diff --git a/ENCSR467LJT/cherimoya.fold_1.log b/ENCSR467LJT/cherimoya.fold_1.log deleted file mode 100644 index 552094e710c34200fdcdfe420b5fc0874029721e..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2157 29.004281997680664 4.345808029174805 218.90696716308594 0.6240341067314148 449.0096435546875 0.16295403242111206 0.69403654 8.438509941101074 True -1 4314 24.021985054016113 0.6386809349060059 241.06048583984375 0.5079025030136108 404.040283203125 0.2260616570711136 0.7839637 3.3013267517089844 True -2 6471 24.024271488189697 0.6312589645385742 238.79151916503906 0.6175346374511719 383.984375 0.24548758566379547 0.81908804 1.943947434425354 True -3 8628 24.009345769882202 0.6795654296875 245.93350219726562 0.4412629008293152 378.0001220703125 0.25167781114578247 0.8323945 1.2293639183044434 True -4 10785 24.097275733947754 0.635286808013916 206.729736328125 0.6342784762382507 374.59051513671875 0.2575288712978363 0.83706415 1.0509233474731445 True -5 12942 24.044113159179688 0.6407620906829834 302.634521484375 0.42338836193084717 372.49212646484375 0.2616983652114868 0.83978444 0.9428375959396362 True -6 15099 24.053487539291382 0.6465814113616943 212.68629455566406 0.47745615243911743 371.84735107421875 0.2621639668941498 0.8438901 0.8561076521873474 True -7 17256 24.05965828895569 0.6467432975769043 282.2359924316406 0.5857601165771484 370.897216796875 0.2624569833278656 0.85293925 0.796745777130127 True -8 19413 24.0460262298584 25.18232035636902 275.90167236328125 0.38854432106018066 369.091064453125 0.2652784287929535 0.86341935 0.7094709873199463 True -9 21570 24.83612370491028 0.6560506820678711 267.37786865234375 0.4230048656463623 368.2701416015625 0.2666720449924469 0.87039924 0.6258006691932678 True -10 23727 24.090052127838135 1.178523302078247 277.1533203125 0.4519943594932556 366.1001281738281 0.27013644576072693 0.87567234 0.5658227205276489 True -11 25884 24.02673649787903 0.6588599681854248 249.92576599121094 0.490795373916626 364.00750732421875 0.2733776569366455 0.8798358 0.52211594581604 True -12 28041 23.95829486846924 0.6287455558776855 251.02841186523438 0.40349718928337097 363.8341369628906 0.273017942905426 0.885031 0.4878336489200592 True -13 30198 23.987942218780518 1.4508624076843262 206.88294982910156 0.3934142589569092 363.106689453125 0.27327683568000793 0.8893095 0.46259286999702454 True -14 32355 24.025190114974976 0.6436264514923096 261.58477783203125 0.3364369571208954 362.2783203125 0.2753002941608429 0.8920312 0.4404471218585968 True -15 34512 23.9960196018219 0.6206316947937012 224.39749145507812 0.3925866484642029 361.7306823730469 0.2750157415866852 0.8936193 0.42792418599128723 True -16 36669 24.014865398406982 0.627155065536499 190.0569610595703 0.4033634662628174 361.76873779296875 0.275055468082428 0.89398026 0.4234595000743866 True -17 38826 23.524739503860474 0.6261730194091797 258.2326354980469 0.3021607995033264 361.8433532714844 0.275272399187088 0.89234036 0.4288408160209656 False -18 40983 23.551204919815063 0.629690408706665 266.8482971191406 0.31008678674697876 361.94122314453125 0.27511587738990784 0.89148706 0.43459853529930115 False -19 43140 23.482784032821655 0.6055786609649658 212.9467010498047 0.31127557158470154 362.484619140625 0.27419614791870117 0.89009255 0.4396456182003021 False diff --git a/ENCSR467LJT/cherimoya.fold_1.performance.tsv b/ENCSR467LJT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a07fbae27cb8928b3924517c22ba2e0168b9f7fc..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.76873779296875 0.4903869032859802 0.27505549788475037 0.09896761924028397 0.8939802646636963 0.8504928350448608 0.4234595000743866 \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_2.evaluate.json b/ENCSR467LJT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8c5285bdce5d68f926fb083aac879fb1a2141121..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020DFW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_2.fit.json b/ENCSR467LJT/cherimoya.fold_2.fit.json deleted file mode 100644 index 807fbd31700b17770d9d52be10d2c70b8597bb4d..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF020DFW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_2.log b/ENCSR467LJT/cherimoya.fold_2.log deleted file mode 100644 index 2412d8c7a6d2f8511514dfdf973aaa4bfcbb5842..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2328 30.957398891448975 4.369951009750366 298.36669921875 0.5723681449890137 383.8170471191406 0.15430963039398193 0.67602044 6.674931526184082 True -1 4656 25.834409475326538 0.5553956031799316 321.53924560546875 0.8425177931785583 336.7909851074219 0.21749556064605713 0.7919923 2.389535427093506 True -2 6984 25.872389793395996 0.47730278968811035 332.1898193359375 0.7479868531227112 325.02471923828125 0.22616839408874512 0.81105506 1.261574387550354 True -3 9312 25.82416534423828 1.5137896537780762 368.2694091796875 0.7534233331680298 321.6292419433594 0.23056969046592712 0.8158381 0.8802744746208191 True -4 11640 25.884589433670044 0.46796464920043945 256.4305419921875 0.7111275792121887 319.89154052734375 0.2332727462053299 0.8203136 0.790863573551178 True -5 13968 25.866905689239502 0.47620630264282227 254.88096618652344 0.5054042935371399 317.840087890625 0.23679856956005096 0.82807255 0.7704029679298401 True -6 16296 25.863130807876587 0.4734492301940918 250.1759033203125 0.6042872071266174 317.11376953125 0.23828363418579102 0.8370407 0.7167477011680603 True -7 18624 25.90097689628601 0.4758446216583252 231.944091796875 0.48279452323913574 315.8995666503906 0.24002127349376678 0.8434878 0.6686790585517883 True -8 20952 25.824932098388672 0.4680445194244385 247.0543212890625 0.4901338815689087 314.7852478027344 0.24228082597255707 0.8480986 0.5795819163322449 True -9 23280 25.81705665588379 0.7755386829376221 193.10928344726562 0.484529972076416 314.0762023925781 0.24341243505477905 0.8530997 0.5499141216278076 True -10 25608 25.84494185447693 0.4955921173095703 174.24502563476562 0.5419780611991882 313.95819091796875 0.24390625953674316 0.85722286 0.5268793106079102 True -11 27936 25.887707471847534 0.4758918285369873 257.103271484375 0.5516232252120972 312.4013671875 0.2462950497865677 0.8635692 0.494274377822876 True -12 30264 25.87763261795044 0.4803178310394287 269.21533203125 0.6370142102241516 311.0347900390625 0.24867717921733856 0.8659347 0.46909022331237793 True -13 32592 25.54821538925171 0.48775601387023926 279.34906005859375 0.3036620616912842 310.5636291503906 0.24851831793785095 0.8694566 0.4483329653739929 True -14 34920 25.359986782073975 0.4672698974609375 181.44052124023438 0.27858126163482666 309.88104248046875 0.24877971410751343 0.87297434 0.4305245876312256 True -15 37248 25.400776863098145 0.49015164375305176 296.0634460449219 0.36968332529067993 310.0763244628906 0.24829678237438202 0.874711 0.4207945764064789 True -16 39576 25.3391854763031 0.473949670791626 213.7939453125 0.35844072699546814 309.3413391113281 0.249907985329628 0.8751178 0.4135192036628723 True -17 41904 25.35158395767212 0.4724152088165283 222.5930938720703 0.3652615249156952 309.5668640136719 0.24967442452907562 0.8735285 0.41705322265625 False -18 44232 25.36330008506775 0.4767277240753174 299.79937744140625 0.28422659635543823 310.13916015625 0.24813199043273926 0.87254775 0.4232114851474762 False -19 46560 25.338587999343872 0.46153950691223145 258.6544189453125 0.42853662371635437 310.2540283203125 0.2481793314218521 0.8713608 0.4284152686595917 False diff --git a/ENCSR467LJT/cherimoya.fold_2.performance.tsv b/ENCSR467LJT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cffd413be8743e89c0b949cce464eba6b7167a05..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.3413391113281 0.5117379426956177 0.249907985329628 0.08273471146821976 0.8751177787780762 0.8132820129394531 0.4135192036628723 \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_3.evaluate.json b/ENCSR467LJT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cac7ca8eacfa3410b440fdc9743fb9196b049c04..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020DFW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_3.fit.json b/ENCSR467LJT/cherimoya.fold_3.fit.json deleted file mode 100644 index 67e713c6be9032e324e92b02bce9e3ddbf98deab..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF020DFW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_3.log b/ENCSR467LJT/cherimoya.fold_3.log deleted file mode 100644 index 838585f60ea54749214357225354e0334e923737..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2220 29.373500108718872 4.014675855636597 237.9110107421875 0.7583791017532349 377.0010681152344 0.1640334129333496 0.65754473 7.050030708312988 True -1 4440 24.672168254852295 0.585848331451416 223.41761779785156 0.5494495630264282 339.81207275390625 0.22099129855632782 0.7603483 2.7817165851593018 True -2 6660 24.69326400756836 0.44088292121887207 274.42578125 0.6891855597496033 330.27203369140625 0.22791382670402527 0.7777716 2.0235610008239746 True -3 8880 24.679396152496338 0.4665224552154541 307.3570861816406 0.8959121704101562 323.72265625 0.2367897480726242 0.7927507 1.2830734252929688 True -4 11100 24.719976663589478 0.47878551483154297 288.76641845703125 0.4867706298828125 320.9180603027344 0.24076971411705017 0.8042237 1.064479112625122 True -5 13320 24.656165838241577 0.4409949779510498 267.31512451171875 0.705441415309906 319.04827880859375 0.24500979483127594 0.813288 0.9328219294548035 True -6 15540 24.680514812469482 0.44230222702026367 211.9906005859375 0.4786945581436157 318.4001159667969 0.2458130568265915 0.82122916 0.8856309652328491 True -7 17760 24.670480012893677 2.8332014083862305 238.42501831054688 0.4362431466579437 317.1965637207031 0.24773447215557098 0.8250792 0.8061318397521973 True -8 19980 24.79328179359436 0.6447129249572754 235.80941772460938 0.6067725419998169 316.7680358886719 0.24835945665836334 0.82991713 0.7505665421485901 True -9 22200 24.6892511844635 1.1776378154754639 218.4635772705078 0.7052568197250366 315.6273193359375 0.2504734694957733 0.8414965 0.6552781462669373 True -10 24420 24.72346806526184 0.45548224449157715 282.8542175292969 0.4025379419326782 313.932861328125 0.25383973121643066 0.8482022 0.6227776408195496 True -11 26640 24.81953763961792 0.4810347557067871 254.3394012451172 0.4130623936653137 313.1915283203125 0.2548346519470215 0.8537328 0.5601872801780701 True -12 28860 25.251795291900635 8.261584997177124 212.186279296875 0.42780470848083496 312.1534423828125 0.25590330362319946 0.8615689 0.5023173093795776 True -13 31080 24.707439184188843 0.4438023567199707 249.89932250976562 0.4790124297142029 311.10601806640625 0.25762274861335754 0.8664647 0.4797164797782898 True -14 33300 24.762505531311035 0.4501333236694336 261.9554138183594 0.3606957197189331 310.6464538574219 0.25831636786460876 0.8709837 0.4647753834724426 True -15 35520 24.71336317062378 0.45760655403137207 248.986572265625 0.4202633500099182 309.98138427734375 0.2592966854572296 0.8715249 0.4531456232070923 True -16 37740 24.739706993103027 0.4594602584838867 268.5704650878906 0.24075326323509216 309.70355224609375 0.2592305839061737 0.8760969 0.4386473298072815 True -17 39960 24.68956208229065 0.43525242805480957 251.80593872070312 0.5225629806518555 309.90411376953125 0.25825008749961853 0.873098 0.43833616375923157 False -18 42180 24.711355924606323 0.7237522602081299 269.1609191894531 0.2779829502105713 310.0084533691406 0.2581581175327301 0.873092 0.4434809684753418 False -19 44400 24.700833797454834 1.02180814743042 222.86453247070312 0.25582826137542725 310.0467529296875 0.2582261264324188 0.8711389 0.44543492794036865 False diff --git a/ENCSR467LJT/cherimoya.fold_3.performance.tsv b/ENCSR467LJT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4b4aa70fb1bd4692bda9ac97a46cccabe636d84f..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.70355224609375 0.5064390301704407 0.2592305839061737 0.08393268287181854 0.8760969042778015 0.8067934513092041 0.4386473298072815 \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_4.evaluate.json b/ENCSR467LJT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ad79cca0a7d39e07163bbae419df35c16bf49469..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020DFW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_4.fit.json b/ENCSR467LJT/cherimoya.fold_4.fit.json deleted file mode 100644 index 77c7e71f1d856763fa76ee7f8b738d6337c25993..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF020DFW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR467LJT/cherimoya.fold_4.log b/ENCSR467LJT/cherimoya.fold_4.log deleted file mode 100644 index 899a252bea1b7870bbfa29a7f60aefca1a6faf64..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2242 29.40229821205139 4.798060417175293 243.32864379882812 0.8159230947494507 329.9683837890625 0.1522715836763382 0.6785965 5.749883651733398 True -1 4484 25.35064721107483 2.277557849884033 239.90257263183594 0.8595479726791382 297.38958740234375 0.20439429581165314 0.7832976 2.2277207374572754 True -2 6726 25.04464054107666 0.4952981472015381 276.698486328125 0.5510237812995911 289.6305236816406 0.2117518037557602 0.8001197 1.3835175037384033 True -3 8968 25.01275134086609 0.4708080291748047 197.98829650878906 0.5497087836265564 285.3414611816406 0.2158796191215515 0.8066834 0.9143130779266357 True -4 11210 25.024911165237427 0.4567553997039795 232.31439208984375 0.5379490852355957 282.89141845703125 0.21926866471767426 0.8185195 0.6931158900260925 True -5 13452 25.002095460891724 0.45445752143859863 263.29364013671875 0.8633220195770264 281.1848449707031 0.22243599593639374 0.82252294 0.6576765179634094 True -6 15694 24.958878993988037 0.4538722038269043 198.30810546875 0.7167954444885254 279.59881591796875 0.2257377654314041 0.8278702 0.6221991777420044 True -7 17936 24.950188636779785 0.4512791633605957 232.228515625 0.5131058692932129 279.0624084472656 0.22618955373764038 0.8352064 0.568234384059906 True -8 20178 25.019976139068604 0.45183444023132324 232.2249755859375 0.43961232900619507 278.0964050292969 0.22751228511333466 0.8421569 0.5267385244369507 True -9 22420 24.993887186050415 0.4636268615722656 253.37081909179688 0.4464433491230011 277.7956848144531 0.22725602984428406 0.84883064 0.49012118577957153 True -10 24662 24.962198972702026 0.4574863910675049 227.00833129882812 0.5691692233085632 276.6934509277344 0.23010119795799255 0.8533354 0.45726674795150757 True -11 26904 24.92859196662903 0.460446834564209 263.83538818359375 0.4608685374259949 275.7777099609375 0.2318161278963089 0.85756135 0.43294140696525574 True -12 29146 25.019882678985596 0.6262338161468506 301.388671875 0.49216729402542114 275.59600830078125 0.23111554980278015 0.8629033 0.40099719166755676 True -13 31388 25.040348291397095 0.4608278274536133 175.54190063476562 0.5945791602134705 274.8765869140625 0.23280684649944305 0.86674607 0.3906096816062927 True -14 33630 25.001235246658325 1.3581666946411133 223.85963439941406 0.2824428379535675 274.3114318847656 0.23390182852745056 0.8691913 0.38023456931114197 True -15 35872 25.01939582824707 0.4562251567840576 176.67539978027344 0.33403903245925903 274.68658447265625 0.2329588085412979 0.8731895 0.37201666831970215 True -16 38114 25.077432870864868 9.207828998565674 200.94464111328125 0.291690468788147 274.506103515625 0.23341098427772522 0.8732759 0.36817067861557007 True -17 40356 25.05478286743164 0.46390295028686523 234.20565795898438 0.3048962652683258 274.3995056152344 0.23402093350887299 0.87385345 0.37039610743522644 True -18 42598 25.05311346054077 0.45523595809936523 299.55242919921875 0.355121910572052 274.883544921875 0.23348468542099 0.8717356 0.37505394220352173 False -19 44840 25.078444719314575 0.4569435119628906 246.9058837890625 0.28614816069602966 275.0286560058594 0.2333877980709076 0.8716158 0.3795240521430969 False diff --git a/ENCSR467LJT/cherimoya.fold_4.performance.tsv b/ENCSR467LJT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8d24006baed215b73045abd6c67e6109446a2c20..0000000000000000000000000000000000000000 --- a/ENCSR467LJT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -274.3995056152344 0.5255016684532166 0.23402093350887299 0.07348351925611496 0.8738534450531006 0.7927107214927673 0.37039610743522644 \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_0.evaluate.json b/ENCSR468AKF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 89fae19a7745f22004e3eeddd90b70597c9d117d..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802PTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_0.fit.json b/ENCSR468AKF/cherimoya.fold_0.fit.json deleted file mode 100644 index f82b6cfc0195ea8c61a16872dbbbb548907ad57f..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_0.log b/ENCSR468AKF/cherimoya.fold_0.log deleted file mode 100644 index 3d321fc3c36830f39ac6c1533d3dc5b18c68b38d..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2700 34.53184628486633 4.246556758880615 540.1788330078125 0.5354247093200684 870.1289672851562 0.1465969681739807 0.7047552 5.779707908630371 True -1 5400 30.084356546401978 0.6116464138031006 586.654541015625 0.4267949163913727 805.9110717773438 0.18598568439483643 0.7465209 2.123725652694702 True -2 8100 30.071836709976196 4.891034364700317 789.7887573242188 0.4573359787464142 790.0303344726562 0.1915401965379715 0.7574442 1.9253629446029663 True -3 10800 30.136012077331543 1.200418472290039 562.2957763671875 0.3892439901828766 777.0252075195312 0.19608677923679352 0.7673519 1.37836754322052 True -4 13500 30.0900616645813 1.30403470993042 598.7669677734375 0.4435843229293823 773.0532836914062 0.19925262033939362 0.76985687 1.6410889625549316 True -5 16200 30.086731672286987 1.41023588180542 565.0001220703125 0.44866424798965454 768.3670043945312 0.20251795649528503 0.7716579 1.0203944444656372 True -6 18900 30.07952094078064 0.8307838439941406 699.30517578125 0.46853065490722656 763.350341796875 0.20508119463920593 0.7791775 0.9040338397026062 True -7 21600 30.08034324645996 0.7563855648040771 610.825439453125 0.4682616591453552 759.7859497070312 0.20704729855060577 0.7781309 0.8864566087722778 False -8 24300 30.17010259628296 1.0950257778167725 655.1136474609375 0.30057525634765625 755.616943359375 0.20940124988555908 0.79048896 0.791576087474823 True -9 27000 30.10038161277771 0.609473466873169 677.555419921875 0.4422271251678467 751.7435302734375 0.21175315976142883 0.7893171 0.6735851168632507 False -10 29700 30.106525182724 0.6115241050720215 588.8417358398438 0.3262351155281067 748.2215576171875 0.21421748399734497 0.80182695 0.5938320159912109 True -11 32400 30.082067728042603 0.5892620086669922 604.8009033203125 0.41578638553619385 745.0718383789062 0.21677570044994354 0.8057326 0.5276010036468506 True -12 35100 30.117863655090332 0.6165018081665039 597.7386474609375 0.2968935966491699 741.156982421875 0.21876615285873413 0.8216236 0.452260822057724 True -13 37800 30.03753972053528 0.6158668994903564 650.5154418945312 0.42246735095977783 738.3958740234375 0.22018657624721527 0.8292709 0.38825592398643494 True -14 40500 29.635724544525146 0.619408130645752 527.0230712890625 0.3252446949481964 736.2117309570312 0.22139514982700348 0.8380458 0.3401283919811249 True -15 43200 29.61504888534546 0.5852797031402588 648.791259765625 0.37145453691482544 734.0404663085938 0.22253572940826416 0.84548116 0.30396586656570435 True -16 45900 29.492364168167114 0.9941599369049072 560.885009765625 0.304751455783844 732.7819213867188 0.22319556772708893 0.85011566 0.28326183557510376 True -17 48600 29.56808590888977 4.765033483505249 581.6475830078125 0.26267024874687195 732.7562255859375 0.2233169823884964 0.85282695 0.27046090364456177 True -18 51300 29.5568265914917 1.3330333232879639 717.1151123046875 0.4670168161392212 732.7011108398438 0.22328726947307587 0.8518253 0.2657153308391571 False -19 54000 29.53577160835266 1.837637186050415 742.416748046875 0.22048808634281158 733.718505859375 0.2222825288772583 0.8511464 0.2678168714046478 False diff --git a/ENCSR468AKF/cherimoya.fold_0.performance.tsv b/ENCSR468AKF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4eec75293d45a0e8fae19ef4da75a9070b4f60c7..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -732.7562255859375 0.5181871652603149 0.2233169823884964 0.07858559489250183 0.8528269529342651 0.775798499584198 0.27046090364456177 \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_1.evaluate.json b/ENCSR468AKF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6ad443cceeecdfbb27058af4a5265ac5264aa23e..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802PTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_1.fit.json b/ENCSR468AKF/cherimoya.fold_1.fit.json deleted file mode 100644 index 7cdc7b8be35aa515fc7e9bd13ad046a0a7e4d904..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_1.log b/ENCSR468AKF/cherimoya.fold_1.log deleted file mode 100644 index a5023f4967c414c50e0dfe87f1c988a884f4b32f..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2700 35.110148429870605 5.31849217414856 740.217529296875 0.6163145303726196 1067.446044921875 0.16267447173595428 0.70454526 6.341463088989258 True -1 5400 30.078912258148193 1.159745216369629 670.8892211914062 0.30731716752052307 981.2007446289062 0.2119743674993515 0.7543692 2.5257065296173096 True -2 8100 30.215314865112305 0.6675901412963867 862.816650390625 0.6436439752578735 968.0450439453125 0.21466664969921112 0.7584295 1.5596991777420044 True -3 10800 30.02474808692932 0.6845800876617432 583.52978515625 0.3188720941543579 944.7877807617188 0.22015444934368134 0.77422255 1.2356407642364502 True -4 13500 30.058167695999146 0.6723315715789795 739.2084350585938 0.5980415344238281 932.7781982421875 0.22591452300548553 0.7799988 1.2489533424377441 True -5 16200 30.049926280975342 0.6717357635498047 684.2567138671875 0.4007314443588257 922.8765258789062 0.23060087859630585 0.789666 1.2157261371612549 True -6 18900 30.03618359565735 0.682044506072998 629.4078369140625 0.38477009534835815 912.6483764648438 0.23569422960281372 0.8004368 0.9315680265426636 True -7 21600 30.00295925140381 0.6860721111297607 680.3038330078125 0.6521528959274292 904.23486328125 0.23975525796413422 0.8099597 0.7661095261573792 True -8 24300 30.059695720672607 0.6828789710998535 638.947998046875 0.45898112654685974 898.083251953125 0.24376904964447021 0.81484216 0.7529616355895996 True -9 27000 30.012684106826782 0.6907365322113037 544.0966186523438 0.3254051208496094 892.6824951171875 0.2463182955980301 0.8188436 0.6664518713951111 True -10 29700 29.862866163253784 0.9076955318450928 803.6492309570312 0.3582063615322113 888.966552734375 0.2486461102962494 0.8258992 0.612616240978241 True -11 32400 29.481706619262695 0.6901493072509766 512.0106201171875 0.2903206944465637 882.3929443359375 0.2517603039741516 0.83429813 0.5307910442352295 True -12 35100 29.58592915534973 0.6830568313598633 628.1718139648438 0.42885246872901917 879.8851318359375 0.2532693147659302 0.8367135 0.49500030279159546 True -13 37800 29.493680715560913 0.6839761734008789 507.939208984375 0.4495972692966461 875.9747924804688 0.25507116317749023 0.8429923 0.44097089767456055 True -14 40500 29.53846526145935 0.6784670352935791 660.6773681640625 0.5520167350769043 873.6510009765625 0.25596195459365845 0.8479814 0.4074352979660034 True -15 43200 29.538565635681152 0.6865084171295166 596.874755859375 0.29975640773773193 871.2749633789062 0.2570219039916992 0.8548362 0.3738476634025574 True -16 45900 29.515236377716064 0.6895921230316162 616.0631103515625 0.2620546519756317 870.9697265625 0.2570396363735199 0.85755116 0.34989216923713684 True -17 48600 29.561330318450928 0.6885027885437012 628.6565551757812 0.23962578177452087 871.8929443359375 0.2559640109539032 0.861487 0.33034488558769226 True -18 51300 29.432849407196045 0.6692924499511719 574.808837890625 0.22924895584583282 871.0437622070312 0.2567293345928192 0.8615629 0.32718008756637573 True -19 54000 29.55951237678528 0.678765058517456 703.466796875 0.37332046031951904 869.5344848632812 0.25778526067733765 0.8633624 0.3236086368560791 True diff --git a/ENCSR468AKF/cherimoya.fold_1.performance.tsv b/ENCSR468AKF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c832e7bd859e16b2f6e495b785b40af0182bebc2..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -869.5344848632812 0.489761620759964 0.25778526067733765 0.0970606878399849 0.8633623719215393 0.8231304883956909 0.3236086368560791 \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_2.evaluate.json b/ENCSR468AKF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3234ac1d8fe1de4f1a4541f07c862db7ad5cbc21..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802PTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_2.fit.json b/ENCSR468AKF/cherimoya.fold_2.fit.json deleted file mode 100644 index 434d4d79a2ec38c4103bcf4e2c533f67d40a8149..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_2.log b/ENCSR468AKF/cherimoya.fold_2.log deleted file mode 100644 index 15111116ec67a66a3c2df7d4d0e0097d83298ac6..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.76777362823486 4.987877368927002 689.917236328125 0.5091899633407593 913.473876953125 0.15265026688575745 0.6967678 5.281152248382568 True -1 5744 31.95399522781372 15.476282358169556 607.528076171875 0.7963628768920898 836.781005859375 0.19622310996055603 0.7594915 1.695113182067871 True -2 8616 31.99998426437378 16.611762285232544 712.1444091796875 0.6157721877098083 822.9501953125 0.20086580514907837 0.76972383 1.3932147026062012 True -3 11488 32.00192046165466 0.5990731716156006 544.759521484375 0.42191386222839355 807.1456298828125 0.20717492699623108 0.78026706 1.3825420141220093 True -4 14360 31.906893730163574 0.5570902824401855 700.55712890625 0.5043805837631226 804.5193481445312 0.20837385952472687 0.78217286 1.2728381156921387 True -5 17232 31.870599508285522 0.5670163631439209 905.6663818359375 0.680645227432251 796.51513671875 0.21320652961730957 0.78820366 0.9948855638504028 True -6 20104 31.827136516571045 0.5654220581054688 610.865966796875 0.4374069273471832 793.2418823242188 0.2143774777650833 0.79278624 0.9387199878692627 True -7 22976 31.83517098426819 1.1641442775726318 627.3095703125 0.6587705612182617 786.8984375 0.21905767917633057 0.79595166 0.9054584503173828 True -8 25848 31.836780309677124 0.6620094776153564 720.759033203125 0.4709663987159729 781.7841796875 0.22210292518138885 0.8023588 0.8195104598999023 True -9 28720 31.163194179534912 0.5567798614501953 699.9115600585938 0.7167593240737915 779.7433471679688 0.22295255959033966 0.8079195 0.6882292628288269 True -10 31592 31.18947958946228 0.5566184520721436 643.1558837890625 0.36031895875930786 775.9397583007812 0.22571402788162231 0.81731576 0.6246585249900818 True -11 34464 31.27164077758789 0.5602819919586182 545.8026733398438 0.34331485629081726 773.0084228515625 0.22735662758350372 0.8207879 0.5310454368591309 True -12 37336 31.27588129043579 0.5489239692687988 557.034423828125 0.20138156414031982 768.7924194335938 0.22975000739097595 0.8284372 0.45092517137527466 True -13 40208 31.267271757125854 0.5399675369262695 732.2521362304688 0.3669765889644623 765.95849609375 0.23144292831420898 0.8320073 0.4013162851333618 True -14 43080 31.245118379592896 0.546663761138916 624.47412109375 0.1507047414779663 762.9948120117188 0.23300574719905853 0.8382265 0.35457611083984375 True -15 45952 31.23732352256775 0.5604374408721924 614.6566162109375 0.2915021777153015 761.7932739257812 0.23285050690174103 0.84535235 0.322864294052124 True -16 48824 31.27571177482605 0.55084228515625 617.7450561523438 0.22292816638946533 758.5901489257812 0.2346441149711609 0.8504 0.300458163022995 True -17 51696 31.23516535758972 0.5594170093536377 662.895263671875 0.2876027822494507 758.879150390625 0.2340567260980606 0.8532072 0.2880484163761139 True -18 54568 31.30744242668152 0.5471920967102051 712.5159912109375 0.3463767170906067 759.0877075195312 0.23384816944599152 0.8530109 0.28372350335121155 False -19 57440 31.281824350357056 0.5416803359985352 690.4034423828125 0.28306230902671814 761.1979370117188 0.23238971829414368 0.85256577 0.2842600345611572 False diff --git a/ENCSR468AKF/cherimoya.fold_2.performance.tsv b/ENCSR468AKF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index db96107b01af32378738c0271bb12fa815a5815f..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -758.879150390625 0.5100278854370117 0.2340567260980606 0.0877637267112732 0.8532071709632874 0.7905654311180115 0.2880484163761139 \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_3.evaluate.json b/ENCSR468AKF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0e4bf604eb25c38cc3d158c4be6bb9b56e316a21..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802PTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_3.fit.json b/ENCSR468AKF/cherimoya.fold_3.fit.json deleted file mode 100644 index b4c87399bf83ef36d2ddbbdace07d115be61ef3a..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_3.log b/ENCSR468AKF/cherimoya.fold_3.log deleted file mode 100644 index 154eb7f6fe9340f43dbaa849ce704e55cfb487a5..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 35.29062032699585 4.35115122795105 603.5126953125 0.7188969850540161 901.2633056640625 0.15860867500305176 0.6998956 5.545566558837891 True -1 5476 30.432868003845215 0.5868375301361084 599.5777587890625 0.5643138289451599 839.5177612304688 0.19653011858463287 0.7399232 2.207456111907959 True -2 8214 30.471753120422363 0.6059463024139404 704.18017578125 0.5630444884300232 828.5056762695312 0.20165158808231354 0.7423678 1.6849555969238281 True -3 10952 30.408527374267578 0.5795340538024902 555.9869995117188 0.33595389127731323 815.5125732421875 0.20610445737838745 0.76435745 1.277631163597107 True -4 13690 30.35874915122986 0.5655333995819092 958.282470703125 0.4684061110019684 806.5045166015625 0.20946063101291656 0.77313787 1.2439420223236084 True -5 16428 30.38255763053894 0.5681741237640381 773.9354248046875 0.6919560432434082 801.8505859375 0.21203695237636566 0.7781277 1.0485373735427856 True -6 19166 30.398789167404175 0.5745680332183838 702.3316650390625 0.5524909496307373 794.78466796875 0.21673108637332916 0.7801492 0.9654102325439453 True -7 21904 30.41829013824463 0.5764923095703125 685.5820922851562 0.4896143078804016 792.14892578125 0.21822884678840637 0.7867088 0.8436633348464966 True -8 24642 30.430070877075195 0.5759172439575195 613.918701171875 0.4496604800224304 786.9740600585938 0.2223445326089859 0.7873469 0.8034684658050537 True -9 27380 30.42865562438965 0.9279663562774658 566.2606811523438 0.44430065155029297 783.099365234375 0.22452259063720703 0.79378814 0.7336609363555908 True -10 30118 29.893153190612793 2.1205666065216064 573.4056396484375 0.3278481364250183 778.9863891601562 0.227333664894104 0.80329376 0.6252869963645935 True -11 32856 29.796116828918457 0.6189441680908203 710.1932373046875 0.4782615602016449 775.8483276367188 0.22911794483661652 0.8116937 0.554884672164917 True -12 35594 29.820044994354248 0.5765419006347656 644.9088134765625 0.5450025796890259 772.0517578125 0.23119065165519714 0.8199762 0.4998316764831543 True -13 38332 29.798156261444092 0.5573503971099854 535.409912109375 0.42434054613113403 770.5150756835938 0.23197709023952484 0.82693785 0.44355249404907227 True -14 41070 29.784976959228516 0.5763895511627197 630.215576171875 0.30756083130836487 766.5259399414062 0.23389585316181183 0.8403965 0.38449299335479736 True -15 43808 29.77325415611267 2.4492952823638916 560.9559326171875 0.42113107442855835 763.4361572265625 0.23546752333641052 0.84714806 0.3484429121017456 True -16 46546 29.814138174057007 0.5666983127593994 611.4329223632812 0.30768951773643494 762.184326171875 0.23559902608394623 0.8542012 0.31467512249946594 True -17 49284 29.95028519630432 0.5745346546173096 598.6697998046875 0.3409164547920227 760.93896484375 0.23633714020252228 0.8571265 0.30144113302230835 True -18 52022 29.983092546463013 0.601459264755249 743.9840087890625 0.41827213764190674 761.7097778320312 0.23573586344718933 0.85775894 0.2920428216457367 True -19 54760 29.94750738143921 0.5822932720184326 594.3375244140625 0.19299045205116272 761.0687255859375 0.23606762290000916 0.8574681 0.2921421229839325 False diff --git a/ENCSR468AKF/cherimoya.fold_3.performance.tsv b/ENCSR468AKF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4b7bdbf4e574f0e1275ed4db8c7a5f1bfcc5be2e..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -761.7097778320312 0.5096011757850647 0.23573584854602814 0.08410030603408813 0.8577589392662048 0.7952336072921753 0.2920428216457367 \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_4.evaluate.json b/ENCSR468AKF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b6e92a347c13756b5db5418862e3b77b85cc8d53..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802PTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_4.fit.json b/ENCSR468AKF/cherimoya.fold_4.fit.json deleted file mode 100644 index c71fcdf86a14ca5d56ba9255163b85da2f0930d1..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR468AKF/cherimoya.fold_4.log b/ENCSR468AKF/cherimoya.fold_4.log deleted file mode 100644 index 824ec7515ecfc734eb61965e47178388bdf64440..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 36.65672969818115 3.925086736679077 602.6295166015625 0.5058010816574097 810.3133544921875 0.14498166739940643 0.6950701 3.916970729827881 True -1 5740 31.894332885742188 1.054889440536499 729.62890625 0.5241798758506775 760.6547241210938 0.179341122508049 0.73461705 1.6287617683410645 True -2 8610 31.848507165908813 20.881136894226074 541.7992553710938 0.33130964636802673 755.543701171875 0.1808495968580246 0.73900306 1.4010721445083618 True -3 11480 31.90997815132141 0.5816571712493896 617.76416015625 0.3557058870792389 742.29296875 0.18653526902198792 0.7538743 1.084520936012268 True -4 14350 31.838807344436646 0.5883963108062744 551.9675903320312 0.2973549962043762 733.8203735351562 0.19097307324409485 0.76629573 0.9259946942329407 True -5 17220 31.884212255477905 0.5833590030670166 579.2960205078125 0.4731721878051758 727.8948974609375 0.19466713070869446 0.7725602 0.9253594875335693 True -6 20090 31.903775930404663 0.5692753791809082 595.8902587890625 0.39909130334854126 724.6183471679688 0.19692185521125793 0.7713115 0.7485531568527222 False -7 22960 31.78365731239319 0.5699787139892578 710.30908203125 0.45688962936401367 720.8743286132812 0.19934846460819244 0.7771055 0.6922053694725037 True -8 25830 31.884737253189087 0.5825695991516113 567.7037963867188 0.3415842056274414 716.7478637695312 0.2019454538822174 0.78281265 0.6008278727531433 True -9 28700 31.824278354644775 0.5813689231872559 569.2457275390625 0.25725728273391724 712.331298828125 0.2053108811378479 0.78747606 0.5867178440093994 True -10 31570 31.871450185775757 0.5839660167694092 702.747314453125 0.4379296600818634 710.2244873046875 0.20647604763507843 0.7919077 0.508714497089386 True -11 34440 31.55432391166687 0.5637094974517822 566.9411010742188 0.26667559146881104 708.686279296875 0.20691105723381042 0.80169004 0.44186821579933167 True -12 37310 31.282638788223267 0.5647127628326416 643.962646484375 0.28493988513946533 705.6832275390625 0.209548220038414 0.80618775 0.4076055884361267 True -13 40180 31.295836448669434 0.574429988861084 646.8902587890625 0.29192012548446655 702.8076782226562 0.21101818978786469 0.81175226 0.3574290871620178 True -14 43050 31.27675151824951 0.575340986251831 672.7355346679688 0.42766064405441284 701.1837768554688 0.21189025044441223 0.8204361 0.3196117579936981 True -15 45920 31.332534313201904 0.5624172687530518 663.3055419921875 0.21120920777320862 699.9169311523438 0.21236979961395264 0.82734144 0.2917844355106354 True -16 48790 31.22429370880127 1.313843011856079 652.0831298828125 0.1936098039150238 697.4733276367188 0.2139783799648285 0.8308928 0.2753196656703949 True -17 51660 31.258325576782227 0.5787553787231445 601.952880859375 0.2675396203994751 698.6926879882812 0.21330271661281586 0.83333695 0.2662739157676697 True -18 54530 31.371049880981445 2.1235411167144775 593.5293579101562 0.41808873414993286 698.3933715820312 0.21341992914676666 0.834366 0.2649255692958832 True -19 57400 31.30956482887268 0.5842127799987793 656.4630126953125 0.22137300670146942 699.45068359375 0.21269509196281433 0.83483785 0.2649456858634949 True diff --git a/ENCSR468AKF/cherimoya.fold_4.performance.tsv b/ENCSR468AKF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ac3e35c2c99c5e11b506f36042de8d28b8667a34..0000000000000000000000000000000000000000 --- a/ENCSR468AKF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -699.45068359375 0.524977445602417 0.21269510686397552 0.07152768224477768 0.8348378539085388 0.7562339305877686 0.2649456858634949 \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_0.evaluate.json b/ENCSR470QCE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c9d903f76f86b839ecfe0490dab12eb05faf2e16..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF724DCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_0.fit.json b/ENCSR470QCE/cherimoya.fold_0.fit.json deleted file mode 100644 index c5edb7a7010a0d9cb90a98b9e74fd8404321c6ad..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_0.log b/ENCSR470QCE/cherimoya.fold_0.log deleted file mode 100644 index 04fd1614f5dfedc760e1c99ba04b243b0bc620ed..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2189 28.053953409194946 3.484429121017456 185.67962646484375 0.48218926787376404 266.221923828125 0.1358102411031723 0.6755686 5.203961372375488 True -1 4378 24.4992253780365 0.5101828575134277 214.12203979492188 0.5292813777923584 249.59510803222656 0.17847689986228943 0.77221173 1.6616380214691162 True -2 6567 24.59465789794922 0.47454261779785156 235.46212768554688 0.6517711877822876 241.79356384277344 0.19502274692058563 0.795548 1.0399924516677856 True -3 8756 24.539169311523438 0.473466157913208 229.3111114501953 0.48582449555397034 240.32235717773438 0.19622208178043365 0.8042369 0.6416451930999756 True -4 10945 24.540164470672607 0.4790670871734619 259.4090270996094 0.6754955053329468 239.4961395263672 0.19765885174274445 0.8124515 0.6226841807365417 True -5 13134 24.54255962371826 0.47919607162475586 200.816162109375 0.5221608877182007 238.45257568359375 0.2009766548871994 0.8180308 0.5478722453117371 True -6 15323 24.556038856506348 0.473330020904541 212.64923095703125 0.3964870572090149 237.940673828125 0.20172040164470673 0.8271933 0.4933921992778778 True -7 17512 24.5770161151886 0.4681425094604492 239.22796630859375 0.465505987405777 237.3773956298828 0.20378968119621277 0.83443785 0.45561015605926514 True -8 19701 24.596145391464233 0.4692401885986328 195.85157775878906 0.5970571041107178 236.7889404296875 0.2060587853193283 0.8391307 0.43025410175323486 True -9 21890 24.612333059310913 0.4791452884674072 205.19903564453125 0.44339269399642944 236.15065002441406 0.20744745433330536 0.8470647 0.4037206768989563 True -10 24079 24.60275387763977 0.47583699226379395 213.37481689453125 0.5588750839233398 235.56089782714844 0.20920100808143616 0.84968245 0.3747442662715912 True -11 26268 24.555014610290527 0.4752652645111084 190.6841583251953 0.29460474848747253 235.18589782714844 0.2097613662481308 0.85399055 0.3426697254180908 True -12 28457 24.550138235092163 0.4801621437072754 242.9832305908203 0.45178988575935364 234.53330993652344 0.2116590291261673 0.85779786 0.3291322588920593 True -13 30646 24.55565595626831 0.48270273208618164 241.68157958984375 0.30507951974868774 234.30084228515625 0.2119046151638031 0.86407626 0.3119838833808899 True -14 32835 24.54386568069458 0.4854271411895752 211.8201446533203 0.35724809765815735 234.5738525390625 0.21059618890285492 0.86516136 0.3038789629936218 True -15 35024 24.569430351257324 0.48129749298095703 227.66598510742188 0.294256329536438 233.848388671875 0.21269425749778748 0.8673439 0.29746100306510925 True -16 37213 24.542653799057007 0.4831833839416504 219.66795349121094 0.23689240217208862 233.8106231689453 0.21297475695610046 0.86844707 0.2941966950893402 True -17 39402 24.527894258499146 0.4826836585998535 183.1907958984375 0.24651119112968445 234.12001037597656 0.2122344672679901 0.86850137 0.2970339357852936 True -18 41591 25.051077365875244 0.4832437038421631 264.0255432128906 0.19670169055461884 234.197021484375 0.21161732077598572 0.8666403 0.29872408509254456 False -19 43780 24.59147596359253 17.7651686668396 223.74771118164062 0.22705848515033722 234.3199005126953 0.211395263671875 0.8657973 0.3008439242839813 False diff --git a/ENCSR470QCE/cherimoya.fold_0.performance.tsv b/ENCSR470QCE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f474e2e8f4e55ad7b6aae1ce4f8618855fe1734d..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -234.12001037597656 0.540611743927002 0.2122344672679901 0.06027243658900261 0.8685013651847839 0.7890928387641907 0.2970339357852936 \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_1.evaluate.json b/ENCSR470QCE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 201f9a31c545f9d0085bd0210b3e230fc01d990f..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF724DCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_1.fit.json b/ENCSR470QCE/cherimoya.fold_1.fit.json deleted file mode 100644 index 6a839c03d7521071ecd43644cf7b8683c9da2a10..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_1.log b/ENCSR470QCE/cherimoya.fold_1.log deleted file mode 100644 index bb1f53a62929d3dcb2158a7216e4bf15e690c50b..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2156 28.038177013397217 3.5459201335906982 178.22218322753906 0.806788444519043 325.5743713378906 0.14986765384674072 0.67217517 6.2728753089904785 True -1 4312 24.09299111366272 0.63681960105896 144.5338592529297 0.471341073513031 303.78692626953125 0.19974404573440552 0.7784334 2.215684652328491 True -2 6468 24.186156749725342 15.235931158065796 225.92416381835938 0.48742324113845825 295.11669921875 0.21523067355155945 0.8022683 1.2483755350112915 True -3 8624 24.105112314224243 0.6286320686340332 212.00372314453125 0.6040753126144409 290.85028076171875 0.2228430211544037 0.8142588 0.7900233864784241 True -4 10780 24.107173442840576 0.6320648193359375 214.6367950439453 0.5386284589767456 289.75360107421875 0.2249409258365631 0.8144423 0.7336066961288452 True -5 12936 24.094627380371094 0.6336474418640137 202.50511169433594 0.3935820758342743 288.67828369140625 0.2277105301618576 0.8248313 0.67357337474823 True -6 15092 24.117287635803223 0.630840539932251 202.79269409179688 0.41708433628082275 288.3797912597656 0.22831258177757263 0.8299284 0.6505731344223022 True -7 17248 24.114730834960938 0.6206467151641846 221.83377075195312 0.44319218397140503 287.6688537597656 0.23081815242767334 0.8367577 0.6284686326980591 True -8 19404 24.573179006576538 1.6967904567718506 175.0400848388672 0.29271259903907776 286.2613830566406 0.23362436890602112 0.84862274 0.5515958666801453 True -9 21560 24.183651447296143 0.6577596664428711 183.85098266601562 0.41309410333633423 285.35357666015625 0.2357841581106186 0.85691667 0.4566918611526489 True -10 23716 24.176458597183228 1.5152661800384521 237.71102905273438 0.43800264596939087 284.6572570800781 0.23722365498542786 0.8630643 0.42572021484375 True -11 25872 24.238288402557373 0.6444151401519775 222.3145751953125 0.2892971336841583 284.1981506347656 0.23775742948055267 0.8701387 0.39416342973709106 True -12 28028 24.29593253135681 0.6413891315460205 214.49331665039062 0.39600199460983276 283.3816833496094 0.239556223154068 0.8737369 0.37159159779548645 True -13 30184 24.210697412490845 18.50656223297119 178.18748474121094 0.3249233365058899 283.0116271972656 0.24020123481750488 0.87837195 0.34944427013397217 True -14 32340 24.619585275650024 0.6416423320770264 176.04464721679688 0.3423101305961609 282.6043701171875 0.2407577782869339 0.8814518 0.3386766314506531 True -15 34496 24.253156185150146 11.282816886901855 185.15261840820312 0.28332948684692383 282.3055419921875 0.24181945621967316 0.88300985 0.33388277888298035 True -16 36652 24.17428159713745 0.649101734161377 178.77169799804688 0.22996509075164795 282.06842041015625 0.24205128848552704 0.8819213 0.33199721574783325 False -17 38808 24.60648012161255 12.559687376022339 206.04661560058594 0.17394694685935974 282.4331970214844 0.24122992157936096 0.88154334 0.3364088833332062 False -18 40964 24.14548897743225 0.648576021194458 159.74717712402344 0.3264733552932739 282.71942138671875 0.24037431180477142 0.88014716 0.341279000043869 False -19 43120 24.186800003051758 0.6518104076385498 182.0319366455078 0.40171176195144653 282.7771911621094 0.24017535150051117 0.8792935 0.3464365303516388 False diff --git a/ENCSR470QCE/cherimoya.fold_1.performance.tsv b/ENCSR470QCE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8f21b78fa1d1f6c2f078c76391a7857855722879..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -282.3055419921875 0.5158541798591614 0.24181947112083435 0.07448366284370422 0.8830098509788513 0.8392500877380371 0.33388277888298035 \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_2.evaluate.json b/ENCSR470QCE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 29ed59cd626c3cabc9b8bbab44f20d18b9171918..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF724DCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_2.fit.json b/ENCSR470QCE/cherimoya.fold_2.fit.json deleted file mode 100644 index 46e5212f320595478f5229873df305f210396fbb..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_2.log b/ENCSR470QCE/cherimoya.fold_2.log deleted file mode 100644 index 904b7892d3a6316043fb0a0908f7ec6e729e479d..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2309 29.851123094558716 3.436781406402588 212.67486572265625 0.42112523317337036 275.0636291503906 0.14157360792160034 0.66162443 4.543892860412598 True -1 4618 25.872705698013306 0.4951162338256836 179.17239379882812 0.4335213303565979 257.115478515625 0.18565897643566132 0.7609744 1.8543016910552979 True -2 6927 25.860061645507812 0.4790360927581787 196.686279296875 0.3778626322746277 249.60281372070312 0.19800737500190735 0.7941395 0.8871275782585144 True -3 9236 25.818450927734375 0.4762125015258789 250.68289184570312 0.3907815217971802 248.29742431640625 0.1986892968416214 0.8028116 0.5849255919456482 True -4 11545 25.81328535079956 0.48174452781677246 207.35482788085938 0.32820451259613037 246.68765258789062 0.20283620059490204 0.8089092 0.542862057685852 True -5 13854 25.801003217697144 0.48129725456237793 222.9080810546875 0.46573972702026367 245.7892303466797 0.20529070496559143 0.81466144 0.5484494566917419 True -6 16163 25.820956468582153 1.3618991374969482 179.74923706054688 0.32330065965652466 244.4893341064453 0.20840127766132355 0.82240456 0.5089167356491089 True -7 18472 26.169513702392578 11.171697854995728 204.58213806152344 0.3356475532054901 243.83680725097656 0.21007627248764038 0.8206701 0.5122888684272766 False -8 20781 25.795836210250854 0.49501490592956543 193.6127471923828 0.3770497143268585 243.61602783203125 0.20972704887390137 0.8325225 0.4639626741409302 True -9 23090 25.83263325691223 0.9605226516723633 187.31103515625 0.34504061937332153 243.29885864257812 0.21126671135425568 0.8380275 0.4180658459663391 True -10 25399 25.855836153030396 0.4879014492034912 223.55963134765625 0.31802064180374146 242.21060180664062 0.21434302628040314 0.8430057 0.3937205374240875 True -11 27708 25.87834858894348 0.4801979064941406 220.97955322265625 0.30064356327056885 241.8014678955078 0.215298593044281 0.84767807 0.3697737157344818 True -12 30017 25.88324213027954 0.47528910636901855 224.330078125 0.4349142611026764 241.7872314453125 0.21497277915477753 0.85413706 0.3490155041217804 True -13 32326 25.884735107421875 0.47981834411621094 189.90521240234375 0.3396272659301758 241.67303466796875 0.2146369069814682 0.8555057 0.3469763994216919 True -14 34635 25.8657546043396 0.48636698722839355 186.6326904296875 0.3292151093482971 241.04054260253906 0.2165803164243698 0.85995364 0.3331391513347626 True -15 36944 25.805696725845337 0.48168325424194336 152.33334350585938 0.2854883670806885 240.71530151367188 0.21763591468334198 0.8610988 0.3216928541660309 True -16 39253 25.798842191696167 0.48087406158447266 190.0297393798828 0.37832319736480713 240.51272583007812 0.21823656558990479 0.8646128 0.3139536678791046 True -17 41562 25.831438779830933 0.47998476028442383 179.8021240234375 0.2283797562122345 240.6157684326172 0.21799075603485107 0.86158806 0.31596627831459045 False -18 43871 25.842880487442017 0.4835665225982666 169.78717041015625 0.27565932273864746 240.93983459472656 0.21666765213012695 0.8615417 0.3198091685771942 False -19 46180 25.804728746414185 0.4797632694244385 195.81005859375 0.2793314456939697 241.19308471679688 0.21569208800792694 0.8595423 0.32246485352516174 False diff --git a/ENCSR470QCE/cherimoya.fold_2.performance.tsv b/ENCSR470QCE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5b59591dd76b64fb9b596acf4d313175185bba3c..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -240.51272583007812 0.5362424850463867 0.21823656558990479 0.06323893368244171 0.8646128177642822 0.8042017817497253 0.3139536678791046 \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_3.evaluate.json b/ENCSR470QCE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bd8dca6b3e337005e7cb7398c061651849fed50e..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF724DCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_3.fit.json b/ENCSR470QCE/cherimoya.fold_3.fit.json deleted file mode 100644 index b12c0b90c63692852f3df38c44a327a15dd3cf61..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_3.log b/ENCSR470QCE/cherimoya.fold_3.log deleted file mode 100644 index 099003860708f8bca4f06c0ff96b897838d64b3f..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2204 30.13941502571106 3.4148406982421875 225.4474639892578 0.4329558312892914 284.5237731933594 0.14716963469982147 0.6360704 5.239624977111816 True -1 4408 24.744174003601074 0.48598241806030273 179.6117401123047 0.3220161199569702 266.7174377441406 0.19176410138607025 0.7299808 2.143453598022461 True -2 6612 24.69442129135132 0.4755096435546875 226.8425750732422 0.47178366780281067 260.11224365234375 0.20549042522907257 0.76497006 1.3120450973510742 True -3 8816 24.720549821853638 0.4735689163208008 221.0323944091797 0.5211567878723145 258.20440673828125 0.20783047378063202 0.7754449 0.8327914476394653 True -4 11020 24.6652615070343 0.4683840274810791 171.44961547851562 0.47971364855766296 256.5871887207031 0.21125008165836334 0.7904128 0.733562707901001 True -5 13224 24.72859239578247 0.4730093479156494 181.62149047851562 0.204271599650383 255.51071166992188 0.21450601518154144 0.7962587 0.6931695342063904 True -6 15428 24.6882004737854 0.47445011138916016 224.06784057617188 0.5110903978347778 255.2251434326172 0.21515095233917236 0.8020632 0.6767099499702454 True -7 17632 24.66882586479187 0.473111629486084 212.47421264648438 0.45306798815727234 254.48948669433594 0.21687187254428864 0.8089562 0.6281410455703735 True -8 19836 24.6590359210968 8.011810541152954 203.8548583984375 0.4876599907875061 253.94046020507812 0.21840207278728485 0.81988686 0.57257080078125 True -9 22040 24.670385599136353 0.479736328125 162.86703491210938 0.35256537795066833 253.14984130859375 0.22070254385471344 0.82081324 0.5607231259346008 True -10 24244 24.680001974105835 0.483734130859375 226.92208862304688 0.19497208297252655 252.91970825195312 0.22105920314788818 0.8250281 0.5343478322029114 True -11 26448 24.673311710357666 0.48346519470214844 228.63070678710938 0.4169776737689972 251.974853515625 0.2241034358739853 0.83506715 0.49547523260116577 True -12 28652 24.646111011505127 0.47350192070007324 242.4775390625 0.24283510446548462 251.76678466796875 0.22443512082099915 0.83934003 0.4589821398258209 True -13 30856 24.69924235343933 0.46829795837402344 167.40896606445312 0.337030291557312 251.13946533203125 0.22582906484603882 0.8451096 0.4296600818634033 True -14 33060 24.6878023147583 0.4746105670928955 165.08114624023438 0.33067354559898376 250.52391052246094 0.22738860547542572 0.8543183 0.39816609025001526 True -15 35264 24.739877700805664 0.48000168800354004 220.90902709960938 0.49359777569770813 250.39942932128906 0.2268582135438919 0.8594015 0.3723891079425812 True -16 37468 24.742933988571167 0.4791128635406494 193.92938232421875 0.3633904457092285 250.23361206054688 0.22708538174629211 0.8616842 0.35987451672554016 True -17 39672 24.760738134384155 0.47344183921813965 202.12484741210938 0.2175549864768982 250.1761474609375 0.22691963613033295 0.8632059 0.35435765981674194 True -18 41876 24.77829074859619 0.4777836799621582 205.337646484375 0.233820378780365 250.41265869140625 0.22617670893669128 0.86190915 0.35635849833488464 False -19 44080 24.77170491218567 0.4991159439086914 192.58816528320312 0.22809302806854248 250.18408203125 0.2270749807357788 0.8599506 0.35918739438056946 False diff --git a/ENCSR470QCE/cherimoya.fold_3.performance.tsv b/ENCSR470QCE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4e3b4d1fd9885c75dcd629feb659b8a2b79bddb0..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.1761474609375 0.5294259190559387 0.22691960632801056 0.07032044976949692 0.8632059097290039 0.7981179356575012 0.35435765981674194 \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_4.evaluate.json b/ENCSR470QCE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d0480a0dbbfc8f8448619652432c3ad58703445f..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF724DCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_4.fit.json b/ENCSR470QCE/cherimoya.fold_4.fit.json deleted file mode 100644 index 58ad8b39d077565b8e0414a2a1bf319950f61c9e..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470QCE/cherimoya.fold_4.log b/ENCSR470QCE/cherimoya.fold_4.log deleted file mode 100644 index b5f3ae0aa0c3c5cc5be56e9a799655517bba4275..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2253 28.912976026535034 3.3755271434783936 210.02944946289062 0.49273765087127686 248.2058563232422 0.1362442523241043 0.655603 4.307539463043213 True -1 4506 25.238266468048096 0.9698047637939453 210.48297119140625 0.49884289503097534 232.230224609375 0.17567788064479828 0.7649087 1.5130524635314941 True -2 6759 25.231452226638794 0.47677159309387207 179.94598388671875 0.3782283067703247 228.6270751953125 0.1835930198431015 0.77951765 1.0721772909164429 True -3 9012 25.209965467453003 0.47562217712402344 223.74887084960938 0.5451202392578125 226.25047302246094 0.1889856904745102 0.793406 0.6575663089752197 True -4 11265 25.23744487762451 0.4754807949066162 202.11705017089844 0.6877485513687134 225.51075744628906 0.19038031995296478 0.7998334 0.5841609835624695 True -5 13518 25.213996171951294 0.48006415367126465 190.84384155273438 0.4381921887397766 224.40609741210938 0.19400176405906677 0.8090106 0.5107740163803101 True -6 15771 25.188172340393066 0.4877197742462158 264.5885925292969 0.33502495288848877 224.22109985351562 0.1940826177597046 0.8137739 0.4895976483821869 True -7 18024 25.176255226135254 0.47946643829345703 186.68170166015625 0.4892277717590332 223.64341735839844 0.19648586213588715 0.82305264 0.4595073163509369 True -8 20277 25.175557136535645 1.1899049282073975 203.69937133789062 0.4997122883796692 223.07022094726562 0.19754469394683838 0.83205104 0.41521087288856506 True -9 22530 25.18027091026306 0.4763050079345703 152.7584228515625 0.28126728534698486 222.7720947265625 0.1981414258480072 0.8392531 0.38738498091697693 True -10 24783 25.182576894760132 0.478435754776001 192.2261505126953 0.41104769706726074 222.54747009277344 0.19882503151893616 0.8459136 0.3486071228981018 True -11 27036 25.19238519668579 0.6222026348114014 238.53323364257812 0.450155109167099 222.222900390625 0.19982415437698364 0.85047954 0.3335323631763458 True -12 29289 25.207841873168945 0.4781677722930908 180.8585205078125 0.3324562907218933 221.3577880859375 0.2023306041955948 0.8542212 0.3229750096797943 True -13 31542 25.194871425628662 1.5777065753936768 213.74612426757812 0.45856398344039917 221.01722717285156 0.20333795249462128 0.8570605 0.3051137626171112 True -14 33795 25.222569704055786 0.4916553497314453 202.4130401611328 0.3618987798690796 220.6863555908203 0.204422265291214 0.86216253 0.29521694779396057 True -15 36048 25.218684196472168 0.5396485328674316 214.2191925048828 0.24054419994354248 220.80648803710938 0.2036232054233551 0.86493856 0.2835378050804138 True -16 38301 25.209166288375854 0.4870929718017578 250.68182373046875 0.32831183075904846 220.66416931152344 0.20387472212314606 0.866052 0.2791816294193268 True -17 40554 25.281818389892578 0.48472046852111816 229.3896942138672 0.2141808718442917 220.9555206298828 0.20306172966957092 0.8657871 0.2780861556529999 False -18 42807 25.21787929534912 0.48369550704956055 258.3148193359375 0.17927370965480804 220.86778259277344 0.20351824164390564 0.8650375 0.28020504117012024 False -19 45060 25.240694284439087 1.7171497344970703 195.9224853515625 0.2988415062427521 220.95204162597656 0.20322613418102264 0.8629409 0.28320154547691345 False diff --git a/ENCSR470QCE/cherimoya.fold_4.performance.tsv b/ENCSR470QCE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f55215028220ff70e02f1b9c3ac912d2bdb6b14b..0000000000000000000000000000000000000000 --- a/ENCSR470QCE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -220.66416931152344 0.5470066666603088 0.20387475192546844 0.05410902947187424 0.866051971912384 0.782220721244812 0.2791816294193268 \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_0.evaluate.json b/ENCSR470ZNM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 06d13e1a61e7b845300522d1bfcd3cfd78d1228e..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367ILE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_0.fit.json b/ENCSR470ZNM/cherimoya.fold_0.fit.json deleted file mode 100644 index e43635ac3effe26c856aa2a1cd0118d03769692a..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF367ILE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_0.log b/ENCSR470ZNM/cherimoya.fold_0.log deleted file mode 100644 index 1fe1a65e058c542f6f7c72124a5781fb89cf46af..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1647 22.639858722686768 3.182023048400879 172.1744384765625 0.936384916305542 293.58575439453125 0.34216395020484924 0.40223598 10.641328811645508 True -1 3294 18.114643573760986 0.35945773124694824 215.28787231445312 0.7058799266815186 260.7528381347656 0.42983001470565796 0.4624341 4.566600799560547 True -2 4941 18.085789918899536 0.32868313789367676 187.3665313720703 0.9953509569168091 246.668701171875 0.48499229550361633 0.5107096 1.729740023612976 True -3 6588 18.074354887008667 0.6591174602508545 157.21170043945312 0.8030102252960205 241.59326171875 0.5001307725906372 0.5294778 1.0619302988052368 True -4 8235 18.068137884140015 0.33795857429504395 192.71530151367188 0.5221534967422485 239.29196166992188 0.507288932800293 0.5504703 0.7777559757232666 True -5 9882 18.07063937187195 0.33254218101501465 179.24285888671875 0.5710693597793579 238.20741271972656 0.5111461281776428 0.56334996 0.6643248796463013 True -6 11529 18.07145071029663 0.33197808265686035 200.71340942382812 0.5719637870788574 237.39846801757812 0.5142568945884705 0.5736794 0.6372952461242676 True -7 13176 18.08822250366211 0.33153820037841797 183.10198974609375 0.5860143303871155 236.70651245117188 0.5166977643966675 0.58865196 0.5679806470870972 True -8 14823 18.091951370239258 0.3362572193145752 218.04725646972656 0.542564868927002 236.1777801513672 0.5190060138702393 0.5926682 0.5533250570297241 True -9 16470 18.074704885482788 0.33213114738464355 181.3663787841797 0.5596276521682739 235.5755615234375 0.5211447477340698 0.6021423 0.5118942856788635 True -10 18117 18.25624179840088 0.33387041091918945 155.33047485351562 0.3933910131454468 234.98403930664062 0.5232154726982117 0.61010957 0.49712690711021423 True -11 19764 17.89870309829712 0.3289377689361572 189.01458740234375 0.3229737877845764 234.5441131591797 0.5252268314361572 0.6163514 0.47594618797302246 True -12 21411 17.76181149482727 0.3271479606628418 168.06097412109375 0.5134566426277161 234.10760498046875 0.5269357562065125 0.6231939 0.4662898778915405 True -13 23058 17.744423389434814 0.3270456790924072 169.58055114746094 0.5257463455200195 233.6798095703125 0.528268575668335 0.6253856 0.4588340222835541 True -14 24705 17.764918088912964 0.3300156593322754 197.48304748535156 0.2694700062274933 233.38223266601562 0.5294053554534912 0.635094 0.44048067927360535 True -15 26352 17.736587524414062 0.6671595573425293 185.46249389648438 0.40730318427085876 233.19642639160156 0.5299258828163147 0.6390627 0.4377135932445526 True -16 27999 17.774201154708862 0.3261594772338867 182.56883239746094 0.4994007647037506 233.1686248779297 0.5298677086830139 0.6407359 0.4416532516479492 True -17 29646 17.788418292999268 0.532813310623169 166.7677001953125 0.3397291898727417 233.28489685058594 0.5291739702224731 0.6408371 0.4438435435295105 True -18 31293 17.752171277999878 0.3335697650909424 163.42684936523438 0.31865400075912476 233.35812377929688 0.5286437273025513 0.64001477 0.44650933146476746 False -19 32940 17.762319803237915 0.325791597366333 175.41046142578125 0.21573100984096527 233.4447021484375 0.5281107425689697 0.63649684 0.45347070693969727 False diff --git a/ENCSR470ZNM/cherimoya.fold_0.performance.tsv b/ENCSR470ZNM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 33af71ebc99714a39b42fa9560b4efa516797e57..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -233.28489685058594 0.3765620291233063 0.5291739106178284 0.14489306509494781 0.6408370733261108 0.6240420341491699 0.4438435435295105 \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_1.evaluate.json b/ENCSR470ZNM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c3537bfb25bdc732e85ca067710865250bf8db54..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367ILE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_1.fit.json b/ENCSR470ZNM/cherimoya.fold_1.fit.json deleted file mode 100644 index b21b45eb264f49078b4c80b01bd3972c623a9df6..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF367ILE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_1.log b/ENCSR470ZNM/cherimoya.fold_1.log deleted file mode 100644 index 9fb1b78af61e1928970f2bc1310fa2281ef5d871..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1682 23.904930114746094 3.3231351375579834 217.06582641601562 0.7065927386283875 292.5267333984375 0.3442099690437317 0.371494 10.453753471374512 True -1 3364 18.515525817871094 0.38707995414733887 181.8138427734375 0.8328348994255066 260.4916687011719 0.4335775077342987 0.50091714 4.442475318908691 True -2 5046 18.473836421966553 0.370272159576416 197.219970703125 0.5683562755584717 249.0807647705078 0.4768572747707367 0.5413299 1.3547204732894897 True -3 6728 18.687905073165894 0.3770711421966553 195.19496154785156 0.7619726657867432 245.4008331298828 0.4884091317653656 0.5686593 0.6271724104881287 True -4 8410 18.515467643737793 0.3898508548736572 207.15411376953125 0.7879389524459839 244.24375915527344 0.4926070272922516 0.5836292 0.5120171308517456 True -5 10092 18.51235580444336 0.38791680335998535 163.9866485595703 0.5237366557121277 243.6203155517578 0.4955999553203583 0.58890134 0.467410147190094 True -6 11774 18.489994525909424 0.4124009609222412 177.38455200195312 0.4411700963973999 243.25616455078125 0.4974445104598999 0.60473233 0.45167621970176697 True -7 13456 18.517701864242554 0.3708035945892334 199.813232421875 0.7324215173721313 242.58163452148438 0.5001784563064575 0.61492795 0.4405284821987152 True -8 15138 18.49546527862549 0.37906384468078613 194.34912109375 0.5280797481536865 241.8658905029297 0.5029352307319641 0.61801916 0.4360504150390625 True -9 16820 18.464409112930298 0.38547754287719727 185.2231903076172 0.8225098252296448 241.3998260498047 0.5050352811813354 0.62615705 0.4216662645339966 True -10 18502 18.46134901046753 0.379319429397583 209.43649291992188 0.3693113923072815 240.86294555664062 0.5069012641906738 0.63478845 0.4156350791454315 True -11 20184 18.567457914352417 19.85137677192688 189.35169982910156 0.5996161699295044 240.29763793945312 0.5088143348693848 0.6424225 0.4115036129951477 True -12 21866 18.783380270004272 0.3990037441253662 181.14166259765625 0.6549912691116333 239.9340362548828 0.510132908821106 0.6474033 0.407724529504776 True -13 23548 18.516535758972168 1.2431824207305908 185.30178833007812 0.3833342492580414 239.34292602539062 0.5118451714515686 0.6571174 0.3869670629501343 True -14 25230 18.50570583343506 0.3771195411682129 208.7664794921875 0.4077591300010681 238.96800231933594 0.5130320191383362 0.66104376 0.38258641958236694 True -15 26912 18.511388063430786 0.3770020008087158 169.296875 0.4060811698436737 238.78514099121094 0.5134620070457458 0.6679253 0.37784329056739807 True -16 28594 18.467895984649658 0.37119317054748535 161.82376098632812 0.39065346121788025 238.74327087402344 0.5133702158927917 0.6720534 0.3819832503795624 True -17 30276 18.525634765625 0.3837289810180664 167.99746704101562 0.2653040289878845 238.81878662109375 0.5127736330032349 0.6716615 0.38671964406967163 False -18 31958 18.611603260040283 18.889650344848633 185.25344848632812 0.317411333322525 238.9335479736328 0.5122289061546326 0.6707524 0.3905773162841797 False -19 33640 18.569647550582886 0.3767056465148926 158.0023193359375 0.40060365200042725 238.9984893798828 0.5119054317474365 0.67113155 0.39511653780937195 False diff --git a/ENCSR470ZNM/cherimoya.fold_1.performance.tsv b/ENCSR470ZNM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 24f96bd85c0eda034949b43cf24d418b3bf41765..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -238.74327087402344 0.38034868240356445 0.5133702158927917 0.14193490147590637 0.6720533967018127 0.6638380885124207 0.3819832503795624 \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_2.evaluate.json b/ENCSR470ZNM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cd4e69340a06084d26ca6d384145386c1e0b3b6e..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367ILE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_2.fit.json b/ENCSR470ZNM/cherimoya.fold_2.fit.json deleted file mode 100644 index 40101429f86ff74283206cec73c47d5c3adafd9a..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF367ILE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_2.log b/ENCSR470ZNM/cherimoya.fold_2.log deleted file mode 100644 index 87f415b76dd12b2566d86224cb40bda70b5ffdb4..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1760 26.079001903533936 4.312408208847046 211.8170623779297 0.5157699584960938 286.2583923339844 0.3469086289405823 0.4081895 9.418612480163574 True -1 3520 19.381147146224976 0.3856382369995117 199.31942749023438 0.7551755309104919 254.31622314453125 0.437155544757843 0.51472914 4.146252155303955 True -2 5280 19.37236261367798 0.34812164306640625 203.85687255859375 0.6166239976882935 243.8242645263672 0.47879594564437866 0.53598535 1.7015284299850464 True -3 7040 19.362069845199585 0.3189413547515869 194.49569702148438 0.9020490646362305 239.7227020263672 0.4922108054161072 0.56712717 0.9121798872947693 True -4 8800 19.340359926223755 0.34369754791259766 188.405029296875 0.5095949172973633 237.8854522705078 0.4984253942966461 0.59021443 0.6330967545509338 True -5 10560 19.371790647506714 0.32491159439086914 175.46728515625 0.6207015514373779 237.02105712890625 0.5016237497329712 0.6051875 0.5613240599632263 True -6 12320 19.415868997573853 0.6521134376525879 158.18051147460938 0.5494529604911804 236.42398071289062 0.5041361451148987 0.6131161 0.5363305807113647 True -7 14080 19.10709309577942 0.3116779327392578 184.54537963867188 0.527801513671875 235.771240234375 0.5064620971679688 0.619513 0.5175617337226868 True -8 15840 19.018378257751465 0.6135175228118896 160.9329376220703 0.5143511295318604 235.2942657470703 0.5084043741226196 0.6255018 0.511538565158844 True -9 17600 19.023593187332153 0.3167304992675781 191.54757690429688 0.4618135690689087 234.72134399414062 0.5103791356086731 0.6330917 0.4764818847179413 True -10 19360 19.017444372177124 0.3144567012786865 178.9770050048828 0.6215788722038269 234.4619140625 0.511758029460907 0.636072 0.46944886445999146 True -11 21120 19.090081214904785 0.32350683212280273 179.48550415039062 0.5783705711364746 234.00437927246094 0.513168215751648 0.6411591 0.4574367105960846 True -12 22880 19.057782888412476 0.3194880485534668 192.041015625 0.43115687370300293 233.63079833984375 0.5144683122634888 0.6488079 0.44022491574287415 True -13 24640 19.047817707061768 0.3160862922668457 206.4873046875 0.6920251846313477 233.26300048828125 0.5159478187561035 0.6498242 0.43714019656181335 True -14 26400 19.04635739326477 0.313793420791626 193.74148559570312 0.37603485584259033 232.8738555908203 0.5170336365699768 0.6587112 0.42212921380996704 True -15 28160 19.04515242576599 0.32099080085754395 203.85577392578125 0.43563559651374817 232.63368225097656 0.5178377032279968 0.6653499 0.41021987795829773 True -16 29920 18.98551368713379 0.313396692276001 195.05340576171875 0.30124688148498535 232.5895233154297 0.518092155456543 0.6682079 0.4069973826408386 True -17 31680 18.97712755203247 0.31540727615356445 183.2208251953125 0.3192374110221863 232.6159210205078 0.5177973508834839 0.66792357 0.4093661606311798 False -18 33440 18.969703912734985 0.31449031829833984 172.55984497070312 0.41938722133636475 232.7311248779297 0.5172526836395264 0.6642229 0.4179251790046692 False -19 35200 18.996895790100098 0.30918216705322266 192.66543579101562 0.37169697880744934 232.8839569091797 0.5167489647865295 0.66244596 0.42488789558410645 False diff --git a/ENCSR470ZNM/cherimoya.fold_2.performance.tsv b/ENCSR470ZNM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index aedf46dcfa41e7f8d2ed51ae6fb3842b057a22fc..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -232.5895233154297 0.38047462701797485 0.518092155456543 0.1420575976371765 0.6682078838348389 0.6566352844238281 0.4069973826408386 \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_3.evaluate.json b/ENCSR470ZNM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 19d2b7c4133df5c0334efa8262de302f76b3ef7b..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367ILE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_3.fit.json b/ENCSR470ZNM/cherimoya.fold_3.fit.json deleted file mode 100644 index 7627c409b84e157c4049aed2e6507a4d7f25b0f7..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF367ILE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_3.log b/ENCSR470ZNM/cherimoya.fold_3.log deleted file mode 100644 index e38f9bc1ea2cd1efa5428200712f4ff3d2d65292..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1719 23.57309651374817 3.5247156620025635 199.31793212890625 0.8746161460876465 299.6944885253906 0.3509103059768677 0.41096634 10.352458953857422 True -1 3438 18.974493265151978 1.0664725303649902 182.02890014648438 0.7306003570556641 262.0694580078125 0.45058736205101013 0.5175933 4.21959114074707 True -2 5157 18.90482997894287 0.3939499855041504 203.47622680664062 0.6794300079345703 250.46942138671875 0.4928668141365051 0.5340188 1.5633851289749146 True -3 6876 18.909882068634033 0.4824187755584717 172.05624389648438 0.5841067433357239 247.22476196289062 0.5025755763053894 0.5421238 0.9452279806137085 True -4 8595 18.916353940963745 0.4203517436981201 197.400390625 0.5282956957817078 246.01332092285156 0.5067001581192017 0.54709494 0.8462125658988953 True -5 10314 18.926796674728394 0.41199207305908203 172.46438598632812 0.5081526041030884 244.83221435546875 0.5108224153518677 0.5685267 0.7345913648605347 True -6 12033 18.934605836868286 0.38523340225219727 179.7371368408203 0.5684758424758911 243.9944610595703 0.5139088034629822 0.57974446 0.6479580998420715 True -7 13752 18.909197092056274 0.40850186347961426 173.0281982421875 0.5630532503128052 243.38108825683594 0.5162869691848755 0.58627015 0.6199080348014832 True -8 15471 18.928160429000854 0.42051076889038086 191.2998809814453 0.8140047788619995 242.80255126953125 0.5184407234191895 0.59518826 0.5970491766929626 True -9 17190 18.91982650756836 0.39150023460388184 187.6327362060547 0.6164833307266235 242.37448120117188 0.5204170346260071 0.605219 0.5634454488754272 True -10 18909 18.93271780014038 0.4008214473724365 183.9433135986328 0.6418678760528564 241.6662139892578 0.5225866436958313 0.6157947 0.5424126982688904 True -11 20628 18.962514877319336 0.3799433708190918 187.12303161621094 0.4989031255245209 240.9210662841797 0.5249269604682922 0.62497723 0.5218993425369263 True -12 22347 18.940185070037842 9.994856834411621 184.23941040039062 0.5219084620475769 240.41224670410156 0.5266357660293579 0.63547 0.496071994304657 True -13 24066 18.981831312179565 0.6908273696899414 165.9329071044922 0.39205729961395264 239.8203887939453 0.5283945202827454 0.6453594 0.4681009352207184 True -14 25785 18.91621732711792 0.38286900520324707 205.0649871826172 0.3799920380115509 239.41360473632812 0.5297063589096069 0.65403694 0.4596633315086365 True -15 27504 18.93060827255249 0.3638293743133545 195.186279296875 0.3657076358795166 239.17942810058594 0.530446469783783 0.6590639 0.4445078372955322 True -16 29223 18.906091451644897 0.37998127937316895 171.95440673828125 0.3226667046546936 239.1058807373047 0.5305399894714355 0.663203 0.443708211183548 True -17 30942 18.919039487838745 0.3896484375 187.6866455078125 0.27642887830734253 239.15660095214844 0.5300493836402893 0.6613509 0.446684330701828 False -18 32661 18.895445108413696 0.3648245334625244 167.00576782226562 0.32328498363494873 239.22720336914062 0.529520571231842 0.6599218 0.44885703921318054 False -19 34380 18.901135444641113 0.37032270431518555 202.07473754882812 0.28587964177131653 239.31251525878906 0.5291783213615417 0.6577709 0.45042338967323303 False diff --git a/ENCSR470ZNM/cherimoya.fold_3.performance.tsv b/ENCSR470ZNM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5f94a8e59aa6bc808107256561435c263c38a303..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -239.1058807373047 0.372764527797699 0.5305399298667908 0.1478448361158371 0.6632030010223389 0.6513257026672363 0.443708211183548 \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_4.evaluate.json b/ENCSR470ZNM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ce18c1a8db7d9d3b96dbd9e53ed749e34ff89135..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367ILE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_4.fit.json b/ENCSR470ZNM/cherimoya.fold_4.fit.json deleted file mode 100644 index 50487ad40eef184b1c75fe8afb216f2680db9266..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF367ILE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR470ZNM/cherimoya.fold_4.log b/ENCSR470ZNM/cherimoya.fold_4.log deleted file mode 100644 index 69f393356d215f59597726a81eb02eac214bd609..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1770 24.154181957244873 3.316135883331299 200.3251953125 0.898524284362793 290.23095703125 0.3491690456867218 0.41595623 9.950912475585938 True -1 3540 19.456817865371704 0.39987874031066895 171.52407836914062 0.520636796951294 256.03997802734375 0.44709286093711853 0.47906807 3.7829225063323975 True -2 5310 19.471871614456177 0.3706052303314209 214.3909912109375 0.6875643134117126 244.15638732910156 0.49359047412872314 0.4579519 1.667734146118164 False -3 7080 19.483266353607178 0.43689584732055664 176.5350341796875 0.4927583932876587 240.36215209960938 0.5051499009132385 0.50675315 1.0210778713226318 True -4 8850 19.456931352615356 0.4095420837402344 165.6502685546875 0.5765764713287354 239.05392456054688 0.5097703337669373 0.53575295 0.8467066884040833 True -5 10620 19.45178508758545 0.41781067848205566 173.70614624023438 0.6066110134124756 238.3245849609375 0.5122294425964355 0.5587359 0.7460299730300903 True -6 12390 19.47322416305542 0.3378932476043701 215.981689453125 0.6906177997589111 237.55865478515625 0.5151956677436829 0.56775177 0.6807971596717834 True -7 14160 19.371978521347046 0.3333406448364258 184.78514099121094 0.7241228818893433 237.16390991210938 0.5168375968933105 0.572335 0.6946666240692139 True -8 15930 19.043910264968872 0.34547948837280273 177.43408203125 0.5380393266677856 236.54519653320312 0.5190216302871704 0.5882234 0.6211562752723694 True -9 17700 19.08629274368286 0.34111547470092773 177.99745178222656 0.4072912335395813 235.80039978027344 0.521420955657959 0.5966309 0.5513588786125183 True -10 19470 19.096352100372314 0.3347437381744385 168.01373291015625 0.48200350999832153 235.30491638183594 0.523155689239502 0.6020817 0.5375906229019165 True -11 21240 19.125372886657715 0.3336045742034912 163.01409912109375 0.4986472725868225 234.78109741210938 0.5250141024589539 0.60755575 0.5156082510948181 True -12 23010 19.096548318862915 0.3484158515930176 164.05288696289062 0.5137455463409424 234.25840759277344 0.527079701423645 0.6166311 0.4771254062652588 True -13 24780 19.065510511398315 0.3361666202545166 183.98715209960938 0.5049264430999756 233.76193237304688 0.5284111499786377 0.6266289 0.4563257694244385 True -14 26550 19.09136128425598 0.34299230575561523 189.71096801757812 0.48274868726730347 233.38328552246094 0.5297719240188599 0.6332537 0.4490680396556854 True -15 28320 19.0843608379364 0.3372952938079834 168.7891387939453 0.37637588381767273 233.10618591308594 0.5308248996734619 0.6391388 0.4468548893928528 True -16 30090 19.12304925918579 0.34167027473449707 172.66622924804688 0.33462873101234436 233.00535583496094 0.5310123562812805 0.64500713 0.4398888945579529 True -17 31860 19.08089804649353 1.4749529361724854 173.313232421875 0.35225728154182434 233.0952606201172 0.5305254459381104 0.643562 0.4410472810268402 False -18 33630 19.066134214401245 0.3494858741760254 160.6536865234375 0.3444354236125946 233.189453125 0.5300116539001465 0.6399554 0.4503587782382965 False -19 35400 19.07620096206665 0.36916089057922363 192.29556274414062 0.20718272030353546 233.2399139404297 0.5297456383705139 0.6391138 0.45463496446609497 False diff --git a/ENCSR470ZNM/cherimoya.fold_4.performance.tsv b/ENCSR470ZNM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4ab020c596c88a0271b29e62421084d0133263fd..0000000000000000000000000000000000000000 --- a/ENCSR470ZNM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -233.00535583496094 0.374625027179718 0.5310123562812805 0.14543746411800385 0.6450071334838867 0.6228740215301514 0.4398888945579529 \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_0.evaluate.json b/ENCSR471RHG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 71d043bb53c08dde58abaeb4f1f5daaeb1f7c8ed..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF509BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_0.fit.json b/ENCSR471RHG/cherimoya.fold_0.fit.json deleted file mode 100644 index fe8abfff7395248877d64121bd6d895c5a9c01a2..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF509BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_0.log b/ENCSR471RHG/cherimoya.fold_0.log deleted file mode 100644 index 4ad4d9736fdbf0994e124b42178e5d754ec260be..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1802 24.53483486175537 4.435715436935425 293.5318908691406 1.0689040422439575 389.4074401855469 0.1642795354127884 0.6121201 9.706040382385254 True -1 3604 20.034024715423584 0.38307952880859375 224.39047241210938 0.6675724983215332 347.9996337890625 0.24765288829803467 0.72920597 5.097581386566162 True -2 5406 20.00749897956848 0.41998863220214844 321.80889892578125 1.248818278312683 320.7429504394531 0.2890644371509552 0.76005685 2.4873807430267334 True -3 7208 19.9920437335968 0.37349891662597656 250.28741455078125 0.47838836908340454 313.6378479003906 0.3006841838359833 0.7805252 1.474501132965088 True -4 9010 20.032185792922974 0.372844934463501 223.39840698242188 0.6964832544326782 311.2571105957031 0.303526908159256 0.79302096 1.0528714656829834 True -5 10812 20.042263746261597 0.37427663803100586 240.907958984375 1.0103070735931396 308.9941101074219 0.3077000379562378 0.8024676 0.8348037600517273 True -6 12614 20.043452262878418 0.3826737403869629 300.99395751953125 0.5319231748580933 307.49493408203125 0.3112628757953644 0.80685556 0.7632917165756226 True -7 14416 20.02642059326172 0.3630492687225342 184.59226989746094 0.639538049697876 307.19287109375 0.31220918893814087 0.80981153 0.7151403427124023 True -8 16218 20.00848698616028 0.37215328216552734 244.13377380371094 0.718829870223999 305.66162109375 0.315210223197937 0.81620747 0.6564109921455383 True -9 18020 20.014575958251953 0.37436938285827637 288.20428466796875 0.49350506067276 305.2104797363281 0.31582751870155334 0.82266635 0.598918616771698 True -10 19822 20.014243841171265 0.36992549896240234 226.8358154296875 0.7061281204223633 304.1923828125 0.31753209233283997 0.82740027 0.5493460893630981 True -11 21624 20.016376495361328 0.3697528839111328 229.22154235839844 0.6410640478134155 303.8581237792969 0.3178119361400604 0.8305483 0.5334936380386353 True -12 23426 20.020989418029785 0.36851072311401367 339.60162353515625 0.5979248285293579 303.0325622558594 0.3205474615097046 0.83544606 0.5105181336402893 True -13 25228 20.013168811798096 0.3697640895843506 250.1391143798828 0.617542028427124 302.010498046875 0.3229096531867981 0.8398247 0.4913152754306793 True -14 27030 20.012601137161255 0.369722843170166 258.5933837890625 0.5836794376373291 301.4281005859375 0.3233519196510315 0.84336346 0.4833206534385681 True -15 28832 20.02195715904236 0.36855268478393555 208.45928955078125 0.49236834049224854 300.25836181640625 0.32547229528427124 0.8457953 0.4739205539226532 True -16 30634 19.8934485912323 0.376054048538208 292.282958984375 0.5818891525268555 300.98223876953125 0.3241192400455475 0.8477518 0.4690013527870178 True -17 32436 19.60438561439514 0.3714301586151123 258.1415100097656 0.39067110419273376 301.52252197265625 0.3229718506336212 0.84920335 0.46910297870635986 True -18 34238 19.588942766189575 0.37528514862060547 259.87896728515625 0.43607062101364136 301.277099609375 0.32439127564430237 0.8473829 0.4754805266857147 False -19 36040 19.652507781982422 0.37307262420654297 296.6048583984375 0.3003619313240051 301.34332275390625 0.3239593505859375 0.84679556 0.4793090224266052 False diff --git a/ENCSR471RHG/cherimoya.fold_0.performance.tsv b/ENCSR471RHG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 390576cdce2a2370d2b2896a1d2305ae8ea88687..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -301.52252197265625 0.47198542952537537 0.3229718804359436 0.09985879808664322 0.84920334815979 0.8019046187400818 0.46910297870635986 \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_1.evaluate.json b/ENCSR471RHG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 55f6a1fd51feb828fb4877a4ff50564f84cba44a..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF509BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_1.fit.json b/ENCSR471RHG/cherimoya.fold_1.fit.json deleted file mode 100644 index 3c27da722ac349b6d802a2e02d350a9e123f2c3e..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF509BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_1.log b/ENCSR471RHG/cherimoya.fold_1.log deleted file mode 100644 index 7e9799d8490a961d7c7de3921e1b8f8b0bc53c07..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1763 24.139952421188354 3.6391451358795166 232.0242462158203 0.6394776105880737 470.43743896484375 0.17644165456295013 0.60581154 10.755180358886719 True -1 3526 19.575963258743286 0.5565786361694336 282.07574462890625 0.646560549736023 422.82061767578125 0.2594483494758606 0.7250892 5.992752552032471 True -2 5289 19.951382160186768 17.039771556854248 253.99560546875 0.716020941734314 390.3149719238281 0.30436909198760986 0.772127 2.6262757778167725 True -3 7052 19.590572834014893 0.522803544998169 294.68548583984375 1.482679843902588 379.47125244140625 0.3195134997367859 0.7876851 1.503723382949829 True -4 8815 19.616689205169678 0.9596467018127441 256.2748718261719 0.8784316778182983 375.4818115234375 0.3257106840610504 0.80089915 1.1217865943908691 True -5 10578 19.64207148551941 0.5191900730133057 264.5282287597656 0.9664364457130432 373.4353332519531 0.3290226459503174 0.8042488 1.0171350240707397 True -6 12341 19.671255111694336 0.5184440612792969 226.40087890625 0.6359937191009521 371.8025207519531 0.33104878664016724 0.81201714 0.9558688402175903 True -7 14104 19.56248164176941 0.49941062927246094 312.3056640625 0.534497857093811 369.9014587402344 0.3339300751686096 0.82259417 0.8453881144523621 True -8 15867 19.59574007987976 0.5205843448638916 219.90333557128906 0.49025046825408936 367.8787841796875 0.3377697169780731 0.8287656 0.7310035824775696 True -9 17630 19.569041967391968 0.5180301666259766 271.2632751464844 0.47482308745384216 366.4613037109375 0.3391333222389221 0.83237106 0.6782066822052002 True -10 19393 19.64721941947937 11.694621562957764 288.08270263671875 0.7088061571121216 365.3907470703125 0.34173527359962463 0.8367414 0.6427387595176697 True -11 21156 19.59252142906189 0.7479965686798096 309.3039855957031 0.5293870568275452 363.692138671875 0.34479957818984985 0.84103787 0.5945538282394409 True -12 22919 19.592256784439087 13.236075401306152 260.90533447265625 0.6274667382240295 362.1051025390625 0.3475552201271057 0.8481232 0.5853198766708374 True -13 24682 19.570298194885254 0.542438268661499 234.98275756835938 0.6009107828140259 361.4908752441406 0.347659170627594 0.852229 0.545810878276825 True -14 26445 19.56463384628296 1.2643506526947021 198.36734008789062 0.7094460725784302 360.039794921875 0.35080718994140625 0.856048 0.5339807868003845 True -15 28208 19.583026885986328 0.515737771987915 238.2322235107422 0.45775508880615234 360.0752868652344 0.35010966658592224 0.8580196 0.5271396636962891 True -16 29971 19.561867237091064 0.6375267505645752 229.08021545410156 0.5619857311248779 359.781005859375 0.3503199815750122 0.8604963 0.5180814266204834 True -17 31734 19.596940517425537 1.4169983863830566 165.726318359375 0.49711668491363525 360.0079650878906 0.3489629328250885 0.8588127 0.5151915550231934 False -18 33497 19.61808156967163 0.5235297679901123 209.59451293945312 0.28999173641204834 360.3563537597656 0.34871047735214233 0.8589557 0.526459276676178 False -19 35260 19.617735147476196 0.5168302059173584 232.30886840820312 0.3330947756767273 360.8580017089844 0.3476175367832184 0.85795265 0.5275007486343384 False diff --git a/ENCSR471RHG/cherimoya.fold_1.performance.tsv b/ENCSR471RHG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 69ec97b8bbf71ccb1c32ea56ef857ea002ce07f7..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -359.781005859375 0.44840207695961 0.3503199815750122 0.11356475204229355 0.8604962825775146 0.8325821757316589 0.5180814266204834 \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_2.evaluate.json b/ENCSR471RHG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b99f68ce567f35d85c8b0e3a1459269daac93300..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF509BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_2.fit.json b/ENCSR471RHG/cherimoya.fold_2.fit.json deleted file mode 100644 index 9c34461f003b74b6f82cf8c58f2aa731abce754f..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF509BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_2.log b/ENCSR471RHG/cherimoya.fold_2.log deleted file mode 100644 index fea677ccbb25a013183e3f47dd66c84b2152ee69..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1911 25.661938905715942 3.4634058475494385 312.06982421875 1.2879700660705566 410.4935302734375 0.1673346906900406 0.59320015 9.325423240661621 True -1 3822 21.31882905960083 0.4817655086517334 261.17095947265625 0.9835319519042969 365.8985900878906 0.25041261315345764 0.7030231 4.718035697937012 True -2 5733 21.269634246826172 0.3780379295349121 253.78466796875 0.6498544216156006 337.55645751953125 0.28921040892601013 0.7603038 2.0599265098571777 True -3 7644 21.247087955474854 0.375774621963501 277.5111083984375 0.9681518077850342 329.5023498535156 0.2994338870048523 0.77772707 1.2078725099563599 True -4 9555 21.271432161331177 0.3969240188598633 261.65753173828125 0.7806270122528076 327.1656799316406 0.3038395345211029 0.78434145 1.066452145576477 True -5 11466 21.253196239471436 0.39072680473327637 226.3463897705078 0.6280866265296936 323.7586975097656 0.3101343512535095 0.7983768 0.8293565511703491 True -6 13377 21.273767948150635 0.4007573127746582 200.33721923828125 0.5632414817810059 323.7062683105469 0.3098416030406952 0.8002484 0.7863748073577881 True -7 15288 21.25906538963318 0.3949015140533447 252.84963989257812 0.8682695627212524 322.52252197265625 0.31308048963546753 0.80624413 0.7356517910957336 True -8 17199 21.25260877609253 0.39516305923461914 180.47494506835938 0.6286972761154175 321.8750305175781 0.3141774535179138 0.811341 0.6914674639701843 True -9 19110 21.29163432121277 0.38823437690734863 195.42857360839844 0.7468159794807434 320.60516357421875 0.3167725205421448 0.8138045 0.668741762638092 True -10 21021 22.65736413002014 1.364166498184204 215.62782287597656 0.4432596266269684 319.161376953125 0.3198206126689911 0.82441914 0.6045511960983276 True -11 22932 20.91669464111328 0.38634824752807617 255.39508056640625 0.7123775482177734 318.3888854980469 0.320091187953949 0.8292177 0.5833407640457153 True -12 24843 20.89880657196045 0.3958871364593506 247.48809814453125 0.39271748065948486 317.560791015625 0.3214797079563141 0.8329505 0.5630044341087341 True -13 26754 20.833871126174927 0.39687490463256836 263.8283996582031 0.4498707354068756 316.68975830078125 0.32363858819007874 0.8354501 0.5482396483421326 True -14 28665 20.78501844406128 0.3802974224090576 207.98617553710938 0.5407005548477173 316.0328674316406 0.3254472017288208 0.84139544 0.5283408761024475 True -15 30576 20.827858448028564 0.38101983070373535 281.27288818359375 0.7314305901527405 315.18597412109375 0.3268895149230957 0.84427917 0.504536509513855 True -16 32487 20.817696571350098 0.4396402835845947 325.71746826171875 0.34004220366477966 314.9819641113281 0.3263746201992035 0.8471315 0.4944536089897156 True -17 34398 20.88046622276306 0.39289283752441406 267.99212646484375 0.44347769021987915 314.93499755859375 0.3264821469783783 0.8472002 0.4958936274051666 True -18 36309 20.886273860931396 0.3968925476074219 257.8521728515625 0.2768026888370514 315.0392761230469 0.32669326663017273 0.84513575 0.5000145435333252 False -19 38220 20.89447331428528 0.3959968090057373 287.0819396972656 0.3823539614677429 315.56793212890625 0.32504957914352417 0.8437774 0.505438506603241 False diff --git a/ENCSR471RHG/cherimoya.fold_2.performance.tsv b/ENCSR471RHG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7ed2b7bb1a54a83280a599d2fa688f6e5a7b709f..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -314.93499755859375 0.4687458574771881 0.3264821767807007 0.10271184146404266 0.8472002148628235 0.8052756190299988 0.4958936274051666 \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_3.evaluate.json b/ENCSR471RHG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d4370ddca44c25565d32f62ab0dbb5b2ad45d3fe..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF509BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_3.fit.json b/ENCSR471RHG/cherimoya.fold_3.fit.json deleted file mode 100644 index 9c4d41754ed1c1090bf4604c2592133b3caa990b..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF509BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_3.log b/ENCSR471RHG/cherimoya.fold_3.log deleted file mode 100644 index 738cc04dc462fb59d71286dde7116af13570dbc3..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1822 24.768619775772095 3.5404436588287354 300.8095397949219 1.4446803331375122 402.7407531738281 0.1801729053258896 0.59173983 10.480663299560547 True -1 3644 20.214523553848267 0.7757515907287598 225.37229919433594 1.1647051572799683 357.45147705078125 0.2650195360183716 0.72434443 5.289824485778809 True -2 5466 20.242489099502563 0.35944080352783203 316.57440185546875 0.9085506796836853 336.757080078125 0.29594966769218445 0.7592484 2.5143680572509766 True -3 7288 20.23358988761902 0.3604440689086914 244.161376953125 0.6225584745407104 330.154296875 0.307020902633667 0.770486 1.4222387075424194 True -4 9110 20.23709511756897 0.3693115711212158 266.79534912109375 0.8227750062942505 328.2999572753906 0.31109344959259033 0.7731583 1.2704765796661377 True -5 10932 20.181785345077515 0.3606560230255127 235.27391052246094 0.7751390337944031 327.0260009765625 0.3137657344341278 0.7797397 1.09857177734375 True -6 12754 20.194217205047607 0.3613429069519043 259.42730712890625 0.8310420513153076 325.93353271484375 0.31631478667259216 0.7818413 1.053696632385254 True -7 14576 20.20278549194336 8.060860633850098 211.54754638671875 0.6851046681404114 324.3586730957031 0.31994330883026123 0.7889351 0.867211639881134 True -8 16398 20.211264610290527 1.5012080669403076 288.3402099609375 0.6129029989242554 322.6404113769531 0.32347530126571655 0.79370636 0.8205779790878296 True -9 18220 20.20374035835266 0.38350677490234375 253.85833740234375 0.6235345005989075 322.1029052734375 0.3242179751396179 0.7981477 0.7511125206947327 True -10 20042 20.222129583358765 0.9963333606719971 348.9876403808594 0.666804850101471 320.5164794921875 0.32772332429885864 0.8045417 0.7050748467445374 True -11 21864 20.205359935760498 0.36359095573425293 264.87652587890625 0.5932998061180115 319.30963134765625 0.3294253647327423 0.81464016 0.6419721245765686 True -12 23686 20.19899272918701 0.3650836944580078 257.28070068359375 0.6062278151512146 318.43841552734375 0.3314325213432312 0.8208274 0.6176488995552063 True -13 25508 20.232041597366333 0.36302876472473145 195.23135375976562 0.5231664776802063 318.3961486816406 0.33001816272735596 0.8261815 0.5898070335388184 True -14 27330 20.20266842842102 0.3624000549316406 266.97265625 0.9033710956573486 317.8204650878906 0.33177658915519714 0.8326574 0.5735837817192078 True -15 29152 20.197237730026245 0.35720062255859375 228.49278259277344 0.42487046122550964 316.99267578125 0.33286139369010925 0.8367485 0.5446246266365051 True -16 30974 20.21858787536621 0.3692336082458496 238.9007568359375 0.4063197076320648 316.7527160644531 0.33320578932762146 0.8406669 0.5345290899276733 True -17 32796 20.216358184814453 0.3699162006378174 260.9993591308594 0.6291555166244507 316.6692199707031 0.3327455222606659 0.84206086 0.529871940612793 True -18 34618 20.23121213912964 0.3669135570526123 245.6712646484375 0.3650228977203369 316.4202575683594 0.3335128128528595 0.8428352 0.532421350479126 True -19 36440 20.23159670829773 0.3706786632537842 207.15036010742188 0.4203430116176605 316.2256164550781 0.3343021273612976 0.8400597 0.537107527256012 False diff --git a/ENCSR471RHG/cherimoya.fold_3.performance.tsv b/ENCSR471RHG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0e651bb8f0b5f84bb041781edca2b1114ddc509a..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -316.4202575683594 0.4627126455307007 0.3335128128528595 0.10404548794031143 0.8428351879119873 0.8004975318908691 0.532421350479126 \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_4.evaluate.json b/ENCSR471RHG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 91b55d1cbcf7d3386096705ce1e48a0d432f56e6..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF509BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_4.fit.json b/ENCSR471RHG/cherimoya.fold_4.fit.json deleted file mode 100644 index 087634053d4d7534d734d2c6755a7cc43e610197..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF509BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR471RHG/cherimoya.fold_4.log b/ENCSR471RHG/cherimoya.fold_4.log deleted file mode 100644 index fa70b2ef8ae780de95bddfbc9eece401ce7f3ad5..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1830 24.926344633102417 7.146231412887573 231.48489379882812 0.8219759464263916 368.78277587890625 0.1618468165397644 0.5947584 9.0105562210083 True -1 3660 20.320187091827393 0.36195969581604004 250.77479553222656 0.8152743577957153 331.0826416015625 0.24069231748580933 0.70352346 4.402069091796875 True -2 5490 20.300021409988403 0.3796670436859131 321.0987243652344 0.8369259834289551 307.0535888671875 0.2786349952220917 0.75173116 1.9102249145507812 True -3 7320 20.30969786643982 1.650176763534546 274.61322021484375 0.9050940275192261 301.4090576171875 0.288852334022522 0.7654338 1.1331846714019775 True -4 9150 20.279218673706055 0.35540175437927246 268.1417236328125 0.8233990669250488 299.09649658203125 0.29234579205513 0.7743969 0.8569406270980835 True -5 10980 20.302474975585938 0.3609042167663574 302.96783447265625 0.6653063297271729 297.66796875 0.29595497250556946 0.7793639 0.7572345733642578 True -6 12810 20.142760038375854 0.3543405532836914 253.5008544921875 0.7656737565994263 296.5728759765625 0.29834404587745667 0.78847545 0.6735618710517883 True -7 14640 19.891538619995117 0.345552921295166 239.76779174804688 0.5307924747467041 296.0035095214844 0.2995317280292511 0.79156727 0.6480879187583923 True -8 16470 19.91717004776001 0.3496739864349365 268.5833740234375 0.6623783111572266 294.38311767578125 0.3025919795036316 0.79444873 0.6214967966079712 True -9 18300 19.863072872161865 0.35391807556152344 197.31597900390625 0.8393985629081726 293.7149963378906 0.30414673686027527 0.80159444 0.5774446725845337 True -10 20130 19.89525055885315 0.34940457344055176 232.77178955078125 0.7333093881607056 292.4920349121094 0.3072047829627991 0.806399 0.5513821244239807 True -11 21960 19.908620595932007 3.942767858505249 235.2397918701172 0.6743959784507751 291.6739501953125 0.30912163853645325 0.812674 0.533011257648468 True -12 23790 19.910506010055542 0.34587907791137695 221.74644470214844 0.39951926469802856 290.5440979003906 0.3109046518802643 0.8192136 0.5128795504570007 True -13 25620 19.852555990219116 0.3405945301055908 254.98814392089844 0.4435122013092041 290.2071533203125 0.31216302514076233 0.82345647 0.49422749876976013 True -14 27450 19.857047080993652 0.33660221099853516 272.48809814453125 0.3884142339229584 289.5960388183594 0.312954843044281 0.8289875 0.48566779494285583 True -15 29280 19.864489793777466 0.3360412120819092 244.21572875976562 0.48314183950424194 288.9203796386719 0.31502118706703186 0.83128905 0.47761374711990356 True -16 31110 19.922565460205078 0.3362545967102051 227.543701171875 0.5173239707946777 288.98162841796875 0.3142019808292389 0.8334122 0.47892916202545166 True -17 32940 19.91111397743225 0.34777379035949707 245.39962768554688 0.33084550499916077 289.1798095703125 0.31386247277259827 0.8322927 0.48435863852500916 False -18 34770 19.904505968093872 0.3439450263977051 241.0552520751953 0.36058172583580017 288.9478454589844 0.31525149941444397 0.8309726 0.4924207329750061 False -19 36600 19.85598111152649 0.3426823616027832 210.7833251953125 0.2994471490383148 289.2783203125 0.31412142515182495 0.8304311 0.4976251423358917 False diff --git a/ENCSR471RHG/cherimoya.fold_4.performance.tsv b/ENCSR471RHG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5af58e3d70d2b8132e4ce06ba95e4b1cad457dfd..0000000000000000000000000000000000000000 --- a/ENCSR471RHG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -288.98162841796875 0.47793665528297424 0.3142019808292389 0.09428438544273376 0.8334121704101562 0.7852888703346252 0.47892916202545166 \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_0.evaluate.json b/ENCSR473LSX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a8fce6db4b529734e18bf346955e3682828231eb..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF705OLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_0.fit.json b/ENCSR473LSX/cherimoya.fold_0.fit.json deleted file mode 100644 index c09623145c2d2f9767f900235b8c8a8e2e0646e4..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF705OLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_0.log b/ENCSR473LSX/cherimoya.fold_0.log deleted file mode 100644 index e61083be4110e8aa474f1eb5bccdf85e8ae95485..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1402 19.86894702911377 3.3301687240600586 318.98114013671875 1.3450226783752441 285.5008544921875 0.12519638240337372 0.5657075 9.379114151000977 True -1 2804 15.57754635810852 0.3292734622955322 220.95599365234375 1.2244137525558472 259.2053527832031 0.18287138640880585 0.69689685 5.916123867034912 True -2 4206 15.57436203956604 0.3012979030609131 195.24063110351562 0.860626220703125 234.32530212402344 0.22432489693164825 0.77155685 3.4169440269470215 True -3 5608 15.573598623275757 0.29389429092407227 182.5803680419922 1.1866904497146606 222.82659912109375 0.241904154419899 0.7960339 1.4301108121871948 True -4 7010 15.582119941711426 0.27922606468200684 219.2372283935547 0.9565622806549072 219.3127899169922 0.24672497808933258 0.7996053 1.0130207538604736 True -5 8412 15.619594812393188 0.28255319595336914 159.38705444335938 0.9388691186904907 217.8661346435547 0.24870681762695312 0.80414075 0.9073934555053711 True -6 9814 15.563831806182861 0.28600335121154785 136.1591796875 0.7842741012573242 216.12379455566406 0.2516738772392273 0.81383944 0.7838410139083862 True -7 11216 15.576921463012695 0.28359460830688477 197.3594970703125 0.6940213441848755 214.8807830810547 0.2542535662651062 0.81902677 0.7015079855918884 True -8 12618 15.28370714187622 0.2751634120941162 195.9373321533203 0.6672438383102417 213.84188842773438 0.25656381249427795 0.8254711 0.6573522686958313 True -9 14020 15.258299827575684 0.27550745010375977 229.6837921142578 0.6573275923728943 212.6490020751953 0.2593109905719757 0.83079815 0.6274378299713135 True -10 15422 15.264218091964722 0.2755882740020752 184.228515625 0.6542384624481201 212.06263732910156 0.260419100522995 0.83360714 0.5966501832008362 True -11 16824 15.226463556289673 0.27649450302124023 201.07997131347656 0.6375621557235718 210.9371795654297 0.2628612816333771 0.84061396 0.574554443359375 True -12 18226 15.244653463363647 0.2788674831390381 196.033447265625 0.4433143138885498 210.56411743164062 0.263930082321167 0.8443232 0.5403131246566772 True -13 19628 15.249335050582886 0.28006577491760254 142.68838500976562 0.4153118133544922 209.5415802001953 0.2661241292953491 0.8472138 0.5232177376747131 True -14 21030 15.242236137390137 0.2760319709777832 182.7720184326172 0.5180754661560059 208.79359436035156 0.2683022916316986 0.8524122 0.5115957856178284 True -15 22432 15.270176410675049 0.2754349708557129 204.45925903320312 0.5574365854263306 208.1486358642578 0.26995599269866943 0.85288393 0.49769142270088196 True -16 23834 15.232706785202026 0.2764413356781006 236.19320678710938 0.3839089274406433 208.49366760253906 0.2685511112213135 0.85541993 0.4917435944080353 True -17 25236 15.294628858566284 0.504807710647583 226.10772705078125 0.6154755353927612 208.82781982421875 0.2671127915382385 0.8563261 0.4921082556247711 True -18 26638 15.256448745727539 0.27853822708129883 161.87271118164062 0.3583555817604065 209.32470703125 0.26582083106040955 0.85491997 0.49551311135292053 False -19 28040 15.295808792114258 0.33940839767456055 183.30783081054688 0.2278136909008026 209.580322265625 0.26551079750061035 0.8554298 0.49947813153266907 False diff --git a/ENCSR473LSX/cherimoya.fold_0.performance.tsv b/ENCSR473LSX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 119a93183571f49363ffe37e39f27dc01769ff26..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -208.82781982421875 0.5177806615829468 0.26711276173591614 0.07605934888124466 0.8563261032104492 0.815438985824585 0.4921082556247711 \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_1.evaluate.json b/ENCSR473LSX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7146be676c718a1eb136fd9a39b06bce2ad835c3..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF705OLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_1.fit.json b/ENCSR473LSX/cherimoya.fold_1.fit.json deleted file mode 100644 index 18a85387927c7c714297544d14c0d7e03db95f75..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF705OLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_1.log b/ENCSR473LSX/cherimoya.fold_1.log deleted file mode 100644 index 0159923b205936391d48b3ee32dcba53806ef725..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1354 19.311094522476196 3.428842306137085 162.84454345703125 1.3305543661117554 363.2045593261719 0.13437683880329132 0.5092677 12.042430877685547 True -1 2708 15.006650686264038 3.001885414123535 256.2964782714844 0.9461845755577087 329.3794250488281 0.19669808447360992 0.6638291 8.457345962524414 True -2 4062 15.058104753494263 0.40012121200561523 201.75584411621094 1.1436501741409302 295.7106628417969 0.24812079966068268 0.73802733 5.432952404022217 True -3 5416 15.058996200561523 0.4173307418823242 197.88046264648438 0.8238481283187866 279.96197509765625 0.2715224027633667 0.76778454 2.9905011653900146 True -4 6770 15.074570894241333 0.3988070487976074 154.52685546875 0.712378978729248 273.14691162109375 0.2789510190486908 0.7874002 1.9493807554244995 True -5 8124 15.059755563735962 0.3975036144256592 253.21836853027344 0.6846289038658142 269.3521423339844 0.2849648892879486 0.79520446 1.584436297416687 True -6 9478 15.108984231948853 0.40526318550109863 200.5622100830078 0.7191347479820251 266.38092041015625 0.2884976863861084 0.81046134 1.2027816772460938 True -7 10832 15.032440185546875 0.41903138160705566 145.79197692871094 0.650741457939148 264.7802734375 0.29094117879867554 0.81951636 1.0443406105041504 True -8 12186 15.022917032241821 0.40675854682922363 164.45709228515625 1.0043104887008667 262.9486083984375 0.29443877935409546 0.82766235 0.89494788646698 True -9 13540 15.014636278152466 0.40361595153808594 145.0621337890625 0.7785980701446533 262.0458068847656 0.29500794410705566 0.8325291 0.8036658763885498 True -10 14894 15.01557183265686 0.4017362594604492 169.16714477539062 0.7101823091506958 260.6690979003906 0.2987219989299774 0.8355194 0.7538918852806091 True -11 16248 15.020109176635742 0.4009130001068115 210.79434204101562 0.5289531946182251 259.7194519042969 0.3002467155456543 0.8414052 0.7093174457550049 True -12 17602 15.017161130905151 0.40078282356262207 200.2652587890625 0.39534661173820496 258.6072692871094 0.3024384379386902 0.8466768 0.6607171297073364 True -13 18956 15.016408205032349 0.4005603790283203 181.337890625 0.5202428102493286 257.7121887207031 0.3036227226257324 0.85266703 0.6236112117767334 True -14 20310 15.077351808547974 0.4081451892852783 170.31492614746094 0.6101603507995605 256.306396484375 0.3065757751464844 0.85766965 0.6024820804595947 True -15 21664 15.008096933364868 0.40636730194091797 171.552001953125 0.40166616439819336 256.1695861816406 0.30748116970062256 0.8590967 0.5819594264030457 True -16 23018 15.039700508117676 0.4052112102508545 188.6968994140625 0.49371302127838135 256.2046203613281 0.30729958415031433 0.86190873 0.5704817175865173 True -17 24372 15.027895212173462 1.3726365566253662 123.1461181640625 0.4771382212638855 255.9702911376953 0.3068406581878662 0.8629802 0.5684185028076172 True -18 25726 15.032976388931274 0.40724754333496094 172.15328979492188 0.26199254393577576 256.5411071777344 0.30553045868873596 0.8611501 0.5729358196258545 False -19 27080 15.0374915599823 0.40172290802001953 189.42880249023438 0.5685212016105652 256.8340759277344 0.30486974120140076 0.85991037 0.5773687958717346 False diff --git a/ENCSR473LSX/cherimoya.fold_1.performance.tsv b/ENCSR473LSX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bbbcf67d1f80af2c965c435ef6e3a38a073ee309..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -255.9702911376953 0.4884856343269348 0.3068406879901886 0.08954251557588577 0.8629801869392395 0.8385498523712158 0.5684185028076172 \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_2.evaluate.json b/ENCSR473LSX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b336dc056b4656da9c43468e60cadd618cb80d20..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF705OLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_2.fit.json b/ENCSR473LSX/cherimoya.fold_2.fit.json deleted file mode 100644 index 95bc3989727bae1b0ecbdaf24ab949337886a878..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF705OLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_2.log b/ENCSR473LSX/cherimoya.fold_2.log deleted file mode 100644 index ad3173b377cf14575dee800615b0aa643aead09c..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1459 21.078298807144165 3.138854742050171 175.3390350341797 1.09336256980896 301.08758544921875 0.12519964575767517 0.50810313 9.727837562561035 True -1 2918 16.203233003616333 0.33948659896850586 168.71707153320312 1.2600820064544678 269.9068298339844 0.1864606887102127 0.6732904 5.88130521774292 True -2 4377 16.201257705688477 0.2998621463775635 216.84786987304688 0.717192530632019 242.0552520751953 0.23360450565814972 0.7490731 3.483016014099121 True -3 5836 16.095685720443726 0.30731654167175293 140.85025024414062 0.7504945993423462 231.90243530273438 0.24597445130348206 0.7801142 1.7129554748535156 True -4 7295 15.918904542922974 0.30027151107788086 144.1285858154297 0.7406737804412842 227.88685607910156 0.25237444043159485 0.7879091 1.2360281944274902 True -5 8754 15.937970399856567 0.2984035015106201 174.03707885742188 0.700577974319458 225.15090942382812 0.2573411166667938 0.80022895 0.9833528399467468 True -6 10213 15.924073696136475 0.2986133098602295 185.07557678222656 0.7993409633636475 223.81224060058594 0.2591153383255005 0.80826783 0.8654082417488098 True -7 11672 15.900627851486206 0.29715514183044434 228.60714721679688 1.1245501041412354 222.8860321044922 0.2596787214279175 0.81808656 0.77254718542099 True -8 13131 15.914208889007568 0.299274206161499 153.58096313476562 0.47301438450813293 221.649169921875 0.26353222131729126 0.8264516 0.6875360012054443 True -9 14590 15.839586734771729 0.29915404319763184 240.47012329101562 0.509780764579773 220.48854064941406 0.26596298813819885 0.83241636 0.6264801025390625 True -10 16049 15.901459693908691 0.30039024353027344 165.30410766601562 0.5086068511009216 219.4759979248047 0.26799654960632324 0.8361425 0.5973297953605652 True -11 17508 15.89516544342041 0.2948791980743408 201.0850830078125 0.40224456787109375 218.2627716064453 0.27074185013771057 0.8432803 0.5623546838760376 True -12 18967 15.91092824935913 0.28926777839660645 221.97329711914062 0.6182082891464233 217.3245849609375 0.272976279258728 0.84689516 0.541405200958252 True -13 20426 15.87877345085144 0.2893846035003662 109.16012573242188 0.4478774666786194 216.40576171875 0.2750526964664459 0.85252976 0.5183005332946777 True -14 21885 15.85383653640747 0.2912471294403076 215.45559692382812 0.5445674657821655 215.77456665039062 0.27649787068367004 0.85504377 0.5106036067008972 True -15 23344 15.868137121200562 0.29317235946655273 192.34791564941406 0.4406072199344635 215.6352996826172 0.27644240856170654 0.8569982 0.49899351596832275 True -16 24803 15.916290283203125 0.3006880283355713 165.1815185546875 0.736872136592865 215.51568603515625 0.2764943540096283 0.85840267 0.4919455349445343 True -17 26262 15.8994779586792 0.30007100105285645 186.3592071533203 0.3222907781600952 215.61241149902344 0.27628886699676514 0.85967654 0.4953712224960327 True -18 27721 15.86081838607788 0.3008277416229248 193.32797241210938 0.4855881333351135 216.21743774414062 0.27478906512260437 0.85881335 0.5011205077171326 False -19 29180 15.841102600097656 0.29892396926879883 125.57867431640625 0.32053273916244507 216.02317810058594 0.27596768736839294 0.85710615 0.5047826170921326 False diff --git a/ENCSR473LSX/cherimoya.fold_2.performance.tsv b/ENCSR473LSX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e699ea471a58b0dde53ab15b3d1a4ebfa1a20258..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -215.61241149902344 0.5116615295410156 0.27628886699676514 0.07124842703342438 0.8596765398979187 0.8213606476783752 0.4953712224960327 \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_3.evaluate.json b/ENCSR473LSX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 55d2827d1f9627cec87209401e6107d16751e8dd..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF705OLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_3.fit.json b/ENCSR473LSX/cherimoya.fold_3.fit.json deleted file mode 100644 index bc0d7d952ad7f106290601dca05bb66bf6aa1b29..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF705OLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_3.log b/ENCSR473LSX/cherimoya.fold_3.log deleted file mode 100644 index d279dc8a343645eb978cd193471f4800ddba8bd9..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1404 19.841240167617798 3.6333601474761963 233.54513549804688 1.4557254314422607 313.26287841796875 0.13656900823116302 0.5180968 10.691629409790039 True -1 2808 15.581464052200317 1.4785103797912598 149.975830078125 0.8615009784698486 282.9584655761719 0.1970483362674713 0.65151125 7.6921610832214355 True -2 4212 15.621159553527832 0.2797372341156006 165.02545166015625 1.239277958869934 252.98106384277344 0.24758698046207428 0.73436195 3.7112233638763428 True -3 5616 15.59635591506958 0.2691359519958496 202.77197265625 0.8763706684112549 243.8640899658203 0.26109376549720764 0.7697813 1.728615164756775 True -4 7020 15.589317321777344 0.27074122428894043 206.80001831054688 0.8330700993537903 240.3075714111328 0.26613369584083557 0.77751213 1.2811379432678223 True -5 8424 15.591026306152344 0.26425838470458984 230.23895263671875 1.0514724254608154 238.2877197265625 0.27044427394866943 0.784241 1.1689817905426025 True -6 9828 15.58474063873291 0.2644782066345215 205.64385986328125 0.7609439492225647 236.32363891601562 0.2739327549934387 0.79399145 1.0621223449707031 True -7 11232 15.586682796478271 0.2667083740234375 165.86309814453125 0.7214909791946411 233.82203674316406 0.2797608971595764 0.79707855 1.0051618814468384 True -8 12636 15.594208717346191 0.26076698303222656 231.5733642578125 0.6812529563903809 233.3292236328125 0.2799829840660095 0.8052855 0.9481461644172668 True -9 14040 15.595043897628784 0.2651505470275879 186.59048461914062 0.5527408719062805 232.6502685546875 0.28149545192718506 0.81102115 0.8343783020973206 True -10 15444 15.602700233459473 0.28693723678588867 183.46810913085938 0.8801144361495972 231.51083374023438 0.2844298779964447 0.8184104 0.7826262712478638 True -11 16848 15.596535682678223 0.2714564800262451 229.67123413085938 0.750815212726593 229.9303741455078 0.28787070512771606 0.8230207 0.7500119209289551 True -12 18252 15.618979692459106 0.2714264392852783 181.89505004882812 0.5031031966209412 228.9315643310547 0.28952065110206604 0.8294221 0.6998134255409241 True -13 19656 15.603710412979126 0.2676842212677002 178.8924102783203 0.357543408870697 228.2387237548828 0.2901763916015625 0.8372429 0.6587337851524353 True -14 21060 15.622689008712769 0.26822805404663086 210.30133056640625 0.4075375199317932 227.449951171875 0.2920615077018738 0.8442165 0.6190653443336487 True -15 22464 15.606910228729248 0.26026058197021484 228.09690856933594 0.42507100105285645 227.0535125732422 0.29299426078796387 0.8481851 0.5883657336235046 True -16 23868 15.580315828323364 0.2619943618774414 190.8447723388672 0.3402419090270996 226.83590698242188 0.29402801394462585 0.8511874 0.5685290694236755 True -17 25272 15.603718280792236 0.26386499404907227 145.34353637695312 0.3198273777961731 227.03765869140625 0.29276910424232483 0.8512035 0.5601730942726135 True -18 26676 15.592534303665161 0.27126455307006836 213.83096313476562 0.4599283039569855 227.73989868164062 0.290820837020874 0.85022235 0.5626733899116516 False -19 28080 15.584509372711182 0.2720050811767578 162.74249267578125 0.36676374077796936 227.60812377929688 0.2919090986251831 0.85122633 0.56477952003479 True diff --git a/ENCSR473LSX/cherimoya.fold_3.performance.tsv b/ENCSR473LSX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b410ea77b2d1b98b694bca395237099777e10878..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -227.60812377929688 0.5011165142059326 0.2919091284275055 0.08107682317495346 0.8512263298034668 0.8254789113998413 0.56477952003479 \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_4.evaluate.json b/ENCSR473LSX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b98e7c667ae4be6196123533a9538dac54e263f3..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF705OLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_4.fit.json b/ENCSR473LSX/cherimoya.fold_4.fit.json deleted file mode 100644 index 0402d7be7b1712e9f30e508e88f9069b1239180b..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF705OLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR473LSX/cherimoya.fold_4.log b/ENCSR473LSX/cherimoya.fold_4.log deleted file mode 100644 index 06b3265d8e91565214e1564cd8d3b7bbac1dd818..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1388 19.784958124160767 3.1869051456451416 187.38577270507812 1.0332422256469727 270.4323425292969 0.12398706376552582 0.52899784 9.066621780395508 True -1 2776 15.255730628967285 0.2977626323699951 133.6178741455078 0.8217997550964355 246.34312438964844 0.17432901263237 0.674913 5.288265705108643 True -2 4164 15.386125564575195 0.27209901809692383 190.31863403320312 0.6250442266464233 224.2488250732422 0.21248550713062286 0.74622655 3.122030258178711 True -3 5552 15.41244387626648 0.28853368759155273 151.7712860107422 0.7010436058044434 214.1145477294922 0.22905205190181732 0.76919943 1.7428359985351562 True -4 6940 15.425581693649292 0.28264808654785156 188.272705078125 0.8863252401351929 210.66769409179688 0.23643578588962555 0.7795092 1.28180730342865 True -5 8328 15.398014783859253 0.268967866897583 185.17654418945312 0.6890616416931152 208.04995727539062 0.24088706076145172 0.7832685 1.1294240951538086 True -6 9716 15.424187421798706 0.27722907066345215 146.38336181640625 0.6863536238670349 206.9827880859375 0.2433420866727829 0.7931705 1.0269739627838135 True -7 11104 15.475078105926514 0.2687852382659912 184.0845947265625 0.6577494144439697 205.8357696533203 0.24590922892093658 0.8057627 0.8895531892776489 True -8 12492 15.373335361480713 0.2794666290283203 194.2840576171875 0.7952885031700134 204.97654724121094 0.24781273305416107 0.81154007 0.7708855271339417 True -9 13880 15.382187128067017 0.29126501083374023 208.74484252929688 0.7354884147644043 203.4718780517578 0.2516587972640991 0.8170183 0.6944470405578613 True -10 15268 15.372186422348022 0.2714352607727051 152.47352600097656 0.8303298950195312 203.01644897460938 0.2535267770290375 0.82398343 0.6350379586219788 True -11 16656 15.387837409973145 0.2783629894256592 256.22247314453125 0.7734915018081665 202.16159057617188 0.2549828290939331 0.8272561 0.604295015335083 True -12 18044 15.37757396697998 0.27293896675109863 173.32086181640625 0.6899744868278503 201.82290649414062 0.254825621843338 0.8336554 0.5791935324668884 True -13 19432 15.406065940856934 0.30159473419189453 160.96376037597656 0.661652684211731 201.13711547851562 0.256918340921402 0.8397387 0.5475383996963501 True -14 20820 15.393898725509644 0.2812540531158447 180.08956909179688 0.6955533027648926 200.88861083984375 0.2563054859638214 0.8447959 0.5218560695648193 True -15 22208 15.410690069198608 1.3441739082336426 174.92543029785156 0.4423661530017853 200.4629364013672 0.25795960426330566 0.84996456 0.5080620646476746 True -16 23596 15.38995099067688 0.2857480049133301 146.0608673095703 0.5718762278556824 200.20889282226562 0.25839686393737793 0.85145545 0.49579527974128723 True -17 24984 15.424463272094727 0.2789468765258789 197.53379821777344 0.3662283420562744 200.47927856445312 0.25750505924224854 0.85352933 0.49125319719314575 True -18 26372 15.380428791046143 0.28081345558166504 122.99474334716797 0.45225244760513306 200.8406524658203 0.256913959980011 0.85294473 0.4944363832473755 False -19 27760 15.383538007736206 0.27347850799560547 222.3872833251953 0.30068284273147583 200.73301696777344 0.25791114568710327 0.85302114 0.49932870268821716 False diff --git a/ENCSR473LSX/cherimoya.fold_4.performance.tsv b/ENCSR473LSX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6104d7b42f8de17b9744a409d79b1b2f56a1998f..0000000000000000000000000000000000000000 --- a/ENCSR473LSX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -200.47927856445312 0.5243834257125854 0.25750505924224854 0.06198666989803314 0.8535293340682983 0.8058153986930847 0.49125319719314575 \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_0.evaluate.json b/ENCSR474HQW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 43913b3e645dfa6cfa0c16c8c9a96dec79a8115b..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF337LGT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_0.fit.json b/ENCSR474HQW/cherimoya.fold_0.fit.json deleted file mode 100644 index c8ca4be23b67d5a645375845c322cd5742593d53..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF337LGT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_0.log b/ENCSR474HQW/cherimoya.fold_0.log deleted file mode 100644 index 23cf4d7bab61c04b50acf3f5edfdfcd72052f87c..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 33.72878384590149 3.9361417293548584 115.41996002197266 0.4436899721622467 191.78665161132812 0.12003154307603836 0.69743353 3.1140403747558594 True -1 5460 30.03292942047119 0.5764319896697998 144.71824645996094 0.4531134068965912 177.33253479003906 0.15498198568820953 0.7625676 1.7825510501861572 True -2 8190 30.016632318496704 0.5791094303131104 107.19381713867188 0.6516939401626587 174.94940185546875 0.15892814099788666 0.77079403 0.8954588770866394 True -3 10920 29.97792935371399 0.5768802165985107 152.90866088867188 0.654344916343689 172.7674560546875 0.16123639047145844 0.78130776 0.7454033493995667 True -4 13650 30.008529663085938 0.5768377780914307 152.95924377441406 0.6345353126525879 171.3530731201172 0.16337577998638153 0.7964048 0.6267258524894714 True -5 16380 29.955530405044556 0.5769453048706055 138.92971801757812 0.5286730527877808 170.34872436523438 0.16556674242019653 0.8053845 0.6224849820137024 True -6 19110 29.99257731437683 7.904478073120117 142.20407104492188 0.508441686630249 169.06405639648438 0.16871200501918793 0.8099549 0.5904809832572937 True -7 21840 30.135199546813965 0.6124422550201416 162.52052307128906 0.48401105403900146 168.59205627441406 0.16977912187576294 0.81862503 0.5335725545883179 True -8 24570 30.112605810165405 0.5970566272735596 139.22579956054688 0.5816035270690918 167.80987548828125 0.17247001826763153 0.82254535 0.5095383524894714 True -9 27300 30.006837844848633 0.58162522315979 144.87042236328125 0.4850196838378906 167.3174285888672 0.17351499199867249 0.827895 0.46934717893600464 True -10 30030 29.95561456680298 0.585228443145752 127.13992309570312 0.29787248373031616 166.84202575683594 0.1747611165046692 0.8338885 0.43942296504974365 True -11 32760 30.078200101852417 0.5895075798034668 153.1590118408203 0.3403199315071106 166.4050750732422 0.17552193999290466 0.84264493 0.39843809604644775 True -12 35490 29.974220275878906 0.5811119079589844 147.34657287597656 0.5610293745994568 165.77154541015625 0.1778050810098648 0.847018 0.37569308280944824 True -13 38220 29.87005376815796 0.5650472640991211 143.51976013183594 0.3153109550476074 165.40492248535156 0.17863419651985168 0.8500965 0.3571026921272278 True -14 40950 29.365261554718018 0.5803790092468262 141.88771057128906 0.417306512594223 164.8698272705078 0.18022602796554565 0.85525995 0.33427169919013977 True -15 43680 29.3917293548584 0.6458511352539062 127.60060119628906 0.6013388633728027 164.7135772705078 0.18008092045783997 0.8594579 0.32161933183670044 True -16 46410 29.383869171142578 0.5699541568756104 99.92469024658203 0.3173956274986267 164.4766845703125 0.1807825118303299 0.8629327 0.3081647455692291 True -17 49140 29.4845232963562 0.5748293399810791 177.60647583007812 0.30055081844329834 164.6776123046875 0.17971447110176086 0.86283875 0.3049977719783783 False -18 51870 29.41366934776306 0.5803115367889404 125.68721008300781 0.2362394481897354 164.7937774658203 0.17932932078838348 0.86260575 0.30473288893699646 False -19 54600 29.43825602531433 1.1316263675689697 189.93348693847656 0.23478356003761292 164.63612365722656 0.1802428662776947 0.86324024 0.30633583664894104 True diff --git a/ENCSR474HQW/cherimoya.fold_0.performance.tsv b/ENCSR474HQW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f44e79dfbf25374b4ab317b197a13dba162c2f3b..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -164.63612365722656 0.574029803276062 0.1802428960800171 0.04064004495739937 0.8632402420043945 0.7661578059196472 0.30633583664894104 \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_1.evaluate.json b/ENCSR474HQW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1c4e4ab72d1bdb4dcbb5f0b76a327cdbc8e54e2c..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF337LGT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_1.fit.json b/ENCSR474HQW/cherimoya.fold_1.fit.json deleted file mode 100644 index e82a86d0fc691dc3e41447e66449fa3a53a818e2..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF337LGT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_1.log b/ENCSR474HQW/cherimoya.fold_1.log deleted file mode 100644 index a62e6a1c16c197e43cba6431894f347557185280..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 33.76473641395569 3.741321563720703 122.22704315185547 0.31959277391433716 250.33578491210938 0.13440153002738953 0.67519665 4.122862815856934 True -1 5418 29.79615879058838 0.6824591159820557 153.48577880859375 0.7602001428604126 226.68145751953125 0.1825018674135208 0.76664907 2.0071160793304443 True -2 8127 29.77330207824707 0.6761171817779541 137.1790771484375 0.7446208000183105 224.89549255371094 0.18459542095661163 0.77816874 1.2422983646392822 True -3 10836 29.762004852294922 0.6831943988800049 125.34825134277344 0.4946790933609009 220.22145080566406 0.19152992963790894 0.7943508 0.9716761112213135 True -4 13545 29.730432271957397 0.6740622520446777 91.8739013671875 0.657545804977417 219.39910888671875 0.19256073236465454 0.7960744 0.9891101717948914 True -5 16254 29.728843927383423 14.53382158279419 160.17477416992188 0.41394925117492676 216.551513671875 0.19860950112342834 0.8098153 0.8477565050125122 True -6 18963 29.777135133743286 1.881052017211914 157.67054748535156 0.49621230363845825 215.05372619628906 0.20145954191684723 0.81600183 0.8527545928955078 True -7 21672 29.709272146224976 0.6965000629425049 167.5593719482422 0.5783576965332031 213.873046875 0.2034066915512085 0.82545394 0.7850010991096497 True -8 24381 29.778658151626587 0.6933274269104004 130.0186004638672 0.4545317590236664 212.60301208496094 0.20647965371608734 0.8322931 0.7520606517791748 True -9 27090 30.487306594848633 0.6847660541534424 156.5257568359375 0.3946935832500458 212.14976501464844 0.20664054155349731 0.83717316 0.6720407605171204 True -10 29799 29.766690731048584 0.6791689395904541 153.31851196289062 0.4629020094871521 210.58590698242188 0.2099006325006485 0.84595287 0.6160140633583069 True -11 32508 29.77127766609192 0.6913316249847412 168.49282836914062 0.48164916038513184 210.35423278808594 0.21089284121990204 0.8495617 0.5704585313796997 True -12 35217 29.784576177597046 0.6891510486602783 140.48712158203125 0.5223007202148438 209.45712280273438 0.21308912336826324 0.8585935 0.5246085524559021 True -13 37926 29.748518705368042 0.6837608814239502 107.86270141601562 0.5036833882331848 209.07176208496094 0.21360069513320923 0.86292374 0.48564139008522034 True -14 40635 29.764591455459595 0.6904294490814209 102.68081665039062 0.43323367834091187 208.29541015625 0.21510004997253418 0.867693 0.4355987310409546 True -15 43344 29.200857162475586 0.6699614524841309 118.48524475097656 0.3326050043106079 207.6601104736328 0.21609438955783844 0.87336147 0.407898485660553 True -16 46053 29.230223655700684 1.3564238548278809 143.17276000976562 0.4947062134742737 207.18377685546875 0.21713398396968842 0.8760375 0.3862626850605011 True -17 48762 29.223875284194946 0.6766681671142578 142.02880859375 0.3235801160335541 207.4416046142578 0.21610035002231598 0.87867516 0.37331125140190125 True -18 51471 29.19075608253479 0.6799037456512451 146.59596252441406 0.382685124874115 207.76458740234375 0.21496358513832092 0.87737656 0.3722204267978668 False -19 54180 29.177730321884155 22.404978275299072 132.77450561523438 0.34132254123687744 207.78968811035156 0.21528391540050507 0.8767585 0.37351930141448975 False diff --git a/ENCSR474HQW/cherimoya.fold_1.performance.tsv b/ENCSR474HQW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5fdfbe75d5dc285db15b341f0f635133a98081d3..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -207.4416046142578 0.5470328330993652 0.21610035002231598 0.05377655848860741 0.8786751627922058 0.8242815136909485 0.37331125140190125 \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_2.evaluate.json b/ENCSR474HQW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3579240b5414d261acdafb67ee88baadf20ef89a..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF337LGT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_2.fit.json b/ENCSR474HQW/cherimoya.fold_2.fit.json deleted file mode 100644 index 5390b4379f0c2481ceba3134052aeaa2758715e9..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF337LGT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_2.log b/ENCSR474HQW/cherimoya.fold_2.log deleted file mode 100644 index 64e169055e085c96da1948df0876dc3e1b8b5f72..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 35.25441288948059 3.548248767852783 146.6333465576172 0.7341445684432983 204.3858184814453 0.12489312887191772 0.6798089 3.102412700653076 True -1 5752 31.61074447631836 0.5578393936157227 222.29409790039062 0.8370257019996643 186.68724060058594 0.1638319194316864 0.7655486 1.4502863883972168 True -2 8628 31.649965524673462 0.5476794242858887 122.14170837402344 0.5755966901779175 185.7228240966797 0.16515381634235382 0.7623047 0.9623373746871948 False -3 11504 31.631126403808594 0.5507574081420898 151.7168731689453 0.6789716482162476 182.27822875976562 0.17035789787769318 0.78150415 0.7667195796966553 True -4 14380 31.576205253601074 0.5422976016998291 142.965087890625 0.658799409866333 180.61878967285156 0.17361874878406525 0.78943133 0.7078878283500671 True -5 17256 31.604135274887085 0.5473124980926514 116.87894439697266 0.26193320751190186 179.62750244140625 0.17498329281806946 0.7967637 0.7026526927947998 True -6 20132 31.600900173187256 0.547147274017334 139.89842224121094 0.8372944593429565 178.28866577148438 0.1777103841304779 0.80858946 0.6290396451950073 True -7 23008 31.5979905128479 0.5481271743774414 108.83949279785156 0.30213478207588196 177.30787658691406 0.17959856986999512 0.8154262 0.5707420110702515 True -8 25884 31.564950227737427 0.5461671352386475 132.05441284179688 0.5331771969795227 176.74476623535156 0.18115535378456116 0.819523 0.5290237069129944 True -9 28760 31.710513591766357 0.54850172996521 139.88304138183594 0.5369372963905334 176.22988891601562 0.18252713978290558 0.824604 0.4992287755012512 True -10 31636 31.61954951286316 1.0801403522491455 124.94359588623047 0.5197299718856812 175.9326629638672 0.18377667665481567 0.8312018 0.45844054222106934 True -11 34512 31.530914545059204 0.5359807014465332 117.86647033691406 0.3493116497993469 175.3311309814453 0.18489289283752441 0.83688664 0.4196072220802307 True -12 37388 30.973933219909668 0.5425295829772949 111.5607681274414 0.32603269815444946 174.65126037597656 0.18663328886032104 0.8439464 0.4002194404602051 True -13 40264 31.053823947906494 0.5340092182159424 125.05609893798828 0.2574199140071869 174.37966918945312 0.18743866682052612 0.8462634 0.3807033598423004 True -14 43140 31.041977882385254 0.5435893535614014 144.71182250976562 0.45913225412368774 173.59228515625 0.18883663415908813 0.85541534 0.3480047881603241 True -15 46016 31.049731492996216 0.5272815227508545 128.40530395507812 0.3500381410121918 173.38348388671875 0.18903480470180511 0.8575958 0.33393943309783936 True -16 48892 31.054020643234253 0.5413284301757812 153.2366485595703 0.26820462942123413 173.0682830810547 0.1896892637014389 0.8604215 0.32709115743637085 True -17 51768 31.017992734909058 0.5434763431549072 139.7429962158203 0.4191400408744812 173.13108825683594 0.18984566628932953 0.8602503 0.3249882757663727 False -18 54644 31.02825403213501 0.5405879020690918 138.06439208984375 0.3111380338668823 173.10733032226562 0.19003009796142578 0.86115587 0.323237806558609 True -19 57520 31.24445629119873 0.5334672927856445 163.28656005859375 0.22352899610996246 173.33653259277344 0.1892273724079132 0.8608083 0.324074923992157 False diff --git a/ENCSR474HQW/cherimoya.fold_2.performance.tsv b/ENCSR474HQW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 78f87aac367fcebdaa8c60b6b93e8512ea8162c7..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -173.10733032226562 0.5670154094696045 0.19003011286258698 0.04702345281839371 0.8611558675765991 0.7866373062133789 0.323237806558609 \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_3.evaluate.json b/ENCSR474HQW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d1865941b1cfc1e84f67ca6bdb9a2c5271b3485a..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF337LGT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_3.fit.json b/ENCSR474HQW/cherimoya.fold_3.fit.json deleted file mode 100644 index 1dbf32768166e10c18b407ee8323217caebe6f8f..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF337LGT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_3.log b/ENCSR474HQW/cherimoya.fold_3.log deleted file mode 100644 index fd288ab29dd3fbf6b39de90409e0edcb6c466a9a..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.21845316886902 3.70049786567688 112.38935852050781 0.5063422322273254 207.8152618408203 0.1292256861925125 0.65759695 2.9776430130004883 True -1 5500 30.26579523086548 0.5724658966064453 164.88612365722656 0.6152244806289673 191.8029022216797 0.1660875827074051 0.73217326 1.9112160205841064 True -2 8250 30.250841856002808 1.7442731857299805 155.33941650390625 0.49389493465423584 188.78977966308594 0.17061413824558258 0.7293659 1.2757741212844849 False -3 11000 30.228594541549683 0.5526869297027588 129.6959228515625 0.4239515960216522 186.42715454101562 0.17420919239521027 0.7504042 1.0872869491577148 True -4 13750 30.26205825805664 2.0882298946380615 181.25802612304688 0.3895220160484314 185.42095947265625 0.1765212118625641 0.7649777 0.9959415793418884 True -5 16500 30.225656509399414 0.5544800758361816 164.36842346191406 0.6150894165039062 184.2974090576172 0.17848247289657593 0.77310747 0.964258074760437 True -6 19250 30.204283714294434 0.5568571090698242 172.9442596435547 0.6948931217193604 183.56680297851562 0.1799750030040741 0.79110056 0.8283711075782776 True -7 22000 30.27871537208557 0.5653531551361084 163.66937255859375 0.5132229328155518 182.32322692871094 0.1831018626689911 0.7961519 0.8123406171798706 True -8 24750 30.15226149559021 0.5680735111236572 129.5489501953125 0.5242176651954651 181.40814208984375 0.1853354424238205 0.80448115 0.7222081422805786 True -9 27500 29.599426746368408 0.556725025177002 164.35464477539062 0.30512315034866333 180.923095703125 0.18624302744865417 0.81224394 0.6443633437156677 True -10 30250 29.603105306625366 0.5548596382141113 171.55422973632812 0.5274159908294678 179.77171325683594 0.18933726847171783 0.8221112 0.5703113675117493 True -11 33000 29.638562202453613 0.914668083190918 169.52325439453125 0.4200725555419922 179.52978515625 0.1898694783449173 0.8316707 0.5248302817344666 True -12 35750 29.623359203338623 0.8906617164611816 147.1787109375 0.45325732231140137 178.86643981933594 0.1915014237165451 0.83573294 0.4792233109474182 True -13 38500 29.651673793792725 0.5567431449890137 116.86283874511719 0.378259539604187 178.6515655517578 0.19107641279697418 0.8429671 0.4404381811618805 True -14 41250 29.68696427345276 0.5481915473937988 163.74612426757812 0.4943486452102661 177.9409637451172 0.19280309975147247 0.8513818 0.41418924927711487 True -15 44000 29.65558433532715 0.8366715908050537 133.88523864746094 0.32111066579818726 177.45738220214844 0.19426009058952332 0.856586 0.3852773606777191 True -16 46750 29.684386014938354 1.1125199794769287 125.5467529296875 0.3528459072113037 177.1531524658203 0.19488072395324707 0.86125517 0.36272114515304565 True -17 49500 29.638957262039185 0.5505292415618896 125.24415588378906 0.30336567759513855 177.09603881835938 0.1948368102312088 0.8634211 0.35435667634010315 True -18 52250 29.590449333190918 0.5493600368499756 129.32200622558594 0.23569028079509735 177.34664916992188 0.19399088621139526 0.8634964 0.3526199162006378 True -19 55000 29.620308876037598 0.5484590530395508 150.326171875 0.3449530601501465 177.46234130859375 0.19353322684764862 0.86395484 0.3565874397754669 True diff --git a/ENCSR474HQW/cherimoya.fold_3.performance.tsv b/ENCSR474HQW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ce1b9e4af91cd89a5f5b2358d821d5e73d03e0d4..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -177.46234130859375 0.5645689368247986 0.19353322684764862 0.04707021266222 0.8639548420906067 0.7739571928977966 0.3565874397754669 \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_4.evaluate.json b/ENCSR474HQW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8f155e7019820ca7715728e11fb766e21d7d7878..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF337LGT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_4.fit.json b/ENCSR474HQW/cherimoya.fold_4.fit.json deleted file mode 100644 index 829d42da5187755747af4e06cf26254b841b42bb..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF337LGT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474HQW/cherimoya.fold_4.log b/ENCSR474HQW/cherimoya.fold_4.log deleted file mode 100644 index 12f706edd292ce265505dbf75bf050b26da0fc8c..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2837 35.63458204269409 3.565213203430176 139.48171997070312 0.48412299156188965 175.8679962158203 0.11864587664604187 0.6526417 2.597637176513672 True -1 5674 31.316124200820923 0.5916440486907959 174.21389770507812 0.8788573741912842 164.41238403320312 0.14658129215240479 0.7503818 1.2746986150741577 True -2 8511 31.146920204162598 0.9527316093444824 170.76089477539062 0.7309036254882812 162.32716369628906 0.14903759956359863 0.7514175 0.8636859655380249 True -3 11348 31.203349590301514 0.5984780788421631 143.78208923339844 0.48758065700531006 160.13160705566406 0.15440110862255096 0.7710392 0.7425140142440796 True -4 14185 31.159823894500732 0.5908067226409912 180.0137939453125 0.4812890291213989 158.85220336914062 0.1563936471939087 0.7791894 0.6868399381637573 True -5 17022 31.141275644302368 0.5886023044586182 181.8759307861328 0.26981955766677856 157.89459228515625 0.15968693792819977 0.78409165 0.6609161496162415 True -6 19859 30.972336769104004 0.5822129249572754 176.61050415039062 0.36929985880851746 157.04066467285156 0.16154293715953827 0.79147154 0.6064713001251221 True -7 22696 30.56827163696289 0.5850987434387207 138.0773162841797 0.5184606313705444 156.51724243164062 0.1629520207643509 0.7981214 0.585216760635376 True -8 25533 30.558682441711426 0.5767738819122314 160.62460327148438 0.5500402450561523 156.0060577392578 0.16436119377613068 0.80081135 0.5601251125335693 True -9 28370 30.604815006256104 0.5868315696716309 150.34971618652344 0.3121102452278137 155.5678253173828 0.16487479209899902 0.810946 0.47984766960144043 True -10 31207 30.570497274398804 1.3696060180664062 126.54539489746094 0.5067111849784851 154.98728942871094 0.16669727861881256 0.8167585 0.4344479441642761 True -11 34044 30.64289164543152 0.6017754077911377 170.916259765625 0.5126867294311523 154.7251739501953 0.16733303666114807 0.82607394 0.3858543038368225 True -12 36881 30.675550937652588 0.5750501155853271 127.0732421875 0.4532293379306793 154.3013153076172 0.1682528406381607 0.83240646 0.3480849266052246 True -13 39718 30.69549798965454 0.5767631530761719 146.69313049316406 0.34404072165489197 153.9103240966797 0.16922418773174286 0.8367515 0.3350646495819092 True -14 42555 30.61750340461731 0.5887296199798584 119.73794555664062 0.44863319396972656 153.59158325195312 0.17046473920345306 0.84151053 0.31775373220443726 True -15 45392 30.57967233657837 0.5753638744354248 129.6807861328125 0.36811909079551697 153.1122589111328 0.1717189997434616 0.84746 0.30065205693244934 True -16 48229 30.627863883972168 0.5772457122802734 154.4028778076172 0.4044088125228882 153.26406860351562 0.17118822038173676 0.8498686 0.2952303886413574 True -17 51066 30.5592143535614 0.5770623683929443 127.24031066894531 0.3157688081264496 153.171142578125 0.17180155217647552 0.84986025 0.29272082448005676 False -18 53903 30.604118824005127 0.5840942859649658 125.28874206542969 0.2685829997062683 153.42498779296875 0.17050521075725555 0.8514293 0.2931649684906006 True -19 56740 30.601659536361694 0.5794942378997803 161.78189086914062 0.22784298658370972 153.2254180908203 0.17166630923748016 0.8491619 0.2935701906681061 False diff --git a/ENCSR474HQW/cherimoya.fold_4.performance.tsv b/ENCSR474HQW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 15f50987c38ebba8451c03ff2c6d08e649a331b0..0000000000000000000000000000000000000000 --- a/ENCSR474HQW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -153.42498779296875 0.5808425545692444 0.17050521075725555 0.03927215188741684 0.851429283618927 0.7415295839309692 0.2931649684906006 \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_0.evaluate.json b/ENCSR474XFV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9ac3ff5575cb625be72a9cc04eb2316ff4d8e908..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF206TNU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_0.fit.json b/ENCSR474XFV/cherimoya.fold_0.fit.json deleted file mode 100644 index dc332dab2018e672fe1b6c270dd6ca363198a285..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF206TNU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_0.log b/ENCSR474XFV/cherimoya.fold_0.log deleted file mode 100644 index bd708bfcaadf3c15350485ce2fb3efdc7d0a0d6c..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2903 35.66939687728882 3.7281479835510254 394.03106689453125 1.27018404006958 579.824462890625 0.5873283743858337 0.5899161 7.393924713134766 True -1 5806 32.06188941001892 0.6058120727539062 347.4881591796875 0.812480092048645 499.8628234863281 0.6848966479301453 0.5930645 2.5814478397369385 True -2 8709 31.967961072921753 2.287843704223633 385.1492614746094 0.88164222240448 489.509521484375 0.6976171731948853 0.59979194 1.4925637245178223 True -3 11612 32.00116419792175 0.5944650173187256 465.5809326171875 1.3461860418319702 484.4380187988281 0.7048596143722534 0.607797 1.2620114088058472 True -4 14515 32.025182008743286 0.5933568477630615 418.64862060546875 0.6890612244606018 481.13909912109375 0.7089604139328003 0.61430836 1.190443992614746 True -5 17418 31.991403341293335 0.6099405288696289 390.40478515625 0.7249624729156494 478.7720031738281 0.7114903926849365 0.61554736 1.083042860031128 True -6 20321 32.014084339141846 3.243025541305542 392.70416259765625 0.8306629061698914 476.5645751953125 0.714709460735321 0.6138299 1.072685718536377 False -7 23224 32.049814224243164 0.5940172672271729 345.01153564453125 0.9339310526847839 474.6827087402344 0.717158854007721 0.6161185 1.0408824682235718 True -8 26127 31.94545817375183 0.6086406707763672 386.2529296875 0.8260248899459839 472.6173400878906 0.719451904296875 0.6198713 0.9382041096687317 True -9 29030 31.985238790512085 0.5972845554351807 412.7388610839844 0.6424051523208618 470.54791259765625 0.7222422361373901 0.6220567 0.904349684715271 True -10 31933 32.00511193275452 2.520963191986084 338.237060546875 0.8264273405075073 468.84326171875 0.7244200110435486 0.6263096 0.8452423214912415 True -11 34836 32.046916007995605 0.5897741317749023 379.073486328125 0.8700551390647888 466.8841247558594 0.7273942828178406 0.63151854 0.8161761164665222 True -12 37739 32.0031852722168 0.5886363983154297 366.3955993652344 0.5557169914245605 465.05267333984375 0.7297219634056091 0.63496244 0.7771939635276794 True -13 40642 32.04295063018799 0.5951166152954102 352.88775634765625 0.48957833647727966 463.2030029296875 0.7319289445877075 0.6395821 0.7624369263648987 True -14 43545 32.03164625167847 0.5868637561798096 371.88134765625 0.6385051012039185 461.8116149902344 0.7336495518684387 0.6480202 0.7372387647628784 True -15 46448 31.99005126953125 0.5789361000061035 348.833740234375 0.5195766687393188 460.84515380859375 0.734769880771637 0.6517421 0.7179772257804871 True -16 49351 31.425223112106323 0.5893466472625732 326.7750244140625 0.5962926149368286 460.5953674316406 0.7353435754776001 0.65503514 0.7114746570587158 True -17 52254 31.317472457885742 0.5891053676605225 317.5105895996094 0.292322039604187 460.4855041503906 0.7353847026824951 0.65689915 0.7070865631103516 True -18 55157 31.349536895751953 0.5893261432647705 354.61279296875 0.570087194442749 460.8692932128906 0.7347629070281982 0.65711325 0.7124186158180237 True -19 58060 31.32609486579895 0.5791895389556885 315.65423583984375 0.3426783084869385 460.98870849609375 0.7344260811805725 0.6546275 0.7220622301101685 False diff --git a/ENCSR474XFV/cherimoya.fold_0.performance.tsv b/ENCSR474XFV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e50e25007cc48e4a141b9cf512632ec4753cf56a..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -460.8692932128906 0.22481893002986908 0.7347629070281982 0.3163125514984131 0.657113254070282 0.635962724685669 0.7124186158180237 \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_1.evaluate.json b/ENCSR474XFV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6ed8ce31bbad3e4a6ea98e5d768ce798cadbe850..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF206TNU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_1.fit.json b/ENCSR474XFV/cherimoya.fold_1.fit.json deleted file mode 100644 index 11680ccacbc1ba61adab7003f492a7cbc1600040..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF206TNU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_1.log b/ENCSR474XFV/cherimoya.fold_1.log deleted file mode 100644 index f044559648d5a109792dc17816b081cf393061b1..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 35.613359451293945 3.620119333267212 429.37396240234375 0.8801841139793396 633.7210693359375 0.5854350328445435 0.6152116 6.744494915008545 True -1 5742 31.669827461242676 0.7476704120635986 343.39154052734375 0.7457596063613892 545.009521484375 0.686534583568573 0.63607854 2.58257794380188 True -2 8613 31.694620609283447 0.7462642192840576 364.39984130859375 0.8419743776321411 527.7720947265625 0.7049476504325867 0.64825106 1.5086944103240967 True -3 11484 31.653061151504517 7.399517059326172 352.8719482421875 1.032850742340088 518.4218139648438 0.7139215469360352 0.6632597 0.9543097615242004 True -4 14355 31.667728900909424 1.1246256828308105 364.323974609375 0.9276511669158936 515.3124389648438 0.7176333069801331 0.6669198 0.9531661868095398 True -5 17226 31.65159559249878 0.758110761642456 358.9588928222656 1.014030933380127 513.4744873046875 0.7193818688392639 0.6740589 0.8841468691825867 True -6 20097 31.642606019973755 0.7432284355163574 407.0395812988281 0.8640526533126831 510.5136413574219 0.7231776714324951 0.678295 0.9106796383857727 True -7 22968 31.68637490272522 0.7574174404144287 377.91278076171875 0.7264291048049927 507.34637451171875 0.7262002229690552 0.67952055 0.7699135541915894 True -8 25839 32.019694089889526 0.7551627159118652 313.6632995605469 0.9027243852615356 505.5579528808594 0.7283270359039307 0.6849421 0.7316430807113647 True -9 28710 32.03760123252869 30.815917253494263 384.2227783203125 0.8818862438201904 502.51727294921875 0.7317847609519958 0.69844824 0.7236866354942322 True -10 31581 31.834641933441162 0.7566874027252197 335.6197204589844 0.8467879295349121 499.7354736328125 0.7347337007522583 0.70046836 0.6689455509185791 True -11 34452 31.84115195274353 0.757777214050293 395.55487060546875 0.8287541270256042 497.5867004394531 0.7370476126670837 0.7094507 0.6440315842628479 True -12 37323 31.824967622756958 0.7479062080383301 419.22076416015625 0.6459785103797913 495.9822082519531 0.7392604351043701 0.7133172 0.6428816318511963 True -13 40194 31.772929191589355 0.7496247291564941 361.04302978515625 0.5244395732879639 494.39495849609375 0.7414020895957947 0.72397226 0.621086835861206 True -14 43065 31.775522470474243 3.389766216278076 324.939453125 0.8929982781410217 492.6977844238281 0.7431819438934326 0.7312379 0.578487753868103 True -15 45936 31.215065717697144 0.7466087341308594 336.6531982421875 0.724722146987915 491.77398681640625 0.7443228363990784 0.7374756 0.563439130783081 True -16 48807 31.104804754257202 2.4821739196777344 350.1933898925781 0.4646352231502533 491.43572998046875 0.744694173336029 0.74163866 0.5578710436820984 True -17 51678 31.21700358390808 0.7476115226745605 323.44049072265625 0.5604604482650757 491.5263671875 0.7444892525672913 0.7410902 0.5596626996994019 False -18 54549 31.255645275115967 0.7479584217071533 331.9853515625 0.5366278886795044 491.92559814453125 0.7439723014831543 0.7404119 0.5535984635353088 False -19 57420 31.14354395866394 0.746037483215332 339.5318603515625 0.3360568881034851 492.2140197753906 0.743648886680603 0.7386752 0.5600858330726624 False diff --git a/ENCSR474XFV/cherimoya.fold_1.performance.tsv b/ENCSR474XFV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6b8b93be929553b24875e74a0dd7cd3b87398c79..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -491.43572998046875 0.21553634107112885 0.7446940541267395 0.3335573673248291 0.7416386604309082 0.7224727272987366 0.5578710436820984 \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_2.evaluate.json b/ENCSR474XFV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e1fbaf64ebc6f717023106c54efeea416b4e72a3..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF206TNU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_2.fit.json b/ENCSR474XFV/cherimoya.fold_2.fit.json deleted file mode 100644 index 79726dfd2b1832099c17703d2811793352632d3a..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF206TNU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_2.log b/ENCSR474XFV/cherimoya.fold_2.log deleted file mode 100644 index 696316eea55d4106fa894b078fcebb7a094b476b..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3060 37.8260395526886 3.5162312984466553 451.96466064453125 1.3200733661651611 584.0792846679688 0.5929018259048462 0.6125881 6.722370147705078 True -1 6120 33.71399164199829 0.6022322177886963 437.8631591796875 0.7540420293807983 504.7064514160156 0.6836519241333008 0.64325184 2.1033775806427 True -2 9180 33.70372438430786 2.623960494995117 450.1099548339844 1.0694093704223633 493.4573974609375 0.6966875195503235 0.6572826 1.0635535717010498 True -3 12240 33.726961851119995 0.5746898651123047 361.1973876953125 0.803280234336853 488.1036682128906 0.7036380767822266 0.66748154 0.8796883225440979 True -4 15300 33.69951772689819 1.3714354038238525 440.5700378417969 1.0359443426132202 485.0870361328125 0.7070983052253723 0.67355734 0.784731388092041 True -5 18360 33.775763511657715 0.5764198303222656 350.3298645019531 0.7365328073501587 482.7122497558594 0.7105660438537598 0.67554224 0.7972282767295837 True -6 21420 33.80447769165039 0.5848438739776611 353.13470458984375 0.7319139838218689 480.1947937011719 0.7136404514312744 0.6785056 0.749372661113739 True -7 24480 33.744311571121216 15.650798082351685 387.2057800292969 0.9973104000091553 478.0722351074219 0.716291606426239 0.68671304 0.7051498889923096 True -8 27540 33.73708939552307 0.5758049488067627 361.1589050292969 0.9371700286865234 475.313720703125 0.7195577025413513 0.6912052 0.688804566860199 True -9 30600 33.73164486885071 0.5871953964233398 387.65325927734375 0.6742334365844727 473.4176025390625 0.7219824194908142 0.6944015 0.6657727360725403 True -10 33660 33.82649540901184 0.5746910572052002 405.0177001953125 0.6407086849212646 471.0303955078125 0.7250135540962219 0.69960636 0.6521406173706055 True -11 36720 33.73855400085449 0.5880203247070312 462.9739074707031 0.6615492105484009 469.1946716308594 0.7271151542663574 0.7061443 0.629235029220581 True -12 39780 33.5519917011261 0.589555025100708 345.035888671875 0.7211734056472778 467.56170654296875 0.7294766902923584 0.71162564 0.6019957065582275 True -13 42840 33.246052980422974 0.5671865940093994 383.04150390625 0.8009688854217529 465.973876953125 0.7313318848609924 0.71957743 0.58045893907547 True -14 45900 33.24829173088074 1.1799688339233398 311.2529602050781 0.37306860089302063 464.7411804199219 0.7330467700958252 0.7268332 0.5649220943450928 True -15 48960 33.10899567604065 1.1453654766082764 346.80694580078125 0.4338202476501465 463.70806884765625 0.734298825263977 0.7318582 0.5459890961647034 True -16 52020 33.08610010147095 2.7820444107055664 292.52691650390625 0.41187047958374023 463.56268310546875 0.7344854474067688 0.7341079 0.5326601266860962 True -17 55080 33.14748239517212 0.574021577835083 354.340576171875 0.7746252417564392 463.5509338378906 0.7344591021537781 0.73429334 0.5334533452987671 True -18 58140 33.07633924484253 0.5693795680999756 325.1868591308594 0.36258259415626526 463.9039001464844 0.7340027689933777 0.73112106 0.5421915650367737 False -19 61200 33.13205862045288 0.5775134563446045 354.0066223144531 0.2786632776260376 464.1628723144531 0.7336821556091309 0.72989833 0.5467168688774109 False diff --git a/ENCSR474XFV/cherimoya.fold_2.performance.tsv b/ENCSR474XFV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 892c01ff1544b95ded613b06f2d4e5494025b683..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -463.5509338378906 0.22457610070705414 0.7344590425491333 0.3172660171985626 0.7342933416366577 0.7044378519058228 0.5334533452987671 \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_3.evaluate.json b/ENCSR474XFV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e818e362f3655e54e5c909faf5e7f8622b3d8791..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF206TNU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_3.fit.json b/ENCSR474XFV/cherimoya.fold_3.fit.json deleted file mode 100644 index ce4f06e9805c5bd42848d2b2f186e88e2ce510b9..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF206TNU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_3.log b/ENCSR474XFV/cherimoya.fold_3.log deleted file mode 100644 index cb1be555ffb180a5c925fc3caebe5b7da29ff2d5..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2962 36.657416343688965 3.5327510833740234 429.5599670410156 0.8972076177597046 586.1240234375 0.5828710198402405 0.6248401 7.157257080078125 True -1 5924 32.586087465286255 0.591808557510376 429.0184631347656 1.2350208759307861 502.02752685546875 0.6837421655654907 0.6547956 2.610891819000244 True -2 8886 32.596686363220215 0.5707471370697021 394.2612609863281 1.159438967704773 488.2945251464844 0.6978126764297485 0.6703082 1.185648798942566 True -3 11848 32.6415011882782 0.5770449638366699 376.4477233886719 0.7333685159683228 481.1434631347656 0.7058510780334473 0.67967695 1.0055549144744873 True -4 14810 34.167598485946655 0.5707066059112549 444.5541687011719 0.9181897640228271 479.4745788574219 0.7087821960449219 0.6807041 0.9315395355224609 True -5 17772 32.6912956237793 0.5784854888916016 381.2543029785156 0.923308789730072 476.54156494140625 0.711746096611023 0.68522966 0.8346589207649231 True -6 20734 32.709250688552856 0.5689828395843506 371.3829345703125 0.8812140822410583 474.3193359375 0.7148189544677734 0.68962544 0.7271270155906677 True -7 23696 32.82434391975403 0.5879757404327393 397.4131164550781 1.0006204843521118 472.4771423339844 0.7169392108917236 0.6879506 0.7622199058532715 False -8 26658 32.785271644592285 1.712754487991333 411.0496826171875 0.9085707664489746 471.3955078125 0.718656063079834 0.6886756 0.7066927552223206 False -9 29620 32.662461280822754 0.5765986442565918 398.74468994140625 0.5760307312011719 469.4463806152344 0.7215381860733032 0.6940497 0.7150169014930725 True -10 32582 32.85299730300903 0.5747904777526855 384.65203857421875 1.120025396347046 467.41265869140625 0.7237751483917236 0.6963782 0.6941344738006592 True -11 35544 32.2591118812561 0.5629947185516357 317.21136474609375 0.7423577308654785 465.03607177734375 0.7270609736442566 0.70478 0.6465615034103394 True -12 38506 32.18221569061279 0.5702240467071533 375.052001953125 0.741879940032959 463.5723571777344 0.7289635539054871 0.7125473 0.6152255535125732 True -13 41468 32.175302267074585 0.5687143802642822 357.09930419921875 0.505262553691864 461.5907897949219 0.7313739061355591 0.7253538 0.5719893574714661 True -14 44430 32.1729371547699 0.7569723129272461 384.4964904785156 0.6168702840805054 460.4881591796875 0.7331655025482178 0.72561526 0.5602313280105591 True -15 47392 32.188684940338135 1.276388168334961 350.0296325683594 0.48260846734046936 459.498046875 0.7343972325325012 0.73480505 0.5474567413330078 True -16 50354 32.185585498809814 4.383624076843262 363.43878173828125 0.6136576533317566 459.188720703125 0.7351066470146179 0.737241 0.5389785170555115 True -17 53316 32.44201636314392 19.052746534347534 362.2977294921875 0.42305395007133484 459.4054260253906 0.7348564267158508 0.7384239 0.5380139350891113 True -18 56278 32.26939535140991 22.158037185668945 365.5461120605469 0.5138444900512695 459.6684265136719 0.7343608736991882 0.734267 0.5489193201065063 False -19 59240 32.318594455718994 5.950433969497681 387.880615234375 0.31062135100364685 459.9449157714844 0.7340131402015686 0.73348105 0.5553627014160156 False diff --git a/ENCSR474XFV/cherimoya.fold_3.performance.tsv b/ENCSR474XFV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index dd9e6a7796c62839b860afd6c33fd58418808a8b..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.4054260253906 0.22417359054088593 0.7348565459251404 0.31576210260391235 0.7384238839149475 0.708666980266571 0.5380139350891113 \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_4.evaluate.json b/ENCSR474XFV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b3ddfe61d8d98ab08cea29999a1c274fbf721bb8..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF206TNU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_4.fit.json b/ENCSR474XFV/cherimoya.fold_4.fit.json deleted file mode 100644 index ed72fe74c94fc2facd1c417938ec4b4d416dbfea..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF206TNU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR474XFV/cherimoya.fold_4.log b/ENCSR474XFV/cherimoya.fold_4.log deleted file mode 100644 index 0b540a385460b0dbbaa001f68be7b5a207b455c8..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3030 37.43356990814209 3.5116031169891357 442.8426818847656 1.1070399284362793 562.6458129882812 0.5885615944862366 0.60465634 6.096273899078369 True -1 6060 33.41341209411621 0.6097602844238281 383.86712646484375 0.8979198932647705 488.2518005371094 0.6840831637382507 0.6388453 1.7992000579833984 True -2 9090 33.435285329818726 0.6000187397003174 409.24993896484375 0.9139794111251831 475.4241943359375 0.6969242691993713 0.64986557 1.1015220880508423 True -3 12120 33.39622116088867 0.5898125171661377 393.09661865234375 0.8398799896240234 471.682861328125 0.7026750445365906 0.6596034 0.9398056268692017 True -4 15150 33.3701958656311 0.590566873550415 407.72943115234375 0.7876207828521729 469.57330322265625 0.7059993743896484 0.6613654 0.9150066375732422 True -5 18180 33.356422662734985 0.6016244888305664 380.59991455078125 0.6983188390731812 467.86834716796875 0.7082306146621704 0.66445464 0.7814619541168213 True -6 21210 33.35569882392883 0.6008579730987549 359.1846923828125 1.0618594884872437 465.5745849609375 0.7104888558387756 0.6627933 0.7862696647644043 False -7 24240 33.35370898246765 0.6042418479919434 375.97882080078125 0.8662610054016113 463.0538635253906 0.7138159871101379 0.6668794 0.69190514087677 True -8 27270 33.37025809288025 0.5930888652801514 421.3331298828125 0.662293553352356 460.6387634277344 0.7172254323959351 0.67780715 0.6386961340904236 True -9 30300 33.393348932266235 0.6015803813934326 401.4244689941406 0.7092632055282593 458.7391357421875 0.7199487090110779 0.6831374 0.6108958125114441 True -10 33330 33.47217559814453 0.5950336456298828 458.82757568359375 0.7581331729888916 456.8066711425781 0.7224095463752747 0.6862226 0.5779417753219604 True -11 36360 32.731914043426514 0.5928609371185303 379.8260192871094 0.6648471355438232 455.1160888671875 0.7248544096946716 0.69190943 0.5951849222183228 True -12 39390 32.731743812561035 0.5833735466003418 411.8774108886719 0.6214202642440796 453.342529296875 0.7271955013275146 0.6978278 0.5522868037223816 True -13 42420 32.73729920387268 0.5849621295928955 317.705322265625 0.5916862487792969 452.18634033203125 0.7291973233222961 0.7054495 0.5646250247955322 True -14 45450 32.740041971206665 0.6000170707702637 328.12945556640625 0.731113076210022 451.0440673828125 0.7308405637741089 0.71343684 0.548498809337616 True -15 48480 32.712445974349976 0.5838758945465088 384.9153747558594 0.5008574724197388 450.105712890625 0.7320423722267151 0.715011 0.5529420375823975 True -16 51510 32.78317213058472 0.5960156917572021 377.7701721191406 0.6806783676147461 449.6893005371094 0.7324969172477722 0.72064364 0.5403372645378113 True -17 54540 32.75938272476196 0.5930955410003662 372.4227600097656 0.30135029554367065 449.87603759765625 0.7322914004325867 0.7189752 0.5498136281967163 False -18 57570 32.76317095756531 2.3385536670684814 346.479736328125 0.37809598445892334 450.4203796386719 0.7315601706504822 0.7168944 0.5617923140525818 False -19 60600 32.78612232208252 0.6038973331451416 324.88726806640625 0.44843482971191406 450.655029296875 0.7313026189804077 0.715078 0.5693103671073914 False diff --git a/ENCSR474XFV/cherimoya.fold_4.performance.tsv b/ENCSR474XFV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 600e67b542b58745b34328afc3167c5e8a65d742..0000000000000000000000000000000000000000 --- a/ENCSR474XFV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -449.6893005371094 0.22683794796466827 0.7324968576431274 0.31123220920562744 0.7206436395645142 0.6777447462081909 0.5403372645378113 \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_0.evaluate.json b/ENCSR475VQD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 45713cf433d216ba0b8f870da937114175d124e7..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF309WVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_0.fit.json b/ENCSR475VQD/cherimoya.fold_0.fit.json deleted file mode 100644 index 2f0798964cf331c13616774fe2975d14c86d2463..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF309WVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_0.log b/ENCSR475VQD/cherimoya.fold_0.log deleted file mode 100644 index a9f59375034b12027bead5c24e40817b82a050c5..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 33.390130043029785 3.6277825832366943 1034.02197265625 0.9390988349914551 1575.0333251953125 0.310362309217453 0.58974254 9.955367088317871 True -1 5504 30.595484972000122 0.5991072654724121 889.3670654296875 1.168534278869629 1309.6480712890625 0.454939603805542 0.698008 2.7389705181121826 True -2 8256 30.277616500854492 0.599653959274292 887.4969482421875 0.6302981376647949 1277.359375 0.47064462304115295 0.7093654 1.1518479585647583 True -3 11008 30.303937911987305 0.596738338470459 1008.9412231445312 1.0411591529846191 1257.0279541015625 0.47329509258270264 0.72106326 0.7912648320198059 True -4 13760 30.19071054458618 0.5961019992828369 953.1250610351562 0.9373602867126465 1240.3370361328125 0.48162275552749634 0.7348905 0.59388267993927 True -5 16512 30.220274448394775 0.5961058139801025 724.963134765625 0.6121901273727417 1227.1153564453125 0.49100396037101746 0.7380467 0.5880634188652039 True -6 19264 30.29543375968933 0.5990591049194336 916.30126953125 0.6429183483123779 1213.5985107421875 0.49709752202033997 0.7445168 0.48641762137413025 True -7 22016 30.27312660217285 0.5894110202789307 952.04052734375 0.5373805165290833 1207.6348876953125 0.503842830657959 0.7471477 0.5008086562156677 True -8 24768 30.281249046325684 0.5998764038085938 1046.0394287109375 0.7409005165100098 1200.4674072265625 0.5067103505134583 0.7427787 0.4511179029941559 False -9 27520 30.40148401260376 0.6221470832824707 1004.4426879882812 0.5317277908325195 1189.3333740234375 0.5131344199180603 0.7570364 0.4384462833404541 True -10 30272 30.307729959487915 0.6082985401153564 1085.5185546875 0.7184361219406128 1187.4676513671875 0.5128157734870911 0.75881493 0.41589298844337463 True -11 33024 30.327707529067993 0.604358434677124 892.374755859375 0.7977269291877747 1182.7440185546875 0.5153026580810547 0.7697539 0.3918110430240631 True -12 35776 30.297483205795288 0.61289381980896 1014.126953125 0.6177763938903809 1174.8843994140625 0.5205077528953552 0.7805226 0.3687237501144409 True -13 38528 30.383686780929565 1.5217571258544922 998.7003173828125 0.5213978290557861 1169.657470703125 0.5223821997642517 0.7917327 0.3522057831287384 True -14 41280 30.37474298477173 0.6197607517242432 970.192626953125 0.4903809428215027 1163.744140625 0.5266781449317932 0.7971885 0.3482584059238434 True -15 44032 30.44258737564087 0.6104245185852051 763.1009521484375 0.47165369987487793 1160.6630859375 0.5271360874176025 0.80483204 0.33347612619400024 True -16 46784 30.557329893112183 0.6098520755767822 973.321044921875 0.6049826145172119 1159.4219970703125 0.5281875133514404 0.81135637 0.320505827665329 True -17 49536 30.43745446205139 0.6094598770141602 837.5039672851562 0.38439810276031494 1154.58154296875 0.5304767489433289 0.8163717 0.3171154260635376 True -18 52288 30.5883846282959 0.6068909168243408 865.722412109375 0.37612003087997437 1154.759521484375 0.5313705801963806 0.8180192 0.31767284870147705 True -19 55040 32.9097204208374 2.8110573291778564 1006.9992065429688 0.25833266973495483 1156.074951171875 0.5298308730125427 0.81669194 0.31743139028549194 False diff --git a/ENCSR475VQD/cherimoya.fold_0.performance.tsv b/ENCSR475VQD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e99bc30b49fc16eebe3b1da0c46845cd859245c8..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1154.759521484375 0.25880464911460876 0.5313706398010254 0.2820846140384674 0.8180192112922668 0.7508283853530884 0.31767284870147705 \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_1.evaluate.json b/ENCSR475VQD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5ea5e8cbd59afd814e561299de638af23c0e772d..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF309WVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_1.fit.json b/ENCSR475VQD/cherimoya.fold_1.fit.json deleted file mode 100644 index 0866b21c18a0f503be2bdaecddb58279c1b73b75..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF309WVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_1.log b/ENCSR475VQD/cherimoya.fold_1.log deleted file mode 100644 index 85d50a9a13de42d10b5bfb99886e8182afd51cb0..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 34.59571290016174 4.00318455696106 870.039306640625 1.066277027130127 1959.3956298828125 0.31396305561065674 0.6103755 9.588953971862793 True -1 5456 30.494476795196533 12.8060884475708 1415.33056640625 1.4257793426513672 1601.849853515625 0.46474575996398926 0.7121633 3.418916940689087 True -2 8184 30.180924892425537 0.7132596969604492 961.1973876953125 0.8105238676071167 1561.4493408203125 0.48213037848472595 0.71252745 1.9798179864883423 True -3 10912 30.07268452644348 0.6424880027770996 918.876220703125 0.7622302770614624 1514.4913330078125 0.4944057762622833 0.72429514 1.2045955657958984 True -4 13640 30.136357307434082 0.6586563587188721 1072.5535888671875 0.728325366973877 1503.185546875 0.49700239300727844 0.73295665 1.0241484642028809 True -5 16368 33.73453211784363 21.749085903167725 972.5733642578125 1.0149257183074951 1486.6475830078125 0.5031331181526184 0.73746294 0.7407189607620239 True -6 19096 30.288639545440674 4.426677465438843 1022.8035278320312 0.6613247394561768 1479.5164794921875 0.5041729807853699 0.74787694 0.6238559484481812 True -7 21824 30.24153709411621 2.3781280517578125 917.2451171875 0.8018620014190674 1455.916259765625 0.5154421925544739 0.755438 0.5375075936317444 True -8 24552 30.25656008720398 2.927009105682373 851.3192138671875 0.7984201908111572 1451.014404296875 0.5147175788879395 0.7648048 0.5021567344665527 True -9 27280 30.18356490135193 2.1202738285064697 857.1885986328125 0.37653422355651855 1438.857666015625 0.5217574834823608 0.77093554 0.5043627023696899 True -10 30008 30.173556566238403 1.6321723461151123 839.6350708007812 0.6650086641311646 1424.433349609375 0.5260610580444336 0.7816775 0.47252607345581055 True -11 32736 30.17593026161194 1.943450689315796 864.9917602539062 0.6151854991912842 1416.992431640625 0.5287072062492371 0.7939217 0.4336567223072052 True -12 35464 30.443230390548706 3.252936363220215 903.2381591796875 0.5058671236038208 1405.1611328125 0.5333164930343628 0.8023622 0.43147826194763184 True -13 38192 30.35370969772339 1.6778788566589355 894.2646484375 0.5003108382225037 1395.415771484375 0.5365585088729858 0.81340104 0.40999987721443176 True -14 40920 30.35195565223694 1.6666526794433594 755.8154296875 0.4197174906730652 1389.9390869140625 0.538184642791748 0.8216661 0.39502015709877014 True -15 43648 30.279820203781128 1.7943029403686523 1138.1064453125 0.3591051697731018 1381.839111328125 0.5398595929145813 0.83205515 0.36986449360847473 True -16 46376 30.26851487159729 1.4572596549987793 809.6258544921875 0.3472635746002197 1368.3565673828125 0.5463088154792786 0.83711624 0.3686203360557556 True -17 49104 30.27190399169922 3.3855996131896973 953.9627075195312 0.32953137159347534 1364.1463623046875 0.5485466718673706 0.83998793 0.3657633066177368 True -18 51832 30.163728952407837 3.4087905883789062 964.3859252929688 0.41070449352264404 1365.18603515625 0.5458931922912598 0.84079975 0.3618752062320709 True -19 54560 30.14359164237976 3.826476573944092 1096.3873291015625 0.41194114089012146 1367.7569580078125 0.5433915853500366 0.8386294 0.36600908637046814 False diff --git a/ENCSR475VQD/cherimoya.fold_1.performance.tsv b/ENCSR475VQD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b156145a1359fda01ddd59f2688537747b979a8c..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1365.18603515625 0.24552662670612335 0.5458931922912598 0.30830851197242737 0.8407997488975525 0.7846918702125549 0.3618752062320709 \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_2.evaluate.json b/ENCSR475VQD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 26d7e1bef1e34799684ef96e4683b90299e294cd..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF309WVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_2.fit.json b/ENCSR475VQD/cherimoya.fold_2.fit.json deleted file mode 100644 index 98db979a7225a83aef8c01d9eca3b8f15cbd5f9e..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF309WVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_2.log b/ENCSR475VQD/cherimoya.fold_2.log deleted file mode 100644 index fbc2937152b3253f6feb1d3b34f4bb1bb60bde71..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 36.946001291275024 19.746127128601074 1066.8115234375 0.6590461730957031 1658.0537109375 0.31828543543815613 0.6049877 7.665527820587158 True -1 5788 32.01752829551697 0.5820260047912598 1264.358154296875 1.4883239269256592 1373.278564453125 0.4615238308906555 0.6748584 3.4239163398742676 True -2 8682 31.936060428619385 1.8687007427215576 1163.1368408203125 1.200872778892517 1341.5068359375 0.4749869406223297 0.7104694 1.7136770486831665 True -3 11576 31.934232711791992 0.552351713180542 997.3262939453125 0.7544043064117432 1324.6033935546875 0.4786494970321655 0.7166649 1.0972609519958496 True -4 14470 31.96507215499878 0.5435178279876709 1024.08154296875 0.5679775476455688 1306.2943115234375 0.48873281478881836 0.7261718 0.8023942112922668 True -5 17364 31.913994073867798 0.5548934936523438 911.2618408203125 0.6269670724868774 1287.900634765625 0.49757224321365356 0.72883666 0.6880566477775574 True -6 20258 31.931007385253906 0.5404148101806641 1109.7037353515625 0.6203633546829224 1279.7088623046875 0.5024656057357788 0.7360236 0.6306439638137817 True -7 23152 31.870447158813477 0.5461142063140869 1328.89599609375 0.7256696224212646 1268.977294921875 0.5086202621459961 0.73639756 0.5645796060562134 True -8 26046 31.887729167938232 0.5572185516357422 912.4205322265625 0.3926628828048706 1255.848388671875 0.5137112140655518 0.75466317 0.4840107262134552 True -9 28940 31.968072175979614 0.5449602603912354 1024.43359375 0.668248176574707 1249.885498046875 0.5172252655029297 0.75623506 0.46713656187057495 True -10 31834 31.87666630744934 27.701335668563843 848.5379638671875 0.5309586524963379 1246.45263671875 0.5168772339820862 0.76757216 0.44944122433662415 True -11 34728 33.94411778450012 0.5963120460510254 755.2552490234375 0.31489068269729614 1230.7012939453125 0.5257837176322937 0.7759179 0.44215112924575806 True -12 37622 31.978662490844727 3.866797924041748 1189.54736328125 0.3663656413555145 1227.6197509765625 0.5266648530960083 0.78486204 0.43176665902137756 True -13 40516 31.998531103134155 1.4154045581817627 874.2052612304688 0.3837835192680359 1216.8485107421875 0.5331498980522156 0.79354554 0.41182243824005127 True -14 43410 32.02139925956726 0.6630203723907471 691.388671875 0.5948042869567871 1216.4681396484375 0.53056800365448 0.7995424 0.3895636796951294 True -15 46304 32.0643846988678 22.18515706062317 960.6511840820312 0.37760746479034424 1208.0826416015625 0.5357450842857361 0.80695873 0.3730865716934204 True -16 49198 32.228230714797974 0.5386636257171631 912.597412109375 0.35925108194351196 1210.1077880859375 0.5330552458763123 0.81124973 0.3649202883243561 True -17 52092 31.946669340133667 1.545274257659912 861.5484619140625 0.28032445907592773 1204.7818603515625 0.5358228087425232 0.81678927 0.35425594449043274 True -18 54986 31.959728717803955 0.5438656806945801 851.5360717773438 0.4436986744403839 1207.39599609375 0.5347582697868347 0.8167146 0.3493196368217468 False -19 57880 31.94644832611084 0.5437183380126953 754.87646484375 0.2965773642063141 1203.181640625 0.5385968089103699 0.8188966 0.3497375547885895 True diff --git a/ENCSR475VQD/cherimoya.fold_2.performance.tsv b/ENCSR475VQD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ba9471d7a375c9cfeb9d27749cea131e89ef284c..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1203.181640625 0.2542237341403961 0.5385968685150146 0.2894570231437683 0.8188965916633606 0.7524772882461548 0.3497375547885895 \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_3.evaluate.json b/ENCSR475VQD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fd82641e0e8b0e42681be51bbe4cfd91909a3f1c..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF309WVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_3.fit.json b/ENCSR475VQD/cherimoya.fold_3.fit.json deleted file mode 100644 index e9f35037260fb71f0b46f032e80ff09db8ad72d9..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF309WVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_3.log b/ENCSR475VQD/cherimoya.fold_3.log deleted file mode 100644 index 8b89b391d6de54a81013cd8ab2fa5b1bc7933b76..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 41.83719825744629 3.7193920612335205 774.6607055664062 1.0454328060150146 1681.1844482421875 0.3245195150375366 0.63396204 9.538073539733887 True -1 5554 30.96641206741333 0.623213529586792 839.5979614257812 0.6824432611465454 1414.6383056640625 0.45731139183044434 0.70369136 2.2633326053619385 True -2 8331 34.210665702819824 0.5416781902313232 1115.5577392578125 0.8564273118972778 1394.8062744140625 0.4641074538230896 0.7014673 1.2218515872955322 False -3 11108 30.81731653213501 0.5449872016906738 942.8603515625 1.3199361562728882 1356.4117431640625 0.48145410418510437 0.7266015 0.9343857765197754 True -4 13885 30.831781148910522 1.1681849956512451 893.0830078125 0.7552813291549683 1340.751953125 0.48845991492271423 0.72478646 0.712180495262146 False -5 16662 30.944639205932617 0.6501400470733643 823.4280395507812 0.9513895511627197 1339.36328125 0.4906999170780182 0.72594523 0.6305410861968994 False -6 19439 30.836626768112183 0.5535116195678711 1019.23876953125 0.46393322944641113 1327.7373046875 0.49692457914352417 0.7220287 0.5812092423439026 False -7 22216 30.780483722686768 0.5371334552764893 892.8591918945312 0.36271899938583374 1317.158203125 0.5008149743080139 0.73123014 0.5339183211326599 True -8 24993 30.696000337600708 0.5372869968414307 971.2352905273438 0.595034658908844 1309.9315185546875 0.5038686394691467 0.7465265 0.4878631830215454 True -9 27770 30.6574547290802 0.5363376140594482 871.562255859375 0.41741132736206055 1304.6016845703125 0.5069267153739929 0.7497458 0.47521138191223145 True -10 30547 30.668500900268555 1.1506800651550293 904.8299560546875 0.5244214534759521 1294.3348388671875 0.5094921588897705 0.7614318 0.46474385261535645 True -11 33324 30.683109521865845 3.2013278007507324 908.2486572265625 0.5932140350341797 1282.1502685546875 0.5150865912437439 0.77153194 0.43111518025398254 True -12 36101 30.75199794769287 0.5468621253967285 1086.0037841796875 0.7489156723022461 1272.807861328125 0.5167149901390076 0.7812373 0.4340914189815521 True -13 38878 30.78759241104126 0.5443189144134521 1092.327880859375 0.4513343572616577 1254.108154296875 0.5280840396881104 0.7932112 0.40078219771385193 True -14 41655 30.643131017684937 1.3273606300354004 838.353515625 0.648496687412262 1250.7679443359375 0.528411865234375 0.8037831 0.38821765780448914 True -15 44432 30.637026071548462 0.5396425724029541 1137.9837646484375 0.62104332447052 1242.025634765625 0.5306205153465271 0.8109805 0.3666432201862335 True -16 47209 32.868109464645386 26.8001389503479 915.3707275390625 0.2719893157482147 1238.17236328125 0.5328360795974731 0.81694627 0.3550531268119812 True -17 49986 30.74498152732849 13.605446100234985 1053.071533203125 0.32857656478881836 1238.62451171875 0.5313318371772766 0.82245505 0.3475279211997986 True -18 52763 30.67934274673462 29.76647663116455 840.5023193359375 0.22715270519256592 1236.824462890625 0.5348514914512634 0.82202095 0.34604936838150024 False -19 55540 32.134560108184814 0.5279772281646729 918.873046875 0.27996644377708435 1240.1632080078125 0.5300357937812805 0.8236829 0.346880167722702 True diff --git a/ENCSR475VQD/cherimoya.fold_3.performance.tsv b/ENCSR475VQD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d141e640751aa8bc00afdbfae86abfd458265863..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1240.1632080078125 0.25684210658073425 0.5300357937812805 0.287233829498291 0.8236829042434692 0.7541616559028625 0.346880167722702 \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_4.evaluate.json b/ENCSR475VQD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e145cb0de728013289dec88333251eb07c1c50b9..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF309WVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_4.fit.json b/ENCSR475VQD/cherimoya.fold_4.fit.json deleted file mode 100644 index acedbae8e9587abe5f6db8d538737ad6c418cd2d..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF309WVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR475VQD/cherimoya.fold_4.log b/ENCSR475VQD/cherimoya.fold_4.log deleted file mode 100644 index 11fe3138c6c2a28d9a8f4ca38a3247be7ca2ae65..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2893 36.80512189865112 3.640676736831665 935.73388671875 0.7058205604553223 1484.4085693359375 0.321033239364624 0.6207094 8.317870140075684 True -1 5786 31.952230215072632 15.937483549118042 890.8397216796875 1.161792278289795 1265.598388671875 0.4470129609107971 0.70014995 2.5060768127441406 True -2 8679 34.471004247665405 0.6504154205322266 883.7701416015625 0.7459564208984375 1249.7410888671875 0.455717533826828 0.70559573 0.8708608150482178 True -3 11572 32.05955505371094 0.602975606918335 1121.43798828125 0.8401274085044861 1228.603759765625 0.4634658396244049 0.71343917 0.675836443901062 True -4 14465 32.03289771080017 0.6201531887054443 915.728759765625 0.5967026352882385 1206.3150634765625 0.47704869508743286 0.72404385 0.6243724226951599 True -5 17358 31.970812559127808 0.6015338897705078 1055.408447265625 0.8128044009208679 1191.75146484375 0.48560523986816406 0.72685844 0.5749326944351196 True -6 20251 31.92507553100586 0.5966455936431885 972.3350219726562 0.7789864540100098 1184.45556640625 0.4900343120098114 0.7343576 0.4669807553291321 True -7 23144 31.987809896469116 0.6178328990936279 924.9459228515625 0.5431927442550659 1178.3128662109375 0.49345511198043823 0.74064106 0.4339143633842468 True -8 26037 32.000322580337524 0.6141903400421143 878.6012573242188 0.804990291595459 1172.7694091796875 0.49576160311698914 0.7483782 0.4004100561141968 True -9 28930 32.128576040267944 0.6058073043823242 929.577880859375 0.5214439630508423 1161.130126953125 0.5035286545753479 0.75722677 0.37565937638282776 True -10 31823 32.12338900566101 0.6044423580169678 1052.130615234375 0.6141942143440247 1155.125 0.5058775544166565 0.76614004 0.3545909523963928 True -11 34716 32.37487745285034 0.6072754859924316 828.1975708007812 0.5217469930648804 1151.705810546875 0.5072104930877686 0.77529436 0.3409668207168579 True -12 37609 32.117645025253296 0.6070172786712646 856.7615966796875 0.4242677688598633 1145.65087890625 0.509798526763916 0.7815848 0.3258016109466553 True -13 40502 32.085031032562256 0.9385936260223389 1085.762939453125 0.3572496771812439 1137.24267578125 0.516122043132782 0.7926484 0.3109922409057617 True -14 43395 32.031126260757446 0.6145269870758057 780.659423828125 0.4903426766395569 1132.8958740234375 0.5178526639938354 0.8039887 0.3018166124820709 True -15 46288 32.22900986671448 0.6098611354827881 1194.488037109375 0.5104824900627136 1129.940185546875 0.5184249877929688 0.80726874 0.29984763264656067 True -16 49181 31.97956919670105 0.6048007011413574 672.7744140625 0.2747359871864319 1129.5859375 0.5175966024398804 0.8103848 0.294397234916687 True -17 52074 32.11855363845825 0.6154799461364746 908.6062622070312 0.3062375485897064 1125.1253662109375 0.5198731422424316 0.81418157 0.29373306035995483 True -18 54967 31.992687225341797 0.5963525772094727 913.9303588867188 0.305265337228775 1126.693603515625 0.5195942521095276 0.8147567 0.293402761220932 True -19 57860 32.06280493736267 0.5938496589660645 850.9052734375 0.25588488578796387 1124.15087890625 0.5228849649429321 0.8140671 0.29583054780960083 False diff --git a/ENCSR475VQD/cherimoya.fold_4.performance.tsv b/ENCSR475VQD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index dd92a48d195fd80f54f19e66d8c8659805e08ebc..0000000000000000000000000000000000000000 --- a/ENCSR475VQD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1126.693603515625 0.2632647156715393 0.5195942521095276 0.27715790271759033 0.8147566914558411 0.7430017590522766 0.293402761220932 \ No newline at end of file diff --git a/ENCSR476SDZ/cherimoya.fold_3.log b/ENCSR476SDZ/cherimoya.fold_3.log deleted file mode 100644 index 11b6b69085898a1db5caf726ce4a03c67b17fdf0..0000000000000000000000000000000000000000 --- a/ENCSR476SDZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2778 35.60665726661682 3.7646117210388184 194.6226348876953 0.7619783878326416 292.0578308105469 0.1630648523569107 0.5095013 3.1626710891723633 True -1 5556 30.972671031951904 0.5901284217834473 220.039794921875 0.6419937014579773 274.2095642089844 0.24420708417892456 0.607143 1.3576120138168335 True -2 8334 30.910881519317627 0.5813558101654053 203.41151428222656 0.6845886707305908 270.7979736328125 0.2526839077472687 0.6271693 0.6292922496795654 True -3 11112 30.95989990234375 0.5826997756958008 187.84503173828125 0.6019258499145508 269.0165710449219 0.2576245367527008 0.6431981 0.5893930792808533 True -4 13890 30.98412847518921 25.857518672943115 178.52374267578125 0.574255108833313 268.1325378417969 0.26042577624320984 0.6480399 0.5821982026100159 True -5 16668 32.8908052444458 23.269984006881714 189.55068969726562 0.7609878182411194 267.74761962890625 0.2618788480758667 0.6565288 0.5816539525985718 True -6 19446 31.358442068099976 0.5884778499603271 169.03604125976562 0.7139191627502441 267.10552978515625 0.2648160457611084 0.6611845 0.604555070400238 True -7 22224 30.430972814559937 0.5743794441223145 185.38009643554688 0.7035354971885681 266.7102966308594 0.2666214406490326 0.6667499 0.6219416856765747 True -8 25002 30.742568492889404 0.5707049369812012 209.63861083984375 0.4375222325325012 266.5387268066406 0.2672170400619507 0.6678131 0.6381353139877319 True -9 27780 30.295653104782104 0.5942583084106445 227.4688720703125 0.854548454284668 265.6967468261719 0.27081337571144104 0.67341286 0.5980383157730103 True -10 30558 30.658267974853516 6.636922836303711 202.53794860839844 0.6481691598892212 265.3760986328125 0.2726219594478607 0.6809555 0.5641447901725769 True -11 33336 30.526122570037842 0.6261377334594727 177.15699768066406 0.5322842597961426 264.8553161621094 0.2749261260032654 0.6866388 0.5618345737457275 True -12 36114 31.276310205459595 37.918211936950684 187.83688354492188 0.6619428992271423 264.35595703125 0.27744755148887634 0.69578284 0.5511643886566162 True -13 38892 32.218477725982666 0.5962173938751221 191.17660522460938 0.5345883965492249 263.8822937011719 0.27934741973876953 0.70688295 0.5103217363357544 True -14 41670 30.396161317825317 0.573991060256958 197.07968139648438 0.40496012568473816 263.8690185546875 0.2788316607475281 0.71239465 0.4889247417449951 True -15 44448 30.33922028541565 1.2436728477478027 190.21340942382812 0.36176854372024536 263.7010192871094 0.2791743874549866 0.71928066 0.4691848158836365 True -16 47226 30.274755716323853 0.5732717514038086 180.98284912109375 0.32074618339538574 263.4131774902344 0.2806035280227661 0.72401464 0.4570184350013733 True -17 50004 30.30618143081665 0.5731954574584961 178.17984008789062 0.3079470098018646 263.22369384765625 0.2816025912761688 0.72654384 0.45666468143463135 True -18 52782 30.23412299156189 0.5681614875793457 193.85467529296875 0.2904702126979828 263.56829833984375 0.279888391494751 0.7247494 0.45948755741119385 False -19 55560 30.296791315078735 0.5735311508178711 200.03555297851562 0.304394394159317 263.80096435546875 0.27844810485839844 0.72298074 0.46295544505119324 False diff --git a/ENCSR476VJY/cherimoya.fold_0.evaluate.json b/ENCSR476VJY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2047575d9a60341fecab1e6a46d0a3472aa5d6ac..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF454KHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_0.fit.json b/ENCSR476VJY/cherimoya.fold_0.fit.json deleted file mode 100644 index 5d5217aa4acd6e036b044f6c2d63f8c250d5c668..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF454KHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_0.log b/ENCSR476VJY/cherimoya.fold_0.log deleted file mode 100644 index e40b8f1c873e8343a8d88eb57fc672b500a554dc..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1425 20.151267766952515 3.6844053268432617 501.03546142578125 2.0370419025421143 1066.7740478515625 0.4590260684490204 0.5593213 25.615497589111328 True -1 2850 15.671891212463379 0.34865689277648926 414.1459655761719 2.0375707149505615 736.2579345703125 0.6025616526603699 0.64184266 17.94669532775879 True -2 4275 15.625590562820435 0.2631082534790039 494.09832763671875 1.9747669696807861 618.8970947265625 0.6866276860237122 0.6584147 8.288283348083496 True -3 5700 15.62978458404541 0.2734053134918213 493.9063720703125 2.1449780464172363 585.148193359375 0.7118529081344604 0.67220974 2.580533266067505 True -4 7125 15.62642765045166 0.26720571517944336 479.8631896972656 1.7765215635299683 571.0491333007812 0.7228958606719971 0.6764502 1.3837575912475586 True -5 8550 15.624279975891113 0.2617788314819336 408.78564453125 1.98099946975708 562.9020385742188 0.7294378280639648 0.68209743 1.2025870084762573 True -6 9975 15.629525184631348 0.26100754737854004 339.9674072265625 1.6173298358917236 559.9747314453125 0.7319236993789673 0.68668896 1.0744081735610962 True -7 11400 15.620681762695312 0.2607541084289551 479.9926452636719 1.8141179084777832 556.7076416015625 0.7352245450019836 0.68706656 1.0822457075119019 True -8 12825 15.678531408309937 0.27321815490722656 345.5067443847656 1.68117356300354 553.4326782226562 0.7377089262008667 0.6891552 1.1132174730300903 True -9 14250 15.646097421646118 0.6793973445892334 360.6979064941406 1.1498503684997559 549.2462158203125 0.7409669160842896 0.6961391 1.0894578695297241 True -10 15675 15.667227506637573 0.2660408020019531 401.5216064453125 1.2308697700500488 546.6375122070312 0.743247389793396 0.703215 1.0713098049163818 True -11 17100 15.647648334503174 0.5803108215332031 383.2481689453125 1.3023567199707031 542.5775146484375 0.7458972334861755 0.707294 1.0582677125930786 True -12 18525 15.678980827331543 0.2675325870513916 393.13421630859375 1.3539646863937378 540.3643188476562 0.7478196024894714 0.7100565 1.0664029121398926 True -13 19950 15.664374828338623 0.26636433601379395 370.54150390625 0.8757258057594299 538.0126953125 0.7494866847991943 0.71149063 1.0626375675201416 True -14 21375 15.662837743759155 0.26690673828125 459.760986328125 0.9136163592338562 536.3025512695312 0.7503196597099304 0.717813 1.055588722229004 True -15 22800 15.643902063369751 0.2742166519165039 402.6402893066406 1.228956699371338 535.3553466796875 0.7509764432907104 0.721643 1.0606356859207153 True -16 24225 15.6741304397583 0.3501780033111572 431.76849365234375 0.48095089197158813 535.451171875 0.7508033514022827 0.72234964 1.0859075784683228 True -17 25650 15.679025411605835 0.26786112785339355 372.2445068359375 1.1732693910598755 535.8306884765625 0.7503369450569153 0.720777 1.1267075538635254 False -18 27075 15.673557758331299 0.8680515289306641 373.53692626953125 0.6481341123580933 536.6868286132812 0.749386727809906 0.7171598 1.1724371910095215 False -19 28500 15.63677978515625 1.082913875579834 360.42364501953125 0.6126350164413452 537.08056640625 0.7488986253738403 0.71562433 1.2002203464508057 False diff --git a/ENCSR476VJY/cherimoya.fold_0.performance.tsv b/ENCSR476VJY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9bef2cd593ed42e9166966a16f4899bdebc4ede9..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -535.451171875 0.21241235733032227 0.750803530216217 0.340326189994812 0.7223496437072754 0.7191610932350159 1.0859075784683228 \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_1.evaluate.json b/ENCSR476VJY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 59c8223a20888bb77c5d188a185ec3708ed8449f..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF454KHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_1.fit.json b/ENCSR476VJY/cherimoya.fold_1.fit.json deleted file mode 100644 index 9042ec0c8d66b47babdeb3907dc48d2cd132b219..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF454KHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_1.log b/ENCSR476VJY/cherimoya.fold_1.log deleted file mode 100644 index ebd22c6fdb0d8b39029f7e7b314eecaa278a7840..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1391 19.825920343399048 4.2301130294799805 585.5708618164062 2.4876062870025635 1203.7247314453125 0.46621763706207275 0.5014885 27.866981506347656 True -1 2782 15.327754259109497 0.48580312728881836 491.7599182128906 2.2057549953460693 834.5579833984375 0.6055978536605835 0.6215404 18.771581649780273 True -2 4173 15.572474479675293 0.4647712707519531 434.31781005859375 2.4836955070495605 685.4208374023438 0.6979796886444092 0.65482 9.887350082397461 True -3 5564 15.283307075500488 0.452312707901001 483.56317138671875 2.331923246383667 641.7000122070312 0.7272377014160156 0.66816586 3.3079349994659424 True -4 6955 15.276260614395142 0.4554147720336914 337.45458984375 1.5057494640350342 625.152587890625 0.7396290898323059 0.6659033 1.911759853363037 False -5 8346 15.282273530960083 0.44254159927368164 480.83966064453125 1.5209249258041382 617.2076416015625 0.7455260753631592 0.67148983 1.4705137014389038 True -6 9737 15.281124591827393 0.4404871463775635 428.576171875 1.8696478605270386 609.87548828125 0.7496494650840759 0.6857069 1.2934653759002686 True -7 11128 15.26548957824707 0.4554417133331299 393.1746826171875 2.0248475074768066 604.7766723632812 0.7537140250205994 0.69171935 1.208748459815979 True -8 12519 15.28339171409607 0.43903040885925293 362.84185791015625 1.3040363788604736 601.4602661132812 0.7565898299217224 0.6956148 1.1818419694900513 True -9 13910 15.117733478546143 0.4931223392486572 413.55615234375 1.2568705081939697 596.750244140625 0.759614109992981 0.7018547 1.1074169874191284 True -10 15301 14.985968828201294 1.1583523750305176 427.711181640625 1.641464114189148 593.9896850585938 0.7616196274757385 0.7011219 1.1154825687408447 False -11 16692 14.984273195266724 0.44495129585266113 385.3023681640625 1.8818027973175049 590.0498046875 0.7638874053955078 0.70883524 1.0610432624816895 True -12 18083 15.010008573532104 0.44211864471435547 386.50750732421875 1.2362632751464844 587.1732177734375 0.7661277651786804 0.71138847 1.0342016220092773 True -13 19474 15.026427268981934 0.46519899368286133 497.916015625 1.2088017463684082 583.3429565429688 0.7680410146713257 0.7178659 1.0151711702346802 True -14 20865 14.992886066436768 0.44497251510620117 443.8266296386719 1.141692876815796 582.2423095703125 0.7691781520843506 0.72118026 1.0219199657440186 True -15 22256 15.021497249603271 0.43660783767700195 380.689208984375 1.2735010385513306 581.387939453125 0.7692962288856506 0.72403663 1.0337499380111694 True -16 23647 14.988056182861328 0.4349043369293213 332.57281494140625 0.8295981884002686 581.8114624023438 0.769055187702179 0.7271508 1.0675724744796753 True -17 25038 14.97890853881836 0.4356992244720459 361.598876953125 0.6325478553771973 583.1437377929688 0.7681083083152771 0.72907823 1.112221360206604 True -18 26429 14.969393491744995 0.43614792823791504 422.4241943359375 0.5625037550926208 584.0545043945312 0.7670348882675171 0.7289906 1.1596741676330566 False -19 27820 14.972959280014038 0.45021867752075195 338.427001953125 0.5113087892532349 585.0202026367188 0.7664638161659241 0.72761583 1.1896532773971558 False diff --git a/ENCSR476VJY/cherimoya.fold_1.performance.tsv b/ENCSR476VJY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 995fff3c482a04b76937be8f2601acf273e2fe68..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -583.1437377929688 0.19700492918491364 0.7681083083152771 0.36873340606689453 0.7290782332420349 0.74088454246521 1.112221360206604 \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_2.evaluate.json b/ENCSR476VJY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f829fb37cbb934ed8c764935f9e12c3e36c1c193..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF454KHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_2.fit.json b/ENCSR476VJY/cherimoya.fold_2.fit.json deleted file mode 100644 index 0e665c222a08155dabb3bf7604253121c9ef99eb..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF454KHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_2.log b/ENCSR476VJY/cherimoya.fold_2.log deleted file mode 100644 index 1901ad982607cd19ced88250338dd4ea1232e5fc..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1505 21.05350112915039 3.068499803543091 547.0540771484375 2.0811328887939453 1121.37255859375 0.4666465222835541 0.50616693 24.86450958251953 True -1 3010 16.51849937438965 0.2895846366882324 521.8558349609375 2.1383919715881348 771.2970581054688 0.6150991916656494 0.6089283 18.696104049682617 True -2 4515 16.515978574752808 0.2810370922088623 404.78314208984375 1.1983067989349365 637.269287109375 0.7004544734954834 0.65277034 5.644532203674316 True -3 6020 17.813467502593994 14.70304560661316 433.7701110839844 2.225918769836426 602.2149658203125 0.7236344218254089 0.6793175 2.1177985668182373 True -4 7525 16.6423180103302 0.2740671634674072 351.233642578125 1.9195888042449951 591.4530639648438 0.7309187054634094 0.6860112 1.4780805110931396 True -5 9030 16.52857255935669 0.277005672454834 440.66070556640625 1.4193735122680664 585.836669921875 0.7363160848617554 0.68776685 1.3346850872039795 True -6 10535 16.529360055923462 0.27011585235595703 493.2027587890625 1.7105095386505127 581.0869750976562 0.7402506470680237 0.6917463 1.225651741027832 True -7 12040 16.53233790397644 0.7407307624816895 425.0732116699219 1.1173243522644043 576.8439331054688 0.7438033223152161 0.6963112 1.1580657958984375 True -8 13545 16.522634029388428 0.26179981231689453 411.47119140625 1.3069708347320557 572.0225830078125 0.7471640706062317 0.70019346 1.1094592809677124 True -9 15050 16.50943660736084 0.2767210006713867 390.22747802734375 0.8972017168998718 568.7656860351562 0.7492945194244385 0.7026234 1.074479579925537 True -10 16555 16.51016879081726 0.26369619369506836 468.8033142089844 1.1649549007415771 564.9998779296875 0.7518609166145325 0.7060596 1.078340768814087 True -11 18060 16.531995058059692 0.2851600646972656 331.9259948730469 1.2524282932281494 562.789794921875 0.7539986968040466 0.7076804 1.0764715671539307 True -12 19565 16.577685594558716 0.27750420570373535 410.5538024902344 1.4524462223052979 560.2406005859375 0.7558875679969788 0.7147242 1.0699422359466553 True -13 21070 16.569082021713257 0.2766261100769043 390.6405029296875 1.5979310274124146 557.3949584960938 0.7579816579818726 0.7171445 1.053437352180481 True -14 22575 16.561858654022217 0.28420543670654297 368.1488037109375 0.81817626953125 555.5853881835938 0.759186327457428 0.718824 1.063300609588623 True -15 24080 16.508736848831177 0.2630796432495117 372.75421142578125 1.0599689483642578 555.4097900390625 0.7592983841896057 0.7243398 1.0729796886444092 True -16 25585 16.550506114959717 0.26502156257629395 349.6358642578125 0.9764328002929688 555.8678588867188 0.7590502500534058 0.72256464 1.1118563413619995 False -17 27090 16.562469482421875 0.2640249729156494 394.4649658203125 0.6681129932403564 556.4586791992188 0.7583081722259521 0.7225736 1.1624614000320435 False -18 28595 16.553776264190674 0.2777535915374756 429.8238525390625 0.9839005470275879 557.6235961914062 0.7575404047966003 0.7199568 1.216012954711914 False -19 30100 16.51859760284424 0.2795238494873047 335.5110778808594 1.0154953002929688 558.4548950195312 0.7568792104721069 0.71943897 1.243491530418396 False diff --git a/ENCSR476VJY/cherimoya.fold_2.performance.tsv b/ENCSR476VJY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8db27b35ac3cf008dbd626105d98cd07a20c329e..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -555.4097900390625 0.20599067211151123 0.7592983245849609 0.3536587357521057 0.7243397831916809 0.7326741218566895 1.0729796886444092 \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_3.evaluate.json b/ENCSR476VJY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5440672e3a577a84140f72bf5edf9e88b6d6e71e..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF454KHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_3.fit.json b/ENCSR476VJY/cherimoya.fold_3.fit.json deleted file mode 100644 index 6a5949a100d424a12f90c671cb1104b28a9ca7b3..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF454KHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_3.log b/ENCSR476VJY/cherimoya.fold_3.log deleted file mode 100644 index 5162b2611115e73ed29a07e0c778e18ecefc6803..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1454 20.2934730052948 3.3377914428710938 451.0967712402344 1.4515790939331055 1060.4144287109375 0.46939054131507874 0.54343885 26.05110740661621 True -1 2908 15.993752002716064 0.33357667922973633 516.9833984375 1.9669995307922363 739.083251953125 0.6103713512420654 0.6210578 17.58611488342285 True -2 4362 16.050122499465942 0.2883598804473877 405.7861328125 2.326090097427368 632.0374145507812 0.6914485692977905 0.6206254 8.518399238586426 False -3 5816 15.969199180603027 0.2745480537414551 413.2477722167969 1.867874264717102 593.26953125 0.7173243761062622 0.6103957 2.7766499519348145 False -4 7270 15.966437578201294 0.3036816120147705 406.480224609375 1.9604450464248657 583.6806030273438 0.7254704833030701 0.62824285 1.9366458654403687 True -5 8724 15.968337297439575 0.2668757438659668 339.8862609863281 1.6938261985778809 575.3558349609375 0.7307224869728088 0.63606805 1.594653844833374 True -6 10178 15.971020698547363 0.2740464210510254 388.11370849609375 1.7110859155654907 571.4426879882812 0.7344120740890503 0.63925517 1.539968729019165 True -7 11632 16.03069019317627 0.27727794647216797 476.91656494140625 1.6907880306243896 566.58447265625 0.7381969094276428 0.65953535 1.3546479940414429 True -8 13086 15.956693410873413 0.2681543827056885 378.42474365234375 1.4037290811538696 563.42919921875 0.7410080432891846 0.6586593 1.302804946899414 False -9 14540 15.957212924957275 0.2724132537841797 462.6563720703125 1.9028894901275635 559.64208984375 0.7440353035926819 0.6640907 1.2639135122299194 True -10 15994 15.972339868545532 0.26938557624816895 376.60986328125 1.5309752225875854 556.2857055664062 0.7468774318695068 0.6700274 1.2101631164550781 True -11 17448 15.943820238113403 0.2733137607574463 551.56298828125 1.3648728132247925 553.5218505859375 0.7490660548210144 0.67786896 1.1657367944717407 True -12 18902 15.94800877571106 0.2687411308288574 357.57366943359375 2.1699695587158203 550.988037109375 0.7512076497077942 0.6824582 1.1866960525512695 True -13 20356 15.94135069847107 0.268233060836792 385.0234375 1.1733205318450928 548.4401245117188 0.7530235648155212 0.6903566 1.151602029800415 True -14 21810 15.974533081054688 0.2731187343597412 501.12030029296875 1.1789034605026245 546.4443969726562 0.754176139831543 0.6982878 1.1474412679672241 True -15 23264 15.94840693473816 0.27277088165283203 428.14361572265625 1.0898971557617188 546.3267211914062 0.7541683912277222 0.7010662 1.174316167831421 True -16 24718 15.946603536605835 0.2780294418334961 419.7805480957031 0.7928389310836792 546.2811889648438 0.7538284063339233 0.7052921 1.201298713684082 True -17 26172 15.95400094985962 0.2734658718109131 307.28436279296875 0.8009028434753418 546.7260131835938 0.7532841563224792 0.70422876 1.2198877334594727 False -18 27626 15.946815252304077 0.2725391387939453 422.40570068359375 0.9583225250244141 547.2631225585938 0.7523766160011292 0.7046245 1.257788896560669 False -19 29080 15.961333990097046 0.27741026878356934 392.6547546386719 0.8445733785629272 547.7355346679688 0.7516756653785706 0.7024182 1.2828823328018188 False diff --git a/ENCSR476VJY/cherimoya.fold_3.performance.tsv b/ENCSR476VJY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 30ba3319ff2323c78e5c42c823fde931bfb4a3c0..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -546.2811889648438 0.20775333046913147 0.7538284063339233 0.3461850583553314 0.7052921056747437 0.7078889608383179 1.201298713684082 \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_4.evaluate.json b/ENCSR476VJY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8c32fe71fd9fbc62eab5ce14a4cdd06de11334a0..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF454KHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_4.fit.json b/ENCSR476VJY/cherimoya.fold_4.fit.json deleted file mode 100644 index 12672e625d2796a5db1c64601a1612ba70237097..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF454KHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR476VJY/cherimoya.fold_4.log b/ENCSR476VJY/cherimoya.fold_4.log deleted file mode 100644 index b01265e118db10f2b3b55a2ec1653585a59b24b4..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1416 19.85361385345459 3.368176221847534 501.5486755371094 2.1332037448883057 1058.0836181640625 0.45662426948547363 0.5303156 25.685413360595703 True -1 2832 15.55663251876831 0.27793121337890625 501.74603271484375 1.5888140201568604 727.1099243164062 0.6015139818191528 0.6190713 15.9013671875 True -2 4248 15.543943166732788 0.27458691596984863 457.57183837890625 1.3100578784942627 603.5738525390625 0.6884297728538513 0.63534164 6.40598726272583 True -3 5664 15.545719861984253 0.2511584758758545 449.4316101074219 1.7895121574401855 570.494873046875 0.7133632302284241 0.64916897 2.1243810653686523 True -4 7080 15.54443359375 0.2428135871887207 560.8231201171875 2.1421356201171875 558.5358276367188 0.7239544987678528 0.6570788 1.4410881996154785 True -5 8496 15.487092971801758 0.2408461570739746 367.863037109375 1.5266917943954468 552.4453735351562 0.7298383116722107 0.6594503 1.3173787593841553 True -6 9912 15.260315179824829 0.24684667587280273 359.06024169921875 2.073835611343384 547.5758056640625 0.7339677214622498 0.6702425 1.1874427795410156 True -7 11328 15.210828065872192 0.24402856826782227 380.87615966796875 1.4758368730545044 544.4558715820312 0.7369586229324341 0.67068523 1.1953110694885254 True -8 12744 15.26175570487976 0.7327344417572021 345.2703857421875 1.3290486335754395 541.521240234375 0.7396540641784668 0.68382394 1.103895902633667 True -9 14160 15.287993431091309 0.24483561515808105 433.2998962402344 1.092686653137207 537.6967163085938 0.742446780204773 0.6913608 1.0545711517333984 True -10 15576 15.269355535507202 0.24419403076171875 407.1194152832031 1.2272803783416748 535.1998291015625 0.7450673580169678 0.6904994 1.0523349046707153 False -11 16992 15.250284910202026 0.5456640720367432 389.2181091308594 1.060306429862976 533.3118896484375 0.7468367218971252 0.6975662 1.0441975593566895 True -12 18408 15.254710674285889 0.24123215675354004 351.49212646484375 0.9016134738922119 530.2392578125 0.7490894794464111 0.70213675 1.0228008031845093 True -13 19824 15.26498818397522 0.24439167976379395 333.4407653808594 0.9565544128417969 527.5514526367188 0.750553548336029 0.70442474 1.0322351455688477 True -14 21240 15.36817479133606 0.24942708015441895 429.3363037109375 0.8086916208267212 526.4114379882812 0.7515718936920166 0.709033 1.0422438383102417 True -15 22656 15.273572206497192 0.24451684951782227 392.53045654296875 0.9385181665420532 526.21630859375 0.7517582774162292 0.71099365 1.061131238937378 True -16 24072 15.325438737869263 9.419538736343384 343.71612548828125 1.0707768201828003 525.9242553710938 0.7516574859619141 0.7114372 1.084578514099121 True -17 25488 15.803425550460815 0.9455106258392334 390.9574890136719 0.8332538604736328 526.5731811523438 0.750541090965271 0.7088181 1.12214195728302 False -18 26904 15.30484652519226 0.2519235610961914 438.007568359375 0.6358884572982788 527.3253784179688 0.7497836947441101 0.70338446 1.1726264953613281 False -19 28320 15.279978513717651 0.2452704906463623 431.63922119140625 0.5455552339553833 528.11083984375 0.7492163181304932 0.6998874 1.1955153942108154 False diff --git a/ENCSR476VJY/cherimoya.fold_4.performance.tsv b/ENCSR476VJY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 99999fa157ab6da1a6b55f8a21c886891bd7c8bd..0000000000000000000000000000000000000000 --- a/ENCSR476VJY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -525.9242553710938 0.21159149706363678 0.7516573667526245 0.34047338366508484 0.7114372253417969 0.7075744867324829 1.084578514099121 \ No newline at end of file diff --git a/ENCSR476WNA/cherimoya.fold_4.log b/ENCSR476WNA/cherimoya.fold_4.log deleted file mode 100644 index a931bacaef22b08bc6538ad1e74242e00d27b452..0000000000000000000000000000000000000000 --- a/ENCSR476WNA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3306 41.220929861068726 3.7134783267974854 668.1991577148438 0.8587076663970947 918.2532348632812 0.7638850212097168 0.7065331 4.053356647491455 True -1 6612 36.500707149505615 1.5532152652740479 755.0513916015625 0.9343194365501404 803.5403442382812 0.8134856224060059 0.78666633 0.5366874933242798 True -2 9918 36.49182105064392 0.6627099514007568 665.7536010742188 0.5873264074325562 788.4651489257812 0.818666398525238 0.79530287 0.2860284447669983 True -3 13224 36.44518065452576 0.6540658473968506 682.97412109375 0.21560454368591309 782.6778564453125 0.8212009072303772 0.8018831 0.23636741936206818 True -4 16530 36.50835990905762 29.567271947860718 699.822265625 0.23130358755588531 779.0677490234375 0.8231448531150818 0.8073676 0.24523653090000153 True -5 19836 37.108784437179565 0.6773159503936768 607.0245971679688 0.14821206033229828 775.5283203125 0.8242998719215393 0.8097575 0.23665904998779297 True -6 23142 36.71443152427673 30.87247371673584 687.4854736328125 0.5454623103141785 773.7898559570312 0.8254066109657288 0.8159735 0.2261035293340683 True -7 26448 36.5993812084198 25.349024534225464 632.2503662109375 0.313732773065567 769.9172973632812 0.8272221684455872 0.81930757 0.2156914323568344 True -8 29754 35.83592677116394 2.1714558601379395 686.862548828125 0.589832067489624 767.3204345703125 0.8283165097236633 0.8211325 0.2123982161283493 True -9 33060 36.20131969451904 13.780677556991577 638.5160522460938 0.1104583889245987 764.05419921875 0.8306386470794678 0.8279847 0.20353740453720093 True -10 36366 35.86589860916138 0.653282880783081 648.9033203125 0.3673936128616333 761.7908935546875 0.8315172791481018 0.8301955 0.19733363389968872 True -11 39672 35.85783815383911 6.400346040725708 675.0433349609375 0.14541485905647278 759.7274169921875 0.8329259753227234 0.8354264 0.1925078183412552 True -12 42978 35.777849197387695 0.6509804725646973 649.3218994140625 0.13073453307151794 756.0283813476562 0.834847092628479 0.8408045 0.185795858502388 True -13 46284 35.83698654174805 0.6498925685882568 755.0001220703125 0.21002686023712158 754.2410278320312 0.8362700939178467 0.8494336 0.17840541899204254 True -14 49590 35.77696704864502 21.379570960998535 699.88134765625 0.30742597579956055 752.6129760742188 0.8376001119613647 0.8544622 0.1727505773305893 True -15 52896 36.72715210914612 0.6609184741973877 599.7312622070312 0.17539116740226746 751.1581420898438 0.8385222554206848 0.8586396 0.16782239079475403 True -16 56202 35.770665884017944 0.6570284366607666 692.70947265625 0.45623528957366943 750.493408203125 0.8390213251113892 0.8613428 0.16503553092479706 True -17 59508 35.800212383270264 23.97029757499695 677.6959228515625 0.2660667300224304 750.7605590820312 0.838802695274353 0.8538415 0.17310446500778198 False -18 62814 35.90054249763489 0.6549520492553711 675.3446044921875 0.8271673917770386 751.4420166015625 0.838536262512207 0.8546529 0.17570099234580994 False -19 66120 35.75420641899109 0.6469478607177734 647.6231079101562 0.13205565512180328 751.881591796875 0.8383952379226685 0.85144854 0.17879454791545868 False diff --git a/ENCSR478SWA/cherimoya.fold_0.evaluate.json b/ENCSR478SWA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9247560307ebcc1636626db5aaa8cf570d69377a..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693RHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_0.fit.json b/ENCSR478SWA/cherimoya.fold_0.fit.json deleted file mode 100644 index 05a01cea97d76dcff43db110b309505e41a1133e..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF693RHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_0.log b/ENCSR478SWA/cherimoya.fold_0.log deleted file mode 100644 index 3f0ff135e9e5c377f732d133c514ae9e181dd415..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 34.18852233886719 3.5254881381988525 888.8270263671875 1.335923433303833 1366.31298828125 0.24778351187705994 0.50851345 11.878901481628418 True -1 5456 30.36239790916443 0.5785446166992188 925.430908203125 1.6083862781524658 1065.951416015625 0.3652958273887634 0.6422317 4.650028228759766 True -2 8184 30.37266778945923 0.5788252353668213 737.17578125 0.7570862770080566 1049.8480224609375 0.3714005649089813 0.6533742 2.721323251724243 True -3 10912 30.379342794418335 0.5737450122833252 902.6266479492188 1.4976489543914795 1043.0185546875 0.37255406379699707 0.65592974 2.751621723175049 True -4 13640 30.32250428199768 0.5721228122711182 891.4761352539062 0.7702100276947021 1010.1754150390625 0.38224661350250244 0.68031126 1.8014987707138062 True -5 16368 30.323590755462646 0.5708258152008057 769.924560546875 0.8602941036224365 994.5263671875 0.391127347946167 0.68861103 1.6620110273361206 True -6 19096 30.35670495033264 0.5793910026550293 835.31689453125 0.9580749869346619 986.3264770507812 0.39422908425331116 0.69383955 1.503050446510315 True -7 21824 30.307433366775513 0.5799388885498047 853.480224609375 1.2373101711273193 979.0299682617188 0.39721089601516724 0.6980703 1.2858107089996338 True -8 24552 30.304962396621704 0.578118085861206 759.0018920898438 1.1734188795089722 966.6270751953125 0.4035593271255493 0.7086396 1.1584128141403198 True -9 27280 30.338223934173584 0.5931499004364014 612.7947387695312 0.8394587635993958 961.8766479492188 0.4046758711338043 0.71238774 1.0400688648223877 True -10 30008 30.379055738449097 0.5745999813079834 929.7225341796875 1.121154546737671 954.2601318359375 0.4093484580516815 0.7196384 1.0703105926513672 True -11 32736 30.406760215759277 0.5833663940429688 836.3193969726562 0.8124825954437256 947.4280395507812 0.41213539242744446 0.7246847 0.953601598739624 True -12 35464 30.452641010284424 1.624570608139038 846.6570434570312 0.9316595792770386 941.2123413085938 0.4157516658306122 0.732841 0.896591305732727 True -13 38192 30.37995743751526 0.5821785926818848 682.5598754882812 1.1836626529693604 934.3277587890625 0.41836515069007874 0.7387014 0.8595190644264221 True -14 40920 30.382219552993774 0.9014232158660889 827.0171508789062 0.9654382467269897 926.7216186523438 0.4230569303035736 0.74802643 0.8161604404449463 True -15 43648 30.37882375717163 0.5871007442474365 679.584228515625 0.8972409963607788 925.6110229492188 0.42259982228279114 0.75368035 0.7808421850204468 True -16 46376 30.385338068008423 0.6086602210998535 810.1144409179688 0.6617251634597778 921.33544921875 0.4239793121814728 0.759904 0.7486997842788696 True -17 49104 30.38081383705139 0.5893192291259766 725.9573974609375 0.648605465888977 920.2377319335938 0.4242663085460663 0.7615081 0.7332766652107239 True -18 51832 30.586278438568115 0.5922670364379883 703.0106201171875 0.8770262002944946 921.7398681640625 0.42367199063301086 0.7612901 0.7281764149665833 False -19 54560 30.458963632583618 0.5865652561187744 773.986328125 0.8166673183441162 922.952880859375 0.4232493042945862 0.76163614 0.7283810973167419 True diff --git a/ENCSR478SWA/cherimoya.fold_0.performance.tsv b/ENCSR478SWA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 51fc995fc7dda8ba68821605bf2e9379a0d09457..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -922.952880859375 0.36988192796707153 0.42324933409690857 0.18270015716552734 0.7616361379623413 0.7039840817451477 0.7283810973167419 \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_1.evaluate.json b/ENCSR478SWA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a76bf4f0da4d5e273e4f132d43e09f99531752bb..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693RHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_1.fit.json b/ENCSR478SWA/cherimoya.fold_1.fit.json deleted file mode 100644 index fdb3f0c6982428c64c69bdc31e09e25f84e916cb..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF693RHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_1.log b/ENCSR478SWA/cherimoya.fold_1.log deleted file mode 100644 index ac1eb949c4e4695bb18e4c74f3202171505c17bc..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2695 34.00541424751282 3.76237416267395 850.5833740234375 1.3591665029525757 1621.8692626953125 0.2486443966627121 0.5224541 11.428489685058594 True -1 5390 29.97597026824951 0.8178558349609375 936.7364501953125 1.2560721635818481 1275.106201171875 0.3682883381843567 0.6644123 5.5302534103393555 True -2 8085 29.990389108657837 0.8036341667175293 1025.4788818359375 1.1007587909698486 1245.9268798828125 0.377156525850296 0.68598896 3.5450193881988525 True -3 10780 30.09286403656006 9.002156734466553 822.07958984375 1.189056396484375 1216.825927734375 0.38224267959594727 0.69774103 2.8672258853912354 True -4 13475 30.021969079971313 0.8080599308013916 749.6700439453125 1.0192677974700928 1199.4276123046875 0.39064833521842957 0.70488864 2.094101667404175 True -5 16170 30.013896942138672 0.8352236747741699 801.7484130859375 0.8869146704673767 1183.96875 0.39597412943840027 0.70993894 1.8614835739135742 True -6 18865 29.969731092453003 0.8264422416687012 672.8192138671875 0.928214430809021 1179.4200439453125 0.39690181612968445 0.71604884 1.8639302253723145 True -7 21560 29.964287757873535 0.8039534091949463 711.3233642578125 1.0285990238189697 1167.36767578125 0.40222257375717163 0.72211725 1.652902364730835 True -8 24255 29.98163104057312 0.8115124702453613 791.71240234375 1.0027185678482056 1153.400634765625 0.4076072871685028 0.7333211 1.3644981384277344 True -9 26950 29.975586414337158 0.8163354396820068 957.13037109375 0.8377710580825806 1137.19677734375 0.4138559103012085 0.74274516 1.3162628412246704 True -10 29645 30.022026538848877 0.8138043880462646 1029.112548828125 1.1709389686584473 1125.234619140625 0.41800951957702637 0.74916536 1.1912626028060913 True -11 32340 29.981430292129517 0.8092212677001953 785.4571533203125 1.0216104984283447 1115.8076171875 0.4222222566604614 0.75438213 1.1465271711349487 True -12 35035 30.126108169555664 29.19854474067688 702.3919677734375 0.7202681303024292 1109.3233642578125 0.423067569732666 0.7632252 1.0310931205749512 True -13 37730 29.948461294174194 8.893543243408203 653.7808227539062 0.7494499683380127 1096.3485107421875 0.4264630079269409 0.7721136 0.938117265701294 True -14 40425 30.0083167552948 26.080668687820435 680.4049682617188 0.6407385468482971 1089.07275390625 0.4291306436061859 0.7823659 0.8754075169563293 True -15 43120 30.82270050048828 0.8271725177764893 741.178466796875 0.5506493449211121 1082.336181640625 0.4312058985233307 0.7875588 0.8380158543586731 True -16 45815 30.153823614120483 0.8412723541259766 606.6738891601562 0.5691027045249939 1079.872802734375 0.4317615330219269 0.79528344 0.7883322238922119 True -17 48510 29.96166968345642 0.8037707805633545 669.646728515625 0.5314493179321289 1074.304931640625 0.4348762333393097 0.79696065 0.760832667350769 True -18 51205 29.982500314712524 0.812391996383667 686.9991455078125 0.6480406522750854 1076.5755615234375 0.43279632925987244 0.79947215 0.7504439353942871 True -19 53900 30.02822732925415 0.8114359378814697 759.8233642578125 0.5444426536560059 1076.4146728515625 0.4326753318309784 0.7987787 0.7508822679519653 False diff --git a/ENCSR478SWA/cherimoya.fold_1.performance.tsv b/ENCSR478SWA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3c92635c72028632f6d99e683710f13d26fdf986..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1076.5755615234375 0.35756492614746094 0.43279626965522766 0.2072487771511078 0.7994721531867981 0.7603683471679688 0.7504439353942871 \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_2.evaluate.json b/ENCSR478SWA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9707eb0067c6c50206df4a2f94722d4ac7e633c6..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693RHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_2.fit.json b/ENCSR478SWA/cherimoya.fold_2.fit.json deleted file mode 100644 index 33c91075ad750401b7af7f8aff41c017b714c794..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF693RHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_2.log b/ENCSR478SWA/cherimoya.fold_2.log deleted file mode 100644 index 833a21dd228903c286dc6cf3abcdd3668473c832..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.006250619888306 3.4670069217681885 660.9946899414062 1.314723014831543 1379.9520263671875 0.24881254136562347 0.48756468 8.781667709350586 True -1 5794 32.16177415847778 0.6228275299072266 832.408447265625 1.2895539999008179 1074.5823974609375 0.35796570777893066 0.6573157 3.989431619644165 True -2 8691 32.186538219451904 0.9118537902832031 697.3250732421875 1.2577104568481445 1056.0435791015625 0.36343804001808167 0.6664484 3.0976879596710205 True -3 11588 32.21013879776001 0.594186544418335 831.193359375 1.0314671993255615 1021.7598266601562 0.376008003950119 0.6894273 2.7608237266540527 True -4 14485 32.15088176727295 0.6019294261932373 830.77587890625 1.3986644744873047 1018.3363037109375 0.37860336899757385 0.68752414 2.452816963195801 False -5 17382 32.15136384963989 0.5946998596191406 840.388671875 1.195235013961792 1000.0757446289062 0.3857835531234741 0.70102227 1.9077746868133545 True -6 20279 32.139089822769165 0.5832512378692627 832.6689453125 0.8466993570327759 999.0897827148438 0.3855663537979126 0.7099508 1.809415578842163 True -7 23176 32.14388465881348 0.582556962966919 908.4566650390625 0.83356112241745 988.075439453125 0.39016982913017273 0.7200247 1.500200867652893 True -8 26073 32.16939663887024 0.5836760997772217 777.3715209960938 0.9368085265159607 982.2156982421875 0.3918742835521698 0.72580355 1.3184163570404053 True -9 28970 32.202558517456055 0.5923655033111572 621.6165161132812 0.7045573592185974 971.0601806640625 0.39874258637428284 0.73173094 1.2022645473480225 True -10 31867 32.176846504211426 2.746896743774414 1029.2191162109375 0.9862828254699707 965.0117797851562 0.40194642543792725 0.7345557 1.090712308883667 True -11 34764 32.19458746910095 5.499232053756714 757.1346435546875 0.8418632745742798 957.5267944335938 0.4056536555290222 0.7421941 1.0370243787765503 True -12 37661 32.23368453979492 0.6064403057098389 697.7174682617188 1.1328994035720825 949.4423828125 0.4094328284263611 0.74789727 0.9278034567832947 True -13 40558 32.20491051673889 0.5966341495513916 833.3822021484375 0.8654460906982422 944.3204956054688 0.40956243872642517 0.75601673 0.8415536880493164 True -14 43455 32.19163775444031 0.6012609004974365 724.8231201171875 0.8834896087646484 938.4898071289062 0.4112142324447632 0.76334417 0.7855694890022278 True -15 46352 32.25656771659851 0.588700532913208 742.8114013671875 0.8815549612045288 935.2511596679688 0.412229061126709 0.7691498 0.7550054788589478 True -16 49249 32.1986563205719 2.505072832107544 794.1434326171875 0.7817182540893555 931.1511840820312 0.41491320729255676 0.77308923 0.719992995262146 True -17 52146 32.272905111312866 0.5991904735565186 795.8426513671875 0.7879852056503296 929.4105834960938 0.416414737701416 0.77498806 0.7075417637825012 True -18 55043 32.26700687408447 0.7122001647949219 555.9901733398438 0.6670228838920593 928.7908325195312 0.4167335629463196 0.77683944 0.7038348317146301 True -19 57940 32.220564126968384 0.599506139755249 753.9624633789062 0.6882726550102234 931.1485595703125 0.4151148796081543 0.7743178 0.7047581672668457 False diff --git a/ENCSR478SWA/cherimoya.fold_2.performance.tsv b/ENCSR478SWA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e74e09a73f812a1dad52f7fab5332efe5d0ad40c..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -928.7908325195312 0.37358558177948 0.4167335331439972 0.18548321723937988 0.7768394351005554 0.7232244610786438 0.7038348317146301 \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_3.evaluate.json b/ENCSR478SWA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 938390610c53ec40a405791f97a4a6f73d36d79a..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693RHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_3.fit.json b/ENCSR478SWA/cherimoya.fold_3.fit.json deleted file mode 100644 index b7a6023f1aa2ef7b3391c81b99d3051d463cb394..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF693RHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_3.log b/ENCSR478SWA/cherimoya.fold_3.log deleted file mode 100644 index 16ee86f7236b2a1b6b6ddc9c187431fc5af77232..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 34.61519813537598 3.6441667079925537 845.7857055664062 1.2568062543869019 1403.5870361328125 0.26023468375205994 0.5059829 12.130642890930176 True -1 5560 30.86766767501831 0.6035912036895752 841.8919677734375 1.511794090270996 1125.5491943359375 0.37198424339294434 0.6279696 6.718787670135498 True -2 8340 30.938130855560303 0.5902664661407471 938.6878051757812 1.286394715309143 1108.8297119140625 0.3790822923183441 0.63766444 4.961888790130615 True -3 11120 30.987423181533813 0.5944802761077881 923.706298828125 1.231154441833496 1090.3658447265625 0.38505658507347107 0.6599866 3.9187371730804443 True -4 13900 30.922101497650146 1.223062515258789 807.377685546875 1.2426908016204834 1069.5111083984375 0.39323753118515015 0.67431647 2.5626559257507324 True -5 16680 30.87290334701538 0.6073753833770752 1051.723876953125 1.2549294233322144 1055.9951171875 0.3978726267814636 0.68113476 2.1992008686065674 True -6 19460 30.947448015213013 0.5897178649902344 702.4024658203125 1.020006537437439 1046.3565673828125 0.4021128714084625 0.68598616 1.9926602840423584 True -7 22240 30.91044521331787 0.8290367126464844 757.7852783203125 0.906417965888977 1035.0582275390625 0.4068543612957001 0.6952906 1.6724237203598022 True -8 25020 30.882179498672485 0.5886132717132568 849.2061767578125 1.0798369646072388 1026.4437255859375 0.41202107071876526 0.7002421 1.6393952369689941 True -9 27800 30.84062957763672 0.5888521671295166 712.2791137695312 0.9548693895339966 1021.3796997070312 0.4135355055332184 0.70983416 1.3877002000808716 True -10 30580 30.918899536132812 0.5816435813903809 862.5009765625 1.071088194847107 1010.639404296875 0.4179980456829071 0.71188563 1.326421856880188 True -11 33360 30.890928030014038 0.5861203670501709 776.4221801757812 1.5088634490966797 1008.755615234375 0.41654354333877563 0.7188137 1.3013229370117188 True -12 36140 30.88464903831482 0.5847959518432617 841.511962890625 0.996400773525238 997.232666015625 0.422308087348938 0.7268101 1.1053491830825806 True -13 38920 30.89517307281494 0.581045389175415 936.3079223632812 0.541735053062439 986.4344482421875 0.42624059319496155 0.74021435 1.018517017364502 True -14 41700 30.90302562713623 0.5986716747283936 868.6756591796875 0.9232381582260132 980.8895263671875 0.4290836453437805 0.74972355 0.9580428600311279 True -15 44480 30.91182255744934 0.5900769233703613 748.1796264648438 0.6136125326156616 971.1222534179688 0.433990478515625 0.75701076 0.8769972920417786 True -16 47260 30.900665760040283 0.5801968574523926 598.744873046875 0.6012793779373169 969.1483154296875 0.4326576888561249 0.76281637 0.8290395140647888 True -17 50040 30.939321517944336 0.5964679718017578 875.542236328125 0.8066800832748413 967.1892700195312 0.4329525828361511 0.76695806 0.7938594818115234 True -18 52820 30.920531511306763 0.5947568416595459 604.0848388671875 0.6140258312225342 965.9694213867188 0.43463823199272156 0.76944315 0.7849305272102356 True -19 55600 30.89750623703003 0.5905466079711914 648.8656005859375 0.5999300479888916 967.3396606445312 0.4330597221851349 0.7683212 0.786079466342926 False diff --git a/ENCSR478SWA/cherimoya.fold_3.performance.tsv b/ENCSR478SWA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2efe6ae3b439eb90ef4d7ed1d64f41e235377720..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -965.9694213867188 0.3613850772380829 0.43463826179504395 0.19739194214344025 0.769443154335022 0.7156413793563843 0.7849305272102356 \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_4.evaluate.json b/ENCSR478SWA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5e8fa084ba62acef57fb6304184674547767f4bf..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693RHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_4.fit.json b/ENCSR478SWA/cherimoya.fold_4.fit.json deleted file mode 100644 index 80a48d18f1dcc204e4e33ddfba512553f05f90b8..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF693RHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR478SWA/cherimoya.fold_4.log b/ENCSR478SWA/cherimoya.fold_4.log deleted file mode 100644 index 6f8ea7e2ca5eb36cb91b3c61ba89e4d1eb3b8576..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2801 35.074146032333374 3.490515947341919 880.4868774414062 1.1332556009292603 1277.0780029296875 0.24572867155075073 0.4918649 7.586030006408691 True -1 5602 31.183528900146484 1.5801117420196533 874.3032836914062 2.326212167739868 1024.6077880859375 0.35085633397102356 0.6300853 4.63745641708374 True -2 8403 31.16231870651245 0.5594813823699951 853.8466186523438 0.8236224055290222 1003.0449829101562 0.3618680536746979 0.6431892 3.195375680923462 True -3 11204 31.19389057159424 1.0387296676635742 1032.25634765625 1.0351130962371826 981.2671508789062 0.36715152859687805 0.6557756 2.281747579574585 True -4 14005 31.184847354888916 0.5596504211425781 814.3656005859375 1.2824745178222656 961.8273315429688 0.3756599426269531 0.67333484 1.597983717918396 True -5 16806 31.081308841705322 0.5517780780792236 933.128173828125 1.126556396484375 950.11181640625 0.3813875913619995 0.6782984 1.470902919769287 True -6 19607 31.11652183532715 0.5517244338989258 719.7247314453125 0.8888343572616577 944.3323974609375 0.38441991806030273 0.6814661 1.3732843399047852 True -7 22408 31.17056179046631 0.5548958778381348 639.5962524414062 1.3156037330627441 934.9659423828125 0.3895435631275177 0.6852187 1.295433759689331 True -8 25209 31.16147804260254 2.193678379058838 862.6868286132812 0.919086217880249 928.9959106445312 0.39350226521492004 0.695002 1.178619623184204 True -9 28010 31.15810489654541 0.5678761005401611 931.3638305664062 1.035076379776001 920.583984375 0.39808619022369385 0.7008877 1.1452875137329102 True -10 30811 31.178762435913086 0.5569543838500977 765.8173828125 1.1588852405548096 913.1222534179688 0.40143337845802307 0.7091622 0.982038140296936 True -11 33612 31.177573442459106 0.5536530017852783 741.5435791015625 0.8182733058929443 909.3018188476562 0.402837336063385 0.7159205 0.9330557584762573 True -12 36413 31.141175508499146 0.5580074787139893 643.4443359375 0.6541285514831543 902.6856079101562 0.4060843586921692 0.7216586 0.9282160997390747 True -13 39214 31.169361352920532 0.5552620887756348 812.6851806640625 0.9509414434432983 895.2098999023438 0.4096772372722626 0.734816 0.8444302678108215 True -14 42015 31.184765338897705 0.5511338710784912 752.1646728515625 0.7306909561157227 891.11962890625 0.41144829988479614 0.7445647 0.8050501942634583 True -15 44816 31.148320198059082 0.5514805316925049 698.474609375 0.6124293208122253 886.6329345703125 0.4134913980960846 0.7513908 0.7538456916809082 True -16 47617 31.140114307403564 0.549201250076294 656.2559204101562 0.7119059562683105 884.0810546875 0.4154455065727234 0.7593646 0.7252338528633118 True -17 50418 31.149487733840942 0.5492801666259766 902.5926513671875 0.6637870073318481 882.1941528320312 0.41509920358657837 0.7605413 0.7063521146774292 True -18 53219 31.117454051971436 0.5574302673339844 728.0693359375 0.5008631944656372 879.1532592773438 0.4182302951812744 0.76170415 0.703161358833313 True -19 56020 31.220354318618774 0.5489842891693115 687.1759033203125 0.6382863521575928 882.9271850585938 0.41481366753578186 0.762924 0.7034040689468384 True diff --git a/ENCSR478SWA/cherimoya.fold_4.performance.tsv b/ENCSR478SWA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2aa85ecbd531ae6c01032ffe645961aeb9253928..0000000000000000000000000000000000000000 --- a/ENCSR478SWA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -882.9271850585938 0.3763166069984436 0.41481366753578186 0.18103531002998352 0.7629240155220032 0.7087319493293762 0.7034040689468384 \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_0.evaluate.json b/ENCSR480SNC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 321b2331522322ac03b45980c636017723839f16..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF447ONB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_0.fit.json b/ENCSR480SNC/cherimoya.fold_0.fit.json deleted file mode 100644 index 3141b6fec6dc9b8a32bb7ecfac745d01d80f5dc4..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF447ONB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_0.log b/ENCSR480SNC/cherimoya.fold_0.log deleted file mode 100644 index 40d95eaca877cf0f2605029fdd0b7f87597155b8..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 34.82720708847046 16.26038908958435 344.94842529296875 0.44674167037010193 568.6185913085938 0.16735586524009705 0.66363955 5.397401332855225 True -1 5468 30.10033631324768 0.6831517219543457 442.9501953125 0.42865246534347534 521.6974487304688 0.21290600299835205 0.7519956 1.6894553899765015 True -2 8202 30.279961347579956 0.5994446277618408 561.3067016601562 0.4226418435573578 515.9659423828125 0.21586871147155762 0.758624 1.5786488056182861 True -3 10936 30.145869970321655 0.6171925067901611 474.8052673339844 0.38511908054351807 507.68701171875 0.22116976976394653 0.7671672 1.0684854984283447 True -4 13670 30.087817192077637 0.5913105010986328 400.2151184082031 0.4771057963371277 504.20697021484375 0.22388316690921783 0.7786483 0.9065986275672913 True -5 16404 30.170124292373657 0.5718674659729004 451.96331787109375 0.4853779971599579 499.8722839355469 0.2278999537229538 0.7901063 0.724473237991333 True -6 19138 30.13898277282715 0.5866241455078125 416.30853271484375 0.27474820613861084 496.0361328125 0.23204712569713593 0.79809874 0.6334142684936523 True -7 21872 29.711894512176514 1.693171739578247 552.5323486328125 0.29249563813209534 494.2928771972656 0.23308169841766357 0.8059381 0.5773067474365234 True -8 24606 29.5963191986084 0.5741336345672607 433.796630859375 0.6117909550666809 492.1222229003906 0.23584814369678497 0.81352574 0.5397489070892334 True -9 27340 29.62207579612732 0.575225830078125 475.29595947265625 0.306334525346756 491.15325927734375 0.2358933687210083 0.81827676 0.4857141375541687 True -10 30074 29.546739101409912 0.5876646041870117 402.0723571777344 0.25818073749542236 489.3596496582031 0.23913037776947021 0.825691 0.4532923996448517 True -11 32808 29.588970184326172 0.5751967430114746 484.916748046875 0.5345349311828613 486.9595642089844 0.2415982335805893 0.8314635 0.41947057843208313 True -12 35542 29.59523057937622 0.599755048751831 388.2020263671875 0.37669527530670166 486.1109924316406 0.2416919618844986 0.83903825 0.39231058955192566 True -13 38276 29.645068407058716 0.5974278450012207 383.048828125 0.19554349780082703 484.45147705078125 0.24190455675125122 0.8473869 0.3567257225513458 True -14 41010 29.63845920562744 0.5900607109069824 444.8741455078125 0.3506234288215637 483.1546936035156 0.2422242909669876 0.8543368 0.3367650806903839 True -15 43744 29.617424488067627 0.58268141746521 599.3436279296875 0.2869078516960144 481.8841857910156 0.24472562968730927 0.85949075 0.31841781735420227 True -16 46478 29.663906574249268 0.5816304683685303 418.30511474609375 0.5693813562393188 482.3727722167969 0.24309657514095306 0.86204696 0.30781078338623047 True -17 49212 29.66041326522827 0.595198392868042 385.8118896484375 0.19278675317764282 482.7780456542969 0.24277037382125854 0.86328846 0.3009796440601349 True -18 51946 29.668195724487305 0.5812029838562012 427.1923828125 0.35081928968429565 483.3924865722656 0.24237975478172302 0.8628406 0.30353033542633057 False -19 54680 29.64552927017212 0.5789732933044434 337.0706481933594 0.16183951497077942 482.11859130859375 0.24461524188518524 0.8609508 0.3055086135864258 False diff --git a/ENCSR480SNC/cherimoya.fold_0.performance.tsv b/ENCSR480SNC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 368dd306a86cb40dfe188020665bb758a6734eda..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -482.7780456542969 0.48040083050727844 0.24277035892009735 0.09979171305894852 0.8632884621620178 0.8028931021690369 0.3009796440601349 \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_1.evaluate.json b/ENCSR480SNC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ab0efd1ebe50649d3a5eaacf4101b092672ec987..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF447ONB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_1.fit.json b/ENCSR480SNC/cherimoya.fold_1.fit.json deleted file mode 100644 index eaafb283d1cfee34e5ce1a0ce8ad424ce139d1c8..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF447ONB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_1.log b/ENCSR480SNC/cherimoya.fold_1.log deleted file mode 100644 index 5f5737703335dd465bed5ead0a922d3b65fa2a62..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2683 34.43387746810913 4.599441051483154 412.267578125 0.7555944919586182 698.2772216796875 0.1812359094619751 0.66806376 6.646402835845947 True -1 5366 29.617769479751587 0.8016357421875 492.8630676269531 0.5599205493927002 632.0618896484375 0.23720911145210266 0.7739567 2.033623218536377 True -2 8049 29.498849153518677 0.7671711444854736 423.177734375 0.35630837082862854 621.4482421875 0.24021849036216736 0.78679854 1.4769083261489868 True -3 10732 28.936603546142578 0.7539348602294922 427.306640625 0.46690887212753296 608.8460693359375 0.24758674204349518 0.79920036 1.3143987655639648 True -4 13415 28.94202947616577 1.7254085540771484 408.21527099609375 0.43665191531181335 603.083740234375 0.253171443939209 0.8100453 1.1128185987472534 True -5 16098 29.00615358352661 0.7485558986663818 377.83160400390625 0.36507469415664673 600.670654296875 0.2544093430042267 0.81335413 0.9926186800003052 True -6 18781 29.04179310798645 0.7598004341125488 454.11468505859375 0.7393648624420166 595.7552490234375 0.25916776061058044 0.82104945 0.8877242207527161 True -7 21464 28.86632537841797 0.7744057178497314 483.38983154296875 0.4438939690589905 592.6043090820312 0.26290610432624817 0.82928205 0.7749481797218323 True -8 24147 29.007376194000244 0.741710901260376 490.67626953125 0.3981558382511139 591.3878784179688 0.26269736886024475 0.8356612 0.7185204029083252 True -9 26830 28.897682666778564 0.7707231044769287 451.678955078125 0.3246026635169983 588.4696655273438 0.2667226791381836 0.83826566 0.6701458096504211 True -10 29513 28.992960453033447 0.7599313259124756 450.558349609375 0.46511808037757874 587.0310668945312 0.26756563782691956 0.84626615 0.6234621405601501 True -11 32196 28.980626583099365 0.7506580352783203 512.8701171875 0.5129019021987915 584.4874877929688 0.27029916644096375 0.85037154 0.5706478953361511 True -12 34879 28.91391134262085 0.7536981105804443 432.0601806640625 0.3618541359901428 581.5465087890625 0.2735876142978668 0.8593873 0.5069289803504944 True -13 37562 28.9337055683136 0.7647769451141357 323.91680908203125 0.3009239435195923 580.5131225585938 0.27356722950935364 0.8680485 0.4518027603626251 True -14 40245 28.98953652381897 0.7633578777313232 494.7517395019531 0.3704020380973816 577.4950561523438 0.27659469842910767 0.87068814 0.428045392036438 True -15 42928 28.9420645236969 0.7534692287445068 423.43865966796875 0.2999374270439148 577.5352783203125 0.27396729588508606 0.8788541 0.3839598298072815 True -16 45611 29.009868383407593 0.7453773021697998 406.90545654296875 0.5197255611419678 577.5284423828125 0.27394571900367737 0.88034743 0.34971049427986145 True -17 48294 28.983218669891357 24.001163959503174 376.489990234375 0.14314208924770355 575.60400390625 0.2772171199321747 0.88333464 0.33796510100364685 True -18 50977 28.984309673309326 0.7606525421142578 369.782958984375 0.2476661205291748 578.0950317382812 0.273001492023468 0.8818294 0.332499235868454 False -19 53660 29.003637552261353 0.7533035278320312 460.9853820800781 0.25574225187301636 577.2481689453125 0.2755715847015381 0.88027394 0.33311155438423157 False diff --git a/ENCSR480SNC/cherimoya.fold_1.performance.tsv b/ENCSR480SNC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d0111151855a769c147ee6f80228a4f011a1b680..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -575.60400390625 0.45184269547462463 0.2772171199321747 0.12080546468496323 0.8833346366882324 0.8557197451591492 0.33796510100364685 \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_2.evaluate.json b/ENCSR480SNC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8ad32e9fd9fd4b233910c76a647b29ca321e7cf5..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF447ONB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_2.fit.json b/ENCSR480SNC/cherimoya.fold_2.fit.json deleted file mode 100644 index 6e69b8e8c11c2b2e618172cfde4f06981aa44f73..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF447ONB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_2.log b/ENCSR480SNC/cherimoya.fold_2.log deleted file mode 100644 index 28c905dd65aefff610ea246de475b5ccc4585c87..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2867 36.46204233169556 4.276661396026611 496.0114440917969 0.48942941427230835 595.3308715820312 0.16990657150745392 0.65978354 4.969510555267334 True -1 5734 31.58796977996826 0.701103925704956 533.4235229492188 0.4934803247451782 541.8597412109375 0.21750681102275848 0.7471697 1.612275242805481 True -2 8601 33.37199425697327 0.6369247436523438 499.3888854980469 0.45395055413246155 535.431396484375 0.21764682233333588 0.7671808 1.3918769359588623 True -3 11468 30.961508750915527 0.6096069812774658 595.6534423828125 0.5863881707191467 522.4003295898438 0.2273891121149063 0.78759235 0.844607949256897 True -4 14335 30.99403429031372 0.6114885807037354 410.5753173828125 0.3460153639316559 518.2273559570312 0.22998127341270447 0.79910564 0.7152667045593262 True -5 17202 31.01165795326233 0.7028119564056396 361.66864013671875 0.4944301247596741 516.7368774414062 0.23140248656272888 0.8013928 0.6737683415412903 True -6 20069 30.98193073272705 0.6131846904754639 383.92364501953125 0.3640648126602173 515.6693725585938 0.23213757574558258 0.8049258 0.63270503282547 True -7 22936 30.932522296905518 0.7481226921081543 424.119384765625 0.632704496383667 513.1969604492188 0.23577015101909637 0.8132525 0.5691124200820923 True -8 25803 30.91365122795105 0.6092720031738281 493.4103698730469 0.6355619430541992 510.3580322265625 0.2392360270023346 0.81830496 0.5351587533950806 True -9 28670 30.9036226272583 0.61092209815979 436.28338623046875 0.2997562289237976 508.8802185058594 0.2404438853263855 0.82420033 0.4849851429462433 True -10 31537 30.981533765792847 0.6156055927276611 451.2506103515625 0.37051206827163696 507.5040283203125 0.24164791405200958 0.8312241 0.4500688314437866 True -11 34404 31.013493537902832 0.6113133430480957 323.6802673339844 0.36021867394447327 505.78619384765625 0.24306173622608185 0.837552 0.4142826795578003 True -12 37271 31.011343240737915 0.6156201362609863 571.934326171875 0.3642382323741913 503.3129577636719 0.2462664246559143 0.84362215 0.3917984366416931 True -13 40138 30.988262176513672 0.6110432147979736 408.6771240234375 0.29029980301856995 502.3175964355469 0.24610835313796997 0.84893525 0.36495497822761536 True -14 43005 31.014803886413574 0.610471248626709 467.5482482910156 0.276946485042572 500.50775146484375 0.24788768589496613 0.8543384 0.3469955027103424 True -15 45872 30.97762417793274 0.6183600425720215 497.5339050292969 0.4002317190170288 499.7993469238281 0.24778644740581512 0.85933787 0.32904452085494995 True -16 48739 31.035260915756226 1.217632532119751 434.0758361816406 0.15885254740715027 499.69921875 0.24751034379005432 0.8614197 0.31791141629219055 True -17 51606 31.117759466171265 0.6178257465362549 334.9227600097656 0.23153209686279297 498.6813659667969 0.24894864857196808 0.8619562 0.31264135241508484 True -18 54473 31.07704496383667 0.6178503036499023 334.65496826171875 0.3011114001274109 498.7665100097656 0.2486160844564438 0.8593546 0.3145465850830078 False -19 57340 31.071343183517456 0.6242492198944092 432.177978515625 0.15413862466812134 499.540771484375 0.24819064140319824 0.85951793 0.31709226965904236 False diff --git a/ENCSR480SNC/cherimoya.fold_2.performance.tsv b/ENCSR480SNC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 060b4e1f43f852d96b4918002053017d3e815bc9..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -498.6813659667969 0.4742879569530487 0.24894864857196808 0.1020173653960228 0.8619561791419983 0.8236825466156006 0.31264135241508484 \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_3.evaluate.json b/ENCSR480SNC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d8bbfd6a4ce547ad68989805dd9843eea769e22f..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF447ONB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_3.fit.json b/ENCSR480SNC/cherimoya.fold_3.fit.json deleted file mode 100644 index 90d49439a28dedfa6250a874bb5c74be56921461..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF447ONB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_3.log b/ENCSR480SNC/cherimoya.fold_3.log deleted file mode 100644 index 1f93c1214f60cf8598d7ff57c6b7afc502cc5010..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.29773473739624 4.610136032104492 368.356689453125 0.4051005244255066 591.431396484375 0.17801761627197266 0.6327071 5.016735076904297 True -1 5508 30.42229175567627 0.6043343544006348 496.3785400390625 0.39099815487861633 544.1245727539062 0.2233838438987732 0.7237359 1.7767668962478638 True -2 8262 30.452253341674805 0.5946822166442871 424.17840576171875 0.36169809103012085 536.4620361328125 0.22471453249454498 0.75026846 1.3235116004943848 True -3 11016 30.40628981590271 0.586219310760498 453.7442321777344 0.5894558429718018 529.5061645507812 0.231387197971344 0.7583534 1.122014045715332 True -4 13770 30.335858583450317 0.5884783267974854 331.39898681640625 0.3694417476654053 526.0678100585938 0.23603937029838562 0.75877583 1.0491288900375366 True -5 16524 30.32853412628174 0.5820586681365967 334.0578308105469 0.346790075302124 522.24462890625 0.2377629280090332 0.77475363 0.9287174344062805 True -6 19278 30.347095489501953 0.5860803127288818 440.7832946777344 0.5157886743545532 521.9072265625 0.23831486701965332 0.777752 0.8633708953857422 True -7 22032 30.435494661331177 30.293548107147217 373.3103942871094 0.3461989760398865 519.1380615234375 0.24188217520713806 0.78864104 0.79294353723526 True -8 24786 29.96490240097046 0.6044683456420898 427.5992126464844 0.3817668557167053 516.9747924804688 0.2440768927335739 0.7967173 0.6846964359283447 True -9 27540 29.840574264526367 0.5876710414886475 484.0611572265625 0.3269879221916199 516.1868896484375 0.2453569918870926 0.80087614 0.654262900352478 True -10 30294 29.828421354293823 0.6180129051208496 474.6314697265625 0.35560309886932373 514.0855712890625 0.24707528948783875 0.8119125 0.5726534128189087 True -11 33048 29.81459927558899 0.5971980094909668 427.377685546875 0.3424256443977356 511.50274658203125 0.2510443329811096 0.8132607 0.5521156787872314 True -12 35802 29.845240592956543 0.5760762691497803 471.6842956542969 0.40520039200782776 511.0272521972656 0.2501825988292694 0.82258594 0.5099261999130249 True -13 38556 29.711618423461914 1.3622417449951172 430.3104553222656 0.2537713646888733 508.95977783203125 0.25237420201301575 0.8312381 0.4674590229988098 True -14 41310 29.786974906921387 0.5744781494140625 384.8856506347656 0.2343565672636032 507.0633850097656 0.25436079502105713 0.84040034 0.43845024704933167 True -15 44064 29.79244375228882 0.5680079460144043 330.3972473144531 0.4031912684440613 505.576904296875 0.25560471415519714 0.84624565 0.40430012345314026 True -16 46818 29.990591526031494 0.5743939876556396 566.7772216796875 0.24042591452598572 505.2189025878906 0.2552097737789154 0.85280347 0.3764892816543579 True -17 49572 29.824503660202026 0.5740172863006592 387.26483154296875 0.16624245047569275 505.17620849609375 0.25446921586990356 0.85709816 0.3539198040962219 True -18 52326 29.738284587860107 0.5656375885009766 400.65069580078125 0.19799670577049255 505.4856262207031 0.2542593479156494 0.8577998 0.34750455617904663 True -19 55080 29.798137426376343 0.5748159885406494 362.4828186035156 0.18698495626449585 505.6846008300781 0.2539091408252716 0.85652554 0.3469839096069336 False diff --git a/ENCSR480SNC/cherimoya.fold_3.performance.tsv b/ENCSR480SNC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d7321a2a677eb7b746dec31f22a4e8e5832ecc3b..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -505.4856262207031 0.4718139171600342 0.2542593479156494 0.10725811123847961 0.8577998280525208 0.7961992621421814 0.34750455617904663 \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_4.evaluate.json b/ENCSR480SNC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 120aab4bf46bc000a22b7e6e4de6fffdcd205ca6..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF447ONB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_4.fit.json b/ENCSR480SNC/cherimoya.fold_4.fit.json deleted file mode 100644 index d4a9e44498fddbafec9c03fa695039ba3610d171..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF447ONB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR480SNC/cherimoya.fold_4.log b/ENCSR480SNC/cherimoya.fold_4.log deleted file mode 100644 index a24462bc39aec6af6dd8c4400134199db2823a79..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2815 35.34726548194885 5.040513038635254 391.2655944824219 0.5352011919021606 521.2738037109375 0.16124732792377472 0.6413996 4.7564473152160645 True -1 5630 31.092508792877197 14.173015594482422 364.32122802734375 0.43889275193214417 482.1623229980469 0.2062217891216278 0.73124355 1.1747543811798096 True -2 8445 31.010478019714355 1.1078341007232666 444.7860107421875 0.2848406434059143 478.2497253417969 0.2075134813785553 0.73126763 1.1379095315933228 True -3 11260 30.445215463638306 0.571326494216919 360.47955322265625 0.497871994972229 472.69866943359375 0.2126850187778473 0.7445172 0.8004398941993713 True -4 14075 30.3591468334198 1.090989351272583 406.8668518066406 0.6989850997924805 468.6125793457031 0.21479910612106323 0.75730395 0.6694607138633728 True -5 16890 30.45598816871643 0.6046199798583984 380.77178955078125 0.3780982494354248 465.6812744140625 0.2179214358329773 0.765272 0.6220465302467346 True -6 19705 30.46485996246338 0.5697488784790039 390.28070068359375 0.23148760199546814 463.60595703125 0.2197193056344986 0.77581847 0.544597327709198 True -7 22520 30.36220359802246 0.6454308032989502 407.2801513671875 0.314005970954895 461.856201171875 0.2207256555557251 0.78538704 0.4969887435436249 True -8 25335 30.41170859336853 0.5700299739837646 444.85308837890625 0.3116914927959442 459.3179626464844 0.22386857867240906 0.7908932 0.4453188478946686 True -9 28150 30.396473169326782 0.581751823425293 534.01220703125 0.6040446758270264 457.1670837402344 0.2268378883600235 0.80038756 0.4089897572994232 True -10 30965 30.388052463531494 0.5499997138977051 345.2301025390625 0.2531451880931854 455.9237060546875 0.22845150530338287 0.8063412 0.3917560577392578 True -11 33780 30.374708652496338 0.5599925518035889 374.29840087890625 0.30892378091812134 454.59771728515625 0.22942551970481873 0.8120101 0.36939090490341187 True -12 36595 30.369537591934204 0.5716333389282227 417.2669982910156 0.28581881523132324 452.937744140625 0.23054549098014832 0.81940037 0.35484760999679565 True -13 39410 30.430696487426758 0.572706937789917 404.0703430175781 0.34244006872177124 453.25531005859375 0.23009061813354492 0.82524586 0.34068572521209717 True -14 42225 30.40765070915222 0.885427713394165 399.0035705566406 0.262875497341156 451.4851379394531 0.2329750806093216 0.83207333 0.32430121302604675 True -15 45040 30.481627702713013 0.6065211296081543 458.99053955078125 0.21771304309368134 451.3665466308594 0.23224274814128876 0.8390688 0.31296050548553467 True -16 47855 30.402246475219727 0.5620944499969482 515.8943481445312 0.3003194332122803 451.3421325683594 0.23123304545879364 0.844043 0.3037441372871399 True -17 50670 30.4014151096344 0.5699074268341064 372.46551513671875 0.16543598473072052 450.8619689941406 0.23153765499591827 0.8423003 0.30407536029815674 False -18 53485 30.40314269065857 0.5719225406646729 387.2279052734375 0.2376956045627594 450.149658203125 0.23358896374702454 0.8418275 0.30724722146987915 False -19 56300 30.432503938674927 0.5737590789794922 417.4884033203125 0.1431894302368164 450.03448486328125 0.2333349883556366 0.8408188 0.30963221192359924 False diff --git a/ENCSR480SNC/cherimoya.fold_4.performance.tsv b/ENCSR480SNC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c1cc04ea598c93efe85bd25b7ca6ab3786c97be6..0000000000000000000000000000000000000000 --- a/ENCSR480SNC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -451.3421325683594 0.4889635741710663 0.23123306035995483 0.09177783131599426 0.8440430164337158 0.7801345586776733 0.3037441372871399 \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_0.evaluate.json b/ENCSR483RKN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 24c9072f9093880c527337b58e98945c4e3c2f42..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF973ISJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_0.fit.json b/ENCSR483RKN/cherimoya.fold_0.fit.json deleted file mode 100644 index bdd4c989af4e37a6bdea13a2e05ad877ce159762..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF973ISJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_0.log b/ENCSR483RKN/cherimoya.fold_0.log deleted file mode 100644 index c39a99f676a47e3e1a18d1b6f07e2a206de0782c..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2696 34.02973794937134 3.4867305755615234 343.4153747558594 0.8187299966812134 590.0195922851562 0.5439730286598206 0.7214334 7.0230607986450195 True -1 5392 29.843244075775146 0.5210442543029785 345.4237060546875 1.1634337902069092 509.568603515625 0.6295735836029053 0.7458778 1.8060802221298218 True -2 8088 29.85206699371338 0.5103695392608643 406.92022705078125 1.1377094984054565 494.2000427246094 0.6459569931030273 0.7539753 0.9071987271308899 True -3 10784 29.816935539245605 0.5105857849121094 425.7987060546875 0.8048033118247986 488.52203369140625 0.652884304523468 0.74692315 0.7449328899383545 False -4 13480 29.820608854293823 0.9524633884429932 397.705322265625 0.6299537420272827 486.5702209472656 0.6556180119514465 0.74741584 0.7027118802070618 False -5 16176 29.856813669204712 0.7647571563720703 429.49560546875 0.5615786910057068 484.51629638671875 0.6580305099487305 0.7448549 0.6582750678062439 False -6 18872 29.8126802444458 0.5186333656311035 456.9066162109375 0.7585350871086121 482.5071716308594 0.6609086990356445 0.7504518 0.6192929148674011 False -7 21568 29.86304998397827 0.5136985778808594 407.38299560546875 0.6840724945068359 481.1191101074219 0.6626772284507751 0.7511678 0.5798124074935913 False -8 24264 29.899625062942505 1.7310655117034912 301.21246337890625 1.027809739112854 479.4295349121094 0.664851725101471 0.75386107 0.5610345602035522 False -9 26960 29.8541202545166 0.5139553546905518 399.20538330078125 0.6489328742027283 477.77685546875 0.6670132279396057 0.75826883 0.5545600056648254 True -10 29656 29.819762468338013 0.5344135761260986 381.5459289550781 0.643343448638916 475.6585998535156 0.6693753004074097 0.7641283 0.5433990955352783 True -11 32352 29.820377111434937 0.5117630958557129 393.66302490234375 0.9451069831848145 473.54669189453125 0.6718204617500305 0.7688788 0.5219460725784302 True -12 35048 30.610056400299072 0.5147027969360352 427.352294921875 0.7940669059753418 472.2632141113281 0.6734994053840637 0.77657217 0.5013574957847595 True -13 37744 30.165335178375244 0.5558013916015625 404.67010498046875 0.4500974416732788 471.2895812988281 0.6746925711631775 0.7815966 0.48393431305885315 True -14 40440 29.889384984970093 0.5194394588470459 309.0225830078125 0.4447251856327057 470.2112121582031 0.6757282018661499 0.7873957 0.48156461119651794 True -15 43136 29.89725422859192 0.5194666385650635 376.3284912109375 0.38841575384140015 470.1119689941406 0.6759043335914612 0.7884151 0.48964154720306396 True -16 45832 29.84079933166504 0.5088372230529785 364.35723876953125 0.43050429224967957 470.1775817871094 0.6757291555404663 0.7866823 0.5058680176734924 False -17 48528 29.798523426055908 9.82632565498352 412.1273193359375 0.3358406722545624 470.89971923828125 0.6749317646026611 0.78283715 0.5298813581466675 False -18 51224 29.801074028015137 0.5116980075836182 359.8585205078125 0.21189948916435242 471.26123046875 0.6743633151054382 0.77813107 0.5512571930885315 False -19 53920 29.822131395339966 0.513864278793335 340.4218444824219 0.37394315004348755 471.6303405761719 0.6739803552627563 0.7742666 0.5663201212882996 False diff --git a/ENCSR483RKN/cherimoya.fold_0.performance.tsv b/ENCSR483RKN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ebab5f96c52c236c19ec15bc5670a7b67a7ec180..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -470.1119689941406 0.26159459352493286 0.6759043335914612 0.29890626668930054 0.7884150743484497 0.7053580284118652 0.48964154720306396 \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_1.evaluate.json b/ENCSR483RKN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ac63879d9a64b7d35e15be85d80d3644040cc8ad..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF973ISJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_1.fit.json b/ENCSR483RKN/cherimoya.fold_1.fit.json deleted file mode 100644 index d9202f1cc30944ca1a89d9cfb9b686a2f0776a70..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF973ISJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_1.log b/ENCSR483RKN/cherimoya.fold_1.log deleted file mode 100644 index 86ec0fe39205942c6c1c7b07f53d79ac0f28a792..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2807 34.95503258705139 3.8170764446258545 395.06634521484375 0.8664623498916626 646.0250244140625 0.5644577741622925 0.7293169 6.72430419921875 True -1 5614 31.03138494491577 0.8818702697753906 417.51116943359375 0.7652240991592407 560.06103515625 0.6552707552909851 0.74858224 2.024420738220215 True -2 8421 31.065063953399658 0.7096519470214844 376.8416748046875 1.0100041627883911 546.6377563476562 0.6676580905914307 0.7515122 1.0354450941085815 True -3 11228 31.098742723464966 0.7050728797912598 447.0484619140625 0.8162610530853271 539.169677734375 0.6730996966362 0.7542179 0.7973139882087708 True -4 14035 31.09595823287964 0.7132673263549805 388.1965637207031 1.034500002861023 536.7377319335938 0.6757149696350098 0.75843817 0.6694852113723755 True -5 16842 31.146310091018677 0.7105982303619385 392.9520263671875 0.8589463233947754 534.7774658203125 0.6779908537864685 0.76358026 0.6507982015609741 True -6 19649 31.04417634010315 0.7040247917175293 351.9682312011719 0.7923126220703125 533.2654418945312 0.6799492835998535 0.7617945 0.6399906277656555 False -7 22456 31.051913499832153 0.7157163619995117 352.7638854980469 0.8964923620223999 530.8893432617188 0.6823474764823914 0.76708305 0.6021305322647095 True -8 25263 31.096485137939453 0.7078714370727539 359.93402099609375 0.8126726150512695 528.0548095703125 0.6849996447563171 0.7746194 0.5814996361732483 True -9 28070 31.118785619735718 1.4674322605133057 421.9253234863281 0.5023974776268005 526.32275390625 0.6870651245117188 0.7738848 0.5698108673095703 False -10 30877 31.058600664138794 29.560290336608887 368.88751220703125 0.7089840769767761 523.9296875 0.6893295049667358 0.7793706 0.5392642021179199 True -11 33684 31.20662546157837 0.9937589168548584 410.37542724609375 0.5855609178543091 521.708984375 0.6916050910949707 0.781653 0.522867739200592 True -12 36491 31.022486448287964 0.6950225830078125 396.57000732421875 0.6392683982849121 519.8009033203125 0.6935563087463379 0.78888845 0.5024408102035522 True -13 39298 31.00534963607788 0.7086455821990967 354.588623046875 0.5069036483764648 518.300048828125 0.6950862407684326 0.7943472 0.4850929379463196 True -14 42105 31.13749647140503 1.491241455078125 416.4977722167969 0.4723132848739624 517.1927490234375 0.6961658000946045 0.8009615 0.4741211235523224 True -15 44912 31.02948832511902 0.7082598209381104 406.06640625 0.7176938056945801 516.5308227539062 0.6967146396636963 0.80219936 0.47076430916786194 True -16 47719 31.029128789901733 0.7272512912750244 385.99090576171875 0.4912262558937073 516.638671875 0.6965407729148865 0.7995948 0.48355114459991455 False -17 50526 31.266007900238037 0.7085108757019043 331.99603271484375 0.4786933362483978 516.8778686523438 0.6959872245788574 0.7950859 0.5016607046127319 False -18 53333 31.0999858379364 0.704871654510498 382.60308837890625 0.48861899971961975 517.5403442382812 0.6952142119407654 0.7908192 0.5197582244873047 False -19 56140 31.0389621257782 1.2922608852386475 401.78668212890625 0.30465370416641235 517.765380859375 0.6948189735412598 0.7862993 0.5363708138465881 False diff --git a/ENCSR483RKN/cherimoya.fold_1.performance.tsv b/ENCSR483RKN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 383bbc23c3eaa045ff2b95d97fdbc0caecf55e11..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -516.5308227539062 0.24509835243225098 0.6967146396636963 0.32659584283828735 0.8021993637084961 0.759911298751831 0.47076430916786194 \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_2.evaluate.json b/ENCSR483RKN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 331921bd0caf528862c559e23aa8bc5dd0668606..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF973ISJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_2.fit.json b/ENCSR483RKN/cherimoya.fold_2.fit.json deleted file mode 100644 index 3f917a5d2bcf7eb0efbcbe041ba8ba6073105b73..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF973ISJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_2.log b/ENCSR483RKN/cherimoya.fold_2.log deleted file mode 100644 index 0e47a23fa596a28abb865a3401f8a034d03d3603..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 36.43650674819946 3.596651077270508 427.51947021484375 0.7507832646369934 606.1773071289062 0.560091495513916 0.66585356 8.003422737121582 True -1 5800 32.15268611907959 0.7011616230010986 482.3189697265625 1.0805647373199463 529.13427734375 0.6384719610214233 0.69205415 2.490330934524536 True -2 8700 32.12088966369629 0.6835203170776367 343.4062194824219 0.7929736375808716 514.8305053710938 0.6503074169158936 0.69849247 1.4607247114181519 True -3 11600 32.022653579711914 0.6798937320709229 421.8800048828125 0.7717362642288208 509.1434631347656 0.6553223133087158 0.70740086 1.1563256978988647 True -4 14500 32.07833290100098 0.6802124977111816 384.82415771484375 0.6148251891136169 507.2039489746094 0.658065140247345 0.7115839 1.0255672931671143 True -5 17400 32.15450668334961 0.6911754608154297 431.386962890625 0.6570074558258057 504.3250427246094 0.6605459451675415 0.7166556 0.9257934093475342 True -6 20300 32.0479633808136 0.6788408756256104 290.9539794921875 1.0181336402893066 502.1420593261719 0.662415087223053 0.7172892 0.8461515307426453 True -7 23200 32.03461742401123 0.6770856380462646 358.9910583496094 1.0342040061950684 499.9885559082031 0.6649467945098877 0.7214407 0.867008626461029 True -8 26100 32.03729176521301 0.6821079254150391 436.86090087890625 1.1294742822647095 498.9172668457031 0.6666741967201233 0.72131467 0.8301342725753784 False -9 29000 32.00098967552185 0.6787459850311279 450.6671142578125 0.6633007526397705 496.9476013183594 0.6686139106750488 0.71986693 0.8229331970214844 False -10 31900 32.04118084907532 0.6814663410186768 459.66455078125 0.42727479338645935 494.924560546875 0.6703750491142273 0.72377044 0.7485077381134033 True -11 34800 32.02069902420044 0.6810708045959473 371.86956787109375 0.6834993362426758 493.1721496582031 0.6724175810813904 0.7254109 0.7437185049057007 True -12 37700 32.055954456329346 0.6831021308898926 350.49462890625 0.6685798168182373 491.3846435546875 0.6744473576545715 0.7291694 0.7560021281242371 True -13 40600 32.01250910758972 2.6197800636291504 390.312255859375 0.41867372393608093 490.12469482421875 0.6757524609565735 0.734281 0.7122817635536194 True -14 43500 32.07345676422119 0.6923680305480957 397.5067138671875 0.634098470211029 489.05340576171875 0.6769761443138123 0.73726 0.6899287104606628 True -15 46400 32.07026433944702 0.6841139793395996 307.58489990234375 0.5772191882133484 488.3455505371094 0.67732834815979 0.73831093 0.7097530961036682 True -16 49300 32.06241178512573 1.391953468322754 354.8975830078125 0.6440529227256775 488.2052001953125 0.6775118708610535 0.73684156 0.7226018309593201 False -17 52200 32.085489988327026 0.6838204860687256 377.85955810546875 0.38733768463134766 488.7550964355469 0.6768934726715088 0.7340624 0.7447748780250549 False -18 55100 32.09463882446289 0.6813573837280273 322.513427734375 0.3694998025894165 488.8080139160156 0.6764742732048035 0.7303335 0.7671542763710022 False -19 58000 32.02060294151306 0.6784200668334961 331.8492736816406 0.2572217285633087 489.1322937011719 0.6762261986732483 0.72670686 0.7899657487869263 False diff --git a/ENCSR483RKN/cherimoya.fold_2.performance.tsv b/ENCSR483RKN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8f00ff337cbce8df2dded4017ba2ef084cb78843..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -488.3455505371094 0.2565428912639618 0.67732834815979 0.30815389752388 0.7383109331130981 0.6540765762329102 0.7097530961036682 \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_3.evaluate.json b/ENCSR483RKN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2cf5a1db88c5cccd20977a191e5005aa775b2cf6..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF973ISJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_3.fit.json b/ENCSR483RKN/cherimoya.fold_3.fit.json deleted file mode 100644 index e939e15fc879c7cfbc5096660768878bd2ac0ad8..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF973ISJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_3.log b/ENCSR483RKN/cherimoya.fold_3.log deleted file mode 100644 index b6c6ef4a1388dcdb4c76bd90f3bc6b12efd0ef31..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2896 35.94334673881531 3.5239202976226807 339.6300354003906 1.0062613487243652 581.9219970703125 0.5636529922485352 0.67277765 6.277032375335693 True -1 5792 32.01267695426941 0.6746187210083008 413.5809326171875 0.8238108158111572 512.90234375 0.6360330581665039 0.6918512 2.226398468017578 True -2 8688 32.06496977806091 0.6328220367431641 408.21917724609375 1.0131068229675293 499.8305969238281 0.6458182334899902 0.6965775 1.0659115314483643 True -3 11584 31.971081733703613 0.6326603889465332 466.7183837890625 0.7026183009147644 496.13330078125 0.6499989032745361 0.69705135 0.9348506927490234 True -4 14480 31.999459743499756 0.635643720626831 360.8171691894531 0.5462472438812256 493.9963073730469 0.6521028876304626 0.7073913 0.8866065740585327 True -5 17376 31.94890284538269 0.8256795406341553 393.45697021484375 0.8334389925003052 492.69744873046875 0.653744637966156 0.7080738 0.8554123640060425 True -6 20272 32.00422477722168 0.6339311599731445 318.7728271484375 0.6958351135253906 491.9883117675781 0.6552140116691589 0.71301466 0.7951698899269104 True -7 23168 31.9750816822052 0.6305820941925049 327.06976318359375 1.123581886291504 489.6640625 0.6579441428184509 0.71631813 0.7479254603385925 True -8 26064 31.95854902267456 0.6301529407501221 474.2095031738281 0.8634614944458008 488.3680419921875 0.6596124172210693 0.71905965 0.7241324186325073 True -9 28960 31.92775249481201 1.0822868347167969 430.50421142578125 0.8759902119636536 486.79986572265625 0.6613969802856445 0.7243535 0.7102623581886292 True -10 31856 31.92705535888672 0.6300985813140869 408.3825988769531 0.9188085198402405 484.8310241699219 0.6642445921897888 0.72607523 0.687644362449646 True -11 34752 31.95954155921936 2.989607810974121 340.8626403808594 0.43898171186447144 482.7919006347656 0.6657269597053528 0.735403 0.6801842451095581 True -12 37648 31.959335803985596 0.626863956451416 393.265380859375 0.6668577194213867 481.35491943359375 0.6677291989326477 0.7399282 0.65203857421875 True -13 40544 32.004624366760254 0.6409797668457031 313.61767578125 0.6339910626411438 480.1920471191406 0.6692173480987549 0.7420475 0.6358655095100403 True -14 43440 32.05102610588074 0.641472578048706 404.11358642578125 0.6364032030105591 478.8279724121094 0.6703327298164368 0.7507257 0.633467435836792 True -15 46336 32.00498819351196 0.633979320526123 384.08056640625 0.4944005012512207 478.5050354003906 0.670862078666687 0.7543413 0.6315658092498779 True -16 49232 32.051212310791016 0.6527597904205322 429.4039611816406 0.7428303360939026 478.3979797363281 0.6708401441574097 0.753691 0.6465722918510437 False -17 52128 32.00373363494873 0.6380767822265625 455.8787536621094 0.4151449203491211 478.6976318359375 0.6703401803970337 0.75184065 0.6745983958244324 False -18 55024 32.07341718673706 0.6506357192993164 364.4987487792969 0.4358154535293579 479.0443420410156 0.6697703003883362 0.74924845 0.7003176808357239 False -19 57920 32.16448163986206 0.6486053466796875 382.38153076171875 0.3065005838871002 479.28619384765625 0.6694342494010925 0.74390036 0.7183064818382263 False diff --git a/ENCSR483RKN/cherimoya.fold_3.performance.tsv b/ENCSR483RKN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 87c191fd65634b0c44d7949fdbc6dd3d3f0b4210..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -478.5050354003906 0.26155003905296326 0.670862078666687 0.3012862503528595 0.7543413043022156 0.6599986553192139 0.6315658092498779 \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_4.evaluate.json b/ENCSR483RKN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 037e865603e571f4746a8aecb20f5330d34a7329..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF973ISJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_4.fit.json b/ENCSR483RKN/cherimoya.fold_4.fit.json deleted file mode 100644 index 53b6b8429ea3e3a4a195ac2447b152b98f3038f0..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF973ISJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR483RKN/cherimoya.fold_4.log b/ENCSR483RKN/cherimoya.fold_4.log deleted file mode 100644 index 6b6fefe0df972f8a65636c1877b501813f352a02..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 35.475663900375366 3.558502674102783 368.09112548828125 0.6702647805213928 556.3484497070312 0.548405647277832 0.7113567 4.724455833435059 True -1 5744 31.788154125213623 0.48070764541625977 384.83282470703125 1.001294732093811 490.4007873535156 0.627620279788971 0.72709095 1.9955857992172241 True -2 8616 31.703577756881714 0.4632303714752197 395.9182434082031 0.8322191834449768 476.692626953125 0.6420704126358032 0.7238621 1.0744576454162598 False -3 11488 31.66602373123169 0.46858978271484375 300.51788330078125 0.8188600540161133 471.5656433105469 0.6477615237236023 0.72529906 0.8512709140777588 False -4 14360 31.653711318969727 0.4676821231842041 321.1733093261719 0.6342601776123047 469.139404296875 0.6511174440383911 0.73126316 0.7679467797279358 True -5 17232 31.753804683685303 0.4654402732849121 424.0832214355469 0.6320872902870178 467.00970458984375 0.653557300567627 0.73280615 0.7661383748054504 True -6 20104 31.71171283721924 0.46317291259765625 431.057861328125 0.5023130178451538 465.4035949707031 0.6557486057281494 0.73403126 0.6876010298728943 True -7 22976 31.713839292526245 0.46257901191711426 431.0498046875 0.4613158702850342 463.9859924316406 0.657748281955719 0.7288195 0.6756505370140076 False -8 25848 31.700464963912964 0.46379613876342773 415.1246337890625 0.6271347999572754 462.2320556640625 0.6598108410835266 0.7413821 0.6235793828964233 True -9 28720 31.69999384880066 0.46286654472351074 403.34527587890625 0.48534050583839417 460.24957275390625 0.6620466113090515 0.7451633 0.5767927169799805 True -10 31592 31.65211582183838 0.46286487579345703 347.71044921875 0.5647414326667786 458.8300476074219 0.6638365983963013 0.74721813 0.5667494535446167 True -11 34464 31.652868509292603 0.4555182456970215 381.64013671875 1.0215423107147217 457.1381530761719 0.666061282157898 0.7546264 0.5438708066940308 True -12 37336 31.723772525787354 0.46413135528564453 333.2703857421875 0.6534037590026855 455.9986267089844 0.6675650477409363 0.75974846 0.5306681990623474 True -13 40208 31.69430947303772 0.4653458595275879 384.5199279785156 0.7816758155822754 454.2440185546875 0.6696674823760986 0.7704207 0.5037742853164673 True -14 43080 31.72510027885437 0.457582950592041 321.03631591796875 0.46396148204803467 453.5668640136719 0.670951783657074 0.7722736 0.49936285614967346 True -15 45952 31.669148206710815 0.4627716541290283 397.9779968261719 0.5191810727119446 453.28790283203125 0.6713686585426331 0.7771786 0.49405425786972046 True -16 48824 31.678646564483643 0.4685337543487549 356.2030334472656 0.36256253719329834 453.2459716796875 0.6710914969444275 0.77451074 0.5062874555587769 False -17 51696 31.758618593215942 0.47052431106567383 442.066650390625 0.25269815325737 453.6061096191406 0.6704689860343933 0.77336437 0.5227384567260742 False -18 54568 31.797770738601685 0.4798429012298584 404.98699951171875 0.21329228579998016 454.0692138671875 0.6700215935707092 0.7689952 0.5411057472229004 False -19 57440 31.868927240371704 12.690179109573364 430.12249755859375 0.2606884837150574 454.2234191894531 0.6697227358818054 0.76442105 0.5536597967147827 False diff --git a/ENCSR483RKN/cherimoya.fold_4.performance.tsv b/ENCSR483RKN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a720a887e980326eed3cbbde8ac2dee478dd6549..0000000000000000000000000000000000000000 --- a/ENCSR483RKN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -453.28790283203125 0.2656084895133972 0.6713686585426331 0.2915444076061249 0.7771785855293274 0.6896714568138123 0.49405425786972046 \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_0.evaluate.json b/ENCSR484UAU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 742fa6b0fdfb8db51bc9d16d4a37b89fb62e57d6..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF535TQE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_0.fit.json b/ENCSR484UAU/cherimoya.fold_0.fit.json deleted file mode 100644 index 5ec1c43665d12fa36ade70847c087b0d9884ce9c..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF535TQE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_0.log b/ENCSR484UAU/cherimoya.fold_0.log deleted file mode 100644 index 73d3c05cf2834187b662f00011ce218c17ef721e..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2713 33.81993508338928 3.5132896900177 504.4278564453125 0.6355889439582825 730.9210205078125 0.23269355297088623 0.61918336 4.791876792907715 True -1 5426 30.122783660888672 0.5935304164886475 624.4649658203125 0.4836834669113159 651.0692138671875 0.32708626985549927 0.7044923 1.4600976705551147 True -2 8139 30.102484703063965 0.5773823261260986 437.733642578125 0.43639329075813293 637.4966430664062 0.340686172246933 0.7239517 0.7484670877456665 True -3 10852 30.133859872817993 0.5817539691925049 535.665283203125 0.3418613076210022 631.7613525390625 0.3457714915275574 0.7409717 0.5720486640930176 True -4 13565 30.051084280014038 0.5701389312744141 555.5186767578125 0.34643661975860596 628.6292724609375 0.34993603825569153 0.7444516 0.5063239336013794 True -5 16278 29.727710723876953 0.5642471313476562 561.5428466796875 0.32350146770477295 625.750244140625 0.35418829321861267 0.75124675 0.45987468957901 True -6 18991 29.49949884414673 0.57131028175354 467.9881286621094 0.3996749818325043 624.4268798828125 0.35547327995300293 0.75538963 0.46768054366111755 True -7 21704 29.52203679084778 0.5707361698150635 567.7787475585938 0.42892760038375854 622.5265502929688 0.3575455844402313 0.7592387 0.4267401397228241 True -8 24417 29.459836959838867 0.5687286853790283 584.22509765625 0.3352222740650177 620.63134765625 0.3594683110713959 0.76657814 0.4078299105167389 True -9 27130 29.475894927978516 0.5663633346557617 590.126708984375 0.5657713413238525 620.2569580078125 0.3587256968021393 0.7695208 0.39355573058128357 True -10 29843 29.47364568710327 0.571486234664917 543.6032104492188 0.28550034761428833 618.5919799804688 0.36087802052497864 0.7760548 0.37274816632270813 True -11 32556 29.485167264938354 0.8523843288421631 556.5772705078125 0.39093291759490967 616.6924438476562 0.36288443207740784 0.7815372 0.3468685746192932 True -12 35269 29.510438680648804 0.570908784866333 550.2801513671875 0.23701214790344238 615.2007446289062 0.36493852734565735 0.7856951 0.333008348941803 True -13 37982 29.500597715377808 0.5673813819885254 464.4368896484375 0.19248250126838684 613.54931640625 0.3672963082790375 0.7934996 0.31221848726272583 True -14 40695 29.501623392105103 0.5700075626373291 482.7745361328125 0.3293886184692383 612.879638671875 0.3666759133338928 0.79847795 0.2877509593963623 True -15 43408 29.51431941986084 19.2674458026886 492.0746765136719 0.2696618437767029 611.1416015625 0.36958861351013184 0.8051295 0.27561724185943604 True -16 46121 29.65054965019226 0.5749731063842773 550.9176635742188 0.2511715292930603 611.3204345703125 0.3680814802646637 0.8070378 0.264018177986145 True -17 48834 29.6031334400177 0.5596551895141602 584.230224609375 0.25547268986701965 609.7825927734375 0.3710883855819702 0.81077415 0.25963860750198364 True -18 51547 29.501410007476807 1.321183681488037 559.176025390625 0.20850177109241486 610.6268310546875 0.369289368391037 0.8107429 0.2569815516471863 False -19 54260 29.49001693725586 0.5598957538604736 510.9682312011719 0.16875043511390686 610.1198120117188 0.3708195090293884 0.81139123 0.2578481435775757 True diff --git a/ENCSR484UAU/cherimoya.fold_0.performance.tsv b/ENCSR484UAU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2755d9543a52a28b116eb5c984210fa3c544b395..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -610.1198120117188 0.41250109672546387 0.37081947922706604 0.14220349490642548 0.8113912343978882 0.7768889665603638 0.2578481435775757 \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_1.evaluate.json b/ENCSR484UAU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a2c12456586c561d8cc1be1f0057902017a76822..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF535TQE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_1.fit.json b/ENCSR484UAU/cherimoya.fold_1.fit.json deleted file mode 100644 index d52aab11a518d28aa4ff55eed74c1fd2ce12aa18..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF535TQE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_1.log b/ENCSR484UAU/cherimoya.fold_1.log deleted file mode 100644 index c72292f3c51dc1740fee74cf7c31c73893e8d1ce..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2699 33.81984066963196 13.191851377487183 574.409423828125 0.49228209257125854 855.1672973632812 0.2422415316104889 0.640812 5.086943626403809 True -1 5398 29.64909529685974 1.6428241729736328 643.14404296875 0.38266849517822266 755.15576171875 0.34248092770576477 0.7292533 1.843896508216858 True -2 8097 29.64545965194702 0.9101850986480713 459.734619140625 0.32818448543548584 731.992431640625 0.3589842915534973 0.7471682 0.8824068903923035 True -3 10796 29.66766047477722 0.7154281139373779 530.1279907226562 0.5128388404846191 725.540283203125 0.36298105120658875 0.7590452 0.729523241519928 True -4 13495 29.32833433151245 2.618382453918457 567.1270141601562 0.42816147208213806 723.0264892578125 0.3653221130371094 0.76894975 0.6350611448287964 True -5 16194 29.1350519657135 0.7023816108703613 488.0220642089844 0.3975207805633545 718.6539916992188 0.3713080585002899 0.7728122 0.6276106238365173 True -6 18893 29.168472290039062 0.7015397548675537 518.1083984375 0.3239867389202118 715.5774536132812 0.3754361867904663 0.778118 0.6075327396392822 True -7 21592 29.104695796966553 1.0748698711395264 584.6495361328125 0.41663938760757446 712.7001953125 0.37755075097084045 0.7834465 0.5634881258010864 True -8 24291 29.10530138015747 0.6968610286712646 524.5975341796875 0.3118574619293213 711.3447875976562 0.3788478970527649 0.78462386 0.5664621591567993 True -9 26990 29.134502410888672 0.7122604846954346 530.3536376953125 0.48967254161834717 709.7628173828125 0.37980467081069946 0.7921582 0.4714340269565582 True -10 29689 29.138320684432983 0.6996207237243652 540.0506591796875 0.3551185727119446 707.0961303710938 0.38248056173324585 0.794162 0.44926783442497253 True -11 32388 29.06498956680298 0.7086756229400635 624.020263671875 0.5217968821525574 703.7842407226562 0.3861828148365021 0.8035529 0.4126373827457428 True -12 35087 29.05783462524414 0.7004737854003906 478.8472900390625 0.3282005488872528 702.167724609375 0.3877592384815216 0.80838346 0.3796006143093109 True -13 37786 29.053865909576416 0.7026629447937012 500.89373779296875 0.40546566247940063 698.6458740234375 0.3912026286125183 0.8135587 0.3501584827899933 True -14 40485 29.131337642669678 1.785130500793457 481.594482421875 0.2970554232597351 697.7844848632812 0.3923851251602173 0.8167199 0.3197418749332428 True -15 43184 29.133705615997314 0.703559398651123 501.52001953125 0.2841915190219879 696.5846557617188 0.39301836490631104 0.82247436 0.3020539879798889 True -16 45883 29.188427925109863 0.7288012504577637 515.060791015625 0.31610801815986633 695.9954833984375 0.3930472433567047 0.8261553 0.29046961665153503 True -17 48582 29.24966788291931 2.71968674659729 464.791015625 0.33040547370910645 695.2281494140625 0.39349231123924255 0.82761294 0.28382599353790283 True -18 51281 29.285714626312256 0.7207386493682861 545.2901000976562 0.25236767530441284 696.0947265625 0.3923739194869995 0.8272249 0.2811441421508789 False -19 53980 29.18460440635681 0.7076191902160645 541.1094970703125 0.18280208110809326 696.301513671875 0.3925437927246094 0.82623076 0.28232088685035706 False diff --git a/ENCSR484UAU/cherimoya.fold_1.performance.tsv b/ENCSR484UAU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 981b4807a81ee689eb7a9c98a753c8425dc6af41..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -695.2281494140625 0.39205312728881836 0.39349234104156494 0.15983812510967255 0.8276129364967346 0.8076896071434021 0.28382599353790283 \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_2.evaluate.json b/ENCSR484UAU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7b227f405c9049e8943ae9155926f0587be3d827..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF535TQE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_2.fit.json b/ENCSR484UAU/cherimoya.fold_2.fit.json deleted file mode 100644 index 8fdeabc474da245a45695a3195afac534fec35c5..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF535TQE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_2.log b/ENCSR484UAU/cherimoya.fold_2.log deleted file mode 100644 index 5566c61259caf45394701255b1e57fb2143215ed..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 35.437004804611206 4.5680623054504395 542.0067138671875 0.40693819522857666 750.8328857421875 0.24101522564888 0.6295184 4.590363502502441 True -1 5770 31.68061637878418 1.1770412921905518 542.1220703125 0.5708810091018677 663.7147216796875 0.3334040343761444 0.72204465 1.1735564470291138 True -2 8655 31.828364610671997 2.1832237243652344 580.8372192382812 0.5135318636894226 651.4215698242188 0.3435750901699066 0.7384851 0.5952507257461548 True -3 11540 31.740224599838257 0.6355764865875244 554.9033203125 0.4557948708534241 644.6494750976562 0.3502943217754364 0.750355 0.4954891800880432 True -4 14425 31.74737286567688 0.5418901443481445 537.460693359375 0.37906956672668457 641.544189453125 0.35423752665519714 0.7572731 0.4294128715991974 True -5 17310 31.255165338516235 0.5415956974029541 541.2386474609375 0.46323806047439575 640.2361450195312 0.35535717010498047 0.7622555 0.4375191330909729 True -6 20195 31.166240215301514 0.5301780700683594 595.06005859375 0.3664996922016144 637.6717529296875 0.35828787088394165 0.7673942 0.41898706555366516 True -7 23080 31.15527892112732 0.5298054218292236 545.8196411132812 0.42699283361434937 634.6131591796875 0.36300355195999146 0.7705225 0.41713517904281616 True -8 25965 31.074968576431274 0.5283505916595459 507.50042724609375 0.26471686363220215 634.0879516601562 0.36357375979423523 0.7785919 0.39612656831741333 True -9 28850 31.10149908065796 0.5331292152404785 560.8407592773438 0.31977635622024536 632.0250854492188 0.3656289875507355 0.7802951 0.37448665499687195 True -10 31735 31.097161531448364 0.5260484218597412 561.3399658203125 0.47207120060920715 630.5694580078125 0.3669731318950653 0.78460795 0.3654056191444397 True -11 34620 31.07010269165039 3.4803531169891357 541.0311279296875 0.33612173795700073 628.7024536132812 0.36967453360557556 0.7903776 0.3466774523258209 True -12 37505 31.14985418319702 2.1077964305877686 543.2612915039062 0.2805430293083191 626.9046630859375 0.37140926718711853 0.7938711 0.3241179287433624 True -13 40390 31.195512533187866 0.5435054302215576 539.92822265625 0.2477698028087616 625.6281127929688 0.3728831708431244 0.79762214 0.309799462556839 True -14 43275 31.151259422302246 0.5233123302459717 552.0626220703125 0.2859472930431366 623.9971313476562 0.3746943473815918 0.8038123 0.2916485667228699 True -15 46160 31.1709885597229 0.517340898513794 504.4570007324219 0.28077274560928345 622.9615478515625 0.3763056993484497 0.8056708 0.28139016032218933 True -16 49045 31.145371437072754 0.529573917388916 514.1539306640625 0.202777698636055 623.4164428710938 0.3747180700302124 0.8102972 0.2681772708892822 True -17 51930 31.192567586898804 0.9807038307189941 529.8286743164062 0.19202160835266113 622.9213256835938 0.376098096370697 0.8132433 0.2655167281627655 True -18 54815 31.263644695281982 0.5321156978607178 614.7456665039062 0.33592715859413147 623.0048828125 0.37701094150543213 0.81217724 0.26453012228012085 False -19 57700 31.18315553665161 0.5308253765106201 590.6658325195312 0.23809564113616943 622.8136596679688 0.3774595260620117 0.8107106 0.2658850848674774 False diff --git a/ENCSR484UAU/cherimoya.fold_2.performance.tsv b/ENCSR484UAU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 824c8e89ac55a5f2df4927082aa3ec1b8ef4b6a1..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -622.9213256835938 0.4080548882484436 0.376098096370697 0.14290323853492737 0.8132433295249939 0.7848084568977356 0.2655167281627655 \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_3.evaluate.json b/ENCSR484UAU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0daca4b03b73410f1ab01ad61fe4e2ae4f2aac1c..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF535TQE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_3.fit.json b/ENCSR484UAU/cherimoya.fold_3.fit.json deleted file mode 100644 index 4e9a3045cb932abadec9901a66caf1ab0348415b..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF535TQE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_3.log b/ENCSR484UAU/cherimoya.fold_3.log deleted file mode 100644 index a8129a3a5907b34e5e91f2ad9f924f1d63375dac..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.01210808753967 3.514284133911133 526.5489501953125 0.5231273770332336 729.001953125 0.2400733083486557 0.6430667 5.017908573150635 True -1 5492 30.17102885246277 0.581845760345459 558.999267578125 0.4191017150878906 650.8649291992188 0.32493868470191956 0.7343687 1.4467966556549072 True -2 8238 30.147637605667114 0.562002420425415 607.3732299804688 0.4329274296760559 637.6004638671875 0.33736667037010193 0.754237 0.6274181604385376 True -3 10984 30.193990468978882 0.6541731357574463 556.9537353515625 0.4839754104614258 632.6010131835938 0.3436828851699829 0.7611647 0.5489079356193542 True -4 13730 29.798609733581543 0.5680713653564453 512.7391967773438 0.508542537689209 630.388427734375 0.3457358479499817 0.7659108 0.46941304206848145 True -5 16476 29.545117616653442 0.5660686492919922 519.468994140625 0.4563625156879425 628.6031494140625 0.3481748104095459 0.7712317 0.44841820001602173 True -6 19222 29.54772973060608 0.5679607391357422 537.9933471679688 0.6235756278038025 626.1309814453125 0.3519577980041504 0.7740249 0.5038524270057678 True -7 21968 29.614628314971924 0.5644361972808838 489.6852722167969 0.3885083794593811 624.5258178710938 0.35415714979171753 0.77778447 0.4705241918563843 True -8 24714 29.64397621154785 0.5713486671447754 569.9515380859375 0.36953434348106384 624.0714721679688 0.35370075702667236 0.78310776 0.4603026807308197 True -9 27460 29.63385772705078 0.5758905410766602 546.811279296875 0.35200461745262146 620.8204956054688 0.3582966923713684 0.78558546 0.42063960433006287 True -10 30206 29.69154644012451 0.5707356929779053 554.3054809570312 0.3581008017063141 619.4349365234375 0.35900330543518066 0.79219913 0.4192555248737335 True -11 32952 29.779748678207397 2.6090943813323975 535.199951171875 0.27290356159210205 617.5187377929688 0.3613433539867401 0.7941925 0.3968189060688019 True -12 35698 29.718876123428345 0.576416015625 488.3576354980469 0.31736981868743896 614.7021484375 0.3654400110244751 0.801432 0.358458936214447 True -13 38444 29.71579337120056 1.611741304397583 535.1751098632812 0.2694457471370697 613.93994140625 0.3655323088169098 0.8102837 0.33446255326271057 True -14 41190 29.726367712020874 0.5789327621459961 598.7047119140625 0.28076568245887756 612.0369262695312 0.3671482503414154 0.81264764 0.30021369457244873 True -15 43936 29.702091932296753 0.5713255405426025 585.619873046875 0.24228084087371826 611.8590087890625 0.3674170970916748 0.81611323 0.279903382062912 True -16 46682 29.70114803314209 0.5744121074676514 487.9766845703125 0.2597176432609558 610.1859130859375 0.37001845240592957 0.8203128 0.2712259590625763 True -17 49428 29.71699857711792 0.5686287879943848 511.5943298339844 0.21944713592529297 610.2335205078125 0.3689638376235962 0.8225731 0.26283568143844604 True -18 52174 29.694998264312744 0.5774953365325928 495.79486083984375 0.2806878685951233 610.5806274414062 0.3683917224407196 0.8221372 0.26077213883399963 False -19 54920 29.697207927703857 0.5739521980285645 513.9337158203125 0.18479730188846588 611.2033081054688 0.36710891127586365 0.82137465 0.2625845968723297 False diff --git a/ENCSR484UAU/cherimoya.fold_3.performance.tsv b/ENCSR484UAU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 46bf117d60ab97ff8de9350ba6f2c12e377d8dc6..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -610.2335205078125 0.4125426113605499 0.36896374821662903 0.14479923248291016 0.8225731253623962 0.7866696715354919 0.26283568143844604 \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_4.evaluate.json b/ENCSR484UAU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6335a9ff0af03913849c9ddda1c99ef79aaf7cda..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF535TQE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_4.fit.json b/ENCSR484UAU/cherimoya.fold_4.fit.json deleted file mode 100644 index 2a407d746cb802e438d551fa25aa0a5e13908113..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF535TQE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR484UAU/cherimoya.fold_4.log b/ENCSR484UAU/cherimoya.fold_4.log deleted file mode 100644 index d962775dbb121de3ae9295a1b5becaf9541fd34b..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2846 35.1364312171936 3.5814337730407715 536.0716552734375 0.30377209186553955 711.3718872070312 0.2384643405675888 0.6054884 5.057295799255371 True -1 5692 31.296478033065796 0.7033541202545166 516.6685791015625 0.4199081063270569 635.26611328125 0.32830139994621277 0.7023448 1.123593807220459 True -2 8538 31.204631567001343 0.5737948417663574 504.0166320800781 0.3066904842853546 623.1473388671875 0.33986896276474 0.72105974 0.689673662185669 True -3 11384 31.210526704788208 0.5667712688446045 551.7671508789062 0.3577582836151123 617.7238159179688 0.3449634313583374 0.7293118 0.4304165542125702 True -4 14230 30.931257724761963 0.5639684200286865 537.95849609375 0.4540533721446991 615.1060180664062 0.34862077236175537 0.7403787 0.39387786388397217 True -5 17076 30.6579372882843 0.5576541423797607 559.1268310546875 0.4502238929271698 613.9949340820312 0.3493078649044037 0.7431196 0.4438380002975464 True -6 19922 30.66406750679016 0.5688197612762451 542.3742065429688 0.5088505148887634 613.5580444335938 0.34956416487693787 0.748934 0.47159022092819214 True -7 22768 30.704460382461548 0.5616984367370605 462.3215637207031 0.23844391107559204 611.5980834960938 0.3514585793018341 0.7526448 0.46602198481559753 True -8 25614 30.687650680541992 1.0956401824951172 599.5883178710938 0.4133707284927368 609.5880126953125 0.3545708954334259 0.7592132 0.43543195724487305 True -9 28460 30.717971324920654 0.5722832679748535 538.7410278320312 0.3045003116130829 608.0108642578125 0.3567705750465393 0.7646807 0.43348026275634766 True -10 31306 30.661365032196045 0.5597429275512695 487.5249328613281 0.3024411201477051 606.6383056640625 0.3582991063594818 0.77464205 0.366523414850235 True -11 34152 30.692049741744995 0.567685604095459 573.208740234375 0.3740193247795105 604.6908569335938 0.3603079617023468 0.7793354 0.34305986762046814 True -12 36998 30.668238401412964 0.5702919960021973 514.825927734375 0.30744749307632446 602.824951171875 0.36339229345321655 0.78189427 0.3193624019622803 True -13 39844 30.748088598251343 0.5698542594909668 546.30712890625 0.31878697872161865 601.0398559570312 0.36548346281051636 0.78931844 0.30351707339286804 True -14 42690 30.610381841659546 0.5706479549407959 550.78759765625 0.1902327537536621 600.45751953125 0.3649523854255676 0.79598343 0.27854734659194946 True -15 45536 30.60635542869568 1.1268351078033447 482.1151123046875 0.21016854047775269 599.1035766601562 0.3679161071777344 0.80086476 0.2684146463871002 True -16 48382 30.7041494846344 1.8682136535644531 540.1365356445312 0.1498696357011795 598.98779296875 0.3676804304122925 0.8057936 0.25468704104423523 True -17 51228 30.70773196220398 0.6012632846832275 548.3882446289062 0.204230397939682 599.8665771484375 0.3660077452659607 0.80681956 0.2513664960861206 True -18 54074 30.614721059799194 0.5743722915649414 500.55078125 0.25972408056259155 599.5933227539062 0.3664710819721222 0.8045134 0.2521272301673889 False -19 56920 30.60951805114746 0.5717465877532959 497.22943115234375 0.20402824878692627 599.8644409179688 0.36625048518180847 0.80399936 0.2524040639400482 False diff --git a/ENCSR484UAU/cherimoya.fold_4.performance.tsv b/ENCSR484UAU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2d0fa6a8904e168f409b9ed0701b7706771799e6..0000000000000000000000000000000000000000 --- a/ENCSR484UAU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -599.8665771484375 0.414610892534256 0.3660077452659607 0.1364201307296753 0.8068195581436157 0.7731324434280396 0.2513664960861206 \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_0.evaluate.json b/ENCSR485TLP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d52a645fef58bce66d60f9039f4be642d38ed476..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_0.fit.json b/ENCSR485TLP/cherimoya.fold_0.fit.json deleted file mode 100644 index 6bb4337a2003e5d4640c39add904150e704c2e10..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF955VHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_0.log b/ENCSR485TLP/cherimoya.fold_0.log deleted file mode 100644 index 85326bfb261bd27f81209bcf813c829c8d73d347..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3943 49.36127209663391 4.284407377243042 994.1915283203125 1.0877712965011597 1357.16455078125 0.794371485710144 0.80649936 7.176752090454102 True -1 7886 43.49231719970703 0.7783064842224121 1082.6319580078125 0.45805788040161133 1136.9368896484375 0.8620651960372925 0.7924834 0.8490574955940247 False -2 11829 43.396005630493164 1.632054328918457 881.60400390625 0.9712470769882202 1098.8489990234375 0.872173011302948 0.80075765 0.39306947588920593 False -3 15772 43.42506384849548 2.4400718212127686 860.198486328125 0.43953731656074524 1083.2076416015625 0.8770876526832581 0.7959266 0.4016801714897156 False -4 19715 43.55034923553467 0.7645940780639648 838.7627563476562 0.6894969940185547 1074.35888671875 0.8792879581451416 0.8047963 0.39304056763648987 False -5 23658 43.659595251083374 1.2767267227172852 822.6419677734375 0.5059407353401184 1067.6793212890625 0.8811389803886414 0.80894613 0.3814261257648468 True -6 27601 43.69718551635742 15.601614952087402 963.8740844726562 0.6719917058944702 1059.8702392578125 0.8835029602050781 0.80937916 0.3619495630264282 True -7 31544 43.43477535247803 0.7899420261383057 885.798583984375 0.3613755702972412 1052.5963134765625 0.8858567476272583 0.8197569 0.3458586633205414 True -8 35487 43.465049028396606 0.7752912044525146 873.8992919921875 0.696459174156189 1045.6634521484375 0.887936532497406 0.81924546 0.3373413383960724 False -9 39430 43.467090368270874 0.7531235218048096 897.2593994140625 0.6729065179824829 1035.98291015625 0.891380250453949 0.82645094 0.33082935214042664 True -10 43373 43.51283311843872 0.773533821105957 808.62353515625 0.4476107358932495 1028.637939453125 0.893787682056427 0.83308464 0.3091098666191101 True -11 47316 43.43036341667175 0.7841308116912842 869.0987548828125 0.4424861967563629 1022.3074340820312 0.8955804109573364 0.8398087 0.29701870679855347 True -12 51259 43.42834544181824 0.7643954753875732 842.6393432617188 0.48985156416893005 1015.6857299804688 0.8976091742515564 0.84704185 0.28320395946502686 True -13 55202 43.50014662742615 0.7559671401977539 923.0159912109375 0.5735259652137756 1009.49267578125 0.8995558023452759 0.8511207 0.2760999798774719 True -14 59145 43.33794164657593 0.9824099540710449 810.638916015625 0.2829076051712036 1005.4083251953125 0.9009382128715515 0.85630584 0.2719547152519226 True -15 63088 43.574259519577026 0.7702271938323975 778.9564208984375 0.7646461725234985 1001.61474609375 0.9022338390350342 0.8628783 0.2642609179019928 True -16 67031 43.4958860874176 0.7645425796508789 760.8900146484375 0.5024631023406982 999.0502319335938 0.9028242230415344 0.8662145 0.26215049624443054 True -17 70974 43.54184293746948 0.8721866607666016 803.9699096679688 0.39684176445007324 997.9453735351562 0.9028702974319458 0.86848855 0.2605075240135193 True -18 74917 43.44509816169739 0.7648961544036865 879.7025756835938 0.18609412014484406 998.7432250976562 0.9028905630111694 0.8677791 0.26614367961883545 False -19 78860 43.43586182594299 0.7641677856445312 679.19189453125 0.27993375062942505 998.94775390625 0.902763843536377 0.86583847 0.26878106594085693 False diff --git a/ENCSR485TLP/cherimoya.fold_0.performance.tsv b/ENCSR485TLP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2c43cd7715a2abab1fce97fd34405bcbf5ea83e2..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -997.9453735351562 0.0840727910399437 0.9028702974319458 0.6060284376144409 0.8684885501861572 0.8582863807678223 0.2605075240135193 \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_1.evaluate.json b/ENCSR485TLP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9b7e3f230fe61e8f0a24b9321775bfc1d1a8c517..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_1.fit.json b/ENCSR485TLP/cherimoya.fold_1.fit.json deleted file mode 100644 index b63b8c24ed4ca4bc7a8860a6216016d6fd6587b6..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF955VHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_1.log b/ENCSR485TLP/cherimoya.fold_1.log deleted file mode 100644 index ccd8caca81c872dbc797a6873596d295bf153146..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3892 47.4127471446991 4.902919769287109 1017.933837890625 0.910271406173706 1608.8660888671875 0.7899057269096375 0.80706567 5.332895278930664 True -1 7784 42.94096851348877 1.1454181671142578 918.078125 1.008392572402954 1294.0166015625 0.8677277565002441 0.81931454 0.8766112923622131 True -2 11676 42.97195601463318 1.0330002307891846 769.6885986328125 1.0127630233764648 1259.6329345703125 0.8759207129478455 0.8133643 0.42035791277885437 False -3 15568 42.95306921005249 1.0125164985656738 827.8195190429688 0.8118008971214294 1242.1414794921875 0.8802351355552673 0.8196973 0.3751845061779022 True -4 19460 42.924413204193115 2.7569010257720947 800.071533203125 0.5527160167694092 1226.0789794921875 0.8837742805480957 0.8292286 0.35961678624153137 True -5 23352 42.96285057067871 0.9848423004150391 923.4522705078125 0.43367892503738403 1215.1849365234375 0.886202335357666 0.8316738 0.3774959444999695 True -6 27244 43.006669759750366 1.8474934101104736 958.4727783203125 0.6297277212142944 1208.2977294921875 0.8884060382843018 0.83354443 0.37207505106925964 True -7 31136 43.04915976524353 1.069901704788208 809.625 0.5750342607498169 1198.723388671875 0.8907681107521057 0.8398795 0.3302159607410431 True -8 35028 43.05110788345337 0.9962847232818604 821.939208984375 0.5951943397521973 1188.1650390625 0.8933635354042053 0.8447817 0.32035019993782043 True -9 38920 43.052669048309326 1.0045228004455566 873.1146240234375 0.6059125661849976 1178.6285400390625 0.8958292007446289 0.8456941 0.3223407566547394 True -10 42812 43.115878105163574 1.0427658557891846 754.8224487304688 0.44715625047683716 1170.4119873046875 0.8976391553878784 0.8501567 0.3036896586418152 True -11 46704 43.0573091506958 1.0019474029541016 830.2160034179688 0.3787221908569336 1161.6063232421875 0.8998352885246277 0.85393214 0.30144795775413513 True -12 50596 43.041876554489136 1.6371500492095947 839.580810546875 0.36022013425827026 1150.545654296875 0.9020389914512634 0.86097986 0.2842577397823334 True -13 54488 43.11170172691345 1.3461554050445557 810.7520751953125 0.31054213643074036 1142.1219482421875 0.9040136933326721 0.8684305 0.2746627628803253 True -14 58380 43.12192392349243 1.003852128982544 953.410888671875 0.3651530146598816 1134.9151611328125 0.9057523012161255 0.87294835 0.2679785192012787 True -15 62272 43.039159059524536 0.990941047668457 795.5274658203125 0.4644375741481781 1130.210693359375 0.9069720506668091 0.8777204 0.2628323435783386 True -16 66164 43.12628960609436 0.9899539947509766 836.007080078125 1.1197975873947144 1126.3131103515625 0.9076907634735107 0.8826378 0.2527880370616913 True -17 70056 43.03687000274658 0.9866418838500977 787.5673828125 0.21306316554546356 1125.181884765625 0.9078881740570068 0.8826572 0.25353875756263733 True -18 73948 43.05404186248779 32.85794734954834 765.1943359375 0.3265017867088318 1125.9180908203125 0.9078360795974731 0.8833872 0.25560450553894043 True -19 77840 43.046985387802124 1.0139098167419434 692.7734375 0.5586798787117004 1125.9915771484375 0.907746434211731 0.8833681 0.258029580116272 False diff --git a/ENCSR485TLP/cherimoya.fold_1.performance.tsv b/ENCSR485TLP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 07a2bd8d508df33cd1b88c3080d849dbcc3a1ec1..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1125.9180908203125 0.07567016035318375 0.9078360795974731 0.6488298773765564 0.8833872079849243 0.8919945955276489 0.25560450553894043 \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_2.evaluate.json b/ENCSR485TLP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 09dcc624f35777032f527a726913fd642b6ad076..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_2.fit.json b/ENCSR485TLP/cherimoya.fold_2.fit.json deleted file mode 100644 index 65fc626a2b9255d19c43e49ef3d16df42744da77..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF955VHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_2.log b/ENCSR485TLP/cherimoya.fold_2.log deleted file mode 100644 index 35bcef373c692fdc0197df1914b78fa30b0199c0..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4101 48.96969556808472 4.095991611480713 1013.91552734375 0.7797358632087708 1405.7958984375 0.8008745312690735 0.7974104 5.489421367645264 True -1 8202 45.15397906303406 2.366133213043213 934.2770385742188 1.7830212116241455 1182.5849609375 0.8655576705932617 0.8082685 0.6774556636810303 True -2 12303 45.267460346221924 0.8680756092071533 934.2723999023438 0.6244832277297974 1146.200927734375 0.874018132686615 0.81062734 0.42675161361694336 True -3 16404 45.16503310203552 0.8367037773132324 741.1353759765625 1.0785057544708252 1131.33740234375 0.8777680993080139 0.8155404 0.37426066398620605 True -4 20505 45.26118087768555 0.8107011318206787 986.149658203125 1.0327715873718262 1121.666748046875 0.8806437849998474 0.8188013 0.3533550202846527 True -5 24606 45.29132032394409 0.8164641857147217 1053.4599609375 0.8226561546325684 1110.435302734375 0.8835216760635376 0.8243715 0.34310269355773926 True -6 28707 45.19096612930298 0.8250021934509277 970.739013671875 0.5662287473678589 1103.3831787109375 0.8857064843177795 0.8264535 0.33689844608306885 True -7 32808 45.240211486816406 0.8259828090667725 775.57958984375 1.209765076637268 1096.0244140625 0.8875454068183899 0.829443 0.32933658361434937 True -8 36909 45.24481964111328 0.8554177284240723 925.5673828125 0.46975523233413696 1089.0430908203125 0.8897964954376221 0.8317816 0.31952592730522156 True -9 41010 45.171650409698486 0.8277285099029541 865.82568359375 0.6364254355430603 1078.1475830078125 0.8924575448036194 0.83903635 0.3082279562950134 True -10 45111 45.185675382614136 0.82741379737854 965.5840454101562 0.5149979591369629 1072.205078125 0.894385814666748 0.8440725 0.29512280225753784 True -11 49212 45.17009663581848 0.8281540870666504 930.90625 0.3303571045398712 1064.5340576171875 0.8963859677314758 0.84555817 0.2922767102718353 True -12 53313 45.160764932632446 0.8283660411834717 878.4981689453125 0.4341179430484772 1057.802978515625 0.8983857035636902 0.85236007 0.28376901149749756 True -13 57414 45.16549849510193 0.8276371955871582 803.5921630859375 0.7724895477294922 1051.3795166015625 0.900213897228241 0.8562095 0.28297290205955505 True -14 61515 45.220396518707275 0.8111355304718018 827.6863403320312 0.20675387978553772 1045.13037109375 0.9019498825073242 0.8606534 0.27345407009124756 True -15 65616 46.83396005630493 0.8528938293457031 772.629150390625 0.2699848413467407 1041.8994140625 0.9031585454940796 0.866709 0.26995936036109924 True -16 69717 46.30857443809509 0.8474612236022949 802.470947265625 0.29037171602249146 1039.538818359375 0.9037266969680786 0.86980224 0.26689448952674866 True -17 73818 45.45540714263916 0.8306167125701904 648.2567138671875 0.34010541439056396 1038.902587890625 0.903974175453186 0.87252367 0.26765748858451843 True -18 77919 45.215977907180786 0.8643734455108643 823.24267578125 0.25736477971076965 1039.0628662109375 0.9038357734680176 0.8726583 0.27011993527412415 True -19 82020 45.448001861572266 0.8318271636962891 752.205078125 0.19020244479179382 1039.181884765625 0.9038341045379639 0.8725337 0.2717364728450775 False diff --git a/ENCSR485TLP/cherimoya.fold_2.performance.tsv b/ENCSR485TLP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 43d406794dd523d65074a49e39f612a99f6edaf7..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1039.0628662109375 0.08121651411056519 0.9038357734680176 0.6219564080238342 0.8726583123207092 0.8693680763244629 0.27011993527412415 \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_3.evaluate.json b/ENCSR485TLP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 79f0bbecfc9b931d3dc60424534a0288f44f38b5..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_3.fit.json b/ENCSR485TLP/cherimoya.fold_3.fit.json deleted file mode 100644 index 27fe83f6d2c3bdc8a7421765eae0a74757a0cf6f..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF955VHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_3.log b/ENCSR485TLP/cherimoya.fold_3.log deleted file mode 100644 index 42854d448dcbe28a5a870596b14cd7aaa377e6aa..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3996 48.342142820358276 4.2061827182769775 906.7261962890625 0.7705770134925842 1342.5078125 0.8001319169998169 0.7778027 6.950281620025635 True -1 7992 44.123430490493774 1.827925682067871 926.732177734375 0.7890908122062683 1132.5477294921875 0.8637129664421082 0.7479718 0.9133100509643555 False -2 11988 44.06594491004944 0.8123092651367188 839.1029052734375 0.42862385511398315 1102.849365234375 0.8718190789222717 0.7725485 0.47187092900276184 False -3 15984 43.970112323760986 0.8505215644836426 771.147705078125 0.5900470018386841 1089.7255859375 0.8752619624137878 0.7749957 0.4483795464038849 False -4 19980 44.04930329322815 0.7791619300842285 1040.2005615234375 0.698503315448761 1085.0126953125 0.87708580493927 0.77408814 0.4312417507171631 False -5 23976 43.99684000015259 0.778005838394165 931.3732299804688 0.5475445985794067 1078.778564453125 0.8793486952781677 0.7771873 0.43878597021102905 False -6 27972 43.987088680267334 13.016971111297607 962.1027221679688 0.4553939402103424 1071.2945556640625 0.881574273109436 0.77734274 0.4294089376926422 False -7 31968 44.00801110267639 0.761847734451294 960.318115234375 0.5509711503982544 1061.3779296875 0.8837617635726929 0.7817809 0.41409027576446533 True -8 35964 43.96571660041809 0.7761054039001465 865.9271240234375 0.9508199691772461 1054.8916015625 0.886134147644043 0.78767926 0.40788933634757996 True -9 39960 43.95213556289673 0.7846853733062744 894.7980346679688 0.49411740899086 1049.1771240234375 0.8882065415382385 0.7922616 0.39891454577445984 True -10 43956 43.94424533843994 0.779778242111206 879.8865966796875 0.4123120903968811 1044.5565185546875 0.8898730278015137 0.79374176 0.40744829177856445 True -11 47952 44.05596590042114 35.03241491317749 875.684814453125 1.0942045450210571 1037.4200439453125 0.89178067445755 0.8061397 0.3969964385032654 True -12 51948 44.64741063117981 0.7724800109863281 891.2523193359375 0.560683012008667 1030.02392578125 0.8939999938011169 0.81369776 0.37247419357299805 True -13 55944 44.60131239891052 0.7888822555541992 849.3440551757812 0.6531168222427368 1022.8388061523438 0.8958485126495361 0.82136935 0.3672260344028473 True -14 59940 45.16264510154724 7.836637020111084 932.6226806640625 0.324044793844223 1017.191162109375 0.8977341651916504 0.8308729 0.3592786490917206 True -15 63936 44.07606530189514 0.7763118743896484 823.2152709960938 0.3036654591560364 1010.7018432617188 0.8992757201194763 0.83636844 0.33935755491256714 True -16 67932 43.967081785202026 0.7687106132507324 913.7412109375 0.5157113671302795 1006.6128540039062 0.9003122448921204 0.84597 0.3295047879219055 True -17 71928 43.93833923339844 0.7807860374450684 866.4567260742188 0.2361011803150177 1005.1297607421875 0.9006492495536804 0.85083467 0.3188427984714508 True -18 75924 44.04963731765747 2.586190938949585 791.3045043945312 0.3054386377334595 1004.7184448242188 0.9005143642425537 0.8491077 0.3220350742340088 False -19 79920 44.044509410858154 1.9443931579589844 819.3902587890625 0.3418457806110382 1005.172119140625 0.9004717469215393 0.84868413 0.32603779435157776 False diff --git a/ENCSR485TLP/cherimoya.fold_3.performance.tsv b/ENCSR485TLP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 15e3fad9ac54215f1d8df574ec945aeabca43f2f..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1005.1297607421875 0.0847364291548729 0.90064936876297 0.6001594066619873 0.8508346676826477 0.8398938775062561 0.3188427984714508 \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_4.evaluate.json b/ENCSR485TLP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5ddf1032624433011c7a4f015f4291852c3077a5..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VHK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_4.fit.json b/ENCSR485TLP/cherimoya.fold_4.fit.json deleted file mode 100644 index c5723ed98a506a647ed80de600439f5b1308dba2..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF955VHK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485TLP/cherimoya.fold_4.log b/ENCSR485TLP/cherimoya.fold_4.log deleted file mode 100644 index a4e55fe309f10e30ecd820af20b02190bf8be221..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4030 48.61081385612488 4.06664514541626 945.54931640625 0.6607627868652344 1292.7996826171875 0.7958279252052307 0.7945932 6.2774152755737305 True -1 8060 44.43244528770447 0.8354761600494385 926.5457153320312 1.0064882040023804 1087.7261962890625 0.8639473915100098 0.79487157 0.6091856360435486 True -2 12090 44.43410038948059 0.7803559303283691 934.4340209960938 0.9397730827331543 1061.297119140625 0.8714926838874817 0.81010437 0.348476380109787 True -3 16120 44.40730333328247 0.7659220695495605 773.6002807617188 0.7482572793960571 1049.7279052734375 0.8748278617858887 0.8066583 0.39383894205093384 False -4 20150 44.36660981178284 0.7395961284637451 821.042236328125 0.5278006792068481 1037.890380859375 0.8783655762672424 0.8116942 0.37494957447052 True -5 24180 44.46938419342041 1.611037015914917 859.9071044921875 0.7226871848106384 1032.356201171875 0.8800209760665894 0.816463 0.36508578062057495 True -6 28210 44.395395040512085 0.7664308547973633 882.8648681640625 0.7062585353851318 1026.104248046875 0.8821938633918762 0.8199422 0.34355252981185913 True -7 32240 44.39221382141113 0.7805471420288086 969.430908203125 0.4889948070049286 1019.2824096679688 0.8846591711044312 0.82781994 0.322716623544693 True -8 36270 44.623244762420654 0.7765529155731201 841.8922729492188 0.41553589701652527 1010.7379760742188 0.8871646523475647 0.8321843 0.31281328201293945 True -9 40300 44.506558418273926 0.7804791927337646 907.4904174804688 0.5666206479072571 1004.0650634765625 0.8891714811325073 0.8383383 0.2988708019256592 True -10 44330 44.47993302345276 0.7677626609802246 885.9231567382812 0.4521946907043457 996.369384765625 0.8918268084526062 0.84461975 0.2878543734550476 True -11 48360 44.556917667388916 0.7671442031860352 883.4430541992188 0.6222536563873291 990.6936645507812 0.8936772346496582 0.8497174 0.2753807604312897 True -12 52390 44.685776710510254 0.7770059108734131 729.3358154296875 0.5833244323730469 982.8763427734375 0.8958709836006165 0.8541371 0.2677702009677887 True -13 56420 44.51138877868652 2.5528316497802734 759.5260620117188 0.5602142810821533 977.5503540039062 0.8975670337677002 0.86199677 0.25600752234458923 True -14 60450 44.58833408355713 0.7895758152008057 897.4915771484375 0.7218239903450012 971.786865234375 0.8992490768432617 0.864952 0.24823777377605438 True -15 64480 44.4957160949707 0.7687342166900635 814.5032348632812 0.30655431747436523 966.937744140625 0.9006837606430054 0.86983037 0.23935635387897491 True -16 68510 44.47251105308533 0.7648916244506836 817.0598754882812 0.27837371826171875 964.9161376953125 0.9013223052024841 0.8753289 0.23573347926139832 True -17 72540 44.48016381263733 0.7678451538085938 932.180908203125 0.26639020442962646 963.9115600585938 0.9015279412269592 0.87403995 0.23778216540813446 False -18 76570 44.39924120903015 0.770993709564209 865.4981689453125 0.3716110289096832 964.662353515625 0.9014102816581726 0.87594247 0.23882555961608887 True -19 80600 44.475850343704224 0.8069391250610352 804.69580078125 0.3456091284751892 964.9007568359375 0.9013038873672485 0.87404466 0.24200034141540527 False diff --git a/ENCSR485TLP/cherimoya.fold_4.performance.tsv b/ENCSR485TLP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 17ac21aeafe67bdce4c58e9b06ee7efdc409841a..0000000000000000000000000000000000000000 --- a/ENCSR485TLP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -964.662353515625 0.08646410703659058 0.9014101624488831 0.5946635603904724 0.8759424686431885 0.8597735166549683 0.23882555961608887 \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_0.evaluate.json b/ENCSR485UQY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4afdbcc355103da8776b85692f75dde86aa24fdd..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF798GRF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_0.fit.json b/ENCSR485UQY/cherimoya.fold_0.fit.json deleted file mode 100644 index 139637cc90e64b76c8801f8eda02d4eee9255596..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF798GRF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_0.log b/ENCSR485UQY/cherimoya.fold_0.log deleted file mode 100644 index 3c59a570110bcfef4851e81f3711f46637120335..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 36.38145208358765 3.6979305744171143 1184.770263671875 1.149276852607727 1647.15576171875 0.2703242599964142 0.6682336 9.634085655212402 True -1 5518 30.75664710998535 0.6020245552062988 1091.4342041015625 1.5197020769119263 1361.2801513671875 0.3615890443325043 0.75801796 2.5485482215881348 True -2 8277 30.728413820266724 0.5748805999755859 897.8457641601562 0.6079622507095337 1331.99609375 0.37091585993766785 0.7604031 1.3137054443359375 True -3 11036 30.759461879730225 39.937660217285156 844.1817626953125 0.6959167718887329 1319.1419677734375 0.37579968571662903 0.76420003 1.1658023595809937 True -4 13795 30.89612603187561 28.103832721710205 1236.974365234375 0.6776179075241089 1314.3236083984375 0.37682223320007324 0.77344257 1.1417028903961182 True -5 16554 31.673380136489868 0.5755867958068848 1159.31494140625 1.0631065368652344 1300.6029052734375 0.38206005096435547 0.7800076 0.9478586912155151 True -6 19313 30.853372812271118 1.7557072639465332 1074.3468017578125 0.7918784022331238 1291.5552978515625 0.38416793942451477 0.79258776 0.8060704469680786 True -7 22072 30.808688402175903 0.5689938068389893 1006.345703125 0.7973721027374268 1277.6319580078125 0.39061784744262695 0.7980198 0.7811298966407776 True -8 24831 30.924034118652344 0.5950407981872559 1275.0966796875 0.7954239249229431 1271.090087890625 0.39151349663734436 0.80369943 0.7793158888816833 True -9 27590 30.778528928756714 0.5908324718475342 930.3311767578125 0.8840532302856445 1265.8653564453125 0.39302748441696167 0.8097357 0.7830597758293152 True -10 30349 30.76218581199646 0.5744831562042236 1313.5950927734375 0.5177467465400696 1257.0811767578125 0.39589911699295044 0.8141038 0.6940698027610779 True -11 33108 30.81354784965515 0.5643713474273682 939.780029296875 0.7717882990837097 1250.07568359375 0.3986371159553528 0.8209016 0.6657076478004456 True -12 35867 30.772836446762085 2.081223964691162 891.6683349609375 0.6318459510803223 1244.6239013671875 0.39963215589523315 0.8258492 0.5847378373146057 True -13 38626 30.81299066543579 0.5820357799530029 1041.392578125 0.336100697517395 1237.5408935546875 0.4019705653190613 0.8336687 0.5338516235351562 True -14 41385 30.39764380455017 0.5685884952545166 936.2162475585938 0.7273125648498535 1236.280517578125 0.4027276039123535 0.84033114 0.5085534453392029 True -15 44144 30.128249168395996 0.5667097568511963 1021.3362426757812 0.5470482110977173 1229.2740478515625 0.40446895360946655 0.8473922 0.47062429785728455 True -16 46903 30.14976191520691 0.5592002868652344 1070.48486328125 0.46479520201683044 1224.440185546875 0.40626874566078186 0.84860677 0.4468282461166382 True -17 49662 30.09582781791687 1.1453673839569092 942.69189453125 0.7624915838241577 1223.744140625 0.4064328074455261 0.85141325 0.4319772720336914 True -18 52421 30.173436880111694 0.5741839408874512 911.6235961914062 0.4529048502445221 1223.8201904296875 0.40563735365867615 0.85137624 0.42705023288726807 False -19 55180 30.18879747390747 0.5773167610168457 1015.0953369140625 0.3736996054649353 1225.8050537109375 0.4051450490951538 0.85179377 0.4268670082092285 True diff --git a/ENCSR485UQY/cherimoya.fold_0.performance.tsv b/ENCSR485UQY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4e84e4bfa13e726d5f7ecd2fa4b826198612a55f..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1225.8050537109375 0.4016820192337036 0.4051450192928314 0.15155407786369324 0.8517937660217285 0.8050665259361267 0.4268670082092285 \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_1.evaluate.json b/ENCSR485UQY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d82126623505b99a8dc76a81fb969f14bb78c9f8..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF798GRF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_1.fit.json b/ENCSR485UQY/cherimoya.fold_1.fit.json deleted file mode 100644 index c40f131578d20d24aaeb890ec47af6526ac3dcb3..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF798GRF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_1.log b/ENCSR485UQY/cherimoya.fold_1.log deleted file mode 100644 index ef11a12de929969e6e77558312ef094bdcbc6f5f..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2680 34.717498779296875 3.7745490074157715 1241.688232421875 0.9155508279800415 1981.9351806640625 0.2738299071788788 0.6735423 9.569701194763184 True -1 5360 29.751712322235107 1.044708490371704 968.527587890625 0.5236908197402954 1633.0164794921875 0.3712509572505951 0.7526576 3.6779186725616455 True -2 8040 29.634481191635132 0.7414126396179199 1016.868896484375 1.2722262144088745 1586.5172119140625 0.3832690119743347 0.77661663 1.7031348943710327 True -3 10720 29.631452560424805 0.7296931743621826 877.3577270507812 0.7292845845222473 1566.1644287109375 0.38676369190216064 0.7868798 1.305074691772461 True -4 13400 29.61153745651245 0.7317161560058594 1054.521484375 0.7300095558166504 1552.7276611328125 0.3906156122684479 0.7921466 1.5516806840896606 True -5 16080 29.928447246551514 0.7401900291442871 1295.167724609375 1.3496001958847046 1534.2340087890625 0.3967892825603485 0.79863733 1.1028989553451538 True -6 18760 29.59237265586853 0.74289870262146 1259.93017578125 0.8865891098976135 1527.04150390625 0.3980942368507385 0.80732584 0.8900004029273987 True -7 21440 29.630343914031982 2.2692015171051025 932.5717163085938 0.7152890563011169 1511.763916015625 0.40302395820617676 0.81007975 0.8798203468322754 True -8 24120 29.62253165245056 0.74188232421875 775.9253540039062 0.7623693943023682 1506.3458251953125 0.4050343930721283 0.8165107 0.813978374004364 True -9 26800 29.7410991191864 2.4113543033599854 1053.22314453125 0.6370963454246521 1492.4278564453125 0.40914803743362427 0.8257034 0.7989755868911743 True -10 29480 29.72802495956421 0.7427284717559814 1176.09326171875 0.8280223608016968 1485.26171875 0.41071298718452454 0.831604 0.6834561824798584 True -11 32160 29.683977842330933 0.7496368885040283 937.0626831054688 0.5650980472564697 1473.7913818359375 0.41400936245918274 0.8382032 0.7030545473098755 True -12 34840 29.66437005996704 1.3859386444091797 1081.7979736328125 0.46674537658691406 1471.613037109375 0.41369351744651794 0.8431122 0.6218618750572205 True -13 37520 29.63453197479248 2.4564571380615234 840.5140380859375 0.451969176530838 1454.44140625 0.419226735830307 0.8518911 0.5630717277526855 True -14 40200 29.408899784088135 0.7340843677520752 974.842529296875 0.5696320533752441 1450.5860595703125 0.4198395609855652 0.8581146 0.5197054147720337 True -15 42880 29.05590057373047 0.7325820922851562 1040.0849609375 0.5556422472000122 1441.436767578125 0.4223080277442932 0.8606378 0.4911237359046936 True -16 45560 29.106654405593872 0.7453711032867432 889.4412841796875 0.4147920608520508 1440.772705078125 0.4220089316368103 0.86388445 0.4658781588077545 True -17 48240 29.060413360595703 0.7580704689025879 831.215087890625 0.4324887990951538 1440.209228515625 0.4224863648414612 0.8657408 0.4449886679649353 True -18 50920 29.06528902053833 0.7565817832946777 920.13330078125 0.6372234225273132 1444.1922607421875 0.420185387134552 0.866941 0.43951016664505005 True -19 53600 29.035631895065308 0.723142147064209 646.9788208007812 0.4101887345314026 1444.0054931640625 0.4201836884021759 0.8665342 0.4406186044216156 False diff --git a/ENCSR485UQY/cherimoya.fold_1.performance.tsv b/ENCSR485UQY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 60f58c25af2808db0c091a3227c062b95c8a261c..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1444.1922607421875 0.3857762813568115 0.420185387134552 0.17282819747924805 0.866940975189209 0.8438246250152588 0.43951016664505005 \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_2.evaluate.json b/ENCSR485UQY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 34ac9a2ae2490a2c0d8ef55c8f165dcb4d0ccfad..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF798GRF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_2.fit.json b/ENCSR485UQY/cherimoya.fold_2.fit.json deleted file mode 100644 index e1ba0c18d43ab1091263c317f2c475ff85edc2c1..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF798GRF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_2.log b/ENCSR485UQY/cherimoya.fold_2.log deleted file mode 100644 index 648492d8917b26687a32c5c3296fd50f5dc54fd6..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.33870577812195 3.935323715209961 1056.422119140625 0.851486086845398 1727.3541259765625 0.2713078558444977 0.66423416 10.397479057312012 True -1 5772 31.924455165863037 0.6101436614990234 982.107666015625 0.6584892868995667 1431.2227783203125 0.3592942953109741 0.7522219 2.3617191314697266 True -2 8658 31.85431957244873 0.5754261016845703 1140.00537109375 0.8536182641983032 1402.533447265625 0.3667446970939636 0.76715076 1.2074106931686401 True -3 11544 31.9021213054657 0.5746870040893555 1165.178466796875 1.1594338417053223 1385.5797119140625 0.3725448548793793 0.7734122 1.190536618232727 True -4 14430 31.866411447525024 0.5832281112670898 1144.036376953125 0.8468722105026245 1372.9002685546875 0.37697523832321167 0.7804388 0.8587856292724609 True -5 17316 31.881640911102295 0.5716426372528076 1384.3067626953125 0.5768262147903442 1368.4720458984375 0.3781696557998657 0.78657144 0.760043203830719 True -6 20202 31.89686417579651 0.5776023864746094 911.4230346679688 0.8296312689781189 1357.3330078125 0.38215532898902893 0.7931369 0.755981981754303 True -7 23088 31.80090355873108 0.57796311378479 1163.90771484375 0.8600548505783081 1351.9644775390625 0.38382986187934875 0.79732555 0.702185869216919 True -8 25974 31.827660083770752 0.5721452236175537 1065.43701171875 0.538833737373352 1345.936279296875 0.38522616028785706 0.80079687 0.7052818536758423 True -9 28860 31.813438415527344 0.5770959854125977 1213.130126953125 0.8816176652908325 1335.82958984375 0.38938450813293457 0.8065543 0.6737797260284424 True -10 31746 31.84218692779541 1.9739789962768555 1056.2724609375 0.7223252058029175 1330.8428955078125 0.3899584412574768 0.81091005 0.6781135201454163 True -11 34632 31.846490144729614 0.5825772285461426 1006.2213134765625 0.6225028038024902 1324.6815185546875 0.39193588495254517 0.8167831 0.62526935338974 True -12 37518 31.884750366210938 0.5796971321105957 1083.0291748046875 0.5552825331687927 1315.6324462890625 0.3946146070957184 0.8216568 0.5694272518157959 True -13 40404 32.13741087913513 26.198819875717163 869.185791015625 0.5740721225738525 1310.4207763671875 0.3961646258831024 0.82807076 0.5207203030586243 True -14 43290 31.327146291732788 22.18194556236267 1084.5018310546875 0.5450913906097412 1302.7481689453125 0.3987051844596863 0.83245564 0.5001994967460632 True -15 46176 31.688990116119385 0.5770852565765381 1051.154541015625 0.3363274037837982 1298.4730224609375 0.4002460539340973 0.8383588 0.4789455533027649 True -16 49062 31.33520793914795 1.363417625427246 1236.75 0.370026558637619 1298.5523681640625 0.4009536802768707 0.841747 0.4574887454509735 True -17 51948 31.26404595375061 2.146688222885132 1065.6131591796875 0.28414493799209595 1297.0621337890625 0.4012269973754883 0.84301096 0.44753775000572205 True -18 54834 31.24717116355896 0.5960109233856201 1248.5821533203125 0.4034712314605713 1299.840576171875 0.3992884159088135 0.84308237 0.4435758590698242 True -19 57720 31.236383199691772 0.5802395343780518 808.2259521484375 0.38058075308799744 1299.8194580078125 0.3997386693954468 0.84368235 0.4437015652656555 True diff --git a/ENCSR485UQY/cherimoya.fold_2.performance.tsv b/ENCSR485UQY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 933aea7f96f3bc06641e985c751bcbbf5b7319c1..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1299.8194580078125 0.4021543264389038 0.3997386693954468 0.15543292462825775 0.8436823487281799 0.8084811568260193 0.4437015652656555 \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_3.evaluate.json b/ENCSR485UQY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d72dd981d40bf185e0082359c4a45d4e2ae1e61b..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF798GRF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_3.fit.json b/ENCSR485UQY/cherimoya.fold_3.fit.json deleted file mode 100644 index ccecdb52a6e615a79ecdae40eab270cecae85aa4..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF798GRF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_3.log b/ENCSR485UQY/cherimoya.fold_3.log deleted file mode 100644 index f42e0bcab42302bf519040182689c66e82ba57e9..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 35.58041787147522 3.437178134918213 1339.609619140625 0.9005936980247498 1611.4964599609375 0.27947738766670227 0.6751613 9.92193603515625 True -1 5502 30.306453466415405 0.5373008251190186 928.3984985351562 1.0007078647613525 1343.412841796875 0.36722007393836975 0.76146513 2.9681642055511475 True -2 8253 30.37709903717041 0.5197098255157471 1173.03662109375 0.9560469388961792 1309.643798828125 0.37658601999282837 0.7717317 1.4420634508132935 True -3 11004 30.748756408691406 18.586217641830444 955.08984375 0.7779167890548706 1294.2901611328125 0.3797582685947418 0.7807373 1.1822184324264526 True -4 13755 30.40092444419861 0.5267865657806396 949.067626953125 0.8425270318984985 1283.05419921875 0.38425394892692566 0.7855231 1.1188088655471802 True -5 16506 30.40088725090027 0.5331194400787354 1180.75390625 1.015141487121582 1268.0791015625 0.38950490951538086 0.7927037 0.8223918080329895 True -6 19257 30.45182514190674 0.5373046398162842 1341.621826171875 1.1653121709823608 1260.8228759765625 0.39149630069732666 0.7965688 0.7944790720939636 True -7 22008 30.472804307937622 0.525749683380127 940.1534423828125 0.8231620788574219 1255.8331298828125 0.3930957615375519 0.8018974 0.745245099067688 True -8 24759 30.614801168441772 27.00150465965271 1161.062744140625 0.5894637703895569 1253.1187744140625 0.39405450224876404 0.805569 0.7580322623252869 True -9 27510 31.14726424217224 0.5336616039276123 1210.6383056640625 1.0804685354232788 1248.5694580078125 0.39428627490997314 0.8099746 0.6581615805625916 True -10 30261 30.542879343032837 0.5364041328430176 1046.741455078125 0.7576961517333984 1241.440185546875 0.39613640308380127 0.81655604 0.6537395715713501 True -11 33012 30.55306339263916 18.539448022842407 804.89013671875 0.5675497055053711 1228.9691162109375 0.4021899700164795 0.82110023 0.6185979843139648 True -12 35763 30.460187673568726 0.536163330078125 1157.4892578125 0.574867308139801 1224.8721923828125 0.4028175473213196 0.8285394 0.5772490501403809 True -13 38514 30.369563817977905 0.5243468284606934 1143.23974609375 0.39813709259033203 1219.0277099609375 0.4042784571647644 0.83570385 0.5393689870834351 True -14 41265 30.94924521446228 0.7268359661102295 964.5819091796875 0.6384152173995972 1212.318115234375 0.4056393504142761 0.8412079 0.5069873929023743 True -15 44016 30.37917947769165 0.5159704685211182 843.7552490234375 0.45030325651168823 1208.6580810546875 0.4070791006088257 0.8456577 0.4832872748374939 True -16 46767 30.374706983566284 14.098479747772217 964.7742919921875 0.33319979906082153 1207.8768310546875 0.4076929986476898 0.8502148 0.4622878134250641 True -17 49518 32.167134523391724 2.886829137802124 1117.7200927734375 0.6008849740028381 1206.5865478515625 0.4079519212245941 0.8537562 0.4475764334201813 True -18 52269 30.169375896453857 23.054065465927124 1117.701904296875 0.46698132157325745 1205.314453125 0.40948486328125 0.8530532 0.44370248913764954 False -19 55020 29.730413913726807 2.8514204025268555 912.1806640625 0.3863505423069 1205.5804443359375 0.40908268094062805 0.85212654 0.4434766173362732 False diff --git a/ENCSR485UQY/cherimoya.fold_3.performance.tsv b/ENCSR485UQY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bdff9caf4cfaa3b9470468ed2f0e309ec52be49b..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1206.5865478515625 0.39999714493751526 0.4079519212245941 0.15312540531158447 0.8537561893463135 0.8104872703552246 0.4475764334201813 \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_4.evaluate.json b/ENCSR485UQY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6f923d96c6de343a463d58880b09454344bb9d48..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF798GRF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_4.fit.json b/ENCSR485UQY/cherimoya.fold_4.fit.json deleted file mode 100644 index 62c43cf12f53bbb7466b1066b19175a9ace6c404..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF798GRF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR485UQY/cherimoya.fold_4.log b/ENCSR485UQY/cherimoya.fold_4.log deleted file mode 100644 index b23e6d6af9df5ac46f8dc9606e5642444c285934..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2791 35.46205687522888 3.748685121536255 1444.3819580078125 0.6510339975357056 1518.9644775390625 0.27161747217178345 0.658066 11.180281639099121 True -1 5582 31.572995901107788 10.858194828033447 1238.468505859375 0.7762300968170166 1276.0888671875 0.3593786656856537 0.72744364 3.0799055099487305 True -2 8373 30.824663639068604 1.8174190521240234 1223.575927734375 0.6699778437614441 1248.717529296875 0.3654788136482239 0.74170107 1.4303685426712036 True -3 11164 30.992571592330933 2.6152329444885254 1249.8114013671875 0.9317800402641296 1223.3521728515625 0.37452828884124756 0.75386167 1.1817299127578735 True -4 13955 31.062997341156006 0.5960166454315186 995.5184936523438 0.44148093461990356 1215.76806640625 0.37659305334091187 0.7623321 0.9255772233009338 True -5 16746 31.03035306930542 30.76824426651001 1273.357177734375 0.8963808417320251 1211.552490234375 0.3775869607925415 0.7668457 0.8853275179862976 True -6 19537 30.958861589431763 0.5831098556518555 851.2388916015625 0.5585963726043701 1198.6519775390625 0.3831646144390106 0.7738312 0.7211012244224548 True -7 22328 30.81970191001892 0.5898745059967041 865.3101806640625 0.7270318865776062 1193.89208984375 0.384147047996521 0.77687436 0.6739661693572998 True -8 25119 30.76945972442627 0.5766804218292236 1038.0577392578125 0.5698522925376892 1188.51806640625 0.3859007656574249 0.78588516 0.6647289395332336 True -9 27910 30.82553267478943 0.5821259021759033 953.8668823242188 0.7282693386077881 1182.6925048828125 0.3878239393234253 0.7892479 0.6660138368606567 True -10 30701 31.312092781066895 29.841986417770386 945.486083984375 0.45259949564933777 1174.7508544921875 0.39059245586395264 0.797548 0.622982919216156 True -11 33492 30.965132474899292 7.539205074310303 1035.3345947265625 0.5848054885864258 1169.7374267578125 0.39339032769203186 0.80244666 0.5777190327644348 True -12 36283 30.87887191772461 0.5982460975646973 1058.47607421875 0.7995525002479553 1165.9405517578125 0.39493533968925476 0.8107644 0.5556775331497192 True -13 39074 30.837708473205566 0.5833590030670166 805.4782104492188 0.5409481525421143 1159.79638671875 0.3960893154144287 0.818996 0.5130942463874817 True -14 41865 30.845366716384888 0.5835075378417969 1097.564697265625 0.36185622215270996 1154.898193359375 0.3990197777748108 0.82429934 0.4787508249282837 True -15 44656 30.782747983932495 0.5835521221160889 991.7353515625 0.4430079460144043 1155.6878662109375 0.3976917862892151 0.8297102 0.45718351006507874 True -16 47447 30.79088807106018 0.5798935890197754 903.386474609375 0.6133569478988647 1152.323486328125 0.40007826685905457 0.83595437 0.44399693608283997 True -17 50238 30.81156063079834 0.5738112926483154 952.432373046875 0.3509553372859955 1150.728515625 0.40080809593200684 0.83745766 0.4343760907649994 True -18 53029 30.85171341896057 0.6055092811584473 1014.8331298828125 0.3764328956604004 1151.6041259765625 0.4000222682952881 0.8370821 0.42851266264915466 False -19 55820 30.62627100944519 29.472066640853882 860.4246215820312 0.36044415831565857 1153.4896240234375 0.3991800546646118 0.8390762 0.4292055368423462 True diff --git a/ENCSR485UQY/cherimoya.fold_4.performance.tsv b/ENCSR485UQY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 821562bb15bbb70bdb65b351143ce767a03ca174..0000000000000000000000000000000000000000 --- a/ENCSR485UQY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1153.4896240234375 0.4074719548225403 0.39918002486228943 0.1447683870792389 0.8390762209892273 0.787202000617981 0.4292055368423462 \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_0.evaluate.json b/ENCSR487QSB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1b1bd539f598e4ffacc48eb4277c0049869b18d6..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF717MYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_0.fit.json b/ENCSR487QSB/cherimoya.fold_0.fit.json deleted file mode 100644 index 42d958491825d5dec914433fd4898c735904d9a0..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF717MYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_0.log b/ENCSR487QSB/cherimoya.fold_0.log deleted file mode 100644 index ca95f908b678116ac3d434a0cdc509bd41ceaf66..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2651 33.98137068748474 4.139265060424805 457.15350341796875 0.43517863750457764 646.510009765625 0.5584443211555481 0.5216797 8.832610130310059 True -1 5302 29.423362970352173 0.7363247871398926 410.8047180175781 0.609197735786438 553.4594116210938 0.6723966002464294 0.62267834 2.3031458854675293 True -2 7953 29.378737211227417 1.637934923171997 339.0762023925781 0.7934924364089966 541.6962280273438 0.6873058676719666 0.63245654 0.9468070268630981 True -3 10604 29.370740175247192 0.5318088531494141 425.8605651855469 0.43384188413619995 536.8152465820312 0.6923757791519165 0.63700444 0.8149646520614624 True -4 13255 29.364322423934937 0.533238410949707 454.2740478515625 0.5386239290237427 534.1152954101562 0.6958951354026794 0.6505486 0.7302079200744629 True -5 15906 29.370234727859497 0.5256390571594238 449.3547058105469 0.45472806692123413 531.9940795898438 0.6985149383544922 0.6543346 0.6815831661224365 True -6 18557 29.37079882621765 0.5396451950073242 401.8536376953125 0.37806060910224915 530.9535522460938 0.7004576325416565 0.65858966 0.5973830223083496 True -7 21208 29.377674102783203 0.5250904560089111 430.9097595214844 0.45914798974990845 530.738037109375 0.7011290788650513 0.657135 0.6065012812614441 False -8 23859 29.451725959777832 1.3971295356750488 424.114501953125 0.7091435194015503 528.4329223632812 0.7040303945541382 0.6592526 0.5599878430366516 True -9 26510 29.33219575881958 0.5351095199584961 426.0743408203125 0.4419814348220825 526.5645751953125 0.7062536478042603 0.6697836 0.5217964053153992 True -10 29161 29.20738196372986 0.5362091064453125 415.7156066894531 0.4898286461830139 525.1566772460938 0.7079176306724548 0.6765651 0.49389511346817017 True -11 31812 28.796729564666748 0.520423412322998 431.52484130859375 0.42398712038993835 523.8157348632812 0.709929347038269 0.6824842 0.4937117397785187 True -12 34463 28.780681371688843 0.5309066772460938 409.3930969238281 0.39698827266693115 522.26953125 0.7119659781455994 0.6865356 0.48147526383399963 True -13 37114 28.77039861679077 0.6404604911804199 392.6873474121094 0.29704397916793823 520.7635498046875 0.7134456634521484 0.69124347 0.4520736634731293 True -14 39765 28.76508069038391 0.5213041305541992 428.1750793457031 0.3538593649864197 519.8817749023438 0.7147793173789978 0.69751865 0.4445270001888275 True -15 42416 28.763324975967407 0.6287035942077637 387.5201416015625 0.26213401556015015 519.2734375 0.7152710556983948 0.70027584 0.4393032193183899 True -16 45067 28.77872347831726 0.5291931629180908 457.04071044921875 0.3785521388053894 519.2533569335938 0.7152848243713379 0.7032115 0.4362756907939911 True -17 47718 28.81296968460083 8.588768482208252 383.36474609375 0.3306654691696167 519.3409423828125 0.7149405479431152 0.6998686 0.4382972717285156 False -18 50369 29.147040605545044 0.5756785869598389 408.85247802734375 0.1918378472328186 519.6552734375 0.7143650054931641 0.69356734 0.4475504159927368 False -19 53020 28.80804991722107 0.536639928817749 412.0810852050781 0.18805313110351562 519.8588256835938 0.7139922380447388 0.6914303 0.45460131764411926 False diff --git a/ENCSR487QSB/cherimoya.fold_0.performance.tsv b/ENCSR487QSB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f9e7805aa464679fa4a9bd782ecced81d2c9cd95..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -519.2533569335938 0.23035500943660736 0.7152848243713379 0.3394372761249542 0.7032114863395691 0.6514747142791748 0.4362756907939911 \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_1.evaluate.json b/ENCSR487QSB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index daf6f5b37d081ac7de2285bd5e07e1502964f09e..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF717MYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_1.fit.json b/ENCSR487QSB/cherimoya.fold_1.fit.json deleted file mode 100644 index cae9dd913fd2e3473ef62d4096f12618fb792d8f..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF717MYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_1.log b/ENCSR487QSB/cherimoya.fold_1.log deleted file mode 100644 index 1474f3fc274c97e434cf22a9337abbf39b0b908f..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2685 34.25490474700928 3.9350640773773193 391.85040283203125 0.7186745405197144 654.8440551757812 0.5732696056365967 0.5587592 6.022110939025879 True -1 5370 30.007479906082153 0.9245662689208984 468.03350830078125 0.4690786600112915 574.8932495117188 0.6741127371788025 0.64211905 1.7290645837783813 True -2 8055 29.728793621063232 0.6362380981445312 457.65826416015625 0.8072127103805542 565.4159545898438 0.685049295425415 0.67620254 0.7480027675628662 True -3 10740 29.734020471572876 0.6008508205413818 455.30389404296875 0.6428734064102173 561.3209228515625 0.6898864507675171 0.6836042 0.6184861063957214 True -4 13425 29.738965034484863 0.6011016368865967 381.79364013671875 0.396681010723114 559.979736328125 0.6924387812614441 0.68491143 0.6392036080360413 True -5 16110 29.724039554595947 0.60331130027771 451.3019104003906 0.5023348331451416 557.3604125976562 0.6958233714103699 0.6892974 0.5650978088378906 True -6 18795 29.739131927490234 3.3009233474731445 492.09783935546875 0.4152219295501709 556.2283325195312 0.6976421475410461 0.6912901 0.49678605794906616 True -7 21480 29.77375626564026 0.6107103824615479 415.13916015625 0.5613706111907959 555.1176147460938 0.6994100213050842 0.69663733 0.4906056225299835 True -8 24165 29.793039321899414 0.6731212139129639 413.8516845703125 0.5191720724105835 553.67333984375 0.7013850808143616 0.7012495 0.47737085819244385 True -9 26850 29.74950337409973 0.6160447597503662 386.8277587890625 0.6542494297027588 551.8245849609375 0.703659176826477 0.708253 0.4424792230129242 True -10 29535 29.743951320648193 0.6155502796173096 436.33575439453125 0.5132949352264404 549.8101196289062 0.7060238122940063 0.7123855 0.4358249306678772 True -11 32220 29.789374351501465 0.6150813102722168 384.33453369140625 0.582558274269104 548.4295654296875 0.7079351544380188 0.72056615 0.4149979054927826 True -12 34905 29.766048192977905 0.6006491184234619 408.6392822265625 0.4653087258338928 546.783447265625 0.7096317410469055 0.7241065 0.40112775564193726 True -13 37590 29.76221513748169 0.619006872177124 391.93170166015625 0.3853026330471039 544.8658447265625 0.7119195461273193 0.73123866 0.3827926814556122 True -14 40275 29.74547815322876 19.980358600616455 354.3148193359375 0.3126341700553894 544.0677490234375 0.7129470109939575 0.7388298 0.36996668577194214 True -15 42960 30.57721781730652 0.6002318859100342 436.88458251953125 0.428047776222229 543.2216796875 0.7137938737869263 0.74045664 0.36663129925727844 True -16 45645 29.184688091278076 0.5963034629821777 385.8760681152344 0.25641679763793945 542.9295043945312 0.7139871120452881 0.74323434 0.36605891585350037 True -17 48330 29.12922978401184 0.5964651107788086 453.78692626953125 0.18442964553833008 542.8999633789062 0.7139463424682617 0.7434812 0.3668898940086365 True -18 51015 29.12379741668701 0.5961332321166992 494.27630615234375 0.2707798182964325 543.2654418945312 0.7134366631507874 0.73886603 0.376042902469635 False -19 53700 29.116681337356567 0.596773624420166 409.45111083984375 0.23703183233737946 543.2771606445312 0.7130933403968811 0.73559785 0.38253748416900635 False diff --git a/ENCSR487QSB/cherimoya.fold_1.performance.tsv b/ENCSR487QSB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3b2381b129670a3a06c7f6ea02e5ae0e46045390..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -542.8999633789062 0.22546066343784332 0.7139463424682617 0.3533017337322235 0.7434812188148499 0.7183356285095215 0.3668898940086365 \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_2.evaluate.json b/ENCSR487QSB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f6c7599a6747229d6d6b4e4220b2eb6e7b37bef6..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF717MYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_2.fit.json b/ENCSR487QSB/cherimoya.fold_2.fit.json deleted file mode 100644 index 04a43b46f71c223ae9a48a9a2c0244b3bb9f589b..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF717MYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_2.log b/ENCSR487QSB/cherimoya.fold_2.log deleted file mode 100644 index 5ff8cb457400984fab1370f0429f5deb7f62c910..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2811 36.228145122528076 2.8845272064208984 459.05877685546875 0.6670808792114258 631.1726684570312 0.5672230124473572 0.5555643 5.7583136558532715 True -1 5622 31.222167491912842 0.9340176582336426 467.220703125 0.5509326457977295 553.2321166992188 0.6679801344871521 0.64668787 1.6790498495101929 True -2 8433 31.09733247756958 0.5100076198577881 408.76141357421875 0.610783576965332 542.7662353515625 0.6794116497039795 0.66057265 0.788630485534668 True -3 11244 31.124967575073242 1.2683734893798828 489.319091796875 0.583317756652832 539.2186889648438 0.6842430830001831 0.6668571 0.8313466310501099 True -4 14055 31.1364848613739 0.48168182373046875 557.8948974609375 0.4263421595096588 537.9082641601562 0.6864067912101746 0.6747694 0.7351980209350586 True -5 16866 31.14838433265686 0.47299623489379883 417.9079895019531 0.49805742502212524 535.4557495117188 0.6889650821685791 0.67955446 0.6369479894638062 True -6 19677 31.143161296844482 0.46888136863708496 416.2084655761719 0.34960198402404785 533.1593627929688 0.6918409466743469 0.6796644 0.6080230474472046 True -7 22488 31.170028686523438 0.47128868103027344 379.06158447265625 0.3954840898513794 531.7313232421875 0.693419873714447 0.68707716 0.5728877186775208 True -8 25299 31.147955417633057 0.4822118282318115 456.28643798828125 0.5621699690818787 530.6719360351562 0.6952857971191406 0.6884037 0.538621723651886 True -9 28110 31.111116409301758 0.4668772220611572 459.6642761230469 0.42389899492263794 529.0133666992188 0.6972472071647644 0.6918341 0.5068338513374329 True -10 30921 31.138405561447144 0.4735219478607178 413.31817626953125 0.6471630334854126 527.2191162109375 0.6996009945869446 0.6978982 0.49245089292526245 True -11 33732 31.579161882400513 9.713764190673828 441.58154296875 0.4889717996120453 525.5810546875 0.7016348838806152 0.7031906 0.46628522872924805 True -12 36543 31.155471801757812 0.47220420837402344 384.2088623046875 0.47627317905426025 524.1785888671875 0.7034684419631958 0.7079615 0.4517946243286133 True -13 39354 31.12794518470764 0.47063517570495605 388.3555908203125 0.27768227458000183 523.0680541992188 0.7049477100372314 0.7150022 0.4362128674983978 True -14 42165 31.10728430747986 0.46883559226989746 410.96783447265625 0.3573760986328125 522.0938110351562 0.7060901522636414 0.7213069 0.4213051199913025 True -15 44976 31.113661527633667 0.45969724655151367 444.16986083984375 0.2608344852924347 521.7886962890625 0.7066413760185242 0.7227068 0.41253453493118286 True -16 47787 31.212177515029907 0.48058462142944336 402.9306945800781 0.20813170075416565 521.8646850585938 0.7066646218299866 0.72590095 0.4105772078037262 True -17 50598 31.17211389541626 0.4706103801727295 431.946044921875 0.248951256275177 521.8544311523438 0.7062309384346008 0.72407645 0.412546306848526 False -18 53409 31.191929817199707 0.479752779006958 406.83038330078125 0.2808045744895935 522.3165283203125 0.7057167291641235 0.72156155 0.4180997312068939 False -19 56220 31.134843349456787 0.4732527732849121 363.9563293457031 0.3710014224052429 522.5167236328125 0.7054975032806396 0.7180409 0.42257580161094666 False diff --git a/ENCSR487QSB/cherimoya.fold_2.performance.tsv b/ENCSR487QSB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ed8206a1d07593be9cf0721c71b3af1dd0318030..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -521.8646850585938 0.23281197249889374 0.7066646814346313 0.34244608879089355 0.7259009480476379 0.6827089190483093 0.4105772078037262 \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_3.evaluate.json b/ENCSR487QSB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f2c47dd956e51ab7adc9693eb656e405c1854dad..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF717MYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_3.fit.json b/ENCSR487QSB/cherimoya.fold_3.fit.json deleted file mode 100644 index 40388aee644973bafa007aba2b150ce93c9676ec..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF717MYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_3.log b/ENCSR487QSB/cherimoya.fold_3.log deleted file mode 100644 index 73bf542c291224f6412dbae091200ee623a0e23a..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 35.41500210762024 5.387425899505615 421.6468505859375 0.5307273864746094 638.1325073242188 0.5707469582557678 0.5410708 7.145573616027832 True -1 5460 30.258347988128662 0.6758594512939453 432.78363037109375 0.5317261219024658 555.9179077148438 0.6742532253265381 0.60570663 1.9754091501235962 True -2 8190 29.739920616149902 0.6616823673248291 414.527587890625 0.5024755597114563 543.6822509765625 0.6865535378456116 0.62794465 0.8346652388572693 True -3 10920 29.679749250411987 0.5827059745788574 394.25927734375 0.5492997169494629 539.7060546875 0.6910879015922546 0.64388216 0.7422466278076172 True -4 13650 29.66260552406311 0.5842516422271729 446.85162353515625 0.7373729348182678 537.1843872070312 0.6937165856361389 0.6544767 0.6784482002258301 True -5 16380 29.77500295639038 0.5874125957489014 431.3190612792969 0.44713184237480164 535.1703491210938 0.695986807346344 0.65703994 0.6066001653671265 True -6 19110 29.774298667907715 0.5801827907562256 466.35577392578125 0.640713632106781 533.6621704101562 0.6979819536209106 0.6616441 0.5624978542327881 True -7 21840 29.681684494018555 0.5784192085266113 375.73675537109375 0.5762176513671875 531.8340454101562 0.700160562992096 0.66783065 0.5253996253013611 True -8 24570 29.660624742507935 0.5801372528076172 392.16436767578125 0.3570079505443573 530.2327880859375 0.702254593372345 0.67416614 0.5000908970832825 True -9 27300 29.75206708908081 0.5841174125671387 511.1615295410156 0.5131587386131287 528.94384765625 0.7040970325469971 0.678714 0.4753161668777466 True -10 30030 29.75312352180481 0.5776865482330322 412.7374572753906 0.3767956495285034 527.543701171875 0.7057943940162659 0.6815895 0.45995402336120605 True -11 32760 29.742077112197876 0.5901634693145752 390.979248046875 0.4696543216705322 526.2307739257812 0.7076743245124817 0.6865231 0.44937220215797424 True -12 35490 29.733409643173218 0.582754373550415 412.22930908203125 0.4594379961490631 524.9071655273438 0.7093955874443054 0.69458485 0.4397273063659668 True -13 38220 29.776121616363525 0.5828230381011963 364.7555847167969 0.4568631649017334 524.0094604492188 0.7106425166130066 0.70242494 0.437310129404068 True -14 40950 29.69785475730896 0.5801839828491211 400.6192932128906 0.3068600296974182 523.021484375 0.7118993997573853 0.70966315 0.4255969524383545 True -15 43680 29.73976445198059 0.5783030986785889 404.55963134765625 0.3180393576622009 522.1555786132812 0.7127407789230347 0.71283454 0.4221557676792145 True -16 46410 29.67813229560852 0.58107590675354 386.1435546875 0.4117458164691925 521.9361572265625 0.7128357887268066 0.7160019 0.4224815368652344 True -17 49140 29.635050296783447 2.0399115085601807 408.62896728515625 0.29475533962249756 522.2070922851562 0.7124991416931152 0.71456176 0.42626598477363586 False -18 51870 29.632202625274658 0.5927858352661133 431.05645751953125 0.21430574357509613 522.2815551757812 0.7120714783668518 0.710072 0.43846267461776733 False -19 54600 29.782418966293335 0.5757687091827393 446.0495300292969 0.21852849423885345 522.7109985351562 0.7117339968681335 0.70727265 0.4456527829170227 False diff --git a/ENCSR487QSB/cherimoya.fold_3.performance.tsv b/ENCSR487QSB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c6c7ccbcde3255ad05a8c0f1d2af0b95afb62869..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -521.9361572265625 0.22966858744621277 0.7128357887268066 0.3412931561470032 0.7160019278526306 0.6690950989723206 0.4224815368652344 \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_4.evaluate.json b/ENCSR487QSB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 54871ad1c83d83529bae4181dbd0c950e89f760b..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF717MYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_4.fit.json b/ENCSR487QSB/cherimoya.fold_4.fit.json deleted file mode 100644 index 0f5ca4599ca2c7f20cacdaaa4c9b23a32e95d229..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF717MYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR487QSB/cherimoya.fold_4.log b/ENCSR487QSB/cherimoya.fold_4.log deleted file mode 100644 index 567d06277f6b9ee1574b039bfebf5a865eec98ce..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2788 35.70953154563904 3.7811782360076904 486.37335205078125 0.7185637950897217 640.8441772460938 0.5661118030548096 0.5548904 5.964623928070068 True -1 5576 30.904364824295044 0.7605915069580078 457.05316162109375 0.5034730434417725 555.7271118164062 0.674587607383728 0.61118984 1.8734184503555298 True -2 8364 30.931212663650513 0.5429599285125732 429.99884033203125 0.7021626830101013 545.969482421875 0.6872981190681458 0.62213326 0.8019949793815613 True -3 11152 30.920822858810425 0.52724289894104 472.1370849609375 0.4804692566394806 541.566162109375 0.6928423047065735 0.6320438 0.7571529150009155 True -4 13940 30.951002836227417 0.5530438423156738 431.08624267578125 0.5385462045669556 538.2735595703125 0.6970295906066895 0.6400974 0.7030133605003357 True -5 16728 30.911606073379517 0.5575277805328369 417.3701477050781 0.4383322298526764 536.7355346679688 0.6990034580230713 0.65001255 0.5705249309539795 True -6 19516 30.586806535720825 0.5403568744659424 461.34197998046875 0.4191077649593353 534.5742797851562 0.7016173601150513 0.6534145 0.5649368762969971 True -7 22304 30.392062664031982 4.02885103225708 485.453857421875 0.4225349426269531 532.901611328125 0.7038365006446838 0.6595375 0.5342194437980652 True -8 25092 30.415782928466797 0.8599092960357666 403.0045166015625 0.2854403555393219 531.3783569335938 0.7058684229850769 0.6654182 0.5233052372932434 True -9 27880 30.292652130126953 0.5538582801818848 456.019287109375 0.7022577524185181 530.3848266601562 0.7074570655822754 0.6727489 0.5097124576568604 True -10 30668 30.286850929260254 0.5609943866729736 413.21600341796875 0.39179450273513794 528.7642211914062 0.7094162702560425 0.6775909 0.4953233599662781 True -11 33456 30.296209812164307 0.5606098175048828 378.11029052734375 0.4801882207393646 527.1105346679688 0.7115975022315979 0.6866251 0.4670708477497101 True -12 36244 30.41191577911377 0.5580668449401855 469.49554443359375 0.4125797152519226 525.8070678710938 0.7132566571235657 0.69403327 0.45563483238220215 True -13 39032 30.392390727996826 0.5510802268981934 393.38800048828125 0.31633126735687256 524.6339721679688 0.7145776748657227 0.69990176 0.44229862093925476 True -14 41820 30.378445863723755 0.5406477451324463 440.1336364746094 0.3425392210483551 523.6942749023438 0.7158948183059692 0.70585465 0.4371505379676819 True -15 44608 30.352535724639893 0.533942699432373 409.0107727050781 0.2925701141357422 522.738037109375 0.7166708111763 0.7145084 0.423828125 True -16 47396 30.364037036895752 0.5273702144622803 450.48883056640625 0.23261085152626038 522.6170654296875 0.7167084813117981 0.71640766 0.42468351125717163 True -17 50184 30.352149724960327 0.5215952396392822 431.52008056640625 0.2535597085952759 522.633544921875 0.716334879398346 0.71639824 0.4255121350288391 False -18 52972 30.37436318397522 0.5340020656585693 408.0382995605469 0.3083644509315491 522.8826293945312 0.715765655040741 0.7125082 0.43382441997528076 False -19 55760 30.371410608291626 0.531519889831543 434.1573181152344 0.18264968693256378 523.291259765625 0.7153052091598511 0.7093092 0.4385318160057068 False diff --git a/ENCSR487QSB/cherimoya.fold_4.performance.tsv b/ENCSR487QSB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 60ac56bd93e575e130db914b8687471a96b79784..0000000000000000000000000000000000000000 --- a/ENCSR487QSB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -522.6170654296875 0.2292841672897339 0.7167084813117981 0.3416351079940796 0.7164076566696167 0.6558241844177246 0.42468351125717163 \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_0.evaluate.json b/ENCSR488PHT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a97c4ddd29302724d39a70823ab590de262b0237..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390YCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_0.fit.json b/ENCSR488PHT/cherimoya.fold_0.fit.json deleted file mode 100644 index 1e51d0adc6038c3ea7e252d2bb876a9c6bfc2866..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF390YCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_0.log b/ENCSR488PHT/cherimoya.fold_0.log deleted file mode 100644 index a805d23197c6aece4837748d717ce01c3b7edd86..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.369616746902466 4.123852252960205 202.44338989257812 1.087627649307251 340.4670104980469 0.1688404232263565 0.5173938 3.895124912261963 True -1 5494 30.41827130317688 8.844483375549316 248.57801818847656 1.0008304119110107 320.84619140625 0.24008837342262268 0.61463153 1.4412553310394287 True -2 8241 30.519551277160645 2.40956974029541 215.05332946777344 0.8087130784988403 316.2752990722656 0.2491571605205536 0.6318274 0.7963758111000061 True -3 10988 30.452209949493408 2.152007818222046 219.9227294921875 0.7019029855728149 313.73858642578125 0.2567756772041321 0.6398673 0.7198983430862427 True -4 13735 30.419480085372925 13.074913263320923 262.2484130859375 0.7698955535888672 313.191650390625 0.25829994678497314 0.6387084 0.8267104625701904 False -5 16482 30.44512414932251 1.2866291999816895 262.24700927734375 0.8252633810043335 312.5003356933594 0.26069650053977966 0.64149356 0.8010907769203186 True -6 19229 30.42066264152527 0.5861847400665283 270.19158935546875 1.1665338277816772 311.9035949707031 0.262820839881897 0.6515712 0.7584643959999084 True -7 21976 30.409911394119263 0.5783665180206299 227.31637573242188 0.8953135013580322 311.3025817871094 0.2648080587387085 0.6559356 0.7965952754020691 True -8 24723 30.411186456680298 0.576580286026001 212.97357177734375 0.9515578150749207 310.17645263671875 0.2693328857421875 0.66323423 0.7731056213378906 True -9 27470 30.410812616348267 0.5708284378051758 248.00137329101562 0.7951233386993408 309.59130859375 0.2709812521934509 0.6676639 0.75911545753479 True -10 30217 30.428746223449707 15.543887853622437 197.656005859375 0.7726927995681763 309.17462158203125 0.2721763849258423 0.68022394 0.6831927299499512 True -11 32964 30.7393696308136 0.6026880741119385 182.85501098632812 0.414577841758728 308.5627746582031 0.2740837633609772 0.6849439 0.6524782180786133 True -12 35711 30.473008632659912 0.5893082618713379 234.90663146972656 0.6317470073699951 307.6866149902344 0.2768472731113434 0.6932547 0.6002257466316223 True -13 38458 30.47327470779419 0.6026322841644287 241.22268676757812 0.7283062934875488 306.6534118652344 0.2799925208091736 0.70269144 0.5670249462127686 True -14 41205 30.533301830291748 0.5811882019042969 188.59255981445312 0.594631016254425 306.2543029785156 0.2820165157318115 0.7127806 0.5251357555389404 True -15 43952 30.50101375579834 1.0291895866394043 238.63827514648438 0.5952253937721252 305.75848388671875 0.2835346758365631 0.7195984 0.5007440447807312 True -16 46699 29.947128295898438 0.5648894309997559 207.4102783203125 0.5076691508293152 305.25531005859375 0.28481221199035645 0.72581357 0.4721803665161133 True -17 49446 29.879791736602783 7.721520185470581 218.8275909423828 0.3984660804271698 305.16339111328125 0.28472644090652466 0.7289696 0.4657362699508667 True -18 52193 29.896483421325684 0.5677826404571533 259.08856201171875 0.32801374793052673 305.4597473144531 0.2834000885486603 0.7276238 0.46454569697380066 False -19 54940 29.917462825775146 0.5651035308837891 217.30714416503906 0.33206015825271606 305.674072265625 0.282720685005188 0.72698915 0.4685399532318115 False diff --git a/ENCSR488PHT/cherimoya.fold_0.performance.tsv b/ENCSR488PHT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 87e29f230e95159b76cf8c2e8ef70ab6bf4463d7..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -305.16339111328125 0.48976683616638184 0.28472644090652466 0.08417678624391556 0.7289695739746094 0.6707574129104614 0.4657362699508667 \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_1.evaluate.json b/ENCSR488PHT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index db0e5baff0a2e98f9fb7bf05642e55c08fe2067d..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390YCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_1.fit.json b/ENCSR488PHT/cherimoya.fold_1.fit.json deleted file mode 100644 index f523edca18898060bb9422a99bddce8704a994d8..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF390YCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_1.log b/ENCSR488PHT/cherimoya.fold_1.log deleted file mode 100644 index 5d2e4e2d0f1438a8a49975efb8304957592bd631..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 35.19263958930969 4.124634027481079 223.77645874023438 1.0452330112457275 388.6943054199219 0.18065844476222992 0.5614398 4.629870891571045 True -1 5498 30.49011754989624 0.9828369617462158 282.5185546875 0.9422290921211243 364.739990234375 0.2535027265548706 0.6528175 1.7914320230484009 True -2 8247 30.491681575775146 0.6915600299835205 267.5382385253906 1.026671290397644 358.8808898925781 0.2634528577327728 0.66917485 1.1155036687850952 True -3 10996 30.513723134994507 6.206610202789307 206.98609924316406 0.4183885455131531 355.9040222167969 0.26978233456611633 0.6775488 0.8120471239089966 True -4 13745 30.55886960029602 0.7807140350341797 249.41281127929688 0.6990684270858765 354.35137939453125 0.27385514974594116 0.68191916 0.7561887502670288 True -5 16494 30.50426483154297 0.7597382068634033 220.22012329101562 0.6346575021743774 353.39263916015625 0.27710938453674316 0.6869734 0.8326884508132935 True -6 19243 30.585063934326172 0.6862268447875977 239.07691955566406 0.5837932229042053 352.8413391113281 0.2780892550945282 0.6932912 0.8295386433601379 True -7 21992 30.46988534927368 0.6935596466064453 209.94027709960938 0.7431919574737549 351.94061279296875 0.2815192639827728 0.6945467 0.8320013284683228 True -8 24741 30.573465824127197 2.235649824142456 303.1085510253906 0.7594944834709167 350.8670654296875 0.28402048349380493 0.70071256 0.8089829087257385 True -9 27490 30.540796995162964 3.3164069652557373 233.26309204101562 0.6967829465866089 350.299560546875 0.28544697165489197 0.7043247 0.7637973427772522 True -10 30239 29.860763788223267 17.69111919403076 217.21572875976562 0.8215290307998657 350.03216552734375 0.2859688103199005 0.7112069 0.7618332505226135 True -11 32988 29.940839529037476 0.6915760040283203 209.54669189453125 0.5028210282325745 348.50140380859375 0.2907261848449707 0.7180409 0.7280820608139038 True -12 35737 29.96763801574707 0.6840574741363525 223.38327026367188 0.5508190393447876 347.3497314453125 0.2934628129005432 0.72703445 0.6633734703063965 True -13 38486 29.839303016662598 0.6878345012664795 234.4261932373047 0.45473700761795044 346.9894104003906 0.2934127748012543 0.73607016 0.6074666380882263 True -14 41235 29.849576950073242 0.6627926826477051 233.95404052734375 0.5754778981208801 345.7058410644531 0.2965063154697418 0.74454397 0.5681712031364441 True -15 43984 29.827717542648315 0.6647963523864746 225.4455108642578 0.47760313749313354 345.2635192871094 0.29833534359931946 0.75031304 0.5384069681167603 True -16 46733 29.92838716506958 0.6857154369354248 201.2283935546875 0.41056832671165466 344.9852294921875 0.2988463342189789 0.75695896 0.5051283836364746 True -17 49482 29.90343427658081 0.6888599395751953 236.1966094970703 0.4124806523323059 344.8628234863281 0.29879236221313477 0.76130146 0.49153706431388855 True -18 52231 29.870386123657227 0.7226877212524414 254.51522827148438 0.3974151611328125 345.08355712890625 0.2985781133174896 0.75987476 0.49114790558815 False -19 54980 29.848719120025635 0.6896572113037109 264.08734130859375 0.40035155415534973 345.3377685546875 0.29750654101371765 0.7591193 0.49223408102989197 False diff --git a/ENCSR488PHT/cherimoya.fold_1.performance.tsv b/ENCSR488PHT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 521808ff79727529fea1c2d674dd63f804883cc4..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -344.8628234863281 0.4742664098739624 0.29879239201545715 0.0980873554944992 0.7613014578819275 0.712388813495636 0.49153706431388855 \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_2.evaluate.json b/ENCSR488PHT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e8804348d1ecd1f17ffab04c8b21fe48f3c8350b..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390YCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_2.fit.json b/ENCSR488PHT/cherimoya.fold_2.fit.json deleted file mode 100644 index cb7b697b66499331eff2847c164865682971b6e2..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF390YCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_2.log b/ENCSR488PHT/cherimoya.fold_2.log deleted file mode 100644 index c5a4528f564b5217903cc4d5508eec8f751ca4e3..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2907 37.51839232444763 4.241258859634399 260.45013427734375 0.9077139496803284 347.47283935546875 0.1724100112915039 0.5241409 3.446086883544922 True -1 5814 32.26954174041748 0.6043853759765625 219.96923828125 1.228649616241455 327.37835693359375 0.2432180792093277 0.61643785 1.339205026626587 True -2 8721 32.25976085662842 0.5724248886108398 233.8836669921875 0.916106104850769 322.9564514160156 0.251444935798645 0.6289045 1.046571969985962 True -3 11628 32.35004138946533 0.5862841606140137 221.23793029785156 0.7504239082336426 321.1271057128906 0.25507405400276184 0.64009225 0.8491396903991699 True -4 14535 31.59554958343506 0.5250873565673828 233.95166015625 0.8735511898994446 319.4794921875 0.2605915069580078 0.6447968 0.9096972942352295 True -5 17442 31.59944176673889 0.5319938659667969 228.611328125 0.8355966210365295 318.2215270996094 0.2646254897117615 0.6564935 0.9073061347007751 True -6 20349 31.59305214881897 0.5280461311340332 222.47833251953125 0.8041707873344421 317.6402893066406 0.26568761467933655 0.65950227 0.8786308765411377 True -7 23256 31.613439798355103 0.5343494415283203 247.35333251953125 0.6105093955993652 317.0663757324219 0.267841637134552 0.6638061 0.8514969944953918 True -8 26163 31.58206868171692 0.5371701717376709 242.04461669921875 0.5329001545906067 316.2735290527344 0.2704145312309265 0.6703248 0.8365700840950012 True -9 29070 31.548956632614136 0.6291780471801758 248.5780792236328 0.8211930990219116 315.4523010253906 0.2730956971645355 0.6748593 0.8181123733520508 True -10 31977 31.520438194274902 0.5233614444732666 214.78741455078125 0.5464940667152405 314.5793762207031 0.27589869499206543 0.68444943 0.7490289807319641 True -11 34884 31.72314715385437 1.128972053527832 224.45303344726562 0.6975705623626709 314.0704345703125 0.2767865061759949 0.69217753 0.7130606174468994 True -12 37791 31.584341049194336 0.536881685256958 235.97866821289062 0.5204628705978394 313.2209777832031 0.2796808183193207 0.69759315 0.6856347918510437 True -13 40698 31.832180976867676 0.5426297187805176 214.04502868652344 0.5645548105239868 312.7656555175781 0.2809266149997711 0.7046761 0.6209253668785095 True -14 43605 31.751082181930542 0.5461180210113525 221.908935546875 0.708680272102356 311.8854675292969 0.2834749221801758 0.7134242 0.5756182670593262 True -15 46512 31.649115800857544 0.5382566452026367 315.58709716796875 0.48262834548950195 311.5127868652344 0.28359487652778625 0.72200704 0.5309335589408875 True -16 49419 31.67480778694153 0.5562689304351807 234.85061645507812 0.5404659509658813 311.04571533203125 0.2856573760509491 0.7290526 0.507979691028595 True -17 52326 31.866609811782837 0.576155424118042 259.0579528808594 0.40812814235687256 311.1968078613281 0.2838023900985718 0.7322461 0.4939647316932678 True -18 55233 31.772399187088013 0.5591058731079102 230.51942443847656 0.6547337770462036 310.8818359375 0.28594863414764404 0.7329487 0.49240314960479736 True -19 58140 31.721681356430054 0.5146336555480957 254.5198211669922 0.3132445514202118 310.9771423339844 0.2850813865661621 0.73260516 0.4935196340084076 False diff --git a/ENCSR488PHT/cherimoya.fold_2.performance.tsv b/ENCSR488PHT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1bfdf0c0bdf3aed12495260e1c6ea7667d065c6e..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -310.8818359375 0.48751193284988403 0.28594863414764404 0.0842396691441536 0.7329487204551697 0.6849186420440674 0.49240314960479736 \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_3.evaluate.json b/ENCSR488PHT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b7015582ba82acdd5decb07c51f1ef956c9c6599..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390YCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_3.fit.json b/ENCSR488PHT/cherimoya.fold_3.fit.json deleted file mode 100644 index d1b121c91d30666ad480693bcaf245e5e463dae4..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF390YCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_3.log b/ENCSR488PHT/cherimoya.fold_3.log deleted file mode 100644 index 2a5cf898bd032462d481f8fbeaceced099e50395..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2783 35.740832567214966 4.766756772994995 216.90106201171875 0.973147988319397 357.6741943359375 0.1697329431772232 0.563307 3.902491569519043 True -1 5566 30.960042238235474 0.611452579498291 241.36624145507812 1.0962104797363281 338.7084655761719 0.23801681399345398 0.6401575 1.640093207359314 True -2 8349 30.93716287612915 0.6115627288818359 259.1356201171875 0.7276022434234619 332.8756408691406 0.2512735426425934 0.64313126 1.1807206869125366 True -3 11132 30.9842369556427 0.5780003070831299 247.1700897216797 0.8632986545562744 331.3555603027344 0.2545700669288635 0.6459855 1.1866012811660767 True -4 13915 32.0360791683197 0.5942363739013672 299.59893798828125 0.9154534935951233 329.85882568359375 0.26007959246635437 0.6508658 1.2437692880630493 True -5 16698 30.98412775993347 0.6058752536773682 257.38824462890625 0.5719259977340698 328.82757568359375 0.262883722782135 0.6575765 1.0915911197662354 True -6 19481 31.162202835083008 0.6009242534637451 175.65737915039062 0.6980247497558594 328.5452880859375 0.26305046677589417 0.66391367 0.9889567494392395 True -7 22264 30.937650442123413 0.5786538124084473 286.033935546875 0.8402885794639587 327.26129150390625 0.2688134014606476 0.66852367 0.9620506167411804 True -8 25047 30.91202974319458 1.1838479042053223 246.82138061523438 0.4722941517829895 326.75732421875 0.27065348625183105 0.677806 0.89239901304245 True -9 27830 30.959080457687378 0.5829923152923584 252.9429168701172 0.574629545211792 326.0648193359375 0.27162855863571167 0.67833835 0.8471303582191467 True -10 30613 30.85754084587097 0.5802962779998779 295.1097412109375 0.5615143179893494 324.9906311035156 0.27523571252822876 0.6860716 0.7870269417762756 True -11 33396 30.85076093673706 0.5776011943817139 259.6376953125 0.6280514597892761 324.44512939453125 0.2770969271659851 0.6953738 0.7495220899581909 True -12 36179 30.843912363052368 0.5683634281158447 211.8524169921875 0.4040493965148926 323.9385070800781 0.2787533104419708 0.70213735 0.7300048470497131 True -13 38962 30.818779230117798 0.5712852478027344 187.2108154296875 0.8718100786209106 323.105224609375 0.28114667534828186 0.7123262 0.6376866698265076 True -14 41745 30.964166402816772 0.5759549140930176 219.8531494140625 0.49864205718040466 322.81488037109375 0.28282833099365234 0.720504 0.5825366377830505 True -15 44528 30.21250057220459 0.6036570072174072 212.36865234375 0.3681299090385437 322.6454772949219 0.2824306786060333 0.72770274 0.5365797877311707 True -16 47311 30.441643953323364 0.5600674152374268 231.3338623046875 0.653963565826416 322.1293029785156 0.2843340337276459 0.7350522 0.4978431463241577 True -17 50094 30.278331995010376 0.5690686702728271 202.387451171875 0.605369508266449 322.3154296875 0.2829265296459198 0.73608947 0.4911665916442871 True -18 52877 30.32002282142639 0.5765788555145264 252.06149291992188 0.6723592877388 321.7417297363281 0.28553706407546997 0.7367219 0.49429264664649963 True -19 55660 30.25432276725769 0.5727658271789551 189.68951416015625 0.5759625434875488 322.30792236328125 0.2826286852359772 0.7354198 0.49602824449539185 False diff --git a/ENCSR488PHT/cherimoya.fold_3.performance.tsv b/ENCSR488PHT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 31a3f1c7bfe669b51375b982114ef01f41f45c5a..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -321.7417297363281 0.4858208894729614 0.28553706407546997 0.08589766174554825 0.7367218732833862 0.6780737042427063 0.49429264664649963 \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_4.evaluate.json b/ENCSR488PHT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6f91d54445028ff71903a619b2a5c684bc7f2ebd..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390YCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_4.fit.json b/ENCSR488PHT/cherimoya.fold_4.fit.json deleted file mode 100644 index b8b7819ac87bce5cb2cfc752a0bf720a98c63131..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF390YCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR488PHT/cherimoya.fold_4.log b/ENCSR488PHT/cherimoya.fold_4.log deleted file mode 100644 index ef088954ff4f654b07787669334792e9613fb1c4..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 36.852946043014526 4.102207660675049 254.11868286132812 0.6319871544837952 341.51947021484375 0.16939355432987213 0.5287611 3.8306009769439697 True -1 5746 31.89869999885559 0.6507418155670166 215.95108032226562 0.6016623973846436 321.3876953125 0.24184997379779816 0.6106605 1.34360933303833 True -2 8619 31.876193046569824 0.630695104598999 223.41983032226562 0.9581505060195923 317.6151123046875 0.2518637478351593 0.62440014 0.8148220181465149 True -3 11492 31.901297569274902 0.5919718742370605 223.39556884765625 0.6601903438568115 316.4630126953125 0.25313684344291687 0.63385034 0.7121875882148743 True -4 14365 31.89833092689514 0.5905976295471191 204.89573669433594 0.7136895656585693 315.81219482421875 0.2552133798599243 0.6359592 0.7499086260795593 True -5 17238 31.966449975967407 0.6122753620147705 226.77711486816406 1.0191271305084229 314.7841796875 0.2585104703903198 0.6395425 0.7597125768661499 True -6 20111 31.95279026031494 0.6111481189727783 228.80023193359375 0.7729499936103821 314.26324462890625 0.26080432534217834 0.64701223 0.7339761853218079 True -7 22984 32.05655765533447 0.6124739646911621 244.13967895507812 0.7699927687644958 313.639892578125 0.2624679505825043 0.6527935 0.7338969111442566 True -8 25857 31.990471124649048 0.6099660396575928 208.29808044433594 0.7160136699676514 312.84515380859375 0.26600128412246704 0.6586327 0.7299174070358276 True -9 28730 31.339541912078857 0.5939249992370605 254.05511474609375 0.6045952439308167 311.9193420410156 0.2687687575817108 0.6665232 0.6673793196678162 True -10 31603 31.249594688415527 3.0445430278778076 253.60366821289062 0.5673794746398926 311.3738098144531 0.27102383971214294 0.67352515 0.6921565532684326 True -11 34476 31.326682090759277 0.6089520454406738 263.52264404296875 0.7047762870788574 310.5303955078125 0.27485984563827515 0.6821231 0.6215788722038269 True -12 37349 31.344153881072998 1.8125526905059814 219.27142333984375 0.5701484680175781 310.0246887207031 0.2757854163646698 0.6922654 0.5831373333930969 True -13 40222 31.385270833969116 0.6234867572784424 242.0567626953125 0.5662391185760498 309.41754150390625 0.27755895256996155 0.70163214 0.5487420558929443 True -14 43095 31.379299879074097 0.6082704067230225 284.91619873046875 0.8998771905899048 309.02117919921875 0.27849602699279785 0.709417 0.5200521945953369 True -15 45968 31.36922574043274 0.5972917079925537 272.0385437011719 0.6682320833206177 308.6462097167969 0.27958956360816956 0.7170022 0.5017158389091492 True -16 48841 31.359652042388916 0.6130037307739258 235.4131317138672 0.3350481390953064 308.6326904296875 0.2784193754196167 0.7215842 0.4786410331726074 True -17 51714 31.35487675666809 0.6017506122589111 206.5201873779297 0.4522220492362976 308.159912109375 0.28105491399765015 0.7204585 0.4812003970146179 False -18 54587 31.44111394882202 0.6092362403869629 228.33399963378906 0.5113682150840759 308.68310546875 0.2792074680328369 0.72016174 0.4838491976261139 False -19 57460 31.37738609313965 0.6006414890289307 253.06546020507812 0.4804047644138336 308.603759765625 0.2791074514389038 0.7203806 0.4903069734573364 False diff --git a/ENCSR488PHT/cherimoya.fold_4.performance.tsv b/ENCSR488PHT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d16d56bd8df9e61b845a3a8f28a36cf2e3901db5..0000000000000000000000000000000000000000 --- a/ENCSR488PHT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.6326904296875 0.49045515060424805 0.2784193754196167 0.08089279383420944 0.7215842008590698 0.6703202724456787 0.4786410331726074 \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_0.evaluate.json b/ENCSR490MSG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4949263de65c6cb3fecbf4783a93b6d7ba06e5bf..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745DEQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_0.fit.json b/ENCSR490MSG/cherimoya.fold_0.fit.json deleted file mode 100644 index 6a31d74ccb5ecdd5087c340b9dcc31cf5604ba98..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF745DEQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_0.log b/ENCSR490MSG/cherimoya.fold_0.log deleted file mode 100644 index 124f4ba69b50ff2224412ff29a1678b9bf3b3767..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1039 16.304506301879883 3.384284257888794 230.24952697753906 0.11357422173023224 342.58062744140625 0.3996830880641937 0.71770483 16.6366024017334 True -1 2078 11.564056873321533 0.22492599487304688 242.21298217773438 0.10538078844547272 288.6816101074219 0.4780629277229309 0.76726216 4.181867599487305 True -2 3117 11.555853605270386 0.206526517868042 249.28729248046875 0.1300007700920105 277.7785949707031 0.500681459903717 0.78501964 0.9544232487678528 True -3 4156 11.533111572265625 0.2047874927520752 253.87274169921875 0.13135185837745667 270.21044921875 0.5166953802108765 0.8139452 0.2569238841533661 True -4 5195 11.532265901565552 0.20888352394104004 234.51754760742188 0.09071777015924454 267.014404296875 0.5228580832481384 0.8275548 0.17759773135185242 True -5 6234 11.546279430389404 0.19663500785827637 228.71559143066406 0.09404739737510681 266.267822265625 0.5241032242774963 0.82796425 0.1596522182226181 True -6 7273 11.585109233856201 0.1955125331878662 253.07208251953125 0.09698570519685745 265.84344482421875 0.5250092148780823 0.8276877 0.15873520076274872 False -7 8312 11.530156373977661 1.937901258468628 249.06088256835938 0.08429455757141113 265.15875244140625 0.5270739793777466 0.8391405 0.1254660189151764 True -8 9351 11.548444986343384 0.19979166984558105 248.37042236328125 0.08452048152685165 264.816162109375 0.5281588435173035 0.8458492 0.1116952896118164 True -9 10390 11.561712741851807 0.41991400718688965 226.9150848388672 0.08034460246562958 267.6138916015625 0.5203737020492554 0.84767336 0.10788462311029434 True -10 11429 11.387851238250732 0.20264220237731934 226.98947143554688 0.14224497973918915 265.3065185546875 0.5265946984291077 0.85081464 0.09828681498765945 True -11 12468 11.311823606491089 0.19806694984436035 206.05239868164062 0.10300152003765106 264.392333984375 0.5295353531837463 0.85567564 0.09221360832452774 True -12 13507 11.339512348175049 0.19794964790344238 234.7186279296875 0.11261577159166336 263.963134765625 0.530713677406311 0.85905904 0.09000587463378906 True -13 14546 11.336630821228027 0.1982417106628418 233.57473754882812 0.06705442070960999 263.8194580078125 0.5310894846916199 0.8613028 0.08783435076475143 True -14 15585 11.340964078903198 0.1948690414428711 218.85394287109375 0.1076158881187439 263.7821350097656 0.5311799049377441 0.86461556 0.08609583973884583 True -15 16624 11.341941595077515 0.4841885566711426 230.4278564453125 0.06468387693166733 263.914794921875 0.5306233167648315 0.8671513 0.08511024713516235 True -16 17663 11.350882768630981 0.5986588001251221 238.88461303710938 0.08247731626033783 264.2191467285156 0.5291425585746765 0.8671764 0.08428086340427399 True -17 18702 11.334235906600952 0.20757746696472168 213.78848266601562 0.06364760547876358 264.6481018066406 0.5273518562316895 0.8676414 0.08550939708948135 True -18 19741 11.314965009689331 0.20014166831970215 229.56930541992188 0.07119379937648773 265.04644775390625 0.5255966782569885 0.8651476 0.08808852732181549 False -19 20780 11.311211585998535 0.19849562644958496 210.800048828125 0.06077085807919502 265.3451843261719 0.5246446132659912 0.8649712 0.08926329016685486 False diff --git a/ENCSR490MSG/cherimoya.fold_0.performance.tsv b/ENCSR490MSG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cdcfbbc21c5a49b3eaf281c7e1d5cc48be189ceb..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -264.6481018066406 0.3583870828151703 0.5273518562316895 0.17982284724712372 0.8676413893699646 0.8568282127380371 0.08550939708948135 \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_1.evaluate.json b/ENCSR490MSG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index df2ec17c18e8f8f553b96c73f14e44e558a9a750..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745DEQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_1.fit.json b/ENCSR490MSG/cherimoya.fold_1.fit.json deleted file mode 100644 index cf647abe6377cf0d83a64b700e1ba28d3cc7ba74..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF745DEQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_1.log b/ENCSR490MSG/cherimoya.fold_1.log deleted file mode 100644 index c240f9bbfe871940ea2aeb2b6a15338127187a78..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1028 16.163992881774902 3.11796236038208 234.18038940429688 0.12905661761760712 366.1485900878906 0.4131302237510681 0.6208043 17.61111831665039 True -1 2056 11.413070440292358 0.27230381965637207 247.81460571289062 0.16026687622070312 308.3849182128906 0.4890739321708679 0.68494457 5.1976823806762695 True -2 3084 11.40493655204773 0.4952507019042969 215.09823608398438 0.08171756565570831 295.7654113769531 0.515159010887146 0.69405764 1.5813100337982178 True -3 4112 11.357091903686523 0.22909307479858398 258.38653564453125 0.12198157608509064 287.5353698730469 0.5333503484725952 0.76569784 0.40565627813339233 True -4 5140 11.17577838897705 0.2290174961090088 230.45962524414062 0.17886190116405487 283.6728820800781 0.5420766472816467 0.79229134 0.2538870871067047 True -5 6168 11.174797296524048 0.23715424537658691 217.5099639892578 0.1248733252286911 282.3487243652344 0.5451597571372986 0.8003768 0.1398952752351761 True -6 7196 11.169571161270142 1.3272812366485596 216.224365234375 0.11869640648365021 281.7508544921875 0.5466166734695435 0.8016525 0.12390828132629395 True -7 8224 11.179829359054565 0.23012304306030273 244.93374633789062 0.11465980112552643 281.50067138671875 0.5473446846008301 0.80798334 0.11831875145435333 True -8 9252 11.182077169418335 0.23055672645568848 217.8157196044922 0.15023410320281982 281.5737609863281 0.5471743941307068 0.8003554 0.12446872889995575 False -9 10280 11.204003810882568 0.2343888282775879 222.58685302734375 0.09636753797531128 281.2568664550781 0.5480782389640808 0.8049379 0.12185888737440109 False -10 11308 11.19858980178833 0.4884495735168457 262.3584899902344 0.09688218683004379 280.8526916503906 0.5496202707290649 0.81579673 0.11315057426691055 True -11 12336 11.206918478012085 0.23192262649536133 225.74673461914062 0.15764689445495605 280.5477294921875 0.5506857633590698 0.8207045 0.11148788034915924 True -12 13364 11.224026918411255 0.23138880729675293 235.87371826171875 0.060676682740449905 280.5907287597656 0.550495445728302 0.8158439 0.11667323112487793 False -13 14392 11.19320297241211 0.23065853118896484 250.6974334716797 0.10806425660848618 280.30242919921875 0.5514139533042908 0.8262981 0.10939720273017883 True -14 15420 11.184781074523926 0.23865270614624023 225.07855224609375 0.08011306822299957 280.083251953125 0.5517213940620422 0.83167464 0.1063411757349968 True -15 16448 11.206671476364136 0.22878479957580566 235.40493774414062 0.08423636853694916 280.2279968261719 0.5509315133094788 0.8366031 0.10458860546350479 True -16 17476 11.216883659362793 0.2284832000732422 227.45697021484375 0.07175704836845398 280.5910949707031 0.549353837966919 0.83930236 0.101743184030056 True -17 18504 11.21457028388977 0.23726701736450195 224.19357299804688 0.0480559766292572 281.11822509765625 0.5470523834228516 0.84002894 0.10014414042234421 True -18 19532 11.230417728424072 0.5412123203277588 237.29519653320312 0.07272958755493164 281.6961975097656 0.5448848605155945 0.8406472 0.0988551527261734 True -19 20560 11.196114540100098 0.24399089813232422 227.94235229492188 0.04993493854999542 282.1169128417969 0.5432624220848083 0.8397472 0.09865425527095795 False diff --git a/ENCSR490MSG/cherimoya.fold_1.performance.tsv b/ENCSR490MSG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e53c2e9a5bf3134171996bd4f937eee438844415..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -281.6961975097656 0.3445427715778351 0.5448848605155945 0.19164825975894928 0.8406472206115723 0.8467556238174438 0.0988551527261734 \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_2.evaluate.json b/ENCSR490MSG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c317eeff416f39be8a7163d59fb5f6a99e45699b..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745DEQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_2.fit.json b/ENCSR490MSG/cherimoya.fold_2.fit.json deleted file mode 100644 index ea2edbc8723e1a38bae811c7dca7c2c7427da5f6..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF745DEQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_2.log b/ENCSR490MSG/cherimoya.fold_2.log deleted file mode 100644 index 7bf7f34e810e580fc016828a7741d2c03a854706..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1061 16.684556245803833 3.126164197921753 227.09976196289062 0.10867898166179657 346.2391052246094 0.40476688742637634 0.6620384 16.691539764404297 True -1 2122 11.789354801177979 0.29692840576171875 255.40328979492188 0.13051898777484894 293.15594482421875 0.47969889640808105 0.7160413 4.1080708503723145 True -2 3183 11.77833080291748 0.2899606227874756 224.2897491455078 0.10525154322385788 282.3017578125 0.5026626586914062 0.74147296 0.900020956993103 True -3 4244 11.782603025436401 1.1245384216308594 219.07073974609375 0.08805489540100098 275.0805358886719 0.517527163028717 0.77783126 0.24533645808696747 True -4 5305 11.780376672744751 0.21574163436889648 236.81759643554688 0.18964385986328125 270.7080078125 0.5248924493789673 0.79784036 0.1638963222503662 True -5 6366 11.766183614730835 0.22912192344665527 225.74923706054688 0.057105474174022675 270.03253173828125 0.5259670615196228 0.796729 0.14698728919029236 False -6 7427 11.763596296310425 0.21696686744689941 225.8437042236328 0.08058969676494598 269.71405029296875 0.5268110036849976 0.8024302 0.12516365945339203 True -7 8488 11.785602569580078 0.21308374404907227 222.3682098388672 0.12066823989152908 268.9152526855469 0.5290266275405884 0.80982625 0.11424486339092255 True -8 9549 11.79549789428711 0.21593499183654785 232.62432861328125 0.12417463958263397 268.480224609375 0.5302644371986389 0.8168394 0.11231925338506699 True -9 10610 11.776513814926147 0.21762895584106445 243.79379272460938 0.0967678427696228 268.2474060058594 0.5311904549598694 0.8210833 0.11104898899793625 True -10 11671 11.781040906906128 0.21134185791015625 223.9720458984375 0.0941002368927002 267.9764709472656 0.5320427417755127 0.82474583 0.10940419137477875 True -11 12732 11.794985055923462 0.2576785087585449 222.21026611328125 0.07692459225654602 267.82843017578125 0.5326719880104065 0.8258266 0.10719875991344452 True -12 13793 11.776910543441772 0.22040796279907227 221.46969604492188 0.06804907321929932 267.6138000488281 0.533306896686554 0.8290498 0.1048675924539566 True -13 14854 11.761132717132568 0.21227359771728516 219.71861267089844 0.06652834266424179 267.5194396972656 0.533804178237915 0.8325286 0.10332086682319641 True -14 15915 11.78430461883545 0.21610307693481445 249.19744873046875 0.08421361446380615 267.5171203613281 0.5336588621139526 0.83419347 0.10131280869245529 True -15 16976 11.762420654296875 0.21560263633728027 219.6730499267578 0.05290665104985237 267.7275695800781 0.5328502655029297 0.83604217 0.1001083105802536 True -16 18037 11.777859210968018 0.27354955673217773 228.41607666015625 0.0859140008687973 268.1236267089844 0.5313480496406555 0.83548796 0.10000602900981903 False -17 19098 11.795764207839966 0.21174883842468262 221.10618591308594 0.06538090109825134 268.658935546875 0.5292575359344482 0.83412284 0.10154685378074646 False -18 20159 11.798741817474365 0.21198391914367676 239.61691284179688 0.05200408399105072 269.1733703613281 0.5273668766021729 0.8328736 0.10284172743558884 False -19 21220 11.796703815460205 0.21203303337097168 250.33383178710938 0.042219750583171844 269.52691650390625 0.5260094404220581 0.83114266 0.10387323796749115 False diff --git a/ENCSR490MSG/cherimoya.fold_2.performance.tsv b/ENCSR490MSG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8b2af86ec680db33305474865cca5b25b52ce919..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -267.7275695800781 0.3556062877178192 0.5328502058982849 0.18388381600379944 0.8360421657562256 0.8305866122245789 0.1001083105802536 \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_3.evaluate.json b/ENCSR490MSG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4b3945a2ae9a355d40d80de0caa390411d0ea7b5..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745DEQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_3.fit.json b/ENCSR490MSG/cherimoya.fold_3.fit.json deleted file mode 100644 index acba12c852c2879589740cd5f8a6412cbd202362..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF745DEQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_3.log b/ENCSR490MSG/cherimoya.fold_3.log deleted file mode 100644 index 90e6ebb5da3d126cb9ff7e9a51512d91d09f30cd..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1037 15.918944597244263 3.0768909454345703 224.388671875 0.17634257674217224 344.38250732421875 0.4013727605342865 0.69541496 16.831632614135742 True -1 2074 11.502202987670898 0.28089451789855957 234.40338134765625 0.15337151288986206 291.544921875 0.47680288553237915 0.7407395 4.470894813537598 True -2 3111 11.523377418518066 0.21311688423156738 230.886962890625 0.10811696201562881 279.2077941894531 0.5023539662361145 0.7711922 0.8746917247772217 True -3 4148 11.494584798812866 0.2509884834289551 230.86087036132812 0.0771913230419159 271.7088928222656 0.517530620098114 0.79322964 0.2926661968231201 True -4 5185 11.519957065582275 0.21876096725463867 222.99623107910156 0.09841778874397278 268.77874755859375 0.523260235786438 0.8031608 0.18179725110530853 True -5 6222 11.513323068618774 0.20921659469604492 232.34715270996094 0.12445542216300964 268.0623474121094 0.5239191055297852 0.80515766 0.14721238613128662 True -6 7259 11.513927459716797 0.20351672172546387 240.6874542236328 0.0808442160487175 267.10675048828125 0.5262414813041687 0.81501865 0.1316177099943161 True -7 8296 11.512679815292358 0.20762324333190918 225.07510375976562 0.0826631709933281 266.8444519042969 0.5273370742797852 0.81892556 0.12723541259765625 True -8 9333 11.514995574951172 0.6329851150512695 241.6630859375 0.13150238990783691 266.386962890625 0.5288403630256653 0.82289606 0.1254909485578537 True -9 10370 11.521984815597534 0.20211553573608398 239.28900146484375 0.07708615064620972 266.20330810546875 0.529442548751831 0.8260866 0.1176658347249031 True -10 11407 11.522632360458374 0.22137928009033203 253.2981719970703 0.11552451550960541 265.9471130371094 0.5302708148956299 0.8296532 0.11406783014535904 True -11 12444 11.528275728225708 0.2255997657775879 247.8291015625 0.11604824662208557 265.8323059082031 0.5306931138038635 0.8318636 0.1132112443447113 True -12 13481 11.533596277236938 0.21089887619018555 230.42481994628906 0.16477343440055847 265.65765380859375 0.5311849117279053 0.8336632 0.11166726052761078 True -13 14518 11.533275365829468 0.22356319427490234 229.51763916015625 0.09104755520820618 265.5650329589844 0.5312955975532532 0.8359598 0.11064816266298294 True -14 15555 11.546087741851807 0.22234559059143066 224.3297882080078 0.049588073045015335 265.4671630859375 0.531475841999054 0.8361483 0.11203416436910629 True -15 16592 11.494353294372559 0.20465612411499023 231.32484436035156 0.09725865721702576 265.67242431640625 0.5306180715560913 0.8371943 0.11200884729623795 True -16 17629 11.49932336807251 0.20729303359985352 234.68051147460938 0.08950667083263397 266.0143127441406 0.5291396379470825 0.8375551 0.11298606544733047 True -17 18666 11.507184743881226 1.1003730297088623 230.37149047851562 0.04586642608046532 266.58770751953125 0.5271463990211487 0.8368567 0.11438237130641937 False -18 19703 11.555281162261963 0.21746253967285156 239.06463623046875 0.051318176090717316 267.1324462890625 0.5251637101173401 0.8333388 0.11712660640478134 False -19 20740 11.54463791847229 0.2176511287689209 224.50729370117188 0.06848910450935364 267.48199462890625 0.5238754749298096 0.8323256 0.11844673752784729 False diff --git a/ENCSR490MSG/cherimoya.fold_3.performance.tsv b/ENCSR490MSG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2c64acb70d8020e7236ddd7b5f0470d452b7e8ff..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -266.0143127441406 0.35650017857551575 0.5291396379470825 0.18085014820098877 0.8375551104545593 0.8345420956611633 0.11298606544733047 \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_4.evaluate.json b/ENCSR490MSG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7a5da4a1a34474c70d5084d33486802a3b91eb7b..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745DEQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_4.fit.json b/ENCSR490MSG/cherimoya.fold_4.fit.json deleted file mode 100644 index cee5c8778e5045cef68751708f16aeab07c8b985..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF745DEQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR490MSG/cherimoya.fold_4.log b/ENCSR490MSG/cherimoya.fold_4.log deleted file mode 100644 index 71aa3d4a8049ec6cfb83bf829038525139d8c5df..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1012 15.9336256980896 3.281031608581543 243.8087158203125 0.14924857020378113 338.96197509765625 0.3992774784564972 0.71457493 17.090654373168945 True -1 2024 11.258800745010376 0.2751655578613281 254.84002685546875 0.16407018899917603 287.0936279296875 0.4726509749889374 0.76044846 4.8249006271362305 True -2 3036 11.256161451339722 0.2176647186279297 232.062744140625 0.16821062564849854 275.8274230957031 0.4969743490219116 0.7883182 1.1379793882369995 True -3 4048 11.291293621063232 0.21261286735534668 234.76318359375 0.09880747646093369 269.21270751953125 0.5113955736160278 0.81636095 0.27740785479545593 True -4 5060 11.250686883926392 0.21006298065185547 226.294189453125 0.12448351830244064 266.1463623046875 0.5170023441314697 0.8361237 0.14307472109794617 True -5 6072 11.2299964427948 0.2092761993408203 241.84776306152344 0.07751952111721039 264.7915344238281 0.5200401544570923 0.84402645 0.10842705518007278 True -6 7084 11.228941440582275 0.20551252365112305 232.0531005859375 0.11073251813650131 264.1919250488281 0.521561861038208 0.8486259 0.09740329533815384 True -7 8096 11.247007131576538 0.20519089698791504 235.72740173339844 0.12479618191719055 263.8379821777344 0.5230241417884827 0.8550537 0.09126170724630356 True -8 9108 11.266516208648682 0.20571112632751465 253.73831176757812 0.06738290935754776 263.5364685058594 0.5241439342498779 0.85885936 0.08743276447057724 True -9 10120 11.24150013923645 0.20607709884643555 242.96820068359375 0.13672277331352234 263.332763671875 0.5248916745185852 0.8625119 0.08779963850975037 True -10 11132 11.26233434677124 0.20613384246826172 221.33946228027344 0.07750074565410614 262.9813232421875 0.5258990526199341 0.8638141 0.08526376634836197 True -11 12144 11.244047403335571 0.2076127529144287 226.25038146972656 0.0943983644247055 262.80560302734375 0.5267227292060852 0.8665211 0.08263812959194183 True -12 13156 11.296579122543335 0.21388769149780273 242.17886352539062 0.09683803468942642 262.5618896484375 0.5273216962814331 0.86874676 0.08054450154304504 True -13 14168 11.251914739608765 0.207352876663208 222.32875061035156 0.06314218044281006 262.4580993652344 0.5276275873184204 0.8724124 0.07905080914497375 True -14 15180 11.24042272567749 0.20896291732788086 225.48141479492188 0.11103555560112 262.45831298828125 0.5274454951286316 0.87266845 0.07870698720216751 True -15 16192 11.26233434677124 0.21707653999328613 223.4787139892578 0.05662080645561218 262.6875305175781 0.5263476371765137 0.8715846 0.07822690904140472 False -16 17204 11.253700733184814 1.1833157539367676 220.7956085205078 0.06404900550842285 263.1706848144531 0.5245857834815979 0.87215555 0.07942477613687515 False -17 18216 11.235781908035278 0.2105238437652588 220.34857177734375 0.08546283096075058 263.7176818847656 0.5226150751113892 0.87130105 0.08143208920955658 False -18 19228 11.240996837615967 0.20337247848510742 204.76710510253906 0.07678291946649551 264.2176513671875 0.5205422043800354 0.86834586 0.0826556608080864 False -19 20240 11.235145807266235 4.645823001861572 214.12506103515625 0.04174612835049629 264.5939636230469 0.5192248821258545 0.8681037 0.0833471417427063 False diff --git a/ENCSR490MSG/cherimoya.fold_4.performance.tsv b/ENCSR490MSG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 253131fde47f19a8552a4d9eaf41bac78d9c2ac6..0000000000000000000000000000000000000000 --- a/ENCSR490MSG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -262.45831298828125 0.35960066318511963 0.5274454951286316 0.1775292307138443 0.872668445110321 0.860149085521698 0.07870698720216751 \ No newline at end of file diff --git a/ENCSR490UQP/cherimoya.fold_0.performance.tsv b/ENCSR490UQP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6ddd9bf14cc9e7d9bb28e8c922c85bd002256dee..0000000000000000000000000000000000000000 --- a/ENCSR490UQP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -243.5817413330078 0.5021917223930359 0.2778337597846985 0.07243221253156662 0.8755995035171509 0.8584108352661133 0.1185879334807396 \ No newline at end of file diff --git a/ENCSR490UQP/cherimoya.fold_1.performance.tsv b/ENCSR490UQP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2b8b8cf2b821e551c41cd500e4afa72ffaedf952..0000000000000000000000000000000000000000 --- a/ENCSR490UQP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.29345703125 0.4877052903175354 0.29541435837745667 0.07854640483856201 0.8848580121994019 0.8798977732658386 0.13140249252319336 \ No newline at end of file diff --git a/ENCSR490UQP/cherimoya.fold_3.evaluate.json b/ENCSR490UQP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9749c0872ab0f90eaa09d7d6c4948106449a633d..0000000000000000000000000000000000000000 --- a/ENCSR490UQP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF173QGO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR490UQP/cherimoya.fold_4.evaluate.json b/ENCSR490UQP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 63cb6f2e75d211e3aa1aad2878590a98934d0f5d..0000000000000000000000000000000000000000 --- a/ENCSR490UQP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF173QGO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_0.evaluate.json b/ENCSR491VKV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 35e453f15766be7392ae217774c5b15815217a9d..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330SGH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_0.fit.json b/ENCSR491VKV/cherimoya.fold_0.fit.json deleted file mode 100644 index fda465a540189c5ed2c9e4459f83d63ec88b84b8..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF330SGH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_0.log b/ENCSR491VKV/cherimoya.fold_0.log deleted file mode 100644 index 32977840d82413930e3ae0f30d16fe06c4a4ea28..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3081 37.69054675102234 10.316571474075317 642.7581787109375 0.27079737186431885 814.8025512695312 0.7276980876922607 0.6962869 4.558915138244629 True -1 6162 34.059285402297974 0.6436645984649658 580.889892578125 0.44442594051361084 715.8978271484375 0.7838874459266663 0.7455667 0.7480396032333374 True -2 9243 34.14266085624695 1.5923714637756348 595.2015380859375 0.2774463891983032 696.0046997070312 0.7938822507858276 0.75903803 0.2920968234539032 True -3 12324 34.40047574043274 0.6162192821502686 656.8591918945312 0.2784780263900757 690.3583374023438 0.7968102097511292 0.760874 0.24319829046726227 True -4 15405 33.97909116744995 0.6296262741088867 629.6709594726562 0.2949579358100891 687.324951171875 0.7994253635406494 0.7617756 0.250898152589798 True -5 18486 33.96038889884949 0.6614017486572266 581.3946533203125 0.2858709990978241 685.2007446289062 0.8016802072525024 0.76559013 0.2766391932964325 True -6 21567 34.49787616729736 14.235320568084717 621.7576904296875 0.34534457325935364 682.2974243164062 0.8030057549476624 0.76713806 0.2509373724460602 True -7 24648 34.07818341255188 0.6162552833557129 596.166015625 0.226556658744812 679.331298828125 0.8048497438430786 0.7730855 0.2312452793121338 True -8 27729 34.01160979270935 0.6315393447875977 551.5217895507812 0.37218230962753296 676.5968017578125 0.8067545294761658 0.77864707 0.23319131135940552 True -9 30810 33.74468231201172 0.6242866516113281 616.0606689453125 0.32994920015335083 674.02392578125 0.8082054853439331 0.7800454 0.21839435398578644 True -10 33891 33.3072247505188 0.6191678047180176 640.195556640625 0.3834347724914551 672.2263793945312 0.8092796206474304 0.78284687 0.2109532356262207 True -11 36972 33.319823026657104 0.6081886291503906 584.467529296875 0.258786141872406 669.9733276367188 0.8107827305793762 0.78399086 0.20906491577625275 True -12 40053 33.3781840801239 0.6182839870452881 613.6276245117188 0.20250076055526733 667.3271484375 0.81342613697052 0.7922118 0.20326592028141022 True -13 43134 33.38565182685852 2.621354103088379 518.2633056640625 0.6250929236412048 665.2490234375 0.814641535282135 0.79593045 0.19723933935165405 True -14 46215 33.44604229927063 1.4108123779296875 621.4043579101562 0.31374120712280273 662.978759765625 0.8164294958114624 0.80419785 0.18711838126182556 True -15 49296 33.50004482269287 0.6246387958526611 572.131103515625 0.18150681257247925 661.602783203125 0.8177440166473389 0.8087413 0.18481691181659698 True -16 52377 33.333184242248535 15.657337188720703 616.9095458984375 0.25307273864746094 660.9360961914062 0.8182839155197144 0.81246597 0.18182013928890228 True -17 55458 33.34642767906189 0.629798173904419 588.306396484375 0.1693696677684784 660.8070068359375 0.8184476494789124 0.81265914 0.18252219259738922 True -18 58539 33.397382497787476 15.1589937210083 548.8377685546875 0.14654777944087982 660.9413452148438 0.8183634877204895 0.81152135 0.1854972243309021 False -19 61620 33.43529963493347 0.617440938949585 558.4498901367188 0.12629394233226776 661.3660888671875 0.8181372284889221 0.8100528 0.1876489371061325 False diff --git a/ENCSR491VKV/cherimoya.fold_0.performance.tsv b/ENCSR491VKV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b40a5494bd2284bf2e11b3879d6173c96fc525f0..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -660.8070068359375 0.14620190858840942 0.8184476494789124 0.46977710723876953 0.8126591444015503 0.7355254292488098 0.18252219259738922 \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_1.evaluate.json b/ENCSR491VKV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bfadef2da70c34a537cd1f956bab2ed3c4dbe56a..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330SGH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_1.fit.json b/ENCSR491VKV/cherimoya.fold_1.fit.json deleted file mode 100644 index e2b95fe67570b2fb6aca6c965d0b0ae759cfa5c7..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF330SGH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_1.log b/ENCSR491VKV/cherimoya.fold_1.log deleted file mode 100644 index 19858d0d3a8ea5adcd94929e4a1370aea4c16fc8..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3048 37.36608099937439 3.812925338745117 479.7248840332031 0.5508130788803101 932.0439453125 0.7289195656776428 0.6914926 4.567662715911865 True -1 6096 33.65677523612976 2.0230228900909424 599.9439697265625 0.6999205350875854 802.9019775390625 0.7905426621437073 0.7469591 0.8617466688156128 True -2 9144 33.639410734176636 0.7823958396911621 687.06884765625 0.271247923374176 778.32421875 0.8025634288787842 0.76303786 0.4395473897457123 True -3 12192 33.68088102340698 0.7903220653533936 653.91943359375 0.3337981700897217 770.1468505859375 0.8069170713424683 0.7718758 0.39768320322036743 True -4 15240 33.64208459854126 0.7862679958343506 582.5888671875 0.19230550527572632 765.9320678710938 0.8095282316207886 0.7720608 0.3836749792098999 True -5 18288 33.64660573005676 0.83487868309021 615.542724609375 0.2994026839733124 760.549072265625 0.8116034865379333 0.78134644 0.3240728974342346 True -6 21336 33.69030737876892 0.7956483364105225 596.50390625 0.5874302387237549 756.4862060546875 0.8137566447257996 0.7827717 0.32687410712242126 True -7 24384 33.74643039703369 0.8111047744750977 606.142578125 0.2242491990327835 752.0133666992188 0.8161422610282898 0.78877056 0.28343895077705383 True -8 27432 33.174060583114624 0.7800467014312744 545.6295166015625 0.1698899269104004 749.0487670898438 0.8172773122787476 0.7911564 0.27333328127861023 True -9 30480 32.98711061477661 0.7775883674621582 630.9144287109375 0.32262861728668213 744.7943115234375 0.8196942210197449 0.7957052 0.24718253314495087 True -10 33528 33.00252985954285 0.7757253646850586 599.337646484375 0.22304973006248474 741.4168701171875 0.8213122487068176 0.8024826 0.23814934492111206 True -11 36576 32.948280572891235 0.7718267440795898 592.3568115234375 0.19401660561561584 737.915283203125 0.8232876062393188 0.80811024 0.23463228344917297 True -12 39624 32.93969917297363 0.7741618156433105 624.4446411132812 0.31617528200149536 734.90478515625 0.8249897360801697 0.81280476 0.22643984854221344 True -13 42672 32.976425886154175 0.7834188938140869 554.4300537109375 0.24068278074264526 731.9771728515625 0.8268640637397766 0.82438207 0.2169247716665268 True -14 45720 33.27538537979126 11.546776056289673 589.591064453125 0.19778215885162354 729.9454956054688 0.8283851146697998 0.8288897 0.2096877545118332 True -15 48768 32.96446132659912 0.7811441421508789 589.10400390625 0.1192600354552269 727.7782592773438 0.8295950293540955 0.835375 0.20164397358894348 True -16 51816 33.29385447502136 0.7841601371765137 532.83203125 0.15303213894367218 727.1611938476562 0.8301215171813965 0.8388574 0.19904670119285583 True -17 54864 33.00208353996277 2.1868231296539307 623.7501831054688 0.14370808005332947 727.04443359375 0.8302839398384094 0.838708 0.19956333935260773 False -18 57912 33.05822491645813 0.7906239032745361 556.3731079101562 0.18264085054397583 727.6575927734375 0.8299323916435242 0.83555794 0.20230522751808167 False -19 60960 33.30699419975281 24.12088179588318 576.49560546875 0.21501424908638 727.9437866210938 0.8297263979911804 0.83510983 0.20483528077602386 False diff --git a/ENCSR491VKV/cherimoya.fold_1.performance.tsv b/ENCSR491VKV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 172b31c6385291e31ebcf36ed0ab305f5a76df1f..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -727.1611938476562 0.13579851388931274 0.8301215171813965 0.49956199526786804 0.8388574123382568 0.7890331149101257 0.19904670119285583 \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_2.evaluate.json b/ENCSR491VKV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8bd6d4a5427c6fa90f53913c68285b11b28991af..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330SGH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_2.fit.json b/ENCSR491VKV/cherimoya.fold_2.fit.json deleted file mode 100644 index 5fd667de3059738218897363b8d7c81f32f857a6..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF330SGH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_2.log b/ENCSR491VKV/cherimoya.fold_2.log deleted file mode 100644 index 4a53e4e19aa72857916792f4fbb0a97e656c9a2b..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3233 39.94959616661072 4.277800559997559 678.3546142578125 0.36119189858436584 834.6268310546875 0.7340818643569946 0.6733518 4.062724590301514 True -1 6466 35.71572208404541 0.6586019992828369 583.8214721679688 0.881484866142273 731.082763671875 0.7882519960403442 0.7378746 0.6606308817863464 True -2 9699 35.68773007392883 0.640721321105957 614.1082763671875 0.414630651473999 716.0322875976562 0.7953373789787292 0.74751824 0.3209317624568939 True -3 12932 35.8214430809021 0.6370084285736084 631.4761352539062 0.1651516556739807 708.9213256835938 0.7987704277038574 0.75784576 0.2518259882926941 True -4 16165 35.68915104866028 0.6377179622650146 580.1455078125 0.3236355781555176 705.4525146484375 0.8008722066879272 0.76421297 0.24156291782855988 True -5 19398 35.698933362960815 0.6372718811035156 618.1810913085938 0.21017295122146606 702.8641357421875 0.8021469116210938 0.768067 0.2255009561777115 True -6 22631 35.66813588142395 2.2965216636657715 620.20849609375 0.27570146322250366 700.3035888671875 0.8035951256752014 0.76961434 0.22511272132396698 True -7 25864 35.1546266078949 0.6334996223449707 570.9061889648438 0.32384610176086426 697.7623291015625 0.8052257299423218 0.77087575 0.2215951681137085 True -8 29097 35.027519941329956 2.555370330810547 525.985595703125 0.7371586561203003 694.552734375 0.8075776696205139 0.77682024 0.21683619916439056 True -9 32330 35.03785681724548 0.639887809753418 640.09912109375 0.38926050066947937 691.3414306640625 0.8097692728042603 0.78332293 0.21218672394752502 True -10 35563 35.03276515007019 0.6318938732147217 530.7504272460938 0.274299681186676 688.840576171875 0.8118953704833984 0.7895475 0.21761749684810638 True -11 38796 34.94423818588257 0.6345574855804443 594.1019897460938 0.3341633677482605 686.3756713867188 0.8133047223091125 0.7938414 0.20712265372276306 True -12 42029 35.03132176399231 0.6359083652496338 628.186279296875 0.1340928077697754 683.988037109375 0.8147592544555664 0.79929346 0.20514333248138428 True -13 45262 35.48245668411255 0.6376090049743652 596.1290283203125 0.18554159998893738 681.5781860351562 0.8165439963340759 0.80438185 0.20154312252998352 True -14 48495 35.02969312667847 0.6388442516326904 577.632568359375 0.20347066223621368 679.86767578125 0.8184428215026855 0.8086336 0.2013094127178192 True -15 51728 35.046125411987305 0.6341714859008789 577.598388671875 0.1600082814693451 678.6089477539062 0.8193433880805969 0.8118993 0.19496995210647583 True -16 54961 35.04047966003418 0.6355211734771729 529.3555908203125 0.23963990807533264 677.6892700195312 0.8201648592948914 0.8161555 0.1943942904472351 True -17 58194 34.987009048461914 0.6277759075164795 573.1620483398438 0.14079833030700684 677.8915405273438 0.8199846148490906 0.8157228 0.19420990347862244 False -18 61427 35.02623653411865 0.633758544921875 604.0482177734375 0.24785487353801727 678.3279418945312 0.8198184967041016 0.81333375 0.19851645827293396 False -19 64660 35.03039813041687 0.6392812728881836 591.6664428710938 0.21564851701259613 678.719970703125 0.8194946050643921 0.8128442 0.19979237020015717 False diff --git a/ENCSR491VKV/cherimoya.fold_2.performance.tsv b/ENCSR491VKV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0871b16f478e42891e00547742f35822f0fffe8b..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -677.6892700195312 0.14396536350250244 0.8201647996902466 0.47814854979515076 0.8161554932594299 0.7424432635307312 0.1943942904472351 \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_3.evaluate.json b/ENCSR491VKV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bdd8595b846e5a7f8a2917d8922ca4217e183e9e..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330SGH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_3.fit.json b/ENCSR491VKV/cherimoya.fold_3.fit.json deleted file mode 100644 index 44e0aab9ff3ad359f210d5f91bdcc7cb9dcd6593..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF330SGH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_3.log b/ENCSR491VKV/cherimoya.fold_3.log deleted file mode 100644 index 3bf722bd5f03f2549c4f58eaabb616c724d41f0d..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3110 38.59580850601196 3.6664512157440186 578.3960571289062 0.26307225227355957 817.5201416015625 0.7262216210365295 0.66921943 4.689343452453613 True -1 6220 34.24692940711975 0.6321711540222168 605.717041015625 0.2091449499130249 713.4443359375 0.7823312878608704 0.7350941 0.8210465312004089 True -2 9330 34.28522729873657 0.6275715827941895 650.882568359375 0.33292150497436523 695.693359375 0.7928665280342102 0.74022365 0.37992432713508606 True -3 12440 34.35124588012695 0.6147952079772949 629.6799926757812 0.2546963095664978 691.0258178710938 0.796242356300354 0.73729503 0.3241633176803589 False -4 15550 34.349087953567505 0.6052122116088867 649.7561645507812 0.2956879436969757 687.7526245117188 0.7980473041534424 0.7431668 0.32799163460731506 True -5 18660 34.185553789138794 0.6122901439666748 620.893310546875 0.2378145158290863 685.712646484375 0.7987465858459473 0.7425339 0.27878567576408386 False -6 21770 33.8150475025177 0.6157634258270264 694.9081420898438 0.7680015563964844 682.6366577148438 0.8006271719932556 0.7489015 0.25945335626602173 True -7 24880 33.73992943763733 0.6022326946258545 610.1431884765625 0.3071649670600891 679.6265869140625 0.8032673597335815 0.7500428 0.2526648938655853 True -8 27990 33.64172863960266 0.6038992404937744 606.02880859375 0.36221933364868164 677.4513549804688 0.8047601580619812 0.75825083 0.2427198439836502 True -9 31100 33.710357427597046 0.6119740009307861 587.91357421875 0.30633026361465454 675.069580078125 0.8066758513450623 0.76694447 0.24146024882793427 True -10 34210 33.68455243110657 0.6056158542633057 615.3134155273438 0.3790982961654663 672.3629150390625 0.808426558971405 0.7754127 0.2340184599161148 True -11 37320 33.601675033569336 0.6036217212677002 612.1465454101562 0.2250465601682663 669.8595581054688 0.8097648024559021 0.77499723 0.23144324123859406 False -12 40430 33.64689064025879 27.863951921463013 596.4620971679688 0.16269555687904358 667.7969970703125 0.8117740154266357 0.78457844 0.2339201271533966 True -13 43540 33.69965195655823 0.6167733669281006 608.7568359375 0.24838514626026154 665.0344848632812 0.8137099742889404 0.79219735 0.22345773875713348 True -14 46650 33.626864194869995 0.6033413410186768 558.725830078125 0.652320146560669 662.5036010742188 0.8152199387550354 0.7964802 0.21597333252429962 True -15 49760 33.64695119857788 0.604642391204834 566.13037109375 0.16865134239196777 661.0755004882812 0.8165016174316406 0.80400777 0.21099945902824402 True -16 52870 33.627436876297 0.6023635864257812 567.1351318359375 0.20021308958530426 659.7340698242188 0.8171980381011963 0.80680203 0.20777510106563568 True -17 55980 33.77138090133667 0.61397385597229 522.4508056640625 0.6921819448471069 659.748291015625 0.8172427415847778 0.8027559 0.21297067403793335 False -18 59090 33.61140775680542 0.6141607761383057 597.2427978515625 0.1920624077320099 660.27587890625 0.8169441819190979 0.79800034 0.22012992203235626 False -19 62200 33.60410118103027 0.6035099029541016 550.7926025390625 0.4506761431694031 660.3429565429688 0.8167101144790649 0.7953441 0.22341510653495789 False diff --git a/ENCSR491VKV/cherimoya.fold_3.performance.tsv b/ENCSR491VKV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e657c5b39049ea21a87d5632f33575c9c997c771..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -659.7340698242188 0.14797230064868927 0.8171980381011963 0.46295803785324097 0.8068020343780518 0.7192538976669312 0.20777510106563568 \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_4.evaluate.json b/ENCSR491VKV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 73c08f2326abcd00b1803b3f62bdad2198d5142d..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330SGH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_4.fit.json b/ENCSR491VKV/cherimoya.fold_4.fit.json deleted file mode 100644 index e48abeaf1c38d1a10d4ae2d563e3c00c712072fc..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF330SGH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR491VKV/cherimoya.fold_4.log b/ENCSR491VKV/cherimoya.fold_4.log deleted file mode 100644 index dd83b4a5cd4579d93e7e11c31003f1ecbf79ddad..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3203 43.056299924850464 3.5995922088623047 604.2847900390625 0.4021669626235962 790.1437377929688 0.7332263588905334 0.65274394 3.9573447704315186 True -1 6406 35.41236758232117 0.662714958190918 608.8232421875 0.4383057653903961 698.3521118164062 0.7863442301750183 0.72442293 0.668271541595459 True -2 9609 35.45860767364502 0.6683218479156494 590.3150634765625 0.5271544456481934 687.7947998046875 0.793444037437439 0.72712463 0.3235549032688141 True -3 12812 35.50244903564453 0.6589181423187256 643.284423828125 0.36916476488113403 682.3338012695312 0.7966806888580322 0.7336215 0.32766276597976685 True -4 16015 35.10711097717285 1.216181993484497 617.016357421875 0.4406399130821228 679.3203125 0.7985785007476807 0.7419697 0.28105437755584717 True -5 19218 34.67184257507324 0.6373679637908936 620.9859619140625 0.18326273560523987 675.3768310546875 0.8005138039588928 0.74959844 0.26477620005607605 True -6 22421 34.71344304084778 0.6965818405151367 626.4871215820312 0.25271907448768616 672.92041015625 0.8018147349357605 0.74975824 0.23671136796474457 True -7 25624 34.70684576034546 0.6638998985290527 656.4365234375 0.5139468908309937 670.3689575195312 0.8038029074668884 0.7595157 0.2310199737548828 True -8 28827 34.84486746788025 0.6411571502685547 574.893310546875 0.24103376269340515 667.7489013671875 0.8049224019050598 0.7624701 0.21466712653636932 True -9 32030 34.70156145095825 1.7780067920684814 597.2277221679688 0.13153505325317383 664.827392578125 0.806893527507782 0.76565814 0.21052286028862 True -10 35233 34.74636936187744 0.6461899280548096 640.5721435546875 0.23177999258041382 663.0421142578125 0.8084311485290527 0.77076167 0.2110707312822342 True -11 38436 34.70132517814636 0.6392199993133545 575.6456298828125 0.2099095582962036 660.6001586914062 0.8101979494094849 0.7760857 0.21118906140327454 True -12 41639 34.76561951637268 0.6357917785644531 586.45947265625 0.3577095568180084 657.6215209960938 0.812004804611206 0.7836754 0.2000776082277298 True -13 44842 34.70843529701233 0.6331167221069336 572.405029296875 0.22544685006141663 655.2271728515625 0.8138296604156494 0.7924818 0.18977369368076324 True -14 48045 34.86325263977051 0.6337392330169678 572.1536865234375 0.14040127396583557 653.2722778320312 0.8153717517852783 0.8009755 0.1848784238100052 True -15 51248 35.57084107398987 31.23129439353943 587.012451171875 0.16118070483207703 652.5415649414062 0.8163116574287415 0.8037723 0.1827285885810852 True -16 54451 35.005568504333496 1.5516858100891113 567.7272338867188 0.1886405050754547 651.8544311523438 0.8170669078826904 0.80657226 0.1819482296705246 True -17 57654 34.70780324935913 0.6452145576477051 609.8404541015625 0.16925197839736938 651.5255126953125 0.8171582818031311 0.80511636 0.185456320643425 False -18 60857 34.67209005355835 0.6427326202392578 585.9613037109375 0.6058168411254883 652.2235107421875 0.8168998956680298 0.8005394 0.19258147478103638 False -19 64060 34.625383615493774 0.6350429058074951 593.1011962890625 0.139743834733963 652.2520141601562 0.8167527318000793 0.8002127 0.19374841451644897 False diff --git a/ENCSR491VKV/cherimoya.fold_4.performance.tsv b/ENCSR491VKV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5ae153478451bf9f25d4cdf12ce45c342584ef30..0000000000000000000000000000000000000000 --- a/ENCSR491VKV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -651.8544311523438 0.14749811589717865 0.8170669674873352 0.46556663513183594 0.8065722584724426 0.7127880454063416 0.1819482296705246 \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_0.evaluate.json b/ENCSR493IAY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index aa634f0c32a1a99db828f22362ba097d72a32551..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF951TDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_0.fit.json b/ENCSR493IAY/cherimoya.fold_0.fit.json deleted file mode 100644 index d2b27f16260377133b5624a23f0417eee2e9b711..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF951TDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_0.log b/ENCSR493IAY/cherimoya.fold_0.log deleted file mode 100644 index 09ec8cafd791d5a13d0806c9dfa8957abbe0838f..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1424 19.39380431175232 3.4600629806518555 1063.29736328125 1.472914457321167 1956.8974609375 0.16763798892498016 0.52358717 28.1519832611084 True -1 2848 15.765697240829468 0.284618616104126 1048.3515625 1.0399794578552246 1735.8182373046875 0.2710208594799042 0.6112792 13.570756912231445 True -2 4272 16.013089179992676 0.26897239685058594 912.278564453125 1.5376269817352295 1476.4005126953125 0.3767224848270416 0.568871 7.294800281524658 False -3 5696 15.702492952346802 0.2827882766723633 863.0301513671875 1.2107882499694824 1339.4351806640625 0.4165325462818146 0.5729962 4.1128458976745605 False -4 7120 15.698812484741211 0.3016676902770996 837.0535888671875 1.1338367462158203 1269.885986328125 0.43498003482818604 0.60205096 3.3697307109832764 False -5 8544 15.683494567871094 0.8089766502380371 1119.77978515625 1.3708025217056274 1221.989501953125 0.4480612576007843 0.6242439 2.698967456817627 True -6 9968 15.700401782989502 0.28211140632629395 1116.77978515625 1.4205060005187988 1208.7568359375 0.45317986607551575 0.6344911 2.2119405269622803 True -7 11392 15.740355730056763 5.37079119682312 1142.3037109375 0.7845767736434937 1182.108154296875 0.46289384365081787 0.64242417 1.931740641593933 True -8 12816 15.766082525253296 0.2893047332763672 1103.637451171875 1.0138285160064697 1170.6080322265625 0.46510758996009827 0.65407723 1.621509313583374 True -9 14240 15.708381652832031 0.27901387214660645 1039.432373046875 0.8608959317207336 1159.3489990234375 0.46865934133529663 0.6660847 1.372767448425293 True -10 15664 15.71780014038086 0.2760298252105713 1192.888427734375 0.8486477136611938 1153.869140625 0.46903195977211 0.67154384 1.2261782884597778 True -11 17088 15.726296424865723 11.65303373336792 860.971923828125 0.7896105051040649 1139.5712890625 0.47402432560920715 0.68476546 1.0940979719161987 True -12 18512 16.238662242889404 0.3010849952697754 1067.15576171875 0.8704861998558044 1135.139404296875 0.4734637141227722 0.69275856 1.0369383096694946 True -13 19936 15.763303995132446 0.2779407501220703 973.35693359375 0.9642850160598755 1124.6807861328125 0.47798892855644226 0.7025164 0.9783461093902588 True -14 21360 15.751292943954468 0.27549171447753906 892.7301025390625 0.81365966796875 1116.2679443359375 0.48105767369270325 0.7078214 0.9567555785179138 True -15 22784 15.731617212295532 0.2739529609680176 852.5391235351562 0.5395485162734985 1111.9295654296875 0.4819257855415344 0.7156083 0.9254331588745117 True -16 24208 16.062610387802124 11.59840989112854 685.9647216796875 0.7165569067001343 1114.5335693359375 0.4792577922344208 0.7183909 0.9109144806861877 True -17 25632 15.976681470870972 0.2786555290222168 1089.03271484375 0.6060695052146912 1117.652099609375 0.47598183155059814 0.717978 0.9189194440841675 False -18 27056 15.766040802001953 0.2717440128326416 748.6722412109375 0.6580910086631775 1110.3082275390625 0.4811062812805176 0.7157383 0.9357814788818359 False -19 28480 16.02279829978943 4.248629808425903 1082.3819580078125 0.5910504460334778 1118.2593994140625 0.4766411781311035 0.7153551 0.9481180906295776 False diff --git a/ENCSR493IAY/cherimoya.fold_0.performance.tsv b/ENCSR493IAY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d15cfab3193dca3199ee879eb51a737982187235..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1114.5335693359375 0.3153017461299896 0.479257732629776 0.2266272008419037 0.7183908820152283 0.6251939535140991 0.9109144806861877 \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_1.evaluate.json b/ENCSR493IAY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2618e5bf0d27eece4208f7674c0e81e9ff7c5024..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF951TDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_1.fit.json b/ENCSR493IAY/cherimoya.fold_1.fit.json deleted file mode 100644 index 3a8d9e63f41a8c15d7df976be13ab3d1e98b1973..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF951TDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_1.log b/ENCSR493IAY/cherimoya.fold_1.log deleted file mode 100644 index c08bd1215179f8c3dc2cf78e86118eeff7ef934d..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1445 20.19690251350403 18.107388496398926 1596.673095703125 2.3105459213256836 2421.502197265625 0.1808345913887024 0.50638163 31.314481735229492 True -1 2890 15.953143835067749 0.4287681579589844 1012.809814453125 1.6835753917694092 2094.94775390625 0.30191585421562195 0.5613261 14.116414070129395 True -2 4335 15.95763087272644 0.40306973457336426 929.07470703125 0.9975733160972595 1773.769775390625 0.39855509996414185 0.5821692 8.83851432800293 True -3 5780 15.927541017532349 0.41222476959228516 804.0787353515625 1.425071120262146 1611.14306640625 0.43527525663375854 0.61354727 6.098448276519775 True -4 7225 15.942761421203613 0.4038691520690918 1085.9761962890625 1.1166784763336182 1506.581787109375 0.4583337903022766 0.63864857 4.584048271179199 True -5 8670 15.940449237823486 0.3974897861480713 1077.3597412109375 1.5817694664001465 1470.3526611328125 0.46452662348747253 0.6575846 4.31292724609375 True -6 10115 15.943769931793213 0.40570569038391113 1073.1953125 0.9694973230361938 1435.7603759765625 0.47461971640586853 0.6680915 3.158694267272949 True -7 11560 15.974661588668823 0.4095618724822998 839.5283203125 1.1445727348327637 1414.43115234375 0.478758305311203 0.6748008 2.6625843048095703 True -8 13005 15.938100576400757 0.4598524570465088 1135.861083984375 1.1727333068847656 1397.537841796875 0.484085351228714 0.6800161 2.235407590866089 True -9 14450 15.939759731292725 0.41686367988586426 866.1796875 1.6226822137832642 1379.2679443359375 0.4879515767097473 0.69115996 1.806882619857788 True -10 15895 15.966544151306152 0.4079592227935791 984.1152954101562 1.0566885471343994 1368.07958984375 0.49201518297195435 0.69718146 1.646674394607544 True -11 17340 15.963533878326416 0.4098031520843506 944.4725952148438 0.8333522081375122 1349.013916015625 0.4963742792606354 0.71015275 1.4582387208938599 True -12 18785 15.925304889678955 0.411696195602417 837.4120483398438 0.8989523649215698 1337.091064453125 0.4994616210460663 0.7230902 1.2780091762542725 True -13 20230 15.917881488800049 0.40930891036987305 764.877197265625 0.7305243015289307 1325.95556640625 0.5008366703987122 0.7348411 1.1626161336898804 True -14 21675 15.980644941329956 0.40607476234436035 1039.6387939453125 1.0505640506744385 1317.27783203125 0.5033093690872192 0.7408353 1.0689212083816528 True -15 23120 16.003309965133667 21.54554319381714 783.3018798828125 0.6358437538146973 1320.5126953125 0.5013930797576904 0.7470569 1.0186032056808472 True -16 24565 16.19209861755371 0.40926694869995117 764.2689208984375 0.6849783658981323 1311.9400634765625 0.5032950043678284 0.7494647 0.9893811941146851 True -17 26010 16.00186252593994 0.5562684535980225 954.1224365234375 0.6575530767440796 1309.0758056640625 0.5027500987052917 0.7491265 0.9844053983688354 False -18 27455 16.900643825531006 12.104583740234375 849.5427856445312 0.4703391194343567 1318.03564453125 0.49995094537734985 0.748249 0.9895521402359009 False -19 28900 16.001460552215576 0.4178764820098877 798.7137451171875 0.5314055681228638 1320.321044921875 0.49900022149086 0.7446441 0.9942865371704102 False diff --git a/ENCSR493IAY/cherimoya.fold_1.performance.tsv b/ENCSR493IAY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4d9bd6c6163c1fd4a5e46d283205953d710c0a0a..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1311.9400634765625 0.2938820719718933 0.5032950043678284 0.26116079092025757 0.7494646906852722 0.6896454095840454 0.9893811941146851 \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_2.evaluate.json b/ENCSR493IAY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f53d4a2ca67ec70cd3f72c70aaaba5d5b435bffc..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF951TDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_2.fit.json b/ENCSR493IAY/cherimoya.fold_2.fit.json deleted file mode 100644 index 32ef845aa275372ce3b4f1887b720b38f44af313..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF951TDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_2.log b/ENCSR493IAY/cherimoya.fold_2.log deleted file mode 100644 index d2a8036295142025511be39d4c22101c1dd5deaf..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1519 20.86621403694153 3.459587574005127 1174.051513671875 1.8085262775421143 2006.71533203125 0.17471030354499817 0.504762 27.074365615844727 True -1 3038 16.81444239616394 0.3121366500854492 966.69970703125 1.351722002029419 1756.9737548828125 0.30026116967201233 0.5868331 12.685432434082031 True -2 4557 16.83025622367859 0.3045191764831543 905.830078125 1.1269029378890991 1478.75244140625 0.39391881227493286 0.5035444 5.6912970542907715 False -3 6076 16.807612419128418 0.31064867973327637 893.8828125 0.8378933668136597 1359.6817626953125 0.41759979724884033 0.6108337 3.2114486694335938 True -4 7595 16.750720024108887 0.2993502616882324 1102.38818359375 1.9139392375946045 1291.712890625 0.43310919404029846 0.6436366 2.334737539291382 True -5 9114 16.762712478637695 0.31379127502441406 662.9495849609375 0.800145149230957 1250.900146484375 0.44448572397232056 0.65867585 1.8618743419647217 True -6 10633 16.755908966064453 0.2996196746826172 1016.5015869140625 0.7858200073242188 1234.626708984375 0.449680894613266 0.66571206 1.778516173362732 True -7 12152 16.78763747215271 0.3010873794555664 1069.2392578125 1.3049275875091553 1216.6514892578125 0.4564336836338043 0.67395747 1.5710347890853882 True -8 13671 16.763166189193726 0.3025789260864258 1466.9161376953125 1.1271380186080933 1201.301025390625 0.45963066816329956 0.6786363 1.4836989641189575 True -9 15190 16.777653455734253 0.30664777755737305 981.373291015625 1.5900450944900513 1187.9876708984375 0.4655589461326599 0.6821762 1.3785629272460938 True -10 16709 16.770715951919556 0.2959709167480469 773.6002197265625 0.8591458797454834 1178.6644287109375 0.46849584579467773 0.68863714 1.292245864868164 True -11 18228 16.780319452285767 0.30293917655944824 860.2622680664062 1.0086798667907715 1170.2344970703125 0.47089457511901855 0.6951537 1.2025506496429443 True -12 19747 16.782121419906616 0.30112767219543457 1071.1982421875 0.928173303604126 1162.009765625 0.47494685649871826 0.70394945 1.0813864469528198 True -13 21266 16.769007921218872 0.30419015884399414 777.3846435546875 0.6418135762214661 1151.256591796875 0.47728464007377625 0.7117189 1.0299896001815796 True -14 22785 16.72868299484253 0.30205678939819336 855.0841064453125 0.7615885734558105 1145.1552734375 0.4790104031562805 0.72112185 0.9772433638572693 True -15 24304 16.799888610839844 0.30311155319213867 859.9661865234375 0.8034681081771851 1141.1729736328125 0.47951337695121765 0.7281851 0.9367567896842957 True -16 25823 16.79148769378662 0.3104381561279297 678.7415771484375 0.7474930286407471 1140.5015869140625 0.47784873843193054 0.7326266 0.9109923243522644 True -17 27342 16.76612114906311 0.3032650947570801 931.0526123046875 0.5211893320083618 1144.8609619140625 0.47784316539764404 0.73460597 0.9079071283340454 True -18 28861 16.744006872177124 0.30376720428466797 954.1202392578125 0.7260101437568665 1144.2916259765625 0.4779234230518341 0.73338485 0.9166754484176636 False -19 30380 16.818084955215454 0.30933332443237305 748.58740234375 0.7397298216819763 1145.811767578125 0.47857245802879333 0.73047185 0.9245314002037048 False diff --git a/ENCSR493IAY/cherimoya.fold_2.performance.tsv b/ENCSR493IAY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2609f53935f46642cbf308dd38b01a832e78bf88..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1144.8609619140625 0.3144063353538513 0.47784319519996643 0.2311997264623642 0.7346059679985046 0.6564809083938599 0.9079071283340454 \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_3.evaluate.json b/ENCSR493IAY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0b417b7bca8bd0b6156bf2775cf4b4b587a30df0..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF951TDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_3.fit.json b/ENCSR493IAY/cherimoya.fold_3.fit.json deleted file mode 100644 index 2c6c872926d7b50cc898bd65156d346f8844ada6..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF951TDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_3.log b/ENCSR493IAY/cherimoya.fold_3.log deleted file mode 100644 index 1b79a2638501fefb824bea3c0ed79e10e147f317..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1479 20.11344838142395 3.811343193054199 1372.43212890625 1.3705105781555176 1983.083251953125 0.16522632539272308 0.5076366 29.662363052368164 True -1 2958 16.313267946243286 0.5172443389892578 863.66943359375 0.8547073602676392 1744.8443603515625 0.28442856669425964 0.56518096 16.258724212646484 True -2 4437 16.31743812561035 0.9691591262817383 992.6697998046875 1.5919824838638306 1519.7845458984375 0.3777795135974884 0.46435 8.017788887023926 False -3 5916 16.320481538772583 0.32816004753112793 1274.7431640625 1.5165398120880127 1402.2310791015625 0.4081951975822449 0.5500951 4.671090602874756 False -4 7395 16.308852195739746 0.3193795680999756 953.08056640625 1.3312206268310547 1335.1248779296875 0.42714983224868774 0.573371 3.5510811805725098 True -5 8874 16.319965839385986 0.31217479705810547 1008.7843627929688 1.0709874629974365 1306.2337646484375 0.43581974506378174 0.6070482 2.98093318939209 True -6 10353 16.337884187698364 0.30940985679626465 1137.214111328125 1.1015342473983765 1274.85302734375 0.4435056746006012 0.6277481 2.4471566677093506 True -7 11832 16.334715843200684 0.3252372741699219 1016.427734375 1.068489670753479 1261.3697509765625 0.4480879008769989 0.6410531 2.202178716659546 True -8 13311 16.311278820037842 0.3124816417694092 1562.2987060546875 1.1846286058425903 1244.357421875 0.4531387984752655 0.6385618 1.9869709014892578 False -9 14790 16.31375813484192 0.7910251617431641 1031.5052490234375 1.0158016681671143 1236.518798828125 0.45426514744758606 0.6476887 1.7349827289581299 True -10 16269 16.31145405769348 0.6085524559020996 1083.973388671875 1.2605574131011963 1225.29150390625 0.4579588770866394 0.6585627 1.516278862953186 True -11 17748 16.35386061668396 0.3025062084197998 1090.910400390625 0.7449976801872253 1215.90234375 0.4619339108467102 0.6690877 1.3623584508895874 True -12 19227 16.34957242012024 0.3026084899902344 998.9930419921875 1.0931575298309326 1212.74755859375 0.4616297483444214 0.67520696 1.2584502696990967 True -13 20706 16.351240873336792 0.3183751106262207 757.8150024414062 0.9214324355125427 1203.23486328125 0.4646490812301636 0.69120985 1.1601577997207642 True -14 22185 16.352266311645508 0.30378270149230957 811.4849243164062 0.9705436825752258 1193.572021484375 0.46766752004623413 0.7040777 1.0937657356262207 True -15 23664 16.367021799087524 0.3105595111846924 763.7512817382812 1.2478432655334473 1186.51318359375 0.47128739953041077 0.7133354 1.0482844114303589 True -16 25143 16.345752716064453 0.3059046268463135 691.1156005859375 0.49545174837112427 1187.2274169921875 0.4701956808567047 0.7179311 1.0099375247955322 True -17 26622 16.31203031539917 0.3030998706817627 849.5357666015625 0.6709227561950684 1183.840087890625 0.47117453813552856 0.71583086 1.0068800449371338 False -18 28101 16.310399532318115 0.30241847038269043 908.4495239257812 0.7285658121109009 1192.9088134765625 0.4660767912864685 0.7156311 1.0111836194992065 False -19 29580 16.27825927734375 0.3269667625427246 874.777587890625 0.6562168598175049 1197.19140625 0.46375176310539246 0.7159047 1.018676519393921 False diff --git a/ENCSR493IAY/cherimoya.fold_3.performance.tsv b/ENCSR493IAY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 02f79ad6337de98a5e569a929756fd256bbb83c5..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1187.2274169921875 0.3146226704120636 0.4701956510543823 0.2353350818157196 0.7179310917854309 0.6422826647758484 1.0099375247955322 \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_4.evaluate.json b/ENCSR493IAY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 725fc24934940c7ca83868ddddee56f57a504b0b..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF951TDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_4.fit.json b/ENCSR493IAY/cherimoya.fold_4.fit.json deleted file mode 100644 index b448d184f51dc27549186bcec5c9fcbb88c30669..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF951TDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IAY/cherimoya.fold_4.log b/ENCSR493IAY/cherimoya.fold_4.log deleted file mode 100644 index 82a6b64acff450479f96fdbabc2b0ee411709f4c..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1511 20.5147442817688 3.431706666946411 1257.406494140625 1.5255918502807617 1849.6644287109375 0.17502978444099426 0.5052943 26.747554779052734 True -1 3022 16.740025281906128 0.28370213508605957 1428.542724609375 1.2983494997024536 1619.44970703125 0.29631710052490234 0.5753502 12.105829238891602 True -2 4533 16.790047883987427 0.27843308448791504 955.6012573242188 1.1295639276504517 1415.165283203125 0.383152037858963 0.5736796 7.156121253967285 False -3 6044 16.81954312324524 0.285367488861084 1101.8817138671875 1.5110007524490356 1308.930419921875 0.41397732496261597 0.5939692 4.947031497955322 True -4 7555 16.747625589370728 0.2743825912475586 891.523681640625 1.3389308452606201 1256.959228515625 0.42481356859207153 0.61869574 3.164135217666626 True -5 9066 16.68510389328003 0.27173519134521484 961.5932006835938 0.9270291328430176 1225.2537841796875 0.4315659701824188 0.6345745 2.201328992843628 True -6 10577 16.691301107406616 0.27234864234924316 888.95068359375 1.0105680227279663 1198.4764404296875 0.4405798017978668 0.63647884 1.9627526998519897 True -7 12088 16.694239854812622 0.27390003204345703 949.040283203125 0.7668857574462891 1178.18310546875 0.4483915865421295 0.6455811 1.6934077739715576 True -8 13599 16.662663221359253 0.26952624320983887 1016.4227294921875 1.3109018802642822 1158.604736328125 0.4552187919616699 0.6523638 1.5287200212478638 True -9 15110 16.707117319107056 0.2707810401916504 1055.668212890625 1.0743155479431152 1152.37255859375 0.45465517044067383 0.66045773 1.3622230291366577 True -10 16621 16.761645555496216 2.149042844772339 1114.0897216796875 1.4223425388336182 1140.397216796875 0.45883044600486755 0.6673166 1.2583979368209839 True -11 18132 16.768633365631104 7.5256524085998535 1000.3385620117188 0.7513330578804016 1128.821044921875 0.46290963888168335 0.6714163 1.1496738195419312 True -12 19643 16.781364917755127 0.3072519302368164 868.8570556640625 0.6591945886611938 1122.598876953125 0.4658079147338867 0.67748785 1.0781471729278564 True -13 21154 16.864071130752563 0.2711968421936035 1061.17578125 1.1787830591201782 1116.5469970703125 0.46853965520858765 0.68547183 1.0285148620605469 True -14 22665 16.788767337799072 0.273862361907959 921.59521484375 0.9308348298072815 1110.4954833984375 0.46971595287323 0.6952289 0.9816065430641174 True -15 24176 16.82392930984497 0.2801814079284668 824.8160400390625 0.5891391038894653 1112.0810546875 0.46848544478416443 0.7025338 0.9456587433815002 True -16 25687 16.768892288208008 0.27599382400512695 989.4498901367188 0.6123398542404175 1105.8004150390625 0.4719257652759552 0.70786417 0.9304999709129333 True -17 27198 16.749701976776123 1.3726747035980225 716.7965087890625 0.6533962488174438 1109.7003173828125 0.47089189291000366 0.71119416 0.9306797385215759 True -18 28709 16.76047372817993 0.26709413528442383 762.606689453125 0.5437981486320496 1113.038330078125 0.469375342130661 0.7116964 0.9353741407394409 True -19 30220 16.744844675064087 0.9993774890899658 722.275390625 0.4119316339492798 1118.552490234375 0.46515628695487976 0.71003705 0.9420717358589172 False diff --git a/ENCSR493IAY/cherimoya.fold_4.performance.tsv b/ENCSR493IAY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e7708963379a685586655ddc619fe16a7695793d..0000000000000000000000000000000000000000 --- a/ENCSR493IAY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1113.038330078125 0.31891003251075745 0.469375342130661 0.22526787221431732 0.7116963863372803 0.6283459067344666 0.9353741407394409 \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_0.evaluate.json b/ENCSR493IQY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7aecad35c35a32b24ebc7060c699a07abd82a0a5..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF990YWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_0.fit.json b/ENCSR493IQY/cherimoya.fold_0.fit.json deleted file mode 100644 index cb06ca88b45d3ad2fa060224ba917406b9df9b29..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF990YWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_0.log b/ENCSR493IQY/cherimoya.fold_0.log deleted file mode 100644 index 1b1eda4a7eb34e0aaf475d2fd11987fd2d642572..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2073 27.527608156204224 3.719367504119873 289.924072265625 0.9949293732643127 484.1146545410156 0.1604396551847458 0.6565933 9.986601829528809 True -1 4146 23.228035926818848 0.5115902423858643 377.213134765625 0.74580979347229 412.59759521484375 0.2333715856075287 0.7750747 4.19270133972168 True -2 6219 22.877975940704346 0.4448058605194092 379.8602600097656 1.085492491722107 387.5478820800781 0.2519010305404663 0.7947182 2.3363308906555176 True -3 8292 23.241482257843018 22.16336154937744 311.797119140625 0.7241734266281128 380.4934387207031 0.2586468756198883 0.80318093 1.5150146484375 True -4 10365 22.900425910949707 0.44271230697631836 271.8909606933594 0.9979649782180786 376.70794677734375 0.26247096061706543 0.81096745 1.1534985303878784 True -5 12438 22.85160183906555 0.4233088493347168 372.8348388671875 0.8487169146537781 374.3861389160156 0.2651804983615875 0.81814015 1.1050567626953125 True -6 14511 22.93105435371399 0.43051719665527344 351.96319580078125 0.6504984498023987 370.9311218261719 0.26982951164245605 0.8279981 0.9812668561935425 True -7 16584 22.883806943893433 0.7944843769073486 207.44564819335938 0.3865188658237457 368.8504638671875 0.2725403606891632 0.83644086 0.8912460207939148 True -8 18657 22.887678146362305 1.3526461124420166 267.9629211425781 0.6897408962249756 367.1096496582031 0.27493512630462646 0.83646154 0.8358578681945801 True -9 20730 22.9739670753479 0.4324476718902588 428.1360778808594 0.6155718564987183 365.1600036621094 0.2777523398399353 0.84506977 0.7603129744529724 True -10 22803 22.875584363937378 0.42581653594970703 307.7739562988281 0.632370114326477 364.05780029296875 0.27843135595321655 0.85022175 0.6990007162094116 True -11 24876 22.887038707733154 0.5049893856048584 319.8515319824219 0.5076329708099365 362.1687927246094 0.2804358899593353 0.85466343 0.6590017080307007 True -12 26949 22.911087036132812 0.4239208698272705 258.8126220703125 0.6489529013633728 359.7111511230469 0.28338825702667236 0.8573094 0.6209351420402527 True -13 29022 22.923999071121216 0.4350900650024414 288.9192810058594 0.8361081480979919 357.8786926269531 0.28596705198287964 0.8621005 0.5947438478469849 True -14 31095 22.940218210220337 0.4371318817138672 259.8021545410156 0.6749356985092163 356.7569580078125 0.2875318229198456 0.86684793 0.5761176347732544 True -15 33168 22.894845485687256 12.872298002243042 291.83782958984375 0.6412168741226196 356.48651123046875 0.2874673008918762 0.87018746 0.5527541041374207 True -16 35241 23.011757135391235 0.44396328926086426 256.99639892578125 0.530799150466919 357.11553955078125 0.2859109044075012 0.87179846 0.5435997843742371 True -17 37314 23.10505485534668 0.43068790435791016 190.4390869140625 0.5247524380683899 356.7039489746094 0.2863575518131256 0.8712247 0.5396760106086731 False -18 39387 22.890751838684082 0.4263427257537842 258.6123046875 0.32436805963516235 356.5189208984375 0.2871069610118866 0.87266713 0.5411045551300049 True -19 41460 22.868502140045166 0.5499634742736816 274.90032958984375 0.32358336448669434 356.6955871582031 0.28656959533691406 0.87076265 0.5437893867492676 False diff --git a/ENCSR493IQY/cherimoya.fold_0.performance.tsv b/ENCSR493IQY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fed8d491b2b7e87c24a045335d02dce882b10d1b..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -356.5189208984375 0.4910621643066406 0.2871069610118866 0.09596523642539978 0.872667133808136 0.8183444142341614 0.5411045551300049 \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_1.evaluate.json b/ENCSR493IQY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3d816dccbf9d04d870885d4b0bd74729f751822b..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF990YWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_1.fit.json b/ENCSR493IQY/cherimoya.fold_1.fit.json deleted file mode 100644 index f6a12ec29942b7cb5c902f7f00b23aa7748f0227..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF990YWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_1.log b/ENCSR493IQY/cherimoya.fold_1.log deleted file mode 100644 index ca440ad2413055b6086666c675e56db1dd5a6d26..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2012 26.571041584014893 4.030613422393799 267.0955810546875 0.9174847602844238 611.9505615234375 0.1693975329399109 0.6496807 11.796422958374023 True -1 4024 22.249924182891846 0.7003483772277832 377.0379943847656 0.7683597803115845 519.6304321289062 0.258760541677475 0.76145 5.457755088806152 True -2 6036 22.26516032218933 0.6155149936676025 390.31927490234375 1.14302396774292 484.4815979003906 0.27986830472946167 0.7950798 3.0411112308502197 True -3 8048 22.108877420425415 0.6050100326538086 382.7388916015625 1.0617475509643555 474.0745849609375 0.2880820035934448 0.8032274 2.035755157470703 True -4 10060 21.832110166549683 0.6028072834014893 408.1240234375 0.8973997235298157 468.8856506347656 0.29330772161483765 0.8150097 1.7174670696258545 True -5 12072 21.82375454902649 0.602435827255249 276.5938720703125 0.9758784770965576 463.3009948730469 0.2986356019973755 0.8287767 1.3913865089416504 True -6 14084 21.911095142364502 0.6282413005828857 306.97491455078125 0.6148175001144409 460.2432556152344 0.30167925357818604 0.83782166 1.274579644203186 True -7 16096 21.850335836410522 0.6282691955566406 360.84857177734375 0.8944196105003357 458.9256896972656 0.30237260460853577 0.84639347 1.1408213376998901 True -8 18108 21.857084035873413 0.6269996166229248 329.3492126464844 0.7253369092941284 455.7936706542969 0.3060859739780426 0.85572743 1.0039582252502441 True -9 20120 21.837039947509766 1.3489587306976318 270.050048828125 0.6661146879196167 452.9400329589844 0.30976197123527527 0.8599888 0.9156496524810791 True -10 22132 21.92284870147705 0.6281540393829346 358.94879150390625 1.435225248336792 450.63018798828125 0.31079837679862976 0.8660022 0.7820615768432617 True -11 24144 21.88368582725525 0.6220560073852539 285.50262451171875 1.051603078842163 448.7273254394531 0.3133375942707062 0.8700594 0.7514439225196838 True -12 26156 22.039143562316895 0.6149799823760986 179.66903686523438 0.7352718710899353 445.47418212890625 0.31652364134788513 0.8748673 0.7069228291511536 True -13 28168 21.88582968711853 0.6197373867034912 285.5746765136719 0.38607072830200195 443.6249694824219 0.31788647174835205 0.88083625 0.6537612080574036 True -14 30180 21.8948335647583 1.4319586753845215 265.983154296875 0.7573549747467041 441.70123291015625 0.32070329785346985 0.8835888 0.6286056637763977 True -15 32192 21.89537739753723 0.6162052154541016 244.89263916015625 0.5102101564407349 441.81817626953125 0.3185920715332031 0.8843812 0.6019770503044128 True -16 34204 21.985234022140503 0.6095931529998779 266.3995666503906 0.6077051758766174 440.5422668457031 0.31997743248939514 0.88709235 0.5880688428878784 True -17 36216 21.90211009979248 0.6032669544219971 334.79815673828125 0.44195064902305603 441.4483947753906 0.318794846534729 0.8851651 0.5915176868438721 False -18 38228 21.9217631816864 1.6253690719604492 322.6139221191406 0.4979132413864136 443.23846435546875 0.31650716066360474 0.886377 0.6004167199134827 False -19 40240 21.907684803009033 0.6115639209747314 311.60003662109375 0.582425057888031 444.1626281738281 0.3153405785560608 0.8824259 0.6046909689903259 False diff --git a/ENCSR493IQY/cherimoya.fold_1.performance.tsv b/ENCSR493IQY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 357ed6fafc60d19b088b5a8d9c43903c78db6a37..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -440.5422668457031 0.4614863991737366 0.31997746229171753 0.12027386575937271 0.8870923519134521 0.8517258167266846 0.5880688428878784 \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_2.evaluate.json b/ENCSR493IQY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0bc52ad29106b1777c467bf7c97936ca4a51988f..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF990YWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_2.fit.json b/ENCSR493IQY/cherimoya.fold_2.fit.json deleted file mode 100644 index 7624b7bb8c90cfd08ebfebfd2eb36c836b8d25ef..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF990YWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_2.log b/ENCSR493IQY/cherimoya.fold_2.log deleted file mode 100644 index 78710f32fbab7f2ace79d2507099dd47daf4e554..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2171 28.370092630386353 3.683286428451538 230.65725708007812 0.7044124603271484 504.7116394042969 0.16112208366394043 0.6294546 9.369593620300293 True -1 4342 24.00037670135498 0.5229489803314209 283.8272399902344 0.5806658267974854 416.87689208984375 0.2439306080341339 0.7699378 3.711596965789795 True -2 6513 23.979597568511963 0.45413851737976074 309.94549560546875 0.774055540561676 397.8187561035156 0.25495490431785583 0.79387915 2.12848162651062 True -3 8684 23.92757511138916 0.881403923034668 237.51666259765625 0.9746701121330261 391.1516418457031 0.2613794803619385 0.80511564 1.4299273490905762 True -4 10855 23.947328329086304 0.4539790153503418 332.238525390625 0.6442150473594666 386.8114318847656 0.26545968651771545 0.8130419 1.252684473991394 True -5 13026 23.9075767993927 0.45206522941589355 306.7444152832031 1.0425636768341064 383.9418029785156 0.2688928246498108 0.8165962 1.1988390684127808 True -6 15197 23.963123321533203 0.4530370235443115 320.72845458984375 0.9185464978218079 381.6734313964844 0.27173176407814026 0.82603747 1.0855903625488281 True -7 17368 23.975388288497925 0.4523651599884033 339.09857177734375 0.6807563900947571 378.8133850097656 0.27454882860183716 0.8355231 0.9809743762016296 True -8 19539 23.934938430786133 0.45888590812683105 322.39068603515625 0.5391381978988647 377.8763427734375 0.2770145833492279 0.83625937 0.9329569339752197 True -9 21710 23.9188449382782 0.4565920829772949 265.1357116699219 0.9157189130783081 376.927978515625 0.277307391166687 0.8453932 0.8288611173629761 True -10 23881 23.844948530197144 0.45551395416259766 256.8731689453125 0.7462512254714966 374.0473327636719 0.2818784713745117 0.8485216 0.7973802089691162 True -11 26052 23.599124908447266 0.46102309226989746 316.73175048828125 0.6555694341659546 371.5492858886719 0.2846672534942627 0.85399336 0.7368221282958984 True -12 28223 23.517107486724854 0.4587888717651367 336.554443359375 0.6574687957763672 369.6218566894531 0.28546878695487976 0.85805714 0.6844989657402039 True -13 30394 23.478551626205444 0.4622030258178711 262.8087158203125 0.5629061460494995 368.7560729980469 0.28569290041923523 0.861207 0.6286290287971497 True -14 32565 23.5548152923584 0.45778489112854004 282.791015625 0.5401910543441772 366.8612060546875 0.2880602478981018 0.8652015 0.60467928647995 True -15 34736 23.50466299057007 0.4665496349334717 293.9385986328125 0.5132142305374146 366.1365051269531 0.2887490391731262 0.8679022 0.5767430663108826 True -16 36907 23.49319863319397 0.8624703884124756 286.4656677246094 0.34620094299316406 366.25018310546875 0.2882746756076813 0.87112826 0.558991551399231 True -17 39078 23.528790712356567 0.4674491882324219 273.35235595703125 0.5074555277824402 367.2272644042969 0.28735673427581787 0.87003183 0.5581606030464172 False -18 41249 23.54153847694397 18.648797035217285 237.2274932861328 0.2844505310058594 368.2785949707031 0.28572309017181396 0.8692319 0.5597053170204163 False -19 43420 23.81752347946167 0.5419223308563232 244.47213745117188 0.5868869423866272 367.5981750488281 0.2874721586704254 0.8688794 0.5623334050178528 False diff --git a/ENCSR493IQY/cherimoya.fold_2.performance.tsv b/ENCSR493IQY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6e5fae35a116777d26a527c382a0ababe6888055..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -366.25018310546875 0.4875572919845581 0.2882746756076813 0.0973019003868103 0.871128261089325 0.8184831738471985 0.558991551399231 \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_3.evaluate.json b/ENCSR493IQY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 751e67f392ab498b687208bcce2c00921ca5b02f..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF990YWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_3.fit.json b/ENCSR493IQY/cherimoya.fold_3.fit.json deleted file mode 100644 index 720ce0f3ad2d30af1d2b12d6c34d78f91d1a9a10..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF990YWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_3.log b/ENCSR493IQY/cherimoya.fold_3.log deleted file mode 100644 index ae4e1a38229f0f6a3a460a327ce6c67e3527def9..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2078 27.614378929138184 3.9544284343719482 345.33203125 0.8355976939201355 502.87200927734375 0.1698465198278427 0.6249787 10.307415008544922 True -1 4156 22.90903115272522 0.5056228637695312 451.5628356933594 1.6542872190475464 422.1383056640625 0.2512085437774658 0.76281023 4.946683883666992 True -2 6234 22.98310661315918 0.43389463424682617 310.26312255859375 0.9384145736694336 404.7793273925781 0.265956848859787 0.78386056 2.9850804805755615 True -3 8312 22.940816402435303 0.4401078224182129 364.8500671386719 0.7379478216171265 396.33697509765625 0.27604246139526367 0.7964116 1.931062936782837 True -4 10390 23.00329065322876 0.9901564121246338 221.70828247070312 0.7213772535324097 394.35833740234375 0.2784721255302429 0.8056428 1.5761586427688599 True -5 12468 22.9810733795166 0.43190526962280273 213.05540466308594 0.7710781097412109 389.72265625 0.28485843539237976 0.8148417 1.4307540655136108 True -6 14546 22.9293532371521 0.4285542964935303 406.3106689453125 0.5516273379325867 388.5401306152344 0.28553101420402527 0.82011116 1.3490184545516968 True -7 16624 22.93584680557251 0.4325602054595947 302.3230895996094 0.6874345541000366 385.6930236816406 0.28939178586006165 0.8294908 1.2325364351272583 True -8 18702 22.92283058166504 0.43119263648986816 300.1910400390625 0.9127264022827148 383.6234436035156 0.29093050956726074 0.83633363 1.1231775283813477 True -9 20780 22.92892074584961 0.4224419593811035 242.04348754882812 1.0055546760559082 382.3195495605469 0.293097585439682 0.8392998 0.9833078980445862 True -10 22858 22.946856021881104 0.43565940856933594 319.38446044921875 0.7290557622909546 380.00018310546875 0.29531535506248474 0.8474877 0.900951623916626 True -11 24936 22.974091291427612 0.4335317611694336 289.81219482421875 0.6841610074043274 378.7315979003906 0.296208918094635 0.85308886 0.8077077269554138 True -12 27014 23.020020484924316 0.447221040725708 290.4600830078125 0.6993361115455627 376.7110595703125 0.29816848039627075 0.85634524 0.7332970499992371 True -13 29092 23.067071437835693 0.43503499031066895 325.70501708984375 0.3389524221420288 375.4378967285156 0.30028343200683594 0.8601 0.6895697712898254 True -14 31170 23.069437265396118 0.444427490234375 372.2323303222656 0.6279529333114624 373.7469787597656 0.3013659715652466 0.8649405 0.6537089943885803 True -15 33248 23.058024644851685 1.1715590953826904 295.2720947265625 0.4297083616256714 373.239013671875 0.3009827435016632 0.8674323 0.6159882545471191 True -16 35326 23.06257128715515 0.43373990058898926 278.166748046875 0.42290282249450684 372.52423095703125 0.30142492055892944 0.8711625 0.6011892557144165 True -17 37404 23.06781315803528 0.43881964683532715 145.9960479736328 0.5618947744369507 373.53814697265625 0.3010455071926117 0.8696895 0.5959829092025757 False -18 39482 23.07033085823059 0.7938358783721924 263.40130615234375 0.39517742395401 372.7441711425781 0.30258893966674805 0.8698807 0.599587619304657 False -19 41560 23.0487859249115 0.43532276153564453 262.74005126953125 0.3448562026023865 373.3602294921875 0.3007658123970032 0.8680814 0.6058544516563416 False diff --git a/ENCSR493IQY/cherimoya.fold_3.performance.tsv b/ENCSR493IQY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 894e7534c49cb3e276b4da4778be020341bd91e1..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -372.52423095703125 0.479449987411499 0.30142495036125183 0.10919379442930222 0.871162474155426 0.8225087523460388 0.6011892557144165 \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_4.evaluate.json b/ENCSR493IQY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 587ffed80aa89fc087c6d518e90272c826421f6c..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF990YWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_4.fit.json b/ENCSR493IQY/cherimoya.fold_4.fit.json deleted file mode 100644 index 524cd2b2b80edb008608f6e7408db8712552e338..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF990YWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493IQY/cherimoya.fold_4.log b/ENCSR493IQY/cherimoya.fold_4.log deleted file mode 100644 index 671871c1d4f713f980ce3c37fb3c13d53b8c79e7..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2078 27.275808811187744 3.634242057800293 340.8507080078125 1.0733264684677124 434.6124267578125 0.15706655383110046 0.6342899 8.181477546691895 True -1 4156 22.941840887069702 0.5739333629608154 233.01226806640625 1.2792805433273315 369.7833557128906 0.22856709361076355 0.7631813 3.6703085899353027 True -2 6234 22.938173055648804 0.460205078125 287.86468505859375 0.6930885314941406 353.47967529296875 0.23978304862976074 0.7815488 2.051133394241333 True -3 8312 23.179818868637085 15.865751504898071 417.9747619628906 0.8872759342193604 348.2789306640625 0.24423599243164062 0.7862003 1.4095171689987183 True -4 10390 23.053987741470337 0.4729931354522705 270.6897277832031 0.8355445861816406 343.2017822265625 0.25057992339134216 0.8025301 1.0097607374191284 True -5 12468 22.915053844451904 0.43045854568481445 295.16510009765625 0.7688663601875305 339.9415588378906 0.2551566958427429 0.81364393 0.8606193661689758 True -6 14546 22.90343403816223 0.4294283390045166 212.96109008789062 0.8035722970962524 338.3231506347656 0.2560289800167084 0.82079935 0.7878729701042175 True -7 16624 22.890981197357178 0.4231584072113037 394.916748046875 0.6288098692893982 337.4398193359375 0.25726109743118286 0.82322365 0.7726998329162598 True -8 18702 22.956064224243164 0.45296812057495117 308.6329345703125 0.5878324508666992 335.6827392578125 0.2598358690738678 0.8287316 0.7159663438796997 True -9 20780 22.971906423568726 0.43198609352111816 229.3231964111328 0.5928573608398438 334.5387878417969 0.2613680958747864 0.83281296 0.6605674028396606 True -10 22858 22.921244382858276 0.4322388172149658 301.9025573730469 0.6797426342964172 331.7662353515625 0.2652485966682434 0.84125304 0.618776798248291 True -11 24936 22.96114993095398 1.353853702545166 226.7183837890625 0.8022940158843994 330.22698974609375 0.26680290699005127 0.8469672 0.5942639708518982 True -12 27014 22.935730457305908 0.47246670722961426 362.88311767578125 0.5827884674072266 329.5206604003906 0.26831838488578796 0.8495783 0.5819314122200012 True -13 29092 22.96878933906555 0.47166919708251953 356.93621826171875 0.552108645439148 328.5032043457031 0.26944276690483093 0.8559601 0.5526731610298157 True -14 31170 23.070584535598755 0.4441959857940674 266.5610046386719 0.4803623557090759 327.42449951171875 0.27102237939834595 0.86240643 0.5298557877540588 True -15 33248 22.99109387397766 0.4518618583679199 246.882568359375 0.3882361352443695 326.3095397949219 0.27278265357017517 0.86457837 0.5189016461372375 True -16 35326 22.987564086914062 0.4499020576477051 343.8096923828125 0.44278019666671753 326.6108093261719 0.2713657319545746 0.866991 0.5108588337898254 True -17 37404 23.07552194595337 0.4649081230163574 234.31997680664062 0.42030325531959534 327.2618103027344 0.2712327241897583 0.8679794 0.5149317979812622 True -18 39482 23.051600456237793 0.4415931701660156 345.1082763671875 0.72404944896698 327.49664306640625 0.2713681161403656 0.8668181 0.5194288492202759 False -19 41560 22.904389142990112 0.44393467903137207 344.1918640136719 0.2642936706542969 328.0023498535156 0.2710575759410858 0.86497015 0.5215582251548767 False diff --git a/ENCSR493IQY/cherimoya.fold_4.performance.tsv b/ENCSR493IQY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4cfdcb9bef8b8976fb06e651f4c7f5e481ed1680..0000000000000000000000000000000000000000 --- a/ENCSR493IQY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -327.2618103027344 0.5018475651741028 0.2712326943874359 0.08887647092342377 0.8679794073104858 0.8061848282814026 0.5149317979812622 \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_0.evaluate.json b/ENCSR493VDS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d4adc151e218dcc41238a11e6d2738bd76790a8e..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093VHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_0.fit.json b/ENCSR493VDS/cherimoya.fold_0.fit.json deleted file mode 100644 index 36c3f3240fccc22be9ff41d1db5456c9fe28f549..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF093VHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_0.log b/ENCSR493VDS/cherimoya.fold_0.log deleted file mode 100644 index 06e55c646c1edabb054da50d5aaca8bfad24f44b..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 34.89661359786987 4.232014894485474 387.48876953125 0.7902959585189819 563.401123046875 0.21508722007274628 0.58150977 4.142767906188965 True -1 5524 30.717596292495728 0.6268541812896729 401.17974853515625 0.7088515162467957 529.8988647460938 0.2922406494617462 0.6558833 1.4481102228164673 True -2 8286 30.775851726531982 0.6106183528900146 474.7308349609375 0.8052094578742981 521.3403930664062 0.3033298850059509 0.6626351 0.7206440567970276 True -3 11048 30.76791214942932 0.5751287937164307 467.75421142578125 0.48516958951950073 516.664306640625 0.31166934967041016 0.66522753 0.613185703754425 True -4 13810 30.385772466659546 0.5603115558624268 359.1941833496094 0.7002474069595337 512.782470703125 0.32084789872169495 0.6709386 0.48611846566200256 True -5 16572 30.14711904525757 0.5737833976745605 394.2543640136719 0.5271437764167786 510.7998962402344 0.32492855191230774 0.6823412 0.4322216510772705 True -6 19334 30.231534242630005 2.0320231914520264 371.43939208984375 0.7255176305770874 509.4498291015625 0.32922452688217163 0.6793382 0.44619303941726685 False -7 22096 30.28691291809082 0.5743017196655273 348.8819885253906 0.524313747882843 508.8341369628906 0.33036765456199646 0.6723051 0.4338940680027008 False -8 24858 30.18417739868164 0.5770988464355469 400.8455505371094 0.5688404440879822 507.1805419921875 0.33401191234588623 0.68530333 0.40411674976348877 True -9 27620 30.142655849456787 0.5719778537750244 407.5380554199219 0.6491107940673828 505.98223876953125 0.33687537908554077 0.6922796 0.4152795672416687 True -10 30382 30.14260482788086 0.5834224224090576 437.48394775390625 0.345659077167511 504.2764892578125 0.34098848700523376 0.7021447 0.38827618956565857 True -11 33144 30.17859673500061 0.5765049457550049 386.5346374511719 0.310758113861084 503.51422119140625 0.341601699590683 0.7104091 0.3910040855407715 True -12 35906 30.133441925048828 0.5648374557495117 434.263671875 0.3107374906539917 502.5470886230469 0.34281983971595764 0.71887773 0.35882315039634705 True -13 38668 30.11699390411377 0.5720064640045166 429.3853759765625 0.4700663387775421 500.4071044921875 0.347901850938797 0.72829497 0.35516661405563354 True -14 41430 30.12445878982544 0.6353480815887451 338.6497802734375 0.3269088864326477 499.13385009765625 0.35097694396972656 0.7370382 0.3428763151168823 True -15 44192 30.126988887786865 1.4245104789733887 443.4492492675781 0.3001648187637329 499.4722900390625 0.34979379177093506 0.7436211 0.3347349762916565 True -16 46954 30.11052966117859 2.362025022506714 481.12982177734375 0.26477473974227905 498.84075927734375 0.3510090112686157 0.74965787 0.32887789607048035 True -17 49716 30.193294286727905 1.723978042602539 402.656494140625 0.39305830001831055 498.4877624511719 0.3526909649372101 0.75141746 0.328932523727417 True -18 52478 30.184511184692383 1.204164981842041 394.4150085449219 0.3333536982536316 498.17474365234375 0.3533298671245575 0.7505056 0.33338668942451477 False -19 55240 30.11765217781067 0.5562219619750977 412.2859802246094 0.3117062449455261 498.9893798828125 0.3508230149745941 0.7501045 0.3357190489768982 False diff --git a/ENCSR493VDS/cherimoya.fold_0.performance.tsv b/ENCSR493VDS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 77ef7e4ae8740ce6f92b0f1f6b09811ccbeb4954..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -498.4877624511719 0.4136485457420349 0.3526909351348877 0.12811560928821564 0.7514174580574036 0.6491748690605164 0.328932523727417 \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_1.evaluate.json b/ENCSR493VDS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c2e6e83515bee3a08482eeb07c05a9ee754bbb7f..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093VHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_1.fit.json b/ENCSR493VDS/cherimoya.fold_1.fit.json deleted file mode 100644 index 2ea51b911eff6f4912f735c0664424d7ed1de94d..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF093VHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_1.log b/ENCSR493VDS/cherimoya.fold_1.log deleted file mode 100644 index 9edd9f71ae21b706c00368bbe35ade53ca977441..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 35.04623007774353 4.005105972290039 438.83599853515625 0.9491631984710693 634.6953735351562 0.22770798206329346 0.59498227 4.729488849639893 True -1 5498 30.604997873306274 15.831602811813354 405.32977294921875 0.8980244398117065 589.51220703125 0.30437493324279785 0.6871407 1.3137948513031006 True -2 8247 30.69739079475403 1.6313157081604004 477.5506286621094 0.742104709148407 577.4983520507812 0.3215492367744446 0.6996252 0.8106430172920227 True -3 10996 30.674823999404907 2.0832345485687256 474.15350341796875 0.6341047286987305 571.5883178710938 0.3314474821090698 0.71075225 0.7218382954597473 True -4 13745 30.223951816558838 2.1228322982788086 474.68463134765625 0.6892063617706299 568.649169921875 0.3368471562862396 0.7175401 0.6116562485694885 True -5 16494 30.091633081436157 2.07061767578125 426.4337158203125 0.6583030223846436 565.6788330078125 0.34236347675323486 0.7255397 0.5414348840713501 True -6 19243 30.15185809135437 2.0533030033111572 380.8092346191406 0.43267735838890076 563.3355712890625 0.34731295704841614 0.7247768 0.531444787979126 False -7 21992 30.000073194503784 2.5135812759399414 373.3655700683594 0.5309244394302368 562.9811401367188 0.34651637077331543 0.7253215 0.5256795883178711 False -8 24741 29.982795000076294 1.8391032218933105 415.8568115234375 0.6293171644210815 561.4515380859375 0.3486793041229248 0.73391414 0.4822894036769867 True -9 27490 29.971315622329712 0.800767183303833 373.83294677734375 0.550944447517395 558.5349731445312 0.35558173060417175 0.7413031 0.4669705033302307 True -10 30239 29.92460608482361 0.7099361419677734 409.4273376464844 0.2987104654312134 556.6932983398438 0.3573680520057678 0.74797636 0.4549756944179535 True -11 32988 29.910998821258545 0.710404634475708 395.1126403808594 0.4717875123023987 556.0011596679688 0.35755854845046997 0.75223666 0.4278563857078552 True -12 35737 29.93459725379944 0.7136297225952148 401.03204345703125 0.304649293422699 555.2955932617188 0.35917866230010986 0.7615156 0.41525372862815857 True -13 38486 29.918184757232666 0.7213699817657471 374.580322265625 0.41461852192878723 552.786865234375 0.36457085609436035 0.76752365 0.40302368998527527 True -14 41235 29.995454788208008 0.7011640071868896 409.124755859375 0.3479955494403839 551.2056274414062 0.3666600286960602 0.7791879 0.3834473192691803 True -15 43984 29.948410987854004 0.7078719139099121 439.94818115234375 0.5131161212921143 551.1956176757812 0.3652496933937073 0.78531456 0.3642410635948181 True -16 46733 30.033984899520874 0.6975841522216797 342.0771484375 0.3451980948448181 549.723876953125 0.3676231801509857 0.79075676 0.3547614812850952 True -17 49482 30.012625694274902 0.7036831378936768 366.55328369140625 0.20780354738235474 550.3219604492188 0.3661446273326874 0.794032 0.3499361574649811 True -18 52231 30.000428199768066 1.700568675994873 447.6811218261719 0.3286847472190857 550.7239379882812 0.3657321333885193 0.7940158 0.3518868386745453 False -19 54980 30.03332281112671 1.3142495155334473 385.79730224609375 0.4126477837562561 550.1127319335938 0.3673248589038849 0.79169565 0.35360538959503174 False diff --git a/ENCSR493VDS/cherimoya.fold_1.performance.tsv b/ENCSR493VDS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index fb21f9d2f02e4461a76a696bed67ca7dad78ad22..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -550.3219604492188 0.4013363718986511 0.36614465713500977 0.14109911024570465 0.7940319776535034 0.7116875648498535 0.3499361574649811 \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_2.evaluate.json b/ENCSR493VDS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 131a558d36de16f199267904d03a24d223dcb0d0..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093VHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_2.fit.json b/ENCSR493VDS/cherimoya.fold_2.fit.json deleted file mode 100644 index ffe9f251547f4e41f785cdfd840722917caa2be0..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF093VHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_2.log b/ENCSR493VDS/cherimoya.fold_2.log deleted file mode 100644 index 0c9ead8bfb3ab762bd69b6344914f8888259d7a7..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.90707731246948 4.327333450317383 415.48773193359375 0.556391716003418 574.1631469726562 0.22399300336837769 0.5769407 4.491168975830078 True -1 5772 32.13727569580078 0.58740234375 431.863037109375 0.576957106590271 535.5911865234375 0.2996513247489929 0.6554176 1.3277827501296997 True -2 8658 31.772385358810425 0.5633590221405029 384.07806396484375 0.4978524446487427 529.3414306640625 0.30927202105522156 0.6599626 0.6348573565483093 True -3 11544 31.45602512359619 0.5611276626586914 434.8121337890625 0.8281365036964417 523.7261962890625 0.3194829225540161 0.6764526 0.6288359761238098 True -4 14430 31.385631799697876 0.5726757049560547 367.57781982421875 0.8553442358970642 519.2973022460938 0.32813215255737305 0.6801397 0.48470690846443176 True -5 17316 31.472563982009888 0.5651931762695312 398.4687194824219 0.6827431917190552 517.8485107421875 0.33128291368484497 0.68504834 0.4614402949810028 True -6 20202 31.613014936447144 12.596678018569946 412.5672607421875 0.6155774593353271 515.3019409179688 0.33610162138938904 0.70034134 0.434506893157959 True -7 23088 31.496325254440308 0.6023330688476562 382.2660217285156 0.5713940858840942 514.3030395507812 0.33693113923072815 0.700532 0.42814651131629944 True -8 25974 31.4157075881958 9.255874633789062 366.27490234375 0.4245660901069641 513.11181640625 0.3396352231502533 0.7029924 0.4344381093978882 True -9 28860 31.579012393951416 0.6176607608795166 392.7884826660156 0.5648152232170105 511.8221435546875 0.34256094694137573 0.707405 0.41544923186302185 True -10 31746 31.759582996368408 0.5759153366088867 465.2908630371094 0.41469261050224304 510.0225830078125 0.34631550312042236 0.7150138 0.4052083492279053 True -11 34632 31.705281496047974 0.5798280239105225 406.97076416015625 0.3202402889728546 509.34783935546875 0.347098708152771 0.72143716 0.38968005776405334 True -12 37518 31.662795782089233 0.570911169052124 422.940185546875 0.31046903133392334 508.15093994140625 0.3502117693424225 0.72426575 0.38347911834716797 True -13 40404 31.811691284179688 0.6735453605651855 477.391845703125 0.4543676972389221 506.77581787109375 0.3523550033569336 0.7372649 0.3765433132648468 True -14 43290 33.513747692108154 0.5726964473724365 418.3931884765625 0.3601261079311371 506.577880859375 0.3516162633895874 0.74673295 0.35989952087402344 True -15 46176 31.541844606399536 0.5854649543762207 303.8732604980469 0.27825355529785156 505.21649169921875 0.3560839891433716 0.7529413 0.35071948170661926 True -16 49062 31.540050268173218 0.5783047676086426 367.98175048828125 0.33439573645591736 504.63214111328125 0.35573825240135193 0.7578385 0.34121325612068176 True -17 51948 31.42591619491577 0.5755434036254883 342.1285705566406 0.19379469752311707 504.2915954589844 0.35757607221603394 0.7586263 0.3419085741043091 True -18 54834 31.449488639831543 0.5832288265228271 401.5206604003906 0.27847737073898315 504.85699462890625 0.35519149899482727 0.7564787 0.34642690420150757 False -19 57720 31.465680599212646 0.5606482028961182 429.65673828125 0.25334784388542175 505.2138671875 0.35401907563209534 0.757359 0.3496859669685364 False diff --git a/ENCSR493VDS/cherimoya.fold_2.performance.tsv b/ENCSR493VDS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 87acf243c8ef59a960fbcd874df0d3176a4f1ae1..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -504.2915954589844 0.41161179542541504 0.35757607221603394 0.1336565464735031 0.7586262822151184 0.6579146981239319 0.3419085741043091 \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_3.evaluate.json b/ENCSR493VDS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f4f68bea53d8f656d38b809bd4fc4eccd9c3835c..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093VHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_3.fit.json b/ENCSR493VDS/cherimoya.fold_3.fit.json deleted file mode 100644 index 027939d11d25efa26b07a3c683922c48bc1254f6..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF093VHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_3.log b/ENCSR493VDS/cherimoya.fold_3.log deleted file mode 100644 index 3987adad9118d9e1c0375251018c43bc06253216..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2794 35.925498247146606 4.192543983459473 432.4752197265625 0.6353458166122437 577.2783813476562 0.2234146147966385 0.5868774 4.247478485107422 True -1 5588 31.087741136550903 0.6095438003540039 431.69708251953125 0.5275811553001404 542.0049438476562 0.29570889472961426 0.65139544 1.041095495223999 True -2 8382 31.188597440719604 0.6255087852478027 478.5384216308594 0.6915217041969299 534.4780883789062 0.3086008131504059 0.6530487 0.6742081642150879 True -3 11176 31.075793743133545 0.5751485824584961 378.1268615722656 0.49341922998428345 529.9334716796875 0.31786203384399414 0.66526026 0.5742000341415405 True -4 13970 30.42946457862854 0.5735788345336914 395.632080078125 0.39749598503112793 528.8197631835938 0.3190329372882843 0.66996884 0.5352901220321655 True -5 16764 30.421231985092163 0.5593740940093994 402.8387756347656 0.709752082824707 525.3828735351562 0.3263992965221405 0.6729439 0.5117185115814209 True -6 19558 30.384875059127808 0.5727536678314209 408.4043273925781 0.4671841263771057 523.814208984375 0.3292211592197418 0.68354493 0.47670042514801025 True -7 22352 30.366454124450684 0.5666544437408447 447.9668273925781 0.4678173363208771 523.0087890625 0.3309273421764374 0.68171835 0.46351853013038635 False -8 25146 30.44524598121643 0.5756080150604248 412.25128173828125 0.6361086368560791 520.7809448242188 0.33627089858055115 0.6908762 0.45632198452949524 True -9 27940 30.438535451889038 0.5660812854766846 396.889404296875 0.5599839687347412 520.074462890625 0.33680856227874756 0.69727 0.434928297996521 True -10 30734 30.437211513519287 0.5793032646179199 439.31195068359375 0.3427659273147583 518.6138305664062 0.3395952582359314 0.7025739 0.4350213408470154 True -11 33528 30.428550481796265 0.5674564838409424 395.35308837890625 0.5384883880615234 516.8092651367188 0.34319955110549927 0.71446335 0.4160575866699219 True -12 36322 30.47740340232849 0.5763459205627441 449.7933349609375 0.4744153618812561 515.6708984375 0.345279723405838 0.7215289 0.4066601097583771 True -13 39116 30.470927476882935 0.5774028301239014 399.7912902832031 0.3189067542552948 513.8059692382812 0.34849321842193604 0.7333123 0.3912258744239807 True -14 41910 30.443634748458862 0.5621414184570312 372.85015869140625 0.38212981820106506 514.6906127929688 0.34643077850341797 0.743299 0.37370526790618896 True -15 44704 30.414233446121216 0.6189041137695312 404.11065673828125 0.32088857889175415 512.935791015625 0.34951362013816833 0.7488926 0.36119207739830017 True -16 47498 30.409571170806885 2.310361862182617 501.77056884765625 0.3198392987251282 511.75048828125 0.3521566689014435 0.7546458 0.3572135269641876 True -17 50292 30.447264194488525 0.5626866817474365 426.6531066894531 0.3703247010707855 511.5459899902344 0.35283786058425903 0.7576376 0.35228464007377625 True -18 53086 30.463335275650024 0.5667624473571777 367.4853820800781 0.5182960033416748 512.0869140625 0.3508570194244385 0.7575851 0.3560578227043152 False -19 55880 30.43441367149353 0.5699572563171387 395.326416015625 0.2380942702293396 511.9971923828125 0.3514799177646637 0.756217 0.36045926809310913 False diff --git a/ENCSR493VDS/cherimoya.fold_3.performance.tsv b/ENCSR493VDS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f74ee7547fda3e69ae48c7f9973194ac7f50ced5..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -511.5459899902344 0.41201284527778625 0.3528379201889038 0.13314543664455414 0.757637619972229 0.6594395637512207 0.35228464007377625 \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_4.evaluate.json b/ENCSR493VDS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6a280d4c86ba879c5e48900a321858aafab38783..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093VHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_4.fit.json b/ENCSR493VDS/cherimoya.fold_4.fit.json deleted file mode 100644 index 4bbe8e260b1c612d5f88c15c20f34e390c2ceb1a..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF093VHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR493VDS/cherimoya.fold_4.log b/ENCSR493VDS/cherimoya.fold_4.log deleted file mode 100644 index 5458742fa668024e6b91f5174f2bf39cf284230b..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 36.677581548690796 3.253136157989502 373.164794921875 0.45822015404701233 550.427490234375 0.2197743058204651 0.56442267 3.674631357192993 True -1 5758 32.19565749168396 0.5490975379943848 418.1844482421875 0.6379014253616333 517.5707397460938 0.2948245704174042 0.6330953 1.161161184310913 True -2 8637 32.12825679779053 0.5083503723144531 508.24755859375 0.5780061483383179 510.61962890625 0.3028993606567383 0.6419068 0.7343727350234985 True -3 11516 32.12304401397705 0.6354858875274658 388.57220458984375 0.4700172543525696 506.510498046875 0.31058910489082336 0.6562731 0.641557514667511 True -4 14395 31.62200427055359 0.5515005588531494 359.9746398925781 0.6650371551513672 502.267333984375 0.32080915570259094 0.6532922 0.560452401638031 False -5 17274 31.466330766677856 0.5377914905548096 415.63751220703125 0.5123149156570435 501.7026672363281 0.3204706907272339 0.6582563 0.5185472965240479 True -6 20153 31.392504692077637 0.5156543254852295 393.73876953125 0.47058773040771484 500.3511047363281 0.3229198455810547 0.6596107 0.49040424823760986 True -7 23032 31.33670163154602 0.5171525478363037 470.52679443359375 0.5628228187561035 499.0427551269531 0.32597821950912476 0.67037255 0.4515000879764557 True -8 25911 31.400710582733154 0.5238573551177979 488.42529296875 0.45047667622566223 497.4919128417969 0.3295862674713135 0.6708352 0.4258308410644531 True -9 28790 31.474239587783813 0.7534847259521484 397.12127685546875 0.35508206486701965 496.7976379394531 0.33138883113861084 0.67668295 0.42916756868362427 True -10 31669 31.471059799194336 0.5449070930480957 353.15643310546875 0.3762562572956085 495.5274658203125 0.3342815339565277 0.6805276 0.4066939353942871 True -11 34548 31.61996293067932 0.5240564346313477 389.825927734375 0.5725914239883423 492.885009765625 0.34024837613105774 0.6903749 0.4012419879436493 True -12 37427 31.60595178604126 0.5267021656036377 404.7768249511719 0.508523166179657 492.61590576171875 0.3407619893550873 0.6992278 0.3792687654495239 True -13 40306 32.661381483078 0.5226948261260986 424.4048156738281 0.46143943071365356 492.0562438964844 0.3412606716156006 0.70905995 0.37118878960609436 True -14 43185 31.56382656097412 0.5198853015899658 424.1044921875 0.29795703291893005 491.2073974609375 0.34349071979522705 0.72098684 0.36051881313323975 True -15 46064 31.565419673919678 0.522075891494751 380.3389587402344 0.40671977400779724 491.0583801269531 0.3435057997703552 0.73052657 0.3482820689678192 True -16 48943 31.53830647468567 3.2468626499176025 443.85443115234375 0.37205690145492554 490.2116394042969 0.34527450799942017 0.7350726 0.34206974506378174 True -17 51822 31.60343098640442 0.6079020500183105 426.5823974609375 0.43760764598846436 490.7221374511719 0.3448256254196167 0.73756725 0.342893123626709 True -18 54701 31.627513885498047 0.5207653045654297 380.68414306640625 0.3170679807662964 490.1210632324219 0.34662926197052 0.73751867 0.3470844030380249 False -19 57580 31.61620593070984 0.5249297618865967 403.26690673828125 0.3324209153652191 490.21380615234375 0.34647393226623535 0.7356771 0.3503378927707672 False diff --git a/ENCSR493VDS/cherimoya.fold_4.performance.tsv b/ENCSR493VDS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4270b08cc17b7c039671ef97bed5961805b76552..0000000000000000000000000000000000000000 --- a/ENCSR493VDS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -490.7221374511719 0.418376088142395 0.3448256850242615 0.12485384941101074 0.7375672459602356 0.6326066851615906 0.342893123626709 \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_0.evaluate.json b/ENCSR495INQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c673cc6148de265f85cf498bf7d313149bb7c0cc..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF909ROS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_0.fit.json b/ENCSR495INQ/cherimoya.fold_0.fit.json deleted file mode 100644 index b28f0bada3e8e47e7f744525257d2970bd9ac7e9..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF909ROS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_0.log b/ENCSR495INQ/cherimoya.fold_0.log deleted file mode 100644 index 8e93d7fe5581abccbfb95c6a80a6d5ee128a47f0..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1788 23.895649433135986 3.817807197570801 254.1388397216797 1.311753273010254 343.92596435546875 0.15773653984069824 0.45878756 9.01089096069336 True -1 3576 19.631591796875 0.4501330852508545 187.55801391601562 1.3219366073608398 307.2835388183594 0.25975605845451355 0.5834164 5.773616313934326 True -2 5364 19.5960955619812 0.36029863357543945 221.73757934570312 0.6324716210365295 284.4310607910156 0.3102791905403137 0.6032721 3.3566927909851074 True -3 7152 19.628309965133667 0.36133503913879395 170.27969360351562 0.8505604267120361 278.5924987792969 0.32387515902519226 0.59886646 2.345717430114746 False -4 8940 19.601616382598877 0.37227845191955566 222.543212890625 1.0865020751953125 274.93548583984375 0.330546498298645 0.6067979 1.8378874063491821 True -5 10728 19.62058997154236 0.3529367446899414 192.43301391601562 0.8874490857124329 273.6422424316406 0.33307215571403503 0.6188934 1.6289738416671753 True -6 12516 19.62912607192993 0.35286688804626465 303.3113098144531 0.7437609434127808 271.4295959472656 0.33887702226638794 0.63563514 1.2689050436019897 True -7 14304 19.59071636199951 0.3523421287536621 283.0631103515625 0.7766085267066956 270.0050048828125 0.3449825048446655 0.6395272 1.1852304935455322 True -8 16092 19.577232837677002 0.36379265785217285 156.06796264648438 0.6200334429740906 268.3460998535156 0.34938955307006836 0.64989704 1.1147748231887817 True -9 17880 19.63819694519043 0.3637523651123047 160.6507568359375 0.6768743395805359 266.1512451171875 0.3546203076839447 0.66154236 0.9623427391052246 True -10 19668 19.612189769744873 0.3657689094543457 206.66265869140625 0.6928824186325073 265.87835693359375 0.35491955280303955 0.67188865 0.859576940536499 True -11 21456 19.611424207687378 0.3608372211456299 175.9113006591797 0.5591195821762085 264.68975830078125 0.3573748469352722 0.67899364 0.8024421334266663 True -12 23244 19.61418318748474 0.3587949275970459 199.5706787109375 0.7744523882865906 263.893310546875 0.3598705232143402 0.6868444 0.7054699659347534 True -13 25032 19.60267448425293 0.3632650375366211 206.53224182128906 0.5351320505142212 262.8034973144531 0.3626721203327179 0.69877666 0.6486145853996277 True -14 26820 19.62479567527771 0.35996150970458984 264.89178466796875 0.7149509787559509 261.9388122558594 0.36602115631103516 0.70631313 0.621593713760376 True -15 28608 19.639970302581787 0.41443681716918945 221.26980590820312 0.5701393485069275 261.7537536621094 0.36531099677085876 0.71562684 0.5860912799835205 True -16 30396 19.5796115398407 1.2383313179016113 208.81622314453125 0.46565914154052734 261.1555480957031 0.3663597106933594 0.71916896 0.5717728734016418 True -17 32184 19.71506977081299 0.3607184886932373 256.6900634765625 0.43008625507354736 261.5083312988281 0.36512598395347595 0.71971184 0.5678163766860962 True -18 33972 19.632104635238647 0.6691684722900391 187.85980224609375 0.37635958194732666 261.51715087890625 0.36679768562316895 0.71752036 0.5700008869171143 False -19 35760 19.656822443008423 0.3588573932647705 269.3962097167969 0.2723906338214874 261.5976867675781 0.3665454387664795 0.7149165 0.5756348371505737 False diff --git a/ENCSR495INQ/cherimoya.fold_0.performance.tsv b/ENCSR495INQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2a8ce576a09992daf6aa0052b85cbd8a1bbd9057..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -261.5083312988281 0.4658415913581848 0.36512598395347595 0.08442708849906921 0.7197118401527405 0.6524226069450378 0.5678163766860962 \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_1.evaluate.json b/ENCSR495INQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d81a8faf4371bb29d219cfdc800b2f961a6c1b48..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF909ROS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_1.fit.json b/ENCSR495INQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 0aa3790eee6df488389c5a10158681d3aa9ef1fb..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF909ROS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_1.log b/ENCSR495INQ/cherimoya.fold_1.log deleted file mode 100644 index 0e787ff6703c29691fa5851b71c7b3b6b240ce87..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1790 24.133882761001587 3.9937899112701416 295.1257019042969 1.479284405708313 420.95513916015625 0.1616770476102829 0.41870406 10.146525382995605 True -1 3580 19.639037609100342 0.5486173629760742 275.87396240234375 0.9557813405990601 369.7630920410156 0.27817535400390625 0.5899283 6.036787033081055 True -2 5370 19.629070520401 0.4964156150817871 249.7684326171875 1.0220472812652588 342.8823547363281 0.33237525820732117 0.623782 3.476855993270874 True -3 7160 19.64855933189392 0.4972827434539795 238.95880126953125 1.0834932327270508 332.0597229003906 0.34861093759536743 0.63668984 2.446223735809326 True -4 8950 19.408127546310425 0.9545125961303711 263.11444091796875 1.1688215732574463 328.70379638671875 0.3512814939022064 0.6413771 1.8121792078018188 True -5 10740 19.25085973739624 0.5342872142791748 244.50790405273438 0.6444908380508423 326.2220764160156 0.3572549521923065 0.649621 1.4822115898132324 True -6 12530 19.23696780204773 0.478557825088501 211.37355041503906 0.7218804955482483 323.224853515625 0.36399391293525696 0.65976346 1.335890293121338 True -7 14320 19.26107382774353 0.5215370655059814 197.42422485351562 0.52229905128479 322.45147705078125 0.36579084396362305 0.6711827 1.2274510860443115 True -8 16110 19.269100189208984 0.4687631130218506 241.90481567382812 0.902763307094574 319.5292663574219 0.3722708523273468 0.6846163 1.0617611408233643 True -9 17900 19.34133553504944 0.4939079284667969 249.43154907226562 1.1207185983657837 317.5182800292969 0.3762953281402588 0.69558716 0.9453562498092651 True -10 19690 19.296188831329346 0.49806690216064453 290.732177734375 1.2349625825881958 315.4121398925781 0.3799656629562378 0.7066424 0.8316068053245544 True -11 21480 19.27629566192627 1.540787696838379 242.58267211914062 0.79118812084198 315.48193359375 0.38043761253356934 0.71747845 0.7578685283660889 True -12 23270 19.26028275489807 0.48517632484436035 231.83253479003906 0.6302680969238281 314.6014404296875 0.3802887499332428 0.7285616 0.7161580920219421 True -13 25060 19.313897371292114 0.4942893981933594 214.9090576171875 0.5581061840057373 312.8521728515625 0.3842512369155884 0.7382866 0.686413049697876 True -14 26850 19.275755167007446 0.4981379508972168 216.63107299804688 0.6797360777854919 312.19854736328125 0.38419100642204285 0.74596226 0.6615619659423828 True -15 28640 19.26606798171997 0.4846651554107666 182.94073486328125 0.48811352252960205 310.9636535644531 0.3873125910758972 0.7530203 0.6281785368919373 True -16 30430 19.27843713760376 0.47243809700012207 225.53860473632812 0.698915421962738 311.4981994628906 0.38520628213882446 0.7550996 0.6139513850212097 True -17 32220 19.29810643196106 0.48665833473205566 246.8465118408203 0.3889589309692383 310.9911193847656 0.3877561390399933 0.75547296 0.6132841110229492 True -18 34010 19.301098346710205 2.2248213291168213 177.8980712890625 0.44793760776519775 311.670166015625 0.38495221734046936 0.7528676 0.6188972592353821 False -19 35800 19.363813638687134 0.4928739070892334 244.26902770996094 0.38624489307403564 312.1136474609375 0.38400998711586 0.75137717 0.6280835270881653 False diff --git a/ENCSR495INQ/cherimoya.fold_1.performance.tsv b/ENCSR495INQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c71e44046bdef1f4ccfe456153df6ec0c484f6b7..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -310.9911193847656 0.4468252956867218 0.3877561390399933 0.09830957651138306 0.7554729580879211 0.6988223791122437 0.6132841110229492 \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_2.evaluate.json b/ENCSR495INQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 29994164ebcd447a91dfcd539c0461bed9364977..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF909ROS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_2.fit.json b/ENCSR495INQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 5e0cfb6c7268559bf95dd16a6d591db527508568..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF909ROS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_2.log b/ENCSR495INQ/cherimoya.fold_2.log deleted file mode 100644 index ef37ca69f974686b2d0a501bb26782c4e3780ffe..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1899 25.36536478996277 3.8677093982696533 190.36170959472656 1.0821326971054077 359.9730529785156 0.1661277562379837 0.43285456 8.211280822753906 True -1 3798 20.814558506011963 1.7678322792053223 240.2844696044922 1.1836731433868408 315.18804931640625 0.2808837294578552 0.5768473 5.257941246032715 True -2 5697 20.86363649368286 0.3729383945465088 153.86846923828125 1.5124297142028809 296.480712890625 0.3185559809207916 0.61014503 3.2757441997528076 True -3 7596 20.914754390716553 0.36461687088012695 260.56915283203125 0.7908554673194885 290.2176818847656 0.32972365617752075 0.6201049 2.163153886795044 True -4 9495 20.805129051208496 0.35391831398010254 272.58935546875 0.9758462309837341 286.9082946777344 0.3368438184261322 0.63013345 1.8046345710754395 True -5 11394 20.846222162246704 0.3708460330963135 217.71234130859375 0.6667274236679077 285.19805908203125 0.33803579211235046 0.64605427 1.5643104314804077 True -6 13293 20.86530900001526 0.3695671558380127 230.730712890625 1.016284465789795 282.8818359375 0.34526821970939636 0.65674335 1.2931643724441528 True -7 15192 20.85675835609436 0.39406895637512207 221.15113830566406 0.8367512226104736 281.2016296386719 0.3502824008464813 0.6638967 1.1725990772247314 True -8 17091 20.85703206062317 0.3679218292236328 198.72286987304688 0.7117140293121338 279.8414001464844 0.3531811535358429 0.6700241 1.0426130294799805 True -9 18990 20.852386713027954 0.3618326187133789 258.2115478515625 0.8010087013244629 278.0737609863281 0.3578508496284485 0.6778738 0.9529792666435242 True -10 20889 20.874460220336914 5.133317232131958 229.57269287109375 0.5469643473625183 276.333740234375 0.36194130778312683 0.6859462 0.8507833480834961 True -11 22788 20.864720344543457 0.38131237030029297 223.0498504638672 0.7487708330154419 275.4259033203125 0.3646436035633087 0.69575775 0.7838985919952393 True -12 24687 20.852484703063965 0.3642995357513428 244.48681640625 0.4126632511615753 274.25732421875 0.36631786823272705 0.705652 0.735133945941925 True -13 26586 20.824732065200806 0.3623969554901123 252.15257263183594 0.5680564641952515 273.1522216796875 0.3664994239807129 0.71551234 0.6596350073814392 True -14 28485 20.865116357803345 0.362778902053833 234.78610229492188 0.7302913069725037 271.9247741699219 0.36941227316856384 0.72316384 0.626570463180542 True -15 30384 20.84845209121704 0.36321091651916504 176.3982391357422 0.3654147982597351 272.27862548828125 0.36827483773231506 0.73110276 0.6041406393051147 True -16 32283 20.848334312438965 0.36495518684387207 233.68792724609375 0.4674253463745117 271.5751647949219 0.36990177631378174 0.73856777 0.5874565243721008 True -17 34182 20.835498809814453 0.36437535285949707 200.40203857421875 0.8061367273330688 271.6855163574219 0.368602991104126 0.740421 0.575270414352417 True -18 36081 20.900892734527588 0.361328125 209.17611694335938 0.36406221985816956 271.9983825683594 0.36753422021865845 0.73819745 0.5754522681236267 False -19 37980 20.83638048171997 0.38066887855529785 186.02435302734375 0.32710543274879456 272.033447265625 0.3686632215976715 0.7369566 0.5829103589057922 False diff --git a/ENCSR495INQ/cherimoya.fold_2.performance.tsv b/ENCSR495INQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9e50c225ea25407011d4dbbebcaecc30062046bc..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.6855163574219 0.4622940719127655 0.3686029613018036 0.0928177610039711 0.7404209971427917 0.6742926239967346 0.575270414352417 \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_3.evaluate.json b/ENCSR495INQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a7e9c06ed77aad770d10d85a29e606401a089f10..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF909ROS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_3.fit.json b/ENCSR495INQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 48f6de358d90b4d70d17590d125ca36cbc102207..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF909ROS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_3.log b/ENCSR495INQ/cherimoya.fold_3.log deleted file mode 100644 index 0ce6c4d750f5e43a3742b64ec7308f26c3218efe..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1832 24.550482511520386 3.6449625492095947 237.51739501953125 1.0303983688354492 377.26885986328125 0.15929488837718964 0.46004757 9.251936912536621 True -1 3664 20.13136386871338 0.3973395824432373 221.75985717773438 1.1490575075149536 335.5650939941406 0.26347440481185913 0.5816481 6.337131023406982 True -2 5496 20.124322652816772 1.1925604343414307 174.9149932861328 0.8082610368728638 314.1246032714844 0.3151835799217224 0.5948247 3.29164981842041 True -3 7328 20.09423828125 0.397258996963501 195.74612426757812 0.6392017602920532 307.34716796875 0.32635951042175293 0.5991932 2.183530330657959 True -4 9160 20.088330507278442 0.37119102478027344 294.2785339355469 1.3592402935028076 302.91796875 0.33623942732810974 0.6152925 1.7239257097244263 True -5 10992 20.07002091407776 0.3806493282318115 208.49693298339844 1.031970739364624 300.65087890625 0.34076690673828125 0.6259584 1.5764814615249634 True -6 12824 20.108460903167725 0.40880608558654785 218.69613647460938 0.9734971523284912 298.5796813964844 0.34576746821403503 0.636868 1.3855208158493042 True -7 14656 20.191880702972412 2.005448579788208 210.77642822265625 0.4787389039993286 296.8458557128906 0.3501511514186859 0.64231014 1.2006311416625977 True -8 16488 20.106890201568604 0.3712496757507324 197.6615753173828 0.6721377968788147 294.89862060546875 0.3529607057571411 0.654853 1.1094642877578735 True -9 18320 20.113722801208496 0.3708314895629883 202.63043212890625 0.7950729131698608 294.2193908691406 0.3536771237850189 0.6670177 0.9868903160095215 True -10 20152 20.145604372024536 1.5912666320800781 243.80531311035156 0.8270496129989624 292.5221862792969 0.3579702377319336 0.67913526 0.8653407692909241 True -11 21984 20.162856340408325 0.38037896156311035 189.3477783203125 0.6947143077850342 290.3551025390625 0.36388474702835083 0.68814117 0.8186795711517334 True -12 23816 20.140640258789062 0.3778064250946045 185.58395385742188 0.6172362565994263 289.290283203125 0.36499547958374023 0.70233303 0.7444616556167603 True -13 25648 20.092942476272583 0.37637805938720703 173.97845458984375 0.5190784931182861 288.3139343261719 0.3663419783115387 0.7145419 0.6931887865066528 True -14 27480 20.138040781021118 4.274069786071777 253.22927856445312 0.5797265768051147 287.6986389160156 0.3663923740386963 0.7291423 0.650360643863678 True -15 29312 20.112799406051636 9.590064525604248 168.4649200439453 0.42787742614746094 286.7083435058594 0.3687908947467804 0.73719716 0.6088104248046875 True -16 31144 20.309107542037964 0.37578701972961426 195.59912109375 0.4302780330181122 286.8386535644531 0.36835411190986633 0.7436895 0.5964329242706299 True -17 32976 20.167858600616455 0.3970465660095215 196.7971954345703 0.7449654340744019 286.5517272949219 0.3690090775489807 0.74262965 0.5921522974967957 False -18 34808 20.160942554473877 0.38257336616516113 188.37991333007812 0.27737995982170105 286.79620361328125 0.36892715096473694 0.7414838 0.6000674366950989 False -19 36640 20.142003536224365 0.3873448371887207 209.5056915283203 0.3213851749897003 286.6398010253906 0.3697839081287384 0.740678 0.6045106053352356 False diff --git a/ENCSR495INQ/cherimoya.fold_3.performance.tsv b/ENCSR495INQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 68b0b3fcf2e7d2f2c92788c28bac7d2d0ba90b41..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -286.8386535644531 0.4609246850013733 0.3683541417121887 0.09482431411743164 0.7436894774436951 0.6803184747695923 0.5964329242706299 \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_4.evaluate.json b/ENCSR495INQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fc99a765a2c91d1b5fb1d6cfea6850a771eb3d1a..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF909ROS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_4.fit.json b/ENCSR495INQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 6bb4d7dd19fc6f40afc1da27fb7804fe3e34f1f2..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF909ROS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR495INQ/cherimoya.fold_4.log b/ENCSR495INQ/cherimoya.fold_4.log deleted file mode 100644 index 55c2cbac7c0666951009816004ab53ced5a7a98e..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1830 24.43570113182068 3.573077440261841 248.85227966308594 0.9607561230659485 343.5075378417969 0.15314652025699615 0.46796146 7.932397842407227 True -1 3660 20.103532552719116 0.34916043281555176 233.92129516601562 1.0618630647659302 301.8731384277344 0.2716435492038727 0.58186954 5.488650798797607 True -2 5490 20.130404233932495 0.34874629974365234 313.527099609375 0.8309563994407654 284.3099670410156 0.3151467740535736 0.5474904 3.284621000289917 False -3 7320 20.093101501464844 0.3424396514892578 273.39801025390625 0.7606527805328369 278.6361083984375 0.3248351216316223 0.57388127 2.46934175491333 False -4 9150 20.089496612548828 0.34244418144226074 261.64520263671875 0.8708512783050537 274.6905517578125 0.3320154547691345 0.59153694 1.894351601600647 True -5 10980 20.168901205062866 0.34848618507385254 207.79725646972656 0.8332817554473877 272.4370422363281 0.3350052833557129 0.6011858 1.6854476928710938 True -6 12810 20.08149743080139 0.3463585376739502 209.61203002929688 0.7933777570724487 270.59539794921875 0.3390040695667267 0.62589043 1.4654916524887085 True -7 14640 20.08154273033142 1.3121323585510254 212.30572509765625 0.6889723539352417 268.8193054199219 0.3438277840614319 0.6302731 1.2934002876281738 True -8 16470 20.141059160232544 0.3517496585845947 213.59466552734375 0.8285425901412964 267.529296875 0.3463231921195984 0.64237326 1.1585536003112793 True -9 18300 20.131965398788452 0.6283314228057861 230.01119995117188 0.8415563106536865 265.9062194824219 0.35194265842437744 0.6558265 1.0168755054473877 True -10 20130 20.066582202911377 0.3606090545654297 166.27366638183594 0.4808257818222046 264.8636169433594 0.3551166355609894 0.67526186 0.8724969029426575 True -11 21960 20.067814588546753 0.3527982234954834 232.0504150390625 0.8212912082672119 263.7624816894531 0.3567620813846588 0.68592185 0.7792524695396423 True -12 23790 20.07080864906311 0.3427116870880127 210.4173583984375 0.6992427110671997 262.4332580566406 0.3612654507160187 0.6966127 0.7207058668136597 True -13 25620 20.06292700767517 0.34612345695495605 225.15798950195312 0.8612509369850159 261.89105224609375 0.3615157902240753 0.7069246 0.6659157276153564 True -14 27450 20.07981824874878 0.35395264625549316 246.62564086914062 0.6269543170928955 261.365234375 0.3614501953125 0.7167604 0.6196025609970093 True -15 29280 20.07022976875305 0.345797061920166 217.3164825439453 0.4323855936527252 260.073974609375 0.3655514717102051 0.72554475 0.5853191018104553 True -16 31110 19.800270557403564 0.33813023567199707 229.80581665039062 0.5705525875091553 260.3404846191406 0.3640125095844269 0.7287765 0.5641740560531616 True -17 32940 19.67890954017639 0.33705568313598633 176.77566528320312 0.4270883798599243 260.65350341796875 0.36179274320602417 0.73004365 0.5563668608665466 True -18 34770 19.667439222335815 0.3485853672027588 232.18698120117188 0.27857697010040283 261.09375 0.3615495562553406 0.7298499 0.5554768443107605 False -19 36600 19.6792573928833 0.3484506607055664 221.98617553710938 0.34852656722068787 261.3941345214844 0.3602616488933563 0.72772986 0.5594560503959656 False diff --git a/ENCSR495INQ/cherimoya.fold_4.performance.tsv b/ENCSR495INQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index bd836e645a71a94f7ccdb8a4938b4acd7d5efe11..0000000000000000000000000000000000000000 --- a/ENCSR495INQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -260.65350341796875 0.46816107630729675 0.36179277300834656 0.08306892216205597 0.7300436496734619 0.658338189125061 0.5563668608665466 \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_0.evaluate.json b/ENCSR496PSH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index cee58e30bceab6b36bdf8a5dc6099649824e72de..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF320PYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_0.fit.json b/ENCSR496PSH/cherimoya.fold_0.fit.json deleted file mode 100644 index d8757dedf9b58f1be7cc6f2ee8ecb89e0b43733b..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF320PYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_0.log b/ENCSR496PSH/cherimoya.fold_0.log deleted file mode 100644 index 7e991a3d41403be45387bad868fc40bf48af27b4..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 36.407663106918335 39.08405542373657 744.6588134765625 0.5502551794052124 926.1314697265625 0.27964064478874207 0.7300593 5.512833595275879 True -1 5496 30.480807781219482 22.66438603401184 749.23876953125 0.7445452809333801 821.1036376953125 0.3709605634212494 0.7827969 1.3855469226837158 True -2 8244 30.541199922561646 0.6237509250640869 614.6381225585938 0.5582519769668579 807.82080078125 0.3801923096179962 0.7853946 0.7009627819061279 True -3 10992 30.333497047424316 0.5679032802581787 614.156005859375 0.4400450587272644 798.3600463867188 0.3897242248058319 0.79000163 0.5980725288391113 True -4 13740 34.588027000427246 37.767895221710205 642.3724365234375 0.4800119996070862 790.5953979492188 0.39727479219436646 0.7931279 0.4940214455127716 True -5 16488 32.865216970443726 17.684643268585205 722.1632080078125 0.474931538105011 787.8981323242188 0.40000858902931213 0.79862696 0.48209112882614136 True -6 19236 30.623281002044678 0.578181266784668 604.3427124023438 0.42873403429985046 784.3226928710938 0.4037245810031891 0.79803157 0.4106234908103943 False -7 21984 30.458277463912964 0.5909726619720459 605.2314453125 0.46850496530532837 779.8048095703125 0.40800032019615173 0.80548435 0.3521675765514374 True -8 24732 30.443239450454712 0.5778243541717529 540.1044921875 0.3556402325630188 778.037109375 0.41013452410697937 0.8053763 0.34741365909576416 False -9 27480 30.373223543167114 0.5791194438934326 624.3194580078125 0.45777881145477295 776.6881713867188 0.4119316041469574 0.8080689 0.33724087476730347 True -10 30228 30.40522265434265 0.6074817180633545 687.7295532226562 0.2971038222312927 771.3886108398438 0.4162030518054962 0.81428427 0.3190622925758362 True -11 32976 30.518447637557983 0.5919690132141113 701.6548461914062 0.35883212089538574 769.7544555664062 0.4167996048927307 0.8224201 0.3124658167362213 True -12 35724 30.4372398853302 0.5969631671905518 628.243408203125 0.33121544122695923 765.6773071289062 0.4216352701187134 0.8293987 0.30223119258880615 True -13 38472 30.452836275100708 0.5905930995941162 691.177734375 0.5711994767189026 766.7778930664062 0.4186550974845886 0.83263564 0.2951792776584625 True -14 41220 30.465651273727417 0.5989699363708496 576.484619140625 0.28386974334716797 763.045166015625 0.4228442311286926 0.8380447 0.28416886925697327 True -15 43968 30.46187949180603 0.5920264720916748 654.7854614257812 0.22713536024093628 760.6073608398438 0.42480987310409546 0.8421491 0.2780879735946655 True -16 46716 30.416956424713135 0.5919005870819092 706.3076171875 0.3545883893966675 760.3606567382812 0.42554372549057007 0.8468836 0.26969873905181885 True -17 49464 30.417635440826416 1.065230369567871 678.7952880859375 0.3073159456253052 760.7031860351562 0.425116628408432 0.8484138 0.2679186463356018 True -18 52212 30.45230221748352 0.5935802459716797 611.0806274414062 0.21091514825820923 760.6381225585938 0.42688634991645813 0.84850377 0.2676413655281067 True -19 54960 30.397298097610474 0.5962011814117432 669.0430908203125 0.3378727436065674 760.8463745117188 0.42595845460891724 0.84749013 0.2675168812274933 False diff --git a/ENCSR496PSH/cherimoya.fold_0.performance.tsv b/ENCSR496PSH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 18fa4a21be1c603e889aeeaa5289334c92cedcd5..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -760.6381225585938 0.35860225558280945 0.4268863797187805 0.1865531951189041 0.8485037684440613 0.7997302412986755 0.2676413655281067 \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_1.evaluate.json b/ENCSR496PSH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3f2528938bc31ab321995f80182813cef47581b5..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF320PYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_1.fit.json b/ENCSR496PSH/cherimoya.fold_1.fit.json deleted file mode 100644 index b35713d9069475b014069b224d8e0093e07c9552..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF320PYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_1.log b/ENCSR496PSH/cherimoya.fold_1.log deleted file mode 100644 index 7156c5128053e94ba2b5cc762d1f1838d9364d25..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 34.784257650375366 3.9488604068756104 669.4236450195312 0.9285852909088135 1075.0377197265625 0.28131213784217834 0.716152 6.408689498901367 True -1 5406 30.190678119659424 0.8714590072631836 679.092529296875 0.4432782232761383 949.984619140625 0.37930193543434143 0.7780485 1.8905103206634521 True -2 8109 29.855791091918945 29.314699411392212 759.1488037109375 0.49985963106155396 933.4671020507812 0.38880425691604614 0.7861685 0.8481027483940125 True -3 10812 29.868763208389282 44.99090242385864 516.6417846679688 0.32777857780456543 917.2261352539062 0.3976665735244751 0.7957249 0.6451467871665955 True -4 13515 30.29527449607849 1.9748480319976807 641.2811279296875 0.3532574474811554 905.7130126953125 0.4064200520515442 0.80646837 0.5086123943328857 True -5 16218 29.80101251602173 0.7010669708251953 572.9432983398438 0.4540550708770752 898.1117553710938 0.41375532746315 0.8105801 0.4117676317691803 True -6 18921 29.836193084716797 0.7290666103363037 728.2325439453125 0.28411155939102173 892.414794921875 0.4187014400959015 0.81586707 0.40096548199653625 True -7 21624 29.85293698310852 1.3878142833709717 635.0753173828125 0.3780851364135742 888.3516845703125 0.4214467704296112 0.8204078 0.36446264386177063 True -8 24327 29.870927333831787 0.7024991512298584 534.072509765625 0.6050736308097839 883.537109375 0.42658939957618713 0.8236972 0.35010531544685364 True -9 27030 29.834859609603882 0.7191822528839111 571.7432861328125 0.35311388969421387 878.0658569335938 0.4302749037742615 0.8282252 0.3423311114311218 True -10 29733 29.917306661605835 0.7057902812957764 689.5743408203125 0.2921822965145111 875.0186157226562 0.43317779898643494 0.8316208 0.32631295919418335 True -11 32436 29.963435649871826 0.7119157314300537 673.8668212890625 0.38635873794555664 871.2103271484375 0.4363272488117218 0.8363189 0.3156103193759918 True -12 35139 29.962411165237427 0.7077071666717529 540.5908203125 0.1911839097738266 869.167236328125 0.43604084849357605 0.84090006 0.3071689307689667 True -13 37842 29.976096153259277 0.7068312168121338 629.66796875 0.30081743001937866 868.0991821289062 0.436627596616745 0.8442547 0.3051726520061493 True -14 40545 30.038990020751953 0.7041878700256348 642.8382568359375 0.3485267460346222 861.7169189453125 0.44229137897491455 0.8485889 0.2976893484592438 True -15 43248 29.98578643798828 0.7056107521057129 654.298095703125 0.2994200587272644 859.5595703125 0.44322648644447327 0.85393304 0.2914399206638336 True -16 45951 29.976462841033936 0.6997175216674805 553.606201171875 0.2576627731323242 858.3928833007812 0.4440823793411255 0.85570914 0.28691181540489197 True -17 48654 30.079113721847534 0.6982359886169434 615.496826171875 0.3876928687095642 860.1530151367188 0.4418255388736725 0.85849035 0.28404152393341064 True -18 51357 29.87346625328064 19.337888956069946 633.576416015625 0.3155176043510437 858.740966796875 0.4431317448616028 0.8578303 0.28471001982688904 False -19 54060 30.017431497573853 1.6325581073760986 666.4051513671875 0.2975458800792694 859.4076538085938 0.4423326849937439 0.8575502 0.286615252494812 False diff --git a/ENCSR496PSH/cherimoya.fold_1.performance.tsv b/ENCSR496PSH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4f004d799f2d11bbe95defb9c8d9888043c15fde..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -860.1530151367188 0.3420632779598236 0.4418255388736725 0.2046523243188858 0.8584903478622437 0.8264676332473755 0.28404152393341064 \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_2.evaluate.json b/ENCSR496PSH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7b5094312f39ee67f860973e2aa47c0ca317761c..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF320PYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_2.fit.json b/ENCSR496PSH/cherimoya.fold_2.fit.json deleted file mode 100644 index 97ffabf8d8f60f83834a6c02fdf98af03625617d..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF320PYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_2.log b/ENCSR496PSH/cherimoya.fold_2.log deleted file mode 100644 index 010b7df377d8437abedb9779773564e5b41a0c53..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.25891947746277 3.557424545288086 639.8966064453125 0.4577912390232086 956.6124877929688 0.28747129440307617 0.7241347 5.767119407653809 True -1 5754 31.78834843635559 0.5788259506225586 769.2095947265625 0.620238184928894 852.3748779296875 0.3738830089569092 0.7736724 1.3548400402069092 True -2 8631 31.78123426437378 0.55411696434021 624.51513671875 0.7724418044090271 835.1847534179688 0.3843673765659332 0.78463155 0.6175746321678162 True -3 11508 31.768071174621582 2.616203546524048 664.8740234375 0.4002256691455841 825.693603515625 0.3920001685619354 0.7914394 0.5356179475784302 True -4 14385 32.17835021018982 0.5643937587738037 728.010498046875 0.5661177635192871 821.6360473632812 0.395627498626709 0.79704195 0.5016040205955505 True -5 17262 31.75680446624756 0.5588061809539795 617.714599609375 0.5574585199356079 817.13818359375 0.40054357051849365 0.7988586 0.3854067921638489 True -6 20139 31.74411368370056 0.5585951805114746 587.5469970703125 0.45063313841819763 810.4728393554688 0.40703609585762024 0.8018442 0.34965768456459045 True -7 23016 31.723456144332886 0.5739803314208984 699.3525390625 0.4552134573459625 807.093017578125 0.4086231291294098 0.8083061 0.3493275046348572 True -8 25893 31.752458810806274 0.5594875812530518 576.8607788085938 0.46102213859558105 803.0219116210938 0.4135202467441559 0.80916727 0.3344392776489258 True -9 28770 31.778568267822266 0.5533370971679688 562.088623046875 0.31486815214157104 800.8484497070312 0.4151715934276581 0.8103733 0.3283766508102417 True -10 31647 31.82087779045105 0.5652740001678467 707.4007568359375 0.3808315396308899 797.8262329101562 0.4183696508407593 0.8142592 0.32614436745643616 True -11 34524 31.809325695037842 0.5636112689971924 729.4784545898438 0.37647420167922974 793.5714111328125 0.4221193492412567 0.819216 0.30994778871536255 True -12 37401 31.808898210525513 0.5628318786621094 695.8988037109375 0.3529697060585022 790.0197143554688 0.4254658818244934 0.82460153 0.30993881821632385 True -13 40278 31.739404916763306 0.5646531581878662 543.489013671875 0.2595691680908203 786.80126953125 0.4264518916606903 0.8286447 0.29963186383247375 True -14 43155 31.717857837677002 0.562427282333374 692.8771362304688 0.2838519215583801 784.8836669921875 0.42846885323524475 0.83339256 0.2931040823459625 True -15 46032 31.715949058532715 0.5521030426025391 667.583740234375 0.3448602557182312 784.5343017578125 0.42738986015319824 0.83660555 0.2888360917568207 True -16 48909 31.768959045410156 0.5541644096374512 534.139892578125 0.3147701025009155 783.216552734375 0.42914536595344543 0.8395753 0.28393444418907166 True -17 51786 31.92020869255066 0.562105655670166 700.181396484375 0.28596174716949463 782.994140625 0.4297584295272827 0.8402909 0.2854401171207428 True -18 54663 31.723796367645264 0.5612955093383789 627.1029052734375 0.322221964597702 784.17578125 0.4283665716648102 0.8401282 0.2856670618057251 False -19 57540 31.71820044517517 0.5637092590332031 673.2276611328125 0.24801599979400635 783.78955078125 0.42900189757347107 0.8393509 0.2884514629840851 False diff --git a/ENCSR496PSH/cherimoya.fold_2.performance.tsv b/ENCSR496PSH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c0d1b56475dd18c4aee915986ac743114f25095f..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -782.994140625 0.35445040464401245 0.4297584295272827 0.18765278160572052 0.840290904045105 0.7954138517379761 0.2854401171207428 \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_3.evaluate.json b/ENCSR496PSH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d75d4d0dd84629c78a781be31879a233b991887a..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF320PYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_3.fit.json b/ENCSR496PSH/cherimoya.fold_3.fit.json deleted file mode 100644 index b3862ca9b8312ea3248d9b4a04cdd5fd2e84b65d..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF320PYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_3.log b/ENCSR496PSH/cherimoya.fold_3.log deleted file mode 100644 index 747ea3e7c6a1806080098421ec424433dc5cd662..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 35.07603859901428 5.197185516357422 682.0528564453125 0.524869978427887 912.6896362304688 0.28620240092277527 0.73164445 7.148519039154053 True -1 5522 30.555665731430054 0.5373764038085938 704.12353515625 0.4575601816177368 813.9224853515625 0.3736509084701538 0.79228485 2.070004463195801 True -2 8283 30.535815477371216 1.3637261390686035 753.8304443359375 0.5163183212280273 802.5230102539062 0.38207313418388367 0.800061 0.7071748971939087 True -3 11044 30.51757788658142 0.5169448852539062 761.404052734375 0.4579421579837799 790.2118530273438 0.39038917422294617 0.80654246 0.5887656807899475 True -4 13805 30.503382444381714 0.519406795501709 622.4520263671875 0.4280130863189697 785.7523803710938 0.39441052079200745 0.81190866 0.549389123916626 True -5 16566 30.47333264350891 0.521747350692749 642.4359130859375 0.489441841840744 780.0517578125 0.4004163146018982 0.81256104 0.44604960083961487 True -6 19327 30.433873414993286 0.5139577388763428 550.7977294921875 0.4177442789077759 776.4412231445312 0.4028382897377014 0.8173451 0.4233596622943878 True -7 22088 30.451524019241333 0.5212631225585938 711.314208984375 0.4387345314025879 772.9263916015625 0.4072951078414917 0.8175748 0.38797709345817566 True -8 24849 30.45852756500244 0.5147442817687988 624.8284301757812 0.47393304109573364 769.7645874023438 0.4100244343280792 0.8220089 0.3756783604621887 True -9 27610 30.4388689994812 0.5201776027679443 649.1689453125 0.3530139923095703 767.70263671875 0.41256821155548096 0.82182336 0.36896830797195435 False -10 30371 30.58989691734314 0.5190021991729736 592.2449951171875 0.2737235724925995 764.9544067382812 0.4143068790435791 0.8252357 0.34867623448371887 True -11 33132 30.487698078155518 0.5143380165100098 700.0155639648438 0.36922362446784973 761.03515625 0.41821661591529846 0.8323365 0.335254967212677 True -12 35893 30.704455375671387 17.595390796661377 709.4152221679688 0.3390342593193054 758.9705810546875 0.42006605863571167 0.83637834 0.3192766010761261 True -13 38654 30.517255783081055 1.575350046157837 650.3563842773438 0.2862669825553894 756.6666870117188 0.4216615855693817 0.8416834 0.309447318315506 True -14 41415 30.575210094451904 1.788123607635498 653.016845703125 0.22580866515636444 754.1870727539062 0.42376771569252014 0.84868085 0.294176310300827 True -15 44176 30.708681344985962 1.0353319644927979 646.01025390625 0.29252809286117554 750.5661010742188 0.4275124669075012 0.8519742 0.2853452265262604 True -16 46937 30.501834392547607 0.8346090316772461 649.7247924804688 0.309338241815567 750.1963500976562 0.42708587646484375 0.855934 0.27949073910713196 True -17 49698 30.428367614746094 1.539792537689209 627.20654296875 0.2754782736301422 751.4548950195312 0.4251384735107422 0.85650265 0.2774939239025116 True -18 52459 30.464902639389038 1.303328275680542 707.6987915039062 0.3272668123245239 750.33837890625 0.4275662899017334 0.8577361 0.2773609161376953 True -19 55220 30.89240050315857 1.7415595054626465 582.2894897460938 0.1862322986125946 751.4076538085938 0.42606404423713684 0.8572217 0.2775540053844452 False diff --git a/ENCSR496PSH/cherimoya.fold_3.performance.tsv b/ENCSR496PSH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 57bc951b595d46e1fa547fee52e8fdd7f9dd3af3..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -750.33837890625 0.35925060510635376 0.4275663197040558 0.18632565438747406 0.8577361106872559 0.8091837763786316 0.2773609161376953 \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_4.evaluate.json b/ENCSR496PSH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e89f2f9666ade832de5b6553e90dbc4cff0a4d5d..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF320PYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_4.fit.json b/ENCSR496PSH/cherimoya.fold_4.fit.json deleted file mode 100644 index 2b6e231dd195d36a25c8f1bc92366cf8e51a551f..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF320PYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496PSH/cherimoya.fold_4.log b/ENCSR496PSH/cherimoya.fold_4.log deleted file mode 100644 index 94581aac09f712a512406d71c97754cced59c681..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2815 36.060755491256714 5.247415781021118 670.9549560546875 0.5212457180023193 862.0093383789062 0.281707227230072 0.7207429 4.964878559112549 True -1 5630 31.083680152893066 2.670691728591919 818.8602905273438 0.4878610372543335 778.3768920898438 0.3584817349910736 0.7713568 1.2701889276504517 True -2 8445 31.09066390991211 0.5824100971221924 602.8717041015625 0.590468168258667 761.94140625 0.37372705340385437 0.779621 0.7594563961029053 True -3 11260 31.048101663589478 1.3173165321350098 598.2825927734375 0.5991510152816772 754.61474609375 0.3793976604938507 0.7874514 0.6094772815704346 True -4 14075 31.011856079101562 0.577601432800293 520.478759765625 0.5116381645202637 750.119384765625 0.38459596037864685 0.7909393 0.5692774057388306 True -5 16890 31.043899059295654 0.577850341796875 479.74920654296875 0.7400960326194763 746.6221313476562 0.38799816370010376 0.79167014 0.4323030412197113 True -6 19705 31.51665997505188 22.88627862930298 559.569091796875 0.3658486008644104 742.94384765625 0.3927258551120758 0.7966784 0.4204042851924896 True -7 22520 31.313408374786377 0.6053345203399658 757.3363037109375 0.4334944486618042 739.7044067382812 0.3963022530078888 0.7977262 0.37343794107437134 True -8 25335 31.244967699050903 0.5793523788452148 570.6604614257812 0.3074181079864502 735.7166137695312 0.4007522761821747 0.80702335 0.34810736775398254 True -9 28150 31.201600790023804 0.5867407321929932 671.6488037109375 0.5147402882575989 733.7005615234375 0.4022665321826935 0.80987006 0.32552778720855713 True -10 30965 31.375525951385498 0.5862910747528076 623.0150146484375 0.24164068698883057 730.4759521484375 0.40579795837402344 0.8156786 0.3056849241256714 True -11 33780 31.16456913948059 0.5728497505187988 627.3297729492188 0.37005794048309326 727.91796875 0.40845564007759094 0.8186032 0.30693355202674866 True -12 36595 31.11721634864807 0.939300537109375 622.4833984375 0.2921519875526428 725.3213500976562 0.41014087200164795 0.825617 0.28679153323173523 True -13 39410 31.2487530708313 0.5792105197906494 601.3079833984375 0.4319334030151367 723.5392456054688 0.4116002321243286 0.8290705 0.2784229815006256 True -14 42225 31.194533586502075 0.5744869709014893 634.64794921875 0.30530157685279846 721.8641967773438 0.41368773579597473 0.83313006 0.27166226506233215 True -15 45040 31.227686166763306 34.70913290977478 602.7827758789062 0.34247294068336487 720.8305053710938 0.4139024317264557 0.83689785 0.2645474374294281 True -16 47855 31.474015474319458 5.89061713218689 556.8576049804688 0.23355482518672943 720.1179809570312 0.4141966700553894 0.8410853 0.26224082708358765 True -17 50670 31.446154356002808 33.54190397262573 619.0628662109375 0.2565913200378418 721.343994140625 0.4135691225528717 0.8420877 0.25845053791999817 True -18 53485 33.84169411659241 0.588111162185669 689.610107421875 0.23778171837329865 721.0501098632812 0.4135252833366394 0.8411423 0.2598731815814972 False -19 56300 31.427753448486328 0.6102437973022461 631.9157104492188 0.20070961117744446 720.4221801757812 0.4146871268749237 0.8401982 0.26188820600509644 False diff --git a/ENCSR496PSH/cherimoya.fold_4.performance.tsv b/ENCSR496PSH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4234bab369c73e9dbfa288fa442dd299b47dd741..0000000000000000000000000000000000000000 --- a/ENCSR496PSH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -721.343994140625 0.3672406077384949 0.41356906294822693 0.17669351398944855 0.8420876860618591 0.7857762575149536 0.25845053791999817 \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_0.evaluate.json b/ENCSR496UER/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 551bfb11349f9810dd1e81b10bfe9d3a6eefaf21..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215LFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_0.fit.json b/ENCSR496UER/cherimoya.fold_0.fit.json deleted file mode 100644 index 9008430b34f9f665e1c7e00529e4d80389dde357..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF215LFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_0.log b/ENCSR496UER/cherimoya.fold_0.log deleted file mode 100644 index 8865b1d26ab8cf5b91e1f55bc14ab9d83cfc8784..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1982 26.461148262023926 3.4807567596435547 261.75982666015625 1.053607702255249 489.992431640625 0.15330569446086884 0.51914626 9.374471664428711 True -1 3964 21.9992835521698 0.5807244777679443 292.4648742675781 1.0836763381958008 425.1983947753906 0.21844083070755005 0.6809413 4.995296478271484 True -2 5946 22.068875789642334 21.23388957977295 294.78375244140625 1.4586131572723389 401.00396728515625 0.23611262440681458 0.7253229 3.6871085166931152 True -3 7928 22.501734972000122 0.4356241226196289 333.27801513671875 0.9539575576782227 390.74420166015625 0.2422938495874405 0.7393533 1.9182803630828857 True -4 9910 22.00886368751526 0.40284061431884766 294.1935729980469 0.6685935854911804 383.7958679199219 0.2491418868303299 0.74396497 1.4596517086029053 True -5 11892 22.06569242477417 0.4375009536743164 319.60614013671875 0.6833550333976746 378.1645812988281 0.25490400195121765 0.75491124 1.1685616970062256 True -6 13874 21.959829568862915 0.42196011543273926 305.19635009765625 1.0998152494430542 374.4723815917969 0.25797808170318604 0.7660527 1.0890560150146484 True -7 15856 22.015764474868774 0.4155309200286865 445.2333984375 0.7106044292449951 371.70294189453125 0.2598915994167328 0.78168714 0.9691933393478394 True -8 17838 22.027588367462158 0.4228200912475586 296.7120666503906 0.6011149883270264 370.34954833984375 0.2617594301700592 0.789437 0.8668513894081116 True -9 19820 22.025428295135498 0.40355730056762695 253.65707397460938 0.8125839829444885 367.16094970703125 0.2659166753292084 0.7953693 0.8707956671714783 True -10 21802 22.000473260879517 0.41266798973083496 339.3731689453125 0.6923820376396179 365.20068359375 0.2686465382575989 0.8029761 0.7665326595306396 True -11 23784 21.966810703277588 0.40834569931030273 283.3782653808594 0.4704130291938782 363.79644775390625 0.26951825618743896 0.80738515 0.7109789848327637 True -12 25766 22.01166009902954 0.4266808032989502 362.0099792480469 0.49442675709724426 361.1550598144531 0.2720869779586792 0.81560904 0.6637755036354065 True -13 27748 21.96598792076111 0.4148728847503662 238.49008178710938 0.43621426820755005 358.15643310546875 0.2760474681854248 0.8246831 0.6059061288833618 True -14 29730 21.99968934059143 0.42700719833374023 339.1235656738281 0.5920426845550537 356.67669677734375 0.27626925706863403 0.8285172 0.5648503303527832 True -15 31712 22.00887942314148 0.4267566204071045 307.4266052246094 0.28383156657218933 354.8699645996094 0.2785264551639557 0.83281326 0.5332623720169067 True -16 33694 22.00297260284424 0.412189245223999 297.1614990234375 0.46224111318588257 355.1304016113281 0.2773454189300537 0.8359247 0.506852388381958 True -17 35676 21.967079877853394 0.41207456588745117 305.2633056640625 0.3948507606983185 355.25518798828125 0.2778978943824768 0.8371956 0.49496108293533325 True -18 37658 21.989253044128418 0.5051047801971436 289.640380859375 0.2958008646965027 356.1764221191406 0.2766294479370117 0.83790106 0.4949626624584198 True -19 39640 22.055720806121826 0.4031107425689697 291.1103515625 0.2670150101184845 356.07574462890625 0.27644118666648865 0.8361427 0.4970918297767639 False diff --git a/ENCSR496UER/cherimoya.fold_0.performance.tsv b/ENCSR496UER/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2cff19381df0bdb293a284968c39c927210069dc..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -356.1764221191406 0.49137771129608154 0.2766294479370117 0.09246528148651123 0.8379010558128357 0.7889794707298279 0.4949626624584198 \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_1.evaluate.json b/ENCSR496UER/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0540e982cdf8770defae6652c9ba397ecb4f9d39..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215LFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_1.fit.json b/ENCSR496UER/cherimoya.fold_1.fit.json deleted file mode 100644 index 58bf5c012fa0adcef161ef861a313c9f99d6600f..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF215LFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_1.log b/ENCSR496UER/cherimoya.fold_1.log deleted file mode 100644 index 07fe4f2d3658cef2a89a60a7c70cc118b10f1f6d..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1925 26.495872497558594 3.753019094467163 270.88031005859375 0.9422391653060913 616.099365234375 0.16358044743537903 0.49061182 10.823500633239746 True -1 3850 21.356322050094604 0.7214822769165039 407.7433166503906 0.9656899571418762 535.7100830078125 0.23589767515659332 0.6580607 6.024522304534912 True -2 5775 21.342365741729736 0.5621120929718018 389.91644287109375 0.5605688095092773 495.52752685546875 0.26364827156066895 0.7204215 4.124533653259277 True -3 7700 21.36948537826538 0.5540094375610352 351.16619873046875 1.1810358762741089 479.0228576660156 0.27314454317092896 0.72674006 2.552264928817749 True -4 9625 21.394481420516968 0.554999828338623 340.04364013671875 0.5470778942108154 467.4910888671875 0.27874594926834106 0.7470355 1.861809492111206 True -5 11550 21.378976821899414 17.667866230010986 280.89422607421875 0.46414509415626526 459.8916320800781 0.284761518239975 0.76066715 1.6172499656677246 True -6 13475 21.408347129821777 0.5734212398529053 408.9772033691406 0.7466583847999573 454.9265441894531 0.2880305051803589 0.7762859 1.393954873085022 True -7 15400 21.361005783081055 0.564363956451416 388.794189453125 0.5272126197814941 452.2115173339844 0.28918346762657166 0.7864842 1.2837711572647095 True -8 17325 21.393895626068115 0.5826013088226318 347.61431884765625 0.6452220678329468 448.4384765625 0.29392701387405396 0.7956163 1.1605241298675537 True -9 19250 21.404282093048096 0.5660829544067383 281.6044921875 0.6652582287788391 446.2763977050781 0.2957117557525635 0.80402184 1.036392092704773 True -10 21175 21.39641237258911 0.5570626258850098 261.3009948730469 0.7684955596923828 444.7604064941406 0.2960129678249359 0.8123847 0.923999547958374 True -11 23100 21.42338991165161 0.5701861381530762 219.49215698242188 0.5374908447265625 440.4116516113281 0.30037474632263184 0.8206031 0.8428133726119995 True -12 25025 21.374433755874634 0.561316967010498 287.9218444824219 0.6659889221191406 438.0494689941406 0.30274099111557007 0.82060546 0.8110161423683167 True -13 26950 21.339094877243042 0.5665931701660156 304.7691650390625 0.578057587146759 435.1163330078125 0.30453523993492126 0.82948375 0.7152477502822876 True -14 28875 21.334519624710083 0.562711238861084 327.994140625 0.5681546926498413 432.5137023925781 0.30612146854400635 0.8361197 0.6723041534423828 True -15 30800 21.33547830581665 0.5596873760223389 284.53082275390625 0.7809498310089111 430.030517578125 0.30844846367836 0.8425539 0.6296850442886353 True -16 32725 21.337178468704224 0.5556137561798096 373.88629150390625 0.3241930902004242 428.38427734375 0.30915433168411255 0.84535795 0.6010305881500244 True -17 34650 21.382750034332275 0.5651049613952637 269.26373291015625 0.455389142036438 429.2385559082031 0.30773231387138367 0.8479083 0.582389235496521 True -18 36575 21.376612186431885 0.5626022815704346 207.6464080810547 0.4895167946815491 429.03033447265625 0.3087197244167328 0.8464657 0.5744374990463257 False -19 38500 21.374646425247192 0.5568256378173828 279.211669921875 0.37705135345458984 429.8661804199219 0.30719441175460815 0.8470421 0.5754218101501465 False diff --git a/ENCSR496UER/cherimoya.fold_1.performance.tsv b/ENCSR496UER/cherimoya.fold_1.performance.tsv deleted file mode 100644 index feb4b3092403dcb68d6484ca8ad49424bbf66a8a..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -429.2385559082031 0.46608951687812805 0.30773231387138367 0.11220568418502808 0.8479083180427551 0.8137252926826477 0.582389235496521 \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_2.evaluate.json b/ENCSR496UER/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5dc66d36c1d480a0c1494ecf7de7b61a6b93f0cc..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215LFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_2.fit.json b/ENCSR496UER/cherimoya.fold_2.fit.json deleted file mode 100644 index 194abc667b790457b438bd46e54493000403d6f7..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF215LFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_2.log b/ENCSR496UER/cherimoya.fold_2.log deleted file mode 100644 index 079d346b92200d435ff734549d15cfe0d920b98d..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2059 27.99009680747986 3.9136383533477783 324.7377624511719 1.1571247577667236 500.9256896972656 0.14876656234264374 0.48091257 9.083456993103027 True -1 4118 22.839821338653564 0.7854561805725098 405.18621826171875 1.2192389965057373 428.8642578125 0.21562322974205017 0.66521865 5.0099945068359375 True -2 6177 22.82220458984375 0.43289661407470703 330.6017150878906 0.9572860598564148 404.3498840332031 0.2372705489397049 0.72605485 3.0577425956726074 True -3 8236 22.84927272796631 0.4345855712890625 327.4349060058594 0.6317311525344849 391.9205322265625 0.24592043459415436 0.7330306 1.7261930704116821 True -4 10295 22.814348936080933 0.458543062210083 307.28399658203125 1.079399824142456 386.6303405761719 0.24813498556613922 0.74722093 1.3857026100158691 True -5 12354 22.812975883483887 0.4471435546875 341.2166748046875 0.9142090082168579 382.6091003417969 0.2516138255596161 0.75690234 1.2587809562683105 True -6 14413 22.83163571357727 0.43430519104003906 290.60321044921875 0.6865816116333008 377.5921325683594 0.25600898265838623 0.767257 0.9305460453033447 True -7 16472 22.814404010772705 0.4416065216064453 371.22149658203125 0.7302688360214233 375.59747314453125 0.2567048966884613 0.77457416 1.022886872291565 True -8 18531 22.837486267089844 0.4432811737060547 236.4529266357422 0.43762141466140747 372.35198974609375 0.25912901759147644 0.78611284 0.8209035396575928 True -9 20590 22.816087245941162 0.4386422634124756 380.696533203125 0.6863186955451965 368.9385681152344 0.26354286074638367 0.7951798 0.7237272262573242 True -10 22649 22.834853649139404 0.4403231143951416 338.4137268066406 0.7925313711166382 366.98370361328125 0.2650046646595001 0.80639476 0.636387825012207 True -11 24708 22.83223605155945 0.44744443893432617 304.5245666503906 1.1716066598892212 364.9769287109375 0.2679857313632965 0.8127359 0.5934179425239563 True -12 26767 22.841860055923462 0.4415762424468994 375.9210205078125 0.6604901552200317 362.4692687988281 0.2701062858104706 0.81727177 0.5631201267242432 True -13 28826 22.84592366218567 0.8438167572021484 303.4509582519531 0.7753599882125854 360.2449951171875 0.27208787202835083 0.8238877 0.5347481369972229 True -14 30885 22.839299201965332 0.44760775566101074 250.9999237060547 0.3838723301887512 358.4967041015625 0.27288153767585754 0.8285314 0.5209129452705383 True -15 32944 22.84138298034668 0.44246339797973633 305.2964782714844 0.5834307670593262 358.1965026855469 0.2728588283061981 0.8328149 0.5042732954025269 True -16 35003 22.840397119522095 0.44654297828674316 274.8712158203125 0.626103401184082 357.2416076660156 0.27393144369125366 0.83668387 0.49144551157951355 True -17 37062 22.843103885650635 0.46248698234558105 259.5406494140625 0.513504147529602 358.3645324707031 0.2726095914840698 0.83769363 0.48792287707328796 True -18 39121 22.874955892562866 1.3146440982818604 278.6317138671875 0.3100416660308838 358.1556091308594 0.2734813392162323 0.8359204 0.49339529871940613 False -19 41180 22.89861297607422 0.4566357135772705 270.4940185546875 0.34828492999076843 358.00665283203125 0.2742140591144562 0.8350889 0.4950587749481201 False diff --git a/ENCSR496UER/cherimoya.fold_2.performance.tsv b/ENCSR496UER/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c4ec9560c92a8f7bc1c9738d43a8e8dfc5e7679b..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -358.3645324707031 0.49244511127471924 0.2726095914840698 0.09459458291530609 0.8376936316490173 0.7846806049346924 0.48792287707328796 \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_3.evaluate.json b/ENCSR496UER/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b1aa7ae242f206a5a0cfcd465708fcfd94439833..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215LFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_3.fit.json b/ENCSR496UER/cherimoya.fold_3.fit.json deleted file mode 100644 index 94005a9edbf5c87cd9180594bbb51b424fea51d6..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF215LFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_3.log b/ENCSR496UER/cherimoya.fold_3.log deleted file mode 100644 index df9376f94628157962095025441706c67f62d2f5..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1973 26.018561124801636 3.5289032459259033 363.6919250488281 1.1440197229385376 538.3861694335938 0.17088793218135834 0.45134056 9.918157577514648 True -1 3946 21.942670822143555 0.42314577102661133 321.62811279296875 0.8286101222038269 463.1859436035156 0.23514866828918457 0.6336393 5.27088737487793 True -2 5919 21.915482997894287 0.3817250728607178 411.4790344238281 0.911086916923523 441.3868713378906 0.24994294345378876 0.69107884 2.9955785274505615 True -3 7892 21.878580331802368 0.4106478691101074 432.5567321777344 1.014721393585205 424.4049377441406 0.2645963132381439 0.7106625 2.289766311645508 True -4 9865 21.868794202804565 0.38933753967285156 289.25714111328125 0.7452476024627686 416.6166687011719 0.2703081965446472 0.72977823 1.542372465133667 True -5 11838 21.87084460258484 0.3868081569671631 251.92469787597656 0.6496611833572388 410.9714050292969 0.27440783381462097 0.7380221 1.2940587997436523 True -6 13811 21.880304098129272 0.37671351432800293 352.03985595703125 0.9308844208717346 407.3326721191406 0.277614563703537 0.7481082 1.2051478624343872 True -7 15784 21.845134258270264 0.3822143077850342 326.93682861328125 0.8889163732528687 404.4278869628906 0.2826010584831238 0.7478 1.1961867809295654 False -8 17757 21.888331413269043 0.37642741203308105 336.82177734375 0.9205939769744873 401.375732421875 0.28662246465682983 0.75902754 1.0328792333602905 True -9 19730 21.87046480178833 0.3773162364959717 294.74664306640625 0.9212778210639954 399.3713073730469 0.2882843613624573 0.763714 1.0000181198120117 True -10 21703 21.86008095741272 0.3857696056365967 394.45391845703125 1.2828068733215332 396.154541015625 0.2934498190879822 0.7727805 0.9241350889205933 True -11 23676 21.926076412200928 0.382427453994751 339.7369384765625 0.6979234218597412 394.3551330566406 0.29357412457466125 0.7807403 0.8526239395141602 True -12 25649 21.869301795959473 0.39138364791870117 324.9977722167969 0.6944326162338257 391.0439758300781 0.29800644516944885 0.78960925 0.8029801249504089 True -13 27622 21.963428020477295 2.793982744216919 398.71966552734375 0.9393897652626038 388.7633361816406 0.2993168830871582 0.79661244 0.7499589920043945 True -14 29595 21.953543663024902 0.38610005378723145 234.87704467773438 0.64092618227005 387.15069580078125 0.30044957995414734 0.80546695 0.6962940096855164 True -15 31568 21.96100664138794 0.38971877098083496 213.95616149902344 0.41136330366134644 385.796630859375 0.3012792468070984 0.81208 0.6648680567741394 True -16 33541 21.994505167007446 0.3759934902191162 371.25872802734375 0.6278649568557739 385.3045349121094 0.3012162446975708 0.8174264 0.6327779293060303 True -17 35514 21.917421579360962 0.38306164741516113 296.2337646484375 0.4281260073184967 384.7302551269531 0.3018137216567993 0.81838375 0.618463933467865 True -18 37487 21.915355920791626 0.38566136360168457 307.1207580566406 0.3031960725784302 385.1494140625 0.30101537704467773 0.8183702 0.6165421605110168 False -19 39460 21.925995111465454 0.4017775058746338 267.8802490234375 0.5153723359107971 386.2489929199219 0.29916560649871826 0.8177269 0.6174731254577637 False diff --git a/ENCSR496UER/cherimoya.fold_3.performance.tsv b/ENCSR496UER/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7e314237b4b7015bf0237daffcb813eaae8c13ed..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -384.7302551269531 0.47391170263290405 0.3018137216567993 0.10709137469530106 0.8183837532997131 0.7704117298126221 0.618463933467865 \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_4.evaluate.json b/ENCSR496UER/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 092577faed07cd0e06c6851b1842eb6eb5be157c..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215LFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_4.fit.json b/ENCSR496UER/cherimoya.fold_4.fit.json deleted file mode 100644 index 2daa46efd23f3ae83e6703b9e3144652b128ec25..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF215LFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UER/cherimoya.fold_4.log b/ENCSR496UER/cherimoya.fold_4.log deleted file mode 100644 index 4653e27de67fe0a5a3a58ebc71c959e0be7a0b1d..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1973 26.31232213973999 3.687535047531128 383.9310302734375 0.9606149792671204 451.5787048339844 0.15005925297737122 0.4794561 8.637885093688965 True -1 3946 21.94772434234619 0.4309830665588379 278.482666015625 0.858447790145874 390.9561462402344 0.2143896520137787 0.6498571 5.0704545974731445 True -2 5919 21.908510446548462 0.41457390785217285 289.3962097167969 1.3365373611450195 368.873779296875 0.2337978482246399 0.70477057 3.0324504375457764 True -3 7892 21.94327187538147 2.314429521560669 297.0688171386719 0.3965153396129608 359.5144348144531 0.24049802124500275 0.717737 1.537903070449829 True -4 9865 21.940799951553345 0.4118638038635254 196.51608276367188 0.6472272872924805 353.4424133300781 0.24546952545642853 0.7281102 1.1953703165054321 True -5 11838 21.698343753814697 0.4091827869415283 351.1180114746094 0.8232137560844421 349.5732727050781 0.2481265664100647 0.7467813 0.9531112313270569 True -6 13811 21.715320587158203 0.8569135665893555 260.77081298828125 0.9397355318069458 346.34228515625 0.2501825988292694 0.75636846 0.7883138656616211 True -7 15784 21.584168434143066 0.3946096897125244 402.3313903808594 0.7303801774978638 344.17279052734375 0.25269871950149536 0.7626246 0.7304556369781494 True -8 17757 21.595890045166016 0.39458751678466797 380.982177734375 0.7421770095825195 342.7250671386719 0.25423091650009155 0.7714398 0.6962980628013611 True -9 19730 22.77422261238098 8.763481616973877 372.89190673828125 0.6082469820976257 340.12890625 0.25542232394218445 0.7801835 0.6427688002586365 True -10 21703 21.66857385635376 0.39864587783813477 334.196533203125 0.5835237503051758 338.56695556640625 0.2580198645591736 0.78565073 0.6315726041793823 True -11 23676 21.679235219955444 0.40247344970703125 325.0510559082031 0.4089401960372925 336.666259765625 0.2594422698020935 0.79383796 0.5955120921134949 True -12 25649 21.630768299102783 0.3946213722229004 418.354248046875 0.8763682842254639 335.10076904296875 0.2619991898536682 0.80282694 0.5759924054145813 True -13 27622 21.620774030685425 0.393263578414917 243.04544067382812 0.550320029258728 334.2707214355469 0.2629419267177582 0.80925924 0.5438125133514404 True -14 29595 21.585467100143433 0.38840389251708984 228.4196319580078 0.541751503944397 331.9488830566406 0.26574432849884033 0.8151397 0.526172399520874 True -15 31568 21.619813680648804 0.399791955947876 272.7821044921875 0.6311973929405212 331.2431945800781 0.2667388319969177 0.8186866 0.5118683576583862 True -16 33541 21.617812156677246 0.39434266090393066 206.07699584960938 0.4510604739189148 331.4405822753906 0.2659972906112671 0.8250285 0.49885112047195435 True -17 35514 21.80680251121521 0.39311957359313965 296.1263427734375 0.36071065068244934 330.6435546875 0.26711827516555786 0.82759607 0.49237772822380066 True -18 37487 21.604074239730835 0.4033632278442383 292.85205078125 0.37380895018577576 330.91583251953125 0.26738253235816956 0.82779294 0.4911794066429138 True -19 39460 21.608991384506226 0.4018819332122803 249.96531677246094 0.4284142553806305 331.2832946777344 0.26686081290245056 0.82635844 0.4950333833694458 False diff --git a/ENCSR496UER/cherimoya.fold_4.performance.tsv b/ENCSR496UER/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ded1878e975f0873027ae7b6c9fff8cd9f496de7..0000000000000000000000000000000000000000 --- a/ENCSR496UER/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -330.91583251953125 0.4995594024658203 0.26738256216049194 0.08975426107645035 0.8277929425239563 0.7668800950050354 0.4911794066429138 \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_0.evaluate.json b/ENCSR496UJY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 763803c0cd7ca5242e57598b1cfb604d17972baf..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_0.fit.json b/ENCSR496UJY/cherimoya.fold_0.fit.json deleted file mode 100644 index 81806a579ea064cdd628890d257fcc071e03986f..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF006JUZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_0.log b/ENCSR496UJY/cherimoya.fold_0.log deleted file mode 100644 index 70f953b55d4b98df45ee125b5bdef59046f06ea9..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.858882427215576 4.3377532958984375 761.190673828125 0.49555307626724243 988.9481811523438 0.28527355194091797 0.7553791 8.793707847595215 True -1 5500 29.985389709472656 11.478354215621948 566.7457275390625 0.6204866766929626 868.6156005859375 0.36146581172943115 0.8130177 2.269646167755127 True -2 8250 29.98048496246338 0.6029586791992188 683.8936767578125 0.6259093284606934 847.3219604492188 0.3702152371406555 0.81864196 1.093865990638733 True -3 11000 29.920915842056274 0.9552979469299316 735.5390014648438 0.7595808506011963 835.6323852539062 0.37641653418540955 0.8280154 0.9889812469482422 True -4 13750 30.018143892288208 2.87565016746521 635.1781005859375 0.6616103649139404 825.9131469726562 0.3825967311859131 0.8328099 0.6731621623039246 True -5 16500 30.008551359176636 26.966805458068848 629.20166015625 0.3517172038555145 821.5323486328125 0.3846900463104248 0.8377247 0.49615395069122314 True -6 19250 30.454532384872437 0.8419156074523926 573.5064697265625 0.4343513548374176 814.4882202148438 0.389055460691452 0.8430066 0.4540434181690216 True -7 22000 30.314037799835205 0.5998859405517578 731.1085205078125 0.4406370222568512 810.370361328125 0.3924574553966522 0.84678173 0.39878687262535095 True -8 24750 30.019181489944458 38.931888580322266 633.4998779296875 0.4329771399497986 809.2672119140625 0.39245885610580444 0.8496846 0.41707611083984375 True -9 27500 29.998533248901367 10.254920721054077 667.1304321289062 0.45763808488845825 802.4309692382812 0.396617591381073 0.8523248 0.38979142904281616 True -10 30250 29.973752737045288 16.2288761138916 597.6956787109375 0.34851306676864624 798.361572265625 0.39972683787345886 0.8582986 0.3729536533355713 True -11 33000 30.000541925430298 1.6770377159118652 629.7017822265625 0.4542815089225769 794.71630859375 0.402156800031662 0.86220783 0.35506322979927063 True -12 35750 30.49965238571167 0.5923159122467041 696.6229248046875 0.49567294120788574 790.70947265625 0.4046398401260376 0.86646146 0.3341994881629944 True -13 38500 29.945708990097046 0.5872414112091064 766.6432495117188 0.368377685546875 789.4183959960938 0.40472495555877686 0.8709738 0.31762227416038513 True -14 41250 29.94221568107605 1.3235032558441162 578.3724365234375 0.27444201707839966 785.20361328125 0.40850502252578735 0.87645227 0.2993643283843994 True -15 44000 29.978965759277344 21.66441249847412 579.3106689453125 0.21108964085578918 781.3145141601562 0.4111431837081909 0.87836504 0.29211726784706116 True -16 46750 30.410902738571167 24.269333839416504 600.3143920898438 0.23720422387123108 781.3858032226562 0.41000595688819885 0.881841 0.2848999798297882 True -17 49500 30.38842511177063 26.030619859695435 632.8302612304688 0.3012329041957855 781.8816528320312 0.4090886116027832 0.8827038 0.27978795766830444 True -18 52250 32.17087697982788 0.8102552890777588 651.751220703125 0.254428893327713 781.7822875976562 0.4107245206832886 0.88410956 0.27993863821029663 True -19 55000 30.03274703025818 0.5814919471740723 681.2518310546875 0.2043009102344513 781.5411376953125 0.41108858585357666 0.88367105 0.27976348996162415 False diff --git a/ENCSR496UJY/cherimoya.fold_0.performance.tsv b/ENCSR496UJY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 87f0b5e25138348b8f30f776f432a4c57ad05b68..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -781.7822875976562 0.3731943964958191 0.41072455048561096 0.1764950007200241 0.8841095566749573 0.846251368522644 0.27993863821029663 \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_1.evaluate.json b/ENCSR496UJY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2cacab182b3375fc910dd34ba4fcd102462bbd80..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_1.fit.json b/ENCSR496UJY/cherimoya.fold_1.fit.json deleted file mode 100644 index cf085191cbfa03e5fe84b42a9ac0e8f77f0688c8..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF006JUZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_1.log b/ENCSR496UJY/cherimoya.fold_1.log deleted file mode 100644 index 2737e6bec9f466b139b39355c3093e000e5c69f9..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2704 34.19707703590393 3.676312208175659 706.45849609375 0.4236283302307129 1227.3897705078125 0.28604570031166077 0.7475673 8.90760612487793 True -1 5408 29.53928542137146 27.65082550048828 594.9339599609375 0.7206906080245972 1045.703125 0.3768489360809326 0.81163996 2.5331015586853027 True -2 8112 31.61408281326294 33.74526047706604 681.1897583007812 0.469654381275177 1015.9262084960938 0.3910374939441681 0.8194734 1.4751347303390503 True -3 10816 31.205432176589966 17.631309270858765 672.9862060546875 0.4770723581314087 1001.218017578125 0.395942360162735 0.8248322 1.1125051975250244 True -4 13520 29.480944633483887 0.6885745525360107 667.0498046875 0.5021505355834961 996.44580078125 0.3972178101539612 0.83047456 0.9247714877128601 True -5 16224 29.473268032073975 0.6946148872375488 692.4801025390625 0.34293851256370544 982.9225463867188 0.40544015169143677 0.8356153 0.7134186625480652 True -6 18928 29.834594249725342 0.6714813709259033 770.0643920898438 0.35247111320495605 977.098388671875 0.40771862864494324 0.842628 0.6801871061325073 True -7 21632 29.403217792510986 0.6823046207427979 653.907470703125 0.492281973361969 967.8690795898438 0.414116233587265 0.84922177 0.6096423268318176 True -8 24336 29.435659646987915 0.6898345947265625 727.02783203125 0.39083582162857056 963.89501953125 0.4150369465351105 0.8519256 0.5673381090164185 True -9 27040 29.400920391082764 0.6785387992858887 733.0546264648438 0.4595058560371399 957.2295532226562 0.4186730980873108 0.85541284 0.5609061121940613 True -10 29744 29.460180282592773 31.209431886672974 724.7445068359375 0.4739015996456146 950.5293579101562 0.421799898147583 0.85898006 0.5007498264312744 True -11 32448 29.65418577194214 0.6977708339691162 739.414794921875 0.3941824436187744 945.9098510742188 0.42505431175231934 0.866005 0.47381359338760376 True -12 35152 29.480352640151978 0.7098126411437988 708.8321533203125 0.32985159754753113 940.493896484375 0.4271085560321808 0.87115246 0.4261983335018158 True -13 37856 29.640300035476685 0.6891288757324219 737.0528564453125 0.26499977707862854 934.252197265625 0.4312990605831146 0.8762228 0.39966052770614624 True -14 40560 29.44670343399048 0.6944723129272461 705.6421508789062 0.32058483362197876 930.296142578125 0.4328576922416687 0.87910837 0.37487292289733887 True -15 43264 29.55863308906555 0.7009594440460205 609.517822265625 0.297055721282959 925.2255249023438 0.43525537848472595 0.8850419 0.34644627571105957 True -16 45968 29.48648476600647 1.8450684547424316 724.0480346679688 0.2897963523864746 925.861572265625 0.43403998017311096 0.8861406 0.3218059539794922 True -17 48672 29.50990653038025 0.695371150970459 714.5594482421875 0.22514748573303223 924.8738403320312 0.4346016049385071 0.888227 0.31395792961120605 True -18 51376 29.489643812179565 0.6847286224365234 523.8764038085938 0.33267155289649963 924.232177734375 0.4359133839607239 0.8881375 0.3106858730316162 False -19 54080 29.466559886932373 1.6862363815307617 469.596923828125 0.16906148195266724 926.6823120117188 0.43329036235809326 0.8893389 0.3094532787799835 True diff --git a/ENCSR496UJY/cherimoya.fold_1.performance.tsv b/ENCSR496UJY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 383c675fc0cf242fd8819b932e58ba0c68cd7f94..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -926.6823120117188 0.3518029451370239 0.43329036235809326 0.20349372923374176 0.8893389105796814 0.8694007396697998 0.3094532787799835 \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_2.evaluate.json b/ENCSR496UJY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f4746e47a92d7f6431894657d38a25772a5a6f74..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_2.fit.json b/ENCSR496UJY/cherimoya.fold_2.fit.json deleted file mode 100644 index 5a98cd4dd6fc24c2611433aa2ff4a9dab03ff894..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF006JUZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_2.log b/ENCSR496UJY/cherimoya.fold_2.log deleted file mode 100644 index 8eb242158d6e3bbbca538bc32a0e12288098f401..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 36.313570737838745 3.6256370544433594 607.2942504882812 0.5108765363693237 1060.0186767578125 0.28895601630210876 0.75272775 6.551177978515625 True -1 5770 31.406635761260986 0.5763483047485352 834.7019653320312 0.6212971210479736 917.1436767578125 0.36646169424057007 0.81321055 1.7343289852142334 True -2 8655 31.42246174812317 0.5657274723052979 993.47216796875 0.428713321685791 898.870361328125 0.372829794883728 0.82084167 1.0549458265304565 True -3 11540 31.345479726791382 0.578115701675415 772.974365234375 0.5372724533081055 883.5698852539062 0.3807260990142822 0.8268656 0.936473548412323 True -4 14425 31.43053436279297 0.5748491287231445 732.3853149414062 0.42873209714889526 870.2906494140625 0.38709786534309387 0.83505166 0.6262340545654297 True -5 17310 31.407743453979492 0.5678000450134277 734.298583984375 0.3468048572540283 863.1057739257812 0.39181283116340637 0.8397501 0.5748854279518127 True -6 20195 31.389414072036743 0.5721020698547363 642.0930786132812 0.32783573865890503 858.4721069335938 0.39397186040878296 0.84566337 0.5229008793830872 True -7 23080 31.366218328475952 0.5711297988891602 749.7698974609375 0.4777434468269348 853.8810424804688 0.39660757780075073 0.84953624 0.4907594621181488 True -8 25965 31.452255249023438 0.5730597972869873 719.9295654296875 0.367678165435791 847.39501953125 0.4014497995376587 0.8526707 0.5114941000938416 True -9 28850 31.4846932888031 0.5800509452819824 802.5203857421875 0.5063788890838623 845.9011840820312 0.4031864106655121 0.8561704 0.4735420048236847 True -10 31735 31.48404860496521 0.5708754062652588 606.13720703125 0.5587925314903259 842.4112548828125 0.404312402009964 0.85684174 0.46439650654792786 True -11 34620 31.447333812713623 22.20004153251648 759.6192626953125 0.39747437834739685 836.3408203125 0.40907979011535645 0.8624876 0.43605077266693115 True -12 37505 31.44223117828369 0.5776731967926025 802.6903076171875 0.2783264219760895 834.6378173828125 0.409542977809906 0.8644192 0.40659278631210327 True -13 40390 31.971168994903564 0.5783727169036865 571.7744750976562 0.2629467844963074 832.318115234375 0.4101172685623169 0.8715553 0.3650098145008087 True -14 43275 31.47623872756958 0.5705277919769287 560.6107788085938 0.26996129751205444 825.9599609375 0.4141046702861786 0.87369335 0.3418179750442505 True -15 46160 31.46697425842285 1.4143667221069336 811.300537109375 0.29777610301971436 823.7527465820312 0.41638290882110596 0.87951225 0.3148786723613739 True -16 49045 31.497262001037598 0.572629451751709 768.8416748046875 0.27936720848083496 823.2364501953125 0.4171523153781891 0.88119644 0.3009401857852936 True -17 51930 31.438960790634155 0.5645473003387451 798.9093017578125 0.3161476254463196 819.7164306640625 0.41929104924201965 0.88052094 0.2911778390407562 False -18 54815 31.629791975021362 1.1108307838439941 802.611083984375 0.2782224416732788 822.2778930664062 0.41742849349975586 0.8825345 0.2897484600543976 True -19 57700 31.438222885131836 0.5813055038452148 680.6500244140625 0.22102785110473633 822.0137939453125 0.4179600179195404 0.88162714 0.28894779086112976 False diff --git a/ENCSR496UJY/cherimoya.fold_2.performance.tsv b/ENCSR496UJY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index dce4745258f7ab069594bc958da64dd7b1a7ff35..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -822.2778930664062 0.3666294813156128 0.41742852330207825 0.1861015409231186 0.8825345039367676 0.8520697355270386 0.2897484600543976 \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_3.evaluate.json b/ENCSR496UJY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3c40cef5a35b572b469cda903801ce4228c9c4b5..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_3.fit.json b/ENCSR496UJY/cherimoya.fold_3.fit.json deleted file mode 100644 index 9a567128b7f1a38da64365784e96fa2c24299238..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF006JUZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_3.log b/ENCSR496UJY/cherimoya.fold_3.log deleted file mode 100644 index c1ad9b9b9d495314ab27813b68d3dfc44cb47c93..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.67420768737793 3.42220139503479 708.9718017578125 0.6609027981758118 973.5513916015625 0.29825150966644287 0.74512464 7.081936836242676 True -1 5500 29.939659357070923 2.3293440341949463 859.6781005859375 0.491411030292511 854.3759765625 0.36873918771743774 0.8173751 2.0928757190704346 True -2 8250 30.04185724258423 0.5379900932312012 618.2901611328125 0.3208696246147156 831.1047973632812 0.37885209918022156 0.82343435 0.8881531953811646 True -3 11000 29.909640312194824 0.7798998355865479 808.15673828125 0.6011931300163269 815.6874389648438 0.3875138759613037 0.8326428 0.7113963961601257 True -4 13750 29.921514987945557 0.5344557762145996 648.0983276367188 0.43126094341278076 808.6781616210938 0.390419602394104 0.8422586 0.6709544658660889 True -5 16500 29.921506881713867 0.5340514183044434 879.0068969726562 0.42673856019973755 800.984130859375 0.3946530818939209 0.846772 0.6086461544036865 True -6 19250 29.926441431045532 0.5341598987579346 778.4754028320312 0.4027769863605499 799.0609741210938 0.39538833498954773 0.85215807 0.509641706943512 True -7 22000 29.86729645729065 0.5282902717590332 749.462158203125 0.30327701568603516 795.908447265625 0.39658933877944946 0.8561465 0.47814542055130005 True -8 24750 29.928601264953613 1.19586181640625 809.4263916015625 0.4162212312221527 789.186767578125 0.40266284346580505 0.8584382 0.46834632754325867 True -9 27500 29.935102224349976 0.5426650047302246 714.43408203125 0.3793329894542694 786.416748046875 0.4035720229148865 0.86094177 0.429034560918808 True -10 30250 29.923394680023193 1.9889295101165771 768.523681640625 0.36795520782470703 781.7568969726562 0.4076998829841614 0.8638416 0.4165051281452179 True -11 33000 29.942830324172974 0.5378143787384033 620.6668701171875 0.22958332300186157 780.12255859375 0.40830567479133606 0.86587787 0.4035123288631439 True -12 35750 29.898247718811035 1.1904983520507812 761.1470336914062 0.40117815136909485 776.6996459960938 0.4102020561695099 0.8698751 0.3818129897117615 True -13 38500 29.92290472984314 0.5362033843994141 771.26220703125 0.4700384736061096 772.6757202148438 0.4131050705909729 0.873875 0.3521535098552704 True -14 41250 30.545416593551636 0.5328752994537354 772.9176635742188 0.3588842749595642 770.0738525390625 0.41398105025291443 0.879483 0.33340615034103394 True -15 44000 30.009084701538086 0.5335993766784668 756.38671875 0.32805028557777405 768.3672485351562 0.4154503643512726 0.88174707 0.31403717398643494 True -16 46750 29.96630597114563 0.5388891696929932 710.135986328125 0.30603206157684326 769.2095336914062 0.4158415198326111 0.8839475 0.30361536145210266 True -17 49500 29.95321559906006 0.5331015586853027 656.0429077148438 0.35571128129959106 768.015380859375 0.4156467914581299 0.88623166 0.2949366867542267 True -18 52250 29.890795946121216 0.5384218692779541 676.378173828125 0.3523191213607788 767.5291137695312 0.4161315858364105 0.88559103 0.2915292978286743 False -19 55000 30.003023624420166 0.5319039821624756 647.8880615234375 0.2970561981201172 767.8386840820312 0.4152100086212158 0.88544804 0.29264184832572937 False diff --git a/ENCSR496UJY/cherimoya.fold_3.performance.tsv b/ENCSR496UJY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5f624b7f7cfc4efb64d052dd6e6716bd39563db7..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -768.015380859375 0.3715696334838867 0.4156467914581299 0.17804884910583496 0.8862316608428955 0.8464996814727783 0.2949366867542267 \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_4.evaluate.json b/ENCSR496UJY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8dfd6f690a0f04ddd817350a4146992d459167e8..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_4.fit.json b/ENCSR496UJY/cherimoya.fold_4.fit.json deleted file mode 100644 index 4e691d19032f63c436992a30487225521b11c8ce..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF006JUZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR496UJY/cherimoya.fold_4.log b/ENCSR496UJY/cherimoya.fold_4.log deleted file mode 100644 index a729b20a952c776cea47c8e8dd5e11a898df577d..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2794 35.68263030052185 35.18198299407959 714.6183471679688 0.5426373481750488 932.411865234375 0.2835020422935486 0.74335265 6.842878818511963 True -1 5588 30.460171699523926 12.91672158241272 742.1942138671875 0.37036919593811035 823.604736328125 0.35856813192367554 0.8051631 1.9084211587905884 True -2 8382 30.47127079963684 0.7601990699768066 574.72998046875 0.5888644456863403 806.9797973632812 0.36509644985198975 0.80786896 0.92255699634552 True -3 11176 30.372863292694092 18.43538761138916 755.9627685546875 0.7066279053688049 795.0269775390625 0.37104561924934387 0.8163139 0.8213744163513184 True -4 13970 30.733169078826904 0.5884866714477539 622.952392578125 0.5019124150276184 788.171630859375 0.3755122125148773 0.8241173 0.7564731240272522 True -5 16764 31.157864332199097 14.613861322402954 604.985107421875 0.40593892335891724 780.9658813476562 0.37911272048950195 0.8301843 0.5687710642814636 True -6 19558 30.40897846221924 1.4697539806365967 765.8667602539062 0.48810598254203796 776.482421875 0.38279488682746887 0.8337413 0.5061516761779785 True -7 22352 30.527846813201904 21.188075304031372 861.6961059570312 0.37562960386276245 770.8402099609375 0.3868226110935211 0.8424602 0.5099449753761292 True -8 25146 31.543770790100098 18.59139585494995 662.689453125 0.43337973952293396 768.3203735351562 0.3875105082988739 0.8486897 0.49643632769584656 True -9 27940 30.918588876724243 14.480390310287476 706.212158203125 0.3631995916366577 763.7743530273438 0.39182400703430176 0.85231405 0.4800680875778198 True -10 30734 30.48725938796997 7.837914705276489 698.136962890625 0.3320181369781494 760.5554809570312 0.394010066986084 0.85535365 0.46293261647224426 True -11 33528 30.735636472702026 0.6028623580932617 654.9203491210938 0.38356858491897583 755.53369140625 0.39853349328041077 0.85967314 0.42029646039009094 True -12 36322 30.48607087135315 0.6218910217285156 688.8026733398438 0.30819377303123474 754.639892578125 0.39704224467277527 0.86515677 0.38291603326797485 True -13 39116 30.44621753692627 0.5983021259307861 686.305419921875 0.24862952530384064 751.3477172851562 0.4011479616165161 0.86824626 0.3525417745113373 True -14 41910 30.54181718826294 0.5965793132781982 750.0985717773438 0.3788348436355591 748.9351806640625 0.40234631299972534 0.873029 0.31678536534309387 True -15 44704 30.500874757766724 0.5887129306793213 654.2522583007812 0.16423220932483673 747.318359375 0.40324926376342773 0.8772973 0.2938273549079895 True -16 47498 30.6023428440094 1.5412280559539795 660.1220703125 0.19310885667800903 745.767578125 0.4045177102088928 0.87846595 0.2766338288784027 True -17 50292 30.47310447692871 1.116734266281128 752.9830932617188 0.10983498394489288 746.91357421875 0.40383318066596985 0.88028765 0.27034062147140503 True -18 53086 30.4278666973114 0.5984869003295898 652.2453002929688 0.25059768557548523 746.6580810546875 0.4040788412094116 0.8801812 0.2701597511768341 False -19 55880 30.481857299804688 0.5820882320404053 688.6162109375 0.2624892592430115 747.6793212890625 0.40328508615493774 0.87946564 0.27212074398994446 False diff --git a/ENCSR496UJY/cherimoya.fold_4.performance.tsv b/ENCSR496UJY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index efc47d14ed0189c6ed0ec128d70291c3752b12b4..0000000000000000000000000000000000000000 --- a/ENCSR496UJY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -746.91357421875 0.3782053291797638 0.4038331210613251 0.1723267287015915 0.8802876472473145 0.8374304175376892 0.27034062147140503 \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_0.evaluate.json b/ENCSR498FCF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ba81b09769bf2b872d2644195be3520921c85b39..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959DGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_0.fit.json b/ENCSR498FCF/cherimoya.fold_0.fit.json deleted file mode 100644 index fbbb774156baf5f03c637556aa146d17a92d0285..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF959DGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_0.log b/ENCSR498FCF/cherimoya.fold_0.log deleted file mode 100644 index 49cd340f1b881ee8bbbc7abc9453a48a8b094900..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 35.97905254364014 3.633018732070923 394.9418029785156 0.34537333250045776 683.1477661132812 0.23350800573825836 0.73116344 6.593862056732178 True -1 5536 30.24336576461792 0.5717158317565918 442.3260803222656 0.5082615613937378 612.6607055664062 0.27921006083488464 0.786155 2.007593870162964 True -2 8304 30.35456418991089 0.5541584491729736 416.6521301269531 0.42254072427749634 603.0056762695312 0.2849017381668091 0.7861853 1.1207412481307983 True -3 11072 30.459064722061157 0.5526785850524902 509.1595153808594 0.6500271558761597 595.4871826171875 0.2868232727050781 0.7981115 0.9095521569252014 True -4 13840 30.21458411216736 0.5531196594238281 380.6384582519531 0.4055876135826111 588.676513671875 0.28965404629707336 0.8146339 0.7023673057556152 True -5 16608 30.231372833251953 0.5570955276489258 438.31304931640625 0.4182529151439667 583.53515625 0.29294922947883606 0.8168526 0.5326108336448669 True -6 19376 30.375717163085938 0.5478196144104004 413.8004455566406 0.564868688583374 580.8764038085938 0.2941338121891022 0.8274094 0.5162153840065002 True -7 22144 30.14694857597351 0.5491650104522705 388.6130676269531 0.3475458025932312 577.426025390625 0.29801979660987854 0.8305338 0.5179615020751953 True -8 24912 30.151368379592896 0.5478599071502686 464.7667541503906 0.35467949509620667 576.043701171875 0.29789334535598755 0.83713233 0.4515953063964844 True -9 27680 30.20490288734436 0.5527911186218262 473.06707763671875 0.3860604763031006 573.486083984375 0.2993744909763336 0.84561545 0.4086570739746094 True -10 30448 30.183077335357666 1.5690972805023193 499.5582275390625 0.3317389190196991 569.3795166015625 0.30269747972488403 0.85439485 0.37780630588531494 True -11 33216 30.2123064994812 0.5462827682495117 557.0068969726562 0.39300602674484253 568.3003540039062 0.30330726504325867 0.85937154 0.35257723927497864 True -12 35984 30.23887801170349 0.5463767051696777 358.218505859375 0.19107526540756226 565.8977661132812 0.3045148551464081 0.8666475 0.32223352789878845 True -13 38752 30.257094144821167 0.5692234039306641 467.2015686035156 0.3458060324192047 564.1260375976562 0.3069678544998169 0.87032187 0.30182766914367676 True -14 41520 30.35136842727661 0.5647885799407959 428.7495422363281 0.3598131537437439 563.1359252929688 0.30722615122795105 0.87553126 0.28582191467285156 True -15 44288 30.452441215515137 0.5576071739196777 525.8839111328125 0.24949003756046295 563.2073974609375 0.30664536356925964 0.87902874 0.2731499671936035 True -16 47056 30.28504204750061 34.710217237472534 465.435791015625 0.23395252227783203 562.1084594726562 0.30706629157066345 0.88052124 0.26758602261543274 True -17 49824 30.294453620910645 0.5654966831207275 590.8179931640625 0.39540576934814453 562.2677001953125 0.3071325123310089 0.8809485 0.26394739747047424 True -18 52592 30.209866285324097 0.6397466659545898 417.3535461425781 0.16658872365951538 562.3541259765625 0.30747082829475403 0.88202333 0.26488935947418213 True -19 55360 30.253073930740356 1.4754297733306885 461.5978698730469 0.11628734320402145 561.98193359375 0.30794328451156616 0.881115 0.26525458693504333 False diff --git a/ENCSR498FCF/cherimoya.fold_0.performance.tsv b/ENCSR498FCF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9fb993921e6b64a19d081f5ce966c54e1b07b380..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -562.3541259765625 0.43596288561820984 0.30747082829475403 0.12923158705234528 0.8820233345031738 0.8403617739677429 0.26488935947418213 \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_1.evaluate.json b/ENCSR498FCF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1d6f9004579111f5198ec07f0775011b2e2d6f8a..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959DGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_1.fit.json b/ENCSR498FCF/cherimoya.fold_1.fit.json deleted file mode 100644 index 69138b011d9768346f4826dae83009dd375412a0..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF959DGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_1.log b/ENCSR498FCF/cherimoya.fold_1.log deleted file mode 100644 index 49b5c9dc8baa6f96faad20fd000530ddf4af3031..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2683 34.27824091911316 3.8483405113220215 606.1129760742188 1.0320749282836914 827.1448364257812 0.24270319938659668 0.7305153 6.352007865905762 True -1 5366 28.832154989242554 0.7405474185943604 469.6330871582031 0.363263875246048 727.9993896484375 0.29809561371803284 0.78517777 2.2207281589508057 True -2 8049 29.44256567955017 3.078664779663086 534.616455078125 0.46158021688461304 722.0138549804688 0.30377596616744995 0.78963184 1.4849779605865479 True -3 10732 29.3438618183136 0.7452268600463867 556.6751098632812 0.5442874431610107 703.1031494140625 0.30684104561805725 0.81544757 1.1767363548278809 True -4 13415 29.373968362808228 1.2094757556915283 565.8255615234375 0.5692144632339478 699.7975463867188 0.3097309172153473 0.81407773 0.8520863652229309 False -5 16098 29.35336971282959 0.7409501075744629 363.9239501953125 0.3069069981575012 688.4283447265625 0.31750670075416565 0.83068025 0.7542402744293213 True -6 18781 29.23905873298645 0.7281651496887207 584.6747436523438 0.40207213163375854 686.0271606445312 0.3189525604248047 0.8385389 0.7110810279846191 True -7 21464 29.28707242012024 0.7394568920135498 508.6502380371094 0.3186017572879791 685.5634155273438 0.3162330985069275 0.844454 0.6721521019935608 True -8 24147 29.401005744934082 0.7362055778503418 425.10601806640625 0.42668354511260986 678.5123901367188 0.3225664794445038 0.8489566 0.615505576133728 True -9 26830 30.33840250968933 31.695751667022705 520.818115234375 0.3486799895763397 672.6471557617188 0.3261971175670624 0.85623944 0.5582385659217834 True -10 29513 29.41283369064331 3.4214060306549072 364.7774658203125 0.30499202013015747 671.1983642578125 0.3271417021751404 0.86227816 0.507053792476654 True -11 32196 29.29570722579956 0.7922608852386475 472.488525390625 0.40238338708877563 669.5541381835938 0.3275531828403473 0.87063485 0.44369155168533325 True -12 34879 29.371593713760376 0.7427551746368408 382.7823791503906 0.3487008810043335 662.4710083007812 0.33389008045196533 0.8786126 0.3992089629173279 True -13 37562 29.290359020233154 41.17259120941162 535.5062255859375 0.2361886203289032 663.0792236328125 0.3315919041633606 0.88120997 0.3681887686252594 True -14 40245 30.07926630973816 0.7390527725219727 474.1497802734375 0.4313887357711792 661.3956298828125 0.33229687809944153 0.8886706 0.3443068861961365 True -15 42928 29.308303117752075 1.3248672485351562 522.72509765625 0.3172375559806824 657.2627563476562 0.3364572823047638 0.8936384 0.3213316798210144 True -16 45611 29.373352766036987 1.853097915649414 550.4495849609375 0.1676098108291626 657.5081787109375 0.33512258529663086 0.8949315 0.3119966685771942 True -17 48294 29.348674058914185 2.7084994316101074 440.1853942871094 0.16351500153541565 658.1587524414062 0.3351856470108032 0.8963635 0.3076762855052948 True -18 50977 29.39071035385132 1.7606027126312256 478.7157287597656 0.17708763480186462 659.602294921875 0.3334449827671051 0.8953859 0.30923399329185486 False -19 53660 29.450220823287964 5.160703420639038 445.85247802734375 0.1918092668056488 658.8984375 0.33418768644332886 0.89487094 0.3104802370071411 False diff --git a/ENCSR498FCF/cherimoya.fold_1.performance.tsv b/ENCSR498FCF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0a9ff926426ff17fca4778be4b2b4ec79627fa39..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -658.1587524414062 0.41395363211631775 0.3351856470108032 0.14974330365657806 0.8963634967803955 0.8749954104423523 0.3076762855052948 \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_2.evaluate.json b/ENCSR498FCF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 232ce4b2d6badafc259e38c70b2d817d76a01f82..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959DGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_2.fit.json b/ENCSR498FCF/cherimoya.fold_2.fit.json deleted file mode 100644 index b83928b536b0f0307e17129bc84c9f4ec45bc5f5..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF959DGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_2.log b/ENCSR498FCF/cherimoya.fold_2.log deleted file mode 100644 index ed348d29494f1968dd7e81082fb351ffa9bad112..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 37.20932149887085 3.813382387161255 475.50506591796875 0.4505460858345032 743.9073486328125 0.24009425938129425 0.69807965 5.308207035064697 True -1 5788 31.946075916290283 0.5512633323669434 455.91302490234375 0.4837556779384613 661.623779296875 0.2884179651737213 0.78124106 1.8262603282928467 True -2 8682 32.10949659347534 0.5396649837493896 590.8121337890625 0.6485236287117004 655.3151245117188 0.2896732985973358 0.7727722 1.1678715944290161 False -3 11576 32.074732542037964 0.540447473526001 620.1468505859375 0.3927621841430664 641.3386840820312 0.2939436137676239 0.791716 0.904727041721344 True -4 14470 31.868184089660645 0.5395879745483398 438.085693359375 0.4123382270336151 635.9241333007812 0.29892125725746155 0.8018991 0.6793131828308105 True -5 17364 31.861377477645874 0.5382118225097656 542.3387451171875 0.49755701422691345 632.8432006835938 0.29902201890945435 0.81128126 0.6373688578605652 True -6 20258 31.877939224243164 0.5380935668945312 455.4088439941406 0.31858864426612854 626.93896484375 0.3041127920150757 0.8191876 0.5941761136054993 True -7 23152 31.881696224212646 1.3164730072021484 530.1848754882812 0.3255411982536316 623.8268432617188 0.3046616315841675 0.82727504 0.5645124316215515 True -8 26046 32.0402569770813 0.5340461730957031 535.607421875 0.33870813250541687 621.7080688476562 0.3059908449649811 0.8332137 0.5228724479675293 True -9 28940 31.928964376449585 0.5471477508544922 437.34954833984375 0.4007587432861328 618.865234375 0.308052122592926 0.8371089 0.48842594027519226 True -10 31834 31.976948976516724 0.5407485961914062 434.7691955566406 0.41463279724121094 616.9321899414062 0.30959856510162354 0.8414452 0.4483537971973419 True -11 34728 31.89197278022766 27.784769773483276 470.0712890625 0.2761297821998596 614.19921875 0.31087726354599 0.8462811 0.4199991524219513 True -12 37622 32.21734976768494 0.5584192276000977 633.428466796875 0.5193719267845154 612.5962524414062 0.31189242005348206 0.8525242 0.38475531339645386 True -13 40516 31.91342568397522 0.5434246063232422 487.97027587890625 0.2707521319389343 608.1082763671875 0.315993070602417 0.86070615 0.3570505678653717 True -14 43410 31.882535457611084 12.982837677001953 503.55816650390625 0.30484500527381897 608.4637451171875 0.31431347131729126 0.86414933 0.33908963203430176 True -15 46304 32.20613479614258 0.5482597351074219 424.38250732421875 0.34832680225372314 605.2191162109375 0.317331999540329 0.86963624 0.31860965490341187 True -16 49198 32.01405310630798 0.5406949520111084 384.72247314453125 0.20147837698459625 605.6539916992188 0.31743890047073364 0.870924 0.3072606325149536 True -17 52092 32.3424391746521 0.5359487533569336 492.96588134765625 0.24206773936748505 605.6138916015625 0.31686273217201233 0.87209463 0.3014819622039795 True -18 54986 31.932108402252197 25.816558837890625 554.8311767578125 0.1361040472984314 605.4157104492188 0.3169337511062622 0.87324977 0.301053911447525 True -19 57880 32.72880959510803 0.5487091541290283 506.139892578125 0.16415852308273315 605.0205688476562 0.3178601562976837 0.8719923 0.30236729979515076 False diff --git a/ENCSR498FCF/cherimoya.fold_2.performance.tsv b/ENCSR498FCF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 56b9a0e4ab9afbfec3b4ef0e6bc453acbed21530..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -605.4157104492188 0.4252243638038635 0.3169337213039398 0.14001430571079254 0.8732497692108154 0.8442064523696899 0.301053911447525 \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_3.evaluate.json b/ENCSR498FCF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f97629d61b17414b334bdb233b14c21b1692c05a..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959DGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_3.fit.json b/ENCSR498FCF/cherimoya.fold_3.fit.json deleted file mode 100644 index 9f214b359f4cfe5c382682ead33af6f06c698440..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF959DGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_3.log b/ENCSR498FCF/cherimoya.fold_3.log deleted file mode 100644 index f0b88005fa787d78079e57695361da33c6660d62..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2726 34.24143695831299 3.7268450260162354 554.7432861328125 0.23275214433670044 699.1987915039062 0.2429732382297516 0.6765402 6.608083248138428 True -1 5452 29.873053312301636 0.5551755428314209 458.3952941894531 0.3559425473213196 628.2438354492188 0.2910000681877136 0.7403038 1.9474732875823975 True -2 8178 29.90589165687561 30.74790048599243 630.1090698242188 0.3883627653121948 621.8281860351562 0.2922191023826599 0.7444452 1.4256094694137573 True -3 10904 30.070046424865723 33.87585806846619 545.4932861328125 0.5235556960105896 609.3571166992188 0.29872483015060425 0.7664846 1.4546023607254028 True -4 13630 29.765218496322632 28.862021684646606 470.11395263671875 0.23805920779705048 603.3152465820312 0.30134081840515137 0.78630126 0.9109333753585815 True -5 16356 30.839045524597168 0.5490517616271973 445.5184631347656 0.4175485670566559 598.8182983398438 0.30572307109832764 0.7901348 0.8234962224960327 True -6 19082 30.052140712738037 0.5442960262298584 467.38702392578125 0.44793790578842163 598.4938354492188 0.3042615056037903 0.79573566 0.8138595223426819 True -7 21808 29.815787076950073 2.8911430835723877 408.3763732910156 0.3499162793159485 594.9827270507812 0.30792444944381714 0.7999851 0.7523139119148254 True -8 24534 29.788692474365234 30.81607985496521 557.70263671875 0.41036689281463623 592.4392700195312 0.3094956576824188 0.8071389 0.6846826076507568 True -9 27260 30.32224726676941 0.5544342994689941 553.7274169921875 0.2843396067619324 588.9385986328125 0.31212562322616577 0.8146787 0.6276981234550476 True -10 29986 29.8325138092041 0.5413568019866943 621.0260009765625 0.46160754561424255 587.8034057617188 0.3121972680091858 0.8210355 0.5580297112464905 True -11 32712 30.24453330039978 34.024107217788696 455.0923156738281 0.22638922929763794 585.882568359375 0.31397923827171326 0.82791615 0.5021750926971436 True -12 35438 29.86177682876587 0.5420494079589844 582.262451171875 0.4420353174209595 584.5057983398438 0.31537550687789917 0.8363015 0.45889872312545776 True -13 38164 29.980182647705078 0.8778183460235596 524.0084228515625 0.3059711456298828 580.0579833984375 0.3185962438583374 0.84655005 0.4084857702255249 True -14 40890 30.637154579162598 0.5424692630767822 529.6900634765625 0.38014471530914307 579.7236328125 0.3174816370010376 0.8518403 0.3775911033153534 True -15 43616 30.257570505142212 33.4795777797699 497.6393737792969 0.18852457404136658 577.5482177734375 0.3181791305541992 0.8617291 0.3426722586154938 True -16 46342 29.98172640800476 1.3202605247497559 464.09222412109375 0.21352261304855347 577.6348876953125 0.3178795576095581 0.86648816 0.328145295381546 True -17 49068 29.95423936843872 0.5580158233642578 560.3352661132812 0.25271087884902954 575.4142456054688 0.32017379999160767 0.8668593 0.3181648254394531 True -18 51794 30.239104509353638 18.0962975025177 515.968505859375 0.2901313304901123 575.2490234375 0.320819228887558 0.8677112 0.31953445076942444 True -19 54520 29.993253231048584 1.4650194644927979 431.20196533203125 0.26303136348724365 574.5822143554688 0.321634978055954 0.86591077 0.3192448019981384 False diff --git a/ENCSR498FCF/cherimoya.fold_3.performance.tsv b/ENCSR498FCF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c01dd566ba7ec148844932707cc3001902c4fbbb..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -575.2490234375 0.4266851544380188 0.32081925868988037 0.13793042302131653 0.8677111864089966 0.8271687626838684 0.31953445076942444 \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_4.evaluate.json b/ENCSR498FCF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 71fa07e0f05c6c03ca7ec7d313117b1a3fc96804..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959DGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_4.fit.json b/ENCSR498FCF/cherimoya.fold_4.fit.json deleted file mode 100644 index 5f46d44ed77aeba05dde824a063bd6596aa68535..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF959DGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498FCF/cherimoya.fold_4.log b/ENCSR498FCF/cherimoya.fold_4.log deleted file mode 100644 index 2789022ad007d15763fb0200510faa072454571f..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2793 35.198397159576416 3.679065465927124 504.9635314941406 0.5261444449424744 573.9259643554688 0.22685208916664124 0.7033955 5.134708881378174 True -1 5586 30.098082065582275 0.6360366344451904 416.35711669921875 0.396884560585022 522.0941772460938 0.26374709606170654 0.775816 1.4100223779678345 True -2 8379 30.565507650375366 0.6456038951873779 471.22528076171875 0.358814001083374 517.6557006835938 0.2669425904750824 0.7738676 0.7759766578674316 False -3 11172 30.490241289138794 0.6525013446807861 426.2681579589844 0.43754276633262634 512.7603759765625 0.2686907649040222 0.79099125 0.7640443444252014 True -4 13965 30.540968418121338 25.08157253265381 603.8137817382812 0.26138293743133545 508.6851501464844 0.2738090753555298 0.797173 0.565123438835144 True -5 16758 30.99366307258606 0.6468229293823242 483.37646484375 0.4869181513786316 505.51226806640625 0.27505046129226685 0.80475193 0.511861264705658 True -6 19551 31.021896362304688 0.965775728225708 496.0273742675781 0.44583940505981445 502.0128479003906 0.27752673625946045 0.8180257 0.44844502210617065 True -7 22344 30.438930988311768 0.6356117725372314 605.3235473632812 0.5170417428016663 498.6942443847656 0.28027331829071045 0.82438064 0.4177636206150055 True -8 25137 30.445191383361816 0.634310245513916 478.822509765625 0.3606545627117157 498.1428527832031 0.2800678610801697 0.8297133 0.4059217870235443 True -9 27930 30.715728521347046 40.235894203186035 493.26116943359375 0.2950391471385956 496.9243469238281 0.2803894579410553 0.8354253 0.3789155185222626 True -10 30723 30.546225547790527 0.6557838916778564 436.34765625 0.2685048580169678 494.51470947265625 0.28199636936187744 0.8432116 0.3447483479976654 True -11 33516 30.598013162612915 22.60956859588623 474.12872314453125 0.3279631733894348 494.46063232421875 0.28135883808135986 0.8503923 0.3060140609741211 True -12 36309 30.519591331481934 2.384153366088867 466.2854919433594 0.2164442241191864 492.18060302734375 0.2840418517589569 0.8570741 0.279257595539093 True -13 39102 30.562428951263428 0.6724324226379395 415.80859375 0.19797007739543915 490.8706970214844 0.2857186794281006 0.8618034 0.2567799985408783 True -14 41895 30.537898778915405 0.916609525680542 472.3091735839844 0.22443756461143494 490.2833251953125 0.2858963906764984 0.8685846 0.2442837953567505 True -15 44688 30.524540424346924 0.6464905738830566 499.536376953125 0.27868974208831787 488.0953063964844 0.2877833843231201 0.8730633 0.23141026496887207 True -16 47481 30.5218243598938 0.6289138793945312 513.421142578125 0.29432278871536255 488.1420593261719 0.28721749782562256 0.87640834 0.22621312737464905 True -17 50274 30.5659019947052 0.7842304706573486 447.7699890136719 0.19158238172531128 488.0306396484375 0.2885722517967224 0.8759257 0.2265254706144333 False -18 53067 30.548789024353027 0.6365280151367188 346.8785400390625 0.14237579703330994 488.8548889160156 0.28704628348350525 0.87644744 0.22671493887901306 True -19 55860 30.510720014572144 0.636763334274292 476.55242919921875 0.17849819362163544 488.8430480957031 0.28734198212623596 0.8753071 0.2279433012008667 False diff --git a/ENCSR498FCF/cherimoya.fold_4.performance.tsv b/ENCSR498FCF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 556d8592820589a0969d9c927bb2c72034d69f6a..0000000000000000000000000000000000000000 --- a/ENCSR498FCF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -488.8548889160156 0.4536342918872833 0.28704628348350525 0.11044224351644516 0.8764474391937256 0.8380174040794373 0.22671493887901306 \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_0.evaluate.json b/ENCSR498RLX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b33947179c608cca64c9e2d01dc5d1acc52b989f..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF036SGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_0.fit.json b/ENCSR498RLX/cherimoya.fold_0.fit.json deleted file mode 100644 index cd135a2d6f5bc25aef868359b6664f8d434f60f4..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF036SGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_0.log b/ENCSR498RLX/cherimoya.fold_0.log deleted file mode 100644 index d4011148df615f7ba5645c75b08571ab09508a13..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 35.90578556060791 4.176584959030151 327.7049560546875 0.42653560638427734 561.4047241210938 0.2861587703227997 0.69316936 3.972677707672119 True -1 5470 30.75952124595642 14.476776599884033 487.7217712402344 0.2946817874908447 510.76495361328125 0.3569430112838745 0.75798106 1.466810941696167 True -2 8205 29.88329291343689 1.5038611888885498 420.1165771484375 0.28262093663215637 502.0400085449219 0.36533719301223755 0.77488136 0.7837132811546326 True -3 10940 30.171086072921753 19.991150856018066 365.74517822265625 0.33194252848625183 499.19171142578125 0.3677576184272766 0.7845391 0.5831708312034607 True -4 13675 29.819042444229126 19.824485301971436 371.458740234375 0.44060218334198 498.354736328125 0.36717551946640015 0.79105073 0.5651202201843262 True -5 16410 29.76284384727478 1.803147315979004 411.92626953125 0.39068007469177246 497.624755859375 0.36808139085769653 0.7965745 0.5255871415138245 True -6 19145 29.799171209335327 1.4758267402648926 437.5447998046875 0.3157776892185211 494.32568359375 0.37223467230796814 0.80289793 0.4046596884727478 True -7 21880 29.800044536590576 1.583202838897705 494.5661926269531 0.4555864930152893 492.41461181640625 0.3754865527153015 0.807866 0.379877507686615 True -8 24615 29.750367164611816 1.2254014015197754 414.69451904296875 0.21285711228847504 491.4089050292969 0.3771023452281952 0.8144161 0.3598928451538086 True -9 27350 29.78091812133789 1.3080878257751465 501.88470458984375 0.6051779985427856 490.53729248046875 0.37699607014656067 0.8184215 0.3382953107357025 True -10 30085 29.721217393875122 0.9056580066680908 366.41094970703125 0.3323679566383362 489.469970703125 0.3788004219532013 0.82258004 0.3229978680610657 True -11 32820 29.789876699447632 0.8150134086608887 470.8843994140625 0.24600613117218018 488.1923828125 0.3814939260482788 0.8275915 0.3037451505661011 True -12 35555 29.754581928253174 0.5806238651275635 438.3779296875 0.35072463750839233 487.2102355957031 0.3829454481601715 0.8308701 0.2996791899204254 True -13 38290 29.799155473709106 0.5726678371429443 467.30517578125 0.2522448003292084 486.4240417480469 0.38372814655303955 0.83507144 0.28257882595062256 True -14 41025 29.813129425048828 0.5843784809112549 414.369140625 0.2814335227012634 485.6135559082031 0.3842848539352417 0.83840925 0.2736228406429291 True -15 43760 29.794781923294067 0.5808169841766357 466.68682861328125 0.2787231206893921 485.2344055175781 0.3845921754837036 0.8415438 0.26516178250312805 True -16 46495 29.758671045303345 0.5742425918579102 485.73016357421875 0.22691792249679565 485.45953369140625 0.38458362221717834 0.8439707 0.25905224680900574 True -17 49230 29.762174606323242 0.5631077289581299 462.46185302734375 0.1260080337524414 484.49237060546875 0.3865920901298523 0.8459341 0.25797218084335327 True -18 51965 29.755225896835327 0.5626749992370605 385.1443176269531 0.2665249705314636 485.23797607421875 0.3853839039802551 0.84394175 0.259721964597702 False -19 54700 29.781455039978027 0.5711305141448975 466.7457580566406 0.23183852434158325 484.99945068359375 0.38591864705085754 0.8423473 0.2610794007778168 False diff --git a/ENCSR498RLX/cherimoya.fold_0.performance.tsv b/ENCSR498RLX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 95907fdc1851167a0541873699a39c634fbad27a..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -484.49237060546875 0.402817964553833 0.3865920901298523 0.14713194966316223 0.8459340929985046 0.8216161727905273 0.25797218084335327 \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_1.evaluate.json b/ENCSR498RLX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 40dd3ac7cf2afc59202239003ecfebcd4163e3a7..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF036SGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_1.fit.json b/ENCSR498RLX/cherimoya.fold_1.fit.json deleted file mode 100644 index e3155f6cf99f7b1a8163bb5bb1c10d8b22c9300d..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF036SGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_1.log b/ENCSR498RLX/cherimoya.fold_1.log deleted file mode 100644 index 2794ff00c2d62bfb468f018b5ea4bb4675a40bd5..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 35.17978310585022 4.7937304973602295 451.11224365234375 0.5335464477539062 681.05859375 0.29046615958213806 0.70225275 4.480414390563965 True -1 5454 29.90287947654724 0.661013126373291 426.0085144042969 0.5082341432571411 610.3583374023438 0.3723277151584625 0.7767871 1.3845384120941162 True -2 8181 30.363646984100342 0.6382458209991455 414.18182373046875 0.3100489377975464 598.440673828125 0.38362225890159607 0.7890593 0.6951547861099243 True -3 10908 30.355949878692627 0.6873114109039307 366.3569030761719 0.33383452892303467 594.4151611328125 0.38740426301956177 0.7949795 0.7274569869041443 True -4 13635 30.351956844329834 0.6522102355957031 436.624755859375 0.2693352997303009 593.2059936523438 0.3886722922325134 0.7933463 0.7382707595825195 False -5 16362 30.33538055419922 1.8002822399139404 412.809326171875 0.3744125962257385 587.0983276367188 0.39458325505256653 0.81086 0.5462788343429565 True -6 19089 30.367626905441284 0.6655120849609375 412.3110656738281 0.3259980082511902 586.7821655273438 0.39388376474380493 0.81223315 0.5013043284416199 True -7 21816 30.442627906799316 0.6526517868041992 419.5899658203125 0.49342191219329834 584.3255615234375 0.3970458507537842 0.8172754 0.43637749552726746 True -8 24543 30.434144258499146 0.7241005897521973 375.3402099609375 0.49811017513275146 581.37890625 0.401574969291687 0.82395077 0.4418971836566925 True -9 27270 30.438822746276855 0.6654767990112305 402.89837646484375 0.2978925108909607 578.5280151367188 0.4048502743244171 0.82770103 0.403574675321579 True -10 29997 30.358824014663696 0.6477630138397217 420.34375 0.4499202072620392 578.8060302734375 0.40309032797813416 0.83200216 0.40587544441223145 True -11 32724 30.364725589752197 0.6540954113006592 431.2691345214844 0.3866598606109619 577.402587890625 0.40467357635498047 0.837397 0.3858644664287567 True -12 35451 30.428531646728516 0.6565983295440674 455.2724914550781 0.39978617429733276 574.6371459960938 0.4080933928489685 0.84056145 0.36191248893737793 True -13 38178 30.421493768692017 0.6658263206481934 513.6239013671875 0.4409416913986206 573.1002197265625 0.40954962372779846 0.8432996 0.34394869208335876 True -14 40905 30.366493463516235 0.6917088031768799 457.3829345703125 0.2835562527179718 570.8692016601562 0.4127098619937897 0.8500465 0.32084542512893677 True -15 43632 30.480443477630615 0.6859185695648193 329.8429260253906 0.15516915917396545 570.9512939453125 0.4110901355743408 0.8526262 0.30914977192878723 True -16 46359 30.47913432121277 1.6310219764709473 424.01617431640625 0.32821008563041687 571.2280883789062 0.41090694069862366 0.8557749 0.29800787568092346 True -17 49086 30.492231369018555 1.1908900737762451 355.9306640625 0.1794578582048416 571.0950927734375 0.41132795810699463 0.8550663 0.296609103679657 False -18 51813 30.494598150253296 13.844929218292236 393.7403869628906 0.14146025478839874 571.7789916992188 0.4106617867946625 0.8535216 0.29798462986946106 False -19 54540 30.58534002304077 23.115049123764038 444.23553466796875 0.2338961362838745 571.3580322265625 0.41192904114723206 0.8530394 0.3001483678817749 False diff --git a/ENCSR498RLX/cherimoya.fold_1.performance.tsv b/ENCSR498RLX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ccc8b791c9be8d7332330df26f0675d79b01f7c3..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -571.2280883789062 0.3807971775531769 0.41090700030326843 0.16950492560863495 0.8557748794555664 0.8450316786766052 0.29800787568092346 \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_2.evaluate.json b/ENCSR498RLX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0592cddab5044ffaa3a54cfe6819e9e489fe871b..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF036SGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_2.fit.json b/ENCSR498RLX/cherimoya.fold_2.fit.json deleted file mode 100644 index 286a75c4db0eec730e7504d3dc26f50bd0a67236..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF036SGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_2.log b/ENCSR498RLX/cherimoya.fold_2.log deleted file mode 100644 index 47fea47f665874266cad52208ffce129571b2307..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2887 36.85826659202576 3.8557422161102295 422.33154296875 0.33484727144241333 593.4677734375 0.2894297242164612 0.687144 3.762690305709839 True -1 5774 32.158976316452026 0.5640573501586914 525.431396484375 0.5838851928710938 540.6802368164062 0.3593028783798218 0.75994176 1.328456163406372 True -2 8661 31.77108120918274 0.550961971282959 409.35662841796875 0.3918970823287964 529.21484375 0.37220731377601624 0.78057504 0.7945022583007812 True -3 11548 31.424472332000732 0.5439009666442871 419.3477478027344 0.2876017093658447 527.5353393554688 0.3722098171710968 0.7900005 0.5218844413757324 True -4 14435 31.458343982696533 0.529857873916626 577.6273193359375 0.4308852553367615 526.4097290039062 0.3727506697177887 0.79810536 0.48555853962898254 True -5 17322 31.531631231307983 0.5887815952301025 432.58056640625 0.3945446312427521 524.2960815429688 0.3755112588405609 0.804686 0.4654904901981354 True -6 20209 31.529113292694092 0.5388643741607666 423.2522277832031 0.31651395559310913 522.1220703125 0.3783835470676422 0.8080758 0.4245537519454956 True -7 23096 31.518221855163574 1.250946283340454 428.43701171875 0.280551016330719 519.9701538085938 0.38113129138946533 0.81286174 0.40139806270599365 True -8 25983 31.421993494033813 0.5525970458984375 498.7177429199219 0.4808931052684784 518.482666015625 0.3827723264694214 0.8171264 0.3710979223251343 True -9 28870 31.476707220077515 0.5330996513366699 471.320556640625 0.4211071729660034 516.66162109375 0.3854420781135559 0.8204375 0.34982597827911377 True -10 31757 31.589498043060303 0.5456042289733887 333.68701171875 0.31319481134414673 515.0513305664062 0.38806572556495667 0.8257206 0.33896172046661377 True -11 34644 31.446547269821167 0.5422282218933105 380.1726379394531 0.18607884645462036 515.0775146484375 0.3868192732334137 0.82948005 0.32601362466812134 True -12 37531 31.44670009613037 0.5426535606384277 370.7125549316406 0.2573915421962738 515.116455078125 0.3860541582107544 0.8309414 0.3169555366039276 True -13 40418 31.43672466278076 0.5366840362548828 435.53497314453125 0.31104469299316406 513.1791381835938 0.3890271484851837 0.8343818 0.3025413453578949 True -14 43305 31.482981204986572 0.5435750484466553 508.6438293457031 0.3007754683494568 512.3941040039062 0.3907754719257355 0.8394604 0.2957097291946411 True -15 46192 31.422529935836792 0.5498337745666504 412.93511962890625 0.26293662190437317 511.7252197265625 0.391194224357605 0.8419397 0.28237709403038025 True -16 49079 31.39208745956421 0.5586636066436768 469.5355529785156 0.2877645492553711 511.2795104980469 0.3918597996234894 0.84284747 0.27792131900787354 True -17 51966 31.4515438079834 0.5452604293823242 386.90875244140625 0.25049740076065063 509.8446350097656 0.3955940902233124 0.8436236 0.2778783440589905 True -18 54853 31.40351438522339 0.5575611591339111 436.407470703125 0.4198148846626282 511.4822692871094 0.3924787938594818 0.8427797 0.27886855602264404 False -19 57740 31.48715114593506 0.5303206443786621 332.7906188964844 0.19582368433475494 511.4820556640625 0.3922156095504761 0.83983564 0.281188428401947 False diff --git a/ENCSR498RLX/cherimoya.fold_2.performance.tsv b/ENCSR498RLX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6e08fc7be6d5e1a338c5c5da9e2080a4880f01be..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -509.8446350097656 0.3958818018436432 0.3955940902233124 0.1555430293083191 0.8436235785484314 0.8271710276603699 0.2778783440589905 \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_3.evaluate.json b/ENCSR498RLX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7af819dfd3660d558f56a0f1bd5ed87ac7c69679..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF036SGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_3.fit.json b/ENCSR498RLX/cherimoya.fold_3.fit.json deleted file mode 100644 index ca4adb7f74ecf32a8e48d9943e397083a1a0675d..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF036SGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_3.log b/ENCSR498RLX/cherimoya.fold_3.log deleted file mode 100644 index c1661528b0e1628393a9da475d2abff02782d603..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 35.41402530670166 3.7596945762634277 465.0926818847656 0.33420616388320923 558.5183715820312 0.2951347529888153 0.6651977 5.00238561630249 True -1 5494 30.630387783050537 0.6407256126403809 407.19073486328125 0.4008975625038147 507.08746337890625 0.3661818504333496 0.7516917 1.3282119035720825 True -2 8241 30.698094367980957 0.6070539951324463 394.2601623535156 0.34276285767555237 501.0801696777344 0.36922597885131836 0.7685835 0.7646412253379822 True -3 10988 30.8022882938385 0.5906038284301758 457.7058410644531 0.29716354608535767 495.994140625 0.3752148449420929 0.7847338 0.5735366940498352 True -4 13735 30.743019580841064 0.59588623046875 382.0285949707031 0.30669182538986206 494.06195068359375 0.37669554352760315 0.7921608 0.5737771391868591 True -5 16482 30.549479722976685 1.528268575668335 421.83538818359375 0.3574347496032715 492.3252258300781 0.37951603531837463 0.7972336 0.5078265070915222 True -6 19229 30.58475351333618 0.6084420680999756 427.5648193359375 0.2739031910896301 491.734130859375 0.3801036775112152 0.7975645 0.45694825053215027 True -7 21976 30.723942518234253 9.922024726867676 441.38922119140625 0.4147621989250183 489.3916931152344 0.38365408778190613 0.8026262 0.439413845539093 True -8 24723 30.841625690460205 0.5799980163574219 379.4683837890625 0.30530235171318054 487.8102722167969 0.3859705626964569 0.8064065 0.42214444279670715 True -9 27470 30.645158290863037 0.8240349292755127 476.5184326171875 0.4607773423194885 486.7991943359375 0.3871667981147766 0.810706 0.40382036566734314 True -10 30217 30.633203983306885 1.2132079601287842 519.5626220703125 0.43109917640686035 486.1134948730469 0.3878708779811859 0.81339455 0.40191617608070374 True -11 32964 30.72024130821228 0.5739731788635254 431.1942443847656 0.35355234146118164 484.9587097167969 0.38882362842559814 0.8210114 0.36525246500968933 True -12 35711 30.644336938858032 0.5713953971862793 456.35406494140625 0.3952783942222595 484.28106689453125 0.38958266377449036 0.82607114 0.3457726836204529 True -13 38458 30.630635261535645 0.5663204193115234 472.3570251464844 0.40499788522720337 483.48052978515625 0.3909015953540802 0.8280343 0.3273104429244995 True -14 41205 30.635011196136475 0.5746262073516846 443.1387939453125 0.28098851442337036 481.63507080078125 0.3934515416622162 0.83424115 0.3111259639263153 True -15 43952 30.742568492889404 0.5711348056793213 412.277099609375 0.2293614000082016 480.4667663574219 0.3952913284301758 0.8383761 0.2981579601764679 True -16 46699 30.630786895751953 2.934082508087158 476.1733093261719 0.24056412279605865 479.94793701171875 0.3955579102039337 0.8408019 0.28881511092185974 True -17 49446 30.15435767173767 0.5959506034851074 457.67852783203125 0.21038004755973816 480.5541687011719 0.3956458568572998 0.84105545 0.2842194139957428 True -18 52193 30.028716564178467 0.5595660209655762 402.43475341796875 0.17407995462417603 480.3343811035156 0.39567816257476807 0.84134203 0.28514766693115234 True -19 54940 29.890862703323364 0.5549178123474121 401.0428466796875 0.18291130661964417 480.9766540527344 0.3941771686077118 0.83957535 0.28640756011009216 False diff --git a/ENCSR498RLX/cherimoya.fold_3.performance.tsv b/ENCSR498RLX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 76c2adc66b0c39a4914b583e8fa885a94a4a8dda..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -480.3343811035156 0.3992154002189636 0.3956781327724457 0.15050072968006134 0.841342031955719 0.8062094449996948 0.28514766693115234 \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_4.evaluate.json b/ENCSR498RLX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5580203564649689a89d1a4f9bdc7dc15785855f..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF036SGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_4.fit.json b/ENCSR498RLX/cherimoya.fold_4.fit.json deleted file mode 100644 index acd0139083b58a6fd8f76e89a156687983393db1..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF036SGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR498RLX/cherimoya.fold_4.log b/ENCSR498RLX/cherimoya.fold_4.log deleted file mode 100644 index 7673cf77614cb6d65eb1102284f1420e020bc408..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2820 36.06890249252319 4.126012802124023 462.27813720703125 0.4693601727485657 537.708251953125 0.2910290062427521 0.6742823 3.8451011180877686 True -1 5640 31.350958108901978 0.6330764293670654 503.2247619628906 0.6745331287384033 494.9043884277344 0.3533782958984375 0.7385847 1.1128292083740234 True -2 8460 31.334588766098022 0.5923628807067871 494.67388916015625 0.5941734910011292 485.83984375 0.36413490772247314 0.7623196 0.5806236863136292 True -3 11280 31.299710035324097 0.5964250564575195 453.3546142578125 0.41598060727119446 482.871826171875 0.36580145359039307 0.77297217 0.5820831060409546 True -4 14100 31.29423475265503 0.5999610424041748 399.88519287109375 0.30283936858177185 480.9542541503906 0.3671238422393799 0.7879283 0.37035608291625977 True -5 16920 31.288472652435303 1.4740028381347656 483.3929748535156 0.2852255702018738 480.1207580566406 0.36843520402908325 0.78900814 0.3839621841907501 True -6 19740 31.363109588623047 1.4666101932525635 422.24468994140625 0.36733368039131165 477.41204833984375 0.37282896041870117 0.7979641 0.36640632152557373 True -7 22560 31.380215406417847 19.204139947891235 403.88641357421875 0.1710757613182068 476.6125183105469 0.3739369511604309 0.80214626 0.35299503803253174 True -8 25380 31.366902828216553 18.712274312973022 378.478759765625 0.31075039505958557 475.0379943847656 0.37764856219291687 0.8064541 0.35542893409729004 True -9 28200 31.323599338531494 1.2852468490600586 398.3219299316406 0.4467223584651947 474.5581970214844 0.3774012625217438 0.80810124 0.34344935417175293 True -10 31020 31.311019897460938 0.9923286437988281 403.8778076171875 0.26292526721954346 472.23223876953125 0.3819580078125 0.8106467 0.34087520837783813 True -11 33840 31.35962462425232 0.860295295715332 362.57977294921875 0.25633704662323 472.3556213378906 0.3807104527950287 0.81632185 0.32423949241638184 True -12 36660 31.32487726211548 0.617786169052124 393.9990234375 0.28765395283699036 471.701171875 0.3814634084701538 0.81968147 0.31040868163108826 True -13 39480 31.32950186729431 0.6401054859161377 394.1129150390625 0.22122813761234283 471.43658447265625 0.3812759220600128 0.82339483 0.29782482981681824 True -14 42300 31.461364030838013 0.8675868511199951 381.7142639160156 0.22016724944114685 470.88067626953125 0.3821289837360382 0.8291372 0.28305479884147644 True -15 45120 31.06070566177368 17.517845153808594 453.59027099609375 0.21180406212806702 469.84600830078125 0.38414570689201355 0.8322585 0.2750908136367798 True -16 47940 30.72386360168457 1.249666690826416 406.2501525878906 0.27864593267440796 469.0234680175781 0.3855632245540619 0.8342217 0.26963821053504944 True -17 50760 30.853933572769165 1.3251655101776123 421.70318603515625 0.2196355164051056 469.0965270996094 0.3852081298828125 0.83344764 0.2660473883152008 False -18 53580 30.70314645767212 1.1317181587219238 422.2003173828125 0.15011754631996155 469.70672607421875 0.38433411717414856 0.8325769 0.2670578360557556 False -19 56400 30.756598711013794 0.8662765026092529 420.8424072265625 0.2226201593875885 469.4517517089844 0.3851119875907898 0.8320566 0.2695544958114624 False diff --git a/ENCSR498RLX/cherimoya.fold_4.performance.tsv b/ENCSR498RLX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3d0b9a7fa7dc2ad932b2587968797ba54db00e0e..0000000000000000000000000000000000000000 --- a/ENCSR498RLX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -469.0234680175781 0.40481439232826233 0.3855632245540619 0.14491204917430878 0.8342217206954956 0.8065771460533142 0.26963821053504944 \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_0.evaluate.json b/ENCSR499ASS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 606aa7c466587143541999891cb53e1f40fd7e24..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF983ZLW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_0.fit.json b/ENCSR499ASS/cherimoya.fold_0.fit.json deleted file mode 100644 index 0934b4743455b81efd542c27659be2df0b56a5ad..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF983ZLW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_0.log b/ENCSR499ASS/cherimoya.fold_0.log deleted file mode 100644 index 3015fd47e9ba99053519f8bf6ef3c9724afd9e3d..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3612 44.55624461174011 5.099907159805298 391.4053649902344 1.34855318069458 661.089111328125 0.6320779919624329 0.5453474 8.400590896606445 True -1 7224 39.902159214019775 2.520231008529663 349.27069091796875 1.5117971897125244 566.8307495117188 0.7367782592773438 0.556081 2.05904483795166 True -2 10836 39.944772243499756 0.8624975681304932 349.9497985839844 1.0059375762939453 556.4861450195312 0.745617151260376 0.5609119 1.6304305791854858 True -3 14448 39.85367703437805 0.9089066982269287 403.93353271484375 1.2834932804107666 548.7535400390625 0.7528512477874756 0.5657007 1.5334367752075195 True -4 18060 39.86280632019043 0.8638596534729004 361.5985412597656 1.034301996231079 547.115234375 0.7562452554702759 0.5655503 1.7131556272506714 False -5 21672 39.93527841567993 0.8344686031341553 372.564208984375 1.2146130800247192 545.9085693359375 0.7585045099258423 0.5768213 1.70404851436615 True -6 25284 39.949394941329956 0.8301358222961426 410.7954406738281 1.207792043685913 542.7459106445312 0.7620804309844971 0.5777812 1.6143293380737305 True -7 28896 39.92317986488342 0.8282642364501953 304.319580078125 1.1952719688415527 538.9423217773438 0.7654005289077759 0.5876093 1.432841420173645 True -8 32508 40.015828132629395 0.85076904296875 353.9288330078125 1.1513205766677856 535.4584350585938 0.7688949108123779 0.60060275 1.3733961582183838 True -9 36120 39.8693528175354 0.840315580368042 418.25689697265625 1.1123223304748535 532.622802734375 0.7715767025947571 0.6088911 1.336326241493225 True -10 39732 39.91569924354553 0.8336954116821289 426.210693359375 0.9213834404945374 528.8889770507812 0.7747838497161865 0.61574423 1.2221027612686157 True -11 43344 39.79975128173828 2.6275525093078613 383.6941833496094 1.4702165126800537 526.1774291992188 0.7771173715591431 0.6220148 1.1270726919174194 True -12 46956 39.93307685852051 1.4624824523925781 427.01287841796875 0.8302727937698364 522.6619873046875 0.7803278565406799 0.6379855 1.0334848165512085 True -13 50568 39.42605781555176 0.8191008567810059 372.5161437988281 0.7662158012390137 520.2378540039062 0.7822313904762268 0.65057224 0.9994385838508606 True -14 54180 39.200735330581665 2.0072999000549316 402.4352722167969 0.6358340382575989 518.11767578125 0.784309983253479 0.65987855 0.9337398409843445 True -15 57792 39.224761724472046 0.8637974262237549 294.5762939453125 1.3325209617614746 516.39404296875 0.7858153581619263 0.66477966 0.9212749004364014 True -16 61404 39.384615898132324 0.8380424976348877 337.92962646484375 0.6320585012435913 515.3358154296875 0.7866415977478027 0.6723897 0.9034194946289062 True -17 65016 39.29328274726868 0.870431661605835 397.07513427734375 0.5989431142807007 515.0438232421875 0.7867215275764465 0.6744827 0.8932300209999084 True -18 68628 39.27715802192688 1.6683886051177979 349.238525390625 0.38703685998916626 515.1366577148438 0.7864038348197937 0.6729313 0.9011203646659851 False -19 72240 39.26567316055298 0.8513369560241699 347.0086669921875 0.8351420760154724 515.3234252929688 0.7862248420715332 0.6712485 0.90982985496521 False diff --git a/ENCSR499ASS/cherimoya.fold_0.performance.tsv b/ENCSR499ASS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e4dc0c08f6f47b36dd5642695b3ac19c6610bb1a..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -515.0438232421875 0.19037654995918274 0.7867216467857361 0.35650211572647095 0.6744827032089233 0.6650905609130859 0.8932300209999084 \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_1.evaluate.json b/ENCSR499ASS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bb0a045a60c65d4027437133231759c122879d25..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF983ZLW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_1.fit.json b/ENCSR499ASS/cherimoya.fold_1.fit.json deleted file mode 100644 index 4c97483da297bf071fa2c57fdf4ab78268139243..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF983ZLW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_1.log b/ENCSR499ASS/cherimoya.fold_1.log deleted file mode 100644 index 02d673cddbc3dbecba12541dc9ac4574e7180f92..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3728 45.86461424827576 4.332256555557251 337.30401611328125 1.1661274433135986 658.1760864257812 0.6470788717269897 0.6291373 6.669447422027588 True -1 7456 41.17487025260925 1.1274175643920898 395.9580383300781 0.9188441038131714 574.689697265625 0.7420844435691833 0.6084341 2.017571449279785 False -2 11184 41.136324644088745 0.9433093070983887 354.3653259277344 0.8893458843231201 562.0444946289062 0.7514898777008057 0.61414963 1.3556238412857056 False -3 14912 41.20463705062866 0.9531784057617188 354.0823669433594 1.2561708688735962 557.0885009765625 0.7567091584205627 0.613065 1.293603777885437 False -4 18640 42.30318641662598 0.9393980503082275 402.205078125 1.112890601158142 553.5604858398438 0.7601738572120667 0.62404317 1.271111011505127 False -5 22368 41.14552426338196 0.9475677013397217 347.972412109375 1.264771580696106 549.1570434570312 0.7649545073509216 0.62960565 1.2037850618362427 True -6 26096 41.1355185508728 12.726608276367188 333.94561767578125 0.9519751071929932 546.2583618164062 0.7685737609863281 0.6383469 1.1260687112808228 True -7 29824 41.28885746002197 0.9686415195465088 375.9908142089844 0.9522527456283569 543.8281860351562 0.771273136138916 0.64612186 1.0582160949707031 True -8 33552 41.23462438583374 0.961007833480835 418.2989501953125 0.8305128216743469 540.1575317382812 0.7746671438217163 0.65289086 0.9573063850402832 True -9 37280 41.23827886581421 0.9552536010742188 344.3944396972656 1.3582851886749268 537.2970581054688 0.7775204181671143 0.65671736 0.9284718632698059 True -10 41008 40.724608421325684 0.9368512630462646 499.2946472167969 0.9647643566131592 534.3731079101562 0.7802931070327759 0.6658717 0.8335609436035156 True -11 44736 40.43675923347473 19.091678380966187 388.6253967285156 0.943435549736023 531.7564086914062 0.7831748127937317 0.67830104 0.7778136730194092 True -12 48464 40.48729920387268 0.9436423778533936 300.9748840332031 0.8217431306838989 529.2355346679688 0.7855812311172485 0.68300676 0.7757260799407959 True -13 52192 40.44410061836243 0.942624568939209 336.1228332519531 1.043487310409546 527.1085205078125 0.7879021763801575 0.69300795 0.7516980171203613 True -14 55920 40.52564835548401 0.9502394199371338 411.3810119628906 0.737073540687561 524.7888793945312 0.7898834347724915 0.70986503 0.6962808966636658 True -15 59648 40.62810492515564 0.9565768241882324 343.4170837402344 0.8727376461029053 523.3429565429688 0.7914032340049744 0.7184873 0.6607089638710022 True -16 63376 40.472466230392456 0.9367647171020508 362.22784423828125 0.6214642524719238 522.1751708984375 0.7922411561012268 0.72623956 0.6408954858779907 True -17 67104 40.658005475997925 0.9511406421661377 340.8331298828125 0.5941396355628967 521.8624877929688 0.792328417301178 0.7297333 0.6309588551521301 True -18 70832 40.50794196128845 0.9240179061889648 358.7508239746094 0.5576645731925964 522.0052490234375 0.7920434474945068 0.7279963 0.6322137117385864 False -19 74560 40.6074116230011 0.9633784294128418 383.27496337890625 0.5348010659217834 522.1679077148438 0.7918952703475952 0.7293098 0.6347866654396057 False diff --git a/ENCSR499ASS/cherimoya.fold_1.performance.tsv b/ENCSR499ASS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9282cc0468f60368677a3d062e36ab1fff1370bc..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -521.8624877929688 0.1869277060031891 0.792328417301178 0.36412402987480164 0.7297332882881165 0.7376249432563782 0.6309588551521301 \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_2.evaluate.json b/ENCSR499ASS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e33bf37b4871c96096757798bea64e6ae7be0ca0..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF983ZLW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_2.fit.json b/ENCSR499ASS/cherimoya.fold_2.fit.json deleted file mode 100644 index 25efa2f903fa3d94ee5d733201a26789cd82e1ce..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF983ZLW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_2.log b/ENCSR499ASS/cherimoya.fold_2.log deleted file mode 100644 index a0d7f44fc9a2d67ecd1ae0041449080e4f45c6ad..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3903 47.80645418167114 4.247047424316406 451.55084228515625 1.5625059604644775 603.7847900390625 0.6553676724433899 0.61526644 6.311647891998291 True -1 7806 43.150197982788086 1.0711562633514404 455.880615234375 1.0531271696090698 538.48046875 0.7381603121757507 0.6016837 1.5391179323196411 False -2 11709 43.1969153881073 0.7793686389923096 364.962158203125 1.3854267597198486 529.4185791015625 0.7459275126457214 0.61114466 1.1836174726486206 False -3 15612 43.10675311088562 0.7866189479827881 352.00250244140625 0.840137243270874 521.974609375 0.7544020414352417 0.61090887 1.1525967121124268 False -4 19515 43.12961983680725 1.3798155784606934 430.5757751464844 1.0848861932754517 519.5513916015625 0.7571123838424683 0.6239349 1.1564732789993286 True -5 23418 42.50180172920227 1.1342253684997559 354.69390869140625 0.9051780104637146 517.8936767578125 0.7597697377204895 0.6300728 1.0895869731903076 True -6 27321 42.265119552612305 0.785336971282959 366.306396484375 1.2332544326782227 515.061767578125 0.763340175151825 0.63941705 1.0306938886642456 True -7 31224 42.26238536834717 0.777050256729126 422.17193603515625 0.9761105179786682 511.67523193359375 0.7666094303131104 0.6446953 0.9509442448616028 True -8 35127 42.27504324913025 0.780811071395874 384.9439697265625 1.2111694812774658 509.3169250488281 0.7695614695549011 0.65001 0.8532980680465698 True -9 39030 42.233903646469116 31.917781591415405 420.47576904296875 0.9750080704689026 506.7050476074219 0.7723698019981384 0.6598679 0.80987149477005 True -10 42933 42.59359264373779 0.7910425662994385 416.65045166015625 1.0410146713256836 504.02728271484375 0.7754082083702087 0.6654481 0.765934944152832 True -11 46836 42.47946047782898 0.8044946193695068 382.0235290527344 0.7988591194152832 501.0628967285156 0.778295636177063 0.67962927 0.7038343548774719 True -12 50739 42.495561838150024 1.72585129737854 386.14935302734375 0.736640214920044 498.14996337890625 0.7812585234642029 0.68949246 0.6530916690826416 True -13 54642 42.47312927246094 0.7828779220581055 375.25341796875 0.7954396605491638 496.6332702636719 0.783017098903656 0.70010173 0.6424969434738159 True -14 58545 42.41687870025635 0.7913944721221924 378.574462890625 0.776987612247467 494.56683349609375 0.7850221395492554 0.70836836 0.614496111869812 True -15 62448 42.43824005126953 0.8211352825164795 348.5823974609375 1.0383532047271729 493.3384704589844 0.7862339615821838 0.7178097 0.5953582525253296 True -16 66351 42.362714529037476 0.7891216278076172 333.0005798339844 0.6810721158981323 492.71160888671875 0.7866032719612122 0.7251113 0.5862144231796265 True -17 70254 42.56007695198059 0.8493754863739014 347.5858154296875 0.6672839522361755 492.3620910644531 0.7869090437889099 0.72854716 0.5916633605957031 True -18 74157 42.48869705200195 0.7849035263061523 401.3802490234375 0.44713249802589417 492.9501647949219 0.7865471839904785 0.7253685 0.600712776184082 False -19 78060 42.528287172317505 0.7697179317474365 392.4362487792969 0.45479243993759155 492.9238586425781 0.7863690257072449 0.7236649 0.6085677146911621 False diff --git a/ENCSR499ASS/cherimoya.fold_2.performance.tsv b/ENCSR499ASS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c2bd8d129c8d6eac929422881ed83f3dcb521ed0..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -492.3620910644531 0.19279631972312927 0.7869090437889099 0.34783804416656494 0.7285471558570862 0.7282034158706665 0.5916633605957031 \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_3.evaluate.json b/ENCSR499ASS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 065a17894e5540de9f51046d0045ee2c0ec86183..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF983ZLW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_3.fit.json b/ENCSR499ASS/cherimoya.fold_3.fit.json deleted file mode 100644 index bf5b5a8ccf84c57560aee2d21dd6819bc0bc19f2..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF983ZLW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_3.log b/ENCSR499ASS/cherimoya.fold_3.log deleted file mode 100644 index 484f11564a027a55f0d06e3699341a8847fed5cc..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3773 46.292832136154175 4.22943377494812 467.034912109375 1.3808951377868652 559.7302856445312 0.6386871933937073 0.63004667 7.317318916320801 True -1 7546 41.725579500198364 0.9815366268157959 408.9332275390625 1.197808027267456 498.3081359863281 0.7306187748908997 0.58703697 1.7541747093200684 False -2 11319 41.62032866477966 0.7265946865081787 437.3575439453125 1.1811981201171875 489.2080383300781 0.739355206489563 0.6019807 1.1569286584854126 False -3 15092 41.226025104522705 0.7025158405303955 423.34161376953125 0.7394447326660156 482.901123046875 0.7467867732048035 0.60652775 0.9833045601844788 False -4 18865 40.82449197769165 0.7149176597595215 467.9332275390625 1.2325453758239746 481.7705993652344 0.7492755651473999 0.6073787 0.9590381383895874 False -5 22638 40.816224575042725 0.7226119041442871 409.91363525390625 0.8686258792877197 479.3481140136719 0.7522408366203308 0.6169206 0.8945484161376953 False -6 26411 40.85565710067749 0.7196304798126221 419.70123291015625 1.075148582458496 478.0834045410156 0.7539451122283936 0.6200146 0.9078832864761353 False -7 30184 40.810551166534424 0.7092914581298828 412.9698486328125 1.2994821071624756 475.27435302734375 0.7577299475669861 0.63694936 0.8551839590072632 True -8 33957 40.89665651321411 0.7249448299407959 421.0637512207031 1.1261396408081055 473.196533203125 0.7607576251029968 0.64695084 0.8215481042861938 True -9 37730 40.88349890708923 0.7245650291442871 406.6094970703125 0.71087646484375 471.1556091308594 0.7632862329483032 0.65103406 0.7317175269126892 True -10 41503 40.86253595352173 0.7189116477966309 425.906005859375 1.1539671421051025 468.2174072265625 0.766450822353363 0.6698538 0.657551646232605 True -11 45276 40.82780647277832 0.7208073139190674 408.485107421875 0.925007700920105 466.4593811035156 0.7690272927284241 0.6764636 0.606194257736206 True -12 49049 40.91011071205139 0.7116794586181641 408.59161376953125 1.107288122177124 464.1647033691406 0.7713640332221985 0.68788296 0.5763455629348755 True -13 52822 40.994460344314575 0.7102539539337158 354.3869323730469 0.7572444677352905 462.1689453125 0.774020254611969 0.7040904 0.537057638168335 True -14 56595 41.112146854400635 0.7270412445068359 332.87176513671875 0.6535552740097046 460.7942199707031 0.7755045294761658 0.71241367 0.5329659581184387 True -15 60368 41.04081654548645 0.7044925689697266 390.15606689453125 0.8071930408477783 459.619873046875 0.7769731283187866 0.7162942 0.5205689072608948 True -16 64141 40.90915846824646 0.7471201419830322 342.43157958984375 0.5632151961326599 459.1785888671875 0.7773127555847168 0.72175854 0.5178295373916626 True -17 67914 41.702171325683594 23.77598810195923 313.3707275390625 0.8635359406471252 458.9757995605469 0.7775318622589111 0.72412133 0.5209418535232544 True -18 71687 40.967575550079346 0.7244129180908203 370.1710205078125 0.4634503424167633 458.85333251953125 0.7773464918136597 0.7208556 0.531703531742096 False -19 75460 40.91736173629761 0.7430553436279297 396.97686767578125 0.7855253219604492 459.19635009765625 0.7771419882774353 0.7201472 0.5394970774650574 False diff --git a/ENCSR499ASS/cherimoya.fold_3.performance.tsv b/ENCSR499ASS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 52dd36690049f96299900860297db0b65428ffe9..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -458.9757995605469 0.20073281228542328 0.7775319218635559 0.3281833231449127 0.7241213321685791 0.7284143567085266 0.5209418535232544 \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_4.evaluate.json b/ENCSR499ASS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b20019b07c68784a9cd5cb23804d1e4550b63068..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF983ZLW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_4.fit.json b/ENCSR499ASS/cherimoya.fold_4.fit.json deleted file mode 100644 index 9fe4587b0399f375a4fdea44a3ae523fd79718c8..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF983ZLW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499ASS/cherimoya.fold_4.log b/ENCSR499ASS/cherimoya.fold_4.log deleted file mode 100644 index 4ba100207ea09f0e0690b931ce3e84ea5caa4c5e..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3800 46.7272527217865 4.5230185985565186 415.5156555175781 0.9993191957473755 619.6517333984375 0.6428050398826599 0.5210539 8.905113220214844 True -1 7600 41.94794774055481 0.9528710842132568 476.373291015625 1.1195249557495117 539.2296752929688 0.7363439798355103 0.5011538 1.6689486503601074 False -2 11400 41.94479036331177 2.0667998790740967 317.8775634765625 0.9940093159675598 527.9293823242188 0.7470094561576843 0.51816916 1.5170326232910156 False -3 15200 42.00631332397461 0.8385591506958008 326.5821533203125 1.2585877180099487 522.5762939453125 0.7537528276443481 0.53041863 1.4481422901153564 True -4 19000 41.92481279373169 0.8075461387634277 384.4145202636719 0.887225866317749 520.879150390625 0.7558318972587585 0.53301054 1.4938793182373047 True -5 22800 41.86448287963867 0.8053910732269287 402.74127197265625 1.1091562509536743 518.7128295898438 0.7590218782424927 0.53620607 1.4144951105117798 True -6 26600 41.95256972312927 0.817253589630127 397.765380859375 0.8203949928283691 515.347412109375 0.7618802785873413 0.54642755 1.40599524974823 True -7 30400 42.02862000465393 0.8361282348632812 376.31451416015625 0.9815375804901123 512.3383178710938 0.7653539180755615 0.55368924 1.2741883993148804 True -8 34200 42.0464608669281 1.878732442855835 353.33935546875 0.9419002532958984 509.2968444824219 0.7681049108505249 0.563928 1.1450082063674927 True -9 38000 41.995198249816895 0.7982063293457031 411.9667663574219 0.8693206906318665 506.28125 0.7710668444633484 0.56605077 1.1083406209945679 True -10 41800 41.86985111236572 1.1607005596160889 468.8126220703125 0.6993120312690735 503.9363098144531 0.774014413356781 0.57917196 1.0331097841262817 True -11 45600 41.96718406677246 0.8061444759368896 351.0374755859375 0.7173051834106445 500.9683837890625 0.7768934369087219 0.58722925 0.9693381786346436 True -12 49400 42.4231972694397 0.7845578193664551 384.10284423828125 0.46585461497306824 499.34124755859375 0.7790773510932922 0.5946939 0.9730259776115417 True -13 53200 41.96432709693909 0.7996668815612793 303.64459228515625 0.5219366550445557 497.0911560058594 0.7811567187309265 0.6050096 0.90697181224823 True -14 57000 41.514886140823364 0.7800304889678955 408.2922058105469 0.6301180720329285 494.9549255371094 0.7830561995506287 0.6125002 0.8933778405189514 True -15 60800 41.17085599899292 0.7894651889801025 401.65093994140625 0.5831708908081055 493.56683349609375 0.7840515971183777 0.61970246 0.8758395910263062 True -16 64600 41.21176600456238 0.8035752773284912 394.914306640625 0.8308355808258057 492.6134338378906 0.7849776148796082 0.6241742 0.8775977492332458 True -17 68400 41.14494442939758 0.7747776508331299 410.6116943359375 0.34881359338760376 492.11376953125 0.7850073575973511 0.6276273 0.8638755679130554 True -18 72200 41.15916109085083 0.7555503845214844 372.4298095703125 0.9313241243362427 492.37469482421875 0.7847830057144165 0.6276397 0.8763231039047241 True -19 76000 41.11549139022827 0.7541506290435791 335.44537353515625 0.5686640739440918 492.5301818847656 0.7846216559410095 0.6259508 0.8812548518180847 False diff --git a/ENCSR499ASS/cherimoya.fold_4.performance.tsv b/ENCSR499ASS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e70ac18287eda9c6f7746bab270d129c51d3a26b..0000000000000000000000000000000000000000 --- a/ENCSR499ASS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -492.37469482421875 0.1948997527360916 0.784782886505127 0.34291714429855347 0.6276397109031677 0.6309360861778259 0.8763231039047241 \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_0.evaluate.json b/ENCSR499IFY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4873c72eeff1cf55c3f234d9a47472f5dfba65d9..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420TGQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_0.fit.json b/ENCSR499IFY/cherimoya.fold_0.fit.json deleted file mode 100644 index 0297e2d962ce374d1f85e962a5e1ad2276778ec3..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF420TGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_0.log b/ENCSR499IFY/cherimoya.fold_0.log deleted file mode 100644 index 91af74caf0b19684047875e53c8e94a26546de2c..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2717 34.67446255683899 3.627514123916626 1352.810302734375 0.5997034311294556 1974.134033203125 0.2864449620246887 0.5759815 9.86397647857666 True -1 5434 30.133647680282593 0.7464122772216797 1637.54296875 0.6583117842674255 1690.858642578125 0.42929819226264954 0.62428534 3.058941602706909 True -2 8151 30.194246292114258 0.554919958114624 1438.28076171875 0.4941362738609314 1649.88525390625 0.44484972953796387 0.6361919 1.666306734085083 True -3 10868 30.147369146347046 0.554311990737915 1586.9739990234375 0.7403588891029358 1630.1239013671875 0.4502420723438263 0.65594953 1.1242971420288086 True -4 13585 30.19154119491577 1.2959272861480713 1414.2076416015625 0.40325111150741577 1619.654541015625 0.45523640513420105 0.6654872 1.1442945003509521 True -5 16302 30.164001941680908 17.125953197479248 1300.3446044921875 0.4816403388977051 1611.418212890625 0.460075318813324 0.6672253 1.1716914176940918 True -6 19019 29.8122341632843 0.5147943496704102 1296.456298828125 0.4642471671104431 1604.9208984375 0.4631567597389221 0.67297494 0.9023407697677612 True -7 21736 29.5050265789032 2.4525442123413086 1471.7799072265625 0.5618488788604736 1594.8826904296875 0.4677307605743408 0.6748563 0.840586245059967 True -8 24453 29.562814712524414 1.3802099227905273 1259.8248291015625 0.357660174369812 1592.0328369140625 0.469820111989975 0.6792681 0.7503032684326172 True -9 27170 29.649396896362305 1.3149068355560303 1156.70654296875 0.4581719636917114 1585.5235595703125 0.47279906272888184 0.6848883 0.7199370861053467 True -10 29887 29.51881694793701 3.813405752182007 1273.182861328125 0.5285692811012268 1576.0482177734375 0.47752276062965393 0.68990576 0.6485721468925476 True -11 32604 29.55284309387207 0.7667794227600098 1077.7806396484375 0.4397915303707123 1568.6102294921875 0.4807382822036743 0.6963005 0.5835875868797302 True -12 35321 29.577329874038696 0.5307736396789551 1313.48681640625 0.44747233390808105 1568.56884765625 0.479351282119751 0.7055303 0.5507893562316895 True -13 38038 29.534046411514282 16.74735951423645 1292.9852294921875 0.35840073227882385 1557.7598876953125 0.4842158854007721 0.71375287 0.5013670325279236 True -14 40755 29.740066528320312 0.5312316417694092 1282.0478515625 0.33920568227767944 1549.043212890625 0.48823991417884827 0.72439 0.4606063961982727 True -15 43472 29.536656856536865 0.5209462642669678 1300.2698974609375 0.2838044762611389 1543.7496337890625 0.49140220880508423 0.7340294 0.4279283285140991 True -16 46189 29.641868829727173 0.5367166996002197 1317.037353515625 0.3133201003074646 1544.9044189453125 0.48983293771743774 0.7428255 0.3890058696269989 True -17 48906 29.599675178527832 0.5292017459869385 1360.4111328125 0.3155616819858551 1541.658935546875 0.49124160408973694 0.7482737 0.3626517951488495 True -18 51623 29.553512811660767 0.5387992858886719 1247.6483154296875 0.32271838188171387 1542.523681640625 0.4904825985431671 0.7488419 0.3521953225135803 True -19 54340 29.65537190437317 0.5291922092437744 1274.111328125 0.33535823225975037 1539.6243896484375 0.492462694644928 0.75068706 0.3504689931869507 True diff --git a/ENCSR499IFY/cherimoya.fold_0.performance.tsv b/ENCSR499IFY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4c959c81afb8b0dbc918b6bbea4309e315f0083b..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1539.6243896484375 0.2854539155960083 0.492462694644928 0.2702813744544983 0.7506870627403259 0.7035243511199951 0.3504689931869507 \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_1.evaluate.json b/ENCSR499IFY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e78eab564147c055afbbaee82870be3c84d9f3ea..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420TGQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_1.fit.json b/ENCSR499IFY/cherimoya.fold_1.fit.json deleted file mode 100644 index 7995fe6cdfe2dd537ee8c6c939ad3ffdade876f7..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF420TGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_1.log b/ENCSR499IFY/cherimoya.fold_1.log deleted file mode 100644 index fe213047ee8468e0acc5110fd46eb3619e840700..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 35.30713701248169 4.122905254364014 1414.511474609375 0.43453171849250793 2127.944091796875 0.29236093163490295 0.58993196 10.732301712036133 True -1 5480 30.4161057472229 0.7381904125213623 1198.729736328125 0.5432862639427185 1795.42041015625 0.4432610869407654 0.6557019 3.194763660430908 True -2 8220 30.469253063201904 0.7037928104400635 1383.8133544921875 0.6176732778549194 1765.9256591796875 0.450374960899353 0.65963554 2.046412706375122 True -3 10960 29.8155996799469 0.6856637001037598 1253.2200927734375 0.6064103841781616 1734.3701171875 0.4615904986858368 0.68424135 0.9987233877182007 True -4 13700 29.822662591934204 0.6850283145904541 1211.227783203125 0.7231314182281494 1730.410888671875 0.46253594756126404 0.69261646 0.9685631990432739 True -5 16440 29.70830488204956 0.691248893737793 1542.154296875 0.44852858781814575 1717.1104736328125 0.46999284625053406 0.7016048 0.9681766629219055 True -6 19180 29.73186182975769 0.8641488552093506 1056.615966796875 0.45839130878448486 1710.6494140625 0.47263282537460327 0.7104144 1.1450390815734863 True -7 21920 29.794188261032104 0.6789164543151855 1446.3529052734375 0.6618983745574951 1706.5308837890625 0.4740501940250397 0.7162583 0.9137904644012451 True -8 24660 29.735820770263672 0.6926705837249756 1145.483154296875 0.6278011798858643 1695.150634765625 0.4796749949455261 0.71772915 0.9330044388771057 True -9 27400 29.72027611732483 0.6928167343139648 1544.170166015625 0.4921632409095764 1691.453857421875 0.48107007145881653 0.7216521 0.9227518439292908 True -10 30140 29.702443599700928 0.6919798851013184 1287.692138671875 0.5275892019271851 1678.5587158203125 0.48581433296203613 0.72357416 0.8183656930923462 True -11 32880 29.909620761871338 0.6788358688354492 1559.01220703125 0.4114382266998291 1673.2349853515625 0.4882601499557495 0.7325554 0.7251995801925659 True -12 35620 29.74793291091919 0.699167013168335 1218.556884765625 0.2983543276786804 1664.2371826171875 0.4916479289531708 0.7441956 0.6290095448493958 True -13 38360 29.737898588180542 12.12867522239685 1362.912841796875 0.510825514793396 1654.8851318359375 0.4946499168872833 0.75229627 0.5516728162765503 True -14 41100 29.837791919708252 0.7285616397857666 1272.9444580078125 0.32678478956222534 1649.2513427734375 0.49670252203941345 0.75698555 0.483536034822464 True -15 43840 29.78030490875244 0.7118935585021973 1099.4373779296875 0.4744621217250824 1643.239501953125 0.4992653727531433 0.76783055 0.4337133467197418 True -16 46580 29.80100727081299 0.7027943134307861 1147.7679443359375 0.32660484313964844 1635.329833984375 0.5028587579727173 0.7736146 0.3816676139831543 True -17 49320 29.78286600112915 0.6892404556274414 1108.330810546875 0.2907889783382416 1637.650634765625 0.5009424090385437 0.7780157 0.34988993406295776 True -18 52060 29.7418270111084 0.7510409355163574 1114.345458984375 0.2953297793865204 1637.9237060546875 0.5012109279632568 0.77829003 0.33798500895500183 True -19 54800 29.753255367279053 0.6779189109802246 1275.601318359375 0.22694717347621918 1638.3455810546875 0.5009453892707825 0.7773323 0.3343232274055481 False diff --git a/ENCSR499IFY/cherimoya.fold_1.performance.tsv b/ENCSR499IFY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index dd8ba6a5e28b6ed0f79da2116b88b6a832888955..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1637.9237060546875 0.27521830797195435 0.5012109279632568 0.2841946482658386 0.7782900333404541 0.7465741634368896 0.33798500895500183 \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_2.evaluate.json b/ENCSR499IFY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6addf7d186f3035bda8a869d517506f31743a7fe..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420TGQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_2.fit.json b/ENCSR499IFY/cherimoya.fold_2.fit.json deleted file mode 100644 index c0f129e0edf59f1fa91d6e44f82a920282795b23..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF420TGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_2.log b/ENCSR499IFY/cherimoya.fold_2.log deleted file mode 100644 index df3be484b8cd8e6979b0d4fc41857aef24b544ea..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2875 36.40724754333496 4.606258392333984 1124.536865234375 0.473158061504364 1991.4261474609375 0.29566332697868347 0.56868416 10.000475883483887 True -1 5750 31.883114337921143 0.613957405090332 1589.31494140625 0.607629656791687 1703.042236328125 0.4313561022281647 0.6367972 3.1765568256378174 True -2 8625 31.915751934051514 0.5463082790374756 1507.936279296875 0.6282591819763184 1672.8236083984375 0.44224321842193604 0.6455519 1.508218765258789 True -3 11500 31.874549865722656 0.5603547096252441 1412.337890625 0.5441508293151855 1652.0159912109375 0.4501679837703705 0.6634598 1.3841651678085327 True -4 14375 31.87986660003662 0.5757791996002197 1268.302978515625 0.5302631855010986 1642.789306640625 0.45655184984207153 0.6668313 1.3590011596679688 True -5 17250 31.85250949859619 0.5453097820281982 1592.55126953125 0.5148381590843201 1631.0933837890625 0.4608011543750763 0.6789986 0.9284241795539856 True -6 20125 31.83353877067566 0.5569801330566406 1110.09375 0.4337729513645172 1625.189208984375 0.4643639326095581 0.67944914 0.8426267504692078 True -7 23000 31.84433650970459 0.5432538986206055 1191.373046875 0.4430472254753113 1618.5784912109375 0.46726250648498535 0.6865515 0.8166783452033997 True -8 25875 31.83407711982727 0.5434105396270752 1300.3419189453125 0.7419588565826416 1607.88671875 0.47269025444984436 0.68790746 0.6998962163925171 True -9 28750 31.83312964439392 0.5456609725952148 1231.3485107421875 0.3205718994140625 1601.8453369140625 0.475521057844162 0.68927985 0.6680275201797485 True -10 31625 31.83682942390442 0.5526163578033447 1251.7379150390625 0.4755289852619171 1594.6220703125 0.4776691794395447 0.69740605 0.6075413227081299 True -11 34500 31.83215832710266 0.5428249835968018 1350.8621826171875 0.37719646096229553 1589.7384033203125 0.4801635146141052 0.70654565 0.5956172943115234 True -12 37375 31.822746992111206 0.5470411777496338 1222.251708984375 0.35543709993362427 1581.1663818359375 0.4836415946483612 0.71477336 0.5217417478561401 True -13 40250 31.296380758285522 1.1733465194702148 1486.921875 0.6574500799179077 1573.088623046875 0.48684853315353394 0.7265212 0.49730589985847473 True -14 43125 31.209158897399902 0.5532968044281006 1214.077392578125 0.3062475919723511 1567.1217041015625 0.48974257707595825 0.736255 0.4470936357975006 True -15 46000 31.16009759902954 0.5478940010070801 1437.5738525390625 0.4216771721839905 1560.8505859375 0.49237045645713806 0.74771184 0.4117075204849243 True -16 48875 31.23763346672058 0.5391714572906494 1139.524169921875 0.38832470774650574 1559.123779296875 0.4917561709880829 0.75472385 0.377862811088562 True -17 51750 31.255475759506226 0.5405795574188232 1282.619140625 0.34961795806884766 1557.3377685546875 0.4930509626865387 0.75855935 0.353325754404068 True -18 54625 31.254215717315674 1.051056146621704 1327.96875 0.2974882125854492 1552.2510986328125 0.4962790310382843 0.76040983 0.34500691294670105 True -19 57500 31.232775688171387 0.5542583465576172 1133.5728759765625 0.2746424078941345 1555.755615234375 0.493582159280777 0.7606333 0.3410097360610962 True diff --git a/ENCSR499IFY/cherimoya.fold_2.performance.tsv b/ENCSR499IFY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4b5c9aad42e6a7c628274a737fe37b7b61a2eddb..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1555.755615234375 0.28392207622528076 0.4935821294784546 0.273007869720459 0.7606332898139954 0.7181803584098816 0.3410097360610962 \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_3.evaluate.json b/ENCSR499IFY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e2d79a2157248eb39c04a82fc57d4a98fa5d0cb1..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420TGQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_3.fit.json b/ENCSR499IFY/cherimoya.fold_3.fit.json deleted file mode 100644 index 26e979aa7ee9781d07bc46c91f9141dd99c9bee9..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF420TGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_3.log b/ENCSR499IFY/cherimoya.fold_3.log deleted file mode 100644 index 48765d2cf26588b9270294ad3ac77cd21872cdbf..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 35.47966265678406 3.953404188156128 1193.70751953125 0.5643606781959534 1958.447509765625 0.29503482580184937 0.58274096 11.653046607971191 True -1 5564 30.902747631072998 0.6763644218444824 1429.5947265625 0.6440353393554688 1683.7230224609375 0.43096524477005005 0.63632077 3.271989583969116 True -2 8346 30.85911726951599 0.6085190773010254 1224.9808349609375 0.5590737462043762 1657.6097412109375 0.43841105699539185 0.64876956 1.9094959497451782 True -3 11128 30.84184694290161 0.5715458393096924 1590.44287109375 0.4856300354003906 1634.8958740234375 0.4470535218715668 0.66584545 1.2287503480911255 True -4 13910 30.827479362487793 2.9253318309783936 1406.2001953125 0.6157526969909668 1623.5430908203125 0.45316654443740845 0.6743572 1.1342946290969849 True -5 16692 30.434957265853882 0.5829143524169922 1260.21630859375 0.4497578740119934 1617.508544921875 0.45646101236343384 0.6692071 1.195913314819336 False -6 19474 30.24234366416931 1.5423014163970947 1301.107421875 0.5199649930000305 1607.4329833984375 0.46210211515426636 0.67582023 1.1582859754562378 True -7 22256 30.291913509368896 0.7192246913909912 1299.578125 0.45504629611968994 1602.08544921875 0.46460917592048645 0.6855073 0.9339466094970703 True -8 25038 30.25775718688965 0.5796771049499512 1402.03955078125 0.5811465978622437 1596.8616943359375 0.4668337106704712 0.68560576 0.8267370462417603 True -9 27820 30.60576295852661 11.640647411346436 1277.6171875 0.3804302215576172 1588.8309326171875 0.4690380394458771 0.6933777 0.762833833694458 True -10 30602 30.274430990219116 1.0835506916046143 1239.509765625 0.5604186058044434 1579.3927001953125 0.47408998012542725 0.7007954 0.7043654322624207 True -11 33384 30.34424090385437 0.5760207176208496 1246.028564453125 0.43514484167099 1572.475830078125 0.47672614455223083 0.70406014 0.6540537476539612 True -12 36166 30.230666160583496 19.730700254440308 1316.105224609375 0.5243886113166809 1562.85791015625 0.480117529630661 0.7171931 0.568401038646698 True -13 38948 30.41797184944153 0.5707972049713135 1202.4508056640625 0.54865962266922 1555.9632568359375 0.48332926630973816 0.7297123 0.513556182384491 True -14 41730 30.255134344100952 0.5811545848846436 1184.985107421875 0.30323314666748047 1549.6341552734375 0.4863661527633667 0.7362431 0.4836154282093048 True -15 44512 30.273356199264526 0.5833227634429932 1276.626708984375 0.2375372350215912 1545.7916259765625 0.4871992766857147 0.7486713 0.4219638407230377 True -16 47294 30.308149337768555 1.1401445865631104 1377.73095703125 0.3139396905899048 1542.518798828125 0.48825567960739136 0.756982 0.3873344361782074 True -17 50076 30.30926513671875 0.5752828121185303 1208.428466796875 0.44251716136932373 1540.087646484375 0.4890729784965515 0.7602088 0.3643130660057068 True -18 52858 30.880927801132202 0.5971312522888184 1267.3194580078125 0.2815127968788147 1539.05322265625 0.49007582664489746 0.7611441 0.35276952385902405 True -19 55640 30.229929447174072 13.076236724853516 1244.683837890625 0.31810227036476135 1539.2000732421875 0.4899750053882599 0.75864077 0.349621444940567 False diff --git a/ENCSR499IFY/cherimoya.fold_3.performance.tsv b/ENCSR499IFY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index dcd4af9175eaed0e98235caaef8a2829ba96f674..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1539.05322265625 0.2870981693267822 0.49007582664489746 0.26828765869140625 0.7611441016197205 0.7170664668083191 0.35276952385902405 \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_4.evaluate.json b/ENCSR499IFY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0e1b68c2d8a66b527203e8b160cd8948df957f2d..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420TGQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_4.fit.json b/ENCSR499IFY/cherimoya.fold_4.fit.json deleted file mode 100644 index 86787c4e9bd282d561cbbed6d385ad5952e0f1d7..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF420TGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499IFY/cherimoya.fold_4.log b/ENCSR499IFY/cherimoya.fold_4.log deleted file mode 100644 index 1b34172ba0c72abdd27f7a80858147604a17782b..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2822 36.03833031654358 3.9006454944610596 1354.50439453125 0.5409903526306152 1900.9244384765625 0.2816402316093445 0.5681464 10.006600379943848 True -1 5644 31.358610153198242 0.6596784591674805 1388.7017822265625 0.7611548900604248 1647.3590087890625 0.420541912317276 0.61163175 2.8790464401245117 True -2 8466 31.305198431015015 0.5524895191192627 1190.66015625 0.760756254196167 1606.694091796875 0.4341999888420105 0.64543146 1.299455165863037 True -3 11288 31.312896013259888 0.550713300704956 1239.625 0.7312211990356445 1584.216552734375 0.443305104970932 0.661061 1.012210726737976 True -4 14110 31.28880524635315 0.5355679988861084 1357.152587890625 0.6531956195831299 1577.6378173828125 0.44861888885498047 0.6634544 0.8701100945472717 True -5 16932 31.351381063461304 0.5573880672454834 1256.6661376953125 0.5402372479438782 1569.9132080078125 0.45176273584365845 0.6719927 0.9491039514541626 True -6 19754 31.45562505722046 0.5788190364837646 1359.8011474609375 0.5018222332000732 1558.7318115234375 0.45791682600975037 0.67942613 0.724033772945404 True -7 22576 31.46292805671692 0.549823522567749 1430.5048828125 0.5556689500808716 1556.39306640625 0.45839178562164307 0.68365765 0.6563001275062561 True -8 25398 31.49387264251709 0.5534405708312988 1281.454345703125 0.4286232590675354 1551.054443359375 0.46142441034317017 0.68493 0.6324840784072876 True -9 28220 31.4426326751709 14.943725824356079 1359.4608154296875 0.5031630396842957 1543.7911376953125 0.4656640589237213 0.6859098 0.6154865622520447 True -10 31042 31.56572937965393 1.1341266632080078 1370.071044921875 0.43914926052093506 1538.65869140625 0.4676864445209503 0.69212687 0.5869722366333008 True -11 33864 30.805649280548096 0.5407941341400146 1194.6480712890625 0.5009389519691467 1531.218505859375 0.4721413850784302 0.6965399 0.5602373480796814 True -12 36686 30.799019813537598 0.5420806407928467 1337.0216064453125 0.4489815831184387 1522.6883544921875 0.47478094696998596 0.7058031 0.5112009644508362 True -13 39508 30.843793869018555 0.5423696041107178 1243.18017578125 0.2242998331785202 1520.279296875 0.4755840599536896 0.7129027 0.48771679401397705 True -14 42330 30.841046810150146 0.5393662452697754 1110.749755859375 0.4304006099700928 1513.248046875 0.47934776544570923 0.7245798 0.44909727573394775 True -15 45152 30.865939378738403 1.2381610870361328 1150.135009765625 0.44393986463546753 1506.9073486328125 0.48234355449676514 0.7330067 0.41058239340782166 True -16 47974 30.928905725479126 0.5573935508728027 1227.991943359375 0.2981865406036377 1505.666259765625 0.4815863370895386 0.74067414 0.37234294414520264 True -17 50796 30.921013832092285 0.5619606971740723 1158.060791015625 0.30982649326324463 1503.0648193359375 0.4823172390460968 0.7457006 0.34718969464302063 True -18 53618 30.868151426315308 0.5458023548126221 1146.0089111328125 0.2965472936630249 1500.87548828125 0.48378413915634155 0.746473 0.3386576771736145 True -19 56440 30.84552812576294 0.5489497184753418 1253.84423828125 0.2475598156452179 1503.001953125 0.48195329308509827 0.74624586 0.3354070484638214 False diff --git a/ENCSR499IFY/cherimoya.fold_4.performance.tsv b/ENCSR499IFY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c7282fdc63bdfcaf8bace611b7fe0942a6280ce3..0000000000000000000000000000000000000000 --- a/ENCSR499IFY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1500.87548828125 0.2919560670852661 0.48378413915634155 0.26084619760513306 0.7464730143547058 0.699845552444458 0.3386576771736145 \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_0.evaluate.json b/ENCSR499PZA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 59f68924c1850e6feaf31fe17b4e9b19f41e8240..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF792OMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_0.fit.json b/ENCSR499PZA/cherimoya.fold_0.fit.json deleted file mode 100644 index 00e692e002236472a5b01a834ce7b6a129bdbd60..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF792OMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_0.log b/ENCSR499PZA/cherimoya.fold_0.log deleted file mode 100644 index 60ecbb3aa33f5cbb423825b0ad22d4c24a66eab4..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 34.894038915634155 4.290877342224121 172.70285034179688 0.6450122594833374 213.35438537597656 0.10538747161626816 0.7163972 1.9054313898086548 True -1 5528 30.81438136100769 0.7087178230285645 165.74977111816406 0.6639550924301147 206.2701873779297 0.1305704563856125 0.79783934 0.3678073585033417 True -2 8292 30.487263441085815 0.570389986038208 206.00198364257812 0.5204196572303772 204.9622802734375 0.13331082463264465 0.8022145 0.28336429595947266 True -3 11056 30.4055814743042 0.5707626342773438 152.54379272460938 0.5538748502731323 203.43641662597656 0.13854092359542847 0.8106575 0.3015877604484558 True -4 13820 30.383934497833252 0.5684723854064941 201.280517578125 0.484291672706604 202.66265869140625 0.1418958157300949 0.81377465 0.3040939271450043 True -5 16584 30.403774976730347 1.6845707893371582 160.199462890625 0.6450811624526978 202.16348266601562 0.14405557513237 0.8162895 0.30879920721054077 True -6 19348 30.434070587158203 0.5771627426147461 170.14474487304688 0.5879555344581604 201.96949768066406 0.1446024626493454 0.82179224 0.28984084725379944 True -7 22112 30.4177143573761 0.5767049789428711 179.499267578125 0.2910779118537903 201.62881469726562 0.14574593305587769 0.82763517 0.29876822233200073 True -8 24876 30.456174612045288 0.5687201023101807 138.88253784179688 0.46059632301330566 201.2149658203125 0.14748147130012512 0.8296539 0.30043578147888184 True -9 27640 30.466073989868164 0.5843265056610107 152.15567016601562 0.5210181474685669 200.78939819335938 0.14929433166980743 0.8340928 0.2890484631061554 True -10 30404 30.49281334877014 0.5787656307220459 169.72406005859375 0.3455619812011719 200.65179443359375 0.1500481218099594 0.8382512 0.2841081917285919 True -11 33168 30.982288122177124 0.583714485168457 147.1199951171875 0.3309589624404907 200.4849090576172 0.15008601546287537 0.8419458 0.27933841943740845 True -12 35932 30.473584413528442 0.5836949348449707 174.27850341796875 0.39012736082077026 200.14404296875 0.15143036842346191 0.844853 0.2840953767299652 True -13 38696 30.550896406173706 0.572939395904541 178.95712280273438 0.4043756127357483 199.84359741210938 0.15263843536376953 0.84762806 0.2740314304828644 True -14 41460 30.536094903945923 0.5786280632019043 145.3861541748047 0.40839603543281555 199.61061096191406 0.1534634232521057 0.8518464 0.2638329863548279 True -15 44224 30.58677339553833 0.5839104652404785 179.33428955078125 0.34693247079849243 199.29750061035156 0.15480239689350128 0.8542477 0.256475567817688 True -16 46988 30.46568512916565 2.3792190551757812 136.31887817382812 0.3979949355125427 199.32281494140625 0.15434154868125916 0.85453963 0.2567158639431 True -17 49752 30.738531827926636 0.8870956897735596 153.54864501953125 0.38544225692749023 199.36813354492188 0.15376029908657074 0.85515326 0.2528347969055176 True -18 52516 30.186230182647705 0.5827944278717041 116.35138702392578 0.5167697072029114 199.55615234375 0.15351654589176178 0.85619015 0.25087103247642517 True -19 55280 30.070342779159546 0.6935327053070068 177.52679443359375 0.22527983784675598 199.617431640625 0.15339504182338715 0.85614556 0.25252392888069153 False diff --git a/ENCSR499PZA/cherimoya.fold_0.performance.tsv b/ENCSR499PZA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 007c2e7b3d97866f967a950162594ef43b25e309..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -199.55615234375 0.5840795040130615 0.15351656079292297 0.040605541318655014 0.8561901450157166 0.8173772692680359 0.25087103247642517 \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_1.evaluate.json b/ENCSR499PZA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 476fdfb5014ddf469064c55697eacdbc12368933..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF792OMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_1.fit.json b/ENCSR499PZA/cherimoya.fold_1.fit.json deleted file mode 100644 index 0c3f7815ea49e64c23fdadf33356ab6d780a9925..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF792OMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_1.log b/ENCSR499PZA/cherimoya.fold_1.log deleted file mode 100644 index 4db8c685ddfdc48625cc74b1008e9d70ab1b9707..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 34.76456332206726 3.8569605350494385 154.8152313232422 0.34746384620666504 258.9387512207031 0.12183819711208344 0.68465316 3.0572450160980225 True -1 5506 30.42408013343811 1.0741326808929443 175.79058837890625 0.5821595788002014 248.68527221679688 0.1551826447248459 0.80329305 0.542906641960144 True -2 8259 30.321025609970093 0.6767697334289551 175.15103149414062 0.44801753759384155 246.08944702148438 0.16129274666309357 0.8099967 0.42454949021339417 True -3 11012 30.347289323806763 0.9748845100402832 168.47433471679688 0.5098230242729187 243.9477081298828 0.1666039675474167 0.8207944 0.33175384998321533 True -4 13765 30.371564388275146 0.6646907329559326 158.13241577148438 0.599342942237854 243.02525329589844 0.16959825158119202 0.82649857 0.3260273337364197 True -5 16518 30.365625619888306 0.6647686958312988 159.5244140625 0.4202616214752197 242.2947235107422 0.1718262881040573 0.8302743 0.32670333981513977 True -6 19271 30.30871558189392 0.6654641628265381 209.69346618652344 0.3485553562641144 242.26539611816406 0.17140251398086548 0.83423716 0.3263331651687622 True -7 22024 30.270639896392822 0.661959171295166 206.7587432861328 0.4577881693840027 241.9468994140625 0.17213967442512512 0.83711696 0.34437453746795654 True -8 24777 30.34283185005188 0.6698384284973145 155.98895263671875 0.39593684673309326 241.5230255126953 0.1735723614692688 0.8422855 0.3355945348739624 True -9 27530 30.382027864456177 0.6702313423156738 160.60272216796875 0.4306335151195526 240.9008331298828 0.17627327144145966 0.8436844 0.34585922956466675 True -10 30283 30.369823932647705 0.6717967987060547 149.06240844726562 0.40720176696777344 240.12330627441406 0.17911095917224884 0.85024506 0.3271113932132721 True -11 33036 30.370255708694458 1.760636806488037 188.3191375732422 0.35950613021850586 239.95040893554688 0.17921236157417297 0.85240114 0.3058271110057831 True -12 35789 30.349076986312866 0.6796588897705078 179.71478271484375 0.41927772760391235 239.4932403564453 0.18064773082733154 0.8558951 0.3062116205692291 True -13 38542 30.304012298583984 0.6736054420471191 132.27215576171875 0.581000566482544 239.19598388671875 0.18165715038776398 0.8603997 0.299325168132782 True -14 41295 30.320027351379395 0.6737065315246582 174.2642822265625 0.4950169026851654 238.58279418945312 0.18394848704338074 0.8628389 0.29032495617866516 True -15 44048 30.343045234680176 0.6743252277374268 168.05996704101562 0.3136776089668274 238.63406372070312 0.18349401652812958 0.865478 0.2925085723400116 True -16 46801 30.453760385513306 0.674487829208374 167.76608276367188 0.45334553718566895 238.8903350830078 0.18227657675743103 0.86652046 0.2909563183784485 True -17 49554 30.368287324905396 0.6742701530456543 153.22283935546875 0.39060771465301514 238.78652954101562 0.18315881490707397 0.8667362 0.2923818528652191 True -18 52307 30.379656076431274 0.6780903339385986 154.49630737304688 0.31301671266555786 238.5189208984375 0.1842552274465561 0.8652613 0.29086360335350037 False -19 55060 30.213995218276978 0.6720261573791504 174.9665985107422 0.36105698347091675 238.8175811767578 0.1829519420862198 0.86623865 0.29420235753059387 False diff --git a/ENCSR499PZA/cherimoya.fold_1.performance.tsv b/ENCSR499PZA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5385e540cb987698ce2ff55d80b6da0a86d7bfc5..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -238.78652954101562 0.561847448348999 0.18315880000591278 0.05037462338805199 0.8667361736297607 0.8460572957992554 0.2923818528652191 \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_2.evaluate.json b/ENCSR499PZA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 086e07013d752b657ba861386310ea9d989ace2c..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF792OMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_2.fit.json b/ENCSR499PZA/cherimoya.fold_2.fit.json deleted file mode 100644 index 27cc26207a8b5c7617d0ddcb35b76d668350129f..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF792OMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_2.log b/ENCSR499PZA/cherimoya.fold_2.log deleted file mode 100644 index fc08fc3fc870ba92218cd82263a2e31c26b8a7fe..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 36.56461834907532 3.8301095962524414 145.6169891357422 0.7200866937637329 225.3804931640625 0.11327901482582092 0.7038876 2.315485954284668 True -1 5764 31.780986309051514 0.5582799911499023 161.173828125 0.45021262764930725 217.16156005859375 0.14201517403125763 0.79696107 0.5561814308166504 True -2 8646 31.846264839172363 0.605379581451416 171.95657348632812 0.5179961919784546 215.56556701660156 0.14417482912540436 0.81066954 0.30844801664352417 True -3 11528 31.79948592185974 0.5285608768463135 179.82769775390625 0.3564032018184662 213.6731719970703 0.1506951004266739 0.8184135 0.3056313991546631 True -4 14410 31.740426301956177 0.5234992504119873 165.35130310058594 0.4875639081001282 213.0756378173828 0.1523299664258957 0.8248963 0.319451242685318 True -5 17292 31.73664617538452 0.5527060031890869 156.7187957763672 0.36321932077407837 212.65478515625 0.15413755178451538 0.8255292 0.321489542722702 True -6 20174 31.720152378082275 0.5352773666381836 162.21578979492188 0.3699096441268921 212.5068817138672 0.15402022004127502 0.83057344 0.29202866554260254 True -7 23056 31.70166015625 0.5353398323059082 151.64126586914062 0.5760424137115479 212.177978515625 0.15546278655529022 0.83542794 0.28938543796539307 True -8 25938 31.694401741027832 0.5361554622650146 166.17556762695312 0.5425853729248047 211.73974609375 0.15727931261062622 0.83853155 0.28648170828819275 True -9 28820 31.69294762611389 0.5186095237731934 176.92848205566406 0.6032823920249939 211.3804473876953 0.1585291028022766 0.8419763 0.2923952341079712 True -10 31702 31.70397973060608 0.7148880958557129 140.9893798828125 0.5512894988059998 211.1788787841797 0.1590636670589447 0.8425897 0.289985716342926 True -11 34584 31.721899271011353 0.55045485496521 154.92340087890625 0.5339227914810181 210.92266845703125 0.15991666913032532 0.84785867 0.2893873453140259 True -12 37466 31.794649600982666 0.5489592552185059 156.10433959960938 0.35272443294525146 210.53948974609375 0.16155147552490234 0.85039157 0.2881124019622803 True -13 40348 31.785626649856567 0.5490529537200928 181.50564575195312 0.6513078212738037 210.29434204101562 0.1622748225927353 0.85222405 0.2910730540752411 True -14 43230 31.798771381378174 0.5316116809844971 129.6767578125 0.3724207878112793 209.87454223632812 0.16427773237228394 0.85637784 0.2802162766456604 True -15 46112 31.747488737106323 0.5292561054229736 170.8617401123047 0.4708854556083679 209.85577392578125 0.16393223404884338 0.8576212 0.2778889238834381 True -16 48994 31.769575834274292 0.5313067436218262 198.94546508789062 0.3705880045890808 210.11590576171875 0.16282841563224792 0.8594078 0.27800533175468445 True -17 51876 31.483559370040894 0.5424349308013916 151.97264099121094 0.38475918769836426 209.9837188720703 0.16337871551513672 0.8592257 0.27561506628990173 False -18 54758 31.172070264816284 0.5393102169036865 142.56967163085938 0.2712031602859497 210.19004821777344 0.16275809705257416 0.8580919 0.2755494713783264 False -19 57640 31.1819748878479 0.5463347434997559 160.50416564941406 0.2815425395965576 210.0274658203125 0.1637580692768097 0.8573424 0.2755119800567627 False diff --git a/ENCSR499PZA/cherimoya.fold_2.performance.tsv b/ENCSR499PZA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 29839d12f810e8f70ce0839426cdaf52db2d9335..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -210.11590576171875 0.5773230195045471 0.16282843053340912 0.04195769876241684 0.8594077825546265 0.8277314305305481 0.27800533175468445 \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_3.evaluate.json b/ENCSR499PZA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4e048c3fa25f4e3690a29fee6a13c0f4b91e7781..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF792OMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_3.fit.json b/ENCSR499PZA/cherimoya.fold_3.fit.json deleted file mode 100644 index ff16c578ff39e03ddcc9858e699ac972bf5651e4..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF792OMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_3.log b/ENCSR499PZA/cherimoya.fold_3.log deleted file mode 100644 index 99d3f545c73356487331f10ef70826fc737cf0c8..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2788 35.7015438079834 3.818223237991333 200.79171752929688 0.6194214820861816 228.9478302001953 0.10888764262199402 0.7044752 2.2096333503723145 True -1 5576 30.80301332473755 0.615999698638916 167.99200439453125 0.7182657718658447 221.0829620361328 0.13646766543388367 0.8006924 0.546403706073761 True -2 8364 30.801079273223877 0.5686719417572021 181.46392822265625 0.4418866038322449 219.51217651367188 0.1402083933353424 0.8053577 0.40865448117256165 True -3 11152 30.79938769340515 1.2674171924591064 165.78326416015625 0.6087725758552551 218.38694763183594 0.14226092398166656 0.8144439 0.3696155846118927 True -4 13940 30.824923276901245 0.5746941566467285 158.85867309570312 0.5304872989654541 217.9564208984375 0.14410178363323212 0.8194704 0.39471352100372314 True -5 16728 30.755029439926147 14.56448245048523 186.5188751220703 0.672461748123169 217.63775634765625 0.1450319141149521 0.82362145 0.41847267746925354 True -6 19516 31.131755828857422 0.5683426856994629 147.1570587158203 0.6617146730422974 217.06858825683594 0.14729423820972443 0.8263506 0.4067894220352173 True -7 22304 31.221166372299194 0.9714059829711914 180.90631103515625 0.4136941134929657 216.66244506835938 0.1484517604112625 0.83038425 0.40353405475616455 True -8 25092 31.140419960021973 16.56284761428833 162.77313232421875 0.3998439311981201 216.2889862060547 0.14963096380233765 0.83217067 0.40270501375198364 True -9 27880 30.750296354293823 0.5657081604003906 140.2543487548828 0.5531255006790161 215.9886016845703 0.15054211020469666 0.83952767 0.35548943281173706 True -10 30668 30.901814699172974 0.5800881385803223 153.95701599121094 0.48945385217666626 215.52304077148438 0.1522996723651886 0.8451593 0.3559364676475525 True -11 33456 30.810068368911743 0.5782768726348877 186.3524169921875 0.3184248208999634 215.0775604248047 0.15400682389736176 0.84787774 0.35341718792915344 True -12 36244 30.8152916431427 0.5709888935089111 138.9558563232422 0.34507450461387634 214.94667053222656 0.15472158789634705 0.850709 0.34398192167282104 True -13 39032 30.734646797180176 0.5760095119476318 156.07489013671875 0.4079722464084625 214.61964416503906 0.15578724443912506 0.8562675 0.3184534013271332 True -14 41820 30.82109785079956 0.556598424911499 167.22116088867188 0.6034326553344727 214.4578399658203 0.15602704882621765 0.85782367 0.3124942481517792 True -15 44608 30.78665041923523 0.5705969333648682 162.11085510253906 0.4386870265007019 214.14393615722656 0.15707385540008545 0.85967046 0.2972663640975952 True -16 47396 30.77740478515625 0.5598244667053223 135.76821899414062 0.3203270435333252 214.38778686523438 0.15576805174350739 0.86219466 0.29023686051368713 True -17 50184 30.52475118637085 0.9911472797393799 190.0791778564453 0.34031832218170166 214.42637634277344 0.1558229774236679 0.8632693 0.2836036682128906 True -18 52972 30.20913338661194 0.5648519992828369 158.4150390625 0.2982797622680664 214.66172790527344 0.15492476522922516 0.8614704 0.2786237597465515 False -19 55760 30.18556547164917 0.5535533428192139 159.11447143554688 0.3615770936012268 214.6778564453125 0.15475089848041534 0.86271626 0.27764061093330383 False diff --git a/ENCSR499PZA/cherimoya.fold_3.performance.tsv b/ENCSR499PZA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9672b9c76be9f801c464bf55c59b162d124bbd27..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -214.42637634277344 0.5800498127937317 0.1558229774236679 0.04282937943935394 0.8632693290710449 0.8244130611419678 0.2836036682128906 \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_4.evaluate.json b/ENCSR499PZA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e5a8a46270c114f6c4ebc08e4d008b108ec689c9..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF792OMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_4.fit.json b/ENCSR499PZA/cherimoya.fold_4.fit.json deleted file mode 100644 index 7ddbe26bf0783383800b91a647521d4653af3970..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF792OMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR499PZA/cherimoya.fold_4.log b/ENCSR499PZA/cherimoya.fold_4.log deleted file mode 100644 index da3ad8fd8c86f916de1134389c432415b35619cf..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 37.542574882507324 3.8657314777374268 153.45970153808594 0.8557658195495605 212.5267333984375 0.10573223233222961 0.70482844 2.130040168762207 True -1 5756 31.742701530456543 0.6447775363922119 175.37677001953125 0.6512740850448608 205.65194702148438 0.13185225427150726 0.78796107 0.5001990795135498 True -2 8634 31.776726007461548 0.5987763404846191 168.5177459716797 0.5382457375526428 204.10525512695312 0.13588497042655945 0.799516 0.2824447751045227 True -3 11512 31.773318767547607 0.6196279525756836 180.08984375 0.44449788331985474 203.27651977539062 0.13789984583854675 0.80548364 0.2972065806388855 True -4 14390 31.85696268081665 0.6016783714294434 143.08956909179688 0.40232282876968384 202.54928588867188 0.14014913141727448 0.8146741 0.28877151012420654 True -5 17268 31.747979402542114 0.6155331134796143 170.40432739257812 0.515569806098938 202.27919006347656 0.14125347137451172 0.81845206 0.28591805696487427 True -6 20146 31.683995485305786 11.771551847457886 182.8108367919922 0.5057878494262695 201.72018432617188 0.14343546330928802 0.8204159 0.2930275499820709 True -7 23024 31.67974305152893 0.6067500114440918 178.892578125 0.3635900020599365 201.3690643310547 0.14482691884040833 0.82619905 0.29017874598503113 True -8 25902 31.686459064483643 0.6012639999389648 158.562744140625 0.4224644899368286 201.29917907714844 0.1446257382631302 0.8254595 0.3000083863735199 False -9 28780 31.7461838722229 0.6035776138305664 163.09738159179688 0.373806357383728 200.7176513671875 0.14724524319171906 0.8296403 0.2930290997028351 True -10 31658 31.754809617996216 0.6331398487091064 195.03585815429688 0.45796531438827515 200.62545776367188 0.14717984199523926 0.8344499 0.2816618084907532 True -11 34536 31.741188049316406 0.5998032093048096 182.26785278320312 0.37747806310653687 200.677001953125 0.1464643031358719 0.8392746 0.27510496973991394 True -12 37414 31.6716730594635 0.6238033771514893 143.15785217285156 0.5568187236785889 200.14901733398438 0.1489219069480896 0.842685 0.25749874114990234 True -13 40292 32.23827075958252 0.596092700958252 188.2811279296875 0.3511035144329071 199.9148712158203 0.1495850533246994 0.8452856 0.25599128007888794 True -14 43170 31.748947620391846 0.5992507934570312 164.5169677734375 0.2716493606567383 199.70103454589844 0.1507556289434433 0.8498688 0.2492203414440155 True -15 46048 31.859044313430786 0.6078062057495117 148.33383178710938 0.3921917974948883 199.60865783691406 0.1508839726448059 0.8521576 0.25126585364341736 True -16 48926 31.75178837776184 0.6006176471710205 156.44393920898438 0.4524310231208801 199.5110321044922 0.15153712034225464 0.8547968 0.24955056607723236 True -17 51804 31.81880521774292 0.5915334224700928 165.46600341796875 0.3210439085960388 199.74853515625 0.15025044977664948 0.8547302 0.252559095621109 False -18 54682 31.14495587348938 0.5910887718200684 162.96424865722656 0.386687695980072 199.71632385253906 0.15051405131816864 0.85288227 0.2518598437309265 False -19 57560 31.104390144348145 0.5863468647003174 181.50564575195312 0.317310631275177 199.874755859375 0.14982593059539795 0.85284185 0.25337404012680054 False diff --git a/ENCSR499PZA/cherimoya.fold_4.performance.tsv b/ENCSR499PZA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index bcd30048f79736a727d3c60b6a72395c57207403..0000000000000000000000000000000000000000 --- a/ENCSR499PZA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -199.5110321044922 0.5854730606079102 0.15153712034225464 0.038650013506412506 0.854796826839447 0.8146106004714966 0.24955056607723236 \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_0.evaluate.json b/ENCSR501FWC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 44d50ce9aa4a711553fde44315c0041ac6597523..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF154FVS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_0.fit.json b/ENCSR501FWC/cherimoya.fold_0.fit.json deleted file mode 100644 index 59dd6654792309f34fa9a1872d73e22941ca538c..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF154FVS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_0.log b/ENCSR501FWC/cherimoya.fold_0.log deleted file mode 100644 index f29ecc919b371904615aa08ee09ca5269d33359c..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 33.846590518951416 3.3821442127227783 670.84033203125 0.4721047878265381 908.8037109375 0.24821090698242188 0.5785998 6.6357011795043945 True -1 5470 30.09248423576355 0.5417835712432861 626.8067626953125 0.7021762132644653 835.4899291992188 0.3645366430282593 0.61611944 1.1726402044296265 True -2 8205 30.142787218093872 0.5357866287231445 637.6213989257812 0.8558673858642578 825.0568237304688 0.3750252425670624 0.62813914 0.5283694863319397 True -3 10940 30.143316984176636 0.5362319946289062 603.9757080078125 0.6666752099990845 819.850830078125 0.3804812729358673 0.6393685 0.42487284541130066 True -4 13675 30.10854697227478 0.5396461486816406 725.9437255859375 0.8898766040802002 816.8666381835938 0.38215285539627075 0.64835113 0.4037984609603882 True -5 16410 30.08255958557129 0.5366475582122803 637.1802978515625 0.6140596866607666 814.5222778320312 0.3855145573616028 0.65064025 0.40484800934791565 True -6 19145 30.09351921081543 0.5379080772399902 676.2008666992188 0.6011945009231567 811.0681762695312 0.3890955150127411 0.650577 0.4427858889102936 False -7 21880 30.091100692749023 0.546018123626709 687.5698852539062 0.5869342684745789 807.5811157226562 0.39202043414115906 0.6549218 0.4561395049095154 True -8 24615 30.154331922531128 0.5451664924621582 628.521728515625 0.3765312433242798 805.2860717773438 0.3943827450275421 0.65842646 0.4364449083805084 True -9 27350 29.91455101966858 0.5293846130371094 623.0111083984375 0.5732436776161194 804.56298828125 0.39644986391067505 0.65467644 0.4252118170261383 False -10 30085 29.564373254776 0.527883768081665 648.9393920898438 0.5146344900131226 798.4947509765625 0.40005800127983093 0.6583122 0.4242420196533203 False -11 32820 29.530965089797974 2.715796947479248 639.0723266601562 0.5525996685028076 796.162841796875 0.40173235535621643 0.66227 0.40316247940063477 True -12 35555 29.646260976791382 0.5377922058105469 620.86962890625 0.7540687322616577 791.5281982421875 0.4081251323223114 0.6745805 0.3950517177581787 True -13 38290 29.52719235420227 0.5350067615509033 547.9647216796875 0.4959431290626526 788.9094848632812 0.41105252504348755 0.68391573 0.3813178241252899 True -14 41025 29.51198983192444 1.037170171737671 628.8168334960938 0.351330429315567 787.1104125976562 0.41259127855300903 0.69126153 0.37599557638168335 True -15 43760 29.532429456710815 0.539360761642456 577.7631225585938 0.48948919773101807 784.7431640625 0.41481897234916687 0.69819987 0.36044183373451233 True -16 46495 29.56591796875 8.876172304153442 602.4715576171875 0.4385063052177429 785.7188110351562 0.41445159912109375 0.7032451 0.360734224319458 True -17 49230 29.841464042663574 0.5284423828125 646.5471801757812 0.3856855630874634 783.8636474609375 0.4161757826805115 0.7051373 0.3600279986858368 True -18 51965 29.597251415252686 1.2651231288909912 595.8546142578125 0.6036088466644287 783.138427734375 0.41723304986953735 0.7060896 0.3621262013912201 True -19 54700 29.575567722320557 0.5312442779541016 662.367919921875 0.34580719470977783 783.2041015625 0.41784757375717163 0.7049605 0.36720725893974304 False diff --git a/ENCSR501FWC/cherimoya.fold_0.performance.tsv b/ENCSR501FWC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index dea48b8a1f8cea031162990dcb2bff26d9a1a136..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -783.138427734375 0.3361094892024994 0.41723307967185974 0.19355563819408417 0.7060896158218384 0.6561599969863892 0.3621262013912201 \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_1.evaluate.json b/ENCSR501FWC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5f02914fceee9a163008cf52127bdace4aed4d2f..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF154FVS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_1.fit.json b/ENCSR501FWC/cherimoya.fold_1.fit.json deleted file mode 100644 index e3aaf5b83587a0d8aac9caa0da730809f770441e..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF154FVS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_1.log b/ENCSR501FWC/cherimoya.fold_1.log deleted file mode 100644 index 2e14a8e71be84411b7e403b7c74be60c9af3d3a1..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 34.55742788314819 4.4003987312316895 649.1578369140625 0.6867738962173462 1038.042236328125 0.26382049918174744 0.6004958 5.380504608154297 True -1 5564 30.77519202232361 0.7081868648529053 656.1151123046875 0.6826602220535278 954.2167358398438 0.37940263748168945 0.6367445 1.2329368591308594 True -2 8346 30.688053607940674 2.1902804374694824 612.9986572265625 0.7079190611839294 941.6444091796875 0.38879069685935974 0.66123533 0.6059840321540833 True -3 11128 30.72158908843994 0.6706080436706543 749.309814453125 0.7594387531280518 932.808837890625 0.39606860280036926 0.67218244 0.5110132098197937 True -4 13910 30.67490267753601 0.6697976589202881 674.8375244140625 0.5610264539718628 925.5250244140625 0.4007921814918518 0.68350434 0.47574782371520996 True -5 16692 30.6573429107666 0.657041072845459 763.1546630859375 0.5940208435058594 912.073974609375 0.4029359817504883 0.6873919 0.4768037796020508 True -6 19474 30.67461919784546 0.6696319580078125 623.635986328125 0.7622507810592651 902.9466552734375 0.4088394343852997 0.68686223 0.4837704598903656 False -7 22256 30.736268281936646 0.6620602607727051 567.738037109375 0.533110499382019 903.3222045898438 0.40959420800209045 0.68522435 0.48300838470458984 False -8 25038 30.633383750915527 0.6688990592956543 730.8468017578125 0.4246217906475067 897.4720458984375 0.4113282859325409 0.68531215 0.5468090772628784 False -9 27820 30.653238773345947 0.6754393577575684 693.2299194335938 0.5216770172119141 886.107421875 0.41556277871131897 0.6888302 0.528710663318634 True -10 30602 30.62909770011902 0.6638634204864502 646.807373046875 0.6366568803787231 878.4347534179688 0.4187924563884735 0.6898833 0.5408922433853149 True -11 33384 30.382606744766235 0.6600329875946045 543.6190185546875 0.48627370595932007 874.151611328125 0.4225386083126068 0.6951639 0.5493671298027039 True -12 36166 30.120523929595947 0.6501641273498535 694.5496215820312 0.40828198194503784 867.5723266601562 0.42677345871925354 0.71174204 0.47517773509025574 True -13 38948 30.037652492523193 0.6602482795715332 672.4810180664062 0.47585850954055786 865.0672607421875 0.4302479028701782 0.7158591 0.463441401720047 True -14 41730 30.165390014648438 1.285017490386963 661.5360107421875 0.405855268239975 861.7274169921875 0.4308721721172333 0.726561 0.431501179933548 True -15 44512 30.043098211288452 0.6617968082427979 569.711669921875 0.33729422092437744 860.3787231445312 0.4335539638996124 0.73389167 0.4069302976131439 True -16 47294 30.045087099075317 0.6493663787841797 641.7647705078125 0.2837654948234558 858.1510620117188 0.4367731809616089 0.7399086 0.38774266839027405 True -17 50076 30.032795667648315 0.6599977016448975 600.3109741210938 0.44665151834487915 857.30859375 0.4373668432235718 0.74274355 0.3761424422264099 True -18 52858 30.032381772994995 0.6579122543334961 637.2615966796875 0.4157499372959137 858.1788940429688 0.43618080019950867 0.74347824 0.3735020160675049 True -19 55640 30.031729698181152 0.6523728370666504 661.1741943359375 0.3274694085121155 858.1124267578125 0.4359976649284363 0.74121547 0.37485048174858093 False diff --git a/ENCSR501FWC/cherimoya.fold_1.performance.tsv b/ENCSR501FWC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 09349d3fb6a3557ae6e647c1328b1eafa2679be4..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -858.1788940429688 0.31916025280952454 0.43618083000183105 0.21854574978351593 0.7434782385826111 0.7108292579650879 0.3735020160675049 \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_2.evaluate.json b/ENCSR501FWC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a28ca03aef039bad4aeeba6d3c623b30c2e84ab6..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF154FVS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_2.fit.json b/ENCSR501FWC/cherimoya.fold_2.fit.json deleted file mode 100644 index 8fe07d9dadf89c8eaa1d70fda1c4880f58bae5bd..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF154FVS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_2.log b/ENCSR501FWC/cherimoya.fold_2.log deleted file mode 100644 index 42fbd2ddbaea6d90af6b1e5691547d73e9895e79..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2887 35.807071924209595 3.094897747039795 721.236572265625 0.923261284828186 958.280517578125 0.25553351640701294 0.5664108 4.33117151260376 True -1 5774 31.88530397415161 0.4894387722015381 749.121826171875 0.9307835102081299 881.211181640625 0.37389734387397766 0.5970796 0.9208544492721558 True -2 8661 31.824846029281616 0.48603391647338867 854.5425415039062 0.5506610870361328 875.8787841796875 0.37932321429252625 0.6093189 0.5745670795440674 True -3 11548 31.814743757247925 0.49058079719543457 588.2919921875 0.7583951950073242 867.506103515625 0.3854527771472931 0.61403626 0.5447567105293274 True -4 14435 31.84723734855652 0.48637843132019043 847.7144165039062 0.6217005848884583 854.074951171875 0.3887600302696228 0.62144077 0.5591446161270142 True -5 17322 31.844723224639893 0.4887073040008545 730.3029174804688 0.7412598133087158 848.5185546875 0.38970088958740234 0.62701786 0.550803542137146 True -6 20209 31.864075422286987 0.4871063232421875 588.9591064453125 0.6062158942222595 843.4684448242188 0.39326712489128113 0.63274515 0.583704948425293 True -7 23096 31.81113338470459 0.486865758895874 541.265869140625 0.9323164224624634 831.9793701171875 0.39645475149154663 0.64327306 0.5079188942909241 True -8 25983 31.77656102180481 0.4944581985473633 549.2620849609375 0.5626985430717468 825.2779541015625 0.40123680233955383 0.64261204 0.5646950602531433 False -9 28870 31.807687759399414 0.48373913764953613 681.911376953125 0.7023425102233887 827.2261352539062 0.40066927671432495 0.6425077 0.547778844833374 False -10 31757 31.678107500076294 0.48343682289123535 657.1551513671875 0.40095025300979614 822.0093994140625 0.40424466133117676 0.64968616 0.5145931839942932 True -11 34644 31.173290252685547 0.4827897548675537 734.4506225585938 0.5310045480728149 817.7083740234375 0.4085727632045746 0.65744084 0.5077946186065674 True -12 37531 31.248759269714355 0.4798264503479004 704.9710693359375 0.497262179851532 813.6177368164062 0.4107564687728882 0.663332 0.4538079798221588 True -13 40418 31.217531442642212 0.5010769367218018 672.0487670898438 0.4783262014389038 808.437744140625 0.414122611284256 0.6745532 0.4494031071662903 True -14 43305 31.274224996566772 0.48288488388061523 634.147216796875 0.48291051387786865 804.4078369140625 0.41760170459747314 0.6847168 0.41976940631866455 True -15 46192 31.20719623565674 0.4950125217437744 589.1126708984375 0.36672478914260864 801.743408203125 0.4196259677410126 0.6935816 0.39978447556495667 True -16 49079 31.206055164337158 0.48441290855407715 599.9345703125 0.4121849536895752 798.9453735351562 0.42154526710510254 0.69974965 0.38593584299087524 True -17 51966 31.22230315208435 0.48469042778015137 683.0134887695312 0.40385153889656067 799.6863403320312 0.4221828281879425 0.70198387 0.3850252032279968 True -18 54853 31.1910183429718 0.482560396194458 604.875 0.3602621555328369 800.152099609375 0.42145082354545593 0.70157963 0.38329192996025085 False -19 57740 31.253410816192627 0.4945340156555176 784.3812255859375 0.3506796061992645 799.4017944335938 0.4229137897491455 0.7011058 0.3882446885108948 False diff --git a/ENCSR501FWC/cherimoya.fold_2.performance.tsv b/ENCSR501FWC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 23cb20cba49321c0840a18e47b43596bbec3818c..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -799.6863403320312 0.3335328698158264 0.4221828877925873 0.20236815512180328 0.7019838690757751 0.6550608277320862 0.3850252032279968 \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_3.evaluate.json b/ENCSR501FWC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 082c5ab1fe7e858921b85fb5d69498fe9cb8add9..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF154FVS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_3.fit.json b/ENCSR501FWC/cherimoya.fold_3.fit.json deleted file mode 100644 index c2398ef1cb13b3402cef611eece6473af499f6f8..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF154FVS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_3.log b/ENCSR501FWC/cherimoya.fold_3.log deleted file mode 100644 index f5f68d636b6a2d3ae36e34743faeaa54efd7c451..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2805 34.88483953475952 3.671584129333496 718.0076904296875 0.7214740514755249 922.70263671875 0.25752946734428406 0.58544046 6.013462543487549 True -1 5610 30.89737296104431 0.5918464660644531 663.4030151367188 0.863390326499939 854.8283081054688 0.3610455095767975 0.6246832 0.995964527130127 True -2 8415 30.909255743026733 0.569854736328125 618.9486083984375 0.5437143445014954 845.5137939453125 0.3725767731666565 0.63212836 0.5006479024887085 True -3 11220 30.91410541534424 0.5733680725097656 706.0809326171875 0.6087977886199951 840.6101684570312 0.37556710839271545 0.65290076 0.4089425206184387 True -4 14025 31.005621194839478 0.5757548809051514 682.6063842773438 0.6416702270507812 836.2420654296875 0.38026919960975647 0.6526571 0.40647128224372864 False -5 16830 30.978806495666504 0.5686893463134766 619.0364990234375 0.5484760999679565 835.1103515625 0.38157716393470764 0.66033924 0.3990321159362793 True -6 19635 30.934602975845337 0.5731847286224365 662.2117919921875 0.7961844205856323 832.0527954101562 0.3852498531341553 0.6590713 0.40776118636131287 False -7 22440 30.90268087387085 0.5707981586456299 642.072998046875 0.7820501923561096 829.0695190429688 0.3870376646518707 0.66069174 0.41691911220550537 True -8 25245 31.013238668441772 0.5719919204711914 636.05419921875 0.513895571231842 827.636474609375 0.3911285400390625 0.6654834 0.41343629360198975 True -9 28050 30.94452977180481 0.5652501583099365 813.39013671875 0.4684981405735016 825.479248046875 0.3929988145828247 0.6707579 0.4127480089664459 True -10 30855 30.708847522735596 0.5655303001403809 631.026611328125 0.5281592011451721 821.7068481445312 0.3962438106536865 0.6760769 0.4245070815086365 True -11 33660 30.330371379852295 0.5628623962402344 680.6307373046875 0.5575724244117737 819.0111694335938 0.3980541527271271 0.6842096 0.4194457530975342 True -12 36465 30.346367835998535 0.5653560161590576 671.7765502929688 0.36827316880226135 815.51025390625 0.4022696018218994 0.6901023 0.4119614064693451 True -13 39270 30.31318998336792 0.707115650177002 543.6326904296875 0.5279144644737244 813.023193359375 0.4044785797595978 0.6991764 0.389708548784256 True -14 42075 30.448713302612305 0.5789577960968018 575.351806640625 0.5336987376213074 810.7462768554688 0.4076632857322693 0.7067771 0.37828707695007324 True -15 44880 30.353368282318115 0.5694234371185303 719.9852294921875 0.39440834522247314 809.8067016601562 0.40818747878074646 0.71652555 0.35962551832199097 True -16 47685 30.361538648605347 0.5723531246185303 609.5628051757812 0.23805759847164154 806.9711303710938 0.41231653094291687 0.720646 0.3620510697364807 True -17 50490 30.421339511871338 0.569390058517456 750.00830078125 0.38694560527801514 806.7037353515625 0.41274315118789673 0.72216153 0.3559160530567169 True -18 53295 30.373462438583374 2.1410319805145264 554.336181640625 0.48981010913848877 807.1708374023438 0.4118587076663971 0.7225474 0.3568040430545807 True -19 56100 30.406564235687256 0.5736203193664551 639.5995483398438 0.44873592257499695 807.2848510742188 0.4111690819263458 0.72220105 0.3583219647407532 False diff --git a/ENCSR501FWC/cherimoya.fold_3.performance.tsv b/ENCSR501FWC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 98294ec88c58dd69ceb9bed6271c3aae54d71483..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -807.1708374023438 0.33349013328552246 0.4118587076663971 0.20109966397285461 0.7225474119186401 0.6736628413200378 0.3568040430545807 \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_4.evaluate.json b/ENCSR501FWC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5c2291df66cf25ce8ed681d4f226510aa57446bf..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF154FVS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_4.fit.json b/ENCSR501FWC/cherimoya.fold_4.fit.json deleted file mode 100644 index d55e44146fdb4cba6fc561b44c77f122074c41d1..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF154FVS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR501FWC/cherimoya.fold_4.log b/ENCSR501FWC/cherimoya.fold_4.log deleted file mode 100644 index cdc22b7ffa2a15b77e0d56f1ab0c0fc67fcd9af4..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 35.902689695358276 3.6143453121185303 652.182861328125 0.6011883616447449 891.2432861328125 0.2533203363418579 0.56391925 4.353450298309326 True -1 5784 31.84577488899231 0.5934333801269531 664.9183349609375 0.689748227596283 824.96142578125 0.3604302704334259 0.5971856 0.8887988328933716 True -2 8676 31.87652897834778 0.5838439464569092 700.0699462890625 0.6993557214736938 816.9213256835938 0.36698171496391296 0.6305791 0.39471980929374695 True -3 11568 31.90095591545105 2.426584482192993 624.723876953125 0.5938224196434021 812.6708374023438 0.3727705776691437 0.6346919 0.40318283438682556 True -4 14460 31.859917879104614 1.1747872829437256 628.5404052734375 0.9004186391830444 809.7410278320312 0.3748617172241211 0.63281316 0.40865859389305115 False -5 17352 31.868932723999023 0.6191425323486328 627.355712890625 0.4632047712802887 807.3866577148438 0.3769686222076416 0.63427526 0.46322011947631836 False -6 20244 31.90871787071228 0.6004345417022705 755.5318603515625 0.3179931044578552 805.3715209960938 0.38006702065467834 0.63130367 0.5151475071907043 False -7 23136 31.83705449104309 0.5897049903869629 639.166015625 0.47016817331314087 801.8233032226562 0.38198786973953247 0.6409162 0.505357563495636 True -8 26028 31.695728063583374 0.5762405395507812 624.25537109375 0.4445914030075073 798.7837524414062 0.3843471109867096 0.6453972 0.5020110607147217 True -9 28920 31.36660146713257 0.5762588977813721 642.9024658203125 0.5349187254905701 797.2603759765625 0.3869476020336151 0.6497504 0.4982340335845947 True -10 31812 31.286466598510742 0.5839285850524902 688.7664794921875 0.6905410289764404 793.4474487304688 0.3901183605194092 0.6510712 0.5101041197776794 True -11 34704 31.306548357009888 0.9721791744232178 666.6990966796875 0.9709200859069824 789.3988037109375 0.39462149143218994 0.65873414 0.5229437351226807 True -12 37596 31.32197141647339 0.578040599822998 590.28466796875 0.5202987194061279 786.8965454101562 0.39673569798469543 0.66374147 0.508518636226654 True -13 40488 31.264182806015015 0.576848030090332 500.20196533203125 0.4385298490524292 784.6690063476562 0.3991939425468445 0.6724706 0.4781630039215088 True -14 43380 31.287412881851196 0.57547926902771 554.6605834960938 0.45217469334602356 782.2969970703125 0.40218645334243774 0.68321985 0.441156804561615 True -15 46272 31.21785020828247 2.4634013175964355 617.4965209960938 0.35688894987106323 780.490966796875 0.4055277109146118 0.6902753 0.4079884886741638 True -16 49164 31.333311319351196 0.5820693969726562 680.430908203125 0.4124794006347656 779.473876953125 0.4067394435405731 0.69829935 0.3850858807563782 True -17 52056 31.310830116271973 1.64923095703125 551.7411499023438 0.44997119903564453 778.8072509765625 0.4073989689350128 0.69881153 0.3837626278400421 True -18 54948 31.273125886917114 0.5855185985565186 725.2349853515625 0.1979324221611023 778.0338134765625 0.408413827419281 0.69973505 0.37612831592559814 True -19 57840 31.261355876922607 0.5908079147338867 558.82958984375 0.3664962649345398 778.0547485351562 0.4082338809967041 0.6982724 0.3796647787094116 False diff --git a/ENCSR501FWC/cherimoya.fold_4.performance.tsv b/ENCSR501FWC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ac3446c937003c832d2fe205a0f8e635ce9e1da3..0000000000000000000000000000000000000000 --- a/ENCSR501FWC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -778.0338134765625 0.3389911949634552 0.408413827419281 0.19441740214824677 0.6997350454330444 0.6421587467193604 0.37612831592559814 \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_0.evaluate.json b/ENCSR502FPR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index df9c7e0dec05da193c6f680a0e8432caa1c9b93c..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155MMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_0.fit.json b/ENCSR502FPR/cherimoya.fold_0.fit.json deleted file mode 100644 index 344d09a9488db90432ffd32d790ef6fa096a3e79..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF155MMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_0.log b/ENCSR502FPR/cherimoya.fold_0.log deleted file mode 100644 index 9d1ddf96edda71ccd672eca914de196726838570..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.63117861747742 4.071106910705566 446.0443115234375 0.2194463163614273 521.979248046875 0.2584114670753479 0.8219468 3.1804652214050293 True -1 5508 30.58173418045044 1.1126000881195068 435.3155517578125 0.27038365602493286 491.9725341796875 0.3083137273788452 0.86099553 0.762706458568573 True -2 8262 30.9931697845459 0.5941214561462402 440.68353271484375 0.2240387350320816 486.5683898925781 0.3172229528427124 0.8742541 0.29624876379966736 True -3 11016 30.411372661590576 1.8264122009277344 404.1148376464844 0.12136311829090118 484.0053405761719 0.32098183035850525 0.8820508 0.2790983021259308 True -4 13770 30.37946581840515 0.58823561668396 451.52423095703125 0.13164348900318146 483.06951904296875 0.3211604356765747 0.8855027 0.20142485201358795 True -5 16524 30.51894998550415 0.5992801189422607 438.0099182128906 0.21392764151096344 481.953125 0.3230132758617401 0.89368427 0.16883713006973267 True -6 19278 30.558499336242676 0.6022145748138428 408.07073974609375 0.19379517436027527 480.8963623046875 0.32522040605545044 0.89535224 0.15624532103538513 True -7 22032 30.54046106338501 0.5897948741912842 401.29833984375 0.1718984842300415 479.9073486328125 0.3279768228530884 0.8957985 0.1516793817281723 True -8 24786 30.432286739349365 0.5955255031585693 434.2508239746094 0.34334659576416016 479.35833740234375 0.32859253883361816 0.90286136 0.14604836702346802 True -9 27540 29.969505310058594 0.5855934619903564 430.698974609375 0.12257841229438782 478.6481018066406 0.33020713925361633 0.9031641 0.13603700697422028 True -10 30294 29.831007480621338 0.5847640037536621 409.3305969238281 0.17050215601921082 477.6634826660156 0.33145028352737427 0.90867865 0.1276472806930542 True -11 33048 29.774247884750366 0.5825278759002686 428.13067626953125 0.13698935508728027 476.9876708984375 0.33246105909347534 0.90991986 0.12188229709863663 True -12 35802 29.798938512802124 0.5860788822174072 441.76129150390625 0.13474228978157043 476.74395751953125 0.33275023102760315 0.9133612 0.11664381623268127 True -13 38556 29.936373710632324 0.5857181549072266 438.73419189453125 0.16803430020809174 476.2619323730469 0.3336184620857239 0.914149 0.11392176896333694 True -14 41310 29.818081378936768 0.5873322486877441 449.22320556640625 0.12131238728761673 475.6666564941406 0.334409236907959 0.9183217 0.1090802475810051 True -15 44064 29.78337574005127 38.380332231521606 391.8511047363281 0.12056048214435577 474.67779541015625 0.3363548517227173 0.9185775 0.10604813694953918 True -16 46818 30.494216203689575 0.6286375522613525 429.8028564453125 0.2049967348575592 474.52197265625 0.3369254469871521 0.92258525 0.10408446937799454 True -17 49572 32.64511966705322 12.931538343429565 433.21966552734375 0.08822755515575409 474.1455993652344 0.3373163044452667 0.92245346 0.10272347182035446 False -18 52326 29.784950733184814 0.590069055557251 412.29266357421875 0.0995795726776123 475.19354248046875 0.33554980158805847 0.921368 0.10385783761739731 False -19 55080 29.771756410598755 0.6025674343109131 392.832763671875 0.10996561497449875 474.736572265625 0.33710339665412903 0.9231514 0.1035766527056694 True diff --git a/ENCSR502FPR/cherimoya.fold_0.performance.tsv b/ENCSR502FPR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 32e0e9df137574e37011e95b2157a34eb052ad52..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -474.736572265625 0.429859459400177 0.33710339665412903 0.12202398478984833 0.9231513738632202 0.9063543677330017 0.1035766527056694 \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_1.evaluate.json b/ENCSR502FPR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index abf2128be0f123ab0e9f6392ea99f3f641e2566e..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155MMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_1.fit.json b/ENCSR502FPR/cherimoya.fold_1.fit.json deleted file mode 100644 index 85d9aa36c1b73dcf4a88b9cf68115f7cb3dc3354..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF155MMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_1.log b/ENCSR502FPR/cherimoya.fold_1.log deleted file mode 100644 index 4959ffddff1cf40ee01051f62b6d898589b8a1dc..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2721 35.18369102478027 3.8847463130950928 460.59259033203125 0.1735670268535614 584.9313354492188 0.26283717155456543 0.82087904 3.390462636947632 True -1 5442 30.095154523849487 0.6919167041778564 409.4057922363281 0.1309366524219513 551.8324584960938 0.310745507478714 0.8530457 0.8410214781761169 True -2 8163 30.001615285873413 0.6985399723052979 429.958984375 0.28689706325531006 543.8243408203125 0.3218803405761719 0.86903477 0.3082096576690674 True -3 10884 30.06875252723694 0.7034919261932373 445.11572265625 0.22816899418830872 539.2318725585938 0.3279898464679718 0.88004786 0.2569502890110016 True -4 13605 30.08360981941223 0.8966083526611328 387.02374267578125 0.1842738538980484 537.3553466796875 0.3302974998950958 0.88439566 0.2071911245584488 True -5 16326 31.934081554412842 0.6966962814331055 384.5817565917969 0.0973919928073883 535.2440185546875 0.33304065465927124 0.8884602 0.21237143874168396 True -6 19047 30.13216781616211 0.8559041023254395 433.1839599609375 0.213298499584198 533.5722045898438 0.3364717960357666 0.8932058 0.1920185685157776 True -7 21768 30.030073165893555 0.6926102638244629 419.4681396484375 0.30632269382476807 532.2394409179688 0.3390471935272217 0.8980112 0.192128986120224 True -8 24489 30.42669367790222 0.6961345672607422 466.00201416015625 0.25201690196990967 531.0360107421875 0.3406459391117096 0.9002941 0.1844838410615921 True -9 27210 30.11739754676819 0.6934912204742432 467.2572326660156 0.192951500415802 529.9553833007812 0.34139004349708557 0.9040408 0.16658370196819305 True -10 29931 31.017784357070923 29.544880390167236 472.74273681640625 0.1382017731666565 529.14794921875 0.34178626537323 0.90738994 0.15994049608707428 True -11 32652 29.60527515411377 0.7097041606903076 424.37933349609375 0.09371428191661835 528.36767578125 0.34289538860321045 0.9118064 0.14775915443897247 True -12 35373 29.588139057159424 0.71091628074646 489.18890380859375 0.09657084941864014 526.0592041015625 0.34730470180511475 0.9158938 0.14201441407203674 True -13 38094 29.659704208374023 0.7008659839630127 421.3135986328125 0.12470079958438873 525.1921997070312 0.34840208292007446 0.9175265 0.13484859466552734 True -14 40815 29.595866680145264 0.6890463829040527 379.1596374511719 0.14766612648963928 524.56103515625 0.34904995560646057 0.9197696 0.12982599437236786 True -15 43536 29.617223978042603 0.7098636627197266 407.2092590332031 0.08960998058319092 524.3502197265625 0.34880033135414124 0.92345953 0.12279078364372253 True -16 46257 29.558085441589355 0.6974043846130371 419.16748046875 0.07150591909885406 523.6727905273438 0.3502432703971863 0.92473716 0.12056717276573181 True -17 48978 29.557558298110962 0.6836917400360107 450.82037353515625 0.06453356146812439 523.1787719726562 0.35118037462234497 0.9261891 0.11749320477247238 True -18 51699 29.511724948883057 0.7717173099517822 399.1935119628906 0.09275907278060913 522.722412109375 0.3519681394100189 0.92403823 0.11741188913583755 False -19 54420 29.483052015304565 1.0748908519744873 399.4857482910156 0.11410351097583771 524.1864013671875 0.3482838273048401 0.92385596 0.11663910746574402 False diff --git a/ENCSR502FPR/cherimoya.fold_1.performance.tsv b/ENCSR502FPR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3565eb2935710611af632a7a5834f731e6038b42..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -523.1787719726562 0.4172612726688385 0.35118037462234497 0.13559791445732117 0.926189124584198 0.9214537143707275 0.11749320477247238 \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_2.evaluate.json b/ENCSR502FPR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 279ff84c17fa1384fdf7face4d10346e02db67f6..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155MMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_2.fit.json b/ENCSR502FPR/cherimoya.fold_2.fit.json deleted file mode 100644 index 5a92ae610a2fd810355984277af69664dbade46e..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF155MMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_2.log b/ENCSR502FPR/cherimoya.fold_2.log deleted file mode 100644 index 2b6b19c15424de2efaaaee42c2527b17d2056a8c..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 36.6155788898468 4.704557418823242 460.7357177734375 0.19788677990436554 550.5353393554688 0.26083701848983765 0.8137914 3.1554055213928223 True -1 5736 31.717113256454468 14.213930368423462 399.97698974609375 0.16844028234481812 521.5314331054688 0.30869704484939575 0.8562915 0.5428741574287415 True -2 8604 31.85926842689514 0.5603146553039551 438.71514892578125 0.1817859262228012 515.2808227539062 0.31816405057907104 0.8622346 0.24280861020088196 True -3 11472 31.709110975265503 0.5452549457550049 363.0483703613281 0.1566261351108551 511.6832275390625 0.3237154185771942 0.87038296 0.22024820744991302 True -4 14340 31.73158288002014 0.538548469543457 489.4087829589844 0.1823451966047287 511.16796875 0.3241393268108368 0.8745629 0.18646588921546936 True -5 17208 31.766324996948242 0.5464699268341064 422.074462890625 0.22100022435188293 509.7994689941406 0.3263390362262726 0.87801474 0.17588862776756287 True -6 20076 31.818716764450073 0.5464322566986084 420.01031494140625 0.17424838244915009 509.640869140625 0.32574260234832764 0.87989825 0.18221114575862885 True -7 22944 31.626741647720337 0.544529914855957 406.3083801269531 0.23407551646232605 508.05413818359375 0.3284939229488373 0.8833945 0.17472603917121887 True -8 25812 31.65391993522644 0.5382218360900879 415.3857116699219 0.21562746167182922 505.7991638183594 0.3322073221206665 0.88964903 0.16468745470046997 True -9 28680 31.67417287826538 0.5437207221984863 405.62396240234375 0.14879727363586426 505.2193908691406 0.3334178924560547 0.8946446 0.15875859558582306 True -10 31548 31.77095603942871 13.265837669372559 410.3728332519531 0.15355783700942993 504.06805419921875 0.33493781089782715 0.8974407 0.15142321586608887 True -11 34416 32.203484773635864 0.5353920459747314 460.302490234375 0.2302856296300888 503.72857666015625 0.33539339900016785 0.89933217 0.1424172967672348 True -12 37284 31.08274245262146 0.5497567653656006 440.43353271484375 0.12805277109146118 502.6664123535156 0.3366127610206604 0.90476984 0.1339939683675766 True -13 40152 31.009966373443604 0.5394666194915771 443.46685791015625 0.1336565464735031 501.90863037109375 0.337861567735672 0.9052874 0.12784342467784882 True -14 43020 31.197123050689697 0.547093391418457 382.4480895996094 0.13748109340667725 501.6685485839844 0.3387351632118225 0.9097968 0.12276722490787506 True -15 45888 31.16557478904724 0.534346342086792 422.62786865234375 0.07557785511016846 500.8754577636719 0.3394579291343689 0.9122435 0.1210511103272438 True -16 48756 31.184149026870728 0.5560450553894043 390.11822509765625 0.11088062077760696 501.3684387207031 0.3386487066745758 0.91213447 0.11773297935724258 False -17 51624 31.254677295684814 0.5605278015136719 399.97918701171875 0.13171835243701935 501.30322265625 0.33858180046081543 0.9109306 0.11627219617366791 False -18 54492 31.180737257003784 27.59768795967102 413.048583984375 0.09132032841444016 501.4753112792969 0.3387962281703949 0.9124312 0.11670392751693726 True -19 57360 32.07589054107666 0.552659273147583 395.68865966796875 0.05987616628408432 501.6849670410156 0.33842983841896057 0.91328526 0.11640963703393936 True diff --git a/ENCSR502FPR/cherimoya.fold_2.performance.tsv b/ENCSR502FPR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 80a53a0dae13e7931a63049fffa0f859d72ea9dd..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -501.6849670410156 0.4247516691684723 0.33842983841896057 0.1245865598320961 0.9132852554321289 0.9035531282424927 0.11640963703393936 \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_3.evaluate.json b/ENCSR502FPR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e5e02240fb4c029ae2f8f33b2148d109bdccc158..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155MMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_3.fit.json b/ENCSR502FPR/cherimoya.fold_3.fit.json deleted file mode 100644 index e0b3b4d6785e66c2c842eda512c19b362bfd9224..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF155MMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_3.log b/ENCSR502FPR/cherimoya.fold_3.log deleted file mode 100644 index 4f85ffa8996343669bbe6c6d69274d06b7294e5f..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 34.9272346496582 3.62733793258667 432.95672607421875 0.18709337711334229 508.1339111328125 0.2703862190246582 0.81027234 3.087766647338867 True -1 5516 30.439995288848877 0.631361722946167 440.3330078125 0.26893773674964905 483.6894836425781 0.30959442257881165 0.8523778 0.623132050037384 True -2 8274 30.59535837173462 0.8512797355651855 393.1524658203125 0.1819470077753067 476.587158203125 0.3199896514415741 0.87108344 0.2736940085887909 True -3 11032 30.540816068649292 2.1396291255950928 407.6510925292969 0.21980392932891846 473.26129150390625 0.3253938853740692 0.88107336 0.21223463118076324 True -4 13790 30.413058757781982 2.349148988723755 437.7130126953125 0.174140065908432 472.87518310546875 0.32474830746650696 0.8853849 0.16683398187160492 True -5 16548 29.98503279685974 0.5255868434906006 362.11517333984375 0.18960614502429962 471.6854248046875 0.3278987407684326 0.8871255 0.16064772009849548 True -6 19306 30.032889127731323 0.5237407684326172 363.9304504394531 0.15092267096042633 470.7583923339844 0.329552561044693 0.8872116 0.1690572053194046 True -7 22064 29.814072370529175 2.8868680000305176 433.13720703125 0.1519024670124054 470.2712097167969 0.32983797788619995 0.8889204 0.17093853652477264 True -8 24822 29.826781749725342 0.5244643688201904 446.47796630859375 0.11034742742776871 469.58160400390625 0.33104920387268066 0.8927992 0.16827845573425293 True -9 27580 29.92235255241394 0.5585074424743652 517.0411376953125 0.13080273568630219 469.19561767578125 0.33162567019462585 0.8955903 0.15605485439300537 True -10 30338 29.828088521957397 0.5256803035736084 436.30499267578125 0.08994768559932709 467.5336608886719 0.33451423048973083 0.89965034 0.15064354240894318 True -11 33096 30.243247032165527 34.75848913192749 388.131103515625 0.17532773315906525 466.8572692871094 0.33576783537864685 0.904968 0.14212052524089813 True -12 35854 29.9824435710907 0.5326011180877686 354.85418701171875 0.12336461246013641 466.1222229003906 0.3366173505783081 0.9046395 0.13908518850803375 False -13 38612 29.851085424423218 10.27890396118164 391.46820068359375 0.14872756600379944 464.9787292480469 0.3386017382144928 0.9084897 0.13573582470417023 True -14 41370 29.947683811187744 0.5273017883300781 418.4000549316406 0.0788303017616272 465.0953369140625 0.3378181755542755 0.9095092 0.1279323846101761 True -15 44128 29.97926688194275 0.527245283126831 457.3695983886719 0.12754453718662262 464.8714599609375 0.338288813829422 0.91210145 0.12162688374519348 True -16 46886 29.854321002960205 0.5289931297302246 513.2284545898438 0.15616577863693237 464.0188903808594 0.3394755423069 0.91486675 0.11745952814817429 True -17 49644 30.005645751953125 0.5263662338256836 385.2230529785156 0.07931526005268097 464.2213134765625 0.3384629487991333 0.9144866 0.11547259986400604 False -18 52402 29.907618284225464 0.5254697799682617 386.332763671875 0.10491884499788284 464.51593017578125 0.33858567476272583 0.91583866 0.11557154357433319 True -19 55160 29.898341178894043 0.5359432697296143 388.559326171875 0.10348537564277649 464.5162658691406 0.33854639530181885 0.9163373 0.11557751893997192 True diff --git a/ENCSR502FPR/cherimoya.fold_3.performance.tsv b/ENCSR502FPR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9ac0149ee726483c40c3b6694904ce65938239a8..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -464.5162658691406 0.4298417270183563 0.33854636549949646 0.12154730409383774 0.9163373112678528 0.8972566723823547 0.11557751893997192 \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_4.evaluate.json b/ENCSR502FPR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 673e0367c01b9496a60fdee0c27f51528641e773..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155MMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_4.fit.json b/ENCSR502FPR/cherimoya.fold_4.fit.json deleted file mode 100644 index 9061a0dbca97ca2e63128b6c1443d0978b97a401..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF155MMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502FPR/cherimoya.fold_4.log b/ENCSR502FPR/cherimoya.fold_4.log deleted file mode 100644 index 73621e9d4739f041713fccc5864bed99ac6aedd7..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.22031235694885 4.060180187225342 423.6670837402344 0.20671072602272034 479.5939025878906 0.2553516626358032 0.81841224 2.4422948360443115 True -1 5596 30.86441969871521 0.6322178840637207 425.368408203125 0.25598883628845215 456.786376953125 0.29597049951553345 0.85747826 0.5285847783088684 True -2 8394 30.812837600708008 0.6189641952514648 413.8907470703125 0.192692369222641 451.9552307128906 0.303455114364624 0.8688136 0.22772294282913208 True -3 11192 30.947532415390015 0.6173136234283447 408.16253662109375 0.18431024253368378 448.7999267578125 0.30918216705322266 0.87675196 0.21292246878147125 True -4 13990 30.884883165359497 0.6208949089050293 429.3924560546875 0.2567664086818695 447.7324523925781 0.3114166557788849 0.87987566 0.15246054530143738 True -5 16788 31.1197350025177 0.6715619564056396 402.7601318359375 0.1304086446762085 446.0349426269531 0.31475165486335754 0.8875564 0.15046942234039307 True -6 19586 30.976032257080078 0.6412830352783203 425.226806640625 0.1718291938304901 445.47882080078125 0.31547385454177856 0.890998 0.14508463442325592 True -7 22384 31.01905107498169 0.6269881725311279 473.0831298828125 0.1666310727596283 444.9008483886719 0.31623202562332153 0.8940989 0.14445465803146362 True -8 25182 31.2085223197937 0.6300668716430664 471.005859375 0.1433289647102356 444.203857421875 0.31754764914512634 0.8997034 0.14144952595233917 True -9 27980 31.208834886550903 1.2872028350830078 425.8371887207031 0.13047797977924347 443.1628723144531 0.31975480914115906 0.9021333 0.13556930422782898 True -10 30778 32.153284549713135 31.355586290359497 409.6024169921875 0.16159044206142426 442.389892578125 0.32093337178230286 0.9062434 0.12293893843889236 True -11 33576 31.00334858894348 0.6231191158294678 421.9493408203125 0.16925746202468872 441.4722900390625 0.32317855954170227 0.9101154 0.11499952524900436 True -12 36374 30.962833404541016 0.6377377510070801 456.86676025390625 0.14581255614757538 440.9477233886719 0.3237161636352539 0.9132835 0.10904969274997711 True -13 39172 31.42475962638855 0.618187427520752 441.7580871582031 0.17668181657791138 440.3004150390625 0.32456865906715393 0.9151769 0.10467705130577087 True -14 41970 30.868652820587158 0.6164321899414062 419.841064453125 0.07415097951889038 440.4764099121094 0.32408007979393005 0.91856414 0.10255317389965057 True -15 44768 30.52246403694153 1.4088549613952637 382.2134094238281 0.12074865400791168 439.81549072265625 0.3253527283668518 0.9183736 0.0976654440164566 False -16 47566 30.24614667892456 0.6183903217315674 437.5357666015625 0.10150548815727234 439.72747802734375 0.3254612386226654 0.91999286 0.0948135033249855 True -17 50364 30.283741235733032 1.212343692779541 350.824462890625 0.10540829598903656 440.3167724609375 0.32403501868247986 0.92037123 0.09288235753774643 True -18 53162 30.323171854019165 0.608100175857544 402.4372253417969 0.07421071827411652 439.6566467285156 0.3260239362716675 0.9216292 0.09195366501808167 True -19 55960 30.304961919784546 0.6178076267242432 419.92388916015625 0.08724507689476013 439.8840026855469 0.324872225522995 0.9211944 0.09245843440294266 False diff --git a/ENCSR502FPR/cherimoya.fold_4.performance.tsv b/ENCSR502FPR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 10c31943aed07d2bd92b3568529802b3c82bbadb..0000000000000000000000000000000000000000 --- a/ENCSR502FPR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -439.6566467285156 0.4402724504470825 0.3260239362716675 0.11417211592197418 0.9216291904449463 0.9005957841873169 0.09195366501808167 \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_0.evaluate.json b/ENCSR502NDK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 31d110be007c5a3e74752801a33835de72cfeb91..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396LZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_0.fit.json b/ENCSR502NDK/cherimoya.fold_0.fit.json deleted file mode 100644 index 2f5e4fd61d6948163e207db8e95649de44c08ccc..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF396LZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_0.log b/ENCSR502NDK/cherimoya.fold_0.log deleted file mode 100644 index 39a64b184758f52867b5f9361d2acccfe6181d97..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 33.91885185241699 3.5324225425720215 217.01255798339844 0.7052037715911865 293.2553405761719 0.15540970861911774 0.5457705 2.262392282485962 True -1 5490 30.282310962677002 0.5618879795074463 224.29078674316406 0.5046265721321106 280.8511047363281 0.20590423047542572 0.6212456 1.2056156396865845 True -2 8235 29.902924299240112 0.5378813743591309 246.479248046875 0.7542745471000671 276.9647521972656 0.21824783086776733 0.6456566 0.6166574954986572 True -3 10980 29.61855912208557 0.540926456451416 234.73919677734375 0.7588967084884644 274.7216491699219 0.22510042786598206 0.650207 0.5949297547340393 True -4 13725 29.75797390937805 1.5392348766326904 238.02880859375 0.5555466413497925 273.64642333984375 0.22869479656219482 0.66092193 0.6070038080215454 True -5 16470 29.656119346618652 0.5376565456390381 250.37188720703125 0.2666685879230499 272.88287353515625 0.23172910511493683 0.6730991 0.6141861081123352 True -6 19215 29.592160940170288 0.5551106929779053 207.2009735107422 0.581383228302002 272.5345764160156 0.23338846862316132 0.67896414 0.6506490707397461 True -7 21960 30.242124557495117 27.298742294311523 210.0842742919922 0.30196380615234375 271.7615051269531 0.23664116859436035 0.6818564 0.6142696738243103 True -8 24705 29.763561964035034 0.5705630779266357 219.72149658203125 0.6189491748809814 271.0873107910156 0.2391636222600937 0.68862253 0.5753940343856812 True -9 27450 29.78736448287964 0.5664153099060059 248.74539184570312 0.39537233114242554 270.777099609375 0.2402486503124237 0.69725525 0.5280339121818542 True -10 30195 29.700318813323975 0.6404945850372314 217.49725341796875 0.44110792875289917 270.1825256347656 0.2424422949552536 0.70268726 0.4806128144264221 True -11 32940 29.669844388961792 29.41844367980957 250.42025756835938 0.5152535438537598 269.59820556640625 0.24502216279506683 0.7101749 0.4733685553073883 True -12 35685 29.851969242095947 0.5620443820953369 212.48040771484375 0.5522558689117432 269.1727600097656 0.24665242433547974 0.71899307 0.4278768301010132 True -13 38430 31.029627799987793 0.5499908924102783 281.400390625 0.6329869031906128 268.95733642578125 0.24673286080360413 0.7279658 0.40390634536743164 True -14 41175 29.646960973739624 0.5337936878204346 205.45089721679688 0.4238455891609192 268.44927978515625 0.24887987971305847 0.73540425 0.38067957758903503 True -15 43920 29.67943835258484 0.5521087646484375 239.12307739257812 0.5237462520599365 268.3620300292969 0.24883565306663513 0.7415519 0.36100566387176514 True -16 46665 29.643081426620483 0.5576176643371582 183.71224975585938 0.28735587000846863 268.3895568847656 0.24906373023986816 0.74564135 0.3484276533126831 True -17 49410 29.642071962356567 0.6020638942718506 215.9092254638672 0.3106544613838196 268.44976806640625 0.24869003891944885 0.7453982 0.34352347254753113 False -18 52155 29.585406064987183 0.5399110317230225 188.18521118164062 0.39325618743896484 268.3044738769531 0.24944767355918884 0.7437291 0.34481874108314514 False -19 54900 29.63843059539795 1.6397902965545654 202.30056762695312 0.38621756434440613 268.0729675292969 0.25099486112594604 0.7437928 0.3487418293952942 False diff --git a/ENCSR502NDK/cherimoya.fold_0.performance.tsv b/ENCSR502NDK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 18ebf3719fffd60c761f6cb6379853d8b3494378..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -268.3895568847656 0.5103533267974854 0.24906373023986816 0.06897136569023132 0.7456413507461548 0.6813846826553345 0.3484276533126831 \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_1.evaluate.json b/ENCSR502NDK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1c190a43d02698a38e726de7bf37ee98ab6c3a3a..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396LZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_1.fit.json b/ENCSR502NDK/cherimoya.fold_1.fit.json deleted file mode 100644 index c6fa2ff6a5bbf99906f67274404e617a83761420..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF396LZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_1.log b/ENCSR502NDK/cherimoya.fold_1.log deleted file mode 100644 index c15743ec3908bbc30343a338f072e6402b3061eb..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 33.392436504364014 3.6955859661102295 234.72247314453125 0.6844053268432617 333.0515441894531 0.16613075137138367 0.5475355 3.733208656311035 True -1 5470 30.038633108139038 0.9955425262451172 254.6427459716797 0.685877799987793 316.2613220214844 0.22719430923461914 0.6503683 1.389269471168518 True -2 8205 30.124650955200195 0.7103893756866455 236.98916625976562 0.4456484019756317 311.9961853027344 0.2366897165775299 0.67086184 0.8601590394973755 True -3 10940 29.672377586364746 0.6958084106445312 219.01622009277344 0.5091471672058105 309.5274353027344 0.2420548051595688 0.6813158 0.7655410766601562 True -4 13675 29.41641664505005 0.6908547878265381 206.32835388183594 0.47460025548934937 308.1514587402344 0.2467295378446579 0.690776 0.7286878824234009 True -5 16410 29.42766809463501 0.6955966949462891 218.93637084960938 0.3595846891403198 307.3920593261719 0.24917398393154144 0.7001607 0.7252981066703796 True -6 19145 29.43497061729431 0.6944003105163574 184.44821166992188 0.5571109652519226 306.3150329589844 0.25389760732650757 0.7049102 0.8151753544807434 True -7 21880 29.42304277420044 0.6825182437896729 240.23220825195312 0.5477462410926819 305.6224670410156 0.2557464838027954 0.7113297 0.7445447444915771 True -8 24615 29.503746271133423 0.6952090263366699 222.35418701171875 0.4205528795719147 304.7074279785156 0.25869932770729065 0.72432303 0.6644102334976196 True -9 27350 29.448014736175537 0.6950314044952393 206.6939697265625 0.38211697340011597 304.1077880859375 0.2607530653476715 0.7313791 0.6367725729942322 True -10 30085 29.447102785110474 0.7016656398773193 204.56512451171875 0.5096831917762756 302.9775390625 0.26475319266319275 0.74322754 0.5564067363739014 True -11 32820 29.40602445602417 0.6997275352478027 196.2113037109375 0.23662811517715454 302.4423522949219 0.26611876487731934 0.7474669 0.5230950117111206 True -12 35555 29.474720239639282 0.6987555027008057 217.33424377441406 0.4043087065219879 302.0927734375 0.2664145231246948 0.7579527 0.49060237407684326 True -13 38290 29.470173120498657 0.6924426555633545 196.48648071289062 0.3916005492210388 301.7281799316406 0.26759395003318787 0.76460105 0.44121044874191284 True -14 41025 29.45803952217102 1.3412439823150635 206.7003173828125 0.451401025056839 301.3932189941406 0.26758670806884766 0.7756077 0.3945450782775879 True -15 43760 29.566320657730103 0.6927309036254883 204.55743408203125 0.4171053469181061 301.03741455078125 0.2695115804672241 0.7779152 0.37855055928230286 True -16 46495 29.530961275100708 0.7010438442230225 261.6224670410156 0.443912535905838 300.8142395019531 0.2702687084674835 0.7812574 0.3624015152454376 True -17 49230 29.555359601974487 0.7061789035797119 194.22354125976562 0.4917535185813904 300.5664978027344 0.27137327194213867 0.7806639 0.35062074661254883 False -18 51965 29.456451892852783 0.7014346122741699 191.09579467773438 0.5119277238845825 301.2550048828125 0.2681006193161011 0.7791604 0.3517003357410431 False -19 54700 29.53040909767151 0.7041378021240234 186.379638671875 0.28076955676078796 301.26397705078125 0.26857325434684753 0.7787235 0.35381200909614563 False diff --git a/ENCSR502NDK/cherimoya.fold_1.performance.tsv b/ENCSR502NDK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 976d9d6735eb9580d637564613a40f0bfa52fa44..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -300.8142395019531 0.49362966418266296 0.27026867866516113 0.0805874615907669 0.7812573909759521 0.7295743227005005 0.3624015152454376 \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_2.evaluate.json b/ENCSR502NDK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 43c6301eec60fc2a377dd53cb8b3d136e6225b62..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396LZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_2.fit.json b/ENCSR502NDK/cherimoya.fold_2.fit.json deleted file mode 100644 index 0539cdca3c242d5c2109fbadda3b699fda9dd93c..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF396LZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_2.log b/ENCSR502NDK/cherimoya.fold_2.log deleted file mode 100644 index af4ac2947b6421d0c9510186a79f289d79ddb722..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2902 43.99366521835327 5.022582292556763 204.5155792236328 0.7939854264259338 300.7741394042969 0.16415828466415405 0.55382997 2.5677361488342285 True -1 5804 31.90303921699524 0.5439534187316895 230.22576904296875 0.7096072435379028 286.5782470703125 0.215714231133461 0.642583 1.0325453281402588 True -2 8706 31.61549472808838 0.5385191440582275 217.4573211669922 0.4652532935142517 283.2242126464844 0.226008340716362 0.66049045 0.6233825087547302 True -3 11608 31.376953601837158 0.529059886932373 243.94041442871094 0.8476842641830444 280.98291015625 0.23204228281974792 0.6729328 0.47107067704200745 True -4 14510 31.444961309432983 0.527069091796875 201.19802856445312 0.39549410343170166 279.8935241699219 0.2352210432291031 0.68211937 0.46654051542282104 True -5 17412 31.31380033493042 0.5635275840759277 196.32687377929688 0.47264134883880615 279.1880798339844 0.23793014883995056 0.69056505 0.5140679478645325 True -6 20314 31.273378133773804 0.5206513404846191 212.91075134277344 0.4848534166812897 278.4681396484375 0.23998861014842987 0.7022741 0.49835729598999023 True -7 23216 31.331084966659546 0.5313849449157715 235.9281005859375 0.5545693635940552 277.6498107910156 0.24442145228385925 0.7075936 0.4764585494995117 True -8 26118 31.26261830329895 0.528613805770874 234.6192626953125 0.5102521181106567 277.0951232910156 0.24603532254695892 0.71246827 0.47194069623947144 True -9 29020 31.263444900512695 0.5305774211883545 167.66110229492188 0.4803837835788727 276.45098876953125 0.24842974543571472 0.7192051 0.46963703632354736 True -10 31922 31.187865734100342 0.5235230922698975 184.21726989746094 0.39694011211395264 275.8192443847656 0.25103193521499634 0.72602993 0.4336787462234497 True -11 34824 31.228326082229614 0.5311522483825684 241.993408203125 0.35436582565307617 275.4495849609375 0.2523176074028015 0.7317461 0.4198976159095764 True -12 37726 31.286375284194946 0.526425838470459 212.40481567382812 0.42698612809181213 274.8196716308594 0.2549305558204651 0.73789334 0.38913580775260925 True -13 40628 31.238746643066406 1.3177223205566406 223.85760498046875 0.496690958738327 274.76666259765625 0.25442612171173096 0.7404293 0.38292261958122253 True -14 43530 31.26879334449768 0.542172908782959 216.07080078125 0.40628716349601746 274.5741271972656 0.2544606328010559 0.7479046 0.36054229736328125 True -15 46432 31.305383443832397 0.5220150947570801 233.03831481933594 0.42196035385131836 273.98565673828125 0.25721314549446106 0.7522759 0.35068267583847046 True -16 49334 31.32585334777832 0.5371840000152588 242.55047607421875 0.3366226255893707 273.9763488769531 0.2572792172431946 0.7529478 0.34493550658226013 True -17 52236 31.49250888824463 0.5186548233032227 185.01962280273438 0.2363971471786499 274.1598815917969 0.25584977865219116 0.7553915 0.33996403217315674 True -18 55138 31.328049182891846 0.529768705368042 250.6705322265625 0.31538331508636475 274.2626953125 0.2561503052711487 0.7517312 0.34596672654151917 False -19 58040 31.314604997634888 0.5194053649902344 211.4941864013672 0.27263766527175903 274.2267761230469 0.2565242648124695 0.75216264 0.34649187326431274 False diff --git a/ENCSR502NDK/cherimoya.fold_2.performance.tsv b/ENCSR502NDK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 75283435030bb9b20e70b229ee1e20e093bcd283..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -274.0175476074219 0.5057481527328491 0.25761228799819946 0.07606272399425507 0.7528708577156067 0.6946567893028259 0.3467353880405426 \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_3.evaluate.json b/ENCSR502NDK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 11ea84e62d7d1627feb9c71257500c6ca88c315c..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396LZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_3.fit.json b/ENCSR502NDK/cherimoya.fold_3.fit.json deleted file mode 100644 index 9dd48753c840023e0118dff7c7f8004139f902d5..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF396LZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_3.log b/ENCSR502NDK/cherimoya.fold_3.log deleted file mode 100644 index 5e599a92adc7114ec684fac301e2d4c669d3092b..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2805 36.10112977027893 4.328108310699463 205.94898986816406 0.4090504050254822 307.9202575683594 0.16260214149951935 0.56802815 3.0918638706207275 True -1 5610 31.22749638557434 0.6122019290924072 209.6708526611328 0.714654803276062 293.6059265136719 0.2185773253440857 0.6457325 1.2735179662704468 True -2 8415 31.112902641296387 0.5573346614837646 215.306640625 0.8260707855224609 290.8070983886719 0.2270558923482895 0.663355 0.7892205119132996 True -3 11220 31.111759662628174 0.5691566467285156 226.92437744140625 0.5178017616271973 288.65020751953125 0.232267364859581 0.6794805 0.6721780300140381 True -4 14025 31.18554949760437 0.5740883350372314 217.74642944335938 1.030466914176941 287.3536376953125 0.23762357234954834 0.682215 0.6792357563972473 True -5 16830 31.19007110595703 0.565300703048706 213.681640625 0.5238916873931885 286.5032653808594 0.24096064269542694 0.6943052 0.6637400388717651 True -6 19635 31.191522121429443 2.8870699405670166 268.86749267578125 0.40241551399230957 286.3570251464844 0.24209517240524292 0.6973294 0.6504582166671753 True -7 22440 31.198054552078247 0.5722746849060059 214.01478576660156 0.5153878927230835 285.7663879394531 0.24430781602859497 0.7055083 0.6480876803398132 True -8 25245 31.14637565612793 0.5659053325653076 202.95681762695312 0.48388269543647766 285.0748291015625 0.24666421115398407 0.70988435 0.6139938235282898 True -9 28050 31.985915422439575 0.5665922164916992 207.31573486328125 0.46628719568252563 284.3335876464844 0.24921631813049316 0.7176198 0.5657622218132019 True -10 30855 31.133657932281494 0.572335958480835 231.34478759765625 0.35856813192367554 283.7406005859375 0.25090304017066956 0.72907627 0.5171903371810913 True -11 33660 31.141193866729736 0.5729005336761475 196.490966796875 0.42062264680862427 283.58953857421875 0.25152140855789185 0.7319839 0.4932839870452881 True -12 36465 30.847167253494263 1.637878179550171 215.041748046875 0.34969186782836914 283.0715026855469 0.25339293479919434 0.74007386 0.47458454966545105 True -13 39270 30.54866075515747 0.5557281970977783 180.85707092285156 0.3091844320297241 282.62725830078125 0.2550744116306305 0.7497815 0.4133611023426056 True -14 42075 30.58787250518799 0.5704395771026611 187.152099609375 0.40807366371154785 282.260986328125 0.2558479309082031 0.7564855 0.39335495233535767 True -15 44880 30.569355249404907 0.563258171081543 225.2560577392578 0.3236013352870941 282.40460205078125 0.2555105686187744 0.76220316 0.37291863560676575 True -16 47685 31.652552843093872 0.5658104419708252 273.777099609375 0.30378851294517517 281.8476867675781 0.2578006386756897 0.7664903 0.3575012683868408 True -17 50490 30.787062644958496 0.5837562084197998 215.21046447753906 0.21834561228752136 282.0118103027344 0.2567138075828552 0.76798826 0.3474690318107605 True -18 53295 30.79068946838379 0.5719108581542969 214.9296112060547 0.18442583084106445 282.3416442871094 0.2549281716346741 0.7655873 0.34737128019332886 False -19 56100 30.91010308265686 0.5724468231201172 228.333251953125 0.20870667695999146 282.137451171875 0.2564857304096222 0.7663547 0.3508894741535187 False diff --git a/ENCSR502NDK/cherimoya.fold_3.performance.tsv b/ENCSR502NDK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6bb8b667aa2886c29f7267d0506f11f5fc42e57e..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -282.0118103027344 0.5040308237075806 0.2567138075828552 0.06953335553407669 0.7679882645606995 0.7122043371200562 0.3474690318107605 \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_4.evaluate.json b/ENCSR502NDK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2e4aff66d773e78c6c2ce117933099e7106a663b..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396LZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_4.fit.json b/ENCSR502NDK/cherimoya.fold_4.fit.json deleted file mode 100644 index a2a79eaf1affcf34878e5e5b4a311e9fdd322de8..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF396LZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR502NDK/cherimoya.fold_4.log b/ENCSR502NDK/cherimoya.fold_4.log deleted file mode 100644 index 298952c30f4e21ecc8bf22fdaf122c6da071c428..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2875 36.524465799331665 3.6137263774871826 224.3863067626953 0.7094293236732483 292.4367980957031 0.1569870561361313 0.5444717 2.4634101390838623 True -1 5750 32.00231313705444 0.5709996223449707 204.1829833984375 0.722052812576294 279.4698486328125 0.21073617041110992 0.6451821 0.8928601145744324 True -2 8625 31.9257595539093 0.5698351860046387 262.545166015625 0.8095619678497314 277.5399169921875 0.21489104628562927 0.666353 0.6532638072967529 True -3 11500 31.947566986083984 0.5614638328552246 191.8299102783203 0.5909184813499451 275.0777893066406 0.22341258823871613 0.67217743 0.5600754022598267 True -4 14375 31.85726308822632 0.5649862289428711 191.24844360351562 0.6813333034515381 273.97174072265625 0.2277146875858307 0.6786353 0.5725218057632446 True -5 17250 31.934789657592773 1.1666769981384277 216.75201416015625 0.4800320863723755 273.07183837890625 0.23030537366867065 0.68723243 0.5859658122062683 True -6 20125 31.91719937324524 0.555854320526123 205.63018798828125 0.4246668219566345 272.5925598144531 0.23171529173851013 0.6956137 0.5318323969841003 True -7 23000 31.90511417388916 10.830858707427979 201.068359375 0.4364488124847412 271.93524169921875 0.23512643575668335 0.7010287 0.5337406396865845 True -8 25875 35.9398467540741 0.5728871822357178 213.99203491210938 0.45296767354011536 271.4928894042969 0.23639699816703796 0.70528 0.5177586674690247 True -9 28750 31.7774977684021 0.5651252269744873 211.76358032226562 0.5335273742675781 271.0804748535156 0.23843570053577423 0.71060693 0.4739892780780792 True -10 31625 31.376121759414673 0.5577938556671143 227.6993408203125 0.28228604793548584 270.2755432128906 0.24160118401050568 0.7186014 0.443985253572464 True -11 34500 31.42996644973755 0.5555398464202881 252.34210205078125 0.40682464838027954 270.0492248535156 0.2421570122241974 0.72484463 0.4241708815097809 True -12 37375 31.400513410568237 0.5510694980621338 215.8406524658203 0.3654383718967438 269.2591552734375 0.2458847612142563 0.73193324 0.39962074160575867 True -13 40250 31.346972227096558 0.5532972812652588 191.22044372558594 0.5219960808753967 269.3572692871094 0.24488092958927155 0.73842096 0.3834949731826782 True -14 43125 32.63123846054077 5.094334125518799 212.0870361328125 0.5506733059883118 268.8243713378906 0.24674871563911438 0.74361354 0.3591601252555847 True -15 46000 31.38758683204651 1.8929507732391357 220.56451416015625 0.37344563007354736 268.7497253417969 0.24637120962142944 0.7513331 0.34443238377571106 True -16 48875 31.31414771080017 5.578696966171265 219.60446166992188 0.30868059396743774 268.62322998046875 0.24730284512043 0.75611925 0.3332543969154358 True -17 51750 31.325433015823364 1.1156959533691406 182.46987915039062 0.4227873682975769 268.5465087890625 0.24792054295539856 0.75572616 0.3300268054008484 False -18 54625 31.29023504257202 1.0358867645263672 235.5594482421875 0.3111858665943146 268.6840515136719 0.2471746951341629 0.7563454 0.33011168241500854 True -19 57500 31.29338765144348 0.5456860065460205 217.9849395751953 0.32847750186920166 268.8128662109375 0.24658900499343872 0.75510293 0.3309428095817566 False diff --git a/ENCSR502NDK/cherimoya.fold_4.performance.tsv b/ENCSR502NDK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 34df9e2387b12108f45da42ebd32313a91ea99c6..0000000000000000000000000000000000000000 --- a/ENCSR502NDK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -268.6840515136719 0.5111696124076843 0.2471746951341629 0.06541218608617783 0.7563453912734985 0.6889769434928894 0.33011168241500854 \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_0.evaluate.json b/ENCSR503HIB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b24651a3844f57b89908dca138049143c538c8de..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF937XFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_0.fit.json b/ENCSR503HIB/cherimoya.fold_0.fit.json deleted file mode 100644 index 0d18ba4ac0f83d6fb70ed8c37c15ff15a1487f7e..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF937XFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_0.log b/ENCSR503HIB/cherimoya.fold_0.log deleted file mode 100644 index a228b8514cca770930445c5cd8ec446b22d32b17..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.84778189659119 4.615710973739624 999.986572265625 1.5546128749847412 1619.5074462890625 0.33097416162490845 0.40550965 10.989195823669434 True -1 5514 29.871625423431396 0.6881630420684814 1287.49658203125 1.2006999254226685 1428.525390625 0.44059598445892334 0.4802951 4.551417827606201 True -2 8271 30.464009761810303 0.6431739330291748 1010.1217041015625 1.2405813932418823 1389.511474609375 0.45748522877693176 0.5005015 1.8865514993667603 True -3 11028 30.425060033798218 0.6021707057952881 1039.19287109375 1.0958079099655151 1371.873046875 0.46506211161613464 0.5050926 1.2725863456726074 True -4 13785 30.46221423149109 0.6009478569030762 1071.857421875 0.8343639969825745 1370.0355224609375 0.4619511365890503 0.51424587 1.2002291679382324 True -5 16542 29.88818883895874 0.5864355564117432 1011.764892578125 0.9542478322982788 1364.6239013671875 0.46596407890319824 0.5219634 1.0225437879562378 True -6 19299 29.729093074798584 0.5947210788726807 963.1016845703125 0.8847509622573853 1351.8443603515625 0.4728012681007385 0.5365007 0.9484517574310303 True -7 22056 29.776142120361328 0.5902972221374512 1143.9869384765625 0.7630097270011902 1347.81201171875 0.47611290216445923 0.5410024 0.8905292749404907 True -8 24813 29.833750247955322 0.5866687297821045 929.296142578125 0.6284353733062744 1344.0250244140625 0.47862809896469116 0.5480019 0.8535472750663757 True -9 27570 29.739086866378784 0.5921692848205566 1195.644775390625 1.0834887027740479 1335.6171875 0.48346877098083496 0.55758244 0.7929818630218506 True -10 30327 29.74912667274475 0.5856192111968994 1247.0537109375 1.088685154914856 1330.5125732421875 0.48465147614479065 0.57479715 0.7266998291015625 True -11 33084 29.781938314437866 0.8851966857910156 833.0320434570312 0.6249580383300781 1328.399658203125 0.48462042212486267 0.5837341 0.7249860763549805 True -12 35841 29.78947901725769 0.598832368850708 1074.072265625 0.9323040246963501 1313.4205322265625 0.49420273303985596 0.59211504 0.7051777839660645 True -13 38598 29.779776573181152 0.5920932292938232 1242.6884765625 0.6338861584663391 1314.577880859375 0.4916764795780182 0.60301125 0.6745802760124207 True -14 41355 29.772796630859375 2.8065741062164307 932.3956298828125 0.5654356479644775 1307.600341796875 0.49703872203826904 0.6158488 0.6594685912132263 True -15 44112 29.946604013442993 0.6054370403289795 929.4033203125 0.6669143438339233 1302.7052001953125 0.49922627210617065 0.62488425 0.6492069959640503 True -16 46869 29.89193058013916 0.6387977600097656 1079.3995361328125 0.6271045207977295 1299.901123046875 0.5009106993675232 0.6307237 0.6550218462944031 True -17 49626 30.19544506072998 0.617729663848877 941.294921875 0.655677080154419 1300.2138671875 0.5011224150657654 0.63275415 0.6614394187927246 True -18 52383 29.857264757156372 0.6146092414855957 928.0294189453125 0.6771164536476135 1299.6474609375 0.5019903779029846 0.6317032 0.6724048256874084 False -19 55140 29.800776481628418 2.011385679244995 1281.875 0.7423099279403687 1299.8424072265625 0.5018557906150818 0.631595 0.6837006211280823 False diff --git a/ENCSR503HIB/cherimoya.fold_0.performance.tsv b/ENCSR503HIB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 187c337283ec2ec1c1a2b62e7863b6051f856485..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1300.2138671875 0.2537267506122589 0.5011223554611206 0.30784180760383606 0.6327541470527649 0.5814268589019775 0.6614394187927246 \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_1.evaluate.json b/ENCSR503HIB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 69c1c67ac78c7b5b3bd471218d66e9674b53a350..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF937XFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_1.fit.json b/ENCSR503HIB/cherimoya.fold_1.fit.json deleted file mode 100644 index ff30175e62ca5a408e5b1e06889c06dda70102e5..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF937XFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_1.log b/ENCSR503HIB/cherimoya.fold_1.log deleted file mode 100644 index 54c33921de6f198f648ffd462e7193cd6c4d86e4..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2732 34.906821966171265 4.324613571166992 1243.710693359375 1.3639285564422607 1809.9642333984375 0.3257337808609009 0.45286343 9.513416290283203 True -1 5464 30.072826385498047 0.9476845264434814 1076.25048828125 0.8719508647918701 1595.804443359375 0.434781551361084 0.534363 4.3518290519714355 True -2 8196 30.11416983604431 0.9230382442474365 1361.75341796875 1.4065008163452148 1545.91748046875 0.45326554775238037 0.55518633 2.0816657543182373 True -3 10928 30.102749347686768 1.777534008026123 1067.864013671875 0.6494590044021606 1521.25048828125 0.46146076917648315 0.57381636 1.476983666419983 True -4 13660 30.09628129005432 0.7923386096954346 1187.804931640625 1.2017968893051147 1509.18212890625 0.4663161039352417 0.590008 1.0412734746932983 True -5 16392 30.06476092338562 0.7382941246032715 1152.569580078125 1.3815174102783203 1495.1993408203125 0.472131609916687 0.59438515 0.9901222586631775 True -6 19124 29.4764621257782 0.7565124034881592 1082.0224609375 0.6092491149902344 1491.057373046875 0.4718814790248871 0.6043437 0.8579755425453186 True -7 21856 29.518269777297974 0.7557651996612549 973.5153198242188 1.0211588144302368 1476.4346923828125 0.4801962971687317 0.6076089 0.7950263023376465 True -8 24588 29.549238681793213 0.7857398986816406 974.2498779296875 0.7701517343521118 1468.844970703125 0.48367294669151306 0.6156439 0.7851789593696594 True -9 27320 29.474315881729126 0.7719278335571289 950.045166015625 1.00691556930542 1461.6446533203125 0.4871341586112976 0.62611103 0.7505863308906555 True -10 30052 29.682374477386475 0.8039226531982422 872.6796875 0.867477536201477 1452.1693115234375 0.4903911352157593 0.6342814 0.7262614369392395 True -11 32784 29.490652561187744 1.4990971088409424 984.5026245117188 0.8548961877822876 1443.434326171875 0.4947746992111206 0.6441162 0.7523546814918518 True -12 35516 29.53973150253296 0.7571585178375244 1047.22998046875 0.6391379833221436 1436.0313720703125 0.49748748540878296 0.6533366 0.7056012749671936 True -13 38248 29.553194046020508 0.7739517688751221 1069.24609375 0.6151916980743408 1427.7713623046875 0.5019063949584961 0.6593825 0.7027446627616882 True -14 40980 29.544403791427612 0.7757325172424316 1103.552490234375 0.7809336185455322 1423.8787841796875 0.5018178820610046 0.6692907 0.6790659427642822 True -15 43712 29.52711248397827 1.527923583984375 1009.9861450195312 0.4955630898475647 1417.1458740234375 0.5051165223121643 0.67663586 0.6772633790969849 True -16 46444 29.518107891082764 0.7621042728424072 1056.96533203125 0.8236773014068604 1416.4962158203125 0.5044841766357422 0.6811572 0.665753960609436 True -17 49176 29.47493553161621 0.7557022571563721 999.0213623046875 0.6825254559516907 1414.70556640625 0.505905270576477 0.68213993 0.6713652610778809 True -18 51908 29.49144220352173 0.7592628002166748 1011.9601440429688 0.3313591480255127 1417.6409912109375 0.5036720037460327 0.68168926 0.672016978263855 False -19 54640 29.551307439804077 0.7528958320617676 798.49267578125 0.6181328296661377 1414.367919921875 0.5073177814483643 0.67992246 0.676173746585846 False diff --git a/ENCSR503HIB/cherimoya.fold_1.performance.tsv b/ENCSR503HIB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bbf3b629f334bf36266840f6dd3f9b09c29b224a..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1414.70556640625 0.24577267467975616 0.5059052109718323 0.3213341236114502 0.6821399331092834 0.6294341087341309 0.6713652610778809 \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_2.evaluate.json b/ENCSR503HIB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index df789a1c0b0b40f3529d98a409d8eb5d4c029531..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF937XFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_2.fit.json b/ENCSR503HIB/cherimoya.fold_2.fit.json deleted file mode 100644 index a594e601fe78626d57b81e7c1e116bada111576c..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF937XFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_2.log b/ENCSR503HIB/cherimoya.fold_2.log deleted file mode 100644 index 89b40fe5e6db87880e8e241a8ed9e425fd56c962..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2883 36.58229041099548 4.071601152420044 1131.929443359375 1.1596736907958984 1644.417236328125 0.32187798619270325 0.40681386 9.30136489868164 True -1 5766 31.772756099700928 1.2634897232055664 1132.31396484375 1.0844879150390625 1420.8526611328125 0.4443705976009369 0.52417964 2.951349973678589 True -2 8649 31.844021558761597 0.5999941825866699 1205.1312255859375 0.9863570332527161 1386.8563232421875 0.45747989416122437 0.550225 1.2091825008392334 True -3 11532 31.81228542327881 0.6319644451141357 1098.3621826171875 1.1523869037628174 1375.54541015625 0.4621294438838959 0.56265366 0.9794468879699707 True -4 14415 31.803102016448975 0.640505313873291 1158.2935791015625 1.415302038192749 1361.7017822265625 0.47008293867111206 0.57384145 0.8184371590614319 True -5 17298 31.462831735610962 0.5912041664123535 1026.1209716796875 1.0830016136169434 1356.2418212890625 0.4719276428222656 0.57683885 0.7663692235946655 True -6 20181 31.207581996917725 0.6152803897857666 1178.660888671875 0.8358851671218872 1345.9837646484375 0.4783015251159668 0.58813596 0.7681310176849365 True -7 23064 31.1943621635437 0.5876014232635498 943.5961303710938 0.7736208438873291 1345.5313720703125 0.476182758808136 0.59316707 0.75135737657547 True -8 25947 31.229605436325073 0.6041772365570068 1199.930419921875 0.9761834144592285 1336.7275390625 0.482028067111969 0.5955124 0.7058505415916443 True -9 28830 31.259149312973022 0.6190164089202881 1134.93359375 0.6797492504119873 1328.34228515625 0.48606225848197937 0.60603374 0.6673903465270996 True -10 31713 31.266249418258667 0.6168525218963623 1032.66455078125 0.7487989664077759 1325.871337890625 0.48689746856689453 0.61215633 0.647066056728363 True -11 34596 31.219016075134277 0.6045174598693848 1028.535400390625 0.872347891330719 1321.432861328125 0.4871360957622528 0.6187316 0.6400577425956726 True -12 37479 31.233506202697754 0.6011350154876709 1012.3917236328125 0.6366651654243469 1313.4366455078125 0.4924221336841583 0.6281312 0.6292040944099426 True -13 40362 31.226238489151 0.6110033988952637 901.49853515625 0.673396110534668 1309.593505859375 0.49354347586631775 0.634509 0.6281168460845947 True -14 43245 31.274665117263794 0.6076946258544922 1222.2635498046875 0.6287643313407898 1308.080078125 0.49410417675971985 0.64214635 0.6216040253639221 True -15 46128 31.145414113998413 27.15356731414795 1044.1163330078125 0.7030806541442871 1297.3922119140625 0.5012834668159485 0.64933985 0.6197817325592041 True -16 49011 31.29068899154663 0.6557271480560303 1142.477783203125 0.6332396864891052 1299.569580078125 0.4988485276699066 0.65267766 0.621903657913208 True -17 51894 34.04148054122925 0.6020352840423584 881.668212890625 0.39801472425460815 1303.00048828125 0.49667635560035706 0.65534437 0.6357851624488831 True -18 54777 31.254348278045654 0.6007828712463379 851.2802734375 0.7252132892608643 1304.2420654296875 0.49536633491516113 0.6551651 0.644707441329956 False -19 57660 31.174957036972046 0.599118709564209 1081.237548828125 0.3800763487815857 1297.0936279296875 0.5026566982269287 0.65281487 0.6581352353096008 False diff --git a/ENCSR503HIB/cherimoya.fold_2.performance.tsv b/ENCSR503HIB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d81de5f9731229217f2da4920dd2691b24c136c6..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1303.00048828125 0.2557995319366455 0.49667638540267944 0.30312952399253845 0.6553443670272827 0.5993350744247437 0.6357851624488831 \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_3.evaluate.json b/ENCSR503HIB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 67c11a01b585a1d1c4a4eeba0c6db9e7ea3809b8..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF937XFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_3.fit.json b/ENCSR503HIB/cherimoya.fold_3.fit.json deleted file mode 100644 index 03e2b08f345a4f13cc126d1ef90a0190326ade4a..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF937XFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_3.log b/ENCSR503HIB/cherimoya.fold_3.log deleted file mode 100644 index 186d1e69d8fcba58af5c548335230db0404624ef..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2815 35.79929852485657 3.810896873474121 1363.415283203125 1.257115364074707 1672.865234375 0.3332337439060211 0.48273644 11.904967308044434 True -1 5630 31.0493004322052 0.5518534183502197 1045.363525390625 1.1373989582061768 1471.1151123046875 0.43878158926963806 0.5239572 3.3821980953216553 True -2 8445 31.091888904571533 0.5544190406799316 1040.197021484375 1.2466471195220947 1438.0439453125 0.4539218842983246 0.51146716 1.5759272575378418 False -3 11260 30.466094493865967 0.5883729457855225 1229.8922119140625 1.0071834325790405 1428.0858154296875 0.455280065536499 0.5330587 1.2451202869415283 True -4 14075 30.44959545135498 0.6472725868225098 1200.02783203125 1.0904103517532349 1411.102294921875 0.46809762716293335 0.5473114 1.0923962593078613 True -5 16890 30.432871341705322 0.5377049446105957 1113.9359130859375 0.9050571322441101 1401.896484375 0.4685850441455841 0.5579607 0.9599112868309021 True -6 19705 30.433151483535767 0.9071276187896729 989.3951416015625 0.8051130771636963 1395.5250244140625 0.4722000062465668 0.5648257 0.8750928640365601 True -7 22520 30.439804315567017 0.5784165859222412 1119.703857421875 0.7628202438354492 1385.79150390625 0.4767153561115265 0.5791362 0.8493162393569946 True -8 25335 30.52967405319214 0.8712906837463379 1116.594482421875 0.9673687815666199 1383.2000732421875 0.4771122336387634 0.5862501 0.7773687243461609 True -9 28150 30.413143157958984 0.6080403327941895 1174.0687255859375 0.5410394668579102 1376.5899658203125 0.48083242774009705 0.58795863 0.7598421573638916 True -10 30965 30.450187921524048 1.561438798904419 837.8414916992188 1.604332447052002 1365.4664306640625 0.4868941903114319 0.60121983 0.7084227204322815 True -11 33780 30.456523656845093 1.1049621105194092 1301.1572265625 0.8862618803977966 1366.3070068359375 0.48369261622428894 0.6115783 0.7009742259979248 True -12 36595 30.4598491191864 0.7392575740814209 1205.0318603515625 0.9054666757583618 1358.909912109375 0.4878048002719879 0.6192168 0.6802982687950134 True -13 39410 30.481208086013794 0.5430343151092529 1049.263671875 0.7883732318878174 1346.7122802734375 0.49485164880752563 0.62896127 0.6612865924835205 True -14 42225 30.372589111328125 0.5390143394470215 953.4349365234375 0.6372958421707153 1344.7216796875 0.49485427141189575 0.63777626 0.6522167921066284 True -15 45040 30.355939149856567 14.158442497253418 1185.2913818359375 0.7013596892356873 1346.49609375 0.49287542700767517 0.6467692 0.6536769270896912 True -16 47855 30.48330068588257 0.8646690845489502 929.1650390625 0.44338464736938477 1343.1727294921875 0.4957663416862488 0.65350133 0.6507067084312439 True -17 50670 30.459693431854248 0.5486085414886475 1064.1629638671875 1.0668573379516602 1344.2174072265625 0.4948817789554596 0.65856874 0.6523644924163818 True -18 53485 30.47725749015808 0.5412347316741943 950.2760009765625 0.6714674830436707 1345.9735107421875 0.49295011162757874 0.65942657 0.656865656375885 True -19 56300 30.41455388069153 1.0306799411773682 1041.294921875 0.9309998750686646 1345.63232421875 0.4931923449039459 0.65878785 0.666311502456665 False diff --git a/ENCSR503HIB/cherimoya.fold_3.performance.tsv b/ENCSR503HIB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c9e83dca976289a8dd51a2e030b4ffa89c984a7c..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1345.9735107421875 0.2552493214607239 0.4929501414299011 0.3059241473674774 0.6594265699386597 0.6135470271110535 0.656865656375885 \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_4.evaluate.json b/ENCSR503HIB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 49b0a50ea6939db13f1340547e3bc2dfe0297848..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF937XFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_4.fit.json b/ENCSR503HIB/cherimoya.fold_4.fit.json deleted file mode 100644 index 0545980362c6fc92b531486ca7eb592f8bacec7c..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF937XFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503HIB/cherimoya.fold_4.log b/ENCSR503HIB/cherimoya.fold_4.log deleted file mode 100644 index 652c5c00dd0be34b3591fe6a42d28b239c7768a7..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2855 36.28346347808838 4.405566453933716 1057.0164794921875 1.2250609397888184 1608.3360595703125 0.3347429931163788 0.43154395 9.231851577758789 True -1 5710 31.491276025772095 0.5918262004852295 1232.700927734375 1.0001628398895264 1418.18603515625 0.44324350357055664 0.49138302 2.062995195388794 True -2 8565 30.871966123580933 0.5477397441864014 949.35791015625 1.44710111618042 1396.2496337890625 0.45110079646110535 0.50988597 1.3188893795013428 True -3 11420 30.83295202255249 0.5613319873809814 1192.0242919921875 0.9021228551864624 1385.1390380859375 0.4557320475578308 0.5167497 0.9996503591537476 True -4 14275 30.825018882751465 0.5542478561401367 903.5680541992188 0.8265764117240906 1369.3544921875 0.4646550714969635 0.531707 0.8111704587936401 True -5 17130 30.788947343826294 0.549504280090332 993.759033203125 0.9559900164604187 1364.666748046875 0.4657152593135834 0.5382845 0.8390077948570251 True -6 19985 31.77829670906067 21.42101287841797 1026.4752197265625 0.890643835067749 1357.8636474609375 0.46863681077957153 0.53513736 0.7893055081367493 False -7 22840 30.874916791915894 1.4825546741485596 1230.7720947265625 0.8072978258132935 1354.5509033203125 0.4687209129333496 0.55489284 0.7440426349639893 True -8 25695 30.894378900527954 0.5575578212738037 1146.1890869140625 1.0297892093658447 1343.56591796875 0.4763806164264679 0.56193215 0.7311822175979614 True -9 28550 30.796266794204712 0.5495040416717529 1127.260498046875 0.842361569404602 1340.2784423828125 0.4786893427371979 0.5678333 0.7159988284111023 True -10 31405 30.81299924850464 0.5507380962371826 1177.494140625 0.8479659557342529 1330.7589111328125 0.48482295870780945 0.57677984 0.6978143453598022 True -11 34260 30.80494713783264 1.8079051971435547 893.788818359375 0.6528920531272888 1328.645751953125 0.48450967669487 0.5882024 0.6753127574920654 True -12 37115 30.865707874298096 0.5530178546905518 1211.65478515625 1.283677577972412 1322.13134765625 0.4885704219341278 0.5908358 0.6776891946792603 True -13 39970 30.797150373458862 0.5470452308654785 1171.49755859375 0.6231856346130371 1315.227783203125 0.4932052791118622 0.59889305 0.6846325993537903 True -14 42825 30.83781385421753 0.5612890720367432 1054.5499267578125 0.6166195869445801 1313.668701171875 0.49218693375587463 0.60850143 0.6710817813873291 True -15 45680 30.843612909317017 0.5527503490447998 1223.33984375 0.6778032183647156 1312.1798095703125 0.49261465668678284 0.61537665 0.6690139770507812 True -16 48535 30.808982610702515 0.5468409061431885 949.6791381835938 0.7180155515670776 1307.1798095703125 0.4963389039039612 0.6212176 0.6682483553886414 True -17 51390 30.806052446365356 0.5520110130310059 1112.6717529296875 0.6037752628326416 1307.4683837890625 0.4948606491088867 0.62633103 0.6716698408126831 True -18 54245 30.792479038238525 0.5614469051361084 851.9156494140625 0.6595065593719482 1305.4884033203125 0.49677610397338867 0.6266991 0.6850287318229675 True -19 57100 30.822394371032715 0.5521829128265381 930.185546875 0.6085793375968933 1305.2086181640625 0.49685269594192505 0.6253942 0.6882662773132324 False diff --git a/ENCSR503HIB/cherimoya.fold_4.performance.tsv b/ENCSR503HIB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5246bf8b8081ffabab6afdb97cdc7e744cc6cbf6..0000000000000000000000000000000000000000 --- a/ENCSR503HIB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1305.4884033203125 0.2546962797641754 0.49677610397338867 0.3043312132358551 0.6266990900039673 0.5673747658729553 0.6850287318229675 \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_0.evaluate.json b/ENCSR503RWO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6ea50099359c37ad84547f8d8951045125319b5a..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123IGV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_0.fit.json b/ENCSR503RWO/cherimoya.fold_0.fit.json deleted file mode 100644 index ca32d7eeb9083218ee7ce34c6177b940952487aa..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF123IGV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_0.log b/ENCSR503RWO/cherimoya.fold_0.log deleted file mode 100644 index a4a4dcda03ab411c921ce0a2a4751dd561b71770..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 36.53253245353699 3.891496181488037 769.1533813476562 0.59746253490448 1205.8289794921875 0.27295106649398804 0.4972393 10.490944862365723 True -1 5496 30.314520597457886 0.5632479190826416 867.43505859375 0.8480504751205444 1023.139892578125 0.3645654618740082 0.6156213 4.7368059158325195 True -2 8244 30.276169538497925 1.168686866760254 804.4268188476562 0.9637478590011597 1006.7213134765625 0.37336522340774536 0.62660795 2.827826499938965 True -3 10992 30.63029170036316 23.749698877334595 774.736083984375 0.6707178950309753 999.8741455078125 0.37521663308143616 0.6361907 2.4267497062683105 True -4 13740 30.33460807800293 0.6839561462402344 854.9755859375 0.6487016677856445 986.4691162109375 0.38277506828308105 0.64539546 2.4733479022979736 True -5 16488 30.342525243759155 0.5617270469665527 801.156494140625 0.6978219747543335 982.28466796875 0.38394588232040405 0.63657224 1.9517656564712524 False -6 19236 30.233885526657104 0.5599861145019531 844.417724609375 0.8573395013809204 968.2337036132812 0.39029574394226074 0.66533077 1.677215337753296 True -7 21984 30.245670795440674 0.5604007244110107 886.1044921875 0.7131743431091309 955.7735595703125 0.39796724915504456 0.6791535 1.4508554935455322 True -8 24732 30.23445749282837 0.5461325645446777 640.5109252929688 0.6203577518463135 953.5388793945312 0.3973948657512665 0.68904984 1.2214072942733765 True -9 27480 30.233679056167603 0.552865743637085 890.036376953125 0.8495713472366333 946.5283203125 0.4004228413105011 0.700155 1.1519839763641357 True -10 30228 30.267351150512695 0.5498929023742676 789.3770751953125 0.5765265226364136 942.2920532226562 0.40262937545776367 0.70949286 0.9919101595878601 True -11 32976 30.314374446868896 0.5602865219116211 806.5821533203125 0.6858948469161987 933.7960205078125 0.4068257212638855 0.71933645 0.9487782120704651 True -12 35724 30.251599073410034 0.5621278285980225 882.4517822265625 0.7841708660125732 929.6951293945312 0.4074280858039856 0.7308804 0.8110722899436951 True -13 38472 30.33934760093689 0.558661937713623 828.9515991210938 0.5484969615936279 920.9572143554688 0.41227951645851135 0.7402615 0.7393962144851685 True -14 41220 30.275165796279907 0.5611622333526611 600.758056640625 0.3875117301940918 915.044921875 0.41574960947036743 0.74995285 0.6679111123085022 True -15 43968 30.345553398132324 0.548018217086792 728.15283203125 0.4373699426651001 911.62890625 0.41582274436950684 0.756175 0.5917522311210632 True -16 46716 30.23924493789673 0.564699649810791 832.865478515625 0.39210397005081177 910.498291015625 0.41611629724502563 0.7613821 0.5582475066184998 True -17 49464 30.35804557800293 1.581665277481079 746.2981567382812 0.4607424736022949 907.489501953125 0.4188048839569092 0.7620105 0.5340156555175781 True -18 52212 30.292919635772705 0.5680091381072998 754.35498046875 0.36228877305984497 911.0476684570312 0.4158012270927429 0.7612976 0.5282054543495178 False -19 54960 30.26769208908081 0.5827951431274414 793.7012939453125 0.27471452951431274 909.7611083984375 0.4175490140914917 0.7610516 0.5296851992607117 False diff --git a/ENCSR503RWO/cherimoya.fold_0.performance.tsv b/ENCSR503RWO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index dd552ada39fa82ead8666119644057beccbb6a8d..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -907.489501953125 0.36300718784332275 0.4188048839569092 0.18781518936157227 0.7620105147361755 0.7196266651153564 0.5340156555175781 \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_1.evaluate.json b/ENCSR503RWO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 55435c47c600a74328efa19c04cfb100d000a313..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123IGV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_1.fit.json b/ENCSR503RWO/cherimoya.fold_1.fit.json deleted file mode 100644 index 061ca92ef36045c7fac3fba3660b580df59c4a5a..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF123IGV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_1.log b/ENCSR503RWO/cherimoya.fold_1.log deleted file mode 100644 index 50a4bb888819bbb1e5bd2911616148fe5f14bfef..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2716 33.699800968170166 3.6856064796447754 704.7769775390625 0.6376441717147827 1375.24169921875 0.27214205265045166 0.55107397 11.141881942749023 True -1 5432 29.90934681892395 1.6991691589355469 760.211669921875 0.818848729133606 1175.73681640625 0.3698557913303375 0.65171206 5.003729820251465 True -2 8148 29.90642809867859 0.7437407970428467 810.9072265625 0.9618183374404907 1143.3016357421875 0.3844763934612274 0.6674039 2.9095354080200195 True -3 10864 29.949072122573853 0.720637321472168 844.0553588867188 0.8818973898887634 1134.1754150390625 0.3888392746448517 0.67099315 2.6633243560791016 True -4 13580 29.926122665405273 0.7195026874542236 793.6015625 0.7939960956573486 1110.3839111328125 0.4009476602077484 0.6907337 2.448427438735962 True -5 16296 29.938237190246582 0.7252492904663086 762.7529296875 0.6327812671661377 1101.8101806640625 0.40203621983528137 0.70681864 2.310426712036133 True -6 19012 29.95218801498413 0.7198276519775391 870.8798217773438 0.8149250745773315 1089.171875 0.40811288356781006 0.71286315 1.6935049295425415 True -7 21728 29.937336683273315 0.72456955909729 761.5791015625 0.4288998246192932 1083.958251953125 0.40950673818588257 0.7258674 1.5180813074111938 True -8 24444 29.908788204193115 0.724048376083374 870.9542236328125 0.5625855326652527 1075.8035888671875 0.4141692817211151 0.7330551 1.34075129032135 True -9 27160 29.87473464012146 0.7274203300476074 724.2926025390625 0.67592453956604 1068.2476806640625 0.41754451394081116 0.7420067 1.2374142408370972 True -10 29876 29.88943600654602 0.7710094451904297 794.6163330078125 0.7440916895866394 1062.9034423828125 0.41971176862716675 0.7444639 1.1554235219955444 True -11 32592 29.891261339187622 2.184152603149414 805.5706787109375 0.5817518830299377 1050.35009765625 0.42567935585975647 0.7617676 0.9371193647384644 True -12 35308 29.94882583618164 0.7174522876739502 716.58154296875 0.539520800113678 1043.319091796875 0.4276634752750397 0.77142674 0.8241032361984253 True -13 38024 29.9552218914032 0.7231202125549316 716.0459594726562 0.6723083853721619 1034.79248046875 0.430682510137558 0.7779624 0.7347924709320068 True -14 40740 29.86465549468994 0.7365450859069824 733.338623046875 0.45591774582862854 1024.4749755859375 0.4349862039089203 0.78751034 0.6247677803039551 True -15 43456 29.958709955215454 0.7068314552307129 731.6376342773438 0.4362980127334595 1021.9348754882812 0.43567296862602234 0.79533905 0.5734509229660034 True -16 46172 29.91115140914917 14.510299682617188 730.7755737304688 0.40129995346069336 1021.011962890625 0.43462181091308594 0.79856783 0.5322323441505432 True -17 48888 30.053756713867188 0.7191059589385986 795.0379638671875 0.5235432386398315 1022.9521484375 0.4324197471141815 0.8000119 0.5004742741584778 True -18 51604 29.92213535308838 0.7233796119689941 690.15869140625 0.45216912031173706 1018.1256103515625 0.43669748306274414 0.8012636 0.49063029885292053 True -19 54320 29.97718572616577 0.7154145240783691 783.282958984375 0.20296448469161987 1019.9111938476562 0.4356020390987396 0.7982504 0.48970115184783936 False diff --git a/ENCSR503RWO/cherimoya.fold_1.performance.tsv b/ENCSR503RWO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c5721de9b5d47df734d86245e985140209ec9ea1..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1018.1256103515625 0.34691959619522095 0.43669745326042175 0.20667293667793274 0.8012635707855225 0.7744919061660767 0.49063029885292053 \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_2.evaluate.json b/ENCSR503RWO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cde623fbf1b094e05ae5584c6fb78ebdd9648bb9..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123IGV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_2.fit.json b/ENCSR503RWO/cherimoya.fold_2.fit.json deleted file mode 100644 index 3dab4e4ab40ac14b63ec71774dd16368451bc6b8..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF123IGV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_2.log b/ENCSR503RWO/cherimoya.fold_2.log deleted file mode 100644 index 26992b80fffd2ea16476aeee52dd8344f8261985..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2865 35.21116852760315 3.606501340866089 890.4775390625 0.795025110244751 1253.35400390625 0.27146032452583313 0.5021175 9.310494422912598 True -1 5730 31.6194064617157 0.8548121452331543 982.6672973632812 0.8537623882293701 1074.4398193359375 0.3604556918144226 0.60763466 4.531295299530029 True -2 8595 31.605611562728882 0.6932528018951416 755.5877685546875 0.777104377746582 1063.8736572265625 0.36856117844581604 0.6174619 3.1298506259918213 True -3 11460 31.64675521850586 0.6780674457550049 655.5318603515625 0.9796309471130371 1044.840087890625 0.37512263655662537 0.630435 2.635143280029297 True -4 14325 31.592877864837646 0.7115700244903564 756.9967041015625 1.059126615524292 1035.72509765625 0.3776110112667084 0.63535917 2.417377471923828 True -5 17190 31.59775424003601 2.036400556564331 729.6138916015625 0.740084171295166 1012.1268310546875 0.386064350605011 0.6697727 1.7870267629623413 True -6 20055 31.608645915985107 0.598224401473999 689.813720703125 0.6103185415267944 1005.3717041015625 0.3899698555469513 0.6807899 1.805078387260437 True -7 22920 31.584452152252197 0.6016764640808105 816.9904174804688 0.7188625931739807 995.9163208007812 0.3960408866405487 0.6910961 1.5922185182571411 True -8 25785 31.582601308822632 0.5930662155151367 917.5179443359375 0.6030901074409485 993.9093627929688 0.39620688557624817 0.6973134 1.4250155687332153 True -9 28650 31.54931664466858 0.5963850021362305 780.87451171875 0.54676353931427 984.7932739257812 0.402039498090744 0.70865226 1.244503378868103 True -10 31515 31.543922901153564 0.5900404453277588 730.019775390625 0.513701319694519 980.6116943359375 0.4031507670879364 0.71930677 1.1456350088119507 True -11 34380 31.506139516830444 0.7017335891723633 688.9588623046875 0.5438993573188782 973.5473022460938 0.4063360095024109 0.7301235 0.977533757686615 True -12 37245 31.62407636642456 0.6013445854187012 692.2279052734375 0.4974972605705261 967.740234375 0.4088357090950012 0.73743254 0.8412718772888184 True -13 40110 31.59999966621399 0.5827817916870117 773.0780639648438 0.51275235414505 958.7857055664062 0.41461479663848877 0.75078094 0.7181500196456909 True -14 42975 31.586079597473145 0.5999929904937744 755.375 0.4328825771808624 953.7926635742188 0.416715145111084 0.76129204 0.6391310095787048 True -15 45840 31.53511357307434 0.5892374515533447 739.7789916992188 0.5708124041557312 950.8242797851562 0.4162757098674774 0.7671588 0.5844054222106934 True -16 48705 31.504542589187622 0.5897612571716309 691.334716796875 0.3471774458885193 948.5916748046875 0.41705209016799927 0.7708352 0.5457245111465454 True -17 51570 31.583486318588257 0.5997278690338135 809.3909912109375 0.6024252772331238 949.1384887695312 0.41675612330436707 0.7749124 0.5188776254653931 True -18 54435 31.577504873275757 0.6843137741088867 862.29833984375 0.34488481283187866 948.6091918945312 0.4174891710281372 0.77445716 0.5126334428787231 False -19 57300 31.627888202667236 1.1097638607025146 805.862548828125 0.35155123472213745 950.067626953125 0.415732204914093 0.77492124 0.5124629139900208 True diff --git a/ENCSR503RWO/cherimoya.fold_2.performance.tsv b/ENCSR503RWO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8867a059d7d622955800bf30b8438b4b7f80bd47..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -950.067626953125 0.3606989085674286 0.4157322347164154 0.19237719476222992 0.7749212384223938 0.7401326298713684 0.5124629139900208 \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_3.evaluate.json b/ENCSR503RWO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 24c0f3a71192e142b600e33519ee3b5401bd7e77..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123IGV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_3.fit.json b/ENCSR503RWO/cherimoya.fold_3.fit.json deleted file mode 100644 index bb9abbb70352c7d45e9926027cf041662b595cc5..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF123IGV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_3.log b/ENCSR503RWO/cherimoya.fold_3.log deleted file mode 100644 index e42a689517cc22ec72c77c72b114b1686034f59f..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 34.27764844894409 49.14702272415161 815.88671875 0.5888593196868896 1171.614990234375 0.27936768531799316 0.48169982 11.370279312133789 True -1 5534 30.71923041343689 2.339796543121338 985.4898681640625 0.7738912105560303 1011.8396606445312 0.3625980615615845 0.58718526 5.603139400482178 True -2 8301 30.7059268951416 0.5627133846282959 779.7281494140625 0.864877462387085 984.58837890625 0.3755567669868469 0.61675006 3.406033992767334 True -3 11068 30.65222191810608 0.5608150959014893 962.9969482421875 0.7382075190544128 970.0231323242188 0.3819018602371216 0.63843507 2.641883611679077 True -4 13835 30.640226125717163 1.4631986618041992 772.8547973632812 0.8938659429550171 964.2584228515625 0.3851351737976074 0.6296586 2.8144211769104004 False -5 16602 30.71619749069214 0.5586230754852295 891.0707397460938 0.6918784379959106 942.9898681640625 0.39495187997817993 0.6638547 2.039975643157959 True -6 19369 30.764893054962158 0.5633978843688965 937.4429931640625 0.8139569759368896 936.019287109375 0.3978298604488373 0.674637 1.7150968313217163 True -7 22136 30.6732075214386 2.0249016284942627 814.8358154296875 0.6816344857215881 928.6864624023438 0.402671754360199 0.6876389 1.4920648336410522 True -8 24903 30.654284715652466 0.5612471103668213 870.9262084960938 0.7175569534301758 921.6137084960938 0.40734583139419556 0.6946645 1.3483494520187378 True -9 27670 30.650820016860962 0.544621467590332 695.687255859375 0.6194000244140625 916.5272216796875 0.4112893342971802 0.70016295 1.2919868230819702 True -10 30437 30.677483081817627 0.5588412284851074 819.602294921875 0.6719760894775391 909.0787353515625 0.41380488872528076 0.71554303 1.1000760793685913 True -11 33204 30.66630482673645 0.5603265762329102 931.42578125 0.5479950904846191 903.3648071289062 0.416610985994339 0.72348964 0.9960359334945679 True -12 35971 30.665835857391357 0.5495195388793945 889.044189453125 0.7244915962219238 898.7051391601562 0.4194437563419342 0.72906846 0.9131544828414917 True -13 38738 30.525603532791138 0.5436718463897705 644.68017578125 0.5305675268173218 892.7808227539062 0.4228043556213379 0.74088115 0.7712143063545227 True -14 41505 30.051628589630127 0.5397307872772217 814.91748046875 0.5971395969390869 889.5286254882812 0.42309334874153137 0.74971586 0.6822898983955383 True -15 44272 30.047425508499146 0.5444676876068115 743.52099609375 0.7629222273826599 883.7396240234375 0.4268982708454132 0.7598286 0.6179930567741394 True -16 47039 30.046644926071167 1.3078393936157227 829.5603637695312 0.6839762330055237 883.937744140625 0.42616894841194153 0.76277876 0.5675167441368103 True -17 49806 30.04672932624817 0.5498659610748291 759.1846923828125 0.5280161499977112 880.5983276367188 0.42865681648254395 0.76620084 0.5326055884361267 True -18 52573 30.09567928314209 0.5523231029510498 741.6067504882812 0.49808835983276367 882.2217407226562 0.42699629068374634 0.76552016 0.5212610960006714 False -19 55340 30.124675750732422 0.5529711246490479 865.9492797851562 0.49317532777786255 883.2560424804688 0.4257839024066925 0.7656684 0.5200511813163757 False diff --git a/ENCSR503RWO/cherimoya.fold_3.performance.tsv b/ENCSR503RWO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f82654cfb21696e96e06f4a911da6f5401993e9e..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -880.5983276367188 0.35862961411476135 0.42865684628486633 0.19106486439704895 0.766200840473175 0.7243621349334717 0.5326055884361267 \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_4.evaluate.json b/ENCSR503RWO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 71c3267100d069cf5efe1d75d0ce4589eb4f4aca..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123IGV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_4.fit.json b/ENCSR503RWO/cherimoya.fold_4.fit.json deleted file mode 100644 index ec4fdf214884fec927c93fdbcb4c50c51a1a21fe..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF123IGV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503RWO/cherimoya.fold_4.log b/ENCSR503RWO/cherimoya.fold_4.log deleted file mode 100644 index eabb2aa83d0a5b530655134482d4c82c2c7990da..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 35.03907489776611 3.633152961730957 911.8089599609375 1.1361615657806396 1118.9552001953125 0.26853203773498535 0.49487326 9.424169540405273 True -1 5584 31.057433128356934 0.5657370090484619 756.97021484375 0.6857509613037109 966.484130859375 0.35234716534614563 0.60916746 4.109588623046875 True -2 8376 30.96921944618225 0.5544748306274414 867.821533203125 0.8931406736373901 947.5355224609375 0.36243736743927 0.6284669 2.55370831489563 True -3 11168 30.956531286239624 0.5472927093505859 782.4463500976562 0.7175443172454834 933.5537719726562 0.36781394481658936 0.6404465 2.366000175476074 True -4 13960 30.950003147125244 0.5545864105224609 818.4566650390625 0.5460925102233887 921.1920166015625 0.3730483055114746 0.65429926 1.948919415473938 True -5 16752 30.501190423965454 0.550194501876831 905.9449462890625 0.6815756559371948 916.4423828125 0.37395811080932617 0.66223556 1.7156357765197754 True -6 19544 30.32007336616516 0.5492701530456543 755.415771484375 0.5607225298881531 903.7842407226562 0.38279253244400024 0.6764015 1.5043447017669678 True -7 22336 30.405065298080444 0.5394845008850098 740.5137329101562 0.6821292638778687 897.5692749023438 0.38492605090141296 0.684269 1.365338683128357 True -8 25128 30.39501428604126 1.0875005722045898 769.547607421875 0.5089505910873413 891.1425170898438 0.3893366754055023 0.6947335 1.1851129531860352 True -9 27920 30.437502145767212 0.5675127506256104 850.1373291015625 0.936516523361206 888.56103515625 0.39039385318756104 0.7026416 1.0329772233963013 True -10 30712 30.475496530532837 0.5422115325927734 719.5167236328125 0.658588707447052 882.3687744140625 0.3934869170188904 0.7125801 0.9175288081169128 True -11 33504 30.461822032928467 0.5556902885437012 695.8071899414062 0.6724568605422974 876.866943359375 0.396643728017807 0.7236376 0.807880163192749 True -12 36296 30.41598653793335 0.5596203804016113 798.78564453125 0.41227370500564575 873.3427124023438 0.3975764811038971 0.7362643 0.7144567966461182 True -13 39088 30.711877822875977 0.5475809574127197 616.372802734375 0.6181981563568115 865.947021484375 0.40209296345710754 0.74256074 0.6370893716812134 True -14 41880 30.699660778045654 22.739743947982788 762.6687622070312 0.41904380917549133 862.5667114257812 0.40398624539375305 0.7518775 0.5774469375610352 True -15 44672 30.494926929473877 0.5570876598358154 707.528564453125 0.6082577705383301 859.1099853515625 0.40434035658836365 0.7610046 0.5313916206359863 True -16 47464 30.38613510131836 0.5416004657745361 710.2244873046875 0.3136780261993408 856.6282958984375 0.40609437227249146 0.7651249 0.5015170574188232 True -17 50256 30.41693902015686 0.5643472671508789 875.9623413085938 0.3380427360534668 856.1077880859375 0.40745946764945984 0.76819 0.4871528148651123 True -18 53048 30.393949270248413 0.5463724136352539 629.673095703125 0.4514198899269104 858.08349609375 0.4048612117767334 0.7657441 0.48682865500450134 False -19 55840 31.44771695137024 0.5517446994781494 679.3155517578125 0.4302442669868469 858.0763549804688 0.40516597032546997 0.7649268 0.4891141653060913 False diff --git a/ENCSR503RWO/cherimoya.fold_4.performance.tsv b/ENCSR503RWO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 695773deaab7a6bd5c86be2f240f7f859ed3840e..0000000000000000000000000000000000000000 --- a/ENCSR503RWO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -856.1077880859375 0.37093114852905273 0.40745946764945984 0.1812499612569809 0.7681900262832642 0.7189845442771912 0.4871528148651123 \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_0.evaluate.json b/ENCSR503UFM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ca2be9085cf9d42275a7e2d0cf1b9a78bf092253..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743PAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_0.fit.json b/ENCSR503UFM/cherimoya.fold_0.fit.json deleted file mode 100644 index 55eac5c7f4754fd5f89da91270f1ec15af033835..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF743PAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_0.log b/ENCSR503UFM/cherimoya.fold_0.log deleted file mode 100644 index 80ec610208dcd89b2d026c613d000ed57fdee66d..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 34.78400993347168 3.853315830230713 444.09051513671875 0.38448843359947205 569.0137939453125 0.2718468904495239 0.7351059 3.24672269821167 True -1 5482 30.180737733840942 0.6127190589904785 419.1541748046875 0.4431777000427246 526.5463256835938 0.33906352519989014 0.7939513 0.8764721751213074 True -2 8223 30.156588554382324 0.6024277210235596 448.2557373046875 0.3025099039077759 518.980224609375 0.34942159056663513 0.80402917 0.47614049911499023 True -3 10964 30.187286376953125 12.042445659637451 436.7967224121094 0.3773730993270874 514.7897338867188 0.3549222946166992 0.81229085 0.5705288052558899 True -4 13705 30.188703060150146 0.5999927520751953 408.7052917480469 0.3504558503627777 513.2012329101562 0.3575306534767151 0.8185165 0.36369597911834717 True -5 16446 30.14257049560547 0.5916292667388916 468.45745849609375 0.39366310834884644 512.0325317382812 0.36060839891433716 0.8205602 0.35640788078308105 True -6 19187 30.09045934677124 0.617487907409668 419.9455261230469 0.2636837959289551 511.3655090332031 0.36149391531944275 0.82576966 0.3321453034877777 True -7 21928 30.107595682144165 0.6050419807434082 403.3419189453125 0.30336886644363403 510.5918884277344 0.36158105731010437 0.8309674 0.3090425133705139 True -8 24669 29.961442708969116 0.5931310653686523 433.64599609375 0.3834972679615021 508.7472839355469 0.3651447296142578 0.83354926 0.29421135783195496 True -9 27410 29.573368072509766 0.6013495922088623 527.3198852539062 0.25803786516189575 507.751953125 0.3669595718383789 0.8375527 0.2833610475063324 True -10 30151 29.600454330444336 0.6383423805236816 432.017578125 0.3739408254623413 505.9195556640625 0.37021154165267944 0.84241885 0.27736178040504456 True -11 32892 29.584798336029053 0.6092948913574219 448.284423828125 0.1828726828098297 504.7021789550781 0.37210813164711 0.84616965 0.262809157371521 True -12 35633 29.569639682769775 0.5996215343475342 379.1470947265625 0.25268322229385376 503.50677490234375 0.37370428442955017 0.8487917 0.23812226951122284 True -13 38374 29.532118320465088 0.6026344299316406 490.833251953125 0.25900381803512573 503.26312255859375 0.37338513135910034 0.8530245 0.22488108277320862 True -14 41115 29.49450993537903 0.5945186614990234 387.929931640625 0.1872716248035431 501.6104431152344 0.37645038962364197 0.8589505 0.2128317952156067 True -15 43856 30.15732216835022 4.798980712890625 445.6380615234375 0.25049370527267456 500.526611328125 0.3785400092601776 0.8618516 0.20471616089344025 True -16 46597 29.545294761657715 1.098639726638794 462.1490478515625 0.21940100193023682 501.412841796875 0.3764483332633972 0.86379313 0.19972975552082062 True -17 49338 29.521201133728027 0.612736701965332 470.1277160644531 0.24710829555988312 500.4267883300781 0.378774493932724 0.8646503 0.19745098054409027 True -18 52079 29.491851091384888 0.5955874919891357 439.2076721191406 0.18317297101020813 500.5101318359375 0.3785494863986969 0.8652005 0.1955224871635437 True -19 54820 29.488198041915894 0.5927872657775879 399.5620422363281 0.1082814559340477 500.302734375 0.3793017864227295 0.86519265 0.19649966061115265 False diff --git a/ENCSR503UFM/cherimoya.fold_0.performance.tsv b/ENCSR503UFM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b53a29c4e40fc39fb27d07788c7c6d312674217a..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -500.5101318359375 0.3998398184776306 0.3785494863986969 0.14498624205589294 0.8652005195617676 0.8450700640678406 0.1955224871635437 \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_1.evaluate.json b/ENCSR503UFM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 882b12d53ff7cfdb0210e26fba58e95e905dd340..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743PAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_1.fit.json b/ENCSR503UFM/cherimoya.fold_1.fit.json deleted file mode 100644 index 8d82730fe908ff590c92498164c6d6bca2b01396..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF743PAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_1.log b/ENCSR503UFM/cherimoya.fold_1.log deleted file mode 100644 index fc21dbfd4e7072c70d9ccc6974fac28c227b99aa..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2696 34.558887004852295 3.9517886638641357 434.74249267578125 0.4275358021259308 663.21484375 0.2790345847606659 0.7369851 4.990706920623779 True -1 5392 29.660168170928955 1.7585911750793457 378.07220458984375 0.5640606880187988 610.5109252929688 0.35180389881134033 0.7877367 1.1277248859405518 True -2 8088 29.892932415008545 0.7012391090393066 463.9908142089844 0.35683542490005493 598.3754272460938 0.3649107813835144 0.80703634 0.5367664098739624 True -3 10784 29.870572328567505 39.08957028388977 438.61676025390625 0.48981016874313354 593.7293090820312 0.37052813172340393 0.81587243 0.5724037289619446 True -4 13480 29.886942625045776 0.7304506301879883 447.3758544921875 0.38390740752220154 591.0223388671875 0.3744303286075592 0.8201334 0.459236741065979 True -5 16176 29.6141459941864 0.7044613361358643 399.58673095703125 0.30493777990341187 588.9122924804688 0.3773579001426697 0.8242077 0.38073015213012695 True -6 18872 29.61680507659912 0.6967380046844482 418.7822570800781 0.37125375866889954 586.6663818359375 0.37949955463409424 0.8301512 0.3334890902042389 True -7 21568 29.56636929512024 0.6869943141937256 408.21844482421875 0.2484980672597885 585.2725830078125 0.3825337886810303 0.8318918 0.3359124958515167 True -8 24264 29.640597343444824 0.7049212455749512 447.90582275390625 0.5015134811401367 583.7392578125 0.38406288623809814 0.8352595 0.3230498731136322 True -9 26960 29.04641819000244 0.6800689697265625 391.8641052246094 0.19770145416259766 581.4884033203125 0.38717392086982727 0.8431515 0.3025609850883484 True -10 29656 29.02592897415161 0.6798450946807861 434.131591796875 0.21210315823554993 579.8026733398438 0.38890403509140015 0.8457024 0.28335267305374146 True -11 32352 28.996419429779053 0.676560640335083 424.3387451171875 0.19588062167167664 578.2337036132812 0.39072105288505554 0.8490995 0.2720421254634857 True -12 35048 28.96511936187744 0.6770215034484863 531.38720703125 0.21977466344833374 576.033447265625 0.3952336013317108 0.8550271 0.2596902847290039 True -13 37744 28.991774320602417 0.6758987903594971 411.2926940917969 0.2624207139015198 576.4176635742188 0.39293578267097473 0.8606093 0.2412436455488205 True -14 40440 28.985204696655273 0.6727511882781982 378.9215087890625 0.3123105466365814 573.9688720703125 0.39695051312446594 0.8652083 0.22996103763580322 True -15 43136 29.28999400138855 48.73573637008667 401.2199401855469 0.2790997624397278 572.6875610351562 0.3985120356082916 0.87190545 0.21783046424388885 True -16 45832 29.10655403137207 0.7019884586334229 474.8546142578125 0.2264786958694458 573.0820922851562 0.39684993028640747 0.8731427 0.21231649816036224 True -17 48528 28.979295253753662 0.6869640350341797 483.8900146484375 0.19622883200645447 572.207275390625 0.39908960461616516 0.875937 0.20959347486495972 True -18 51224 28.954112768173218 0.6876745223999023 442.5789489746094 0.16139015555381775 572.9214477539062 0.397722065448761 0.8760873 0.2089005410671234 True -19 53920 28.996400833129883 0.6841483116149902 352.92926025390625 0.1543152928352356 572.3213500976562 0.3993704915046692 0.87472636 0.20994554460048676 False diff --git a/ENCSR503UFM/cherimoya.fold_1.performance.tsv b/ENCSR503UFM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c92152a45fb53a80d02ce43490e72db76c9b93c6..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -572.9214477539062 0.3809763193130493 0.397722065448761 0.16402508318424225 0.8760873079299927 0.8634132146835327 0.2089005410671234 \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_2.evaluate.json b/ENCSR503UFM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0b0859efaf097bb6fbbbff6c1d673ced68941132..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743PAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_2.fit.json b/ENCSR503UFM/cherimoya.fold_2.fit.json deleted file mode 100644 index bdb6468dfb9e255768319295750d7a76eedbe7c2..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF743PAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_2.log b/ENCSR503UFM/cherimoya.fold_2.log deleted file mode 100644 index 4ed7be141045abdb0c5b7503d1798aa771a7e0fd..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 36.498472690582275 4.4207634925842285 486.4019775390625 0.3318774104118347 595.8760375976562 0.27792513370513916 0.74128383 3.3434810638427734 True -1 5762 31.708196878433228 1.1431245803833008 469.4454345703125 0.36051082611083984 552.1011962890625 0.34218060970306396 0.79410446 0.802184522151947 True -2 8643 31.732736825942993 0.5881326198577881 525.0831909179688 0.2875435948371887 543.71728515625 0.35369500517845154 0.80114406 0.4876706898212433 True -3 11524 31.76400852203369 0.5789334774017334 461.75921630859375 0.3062676191329956 539.6497192382812 0.35848507285118103 0.8088716 0.4530264735221863 True -4 14405 31.639793157577515 0.5786659717559814 463.88214111328125 0.3517211079597473 537.7744750976562 0.3604452908039093 0.8117027 0.3577108383178711 True -5 17286 32.281147480010986 33.17667770385742 474.86065673828125 0.3354765772819519 537.5224609375 0.35991886258125305 0.81486684 0.3309461176395416 True -6 20167 31.747960329055786 26.57649874687195 462.17724609375 0.31514981389045715 533.9249267578125 0.3663123846054077 0.82207954 0.2700326144695282 True -7 23048 32.22927117347717 1.6702637672424316 390.21295166015625 0.3677646517753601 532.2786254882812 0.3690395951271057 0.82392365 0.26842552423477173 True -8 25929 31.667524814605713 0.5620548725128174 382.4753723144531 0.2117958813905716 531.32568359375 0.3704521358013153 0.8290964 0.25848299264907837 True -9 28810 31.22378134727478 3.479276657104492 458.76416015625 0.21795032918453217 530.1043701171875 0.371839314699173 0.8329972 0.24165162444114685 True -10 31691 31.095548391342163 0.5605497360229492 436.82452392578125 0.3575166165828705 529.1144409179688 0.3731558918952942 0.8371751 0.23233060538768768 True -11 34572 31.04801106452942 0.5528616905212402 509.86016845703125 0.25463277101516724 527.5850830078125 0.3752438724040985 0.8427381 0.22826838493347168 True -12 37453 31.073789358139038 0.5618844032287598 409.2812194824219 0.1962406486272812 526.4732055664062 0.37691766023635864 0.8473447 0.22640332579612732 True -13 40334 31.027414560317993 0.558037519454956 421.20538330078125 0.33895260095596313 526.1611328125 0.3772447407245636 0.8526974 0.21723699569702148 True -14 43215 30.99300265312195 1.7412853240966797 402.5973205566406 0.21801355481147766 524.511474609375 0.37992772459983826 0.8551144 0.20928062498569489 True -15 46096 31.11810851097107 26.137414932250977 403.77716064453125 0.1693355143070221 524.1937866210938 0.38054290413856506 0.86006844 0.20602957904338837 True -16 48977 31.118000984191895 0.5602846145629883 385.593994140625 0.19007089734077454 523.5775756835938 0.3818640410900116 0.86210865 0.20099112391471863 True -17 51858 31.0434467792511 0.5552115440368652 429.35809326171875 0.2085506170988083 523.8931884765625 0.38093098998069763 0.86312586 0.2022664099931717 True -18 54739 31.061808347702026 0.5635113716125488 347.82177734375 0.20382747054100037 524.1475219726562 0.3803103566169739 0.86398643 0.20221088826656342 True -19 57620 31.03696370124817 0.5605020523071289 398.808349609375 0.0910177081823349 523.7421264648438 0.3813256323337555 0.8626351 0.20429570972919464 False diff --git a/ENCSR503UFM/cherimoya.fold_2.performance.tsv b/ENCSR503UFM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4150dce367825d6a79ab10c15755dac21c7c598d..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -524.1475219726562 0.39510130882263184 0.38031041622161865 0.14938364923000336 0.8639864325523376 0.8459706902503967 0.20221088826656342 \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_3.evaluate.json b/ENCSR503UFM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8ff7040eabc733ec460de9e8b666127ac2167a96..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743PAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_3.fit.json b/ENCSR503UFM/cherimoya.fold_3.fit.json deleted file mode 100644 index 597fbd8e714f159233a523113efdff1385231642..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF743PAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_3.log b/ENCSR503UFM/cherimoya.fold_3.log deleted file mode 100644 index 3166763c230e335221bf5ec7817b5125bb4216dd..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 35.1588020324707 21.06841731071472 497.0572509765625 0.47365978360176086 556.4337768554688 0.2811531126499176 0.7226801 4.329962253570557 True -1 5522 30.424386739730835 0.5383005142211914 499.97357177734375 0.47418269515037537 514.8377685546875 0.3427759110927582 0.78416926 0.8747343420982361 True -2 8283 30.074833154678345 1.0229485034942627 465.1911926269531 0.39970287680625916 506.3651428222656 0.3541041910648346 0.8058561 0.5438409447669983 True -3 11044 29.816370964050293 0.5174920558929443 461.7704772949219 0.26590389013290405 502.106201171875 0.3596736490726471 0.81632584 0.4696328639984131 True -4 13805 29.856451749801636 35.05464577674866 472.540771484375 0.5097360014915466 500.6307373046875 0.3622950613498688 0.82275116 0.3670834004878998 True -5 16566 30.177066564559937 0.5224840641021729 393.98870849609375 0.25250107049942017 499.17449951171875 0.364663302898407 0.8261937 0.32035183906555176 True -6 19327 29.89122176170349 0.5117089748382568 439.1211853027344 0.22378507256507874 498.7674255371094 0.36483603715896606 0.8253124 0.31580138206481934 False -7 22088 29.7426974773407 0.5151140689849854 383.3297119140625 0.22865143418312073 497.4489440917969 0.36651191115379333 0.8278097 0.29807934165000916 True -8 24849 30.111610651016235 0.5132644176483154 450.2003173828125 0.25581175088882446 495.92266845703125 0.36921367049217224 0.8333219 0.2932632565498352 True -9 27610 29.687485933303833 0.5150582790374756 478.1855773925781 0.2606125473976135 494.55133056640625 0.37138059735298157 0.8366282 0.28260481357574463 True -10 30371 29.653464794158936 0.5059177875518799 391.0368957519531 0.24761630594730377 493.8938903808594 0.3721025586128235 0.8403696 0.2691604197025299 True -11 33132 29.663272857666016 0.5047523975372314 471.81365966796875 0.18135206401348114 492.2349853515625 0.3753136396408081 0.84588134 0.25360965728759766 True -12 35893 29.778882026672363 0.5083858966827393 443.7944641113281 0.20005229115486145 491.4289245605469 0.37577885389328003 0.8503768 0.24266168475151062 True -13 38654 29.78421187400818 2.050154447555542 404.47955322265625 0.298376202583313 489.8108825683594 0.37788861989974976 0.85505444 0.23109018802642822 True -14 41415 29.884164094924927 1.1887788772583008 426.0025329589844 0.24554504454135895 489.2623291015625 0.37846556305885315 0.8602071 0.21952995657920837 True -15 44176 29.814497470855713 0.5151216983795166 445.3611145019531 0.24796025454998016 489.3395080566406 0.3783979117870331 0.86432153 0.2121938019990921 True -16 46937 29.755000114440918 0.5211474895477295 400.1205749511719 0.20545898377895355 488.11480712890625 0.38034677505493164 0.86799145 0.20513536036014557 True -17 49698 29.709556341171265 0.5108318328857422 452.52630615234375 0.2026730626821518 488.1034240722656 0.3797096610069275 0.87179965 0.2020406424999237 True -18 52459 29.855499982833862 0.5152616500854492 478.55950927734375 0.1356765627861023 487.5290832519531 0.3814924359321594 0.8691716 0.20162594318389893 False -19 55220 29.740442276000977 0.5170824527740479 461.38031005859375 0.1912471503019333 487.94061279296875 0.38052988052368164 0.87003374 0.2020953893661499 False diff --git a/ENCSR503UFM/cherimoya.fold_3.performance.tsv b/ENCSR503UFM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index aab14ea485cf600f0810910a5c89c662a74b7d57..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -488.1034240722656 0.400208979845047 0.3797096610069275 0.1452198624610901 0.871799647808075 0.8431121706962585 0.2020406424999237 \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_4.evaluate.json b/ENCSR503UFM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b250d0dfd9ed8c898f7e9701582923f1cc6f2d0b..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743PAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_4.fit.json b/ENCSR503UFM/cherimoya.fold_4.fit.json deleted file mode 100644 index 3d2c1592ddc0f5f532a369d3a3aff18881e3c910..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF743PAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR503UFM/cherimoya.fold_4.log b/ENCSR503UFM/cherimoya.fold_4.log deleted file mode 100644 index 1375ec632f21cb776308ed4d443dcef562696afa..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2822 36.905813455581665 4.175862789154053 407.0445251464844 0.43623489141464233 538.1303100585938 0.275634765625 0.724976 4.049436569213867 True -1 5644 31.108384609222412 4.555548667907715 423.97320556640625 0.36633002758026123 499.4898681640625 0.33907821774482727 0.7788749 0.7960904836654663 True -2 8466 31.028469562530518 0.5984828472137451 451.1087646484375 0.24220341444015503 494.1053161621094 0.3476196527481079 0.7823112 0.37288427352905273 True -3 11288 31.019679069519043 0.5936601161956787 436.6672058105469 0.3020389676094055 491.6198425292969 0.34796416759490967 0.79873574 0.3332366645336151 True -4 14110 33.158785581588745 0.9520308971405029 424.797607421875 0.2982832193374634 489.40350341796875 0.3517521023750305 0.80533385 0.28692564368247986 True -5 16932 31.011493682861328 0.5832362174987793 392.63031005859375 0.33222025632858276 487.9917297363281 0.3544245958328247 0.8136897 0.30448585748672485 True -6 19754 31.856048107147217 0.5893840789794922 469.8017578125 0.44914329051971436 487.1585693359375 0.3551807999610901 0.81745946 0.29828736186027527 True -7 22576 31.349673986434937 8.905334949493408 465.95343017578125 0.3901912569999695 485.6340026855469 0.35811811685562134 0.82234395 0.2841152846813202 True -8 25398 31.040931940078735 2.9968323707580566 412.0436096191406 0.31085291504859924 484.9438171386719 0.35890668630599976 0.8271922 0.2722261846065521 True -9 28220 31.095876693725586 0.5980980396270752 440.9498596191406 0.2514552175998688 484.2623596191406 0.3596104681491852 0.8288499 0.27530190348625183 True -10 31042 30.971402168273926 0.5891196727752686 409.5643005371094 0.20709499716758728 482.8367004394531 0.36295369267463684 0.83428854 0.25457414984703064 True -11 33864 31.02699303627014 0.5772738456726074 472.3326416015625 0.21941420435905457 480.9393005371094 0.3664294481277466 0.8410139 0.2341013252735138 True -12 36686 31.010627031326294 0.579890251159668 423.86871337890625 0.32397204637527466 481.14874267578125 0.3649437725543976 0.844889 0.23344998061656952 True -13 39508 30.992038011550903 0.6321611404418945 470.26361083984375 0.22045277059078217 479.30841064453125 0.368948757648468 0.8514473 0.21654048562049866 True -14 42330 30.91950821876526 0.5776917934417725 422.1068115234375 0.17498892545700073 479.0162353515625 0.36970821022987366 0.85535276 0.20099417865276337 True -15 45152 30.388211727142334 0.576946496963501 373.2492980957031 0.16260048747062683 478.7630310058594 0.36951643228530884 0.8600911 0.19337522983551025 True -16 47974 30.42226243019104 0.5861029624938965 401.5506286621094 0.21716737747192383 477.99261474609375 0.37125661969184875 0.8613016 0.18861079216003418 True -17 50796 30.53709602355957 0.5798871517181396 384.69586181640625 0.21184366941452026 478.0729675292969 0.37134674191474915 0.8635982 0.18589815497398376 True -18 53618 31.546205520629883 37.72933387756348 421.11077880859375 0.1189299076795578 477.3890075683594 0.373614102602005 0.86384904 0.18635018169879913 True -19 56440 30.458776712417603 0.5976450443267822 460.9986267089844 0.23574119806289673 477.390625 0.3732846677303314 0.8621668 0.18739253282546997 False diff --git a/ENCSR503UFM/cherimoya.fold_4.performance.tsv b/ENCSR503UFM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index df17bf7d942a00e2ce46357ef7cf178fa25f3081..0000000000000000000000000000000000000000 --- a/ENCSR503UFM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -477.3890075683594 0.405070960521698 0.373614102602005 0.13861601054668427 0.8638490438461304 0.8381256461143494 0.18635018169879913 \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_0.evaluate.json b/ENCSR504OUW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7ea882571525cd6302bf53f0f2b1351ad5e314e1..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF461LOV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_0.fit.json b/ENCSR504OUW/cherimoya.fold_0.fit.json deleted file mode 100644 index add682b1f38a78bf00d61f61406ad0c53760c879..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF461LOV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_0.log b/ENCSR504OUW/cherimoya.fold_0.log deleted file mode 100644 index eba182176b3f412976b09ea2e1a87d05f8b7b49c..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1193 17.992666482925415 3.3095006942749023 296.57122802734375 0.814445972442627 644.9241943359375 0.39789968729019165 0.5978528 21.157846450805664 True -1 2386 13.276085615158081 0.26674580574035645 300.2711181640625 1.2921050786972046 487.12615966796875 0.5204634070396423 0.6841407 11.364827156066895 True -2 3579 13.386222839355469 0.22704482078552246 305.2484130859375 0.8941454291343689 411.24749755859375 0.6137234568595886 0.7018596 4.95157527923584 True -3 4772 13.3268301486969 0.22670626640319824 263.6854248046875 0.8765589594841003 382.3837585449219 0.6520079970359802 0.7263465 1.5156782865524292 True -4 5965 13.306386470794678 0.2265911102294922 289.9449462890625 0.8403830528259277 372.9334411621094 0.6627576351165771 0.73645586 0.8181003332138062 True -5 7158 13.376609563827515 0.2252507209777832 234.92996215820312 0.9130159020423889 368.54803466796875 0.6689162254333496 0.74064946 0.6956540942192078 True -6 8351 13.298008918762207 0.2221825122833252 294.96551513671875 0.38381728529930115 365.0929260253906 0.6731725335121155 0.74558705 0.6411279439926147 True -7 9544 13.287026405334473 0.22603940963745117 249.6531982421875 0.7071597576141357 362.59576416015625 0.675662636756897 0.7505318 0.6208724975585938 True -8 10737 13.297945737838745 0.2248234748840332 320.11370849609375 0.5172905325889587 360.3888244628906 0.6787558794021606 0.74838376 0.6105255484580994 False -9 11930 13.273648262023926 0.22748708724975586 295.50787353515625 0.595109760761261 358.6356201171875 0.6811797022819519 0.7575962 0.5907022356987 True -10 13123 13.296114444732666 1.455960988998413 272.341552734375 0.5860430598258972 357.3648681640625 0.6831044554710388 0.7622864 0.5852071642875671 True -11 14316 13.32430911064148 0.2329421043395996 327.48162841796875 0.6103478670120239 356.48529052734375 0.6845287084579468 0.7637908 0.587281346321106 True -12 15509 13.313725233078003 0.2293241024017334 281.5244140625 0.5412224531173706 355.1677551269531 0.6860076785087585 0.76561064 0.5820430517196655 True -13 16702 13.321434259414673 0.22955727577209473 238.6011505126953 0.3567931354045868 354.5600280761719 0.687086284160614 0.76699746 0.5843963623046875 True -14 17895 13.293320417404175 0.2294774055480957 278.09918212890625 0.7812445759773254 353.925537109375 0.688051164150238 0.7713073 0.5798834562301636 True -15 19088 13.309896230697632 0.22523880004882812 273.5009460449219 0.37278884649276733 353.4050598144531 0.6887174844741821 0.775337 0.574242889881134 True -16 20281 13.30710744857788 0.22916960716247559 268.19586181640625 0.4851292371749878 353.6595764160156 0.688357949256897 0.7784148 0.5739240646362305 True -17 21474 13.31546664237976 0.22722458839416504 265.20721435546875 0.2236582636833191 354.1877136230469 0.6874783635139465 0.7768235 0.5853087902069092 False -18 22667 13.305769443511963 0.22917723655700684 240.9274139404297 0.39247381687164307 354.65679931640625 0.6866536140441895 0.77779955 0.6007908582687378 False -19 23860 13.302595853805542 0.5022318363189697 291.8092346191406 0.24892190098762512 355.0254211425781 0.6859952211380005 0.7755846 0.611987292766571 False diff --git a/ENCSR504OUW/cherimoya.fold_0.performance.tsv b/ENCSR504OUW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 244c44cc51c93c15df73b5f43240738e163f3c44..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -353.6595764160156 0.2658758759498596 0.6883580684661865 0.23910614848136902 0.778414785861969 0.7433048486709595 0.5739240646362305 \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_1.evaluate.json b/ENCSR504OUW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e38eb095ebaeac0b7f9225b2469520f6db6d79f3..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF461LOV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_1.fit.json b/ENCSR504OUW/cherimoya.fold_1.fit.json deleted file mode 100644 index 9129bf380246d0f97af7eb2f5215d0a98afda106..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF461LOV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_1.log b/ENCSR504OUW/cherimoya.fold_1.log deleted file mode 100644 index ca77138e7bbe87ae6ae8bd23b7f55d8ad0dd3531..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1169 17.45907163619995 3.792541980743408 331.48590087890625 1.0129776000976562 734.4212036132812 0.40705642104148865 0.51741505 23.2643985748291 True -1 2338 13.053715944290161 0.3701457977294922 323.21746826171875 0.865509569644928 558.0662231445312 0.5212720036506653 0.647737 11.290817260742188 True -2 3507 13.05549144744873 0.36358642578125 251.81105041503906 1.2788177728652954 469.8492126464844 0.6199771761894226 0.6910295 5.39839506149292 True -3 4676 13.056223154067993 0.36344456672668457 252.89907836914062 0.7692397832870483 425.8880615234375 0.6694241166114807 0.7114526 2.1632440090179443 True -4 5845 13.058748245239258 0.36229467391967773 298.822509765625 0.7351992130279541 412.037353515625 0.6818208694458008 0.72953016 1.1691362857818604 True -5 7014 13.47892451286316 19.251545429229736 292.62744140625 0.8068850040435791 405.7067565917969 0.6881001591682434 0.7288176 0.9516786336898804 False -6 8183 14.737006902694702 19.170748949050903 293.44671630859375 0.5433202981948853 401.77691650390625 0.6920084357261658 0.7379096 0.8113217949867249 True -7 9352 13.396979331970215 0.37655162811279297 345.568359375 0.7279289960861206 398.3229675292969 0.6955498456954956 0.7478185 0.7282410860061646 True -8 10521 13.053131580352783 0.36684465408325195 239.90724182128906 0.6407530307769775 396.11431884765625 0.6982890963554382 0.75161624 0.6826567649841309 True -9 11690 13.11507248878479 1.9851093292236328 255.70169067382812 0.7320324182510376 394.2032775878906 0.7007409930229187 0.754895 0.6537525057792664 True -10 12859 13.073099613189697 0.37083935737609863 287.95513916015625 0.675263524055481 392.3536376953125 0.7028031349182129 0.76299244 0.6273595690727234 True -11 14028 12.801697015762329 6.761894702911377 306.4691162109375 0.4386354684829712 390.4659729003906 0.7054010033607483 0.7721242 0.6103015542030334 True -12 15197 12.816420316696167 0.3662078380584717 306.7790832519531 0.5639922618865967 388.9481506347656 0.7071540355682373 0.7780808 0.5902869701385498 True -13 16366 12.85898470878601 0.36206555366516113 284.6607971191406 0.8555783629417419 387.7341003417969 0.7085002064704895 0.7852036 0.5821683406829834 True -14 17535 12.896070718765259 0.709496021270752 264.0780334472656 0.49517935514450073 387.175537109375 0.7089923620223999 0.787367 0.577277421951294 True -15 18704 12.804830312728882 0.36358165740966797 240.0908203125 0.38383960723876953 387.1768798828125 0.709117591381073 0.79121715 0.5753243565559387 True -16 19873 12.766071081161499 0.360851526260376 223.01095581054688 0.2248082309961319 387.511474609375 0.7083063125610352 0.79253 0.5823603272438049 True -17 21042 12.776426076889038 0.36028194427490234 255.0478515625 0.29326415061950684 387.98345947265625 0.7073659896850586 0.7922123 0.597586452960968 False -18 22211 13.3498215675354 3.9312305450439453 221.48046875 0.3540307879447937 388.54608154296875 0.7064064145088196 0.7894423 0.6105811595916748 False -19 23380 12.814573526382446 0.36542510986328125 243.2672882080078 0.2057850956916809 389.09442138671875 0.705653190612793 0.7882457 0.622333288192749 False diff --git a/ENCSR504OUW/cherimoya.fold_1.performance.tsv b/ENCSR504OUW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 03fa7157f03d2bccc2ca750b69beda022869408c..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -387.511474609375 0.2490886151790619 0.7083063125610352 0.25982171297073364 0.7925300002098083 0.7724564075469971 0.5823603272438049 \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_2.evaluate.json b/ENCSR504OUW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 60a95c9a9698f369506ddd8cedc9af50e0ea5a39..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF461LOV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_2.fit.json b/ENCSR504OUW/cherimoya.fold_2.fit.json deleted file mode 100644 index 1ec6a477463796d36466649c5ab929440d4c89af..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF461LOV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_2.log b/ENCSR504OUW/cherimoya.fold_2.log deleted file mode 100644 index f3acb51c4e9c87cc988f39436adf39f133fa2693..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1258 18.605178356170654 3.339773178100586 323.9007873535156 1.0609993934631348 677.817626953125 0.40930524468421936 0.5461824 21.234716415405273 True -1 2516 14.050381660461426 0.2594618797302246 274.33551025390625 0.8789137601852417 508.651611328125 0.5337963104248047 0.6619159 10.510113716125488 True -2 3774 14.04252552986145 0.24981284141540527 303.05914306640625 1.340256690979004 435.7334289550781 0.6268031001091003 0.69902074 5.024651050567627 True -3 5032 14.010539293289185 0.25188612937927246 286.64599609375 0.6598992347717285 401.28997802734375 0.6612987518310547 0.73007846 2.08103084564209 True -4 6290 14.014907598495483 0.29004788398742676 294.6859130859375 0.9711694717407227 389.2496032714844 0.6716309785842896 0.7400017 1.064449667930603 True -5 7548 14.003483772277832 0.2491917610168457 251.41799926757812 0.8544963598251343 384.6272888183594 0.6759641766548157 0.7478876 0.8136783838272095 True -6 8806 14.020278930664062 1.1231615543365479 280.95111083984375 0.8013151288032532 381.8289489746094 0.6797906756401062 0.7528679 0.7147217988967896 True -7 10064 14.0376296043396 0.25741124153137207 296.31658935546875 0.749426007270813 378.24853515625 0.6837357878684998 0.7579488 0.6577847003936768 True -8 11322 14.0243239402771 0.2501974105834961 274.8341369628906 0.6862062215805054 376.4570617675781 0.686334490776062 0.76393324 0.6456700563430786 True -9 12580 14.047743082046509 0.2548365592956543 259.5093078613281 0.581847071647644 374.15020751953125 0.6888419389724731 0.7668713 0.6144325733184814 True -10 13838 14.085162878036499 0.2522258758544922 262.4989013671875 0.4332180619239807 372.48724365234375 0.6910087466239929 0.77016807 0.6074939966201782 True -11 15096 14.058379888534546 0.25756144523620605 252.33917236328125 0.4771393835544586 371.17901611328125 0.6930294036865234 0.7772182 0.592018187046051 True -12 16354 14.087086915969849 0.25289368629455566 274.665283203125 0.627016544342041 369.11236572265625 0.6952075958251953 0.78454894 0.5750760436058044 True -13 17612 14.04690170288086 0.2527732849121094 298.4676208496094 0.5511020421981812 368.1632080078125 0.6966567039489746 0.7906689 0.5568931698799133 True -14 18870 14.051314353942871 0.2499856948852539 308.2144775390625 0.5575155019760132 367.31646728515625 0.6973507404327393 0.791336 0.5605906844139099 True -15 20128 14.105850219726562 0.25151658058166504 265.7983703613281 0.36704879999160767 367.0361633300781 0.6973726153373718 0.7956559 0.5622096061706543 True -16 21386 14.053227424621582 0.2544097900390625 281.6751708984375 0.4078264832496643 367.1676330566406 0.6969764828681946 0.79588914 0.5657560229301453 True -17 22644 14.045060873031616 0.2539849281311035 219.56895446777344 0.5061918497085571 367.4963684082031 0.696049153804779 0.7937316 0.5789202451705933 False -18 23902 14.034503936767578 0.24995732307434082 240.02133178710938 0.24306970834732056 367.9861145019531 0.6951467990875244 0.7939175 0.5905279517173767 False -19 25160 14.06373405456543 0.25070714950561523 300.71942138671875 0.18455809354782104 368.212890625 0.6945556402206421 0.79317546 0.597356379032135 False diff --git a/ENCSR504OUW/cherimoya.fold_2.performance.tsv b/ENCSR504OUW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 541bdfedb8c4d482a069bccc6e876e05cd746381..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -367.1676330566406 0.2595292031764984 0.6969764232635498 0.25264105200767517 0.795889139175415 0.7725080847740173 0.5657560229301453 \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_3.evaluate.json b/ENCSR504OUW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 94e2fac78ed8efd9e4d711acd98f506f60439f09..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF461LOV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_3.fit.json b/ENCSR504OUW/cherimoya.fold_3.fit.json deleted file mode 100644 index 4f7d36f8a06c8aaf607b5efc1369964ac39efc0a..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF461LOV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_3.log b/ENCSR504OUW/cherimoya.fold_3.log deleted file mode 100644 index 14dd7d2ba156c16d348eb27a4ea33643d49bba93..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1214 17.731832265853882 3.4611618518829346 327.9200439453125 1.4210573434829712 645.0399780273438 0.4025309681892395 0.5498087 21.69818115234375 True -1 2428 13.557628631591797 0.2720911502838135 323.22723388671875 1.1324872970581055 486.67626953125 0.5234065651893616 0.64210546 11.280959129333496 True -2 3642 13.547465801239014 14.767093181610107 327.00274658203125 1.0007226467132568 418.4555358886719 0.6110718846321106 0.66830266 5.229127883911133 True -3 4856 18.122368574142456 12.57553744316101 261.90777587890625 1.091794729232788 388.864013671875 0.6510482430458069 0.7006426 1.9502599239349365 True -4 6070 13.512902736663818 0.2676231861114502 295.50360107421875 1.1641021966934204 380.1561584472656 0.6618237495422363 0.70420283 1.18605375289917 True -5 7284 13.515041828155518 5.24506950378418 255.38424682617188 0.7116702795028687 375.90960693359375 0.6667816638946533 0.704492 0.9375309944152832 True -6 8498 15.547933340072632 13.302974462509155 293.3285217285156 0.6398804783821106 373.6808776855469 0.6701065897941589 0.7126367 0.7853941917419434 True -7 9712 14.76794147491455 0.2667386531829834 333.003662109375 0.6717404127120972 371.2431335449219 0.6732540726661682 0.71944195 0.6938912272453308 True -8 10926 13.526888847351074 0.9183633327484131 315.61663818359375 0.9457370042800903 369.16693115234375 0.6765680909156799 0.7218499 0.6769760251045227 True -9 12140 13.53392243385315 0.25615358352661133 261.78094482421875 0.39951786398887634 367.3910217285156 0.6792862415313721 0.7292313 0.6574777960777283 True -10 13354 13.556575298309326 0.263810396194458 303.5945129394531 0.5847233533859253 365.7956237792969 0.681704580783844 0.7307235 0.6511461734771729 True -11 14568 13.54179859161377 0.2580251693725586 270.1185607910156 0.6670025587081909 363.8641052246094 0.6843340396881104 0.7342464 0.6343494653701782 True -12 15782 13.549200773239136 0.2577683925628662 247.96221923828125 0.47397956252098083 362.51153564453125 0.6865993142127991 0.7456682 0.6236903667449951 True -13 16996 13.531741619110107 0.2576897144317627 237.06214904785156 0.358487606048584 361.00164794921875 0.6882330775260925 0.75215685 0.6119074821472168 True -14 18210 13.522712707519531 0.26406121253967285 261.0106201171875 0.4363170862197876 360.4535217285156 0.6890819072723389 0.7601077 0.597032368183136 True -15 19424 13.352232933044434 0.2567265033721924 306.04022216796875 0.4278576672077179 360.1289367675781 0.6893489956855774 0.7659321 0.5966888666152954 True -16 20638 13.28333044052124 0.2561028003692627 252.35348510742188 0.4728457033634186 360.0910339355469 0.6891778707504272 0.7682536 0.605159342288971 True -17 21852 13.295794486999512 0.2581751346588135 296.83154296875 0.17292973399162292 360.1981506347656 0.6883329153060913 0.76737314 0.6232872009277344 False -18 23066 13.330641984939575 0.25870585441589355 239.7915802001953 0.30115196108818054 360.5378723144531 0.6874785423278809 0.7666843 0.639900267124176 False -19 24280 13.27754259109497 0.2534823417663574 270.0689697265625 0.30259737372398376 360.7727966308594 0.6868851184844971 0.76516813 0.6531600952148438 False diff --git a/ENCSR504OUW/cherimoya.fold_3.performance.tsv b/ENCSR504OUW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 68ec92643b3f9221177788c268ca51c0361c9367..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -360.0910339355469 0.26333996653556824 0.6891779899597168 0.24614974856376648 0.7682536244392395 0.7390032410621643 0.605159342288971 \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_4.evaluate.json b/ENCSR504OUW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 766e3731b8b9a7cd71ba92fbc4770a2dcecda05f..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF461LOV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_4.fit.json b/ENCSR504OUW/cherimoya.fold_4.fit.json deleted file mode 100644 index 8d822075484775f2fd78777f6e8452b5b493d4cd..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF461LOV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR504OUW/cherimoya.fold_4.log b/ENCSR504OUW/cherimoya.fold_4.log deleted file mode 100644 index 2422a6876335e3b16ccdd44c0274c714cd058b5c..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1199 17.804030179977417 3.1579596996307373 292.8196716308594 1.0711098909378052 631.0468139648438 0.3978408873081207 0.5513037 20.968181610107422 True -1 2398 13.423258781433105 0.24204230308532715 272.40557861328125 0.9977052807807922 477.4310302734375 0.5145332217216492 0.6537561 10.946627616882324 True -2 3597 13.409485578536987 0.23775243759155273 253.3265380859375 0.934462308883667 407.3770446777344 0.6073242425918579 0.69156826 4.634525775909424 True -3 4796 13.410935878753662 0.23177242279052734 261.88409423828125 0.7754539251327515 374.34149169921875 0.6439909338951111 0.7059132 1.5777287483215332 True -4 5995 13.368968486785889 0.22883105278015137 315.974609375 0.7078601121902466 366.15283203125 0.6537376642227173 0.71193707 0.9932371973991394 True -5 7194 13.381375551223755 0.2296912670135498 298.71063232421875 0.6903330087661743 361.38214111328125 0.6591973304748535 0.7239169 0.7945727705955505 True -6 8393 13.368073463439941 0.35701465606689453 275.47552490234375 0.6886869668960571 358.13482666015625 0.6640236973762512 0.72684354 0.7443377375602722 True -7 9592 13.455198287963867 9.594121217727661 292.9495849609375 0.7284928560256958 356.48309326171875 0.6663274765014648 0.7351308 0.7030123472213745 True -8 10791 13.418290853500366 0.24435210227966309 264.09185791015625 0.6015195846557617 354.2940979003906 0.6689993739128113 0.7386349 0.6759241819381714 True -9 11990 13.39775276184082 0.23429560661315918 309.5482177734375 0.6121910810470581 353.1063537597656 0.6708679795265198 0.74122226 0.656406044960022 True -10 13189 13.378523588180542 0.5515451431274414 221.84014892578125 0.7816314101219177 351.3235778808594 0.6732034087181091 0.7520399 0.6303364038467407 True -11 14388 13.396132946014404 0.23262476921081543 272.9012451171875 0.5385974645614624 349.73675537109375 0.6750862002372742 0.75606966 0.6182590126991272 True -12 15587 13.379223585128784 0.2322545051574707 264.8880920410156 0.5784801840782166 348.9259948730469 0.6763766407966614 0.76196504 0.5995569229125977 True -13 16786 13.371074199676514 0.23189783096313477 260.62579345703125 0.5108824968338013 347.6805419921875 0.6780474185943604 0.77146107 0.5825997591018677 True -14 17985 13.675214767456055 4.951464653015137 282.0574951171875 0.3509262204170227 347.42236328125 0.6787710785865784 0.7762419 0.5698320269584656 True -15 19184 13.408353805541992 0.23359322547912598 232.27259826660156 0.5704225897789001 346.98681640625 0.6792646050453186 0.77891314 0.5735521912574768 True -16 20383 13.372491121292114 0.22982382774353027 278.6690368652344 0.3582311272621155 347.13421630859375 0.6793292164802551 0.780817 0.5746856927871704 True -17 21582 13.982083320617676 13.689926147460938 275.2232666015625 0.3449813723564148 347.8103332519531 0.6783677935600281 0.7809776 0.5836639404296875 True -18 22781 16.98114824295044 11.621964693069458 246.38121032714844 0.3469583988189697 348.3399353027344 0.67760169506073 0.7792323 0.6027086973190308 False -19 23980 14.048376321792603 0.23287725448608398 279.9482727050781 0.21422179043293 348.7221374511719 0.6769838929176331 0.7774122 0.6160101294517517 False diff --git a/ENCSR504OUW/cherimoya.fold_4.performance.tsv b/ENCSR504OUW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 669f91564aee3afbd077a0f9c31c042282b8cedb..0000000000000000000000000000000000000000 --- a/ENCSR504OUW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -347.8103332519531 0.27089381217956543 0.6783677935600281 0.2377931922674179 0.7809776067733765 0.7421690821647644 0.5836639404296875 \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_0.evaluate.json b/ENCSR507DQC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e82afc804544acd1423d7a46e7f3b87d638c217b..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791UDQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_0.fit.json b/ENCSR507DQC/cherimoya.fold_0.fit.json deleted file mode 100644 index 7d7979f08b33b0b6205fc048306912480e2a2cbf..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF791UDQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_0.log b/ENCSR507DQC/cherimoya.fold_0.log deleted file mode 100644 index aeaf738f26b4721618548f461b3dbaa404cb7684..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 33.74638080596924 20.901689052581787 919.3814697265625 1.0944150686264038 1171.052001953125 0.29944750666618347 0.64794576 9.627677917480469 True -1 5472 31.01077151298523 0.5908927917480469 776.3707275390625 0.8335774540901184 926.2521362304688 0.4522339105606079 0.68648225 3.856254816055298 True -2 8208 30.13008141517639 0.5451185703277588 628.7630615234375 0.9131062626838684 903.1806640625 0.46347329020500183 0.6990576 2.2080483436584473 True -3 10944 30.12763738632202 0.5378837585449219 780.5401000976562 1.0639631748199463 891.5651245117188 0.47258248925209045 0.70659626 1.8658666610717773 True -4 13680 30.113837718963623 0.546661376953125 713.5595092773438 0.73897385597229 880.0291748046875 0.4819662272930145 0.7130616 1.8435324430465698 True -5 16416 30.055793523788452 0.5396881103515625 474.5581359863281 1.0249111652374268 877.35888671875 0.48437172174453735 0.7085008 1.5227422714233398 False -6 19152 30.042434453964233 0.5436625480651855 643.721435546875 0.9996147155761719 872.02587890625 0.48753467202186584 0.7195814 1.34996497631073 True -7 21888 30.071362018585205 0.5449340343475342 749.3043212890625 1.1582996845245361 866.7559814453125 0.49193936586380005 0.719719 1.2859346866607666 True -8 24624 30.065290212631226 0.5416889190673828 587.7424926757812 0.48647207021713257 858.8440551757812 0.4972159266471863 0.73154545 1.1041042804718018 True -9 27360 30.02949070930481 0.5474445819854736 705.35400390625 0.799403727054596 856.4689331054688 0.49809107184410095 0.73211116 1.0702584981918335 True -10 30096 30.078704833984375 0.5439856052398682 792.8209228515625 0.7932582497596741 850.15478515625 0.5030240416526794 0.7376092 0.9645005464553833 True -11 32832 30.08410096168518 0.5403664112091064 767.23974609375 0.633042573928833 845.9267578125 0.5057778358459473 0.7458729 0.8905354142189026 True -12 35568 30.12292194366455 0.5445334911346436 883.9703369140625 0.5420979261398315 837.4464721679688 0.5124584436416626 0.7499977 0.8003385066986084 True -13 38304 30.02375626564026 2.0193850994110107 759.3088989257812 0.6328151226043701 833.8064575195312 0.5140422582626343 0.7613445 0.6874900460243225 True -14 41040 30.0976402759552 0.5384426116943359 605.751708984375 0.6232427358627319 830.49072265625 0.5165281295776367 0.7691411 0.6342055201530457 True -15 43776 30.04443621635437 0.5461187362670898 641.0928344726562 0.5612746477127075 826.8275146484375 0.5189705491065979 0.7759672 0.5814591646194458 True -16 46512 29.539154767990112 0.7915060520172119 653.7999267578125 0.8543100953102112 824.5855102539062 0.5213987827301025 0.77953184 0.5497787594795227 True -17 49248 29.803534507751465 0.5334219932556152 545.2183227539062 0.7182856798171997 823.9652709960938 0.5220526456832886 0.7838038 0.5313344597816467 True -18 51984 29.520493984222412 0.5397188663482666 605.1265869140625 0.544858455657959 826.167724609375 0.5197672247886658 0.785301 0.5271642208099365 True -19 54720 29.52993154525757 0.5393288135528564 761.8074951171875 0.5648313164710999 825.3624267578125 0.5207550525665283 0.7845107 0.5264183282852173 False diff --git a/ENCSR507DQC/cherimoya.fold_0.performance.tsv b/ENCSR507DQC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 25543d157344c41cfa6094d2b21ca38885d22ab3..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -826.167724609375 0.3042134642601013 0.5197672843933105 0.23601704835891724 0.7853010296821594 0.7256900072097778 0.5271642208099365 \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_1.evaluate.json b/ENCSR507DQC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ae60f1e919ede9bfbfa52a87f7fade81d7c8ae1f..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791UDQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_1.fit.json b/ENCSR507DQC/cherimoya.fold_1.fit.json deleted file mode 100644 index fc489776370452b54b5bb4ac86dd0af0c1b9eb61..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF791UDQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_1.log b/ENCSR507DQC/cherimoya.fold_1.log deleted file mode 100644 index 1c2a45647bb491747d73812a8a9a6dbc72c65d71..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2687 33.320581674575806 3.7699637413024902 730.5931396484375 0.6566847562789917 1378.7275390625 0.29944226145744324 0.6510533 8.856229782104492 True -1 5374 29.611742734909058 2.708167791366577 603.0504760742188 0.7260944247245789 1082.236083984375 0.45494696497917175 0.6948189 4.672653675079346 True -2 8061 29.59883213043213 0.7813444137573242 714.3538818359375 1.1767528057098389 1055.9686279296875 0.4686766266822815 0.7102742 2.69022798538208 True -3 10748 29.5782253742218 0.7316548824310303 595.879150390625 0.8968768119812012 1040.1754150390625 0.47981518507003784 0.72741276 2.0677075386047363 True -4 13435 29.578437089920044 0.7312581539154053 924.7205810546875 0.9525683522224426 1030.6124267578125 0.48613741993904114 0.7330099 1.9298290014266968 True -5 16122 29.540499210357666 0.7436878681182861 839.8809814453125 0.885633111000061 1021.1625366210938 0.492278516292572 0.7414207 1.7342623472213745 True -6 18809 29.544580698013306 0.7328841686248779 856.2911376953125 0.7511004209518433 1013.0241088867188 0.499277263879776 0.74562395 1.6326996088027954 True -7 21496 29.54423713684082 0.7468171119689941 807.5126342773438 0.9204602241516113 1007.0518798828125 0.5019543766975403 0.7432751 1.4329544305801392 False -8 24183 29.55048394203186 0.742844820022583 647.9039916992188 0.8727272748947144 998.689697265625 0.5078543424606323 0.74903405 1.429756999015808 True -9 26870 29.560482025146484 0.7780036926269531 748.9427490234375 0.7892318964004517 989.7232666015625 0.5148606896400452 0.75377613 1.2432869672775269 True -10 29557 29.567330837249756 0.7413101196289062 714.6860961914062 0.9331094622612 983.2793579101562 0.5176701545715332 0.7583295 1.1559560298919678 True -11 32244 29.554542064666748 0.742772102355957 816.419677734375 0.7756875157356262 976.90087890625 0.5200470089912415 0.76727676 1.023493766784668 True -12 34931 29.51745343208313 0.7292101383209229 709.619873046875 0.8586819767951965 970.909423828125 0.5228015184402466 0.7709341 0.8885943293571472 True -13 37618 29.577045440673828 0.7416422367095947 543.9995727539062 0.6485214233398438 967.3374633789062 0.5228713154792786 0.7811986 0.776035487651825 True -14 40305 29.540487051010132 0.7458465099334717 565.453125 0.6080420017242432 960.947509765625 0.5274812579154968 0.78820115 0.6838828325271606 True -15 42992 29.551893949508667 0.7352442741394043 757.5692749023438 0.7539434432983398 956.32177734375 0.5305948853492737 0.7956741 0.6188697814941406 True -16 45679 29.53709077835083 0.74049973487854 570.2066650390625 0.4591437578201294 956.4671020507812 0.5291066765785217 0.8018194 0.579428493976593 True -17 48366 29.06489896774292 0.7367706298828125 615.74462890625 0.5314499139785767 954.8154296875 0.5300278067588806 0.80388856 0.5507826209068298 True -18 51053 29.006494283676147 1.5386440753936768 719.8873291015625 0.48729318380355835 956.803466796875 0.5283489227294922 0.8041357 0.5451229214668274 True -19 53740 29.0717990398407 0.7428438663482666 618.9375 0.9371320605278015 952.916259765625 0.5327004790306091 0.8034955 0.5449581742286682 False diff --git a/ENCSR507DQC/cherimoya.fold_1.performance.tsv b/ENCSR507DQC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b5b0936b10b3395378676ac77c4062db34de72b3..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -956.803466796875 0.2891530692577362 0.5283489227294922 0.263356477022171 0.8041356801986694 0.7692275643348694 0.5451229214668274 \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_2.evaluate.json b/ENCSR507DQC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1729a9f5df8d44eeb7df309327e3bb42bb6b6f6a..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791UDQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_2.fit.json b/ENCSR507DQC/cherimoya.fold_2.fit.json deleted file mode 100644 index a4dba4af06712883dc9ef95218b90ebe67bc8452..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF791UDQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_2.log b/ENCSR507DQC/cherimoya.fold_2.log deleted file mode 100644 index eb9e5cbe26fdf4c28c86353771cac00d23367dfb..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2889 35.34761929512024 3.795585870742798 801.858154296875 0.9413830041885376 1251.577392578125 0.3108997344970703 0.6454823 8.060416221618652 True -1 5778 32.0897171497345 0.5513856410980225 643.59716796875 0.972686231136322 987.4580688476562 0.455838680267334 0.6874428 3.2604167461395264 True -2 8667 31.81704616546631 0.7321457862854004 665.6378784179688 0.8843125700950623 964.4183959960938 0.4730229377746582 0.70318234 2.0697038173675537 True -3 11556 31.79620385169983 2.538381338119507 690.6297607421875 0.6539995670318604 952.3386840820312 0.4810059666633606 0.71151215 2.0739307403564453 True -4 14445 31.869451761245728 0.7486424446105957 879.9393310546875 0.9706733822822571 946.7275390625 0.48712095618247986 0.71250176 1.8895915746688843 True -5 17334 31.73677659034729 0.53641676902771 664.5408935546875 0.8006218671798706 944.3822021484375 0.48796454071998596 0.71600246 1.7773241996765137 True -6 20223 31.687057495117188 3.7907662391662598 770.2742309570312 0.8832026720046997 939.543212890625 0.4930724799633026 0.7108925 1.6479196548461914 False -7 23112 31.767951488494873 0.5281932353973389 601.773681640625 1.1728768348693848 932.1702880859375 0.4965696632862091 0.7188352 1.3522448539733887 True -8 26001 31.783255577087402 0.5331599712371826 731.4349975585938 0.5806428790092468 927.1633911132812 0.5010752081871033 0.71622014 1.3869965076446533 False -9 28890 31.879271984100342 0.542163610458374 655.152587890625 0.9968292117118835 915.4190063476562 0.5068901181221008 0.7261001 1.202193021774292 True -10 31779 31.85562777519226 0.5344221591949463 773.7061767578125 0.7074025273323059 910.3956909179688 0.510696530342102 0.73386806 1.0725007057189941 True -11 34668 31.779711723327637 0.5318331718444824 801.4658203125 0.6775305271148682 902.5712890625 0.5142110586166382 0.73912364 0.9842308163642883 True -12 37557 31.78400492668152 0.5361261367797852 685.4393920898438 0.4540911614894867 896.1797485351562 0.5191369652748108 0.7515198 0.8443047404289246 True -13 40446 31.73529076576233 1.2176122665405273 861.854736328125 0.8360171318054199 888.6414184570312 0.524041473865509 0.76316494 0.7417957782745361 True -14 43335 31.831579446792603 0.5399746894836426 843.1400756835938 0.6050528287887573 887.4164428710938 0.5230116248130798 0.77018017 0.6648033857345581 True -15 46224 31.77673101425171 0.536607027053833 658.4219360351562 0.5385327339172363 884.5536499023438 0.5249564051628113 0.7775309 0.6084997057914734 True -16 49113 31.798970699310303 0.5490462779998779 646.6870727539062 0.5426669120788574 880.5307006835938 0.5281007885932922 0.78181326 0.5658169984817505 True -17 52002 31.562967538833618 0.5262837409973145 818.5294799804688 0.33792251348495483 881.9864501953125 0.5264452695846558 0.78508055 0.5495935678482056 True -18 54891 31.135275840759277 2.0492427349090576 726.0806274414062 0.4483046233654022 883.3540649414062 0.5267170667648315 0.78739583 0.5383307337760925 True -19 57780 31.168603658676147 0.5268816947937012 773.203857421875 0.5026499629020691 884.2861328125 0.5249148607254028 0.78647643 0.5401482582092285 False diff --git a/ENCSR507DQC/cherimoya.fold_2.performance.tsv b/ENCSR507DQC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d7881bf78e2e054e453b91ab9c9b492ac8da9174..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -883.3540649414062 0.29611891508102417 0.5267170071601868 0.2507355213165283 0.7873958349227905 0.7454881072044373 0.5383307337760925 \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_3.evaluate.json b/ENCSR507DQC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9635b8b183d83d5c210a7018f1625c9bf9baf9a0..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791UDQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_3.fit.json b/ENCSR507DQC/cherimoya.fold_3.fit.json deleted file mode 100644 index 324c46e0edbe7aef17b883770bb6ba17a18ee99d..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF791UDQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_3.log b/ENCSR507DQC/cherimoya.fold_3.log deleted file mode 100644 index 9ee6d609d45ce393b50bfae97fee8c288007d615..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 34.64501476287842 4.442162275314331 854.0784912109375 0.9069475531578064 1172.7620849609375 0.3147008717060089 0.65462595 8.412473678588867 True -1 5560 30.636393785476685 0.572822093963623 812.8923950195312 1.2153105735778809 937.9772338867188 0.44839173555374146 0.6989864 3.884978771209717 True -2 8340 30.61928081512451 0.5649008750915527 712.4405517578125 1.1273014545440674 909.6762084960938 0.4685174822807312 0.71505684 2.8513665199279785 True -3 11120 30.699630737304688 0.5911805629730225 774.8234252929688 1.2618958950042725 899.1427612304688 0.47543519735336304 0.72465104 2.2289609909057617 True -4 13900 30.67120051383972 0.601945161819458 539.619873046875 0.6288684010505676 892.6534423828125 0.48099032044410706 0.7279616 1.7497336864471436 True -5 16680 30.58836531639099 0.5645887851715088 678.542724609375 0.657495379447937 888.2263793945312 0.48304083943367004 0.72905654 1.483845591545105 True -6 19460 30.606647729873657 1.6462836265563965 672.4365234375 0.7745510339736938 885.306884765625 0.48503169417381287 0.7284597 1.4239349365234375 False -7 22240 30.68586564064026 0.5673813819885254 787.7757568359375 0.8386690616607666 879.7765502929688 0.49079179763793945 0.73348737 1.4008886814117432 True -8 25020 30.696781158447266 0.5608320236206055 884.08544921875 0.5172048807144165 871.1163330078125 0.4955735206604004 0.7361009 1.2595771551132202 True -9 27800 30.653769731521606 2.1934282779693604 729.2879638671875 1.0138483047485352 867.4495849609375 0.4979110360145569 0.740308 1.2107609510421753 True -10 30580 30.574284315109253 0.546647310256958 607.129638671875 0.8509036898612976 858.0233154296875 0.505378007888794 0.74691206 1.0449773073196411 True -11 33360 30.58394765853882 2.4484097957611084 687.619873046875 0.7292720079421997 854.4166259765625 0.5065938830375671 0.75505567 0.87917160987854 True -12 36140 30.116690397262573 0.5418155193328857 813.883056640625 0.7743105888366699 845.9464721679688 0.5126664638519287 0.76569074 0.8325482606887817 True -13 38920 30.02768635749817 0.5425117015838623 748.3795776367188 0.5757306218147278 841.82275390625 0.5138301849365234 0.7756444 0.7410797476768494 True -14 41700 29.995412349700928 2.3529558181762695 645.653564453125 0.7308260202407837 838.2548828125 0.5162045955657959 0.783994 0.6654701232910156 True -15 44480 30.094609022140503 0.5532715320587158 741.98486328125 0.6473314166069031 833.8999633789062 0.5184974074363708 0.7899379 0.6125835180282593 True -16 47260 30.078805446624756 0.552649974822998 704.7247314453125 0.5218464732170105 833.776123046875 0.5186846256256104 0.79707474 0.562439501285553 True -17 50040 30.049002408981323 4.822288751602173 658.005859375 0.7121928334236145 831.8143920898438 0.5206473469734192 0.7995697 0.5455008745193481 True -18 52820 30.075998783111572 24.348808765411377 801.1090698242188 0.3763316571712494 832.4925537109375 0.5197709798812866 0.7996092 0.5383676886558533 True -19 55600 30.627978563308716 0.5879707336425781 592.6204833984375 0.5817850828170776 830.7980346679688 0.5214873552322388 0.80101985 0.5361815094947815 True diff --git a/ENCSR507DQC/cherimoya.fold_3.performance.tsv b/ENCSR507DQC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e5afeb33350ab2781077c9f535330e8267061ca8..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -830.7980346679688 0.30228880047798157 0.5214873552322388 0.24221034348011017 0.8010198473930359 0.7462626099586487 0.5361815094947815 \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_4.evaluate.json b/ENCSR507DQC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7aa492531ad0958a656e853bc50c2f5288c1e190..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791UDQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_4.fit.json b/ENCSR507DQC/cherimoya.fold_4.fit.json deleted file mode 100644 index 01cdca581d9fc736fb4a20771a9c035721e16def..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF791UDQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507DQC/cherimoya.fold_4.log b/ENCSR507DQC/cherimoya.fold_4.log deleted file mode 100644 index e478cc5709be47fd15d11b2da01d1cd41bc984af..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2826 34.91752099990845 3.573117733001709 858.9798583984375 1.2192041873931885 1095.1573486328125 0.30254510045051575 0.6341174 6.517588138580322 True -1 5652 31.127747774124146 1.828601360321045 845.523681640625 0.8964710235595703 883.4968872070312 0.4406186044216156 0.66893864 4.006909370422363 True -2 8478 31.144348621368408 0.5423524379730225 757.468017578125 0.9125322103500366 858.3545532226562 0.46054625511169434 0.6907493 2.030735731124878 True -3 11304 31.183295726776123 0.5361347198486328 698.5300903320312 0.6034482717514038 847.531982421875 0.4677223563194275 0.69970804 1.984145998954773 True -4 14130 31.13180375099182 0.5506658554077148 675.6089477539062 0.8665938377380371 839.5372924804688 0.4747388958930969 0.7020597 1.8933169841766357 True -5 16956 31.18790102005005 0.5496153831481934 823.3760986328125 0.9901425242424011 835.1681518554688 0.4778696298599243 0.70588803 1.6377196311950684 True -6 19782 31.141912937164307 0.5484211444854736 653.8461303710938 0.732758641242981 828.8135986328125 0.48398593068122864 0.7044378 1.4498966932296753 False -7 22608 30.955742597579956 0.5370049476623535 846.2171630859375 0.8586157560348511 823.7295532226562 0.4884321689605713 0.7095225 1.342637062072754 True -8 25434 30.47533416748047 0.5377283096313477 671.632568359375 0.513474702835083 819.226806640625 0.4906158745288849 0.7169322 1.1755104064941406 True -9 28260 30.870965719223022 0.5417904853820801 615.7359619140625 0.6975681781768799 814.48291015625 0.4947497248649597 0.7218133 1.0256597995758057 True -10 31086 30.58389139175415 0.5440959930419922 743.863525390625 0.8047630190849304 811.54638671875 0.49573007225990295 0.73079985 0.9389631152153015 True -11 33912 30.501790285110474 0.5413177013397217 595.3427734375 0.3784683346748352 803.9152221679688 0.50201416015625 0.7384441 0.8331947326660156 True -12 36738 30.50949788093567 0.5341968536376953 515.1165771484375 0.7448906898498535 798.5139770507812 0.5058697462081909 0.74602264 0.7704569697380066 True -13 39564 30.57703447341919 0.5406520366668701 756.3602294921875 0.47764819860458374 794.8277587890625 0.5085045695304871 0.7551997 0.669590950012207 True -14 42390 30.564271211624146 0.5416383743286133 575.1785888671875 0.5977878570556641 790.16943359375 0.5135131478309631 0.76368463 0.6202700138092041 True -15 45216 30.516788482666016 0.9210751056671143 749.3697509765625 0.504656195640564 789.2294311523438 0.5121774673461914 0.7707329 0.5639392733573914 True -16 48042 30.57402992248535 0.5544018745422363 587.1302490234375 0.5391745567321777 788.8040161132812 0.511904776096344 0.77642494 0.540549099445343 True -17 50868 30.60710096359253 0.546612024307251 553.4664306640625 0.43552643060684204 787.626953125 0.5143414735794067 0.78096944 0.5170080065727234 True -18 53694 30.55867838859558 0.5406415462493896 563.4987182617188 0.3600998520851135 786.4268188476562 0.5159856677055359 0.78124225 0.5109593272209167 True -19 56520 30.615191221237183 0.5376265048980713 539.911376953125 0.3896791934967041 788.6293334960938 0.513351559638977 0.78040195 0.5119905471801758 False diff --git a/ENCSR507DQC/cherimoya.fold_4.performance.tsv b/ENCSR507DQC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 37d3a1d06723429302164b2808ad0909202a1133..0000000000000000000000000000000000000000 --- a/ENCSR507DQC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -786.4268188476562 0.30817997455596924 0.5159856677055359 0.23151671886444092 0.7812422513961792 0.7151646614074707 0.5109593272209167 \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_0.evaluate.json b/ENCSR507GFJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0ed9749fa63fad3583890b721e25892b58d75ee5..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330QCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_0.fit.json b/ENCSR507GFJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 407ac47659c73f3c6645210640f937cf01d67fc4..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF330QCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_0.log b/ENCSR507GFJ/cherimoya.fold_0.log deleted file mode 100644 index fc6c3f67fea7a6f28f8e6cb1a53f84ebf1721ee1..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 34.89515161514282 3.8564698696136475 775.81689453125 0.75569748878479 1284.044921875 0.26226818561553955 0.6355708 9.885519981384277 True -1 5512 30.384660720825195 0.736149787902832 1038.0672607421875 0.5176072716712952 1126.9591064453125 0.37532952427864075 0.6887847 1.873595952987671 True -2 8268 30.46424174308777 0.659947395324707 967.5374755859375 0.8823593854904175 1106.1085205078125 0.38936081528663635 0.6989373 0.9947301745414734 True -3 11024 30.001044511795044 0.6236178874969482 826.5819091796875 0.48773306608200073 1095.0672607421875 0.39600205421447754 0.70833874 0.7846221327781677 True -4 13780 29.80220055580139 0.6139616966247559 898.1512451171875 0.8901872634887695 1085.32177734375 0.4008942246437073 0.71921337 0.6036423444747925 True -5 16536 29.83669948577881 0.6115157604217529 1017.2264404296875 0.7841407060623169 1080.829833984375 0.4041568636894226 0.71935576 0.5806782841682434 True -6 19292 29.78663420677185 0.598224401473999 839.729736328125 0.8756653070449829 1078.390869140625 0.4035015106201172 0.7269181 0.5075924396514893 True -7 22048 29.769911766052246 1.0028882026672363 820.53759765625 0.5688009262084961 1072.0941162109375 0.4091121256351471 0.73887336 0.4625548720359802 True -8 24804 29.839632034301758 2.2541921138763428 906.5606689453125 0.5353900194168091 1064.394775390625 0.4161891043186188 0.73939306 0.447305828332901 True -9 27560 29.815425157546997 0.6158726215362549 906.8125 0.47079095244407654 1061.8896484375 0.4163455665111542 0.75296235 0.4089374244213104 True -10 30316 29.850695610046387 0.6150035858154297 799.7720947265625 0.539151132106781 1058.0389404296875 0.4193803369998932 0.7635258 0.38584598898887634 True -11 33072 29.78487753868103 0.6149590015411377 950.2667236328125 0.4418194890022278 1054.3343505859375 0.4214170575141907 0.7714202 0.3708321154117584 True -12 35828 29.824229955673218 0.6143050193786621 978.993896484375 0.3572486340999603 1049.592041015625 0.4251178205013275 0.7837811 0.3487239480018616 True -13 38584 31.01939845085144 15.135601282119751 855.8121337890625 0.6093370914459229 1049.0306396484375 0.4245721995830536 0.78987646 0.33202511072158813 True -14 41340 29.860561847686768 1.0050134658813477 862.216796875 0.2917608916759491 1045.7935791015625 0.42616698145866394 0.8009888 0.31545355916023254 True -15 44096 29.853468656539917 1.0530755519866943 820.77490234375 0.31466448307037354 1041.13818359375 0.4299997091293335 0.8096484 0.31304123997688293 True -16 46852 29.883177280426025 0.6276302337646484 868.2127685546875 0.4019438326358795 1040.6087646484375 0.4309000074863434 0.814185 0.3044379651546478 True -17 49608 29.895681142807007 0.6063740253448486 1001.3953247070312 0.28460296988487244 1036.8067626953125 0.43430784344673157 0.8161239 0.3065447211265564 True -18 52364 29.774145364761353 0.627173900604248 706.9895629882812 0.47514015436172485 1039.3232421875 0.43205997347831726 0.8164642 0.3071018159389496 True -19 55120 29.87027072906494 0.6181037425994873 719.7686767578125 0.3141497075557709 1042.8258056640625 0.42731884121894836 0.8182042 0.30755922198295593 True diff --git a/ENCSR507GFJ/cherimoya.fold_0.performance.tsv b/ENCSR507GFJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f94149f99578ef2e63638ee9a72c8e740b5473b5..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1042.8258056640625 0.3275320529937744 0.427318811416626 0.21272435784339905 0.8182042241096497 0.7589033246040344 0.30755922198295593 \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_1.evaluate.json b/ENCSR507GFJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5f5577303fa064c5ce9e29f65c8ab4c3e902ca20..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330QCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_1.fit.json b/ENCSR507GFJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 2ce4d1d9a9f53358952417919c9d3fbc44a6bb91..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF330QCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_1.log b/ENCSR507GFJ/cherimoya.fold_1.log deleted file mode 100644 index 1e3dab5901d6add8ed46d5f48455d6847aa60424..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 34.70638179779053 20.601330757141113 748.1052856445312 0.7964950799942017 1520.582275390625 0.2721131443977356 0.64053106 7.614141941070557 True -1 5472 29.83192229270935 13.224162340164185 1005.806396484375 0.6686210036277771 1317.1600341796875 0.3943782150745392 0.6965201 2.7633869647979736 True -2 8208 30.225614309310913 4.3647074699401855 937.732177734375 0.7156374454498291 1287.9630126953125 0.409468412399292 0.7235184 0.9753863215446472 True -3 10944 31.199424743652344 0.9824609756469727 853.9799194335938 0.6864140629768372 1263.21142578125 0.41982972621917725 0.74651116 0.7741701602935791 True -4 13680 31.389919996261597 0.6835589408874512 584.7530517578125 0.36743873357772827 1252.944580078125 0.4270155727863312 0.74894404 0.6869767904281616 True -5 16416 30.26663851737976 0.7872929573059082 872.4708251953125 0.5297454595565796 1252.157470703125 0.4275292456150055 0.75775564 0.5546756386756897 True -6 19152 30.33389163017273 0.7288758754730225 834.8544921875 0.6605725288391113 1244.4725341796875 0.43012288212776184 0.76318425 0.5469560027122498 True -7 21888 30.212809324264526 0.7178821563720703 944.37353515625 0.6735574007034302 1234.168212890625 0.4378126263618469 0.77141386 0.4869130551815033 True -8 24624 30.295777320861816 1.5529670715332031 987.12744140625 0.7635879516601562 1226.6290283203125 0.44008341431617737 0.77562183 0.47014638781547546 True -9 27360 30.360530138015747 0.7097089290618896 884.4259033203125 0.3555668890476227 1221.375244140625 0.44126617908477783 0.78376573 0.44448214769363403 True -10 30096 30.22142744064331 0.7101681232452393 996.87109375 0.4373909831047058 1211.35400390625 0.4482388198375702 0.793427 0.4192451238632202 True -11 32832 30.295562982559204 0.7106618881225586 848.0439453125 0.6951116919517517 1206.5042724609375 0.44889459013938904 0.8021999 0.4059567451477051 True -12 35568 30.181872844696045 0.9004857540130615 849.5711669921875 0.4825695753097534 1199.511962890625 0.4533586800098419 0.8106836 0.3803216516971588 True -13 38304 30.19482660293579 0.7065060138702393 947.327392578125 0.5224010944366455 1192.65771484375 0.45692044496536255 0.8166617 0.3841319680213928 True -14 41040 30.201539039611816 0.6929328441619873 893.2422485351562 0.4625593423843384 1188.0203857421875 0.46032413840293884 0.82425827 0.371516615152359 True -15 43776 30.17571997642517 0.6865084171295166 752.3256225585938 0.49756020307540894 1187.5289306640625 0.4588678181171417 0.8318736 0.3566448986530304 True -16 46512 30.21068835258484 0.6945221424102783 970.7120971679688 0.24351897835731506 1188.9276123046875 0.4576399624347687 0.83719707 0.3489319980144501 True -17 49248 30.144471168518066 7.487746715545654 765.742431640625 0.42437613010406494 1186.899658203125 0.458589106798172 0.8380495 0.34568530321121216 True -18 51984 30.246034383773804 0.6966063976287842 769.2823486328125 0.2880123257637024 1188.447265625 0.45670390129089355 0.8408825 0.3447871804237366 True -19 54720 30.235386848449707 0.7121191024780273 717.2018432617188 0.27667713165283203 1185.1063232421875 0.4598146975040436 0.8394125 0.3493230938911438 False diff --git a/ENCSR507GFJ/cherimoya.fold_1.performance.tsv b/ENCSR507GFJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 378c85472bfe2995441f84ff9b1639f66d019aae..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1188.447265625 0.3068252205848694 0.45670393109321594 0.24291887879371643 0.8408824801445007 0.7950400114059448 0.3447871804237366 \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_2.evaluate.json b/ENCSR507GFJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b87364f7fd5b77b1f85a756aa18d4c730845a43c..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330QCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_2.fit.json b/ENCSR507GFJ/cherimoya.fold_2.fit.json deleted file mode 100644 index cd5c4781689e6189b95b80712ae0197a8946a761..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF330QCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_2.log b/ENCSR507GFJ/cherimoya.fold_2.log deleted file mode 100644 index 79a8e956b538801c854cf9f93bc80f4d579240d2..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2903 36.73446869850159 3.69535756111145 1184.6385498046875 0.5907320976257324 1362.747314453125 0.265733927488327 0.6391767 6.17323637008667 True -1 5806 32.52092790603638 0.5385274887084961 699.5916137695312 1.2655255794525146 1183.320556640625 0.38476327061653137 0.6918591 1.7807708978652954 True -2 8709 31.995476722717285 1.5057330131530762 925.79296875 0.6866864562034607 1162.5638427734375 0.39686644077301025 0.71302015 0.9129480123519897 True -3 11612 32.002687215805054 0.5092129707336426 1015.35888671875 0.5849424004554749 1148.4754638671875 0.4046471118927002 0.7197685 0.7052735090255737 True -4 14515 31.99113178253174 0.5018506050109863 934.702880859375 0.4939814805984497 1133.5047607421875 0.41517192125320435 0.73068947 0.584173858165741 True -5 17418 31.984886169433594 0.5077650547027588 1012.52783203125 0.7218677401542664 1129.94970703125 0.4138276278972626 0.7428102 0.5370826125144958 True -6 20321 32.036248207092285 0.501945972442627 816.7344360351562 0.5034122467041016 1125.139404296875 0.4179585576057434 0.7448664 0.5011930465698242 True -7 23224 31.961753129959106 0.8609025478363037 803.375 0.5670636892318726 1117.6160888671875 0.4241340458393097 0.74921703 0.4932061433792114 True -8 26127 32.06848740577698 0.5068628787994385 845.3446044921875 0.7289676070213318 1115.8309326171875 0.42365366220474243 0.7576445 0.4608544409275055 True -9 29030 32.011611223220825 0.5060157775878906 757.0545043945312 0.5264416337013245 1108.55859375 0.42895445227622986 0.76292956 0.4341912567615509 True -10 31933 31.96952223777771 0.5079245567321777 772.8226318359375 0.3278573751449585 1105.3878173828125 0.42951059341430664 0.77396965 0.3992433547973633 True -11 34836 31.983201265335083 0.5121872425079346 895.861572265625 0.684195876121521 1099.823974609375 0.4327208995819092 0.7841815 0.3791186809539795 True -12 37739 32.040953159332275 0.5087893009185791 842.0859375 0.42109954357147217 1096.1817626953125 0.43571367859840393 0.79018337 0.3752584159374237 True -13 40642 31.977494955062866 0.5271737575531006 987.8841552734375 0.593659520149231 1090.4781494140625 0.43901771306991577 0.7984747 0.3582143187522888 True -14 43545 31.987379789352417 0.5536270141601562 835.246337890625 0.3469862937927246 1090.2978515625 0.43982768058776855 0.8062616 0.35431405901908875 True -15 46448 32.02218222618103 0.500708818435669 838.3256225585938 0.4034580886363983 1083.9705810546875 0.4431706666946411 0.8123326 0.3515932857990265 True -16 49351 32.026209354400635 0.5011122226715088 881.919189453125 0.4023387134075165 1085.849853515625 0.44096189737319946 0.81396145 0.3466677963733673 True -17 52254 31.997759342193604 0.5056014060974121 601.113525390625 0.27545368671417236 1084.1920166015625 0.4433327615261078 0.8164616 0.347514271736145 True -18 55157 32.010499238967896 2.0981924533843994 746.5235595703125 0.34479498863220215 1085.3170166015625 0.4418334662914276 0.8181342 0.34435656666755676 True -19 58060 32.11402487754822 0.5121619701385498 772.86962890625 0.37708041071891785 1085.369873046875 0.44206705689430237 0.8193 0.34351813793182373 True diff --git a/ENCSR507GFJ/cherimoya.fold_2.performance.tsv b/ENCSR507GFJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 783c3da6743734217ce0d3ac3be8751ef901ceaa..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1085.369873046875 0.31834304332733154 0.44206702709198 0.22421671450138092 0.8192999958992004 0.7644189596176147 0.34351813793182373 \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_3.evaluate.json b/ENCSR507GFJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fd5fb949221ce83b3122255dc343c472a89c54bb..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330QCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_3.fit.json b/ENCSR507GFJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 60ea60b0a863acb02e73d6ee7d56aa6bc72185ad..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF330QCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_3.log b/ENCSR507GFJ/cherimoya.fold_3.log deleted file mode 100644 index e505fca6f87838acbf7067605031204d82fe5084..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2778 35.21090817451477 8.82704758644104 940.5869750976562 1.0628958940505981 1388.1700439453125 0.2670048177242279 0.65647537 10.045517921447754 True -1 5556 30.601088047027588 0.713047981262207 886.1488037109375 0.9485408663749695 1223.01123046875 0.375381737947464 0.7179245 2.297262191772461 True -2 8334 30.695146322250366 0.6326684951782227 712.1510620117188 0.804659366607666 1200.5743408203125 0.3864639103412628 0.73768485 0.983366847038269 True -3 11112 30.607649087905884 0.5748937129974365 1032.987548828125 0.6276676654815674 1188.99072265625 0.3948393762111664 0.74056876 0.7708751559257507 True -4 13890 30.635377645492554 0.5850119590759277 918.3121337890625 0.6995250582695007 1180.4501953125 0.3998189866542816 0.74845505 0.682718813419342 True -5 16668 30.60469388961792 0.5924925804138184 922.168212890625 0.8851526975631714 1174.22314453125 0.4044681489467621 0.75122875 0.5837807059288025 True -6 19446 30.72623109817505 0.6189179420471191 811.5628662109375 0.6757845878601074 1167.050048828125 0.4095294773578644 0.7522424 0.5296565294265747 True -7 22224 30.599633932113647 0.5802428722381592 891.5701904296875 0.6170244216918945 1164.3856201171875 0.41130557656288147 0.75801945 0.5006265640258789 True -8 25002 30.571060180664062 1.2578859329223633 744.9306640625 0.6243482828140259 1157.894775390625 0.4156511723995209 0.76528615 0.46394091844558716 True -9 27780 30.704912662506104 0.5752618312835693 898.8519287109375 0.5731536149978638 1155.2098388671875 0.41647759079933167 0.7750746 0.44201919436454773 True -10 30558 30.6710786819458 0.5656778812408447 785.3091430664062 0.590674638748169 1152.609130859375 0.41847649216651917 0.77646387 0.41918981075286865 True -11 33336 30.711463928222656 0.5765805244445801 844.4498901367188 0.7204478979110718 1146.1845703125 0.42200416326522827 0.7856718 0.39936208724975586 True -12 36114 30.677228927612305 0.6309740543365479 821.3844604492188 0.6950443387031555 1140.202392578125 0.4265803396701813 0.7955333 0.37651684880256653 True -13 38892 30.705661058425903 0.571923017501831 860.1376342773438 0.5927120447158813 1137.37890625 0.4267619848251343 0.80422896 0.36525383591651917 True -14 41670 30.633298635482788 19.19888663291931 820.1204223632812 0.413953959941864 1132.075927734375 0.4303324222564697 0.8155025 0.3454605042934418 True -15 44448 30.671085596084595 1.0766031742095947 871.6448974609375 0.3481699526309967 1133.8740234375 0.4286035895347595 0.82294756 0.3333205580711365 True -16 47226 30.777466773986816 1.1808440685272217 920.146484375 0.5942114591598511 1126.93115234375 0.4319419264793396 0.8286159 0.3269351124763489 True -17 50004 30.676788091659546 19.981314659118652 828.366943359375 0.3827531933784485 1124.5469970703125 0.43387502431869507 0.82985055 0.3225772976875305 True -18 52782 30.62471032142639 0.5605776309967041 576.4324951171875 0.4386928379535675 1124.9310302734375 0.4332473874092102 0.83044016 0.32329633831977844 True -19 55560 30.703586101531982 0.5708789825439453 957.2620849609375 0.2432226687669754 1123.9974365234375 0.4343222677707672 0.8318607 0.32600489258766174 True diff --git a/ENCSR507GFJ/cherimoya.fold_3.performance.tsv b/ENCSR507GFJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c1c40a6bc5cf46d1f697348d28a4a0358feadb34..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1123.9974365234375 0.31990325450897217 0.4343222379684448 0.22630088031291962 0.8318607211112976 0.7777613997459412 0.32600489258766174 \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_4.evaluate.json b/ENCSR507GFJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3ed1adb7bb2ea1ba9bc6cd212ab9c320598f6881..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF330QCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_4.fit.json b/ENCSR507GFJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 40a64085f1b815ddf4c92a68f1c32c47231a92db..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF330QCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507GFJ/cherimoya.fold_4.log b/ENCSR507GFJ/cherimoya.fold_4.log deleted file mode 100644 index 7415808048a4c6c2c3426ce439185bd093956e1c..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 36.3437716960907 5.015207529067993 1114.7467041015625 0.6021493077278137 1255.2890625 0.2588764429092407 0.65566957 8.253643989562988 True -1 5762 31.821675539016724 1.061997652053833 933.2508544921875 0.8763023018836975 1115.8543701171875 0.3684234321117401 0.7150769 1.6968342065811157 True -2 8643 31.792744159698486 0.6241698265075684 916.0045166015625 0.7240612506866455 1096.950439453125 0.37845027446746826 0.7251312 0.6532077193260193 True -3 11524 31.72511076927185 0.6402628421783447 829.53271484375 0.7625201940536499 1082.015625 0.3861660361289978 0.73579055 0.46425315737724304 True -4 14405 31.79946494102478 9.188199996948242 761.2205810546875 0.5274666547775269 1078.4281005859375 0.38809800148010254 0.739422 0.41447484493255615 True -5 17286 31.75227999687195 1.5809178352355957 757.0509033203125 0.6253741979598999 1068.81982421875 0.3951023519039154 0.74941635 0.36804288625717163 True -6 20167 31.745588779449463 1.1456284523010254 998.45947265625 0.9537637829780579 1063.9119873046875 0.39736464619636536 0.7553883 0.3556516766548157 True -7 23048 31.747114181518555 8.18223786354065 885.3284912109375 1.1557965278625488 1057.1778564453125 0.40217044949531555 0.7667617 0.34211114048957825 True -8 25929 31.797096967697144 0.650270938873291 884.3482666015625 0.6590015888214111 1056.1214599609375 0.40259549021720886 0.7748158 0.32792791724205017 True -9 28810 31.757915258407593 0.6123638153076172 873.5933227539062 0.4751015305519104 1050.2720947265625 0.40779417753219604 0.77736694 0.3216565251350403 True -10 31691 31.845701932907104 0.6274724006652832 916.1217041015625 0.523551344871521 1046.6578369140625 0.4097171723842621 0.7865772 0.3108865022659302 True -11 34572 31.81589651107788 0.6402955055236816 754.1605834960938 0.45395922660827637 1042.080810546875 0.414143830537796 0.7902896 0.30910971760749817 True -12 37453 31.93670082092285 0.6346337795257568 874.803955078125 0.33824217319488525 1040.4725341796875 0.4145503342151642 0.79663175 0.2989746332168579 True -13 40334 31.912229776382446 0.6254158020019531 774.1552734375 0.32840245962142944 1035.764892578125 0.41782933473587036 0.8069588 0.2902790606021881 True -14 43215 31.967000246047974 0.6247663497924805 695.57373046875 0.4550095200538635 1034.809326171875 0.41821348667144775 0.81317586 0.2841555178165436 True -15 46096 31.807879209518433 0.8743572235107422 788.9050903320312 0.33154505491256714 1032.0855712890625 0.4198805093765259 0.81919265 0.28040680289268494 True -16 48977 31.8256196975708 0.6407475471496582 863.2247924804688 0.22774070501327515 1029.6712646484375 0.42227768898010254 0.8222575 0.28010326623916626 True -17 51858 31.917709350585938 0.6210856437683105 687.2022705078125 0.4159998595714569 1030.1123046875 0.4216800332069397 0.82547194 0.2795238792896271 True -18 54739 31.650070190429688 0.6089775562286377 819.6008911132812 0.15238577127456665 1030.9517822265625 0.4205613434314728 0.8239134 0.2837677001953125 False -19 57620 31.147711038589478 0.6139683723449707 851.7933349609375 0.19522438943386078 1029.01220703125 0.42322471737861633 0.8234893 0.28472447395324707 False diff --git a/ENCSR507GFJ/cherimoya.fold_4.performance.tsv b/ENCSR507GFJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 47a1ac95b1539178548a63130d905ae41d03587d..0000000000000000000000000000000000000000 --- a/ENCSR507GFJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1030.1123046875 0.33013835549354553 0.4216800332069397 0.21097806096076965 0.8254719376564026 0.7651880979537964 0.2795238792896271 \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_0.evaluate.json b/ENCSR507XBY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c76ae4c9979fe942516b420f4995e05d260e05e7..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723WLU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_0.fit.json b/ENCSR507XBY/cherimoya.fold_0.fit.json deleted file mode 100644 index 38fb673c103a6ffbbbeeded927a39b79c95f5e22..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF723WLU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_0.log b/ENCSR507XBY/cherimoya.fold_0.log deleted file mode 100644 index 30fbe2a1b82248f3691d689bcba2b1a884784f93..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1445 21.190799951553345 43.66708588600159 548.994873046875 1.6024069786071777 965.9094848632812 0.16065597534179688 0.49817887 19.55600357055664 True -1 2890 17.35884928703308 0.3134171962738037 374.50482177734375 1.443122386932373 830.6751098632812 0.25317084789276123 0.65706825 11.998758316040039 True -2 4335 15.945126056671143 0.29039645195007324 639.2861328125 1.3055431842803955 713.028564453125 0.3193507790565491 0.69443655 6.370741844177246 True -3 5780 17.411657571792603 17.89043354988098 685.4591674804688 1.4392476081848145 670.1829223632812 0.33924180269241333 0.69704 4.3179097175598145 True -4 7225 16.64939594268799 0.3138713836669922 468.080810546875 1.0107091665267944 653.1578369140625 0.35105401277542114 0.70539236 3.186628818511963 True -5 8670 15.954818964004517 0.2967801094055176 750.8320922851562 1.1080994606018066 644.6244506835938 0.3579290211200714 0.71144485 2.3922653198242188 True -6 10115 15.935325622558594 1.1412506103515625 491.1922912597656 1.0296969413757324 635.4402465820312 0.36626100540161133 0.72394854 1.9762731790542603 True -7 11560 16.512086391448975 0.2937953472137451 424.6857604980469 0.8013540506362915 632.104736328125 0.3678246736526489 0.73798645 1.6253517866134644 True -8 13005 15.936765670776367 0.28955698013305664 379.712890625 0.9492483735084534 626.1926879882812 0.3711950480937958 0.7480368 1.3916547298431396 True -9 14450 15.921780824661255 0.2876760959625244 372.91656494140625 1.2351021766662598 617.3184204101562 0.37848952412605286 0.75379384 1.2060972452163696 True -10 15895 16.075390100479126 0.28176188468933105 499.3210144042969 0.8505358695983887 613.7310791015625 0.3796163499355316 0.76731247 1.0291659832000732 True -11 17340 15.921770334243774 0.28603243827819824 459.5859680175781 0.7641029357910156 609.2337036132812 0.3823447823524475 0.7760148 0.9653932452201843 True -12 18785 15.916706323623657 0.7252755165100098 524.7117919921875 0.6651707887649536 604.2445678710938 0.3861488103866577 0.7822666 0.9131360054016113 True -13 20230 15.983725309371948 0.28792333602905273 544.6978149414062 0.9908546805381775 602.9078979492188 0.3857273757457733 0.787652 0.8774062991142273 True -14 21675 15.930651187896729 0.9978606700897217 442.15252685546875 0.6540525555610657 599.0206909179688 0.38769036531448364 0.79525465 0.8332623243331909 True -15 23120 16.055683135986328 0.2864711284637451 458.9677734375 0.6251758337020874 596.1458129882812 0.3895280957221985 0.8006531 0.8172600865364075 True -16 24565 15.90035891532898 0.2845039367675781 432.70684814453125 0.6907204389572144 594.5761108398438 0.38948750495910645 0.8035664 0.7971813678741455 True -17 26010 17.764416217803955 13.726390838623047 496.7068176269531 0.4003812074661255 594.1624145507812 0.38931360840797424 0.8073869 0.78415447473526 True -18 27455 16.681400060653687 0.2858924865722656 425.497802734375 0.5734464526176453 599.2650756835938 0.3843608498573303 0.80714244 0.7831728458404541 False -19 28900 15.932366847991943 0.7527856826782227 474.21246337890625 0.8664608001708984 596.49609375 0.3881336748600006 0.8066862 0.7897270321846008 False diff --git a/ENCSR507XBY/cherimoya.fold_0.performance.tsv b/ENCSR507XBY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5159b8bfdb256e0fe86da0bf6e677748e0e3170c..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -594.1624145507812 0.40605807304382324 0.38931360840797424 0.15212935209274292 0.8073868751525879 0.7720086574554443 0.78415447473526 \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_1.evaluate.json b/ENCSR507XBY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7c9d303e20601960000c99f0cf8ef729dbe6f22a..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723WLU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_1.fit.json b/ENCSR507XBY/cherimoya.fold_1.fit.json deleted file mode 100644 index dec4e2629e51621764b62c80a7e2d39e53be2a77..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF723WLU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_1.log b/ENCSR507XBY/cherimoya.fold_1.log deleted file mode 100644 index 77cb925cfbf912e0bb94cf737764431349aa61b7..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1401 20.02485752105713 3.20198917388916 750.02490234375 1.3434888124465942 1133.2623291015625 0.16807404160499573 0.4531079 22.295516967773438 True -1 2802 15.558410406112671 1.3914954662322998 386.57501220703125 1.1411323547363281 978.7169799804688 0.2604302763938904 0.62335104 14.306262969970703 True -2 4203 15.509053707122803 0.9656870365142822 431.8153991699219 0.8816221952438354 841.8670043945312 0.32812777161598206 0.71380424 6.606966972351074 True -3 5604 15.345866441726685 0.42377734184265137 373.931396484375 1.2364146709442139 782.3775634765625 0.3512514531612396 0.73727214 4.170865058898926 True -4 7005 15.202892303466797 0.4626626968383789 556.999267578125 0.9561864137649536 757.40234375 0.3650636076927185 0.74986666 3.215324640274048 True -5 8406 15.203437805175781 0.4522266387939453 502.661376953125 1.095684289932251 743.6609497070312 0.37173280119895935 0.76446426 2.1521902084350586 True -6 9807 15.209054470062256 0.4283168315887451 456.70733642578125 0.85011887550354 734.5975341796875 0.3779834508895874 0.7718134 1.7390908002853394 True -7 11208 15.187288284301758 0.4312403202056885 502.17864990234375 0.9855311512947083 725.935791015625 0.38309571146965027 0.7823232 1.3695719242095947 True -8 12609 15.203965663909912 0.42486095428466797 404.97686767578125 1.1553122997283936 718.0133056640625 0.38793420791625977 0.78952324 1.171292781829834 True -9 14010 15.195734739303589 0.41965365409851074 542.7872924804688 1.3594343662261963 714.4675903320312 0.3902662396430969 0.7921687 1.1049268245697021 True -10 15411 15.178279399871826 0.59914231300354 487.90496826171875 0.9360834360122681 709.40869140625 0.3934222161769867 0.7984817 1.0418808460235596 True -11 16812 15.188910245895386 0.4329080581665039 571.82275390625 1.227813482284546 703.85107421875 0.3967345356941223 0.80481714 0.9530590772628784 True -12 18213 15.586802244186401 9.518775463104248 593.9232177734375 1.3215889930725098 696.1793212890625 0.40178921818733215 0.80968624 0.8974072337150574 True -13 19614 15.250881910324097 0.4496273994445801 442.35455322265625 1.2101134061813354 694.43359375 0.4019203782081604 0.8174363 0.8508036136627197 True -14 21015 15.16730785369873 0.7258987426757812 441.89593505859375 0.8661909699440002 690.2493896484375 0.4034208059310913 0.82486564 0.8034486174583435 True -15 22416 15.19754147529602 0.4240376949310303 440.5899963378906 0.5302385091781616 684.530517578125 0.40870675444602966 0.8300033 0.7794656753540039 True -16 23817 15.219285011291504 0.42415595054626465 323.5587158203125 0.7427043318748474 684.314453125 0.40769943594932556 0.83085084 0.7663078308105469 True -17 25218 15.234498262405396 0.42430591583251953 525.84033203125 0.5812357068061829 685.0601806640625 0.407587468624115 0.8332493 0.7689990401268005 True -18 26619 15.25191354751587 0.42295336723327637 475.7567138671875 0.4932045340538025 688.3956298828125 0.4048985242843628 0.83287364 0.7705020308494568 False -19 28020 15.233415603637695 0.4393603801727295 352.17022705078125 0.5768955945968628 687.8184204101562 0.4061554968357086 0.83254915 0.7781006693840027 False diff --git a/ENCSR507XBY/cherimoya.fold_1.performance.tsv b/ENCSR507XBY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bc93e29e6fa3b5e6f75a9a3c573d7bdddfc47a16..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -685.0601806640625 0.3887477219104767 0.40758752822875977 0.1735069453716278 0.8332492709159851 0.8108927011489868 0.7689990401268005 \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_2.evaluate.json b/ENCSR507XBY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 36657fb78302c28a6cfea9b881cb0be0dd06a25a..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723WLU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_2.fit.json b/ENCSR507XBY/cherimoya.fold_2.fit.json deleted file mode 100644 index 40f536cc747a22bc0048848313b79e1f4a5725d6..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF723WLU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_2.log b/ENCSR507XBY/cherimoya.fold_2.log deleted file mode 100644 index afeb1291e15f8fbaf7a8496df0ea68ef901df64a..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1513 21.483150005340576 3.1424763202667236 717.5317993164062 1.8718748092651367 978.2022705078125 0.16316093504428864 0.4455179 19.692058563232422 True -1 3026 16.75212335586548 0.3248860836029053 540.7134399414062 1.371504783630371 831.4771728515625 0.2561442255973816 0.6263415 12.495723724365234 True -2 4539 16.786043405532837 0.8386015892028809 490.4490966796875 1.1832334995269775 705.7381591796875 0.32041847705841064 0.69588494 5.763038158416748 True -3 6052 16.766505002975464 0.3129608631134033 505.0804138183594 1.2406175136566162 660.2942504882812 0.34311991930007935 0.7321238 3.1689956188201904 True -4 7565 16.779760360717773 0.3110649585723877 630.29541015625 1.239650011062622 648.9061889648438 0.34837791323661804 0.7463395 2.1963183879852295 True -5 9078 16.748358488082886 0.3552401065826416 490.3623046875 1.0835775136947632 640.5574340820312 0.3540424406528473 0.7568736 1.770448923110962 True -6 10591 16.837873935699463 0.33458995819091797 373.2955322265625 1.069983959197998 634.3700561523438 0.3583846688270569 0.7634304 1.3378171920776367 True -7 12104 16.730340242385864 1.1175954341888428 347.1481628417969 1.2322711944580078 628.2041625976562 0.3623718023300171 0.77283907 1.1270211935043335 True -8 13617 16.797544240951538 0.30584001541137695 520.3212890625 1.0502283573150635 625.963134765625 0.3635075092315674 0.7804386 1.043485164642334 True -9 15130 16.718257665634155 0.30875110626220703 470.0142822265625 1.1488919258117676 616.4517211914062 0.3702828884124756 0.78530306 0.9733525514602661 True -10 16643 16.86962080001831 0.3084745407104492 498.4288635253906 0.8878520727157593 612.5127563476562 0.3725207448005676 0.7887801 0.9195035696029663 True -11 18156 16.736923217773438 0.5218689441680908 542.169677734375 0.772121250629425 609.1072998046875 0.3753453493118286 0.7952263 0.8842151165008545 True -12 19669 16.785425901412964 0.30910253524780273 511.3188781738281 0.597565770149231 604.65234375 0.3776251971721649 0.80030453 0.8411615490913391 True -13 21182 16.794690370559692 0.3139364719390869 458.52752685546875 0.6595028638839722 598.5797119140625 0.38280439376831055 0.8065879 0.7957836389541626 True -14 22695 16.73282289505005 0.3047349452972412 558.8112182617188 0.586228609085083 596.012451171875 0.383999228477478 0.81176674 0.7874406576156616 True -15 24208 16.755641222000122 0.2990548610687256 397.8146057128906 0.8276264667510986 593.9159545898438 0.38509511947631836 0.8167369 0.7612178921699524 True -16 25721 16.717103958129883 0.40304994583129883 470.59832763671875 0.6995507478713989 594.790283203125 0.3840163052082062 0.81792843 0.7537423968315125 True -17 27234 16.80194330215454 0.31907224655151367 424.30279541015625 0.8648776412010193 597.05029296875 0.3813666105270386 0.81814414 0.756759524345398 True -18 28747 16.76415514945984 0.31876659393310547 421.77764892578125 0.5246800184249878 596.5951538085938 0.38265207409858704 0.81681895 0.7628805041313171 False -19 30260 16.774362087249756 0.8394010066986084 499.52984619140625 0.26536494493484497 596.6326904296875 0.3833130896091461 0.81583875 0.7726077437400818 False diff --git a/ENCSR507XBY/cherimoya.fold_2.performance.tsv b/ENCSR507XBY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a9bdf89bcbce7d3f7c39b42db0f1f3a65d9ec122..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -597.05029296875 0.41009145975112915 0.3813665509223938 0.15328149497509003 0.8181441426277161 0.7844096422195435 0.756759524345398 \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_3.evaluate.json b/ENCSR507XBY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f45fd747dab1d533bf147d3fadc3cbb15f3fd128..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723WLU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_3.fit.json b/ENCSR507XBY/cherimoya.fold_3.fit.json deleted file mode 100644 index d0543c9556406835583c7d378e4e607f141b1b41..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF723WLU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_3.log b/ENCSR507XBY/cherimoya.fold_3.log deleted file mode 100644 index 50fdae4216bbbc287206e76fa26f68cb542b71b4..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1454 20.653546810150146 3.918917179107666 454.7314453125 1.3223638534545898 983.276611328125 0.17836317420005798 0.46041724 20.50981330871582 True -1 2908 16.126428604125977 1.6650111675262451 580.3401489257812 1.0506089925765991 842.5888061523438 0.2714443504810333 0.626187 12.833931922912598 True -2 4362 15.782566547393799 0.28252172470092773 595.1497192382812 1.429757833480835 728.999267578125 0.3341825008392334 0.6803678 6.102406978607178 True -3 5816 15.764743328094482 0.3034083843231201 468.78948974609375 0.8884680271148682 697.5616455078125 0.35100647807121277 0.70785123 3.1363096237182617 True -4 7270 15.797993659973145 0.28788018226623535 340.0083923339844 0.8484163880348206 684.021484375 0.3585142493247986 0.7262016 2.40954327583313 True -5 8724 15.752568006515503 1.1469225883483887 495.8402099609375 1.0132652521133423 674.0137329101562 0.3644201159477234 0.737338 1.9630863666534424 True -6 10178 15.788393259048462 1.4563801288604736 646.4566650390625 1.553895115852356 665.8485717773438 0.3708206117153168 0.7469234 1.5184201002120972 True -7 11632 15.76549744606018 0.2829146385192871 599.1148071289062 1.0926241874694824 659.3505249023438 0.375430703163147 0.7461923 1.4171148538589478 False -8 13086 16.22627282142639 5.381711483001709 552.07080078125 0.7113288640975952 654.6311645507812 0.37923818826675415 0.75045604 1.2620317935943604 True -9 14540 15.774124383926392 0.29232144355773926 519.5695190429688 1.0214289426803589 650.5982666015625 0.3822506368160248 0.75999147 1.156269907951355 True -10 15994 15.798316717147827 0.2863438129425049 513.6922607421875 0.49732860922813416 645.297119140625 0.3849392235279083 0.7672176 1.0980364084243774 True -11 17448 15.758128643035889 0.32088232040405273 527.7640380859375 1.0987515449523926 639.4805908203125 0.38890644907951355 0.7742315 1.0365643501281738 True -12 18902 15.774156332015991 0.3051745891571045 464.40960693359375 0.9923038482666016 633.6275024414062 0.3920386731624603 0.779219 0.9806304574012756 True -13 20356 15.780312776565552 0.2790243625640869 347.53594970703125 0.5502580404281616 630.437744140625 0.3938230574131012 0.7892094 0.928710401058197 True -14 21810 15.79093050956726 4.95191216468811 576.2432861328125 1.1503385305404663 623.245849609375 0.3981724977493286 0.79763967 0.8740288019180298 True -15 23264 15.822346448898315 0.296722412109375 532.061279296875 0.5897384881973267 624.1978149414062 0.3957624137401581 0.8023635 0.85801762342453 True -16 24718 15.806281089782715 0.2839620113372803 394.42279052734375 0.6069971323013306 623.6721801757812 0.3962719142436981 0.80682814 0.8317951560020447 True -17 26172 15.80068588256836 0.2858390808105469 394.818115234375 0.5102300643920898 620.7955322265625 0.39845478534698486 0.8089239 0.8202784657478333 True -18 27626 15.818833351135254 0.2875068187713623 404.44439697265625 0.48532208800315857 624.2325439453125 0.39520904421806335 0.8095015 0.8233582973480225 True -19 29080 15.828808546066284 0.28020167350769043 492.3168029785156 0.5673097372055054 623.6690673828125 0.39552929997444153 0.80878556 0.8235070705413818 False diff --git a/ENCSR507XBY/cherimoya.fold_3.performance.tsv b/ENCSR507XBY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9220770748a08077bb43de9a3756779c6d715f2c..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -624.2325439453125 0.3986521065235138 0.39520904421806335 0.1568964123725891 0.8095015287399292 0.7736201286315918 0.8233582973480225 \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_4.evaluate.json b/ENCSR507XBY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a154e88d8f1cbb67c601b08bdf0b463e0dec5ebf..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723WLU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_4.fit.json b/ENCSR507XBY/cherimoya.fold_4.fit.json deleted file mode 100644 index cadec202ef55b5d5f9a29013ca4d47c445105df7..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF723WLU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR507XBY/cherimoya.fold_4.log b/ENCSR507XBY/cherimoya.fold_4.log deleted file mode 100644 index cca6d16ccf7f3bf6ab541961f7ed632bdd3619f4..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1430 20.605711698532104 3.1015989780426025 698.8475341796875 1.8463711738586426 900.7052001953125 0.16126032173633575 0.46547967 18.767194747924805 True -1 2860 15.853924751281738 0.3392767906188965 468.63543701171875 1.270707368850708 771.5905151367188 0.2555270493030548 0.62532675 11.637025833129883 True -2 4290 15.854430913925171 0.2686939239501953 364.522705078125 0.8293542861938477 676.9063110351562 0.31694507598876953 0.6789558 6.113188743591309 True -3 5720 15.816422700881958 0.26825976371765137 552.8862915039062 1.0836098194122314 637.3441772460938 0.33511921763420105 0.68364644 3.6463782787323 True -4 7150 15.845618486404419 0.26891160011291504 526.721435546875 1.199737310409546 620.1795654296875 0.34410327672958374 0.71726865 2.376340389251709 True -5 8580 15.804720163345337 5.771168947219849 450.4847412109375 1.2898719310760498 608.1250610351562 0.35129886865615845 0.7263124 1.9179543256759644 True -6 10010 16.121840715408325 0.2735433578491211 611.1661376953125 1.0890848636627197 600.7117309570312 0.3561907112598419 0.7353284 1.5931178331375122 True -7 11440 15.81244945526123 0.2712593078613281 407.67474365234375 0.952444314956665 597.7539672851562 0.35776451230049133 0.7434764 1.2210854291915894 True -8 12870 16.082854986190796 0.2720608711242676 507.51666259765625 1.0676382780075073 591.80419921875 0.36241811513900757 0.7448373 1.060309648513794 True -9 14300 15.827605247497559 0.2718923091888428 415.658447265625 0.9931968450546265 588.469482421875 0.36482205986976624 0.7528305 1.0137197971343994 True -10 15730 15.833767652511597 0.2717247009277344 432.7286071777344 0.8219802975654602 581.0132446289062 0.37090563774108887 0.76123136 0.943360447883606 True -11 17160 15.836650848388672 0.2629690170288086 575.0132446289062 1.0683246850967407 578.6842651367188 0.3720850646495819 0.7691955 0.906865656375885 True -12 18590 15.838157415390015 0.26836061477661133 556.75830078125 0.9083033800125122 575.391357421875 0.3743552565574646 0.7750265 0.8702901601791382 True -13 20020 15.81892991065979 0.2703683376312256 513.3277587890625 0.5261497497558594 573.4465942382812 0.37605226039886475 0.78303796 0.8428862690925598 True -14 21450 15.833411931991577 0.2829153537750244 560.6529541015625 0.8820205926895142 571.2603759765625 0.3778131306171417 0.7919968 0.8084750771522522 True -15 22880 15.846731662750244 0.2721395492553711 460.1788635253906 0.5212211012840271 568.2311401367188 0.37996840476989746 0.79976374 0.781491219997406 True -16 24310 15.759668588638306 0.26404905319213867 546.6778564453125 0.9399740099906921 568.7761840820312 0.37913447618484497 0.80424154 0.7679292559623718 True -17 25740 15.522695302963257 0.2649507522583008 349.3500061035156 0.5305594205856323 569.31982421875 0.3789243996143341 0.80576724 0.7637321949005127 True -18 27170 15.51567530632019 0.2655375003814697 384.61474609375 0.6525129675865173 572.5880126953125 0.3758087754249573 0.8044085 0.7700179219245911 False -19 28600 15.504237651824951 0.268787145614624 605.9361572265625 0.40833961963653564 572.1876831054688 0.3773126006126404 0.8038715 0.7744615077972412 False diff --git a/ENCSR507XBY/cherimoya.fold_4.performance.tsv b/ENCSR507XBY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 09beb23d1d6723dc09d7bf7357eae76e5f3b1e62..0000000000000000000000000000000000000000 --- a/ENCSR507XBY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -569.31982421875 0.413118839263916 0.3789243996143341 0.14554418623447418 0.8057672381401062 0.7640283107757568 0.7637321949005127 \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_0.evaluate.json b/ENCSR510GRY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2956b3998fec8b567d8da1feb2d24eacc27b55ab..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF104DKS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_0.fit.json b/ENCSR510GRY/cherimoya.fold_0.fit.json deleted file mode 100644 index 979a31e2c8f64f8fedce5dd05e822ab2f53dd8f3..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF104DKS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_0.log b/ENCSR510GRY/cherimoya.fold_0.log deleted file mode 100644 index 64584a6d9d942f56710192cf3ed7c609a7357106..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.451411962509155 3.5999505519866943 427.41131591796875 0.31359434127807617 452.3066101074219 0.22878509759902954 0.8286577 3.4011197090148926 True -1 5488 30.55187749862671 0.6144287586212158 363.9635009765625 0.3202633857727051 429.4892883300781 0.27218666672706604 0.85936385 0.8740828037261963 True -2 8232 30.428719520568848 0.6035053730010986 337.03912353515625 0.31002673506736755 424.5424499511719 0.28148677945137024 0.8730278 0.3765418231487274 True -3 10976 30.389338970184326 0.6038005352020264 403.1236572265625 0.22821548581123352 422.4076843261719 0.2858692705631256 0.8783428 0.296522319316864 True -4 13720 30.39102602005005 0.6043710708618164 402.32843017578125 0.2860032916069031 420.8068542480469 0.2884504497051239 0.881702 0.23239180445671082 True -5 16464 30.411590576171875 0.6005487442016602 405.941650390625 0.20770753920078278 420.8096923828125 0.2884354889392853 0.8863052 0.24023762345314026 True -6 19208 30.45375108718872 0.6100914478302002 379.882080078125 0.220640629529953 419.90972900390625 0.2901703715324402 0.89017844 0.2308659702539444 True -7 21952 30.430575609207153 0.6085407733917236 433.049072265625 0.18392875790596008 418.8879699707031 0.29210686683654785 0.8921529 0.22444850206375122 True -8 24696 30.398279905319214 0.6947500705718994 264.2471008300781 0.14414793252944946 418.32440185546875 0.2934474050998688 0.895935 0.19673870503902435 True -9 27440 30.364118099212646 0.9005820751190186 346.735595703125 0.20374739170074463 417.58551025390625 0.2944413423538208 0.8972108 0.1881939321756363 True -10 30184 30.387935161590576 0.9590480327606201 349.64324951171875 0.21659421920776367 416.6181640625 0.2969874441623688 0.9009034 0.17326779663562775 True -11 32928 30.39413094520569 2.4453210830688477 314.79949951171875 0.17540094256401062 416.0370788574219 0.29782459139823914 0.90336597 0.16142389178276062 True -12 35672 30.47301435470581 1.2033963203430176 344.16827392578125 0.2861431837081909 414.6307373046875 0.3007902503013611 0.90720093 0.1483723372220993 True -13 38416 30.41295886039734 1.408496618270874 386.46783447265625 0.10082188993692398 414.6229553222656 0.2999285161495209 0.9091228 0.1409187614917755 True -14 41160 30.48609232902527 2.3787312507629395 377.68719482421875 0.1508626639842987 414.2544250488281 0.3005899488925934 0.9114832 0.13132870197296143 True -15 43904 30.476436853408813 2.180851459503174 447.84844970703125 0.14921000599861145 414.03662109375 0.3010854423046112 0.9113843 0.1255226582288742 False -16 46648 30.46082091331482 1.4711239337921143 333.957275390625 0.12942230701446533 413.4984436035156 0.3025054335594177 0.9137104 0.1213846281170845 True -17 49392 30.463672876358032 2.2187395095825195 351.4524841308594 0.19706019759178162 413.5738830566406 0.30205437541007996 0.9122962 0.11941707879304886 False -18 52136 29.993876457214355 1.0475406646728516 357.45892333984375 0.1273183524608612 414.0572814941406 0.3010001480579376 0.9117525 0.12136424332857132 False -19 54880 29.851582288742065 0.6022915840148926 350.0352783203125 0.16238604485988617 414.0810852050781 0.3012012243270874 0.91170967 0.12169020622968674 False diff --git a/ENCSR510GRY/cherimoya.fold_0.performance.tsv b/ENCSR510GRY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e95fbb359142ba913a7810780dc5517f1ed680c6..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -413.4984436035156 0.4658648371696472 0.3025054335594177 0.09782049059867859 0.9137104153633118 0.8880415558815002 0.1213846281170845 \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_1.evaluate.json b/ENCSR510GRY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8eafb05fbf8b5ac9630dd7d91eaa7b1832d27672..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF104DKS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_1.fit.json b/ENCSR510GRY/cherimoya.fold_1.fit.json deleted file mode 100644 index 5407ad10471b4995cf0e59e4f9cf183f1086dbb6..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF104DKS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_1.log b/ENCSR510GRY/cherimoya.fold_1.log deleted file mode 100644 index e0bc4552f26f46387beb44d71b5bc9779694b666..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2698 33.551302671432495 4.041899919509888 422.13507080078125 0.2793000042438507 527.1133422851562 0.2370028793811798 0.81829476 4.162268161773682 True -1 5396 30.0131893157959 0.6717662811279297 373.0909423828125 0.1887359619140625 499.25531005859375 0.2849196493625641 0.8498789 0.8276003003120422 True -2 8094 29.933764696121216 0.6680452823638916 355.15625 0.21821242570877075 492.04229736328125 0.2949988543987274 0.86310863 0.5996358394622803 True -3 10792 29.908641815185547 0.9730329513549805 373.58428955078125 0.21070435643196106 488.07073974609375 0.30097970366477966 0.8725451 0.301718145608902 True -4 13490 29.946402549743652 4.559860706329346 377.88653564453125 0.16101685166358948 486.2589111328125 0.30316564440727234 0.8792074 0.2356639802455902 True -5 16188 29.92733907699585 0.6799955368041992 370.7496337890625 0.15962956845760345 484.0945739746094 0.3077080547809601 0.8831286 0.2250770926475525 True -6 18886 29.92704200744629 0.6625659465789795 390.0162658691406 0.19915997982025146 482.84808349609375 0.3091330826282501 0.8870495 0.22346378862857819 True -7 21584 30.451974153518677 0.6831057071685791 378.0418701171875 0.16347697377204895 481.784423828125 0.31068387627601624 0.8917714 0.20155714452266693 True -8 24282 30.07271695137024 0.6642682552337646 417.05560302734375 0.19932861626148224 480.21307373046875 0.3134608566761017 0.89646393 0.18729229271411896 True -9 26980 30.050159215927124 0.6673622131347656 374.359130859375 0.1917594075202942 479.9419860839844 0.31394004821777344 0.89681995 0.17973148822784424 True -10 29678 30.039656162261963 0.6793501377105713 365.5167541503906 0.2699184715747833 478.56597900390625 0.3160582184791565 0.90145546 0.17042548954486847 True -11 32376 29.970313787460327 0.6777136325836182 368.98004150390625 0.19739681482315063 477.90325927734375 0.3169434666633606 0.90579826 0.16270840167999268 True -12 35074 29.955920934677124 0.6722414493560791 352.75079345703125 0.1197512298822403 476.0325012207031 0.3205541968345642 0.90811133 0.15622320771217346 True -13 37772 29.99647355079651 4.523944616317749 394.7381286621094 0.1399994045495987 475.30517578125 0.321508526802063 0.9115288 0.14747686684131622 True -14 40470 29.974789142608643 0.7060301303863525 361.33270263671875 0.16970893740653992 474.6828918457031 0.3217447102069855 0.9146448 0.14242984354496002 True -15 43168 29.960423946380615 0.6777472496032715 370.45074462890625 0.17124108970165253 474.5574645996094 0.3222404718399048 0.91532767 0.13921701908111572 True -16 45866 29.969825506210327 0.6636636257171631 349.65509033203125 0.15085157752037048 473.9309997558594 0.32322078943252563 0.9177723 0.13681693375110626 True -17 48564 29.984967470169067 0.6622600555419922 374.38726806640625 0.13729244470596313 474.0225830078125 0.3236437141895294 0.9178924 0.135237917304039 True -18 51262 29.985540628433228 0.6762537956237793 400.06915283203125 0.07345956563949585 475.12432861328125 0.32107511162757874 0.91944826 0.13415303826332092 True -19 53960 29.822073221206665 0.658994197845459 376.8608703613281 0.11535772681236267 475.2266845703125 0.3209576904773712 0.9179238 0.13495895266532898 False diff --git a/ENCSR510GRY/cherimoya.fold_1.performance.tsv b/ENCSR510GRY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index eb69ee760896c6536f10c7c62bcb47d41cff6586..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.12432861328125 0.4472885727882385 0.32107505202293396 0.11299527436494827 0.9194482564926147 0.9104849100112915 0.13415303826332092 \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_2.evaluate.json b/ENCSR510GRY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 659b39c3876a7776b6a9f7dd1f13736a3ee5149d..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF104DKS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_2.fit.json b/ENCSR510GRY/cherimoya.fold_2.fit.json deleted file mode 100644 index 156cd3335439c66c7c0e071b58999f0167b57301..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF104DKS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_2.log b/ENCSR510GRY/cherimoya.fold_2.log deleted file mode 100644 index 7e41dede523fa306900dc93f4d9112b7f85ad341..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2867 35.67631721496582 3.5179708003997803 340.25323486328125 0.3346804976463318 478.095947265625 0.23208709061145782 0.81440634 2.9548768997192383 True -1 5734 31.935812950134277 0.5719199180603027 376.12579345703125 0.37002310156822205 453.2763366699219 0.27783507108688354 0.85519147 0.6699423789978027 True -2 8601 31.80417561531067 0.5538513660430908 366.5975036621094 0.6851238012313843 449.46697998046875 0.28244030475616455 0.8633611 0.3634238839149475 True -3 11468 31.80013370513916 0.5539016723632812 367.58880615234375 0.20483258366584778 445.86114501953125 0.28814640641212463 0.86969227 0.22514274716377258 True -4 14335 31.771875381469727 0.5534393787384033 367.8460998535156 0.26750409603118896 446.58740234375 0.2872893214225769 0.8694761 0.18951518833637238 False -5 17202 31.831716060638428 0.557610273361206 349.156494140625 0.21276052296161652 443.71484375 0.2918998599052429 0.8734471 0.19722862541675568 True -6 20069 31.817699670791626 0.5561950206756592 341.0214538574219 0.2265244424343109 442.4361572265625 0.29484298825263977 0.8793514 0.19023443758487701 True -7 22936 32.36007881164551 5.060759782791138 366.8436279296875 0.24123609066009521 441.2625427246094 0.29631364345550537 0.88253087 0.18843749165534973 True -8 25803 31.85338044166565 0.5724589824676514 389.68157958984375 0.30171999335289 441.0440368652344 0.29691243171691895 0.8826119 0.2006630301475525 True -9 28670 31.828683614730835 0.8576846122741699 376.4117431640625 0.18694666028022766 439.5669860839844 0.29919132590293884 0.8881642 0.18436199426651 True -10 31537 31.889970302581787 0.5586583614349365 448.053955078125 0.16247130930423737 438.5124206542969 0.30218708515167236 0.890286 0.1780952662229538 True -11 34404 31.80910587310791 0.5546019077301025 294.421142578125 0.21094101667404175 438.5870056152344 0.30078810453414917 0.89238244 0.1724804788827896 True -12 37271 31.796857595443726 0.5621201992034912 381.62164306640625 0.21865785121917725 437.9434509277344 0.3023940324783325 0.89439154 0.16106469929218292 True -13 40138 31.849881410598755 0.5601027011871338 377.27642822265625 0.1256408542394638 436.9176330566406 0.3040939271450043 0.89754033 0.15113496780395508 True -14 43005 31.82352066040039 0.5551424026489258 407.34014892578125 0.1441681832075119 436.6372375488281 0.30436986684799194 0.8986052 0.14463335275650024 True -15 45872 31.820729732513428 0.5634288787841797 322.65509033203125 0.13745978474617004 435.96624755859375 0.30550140142440796 0.9018668 0.14012371003627777 True -16 48739 31.81222438812256 0.5596654415130615 386.893310546875 0.1519259661436081 435.88702392578125 0.3055855631828308 0.90374845 0.13693007826805115 True -17 51606 31.814794540405273 0.5556755065917969 417.043701171875 0.0858711302280426 436.19671630859375 0.304934561252594 0.90385383 0.13588246703147888 True -18 54473 31.820528507232666 0.5591630935668945 349.0505065917969 0.12295272201299667 435.66400146484375 0.3067232668399811 0.9028944 0.13594527542591095 False -19 57340 31.760679006576538 0.5543286800384521 377.26434326171875 0.11852070689201355 435.8124084472656 0.30624574422836304 0.90313524 0.13701438903808594 False diff --git a/ENCSR510GRY/cherimoya.fold_2.performance.tsv b/ENCSR510GRY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 62cedd17e1ded0723485d29dec1fdab0cc2ef67d..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -436.19671630859375 0.4604766070842743 0.304934561252594 0.10209572315216064 0.9038538336753845 0.887022852897644 0.13588246703147888 \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_3.evaluate.json b/ENCSR510GRY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8d1016b7f2f8ea595de85bcd143a1f362f792cb6..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF104DKS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_3.fit.json b/ENCSR510GRY/cherimoya.fold_3.fit.json deleted file mode 100644 index d774f13358b1ba125f4c7064076d3fe26e8576da..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF104DKS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_3.log b/ENCSR510GRY/cherimoya.fold_3.log deleted file mode 100644 index 232044090209ab7e19bf081f6f207d09712d73a5..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2725 34.445308208465576 2.743271827697754 349.9253234863281 0.2340136617422104 446.6889343261719 0.2353023737668991 0.80159116 3.844015121459961 True -1 5450 30.28564977645874 0.48856019973754883 352.4132995605469 0.3525538444519043 423.20440673828125 0.27925407886505127 0.8527704 0.6790293455123901 True -2 8175 30.19921636581421 0.4845740795135498 365.33282470703125 0.3018442690372467 419.7303466796875 0.2844650149345398 0.8609682 0.30085161328315735 True -3 10900 30.182533502578735 0.4779806137084961 364.99554443359375 0.3985127806663513 416.4144287109375 0.2903532087802887 0.8701154 0.26247096061706543 True -4 13625 30.21150493621826 0.4796180725097656 402.6058349609375 0.24948278069496155 416.03631591796875 0.2898918092250824 0.8756093 0.24427315592765808 True -5 16350 30.232264041900635 0.48805761337280273 375.29022216796875 0.23509636521339417 414.31951904296875 0.29311224818229675 0.8804934 0.21450525522232056 True -6 19075 30.260562419891357 0.4848613739013672 414.52154541015625 0.23073288798332214 413.1141662597656 0.2959357798099518 0.8869588 0.19271641969680786 True -7 21800 30.23695969581604 0.49098849296569824 358.9671936035156 0.1789110004901886 412.50579833984375 0.29705342650413513 0.8875607 0.19852575659751892 True -8 24525 30.222663640975952 0.4899330139160156 398.0775146484375 0.25916486978530884 411.43536376953125 0.2993822693824768 0.89319664 0.18447689712047577 True -9 27250 30.205751180648804 1.0438611507415771 406.6182861328125 0.27752023935317993 411.39605712890625 0.29921188950538635 0.8952384 0.1748727262020111 True -10 29975 30.249947547912598 0.4846174716949463 360.1897888183594 0.18094530701637268 410.4823913574219 0.30167877674102783 0.8953095 0.17020724713802338 True -11 32700 30.252355337142944 0.4882700443267822 397.61285400390625 0.22020798921585083 409.32623291015625 0.3039972186088562 0.9003321 0.16197435557842255 True -12 35425 30.267735242843628 0.4854624271392822 379.0863037109375 0.15241876244544983 408.76263427734375 0.3050224184989929 0.9004602 0.15539079904556274 True -13 38150 30.275625944137573 0.4864692687988281 360.121826171875 0.10073532909154892 408.5496826171875 0.3045041859149933 0.9021338 0.14869998395442963 True -14 40875 30.27312135696411 0.48500943183898926 376.1497802734375 0.19250580668449402 407.65228271484375 0.30651548504829407 0.90543056 0.1404193937778473 True -15 43600 30.301908254623413 0.48516297340393066 336.1416931152344 0.14993199706077576 407.81121826171875 0.30527541041374207 0.908241 0.13625787198543549 True -16 46325 30.271381855010986 1.7446599006652832 420.7008972167969 0.0998799055814743 407.35345458984375 0.3069905638694763 0.9088993 0.132707417011261 True -17 49050 30.219932317733765 0.4816923141479492 402.6665954589844 0.264522910118103 407.256591796875 0.30716177821159363 0.9103014 0.12909053266048431 True -18 51775 30.3173508644104 0.48300933837890625 431.921630859375 0.10517704486846924 407.4382019042969 0.30615270137786865 0.9118058 0.1288570612668991 True -19 54500 30.412592887878418 0.49481773376464844 328.82177734375 0.17226681113243103 407.2709655761719 0.3073141574859619 0.91036856 0.12929213047027588 False diff --git a/ENCSR510GRY/cherimoya.fold_3.performance.tsv b/ENCSR510GRY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2590ffcc0ddc45a8dbfef55ea2c9acb0f50dede4..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -407.4382019042969 0.4644308090209961 0.30615270137786865 0.10215197503566742 0.9118058085441589 0.8785030245780945 0.1288570612668991 \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_4.evaluate.json b/ENCSR510GRY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b5b7f7b601dccfd67ee73743102e608abd58ed44..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF104DKS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_4.fit.json b/ENCSR510GRY/cherimoya.fold_4.fit.json deleted file mode 100644 index 5336fbf4a067526c911679892b3660a931e454d3..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF104DKS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR510GRY/cherimoya.fold_4.log b/ENCSR510GRY/cherimoya.fold_4.log deleted file mode 100644 index c4a3eae45732afc0ef747d785656a6409181f574..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2830 34.72645902633667 3.767535924911499 344.3843688964844 0.27858537435531616 415.3174133300781 0.22552762925624847 0.8219259 2.8059349060058594 True -1 5660 31.53190588951111 0.6746394634246826 348.9952697753906 0.25187963247299194 397.5290832519531 0.26356399059295654 0.85133857 0.5460861921310425 True -2 8490 31.384034395217896 0.6561288833618164 393.35784912109375 0.24142338335514069 392.33251953125 0.27211102843284607 0.866197 0.2223830372095108 True -3 11320 31.40884304046631 0.6465394496917725 403.435302734375 0.37152528762817383 390.7151184082031 0.27402663230895996 0.8754935 0.19536209106445312 True -4 14150 31.38847279548645 13.827093362808228 388.302978515625 0.21656125783920288 389.4464111328125 0.2771483063697815 0.8822722 0.1690238118171692 True -5 16980 32.89070987701416 0.7260568141937256 330.062255859375 0.27732717990875244 388.7257995605469 0.27835479378700256 0.8834627 0.1542578637599945 True -6 19810 31.403358697891235 0.6588616371154785 350.5451354980469 0.1441432237625122 388.386962890625 0.27838581800460815 0.8874226 0.15710628032684326 True -7 22640 31.551974534988403 0.6515696048736572 309.120361328125 0.1913769245147705 387.63909912109375 0.28043562173843384 0.891072 0.14471660554409027 True -8 25470 31.450645685195923 0.6560173034667969 349.94342041015625 0.2201036512851715 387.0053405761719 0.28232541680336 0.8969349 0.1459297090768814 True -9 28300 31.39871835708618 1.066495656967163 374.3892822265625 0.20556926727294922 385.9397888183594 0.2842705249786377 0.8985038 0.1436477154493332 True -10 31130 31.434584140777588 1.7278468608856201 371.76910400390625 0.21250903606414795 385.2507019042969 0.28577956557273865 0.9003165 0.14299865067005157 True -11 33960 31.505150318145752 0.6525187492370605 289.234130859375 0.17093883454799652 384.5638122558594 0.2873587906360626 0.90387565 0.1328079253435135 True -12 36790 31.376184940338135 4.815270185470581 415.5155944824219 0.1357118785381317 384.23333740234375 0.2878943383693695 0.9045677 0.1278194636106491 True -13 39620 31.56380844116211 1.932142972946167 334.9623718261719 0.13329318165779114 383.89593505859375 0.288337767124176 0.9070331 0.12168192118406296 True -14 42450 31.56899404525757 2.51104998588562 363.6905822753906 0.1534266173839569 383.383056640625 0.28983786702156067 0.91086245 0.11496978998184204 True -15 45280 31.48196530342102 30.03491234779358 366.10638427734375 0.14302122592926025 383.2395324707031 0.29043275117874146 0.9138136 0.10999397933483124 True -16 48110 31.47212839126587 0.7217435836791992 326.2490234375 0.07836851477622986 383.2623291015625 0.2899194061756134 0.9145045 0.10750450193881989 True -17 50940 31.40774130821228 0.636744499206543 360.15399169921875 0.07123857736587524 383.18341064453125 0.2904335856437683 0.9136417 0.10538281500339508 False -18 53770 31.357112169265747 0.6525368690490723 333.0713195800781 0.21958763897418976 383.1825866699219 0.29019540548324585 0.9153931 0.10540737956762314 True -19 56600 31.416959285736084 0.636223316192627 364.7657165527344 0.11668418347835541 383.0611267089844 0.2909923195838928 0.91303545 0.10558842867612839 False diff --git a/ENCSR510GRY/cherimoya.fold_4.performance.tsv b/ENCSR510GRY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index df718adc6d2872c79a7f55f07b12184ac3b2fd73..0000000000000000000000000000000000000000 --- a/ENCSR510GRY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -383.1825866699219 0.4764755070209503 0.29019543528556824 0.09202171862125397 0.9153931140899658 0.8814512491226196 0.10540737956762314 \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_0.evaluate.json b/ENCSR511GQA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4f8ce5f17abf82f3566c32b37c8bcb0156b334dc..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF319MZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_0.fit.json b/ENCSR511GQA/cherimoya.fold_0.fit.json deleted file mode 100644 index 54beeddb9068c7c2267c0ab1d073b987a00f0bff..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF319MZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_0.log b/ENCSR511GQA/cherimoya.fold_0.log deleted file mode 100644 index acd0707e099c34ca5d5e93ec1f3adf380b4e475f..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 34.30706191062927 13.430832624435425 115.07975769042969 0.6271015405654907 143.15988159179688 0.11616361886262894 0.5120652 1.9152476787567139 True -1 5486 32.045154333114624 0.6235613822937012 86.73277282714844 0.560728907585144 135.6470489501953 0.1700989454984665 0.5941998 1.0506967306137085 True -2 8229 30.60097622871399 0.6077773571014404 125.54733276367188 0.6210216879844666 133.5543670654297 0.18281525373458862 0.61503017 0.6740275621414185 True -3 10972 30.61609387397766 0.5980551242828369 94.39801788330078 0.5184642672538757 132.77334594726562 0.18555687367916107 0.62906194 0.4975001811981201 True -4 13715 30.582446575164795 0.8613040447235107 108.55428314208984 0.46151310205459595 132.36036682128906 0.18725097179412842 0.6313809 0.4887871742248535 True -5 16458 30.66341209411621 0.6307976245880127 105.97650146484375 0.4527343213558197 131.98240661621094 0.18981197476387024 0.6368103 0.4911177158355713 True -6 19201 30.618005752563477 0.606130838394165 110.41453552246094 0.35506492853164673 131.3913116455078 0.19546116888523102 0.6428066 0.5130602717399597 True -7 21944 30.639541625976562 0.5968320369720459 129.90774536132812 0.5070686340332031 131.21334838867188 0.19631396234035492 0.6482095 0.468992680311203 True -8 24687 30.62954616546631 1.2040741443634033 121.17713928222656 0.5000898241996765 130.9986572265625 0.197805717587471 0.65187085 0.4820605516433716 True -9 27430 30.690361261367798 0.5971930027008057 77.87498474121094 0.597385823726654 130.77627563476562 0.19987718760967255 0.65768594 0.45968496799468994 True -10 30173 30.61042022705078 0.6037182807922363 99.15225219726562 0.43901270627975464 130.451904296875 0.20245954394340515 0.66089314 0.4572213888168335 True -11 32916 30.59355664253235 0.5945992469787598 103.38133239746094 0.5224261283874512 130.2832489013672 0.20312733948230743 0.6733552 0.41744256019592285 True -12 35659 30.60727596282959 0.5942142009735107 116.80560302734375 0.3044908046722412 129.84339904785156 0.20674964785575867 0.6831958 0.3928721845149994 True -13 38402 30.610414028167725 0.587054967880249 100.75538635253906 0.35816752910614014 129.59341430664062 0.20878078043460846 0.6946622 0.3587990403175354 True -14 41145 30.699215412139893 0.5970089435577393 102.879638671875 0.29915887117385864 129.47488403320312 0.20905078947544098 0.7025066 0.3298030495643616 True -15 43888 30.635310411453247 0.6055288314819336 109.14599609375 0.2934340834617615 129.1688995361328 0.21203580498695374 0.7105764 0.31510359048843384 True -16 46631 30.638376474380493 0.5970487594604492 126.58003997802734 0.2821337580680847 129.15518188476562 0.21151769161224365 0.71498936 0.29980289936065674 True -17 49374 30.61423397064209 0.5895988941192627 99.47468566894531 0.244520902633667 129.02232360839844 0.21313920617103577 0.7194606 0.2907246947288513 True -18 52117 30.623520135879517 0.5954535007476807 99.83527374267578 0.4040229916572571 129.0845184326172 0.21173177659511566 0.7217315 0.2878657877445221 True -19 54860 30.694042921066284 0.6062135696411133 120.748046875 0.3206373453140259 129.1224822998047 0.2116755247116089 0.7210116 0.28997331857681274 False diff --git a/ENCSR511GQA/cherimoya.fold_0.performance.tsv b/ENCSR511GQA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1475b7207d6a2941f76ba495ea8ac165b63be26e..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -129.0845184326172 0.5697447061538696 0.21173174679279327 0.035047125071287155 0.7217314839363098 0.6569945216178894 0.2878657877445221 \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_1.evaluate.json b/ENCSR511GQA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 78493778f1e6240944beab293140f2352f19df76..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF319MZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_1.fit.json b/ENCSR511GQA/cherimoya.fold_1.fit.json deleted file mode 100644 index 3731ae65d669696a1cae26e44baff4ba0cb4dfa1..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF319MZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_1.log b/ENCSR511GQA/cherimoya.fold_1.log deleted file mode 100644 index baf08fa5fc28eb199d15609c5254802001409757..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.024014949798584 3.6462295055389404 98.11441802978516 0.5957413911819458 163.74026489257812 0.12048612534999847 0.54533625 1.9902266263961792 True -1 5488 30.319249391555786 0.7649388313293457 100.60492706298828 0.575255274772644 153.8873748779297 0.18409383296966553 0.640464 1.0541962385177612 True -2 8232 30.356419801712036 0.730759859085083 96.72093963623047 0.790932834148407 151.52186584472656 0.19439847767353058 0.64521754 0.6608661413192749 True -3 10976 30.30812907218933 1.696138858795166 110.40306091308594 0.6532090902328491 150.42689514160156 0.19960808753967285 0.65770614 0.5403891801834106 True -4 13720 33.04709076881409 6.206472635269165 111.75563049316406 0.4141782224178314 149.92947387695312 0.2021854817867279 0.66922987 0.5291079878807068 True -5 16464 30.425740242004395 0.7286741733551025 123.03295135498047 0.4500542879104614 149.5193634033203 0.20528191328048706 0.6796307 0.5100796222686768 True -6 19208 30.42285704612732 0.7422442436218262 114.81985473632812 0.5015484690666199 148.94862365722656 0.20807935297489166 0.69167876 0.4929805099964142 True -7 21952 30.35205364227295 0.731473445892334 114.57428741455078 0.4319528639316559 148.7558135986328 0.20857612788677216 0.7000299 0.4705042541027069 True -8 24696 30.314409971237183 0.7228035926818848 99.58267211914062 0.5930575728416443 148.41246032714844 0.21029405295848846 0.70203835 0.47417184710502625 True -9 27440 30.302252054214478 0.7390234470367432 98.35443115234375 0.5129806995391846 148.11875915527344 0.21224567294120789 0.70588785 0.4600696563720703 True -10 30184 30.398805379867554 1.6634955406188965 130.18357849121094 0.5155828595161438 147.51898193359375 0.21662183105945587 0.7136564 0.4309820234775543 True -11 32928 30.75276803970337 0.7358012199401855 97.75371551513672 0.44681841135025024 147.20294189453125 0.21767249703407288 0.72382987 0.4197351336479187 True -12 35672 30.367294549942017 0.7276537418365479 114.77468872070312 0.3360385596752167 146.84939575195312 0.2204478234052658 0.72974247 0.3673906922340393 True -13 38416 30.39456605911255 0.7393894195556641 115.21270751953125 0.2975269854068756 146.4130401611328 0.22333846986293793 0.73812675 0.35293105244636536 True -14 41160 30.383233547210693 0.734138011932373 119.92768859863281 0.4068208932876587 146.2605438232422 0.22391238808631897 0.7499478 0.33681413531303406 True -15 43904 30.385236978530884 0.7168519496917725 97.71617126464844 0.2901698648929596 145.97970581054688 0.22568291425704956 0.7547171 0.32361161708831787 True -16 46648 30.35013246536255 0.7229743003845215 102.82865905761719 0.3944806456565857 145.86920166015625 0.22599071264266968 0.7611284 0.3140469491481781 True -17 49392 30.342320203781128 0.7325372695922852 106.16273498535156 0.3480221629142761 146.01864624023438 0.224457249045372 0.7638733 0.30987754464149475 True -18 52136 30.35318374633789 0.8457849025726318 108.03764343261719 0.2911915183067322 145.99256896972656 0.22519513964653015 0.7641174 0.3075959086418152 True -19 54880 30.379381895065308 0.7374827861785889 95.01345825195312 0.1695190966129303 145.88595581054688 0.2260473370552063 0.7638942 0.30685338377952576 False diff --git a/ENCSR511GQA/cherimoya.fold_1.performance.tsv b/ENCSR511GQA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 91c2555b5149e61b4eea963e82148a1b2a1dfbeb..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -145.99256896972656 0.5577592849731445 0.22519513964653015 0.041612785309553146 0.764117419719696 0.7036423087120056 0.3075959086418152 \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_2.evaluate.json b/ENCSR511GQA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ac113422bf06ce7cf86a12943c2b42f8b54187cc..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF319MZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_2.fit.json b/ENCSR511GQA/cherimoya.fold_2.fit.json deleted file mode 100644 index 254672ccf2a74aaa7a91b1c6977bbf35537a549e..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF319MZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_2.log b/ENCSR511GQA/cherimoya.fold_2.log deleted file mode 100644 index a8a4ff689a628252475dbe56d93bfb8ab4aea0c8..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 37.08210825920105 3.58591628074646 113.03128051757812 0.6119798421859741 146.20443725585938 0.12096605449914932 0.5264425 1.714333415031433 True -1 5800 32.39145541191101 0.552217960357666 100.61245727539062 0.5244251489639282 137.96609497070312 0.17815637588500977 0.6179409 0.8323711156845093 True -2 8700 32.449615240097046 0.5447320938110352 107.63957214355469 0.31907081604003906 135.81666564941406 0.1891765296459198 0.63641894 0.5244604349136353 True -3 11600 32.435423135757446 0.5453701019287109 112.87130737304688 0.6461852788925171 134.9345703125 0.19401238858699799 0.64600044 0.41468358039855957 True -4 14500 32.48056483268738 0.5472772121429443 96.12588500976562 0.46837118268013 134.6907501220703 0.19541563093662262 0.65165365 0.42916131019592285 True -5 17400 32.426743030548096 15.35504961013794 112.20695495605469 0.40597647428512573 134.32373046875 0.19798800349235535 0.65653104 0.4435479938983917 True -6 20300 32.83981513977051 0.5536832809448242 117.42364501953125 0.5452442169189453 134.15025329589844 0.1980362981557846 0.6643902 0.44367679953575134 True -7 23200 32.45474576950073 0.5522422790527344 87.60818481445312 0.4755517840385437 133.72740173339844 0.20131871104240417 0.66682005 0.4329836368560791 True -8 26100 32.395079374313354 0.5481452941894531 109.37040710449219 0.5848119854927063 133.44810485839844 0.2038678228855133 0.67598987 0.4294210970401764 True -9 29000 32.43536925315857 0.5450901985168457 120.82109832763672 0.46741610765457153 133.13742065429688 0.2057839334011078 0.68013906 0.41500988602638245 True -10 31900 32.39268231391907 0.5394012928009033 113.18330383300781 0.6488124132156372 132.8304901123047 0.20811615884304047 0.6852484 0.40590474009513855 True -11 34800 32.39680361747742 24.968912601470947 96.85693359375 0.5191887021064758 132.443603515625 0.21079054474830627 0.69819 0.3496486246585846 True -12 37700 32.623125314712524 0.5439243316650391 118.54196166992188 0.3315753936767578 132.1046905517578 0.21361634135246277 0.70811665 0.33364352583885193 True -13 40600 32.534170627593994 0.5460331439971924 87.24917602539062 0.4513883590698242 131.94691467285156 0.21424390375614166 0.7172309 0.31329625844955444 True -14 43500 32.41101121902466 8.1499764919281 90.96435546875 0.3787107765674591 131.6886444091797 0.21587038040161133 0.72356725 0.30194100737571716 True -15 46400 32.550891399383545 0.5846114158630371 121.38233947753906 0.2729470729827881 131.4803924560547 0.21770702302455902 0.73136866 0.29009026288986206 True -16 49300 32.43152165412903 2.2203328609466553 106.95088958740234 0.37193071842193604 131.46278381347656 0.217513307929039 0.73709244 0.2880263924598694 True -17 52200 32.6259708404541 0.5754706859588623 101.19075012207031 0.23246020078659058 131.46722412109375 0.2171492874622345 0.7392559 0.28250283002853394 True -18 55100 32.900521755218506 1.049112319946289 105.44763946533203 0.41324055194854736 131.44207763671875 0.21749849617481232 0.7396016 0.28416064381599426 True -19 58000 32.826528549194336 0.9984838962554932 106.8192138671875 0.30168771743774414 131.42648315429688 0.21788008511066437 0.73995966 0.2845363914966583 True diff --git a/ENCSR511GQA/cherimoya.fold_2.performance.tsv b/ENCSR511GQA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c7110cb6cf1e84176c29de746f470cbbc360cd42..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -131.42648315429688 0.5658341646194458 0.21788008511066437 0.03641072288155556 0.7399596571922302 0.6811574101448059 0.2845363914966583 \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_3.evaluate.json b/ENCSR511GQA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3317ef615129fcccc718101008db30af83b7738f..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF319MZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_3.fit.json b/ENCSR511GQA/cherimoya.fold_3.fit.json deleted file mode 100644 index e94778b9ad1b38e4fde1989082428990db93c9f8..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF319MZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_3.log b/ENCSR511GQA/cherimoya.fold_3.log deleted file mode 100644 index ef0959e89438c756864424b2a2f96d8fce267966..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2788 34.78590512275696 3.6659867763519287 117.00581359863281 0.7640363574028015 150.42486572265625 0.11745394021272659 0.5467464 1.9066599607467651 True -1 5576 30.90767002105713 0.6048970222473145 120.3184814453125 0.44096946716308594 142.2472381591797 0.17670483887195587 0.6293422 0.9543124437332153 True -2 8364 31.339425802230835 0.6015560626983643 104.73191833496094 0.45382681488990784 140.24917602539062 0.18642283976078033 0.6436986 0.5229059457778931 True -3 11152 30.85178232192993 0.5965089797973633 131.816650390625 0.29125988483428955 139.43844604492188 0.18997898697853088 0.656755 0.5175775289535522 True -4 13940 30.861337423324585 0.6066794395446777 116.71127319335938 0.3378589153289795 138.92926025390625 0.19365619122982025 0.6546425 0.5353865623474121 False -5 16728 30.82518434524536 0.5937762260437012 102.60270690917969 0.35334309935569763 138.65936279296875 0.19571121037006378 0.66190773 0.5178146362304688 True -6 19516 31.026612997055054 0.6029479503631592 94.13723754882812 0.5947141647338867 138.28387451171875 0.19825580716133118 0.6678415 0.5244976878166199 True -7 22304 31.0021071434021 0.6008353233337402 84.99384307861328 0.707526445388794 138.2103729248047 0.19820928573608398 0.6671192 0.5036426782608032 False -8 25092 30.890048503875732 0.6021995544433594 93.30419921875 0.35664570331573486 137.89691162109375 0.20041494071483612 0.67542255 0.4612269103527069 True -9 27880 30.846176624298096 0.5996048450469971 101.0982666015625 0.31427618861198425 137.62142944335938 0.20335742831230164 0.6783841 0.43056052923202515 True -10 30668 30.83095145225525 0.5973067283630371 103.04624938964844 0.3895900249481201 137.3135223388672 0.20503383874893188 0.6852852 0.41228383779525757 True -11 33456 30.857649326324463 0.599682092666626 91.93333435058594 0.4178691506385803 137.01513671875 0.20765672624111176 0.68997365 0.4186975955963135 True -12 36244 30.90411615371704 0.5969090461730957 74.1390609741211 0.4372285008430481 136.6122283935547 0.21056777238845825 0.70089334 0.37814679741859436 True -13 39032 30.902955055236816 0.5993974208831787 90.43202209472656 0.5878562927246094 136.2044677734375 0.21368247270584106 0.7130125 0.36314281821250916 True -14 41820 30.85513472557068 0.5994997024536133 96.93408966064453 0.3913452625274658 136.01025390625 0.2143247425556183 0.7243856 0.33989936113357544 True -15 44608 30.858173847198486 0.5961973667144775 117.47463989257812 0.3418329358100891 135.8704833984375 0.21528872847557068 0.7315155 0.3193057179450989 True -16 47396 30.902425289154053 0.5999162197113037 95.8576889038086 0.27361786365509033 135.9036865234375 0.21431434154510498 0.73695993 0.309761643409729 True -17 50184 30.897003889083862 0.6051459312438965 107.24225616455078 0.3392345607280731 136.04762268066406 0.21334458887577057 0.74112314 0.2998608350753784 True -18 52972 30.88528060913086 0.6006863117218018 117.91761779785156 0.38714829087257385 135.90684509277344 0.21486793458461761 0.7424573 0.2989005744457245 True -19 55760 30.962335109710693 0.6017115116119385 113.29096221923828 0.32735422253608704 135.87600708007812 0.21545130014419556 0.74208224 0.2980121076107025 False diff --git a/ENCSR511GQA/cherimoya.fold_3.performance.tsv b/ENCSR511GQA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8c3beef9445f899c82822a9e6b63dd26f671f71b..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -135.90684509277344 0.5665637850761414 0.2148679494857788 0.035973403602838516 0.7424572706222534 0.6790615320205688 0.2989005744457245 \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_4.evaluate.json b/ENCSR511GQA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c7f0c3e4a5bfc1a92fa5a16c160285ad04c4f058..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF319MZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_4.fit.json b/ENCSR511GQA/cherimoya.fold_4.fit.json deleted file mode 100644 index ff7b03edb90751a0c66038b2ee1b558cbd3b6b13..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF319MZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511GQA/cherimoya.fold_4.log b/ENCSR511GQA/cherimoya.fold_4.log deleted file mode 100644 index d54e9caa73a70cf9b9738e6cd37c54c1e2cfd7c0..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 35.99028038978577 3.4702506065368652 117.08970642089844 0.5405063033103943 141.52557373046875 0.11614777147769928 0.5203538 1.2710156440734863 True -1 5770 32.18994617462158 0.6964223384857178 115.15057373046875 0.5721179842948914 134.41860961914062 0.17110584676265717 0.60583407 0.9100894331932068 True -2 8655 32.309699296951294 9.192779541015625 99.58990478515625 0.6024773120880127 132.81019592285156 0.179452046751976 0.6174911 0.559444785118103 True -3 11540 32.24525713920593 0.613591194152832 102.42875671386719 0.498809278011322 131.8057098388672 0.183616504073143 0.6248767 0.5374622941017151 True -4 14425 32.305792808532715 0.6147580146789551 110.00887298583984 0.42735958099365234 131.25177001953125 0.18708530068397522 0.6363635 0.5346591472625732 True -5 17310 32.242080211639404 0.6094634532928467 114.19290924072266 0.4825453758239746 131.08984375 0.18813170492649078 0.643631 0.5619891881942749 True -6 20195 32.185447216033936 0.6042261123657227 105.88750457763672 0.4441795349121094 130.7993927001953 0.19018761813640594 0.6464721 0.5914354920387268 True -7 23080 32.214457750320435 1.1867148876190186 118.760498046875 0.6375678777694702 130.49160766601562 0.19305139780044556 0.64920115 0.5843349695205688 True -8 25965 32.192548513412476 15.982328176498413 102.2826156616211 0.32669302821159363 130.17208862304688 0.19556258618831635 0.65209335 0.5568583011627197 True -9 28850 32.74369812011719 0.6159484386444092 84.19813537597656 0.5411930084228516 129.94984436035156 0.19791972637176514 0.6556798 0.527131974697113 True -10 31735 32.25555181503296 0.6123337745666504 108.2684555053711 0.44179481267929077 129.7310791015625 0.19927875697612762 0.6648421 0.49646878242492676 True -11 34620 32.302709102630615 0.6153774261474609 118.15477752685547 0.4184074401855469 129.4200897216797 0.20139215886592865 0.6784589 0.41153684258461 True -12 37505 32.23022413253784 0.6144058704376221 105.7703857421875 0.3781752586364746 129.0830078125 0.20358909666538239 0.690296 0.37463274598121643 True -13 40390 32.23758268356323 0.6040134429931641 97.0293197631836 0.285203218460083 128.87728881835938 0.2048284113407135 0.7044369 0.3334721624851227 True -14 43275 32.227123737335205 0.6025376319885254 110.8595199584961 0.36430686712265015 128.59259033203125 0.2067740559577942 0.71199673 0.31088754534721375 True -15 46160 32.231478691101074 0.6154124736785889 87.98970031738281 0.31350183486938477 128.41238403320312 0.20784179866313934 0.72017014 0.2959815263748169 True -16 49045 32.527090072631836 0.6066057682037354 100.77081298828125 0.3319908082485199 128.38717651367188 0.208069309592247 0.72461325 0.2869738042354584 True -17 51930 32.2314453125 0.6082885265350342 110.04051208496094 0.3494153618812561 128.40133666992188 0.20766089856624603 0.7277952 0.2814716696739197 True -18 54815 32.25225043296814 0.6167926788330078 108.46559143066406 0.38290971517562866 128.4066619873047 0.20768055319786072 0.7278375 0.2789033353328705 True -19 57700 32.244160413742065 1.4196124076843262 96.4892578125 0.30693405866622925 128.46401977539062 0.20697666704654694 0.7274455 0.27966979146003723 False diff --git a/ENCSR511GQA/cherimoya.fold_4.performance.tsv b/ENCSR511GQA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7644b100b362351818175ac9938ad478f83a2281..0000000000000000000000000000000000000000 --- a/ENCSR511GQA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -128.4066619873047 0.5716069936752319 0.20768055319786072 0.035467810928821564 0.7278375029563904 0.6671987771987915 0.2789033353328705 \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_0.evaluate.json b/ENCSR511PFY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index eeb38b9aaf733f185dc653230b593236ca885ff1..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178PUT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_0.fit.json b/ENCSR511PFY/cherimoya.fold_0.fit.json deleted file mode 100644 index cbebd90070fb22e7df6dbb893f746d48b0f9c1ca..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF178PUT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_0.log b/ENCSR511PFY/cherimoya.fold_0.log deleted file mode 100644 index e4c4db44cb1729dd87579171b0e2646792502246..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 35.66797471046448 3.4460394382476807 690.3796997070312 0.723801851272583 744.9871826171875 0.20155178010463715 0.7424841 5.977715969085693 True -1 5484 30.26557445526123 1.1817364692687988 667.6050415039062 0.4253845512866974 686.6704711914062 0.25509607791900635 0.78850377 1.6824285984039307 True -2 8226 30.32190442085266 0.6025753021240234 439.2621765136719 0.4745430052280426 671.5448608398438 0.2663312256336212 0.80393887 0.8198159337043762 True -3 10968 30.24471116065979 0.6048450469970703 610.2626953125 0.6107972860336304 663.6725463867188 0.27376601099967957 0.8106583 0.6962441802024841 True -4 13710 30.408211708068848 0.5949070453643799 550.1702270507812 0.6467726826667786 660.8112182617188 0.27489665150642395 0.81598586 0.6618180871009827 True -5 16452 30.305234909057617 0.6231603622436523 476.91558837890625 0.25324827432632446 654.5435180664062 0.2811318039894104 0.8253616 0.47947874665260315 True -6 19194 30.240628242492676 0.5946834087371826 532.0166625976562 0.35980504751205444 653.3759765625 0.2815026342868805 0.8313944 0.4807606041431427 True -7 21936 30.23906397819519 0.5946614742279053 676.5850219726562 0.5669345855712891 649.89013671875 0.285701185464859 0.83532256 0.47590166330337524 True -8 24678 30.233314990997314 0.5927293300628662 460.16949462890625 0.256803423166275 646.1917724609375 0.28956887125968933 0.8411557 0.4423048496246338 True -9 27420 30.179912328720093 1.2562222480773926 529.6807250976562 0.5676020383834839 645.5350952148438 0.2896271049976349 0.84547037 0.4337172508239746 True -10 30162 30.106541395187378 0.5947709083557129 728.6039428710938 0.5387614369392395 643.9024047851562 0.2918194830417633 0.8482845 0.396043986082077 True -11 32904 30.174376726150513 0.7557227611541748 524.3792724609375 0.3782899081707001 639.820068359375 0.2964906096458435 0.85306674 0.3529174327850342 True -12 35646 29.99660873413086 0.5763816833496094 604.07421875 0.42830657958984375 638.4685668945312 0.2970753014087677 0.85738355 0.3272044062614441 True -13 38388 29.595473527908325 0.58249831199646 563.0679931640625 0.4294848144054413 635.8375854492188 0.2999557852745056 0.8607551 0.30493056774139404 True -14 41130 30.354278087615967 0.6123611927032471 493.21649169921875 0.3376429080963135 634.6326293945312 0.30019330978393555 0.8631213 0.29073798656463623 True -15 43872 30.404658317565918 0.5828728675842285 556.0262451171875 0.39825528860092163 633.2347412109375 0.302273690700531 0.86554277 0.2776511013507843 True -16 46614 29.576411724090576 0.5726141929626465 463.492919921875 0.36970096826553345 632.7453002929688 0.30244678258895874 0.86762613 0.26586413383483887 True -17 49356 29.54269027709961 0.593836784362793 499.5329895019531 0.2223774790763855 633.1615600585938 0.3020784258842468 0.8695832 0.26360565423965454 True -18 52098 29.579385995864868 0.6158554553985596 540.5614013671875 0.42701011896133423 633.4027709960938 0.30156612396240234 0.86905754 0.26201358437538147 False -19 54840 29.60271906852722 2.022627353668213 660.395751953125 0.20840290188789368 633.3652954101562 0.3020990788936615 0.8688281 0.26246997714042664 False diff --git a/ENCSR511PFY/cherimoya.fold_0.performance.tsv b/ENCSR511PFY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5823417fb2bb49cdea4ba305ed4234e38f3fa942..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -633.1615600585938 0.46650153398513794 0.3020784258842468 0.10636770725250244 0.8695831894874573 0.8259862661361694 0.26360565423965454 \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_1.evaluate.json b/ENCSR511PFY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1269d878689dca6cefcfaab3e230690a6a7d955a..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178PUT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_1.fit.json b/ENCSR511PFY/cherimoya.fold_1.fit.json deleted file mode 100644 index ae50542a7d83ccbf47c599bc890fe34045cac60d..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF178PUT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_1.log b/ENCSR511PFY/cherimoya.fold_1.log deleted file mode 100644 index 4b6f884841e1c62d1501f478e09bfb53a1f8b571..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 35.321707248687744 4.104472398757935 631.8119506835938 0.6295450925827026 869.390625 0.2048109620809555 0.73087174 6.376563549041748 True -1 5410 29.70394778251648 1.1092033386230469 566.154296875 0.7023237943649292 781.4461059570312 0.2723231315612793 0.79145 1.641239047050476 True -2 8115 29.69949769973755 0.7715163230895996 549.4414672851562 0.4992077946662903 768.62109375 0.28103575110435486 0.8080656 0.898037850856781 True -3 10820 29.6793372631073 0.7371120452880859 505.25335693359375 0.3687703013420105 757.4559936523438 0.2893124222755432 0.81551915 0.7359021902084351 True -4 13525 29.69905924797058 0.6992225646972656 430.1114501953125 0.436840683221817 751.8560180664062 0.292322039604187 0.82241595 0.6262300610542297 True -5 16230 29.697147130966187 0.7372238636016846 554.459716796875 0.4315202832221985 744.8368530273438 0.2977192997932434 0.8297491 0.5208644866943359 True -6 18935 29.6887366771698 0.826305627822876 484.4934997558594 0.490967333316803 744.0777587890625 0.2990915775299072 0.83430326 0.4980247914791107 True -7 21640 29.73397469520569 0.7058184146881104 520.8053588867188 0.316060334444046 736.4827880859375 0.3046943247318268 0.8400164 0.4578012526035309 True -8 24345 29.8081533908844 0.7007184028625488 413.71441650390625 0.3238753378391266 732.716796875 0.30827996134757996 0.84490925 0.4445350170135498 True -9 27050 29.719780683517456 0.7249047756195068 441.87384033203125 0.4328794479370117 729.2559814453125 0.310454398393631 0.8519192 0.4297811686992645 True -10 29755 29.815778970718384 0.7220511436462402 539.816650390625 0.4911941885948181 727.0364990234375 0.31313663721084595 0.85273254 0.4138309955596924 True -11 32460 30.14414954185486 7.640634059906006 423.71905517578125 0.30053627490997314 723.1879272460938 0.31522050499916077 0.8621762 0.3557661473751068 True -12 35165 29.304906845092773 0.7242121696472168 501.16204833984375 0.36234474182128906 719.273681640625 0.3186911642551422 0.86515397 0.3356058895587921 True -13 37870 29.29798150062561 0.7737126350402832 439.6692199707031 0.3121241331100464 716.5343017578125 0.3211180567741394 0.868718 0.31380927562713623 True -14 40575 29.227198362350464 0.7193787097930908 595.534423828125 0.31419023871421814 715.7921752929688 0.32114487886428833 0.872103 0.3081846237182617 True -15 43280 29.205843210220337 0.7255368232727051 518.223876953125 0.3150852620601654 712.454833984375 0.32443687319755554 0.8756757 0.29540935158729553 True -16 45985 29.217247009277344 0.712482213973999 529.3944702148438 0.2638043463230133 713.9559326171875 0.3223857581615448 0.8776266 0.2885757088661194 True -17 48690 29.196425437927246 0.7102868556976318 528.0855712890625 0.3409305214881897 712.9227294921875 0.32386329770088196 0.8786555 0.2846061587333679 True -18 51395 29.171194553375244 0.7002890110015869 511.7832336425781 0.24675020575523376 711.9169921875 0.3246854245662689 0.8800497 0.28504300117492676 True -19 54100 29.17361569404602 0.7169950008392334 475.337158203125 0.3906136751174927 712.3289184570312 0.32452672719955444 0.8777388 0.28689321875572205 False diff --git a/ENCSR511PFY/cherimoya.fold_1.performance.tsv b/ENCSR511PFY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c55667087f3ea8124332711d28c1d7d14e54a4e8..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -711.9169921875 0.4495648443698883 0.3246854245662689 0.11811274290084839 0.8800497055053711 0.8570594787597656 0.28504300117492676 \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_2.evaluate.json b/ENCSR511PFY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 61a5f7cdaf5298da29784011273e3f0b1fc29d72..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178PUT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_2.fit.json b/ENCSR511PFY/cherimoya.fold_2.fit.json deleted file mode 100644 index a6afc31502838c5329b1d2a4143d9003b7e4d8ca..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF178PUT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_2.log b/ENCSR511PFY/cherimoya.fold_2.log deleted file mode 100644 index ac2a78fe3b7a5abafa1131209f1ec281e364dc40..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2867 37.21556901931763 4.028754234313965 626.5887451171875 0.6587865352630615 782.4813232421875 0.2048063576221466 0.73435324 4.322983741760254 True -1 5734 31.59834384918213 0.7177679538726807 573.1544189453125 0.5070285797119141 713.7825317382812 0.2628389894962311 0.784612 1.416494607925415 True -2 8601 31.507511615753174 0.5500223636627197 715.4090576171875 0.425692617893219 699.2909545898438 0.2714981138706207 0.7876929 0.747592568397522 True -3 11468 31.507364988327026 0.5600571632385254 583.9228515625 0.39242202043533325 691.593017578125 0.2760182321071625 0.8003778 0.7786842584609985 True -4 14335 31.527278423309326 0.5766031742095947 461.27069091796875 0.3930940628051758 685.1836547851562 0.28226858377456665 0.8117225 0.5712414383888245 True -5 17202 31.506783723831177 0.5590729713439941 541.5540771484375 0.3256106376647949 682.1530151367188 0.2843051254749298 0.81757444 0.5651845335960388 True -6 20069 31.54583740234375 0.561150074005127 564.272705078125 0.4458272159099579 679.0231323242188 0.2880476117134094 0.8226286 0.5772771239280701 True -7 22936 31.540724515914917 0.560692548751831 559.7522583007812 0.4469909071922302 675.15380859375 0.2919803857803345 0.8271243 0.5489447116851807 True -8 25803 31.53097701072693 0.559727668762207 492.5105895996094 0.3827349841594696 672.728759765625 0.2943747639656067 0.82984245 0.5280801057815552 True -9 28670 31.55246591567993 0.5594005584716797 605.065673828125 0.394672155380249 671.2954711914062 0.2947651147842407 0.8357948 0.48106157779693604 True -10 31537 31.04566478729248 0.5546958446502686 600.2765502929688 0.3658292889595032 667.8005981445312 0.29830262064933777 0.8415119 0.42399242520332336 True -11 34404 30.92165780067444 0.5541794300079346 589.0782470703125 0.3320590853691101 664.7391967773438 0.3005867004394531 0.84467787 0.3702694773674011 True -12 37271 31.056248664855957 0.5643813610076904 485.8758544921875 0.4081810414791107 661.783203125 0.3048528730869293 0.849268 0.34856513142585754 True -13 40138 31.001566410064697 0.5571749210357666 498.2412109375 0.3372775912284851 658.9185180664062 0.30739909410476685 0.85509485 0.3302081227302551 True -14 43005 30.988826990127563 0.5503668785095215 549.6949462890625 0.3173254132270813 658.0924682617188 0.30756446719169617 0.8576409 0.3073596954345703 True -15 45872 30.94845724105835 0.5520420074462891 475.06573486328125 0.35366153717041016 656.46875 0.30885186791419983 0.8600823 0.292348712682724 True -16 48739 30.954723119735718 1.1533048152923584 503.1698303222656 0.34309619665145874 655.5608520507812 0.3105320930480957 0.8634005 0.28246307373046875 True -17 51606 30.946441411972046 0.5598087310791016 486.5372009277344 0.26681578159332275 656.3809204101562 0.3086572587490082 0.8635688 0.2781285345554352 True -18 54473 30.907933950424194 0.5479311943054199 502.38458251953125 0.3043656051158905 656.8642578125 0.30869171023368835 0.86412627 0.27773788571357727 True -19 57340 30.898370504379272 0.5650136470794678 578.365966796875 0.2238243669271469 655.2869873046875 0.31101399660110474 0.8623387 0.27745965123176575 False diff --git a/ENCSR511PFY/cherimoya.fold_2.performance.tsv b/ENCSR511PFY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d70b08c05bbb3dd374fe1c6b31bc8906a0800ae2..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -656.8642578125 0.46075740456581116 0.30869171023368835 0.11274514347314835 0.8641262650489807 0.8271323442459106 0.27773788571357727 \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_3.evaluate.json b/ENCSR511PFY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 02c8f78b93a981879a3b1761cb5d49035ff693e6..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178PUT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_3.fit.json b/ENCSR511PFY/cherimoya.fold_3.fit.json deleted file mode 100644 index 015ed4e5feb582eaa6d68d3e9dd4e5f5edbb2874..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF178PUT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_3.log b/ENCSR511PFY/cherimoya.fold_3.log deleted file mode 100644 index e5a84a2189db33729ebf0ad6a2f49eefe6ebf186..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 35.17214059829712 3.5213258266448975 717.52978515625 0.5822563171386719 760.6336059570312 0.21064238250255585 0.73464656 4.9851460456848145 True -1 5504 30.280479192733765 0.6672959327697754 652.5635375976562 0.649550199508667 692.0278930664062 0.2688181698322296 0.80759186 1.4606398344039917 True -2 8256 30.410892009735107 0.5360960960388184 633.0113525390625 0.5555287599563599 682.39697265625 0.27559611201286316 0.8121737 0.7163916826248169 True -3 11008 30.46209955215454 20.95093321800232 535.1303100585938 0.4793354868888855 677.8963012695312 0.2793511748313904 0.8168374 0.9168492555618286 True -4 13760 30.189010858535767 0.5598227977752686 578.891357421875 0.525601327419281 671.5667114257812 0.286093533039093 0.8249674 0.6968678832054138 True -5 16512 30.247765064239502 0.7643477916717529 515.810302734375 0.6693589687347412 669.200927734375 0.2873248755931854 0.8283634 0.6423942446708679 True -6 19264 30.237865447998047 0.5339455604553223 518.0581665039062 0.4540672302246094 666.1097412109375 0.2908218204975128 0.8332235 0.5788453817367554 True -7 22016 30.225459098815918 27.77892541885376 414.76171875 0.4098035991191864 662.511474609375 0.2936757504940033 0.8373686 0.5897442698478699 True -8 24768 30.23366641998291 0.546605110168457 456.2744140625 0.35924503207206726 659.3546142578125 0.2966495454311371 0.8411248 0.5119720697402954 True -9 27520 30.80512571334839 0.5372133255004883 598.8320922851562 0.47403618693351746 656.1018676757812 0.30051130056381226 0.8445949 0.4910193979740143 True -10 30272 30.294551849365234 0.529465913772583 554.4791259765625 0.38813722133636475 654.0654296875 0.30298274755477905 0.8499871 0.46967947483062744 True -11 33024 30.9646577835083 26.310951948165894 543.7344970703125 0.43236327171325684 651.9730834960938 0.30403634905815125 0.8538663 0.4357999563217163 True -12 35776 29.839837789535522 1.7753362655639648 527.8379516601562 0.4168817400932312 650.195556640625 0.3060198128223419 0.85580945 0.385378897190094 True -13 38528 29.686989545822144 0.5206058025360107 817.0689697265625 0.27982097864151 648.2745361328125 0.3079197108745575 0.86104715 0.35625070333480835 True -14 41280 29.67310333251953 0.5270810127258301 444.7272644042969 0.3629950284957886 646.236328125 0.30906757712364197 0.86612886 0.32069647312164307 True -15 44032 29.689760208129883 0.5272846221923828 437.9205322265625 0.21747972071170807 643.8427734375 0.3118359446525574 0.8696251 0.2993341088294983 True -16 46784 29.82047939300537 0.5345702171325684 584.0675048828125 0.3242609202861786 643.5715942382812 0.3116244971752167 0.8711762 0.2857794761657715 True -17 49536 29.7175133228302 0.8609862327575684 574.3007202148438 0.3291260302066803 644.10107421875 0.3105272650718689 0.8728474 0.27843084931373596 True -18 52288 29.703585624694824 0.5319280624389648 467.0332336425781 0.30252498388290405 643.8609619140625 0.3113299608230591 0.8729676 0.27715614438056946 True -19 55040 29.652488470077515 0.531965970993042 472.39794921875 0.2788817882537842 643.344482421875 0.31190064549446106 0.8731606 0.27663087844848633 True diff --git a/ENCSR511PFY/cherimoya.fold_3.performance.tsv b/ENCSR511PFY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 74ae50ddaffeb5a317c7ec8402c75bf50c49a9e9..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -643.344482421875 0.4610399603843689 0.3119005858898163 0.11264172196388245 0.8731606006622314 0.8299307823181152 0.27663087844848633 \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_4.evaluate.json b/ENCSR511PFY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0f728d2b71b2dff420e2ce70a2cb0b2a847895d3..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178PUT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_4.fit.json b/ENCSR511PFY/cherimoya.fold_4.fit.json deleted file mode 100644 index c3400134aa29b3a79454c4055975f3eee6ea92d7..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF178PUT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR511PFY/cherimoya.fold_4.log b/ENCSR511PFY/cherimoya.fold_4.log deleted file mode 100644 index 6ac4fcadd8575581c6cb11f063dea3dea4f19fea..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2823 35.88251066207886 3.85709810256958 517.44677734375 0.570126473903656 697.0584716796875 0.197719007730484 0.727654 5.431576251983643 True -1 5646 31.174264907836914 0.6425848007202148 639.164306640625 0.5896405577659607 644.0366821289062 0.24774450063705444 0.77874184 1.4401453733444214 True -2 8469 31.13154411315918 0.6133551597595215 545.79638671875 0.5512752532958984 634.0635375976562 0.25720396637916565 0.78763735 0.7705907225608826 True -3 11292 31.13326072692871 0.6115756034851074 486.5669250488281 0.3874059021472931 627.7523803710938 0.2626272737979889 0.7969933 0.6646361351013184 True -4 14115 31.113972425460815 0.6104898452758789 551.303955078125 0.3848593831062317 623.381591796875 0.26682332158088684 0.8062476 0.5780357718467712 True -5 16938 31.17250394821167 0.6092572212219238 525.8372802734375 0.8972251415252686 619.8198852539062 0.2700207233428955 0.8080172 0.5112887024879456 True -6 19761 31.113046407699585 0.6091911792755127 582.9000244140625 0.5459903478622437 616.716552734375 0.2722682058811188 0.8191053 0.44774022698402405 True -7 22584 31.10358691215515 0.6392245292663574 512.646484375 0.24955669045448303 613.5405883789062 0.2759561836719513 0.821943 0.4497840702533722 True -8 25407 31.152353525161743 0.6352195739746094 483.8339538574219 0.48383307456970215 612.4663696289062 0.2771443724632263 0.82658 0.4592455327510834 True -9 28230 31.078195095062256 0.6197431087493896 632.0777587890625 0.30367404222488403 609.1565551757812 0.2806151211261749 0.8327393 0.4288007318973541 True -10 31053 30.992156744003296 21.96806025505066 548.3516845703125 0.43867114186286926 606.3121337890625 0.28396910429000854 0.83694917 0.4136781394481659 True -11 33876 31.120971202850342 0.6334817409515381 554.6720581054688 0.4168063998222351 604.1267700195312 0.28646036982536316 0.8441108 0.36343294382095337 True -12 36699 30.772466897964478 0.7038130760192871 511.324951171875 0.3155681788921356 602.4921875 0.2876649498939514 0.84878117 0.3338339924812317 True -13 39522 30.579468250274658 0.6154723167419434 500.7901611328125 0.32331204414367676 600.5704956054688 0.2894496023654938 0.85449255 0.31540369987487793 True -14 42345 30.502155303955078 0.6148710250854492 571.7007446289062 0.2948457598686218 598.7733154296875 0.29088833928108215 0.85779744 0.2888944149017334 True -15 45168 30.485130786895752 0.6079709529876709 446.91033935546875 0.3039131760597229 597.9575805664062 0.29182857275009155 0.8630735 0.2698865532875061 True -16 47991 30.54915690422058 1.1299991607666016 529.7310791015625 0.367950975894928 597.2748413085938 0.2933894991874695 0.8645075 0.2600659430027008 True -17 50814 30.519888877868652 0.610802173614502 500.8524169921875 0.216448575258255 597.563232421875 0.29265016317367554 0.86607885 0.2557484805583954 True -18 53637 30.42186999320984 0.6006805896759033 492.3477783203125 0.19962620735168457 597.7124633789062 0.2927665412425995 0.86506754 0.25310105085372925 False -19 56460 30.445287227630615 0.603276252746582 425.09307861328125 0.3035200834274292 598.3050537109375 0.2918599247932434 0.8656694 0.25322237610816956 False diff --git a/ENCSR511PFY/cherimoya.fold_4.performance.tsv b/ENCSR511PFY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 735d36f9bd4997630113610533d3b5dd9a17477f..0000000000000000000000000000000000000000 --- a/ENCSR511PFY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -597.563232421875 0.4751081168651581 0.2926501929759979 0.1014765128493309 0.8660788536071777 0.8201214671134949 0.2557484805583954 \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_0.evaluate.json b/ENCSR512CWR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ec6c7bebc557c38177687bc0d161279d192b9486..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625IND.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_0.fit.json b/ENCSR512CWR/cherimoya.fold_0.fit.json deleted file mode 100644 index 1dc3c86e83110d8e8378feaaac9cf0170d0cc147..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF625IND.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_0.log b/ENCSR512CWR/cherimoya.fold_0.log deleted file mode 100644 index 3f26fd5f146c2674b7ae85528921ede7e3a8d8ca..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 34.93187189102173 5.443740367889404 1345.13330078125 0.5433173179626465 1938.684814453125 0.29440033435821533 0.56622356 7.892180442810059 True -1 5462 30.575643062591553 0.5358123779296875 1290.492919921875 0.9380189180374146 1683.0941162109375 0.42050057649612427 0.64066565 1.5183067321777344 True -2 8193 30.511074781417847 0.5387389659881592 1455.040771484375 0.8648124933242798 1643.413818359375 0.4361548125743866 0.65417844 0.588169276714325 True -3 10924 30.65181612968445 2.0398411750793457 1479.94091796875 0.7535814046859741 1620.9000244140625 0.44698360562324524 0.6493829 0.503987193107605 False -4 13655 30.49380326271057 1.5187973976135254 1342.0369873046875 0.5052822828292847 1618.2442626953125 0.44579723477363586 0.6511994 0.47995737195014954 False -5 16386 30.463704586029053 0.5079011917114258 1238.095947265625 0.5493324995040894 1603.774658203125 0.4555022120475769 0.66579664 0.5214090943336487 True -6 19117 30.494677782058716 0.5139865875244141 1334.020751953125 0.6889487504959106 1595.9891357421875 0.4593404233455658 0.6695323 0.45589974522590637 True -7 21848 30.474601984024048 0.5153014659881592 1327.7977294921875 0.6751658916473389 1589.0018310546875 0.4632319211959839 0.6711926 0.4436076879501343 True -8 24579 30.516419172286987 7.038751840591431 1346.9921875 0.5389710068702698 1580.9659423828125 0.46760496497154236 0.67449075 0.4614216089248657 True -9 27310 30.57623529434204 0.5197854042053223 1089.517333984375 0.4699961841106415 1577.5274658203125 0.47025609016418457 0.6812511 0.46305128931999207 True -10 30041 30.85887336730957 3.5294599533081055 1302.7108154296875 0.4230276644229889 1572.812744140625 0.47251129150390625 0.6871905 0.4434359073638916 True -11 32772 30.546445846557617 0.5134704113006592 1432.767822265625 0.40320634841918945 1563.2637939453125 0.4778023660182953 0.70128936 0.430421382188797 True -12 35503 30.278643131256104 0.5238997936248779 1202.1607666015625 0.4595666527748108 1557.4139404296875 0.4815523326396942 0.71260804 0.4208478331565857 True -13 38234 29.856532096862793 0.5036981105804443 1333.819580078125 0.4926287829875946 1552.615966796875 0.4831324517726898 0.72436154 0.4111664891242981 True -14 40965 29.79812479019165 0.49953722953796387 1231.31787109375 0.3834287226200104 1541.262451171875 0.4904664158821106 0.7357263 0.3770141005516052 True -15 43696 30.207069396972656 0.5099191665649414 1160.1400146484375 0.41839081048965454 1538.473876953125 0.4907696545124054 0.7437259 0.3649667501449585 True -16 46427 29.925392389297485 25.771586179733276 1378.2041015625 0.42082011699676514 1540.8585205078125 0.488449364900589 0.75166124 0.35181236267089844 True -17 49158 30.02203345298767 0.5259134769439697 1400.849365234375 0.3560718297958374 1538.9981689453125 0.49079740047454834 0.75468385 0.3459630012512207 True -18 51889 30.043203830718994 26.791208744049072 1263.1478271484375 0.3230020999908447 1536.9114990234375 0.4917447566986084 0.754737 0.3454771935939789 True -19 54620 30.781770706176758 25.11540198326111 1214.306884765625 0.315240740776062 1535.6552734375 0.49280503392219543 0.7542109 0.3454194962978363 False diff --git a/ENCSR512CWR/cherimoya.fold_0.performance.tsv b/ENCSR512CWR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index bf5075fc4aee65d25c03aad47ff9e3cedac83690..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1536.9114990234375 0.26930341124534607 0.4917447865009308 0.2764090597629547 0.7547370195388794 0.7001654505729675 0.3454771935939789 \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_1.evaluate.json b/ENCSR512CWR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index fb23794f737806b1b5b91bdc7011ecdea6d8444a..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625IND.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_1.fit.json b/ENCSR512CWR/cherimoya.fold_1.fit.json deleted file mode 100644 index 73c9aad4544b03e7e0eace662de84c49346a400b..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF625IND.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_1.log b/ENCSR512CWR/cherimoya.fold_1.log deleted file mode 100644 index 7fb8bfbbfa86e729e29954ffc8af0bb22b4f6d44..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 33.719350814819336 3.6604442596435547 1494.8389892578125 0.7830994129180908 2223.0107421875 0.2999148368835449 0.608551 10.140738487243652 True -1 5424 29.906697273254395 0.6932241916656494 1236.778564453125 0.8410826921463013 1927.93115234375 0.42754101753234863 0.6504194 2.449476480484009 True -2 8136 29.853066444396973 0.6827967166900635 1182.33642578125 0.7516642212867737 1871.7520751953125 0.44874897599220276 0.67393214 1.0397107601165771 True -3 10848 29.832717895507812 0.676506757736206 1281.43359375 0.8194960355758667 1836.59521484375 0.4584819972515106 0.683839 0.7750830054283142 True -4 13560 29.93985867500305 0.679558277130127 1404.7806396484375 0.7209720611572266 1821.3896484375 0.4636200964450836 0.6907147 0.6998438835144043 True -5 16272 29.870640993118286 0.6770563125610352 1261.5545654296875 0.5030666589736938 1806.7681884765625 0.46904054284095764 0.69977444 0.5762614607810974 True -6 18984 29.823305368423462 0.6819765567779541 1231.14111328125 0.9040895700454712 1801.940673828125 0.47109511494636536 0.69848514 0.4896756708621979 False -7 21696 29.82125163078308 0.6792943477630615 1285.62646484375 0.43406274914741516 1788.4481201171875 0.47680577635765076 0.70798004 0.4775008261203766 True -8 24408 29.803500413894653 1.4181270599365234 1119.0113525390625 0.516801118850708 1779.475830078125 0.4820498526096344 0.71269625 0.46688786149024963 True -9 27120 29.860066175460815 0.6745092868804932 1368.2802734375 0.6489028930664062 1772.55859375 0.48362627625465393 0.7204592 0.4413597583770752 True -10 29832 29.782261848449707 0.67325758934021 1239.050048828125 0.462791383266449 1763.1485595703125 0.4883958101272583 0.72539073 0.43462449312210083 True -11 32544 29.789833784103394 0.6727807521820068 1184.327880859375 0.4162040948867798 1750.2174072265625 0.49367859959602356 0.73525184 0.41782480478286743 True -12 35256 29.84643244743347 1.9611833095550537 1252.8128662109375 0.44481387734413147 1745.81787109375 0.49530646204948425 0.7455425 0.4090910255908966 True -13 37968 29.892237663269043 2.0040910243988037 1386.741455078125 0.415772944688797 1737.026611328125 0.49882081151008606 0.75687504 0.39263448119163513 True -14 40680 29.957090616226196 0.6900677680969238 1241.987548828125 0.4531823694705963 1728.2171630859375 0.5023896098136902 0.7674233 0.3784424662590027 True -15 43392 29.619208097457886 0.689633846282959 1167.8486328125 0.39840883016586304 1727.4654541015625 0.503680944442749 0.775251 0.37128403782844543 True -16 46104 29.255983352661133 0.6885974407196045 1021.5650024414062 0.2784125804901123 1720.603271484375 0.5062553286552429 0.7805737 0.36147502064704895 True -17 48816 29.217517852783203 0.6911818981170654 1199.946044921875 0.3714770972728729 1722.1904296875 0.504921555519104 0.7841977 0.35887303948402405 True -18 51528 29.29996156692505 0.686269998550415 1360.120849609375 0.20852863788604736 1725.867431640625 0.502977192401886 0.78667116 0.3581812381744385 True -19 54240 29.22551131248474 0.6837430000305176 1110.0416259765625 0.19161507487297058 1721.0115966796875 0.5065221786499023 0.7861638 0.3599436283111572 False diff --git a/ENCSR512CWR/cherimoya.fold_1.performance.tsv b/ENCSR512CWR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index fe6a1c57cb9fd317d1dc9f9324be1650df517077..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1725.867431640625 0.2560909688472748 0.5029771327972412 0.2984345853328705 0.7866711616516113 0.7516195178031921 0.3581812381744385 \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_2.evaluate.json b/ENCSR512CWR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 43a7a1df6757560e1d0ac547b09d8dbe41170ff1..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625IND.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_2.fit.json b/ENCSR512CWR/cherimoya.fold_2.fit.json deleted file mode 100644 index 9d002c96571206a53a5ccee68c3385a9ca2f9695..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF625IND.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_2.log b/ENCSR512CWR/cherimoya.fold_2.log deleted file mode 100644 index 487946a9e491d677dcee883f8d8229a36724c134..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2860 35.172919034957886 3.793687343597412 1526.630859375 0.8908205032348633 1980.8212890625 0.30468517541885376 0.5813212 4.626696586608887 True -1 5720 31.495139122009277 0.5369343757629395 1456.4268798828125 0.9062709212303162 1717.33935546875 0.42572394013404846 0.66823846 1.4871505498886108 True -2 8580 31.50316095352173 0.5170121192932129 1373.22021484375 0.9190430641174316 1673.603515625 0.442731112241745 0.67864627 0.6340407133102417 True -3 11440 31.541134119033813 0.527493953704834 1414.062744140625 0.8793420195579529 1657.2381591796875 0.4481643736362457 0.6852251 0.4875330626964569 True -4 14300 31.56700873374939 0.5217363834381104 1388.431884765625 0.6816514134407043 1646.0482177734375 0.45352986454963684 0.69088537 0.4585013687610626 True -5 17160 31.442776441574097 0.5168752670288086 1587.7257080078125 0.8866574764251709 1633.1021728515625 0.4601982533931732 0.6896778 0.5195877552032471 False -6 20020 31.4220073223114 0.5171494483947754 1296.6748046875 0.4668986201286316 1627.029052734375 0.46241533756256104 0.6951149 0.472670316696167 True -7 22880 31.463005542755127 0.5139665603637695 1372.8779296875 0.5748339891433716 1623.1505126953125 0.4643765687942505 0.6951458 0.49106621742248535 True -8 25740 31.488343000411987 1.5572068691253662 1331.2176513671875 0.5567525625228882 1612.5386962890625 0.4705464243888855 0.6913287 0.4426476061344147 False -9 28600 31.631686687469482 1.4840788841247559 1437.9447021484375 0.48136958479881287 1607.569091796875 0.47416919469833374 0.69906163 0.45945504307746887 True -10 31460 31.552835941314697 0.5236659049987793 1262.615478515625 0.5104262828826904 1600.6527099609375 0.4769425392150879 0.69990456 0.42133012413978577 True -11 34320 31.45902109146118 0.5234849452972412 1348.162109375 0.40864238142967224 1591.7977294921875 0.48186731338500977 0.7073519 0.4312661290168762 True -12 37180 31.430732011795044 0.5149016380310059 1157.349853515625 0.5235401391983032 1584.8653564453125 0.4848399758338928 0.7184153 0.4076277017593384 True -13 40040 31.41141700744629 0.5204980373382568 1361.8076171875 0.40296196937561035 1580.1279296875 0.4868936538696289 0.7293788 0.38883519172668457 True -14 42900 31.43971300125122 0.5230317115783691 1404.4639892578125 0.5746670961380005 1573.6697998046875 0.4903877377510071 0.7378624 0.3768589496612549 True -15 45760 30.850994348526 0.5210056304931641 1230.364013671875 0.3144058287143707 1570.38720703125 0.4910314083099365 0.74720335 0.3633260130882263 True -16 48620 30.845407962799072 0.5088908672332764 1204.8929443359375 0.2752074599266052 1564.3426513671875 0.4938269257545471 0.75361896 0.35410958528518677 True -17 51480 30.848162412643433 0.5189170837402344 1287.385009765625 0.3186180591583252 1567.32080078125 0.49255988001823425 0.7562755 0.35067206621170044 True -18 54340 30.832444667816162 0.512561559677124 1225.9581298828125 0.3137930631637573 1567.2972412109375 0.49208498001098633 0.7573536 0.34924080967903137 True -19 57200 30.8205988407135 0.5153331756591797 1398.914306640625 0.3495638966560364 1562.700927734375 0.4954845607280731 0.75702816 0.35199880599975586 False diff --git a/ENCSR512CWR/cherimoya.fold_2.performance.tsv b/ENCSR512CWR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a0c0f8e31c6351953a00a6ae04d217feb2b3886f..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1567.2972412109375 0.26809877157211304 0.4920850396156311 0.281004399061203 0.7573536038398743 0.708452045917511 0.34924080967903137 \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_3.evaluate.json b/ENCSR512CWR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e3d0ebf1b5cd702d5742384b61380f349e2b706d..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625IND.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_3.fit.json b/ENCSR512CWR/cherimoya.fold_3.fit.json deleted file mode 100644 index 6f6bf915ad8200236636ecc16da6e2821b6d0c8d..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF625IND.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_3.log b/ENCSR512CWR/cherimoya.fold_3.log deleted file mode 100644 index 34dce606757c83db385076b5f01a7716421d6911..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2771 34.17022109031677 3.6302566528320312 1437.82763671875 0.6265486478805542 1967.2591552734375 0.298636794090271 0.5830466 6.798289775848389 True -1 5542 30.54591941833496 8.965537309646606 1473.939453125 0.9388465285301208 1695.966064453125 0.430097371339798 0.6670629 1.5614293813705444 True -2 8313 30.57993173599243 2.2712275981903076 1196.74658203125 0.6436960101127625 1667.4923095703125 0.44088271260261536 0.66967136 0.8054471611976624 True -3 11084 30.52478861808777 29.510465145111084 1451.5604248046875 0.8122886419296265 1646.02294921875 0.4522916376590729 0.6730293 0.8027995228767395 True -4 13855 30.576253414154053 0.5673577785491943 1264.4056396484375 0.6250205039978027 1641.947998046875 0.4527643918991089 0.67260367 0.6721500754356384 False -5 16626 30.713991165161133 0.5474953651428223 1421.183349609375 0.7196544408798218 1634.88427734375 0.4564107060432434 0.66895354 0.5905335545539856 False -6 19397 30.498029947280884 0.5558350086212158 1294.11376953125 0.5524681806564331 1624.9791259765625 0.460631787776947 0.67210084 0.47724300622940063 False -7 22168 30.67552638053894 0.5575664043426514 1337.3056640625 0.6135683059692383 1618.32080078125 0.4630129933357239 0.6692454 0.47149714827537537 False -8 24939 30.564226388931274 0.5520949363708496 1344.3214111328125 0.4000902771949768 1610.983642578125 0.4673699140548706 0.67474914 0.43061333894729614 True -9 27710 30.522399187088013 0.5518724918365479 1452.524169921875 0.535664439201355 1604.8641357421875 0.47064730525016785 0.6861975 0.41183212399482727 True -10 30481 30.458534717559814 0.5471224784851074 1264.3873291015625 0.575392484664917 1600.5970458984375 0.4723029136657715 0.70091695 0.40595126152038574 True -11 33252 30.496129274368286 0.5467052459716797 1314.698486328125 0.4622698426246643 1593.43603515625 0.4759642481803894 0.7154921 0.3925175368785858 True -12 36023 30.851516246795654 0.5551331043243408 1346.523681640625 0.4896966218948364 1585.6121826171875 0.4799777567386627 0.72681314 0.3832603394985199 True -13 38794 30.507907152175903 0.5458080768585205 1154.9176025390625 0.41420042514801025 1576.1826171875 0.48567819595336914 0.73593074 0.3746776282787323 True -14 41565 30.44477868080139 0.5499253273010254 1118.072265625 0.4721665382385254 1572.1063232421875 0.4884180426597595 0.7482213 0.3662344515323639 True -15 44336 30.43372082710266 0.5510375499725342 1237.5733642578125 0.2707441449165344 1572.6734619140625 0.4852575361728668 0.7551148 0.3513484001159668 True -16 47107 29.970311880111694 0.5434045791625977 1254.020751953125 0.2901064157485962 1565.8477783203125 0.4893668591976166 0.7624883 0.3490663468837738 True -17 49878 29.8147394657135 1.2175967693328857 1044.0731201171875 0.3242560625076294 1562.18212890625 0.49184659123420715 0.76617783 0.3456416726112366 True -18 52649 29.900663375854492 0.5410828590393066 1304.404296875 0.18822944164276123 1565.00537109375 0.49084505438804626 0.7668774 0.3454441428184509 True -19 55420 29.893083572387695 0.5540683269500732 1165.8939208984375 0.2602477967739105 1567.5294189453125 0.48934412002563477 0.76729465 0.34733057022094727 True diff --git a/ENCSR512CWR/cherimoya.fold_3.performance.tsv b/ENCSR512CWR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4af3267cc6e07bc3ffdf3ddd9ec1414f91eaad10..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1567.5294189453125 0.2677313983440399 0.4893440902233124 0.2814670205116272 0.7672946453094482 0.7157186269760132 0.34733057022094727 \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_4.evaluate.json b/ENCSR512CWR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0f280b8519a959bdfe32762d1ce1425d02acef3c..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625IND.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_4.fit.json b/ENCSR512CWR/cherimoya.fold_4.fit.json deleted file mode 100644 index b6a74767f3b64f0f87aafdeb800d67f6817d9ff3..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF625IND.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512CWR/cherimoya.fold_4.log b/ENCSR512CWR/cherimoya.fold_4.log deleted file mode 100644 index ac4f599cba59d1a3f58114490495aacbb30be267..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2856 35.1148796081543 3.626781463623047 1385.1956787109375 1.0408223867416382 1892.5784912109375 0.3026217222213745 0.5674953 6.198437690734863 True -1 5712 31.412006855010986 0.5718390941619873 1204.0380859375 0.48144638538360596 1667.8179931640625 0.42051127552986145 0.6438837 1.9287261962890625 True -2 8568 31.586878299713135 0.5967237949371338 1267.8233642578125 0.679149866104126 1621.854736328125 0.44084781408309937 0.6525179 0.7660248279571533 True -3 11424 31.46639347076416 2.7654378414154053 1280.7283935546875 0.902679443359375 1602.10595703125 0.4494812786579132 0.6574492 0.6473305821418762 True -4 14280 31.55862855911255 0.5730550289154053 1339.40380859375 0.5593066811561584 1592.7430419921875 0.4529191851615906 0.66186476 0.5825477242469788 True -5 17136 31.4340603351593 0.5505867004394531 1441.85302734375 0.6289429664611816 1584.22607421875 0.45721617341041565 0.66468585 0.6163873076438904 True -6 19992 31.443244457244873 0.5658359527587891 1273.5660400390625 0.42672693729400635 1581.5753173828125 0.45830968022346497 0.6593684 0.49769842624664307 False -7 22848 31.440502405166626 0.5575127601623535 1210.20556640625 0.5140682458877563 1571.2919921875 0.4648398756980896 0.65628624 0.5346007943153381 False -8 25704 31.428054571151733 0.5667910575866699 1449.348388671875 0.5857722759246826 1568.4512939453125 0.46612071990966797 0.6536859 0.5125124454498291 False -9 28560 31.369385719299316 0.5610344409942627 1403.4388427734375 0.3491474688053131 1562.568115234375 0.4707358777523041 0.66754544 0.49879154562950134 True -10 31416 31.363879680633545 0.5658063888549805 1449.202392578125 0.5124682784080505 1557.0689697265625 0.47289732098579407 0.6772381 0.47358670830726624 True -11 34272 31.43274450302124 0.5564353466033936 1416.2518310546875 0.3461264371871948 1545.340087890625 0.4798506200313568 0.6922876 0.4449736773967743 True -12 37128 31.454060554504395 0.5560903549194336 1105.8397216796875 0.515113353729248 1541.4305419921875 0.48164868354797363 0.7008926 0.4290961027145386 True -13 39984 31.43168568611145 0.5597410202026367 1359.39990234375 0.4253425896167755 1534.1729736328125 0.4857504367828369 0.7140756 0.4001428484916687 True -14 42840 31.41428232192993 0.566941499710083 1198.5263671875 0.41878920793533325 1531.91845703125 0.48523619771003723 0.72708505 0.37375906109809875 True -15 45696 31.166142225265503 0.5498766899108887 1251.1943359375 0.32829195261001587 1528.895263671875 0.48789724707603455 0.7360195 0.36132922768592834 True -16 48552 30.789449453353882 0.5603835582733154 1297.227783203125 0.36782804131507874 1526.0765380859375 0.4895409643650055 0.74348843 0.3541865646839142 True -17 51408 30.903112411499023 0.5567150115966797 1245.0401611328125 0.2058659940958023 1523.2501220703125 0.49057960510253906 0.7486167 0.3419988453388214 True -18 54264 30.773967027664185 0.5493757724761963 1210.88623046875 0.24662280082702637 1521.3621826171875 0.4907996356487274 0.74789625 0.33994483947753906 False -19 57120 30.949889183044434 0.5615150928497314 1153.003662109375 0.4862931966781616 1525.154296875 0.48854944109916687 0.74847895 0.3422803580760956 False diff --git a/ENCSR512CWR/cherimoya.fold_4.performance.tsv b/ENCSR512CWR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1ffff4aa91692f713a5fb43079e8d1a9a003172a..0000000000000000000000000000000000000000 --- a/ENCSR512CWR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1523.2501220703125 0.2691587805747986 0.49057960510253906 0.27848294377326965 0.7486166954040527 0.6980167031288147 0.3419988453388214 \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_0.evaluate.json b/ENCSR512FHU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 230380c4327a06cda05292a3d13833525047ecd0..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF944ETK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_0.fit.json b/ENCSR512FHU/cherimoya.fold_0.fit.json deleted file mode 100644 index 908ad1ed55bc06e7218d8632463c7dcf3cd245df..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF944ETK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_0.log b/ENCSR512FHU/cherimoya.fold_0.log deleted file mode 100644 index 75163ee09511d21c1ee80a5148437f9a2664c870..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2195 28.037662267684937 3.4465019702911377 304.8706359863281 0.7600032687187195 447.9979248046875 0.4559750556945801 0.5874201 8.981527328491211 True -1 4390 24.16885733604431 0.45992565155029297 289.6903076171875 0.8243427276611328 380.81573486328125 0.5706766247749329 0.6518222 3.5132150650024414 True -2 6585 24.18750810623169 0.44385457038879395 314.2801818847656 0.7508419156074524 365.4713439941406 0.6004582047462463 0.66628486 1.0967943668365479 True -3 8780 24.197004318237305 0.4389638900756836 270.14154052734375 0.6883271336555481 360.5763244628906 0.6085241436958313 0.6689121 0.7670278549194336 True -4 10975 24.171294927597046 0.4447803497314453 311.27117919921875 0.9447908401489258 358.90606689453125 0.6115408539772034 0.6748696 0.76410973072052 True -5 13170 24.211195707321167 0.4457128047943115 300.8387145996094 1.057393193244934 357.37493896484375 0.6147714257240295 0.6817274 0.7231383323669434 True -6 15365 24.1731595993042 0.4495692253112793 259.1046447753906 0.76678866147995 356.3573913574219 0.6168929934501648 0.68678266 0.6821110844612122 True -7 17560 24.180261850357056 0.4618206024169922 299.4273986816406 0.8452788591384888 355.36407470703125 0.6188319325447083 0.69092935 0.6588591933250427 True -8 19755 24.23269772529602 0.46646785736083984 291.99127197265625 0.6676034927368164 354.3139343261719 0.6210185885429382 0.6985959 0.6202933192253113 True -9 21950 24.229928970336914 0.4452533721923828 238.88294982910156 0.6090990304946899 353.5504150390625 0.6228607296943665 0.70542663 0.5875806212425232 True -10 24145 24.85249972343445 0.4441869258880615 254.16558837890625 0.6439355611801147 352.5202941894531 0.6248101592063904 0.7075173 0.5540392398834229 True -11 26340 24.2565815448761 1.1050214767456055 283.2536926269531 0.5990108847618103 351.87042236328125 0.6261459589004517 0.7140541 0.5511985421180725 True -12 28535 24.290836334228516 0.4398183822631836 304.60894775390625 0.5217140913009644 350.9944763183594 0.6275798082351685 0.71893966 0.5352805256843567 True -13 30730 24.26523995399475 0.4340078830718994 220.33709716796875 0.45469892024993896 350.0684509277344 0.6292128562927246 0.7251536 0.5228868722915649 True -14 32925 24.144105434417725 0.4376232624053955 242.75387573242188 0.4905852973461151 349.7045593261719 0.6300281286239624 0.72762203 0.5232623815536499 True -15 35120 24.138543605804443 0.4362201690673828 291.9624938964844 0.39663973450660706 349.3702087402344 0.630382239818573 0.72972804 0.5228345394134521 True -16 37315 24.10746121406555 0.4343843460083008 260.2829895019531 0.3145264983177185 349.4367980957031 0.6302168369293213 0.7269367 0.5290114879608154 False -17 39510 24.139544010162354 0.42980456352233887 252.31948852539062 0.4084641933441162 349.7696533203125 0.6295861601829529 0.7259643 0.5413795709609985 False -18 41705 24.14116907119751 1.636350154876709 252.19595336914062 0.36370038986206055 350.0231628417969 0.6289018988609314 0.7196359 0.5616788864135742 False -19 43900 24.171562433242798 0.44125986099243164 324.51287841796875 0.2856329679489136 350.1877136230469 0.6284389495849609 0.716535 0.5691496133804321 False diff --git a/ENCSR512FHU/cherimoya.fold_0.performance.tsv b/ENCSR512FHU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 01489dcf419597765084b98fb15a4a89667de8e9..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -349.3702087402344 0.3019154667854309 0.630382239818573 0.22966983914375305 0.7297280430793762 0.6820583939552307 0.5228345394134521 \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_1.evaluate.json b/ENCSR512FHU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3e3ad3af2a5cd119ac8b03db63f6126bb02fb220..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF944ETK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_1.fit.json b/ENCSR512FHU/cherimoya.fold_1.fit.json deleted file mode 100644 index d3b0d13ea36bbf793861492069bb563540bea07f..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF944ETK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_1.log b/ENCSR512FHU/cherimoya.fold_1.log deleted file mode 100644 index 67c894a40891527a55ab707215caf5d54de3ce01..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2229 28.97888684272766 3.4331839084625244 284.70343017578125 0.7933122515678406 452.1197204589844 0.46793997287750244 0.5795259 9.61151123046875 True -1 4458 24.817642211914062 0.524235725402832 318.4286804199219 0.8471126556396484 393.1782531738281 0.5768828988075256 0.66615504 3.305999755859375 True -2 6687 24.812683820724487 0.5037217140197754 315.28857421875 0.8896608352661133 378.1842346191406 0.6058825850486755 0.6817557 0.9347772598266602 True -3 8916 24.760733366012573 0.49854612350463867 318.54205322265625 0.6074358224868774 372.7430725097656 0.6134410500526428 0.69678885 0.677612841129303 True -4 11145 24.769597053527832 0.5229158401489258 247.37966918945312 0.8874356150627136 371.2667541503906 0.6163913011550903 0.70274115 0.6316202282905579 True -5 13374 24.737305164337158 0.4984769821166992 280.783935546875 0.6890795826911926 369.979736328125 0.618955135345459 0.70476246 0.6065415143966675 True -6 15603 24.73662781715393 0.4979379177093506 289.1061706542969 0.4658238887786865 368.7647399902344 0.6211536526679993 0.71175 0.5687173008918762 True -7 17832 24.731361865997314 0.5034925937652588 263.4089660644531 0.8392946124076843 368.16705322265625 0.6229457259178162 0.71589285 0.5457928776741028 True -8 20061 24.729209899902344 1.012418270111084 265.170166015625 0.5868462920188904 367.1808166503906 0.6251612305641174 0.7203087 0.5448994636535645 True -9 22290 24.80141592025757 0.5030279159545898 244.82168579101562 0.8047515749931335 366.440185546875 0.626816987991333 0.72538805 0.5316734313964844 True -10 24519 24.807318210601807 0.5080668926239014 242.56011962890625 0.40177905559539795 365.4510803222656 0.6285984516143799 0.7273785 0.5095138549804688 True -11 26748 24.776257276535034 0.5087003707885742 238.0667266845703 0.5920237302780151 364.30877685546875 0.6306701302528381 0.731952 0.5045755505561829 True -12 28977 24.766495943069458 0.5092074871063232 285.0265808105469 0.4498271346092224 363.52044677734375 0.6323089003562927 0.73988926 0.48882532119750977 True -13 31206 24.821002960205078 0.5030181407928467 269.8216247558594 0.434444785118103 362.9696960449219 0.6334991455078125 0.74412286 0.4832576513290405 True -14 33435 24.74880051612854 0.503925085067749 256.1712341308594 0.5869812965393066 362.3663330078125 0.6346206665039062 0.7508272 0.4734255075454712 True -15 35664 24.768040657043457 0.5015525817871094 254.906982421875 0.48613715171813965 362.178955078125 0.6348374485969543 0.7549094 0.4672935903072357 True -16 37893 24.77422595024109 0.5070040225982666 269.61529541015625 0.3006800413131714 362.1897888183594 0.6346858739852905 0.75490934 0.4698529541492462 False -17 40122 24.782823085784912 0.5025348663330078 278.3163146972656 0.3496888279914856 362.4046630859375 0.6339070796966553 0.75176793 0.4778602719306946 False -18 42351 24.730687379837036 0.501183032989502 223.9134979248047 0.32140570878982544 362.6238708496094 0.6331076622009277 0.748014 0.49250489473342896 False -19 44580 24.782851934432983 0.5020787715911865 254.30523681640625 0.389262855052948 362.83929443359375 0.6326930522918701 0.7440603 0.5001760721206665 False diff --git a/ENCSR512FHU/cherimoya.fold_1.performance.tsv b/ENCSR512FHU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4e1caa415d396724d081d254ce2804ce70ac3024..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -362.178955078125 0.2958209216594696 0.6348375082015991 0.23696738481521606 0.7549093961715698 0.7404690384864807 0.4672935903072357 \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_2.evaluate.json b/ENCSR512FHU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bcac536f1b9d518caab74c6a83d8620eddad053d..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF944ETK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_2.fit.json b/ENCSR512FHU/cherimoya.fold_2.fit.json deleted file mode 100644 index 42b39227973d720b83e8eada1b89008a3735db88..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF944ETK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_2.log b/ENCSR512FHU/cherimoya.fold_2.log deleted file mode 100644 index 81c6f20b53caba2f00afc3c347b86e0bbb77c4f1..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2329 29.560295343399048 3.290104866027832 294.9385986328125 1.1943511962890625 447.3568420410156 0.46569564938545227 0.59502447 6.958278656005859 True -1 4658 25.73948860168457 0.4409055709838867 298.2059326171875 0.7941235303878784 386.0034484863281 0.5715447664260864 0.6626023 2.65242075920105 True -2 6987 25.680222272872925 0.47133708000183105 299.41845703125 0.4829443693161011 371.8043212890625 0.597271740436554 0.6682862 1.1510456800460815 True -3 9316 25.7249174118042 0.42543721199035645 350.16595458984375 0.6124494075775146 367.4750061035156 0.6044436693191528 0.68516695 0.855680525302887 True -4 11645 25.62807869911194 1.801640510559082 318.26104736328125 0.534395694732666 366.3315124511719 0.607062041759491 0.6855293 0.8392009139060974 True -5 13974 25.71128797531128 0.43456554412841797 317.6104736328125 0.6696511507034302 364.6318664550781 0.609886646270752 0.68884563 0.7907191514968872 True -6 16303 25.695157289505005 0.42574119567871094 278.2288513183594 0.6923398971557617 363.350830078125 0.6123821139335632 0.68959314 0.7491078972816467 True -7 18632 25.646470069885254 0.4250168800354004 253.0563201904297 0.598330557346344 361.9725036621094 0.6147635579109192 0.69413143 0.7161033153533936 True -8 20961 25.748249292373657 0.43274760246276855 255.91896057128906 0.5282540321350098 360.9239196777344 0.617026686668396 0.69673437 0.6732452511787415 True -9 23290 25.712456703186035 0.42574238777160645 252.58493041992188 0.571732223033905 359.7942810058594 0.6192121505737305 0.70469266 0.6304464936256409 True -10 25619 25.713600397109985 0.42630791664123535 278.3322448730469 0.4257795810699463 358.6019287109375 0.6216230988502502 0.70865357 0.5956571102142334 True -11 27948 25.66981339454651 0.4258086681365967 245.40289306640625 0.3630515933036804 357.69219970703125 0.6234850883483887 0.7162381 0.5729106068611145 True -12 30277 25.71391487121582 0.4256908893585205 254.8767547607422 0.4755849838256836 356.93963623046875 0.6250491738319397 0.7213677 0.5593087673187256 True -13 32606 25.650755405426025 0.4276611804962158 221.28457641601562 0.5349285006523132 356.1144714355469 0.6264554262161255 0.7237489 0.5477569699287415 True -14 34935 25.6406672000885 0.4224727153778076 249.58624267578125 0.5078257918357849 355.80462646484375 0.627346396446228 0.72866005 0.5390236377716064 True -15 37264 25.862205028533936 0.43008995056152344 281.22821044921875 0.42735931277275085 355.5144348144531 0.6277632713317871 0.73464906 0.5296737551689148 True -16 39593 25.74608063697815 0.9736142158508301 283.70147705078125 0.4771699607372284 355.60345458984375 0.6275048851966858 0.7369115 0.5326579213142395 True -17 41922 25.752331733703613 0.4289238452911377 260.82562255859375 0.3017555773258209 355.6287841796875 0.6270856857299805 0.7351921 0.5425118803977966 False -18 44251 25.688969135284424 1.0799996852874756 251.8739776611328 0.31531792879104614 355.82586669921875 0.626499354839325 0.73089707 0.5576990246772766 False -19 46580 25.876590967178345 0.42543888092041016 268.7783508300781 0.29896628856658936 356.09210205078125 0.6262032389640808 0.72825503 0.5659650564193726 False diff --git a/ENCSR512FHU/cherimoya.fold_2.performance.tsv b/ENCSR512FHU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 43e312c1caaa36c6ffe609cd416ae8d62401f6f1..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -355.60345458984375 0.3020171523094177 0.6275048851966858 0.23448146879673004 0.7369114756584167 0.694687008857727 0.5326579213142395 \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_3.evaluate.json b/ENCSR512FHU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 979bcde4c902cad068d8597f7f497fdbefc1bd2d..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF944ETK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_3.fit.json b/ENCSR512FHU/cherimoya.fold_3.fit.json deleted file mode 100644 index 6b2f006f1120ac31e07c56e546bba351e90a27a8..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF944ETK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_3.log b/ENCSR512FHU/cherimoya.fold_3.log deleted file mode 100644 index 5505971bc68f87916066b6cb3a2ca698a8b9cc56..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2269 28.929285526275635 3.534256935119629 293.368408203125 0.9377307891845703 450.2358703613281 0.46586528420448303 0.59242594 10.86281967163086 True -1 4538 25.37259793281555 0.49782347679138184 236.03952026367188 0.7559599876403809 383.9898376464844 0.5778137445449829 0.66383857 3.665055274963379 True -2 6807 25.007535696029663 0.48593568801879883 289.0778503417969 0.8991314172744751 372.2884216308594 0.5996980667114258 0.638243 1.2349629402160645 False -3 9076 25.016382932662964 0.48105311393737793 278.0943908691406 0.637569785118103 367.0447998046875 0.6085057854652405 0.6510704 0.8862771987915039 False -4 11345 25.06987690925598 1.5609652996063232 290.74053955078125 0.5858201384544373 365.03826904296875 0.6121169924736023 0.66038287 0.849546492099762 False -5 13614 25.01194453239441 0.48059558868408203 260.0931091308594 0.6286042332649231 363.89093017578125 0.6143823266029358 0.6749423 0.8363950848579407 True -6 15883 25.010161638259888 19.61137580871582 267.4054870605469 0.7184916734695435 362.2397766113281 0.617281973361969 0.6829441 0.7438163161277771 True -7 18152 25.555287837982178 0.4924933910369873 301.21270751953125 0.7417266964912415 361.3919677734375 0.6190937757492065 0.6864128 0.7489655613899231 True -8 20421 25.130627155303955 0.5724778175354004 271.1441650390625 0.7653502225875854 360.46307373046875 0.6211164593696594 0.69222623 0.689179539680481 True -9 22690 25.109403371810913 0.482316255569458 286.90545654296875 0.6065640449523926 359.4549560546875 0.6229234337806702 0.69755864 0.6742078065872192 True -10 24959 25.147145748138428 0.4809741973876953 272.5539855957031 0.50909024477005 358.34576416015625 0.6252962350845337 0.7052676 0.6268665194511414 True -11 27228 25.07053565979004 0.4801633358001709 250.72010803222656 0.42771872878074646 357.322021484375 0.6268377900123596 0.7082423 0.6047013998031616 True -12 29497 25.12283182144165 0.4829087257385254 266.18023681640625 0.4940999150276184 356.47027587890625 0.6284618377685547 0.7167897 0.5747442245483398 True -13 31766 25.07945203781128 0.4855053424835205 301.3331604003906 0.518340528011322 355.5487976074219 0.6302247643470764 0.72465444 0.5429474711418152 True -14 34035 25.10806632041931 0.4869344234466553 258.799072265625 0.4609909951686859 355.19940185546875 0.6308392882347107 0.72795457 0.5346090793609619 True -15 36304 25.065484285354614 0.4803187847137451 270.15264892578125 0.4033363461494446 354.9493408203125 0.6312389373779297 0.73240215 0.5348768830299377 True -16 38573 25.002901554107666 7.1109230518341064 329.5980224609375 0.27987140417099 355.0634460449219 0.6309702396392822 0.7316901 0.5456740856170654 False -17 40842 25.13526940345764 0.48297667503356934 254.5897979736328 0.4772056043148041 355.35455322265625 0.6302156448364258 0.7307832 0.553390383720398 False -18 43111 25.08433485031128 1.9376847743988037 259.98486328125 0.24938403069972992 355.6200256347656 0.6296036839485168 0.72814286 0.5682141780853271 False -19 45380 25.103507041931152 0.48592305183410645 293.8224792480469 0.2914620637893677 355.859619140625 0.629134476184845 0.72604954 0.5774896740913391 False diff --git a/ENCSR512FHU/cherimoya.fold_3.performance.tsv b/ENCSR512FHU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b507079688b60a95f8dd0f0a8161c84904397453..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -354.9493408203125 0.2987978756427765 0.6312389373779297 0.2337709665298462 0.7324021458625793 0.6974181532859802 0.5348768830299377 \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_4.evaluate.json b/ENCSR512FHU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8c500356bd8bba0e134196568490e8a3ae0fbd0e..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF944ETK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_4.fit.json b/ENCSR512FHU/cherimoya.fold_4.fit.json deleted file mode 100644 index 842e1fd97dcbab0c7e21515d36a7dcdc6454f8ea..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF944ETK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512FHU/cherimoya.fold_4.log b/ENCSR512FHU/cherimoya.fold_4.log deleted file mode 100644 index e89061e2433394c69034c573b359f6627d29f0b9..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2308 29.540403366088867 3.3329999446868896 311.5556945800781 0.826446533203125 449.740234375 0.46476131677627563 0.6268059 9.606395721435547 True -1 4616 25.448524475097656 0.44857001304626465 265.0242919921875 0.793095588684082 386.2557373046875 0.5814154744148254 0.65192795 3.0675015449523926 True -2 6924 25.447131395339966 0.44834470748901367 277.32965087890625 0.9142202138900757 373.7362365722656 0.6026689410209656 0.6708513 1.070050835609436 True -3 9232 25.457653760910034 0.8224215507507324 279.0534973144531 1.3570979833602905 368.6803283691406 0.6103403568267822 0.6846359 0.8700695633888245 True -4 11540 25.430190563201904 0.4458749294281006 285.11895751953125 0.6818331480026245 366.6879577636719 0.61412113904953 0.6832931 0.8200942277908325 False -5 13848 25.499082565307617 1.3405537605285645 246.6304931640625 0.6380590200424194 364.9645080566406 0.6173192858695984 0.68432856 0.7417482733726501 False -6 16156 25.493053913116455 0.45188379287719727 285.979736328125 0.47949469089508057 364.0308532714844 0.6198139190673828 0.68270874 0.7255412936210632 False -7 18464 25.445723295211792 0.44847750663757324 243.95187377929688 0.524429202079773 362.9178466796875 0.6219942569732666 0.68566024 0.7069593071937561 True -8 20772 25.380934715270996 0.4458615779876709 260.0845031738281 0.6953480243682861 361.77044677734375 0.6242882013320923 0.69578326 0.6829037666320801 True -9 23080 25.394163131713867 1.8780837059020996 269.32293701171875 0.6223669052124023 360.935302734375 0.626017153263092 0.70549124 0.6338090300559998 True -10 25388 25.460225343704224 0.44464945793151855 281.18475341796875 0.5970458984375 360.0534973144531 0.628240704536438 0.7060227 0.6138926148414612 True -11 27696 25.412331342697144 0.44727039337158203 282.63922119140625 0.5031446218490601 358.9085998535156 0.6302069425582886 0.7155034 0.5808061957359314 True -12 30004 25.412407636642456 0.45195984840393066 258.9571533203125 0.4987827241420746 358.0435791015625 0.6317372918128967 0.7219429 0.5613764524459839 True -13 32312 25.353694438934326 0.4439272880554199 253.7218017578125 0.5412557721138 357.3176574707031 0.6332106590270996 0.7284105 0.5436930656433105 True -14 34620 25.38055157661438 0.44660019874572754 237.10189819335938 0.7125812768936157 356.7355041503906 0.6341835260391235 0.7322537 0.5339483022689819 True -15 36928 25.37732243537903 0.45130038261413574 319.73992919921875 0.42866647243499756 356.43914794921875 0.6346719264984131 0.736495 0.5295372605323792 True -16 39236 25.381481885910034 0.44040799140930176 215.61131286621094 0.2933756113052368 356.48114013671875 0.6344138979911804 0.73604023 0.5395501255989075 False -17 41544 25.372146129608154 0.4427769184112549 259.2353515625 0.2900333106517792 356.6694641113281 0.6338655948638916 0.7356499 0.5446140170097351 False -18 43852 25.385531425476074 1.3344862461090088 264.7728271484375 0.39932727813720703 356.960205078125 0.6332444548606873 0.7316324 0.5525099039077759 False -19 46160 25.79552721977234 0.4471292495727539 236.83509826660156 0.19541481137275696 357.065185546875 0.6328654289245605 0.7280996 0.5615264773368835 False diff --git a/ENCSR512FHU/cherimoya.fold_4.performance.tsv b/ENCSR512FHU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6a99ebb037d15c3a9058a1ab69b6b4ee68adf947..0000000000000000000000000000000000000000 --- a/ENCSR512FHU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -356.43914794921875 0.2979371249675751 0.6346718072891235 0.23585501313209534 0.7364950180053711 0.6860485672950745 0.5295372605323792 \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_0.evaluate.json b/ENCSR512YXO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index dfd952fa4ab38f22d78e4f3c2703c54f8d1a5b5e..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF582MTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_0.fit.json b/ENCSR512YXO/cherimoya.fold_0.fit.json deleted file mode 100644 index 4358f254599fd312a0a3f276ac9bffe1ee64d15f..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF582MTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_0.log b/ENCSR512YXO/cherimoya.fold_0.log deleted file mode 100644 index 21c766b8191d8e16c0f80ae2974560672156d37c..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2091 27.699431896209717 5.2094316482543945 305.2384033203125 0.6185692548751831 494.9280090332031 0.46211832761764526 0.5458972 10.683547973632812 True -1 4182 22.688786268234253 0.509413480758667 355.00146484375 0.6742624640464783 418.7065124511719 0.5851778388023376 0.61896676 4.381659984588623 True -2 6273 23.011515140533447 0.43483400344848633 330.3407287597656 0.9257867336273193 402.48406982421875 0.6155545711517334 0.6352897 1.1290321350097656 True -3 8364 23.057132720947266 0.4851686954498291 284.27197265625 0.6858924627304077 397.2001953125 0.625714123249054 0.64532983 0.7299196720123291 True -4 10455 23.002209663391113 0.43600010871887207 356.22271728515625 0.4276566505432129 394.9065856933594 0.6294964551925659 0.6502849 0.7201989889144897 True -5 12546 23.025671005249023 0.5168583393096924 396.92413330078125 1.0073397159576416 393.62939453125 0.6324604749679565 0.65636927 0.7212951183319092 True -6 14637 24.08634066581726 0.4300203323364258 311.2811279296875 0.8175603747367859 392.2327880859375 0.6352188587188721 0.65541065 0.673507809638977 False -7 16728 23.007834434509277 0.526909589767456 268.4653015136719 0.7015825510025024 391.38006591796875 0.6370499134063721 0.6555994 0.6640641689300537 False -8 18819 23.03857421875 0.43916988372802734 272.43707275390625 1.0085185766220093 390.3038635253906 0.6388363838195801 0.66651726 0.6192333102226257 True -9 20910 23.02131962776184 0.5021827220916748 303.46722412109375 0.5302858352661133 389.189208984375 0.6412362456321716 0.6707657 0.5872593522071838 True -10 23001 23.017327070236206 0.5042526721954346 308.0845947265625 0.6417850255966187 388.1781921386719 0.6428154706954956 0.679987 0.5716675519943237 True -11 25092 22.98026704788208 0.47196531295776367 307.16986083984375 0.6288608312606812 387.0093688964844 0.644953191280365 0.6873975 0.5454098582267761 True -12 27183 23.01030206680298 0.9795677661895752 346.2568359375 0.46782386302948 386.2148132324219 0.6467260718345642 0.6931329 0.5281710028648376 True -13 29274 23.025671005249023 0.42582082748413086 354.5991516113281 0.6058856248855591 385.2372131347656 0.6483083367347717 0.7000376 0.5178579688072205 True -14 31365 23.103841066360474 0.4432492256164551 308.35986328125 0.5967261791229248 385.0631103515625 0.6493465900421143 0.70495445 0.5137989521026611 True -15 33456 23.016902923583984 0.44388365745544434 315.175537109375 0.4959346354007721 384.3983459472656 0.6498163938522339 0.7089759 0.5145377516746521 True -16 35547 23.022485971450806 0.4340245723724365 353.06170654296875 0.376303493976593 385.18621826171875 0.6496486663818359 0.71105295 0.5141348242759705 True -17 37638 23.02465558052063 0.4432976245880127 327.579345703125 0.37677621841430664 384.43634033203125 0.6493569016456604 0.7100829 0.5248357653617859 False -18 39729 23.013916015625 0.42842698097229004 271.86053466796875 0.43871739506721497 385.07171630859375 0.6488473415374756 0.7086699 0.5329169034957886 False -19 41820 22.99473786354065 0.4352579116821289 297.350830078125 0.27396148443222046 384.7741394042969 0.648457407951355 0.70614606 0.5429123044013977 False diff --git a/ENCSR512YXO/cherimoya.fold_0.performance.tsv b/ENCSR512YXO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ed63f043f0ae7f893a119a4f9049b9dfaec7f41a..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -385.18621826171875 0.28578075766563416 0.6496486067771912 0.25052472949028015 0.7110529541969299 0.6677030920982361 0.5141348242759705 \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_1.evaluate.json b/ENCSR512YXO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f298e1477a0b919fe54dc09e0c0a19d609fe7008..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF582MTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_1.fit.json b/ENCSR512YXO/cherimoya.fold_1.fit.json deleted file mode 100644 index fc18b6e2311730cd9411b778b9229b4dc5de851a..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF582MTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_1.log b/ENCSR512YXO/cherimoya.fold_1.log deleted file mode 100644 index e1689aec826c0b7cb33fcc66789380b1c4cd42c7..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2129 27.94985032081604 3.833975076675415 260.4208679199219 1.0479364395141602 501.2695617675781 0.4715516269207001 0.5575678 8.915641784667969 True -1 4258 23.31524133682251 0.5374858379364014 270.9316101074219 0.8952741622924805 430.4972229003906 0.5879769921302795 0.6404672 3.4921395778656006 True -2 6387 23.393643379211426 0.5273103713989258 357.4546203613281 0.5882911682128906 417.5196838378906 0.6125547289848328 0.64932865 1.0375882387161255 True -3 8516 23.388298511505127 1.6740913391113281 358.2476806640625 0.8595862984657288 412.00335693359375 0.6224058866500854 0.6703949 0.7760096192359924 True -4 10645 23.436395406723022 0.6896753311157227 284.70306396484375 0.43159759044647217 410.4242858886719 0.6256851553916931 0.6867111 0.6451485753059387 True -5 12774 23.18307852745056 0.49788379669189453 313.56329345703125 0.7542634010314941 409.0223693847656 0.628207802772522 0.69182074 0.6457719206809998 True -6 14903 23.054901361465454 15.081362962722778 325.30963134765625 0.5192624926567078 407.8335266113281 0.6307171583175659 0.6947147 0.5992305278778076 True -7 17032 22.981435537338257 0.5038447380065918 329.3622131347656 0.4676234722137451 406.9320068359375 0.6323719024658203 0.6959174 0.585716962814331 True -8 19161 23.025628805160522 0.501173734664917 299.0018005371094 0.6523975133895874 405.77618408203125 0.6347496509552002 0.7045511 0.5549299716949463 True -9 21290 22.999020099639893 0.606658935546875 348.33953857421875 0.4816824197769165 404.9715881347656 0.6367915272712708 0.70753735 0.5223494172096252 True -10 23419 22.952505826950073 0.4925224781036377 323.0104675292969 0.5907000303268433 403.6384582519531 0.6388489603996277 0.71616685 0.500659167766571 True -11 25548 22.933295011520386 0.49104785919189453 288.8382263183594 0.6139380931854248 402.71075439453125 0.640623927116394 0.72299933 0.48900672793388367 True -12 27677 22.93823766708374 0.4969956874847412 246.99713134765625 0.6520686149597168 401.9476318359375 0.6420851945877075 0.72557193 0.48009055852890015 True -13 29806 22.946266651153564 0.4954047203063965 278.63238525390625 0.45116543769836426 401.1886901855469 0.6435738205909729 0.73065543 0.46757373213768005 True -14 31935 22.96038818359375 14.40159797668457 353.1129150390625 0.45946651697158813 400.5175476074219 0.6446941494941711 0.73855317 0.4555313289165497 True -15 34064 23.00199031829834 0.4891688823699951 307.6872863769531 0.5320255756378174 400.1249084472656 0.6451953053474426 0.7414413 0.4540051817893982 True -16 36193 22.959351778030396 0.49800729751586914 330.6636962890625 0.3884364366531372 400.03497314453125 0.6452219486236572 0.74583364 0.4482792913913727 True -17 38322 22.923864364624023 1.4099266529083252 274.51763916015625 0.24487119913101196 400.15130615234375 0.6448723673820496 0.7457089 0.45340314507484436 False -18 40451 23.061421394348145 0.49004077911376953 310.31671142578125 0.23639312386512756 400.2018127441406 0.6445510983467102 0.74257994 0.4639105796813965 False -19 42580 22.96206307411194 0.4986093044281006 311.205322265625 0.4437214434146881 400.37493896484375 0.6441822648048401 0.73785704 0.4718737304210663 False diff --git a/ENCSR512YXO/cherimoya.fold_1.performance.tsv b/ENCSR512YXO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2813d089cd60000935127b8cacf22c058ad325a7..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -400.03497314453125 0.2835976481437683 0.6452219486236572 0.2597196102142334 0.7458336353302002 0.732426106929779 0.4482792913913727 \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_2.evaluate.json b/ENCSR512YXO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 70875a74be6f375de052bf6b0091acdb0484c6ce..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF582MTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_2.fit.json b/ENCSR512YXO/cherimoya.fold_2.fit.json deleted file mode 100644 index 719a123cd8fc277ae76850a7912eb19b42a690fb..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF582MTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_2.log b/ENCSR512YXO/cherimoya.fold_2.log deleted file mode 100644 index c0a30bea89ce4ed702a1e1cb03a89259b58fcb5d..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2234 29.416663885116577 3.5645389556884766 308.7354736328125 0.7878384590148926 484.06317138671875 0.46884122490882874 0.5511637 9.332275390625 True -1 4468 24.621174335479736 0.4825148582458496 336.64654541015625 0.7255951762199402 415.5693054199219 0.5878419280052185 0.61741376 3.5270798206329346 True -2 6702 24.58484387397766 0.43058180809020996 313.8551025390625 0.6918073892593384 403.8148498535156 0.6107224225997925 0.61877185 1.2667217254638672 True -3 8936 24.52720284461975 0.4137129783630371 271.2293701171875 1.0643599033355713 398.05047607421875 0.6189824938774109 0.637728 0.8431043028831482 True -4 11170 24.44872808456421 0.4079720973968506 341.2947082519531 0.5131193399429321 396.23175048828125 0.622181236743927 0.6447288 0.8057989478111267 True -5 13404 24.126188039779663 0.40963006019592285 294.00653076171875 0.5894002914428711 395.2527160644531 0.6242464780807495 0.6466218 0.8106880784034729 True -6 15638 24.14651656150818 5.626519441604614 311.50396728515625 0.7323850989341736 393.70391845703125 0.6271435618400574 0.65531826 0.7896795868873596 True -7 17872 24.12523102760315 0.4132401943206787 311.3721923828125 0.6946308612823486 392.21209716796875 0.6298161745071411 0.6615391 0.7539727091789246 True -8 20106 24.09942317008972 0.406353235244751 289.0843811035156 0.6140743494033813 391.1547546386719 0.6315287351608276 0.67051953 0.7162596583366394 True -9 22340 24.086427688598633 0.4102749824523926 302.90350341796875 0.675981879234314 389.8200988769531 0.6340006589889526 0.6794684 0.6192303895950317 True -10 24574 24.11273694038391 1.3549182415008545 274.4311218261719 0.6928698420524597 388.7791442871094 0.6360135078430176 0.68354964 0.5858163833618164 True -11 26808 24.287665605545044 7.912052154541016 304.86553955078125 0.4286564290523529 387.96875 0.6378951072692871 0.6937171 0.5485022664070129 True -12 29042 24.107802391052246 0.4159572124481201 319.56915283203125 0.5822149515151978 387.0570068359375 0.6395934820175171 0.70109993 0.539297878742218 True -13 31276 24.123090505599976 0.9306540489196777 322.6831359863281 0.6203616857528687 386.3438415527344 0.6409062743186951 0.7058368 0.5250700116157532 True -14 33510 24.07863163948059 0.40510106086730957 348.1470031738281 0.28565335273742676 385.99151611328125 0.6417200565338135 0.7125709 0.5063228607177734 True -15 35744 24.071858167648315 0.4526529312133789 289.7743225097656 0.5899621844291687 385.5412292480469 0.6424301862716675 0.7183569 0.5051404237747192 True -16 37978 24.05083656311035 0.40961194038391113 251.38345336914062 0.3939734399318695 385.4981384277344 0.6426604390144348 0.72237897 0.5006210803985596 True -17 40212 24.09130024909973 0.40134692192077637 296.9229736328125 0.2889368534088135 385.66107177734375 0.6420847773551941 0.7199519 0.5091554522514343 False -18 42446 24.0798122882843 0.4006474018096924 265.36651611328125 0.35096725821495056 385.8802795410156 0.641532838344574 0.7173976 0.5160365700721741 False -19 44680 24.088375091552734 0.3980865478515625 301.4276428222656 0.21758444607257843 386.1127624511719 0.6412566900253296 0.71630484 0.5236429572105408 False diff --git a/ENCSR512YXO/cherimoya.fold_2.performance.tsv b/ENCSR512YXO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5e019e4303806e44276dbb498b31c628b28a789d..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -385.4981384277344 0.2885251045227051 0.6426604390144348 0.25120484828948975 0.7223789691925049 0.6875089406967163 0.5006210803985596 \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_3.evaluate.json b/ENCSR512YXO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e3ad4977fc1fb0a0d5634de3233cc3832cc2c7b2..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF582MTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_3.fit.json b/ENCSR512YXO/cherimoya.fold_3.fit.json deleted file mode 100644 index c37f0994353ffe42e7d37b2579b0cdade065fa33..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF582MTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_3.log b/ENCSR512YXO/cherimoya.fold_3.log deleted file mode 100644 index 703b492157299ff00db78dd15d744ea6b135bab6..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2168 28.740907907485962 3.5510966777801514 293.197998046875 0.9110686779022217 492.87103271484375 0.4719047546386719 0.54430693 9.694198608398438 True -1 4336 23.86999201774597 0.6159999370574951 316.31744384765625 0.8642510175704956 419.4210205078125 0.5930110812187195 0.6052189 4.211275100708008 True -2 6504 23.815415620803833 0.46212124824523926 314.81195068359375 0.9386765360832214 406.02252197265625 0.6176260709762573 0.62040424 1.5958956480026245 True -3 8672 23.809637308120728 0.45392656326293945 279.9964294433594 0.662202000617981 401.1120910644531 0.6267938017845154 0.6284596 1.0657048225402832 True -4 10840 23.811161518096924 0.4542403221130371 303.104736328125 0.6004947423934937 398.6961364746094 0.631658673286438 0.6360445 0.9539154767990112 True -5 13008 23.821175575256348 0.4558224678039551 303.5076904296875 0.74763023853302 397.57440185546875 0.6336014270782471 0.63970774 0.9230499267578125 True -6 15176 23.853498458862305 1.0221099853515625 265.45849609375 0.6886651515960693 396.4385986328125 0.6357335448265076 0.6414232 0.8746515512466431 True -7 17344 23.5511736869812 0.4587516784667969 253.76939392089844 0.5546042323112488 395.9161376953125 0.6371251344680786 0.6516172 0.8042092323303223 True -8 19512 23.355623483657837 0.4602792263031006 294.12823486328125 0.4545622169971466 394.6361083984375 0.6389813423156738 0.66267866 0.7884177565574646 True -9 21680 23.334285736083984 0.459758996963501 277.25299072265625 0.9502317905426025 393.5827331542969 0.640933632850647 0.6703739 0.6930306553840637 True -10 23848 23.379108905792236 0.45832133293151855 301.2212829589844 0.5153789520263672 392.4510192871094 0.643197774887085 0.6781896 0.6637890934944153 True -11 26016 23.367243766784668 0.45928215980529785 279.78265380859375 0.6114316582679749 391.7532958984375 0.6448856592178345 0.6822978 0.643779993057251 True -12 28184 23.397305488586426 0.4586524963378906 299.38836669921875 0.4226664900779724 391.2377014160156 0.645913302898407 0.69116896 0.6155884861946106 True -13 30352 23.372496604919434 0.45793914794921875 327.30615234375 0.5869108438491821 390.10687255859375 0.6474721431732178 0.69848335 0.5784807801246643 True -14 32520 23.356187105178833 0.45847439765930176 311.9436950683594 0.40920597314834595 389.690185546875 0.6484070420265198 0.70365393 0.5603509545326233 True -15 34688 23.359676837921143 0.45925045013427734 265.6546630859375 0.3241838216781616 389.1006774902344 0.6488656401634216 0.70609766 0.5466254353523254 True -16 36856 23.394830226898193 1.5086045265197754 288.86944580078125 0.5048716068267822 389.3458251953125 0.6487991809844971 0.7103073 0.5372538566589355 True -17 39024 23.41871953010559 0.4643259048461914 296.1211242675781 0.32307496666908264 389.1138916015625 0.6485666036605835 0.706621 0.5378680229187012 False -18 41192 23.358404874801636 0.4645805358886719 276.45355224609375 0.3072523772716522 389.4024963378906 0.6480400562286377 0.70445573 0.549480140209198 False -19 43360 23.35650658607483 0.4617116451263428 271.079833984375 0.3091156482696533 389.4087829589844 0.6477681398391724 0.70114416 0.5548030138015747 False diff --git a/ENCSR512YXO/cherimoya.fold_3.performance.tsv b/ENCSR512YXO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 507f821a8f1d370112c398d69f6fc2c8011c386c..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -389.3458251953125 0.2842985689640045 0.6487991809844971 0.2539339065551758 0.7103073000907898 0.6738437414169312 0.5372538566589355 \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_4.evaluate.json b/ENCSR512YXO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 03a2a5223cad1e1eff5e665c027b2b3cdc90997f..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF582MTA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_4.fit.json b/ENCSR512YXO/cherimoya.fold_4.fit.json deleted file mode 100644 index b0a914736c2146c6dc1f55c8ff083ef42b8f3182..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF582MTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR512YXO/cherimoya.fold_4.log b/ENCSR512YXO/cherimoya.fold_4.log deleted file mode 100644 index 46b36df6a0f6e3f2a0ad9e1ddaaccda700a924f9..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2233 29.198657751083374 4.4895265102386475 312.475341796875 0.8339043855667114 487.77313232421875 0.4677378237247467 0.5641206 9.362822532653809 True -1 4466 24.50377082824707 0.6351003646850586 298.49151611328125 1.1625193357467651 416.03759765625 0.593977689743042 0.59894484 3.4734411239624023 True -2 6699 24.519506454467773 0.4297831058502197 337.3309631347656 0.658025860786438 401.9065246582031 0.6191080212593079 0.61242265 0.9785715341567993 True -3 8932 24.494232654571533 0.4270474910736084 381.6393127441406 0.8104100823402405 397.0496826171875 0.6280864477157593 0.64023083 0.7538658976554871 True -4 11165 24.564769506454468 0.8310425281524658 315.28814697265625 0.39907360076904297 394.9939270019531 0.6320675015449524 0.6463778 0.720679759979248 True -5 13398 24.570582151412964 0.4298412799835205 307.9283142089844 0.7392280101776123 393.4713439941406 0.6351455450057983 0.65471816 0.6979994773864746 True -6 15631 24.52755355834961 0.4294612407684326 346.76898193359375 0.6394690275192261 392.4878845214844 0.6373154520988464 0.66018087 0.6843207478523254 True -7 17864 24.516117334365845 0.43230748176574707 351.3074035644531 0.7813551425933838 391.1861267089844 0.6398258805274963 0.66406757 0.6484844088554382 True -8 20097 24.545847415924072 0.42740488052368164 354.3072814941406 0.6984940767288208 390.4421691894531 0.6417972445487976 0.67353535 0.6167142391204834 True -9 22330 24.56244206428528 1.5774590969085693 277.22479248046875 0.34121695160865784 389.5452880859375 0.6438526511192322 0.6749424 0.5759127736091614 True -10 24563 24.546441793441772 0.4248359203338623 289.0117492675781 0.6037823557853699 388.4888610839844 0.6456711888313293 0.68216544 0.5711397528648376 True -11 26796 24.571739435195923 0.4412977695465088 285.6921691894531 0.4930703043937683 387.2435302734375 0.647761344909668 0.68861246 0.5467531085014343 True -12 29029 24.602411031723022 0.42999911308288574 296.0928039550781 0.35937899351119995 387.05938720703125 0.6491068601608276 0.6955514 0.5344456434249878 True -13 31262 24.56874370574951 0.43137454986572266 276.6919860839844 0.5242024660110474 385.7239990234375 0.6504387855529785 0.7033585 0.5202862024307251 True -14 33495 24.560375452041626 0.4318416118621826 306.2230224609375 0.5168453454971313 384.7126159667969 0.6516167521476746 0.7089471 0.5083123445510864 True -15 35728 24.50063729286194 0.4424262046813965 274.1094665527344 0.49279654026031494 385.00543212890625 0.6519414186477661 0.711339 0.5088843703269958 True -16 37961 24.178332090377808 0.4258432388305664 304.2879638671875 0.35152900218963623 384.7509460449219 0.6516990065574646 0.71356726 0.5108273029327393 True -17 40194 24.039245128631592 0.42607593536376953 281.8013000488281 0.2778577208518982 384.7495422363281 0.6512077450752258 0.7128959 0.5212609171867371 False -18 42427 24.054102659225464 0.4201653003692627 284.3407287597656 0.2158607542514801 385.14715576171875 0.6506021022796631 0.7081321 0.534271776676178 False -19 44660 24.068493127822876 0.4358394145965576 316.0394287109375 0.3799603581428528 385.1177978515625 0.6502169966697693 0.7062029 0.5436909198760986 False diff --git a/ENCSR512YXO/cherimoya.fold_4.performance.tsv b/ENCSR512YXO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b1d56b55a4ce48ea86def173848a4663f4295d20..0000000000000000000000000000000000000000 --- a/ENCSR512YXO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -384.7509460449219 0.2856042683124542 0.6516990065574646 0.25326117873191833 0.7135672569274902 0.663287341594696 0.5108273029327393 \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_0.evaluate.json b/ENCSR513EVP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index aa3ff202764d8c785e5faeac6724b56fc27b0507..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF927NMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_0.fit.json b/ENCSR513EVP/cherimoya.fold_0.fit.json deleted file mode 100644 index 1c1461d67c6b377ed1ff9c09c68258ad4b2320df..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF927NMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_0.log b/ENCSR513EVP/cherimoya.fold_0.log deleted file mode 100644 index 62ce8f64d1ceeb1c46e4e88542c2f08c56ac936c..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1061 16.07774591445923 3.0576577186584473 293.4938659667969 0.6392605900764465 480.0769958496094 0.3814335763454437 0.64017844 19.8725528717041 True -1 2122 11.669138431549072 0.2131664752960205 273.3023681640625 0.8543221950531006 378.6073303222656 0.4770752191543579 0.7169984 9.411086082458496 True -2 3183 11.67612099647522 0.20490789413452148 239.21336364746094 0.8307676911354065 343.1085510253906 0.5369014143943787 0.74069417 4.393661975860596 True -3 4244 11.704439640045166 0.2395322322845459 270.75244140625 0.5288160443305969 315.3443298339844 0.5864700675010681 0.7590956 2.0333542823791504 True -4 5305 11.656782627105713 0.21055126190185547 209.22698974609375 0.5458590984344482 305.0050048828125 0.6028596758842468 0.7855775 0.9065142869949341 True -5 6366 11.679333209991455 0.20477747917175293 251.16497802734375 0.5635393261909485 301.0062255859375 0.6089472770690918 0.7960647 0.5231660008430481 True -6 7427 11.649569034576416 0.21406865119934082 237.79273986816406 0.3011960983276367 299.10333251953125 0.6124143004417419 0.79931283 0.4330776333808899 True -7 8488 11.641324520111084 0.21027541160583496 255.70834350585938 0.29473876953125 297.6437683105469 0.614881694316864 0.8007074 0.40457502007484436 True -8 9549 11.647323608398438 0.30940794944763184 288.8226623535156 0.41309699416160583 296.52783203125 0.6166121959686279 0.80832803 0.3816724121570587 True -9 10610 11.68742299079895 0.205796480178833 219.2452392578125 0.289408802986145 295.5986022949219 0.6187114715576172 0.8138317 0.3744184374809265 True -10 11671 11.667775869369507 0.2056884765625 240.0948486328125 0.2687751054763794 294.77398681640625 0.6202569007873535 0.823036 0.35969969630241394 True -11 12732 11.657701969146729 0.20766425132751465 236.03073120117188 0.31816524267196655 293.91766357421875 0.6220543384552002 0.8235319 0.3540515601634979 True -12 13793 11.695850133895874 1.0668816566467285 212.3670654296875 0.25493836402893066 293.431884765625 0.6234670281410217 0.82679474 0.34745824337005615 True -13 14854 11.665810108184814 0.21052241325378418 230.27066040039062 0.25937971472740173 293.13629150390625 0.6243770718574524 0.8323237 0.33791583776474 True -14 15915 11.673231363296509 0.28713154792785645 215.30807495117188 0.27756404876708984 292.8238525390625 0.6250392198562622 0.836966 0.3319171965122223 True -15 16976 11.689751386642456 0.2127704620361328 189.4357452392578 0.21121765673160553 292.7831115722656 0.6252689957618713 0.8402004 0.3289077579975128 True -16 18037 11.65612268447876 0.21301531791687012 209.01272583007812 0.2406509965658188 292.8398132324219 0.6248275637626648 0.8406642 0.33125951886177063 True -17 19098 11.679126501083374 0.21499276161193848 205.0130615234375 0.1831672638654709 293.3048400878906 0.6236121654510498 0.84141237 0.3372915983200073 True -18 20159 11.647283554077148 0.21022439002990723 210.32728576660156 0.16969366371631622 293.607421875 0.6225289106369019 0.8404798 0.34692004323005676 False -19 21220 11.684966564178467 0.20597076416015625 241.7342071533203 0.1694251298904419 294.0230712890625 0.6216405630111694 0.8398659 0.3540199398994446 False diff --git a/ENCSR513EVP/cherimoya.fold_0.performance.tsv b/ENCSR513EVP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a4dc9229441ffc3d8256efed0c0b935935794489..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -293.3048400878906 0.3106289207935333 0.6236121654510498 0.20130884647369385 0.841412365436554 0.8090451955795288 0.3372915983200073 \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_1.evaluate.json b/ENCSR513EVP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2860d25d7551d5a34523901e3f1f0bea58fe0c84..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF927NMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_1.fit.json b/ENCSR513EVP/cherimoya.fold_1.fit.json deleted file mode 100644 index 88f7548b95e5847099674319b335a000b4c30613..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF927NMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_1.log b/ENCSR513EVP/cherimoya.fold_1.log deleted file mode 100644 index c28764a28557db7bde0818b07bb099ba6a9cd948..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1038 16.457667350769043 2.8818233013153076 214.32861328125 0.5506161451339722 534.3370971679688 0.3928009867668152 0.5472047 21.436805725097656 True -1 2076 11.436155319213867 0.30614399909973145 244.89556884765625 0.6064386367797852 422.50360107421875 0.4887472689151764 0.66869026 10.017987251281738 True -2 3114 11.696971893310547 20.26023244857788 244.93492126464844 0.5100964307785034 377.28662109375 0.5568958520889282 0.7208012 4.550839424133301 True -3 4152 11.439782619476318 0.3102998733520508 221.80108642578125 0.41862303018569946 344.25665283203125 0.6124176979064941 0.7533485 1.88114595413208 True -4 5190 11.383644342422485 0.30086708068847656 259.2013854980469 0.4144187867641449 331.9837646484375 0.6310392022132874 0.7748164 1.0030370950698853 True -5 6228 11.408976554870605 0.7135679721832275 261.88751220703125 0.4983394742012024 327.6141357421875 0.6378010511398315 0.7844445 0.6464376449584961 True -6 7266 11.395633220672607 0.2963836193084717 249.18228149414062 0.4351996183395386 325.121337890625 0.6416646838188171 0.7972186 0.4564306437969208 True -7 8304 11.400583505630493 0.28835058212280273 242.7469482421875 0.512326717376709 323.7787780761719 0.6441894769668579 0.80485743 0.4231478273868561 True -8 9342 12.00869345664978 17.24393320083618 235.33558654785156 0.44721153378486633 322.4725646972656 0.6464664936065674 0.80657756 0.40533536672592163 True -9 10380 11.671066045761108 0.3048980236053467 208.08998107910156 0.31865301728248596 321.2662353515625 0.6487950086593628 0.8105199 0.39069268107414246 True -10 11418 11.393646001815796 0.3004910945892334 249.42303466796875 0.571262538433075 320.2015686035156 0.6508539915084839 0.8196986 0.36764171719551086 True -11 12456 11.380737781524658 0.3003537654876709 226.79026794433594 0.3203169107437134 319.4070739746094 0.6522400975227356 0.8228261 0.3602491021156311 True -12 13494 11.416933298110962 0.4529285430908203 240.3006591796875 0.457669198513031 318.6159973144531 0.6535448431968689 0.82758474 0.3494877219200134 True -13 14532 11.39754056930542 0.2905905246734619 230.597900390625 0.3814650774002075 318.1878356933594 0.654251217842102 0.83275306 0.3403465151786804 True -14 15570 11.418175220489502 0.2895512580871582 244.5856475830078 0.2555909752845764 318.1221618652344 0.6545167565345764 0.8368458 0.33861982822418213 True -15 16608 11.426463603973389 0.28928709030151367 240.68417358398438 0.2455729991197586 318.1353454589844 0.6542795896530151 0.83853966 0.34066763520240784 True -16 17646 11.434781551361084 0.2937932014465332 240.31736755371094 0.2289227843284607 318.46380615234375 0.6533562541007996 0.839971 0.34441205859184265 True -17 18684 11.426966905593872 0.2955629825592041 181.8754119873047 0.13461627066135406 319.1601257324219 0.6519158482551575 0.83793724 0.35432785749435425 False -18 19722 11.41998028755188 0.2979164123535156 204.55763244628906 0.19125434756278992 319.54876708984375 0.6506345868110657 0.8361902 0.3678373694419861 False -19 20760 11.456263303756714 0.2891528606414795 252.33059692382812 0.09560935199260712 320.0263977050781 0.649599552154541 0.83559364 0.37650930881500244 False diff --git a/ENCSR513EVP/cherimoya.fold_1.performance.tsv b/ENCSR513EVP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0c407c6bef9cc89c25ddbd6b2a5961ea4b85fa5a..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -318.46380615234375 0.289547860622406 0.6533562541007996 0.22112593054771423 0.8399710059165955 0.8154870867729187 0.34441205859184265 \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_2.evaluate.json b/ENCSR513EVP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f3560cad65d792a5516ef8c6bb60e05d158416de..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF927NMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_2.fit.json b/ENCSR513EVP/cherimoya.fold_2.fit.json deleted file mode 100644 index b99320cbf1a8b7d8297eaf19b95a98fec8643973..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF927NMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_2.log b/ENCSR513EVP/cherimoya.fold_2.log deleted file mode 100644 index 26c69e26010a62059718031f718bf6691d31f2c3..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1111 16.74324607849121 3.1196393966674805 244.1977081298828 0.8956313729286194 491.30767822265625 0.38736847043037415 0.5820131 19.34238052368164 True -1 2222 12.242914199829102 1.3033556938171387 234.9928741455078 0.43774664402008057 389.6596984863281 0.4824327528476715 0.69263685 8.400191307067871 True -2 3333 12.242703914642334 10.23462724685669 275.18548583984375 0.42806512117385864 346.0013732910156 0.5510786771774292 0.7379217 3.6274564266204834 True -3 4444 12.500813722610474 0.2473468780517578 219.88331604003906 0.6350529193878174 319.17913818359375 0.5963233709335327 0.77701753 1.3546189069747925 True -4 5555 12.189385414123535 0.2328510284423828 278.88201904296875 0.39109188318252563 310.089599609375 0.6088405847549438 0.7934637 0.6295301914215088 True -5 6666 12.198716878890991 0.23545598983764648 224.11280822753906 0.5992335081100464 306.7081298828125 0.6141025424003601 0.800525 0.488887220621109 True -6 7777 12.228361129760742 0.2422647476196289 254.8492431640625 0.41680747270584106 304.6547546386719 0.6173226237297058 0.80424666 0.4256516098976135 True -7 8888 12.2305428981781 0.23714423179626465 293.49444580078125 0.4599163830280304 303.6874694824219 0.6193566918373108 0.8020826 0.4057842493057251 False -8 9999 12.249597549438477 0.23189568519592285 223.96356201171875 0.4086351692676544 302.52899169921875 0.6215816736221313 0.80930156 0.393957257270813 True -9 11110 11.978211641311646 0.22957706451416016 232.80459594726562 0.6360596418380737 301.557373046875 0.6233125329017639 0.8136595 0.38785797357559204 True -10 12221 11.975227355957031 0.23265790939331055 213.26988220214844 0.43022826313972473 301.00054931640625 0.6245452165603638 0.8167276 0.3815140128135681 True -11 13332 12.101738929748535 0.24409914016723633 245.66575622558594 0.5214033126831055 300.21441650390625 0.6262316107749939 0.8184273 0.3785783648490906 True -12 14443 11.999985694885254 0.23656344413757324 245.18624877929688 0.348757266998291 299.71343994140625 0.627438485622406 0.823367 0.371433287858963 True -13 15554 12.00955843925476 0.23259449005126953 225.63328552246094 0.24306972324848175 299.32305908203125 0.6284511685371399 0.8285106 0.3631127178668976 True -14 16665 11.97644853591919 1.0480291843414307 222.43777465820312 0.22525939345359802 298.9637451171875 0.6292482018470764 0.8299531 0.3577768802642822 True -15 17776 12.001504182815552 0.24172663688659668 233.65042114257812 0.23389551043510437 298.9803771972656 0.6290175318717957 0.832775 0.35754773020744324 True -16 18887 11.985252141952515 0.2323145866394043 184.01454162597656 0.21579420566558838 299.113525390625 0.6284597516059875 0.83179307 0.36291390657424927 False -17 19998 11.963248491287231 0.23226189613342285 261.70391845703125 0.1559879034757614 299.608154296875 0.6271377801895142 0.8297742 0.37169522047042847 False -18 21109 11.976351499557495 0.2301774024963379 244.20797729492188 0.18827950954437256 300.1817626953125 0.6258335113525391 0.8276414 0.3780038058757782 False -19 22220 11.987218141555786 0.23630475997924805 221.71726989746094 0.1144467443227768 300.5146484375 0.6251824498176575 0.8249933 0.3837677538394928 False diff --git a/ENCSR513EVP/cherimoya.fold_2.performance.tsv b/ENCSR513EVP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e6ef94e4d7191e61b7867edfdad19147fffa02cd..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -298.9803771972656 0.30602994561195374 0.6290175318717957 0.2082533985376358 0.8327749967575073 0.7995730638504028 0.35754773020744324 \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_3.evaluate.json b/ENCSR513EVP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 73ac1ceb3e446149aa8e01547899098a7f7f9a1c..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF927NMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_3.fit.json b/ENCSR513EVP/cherimoya.fold_3.fit.json deleted file mode 100644 index 9fa059a280dd46999244cc7fd55287754fd492c6..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF927NMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_3.log b/ENCSR513EVP/cherimoya.fold_3.log deleted file mode 100644 index 66910a8be6f7cad181964969178c9872b98cdbe6..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1073 16.331378936767578 3.3626396656036377 282.8111572265625 0.6969424486160278 486.20367431640625 0.3885563910007477 0.5696358 19.7376708984375 True -1 2146 11.83740234375 0.23525595664978027 271.186767578125 0.6313296556472778 386.15008544921875 0.48745429515838623 0.6462315 10.191191673278809 True -2 3219 11.859325647354126 0.2301638126373291 279.12908935546875 0.38522452116012573 347.9078674316406 0.5509910583496094 0.6731947 4.64345121383667 True -3 4292 11.83090877532959 0.2246387004852295 212.55494689941406 0.40217751264572144 321.5069580078125 0.5970486998558044 0.6979485 1.6946600675582886 True -4 5365 11.828147411346436 2.1618175506591797 228.2423095703125 0.45822420716285706 312.0990295410156 0.6118583679199219 0.73402923 0.7893067598342896 True -5 6438 11.80646276473999 2.0018680095672607 243.25442504882812 0.3887821435928345 309.2787780761719 0.6160482168197632 0.74980325 0.4862455129623413 True -6 7511 11.790225267410278 0.2233126163482666 242.041259765625 0.41902804374694824 307.8129577636719 0.6190758943557739 0.7571231 0.43521827459335327 True -7 8584 11.794753789901733 8.46463131904602 263.4730224609375 0.4921606779098511 306.6937561035156 0.6213101744651794 0.766018 0.415927529335022 True -8 9657 14.613775968551636 16.87187886238098 249.5973358154297 0.36489859223365784 305.58953857421875 0.6235610842704773 0.7705038 0.4101705253124237 True -9 10730 12.760730266571045 0.23464393615722656 248.74679565429688 0.4401836395263672 304.8283996582031 0.6259995698928833 0.77646965 0.40575143694877625 True -10 11803 11.788612365722656 0.2245314121246338 233.47637939453125 0.4659079313278198 303.9222412109375 0.6279916167259216 0.7811503 0.400518000125885 True -11 12876 11.853447437286377 0.2217710018157959 248.81109619140625 0.27245867252349854 303.2265625 0.6293249726295471 0.7841681 0.3959113359451294 True -12 13949 11.867256879806519 0.22308611869812012 242.3613739013672 0.33085423707962036 302.61431884765625 0.6304971575737 0.7884049 0.3916113078594208 True -13 15022 11.829102277755737 5.694703102111816 217.8368377685547 0.39114972949028015 302.0862121582031 0.6315326690673828 0.7920004 0.38927972316741943 True -14 16095 11.826553106307983 0.22286653518676758 227.91873168945312 0.28850287199020386 301.6670227050781 0.6323391795158386 0.7999259 0.3822363615036011 True -15 17168 11.787521600723267 0.2599484920501709 223.0106201171875 0.30773282051086426 301.66925048828125 0.6322113871574402 0.80111426 0.38867703080177307 True -16 18241 11.789950370788574 7.8596813678741455 216.641845703125 0.3084544837474823 301.75323486328125 0.6314843893051147 0.80337507 0.3982667326927185 True -17 19314 12.04121208190918 0.22312688827514648 221.7330322265625 0.18142415583133698 302.0526123046875 0.6305223107337952 0.8040067 0.40728428959846497 True -18 20387 11.77497386932373 0.22016143798828125 193.2190399169922 0.20748548209667206 302.3236999511719 0.6294954419136047 0.80436814 0.4195196330547333 True -19 21460 11.79660677909851 9.318161249160767 248.9976806640625 0.21402058005332947 302.4938659667969 0.6286999583244324 0.8025554 0.42608481645584106 False diff --git a/ENCSR513EVP/cherimoya.fold_3.performance.tsv b/ENCSR513EVP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 04051d44a42484eb5080afb664db5d326a51e927..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.3236999511719 0.3039781451225281 0.6294954419136047 0.20832432806491852 0.8043681383132935 0.7766380310058594 0.4195196330547333 \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_4.evaluate.json b/ENCSR513EVP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b29531256ed012137338ce387789978194effc9c..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF927NMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_4.fit.json b/ENCSR513EVP/cherimoya.fold_4.fit.json deleted file mode 100644 index 3f54e676b419134a982cd1afbc303b2d3d1db711..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF927NMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR513EVP/cherimoya.fold_4.log b/ENCSR513EVP/cherimoya.fold_4.log deleted file mode 100644 index fe3abebb04a583812ff6d147b72b041f97bdd7cf..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1061 16.02400827407837 3.159066915512085 248.75563049316406 0.6575866341590881 453.4059143066406 0.37675872445106506 0.60884833 18.722673416137695 True -1 2122 11.680552005767822 0.2114267349243164 274.0598449707031 0.6524295806884766 361.1381530761719 0.46901679039001465 0.7103615 7.492491245269775 True -2 3183 11.791365146636963 11.992663383483887 211.9266357421875 0.47848987579345703 322.8105163574219 0.5328172445297241 0.7658469 3.1314306259155273 True -3 4244 11.988751411437988 11.162596225738525 232.13995361328125 0.5471733212471008 298.6280212402344 0.5728083252906799 0.78602755 1.4111305475234985 True -4 5305 11.969360828399658 7.091388463973999 252.2984161376953 0.5529902577400208 290.8187561035156 0.5850018262863159 0.7942239 0.7470578551292419 True -5 6366 11.679871559143066 0.2062668800354004 240.41943359375 0.4589424133300781 287.8294372558594 0.588981568813324 0.7978268 0.42231684923171997 True -6 7427 11.700398206710815 0.2135164737701416 236.3724365234375 0.32561925053596497 286.2217712402344 0.5922320485115051 0.7989585 0.38365787267684937 True -7 8488 11.645291090011597 0.20516014099121094 234.97537231445312 0.3655593991279602 285.2784118652344 0.5939416289329529 0.8023536 0.3764449954032898 True -8 9549 11.647308826446533 0.2039787769317627 209.61492919921875 0.3896353542804718 284.4477233886719 0.5964473485946655 0.80547285 0.37214910984039307 True -9 10610 11.70905613899231 0.4647819995880127 246.16807556152344 0.45548415184020996 283.48724365234375 0.5983927845954895 0.80727965 0.37045979499816895 True -10 11671 11.636592626571655 0.7085592746734619 265.27093505859375 0.45146340131759644 282.6500549316406 0.6003164649009705 0.8184905 0.3590807020664215 True -11 12732 11.624709606170654 0.20711088180541992 276.69873046875 0.36614784598350525 281.91802978515625 0.602014422416687 0.82390505 0.34789177775382996 True -12 13793 11.969331979751587 13.441901922225952 206.77769470214844 0.3526250422000885 281.37506103515625 0.6032837629318237 0.82829404 0.33804547786712646 True -13 14854 12.070249319076538 0.20665192604064941 226.3465576171875 0.2853793799877167 281.05767822265625 0.6045817732810974 0.8304217 0.3341412842273712 True -14 15915 11.682831525802612 0.2077653408050537 253.04425048828125 0.25601285696029663 280.9115905761719 0.6051222681999207 0.8358083 0.3278639316558838 True -15 16976 11.651547908782959 0.21123361587524414 205.11380004882812 0.20972877740859985 280.9951171875 0.6050025224685669 0.8380644 0.3266657888889313 True -16 18037 11.661580085754395 0.20840072631835938 185.41024780273438 0.21794044971466064 281.1830139160156 0.6046631932258606 0.8373436 0.328050434589386 False -17 19098 11.65681767463684 0.20778656005859375 182.64297485351562 0.14782844483852386 281.61334228515625 0.6038421392440796 0.83658344 0.33651766180992126 False -18 20159 11.669537782669067 1.2440574169158936 257.05523681640625 0.1366167962551117 281.9780578613281 0.6030840277671814 0.8338524 0.34494221210479736 False -19 21220 11.521633863449097 0.20230698585510254 216.18377685546875 0.15734250843524933 282.1781921386719 0.6023989915847778 0.8339277 0.3507848083972931 False diff --git a/ENCSR513EVP/cherimoya.fold_4.performance.tsv b/ENCSR513EVP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6cc9e60e5fbc7187669ad7a8eacc092fa63cd655..0000000000000000000000000000000000000000 --- a/ENCSR513EVP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -280.9951171875 0.3203979432582855 0.6050025224685669 0.19364404678344727 0.8380643725395203 0.7985682487487793 0.3266657888889313 \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_0.evaluate.json b/ENCSR515CDW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f2017fe1637e9a1511404b60c6214ec965c8d348..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118KSS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_0.fit.json b/ENCSR515CDW/cherimoya.fold_0.fit.json deleted file mode 100644 index 92d570abcac7ca15f469e4669b1daacaebced580..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF118KSS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_0.log b/ENCSR515CDW/cherimoya.fold_0.log deleted file mode 100644 index 7935945d63f7ea945a53b583f94a97593f5fa915..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 594 10.637414932250977 2.930396318435669 112.0223159790039 0.14955362677574158 148.00094604492188 0.2209409773349762 0.73019195 11.198087692260742 True -1 1188 6.451858758926392 0.1325216293334961 100.27848052978516 0.20398075878620148 132.78189086914062 0.27316153049468994 0.77412987 6.799453258514404 True -2 1782 6.473031759262085 0.12407279014587402 95.9189224243164 0.18684527277946472 124.73101806640625 0.299272745847702 0.79225343 2.6304967403411865 True -3 2376 6.4656453132629395 0.12549185752868652 95.39005279541016 0.12685343623161316 121.21253967285156 0.31356722116470337 0.79573447 0.8639851808547974 True -4 2970 6.450461149215698 0.1264505386352539 94.68035125732422 0.1318599283695221 118.82299041748047 0.32479920983314514 0.8020437 0.43516379594802856 True -5 3564 6.4426186084747314 0.12491536140441895 94.64208984375 0.18286176025867462 117.15816497802734 0.3322054445743561 0.8065858 0.3111926019191742 True -6 4158 6.441380977630615 0.12459278106689453 95.82976531982422 0.16850075125694275 116.12183380126953 0.33721861243247986 0.81448025 0.21874147653579712 True -7 4752 6.441308259963989 0.12460684776306152 91.5556640625 0.20083312690258026 115.55060577392578 0.3402649164199829 0.82138693 0.174764484167099 True -8 5346 6.441108465194702 0.12692642211914062 100.27754974365234 0.12560376524925232 115.21651458740234 0.3422614336013794 0.82744735 0.15125243365764618 True -9 5940 6.446857929229736 3.7396695613861084 105.97166442871094 0.1218886524438858 115.05806732177734 0.34329473972320557 0.8314364 0.13782627880573273 True -10 6534 6.5211522579193115 2.5069258213043213 102.53216552734375 0.1029573380947113 114.96376037597656 0.34388619661331177 0.83363867 0.12726140022277832 True -11 7128 6.480048179626465 0.1251370906829834 88.43106079101562 0.11868777126073837 114.91483306884766 0.3440153896808624 0.8369588 0.12117868661880493 True -12 7722 6.442028760910034 0.3816993236541748 99.81192016601562 0.09722542762756348 114.88238525390625 0.3438977301120758 0.8389315 0.11699777841567993 True -13 8316 6.4463951587677 1.1597068309783936 102.92442321777344 0.06958138942718506 114.92073822021484 0.34327104687690735 0.84134454 0.11547258496284485 True -14 8910 6.486165523529053 0.1282365322113037 103.34703063964844 0.12322115153074265 115.0079574584961 0.3422457277774811 0.8416556 0.11417105793952942 True -15 9504 6.495482921600342 0.12506604194641113 97.4491958618164 0.10635680705308914 115.19212341308594 0.3404007852077484 0.84570205 0.1123846173286438 True -16 10098 6.478415489196777 0.1283435821533203 95.86609649658203 0.07947279512882233 115.45657348632812 0.33791860938072205 0.84528846 0.1100846379995346 False -17 10692 6.479409217834473 0.12656784057617188 85.1023178100586 0.11718078702688217 115.76139068603516 0.3350847661495209 0.8465538 0.10792037844657898 True -18 11286 6.4512035846710205 0.12633538246154785 97.23883056640625 0.08163616061210632 116.14409637451172 0.3319801688194275 0.8484212 0.10696414858102798 True -19 11880 6.44659686088562 0.12537074089050293 97.54701232910156 0.10148020088672638 116.47215270996094 0.32933780550956726 0.8476185 0.10671203583478928 False diff --git a/ENCSR515CDW/cherimoya.fold_0.performance.tsv b/ENCSR515CDW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c30a56504259133d9b58ca427b0a530b3169d8a7..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -116.14409637451172 0.5002366304397583 0.3319801390171051 0.0640321671962738 0.8484212160110474 0.8163056373596191 0.10696414858102798 \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_1.evaluate.json b/ENCSR515CDW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6272669b8c076c5fa1a3b9d81788276d741bd986..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118KSS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_1.fit.json b/ENCSR515CDW/cherimoya.fold_1.fit.json deleted file mode 100644 index e580fa0ca792ea9ddd47c71f02a8f159565ae52f..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF118KSS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_1.log b/ENCSR515CDW/cherimoya.fold_1.log deleted file mode 100644 index 2c6eac4f6ec44f2b86586929970585a95f98afd2..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 589 10.729563236236572 3.2984261512756348 107.74229431152344 0.2569739818572998 162.73609924316406 0.23015595972537994 -0.29630822 11.99518871307373 True -1 1178 6.416067600250244 0.16409707069396973 104.40129089355469 0.132558673620224 146.01271057128906 0.28342652320861816 0.7147654 7.748120307922363 True -2 1767 6.417374610900879 0.1543726921081543 103.76333618164062 0.1949501782655716 136.7016143798828 0.3110707700252533 0.7520512 2.996103286743164 True -3 2356 6.405789375305176 0.1519935131072998 103.17940521240234 0.17501233518123627 132.31478881835938 0.3293835520744324 0.76807797 0.9204497337341309 True -4 2945 6.427351474761963 5.753040552139282 112.34244537353516 0.27993229031562805 129.58755493164062 0.3416857123374939 0.7696771 0.37863028049468994 True -5 3534 6.577863693237305 7.500901937484741 104.72979736328125 0.19510141015052795 127.81004333496094 0.3495445251464844 0.7685114 0.2776528596878052 False -6 4123 6.508951902389526 0.15282320976257324 104.5926284790039 0.14208808541297913 126.82878875732422 0.35353797674179077 0.77101123 0.2573886215686798 True -7 4712 6.383058786392212 0.1517496109008789 111.53553009033203 0.15105441212654114 126.16667175292969 0.3570308983325958 0.785108 0.20218227803707123 True -8 5301 6.375512599945068 0.14972138404846191 89.36913299560547 0.2435895949602127 125.73436737060547 0.35946154594421387 0.79704237 0.16942444443702698 True -9 5890 6.395150899887085 0.15099644660949707 110.55401611328125 0.10272125899791718 125.55421447753906 0.36050117015838623 0.80805194 0.15427856147289276 True -10 6479 6.406810522079468 0.4964790344238281 87.29753112792969 0.17765410244464874 125.45128631591797 0.3611057996749878 0.8105512 0.14156420528888702 True -11 7068 6.416589260101318 0.1537017822265625 105.257568359375 0.18009576201438904 125.3298110961914 0.36201682686805725 0.8167861 0.13746313750743866 True -12 7657 6.425423860549927 0.1508779525756836 90.77132415771484 0.12350291758775711 125.27963256835938 0.36237797141075134 0.8214197 0.13398344814777374 True -13 8246 6.3975653648376465 0.15158796310424805 92.76252746582031 0.13851004838943481 125.30404663085938 0.36222878098487854 0.8261136 0.13162237405776978 True -14 8835 6.3979573249816895 0.14905214309692383 98.88874816894531 0.16277776658535004 125.39197540283203 0.3612295687198639 0.8311796 0.12850560247898102 True -15 9424 6.404074192047119 0.1489555835723877 95.0073471069336 0.11638841778039932 125.56982421875 0.3594890534877777 0.8348455 0.12590403854846954 True -16 10013 6.489801406860352 7.210178852081299 84.44059753417969 0.18440395593643188 125.8934326171875 0.3566697835922241 0.84011394 0.12224472314119339 True -17 10602 6.65320611000061 10.195578336715698 93.24113464355469 0.14501798152923584 126.3400650024414 0.35273393988609314 0.8410863 0.11767800152301788 True -18 11191 6.581136703491211 0.15291833877563477 99.19828796386719 0.14129230380058289 126.83221435546875 0.34868842363357544 0.84376454 0.11474528908729553 True -19 11780 6.410546779632568 0.14969515800476074 91.41056060791016 0.13617779314517975 127.30132293701172 0.34529900550842285 0.84496814 0.11299839615821838 True diff --git a/ENCSR515CDW/cherimoya.fold_1.performance.tsv b/ENCSR515CDW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index fb41121772752ce6a5b65304660aff96c03566a4..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -127.30132293701172 0.48763903975486755 0.34529897570610046 0.07457073032855988 0.8449681401252747 0.8450897932052612 0.11299839615821838 \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_2.evaluate.json b/ENCSR515CDW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e12a3b3f01a4bea208fd4a57d849b3a4d807407d..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118KSS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_2.fit.json b/ENCSR515CDW/cherimoya.fold_2.fit.json deleted file mode 100644 index d2742140b5a78a269640d4c649087ad7a0ceb6df..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF118KSS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_2.log b/ENCSR515CDW/cherimoya.fold_2.log deleted file mode 100644 index 93c1e925e0c8e0958b1f31410679349c20b17d68..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 624 11.365245342254639 8.726739645004272 96.33377075195312 0.3427739143371582 153.5321807861328 0.22992676496505737 0.71375376 11.391252517700195 True -1 1248 6.983360290527344 5.310684442520142 100.44274139404297 0.21575161814689636 137.25306701660156 0.28019729256629944 0.7344711 6.8416266441345215 True -2 1872 6.832970142364502 0.13003230094909668 103.22970581054688 0.18438130617141724 129.43405151367188 0.30638572573661804 0.7639527 2.946427345275879 True -3 2496 6.7706568241119385 0.12371182441711426 104.99848175048828 0.1941230148077011 126.0837631225586 0.32014000415802 0.7692296 0.9354944229125977 True -4 3120 6.763987302780151 0.12353873252868652 101.2932357788086 0.1672479659318924 123.34871673583984 0.33191171288490295 0.78025836 0.3770449161529541 True -5 3744 6.7699902057647705 1.0827617645263672 100.9177474975586 0.09838402271270752 121.46144104003906 0.340745210647583 0.79114324 0.23430867493152618 True -6 4368 6.79189395904541 0.12318015098571777 106.93592834472656 0.20202434062957764 120.53683471679688 0.3445214331150055 0.79570544 0.1867944896221161 True -7 4992 6.774795293807983 0.12368297576904297 106.2887191772461 0.12855736911296844 119.9769287109375 0.34741905331611633 0.8026838 0.14250394701957703 True -8 5616 6.779224395751953 0.1240234375 103.65776062011719 0.20237073302268982 119.64806365966797 0.3498780131340027 0.8094378 0.1302027404308319 True -9 6240 6.780788421630859 0.12446403503417969 99.53595733642578 0.13197490572929382 119.4505386352539 0.35137203335762024 0.8148057 0.12748631834983826 True -10 6864 6.782918214797974 0.12490057945251465 114.68121337890625 0.17619964480400085 119.3151626586914 0.3524050712585449 0.8191221 0.12683221697807312 True -11 7488 6.771550416946411 0.12551355361938477 89.55181884765625 0.1579747498035431 119.24495697021484 0.3527592718601227 0.82200116 0.12701134383678436 True -12 8112 6.767414331436157 0.12546682357788086 102.17013549804688 0.15177468955516815 119.18109130859375 0.35296282172203064 0.8244041 0.12553048133850098 True -13 8736 6.7693798542022705 0.12624263763427734 97.08293914794922 0.20852848887443542 119.20730590820312 0.35270681977272034 0.8297758 0.12389242649078369 True -14 9360 6.742339849472046 0.35531067848205566 98.11058807373047 0.12008180469274521 119.24579620361328 0.3520983159542084 0.8317648 0.12073341757059097 True -15 9984 6.745298147201538 0.1252737045288086 100.70948791503906 0.08697764575481415 119.392333984375 0.3504352271556854 0.8322412 0.11816002428531647 True -16 10608 6.679761648178101 0.1260380744934082 94.7304916381836 0.11206567287445068 119.68404388427734 0.3477551341056824 0.83530384 0.11588272452354431 True -17 11232 6.650617837905884 0.12655425071716309 90.93589782714844 0.11595818400382996 120.07975769042969 0.34440910816192627 0.8348479 0.1144377812743187 False -18 11856 6.6448655128479 0.5585470199584961 97.18203735351562 0.11987385153770447 120.50867462158203 0.34072405099868774 0.8325703 0.11486842483282089 False -19 12480 6.6749677658081055 0.12325787544250488 98.32378387451172 0.08212663978338242 120.8917465209961 0.33779942989349365 0.83272403 0.11566585302352905 False diff --git a/ENCSR515CDW/cherimoya.fold_2.performance.tsv b/ENCSR515CDW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2a21426e02dc8d44d93c90e96847c94f712d8080..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -119.68404388427734 0.4920213222503662 0.34775519371032715 0.07238086313009262 0.8353038430213928 0.8224009275436401 0.11588272452354431 \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_3.evaluate.json b/ENCSR515CDW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a58835112ba7da215d152312ab29a7ba5998312f..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118KSS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_3.fit.json b/ENCSR515CDW/cherimoya.fold_3.fit.json deleted file mode 100644 index 1e430051b650d84f557543c8c7d5b96e90b2720b..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF118KSS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_3.log b/ENCSR515CDW/cherimoya.fold_3.log deleted file mode 100644 index b39bc9f9a746f27e2055b226f5ddb0831e4e8fb6..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 609 11.174257516860962 3.0877044200897217 93.19154357910156 0.22306708991527557 149.11212158203125 0.22515764832496643 0.657256 11.207500457763672 True -1 1218 6.624547004699707 0.5990674495697021 103.00518798828125 0.18457075953483582 133.37155151367188 0.2767201066017151 0.7434023 6.786224842071533 True -2 1827 6.803768157958984 6.602089166641235 108.33750915527344 0.14271341264247894 125.28426361083984 0.30404311418533325 0.76695627 2.669238567352295 True -3 2436 6.705902576446533 0.12761950492858887 105.48130798339844 0.1884235441684723 121.71973419189453 0.3193279802799225 0.7769081 0.7225590944290161 True -4 3045 6.612814664840698 0.13047337532043457 106.00833129882812 0.1733613908290863 119.57025146484375 0.3281767964363098 0.7794448 0.26319101452827454 True -5 3654 6.608064889907837 0.126878023147583 98.54434204101562 0.11287154257297516 117.95266723632812 0.3352636694908142 0.7884397 0.19190585613250732 True -6 4263 6.617732048034668 0.12501978874206543 98.46302795410156 0.16758865118026733 117.08749389648438 0.3390648663043976 0.7927959 0.20318220555782318 True -7 4872 6.619016408920288 0.4523766040802002 100.43963623046875 0.1891700029373169 116.54470825195312 0.3420766592025757 0.80075336 0.17323052883148193 True -8 5481 6.605597019195557 0.1254575252532959 104.44438171386719 0.09818963706493378 116.13661193847656 0.34454378485679626 0.80868316 0.15187299251556396 True -9 6090 6.613765716552734 0.35488152503967285 95.00038146972656 0.11222857236862183 115.90357971191406 0.34601685404777527 0.8163332 0.1392451673746109 True -10 6699 6.6018030643463135 0.12686991691589355 92.03466796875 0.22212359309196472 115.76837921142578 0.3470202386379242 0.8222288 0.12873795628547668 True -11 7308 6.606691837310791 0.12494516372680664 104.9940414428711 0.13279099762439728 115.65943145751953 0.34768152236938477 0.8262833 0.12381505221128464 True -12 7917 6.608800649642944 0.12677836418151855 93.39765930175781 0.14381572604179382 115.63922882080078 0.3478063941001892 0.82968605 0.12134052067995071 True -13 8526 6.743364572525024 8.199392080307007 106.19895935058594 0.1529877483844757 115.62848663330078 0.3476451337337494 0.83355284 0.11956384032964706 True -14 9135 6.9364013671875 8.144159078598022 87.28666687011719 0.16276061534881592 115.70030975341797 0.3469395041465759 0.83553314 0.1189584881067276 True -15 9744 6.765279293060303 0.14487767219543457 102.08221435546875 0.15769582986831665 115.86604309082031 0.3455606698989868 0.8355492 0.11730888485908508 True -16 10353 6.616673946380615 0.12770438194274902 95.26443481445312 0.1608259081840515 116.097900390625 0.3432598412036896 0.83786327 0.11595248430967331 True -17 10962 6.6160337924957275 0.126129150390625 107.79835510253906 0.07828183472156525 116.44025421142578 0.3402518928050995 0.8370687 0.11466086655855179 False -18 11571 6.6310131549835205 0.4082832336425781 103.63697814941406 0.1586296260356903 116.82418060302734 0.33686748147010803 0.8366557 0.11420776695013046 False -19 12180 6.6205010414123535 0.2851097583770752 87.40860748291016 0.12930932641029358 117.17045593261719 0.3339478671550751 0.8370333 0.11500576138496399 False diff --git a/ENCSR515CDW/cherimoya.fold_3.performance.tsv b/ENCSR515CDW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 458890798b8b7efe48099bc55ed6c7b526b7bbbe..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -116.097900390625 0.49709442257881165 0.3432598412036896 0.07163114100694656 0.8378632664680481 0.8204188346862793 0.11595248430967331 \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_4.evaluate.json b/ENCSR515CDW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b894bec10b703906ec68ddd7a52efd08f8393783..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118KSS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_4.fit.json b/ENCSR515CDW/cherimoya.fold_4.fit.json deleted file mode 100644 index 280ee6787fd199f0b13e9a9325da8ac97b385161..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF118KSS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515CDW/cherimoya.fold_4.log b/ENCSR515CDW/cherimoya.fold_4.log deleted file mode 100644 index 2edb59dc4f5cbfc84e984bda0069dd6ef429e201..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 601 11.06887936592102 2.4383490085601807 112.73719787597656 0.30201485753059387 145.3826446533203 0.22238337993621826 0.74843425 10.929327964782715 True -1 1202 6.531779527664185 0.11519241333007812 98.36058044433594 0.28240665793418884 130.47882080078125 0.27141180634498596 0.7659367 6.61228609085083 True -2 1803 6.522332429885864 0.1530449390411377 101.57881164550781 0.24721170961856842 122.85589599609375 0.2980533242225647 0.78625757 2.6811561584472656 True -3 2404 6.579439878463745 0.7548112869262695 104.55490112304688 0.15626242756843567 119.42080688476562 0.3118545711040497 0.79567623 0.8043197989463806 True -4 3005 6.531408786773682 0.11250543594360352 106.12710571289062 0.24984654784202576 116.69452667236328 0.32368016242980957 0.7965273 0.2518227994441986 True -5 3606 6.523644208908081 0.11213302612304688 95.86970520019531 0.15901044011116028 115.29181671142578 0.3299720883369446 0.8007375 0.19993960857391357 True -6 4207 6.522773504257202 0.11243247985839844 97.04685974121094 0.17258700728416443 114.4746322631836 0.3344050645828247 0.8123287 0.1685122549533844 True -7 4808 6.5219433307647705 0.1130375862121582 108.39219665527344 0.17446370422840118 114.02999114990234 0.33721423149108887 0.8212514 0.1461820751428604 True -8 5409 6.625425338745117 5.7266151905059814 100.79174041748047 0.1451791226863861 113.77413177490234 0.3388769030570984 0.8284356 0.13235419988632202 True -9 6010 6.6773576736450195 7.765261173248291 104.89788055419922 0.17785708606243134 113.62487030029297 0.33988887071609497 0.83406323 0.11888832598924637 True -10 6611 6.645451307296753 0.11320161819458008 97.80111694335938 0.12619751691818237 113.48320770263672 0.34080255031585693 0.8393883 0.10836482793092728 True -11 7212 6.506158113479614 0.11142754554748535 89.28175354003906 0.11633775383234024 113.4332504272461 0.34120845794677734 0.8433885 0.10442457348108292 True -12 7813 6.513471364974976 0.11141157150268555 91.78715515136719 0.16649700701236725 113.44706726074219 0.341238796710968 0.8477744 0.10200981050729752 True -13 8414 6.52072811126709 0.11283397674560547 88.73209381103516 0.20825809240341187 113.45382690429688 0.34096112847328186 0.850098 0.10278551280498505 True -14 9015 6.543689250946045 0.13716554641723633 93.65789794921875 0.15789714455604553 113.5211410522461 0.3401627540588379 0.8509319 0.10153554379940033 True -15 9616 6.544065713882446 0.11325645446777344 83.46256256103516 0.11278611421585083 113.71553039550781 0.33844825625419617 0.8521793 0.10128475725650787 True -16 10217 6.536505937576294 0.1106574535369873 94.90957641601562 0.12874901294708252 114.00267028808594 0.3360018730163574 0.8520649 0.0996437594294548 False -17 10818 6.537612676620483 0.11139798164367676 91.54071044921875 0.1458374559879303 114.35511779785156 0.33310332894325256 0.8524197 0.09855079650878906 True -18 11419 6.540695905685425 0.11073994636535645 95.98658752441406 0.11800406873226166 114.76604461669922 0.32977667450904846 0.851433 0.09740914404392242 False -19 12020 6.524179220199585 0.11010909080505371 97.33634185791016 0.1351580023765564 115.1131362915039 0.3270653188228607 0.85029113 0.09750887006521225 False diff --git a/ENCSR515CDW/cherimoya.fold_4.performance.tsv b/ENCSR515CDW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a5fa32b2446c30031dbfa43dfa51fd8cf4f85631..0000000000000000000000000000000000000000 --- a/ENCSR515CDW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -114.35511779785156 0.5013558864593506 0.3331032991409302 0.06401444226503372 0.8524196743965149 0.8170698285102844 0.09855079650878906 \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_0.evaluate.json b/ENCSR515DVK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5adad924d245481fa28ee3a79499b52178294256..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF404TWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_0.fit.json b/ENCSR515DVK/cherimoya.fold_0.fit.json deleted file mode 100644 index 7643cd08c63ef59a3adcccbff3e24900a0ce795c..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF404TWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_0.log b/ENCSR515DVK/cherimoya.fold_0.log deleted file mode 100644 index 61d4f5c1e8a76350829312d778a3452697b9aead..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2147 28.717278718948364 3.6716268062591553 166.80596923828125 0.5480329990386963 198.7346954345703 0.09558675438165665 0.6497874 4.154404640197754 True -1 4294 23.8688542842865 0.7870652675628662 169.37423706054688 0.2636961340904236 187.7620849609375 0.13269859552383423 0.75085604 1.492153286933899 True -2 6441 23.87129306793213 0.48516130447387695 133.12197875976562 0.2907799184322357 180.9055633544922 0.14618580043315887 0.77049506 0.7083555459976196 True -3 8588 23.85741138458252 0.4471402168273926 152.6924591064453 0.2989863455295563 179.68887329101562 0.14897581934928894 0.77777046 0.5147605538368225 True -4 10735 23.820101261138916 1.5409893989562988 152.4793243408203 0.41824811697006226 179.19554138183594 0.1500760316848755 0.78435576 0.460582971572876 True -5 12882 23.874892234802246 0.6395936012268066 142.77713012695312 0.6470137238502502 178.6390380859375 0.15220728516578674 0.7878213 0.4552988111972809 True -6 15029 23.84624481201172 0.4573845863342285 134.12677001953125 0.5007131099700928 177.94371032714844 0.15415434539318085 0.79909915 0.39927783608436584 True -7 17176 23.89106297492981 0.44459009170532227 142.86660766601562 0.28663909435272217 177.53077697753906 0.1549580991268158 0.8073769 0.3717126250267029 True -8 19323 23.849200010299683 0.4535343647003174 139.23489379882812 0.29756850004196167 176.79617309570312 0.1573791801929474 0.817108 0.33662742376327515 True -9 21470 23.82959485054016 0.4379613399505615 159.8663330078125 0.47458821535110474 176.6702423095703 0.15766841173171997 0.8233417 0.32328909635543823 True -10 23617 23.927698612213135 0.45146918296813965 124.63768768310547 0.47427916526794434 176.26028442382812 0.15866078436374664 0.83109707 0.3010418713092804 True -11 25764 23.825241088867188 0.4516115188598633 138.48451232910156 0.49510976672172546 175.81809997558594 0.16005733609199524 0.8368628 0.28274425864219666 True -12 27911 23.836582899093628 0.4379537105560303 160.6357421875 0.2380724847316742 175.45811462402344 0.16123135387897491 0.84316844 0.27575626969337463 True -13 30058 23.837985277175903 0.4514470100402832 151.67767333984375 0.38082200288772583 175.1844024658203 0.16192758083343506 0.84808594 0.2602185904979706 True -14 32205 23.826402187347412 0.44579124450683594 154.9110565185547 0.2421208769083023 174.91006469726562 0.16272832453250885 0.8523037 0.2536002993583679 True -15 34352 23.871508836746216 0.44193100929260254 160.98342895507812 0.35694289207458496 174.79612731933594 0.16293959319591522 0.85302275 0.24572409689426422 True -16 36499 23.863207578659058 1.467550277709961 154.67442321777344 0.18546245992183685 174.87619018554688 0.16249023377895355 0.8572502 0.23859715461730957 True -17 38646 23.878010272979736 0.4630916118621826 134.83499145507812 0.198468878865242 175.0836639404297 0.16164304316043854 0.8589098 0.2372388392686844 True -18 40793 23.880232334136963 0.4331810474395752 150.10899353027344 0.21488851308822632 174.87960815429688 0.16236025094985962 0.856161 0.2394450604915619 False -19 42940 23.899049282073975 0.44372057914733887 129.52569580078125 0.20909345149993896 174.8292999267578 0.16285760700702667 0.8564461 0.24159803986549377 False diff --git a/ENCSR515DVK/cherimoya.fold_0.performance.tsv b/ENCSR515DVK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ad202f0502430d91302dff80dabe7b6309f3d64d..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -175.0836639404297 0.57962965965271 0.16164304316043854 0.044599518179893494 0.8589097857475281 0.7581555247306824 0.2372388392686844 \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_1.evaluate.json b/ENCSR515DVK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6037d1742d602cc9a3b03ad3c3a69bc5a6c7f9ac..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF404TWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_1.fit.json b/ENCSR515DVK/cherimoya.fold_1.fit.json deleted file mode 100644 index 4de8c66cf5b758e644127d9aecf18d6e56682275..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF404TWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_1.log b/ENCSR515DVK/cherimoya.fold_1.log deleted file mode 100644 index df6d3968ab7ef012f7cdfd24571cc5e085c6b31a..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2121 29.13173198699951 4.920192718505859 165.09371948242188 0.34048283100128174 241.36456298828125 0.11051212251186371 0.6224538 5.01155424118042 True -1 4242 23.58638095855713 0.6121954917907715 176.58206176757812 0.587233304977417 226.7948455810547 0.15641482174396515 0.74291545 1.9436707496643066 True -2 6363 23.648725032806396 0.6227734088897705 161.7130126953125 0.42485690116882324 219.74288940429688 0.16887503862380981 0.7568411 1.2471598386764526 True -3 8484 23.636772871017456 17.968520164489746 143.23721313476562 0.48603689670562744 217.45042419433594 0.17191800475120544 0.76945704 0.7466586232185364 True -4 10605 23.340999841690063 0.6220123767852783 141.07972717285156 0.2761090397834778 214.85633850097656 0.1782967448234558 0.7819551 0.6281671524047852 True -5 12726 23.186258792877197 0.5901346206665039 129.25209045410156 0.308455228805542 213.54373168945312 0.18143148720264435 0.7971002 0.5580821633338928 True -6 14847 23.186083555221558 0.602851152420044 119.20489501953125 0.3194277286529541 212.54296875 0.18371330201625824 0.8067198 0.5278295874595642 True -7 16968 23.17630124092102 0.5837132930755615 179.2509307861328 0.2994179129600525 212.0087127685547 0.18546268343925476 0.81263536 0.4950224459171295 True -8 19089 23.18180561065674 0.5871570110321045 128.71017456054688 0.4389555752277374 211.0963134765625 0.18810610473155975 0.8241743 0.45684802532196045 True -9 21210 23.158113956451416 0.592505931854248 140.52560424804688 0.2891313433647156 210.80621337890625 0.1886124461889267 0.8321615 0.4243320822715759 True -10 23331 23.265848636627197 0.590825080871582 169.0783233642578 0.47792428731918335 209.96556091308594 0.19153884053230286 0.8410128 0.3919178545475006 True -11 25452 23.166926383972168 0.8641676902770996 127.67459106445312 0.3811051845550537 209.7174072265625 0.19201229512691498 0.84462184 0.3873624801635742 True -12 27573 23.16855216026306 1.5875349044799805 129.11788940429688 0.27610570192337036 209.27072143554688 0.19331753253936768 0.8537558 0.3555249273777008 True -13 29694 23.179077863693237 0.5747556686401367 140.3594970703125 0.24764484167099 208.88775634765625 0.19420306384563446 0.8597391 0.331049382686615 True -14 31815 23.1603000164032 0.5922439098358154 141.33108520507812 0.22249211370944977 208.17356872558594 0.1959317922592163 0.86596066 0.311605840921402 True -15 33936 23.195899724960327 0.5752074718475342 196.42764282226562 0.3539741039276123 208.16275024414062 0.19608692824840546 0.8694734 0.30352282524108887 True -16 36057 23.081384897232056 0.5777263641357422 132.85159301757812 0.3366285562515259 208.0070037841797 0.19661565124988556 0.8724498 0.28782549500465393 True -17 38178 23.171313047409058 0.5796148777008057 169.61631774902344 0.251934289932251 208.07635498046875 0.19613038003444672 0.8722727 0.28341540694236755 False -18 40299 23.2698016166687 0.5818443298339844 142.69239807128906 0.17228983342647552 208.4270782470703 0.19458959996700287 0.8722153 0.28317683935165405 False -19 42420 23.24836492538452 0.5809779167175293 145.09432983398438 0.23740750551223755 208.3916778564453 0.1950034648180008 0.8707023 0.2859722673892975 False diff --git a/ENCSR515DVK/cherimoya.fold_1.performance.tsv b/ENCSR515DVK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6230d7c65996cce92a07191457fb3132d34001e1..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -208.0070037841797 0.5557740330696106 0.19661565124988556 0.048870351165533066 0.8724498152732849 0.8206611275672913 0.28782549500465393 \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_2.evaluate.json b/ENCSR515DVK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 595d45c2435d154b416eecd9d1e2248208ac0e3f..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF404TWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_2.fit.json b/ENCSR515DVK/cherimoya.fold_2.fit.json deleted file mode 100644 index c86c0ef24ebdce8656f244361b4dfe3651b1b71c..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF404TWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_2.log b/ENCSR515DVK/cherimoya.fold_2.log deleted file mode 100644 index fc06c54332c53a476f02f5b524a86efa16b4af0d..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2256 29.74513006210327 3.6978299617767334 186.64056396484375 0.6596652269363403 209.5569610595703 0.09995707124471664 0.6311759 3.5729727745056152 True -1 4512 25.068751096725464 0.6664981842041016 167.43997192382812 0.3812081813812256 197.46482849121094 0.1407465636730194 0.74293727 1.2965208292007446 True -2 6768 25.06466794013977 0.4442141056060791 176.19332885742188 0.68173748254776 191.08602905273438 0.15152984857559204 0.7567754 0.643401563167572 True -3 9024 25.031031131744385 0.4501152038574219 175.96653747558594 0.374178409576416 189.423828125 0.15313692390918732 0.7757319 0.543039858341217 True -4 11280 25.04171919822693 0.44312214851379395 151.61239624023438 0.46848607063293457 188.3333740234375 0.15610888600349426 0.78433657 0.5542872548103333 True -5 13536 25.005557775497437 0.4459378719329834 179.30892944335938 0.32917794585227966 186.66810607910156 0.16116510331630707 0.7914983 0.5169450640678406 True -6 15792 25.015711784362793 0.45357179641723633 179.11077880859375 0.4544144868850708 185.8863983154297 0.1626359075307846 0.80450463 0.45562005043029785 True -7 18048 25.00758934020996 0.4522221088409424 165.98190307617188 0.5461779832839966 185.16770935058594 0.165265753865242 0.8089564 0.43863445520401 True -8 20304 24.998234510421753 0.45273447036743164 152.5445098876953 0.2882826626300812 184.4746856689453 0.16748006641864777 0.81882256 0.391340970993042 True -9 22560 24.99951481819153 0.44902849197387695 167.5331573486328 0.2886762320995331 184.1422882080078 0.16820751130580902 0.8235264 0.37859275937080383 True -10 24816 25.05590319633484 0.45012760162353516 166.52340698242188 0.24930699169635773 183.73501586914062 0.16957643628120422 0.83038616 0.3504902720451355 True -11 27072 24.54521346092224 2.700735092163086 170.7660675048828 0.3037627935409546 183.30426025390625 0.17035187780857086 0.8374739 0.32493990659713745 True -12 29328 24.56044888496399 0.45596766471862793 147.42864990234375 0.3464926779270172 183.0345001220703 0.17080256342887878 0.8426181 0.30599188804626465 True -13 31584 24.56103014945984 0.4469449520111084 148.28941345214844 0.29522964358329773 182.7604217529297 0.17166292667388916 0.846815 0.29172495007514954 True -14 33840 24.527915954589844 0.4503908157348633 150.20680236816406 0.2647186815738678 182.3296356201172 0.17337991297245026 0.851002 0.27973613142967224 True -15 36096 24.594011306762695 0.4393773078918457 128.56719970703125 0.207896426320076 182.27593994140625 0.1731218844652176 0.85298336 0.2692294418811798 True -16 38352 24.559552669525146 0.44042468070983887 163.05184936523438 0.22923028469085693 182.14065551757812 0.17354287207126617 0.8552183 0.26306286454200745 True -17 40608 24.64540672302246 20.436131954193115 148.4368133544922 0.23966147005558014 182.07797241210938 0.17407089471817017 0.8546717 0.2591823935508728 False -18 42864 24.72911787033081 0.456829309463501 161.2970428466797 0.24674077332019806 182.31605529785156 0.1728229820728302 0.85345674 0.2609860897064209 False -19 45120 24.55710506439209 0.45501255989074707 168.78890991210938 0.2355196624994278 182.5094451904297 0.17210939526557922 0.85381424 0.2627957761287689 False diff --git a/ENCSR515DVK/cherimoya.fold_2.performance.tsv b/ENCSR515DVK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cb56e052348f5b5fb44c16b4ca8fcd706ee102f8..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -182.14065551757812 0.572480320930481 0.17354285717010498 0.041413553059101105 0.8552182912826538 0.7758199572563171 0.26306286454200745 \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_3.evaluate.json b/ENCSR515DVK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2b3e54f4b8b56586cba4ed76d2cedabc15055c6f..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF404TWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_3.fit.json b/ENCSR515DVK/cherimoya.fold_3.fit.json deleted file mode 100644 index 90657735c411d4e304a4bea2c5b5e76dff1bf115..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF404TWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_3.log b/ENCSR515DVK/cherimoya.fold_3.log deleted file mode 100644 index e7b786481670149db35dfd0325c627d916833e17..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2162 29.906538486480713 4.117503881454468 160.96585083007812 0.3799612820148468 209.57406616210938 0.10257828235626221 0.6119418 4.35736083984375 True -1 4324 24.055732011795044 0.4834897518157959 133.75262451171875 0.5110676884651184 198.40953063964844 0.14164398610591888 0.71724 1.6966558694839478 True -2 6486 24.235697507858276 23.938799142837524 132.60577392578125 0.305813193321228 192.9359893798828 0.15130284428596497 0.72950196 0.9894586801528931 True -3 8648 24.048705577850342 0.417926549911499 119.23387908935547 0.22551220655441284 191.51104736328125 0.15363669395446777 0.7379816 0.7408958673477173 True -4 10810 24.019468307495117 0.4292175769805908 143.65390014648438 0.2942202389240265 190.57183837890625 0.15623226761817932 0.7466554 0.6538165211677551 True -5 12972 24.020917415618896 0.4338715076446533 170.6759033203125 0.3409687578678131 189.40689086914062 0.15961070358753204 0.7674729 0.5729415416717529 True -6 15134 23.951759815216064 0.4265625476837158 162.9542236328125 0.3293916583061218 188.3601837158203 0.16310657560825348 0.7854282 0.5074310302734375 True -7 17296 23.93707036972046 0.42471790313720703 136.4239044189453 0.3742768168449402 187.6231231689453 0.1652774065732956 0.8011335 0.4539240598678589 True -8 19458 23.96364116668701 1.096853494644165 176.59002685546875 0.3716886341571808 187.1224822998047 0.16656756401062012 0.8077768 0.43810293078422546 True -9 21620 24.007805109024048 0.4261505603790283 203.6434783935547 0.43199312686920166 186.80282592773438 0.1676914542913437 0.8181221 0.38096070289611816 True -10 23782 23.972014904022217 0.4327261447906494 163.81829833984375 0.2986931800842285 186.43687438964844 0.16893896460533142 0.8246405 0.3660285770893097 True -11 25944 23.974997997283936 0.4380779266357422 124.31280517578125 0.33448854088783264 185.74366760253906 0.17131151258945465 0.83603567 0.3320505917072296 True -12 28106 23.9774432182312 0.6959397792816162 126.09881591796875 0.23976176977157593 185.5824737548828 0.17168521881103516 0.83970654 0.318043977022171 True -13 30268 24.00966238975525 0.42923426628112793 154.68511962890625 0.2688000500202179 185.25747680664062 0.17257964611053467 0.84570885 0.30595654249191284 True -14 32430 23.997841119766235 0.4520223140716553 156.69883728027344 0.26521623134613037 184.75430297851562 0.17426642775535583 0.85088104 0.2931539714336395 True -15 34592 23.989213466644287 0.6356751918792725 140.54443359375 0.2996843755245209 184.85755920410156 0.17318765819072723 0.85503507 0.28325971961021423 True -16 36754 24.070108652114868 14.728103160858154 131.5120849609375 0.33188289403915405 184.7382354736328 0.17352207005023956 0.85618514 0.2746541500091553 True -17 38916 24.45917558670044 0.5146875381469727 149.69386291503906 0.32425975799560547 184.81732177734375 0.17286072671413422 0.8584689 0.2702167332172394 True -18 41078 23.576687812805176 0.42316651344299316 163.3375701904297 0.1690618395805359 184.60963439941406 0.17383965849876404 0.8592135 0.2713761627674103 True -19 43240 23.53925347328186 0.4971432685852051 168.23944091796875 0.1510174721479416 184.84329223632812 0.1727738380432129 0.8578802 0.2717096209526062 False diff --git a/ENCSR515DVK/cherimoya.fold_3.performance.tsv b/ENCSR515DVK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b634e9e589352455bd8a7afb1acd5755596b8468..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -184.60963439941406 0.5722907781600952 0.17383964359760284 0.04143000394105911 0.8592134714126587 0.7937265634536743 0.2713761627674103 \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_4.evaluate.json b/ENCSR515DVK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d7c73e3ead37217bcacd317e19b7f08cdfbaa8a1..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF404TWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_4.fit.json b/ENCSR515DVK/cherimoya.fold_4.fit.json deleted file mode 100644 index 131837278ce3632e5a54b5d35933088163b0fd57..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF404TWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515DVK/cherimoya.fold_4.log b/ENCSR515DVK/cherimoya.fold_4.log deleted file mode 100644 index 405c4117ed87f3f5ff908d7455a9a14c98040387..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2209 28.942076683044434 3.563242197036743 133.0967254638672 0.43850070238113403 186.17079162597656 0.09787843376398087 0.6257807 3.7482287883758545 True -1 4418 24.785940408706665 6.366396427154541 153.62045288085938 0.35144394636154175 177.75160217285156 0.13015641272068024 0.7286275 1.2490452527999878 True -2 6627 24.584447860717773 0.45740723609924316 131.7191925048828 0.43820956349372864 173.84364318847656 0.136936753988266 0.74309707 0.6708109974861145 True -3 8836 24.60771679878235 0.49364638328552246 141.49264526367188 0.2646300196647644 172.37002563476562 0.13831283152103424 0.7582072 0.4832324683666229 True -4 11045 24.971611976623535 13.129862308502197 146.71640014648438 0.4304967522621155 170.6673583984375 0.14322176575660706 0.7734544 0.4344105124473572 True -5 13254 24.47585368156433 0.4535553455352783 159.6554718017578 0.4314533472061157 170.0889129638672 0.1445046067237854 0.7827472 0.3722184896469116 True -6 15463 24.761794090270996 0.4514899253845215 168.6353759765625 0.40868112444877625 169.3247528076172 0.14779867231845856 0.7905719 0.3716437816619873 True -7 17672 24.442399263381958 0.4617350101470947 141.45166015625 0.2934362292289734 168.9268035888672 0.14866383373737335 0.8022159 0.3262689411640167 True -8 19881 24.491003036499023 0.45978355407714844 140.65707397460938 0.33570387959480286 168.37464904785156 0.15062706172466278 0.8113524 0.3031422197818756 True -9 22090 24.572762489318848 5.990833520889282 179.87606811523438 0.26981157064437866 168.0352325439453 0.15167281031608582 0.81904507 0.28351181745529175 True -10 24299 24.528229475021362 0.4628760814666748 163.50143432617188 0.3095674216747284 167.67593383789062 0.15279613435268402 0.8272651 0.2721153497695923 True -11 26508 24.58163094520569 0.6510398387908936 134.23159790039062 0.23649004101753235 167.1860809326172 0.1545596867799759 0.8316098 0.2664676606655121 True -12 28717 24.548417806625366 0.45050621032714844 161.8264617919922 0.33228349685668945 167.15492248535156 0.15464581549167633 0.83663344 0.25846028327941895 True -13 30926 24.703040599822998 22.54197883605957 128.2591552734375 0.27748918533325195 166.96376037597656 0.1554088443517685 0.8401985 0.2510821521282196 True -14 33135 24.4958016872406 0.45311856269836426 168.33741760253906 0.26965075731277466 166.75814819335938 0.15592488646507263 0.84431183 0.24182264506816864 True -15 35344 24.717156887054443 0.44853639602661133 127.25691223144531 0.23727953433990479 166.4976806640625 0.15724769234657288 0.8459248 0.23532633483409882 True -16 37553 24.59476351737976 0.4493861198425293 145.150390625 0.18395930528640747 166.4159698486328 0.1573324054479599 0.8475367 0.23270946741104126 True -17 39762 24.543479681015015 0.44020605087280273 138.2550048828125 0.26814866065979004 166.5057830810547 0.1568393111228943 0.84836954 0.23203663527965546 True -18 41971 24.563031435012817 0.44318151473999023 154.64401245117188 0.3785673677921295 166.70266723632812 0.15557369589805603 0.84647495 0.23352272808551788 False -19 44180 24.714698553085327 0.45131683349609375 168.40093994140625 0.19734519720077515 166.74984741210938 0.1556718647480011 0.846901 0.23538003861904144 False diff --git a/ENCSR515DVK/cherimoya.fold_4.performance.tsv b/ENCSR515DVK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7ff80afe9e54cfa59d55021ae0d12ed7894f9a70..0000000000000000000000000000000000000000 --- a/ENCSR515DVK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -166.5057830810547 0.5842837691307068 0.15683932602405548 0.04012056067585945 0.8483695387840271 0.750062882900238 0.23203663527965546 \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_0.evaluate.json b/ENCSR515EWI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d4e263603ff637d83ada50b7472f2360188b6ae6..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF008OXU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_0.fit.json b/ENCSR515EWI/cherimoya.fold_0.fit.json deleted file mode 100644 index fb440c97d7f665ee66bba5ec8367680ac7717af9..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF008OXU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_0.log b/ENCSR515EWI/cherimoya.fold_0.log deleted file mode 100644 index ee65a1460e2bff7f6bc461e37029bc31e517742b..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.704002141952515 4.238152980804443 1196.898193359375 1.7158632278442383 1666.945068359375 0.2740548849105835 0.45083618 9.783740043640137 True -1 5454 30.014777421951294 1.9317927360534668 1177.4993896484375 1.5089020729064941 1441.62255859375 0.3849088251590729 0.49503535 5.897542953491211 True -2 8181 30.196776390075684 0.622990608215332 982.4080200195312 1.2336416244506836 1420.8111572265625 0.3971468210220337 0.4940997 5.63916015625 False -3 10908 30.1733238697052 0.5965690612792969 908.4129638671875 1.3934690952301025 1399.5634765625 0.4061385989189148 0.4953998 5.846889019012451 True -4 13635 30.104196310043335 0.6006853580474854 818.1287841796875 1.5619398355484009 1378.8262939453125 0.41864603757858276 0.49628595 4.822218418121338 True -5 16362 30.076590061187744 0.5991311073303223 946.9236450195312 1.4380624294281006 1368.0947265625 0.42148637771606445 0.50303483 4.0154924392700195 True -6 19089 30.078899145126343 0.6021327972412109 1148.609130859375 1.3136475086212158 1351.1026611328125 0.431225061416626 0.5229001 3.3231844902038574 True -7 21816 30.125563383102417 0.5916914939880371 1072.062744140625 1.157836675643921 1345.5931396484375 0.43290460109710693 0.5295341 3.154430389404297 True -8 24543 30.11937689781189 1.1100575923919678 916.009521484375 0.9186071157455444 1330.9451904296875 0.43888112902641296 0.5522314 2.604944944381714 True -9 27270 30.093793153762817 0.5886209011077881 1104.441650390625 1.3385026454925537 1320.8905029296875 0.4465944170951843 0.5537781 2.378681182861328 True -10 29997 30.105322122573853 0.5880341529846191 994.603515625 0.9677077531814575 1314.3612060546875 0.44731763005256653 0.57424265 2.1224403381347656 True -11 32724 30.039123058319092 0.5895595550537109 954.73486328125 1.0421035289764404 1305.342529296875 0.451616495847702 0.5858794 1.782902717590332 True -12 35451 30.101516485214233 0.5884523391723633 877.1692504882812 1.0468533039093018 1303.11279296875 0.449895977973938 0.60135037 1.645357370376587 True -13 38178 30.109256744384766 0.5802161693572998 872.539306640625 1.2319300174713135 1289.497314453125 0.4586825668811798 0.61230683 1.4797532558441162 True -14 40905 30.09835457801819 0.5883729457855225 919.36474609375 1.0135548114776611 1284.5648193359375 0.45916616916656494 0.62479603 1.3149045705795288 True -15 43632 30.077510833740234 0.5813226699829102 847.44189453125 0.7797929048538208 1277.4732666015625 0.46155357360839844 0.6345723 1.1965765953063965 True -16 46359 30.179454565048218 0.6029248237609863 930.3408203125 0.6769311428070068 1274.245849609375 0.4614366590976715 0.64117503 1.104706048965454 True -17 49086 30.086233615875244 0.6015839576721191 784.9412231445312 0.8619548082351685 1277.2281494140625 0.4600585997104645 0.6422756 1.0607959032058716 True -18 51813 30.118900775909424 1.5965137481689453 1050.3917236328125 0.7605273723602295 1275.2135009765625 0.4610714018344879 0.6403705 1.0413752794265747 False -19 54540 30.051265954971313 0.6028022766113281 932.01953125 0.6246532797813416 1276.938232421875 0.46003013849258423 0.6382866 1.0401192903518677 False diff --git a/ENCSR515EWI/cherimoya.fold_0.performance.tsv b/ENCSR515EWI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 246c00257c0cb88b022f1f9572c7595442eb4430..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1277.2281494140625 0.29877275228500366 0.4600585997104645 0.2690218985080719 0.6422755718231201 0.6138477921485901 1.0607959032058716 \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_1.evaluate.json b/ENCSR515EWI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4d8d4de1109a1c585bf313927965a8a82629defa..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF008OXU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_1.fit.json b/ENCSR515EWI/cherimoya.fold_1.fit.json deleted file mode 100644 index 2e8b2c0d58ac6a709a8ed362404694fe37ba0db7..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF008OXU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_1.log b/ENCSR515EWI/cherimoya.fold_1.log deleted file mode 100644 index a9ddcf87983a5bb1c3c0701141677c6a4d712d82..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2670 34.231876611709595 4.857626914978027 1200.315673828125 2.3714613914489746 1792.5654296875 0.2703227996826172 0.47890222 11.058558464050293 True -1 5340 29.358562231063843 0.8597073554992676 1084.1988525390625 2.051680564880371 1555.924072265625 0.3809911012649536 0.54896116 6.239687919616699 True -2 8010 29.50270128250122 0.8038027286529541 840.1942138671875 1.4335167407989502 1541.5079345703125 0.3876535892486572 0.53573716 4.433747291564941 False -3 10680 29.367032766342163 0.7999882698059082 941.18896484375 1.0830364227294922 1496.1053466796875 0.4046395421028137 0.5535148 3.1754813194274902 True -4 13350 29.28285837173462 0.7992503643035889 1091.083251953125 1.4558422565460205 1475.609619140625 0.4149511456489563 0.56477857 2.9975621700286865 True -5 16020 29.100938320159912 0.8084232807159424 1182.4862060546875 1.2163457870483398 1455.493408203125 0.42511266469955444 0.5745084 2.9473021030426025 True -6 18690 28.815385103225708 1.2563273906707764 1127.0966796875 1.7031021118164062 1450.6990966796875 0.4252798855304718 0.5803863 2.836700201034546 True -7 21360 28.8680260181427 0.7714884281158447 964.4410400390625 1.2576475143432617 1435.4261474609375 0.4329544007778168 0.58918697 2.632404088973999 True -8 24030 28.77942728996277 2.3201839923858643 818.1976318359375 1.296738862991333 1421.2802734375 0.4390084743499756 0.6002974 2.381356954574585 True -9 26700 28.754165649414062 0.7821943759918213 985.3705444335938 1.3799078464508057 1415.8975830078125 0.44208604097366333 0.6091014 2.182666301727295 True -10 29370 28.79729676246643 0.7792418003082275 755.0845947265625 1.2739359140396118 1404.06494140625 0.44617438316345215 0.6200169 1.9045600891113281 True -11 32040 28.77509570121765 0.7674002647399902 1031.7918701171875 1.076497197151184 1398.5821533203125 0.447368860244751 0.63146245 1.7220842838287354 True -12 34710 29.325722455978394 0.765904426574707 779.6537475585938 0.7149912118911743 1383.11669921875 0.4538417160511017 0.6411222 1.569548487663269 True -13 37380 28.794244050979614 0.7980527877807617 1052.8221435546875 0.9195603132247925 1374.9119873046875 0.45769885182380676 0.65171874 1.5131250619888306 True -14 40050 28.92679452896118 0.7972173690795898 750.3236083984375 0.8635401725769043 1368.251953125 0.4600967466831207 0.66248137 1.3815494775772095 True -15 42720 28.801976680755615 1.0046095848083496 1098.197265625 0.9134876728057861 1360.713623046875 0.4620177149772644 0.6695106 1.2769030332565308 True -16 45390 28.810473918914795 0.7894389629364014 1021.5221557617188 0.844650387763977 1362.1568603515625 0.45974063873291016 0.6737642 1.1964538097381592 True -17 48060 28.83953094482422 0.7761647701263428 1007.328125 1.17781400680542 1359.463623046875 0.46095067262649536 0.6724337 1.1277971267700195 False -18 50730 28.819230556488037 0.776709794998169 758.6763305664062 0.8544954061508179 1355.4920654296875 0.46377667784690857 0.6702597 1.1152328252792358 False -19 53400 28.831472396850586 0.757612943649292 1022.445068359375 0.7728739976882935 1360.856201171875 0.45961153507232666 0.6669536 1.1190340518951416 False diff --git a/ENCSR515EWI/cherimoya.fold_1.performance.tsv b/ENCSR515EWI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ec0e6c27ea8be4e93bc32b2192faf3d919e69a6b..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1362.1568603515625 0.2942645847797394 0.45974063873291016 0.2784287929534912 0.6737642288208008 0.6533227562904358 1.1964538097381592 \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_2.evaluate.json b/ENCSR515EWI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c47115954b27a274f363844360859d7000d21823..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF008OXU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_2.fit.json b/ENCSR515EWI/cherimoya.fold_2.fit.json deleted file mode 100644 index a1299528621b772312ef761c9d603cda2a2e1c91..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF008OXU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_2.log b/ENCSR515EWI/cherimoya.fold_2.log deleted file mode 100644 index e5203b91e4829980905f8505b8adee6eaf143ce2..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2850 37.80393147468567 3.9744701385498047 1131.95263671875 1.5072417259216309 1710.9417724609375 0.27559608221054077 0.47218987 11.43631362915039 True -1 5700 31.660489320755005 0.7173449993133545 1057.90673828125 1.1610026359558105 1476.4261474609375 0.38779786229133606 0.5082489 6.093273162841797 True -2 8550 31.35423231124878 0.5829780101776123 1086.644287109375 1.5185067653656006 1463.2208251953125 0.39418694376945496 0.5151324 4.415032863616943 True -3 11400 31.350026845932007 0.5870513916015625 1051.4564208984375 1.181666612625122 1446.1455078125 0.39837729930877686 0.53216463 3.4189023971557617 True -4 14250 31.367122411727905 0.58719801902771 1190.5205078125 1.1863354444503784 1419.658203125 0.4116426408290863 0.5384915 3.27359938621521 True -5 17100 31.314425468444824 0.5859215259552002 1222.415283203125 1.2597100734710693 1408.9805908203125 0.41840505599975586 0.53792405 2.9451096057891846 False -6 19950 31.321430683135986 0.6160423755645752 1002.311767578125 1.1892905235290527 1392.5361328125 0.4264248311519623 0.5503511 2.816932201385498 True -7 22800 31.362119436264038 0.5873064994812012 872.6470947265625 1.0216213464736938 1385.6689453125 0.42965978384017944 0.55875814 2.7609503269195557 True -8 25650 31.54403066635132 22.77826476097107 1320.9012451171875 1.14717698097229 1376.8109130859375 0.43372413516044617 0.5661969 2.485379219055176 True -9 28500 31.36273169517517 0.8348238468170166 940.0385131835938 1.0815227031707764 1364.1778564453125 0.43867596983909607 0.5750968 2.2520735263824463 True -10 31350 31.084274291992188 1.7578721046447754 1036.424560546875 0.8465195894241333 1351.784912109375 0.44483062624931335 0.5878126 2.0789849758148193 True -11 34200 30.73003315925598 1.754108190536499 1040.7833251953125 1.3827433586120605 1344.327392578125 0.44586947560310364 0.5980123 1.950200080871582 True -12 37050 30.788989067077637 1.6294975280761719 845.3732299804688 1.1569570302963257 1331.5902099609375 0.450909823179245 0.61345905 1.697933316230774 True -13 39900 30.87836480140686 9.624987840652466 905.0968017578125 1.196542739868164 1318.856201171875 0.45596426725387573 0.62730265 1.5040192604064941 True -14 42750 30.780128955841064 4.993265151977539 1061.386474609375 0.7697768211364746 1308.629150390625 0.4605366885662079 0.6405396 1.3491812944412231 True -15 45600 30.82115387916565 4.768197536468506 1083.397216796875 0.7773579359054565 1301.5328369140625 0.46398669481277466 0.65268904 1.1910489797592163 True -16 48450 30.83096718788147 0.5856680870056152 959.6322021484375 0.6970217227935791 1305.1251220703125 0.4607270658016205 0.6575333 1.1082301139831543 True -17 51300 30.773264408111572 0.5829975605010986 824.6309814453125 0.9937142133712769 1305.0428466796875 0.46069827675819397 0.6596698 1.0451831817626953 True -18 54150 30.714006185531616 0.5795743465423584 967.17626953125 0.5150889158248901 1306.7418212890625 0.46039530634880066 0.656889 1.028303623199463 False -19 57000 30.720816135406494 0.5718317031860352 957.8884887695312 1.033708095550537 1306.9327392578125 0.4602143466472626 0.6560889 1.0252195596694946 False diff --git a/ENCSR515EWI/cherimoya.fold_2.performance.tsv b/ENCSR515EWI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 658f903df605fc7e923548fd37f81c1d77b7e2c3..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1305.0428466796875 0.29595789313316345 0.46069830656051636 0.27591845393180847 0.659669816493988 0.6304759383201599 1.0451831817626953 \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_3.evaluate.json b/ENCSR515EWI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 84ca9be39393c14039b7067b7e9126843ef93c32..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF008OXU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_3.fit.json b/ENCSR515EWI/cherimoya.fold_3.fit.json deleted file mode 100644 index d3f929e2c320f8f0b72988a8921932c3b5b5c303..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF008OXU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_3.log b/ENCSR515EWI/cherimoya.fold_3.log deleted file mode 100644 index af700d34639fc8f8db7a987691a1828df8e397f7..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 35.45389723777771 4.0590596199035645 1183.888427734375 1.622525930404663 1755.5733642578125 0.2849327623844147 0.4917465 10.49776554107666 True -1 5554 30.5484037399292 0.6826744079589844 1286.268798828125 1.3616231679916382 1535.9024658203125 0.3933086693286896 0.48701724 8.821442604064941 False -2 8331 30.543878078460693 0.61165452003479 1186.498779296875 1.879496693611145 1507.8973388671875 0.4025423526763916 0.48699018 6.128023147583008 False -3 11108 30.4605553150177 0.5795984268188477 902.3231201171875 1.105772852897644 1479.0220947265625 0.4162313640117645 0.516936 4.673367977142334 True -4 13885 30.49622941017151 0.5629398822784424 902.1181640625 1.6897501945495605 1464.677978515625 0.4223230481147766 0.51548636 3.837470769882202 False -5 16662 30.48324680328369 0.598665714263916 1109.588134765625 1.0061209201812744 1459.4722900390625 0.4233439862728119 0.5145075 3.574422597885132 False -6 19439 30.45426917076111 0.575472354888916 1035.76953125 1.6627004146575928 1439.895751953125 0.43521788716316223 0.5243732 3.3004562854766846 True -7 22216 30.508471250534058 0.6146128177642822 922.6026000976562 0.9481603503227234 1429.4620361328125 0.43943071365356445 0.53438854 2.853022336959839 True -8 24993 30.49763584136963 0.5893099308013916 885.81103515625 1.6310893297195435 1419.030029296875 0.44469574093818665 0.5417612 2.590897560119629 True -9 27770 30.462242603302002 0.5895509719848633 928.523681640625 0.7184470295906067 1410.1019287109375 0.44964107871055603 0.55560476 2.366819143295288 True -10 30547 30.470889568328857 0.5680794715881348 794.91455078125 1.1948028802871704 1403.1453857421875 0.4514595866203308 0.5664592 2.0309345722198486 True -11 33324 30.49394679069519 0.5733864307403564 1104.5390625 0.7771874666213989 1396.1318359375 0.45394468307495117 0.57725966 1.8069565296173096 True -12 36101 30.517927646636963 0.5661430358886719 1050.727294921875 1.1041795015335083 1381.35693359375 0.46224549412727356 0.5948128 1.6690698862075806 True -13 38878 30.560084342956543 0.8667538166046143 889.5372314453125 0.8703073263168335 1377.1397705078125 0.46162474155426025 0.61702436 1.5154433250427246 True -14 41655 30.601905345916748 2.219172239303589 1026.57666015625 0.8272159099578857 1358.4757080078125 0.47033923864364624 0.63261133 1.3486230373382568 True -15 44432 30.142901182174683 1.5720107555389404 865.5821533203125 0.7758007049560547 1359.0157470703125 0.4701245427131653 0.6449538 1.2373948097229004 True -16 47209 30.02698850631714 0.5909514427185059 989.103271484375 0.8486863970756531 1354.1124267578125 0.47163182497024536 0.65325594 1.1501606702804565 True -17 49986 29.97438907623291 0.5829005241394043 813.8617553710938 0.705101490020752 1353.4725341796875 0.47146421670913696 0.6557288 1.073627233505249 True -18 52763 29.96227526664734 0.5815057754516602 781.9064331054688 0.6608179211616516 1356.7169189453125 0.4677013158798218 0.6554564 1.053697109222412 False -19 55540 29.947192430496216 0.5739972591400146 764.97314453125 1.1358873844146729 1358.290283203125 0.4671383500099182 0.65169126 1.0524448156356812 False diff --git a/ENCSR515EWI/cherimoya.fold_3.performance.tsv b/ENCSR515EWI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e478075e2489ac33e5ba634019c5b422dee82245..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1353.4725341796875 0.2891135513782501 0.47146421670913696 0.2821696102619171 0.655728816986084 0.6315208673477173 1.073627233505249 \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_4.evaluate.json b/ENCSR515EWI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c6da89e8d0b4c5e67d7e5f77228efee69edf4a82..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF008OXU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_4.fit.json b/ENCSR515EWI/cherimoya.fold_4.fit.json deleted file mode 100644 index 27ee7cc57ea432fc285a8be746267d6b72e01dd6..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF008OXU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515EWI/cherimoya.fold_4.log b/ENCSR515EWI/cherimoya.fold_4.log deleted file mode 100644 index f318503f53814ffc9e6ee51eb281561e55e0a596..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2827 35.522640228271484 3.888547420501709 1316.8284912109375 1.387977957725525 1607.509033203125 0.2747651934623718 0.45173326 9.530202865600586 True -1 5654 31.079267024993896 0.5428867340087891 1076.09130859375 1.0134049654006958 1415.3948974609375 0.38331446051597595 0.46832797 6.748990535736084 True -2 8481 31.119340181350708 0.5581495761871338 1225.1904296875 1.5345652103424072 1389.5753173828125 0.39836493134498596 0.4896086 4.708650588989258 True -3 11308 31.046701669692993 0.5390815734863281 965.6561279296875 1.147001028060913 1370.76220703125 0.4065556228160858 0.48613915 3.622471332550049 False -4 14135 31.085197687149048 0.5356757640838623 921.2169799804688 0.9809435606002808 1354.615966796875 0.41350021958351135 0.49727473 3.0288355350494385 True -5 16962 31.030105352401733 0.8877813816070557 921.3753051757812 1.0029648542404175 1336.65966796875 0.423499196767807 0.5213912 2.6746697425842285 True -6 19789 31.039294004440308 16.460398197174072 757.5826416015625 1.148831844329834 1329.0548095703125 0.4266602396965027 0.5329945 2.247053623199463 True -7 22616 31.636889219284058 0.5439956188201904 1193.41796875 1.952648401260376 1312.586669921875 0.43628162145614624 0.54094523 2.0400755405426025 True -8 25443 31.120922088623047 0.5421669483184814 978.8775024414062 1.1643431186676025 1303.5609130859375 0.4415619671344757 0.5454226 1.996928334236145 True -9 28270 31.09335231781006 0.5538358688354492 1028.244384765625 1.4148709774017334 1299.072509765625 0.44503718614578247 0.5562868 1.858583927154541 True -10 31097 31.09869694709778 0.5651841163635254 1183.720458984375 1.3235725164413452 1293.5206298828125 0.4472600519657135 0.5621324 1.7530583143234253 True -11 33924 31.053197622299194 0.5526807308197021 742.2444458007812 1.1670148372650146 1280.2652587890625 0.4547772705554962 0.5689459 1.644469976425171 True -12 36751 31.031723976135254 0.535266637802124 949.731201171875 1.2821731567382812 1275.0948486328125 0.4548543691635132 0.58120227 1.549642562866211 True -13 39578 31.064746618270874 0.5368964672088623 991.5665893554688 1.1191492080688477 1267.763916015625 0.4590606391429901 0.5973425 1.375317096710205 True -14 42405 31.833815336227417 6.328233003616333 1152.4287109375 1.0535558462142944 1259.9306640625 0.46300044655799866 0.60799277 1.252502202987671 True -15 45232 31.02919363975525 0.5494992733001709 914.921142578125 1.1249566078186035 1253.4266357421875 0.4663180708885193 0.6212337 1.1528592109680176 True -16 48059 31.04389524459839 0.5504367351531982 1095.899658203125 0.9033057689666748 1252.0166015625 0.46611472964286804 0.63003373 1.062796711921692 True -17 50886 31.262548446655273 24.879589796066284 929.0211181640625 0.7240478992462158 1249.1214599609375 0.466326504945755 0.6334762 1.0126539468765259 True -18 53713 31.166234493255615 1.7805991172790527 1033.3585205078125 0.8394061326980591 1251.8388671875 0.46467915177345276 0.63412917 1.0004477500915527 True -19 56540 31.128361701965332 0.548419713973999 899.2222290039062 0.7028756141662598 1254.8272705078125 0.4621686041355133 0.6327 1.0047118663787842 False diff --git a/ENCSR515EWI/cherimoya.fold_4.performance.tsv b/ENCSR515EWI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d45aeacabfd2f54cc86747edf15fa94f6afc90c3..0000000000000000000000000000000000000000 --- a/ENCSR515EWI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1251.8388671875 0.2977399528026581 0.464679092168808 0.26986679434776306 0.6341291666030884 0.6054292917251587 1.0004477500915527 \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_0.evaluate.json b/ENCSR515PDV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 180cf4711dd59ff3b0aa0ff712393f6c7f9b623c..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF739NRO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_0.fit.json b/ENCSR515PDV/cherimoya.fold_0.fit.json deleted file mode 100644 index ccefd43e1aa442cd8a71bb219a33d3ef1b653c38..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF739NRO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_0.log b/ENCSR515PDV/cherimoya.fold_0.log deleted file mode 100644 index f284705b63f71bc8e1d784528a451e2539143502..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 33.75981092453003 3.579484224319458 548.0015869140625 0.37354108691215515 730.068359375 0.17828057706356049 0.75728005 4.393212795257568 True -1 5470 30.204542875289917 0.5648319721221924 520.3946533203125 0.3102456033229828 693.9620971679688 0.20686781406402588 0.8139533 1.005897045135498 True -2 8205 30.2109534740448 0.5504283905029297 616.1173095703125 0.42715227603912354 687.1787109375 0.2120644599199295 0.8201514 0.5669862031936646 True -3 10940 30.189677715301514 0.5429611206054688 509.4622497558594 0.29550501704216003 683.5034790039062 0.21423597633838654 0.8263205 0.5207397937774658 True -4 13675 30.148888111114502 0.7776527404785156 512.940673828125 0.2200973927974701 680.4344482421875 0.21821069717407227 0.829346 0.5032398104667664 True -5 16410 30.195581674575806 1.0350573062896729 485.80474853515625 0.32849228382110596 679.223388671875 0.21810869872570038 0.8358609 0.420639306306839 True -6 19145 30.245566606521606 1.5867505073547363 567.352294921875 0.3278428018093109 677.1297607421875 0.22011449933052063 0.8438257 0.36700692772865295 True -7 21880 29.95131778717041 0.5417630672454834 635.281982421875 0.2751384973526001 675.1676025390625 0.22115746140480042 0.85089266 0.34331467747688293 True -8 24615 29.585081100463867 0.5415823459625244 681.8191528320312 0.30619436502456665 674.655517578125 0.22218257188796997 0.8545373 0.3200015723705292 True -9 27350 29.615336894989014 0.5477049350738525 613.7057495117188 0.29177701473236084 672.0457763671875 0.22410090267658234 0.86406237 0.29270675778388977 True -10 30085 29.605650663375854 0.5417354106903076 591.9288940429688 0.26170727610588074 670.6172485351562 0.22547805309295654 0.868998 0.2728857696056366 True -11 32820 29.65675640106201 0.5646793842315674 602.1337890625 0.3379351496696472 670.3372802734375 0.22564774751663208 0.875726 0.2484411746263504 True -12 35555 29.670302629470825 0.5689818859100342 625.0640869140625 0.2763270139694214 668.2879638671875 0.22747495770454407 0.8820478 0.23632760345935822 True -13 38290 29.602705717086792 0.5548267364501953 701.0778198242188 0.2047334760427475 666.2420654296875 0.23019817471504211 0.88440704 0.22578208148479462 True -14 41025 29.739110946655273 0.5550148487091064 557.2584838867188 0.1928054690361023 667.2777709960938 0.22810831665992737 0.8872105 0.21388395130634308 True -15 43760 29.75299310684204 0.55548095703125 558.3785400390625 0.2734541594982147 666.7985229492188 0.22900721430778503 0.8900044 0.20431837439537048 True -16 46495 29.636967420578003 0.5515217781066895 572.2813110351562 0.13063938915729523 666.5050048828125 0.22905965149402618 0.8913806 0.19931641221046448 True -17 49230 29.711371898651123 0.5642135143280029 610.244140625 0.13071303069591522 667.385498046875 0.2275017946958542 0.8910744 0.19601379334926605 False -18 51965 29.573641300201416 0.5493488311767578 541.9122314453125 0.13975751399993896 667.0090942382812 0.22897246479988098 0.89083946 0.1986464560031891 False -19 54700 29.56848168373108 2.323052167892456 555.2423095703125 0.17155933380126953 667.9172973632812 0.22771161794662476 0.89075696 0.19952423870563507 False diff --git a/ENCSR515PDV/cherimoya.fold_0.performance.tsv b/ENCSR515PDV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ff11ab2b2df6a82c8b850f9ade48cd748d25cdf2..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -666.5050048828125 0.486372709274292 0.22905965149402618 0.09617789089679718 0.8913806080818176 0.8508462905883789 0.19931641221046448 \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_1.evaluate.json b/ENCSR515PDV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2eb53e14a8a9fab04f01a2370d14be7a6dc7a8a8..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF739NRO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_1.fit.json b/ENCSR515PDV/cherimoya.fold_1.fit.json deleted file mode 100644 index 8b7c5b83817c99ea48b94c8487c9f7a39b9c65bf..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF739NRO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_1.log b/ENCSR515PDV/cherimoya.fold_1.log deleted file mode 100644 index f45e5740be292cf0fa49ee1080a5594b95e96739..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 33.80292987823486 3.578997850418091 505.88385009765625 0.33993300795555115 855.4202270507812 0.19262684881687164 0.7343067 5.325064659118652 True -1 5418 29.85434579849243 0.7370705604553223 600.491455078125 0.26537758111953735 806.349365234375 0.2292836457490921 0.8044274 1.4460468292236328 True -2 8127 29.90889573097229 0.7032785415649414 570.4365844726562 0.5157502889633179 798.1489868164062 0.23214146494865417 0.8169123 0.7269195914268494 True -3 10836 29.882856607437134 0.7125356197357178 575.2706298828125 0.43967846035957336 792.8748168945312 0.23680859804153442 0.82826114 0.6106744408607483 True -4 13545 29.907675981521606 0.7148330211639404 625.83935546875 0.3253854215145111 788.23046875 0.24068132042884827 0.8349819 0.5555082559585571 True -5 16254 29.90601134300232 0.7112445831298828 564.6532592773438 0.1728520691394806 787.7359619140625 0.24100783467292786 0.835661 0.45793524384498596 True -6 18963 29.946439266204834 1.6938586235046387 559.6429443359375 0.3016711175441742 785.6510009765625 0.24214354157447815 0.8432799 0.4321257770061493 True -7 21672 29.951903581619263 0.7150366306304932 668.8220825195312 0.31196972727775574 784.5689697265625 0.24252012372016907 0.84616905 0.4269302487373352 True -8 24381 29.929307222366333 0.7124042510986328 703.552001953125 0.2893052101135254 783.013671875 0.2439872771501541 0.85249335 0.3951454162597656 True -9 27090 29.5420880317688 2.2266597747802734 565.992431640625 0.2620161175727844 780.0198364257812 0.2465425580739975 0.8599312 0.37109068036079407 True -10 29799 29.357866048812866 0.7109212875366211 617.4588012695312 0.26129448413848877 778.8668823242188 0.247402161359787 0.8674196 0.35262632369995117 True -11 32508 29.347169399261475 0.7087349891662598 597.919677734375 0.240778386592865 777.1554565429688 0.2491884082555771 0.87250584 0.32040315866470337 True -12 35217 29.33873224258423 0.7086787223815918 604.1896362304688 0.234757661819458 773.8490600585938 0.2525572180747986 0.8785666 0.30165448784828186 True -13 37926 29.350660800933838 0.7093660831451416 673.8507080078125 0.412842333316803 773.1663818359375 0.2523657977581024 0.8850355 0.27803152799606323 True -14 40635 29.366860389709473 0.7032732963562012 594.001953125 0.29808902740478516 771.7600708007812 0.2527126371860504 0.888657 0.26768186688423157 True -15 43344 29.304845571517944 0.7087829113006592 628.5259399414062 0.35803672671318054 771.5617065429688 0.2536414563655853 0.8899325 0.2653915584087372 True -16 46053 29.27169895172119 0.7089712619781494 528.2542724609375 0.18356569111347198 770.997802734375 0.25413399934768677 0.8933141 0.25347110629081726 True -17 48762 29.265907764434814 0.6901748180389404 585.358154296875 0.18908843398094177 771.7540283203125 0.25343194603919983 0.893244 0.2520032823085785 False -18 51471 29.27716326713562 0.7099590301513672 545.9755859375 0.08948853611946106 774.569580078125 0.2508348226547241 0.89111537 0.25191646814346313 False -19 54180 29.334423065185547 0.6979954242706299 548.340087890625 0.13527821004390717 773.9144897460938 0.2512560188770294 0.89062726 0.25163424015045166 False diff --git a/ENCSR515PDV/cherimoya.fold_1.performance.tsv b/ENCSR515PDV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 01d30561557474aaf53fa86852c30c7d1002661a..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -770.997802734375 0.4627360701560974 0.2541339695453644 0.11451155692338943 0.8933141231536865 0.8709763288497925 0.25347110629081726 \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_2.evaluate.json b/ENCSR515PDV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 75818c43d62f42e6f1f427a6dbfc10cb88d04795..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF739NRO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_2.fit.json b/ENCSR515PDV/cherimoya.fold_2.fit.json deleted file mode 100644 index 16e42761dcd46ce5905e7e192c4a77e20d8aa34d..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF739NRO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_2.log b/ENCSR515PDV/cherimoya.fold_2.log deleted file mode 100644 index 34ed31b9ed4067eb61627daa627741442948afc5..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 35.347068786621094 3.686133861541748 584.276123046875 0.39246129989624023 757.1976318359375 0.1852552741765976 0.7348388 4.4265007972717285 True -1 5744 31.723219394683838 0.5716993808746338 668.10888671875 0.4404520094394684 719.779296875 0.21468393504619598 0.8013478 1.183305025100708 True -2 8616 31.691506385803223 0.5584726333618164 598.2978515625 0.47118666768074036 712.9381713867188 0.21614199876785278 0.81832 0.535775899887085 True -3 11488 31.646687030792236 0.5515456199645996 510.0517578125 0.2882910668849945 708.0419921875 0.22072575986385345 0.83006024 0.5134396553039551 True -4 14360 31.705830335617065 3.6115167140960693 590.8909912109375 0.2747965455055237 706.1210327148438 0.22260797023773193 0.8352961 0.41940122842788696 True -5 17232 31.668877840042114 0.5720176696777344 554.2682495117188 0.5118943452835083 704.240234375 0.22390855848789215 0.8407583 0.3866601288318634 True -6 20104 31.671142578125 0.5562887191772461 521.92333984375 0.30624186992645264 702.8442993164062 0.22545519471168518 0.84541696 0.3714134991168976 True -7 22976 31.65386700630188 0.5623495578765869 530.5250854492188 0.16439613699913025 700.5206909179688 0.2271953821182251 0.85284215 0.3329958915710449 True -8 25848 31.660538911819458 0.5635747909545898 593.0606689453125 0.2451944351196289 700.1158447265625 0.22784416377544403 0.85695046 0.31805944442749023 True -9 28720 31.005935668945312 0.5515055656433105 609.8446655273438 0.3412439227104187 698.1605834960938 0.2302217334508896 0.86011547 0.3051014840602875 True -10 31592 31.02686333656311 0.5582566261291504 591.3064575195312 0.2643689215183258 698.9854736328125 0.2280949205160141 0.86383533 0.2734970152378082 True -11 34464 31.091219186782837 0.5588812828063965 552.2586059570312 0.23368896543979645 697.5076904296875 0.22976535558700562 0.86921173 0.26078173518180847 True -12 37336 31.104129314422607 3.743413209915161 531.97314453125 0.2352651208639145 695.6264038085938 0.2322573959827423 0.87086546 0.25066623091697693 True -13 40208 31.10091519355774 0.5660715103149414 538.0263061523438 0.24290084838867188 696.2481079101562 0.2309332937002182 0.8771029 0.23663756251335144 True -14 43080 31.07384467124939 0.5711123943328857 699.7313842773438 0.22692489624023438 694.93359375 0.2317994385957718 0.88157594 0.22686900198459625 True -15 45952 31.10043716430664 0.5710763931274414 638.3212890625 0.247538223862648 694.7100219726562 0.23179225623607635 0.8832003 0.21806879341602325 True -16 48824 31.152114868164062 0.5671982765197754 599.1351318359375 0.134409561753273 692.8059692382812 0.2337212711572647 0.8866777 0.2119394689798355 True -17 51696 31.129462957382202 0.5658152103424072 523.4922485351562 0.20566979050636292 692.9913940429688 0.23447079956531525 0.8847556 0.21212780475616455 False -18 54568 31.10314655303955 0.5530693531036377 582.9769287109375 0.11291187256574631 693.0433349609375 0.2342388927936554 0.88410234 0.2145593762397766 False -19 57440 31.08345866203308 0.5562186241149902 606.9112548828125 0.1528259664773941 693.9773559570312 0.23245173692703247 0.88220704 0.21737387776374817 False diff --git a/ENCSR515PDV/cherimoya.fold_2.performance.tsv b/ENCSR515PDV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0093c798c114cd55e579b86bed8a1fe310a320e0..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -692.8059692382812 0.48026353120803833 0.2337213158607483 0.10362593084573746 0.8866776823997498 0.8603049516677856 0.2119394689798355 \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_3.evaluate.json b/ENCSR515PDV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 31265e2cea247bd41e82c94e536eb1317b0a2654..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF739NRO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_3.fit.json b/ENCSR515PDV/cherimoya.fold_3.fit.json deleted file mode 100644 index 5dec626d53fd06e0e27c83f3af2114f97a7ed433..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF739NRO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_3.log b/ENCSR515PDV/cherimoya.fold_3.log deleted file mode 100644 index 4e3b5534836fb1cee521979362d477f104efc2ce..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 33.847222089767456 3.51281476020813 542.6924438476562 0.3873136043548584 719.4592895507812 0.18815147876739502 0.7045266 4.408671855926514 True -1 5458 30.209442138671875 0.5778999328613281 594.12353515625 0.3281288743019104 684.3356323242188 0.21561399102210999 0.77294916 1.116264820098877 True -2 8187 30.513959407806396 0.5704219341278076 645.88134765625 0.2835935652256012 676.4103393554688 0.220399871468544 0.8049752 0.5778456926345825 True -3 10916 30.14806365966797 0.5746238231658936 685.0686645507812 0.3165856599807739 672.7637939453125 0.22436478734016418 0.81020474 0.4527225196361542 True -4 13645 30.13163447380066 0.5752220153808594 547.8922119140625 0.2786126136779785 672.8212280273438 0.22313830256462097 0.81647635 0.5303669571876526 True -5 16374 30.160638570785522 0.5746793746948242 591.56884765625 0.3177458345890045 671.0994262695312 0.2246095985174179 0.8193405 0.3850056231021881 True -6 19103 30.180209636688232 0.5706593990325928 618.2136840820312 0.4094802439212799 668.672119140625 0.22793085873126984 0.8204964 0.3993131220340729 True -7 21832 30.08660912513733 0.5655519962310791 604.3314208984375 0.4030165672302246 667.3515625 0.22961975634098053 0.8224417 0.388800710439682 True -8 24561 29.98759388923645 1.0804874897003174 724.73095703125 0.36609843373298645 665.6481323242188 0.23091861605644226 0.8263051 0.3797249495983124 True -9 27290 29.5279061794281 0.5614776611328125 552.55419921875 0.33595576882362366 665.3789672851562 0.23013989627361298 0.8329381 0.36420854926109314 True -10 30019 29.507739067077637 0.5685241222381592 565.4996337890625 0.24117133021354675 664.6510009765625 0.23107829689979553 0.8360679 0.3420945107936859 True -11 32748 29.528237104415894 0.56557297706604 604.6585083007812 0.33653438091278076 663.314453125 0.23221491277217865 0.84207445 0.3326342701911926 True -12 35477 29.563263654708862 0.5703895092010498 648.4402465820312 0.253934770822525 662.6340942382812 0.23226921260356903 0.8491389 0.31397879123687744 True -13 38206 29.523499488830566 0.5646343231201172 620.0567016601562 0.2868671119213104 661.8232421875 0.2334202378988266 0.8585004 0.2882116436958313 True -14 40935 29.54255747795105 0.5623331069946289 732.6627807617188 0.33498817682266235 660.16357421875 0.23529653251171112 0.8625836 0.2737082839012146 True -15 43664 29.52991271018982 0.564802885055542 585.2158203125 0.2606715261936188 660.7091064453125 0.23408851027488708 0.86832315 0.2613435685634613 True -16 46393 29.543863534927368 0.5711209774017334 563.8614501953125 0.18467475473880768 660.9503173828125 0.23389498889446259 0.87090397 0.25246676802635193 True -17 49122 29.50911021232605 0.5603621006011963 586.22607421875 0.1892356425523758 661.0830688476562 0.23432600498199463 0.8743012 0.24502024054527283 True -18 51851 29.560159921646118 0.5615603923797607 579.1484985351562 0.12263602763414383 660.68994140625 0.23487809300422668 0.87410605 0.24405686557292938 False -19 54580 29.57352566719055 0.5673775672912598 580.3156127929688 0.19012236595153809 660.7691040039062 0.2345888763666153 0.873174 0.2446436583995819 False diff --git a/ENCSR515PDV/cherimoya.fold_3.performance.tsv b/ENCSR515PDV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3a714f850fc1cb386ffe280b2512db1acc3e2d99..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -661.0830688476562 0.4840215742588043 0.23432599008083344 0.09728094935417175 0.8743011951446533 0.838985800743103 0.24502024054527283 \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_4.evaluate.json b/ENCSR515PDV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 807ce7c239309545a4312b54f26a919abd85e1e1..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF739NRO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_4.fit.json b/ENCSR515PDV/cherimoya.fold_4.fit.json deleted file mode 100644 index 32aa1b0fc5f5af7b26899deab03a7eb0237116f6..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF739NRO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR515PDV/cherimoya.fold_4.log b/ENCSR515PDV/cherimoya.fold_4.log deleted file mode 100644 index 208a42ae6c040f6c3814bfb9ba4c681c1a68aaf3..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2817 35.20748448371887 3.647864818572998 692.488037109375 0.5659971833229065 644.3340454101562 0.1767168790102005 0.7407721 3.841243028640747 True -1 5634 31.16736936569214 0.6625235080718994 635.3993530273438 0.29369238018989563 619.972412109375 0.19843973219394684 0.79737383 0.962283194065094 True -2 8451 31.16484832763672 0.6375491619110107 632.517578125 0.24228346347808838 612.2572021484375 0.20108069479465485 0.8197764 0.43320611119270325 True -3 11268 31.26984453201294 0.6358723640441895 635.574462890625 0.33902567625045776 609.7030029296875 0.2031598836183548 0.8235618 0.3845910131931305 True -4 14085 31.18144917488098 0.6262950897216797 548.1495361328125 0.28518810868263245 607.2384033203125 0.2050551176071167 0.82927006 0.37907207012176514 True -5 16902 31.13809061050415 0.6216475963592529 616.525146484375 0.33479124307632446 605.2127075195312 0.20745952427387238 0.8370047 0.3021755516529083 True -6 19719 31.212074518203735 0.6323695182800293 590.1951904296875 0.27901434898376465 603.6702880859375 0.20873446762561798 0.84241617 0.28773778676986694 True -7 22536 31.13691282272339 0.6239826679229736 524.857666015625 0.24805940687656403 602.5372314453125 0.20966856181621552 0.8476099 0.27044010162353516 True -8 25353 31.123281478881836 0.6171853542327881 616.1557006835938 0.26811766624450684 602.252197265625 0.20955251157283783 0.85313106 0.24985460937023163 True -9 28170 30.867630004882812 0.6186943054199219 545.46142578125 0.26033568382263184 600.7318115234375 0.2119247317314148 0.8560745 0.24249152839183807 True -10 30987 30.397751808166504 0.6181890964508057 540.3800048828125 0.23910388350486755 599.8272705078125 0.21257384121418 0.86374193 0.2227071225643158 True -11 33804 30.415018320083618 0.6207051277160645 555.3712158203125 0.3625611662864685 599.3124389648438 0.2127331644296646 0.8697361 0.21064290404319763 True -12 36621 30.45204448699951 0.6179788112640381 589.1129760742188 0.18860992789268494 597.96923828125 0.21354971826076508 0.8733633 0.20271910727024078 True -13 39438 30.489667654037476 1.4396767616271973 518.485107421875 0.2416650503873825 597.253662109375 0.21465124189853668 0.8775665 0.1983102709054947 True -14 42255 30.47399091720581 0.6216528415679932 520.5701904296875 0.19513186812400818 597.4865112304688 0.2148541808128357 0.8807112 0.18947148323059082 True -15 45072 30.549663305282593 0.6149423122406006 522.557373046875 0.15636548399925232 597.1929931640625 0.2149479240179062 0.88481426 0.18369309604167938 True -16 47889 30.468268871307373 0.6151859760284424 457.0763854980469 0.11596975475549698 597.1386108398438 0.21466371417045593 0.8837896 0.18161575496196747 False -17 50706 30.494391202926636 0.6133816242218018 610.89599609375 0.139481782913208 597.3146362304688 0.21427403390407562 0.88438994 0.18192903697490692 False -18 53523 30.50038743019104 0.6092896461486816 618.482421875 0.12526172399520874 597.2041015625 0.21456512808799744 0.8826111 0.18309542536735535 False -19 56340 30.556950330734253 0.617516040802002 496.24786376953125 0.16184745728969574 597.4696655273438 0.21414507925510406 0.8828859 0.18454554677009583 False diff --git a/ENCSR515PDV/cherimoya.fold_4.performance.tsv b/ENCSR515PDV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5b8c3445301b7f63bc5f00b86fbf40763452c017..0000000000000000000000000000000000000000 --- a/ENCSR515PDV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -597.1929931640625 0.5012457966804504 0.2149479240179062 0.08907733112573624 0.8848142623901367 0.8494909405708313 0.18369309604167938 \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_0.evaluate.json b/ENCSR516RTV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 833bdf7b201072393466d52e08d655d0cefc18a6..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF703MBI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_0.fit.json b/ENCSR516RTV/cherimoya.fold_0.fit.json deleted file mode 100644 index 6e3241cc3b222891fd968dbe21e0e4f0f3dc8388..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF703MBI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_0.log b/ENCSR516RTV/cherimoya.fold_0.log deleted file mode 100644 index 634869cb1bf46543aaffd7a9d35bb010f01f6675..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 36.049540519714355 3.567673444747925 406.93682861328125 0.26720064878463745 594.0538330078125 0.29997381567955017 0.81323683 5.2319746017456055 True -1 5526 30.79099941253662 0.5943281650543213 476.47674560546875 0.4387722611427307 540.690185546875 0.36920562386512756 0.8511864 1.2867403030395508 True -2 8289 31.307049989700317 0.579988956451416 516.1378784179688 0.30403369665145874 529.719482421875 0.3839123845100403 0.86320865 0.47055432200431824 True -3 11052 30.825138807296753 0.5845687389373779 463.21685791015625 0.3463059067726135 522.8843383789062 0.391035795211792 0.86887354 0.4443129301071167 True -4 13815 30.788841009140015 2.539924383163452 415.2897033691406 0.2609703838825226 519.748779296875 0.3948688805103302 0.8766635 0.30852413177490234 True -5 16578 30.812655925750732 0.5879766941070557 396.4705810546875 0.1826663464307785 520.4552612304688 0.39199671149253845 0.87583345 0.257455050945282 False -6 19341 30.80445647239685 18.765167713165283 468.73388671875 0.31427299976348877 516.0476684570312 0.3999108076095581 0.88164145 0.24214884638786316 True -7 22104 31.47596526145935 0.5893526077270508 466.90032958984375 0.22964471578598022 514.894775390625 0.40116646885871887 0.8873946 0.22870118916034698 True -8 24867 30.800538063049316 0.6622607707977295 433.50164794921875 0.17138966917991638 513.4668579101562 0.4030601978302002 0.8892479 0.23633255064487457 True -9 27630 30.864226818084717 2.543649673461914 408.3628234863281 0.21651171147823334 511.7266845703125 0.40523988008499146 0.89196694 0.22896265983581543 True -10 30393 30.85987138748169 0.5957260131835938 463.3944091796875 0.2613568902015686 509.7821350097656 0.40785089135169983 0.8960038 0.21941672265529633 True -11 33156 30.86493682861328 0.6038370132446289 433.8390197753906 0.22987288236618042 508.4917907714844 0.4097059369087219 0.89822334 0.19626738131046295 True -12 35919 30.83815860748291 0.5897371768951416 429.6639404296875 0.18976342678070068 506.6839599609375 0.41189226508140564 0.90274704 0.1960611790418625 True -13 38682 30.796942472457886 1.6412713527679443 440.6721496582031 0.18626272678375244 506.2690124511719 0.41236042976379395 0.90697724 0.1792391687631607 True -14 41445 30.855100870132446 0.5904245376586914 475.811279296875 0.17132800817489624 504.6225891113281 0.41398394107818604 0.9085796 0.17145314812660217 True -15 44208 31.08470606803894 0.5870883464813232 390.1384582519531 0.2031792551279068 503.1549377441406 0.41627103090286255 0.9104433 0.16425441205501556 True -16 46971 30.26909351348877 0.5799281597137451 467.79632568359375 0.19433826208114624 502.70465087890625 0.41624197363853455 0.9129685 0.15993686020374298 True -17 49734 30.263758659362793 0.5801341533660889 490.8871765136719 0.11993227154016495 503.247314453125 0.41614285111427307 0.9127836 0.1579791009426117 False -18 52497 30.321378707885742 0.5906319618225098 474.6510009765625 0.14154782891273499 503.3385314941406 0.4158630967140198 0.9122896 0.15785957872867584 False -19 55260 30.198018312454224 0.5795097351074219 512.1889038085938 0.13967594504356384 502.9533996582031 0.41714370250701904 0.91183925 0.15861600637435913 False diff --git a/ENCSR516RTV/cherimoya.fold_0.performance.tsv b/ENCSR516RTV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 430646a2ff3a60c9188de263f4368e788208e10e..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -502.70465087890625 0.38247939944267273 0.41624191403388977 0.15874505043029785 0.9129685163497925 0.8918706774711609 0.15993686020374298 \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_1.evaluate.json b/ENCSR516RTV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index de14fc373aa9e8b6629dde27a2871b998a0409d5..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF703MBI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_1.fit.json b/ENCSR516RTV/cherimoya.fold_1.fit.json deleted file mode 100644 index d7a0b1e286ce0f21d5297a09965a074ca64b631a..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF703MBI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_1.log b/ENCSR516RTV/cherimoya.fold_1.log deleted file mode 100644 index 640e582ace6f64e5425fd624f48c863fcf42e22f..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 34.90899395942688 3.9490790367126465 496.7685852050781 0.35591238737106323 704.5440063476562 0.2997474670410156 0.8017299 5.907251358032227 True -1 5418 30.205344200134277 3.1225764751434326 382.2328796386719 0.34797587990760803 635.57666015625 0.3756813108921051 0.8352977 1.4003331661224365 True -2 8127 30.170634984970093 0.6782016754150391 392.39141845703125 0.2399752140045166 621.9451904296875 0.39068880677223206 0.8522949 0.6932858824729919 True -3 10836 30.21204924583435 0.6967153549194336 486.4925537109375 0.3370298743247986 615.0315551757812 0.39696988463401794 0.861691 0.6516260504722595 True -4 13545 30.237927436828613 0.6724488735198975 532.6854248046875 0.3922799229621887 608.3458862304688 0.40378862619400024 0.8656173 0.48411667346954346 True -5 16254 30.264141082763672 0.688391923904419 406.9088439941406 0.2622218132019043 604.487060546875 0.40756574273109436 0.87355787 0.38976168632507324 True -6 18963 30.252596139907837 0.6787056922912598 474.2721252441406 0.38058942556381226 604.5385131835938 0.40762409567832947 0.8770592 0.3551581799983978 True -7 21672 30.19367742538452 0.6819913387298584 423.41839599609375 0.2927120625972748 600.2737426757812 0.41199830174446106 0.8828424 0.3298260569572449 True -8 24381 30.250831127166748 0.6913046836853027 516.9114379882812 0.2557685971260071 597.7377319335938 0.4141634404659271 0.8854328 0.3114980161190033 True -9 27090 30.19708228111267 0.6828703880310059 449.8033142089844 0.1750313639640808 594.50341796875 0.4192729890346527 0.8886121 0.304674357175827 True -10 29799 30.198949098587036 0.6831705570220947 447.7259216308594 0.21989858150482178 591.756591796875 0.4229086935520172 0.8932144 0.28449833393096924 True -11 32508 30.26940941810608 0.6817622184753418 468.4716796875 0.20274418592453003 588.4146118164062 0.4265158474445343 0.89655447 0.273654580116272 True -12 35217 30.280441522598267 2.707622528076172 423.763427734375 0.1503702700138092 586.2293701171875 0.4280683994293213 0.90211457 0.23941856622695923 True -13 37926 30.36475110054016 0.7038087844848633 347.35906982421875 0.17659074068069458 584.6260986328125 0.4299495220184326 0.90545404 0.22441549599170685 True -14 40635 30.307515144348145 0.693134069442749 422.330078125 0.15603452920913696 581.9915771484375 0.43296441435813904 0.91120154 0.20406915247440338 True -15 43344 30.283336400985718 0.6945493221282959 427.56085205078125 0.14101576805114746 579.5026245117188 0.4363533854484558 0.9119433 0.19222941994667053 True -16 46053 30.852018117904663 38.15001368522644 439.284912109375 0.15465259552001953 579.8091430664062 0.43553808331489563 0.912295 0.1867869645357132 True -17 48762 30.03668189048767 0.7150635719299316 433.8573913574219 0.1432841718196869 579.9917602539062 0.43423235416412354 0.9153496 0.18177530169487 True -18 51471 29.783018350601196 0.6785862445831299 470.2320556640625 0.15461483597755432 579.9969482421875 0.43460169434547424 0.91365397 0.1811000555753708 False -19 54180 29.725608825683594 3.032024621963501 467.12908935546875 0.13760188221931458 580.264892578125 0.43381914496421814 0.9142258 0.18050901591777802 False diff --git a/ENCSR516RTV/cherimoya.fold_1.performance.tsv b/ENCSR516RTV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b301504fde952c3747306c83d07c984bdd378a0c..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -579.9917602539062 0.36510133743286133 0.43423232436180115 0.1801718920469284 0.9153496026992798 0.9077931046485901 0.18177530169487 \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_2.evaluate.json b/ENCSR516RTV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ae48e080f4480105ffd6df15574de3887f337f62..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF703MBI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_2.fit.json b/ENCSR516RTV/cherimoya.fold_2.fit.json deleted file mode 100644 index cc3152a352b5bf1386b914ed1193f75d09663d02..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF703MBI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_2.log b/ENCSR516RTV/cherimoya.fold_2.log deleted file mode 100644 index 4fb0c50a417be9a3b77f37d4d8c65dd031302182..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 37.3090341091156 32.40190649032593 406.5523376464844 0.27717918157577515 616.8072509765625 0.305573970079422 0.80965626 4.213682174682617 True -1 5762 32.75605487823486 0.6171326637268066 460.357421875 0.3158688247203827 562.6577758789062 0.3751978874206543 0.84331834 1.161028265953064 True -2 8643 37.034584522247314 8.393532514572144 438.96038818359375 0.2782948613166809 554.1693725585938 0.382196307182312 0.8530228 0.5354003310203552 True -3 11524 32.173322439193726 2.1013998985290527 442.0901794433594 0.2878197431564331 548.8350830078125 0.3864327371120453 0.86023885 0.47866448760032654 True -4 14405 32.15781879425049 1.4595396518707275 482.2591552734375 0.30920737981796265 544.6911010742188 0.39163196086883545 0.8649711 0.33774465322494507 True -5 17286 32.233232736587524 2.2096569538116455 439.7303161621094 0.2682831883430481 540.1419067382812 0.3979485332965851 0.86912525 0.3134285807609558 True -6 20167 32.16836404800415 1.7546591758728027 367.81402587890625 0.22431805729866028 538.7604370117188 0.3997814357280731 0.87479484 0.26857829093933105 True -7 23048 37.23513460159302 28.6122088432312 505.4350891113281 0.23305392265319824 536.8637084960938 0.4021555185317993 0.87329304 0.2879640460014343 False -8 25929 32.137208223342896 1.1937000751495361 466.5368957519531 0.3455342650413513 535.255615234375 0.4041723608970642 0.88059735 0.24633069336414337 True -9 28810 32.174103021621704 0.5694108009338379 425.83990478515625 0.28891634941101074 532.2051391601562 0.4084930419921875 0.88469344 0.22548983991146088 True -10 31691 32.09546709060669 0.5647215843200684 392.693603515625 0.28984135389328003 530.7882080078125 0.41035085916519165 0.8887099 0.21240472793579102 True -11 34572 32.15374255180359 0.5594680309295654 386.1924133300781 0.3319324254989624 530.0673217773438 0.41073617339134216 0.89046085 0.21354159712791443 True -12 37453 33.35294151306152 38.24515914916992 412.276123046875 0.2085823118686676 527.6303100585938 0.4152088463306427 0.89482594 0.20163151621818542 True -13 40334 32.25056171417236 0.5696163177490234 385.8533935546875 0.16538697481155396 524.647216796875 0.4200064241886139 0.89882845 0.1909063756465912 True -14 43215 32.212234020233154 0.5631184577941895 491.24530029296875 0.1341823786497116 524.5852661132812 0.41921859979629517 0.9003701 0.1856023520231247 True -15 46096 32.15305161476135 1.2891607284545898 423.3329772949219 0.1623847931623459 524.979248046875 0.41821351647377014 0.90150523 0.1796451359987259 True -16 48977 32.139249086380005 0.5662145614624023 468.69647216796875 0.10998301953077316 523.9853515625 0.4189586937427521 0.902861 0.17741265892982483 True -17 51858 33.09362053871155 37.00879693031311 396.8070373535156 0.13853245973587036 524.4642944335938 0.4184780418872833 0.9041795 0.1753249317407608 True -18 54739 31.99534034729004 0.561091423034668 405.66900634765625 0.18925350904464722 523.9257202148438 0.42014166712760925 0.9031015 0.17628411948680878 False -19 57620 31.709395170211792 0.5730280876159668 450.86700439453125 0.11960907280445099 523.9158325195312 0.42029082775115967 0.9026287 0.17744119465351105 False diff --git a/ENCSR516RTV/cherimoya.fold_2.performance.tsv b/ENCSR516RTV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 15c76c8910e7930577fa5b483f10564cbea29ad9..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -524.4642944335938 0.37847885489463806 0.4184780418872833 0.1620544046163559 0.9041795134544373 0.8898681402206421 0.1753249317407608 \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_3.evaluate.json b/ENCSR516RTV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7f3c662493b2ef5a99e7a08b888f0f8f3ac45030..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF703MBI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_3.fit.json b/ENCSR516RTV/cherimoya.fold_3.fit.json deleted file mode 100644 index 9f78897b21bc1988a1fed18b28e7d027f33f8573..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF703MBI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_3.log b/ENCSR516RTV/cherimoya.fold_3.log deleted file mode 100644 index 20249f84697803e894c4a3de939ebd0d7d525880..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 35.35371494293213 3.448758125305176 472.3841552734375 0.3140139877796173 580.860595703125 0.3141658902168274 0.8048179 4.841262340545654 True -1 5510 30.708922863006592 0.5451018810272217 445.9459533691406 0.519544243812561 533.1511840820312 0.3799740970134735 0.8444011 1.131910800933838 True -2 8265 30.748387098312378 0.5297343730926514 520.042724609375 0.3143307864665985 520.6602172851562 0.3932284414768219 0.8582926 0.5420154929161072 True -3 11020 30.668148517608643 0.5473062992095947 416.79248046875 0.24158939719200134 520.1594848632812 0.3927611708641052 0.8602881 0.513443112373352 True -4 13775 30.704181909561157 0.5351643562316895 458.2278137207031 0.28773415088653564 513.812744140625 0.3998425304889679 0.86873597 0.3786197304725647 True -5 16530 30.692052841186523 0.5326611995697021 394.6322326660156 0.19336126744747162 513.1151733398438 0.4006253182888031 0.8660145 0.4242400527000427 False -6 19285 30.707817316055298 2.474268913269043 447.87884521484375 0.27354171872138977 508.7503967285156 0.40748462080955505 0.87575316 0.3155927360057831 True -7 22040 30.76810646057129 12.438111543655396 396.89764404296875 0.26170727610588074 507.23870849609375 0.40832361578941345 0.88197017 0.2768710255622864 True -8 24795 36.149136781692505 14.528376579284668 550.1397094726562 0.19982293248176575 505.2420654296875 0.41043469309806824 0.88550854 0.2620587646961212 True -9 27550 30.845468282699585 16.03202223777771 333.77496337890625 0.3333531320095062 503.6239318847656 0.4127117991447449 0.88620645 0.23954373598098755 True -10 30305 30.80997133255005 33.41638469696045 417.1764221191406 0.15169452130794525 501.6287841796875 0.41618311405181885 0.8905269 0.23215104639530182 True -11 33060 30.901928901672363 0.5548419952392578 504.72833251953125 0.1514914333820343 500.3332214355469 0.4171227812767029 0.89387006 0.2169703245162964 True -12 35815 30.75591230392456 1.5938572883605957 434.4697570800781 0.24790966510772705 498.5077209472656 0.4200707674026489 0.8975747 0.2031652331352234 True -13 38570 30.74685549736023 0.5316441059112549 372.4271545410156 0.14886508882045746 498.0587158203125 0.4190863370895386 0.901262 0.19806966185569763 True -14 41325 30.72225284576416 0.5294342041015625 375.150390625 0.19686836004257202 496.7445068359375 0.4206397831439972 0.9029934 0.1846710741519928 True -15 44080 30.708643913269043 0.5272159576416016 455.98394775390625 0.2641173303127289 495.4619140625 0.42313188314437866 0.90678334 0.18133054673671722 True -16 46835 30.650453090667725 0.5266923904418945 381.866455078125 0.1494918167591095 494.6554260253906 0.4249162971973419 0.9080624 0.17563974857330322 True -17 49590 30.66511344909668 0.5349266529083252 441.03277587890625 0.214142844080925 494.8631591796875 0.4237774908542633 0.90878874 0.1731969118118286 True -18 52345 31.185702323913574 8.033775329589844 464.10833740234375 0.12417121976613998 495.59197998046875 0.42267441749572754 0.9109261 0.17302186787128448 True -19 55100 30.163216590881348 0.5292294025421143 509.4715576171875 0.12886664271354675 494.9991760253906 0.42421936988830566 0.91007066 0.1729804128408432 False diff --git a/ENCSR516RTV/cherimoya.fold_3.performance.tsv b/ENCSR516RTV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d4b2abe25d6a694e4a9eef49528ffebf3e6932b8..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -495.59197998046875 0.37974122166633606 0.4226744771003723 0.15961474180221558 0.910926103591919 0.8806101679801941 0.17302186787128448 \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_4.evaluate.json b/ENCSR516RTV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 983ba72ba69d97956df494834a4a78f9b8b7a64f..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF703MBI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_4.fit.json b/ENCSR516RTV/cherimoya.fold_4.fit.json deleted file mode 100644 index 2f21527712ee4d9bf669b4efd434b645a4d7f73d..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF703MBI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516RTV/cherimoya.fold_4.log b/ENCSR516RTV/cherimoya.fold_4.log deleted file mode 100644 index 4a33edae210d3abf8e6e1a2a70f76722d36daa4a..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2789 35.962899923324585 3.816659450531006 414.70635986328125 0.3590599298477173 555.0827026367188 0.30414772033691406 0.80859345 4.4517669677734375 True -1 5578 31.1052029132843 0.6232397556304932 399.5483703613281 0.21469002962112427 505.16241455078125 0.36824309825897217 0.8366986 0.9405091404914856 True -2 8367 31.122685194015503 0.6013274192810059 410.65521240234375 0.311140775680542 496.52069091796875 0.37970536947250366 0.8520376 0.449403315782547 True -3 11156 31.04189682006836 0.5981900691986084 352.1446533203125 0.3138999342918396 494.0234680175781 0.38047507405281067 0.8599141 0.4156615138053894 True -4 13945 31.03526210784912 0.5994575023651123 503.05889892578125 0.2918764054775238 490.760986328125 0.3865886628627777 0.8620653 0.30581480264663696 True -5 16734 32.8741614818573 2.5527584552764893 412.65167236328125 0.5002402067184448 488.01470947265625 0.39127519726753235 0.87236625 0.2852039635181427 True -6 19523 31.281248331069946 1.0542330741882324 432.978271484375 0.1947903335094452 486.55438232421875 0.3933441638946533 0.87370175 0.276205450296402 True -7 22312 31.149765968322754 0.5986809730529785 365.08331298828125 0.2311040610074997 484.9586486816406 0.3949085772037506 0.87820023 0.25886839628219604 True -8 25101 31.10749101638794 0.5935385227203369 528.681884765625 0.3653012216091156 483.58154296875 0.39685243368148804 0.8829466 0.25122758746147156 True -9 27890 31.08840823173523 0.602158784866333 423.0964660644531 0.28790873289108276 481.2765197753906 0.40083804726600647 0.8859746 0.2161862850189209 True -10 30679 31.30884838104248 0.5978145599365234 462.50933837890625 0.13712021708488464 480.8435363769531 0.40066707134246826 0.8909802 0.20888639986515045 True -11 33468 31.283814907073975 0.5963494777679443 457.67681884765625 0.15580902993679047 478.6604919433594 0.404836505651474 0.8955693 0.19317710399627686 True -12 36257 31.158929109573364 0.6121695041656494 417.1844177246094 0.20663884282112122 477.2132263183594 0.4068591296672821 0.8978485 0.1772272139787674 True -13 39046 31.219065189361572 0.6031594276428223 425.5658264160156 0.2622382640838623 476.2585144042969 0.4084053337574005 0.90169555 0.16895166039466858 True -14 41835 31.128979921340942 0.5941073894500732 416.22393798828125 0.16895964741706848 476.21319580078125 0.40807586908340454 0.90462476 0.1611819565296173 True -15 44624 31.11689043045044 0.5986912250518799 432.2315979003906 0.1775585114955902 474.7685546875 0.41078007221221924 0.9083851 0.155137300491333 True -16 47413 31.124221801757812 0.5934617519378662 468.92669677734375 0.15687525272369385 476.037109375 0.40803831815719604 0.9097655 0.15062661468982697 True -17 50202 31.057109832763672 2.6189382076263428 389.2660827636719 0.16849640011787415 475.0190124511719 0.4094581604003906 0.91054356 0.14772188663482666 True -18 52991 30.64839816093445 32.00367045402527 461.48040771484375 0.15562856197357178 475.1429138183594 0.4099436104297638 0.91084534 0.14788201451301575 True -19 55780 31.591805458068848 1.5487370491027832 401.67950439453125 0.17674878239631653 475.2300720214844 0.4096413552761078 0.91122293 0.1486101746559143 True diff --git a/ENCSR516RTV/cherimoya.fold_4.performance.tsv b/ENCSR516RTV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a808c89aeda44f2f166c2212e70389fe3631c668..0000000000000000000000000000000000000000 --- a/ENCSR516RTV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.2300720214844 0.3886658847332001 0.4096413552761078 0.15258169174194336 0.9112229347229004 0.8838986158370972 0.1486101746559143 \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_0.evaluate.json b/ENCSR516YAD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 22c05dcbcb046f2cce67e8c04e31dbec45607972..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354JBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_0.fit.json b/ENCSR516YAD/cherimoya.fold_0.fit.json deleted file mode 100644 index 6472f9d50caf5de6a7c6e60e46fbc6aadcee8158..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF354JBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_0.log b/ENCSR516YAD/cherimoya.fold_0.log deleted file mode 100644 index 72f648c384e9ddc06e8a9b367abbb287fa05dd87..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2981 38.035120487213135 3.70487642288208 657.0416870117188 0.9300507307052612 871.2488403320312 0.6569845676422119 0.71536875 12.056520462036133 True -1 5962 34.76650619506836 21.710355520248413 599.1181640625 1.3759276866912842 719.7512817382812 0.7366079092025757 0.75319874 2.494415044784546 True -2 8943 33.42452883720398 0.6179180145263672 717.5362548828125 1.3706820011138916 695.0731811523438 0.7504971027374268 0.7550703 1.0328508615493774 True -3 11924 33.44198179244995 0.6388115882873535 503.1083984375 1.6617040634155273 687.2871704101562 0.7558653354644775 0.75332326 0.9223227500915527 False -4 14905 33.50909614562988 0.6221926212310791 671.522216796875 1.4908841848373413 681.1781616210938 0.7600011825561523 0.75937444 0.7889902591705322 True -5 17886 33.483837366104126 1.0627110004425049 646.6599731445312 1.3761353492736816 676.6443481445312 0.761906623840332 0.7570874 0.7363293766975403 False -6 20867 33.391061544418335 0.6285314559936523 617.997802734375 1.5452234745025635 673.596435546875 0.7640243172645569 0.76464725 0.7222299575805664 True -7 23848 33.47421169281006 0.6267223358154297 696.6712646484375 1.3586690425872803 669.4264526367188 0.7668593525886536 0.76658714 0.7037807106971741 True -8 26829 33.405436992645264 0.6325852870941162 571.836181640625 0.6732858419418335 667.2288818359375 0.7687973380088806 0.7721824 0.6877861618995667 True -9 29810 33.499645948410034 0.6254544258117676 592.655029296875 0.7660585641860962 662.9368286132812 0.7708688378334045 0.7745271 0.6626085638999939 True -10 32791 33.39888000488281 0.6425714492797852 517.1903076171875 0.9688119292259216 659.5633544921875 0.7733303308486938 0.77850205 0.6614044308662415 True -11 35772 33.31216502189636 0.6146581172943115 549.4921264648438 0.7680830955505371 655.7206420898438 0.7754842638969421 0.7881068 0.6372926831245422 True -12 38753 35.23701739311218 32.602051973342896 492.4049072265625 0.620875358581543 652.266357421875 0.7777112126350403 0.7938227 0.6111077070236206 True -13 41734 32.795429944992065 0.6183147430419922 475.0214538574219 0.7544651031494141 648.6383666992188 0.7800145149230957 0.7985123 0.5920490026473999 True -14 44715 32.61508917808533 0.6057679653167725 548.990234375 0.6026185154914856 645.8040771484375 0.7818375825881958 0.8076064 0.573733925819397 True -15 47696 32.62080478668213 0.6047279834747314 509.55621337890625 0.4484289586544037 644.0592651367188 0.7831670045852661 0.8125972 0.5787436962127686 True -16 50677 32.588523387908936 0.6134474277496338 455.7335205078125 0.6720072627067566 642.9432373046875 0.7838271856307983 0.8141608 0.5819635987281799 True -17 53658 32.606041431427 0.6111512184143066 467.5328369140625 0.5467000007629395 642.839599609375 0.783815860748291 0.81321716 0.5890557765960693 False -18 56639 32.56110405921936 0.6150193214416504 558.82421875 0.5750340223312378 643.4629516601562 0.7835478186607361 0.81331766 0.5995945334434509 False -19 59620 32.5863516330719 1.089198350906372 510.9584045410156 0.5789928436279297 643.9122314453125 0.7832660675048828 0.8131606 0.6055787801742554 False diff --git a/ENCSR516YAD/cherimoya.fold_0.performance.tsv b/ENCSR516YAD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ebe4e80f4a4551777cd59cbfe7b92bcb71deaa0c..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -642.9432373046875 0.18137861788272858 0.7838271856307983 0.40272292494773865 0.8141608238220215 0.7644818425178528 0.5819635987281799 \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_1.evaluate.json b/ENCSR516YAD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0c7934141f1e5503f8700a7a7951fa5f66db7ecb..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354JBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_1.fit.json b/ENCSR516YAD/cherimoya.fold_1.fit.json deleted file mode 100644 index 79fc9f199e122e6241b2536a795133cfa5b4c309..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF354JBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_1.log b/ENCSR516YAD/cherimoya.fold_1.log deleted file mode 100644 index aa2e9f1d392f29fe09103fff293d2f67100df85a..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2974 38.32934379577637 4.723412036895752 511.3434143066406 1.9864599704742432 1048.781982421875 0.6749208569526672 0.71521103 8.703941345214844 True -1 5948 33.26167273521423 0.8198480606079102 533.9284057617188 0.9538309574127197 858.872802734375 0.7504715919494629 0.76392156 2.8504488468170166 True -2 8922 33.23064923286438 0.7561354637145996 565.198486328125 1.1663415431976318 830.8600463867188 0.7632364630699158 0.76900214 1.5336672067642212 True -3 11896 33.226144552230835 0.7520925998687744 549.45556640625 0.8592663407325745 816.9019775390625 0.7703073024749756 0.7746908 1.2101045846939087 True -4 14870 33.314610719680786 1.469334363937378 627.803466796875 1.4177186489105225 808.7400512695312 0.7733856439590454 0.77571046 0.9410072565078735 True -5 17844 33.17779231071472 0.7589383125305176 507.88861083984375 1.2352975606918335 800.6080322265625 0.7775276899337769 0.7775178 0.9095142483711243 True -6 20818 33.11682677268982 0.7414908409118652 436.40777587890625 1.6821578741073608 795.998046875 0.7794919013977051 0.78133863 0.8116887211799622 True -7 23792 33.17817997932434 0.7552540302276611 560.297607421875 0.9322628974914551 791.2006225585938 0.78160160779953 0.7852308 0.7720288634300232 True -8 26766 33.12154006958008 42.776400089263916 552.7601318359375 0.8716160655021667 786.1087646484375 0.7842446565628052 0.78961915 0.7500119209289551 True -9 29740 33.22676372528076 1.3197104930877686 505.7115173339844 1.0056079626083374 779.9657592773438 0.787077784538269 0.7954632 0.6943737864494324 True -10 32714 33.13354825973511 1.5736119747161865 476.68304443359375 1.0088591575622559 774.2807006835938 0.7893701195716858 0.798572 0.6615481972694397 True -11 35688 33.01545977592468 0.7353405952453613 668.2916259765625 0.794463574886322 769.0015258789062 0.7919264435768127 0.80513406 0.6303409337997437 True -12 38662 32.68404507637024 1.7831647396087646 544.3487548828125 0.9407142996788025 763.7888793945312 0.7939305305480957 0.80967647 0.6152437925338745 True -13 41636 32.72819924354553 0.7421221733093262 534.5748901367188 0.882617175579071 759.470947265625 0.7960578203201294 0.8156066 0.5961708426475525 True -14 44610 32.49962115287781 0.7337987422943115 558.7675170898438 0.7864842414855957 756.502197265625 0.7976349592208862 0.8211972 0.5954633951187134 True -15 47584 32.50211548805237 0.742328405380249 494.6797790527344 0.5366549491882324 754.6663208007812 0.798793613910675 0.8263702 0.5826843976974487 True -16 50558 32.520846366882324 0.7443788051605225 487.6639404296875 0.6762837767601013 753.6441040039062 0.7993390560150146 0.8304918 0.5787115693092346 True -17 53532 32.53808283805847 0.73624587059021 547.15380859375 0.787879467010498 753.7304077148438 0.7994211912155151 0.8302272 0.5907586812973022 False -18 56506 32.5966100692749 0.7309243679046631 522.7413940429688 0.6300203800201416 754.0242309570312 0.7992210388183594 0.8297402 0.6024976372718811 False -19 59480 32.463594913482666 34.06311893463135 467.8216552734375 0.5373889207839966 754.5813598632812 0.7990733981132507 0.8308155 0.6085681915283203 True diff --git a/ENCSR516YAD/cherimoya.fold_1.performance.tsv b/ENCSR516YAD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e739bacb3e5cf2c092beba0cd9284d415c751efe..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -754.5813598632812 0.16415375471115112 0.7990733981132507 0.4541182816028595 0.8308154940605164 0.8098730444908142 0.6085681915283203 \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_2.evaluate.json b/ENCSR516YAD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 68d08c19b92195e8a5ef2fc8008b2823268c0f4c..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354JBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_2.fit.json b/ENCSR516YAD/cherimoya.fold_2.fit.json deleted file mode 100644 index 718f237c1250dc1abe330aa47f6898bb17f99587..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF354JBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_2.log b/ENCSR516YAD/cherimoya.fold_2.log deleted file mode 100644 index ea2e7918af58a41a8f14ed6fd93bf2d8af928dac..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3205 40.16744589805603 4.538222074508667 494.6056823730469 1.6031827926635742 925.172607421875 0.6738299131393433 0.7138239 8.262327194213867 True -1 6410 35.84869027137756 2.1897640228271484 392.6217041015625 1.8613371849060059 776.696533203125 0.7412794232368469 0.7663354 1.8921325206756592 True -2 9615 35.748303174972534 0.7589635848999023 597.4880981445312 1.5975182056427002 752.9881591796875 0.751630961894989 0.7732103 1.1130539178848267 True -3 12820 35.75030493736267 0.5877931118011475 661.3861083984375 1.3653452396392822 743.5146484375 0.7562751770019531 0.7805451 0.85036301612854 True -4 16025 35.74763512611389 0.5853030681610107 560.177734375 1.0923337936401367 736.9208374023438 0.7613757252693176 0.7839916 0.734470546245575 True -5 19230 35.67853498458862 1.4738445281982422 408.59381103515625 0.9031240940093994 732.591796875 0.7639416456222534 0.78694475 0.6661496758460999 True -6 22435 35.760600090026855 0.5829012393951416 509.7376708984375 1.4144973754882812 726.2609252929688 0.7663047909736633 0.78824997 0.6587104201316833 True -7 25640 35.768462896347046 0.6040620803833008 583.6057739257812 0.8161718249320984 721.5601196289062 0.7686441540718079 0.79245645 0.6373527646064758 True -8 28845 35.819122076034546 0.5827915668487549 541.0247802734375 0.9709227085113525 716.8469848632812 0.7709178924560547 0.7954713 0.6331925392150879 True -9 32050 35.12628436088562 0.585355281829834 557.8331298828125 0.7241685390472412 711.8262329101562 0.773978590965271 0.7991857 0.6173697710037231 True -10 35255 34.9994637966156 0.578934907913208 536.0159912109375 0.9030859470367432 706.4050903320312 0.7764354348182678 0.8044323 0.6106777191162109 True -11 38460 35.15746784210205 0.5704054832458496 509.6370849609375 0.6381201148033142 701.9339599609375 0.7789978981018066 0.80616874 0.601559042930603 True -12 41665 35.01017928123474 0.5975503921508789 531.2724609375 0.7492009997367859 697.8838500976562 0.7814413905143738 0.8120023 0.597661018371582 True -13 44870 35.21186065673828 0.5913522243499756 575.6541137695312 1.0578272342681885 693.377197265625 0.7836413979530334 0.816804 0.590901255607605 True -14 48075 35.073277950286865 0.5879549980163574 549.3651123046875 0.7102347612380981 691.206298828125 0.7852387428283691 0.8202887 0.5795995593070984 True -15 51280 35.233548402786255 7.751216650009155 400.4678955078125 0.9876036047935486 688.9346923828125 0.7865614891052246 0.82474935 0.5733349919319153 True -16 54485 35.38231706619263 0.5987453460693359 521.13037109375 0.7594636678695679 688.4158325195312 0.7874212265014648 0.8292959 0.565788984298706 True -17 57690 35.74667716026306 25.373964548110962 491.7474365234375 0.7107807397842407 688.1849365234375 0.787590503692627 0.82805425 0.5766738057136536 False -18 60895 41.358221769332886 0.5998978614807129 513.16259765625 0.6486226320266724 688.4680786132812 0.7873967885971069 0.826427 0.5846091508865356 False -19 64100 35.52085566520691 0.5860130786895752 428.6036682128906 0.42069536447525024 689.1480102539062 0.787126898765564 0.82544976 0.5929995775222778 False diff --git a/ENCSR516YAD/cherimoya.fold_2.performance.tsv b/ENCSR516YAD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 22f37ecb1795921dbd21e1b2d45112cdb10160bd..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -688.4158325195312 0.1763799488544464 0.7874212265014648 0.42141321301460266 0.8292958736419678 0.7915164828300476 0.565788984298706 \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_3.evaluate.json b/ENCSR516YAD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index dfd0efbff4d061257439ed7177f2cc797792b83d..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354JBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_3.fit.json b/ENCSR516YAD/cherimoya.fold_3.fit.json deleted file mode 100644 index a711ef080caf83aaaf3c0acf29adb545372e0cb0..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF354JBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_3.log b/ENCSR516YAD/cherimoya.fold_3.log deleted file mode 100644 index ea9e868d88a7ef7d495905cd7bad5bf8c517a3cf..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3051 40.570958375930786 3.818302631378174 599.0943603515625 1.1948553323745728 878.166748046875 0.6620775461196899 0.70126694 7.938440322875977 True -1 6102 34.06791138648987 0.6308443546295166 546.171875 1.4739505052566528 723.4650268554688 0.7363272309303284 0.74520284 2.1127092838287354 True -2 9153 34.155855655670166 0.5862517356872559 455.90704345703125 1.3293626308441162 703.9166870117188 0.7470588684082031 0.7519702 1.0501443147659302 True -3 12204 34.014585733413696 11.049319982528687 530.4415893554688 1.5072957277297974 691.3451538085938 0.7546783089637756 0.75518674 0.9262368679046631 True -4 15255 34.87562608718872 0.5949540138244629 572.0599365234375 1.324958086013794 685.6249389648438 0.7591488361358643 0.75546 0.8167244791984558 True -5 18306 34.16483426094055 0.5889909267425537 614.7069091796875 1.1161746978759766 680.661865234375 0.7624752521514893 0.7594892 0.7697814106941223 True -6 21357 34.05707097053528 0.5793502330780029 585.419189453125 1.102886438369751 676.2597045898438 0.7654033303260803 0.7616436 0.7175450325012207 True -7 24408 34.276819705963135 0.5945446491241455 621.9637451171875 0.6194484829902649 672.5115356445312 0.7675929665565491 0.7623025 0.7051308751106262 True -8 27459 33.35138273239136 0.5808625221252441 535.076904296875 1.132903814315796 668.7389526367188 0.7701186537742615 0.7634197 0.7081228494644165 True -9 30510 33.3134548664093 0.583465576171875 604.322021484375 0.9070969820022583 664.0045166015625 0.7725107669830322 0.7656632 0.6852907538414001 True -10 33561 33.40823841094971 24.058103799819946 567.9351196289062 1.1785465478897095 660.937255859375 0.7745341658592224 0.77289724 0.6675492525100708 True -11 36612 36.009469509124756 0.5817360877990723 579.1104736328125 0.7472085952758789 657.8316040039062 0.7762722373008728 0.779355 0.6590853929519653 True -12 39663 33.45542788505554 1.4460721015930176 672.4741821289062 0.8739020824432373 653.9459838867188 0.7785093784332275 0.78619736 0.6399266123771667 True -13 42714 33.43225574493408 1.503629207611084 525.9923706054688 0.5600616931915283 651.5250244140625 0.7803032398223877 0.7917153 0.6343222260475159 True -14 45765 33.4524040222168 0.5872852802276611 446.86016845703125 0.5528739094734192 649.6472778320312 0.781474769115448 0.80142796 0.6184126138687134 True -15 48816 34.5120804309845 0.5917482376098633 538.3446655273438 0.7378134727478027 647.4194946289062 0.782539963722229 0.804414 0.6150781512260437 True -16 51867 35.384820222854614 33.43654489517212 612.5671997070312 0.5596898794174194 646.9910278320312 0.783013641834259 0.80598897 0.6226344704627991 True -17 54918 33.89476299285889 0.581254243850708 492.8429870605469 0.6849738359451294 647.1774291992188 0.7829135060310364 0.80741125 0.6327387690544128 True -18 57969 33.428688526153564 0.5747644901275635 423.32373046875 0.48532119393348694 648.06005859375 0.782343327999115 0.80864537 0.6485803723335266 True -19 61020 33.33156991004944 0.8340754508972168 518.0442504882812 0.29798465967178345 648.1849975585938 0.7821498513221741 0.80775326 0.651736855506897 False diff --git a/ENCSR516YAD/cherimoya.fold_3.performance.tsv b/ENCSR516YAD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bc5c0cca301b5672bbc045b962bf65b9cbe187db..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -648.06005859375 0.1817859560251236 0.7823433876037598 0.39946407079696655 0.8086453676223755 0.7512203454971313 0.6485803723335266 \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_4.evaluate.json b/ENCSR516YAD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 21d0014102526aebb577b4f017d20e294cb6b4dd..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354JBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_4.fit.json b/ENCSR516YAD/cherimoya.fold_4.fit.json deleted file mode 100644 index 727ddc65e60731cb3e18d2725c1b775f0d4cb257..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF354JBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR516YAD/cherimoya.fold_4.log b/ENCSR516YAD/cherimoya.fold_4.log deleted file mode 100644 index 709bcf56ef7af94c68e67553563c131352f24851..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3083 39.12562870979309 34.30328893661499 517.0584106445312 1.8001458644866943 808.4417724609375 0.6593064069747925 0.707988 9.351292610168457 True -1 6166 34.72077512741089 0.6715574264526367 500.3938293457031 1.7614095211029053 689.493408203125 0.7305195331573486 0.75014275 2.7333524227142334 True -2 9249 34.442950963974 0.6480731964111328 539.1891479492188 1.3151918649673462 665.9037475585938 0.745654284954071 0.7567068 1.4427720308303833 True -3 12332 34.35745549201965 0.6446235179901123 557.1317749023438 0.9929443001747131 655.7874755859375 0.7532525658607483 0.75983655 0.9471438527107239 True -4 15415 34.367511510849 0.9891948699951172 665.7044067382812 1.476269006729126 650.7177734375 0.7570312023162842 0.75964785 0.7861828207969666 False -5 18498 34.67531442642212 25.458807468414307 614.3458862304688 1.1013466119766235 646.1119995117188 0.7597663998603821 0.7594878 0.7416324615478516 False -6 21581 34.64712452888489 38.04997801780701 628.7080078125 0.9570946097373962 643.0537719726562 0.7623602151870728 0.7597394 0.6809148192405701 False -7 24664 35.29189848899841 30.364977836608887 588.1175537109375 1.1478209495544434 638.8734741210938 0.7644444704055786 0.77050614 0.6174901127815247 True -8 27747 33.73211908340454 0.6525909900665283 540.4286499023438 0.928102970123291 635.5596923828125 0.7670014500617981 0.7769924 0.5975619554519653 True -9 30830 33.763155460357666 0.6513049602508545 505.3433837890625 0.8386003971099854 632.0323486328125 0.7694492340087891 0.7810586 0.5800253748893738 True -10 33913 33.95223379135132 1.4068634510040283 490.1817932128906 0.9313105344772339 628.17919921875 0.7720430493354797 0.7832987 0.5744608640670776 True -11 36996 33.87060594558716 1.1056711673736572 496.9101867675781 0.6400958299636841 624.3499145507812 0.7742564082145691 0.78950197 0.5582315325737 True -12 40079 33.89386701583862 0.6641488075256348 502.8771667480469 0.8213841915130615 621.1430053710938 0.7765898704528809 0.7931802 0.5512627363204956 True -13 43162 33.80589032173157 0.6467962265014648 562.9667358398438 0.8761885166168213 618.9783325195312 0.7785331606864929 0.7995101 0.5373263955116272 True -14 46245 34.1220645904541 16.08379554748535 554.7517700195312 0.814200222492218 616.462890625 0.7803736329078674 0.80529886 0.5273163914680481 True -15 49328 34.79809761047363 34.310622692108154 453.93902587890625 0.8624992370605469 615.2058715820312 0.7815361618995667 0.8075211 0.5229701399803162 True -16 52411 35.27365279197693 35.72148847579956 498.67803955078125 0.7982929944992065 614.48583984375 0.782159686088562 0.81160045 0.5266897082328796 True -17 55494 34.370574712753296 0.6419095993041992 380.02508544921875 1.0122170448303223 614.6796264648438 0.7819358110427856 0.81011015 0.5370596647262573 False -18 58577 33.71050453186035 0.6287820339202881 462.82574462890625 0.5546175837516785 615.6451416015625 0.7816188335418701 0.8087541 0.5502731204032898 False -19 61660 33.65968728065491 0.6412041187286377 525.6764526367188 0.6801034212112427 616.07861328125 0.7813736796379089 0.8065611 0.5577673316001892 False diff --git a/ENCSR516YAD/cherimoya.fold_4.performance.tsv b/ENCSR516YAD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d6ec77e26eb69043c28998251a75772e85c2f474..0000000000000000000000000000000000000000 --- a/ENCSR516YAD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -614.48583984375 0.18458783626556396 0.782159686088562 0.39151298999786377 0.8116004467010498 0.7589452862739563 0.5266897082328796 \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_0.evaluate.json b/ENCSR517NHP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c748c46eadd491e97dfafde9c6014eeef7674431..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF530BGE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_0.fit.json b/ENCSR517NHP/cherimoya.fold_0.fit.json deleted file mode 100644 index e65d82fe273134b98f48c1d710ae9dd6f303fec1..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF530BGE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_0.log b/ENCSR517NHP/cherimoya.fold_0.log deleted file mode 100644 index 30b473fa9de364cf50b2650280da98d1f2f14457..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.85888743400574 3.542781352996826 452.6319580078125 1.0957163572311401 591.62353515625 0.20857058465480804 0.51191425 5.443037986755371 True -1 5510 30.277058124542236 0.5847127437591553 397.862548828125 0.927524983882904 538.950927734375 0.32154524326324463 0.6344865 2.007070302963257 True -2 8265 30.29828119277954 0.60260009765625 387.81219482421875 0.743252158164978 530.7111206054688 0.33327654004096985 0.6326713 0.9448941946029663 False -3 11020 30.2601478099823 0.5755276679992676 440.45819091796875 1.6600595712661743 526.4786376953125 0.3407956659793854 0.64295775 0.70905601978302 True -4 13775 30.344867944717407 0.5701501369476318 426.952880859375 0.9073910713195801 524.080810546875 0.3454836905002594 0.65667725 0.6697515249252319 True -5 16530 30.350449562072754 4.336776971817017 411.91485595703125 0.7733156681060791 523.25927734375 0.347018301486969 0.6550997 0.6461634039878845 False -6 19285 30.329684257507324 0.651334285736084 338.6464538574219 0.6483774781227112 521.4935913085938 0.35093584656715393 0.66455996 0.6468849182128906 True -7 22040 30.31592869758606 0.6059997081756592 492.99859619140625 0.7021307945251465 520.7357788085938 0.35211727023124695 0.6727032 0.6337738037109375 True -8 24795 30.388997793197632 0.589482307434082 414.7160949707031 0.42069992423057556 518.4180908203125 0.35724255442619324 0.67689496 0.6017937660217285 True -9 27550 30.43580198287964 0.5790929794311523 408.50787353515625 0.8053740859031677 517.7108764648438 0.35827726125717163 0.6833401 0.6119931936264038 True -10 30305 29.876660346984863 0.5803086757659912 421.487548828125 0.7677018046379089 515.8224487304688 0.3611522614955902 0.6940055 0.5967702269554138 True -11 33060 29.737701892852783 0.5785408020019531 426.43817138671875 0.416503369808197 514.36669921875 0.3635181486606598 0.7053836 0.5509343147277832 True -12 35815 29.737340927124023 0.5798475742340088 363.73046875 0.5011003613471985 512.5603637695312 0.3680335283279419 0.7140325 0.5129336714744568 True -13 38570 29.766801118850708 0.5802993774414062 373.30230712890625 0.6009091138839722 510.999267578125 0.37081611156463623 0.72505516 0.4793754816055298 True -14 41325 29.75270938873291 0.5862364768981934 365.1787414550781 0.6043241024017334 510.1739196777344 0.3721778988838196 0.7373322 0.4581068456172943 True -15 44080 29.75234580039978 0.5827257633209229 429.8500671386719 0.40674054622650146 509.2559509277344 0.3742971122264862 0.74476194 0.4330768883228302 True -16 46835 29.73492431640625 1.1966068744659424 453.5548095703125 0.7588340044021606 509.5918884277344 0.3730447292327881 0.7462259 0.4275397062301636 True -17 49590 29.762319803237915 0.5681726932525635 424.29486083984375 0.24138855934143066 508.36785888671875 0.37673547863960266 0.749951 0.4244373142719269 True -18 52345 29.82313084602356 0.5849525928497314 430.2128601074219 0.4643478989601135 508.7336120605469 0.3761424422264099 0.7494149 0.4250721037387848 False -19 55100 29.8108229637146 0.5842645168304443 429.6164855957031 0.24814292788505554 508.77685546875 0.375936359167099 0.7483971 0.4293505549430847 False diff --git a/ENCSR517NHP/cherimoya.fold_0.performance.tsv b/ENCSR517NHP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 221bb8a04419c70bb59607c53db3a6cd5c96d80a..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -508.36785888671875 0.4075809121131897 0.37673547863960266 0.14078794419765472 0.7499510049819946 0.6983224749565125 0.4244373142719269 \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_1.evaluate.json b/ENCSR517NHP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 36798bfbdd3936a797273256aa6ad5ee9871a5d5..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF530BGE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_1.fit.json b/ENCSR517NHP/cherimoya.fold_1.fit.json deleted file mode 100644 index d61c4e60380057a85cda5866a5d2e88b03fc62c6..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF530BGE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_1.log b/ENCSR517NHP/cherimoya.fold_1.log deleted file mode 100644 index 1d0028b50debae8ca49857754e56c361a8d32185..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 34.89186429977417 3.510589838027954 553.6018676757812 0.7748068571090698 686.9218139648438 0.21128539741039276 0.5654216 5.976193428039551 True -1 5504 30.58993148803711 0.9569015502929688 411.9498291015625 0.8562647700309753 616.9495239257812 0.3354802131652832 0.6723731 2.2449371814727783 True -2 8256 30.31705403327942 0.65411376953125 380.5923767089844 0.7836600542068481 603.5860595703125 0.3538573682308197 0.68305063 0.9387087225914001 True -3 11008 30.335711002349854 0.6544942855834961 471.35040283203125 1.089011788368225 600.4002685546875 0.3566344976425171 0.68983895 0.8098500967025757 True -4 13760 30.327646017074585 0.6561880111694336 468.361328125 0.5879632234573364 598.2554321289062 0.35916683077812195 0.7054684 0.8215707540512085 True -5 16512 30.26586604118347 0.6568219661712646 398.1035461425781 1.0155456066131592 595.831298828125 0.3638860583305359 0.7120824 0.7783101201057434 True -6 19264 30.334244966506958 0.6849491596221924 316.9324645996094 1.2680290937423706 593.8396606445312 0.36704474687576294 0.71985584 0.7119482755661011 True -7 22016 30.36997699737549 0.684077262878418 332.8128662109375 0.44760698080062866 592.4026489257812 0.3690774738788605 0.72168666 0.7088477611541748 True -8 24768 30.2833149433136 18.628646850585938 337.3245849609375 0.4496667981147766 589.8893432617188 0.37281301617622375 0.72966063 0.6427118182182312 True -9 27520 30.27892804145813 1.6806907653808594 442.3979797363281 0.5575450658798218 588.0899658203125 0.37592533230781555 0.7353219 0.6060170531272888 True -10 30272 30.30042004585266 0.6846566200256348 382.18536376953125 0.6612132787704468 586.4561767578125 0.37794479727745056 0.74427277 0.5702541470527649 True -11 33024 30.30073833465576 0.6831021308898926 333.1120300292969 0.7018319368362427 582.66845703125 0.3848140239715576 0.7529233 0.5445737838745117 True -12 35776 30.017800331115723 0.6656966209411621 455.3791809082031 0.619362473487854 582.3333740234375 0.3852623403072357 0.75937814 0.53842693567276 True -13 38528 29.776204109191895 0.6773867607116699 360.077392578125 0.5192899703979492 580.212646484375 0.38839009404182434 0.7697552 0.49320411682128906 True -14 41280 29.717072010040283 0.6767783164978027 348.0000305175781 0.5414707064628601 579.1270141601562 0.3894749879837036 0.7758476 0.4737032353878021 True -15 44032 29.719760417938232 0.6570484638214111 402.3902282714844 0.4154316782951355 578.8309326171875 0.39137932658195496 0.7825745 0.4497591257095337 True -16 46784 29.71846079826355 0.680213212966919 369.55462646484375 0.4300738275051117 577.4738159179688 0.39303743839263916 0.78783166 0.4371059536933899 True -17 49536 29.7454195022583 0.685713529586792 404.669921875 0.4514472484588623 578.2216186523438 0.39056286215782166 0.79070735 0.4322149455547333 True -18 52288 29.72282385826111 0.8090507984161377 402.4956970214844 0.5139174461364746 576.9151611328125 0.39406055212020874 0.79018956 0.4354977607727051 False -19 55040 29.68268132209778 0.6744983196258545 391.84576416015625 0.20567449927330017 576.6307373046875 0.39429938793182373 0.7894259 0.4375607967376709 False diff --git a/ENCSR517NHP/cherimoya.fold_1.performance.tsv b/ENCSR517NHP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bdc1ccbf46d2a06db24977934230a488cda59c4b..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -578.2216186523438 0.39101263880729675 0.39056289196014404 0.1564360409975052 0.7907073497772217 0.7545517683029175 0.4322149455547333 \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_2.evaluate.json b/ENCSR517NHP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9dfb75dbe990ed7701d213fdcbd5bc2c68a0327f..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF530BGE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_2.fit.json b/ENCSR517NHP/cherimoya.fold_2.fit.json deleted file mode 100644 index bc7ae9b298a74fc8ba41055ff08ea471b87732b0..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF530BGE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_2.log b/ENCSR517NHP/cherimoya.fold_2.log deleted file mode 100644 index 0caa8732ac399dcb31a1b512f2ed2f61b1d645ee..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2920 36.64754104614258 3.6805174350738525 401.656982421875 0.7202388644218445 604.2059936523438 0.21856410801410675 0.5420284 6.763792514801025 True -1 5840 32.22103834152222 0.5549676418304443 383.3689270019531 0.9640332460403442 547.7606201171875 0.3275706171989441 0.636709 1.8847547769546509 True -2 8760 32.14634108543396 0.5406694412231445 402.88775634765625 0.6985613107681274 539.7176513671875 0.3412174582481384 0.64933586 0.9607157707214355 True -3 11680 32.157315254211426 1.530684471130371 497.27484130859375 0.7249971032142639 535.9673461914062 0.3458137512207031 0.6635237 0.7519776225090027 True -4 14600 32.14090061187744 0.5358047485351562 384.90386962890625 0.7784231305122375 533.6109008789062 0.35031968355178833 0.67416066 0.745620608329773 True -5 17520 32.18360447883606 0.5372679233551025 498.65496826171875 0.5948079824447632 531.2081298828125 0.35595589876174927 0.6735871 0.7472331523895264 False -6 20440 32.121596813201904 0.522202730178833 404.3746337890625 0.6409514546394348 529.7484130859375 0.35868218541145325 0.6764266 0.6755024790763855 True -7 23360 32.18383598327637 0.5363233089447021 334.50537109375 0.6324268579483032 528.8917236328125 0.3592330813407898 0.6795112 0.7140563130378723 True -8 26280 32.13646912574768 1.2846109867095947 412.158447265625 0.7930833101272583 526.7861328125 0.3637826442718506 0.68499684 0.6924053430557251 True -9 29200 32.127434492111206 0.5251271724700928 316.130615234375 0.49521392583847046 526.1747436523438 0.3646126389503479 0.69055426 0.6524500250816345 True -10 32120 31.567660570144653 0.5238363742828369 404.8807373046875 0.6975823044776917 524.7200317382812 0.36599645018577576 0.6980156 0.6369612216949463 True -11 35040 31.61061716079712 0.5245015621185303 456.75018310546875 0.5391795635223389 522.887939453125 0.3699698746204376 0.7050282 0.5958230495452881 True -12 37960 31.575096368789673 0.5278759002685547 455.5608215332031 0.6437898278236389 520.7279663085938 0.37426885962486267 0.71666574 0.5470340847969055 True -13 40880 31.52304697036743 0.5354156494140625 431.60400390625 0.5347309112548828 518.9088745117188 0.37901589274406433 0.7267196 0.5216876864433289 True -14 43800 31.594365119934082 0.5304961204528809 334.781982421875 0.42440277338027954 517.8976440429688 0.3793051838874817 0.7352568 0.48852571845054626 True -15 46720 31.566700220108032 0.517315149307251 390.97210693359375 0.32689404487609863 517.1301879882812 0.3809138238430023 0.74223584 0.46890518069267273 True -16 49640 31.537810564041138 0.5241043567657471 391.01593017578125 0.37946176528930664 517.6358642578125 0.3789065480232239 0.7507296 0.4492572844028473 True -17 52560 31.558749198913574 0.5282468795776367 401.2076416015625 0.5063774585723877 517.573486328125 0.37935203313827515 0.75381637 0.4434169828891754 True -18 55480 31.54311776161194 0.5271844863891602 448.7210998535156 0.3091733455657959 517.3896484375 0.3799991011619568 0.7543169 0.4445546865463257 True -19 58400 31.54769229888916 0.519171953201294 378.7840576171875 0.3376016616821289 517.5852661132812 0.3797183930873871 0.7555324 0.4448903501033783 True diff --git a/ENCSR517NHP/cherimoya.fold_2.performance.tsv b/ENCSR517NHP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ca246ee277a09fd8f449ae4c7a81550533f7ea0a..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -517.5852661132812 0.405828595161438 0.3797183930873871 0.14176012575626373 0.7555323839187622 0.7036612033843994 0.4448903501033783 \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_3.evaluate.json b/ENCSR517NHP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bd3a16fc461461e426825b8d893a60fc2a8b8be1..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF530BGE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_3.fit.json b/ENCSR517NHP/cherimoya.fold_3.fit.json deleted file mode 100644 index 61efb7e5731985b64fde55dc6ea3a6a77ff8f0f1..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF530BGE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_3.log b/ENCSR517NHP/cherimoya.fold_3.log deleted file mode 100644 index 34d6cc84c1a88026100bd9ddf59d68c3b88de8f9..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 35.16010570526123 4.040959119796753 434.19622802734375 1.2053405046463013 619.4506225585938 0.21786321699619293 0.5491623 5.36591911315918 True -1 5544 30.507050275802612 0.6254842281341553 366.9256591796875 0.9422168731689453 565.7882080078125 0.32509881258010864 0.64958864 1.7156985998153687 True -2 8316 30.554887771606445 0.5877819061279297 444.6336364746094 0.6949790716171265 557.0452270507812 0.3401760160923004 0.65445983 0.8766589164733887 True -3 11088 30.512969493865967 0.5943310260772705 422.510009765625 0.6030666828155518 554.3106079101562 0.3434377908706665 0.6695508 0.7304636240005493 True -4 13860 30.571561098098755 0.5931880474090576 477.68768310546875 0.6721742153167725 553.21044921875 0.34525802731513977 0.67383194 0.7135428190231323 True -5 16632 30.487542629241943 1.4084422588348389 380.9082946777344 0.6661654710769653 551.4409790039062 0.3509199321269989 0.67532516 0.7759668827056885 True -6 19404 30.439185619354248 1.9987990856170654 481.0848388671875 0.6703866124153137 550.934326171875 0.35113081336021423 0.6779116 0.7685683965682983 True -7 22176 30.57352566719055 0.6121032238006592 466.0879821777344 0.655127227306366 549.543212890625 0.3538365066051483 0.6835712 0.7339652180671692 True -8 24948 30.4627685546875 0.625164270401001 375.1014709472656 0.7800389528274536 547.6504516601562 0.35753723978996277 0.6935913 0.6649575233459473 True -9 27720 30.04227066040039 0.5785560607910156 445.253662109375 0.4988548457622528 546.0707397460938 0.36057308316230774 0.69200784 0.6749933362007141 False -10 30492 30.0543372631073 0.5777099132537842 480.28741455078125 0.7944981455802917 545.151123046875 0.36269983649253845 0.70073396 0.6147507429122925 True -11 33264 29.96493649482727 0.9077045917510986 402.2086181640625 0.41420674324035645 543.5165405273438 0.36628004908561707 0.7048673 0.585127055644989 True -12 36036 29.943665742874146 0.5869474411010742 427.11395263671875 0.7322656512260437 542.572021484375 0.3665933609008789 0.715466 0.559148907661438 True -13 38808 29.948907613754272 0.5904707908630371 327.3526916503906 0.6533648371696472 541.7744140625 0.3673558533191681 0.7253205 0.5153714418411255 True -14 41580 29.920594930648804 0.5891311168670654 368.0584716796875 0.6111835241317749 538.6472778320312 0.37434151768684387 0.7375342 0.48861655592918396 True -15 44352 29.94982409477234 0.5809769630432129 483.19915771484375 0.39955657720565796 538.0131225585938 0.3742040693759918 0.7480375 0.46573111414909363 True -16 47124 29.92492437362671 0.5766892433166504 386.09173583984375 0.29050731658935547 537.9371337890625 0.3747633993625641 0.7534398 0.4538838863372803 True -17 49896 29.958874702453613 0.5834879875183105 369.44146728515625 0.613669753074646 537.301025390625 0.37541571259498596 0.7570037 0.4472508132457733 True -18 52668 29.942752599716187 1.4836845397949219 394.457763671875 0.34104979038238525 538.55810546875 0.37261253595352173 0.7553945 0.45534417033195496 False -19 55440 29.973037719726562 0.5771620273590088 382.91705322265625 0.21433192491531372 537.147216796875 0.3766736686229706 0.7558414 0.46327608823776245 False diff --git a/ENCSR517NHP/cherimoya.fold_3.performance.tsv b/ENCSR517NHP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9f36b1d693961daad538040fec2de916c20f71d4..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -537.301025390625 0.4028066098690033 0.3754156529903412 0.1459999978542328 0.7570037245750427 0.7113544940948486 0.4472508132457733 \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_4.evaluate.json b/ENCSR517NHP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3fc88a31ac2487036314379944135fd529fad7f2..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF530BGE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_4.fit.json b/ENCSR517NHP/cherimoya.fold_4.fit.json deleted file mode 100644 index 29c6a5b9954516fd299b2f71794ca4fdc1cc98e7..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF530BGE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR517NHP/cherimoya.fold_4.log b/ENCSR517NHP/cherimoya.fold_4.log deleted file mode 100644 index 772084f4e3934afa98998d1320bcce0041194a12..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2854 35.79303765296936 3.5645036697387695 508.68707275390625 0.8440384864807129 596.3106689453125 0.2120441496372223 0.51766294 4.369733810424805 True -1 5708 31.449716567993164 0.685936689376831 428.5135498046875 0.6626280546188354 546.202880859375 0.32234734296798706 0.6146201 1.6006962060928345 True -2 8562 31.407872200012207 3.811387062072754 431.8036804199219 0.6168618202209473 538.9365234375 0.3325430452823639 0.62780964 0.7287005186080933 True -3 11416 31.468112468719482 0.6051461696624756 375.71905517578125 0.7176474928855896 534.563232421875 0.34043678641319275 0.6388274 0.595856785774231 True -4 14270 31.399051666259766 0.5966954231262207 371.37860107421875 0.6602045297622681 531.9308471679688 0.3451595604419708 0.64922845 0.5923431515693665 True -5 17124 31.393020153045654 0.6043376922607422 448.14312744140625 1.0204823017120361 530.662841796875 0.3482758700847626 0.6527531 0.6231178045272827 True -6 19978 31.38392162322998 0.5927650928497314 303.6501159667969 0.814910888671875 529.6607055664062 0.3507979214191437 0.660058 0.5839267373085022 True -7 22832 31.36856985092163 0.5997538566589355 379.7598876953125 0.5523648858070374 528.7425537109375 0.3540007770061493 0.6639894 0.5866115689277649 True -8 25686 31.423762321472168 0.5884034633636475 535.3606567382812 0.6826770901679993 527.2568359375 0.35551950335502625 0.67514724 0.5774703621864319 True -9 28540 31.326151609420776 0.6115355491638184 393.3914794921875 0.6801085472106934 525.6948852539062 0.3589317500591278 0.68057597 0.529386043548584 True -10 31394 30.945810317993164 0.5859031677246094 458.7770690917969 0.5342447757720947 524.3258666992188 0.3613041937351227 0.68916583 0.5334511399269104 True -11 34248 30.94049882888794 0.5850083827972412 443.2032165527344 0.5866895914077759 522.6240844726562 0.36535337567329407 0.69691825 0.5406475067138672 True -12 37102 30.931422233581543 0.5944952964782715 366.6470947265625 0.701728343963623 521.60498046875 0.36776721477508545 0.7066817 0.4951193630695343 True -13 39956 30.847697734832764 1.322319746017456 306.8543395996094 0.5747427344322205 519.8099975585938 0.37063169479370117 0.7157476 0.4752679467201233 True -14 42810 30.84155249595642 0.5865869522094727 373.21923828125 0.48783695697784424 519.051513671875 0.3723215162754059 0.7254614 0.4562581181526184 True -15 45664 30.80970025062561 0.5914897918701172 419.0654296875 0.5758391618728638 519.4647827148438 0.37086552381515503 0.7329975 0.4410989284515381 True -16 48518 30.834953784942627 0.5824675559997559 395.7010498046875 0.6582887172698975 518.43603515625 0.3728269636631012 0.738127 0.4363881051540375 True -17 51372 30.8517427444458 0.594139575958252 372.41864013671875 0.8943865895271301 518.0391235351562 0.37395334243774414 0.74073017 0.43410640954971313 True -18 54226 30.948320865631104 0.5970296859741211 473.3791809082031 0.3782811760902405 518.15380859375 0.3738418221473694 0.74306 0.4365091025829315 True -19 57080 31.063128232955933 0.5939781665802002 355.25640869140625 0.5335647463798523 517.5296020507812 0.37585797905921936 0.7428779 0.4403919279575348 False diff --git a/ENCSR517NHP/cherimoya.fold_4.performance.tsv b/ENCSR517NHP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d4d04d247ab6c4c97a9c466eb0c7393ae8f223ce..0000000000000000000000000000000000000000 --- a/ENCSR517NHP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -518.15380859375 0.4057163894176483 0.3738418519496918 0.14312614500522614 0.7430599927902222 0.6930988430976868 0.4365091025829315 \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_0.evaluate.json b/ENCSR518JGY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6c357df5d626a82341fa12307988369f2814209d..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF223XDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_0.fit.json b/ENCSR518JGY/cherimoya.fold_0.fit.json deleted file mode 100644 index 55d28126d2f7398355acea1f40cad5771cce47e2..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF223XDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_0.log b/ENCSR518JGY/cherimoya.fold_0.log deleted file mode 100644 index fa0ca62677f22b759ff37a9d8cc9670b09f543ed..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2711 34.305806398391724 4.3242409229278564 240.25587463378906 0.9290928840637207 363.4954833984375 0.18632756173610687 0.31480882 2.9925761222839355 True -1 5422 30.04336452484131 0.5655221939086914 239.5166473388672 0.7313898801803589 320.8868103027344 0.30124637484550476 0.48754025 1.8993630409240723 True -2 8133 30.092503309249878 0.5422301292419434 231.3107452392578 0.47516578435897827 313.8741455078125 0.31479352712631226 0.5126072 1.20238196849823 True -3 10844 30.147293090820312 0.5562877655029297 249.3035430908203 0.6644583940505981 310.8291931152344 0.3215269446372986 0.5249449 0.8623785972595215 True -4 13555 30.130838871002197 0.8296654224395752 230.00650024414062 0.3951554298400879 308.2159118652344 0.3289104402065277 0.5403809 0.7551232576370239 True -5 16266 30.03235626220703 0.5421795845031738 228.75164794921875 0.7304965257644653 307.044921875 0.3319728672504425 0.55302495 0.7404311895370483 True -6 18977 30.00800657272339 0.5569453239440918 258.4190368652344 0.4372202455997467 306.55230712890625 0.3327917158603668 0.5666677 0.716629147529602 True -7 21688 30.00665807723999 0.548290491104126 194.87120056152344 0.5973893404006958 305.4071350097656 0.33558011054992676 0.57734615 0.6501259803771973 True -8 24399 29.982666492462158 0.7861769199371338 225.3761444091797 0.5756465196609497 304.46966552734375 0.33788028359413147 0.5899136 0.6127650141716003 True -9 27110 30.019368886947632 0.5914404392242432 226.45693969726562 0.4422377347946167 304.1412353515625 0.33837276697158813 0.59732014 0.5704631805419922 True -10 29821 30.2268123626709 21.106292486190796 203.22056579589844 0.3912452459335327 302.9080505371094 0.34278976917266846 0.6097584 0.5509441494941711 True -11 32532 30.13993763923645 0.5570249557495117 265.22802734375 0.39535683393478394 302.5694580078125 0.3423597812652588 0.6218477 0.5077276825904846 True -12 35243 30.07327914237976 0.5508856773376465 223.60137939453125 0.4637441337108612 301.82666015625 0.3444947600364685 0.632878 0.4915050268173218 True -13 37954 30.18584370613098 0.5668220520019531 227.26577758789062 0.310039222240448 300.9609680175781 0.3470733165740967 0.64522076 0.4688781797885895 True -14 40665 30.270673751831055 0.558819055557251 236.87713623046875 0.5625321865081787 300.3314208984375 0.34771689772605896 0.6599093 0.4461546540260315 True -15 43376 29.829654455184937 0.5535099506378174 258.39483642578125 0.46433025598526 299.74481201171875 0.34918084740638733 0.6685148 0.428401380777359 True -16 46087 29.543309211730957 0.5494141578674316 240.70999145507812 0.35541078448295593 299.5222473144531 0.3495369851589203 0.6752724 0.41956841945648193 True -17 48798 29.50049328804016 0.5482485294342041 236.87457275390625 0.34286242723464966 299.19061279296875 0.35075631737709045 0.6760869 0.41629570722579956 True -18 51509 29.56356430053711 0.5448367595672607 236.3121337890625 0.36050063371658325 299.3324890136719 0.34962916374206543 0.6759473 0.4176059663295746 False -19 54220 29.610377311706543 0.5466790199279785 267.47857666015625 0.23646512627601624 299.2523193359375 0.3505401909351349 0.67501473 0.4214285612106323 False diff --git a/ENCSR518JGY/cherimoya.fold_0.performance.tsv b/ENCSR518JGY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f824a17747b0a5773cab2c14087cfcaeb1fa6ab7..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -299.19061279296875 0.4561867415904999 0.35075631737709045 0.09431372582912445 0.6760869026184082 0.6370896697044373 0.41629570722579956 \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_1.evaluate.json b/ENCSR518JGY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 38ecda070ff055230d433ddcf8f929d0a157b970..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF223XDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_1.fit.json b/ENCSR518JGY/cherimoya.fold_1.fit.json deleted file mode 100644 index 27c5fe6295093179fa7c773df308d74556737299..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF223XDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_1.log b/ENCSR518JGY/cherimoya.fold_1.log deleted file mode 100644 index b96e327e83dea73a3de5db91b4779f99a55227cb..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 34.222676515579224 4.6645731925964355 327.67437744140625 0.6590452194213867 391.6568908691406 0.19142600893974304 0.33786073 3.029214382171631 True -1 5466 30.37765669822693 0.7100720405578613 276.4029846191406 0.8554369807243347 343.0599670410156 0.3111781179904938 0.52498597 2.306093454360962 True -2 8199 30.337190866470337 0.672102689743042 279.18048095703125 0.659848690032959 337.43157958984375 0.3229549825191498 0.5287299 1.3971519470214844 True -3 10932 30.326530694961548 1.470658540725708 259.9447326660156 0.6247837543487549 333.2949523925781 0.32951509952545166 0.55199236 0.7812691330909729 True -4 13665 30.322765827178955 0.673654317855835 229.19412231445312 0.5156595706939697 330.9014587402344 0.33391207456588745 0.5662218 0.6834836602210999 True -5 16398 30.42073106765747 0.6678614616394043 247.48480224609375 0.4793524146080017 329.44671630859375 0.3376566469669342 0.58046 0.6879879236221313 True -6 19131 30.401702880859375 0.6600208282470703 215.06045532226562 0.4188644587993622 327.1032409667969 0.34405848383903503 0.59198475 0.6182817816734314 True -7 21864 30.374922037124634 0.651667594909668 200.244384765625 0.531632125377655 326.264892578125 0.3460667133331299 0.59806776 0.6183061599731445 True -8 24597 30.281574964523315 0.6639688014984131 242.79965209960938 0.5509809851646423 324.7803955078125 0.3506534993648529 0.6096605 0.5637015700340271 True -9 27330 30.34037160873413 13.01554799079895 214.5831756591797 0.48369836807250977 324.3835754394531 0.34936457872390747 0.6240735 0.5304370522499084 True -10 30063 30.39517378807068 32.65842652320862 208.27777099609375 0.4011676013469696 323.69964599609375 0.35094448924064636 0.6328249 0.5329422354698181 True -11 32796 30.417098999023438 0.6600761413574219 268.41668701171875 0.5579605102539062 322.48126220703125 0.3545861542224884 0.64686364 0.5093830227851868 True -12 35529 30.35593557357788 0.6493048667907715 240.3502960205078 0.34712380170822144 321.4117126464844 0.3572195768356323 0.660464 0.4913055896759033 True -13 38262 30.02303957939148 0.6435165405273438 255.47052001953125 0.4660612642765045 320.7635803222656 0.3584751486778259 0.6736894 0.47702792286872864 True -14 40995 29.707952737808228 0.643796443939209 274.1805725097656 0.4564962685108185 320.02886962890625 0.3597770631313324 0.68415165 0.4603814482688904 True -15 43728 29.712379693984985 0.645510196685791 256.6228942871094 0.4749259948730469 319.6624450683594 0.36035460233688354 0.69689554 0.4390456974506378 True -16 46461 29.780863285064697 0.6615338325500488 212.48165893554688 0.2857089638710022 319.2848815917969 0.3609881103038788 0.70561284 0.42849430441856384 True -17 49194 29.775405168533325 0.642115592956543 286.22088623046875 0.3397849202156067 319.44683837890625 0.3605472147464752 0.7061906 0.42626726627349854 True -18 51927 29.716179847717285 0.6556189060211182 217.53070068359375 0.44013267755508423 319.63616943359375 0.35961270332336426 0.70700127 0.42526212334632874 True -19 54660 29.710254430770874 0.645348310470581 284.60400390625 0.2978856563568115 319.18145751953125 0.36221152544021606 0.7066028 0.4280620813369751 False diff --git a/ENCSR518JGY/cherimoya.fold_1.performance.tsv b/ENCSR518JGY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c56b38877d4c729ae6ed79699e4ed4af6dd48443..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -319.63616943359375 0.4469511806964874 0.35961273312568665 0.10344188660383224 0.707001268863678 0.6754365563392639 0.42526212334632874 \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_2.evaluate.json b/ENCSR518JGY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5d43c70845e71bd5fe07e15531e7c6bcf16b27b5..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF223XDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_2.fit.json b/ENCSR518JGY/cherimoya.fold_2.fit.json deleted file mode 100644 index 542bc1202bfda81ce87d2178e70c05e812b36178..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF223XDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_2.log b/ENCSR518JGY/cherimoya.fold_2.log deleted file mode 100644 index df1a690a6629d3fa62217e2601cd1b71bc8f7e8a..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2849 34.94441795349121 3.8237576484680176 237.5021209716797 0.6575983762741089 362.3907470703125 0.19204001128673553 0.31425965 3.43206787109375 True -1 5698 31.310336351394653 0.5536220073699951 293.40667724609375 0.573947012424469 318.2736511230469 0.30568447709083557 0.49202204 1.9158692359924316 True -2 8547 31.288367986679077 0.5118134021759033 211.28652954101562 0.5596418380737305 312.48876953125 0.31723901629447937 0.512169 1.2155650854110718 True -3 11396 31.259066820144653 0.5035014152526855 237.67727661132812 0.8535178899765015 308.84100341796875 0.327139288187027 0.5402204 0.9286743402481079 True -4 14245 31.37487816810608 0.5115609169006348 253.955322265625 0.7201510071754456 307.1993103027344 0.33001330494880676 0.5522784 0.7947289347648621 True -5 17094 31.30450987815857 0.5089948177337646 281.8358154296875 0.746496319770813 306.022705078125 0.33284565806388855 0.5641514 0.6929476261138916 True -6 19943 31.22682213783264 0.510613203048706 234.28060913085938 0.573367714881897 305.3719177246094 0.33309683203697205 0.57206583 0.6341297626495361 True -7 22792 31.23219633102417 2.120539426803589 232.67486572265625 0.5410952568054199 304.3316650390625 0.335766077041626 0.5813992 0.6020973920822144 True -8 25641 31.33448886871338 0.5322186946868896 263.643310546875 0.7543990015983582 302.91973876953125 0.34092745184898376 0.58922917 0.5675880908966064 True -9 28490 31.275854110717773 0.5089941024780273 270.8726806640625 0.5329389572143555 302.330078125 0.34202852845191956 0.59986097 0.5353730320930481 True -10 31339 31.225518941879272 0.514545202255249 252.92257690429688 0.7578198313713074 301.3198547363281 0.3443674147129059 0.61395955 0.5123878717422485 True -11 34188 31.31477403640747 0.5089428424835205 221.91549682617188 0.3389524221420288 300.333984375 0.34718072414398193 0.62765115 0.4966936707496643 True -12 37037 31.058095693588257 0.5122706890106201 240.90403747558594 0.582793116569519 300.2685546875 0.3456554412841797 0.64086944 0.4717491567134857 True -13 39886 31.16273832321167 23.542620182037354 261.3492736816406 0.5144912600517273 299.07061767578125 0.3495066165924072 0.65303147 0.45262736082077026 True -14 42735 30.65752673149109 15.80805778503418 271.89788818359375 0.6387659311294556 297.73193359375 0.3543062210083008 0.6656017 0.4351292550563812 True -15 45584 30.74466848373413 0.5073356628417969 242.70297241210938 0.2769661247730255 297.6285400390625 0.3530309796333313 0.67795384 0.41825515031814575 True -16 48433 30.705298900604248 0.5065088272094727 246.16888427734375 0.24526207149028778 297.579345703125 0.35280507802963257 0.682924 0.409240186214447 True -17 51282 30.662145137786865 0.5008618831634521 242.47509765625 0.2564302980899811 297.6058654785156 0.3523868918418884 0.68731976 0.4058349132537842 True -18 54131 30.61415410041809 0.5011732578277588 279.92138671875 0.2845565676689148 297.4111022949219 0.35340020060539246 0.68730795 0.40521928668022156 False -19 56980 30.616767406463623 0.5019567012786865 246.19155883789062 0.2512003481388092 297.3895263671875 0.35375577211380005 0.68701416 0.40814897418022156 False diff --git a/ENCSR518JGY/cherimoya.fold_2.performance.tsv b/ENCSR518JGY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 34c84d5602f4caac3f9f63a26641f6b14de71a96..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -297.6058654785156 0.4548245668411255 0.3523868918418884 0.09819339215755463 0.6873197555541992 0.6512265205383301 0.4058349132537842 \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_3.evaluate.json b/ENCSR518JGY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 88264cb67aaf2f3cd4dff7db5b4e628e66c2b1ab..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF223XDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_3.fit.json b/ENCSR518JGY/cherimoya.fold_3.fit.json deleted file mode 100644 index 586dbc60f8d5b147463f3b918a564fe149738ab9..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF223XDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_3.log b/ENCSR518JGY/cherimoya.fold_3.log deleted file mode 100644 index cf381094d1bc3e4ad499d1eb685c072858cf230a..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 34.40207624435425 3.4948208332061768 235.88916015625 0.5619903802871704 376.2784729003906 0.19557800889015198 0.3479518 3.554166555404663 True -1 5564 30.54279661178589 0.5745432376861572 307.6151123046875 0.7508432269096375 330.6273498535156 0.31165069341659546 0.4982458 1.9358536005020142 True -2 8346 30.56314992904663 0.5616190433502197 264.56317138671875 0.5158345103263855 325.7435302734375 0.32009145617485046 0.49775812 1.3427895307540894 False -3 11128 30.531691551208496 0.6154639720916748 254.28233337402344 0.6344548463821411 323.2403259277344 0.32639995217323303 0.5046127 1.07231605052948 True -4 13910 30.504616022109985 0.5621232986450195 258.0244445800781 0.6377938389778137 321.79522705078125 0.33095693588256836 0.5248502 0.9714166522026062 True -5 16692 30.442253589630127 0.563826322555542 304.27801513671875 0.6297178268432617 319.7040710449219 0.33639752864837646 0.53225595 0.8736898899078369 True -6 19474 30.505253314971924 0.5638906955718994 220.2508544921875 0.6093143224716187 318.8791809082031 0.3371010422706604 0.54266506 0.8114262223243713 True -7 22256 30.47495675086975 0.5641984939575195 248.64724731445312 0.6720158457756042 317.4925842285156 0.3403453826904297 0.5558782 0.7499806880950928 True -8 25038 30.52718448638916 0.5645956993103027 245.66162109375 0.49946340918540955 316.2837829589844 0.3439589738845825 0.57219607 0.7045047879219055 True -9 27820 30.495563507080078 0.5631115436553955 222.0259552001953 0.3973691761493683 315.19940185546875 0.34565091133117676 0.59121597 0.636530876159668 True -10 30602 30.47248339653015 0.5729410648345947 274.90185546875 0.4632977843284607 314.58502197265625 0.3464893102645874 0.60325056 0.6003232002258301 True -11 33384 30.105164527893066 0.5824658870697021 214.83154296875 0.37706559896469116 314.0983581542969 0.34696465730667114 0.61783373 0.5563892722129822 True -12 36166 30.107733964920044 0.5733892917633057 237.69497680664062 0.49561575055122375 312.6671142578125 0.3510778546333313 0.6335937 0.5096464157104492 True -13 38948 30.10096788406372 0.5685441493988037 264.30230712890625 0.46258413791656494 312.15838623046875 0.35151946544647217 0.6506661 0.4742104709148407 True -14 41730 30.049317121505737 0.5717716217041016 283.92803955078125 0.48720666766166687 311.0380859375 0.3548445403575897 0.66514677 0.455215185880661 True -15 44512 30.149733543395996 0.5722923278808594 258.4398498535156 0.3759227395057678 310.7154541015625 0.3556942939758301 0.6792187 0.43553653359413147 True -16 47294 30.12115216255188 0.5765945911407471 247.64993286132812 0.339484840631485 309.9314880371094 0.35735028982162476 0.6887974 0.4226413369178772 True -17 50076 30.030285835266113 2.656226873397827 250.1719970703125 0.37004244327545166 310.0960998535156 0.3561564087867737 0.69196904 0.4220312535762787 True -18 52858 30.017472505569458 15.217190504074097 252.5543670654297 0.24335195124149323 309.8233337402344 0.3577275574207306 0.691865 0.4222032427787781 False -19 55640 30.421395540237427 0.5811569690704346 244.45945739746094 0.20748980343341827 309.8102722167969 0.3574358820915222 0.6904675 0.42578643560409546 False diff --git a/ENCSR518JGY/cherimoya.fold_3.performance.tsv b/ENCSR518JGY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3ef9d81900d412ccf1d5435d573ea7c18a943bb5..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -310.0960998535156 0.4514274001121521 0.3561564087867737 0.09768430888652802 0.6919690370559692 0.6459699273109436 0.4220312535762787 \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_4.evaluate.json b/ENCSR518JGY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 26ed0893a53a9314b8ba27335ba75d5b130638fc..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF223XDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_4.fit.json b/ENCSR518JGY/cherimoya.fold_4.fit.json deleted file mode 100644 index 30a37e8fe997aea0d56f81d4f1bc0d15289ba113..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF223XDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518JGY/cherimoya.fold_4.log b/ENCSR518JGY/cherimoya.fold_4.log deleted file mode 100644 index edf9a47807cef808dac1a2ca4353beec4e3028b0..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 35.6649055480957 3.452897548675537 207.61009216308594 0.7737005949020386 359.8361511230469 0.19528180360794067 0.31152216 3.1515705585479736 True -1 5754 31.95275616645813 0.6216692924499512 295.60693359375 0.6427595019340515 315.8876953125 0.30838337540626526 0.48600736 1.4216052293777466 True -2 8631 31.904022932052612 0.5499351024627686 234.6068115234375 0.5117926001548767 311.8665466308594 0.31593626737594604 0.49781817 0.9742916822433472 True -3 11508 31.959980487823486 0.5447537899017334 277.42724609375 0.6458895206451416 309.3694763183594 0.31973835825920105 0.52451146 0.6891838312149048 True -4 14385 31.929203987121582 0.545945405960083 267.0478210449219 0.6051133275032043 307.3585510253906 0.3250729441642761 0.538819 0.6065854430198669 True -5 17262 32.055766582489014 0.5565369129180908 285.816650390625 0.5080310106277466 305.69854736328125 0.32902827858924866 0.5508367 0.5906895995140076 True -6 20139 32.71787977218628 0.5729498863220215 232.522216796875 0.6001094579696655 304.275146484375 0.33350732922554016 0.5642619 0.5805830955505371 True -7 23016 32.10391283035278 1.9217383861541748 279.23931884765625 0.5085756778717041 303.2830810546875 0.33580490946769714 0.5744684 0.5281100273132324 True -8 25893 32.14941954612732 0.5698716640472412 238.7059326171875 0.4743630290031433 302.77142333984375 0.33728834986686707 0.5851516 0.5101534724235535 True -9 28770 32.08746790885925 0.5587770938873291 237.28616333007812 0.3480087220668793 302.01123046875 0.339216947555542 0.5959214 0.5097594261169434 True -10 31647 31.72256350517273 0.5491037368774414 250.97848510742188 0.5736644268035889 301.5038146972656 0.341117262840271 0.60433537 0.49675253033638 True -11 34524 31.52675485610962 0.6329755783081055 255.62734985351562 0.28507179021835327 300.6593933105469 0.3428672254085541 0.6176944 0.4903307557106018 True -12 37401 31.477102041244507 0.5664007663726807 226.53118896484375 0.4344457983970642 300.1276550292969 0.34436872601509094 0.632452 0.4749283492565155 True -13 40278 31.360210418701172 0.5452444553375244 240.2877197265625 0.4492650032043457 299.4354553222656 0.3454793095588684 0.64671504 0.45017749071121216 True -14 43155 31.393187999725342 0.5510857105255127 233.06390380859375 0.26546579599380493 298.9457702636719 0.3460465371608734 0.65918297 0.4353491961956024 True -15 46032 31.364043951034546 0.5493113994598389 281.5924072265625 0.36326363682746887 298.3890686035156 0.3479175865650177 0.66942835 0.4227316975593567 True -16 48909 31.318342208862305 0.5427627563476562 235.635986328125 0.3810742497444153 298.1125793457031 0.34852614998817444 0.67711264 0.41402581334114075 True -17 51786 31.326643705368042 0.5432026386260986 228.49319458007812 0.288468599319458 298.16070556640625 0.34800639748573303 0.679973 0.41146641969680786 True -18 54663 31.288939714431763 0.5440633296966553 259.3576965332031 0.35796695947647095 298.0391540527344 0.34899693727493286 0.6794916 0.4154096841812134 False -19 57540 31.308247804641724 0.5481171607971191 257.8271484375 0.30772241950035095 298.3046569824219 0.34781983494758606 0.67888635 0.41873103380203247 False diff --git a/ENCSR518JGY/cherimoya.fold_4.performance.tsv b/ENCSR518JGY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index de7610dc9e2d9f1766f25ad6a464018176e9c0f0..0000000000000000000000000000000000000000 --- a/ENCSR518JGY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -298.16070556640625 0.45684510469436646 0.34800639748573303 0.0941992923617363 0.6799730062484741 0.6359823346138 0.41146641969680786 \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_0.evaluate.json b/ENCSR518WRP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1e3838715960124a3479b3a7afaec2a3a0ce2ee3..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF980SPA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_0.fit.json b/ENCSR518WRP/cherimoya.fold_0.fit.json deleted file mode 100644 index 9df225df81fe78ce36e8d1cc5064ac77f7597718..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF980SPA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_0.log b/ENCSR518WRP/cherimoya.fold_0.log deleted file mode 100644 index c498c7b8e7e496738ebbf5b0effdacbb9684b194..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 35.45736742019653 4.1365907192230225 422.01824951171875 0.21592943370342255 642.0084228515625 0.3222035765647888 0.79382336 3.9223599433898926 True -1 5530 30.43259358406067 0.5914220809936523 460.7135009765625 0.2714296877384186 592.1729736328125 0.3878253996372223 0.8408792 1.0447665452957153 True -2 8295 30.487858772277832 0.5797150135040283 501.260986328125 0.39372795820236206 579.7872924804688 0.4013780653476715 0.86121553 0.35385552048683167 True -3 11060 30.471569299697876 0.5659964084625244 487.8998107910156 0.31422191858291626 575.609619140625 0.4065198302268982 0.866236 0.3029312491416931 True -4 13825 30.52025532722473 0.580643892288208 553.721923828125 0.3697983920574188 574.3865966796875 0.4077865481376648 0.86928326 0.27468180656433105 True -5 16590 30.47708487510681 0.5809152126312256 542.8067626953125 0.194243922829628 573.7540893554688 0.40728992223739624 0.8736479 0.2365836799144745 True -6 19355 30.497623205184937 0.5705010890960693 423.1912841796875 0.20095692574977875 569.6592407226562 0.4140613079071045 0.87920797 0.21207784116268158 True -7 22120 30.430104732513428 0.5767662525177002 445.4428405761719 0.21388287842273712 568.8536987304688 0.4150488078594208 0.8830345 0.21464134752750397 True -8 24885 30.44023823738098 0.5773043632507324 449.5142822265625 0.1383214294910431 566.94775390625 0.4176108241081238 0.888694 0.21147462725639343 True -9 27650 30.161277055740356 0.572869062423706 526.5557861328125 0.15616312623023987 565.148193359375 0.42052894830703735 0.89204913 0.19445982575416565 True -10 30415 29.876871347427368 0.5729012489318848 469.2879333496094 0.12758734822273254 564.7227783203125 0.42070716619491577 0.8962022 0.19000105559825897 True -11 33180 29.871519804000854 0.5713911056518555 578.1670532226562 0.1435869336128235 562.2021484375 0.4235571026802063 0.8964507 0.177244171500206 True -12 35945 29.86329174041748 0.5691213607788086 468.08880615234375 0.20689626038074493 561.3176879882812 0.42524954676628113 0.90028244 0.1756686270236969 True -13 38710 29.872068405151367 0.5728731155395508 495.6146240234375 0.16142117977142334 560.6994018554688 0.4262544810771942 0.9043014 0.16659365594387054 True -14 41475 29.8635356426239 0.5660815238952637 515.0873413085938 0.21309930086135864 559.6304931640625 0.4274733364582062 0.9071429 0.15759199857711792 True -15 44240 29.897467851638794 0.5774013996124268 456.1551513671875 0.1470699906349182 559.5164184570312 0.4272692799568176 0.9105414 0.1487599015235901 True -16 47005 29.907577514648438 0.5788183212280273 564.6798095703125 0.14978095889091492 558.79052734375 0.4278550446033478 0.9098393 0.1459052562713623 False -17 49770 29.901901245117188 0.5703835487365723 505.93951416015625 0.16933929920196533 559.2515258789062 0.42699921131134033 0.91169447 0.14358186721801758 True -18 52535 29.857602834701538 0.5866725444793701 512.6046142578125 0.09052848815917969 559.6055297851562 0.42655086517333984 0.91202116 0.14350853860378265 True -19 55300 30.005892515182495 10.693766117095947 419.000732421875 0.1352851390838623 559.9773559570312 0.42600682377815247 0.91181123 0.14424484968185425 False diff --git a/ENCSR518WRP/cherimoya.fold_0.performance.tsv b/ENCSR518WRP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1d2f153db11e61302e577ac8a159d98ab413208f..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -559.6055297851562 0.3673560321331024 0.42655086517333984 0.1719798892736435 0.9120211601257324 0.8905710577964783 0.14350853860378265 \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_1.evaluate.json b/ENCSR518WRP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 32f113a8168bc951e12c49734c0ea0b317991157..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF980SPA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_1.fit.json b/ENCSR518WRP/cherimoya.fold_1.fit.json deleted file mode 100644 index 3eb4afa1c542e5c28e58639fec3ed8ff1c000232..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF980SPA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_1.log b/ENCSR518WRP/cherimoya.fold_1.log deleted file mode 100644 index d77532a0c7f2c4002abef9e2e52d9830709d9f6f..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2706 34.65802192687988 4.28958535194397 491.225830078125 0.307150661945343 730.5562744140625 0.3149471580982208 0.78353643 5.631443977355957 True -1 5412 29.908662796020508 0.8610339164733887 490.6930236816406 0.30756622552871704 663.6444091796875 0.39280667901039124 0.84115094 1.0693868398666382 True -2 8118 29.83906102180481 0.7116091251373291 533.98291015625 0.3350203335285187 648.6625366210938 0.408067524433136 0.85302824 0.4615500271320343 True -3 10824 29.85226821899414 0.6937553882598877 488.6215515136719 0.2152285873889923 641.4915161132812 0.4147839844226837 0.8675501 0.3490830063819885 True -4 13530 29.882898807525635 0.6918809413909912 495.6848449707031 0.22006645798683167 638.0867919921875 0.418072372674942 0.8724205 0.32934126257896423 True -5 16236 29.82328200340271 0.709895133972168 449.18634033203125 0.25998613238334656 634.4396362304688 0.4234795868396759 0.87721187 0.2840646505355835 True -6 18942 29.845036506652832 0.7150654792785645 502.4341125488281 0.21898046135902405 633.130126953125 0.4248436987400055 0.88083446 0.2869291305541992 True -7 21648 29.81731343269348 0.7086231708526611 439.65673828125 0.36869698762893677 629.9700927734375 0.42860302329063416 0.88533515 0.25709280371665955 True -8 24354 29.755733251571655 0.6976046562194824 483.2237854003906 0.15797121822834015 628.6653442382812 0.43008503317832947 0.8895093 0.24363350868225098 True -9 27060 29.27734661102295 0.7062404155731201 363.96783447265625 0.4245608448982239 626.6427612304688 0.4322606325149536 0.8919272 0.2319398820400238 True -10 29766 29.24583077430725 0.7086372375488281 539.728271484375 0.30783042311668396 625.8310546875 0.43261831998825073 0.89549536 0.21613138914108276 True -11 32472 29.249008655548096 0.6921443939208984 487.1120910644531 0.17761151492595673 622.596435546875 0.4370637834072113 0.8995704 0.21202649176120758 True -12 35178 29.26402187347412 0.7058768272399902 398.0321044921875 0.2660555839538574 621.462890625 0.4369116425514221 0.9030319 0.1949346512556076 True -13 37884 29.322466373443604 0.7057337760925293 470.71612548828125 0.12635907530784607 620.2078247070312 0.4377182722091675 0.90794206 0.18571215867996216 True -14 40590 29.253073692321777 0.7070791721343994 464.93988037109375 0.17612293362617493 619.337890625 0.4390272796154022 0.9100065 0.17602500319480896 True -15 43296 29.333173274993896 0.7262358665466309 465.80474853515625 0.1579175442457199 617.7806396484375 0.44137042760849 0.9144239 0.16581031680107117 True -16 46002 29.341593742370605 0.7199933528900146 437.3620910644531 0.12541279196739197 618.1614379882812 0.44054052233695984 0.9169015 0.1580510437488556 True -17 48708 29.34015202522278 1.5415189266204834 462.9954833984375 0.14165490865707397 618.2201538085938 0.44055745005607605 0.91769266 0.15467193722724915 True -18 51414 29.32925581932068 0.7068815231323242 414.2122497558594 0.11761408299207687 618.4534912109375 0.43945321440696716 0.9181203 0.1531660258769989 True -19 54120 29.299145221710205 0.75858473777771 444.5743713378906 0.10872533172369003 617.8304443359375 0.44159209728240967 0.91856 0.15395717322826385 True diff --git a/ENCSR518WRP/cherimoya.fold_1.performance.tsv b/ENCSR518WRP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8c34a5da5613fbd20bedf76a1b55bd509c0a8de7..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -617.8304443359375 0.35509631037712097 0.4415920376777649 0.18764810264110565 0.9185600280761719 0.9107083082199097 0.15395717322826385 \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_2.evaluate.json b/ENCSR518WRP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9b6547d2c69d9259efa738486ad44fb20f8f9e89..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF980SPA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_2.fit.json b/ENCSR518WRP/cherimoya.fold_2.fit.json deleted file mode 100644 index 040801f82c8fc21d9c36fff314c05d4b510fa7ba..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF980SPA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_2.log b/ENCSR518WRP/cherimoya.fold_2.log deleted file mode 100644 index aba6efdb5fa69959c10b959f67d17fce6ab1c393..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 36.206111907958984 4.257847785949707 489.19293212890625 0.35587120056152344 673.4710693359375 0.3218957185745239 0.78885454 4.482258319854736 True -1 5740 31.65713357925415 0.5706591606140137 388.85125732421875 0.2222961038351059 614.2021484375 0.396738201379776 0.8399251 1.0688965320587158 True -2 8610 31.68044400215149 0.5709145069122314 411.4196472167969 0.28563031554222107 604.4932861328125 0.406137615442276 0.8517376 0.37473124265670776 True -3 11480 31.648210048675537 0.5569581985473633 474.11212158203125 0.2744961977005005 600.4150390625 0.4102293848991394 0.85945415 0.32502955198287964 True -4 14350 31.67911458015442 0.5650157928466797 521.989990234375 0.28612446784973145 598.064697265625 0.41230103373527527 0.8648423 0.27234458923339844 True -5 17220 31.62629771232605 0.5489227771759033 427.6875 0.26547756791114807 596.4215698242188 0.41543805599212646 0.8660376 0.24767445027828217 True -6 20090 31.654818296432495 0.5720231533050537 445.50567626953125 0.23737835884094238 594.982177734375 0.41654807329177856 0.8716691 0.23009908199310303 True -7 22960 31.432706117630005 0.6402838230133057 447.2353515625 0.2579481303691864 592.7103271484375 0.4198981523513794 0.8764419 0.23489409685134888 True -8 25830 31.018219709396362 0.6963486671447754 492.0767822265625 0.20059065520763397 591.00341796875 0.42155537009239197 0.87866837 0.22214704751968384 True -9 28700 31.0599582195282 0.550243616104126 518.7030029296875 0.13481830060482025 590.1572875976562 0.42252352833747864 0.8802359 0.21668972074985504 True -10 31570 31.06671166419983 0.5783452987670898 470.8376159667969 0.2669490575790405 588.9617309570312 0.42386943101882935 0.8857263 0.1987524777650833 True -11 34440 31.031155347824097 0.6024420261383057 430.646728515625 0.14605148136615753 587.6780395507812 0.42493903636932373 0.888596 0.19936612248420715 True -12 37310 31.09245467185974 0.5615575313568115 484.59259033203125 0.12794287502765656 586.056884765625 0.4271326959133148 0.89358723 0.1890498697757721 True -13 40180 31.051642656326294 0.5620405673980713 457.13238525390625 0.18689921498298645 584.4700317382812 0.4291762113571167 0.8973537 0.17760351300239563 True -14 43050 31.05982255935669 0.5607547760009766 456.39215087890625 0.11064301431179047 583.2985229492188 0.43005701899528503 0.89941096 0.17121031880378723 True -15 45920 31.104302167892456 0.8378374576568604 501.163330078125 0.13390615582466125 582.8037109375 0.4306148886680603 0.900571 0.16436198353767395 True -16 48790 31.099743843078613 0.5662086009979248 427.43939208984375 0.08710876107215881 582.08740234375 0.43064287304878235 0.9046081 0.1577492654323578 True -17 51660 31.059977531433105 0.560215950012207 477.7219543457031 0.23161467909812927 582.0801391601562 0.4321013391017914 0.9035742 0.1556461602449417 False -18 54530 31.05492877960205 0.5612077713012695 455.40655517578125 0.14229214191436768 582.45361328125 0.4312009811401367 0.90488416 0.15586340427398682 True -19 57400 31.044004201889038 0.5687282085418701 467.74005126953125 0.11324507743120193 583.2098388671875 0.42972102761268616 0.90314645 0.15623746812343597 False diff --git a/ENCSR518WRP/cherimoya.fold_2.performance.tsv b/ENCSR518WRP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4937c6f803db5164c56ee037926811334d0b2c5b..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -582.45361328125 0.362884521484375 0.4312009811401367 0.17764942348003387 0.9048841595649719 0.8891754150390625 0.15586340427398682 \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_3.evaluate.json b/ENCSR518WRP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 89d8d64561f147f6ad296ff5afd502057fdb7a49..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF980SPA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_3.fit.json b/ENCSR518WRP/cherimoya.fold_3.fit.json deleted file mode 100644 index c2f81dcf9a22215c6106930629cc93d7f6b32d11..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF980SPA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_3.log b/ENCSR518WRP/cherimoya.fold_3.log deleted file mode 100644 index edb5f1c31b31aabcd565c808f8758ed3591cf1f0..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 35.06263089179993 4.3645570278167725 625.9682006835938 0.33249300718307495 623.3543090820312 0.32738280296325684 0.7695122 4.506228923797607 True -1 5524 30.466144800186157 1.105344533920288 495.2278747558594 0.2671687602996826 571.3013305664062 0.39736583828926086 0.83666146 0.8067194223403931 True -2 8286 30.49764347076416 21.806200742721558 474.8641662597656 0.3237641453742981 560.9189453125 0.40669429302215576 0.85133415 0.3705373704433441 True -3 11048 30.66700267791748 0.5555846691131592 469.44873046875 0.3348233699798584 557.0609130859375 0.41279977560043335 0.86177635 0.30690738558769226 True -4 13810 30.71647310256958 0.528052568435669 509.6434020996094 0.34133702516555786 556.8018798828125 0.41217970848083496 0.8597498 0.299638569355011 False -5 16572 30.480788230895996 0.586406946182251 558.0709838867188 0.20936980843544006 554.6466674804688 0.4151407778263092 0.8645947 0.2779120206832886 True -6 19334 30.428417682647705 0.5140724182128906 481.5680847167969 0.1804886758327484 554.1871337890625 0.41538602113723755 0.86683404 0.2889965772628784 True -7 22096 29.945507764816284 0.5255706310272217 530.5654296875 0.29703468084335327 551.5243530273438 0.41910818219184875 0.8691135 0.2681916356086731 True -8 24858 29.914806604385376 0.521571159362793 424.5506896972656 0.2307640165090561 551.0282592773438 0.4186531603336334 0.8738546 0.25536617636680603 True -9 27620 29.912319898605347 0.5220255851745605 484.7687072753906 0.1601896584033966 549.69970703125 0.4216797947883606 0.8751621 0.26196396350860596 True -10 30382 29.9313223361969 0.5209872722625732 478.8767395019531 0.25943687558174133 547.51123046875 0.4243198037147522 0.88019705 0.23906956613063812 True -11 33144 29.872674226760864 0.5099964141845703 513.503662109375 0.10074694454669952 545.9285278320312 0.42628464102745056 0.88459253 0.22295716404914856 True -12 35906 30.318201303482056 0.5179898738861084 405.7715759277344 0.1469649076461792 544.56787109375 0.42779356241226196 0.88911414 0.21024954319000244 True -13 38668 29.934480905532837 0.5149805545806885 488.5420227050781 0.18110355734825134 541.77490234375 0.4319188892841339 0.8948578 0.19232283532619476 True -14 41430 29.89838194847107 0.5107743740081787 520.8239135742188 0.14008796215057373 541.9324340820312 0.43094301223754883 0.8983595 0.18134252727031708 True -15 44192 29.98442554473877 0.5191066265106201 447.6184387207031 0.08104902505874634 541.3802490234375 0.43179526925086975 0.90159816 0.17277511954307556 True -16 46954 29.942832708358765 0.5192937850952148 463.9686279296875 0.12543323636054993 541.1572265625 0.4312322437763214 0.9063784 0.16427595913410187 True -17 49716 29.91577386856079 0.5194869041442871 502.22479248046875 0.19177058339118958 540.2584838867188 0.432610422372818 0.90553534 0.16112206876277924 False -18 52478 29.88694167137146 0.5215651988983154 480.5509948730469 0.10598821938037872 540.2982177734375 0.4322051703929901 0.907351 0.15997877717018127 True -19 55240 29.873833656311035 0.5192885398864746 485.5489196777344 0.09682506322860718 540.6884765625 0.4319039583206177 0.90643084 0.15952394902706146 False diff --git a/ENCSR518WRP/cherimoya.fold_3.performance.tsv b/ENCSR518WRP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bfb60bea5e54186f038058d1085ce50decd03f53..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -540.2982177734375 0.3671523928642273 0.4322051405906677 0.17165446281433105 0.907351016998291 0.8849857449531555 0.15997877717018127 \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_4.evaluate.json b/ENCSR518WRP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f6d76eb582825684edbe00d312c43296c446ae80..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF980SPA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_4.fit.json b/ENCSR518WRP/cherimoya.fold_4.fit.json deleted file mode 100644 index c176ff45eb691def0ae6303484496c6be77e810a..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF980SPA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518WRP/cherimoya.fold_4.log b/ENCSR518WRP/cherimoya.fold_4.log deleted file mode 100644 index 6facac6fb5a2d5a57b44eec0adcee4b90bcb9aef..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2797 35.67115330696106 3.9175312519073486 439.627685546875 0.19220399856567383 586.3576049804688 0.3206619918346405 0.7863542 3.55371356010437 True -1 5594 30.810189247131348 0.7200205326080322 512.4489135742188 0.3928943872451782 539.4754028320312 0.38557231426239014 0.8388631 0.7634108066558838 True -2 8391 30.861371755599976 0.6148719787597656 522.5073852539062 0.24479591846466064 533.0978393554688 0.39100024104118347 0.8471027 0.3691304922103882 True -3 11188 30.879011154174805 0.5980963706970215 530.9111938476562 0.2969602048397064 531.0819091796875 0.39222148060798645 0.85244524 0.31704357266426086 True -4 13985 30.859644174575806 0.6076655387878418 475.9136657714844 0.2325868159532547 527.38623046875 0.3983171582221985 0.8638669 0.24791790544986725 True -5 16782 30.843639373779297 1.3194198608398438 503.7502746582031 0.30153000354766846 526.3372192382812 0.3998512327671051 0.8681112 0.20387284457683563 True -6 19579 30.56968879699707 0.5895147323608398 469.1478271484375 0.41463857889175415 524.8065185546875 0.40201079845428467 0.87340313 0.19061318039894104 True -7 22376 30.24529242515564 0.6133542060852051 436.22454833984375 0.18127089738845825 522.3491821289062 0.40586933493614197 0.8781241 0.19125960767269135 True -8 25173 30.248627424240112 1.8254077434539795 404.17999267578125 0.2824455797672272 521.6121826171875 0.40596136450767517 0.8815162 0.18179161846637726 True -9 27970 30.309258222579956 2.651400327682495 541.482177734375 0.3133544921875 520.1282348632812 0.4092223644256592 0.8865109 0.17735129594802856 True -10 30767 30.262360334396362 0.5902848243713379 477.1920166015625 0.16105031967163086 520.2138061523438 0.4080963134765625 0.8893241 0.18040943145751953 True -11 33564 30.306270837783813 0.6069316864013672 414.8849792480469 0.1563940942287445 518.8436889648438 0.4103785455226898 0.8936221 0.17111967504024506 True -12 36361 30.30211305618286 0.6054003238677979 552.78857421875 0.23019954562187195 517.8972778320312 0.41134577989578247 0.8957324 0.16382217407226562 True -13 39158 30.273988008499146 2.5663609504699707 443.24493408203125 0.16929489374160767 517.0125122070312 0.41222938895225525 0.89974797 0.15424394607543945 True -14 41955 30.265625476837158 0.6161751747131348 495.4093017578125 0.16070497035980225 516.6997680664062 0.4133133292198181 0.9025863 0.1460365653038025 True -15 44752 30.445656299591064 0.6178600788116455 490.73919677734375 0.13658377528190613 515.9625244140625 0.4144260883331299 0.9076563 0.1403183490037918 True -16 47549 30.29656720161438 0.6163394451141357 452.182373046875 0.1026766449213028 515.1908569335938 0.4154634177684784 0.9104829 0.13567644357681274 True -17 50346 30.281806230545044 0.5889966487884521 446.2806396484375 0.09875284135341644 515.03564453125 0.4164007008075714 0.91012895 0.13196739554405212 False -18 53143 30.43385124206543 0.5847647190093994 469.3355712890625 0.10274849832057953 515.9388427734375 0.4146595597267151 0.91238576 0.132048100233078 True -19 55940 30.368940114974976 0.5941057205200195 502.01934814453125 0.08775204420089722 515.2544555664062 0.41639986634254456 0.9108337 0.13207311928272247 False diff --git a/ENCSR518WRP/cherimoya.fold_4.performance.tsv b/ENCSR518WRP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 64446f4b58032faef4d38d80af7fd0c9731bba9c..0000000000000000000000000000000000000000 --- a/ENCSR518WRP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -515.9388427734375 0.3789754807949066 0.4146595597267151 0.16078801453113556 0.9123857617378235 0.8881402015686035 0.132048100233078 \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_0.evaluate.json b/ENCSR518YYX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index cee401ddbbac6e5f44b87215a2d5813c8f06999c..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187POQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_0.fit.json b/ENCSR518YYX/cherimoya.fold_0.fit.json deleted file mode 100644 index f4ef424ec6b2525ed5a2300471f359b414405be6..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF187POQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_0.log b/ENCSR518YYX/cherimoya.fold_0.log deleted file mode 100644 index fb2d63303ad850edd5f48e6323c1fffab20bdaef..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2490 35.712074756622314 5.36006236076355 456.74591064453125 0.906299352645874 849.3466796875 0.20822389423847198 0.61807233 9.730223655700684 True -1 4980 28.445724725723267 30.911813974380493 617.767822265625 1.3965742588043213 718.37451171875 0.2908315658569336 0.7361702 4.221474647521973 True -2 7470 27.672241687774658 2.6088733673095703 599.859375 0.8446593284606934 690.648681640625 0.3087390959262848 0.75687724 2.351351499557495 True -3 9960 27.694248914718628 0.5030443668365479 687.3275146484375 1.4204001426696777 679.1050415039062 0.31614404916763306 0.7697246 1.6219699382781982 True -4 12450 27.664777994155884 1.017273187637329 656.3011474609375 1.088496208190918 672.2266235351562 0.3213363289833069 0.7776443 1.2416197061538696 True -5 14940 27.623829126358032 0.503608226776123 485.6337585449219 1.0311450958251953 666.615234375 0.32636746764183044 0.78465307 1.130509614944458 True -6 17430 28.134755849838257 34.51485276222229 540.4174194335938 0.8414482474327087 661.864501953125 0.32878586649894714 0.7923853 1.1220258474349976 True -7 19920 28.460216522216797 1.440600872039795 329.93505859375 0.7742599248886108 656.9757690429688 0.3320469558238983 0.80080575 0.923140823841095 True -8 22410 27.551254272460938 0.49937963485717773 637.3272094726562 1.0255398750305176 654.4885864257812 0.3336260914802551 0.80356354 0.8838245868682861 True -9 24900 27.064653158187866 0.5015270709991455 475.5221252441406 1.0541629791259766 653.088623046875 0.3344089984893799 0.8106649 0.8172690272331238 True -10 27390 27.10741686820984 0.49134397506713867 608.9822998046875 0.7581641674041748 647.9412231445312 0.33910810947418213 0.8172721 0.7976318597793579 True -11 29880 27.05470895767212 0.49272871017456055 695.4498291015625 0.7183760404586792 645.9022827148438 0.33931952714920044 0.82246536 0.7600907683372498 True -12 32370 27.058588981628418 13.6012704372406 553.0050048828125 0.503288984298706 641.9682006835938 0.3435156047344208 0.8264672 0.7142354846000671 True -13 34860 27.16154718399048 0.49822354316711426 531.1837768554688 0.6929808855056763 636.296630859375 0.346319317817688 0.8331031 0.6852699518203735 True -14 37350 27.20221781730652 0.4976332187652588 434.7374572753906 0.7591363787651062 635.3849487304688 0.3468777537345886 0.83692735 0.6550922989845276 True -15 39840 27.206547737121582 0.498518705368042 454.24359130859375 0.676318883895874 632.1635131835938 0.35079774260520935 0.8413602 0.6292527914047241 True -16 42330 27.314129114151 0.5052511692047119 591.312255859375 0.44222187995910645 633.435791015625 0.3477928042411804 0.84324175 0.6195228099822998 True -17 44820 27.246049165725708 0.503044605255127 438.47540283203125 0.4501267671585083 633.3405151367188 0.34755992889404297 0.84481555 0.6115354895591736 True -18 47310 27.45416259765625 0.5070626735687256 548.758544921875 0.4945833086967468 632.8631591796875 0.34769344329833984 0.8423373 0.6168658137321472 False -19 49800 27.43000078201294 20.520568370819092 599.457763671875 0.501966118812561 633.8345336914062 0.3471841812133789 0.8422603 0.6205877661705017 False diff --git a/ENCSR518YYX/cherimoya.fold_0.performance.tsv b/ENCSR518YYX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b15d880fe0b26963d79d2b12249fc1d093bff51c..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -633.3405151367188 0.42655983567237854 0.34755998849868774 0.14796645939350128 0.8448155522346497 0.7859269380569458 0.6115354895591736 \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_1.evaluate.json b/ENCSR518YYX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8e04030a5e81406ae0e0ee1fa8ddbb608e7f0886..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187POQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_1.fit.json b/ENCSR518YYX/cherimoya.fold_1.fit.json deleted file mode 100644 index d6150c8d41f1e7009b2f31d8fcda8d9e8eff0eb4..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF187POQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_1.log b/ENCSR518YYX/cherimoya.fold_1.log deleted file mode 100644 index 5422699c6ac4f64d9fee5d975c48bb98fa220f45..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2416 37.07574534416199 3.8047966957092285 473.12628173828125 1.154976487159729 1015.2551879882812 0.21149958670139313 0.6148661 10.327272415161133 True -1 4832 27.240830421447754 11.408546686172485 611.7001953125 1.0002481937408447 841.9671630859375 0.3111538290977478 0.76201445 5.205883979797363 True -2 7248 26.84967875480652 0.7019829750061035 608.9398803710938 1.4020129442214966 817.2423706054688 0.3260079026222229 0.7710597 3.1223597526550293 True -3 9664 26.916625261306763 0.721034049987793 496.2191162109375 0.8632848858833313 798.8024291992188 0.336078017950058 0.78123397 2.2719109058380127 True -4 12080 26.900927543640137 0.7094156742095947 483.96722412109375 0.7541799545288086 792.362548828125 0.33803826570510864 0.7941976 1.8366349935531616 True -5 14496 26.9675509929657 0.7084283828735352 505.1116027832031 0.8395325541496277 782.6963500976562 0.34374016523361206 0.8083655 1.511171817779541 True -6 16912 26.858684062957764 51.293349742889404 540.20361328125 1.0373499393463135 778.7623901367188 0.34710362553596497 0.8149584 1.3296786546707153 True -7 19328 26.935080766677856 0.8228743076324463 599.7193603515625 0.7743126749992371 772.4514770507812 0.3510741889476776 0.82119936 1.273512840270996 True -8 21744 26.877065181732178 0.7106232643127441 511.22882080078125 0.9658275842666626 769.6557006835938 0.352662056684494 0.8238336 1.0904922485351562 True -9 24160 26.8410964012146 2.1510910987854004 486.201416015625 0.7540847063064575 765.5601196289062 0.3556734025478363 0.8297364 1.0357459783554077 True -10 26576 26.58725118637085 0.6904034614562988 614.6217041015625 0.6702791452407837 761.1415405273438 0.3588312566280365 0.83816344 0.9104816913604736 True -11 28992 26.261365175247192 0.7051684856414795 605.6965942382812 0.7959522604942322 758.6652221679688 0.3603425920009613 0.84304196 0.8808422684669495 True -12 31408 26.24132204055786 0.7054691314697266 558.921630859375 0.7355353832244873 755.295166015625 0.36062443256378174 0.84835577 0.8349525928497314 True -13 33824 26.242305040359497 0.6986846923828125 558.5660400390625 0.7302970290184021 745.0348510742188 0.3672187924385071 0.8525724 0.751623272895813 True -14 36240 26.30628776550293 0.6916196346282959 730.833984375 1.0298103094100952 742.98046875 0.3682212829589844 0.8582907 0.7110703587532043 True -15 38656 26.22775363922119 2.986926317214966 513.5360107421875 0.5849930047988892 739.1080932617188 0.3698703646659851 0.8607702 0.6815192699432373 True -16 41072 26.344223976135254 0.7098231315612793 564.7135009765625 0.5556743144989014 739.3463745117188 0.37005266547203064 0.8614755 0.6581020355224609 True -17 43488 26.247563123703003 1.5043458938598633 575.3416748046875 0.5887665748596191 740.13525390625 0.36950576305389404 0.86213815 0.6495898962020874 True -18 45904 26.28499984741211 0.7031629085540771 446.1854248046875 0.9113385677337646 739.0139770507812 0.37012168765068054 0.8601091 0.6511679291725159 False -19 48320 26.35282850265503 0.7105152606964111 539.7767333984375 0.5098078846931458 738.2157592773438 0.37117433547973633 0.8587703 0.6538943648338318 False diff --git a/ENCSR518YYX/cherimoya.fold_1.performance.tsv b/ENCSR518YYX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0e0b73b8052b9172f53ae6f77cc84936bc5deb77..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -740.13525390625 0.40669384598731995 0.36950576305389404 0.1728183925151825 0.8621381521224976 0.8214448690414429 0.6495898962020874 \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_2.evaluate.json b/ENCSR518YYX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 63246a9923c63563b50a7ab0872009becf11001c..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187POQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_2.fit.json b/ENCSR518YYX/cherimoya.fold_2.fit.json deleted file mode 100644 index 06f78e91ecdbd240829226411c26b451870202a8..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF187POQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_2.log b/ENCSR518YYX/cherimoya.fold_2.log deleted file mode 100644 index 38c01ac20b0d5c8a369b832296037ea3d533f8a2..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2604 33.26324486732483 9.980729818344116 613.65185546875 1.1639608144760132 861.44091796875 0.20612381398677826 0.6032563 8.451102256774902 True -1 5208 28.95844841003418 0.569159984588623 553.2128295898438 1.0410399436950684 727.1757202148438 0.285724014043808 0.7330689 3.907411575317383 True -2 7812 28.981398344039917 0.5572857856750488 547.8473510742188 1.29988431930542 701.3363037109375 0.29979974031448364 0.7453678 2.6182408332824707 True -3 10416 28.886541604995728 0.5481905937194824 435.6528015136719 0.7800348401069641 687.1651611328125 0.307736337184906 0.769596 1.8221361637115479 True -4 13020 28.878997087478638 0.5623548030853271 565.9119262695312 1.4140840768814087 676.8048095703125 0.3137478828430176 0.7844868 1.4676178693771362 True -5 15624 28.912748336791992 0.5442218780517578 600.026611328125 1.1225334405899048 672.69580078125 0.31580373644828796 0.7961099 1.2089836597442627 True -6 18228 28.893213748931885 0.5485720634460449 535.8574829101562 0.9142920970916748 667.1050415039062 0.31989234685897827 0.8027645 1.0970985889434814 True -7 20832 28.865735054016113 0.5471131801605225 615.5850830078125 0.9390168190002441 661.5888671875 0.322674423456192 0.81185895 0.9152384400367737 True -8 23436 28.856295347213745 0.5433096885681152 584.39111328125 0.5159878730773926 661.2899780273438 0.32344427704811096 0.8143648 0.9219403862953186 True -9 26040 28.951824188232422 0.5466458797454834 618.732421875 0.8584942817687988 654.8336791992188 0.328156054019928 0.820917 0.821907639503479 True -10 28644 28.985875844955444 0.5430002212524414 523.0350341796875 0.4999012351036072 651.1295776367188 0.33000004291534424 0.823541 0.7843254208564758 True -11 31248 29.03001379966736 0.5631701946258545 460.1572570800781 0.7792156338691711 647.8616943359375 0.33279845118522644 0.83015776 0.7607376575469971 True -12 33852 29.002886056900024 0.5404889583587646 548.3087158203125 0.5159666538238525 646.3009643554688 0.3343900442123413 0.8346486 0.7165254354476929 True -13 36456 28.54523777961731 1.3454124927520752 573.43603515625 0.5439357757568359 641.8292236328125 0.33848243951797485 0.8389639 0.6875061988830566 True -14 39060 28.359055042266846 0.5420870780944824 709.5157470703125 0.7479984760284424 641.3865356445312 0.3382627069950104 0.84247607 0.6399176716804504 True -15 41664 28.407008171081543 0.5432415008544922 539.86474609375 0.45192256569862366 639.1686401367188 0.33994725346565247 0.846007 0.6185429096221924 True -16 44268 28.41410207748413 0.5421090126037598 505.83953857421875 0.4672708511352539 638.1657104492188 0.34027281403541565 0.84798306 0.5999610424041748 True -17 46872 28.334012031555176 0.5415909290313721 501.6325988769531 0.6221569180488586 639.3914794921875 0.33978039026260376 0.84623075 0.5971989035606384 False -18 49476 28.305474042892456 0.525559663772583 571.7799682617188 0.5343379378318787 640.37646484375 0.33962225914001465 0.8446862 0.6037958860397339 False -19 52080 28.323130130767822 0.5374042987823486 566.514404296875 0.30926787853240967 641.5248413085938 0.33839598298072815 0.8450123 0.6060634255409241 False diff --git a/ENCSR518YYX/cherimoya.fold_2.performance.tsv b/ENCSR518YYX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f01d4f30e4ad85d203faa8b3aeaa87313077c21e..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -638.1657104492188 0.42893102765083313 0.34027281403541565 0.15019401907920837 0.8479830622673035 0.7926451563835144 0.5999610424041748 \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_3.evaluate.json b/ENCSR518YYX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 96c493c9cc48df253ef4514148db1aff9a4a30fa..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187POQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_3.fit.json b/ENCSR518YYX/cherimoya.fold_3.fit.json deleted file mode 100644 index 95a744dc1867ffb6450ca8aa1f1a73713b23f1ed..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF187POQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_3.log b/ENCSR518YYX/cherimoya.fold_3.log deleted file mode 100644 index fd79dc70da81a5daf2bd8cc34e3d3b3602bfc2bf..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2507 32.188183546066284 2.8803696632385254 491.49322509765625 1.07716703414917 871.4566650390625 0.22401198744773865 0.6018946 8.238944053649902 True -1 5014 27.945327281951904 0.45129871368408203 526.7025756835938 0.9661982655525208 739.5424194335938 0.3072092831134796 0.7266198 4.3423075675964355 True -2 7521 27.885468006134033 0.4426848888397217 485.3916931152344 0.8301258087158203 714.14794921875 0.3257123827934265 0.7393519 2.8792972564697266 True -3 10028 27.866503953933716 0.44527769088745117 519.3009033203125 0.8802012205123901 707.6663208007812 0.33016806840896606 0.74117184 2.63746976852417 True -4 12535 27.868542909622192 0.43872761726379395 433.32244873046875 0.7259136438369751 701.2581176757812 0.3342108726501465 0.7538678 2.130282163619995 True -5 15042 27.841679096221924 0.45213818550109863 660.201904296875 0.7424878478050232 695.7100219726562 0.33649444580078125 0.7649333 1.800349235534668 True -6 17549 27.875075340270996 0.43965816497802734 566.0970458984375 0.8893566131591797 689.0645751953125 0.3430510461330414 0.77240896 1.5068358182907104 True -7 20056 27.95861577987671 0.7742128372192383 502.3308410644531 1.074247121810913 684.952392578125 0.34529227018356323 0.7740773 1.35059654712677 True -8 22563 27.87539553642273 0.4595823287963867 434.936279296875 0.7248759269714355 683.21435546875 0.3467949330806732 0.78196776 1.259784460067749 True -9 25070 27.859655618667603 0.4412555694580078 627.6574096679688 1.0254757404327393 678.69775390625 0.3512682616710663 0.7847034 1.1567753553390503 True -10 27577 27.890872955322266 0.44357728958129883 571.9057006835938 0.9865689873695374 676.0248413085938 0.3522661030292511 0.7891468 1.1264747381210327 True -11 30084 27.886451482772827 0.4447801113128662 636.4713745117188 0.7896239757537842 673.8431396484375 0.35341599583625793 0.7955558 1.0477004051208496 True -12 32591 27.88413906097412 23.98488712310791 594.970703125 0.7174298763275146 668.9513549804688 0.35740455985069275 0.8023314 0.9535824060440063 True -13 35098 28.047624588012695 0.4527280330657959 628.1851806640625 0.7703997492790222 666.06005859375 0.3593937158584595 0.80920684 0.874994695186615 True -14 37605 27.494712114334106 0.44437456130981445 481.1939697265625 0.7662213444709778 662.950439453125 0.3610091209411621 0.8176174 0.8201535940170288 True -15 40112 27.291659593582153 0.4447672367095947 597.37744140625 0.43131130933761597 659.2318115234375 0.3637635409832001 0.82647616 0.7621412873268127 True -16 42619 27.293558359146118 0.44310688972473145 433.48297119140625 0.5382664203643799 658.5909423828125 0.3636661171913147 0.8310419 0.7195485830307007 True -17 45126 27.258142232894897 0.43429112434387207 530.9763793945312 0.7881094217300415 659.4154663085938 0.36345207691192627 0.8334435 0.7035553455352783 True -18 47633 27.365452766418457 0.4562981128692627 604.8695068359375 0.4568352997303009 659.6143188476562 0.36312395334243774 0.83384085 0.7018995881080627 True -19 50140 27.43961477279663 0.4489004611968994 516.345458984375 0.5722842216491699 659.6624755859375 0.3626003563404083 0.83411837 0.7024791836738586 True diff --git a/ENCSR518YYX/cherimoya.fold_3.performance.tsv b/ENCSR518YYX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a1707bb2c69aebeceb40d1e4a8375cfd13a7caf9..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -659.6624755859375 0.4147544503211975 0.3626003861427307 0.15442293882369995 0.8341183662414551 0.7824581265449524 0.7024791836738586 \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_4.evaluate.json b/ENCSR518YYX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 66cddcf86c040dab57f093a319c52bd10b2adaf2..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187POQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_4.fit.json b/ENCSR518YYX/cherimoya.fold_4.fit.json deleted file mode 100644 index d25a1afd5ed43dd3f091a2b5a2f2832ba8fbee93..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF187POQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR518YYX/cherimoya.fold_4.log b/ENCSR518YYX/cherimoya.fold_4.log deleted file mode 100644 index b786eeb0141c178ed8c9487f91a6d8436ded81e7..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2497 32.24043679237366 4.367401123046875 682.9732055664062 1.3205199241638184 808.4221801757812 0.20929375290870667 0.59152246 9.407201766967773 True -1 4994 27.69462275505066 0.4806222915649414 612.2785034179688 1.3634440898895264 684.7362060546875 0.29115161299705505 0.72167915 3.8585684299468994 True -2 7491 27.76659345626831 0.47100329399108887 442.02935791015625 0.7466071844100952 663.5447998046875 0.3086939752101898 0.73929363 2.784914493560791 True -3 9988 27.758646488189697 0.4691743850708008 609.3350830078125 0.9236476421356201 651.1332397460938 0.3156939446926117 0.75220597 1.6811362504959106 True -4 12485 28.666410446166992 23.895357847213745 504.04241943359375 0.7948250770568848 644.1045532226562 0.3199433982372284 0.7629934 1.494059681892395 True -5 14982 29.087366580963135 0.47539210319519043 424.1563415527344 1.140848994255066 639.5299682617188 0.32367897033691406 0.76564085 1.3845332860946655 True -6 17479 27.702114582061768 0.4688091278076172 424.21160888671875 0.9712509512901306 634.9710693359375 0.32664772868156433 0.77730995 1.223766803741455 True -7 19976 27.794742345809937 2.2798430919647217 417.16192626953125 0.7364883422851562 634.4195556640625 0.32808223366737366 0.7797744 1.1779887676239014 True -8 22473 27.749124765396118 1.3325250148773193 409.73211669921875 0.9028033018112183 630.439208984375 0.330928772687912 0.7867162 1.0736972093582153 True -9 24970 27.77501893043518 0.4604959487915039 408.0074462890625 0.830359935760498 625.6502075195312 0.33329442143440247 0.7937981 1.016519546508789 True -10 27467 27.81870985031128 0.4678525924682617 607.9391479492188 0.7027053236961365 624.6175537109375 0.3343828022480011 0.7998111 0.9541505575180054 True -11 29964 27.744457006454468 0.46776342391967773 486.8867492675781 0.7575629949569702 621.0266723632812 0.33750829100608826 0.8062611 0.8867572546005249 True -12 32461 27.72044062614441 0.46558594703674316 414.08111572265625 0.8017737865447998 617.735107421875 0.3401170074939728 0.81463003 0.8176019191741943 True -13 34958 27.695307970046997 0.46752285957336426 504.73004150390625 0.8678609132766724 613.3817749023438 0.3435658812522888 0.82353395 0.7472106218338013 True -14 37455 27.74144959449768 0.4678671360015869 461.50665283203125 0.9013064503669739 611.6881103515625 0.34368544816970825 0.8299588 0.6743641495704651 True -15 39952 28.252251625061035 24.653466939926147 543.5602416992188 0.5582550764083862 607.9033813476562 0.3471892476081848 0.83561456 0.6370315551757812 True -16 42449 28.679372549057007 0.49135875701904297 529.116943359375 0.4065677225589752 608.7027587890625 0.3457641005516052 0.83811235 0.6136019229888916 True -17 44946 27.324330806732178 0.4655439853668213 456.2443542480469 0.700272798538208 611.3643798828125 0.34295007586479187 0.83853847 0.6071388125419617 True -18 47443 27.13138437271118 0.46561741828918457 503.716796875 0.4302411675453186 609.9780883789062 0.3455117344856262 0.8404903 0.6076626181602478 True -19 49940 27.13730549812317 0.4654686450958252 439.22149658203125 0.46846556663513184 610.880859375 0.34439077973365784 0.8385781 0.6120139956474304 False diff --git a/ENCSR518YYX/cherimoya.fold_4.performance.tsv b/ENCSR518YYX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0929a622b09c430c712305abdf23cb49ffbe1d5d..0000000000000000000000000000000000000000 --- a/ENCSR518YYX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -609.9780883789062 0.42936718463897705 0.3455117344856262 0.14391933381557465 0.8404902815818787 0.785511314868927 0.6076626181602478 \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_0.evaluate.json b/ENCSR520WTV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1d1c67edb043bc4241ac731e8c9e4ba385548de4..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098JOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_0.fit.json b/ENCSR520WTV/cherimoya.fold_0.fit.json deleted file mode 100644 index 815ce84502d6097f47ec18f171844fcb9d1b17b9..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF098JOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_0.log b/ENCSR520WTV/cherimoya.fold_0.log deleted file mode 100644 index c824f15e7a249307173f534eb82502726fd1e1a7..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 34.78742575645447 4.650870323181152 1273.847900390625 0.7642412185668945 1625.5810546875 0.3410112261772156 0.54789823 7.499304294586182 True -1 5554 30.750295639038086 0.6978776454925537 1035.661865234375 0.8260204792022705 1437.40576171875 0.41559112071990967 0.63030356 3.1747114658355713 True -2 8331 30.78846287727356 0.6808412075042725 1405.896240234375 0.7812241315841675 1400.028564453125 0.4252382218837738 0.648339 1.9612210988998413 True -3 11108 30.710228443145752 0.6654698848724365 1311.860107421875 0.8850224018096924 1366.2889404296875 0.43822169303894043 0.66338336 1.601867914199829 True -4 13885 30.670229196548462 1.2071647644042969 1404.210205078125 1.0069310665130615 1356.5498046875 0.44044771790504456 0.66455436 1.4688994884490967 True -5 16662 30.66510772705078 0.6771352291107178 1133.9580078125 0.873467206954956 1341.8905029296875 0.44668111205101013 0.6809409 1.0592230558395386 True -6 19439 30.789156436920166 0.7046630382537842 964.281494140625 0.5780723094940186 1329.9835205078125 0.44870296120643616 0.68302274 1.065177083015442 True -7 22216 30.69679045677185 0.6794352531433105 1157.822998046875 0.5774328708648682 1316.161865234375 0.45423656702041626 0.7024447 0.9119240045547485 True -8 24993 30.647966384887695 0.6690592765808105 1013.3065185546875 0.5609447956085205 1306.09326171875 0.4588738679885864 0.7160053 0.8245880007743835 True -9 27770 30.652917623519897 0.6821684837341309 1091.61767578125 0.5701549649238586 1296.1448974609375 0.4604293406009674 0.7342158 0.7468986511230469 True -10 30547 30.65162467956543 0.6687633991241455 1014.1533203125 0.43036526441574097 1285.5152587890625 0.4656974673271179 0.74433327 0.7097287178039551 True -11 33324 30.80855417251587 0.687708854675293 996.52783203125 0.6161459684371948 1274.7208251953125 0.46994638442993164 0.75500363 0.6341999769210815 True -12 36101 30.85426902770996 0.7639307975769043 1050.2139892578125 0.6401994228363037 1267.919677734375 0.47103357315063477 0.7641583 0.5582386255264282 True -13 38878 30.862468957901 0.6780290603637695 1091.4295654296875 0.42375892400741577 1261.060546875 0.4729457199573517 0.7715942 0.49020761251449585 True -14 41655 30.977248191833496 0.6908259391784668 924.7151489257812 0.5609067678451538 1253.518310546875 0.4739391505718231 0.77936465 0.43057146668434143 True -15 44432 30.797444581985474 0.6823046207427979 1004.460693359375 0.398037314414978 1249.970703125 0.474478542804718 0.78327936 0.4039258062839508 True -16 47209 30.82852029800415 0.7392787933349609 1370.6160888671875 0.569084644317627 1244.7376708984375 0.47536879777908325 0.7883713 0.37834587693214417 True -17 49986 30.88933253288269 0.6789393424987793 1049.9814453125 0.471851110458374 1241.01220703125 0.4782249331474304 0.79328203 0.3615301847457886 True -18 52763 30.876956701278687 0.6783862113952637 1155.8990478515625 0.39596694707870483 1243.6519775390625 0.4764615595340729 0.79343474 0.35695597529411316 True -19 55540 30.90757656097412 0.6838645935058594 1167.373046875 0.5517165660858154 1241.410888671875 0.478249728679657 0.7926035 0.3562622666358948 False diff --git a/ENCSR520WTV/cherimoya.fold_0.performance.tsv b/ENCSR520WTV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 09b60e80609dae0d6c291e7d3a4228969b2905c7..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1243.6519775390625 0.29162147641181946 0.4764615595340729 0.2640472650527954 0.793434739112854 0.7574236392974854 0.35695597529411316 \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_1.evaluate.json b/ENCSR520WTV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 114984ac92e0198636f93e38a9293e9f3641345a..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098JOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_1.fit.json b/ENCSR520WTV/cherimoya.fold_1.fit.json deleted file mode 100644 index 5a3f5356276ef71b3b762e322c71433bf25bcff5..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF098JOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_1.log b/ENCSR520WTV/cherimoya.fold_1.log deleted file mode 100644 index c0ba2df14bd3b1e5494a5df4f28fe95d08672a2d..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2663 33.523810625076294 4.807075262069702 1221.69482421875 0.7328184843063354 2169.1044921875 0.36398714780807495 0.43341812 10.982966423034668 True -1 5326 29.44237971305847 30.404008865356445 1106.642822265625 0.6881462335586548 1880.363037109375 0.45228588581085205 0.47275653 5.43705415725708 True -2 7989 29.47119688987732 24.148271799087524 1180.7242431640625 0.7890162467956543 1851.997314453125 0.4626287519931793 0.4689005 3.416886568069458 False -3 10652 29.436010122299194 0.8172380924224854 1297.506103515625 0.7419710755348206 1803.2974853515625 0.4736705720424652 0.4790982 2.867507219314575 True -4 13315 30.13412642478943 0.8229517936706543 1660.057861328125 1.0707684755325317 1774.5531005859375 0.48219817876815796 0.4858021 2.649653196334839 True -5 15978 29.38413643836975 0.810211181640625 1171.3797607421875 0.578830897808075 1764.530029296875 0.4850535988807678 0.49414834 2.6284401416778564 True -6 18641 29.39551019668579 0.7939579486846924 1114.13525390625 0.5008286237716675 1741.736083984375 0.49266475439071655 0.4987021 2.6204326152801514 True -7 21304 29.362853527069092 0.806025505065918 858.1465454101562 0.5459356307983398 1726.6263427734375 0.49918344616889954 0.50590265 2.201094627380371 True -8 23967 29.37191867828369 0.7944839000701904 1229.112548828125 0.5900334119796753 1721.4615478515625 0.4995128810405731 0.5092427 2.064202070236206 True -9 26630 29.374537229537964 1.3397090435028076 940.7305908203125 0.4766111671924591 1708.5146484375 0.50370192527771 0.5121827 1.8607592582702637 True -10 29293 29.35489511489868 0.7888498306274414 1211.1168212890625 0.6731733083724976 1696.002685546875 0.5072317719459534 0.5175928 1.7809809446334839 True -11 31956 29.354886770248413 0.790766716003418 1192.868408203125 0.6378239989280701 1687.576904296875 0.5101944208145142 0.52180576 1.7471206188201904 True -12 34619 29.38792061805725 0.7845361232757568 1082.6033935546875 0.633228063583374 1673.4932861328125 0.5145732760429382 0.52307093 1.6184712648391724 True -13 37282 29.43824076652527 0.7944700717926025 1052.4052734375 0.4010925889015198 1668.9468994140625 0.5147553086280823 0.5290787 1.504044771194458 True -14 39945 29.396191596984863 1.8979671001434326 1059.75244140625 0.37471503019332886 1652.5556640625 0.5197393298149109 0.5334297 1.4066790342330933 True -15 42608 29.428611278533936 0.7841603755950928 1072.767578125 0.42087626457214355 1650.369140625 0.5188637375831604 0.53555983 1.3141127824783325 True -16 45271 29.44857668876648 0.7946538925170898 935.5980834960938 0.4367613196372986 1649.2962646484375 0.5163376331329346 0.53877616 1.2433412075042725 True -17 47934 29.38347291946411 0.7914679050445557 1009.3499755859375 0.369872123003006 1645.0638427734375 0.5198190808296204 0.54003525 1.2035374641418457 True -18 50597 29.385695934295654 0.804520845413208 1040.6619873046875 0.23618489503860474 1641.895263671875 0.5210236310958862 0.5389292 1.1907211542129517 False -19 53260 29.4177348613739 0.7811374664306641 984.5828857421875 0.3391401767730713 1640.9757080078125 0.5216314196586609 0.5375436 1.1858007907867432 False diff --git a/ENCSR520WTV/cherimoya.fold_1.performance.tsv b/ENCSR520WTV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 61e89b9cf5aef53b435bae67be0b99c68e006d5d..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1645.0638427734375 0.251966267824173 0.5198190212249756 0.3264290690422058 0.5400352478027344 0.49992647767066956 1.2035374641418457 \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_2.evaluate.json b/ENCSR520WTV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4f78d9984516756096ce54c61db72f3b31679346..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098JOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_2.fit.json b/ENCSR520WTV/cherimoya.fold_2.fit.json deleted file mode 100644 index 1aa5cae568111e1cb9cdff987f0610e25adc30fa..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF098JOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_2.log b/ENCSR520WTV/cherimoya.fold_2.log deleted file mode 100644 index 4099edf2991a0588e03531bfdae953e261d97b03..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2907 35.847832918167114 3.517367362976074 1088.88525390625 0.7964584827423096 1795.6536865234375 0.34432047605514526 0.5235299 7.2470927238464355 True -1 5814 32.18192505836487 0.5380167961120605 1010.1803588867188 0.5563392639160156 1532.050048828125 0.43640974164009094 0.6386711 2.511707305908203 True -2 8721 32.15471577644348 0.9097621440887451 1278.5361328125 0.7294450998306274 1518.2861328125 0.44017142057418823 0.63593084 1.4902243614196777 False -3 11628 32.144864559173584 0.5272462368011475 1255.904296875 0.555870771408081 1480.472900390625 0.45160049200057983 0.65398306 1.5931766033172607 True -4 14535 32.047470569610596 0.5216138362884521 1264.5008544921875 0.746200680732727 1449.8131103515625 0.4627050459384918 0.6732495 1.4509729146957397 True -5 17442 32.09022784233093 0.521317720413208 1267.0128173828125 0.5912773609161377 1446.6729736328125 0.462819367647171 0.68614364 1.561156153678894 True -6 20349 32.10033440589905 0.5411584377288818 1374.529296875 0.42690569162368774 1423.034423828125 0.4715452492237091 0.7025505 1.006555438041687 True -7 23256 32.108304500579834 0.5205180644989014 1120.30224609375 0.5919420123100281 1416.4027099609375 0.47276389598846436 0.70596874 0.901554524898529 True -8 26163 32.07806992530823 0.7181599140167236 1175.74365234375 0.33665111660957336 1405.5926513671875 0.4768027663230896 0.7209936 0.7768964171409607 True -9 29070 32.1240599155426 0.5169777870178223 1055.750732421875 0.5134105086326599 1395.1800537109375 0.47865453362464905 0.73522484 0.6827002167701721 True -10 31977 32.086591720581055 0.5253171920776367 1096.42236328125 0.596917986869812 1381.937744140625 0.4841509759426117 0.7451233 0.6513499021530151 True -11 34884 32.03036665916443 1.5689241886138916 1167.66845703125 0.37096333503723145 1372.5206298828125 0.48808753490448 0.7531718 0.6100035309791565 True -12 37791 32.07413578033447 1.3585150241851807 1117.720703125 0.43034082651138306 1367.5357666015625 0.48844683170318604 0.7617306 0.5498639345169067 True -13 40698 32.10849213600159 0.5261964797973633 1066.1324462890625 0.4477687478065491 1359.9560546875 0.49115535616874695 0.76839226 0.5006807446479797 True -14 43605 32.08820033073425 0.523695707321167 1087.0810546875 0.5137094855308533 1349.3995361328125 0.49406424164772034 0.7764332 0.45064643025398254 True -15 46512 32.096760749816895 0.5230672359466553 912.4954833984375 0.34037381410598755 1344.6025390625 0.497383177280426 0.78501004 0.41428375244140625 True -16 49419 32.12280058860779 0.5243940353393555 1286.3177490234375 0.5097262859344482 1344.1246337890625 0.4952819049358368 0.7889963 0.39605769515037537 True -17 52326 32.139305114746094 0.5324437618255615 1074.0728759765625 0.35512325167655945 1341.611083984375 0.4973919689655304 0.79183745 0.38163772225379944 True -18 55233 32.12864375114441 0.5293028354644775 1063.92919921875 0.24318931996822357 1341.0682373046875 0.4975913465023041 0.79537076 0.3776688277721405 True -19 58140 32.15273666381836 0.5273144245147705 1024.7857666015625 0.2943771183490753 1342.04931640625 0.4970734715461731 0.79276174 0.3794245421886444 False diff --git a/ENCSR520WTV/cherimoya.fold_2.performance.tsv b/ENCSR520WTV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3138d5ec1d128f3f5ba732372c103f9bb9b4a868..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1341.0682373046875 0.27906936407089233 0.4975913465023041 0.2836518883705139 0.7953707575798035 0.7637515068054199 0.3776688277721405 \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_3.evaluate.json b/ENCSR520WTV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c0406e5cf3b75c9b394b78181d6314e64de66ac9..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098JOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_3.fit.json b/ENCSR520WTV/cherimoya.fold_3.fit.json deleted file mode 100644 index 7a68fece99a8c3dae574a41687a564522e445376..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF098JOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_3.log b/ENCSR520WTV/cherimoya.fold_3.log deleted file mode 100644 index dc8574e61f109a1e58c11effc0382bc64bc6b926..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 34.078033208847046 7.360541343688965 1256.2923583984375 0.8069196939468384 1805.5679931640625 0.34026476740837097 0.51341957 8.081938743591309 True -1 5460 30.198598384857178 0.5453402996063232 1042.3809814453125 0.6543606519699097 1581.4754638671875 0.43038222193717957 0.5916248 3.352294683456421 True -2 8190 30.16707444190979 0.5465824604034424 1311.183837890625 0.70685875415802 1532.015625 0.4444538652896881 0.6099328 2.2612640857696533 True -3 10920 30.140739917755127 0.5344853401184082 1164.6949462890625 0.7102550268173218 1490.9677734375 0.45419883728027344 0.6299668 2.0896289348602295 True -4 13650 30.077014207839966 0.526421308517456 1317.60205078125 0.7073224782943726 1470.4267578125 0.4612770080566406 0.64237493 2.15324068069458 True -5 16380 30.105376482009888 0.5278398990631104 1360.226318359375 0.7838611602783203 1447.7420654296875 0.46851930022239685 0.66009355 1.5702033042907715 True -6 19110 30.079094171524048 0.5242359638214111 1322.4296875 0.8157193660736084 1428.865966796875 0.475746214389801 0.6771571 1.2508502006530762 True -7 21840 30.090474605560303 0.526132345199585 1180.953369140625 0.7564067840576172 1414.3388671875 0.4812067151069641 0.6949534 1.1571117639541626 True -8 24570 30.090637683868408 0.5332608222961426 1486.703369140625 0.8344894647598267 1403.022705078125 0.48438698053359985 0.7024288 1.0124231576919556 True -9 27300 30.139360666275024 1.067138433456421 1104.8505859375 0.3894246220588684 1392.956298828125 0.4880538582801819 0.71816206 0.8813970685005188 True -10 30030 30.120169639587402 1.3681049346923828 1517.820068359375 0.6328754425048828 1386.701171875 0.4897461235523224 0.7245998 0.8370158672332764 True -11 32760 30.14215898513794 0.536158561706543 1194.8525390625 0.4813244938850403 1377.0419921875 0.4921659827232361 0.7400117 0.7430682182312012 True -12 35490 30.115861415863037 0.520054817199707 1216.5869140625 0.50986647605896 1365.7979736328125 0.497947096824646 0.74977136 0.6528975963592529 True -13 38220 30.087916374206543 0.5269279479980469 1057.4915771484375 0.509311318397522 1356.531005859375 0.500786304473877 0.75956553 0.5718876719474792 True -14 40950 30.18979287147522 0.5399844646453857 1055.8238525390625 0.5256743431091309 1348.6966552734375 0.5020567774772644 0.7705247 0.5097162127494812 True -15 43680 30.116060972213745 0.5314171314239502 1125.510498046875 0.4037165641784668 1349.36865234375 0.500700831413269 0.7772925 0.4768155515193939 True -16 46410 30.156256914138794 0.5382354259490967 1088.0994873046875 0.3988371193408966 1341.0101318359375 0.5038673877716064 0.7827134 0.44281041622161865 True -17 49140 30.14986276626587 1.554842472076416 1220.765380859375 0.5095670819282532 1339.6158447265625 0.5044900178909302 0.7890667 0.4200572669506073 True -18 51870 30.216432094573975 0.5434746742248535 1067.94970703125 0.6966128945350647 1336.8358154296875 0.506030797958374 0.7882047 0.4140235185623169 False -19 54600 30.214271783828735 0.5319287776947021 1037.3223876953125 0.4391319453716278 1339.9227294921875 0.5035806894302368 0.7884623 0.41273781657218933 False diff --git a/ENCSR520WTV/cherimoya.fold_3.performance.tsv b/ENCSR520WTV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 304bc729737c5a201877fee034fc8ae6372ed17c..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1339.6158447265625 0.27783915400505066 0.5044900178909302 0.28725090622901917 0.7890666723251343 0.7569328546524048 0.4200572669506073 \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_4.evaluate.json b/ENCSR520WTV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5f48dfb49aa0dd2cf70e78db1a176b067ff6c0b5..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098JOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_4.fit.json b/ENCSR520WTV/cherimoya.fold_4.fit.json deleted file mode 100644 index afe6094a01af51250ffad6d1f1f163f328835685..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF098JOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR520WTV/cherimoya.fold_4.log b/ENCSR520WTV/cherimoya.fold_4.log deleted file mode 100644 index 509b4a750b51db608543e1e2a970daaadbb1bedf..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 34.89331912994385 3.636014699935913 1370.1754150390625 0.7410218715667725 1676.15869140625 0.33754396438598633 0.50795907 8.448206901550293 True -1 5516 30.468557357788086 0.5582339763641357 1702.807373046875 0.8211820125579834 1459.0775146484375 0.42478570342063904 0.6069039 2.855638027191162 True -2 8274 30.46946406364441 2.275895595550537 1102.6771240234375 0.6526784896850586 1427.522216796875 0.4351871907711029 0.6124303 1.5583469867706299 True -3 11032 30.515097856521606 0.5553197860717773 1228.951904296875 0.5958934426307678 1376.57275390625 0.4503050744533539 0.65432703 1.1124762296676636 True -4 13790 30.473867416381836 0.5406947135925293 1018.634033203125 0.5024377107620239 1346.3502197265625 0.4632422924041748 0.67016584 0.9997453093528748 True -5 16548 30.413301706314087 0.5395233631134033 1196.845947265625 0.6432901620864868 1335.254150390625 0.46635767817497253 0.6806702 1.079807996749878 True -6 19306 30.466388463974 0.5449390411376953 1168.095703125 0.4783439040184021 1329.0975341796875 0.46923741698265076 0.68593824 0.8185817003250122 True -7 22064 30.45906138420105 0.541635274887085 1000.5563354492188 0.4434461295604706 1327.2333984375 0.4680155813694 0.68635064 0.9825215339660645 True -8 24822 30.42256760597229 5.219475030899048 1229.3330078125 0.5144715905189514 1324.0518798828125 0.4701137840747833 0.6826867 0.8229882121086121 False -9 27580 30.640401363372803 0.5571098327636719 1315.177001953125 0.4257926642894745 1304.1898193359375 0.47917380928993225 0.7122248 0.7058603763580322 True -10 30338 30.537133932113647 0.5559768676757812 954.485595703125 0.40898922085762024 1288.9434814453125 0.4849024713039398 0.7373489 0.5813697576522827 True -11 33096 30.44711923599243 0.5316324234008789 1233.975341796875 0.4316375255584717 1282.796875 0.4835062026977539 0.75105584 0.5087905526161194 True -12 35854 30.49171209335327 0.5459163188934326 1110.6285400390625 0.5100365877151489 1272.5364990234375 0.4880581498146057 0.76095706 0.4775078296661377 True -13 38612 30.491581439971924 0.5435178279876709 1146.900146484375 0.770619809627533 1265.9903564453125 0.49066871404647827 0.77187437 0.4415654242038727 True -14 41370 30.535426378250122 0.5325527191162109 1081.6175537109375 0.4678196907043457 1261.2230224609375 0.4928816556930542 0.7773995 0.41261962056159973 True -15 44128 30.579087495803833 0.5414302349090576 1259.1158447265625 0.6593165993690491 1253.3011474609375 0.4964878261089325 0.78549886 0.3885120153427124 True -16 46886 30.494725227355957 0.5330061912536621 1066.691162109375 0.31833416223526 1254.1881103515625 0.4951927959918976 0.7915027 0.3736581802368164 True -17 49644 30.47586441040039 0.5413370132446289 998.4876708984375 0.256022572517395 1252.418212890625 0.49606677889823914 0.7926028 0.36932530999183655 True -18 52402 30.49804973602295 0.535336971282959 1091.8878173828125 0.3322189152240753 1255.724609375 0.4953697621822357 0.790709 0.36770644783973694 False -19 55160 30.410574913024902 0.5421862602233887 1086.0579833984375 0.29103317856788635 1253.672119140625 0.497126042842865 0.7915537 0.36769819259643555 False diff --git a/ENCSR520WTV/cherimoya.fold_4.performance.tsv b/ENCSR520WTV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 034dbe2f27949b59e50303fe599d58b479446b6f..0000000000000000000000000000000000000000 --- a/ENCSR520WTV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1252.418212890625 0.285485178232193 0.4960668087005615 0.2723413407802582 0.7926027774810791 0.7516343593597412 0.36932530999183655 \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_0.evaluate.json b/ENCSR522FGG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index aebdea315922425086fe6734fc2f6325dd797ddf..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_0.fit.json b/ENCSR522FGG/cherimoya.fold_0.fit.json deleted file mode 100644 index 370ad94a85d3b1cfb385e3fb09d240c9ba9f3da1..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF187OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_0.log b/ENCSR522FGG/cherimoya.fold_0.log deleted file mode 100644 index 5e96fed12e372500215027cba67b2ca8d352b907..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2231 29.426486015319824 4.4639153480529785 164.67416381835938 0.3049979507923126 153.85678100585938 0.09901108592748642 0.7173112 2.7526378631591797 True -1 4462 24.613029956817627 0.507831335067749 131.8546905517578 0.594480574131012 149.30987548828125 0.1383712887763977 0.79013723 0.5730849504470825 True -2 6693 24.55354142189026 0.45696139335632324 99.98477172851562 0.4027431905269623 146.777099609375 0.15441834926605225 0.80713993 0.2963087856769562 True -3 8924 24.567988634109497 0.4565308094024658 119.34228515625 0.46361008286476135 145.2033233642578 0.16154205799102783 0.8149565 0.27050381898880005 True -4 11155 24.493959426879883 12.085430145263672 147.44798278808594 0.5142901539802551 144.4495849609375 0.16517174243927002 0.8220973 0.27861443161964417 True -5 13386 24.098427057266235 0.4630892276763916 129.2235870361328 0.20430788397789001 144.068359375 0.167230486869812 0.82532996 0.2844397723674774 True -6 15617 24.064340114593506 0.46590542793273926 114.8414306640625 0.2522338032722473 143.73794555664062 0.16911084949970245 0.829761 0.2823362946510315 True -7 17848 24.04586172103882 0.45611071586608887 122.7574462890625 0.37509119510650635 143.47169494628906 0.17185647785663605 0.8339178 0.25785672664642334 True -8 20079 24.059265613555908 0.45421385765075684 127.15812683105469 0.4639158844947815 143.21160888671875 0.1733824908733368 0.83839184 0.2445766031742096 True -9 22310 24.1477689743042 0.4570484161376953 113.66246032714844 0.4801541566848755 143.19654846191406 0.1734233945608139 0.83965796 0.24494853615760803 True -10 24541 24.07498788833618 0.45475149154663086 135.855224609375 0.2727311849594116 142.9766387939453 0.17491675913333893 0.84509116 0.23569081723690033 True -11 26772 24.04826593399048 0.46387529373168945 107.67054748535156 0.5253714323043823 142.6796112060547 0.17738765478134155 0.84844035 0.22633647918701172 True -12 29003 24.059179306030273 1.2680027484893799 123.53504943847656 0.32665562629699707 142.6611328125 0.17750178277492523 0.8512445 0.21989558637142181 True -13 31234 24.059273719787598 1.1686363220214844 115.60848999023438 0.4085715115070343 142.6033935546875 0.17765192687511444 0.85399693 0.2154850959777832 True -14 33465 24.092743158340454 0.4576430320739746 111.16168212890625 0.24174916744232178 142.43157958984375 0.17859670519828796 0.85739714 0.21107268333435059 True -15 35696 24.135180950164795 0.462296724319458 133.51226806640625 0.2382800132036209 142.33238220214844 0.17941351234912872 0.8595318 0.20375771820545197 True -16 37927 24.070360898971558 0.4487731456756592 105.54570007324219 0.23072963953018188 142.28929138183594 0.17991240322589874 0.8595341 0.2020765244960785 True -17 40158 24.082518815994263 0.4519035816192627 122.22799682617188 0.1684184968471527 142.41445922851562 0.17888836562633514 0.86101276 0.20233072340488434 True -18 42389 24.124891996383667 0.4530661106109619 121.4410400390625 0.18289777636528015 142.28697204589844 0.17960846424102783 0.8590466 0.20463840663433075 False -19 44620 24.068798542022705 0.4489624500274658 128.64596557617188 0.22894087433815002 142.4695587158203 0.17773273587226868 0.8591833 0.20606249570846558 False diff --git a/ENCSR522FGG/cherimoya.fold_0.performance.tsv b/ENCSR522FGG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e099bc33f5be62b3f5b8484c514efc1cde20ee5a..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -142.41445922851562 0.5790261626243591 0.17888836562633514 0.033930208534002304 0.8610127568244934 0.7976807355880737 0.20233072340488434 \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_1.evaluate.json b/ENCSR522FGG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index aba5579e3b7160e00a1b8fd49c6856967c4bb5ed..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_1.fit.json b/ENCSR522FGG/cherimoya.fold_1.fit.json deleted file mode 100644 index ab0d34114c8cf95530170fbde2e466a86c06cb4e..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF187OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_1.log b/ENCSR522FGG/cherimoya.fold_1.log deleted file mode 100644 index 672c26cdb7497818f55a2301809fa8b68fbe3e43..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2216 28.761547803878784 4.549429178237915 135.21807861328125 0.4935314655303955 181.8164520263672 0.10948381572961807 0.69822544 3.2070658206939697 True -1 4432 24.371021509170532 0.6238718032836914 116.64143371582031 0.27197813987731934 175.5728302001953 0.15785357356071472 0.7747252 0.9118207693099976 True -2 6648 24.346094608306885 1.0657339096069336 114.92105102539062 0.3441607654094696 171.8549346923828 0.1755104660987854 0.8084439 0.5066892504692078 True -3 8864 24.334277868270874 0.5881626605987549 101.53451538085938 0.36646023392677307 169.7724609375 0.18522971868515015 0.8177564 0.3960266709327698 True -4 11080 23.98035430908203 0.8866314888000488 93.14913940429688 0.370919793844223 169.23866271972656 0.18773749470710754 0.82446736 0.3431892991065979 True -5 13296 23.90617537498474 0.5737428665161133 127.25251770019531 0.30508190393447876 168.94976806640625 0.1885296106338501 0.8274784 0.34426775574684143 True -6 15512 23.882802486419678 0.5673356056213379 121.67860412597656 0.3179541826248169 168.3917236328125 0.19247199594974518 0.8326515 0.33455365896224976 True -7 17728 23.954704523086548 0.5695085525512695 131.45489501953125 0.3760380744934082 168.3442840576172 0.19240358471870422 0.8377918 0.31326359510421753 True -8 19944 23.963587760925293 0.5701451301574707 101.21443176269531 0.25864097476005554 168.21763610839844 0.192729189991951 0.8425403 0.29415637254714966 True -9 22160 23.91521120071411 0.5817728042602539 117.92180633544922 0.26464319229125977 167.8740234375 0.19530227780342102 0.8456433 0.27314314246177673 True -10 24376 23.95105218887329 0.580054759979248 129.62982177734375 0.24256518483161926 167.57315063476562 0.19738340377807617 0.84983546 0.2674563229084015 True -11 26592 23.89263653755188 12.758785963058472 123.64749145507812 0.2140512317419052 167.45114135742188 0.19798602163791656 0.8559995 0.2551230192184448 True -12 28808 24.02180814743042 0.596712589263916 114.95944213867188 0.23739859461784363 167.2641143798828 0.19933170080184937 0.85888946 0.2470398247241974 True -13 31024 24.01923942565918 0.5986428260803223 112.0478744506836 0.3062910735607147 166.97610473632812 0.20079907774925232 0.859668 0.24499037861824036 True -14 33240 23.928481578826904 0.5871231555938721 102.2244873046875 0.3096940517425537 166.95205688476562 0.2011060118675232 0.8645137 0.23269227147102356 True -15 35456 24.0123770236969 0.5760018825531006 134.26260375976562 0.2046222984790802 166.89178466796875 0.20133613049983978 0.8668423 0.22769597172737122 True -16 37672 24.00283932685852 0.5760824680328369 131.77963256835938 0.23341581225395203 166.94691467285156 0.20056916773319244 0.8680502 0.22050513327121735 True -17 39888 23.951255559921265 1.42218017578125 121.24017333984375 0.14428427815437317 167.0211181640625 0.19983641803264618 0.86923754 0.22304123640060425 True -18 42104 24.021132946014404 0.597649335861206 113.92710876464844 0.1960727572441101 167.072265625 0.19995911419391632 0.86752945 0.22492246329784393 False -19 44320 23.948766231536865 0.5991325378417969 123.2000732421875 0.21700169146060944 167.1597442626953 0.1991119533777237 0.86751634 0.22688785195350647 False diff --git a/ENCSR522FGG/cherimoya.fold_1.performance.tsv b/ENCSR522FGG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b0a6fa1f3d35d8e7a394edec6d79f694c6d52e01..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -167.0211181640625 0.5618200302124023 0.19983640313148499 0.03928365930914879 0.8692375421524048 0.8377929329872131 0.22304123640060425 \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_2.evaluate.json b/ENCSR522FGG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d8bbe68a231a1bc0c88b866010e5848468586178..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_2.fit.json b/ENCSR522FGG/cherimoya.fold_2.fit.json deleted file mode 100644 index 7a7612f83eda7f2b4a0ce642ebb97e3ec7431609..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF187OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_2.log b/ENCSR522FGG/cherimoya.fold_2.log deleted file mode 100644 index c57fcb37707330ee92fb2ea5c273f09955b9fb43..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2351 30.793920040130615 3.3911378383636475 129.1663055419922 0.4602004587650299 159.81370544433594 0.10245861113071442 0.69981277 2.539080858230591 True -1 4702 25.922247409820557 1.6214747428894043 140.24932861328125 0.36429160833358765 154.09165954589844 0.14729413390159607 0.7795539 0.6800382733345032 True -2 7053 25.8717679977417 0.4506397247314453 121.59551239013672 0.33938589692115784 151.13522338867188 0.16364885866641998 0.81168073 0.31474125385284424 True -3 9404 25.9109468460083 0.45211291313171387 105.95272064208984 0.24949517846107483 149.8351593017578 0.16861507296562195 0.8210672 0.28157344460487366 True -4 11755 25.853471517562866 0.44910287857055664 131.900390625 0.24308569729328156 149.47494506835938 0.1697946935892105 0.82648575 0.2750277817249298 True -5 14106 25.956902742385864 0.44773411750793457 120.37838745117188 0.36773449182510376 148.9001922607422 0.1747523993253708 0.8330494 0.2827266454696655 True -6 16457 25.912859439849854 12.961647987365723 118.95523071289062 0.4118622839450836 148.6864013671875 0.17617559432983398 0.8366765 0.2861303389072418 True -7 18808 26.012598276138306 0.44581103324890137 137.13967895507812 0.39486709237098694 148.55831909179688 0.17667219042778015 0.839051 0.27954575419425964 True -8 21159 25.81725764274597 0.44435811042785645 129.7514190673828 0.3573817014694214 148.2872772216797 0.17834943532943726 0.84097725 0.2652254104614258 True -9 23510 25.848467111587524 1.4658842086791992 155.92529296875 0.21767468750476837 147.9447021484375 0.18071068823337555 0.84534335 0.25347450375556946 True -10 25861 25.87137770652771 0.434262752532959 119.83045959472656 0.19555923342704773 147.73011779785156 0.18203310668468475 0.8481881 0.23654235899448395 True -11 28212 25.36044144630432 0.4333491325378418 98.82373809814453 0.3074047565460205 147.71566772460938 0.18188396096229553 0.85114247 0.22206532955169678 True -12 30563 25.326589345932007 0.43384456634521484 105.92951202392578 0.24846217036247253 147.5763397216797 0.183015838265419 0.8553024 0.22228822112083435 True -13 32914 25.3289315700531 0.44144320487976074 117.14060974121094 0.2754538655281067 147.39236450195312 0.18433010578155518 0.85891986 0.21610628068447113 True -14 35265 25.321911811828613 0.43984484672546387 135.10975646972656 0.1444925218820572 147.30279541015625 0.18469060957431793 0.8609048 0.21229276061058044 True -15 37616 25.325141668319702 0.43424081802368164 112.99107360839844 0.27990782260894775 147.3059539794922 0.1845368891954422 0.8627857 0.21054953336715698 True -16 39967 25.29332971572876 0.4381825923919678 121.79936981201172 0.17626890540122986 147.24461364746094 0.1851699948310852 0.8624985 0.20825590193271637 False -17 42318 25.350496530532837 0.4448666572570801 119.83007049560547 0.19119147956371307 147.32882690429688 0.1843099147081375 0.86380655 0.20783469080924988 True -18 44669 25.325854063034058 0.4322042465209961 151.27590942382812 0.16115164756774902 147.37457275390625 0.184362530708313 0.862398 0.2093227505683899 False -19 47020 25.336410522460938 0.4457275867462158 130.408203125 0.11657171696424484 147.47592163085938 0.1835102140903473 0.861987 0.21002759039402008 False diff --git a/ENCSR522FGG/cherimoya.fold_2.performance.tsv b/ENCSR522FGG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 531c50bd4d75db41787b392fcace1ab9e2ed2ef1..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -147.32882690429688 0.5746361017227173 0.1843099445104599 0.03513413295149803 0.8638065457344055 0.812860906124115 0.20783469080924988 \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_3.evaluate.json b/ENCSR522FGG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 38ad070f614056b63e092f1da9ab26cd246b53df..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_3.fit.json b/ENCSR522FGG/cherimoya.fold_3.fit.json deleted file mode 100644 index 0fa2e699c9ec170946812598e2c8f1806fdfae57..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF187OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_3.log b/ENCSR522FGG/cherimoya.fold_3.log deleted file mode 100644 index 597fde2df334340d01db0e1f706b22558a5fb1ef..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2263 29.72469401359558 3.6267037391662598 111.67239379882812 0.32488831877708435 159.85714721679688 0.10174768418073654 0.7020802 2.9088401794433594 True -1 4526 24.963287353515625 0.511643648147583 121.71839904785156 0.3809131979942322 154.96939086914062 0.14132358133792877 0.79539084 0.733213484287262 True -2 6789 24.904282569885254 0.45734739303588867 116.70857238769531 0.3870306611061096 151.9253692626953 0.1579275131225586 0.8224256 0.3481036126613617 True -3 9052 24.896438121795654 0.4560210704803467 134.41488647460938 0.39422404766082764 150.71299743652344 0.1645902693271637 0.8289637 0.32959794998168945 True -4 11315 24.912395238876343 0.4774460792541504 99.65084838867188 0.276758074760437 150.01380920410156 0.1692495048046112 0.8339001 0.31720253825187683 True -5 13578 24.897440195083618 12.24625539779663 121.75157165527344 0.318421334028244 149.83206176757812 0.17059096693992615 0.8351875 0.34387388825416565 True -6 15841 25.083144664764404 0.46992921829223633 126.37373352050781 0.3340396285057068 149.82862854003906 0.16991190612316132 0.8377221 0.33735451102256775 True -7 18104 24.869495153427124 0.46691250801086426 138.25003051757812 0.30974921584129333 149.65907287597656 0.1715066283941269 0.83898324 0.3352518379688263 True -8 20367 24.82978129386902 0.4612584114074707 106.79783630371094 0.3316326141357422 149.54034423828125 0.17237526178359985 0.8434768 0.32285282015800476 True -9 22630 24.870190382003784 0.45508265495300293 124.47132873535156 0.2751455307006836 149.29739379882812 0.17406094074249268 0.8470815 0.3080671727657318 True -10 24893 24.871044397354126 0.47057414054870605 123.88093566894531 0.28891903162002563 149.1495361328125 0.17503152787685394 0.8539657 0.2937505841255188 True -11 27156 24.932783603668213 0.47150564193725586 126.76396179199219 0.3800821900367737 148.9219512939453 0.17698146402835846 0.85669035 0.27847328782081604 True -12 29419 24.89402937889099 0.45841121673583984 128.63739013671875 0.290500670671463 148.89857482910156 0.1764623373746872 0.8576703 0.2632675766944885 True -13 31682 24.903639554977417 0.4733312129974365 107.4983139038086 0.21492817997932434 148.62298583984375 0.17909371852874756 0.8628284 0.24795599281787872 True -14 33945 24.89865469932556 0.4705789089202881 134.0928497314453 0.21173545718193054 148.7222900390625 0.1774006336927414 0.86284953 0.23684890568256378 True -15 36208 24.84389328956604 0.9123845100402832 127.62535095214844 0.26734018325805664 148.5392608642578 0.17931097745895386 0.8670402 0.22772549092769623 True -16 38471 24.8562912940979 0.4692676067352295 124.67741394042969 0.26028722524642944 148.53834533691406 0.17880362272262573 0.86854696 0.22047969698905945 True -17 40734 24.882355451583862 0.48189830780029297 104.61734008789062 0.37746304273605347 148.53427124023438 0.179067000746727 0.868653 0.21533526480197906 True -18 42997 24.835891485214233 0.4527146816253662 107.29518127441406 0.1902564913034439 148.62156677246094 0.1783447563648224 0.8643206 0.2166559100151062 False -19 45260 24.439948797225952 0.4686703681945801 104.82698059082031 0.16537338495254517 148.56683349609375 0.17896495759487152 0.863205 0.21814978122711182 False diff --git a/ENCSR522FGG/cherimoya.fold_3.performance.tsv b/ENCSR522FGG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7256ef6142b61a25e3d47a95b0db2cce512fac61..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -148.53427124023438 0.5767671465873718 0.17906701564788818 0.034374017268419266 0.8686529994010925 0.8095249533653259 0.21533526480197906 \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_4.evaluate.json b/ENCSR522FGG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fb5c43ccad8ee65ee3d3306dfd20c3b643811d1b..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_4.fit.json b/ENCSR522FGG/cherimoya.fold_4.fit.json deleted file mode 100644 index 4984409a7d7b045329052dd4723ff84c34decb2c..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF187OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR522FGG/cherimoya.fold_4.log b/ENCSR522FGG/cherimoya.fold_4.log deleted file mode 100644 index 1ea172c4832041ac9868e873274abd66a05a06e3..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2324 31.033624410629272 3.498044490814209 139.0728759765625 0.4395817220211029 149.1485137939453 0.09788962453603745 0.70225066 2.416658401489258 True -1 4648 25.66741943359375 0.49047064781188965 125.15859985351562 0.2844277620315552 144.20445251464844 0.13907665014266968 0.78483444 0.5932639241218567 True -2 6972 25.575004816055298 0.528181791305542 109.18467712402344 0.38688522577285767 141.9932098388672 0.15272070467472076 0.80027074 0.3150465786457062 True -3 9296 25.55732274055481 0.4643111228942871 130.7028350830078 0.44356074929237366 140.85739135742188 0.15764844417572021 0.8136203 0.25501367449760437 True -4 11620 25.527970552444458 2.005964756011963 107.72013092041016 0.4092983901500702 140.21791076660156 0.16181817650794983 0.8200099 0.24375233054161072 True -5 13944 25.630804300308228 0.516852617263794 121.5067138671875 0.3189328908920288 139.76971435546875 0.1650594025850296 0.82348305 0.2492900788784027 True -6 16268 25.62212634086609 0.47277307510375977 131.8827667236328 0.40673747658729553 139.7405548095703 0.1642700880765915 0.82941014 0.23160633444786072 True -7 18592 25.592984199523926 0.49406981468200684 122.87357330322266 0.44368481636047363 139.49378967285156 0.1667027771472931 0.83255225 0.22874172031879425 True -8 20916 25.5312180519104 0.5261428356170654 116.01554870605469 0.358299195766449 139.3144073486328 0.1672448366880417 0.83456635 0.22476178407669067 True -9 23240 25.609695434570312 0.47098517417907715 120.60448455810547 0.28819143772125244 139.08877563476562 0.1692378669977188 0.83973837 0.219061017036438 True -10 25564 25.568164110183716 0.46649861335754395 113.95045471191406 0.3690856695175171 138.92465209960938 0.1704750657081604 0.84199286 0.21642948687076569 True -11 27888 25.60189986228943 0.4772460460662842 103.16938781738281 0.12748228013515472 138.7763214111328 0.171718567609787 0.8434127 0.21009239554405212 True -12 30212 25.551717042922974 0.47026872634887695 125.40777587890625 0.23587898910045624 138.5984649658203 0.1734446883201599 0.8476023 0.20596769452095032 True -13 32536 25.66336417198181 0.4740264415740967 123.45223999023438 0.3785856366157532 138.5189971923828 0.17406924068927765 0.8502059 0.20028342306613922 True -14 34860 25.548380136489868 0.47716212272644043 92.12370300292969 0.1976507604122162 138.52723693847656 0.17401611804962158 0.8516317 0.2017805129289627 True -15 37184 25.587181329727173 0.4572439193725586 126.70723724365234 0.1513301134109497 138.4644317626953 0.17422953248023987 0.8526434 0.20147916674613953 True -16 39508 25.558286666870117 0.46834802627563477 115.31800079345703 0.24921715259552002 138.39515686035156 0.1744920313358307 0.8549019 0.19683873653411865 True -17 41832 25.606571674346924 0.46009397506713867 91.92798614501953 0.15801122784614563 138.4620819091797 0.174184188246727 0.85570055 0.19674110412597656 True -18 44156 25.58610463142395 0.4647183418273926 101.09514617919922 0.22135670483112335 138.5079803466797 0.17371080815792084 0.8549426 0.1999281346797943 False -19 46480 25.594875812530518 19.3852322101593 104.73851776123047 0.1397673338651657 138.61663818359375 0.1727592796087265 0.8530762 0.2024073302745819 False diff --git a/ENCSR522FGG/cherimoya.fold_4.performance.tsv b/ENCSR522FGG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 40893baa56c3523569d296775546c73073b309ed..0000000000000000000000000000000000000000 --- a/ENCSR522FGG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -138.4620819091797 0.5821552276611328 0.1741841733455658 0.02969415858387947 0.8557005524635315 0.7888574600219727 0.19674110412597656 \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_0.evaluate.json b/ENCSR524CPZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7cd54e4320f1650b2239c1b59f71b40792dcf2da..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF076YVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_0.fit.json b/ENCSR524CPZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 783bd1ca2c3704bc9c9101fbd114b4f50ffc8e1f..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF076YVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_0.log b/ENCSR524CPZ/cherimoya.fold_0.log deleted file mode 100644 index a3da3f056c43fb4f84431e6dd51d9eaf09e9101d..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2684 35.70587229728699 11.416412353515625 363.67529296875 0.6319315433502197 608.3701171875 0.53742516040802 0.5606739 6.775699615478516 True -1 5368 30.01294207572937 24.536083221435547 461.2677001953125 0.7304597496986389 513.225341796875 0.6514233350753784 0.640225 2.1844699382781982 True -2 8052 30.48838710784912 0.5925986766815186 336.101318359375 0.5486606955528259 502.0627746582031 0.6647250056266785 0.65687835 0.9368966817855835 True -3 10736 30.017704725265503 1.603344440460205 400.4253845214844 0.5006933808326721 496.5588073730469 0.6710526347160339 0.6649925 0.7559130191802979 True -4 13420 30.18186855316162 1.4873812198638916 360.85772705078125 0.4643671214580536 494.2677307128906 0.6735778450965881 0.667674 0.7239411473274231 True -5 16104 29.991235733032227 0.5552976131439209 375.9240417480469 0.49664342403411865 492.3847351074219 0.6764360666275024 0.66884077 0.6545712947845459 True -6 18788 30.04969334602356 0.5489134788513184 366.5286560058594 0.5679024457931519 490.6554260253906 0.6790586709976196 0.671458 0.594240128993988 True -7 21472 30.015174627304077 0.5517325401306152 375.61798095703125 0.5736873149871826 489.4751281738281 0.6803401708602905 0.6759417 0.6007128357887268 True -8 24156 29.952139377593994 0.5505633354187012 443.3299560546875 0.44848302006721497 487.58258056640625 0.6823679208755493 0.68097043 0.5635976791381836 True -9 26840 29.955724000930786 0.5548362731933594 432.0121154785156 0.6753871440887451 485.90045166015625 0.6846491098403931 0.6890233 0.5142170190811157 True -10 29524 29.978501319885254 0.5638172626495361 405.388671875 0.41827625036239624 484.12841796875 0.6866223812103271 0.69528013 0.5069338083267212 True -11 32208 29.947434663772583 0.5499663352966309 383.2414855957031 0.34212732315063477 482.4029846191406 0.688590407371521 0.7066669 0.4677274823188782 True -12 34892 29.935667276382446 0.5636799335479736 392.576171875 0.4528517723083496 480.65069580078125 0.6905975937843323 0.71126217 0.4682399332523346 True -13 37576 29.986770391464233 1.1011841297149658 431.3536376953125 0.5618131160736084 479.2009582519531 0.692457914352417 0.7183431 0.4552065432071686 True -14 40260 29.963876008987427 0.5619993209838867 440.6141662597656 0.346142441034317 477.7565612792969 0.6940096616744995 0.72581357 0.447537362575531 True -15 42944 29.92570209503174 0.7397477626800537 437.06524658203125 0.38597503304481506 477.214111328125 0.6947475075721741 0.72759163 0.4451935589313507 True -16 45628 29.916028022766113 0.5506434440612793 383.82391357421875 0.35524052381515503 476.94677734375 0.6948804259300232 0.7300215 0.4472375810146332 True -17 48312 29.819271564483643 0.7622406482696533 396.81402587890625 0.3364339768886566 477.1601867675781 0.6946149468421936 0.7280203 0.45485812425613403 False -18 50996 29.99510383605957 0.561448335647583 383.3658447265625 0.26548299193382263 477.44256591796875 0.6941869258880615 0.7257739 0.4623531103134155 False -19 53680 30.160956144332886 0.5615100860595703 348.0949401855469 0.2217661440372467 477.6871032714844 0.693901777267456 0.72234684 0.4683414697647095 False diff --git a/ENCSR524CPZ/cherimoya.fold_0.performance.tsv b/ENCSR524CPZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7d315a5473ee81fa7c9901da1c3bb092442a935b..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -476.94677734375 0.2477569431066513 0.6948804259300232 0.3058442771434784 0.7300214767456055 0.6504892110824585 0.4472375810146332 \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_1.evaluate.json b/ENCSR524CPZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c57c9275368d1f73c99f611ff71a18f9513d4e9a..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF076YVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_1.fit.json b/ENCSR524CPZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 13193f56b1562868922fa52fe0342a6a25873dbf..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF076YVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_1.log b/ENCSR524CPZ/cherimoya.fold_1.log deleted file mode 100644 index f69811125098c2f1f736e8ae1ff69826fbfe0e8c..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 35.313430070877075 4.128961086273193 351.77752685546875 0.6364266276359558 634.4019165039062 0.5553943514823914 0.5950062 8.25375747680664 True -1 5482 30.526422262191772 0.7829351425170898 373.1395568847656 0.6667670011520386 550.981201171875 0.6608093976974487 0.6796124 1.8555582761764526 True -2 8223 30.171452283859253 0.6328942775726318 381.200927734375 0.6387909650802612 539.2981567382812 0.6733776926994324 0.69886684 0.8473225831985474 True -3 10964 29.90606379508972 0.6120622158050537 367.1963806152344 0.6937057971954346 534.5640869140625 0.6793149709701538 0.7050431 0.7511254549026489 True -4 13705 29.8295795917511 0.6159031391143799 427.9368896484375 0.6557936072349548 532.302734375 0.6828938126564026 0.71151805 0.685045599937439 True -5 16446 29.827547073364258 0.6000111103057861 495.93634033203125 0.5488628149032593 529.9672241210938 0.6857048273086548 0.7138464 0.6249609589576721 True -6 19187 29.861720323562622 1.467376947402954 475.852294921875 0.5810433626174927 527.2532958984375 0.6886539459228516 0.7195727 0.5779605507850647 True -7 21928 29.8430335521698 0.6050398349761963 348.99853515625 0.5266423225402832 525.2764282226562 0.6911813020706177 0.72383726 0.5563929080963135 True -8 24669 29.889935731887817 0.6148695945739746 406.1060791015625 0.6734708547592163 523.89453125 0.6930372714996338 0.7277431 0.5372216105461121 True -9 27410 29.848536491394043 0.6654760837554932 357.4161376953125 0.49923789501190186 521.8916625976562 0.6952388882637024 0.7327592 0.5070483088493347 True -10 30151 29.919516563415527 0.6087906360626221 434.2455139160156 0.5028417110443115 519.9067993164062 0.696933925151825 0.7389399 0.48319825530052185 True -11 32892 29.87113881111145 0.5834066867828369 471.96990966796875 0.39888566732406616 518.52587890625 0.6987231373786926 0.74546766 0.47641608119010925 True -12 35633 29.862175226211548 1.0035722255706787 413.67218017578125 0.5752202868461609 517.0382690429688 0.7005094289779663 0.75102574 0.456596314907074 True -13 38374 29.849785089492798 0.5960650444030762 391.11871337890625 0.5003482103347778 515.3245849609375 0.702083945274353 0.7600327 0.426418662071228 True -14 41115 29.91741180419922 0.6067967414855957 354.0050964355469 0.48231980204582214 513.8992309570312 0.7036741971969604 0.7647256 0.41596975922584534 True -15 43856 29.98029351234436 0.6063690185546875 386.384765625 0.3217718005180359 513.1575927734375 0.7044728994369507 0.7701176 0.4048451781272888 True -16 46597 29.956087589263916 0.6243972778320312 378.8402404785156 0.4285539984703064 512.7002563476562 0.7045862078666687 0.77313447 0.39984914660453796 True -17 49338 30.10498046875 21.817922830581665 330.15472412109375 0.337980717420578 512.890625 0.7043085098266602 0.7706239 0.40411707758903503 False -18 52079 30.119834423065186 0.6387722492218018 360.29095458984375 0.20856072008609772 513.0521240234375 0.7037860751152039 0.7673884 0.40965530276298523 False -19 54820 30.070352792739868 0.6369826793670654 357.06781005859375 0.2878420054912567 513.3321533203125 0.7034732699394226 0.7659129 0.41562727093696594 False diff --git a/ENCSR524CPZ/cherimoya.fold_1.performance.tsv b/ENCSR524CPZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0c7e3640733690ccf77cdcf0b55e03dd03090bc0..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -512.7002563476562 0.2374771237373352 0.7045862078666687 0.3259204626083374 0.7731344699859619 0.7208091616630554 0.39984914660453796 \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_2.evaluate.json b/ENCSR524CPZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cbcfa4709614a58b60390b8d5d2255deb63f95a2..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF076YVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_2.fit.json b/ENCSR524CPZ/cherimoya.fold_2.fit.json deleted file mode 100644 index bf885ab102dd05323a52a5b2ddeab9f8367e0a6b..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF076YVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_2.log b/ENCSR524CPZ/cherimoya.fold_2.log deleted file mode 100644 index 43e83482d90f0db27debc4874aeb6251319d8e51..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2855 38.235358238220215 4.015523195266724 450.84002685546875 0.5793290734291077 601.1235961914062 0.5464966297149658 0.5797416 5.8743109703063965 True -1 5710 31.807719945907593 0.6274588108062744 417.791015625 0.72976154088974 518.0855712890625 0.6500973105430603 0.6782521 1.641312599182129 True -2 8565 31.75239062309265 0.5220112800598145 402.53961181640625 0.588863730430603 506.9408874511719 0.6622044444084167 0.6917496 0.833202064037323 True -3 11420 31.343579530715942 0.5138332843780518 408.9765625 0.9207320213317871 503.2030029296875 0.6672506928443909 0.69180006 0.8507120609283447 True -4 14275 31.123713970184326 0.8611209392547607 440.13446044921875 0.3927656412124634 500.8001708984375 0.6704177856445312 0.6996569 0.7836080193519592 True -5 17130 31.05032181739807 2.288510799407959 464.7396240234375 0.4894521236419678 498.6710510253906 0.6725857257843018 0.7001261 0.6618971824645996 True -6 19985 31.089295625686646 0.5189778804779053 358.8365783691406 0.5036871433258057 497.6540832519531 0.6748306751251221 0.7067401 0.6345398426055908 True -7 22840 31.049480438232422 0.5462234020233154 424.05389404296875 0.5176886916160583 495.59759521484375 0.6771029829978943 0.7078872 0.5952035188674927 True -8 25695 31.027408838272095 0.5169713497161865 334.4364318847656 0.579129159450531 493.4685974121094 0.6792753338813782 0.7153647 0.5554042458534241 True -9 28550 31.025773286819458 0.5150871276855469 386.54827880859375 0.5389440655708313 491.0912170410156 0.6815987825393677 0.7193539 0.5246210694313049 True -10 31405 31.134459972381592 0.528733491897583 386.56842041015625 0.5412770509719849 489.553955078125 0.6831682324409485 0.7210675 0.5133607387542725 True -11 34260 31.09549379348755 0.5282080173492432 319.39215087890625 0.33990833163261414 487.7546081542969 0.6854467988014221 0.72695243 0.49626532196998596 True -12 37115 31.068472385406494 0.5275595188140869 368.12310791015625 0.5937920808792114 486.058837890625 0.6872274875640869 0.7325032 0.4705239534378052 True -13 39970 31.0992271900177 0.5286352634429932 396.8740539550781 0.37260812520980835 484.51007080078125 0.6889027953147888 0.73916817 0.45695796608924866 True -14 42825 31.13136911392212 0.5561151504516602 374.1646423339844 0.3663952052593231 483.2288513183594 0.6904016137123108 0.74636555 0.43506699800491333 True -15 45680 31.102328062057495 0.538243293762207 438.26275634765625 0.36796173453330994 482.59454345703125 0.691164493560791 0.752676 0.42874401807785034 True -16 48535 31.095066785812378 0.5148677825927734 417.0908508300781 0.2958419919013977 482.22802734375 0.6915256977081299 0.7565486 0.4225824177265167 True -17 51390 31.101634740829468 0.5725193023681641 352.50921630859375 0.28768205642700195 482.1914367675781 0.6913692355155945 0.754924 0.4224117398262024 False -18 54245 31.130439043045044 0.5193037986755371 372.5177001953125 0.25849542021751404 482.5717468261719 0.6909524202346802 0.75367045 0.42766380310058594 False -19 57100 31.153655529022217 0.5314943790435791 419.8226318359375 0.18733905255794525 482.78125 0.6906461715698242 0.7517413 0.43242204189300537 False diff --git a/ENCSR524CPZ/cherimoya.fold_2.performance.tsv b/ENCSR524CPZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 74122cec59b69012d79f3cece5aa6c2205dbcc77..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -482.22802734375 0.24829910695552826 0.6915256381034851 0.30831605195999146 0.7565485835075378 0.6811665892601013 0.4225824177265167 \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_3.evaluate.json b/ENCSR524CPZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ac423cb146fe066953407d83e837354626884026..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF076YVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_3.fit.json b/ENCSR524CPZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 8add30310d516aba1f5df61e2ec12d73ac8cacd4..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF076YVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_3.log b/ENCSR524CPZ/cherimoya.fold_3.log deleted file mode 100644 index 20c304e572ec1947444ffa56d091c08c48ff6c5d..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2800 35.611544370651245 4.490044355392456 380.38250732421875 0.46073079109191895 601.6544189453125 0.5503854155540466 0.5692736 6.623202323913574 True -1 5600 31.128345251083374 0.6525156497955322 359.61126708984375 0.47474363446235657 521.4102172851562 0.6538830995559692 0.6526469 1.8450376987457275 True -2 8400 31.135452270507812 0.6176166534423828 463.93511962890625 0.5547865629196167 509.1722106933594 0.666629433631897 0.65710527 0.8625307083129883 True -3 11200 31.114285469055176 0.6370761394500732 415.38739013671875 0.765174388885498 504.4326171875 0.6718752384185791 0.6688282 0.8403668999671936 True -4 14000 30.732453107833862 0.579204797744751 395.70355224609375 0.4595567584037781 501.6728820800781 0.6750173568725586 0.67853975 0.7690243124961853 True -5 16800 30.504799604415894 0.5918292999267578 332.6265869140625 0.49740391969680786 500.6021728515625 0.6767581701278687 0.66712 0.746100664138794 False -6 19600 30.462428092956543 0.5830223560333252 364.981689453125 0.5589606761932373 499.156005859375 0.6792162656784058 0.67679864 0.6286041736602783 False -7 22400 30.49133276939392 0.5807945728302002 344.5762939453125 0.6249300837516785 497.099853515625 0.6811589002609253 0.6832588 0.5938945412635803 True -8 25200 30.480060815811157 0.5845615863800049 435.0587158203125 0.4562660753726959 495.60321044921875 0.6829522252082825 0.6928731 0.5745707154273987 True -9 28000 30.500383615493774 0.5978071689605713 434.7071838378906 0.5373026132583618 494.47174072265625 0.6846812963485718 0.69326115 0.5515910387039185 True -10 30800 30.500306129455566 0.5914971828460693 431.526123046875 0.5888134241104126 492.1537780761719 0.6869031190872192 0.70575106 0.5230022072792053 True -11 33600 30.52836275100708 0.5994911193847656 385.4967041015625 0.4152810871601105 490.7940368652344 0.6883918046951294 0.70819485 0.5243552327156067 True -12 36400 30.481029272079468 0.5956206321716309 367.30401611328125 0.4214302897453308 488.6947021484375 0.6903558969497681 0.7193694 0.48972851037979126 True -13 39200 30.45866107940674 0.5842947959899902 359.2139587402344 0.3266339600086212 487.1517028808594 0.6924166083335876 0.72660506 0.4689966142177582 True -14 42000 30.47053074836731 13.872196674346924 384.04669189453125 0.399994820356369 486.1033935546875 0.6934807896614075 0.7313664 0.4653787910938263 True -15 44800 30.51825737953186 13.261642932891846 407.28167724609375 0.22856321930885315 485.0693664550781 0.6943034529685974 0.7393885 0.4504401981830597 True -16 47600 30.698269367218018 0.5996987819671631 400.916748046875 0.47830504179000854 484.5181579589844 0.6946664452552795 0.74196196 0.4482490122318268 True -17 50400 31.145994663238525 0.5835886001586914 383.896728515625 0.23868758976459503 484.7475891113281 0.6943879723548889 0.74179584 0.44724494218826294 False -18 53200 30.814453840255737 9.681477308273315 415.74237060546875 0.23613348603248596 485.0129089355469 0.6939949989318848 0.7372201 0.45486393570899963 False -19 56000 30.54081130027771 22.999833345413208 415.34649658203125 0.1899610161781311 485.0116882324219 0.6936741471290588 0.7369358 0.4608159363269806 False diff --git a/ENCSR524CPZ/cherimoya.fold_3.performance.tsv b/ENCSR524CPZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 116ce6b6023d673a7a407509011a6c3ebb65149d..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -484.5181579589844 0.24638532102108002 0.6946664452552795 0.3104819357395172 0.7419619560241699 0.6671594381332397 0.4482490122318268 \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_4.evaluate.json b/ENCSR524CPZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a9d20a8cd2c119fff4e45eb4023e786655a790fc..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF076YVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_4.fit.json b/ENCSR524CPZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 58627ef4424321a7166eb9cbe154051b6f79456d..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF076YVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524CPZ/cherimoya.fold_4.log b/ENCSR524CPZ/cherimoya.fold_4.log deleted file mode 100644 index 337c869c253548f5d1be8afd71fed6c58f8cf868..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2893 36.75142240524292 3.7757842540740967 398.47198486328125 0.5560447573661804 594.6652221679688 0.5503779649734497 0.5913734 5.539970397949219 True -1 5786 32.14493417739868 0.7810463905334473 362.34423828125 0.8170965909957886 512.8348999023438 0.6550354361534119 0.6525472 1.998784065246582 True -2 8679 31.705432653427124 0.5558717250823975 328.762451171875 0.6479605436325073 502.275146484375 0.6666717529296875 0.6567183 0.9513503313064575 True -3 11572 31.543757438659668 0.5417861938476562 391.86651611328125 0.497580885887146 497.8320617675781 0.6715508699417114 0.6672215 1.0394296646118164 True -4 14465 31.487874269485474 0.6260788440704346 467.8765869140625 0.5366947054862976 494.6731872558594 0.6753439903259277 0.672424 0.702972412109375 True -5 17358 31.481548309326172 0.5380842685699463 382.0831604003906 0.7364538908004761 492.447998046875 0.6789602041244507 0.6683766 0.6831222772598267 False -6 20251 31.469436168670654 0.5438277721405029 380.51812744140625 0.601872444152832 491.2062072753906 0.6808018684387207 0.67505366 0.6642837524414062 True -7 23144 31.513741970062256 0.5427942276000977 374.595947265625 0.49046915769577026 489.687744140625 0.6828680038452148 0.6824373 0.6413055658340454 True -8 26037 31.519878387451172 0.5428590774536133 390.85235595703125 0.6423105001449585 487.49896240234375 0.6850754022598267 0.6877805 0.5967855453491211 True -9 28930 31.436532735824585 0.5425453186035156 391.08197021484375 0.43915027379989624 486.37237548828125 0.6868915557861328 0.6909163 0.5641871690750122 True -10 31823 31.46688675880432 0.5356495380401611 409.6603088378906 0.4560917317867279 484.3982238769531 0.6892563104629517 0.6995261 0.5250214338302612 True -11 34716 32.34474420547485 3.044515609741211 432.59075927734375 0.33838483691215515 483.14068603515625 0.6910794377326965 0.70315856 0.49624791741371155 True -12 37609 31.532512664794922 1.647258996963501 419.42779541015625 0.4598615765571594 481.4945068359375 0.6930925846099854 0.71287185 0.4823251962661743 True -13 40502 31.524249792099 0.5329704284667969 402.5598449707031 0.4106127917766571 480.01678466796875 0.6950322985649109 0.72238296 0.4534353017807007 True -14 43395 31.526655912399292 0.5459790229797363 385.8106994628906 0.37866464257240295 478.99578857421875 0.6962089538574219 0.7307702 0.4414607882499695 True -15 46288 31.451601266860962 0.5454163551330566 363.1611328125 0.32199883460998535 477.8208923339844 0.6972354054450989 0.737051 0.43166396021842957 True -16 49181 31.43736743927002 0.5424544811248779 406.709228515625 0.3266669511795044 477.5190734863281 0.6976933479309082 0.7396092 0.42803719639778137 True -17 52074 31.44183039665222 0.5416882038116455 385.9442138671875 0.3953911364078522 477.5997314453125 0.6974483728408813 0.7391275 0.42844098806381226 False -18 54967 31.51365876197815 0.5352745056152344 353.65667724609375 0.20863914489746094 477.9386291503906 0.6970131993293762 0.73762685 0.43387264013290405 False -19 57860 31.581498384475708 0.532923698425293 338.8973388671875 0.34906071424484253 478.2615051269531 0.6966654658317566 0.73359054 0.43911629915237427 False diff --git a/ENCSR524CPZ/cherimoya.fold_4.performance.tsv b/ENCSR524CPZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fafdcc15f243442c45709facdba492db331f992f..0000000000000000000000000000000000000000 --- a/ENCSR524CPZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -477.5190734863281 0.24647288024425507 0.697693407535553 0.308749794960022 0.7396091818809509 0.6454979181289673 0.42803719639778137 \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_0.evaluate.json b/ENCSR524QBS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 454a49b7baaefdc0de55749f5c8bd5cee08e8b11..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF397NJB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_0.fit.json b/ENCSR524QBS/cherimoya.fold_0.fit.json deleted file mode 100644 index 101c40ab86cfa04f70df91f2d093686afc7e4c59..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF397NJB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_0.log b/ENCSR524QBS/cherimoya.fold_0.log deleted file mode 100644 index 3b684f70946ddc378beba52b487d87880d354186..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 35.16487407684326 4.031581878662109 581.9971313476562 0.3327915668487549 792.9828491210938 0.1944749653339386 0.80600464 3.7129616737365723 True -1 5506 30.24484920501709 0.5977275371551514 594.3590087890625 0.22198015451431274 757.0128784179688 0.22346600890159607 0.83535796 0.849144458770752 True -2 8259 30.269782781600952 0.5786595344543457 655.6605224609375 0.29393601417541504 749.140869140625 0.22797870635986328 0.8525394 0.39184606075286865 True -3 11012 30.263821601867676 0.5916144847869873 565.53466796875 0.18891122937202454 745.1145629882812 0.23119333386421204 0.85941523 0.3673866391181946 True -4 13765 30.24685525894165 0.5768260955810547 655.1880493164062 0.1511572152376175 740.8724975585938 0.23525643348693848 0.8620744 0.24864216148853302 True -5 16518 30.301363229751587 0.5792088508605957 649.1781616210938 0.13504071533679962 738.8457641601562 0.23691412806510925 0.8686275 0.2158200591802597 True -6 19271 30.241679430007935 0.5793743133544922 575.4027099609375 0.14221835136413574 739.582763671875 0.23613886535167694 0.86941034 0.259691447019577 True -7 22024 30.200385093688965 0.5774974822998047 716.73095703125 0.2241407185792923 736.5100708007812 0.23919332027435303 0.8731194 0.2339162677526474 True -8 24777 30.308895111083984 0.5799262523651123 691.389404296875 0.19171668589115143 735.4766845703125 0.24000132083892822 0.87380683 0.21419455111026764 True -9 27530 30.1891348361969 0.5804886817932129 603.4921875 0.1190413162112236 733.84912109375 0.24180732667446136 0.88026655 0.19400861859321594 True -10 30283 30.3526029586792 0.5875964164733887 630.2554931640625 0.1685054451227188 732.4462890625 0.24308788776397705 0.8825301 0.18552738428115845 True -11 33036 30.11385464668274 0.5966091156005859 744.576171875 0.22590118646621704 730.7994995117188 0.24499471485614777 0.8866744 0.16712740063667297 True -12 35789 29.795461416244507 1.1301460266113281 649.3441162109375 0.17331117391586304 729.7089233398438 0.24550345540046692 0.8897627 0.15707604587078094 True -13 38542 29.83319091796875 0.5852189064025879 515.1029052734375 0.15258166193962097 728.3648071289062 0.24693411588668823 0.8941053 0.14580194652080536 True -14 41295 29.83555555343628 0.5840866565704346 701.373046875 0.15446819365024567 728.3292846679688 0.24643079936504364 0.8970377 0.13846594095230103 True -15 44048 29.849562644958496 0.6010355949401855 668.6859130859375 0.18918761610984802 726.9326782226562 0.24775952100753784 0.90174586 0.12772658467292786 True -16 46801 29.730517148971558 0.5692489147186279 616.3985595703125 0.055274441838264465 726.6268310546875 0.2476857602596283 0.9034643 0.12140212208032608 True -17 49554 29.712743043899536 0.5683238506317139 665.6087036132812 0.11972464621067047 726.1508178710938 0.2485601007938385 0.90513563 0.11816238611936569 True -18 52307 29.775288581848145 0.679279088973999 524.09228515625 0.13536682724952698 726.5902099609375 0.24813318252563477 0.9052277 0.11746551841497421 True -19 55060 29.679572343826294 0.5775022506713867 635.71044921875 0.1844298243522644 727.5167846679688 0.2466590851545334 0.9054597 0.11725002527236938 True diff --git a/ENCSR524QBS/cherimoya.fold_0.performance.tsv b/ENCSR524QBS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 68970bc80ea5ce021ea0a993f89ce8fb65eb807b..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -727.5167846679688 0.4938820004463196 0.24665910005569458 0.08572200685739517 0.9054597020149231 0.8749881982803345 0.11725002527236938 \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_1.evaluate.json b/ENCSR524QBS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2209f9a370d97f776785de82210d5201da7566a2..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF397NJB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_1.fit.json b/ENCSR524QBS/cherimoya.fold_1.fit.json deleted file mode 100644 index a5ea5f7eb9e9cf9aff2474e306e5fe0e099f4eeb..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF397NJB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_1.log b/ENCSR524QBS/cherimoya.fold_1.log deleted file mode 100644 index 01d1146032241d56728ef4307b81fdad2cbcde97..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 34.73369073867798 4.06025505065918 697.9290161132812 0.2556420564651489 930.5352172851562 0.20546743273735046 0.80070466 3.956773281097412 True -1 5466 30.080623388290405 0.7483603954315186 651.58349609375 0.23255260288715363 887.1947631835938 0.23861196637153625 0.8417808 1.0312097072601318 True -2 8199 30.018736839294434 0.7134292125701904 714.1790161132812 0.24222765862941742 868.0982666015625 0.2502540349960327 0.8570592 0.3678809404373169 True -3 10932 30.02319312095642 0.62489914894104 578.1669311523438 0.1959683746099472 864.8981323242188 0.25112342834472656 0.8589722 0.34981483221054077 True -4 13665 30.022371768951416 0.6409182548522949 679.863525390625 0.16228508949279785 862.740478515625 0.25217312574386597 0.86525625 0.38149863481521606 True -5 16398 30.074405193328857 0.6363646984100342 773.5439453125 0.4309806823730469 861.1553955078125 0.2533099949359894 0.86632633 0.26916369795799255 True -6 19131 30.058115482330322 0.6344647407531738 650.5560913085938 0.16591952741146088 855.8598022460938 0.25827673077583313 0.8734454 0.26136431097984314 True -7 21864 30.03162670135498 0.6462645530700684 556.2973022460938 0.15767189860343933 852.5980224609375 0.2610326111316681 0.8775276 0.23852850496768951 True -8 24597 29.993165731430054 0.6487071514129639 734.815185546875 0.20615103840827942 850.1557006835938 0.26321226358413696 0.8803907 0.24359753727912903 True -9 27330 29.99670958518982 0.6392395496368408 600.1915893554688 0.15148289501667023 848.0301513671875 0.2649567425251007 0.88604856 0.22770853340625763 True -10 30063 30.020238876342773 0.6480374336242676 664.5798950195312 0.26930028200149536 845.8549194335938 0.2666594982147217 0.88951164 0.22017556428909302 True -11 32796 29.774169921875 0.6323893070220947 673.8113403320312 0.20636707544326782 844.3778686523438 0.2683151066303253 0.8919445 0.2049618810415268 True -12 35529 29.478188514709473 0.6388211250305176 649.8875732421875 0.2552092671394348 843.2049560546875 0.26909708976745605 0.89433986 0.20217905938625336 True -13 38262 29.479618072509766 0.6341922283172607 613.8231811523438 0.1383432000875473 840.2908325195312 0.27104803919792175 0.89999646 0.17810621857643127 True -14 40995 29.47460961341858 0.640221118927002 693.8433837890625 0.10673780739307404 839.5897216796875 0.27162086963653564 0.90422016 0.1637534648180008 True -15 43728 29.4899001121521 0.6425342559814453 590.6588134765625 0.129573792219162 838.4489135742188 0.27243027091026306 0.9067842 0.15117309987545013 True -16 46461 29.53593373298645 0.6439559459686279 567.0330200195312 0.12004321813583374 837.2662353515625 0.2728802263736725 0.9102083 0.1421889215707779 True -17 49194 29.483211040496826 0.6462080478668213 661.3634033203125 0.08030837774276733 837.0872192382812 0.2732786238193512 0.91284776 0.1373974233865738 True -18 51927 29.443268537521362 0.6449897289276123 632.4440307617188 0.10057561099529266 837.563720703125 0.2726753056049347 0.9130913 0.13518059253692627 True -19 54660 29.42264175415039 0.7061784267425537 560.6929931640625 0.14414292573928833 836.8397216796875 0.27346688508987427 0.91200715 0.13566595315933228 False diff --git a/ENCSR524QBS/cherimoya.fold_1.performance.tsv b/ENCSR524QBS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index eba12eb0ed9682d6a5a581efd53576cd18bcd0ac..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -837.563720703125 0.47097253799438477 0.2726753056049347 0.10339392721652985 0.9130913019180298 0.9002526998519897 0.13518059253692627 \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_2.evaluate.json b/ENCSR524QBS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f8bfe2b2835294d3207de18bb7753d67b023fb13..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF397NJB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_2.fit.json b/ENCSR524QBS/cherimoya.fold_2.fit.json deleted file mode 100644 index f7e7d0da350e89d8cbc6dbf918753905faee33d3..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF397NJB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_2.log b/ENCSR524QBS/cherimoya.fold_2.log deleted file mode 100644 index 73211e595b6a11aac69d300de553669a67c81b91..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2895 36.41343140602112 4.218965768814087 660.690185546875 0.15805171430110931 837.0153198242188 0.19581261277198792 0.80175436 3.0789034366607666 True -1 5790 31.90419101715088 0.559849739074707 674.908935546875 0.25969329476356506 796.0957641601562 0.2274433821439743 0.8412043 0.6808626651763916 True -2 8685 31.915661811828613 0.5601537227630615 698.286865234375 0.20686794817447662 788.1656494140625 0.23072586953639984 0.8468981 0.2972685992717743 True -3 11580 31.89758610725403 0.517237663269043 597.5228271484375 0.1615886390209198 784.8634643554688 0.23243485391139984 0.8520559 0.2676461338996887 True -4 14475 31.87411069869995 0.5448007583618164 576.757568359375 0.1784142553806305 780.200927734375 0.23768411576747894 0.8559249 0.28062552213668823 True -5 17370 31.862449169158936 0.540773868560791 660.3583374023438 0.16759832203388214 776.181640625 0.2412102371454239 0.86325157 0.2426605075597763 True -6 20265 31.89224648475647 1.3760840892791748 609.9533081054688 0.126284658908844 774.6405029296875 0.2419482320547104 0.86800075 0.2016388177871704 True -7 23160 31.872979640960693 0.555234432220459 655.2776489257812 0.17591962218284607 774.4364013671875 0.24155856668949127 0.8687085 0.19976255297660828 True -8 26055 31.780569791793823 0.5452642440795898 579.3801879882812 0.12410204857587814 771.5977783203125 0.244766965508461 0.87524843 0.19815322756767273 True -9 28950 31.770029306411743 0.5515339374542236 620.06982421875 0.15608951449394226 770.223876953125 0.24553991854190826 0.8783383 0.1860506683588028 True -10 31845 31.862284183502197 16.500279664993286 576.5650634765625 0.16804224252700806 769.0028686523438 0.24667635560035706 0.8825783 0.16810092329978943 True -11 34740 32.46650433540344 0.5408902168273926 583.4237670898438 0.14032909274101257 766.936767578125 0.24927067756652832 0.88622993 0.1618531048297882 True -12 37635 31.235780715942383 0.5658700466156006 596.57958984375 0.13631364703178406 766.4096069335938 0.24846838414669037 0.8877687 0.15441755950450897 True -13 40530 31.2911274433136 1.3626563549041748 605.2413940429688 0.16227760910987854 763.8695678710938 0.2515428960323334 0.8914032 0.15021009743213654 True -14 43425 31.242059469223022 1.101787805557251 691.2487182617188 0.11838989704847336 763.3668212890625 0.2515520751476288 0.89352924 0.14306952059268951 True -15 46320 31.239898920059204 0.5785324573516846 627.183349609375 0.2182081788778305 763.1608276367188 0.2518843114376068 0.89641565 0.13804329931735992 True -16 49215 31.37186312675476 0.55735182762146 698.2487182617188 0.17529956996440887 763.980712890625 0.2507745027542114 0.89706004 0.1347285956144333 True -17 52110 31.372694492340088 0.5619432926177979 610.1385498046875 0.14211030304431915 763.8931884765625 0.2507537603378296 0.8981548 0.13160477578639984 True -18 55005 31.275524854660034 1.0367376804351807 681.6951904296875 0.0888260155916214 763.1773071289062 0.2517409920692444 0.8975101 0.1315309852361679 False -19 57900 31.272841453552246 0.5554623603820801 627.8158569335938 0.10008278489112854 763.4468383789062 0.25146472454071045 0.89792156 0.13217750191688538 False diff --git a/ENCSR524QBS/cherimoya.fold_2.performance.tsv b/ENCSR524QBS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bcf7d528538ccfa762f8a7456afee02e9064afa5..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -763.8931884765625 0.48772263526916504 0.2507537305355072 0.09086240082979202 0.8981547951698303 0.8801141977310181 0.13160477578639984 \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_3.evaluate.json b/ENCSR524QBS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 549ba0fecce77096fa9ef5fd0586537f694ebab5..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF397NJB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_3.fit.json b/ENCSR524QBS/cherimoya.fold_3.fit.json deleted file mode 100644 index 846080456a24f55ff3d1c36b7e7f93511302ff8a..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF397NJB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_3.log b/ENCSR524QBS/cherimoya.fold_3.log deleted file mode 100644 index cd9f6e3e500f953798f168c6252b3f09d0bdc2e0..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.71567416191101 4.091453790664673 728.00390625 0.18518830835819244 788.636474609375 0.19733977317810059 0.79242533 3.7523484230041504 True -1 5510 30.305892944335938 0.5667171478271484 630.4517211914062 0.2736670970916748 750.5672607421875 0.22612880170345306 0.833022 0.7030771970748901 True -2 8265 30.284838438034058 0.6272549629211426 814.670166015625 0.21593032777309418 742.3580322265625 0.232449471950531 0.8498381 0.3184465765953064 True -3 11020 30.32342767715454 0.5459780693054199 717.7522583007812 0.24466468393802643 738.1754150390625 0.23572030663490295 0.855943 0.31023097038269043 True -4 13775 30.228968858718872 0.5557324886322021 616.4249267578125 0.10576099902391434 737.025146484375 0.2368617057800293 0.85390276 0.2687760889530182 False -5 16530 30.264429569244385 0.5536165237426758 690.0559692382812 0.29396313428878784 734.1388549804688 0.2392730861902237 0.8601859 0.2571852505207062 True -6 19285 30.293912172317505 0.5637948513031006 627.34130859375 0.18914486467838287 731.9386596679688 0.24073584377765656 0.86541355 0.2372419834136963 True -7 22040 30.367874145507812 0.5553760528564453 666.4817504882812 0.13274982571601868 730.2723388671875 0.2415512204170227 0.87037885 0.2309894561767578 True -8 24795 30.303627252578735 0.5553920269012451 609.8950805664062 0.229291170835495 728.3217163085938 0.24453294277191162 0.8735472 0.23738926649093628 True -9 27550 30.27101755142212 1.298492670059204 592.6910400390625 0.19856254756450653 727.49072265625 0.24521419405937195 0.874597 0.2525993585586548 True -10 30305 30.464224576950073 7.828073263168335 684.602294921875 0.1533839851617813 726.385498046875 0.2459944188594818 0.8801988 0.21766731142997742 True -11 33060 29.733960390090942 1.4223289489746094 606.446533203125 0.20482784509658813 724.8683471679688 0.24746327102184296 0.8822926 0.19627892971038818 True -12 35815 29.685277462005615 1.198617935180664 585.1220092773438 0.17768658697605133 723.8696899414062 0.24806411564350128 0.88683796 0.1793113648891449 True -13 38570 29.757538318634033 0.5558810234069824 680.0279541015625 0.09071680903434753 722.7109985351562 0.24908800423145294 0.8908743 0.16528065502643585 True -14 41325 29.733779191970825 0.551182746887207 632.1798095703125 0.17674604058265686 720.8446044921875 0.2512170374393463 0.8927469 0.15664885938167572 True -15 44080 29.743281841278076 0.5572597980499268 698.540771484375 0.1269414722919464 719.7568359375 0.2521314024925232 0.89788914 0.14800895750522614 True -16 46835 29.847635507583618 0.552567720413208 701.2904663085938 0.19379951059818268 720.8999633789062 0.2505265176296234 0.8978867 0.14006274938583374 False -17 49590 29.831021070480347 0.557201623916626 667.158203125 0.07489089667797089 719.9771118164062 0.2514170706272125 0.89993846 0.13432610034942627 True -18 52345 29.798891067504883 0.5750584602355957 595.745361328125 0.13932645320892334 720.6300048828125 0.25060003995895386 0.8993018 0.13273930549621582 False -19 55100 30.06265902519226 0.5643916130065918 642.049560546875 0.10886010527610779 721.3173828125 0.24968893826007843 0.9012012 0.13212993741035461 True diff --git a/ENCSR524QBS/cherimoya.fold_3.performance.tsv b/ENCSR524QBS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0a9ba201862008b2c1057cba382e057538994ed1..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -721.3173828125 0.4924248456954956 0.24968896806240082 0.08588455617427826 0.9012011885643005 0.8647316098213196 0.13212993741035461 \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_4.evaluate.json b/ENCSR524QBS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index dc4131ec3fcea0cf247c562b6ce333e2fcbebab4..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF397NJB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_4.fit.json b/ENCSR524QBS/cherimoya.fold_4.fit.json deleted file mode 100644 index af0f8cc435a2b5cc794853adbe4ca04104d65fb0..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF397NJB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QBS/cherimoya.fold_4.log b/ENCSR524QBS/cherimoya.fold_4.log deleted file mode 100644 index 80f2e6cfad190cb01dfe5115af9b2769496f7128..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 35.49828100204468 5.052124500274658 754.7249755859375 0.15918637812137604 755.842529296875 0.1914910078048706 0.80625594 3.3819499015808105 True -1 5564 30.620152711868286 0.6484842300415039 619.0142211914062 0.23174217343330383 726.8245239257812 0.2169487178325653 0.8394679 0.6038151383399963 True -2 8346 30.62766170501709 0.6018908023834229 682.6522827148438 0.26699551939964294 718.7636108398438 0.22171741724014282 0.851041 0.2804214358329773 True -3 11128 30.558388233184814 0.6101536750793457 642.0550537109375 0.23360875248908997 718.0447387695312 0.22262480854988098 0.85196483 0.23334144055843353 True -4 13910 30.551273345947266 0.604705810546875 615.935302734375 0.17426401376724243 714.5071411132812 0.2261035442352295 0.85611355 0.305359810590744 True -5 16692 30.58522915840149 0.6110670566558838 669.76416015625 0.17611682415008545 712.4522705078125 0.22847890853881836 0.85796994 0.25894322991371155 True -6 19474 30.567820072174072 0.6107842922210693 581.870849609375 0.20344975590705872 711.0969848632812 0.22986342012882233 0.85965943 0.23545922338962555 True -7 22256 30.56117582321167 0.6048755645751953 711.7188110351562 0.19288577139377594 709.3592529296875 0.23098616302013397 0.8663594 0.21373030543327332 True -8 25038 30.589925050735474 0.6025774478912354 717.7943115234375 0.29312679171562195 707.6136474609375 0.2328261137008667 0.8691126 0.2079276442527771 True -9 27820 30.590895175933838 0.6115319728851318 702.3853759765625 0.13738924264907837 706.8582763671875 0.2328382134437561 0.8727023 0.19450710713863373 True -10 30602 30.619917392730713 0.6052646636962891 661.1541748046875 0.13696050643920898 705.1400146484375 0.23481853306293488 0.8766409 0.1849571168422699 True -11 33384 30.462860107421875 0.6130163669586182 711.8050537109375 0.22176006436347961 704.1438598632812 0.23586255311965942 0.882841 0.17033185064792633 True -12 36166 30.038174152374268 0.5947656631469727 706.6875610351562 0.17949801683425903 702.6690673828125 0.23755121231079102 0.88660085 0.1590685248374939 True -13 38948 30.013786554336548 0.5911753177642822 745.871826171875 0.11352318525314331 702.0553588867188 0.23789814114570618 0.8897536 0.1492268145084381 True -14 41730 30.03663730621338 0.6046295166015625 640.28173828125 0.20938873291015625 701.1129760742188 0.23873281478881836 0.8953494 0.13871796429157257 True -15 44512 30.047473430633545 0.6019601821899414 656.12744140625 0.20964547991752625 699.4515991210938 0.2406473606824875 0.8980467 0.12857793271541595 True -16 47294 30.05240225791931 0.6122987270355225 664.493408203125 0.11241387575864792 700.2200317382812 0.2396470308303833 0.90137774 0.11907706409692764 True -17 50076 30.047470092773438 0.5948529243469238 602.9483642578125 0.07456725090742111 700.2477416992188 0.23956580460071564 0.9022472 0.1144489273428917 True -18 52858 30.054778337478638 0.6079573631286621 521.564453125 0.09631600975990295 700.587890625 0.23944343626499176 0.90259916 0.1129695326089859 True -19 55640 30.0427508354187 0.6069462299346924 612.5861206054688 0.11856378614902496 700.4481201171875 0.23977065086364746 0.9019528 0.11239980906248093 False diff --git a/ENCSR524QBS/cherimoya.fold_4.performance.tsv b/ENCSR524QBS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1b0d8521dabfc5f4e38f7cc91bfb8dbf136380cc..0000000000000000000000000000000000000000 --- a/ENCSR524QBS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -700.587890625 0.49976128339767456 0.23944343626499176 0.08379695564508438 0.9025991559028625 0.8672158718109131 0.1129695326089859 \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_0.evaluate.json b/ENCSR524QPZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 74c29453211edc9dae98690fe9f323ac42359d55..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF887HGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_0.fit.json b/ENCSR524QPZ/cherimoya.fold_0.fit.json deleted file mode 100644 index a8280f5af10eacac9f5351cd7e0e7de5f22c21b7..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF887HGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_0.log b/ENCSR524QPZ/cherimoya.fold_0.log deleted file mode 100644 index 6d7753caaa8c5215d1332b4169f06a585a396be9..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 35.20068955421448 4.080248117446899 287.31304931640625 0.351199746131897 387.50787353515625 0.2764105200767517 0.82010216 3.813957452774048 True -1 5514 30.768022298812866 0.8026282787322998 296.43707275390625 0.3448091149330139 359.2458801269531 0.34042873978614807 0.8315765 1.079520344734192 True -2 8271 30.752938508987427 0.7321841716766357 282.7319641113281 0.26932579278945923 354.0110778808594 0.3502269983291626 0.8486274 0.6427756547927856 True -3 11028 30.741870641708374 0.6097128391265869 360.45782470703125 0.22644156217575073 352.4494934082031 0.3531942665576935 0.8526529 0.438657283782959 True -4 13785 30.724548816680908 0.6138832569122314 251.62063598632812 0.27037864923477173 349.8941345214844 0.35848528146743774 0.860677 0.3870590329170227 True -5 16542 30.779249906539917 1.0968921184539795 274.9146423339844 0.29451462626457214 349.4635009765625 0.3592454195022583 0.86297506 0.38232335448265076 True -6 19299 30.70714807510376 0.6143884658813477 328.3912658691406 0.28192102909088135 348.7072448730469 0.3612965941429138 0.86576617 0.3235201835632324 True -7 22056 30.696632146835327 0.6167030334472656 274.0850524902344 0.15645483136177063 347.1288146972656 0.3651352822780609 0.8720954 0.29825347661972046 True -8 24813 30.68858313560486 0.6097579002380371 268.9754638671875 0.2431415617465973 346.23870849609375 0.36755669116973877 0.87596923 0.2722613215446472 True -9 27570 30.664402961730957 0.6192071437835693 318.28961181640625 0.32195818424224854 345.11639404296875 0.3697865903377533 0.879608 0.26610010862350464 True -10 30327 30.58905792236328 0.6458516120910645 293.4773254394531 0.2553638219833374 345.2483215332031 0.36809295415878296 0.88428 0.2360575795173645 True -11 33084 30.0724675655365 0.5965695381164551 314.34674072265625 0.24748864769935608 343.4543151855469 0.3728983402252197 0.8872609 0.21643981337547302 True -12 35841 30.027360439300537 0.63020920753479 294.32977294921875 0.15873374044895172 342.9748840332031 0.3732598125934601 0.8904599 0.20112794637680054 True -13 38598 30.093827962875366 0.6392428874969482 318.1396789550781 0.2434903085231781 342.29815673828125 0.3739410638809204 0.8945674 0.18179886043071747 True -14 41355 30.04031276702881 0.6281552314758301 302.88067626953125 0.2184860110282898 341.42547607421875 0.37610137462615967 0.900709 0.1678992211818695 True -15 44112 30.039205312728882 0.6079621315002441 266.52734375 0.15275484323501587 340.8633728027344 0.3763972520828247 0.9033126 0.15796416997909546 True -16 46869 30.071899890899658 0.6068978309631348 304.502197265625 0.21317532658576965 340.4295349121094 0.3780004382133484 0.90509605 0.15065915882587433 True -17 49626 30.06122899055481 0.9972391128540039 317.6798400878906 0.1636635661125183 340.36370849609375 0.3783211410045624 0.906991 0.14736707508563995 True -18 52383 30.102680444717407 0.6352307796478271 319.5191650390625 0.16336068511009216 340.71563720703125 0.37631791830062866 0.90534586 0.14658553898334503 False -19 55140 30.1115300655365 0.6169850826263428 287.1272277832031 0.27157068252563477 340.6117248535156 0.37777477502822876 0.9061635 0.14695073664188385 False diff --git a/ENCSR524QPZ/cherimoya.fold_0.performance.tsv b/ENCSR524QPZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1ad6488124174cfe5a6166be0fb529e972328fc3..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -340.36370849609375 0.42939162254333496 0.3783211410045624 0.11459430307149887 0.9069910049438477 0.87547367811203 0.14736707508563995 \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_1.evaluate.json b/ENCSR524QPZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c80d0bc70be717bef859566b139bc6c499637392..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF887HGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_1.fit.json b/ENCSR524QPZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 0a0f389a952e45886d1cfdf838c5d6a5a19a0bf5..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF887HGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_1.log b/ENCSR524QPZ/cherimoya.fold_1.log deleted file mode 100644 index 9ec27bfd5065db38768be678c2071488a359b39e..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2682 34.772215366363525 6.25081729888916 313.8785400390625 0.3297145366668701 457.5797119140625 0.2794618606567383 0.8135221 4.5956711769104 True -1 5364 29.93248987197876 3.3296384811401367 319.7288818359375 0.40715450048446655 418.55010986328125 0.35396358370780945 0.83540905 1.2834171056747437 True -2 8046 29.956925630569458 0.8159468173980713 302.2115478515625 0.2715894877910614 413.0792236328125 0.36007073521614075 0.8538669 0.712510883808136 True -3 10728 29.868208646774292 1.0002903938293457 284.18206787109375 0.19167375564575195 409.1626281738281 0.36655393242836 0.8626955 0.5119993686676025 True -4 13410 29.851149320602417 1.9790065288543701 310.607421875 0.3451829254627228 406.715576171875 0.3698049783706665 0.86665154 0.3919472098350525 True -5 16092 29.920498609542847 0.7379050254821777 348.3727722167969 0.2442253828048706 404.91064453125 0.373359352350235 0.8715907 0.34184277057647705 True -6 18774 29.86736297607422 0.7522943019866943 323.57623291015625 0.23648078739643097 402.8841247558594 0.37780994176864624 0.8760085 0.32309189438819885 True -7 21456 29.849052667617798 0.751201868057251 278.0548095703125 0.22695910930633545 401.5245666503906 0.37954312562942505 0.8808218 0.2796081304550171 True -8 24138 29.811364889144897 0.7316069602966309 289.326904296875 0.2602236568927765 400.2804870605469 0.38217052817344666 0.884545 0.2754259407520294 True -9 26820 29.809903144836426 0.7275772094726562 304.10760498046875 0.24610774219036102 399.0881042480469 0.38300567865371704 0.8906997 0.24705550074577332 True -10 29502 29.799999713897705 1.541963815689087 254.2560577392578 0.25585073232650757 398.5345458984375 0.38385966420173645 0.8913768 0.24743258953094482 True -11 32184 29.260476112365723 0.7472507953643799 293.612060546875 0.2517468333244324 397.3056640625 0.38596633076667786 0.8937513 0.23329943418502808 True -12 34866 29.328177213668823 16.625232934951782 302.67608642578125 0.24031126499176025 396.2475280761719 0.38813722133636475 0.89860684 0.21661143004894257 True -13 37548 29.296541929244995 1.433068037033081 315.7367858886719 0.20081225037574768 394.35418701171875 0.3908320367336273 0.9011644 0.20658017694950104 True -14 40230 29.268227338790894 0.7460331916809082 296.60589599609375 0.19735297560691833 393.2548828125 0.3926869034767151 0.90619403 0.19455762207508087 True -15 42912 29.182526111602783 0.7501101493835449 330.866943359375 0.2909861207008362 392.92169189453125 0.39350125193595886 0.90885407 0.1894824206829071 True -16 45594 29.28475022315979 0.7245357036590576 275.614990234375 0.10478731244802475 392.7040100097656 0.39337578415870667 0.9089148 0.17897501587867737 True -17 48276 29.223501443862915 0.7246708869934082 336.5802307128906 0.15691988170146942 392.3003845214844 0.3942711055278778 0.91185886 0.17251911759376526 True -18 50958 29.220837593078613 0.7372026443481445 311.860595703125 0.19250141084194183 392.121826171875 0.39409229159355164 0.9106803 0.17020511627197266 False -19 53640 29.192063570022583 0.7626357078552246 281.7276306152344 0.1761787235736847 392.8122863769531 0.3917849063873291 0.91101944 0.1704929918050766 False diff --git a/ENCSR524QPZ/cherimoya.fold_1.performance.tsv b/ENCSR524QPZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 89a726db1eacabd39e915e785c8ea257a540a23c..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -392.3003845214844 0.413917601108551 0.3942711055278778 0.13102106750011444 0.911858856678009 0.8971050977706909 0.17251911759376526 \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_2.evaluate.json b/ENCSR524QPZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c69a92f7e22c8f2529ad7386057b9e3c60792a13..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF887HGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_2.fit.json b/ENCSR524QPZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 84dd0d6ca0454bd9b3ee0a36011f87171001cfd0..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF887HGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_2.log b/ENCSR524QPZ/cherimoya.fold_2.log deleted file mode 100644 index 50efbc927495018fdd8d1bfda53d857e027a71bc..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2893 36.55315947532654 4.350852727890015 295.34619140625 0.234539195895195 416.55194091796875 0.2758405804634094 0.8107406 3.748812675476074 True -1 5786 32.05672645568848 0.9770591259002686 313.37066650390625 0.3442481756210327 384.0174255371094 0.3421539068222046 0.8230359 1.0551400184631348 True -2 8679 32.28386378288269 0.6028797626495361 349.5999450683594 0.38152360916137695 377.28045654296875 0.35356268286705017 0.8455134 0.654385507106781 True -3 11572 31.517385005950928 0.5716159343719482 351.04754638671875 0.3227158188819885 374.75323486328125 0.3582388162612915 0.85339856 0.4617964029312134 True -4 14465 31.524770498275757 0.5712180137634277 315.4134826660156 0.19319668412208557 372.4967041015625 0.3612314462661743 0.8578257 0.3011537194252014 True -5 17358 31.495896816253662 0.5612962245941162 327.02410888671875 0.2672697901725769 370.73443603515625 0.3653183877468109 0.86230373 0.2649604380130768 True -6 20251 31.528326272964478 1.0009396076202393 342.18359375 0.2921578288078308 369.3100891113281 0.36841583251953125 0.8657379 0.2609739303588867 True -7 23144 31.57112956047058 0.6429798603057861 254.4691162109375 0.354559063911438 368.788330078125 0.3693114221096039 0.87025195 0.2561745345592499 True -8 26037 31.52608036994934 0.5944509506225586 340.39007568359375 0.21327777206897736 367.5033874511719 0.3716995418071747 0.87372404 0.241532564163208 True -9 28930 31.52730655670166 0.5983579158782959 349.72076416015625 0.3063925504684448 367.0460205078125 0.3721727132797241 0.87765557 0.2327532172203064 True -10 31823 31.53147292137146 0.5760915279388428 262.6117858886719 0.14558058977127075 365.65264892578125 0.37514281272888184 0.88218385 0.21113955974578857 True -11 34716 31.58967876434326 0.5797250270843506 257.145751953125 0.3040931820869446 364.2347106933594 0.3790961503982544 0.88744354 0.20639590919017792 True -12 37609 31.50224781036377 1.9795663356781006 234.73629760742188 0.1122540831565857 363.5967712402344 0.37926188111305237 0.8910708 0.2009984850883484 True -13 40502 31.593327522277832 0.5772204399108887 299.99395751953125 0.19151701033115387 363.2746276855469 0.3791894316673279 0.8921632 0.1921084225177765 True -14 43395 31.549156665802002 0.760955810546875 334.19549560546875 0.22564175724983215 362.37115478515625 0.3813331425189972 0.8952411 0.1814609169960022 True -15 46288 31.661677837371826 0.5699145793914795 312.1325988769531 0.14263533055782318 361.97772216796875 0.3825579285621643 0.89923495 0.17248544096946716 True -16 49181 31.59662914276123 0.5800468921661377 365.67779541015625 0.11733237653970718 362.1809997558594 0.3815663158893585 0.9015476 0.16529567539691925 True -17 52074 31.53649663925171 0.5637786388397217 272.5885314941406 0.18158790469169617 361.5860290527344 0.383226215839386 0.90109974 0.16085754334926605 False -18 54967 31.51385498046875 0.5720868110656738 295.83978271484375 0.11727719753980637 362.5703430175781 0.380808562040329 0.9014628 0.1601206213235855 False -19 57860 31.490241765975952 0.5793616771697998 303.3846130371094 0.1442614197731018 361.7909851074219 0.38351723551750183 0.9009826 0.16091309487819672 False diff --git a/ENCSR524QPZ/cherimoya.fold_2.performance.tsv b/ENCSR524QPZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 345f96313ada64b86bd1e1406970ce1eee99dd86..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -362.1809997558594 0.4240836799144745 0.3815663456916809 0.12288479506969452 0.9015476107597351 0.8823536038398743 0.16529567539691925 \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_3.evaluate.json b/ENCSR524QPZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f4b91d9d98e75796d4372e7ba503bdf4f0ecd80c..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF887HGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_3.fit.json b/ENCSR524QPZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 4249952056f1a05380d4e5e47de222c290887351..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF887HGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_3.log b/ENCSR524QPZ/cherimoya.fold_3.log deleted file mode 100644 index f13f8a53a5438c523e36283224160d49905bcb5a..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 35.374512910842896 3.9023079872131348 310.2883605957031 0.4221789836883545 388.1380310058594 0.28350117802619934 0.8035286 4.69771146774292 True -1 5524 30.801417350769043 0.589167594909668 351.7925720214844 0.3647848069667816 357.86322021484375 0.3473553955554962 0.82250637 1.1235114336013794 True -2 8286 30.841689825057983 0.570204496383667 293.64404296875 0.25144028663635254 351.9823303222656 0.3576493561267853 0.85483223 0.553634524345398 True -3 11048 30.81182837486267 3.3079299926757812 302.55072021484375 0.2556374669075012 348.8858642578125 0.36409658193588257 0.8639151 0.3398524224758148 True -4 13810 30.85944676399231 0.5948703289031982 300.52337646484375 0.34325653314590454 346.9891662597656 0.36676880717277527 0.8656788 0.26624026894569397 True -5 16572 30.98711061477661 0.5672061443328857 369.1249694824219 0.5269696116447449 346.4386901855469 0.36767539381980896 0.8675341 0.26215025782585144 True -6 19334 30.91559910774231 0.5616602897644043 283.5645446777344 0.14887794852256775 344.7611083984375 0.3709224462509155 0.8752219 0.23915602266788483 True -7 22096 30.37179660797119 0.5443274974822998 299.64300537109375 0.22931025922298431 344.09283447265625 0.37176141142845154 0.8800224 0.22916477918624878 True -8 24858 30.26080632209778 1.9070167541503906 367.10687255859375 0.21747750043869019 343.1080322265625 0.37478822469711304 0.8828156 0.21343091130256653 True -9 27620 30.241119861602783 1.866159439086914 300.8855895996094 0.1610656976699829 342.4040832519531 0.3764091730117798 0.8836416 0.20809146761894226 True -10 30382 30.28438711166382 0.5667140483856201 288.5226745605469 0.21433013677597046 341.4577331542969 0.37758928537368774 0.8885014 0.19243992865085602 True -11 33144 30.239359617233276 0.5550742149353027 319.76239013671875 0.2958010137081146 340.60211181640625 0.37856268882751465 0.89392054 0.18391388654708862 True -12 35906 30.2491934299469 1.6211185455322266 391.399169921875 0.3609098494052887 339.82958984375 0.38004055619239807 0.89546394 0.1783653199672699 True -13 38668 30.309707641601562 0.5492773056030273 333.37713623046875 0.15515965223312378 338.30517578125 0.3826741874217987 0.89841956 0.1717618852853775 True -14 41430 30.410759687423706 0.5487933158874512 322.7061767578125 0.2863655090332031 338.1224060058594 0.3817284405231476 0.90139586 0.16902180016040802 True -15 44192 30.293395519256592 0.5509059429168701 357.634521484375 0.19972798228263855 337.7251281738281 0.38281533122062683 0.90375274 0.1643366515636444 True -16 46954 30.243630409240723 11.095248937606812 268.2775573730469 0.24347230792045593 337.219482421875 0.3844817876815796 0.9039574 0.1612721085548401 True -17 49716 30.729910850524902 0.5450897216796875 345.3787841796875 0.18534940481185913 337.1141357421875 0.38424429297447205 0.90724593 0.158207505941391 True -18 52478 30.40824556350708 0.5552961826324463 272.73956298828125 0.28582221269607544 337.0663146972656 0.38401737809181213 0.90717 0.1568703055381775 False -19 55240 30.340451955795288 1.4050030708312988 325.04180908203125 0.12388955056667328 337.17633056640625 0.3850373923778534 0.90681624 0.15700052678585052 False diff --git a/ENCSR524QPZ/cherimoya.fold_3.performance.tsv b/ENCSR524QPZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ac5988dd51b384a5f3f79c87c29b18b148df86c1..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -337.1141357421875 0.4258137345314026 0.38424426317214966 0.11678869277238846 0.907245934009552 0.8649172782897949 0.158207505941391 \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_4.evaluate.json b/ENCSR524QPZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 592ed66781c575dcb1605622d2f4977cdfe93e98..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF887HGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_4.fit.json b/ENCSR524QPZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 9b1ea9a2c80774b9c5fdbee2e347ec3de9f51a2f..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF887HGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR524QPZ/cherimoya.fold_4.log b/ENCSR524QPZ/cherimoya.fold_4.log deleted file mode 100644 index 4283b8a19773593d6d399eea95589d5e4011cd2e..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2787 35.90912413597107 4.441678762435913 265.6379089355469 0.19025833904743195 368.1069030761719 0.27616065740585327 0.80847746 3.518580436706543 True -1 5574 31.1177921295166 0.8199954032897949 285.74859619140625 0.39361658692359924 342.2281799316406 0.3385898768901825 0.81249446 0.8711578845977783 True -2 8361 31.023520469665527 0.6771137714385986 282.6331481933594 0.20274361968040466 338.2392578125 0.3455752730369568 0.8336809 0.5275796055793762 True -3 11148 31.00183653831482 0.6666464805603027 291.407958984375 0.2066396325826645 334.89532470703125 0.35207056999206543 0.85065085 0.36009782552719116 True -4 13935 31.074820041656494 0.6341676712036133 308.4344177246094 0.3308072090148926 332.8013610839844 0.35563451051712036 0.85392416 0.23628933727741241 True -5 16722 31.056018114089966 0.6466174125671387 306.28631591796875 0.1799977868795395 331.01806640625 0.36013340950012207 0.8586178 0.2246328592300415 True -6 19509 31.08817219734192 0.634235143661499 320.037109375 0.1971036046743393 329.9857482910156 0.3635571300983429 0.8673787 0.21005012094974518 True -7 22296 31.08614158630371 0.6268002986907959 283.3726806640625 0.28910624980926514 329.6690979003906 0.3632887005805969 0.87135243 0.1938062161207199 True -8 25083 31.039865493774414 0.6346876621246338 296.2884826660156 0.2639615535736084 328.7870178222656 0.36488962173461914 0.87508816 0.18937651813030243 True -9 27870 31.058550596237183 0.629000186920166 274.099365234375 0.15108837187290192 328.1189880371094 0.3658274710178375 0.88157684 0.17839530110359192 True -10 30657 31.05441904067993 0.6218652725219727 293.6922912597656 0.29661649465560913 327.3784484863281 0.36887475848197937 0.88390225 0.1714637279510498 True -11 33444 30.64437985420227 0.6119253635406494 351.1479797363281 0.138005793094635 326.4311828613281 0.3707101345062256 0.88679546 0.1642499566078186 True -12 36231 30.483909130096436 0.6014153957366943 313.238525390625 0.18660211563110352 325.7274169921875 0.37173035740852356 0.89123774 0.16081248223781586 True -13 39018 30.425536394119263 0.6390526294708252 303.3737487792969 0.1960430145263672 325.5909729003906 0.371957004070282 0.8944501 0.15801085531711578 True -14 41805 30.40069270133972 0.5997104644775391 282.03009033203125 0.19629549980163574 325.2677917480469 0.3723101019859314 0.8958549 0.15255168080329895 True -15 44592 30.3689603805542 0.6196236610412598 282.2064208984375 0.15634486079216003 324.530517578125 0.37420493364334106 0.90196884 0.1472093164920807 True -16 47379 30.385143041610718 0.6154842376708984 343.2061767578125 0.14739015698432922 324.4844055175781 0.37486380338668823 0.90132356 0.1440303921699524 False -17 50166 30.377522230148315 0.6010243892669678 277.47802734375 0.12323658168315887 324.8009338378906 0.3720206022262573 0.90302706 0.14045679569244385 True -18 52953 30.403632640838623 0.6198306083679199 257.40863037109375 0.15957175195217133 324.921875 0.3733545243740082 0.90436137 0.1403656154870987 True -19 55740 30.39187502861023 0.6210360527038574 295.14404296875 0.1737070232629776 324.7635192871094 0.3741339445114136 0.9028016 0.1412419080734253 False diff --git a/ENCSR524QPZ/cherimoya.fold_4.performance.tsv b/ENCSR524QPZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ed4c7725352f3c6fda50303d91673cc28fd24fec..0000000000000000000000000000000000000000 --- a/ENCSR524QPZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.921875 0.43366801738739014 0.3733544945716858 0.11287497729063034 0.904361367225647 0.8670161366462708 0.1403656154870987 \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_0.evaluate.json b/ENCSR528YDD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8f9c86d4d929a01b684978c0ed5b2e5c28cdbf3c..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF245PLY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_0.fit.json b/ENCSR528YDD/cherimoya.fold_0.fit.json deleted file mode 100644 index 599d741481422bec617874fffcc6e4d084dcf3fd..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF245PLY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_0.log b/ENCSR528YDD/cherimoya.fold_0.log deleted file mode 100644 index 7f3566e2e58ebe51721955ad7e59d6fc47cdd1cf..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2322 30.447548627853394 3.660457134246826 283.36053466796875 0.7430112361907959 502.781494140625 0.48130089044570923 0.5234203 7.624915599822998 True -1 4644 25.892657995224 0.5287952423095703 296.822021484375 0.9953751564025879 423.0199279785156 0.6110619902610779 0.60261196 2.629279375076294 True -2 6966 25.887745141983032 0.4595344066619873 291.39447021484375 0.8253390192985535 411.1941223144531 0.6305339336395264 0.60663277 1.115050196647644 True -3 9288 25.855676889419556 0.46703219413757324 338.88702392578125 0.8361843228340149 405.43389892578125 0.6397148966789246 0.6185395 0.8150032758712769 True -4 11610 25.872427463531494 0.46901965141296387 368.61334228515625 0.7941973209381104 403.9390869140625 0.6432517766952515 0.6254326 0.751381516456604 True -5 13932 25.888202905654907 0.46030330657958984 349.8555603027344 0.5605926513671875 402.1866149902344 0.6462708115577698 0.6289908 0.7362127900123596 True -6 16254 25.910035848617554 0.46616673469543457 328.4197692871094 0.5826910734176636 401.58001708984375 0.6483513712882996 0.62804705 0.7248509526252747 False -7 18576 25.910038709640503 0.4658386707305908 320.0931396484375 0.7022439241409302 400.2210998535156 0.650509238243103 0.63218033 0.6878241896629333 True -8 20898 25.84720492362976 0.4686002731323242 284.6360778808594 0.5629330277442932 398.89569091796875 0.6529118418693542 0.64163935 0.6414123177528381 True -9 23220 25.862359285354614 0.4662439823150635 357.77789306640625 0.6464475393295288 396.993408203125 0.6560592651367188 0.6469845 0.5985246896743774 True -10 25542 25.855282068252563 0.9099822044372559 271.70513916015625 0.4841412305831909 395.9500427246094 0.6579641699790955 0.6524149 0.5828049778938293 True -11 27864 25.51535725593567 0.4568214416503906 287.53314208984375 0.5918501019477844 394.85565185546875 0.6597261428833008 0.65940034 0.5519328117370605 True -12 30186 25.445452213287354 0.4550180435180664 348.9378662109375 0.4656922221183777 393.8254699707031 0.66117924451828 0.66601616 0.5398909449577332 True -13 32508 25.43194079399109 0.4461336135864258 283.3633117675781 0.42384403944015503 392.3416748046875 0.6631993055343628 0.67166805 0.5254665613174438 True -14 34830 25.41768193244934 0.4628903865814209 316.6052551269531 0.33642327785491943 391.88116455078125 0.66447514295578 0.6781432 0.5144924521446228 True -15 37152 25.396189212799072 0.49802446365356445 351.92938232421875 0.3522578477859497 391.27679443359375 0.6651287078857422 0.6851259 0.5045850872993469 True -16 39474 25.421765327453613 0.45760679244995117 287.4228515625 0.25763389468193054 391.31915283203125 0.6651012897491455 0.68936473 0.503375232219696 True -17 41796 25.376885175704956 0.4557228088378906 329.11572265625 0.34426698088645935 391.54827880859375 0.6645851135253906 0.68743926 0.5087558627128601 False -18 44118 25.38081455230713 0.4645838737487793 300.88140869140625 0.19403284788131714 391.9599914550781 0.6639876365661621 0.6822795 0.5251170992851257 False -19 46440 25.374850273132324 0.4592862129211426 265.3718566894531 0.1896577775478363 391.8273620605469 0.6636723875999451 0.6790612 0.5271983742713928 False diff --git a/ENCSR528YDD/cherimoya.fold_0.performance.tsv b/ENCSR528YDD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fe2a0c42f488f5ca9d484536cd5e9265a49cb918..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -391.31915283203125 0.2761077880859375 0.6651012897491455 0.256287544965744 0.6893647313117981 0.6448444128036499 0.503375232219696 \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_1.evaluate.json b/ENCSR528YDD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 62e2cd79e6e50b644d33b8eecf4356ea6c6b7871..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF245PLY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_1.fit.json b/ENCSR528YDD/cherimoya.fold_1.fit.json deleted file mode 100644 index 50a4c851becb105b08a72d6a799aba26a2ce3847..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF245PLY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_1.log b/ENCSR528YDD/cherimoya.fold_1.log deleted file mode 100644 index a820813fc10db91589a1e030600fb63996fa3b44..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2362 30.94306230545044 3.8530824184417725 358.7371520996094 0.835737943649292 502.2442321777344 0.49355247616767883 0.51648605 7.521088600158691 True -1 4724 26.307842016220093 0.7859282493591309 341.57904052734375 0.9497252702713013 434.3406677246094 0.6069474816322327 0.61761373 2.3491475582122803 True -2 7086 26.379401922225952 0.576021671295166 335.6252136230469 0.6191685795783997 422.2808837890625 0.6280030012130737 0.6250359 0.7234729528427124 True -3 9448 26.335718154907227 0.5289671421051025 362.41229248046875 0.572487473487854 416.5811767578125 0.6384474039077759 0.6468474 0.5316727757453918 True -4 11810 26.348368167877197 0.5783669948577881 327.1776123046875 0.7672615647315979 414.5195617675781 0.6424733996391296 0.65610325 0.5046759247779846 True -5 14172 26.304486751556396 0.5217604637145996 356.3155517578125 0.7513126730918884 413.4616394042969 0.6457338929176331 0.6582087 0.4968358874320984 True -6 16534 26.28658103942871 0.52728271484375 307.6092224121094 0.5188901424407959 411.6844177246094 0.6488279700279236 0.6629789 0.49219223856925964 True -7 18896 26.345728874206543 0.5428676605224609 312.351318359375 0.6467720866203308 410.7603759765625 0.6506150364875793 0.66820693 0.48431503772735596 True -8 21258 26.372223377227783 10.632611513137817 350.2332763671875 0.6846565008163452 409.4707946777344 0.6531567573547363 0.6731029 0.4713973104953766 True -9 23620 26.344586849212646 0.5337762832641602 307.98394775390625 0.6736817955970764 408.2532958984375 0.6553757786750793 0.680238 0.4588782489299774 True -10 25982 26.368836641311646 0.5545389652252197 331.71514892578125 0.4699528217315674 407.130615234375 0.6575998067855835 0.68433225 0.4598862826824188 True -11 28344 26.3589448928833 0.5289015769958496 291.5824890136719 0.929949164390564 406.3050231933594 0.659052312374115 0.6910817 0.4534681439399719 True -12 30706 26.368542671203613 0.5307178497314453 273.26629638671875 0.46096473932266235 405.3638916015625 0.6606457233428955 0.6983686 0.44215714931488037 True -13 33068 26.28665781021118 0.5319187641143799 318.89794921875 0.3977161943912506 404.3513488769531 0.6622179746627808 0.7072913 0.4411894977092743 True -14 35430 26.406428337097168 0.5584468841552734 262.570556640625 0.5321317315101624 403.69903564453125 0.6634981632232666 0.7134233 0.43042731285095215 True -15 37792 26.474549055099487 0.5491275787353516 297.6250915527344 0.44668716192245483 403.0551452636719 0.6643084287643433 0.7160857 0.4292023479938507 True -16 40154 26.464757204055786 0.5336837768554688 283.56488037109375 0.4734376072883606 402.84857177734375 0.6643282771110535 0.7172556 0.4304448664188385 True -17 42516 26.453203201293945 0.5470170974731445 298.36309814453125 0.35425907373428345 402.8255310058594 0.6639694571495056 0.71754634 0.4339189827442169 True -18 44878 26.437083959579468 9.819926977157593 300.0540771484375 0.27894943952560425 403.0592041015625 0.6633816957473755 0.71345025 0.4441572427749634 False -19 47240 26.336033582687378 0.5339062213897705 272.08740234375 0.32106906175613403 403.1351623535156 0.6631024479866028 0.7097961 0.4532988965511322 False diff --git a/ENCSR528YDD/cherimoya.fold_1.performance.tsv b/ENCSR528YDD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 276b9ef0cfe95cb608f8e3c9743c3ba7df86e3f1..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -402.8255310058594 0.2734907269477844 0.6639694571495056 0.2631830871105194 0.7175463438034058 0.7035940289497375 0.4339189827442169 \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_2.evaluate.json b/ENCSR528YDD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7cd27e06fd575c663151ebf7efe79578488c0593..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF245PLY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_2.fit.json b/ENCSR528YDD/cherimoya.fold_2.fit.json deleted file mode 100644 index f1deec07a19486bba985a85e5a6828ef6eac8746..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF245PLY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_2.log b/ENCSR528YDD/cherimoya.fold_2.log deleted file mode 100644 index c96245c0e93003891f5d61dd07e699023112cb87..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2474 32.18121266365051 3.978447198867798 330.67584228515625 0.7915843725204468 489.83880615234375 0.4926208257675171 0.54136443 7.445662975311279 True -1 4948 27.610321760177612 12.298061847686768 274.8522033691406 0.5821980237960815 422.9906005859375 0.6110637784004211 0.606555 2.735044240951538 True -2 7422 27.569030046463013 0.4597623348236084 321.4072265625 0.8032562136650085 411.75494384765625 0.6275558471679688 0.6243075 1.099648118019104 True -3 9896 27.597769498825073 0.4530603885650635 255.33787536621094 0.5064563751220703 407.3663024902344 0.6352820992469788 0.6323298 0.8275907039642334 True -4 12370 27.629364252090454 0.4707145690917969 279.521484375 0.6995484828948975 405.3735656738281 0.6390716433525085 0.63767725 0.7139485478401184 True -5 14844 27.5759379863739 0.45151281356811523 327.0422668457031 0.5163553357124329 403.99407958984375 0.6420906186103821 0.6412523 0.6847870945930481 True -6 17318 27.517568111419678 0.4493749141693115 362.037841796875 0.6211646795272827 402.7209777832031 0.6440489888191223 0.64527696 0.6723202466964722 True -7 19792 27.618785858154297 0.4499855041503906 292.3966064453125 0.7330106496810913 401.5295104980469 0.6462836265563965 0.6506712 0.6410149931907654 True -8 22266 27.88480806350708 16.051494121551514 291.0873718261719 0.5868692398071289 400.2413635253906 0.6489996910095215 0.65442634 0.6050623059272766 True -9 24740 27.60369038581848 0.45380187034606934 305.56219482421875 0.44307461380958557 398.480224609375 0.651006817817688 0.66011965 0.5693162679672241 True -10 27214 27.64997673034668 0.45937347412109375 302.0115966796875 0.6486660242080688 398.0852355957031 0.652840256690979 0.66894865 0.5458513498306274 True -11 29688 27.617061614990234 0.45230650901794434 303.88250732421875 0.48323091864585876 396.7993469238281 0.6545425653457642 0.67522067 0.525521993637085 True -12 32162 27.62017583847046 0.45087671279907227 323.8704528808594 0.5071969032287598 395.86712646484375 0.6564269065856934 0.6814859 0.5233557224273682 True -13 34636 27.58479332923889 0.4597618579864502 286.3557434082031 0.5414289236068726 394.3114929199219 0.657814085483551 0.68465286 0.51047283411026 True -14 37110 27.603766202926636 0.45302867889404297 249.61126708984375 0.38951000571250916 393.65643310546875 0.6590285897254944 0.69360995 0.49339646100997925 True -15 39584 27.59177303314209 0.4496781826019287 305.0458068847656 0.4913267195224762 393.644775390625 0.6599567532539368 0.697862 0.4853007197380066 True -16 42058 27.511128902435303 0.45125484466552734 299.7698669433594 0.3627816438674927 393.511962890625 0.660037100315094 0.69896513 0.4871504604816437 True -17 44532 27.546470165252686 0.4457571506500244 321.80169677734375 0.4117905795574188 393.56927490234375 0.6596672534942627 0.69795537 0.4940132796764374 False -18 47006 27.549115896224976 0.44382190704345703 316.1744079589844 0.23431585729122162 393.5426330566406 0.6591461896896362 0.6970378 0.4992399215698242 False -19 49480 27.555479526519775 0.7793748378753662 288.0440979003906 0.2983313202857971 393.346923828125 0.6588844060897827 0.69652444 0.5018279552459717 False diff --git a/ENCSR528YDD/cherimoya.fold_2.performance.tsv b/ENCSR528YDD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 911311092aeec58ebeb89f3ca4a92db42b36b669..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -393.511962890625 0.27740663290023804 0.6600371599197388 0.2586088478565216 0.6989651322364807 0.667259931564331 0.4871504604816437 \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_3.evaluate.json b/ENCSR528YDD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fc7ec213eb6c6707949afd52f16d42bbacfe871c..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF245PLY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_3.fit.json b/ENCSR528YDD/cherimoya.fold_3.fit.json deleted file mode 100644 index 324d9ded168176154c986d6c98ed4285da8698d3..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF245PLY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_3.log b/ENCSR528YDD/cherimoya.fold_3.log deleted file mode 100644 index e5cc2c2ad5a3550abf61b7807f5838def0dd0094..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2427 31.7936692237854 3.706613779067993 278.19403076171875 0.5867004990577698 502.9053039550781 0.49638715386390686 0.5284527 8.953398704528809 True -1 4854 26.85295557975769 0.5352499485015869 321.92529296875 0.6747972965240479 429.42181396484375 0.6164098978042603 0.5909716 2.876431465148926 True -2 7281 27.002166748046875 0.5345869064331055 354.3246154785156 0.6126161813735962 418.29718017578125 0.6337831616401672 0.5997413 1.110313892364502 True -3 9708 27.00071954727173 0.5191638469696045 320.0679931640625 0.748987078666687 414.2283020019531 0.6395673751831055 0.6093352 1.0647656917572021 True -4 12135 27.082176446914673 0.611168622970581 331.3200378417969 0.6838337182998657 412.1230773925781 0.64335697889328 0.62373143 0.983238697052002 True -5 14562 27.068418741226196 0.5001957416534424 349.63323974609375 0.5778348445892334 410.0629577636719 0.6466202139854431 0.6342123 0.8078145980834961 True -6 16989 27.029460430145264 0.5140194892883301 311.48724365234375 0.6169551610946655 408.903076171875 0.6488091945648193 0.63659096 0.7593591809272766 True -7 19416 27.036750078201294 0.572648286819458 279.28729248046875 0.4733760356903076 407.4347229003906 0.6514507532119751 0.63757604 0.7082031965255737 True -8 21843 27.060497999191284 0.49866557121276855 325.89874267578125 0.4197818636894226 406.3705749511719 0.6534806489944458 0.6479067 0.6448725461959839 True -9 24270 27.053638219833374 0.504361629486084 325.352294921875 0.5491693019866943 405.2820739746094 0.6554881930351257 0.65094423 0.6242812871932983 True -10 26697 27.11275339126587 0.5243208408355713 263.10107421875 0.747002363204956 404.04180908203125 0.6576946973800659 0.6626702 0.6051737070083618 True -11 29124 27.032710313796997 0.49894213676452637 287.2398376464844 0.5286470651626587 402.9360656738281 0.6595818996429443 0.6723276 0.5724803805351257 True -12 31551 27.119826316833496 0.5076580047607422 300.77001953125 0.2940328121185303 401.6694641113281 0.6617998480796814 0.68349457 0.5444719195365906 True -13 33978 27.10166311264038 0.5107114315032959 292.4068603515625 0.3241491913795471 400.6308288574219 0.6634530425071716 0.69400144 0.5108430981636047 True -14 36405 27.11254620552063 1.670804738998413 296.500732421875 0.5107334852218628 399.59637451171875 0.664684534072876 0.7013167 0.5076321363449097 True -15 38832 27.115310668945312 0.514937162399292 316.411865234375 0.45578938722610474 398.8920593261719 0.6656526923179626 0.7107038 0.488038033246994 True -16 41259 27.10485076904297 0.8008346557617188 330.0047607421875 0.45263928174972534 398.64703369140625 0.6659275889396667 0.713351 0.48493602871894836 True -17 43686 27.08525252342224 0.5040450096130371 304.49365234375 0.2325633466243744 398.7981872558594 0.6656829118728638 0.71277297 0.482075959444046 False -18 46113 27.084675312042236 0.504263162612915 306.79644775390625 0.3277585506439209 398.952392578125 0.6651928424835205 0.70942944 0.4863124191761017 False -19 48540 27.11179828643799 0.5070736408233643 300.6395568847656 0.38930559158325195 399.0422058105469 0.6648509502410889 0.7096882 0.49413466453552246 False diff --git a/ENCSR528YDD/cherimoya.fold_3.performance.tsv b/ENCSR528YDD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 94e1847f55b95521ed824c45ae77e8553e93ff42..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -398.64703369140625 0.27261224389076233 0.6659275889396667 0.264094740152359 0.7133510112762451 0.6826986074447632 0.48493602871894836 \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_4.evaluate.json b/ENCSR528YDD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index dd76dc5942e5ba4581576b95026be3b6e0d1ea89..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF245PLY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_4.fit.json b/ENCSR528YDD/cherimoya.fold_4.fit.json deleted file mode 100644 index fd37dd53a639756a2e67a188d14890c41dd99082..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF245PLY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR528YDD/cherimoya.fold_4.log b/ENCSR528YDD/cherimoya.fold_4.log deleted file mode 100644 index 8f2ffd7ba6c12854547b4bc0436fae5c869c3f4c..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2472 32.20767855644226 4.464901447296143 335.1128845214844 0.8535656929016113 502.67156982421875 0.49434375762939453 0.5656132 7.550416946411133 True -1 4944 27.501883268356323 0.5238802433013916 300.4013366699219 0.6356749534606934 433.23065185546875 0.614761233329773 0.6002476 2.1795458793640137 True -2 7416 27.58130383491516 0.5336306095123291 353.22265625 0.784167468547821 420.9697570800781 0.6359146237373352 0.61594224 0.9134573340415955 True -3 9888 27.597386360168457 0.5363812446594238 326.79534912109375 0.7214654088020325 415.9952392578125 0.6442997455596924 0.63205534 0.7579663395881653 True -4 12360 27.59320068359375 2.166215419769287 290.63360595703125 0.7353813648223877 413.6546630859375 0.6484432220458984 0.6467643 0.663730263710022 True -5 14832 27.54463028907776 0.4651029109954834 304.04693603515625 0.5382388830184937 412.5238037109375 0.6505752205848694 0.6481207 0.6645864248275757 True -6 17304 27.292332410812378 0.4628787040710449 290.4614562988281 0.5883939266204834 410.35565185546875 0.6545027494430542 0.657203 0.6263410449028015 True -7 19776 27.06561827659607 0.48925352096557617 298.28375244140625 0.467144250869751 409.2772216796875 0.6566356420516968 0.6592622 0.6208886504173279 True -8 22248 27.061155080795288 0.45763731002807617 294.3377685546875 0.6509480476379395 407.60882568359375 0.659209668636322 0.667301 0.548252522945404 True -9 24720 26.961250066757202 0.462019681930542 333.3616943359375 0.5229830741882324 406.5714416503906 0.6614635586738586 0.6756419 0.5520232915878296 True -10 27192 27.10544443130493 0.46058011054992676 366.03546142578125 0.42262810468673706 404.8287353515625 0.6636173129081726 0.678439 0.5357354283332825 True -11 29664 27.02929186820984 0.45816707611083984 275.24273681640625 0.34892821311950684 404.1331787109375 0.6654435396194458 0.68136364 0.5366743206977844 True -12 32136 27.014782905578613 0.47952985763549805 314.9569091796875 0.5168799757957458 402.8997497558594 0.667263925075531 0.6853282 0.5209330320358276 True -13 34608 27.030441522598267 1.3460078239440918 263.2713928222656 0.4269002676010132 401.8337707519531 0.669187068939209 0.68784946 0.5077694654464722 True -14 37080 27.02659273147583 0.48505496978759766 310.97662353515625 0.550544261932373 400.7913818359375 0.6706504821777344 0.69378275 0.4975842237472534 True -15 39552 26.972355365753174 0.4850468635559082 307.8467102050781 0.36975401639938354 400.3104553222656 0.6711808443069458 0.6994814 0.49130961298942566 True -16 42024 27.040297508239746 0.4613656997680664 280.106689453125 0.3596373498439789 400.7940979003906 0.6711322069168091 0.6987016 0.4888527989387512 False -17 44496 27.019837141036987 0.4663858413696289 307.05889892578125 0.2382500022649765 401.19024658203125 0.670693039894104 0.69795984 0.49345046281814575 False -18 46968 27.01710796356201 0.47817015647888184 294.4241943359375 0.4279942512512207 400.79949951171875 0.6702277660369873 0.6939521 0.5075414776802063 False -19 49440 27.072770357131958 0.47382140159606934 285.2025146484375 0.28636693954467773 401.46148681640625 0.6699020862579346 0.6888853 0.5126679539680481 False diff --git a/ENCSR528YDD/cherimoya.fold_4.performance.tsv b/ENCSR528YDD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2faec0105a1745ac421ce9d6fb800b7fbf8cbc11..0000000000000000000000000000000000000000 --- a/ENCSR528YDD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -400.3104553222656 0.2715599238872528 0.6711808443069458 0.26490363478660583 0.6994814276695251 0.6507730484008789 0.49130961298942566 \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_0.evaluate.json b/ENCSR530XBF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b413c1076b31d75a2e0c17f9976f723e532181ca..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF913NQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_0.fit.json b/ENCSR530XBF/cherimoya.fold_0.fit.json deleted file mode 100644 index 939d8bf884ee14787042e438542cc360f57dfd94..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF913NQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_0.log b/ENCSR530XBF/cherimoya.fold_0.log deleted file mode 100644 index 177f4af58451cd5302ba939e7d216f104fad5e4b..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3827 47.29053020477295 4.0871806144714355 805.653076171875 1.4439520835876465 1189.539306640625 0.7113823890686035 0.6866207 8.46304988861084 True -1 7654 42.39401602745056 0.9899106025695801 835.2823486328125 1.2389042377471924 990.9373168945312 0.7869560718536377 0.69331646 2.149015188217163 True -2 11481 42.34420418739319 0.8349549770355225 869.087646484375 0.9893726706504822 969.9716186523438 0.7936811447143555 0.6991704 1.4798269271850586 True -3 15308 42.31002879142761 0.7443079948425293 900.0614013671875 1.1350157260894775 954.8220825195312 0.8002534508705139 0.70515966 1.4398927688598633 True -4 19135 42.29639935493469 0.7447938919067383 883.6380004882812 0.7621386051177979 949.048583984375 0.8027215600013733 0.70256025 1.4286035299301147 False -5 22962 42.4251823425293 30.433488845825195 895.01123046875 1.734405755996704 940.05322265625 0.8068569898605347 0.7037651 1.3820372819900513 False -6 26789 45.06623911857605 33.58491277694702 870.7259521484375 0.8651931881904602 934.8413696289062 0.809325635433197 0.7000789 1.3585503101348877 False -7 30616 42.50918173789978 0.7494034767150879 914.4191284179688 1.099428415298462 928.586669921875 0.811815083026886 0.7062091 1.3556897640228271 True -8 34443 42.46294689178467 0.7935590744018555 754.2234497070312 0.8850067853927612 917.9678955078125 0.8154720664024353 0.7160561 1.2193375825881958 True -9 38270 42.35488748550415 1.087144374847412 730.1900634765625 1.051772952079773 909.4833984375 0.8188962340354919 0.71730274 1.090141773223877 True -10 42097 42.42071509361267 0.758289098739624 828.7318115234375 0.7464859485626221 901.1036376953125 0.8217935562133789 0.7205899 1.0382697582244873 True -11 45924 42.38792371749878 0.7533292770385742 781.5408325195312 1.0244169235229492 891.58349609375 0.8253252506256104 0.7304181 0.9026517271995544 True -12 49751 42.29882073402405 0.7476308345794678 754.4444580078125 1.4071767330169678 883.5136108398438 0.8282542824745178 0.7366415 0.8392124176025391 True -13 53578 41.529194831848145 0.792574405670166 627.793701171875 1.2256648540496826 877.0032958984375 0.8311182856559753 0.7467639 0.784686267375946 True -14 57405 41.638038873672485 0.7617456912994385 720.4234619140625 0.8439256548881531 871.5731201171875 0.8338419198989868 0.7550895 0.762390673160553 True -15 61232 41.64031410217285 0.7370102405548096 671.8502807617188 0.5661424398422241 867.6526489257812 0.8356355428695679 0.7629277 0.7036445736885071 True -16 65059 41.55828905105591 1.0587489604949951 692.0064697265625 0.9471790790557861 865.1630859375 0.8367747664451599 0.7657843 0.6732395887374878 True -17 68886 41.59589672088623 0.7397329807281494 620.6401977539062 0.8115930557250977 865.2042236328125 0.8369020819664001 0.7683047 0.6538264751434326 True -18 72713 41.54014825820923 0.7502076625823975 628.6813354492188 0.5013013482093811 866.6475219726562 0.8365925550460815 0.76778257 0.6472455859184265 False -19 76540 41.53772568702698 0.7483365535736084 579.131591796875 0.49462804198265076 867.0103759765625 0.8364173173904419 0.7665009 0.6470968127250671 False diff --git a/ENCSR530XBF/cherimoya.fold_0.performance.tsv b/ENCSR530XBF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 34c3888756f03cf8639994ed7ac78eb64e640312..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -865.2042236328125 0.13350346684455872 0.8369021415710449 0.5037124156951904 0.768304705619812 0.7175329923629761 0.6538264751434326 \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_1.evaluate.json b/ENCSR530XBF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 80e7750fc7b5059b5fde05972ce1286c7cd5d367..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF913NQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_1.fit.json b/ENCSR530XBF/cherimoya.fold_1.fit.json deleted file mode 100644 index 0aeb629c15da4354a95d59edbc6f6ffad1e3c7c6..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF913NQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_1.log b/ENCSR530XBF/cherimoya.fold_1.log deleted file mode 100644 index 507b0b83b14b433dc9ed74d159542c7a97a68c83..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3797 47.645561933517456 4.409583806991577 972.1640625 1.368931770324707 1386.4591064453125 0.7203965187072754 0.70702416 8.617960929870605 True -1 7594 42.168763160705566 1.081265926361084 671.355224609375 1.5505008697509766 1139.3629150390625 0.7974787354469299 0.73268116 2.641246795654297 True -2 11391 42.122822523117065 1.059988021850586 693.2286987304688 0.9068368673324585 1114.302490234375 0.8053798675537109 0.7426647 1.8043594360351562 True -3 15188 42.14066481590271 1.9217021465301514 798.8958740234375 1.0641157627105713 1095.134765625 0.8111472725868225 0.74581385 1.4590224027633667 True -4 18985 42.161821126937866 0.9988007545471191 768.1168212890625 1.5221672058105469 1080.4794921875 0.8152129650115967 0.74627876 1.231472373008728 True -5 22782 42.10111141204834 0.9944336414337158 813.5919799804688 1.5327105522155762 1072.65478515625 0.8179739713668823 0.7500808 1.2734931707382202 True -6 26579 42.01579451560974 0.9902787208557129 817.688232421875 1.4462347030639648 1061.464111328125 0.8208383917808533 0.75167537 1.102315068244934 True -7 30376 41.93673753738403 1.996208667755127 702.82275390625 1.2801792621612549 1052.1639404296875 0.8233985900878906 0.7549696 1.0027698278427124 True -8 34173 41.24677658081055 0.9916737079620361 762.8607788085938 1.1594561338424683 1044.31201171875 0.8260306715965271 0.7580457 1.0423438549041748 True -9 37970 41.34911108016968 1.0267128944396973 690.5162353515625 1.014139175415039 1037.4222412109375 0.828653872013092 0.75899106 1.0640947818756104 True -10 41767 41.355308532714844 0.9933445453643799 650.947021484375 1.1581828594207764 1026.3692626953125 0.8315525650978088 0.7647883 1.03432035446167 True -11 45564 41.37685489654541 1.0052738189697266 836.5670166015625 0.722476601600647 1019.2512817382812 0.8342280983924866 0.7681753 0.9927511811256409 True -12 49361 41.37505078315735 0.9882423877716064 775.9554443359375 0.6301957964897156 1004.8361206054688 0.8379076719284058 0.7744993 0.8208427429199219 True -13 53158 41.33199858665466 0.9801535606384277 794.1748046875 0.8190135359764099 996.5419921875 0.8410468101501465 0.7817651 0.7963705062866211 True -14 56955 41.33637022972107 0.9815130233764648 708.2015991210938 0.49571987986564636 988.94580078125 0.8434138894081116 0.7888329 0.7501537799835205 True -15 60752 41.297508239746094 2.1432700157165527 734.5069580078125 0.7518854141235352 983.6194458007812 0.8454167246818542 0.7942609 0.6963046789169312 True -16 64549 41.260085344314575 0.9939265251159668 677.748779296875 0.6268472671508789 980.475341796875 0.8463963866233826 0.7971777 0.6616058349609375 True -17 68346 41.180415391922 1.0042877197265625 746.69970703125 0.414638876914978 980.8811645507812 0.8464595079421997 0.79941446 0.648705244064331 True -18 72143 41.129956007003784 0.9725520610809326 800.3783569335938 0.5870767831802368 982.95751953125 0.8461751341819763 0.8007441 0.6344180703163147 True -19 75940 41.144227504730225 1.0040597915649414 656.8208618164062 0.6146774291992188 984.29443359375 0.8457343578338623 0.7981115 0.6393808722496033 False diff --git a/ENCSR530XBF/cherimoya.fold_1.performance.tsv b/ENCSR530XBF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7c7f9714ad8fd9af46e462b6c95c584af879242c..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -982.95751953125 0.12229511886835098 0.8461750149726868 0.5417104363441467 0.8007441163063049 0.7722192406654358 0.6344180703163147 \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_2.evaluate.json b/ENCSR530XBF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 724f1a08f483a3614cc78ff8342d0e3affa07d73..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF913NQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_2.fit.json b/ENCSR530XBF/cherimoya.fold_2.fit.json deleted file mode 100644 index f078e6bdd75209f55504bfa99e050256d0ab530c..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF913NQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_2.log b/ENCSR530XBF/cherimoya.fold_2.log deleted file mode 100644 index 0c0fd7985c752e6b68d1c03736039ebaa3f67dd9..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4029 49.464683532714844 4.17685604095459 851.054443359375 1.2541745901107788 1261.556396484375 0.7235961556434631 0.6810109 8.187108039855957 True -1 8058 44.72420334815979 0.7801778316497803 892.114501953125 1.060858964920044 1057.7471923828125 0.7976667284965515 0.7053275 1.9589767456054688 True -2 12087 44.70167541503906 1.95387864112854 842.45556640625 1.4190055131912231 1037.3570556640625 0.8047807216644287 0.71426874 1.2900716066360474 True -3 16116 43.99215912818909 0.9010555744171143 671.684326171875 0.8188751935958862 1021.7315673828125 0.8090652823448181 0.7186093 1.135960340499878 True -4 20145 43.76907920837402 0.7568821907043457 667.15234375 1.562658429145813 1013.0673828125 0.813303530216217 0.7208962 1.3157281875610352 True -5 24174 43.68620562553406 2.3580856323242188 770.7211303710938 1.0971516370773315 1004.8433227539062 0.8165357708930969 0.7216399 1.3250443935394287 True -6 28203 43.724854707717896 0.753251314163208 805.6241455078125 0.6706749200820923 995.0196533203125 0.8191807270050049 0.72791487 1.2371437549591064 True -7 32232 43.739402055740356 19.476827383041382 737.1881713867188 0.8489426970481873 986.576904296875 0.8220452666282654 0.72844434 1.238359808921814 True -8 36261 43.767900466918945 0.7608852386474609 850.3687744140625 1.223069190979004 978.9213256835938 0.8247854113578796 0.73018175 1.1413917541503906 True -9 40290 43.739349365234375 0.7862672805786133 796.80517578125 1.308181643486023 969.7418212890625 0.8278000354766846 0.73164594 1.1230827569961548 True -10 44319 43.788727045059204 0.7572715282440186 791.580078125 0.7289741039276123 960.7962646484375 0.8308079242706299 0.7364684 1.0206888914108276 True -11 48348 43.6777663230896 0.7578227519989014 784.82861328125 0.7851114273071289 953.5009765625 0.8336400389671326 0.73857653 0.9786519408226013 True -12 52377 43.697322607040405 0.75826096534729 610.9176025390625 0.661200761795044 944.5344848632812 0.8361701369285583 0.7460174 0.9164193868637085 True -13 56406 43.69403076171875 0.7594864368438721 681.159423828125 0.9565083980560303 938.3492431640625 0.8388504385948181 0.751762 0.8346124887466431 True -14 60435 43.71325373649597 0.756523609161377 610.9537353515625 0.6798566579818726 931.5064697265625 0.841235876083374 0.75386477 0.806434690952301 True -15 64464 43.71701622009277 1.6612155437469482 663.865478515625 0.5202227234840393 926.0113525390625 0.8434979915618896 0.76032954 0.7548596262931824 True -16 68493 43.73632788658142 0.7570211887359619 733.9281005859375 0.6002158522605896 924.4404907226562 0.8444312810897827 0.76394606 0.7250673174858093 True -17 72522 43.67743802070618 1.5130698680877686 557.0636596679688 0.8579584360122681 924.012939453125 0.8445532321929932 0.7645065 0.6984612345695496 True -18 76551 43.85385584831238 0.7699403762817383 541.597900390625 0.9174533486366272 924.91943359375 0.8442047834396362 0.7647946 0.6944878697395325 True -19 80580 44.68274450302124 0.7935948371887207 615.0836791992188 0.43952593207359314 926.4085693359375 0.8438610434532166 0.76396775 0.6991026401519775 False diff --git a/ENCSR530XBF/cherimoya.fold_2.performance.tsv b/ENCSR530XBF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6efddb95ce82227cc35b14c7d56286621a4cbfad..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -924.91943359375 0.12631851434707642 0.8442047834396362 0.5254617929458618 0.7647945880889893 0.725878894329071 0.6944878697395325 \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_3.evaluate.json b/ENCSR530XBF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 69d5aa0ee678cace83d83c3fed37fe964296926d..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF913NQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_3.fit.json b/ENCSR530XBF/cherimoya.fold_3.fit.json deleted file mode 100644 index 4721c541118f0ccd3f06af5813c3c09b8f261629..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF913NQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_3.log b/ENCSR530XBF/cherimoya.fold_3.log deleted file mode 100644 index 6b5c835b08d15e27bd2efb39dc75076f37bbde8a..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3887 47.884328842163086 3.770949602127075 825.5490112304688 1.2156130075454712 1190.387451171875 0.7166539430618286 0.6989294 7.682374477386475 True -1 7774 42.496620893478394 0.9832005500793457 844.1137084960938 1.4320623874664307 998.2791137695312 0.7888089418411255 0.7156692 2.555001735687256 True -2 11661 43.00295162200928 0.8095481395721436 705.442138671875 1.0845288038253784 976.4921264648438 0.7975931763648987 0.7160974 1.8010640144348145 True -3 15548 42.999943256378174 0.7619884014129639 807.5687255859375 1.11466646194458 963.0679321289062 0.8031079173088074 0.71888673 1.6188328266143799 True -4 19435 43.05048227310181 0.7813429832458496 759.44970703125 0.8508527874946594 952.18017578125 0.8069917559623718 0.72461873 1.2228268384933472 True -5 23322 43.002522706985474 0.7799746990203857 733.7305908203125 1.265005111694336 948.0877075195312 0.8089239001274109 0.7209046 1.176600456237793 False -6 27209 43.06742835044861 0.7837538719177246 914.4514770507812 0.8400379419326782 942.9910278320312 0.8112372159957886 0.7286003 1.144942283630371 True -7 31096 43.13570952415466 0.7675642967224121 742.5203857421875 0.9511836767196655 930.4775390625 0.8148573040962219 0.7309964 0.9975364208221436 True -8 34983 43.104727268218994 0.7808027267456055 833.6241455078125 0.8874263763427734 923.311279296875 0.8178178071975708 0.7381771 1.000177025794983 True -9 38870 43.1064350605011 0.7759394645690918 696.5291748046875 0.8984524011611938 920.663818359375 0.8191406726837158 0.73943377 0.917252779006958 True -10 42757 43.0671968460083 0.7826297283172607 884.669921875 0.838708221912384 910.7105102539062 0.8227713108062744 0.74208033 0.8841405510902405 True -11 46644 43.47807192802429 0.7797544002532959 753.877685546875 1.0719155073165894 904.6348876953125 0.8255963325500488 0.7470887 0.8470664620399475 True -12 50531 43.12696933746338 0.7671773433685303 713.7887573242188 0.5717661380767822 895.8861083984375 0.8286933898925781 0.75684315 0.787613570690155 True -13 54418 43.040321826934814 0.7739012241363525 689.1325073242188 0.8846396803855896 888.6200561523438 0.8317878246307373 0.7609499 0.7451609373092651 True -14 58305 43.10776233673096 0.7713108062744141 806.8914794921875 0.6106280088424683 883.3515014648438 0.8343638181686401 0.7684156 0.690752387046814 True -15 62192 43.08181881904602 0.7764933109283447 699.8707275390625 0.609722375869751 878.89111328125 0.836098849773407 0.7729745 0.6771394610404968 True -16 66079 42.98075842857361 0.7510955333709717 755.0856323242188 0.7556964755058289 877.9212036132812 0.8369994759559631 0.7765304 0.6591761112213135 True -17 69966 42.19718265533447 0.7607150077819824 596.5728759765625 0.6913671493530273 878.5015869140625 0.8370335102081299 0.7761799 0.6527221202850342 False -18 73853 42.2289662361145 0.7548012733459473 653.0303955078125 0.4883592128753662 880.18701171875 0.8366683125495911 0.77561027 0.6468484401702881 False -19 77740 42.1512348651886 1.6740188598632812 511.79241943359375 0.7606725692749023 880.98974609375 0.8363990187644958 0.77465355 0.6524717211723328 False diff --git a/ENCSR530XBF/cherimoya.fold_3.performance.tsv b/ENCSR530XBF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 308af0b69e4f1d14a7c32283ce80ca50f485ef24..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -877.9212036132812 0.13206401467323303 0.8369994759559631 0.5055996775627136 0.776530385017395 0.7305293083190918 0.6591761112213135 \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_4.evaluate.json b/ENCSR530XBF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0b2c8f76c9b02575279ba60c122d5dd7ced69624..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF913NQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_4.fit.json b/ENCSR530XBF/cherimoya.fold_4.fit.json deleted file mode 100644 index ae1c296a2535cf00cbd4cf5ddd963018485d7e79..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF913NQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR530XBF/cherimoya.fold_4.log b/ENCSR530XBF/cherimoya.fold_4.log deleted file mode 100644 index 52121c4368434360410995e58966bd2e1593f4c7..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3944 48.530966997146606 3.8355491161346436 860.2379150390625 1.4376599788665771 1154.8095703125 0.711902916431427 0.67218137 6.883418560028076 True -1 7888 43.737616300582886 0.8566405773162842 852.71533203125 1.3383536338806152 974.4299926757812 0.7838001251220703 0.69770384 2.745544195175171 True -2 11832 43.6874577999115 0.8341860771179199 725.419189453125 1.1984474658966064 959.4844970703125 0.7892552018165588 0.70141643 1.2086896896362305 True -3 15776 43.69595551490784 0.7808151245117188 738.864501953125 1.0800657272338867 939.5860595703125 0.7975226044654846 0.7071937 1.0066161155700684 True -4 19720 43.62403678894043 2.526970386505127 597.1473999023438 1.0492706298828125 931.0068969726562 0.8010263442993164 0.7058058 1.1742591857910156 False -5 23664 43.72925066947937 0.7874712944030762 802.9296264648438 0.864863395690918 921.0650634765625 0.8051819205284119 0.7047562 1.0576002597808838 False -6 27608 43.65509009361267 0.7891507148742676 634.7733154296875 0.8778297901153564 916.2465209960938 0.8081311583518982 0.70926607 1.0810744762420654 True -7 31552 43.661197900772095 1.130671501159668 771.2984619140625 0.877781867980957 907.7119750976562 0.8116412162780762 0.7118751 1.1476364135742188 True -8 35496 43.71966218948364 0.783592939376831 830.4046630859375 0.9266217350959778 901.6378173828125 0.8140976428985596 0.71539706 1.1787711381912231 True -9 39440 43.70492172241211 0.8535196781158447 761.879150390625 0.7988278865814209 893.5548095703125 0.8173838257789612 0.71955556 1.103806734085083 True -10 43384 43.76093602180481 0.7773048877716064 679.84619140625 0.9013127088546753 883.0568237304688 0.8206754326820374 0.721729 0.9631140232086182 True -11 47328 43.39643883705139 0.7623956203460693 692.131591796875 0.6813547611236572 876.2738037109375 0.823493480682373 0.7255674 0.8652203679084778 True -12 51272 43.2211537361145 0.8126533031463623 765.8801879882812 1.082196831703186 867.6927490234375 0.8265548348426819 0.7364832 0.8020926117897034 True -13 55216 42.84043550491333 0.7741756439208984 750.5604248046875 0.661227822303772 862.54736328125 0.8293548822402954 0.7394064 0.7764438986778259 True -14 59160 42.75747323036194 0.7882697582244873 669.044189453125 0.8583402037620544 856.5203857421875 0.8319427967071533 0.7454152 0.7330172657966614 True -15 63104 42.84071683883667 0.7744603157043457 707.2263793945312 0.618357241153717 853.9881591796875 0.8334800004959106 0.75247395 0.6982369422912598 True -16 67048 42.88034725189209 0.7764761447906494 727.0707397460938 0.5336580276489258 851.2251586914062 0.8348284959793091 0.7573271 0.6749204993247986 True -17 70992 42.753902435302734 0.7730116844177246 526.9126586914062 0.59257972240448 851.63818359375 0.8348773717880249 0.7582891 0.6597467660903931 True -18 74936 42.82731771469116 0.7790348529815674 684.9847412109375 0.5702317953109741 852.681396484375 0.8344357013702393 0.75700784 0.6589116454124451 False -19 78880 42.76423215866089 0.776360034942627 699.838623046875 0.3201945424079895 854.1038208007812 0.8341820240020752 0.75511676 0.6638278365135193 False diff --git a/ENCSR530XBF/cherimoya.fold_4.performance.tsv b/ENCSR530XBF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d13cfc2c5e2e170ef5fff3bf73af0e9d64e1ee8f..0000000000000000000000000000000000000000 --- a/ENCSR530XBF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -851.63818359375 0.1347772777080536 0.8348773717880249 0.5003024935722351 0.758289098739624 0.699091374874115 0.6597467660903931 \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_0.evaluate.json b/ENCSR531AYV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 516f10f8550231a54ec22ba696b15c8ca52f50cb..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF241HZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_0.fit.json b/ENCSR531AYV/cherimoya.fold_0.fit.json deleted file mode 100644 index 2b7168fc499770234841062a5609cfa2ee03303b..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF241HZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_0.log b/ENCSR531AYV/cherimoya.fold_0.log deleted file mode 100644 index 40e88e82de2a9f29465e543b2f382d1710cddf29..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 34.831268072128296 3.9106030464172363 155.89610290527344 0.4190872013568878 256.21148681640625 0.13391467928886414 0.7150855 3.817230224609375 True -1 5512 30.479568243026733 0.6171236038208008 294.55072021484375 0.6561094522476196 231.84156799316406 0.16755658388137817 0.7980551 1.6551295518875122 True -2 8268 30.474287271499634 0.6083006858825684 187.99090576171875 0.5038648843765259 230.14744567871094 0.16903334856033325 0.7701168 1.117235541343689 False -3 11024 30.40659761428833 0.5685796737670898 214.36846923828125 0.5135683417320251 226.07601928710938 0.1726013422012329 0.8101738 0.7519252896308899 True -4 13780 30.402581453323364 0.8570067882537842 174.25555419921875 0.4213566780090332 224.0340118408203 0.17471624910831451 0.8184828 0.6386042833328247 True -5 16536 30.372864723205566 0.5645439624786377 185.92333984375 0.47543174028396606 222.1146697998047 0.17662948369979858 0.8317504 0.6032280325889587 True -6 19292 30.349632024765015 0.5547051429748535 203.14117431640625 0.3285166621208191 220.659912109375 0.17857658863067627 0.8405237 0.5366732478141785 True -7 22048 30.3298978805542 0.5631875991821289 182.485595703125 0.35618942975997925 219.8461456298828 0.18068014085292816 0.84199786 0.520203173160553 True -8 24804 30.300034284591675 0.548201322555542 203.02798461914062 0.3364567756652832 218.77723693847656 0.18180018663406372 0.84688395 0.48196062445640564 True -9 27560 30.30849289894104 0.5642526149749756 196.1918182373047 0.6595901846885681 217.77467346191406 0.18392807245254517 0.8524175 0.4418952763080597 True -10 30316 30.327571392059326 0.5660049915313721 190.18701171875 0.4828298091888428 217.1750030517578 0.18466919660568237 0.85752434 0.40851104259490967 True -11 33072 30.31900191307068 0.5543687343597412 159.90048217773438 0.2971782684326172 216.34446716308594 0.18640217185020447 0.8632443 0.36764469742774963 True -12 35828 29.730777502059937 0.5545496940612793 144.69125366210938 0.28520217537879944 216.02667236328125 0.18677541613578796 0.86400115 0.3537333011627197 True -13 38584 29.76686429977417 0.5596737861633301 161.63531494140625 0.32127195596694946 215.7210235595703 0.1867746263742447 0.8681005 0.3305368423461914 True -14 41340 29.7607479095459 0.5545084476470947 241.6195831298828 0.4918692111968994 214.70608520507812 0.18816721439361572 0.876105 0.30459946393966675 True -15 44096 29.82773995399475 0.5599358081817627 207.13400268554688 0.3756200075149536 214.62539672851562 0.18830323219299316 0.87873137 0.29174044728279114 True -16 46852 29.75427746772766 0.5543322563171387 204.01687622070312 0.27346304059028625 213.82908630371094 0.18936893343925476 0.8814106 0.2781825661659241 True -17 49608 29.8397855758667 0.5585837364196777 145.62908935546875 0.2953917384147644 213.9960479736328 0.1888992190361023 0.88261205 0.2730202376842499 True -18 52364 29.834731101989746 0.5608491897583008 163.05992126464844 0.2837420105934143 214.39939880371094 0.1883532702922821 0.8825507 0.27541059255599976 False -19 55120 29.78788685798645 0.5627126693725586 181.30227661132812 0.22457753121852875 214.25802612304688 0.1889066994190216 0.88148445 0.27656087279319763 False diff --git a/ENCSR531AYV/cherimoya.fold_0.performance.tsv b/ENCSR531AYV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e963d2c9005b4f35eb45d04831bc40aabe85fa46..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -213.9960479736328 0.5634400844573975 0.1888992190361023 0.05240898206830025 0.8826120495796204 0.7982174754142761 0.2730202376842499 \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_1.evaluate.json b/ENCSR531AYV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 83cb96a3b916cfe6cc3ba40b72d7d13b22648387..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF241HZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_1.fit.json b/ENCSR531AYV/cherimoya.fold_1.fit.json deleted file mode 100644 index 32b86ab4c05b8be4ee75aca9dbfe822c1c02fbae..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF241HZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_1.log b/ENCSR531AYV/cherimoya.fold_1.log deleted file mode 100644 index 934be3bfee26733ec9350999c2be397e0e8327cb..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2720 34.3820915222168 5.189371347427368 187.41836547851562 0.395305335521698 325.58795166015625 0.14408908784389496 0.6831367 4.543821811676025 True -1 5440 30.021005630493164 1.0230846405029297 239.58633422851562 0.497630774974823 298.4996337890625 0.18040311336517334 0.7418141 2.4212684631347656 True -2 8160 30.050774097442627 0.7741644382476807 206.89041137695312 0.753778338432312 289.62255859375 0.18926848471164703 0.7575825 1.6086982488632202 True -3 10880 29.953866004943848 0.8892972469329834 195.23658752441406 0.5458877086639404 283.73980712890625 0.1947993040084839 0.78482103 1.2762517929077148 True -4 13600 29.975426197052002 1.0046472549438477 217.80987548828125 0.6391733288764954 278.35711669921875 0.20024192333221436 0.8064126 1.1441256999969482 True -5 16320 29.945136070251465 1.9641802310943604 176.93203735351562 0.42017561197280884 277.332763671875 0.2016420066356659 0.8105196 1.0511460304260254 True -6 19040 29.96764039993286 1.4100401401519775 136.88998413085938 0.2266160249710083 274.651611328125 0.20504312217235565 0.8170288 0.9181106686592102 True -7 21760 29.954150676727295 0.9519872665405273 181.998046875 0.3775213360786438 272.76629638671875 0.20727768540382385 0.8254688 0.8099547624588013 True -8 24480 29.90563941001892 0.7033853530883789 208.79637145996094 0.3801615536212921 270.6181945800781 0.21030065417289734 0.83818966 0.6859706044197083 True -9 27200 29.90060520172119 0.7072851657867432 195.63467407226562 0.33236491680145264 269.8051452636719 0.21104416251182556 0.8465944 0.6276320219039917 True -10 29920 29.916728258132935 0.6993124485015869 168.43263244628906 0.3592439889907837 268.3211364746094 0.21330568194389343 0.8515189 0.5766282081604004 True -11 32640 29.92776608467102 1.6360564231872559 174.80279541015625 0.33931058645248413 267.1041259765625 0.21404775977134705 0.85942006 0.5280560851097107 True -12 35360 29.582411766052246 1.3811290264129639 175.40853881835938 0.34213119745254517 265.27197265625 0.2164362072944641 0.8687229 0.4776517450809479 True -13 38080 29.453019618988037 16.17965292930603 143.2330322265625 0.27342474460601807 264.6109619140625 0.21738116443157196 0.8752433 0.4389810562133789 True -14 40800 29.438058853149414 21.671701669692993 175.6811981201172 0.3554779887199402 263.2121887207031 0.21872368454933167 0.8833332 0.4034386873245239 True -15 43520 29.572977304458618 0.6977310180664062 176.22589111328125 0.33165112137794495 262.7373046875 0.21841058135032654 0.8880041 0.372083455324173 True -16 46240 29.42971897125244 0.6908431053161621 140.4889678955078 0.26570916175842285 261.84075927734375 0.2205921709537506 0.8930608 0.3501487374305725 True -17 48960 29.51821517944336 0.6993494033813477 182.94688415527344 0.3190736174583435 262.5578918457031 0.21857213973999023 0.8930027 0.34488269686698914 False -18 51680 29.369706630706787 0.7042343616485596 182.13363647460938 0.2607223391532898 263.1941223144531 0.21658024191856384 0.890803 0.3445478677749634 False -19 54400 29.41501760482788 0.7120532989501953 164.4075927734375 0.2556159496307373 263.07696533203125 0.21759358048439026 0.8896501 0.3459121286869049 False diff --git a/ENCSR531AYV/cherimoya.fold_1.performance.tsv b/ENCSR531AYV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7112d1d2220656b0d07e6b5144b357489bbf6592..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -261.84075927734375 0.5395421385765076 0.22059215605258942 0.06713464111089706 0.8930608034133911 0.8416184782981873 0.3501487374305725 \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_2.evaluate.json b/ENCSR531AYV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 710154a3a370f9eafc448c1a624ddf668a83e794..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF241HZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_2.fit.json b/ENCSR531AYV/cherimoya.fold_2.fit.json deleted file mode 100644 index f5c2c2c664af0a6105b4ce9369332292ef353db3..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF241HZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_2.log b/ENCSR531AYV/cherimoya.fold_2.log deleted file mode 100644 index 8d236efd4192124bd7518a38379cf77e9ebedf10..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2859 35.94735646247864 3.721242904663086 197.28065490722656 0.4870298206806183 263.2716064453125 0.1358875334262848 0.68898946 3.7758584022521973 True -1 5718 31.56433343887329 0.6998419761657715 264.71624755859375 0.5482291579246521 238.46493530273438 0.16907206177711487 0.79161716 1.6122865676879883 True -2 8577 31.506223678588867 0.6631078720092773 190.5164031982422 0.45085662603378296 235.1329803466797 0.17179009318351746 0.7808123 1.0528852939605713 False -3 11436 31.515218257904053 0.5843119621276855 141.91851806640625 0.5710668563842773 229.07652282714844 0.17782922089099884 0.8170245 0.6742123961448669 True -4 14295 31.449101209640503 1.3531501293182373 146.46372985839844 0.625679612159729 227.65464782714844 0.17818373441696167 0.82551146 0.6344203352928162 True -5 17154 31.517249822616577 0.5936017036437988 200.64613342285156 0.3882048726081848 226.01739501953125 0.18037952482700348 0.834363 0.5623868107795715 True -6 20013 31.488362789154053 0.5960307121276855 260.2091979980469 0.44828349351882935 224.40628051757812 0.18326525390148163 0.8411905 0.5495524406433105 True -7 22872 31.534412622451782 0.5900464057922363 149.57443237304688 0.32384192943573 223.689697265625 0.18384678661823273 0.8446739 0.5011922717094421 True -8 25731 31.504745960235596 0.5886454582214355 245.2364044189453 0.4838671386241913 222.46746826171875 0.18523572385311127 0.8517375 0.45917755365371704 True -9 28590 31.458723068237305 0.6061084270477295 188.37472534179688 0.4075400233268738 221.3793182373047 0.18784233927726746 0.8551205 0.44294777512550354 True -10 31449 30.9183349609375 0.5911855697631836 123.02384948730469 0.5228941440582275 220.82777404785156 0.18851324915885925 0.8594319 0.41385433077812195 True -11 34308 30.905577659606934 0.5796632766723633 124.90774536132812 0.23742607235908508 220.8336639404297 0.18749813735485077 0.86307347 0.37491682171821594 True -12 37167 30.876314163208008 0.5848219394683838 177.95663452148438 0.31278160214424133 219.9658660888672 0.18927882611751556 0.86801285 0.3582562208175659 True -13 40026 30.90121364593506 0.5737948417663574 120.6620101928711 0.4438842535018921 218.65415954589844 0.19227798283100128 0.8701194 0.3335132300853729 True -14 42885 30.92938208580017 1.035505771636963 201.16018676757812 0.24062779545783997 218.53155517578125 0.19118468463420868 0.87743264 0.3081829249858856 True -15 45744 30.93178391456604 0.5878088474273682 155.62789916992188 0.17088261246681213 217.83973693847656 0.19323408603668213 0.880721 0.2893296778202057 True -16 48603 30.953279972076416 0.5743489265441895 181.12550354003906 0.19349902868270874 217.8194122314453 0.1924307644367218 0.883399 0.2789788544178009 True -17 51462 30.937421798706055 0.6215288639068604 177.62818908691406 0.22895291447639465 217.35733032226562 0.19370776414871216 0.8855326 0.27201056480407715 True -18 54321 30.891379833221436 0.5891764163970947 170.818359375 0.16998723149299622 217.52072143554688 0.19304350018501282 0.88452095 0.27172383666038513 False -19 57180 30.908023357391357 0.582038164138794 249.91122436523438 0.23933157324790955 218.04627990722656 0.1913788616657257 0.88326806 0.2723013162612915 False diff --git a/ENCSR531AYV/cherimoya.fold_2.performance.tsv b/ENCSR531AYV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index eb6f5d55bd57db76f099e7b426f40274ff4cf957..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -217.35733032226562 0.5598961710929871 0.19370777904987335 0.052143726497888565 0.8855326175689697 0.8188206553459167 0.27201056480407715 \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_3.evaluate.json b/ENCSR531AYV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d71e4a0e695fc75ac87781ebf52828bf9e0489f6..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF241HZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_3.fit.json b/ENCSR531AYV/cherimoya.fold_3.fit.json deleted file mode 100644 index f4aafa3ef16151b29fe415421328559f566dd98a..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF241HZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_3.log b/ENCSR531AYV/cherimoya.fold_3.log deleted file mode 100644 index 6264d195d8bdb0204805c5d8fb366529262fbd2f..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 35.14383006095886 3.344324827194214 227.95852661132812 0.6335066556930542 267.46600341796875 0.1403692215681076 0.65755093 4.3011579513549805 True -1 5458 30.113901138305664 0.580575704574585 152.68429565429688 0.4401029050350189 244.25241088867188 0.17408685386180878 0.7421717 1.7862887382507324 True -2 8187 30.451539039611816 0.5379197597503662 166.68167114257812 0.4518531262874603 241.85699462890625 0.17501921951770782 0.7563165 1.175215244293213 True -3 10916 30.07980990409851 0.5040132999420166 227.47947692871094 0.5084220767021179 236.84986877441406 0.17955884337425232 0.79623896 0.8072848916053772 True -4 13645 30.029191970825195 0.972252368927002 155.14385986328125 0.3314480781555176 234.43743896484375 0.18234100937843323 0.7986373 0.808809220790863 True -5 16374 30.046197175979614 1.2855794429779053 143.29881286621094 0.31809914112091064 232.5391082763672 0.18564322590827942 0.8043933 0.760376513004303 True -6 19103 30.028951168060303 0.5833389759063721 259.5546569824219 0.6073775291442871 231.38218688964844 0.1874937266111374 0.8068537 0.7270881533622742 True -7 21832 30.08630871772766 0.5108633041381836 172.929443359375 0.6058675050735474 231.26171875 0.18689396977424622 0.8100001 0.709408700466156 True -8 24561 30.044898509979248 0.49481678009033203 196.49221801757812 0.40035325288772583 229.99253845214844 0.1883423924446106 0.81774485 0.6186193227767944 True -9 27290 30.0397789478302 1.4084656238555908 210.06797790527344 0.2528221011161804 229.2827606201172 0.1889139711856842 0.8264394 0.5648045539855957 True -10 30019 30.067410707473755 0.5076849460601807 167.0892333984375 0.28549665212631226 227.75680541992188 0.19220687448978424 0.8297204 0.5364466309547424 True -11 32748 29.67863965034485 0.48873281478881836 223.9047393798828 0.37203139066696167 226.6377716064453 0.1941744089126587 0.8370209 0.5067090392112732 True -12 35477 29.5112202167511 0.5053179264068604 205.94827270507812 0.20954099297523499 225.8242950439453 0.19549813866615295 0.8470355 0.45105552673339844 True -13 38206 29.497348070144653 0.5015020370483398 184.46914672851562 0.5043078660964966 224.74945068359375 0.19660955667495728 0.852579 0.42166149616241455 True -14 40935 29.518718719482422 0.5144624710083008 139.4331512451172 0.21693819761276245 224.43641662597656 0.19633696973323822 0.85929734 0.39455723762512207 True -15 43664 29.50629687309265 0.5141634941101074 180.67935180664062 0.4539342522621155 223.74119567871094 0.19685927033424377 0.86557853 0.3680625557899475 True -16 46393 29.52175235748291 0.5054190158843994 184.7574462890625 0.1486009955406189 223.4739227294922 0.19693593680858612 0.86867434 0.35122454166412354 True -17 49122 29.54484486579895 0.5129952430725098 154.46603393554688 0.2610374391078949 223.297119140625 0.1977114975452423 0.87204695 0.33703237771987915 True -18 51851 29.525683641433716 0.7627193927764893 184.6409454345703 0.29409775137901306 223.07907104492188 0.19816026091575623 0.87201303 0.333700031042099 False -19 54580 29.562549114227295 0.5028502941131592 172.12338256835938 0.19929197430610657 223.0157928466797 0.19847941398620605 0.87214947 0.33317235112190247 True diff --git a/ENCSR531AYV/cherimoya.fold_3.performance.tsv b/ENCSR531AYV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9b4e7d1bc37d2b61a1d6b0bf860daad2687fdd5c..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.0157928466797 0.557019054889679 0.19847941398620605 0.05561579391360283 0.8721494674682617 0.8059119582176208 0.33317235112190247 \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_4.evaluate.json b/ENCSR531AYV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 59a06f78eb20c598c56d5edc5f4fc0fcde463f1a..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF241HZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_4.fit.json b/ENCSR531AYV/cherimoya.fold_4.fit.json deleted file mode 100644 index 0658ab49c4e3d642e515ab9cbc88ea152ee42246..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF241HZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531AYV/cherimoya.fold_4.log b/ENCSR531AYV/cherimoya.fold_4.log deleted file mode 100644 index df45e60a6ac456ce03c8ceffa094fb1f6512fc60..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 35.42778205871582 5.842074155807495 189.82327270507812 0.40253502130508423 219.93902587890625 0.1298660933971405 0.68660593 3.046107292175293 True -1 5612 30.936424255371094 1.5982847213745117 149.6031494140625 0.6010957956314087 202.48765563964844 0.15814943611621857 0.76872635 1.2702507972717285 True -2 8418 30.99661684036255 17.05317711830139 136.99093627929688 0.426615834236145 199.30152893066406 0.16030411422252655 0.8022407 0.6014008522033691 True -3 11224 31.13808798789978 0.6175048351287842 196.03875732421875 0.3611573278903961 198.0697479248047 0.1610061079263687 0.8047222 0.4918581545352936 True -4 14030 31.455368995666504 0.6088504791259766 212.67514038085938 0.39999258518218994 195.78041076660156 0.16360187530517578 0.81748796 0.4395199418067932 True -5 16836 30.96514892578125 0.6080186367034912 209.3323974609375 0.5086751580238342 195.19247436523438 0.16458846628665924 0.8174251 0.42157429456710815 False -6 19642 30.92778182029724 0.606654167175293 142.9105682373047 0.36737847328186035 193.5412139892578 0.1673830896615982 0.8270423 0.40249961614608765 True -7 22448 30.8358371257782 0.6071832180023193 242.5199432373047 0.6264424920082092 192.67166137695312 0.16923195123672485 0.83306336 0.3905722498893738 True -8 25254 30.88885259628296 0.5984063148498535 160.68751525878906 0.3895983099937439 192.1520233154297 0.16981546580791473 0.8371059 0.3676336407661438 True -9 28060 30.917529582977295 0.6079192161560059 162.98300170898438 0.24150806665420532 191.89828491210938 0.16987590491771698 0.84102565 0.35307857394218445 True -10 30866 30.936885118484497 0.6070499420166016 160.43038940429688 0.4433514177799225 191.03509521484375 0.1720786839723587 0.8467382 0.32789722084999084 True -11 33672 31.21323800086975 10.647820949554443 139.36805725097656 0.18737658858299255 191.097900390625 0.17140072584152222 0.8497399 0.32326310873031616 True -12 36478 30.825813055038452 1.2687773704528809 200.4217529296875 0.46581530570983887 190.50338745117188 0.17290635406970978 0.85426193 0.30054971575737 True -13 39284 30.378011226654053 1.5890114307403564 207.48431396484375 0.4107353091239929 189.93118286132812 0.17374496161937714 0.85916233 0.2903294861316681 True -14 42090 30.395423412322998 1.394117832183838 168.76019287109375 0.2565336227416992 189.18527221679688 0.17523790895938873 0.8631161 0.2726418375968933 True -15 44896 30.420989513397217 0.9668562412261963 207.01263427734375 0.29004472494125366 189.00302124023438 0.1750604212284088 0.8676867 0.25992023944854736 True -16 47702 30.393145084381104 0.6142432689666748 159.88552856445312 0.27669429779052734 188.94688415527344 0.17524172365665436 0.8695528 0.2490762621164322 True -17 50508 30.417943716049194 0.6472411155700684 184.23727416992188 0.285607248544693 189.32357788085938 0.17356126010417938 0.8730626 0.2433244287967682 True -18 53314 30.40029287338257 0.6110935211181641 165.589599609375 0.24720360338687897 189.1122283935547 0.1743125170469284 0.87097615 0.24346418678760529 False -19 56120 30.419722318649292 0.6073522567749023 199.30787658691406 0.23730742931365967 189.2398223876953 0.17442259192466736 0.87153864 0.24459528923034668 False diff --git a/ENCSR531AYV/cherimoya.fold_4.performance.tsv b/ENCSR531AYV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index af83f11bcd2611d37e39b80ce47a38eb9a0059ff..0000000000000000000000000000000000000000 --- a/ENCSR531AYV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -189.32357788085938 0.5748679041862488 0.17356126010417938 0.04380228370428085 0.8730626106262207 0.7865329384803772 0.2433244287967682 \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_0.evaluate.json b/ENCSR531HPD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 79cc5d9f2ac0b02263b48bec290ffc88e3cfdd7e..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551PIV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_0.fit.json b/ENCSR531HPD/cherimoya.fold_0.fit.json deleted file mode 100644 index 3aa1fc4261d8b2dcd3368fda1751e0a8a46dc8ef..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF551PIV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_0.log b/ENCSR531HPD/cherimoya.fold_0.log deleted file mode 100644 index 3916f354ba4f60caeca1319bd3bd27cbb9912a51..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2625 34.560840129852295 19.555472373962402 169.37606811523438 0.8127958178520203 258.9583435058594 0.1466013640165329 0.5731335 3.3043360710144043 True -1 5250 28.746918201446533 0.9321095943450928 190.70388793945312 0.5609104633331299 244.18084716796875 0.21500933170318604 0.64566 1.515488624572754 True -2 7875 29.297934532165527 0.5077669620513916 200.14007568359375 0.9248767495155334 240.01039123535156 0.22981256246566772 0.6505109 1.1396540403366089 True -3 10500 29.12963557243347 0.5013484954833984 163.3278350830078 0.5224894881248474 238.5765380859375 0.2342638522386551 0.67106867 0.9764910340309143 True -4 13125 28.695170402526855 0.5151700973510742 154.87176513671875 1.175742268562317 238.1092987060547 0.23715996742248535 0.68588316 0.8175355792045593 True -5 15750 28.669593572616577 0.510474443435669 130.05035400390625 0.4867008924484253 237.66592407226562 0.23895621299743652 0.6889641 0.7875636219978333 True -6 18375 28.855131149291992 0.5043590068817139 207.87887573242188 0.7809527516365051 236.9034881591797 0.24266919493675232 0.6913773 0.7699604034423828 True -7 21000 28.695618391036987 0.5048861503601074 195.93710327148438 0.7266231775283813 236.73719787597656 0.2432081550359726 0.6972532 0.7467569708824158 True -8 23625 29.106761932373047 27.744954586029053 150.82379150390625 0.5648969411849976 236.16334533691406 0.2464810609817505 0.7032158 0.6957418322563171 True -9 26250 28.828152179718018 0.5074074268341064 180.5001678466797 0.6688148975372314 235.56153869628906 0.24810904264450073 0.70976394 0.6356420516967773 True -10 28875 28.65825629234314 0.5176668167114258 200.58154296875 0.5450277924537659 235.2867431640625 0.24950358271598816 0.7125359 0.6090484261512756 True -11 31500 28.653083324432373 0.5345289707183838 223.96453857421875 0.8687624931335449 234.8276824951172 0.2512688934803009 0.7211803 0.5646184682846069 True -12 34125 28.564953565597534 1.8820981979370117 256.08740234375 0.5419062376022339 234.3866424560547 0.2535845637321472 0.72883004 0.5378001928329468 True -13 36750 28.602890491485596 0.5033373832702637 186.81057739257812 0.6051345467567444 234.25665283203125 0.25359731912612915 0.7352922 0.4913472533226013 True -14 39375 28.594791412353516 0.5083372592926025 180.227294921875 0.5003044605255127 234.0532684326172 0.25450581312179565 0.7417702 0.47494691610336304 True -15 42000 28.648110151290894 0.5086514949798584 224.02706909179688 0.44557780027389526 233.56198120117188 0.25695058703422546 0.74908495 0.44663360714912415 True -16 44625 28.84234094619751 39.01489567756653 217.70729064941406 0.39348042011260986 233.7255859375 0.25596708059310913 0.7539492 0.4288273751735687 True -17 47250 28.760188341140747 0.5152842998504639 168.39678955078125 0.32489195466041565 233.7502899169922 0.25608572363853455 0.7559573 0.42207297682762146 True -18 49875 28.674705505371094 0.5084481239318848 197.2430877685547 0.4182182550430298 233.374267578125 0.25838932394981384 0.7544438 0.4280986785888672 False -19 52500 28.63473892211914 0.49639129638671875 213.57492065429688 0.3526010513305664 233.5965118408203 0.2568298578262329 0.75115746 0.43044236302375793 False diff --git a/ENCSR531HPD/cherimoya.fold_0.performance.tsv b/ENCSR531HPD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cbbb9b3396c4cb5bc19b468a1cfa607fe34b9f42..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -233.7502899169922 0.5184352993965149 0.25608569383621216 0.06344234943389893 0.755957305431366 0.7012043595314026 0.42207297682762146 \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_1.evaluate.json b/ENCSR531HPD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 241f3924d61537d1794f7dfc25e508098c03b729..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551PIV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_1.fit.json b/ENCSR531HPD/cherimoya.fold_1.fit.json deleted file mode 100644 index 73eca5cf1c258e7350167e2ade067abf59fa1266..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF551PIV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_1.log b/ENCSR531HPD/cherimoya.fold_1.log deleted file mode 100644 index a5cff24458bcfe0613e85ffa2a8ed1071a9e8dc4..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2628 34.09369397163391 4.182138681411743 185.34414672851562 0.9712283611297607 293.1834411621094 0.15348701179027557 0.5754288 3.916917085647583 True -1 5256 29.25684666633606 0.7181928157806396 177.9344482421875 0.7032127976417542 275.49835205078125 0.22865141928195953 0.6734683 1.5259407758712769 True -2 7884 29.23839235305786 0.6784172058105469 190.8575439453125 0.7704717516899109 270.89129638671875 0.2418162077665329 0.67612165 1.0319287776947021 True -3 10512 28.72009587287903 0.6737244129180908 191.27944946289062 0.507718026638031 268.55029296875 0.2494884729385376 0.69529325 0.8117328882217407 True -4 13140 28.68848443031311 11.450856447219849 171.32388305664062 1.0150856971740723 267.1802673339844 0.2552228271961212 0.71010405 0.6722989082336426 True -5 15768 28.716196060180664 0.6779320240020752 132.95755004882812 0.47113877534866333 266.223388671875 0.2594003677368164 0.7172325 0.6142004728317261 True -6 18396 28.916302919387817 0.6899988651275635 198.66229248046875 0.7870867252349854 265.888427734375 0.26134851574897766 0.7208413 0.6617056727409363 True -7 21024 28.596002340316772 0.6695544719696045 151.8817596435547 0.7024879455566406 265.20556640625 0.263510137796402 0.7312014 0.5867010951042175 True -8 23652 28.65939426422119 0.679612398147583 231.39219665527344 0.7502472400665283 265.109619140625 0.2636030912399292 0.7370599 0.5682103633880615 True -9 26280 28.572795867919922 0.6814441680908203 166.50286865234375 0.5137819647789001 264.3194885253906 0.2666631042957306 0.7428455 0.5211277008056641 True -10 28908 28.622918844223022 0.6716594696044922 210.57650756835938 0.4556887149810791 263.49322509765625 0.27069011330604553 0.74930775 0.5168032050132751 True -11 31536 28.63391637802124 1.4623072147369385 189.68626403808594 0.6324469447135925 263.6680908203125 0.26946189999580383 0.7535679 0.4891035854816437 True -12 34164 28.738683938980103 9.618072032928467 183.66741943359375 0.5017187595367432 262.8465270996094 0.2725563645362854 0.7612545 0.4752075672149658 True -13 36792 29.01487421989441 0.6856734752655029 190.1577606201172 0.5813452005386353 262.5549621582031 0.2732934355735779 0.764954 0.4544367790222168 True -14 39420 29.144405841827393 38.10882878303528 145.0133056640625 0.5093362331390381 262.11907958984375 0.27440282702445984 0.7699309 0.44540882110595703 True -15 42048 28.663408517837524 0.6804895401000977 150.19839477539062 0.5680528879165649 261.84552001953125 0.27597153186798096 0.7748304 0.42909225821495056 True -16 44676 28.62045931816101 0.6648497581481934 171.9319610595703 0.4245690703392029 261.9468994140625 0.27586713433265686 0.7778516 0.4265161156654358 True -17 47304 28.603418827056885 0.6824436187744141 192.1766357421875 0.5693949460983276 261.8877258300781 0.27551090717315674 0.77966654 0.42539724707603455 True -18 49932 28.691795110702515 0.6756525039672852 199.18109130859375 0.4742945432662964 261.8561706542969 0.27642250061035156 0.7800409 0.4298919439315796 True -19 52560 28.60683584213257 0.6729001998901367 198.18463134765625 0.3460026979446411 261.9009704589844 0.27623915672302246 0.7786804 0.4335014820098877 False diff --git a/ENCSR531HPD/cherimoya.fold_1.performance.tsv b/ENCSR531HPD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 02214fcd3ed9555bbf3f792839e957182873f793..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -261.8561706542969 0.5021727681159973 0.2764224410057068 0.07305920869112015 0.7800409197807312 0.7442319393157959 0.4298919439315796 \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_2.evaluate.json b/ENCSR531HPD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 579a06b43a1c0a36e2424d30f87f0ea125173041..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551PIV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_2.fit.json b/ENCSR531HPD/cherimoya.fold_2.fit.json deleted file mode 100644 index 8730381f477e7169fac070c0454b75b8479f7a87..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF551PIV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_2.log b/ENCSR531HPD/cherimoya.fold_2.log deleted file mode 100644 index 9d409fc6df243cf4905022469c8db707ec4076b6..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.20643949508667 3.6546101570129395 156.8596954345703 0.8828041553497314 264.765869140625 0.14912183582782745 0.5672447 3.4601263999938965 True -1 5508 30.663047790527344 0.8507702350616455 175.5708465576172 0.750731348991394 249.0884246826172 0.21847042441368103 0.64666224 1.0270296335220337 True -2 8262 32.71014976501465 28.969565868377686 166.4529266357422 0.8483538627624512 244.91685485839844 0.23226769268512726 0.66531557 0.7156386375427246 True -3 11016 31.382867097854614 0.5151379108428955 209.91116333007812 0.9709469079971313 242.59902954101562 0.2413656860589981 0.68209124 0.6557268500328064 True -4 13770 30.513539791107178 23.57097601890564 186.99923706054688 1.2732746601104736 242.014404296875 0.24394455552101135 0.6896415 0.6202159523963928 True -5 16524 30.420710802078247 0.5417225360870361 147.28173828125 0.9048760533332825 241.28936767578125 0.24664057791233063 0.69953173 0.6269798278808594 True -6 19278 30.112316370010376 0.5114536285400391 160.27334594726562 0.6378939151763916 241.18240356445312 0.2466522455215454 0.7047124 0.6057996153831482 True -7 22032 30.08169460296631 0.504727840423584 182.00994873046875 0.566114604473114 240.5496368408203 0.24966485798358917 0.7090817 0.5791229009628296 True -8 24786 30.051851511001587 0.5023679733276367 187.575927734375 0.5674617290496826 240.09312438964844 0.251992791891098 0.71430624 0.5793658494949341 True -9 27540 30.04210114479065 1.6920835971832275 209.7938995361328 0.47581928968429565 239.2635955810547 0.25613126158714294 0.7167358 0.536038339138031 True -10 30294 30.017030715942383 0.5057122707366943 182.67547607421875 0.8178693056106567 239.0281982421875 0.25677815079689026 0.7239349 0.5287650227546692 True -11 33048 29.983569622039795 0.505413293838501 195.64105224609375 0.5350764393806458 238.6025390625 0.25759971141815186 0.7296523 0.4871482253074646 True -12 35802 29.98676872253418 0.5145769119262695 206.3621368408203 0.5175803899765015 237.84364318847656 0.2613344192504883 0.7323622 0.4715854525566101 True -13 38556 29.986944913864136 0.761681318283081 207.3685302734375 0.441989541053772 237.77392578125 0.26160767674446106 0.7405607 0.44393667578697205 True -14 41310 30.091496467590332 0.5059716701507568 216.90789794921875 0.457075834274292 237.45184326171875 0.262747585773468 0.74617577 0.4389095604419708 True -15 44064 30.030388355255127 0.506939172744751 209.72930908203125 0.3664144277572632 236.87852478027344 0.2655772268772125 0.75176144 0.4254257082939148 True -16 46818 30.031992197036743 0.5080399513244629 185.22801208496094 0.442975789308548 237.14002990722656 0.2636188864707947 0.75490224 0.4217430055141449 True -17 49572 31.08613395690918 30.77992296218872 210.6273193359375 0.5157719850540161 237.2787628173828 0.2625661790370941 0.75599116 0.4213891625404358 True -18 52326 31.96098041534424 0.511737585067749 191.47525024414062 0.36846408247947693 237.1212921142578 0.26366275548934937 0.75431305 0.4264204502105713 False -19 55080 30.070292234420776 0.5049419403076172 170.04566955566406 0.42641156911849976 237.27435302734375 0.26276957988739014 0.75381565 0.43116098642349243 False diff --git a/ENCSR531HPD/cherimoya.fold_2.performance.tsv b/ENCSR531HPD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8c2eb400ba7347a53abe3aa35d0c7aeb6edd7413..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -237.2787628173828 0.5146311521530151 0.2625661790370941 0.06642656773328781 0.7559911608695984 0.7107571959495544 0.4213891625404358 \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_3.evaluate.json b/ENCSR531HPD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e590f5f67a3ede78ce3acc8ca93c9a0b7f4e7e4b..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551PIV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_3.fit.json b/ENCSR531HPD/cherimoya.fold_3.fit.json deleted file mode 100644 index d9a15d48ff37b2a973d89a214f58d9939986a68f..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF551PIV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_3.log b/ENCSR531HPD/cherimoya.fold_3.log deleted file mode 100644 index e24382ffd32c2d5cc4222ee3d6c1b4792b05b20f..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2673 34.75866341590881 15.853053569793701 166.9562530517578 0.8946161270141602 268.57666015625 0.14505326747894287 0.5754917 4.066567420959473 True -1 5346 29.603018283843994 0.8210036754608154 161.95498657226562 0.7860910296440125 253.88046264648438 0.21293987333774567 0.6579268 1.7847342491149902 True -2 8019 29.33297109603882 0.5646681785583496 159.62313842773438 1.046441912651062 250.4896240234375 0.22478532791137695 0.6670333 0.9814251065254211 True -3 10692 29.15781593322754 0.5472557544708252 201.18417358398438 0.5371476411819458 248.3394012451172 0.23324927687644958 0.6913225 0.7711194753646851 True -4 13365 29.22156524658203 0.5479166507720947 161.94155883789062 0.5757623910903931 247.62307739257812 0.23635785281658173 0.69731826 0.7820576429367065 True -5 16038 29.116760969161987 1.5978734493255615 197.23683166503906 0.8060564398765564 246.70562744140625 0.24103733897209167 0.6955756 0.7905082702636719 False -6 18711 29.10535454750061 0.6948723793029785 178.2002410888672 0.6329458951950073 246.25115966796875 0.2423214316368103 0.7045239 0.7474658489227295 True -7 21384 29.178906202316284 0.5497145652770996 179.62249755859375 0.7309987545013428 245.92929077148438 0.24404621124267578 0.70654935 0.7100680470466614 True -8 24057 29.165509700775146 0.5368895530700684 186.2863006591797 0.799366295337677 245.77842712402344 0.24496616423130035 0.7113008 0.668639600276947 True -9 26730 29.159887313842773 0.5895090103149414 217.52853393554688 0.7560752034187317 245.10084533691406 0.24793387949466705 0.71602905 0.6071274876594543 True -10 29403 29.117523431777954 0.5347561836242676 162.17623901367188 0.48415637016296387 244.8173828125 0.24846747517585754 0.7217265 0.5595722794532776 True -11 32076 29.088263273239136 0.5352082252502441 159.14181518554688 0.6406844854354858 244.20730590820312 0.25126683712005615 0.73182845 0.5447397232055664 True -12 34749 29.1530499458313 0.5249435901641846 171.420654296875 0.6011536121368408 244.10646057128906 0.25137123465538025 0.7368117 0.49763473868370056 True -13 37422 29.281538486480713 0.5571305751800537 222.47019958496094 0.4250328540802002 243.82997131347656 0.25274157524108887 0.74321824 0.48379257321357727 True -14 40095 30.31938600540161 34.414533376693726 162.37460327148438 0.4475773572921753 243.03245544433594 0.25643250346183777 0.7505075 0.4609520733356476 True -15 42768 29.564233779907227 22.034175872802734 215.4794921875 0.6322743892669678 243.21224975585938 0.25463855266571045 0.754835 0.45303982496261597 True -16 45441 30.432489156723022 0.5482332706451416 191.9438934326172 0.35932624340057373 243.02496337890625 0.2554788589477539 0.7583138 0.444940447807312 True -17 48114 29.292423963546753 0.5653812885284424 174.4273223876953 0.36280202865600586 243.1375274658203 0.25482502579689026 0.75838107 0.44118350744247437 True -18 50787 29.29838538169861 0.5506207942962646 151.1099395751953 0.3288649618625641 243.13868713378906 0.25487634539604187 0.75588274 0.4472241997718811 False -19 53460 29.271644592285156 0.5629920959472656 164.48526000976562 0.26407429575920105 243.1704559326172 0.25519099831581116 0.7565742 0.4521586000919342 False diff --git a/ENCSR531HPD/cherimoya.fold_3.performance.tsv b/ENCSR531HPD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ece4be1a1a9e59bb89b70c7e5440f50196ab0079..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -243.1375274658203 0.5164470076560974 0.25482505559921265 0.06422150135040283 0.7583810687065125 0.7138099670410156 0.44118350744247437 \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_4.evaluate.json b/ENCSR531HPD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 506ae3d653901f98a9221bb48c7ba2720058e7eb..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551PIV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_4.fit.json b/ENCSR531HPD/cherimoya.fold_4.fit.json deleted file mode 100644 index bca4d8d367576524b1e1a5f7ae889ee23e2568c8..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF551PIV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_4.log b/ENCSR531HPD/cherimoya.fold_4.log deleted file mode 100644 index 7fa6ca24142a6926109e231440e1dcc02984c5b3..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 34.59952640533447 3.5496878623962402 163.7112579345703 0.9512638449668884 252.96157836914062 0.14540943503379822 0.5651058 2.999044895172119 True -1 5486 30.563446521759033 1.081989049911499 177.4964599609375 0.8276826739311218 239.92355346679688 0.207870215177536 0.6533909 1.2613481283187866 True -2 8229 30.52499032020569 0.8944830894470215 187.12396240234375 0.9096767902374268 235.59466552734375 0.22620634734630585 0.66339296 0.6399416327476501 True -3 10972 30.56119418144226 0.5270752906799316 220.7234344482422 1.3932284116744995 234.11392211914062 0.23014427721500397 0.6764441 0.6395958662033081 True -4 13715 31.098575115203857 0.5299651622772217 181.38558959960938 0.6711726188659668 233.24607849121094 0.23448914289474487 0.6828313 0.6293184161186218 True -5 16458 30.50901484489441 0.5257220268249512 164.14431762695312 0.8788723945617676 233.09341430664062 0.23485641181468964 0.6883417 0.6495944261550903 True -6 19201 30.502129554748535 0.5317671298980713 182.3126220703125 0.7394883632659912 232.21495056152344 0.23885923624038696 0.69049805 0.6053247451782227 True -7 21944 30.789679765701294 0.5265500545501709 225.14569091796875 0.4797365665435791 232.20339965820312 0.2381264716386795 0.69463575 0.5783756971359253 True -8 24687 30.558215856552124 30.650010347366333 176.37496948242188 0.6296310424804688 231.39761352539062 0.24254865944385529 0.70101875 0.570362389087677 True -9 27430 33.677168130874634 0.5807654857635498 228.465087890625 0.628433883190155 231.03713989257812 0.24435840547084808 0.70456374 0.5510858297348022 True -10 30173 29.911656618118286 0.5245752334594727 188.27609252929688 0.6171810626983643 230.90318298339844 0.24473659694194794 0.7124677 0.5156976580619812 True -11 32916 29.976733207702637 0.5316262245178223 149.44725036621094 0.3523232340812683 230.5139923095703 0.24632589519023895 0.71807814 0.4930874705314636 True -12 35659 29.96547794342041 0.5215516090393066 164.6483612060547 0.5002894401550293 230.08236694335938 0.24771828949451447 0.7267218 0.4701123833656311 True -13 38402 29.90103030204773 0.520927906036377 207.28591918945312 0.4266227185726166 229.71926879882812 0.24907100200653076 0.7323492 0.4487185478210449 True -14 41145 29.914810180664062 0.5222001075744629 179.00538635253906 0.693747878074646 229.4534149169922 0.2509925365447998 0.7379989 0.44114378094673157 True -15 43888 29.892983198165894 0.5177829265594482 172.64878845214844 0.4449523389339447 229.1542205810547 0.25237953662872314 0.7435391 0.43700700998306274 True -16 46631 29.94146490097046 0.5185427665710449 199.939453125 0.36058205366134644 228.96421813964844 0.2527044713497162 0.74859464 0.42411670088768005 True -17 49374 29.887670755386353 1.25632905960083 172.39871215820312 0.42051732540130615 229.1538543701172 0.2521646320819855 0.7509879 0.41876888275146484 True -18 52117 29.953002214431763 0.5234503746032715 153.07199096679688 0.5078379511833191 229.26551818847656 0.2515887916088104 0.7508149 0.4199123680591583 False -19 54860 29.862521409988403 0.9099996089935303 144.9796905517578 0.3342633843421936 229.29119873046875 0.25140613317489624 0.75024754 0.4232146143913269 False diff --git a/ENCSR531HPD/cherimoya.fold_4.performance.tsv b/ENCSR531HPD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f616ac265971e4a8f6ae0b9e52fa534d39e4131c..0000000000000000000000000000000000000000 --- a/ENCSR531HPD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -229.1538543701172 0.5215293169021606 0.2521646320819855 0.060329001396894455 0.7509878873825073 0.6989354491233826 0.41876888275146484 \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_0.evaluate.json b/ENCSR531UVE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 28534a391579c5d1c8eb0bf0f5bc516732eb1143..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF240OZT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_0.fit.json b/ENCSR531UVE/cherimoya.fold_0.fit.json deleted file mode 100644 index e4a4e5d688ff7bc115226f853db8c522d740a9e5..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF240OZT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_0.log b/ENCSR531UVE/cherimoya.fold_0.log deleted file mode 100644 index 97a1e5c8df9130f7c3bf008828b3f7f275aa07be..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 35.122586727142334 3.9187793731689453 311.6910400390625 0.344646692276001 385.87042236328125 0.1448649764060974 0.753564 3.5023679733276367 True -1 5470 30.35248064994812 0.5861201286315918 322.1400451660156 0.48376888036727905 365.07550048828125 0.1721348762512207 0.80871475 1.1196097135543823 True -2 8205 30.311251163482666 0.5587449073791504 256.24420166015625 0.23166990280151367 360.7004699707031 0.17618225514888763 0.8121418 0.9430346488952637 True -3 10940 30.31806492805481 0.5495824813842773 315.58837890625 0.38751220703125 357.9563903808594 0.17879486083984375 0.80778146 0.5704268217086792 False -4 13675 30.298306465148926 0.5581972599029541 381.294677734375 0.31165507435798645 355.8136901855469 0.18068882822990417 0.82221884 0.4764712154865265 True -5 16410 30.066186904907227 0.5536720752716064 323.2724304199219 0.36105072498321533 354.0496826171875 0.183031365275383 0.83046526 0.43621984124183655 True -6 19145 29.67007541656494 0.5471255779266357 257.8870849609375 0.29068470001220703 353.05828857421875 0.18508243560791016 0.8335351 0.4016522467136383 True -7 21880 29.714508295059204 0.5798654556274414 296.0721740722656 0.35496801137924194 351.5404052734375 0.18763142824172974 0.8419123 0.3636248707771301 True -8 24615 29.68776512145996 0.5551338195800781 335.5370178222656 0.43520358204841614 351.14794921875 0.1874994933605194 0.8459219 0.3355535864830017 True -9 27350 29.684086561203003 0.5523819923400879 361.09423828125 0.28139781951904297 349.8141784667969 0.18986161053180695 0.8517606 0.30551037192344666 True -10 30085 29.81684708595276 0.6156187057495117 279.111328125 0.25043976306915283 349.3066101074219 0.1904619038105011 0.85798943 0.283599853515625 True -11 32820 29.762035131454468 0.5551190376281738 348.07659912109375 0.23912519216537476 348.34576416015625 0.19269292056560516 0.8598482 0.27001500129699707 True -12 35555 29.762722730636597 0.6524455547332764 279.2411193847656 0.25045451521873474 348.13189697265625 0.19201232492923737 0.8696948 0.24093890190124512 True -13 38290 29.82399082183838 0.561164379119873 251.6973876953125 0.14986486732959747 347.3213806152344 0.19338098168373108 0.8753373 0.22428466379642487 True -14 41025 29.812657117843628 0.5586991310119629 256.9332580566406 0.18935921788215637 346.33074951171875 0.1947098821401596 0.8806513 0.21250887215137482 True -15 43760 29.78648090362549 0.5534119606018066 316.5307922363281 0.12959076464176178 346.4274597167969 0.1943720281124115 0.8850254 0.20726482570171356 True -16 46495 29.715905904769897 0.5560667514801025 278.9757385253906 0.16221965849399567 346.1702575683594 0.194022998213768 0.8860273 0.20233891904354095 True -17 49230 29.77906847000122 1.3910701274871826 347.8442077636719 0.2003939002752304 345.4120788574219 0.19633813202381134 0.8860524 0.20062939822673798 True -18 51965 29.84608292579651 0.5787234306335449 269.11016845703125 0.2577391564846039 346.1646728515625 0.19535860419273376 0.88674366 0.2007663995027542 True -19 54700 29.810811042785645 0.5659663677215576 261.3143615722656 0.20095866918563843 346.1517639160156 0.19457830488681793 0.8842061 0.20300690829753876 False diff --git a/ENCSR531UVE/cherimoya.fold_0.performance.tsv b/ENCSR531UVE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 90ca30d82e1dc3cd2150c8e1dbde00ff3d2a2e9c..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -346.1646728515625 0.5354099869728088 0.19535858929157257 0.06139736995100975 0.8867436647415161 0.8256754279136658 0.2007663995027542 \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_1.evaluate.json b/ENCSR531UVE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 65b402e66d2fbaf93a7dc16d13bc698f2eeed6f8..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF240OZT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_1.fit.json b/ENCSR531UVE/cherimoya.fold_1.fit.json deleted file mode 100644 index 54743bf788e657dbe0be34d11d90a313a6f43649..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF240OZT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_1.log b/ENCSR531UVE/cherimoya.fold_1.log deleted file mode 100644 index 7f95ec806881deb5428a78c3f3983a5bd4fe9996..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 35.22947812080383 5.39579963684082 256.8387145996094 0.20363280177116394 476.8255920410156 0.158113494515419 0.7247813 4.44895076751709 True -1 5462 30.321585178375244 1.6490812301635742 361.16937255859375 0.5300732851028442 444.6584777832031 0.19596068561077118 0.8002146 1.5656368732452393 True -2 8193 30.24805498123169 1.4417216777801514 316.29595947265625 0.19991227984428406 445.1537170410156 0.19412046670913696 0.7743569 1.249705195426941 False -3 10924 30.263811588287354 6.524834871292114 245.43740844726562 0.33580482006073 434.2943420410156 0.2036324143409729 0.80476296 0.8576895594596863 True -4 13655 30.200143098831177 1.0851504802703857 305.2985534667969 0.5082496404647827 429.6488342285156 0.20929020643234253 0.8308934 0.6321602463722229 True -5 16386 30.199915885925293 0.7122642993927002 322.67608642578125 0.354608952999115 428.76171875 0.21012936532497406 0.8376686 0.5826829671859741 True -6 19117 30.19062876701355 0.691171407699585 295.8245849609375 0.2706090807914734 427.517333984375 0.21141280233860016 0.83643 0.5906408429145813 False -7 21848 30.245959043502808 0.6928389072418213 338.8674011230469 0.4636637270450592 424.9107360839844 0.21443650126457214 0.8443176 0.5140684247016907 True -8 24579 30.33292841911316 0.6775035858154297 235.1506805419922 0.20288947224617004 422.8736267089844 0.21643708646297455 0.850415 0.4670584201812744 True -9 27310 30.195066928863525 1.4238488674163818 297.13800048828125 0.30420947074890137 421.90838623046875 0.21854831278324127 0.85313964 0.45167651772499084 True -10 30041 30.27654790878296 0.6731932163238525 318.813232421875 0.23676806688308716 420.8119201660156 0.2189355343580246 0.8596611 0.4397381544113159 True -11 32772 30.311237335205078 0.6910438537597656 327.8025817871094 0.23888099193572998 418.9101867675781 0.2221023142337799 0.86800814 0.377378910779953 True -12 35503 30.268134593963623 0.6834852695465088 240.9608612060547 0.28474628925323486 418.88201904296875 0.22143220901489258 0.8727074 0.3519388735294342 True -13 38234 30.222656726837158 0.6753690242767334 328.4259338378906 0.2503509521484375 417.44342041015625 0.22325490415096283 0.8818478 0.3195500075817108 True -14 40965 30.30127191543579 25.325313806533813 264.4687805175781 0.1664448380470276 416.0023193359375 0.22490543127059937 0.8859491 0.293334424495697 True -15 43696 30.36872434616089 0.676896333694458 291.992431640625 0.2820722460746765 415.7950134277344 0.22503529489040375 0.8897917 0.2788350582122803 True -16 46427 30.34925413131714 0.7076766490936279 255.466796875 0.3032856583595276 414.7941589355469 0.2260747253894806 0.8937992 0.25978079438209534 True -17 49158 30.29822039604187 0.6790344715118408 251.47711181640625 0.19218948483467102 415.23614501953125 0.22511233389377594 0.897148 0.2522246539592743 True -18 51889 30.238222360610962 0.6693100929260254 349.5050048828125 0.21724064648151398 415.16827392578125 0.2248474657535553 0.89338315 0.2538039982318878 False -19 54620 30.289827585220337 0.6652920246124268 366.53863525390625 0.14240464568138123 415.6308898925781 0.22398057579994202 0.89419967 0.255733847618103 False diff --git a/ENCSR531UVE/cherimoya.fold_1.performance.tsv b/ENCSR531UVE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9a7e31726dbd2fbb7e98ff1207f3571dc4e99add..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -415.23614501953125 0.5102502703666687 0.22511231899261475 0.0766431987285614 0.8971480131149292 0.863277018070221 0.2522246539592743 \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_2.evaluate.json b/ENCSR531UVE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9e7790369b4e10228f241ce297f8c9fa124da842..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF240OZT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_2.fit.json b/ENCSR531UVE/cherimoya.fold_2.fit.json deleted file mode 100644 index 02e6d98900bdb67dee9004f8efda843be216f81e..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF240OZT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_2.log b/ENCSR531UVE/cherimoya.fold_2.log deleted file mode 100644 index 3aac4b2ac17d5f0407a38a1cc88d93796406a1b5..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2866 36.35463547706604 3.753096342086792 347.8899230957031 0.38315290212631226 410.2716369628906 0.1484881192445755 0.7301435 3.174135446548462 True -1 5732 31.768813610076904 0.7060544490814209 291.8123779296875 0.3325820565223694 386.8511962890625 0.1788928359746933 0.7927767 1.0538185834884644 True -2 8598 31.20508623123169 0.5676608085632324 263.512939453125 0.30441269278526306 379.5702819824219 0.18454308807849884 0.8113994 0.8753510117530823 True -3 11464 31.064748287200928 0.5363748073577881 327.3501892089844 0.5972440242767334 378.62060546875 0.18463827669620514 0.81246334 0.6494333744049072 True -4 14330 31.102559804916382 0.8695423603057861 323.72979736328125 0.26653361320495605 375.8089294433594 0.18864324688911438 0.8240874 0.5198360681533813 True -5 17196 31.14647078514099 1.0347037315368652 301.83251953125 0.2300182282924652 373.4884948730469 0.1914891004562378 0.83146447 0.43091753125190735 True -6 20062 31.184361219406128 0.5452783107757568 269.9569091796875 0.3441436290740967 371.4861145019531 0.1940077394247055 0.8385131 0.39895471930503845 True -7 22928 31.109007835388184 0.5314083099365234 311.6373291015625 0.27793288230895996 371.70758056640625 0.1933673471212387 0.8440731 0.35717132687568665 True -8 25794 31.120413064956665 0.5315139293670654 319.35015869140625 0.3016093969345093 370.11212158203125 0.1962146908044815 0.8478533 0.31689682602882385 True -9 28660 31.063233375549316 0.5449957847595215 277.8990173339844 0.249466210603714 369.2518310546875 0.19656836986541748 0.8554672 0.29859161376953125 True -10 31526 31.087316274642944 0.5448284149169922 299.75146484375 0.29264530539512634 367.20574951171875 0.20030830800533295 0.85908926 0.27945011854171753 True -11 34392 31.09931230545044 0.543724536895752 275.9916687011719 0.265472948551178 366.71514892578125 0.20072834193706512 0.86285365 0.26232555508613586 True -12 37258 31.14185667037964 0.5598218441009521 251.638427734375 0.257268488407135 366.38201904296875 0.201184943318367 0.8679917 0.25345298647880554 True -13 40124 31.156675338745117 2.4676008224487305 315.0807189941406 0.33903229236602783 365.9237976074219 0.20151205360889435 0.8744236 0.23972126841545105 True -14 42990 31.271907806396484 0.5775754451751709 278.6878967285156 0.3054976463317871 365.02410888671875 0.20309482514858246 0.8771839 0.23021447658538818 True -15 45856 32.34159207344055 0.5616440773010254 345.56719970703125 0.19589337706565857 364.4888916015625 0.20334786176681519 0.8793725 0.22456414997577667 True -16 48722 31.352393865585327 0.5653655529022217 258.5565490722656 0.15079852938652039 364.41546630859375 0.2037104368209839 0.8820176 0.21975861489772797 True -17 51588 31.411607265472412 2.135118246078491 297.01220703125 0.14335128664970398 364.6909484863281 0.20344823598861694 0.8830563 0.21810202300548553 True -18 54454 31.356637239456177 2.8213977813720703 291.46417236328125 0.23254311084747314 364.2469177246094 0.20410007238388062 0.8812019 0.21889661252498627 False -19 57320 31.34533166885376 0.6629722118377686 280.0752258300781 0.14688308537006378 364.8944091796875 0.2018418163061142 0.8799813 0.22056424617767334 False diff --git a/ENCSR531UVE/cherimoya.fold_2.performance.tsv b/ENCSR531UVE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ef0f78c93a59fc035a974cb92a2f7ef781a62d44..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -364.6909484863281 0.5279581546783447 0.20344823598861694 0.06642317771911621 0.8830562829971313 0.8341880440711975 0.21810202300548553 \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_3.evaluate.json b/ENCSR531UVE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 882c3580167f6ef7b75752c11048b27aeea365b1..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF240OZT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_3.fit.json b/ENCSR531UVE/cherimoya.fold_3.fit.json deleted file mode 100644 index 4fe63aa151d43928db157256a2ae4a43d3c620af..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF240OZT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_3.log b/ENCSR531UVE/cherimoya.fold_3.log deleted file mode 100644 index a67db279e2088cf7914c34963fbff0c3499a29b0..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2723 35.056918144226074 3.8537347316741943 248.370361328125 0.43999946117401123 394.4321594238281 0.15286029875278473 0.7014264 4.046258449554443 True -1 5446 30.24739170074463 0.6233718395233154 269.150634765625 0.2871410846710205 372.9365539550781 0.18061260879039764 0.75781614 1.356576681137085 True -2 8169 30.030986309051514 0.585247278213501 308.3763732910156 0.30962681770324707 370.47662353515625 0.18452098965644836 0.78401357 1.2065706253051758 True -3 10892 29.60396409034729 0.5576345920562744 313.6204833984375 0.5646669864654541 365.7562255859375 0.18881957232952118 0.7712399 0.8100480437278748 False -4 13615 29.604515552520752 0.5539214611053467 293.5895080566406 0.2541353106498718 364.3901062011719 0.18938252329826355 0.79200274 0.6101831197738647 True -5 16338 29.59137773513794 0.5551958084106445 303.7119140625 0.2337471842765808 363.03619384765625 0.1912233531475067 0.7973678 0.5409837961196899 True -6 19061 29.56965732574463 0.5831584930419922 361.1824645996094 0.3237640857696533 361.3064880371094 0.1934480518102646 0.80723464 0.4991582930088043 True -7 21784 29.530633449554443 0.5560615062713623 332.89691162109375 0.32647550106048584 360.2111511230469 0.1950272172689438 0.81212974 0.46591320633888245 True -8 24507 29.56715440750122 0.5863208770751953 333.613037109375 0.30580559372901917 358.8473815917969 0.19715651869773865 0.8249383 0.4263584613800049 True -9 27230 29.556784629821777 0.5637483596801758 310.60638427734375 0.26507607102394104 357.4041442871094 0.19929012656211853 0.8305065 0.39231428503990173 True -10 29953 29.514373064041138 0.5702710151672363 360.92974853515625 0.322634756565094 357.328125 0.19974248111248016 0.83637303 0.3554069995880127 True -11 32676 29.532952308654785 0.5872557163238525 296.437744140625 0.3617936074733734 357.0064392089844 0.20024974644184113 0.84399265 0.3390539288520813 True -12 35399 29.62294340133667 0.5473027229309082 260.3912048339844 0.3170076608657837 356.2933044433594 0.20099011063575745 0.8499555 0.31859827041625977 True -13 38122 29.610047817230225 0.5588443279266357 268.1817321777344 0.3655228018760681 355.4572448730469 0.20197975635528564 0.85599893 0.2992008626461029 True -14 40845 29.51044464111328 0.5581703186035156 252.3966064453125 0.25730156898498535 354.1832580566406 0.20383715629577637 0.8621322 0.2822628915309906 True -15 43568 29.5293710231781 0.5536584854125977 293.3236999511719 0.35114550590515137 353.601318359375 0.20470283925533295 0.86740386 0.2670207917690277 True -16 46291 29.63627290725708 0.5599977970123291 296.07794189453125 0.1872251033782959 353.60540771484375 0.2038850337266922 0.8710778 0.25168222188949585 True -17 49014 29.689868211746216 0.566472053527832 283.0412902832031 0.15019908547401428 353.5054626464844 0.2042277604341507 0.8747623 0.24465137720108032 True -18 51737 31.62296199798584 2.7305400371551514 231.99244689941406 0.13006380200386047 353.53729248046875 0.20455074310302734 0.8744669 0.2424076944589615 False -19 54460 29.94309163093567 0.5542824268341064 259.7159423828125 0.14770101010799408 353.823486328125 0.20363430678844452 0.8736638 0.24271491169929504 False diff --git a/ENCSR531UVE/cherimoya.fold_3.performance.tsv b/ENCSR531UVE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index dc92d64994da67dc7ecfc143e28a959f4cb585a3..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -353.5054626464844 0.529239296913147 0.2042277753353119 0.06170567125082016 0.8747622966766357 0.8190514445304871 0.24465137720108032 \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_4.evaluate.json b/ENCSR531UVE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a2ec15a6b4f7c70fea430aaa83b2ffc2f3632198..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF240OZT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_4.fit.json b/ENCSR531UVE/cherimoya.fold_4.fit.json deleted file mode 100644 index 2be11e8c56339add661aeba971bfbf09fbe70635..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF240OZT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR531UVE/cherimoya.fold_4.log b/ENCSR531UVE/cherimoya.fold_4.log deleted file mode 100644 index 3c5dc5f38a1e98bb3265b70a3a7a8ab7a03c0461..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2820 36.11890435218811 4.131143569946289 284.496826171875 0.5540528297424316 335.406005859375 0.1398901343345642 0.73129696 3.3273885250091553 True -1 5640 31.32885193824768 1.8678243160247803 287.84124755859375 0.28683894872665405 320.5038757324219 0.1632571816444397 0.786874 1.0061743259429932 True -2 8460 31.332230806350708 0.7543492317199707 293.6742858886719 0.514815092086792 317.7484436035156 0.16654261946678162 0.78253895 0.7036628723144531 False -3 11280 31.318109273910522 0.6603100299835205 319.9246826171875 0.3543858230113983 316.73309326171875 0.1672704964876175 0.78210557 0.4747426509857178 False -4 14100 31.260340213775635 0.7071094512939453 280.7119445800781 0.19750618934631348 315.23577880859375 0.16943024098873138 0.79516035 0.45006415247917175 True -5 16920 31.315743923187256 0.6779694557189941 302.32342529296875 0.31598585844039917 314.2386169433594 0.17076678574085236 0.7987213 0.3991219401359558 True -6 19740 31.231379508972168 0.6627964973449707 255.84317016601562 0.340900719165802 313.447265625 0.17187261581420898 0.81064934 0.3850274085998535 True -7 22560 31.218108654022217 1.0978517532348633 271.0081787109375 0.1708747148513794 312.47808837890625 0.17229063808918 0.8204124 0.3263933062553406 True -8 25380 31.47939968109131 0.6738286018371582 251.9982147216797 0.26918932795524597 311.8365173339844 0.17364223301410675 0.82460594 0.30142271518707275 True -9 28200 30.962185382843018 0.7234575748443604 375.7828063964844 0.322742760181427 311.4936828613281 0.17405714094638824 0.82769686 0.2837626338005066 True -10 31020 30.89485239982605 1.4053676128387451 274.3304748535156 0.30541396141052246 310.2988586425781 0.1766025424003601 0.83647484 0.26308557391166687 True -11 33840 30.93898916244507 5.742107152938843 305.1172790527344 0.2337431013584137 310.22216796875 0.1758391261100769 0.8441443 0.23578716814517975 True -12 36660 31.03985095024109 1.1002469062805176 336.550537109375 0.37052327394485474 309.61712646484375 0.17760509252548218 0.8512697 0.22140859067440033 True -13 39480 30.95290446281433 1.1347784996032715 341.40789794921875 0.19373179972171783 309.17559814453125 0.17824344336986542 0.8595942 0.2076636403799057 True -14 42300 31.024641036987305 0.7633645534515381 324.44781494140625 0.22802132368087769 308.1452941894531 0.17990544438362122 0.86367095 0.19881097972393036 True -15 45120 30.843817472457886 0.6838569641113281 308.37249755859375 0.2515590190887451 308.075927734375 0.17961034178733826 0.86865634 0.1908765584230423 True -16 47940 30.86387586593628 0.6707186698913574 296.14263916015625 0.21246375143527985 307.8395690917969 0.1798979640007019 0.8698348 0.18562529981136322 True -17 50760 30.814634799957275 0.7048366069793701 319.71917724609375 0.15024328231811523 307.81298828125 0.17971910536289215 0.87214637 0.18266147375106812 True -18 53580 30.88170552253723 0.6534647941589355 273.5455322265625 0.19425660371780396 308.1911315917969 0.1791447252035141 0.8713132 0.1830577552318573 False -19 56400 31.076713800430298 0.6604807376861572 286.2735290527344 0.21041271090507507 308.50146484375 0.1789107620716095 0.870058 0.18384301662445068 False diff --git a/ENCSR531UVE/cherimoya.fold_4.performance.tsv b/ENCSR531UVE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f11da22f22a55436116a0729aea88475f8808927..0000000000000000000000000000000000000000 --- a/ENCSR531UVE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -307.81298828125 0.5483525991439819 0.17971909046173096 0.0537780299782753 0.8721463680267334 0.8066622018814087 0.18266147375106812 \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_0.evaluate.json b/ENCSR532DBH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2da64a6d794da0ffe22390b2b991dc227875412a..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF158EVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_0.fit.json b/ENCSR532DBH/cherimoya.fold_0.fit.json deleted file mode 100644 index 1e49f1607813c7f70810de6364c1850016436e21..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF158EVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_0.log b/ENCSR532DBH/cherimoya.fold_0.log deleted file mode 100644 index 6637b922051eb2ebeb7f2822b90480ba2b887cb6..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.21042847633362 3.5235514640808105 428.43841552734375 0.41506192088127136 569.0758666992188 0.27011537551879883 0.6909876 4.867426872253418 True -1 5488 30.37489891052246 0.6019928455352783 382.5090026855469 0.49288952350616455 508.6158447265625 0.34157195687294006 0.76125944 1.3969491720199585 True -2 8232 30.43453574180603 0.5814015865325928 454.2693786621094 0.4560318887233734 500.7260437011719 0.34674394130706787 0.7821983 0.6710036396980286 True -3 10976 30.41519594192505 0.5893909931182861 459.06890869140625 0.23925766348838806 495.730712890625 0.3534281551837921 0.78830934 0.7213525176048279 True -4 13720 30.43819832801819 0.581392765045166 394.43731689453125 0.304640531539917 493.1949462890625 0.3553958535194397 0.79781234 0.5149281024932861 True -5 16464 30.396547317504883 0.5811336040496826 488.3233337402344 0.3854135572910309 489.6175231933594 0.359782338142395 0.8062103 0.4857015311717987 True -6 19208 30.371617317199707 28.841466426849365 413.8619384765625 0.24415898323059082 488.6942443847656 0.36086323857307434 0.8127536 0.4632188677787781 True -7 21952 30.502588987350464 0.5910820960998535 430.88018798828125 0.23988419771194458 487.30242919921875 0.3616050183773041 0.8174615 0.4305967390537262 True -8 24696 30.400946140289307 0.5940451622009277 366.5628967285156 0.19997401535511017 485.4417419433594 0.3640919625759125 0.8203248 0.3917829394340515 True -9 27440 30.42138910293579 0.5872094631195068 355.97552490234375 0.36559662222862244 483.0762634277344 0.3680941164493561 0.8251129 0.3920040428638458 True -10 30184 30.404667615890503 0.5933921337127686 440.0045471191406 0.4971790015697479 482.62200927734375 0.3681063652038574 0.82725334 0.370328813791275 True -11 32928 30.39673686027527 1.57371187210083 456.66546630859375 0.3302108943462372 482.03741455078125 0.3684113025665283 0.83457714 0.3310627341270447 True -12 35672 30.424680471420288 0.5920994281768799 481.18389892578125 0.3330309987068176 480.37109375 0.3705877661705017 0.83509386 0.3187333047389984 True -13 38416 30.399120569229126 0.8837888240814209 471.04052734375 0.31539851427078247 478.94146728515625 0.3732635974884033 0.84136415 0.29784974455833435 True -14 41160 30.488865852355957 0.5897274017333984 430.2377624511719 0.26576584577560425 477.6923522949219 0.3743033707141876 0.84612864 0.27641865611076355 True -15 43904 30.44102382659912 0.583179235458374 380.05157470703125 0.3521959185600281 477.2753601074219 0.37413081526756287 0.85021186 0.2595018148422241 True -16 46648 30.47652792930603 0.5829455852508545 434.61029052734375 0.3568183183670044 475.19598388671875 0.37835416197776794 0.85147065 0.2481236457824707 True -17 49392 30.463054656982422 0.6012101173400879 501.322265625 0.360276997089386 476.3606262207031 0.3750709891319275 0.8544318 0.24243853986263275 True -18 52136 30.39785933494568 0.6104884147644043 333.9447021484375 0.2393442541360855 476.6080017089844 0.37477734684944153 0.8525291 0.2413412481546402 False -19 54880 30.39314603805542 21.70069718360901 462.4916076660156 0.1776168942451477 477.0224609375 0.37372684478759766 0.8524582 0.24169489741325378 False diff --git a/ENCSR532DBH/cherimoya.fold_0.performance.tsv b/ENCSR532DBH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f2c0258348693bd89a6bb936905ffce5771600cf..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -476.3606262207031 0.41734135150909424 0.3750710189342499 0.13004811108112335 0.8544318079948425 0.8356993198394775 0.24243853986263275 \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_1.evaluate.json b/ENCSR532DBH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1c3357ddb6067404305d93c6a55c7ef8842d6c2e..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF158EVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_1.fit.json b/ENCSR532DBH/cherimoya.fold_1.fit.json deleted file mode 100644 index 91a0db9fa6ffa572a823ffca80fa0da08c974df2..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF158EVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_1.log b/ENCSR532DBH/cherimoya.fold_1.log deleted file mode 100644 index de3c46507a1173fa4c91c85660bfc7a46a4070e4..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 33.736934661865234 3.862126111984253 503.27056884765625 0.38146746158599854 685.4658203125 0.2738548517227173 0.70204604 5.596576690673828 True -1 5424 29.751418113708496 12.740041971206665 432.50946044921875 0.38753741979599 607.1673583984375 0.3545588552951813 0.7716495 1.5665823221206665 True -2 8136 29.789404153823853 0.667961835861206 414.1566467285156 0.5022275447845459 592.5319213867188 0.3661956489086151 0.7883111 0.9047130346298218 True -3 10848 29.77204990386963 0.6621038913726807 477.9526672363281 0.2962017357349396 586.0204467773438 0.37214887142181396 0.7991871 0.5992130637168884 True -4 13560 29.789252996444702 0.6633524894714355 464.5751953125 0.30601590871810913 586.7555541992188 0.373370885848999 0.7945702 0.6051073670387268 False -5 16272 29.82034683227539 0.6556172370910645 439.0018310546875 0.4333116114139557 579.56591796875 0.3788090944290161 0.8105709 0.48866960406303406 True -6 18984 29.7853000164032 0.6625399589538574 408.1739807128906 0.2517353892326355 577.1112060546875 0.38060352206230164 0.8158581 0.43530434370040894 True -7 21696 29.765704870224 0.6627888679504395 395.5205078125 0.35843920707702637 573.5523071289062 0.38338765501976013 0.82414985 0.39633017778396606 True -8 24408 29.753408908843994 0.65614914894104 486.1712646484375 0.3125154972076416 571.8165893554688 0.3851189911365509 0.8278302 0.3826855421066284 True -9 27120 29.778997659683228 0.654759407043457 363.7669677734375 0.3081364035606384 569.788330078125 0.3868950307369232 0.8331447 0.3933132290840149 True -10 29832 29.75977659225464 0.6637270450592041 457.022216796875 0.2628255784511566 567.4761962890625 0.38905325531959534 0.83892787 0.37629929184913635 True -11 32544 29.760262489318848 0.6624631881713867 448.4439697265625 0.2892419397830963 564.8869018554688 0.392596572637558 0.8438461 0.34758931398391724 True -12 35256 29.747907638549805 0.9723482131958008 434.86614990234375 0.23017367720603943 563.6641845703125 0.39306989312171936 0.84773105 0.331659197807312 True -13 37968 29.868568420410156 0.6735920906066895 419.0645446777344 0.3165857195854187 561.8070678710938 0.3949049711227417 0.85137683 0.30733782052993774 True -14 40680 29.86361598968506 0.6700139045715332 492.5885009765625 0.20160186290740967 559.4386596679688 0.3972328007221222 0.8577048 0.29305794835090637 True -15 43392 29.765192985534668 0.6588606834411621 394.1578369140625 0.19543994963169098 558.2788696289062 0.39799395203590393 0.86133343 0.28430238366127014 True -16 46104 29.78739595413208 0.6596448421478271 403.9828796386719 0.4752289056777954 558.5184936523438 0.39814701676368713 0.86582184 0.27214401960372925 True -17 48816 29.806917428970337 0.6717283725738525 422.7511291503906 0.26544511318206787 557.938232421875 0.39857789874076843 0.86755747 0.26664498448371887 True -18 51528 29.746397972106934 0.6699810028076172 445.6499328613281 0.1999652087688446 559.2533569335938 0.3963271677494049 0.8663571 0.26452285051345825 False -19 54240 29.760590076446533 0.6572179794311523 387.2603454589844 0.24449706077575684 558.615966796875 0.39767542481422424 0.86559826 0.2673676311969757 False diff --git a/ENCSR532DBH/cherimoya.fold_1.performance.tsv b/ENCSR532DBH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2682bebbbb0c555d1327e97b5083b7c541aa06ec..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -557.938232421875 0.39704179763793945 0.39857786893844604 0.15568211674690247 0.8675574660301208 0.8607326149940491 0.26664498448371887 \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_2.evaluate.json b/ENCSR532DBH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5982eb2a1184079da27956edc50e6b6aa4601b83..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF158EVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_2.fit.json b/ENCSR532DBH/cherimoya.fold_2.fit.json deleted file mode 100644 index 1303ce7285e83669bbd594d5cc192058ccd8f4eb..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF158EVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_2.log b/ENCSR532DBH/cherimoya.fold_2.log deleted file mode 100644 index 910829a0509551447739cb5f3d4b5872e8e4fe87..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 93.84762024879456 3.508143424987793 515.6705322265625 0.4288380742073059 607.2492065429688 0.27275967597961426 0.69059104 4.316257476806641 True -1 5758 31.933958530426025 0.5524625778198242 396.89801025390625 0.4380677342414856 543.220458984375 0.34569644927978516 0.7610943 1.4096835851669312 True -2 8637 31.94351840019226 0.5546984672546387 362.6526184082031 0.3375625014305115 533.0502319335938 0.3559655547142029 0.78117836 0.6832910180091858 True -3 11516 31.930644750595093 3.076157569885254 534.54052734375 0.4888269007205963 527.0114135742188 0.36183255910873413 0.7915114 0.6497159004211426 True -4 14395 31.94415283203125 0.5581212043762207 418.5540771484375 0.22413554787635803 522.8873901367188 0.36533451080322266 0.8037088 0.5101615786552429 True -5 17274 31.913275003433228 0.5480601787567139 462.75762939453125 0.43365588784217834 521.0450439453125 0.36645591259002686 0.81047195 0.41227686405181885 True -6 20153 31.93624973297119 0.543715238571167 341.0694580078125 0.2701552212238312 519.6583251953125 0.36863696575164795 0.8140646 0.4023810029029846 True -7 23032 31.945099115371704 1.170226812362671 413.419921875 0.33180931210517883 517.88134765625 0.3702429234981537 0.8222256 0.38102608919143677 True -8 25911 31.993342399597168 0.5535991191864014 440.2498779296875 0.26327216625213623 516.1907958984375 0.3719433844089508 0.82289445 0.37373337149620056 True -9 28790 31.9863383769989 0.5443241596221924 478.8153991699219 0.3614516854286194 514.6962280273438 0.37379539012908936 0.82695305 0.37092268466949463 True -10 31669 31.944608449935913 0.5544521808624268 401.5323486328125 0.258341908454895 513.3271484375 0.37529581785202026 0.83248687 0.3551877737045288 True -11 34548 31.954744338989258 0.5522816181182861 375.4288635253906 0.15321475267410278 512.06201171875 0.37668171525001526 0.8380167 0.32288819551467896 True -12 37427 31.966849088668823 0.5557708740234375 435.32794189453125 0.36311882734298706 510.7101745605469 0.3781774938106537 0.8413459 0.317227303981781 True -13 40306 31.905377864837646 0.544471025466919 403.5343322753906 0.2897745668888092 507.86529541015625 0.3824896514415741 0.84791464 0.30052682757377625 True -14 43185 31.90833854675293 0.5418000221252441 433.14678955078125 0.29668575525283813 507.1952209472656 0.38268786668777466 0.8525742 0.2787766754627228 True -15 46064 31.92371916770935 0.5412135124206543 444.01708984375 0.1709708571434021 506.8952941894531 0.38222506642341614 0.8539599 0.2664538323879242 True -16 48943 31.94027042388916 0.5421900749206543 456.8326110839844 0.23153215646743774 507.0674133300781 0.38158032298088074 0.8567986 0.25756189227104187 True -17 51822 31.983856678009033 0.5360150337219238 386.58197021484375 0.19060471653938293 506.48370361328125 0.38297802209854126 0.85578465 0.25004440546035767 False -18 54701 31.936237335205078 0.8185656070709229 400.63116455078125 0.1995515525341034 506.0216064453125 0.3839000463485718 0.85611933 0.25057074427604675 False -19 57580 31.426321506500244 0.5484282970428467 428.51165771484375 0.17483143508434296 507.7211608886719 0.380222886800766 0.8548833 0.2513905167579651 False diff --git a/ENCSR532DBH/cherimoya.fold_2.performance.tsv b/ENCSR532DBH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 64800c334b106e0b301d8efb57a5fd5b475a1c48..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -507.0674133300781 0.41026896238327026 0.38158032298088074 0.14030174911022186 0.8567985892295837 0.8413578271865845 0.25756189227104187 \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_3.evaluate.json b/ENCSR532DBH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 072d1b09d8b85af62061f59666daa914e18cdf8d..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF158EVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_3.fit.json b/ENCSR532DBH/cherimoya.fold_3.fit.json deleted file mode 100644 index 3c462cb3950fc2d0ce516532a3e161d996044b82..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF158EVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_3.log b/ENCSR532DBH/cherimoya.fold_3.log deleted file mode 100644 index c46f2e2c3b2d562acc09c2cfd85c927d4ee2106d..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 34.27625489234924 3.441253900527954 469.39971923828125 0.4201091527938843 560.4410400390625 0.2837308645248413 0.6720403 4.690418720245361 True -1 5496 30.416825771331787 0.5593841075897217 379.3661193847656 0.3308609426021576 504.8167419433594 0.348609983921051 0.74943024 1.471876621246338 True -2 8244 30.433325052261353 0.5311894416809082 460.1043701171875 0.3646628260612488 494.1348571777344 0.35868561267852783 0.77655214 0.6585312485694885 True -3 10992 30.421074390411377 0.5369281768798828 465.39251708984375 0.37617045640945435 488.9821472167969 0.36423149704933167 0.7872313 0.5540279150009155 True -4 13740 30.42172145843506 0.5373833179473877 452.06298828125 0.4428500533103943 485.78887939453125 0.367780476808548 0.79695773 0.5165352821350098 True -5 16488 30.48321843147278 0.5480823516845703 422.32733154296875 0.3291206657886505 483.8176574707031 0.3693048357963562 0.8006669 0.5016711950302124 True -6 19236 30.456955432891846 0.5703983306884766 522.2833251953125 0.5512169003486633 482.2946472167969 0.3705510199069977 0.8064414 0.4643097221851349 True -7 21984 30.403951406478882 0.5472207069396973 425.21673583984375 0.3737673759460449 479.9624328613281 0.3737121820449829 0.81194794 0.4472176134586334 True -8 24732 30.436198234558105 0.5401804447174072 368.484130859375 0.4553026556968689 479.28033447265625 0.3735823631286621 0.81639016 0.4463827610015869 True -9 27480 30.406582832336426 1.7007153034210205 452.7032470703125 0.40326929092407227 477.9593505859375 0.3753921389579773 0.8190267 0.4073795974254608 True -10 30228 30.459559202194214 0.5452554225921631 436.4659729003906 0.3678731322288513 477.03948974609375 0.37623506784439087 0.8238569 0.38484683632850647 True -11 32976 30.40133833885193 0.5609133243560791 435.9991149902344 0.1907287836074829 473.9877014160156 0.3800809383392334 0.82839006 0.36202046275138855 True -12 35724 30.552624940872192 0.5538382530212402 375.21307373046875 0.3021491765975952 473.76025390625 0.3790581226348877 0.8325139 0.3332059979438782 True -13 38472 30.418437242507935 0.5429403781890869 410.3049621582031 0.2125384658575058 471.1778869628906 0.3836728632450104 0.83681756 0.3166355490684509 True -14 41220 30.421635389328003 0.5538997650146484 375.59429931640625 0.23444120585918427 470.0087585449219 0.38502204418182373 0.8418042 0.2988574504852295 True -15 43968 30.460853815078735 0.5403690338134766 391.6646728515625 0.3103425204753876 470.3851318359375 0.3834640383720398 0.84694153 0.2859305441379547 True -16 46716 30.44030523300171 13.070592164993286 365.40789794921875 0.2725974917411804 469.929931640625 0.38427019119262695 0.8483939 0.2784908413887024 True -17 49464 30.510191917419434 0.5583865642547607 465.173828125 0.22903653979301453 469.4684753417969 0.3841001093387604 0.8486652 0.2713749408721924 True -18 52212 30.5000057220459 0.5493597984313965 386.0302734375 0.21563264727592468 469.1043395996094 0.38466542959213257 0.84827524 0.269406259059906 False -19 54960 30.010393381118774 0.5356094837188721 428.4232482910156 0.2179725468158722 469.76214599609375 0.38290464878082275 0.8493028 0.27055495977401733 True diff --git a/ENCSR532DBH/cherimoya.fold_3.performance.tsv b/ENCSR532DBH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b3a4aefad2a98f872429f5916c32159730430010..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -469.76214599609375 0.41266220808029175 0.38290467858314514 0.13836035132408142 0.8493028283119202 0.8233964443206787 0.27055495977401733 \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_4.evaluate.json b/ENCSR532DBH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2d4a9c32c98dc476b4a77badc1e5e6ca534e0d79..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF158EVM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_4.fit.json b/ENCSR532DBH/cherimoya.fold_4.fit.json deleted file mode 100644 index 74bbc3cd7e90bc8b6e21829761df31c967a9fd9a..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF158EVM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR532DBH/cherimoya.fold_4.log b/ENCSR532DBH/cherimoya.fold_4.log deleted file mode 100644 index 061647f3ea021cc33747568ed53fea3327a6d521..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2829 34.705124855041504 3.558192014694214 408.3204345703125 0.6653953790664673 542.8949584960938 0.27415895462036133 0.6700315 4.220296859741211 True -1 5658 31.043895959854126 0.59755539894104 401.871826171875 0.3979095220565796 487.6902160644531 0.34240275621414185 0.7514303 1.3236329555511475 True -2 8487 31.04980707168579 0.5834228992462158 498.9226989746094 0.49276047945022583 479.1164855957031 0.3528820276260376 0.7682913 0.9527317881584167 True -3 11316 31.01883053779602 0.5854084491729736 378.8780822753906 0.37494295835494995 475.8143615722656 0.35412487387657166 0.77761805 0.5550013184547424 True -4 14145 31.026665210723877 0.5861356258392334 345.72052001953125 0.4594091773033142 473.0060729980469 0.3584684729576111 0.7832134 0.41001519560813904 True -5 16974 31.02275848388672 0.5826058387756348 371.88201904296875 0.4664192497730255 472.0303649902344 0.3579925000667572 0.7892707 0.39460405707359314 True -6 19803 31.033366918563843 0.5860276222229004 400.14947509765625 0.7623138427734375 471.8224792480469 0.3574429154396057 0.79289895 0.379525750875473 True -7 22632 31.074805974960327 0.5880160331726074 446.5540771484375 0.31102731823921204 469.6806945800781 0.36051544547080994 0.80172944 0.36229705810546875 True -8 25461 31.086754083633423 0.5775749683380127 375.74041748046875 0.23116005957126617 468.19219970703125 0.36253705620765686 0.80832624 0.33799490332603455 True -9 28290 31.08689045906067 0.5882894992828369 365.6509704589844 0.30824822187423706 466.1628723144531 0.3656023144721985 0.8117254 0.32398468255996704 True -10 31119 31.029174089431763 1.4614806175231934 584.7105712890625 0.46965712308883667 465.6733093261719 0.3660939335823059 0.8175198 0.3103034496307373 True -11 33948 31.091185808181763 0.5922605991363525 494.86865234375 0.4101399779319763 463.7737121582031 0.36835697293281555 0.82122314 0.29377034306526184 True -12 36777 31.052644968032837 0.6140093803405762 427.26556396484375 0.3746412992477417 463.0706787109375 0.36896130442619324 0.828776 0.2731871008872986 True -13 39606 31.082637786865234 0.5896246433258057 462.3836669921875 0.20723988115787506 462.0954895019531 0.3697132468223572 0.8339877 0.26887282729148865 True -14 42435 31.074110746383667 0.5928425788879395 386.0398254394531 0.19724388420581818 460.71905517578125 0.3726162910461426 0.8388159 0.2583629786968231 True -15 45264 31.100940942764282 0.5998613834381104 391.52703857421875 0.24057847261428833 460.222900390625 0.3727809488773346 0.84461975 0.24516141414642334 True -16 48093 31.067814588546753 0.5897021293640137 443.7900695800781 0.32883936166763306 459.7433166503906 0.37292832136154175 0.8477627 0.24149340391159058 True -17 50922 31.114041328430176 0.5843467712402344 392.31396484375 0.3260766863822937 459.9590759277344 0.3733333647251129 0.84952825 0.23749639093875885 True -18 53751 30.86614155769348 0.84702467918396 494.2793884277344 0.205393984913826 460.30914306640625 0.3729194104671478 0.8481167 0.23808205127716064 False -19 56580 30.58982491493225 0.594651460647583 393.9329528808594 0.1910112500190735 460.13861083984375 0.3731671869754791 0.8468269 0.24076725542545319 False diff --git a/ENCSR532DBH/cherimoya.fold_4.performance.tsv b/ENCSR532DBH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index bd4396e4a207e456fd358932f642ad41ae1b3d1f..0000000000000000000000000000000000000000 --- a/ENCSR532DBH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.9590759277344 0.4194411337375641 0.3733333647251129 0.1308029294013977 0.8495282530784607 0.8290888667106628 0.23749639093875885 \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_0.evaluate.json b/ENCSR533VAF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 045f83a1cd37336346bf9d8528bc9eb4dfb7c652..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791WMC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_0.fit.json b/ENCSR533VAF/cherimoya.fold_0.fit.json deleted file mode 100644 index aa456714af80bb65316ac6f84e72f01e7aba6291..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF791WMC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_0.log b/ENCSR533VAF/cherimoya.fold_0.log deleted file mode 100644 index cb9fb451fd20653486ba0214c69868ce97781049..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2726 34.75569939613342 3.4689741134643555 262.1936340332031 1.3837437629699707 318.7282409667969 0.1479157954454422 0.37899858 3.147116184234619 True -1 5452 29.950002908706665 0.6015844345092773 293.59246826171875 0.706261157989502 310.9517822265625 0.18573375046253204 0.47069117 1.1676560640335083 True -2 8178 29.95788049697876 0.5718233585357666 230.21778869628906 0.8563613891601562 309.2847595214844 0.19190357625484467 0.48837695 0.6542763113975525 True -3 10904 29.93621277809143 0.5265254974365234 197.91998291015625 1.12606942653656 308.12384033203125 0.1948261260986328 0.5082589 0.6665847897529602 True -4 13630 29.975116729736328 0.5460629463195801 205.05166625976562 0.9877660870552063 307.1226501464844 0.19875340163707733 0.5145389 0.7125906348228455 True -5 16356 29.91849637031555 0.5568697452545166 264.46710205078125 0.6705758571624756 306.4511413574219 0.20209231972694397 0.51577866 0.7430902123451233 True -6 19082 29.88792324066162 0.5299842357635498 209.78598022460938 0.8878070712089539 306.03948974609375 0.20306001603603363 0.5162255 0.7278688549995422 True -7 21808 29.900545835494995 0.5303335189819336 239.83349609375 0.7753968238830566 306.0736083984375 0.20299500226974487 0.51894885 0.7708745002746582 True -8 24534 29.880985736846924 0.5228769779205322 223.14927673339844 0.6472511291503906 305.4939880371094 0.2057100087404251 0.52244097 0.7272468209266663 True -9 27260 29.891871690750122 0.5313410758972168 218.53257751464844 0.7287167310714722 305.0498352050781 0.2078898847103119 0.52629083 0.7068106532096863 True -10 29986 29.970730543136597 0.5306549072265625 189.6038818359375 0.6301758289337158 304.82342529296875 0.2087640017271042 0.5369583 0.6858130097389221 True -11 32712 29.932223558425903 0.5249924659729004 256.0455017089844 0.5665069818496704 304.452392578125 0.210663840174675 0.5416315 0.6703469157218933 True -12 35438 29.91540217399597 0.8037045001983643 221.24728393554688 0.6943590641021729 303.9689636230469 0.2126544862985611 0.55414295 0.606229841709137 True -13 38164 29.990155458450317 27.186897039413452 254.15188598632812 0.8806780576705933 303.72308349609375 0.21390575170516968 0.5610306 0.5745135545730591 True -14 40890 29.51766324043274 0.5951211452484131 247.75173950195312 0.41505247354507446 303.9976806640625 0.21196028590202332 0.5675829 0.5332019329071045 True -15 43616 29.374907732009888 0.5272209644317627 204.50375366210938 0.584363579750061 303.7392272949219 0.2131987065076828 0.57478815 0.5084502696990967 True -16 46342 29.348062992095947 0.5267610549926758 246.08187866210938 0.4566015601158142 303.40570068359375 0.21494217216968536 0.5790619 0.49921783804893494 True -17 49068 29.398363828659058 1.3168432712554932 198.14254760742188 0.6971601843833923 303.555419921875 0.21410036087036133 0.57994586 0.5123116970062256 True -18 51794 29.36598563194275 0.5330493450164795 246.3098907470703 0.592558741569519 303.88189697265625 0.21259337663650513 0.57588136 0.5191575288772583 False -19 54520 29.335726022720337 0.520183801651001 219.23764038085938 0.3114916980266571 303.904052734375 0.21249398589134216 0.5741556 0.5288299322128296 False diff --git a/ENCSR533VAF/cherimoya.fold_0.performance.tsv b/ENCSR533VAF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 64b7fc89b9dba0f18b94b26ba821f6e672d5bc41..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -303.555419921875 0.5125478506088257 0.21410034596920013 0.07036416977643967 0.5799458622932434 0.5827717185020447 0.5123116970062256 \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_1.evaluate.json b/ENCSR533VAF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 82b34543fce757612485e473cad14663903833a3..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791WMC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_1.fit.json b/ENCSR533VAF/cherimoya.fold_1.fit.json deleted file mode 100644 index 1a52dc81fe528794285758b61cd8773ac237a9df..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF791WMC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_1.log b/ENCSR533VAF/cherimoya.fold_1.log deleted file mode 100644 index 5a11f81a5c149c73cbe5b81587be27703f05b273..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2791 35.76683592796326 3.4905829429626465 218.05563354492188 0.9555074572563171 344.8061218261719 0.15943212807178497 0.40254846 2.7727346420288086 True -1 5582 30.65449070930481 0.6980335712432861 309.7716064453125 0.9674369096755981 336.62994384765625 0.1948096752166748 0.49281 1.39525306224823 True -2 8373 30.69778847694397 0.7170248031616211 236.44638061523438 0.7895901799201965 333.7506103515625 0.20541250705718994 0.50605434 0.7402170896530151 True -3 11164 30.644213438034058 0.6856515407562256 259.9682312011719 1.0870881080627441 332.656982421875 0.20884382724761963 0.53123 0.6963995695114136 True -4 13955 30.637977838516235 0.662255048751831 171.36968994140625 1.128786563873291 331.8754577636719 0.21071547269821167 0.5478605 0.6176906824111938 True -5 16746 30.666244745254517 0.6680750846862793 235.9532470703125 0.7821763157844543 330.90606689453125 0.21445675194263458 0.5586793 0.5850184559822083 True -6 19537 30.59441590309143 0.9161067008972168 222.42454528808594 0.6726397275924683 330.5375671386719 0.2152504175901413 0.56374943 0.5670018792152405 True -7 22328 30.649453163146973 1.9501192569732666 296.2199401855469 0.803328275680542 329.934814453125 0.21798162162303925 0.5706254 0.5519871115684509 True -8 25119 30.651975393295288 13.194061040878296 228.06198120117188 1.2613012790679932 329.6247253417969 0.21874330937862396 0.56948376 0.5687508583068848 False -9 27910 30.655290603637695 9.003521203994751 205.84982299804688 0.5734358429908752 328.9398498535156 0.22172842919826508 0.5748043 0.5499498248100281 True -10 30701 30.733376502990723 1.6380131244659424 249.07357788085938 0.7646318078041077 328.5290222167969 0.22300297021865845 0.58163756 0.5390931367874146 True -11 33492 30.68363380432129 0.6755473613739014 253.99795532226562 0.6586397290229797 328.1786193847656 0.22474217414855957 0.5899555 0.5318750739097595 True -12 36283 30.685649156570435 1.3801124095916748 182.93301391601562 0.6863313317298889 327.7667236328125 0.22646674513816833 0.59227014 0.5224003791809082 True -13 39074 30.634100914001465 0.659205436706543 238.68228149414062 0.8266651034355164 327.7367248535156 0.22582419216632843 0.6007009 0.5043347477912903 True -14 41865 30.629108428955078 1.1074950695037842 224.64007568359375 0.370479017496109 327.6579895019531 0.2266124188899994 0.60862374 0.49328720569610596 True -15 44656 30.202207326889038 0.68623948097229 243.58392333984375 0.4872283637523651 326.8545837402344 0.23085196316242218 0.6148805 0.4811248779296875 True -16 47447 30.134774923324585 3.9986917972564697 235.50704956054688 0.5985500812530518 326.9296875 0.22902372479438782 0.62207586 0.4834822714328766 True -17 50238 30.028671503067017 0.6565837860107422 236.7850341796875 0.6278546452522278 327.0588073730469 0.22840765118598938 0.6220027 0.4905569851398468 False -18 53029 30.026203632354736 0.6605920791625977 257.5966796875 0.37199926376342773 327.5883483886719 0.22639602422714233 0.62034136 0.5044644474983215 False -19 55820 30.037670373916626 0.6573581695556641 204.31170654296875 0.7641268372535706 327.49188232421875 0.22672860324382782 0.61905164 0.511093020439148 False diff --git a/ENCSR533VAF/cherimoya.fold_1.performance.tsv b/ENCSR533VAF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f3655ef4464e9f25f3c3ef1bfdbc37419f7588c7..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.9296875 0.5001729726791382 0.229023739695549 0.0753750205039978 0.6220758557319641 0.6333523988723755 0.4834822714328766 \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_2.evaluate.json b/ENCSR533VAF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d85597078fc7f762141010af088162d042c10dd9..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791WMC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_2.fit.json b/ENCSR533VAF/cherimoya.fold_2.fit.json deleted file mode 100644 index e2819aceec75e9f5e0cb566d964e022d3e56d32b..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF791WMC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_2.log b/ENCSR533VAF/cherimoya.fold_2.log deleted file mode 100644 index 43df1d57c4c7cad7f7855f69dceed3c8144e451c..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2883 36.531545639038086 3.5002291202545166 212.79025268554688 0.9898600578308105 318.39410400390625 0.15239939093589783 0.3829501 2.493870735168457 True -1 5766 31.704249620437622 1.5345561504364014 238.9248504638672 1.3978486061096191 310.13568115234375 0.18949201703071594 0.4584594 1.2350858449935913 True -2 8649 31.746362447738647 0.6677417755126953 209.18658447265625 0.9341067671775818 308.06732177734375 0.19572468101978302 0.46840352 0.6701818704605103 True -3 11532 31.68201446533203 0.5190093517303467 231.51849365234375 1.0742331743240356 306.811767578125 0.2000049650669098 0.4872135 0.6108658313751221 True -4 14415 31.800456285476685 0.5190906524658203 201.0107421875 0.7668348550796509 306.2316589355469 0.20245261490345 0.49388146 0.6010168194770813 True -5 17298 31.757888078689575 0.598616361618042 290.0791015625 1.011918544769287 305.7852783203125 0.20460499823093414 0.50416285 0.6214107871055603 True -6 20181 31.623759508132935 0.5329129695892334 274.5315856933594 0.555198073387146 305.2807312011719 0.20657698810100555 0.51025844 0.6417416930198669 True -7 23064 31.625430583953857 0.5311064720153809 272.8265686035156 0.8101558685302734 304.703125 0.2094200849533081 0.5176492 0.6638815402984619 True -8 25947 31.6380136013031 0.5393962860107422 300.59149169921875 0.6997367143630981 304.71875 0.2086843103170395 0.52261657 0.6778132319450378 True -9 28830 31.69278049468994 0.5401580333709717 241.91595458984375 0.8828003406524658 304.3814392089844 0.21028052270412445 0.52721757 0.680309534072876 True -10 31713 31.69006848335266 0.5430850982666016 226.84027099609375 0.54527348279953 304.0567321777344 0.211373969912529 0.53515446 0.6535292863845825 True -11 34596 31.712393522262573 1.0542802810668945 234.95440673828125 0.8332887291908264 303.40863037109375 0.2147701531648636 0.5470977 0.6206277012825012 True -12 37479 31.63339138031006 10.3832528591156 244.88552856445312 0.6795775890350342 303.121337890625 0.2158403992652893 0.5510219 0.5987681150436401 True -13 40362 31.083245038986206 0.5462524890899658 234.03936767578125 0.9115680456161499 303.0908508300781 0.21535885334014893 0.56301284 0.5520862340927124 True -14 43245 31.081176042556763 0.543109655380249 275.3948059082031 0.6583573818206787 302.74176025390625 0.21719402074813843 0.57061183 0.5204622149467468 True -15 46128 31.087432861328125 0.524406909942627 205.91201782226562 0.7734901905059814 302.5802917480469 0.21787671744823456 0.57614654 0.5149450898170471 True -16 49011 31.061526775360107 0.5326335430145264 242.12533569335938 0.6234874725341797 302.9117736816406 0.21601687371730804 0.57967365 0.5149672031402588 True -17 51894 31.085578203201294 13.729900121688843 245.65359497070312 0.8005831837654114 302.6816711425781 0.21712753176689148 0.5808425 0.5219102501869202 True -18 54777 31.077985048294067 0.7134711742401123 212.7780303955078 0.6644666790962219 303.0090026855469 0.2153140753507614 0.5805155 0.5281935930252075 False -19 57660 31.123619079589844 0.5436005592346191 242.22512817382812 0.510259211063385 302.8671875 0.21616101264953613 0.57881343 0.5374936461448669 False diff --git a/ENCSR533VAF/cherimoya.fold_2.performance.tsv b/ENCSR533VAF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8f0ce21031f364b96a6f001b41af30d0f2fa3a5e..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.6816711425781 0.5115630030632019 0.21712753176689148 0.07340985536575317 0.5808424949645996 0.5885162949562073 0.5219102501869202 \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_3.evaluate.json b/ENCSR533VAF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7eddcf7bf3cb6b39c990e8c6e447f07b1d595e09..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791WMC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_3.fit.json b/ENCSR533VAF/cherimoya.fold_3.fit.json deleted file mode 100644 index 97b5706f38432c27a26e5a9d9abc2a01d5f9adc4..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF791WMC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_3.log b/ENCSR533VAF/cherimoya.fold_3.log deleted file mode 100644 index 6979db5b62f3c2b29ff8edde7f2ab4f663e75f01..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2807 35.745463371276855 3.906964063644409 251.45018005371094 0.7999787330627441 337.8988342285156 0.15388165414333344 0.42311653 2.7942545413970947 True -1 5614 30.83612871170044 0.629443883895874 253.21875 0.985885739326477 330.6598815917969 0.18627996742725372 0.47793782 1.3366628885269165 True -2 8421 30.882925271987915 10.205082178115845 231.1416778564453 0.9357472658157349 328.3824462890625 0.19475823640823364 0.49960822 0.8585292100906372 True -3 11228 30.844107627868652 0.6361532211303711 239.7585906982422 0.9462730884552002 326.8824157714844 0.19907903671264648 0.52387077 0.7366507649421692 True -4 14035 30.90945339202881 8.468185186386108 278.87078857421875 0.7510957717895508 326.4187316894531 0.20032456517219543 0.5294533 0.8145973086357117 True -5 16842 30.853935718536377 0.6058447360992432 224.08261108398438 0.8237192630767822 325.949951171875 0.20214290916919708 0.5428107 0.8127074241638184 True -6 19649 30.90354323387146 0.6044974327087402 242.7713623046875 0.8878085613250732 325.3651428222656 0.20506122708320618 0.5459413 0.8133050203323364 True -7 22456 30.838634729385376 2.236537218093872 220.614501953125 0.8072463870048523 325.0513000488281 0.20673096179962158 0.5540875 0.7902990579605103 True -8 25263 30.85096526145935 0.6041324138641357 259.555908203125 0.9269677996635437 324.8055725097656 0.2069120556116104 0.55550826 0.7841534614562988 True -9 28070 30.326476573944092 0.6011137962341309 223.81568908691406 0.9066241979598999 324.5408630371094 0.2077297419309616 0.56604975 0.7489902973175049 True -10 30877 30.244174003601074 0.5899994373321533 256.3293762207031 0.6794297695159912 323.6842346191406 0.21170233190059662 0.57123643 0.7326065897941589 True -11 33684 30.220641374588013 0.5975306034088135 232.51515197753906 0.540151834487915 323.2550354003906 0.21325290203094482 0.58332086 0.6834025979042053 True -12 36491 30.262600421905518 0.6106946468353271 218.21800231933594 0.8990594148635864 323.181884765625 0.2134590744972229 0.5903179 0.6229149699211121 True -13 39298 30.235811471939087 0.6021029949188232 260.5242919921875 0.6866788864135742 322.8782043457031 0.21479398012161255 0.6006634 0.5812987089157104 True -14 42105 30.25308322906494 0.586916446685791 230.33348083496094 0.7693253755569458 322.6492004394531 0.21520674228668213 0.608217 0.5442707538604736 True -15 44912 30.318859577178955 0.5908942222595215 310.980712890625 0.7610718011856079 322.4684753417969 0.2159128040075302 0.613851 0.5158668756484985 True -16 47719 30.345571756362915 0.6111981868743896 238.97561645507812 0.5175390243530273 322.59735107421875 0.2153661549091339 0.61546874 0.5081987977027893 True -17 50526 30.282253742218018 0.5828897953033447 228.8519287109375 0.5297688245773315 322.5638122558594 0.21539723873138428 0.6177186 0.5044452548027039 True -18 53333 30.306206703186035 0.5971524715423584 255.8570556640625 0.5797285437583923 322.63336181640625 0.21528677642345428 0.61521953 0.5061649680137634 False -19 56140 30.296359062194824 0.59378981590271 231.92166137695312 0.3131345510482788 322.7373962402344 0.21456795930862427 0.6127394 0.5125707387924194 False diff --git a/ENCSR533VAF/cherimoya.fold_3.performance.tsv b/ENCSR533VAF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 85e46867a613019949c0379663d66e390b18b4d3..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -322.5638122558594 0.5065193176269531 0.21539723873138428 0.0752635970711708 0.6177185773849487 0.6148644685745239 0.5044452548027039 \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_4.evaluate.json b/ENCSR533VAF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8fc678c9554b5b23e788af10d4276f866b305e66..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791WMC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_4.fit.json b/ENCSR533VAF/cherimoya.fold_4.fit.json deleted file mode 100644 index f30563d4808bd6c40e4ee41079db5ed07e6de36a..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF791WMC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533VAF/cherimoya.fold_4.log b/ENCSR533VAF/cherimoya.fold_4.log deleted file mode 100644 index 368b25d112b31eb1c16a377a39ac3d2d3576aeeb..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2910 36.74919152259827 3.9821465015411377 256.59063720703125 0.9472694396972656 328.14605712890625 0.1578851193189621 0.3809476 2.732304334640503 True -1 5820 31.972875356674194 0.6214923858642578 242.5154266357422 1.1360065937042236 320.711181640625 0.18958371877670288 0.43992093 1.2417093515396118 True -2 8730 32.0549955368042 0.5807280540466309 271.5821533203125 0.8402754068374634 318.7453918457031 0.19717197120189667 0.45052096 0.7811141014099121 True -3 11640 32.00425839424133 0.5798790454864502 204.18991088867188 0.8495254516601562 317.7735595703125 0.19962526857852936 0.4716221 0.7765541672706604 True -4 14550 32.00196886062622 0.5800464153289795 204.9320526123047 0.8064355850219727 317.0403747558594 0.20279540121555328 0.48283586 0.7155007719993591 True -5 17460 32.016799449920654 3.8355894088745117 237.439208984375 0.6079176068305969 317.2438659667969 0.20078061521053314 0.48837376 0.7182140946388245 True -6 20370 31.657375812530518 0.5846846103668213 238.6022186279297 0.7618920803070068 316.6592102050781 0.2037559598684311 0.49135962 0.7307257056236267 True -7 23280 31.41416096687317 4.4891557693481445 225.72657775878906 0.8813116550445557 316.09857177734375 0.2063189446926117 0.48860306 0.7987679839134216 False -8 26190 31.382532119750977 0.5714108943939209 211.0096435546875 0.9458934664726257 315.5550231933594 0.20868977904319763 0.4985019 0.7957543730735779 True -9 29100 31.399407625198364 0.5836963653564453 278.9244384765625 0.8482505083084106 315.3160705566406 0.2094816416501999 0.5097208 0.7446238398551941 True -10 32010 31.372058153152466 0.5788962841033936 226.80552673339844 0.865865170955658 315.0453796386719 0.21061815321445465 0.5132006 0.7215850353240967 True -11 34920 31.333298683166504 0.5800211429595947 233.79046630859375 0.5483949184417725 314.606201171875 0.2123212218284607 0.52426046 0.7100377082824707 True -12 37830 31.250650882720947 0.5796253681182861 239.33087158203125 0.7327510118484497 314.59881591796875 0.21222761273384094 0.5306553 0.692484974861145 True -13 40740 31.320751905441284 0.5779094696044922 248.88214111328125 0.5082197189331055 313.90850830078125 0.2152104526758194 0.5397934 0.6488742828369141 True -14 43650 31.30273127555847 1.760667324066162 225.28155517578125 0.9951975345611572 313.6943359375 0.2158767431974411 0.54968685 0.6294955015182495 True -15 46560 32.344199419021606 10.352709293365479 267.5430908203125 0.5519408583641052 313.3828125 0.21699737012386322 0.557932 0.5835256576538086 True -16 49470 31.493684768676758 0.5761773586273193 234.123291015625 0.5614145994186401 314.050048828125 0.21338649094104767 0.5632808 0.5617797374725342 True -17 52380 31.544479846954346 19.275691986083984 238.3072509765625 0.5100651383399963 313.7571716308594 0.21536536514759064 0.56830496 0.5552510619163513 True -18 55290 31.7781081199646 23.24284029006958 219.02389526367188 0.513227105140686 313.7983703613281 0.21527951955795288 0.56570464 0.5578751564025879 False -19 58200 31.59530210494995 0.5910935401916504 255.05426025390625 0.556884765625 313.84466552734375 0.21530750393867493 0.56442815 0.5690754652023315 False diff --git a/ENCSR533VAF/cherimoya.fold_4.performance.tsv b/ENCSR533VAF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0c8c1de8263e81baca85fb4042c34d292850b4af..0000000000000000000000000000000000000000 --- a/ENCSR533VAF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -313.7571716308594 0.5089114308357239 0.21536536514759064 0.0724942684173584 0.5683049559593201 0.573429524898529 0.5552510619163513 \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_0.evaluate.json b/ENCSR533WFB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 47ebbe76fb30ea1c5a8073b3e093ab1286b0b833..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF381NLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_0.fit.json b/ENCSR533WFB/cherimoya.fold_0.fit.json deleted file mode 100644 index ed45dea7c6892c031d8abcc626cc93dcd63b5382..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF381NLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_0.log b/ENCSR533WFB/cherimoya.fold_0.log deleted file mode 100644 index 1d68f0f04de00e175f6c1cb5a0714e25872ff6ea..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1452 20.489266872406006 3.4662864208221436 271.01031494140625 0.21693211793899536 438.6607360839844 0.4901268780231476 0.66345525 15.295307159423828 True -1 2904 16.046885013580322 0.43978357315063477 322.1309814453125 0.3637242615222931 360.676025390625 0.589704155921936 0.75880575 2.5806565284729004 True -2 4356 16.006564140319824 0.30703306198120117 296.70037841796875 0.16161569952964783 343.44635009765625 0.6207531094551086 0.77691996 0.43431204557418823 True -3 5808 16.023306608200073 0.30478549003601074 280.24737548828125 0.25440514087677 334.7294006347656 0.6339063048362732 0.78761923 0.2159530073404312 True -4 7260 16.010161638259888 0.30954933166503906 276.43829345703125 0.19738489389419556 332.13275146484375 0.6401911377906799 0.79985625 0.18529564142227173 True -5 8712 16.003662824630737 0.36377859115600586 285.17071533203125 0.22038091719150543 330.4327392578125 0.6442257165908813 0.8057663 0.17657987773418427 True -6 10164 16.02360701560974 0.2916390895843506 268.61993408203125 0.17170915007591248 329.518310546875 0.6466571092605591 0.8141622 0.16082985699176788 True -7 11616 16.032710790634155 0.2979142665863037 302.33831787109375 0.1903100311756134 329.13751220703125 0.6478579640388489 0.8175113 0.14453771710395813 True -8 13068 16.04663610458374 0.2952587604522705 299.28082275390625 0.15035732090473175 328.433837890625 0.6495493054389954 0.82241404 0.13702748715877533 True -9 14520 15.999715805053711 0.7867751121520996 293.13299560546875 0.17774389684200287 327.85504150390625 0.6508038640022278 0.82618755 0.13718874752521515 True -10 15972 16.026683807373047 0.5498383045196533 280.82794189453125 0.12408849596977234 327.3058166503906 0.6521816849708557 0.83093935 0.12957149744033813 True -11 17424 16.011662483215332 0.29729342460632324 280.9130859375 0.11718524247407913 326.8608703613281 0.6534685492515564 0.83251923 0.12321264296770096 True -12 18876 16.02098512649536 0.3051869869232178 290.479248046875 0.12275603413581848 326.4939880371094 0.6543845534324646 0.8371447 0.12088989466428757 True -13 20328 16.078296184539795 0.30449867248535156 275.55352783203125 0.08135257661342621 326.15826416015625 0.6551609635353088 0.83969754 0.11847177892923355 True -14 21780 15.999791383743286 0.3017618656158447 307.56781005859375 0.16136600077152252 326.0047912597656 0.6554994583129883 0.8401565 0.11766576766967773 True -15 23232 16.0367431640625 0.29755330085754395 298.083251953125 0.10469494760036469 325.84130859375 0.6556777358055115 0.8419715 0.1180063858628273 True -16 24684 16.022555589675903 0.29549717903137207 282.775390625 0.0859847217798233 326.04095458984375 0.6554054617881775 0.84216 0.11782487481832504 True -17 26136 16.08180260658264 0.3105733394622803 302.8504638671875 0.11992105841636658 326.29730224609375 0.6546859741210938 0.8423186 0.11884227395057678 True -18 27588 15.99816083908081 0.30857038497924805 287.68829345703125 0.06020299345254898 326.49029541015625 0.6540715098381042 0.8393012 0.12112975120544434 False -19 29040 16.0439875125885 0.3071873188018799 279.61212158203125 0.07541745901107788 326.6502990722656 0.6536450982093811 0.83882487 0.12303256243467331 False diff --git a/ENCSR533WFB/cherimoya.fold_0.performance.tsv b/ENCSR533WFB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cd853cf4fb74ec7d33f96d41f72ba456b3ead252..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.29730224609375 0.28047576546669006 0.6546860337257385 0.24127867817878723 0.842318594455719 0.7735150456428528 0.11884227395057678 \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_1.evaluate.json b/ENCSR533WFB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bf229c00ff2f1359554185a6b7cc89fc022800f0..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF381NLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_1.fit.json b/ENCSR533WFB/cherimoya.fold_1.fit.json deleted file mode 100644 index 725b4f2f58fb77de78ef94d5145e5198a007f92d..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF381NLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_1.log b/ENCSR533WFB/cherimoya.fold_1.log deleted file mode 100644 index f6ccf55802f25004e2929b4a6771798249fe1138..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1426 20.590219736099243 3.6898908615112305 308.26776123046875 0.2861569821834564 501.1097106933594 0.5022197365760803 0.57753664 16.502992630004883 True -1 2852 15.792163133621216 9.75840425491333 302.4976501464844 0.20092493295669556 408.9167785644531 0.6029300093650818 0.7330642 3.1096079349517822 True -2 4278 15.765286207199097 0.40735459327697754 322.9876708984375 0.25406888127326965 383.7861633300781 0.6440277695655823 0.75921285 0.8177298903465271 True -3 5704 15.750885248184204 0.40214037895202637 279.288818359375 0.15014658868312836 371.44207763671875 0.6637225151062012 0.7771607 0.3623431324958801 True -4 7130 15.708914756774902 0.8863387107849121 297.6001892089844 0.13145512342453003 367.7508850097656 0.6699685454368591 0.79165703 0.26202335953712463 True -5 8556 15.734968423843384 0.4006023406982422 280.28369140625 0.1575472354888916 367.1656188964844 0.6713176965713501 0.7921593 0.20606303215026855 True -6 9982 15.727819204330444 0.4021000862121582 264.8211669921875 0.13481926918029785 366.05029296875 0.6737757921218872 0.7985403 0.1923632025718689 True -7 11408 15.716836214065552 0.40602779388427734 282.9441223144531 0.2112647294998169 365.0995178222656 0.6759598255157471 0.80756646 0.18213675916194916 True -8 12834 15.700594902038574 0.4136631488800049 290.657958984375 0.17604821920394897 364.6786804199219 0.676598310470581 0.8108854 0.19285182654857635 True -9 14260 15.737540245056152 0.3998701572418213 280.94830322265625 0.1478031873703003 364.1252746582031 0.6777737736701965 0.81657165 0.1979425549507141 True -10 15686 15.738614559173584 0.410503625869751 267.80181884765625 0.12064755707979202 363.2272033691406 0.6798179745674133 0.8226494 0.1757902354001999 True -11 17112 15.720030784606934 0.4043998718261719 307.3724365234375 0.22223404049873352 362.67327880859375 0.6810376048088074 0.827121 0.16361546516418457 True -12 18538 15.719840049743652 0.39793992042541504 307.4910888671875 0.15686053037643433 362.1985168457031 0.681979238986969 0.83098364 0.15554915368556976 True -13 19964 15.770232915878296 0.4079287052154541 283.6933898925781 0.09322789311408997 361.86590576171875 0.6826422810554504 0.83366805 0.15388894081115723 True -14 21390 15.75744104385376 0.40845823287963867 302.77178955078125 0.1791514754295349 361.5770568847656 0.683300793170929 0.8370197 0.15166786313056946 True -15 22816 15.753241300582886 1.084122896194458 271.50738525390625 0.10859955102205276 361.60870361328125 0.6830790638923645 0.83961046 0.14910858869552612 True -16 24242 15.737598180770874 1.2844221591949463 294.9173278808594 0.06215387582778931 361.8291320800781 0.6824043393135071 0.8397966 0.14688672125339508 True -17 25668 15.589030265808105 0.3889012336730957 268.67999267578125 0.09682002663612366 362.1668395996094 0.6813599467277527 0.8388282 0.14769300818443298 False -18 27094 15.433404445648193 0.3963649272918701 267.39300537109375 0.12386322021484375 362.4785461425781 0.6804441213607788 0.83707076 0.14832961559295654 False -19 28520 15.459267616271973 2.572721481323242 274.27398681640625 0.07262104749679565 362.7008056640625 0.6798057556152344 0.8350371 0.14996270835399628 False diff --git a/ENCSR533WFB/cherimoya.fold_1.performance.tsv b/ENCSR533WFB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c7798854b77350916c33e3f33ee53011f9a2c6f6..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.8291320800781 0.26105788350105286 0.6824043393135071 0.2663765251636505 0.8397966027259827 0.7942025661468506 0.14688672125339508 \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_2.evaluate.json b/ENCSR533WFB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c496eb6593fc44c5e617e4ecbb7af2d3441049b4..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF381NLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_2.fit.json b/ENCSR533WFB/cherimoya.fold_2.fit.json deleted file mode 100644 index 6a448d19a9db7ac5a4c38c5678cfbe6459a7f3f9..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF381NLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_2.log b/ENCSR533WFB/cherimoya.fold_2.log deleted file mode 100644 index 5b9cdb8450e54e6750a907877f8d8c3ff98159ab..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1528 21.740942239761353 4.540281057357788 324.0545654296875 0.2454279661178589 454.5464172363281 0.5003194808959961 0.6140396 13.647542953491211 True -1 3056 16.863451719284058 0.4111495018005371 269.26837158203125 0.22441741824150085 374.5048522949219 0.5981764793395996 0.75966465 2.1654796600341797 True -2 4584 16.928200721740723 0.3126513957977295 295.25018310546875 0.17177601158618927 355.3634948730469 0.6304304599761963 0.7860367 0.4403665363788605 True -3 6112 16.841007709503174 0.3208298683166504 286.5194396972656 0.1734311580657959 346.8905944824219 0.6458498239517212 0.7983844 0.28756746649742126 True -4 7640 16.565917015075684 0.2897634506225586 296.3813781738281 0.19750502705574036 343.7284851074219 0.6510095000267029 0.8093664 0.2422804981470108 True -5 9168 16.57535982131958 0.295912504196167 271.2437438964844 0.19505009055137634 342.84869384765625 0.6527190208435059 0.8138902 0.18585093319416046 True -6 10696 16.567078590393066 0.2925279140472412 281.5075378417969 0.15888801217079163 342.0520324707031 0.6551775336265564 0.81826884 0.17420394718647003 True -7 12224 16.54832434654236 0.29448843002319336 299.1054992675781 0.18971645832061768 341.4686584472656 0.6562814712524414 0.8226187 0.163282573223114 True -8 13752 16.53261089324951 0.29196715354919434 260.395751953125 0.10206232219934464 340.895751953125 0.6577999591827393 0.8247238 0.156280979514122 True -9 15280 16.562899112701416 0.2968013286590576 292.09808349609375 0.17423123121261597 340.2360534667969 0.6591569781303406 0.82632 0.1522054672241211 True -10 16808 16.566338539123535 0.29593610763549805 294.1885681152344 0.14799216389656067 339.58258056640625 0.6604802012443542 0.8272242 0.1494048684835434 True -11 18336 16.56156873703003 1.7286028861999512 321.3419189453125 0.14702022075653076 339.0580139160156 0.6620246767997742 0.83068407 0.14233796298503876 True -12 19864 16.56882119178772 0.29930806159973145 287.943359375 0.14897923171520233 338.4438781738281 0.663354218006134 0.83227175 0.13921666145324707 True -13 21392 16.53856348991394 0.30478549003601074 303.52508544921875 0.16782228648662567 337.92822265625 0.6644022464752197 0.8345208 0.13865308463573456 True -14 22920 16.57962727546692 0.3046600818634033 257.03314208984375 0.1206410676240921 337.7627868652344 0.6648630499839783 0.8348147 0.13710561394691467 True -15 24448 16.540897369384766 0.30269861221313477 263.550048828125 0.07391898334026337 337.68267822265625 0.6649588942527771 0.83682233 0.1384202092885971 True -16 25976 16.576102256774902 0.30464673042297363 271.58795166015625 0.1396898776292801 337.7995910644531 0.6645371913909912 0.8341066 0.13939832150936127 False -17 27504 16.540786266326904 0.3155064582824707 281.68084716796875 0.08824172616004944 338.0935974121094 0.6637352705001831 0.8321616 0.14297038316726685 False -18 29032 16.576497316360474 1.109151840209961 269.32763671875 0.09949691593647003 338.32763671875 0.6630092263221741 0.8305272 0.14470411837100983 False -19 30560 16.57037878036499 0.304823637008667 274.18304443359375 0.09707015752792358 338.50677490234375 0.6625786423683167 0.8306403 0.14512264728546143 False diff --git a/ENCSR533WFB/cherimoya.fold_2.performance.tsv b/ENCSR533WFB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d7c503885fc5e5243cf96de437899929b97fd4c7..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -337.68267822265625 0.27394846081733704 0.6649587750434875 0.2510046362876892 0.8368223309516907 0.7714588642120361 0.1384202092885971 \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_3.evaluate.json b/ENCSR533WFB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a7f9335431a1902c9c90b1e75617aff77437a54d..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF381NLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_3.fit.json b/ENCSR533WFB/cherimoya.fold_3.fit.json deleted file mode 100644 index 7530691eae164876f579a11c63edda5610eb8be9..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF381NLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_3.log b/ENCSR533WFB/cherimoya.fold_3.log deleted file mode 100644 index 7774160b0ff20f57abf164b84e154c58ab676a21..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1472 20.925848722457886 19.238182306289673 310.20166015625 0.2363763153553009 446.57806396484375 0.4947117269039154 0.6212588 14.679702758789062 True -1 2944 16.36963987350464 0.3606560230255127 274.8165283203125 0.20493200421333313 368.23846435546875 0.594468355178833 0.73664796 2.6521337032318115 True -2 4416 16.25766372680664 0.35628819465637207 291.27105712890625 0.265870600938797 347.5624084472656 0.6280045509338379 0.7415226 0.5004048943519592 True -3 5888 17.09260129928589 5.81647253036499 263.91876220703125 0.17569813132286072 339.54541015625 0.6415621638298035 0.766747 0.2413097620010376 True -4 7360 16.257663249969482 0.3165578842163086 292.95489501953125 0.16454076766967773 337.39892578125 0.6470789313316345 0.78059524 0.21270118653774261 True -5 8832 16.26063632965088 0.3179972171783447 298.84442138671875 0.1444571316242218 336.6175231933594 0.6492130756378174 0.7860851 0.1823708862066269 True -6 10304 16.256776094436646 0.31137561798095703 289.32513427734375 0.1616382896900177 336.467529296875 0.6494922041893005 0.7876506 0.1742728352546692 True -7 11776 16.259249687194824 0.3156626224517822 295.5205383300781 0.17025579512119293 335.6875915527344 0.6518766283988953 0.7852029 0.17065268754959106 False -8 13248 16.2531795501709 0.8949384689331055 295.57635498046875 0.11091894656419754 335.4074401855469 0.6529808640480042 0.78550845 0.1678096204996109 False -9 14720 16.25689125061035 0.5213272571563721 279.65460205078125 0.18666476011276245 334.8701171875 0.6541887521743774 0.78904015 0.16679801046848297 True -10 16192 16.20075297355652 0.30966830253601074 276.46337890625 0.11718863248825073 334.3687744140625 0.6555137038230896 0.7879346 0.16734546422958374 False -11 17664 16.2205331325531 0.41353654861450195 300.81427001953125 0.11229317635297775 334.0185241699219 0.6564986705780029 0.7898798 0.1655629426240921 True -12 19136 16.277300596237183 0.3100619316101074 302.7851867675781 0.15623146295547485 333.6280212402344 0.657606840133667 0.79403013 0.16432546079158783 True -13 20608 16.292180061340332 0.34274864196777344 284.2022705078125 0.1276930272579193 333.3016357421875 0.6583899855613708 0.7967544 0.1633332520723343 True -14 22080 16.254688024520874 0.31601715087890625 285.09344482421875 0.137131005525589 333.2462158203125 0.6585663557052612 0.79783505 0.16301123797893524 True -15 23552 16.232226133346558 0.3110065460205078 288.09454345703125 0.10244329273700714 333.1368713378906 0.6587284803390503 0.7986024 0.16200292110443115 True -16 25024 16.211371660232544 0.31394505500793457 309.802490234375 0.06611248850822449 333.33038330078125 0.6582870483398438 0.8010003 0.16231611371040344 True -17 26496 16.206388473510742 0.31404972076416016 285.6082763671875 0.072801873087883 333.57513427734375 0.6576278805732727 0.798682 0.16612176597118378 False -18 27968 16.23827362060547 1.1892802715301514 270.3521728515625 0.11230398714542389 333.86712646484375 0.6569523811340332 0.79979044 0.1686977595090866 False -19 29440 15.96453070640564 0.31496524810791016 265.16424560546875 0.07451450079679489 334.08367919921875 0.6565393209457397 0.7966582 0.16985152661800385 False diff --git a/ENCSR533WFB/cherimoya.fold_3.performance.tsv b/ENCSR533WFB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 661341881b2064d203eaa2cc4c5b81a9ddf8e9d3..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -333.33038330078125 0.2776791453361511 0.6582871079444885 0.2453317791223526 0.8010002970695496 0.7517051696777344 0.16231611371040344 \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_4.evaluate.json b/ENCSR533WFB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d3c282e63535df8923ca1b234cfa084c66ad3ff6..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF381NLQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_4.fit.json b/ENCSR533WFB/cherimoya.fold_4.fit.json deleted file mode 100644 index e29872e3c0b34da92b368b70294de4d86410cc51..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF381NLQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR533WFB/cherimoya.fold_4.log b/ENCSR533WFB/cherimoya.fold_4.log deleted file mode 100644 index c0487280e327fdbff9756ab859f38d881f8a320b..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1479 20.805954694747925 3.7053446769714355 302.7317199707031 0.21092863380908966 432.4460754394531 0.4947100877761841 0.6411362 14.508234024047852 True -1 2958 16.36239767074585 0.3114190101623535 300.96038818359375 0.2433820217847824 358.3788757324219 0.5918351411819458 0.74734414 2.153911828994751 True -2 4437 16.39686679840088 0.3148956298828125 297.65350341796875 0.20538446307182312 340.7395935058594 0.6243454813957214 0.77519685 0.6119015216827393 True -3 5916 16.340841054916382 0.2922995090484619 295.4596862792969 0.1840803176164627 332.2243957519531 0.6390541791915894 0.7975062 0.284950315952301 True -4 7395 16.357147693634033 0.2863907814025879 274.90460205078125 0.2005401998758316 330.12762451171875 0.6423327922821045 0.8040588 0.24672989547252655 True -5 8874 16.34516406059265 0.34883952140808105 280.6396484375 0.14735902845859528 329.10791015625 0.6444597244262695 0.8195011 0.15161453187465668 True -6 10353 16.35964012145996 0.28774499893188477 292.54254150390625 0.16273626685142517 328.51800537109375 0.6466039419174194 0.82165086 0.14196056127548218 True -7 11832 16.35409641265869 0.28754115104675293 301.91363525390625 0.226580411195755 328.21337890625 0.6472963690757751 0.82265735 0.13689233362674713 True -8 13311 16.086485147476196 0.2902705669403076 274.17669677734375 0.16336195170879364 327.64141845703125 0.6486416459083557 0.8308226 0.12464772164821625 True -9 14790 16.05876636505127 0.5629098415374756 292.80133056640625 0.19361832737922668 327.2953186035156 0.6496941447257996 0.83241415 0.12369505316019058 True -10 16269 16.036613702774048 0.3240842819213867 267.65252685546875 0.1547255516052246 326.88372802734375 0.6504135727882385 0.83668405 0.11841798573732376 True -11 17748 16.040358304977417 0.28366899490356445 273.1361389160156 0.0924522876739502 326.4539794921875 0.6516417264938354 0.8383425 0.12398312240839005 True -12 19227 16.041254997253418 0.28394222259521484 286.5580749511719 0.11809754371643066 325.9683837890625 0.6525934934616089 0.84123343 0.11352144181728363 True -13 20706 16.007043600082397 0.28450918197631836 290.7484130859375 0.09182213246822357 325.6143493652344 0.6534916758537292 0.8459133 0.10982122272253036 True -14 22185 16.04795527458191 0.2829756736755371 278.90283203125 0.08503253757953644 325.45257568359375 0.6539610028266907 0.84545606 0.10967446863651276 False -15 23664 16.078967094421387 0.28331756591796875 257.7952880859375 0.06865238398313522 325.34075927734375 0.6541275382041931 0.8463362 0.11160513013601303 True -16 25143 16.080856561660767 0.28891706466674805 273.44476318359375 0.09418727457523346 325.51385498046875 0.6538865566253662 0.8452496 0.11495040357112885 False -17 26622 16.089704036712646 0.2949976921081543 283.57135009765625 0.08068504929542542 325.67071533203125 0.6533586382865906 0.84352535 0.11779345571994781 False -18 28101 16.10441303253174 0.29012227058410645 269.4913024902344 0.09466510266065598 325.91241455078125 0.6526124477386475 0.84262866 0.12198872119188309 False -19 29580 16.061464309692383 0.9330620765686035 288.4703063964844 0.09772532433271408 326.1089782714844 0.6521661281585693 0.8409507 0.12289983779191971 False diff --git a/ENCSR533WFB/cherimoya.fold_4.performance.tsv b/ENCSR533WFB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 72f69c0c9a8353851e6d18448397407c2c7f9179..0000000000000000000000000000000000000000 --- a/ENCSR533WFB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -325.34075927734375 0.28044095635414124 0.6541275382041931 0.23997104167938232 0.8463361859321594 0.7743971943855286 0.11160513013601303 \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_0.evaluate.json b/ENCSR539WBA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 89a1032815eac91447430dceaf20475e0298f65b..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF858XXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_0.fit.json b/ENCSR539WBA/cherimoya.fold_0.fit.json deleted file mode 100644 index a0abd191974e2f461d754971999a2537873a4d37..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF858XXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_0.log b/ENCSR539WBA/cherimoya.fold_0.log deleted file mode 100644 index 2e16228e377aabf938ccd43245e3077c63de4e54..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2725 34.83401536941528 4.7293312549591064 960.6893310546875 0.8713008165359497 1119.4105224609375 0.3019947409629822 0.58977413 6.9039387702941895 True -1 5450 30.355715036392212 0.6199383735656738 639.6754760742188 1.1912412643432617 923.9529418945312 0.42169517278671265 0.6548159 3.7106902599334717 True -2 8175 30.346623182296753 0.6139335632324219 835.06005859375 1.0164599418640137 898.941162109375 0.434835821390152 0.655329 2.7296197414398193 True -3 10900 30.33133363723755 0.6208755970001221 701.544677734375 0.8767076730728149 875.6654663085938 0.44541189074516296 0.66472125 2.278935194015503 True -4 13625 30.323206424713135 0.6488020420074463 725.8375244140625 0.8732799291610718 857.221435546875 0.45444777607917786 0.6676723 2.008283853530884 True -5 16350 30.377467393875122 0.5964345932006836 820.3331298828125 1.027193307876587 848.3656616210938 0.4598498046398163 0.6752819 1.8090174198150635 True -6 19075 30.360227584838867 0.6088566780090332 768.688232421875 0.6287801861763 842.5369262695312 0.4631443917751312 0.67407215 1.4520409107208252 False -7 21800 30.39682650566101 0.5985338687896729 742.0067138671875 1.0703210830688477 835.432861328125 0.46845725178718567 0.67587566 1.3467580080032349 True -8 24525 30.340445041656494 0.6026458740234375 678.8292846679688 0.8619108200073242 827.98193359375 0.47351881861686707 0.6836665 1.2356654405593872 True -9 27250 30.326826333999634 0.5886819362640381 629.5476684570312 1.0292949676513672 822.8967895507812 0.47609207034111023 0.6907361 1.188567042350769 True -10 29975 30.369104623794556 0.5966854095458984 559.2601318359375 0.860804557800293 817.609619140625 0.4791228175163269 0.7001786 1.2010364532470703 True -11 32700 30.339481592178345 0.5941126346588135 771.3358764648438 0.9007135629653931 810.7720336914062 0.48432114720344543 0.7075143 1.1050355434417725 True -12 35425 30.471298694610596 0.6163985729217529 598.435791015625 0.8494677543640137 800.9754638671875 0.4904569387435913 0.7158425 1.0130788087844849 True -13 38150 30.465030431747437 0.6107118129730225 540.0142822265625 0.7425782680511475 798.137939453125 0.49145373702049255 0.7256419 0.8968141674995422 True -14 40875 30.493609189987183 0.6104695796966553 663.093994140625 0.589163064956665 793.3394775390625 0.4940347373485565 0.7342176 0.7673579454421997 True -15 43600 30.422950983047485 0.8497631549835205 684.4051513671875 0.8406847715377808 787.9260864257812 0.49861565232276917 0.74137354 0.6913775205612183 True -16 46325 30.48462462425232 0.620577335357666 624.256103515625 0.5866531133651733 784.3689575195312 0.501994252204895 0.7479434 0.6344286799430847 True -17 49050 30.4685800075531 0.619133710861206 753.3792724609375 0.6055786609649658 785.9404296875 0.5001726746559143 0.75058365 0.6057348251342773 True -18 51775 30.669180393218994 20.447970867156982 660.0354614257812 0.7406499981880188 785.7620239257812 0.5009288191795349 0.7499289 0.59847491979599 False -19 54500 31.05309224128723 0.6042404174804688 658.3670654296875 0.5004296898841858 786.470947265625 0.5000965595245361 0.74968046 0.5936569571495056 False diff --git a/ENCSR539WBA/cherimoya.fold_0.performance.tsv b/ENCSR539WBA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 20f3bb43500a4b29823711d719679924c8b3bda5..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -785.9404296875 0.3190411329269409 0.5001726150512695 0.22028803825378418 0.7505836486816406 0.6852352619171143 0.6057348251342773 \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_1.evaluate.json b/ENCSR539WBA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 208745fe5ddc89a90a6ae006a8d2e96928f4da77..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF858XXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_1.fit.json b/ENCSR539WBA/cherimoya.fold_1.fit.json deleted file mode 100644 index 411963b14406240c9aa94d40da9d2e783f580fff..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF858XXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_1.log b/ENCSR539WBA/cherimoya.fold_1.log deleted file mode 100644 index 493ae4e71c111320806a251085979de903969d8d..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 34.569047689437866 3.8929553031921387 927.1727294921875 0.7259517312049866 1347.531005859375 0.30166950821876526 0.60143876 7.952386856079102 True -1 5406 30.09499478340149 0.8812835216522217 868.8345947265625 0.9261394739151001 1096.184326171875 0.4315814971923828 0.66912127 5.16787576675415 True -2 8109 30.102078199386597 0.7394299507141113 712.1988525390625 0.6403089165687561 1073.968994140625 0.4428171217441559 0.6713188 3.477924108505249 True -3 10812 30.121716022491455 0.7336757183074951 617.7113037109375 1.0457849502563477 1043.9888916015625 0.4546106159687042 0.68308055 2.640892744064331 True -4 13515 30.31173014640808 0.7508838176727295 651.0851440429688 0.5210683345794678 1018.712890625 0.4650219976902008 0.6896545 2.0899198055267334 True -5 16218 30.087759256362915 0.7412188053131104 811.5623779296875 1.1793653964996338 1006.385498046875 0.4724123477935791 0.68923587 1.8742315769195557 False -6 18921 30.120587825775146 0.725999116897583 783.7569580078125 0.7109088897705078 998.1099243164062 0.47525715827941895 0.6928098 1.7589986324310303 True -7 21624 30.060800790786743 0.7338395118713379 830.519775390625 0.8976775407791138 985.0652465820312 0.4829949736595154 0.70052165 1.4396473169326782 True -8 24327 30.118852853775024 0.7329630851745605 703.248291015625 0.7533461451530457 978.9609375 0.48693951964378357 0.7099703 1.43093740940094 True -9 27030 30.07256531715393 0.7220301628112793 834.9483642578125 0.9323136806488037 968.4400024414062 0.49154436588287354 0.7177904 1.3728941679000854 True -10 29733 30.103943347930908 0.7309410572052002 516.4609375 0.8772380352020264 959.08740234375 0.4967100918292999 0.7223296 1.4457991123199463 True -11 32436 30.152952432632446 0.7358570098876953 646.2189331054688 0.8526649475097656 950.2939453125 0.5006290674209595 0.730297 1.211969256401062 True -12 35139 30.089277982711792 1.6745445728302002 568.097900390625 0.7185830473899841 946.212646484375 0.5010232925415039 0.7393888 1.1517291069030762 True -13 37842 30.173997402191162 0.7602732181549072 534.590576171875 0.7450791597366333 934.5610961914062 0.5069924592971802 0.75102144 0.9676137566566467 True -14 40545 30.122747898101807 0.7744531631469727 582.518798828125 0.973312258720398 927.5588989257812 0.5110793709754944 0.75704116 0.8712717890739441 True -15 43248 30.141401529312134 0.7379162311553955 740.5103759765625 0.6779442429542542 924.779541015625 0.5101515650749207 0.7638134 0.7498049139976501 True -16 45951 30.16814684867859 0.77402663230896 711.1771240234375 0.6172440648078918 920.0411376953125 0.5128509998321533 0.7690278 0.6855699419975281 True -17 48654 30.563739776611328 0.7304737567901611 595.610107421875 0.5995559692382812 914.9624633789062 0.5169466733932495 0.77208316 0.6424794793128967 True -18 51357 30.164543390274048 0.7433905601501465 645.8157958984375 0.6639840006828308 916.1135864257812 0.515051007270813 0.77428776 0.6224316954612732 True -19 54060 30.15587043762207 0.7468996047973633 483.6440734863281 0.6228656768798828 919.2454223632812 0.5125995874404907 0.77249736 0.6163541078567505 False diff --git a/ENCSR539WBA/cherimoya.fold_1.performance.tsv b/ENCSR539WBA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d54752fed1ec337e42aae43bf16a90c86c62888d..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -916.1135864257812 0.3030344247817993 0.515051007270813 0.24527306854724884 0.774287760257721 0.7323417663574219 0.6224316954612732 \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_2.evaluate.json b/ENCSR539WBA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ec3f9766e16d01e14af5b0acd7229f3b6fb28fb2..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF858XXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_2.fit.json b/ENCSR539WBA/cherimoya.fold_2.fit.json deleted file mode 100644 index 7cd78da5649b94897a67d254b72e40cb50229201..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF858XXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_2.log b/ENCSR539WBA/cherimoya.fold_2.log deleted file mode 100644 index 7a8b75e0bff7f36bbe9dac59ba6804a04232e97b..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 36.58228874206543 3.8894004821777344 747.9025268554688 0.8727337121963501 1185.583251953125 0.31223127245903015 0.58935636 6.433857440948486 True -1 5784 32.53362822532654 0.5850532054901123 823.7039794921875 0.8672060370445251 972.9554443359375 0.43205976486206055 0.6428229 4.677946090698242 True -2 8676 32.26209354400635 0.5886471271514893 846.4888305664062 0.9045855402946472 955.8948364257812 0.43745729327201843 0.65893936 2.684941530227661 True -3 11568 31.85856032371521 0.5678081512451172 838.5363159179688 1.2121763229370117 935.7205200195312 0.44781824946403503 0.66317755 2.6543381214141846 True -4 14460 31.518330812454224 0.5672619342803955 730.393798828125 0.8360176682472229 917.7892456054688 0.4557945430278778 0.6750652 1.8165501356124878 True -5 17352 31.586249113082886 0.5713739395141602 870.0106201171875 0.9532725214958191 906.83837890625 0.4614897072315216 0.6734185 1.6994214057922363 False -6 20244 31.525959491729736 0.5601906776428223 720.8167114257812 0.6623976230621338 897.159423828125 0.4674190580844879 0.6742871 1.7479280233383179 False -7 23136 31.527445316314697 0.5682780742645264 883.9109497070312 1.036106824874878 890.05712890625 0.47202685475349426 0.68180287 1.7812516689300537 True -8 26028 31.543277263641357 0.5593395233154297 717.5138549804688 0.8154332637786865 881.4155883789062 0.4789452850818634 0.68414044 1.6126797199249268 True -9 28920 31.520787239074707 0.5709528923034668 992.4577026367188 1.24226975440979 874.437744140625 0.48213398456573486 0.6898879 1.390231728553772 True -10 31812 31.52550506591797 0.5756113529205322 570.625 0.818313479423523 866.4467163085938 0.485790878534317 0.70032 1.2933087348937988 True -11 34704 31.596803426742554 0.5718719959259033 614.1163330078125 0.6470295190811157 856.10205078125 0.4931420683860779 0.7095648 1.1119993925094604 True -12 37596 31.60738253593445 0.563377857208252 590.38916015625 0.6975910067558289 849.8157958984375 0.4968779385089874 0.71583873 1.0167299509048462 True -13 40488 31.607733726501465 0.5712928771972656 618.222900390625 1.0089187622070312 846.2650756835938 0.49735480546951294 0.7216133 0.8927258849143982 True -14 43380 31.507194995880127 0.5695450305938721 624.4253540039062 0.5762708187103271 840.3487548828125 0.5010860562324524 0.7286977 0.7884969115257263 True -15 46272 31.497304677963257 2.5321788787841797 832.1761474609375 0.5232699513435364 836.2247924804688 0.5040051937103271 0.73573655 0.7144657969474792 True -16 49164 31.573259353637695 0.621910810470581 691.393798828125 0.5524160861968994 832.9226684570312 0.5053856372833252 0.73957783 0.68560391664505 True -17 52056 31.74122977256775 0.586514949798584 536.9456787109375 0.48109135031700134 833.2861938476562 0.505482017993927 0.7424375 0.644563615322113 True -18 54948 31.608691453933716 0.5771818161010742 584.0589599609375 0.4754785895347595 834.5534057617188 0.5055322051048279 0.7418411 0.6354085206985474 False -19 57840 31.54724097251892 0.5833015441894531 459.3717346191406 0.6761982440948486 834.7210083007812 0.5050833225250244 0.74130404 0.6345572471618652 False diff --git a/ENCSR539WBA/cherimoya.fold_2.performance.tsv b/ENCSR539WBA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1b334aaaaaf5a1d3720a4cc6b5b67be048308e6b..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -833.2861938476562 0.31327012181282043 0.505482017993927 0.22978618741035461 0.742437481880188 0.6880282163619995 0.644563615322113 \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_3.evaluate.json b/ENCSR539WBA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 15542b2146034501fc4635652f78825cadc6b128..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF858XXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_3.fit.json b/ENCSR539WBA/cherimoya.fold_3.fit.json deleted file mode 100644 index cdceca76c1f090bff2c951d536a0826a7f3edde6..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF858XXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_3.log b/ENCSR539WBA/cherimoya.fold_3.log deleted file mode 100644 index fa3a3e33bd445ae2683722965756887a13731772..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 35.65935468673706 3.871384859085083 753.5322265625 1.2569355964660645 1118.40576171875 0.3115888237953186 0.60741574 8.815874099731445 True -1 5528 30.800623178482056 0.5979197025299072 771.0399169921875 0.8967798948287964 922.864013671875 0.4284624457359314 0.6638596 4.023214340209961 True -2 8292 30.894723176956177 0.5804262161254883 691.479248046875 0.9452792406082153 908.5307006835938 0.43357765674591064 0.6797933 2.3321776390075684 True -3 11056 30.743409633636475 0.5537261962890625 777.5139770507812 0.8401138782501221 882.5147705078125 0.4474131166934967 0.6863814 2.6352651119232178 True -4 13820 30.791566371917725 0.5659377574920654 723.6400146484375 0.9834452867507935 872.4544677734375 0.4509356915950775 0.6878412 1.7400461435317993 True -5 16584 30.735700368881226 0.5716919898986816 651.3429565429688 0.9036271572113037 857.9788818359375 0.46000394225120544 0.69021106 1.6769859790802002 True -6 19348 30.7527596950531 1.5193147659301758 632.6835327148438 0.9447712898254395 851.9197998046875 0.4646526277065277 0.69936186 1.44730544090271 True -7 22112 30.827574014663696 0.5957949161529541 710.3331298828125 0.7603490352630615 841.4978637695312 0.4702240526676178 0.7009414 1.4047341346740723 True -8 24876 30.34335160255432 0.5479705333709717 835.5822143554688 1.1916499137878418 832.9463500976562 0.47618362307548523 0.70646644 1.3026256561279297 True -9 27640 30.103917360305786 0.5496456623077393 765.890380859375 0.8081675171852112 823.3076171875 0.48260948061943054 0.7130873 1.2116780281066895 True -10 30404 30.056118965148926 0.5740034580230713 633.272216796875 0.6688605546951294 819.3873291015625 0.4856557250022888 0.72301185 1.2334333658218384 True -11 33168 30.079021453857422 0.5588414669036865 717.1905517578125 0.7352901101112366 812.64501953125 0.4885883629322052 0.728946 1.135930061340332 True -12 35932 30.16115927696228 1.8503551483154297 625.2373046875 0.7767770886421204 808.6682739257812 0.48961466550827026 0.7376496 1.024549126625061 True -13 38696 30.12190818786621 0.5414729118347168 809.4259033203125 0.6862278580665588 800.6624755859375 0.49652227759361267 0.7452803 0.9081709980964661 True -14 41460 30.14560055732727 0.5748963356018066 645.4240112304688 0.5065452456474304 795.1758422851562 0.49907758831977844 0.75197774 0.803203821182251 True -15 44224 30.19285225868225 0.5710844993591309 781.82568359375 0.7501480579376221 791.4342651367188 0.4991225302219391 0.76078373 0.7196424603462219 True -16 46988 30.18485951423645 0.5691530704498291 676.9329833984375 0.7900422811508179 788.4705810546875 0.5035937428474426 0.7648899 0.6533557772636414 True -17 49752 30.178516387939453 0.5591981410980225 729.365478515625 0.6571415662765503 787.9498291015625 0.5031113028526306 0.76624775 0.6137212514877319 True -18 52516 30.134204149246216 0.5753662586212158 601.1328125 0.4023416042327881 789.3392333984375 0.5025929808616638 0.76526576 0.6022801399230957 False -19 55280 30.097150802612305 0.5901379585266113 708.0901489257812 0.7079368829727173 791.6213989257812 0.499906063079834 0.76422155 0.6027488112449646 False diff --git a/ENCSR539WBA/cherimoya.fold_3.performance.tsv b/ENCSR539WBA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 480413a76ad49bde7785c716949030c90a251d79..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -787.9498291015625 0.3167210519313812 0.5031113624572754 0.22530071437358856 0.7662477493286133 0.7036142349243164 0.6137212514877319 \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_4.evaluate.json b/ENCSR539WBA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 004e509b2246b8550d1f1558c4351e8c1c2cff9e..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF858XXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_4.fit.json b/ENCSR539WBA/cherimoya.fold_4.fit.json deleted file mode 100644 index 525a2ecddac48722677b018e75417ceca0ded601..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF858XXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR539WBA/cherimoya.fold_4.log b/ENCSR539WBA/cherimoya.fold_4.log deleted file mode 100644 index 448d8f34c6e1cd36ee95703cf1dde59bed3ec021..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2820 36.21890926361084 3.9268462657928467 766.9956665039062 1.2111334800720215 1056.48486328125 0.30186545848846436 0.58277273 6.619998455047607 True -1 5640 31.451277017593384 1.905608892440796 680.9738159179688 1.5732773542404175 874.5370483398438 0.41947057843208313 0.63888425 4.079901218414307 True -2 8460 31.539844512939453 0.6027212142944336 502.937744140625 0.8952324390411377 861.3026123046875 0.4282657504081726 0.6429285 2.441852569580078 True -3 11280 31.65363097190857 0.6170051097869873 678.178466796875 0.7893656492233276 836.4326171875 0.44140952825546265 0.6550343 1.9755820035934448 True -4 14100 31.56918954849243 0.6224350929260254 655.5596313476562 0.7886185050010681 820.5984497070312 0.4519720673561096 0.6581131 1.3898001909255981 True -5 16920 31.56885313987732 0.6129229068756104 845.6543579101562 0.8240801095962524 814.0667724609375 0.45508044958114624 0.66172075 1.2152098417282104 True -6 19740 31.528188705444336 0.5975437164306641 723.6990966796875 1.1234614849090576 806.3826904296875 0.46207085251808167 0.6591836 1.210236668586731 False -7 22560 31.52440333366394 0.5925946235656738 566.40185546875 0.7345543503761292 801.46044921875 0.464840292930603 0.6644159 1.299971580505371 True -8 25380 31.41630721092224 0.5871326923370361 743.5693359375 0.9533259868621826 794.1629638671875 0.46947309374809265 0.6697791 1.2182811498641968 True -9 28200 31.290977716445923 1.185638427734375 603.9593505859375 0.47794967889785767 789.3560791015625 0.4739823639392853 0.67619944 1.203704595565796 True -10 31020 30.75374484062195 20.584516286849976 684.0157470703125 0.7785813808441162 785.3407592773438 0.47603872418403625 0.6826468 1.0990989208221436 True -11 33840 31.18515181541443 1.149766206741333 535.3126220703125 0.7428079843521118 780.8128662109375 0.47790247201919556 0.69167244 1.0894381999969482 True -12 36660 30.979124546051025 1.6303176879882812 513.7072143554688 0.5937741994857788 771.5621337890625 0.4863235354423523 0.6969544 0.9662677049636841 True -13 39480 30.832700490951538 0.6595361232757568 569.1612548828125 0.5997169017791748 766.796142578125 0.48898375034332275 0.70531857 0.8832218050956726 True -14 42300 30.92513418197632 0.5938453674316406 594.0291748046875 0.6501392126083374 762.7615356445312 0.4913957118988037 0.715964 0.7706637978553772 True -15 45120 30.799591064453125 0.588653564453125 573.218017578125 0.4833064675331116 756.1771850585938 0.4963771104812622 0.72264826 0.6997369527816772 True -16 47940 30.86733078956604 0.5947937965393066 531.017578125 0.759462833404541 755.8040771484375 0.4959243834018707 0.7292497 0.6404219269752502 True -17 50760 30.92066478729248 0.5877947807312012 676.443603515625 0.5495704412460327 755.3547973632812 0.4951815605163574 0.73291665 0.6142348647117615 True -18 53580 30.90133571624756 0.59309983253479 533.11279296875 0.3864515721797943 755.104736328125 0.49541348218917847 0.73278356 0.6013543605804443 False -19 56400 30.84460759162903 0.5982365608215332 491.83233642578125 0.42416712641716003 753.69921875 0.4975675940513611 0.7326529 0.5998715162277222 False diff --git a/ENCSR539WBA/cherimoya.fold_4.performance.tsv b/ENCSR539WBA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b8f68231d29a029ef79bce86d59d97151ee10a56..0000000000000000000000000000000000000000 --- a/ENCSR539WBA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -755.3547973632812 0.3219678997993469 0.49518153071403503 0.21985527873039246 0.7329166531562805 0.6654066443443298 0.6142348647117615 \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_0.evaluate.json b/ENCSR540BML/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 322637cc9bb3a1b3c84d59b13c56c04289c5388a..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326AQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_0.fit.json b/ENCSR540BML/cherimoya.fold_0.fit.json deleted file mode 100644 index ba328e13bf6fbba5d55e5c3692e0038145a368a2..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF326AQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_0.log b/ENCSR540BML/cherimoya.fold_0.log deleted file mode 100644 index 06b7ba9612bdcc8f1eff56741b3068b21ff726e3..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2141 27.441134691238403 3.327382802963257 385.5419616699219 0.4392402768135071 496.8718566894531 0.5450437068939209 0.6915864 8.648773193359375 True -1 4282 23.826602935791016 0.43596720695495605 379.76446533203125 0.3031943440437317 425.8354797363281 0.6294552087783813 0.76589394 1.1195014715194702 True -2 6423 23.86251449584961 0.4211881160736084 304.5017395019531 0.4388597309589386 411.86407470703125 0.6478957533836365 0.7815371 0.4520387053489685 True -3 8564 23.857242107391357 0.41848111152648926 359.3904724121094 0.30352190136909485 406.2040710449219 0.6557149291038513 0.79246575 0.3790128827095032 True -4 10705 23.812278747558594 0.4157562255859375 395.8890075683594 0.36349955201148987 404.52032470703125 0.6577185988426208 0.7967966 0.2953355610370636 True -5 12846 23.815619230270386 0.41767430305480957 357.00750732421875 0.3001369833946228 403.1941223144531 0.6596893668174744 0.80047935 0.31102240085601807 True -6 14987 23.824910402297974 0.414975643157959 330.70513916015625 0.28655678033828735 401.2099914550781 0.6629549860954285 0.8079689 0.2625282406806946 True -7 17128 23.744477033615112 0.41466522216796875 294.4739685058594 0.28375357389450073 399.8802185058594 0.6650688052177429 0.80732536 0.25697946548461914 False -8 19269 23.833715200424194 0.4176669120788574 333.02166748046875 0.280077189207077 399.01141357421875 0.6665501594543457 0.8079079 0.24700960516929626 False -9 21410 23.80238914489746 0.48910069465637207 355.46319580078125 0.27538228034973145 398.1434631347656 0.6679521799087524 0.8106895 0.24219833314418793 True -10 23551 23.768261432647705 0.42053675651550293 299.80975341796875 0.32052043080329895 397.2139587402344 0.6693750023841858 0.8130214 0.23585271835327148 True -11 25692 23.771774768829346 0.4165503978729248 337.5030517578125 0.2407575249671936 396.63922119140625 0.670508623123169 0.8167201 0.23550640046596527 True -12 27833 23.770456552505493 0.4138906002044678 342.87335205078125 0.23553839325904846 395.9162292480469 0.6719141602516174 0.81973165 0.24079500138759613 True -13 29974 23.771770477294922 0.41309285163879395 368.0013427734375 0.21569925546646118 395.458740234375 0.6727768182754517 0.82324266 0.23347924649715424 True -14 32115 23.77919054031372 2.4992921352386475 346.5909423828125 0.28739866614341736 395.094970703125 0.6736247539520264 0.82823545 0.22979134321212769 True -15 34256 23.85574245452881 0.43543195724487305 352.6138000488281 0.18403369188308716 394.9034118652344 0.6738817095756531 0.8280739 0.2349030077457428 False -16 36397 23.84834861755371 0.4219069480895996 352.8537902832031 0.2194608449935913 395.1053771972656 0.6736763715744019 0.8291718 0.23566345870494843 True -17 38538 24.09778928756714 6.391459226608276 348.837890625 0.16709360480308533 395.4329528808594 0.6730625033378601 0.8258946 0.24028398096561432 False -18 40679 23.85926342010498 0.42902183532714844 331.06640625 0.1756114512681961 395.8680419921875 0.6723950505256653 0.82285786 0.2446867972612381 False -19 42820 23.860563039779663 0.4245622158050537 361.1568603515625 0.15750211477279663 396.01495361328125 0.6720098853111267 0.82062536 0.24948641657829285 False diff --git a/ENCSR540BML/cherimoya.fold_0.performance.tsv b/ENCSR540BML/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f9a9cce1acf91e0932300724bc8d10168a1fa77d..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -395.1053771972656 0.2622493803501129 0.6736763715744019 0.2800312936306 0.8291717767715454 0.7655067443847656 0.23566345870494843 \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_1.evaluate.json b/ENCSR540BML/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3857f6a97972b412f9aa2014a4097b63e8dd3ba8..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326AQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_1.fit.json b/ENCSR540BML/cherimoya.fold_1.fit.json deleted file mode 100644 index a7d91fb27acaca844cec7b44408962a07fb50e2f..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF326AQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_1.log b/ENCSR540BML/cherimoya.fold_1.log deleted file mode 100644 index 6ccbd0692235927ca455cb352f1d539de84194fa..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2097 26.926942348480225 3.469214677810669 369.3485412597656 0.38056397438049316 561.38720703125 0.5563169717788696 0.65527713 7.761431694030762 True -1 4194 23.081196784973145 0.5751211643218994 361.94171142578125 0.4694820046424866 478.24908447265625 0.6441514492034912 0.7385497 1.4357316493988037 True -2 6291 23.16080141067505 0.5620474815368652 337.3399353027344 0.27298325300216675 455.347412109375 0.673774242401123 0.7755646 0.5218090415000916 True -3 8388 23.081884622573853 0.5577609539031982 377.72760009765625 0.35140448808670044 448.8126220703125 0.6805916428565979 0.78651255 0.3708145022392273 True -4 10485 23.091211557388306 0.5591247081756592 292.9754638671875 0.3388568162918091 445.73663330078125 0.6849417686462402 0.7976723 0.3429114520549774 True -5 12582 23.099063396453857 0.5602078437805176 350.18328857421875 0.23453573882579803 443.8216247558594 0.6871091723442078 0.8007039 0.29790717363357544 True -6 14679 23.06093716621399 3.7731544971466064 324.55047607421875 0.35584786534309387 442.46331787109375 0.6891195178031921 0.80481774 0.28862905502319336 True -7 16776 23.14256739616394 0.5589849948883057 349.4101257324219 0.3927300274372101 441.07086181640625 0.6912311911582947 0.8096274 0.2699974477291107 True -8 18873 23.110739946365356 0.5624110698699951 321.8914794921875 0.25003159046173096 440.00762939453125 0.692530632019043 0.81401265 0.26064449548721313 True -9 20970 23.029271125793457 1.2112340927124023 344.4658203125 0.2855769991874695 439.2255554199219 0.6938151717185974 0.816166 0.27152204513549805 True -10 23067 23.101435661315918 1.4973154067993164 368.78533935546875 0.39438048005104065 438.1502380371094 0.6956671476364136 0.81812865 0.2663472294807434 True -11 25164 23.094231128692627 0.5712692737579346 298.33306884765625 0.4295841455459595 437.2215270996094 0.6971418261528015 0.82106763 0.25874266028404236 True -12 27261 23.192466020584106 5.820565700531006 321.19921875 0.24261927604675293 436.4940185546875 0.6982782483100891 0.82634604 0.25881409645080566 True -13 29358 23.132152318954468 0.5592374801635742 331.53607177734375 0.31844472885131836 435.83209228515625 0.6991021037101746 0.8281848 0.2507408559322357 True -14 31455 23.117344856262207 0.56589674949646 318.87860107421875 0.21717041730880737 435.4560546875 0.6998845338821411 0.8321274 0.2470782846212387 True -15 33552 23.029348611831665 0.553774356842041 344.017822265625 0.11338935792446136 435.2383728027344 0.7003882527351379 0.83448017 0.24727989733219147 True -16 35649 23.06105947494507 1.0937714576721191 329.57525634765625 0.159899041056633 435.51239013671875 0.6999236941337585 0.83486474 0.250512957572937 True -17 37746 23.024781703948975 0.5612902641296387 323.0433349609375 0.15593202412128448 436.01312255859375 0.6991811394691467 0.83237123 0.25527423620224 False -18 39843 23.03292441368103 0.5555202960968018 326.830810546875 0.12821213901042938 436.54693603515625 0.6983041167259216 0.82788754 0.26109883189201355 False -19 41940 23.043235301971436 0.5554194450378418 320.8632507324219 0.0876430869102478 436.8448486328125 0.6977590918540955 0.82459456 0.26479828357696533 False diff --git a/ENCSR540BML/cherimoya.fold_1.performance.tsv b/ENCSR540BML/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 462d614e57637815492957c37fe2e1057e2e1086..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -435.51239013671875 0.24342580139636993 0.6999236941337585 0.3090902864933014 0.8348647356033325 0.8039440512657166 0.250512957572937 \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_2.evaluate.json b/ENCSR540BML/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 37546b106ea900cd8433b5f1cdd2475281838b0d..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326AQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_2.fit.json b/ENCSR540BML/cherimoya.fold_2.fit.json deleted file mode 100644 index 63ffb125e84470c273e11154ebaea5d1c43873ea..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF326AQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_2.log b/ENCSR540BML/cherimoya.fold_2.log deleted file mode 100644 index 3934432e70df62d57ccb5521a700f3ef96109f32..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2244 28.97191834449768 3.7856950759887695 342.28436279296875 0.39667272567749023 515.2855834960938 0.557144284248352 0.67040014 6.658508777618408 True -1 4488 24.92242455482483 0.44779157638549805 341.35137939453125 0.47382670640945435 444.70843505859375 0.638348400592804 0.7579078 1.1281037330627441 True -2 6732 24.92328190803528 0.427196741104126 326.2017822265625 0.3904535472393036 427.95770263671875 0.6604920625686646 0.78311616 0.41783443093299866 True -3 8976 24.93682599067688 0.4368109703063965 337.768310546875 0.3633476495742798 422.5665283203125 0.6670117974281311 0.794709 0.3355998694896698 True -4 11220 24.926612377166748 0.43552255630493164 332.7005310058594 0.3157341480255127 421.3408203125 0.6683900952339172 0.79994315 0.31510719656944275 True -5 13464 24.87518310546875 0.4312746524810791 341.81732177734375 0.2764475643634796 420.2448425292969 0.6705538630485535 0.7991557 0.29799169301986694 False -6 15708 24.883599281311035 21.19589900970459 344.66156005859375 0.4124940037727356 419.4463806152344 0.6714186668395996 0.80648464 0.3152531683444977 True -7 17952 25.38002920150757 0.44588255882263184 345.2435302734375 0.1922963261604309 417.5290832519531 0.6744085550308228 0.80933094 0.29141172766685486 True -8 20196 25.572417736053467 2.333109140396118 325.71337890625 0.3774999678134918 416.5597839355469 0.6758692264556885 0.80984277 0.27104127407073975 True -9 22440 24.989621877670288 0.43451523780822754 353.6205749511719 0.22222575545310974 415.7384033203125 0.6775022745132446 0.81344306 0.2792956531047821 True -10 24684 25.73198366165161 10.042022466659546 353.2767333984375 0.2743357717990875 414.6697692871094 0.679029643535614 0.81915987 0.27279287576675415 True -11 26928 25.78978419303894 0.43990564346313477 285.54168701171875 0.29160022735595703 413.5835876464844 0.6809244155883789 0.8222136 0.2709754705429077 True -12 29172 25.063650369644165 0.4313547611236572 367.83734130859375 0.2350746989250183 412.9222106933594 0.6818469166755676 0.82406235 0.26779115200042725 True -13 31416 25.02940273284912 0.431323766708374 327.38995361328125 0.20522846281528473 412.32977294921875 0.6827907562255859 0.82693523 0.26116323471069336 True -14 33660 25.03336477279663 0.43230676651000977 316.89263916015625 0.2055974006652832 411.98651123046875 0.6834946870803833 0.8307009 0.25538429617881775 True -15 35904 25.030741453170776 0.4779024124145508 317.6457214355469 0.24697056412696838 411.907958984375 0.6837621927261353 0.8317473 0.25542736053466797 True -16 38148 25.06319808959961 0.4500865936279297 298.2084045410156 0.18594878911972046 412.1002502441406 0.6835104823112488 0.8309291 0.2542690336704254 False -17 40392 25.048146724700928 0.4442462921142578 319.62200927734375 0.2197759598493576 412.3193664550781 0.6828509569168091 0.8276364 0.25717300176620483 False -18 42636 25.092722415924072 1.3944013118743896 332.63763427734375 0.19321304559707642 412.707275390625 0.6821761727333069 0.82421327 0.26017695665359497 False -19 44880 25.036317825317383 2.028182029724121 340.58929443359375 0.14118143916130066 412.9781494140625 0.6817610859870911 0.8232362 0.2616712749004364 False diff --git a/ENCSR540BML/cherimoya.fold_2.performance.tsv b/ENCSR540BML/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 96819db03f3b3a19c07188aa326d58f350a14e8c..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -411.907958984375 0.25487643480300903 0.6837621331214905 0.2931174337863922 0.83174729347229 0.7825500965118408 0.25542736053466797 \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_3.evaluate.json b/ENCSR540BML/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a8030df7776d7dd4c94e4dd9c122143e891774fe..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326AQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_3.fit.json b/ENCSR540BML/cherimoya.fold_3.fit.json deleted file mode 100644 index 229ba493385ec1f89f60982670adc2ca783723a2..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF326AQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_3.log b/ENCSR540BML/cherimoya.fold_3.log deleted file mode 100644 index 9144b917f8917bdc6b8d46fab83cca80bd0bde50..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2177 27.89810347557068 3.3289198875427246 388.2001647949219 0.4702029228210449 502.2075500488281 0.5461698770523071 0.68829995 7.97366189956665 True -1 4354 24.204484224319458 0.43105363845825195 345.7889709472656 0.384368360042572 429.84881591796875 0.6286213994026184 0.76692986 1.3082524538040161 True -2 6531 24.024404287338257 0.4242868423461914 398.25201416015625 0.3249672055244446 413.1484069824219 0.6519408822059631 0.7877873 0.4126833975315094 True -3 8708 24.01828670501709 0.4201192855834961 346.998291015625 0.48925328254699707 408.398193359375 0.6581519842147827 0.7996611 0.35080984234809875 True -4 10885 24.055434703826904 0.4198610782623291 342.8218078613281 0.3241752088069916 406.9310607910156 0.6598766446113586 0.80699354 0.2710925340652466 True -5 13062 23.995327949523926 0.41935205459594727 375.32568359375 0.3776843547821045 405.7039489746094 0.6619554162025452 0.809326 0.2588628828525543 True -6 15239 24.002551317214966 0.41681814193725586 308.2783508300781 0.26478010416030884 404.78814697265625 0.6635561585426331 0.8106773 0.2591768503189087 True -7 17416 23.9255428314209 0.4218177795410156 372.6716613769531 0.23767830431461334 403.7041015625 0.664966881275177 0.8079051 0.25969398021698 False -8 19593 23.97050642967224 0.4189486503601074 363.69854736328125 0.3074913024902344 403.0399475097656 0.6663236618041992 0.8116843 0.25391992926597595 True -9 21770 23.993422508239746 0.41935110092163086 312.04986572265625 0.35368818044662476 402.18572998046875 0.6677637100219727 0.811707 0.2546621263027191 True -10 23947 23.981165409088135 0.41533994674682617 374.60064697265625 0.27593010663986206 401.2603454589844 0.6691515445709229 0.81255364 0.25445714592933655 True -11 26124 24.011757850646973 1.4238479137420654 298.58905029296875 0.27147945761680603 400.51025390625 0.670595109462738 0.813737 0.2550140917301178 True -12 28301 24.11643147468567 0.4202587604522705 308.87890625 0.19985204935073853 399.788330078125 0.6723110675811768 0.81968343 0.25419187545776367 True -13 30478 23.994786739349365 0.4148247241973877 371.6632080078125 0.19075307250022888 399.2443542480469 0.6731495261192322 0.82002366 0.25315892696380615 True -14 32655 23.995856761932373 0.4181020259857178 327.20831298828125 0.21545156836509705 398.7638244628906 0.6739846467971802 0.82338053 0.25052201747894287 True -15 34832 24.019033908843994 4.9936957359313965 338.65472412109375 0.2920764684677124 398.7093505859375 0.6745414137840271 0.82467335 0.25158601999282837 True -16 37009 24.390281677246094 0.4159581661224365 331.7442321777344 0.19449880719184875 398.77520751953125 0.674209475517273 0.8257374 0.25461748242378235 True -17 39186 23.953250408172607 0.41382265090942383 316.780517578125 0.12998124957084656 398.9988098144531 0.6737418174743652 0.8231908 0.258055180311203 False -18 41363 23.969098806381226 0.41364264488220215 329.80523681640625 0.12860211730003357 399.5228271484375 0.6729142069816589 0.8189292 0.2642233669757843 False -19 43540 24.008060932159424 0.4129810333251953 331.14404296875 0.0939791277050972 399.6190490722656 0.6726084351539612 0.81692713 0.26633143424987793 False diff --git a/ENCSR540BML/cherimoya.fold_3.performance.tsv b/ENCSR540BML/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 586cf3e8d43a034f30d97c0bb3e5e05b2c1b92e1..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -398.77520751953125 0.26138031482696533 0.6742094159126282 0.2821551263332367 0.8257374167442322 0.7662911415100098 0.25461748242378235 \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_4.evaluate.json b/ENCSR540BML/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a20dd0cf523da6b938ebbf2499a73afc23595d15..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326AQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_4.fit.json b/ENCSR540BML/cherimoya.fold_4.fit.json deleted file mode 100644 index 8051a06672f328b9db9e8157e497427adf1773db..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF326AQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540BML/cherimoya.fold_4.log b/ENCSR540BML/cherimoya.fold_4.log deleted file mode 100644 index bd368a48ea07e371ec4e8c8c2b414af3bf306b88..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2188 27.661426067352295 3.2841989994049072 346.17010498046875 0.2849453091621399 489.4620666503906 0.5472755432128906 0.68229306 6.618194580078125 True -1 4376 24.111960411071777 0.42834925651550293 308.47216796875 0.4707525968551636 423.4173889160156 0.6276034712791443 0.7516839 1.2641284465789795 True -2 6564 24.151090145111084 0.43990254402160645 332.453857421875 0.29669421911239624 408.58502197265625 0.6494576930999756 0.77503914 0.43907979130744934 True -3 8752 24.210845232009888 0.430300235748291 412.10296630859375 0.3813819885253906 403.0040588378906 0.6558794975280762 0.7849984 0.41345542669296265 True -4 10940 24.15595507621765 1.9080042839050293 331.8957214355469 0.2741782069206238 400.9642639160156 0.6591030359268188 0.79339164 0.37391048669815063 True -5 13128 24.220966577529907 0.4621284008026123 375.8518981933594 0.39113110303878784 399.4580383300781 0.6610193848609924 0.79534596 0.3324320316314697 True -6 15316 24.277008295059204 0.8338603973388672 359.0003356933594 0.2043178677558899 398.4104919433594 0.6626632809638977 0.80085087 0.30502447485923767 True -7 17504 24.12894558906555 8.615566968917847 383.5873107910156 0.4295090138912201 397.4419250488281 0.6644096970558167 0.8033262 0.28744712471961975 True -8 19692 24.14002513885498 0.4348747730255127 371.86273193359375 0.17661304771900177 396.5317687988281 0.6656218767166138 0.80614394 0.2802290618419647 True -9 21880 24.209158182144165 0.43268871307373047 345.2399597167969 0.3328896462917328 395.66668701171875 0.667083740234375 0.8130106 0.2578367590904236 True -10 24068 24.06235432624817 0.4245719909667969 331.80712890625 0.37385308742523193 394.9627685546875 0.6683640480041504 0.81688327 0.25148501992225647 True -11 26256 24.04305601119995 22.131399154663086 309.9327697753906 0.14993517100811005 394.0693664550781 0.6698481440544128 0.8203573 0.253388911485672 True -12 28444 24.259548902511597 1.139833688735962 325.17950439453125 0.25123611092567444 393.56793212890625 0.6709044575691223 0.82646686 0.24611544609069824 True -13 30632 24.23961043357849 0.42716455459594727 332.098388671875 0.25627273321151733 392.9868469238281 0.6718184947967529 0.83082676 0.24066264927387238 True -14 32820 24.111624002456665 0.4251115322113037 325.6159973144531 0.16765274107456207 392.7039794921875 0.6723218560218811 0.83250445 0.23368307948112488 True -15 35008 24.04064965248108 2.060560703277588 324.70770263671875 0.23941607773303986 392.6426696777344 0.6726650595664978 0.83659434 0.23024901747703552 True -16 37196 24.265339851379395 0.4221501350402832 359.5730285644531 0.15045326948165894 392.8374328613281 0.6722406148910522 0.8346866 0.2320883423089981 False -17 39384 24.05479335784912 0.4194667339324951 359.1985168457031 0.19753813743591309 393.2617492675781 0.6715573072433472 0.83246654 0.2347586303949356 False -18 41572 24.02225971221924 0.41692185401916504 441.37255859375 0.1386880874633789 393.59326171875 0.670774519443512 0.8294731 0.23992295563220978 False -19 43760 24.042035579681396 0.42113637924194336 302.8778076171875 0.1438043713569641 393.8681335449219 0.6703401803970337 0.82620865 0.24299746751785278 False diff --git a/ENCSR540BML/cherimoya.fold_4.performance.tsv b/ENCSR540BML/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 72dc09764ad32e7d77948cc98a9ebda53aa6dc35..0000000000000000000000000000000000000000 --- a/ENCSR540BML/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -392.6426696777344 0.2630985975265503 0.6726650595664978 0.2796347141265869 0.8365943431854248 0.7734586000442505 0.23024901747703552 \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_0.evaluate.json b/ENCSR540PVZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 766fa30a9f6a66d6d84014a06087c08b58b96547..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF295MKE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_0.fit.json b/ENCSR540PVZ/cherimoya.fold_0.fit.json deleted file mode 100644 index d91bea478d7f5a7f37d8056c0a8963fc23b88f79..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF295MKE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_0.log b/ENCSR540PVZ/cherimoya.fold_0.log deleted file mode 100644 index a7f434afb705776c3bae6177f04c94e6bbb55c73..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.127739667892456 3.551118850708008 155.8099365234375 0.5085468888282776 215.12730407714844 0.14119349420070648 0.6695464 2.892683744430542 True -1 5488 30.384915590286255 0.5826935768127441 172.6747589111328 0.741523802280426 205.01454162597656 0.1957898586988449 0.71746725 0.932661771774292 True -2 8232 30.311221599578857 0.5617341995239258 160.14321899414062 0.5517839789390564 201.82241821289062 0.20920036733150482 0.7350962 0.42863911390304565 True -3 10976 30.311227798461914 0.5625479221343994 194.1973876953125 0.5944513082504272 200.7215576171875 0.21342699229717255 0.7456105 0.3397754728794098 True -4 13720 30.252763509750366 2.0027050971984863 187.63455200195312 0.39604586362838745 199.87298583984375 0.2174331545829773 0.74594194 0.33693984150886536 True -5 16464 30.315692901611328 0.5607287883758545 211.070556640625 0.6173238754272461 199.648681640625 0.2187783569097519 0.7488769 0.3377123773097992 True -6 19208 30.230987310409546 0.5680806636810303 148.61134338378906 0.5864970088005066 198.93194580078125 0.2233801931142807 0.7508717 0.36667221784591675 True -7 21952 30.218023538589478 0.5687999725341797 194.019775390625 0.596204936504364 198.4656219482422 0.22548776865005493 0.752759 0.3757780194282532 True -8 24696 30.274081707000732 0.562291145324707 185.46630859375 0.36197274923324585 198.3131866455078 0.22622625529766083 0.7548302 0.3662211298942566 True -9 27440 30.002634048461914 0.5478019714355469 122.00053405761719 0.4017898440361023 198.09133911132812 0.22745560109615326 0.75592834 0.37000131607055664 True -10 30184 29.66252589225769 0.5471866130828857 178.97903442382812 0.344461590051651 197.41033935546875 0.2315451055765152 0.75840753 0.35057181119918823 True -11 32928 29.720519304275513 0.5514545440673828 152.32652282714844 0.6347057819366455 197.28575134277344 0.23245106637477875 0.7618627 0.34051498770713806 True -12 35672 29.633588314056396 0.554661750793457 139.5762939453125 0.3427673578262329 196.8093719482422 0.23497258126735687 0.7655533 0.3295226991176605 True -13 38416 29.678727626800537 0.5607032775878906 170.18304443359375 0.42359280586242676 196.56173706054688 0.2359200417995453 0.77507234 0.32032421231269836 True -14 41160 29.676628589630127 0.5507144927978516 161.90414428710938 0.4440145194530487 196.25732421875 0.23766779899597168 0.778235 0.31472089886665344 True -15 43904 29.700437545776367 0.5554687976837158 129.32298278808594 0.31955045461654663 195.9746856689453 0.2389708012342453 0.78526294 0.3090677559375763 True -16 46648 29.669593334197998 0.5573263168334961 155.109375 0.4337373971939087 196.0758819580078 0.23817208409309387 0.7893371 0.2943682074546814 True -17 49392 29.67393684387207 1.2930924892425537 158.19378662109375 0.2375357747077942 195.807373046875 0.24051058292388916 0.790534 0.2919204831123352 True -18 52136 29.68233060836792 1.0626566410064697 153.3677215576172 0.24507759511470795 195.9062957763672 0.23958176374435425 0.7907783 0.29016077518463135 True -19 54880 29.65729808807373 0.5571105480194092 136.32537841796875 0.326185941696167 195.955078125 0.23939795792102814 0.78961927 0.2918953001499176 False diff --git a/ENCSR540PVZ/cherimoya.fold_0.performance.tsv b/ENCSR540PVZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a06731488126dfd189060d3f6750fc9223dd7f3d..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -195.9062957763672 0.5369882583618164 0.23958176374435425 0.0521656833589077 0.7907782793045044 0.7323403358459473 0.29016077518463135 \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_1.evaluate.json b/ENCSR540PVZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ee958dd051eb9b4bb053e27de316612e901e2018..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF295MKE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_1.fit.json b/ENCSR540PVZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 6438e07b8ef2f45512215d93722f2cddcf5e4c09..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF295MKE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_1.log b/ENCSR540PVZ/cherimoya.fold_1.log deleted file mode 100644 index 3a581372b7393929f6376d9da904ae44291b13f7..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 33.969298124313354 4.776435613632202 194.63632202148438 0.5655163526535034 247.83432006835938 0.14533260464668274 0.66119415 3.6917972564697266 True -1 5424 29.9813232421875 1.6405951976776123 158.11856079101562 0.4725235402584076 234.608154296875 0.2100781947374344 0.7328822 0.7621116638183594 True -2 8136 30.026920795440674 1.9011244773864746 180.221923828125 0.5737956762313843 231.62216186523438 0.2224123477935791 0.7429772 0.477809339761734 True -3 10848 29.935335397720337 1.7927498817443848 170.90036010742188 0.5775799751281738 229.39971923828125 0.22921861708164215 0.75088334 0.4230959415435791 True -4 13560 29.9617919921875 1.4124855995178223 143.43405151367188 0.6557813882827759 228.3953857421875 0.23397472500801086 0.75857 0.47703027725219727 True -5 16272 29.957549333572388 1.2578344345092773 152.88050842285156 0.7976737022399902 227.78086853027344 0.2364186942577362 0.75870806 0.5252600312232971 True -6 18984 29.88470458984375 0.6933858394622803 163.70919799804688 0.4577329754829407 226.8317108154297 0.24117878079414368 0.7611454 0.5283557176589966 True -7 21696 29.894930601119995 0.6962838172912598 158.8038330078125 0.3309175670146942 226.74972534179688 0.24174407124519348 0.7610216 0.5484285950660706 False -8 24408 29.737597227096558 0.6874029636383057 180.4659881591797 0.45714569091796875 226.00018310546875 0.2448166012763977 0.76560146 0.5343216061592102 True -9 27120 29.290914297103882 0.6960928440093994 186.4169158935547 0.39043936133384705 225.6439666748047 0.24701163172721863 0.76819164 0.516965925693512 True -10 29832 29.37432074546814 0.6919195652008057 128.08755493164062 0.714353621006012 225.37158203125 0.2476889044046402 0.7710754 0.5147169232368469 True -11 32544 29.31466054916382 0.6769814491271973 157.62393188476562 0.5177368521690369 225.01084899902344 0.24994629621505737 0.77514863 0.515576958656311 True -12 35256 29.307982683181763 0.6919560432434082 149.7289276123047 0.43279361724853516 224.63526916503906 0.2512533664703369 0.78263944 0.45132917165756226 True -13 37968 29.34025502204895 0.6855490207672119 124.61155700683594 0.4248773455619812 224.00303649902344 0.254861444234848 0.7852615 0.43792200088500977 True -14 40680 29.32016658782959 0.6878178119659424 136.22030639648438 0.27430903911590576 223.6479034423828 0.2564135491847992 0.79176927 0.40349286794662476 True -15 43392 29.303826570510864 0.687089204788208 181.20623779296875 0.3705924153327942 223.6586456298828 0.25561270117759705 0.79993427 0.3775642514228821 True -16 46104 29.3179874420166 0.6857125759124756 114.62351989746094 0.4073418974876404 223.30189514160156 0.25809261202812195 0.8037564 0.3452083468437195 True -17 48816 29.38392734527588 3.676391839981079 159.92898559570312 0.2606178820133209 223.5733642578125 0.25620779395103455 0.8059081 0.33282652497291565 True -18 51528 29.361690521240234 0.6925714015960693 175.07232666015625 0.24608798325061798 223.4383087158203 0.2568560242652893 0.8044071 0.326360821723938 False -19 54240 29.468211889266968 0.6914081573486328 166.27903747558594 0.22186680138111115 223.32568359375 0.25786828994750977 0.80469644 0.32437506318092346 False diff --git a/ENCSR540PVZ/cherimoya.fold_1.performance.tsv b/ENCSR540PVZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b50cb1cd4b170a4a60306a19744c388794a92b63..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.5733642578125 0.5216089487075806 0.25620779395103455 0.062350936233997345 0.8059080839157104 0.7684692740440369 0.33282652497291565 \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_2.evaluate.json b/ENCSR540PVZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1429f5c8dd6e1b85460722d22c874f75857615f2..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF295MKE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_2.fit.json b/ENCSR540PVZ/cherimoya.fold_2.fit.json deleted file mode 100644 index ce9dac8b84508e839dc5cd4735d011df789b4dc0..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF295MKE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_2.log b/ENCSR540PVZ/cherimoya.fold_2.log deleted file mode 100644 index 6d534be5b7d6c0f3be13a95e698031f6c583f3e4..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 35.557350158691406 3.4117298126220703 165.97854614257812 0.5929184556007385 222.1366424560547 0.14448952674865723 0.6598416 2.5963001251220703 True -1 5748 31.898892879486084 0.5377168655395508 139.12258911132812 0.6718064546585083 210.3694305419922 0.20538192987442017 0.72540545 0.8265619874000549 True -2 8622 31.76894998550415 0.5226750373840332 195.45152282714844 0.5722519159317017 208.2503662109375 0.2125428169965744 0.73748964 0.5077386498451233 True -3 11496 31.72919750213623 0.528660774230957 162.64390563964844 0.6798524856567383 207.28077697753906 0.21477727591991425 0.7457661 0.44135671854019165 True -4 14370 31.665610790252686 0.5329766273498535 139.7462921142578 0.7805519104003906 206.11611938476562 0.22068314254283905 0.75000924 0.46866223216056824 True -5 17244 31.674405097961426 0.525925874710083 149.20513916015625 0.46552759408950806 205.3182830810547 0.22502604126930237 0.7485801 0.4784930646419525 False -6 20118 31.742071628570557 0.528223991394043 153.3272705078125 0.5286856889724731 204.91876220703125 0.22704438865184784 0.75196546 0.48562225699424744 True -7 22992 31.686116695404053 0.5321743488311768 125.99729919433594 0.5371878147125244 204.3535614013672 0.23072534799575806 0.75393957 0.4688626229763031 True -8 25866 31.491262197494507 0.5274157524108887 152.79905700683594 0.356990247964859 203.81947326660156 0.23340044915676117 0.75520945 0.4633485674858093 True -9 28740 31.819337606430054 0.523972749710083 185.98394775390625 0.5790191888809204 203.34739685058594 0.2359316200017929 0.75915223 0.45656952261924744 True -10 31614 31.158068895339966 0.526930570602417 153.502197265625 0.5184611678123474 202.994873046875 0.23858775198459625 0.762965 0.4621378183364868 True -11 34488 31.170485496520996 0.6855976581573486 164.27691650390625 0.47448623180389404 202.77786254882812 0.2389332503080368 0.76336855 0.4407964050769806 True -12 37362 31.040207147598267 0.7252373695373535 138.59532165527344 0.511455237865448 202.5614013671875 0.24015595018863678 0.7680359 0.4345017075538635 True -13 40236 31.07657766342163 0.533348798751831 154.3485565185547 0.43388086557388306 202.0175018310547 0.24287618696689606 0.77441835 0.4032188653945923 True -14 43110 31.139536142349243 0.5240159034729004 161.9603271484375 0.35405343770980835 201.9752197265625 0.2428179234266281 0.7814847 0.3704010546207428 True -15 45984 31.059434413909912 0.532489538192749 170.96202087402344 0.4179956316947937 201.54287719726562 0.24597285687923431 0.78788185 0.3410780727863312 True -16 48858 31.1283118724823 0.5282618999481201 160.681640625 0.3146018981933594 201.402099609375 0.246337890625 0.79312986 0.3181595802307129 True -17 51732 31.1222026348114 0.5416052341461182 159.00527954101562 0.33539435267448425 201.41810607910156 0.24637572467327118 0.79403794 0.30835968255996704 True -18 54606 31.26306462287903 0.5309967994689941 129.75961303710938 0.30601000785827637 201.49102783203125 0.2456052601337433 0.79203963 0.3065880835056305 False -19 57480 31.23665761947632 0.527698278427124 137.11500549316406 0.26598453521728516 201.71327209472656 0.24424581229686737 0.79106855 0.30709508061408997 False diff --git a/ENCSR540PVZ/cherimoya.fold_2.performance.tsv b/ENCSR540PVZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6c32b1222629046728380f1ad795a5a544ab5615..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.41810607910156 0.5327686071395874 0.24637572467327118 0.05320965126156807 0.794037938117981 0.7425695657730103 0.30835968255996704 \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_3.evaluate.json b/ENCSR540PVZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c1637ea5ff3ddda9bddf53e146109b0174bffe4d..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF295MKE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_3.fit.json b/ENCSR540PVZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 32f752390c766c07c7f39acd965b783e9f5a9ca6..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF295MKE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_3.log b/ENCSR540PVZ/cherimoya.fold_3.log deleted file mode 100644 index 51251450ba6bb3e0d8e196546b2f0f1c36614bc7..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.377565145492554 3.4377617835998535 186.8992462158203 0.6783909797668457 227.1232147216797 0.13870039582252502 0.6637339 2.9794113636016846 True -1 5498 30.41170573234558 0.5676436424255371 200.58633422851562 0.7623010873794556 216.30624389648438 0.19595175981521606 0.7277977 0.8400075435638428 True -2 8247 30.312405586242676 1.6407864093780518 170.44296264648438 0.44256502389907837 213.22842407226562 0.20963986217975616 0.74086696 0.5241307616233826 True -3 10996 30.339839458465576 1.1380455493927002 183.7550506591797 0.4770907759666443 211.7424774169922 0.2156093716621399 0.7470045 0.49076205492019653 True -4 13745 30.30618977546692 0.5763154029846191 132.23916625976562 0.5486786365509033 211.43484497070312 0.215964674949646 0.74604726 0.5447118282318115 False -5 16494 30.33228373527527 0.5670831203460693 104.5587387084961 0.45561879873275757 210.8690185546875 0.21940270066261292 0.7491052 0.5346364378929138 True -6 19243 30.379186153411865 0.5822439193725586 168.25790405273438 0.8677109479904175 210.33535766601562 0.22310295701026917 0.75096345 0.5536536574363708 True -7 21992 30.39884901046753 0.571185827255249 151.90579223632812 0.4122031331062317 210.0077362060547 0.22411416471004486 0.7536296 0.550672709941864 True -8 24741 29.87666130065918 0.5511643886566162 188.23902893066406 0.4230576157569885 209.630615234375 0.22727754712104797 0.7546255 0.552302360534668 True -9 27490 29.799408674240112 0.5598762035369873 146.33489990234375 0.3898378014564514 209.4211883544922 0.2279590368270874 0.7610316 0.5658568143844604 True -10 30239 29.76920175552368 0.5606968402862549 159.13534545898438 0.7453562021255493 209.02850341796875 0.22960306704044342 0.7654323 0.5477449893951416 True -11 32988 29.74091911315918 0.9303536415100098 135.25741577148438 0.5561848282814026 208.94091796875 0.22983302175998688 0.7666574 0.5429413318634033 True -12 35737 29.80080008506775 0.5751020908355713 134.83148193359375 0.38181012868881226 208.2669219970703 0.23468807339668274 0.77217317 0.49185535311698914 True -13 38486 29.80863308906555 0.5599472522735596 149.95008850097656 0.4217802882194519 208.22232055664062 0.23409859836101532 0.7786814 0.45021721720695496 True -14 41235 29.854228019714355 0.5594394207000732 178.72976684570312 0.3529408872127533 207.882080078125 0.23567403852939606 0.7852615 0.4135580062866211 True -15 43984 29.72490954399109 0.5529496669769287 150.30482482910156 0.23094119131565094 207.8061065673828 0.23580557107925415 0.79049236 0.36601608991622925 True -16 46733 29.718087434768677 0.5532679557800293 160.01516723632812 0.3895333409309387 207.4865264892578 0.23802244663238525 0.7949848 0.3345915675163269 True -17 49482 29.748889207839966 0.5548539161682129 178.28131103515625 0.3927668333053589 207.49072265625 0.2375074177980423 0.79733527 0.31994977593421936 True -18 52231 29.71089792251587 0.5512435436248779 180.438232421875 0.3542636036872864 207.4847412109375 0.237117737531662 0.79805094 0.3145543932914734 True -19 54980 29.725963830947876 0.5537559986114502 148.50143432617188 0.29765936732292175 207.50265502929688 0.23741427063941956 0.79630846 0.315094530582428 False diff --git a/ENCSR540PVZ/cherimoya.fold_3.performance.tsv b/ENCSR540PVZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 21e75fd5063d3e2f6d20c1cd250f056c98215b3a..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -207.4847412109375 0.5343943238258362 0.2371177077293396 0.05336330085992813 0.7980509400367737 0.7421733736991882 0.3145543932914734 \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_4.evaluate.json b/ENCSR540PVZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e5710a02cc265a684c6f3990aa23480175c61496..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF295MKE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_4.fit.json b/ENCSR540PVZ/cherimoya.fold_4.fit.json deleted file mode 100644 index d848922e65a7fd9e03cbdb79796d1dd484a7918c..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF295MKE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540PVZ/cherimoya.fold_4.log b/ENCSR540PVZ/cherimoya.fold_4.log deleted file mode 100644 index 495a69943cc532f5e407de26f24f6798f3c18c90..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2831 35.18231201171875 3.5829362869262695 167.08160400390625 0.63406902551651 212.59188842773438 0.1360856145620346 0.6603152 2.157933473587036 True -1 5662 31.38564443588257 0.6331746578216553 149.58314514160156 0.567050576210022 203.14010620117188 0.1900310218334198 0.72393787 0.8286940455436707 True -2 8493 31.339888334274292 0.608201265335083 150.684814453125 0.6078001260757446 200.23184204101562 0.2031322419643402 0.73483133 0.44782862067222595 True -3 11324 31.288386344909668 0.6080102920532227 146.03262329101562 0.5416797399520874 199.4066162109375 0.20507469773292542 0.73876494 0.3979518711566925 True -4 14155 31.217100143432617 0.6165914535522461 184.973388671875 0.5525585412979126 198.52316284179688 0.21007747948169708 0.7446891 0.3965466022491455 True -5 16986 31.22776985168457 0.6034832000732422 156.16476440429688 0.568577229976654 198.23690795898438 0.21210646629333496 0.74584717 0.41496822237968445 True -6 19817 31.172266244888306 0.6067674160003662 176.83770751953125 0.4936053454875946 198.0006866455078 0.2132110297679901 0.74874806 0.397647887468338 True -7 22648 31.20525622367859 0.6017827987670898 158.74771118164062 0.4045068621635437 197.4869842529297 0.21611729264259338 0.75393707 0.39301976561546326 True -8 25479 31.149234294891357 0.6039979457855225 147.05477905273438 0.3655666708946228 197.1149444580078 0.21834291517734528 0.7540424 0.38554680347442627 True -9 28310 30.629457712173462 0.6023719310760498 188.10528564453125 0.3776831328868866 196.87828063964844 0.21973152458667755 0.75823987 0.3869355022907257 True -10 31141 30.63276171684265 0.6689050197601318 180.51661682128906 0.3811001777648926 196.10658264160156 0.22459056973457336 0.76032966 0.3709433376789093 True -11 33972 30.65034294128418 5.273282289505005 150.49871826171875 0.2790392339229584 196.22259521484375 0.22338831424713135 0.76607025 0.3606979548931122 True -12 36803 30.688905000686646 15.107319355010986 162.41848754882812 0.48167121410369873 195.68875122070312 0.22698606550693512 0.7707945 0.345816045999527 True -13 39634 30.9685378074646 0.6166021823883057 155.45123291015625 0.49044278264045715 195.52719116210938 0.22869746387004852 0.77483845 0.32923948764801025 True -14 42465 30.698566675186157 0.6068840026855469 134.31248474121094 0.4553599953651428 195.10980224609375 0.2303408831357956 0.7824537 0.3079064190387726 True -15 45296 30.7061767578125 0.6000838279724121 161.90097045898438 0.28807729482650757 194.9232177734375 0.23110759258270264 0.78697056 0.29613256454467773 True -16 48127 30.687763214111328 0.6222555637359619 149.13720703125 0.20154595375061035 195.2113494873047 0.22852399945259094 0.7895882 0.2861041724681854 True -17 50958 30.80962371826172 0.6023142337799072 157.1927032470703 0.2394237518310547 194.8780059814453 0.2319696843624115 0.7923624 0.28009793162345886 True -18 53789 30.71904683113098 0.6078908443450928 147.970458984375 0.36435845494270325 194.87051391601562 0.23169001936912537 0.79189605 0.27590838074684143 False -19 56620 30.70738458633423 0.5994784832000732 133.332275390625 0.2002021074295044 195.00975036621094 0.23033039271831512 0.79136986 0.2773067057132721 False diff --git a/ENCSR540PVZ/cherimoya.fold_4.performance.tsv b/ENCSR540PVZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0a7a6999a00dfece288c96dcc17c2654c541e1f9..0000000000000000000000000000000000000000 --- a/ENCSR540PVZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -194.8780059814453 0.5404324531555176 0.2319696992635727 0.05036015063524246 0.7923623919487 0.7273198962211609 0.28009793162345886 \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_0.evaluate.json b/ENCSR540VTN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6c3e46ce2ba1aa26d0c01dd0de47d762cb8a7377..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF683FCI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_0.fit.json b/ENCSR540VTN/cherimoya.fold_0.fit.json deleted file mode 100644 index d4ebe1673009adcdfadcacdb8f583458f98c29b3..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF683FCI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_0.log b/ENCSR540VTN/cherimoya.fold_0.log deleted file mode 100644 index c9b712eba605f0e724705465aa69583b153c601b..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1986 26.27893328666687 3.563920736312866 414.7596435546875 0.8994771838188171 512.878662109375 0.1648710072040558 0.5736494 9.260295867919922 True -1 3972 21.835491180419922 0.43567347526550293 524.5052490234375 1.278905987739563 439.4959411621094 0.24195528030395508 0.7390395 3.9423434734344482 True -2 5958 21.833946466445923 0.787055492401123 303.70050048828125 0.666746973991394 418.0300598144531 0.2578833997249603 0.7522488 2.8362531661987305 True -3 7944 21.90815830230713 0.42133092880249023 326.96221923828125 0.8719115257263184 408.08453369140625 0.26386624574661255 0.7596656 2.5167741775512695 True -4 9930 21.84862995147705 0.4253060817718506 344.94635009765625 0.8726621270179749 399.0581359863281 0.2712152898311615 0.76487225 1.369931936264038 True -5 11916 21.8343722820282 0.41867733001708984 356.7375183105469 0.4586344361305237 396.2675476074219 0.27349478006362915 0.7765369 1.098686695098877 True -6 13902 21.8440420627594 0.41251659393310547 430.0654602050781 0.7992943525314331 391.5509338378906 0.27927759289741516 0.77853036 1.0257972478866577 True -7 15888 21.80473017692566 0.42452526092529297 397.4804382324219 0.7292865514755249 387.7511291503906 0.28252944350242615 0.79032874 0.968623161315918 True -8 17874 21.8074791431427 0.4250192642211914 358.49615478515625 0.5344139337539673 385.146728515625 0.28521689772605896 0.794862 0.8197777271270752 True -9 19860 21.809141874313354 0.417858362197876 428.07586669921875 0.42757299542427063 381.73590087890625 0.2885774075984955 0.80601203 0.6878857016563416 True -10 21846 21.818586826324463 0.4086165428161621 320.6766052246094 0.3507630228996277 379.8147888183594 0.29019102454185486 0.81534255 0.5846039056777954 True -11 23832 21.868773221969604 0.41677045822143555 293.0145263671875 0.46226537227630615 377.1107482910156 0.29316025972366333 0.8209699 0.5401044487953186 True -12 25818 21.86651086807251 0.4353141784667969 250.6708221435547 0.5032414793968201 374.751953125 0.29487770795822144 0.82926345 0.493392676115036 True -13 27804 21.847049236297607 0.4628784656524658 356.148193359375 0.3649718165397644 373.69049072265625 0.29453203082084656 0.83474106 0.4600282907485962 True -14 29790 21.850411653518677 0.445831298828125 340.22735595703125 0.3003699779510498 370.7043151855469 0.2993420660495758 0.8399147 0.4411262571811676 True -15 31776 21.856861114501953 0.4104306697845459 262.06219482421875 0.3068833351135254 369.5268859863281 0.3002566695213318 0.8447141 0.4250645339488983 True -16 33762 21.880984783172607 1.0122292041778564 342.3984375 0.33022019267082214 369.0104064941406 0.301776647567749 0.84658855 0.4103293716907501 True -17 35748 21.840734243392944 0.416393518447876 300.6213684082031 0.5129586458206177 368.96453857421875 0.3020972013473511 0.84891456 0.4070597290992737 True -18 37734 21.850118398666382 0.4201183319091797 280.540771484375 0.3189755082130432 369.3306579589844 0.30086636543273926 0.8467785 0.41005656123161316 False -19 39720 21.866297960281372 0.42889952659606934 347.8534240722656 0.3908870220184326 371.0181884765625 0.29782620072364807 0.8458153 0.4120057225227356 False diff --git a/ENCSR540VTN/cherimoya.fold_0.performance.tsv b/ENCSR540VTN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fcb9a695d92205534fc92155135e09b38d33040d..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -368.96453857421875 0.4748538136482239 0.30209723114967346 0.09844470024108887 0.8489145636558533 0.7913937568664551 0.4070597290992737 \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_1.evaluate.json b/ENCSR540VTN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a045ecce3a227d21d471d75fec6609ae806791f9..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF683FCI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_1.fit.json b/ENCSR540VTN/cherimoya.fold_1.fit.json deleted file mode 100644 index dc62b665a28fba1007e4c12fac80ea76195d36a2..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF683FCI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_1.log b/ENCSR540VTN/cherimoya.fold_1.log deleted file mode 100644 index d59c5f3cca4dfdc0359613a281e5a7062c0d1d88..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1939 25.744640111923218 3.6800246238708496 406.1226806640625 0.8051018118858337 664.9114990234375 0.17582079768180847 0.5492315 11.743592262268066 True -1 3878 21.33327889442444 0.9741880893707275 322.9161071777344 1.1373281478881836 568.93896484375 0.25730475783348083 0.70588475 5.0963053703308105 True -2 5817 21.3693585395813 0.553081750869751 265.9027099609375 0.5198467969894409 526.5235595703125 0.2853702902793884 0.727055 3.1591598987579346 True -3 7756 21.343329668045044 0.5759837627410889 383.364990234375 0.7701934576034546 513.3731689453125 0.2906858026981354 0.7504276 1.8025882244110107 True -4 9695 21.165847301483154 0.5503931045532227 333.4324035644531 0.6685499548912048 500.8799133300781 0.30222800374031067 0.77327704 1.3707839250564575 True -5 11634 20.918670892715454 0.5400879383087158 328.3419494628906 0.6586555242538452 495.4440612792969 0.3074458837509155 0.7810079 1.2497406005859375 True -6 13573 20.918991804122925 0.5398385524749756 273.0227355957031 0.5411202311515808 486.2098388671875 0.31540125608444214 0.7936599 1.1301426887512207 True -7 15512 21.03329300880432 0.564852237701416 319.6039733886719 1.4183971881866455 484.6172790527344 0.31680211424827576 0.801416 1.080422282218933 True -8 17451 20.96116542816162 0.57550048828125 314.4310607910156 0.8209761381149292 480.576171875 0.32087334990501404 0.8125758 0.9647625684738159 True -9 19390 20.994351148605347 0.5679965019226074 274.32037353515625 0.6807429790496826 475.50079345703125 0.3248240649700165 0.82378274 0.8244078755378723 True -10 21329 21.04435157775879 1.4631710052490234 271.244873046875 0.5826945304870605 471.927978515625 0.3287654519081116 0.8276694 0.7840800285339355 True -11 23268 21.01495885848999 0.5677227973937988 308.3117370605469 0.4775732159614563 470.18609619140625 0.3290292024612427 0.83454263 0.6854772567749023 True -12 25207 21.011332988739014 0.5988597869873047 352.78546142578125 0.5067206025123596 465.6492004394531 0.33377090096473694 0.8401992 0.6393972039222717 True -13 27146 21.031809329986572 0.5606203079223633 379.368896484375 0.4202122092247009 462.8692932128906 0.3351062536239624 0.84663236 0.5713610649108887 True -14 29085 20.996445178985596 0.5562577247619629 272.4267883300781 0.37827974557876587 459.4987487792969 0.33753520250320435 0.85198647 0.540932297706604 True -15 31024 21.003548860549927 0.5664088726043701 318.91632080078125 0.3916349411010742 458.7895812988281 0.3369637727737427 0.85665596 0.5097633004188538 True -16 32963 20.934645652770996 0.5826370716094971 330.2442626953125 0.4580724537372589 458.02374267578125 0.33712679147720337 0.859717 0.4908333420753479 True -17 34902 20.924944639205933 0.5616896152496338 292.0557861328125 0.3141686022281647 459.1599426269531 0.335082471370697 0.86104614 0.47925034165382385 True -18 36841 21.011253833770752 1.2338721752166748 388.0585021972656 0.2899773120880127 459.0616455078125 0.3359977602958679 0.8595565 0.47829219698905945 False -19 38780 21.071296453475952 0.5502481460571289 320.87969970703125 0.35420873761177063 458.4686279296875 0.33744484186172485 0.8598211 0.4790154695510864 False diff --git a/ENCSR540VTN/cherimoya.fold_1.performance.tsv b/ENCSR540VTN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0577c3f51842137760702b3e0d65c0870a7ff0cb..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.1599426269531 0.4461311995983124 0.335082471370697 0.12633070349693298 0.8610461354255676 0.828359067440033 0.47925034165382385 \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_2.evaluate.json b/ENCSR540VTN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b2ffce7b186318d595409038a470bafc16e17f0b..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF683FCI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_2.fit.json b/ENCSR540VTN/cherimoya.fold_2.fit.json deleted file mode 100644 index 96f2266855cfab30c80a7736f922514c03a684bf..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF683FCI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_2.log b/ENCSR540VTN/cherimoya.fold_2.log deleted file mode 100644 index 0d73e7785e397b619bad2a2a89c74afc1c5924d2..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2089 27.414708375930786 3.6047019958496094 373.483642578125 0.6765232682228088 543.75732421875 0.16934634745121002 0.54996395 8.072484016418457 True -1 4178 23.221980094909668 0.49286627769470215 451.3979187011719 0.9183855652809143 458.3328857421875 0.2510085999965668 0.7315344 3.7411105632781982 True -2 6267 22.99823808670044 0.42593860626220703 411.59722900390625 0.7400943040847778 434.9918212890625 0.266470342874527 0.7337574 2.54443359375 True -3 8356 22.95315670967102 0.42553210258483887 319.23333740234375 0.7359874248504639 424.9006652832031 0.27146846055984497 0.7597616 1.3220287561416626 True -4 10445 22.92706608772278 8.204959630966187 409.7427673339844 0.7808800339698792 416.7886962890625 0.27655065059661865 0.7745765 1.0400769710540771 True -5 12534 22.964561462402344 0.5258152484893799 307.88165283203125 0.39964789152145386 413.6078796386719 0.2789889872074127 0.7835509 0.9382777214050293 True -6 14623 22.92853093147278 0.42851686477661133 274.11962890625 0.5145923495292664 407.5845031738281 0.2841019034385681 0.79277605 0.992679238319397 True -7 16712 22.59276580810547 0.42568159103393555 429.79400634765625 0.4949963092803955 403.23516845703125 0.2884308695793152 0.8045055 0.8679773807525635 True -8 18801 22.49543857574463 0.44472813606262207 373.5760498046875 0.46604031324386597 401.05743408203125 0.29015809297561646 0.81042355 0.7380298376083374 True -9 20890 22.510152578353882 1.5943326950073242 320.3997802734375 0.5980939269065857 398.87579345703125 0.29227563738822937 0.81709796 0.6681654453277588 True -10 22979 22.581294298171997 0.43224310874938965 355.6242370605469 0.45677661895751953 396.9112243652344 0.29414352774620056 0.82336384 0.6058385372161865 True -11 25068 22.55107069015503 0.4277195930480957 317.79937744140625 0.5988717079162598 394.6276550292969 0.29640015959739685 0.82789177 0.557716965675354 True -12 27157 22.617276430130005 0.4349384307861328 449.7104797363281 0.45811551809310913 390.8316955566406 0.30146583914756775 0.8349629 0.5097646713256836 True -13 29246 22.673497915267944 0.4253420829772949 337.1070556640625 0.7244337797164917 389.90252685546875 0.30155205726623535 0.841391 0.4787047803401947 True -14 31335 22.489042043685913 0.43443751335144043 496.70355224609375 0.5214444994926453 388.3428039550781 0.30278170108795166 0.84636724 0.45421019196510315 True -15 33424 23.31243324279785 6.760801553726196 389.2122802734375 0.36665838956832886 385.9465026855469 0.3057279586791992 0.8492837 0.4299439489841461 True -16 35513 22.49334979057312 17.18649435043335 317.346923828125 0.3504754602909088 385.3791198730469 0.30680254101753235 0.85364985 0.41516491770744324 True -17 37602 22.915599584579468 0.42160511016845703 258.451904296875 0.27780935168266296 385.7957763671875 0.30493417382240295 0.8527136 0.4111018478870392 False -18 39691 22.6714608669281 11.453171253204346 279.6394958496094 0.44440963864326477 386.4754638671875 0.3044123649597168 0.85217845 0.4135845899581909 False -19 41780 22.534576892852783 0.4264183044433594 190.90447998046875 0.20131926238536835 386.647216796875 0.3049263656139374 0.8509754 0.41662609577178955 False diff --git a/ENCSR540VTN/cherimoya.fold_2.performance.tsv b/ENCSR540VTN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ed94053c08195e91ec8b6076ffa31efedcdf9900..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -385.3791198730469 0.46914511919021606 0.30680254101753235 0.10624530911445618 0.8536498546600342 0.7919835448265076 0.41516491770744324 \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_3.evaluate.json b/ENCSR540VTN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a39f38f786cccf93aa8c796c115bb26aaa48e4a0..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF683FCI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_3.fit.json b/ENCSR540VTN/cherimoya.fold_3.fit.json deleted file mode 100644 index 8a210526d494b3de0d15bd6140a183eba1db8b03..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF683FCI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_3.log b/ENCSR540VTN/cherimoya.fold_3.log deleted file mode 100644 index 949d4f4172c0be7641372dc2f8f33beaa80682df..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1982 26.21903419494629 4.070003032684326 380.14361572265625 0.9023677110671997 559.7717895507812 0.18178562819957733 0.5201959 10.07873249053955 True -1 3964 21.8699209690094 0.6069238185882568 398.5716857910156 0.7139418125152588 484.2779541015625 0.25872495770454407 0.69023705 5.2756781578063965 True -2 5946 21.807345151901245 0.4009559154510498 417.4548034667969 0.8186162114143372 454.176513671875 0.2774469554424286 0.7170693 3.0233798027038574 True -3 7928 21.925668954849243 0.4127376079559326 385.93707275390625 0.5772738456726074 444.4224853515625 0.2851752042770386 0.73463243 1.8927922248840332 True -4 9910 21.773615837097168 0.4148521423339844 320.4144592285156 0.8473269939422607 437.94989013671875 0.28856682777404785 0.74822074 1.2970370054244995 True -5 11892 21.785860776901245 0.3886241912841797 327.36669921875 0.592490553855896 431.998291015625 0.29433026909828186 0.75525147 1.1297980546951294 True -6 13874 21.929810523986816 1.062619686126709 328.85687255859375 0.8404163122177124 426.2637023925781 0.3003736436367035 0.7694255 1.028335452079773 True -7 15856 21.793948650360107 0.4113790988922119 367.9049072265625 0.5815150141716003 423.2828063964844 0.304004430770874 0.77801085 0.961925745010376 True -8 17838 21.808318376541138 0.4032456874847412 317.6396789550781 0.3851972818374634 421.4046936035156 0.3043726086616516 0.7860517 0.8725292086601257 True -9 19820 21.81411600112915 0.4068176746368408 407.70123291015625 0.47505974769592285 417.3669738769531 0.30807071924209595 0.79609567 0.7561965584754944 True -10 21802 21.79914951324463 0.389240026473999 384.62335205078125 0.46421515941619873 414.9410400390625 0.3109819293022156 0.8011306 0.717838704586029 True -11 23784 21.78697919845581 0.38767027854919434 281.98876953125 0.47660601139068604 413.2322692871094 0.31175196170806885 0.8077713 0.6481449604034424 True -12 25766 21.819575309753418 0.3924586772918701 385.4056091308594 0.4770830571651459 409.8879089355469 0.3154183328151703 0.81382304 0.6296442747116089 True -13 27748 21.799067974090576 0.41156435012817383 309.6575927734375 0.673184871673584 406.4131774902344 0.3192282021045685 0.82111764 0.5862531661987305 True -14 29730 21.803489208221436 0.40365171432495117 386.31036376953125 0.2749933898448944 405.4985656738281 0.3199969232082367 0.82882607 0.5495613813400269 True -15 31712 21.765565872192383 0.39055538177490234 354.9239196777344 0.3028600215911865 404.47552490234375 0.3206707239151001 0.8330081 0.5193736553192139 True -16 33694 23.786096334457397 8.02642560005188 305.89532470703125 0.3580445647239685 403.88714599609375 0.32086411118507385 0.83751273 0.4955746829509735 True -17 35676 21.57213282585144 0.40766310691833496 264.9191589355469 0.44216784834861755 404.2814025878906 0.3199848532676697 0.83855474 0.4883510172367096 True -18 37658 21.48753070831299 0.39059996604919434 277.666748046875 0.28623583912849426 404.138916015625 0.320652574300766 0.8398042 0.48729342222213745 True -19 39640 21.40848994255066 0.40522027015686035 248.76593017578125 0.22435277700424194 404.05767822265625 0.3212955594062805 0.83929306 0.48800423741340637 False diff --git a/ENCSR540VTN/cherimoya.fold_3.performance.tsv b/ENCSR540VTN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c9a50521fa26182982c42f82588ebcc99868a92d..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -404.138916015625 0.45943567156791687 0.320652574300766 0.11369723081588745 0.8398041725158691 0.7857499718666077 0.48729342222213745 \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_4.evaluate.json b/ENCSR540VTN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 44ca824adf79ef4218aff7503f94686be3998cc6..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF683FCI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_4.fit.json b/ENCSR540VTN/cherimoya.fold_4.fit.json deleted file mode 100644 index 74d6491917827e07cae5cbc88ac3a82887263c02..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF683FCI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR540VTN/cherimoya.fold_4.log b/ENCSR540VTN/cherimoya.fold_4.log deleted file mode 100644 index da39ca6cc6a252d8eb4c6b670af085a269b33254..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2002 26.519220113754272 3.7366137504577637 294.26165771484375 0.7136874198913574 480.3767395019531 0.1686144769191742 0.5382937 8.589376449584961 True -1 4004 22.04093599319458 0.5075535774230957 337.208251953125 0.8747150301933289 415.9401550292969 0.2383360117673874 0.7081663 3.0242555141448975 True -2 6006 22.00898265838623 0.4097561836242676 358.191162109375 0.6345494985580444 395.61590576171875 0.2545114755630493 0.7186463 1.9310681819915771 True -3 8008 22.019857168197632 0.40866971015930176 274.35150146484375 0.6548295021057129 384.7010498046875 0.26130351424217224 0.71842635 1.452674388885498 False -4 10010 21.990217685699463 0.40790820121765137 315.18939208984375 0.789395809173584 378.8139343261719 0.26427748799324036 0.7453548 1.174290657043457 True -5 12012 22.008908987045288 4.7156171798706055 387.4944152832031 0.5863760709762573 374.0710144042969 0.26865944266319275 0.7596618 1.0578219890594482 True -6 14014 22.05832290649414 0.41548895835876465 367.9779052734375 0.5509580373764038 371.85650634765625 0.27264150977134705 0.76312083 0.9602579474449158 True -7 16016 22.01614236831665 0.417128324508667 368.5597229003906 0.7208652496337891 368.6949462890625 0.27517133951187134 0.7752017 0.8768163919448853 True -8 18018 22.031179428100586 0.4068782329559326 444.3445129394531 0.5513179898262024 365.5509338378906 0.27894648909568787 0.78602004 0.7771521806716919 True -9 20020 22.020431518554688 0.42025208473205566 261.72772216796875 0.551853597164154 364.05645751953125 0.2810889482498169 0.7935188 0.6956195831298828 True -10 22022 22.012444734573364 1.1548657417297363 259.9143371582031 0.35488951206207275 361.9790954589844 0.28354236483573914 0.7993672 0.6380787491798401 True -11 24024 22.048861026763916 0.4186422824859619 509.3205261230469 0.5075783729553223 360.7933349609375 0.284475177526474 0.8065492 0.5830898880958557 True -12 26026 22.021827459335327 0.41173768043518066 369.8651123046875 0.6259269714355469 357.4889831542969 0.2887192666530609 0.815714 0.5156323909759521 True -13 28028 22.017951250076294 0.40617990493774414 306.760986328125 0.5004099011421204 356.62982177734375 0.2884669005870819 0.8221321 0.4770250916481018 True -14 30030 22.04878044128418 0.4117705821990967 267.2125244140625 0.3095272183418274 354.3338928222656 0.29228392243385315 0.8284432 0.45214346051216125 True -15 32032 22.047547340393066 0.6263473033905029 418.8895568847656 0.3693479299545288 353.7982482910156 0.29133340716362 0.83252704 0.4368402659893036 True -16 34034 22.054855823516846 0.4013690948486328 303.12969970703125 0.33420759439468384 354.4581298828125 0.28920266032218933 0.8352927 0.42406708002090454 True -17 36036 22.064605474472046 0.41260504722595215 274.9534606933594 0.16543026268482208 354.03369140625 0.29105621576309204 0.8343835 0.42266765236854553 False -18 38038 22.059134483337402 0.4070916175842285 329.51043701171875 0.32516708970069885 354.3418884277344 0.29106631875038147 0.8346808 0.421207070350647 False -19 40040 22.055800437927246 0.413377046585083 350.0399169921875 0.24144072830677032 355.2016296386719 0.2894851267337799 0.8330983 0.422378271818161 False diff --git a/ENCSR540VTN/cherimoya.fold_4.performance.tsv b/ENCSR540VTN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8c7ac8c3ee5ce303798cb142a8a1c2611e77bdc9..0000000000000000000000000000000000000000 --- a/ENCSR540VTN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -354.4581298828125 0.4814088046550751 0.28920266032218933 0.10151471197605133 0.8352926969528198 0.773563802242279 0.42406708002090454 \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_0.evaluate.json b/ENCSR541IET/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4a822fc1e8a2dc24e876d61c29659c1b86d8e334..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF368BPI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_0.fit.json b/ENCSR541IET/cherimoya.fold_0.fit.json deleted file mode 100644 index d214e6a7cf980a67c4dc1ba86168b385b5d533f7..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF368BPI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_0.log b/ENCSR541IET/cherimoya.fold_0.log deleted file mode 100644 index 64dbf1fe21290b852a11272dbfb9c6ddd3a2f759..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 35.33452010154724 4.396835803985596 950.8843994140625 0.38410359621047974 1245.335205078125 0.29501473903656006 0.7120326 6.714410305023193 True -1 5472 30.34765315055847 0.5757796764373779 857.900390625 0.494462251663208 1065.8143310546875 0.40002983808517456 0.8147946 1.6392327547073364 True -2 8208 30.488508939743042 0.5942296981811523 881.3528442382812 0.47713911533355713 1035.7059326171875 0.4155474603176117 0.82670796 0.7583183646202087 True -3 10944 30.363932609558105 0.5723185539245605 835.7244262695312 0.3583395779132843 1025.6099853515625 0.4218350946903229 0.83225536 0.6847803592681885 True -4 13680 30.376620292663574 0.5745499134063721 887.7941284179688 0.4631604552268982 1018.9810180664062 0.42520856857299805 0.8392747 0.5259963274002075 True -5 16416 30.406302213668823 0.5443189144134521 883.202392578125 0.3435174822807312 1013.30908203125 0.429278701543808 0.8468546 0.5200937986373901 True -6 19152 30.20971989631653 0.5657331943511963 866.1123046875 0.280910462141037 1006.6069946289062 0.43288272619247437 0.85160136 0.36887407302856445 True -7 21888 29.79845690727234 0.5726985931396484 787.68798828125 0.2594659924507141 1002.65673828125 0.43638017773628235 0.8558327 0.3534058928489685 True -8 24624 29.808459758758545 0.5690481662750244 972.1781005859375 0.45726463198661804 999.9451293945312 0.43772393465042114 0.8597114 0.353583425283432 True -9 27360 29.74770188331604 0.5762777328491211 877.9224853515625 0.3117104768753052 995.6317138671875 0.4415197968482971 0.86189157 0.3166128695011139 True -10 30096 29.8681800365448 0.57755446434021 859.453369140625 0.34022024273872375 991.5476684570312 0.4431016743183136 0.86855865 0.29060813784599304 True -11 32832 29.84485697746277 12.612436294555664 739.9255981445312 0.2371976524591446 988.1149291992188 0.4447880983352661 0.8716144 0.2657511532306671 True -12 35568 29.844417333602905 0.666679859161377 816.5599365234375 0.2238684594631195 985.7470092773438 0.44584566354751587 0.8781639 0.24983327090740204 True -13 38304 29.91270661354065 0.5793490409851074 796.5474853515625 0.27443984150886536 980.4254760742188 0.449838787317276 0.88242215 0.24019967019557953 True -14 41040 30.043901443481445 0.5807812213897705 823.2468872070312 0.3007047772407532 979.1420288085938 0.450186550617218 0.88612497 0.22703693807125092 True -15 43776 30.040313720703125 0.5830481052398682 788.7675170898438 0.1847987174987793 974.7002563476562 0.45465609431266785 0.8883215 0.21673108637332916 True -16 46512 30.02757215499878 0.5817279815673828 769.759521484375 0.2175913155078888 973.4187622070312 0.45457231998443604 0.8901181 0.2120320051908493 True -17 49248 30.042853832244873 0.5797510147094727 881.004150390625 0.15262307226657867 973.8873291015625 0.45353275537490845 0.89157647 0.21040503680706024 True -18 51984 30.09439444541931 0.577275276184082 830.0382080078125 0.30198556184768677 975.9147338867188 0.45291557908058167 0.89159906 0.2120215743780136 True -19 54720 30.00460410118103 0.5797972679138184 788.1837768554688 0.2022375464439392 974.9840087890625 0.45409029722213745 0.89180636 0.21152523159980774 True diff --git a/ENCSR541IET/cherimoya.fold_0.performance.tsv b/ENCSR541IET/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 76d4c8bd54a861bb9b46391a83ba6919bb6f595f..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -974.9840087890625 0.31697675585746765 0.45409029722213745 0.22622518241405487 0.8918063640594482 0.8522992134094238 0.21152523159980774 \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_1.evaluate.json b/ENCSR541IET/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7ec3edd9db378c7bad43d22e6944d30f1c30ef74..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF368BPI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_1.fit.json b/ENCSR541IET/cherimoya.fold_1.fit.json deleted file mode 100644 index f9c1473ea88e3248958a1b6901804587ba7502d2..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF368BPI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_1.log b/ENCSR541IET/cherimoya.fold_1.log deleted file mode 100644 index 675d6c2218e626e3cd5e507620d135f38cc3502b..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2715 34.77984666824341 4.061976671218872 965.4365234375 0.6268641948699951 1454.2220458984375 0.3008938133716583 0.71086925 7.26547384262085 True -1 5430 30.095661878585815 0.733144998550415 826.0490112304688 0.42528456449508667 1231.9149169921875 0.41598260402679443 0.81241494 1.8095543384552002 True -2 8145 30.122966766357422 0.6902318000793457 715.736083984375 0.31489431858062744 1192.3974609375 0.43222758173942566 0.82819974 0.7975041270256042 True -3 10860 30.112406969070435 0.682199239730835 809.2302856445312 0.3249090611934662 1173.7049560546875 0.4400656521320343 0.8392082 0.5637578964233398 True -4 13575 30.1126925945282 0.6856708526611328 869.13671875 0.43685442209243774 1165.594482421875 0.4447280764579773 0.8450148 0.514413595199585 True -5 16290 30.141313791275024 2.3267619609832764 827.1273193359375 0.4427618682384491 1159.5848388671875 0.44802752137184143 0.854599 0.515722930431366 True -6 19005 30.16498827934265 0.7062797546386719 688.3997802734375 0.2980342507362366 1153.734619140625 0.45033422112464905 0.85838383 0.460970938205719 True -7 21720 30.15947127342224 0.7072267532348633 862.3935546875 0.3478139042854309 1147.840087890625 0.45432114601135254 0.8617248 0.4063030779361725 True -8 24435 30.214004039764404 0.6837503910064697 905.6119384765625 0.4645599126815796 1140.6588134765625 0.45924320816993713 0.8643208 0.3804795444011688 True -9 27150 30.145607471466064 0.7058639526367188 935.3504638671875 0.24508754909038544 1139.0831298828125 0.4587109088897705 0.86859643 0.353061705827713 True -10 29865 30.14679741859436 0.703380823135376 826.7271118164062 0.2977055311203003 1129.958740234375 0.4633067548274994 0.8770128 0.30588701367378235 True -11 32580 30.112751245498657 0.6885533332824707 715.3157958984375 0.17130598425865173 1124.1121826171875 0.4663165211677551 0.8792259 0.29595571756362915 True -12 35295 30.19851303100586 0.6892845630645752 799.3341674804688 0.19869574904441833 1119.5582275390625 0.4688604176044464 0.8831997 0.27437055110931396 True -13 38010 30.64956831932068 0.6965243816375732 772.435302734375 0.3061673641204834 1116.8388671875 0.46854251623153687 0.8892829 0.25406062602996826 True -14 40725 30.216898202896118 0.7019193172454834 842.8195190429688 0.22439469397068024 1111.6383056640625 0.47187530994415283 0.89314896 0.23378537595272064 True -15 43440 30.135751962661743 0.6937148571014404 943.7070922851562 0.19915202260017395 1110.4365234375 0.47260582447052 0.8963966 0.2243276983499527 True -16 46155 29.71854019165039 0.9519133567810059 891.3271484375 0.18577438592910767 1106.71728515625 0.4752902686595917 0.89883214 0.21749347448349 True -17 48870 29.63728904724121 0.6800310611724854 817.1697998046875 0.1840459108352661 1106.5537109375 0.47419729828834534 0.9023539 0.21332186460494995 True -18 51585 29.67304277420044 0.7111964225769043 986.9698486328125 0.1879877746105194 1105.3992919921875 0.476154088973999 0.9005206 0.21273571252822876 False -19 54300 29.59439206123352 0.6715888977050781 749.852783203125 0.11197420954704285 1107.2293701171875 0.47477054595947266 0.90042937 0.21371230483055115 False diff --git a/ENCSR541IET/cherimoya.fold_1.performance.tsv b/ENCSR541IET/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1737a38e3beabc7565d4fbd00a13ffad2b1fb95b..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1106.5537109375 0.2970271408557892 0.47419729828834534 0.25504958629608154 0.9023538827896118 0.8835648894309998 0.21332186460494995 \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_2.evaluate.json b/ENCSR541IET/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8b2c04194e8552c3c6d8bcb3f8e6c28fa43e47d5..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF368BPI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_2.fit.json b/ENCSR541IET/cherimoya.fold_2.fit.json deleted file mode 100644 index 9782c5e5cb1b6265aedf8f3aae3b5279e417e6a0..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF368BPI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_2.log b/ENCSR541IET/cherimoya.fold_2.log deleted file mode 100644 index eddce52bc8c9a029c7852579662d4ff0387b6cac..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 36.45797562599182 3.6372880935668945 957.578857421875 0.41220635175704956 1284.55322265625 0.3008424937725067 0.70140046 6.606267929077148 True -1 5740 31.812439680099487 0.70770263671875 889.5576782226562 0.48656314611434937 1091.9569091796875 0.40142688155174255 0.81112677 1.4854519367218018 True -2 8610 31.85248327255249 0.5439074039459229 1061.630615234375 0.7138581275939941 1065.866455078125 0.41381677985191345 0.8223628 0.7212477922439575 True -3 11480 31.87560534477234 1.2850918769836426 841.623046875 0.3593704104423523 1054.2418212890625 0.41942864656448364 0.83017486 0.5280340909957886 True -4 14350 31.909295320510864 0.9657478332519531 825.6411743164062 0.26379069685935974 1042.42529296875 0.4272991716861725 0.8379769 0.5018014907836914 True -5 17220 31.89410376548767 0.5729761123657227 931.2755126953125 0.38024264574050903 1036.853515625 0.4303148090839386 0.84359103 0.4907129406929016 True -6 20090 31.528733491897583 0.551713228225708 790.9615478515625 0.2498602271080017 1032.2548828125 0.4331241250038147 0.8488837 0.42320501804351807 True -7 22960 31.22830629348755 0.5458559989929199 921.190185546875 0.2405044436454773 1026.1302490234375 0.43622124195098877 0.8551946 0.3666398823261261 True -8 25830 31.27859401702881 0.5463006496429443 838.69140625 0.3398105502128601 1018.4978637695312 0.44224485754966736 0.85700065 0.3455948829650879 True -9 28700 31.231773614883423 19.54622507095337 812.669921875 0.23346567153930664 1016.3013305664062 0.4437595009803772 0.8628782 0.3076494038105011 True -10 31570 31.459603309631348 0.5442962646484375 884.006591796875 0.3140534460544586 1013.0399780273438 0.44468626379966736 0.8635017 0.2971872091293335 True -11 34440 31.229901790618896 1.1648705005645752 884.67578125 0.22613516449928284 1008.1868896484375 0.4474183917045593 0.8697515 0.2797125577926636 True -12 37310 31.226421356201172 0.5542237758636475 881.282470703125 0.24096067249774933 1004.0927124023438 0.4501795172691345 0.8744495 0.2614380121231079 True -13 40180 31.262577056884766 0.549140453338623 951.5719604492188 0.21346107125282288 1000.6578369140625 0.4516436755657196 0.87770724 0.25065258145332336 True -14 43050 31.278364896774292 1.1253571510314941 878.654052734375 0.21770775318145752 999.7982788085938 0.45229437947273254 0.88117325 0.2339165210723877 True -15 45920 31.405588388442993 0.5594909191131592 852.1449584960938 0.25777965784072876 997.0231323242188 0.4537960886955261 0.88293016 0.23043973743915558 True -16 48790 31.246569633483887 0.5376846790313721 825.84375 0.18995192646980286 998.0155029296875 0.45366424322128296 0.88416946 0.22479936480522156 True -17 51660 31.21313977241516 0.5457212924957275 679.5171508789062 0.20095080137252808 996.9609375 0.45420458912849426 0.8859304 0.22164875268936157 True -18 54530 31.235694408416748 0.5547246932983398 981.7838134765625 0.19151735305786133 996.8629760742188 0.4549811780452728 0.88583136 0.2213108241558075 False -19 57400 31.254411697387695 0.5529043674468994 895.7138671875 0.10619297623634338 997.7128295898438 0.45302027463912964 0.8866261 0.22203773260116577 True diff --git a/ENCSR541IET/cherimoya.fold_2.performance.tsv b/ENCSR541IET/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 82bb8dcfda3ad654311f5bc2fc8602345bf33fbe..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -997.7128295898438 0.3146505653858185 0.453020304441452 0.22927536070346832 0.886626124382019 0.8562600016593933 0.22203773260116577 \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_3.evaluate.json b/ENCSR541IET/cherimoya.fold_3.evaluate.json deleted file mode 100644 index effc865fdb1b44b4f95b338caf308224899a38a2..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF368BPI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_3.fit.json b/ENCSR541IET/cherimoya.fold_3.fit.json deleted file mode 100644 index cf7ce9f96a2799b1e277dddabc5e9a18f8db7789..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF368BPI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_3.log b/ENCSR541IET/cherimoya.fold_3.log deleted file mode 100644 index 962485408a3e0cc6316f7a04b72bffface956400..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 35.22773623466492 3.9157752990722656 954.6539916992188 0.3472248315811157 1234.0670166015625 0.30541571974754333 0.7127516 8.24299430847168 True -1 5520 30.656270503997803 0.563286304473877 936.6766967773438 0.5576211214065552 1068.5516357421875 0.4006078541278839 0.8061845 2.034010887145996 True -2 8280 30.632929801940918 0.5539555549621582 835.6075439453125 0.37772125005722046 1045.2667236328125 0.4142809212207794 0.81827945 0.8033626675605774 True -3 11040 30.61099338531494 0.5510361194610596 848.4566040039062 0.2741736173629761 1030.5537109375 0.42272406816482544 0.8298662 0.5549590587615967 True -4 13800 30.639050245285034 0.5543317794799805 742.814208984375 0.2911474108695984 1026.264892578125 0.42348766326904297 0.8395919 0.465216726064682 True -5 16560 30.645135641098022 0.5427711009979248 796.5023803710938 0.3353162109851837 1020.4403076171875 0.4277612566947937 0.8430451 0.42085471749305725 True -6 19320 30.597788333892822 0.9471993446350098 863.4296875 0.2618195414543152 1015.5166015625 0.43153342604637146 0.8461635 0.4211755692958832 True -7 22080 30.68901252746582 0.5644943714141846 831.18701171875 0.32201847434043884 1013.3466796875 0.4327698051929474 0.84807163 0.40951743721961975 True -8 24840 30.659613132476807 0.5569217205047607 771.469482421875 0.25653234124183655 1008.8760986328125 0.4355422258377075 0.85028577 0.39666426181793213 True -9 27600 30.64133334159851 0.5619847774505615 791.16455078125 0.2616836130619049 1006.2197265625 0.43652719259262085 0.85346174 0.36221492290496826 True -10 30360 30.42647933959961 0.5615129470825195 730.9069213867188 0.3350832462310791 1002.7185668945312 0.4401107132434845 0.8551003 0.35511380434036255 True -11 33120 30.107940435409546 0.5486693382263184 723.1846923828125 0.3036378026008606 998.6586303710938 0.4423741102218628 0.8579676 0.32122740149497986 True -12 35880 30.12914276123047 0.5551319122314453 832.7125244140625 0.3366791605949402 991.7617797851562 0.44690990447998047 0.8643896 0.2998271584510803 True -13 38640 30.13301944732666 0.5505082607269287 835.92431640625 0.2835202217102051 990.814453125 0.44736379384994507 0.8723045 0.28163620829582214 True -14 41400 30.075589179992676 0.5441491603851318 820.83251953125 0.21544219553470612 984.8881225585938 0.45109936594963074 0.8782067 0.25997138023376465 True -15 44160 30.050382614135742 0.5558288097381592 745.7078857421875 0.1770249903202057 984.4774169921875 0.45087507367134094 0.88334125 0.24281969666481018 True -16 46920 30.073184490203857 0.5581519603729248 867.88720703125 0.19840028882026672 983.2907104492188 0.45116740465164185 0.8857826 0.235536590218544 True -17 49680 30.11029553413391 0.5574395656585693 800.8182373046875 0.2159145474433899 980.0758056640625 0.452643483877182 0.88717896 0.231883242726326 True -18 52440 30.119218111038208 0.5460591316223145 829.0365600585938 0.1289561539888382 981.16796875 0.4530181884765625 0.888539 0.2301846593618393 True -19 55200 30.116705179214478 0.5574517250061035 772.1282958984375 0.1754053384065628 979.6924438476562 0.4540264904499054 0.88733083 0.2306901514530182 False diff --git a/ENCSR541IET/cherimoya.fold_3.performance.tsv b/ENCSR541IET/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1b7016ddcf397f4af2a93c341c95ff7531c3ccfe..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -981.16796875 0.3162006139755249 0.4530181586742401 0.22879312932491302 0.8885390162467957 0.853180468082428 0.2301846593618393 \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_4.evaluate.json b/ENCSR541IET/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 47cd52147475bae2e535ac8f9b9a4505b3c08008..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF368BPI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_4.fit.json b/ENCSR541IET/cherimoya.fold_4.fit.json deleted file mode 100644 index bc92799e247deafa2a8955d6237548694b92b00c..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF368BPI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541IET/cherimoya.fold_4.log b/ENCSR541IET/cherimoya.fold_4.log deleted file mode 100644 index 49f68b7ac8f6a8416cec4b5f06093d647f80b188..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2828 36.02095818519592 4.347502708435059 811.7449340820312 0.21143890917301178 1178.89599609375 0.2985174357891083 0.6987524 5.318177223205566 True -1 5656 31.481018543243408 0.6240146160125732 897.7199096679688 0.4629201292991638 1017.564453125 0.3953143358230591 0.80823714 1.3295530080795288 True -2 8484 31.449744701385498 1.6242690086364746 876.6121826171875 0.3233264088630676 991.4578857421875 0.4120853543281555 0.8153368 0.6777547001838684 True -3 11312 31.40903615951538 1.8488352298736572 1026.2322998046875 0.23434507846832275 983.112060546875 0.4164724349975586 0.82265556 0.46536827087402344 True -4 14140 31.46241283416748 0.5960476398468018 993.2506103515625 0.48590198159217834 973.8397827148438 0.42306584119796753 0.8312352 0.45640790462493896 True -5 16968 31.427549362182617 0.5693457126617432 903.1768188476562 0.3098205029964447 970.7780151367188 0.423981636762619 0.8393357 0.4101581871509552 True -6 19796 31.36911416053772 0.5767958164215088 959.2345581054688 0.41438961029052734 966.66455078125 0.4278402328491211 0.8416822 0.3716087341308594 True -7 22624 31.318456172943115 0.5755569934844971 852.35498046875 0.2907877564430237 961.1179809570312 0.43193480372428894 0.84903824 0.3233034908771515 True -8 25452 31.33182692527771 0.577664852142334 844.9072875976562 0.3124149739742279 960.705810546875 0.43230804800987244 0.8488865 0.3066282868385315 False -9 28280 31.361781120300293 0.5602016448974609 746.5643310546875 0.25325584411621094 953.8745727539062 0.4363069236278534 0.8529498 0.30043503642082214 True -10 31108 31.33729124069214 0.5703613758087158 888.4360961914062 0.23806869983673096 948.91357421875 0.4410448372364044 0.8572572 0.2836095988750458 True -11 33936 31.330098628997803 0.581261157989502 783.233642578125 0.1943184733390808 946.8961791992188 0.441866397857666 0.8617027 0.2648890018463135 True -12 36764 31.362624168395996 0.5682590007781982 821.281982421875 0.34186527132987976 942.6144409179688 0.4446330666542053 0.8679113 0.24655713140964508 True -13 39592 31.29793357849121 0.5713636875152588 773.154052734375 0.22801902890205383 942.7744140625 0.4446178376674652 0.8715594 0.2413220852613449 True -14 42420 31.079530239105225 0.5753223896026611 829.2520751953125 0.2456657588481903 938.7294311523438 0.4468343257904053 0.87666476 0.2246541976928711 True -15 45248 30.787741661071777 1.7519309520721436 821.9085693359375 0.2088700383901596 937.9210205078125 0.4465370178222656 0.8821489 0.21684500575065613 True -16 48076 30.832369089126587 0.5686016082763672 739.4334106445312 0.14332303404808044 935.6477661132812 0.4485764503479004 0.88487756 0.20883771777153015 True -17 50904 30.85180425643921 0.5677568912506104 849.5620727539062 0.1530618965625763 936.2764892578125 0.4482972025871277 0.8872461 0.20587868988513947 True -18 53732 30.879204750061035 0.5548264980316162 784.5113525390625 0.13904744386672974 938.4932861328125 0.4460078775882721 0.885281 0.205549955368042 False -19 56560 30.822887897491455 0.5614745616912842 830.7705078125 0.1148853749036789 938.4187622070312 0.4461718797683716 0.8856049 0.2062431275844574 False diff --git a/ENCSR541IET/cherimoya.fold_4.performance.tsv b/ENCSR541IET/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0525c682e46cb85183b1bf94d363160e4f010997..0000000000000000000000000000000000000000 --- a/ENCSR541IET/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -936.2764892578125 0.3210841715335846 0.4482972025871277 0.2213275283575058 0.8872460722923279 0.8384620547294617 0.20587868988513947 \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_0.evaluate.json b/ENCSR541JMK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a4187220f07a1058d79d6aa8a112f3c75e319cd4..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702NNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_0.fit.json b/ENCSR541JMK/cherimoya.fold_0.fit.json deleted file mode 100644 index 517928e4879936d4d2fc01eee54bff413b19f5f1..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF702NNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_0.log b/ENCSR541JMK/cherimoya.fold_0.log deleted file mode 100644 index d72a808541fe28741158ad1cbdcd5bb5031d48ad..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.97012376785278 10.702864646911621 927.5426025390625 0.8977429866790771 1212.8564453125 0.2534785270690918 0.6056941 6.441163063049316 True -1 5476 30.479450225830078 0.6092016696929932 944.3305053710938 0.7242776155471802 1037.8465576171875 0.35932183265686035 0.69532955 3.057487964630127 True -2 8214 30.0591037273407 0.5697021484375 744.3411865234375 0.7128888368606567 1016.061279296875 0.3670055866241455 0.69602346 1.77212655544281 True -3 10952 29.841701984405518 1.4511125087738037 594.5584106445312 0.7319363951683044 998.7033081054688 0.37654468417167664 0.70619774 1.4243170022964478 True -4 13690 29.782503366470337 0.889737606048584 855.3157958984375 0.625028669834137 984.4595947265625 0.3845159113407135 0.71329737 1.3307417631149292 True -5 16428 29.780919790267944 0.574918270111084 1073.7574462890625 0.8605064749717712 981.2408447265625 0.38407278060913086 0.7181208 1.2349598407745361 True -6 19166 29.776369333267212 0.557579517364502 1031.773681640625 0.6904271245002747 973.0963745117188 0.38982194662094116 0.7267807 1.0401595830917358 True -7 21904 29.82123303413391 0.5611705780029297 771.219482421875 0.7695872783660889 969.8274536132812 0.39129438996315 0.72577566 0.9451338052749634 False -8 24642 29.768720388412476 0.8925795555114746 857.9818725585938 0.6979671716690063 964.1508178710938 0.396651953458786 0.72768563 0.9235324859619141 True -9 27380 29.76302719116211 0.557941198348999 848.3787841796875 0.6210715770721436 960.167236328125 0.39922231435775757 0.7367191 0.8505862951278687 True -10 30118 29.78195881843567 0.5741772651672363 796.6200561523438 0.49107563495635986 955.6416015625 0.40162912011146545 0.7432788 0.8080815672874451 True -11 32856 29.821945905685425 0.5672900676727295 918.08251953125 0.6638228297233582 951.5673828125 0.40344107151031494 0.751292 0.7224754691123962 True -12 35594 29.761731386184692 0.5641849040985107 863.6121826171875 0.6419728994369507 946.805908203125 0.40557485818862915 0.7600833 0.6769894361495972 True -13 38332 29.82394051551819 0.5728836059570312 644.94384765625 0.3683876395225525 943.1737060546875 0.4075593054294586 0.76741946 0.618752658367157 True -14 41070 29.849180221557617 0.5727739334106445 718.2343139648438 0.4380657374858856 938.2277221679688 0.41084912419319153 0.77558136 0.5595322251319885 True -15 43808 29.84111714363098 0.5639996528625488 724.7973022460938 0.5086390972137451 935.4295043945312 0.4117625057697296 0.78339386 0.5133811235427856 True -16 46546 29.816272020339966 0.5629100799560547 730.2838134765625 0.30693715810775757 933.599365234375 0.4122689664363861 0.7889975 0.48032841086387634 True -17 49284 29.804742097854614 0.5700216293334961 774.8139038085938 0.4168359041213989 932.9307861328125 0.4132404625415802 0.79319996 0.46209704875946045 True -18 52022 29.841273069381714 0.5569462776184082 1000.6290283203125 0.4224262833595276 932.3111572265625 0.412878155708313 0.793728 0.45423364639282227 True -19 54760 29.84093165397644 20.455568552017212 645.46240234375 0.4706002473831177 931.7314453125 0.41370195150375366 0.7929627 0.4557189643383026 False diff --git a/ENCSR541JMK/cherimoya.fold_0.performance.tsv b/ENCSR541JMK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b1ccd9d492800557429033cd8902cee512c11ee5..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -932.3111572265625 0.3773930072784424 0.412878155708313 0.17336690425872803 0.7937279939651489 0.7475229501724243 0.45423364639282227 \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_1.evaluate.json b/ENCSR541JMK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6c539a8f769bcf7e7540c8a46146c41f94a37a8c..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702NNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_1.fit.json b/ENCSR541JMK/cherimoya.fold_1.fit.json deleted file mode 100644 index ada116dfb6885a36a677fb9051bbe3011793840d..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF702NNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_1.log b/ENCSR541JMK/cherimoya.fold_1.log deleted file mode 100644 index a89a30cc9391dfabd5b98ea3474a132b752681e0..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2686 34.669408321380615 4.292829513549805 759.218994140625 0.645088255405426 1421.1680908203125 0.2613174617290497 0.62267923 7.1945672035217285 True -1 5372 29.88833713531494 1.8143925666809082 995.8364868164062 0.8480498790740967 1199.2166748046875 0.3742845058441162 0.7048547 3.54453444480896 True -2 8058 29.929323196411133 1.9463183879852295 725.757568359375 0.7468018531799316 1169.7691650390625 0.38636067509651184 0.7121532 2.2529985904693604 True -3 10744 29.891175508499146 0.7395679950714111 784.2265014648438 0.7490604519844055 1155.696533203125 0.3914774954319 0.72117984 1.8340210914611816 True -4 13430 29.839610815048218 0.7549185752868652 723.4219970703125 0.6828985214233398 1146.052001953125 0.39480462670326233 0.72970235 1.717139720916748 True -5 16116 29.62210702896118 0.7234423160552979 930.583251953125 0.5474790930747986 1132.1441650390625 0.40311774611473083 0.7387439 1.4888529777526855 True -6 18802 29.272369861602783 0.7189788818359375 746.7279663085938 0.7457827925682068 1128.2210693359375 0.4053022563457489 0.7418848 1.3294070959091187 True -7 21488 29.303266763687134 0.7271707057952881 911.441650390625 0.7339388728141785 1122.101806640625 0.40893784165382385 0.74634856 1.3140205144882202 True -8 24174 29.26065230369568 0.7182261943817139 981.4373779296875 0.6602045893669128 1116.6473388671875 0.4127391278743744 0.75292134 1.2301139831542969 True -9 26860 29.25388765335083 1.8230338096618652 926.0931396484375 0.5293253064155579 1118.921630859375 0.4112444221973419 0.751528 1.1683545112609863 False -10 29546 29.284504652023315 0.7131497859954834 626.6739501953125 0.44892221689224243 1103.383056640625 0.4174790680408478 0.76448274 0.9927229881286621 True -11 32232 29.277453184127808 0.7127866744995117 672.4034423828125 0.746943473815918 1098.3505859375 0.4192579388618469 0.77434194 0.9154300093650818 True -12 34918 29.338223934173584 0.7262699604034424 868.6012573242188 0.4122914671897888 1087.4266357421875 0.42500680685043335 0.7836154 0.8211042881011963 True -13 37604 29.323741674423218 0.7167186737060547 814.1361083984375 0.5408923625946045 1081.1829833984375 0.42828449606895447 0.79142886 0.7553985118865967 True -14 40290 29.28990387916565 0.7255411148071289 756.165771484375 0.4753376245498657 1078.3760986328125 0.42860618233680725 0.7982753 0.6583957672119141 True -15 42976 29.261704683303833 0.7419915199279785 792.2718505859375 0.4109615683555603 1071.5164794921875 0.4328451454639435 0.80476654 0.582933783531189 True -16 45662 29.254973649978638 1.374075174331665 711.24169921875 0.21840429306030273 1071.921875 0.43086081743240356 0.80894774 0.5195884704589844 True -17 48348 29.300200700759888 0.7269361019134521 818.3157348632812 0.3332626223564148 1067.7623291015625 0.4333682656288147 0.8102764 0.49093949794769287 True -18 51034 29.331613779067993 0.7223331928253174 723.6882934570312 0.47042933106422424 1065.242431640625 0.4363582730293274 0.8117467 0.47958263754844666 True -19 53720 29.382301807403564 0.7216861248016357 703.5260009765625 0.3363114297389984 1073.3138427734375 0.42858684062957764 0.81094176 0.47762203216552734 False diff --git a/ENCSR541JMK/cherimoya.fold_1.performance.tsv b/ENCSR541JMK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c6b60a1100bb1261d87868cc58de85f7e8521487..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1065.242431640625 0.3581160306930542 0.4363582730293274 0.19613590836524963 0.8117467164993286 0.7818346619606018 0.47958263754844666 \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_2.evaluate.json b/ENCSR541JMK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 52c0bde6c4b0d868a23c123d27c22144ce547799..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702NNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_2.fit.json b/ENCSR541JMK/cherimoya.fold_2.fit.json deleted file mode 100644 index f675e8e08af3c7709633a766e822f530849463b8..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF702NNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_2.log b/ENCSR541JMK/cherimoya.fold_2.log deleted file mode 100644 index 5fae87265e6b84902657c129fa2145dbff11d25b..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 36.70928382873535 3.6670453548431396 714.3637084960938 1.1394834518432617 1257.0350341796875 0.25666698813438416 0.6060594 5.724250316619873 True -1 5784 32.226030588150024 1.3389966487884521 964.564453125 1.0072641372680664 1074.3165283203125 0.36077263951301575 0.6941062 3.427384614944458 True -2 8676 32.18473505973816 1.4216761589050293 901.0462036132812 0.6841399073600769 1052.59716796875 0.3721545934677124 0.7006219 2.067837953567505 True -3 11568 32.146854877471924 0.6277563571929932 935.56689453125 1.0466957092285156 1033.48291015625 0.37950649857521057 0.7117877 1.5760079622268677 True -4 14460 32.117037773132324 0.5637681484222412 855.0802001953125 0.8142314553260803 1023.9312133789062 0.38323208689689636 0.7171137 1.247865915298462 True -5 17352 32.095972776412964 0.6040761470794678 729.674072265625 0.5965895056724548 1014.4457397460938 0.3892023265361786 0.7254284 1.1863813400268555 True -6 20244 32.066015005111694 0.5461540222167969 896.4196166992188 0.7567487955093384 1011.087890625 0.3895876407623291 0.7347886 1.0575051307678223 True -7 23136 32.110270977020264 0.6938683986663818 884.23828125 0.6631966829299927 1006.09765625 0.3926732540130615 0.7374407 1.0155986547470093 True -8 26028 31.78107786178589 0.5613057613372803 835.100830078125 0.6535753011703491 998.8704833984375 0.39637160301208496 0.7431578 0.9096684455871582 True -9 28920 31.5362331867218 0.5549652576446533 778.8480834960938 0.6691761016845703 994.080078125 0.4002675414085388 0.7473919 0.8522188663482666 True -10 31812 31.42557430267334 0.5577552318572998 901.4605102539062 0.6978017091751099 987.6716918945312 0.4039202630519867 0.75313294 0.7714537978172302 True -11 34704 31.472074508666992 0.5533232688903809 804.153076171875 0.42625948786735535 984.4937744140625 0.4058151841163635 0.7623343 0.7152776122093201 True -12 37596 31.50395965576172 0.8209543228149414 842.7882080078125 0.48356157541275024 979.6688842773438 0.4073895812034607 0.77099055 0.6544297933578491 True -13 40488 31.472070693969727 0.5724525451660156 716.5564575195312 0.3338907063007355 974.8359375 0.4100908935070038 0.77730036 0.5896963477134705 True -14 43380 31.481539249420166 0.5511422157287598 792.2415771484375 0.37063467502593994 970.6260986328125 0.41322529315948486 0.7841403 0.538604199886322 True -15 46272 31.564995765686035 0.5678715705871582 787.6751708984375 0.42069002985954285 967.5206298828125 0.4147958755493164 0.7879282 0.4980686604976654 True -16 49164 31.468494653701782 0.5459752082824707 725.8265380859375 0.3386056423187256 967.0237426757812 0.41502827405929565 0.79176426 0.4739065170288086 True -17 52056 31.542940616607666 0.5606546401977539 811.53271484375 0.4238741397857666 966.6569213867188 0.41532671451568604 0.7938098 0.46323347091674805 True -18 54948 31.484427452087402 0.5547194480895996 780.0625610351562 0.41213518381118774 967.6353759765625 0.4145289957523346 0.79406965 0.4579908549785614 True -19 57840 31.458159923553467 0.5547966957092285 740.276123046875 0.34711581468582153 967.4129638671875 0.41473114490509033 0.7950529 0.4588474929332733 True diff --git a/ENCSR541JMK/cherimoya.fold_2.performance.tsv b/ENCSR541JMK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7afbf08321bfa6082073d09e725c3038c33d91a2..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -967.4129638671875 0.374270498752594 0.41473114490509033 0.17821893095970154 0.7950528860092163 0.7574446201324463 0.4588474929332733 \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_3.evaluate.json b/ENCSR541JMK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index db4dbace561bc2b0466a68f3caca81fee16a5464..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702NNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_3.fit.json b/ENCSR541JMK/cherimoya.fold_3.fit.json deleted file mode 100644 index dfd9a1e98dde5d5d95acf9db0beb8d46f0730004..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF702NNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_3.log b/ENCSR541JMK/cherimoya.fold_3.log deleted file mode 100644 index f6e2c0965c10d8955e8ddc7defab3c20a57d6482..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 35.44097590446472 4.440364360809326 876.506103515625 0.8118337392807007 1183.6729736328125 0.25950607657432556 0.6087692 6.755319595336914 True -1 5564 30.9396493434906 10.128827810287476 1101.251953125 1.0913589000701904 1016.4645385742188 0.3582111597061157 0.7053595 2.8799355030059814 True -2 8346 30.919251680374146 18.613125801086426 770.667236328125 0.9213650822639465 990.6134643554688 0.3717275857925415 0.7051843 1.629097819328308 False -3 11128 30.946569681167603 0.5154671669006348 720.2105712890625 0.7876880764961243 977.5870361328125 0.37664052844047546 0.71396315 1.2723907232284546 True -4 13910 30.90246820449829 0.6195507049560547 991.463134765625 0.7023372054100037 963.8430786132812 0.38308948278427124 0.718499 1.165926218032837 True -5 16692 30.95186710357666 0.5653586387634277 987.1488037109375 0.5686005353927612 957.8095092773438 0.3860516846179962 0.7244402 1.07879638671875 True -6 19474 30.91102433204651 0.5256514549255371 704.9810180664062 0.48195523023605347 949.7542724609375 0.38994431495666504 0.7349594 0.8703399300575256 True -7 22256 30.89173722267151 0.5290441513061523 624.7503051757812 0.6346755623817444 943.25537109375 0.39366936683654785 0.7403683 0.7699815034866333 True -8 25038 30.480035305023193 0.5280053615570068 982.63232421875 0.7920734286308289 942.3916625976562 0.3933779001235962 0.7444414 0.771641731262207 True -9 27820 30.24651336669922 0.5285472869873047 696.1837158203125 0.49022823572158813 935.9422607421875 0.3981749415397644 0.7497725 0.7128131985664368 True -10 30602 30.24389386177063 0.5282754898071289 900.5089111328125 0.5135608315467834 931.4999389648438 0.400031179189682 0.7604587 0.6830142736434937 True -11 33384 30.253475189208984 12.476175546646118 766.3201293945312 0.4025183618068695 923.6533813476562 0.40486568212509155 0.7683577 0.6147490739822388 True -12 36166 30.28743267059326 0.5273499488830566 775.2705688476562 0.5554971694946289 921.6619873046875 0.4066331088542938 0.77353185 0.6073842644691467 True -13 38948 30.30758786201477 0.5418350696563721 806.306396484375 0.5457873344421387 914.6190795898438 0.41049864888191223 0.78501326 0.5701839327812195 True -14 41730 30.336440801620483 0.5808041095733643 949.2545166015625 0.40078920125961304 910.4610595703125 0.4122869372367859 0.7896329 0.5356806516647339 True -15 44512 30.290401220321655 0.5314509868621826 754.44677734375 0.3576923608779907 909.6661376953125 0.4121319651603699 0.79701823 0.4925893545150757 True -16 47294 30.5041925907135 0.5319020748138428 756.560791015625 0.36599797010421753 908.4485473632812 0.4131147563457489 0.8002284 0.4748004674911499 True -17 50076 30.405491828918457 0.5184388160705566 753.727294921875 0.5357476472854614 908.75537109375 0.41323092579841614 0.804465 0.45772168040275574 True -18 52858 30.41547441482544 0.5474331378936768 719.270751953125 0.38800525665283203 909.7549438476562 0.41328591108322144 0.80363053 0.45286378264427185 False -19 55640 30.41269850730896 0.5310192108154297 769.9724731445312 0.36676210165023804 908.1757202148438 0.41505950689315796 0.8028202 0.4544495642185211 False diff --git a/ENCSR541JMK/cherimoya.fold_3.performance.tsv b/ENCSR541JMK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9d71afce9d824c23578760348d9f2759487d11d1..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -908.75537109375 0.37840598821640015 0.4132309854030609 0.1734647899866104 0.8044649958610535 0.7504904270172119 0.45772168040275574 \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_4.evaluate.json b/ENCSR541JMK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 29fd9496e290337e3774651d655d0c702979d188..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702NNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_4.fit.json b/ENCSR541JMK/cherimoya.fold_4.fit.json deleted file mode 100644 index a897e37ebe973b6782a66fe17a5f04b268578702..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF702NNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541JMK/cherimoya.fold_4.log b/ENCSR541JMK/cherimoya.fold_4.log deleted file mode 100644 index 6c44746ee3e8737868c1bec397ff308470948f82..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 35.83143472671509 4.378762245178223 735.1928100585938 0.6982994675636292 1126.025634765625 0.2520464360713959 0.59618914 5.126842021942139 True -1 5606 31.222047090530396 0.603959321975708 774.8782958984375 0.6495742797851562 971.6442260742188 0.35038161277770996 0.682947 2.6798253059387207 True -2 8409 31.16581654548645 0.5539734363555908 828.7105102539062 0.48724067211151123 946.8964233398438 0.36427149176597595 0.6901247 1.7541958093643188 True -3 11212 31.236790657043457 0.5541110038757324 757.490478515625 0.5628349184989929 930.8828125 0.3738957345485687 0.69834214 1.3040735721588135 True -4 14015 31.164031744003296 0.5552804470062256 768.1075439453125 0.6281173229217529 924.3078002929688 0.37655290961265564 0.71211016 1.5023472309112549 True -5 16818 31.156760931015015 0.640744686126709 896.1280517578125 0.7375312447547913 920.0953979492188 0.3773542046546936 0.71362406 1.1161030530929565 True -6 19621 31.16160821914673 0.5552442073822021 600.0050659179688 0.5179646611213684 911.9783935546875 0.3835988938808441 0.71865714 1.0212595462799072 True -7 22424 30.523810386657715 2.5706324577331543 655.2636108398438 0.42317163944244385 908.2348022460938 0.38544774055480957 0.72055614 0.9598210453987122 True -8 25227 30.607182025909424 0.5994603633880615 678.6964111328125 0.46020498871803284 898.8468627929688 0.3909635841846466 0.7293677 0.877765953540802 True -9 28030 30.570892810821533 0.5755586624145508 780.7116088867188 0.4367887079715729 895.154296875 0.3935927152633667 0.7352427 0.8130020499229431 True -10 30833 30.659021139144897 0.580474853515625 712.2391357421875 0.39611414074897766 890.7894897460938 0.39614030718803406 0.74161315 0.705785870552063 True -11 33636 30.69404101371765 0.5841515064239502 705.2049560546875 0.4552405774593353 886.7001342773438 0.3987199664115906 0.74973375 0.6625077128410339 True -12 36439 30.596368312835693 0.5877125263214111 637.1434936523438 0.4384240508079529 880.0557861328125 0.40310412645339966 0.7575546 0.6230536699295044 True -13 39242 30.67832589149475 0.5730867385864258 644.1223754882812 0.341314435005188 879.4744873046875 0.401725172996521 0.7680491 0.5646907091140747 True -14 42045 30.614641427993774 0.7762129306793213 834.230224609375 0.4866875410079956 872.8472900390625 0.4064067304134369 0.77537996 0.5193986892700195 True -15 44848 30.64798140525818 0.5620999336242676 545.152587890625 0.2494415044784546 873.6984252929688 0.4054114520549774 0.7819723 0.4765607714653015 True -16 47651 30.6455397605896 0.5690572261810303 670.0232543945312 0.32992956042289734 872.0590209960938 0.4066566228866577 0.78709537 0.45168593525886536 True -17 50454 30.6129789352417 0.5448696613311768 833.7222900390625 0.4465652108192444 872.3522338867188 0.4063897728919983 0.7908136 0.432957261800766 True -18 53257 30.594481468200684 0.5595333576202393 811.8851318359375 0.24370160698890686 871.5674438476562 0.4077780246734619 0.79106104 0.4273741543292999 True -19 56060 30.48262095451355 0.5397319793701172 628.8016357421875 0.3195318579673767 873.6021728515625 0.4061852693557739 0.7904213 0.42832911014556885 False diff --git a/ENCSR541JMK/cherimoya.fold_4.performance.tsv b/ENCSR541JMK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 19217e01e2b3ace6f727b4d15a8a6691222c2d5d..0000000000000000000000000000000000000000 --- a/ENCSR541JMK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -871.5674438476562 0.3842647671699524 0.4077780246734619 0.16661851108074188 0.7910610437393188 0.7376992702484131 0.4273741543292999 \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_0.evaluate.json b/ENCSR541KFY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 41b4396f9b338cdb55770a5edde3951bff65eaa7..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236XGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_0.fit.json b/ENCSR541KFY/cherimoya.fold_0.fit.json deleted file mode 100644 index 5eaf8ed72e08348cb81d4fb966e5ba298ab7246c..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF236XGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_0.log b/ENCSR541KFY/cherimoya.fold_0.log deleted file mode 100644 index 07d8efa12a3f4ba9948a6b9a7c7e4be325470b1c..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3648 45.153974771499634 11.799616575241089 420.0296630859375 0.575494647026062 584.7117919921875 0.6669425368309021 0.7477849 3.8159031867980957 True -1 7296 40.76462769508362 0.7355976104736328 367.2464599609375 0.7874143719673157 517.9537353515625 0.7418004274368286 0.75833595 0.6204867959022522 True -2 10944 40.6327269077301 0.7142300605773926 422.5705261230469 0.975653886795044 508.5047302246094 0.7505171895027161 0.77300715 0.4159957468509674 True -3 14592 40.660911560058594 0.7045550346374512 366.13226318359375 0.778404712677002 503.4984130859375 0.756428062915802 0.7704333 0.381693035364151 False -4 18240 40.564738750457764 0.7101550102233887 414.1411437988281 0.912106990814209 501.625244140625 0.7590878009796143 0.7765899 0.36541590094566345 True -5 21888 40.60171627998352 0.7034401893615723 394.7262268066406 0.4461987614631653 499.31488037109375 0.7619502544403076 0.7804912 0.3636658489704132 True -6 25536 40.66145467758179 1.473839521408081 363.9778137207031 0.7899162769317627 498.30499267578125 0.7633393406867981 0.7779327 0.3676406741142273 False -7 29184 40.715625047683716 0.7046215534210205 431.97467041015625 0.5805016160011292 496.3400573730469 0.7653698921203613 0.7841715 0.35236966609954834 True -8 32832 40.630037784576416 0.6948583126068115 379.5533752441406 0.603291928768158 494.3123474121094 0.7681228518486023 0.7923854 0.3376227021217346 True -9 36480 40.60772347450256 0.6985080242156982 371.4300537109375 0.6277089715003967 492.68359375 0.7701853513717651 0.794189 0.32734647393226624 True -10 40128 40.61763143539429 0.6950335502624512 469.18035888671875 0.40681540966033936 490.74566650390625 0.7727091908454895 0.8011016 0.31975674629211426 True -11 43776 40.65124535560608 0.7122583389282227 369.98345947265625 0.5537675023078918 488.74774169921875 0.7749780416488647 0.80403125 0.3132447600364685 True -12 47424 40.647292613983154 0.7077794075012207 404.2588806152344 0.5673770904541016 487.0825500488281 0.7768686413764954 0.81223565 0.30356889963150024 True -13 51072 40.1984965801239 0.7031607627868652 410.234375 0.4819449484348297 485.1481628417969 0.7791780829429626 0.81706893 0.2947947680950165 True -14 54720 39.90449357032776 0.7023129463195801 353.01708984375 0.36055517196655273 483.66278076171875 0.7810458540916443 0.82364845 0.28974953293800354 True -15 58368 39.89345026016235 1.6463606357574463 311.88665771484375 0.24881906807422638 482.75244140625 0.7821269035339355 0.83049816 0.28238385915756226 True -16 62016 40.03151178359985 1.3985564708709717 397.8803405761719 0.5579394698143005 481.9507141113281 0.7830307483673096 0.8334136 0.28369536995887756 True -17 65664 42.95295524597168 21.376477241516113 341.62188720703125 0.48910701274871826 481.5509948730469 0.7832595705986023 0.8347713 0.28386160731315613 True -18 69312 39.90352153778076 0.8364849090576172 406.69622802734375 0.2703338861465454 481.7369384765625 0.7832233309745789 0.8352253 0.28650176525115967 True -19 72960 39.81857347488403 0.7030930519104004 361.60101318359375 0.19481024146080017 481.7992248535156 0.7830893993377686 0.8346365 0.29001468420028687 False diff --git a/ENCSR541KFY/cherimoya.fold_0.performance.tsv b/ENCSR541KFY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b15aca5f8b0e9bbfe3ba1f4b9463dfcc3141a048..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -481.7369384765625 0.19148384034633636 0.7832233309745789 0.3452203869819641 0.8352252840995789 0.8096793293952942 0.28650176525115967 \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_1.evaluate.json b/ENCSR541KFY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 20daea71123d90f349ac27f6f61f94928ee14da4..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236XGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_1.fit.json b/ENCSR541KFY/cherimoya.fold_1.fit.json deleted file mode 100644 index 9970d259410f105fa88b71d9f691dc64ead4a1aa..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF236XGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_1.log b/ENCSR541KFY/cherimoya.fold_1.log deleted file mode 100644 index e3e1d58c6c5fb963f7d60e0ad33113e41a0f7f79..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3674 46.35824227333069 8.052626371383667 501.6317443847656 0.5589847564697266 663.565673828125 0.6787056922912598 0.7478719 3.7564995288848877 True -1 7348 41.03904843330383 0.884474515914917 423.35595703125 0.8169958591461182 585.5086669921875 0.7522591352462769 0.7675762 0.6261892318725586 True -2 11022 40.97693967819214 5.688014268875122 393.2092590332031 0.44955623149871826 574.556396484375 0.7614958882331848 0.7763456 0.4836848974227905 True -3 14696 41.16942024230957 0.869520902633667 459.4203186035156 0.46386200189590454 570.2229614257812 0.7657346725463867 0.7875273 0.4008108973503113 True -4 18370 41.00120830535889 1.1689386367797852 398.4019775390625 0.8951727151870728 565.9520263671875 0.7698554396629333 0.7909154 0.39918628334999084 True -5 22044 41.07515835762024 0.8672599792480469 394.3196716308594 0.6024502515792847 563.3558959960938 0.7724842429161072 0.7931763 0.39549964666366577 True -6 25718 41.08082413673401 0.8838839530944824 349.68853759765625 0.8705750107765198 560.8779296875 0.7751203775405884 0.7875495 0.40394431352615356 False -7 29392 41.34949254989624 0.8639376163482666 442.34381103515625 0.44071727991104126 558.1324462890625 0.7775608897209167 0.7926164 0.3848680555820465 False -8 33066 41.14282512664795 0.8710677623748779 371.80462646484375 0.43995508551597595 555.5103759765625 0.7804297804832458 0.7993977 0.37401068210601807 True -9 36740 40.27953338623047 0.839285135269165 383.991943359375 0.624253511428833 553.6409912109375 0.7825222611427307 0.80152327 0.36519530415534973 True -10 40414 40.46145677566528 49.40719532966614 402.20001220703125 0.4935098886489868 550.4577026367188 0.7851372957229614 0.808425 0.34629184007644653 True -11 44088 40.354593992233276 1.3544025421142578 466.6986999511719 0.41374528408050537 547.3271484375 0.7877856492996216 0.8145647 0.33404436707496643 True -12 47762 40.478739976882935 0.8670551776885986 395.401123046875 0.4566042423248291 545.1900634765625 0.7898474335670471 0.8234408 0.3205813765525818 True -13 51436 40.23874568939209 0.8472950458526611 354.5994873046875 0.39348381757736206 543.3518676757812 0.7918921709060669 0.8307177 0.30868029594421387 True -14 55110 40.241870403289795 0.8395781517028809 433.2980041503906 0.2831864655017853 541.4397583007812 0.7936675548553467 0.8353198 0.3009515404701233 True -15 58784 40.16961455345154 0.8457472324371338 400.2540283203125 0.2559332251548767 539.8416137695312 0.7954561710357666 0.84186643 0.29207518696784973 True -16 62458 41.23496675491333 18.620570182800293 392.2331848144531 0.3782576024532318 538.7474975585938 0.7965139150619507 0.84711426 0.2901536226272583 True -17 66132 40.48339056968689 0.8431646823883057 371.5393371582031 0.2920014262199402 538.2230224609375 0.7969083786010742 0.84809446 0.290475457906723 True -18 69806 40.39962983131409 1.8789875507354736 350.8653259277344 0.33756113052368164 538.5243530273438 0.7968802452087402 0.8471789 0.29220402240753174 False -19 73480 40.47914528846741 11.50078535079956 380.4088134765625 0.24015484750270844 538.468017578125 0.7967299818992615 0.84859806 0.29739341139793396 True diff --git a/ENCSR541KFY/cherimoya.fold_1.performance.tsv b/ENCSR541KFY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 49b916b9bedaf8680c69475557b516f59fd23297..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -538.468017578125 0.178910493850708 0.7967299818992615 0.37926703691482544 0.848598062992096 0.8471920490264893 0.29739341139793396 \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_2.evaluate.json b/ENCSR541KFY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9ced8e5a2b93734a7aa5c7df86faf9f04340649a..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236XGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_2.fit.json b/ENCSR541KFY/cherimoya.fold_2.fit.json deleted file mode 100644 index c1b026a151a3c1e4384658c84a3bb4656d3591ab..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF236XGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_2.log b/ENCSR541KFY/cherimoya.fold_2.log deleted file mode 100644 index 3ae40e9858b91a809deb9f94e7cb5270c8c7501a..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3813 47.17224669456482 3.694103240966797 361.30389404296875 0.7503291368484497 607.0266723632812 0.6779674887657166 0.73928124 3.307594060897827 True -1 7626 42.64153528213501 0.7606039047241211 470.29876708984375 0.553862452507019 542.7030639648438 0.7470121383666992 0.7572115 0.7370526790618896 True -2 11439 42.86649751663208 0.7288744449615479 372.5640563964844 0.5134679079055786 532.9488525390625 0.7548365592956543 0.7748735 0.5076397061347961 True -3 15252 43.19980525970459 0.7204442024230957 461.96551513671875 0.3972025215625763 527.7612915039062 0.7598890662193298 0.77587044 0.4430408477783203 True -4 19065 41.64328622817993 0.7155723571777344 408.6725769042969 0.5618647336959839 525.62109375 0.7624468803405762 0.77989787 0.43853795528411865 True -5 22878 41.72365093231201 0.870319128036499 430.5550537109375 0.4288499355316162 523.6278686523438 0.7648221254348755 0.78326017 0.4102204442024231 True -6 26691 41.8161256313324 0.7375686168670654 404.4994201660156 0.5462762713432312 522.19091796875 0.7664281725883484 0.7893523 0.38707098364830017 True -7 30504 41.67525601387024 0.7253038883209229 377.82470703125 0.5421217679977417 519.8038940429688 0.7691266536712646 0.7877351 0.39047032594680786 False -8 34317 41.744627952575684 0.7228007316589355 354.02630615234375 0.35293734073638916 517.3063354492188 0.7717886567115784 0.79375845 0.3654569685459137 True -9 38130 41.56092047691345 0.7245533466339111 338.4150390625 0.43209540843963623 514.8341674804688 0.7743149399757385 0.8000557 0.34808745980262756 True -10 41943 41.79586744308472 0.7176780700683594 432.0855407714844 0.6882064342498779 512.3287353515625 0.7767704725265503 0.8046126 0.3432289659976959 True -11 45756 41.77630877494812 0.719085693359375 340.730712890625 0.3654966950416565 510.3393249511719 0.7787651419639587 0.80993545 0.3334892690181732 True -12 49569 41.65544247627258 0.7240915298461914 390.5293273925781 0.4027518928050995 508.333984375 0.7811412215232849 0.81751466 0.32102707028388977 True -13 53382 41.73977279663086 1.325390100479126 424.1225280761719 0.3328017592430115 506.155517578125 0.7835336327552795 0.82147807 0.3205164968967438 True -14 57195 41.761409521102905 0.7430379390716553 369.52679443359375 0.4577537178993225 504.1375732421875 0.7851976156234741 0.82773346 0.31715232133865356 True -15 61008 41.700419425964355 1.4034745693206787 389.9129638671875 0.3126252293586731 502.8465270996094 0.7866735458374023 0.8335957 0.30623865127563477 True -16 64821 41.63988971710205 0.7112941741943359 394.37908935546875 0.27794259786605835 501.9990539550781 0.7874007821083069 0.83725274 0.3023698031902313 True -17 68634 41.733234167099 0.7081732749938965 381.40216064453125 0.25035637617111206 501.3201904296875 0.7878270149230957 0.8391854 0.3036095201969147 True -18 72447 41.72155046463013 0.7185375690460205 346.62615966796875 0.22126974165439606 501.20916748046875 0.7878501415252686 0.83820325 0.3031059503555298 False -19 76260 41.64500427246094 3.589217185974121 364.4581298828125 0.1729518175125122 501.5741271972656 0.7877597808837891 0.83866966 0.30533701181411743 False diff --git a/ENCSR541KFY/cherimoya.fold_2.performance.tsv b/ENCSR541KFY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a08e3e10c092fc5056e0bf57a32108e6cce9150a..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -501.3201904296875 0.18671436607837677 0.7878270149230957 0.3571484386920929 0.8391854166984558 0.8200089931488037 0.3036095201969147 \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_3.evaluate.json b/ENCSR541KFY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fad93bf9ffacf212f619dc78408842574f7ca672..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236XGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_3.fit.json b/ENCSR541KFY/cherimoya.fold_3.fit.json deleted file mode 100644 index fda671898f024b7e91c7c8c170eedba733027ebf..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF236XGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_3.log b/ENCSR541KFY/cherimoya.fold_3.log deleted file mode 100644 index ddca923042cb898b4fca9c71e97396282bfb63e6..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3727 45.8928747177124 6.07905387878418 463.20123291015625 0.5031700134277344 584.8892211914062 0.679266631603241 0.7359033 4.086421012878418 True -1 7454 41.65836524963379 0.7419097423553467 416.2001037597656 0.7524552345275879 525.9483642578125 0.7438888549804688 0.7149538 0.6785463094711304 False -2 11181 41.60387396812439 40.079031467437744 394.05548095703125 0.6297973394393921 517.2072143554688 0.7515666484832764 0.7492068 0.5000948309898376 True -3 14908 42.11487531661987 0.7326250076293945 416.9376220703125 0.522235631942749 512.4851684570312 0.7572198510169983 0.7519185 0.4332498013973236 True -4 18635 41.58993935585022 0.7274727821350098 473.454345703125 0.5778093338012695 509.9142150878906 0.760165274143219 0.7585953 0.41146203875541687 True -5 22362 41.53203535079956 0.7193450927734375 368.1866455078125 0.4984142482280731 507.9948425292969 0.7626075744628906 0.75908643 0.41528400778770447 True -6 26089 41.60801386833191 0.7260315418243408 449.8172607421875 0.5687656402587891 506.009033203125 0.7652020454406738 0.76367927 0.4093994200229645 True -7 29816 41.56272912025452 1.4470901489257812 389.9136962890625 0.4815487861633301 504.1883239746094 0.7676955461502075 0.76492226 0.40170904994010925 True -8 33543 41.61370801925659 1.389794111251831 396.3194580078125 0.4590834975242615 502.26971435546875 0.7699800729751587 0.762507 0.3966405987739563 False -9 37270 41.72152066230774 0.7341268062591553 439.0028076171875 0.4731462597846985 500.4044189453125 0.7718860507011414 0.77269703 0.38201409578323364 True -10 40997 41.72815561294556 38.73187589645386 309.7879638671875 0.6277640461921692 498.7314453125 0.774248480796814 0.7748633 0.37915533781051636 True -11 44724 42.127002477645874 0.7395570278167725 467.21148681640625 0.461062490940094 496.5126647949219 0.7765034437179565 0.78443986 0.3601689636707306 True -12 48451 41.83220648765564 0.7350122928619385 405.31134033203125 0.3203590214252472 494.71478271484375 0.7785751819610596 0.7882355 0.3569038212299347 True -13 52178 41.78751587867737 0.7271482944488525 397.36199951171875 0.45955726504325867 492.851318359375 0.7803582549095154 0.79612684 0.3447859585285187 True -14 55905 41.72689938545227 0.7225887775421143 433.86083984375 0.674811601638794 491.2992248535156 0.7819686532020569 0.8029834 0.343292236328125 True -15 59632 41.861029863357544 0.7155635356903076 384.1800231933594 0.3439931869506836 489.9375 0.7833447456359863 0.8098429 0.33683645725250244 True -16 63359 41.095009088516235 0.7416679859161377 363.6808776855469 0.4312170147895813 489.3768005371094 0.783893346786499 0.813776 0.33476388454437256 True -17 67086 40.95842885971069 0.7201476097106934 382.8798828125 0.42070943117141724 488.89739990234375 0.7841838002204895 0.8193066 0.32989734411239624 True -18 70813 40.82197856903076 0.7396907806396484 381.93560791015625 0.36543959379196167 489.0397033691406 0.7841114401817322 0.81946146 0.3347929120063782 True -19 74540 40.906017541885376 0.7214264869689941 394.0797119140625 0.34160909056663513 488.9505310058594 0.7839915752410889 0.8188138 0.33649009466171265 False diff --git a/ENCSR541KFY/cherimoya.fold_3.performance.tsv b/ENCSR541KFY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3dc9e30bb6c40f479bec133ebf8720a5315d5259..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -489.0397033691406 0.18914689123630524 0.7841114401817322 0.34675371646881104 0.819461464881897 0.7950943112373352 0.3347929120063782 \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_4.evaluate.json b/ENCSR541KFY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 20644f41244a275d0af95e73c8f873d0ceacf931..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236XGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_4.fit.json b/ENCSR541KFY/cherimoya.fold_4.fit.json deleted file mode 100644 index 8ce2387524cd49baae72ea8e55e7cca9d98133ee..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF236XGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541KFY/cherimoya.fold_4.log b/ENCSR541KFY/cherimoya.fold_4.log deleted file mode 100644 index 2539b232a1732438761948303d23c1b040df09cd..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3795 47.13567852973938 3.7567672729492188 444.1690368652344 0.6979584693908691 559.1045532226562 0.6711987257003784 0.74495465 3.214249610900879 True -1 7590 42.295063972473145 0.7481625080108643 451.256103515625 1.0436372756958008 501.7237548828125 0.739916205406189 0.75667 0.5914937853813171 True -2 11385 42.450446367263794 1.4013235569000244 423.248291015625 0.5949658155441284 495.3471984863281 0.7461637258529663 0.77998793 0.45931777358055115 True -3 15180 42.32614350318909 0.7330844402313232 421.5048522949219 0.5291244983673096 491.2893981933594 0.7503176331520081 0.77889115 0.3886280357837677 False -4 18975 43.20692801475525 0.7332096099853516 402.5377197265625 0.49082818627357483 487.9698181152344 0.7544329762458801 0.78383744 0.358408659696579 True -5 22770 42.28649044036865 1.0029857158660889 316.04840087890625 1.0156421661376953 486.0044860839844 0.7564070820808411 0.7895528 0.353128582239151 True -6 26565 42.27177405357361 0.7386465072631836 456.35931396484375 0.4201720654964447 483.23345947265625 0.7597740888595581 0.7928941 0.3489193022251129 True -7 30360 42.30145573616028 0.7315070629119873 324.7054443359375 0.508446455001831 481.5982971191406 0.7615144848823547 0.79819393 0.34443649649620056 True -8 34155 42.305498123168945 0.7247624397277832 412.9031066894531 0.4421231150627136 479.7620544433594 0.7639418244361877 0.8030656 0.32883545756340027 True -9 37950 42.27881574630737 0.7255995273590088 435.83551025390625 0.37416577339172363 477.9068298339844 0.7664589881896973 0.80725175 0.3143990933895111 True -10 41745 42.28475761413574 36.901676177978516 427.7891540527344 0.46768468618392944 475.6409912109375 0.7689968347549438 0.81166 0.30781200528144836 True -11 45540 41.67409324645996 0.7144992351531982 401.73126220703125 0.6488341689109802 473.7291564941406 0.7711201310157776 0.81608194 0.2972522974014282 True -12 49335 41.42981314659119 0.714287519454956 378.21240234375 0.5613440871238708 472.4326477050781 0.7726684808731079 0.82469076 0.28419798612594604 True -13 53130 41.592426776885986 0.7210793495178223 369.84600830078125 0.4558490514755249 470.8738708496094 0.7746139168739319 0.82970035 0.27451497316360474 True -14 56925 41.500409841537476 0.7221074104309082 370.84271240234375 0.3065527379512787 468.9898986816406 0.7769398093223572 0.83770317 0.2653217017650604 True -15 60720 41.5157995223999 0.717693567276001 422.6996765136719 0.35529470443725586 467.96112060546875 0.7783655524253845 0.8425219 0.26083624362945557 True -16 64515 41.593278646469116 2.662804126739502 375.221923828125 0.37425869703292847 467.3499755859375 0.7790794372558594 0.84644175 0.2556201219558716 True -17 68310 41.63306641578674 1.3562979698181152 367.2857666015625 0.44158029556274414 466.99261474609375 0.7792161107063293 0.84758466 0.2572322189807892 True -18 72105 41.54752588272095 44.3251793384552 385.48138427734375 0.23150278627872467 467.0162353515625 0.7792021036148071 0.84918046 0.2595587968826294 True -19 75900 41.92377042770386 40.54324674606323 409.5048828125 0.21495521068572998 467.1307678222656 0.7791199088096619 0.84705 0.2620179355144501 False diff --git a/ENCSR541KFY/cherimoya.fold_4.performance.tsv b/ENCSR541KFY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9e59dd4078302c0551bd5c0b04572fb29f933868..0000000000000000000000000000000000000000 --- a/ENCSR541KFY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -467.0162353515625 0.19560544192790985 0.7792021036148071 0.3365415632724762 0.8491804599761963 0.8213920593261719 0.2595587968826294 \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_0.evaluate.json b/ENCSR541UPY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ae5f65e92b657458444c872b96dcca534aeb5d10..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF620OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_0.fit.json b/ENCSR541UPY/cherimoya.fold_0.fit.json deleted file mode 100644 index 6c859cff09a944961bd432ebf22171b1bf94fbf7..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF620OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_0.log b/ENCSR541UPY/cherimoya.fold_0.log deleted file mode 100644 index 5329a146298f6fffd29d84fa63d0b9cf4fbad83f..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2718 34.60190224647522 4.084294557571411 389.94854736328125 0.9259612560272217 530.8206176757812 0.1810268759727478 0.6136695 4.0096049308776855 True -1 5436 29.932530641555786 1.189253330230713 327.7249450683594 0.5504969358444214 476.72119140625 0.2712230682373047 0.7031862 1.4933899641036987 True -2 8154 30.074196100234985 0.5960538387298584 364.297119140625 0.7383089065551758 466.4998474121094 0.2855766713619232 0.7179727 0.8909203410148621 True -3 10872 30.004348754882812 0.7203965187072754 356.5076599121094 0.805141806602478 463.7340087890625 0.28748247027397156 0.73188937 0.657991349697113 True -4 13590 29.95713186264038 0.5827803611755371 439.62432861328125 0.5858039855957031 461.5547790527344 0.2914741635322571 0.73935175 0.5740957260131836 True -5 16308 29.956321239471436 1.3232486248016357 383.1535339355469 0.840573251247406 459.6723327636719 0.29443252086639404 0.748481 0.5109280943870544 True -6 19026 29.975325345993042 0.5922684669494629 366.53070068359375 0.6554880738258362 458.27734375 0.2967972755432129 0.7512357 0.5188952088356018 True -7 21744 30.00700569152832 0.5669169425964355 429.83154296875 0.6990395784378052 457.2752380371094 0.2984734773635864 0.7532002 0.4832337200641632 True -8 24462 30.003458976745605 1.9317281246185303 412.7461242675781 0.6806672811508179 455.2345886230469 0.3021913766860962 0.7572745 0.4735201895236969 True -9 27180 30.053699016571045 0.6062102317810059 336.787109375 0.5729859471321106 453.758544921875 0.30487412214279175 0.76285505 0.4508073925971985 True -10 29898 30.090617418289185 0.6091725826263428 309.4210510253906 0.26725709438323975 452.0729064941406 0.3069995045661926 0.7693446 0.4336714744567871 True -11 32616 30.172698736190796 0.5944900512695312 382.4203186035156 0.4957490563392639 450.99249267578125 0.3090939223766327 0.7732888 0.4287342131137848 True -12 35334 30.143040657043457 0.5809545516967773 377.7099304199219 0.32007813453674316 449.90484619140625 0.3113676607608795 0.7770526 0.421914279460907 True -13 38052 30.162402153015137 0.6239297389984131 351.9416809082031 0.5238850116729736 448.94110107421875 0.31293749809265137 0.78142416 0.4171643853187561 True -14 40770 30.108078718185425 0.5503833293914795 424.0487060546875 0.4697190523147583 448.55999755859375 0.31281495094299316 0.7896203 0.4039090871810913 True -15 43488 30.118743181228638 0.5763270854949951 364.90338134765625 0.5229064226150513 448.2121276855469 0.31245988607406616 0.7931409 0.3957870304584503 True -16 46206 30.039841413497925 0.575855016708374 375.7467041015625 0.3647845685482025 448.4303894042969 0.3121276795864105 0.7945973 0.39550915360450745 True -17 48924 30.056677103042603 0.5972435474395752 422.6792907714844 0.2788509726524353 448.5980224609375 0.3110271394252777 0.7943831 0.40105322003364563 False -18 51642 30.044306993484497 0.5533628463745117 360.9064636230469 0.3114529848098755 449.0609130859375 0.31064701080322266 0.7913421 0.4088903069496155 False -19 54360 30.032996654510498 0.5644919872283936 341.09515380859375 0.6302132606506348 448.3421936035156 0.312238872051239 0.78957546 0.4137668013572693 False diff --git a/ENCSR541UPY/cherimoya.fold_0.performance.tsv b/ENCSR541UPY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9bec6d145fba9e9232c1fa59d08e3bb5b8eb0ff8..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -448.4303894042969 0.4481724798679352 0.3121276795864105 0.11094599217176437 0.794597327709198 0.7349138855934143 0.39550915360450745 \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_1.evaluate.json b/ENCSR541UPY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c1b1ff58ca2c1efdad37b1bd993bc3e93c0fe0ea..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF620OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_1.fit.json b/ENCSR541UPY/cherimoya.fold_1.fit.json deleted file mode 100644 index 46b08bbf846f0123e4bc8bc01586693bb2b0d2f6..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF620OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_1.log b/ENCSR541UPY/cherimoya.fold_1.log deleted file mode 100644 index 3e5816593be2b4b7c6a04123de60a7aac7e81351..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 34.57951045036316 4.732118606567383 406.1475830078125 0.6730147004127502 630.5767822265625 0.19538037478923798 0.6042369 5.85123348236084 True -1 5418 29.9109206199646 0.7780318260192871 340.3175048828125 0.6419597268104553 559.7110595703125 0.2992267608642578 0.6999412 1.9263702630996704 True -2 8127 29.92414903640747 0.7338488101959229 362.2724609375 0.5989649891853333 547.2205810546875 0.3124105930328369 0.7231224 1.0683234930038452 True -3 10836 29.86832618713379 0.7207937240600586 410.48663330078125 0.35304853320121765 541.3588256835938 0.3163051903247833 0.7419439 0.8929875493049622 True -4 13545 29.855496168136597 0.7282733917236328 354.35321044921875 0.5689059495925903 539.0967407226562 0.31934550404548645 0.7507061 0.7959238886833191 True -5 16254 29.91431450843811 0.7177424430847168 349.7054443359375 0.4792565405368805 537.1434326171875 0.322205126285553 0.75180745 0.686051070690155 True -6 18963 29.89685082435608 0.7267971038818359 343.81561279296875 0.3673110008239746 532.9741821289062 0.3290174603462219 0.7563321 0.6488441824913025 True -7 21672 29.944311141967773 0.9349098205566406 340.39862060546875 0.4793519377708435 532.3578491210938 0.329723060131073 0.7611063 0.5762705206871033 True -8 24381 29.897544384002686 0.7335233688354492 393.08123779296875 0.48473262786865234 530.7670288085938 0.33039915561676025 0.766078 0.5553544759750366 True -9 27090 29.871440649032593 2.196918487548828 309.20074462890625 0.32140499353408813 528.0313720703125 0.33442962169647217 0.77117115 0.5420203804969788 True -10 29799 29.87203598022461 0.7288112640380859 364.47430419921875 0.3846989870071411 526.5548706054688 0.33684808015823364 0.77795404 0.49632588028907776 True -11 32508 29.833407878875732 0.7179243564605713 347.923828125 0.4756420850753784 525.41357421875 0.3380516767501831 0.78113365 0.48773688077926636 True -12 35217 29.865262746810913 0.7420272827148438 370.2669677734375 0.4024818539619446 523.0075073242188 0.34173768758773804 0.78732425 0.4793327748775482 True -13 37926 29.935129404067993 2.9225447177886963 428.82501220703125 0.43045616149902344 521.302734375 0.3439721465110779 0.79180044 0.4743710458278656 True -14 40635 30.320417165756226 0.7445030212402344 367.58599853515625 0.46092405915260315 520.2982177734375 0.3455900251865387 0.7990113 0.45525702834129333 True -15 43344 29.883628368377686 0.724452018737793 351.22772216796875 0.5261568427085876 520.4854736328125 0.34411555528640747 0.80536467 0.447831928730011 True -16 46053 29.947203636169434 0.7306993007659912 358.73944091796875 0.27403420209884644 521.3488159179688 0.34158629179000854 0.80464333 0.44845500588417053 False -17 48762 29.947129487991333 0.7262330055236816 335.09393310546875 0.17299562692642212 520.7445068359375 0.34381937980651855 0.80477387 0.45056596398353577 False -18 51471 29.932509899139404 0.7256984710693359 408.89471435546875 0.2422296702861786 521.16552734375 0.34339639544487 0.80447376 0.4587382376194 False -19 54180 29.901501178741455 0.71584153175354 338.79547119140625 0.2629299759864807 520.8590698242188 0.3444112539291382 0.8031674 0.46651479601860046 False diff --git a/ENCSR541UPY/cherimoya.fold_1.performance.tsv b/ENCSR541UPY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6ed5ea41283428e894146c918738f03bd1a3e625..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -520.4854736328125 0.42217206954956055 0.34411555528640747 0.13211388885974884 0.8053646683692932 0.7664552927017212 0.447831928730011 \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_2.evaluate.json b/ENCSR541UPY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index df70825c7a8c4a81f2c4de31e355b7f0e6f53139..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF620OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_2.fit.json b/ENCSR541UPY/cherimoya.fold_2.fit.json deleted file mode 100644 index 67ae7ba3130b0ced8f6ae0ac3f633a85132331ed..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF620OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_2.log b/ENCSR541UPY/cherimoya.fold_2.log deleted file mode 100644 index 2bfeb3da73c9ce8761179e446bcc55580420acb8..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.8072247505188 4.611217975616455 471.65264892578125 0.4473031759262085 544.641845703125 0.18960236012935638 0.57918435 3.837066173553467 True -1 5794 32.029611587524414 1.3630244731903076 320.82733154296875 0.540310263633728 484.7473449707031 0.2800646424293518 0.696682 1.0053850412368774 True -2 8691 31.993586778640747 0.5841109752655029 418.4258117675781 0.6748942136764526 478.1769104003906 0.28732141852378845 0.71584207 0.6937956809997559 True -3 11588 31.966710090637207 0.7864642143249512 340.1484375 0.555144190788269 474.27557373046875 0.2921176254749298 0.72600096 0.5897876024246216 True -4 14485 31.963299036026 0.6575343608856201 450.200927734375 0.6105101108551025 472.0028991699219 0.2977394163608551 0.7279542 0.5843169689178467 True -5 17382 31.998354196548462 0.5872442722320557 408.92431640625 0.3820968270301819 470.4141540527344 0.29916471242904663 0.7327047 0.5482441186904907 True -6 20279 31.95169997215271 0.5631904602050781 400.3970947265625 0.5390748977661133 467.61151123046875 0.3039062023162842 0.7416891 0.5164369940757751 True -7 23176 31.90138006210327 0.5583982467651367 355.6551513671875 0.39402833580970764 467.0696105957031 0.30460992455482483 0.74191254 0.5180166363716125 True -8 26073 31.940021276474 0.5665919780731201 388.84600830078125 0.4322856068611145 464.8531799316406 0.30908724665641785 0.7471562 0.5022546648979187 True -9 28970 32.105639934539795 0.5615952014923096 350.265380859375 0.5641461610794067 463.40740966796875 0.31191858649253845 0.7518275 0.4853128492832184 True -10 31867 31.98488187789917 0.563011646270752 391.1526184082031 0.5123473405838013 462.3451232910156 0.31253719329833984 0.7556483 0.4767717123031616 True -11 34764 31.99518370628357 1.7106001377105713 397.44281005859375 0.299638032913208 461.59130859375 0.3137989342212677 0.7593887 0.4637472331523895 True -12 37661 32.07080912590027 0.5708966255187988 418.9205322265625 0.3800932765007019 459.9295959472656 0.3166203200817108 0.76319 0.4549283981323242 True -13 40558 32.03651523590088 0.5721297264099121 342.92242431640625 0.45483607053756714 458.6405029296875 0.3195532560348511 0.77165693 0.44144922494888306 True -14 43455 31.969686269760132 19.26231861114502 375.3221435546875 0.43584781885147095 458.4608459472656 0.31906017661094666 0.7777132 0.43350544571876526 True -15 46352 32.2874972820282 0.6781299114227295 400.7839660644531 0.3496183454990387 457.5296630859375 0.32080399990081787 0.7826207 0.42818525433540344 True -16 49249 32.00372576713562 0.559920072555542 396.5586242675781 0.3698044419288635 457.8603210449219 0.3196486830711365 0.7844875 0.426789790391922 True -17 52146 32.00046443939209 0.571887731552124 332.4881896972656 0.27118998765945435 458.1882019042969 0.31884029507637024 0.78332806 0.4300196170806885 False -18 55043 32.0199830532074 1.2554686069488525 422.971435546875 0.4407283663749695 457.5822448730469 0.3207109570503235 0.7828829 0.43511560559272766 False -19 57940 31.67695188522339 1.79518723487854 336.03411865234375 0.27886730432510376 458.0886535644531 0.3188617527484894 0.78099984 0.44120144844055176 False diff --git a/ENCSR541UPY/cherimoya.fold_2.performance.tsv b/ENCSR541UPY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 005f6f0942903b869d79364dde742652cf49662a..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -457.8603210449219 0.44330599904060364 0.3196486234664917 0.11700285226106644 0.7844874858856201 0.7350140810012817 0.426789790391922 \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_3.evaluate.json b/ENCSR541UPY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 590f528c77bec645c25550d82505511c30d1e085..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF620OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_3.fit.json b/ENCSR541UPY/cherimoya.fold_3.fit.json deleted file mode 100644 index d81bc1b6eff7db3f4748a23a238e43eeba6b6d92..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF620OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_3.log b/ENCSR541UPY/cherimoya.fold_3.log deleted file mode 100644 index 66f1f2a5a9475f51d0e50818e10df0719332362e..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 36.34290099143982 4.201625823974609 411.6514892578125 0.4352613091468811 557.0037231445312 0.19586142897605896 0.6046926 4.236105442047119 True -1 5508 30.448487997055054 0.618816614151001 419.6359558105469 0.8759337663650513 506.2104187011719 0.2755870223045349 0.68518966 1.5793055295944214 True -2 8262 30.726699352264404 0.6050930023193359 384.9604187011719 0.7279754877090454 497.6356506347656 0.28502991795539856 0.70398676 0.9822945594787598 True -3 11016 30.407339572906494 0.5820906162261963 350.4105224609375 0.613578200340271 492.4419250488281 0.2932140529155731 0.70955366 0.7725592851638794 True -4 13770 30.402393102645874 0.5890467166900635 358.04315185546875 0.5311987400054932 491.5060729980469 0.292454332113266 0.72232574 0.6844485402107239 True -5 16524 30.394851207733154 0.5830478668212891 318.3007507324219 0.6985650062561035 487.84051513671875 0.2986978590488434 0.727838 0.5910985469818115 True -6 19278 30.381567001342773 0.5961487293243408 407.02630615234375 0.4903466999530792 486.931396484375 0.2995367646217346 0.73503786 0.5482525825500488 True -7 22032 30.38472819328308 0.9784610271453857 354.61614990234375 0.34701383113861084 485.467529296875 0.30249515175819397 0.7361219 0.5427715182304382 True -8 24786 30.468111038208008 0.5938796997070312 408.6668395996094 0.4611721634864807 484.501220703125 0.3036485016345978 0.74236095 0.5274621248245239 True -9 27540 30.4010488986969 0.6104176044464111 339.4679870605469 0.5522769689559937 482.58636474609375 0.30734896659851074 0.7500592 0.507594883441925 True -10 30294 30.372169971466064 0.5949642658233643 356.44036865234375 0.5716251134872437 481.3970947265625 0.3086692690849304 0.75877094 0.4957998991012573 True -11 33048 30.411586046218872 0.5909042358398438 416.9765625 0.5194974541664124 480.7835998535156 0.3096499443054199 0.76269644 0.48183244466781616 True -12 35802 30.385116815567017 0.5737900733947754 337.3564147949219 0.308363676071167 478.48760986328125 0.31384626030921936 0.7713986 0.46209055185317993 True -13 38556 30.453206777572632 0.5783224105834961 409.26824951171875 0.46060290932655334 478.08734130859375 0.31342214345932007 0.776408 0.4550316631793976 True -14 41310 30.37602925300598 0.5735223293304443 474.372802734375 0.48468419909477234 477.0712585449219 0.3145580589771271 0.7843474 0.44454580545425415 True -15 44064 30.445576429367065 0.5920286178588867 315.9493713378906 0.288534015417099 476.5531311035156 0.3157188296318054 0.7927262 0.43277642130851746 True -16 46818 30.428640127182007 1.8640789985656738 358.59332275390625 0.3050266206264496 477.09307861328125 0.31420230865478516 0.7963147 0.42806166410446167 True -17 49572 30.502350091934204 15.524711608886719 354.11505126953125 0.30136075615882874 476.65399169921875 0.31476569175720215 0.796592 0.4313950538635254 True -18 52326 30.739243745803833 0.5951616764068604 358.42236328125 0.29522866010665894 477.59716796875 0.3124232888221741 0.7971604 0.4375448524951935 True -19 55080 29.82871437072754 0.588306188583374 396.39093017578125 0.2305847704410553 477.42840576171875 0.3133201003074646 0.7958248 0.4406898319721222 False diff --git a/ENCSR541UPY/cherimoya.fold_3.performance.tsv b/ENCSR541UPY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 433d0a0b95f3c8b1f76500b578ef8b38943748fd..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -477.59716796875 0.4433739185333252 0.3124232888221741 0.11576355248689651 0.7971603870391846 0.7424354553222656 0.4375448524951935 \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_4.evaluate.json b/ENCSR541UPY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1f84a59d3fc002d5a0a73ab552ed0310ea22621f..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF620OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_4.fit.json b/ENCSR541UPY/cherimoya.fold_4.fit.json deleted file mode 100644 index 5cb9787585aa83236b6da3320955a1b12a3ea3dd..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF620OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR541UPY/cherimoya.fold_4.log b/ENCSR541UPY/cherimoya.fold_4.log deleted file mode 100644 index 59ec55c2e06a31ab8db80dd0e4d62b4054e3586f..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2801 35.74315118789673 4.228145122528076 363.4241943359375 0.7628423571586609 506.96160888671875 0.18278400599956512 0.5855379 3.741966962814331 True -1 5602 30.892771244049072 1.3949661254882812 366.02764892578125 0.7251026630401611 458.45697021484375 0.2645728886127472 0.686285 1.1338499784469604 True -2 8403 30.899802446365356 0.6705677509307861 404.46685791015625 0.9121202230453491 452.83685302734375 0.2711935341358185 0.70341855 0.6833480000495911 True -3 11204 30.878483295440674 0.5945389270782471 394.98748779296875 0.6358357667922974 448.6315002441406 0.27725228667259216 0.713686 0.5703650116920471 True -4 14005 30.925700426101685 0.6393156051635742 330.6691589355469 0.3829515874385834 445.98736572265625 0.28182631731033325 0.72909975 0.5619014501571655 True -5 16806 30.94784140586853 2.147817373275757 419.2440185546875 0.5175813436508179 444.4285888671875 0.2838689088821411 0.7357571 0.5524629354476929 True -6 19607 30.977712392807007 1.1868793964385986 368.9083251953125 0.5415807962417603 443.05743408203125 0.2862509489059448 0.73891497 0.5116052627563477 True -7 22408 30.87446904182434 0.5848338603973389 403.46710205078125 0.5269345045089722 442.8455505371094 0.2860371172428131 0.7429433 0.4881786108016968 True -8 25209 30.94500756263733 0.6040277481079102 310.22515869140625 0.4957461953163147 441.6618957519531 0.28825926780700684 0.74726474 0.47248825430870056 True -9 28010 30.920657873153687 0.6100504398345947 373.46136474609375 0.3802599310874939 439.409912109375 0.2931218147277832 0.7539095 0.4487069547176361 True -10 30811 30.935306072235107 0.5919063091278076 390.8408508300781 0.3237078785896301 439.0405578613281 0.29229700565338135 0.7591601 0.4362637996673584 True -11 33612 30.97102117538452 0.6044595241546631 367.2757568359375 0.5310617685317993 437.31427001953125 0.2964094877243042 0.7643532 0.4298906624317169 True -12 36413 30.924421787261963 0.5959548950195312 367.28369140625 0.4684467613697052 436.0776672363281 0.29873228073120117 0.7683005 0.4152197241783142 True -13 39214 30.960313081741333 0.6042563915252686 331.1631164550781 0.6246415376663208 435.2895812988281 0.30040958523750305 0.77484244 0.4058634340763092 True -14 42015 31.00450372695923 0.6984431743621826 389.7745666503906 0.381966233253479 434.58740234375 0.3009733557701111 0.78142214 0.39765650033950806 True -15 44816 30.949261903762817 23.946166276931763 420.278564453125 0.35964447259902954 434.43634033203125 0.30130913853645325 0.78579986 0.39081650972366333 True -16 47617 30.825050830841064 1.0124835968017578 396.6357116699219 0.4140688180923462 434.5373840332031 0.30113473534584045 0.78751886 0.3921663761138916 True -17 50418 30.39386820793152 1.7144575119018555 334.19354248046875 0.22582519054412842 433.76715087890625 0.3025398552417755 0.7868257 0.3959512412548065 False -18 53219 30.550626039505005 1.6507086753845215 374.79937744140625 0.24181067943572998 433.86737060546875 0.30357626080513 0.7852107 0.4042193591594696 False -19 56020 30.49389386177063 1.4100894927978516 401.070556640625 0.22751164436340332 434.9845886230469 0.30007264018058777 0.7829037 0.4085693359375 False diff --git a/ENCSR541UPY/cherimoya.fold_4.performance.tsv b/ENCSR541UPY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5481b204279d99cf217c008d2053be2818e71aa8..0000000000000000000000000000000000000000 --- a/ENCSR541UPY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -434.5373840332031 0.4541018605232239 0.30113473534584045 0.10485491156578064 0.7875188589096069 0.7296323776245117 0.3921663761138916 \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_0.evaluate.json b/ENCSR542RNG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4acc130c90cfe438a26ccb97581323d19b52b136..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF848SUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_0.fit.json b/ENCSR542RNG/cherimoya.fold_0.fit.json deleted file mode 100644 index 1872a676a5fad61092eed25fd69a82a9d892aa53..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF848SUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_0.log b/ENCSR542RNG/cherimoya.fold_0.log deleted file mode 100644 index e6e6d0b20005aed1fb38991a7be1a07dcc62b6e4..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3858 54.99457311630249 3.866973638534546 852.1721801757812 0.94646817445755 1216.937255859375 0.7083234190940857 0.71530956 7.767544269561768 True -1 7716 43.138270139694214 0.8136086463928223 817.5722045898438 1.3784528970718384 1006.9430541992188 0.8008385896682739 0.7250633 1.07377028465271 True -2 11574 42.97616744041443 0.7514781951904297 737.07568359375 0.8320143818855286 993.4989013671875 0.8045570850372314 0.7255781 0.8564484715461731 True -3 15432 43.06847357749939 0.7569494247436523 719.887451171875 1.1278717517852783 974.5609130859375 0.8119600415229797 0.7103555 0.8305653929710388 False -4 19290 48.37639260292053 5.5857789516448975 702.6331787109375 0.6789525151252747 965.888916015625 0.8154041767120361 0.7133254 0.8278743624687195 False -5 23148 43.476141929626465 10.501891136169434 688.1998291015625 1.1461421251296997 962.4633178710938 0.8169475197792053 0.7102707 0.8192687034606934 False -6 27006 43.10264325141907 14.60069727897644 762.22216796875 0.7721232175827026 952.6182250976562 0.8210223913192749 0.70890707 0.7995041608810425 False -7 30864 43.140252113342285 0.771686315536499 810.5862426757812 0.8196187019348145 942.4396362304688 0.8250179886817932 0.7162308 0.7629121541976929 False -8 34722 42.95262575149536 1.4693260192871094 790.2589111328125 0.7646871209144592 936.6019897460938 0.8272135257720947 0.72769797 0.7151593565940857 True -9 38580 42.984012842178345 55.19528079032898 668.9362182617188 1.321239948272705 929.3490600585938 0.8296521902084351 0.7362476 0.6973730325698853 True -10 42438 43.451345920562744 0.8211648464202881 798.2346801757812 0.44889774918556213 919.4984741210938 0.8329743146896362 0.7432648 0.674408495426178 True -11 46296 43.13197565078735 0.7618198394775391 784.692138671875 0.7998147010803223 911.6146850585938 0.8361707925796509 0.7527274 0.6566400527954102 True -12 50154 42.99237775802612 0.7675762176513672 592.359375 1.1635315418243408 904.3204956054688 0.838866114616394 0.76061904 0.6259241700172424 True -13 54012 42.45104932785034 0.7640962600708008 679.815673828125 0.8642853498458862 898.767578125 0.8413091897964478 0.76872474 0.6323541402816772 True -14 57870 42.05762267112732 42.286850929260254 567.553955078125 0.7857400178909302 893.2018432617188 0.8435141444206238 0.7790517 0.5992178916931152 True -15 61728 42.93061828613281 19.543527841567993 686.685791015625 0.6220351457595825 888.4669799804688 0.8454092144966125 0.7842643 0.581978976726532 True -16 65586 42.88713359832764 4.902953386306763 688.5780029296875 0.5756613612174988 887.0470581054688 0.846444308757782 0.7896096 0.5830097794532776 True -17 69444 43.00469207763672 29.920071125030518 773.455810546875 0.6913305521011353 886.161865234375 0.8467065095901489 0.79207575 0.5854182243347168 True -18 73302 42.310548067092896 0.768441915512085 715.07666015625 0.4870592951774597 887.2893676757812 0.846397876739502 0.79247355 0.5868018269538879 True -19 77160 42.284229040145874 0.7675755023956299 670.35791015625 0.5042320489883423 888.4339599609375 0.846201479434967 0.7904574 0.5919274687767029 False diff --git a/ENCSR542RNG/cherimoya.fold_0.performance.tsv b/ENCSR542RNG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 47ff3cb1842987fe70a0ba620ca96d2f6c9ba23b..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -887.2893676757812 0.1292959749698639 0.8463977575302124 0.5148125886917114 0.792473554611206 0.7373596429824829 0.5868018269538879 \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_1.evaluate.json b/ENCSR542RNG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 996cfa5095507e2eaecc53de4bc9d2c33497e181..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF848SUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_1.fit.json b/ENCSR542RNG/cherimoya.fold_1.fit.json deleted file mode 100644 index f2f136eaa824e0bc05fd40a6d221acce9d02889c..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF848SUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_1.log b/ENCSR542RNG/cherimoya.fold_1.log deleted file mode 100644 index d2d818c6bdbac21bea61ccf3aed3f8cb5c695671..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3802 47.23675775527954 3.9891412258148193 757.4688720703125 1.381105661392212 1414.725341796875 0.7062004208564758 0.7152929 10.04632568359375 True -1 7604 42.31845283508301 1.0275673866271973 806.0693359375 1.168737530708313 1133.2872314453125 0.8116520047187805 0.7392909 1.5620100498199463 True -2 11406 42.28496718406677 2.176903486251831 959.332763671875 0.8863658905029297 1109.1387939453125 0.8183193802833557 0.73496187 0.9293069243431091 False -3 15208 42.465025424957275 1.0058937072753906 975.6541748046875 0.8490999937057495 1093.9375 0.8225564956665039 0.74571264 0.802011251449585 True -4 19010 42.32112193107605 1.013404369354248 780.0392456054688 0.9843268394470215 1083.159912109375 0.8262161016464233 0.7421487 0.8051013350486755 False -5 22812 41.69554924964905 1.0389509201049805 849.077392578125 1.0097146034240723 1074.3419189453125 0.828728199005127 0.7469627 0.7808659076690674 True -6 26614 41.765174865722656 1.0938620567321777 679.8992919921875 0.8409725427627563 1064.8538818359375 0.8311516642570496 0.7544872 0.7590027451515198 True -7 30416 41.877084493637085 45.24791741371155 707.5771484375 1.0609172582626343 1054.5042724609375 0.8343545198440552 0.75898254 0.7005137205123901 True -8 34218 41.620078802108765 1.6803009510040283 767.8450927734375 0.7725012898445129 1045.7091064453125 0.8374661207199097 0.7656221 0.6784831881523132 True -9 38020 41.595731019973755 1.0379185676574707 691.5523681640625 0.8624855279922485 1037.707275390625 0.8402116298675537 0.773169 0.6710172891616821 True -10 41822 42.00013732910156 18.063525915145874 737.1217651367188 1.3157522678375244 1027.616455078125 0.8431434631347656 0.7781016 0.6523278951644897 True -11 45624 43.121132373809814 1.0263655185699463 642.889892578125 0.9330918788909912 1019.6233520507812 0.8451243042945862 0.7833391 0.6470349431037903 True -12 49426 43.80202627182007 16.133118867874146 668.4659423828125 0.9833295941352844 1011.4327392578125 0.8481406569480896 0.79292184 0.6125525236129761 True -13 53228 41.66512441635132 1.9175238609313965 821.0122680664062 0.5379266738891602 1001.9113159179688 0.8510989546775818 0.7997089 0.5792953372001648 True -14 57030 41.5976140499115 1.0196495056152344 662.9147338867188 0.5260555744171143 996.9573364257812 0.85312819480896 0.80832183 0.5826447010040283 True -15 60832 41.691389083862305 1.007216453552246 737.46435546875 0.5829136371612549 991.744140625 0.8547382354736328 0.8136629 0.5693624019622803 True -16 64634 44.12417507171631 18.656015634536743 640.545166015625 0.891299843788147 988.7164306640625 0.855949878692627 0.8204242 0.563519299030304 True -17 68436 41.64422869682312 0.9915111064910889 677.2415771484375 0.8382232189178467 989.5069580078125 0.8561490178108215 0.8204869 0.56264728307724 True -18 72238 41.70675325393677 2.8683340549468994 644.752685546875 0.6510155200958252 989.9873657226562 0.855803906917572 0.8201951 0.5678454637527466 False -19 76040 41.68108081817627 1.0209956169128418 773.4471435546875 0.48440128564834595 990.9664306640625 0.8556310534477234 0.8200052 0.5695059299468994 False diff --git a/ENCSR542RNG/cherimoya.fold_1.performance.tsv b/ENCSR542RNG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 34a065b8b2502bfc0f30297413527a27c5a60a98..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -989.5069580078125 0.11737740784883499 0.8561490178108215 0.5541078448295593 0.8204869031906128 0.7917125821113586 0.56264728307724 \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_2.evaluate.json b/ENCSR542RNG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bb1ab3eed731fbe3870a72b4d17bec414eda1a96..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF848SUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_2.fit.json b/ENCSR542RNG/cherimoya.fold_2.fit.json deleted file mode 100644 index a2bf254f037d605edb102b2ed14888e3a80842ff..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF848SUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_2.log b/ENCSR542RNG/cherimoya.fold_2.log deleted file mode 100644 index 4e275c203086bf16bffe2c64a4b400429e721d8f..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4049 51.885791063308716 3.864137649536133 971.2303466796875 1.8868236541748047 1261.4881591796875 0.7179859280586243 0.71824753 8.424376487731934 True -1 8098 45.175981760025024 0.7980794906616211 691.207763671875 1.6025065183639526 1052.119140625 0.8073781728744507 0.73448956 1.3017678260803223 True -2 12147 45.498903036117554 1.2048685550689697 1036.533447265625 1.3766283988952637 1027.9874267578125 0.8129364252090454 0.7332685 0.7600990533828735 False -3 16196 45.25554156303406 0.7937359809875488 723.5399169921875 0.9154188632965088 1008.6895751953125 0.8186778426170349 0.72734797 0.6951072812080383 False -4 20245 45.32257032394409 3.3544459342956543 650.61181640625 1.0667035579681396 1003.07177734375 0.821870744228363 0.7364985 0.7009600400924683 True -5 24294 50.09802460670471 4.680120468139648 773.4697875976562 0.8087535500526428 992.9893188476562 0.8249032497406006 0.7386932 0.6810845136642456 True -6 28343 45.44093656539917 0.8412477970123291 776.1689453125 1.3634955883026123 985.6795654296875 0.8277099132537842 0.7484434 0.682833194732666 True -7 32392 45.07412075996399 0.7965869903564453 805.4251708984375 1.1126433610916138 979.1503295898438 0.8294833302497864 0.75015503 0.6666940450668335 True -8 36441 45.28906226158142 0.794274091720581 738.28857421875 1.2907079458236694 969.2703247070312 0.8327586650848389 0.75572634 0.6468575596809387 True -9 40490 45.28050231933594 0.7907874584197998 619.5155029296875 1.087306022644043 962.593017578125 0.835588812828064 0.7590592 0.6377199292182922 True -10 44539 45.01892113685608 0.7892241477966309 780.2010498046875 0.8396674394607544 956.9742431640625 0.8376005291938782 0.7681172 0.6214178204536438 True -11 48588 44.44150424003601 0.7816557884216309 740.9903564453125 0.6478908061981201 950.641845703125 0.8401577472686768 0.77225167 0.6169936656951904 True -12 52637 44.23636722564697 0.7890353202819824 678.728271484375 0.5608643293380737 942.9799194335938 0.8426633477210999 0.7806267 0.6017928719520569 True -13 56686 44.457342863082886 27.278462648391724 770.8907470703125 0.6917964816093445 937.1830444335938 0.8450452089309692 0.7842373 0.6033679246902466 True -14 60735 45.95508337020874 40.446500062942505 691.9501342773438 0.5587007403373718 931.949462890625 0.847009539604187 0.79140043 0.5922465920448303 True -15 64784 45.374215602874756 0.7854483127593994 751.1841430664062 0.5913234949111938 929.1726684570312 0.8488308787345886 0.79706705 0.5728628635406494 True -16 68833 44.43905520439148 0.8001699447631836 706.17333984375 1.1235368251800537 926.809326171875 0.8496644496917725 0.80056995 0.576994001865387 True -17 72882 44.47675132751465 0.7850210666656494 648.44140625 0.7243807315826416 926.72509765625 0.8500668406486511 0.80327135 0.5739961862564087 True -18 76931 44.30717849731445 0.7848086357116699 797.0972290039062 0.5106189250946045 927.3837890625 0.8499197959899902 0.80335355 0.5713895559310913 True -19 80980 44.889904260635376 39.6369206905365 741.72998046875 0.5528318881988525 928.123779296875 0.84969162940979 0.80236465 0.5758021473884583 False diff --git a/ENCSR542RNG/cherimoya.fold_2.performance.tsv b/ENCSR542RNG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a2d6d7f43ca78e28f4912c9dce6ab5982c23d063..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -927.3837890625 0.1247217133641243 0.8499196171760559 0.5324589014053345 0.8033535480499268 0.7613677978515625 0.5713895559310913 \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_3.evaluate.json b/ENCSR542RNG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 152f4d917ca0b0f976d196a4978d89ff716dedf4..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF848SUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_3.fit.json b/ENCSR542RNG/cherimoya.fold_3.fit.json deleted file mode 100644 index 90b251d8390c330d47772e01dfca515f4b75ac78..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF848SUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_3.log b/ENCSR542RNG/cherimoya.fold_3.log deleted file mode 100644 index a3372a2fcc5a9f7ff2b4710609e855ca28df5f5c..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3890 49.980205059051514 3.7521090507507324 1019.8190307617188 1.266366958618164 1170.4593505859375 0.7033655047416687 0.71443963 7.734427452087402 True -1 7780 43.328407526016235 0.7403581142425537 759.5247802734375 1.0477803945541382 976.0560913085938 0.7967928051948547 0.72043675 1.3618119955062866 True -2 11670 43.535563468933105 0.7327854633331299 723.7799072265625 1.198675513267517 960.42529296875 0.8020576238632202 0.70575166 0.891371488571167 False -3 15560 49.462846994400024 0.7241866588592529 732.882568359375 1.1555769443511963 941.0474853515625 0.8091190457344055 0.7141787 0.7693615555763245 False -4 19450 42.655861377716064 0.7091307640075684 830.5413208007812 1.0261479616165161 933.551025390625 0.8119826912879944 0.7119645 0.8212665915489197 False -5 23340 42.421757221221924 0.7234759330749512 782.262939453125 0.8169387578964233 923.9179077148438 0.8158581852912903 0.7176628 0.7690327167510986 False -6 27230 42.450517416000366 0.7074036598205566 729.410888671875 1.21805739402771 917.2012329101562 0.8183403015136719 0.722756 0.7212831974029541 True -7 31120 42.348681688308716 1.4343252182006836 699.0328369140625 0.7811546921730042 910.321044921875 0.8213982582092285 0.73449177 0.6867260932922363 True -8 35010 43.196269273757935 0.7173357009887695 692.2625732421875 0.7672593593597412 902.7274169921875 0.8243594765663147 0.7362186 0.6727076768875122 True -9 38900 46.69434905052185 12.16369080543518 803.745849609375 0.8666698336601257 896.598876953125 0.8266112208366394 0.74561894 0.6532148718833923 True -10 42790 42.56560015678406 0.7122952938079834 678.4202270507812 0.870805025100708 890.3111572265625 0.8293390274047852 0.7496536 0.6417708992958069 True -11 46680 42.527859926223755 0.7230844497680664 600.257568359375 0.9966459274291992 884.0826416015625 0.83197420835495 0.75758064 0.6283835172653198 True -12 50570 42.447914838790894 0.707484245300293 768.2146606445312 0.9776067733764648 877.0006713867188 0.8345171213150024 0.765536 0.6062942147254944 True -13 54460 42.43651294708252 2.2891669273376465 722.13232421875 0.752151370048523 871.9923706054688 0.8369253277778625 0.7749837 0.5903064012527466 True -14 58350 44.08280849456787 21.579660415649414 739.2039184570312 0.7555253505706787 865.6632690429688 0.8392274975776672 0.78160447 0.5699695348739624 True -15 62240 42.4329719543457 0.7226293087005615 724.0056762695312 0.5368724465370178 862.4743041992188 0.8411747217178345 0.7919344 0.554268479347229 True -16 66130 42.45476460456848 0.7155239582061768 717.4568481445312 0.5907077789306641 859.8069458007812 0.8423948287963867 0.7950595 0.5593731999397278 True -17 70020 46.72649049758911 0.7134597301483154 655.7344360351562 0.46437162160873413 859.8854370117188 0.8426147103309631 0.79658407 0.5621242523193359 True -18 73910 42.43252158164978 0.7109899520874023 663.8658447265625 0.6440916657447815 860.88330078125 0.8423404097557068 0.7975171 0.5646209716796875 True -19 77800 42.47709631919861 6.51832914352417 644.1756591796875 0.549017071723938 861.266845703125 0.8422502279281616 0.7976041 0.5665343999862671 True diff --git a/ENCSR542RNG/cherimoya.fold_3.performance.tsv b/ENCSR542RNG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 49fe69e87f6490b1ae6b634f1d7324f49d1cf13a..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -861.266845703125 0.13301339745521545 0.8422501683235168 0.5011178851127625 0.7976040840148926 0.7445084452629089 0.5665343999862671 \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_4.evaluate.json b/ENCSR542RNG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1d1547c2b047dec1dc804a6186bd45f124ce5a04..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF848SUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_4.fit.json b/ENCSR542RNG/cherimoya.fold_4.fit.json deleted file mode 100644 index 1de5ce9e7af402884ee9f8c99bb695be52e99108..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF848SUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_4.log b/ENCSR542RNG/cherimoya.fold_4.log deleted file mode 100644 index b59da1f3c35feac0034e2390d21bd1d581281b29..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3953 48.88255071640015 3.8429689407348633 766.64013671875 1.1740391254425049 1167.7037353515625 0.70194411277771 0.7063695 7.970501899719238 True -1 7906 44.14253211021423 0.7803092002868652 971.4627685546875 1.0601215362548828 971.6085205078125 0.7973901033401489 0.7079677 1.2696458101272583 True -2 11859 44.0568687915802 0.7640562057495117 735.9658203125 1.4258346557617188 947.900634765625 0.8057700395584106 0.7073924 0.8063812851905823 False -3 15812 44.09100580215454 40.63368344306946 846.125 1.37154221534729 934.5757446289062 0.8106457591056824 0.70651686 0.7706533670425415 False -4 19765 44.837043046951294 0.7803611755371094 921.0985717773438 1.0630676746368408 923.9440307617188 0.8144450783729553 0.71592367 0.7267467379570007 True -5 23718 44.02761745452881 0.7748498916625977 720.22509765625 0.9731302261352539 916.8574829101562 0.8166905641555786 0.71327245 0.7384147644042969 False -6 27671 44.02836036682129 1.1818153858184814 664.8871459960938 1.1012687683105469 911.1494750976562 0.8194709420204163 0.72390115 0.6821557879447937 True -7 31624 44.07195258140564 0.7721872329711914 869.9765625 1.3083198070526123 905.4577026367188 0.8218573331832886 0.7253552 0.6664631962776184 True -8 35577 44.032628536224365 0.774885892868042 771.2213745117188 0.7786352038383484 897.715087890625 0.8247923851013184 0.73015654 0.6653111577033997 True -9 39530 43.99532461166382 0.7751264572143555 752.8259887695312 1.0747647285461426 892.56298828125 0.8268252015113831 0.73127395 0.6668863296508789 True -10 43483 44.04969620704651 0.7649035453796387 750.9400024414062 1.1145262718200684 885.3528442382812 0.8299493193626404 0.7377168 0.6435897350311279 True -11 47436 44.060343742370605 0.7724237442016602 671.0751953125 1.291066288948059 879.88525390625 0.8322270512580872 0.7438201 0.6315396428108215 True -12 51389 44.20121121406555 0.7843964099884033 647.4534912109375 0.9355272054672241 872.9519653320312 0.8349729776382446 0.75380045 0.6115294694900513 True -13 55342 44.1650116443634 0.7580828666687012 699.783203125 1.3200279474258423 867.6729736328125 0.8375316858291626 0.7670745 0.59330153465271 True -14 59295 43.36156725883484 0.7727952003479004 676.8795166015625 0.9103851318359375 862.5407104492188 0.8396193981170654 0.7706148 0.5828678011894226 True -15 63248 43.20098304748535 0.7701020240783691 729.4370727539062 0.8647620677947998 860.2400512695312 0.8415632247924805 0.7801741 0.5786194801330566 True -16 67201 43.24005126953125 0.7668313980102539 689.9721069335938 0.5431023836135864 858.271240234375 0.8426693081855774 0.78494 0.5686450004577637 True -17 71154 43.17317056655884 2.1628222465515137 702.99951171875 0.5918188095092773 857.8704223632812 0.8430769443511963 0.7888178 0.5749574899673462 True -18 75107 43.1470890045166 1.7785592079162598 636.3587646484375 0.6595798134803772 857.8896484375 0.8430962562561035 0.7881876 0.5764039754867554 False -19 79060 43.30102801322937 0.7713708877563477 636.735107421875 0.6302007436752319 858.7112426757812 0.8430718183517456 0.7882731 0.5811408758163452 False diff --git a/ENCSR542RNG/cherimoya.fold_4.performance.tsv b/ENCSR542RNG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fa42273c8e4b4355ba0b72cdb6e39bfeb8a1637d..0000000000000000000000000000000000000000 --- a/ENCSR542RNG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -857.8704223632812 0.13263064622879028 0.8430769443511963 0.5032305717468262 0.788817822933197 0.7237371206283569 0.5749574899673462 \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_0.evaluate.json b/ENCSR543WNA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c6f9706ae02858afc6d015853d8960e41cdebfa7..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF604AIP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_0.fit.json b/ENCSR543WNA/cherimoya.fold_0.fit.json deleted file mode 100644 index 1d9b7a0b5d2d99a5f19b32bdda21ac0834592713..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF604AIP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_0.log b/ENCSR543WNA/cherimoya.fold_0.log deleted file mode 100644 index 5c4c5248308a53879a262207a87505770108db09..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1794 26.046070098876953 3.541969060897827 282.63946533203125 0.7451860904693604 379.2081604003906 0.14507803320884705 0.73403126 8.867040634155273 True -1 3588 20.027679443359375 0.40371036529541016 309.34429931640625 0.5032590627670288 359.1720886230469 0.19678856432437897 0.7984607 2.873234748840332 True -2 5382 19.98171901702881 0.3613905906677246 307.8018798828125 0.7044922113418579 344.7670593261719 0.22312265634536743 0.82840437 1.2664774656295776 True -3 7176 19.909373998641968 0.35617923736572266 263.56524658203125 0.46471455693244934 339.0238952636719 0.2335064858198166 0.8400598 0.8559779524803162 True -4 8970 19.94684362411499 0.3538339138031006 311.1779479980469 0.5671329498291016 337.33013916015625 0.2367527037858963 0.8461155 0.6933274865150452 True -5 10764 19.91163182258606 0.3538942337036133 262.3465576171875 0.44971540570259094 336.5881042480469 0.23847702145576477 0.852008 0.6211197972297668 True -6 12558 19.9223849773407 0.5889050960540771 238.92263793945312 0.3891221284866333 335.6888122558594 0.2411576360464096 0.8560733 0.5633162260055542 True -7 14352 19.959911823272705 0.351715087890625 306.0386962890625 0.39103591442108154 335.15814208984375 0.2420126050710678 0.861734 0.5073389410972595 True -8 16146 19.908130407333374 0.3624730110168457 365.0766906738281 0.6108700633049011 334.64874267578125 0.24320265650749207 0.86558944 0.46369707584381104 True -9 17940 19.975694179534912 0.35054469108581543 214.17160034179688 0.5802921056747437 333.32293701171875 0.24661745131015778 0.87017727 0.43275877833366394 True -10 19734 19.900289297103882 0.35886049270629883 321.07269287109375 0.48164093494415283 332.50738525390625 0.24837473034858704 0.87186193 0.4180489182472229 True -11 21528 19.920066118240356 0.7331352233886719 305.41949462890625 0.44599637389183044 332.4834899902344 0.24880847334861755 0.87641406 0.41133105754852295 True -12 23322 19.87733030319214 0.34693336486816406 326.1181945800781 0.3444739580154419 332.18157958984375 0.2488437294960022 0.876858 0.3945448100566864 True -13 25116 19.9134738445282 0.35793209075927734 303.67388916015625 0.4355055093765259 332.26092529296875 0.2485753297805786 0.8810386 0.38418397307395935 True -14 26910 19.880242824554443 1.2011620998382568 302.0735778808594 0.2724853456020355 331.4996337890625 0.25026971101760864 0.88103914 0.37302887439727783 True -15 28704 19.880977630615234 0.34945011138916016 196.55917358398438 0.26999467611312866 331.4507751464844 0.25027936697006226 0.8815719 0.3711830973625183 True -16 30498 19.874109745025635 0.3528423309326172 340.1699523925781 0.38833582401275635 331.5315246582031 0.2502553164958954 0.8821195 0.37322670221328735 True -17 32292 19.912691831588745 0.3529484272003174 241.59642028808594 0.3118964731693268 332.1411437988281 0.24866323173046112 0.87956077 0.3843485116958618 False -18 34086 19.880003690719604 0.34888315200805664 261.18585205078125 0.2591773271560669 331.93377685546875 0.2494354546070099 0.8778442 0.3967641294002533 False -19 35880 19.873892068862915 0.8707013130187988 214.77059936523438 0.4050791263580322 332.2475280761719 0.2480858862400055 0.8763939 0.404977411031723 False diff --git a/ENCSR543WNA/cherimoya.fold_0.performance.tsv b/ENCSR543WNA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ad76beb21b962823483069eea4c5081c9cb2aa61..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -331.5315246582031 0.5024058818817139 0.2502553164958954 0.08649685233831406 0.8821194767951965 0.8337530493736267 0.37322670221328735 \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_1.evaluate.json b/ENCSR543WNA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9269d119f906d9010e661708def632f3cbe79fd6..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF604AIP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_1.fit.json b/ENCSR543WNA/cherimoya.fold_1.fit.json deleted file mode 100644 index 298f8cc433689c645d9eedbdad6889ed2407ffd8..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF604AIP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_1.log b/ENCSR543WNA/cherimoya.fold_1.log deleted file mode 100644 index 72f423f9a76fc6b9aa21dfd5c8c9540a6573537e..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1751 23.99779725074768 4.09239649772644 285.69842529296875 0.8264100551605225 442.969482421875 0.1562662571668625 0.7209297 10.535320281982422 True -1 3502 19.52481961250305 1.3879685401916504 256.29302978515625 0.5131968855857849 421.47467041015625 0.20809204876422882 0.77634114 4.006648063659668 True -2 5253 19.097355127334595 0.5401861667633057 258.98944091796875 0.7965409159660339 400.2658386230469 0.2457347959280014 0.8265707 1.759672999382019 True -3 7004 19.06720232963562 0.5550475120544434 285.44464111328125 0.46735405921936035 393.7142639160156 0.2556237280368805 0.849429 1.0480821132659912 True -4 8755 19.004464626312256 0.5232763290405273 217.50228881835938 0.635100781917572 391.6254577636719 0.2601820230484009 0.86072683 0.7574687600135803 True -5 10506 19.102202653884888 0.525972843170166 274.7141418457031 0.6254727840423584 389.9839172363281 0.26376673579216003 0.86170715 0.6858890056610107 True -6 12257 19.029932498931885 0.5158796310424805 329.1883544921875 0.7549950480461121 389.1551818847656 0.2655545771121979 0.8677686 0.6389375925064087 True -7 14008 19.022040367126465 0.5253558158874512 272.1180725097656 0.37233105301856995 388.47869873046875 0.26737159490585327 0.8740138 0.5727497339248657 True -8 15759 19.080180168151855 0.5340940952301025 261.6995849609375 0.2976565957069397 387.6956787109375 0.2691376507282257 0.87733275 0.5246233940124512 True -9 17510 19.073752403259277 0.5364515781402588 212.39529418945312 0.42076340317726135 386.87957763671875 0.2708180546760559 0.87946546 0.47845953702926636 True -10 19261 19.028529405593872 0.5345284938812256 249.90850830078125 0.47756412625312805 386.2926330566406 0.27186575531959534 0.8844305 0.4529247283935547 True -11 21012 19.036981344223022 0.5367658138275146 292.27679443359375 0.43269315361976624 385.17474365234375 0.27422183752059937 0.88583845 0.4164828956127167 True -12 22763 19.02815890312195 0.525639533996582 263.85198974609375 0.41547635197639465 384.8321838378906 0.2754404842853546 0.88860416 0.40320539474487305 True -13 24514 19.0278217792511 0.5339767932891846 279.7813720703125 0.42657744884490967 384.4802551269531 0.27636173367500305 0.8910532 0.3945954740047455 True -14 26265 19.021789073944092 0.527930736541748 330.826171875 0.4311539828777313 383.89306640625 0.2774471342563629 0.8938025 0.3818015456199646 True -15 28016 19.02348494529724 0.5337717533111572 278.61114501953125 0.24003489315509796 384.5901794433594 0.2750270962715149 0.8926467 0.3885735273361206 False -16 29767 19.015586853027344 1.3239777088165283 306.4927978515625 0.35750293731689453 384.29864501953125 0.27617955207824707 0.88991946 0.3951699733734131 False -17 31518 19.07449507713318 0.5229015350341797 229.03927612304688 0.16537028551101685 384.9552307128906 0.2741463780403137 0.88899064 0.4127599895000458 False -18 33269 19.07515525817871 0.5275881290435791 215.3251953125 0.2433401346206665 385.2408447265625 0.2732153832912445 0.88647234 0.4267651438713074 False -19 35020 19.070663690567017 0.5899298191070557 282.9792785644531 0.2812635898590088 385.9264221191406 0.2714534103870392 0.88411367 0.43844476342201233 False diff --git a/ENCSR543WNA/cherimoya.fold_1.performance.tsv b/ENCSR543WNA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e93bc3c0a437bd05b437a9b35f282a654a485179..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -383.89306640625 0.47844377160072327 0.2774471640586853 0.10212460905313492 0.8938025236129761 0.8724866509437561 0.3818015456199646 \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_2.evaluate.json b/ENCSR543WNA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1bc93d3905c16d41b38770fa938071239eebd714..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF604AIP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_2.fit.json b/ENCSR543WNA/cherimoya.fold_2.fit.json deleted file mode 100644 index 724fbee4bdf7229b397d1c32642b772833bd42c8..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF604AIP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_2.log b/ENCSR543WNA/cherimoya.fold_2.log deleted file mode 100644 index 5b29f46c9ffa821b5799c71e44c648b47fb2e7cc..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1899 25.524056434631348 3.601783514022827 269.8285827636719 0.8390458226203918 397.0979309082031 0.1517074853181839 0.7145524 8.082562446594238 True -1 3798 21.10575819015503 0.445446252822876 255.9364013671875 0.5081459283828735 373.7539978027344 0.2079954594373703 0.77213436 3.135678768157959 True -2 5697 21.0969455242157 0.388777494430542 266.0727844238281 0.6471983194351196 358.1065368652344 0.23292729258537292 0.82151616 1.588539481163025 True -3 7596 21.084101915359497 0.3685574531555176 257.7016906738281 0.9175595045089722 352.9466857910156 0.24156945943832397 0.8347748 0.7993380427360535 True -4 9495 21.06365990638733 0.3761942386627197 357.543701171875 0.6291985511779785 351.2007751464844 0.2453891634941101 0.84220153 0.6664616465568542 True -5 11394 21.020657062530518 0.3689608573913574 258.26397705078125 0.58418208360672 350.23626708984375 0.247628852725029 0.84743553 0.6227210760116577 True -6 13293 21.078233242034912 0.5753953456878662 285.28564453125 0.3919970393180847 349.5690612792969 0.24958661198616028 0.8529627 0.5885291695594788 True -7 15192 21.068687438964844 0.3802783489227295 239.50582885742188 0.47716933488845825 348.5865478515625 0.2521647810935974 0.8592344 0.5429145097732544 True -8 17091 21.086594343185425 0.3678429126739502 226.0623779296875 0.508741021156311 347.9921569824219 0.25233784317970276 0.8633026 0.5147542357444763 True -9 18990 21.113818168640137 0.37934327125549316 262.22503662109375 0.3555890619754791 347.6941223144531 0.25375303626060486 0.8644937 0.4802163541316986 True -10 20889 20.658146619796753 0.3645358085632324 293.5465087890625 0.33373624086380005 346.7822570800781 0.2560025155544281 0.86894584 0.43477585911750793 True -11 22788 20.68379855155945 0.37137770652770996 233.90151977539062 0.3483191132545471 346.37921142578125 0.25732114911079407 0.87224585 0.4167599081993103 True -12 24687 20.696035146713257 0.3682994842529297 262.413330078125 0.662642240524292 345.6114807128906 0.2586812674999237 0.8741746 0.4044231176376343 True -13 26586 20.722408294677734 0.37576937675476074 300.80267333984375 0.2968409061431885 345.3855895996094 0.2594805657863617 0.8764138 0.39802786707878113 True -14 28485 20.644590854644775 0.37431764602661133 265.4597473144531 0.5320224165916443 344.8910827636719 0.260267436504364 0.87797755 0.39371436834335327 True -15 30384 20.645089626312256 0.3715221881866455 289.00634765625 0.34522438049316406 344.8236389160156 0.26059889793395996 0.87808895 0.38866347074508667 True -16 32283 20.681296586990356 0.3712775707244873 286.22955322265625 0.2549433708190918 344.9828796386719 0.25960180163383484 0.8777503 0.3909370005130768 False -17 34182 20.68539333343506 0.3665032386779785 232.89451599121094 0.24450340867042542 345.1898498535156 0.2591806650161743 0.8759831 0.39847999811172485 False -18 36081 20.65248966217041 0.3709084987640381 278.90667724609375 0.23479190468788147 345.6496887207031 0.2578379809856415 0.8747816 0.40827709436416626 False -19 37980 20.640340089797974 0.37100934982299805 263.69482421875 0.3377552628517151 346.0411071777344 0.25684213638305664 0.8738355 0.41410747170448303 False diff --git a/ENCSR543WNA/cherimoya.fold_2.performance.tsv b/ENCSR543WNA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ffa45f7d59dac933e87cb644c135fdcaeceb7ff3..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -344.8236389160156 0.49457287788391113 0.26059889793395996 0.09266108274459839 0.8780889511108398 0.8478227257728577 0.38866347074508667 \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_3.evaluate.json b/ENCSR543WNA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e1f2503b731a4298f6a9f9c8a408fa2c88f78a30..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF604AIP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_3.fit.json b/ENCSR543WNA/cherimoya.fold_3.fit.json deleted file mode 100644 index 5d7efd291639e83cab400ea95b365260ea1279a1..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF604AIP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_3.log b/ENCSR543WNA/cherimoya.fold_3.log deleted file mode 100644 index fa5b9bf7e8d62ffcc96b543af10fde00cbde50e2..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1814 24.738755702972412 3.5815062522888184 285.00885009765625 0.6405868530273438 377.3420715332031 0.15463146567344666 0.6973423 9.345430374145508 True -1 3628 20.099421739578247 0.431384801864624 305.5991516113281 0.6536256074905396 356.669677734375 0.20583848655223846 0.7849225 3.157008409500122 True -2 5442 20.18947982788086 0.3796696662902832 259.4311218261719 0.4611528515815735 343.0481262207031 0.22864075005054474 0.8227376 1.6131322383880615 True -3 7256 20.14747905731201 0.3834803104400635 260.70703125 0.352424681186676 339.928955078125 0.23599836230278015 0.82634866 1.0523710250854492 True -4 9070 20.12722158432007 1.0791409015655518 237.55166625976562 0.9090402126312256 339.1673278808594 0.23692524433135986 0.83567053 0.8622123003005981 True -5 10884 20.087416887283325 0.3686795234680176 287.60614013671875 0.6152393817901611 338.7413024902344 0.23826579749584198 0.8368148 0.8026251792907715 True -6 12698 20.091804265975952 2.502568483352661 207.52291870117188 0.5257055759429932 337.9275207519531 0.24041993916034698 0.8442543 0.7225171327590942 True -7 14512 20.14704704284668 0.3854811191558838 346.8038635253906 0.45609980821609497 337.0120849609375 0.24276646971702576 0.8498052 0.6702618598937988 True -8 16326 20.11996841430664 0.37719106674194336 233.80831909179688 0.23257800936698914 335.6289978027344 0.24698543548583984 0.8550185 0.6261019110679626 True -9 18140 20.13266086578369 0.3793022632598877 248.4476318359375 0.43772992491722107 335.32806396484375 0.24758420884609222 0.85963535 0.5768025517463684 True -10 19954 20.11686658859253 0.39536046981811523 264.483642578125 0.4703254699707031 334.93011474609375 0.24778537452220917 0.8655383 0.5165302753448486 True -11 21768 20.15225100517273 0.3824272155761719 280.865478515625 0.5581750869750977 333.94732666015625 0.25077253580093384 0.8697613 0.48227423429489136 True -12 23582 20.118838787078857 0.3691549301147461 310.25579833984375 0.6199973821640015 333.6537170410156 0.25138676166534424 0.87411773 0.4344550669193268 True -13 25396 20.146657943725586 0.37758731842041016 278.7177734375 0.47441044449806213 333.1581115722656 0.2515682578086853 0.8783867 0.41287699341773987 True -14 27210 20.11054539680481 0.37258100509643555 295.32379150390625 0.23367354273796082 333.2585754394531 0.25180768966674805 0.8817105 0.3987441956996918 True -15 29024 20.207343339920044 0.3729720115661621 265.73333740234375 0.3553730845451355 332.5262451171875 0.25295671820640564 0.8835555 0.3911682367324829 True -16 30838 20.23358392715454 0.3889172077178955 239.35635375976562 0.38404446840286255 333.0021667480469 0.2517356872558594 0.8816893 0.39608487486839294 False -17 32652 20.15920066833496 0.37093377113342285 302.2532958984375 0.25052589178085327 332.8879699707031 0.2522118091583252 0.88134444 0.40411001443862915 False -18 34466 20.109609603881836 0.3661203384399414 246.42857360839844 0.28232964873313904 333.6203918457031 0.250455766916275 0.8802131 0.4139343798160553 False -19 36280 20.104928731918335 0.36612820625305176 305.65386962890625 0.19672153890132904 333.76568603515625 0.2500838339328766 0.8786882 0.4179864823818207 False diff --git a/ENCSR543WNA/cherimoya.fold_3.performance.tsv b/ENCSR543WNA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d2d24020c03abb2611870bb654e52627d44b99a8..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -332.5262451171875 0.49946126341819763 0.25295671820640564 0.08790075033903122 0.8835554718971252 0.8417057394981384 0.3911682367324829 \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_4.evaluate.json b/ENCSR543WNA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7460230894e10d825724f330855947e08c7edea0..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF604AIP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_4.fit.json b/ENCSR543WNA/cherimoya.fold_4.fit.json deleted file mode 100644 index e721b3398105b30b0467a119bee8a207fa34446b..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF604AIP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR543WNA/cherimoya.fold_4.log b/ENCSR543WNA/cherimoya.fold_4.log deleted file mode 100644 index fc356f54a8e981647e5639eba476bdb1f5f28800..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1821 25.929715871810913 3.6528191566467285 312.9476318359375 0.7000333666801453 354.8951416015625 0.14199769496917725 0.70877856 9.039634704589844 True -1 3642 20.234869480133057 0.3616776466369629 347.044677734375 0.6706061363220215 337.4867858886719 0.18941964209079742 0.777157 2.9645562171936035 True -2 5463 20.24718689918518 0.3391702175140381 254.32176208496094 0.5587964057922363 322.6685485839844 0.2169727236032486 0.8210004 1.3070749044418335 True -3 7284 20.24220633506775 0.3368232250213623 228.91604614257812 0.3922347128391266 319.0607604980469 0.22280095517635345 0.8343335 0.8437923192977905 True -4 9105 20.227378129959106 0.36379337310791016 249.16043090820312 0.6412904262542725 317.3710021972656 0.22688491642475128 0.8450271 0.6174238324165344 True -5 10926 20.2498676776886 0.3422257900238037 239.45196533203125 0.352485716342926 316.8453674316406 0.22756339609622955 0.8486346 0.5749729871749878 True -6 12747 20.1778666973114 0.3422574996948242 369.02252197265625 0.56146240234375 315.72882080078125 0.23084279894828796 0.8497499 0.5471584796905518 True -7 14568 20.13475728034973 0.34052395820617676 229.86019897460938 0.53035569190979 315.14520263671875 0.23182572424411774 0.85567427 0.5060079097747803 True -8 16389 19.78214454650879 0.34055328369140625 249.03616333007812 0.44077828526496887 315.04742431640625 0.23228983581066132 0.8605791 0.459459125995636 True -9 18210 19.776893615722656 0.876091718673706 264.5375671386719 0.4327816069126129 313.6009521484375 0.23603731393814087 0.8651626 0.43008720874786377 True -10 20031 19.859474658966064 0.3508884906768799 293.3324279785156 0.6245564222335815 314.2642517089844 0.23379111289978027 0.8687824 0.4130966365337372 True -11 21852 19.83189582824707 0.34722399711608887 354.23541259765625 0.3817708492279053 313.6749267578125 0.23504064977169037 0.8724922 0.3984234631061554 True -12 23673 19.818598747253418 0.3447704315185547 256.81939697265625 0.5389448404312134 312.9921569824219 0.23665419220924377 0.8761949 0.3816850483417511 True -13 25494 19.861533641815186 0.34226369857788086 243.25759887695312 0.5739760398864746 312.3550720214844 0.2384374588727951 0.88048345 0.35934463143348694 True -14 27315 19.838939428329468 0.34099578857421875 264.1201477050781 0.3815462291240692 312.068115234375 0.23929674923419952 0.8822482 0.3529476225376129 True -15 29136 19.82709050178528 0.34098339080810547 204.39358520507812 0.3700430989265442 311.90020751953125 0.2401283234357834 0.88139033 0.3512982130050659 False -16 30957 19.790815353393555 0.35906362533569336 250.40028381347656 0.38817262649536133 312.3919372558594 0.2383248507976532 0.8823988 0.3542005717754364 True -17 32778 19.784375429153442 0.3383760452270508 230.13870239257812 0.25930243730545044 312.90374755859375 0.23701351881027222 0.87975943 0.36569178104400635 False -18 34599 19.785576820373535 0.34223294258117676 273.4881591796875 0.19561947882175446 313.2279052734375 0.236627995967865 0.8772313 0.3736635446548462 False -19 36420 19.822493076324463 0.3572049140930176 281.90753173828125 0.23549075424671173 313.2909240722656 0.23615208268165588 0.8755643 0.3798637092113495 False diff --git a/ENCSR543WNA/cherimoya.fold_4.performance.tsv b/ENCSR543WNA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c9c4c2c4728805e76b1dd50bd1b61acee025d175..0000000000000000000000000000000000000000 --- a/ENCSR543WNA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -312.3919372558594 0.5110936164855957 0.2383248507976532 0.08041349798440933 0.882398784160614 0.8338000178337097 0.3542005717754364 \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_0.evaluate.json b/ENCSR544KDB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5510ee4be17694df45a207df3835788886decd83..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029ZPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_0.fit.json b/ENCSR544KDB/cherimoya.fold_0.fit.json deleted file mode 100644 index 806cbbcd095f3894c5c93441814b5bd137fd7381..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF029ZPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_0.log b/ENCSR544KDB/cherimoya.fold_0.log deleted file mode 100644 index 640116df01ff21e730d341cb7bd0eec34d4cbe20..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2124 28.5175039768219 3.3007214069366455 214.21926879882812 0.6199235916137695 301.4796447753906 0.126241996884346 0.6126493 5.154959201812744 True -1 4248 23.554691314697266 0.5073959827423096 245.6168212890625 0.6324906349182129 289.6149597167969 0.18614695966243744 0.67849505 1.5475596189498901 True -2 6372 23.49927067756653 0.41190075874328613 272.3811340332031 0.679412305355072 280.253662109375 0.2184009999036789 0.7209895 0.6701080799102783 True -3 8496 23.561686992645264 0.4093918800354004 275.6773986816406 0.5665327310562134 278.1252746582031 0.22514280676841736 0.7363597 0.5254652500152588 True -4 10620 23.533806800842285 0.40850019454956055 257.896484375 0.446754515171051 277.0450744628906 0.22733546793460846 0.74609184 0.4619685113430023 True -5 12744 23.436561346054077 0.40758705139160156 289.62652587890625 0.7041141390800476 276.3162536621094 0.22975552082061768 0.7464864 0.4504745602607727 True -6 14868 23.42595911026001 0.40369105339050293 253.82559204101562 0.5991002917289734 276.2183837890625 0.22986796498298645 0.7565696 0.43982577323913574 True -7 16992 23.40030550956726 1.0698997974395752 237.98086547851562 0.9278068542480469 275.5071105957031 0.23316098749637604 0.75939685 0.4483778476715088 True -8 19116 23.417405128479004 0.4060239791870117 250.5426483154297 0.5182427167892456 274.8228759765625 0.23612576723098755 0.76747984 0.42280885577201843 True -9 21240 23.408060312271118 0.39754509925842285 269.3205261230469 0.6515966653823853 274.59649658203125 0.23670251667499542 0.7689463 0.4078309237957001 True -10 23364 23.405974864959717 0.39794445037841797 241.161865234375 0.38619378209114075 274.0644836425781 0.23926162719726562 0.7765048 0.3807770311832428 True -11 25488 23.431046962738037 0.39688539505004883 198.89508056640625 0.359805703163147 273.6759338378906 0.24069038033485413 0.7781433 0.3706178367137909 True -12 27612 23.410438537597656 0.40723133087158203 184.2808380126953 0.46453946828842163 273.0982360839844 0.24291962385177612 0.7845774 0.3591662049293518 True -13 29736 23.40177822113037 0.40807437896728516 220.27215576171875 0.6361294984817505 272.52703857421875 0.24476562440395355 0.7909805 0.3502950072288513 True -14 31860 23.41817593574524 1.9865655899047852 213.56170654296875 0.2774040400981903 272.5955505371094 0.2441960722208023 0.79053855 0.351142019033432 False -15 33984 23.505517959594727 0.4147071838378906 222.25448608398438 0.25863227248191833 272.681396484375 0.2440553605556488 0.79179764 0.35086655616760254 True -16 36108 23.394836902618408 16.706169843673706 215.29556274414062 0.23277831077575684 272.62005615234375 0.24429479241371155 0.7924146 0.3563147485256195 True -17 38232 23.730467319488525 0.4103977680206299 251.55783081054688 0.31164562702178955 272.802978515625 0.24374951422214508 0.7923818 0.36748749017715454 False -18 40356 23.62364149093628 22.59518814086914 204.77662658691406 0.25680118799209595 273.05291748046875 0.24212540686130524 0.78951293 0.3812921345233917 False -19 42480 23.459064245224 0.4210019111633301 240.8787841796875 0.183576762676239 272.87530517578125 0.24327297508716583 0.7850505 0.38706815242767334 False diff --git a/ENCSR544KDB/cherimoya.fold_0.performance.tsv b/ENCSR544KDB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 51bce720ddee8f1f4ecf82e130052c96f17ad567..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -272.62005615234375 0.5115610361099243 0.24429479241371155 0.07135948538780212 0.7924146056175232 0.7641311287879944 0.3563147485256195 \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_1.evaluate.json b/ENCSR544KDB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index db9c5777d1982c8f9863d5a18b27130c105e6481..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029ZPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_1.fit.json b/ENCSR544KDB/cherimoya.fold_1.fit.json deleted file mode 100644 index 2b4da3f2a12d8e56adfdd49a0c56ec5b42132f38..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF029ZPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_1.log b/ENCSR544KDB/cherimoya.fold_1.log deleted file mode 100644 index 5a10a2a54ae4d10b15ee104f06caadb3461cb5c5..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2107 27.923818826675415 3.5873048305511475 210.0440673828125 0.8028057813644409 356.91522216796875 0.13955816626548767 0.58231795 6.3819379806518555 True -1 4214 23.28510808944702 1.3764264583587646 243.802734375 0.7257765531539917 341.2721862792969 0.20911794900894165 0.6641378 1.8947017192840576 True -2 6321 23.26289463043213 1.1880300045013428 257.4775390625 0.5815732479095459 330.439697265625 0.24120639264583588 0.72614354 0.8244478106498718 True -3 8428 23.53965711593628 0.6112864017486572 217.696044921875 0.6097490787506104 327.430419921875 0.24834351241588593 0.7433779 0.5679944753646851 True -4 10535 23.254199743270874 2.104543447494507 202.84185791015625 0.5940378904342651 325.7989807128906 0.25119534134864807 0.755516 0.49546152353286743 True -5 12642 23.23464608192444 0.5950424671173096 209.2431640625 0.5850362777709961 324.9694519042969 0.2530530095100403 0.7583652 0.46292611956596375 True -6 14749 23.247050523757935 29.941622972488403 172.83384704589844 0.4351192116737366 324.22955322265625 0.25520187616348267 0.76548505 0.44874298572540283 True -7 16856 23.598604917526245 0.619171142578125 199.3678436279297 0.5235434770584106 323.6691589355469 0.25749772787094116 0.7665151 0.4470455050468445 True -8 18963 23.288027048110962 0.5798587799072266 249.87109375 0.42887765169143677 322.96734619140625 0.25915729999542236 0.7720497 0.4108866751194 True -9 21070 23.282419443130493 1.5547502040863037 175.40223693847656 0.5842813849449158 321.9568176269531 0.26294460892677307 0.7740127 0.40431344509124756 True -10 23177 23.284107446670532 0.6879632472991943 177.31808471679688 0.4741499423980713 321.5097961425781 0.26484641432762146 0.78051394 0.3926234245300293 True -11 25284 23.273660898208618 0.6975078582763672 202.60546875 0.45614808797836304 321.2923583984375 0.2653961777687073 0.7837133 0.37859660387039185 True -12 27391 23.283529043197632 1.1659512519836426 240.00245666503906 0.5830239057540894 320.75482177734375 0.2671622931957245 0.789007 0.3737984597682953 True -13 29498 23.46074390411377 0.5768442153930664 238.710693359375 0.40799832344055176 320.8351135253906 0.2661771774291992 0.7942855 0.3660070598125458 True -14 31605 23.25187087059021 38.83931851387024 213.91064453125 0.47282522916793823 320.4886779785156 0.26779627799987793 0.7966467 0.3684326112270355 True -15 33712 23.391929388046265 0.600604772567749 264.2377014160156 0.3866994380950928 319.717041015625 0.2707158029079437 0.79917234 0.3743263781070709 True -16 35819 23.579259395599365 25.037124156951904 214.277587890625 0.27314016222953796 319.9645080566406 0.26947182416915894 0.79832715 0.39036086201667786 False -17 37926 23.33677864074707 0.5919947624206543 195.129638671875 0.3236003816127777 320.3984375 0.2678859233856201 0.7962597 0.4133855700492859 False -18 40033 23.36352038383484 1.4625096321105957 203.42776489257812 0.21908575296401978 320.2854919433594 0.2683314383029938 0.79165304 0.4352700710296631 False -19 42140 23.244808197021484 0.588515043258667 185.97332763671875 0.3468189835548401 320.5545349121094 0.2672208845615387 0.78903663 0.4491880536079407 False diff --git a/ENCSR544KDB/cherimoya.fold_1.performance.tsv b/ENCSR544KDB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5dfab7528dff1c1357a6b95365c3a1effce6f5a7..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -319.717041015625 0.48727869987487793 0.27071574330329895 0.08008400350809097 0.7991723418235779 0.7781684398651123 0.3743263781070709 \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_2.evaluate.json b/ENCSR544KDB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 483ac013fd3d1a79dd8db34a803bb984c59fa62c..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029ZPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_2.fit.json b/ENCSR544KDB/cherimoya.fold_2.fit.json deleted file mode 100644 index bf63472eee6425d691f7b253b7d16656c471aaa8..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF029ZPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_2.log b/ENCSR544KDB/cherimoya.fold_2.log deleted file mode 100644 index 327d742d99acbbe72ec680b694a685b678721c59..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2262 31.568872451782227 3.263263463973999 188.00247192382812 0.4549218416213989 314.1556701660156 0.13516750931739807 0.5769668 5.000245571136475 True -1 4524 25.22068166732788 10.459624767303467 239.82504272460938 0.5976314544677734 299.4687194824219 0.20421242713928223 0.67393726 1.376423954963684 True -2 6786 25.021965742111206 0.9674324989318848 260.39935302734375 0.6836634874343872 291.0145263671875 0.22792308032512665 0.70820767 0.6404496431350708 True -3 9048 24.981315851211548 0.4209311008453369 251.71746826171875 0.47180047631263733 288.7308044433594 0.2342836558818817 0.73056763 0.4786834716796875 True -4 11310 24.93718957901001 0.42292070388793945 215.6847686767578 0.7125937938690186 287.7894592285156 0.2369803786277771 0.73584074 0.4629096984863281 True -5 13572 24.926230907440186 0.421489953994751 256.5333251953125 0.6948376893997192 287.0697021484375 0.23876531422138214 0.74083465 0.45251911878585815 True -6 15834 24.921220779418945 0.4130990505218506 258.8082275390625 0.4570181965827942 286.2336120605469 0.24183334410190582 0.7398438 0.46061185002326965 False -7 18096 24.964588165283203 0.4120442867279053 215.13966369628906 0.4057520627975464 285.77142333984375 0.24333912134170532 0.7567132 0.4104141592979431 True -8 20358 25.01551628112793 0.4296839237213135 274.09014892578125 0.37290894985198975 285.42059326171875 0.24461856484413147 0.76295835 0.39562246203422546 True -9 22620 25.05013132095337 0.42525434494018555 200.685546875 0.5510755777359009 284.6820983886719 0.24805575609207153 0.76521987 0.4011535048484802 True -10 24882 24.923047304153442 0.41916847229003906 214.46728515625 0.6313260197639465 284.70733642578125 0.24688807129859924 0.7701264 0.39166146516799927 True -11 27144 24.990412712097168 0.41647815704345703 199.85195922851562 0.538928210735321 284.1209411621094 0.24934691190719604 0.77587396 0.3768714368343353 True -12 29406 24.980657815933228 4.392163991928101 220.6719970703125 0.5634739398956299 283.7366027832031 0.2501692473888397 0.7785891 0.37729787826538086 True -13 31668 25.241013288497925 0.4296097755432129 216.987060546875 0.6808282136917114 283.3366394042969 0.25190967321395874 0.7813888 0.37563493847846985 True -14 33930 24.958813667297363 0.41626906394958496 191.0843048095703 0.26918676495552063 283.1383361816406 0.2523441016674042 0.78428096 0.371960312128067 True -15 36192 25.001821756362915 0.42931222915649414 255.68878173828125 0.27689242362976074 282.783447265625 0.25335192680358887 0.78376883 0.3771544396877289 False -16 38454 25.01287031173706 1.0041160583496094 272.41070556640625 0.2889544367790222 282.625244140625 0.254144549369812 0.7843818 0.38925856351852417 True -17 40716 24.98773431777954 0.4236311912536621 192.39540100097656 0.2837797999382019 283.0588684082031 0.252197802066803 0.77873635 0.4058452844619751 False -18 42978 24.948857307434082 0.41521358489990234 244.71261596679688 0.2388254553079605 283.2686767578125 0.2516552805900574 0.7764737 0.4215405583381653 False -19 45240 25.01544713973999 0.4191458225250244 275.37646484375 0.2165774405002594 283.35784912109375 0.25126564502716064 0.77293265 0.4338073432445526 False diff --git a/ENCSR544KDB/cherimoya.fold_2.performance.tsv b/ENCSR544KDB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b84618ad07f32b4e4471404e891032c56ab4b7a5..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -282.625244140625 0.5046733021736145 0.254144549369812 0.07353280484676361 0.7843818068504333 0.7586753368377686 0.38925856351852417 \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_3.evaluate.json b/ENCSR544KDB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 68692566fb43d08e52312e4912cc707a54fd3618..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029ZPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_3.fit.json b/ENCSR544KDB/cherimoya.fold_3.fit.json deleted file mode 100644 index 6fe666b2252281127452e026bf2e9123d2ee4b65..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF029ZPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_3.log b/ENCSR544KDB/cherimoya.fold_3.log deleted file mode 100644 index c9dffa81552547706f47e16a92323f73c598e3dc..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2168 28.906919717788696 4.810801029205322 245.97744750976562 0.5644130706787109 330.0960388183594 0.13718608021736145 0.5943512 6.404528617858887 True -1 4336 24.066559314727783 9.544427871704102 258.57281494140625 0.5751935839653015 317.2486877441406 0.1944316178560257 0.6708923 1.7464144229888916 True -2 6504 28.234954118728638 21.486058950424194 233.43414306640625 0.604221522808075 309.557861328125 0.22042013704776764 0.71638775 0.6567709445953369 True -3 8672 24.20776343345642 0.4557952880859375 210.69277954101562 0.5623178482055664 307.39013671875 0.22457441687583923 0.73282105 0.5331000685691833 True -4 10840 24.076619386672974 0.7351169586181641 277.5115966796875 0.6353074908256531 305.6119079589844 0.23004035651683807 0.74106705 0.4995774030685425 True -5 13008 24.02830934524536 0.4491157531738281 233.63876342773438 0.6117151379585266 305.28485107421875 0.23064331710338593 0.74753714 0.49841395020484924 True -6 15176 23.944831132888794 0.47560715675354004 243.17417907714844 0.7976593971252441 304.6549072265625 0.23240666091442108 0.75580585 0.4838051497936249 True -7 17344 23.969602584838867 0.618657112121582 233.5040283203125 0.3470558524131775 304.1996765136719 0.23461933434009552 0.76027095 0.46279388666152954 True -8 19512 23.98160409927368 17.118415594100952 205.1991729736328 0.6891809701919556 303.60711669921875 0.2373262494802475 0.7640773 0.44992876052856445 True -9 21680 24.55229687690735 0.48637938499450684 199.59634399414062 0.42740094661712646 303.1939392089844 0.23825716972351074 0.76957494 0.43376949429512024 True -10 23848 25.59311580657959 26.466690063476562 257.1255187988281 0.43557241559028625 302.7879943847656 0.23929913341999054 0.77587724 0.41708192229270935 True -11 26016 24.01630711555481 0.5190331935882568 202.24835205078125 0.48514336347579956 301.9455871582031 0.24274922907352448 0.7812065 0.3991639316082001 True -12 28184 24.01277780532837 0.44881176948547363 249.5338897705078 0.34178483486175537 301.7231140136719 0.24330638349056244 0.7880652 0.3892424702644348 True -13 30352 24.289688110351562 0.45037364959716797 200.01754760742188 0.30095577239990234 301.59454345703125 0.2439243197441101 0.79269433 0.3827616572380066 True -14 32520 23.93371295928955 0.45901942253112793 244.2603759765625 0.4370572566986084 300.9028625488281 0.24575744569301605 0.7969682 0.3788195848464966 True -15 34688 23.99813985824585 0.44829463958740234 268.1716613769531 0.41125601530075073 301.0798034667969 0.24440507590770721 0.8006824 0.3768533170223236 True -16 36856 24.053337812423706 0.4531974792480469 235.0922393798828 0.30624324083328247 301.1899719238281 0.24410183727741241 0.8011335 0.3838699460029602 True -17 39024 24.15345001220703 0.45386791229248047 226.19015502929688 0.32778051495552063 301.37579345703125 0.24421845376491547 0.798077 0.4038732349872589 False -18 41192 24.061620473861694 0.45861244201660156 189.62661743164062 0.23328392207622528 301.75958251953125 0.2423228919506073 0.7963568 0.4225618541240692 False -19 43360 24.057957887649536 23.089718341827393 258.3369140625 0.25458431243896484 301.8323059082031 0.24189141392707825 0.7927511 0.4350699186325073 False diff --git a/ENCSR544KDB/cherimoya.fold_3.performance.tsv b/ENCSR544KDB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 00b940a980f63cea88044e886d53689151a2f20f..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -301.1899719238281 0.5039493441581726 0.2441018521785736 0.07528107613325119 0.8011335134506226 0.7802696228027344 0.3838699460029602 \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_4.evaluate.json b/ENCSR544KDB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c5bd05b17a61c71226603ae38d5ad51a3b9fc724..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029ZPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_4.fit.json b/ENCSR544KDB/cherimoya.fold_4.fit.json deleted file mode 100644 index d6746e613b0f6ab361a15c7b4d846625cc4d20e3..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF029ZPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR544KDB/cherimoya.fold_4.log b/ENCSR544KDB/cherimoya.fold_4.log deleted file mode 100644 index c2d5142717323508b23113e88824401e9a0461b3..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2214 29.11467456817627 3.299748420715332 216.73941040039062 0.5347009897232056 301.2166748046875 0.13147416710853577 0.59149826 5.278336048126221 True -1 4428 24.454058170318604 0.4358243942260742 224.33987426757812 0.5874905586242676 288.0079650878906 0.19719263911247253 0.67455274 1.353834867477417 True -2 6642 24.45269513130188 0.4147450923919678 259.4864807128906 0.6739457845687866 281.1885070800781 0.2173614799976349 0.72086 0.5654623508453369 True -3 8856 24.451160669326782 1.159531831741333 234.361328125 0.7618338465690613 278.8397216796875 0.22351589798927307 0.73441803 0.4566101133823395 True -4 11070 24.446819305419922 2.6391234397888184 194.46800231933594 0.42485910654067993 277.6108703613281 0.22734014689922333 0.7420802 0.43331098556518555 True -5 13284 24.483293056488037 0.41153383255004883 231.2479248046875 0.3349284529685974 277.0736999511719 0.22848562896251678 0.74394625 0.4429858326911926 True -6 15498 24.476177215576172 18.87001943588257 211.0211181640625 0.5496025681495667 276.5856018066406 0.23062127828598022 0.7500301 0.42490413784980774 True -7 17712 25.156839609146118 12.12141466140747 212.29531860351562 0.600959062576294 276.20989990234375 0.2312590479850769 0.7606058 0.39927995204925537 True -8 19926 24.48923683166504 0.41664814949035645 220.8402557373047 0.5484702587127686 275.78082275390625 0.23282839357852936 0.76184005 0.391457736492157 True -9 22140 24.390767335891724 0.4213995933532715 230.66268920898438 0.5822376608848572 275.32781982421875 0.2350553423166275 0.76622385 0.37417110800743103 True -10 24354 24.42685031890869 0.41606831550598145 198.0225067138672 0.5575937628746033 274.88818359375 0.23659271001815796 0.77113795 0.36595872044563293 True -11 26568 24.441372871398926 0.41446900367736816 220.60914611816406 0.4251524806022644 274.59515380859375 0.23815923929214478 0.77663493 0.35672274231910706 True -12 28782 24.469910144805908 0.4128537178039551 252.6287841796875 0.7206363677978516 274.12152099609375 0.2395447939634323 0.7788369 0.35378891229629517 True -13 30996 24.43647003173828 0.4184713363647461 218.5159912109375 0.5840250253677368 273.79473876953125 0.2413059026002884 0.78473616 0.34780389070510864 True -14 33210 24.437151193618774 0.42159128189086914 212.86688232421875 0.5859000086784363 273.9981689453125 0.24013124406337738 0.7885872 0.3451306223869324 True -15 35424 24.545209884643555 1.8261547088623047 240.42987060546875 0.39327213168144226 273.7651062011719 0.24031996726989746 0.79086417 0.3475338816642761 True -16 37638 24.539804458618164 0.41793394088745117 220.2823486328125 0.31482332944869995 274.03179931640625 0.23943723738193512 0.79019773 0.3559444844722748 False -17 39852 25.220804452896118 23.57610559463501 249.0293731689453 0.3178839683532715 274.3336181640625 0.2381354421377182 0.7886803 0.3692485988140106 False -18 42066 24.494953393936157 0.4300365447998047 213.7235565185547 0.43716907501220703 274.0199890136719 0.23983658850193024 0.78506136 0.38374558091163635 False -19 44280 24.51622986793518 0.43029022216796875 188.15127563476562 0.24396640062332153 274.1996765136719 0.23853467404842377 0.78330874 0.39395013451576233 False diff --git a/ENCSR544KDB/cherimoya.fold_4.performance.tsv b/ENCSR544KDB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 156a719df60796e539c469a4f92db7eb49e36ab9..0000000000000000000000000000000000000000 --- a/ENCSR544KDB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -273.7651062011719 0.5125816464424133 0.24031996726989746 0.06884398311376572 0.7908641695976257 0.7629641890525818 0.3475338816642761 \ No newline at end of file diff --git a/ENCSR545KQR/cherimoya.fold_0.log b/ENCSR545KQR/cherimoya.fold_0.log deleted file mode 100644 index e75dd56384d9792fda1d858949e61b6442508449..0000000000000000000000000000000000000000 --- a/ENCSR545KQR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2706 34.34456729888916 3.424816846847534 268.888916015625 1.7650750875473022 370.14453125 0.19138596951961517 0.30893123 6.308672904968262 True -1 5412 30.12266731262207 0.5542442798614502 298.4007568359375 1.2362957000732422 313.20379638671875 0.3370121419429779 0.42064568 4.728920936584473 True -2 8118 30.973795413970947 25.592092275619507 248.99285888671875 1.269421100616455 306.7262268066406 0.3490716814994812 0.4466925 3.4159741401672363 True -3 10824 29.757444858551025 0.5418319702148438 217.3057861328125 0.7488358020782471 302.36798095703125 0.3577685058116913 0.47456622 2.5216567516326904 True -4 13530 29.741146087646484 3.1598105430603027 230.92176818847656 1.4626544713974 300.6850891113281 0.3615672290325165 0.4898796 2.226470947265625 True -5 16236 29.810391664505005 0.5366249084472656 201.67506408691406 0.8724018931388855 299.4938659667969 0.36489221453666687 0.49998084 2.0708959102630615 True -6 18942 29.901094913482666 0.5347588062286377 262.65362548828125 1.0520986318588257 298.2873229980469 0.36843979358673096 0.51369953 1.827877402305603 True -7 21648 29.162455797195435 0.5583641529083252 201.80096435546875 0.788490891456604 297.237548828125 0.37151604890823364 0.5189641 1.7418689727783203 True -8 24354 29.19587802886963 0.5304031372070312 209.15359497070312 0.7651510238647461 296.69635009765625 0.3727973997592926 0.52860594 1.598589301109314 True -9 27060 29.16886329650879 0.5240700244903564 211.80648803710938 0.7182394862174988 294.9583740234375 0.37851718068122864 0.53695077 1.3808369636535645 True -10 29766 29.17333459854126 0.5318360328674316 228.74343872070312 1.0876576900482178 294.1310119628906 0.3810722231864929 0.53836817 1.4048281908035278 True -11 32472 29.219723224639893 0.5201976299285889 198.39324951171875 0.8944105505943298 293.4349365234375 0.3821062445640564 0.5526653 1.2567822933197021 True -12 35178 29.22126793861389 1.8253607749938965 229.2601318359375 0.8710716962814331 291.8504943847656 0.3864811956882477 0.5614125 1.0753943920135498 True -13 37884 29.287678480148315 0.5531926155090332 232.4560089111328 0.5373097062110901 290.429443359375 0.38947635889053345 0.5780017 0.976388156414032 True -14 40590 29.715937614440918 39.6144859790802 263.43975830078125 0.8709205985069275 290.08953857421875 0.3900194764137268 0.5912686 0.8846378922462463 True -15 43296 29.87345790863037 0.54197096824646 200.411376953125 1.0678435564041138 288.63580322265625 0.394917756319046 0.602111 0.7836482524871826 True -16 46002 29.23648166656494 0.5427014827728271 207.10214233398438 0.44748908281326294 288.7742919921875 0.3925224840641022 0.6060964 0.7423796057701111 True -17 48708 29.354899883270264 28.999557971954346 240.36624145507812 0.6078786849975586 288.4067077636719 0.39418235421180725 0.6104899 0.7085719108581543 True -18 51414 29.764233112335205 0.6665496826171875 242.16058349609375 0.3688350021839142 288.0682678222656 0.3949122726917267 0.61044186 0.6985066533088684 False -19 54120 29.14035987854004 0.5520117282867432 185.50074768066406 0.43523043394088745 288.313720703125 0.39384254813194275 0.6099326 0.6989901065826416 False diff --git a/ENCSR545KQR/cherimoya.fold_2.fit.json b/ENCSR545KQR/cherimoya.fold_2.fit.json deleted file mode 100644 index c5b38e39a53a473096eb4661eb357b646e0b5ae6..0000000000000000000000000000000000000000 --- a/ENCSR545KQR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF701PJJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR545KQR/cherimoya.fold_3.fit.json b/ENCSR545KQR/cherimoya.fold_3.fit.json deleted file mode 100644 index 658599ddbcd781043f258d66d8154a548051f794..0000000000000000000000000000000000000000 --- a/ENCSR545KQR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF701PJJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_0.evaluate.json b/ENCSR545UJP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6feede74bb4633be569aec85fad552780e5cac08..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF773VTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_0.fit.json b/ENCSR545UJP/cherimoya.fold_0.fit.json deleted file mode 100644 index d8a383301e5d0dd6bf4c28ae1d2dbc06bf2fd950..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF773VTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_0.log b/ENCSR545UJP/cherimoya.fold_0.log deleted file mode 100644 index 838d08fe6790ca89ba581b2bf3e36c0d5515eb34..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1808 23.78858971595764 3.844238758087158 420.95379638671875 0.9771579504013062 766.2969360351562 0.5156300067901611 0.58497953 17.277278900146484 True -1 3616 20.14022660255432 0.5536971092224121 430.194580078125 1.3445932865142822 579.6377563476562 0.6340605616569519 0.6698429 7.732200622558594 True -2 5424 20.15366005897522 0.3538646697998047 399.26739501953125 1.1507482528686523 527.235107421875 0.6945399045944214 0.68248534 2.5067813396453857 True -3 7232 20.130600929260254 0.3656468391418457 425.82958984375 1.039182424545288 513.3514404296875 0.7062485218048096 0.6996297 1.338164210319519 True -4 9040 20.097806453704834 0.36324572563171387 386.52874755859375 0.8475309610366821 506.80810546875 0.7120141983032227 0.70400596 0.9712684750556946 True -5 10848 20.103861331939697 0.37062501907348633 419.1732177734375 0.7108627557754517 503.5122375488281 0.7160099744796753 0.7098739 0.862432062625885 True -6 12656 20.35341167449951 15.878084659576416 395.1251220703125 1.1717009544372559 501.9733581542969 0.7180773615837097 0.7091568 0.8450028300285339 False -7 14464 20.145878314971924 0.3693244457244873 405.95123291015625 1.048330307006836 499.59503173828125 0.7214182019233704 0.7190891 0.7727311849594116 True -8 16272 20.18379306793213 0.3714592456817627 335.55755615234375 1.4536817073822021 497.5722961425781 0.7242059707641602 0.7212042 0.7537007331848145 True -9 18080 20.13800048828125 7.602217435836792 460.5942077636719 0.8276799321174622 495.44921875 0.7266486883163452 0.72866523 0.7337451577186584 True -10 19888 20.57389259338379 0.36783504486083984 431.56365966796875 0.920531153678894 493.6345520019531 0.728662371635437 0.73717666 0.7197292447090149 True -11 21696 20.2476487159729 0.3650021553039551 414.5812683105469 1.016364336013794 491.8012390136719 0.7303335666656494 0.73973125 0.7153806090354919 True -12 23504 20.166986227035522 0.3905055522918701 409.02410888671875 0.9895347952842712 490.2759094238281 0.7317473292350769 0.7528548 0.6787458658218384 True -13 25312 20.226329803466797 0.37279486656188965 432.35009765625 0.40369555354118347 489.1893005371094 0.7330008149147034 0.7525942 0.6796674728393555 False -14 27120 20.234726667404175 0.365602970123291 427.4812927246094 0.46028932929039 488.5743713378906 0.7335797548294067 0.75485045 0.6874319911003113 True -15 28928 20.183061122894287 0.3609955310821533 412.85296630859375 0.8880208730697632 488.2958679199219 0.733635663986206 0.7590726 0.6854212880134583 True -16 30736 20.319530248641968 0.3615567684173584 354.5256652832031 0.45790836215019226 488.272216796875 0.7336258888244629 0.75775397 0.7009802460670471 False -17 32544 20.198620557785034 12.099626541137695 384.0029296875 0.531209409236908 488.6438293457031 0.7329782843589783 0.75691336 0.7278198599815369 False -18 34352 20.934305429458618 0.37303781509399414 388.3941650390625 0.46192213892936707 489.24688720703125 0.7322292327880859 0.7514743 0.75251704454422 False -19 36160 20.168843269348145 0.38043713569641113 362.78265380859375 0.4784838557243347 489.641357421875 0.7318825125694275 0.7494152 0.774215042591095 False diff --git a/ENCSR545UJP/cherimoya.fold_0.performance.tsv b/ENCSR545UJP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f5a0260a94fafe72bf09fa4946e8b5913e6948dc..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -488.2958679199219 0.22637559473514557 0.7336357235908508 0.3318183422088623 0.7590726017951965 0.7286076545715332 0.6854212880134583 \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_1.evaluate.json b/ENCSR545UJP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 956d7e67f14dd6b79f96687f2dd19518257f7ca1..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF773VTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_1.fit.json b/ENCSR545UJP/cherimoya.fold_1.fit.json deleted file mode 100644 index edb24757960ab84cd9e4ab55057ec9dc5259ceb4..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF773VTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_1.log b/ENCSR545UJP/cherimoya.fold_1.log deleted file mode 100644 index db726d30139997ff6aae7ec3b6d850de7a6278cd..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1773 23.510185718536377 4.276073694229126 348.9590759277344 1.149435043334961 879.3821411132812 0.5268903970718384 0.56991756 17.476415634155273 True -1 3546 19.692107677459717 0.5843312740325928 466.6653747558594 1.2359745502471924 659.0057983398438 0.6496738195419312 0.6756517 8.96557903289795 True -2 5319 19.68980360031128 0.704481840133667 403.0112609863281 0.9328190088272095 593.3986206054688 0.7145028710365295 0.6987937 3.4034218788146973 True -3 7092 19.71584415435791 0.6562240123748779 416.69244384765625 1.3823821544647217 573.11376953125 0.728473961353302 0.71451306 1.6176795959472656 True -4 8865 19.682087182998657 0.5588347911834717 466.1863098144531 1.3188869953155518 566.100830078125 0.73432856798172 0.7266663 1.0908446311950684 True -5 10638 19.703811168670654 0.56215500831604 365.2841796875 1.3221852779388428 562.3060913085938 0.7370913624763489 0.7371792 0.8992971777915955 True -6 12411 19.68550395965576 0.643996000289917 336.5089111328125 0.8707067966461182 559.179443359375 0.7399712204933167 0.7484939 0.7929279804229736 True -7 14184 19.700181245803833 1.0082905292510986 390.4706115722656 1.0208020210266113 556.6817626953125 0.7424793839454651 0.75716066 0.7513822913169861 True -8 15957 19.71670126914978 0.5467836856842041 425.26800537109375 0.669186532497406 554.0430908203125 0.745549738407135 0.7594201 0.7341650724411011 True -9 17730 19.715135097503662 0.5723557472229004 460.3606872558594 1.0088701248168945 552.4659423828125 0.7471756935119629 0.76405513 0.7302194237709045 True -10 19503 19.730727672576904 0.5692524909973145 456.256591796875 0.7402088642120361 549.8159790039062 0.7493770122528076 0.77090025 0.6856220364570618 True -11 21276 19.68830919265747 0.5580911636352539 323.43414306640625 1.037431240081787 548.439453125 0.7507259845733643 0.77583855 0.6791025996208191 True -12 23049 19.68520450592041 0.5546393394470215 417.47802734375 0.7605586051940918 547.1014404296875 0.7524611353874207 0.7793371 0.6844859719276428 True -13 24822 19.713072776794434 0.5529625415802002 384.51898193359375 0.6203729510307312 545.3140258789062 0.7536643743515015 0.78306663 0.6655346155166626 True -14 26595 19.737651824951172 0.5478181838989258 382.10113525390625 0.9113363027572632 543.9237060546875 0.754636287689209 0.7858935 0.6545325517654419 True -15 28368 19.714998483657837 0.5681469440460205 384.88970947265625 0.8308397531509399 543.703857421875 0.7551908493041992 0.7904517 0.6617845296859741 True -16 30141 19.675225019454956 0.5741672515869141 362.53070068359375 0.3501153886318207 543.89501953125 0.7550632953643799 0.78737056 0.6816896200180054 False -17 31914 19.711509943008423 0.5458533763885498 367.81878662109375 0.3106561303138733 544.3717041015625 0.7544132471084595 0.78307533 0.7216796278953552 False -18 33687 19.699155569076538 0.5582625865936279 342.57305908203125 0.23481088876724243 544.9854125976562 0.7537602186203003 0.77718973 0.7628130912780762 False -19 35460 19.696228742599487 2.284576892852783 400.25701904296875 0.3650968670845032 545.2586669921875 0.7532581090927124 0.7760719 0.7781979441642761 False diff --git a/ENCSR545UJP/cherimoya.fold_1.performance.tsv b/ENCSR545UJP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0b83857d664f830247ad9c6bc7dd260aae742d0f..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -543.703857421875 0.20748230814933777 0.755190908908844 0.36559218168258667 0.79045170545578 0.7806159853935242 0.6617845296859741 \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_2.evaluate.json b/ENCSR545UJP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1ab670d2c65460c4f63f747ba208a17c3dfbba78..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF773VTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_2.fit.json b/ENCSR545UJP/cherimoya.fold_2.fit.json deleted file mode 100644 index 07ae77bac9b087ba4450caf5e299d6fa30d0d61a..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF773VTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_2.log b/ENCSR545UJP/cherimoya.fold_2.log deleted file mode 100644 index b291ebfac0efa105e5324acb2903e882b91f5698..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1910 24.91165018081665 4.0009894371032715 412.6239318847656 1.315800428390503 788.7363891601562 0.5238186120986938 0.5729901 17.48688507080078 True -1 3820 21.26683759689331 0.417935848236084 509.830078125 1.0609288215637207 598.7887573242188 0.6491567492485046 0.6840762 6.997229099273682 True -2 5730 21.269508361816406 0.9739973545074463 401.4327087402344 0.9472679495811462 546.0274658203125 0.7004493474960327 0.7091715 1.7100214958190918 True -3 7640 21.282273292541504 0.39793825149536133 320.9576110839844 0.802983283996582 531.3106079101562 0.7106108069419861 0.7198211 0.8748588562011719 True -4 9550 21.255077362060547 0.4539003372192383 434.0544128417969 1.0096501111984253 525.9705200195312 0.7156977653503418 0.72756106 0.8515928983688354 True -5 11460 21.262937307357788 0.5776703357696533 435.6844482421875 0.8563277721405029 522.309814453125 0.7185532450675964 0.73298067 0.8113246560096741 True -6 13370 21.304768085479736 0.3976154327392578 428.61370849609375 1.0177783966064453 519.783935546875 0.7216699123382568 0.74006444 0.7808407545089722 True -7 15280 21.27385401725769 0.3972744941711426 329.80340576171875 1.410972237586975 517.0142822265625 0.7242088913917542 0.743467 0.7545260787010193 True -8 17190 21.221385717391968 0.40010809898376465 449.55450439453125 0.668869137763977 514.9337158203125 0.7267323732376099 0.7441497 0.744948148727417 True -9 19100 21.218334913253784 0.38820338249206543 333.60150146484375 0.8413137197494507 512.7460327148438 0.7290511727333069 0.7485159 0.7252429723739624 True -10 21010 21.20073938369751 0.3943333625793457 390.08544921875 0.8184370994567871 510.7425842285156 0.7314609885215759 0.75118417 0.7024621963500977 True -11 22920 21.223646879196167 0.8378410339355469 383.864501953125 0.8185879588127136 509.57843017578125 0.7327191829681396 0.75606084 0.6921190619468689 True -12 24830 21.246896743774414 0.9027531147003174 395.4342956542969 0.9451823234558105 507.46026611328125 0.7346174120903015 0.7616684 0.6747989058494568 True -13 26740 21.23125696182251 0.39830708503723145 369.25396728515625 0.7835170030593872 506.1912841796875 0.7358938455581665 0.7669289 0.6646572351455688 True -14 28650 21.246565341949463 0.40129685401916504 440.09283447265625 0.4591245651245117 505.56732177734375 0.7367684245109558 0.7705573 0.6647509336471558 True -15 30560 21.339237213134766 0.39258813858032227 316.1818542480469 0.4416126608848572 505.21484375 0.7372130751609802 0.7723796 0.6678250432014465 True -16 32470 21.31239914894104 0.39031505584716797 408.5014343261719 0.430242657661438 505.3879089355469 0.7372158765792847 0.7714836 0.6907800436019897 False -17 34380 21.31502938270569 0.39317774772644043 389.81036376953125 0.4212346374988556 505.8593444824219 0.7367045283317566 0.7701324 0.7137803435325623 False -18 36290 21.303001880645752 9.838311195373535 362.21514892578125 0.3378868103027344 506.3451232910156 0.7361211180686951 0.7664052 0.7431202530860901 False -19 38200 21.350804805755615 0.4147055149078369 373.1724853515625 0.33095699548721313 506.7929992675781 0.735764741897583 0.76206267 0.7621881365776062 False diff --git a/ENCSR545UJP/cherimoya.fold_2.performance.tsv b/ENCSR545UJP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f1da57ba29262ac41d3a3e8753c50b2bbd8df7d5..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -505.21484375 0.22176972031593323 0.737213134765625 0.34294450283050537 0.7723795771598816 0.7532352209091187 0.6678250432014465 \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_3.evaluate.json b/ENCSR545UJP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f938b2dcdc0889eb2c3d20c3f1260761969ef0b3..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF773VTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_3.fit.json b/ENCSR545UJP/cherimoya.fold_3.fit.json deleted file mode 100644 index 6e351c047dd50b47f5632965688d5bab38083e14..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF773VTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_3.log b/ENCSR545UJP/cherimoya.fold_3.log deleted file mode 100644 index e252ec5cccc7eaaf4d79d7a56263bfe45cb50a88..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1847 24.414623737335205 3.6638052463531494 303.0438537597656 1.892432451248169 788.2463989257812 0.5314624309539795 0.5729719 18.2999210357666 True -1 3694 20.491462230682373 0.6036128997802734 425.21783447265625 1.111997365951538 595.8057861328125 0.6546911597251892 0.6532279 8.073966979980469 True -2 5541 20.494227409362793 0.38709425926208496 407.325439453125 0.9560332894325256 548.0159912109375 0.7023587226867676 0.6656776 2.2612946033477783 True -3 7388 20.53519058227539 0.41536378860473633 421.58294677734375 0.6594765782356262 532.8408203125 0.7132794857025146 0.6650405 1.2015939950942993 False -4 9235 20.48489022254944 0.7581956386566162 441.2030334472656 0.7173628807067871 528.47119140625 0.717805027961731 0.6807073 1.037115216255188 True -5 11082 20.51218891143799 0.41080641746520996 454.2264099121094 0.8516468405723572 526.0738525390625 0.7203854322433472 0.68736863 0.9749299883842468 True -6 12929 20.498996019363403 0.4194755554199219 362.5020751953125 1.2349824905395508 522.8407592773438 0.7239679098129272 0.6921123 0.9267484545707703 True -7 14776 20.648534297943115 0.42693257331848145 496.8419189453125 0.7145671844482422 522.0945434570312 0.7257785201072693 0.6978769 0.8701642155647278 True -8 16623 20.550190925598145 1.09676194190979 337.3582763671875 0.9042069911956787 519.8002319335938 0.7280359864234924 0.70592827 0.8338419795036316 True -9 18470 20.618433713912964 0.3911147117614746 436.56805419921875 0.826553225517273 517.6785278320312 0.7303136587142944 0.7122374 0.8346126675605774 True -10 20317 20.61858892440796 0.9148750305175781 412.9453125 0.46216854453086853 516.7742309570312 0.731787383556366 0.71492606 0.8222197890281677 True -11 22164 20.62787175178528 10.354506969451904 428.5849304199219 0.771281898021698 514.6878051757812 0.7340041399002075 0.7205924 0.8021068572998047 True -12 24011 22.004236459732056 0.4099085330963135 422.7475280761719 0.5138249397277832 513.453369140625 0.734916090965271 0.7334744 0.7599289417266846 True -13 25858 20.55561351776123 0.462749719619751 430.8517761230469 0.6621018648147583 511.87548828125 0.7364581823348999 0.7409989 0.7671398520469666 True -14 27705 20.53191566467285 0.4684715270996094 358.31817626953125 0.47090989351272583 510.9215393066406 0.7373594641685486 0.7440647 0.7557331323623657 True -15 29552 20.634995937347412 0.4150362014770508 344.9171142578125 0.4178312420845032 510.0055236816406 0.7380549311637878 0.74945575 0.7562852501869202 True -16 31399 20.509122371673584 0.3869929313659668 345.0872802734375 0.4729706048965454 510.43804931640625 0.7376171350479126 0.7490569 0.7864837050437927 False -17 33246 20.631035804748535 0.41698479652404785 345.058349609375 0.3880663812160492 510.8992919921875 0.7370750308036804 0.74615765 0.8189713358879089 False -18 35093 20.62716507911682 0.43433189392089844 464.19403076171875 0.3063466548919678 511.55511474609375 0.7365225553512573 0.74067914 0.8568292856216431 False -19 36940 20.621082544326782 0.38773274421691895 406.1315002441406 0.415080726146698 511.8543701171875 0.7360861897468567 0.73767304 0.880776047706604 False diff --git a/ENCSR545UJP/cherimoya.fold_3.performance.tsv b/ENCSR545UJP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 67aa0de674ae7cb0b62be90bd0b1d0ae2cad5364..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -510.0055236816406 0.21937939524650574 0.7380548715591431 0.3445131182670593 0.7494557499885559 0.7256057262420654 0.7562852501869202 \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_4.evaluate.json b/ENCSR545UJP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4ca33d2ba55ccb47af0c1f251a30af960a8af2bd..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF773VTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_4.fit.json b/ENCSR545UJP/cherimoya.fold_4.fit.json deleted file mode 100644 index 1d18fc85c8e3ea543757d715aae2cc56520e233d..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF773VTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR545UJP/cherimoya.fold_4.log b/ENCSR545UJP/cherimoya.fold_4.log deleted file mode 100644 index 0982ab53bcc75ad2c6e8e75ade56d2aab389ba6d..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1834 24.200298070907593 3.486652135848999 458.9599914550781 1.2670068740844727 744.959716796875 0.5187569856643677 0.5668743 17.110260009765625 True -1 3668 20.383800983428955 10.978067636489868 479.98834228515625 1.6549086570739746 569.1187133789062 0.6382579803466797 0.6528407 7.927190780639648 True -2 5502 20.745638132095337 0.39763569831848145 454.3210144042969 1.2080557346343994 518.6256103515625 0.6949554681777954 0.67255586 2.1765942573547363 True -3 7336 20.414904832839966 0.42891645431518555 390.07708740234375 1.1905326843261719 505.43621826171875 0.7063905596733093 0.6715836 1.0858465433120728 False -4 9170 20.450270414352417 0.3805408477783203 362.33251953125 1.0560386180877686 500.62384033203125 0.7104711532592773 0.6864482 0.8376226425170898 True -5 11004 20.4782497882843 0.4175410270690918 406.2279968261719 1.215604305267334 498.1184997558594 0.7136297821998596 0.69091266 0.8177335262298584 True -6 12838 20.469581604003906 0.3758227825164795 346.28472900390625 1.4888595342636108 495.80963134765625 0.7164574265480042 0.69426626 0.8027963042259216 True -7 14672 20.49554705619812 0.34716296195983887 400.37310791015625 1.320199728012085 493.4390563964844 0.7191289067268372 0.6918723 0.7970340847969055 False -8 16506 20.458230018615723 0.35330748558044434 440.01934814453125 0.7991816997528076 491.2210388183594 0.7217625975608826 0.70037955 0.7742519974708557 True -9 18340 20.481987476348877 0.3514115810394287 354.52423095703125 0.7110061645507812 490.07891845703125 0.723492443561554 0.7081385 0.7601712346076965 True -10 20174 20.42688012123108 1.0953946113586426 380.9275207519531 0.6338222026824951 488.1756286621094 0.7251895070075989 0.71176 0.7535133361816406 True -11 22008 20.555082321166992 0.34188246726989746 336.1142578125 1.0260913372039795 486.79852294921875 0.7271474599838257 0.718167 0.7502048015594482 True -12 23842 20.392242193222046 0.33946752548217773 407.40106201171875 0.7066686153411865 485.3220520019531 0.7289487719535828 0.72237146 0.7342236042022705 True -13 25676 20.40361499786377 0.36005735397338867 432.60308837890625 0.6961814165115356 484.1217041015625 0.7300742864608765 0.7312935 0.7207437753677368 True -14 27510 20.41678237915039 0.35764503479003906 439.49859619140625 0.5096310377120972 483.1883239746094 0.7313276529312134 0.73807526 0.709796130657196 True -15 29344 20.43050718307495 0.3434445858001709 439.8447265625 0.38069581985473633 483.24493408203125 0.7312483191490173 0.7437886 0.7110370397567749 True -16 31178 20.417165994644165 0.3599274158477783 317.3279113769531 0.5809196829795837 483.0240478515625 0.7308250069618225 0.74568886 0.7254005074501038 True -17 33012 20.43460488319397 0.35604381561279297 317.31427001953125 0.6029797792434692 483.7947692871094 0.730209231376648 0.7419229 0.7565556168556213 False -18 34846 20.406871795654297 0.3500046730041504 361.8505554199219 0.5555939674377441 484.0258483886719 0.729671835899353 0.74028116 0.7761672735214233 False -19 36680 20.451157331466675 0.3454141616821289 376.7110900878906 0.3032461404800415 484.2809143066406 0.729423463344574 0.740004 0.7943958044052124 False diff --git a/ENCSR545UJP/cherimoya.fold_4.performance.tsv b/ENCSR545UJP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c5df4502ada4ad8652b00e519a74fa9afe99f2db..0000000000000000000000000000000000000000 --- a/ENCSR545UJP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -483.0240478515625 0.22772204875946045 0.7308250665664673 0.3314143121242523 0.7456888556480408 0.7068782448768616 0.7254005074501038 \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_0.evaluate.json b/ENCSR548KIL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 94c21f3a00294de360ba17a9439d593d78a7fcbf..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF419ROQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_0.fit.json b/ENCSR548KIL/cherimoya.fold_0.fit.json deleted file mode 100644 index 04884bb534a70a23d43f0450499bb4c3ed90d2f5..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF419ROQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_0.log b/ENCSR548KIL/cherimoya.fold_0.log deleted file mode 100644 index fce22b984d4852d22cad4f1698a096d4108a7c32..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2328 30.384944438934326 3.9646077156066895 268.4827880859375 0.6158499717712402 369.4256591796875 0.4627833068370819 0.6577519 5.564014911651611 True -1 4656 25.82751441001892 0.4887559413909912 266.59808349609375 0.45121335983276367 323.3487854003906 0.5721554756164551 0.7113512 1.5606269836425781 True -2 6984 25.816688299179077 0.46211910247802734 242.23007202148438 0.5247610211372375 315.01422119140625 0.5926939845085144 0.701579 0.5379467010498047 False -3 9312 25.84465789794922 0.47080159187316895 263.02825927734375 0.4616923928260803 311.69903564453125 0.5986033082008362 0.70232815 0.4228285849094391 False -4 11640 25.958611726760864 29.793078184127808 226.7880859375 0.6159751415252686 310.75408935546875 0.6010568737983704 0.7155464 0.387369304895401 True -5 13968 27.00542902946472 0.4870426654815674 252.6866455078125 0.46056199073791504 309.88446044921875 0.6037634015083313 0.70318663 0.39220067858695984 False -6 16296 25.929508447647095 0.4794504642486572 258.86578369140625 0.5208079814910889 308.7874450683594 0.6062974333763123 0.7138422 0.3807065784931183 False -7 18624 25.814847469329834 0.4636566638946533 272.93341064453125 0.3714246153831482 308.08245849609375 0.60830157995224 0.7170227 0.39013320207595825 True -8 20952 25.795001745224 0.47118282318115234 260.34613037109375 0.38873714208602905 307.0264587402344 0.6109159588813782 0.72199255 0.3720332086086273 True -9 23280 25.79062247276306 0.4693279266357422 227.4323272705078 0.4264569878578186 306.13043212890625 0.6134047508239746 0.7324252 0.35988083481788635 True -10 25608 25.89191198348999 25.30289602279663 250.998779296875 0.43783897161483765 305.3792724609375 0.6154927015304565 0.73695177 0.36011505126953125 True -11 27936 28.003969192504883 0.46938037872314453 273.80352783203125 0.4381710886955261 304.62945556640625 0.6174520254135132 0.74004227 0.3552148938179016 True -12 30264 28.423121690750122 29.29991602897644 317.5907897949219 0.33385002613067627 303.9360046386719 0.6191255450248718 0.74812025 0.34650757908821106 True -13 32592 28.76363444328308 27.056923627853394 276.0075378417969 0.33173173666000366 303.4269714355469 0.6205482482910156 0.7553908 0.34009119868278503 True -14 34920 27.656843900680542 0.46531033515930176 292.5889892578125 0.30469149351119995 302.9789123535156 0.6217352151870728 0.7629957 0.33275315165519714 True -15 37248 25.824366331100464 0.4618346691131592 243.76199340820312 0.3100067377090454 302.7698669433594 0.6225348711013794 0.7671792 0.33445504307746887 True -16 39576 25.81504225730896 0.46987223625183105 189.92703247070312 0.4031403064727783 302.6933898925781 0.6227370500564575 0.7690691 0.33863091468811035 True -17 41904 25.80455231666565 0.8299338817596436 272.6444091796875 0.29357314109802246 302.8781433105469 0.6223821043968201 0.76889205 0.3446153402328491 False -18 44232 25.93056321144104 0.4684631824493408 208.57066345214844 0.27013546228408813 303.0529479980469 0.6217952966690063 0.76710343 0.35237371921539307 False -19 46560 25.767547369003296 0.4664790630340576 271.470947265625 0.22649487853050232 303.1839294433594 0.6214451193809509 0.7661149 0.3565613925457001 False diff --git a/ENCSR548KIL/cherimoya.fold_0.performance.tsv b/ENCSR548KIL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4799de630c2cfb62e9e0ce51377e3b24ad92c680..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.6933898925781 0.3104653060436249 0.6227370500564575 0.20998983085155487 0.7690690755844116 0.729572057723999 0.33863091468811035 \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_1.evaluate.json b/ENCSR548KIL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ce8b50606fe431fce763bf7bd9a534ff73666241..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF419ROQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_1.fit.json b/ENCSR548KIL/cherimoya.fold_1.fit.json deleted file mode 100644 index 3ee8c885f380a3a787bfa507be2d315fd75cd21a..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF419ROQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_1.log b/ENCSR548KIL/cherimoya.fold_1.log deleted file mode 100644 index 4e36d6f2ff7d4c27024ea53493c25cafe52a47a5..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2287 32.92327833175659 3.6912548542022705 239.05447387695312 0.6168938279151917 409.32342529296875 0.47485285997390747 0.6438796 5.521465301513672 True -1 4574 25.690556287765503 22.31648898124695 306.54376220703125 0.3488655090332031 356.22100830078125 0.582662045955658 0.709692 2.0294036865234375 True -2 6861 26.006134510040283 33.945666790008545 269.967529296875 0.6510567665100098 344.4928283691406 0.6101022362709045 0.73361224 0.6279695630073547 True -3 9148 26.126280784606934 35.20894408226013 334.9657287597656 0.8036618828773499 340.3762512207031 0.6184782385826111 0.74890727 0.3729742467403412 True -4 11435 25.671470880508423 0.6341569423675537 268.42535400390625 0.7129811644554138 339.2259216308594 0.6211942434310913 0.75348353 0.3824068307876587 True -5 13722 25.344931840896606 0.6172952651977539 234.2719268798828 0.6358349919319153 338.3086853027344 0.6234279870986938 0.75543976 0.3589528799057007 True -6 16009 25.322633743286133 0.6247899532318115 225.34152221679688 0.38391223549842834 337.3759765625 0.6259902119636536 0.75613075 0.3835277855396271 True -7 18296 25.22449493408203 0.7793416976928711 225.58114624023438 0.4814096689224243 336.1039123535156 0.6287222504615784 0.76318556 0.36340415477752686 True -8 20583 25.235267400741577 0.6158056259155273 228.18983459472656 0.5139771699905396 335.2095031738281 0.6307719945907593 0.7652707 0.3672969937324524 True -9 22870 25.252103805541992 1.3266487121582031 234.8905487060547 0.3820967674255371 334.56915283203125 0.6324390172958374 0.76602 0.3701932430267334 True -10 25157 25.568846225738525 27.09371280670166 253.5141143798828 0.5235544443130493 333.6640319824219 0.634567379951477 0.7719383 0.3542630672454834 True -11 27444 25.269670009613037 39.110583543777466 251.7818603515625 0.3400841951370239 333.013916015625 0.6363862156867981 0.7742609 0.35785868763923645 True -12 29731 25.253616333007812 1.4236407279968262 224.27517700195312 0.3578583896160126 332.4281005859375 0.6377813220024109 0.77877355 0.34446969628334045 True -13 32018 25.26568865776062 0.6133193969726562 289.7217102050781 0.38709843158721924 331.992431640625 0.639075756072998 0.7827859 0.35379672050476074 True -14 34305 25.283711433410645 0.6265153884887695 237.3237762451172 0.4402620196342468 331.5246276855469 0.6404041051864624 0.78636414 0.3457634150981903 True -15 36592 25.348013401031494 0.6154782772064209 216.9618377685547 0.36405399441719055 331.3271484375 0.6409062743186951 0.7897287 0.33688563108444214 True -16 38879 25.226933479309082 0.6208348274230957 260.03338623046875 0.26756542921066284 331.2405700683594 0.6410564184188843 0.79342496 0.33553725481033325 True -17 41166 25.273972272872925 0.6097285747528076 249.90101623535156 0.26027384400367737 331.4721374511719 0.6406228542327881 0.79177153 0.33583590388298035 False -18 43453 25.29281497001648 0.6190330982208252 263.07135009765625 0.2704775631427765 331.76251220703125 0.640019953250885 0.7887159 0.34198227524757385 False -19 45740 25.2696795463562 0.6063528060913086 235.0146484375 0.23841556906700134 331.8811340332031 0.6395530700683594 0.7862286 0.3503260910511017 False diff --git a/ENCSR548KIL/cherimoya.fold_1.performance.tsv b/ENCSR548KIL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 221a71bf01fe845f3a1efedf0a8137189eac423a..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -331.2405700683594 0.29523831605911255 0.6410564184188843 0.22938761115074158 0.7934249639511108 0.7733249068260193 0.33553725481033325 \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_2.evaluate.json b/ENCSR548KIL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d59f0efaa1c823d0f50cea2c371496dec5062827..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF419ROQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_2.fit.json b/ENCSR548KIL/cherimoya.fold_2.fit.json deleted file mode 100644 index bf8161f6855e14e090529db69cb9c741711085b1..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF419ROQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_2.log b/ENCSR548KIL/cherimoya.fold_2.log deleted file mode 100644 index aa5abe2b9b807b1a431c0d84e5027a628783a8d8..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2449 31.78737473487854 3.578920841217041 266.8169250488281 0.7934021949768066 377.642333984375 0.47069743275642395 0.6676122 5.171520233154297 True -1 4898 27.059197187423706 0.4801931381225586 245.54830932617188 0.6365244388580322 330.96697998046875 0.5829087495803833 0.7132886 1.2942131757736206 True -2 7347 27.00603985786438 0.4646596908569336 224.060302734375 0.6129699349403381 322.40728759765625 0.5995626449584961 0.7320452 0.4735390245914459 True -3 9796 27.02996039390564 4.048332214355469 250.992431640625 0.799046516418457 319.58465576171875 0.6048235893249512 0.7417298 0.3866384029388428 True -4 12245 27.072460651397705 0.4695243835449219 274.3931579589844 0.45692405104637146 317.95831298828125 0.609032928943634 0.74633294 0.3772674798965454 True -5 14694 27.036044359207153 0.46271848678588867 255.13706970214844 0.4573143720626831 316.769287109375 0.612082302570343 0.7485966 0.3734407424926758 True -6 17143 27.1095769405365 0.4750518798828125 265.837158203125 0.5354686379432678 316.0218505859375 0.6140601634979248 0.7520957 0.3756882846355438 True -7 19592 27.049474000930786 0.46854305267333984 294.06072998046875 0.3602904677391052 315.33203125 0.6161562204360962 0.7519726 0.3621422350406647 False -8 22041 27.022085428237915 0.46842193603515625 308.0319519042969 0.3800753951072693 314.38006591796875 0.6184062361717224 0.7512004 0.3580152988433838 False -9 24490 27.013556480407715 1.6404144763946533 240.10968017578125 0.3291035294532776 313.708740234375 0.6202801465988159 0.75978553 0.3484441936016083 True -10 26939 27.028982400894165 0.4624826908111572 265.30670166015625 0.36317816376686096 312.95037841796875 0.6225529909133911 0.7632344 0.34087976813316345 True -11 29388 27.008065700531006 0.4709339141845703 269.01727294921875 0.27200180292129517 312.019287109375 0.6247667074203491 0.7659011 0.33501604199409485 True -12 31837 27.101311922073364 0.4706308841705322 268.7216491699219 0.4844094514846802 311.4620666503906 0.6264123916625977 0.7693204 0.3279615342617035 True -13 34286 27.047321796417236 0.46655988693237305 265.8134765625 0.40221914649009705 310.895751953125 0.6279948949813843 0.7781409 0.32012826204299927 True -14 36735 27.012991666793823 0.4626297950744629 239.56036376953125 0.4044933617115021 310.4894104003906 0.6291704177856445 0.7816843 0.31904423236846924 True -15 39184 27.028407335281372 0.4726533889770508 260.19635009765625 0.25688180327415466 310.374267578125 0.6295680403709412 0.78436077 0.3201950490474701 True -16 41633 27.064488887786865 0.46793246269226074 249.15264892578125 0.3187929093837738 310.38226318359375 0.6296626925468445 0.7861104 0.32283633947372437 True -17 44082 27.059089422225952 0.4719424247741699 261.4408264160156 0.27914538979530334 310.53924560546875 0.6291695833206177 0.785191 0.32896146178245544 False -18 46531 27.091298818588257 0.4634740352630615 265.1694030761719 0.20740750432014465 310.701416015625 0.6285187602043152 0.78263885 0.3347752094268799 False -19 48980 27.01568102836609 22.64236831665039 236.99801635742188 0.28188878297805786 310.8497009277344 0.6281300187110901 0.7819721 0.34100452065467834 False diff --git a/ENCSR548KIL/cherimoya.fold_2.performance.tsv b/ENCSR548KIL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b8224079c172fef849692dea06f80776d2091c3b..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -310.38226318359375 0.3057132065296173 0.6296626925468445 0.21676895022392273 0.7861104011535645 0.7547433972358704 0.32283633947372437 \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_3.evaluate.json b/ENCSR548KIL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 01a409c9e278b6a3b0d4765b3d2e0a42fdbc7ac3..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF419ROQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_3.fit.json b/ENCSR548KIL/cherimoya.fold_3.fit.json deleted file mode 100644 index 16b6e2209ee202f4506e034c57fd2798797db5e2..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF419ROQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_3.log b/ENCSR548KIL/cherimoya.fold_3.log deleted file mode 100644 index 945ca4d4b461db6203f2252608530bf3cc74a870..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2382 31.690685272216797 3.3619277477264404 272.09259033203125 0.74614417552948 374.3957214355469 0.4626334309577942 0.648779 5.6461005210876465 True -1 4764 26.42971110343933 0.47696828842163086 270.19293212890625 0.6712855100631714 325.6938781738281 0.5739823579788208 0.7047409 1.6914550065994263 True -2 7146 26.51788592338562 0.45183420181274414 215.7581024169922 0.5892537832260132 316.6356201171875 0.5930725336074829 0.71458614 0.5343613028526306 True -3 9528 26.270335912704468 1.8819212913513184 252.96563720703125 0.5634971261024475 313.0084228515625 0.6011398434638977 0.7252586 0.427751362323761 True -4 11910 26.372755527496338 0.45094895362854004 249.31097412109375 0.7406371831893921 311.4681396484375 0.6048115491867065 0.73068035 0.3976462781429291 True -5 14292 26.261924743652344 0.44829416275024414 268.8810729980469 0.5563920736312866 310.3332214355469 0.6077133417129517 0.7343532 0.39788493514060974 True -6 16674 26.363689422607422 0.4489705562591553 276.56317138671875 0.5267724394798279 309.6128234863281 0.6097805500030518 0.7331597 0.408329039812088 False -7 19056 26.295547008514404 29.235413074493408 231.4584197998047 0.5696017742156982 308.8509216308594 0.6116216778755188 0.7391562 0.4072701036930084 True -8 21438 26.482036113739014 0.4769761562347412 229.170654296875 0.46454256772994995 308.19677734375 0.6133422255516052 0.73891413 0.4099086821079254 False -9 23820 26.334977626800537 0.4530210494995117 257.10186767578125 0.4280507266521454 307.49334716796875 0.6153537034988403 0.74271756 0.40740764141082764 True -10 26202 26.300073623657227 0.4535391330718994 234.69761657714844 0.3679097890853882 306.85491943359375 0.6170052289962769 0.7414696 0.41923779249191284 False -11 28584 26.450122594833374 0.4564244747161865 245.15249633789062 0.3454500734806061 306.1796875 0.6193225979804993 0.7499803 0.40025001764297485 True -12 30966 26.33385920524597 0.4623117446899414 261.0821533203125 0.3009105920791626 305.45318603515625 0.6211953163146973 0.755545 0.38778573274612427 True -13 33348 26.387753009796143 0.4525892734527588 248.55938720703125 0.389650821685791 305.0059509277344 0.6223582625389099 0.76337564 0.3785308599472046 True -14 35730 26.419391632080078 1.2511296272277832 254.80577087402344 0.3552936315536499 304.48187255859375 0.6236661672592163 0.7695683 0.3675021231174469 True -15 38112 30.031309127807617 11.190649032592773 230.01266479492188 0.25932130217552185 304.2594299316406 0.6244555711746216 0.77421904 0.3607071042060852 True -16 40494 26.442763805389404 0.4534604549407959 233.43716430664062 0.34554022550582886 304.0796203613281 0.6246777772903442 0.77929896 0.35309165716171265 True -17 42876 26.461129426956177 0.4541618824005127 270.4375915527344 0.273773193359375 304.3335266113281 0.624406635761261 0.77923393 0.35231149196624756 False -18 45258 26.475011825561523 1.9012367725372314 232.42449951171875 0.4758228063583374 304.4701232910156 0.623867392539978 0.77770966 0.3569408655166626 False -19 47640 26.43576979637146 0.4522087574005127 225.11019897460938 0.3020588159561157 304.62396240234375 0.6235517859458923 0.7778763 0.36055809259414673 False diff --git a/ENCSR548KIL/cherimoya.fold_3.performance.tsv b/ENCSR548KIL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2334990450ffdd113ca40e70690b561a06c97f79..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -304.0796203613281 0.30975255370140076 0.6246777176856995 0.21132178604602814 0.7792989611625671 0.7408578395843506 0.35309165716171265 \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_4.evaluate.json b/ENCSR548KIL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 521b659fb60db12d1ac914b8c43aee5b8e6217f2..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF419ROQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_4.fit.json b/ENCSR548KIL/cherimoya.fold_4.fit.json deleted file mode 100644 index 7d2038e5eca89982a549ac0f8c00a2413ac9d42c..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF419ROQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KIL/cherimoya.fold_4.log b/ENCSR548KIL/cherimoya.fold_4.log deleted file mode 100644 index 0df61ef292083136820383a5bf96114e68d22eb1..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2399 31.097761631011963 3.567946195602417 283.5760192871094 0.5253280997276306 358.6585998535156 0.46016910672187805 0.6505994 4.9162278175354 True -1 4798 26.615376472473145 1.1273894309997559 287.043701171875 0.9227359294891357 311.6361389160156 0.5727722644805908 0.7119588 1.5423612594604492 True -2 7197 26.49560570716858 0.46885228157043457 265.1142578125 0.443167507648468 304.8533935546875 0.5881596803665161 0.72526085 0.46286240220069885 True -3 9596 26.547832489013672 0.46036291122436523 291.7411193847656 0.5176715850830078 302.0522155761719 0.5949736833572388 0.7260457 0.3609044849872589 True -4 11995 27.196972608566284 30.741320848464966 225.4560089111328 0.3951103687286377 300.51446533203125 0.5993515849113464 0.72875065 0.3544420897960663 True -5 14394 26.84642767906189 0.620779275894165 269.34686279296875 0.4685455560684204 299.85552978515625 0.60115647315979 0.72813714 0.3637045621871948 False -6 16793 26.516768217086792 0.47418951988220215 227.61793518066406 0.4580073356628418 299.02740478515625 0.6033938527107239 0.73168224 0.3647002577781677 True -7 19192 26.591259002685547 0.4801795482635498 255.83123779296875 0.3413379490375519 298.4095764160156 0.6050353050231934 0.73509437 0.37503692507743835 True -8 21591 26.690576791763306 23.222646474838257 268.0167236328125 0.4164443016052246 297.5625305175781 0.6073786020278931 0.7397081 0.3759599030017853 True -9 23990 28.240973949432373 0.48732566833496094 248.4010009765625 0.46587687730789185 297.11260986328125 0.6090384125709534 0.7406907 0.3680189549922943 True -10 26389 26.716135501861572 0.47864365577697754 220.14794921875 0.3026910126209259 296.2430419921875 0.6110807657241821 0.7420512 0.357827752828598 True -11 28788 26.72160816192627 0.47229623794555664 234.25350952148438 0.3415406346321106 295.73699951171875 0.6128044724464417 0.7467584 0.3482973873615265 True -12 31187 26.57224702835083 0.4718208312988281 240.45718383789062 0.5393388271331787 295.02239990234375 0.614671528339386 0.7563545 0.33772796392440796 True -13 33586 28.974466800689697 19.567991971969604 224.2904815673828 0.33123940229415894 294.5072937011719 0.6161004900932312 0.76014173 0.3322969973087311 True -14 35985 26.938172578811646 0.4787633419036865 212.65371704101562 0.3309333324432373 294.2333679199219 0.6171693205833435 0.7680933 0.3262729048728943 True -15 38384 26.643064498901367 1.6178107261657715 237.43870544433594 0.3322920501232147 294.07330322265625 0.618044376373291 0.772128 0.32544875144958496 True -16 40783 26.65119504928589 0.5093348026275635 226.02081298828125 0.33613190054893494 293.6971130371094 0.6181302070617676 0.7732064 0.3287230134010315 True -17 43182 26.73035454750061 0.4689006805419922 245.5533447265625 0.2706849277019501 294.18975830078125 0.6178105473518372 0.7747818 0.33193764090538025 True -18 45581 26.67106342315674 0.4662339687347412 285.06683349609375 0.26103675365448 294.2926940917969 0.6171262860298157 0.7718908 0.33875155448913574 False -19 47980 26.67106580734253 0.47057628631591797 255.78965759277344 0.23123185336589813 294.1849365234375 0.6167393922805786 0.7691565 0.34361201524734497 False diff --git a/ENCSR548KIL/cherimoya.fold_4.performance.tsv b/ENCSR548KIL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0944dfdb4c9c680083dd66db1e53d913c8b28517..0000000000000000000000000000000000000000 --- a/ENCSR548KIL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -294.18975830078125 0.3151848614215851 0.6178105473518372 0.20376162230968475 0.7747818231582642 0.7204341888427734 0.33193764090538025 \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_0.evaluate.json b/ENCSR548KXH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4868a817ddd8c31438653814186921cae6617a18..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF595ODH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_0.fit.json b/ENCSR548KXH/cherimoya.fold_0.fit.json deleted file mode 100644 index 1a0f864d77d654bc5f57caca428ef139a6298725..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF595ODH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_0.log b/ENCSR548KXH/cherimoya.fold_0.log deleted file mode 100644 index 25646135fbe65f3d1935df68b05f4e78c4124ab0..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.97687292098999 3.805570125579834 194.21478271484375 1.2262932062149048 245.7843475341797 0.14706915616989136 0.7063982 3.8287410736083984 True -1 5518 30.98959517478943 0.5440928936004639 180.3859405517578 0.6321334838867188 223.44793701171875 0.1942516267299652 0.7886295 1.421005368232727 True -2 8277 30.696091890335083 0.5370163917541504 224.9141845703125 0.5948076248168945 220.3707275390625 0.1984015256166458 0.7895094 1.026465892791748 True -3 11036 30.68493103981018 0.5657684803009033 186.75595092773438 0.8876919746398926 218.1577911376953 0.203891322016716 0.79932225 0.8816893696784973 True -4 13795 30.623265743255615 1.2137610912322998 148.86936950683594 0.5658241510391235 217.50442504882812 0.20378540456295013 0.81116164 0.7854017615318298 True -5 16554 30.523428440093994 0.5351896286010742 199.55296325683594 0.6373517513275146 216.2576904296875 0.20808303356170654 0.81674933 0.6942175626754761 True -6 19313 30.51906991004944 0.567528486251831 166.65286254882812 0.5355641841888428 215.3372039794922 0.21055176854133606 0.8249674 0.6310381293296814 True -7 22072 30.49190402030945 0.5329389572143555 173.86907958984375 0.6513012051582336 214.35389709472656 0.2126792073249817 0.8320392 0.6225864887237549 True -8 24831 30.720776557922363 0.5231611728668213 194.22607421875 0.5210716128349304 213.8260040283203 0.21406210958957672 0.8358157 0.5986465811729431 True -9 27590 30.462172746658325 0.5205559730529785 148.10694885253906 0.5663203597068787 213.04042053222656 0.21627265214920044 0.8435071 0.5482487082481384 True -10 30349 30.450896978378296 0.5197362899780273 187.42828369140625 0.42505359649658203 212.32652282714844 0.21815381944179535 0.84950256 0.5068401098251343 True -11 33108 30.388968229293823 0.5205914974212646 146.83570861816406 0.5381626486778259 212.234619140625 0.21805904805660248 0.85563046 0.4695383310317993 True -12 35867 31.006213426589966 18.6734561920166 122.28900909423828 0.37160390615463257 211.73683166503906 0.21907277405261993 0.85951996 0.4502731263637543 True -13 38626 30.42747211456299 0.5278544425964355 137.79086303710938 0.38742879033088684 211.21876525878906 0.22038201987743378 0.8650801 0.4282090365886688 True -14 41385 30.41720986366272 0.5161535739898682 163.71368408203125 0.5305731892585754 210.6684112548828 0.221957266330719 0.8680462 0.4108954071998596 True -15 44144 29.831482410430908 19.330265522003174 161.98385620117188 0.4370878040790558 210.07904052734375 0.22246631979942322 0.86822224 0.39648541808128357 True -16 46903 29.813047885894775 0.5092916488647461 150.6465301513672 0.33064717054367065 210.19187927246094 0.22151316702365875 0.87192905 0.38629570603370667 True -17 49662 29.89974546432495 0.5034527778625488 145.02764892578125 0.556475043296814 210.01504516601562 0.22243531048297882 0.87229484 0.385783851146698 True -18 52421 30.416768312454224 0.5131237506866455 146.8350830078125 0.22028975188732147 210.17759704589844 0.22192800045013428 0.86992943 0.38499364256858826 False -19 55180 29.79243540763855 22.2480206489563 177.22909545898438 0.38380104303359985 210.17068481445312 0.2219298779964447 0.8699232 0.38727807998657227 False diff --git a/ENCSR548KXH/cherimoya.fold_0.performance.tsv b/ENCSR548KXH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 90f2b7171d7df0e32a41133374d4ddb66405d6d8..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -210.01504516601562 0.5445663928985596 0.22243531048297882 0.06162761151790619 0.8722948431968689 0.7954837679862976 0.385783851146698 \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_1.evaluate.json b/ENCSR548KXH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7df104a3c182453405ce5127eb159046e8d0e787..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF595ODH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_1.fit.json b/ENCSR548KXH/cherimoya.fold_1.fit.json deleted file mode 100644 index 8dcac678581d7dcb7c15ee29f2e0d56b88736697..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF595ODH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_1.log b/ENCSR548KXH/cherimoya.fold_1.log deleted file mode 100644 index 4b1bdaf043f7c8c167e92e2e90deb3ba3b9542ec..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2714 34.9050452709198 4.142647981643677 258.44891357421875 0.5460233688354492 286.5671691894531 0.154796302318573 0.7113764 4.445284366607666 True -1 5428 29.97079086303711 0.781527042388916 175.03244018554688 0.3945191502571106 260.9534912109375 0.204671710729599 0.8012224 2.03289532661438 True -2 8142 30.05061960220337 1.221907377243042 206.1727294921875 0.6579971313476562 257.6361999511719 0.20939293503761292 0.804321 1.2330994606018066 True -3 10856 29.9181067943573 13.096652269363403 173.89064025878906 0.5095784664154053 253.94837951660156 0.2157600075006485 0.8164476 1.0327463150024414 True -4 13570 33.52106165885925 0.7408359050750732 181.2703857421875 0.9062398672103882 252.0631103515625 0.2184850424528122 0.8249403 0.929359495639801 True -5 16284 36.01003909111023 14.088462829589844 177.43905639648438 0.46729710698127747 250.65525817871094 0.22083351016044617 0.8349939 0.8664863705635071 True -6 18998 29.904882669448853 48.66118764877319 130.90496826171875 0.6457259058952332 249.3061065673828 0.22295542061328888 0.8390478 0.8013954758644104 True -7 21712 29.913275480270386 10.50050163269043 153.98101806640625 0.4657961130142212 248.20436096191406 0.22549477219581604 0.8486637 0.7429031729698181 True -8 24426 29.905442714691162 4.149040937423706 202.88986206054688 0.571465015411377 247.22964477539062 0.22751756012439728 0.8577845 0.68891841173172 True -9 27140 29.948235273361206 45.99632525444031 151.99220275878906 0.5275862216949463 246.8192138671875 0.22837795317173004 0.86330193 0.6423599720001221 True -10 29854 29.911009311676025 0.7288546562194824 152.31845092773438 0.5029172897338867 246.25753784179688 0.22936467826366425 0.86953866 0.5557090640068054 True -11 32568 29.939713716506958 47.024895429611206 148.8267059326172 0.4263852834701538 244.90122985839844 0.23220284283161163 0.8738363 0.520527720451355 True -12 35282 29.774553775787354 0.7297120094299316 160.33148193359375 0.42781496047973633 244.44009399414062 0.23288385570049286 0.88049597 0.48182258009910583 True -13 37996 29.51480793952942 0.7286770343780518 135.73565673828125 0.4130569398403168 243.76052856445312 0.23432180285453796 0.8833258 0.4518115818500519 True -14 40710 31.73484516143799 0.7174429893493652 204.06930541992188 0.48063746094703674 243.0740966796875 0.2360679656267166 0.8876548 0.4226396679878235 True -15 43424 29.480388879776 39.934462547302246 163.2592315673828 0.5159574151039124 242.3664093017578 0.23754943907260895 0.8895085 0.41199326515197754 True -16 46138 29.42064380645752 0.7291538715362549 176.1218719482422 0.3463391363620758 242.40623474121094 0.23665742576122284 0.8922642 0.3977789878845215 True -17 48852 29.307093143463135 0.7325575351715088 108.30656433105469 0.5307894945144653 242.03909301757812 0.2379099428653717 0.89176106 0.39801037311553955 False -18 51566 29.550400495529175 17.29797339439392 157.725341796875 0.24278146028518677 242.63829040527344 0.236290842294693 0.8909855 0.40073853731155396 False -19 54280 29.36702060699463 3.2143471240997314 132.6613006591797 0.1898288130760193 242.72885131835938 0.2363569140434265 0.8902228 0.40397894382476807 False diff --git a/ENCSR548KXH/cherimoya.fold_1.performance.tsv b/ENCSR548KXH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 31b4837dc6c2fe43735680a2673e37d7d710d06b..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -242.40623474121094 0.5308476686477661 0.23665742576122284 0.06685850769281387 0.892264187335968 0.8365224599838257 0.3977789878845215 \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_2.evaluate.json b/ENCSR548KXH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9ad099e65a17ef5dc85f88acf4843338060c3673..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF595ODH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_2.fit.json b/ENCSR548KXH/cherimoya.fold_2.fit.json deleted file mode 100644 index cfae8c5098708399a2255fc48ce3abe5f646e76c..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF595ODH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_2.log b/ENCSR548KXH/cherimoya.fold_2.log deleted file mode 100644 index a8b3ba04c0fed2029bb23afb05d270f9c9c551df..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 36.30409836769104 3.5472817420959473 133.3991241455078 0.39669376611709595 262.39996337890625 0.15389052033424377 0.68559957 3.4551053047180176 True -1 5764 32.11231088638306 0.5226893424987793 177.07571411132812 0.5944554805755615 235.8655242919922 0.20453709363937378 0.7851522 1.7589486837387085 True -2 8646 31.59605050086975 0.5119848251342773 174.83132934570312 0.780013382434845 231.9874267578125 0.21012476086616516 0.7989602 0.9479569792747498 True -3 11528 31.522920608520508 0.5178563594818115 141.08230590820312 0.32985013723373413 230.74032592773438 0.21193087100982666 0.8026883 0.7889012098312378 True -4 14410 31.525452136993408 22.30084252357483 218.6399383544922 0.586266040802002 229.95872497558594 0.21309827268123627 0.80902225 0.7724613547325134 True -5 17292 32.900187253952026 0.5282721519470215 216.08358764648438 0.5265990495681763 228.37498474121094 0.21766844391822815 0.81814593 0.6939660906791687 True -6 20174 32.71635675430298 0.9100570678710938 115.45402526855469 0.34021955728530884 227.19873046875 0.22040794789791107 0.8271786 0.6516210436820984 True -7 23056 31.529760360717773 0.5089848041534424 210.0782470703125 0.6871394515037537 226.84814453125 0.2221057116985321 0.83162653 0.626180112361908 True -8 25938 31.51370620727539 0.5092086791992188 190.12838745117188 0.7139012813568115 226.45257568359375 0.22221432626247406 0.83834964 0.5757250785827637 True -9 28820 34.149155139923096 34.49082803726196 152.67433166503906 0.8556450605392456 225.7806396484375 0.2235962301492691 0.84445095 0.5304826498031616 True -10 31702 31.464280366897583 0.5047605037689209 159.70846557617188 0.3058425188064575 225.01528930664062 0.2254900187253952 0.8486533 0.5112146139144897 True -11 34584 31.24559211730957 21.11336588859558 184.0638427734375 0.47550374269485474 224.4628143310547 0.2263994663953781 0.8515772 0.4845527410507202 True -12 37466 31.043760061264038 2.0139009952545166 265.7978515625 0.6725330948829651 223.96932983398438 0.22767367959022522 0.8542376 0.4650844931602478 True -13 40348 31.185522317886353 0.5325062274932861 144.05023193359375 0.4285341501235962 223.7821044921875 0.2278691530227661 0.85800284 0.44881218671798706 True -14 43230 31.36646842956543 0.6944546699523926 121.15312194824219 0.3315449059009552 223.29034423828125 0.22909888625144958 0.86187756 0.43541499972343445 True -15 46112 31.179096460342407 0.49773526191711426 133.79251098632812 0.37394222617149353 222.88079833984375 0.2306358814239502 0.8646712 0.42053353786468506 True -16 48994 31.115107536315918 0.4959862232208252 210.0599365234375 0.4456193745136261 222.89060974121094 0.2302653044462204 0.86471176 0.417108416557312 True -17 51876 31.141412258148193 0.4969158172607422 131.57960510253906 0.32244718074798584 222.63319396972656 0.23139424622058868 0.86554205 0.4121950566768646 True -18 54758 31.172980070114136 0.5057113170623779 186.44985961914062 0.2823304533958435 222.99966430664062 0.2303657978773117 0.86246985 0.4159819483757019 False -19 57640 31.026254177093506 0.4988126754760742 189.54171752929688 0.3340992033481598 223.07467651367188 0.23028205335140228 0.8623434 0.4200146496295929 False diff --git a/ENCSR548KXH/cherimoya.fold_2.performance.tsv b/ENCSR548KXH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 15cf1fcc64712ccce5712ab32886c67a96c8e3c2..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -222.63319396972656 0.5373665690422058 0.23139424622058868 0.06037720665335655 0.8655420541763306 0.8033905625343323 0.4121950566768646 \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_3.evaluate.json b/ENCSR548KXH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b300f98fc3af10a429eeb31d753d405d8e8f7591..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF595ODH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_3.fit.json b/ENCSR548KXH/cherimoya.fold_3.fit.json deleted file mode 100644 index 6419e9eaaaf5139d19b26a833e6468e0dc2497ad..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF595ODH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_3.log b/ENCSR548KXH/cherimoya.fold_3.log deleted file mode 100644 index ad2128fbbeb2a6773889577f6d394c371c0b0360..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 34.95574736595154 3.579022169113159 147.6080780029297 1.0555025339126587 259.3016052246094 0.156208336353302 0.6494169 4.355233192443848 True -1 5504 30.112754821777344 0.5198428630828857 178.40176391601562 0.83277428150177 236.90203857421875 0.20209504663944244 0.76348776 2.1887857913970947 True -2 8256 30.136340379714966 32.57846426963806 182.30047607421875 0.6138701438903809 233.99159240722656 0.20764422416687012 0.76845413 1.1513643264770508 True -3 11008 30.273653507232666 0.5091042518615723 148.05447387695312 0.49054908752441406 232.38226318359375 0.21055768430233002 0.771756 1.0705797672271729 True -4 13760 30.04912281036377 0.5139455795288086 141.5199737548828 0.4629325270652771 230.75161743164062 0.214365616440773 0.784095 1.0266107320785522 True -5 16512 29.98586678504944 1.9142577648162842 141.72885131835938 0.524214506149292 229.62728881835938 0.21708008646965027 0.797029 0.9664254784584045 True -6 19264 30.032381296157837 0.5148723125457764 166.05392456054688 0.42686331272125244 228.39959716796875 0.22118395566940308 0.8016513 0.9341096878051758 True -7 22016 30.001782417297363 0.5133554935455322 129.78550720214844 0.46872878074645996 227.29226684570312 0.22379818558692932 0.8108994 0.887302041053772 True -8 24768 29.96113634109497 0.5136322975158691 301.9339904785156 0.876778781414032 227.31089782714844 0.22353224456310272 0.8155761 0.81223464012146 True -9 27520 29.98030400276184 0.5061514377593994 142.04293823242188 0.5208349823951721 226.41891479492188 0.22495350241661072 0.82556987 0.7682833671569824 True -10 30272 29.653751134872437 0.5020170211791992 139.05191040039062 0.5157392024993896 225.3524627685547 0.22868627309799194 0.8324931 0.6825240850448608 True -11 33024 29.499727249145508 21.10876226425171 186.69500732421875 0.47654664516448975 225.07017517089844 0.2291998714208603 0.8362766 0.6445432305335999 True -12 35776 29.600075006484985 0.5039210319519043 170.646240234375 0.4465605616569519 224.3210906982422 0.2304982990026474 0.84682465 0.5876891613006592 True -13 38528 29.489186763763428 0.5038840770721436 144.06704711914062 0.4626520872116089 223.6151580810547 0.23205788433551788 0.85232794 0.5422510504722595 True -14 41280 29.537394285202026 20.325602054595947 215.57611083984375 0.4141504764556885 222.6782684326172 0.23422297835350037 0.85733414 0.5024120211601257 True -15 44032 29.86331558227539 0.5130722522735596 178.2879638671875 0.350233793258667 222.080322265625 0.23567163944244385 0.86215687 0.47100046277046204 True -16 46784 29.50156545639038 0.5058419704437256 114.9688949584961 0.3614574074745178 222.68719482421875 0.2332572489976883 0.86525846 0.4523202180862427 True -17 49536 29.531548500061035 0.5005357265472412 200.76156616210938 0.19676613807678223 222.47833251953125 0.2343698889017105 0.8657077 0.4392671585083008 True -18 52288 29.535076379776 0.5032954216003418 167.3795166015625 0.3088361620903015 222.1524200439453 0.23510442674160004 0.8678133 0.43979349732398987 True -19 55040 29.479636430740356 0.507749080657959 133.6591033935547 0.5248250365257263 222.20082092285156 0.23503096401691437 0.8656781 0.4394548237323761 False diff --git a/ENCSR548KXH/cherimoya.fold_3.performance.tsv b/ENCSR548KXH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ccf90048ba12086769f2d345205ff5ab961ad805..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -222.1524200439453 0.5354998111724854 0.23510441184043884 0.06182507053017616 0.8678132891654968 0.7928350567817688 0.43979349732398987 \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_4.evaluate.json b/ENCSR548KXH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 40b83236f02684b17afd845607f28a880b47b117..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF595ODH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_4.fit.json b/ENCSR548KXH/cherimoya.fold_4.fit.json deleted file mode 100644 index ee1e7e49a0ca22898ee5a39f1c78ee26b72288da..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF595ODH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548KXH/cherimoya.fold_4.log b/ENCSR548KXH/cherimoya.fold_4.log deleted file mode 100644 index cdfc91730cc6a0672f4d9da0b151e9011d8db81e..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2829 35.91930913925171 3.6205146312713623 177.46176147460938 0.6360141038894653 204.87948608398438 0.1352362036705017 0.67336684 3.1704909801483154 True -1 5658 31.22619891166687 0.603834867477417 180.82763671875 0.8458930253982544 188.84381103515625 0.1718420386314392 0.7758519 1.4680204391479492 True -2 8487 31.242632389068604 1.3398542404174805 149.54364013671875 0.4700281023979187 186.96815490722656 0.1745690256357193 0.7815335 0.7974830865859985 True -3 11316 31.177452325820923 5.221011638641357 155.83151245117188 0.5226806402206421 185.08108520507812 0.17881254851818085 0.79167277 0.7397276759147644 True -4 14145 32.550291776657104 25.77910041809082 140.267333984375 0.5626109838485718 183.813720703125 0.1808602213859558 0.80098236 0.6780134439468384 True -5 16974 32.169677734375 37.16241264343262 126.73148345947266 0.4396444857120514 183.0390167236328 0.18337342143058777 0.80935746 0.663993239402771 True -6 19803 32.251524925231934 8.18473196029663 231.56626892089844 0.6391711831092834 181.9093017578125 0.18755114078521729 0.8145046 0.631783664226532 True -7 22632 31.217479467391968 0.6298863887786865 144.94375610351562 0.6623181700706482 181.38333129882812 0.1880924552679062 0.82417816 0.5802249312400818 True -8 25461 31.263811349868774 0.6022634506225586 149.37730407714844 0.5555175542831421 181.05938720703125 0.18924154341220856 0.82631767 0.5594737529754639 True -9 28290 31.138212203979492 0.5907444953918457 166.86285400390625 0.703310489654541 180.76124572753906 0.18983647227287292 0.8323674 0.5119735598564148 True -10 31119 30.833468914031982 1.0331087112426758 149.93719482421875 0.42098864912986755 180.13963317871094 0.1910025179386139 0.8426344 0.4694538414478302 True -11 33948 30.606956481933594 27.2530996799469 209.634765625 0.3660181164741516 179.86997985839844 0.19201745092868805 0.84681886 0.43612292408943176 True -12 36777 31.052118062973022 0.5912337303161621 236.62774658203125 0.464861124753952 179.01109313964844 0.1948050856590271 0.85146236 0.4068146347999573 True -13 39606 31.20908212661743 24.338068962097168 191.25534057617188 0.5166799426078796 178.6774444580078 0.19558671116828918 0.85594726 0.3830086886882782 True -14 42435 30.67011857032776 13.646824598312378 112.02438354492188 0.6081956624984741 178.9520721435547 0.19422073662281036 0.86062956 0.3610318601131439 True -15 45264 30.627989053726196 0.5911097526550293 196.69483947753906 0.44709068536758423 178.7111053466797 0.19519656896591187 0.8650445 0.3474877178668976 True -16 48093 30.59332799911499 0.5847859382629395 156.49746704101562 0.32489243149757385 178.33029174804688 0.1959063559770584 0.86637974 0.34141331911087036 True -17 50922 31.38261866569519 34.064826250076294 180.71627807617188 0.2761351466178894 178.30921936035156 0.19626468420028687 0.86599624 0.3397393822669983 False -18 53751 30.88600993156433 0.622856616973877 122.98756408691406 0.34385180473327637 178.46844482421875 0.19582034647464752 0.8659397 0.3395707309246063 False -19 56580 30.646132946014404 0.7409648895263672 120.86756896972656 0.26866480708122253 178.69496154785156 0.1947326809167862 0.86447114 0.34025371074676514 False diff --git a/ENCSR548KXH/cherimoya.fold_4.performance.tsv b/ENCSR548KXH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9df91de54a59f888d6cea65af8fa9da28f7d0451..0000000000000000000000000000000000000000 --- a/ENCSR548KXH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -178.33029174804688 0.5641010999679565 0.1959063708782196 0.04838442802429199 0.8663797378540039 0.768791139125824 0.34141331911087036 \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_0.evaluate.json b/ENCSR548QCP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index deab8a243e41654981e1c8ed0413fffd350d41cc..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326FMD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_0.fit.json b/ENCSR548QCP/cherimoya.fold_0.fit.json deleted file mode 100644 index ba28de36c41c6a482b77ccb1d042aa097d4dbe62..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF326FMD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_0.log b/ENCSR548QCP/cherimoya.fold_0.log deleted file mode 100644 index 4ab3d84ee8c1d523412dc3c7fd5c48ed77048348..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1708 22.88782286643982 3.4952304363250732 338.297607421875 0.3165304958820343 539.3734130859375 0.5057245492935181 0.6408152 12.768898963928223 True -1 3416 19.053239822387695 0.36574745178222656 364.663818359375 0.40779736638069153 447.7506103515625 0.5962954759597778 0.7278827 2.2523996829986572 True -2 5124 18.984169006347656 0.35675716400146484 347.6609802246094 0.31311386823654175 421.70660400390625 0.6292728185653687 0.75981456 0.6268770694732666 True -3 6832 18.9454402923584 0.3507523536682129 332.99053955078125 0.3324548006057739 413.50860595703125 0.639020562171936 0.77341706 0.39367640018463135 True -4 8540 18.99841022491455 8.034907341003418 384.27978515625 0.41370224952697754 409.1363830566406 0.6446488499641418 0.7847167 0.37559986114501953 True -5 10248 18.950544357299805 0.3602783679962158 364.8712158203125 0.29478582739830017 407.7181091308594 0.6469743847846985 0.7918688 0.3135683536529541 True -6 11956 21.6182382106781 3.6556825637817383 370.6543273925781 0.4755209684371948 406.28765869140625 0.6485384106636047 0.7940112 0.29316267371177673 True -7 13664 18.951316595077515 0.35265493392944336 359.87176513671875 0.33735033869743347 405.31298828125 0.6505359411239624 0.7988948 0.2822795510292053 True -8 15372 18.95215392112732 0.35206103324890137 351.552001953125 0.16790452599525452 404.1103820800781 0.6521032452583313 0.80325186 0.27725809812545776 True -9 17080 18.94233727455139 0.3454442024230957 368.5638427734375 0.2861233055591583 403.3586120605469 0.6534478068351746 0.8053022 0.27167627215385437 True -10 18788 18.93960189819336 0.3505265712738037 337.6063232421875 0.2059778869152069 402.4141540527344 0.6552661061286926 0.8097213 0.2659156322479248 True -11 20496 18.93093180656433 0.34955787658691406 344.19061279296875 0.24815845489501953 401.3792419433594 0.6571061015129089 0.8118467 0.262295663356781 True -12 22204 18.94498562812805 1.1821014881134033 329.1385192871094 0.2894907295703888 400.5874328613281 0.6585461497306824 0.8154456 0.2620287239551544 True -13 23912 18.964194536209106 1.5039074420928955 306.79718017578125 0.213990718126297 400.064208984375 0.6595048308372498 0.8145409 0.2577190399169922 False -14 25620 18.96589159965515 0.35265374183654785 323.7369079589844 0.14968575537204742 399.80413818359375 0.6602854132652283 0.8190826 0.25445061922073364 True -15 27328 18.936158657073975 0.34671759605407715 304.296630859375 0.192402184009552 399.6960754394531 0.6607339978218079 0.819542 0.2539496421813965 True -16 29036 18.949337482452393 0.34908461570739746 313.73358154296875 0.10789775848388672 399.9591369628906 0.6602567434310913 0.8187565 0.25580161809921265 False -17 30744 18.956858158111572 0.3465394973754883 352.09918212890625 0.17350006103515625 400.4134216308594 0.6594420075416565 0.8165462 0.26072874665260315 False -18 32452 18.94773006439209 0.35003662109375 320.191162109375 0.12019321322441101 400.9581298828125 0.6584896445274353 0.8137383 0.2666892409324646 False -19 34160 18.934080362319946 0.34665822982788086 364.78643798828125 0.09843990206718445 401.3003234863281 0.6579761505126953 0.8088887 0.2723022699356079 False diff --git a/ENCSR548QCP/cherimoya.fold_0.performance.tsv b/ENCSR548QCP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3b7c1183702e1bd66545ec64393d749a1e72f5fe..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -399.6960754394531 0.26755207777023315 0.6607340574264526 0.27834823727607727 0.8195419907569885 0.7846648693084717 0.2539496421813965 \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_1.evaluate.json b/ENCSR548QCP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 41c8cdfe83fb4daf0d63187d231a940745276cce..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326FMD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_1.fit.json b/ENCSR548QCP/cherimoya.fold_1.fit.json deleted file mode 100644 index 2040921169d5c3d0117de4f86cd613b407ac1e60..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF326FMD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_1.log b/ENCSR548QCP/cherimoya.fold_1.log deleted file mode 100644 index db42295131241c7c2c078e6c6872ea3d03d975ba..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1660 22.26013159751892 3.462111711502075 351.3147277832031 0.4995564818382263 616.5897216796875 0.518583357334137 0.6050652 15.264837265014648 True -1 3320 18.40350651741028 0.5075850486755371 324.1314392089844 0.3872307538986206 507.10906982421875 0.6117574572563171 0.7154977 3.1589372158050537 True -2 4980 18.446199893951416 0.4920055866241455 391.5721740722656 0.31209754943847656 473.79779052734375 0.6519376039505005 0.747521 1.0992685556411743 True -3 6640 18.40777039527893 0.4807276725769043 282.75970458984375 0.25214171409606934 459.4826354980469 0.6689759492874146 0.7733441 0.46067509055137634 True -4 8300 18.435223817825317 0.48561763763427734 383.73724365234375 0.4312819242477417 455.3358154296875 0.6735233068466187 0.7879254 0.3759855031967163 True -5 9960 18.43219518661499 0.6667098999023438 335.38134765625 0.228577122092247 453.1051025390625 0.6759561896324158 0.79691356 0.3321831226348877 True -6 11620 18.470234632492065 0.49148058891296387 362.204345703125 0.43462711572647095 451.2601318359375 0.6788187623023987 0.8030743 0.30231451988220215 True -7 13280 18.45402765274048 0.48822021484375 369.2337646484375 0.2150951325893402 449.6789855957031 0.6816260814666748 0.80832714 0.29470375180244446 True -8 14940 18.515734434127808 2.0306005477905273 386.04229736328125 0.2689793109893799 448.3123474121094 0.6835643649101257 0.81324553 0.2831728160381317 True -9 16600 18.47208046913147 1.0499343872070312 368.8336486816406 0.37634599208831787 446.9674377441406 0.6855466961860657 0.81538415 0.27080976963043213 True -10 18260 18.489998817443848 0.4978625774383545 380.7920837402344 0.18431101739406586 445.8170166015625 0.6871436834335327 0.81995404 0.2678099572658539 True -11 19920 18.506326913833618 0.4938807487487793 314.48846435546875 0.35009700059890747 444.7122802734375 0.6889129877090454 0.8239318 0.2622638940811157 True -12 21580 18.49502992630005 0.8029401302337646 373.47406005859375 0.2369794398546219 444.0269775390625 0.6902230381965637 0.8258503 0.2603658139705658 True -13 23240 18.467278242111206 0.9498515129089355 379.53619384765625 0.2297767549753189 443.4825744628906 0.6910929083824158 0.82736725 0.2565970718860626 True -14 24900 18.500178575515747 0.5027425289154053 363.0320739746094 0.23732022941112518 443.031005859375 0.6918321251869202 0.82974476 0.25248292088508606 True -15 26560 18.460229635238647 0.4919719696044922 313.6273498535156 0.19036860764026642 442.9395751953125 0.6920851469039917 0.83162856 0.2538788318634033 True -16 28220 18.45645499229431 0.506915807723999 343.0094299316406 0.14167553186416626 443.3551330566406 0.6915876865386963 0.8317249 0.2591513395309448 True -17 29880 18.419842004776 1.9038255214691162 319.9485168457031 0.13630050420761108 444.0435791015625 0.6905437111854553 0.8285768 0.2649216949939728 False -18 31540 18.478607416152954 0.4920797348022461 347.9847717285156 0.14166821539402008 444.5776062011719 0.6896604299545288 0.8252888 0.2704712152481079 False -19 33200 18.406592845916748 0.49706554412841797 354.16339111328125 0.11201737076044083 444.8584899902344 0.6890257000923157 0.82286084 0.2741215229034424 False diff --git a/ENCSR548QCP/cherimoya.fold_1.performance.tsv b/ENCSR548QCP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e8b60a0e4d016132263ca4f300fd39c6526bcb29..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -443.3551330566406 0.24536971747875214 0.6915876865386963 0.30789420008659363 0.8317248821258545 0.8158453106880188 0.2591513395309448 \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_2.evaluate.json b/ENCSR548QCP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cc03ac3452842e8ce2006a45b58c324e6650e826..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326FMD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_2.fit.json b/ENCSR548QCP/cherimoya.fold_2.fit.json deleted file mode 100644 index 6f244eb5dc07811cea8eb6d272c9e79de04550a2..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF326FMD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_2.log b/ENCSR548QCP/cherimoya.fold_2.log deleted file mode 100644 index 1a583a373a6d4dc8fc6a1271c5ed22068a0671cc..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1768 24.32794213294983 3.3515632152557373 351.29754638671875 0.4343445897102356 557.9745483398438 0.5120090246200562 0.61091185 12.980264663696289 True -1 3536 19.731801986694336 0.4201991558074951 343.6041259765625 0.27053263783454895 460.3326110839844 0.6049156188964844 0.7226184 2.3598639965057373 True -2 5304 19.7262065410614 0.3700244426727295 356.1468811035156 0.2577323913574219 432.2938232421875 0.6385757327079773 0.7683695 0.6872462034225464 True -3 7072 19.775649785995483 4.893594980239868 380.0604248046875 0.29123637080192566 424.2696533203125 0.6484322547912598 0.7853584 0.39023903012275696 True -4 8840 19.714046955108643 2.236253023147583 361.177490234375 0.30449378490448 421.3782653808594 0.6521514654159546 0.7962738 0.32940930128097534 True -5 10608 19.7420814037323 0.4063377380371094 356.5524597167969 0.3399198055267334 419.5514831542969 0.6540877223014832 0.80216 0.28385984897613525 True -6 12376 21.816553115844727 9.85119891166687 381.22491455078125 0.3639274835586548 418.3345031738281 0.6560418009757996 0.8050665 0.28315502405166626 True -7 14144 19.867180585861206 0.3757467269897461 320.7635498046875 0.24146096408367157 417.25146484375 0.6583454608917236 0.80916077 0.30681753158569336 True -8 15912 19.791927099227905 0.43193769454956055 349.386474609375 0.293829083442688 416.1764831542969 0.6597771048545837 0.81129247 0.2829799950122833 True -9 17680 19.73459219932556 0.3697028160095215 355.51708984375 0.23008248209953308 414.9027099609375 0.661929726600647 0.81607276 0.268256276845932 True -10 19448 19.77017092704773 0.8865725994110107 341.81365966796875 0.19270431995391846 413.9006652832031 0.6637687683105469 0.8199184 0.27123263478279114 True -11 21216 19.743598699569702 0.3677704334259033 336.8539123535156 0.3041353225708008 412.9152526855469 0.6650986075401306 0.82029545 0.2620272636413574 True -12 22984 19.77680730819702 0.3791158199310303 385.481689453125 0.33785563707351685 412.2854919433594 0.6663185954093933 0.82108384 0.26254844665527344 True -13 24752 19.793872594833374 0.8008952140808105 334.9234924316406 0.2537229657173157 411.6212463378906 0.6677535772323608 0.8240877 0.25991490483283997 True -14 26520 19.773117303848267 1.434591293334961 390.2862548828125 0.31074008345603943 411.1036682128906 0.6686553955078125 0.82691985 0.2548294961452484 True -15 28288 19.768505573272705 0.372222900390625 334.65673828125 0.21002107858657837 411.3316345214844 0.6688007712364197 0.82735616 0.2583455443382263 True -16 30056 19.794060945510864 0.3675079345703125 313.647705078125 0.14831173419952393 411.3795471191406 0.6685672402381897 0.82696635 0.2617444694042206 False -17 31824 19.708925008773804 0.3648946285247803 341.7934875488281 0.1827830970287323 411.851318359375 0.6678921580314636 0.82287335 0.26569730043411255 False -18 33592 20.10752558708191 0.3806934356689453 328.9869384765625 0.11492647975683212 412.160400390625 0.6672030687332153 0.819911 0.26890236139297485 False -19 35360 19.797926902770996 0.3640937805175781 305.88519287109375 0.10775288939476013 412.3831787109375 0.6666796803474426 0.81899726 0.26936525106430054 False diff --git a/ENCSR548QCP/cherimoya.fold_2.performance.tsv b/ENCSR548QCP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5d37a0a1c92c280504e6b4449f568240c80c1927..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -411.3316345214844 0.26166069507598877 0.6688008308410645 0.2867772877216339 0.8273561596870422 0.7938207983970642 0.2583455443382263 \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_3.evaluate.json b/ENCSR548QCP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7ad22bbe359c5b2e517909d22db98353a065d52a..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326FMD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_3.fit.json b/ENCSR548QCP/cherimoya.fold_3.fit.json deleted file mode 100644 index a7ea8b054f65f9741eebaad70e2dfb8d09e5542b..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF326FMD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_3.log b/ENCSR548QCP/cherimoya.fold_3.log deleted file mode 100644 index e816be4e7d79ffaa371963f2f0c70f70e28f33f3..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1726 23.900119066238403 4.002991437911987 374.115234375 0.41552209854125977 545.7206420898438 0.5071688294410706 0.61819583 12.70479679107666 True -1 3452 18.986440181732178 0.35669851303100586 361.4581298828125 0.21676212549209595 452.77227783203125 0.6009853482246399 0.7234406 2.509230375289917 True -2 5178 19.236610889434814 0.32869720458984375 381.44171142578125 0.30695074796676636 427.7898864746094 0.6307992935180664 0.74822557 0.5211913585662842 True -3 6904 19.226829051971436 0.327345609664917 408.0924072265625 0.3205380141735077 416.8265380859375 0.6434797644615173 0.77149284 0.4162072539329529 True -4 8630 19.04830813407898 0.3218421936035156 314.54718017578125 0.264411598443985 413.6944885253906 0.6469120979309082 0.78101933 0.3368230164051056 True -5 10356 18.823156356811523 0.3191533088684082 344.6111755371094 0.32122930884361267 411.57916259765625 0.6496915817260742 0.7899958 0.30608615279197693 True -6 12082 18.83999276161194 1.1089682579040527 358.7221374511719 0.2967097759246826 410.1396179199219 0.6512916088104248 0.795725 0.2979829013347626 True -7 13808 18.848860263824463 0.3266489505767822 379.538818359375 0.22937244176864624 408.6754455566406 0.6538835167884827 0.79998213 0.27887898683547974 True -8 15534 18.9110209941864 0.3183786869049072 357.48046875 0.25883597135543823 407.59564208984375 0.6555724143981934 0.8017829 0.2716965675354004 True -9 17260 19.058186531066895 0.3290238380432129 346.10980224609375 0.2763887643814087 406.6742858886719 0.6573875546455383 0.80597866 0.2755744159221649 True -10 18986 18.85649609565735 0.32913708686828613 336.90826416015625 0.2163415402173996 405.882568359375 0.6590819954872131 0.80977345 0.2725691497325897 True -11 20712 18.863871097564697 0.3281433582305908 355.57513427734375 0.26603782176971436 405.105224609375 0.6603714823722839 0.8121092 0.2752428948879242 True -12 22438 18.863808393478394 1.2277696132659912 350.39593505859375 0.30016177892684937 404.7605895996094 0.6612178087234497 0.8159762 0.26665619015693665 True -13 24164 18.876446962356567 0.3246455192565918 323.9184265136719 0.2366756945848465 404.3017272949219 0.6622244715690613 0.81721056 0.2678026556968689 True -14 25890 18.857488870620728 12.474408388137817 362.3704528808594 0.19931486248970032 403.9172058105469 0.6631015539169312 0.81836146 0.26961469650268555 True -15 27616 18.8868625164032 0.3267385959625244 321.31494140625 0.15652140974998474 403.9984130859375 0.6632769107818604 0.82073385 0.26768067479133606 True -16 29342 18.849498510360718 0.33818912506103516 346.9818115234375 0.22011013329029083 404.1640319824219 0.6627075672149658 0.82026404 0.26810017228126526 False -17 31068 18.933504343032837 0.3225846290588379 323.59967041015625 0.17426258325576782 404.4862365722656 0.6622341871261597 0.8160074 0.2685449421405792 False -18 32794 18.854054927825928 0.3200702667236328 339.714111328125 0.12129739671945572 404.8540954589844 0.6614040732383728 0.8157315 0.27220484614372253 False -19 34520 18.825164794921875 0.3236079216003418 339.71630859375 0.10103639960289001 405.080810546875 0.6609406471252441 0.8122793 0.274834543466568 False diff --git a/ENCSR548QCP/cherimoya.fold_3.performance.tsv b/ENCSR548QCP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e68fd51243c939868e2fbaa6122028699967aad0..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -403.9984130859375 0.2653132677078247 0.6632769107818604 0.2822660207748413 0.8207338452339172 0.7838202714920044 0.26768067479133606 \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_4.evaluate.json b/ENCSR548QCP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 442040850ed072c76b785e90d40d5455863b119f..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF326FMD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_4.fit.json b/ENCSR548QCP/cherimoya.fold_4.fit.json deleted file mode 100644 index 3e2b331b4ca4f926a53e47ce98853981c95a6a6f..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF326FMD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR548QCP/cherimoya.fold_4.log b/ENCSR548QCP/cherimoya.fold_4.log deleted file mode 100644 index 0428b78d6a3e7798c8df50f196e8aa73febec6cb..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1730 23.8379328250885 3.307807207107544 427.85479736328125 0.35208654403686523 529.653564453125 0.5101999640464783 0.62102944 12.631600379943848 True -1 3460 19.2658793926239 0.34982943534851074 355.78582763671875 0.36722639203071594 442.44818115234375 0.5982868075370789 0.7138794 2.234820604324341 True -2 5190 19.278417825698853 0.3414347171783447 347.48846435546875 0.39353349804878235 419.7865295410156 0.630933940410614 0.75196034 0.6239412426948547 True -3 6920 19.295480966567993 0.3394913673400879 362.57330322265625 0.39653992652893066 408.7395935058594 0.6433526873588562 0.7730882 0.3887752890586853 True -4 8650 19.25835371017456 0.33462047576904297 337.8250732421875 0.2327374666929245 407.27996826171875 0.6449640989303589 0.7772982 0.4001171588897705 True -5 10380 19.255234956741333 13.871503353118896 319.7608642578125 0.259864866733551 404.2819519042969 0.6497828364372253 0.79231715 0.3143802285194397 True -6 12110 22.857483625411987 13.597689628601074 382.1189880371094 0.24221618473529816 402.93951416015625 0.6521003246307373 0.80132043 0.28674501180648804 True -7 13840 19.34633708000183 0.3341860771179199 337.85369873046875 0.31663304567337036 401.80059814453125 0.6541001200675964 0.8078338 0.2747454345226288 True -8 15570 19.297211408615112 0.33599114418029785 362.1211242675781 0.26907584071159363 401.2602844238281 0.6557837128639221 0.807503 0.28435322642326355 False -9 17300 19.293033599853516 0.32861804962158203 312.06103515625 0.41258642077445984 399.83599853515625 0.6574746966362 0.8097539 0.2826501727104187 True -10 19030 19.32723069190979 0.33720898628234863 354.17822265625 0.29929274320602417 398.9541931152344 0.6591085195541382 0.8160948 0.2601034641265869 True -11 20760 19.260151386260986 0.33761096000671387 353.8729553222656 0.15535402297973633 398.06927490234375 0.6603672504425049 0.81711537 0.24893809854984283 True -12 22490 19.286221265792847 6.306303262710571 429.288818359375 0.22626256942749023 397.3258056640625 0.6615161895751953 0.82197905 0.23875972628593445 True -13 24220 19.32867956161499 2.609956741333008 330.5526428222656 0.18222682178020477 397.05279541015625 0.6623170971870422 0.82326776 0.23847666382789612 True -14 25950 18.938134908676147 0.3307921886444092 326.6669006347656 0.22490864992141724 396.4765319824219 0.6632319092750549 0.8301501 0.23524104058742523 True -15 27680 19.00583815574646 0.347628116607666 346.160400390625 0.1316644251346588 396.2721862792969 0.6638234853744507 0.8290911 0.23588599264621735 False -16 29410 19.097038984298706 0.7656943798065186 340.73175048828125 0.14399851858615875 396.7249755859375 0.6634483933448792 0.8301283 0.23819148540496826 False -17 31140 19.046716928482056 0.33837437629699707 372.77935791015625 0.05915461853146553 397.0618591308594 0.6628434062004089 0.8254998 0.24441614747047424 False -18 32870 19.043785333633423 0.3353993892669678 325.7074890136719 0.08091798424720764 397.5497741699219 0.6619319915771484 0.82012045 0.24956510961055756 False -19 34600 20.043937921524048 0.33896613121032715 314.0579833984375 0.13557904958724976 397.7167663574219 0.6613658666610718 0.81929207 0.25134268403053284 False diff --git a/ENCSR548QCP/cherimoya.fold_4.performance.tsv b/ENCSR548QCP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5903117ec3a6bacc3611ec31225860fc2c4a61d4..0000000000000000000000000000000000000000 --- a/ENCSR548QCP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -396.4765319824219 0.266337513923645 0.6632319688796997 0.2795385718345642 0.8301501274108887 0.7905892133712769 0.23524104058742523 \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_0.evaluate.json b/ENCSR550UWM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a0546291067a84b294a95970a2fec5edc905142d..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF829DQY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_0.fit.json b/ENCSR550UWM/cherimoya.fold_0.fit.json deleted file mode 100644 index a31f34ac5176f1e391cae51d5027daae0401b044..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF829DQY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_0.log b/ENCSR550UWM/cherimoya.fold_0.log deleted file mode 100644 index 04b1ecaaca9fbfdf8429d5eef62577d2572e124f..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.23382830619812 4.360194444656372 179.96554565429688 0.9214144349098206 228.90652465820312 0.14820967614650726 0.7312889 3.0549817085266113 True -1 5500 30.452537298202515 0.9023594856262207 186.73080444335938 0.5898621082305908 217.36822509765625 0.20861105620861053 0.77241796 0.9814773201942444 True -2 8250 30.52065396308899 0.5537047386169434 178.3874053955078 0.7450746893882751 213.93466186523438 0.21972760558128357 0.77899855 0.6353008151054382 True -3 11000 30.351804971694946 0.5668225288391113 185.67495727539062 0.663983941078186 212.1254119873047 0.2271076738834381 0.7834561 0.5800450444221497 True -4 13750 29.8369300365448 17.99570608139038 216.69361877441406 0.5734525918960571 211.3001251220703 0.23165415227413177 0.78365546 0.6507228016853333 True -5 16500 29.855543851852417 0.5871410369873047 146.724853515625 0.4707092344760895 210.84266662597656 0.2331438958644867 0.78670555 0.6065506935119629 True -6 19250 29.815242528915405 0.5825517177581787 164.43960571289062 0.7278225421905518 210.28367614746094 0.23543106019496918 0.7924463 0.5977585911750793 True -7 22000 29.840984344482422 0.578655481338501 173.18667602539062 0.7249470949172974 209.88844299316406 0.2376088947057724 0.7907987 0.5601598620414734 False -8 24750 29.815710306167603 0.593914270401001 130.13534545898438 0.7174399495124817 209.4824676513672 0.23923878371715546 0.79474413 0.5279234051704407 True -9 27500 29.81309700012207 0.5633285045623779 152.93743896484375 0.5842106342315674 208.8370819091797 0.24321424961090088 0.7949184 0.5348607897758484 True -10 30250 29.8121817111969 1.380960464477539 177.89390563964844 0.4838038384914398 208.53436279296875 0.24467585980892181 0.79993224 0.5042503476142883 True -11 33000 29.95062780380249 1.70676589012146 174.12294006347656 0.5014582872390747 208.30274963378906 0.24561239778995514 0.80332243 0.4670756757259369 True -12 35750 29.91042160987854 1.8139126300811768 122.86812591552734 0.25323718786239624 207.94781494140625 0.2479221522808075 0.8035605 0.44428014755249023 True -13 38500 29.90751886367798 1.6905896663665771 178.04478454589844 0.46648308634757996 207.6050567626953 0.24895049631595612 0.80801433 0.4165571331977844 True -14 41250 29.82603645324707 1.5219981670379639 167.93368530273438 0.5950479507446289 207.027099609375 0.2516374886035919 0.81362617 0.393160879611969 True -15 44000 29.88494634628296 2.309107542037964 184.19349670410156 0.6034922003746033 206.81138610839844 0.2525911033153534 0.8170246 0.37261560559272766 True -16 46750 29.83925461769104 1.5279686450958252 190.47129821777344 0.41256940364837646 206.78028869628906 0.25327035784721375 0.821873 0.35819628834724426 True -17 49500 29.986920833587646 2.0794193744659424 223.68692016601562 0.33456939458847046 206.7683563232422 0.2533794939517975 0.8230884 0.3501449227333069 True -18 52250 29.939684629440308 1.511521816253662 160.13710021972656 0.22888685762882233 206.91871643066406 0.25263071060180664 0.82319105 0.34839993715286255 True -19 55000 29.922410488128662 1.704662561416626 151.74850463867188 0.4196354150772095 206.80169677734375 0.25371265411376953 0.8222545 0.35062408447265625 False diff --git a/ENCSR550UWM/cherimoya.fold_0.performance.tsv b/ENCSR550UWM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 45d6b7a6fa94da2d0d46d142a9cd97a4153e3f59..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -206.91871643066406 0.5286707282066345 0.25263068079948425 0.0554145872592926 0.8231910467147827 0.7623738646507263 0.34839993715286255 \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_1.evaluate.json b/ENCSR550UWM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5622f34e38eacd87460cafc201c37ea7193fa4f6..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF829DQY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_1.fit.json b/ENCSR550UWM/cherimoya.fold_1.fit.json deleted file mode 100644 index 0bb5630eccae8e93cc6c94da2dad38498be2d56a..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF829DQY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_1.log b/ENCSR550UWM/cherimoya.fold_1.log deleted file mode 100644 index 280fd2beba870743676095332197b171f94f5968..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 34.598424434661865 3.8806533813476562 178.68431091308594 0.7015864849090576 270.341064453125 0.15663139522075653 0.72609365 3.4300484657287598 True -1 5410 29.992149829864502 0.7737331390380859 199.40530395507812 0.943767786026001 254.85765075683594 0.22663429379463196 0.77067024 1.2962318658828735 True -2 8115 29.960909128189087 0.765458345413208 179.3448944091797 0.7178979516029358 250.42857360839844 0.24030748009681702 0.78422683 0.7843714952468872 True -3 10820 29.528337240219116 0.7003388404846191 173.70632934570312 0.7300587892532349 248.4001922607422 0.2472279965877533 0.7913638 0.6881729364395142 True -4 13525 29.330633878707886 0.7007582187652588 196.76315307617188 0.614712655544281 247.60308837890625 0.25033292174339294 0.79489285 0.7046986818313599 True -5 16230 29.345632314682007 0.6984879970550537 164.20196533203125 0.6009385585784912 246.60179138183594 0.255330353975296 0.7995902 0.7454602122306824 True -6 18935 29.368250131607056 0.7033329010009766 162.61660766601562 0.4695640206336975 246.31524658203125 0.25592416524887085 0.8014297 0.713962733745575 True -7 21640 29.32146716117859 0.6971523761749268 147.9974365234375 0.8586981296539307 245.74050903320312 0.2583126723766327 0.80169135 0.6990429759025574 True -8 24345 29.38319754600525 0.8377673625946045 145.82452392578125 0.6610985994338989 244.96046447753906 0.2625858783721924 0.80538243 0.7012882232666016 True -9 27050 29.307490825653076 0.69576096534729 129.04066467285156 0.5010362863540649 244.36456298828125 0.26505449414253235 0.80898124 0.6739786863327026 True -10 29755 29.29508376121521 0.6856629848480225 127.15765380859375 0.4805266261100769 243.81268310546875 0.267374187707901 0.809333 0.6515139937400818 True -11 32460 29.366197109222412 0.7057955265045166 204.2742919921875 0.6502246260643005 243.618896484375 0.2677639424800873 0.8150218 0.5593741536140442 True -12 35165 29.393983602523804 0.7013628482818604 143.13455200195312 0.4310988485813141 243.5064697265625 0.268135666847229 0.8189072 0.5424522757530212 True -13 37870 29.431616067886353 0.6908073425292969 169.79461669921875 0.617412805557251 242.72975158691406 0.2713811695575714 0.8229917 0.5052707195281982 True -14 40575 29.329303741455078 0.7026548385620117 153.17431640625 0.6814802885055542 242.2378387451172 0.2729467749595642 0.8288614 0.4769199788570404 True -15 43280 29.334944486618042 2.611973524093628 145.32208251953125 0.4033203125 242.30255126953125 0.2722870111465454 0.83173347 0.43585294485092163 True -16 45985 29.38324761390686 0.7049093246459961 141.3042449951172 0.4237402081489563 241.82763671875 0.27426961064338684 0.8365446 0.412172794342041 True -17 48690 29.36866283416748 0.6991918087005615 168.98660278320312 0.2992517948150635 241.9805908203125 0.27384090423583984 0.8371219 0.3893531858921051 True -18 51395 29.377631425857544 0.6971356868743896 166.43655395507812 0.3410983085632324 242.18751525878906 0.27241694927215576 0.8376021 0.3887556493282318 True -19 54100 29.372725009918213 0.6974444389343262 174.72738647460938 0.290951132774353 242.0633087158203 0.27359604835510254 0.8373207 0.3870200216770172 False diff --git a/ENCSR550UWM/cherimoya.fold_1.performance.tsv b/ENCSR550UWM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 87df6489c0341f30848d13d8f7e92d9c61fd570d..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -242.18751525878906 0.5098865032196045 0.2724169194698334 0.06954735517501831 0.8376020789146423 0.8059144616127014 0.3887556493282318 \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_2.evaluate.json b/ENCSR550UWM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 093612fa0b57d5b2d4c3805efa001b0dfa9565d1..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF829DQY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_2.fit.json b/ENCSR550UWM/cherimoya.fold_2.fit.json deleted file mode 100644 index cdddeb90ac19f5396339d1c096480c94794b12f9..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF829DQY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_2.log b/ENCSR550UWM/cherimoya.fold_2.log deleted file mode 100644 index 48140bd466f042b8b3c3e7c8804e2268ab575b80..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.90618348121643 3.4038805961608887 150.57701110839844 0.8155105113983154 242.15829467773438 0.1538597047328949 0.7200143 3.1730799674987793 True -1 5744 31.82278800010681 0.557236909866333 149.33274841308594 0.8197567462921143 228.68719482421875 0.21604228019714355 0.7695154 0.9343708157539368 True -2 8616 31.298011541366577 0.5928566455841064 154.81881713867188 0.566329836845398 225.5427703857422 0.22653156518936157 0.78267044 0.5668626427650452 True -3 11488 31.221837043762207 0.5322051048278809 189.90420532226562 0.6965274810791016 224.29917907714844 0.23053514957427979 0.7830702 0.5702382922172546 True -4 14360 31.252275466918945 0.5361526012420654 177.9740753173828 0.5377137660980225 223.30657958984375 0.23455046117305756 0.78762436 0.5893663763999939 True -5 17232 31.089327812194824 0.5330710411071777 181.0836944580078 0.4778411388397217 222.4323272705078 0.2388642281293869 0.78844744 0.568673849105835 True -6 20104 31.096526622772217 0.5332181453704834 174.90509033203125 0.6673793792724609 221.74978637695312 0.24256815016269684 0.7905106 0.5441839098930359 True -7 22976 31.1294846534729 0.5226113796234131 151.50149536132812 0.6592109203338623 221.58763122558594 0.2437487691640854 0.7929695 0.5370702743530273 True -8 25848 31.105541706085205 0.5336000919342041 150.81744384765625 0.787696361541748 221.13616943359375 0.24558137357234955 0.7956342 0.573660671710968 True -9 28720 31.136707544326782 0.5215973854064941 183.80340576171875 0.5449445247650146 220.60992431640625 0.24769245088100433 0.79697955 0.5391432046890259 True -10 31592 31.130571365356445 0.5336582660675049 151.02841186523438 0.4443604648113251 220.16061401367188 0.2495594620704651 0.79692477 0.5393625497817993 False -11 34464 31.201634883880615 0.5355820655822754 137.268798828125 0.4215661883354187 219.48634338378906 0.25330090522766113 0.7994547 0.5150311589241028 True -12 37336 31.192963123321533 0.5528554916381836 142.06103515625 0.5097222924232483 219.26515197753906 0.25409942865371704 0.8029323 0.4854218065738678 True -13 40208 31.17615056037903 0.5560522079467773 132.0072479248047 0.5100220441818237 218.73292541503906 0.25727054476737976 0.80700004 0.45657801628112793 True -14 43080 31.193345308303833 0.5345416069030762 164.0699462890625 0.5544323921203613 218.68421936035156 0.2570998966693878 0.8118038 0.4406866729259491 True -15 45952 31.205430507659912 0.5389373302459717 198.624267578125 0.3860160708427429 218.34103393554688 0.2590469717979431 0.8161875 0.4173751771450043 True -16 48824 31.231995344161987 0.5342400074005127 183.32749938964844 0.5919113755226135 218.25106811523438 0.2594960331916809 0.82051367 0.4018457233905792 True -17 51696 31.1804780960083 0.5344552993774414 139.57876586914062 0.5373203158378601 218.51953125 0.2571066915988922 0.8218495 0.3847784698009491 True -18 54568 31.170552015304565 0.518211841583252 156.926513671875 0.44479480385780334 218.425048828125 0.2587736248970032 0.8211024 0.3820585608482361 False -19 57440 31.18607211112976 0.5245492458343506 170.85208129882812 0.3943926692008972 218.284912109375 0.258862167596817 0.82127875 0.37990185618400574 False diff --git a/ENCSR550UWM/cherimoya.fold_2.performance.tsv b/ENCSR550UWM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d3f4657ae8d9d1bdec51fd3a209703bc0e2444ea..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -218.51953125 0.5229839086532593 0.2571066915988922 0.06166334077715874 0.821849524974823 0.7736683487892151 0.3847784698009491 \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_3.evaluate.json b/ENCSR550UWM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ff1b469169ca5162d8f04d7b1db7321b1e297f62..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF829DQY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_3.fit.json b/ENCSR550UWM/cherimoya.fold_3.fit.json deleted file mode 100644 index 619de1b7153c37c0abad71913a53558ce2ab4859..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF829DQY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_3.log b/ENCSR550UWM/cherimoya.fold_3.log deleted file mode 100644 index 380667c6227254f7d7ecc058fa62b8b08e8a2100..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 35.0815372467041 3.4681458473205566 160.3437042236328 0.8447116017341614 241.40765380859375 0.14922837913036346 0.7266117 3.931046724319458 True -1 5496 30.476423978805542 0.6113407611846924 160.99822998046875 0.5969408750534058 229.153076171875 0.20844487845897675 0.7803047 0.9998782873153687 True -2 8244 30.524382829666138 0.5461437702178955 174.78802490234375 0.5264175534248352 226.32086181640625 0.21904444694519043 0.7889563 0.5758848190307617 True -3 10992 29.90907859802246 4.597945213317871 206.19569396972656 0.651892900466919 224.83963012695312 0.22453869879245758 0.79169756 0.5614393353462219 True -4 13740 29.865947723388672 0.5718965530395508 145.20016479492188 0.6240891218185425 223.7423095703125 0.23017637431621552 0.7943342 0.5226973295211792 True -5 16488 29.78420877456665 0.5421023368835449 181.30722045898438 0.8176136016845703 223.48037719726562 0.23171564936637878 0.79804754 0.5405920147895813 True -6 19236 29.831554174423218 0.5376787185668945 195.35997009277344 0.572681188583374 223.13189697265625 0.23345667123794556 0.79784423 0.5660443305969238 False -7 21984 29.833362102508545 0.5473294258117676 146.8552703857422 0.883048415184021 222.45555114746094 0.2371458262205124 0.7984025 0.5713276267051697 True -8 24732 29.799436807632446 0.5464684963226318 181.75741577148438 0.4889189302921295 222.1719970703125 0.23885349929332733 0.8000512 0.5946553349494934 True -9 27480 29.80914282798767 0.5433907508850098 166.65733337402344 0.6940525770187378 221.95556640625 0.23983700573444366 0.8003201 0.5889416933059692 True -10 30228 29.837660789489746 0.9283246994018555 151.60540771484375 0.6210827827453613 221.08604431152344 0.2440238744020462 0.8032321 0.5505962371826172 True -11 32976 29.859461784362793 0.5527489185333252 185.93115234375 0.5645738244056702 221.16029357910156 0.24387295544147491 0.8045713 0.5248808860778809 True -12 35724 29.801725387573242 0.5349342823028564 147.62911987304688 0.7236436605453491 220.91078186035156 0.2439027726650238 0.8089392 0.48542913794517517 True -13 38472 29.79904270172119 0.5401275157928467 179.75790405273438 0.2780551016330719 220.5828857421875 0.24613319337368011 0.8157401 0.44362008571624756 True -14 41220 29.779038190841675 1.0176942348480225 179.31826782226562 0.3179525136947632 220.32400512695312 0.24771200120449066 0.8188945 0.4385230541229248 True -15 43968 29.78445863723755 0.5473935604095459 149.75057983398438 0.6028330326080322 220.00645446777344 0.24891142547130585 0.82597035 0.41178977489471436 True -16 46716 29.781851053237915 0.542877197265625 154.15521240234375 0.2767948806285858 219.71075439453125 0.2508656978607178 0.828829 0.39022210240364075 True -17 49464 29.807517051696777 0.5484378337860107 141.2730712890625 0.3312351703643799 219.76780700683594 0.24978308379650116 0.82909787 0.37822824716567993 True -18 52212 29.827253818511963 0.5504052639007568 168.99853515625 0.39634257555007935 219.7638702392578 0.2504177391529083 0.8309306 0.3723828196525574 True -19 54960 29.767682313919067 0.5417940616607666 166.09310913085938 0.3202773928642273 219.6480712890625 0.25135132670402527 0.8288119 0.37721675634384155 False diff --git a/ENCSR550UWM/cherimoya.fold_3.performance.tsv b/ENCSR550UWM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c220c302c79905fa2595a6fafa8325f806cef286..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.7638702392578 0.5265447497367859 0.2504177689552307 0.06035255640745163 0.8309305906295776 0.7713311314582825 0.3723828196525574 \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_4.evaluate.json b/ENCSR550UWM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 73d99305f3ecd0e712c7ad5373fe7ec225cdec2c..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF829DQY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_4.fit.json b/ENCSR550UWM/cherimoya.fold_4.fit.json deleted file mode 100644 index 18d70c13219c05134198130ee992e09886a37285..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF829DQY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_4.log b/ENCSR550UWM/cherimoya.fold_4.log deleted file mode 100644 index 4dcea143f030d553440e4b3aec46a51ca1d6d7a0..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2819 35.13904094696045 3.8332953453063965 185.7559814453125 0.573194146156311 226.45005798339844 0.14753741025924683 0.72364885 2.7677197456359863 True -1 5638 31.242531538009644 0.6781220436096191 165.69384765625 0.6847167015075684 215.92288208007812 0.20261012017726898 0.7661011 1.0394662618637085 True -2 8457 31.270735502243042 0.5915946960449219 189.80902099609375 0.7198030948638916 213.5745849609375 0.21359746158123016 0.77338153 0.5090281963348389 True -3 11276 31.164594411849976 1.5172626972198486 159.5797119140625 0.696236789226532 211.53758239746094 0.2210594266653061 0.7791079 0.4931983947753906 True -4 14095 31.246740579605103 1.5663814544677734 162.501953125 0.7045926451683044 210.63597106933594 0.22466495633125305 0.7788021 0.5087109208106995 False -5 16914 30.74678897857666 0.5874216556549072 153.62939453125 0.604546844959259 210.3413543701172 0.2255527377128601 0.7796016 0.5167539119720459 True -6 19733 30.546688556671143 14.808748722076416 203.8770751953125 0.7475895285606384 209.5458526611328 0.2296423614025116 0.7837099 0.4985641539096832 True -7 22552 30.613129138946533 0.5926854610443115 128.7015380859375 0.3125956058502197 209.0884246826172 0.23210763931274414 0.7864815 0.4856151044368744 True -8 25371 30.560811758041382 0.5856373310089111 125.38435363769531 0.5918996334075928 208.70301818847656 0.2341686338186264 0.7845815 0.4900720715522766 False -9 28190 30.55593967437744 0.6004934310913086 182.06954956054688 0.5252044200897217 208.54776000976562 0.23449629545211792 0.7864503 0.48059654235839844 False -10 31009 30.594237565994263 0.6014819145202637 136.99436950683594 0.37929272651672363 208.26841735839844 0.23618200421333313 0.7905977 0.4624636769294739 True -11 33828 30.686716079711914 1.021592378616333 190.65603637695312 0.4274270534515381 207.6683349609375 0.23945391178131104 0.79394686 0.46440622210502625 True -12 36647 30.557384490966797 1.2253155708312988 166.7265167236328 0.6013873219490051 207.5436553955078 0.23986975848674774 0.7985833 0.42327880859375 True -13 39466 30.533390760421753 0.59670090675354 153.46278381347656 0.5835111141204834 207.2914581298828 0.24044889211654663 0.80536425 0.41762396693229675 True -14 42285 30.51063060760498 0.6053385734558105 183.17376708984375 0.5192939043045044 206.98428344726562 0.24241578578948975 0.8087963 0.3985501825809479 True -15 45104 30.525573015213013 0.6094303131103516 193.6888427734375 0.3770119845867157 206.57659912109375 0.24431222677230835 0.81546944 0.3817408084869385 True -16 47923 30.551417589187622 0.6084959506988525 191.29672241210938 0.2609569728374481 206.49978637695312 0.2453635036945343 0.81907797 0.36534303426742554 True -17 50742 30.70398235321045 0.5994281768798828 159.4173583984375 0.39927244186401367 206.6683807373047 0.24429090321063995 0.82019025 0.35384976863861084 True -18 53561 30.69869041442871 1.0323784351348877 181.66107177734375 0.2570072412490845 206.88429260253906 0.2431410402059555 0.8200353 0.35063156485557556 False -19 56380 30.676053285598755 0.6225831508636475 189.9359130859375 0.3080635666847229 206.77613830566406 0.24431006610393524 0.81899667 0.34952405095100403 False diff --git a/ENCSR550UWM/cherimoya.fold_4.performance.tsv b/ENCSR550UWM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1f9c6c9702999bb398682d87ee3d9074342d9d8a..0000000000000000000000000000000000000000 --- a/ENCSR550UWM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -206.6683807373047 0.531912624835968 0.24429088830947876 0.05944367125630379 0.8201902508735657 0.7572583556175232 0.35384976863861084 \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_0.evaluate.json b/ENCSR552QUA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c1bd0a31a468aa22d0332639afcfa7cfa782d4e9..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF214AAW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_0.fit.json b/ENCSR552QUA/cherimoya.fold_0.fit.json deleted file mode 100644 index 1774e3fa370eb2898daad4e1d4e57d69e873868e..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF214AAW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_0.log b/ENCSR552QUA/cherimoya.fold_0.log deleted file mode 100644 index cb914bc9f0a893f68d6e4e5f504a7f3b13a78c72..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3343 41.331109046936035 4.832126140594482 631.557861328125 0.31624189019203186 838.784912109375 0.7273296117782593 0.64523673 3.069894552230835 True -1 6686 36.27658033370972 0.8946897983551025 616.9300537109375 0.4267807602882385 721.3967895507812 0.7989086508750916 0.71447945 0.7016899585723877 True -2 10029 36.96533441543579 0.7324519157409668 683.087646484375 0.3552922010421753 707.3344116210938 0.806800365447998 0.7293033 0.3687538802623749 True -3 13372 36.932207345962524 0.685737133026123 591.9957275390625 0.3374458849430084 701.4417724609375 0.8099048137664795 0.7328069 0.38238683342933655 True -4 16715 37.544835567474365 0.6878080368041992 583.3258056640625 0.41597795486450195 699.77392578125 0.8109422326087952 0.7357978 0.33468323945999146 True -5 20058 36.99670124053955 0.6957354545593262 572.0323486328125 0.2819739580154419 696.954833984375 0.8133977651596069 0.7362427 0.32040515542030334 True -6 23401 36.955387592315674 0.6884403228759766 680.59521484375 0.3845294713973999 694.9561157226562 0.8148771524429321 0.729714 0.3093855381011963 False -7 26744 36.94647550582886 0.6920862197875977 582.7401123046875 0.4039863646030426 691.262451171875 0.8173045516014099 0.7372984 0.2976396977901459 True -8 30087 36.93842625617981 0.6912930011749268 627.9044799804688 0.3132007122039795 689.3123779296875 0.8191843628883362 0.7460867 0.29629984498023987 True -9 33430 36.85144877433777 1.0287106037139893 644.244140625 0.3306199312210083 686.8965454101562 0.8207684755325317 0.74962604 0.28832244873046875 True -10 36773 36.961599588394165 0.6929523944854736 593.531982421875 0.20174658298492432 684.7330322265625 0.8225224018096924 0.7498954 0.2839449942111969 True -11 40116 37.021286964416504 0.7112445831298828 641.7940673828125 0.2944999933242798 682.2759399414062 0.8241587281227112 0.76172286 0.27516791224479675 True -12 43459 36.936039209365845 0.6974308490753174 565.8702392578125 0.32159751653671265 679.8318481445312 0.8258302807807922 0.76910824 0.26780784130096436 True -13 46802 36.862287521362305 25.112130403518677 537.8844604492188 0.32128721475601196 677.8850708007812 0.8277523517608643 0.77774364 0.26067426800727844 True -14 50145 36.99845767021179 1.8250043392181396 632.2273559570312 0.24719354510307312 675.6744384765625 0.8297164440155029 0.7875688 0.25106188654899597 True -15 53488 36.91078519821167 0.678565502166748 639.7552490234375 0.29360827803611755 674.6417846679688 0.8306014537811279 0.794777 0.2464084029197693 True -16 56831 36.84201169013977 0.6756815910339355 601.5072631835938 0.2573000192642212 674.313232421875 0.831157386302948 0.7963445 0.24422958493232727 True -17 60174 36.81249785423279 0.6727859973907471 526.3239135742188 0.1672387421131134 674.5123901367188 0.8310882449150085 0.79549885 0.24537795782089233 False -18 63517 36.4470751285553 1.5838961601257324 609.1041259765625 0.1809738278388977 674.92041015625 0.83087158203125 0.7953657 0.24710947275161743 False -19 66860 36.16930079460144 0.6772170066833496 580.8350219726562 0.1619454026222229 675.1148681640625 0.8306805491447449 0.79314375 0.24931423366069794 False diff --git a/ENCSR552QUA/cherimoya.fold_0.performance.tsv b/ENCSR552QUA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8bcc31132c2a8c65acb52aa5c9395c2df5a61994..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -674.313232421875 0.1411319077014923 0.831157386302948 0.4777047038078308 0.796344518661499 0.731016993522644 0.24422958493232727 \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_1.evaluate.json b/ENCSR552QUA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4e1bf938563061b1848daf21bdef72a97e3b1cf7..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF214AAW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_1.fit.json b/ENCSR552QUA/cherimoya.fold_1.fit.json deleted file mode 100644 index 4af257fcee7da24669ee60e9afcaff821ac6cc3d..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF214AAW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_1.log b/ENCSR552QUA/cherimoya.fold_1.log deleted file mode 100644 index b7b877c189baa14c9a5ec2f9342213d62171810e..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3296 41.35463857650757 4.353759527206421 570.1617431640625 0.4476976692676544 938.3569946289062 0.7312977910041809 0.67106354 3.7527012825012207 True -1 6592 36.385777950286865 3.3890583515167236 620.5654296875 0.2855064570903778 795.0477294921875 0.8073787689208984 0.737256 1.1220176219940186 True -2 9888 36.419374227523804 1.5100581645965576 673.8650512695312 0.34410858154296875 779.0801391601562 0.8149695992469788 0.7425803 0.5623669028282166 True -3 13184 36.47499346733093 0.8939666748046875 658.58056640625 0.4020633101463318 772.4907836914062 0.8175216317176819 0.7515756 0.4488188922405243 True -4 16480 36.583945512771606 0.8872251510620117 653.640380859375 0.3349742889404297 768.3073120117188 0.8199784159660339 0.7550993 0.4279000461101532 True -5 19776 36.52294850349426 0.8918097019195557 587.0880126953125 0.30287763476371765 765.4335327148438 0.8218006491661072 0.7513742 0.3795104920864105 False -6 23072 36.3768413066864 0.9156930446624756 623.5464477539062 0.39951449632644653 761.6896362304688 0.8238801956176758 0.7556576 0.3955521881580353 True -7 26368 36.364086389541626 0.9108610153198242 573.466796875 0.3262157440185547 757.6109619140625 0.8266436457633972 0.76585776 0.36856508255004883 True -8 29664 36.42555284500122 0.8794138431549072 603.9426879882812 0.22825126349925995 754.38720703125 0.8284837603569031 0.7693169 0.3481091856956482 True -9 32960 36.55120325088501 0.8922619819641113 647.5776977539062 0.2968769669532776 750.5447387695312 0.8307677507400513 0.7792784 0.3298168480396271 True -10 36256 36.61461639404297 10.58483099937439 661.5294799804688 0.295829713344574 747.2750854492188 0.8325564861297607 0.78610826 0.3082497715950012 True -11 39552 36.548218727111816 0.9070937633514404 558.898193359375 0.3621387779712677 744.8777465820312 0.8342445492744446 0.79356354 0.3022565245628357 True -12 42848 36.555925607681274 2.325063943862915 568.1419677734375 0.23898789286613464 741.6572875976562 0.8363858461380005 0.80254793 0.2875574827194214 True -13 46144 36.486759185791016 0.8793892860412598 513.012939453125 0.204693004488945 738.8931274414062 0.8384974598884583 0.8096063 0.2865159213542938 True -14 49440 36.407092809677124 0.874866247177124 528.0443115234375 0.17305225133895874 735.9449462890625 0.840192973613739 0.8169646 0.26966696977615356 True -15 52736 35.90180945396423 0.889937162399292 550.90869140625 0.20979878306388855 734.4066162109375 0.8414063453674316 0.822944 0.25938525795936584 True -16 56032 35.765042781829834 0.9086897373199463 505.515869140625 0.1793006956577301 733.8035278320312 0.841923713684082 0.82513434 0.25518906116485596 True -17 59328 35.80021333694458 0.8960185050964355 547.9891357421875 0.15442535281181335 734.0017700195312 0.8418332934379578 0.8273106 0.25130701065063477 True -18 62624 35.66029357910156 0.8719651699066162 575.9869384765625 0.15197394788265228 734.5470581054688 0.8415670394897461 0.8264459 0.2520129382610321 False -19 65920 35.65899467468262 0.8756320476531982 548.591796875 0.20722761750221252 735.1231079101562 0.8413313627243042 0.8257752 0.25448077917099 False diff --git a/ENCSR552QUA/cherimoya.fold_1.performance.tsv b/ENCSR552QUA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8d3ecda8d0abc25e1c38c12a8b9467eedf940ff9..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -734.0017700195312 0.13134171068668365 0.8418332934379578 0.5086120367050171 0.8273106217384338 0.7861670851707458 0.25130701065063477 \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_2.evaluate.json b/ENCSR552QUA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9bd9ec93a47e0862895952e4c9db060472fa22ca..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF214AAW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_2.fit.json b/ENCSR552QUA/cherimoya.fold_2.fit.json deleted file mode 100644 index 26ec02d53044d026be0ccacd8aed3eaceecad7c8..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF214AAW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_2.log b/ENCSR552QUA/cherimoya.fold_2.log deleted file mode 100644 index 1fdce0fa5b822b8f9ff94f9929d3d0d94ceca3a5..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3524 43.38535118103027 3.7368388175964355 634.1325073242188 0.36996573209762573 851.2135009765625 0.738200306892395 0.6524596 3.8776638507843018 True -1 7048 38.77085900306702 0.8082213401794434 625.3741455078125 0.5083857178688049 741.7813720703125 0.8004172444343567 0.74166185 0.9719523191452026 True -2 10572 38.72885751724243 0.6635777950286865 652.1072998046875 0.4579039514064789 730.1807250976562 0.8063687086105347 0.74821544 0.43572989106178284 True -3 14096 38.70851182937622 0.6672108173370361 621.6080322265625 0.4204661250114441 724.6886596679688 0.8095317482948303 0.75190663 0.4674818217754364 True -4 17620 38.82280349731445 1.597221851348877 660.26318359375 0.3565337061882019 721.8577270507812 0.8120785355567932 0.75809807 0.374066025018692 True -5 21144 38.75356459617615 0.6864564418792725 600.656982421875 0.30781811475753784 719.1910400390625 0.8135198354721069 0.75721 0.31467342376708984 False -6 24668 38.7660768032074 0.7943997383117676 593.9007568359375 0.23291374742984772 716.3703002929688 0.8151745200157166 0.75904405 0.3136700689792633 True -7 28192 38.805095195770264 0.6716561317443848 539.5582885742188 0.35731738805770874 713.628662109375 0.8167827129364014 0.75898427 0.2970430850982666 False -8 31716 38.6926383972168 18.715426206588745 603.9881591796875 0.4705863893032074 710.3911743164062 0.8190447092056274 0.76666266 0.28776660561561584 True -9 35240 38.91118359565735 25.786542177200317 592.14208984375 0.28862982988357544 706.8594970703125 0.8214002251625061 0.77707994 0.2840612232685089 True -10 38764 38.81716203689575 0.6783163547515869 651.32373046875 0.33085042238235474 704.7073974609375 0.8230206966400146 0.78158206 0.2774219810962677 True -11 42288 38.006003618240356 0.6609015464782715 654.478515625 0.22934652864933014 701.3800048828125 0.8250522613525391 0.78880984 0.2739446461200714 True -12 45812 37.92722272872925 0.6679511070251465 555.2117919921875 0.21961650252342224 699.583984375 0.8266105055809021 0.7957164 0.26253917813301086 True -13 49336 37.926048040390015 0.6729762554168701 615.4490966796875 0.36332184076309204 697.0267944335938 0.8284422159194946 0.79811776 0.2630223333835602 True -14 52860 38.01586961746216 1.9236564636230469 617.115234375 0.2595375180244446 695.07666015625 0.8301259875297546 0.8036353 0.2588704228401184 True -15 56384 38.028125047683716 0.6928932666778564 574.9407958984375 0.2688853144645691 693.6427612304688 0.8312907218933105 0.80924517 0.251731276512146 True -16 59908 38.09786605834961 0.6685051918029785 670.1290893554688 0.1666329950094223 692.8216552734375 0.8318842053413391 0.8109541 0.2457563877105713 True -17 63432 38.085166692733765 0.6766326427459717 557.55224609375 0.1831803172826767 692.5515747070312 0.8320713043212891 0.8124115 0.24451075494289398 True -18 66956 38.13576078414917 0.671802282333374 601.1551513671875 0.12705421447753906 693.1456298828125 0.831824004650116 0.81335527 0.24432280659675598 True -19 70480 38.01344108581543 0.673560380935669 639.55322265625 0.18412378430366516 693.12109375 0.831597626209259 0.8119533 0.24615544080734253 False diff --git a/ENCSR552QUA/cherimoya.fold_2.performance.tsv b/ENCSR552QUA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d9d126bae40dc1b13d196ac3b5703dcdcb7a862c..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -693.1456298828125 0.13896560668945312 0.831824004650116 0.48897451162338257 0.8133552670478821 0.7541281580924988 0.24432280659675598 \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_3.evaluate.json b/ENCSR552QUA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 62fec5df3f9d1339e02d1e3475a057b63b5330bd..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF214AAW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_3.fit.json b/ENCSR552QUA/cherimoya.fold_3.fit.json deleted file mode 100644 index eac9bb49929b13defaabe76a7419ad7405ec106c..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF214AAW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_3.log b/ENCSR552QUA/cherimoya.fold_3.log deleted file mode 100644 index 8553c277bdabf276a886add1f60b99d5435d74d6..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3394 42.52382183074951 4.201674461364746 669.65087890625 0.4843443036079407 826.56982421875 0.7293602824211121 0.6556562 4.228525161743164 True -1 6788 37.33300471305847 0.6880121231079102 593.9839477539062 0.5504123568534851 718.2550048828125 0.7961869239807129 0.7273851 0.7821418046951294 True -2 10182 37.355889320373535 0.8817431926727295 566.5197143554688 0.33387142419815063 707.3624877929688 0.8017061352729797 0.7332394 0.3657779395580292 True -3 13576 37.34394693374634 0.6754846572875977 634.472900390625 0.37895187735557556 700.2662353515625 0.8062854409217834 0.737613 0.3375440239906311 True -4 16970 37.38281035423279 0.6753413677215576 602.1143798828125 0.3105969727039337 697.9056396484375 0.8076903223991394 0.7391614 0.338855504989624 True -5 20364 37.49689745903015 0.664569616317749 590.1575927734375 0.2733131945133209 694.2555541992188 0.810658872127533 0.7461146 0.3215349316596985 True -6 23758 37.56285762786865 6.731389284133911 649.5587768554688 0.31442299485206604 691.7172241210938 0.812903642654419 0.74671626 0.32527732849121094 True -7 27152 37.15676474571228 0.6768836975097656 620.9695434570312 0.2048550248146057 689.990478515625 0.8143318891525269 0.75114965 0.3195718228816986 True -8 30546 36.78692436218262 0.6516444683074951 651.1790771484375 0.3596421480178833 686.0167236328125 0.8165958523750305 0.75375444 0.3147582411766052 True -9 33940 36.76635193824768 0.6527447700500488 646.8695068359375 0.25605830550193787 684.094970703125 0.8182120323181152 0.7637473 0.309567391872406 True -10 37334 36.78833484649658 0.6557443141937256 606.2882080078125 0.29510200023651123 681.3218383789062 0.8202205300331116 0.76837844 0.31829193234443665 True -11 40728 36.77373170852661 0.6542763710021973 615.6815185546875 0.29811614751815796 678.7005615234375 0.8220831751823425 0.7719277 0.2964995503425598 True -12 44122 36.759042263031006 0.6514661312103271 585.77294921875 0.3216676115989685 676.22216796875 0.8240190148353577 0.7813258 0.28590238094329834 True -13 47516 36.661255836486816 0.6519968509674072 536.2859497070312 0.29358384013175964 673.600341796875 0.8258385062217712 0.78634906 0.27156761288642883 True -14 50910 36.62864685058594 0.6510143280029297 655.740966796875 0.22040611505508423 671.8242797851562 0.8272743821144104 0.79317844 0.26340290904045105 True -15 54304 36.62877655029297 0.6421458721160889 566.1776733398438 0.19808422029018402 670.3900756835938 0.8284760117530823 0.7964576 0.2604670226573944 True -16 57698 36.599984645843506 0.6506812572479248 585.027587890625 0.25170761346817017 669.8353271484375 0.8292131423950195 0.80270934 0.256544828414917 True -17 61092 36.668256759643555 0.6508190631866455 620.0490112304688 0.1447353959083557 669.9434204101562 0.8292542695999146 0.8014755 0.253986120223999 False -18 64486 36.64275121688843 1.7320983409881592 614.9693603515625 0.18190857768058777 670.1810913085938 0.829089343547821 0.8014131 0.2566637694835663 False -19 67880 36.58735132217407 0.6504485607147217 599.3394775390625 0.1501329392194748 670.4490966796875 0.8289023041725159 0.7993727 0.2580066919326782 False diff --git a/ENCSR552QUA/cherimoya.fold_3.performance.tsv b/ENCSR552QUA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 94b8140247da7acddddfa870c9705b3319e7fe78..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -669.8353271484375 0.14279302954673767 0.8292130827903748 0.4722238779067993 0.8027093410491943 0.7351518869400024 0.256544828414917 \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_4.evaluate.json b/ENCSR552QUA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b06e6d8e4e773e70d4ca2622600642c23fb1d1aa..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF214AAW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_4.fit.json b/ENCSR552QUA/cherimoya.fold_4.fit.json deleted file mode 100644 index 0fca18e93e721132201e584259a0df8c9c80e27a..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF214AAW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552QUA/cherimoya.fold_4.log b/ENCSR552QUA/cherimoya.fold_4.log deleted file mode 100644 index 1c4061ef878594684eff9b9586d65e7fd1570212..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3433 42.61252999305725 4.362224102020264 576.7265014648438 0.3318859934806824 808.26025390625 0.7308769226074219 0.6175915 3.3585734367370605 True -1 6866 37.734057903289795 0.7087764739990234 588.3822021484375 0.4445755183696747 709.3424072265625 0.7972248792648315 0.6942624 0.7748029828071594 True -2 10299 37.765912771224976 0.7299442291259766 614.373291015625 0.3012353479862213 696.4404296875 0.8043106198310852 0.7102893 0.3595008850097656 True -3 13732 37.740437030792236 0.7388200759887695 554.2685546875 0.4504324793815613 691.4765625 0.8066999912261963 0.71180224 0.3409753143787384 True -4 17165 37.881919384002686 0.6806113719940186 715.5509643554688 0.3198237419128418 688.9009399414062 0.808374285697937 0.7192927 0.31168681383132935 True -5 20598 37.16234588623047 0.6921672821044922 657.416015625 0.4579899311065674 686.5597534179688 0.8097642660140991 0.72376406 0.296964555978775 True -6 24031 37.11490058898926 0.6761093139648438 588.8709106445312 0.3592131733894348 682.9884033203125 0.8128340244293213 0.72836745 0.301133930683136 True -7 27464 36.96594786643982 0.6729769706726074 650.3567504882812 0.3227574825286865 680.9149169921875 0.8142560124397278 0.7331997 0.2899210453033447 True -8 30897 36.96593427658081 0.7722768783569336 575.7073974609375 0.23469121754169464 678.5709838867188 0.8161386251449585 0.7364643 0.2857246696949005 True -9 34330 37.06623029708862 0.7056429386138916 592.7291259765625 0.24457576870918274 676.1994018554688 0.818035900592804 0.7425092 0.2845073938369751 True -10 37763 37.08772373199463 2.478597640991211 508.325439453125 0.20824700593948364 674.0308837890625 0.8200494647026062 0.75107837 0.28180140256881714 True -11 41196 36.991241455078125 0.6848568916320801 611.7367553710938 0.24499821662902832 671.5027465820312 0.8213866353034973 0.7584859 0.26903194189071655 True -12 44629 37.01511287689209 0.6831648349761963 623.7608642578125 0.3398251235485077 669.69580078125 0.8230654001235962 0.76490945 0.2657349109649658 True -13 48062 37.05604577064514 1.0769827365875244 597.0538330078125 0.24339959025382996 667.167724609375 0.8250848054885864 0.7766154 0.25719964504241943 True -14 51495 37.05254912376404 0.67020583152771 587.764404296875 0.25301286578178406 665.68701171875 0.8266646265983582 0.78234196 0.2509159445762634 True -15 54928 37.068244218826294 13.127068281173706 544.9564208984375 0.1468421369791031 664.2000122070312 0.8279510736465454 0.7871473 0.24548956751823425 True -16 58361 37.00870108604431 0.6819977760314941 528.3179931640625 0.1895555704832077 663.7098999023438 0.8283866047859192 0.7933028 0.2408430427312851 True -17 61794 37.06122064590454 0.6822874546051025 544.4540405273438 0.1694379597902298 663.5681762695312 0.8284652233123779 0.7949464 0.2402462363243103 True -18 65227 37.02442169189453 0.6700623035430908 533.3087768554688 0.2356749176979065 663.9642944335938 0.8282204866409302 0.7940711 0.2408556342124939 False -19 68660 37.05501079559326 0.6799755096435547 555.994140625 0.1765443980693817 664.2694702148438 0.8280360102653503 0.7936218 0.24236764013767242 False diff --git a/ENCSR552QUA/cherimoya.fold_4.performance.tsv b/ENCSR552QUA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c53dcfff38d9758f08ff5f396a18007af1468740..0000000000000000000000000000000000000000 --- a/ENCSR552QUA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -663.5681762695312 0.14311592280864716 0.8284652233123779 0.47366857528686523 0.7949463725090027 0.7259802222251892 0.2402462363243103 \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_0.evaluate.json b/ENCSR552RKI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index eed3ed08ab2259905ed02036e861f14e723903d5..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF260RYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_0.fit.json b/ENCSR552RKI/cherimoya.fold_0.fit.json deleted file mode 100644 index 3ebe4cf6eee1b44035b1d0d7b63824dec350dd3c..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF260RYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_0.log b/ENCSR552RKI/cherimoya.fold_0.log deleted file mode 100644 index f0f60cccbc2f7cf0c2ad5777ecf6dc1046c5ac35..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.888001918792725 4.30383038520813 687.7509765625 0.16723419725894928 868.1805419921875 0.24098901450634003 0.70247716 5.531427383422852 True -1 5454 30.271082878112793 0.5785627365112305 722.966552734375 0.38607925176620483 804.0471801757812 0.3082810938358307 0.7532413 1.394771933555603 True -2 8181 30.32468342781067 2.222673177719116 747.77001953125 0.32843291759490967 789.86572265625 0.3207152485847473 0.7635056 0.9447045922279358 True -3 10908 30.338239669799805 2.16306734085083 625.4979248046875 0.3906646966934204 780.0444946289062 0.33149614930152893 0.7905004 0.7817867398262024 True -4 13635 30.513975858688354 27.929538249969482 750.0052490234375 0.19662213325500488 777.3392944335938 0.3344985842704773 0.79411525 0.7128793001174927 True -5 16362 30.361233472824097 0.807154655456543 621.3743896484375 0.31443363428115845 774.4298095703125 0.3372458517551422 0.80209196 0.5975251793861389 True -6 19089 30.271335124969482 0.5617103576660156 632.3111572265625 0.27303940057754517 772.5648803710938 0.33996281027793884 0.802632 0.5631539821624756 True -7 21816 30.28804326057434 0.5653269290924072 628.636474609375 0.2348743975162506 770.4354248046875 0.3421354591846466 0.8091156 0.5070791840553284 True -8 24543 30.309876203536987 1.1817386150360107 661.119140625 0.49945318698883057 769.4556274414062 0.3428098261356354 0.8133136 0.47176796197891235 True -9 27270 30.29058313369751 0.5537521839141846 691.9889526367188 0.24546808004379272 765.7451171875 0.34732726216316223 0.81835544 0.4571983814239502 True -10 29997 30.32216453552246 21.028234004974365 626.1927490234375 0.28218352794647217 765.1104736328125 0.34803271293640137 0.821832 0.42120811343193054 True -11 32724 30.240741729736328 0.5560088157653809 621.2091064453125 0.24932189285755157 763.2071533203125 0.34931260347366333 0.82859486 0.3661753535270691 True -12 35451 30.2604238986969 0.5632009506225586 671.4039916992188 0.3408394455909729 760.0217895507812 0.35336214303970337 0.83324564 0.3195239305496216 True -13 38178 30.570526838302612 0.5577683448791504 666.3902587890625 0.30941909551620483 759.4608764648438 0.35404303669929504 0.8384188 0.2965736985206604 True -14 40905 30.28645086288452 0.5636036396026611 544.1299438476562 0.24813000857830048 758.7122802734375 0.3549034297466278 0.8465942 0.26662713289260864 True -15 43632 30.25792145729065 0.5609278678894043 662.1956787109375 0.14282840490341187 757.0678100585938 0.35616669058799744 0.8493565 0.24399395287036896 True -16 46359 30.27860140800476 2.5906407833099365 636.4073486328125 0.19860407710075378 757.004638671875 0.3562716245651245 0.85274166 0.23053964972496033 True -17 49086 30.287334203720093 0.5600738525390625 640.796630859375 0.21797770261764526 756.2219848632812 0.357032835483551 0.85387605 0.22193361818790436 True -18 51813 30.22957944869995 0.5586585998535156 705.2879638671875 0.1587998867034912 756.8016357421875 0.3566865026950836 0.85413325 0.21741747856140137 True -19 54540 30.330448865890503 0.5642430782318115 760.7071533203125 0.1800396740436554 757.3494262695312 0.35643142461776733 0.85309684 0.21753542125225067 False diff --git a/ENCSR552RKI/cherimoya.fold_0.performance.tsv b/ENCSR552RKI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7c0205f82d57b32c1f9286413b1802c53ac0d199..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -756.8016357421875 0.396427720785141 0.3566865026950836 0.14777909219264984 0.8541332483291626 0.8158775568008423 0.21741747856140137 \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_1.evaluate.json b/ENCSR552RKI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a5eb2cdc002ac50f420b6ac1a3323054d427d294..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF260RYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_1.fit.json b/ENCSR552RKI/cherimoya.fold_1.fit.json deleted file mode 100644 index d34c5300b6fa42eb67592634a752efb47d8592f6..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF260RYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_1.log b/ENCSR552RKI/cherimoya.fold_1.log deleted file mode 100644 index 0e2c1e357c4ea159310c50529176dd8c5307c1df..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2719 33.735029220581055 3.6418676376342773 667.0436401367188 0.41164785623550415 983.0667724609375 0.24796250462532043 0.7167013 6.997073650360107 True -1 5438 29.912940740585327 0.7079870700836182 729.2721557617188 0.5863887667655945 903.49072265625 0.32468101382255554 0.7816097 1.6394059658050537 True -2 8157 29.884480237960815 0.7086765766143799 603.1221923828125 0.30095309019088745 882.5455322265625 0.3441266119480133 0.80844665 0.6704784035682678 True -3 10876 29.902727842330933 0.7053630352020264 593.0677490234375 0.2651762366294861 876.5120849609375 0.34779199957847595 0.8178475 0.5702701807022095 True -4 13595 30.14023518562317 0.6983227729797363 623.81494140625 0.30866679549217224 871.9465942382812 0.3525296151638031 0.82320416 0.5839992165565491 True -5 16314 29.89574646949768 0.7011713981628418 681.5480346679688 0.3069070875644684 868.1221923828125 0.356954962015152 0.8291616 0.5236595273017883 True -6 19033 29.859259128570557 0.706078290939331 619.0625 0.2955358922481537 866.2539672851562 0.3592720925807953 0.83186865 0.4579559862613678 True -7 21752 29.88436985015869 0.7009665966033936 682.5931396484375 0.4108281135559082 864.3726196289062 0.36038652062416077 0.8392837 0.4419185519218445 True -8 24471 29.881659984588623 1.5569632053375244 685.4609985351562 0.32629042863845825 862.1066284179688 0.3625432848930359 0.84311223 0.40217551589012146 True -9 27190 29.909827947616577 1.3740153312683105 621.6630859375 0.2319892942905426 860.7213134765625 0.363899290561676 0.84613866 0.3773953318595886 True -10 29909 29.96824049949646 2.15923810005188 659.257080078125 0.16957378387451172 858.1074829101562 0.36630892753601074 0.8525501 0.3451257348060608 True -11 32628 29.940492391586304 0.7020649909973145 720.730712890625 0.30724790692329407 855.3556518554688 0.3692607879638672 0.85633785 0.3256968855857849 True -12 35347 29.916845321655273 0.6964411735534668 610.267822265625 0.33328187465667725 852.3768920898438 0.37183713912963867 0.8624787 0.301270067691803 True -13 38066 29.89309787750244 0.6946461200714111 800.907470703125 0.3876025080680847 850.9468994140625 0.3726930320262909 0.8656032 0.2708287835121155 True -14 40785 29.9268159866333 0.7024824619293213 640.863525390625 0.3078961968421936 848.886474609375 0.37473902106285095 0.86921114 0.25801822543144226 True -15 43504 29.918709993362427 0.7144250869750977 572.10400390625 0.2763013243675232 848.743896484375 0.37395402789115906 0.87384367 0.2375582754611969 True -16 46223 29.94026470184326 0.7159671783447266 548.0001831054688 0.17697525024414062 848.61376953125 0.37411442399024963 0.87434316 0.22271041572093964 True -17 48942 29.717007398605347 0.7070419788360596 664.7579956054688 0.16941657662391663 848.2662353515625 0.3759121894836426 0.875976 0.21583127975463867 True -18 51661 29.337925672531128 0.6922392845153809 574.8563232421875 0.2478400319814682 847.5440063476562 0.3761536777019501 0.87483597 0.21389321982860565 False -19 54380 29.321083068847656 1.0994288921356201 593.8153076171875 0.15897917747497559 848.3252563476562 0.3747541308403015 0.87359554 0.21193361282348633 False diff --git a/ENCSR552RKI/cherimoya.fold_1.performance.tsv b/ENCSR552RKI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c96dbd79e0cf6700e53ab76aafba25e07b1d82c4..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -848.2662353515625 0.3780015707015991 0.3759121894836426 0.16838710010051727 0.875976026058197 0.8518220782279968 0.21583127975463867 \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_2.evaluate.json b/ENCSR552RKI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b0a2ec5c692c7fa9e7068151253cec2037a72325..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF260RYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_2.fit.json b/ENCSR552RKI/cherimoya.fold_2.fit.json deleted file mode 100644 index 78a9b432c84a0c0ff8b2adbff07335890c4ed6e4..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF260RYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_2.log b/ENCSR552RKI/cherimoya.fold_2.log deleted file mode 100644 index 5667f9401de7953471789c5dc606f3be2c0519ad..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 35.38744282722473 3.2443737983703613 694.4537963867188 0.38337552547454834 908.9461059570312 0.24534589052200317 0.69217056 5.853374004364014 True -1 5744 31.703652143478394 0.565239429473877 602.9500732421875 0.4181603491306305 833.2442626953125 0.3210565745830536 0.7651146 1.605109691619873 True -2 8616 31.707971811294556 0.5169551372528076 615.9382934570312 0.35625746846199036 819.168212890625 0.33273518085479736 0.7862765 0.7689815163612366 True -3 11488 31.719994068145752 3.866300106048584 618.3551025390625 0.39822936058044434 813.6309204101562 0.33841538429260254 0.7982277 0.5697768926620483 True -4 14360 31.77961564064026 0.522801399230957 588.46630859375 0.35737520456314087 810.41552734375 0.3423466980457306 0.80281675 0.6399086713790894 True -5 17232 31.629545211791992 0.5179615020751953 660.8924560546875 0.27657389640808105 807.8779296875 0.34470516443252563 0.8073565 0.48254266381263733 True -6 20104 34.00329899787903 12.529919147491455 617.8112182617188 0.39468371868133545 806.4020385742188 0.3477221131324768 0.811481 0.4942062199115753 True -7 22976 31.762796640396118 0.5193631649017334 589.1053466796875 0.3197280168533325 805.7713623046875 0.34774893522262573 0.8147037 0.45414021611213684 True -8 25848 31.65009331703186 0.5226473808288574 610.2022705078125 0.2756722867488861 803.369873046875 0.3502252697944641 0.81714684 0.41593122482299805 True -9 28720 31.667356729507446 0.545621395111084 672.9017333984375 0.3214268982410431 802.9669799804688 0.35024115443229675 0.82221836 0.3876100182533264 True -10 31592 31.642157554626465 0.5232584476470947 729.2276611328125 0.27159762382507324 800.323974609375 0.35295337438583374 0.82720506 0.3626582622528076 True -11 34464 31.607600212097168 0.519895076751709 662.3671875 0.14263634383678436 797.8446044921875 0.3544130027294159 0.83441633 0.3304207921028137 True -12 37336 31.628989934921265 0.5200095176696777 636.8555297851562 0.19902129471302032 795.536865234375 0.3578568994998932 0.8386289 0.31221917271614075 True -13 40208 31.575955152511597 0.5144307613372803 539.5567626953125 0.2655991017818451 794.4618530273438 0.35938072204589844 0.8424913 0.28960758447647095 True -14 43080 31.550138235092163 0.5170187950134277 724.375732421875 0.17736169695854187 793.5479125976562 0.35950303077697754 0.8481073 0.26893720030784607 True -15 45952 31.60021710395813 0.5225265026092529 727.8377685546875 0.253510057926178 792.1605224609375 0.3611360788345337 0.8492375 0.2518215477466583 True -16 48824 31.31502413749695 0.9252688884735107 591.552978515625 0.19058331847190857 790.4310302734375 0.3633563220500946 0.8517061 0.23827476799488068 True -17 51696 30.91713833808899 0.4938991069793701 615.046875 0.2331480234861374 791.9957275390625 0.3614408075809479 0.85510063 0.23123197257518768 True -18 54568 30.98352074623108 0.5006606578826904 636.9625244140625 0.1621318906545639 791.1845092773438 0.3626580834388733 0.8545045 0.22863872349262238 False -19 57440 30.922658443450928 0.5004441738128662 796.116455078125 0.21277830004692078 791.0072021484375 0.3624976575374603 0.85274065 0.22925536334514618 False diff --git a/ENCSR552RKI/cherimoya.fold_2.performance.tsv b/ENCSR552RKI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0a4cd7d34e5525f17ebb32a52e33ac8b5337785e..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -791.9957275390625 0.3905046880245209 0.3614408075809479 0.15514269471168518 0.8551006317138672 0.8225218057632446 0.23123197257518768 \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_3.evaluate.json b/ENCSR552RKI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bd8d30321ba1f6cb2113c99565bd3e14acbaeae8..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF260RYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_3.fit.json b/ENCSR552RKI/cherimoya.fold_3.fit.json deleted file mode 100644 index 6dc5ef49a996f8ad040e1113b55ffe7e8afbe7f2..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF260RYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_3.log b/ENCSR552RKI/cherimoya.fold_3.log deleted file mode 100644 index 6e56242becef34a4bc03d5fc83a7956adc96a9c8..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 33.77470016479492 3.5086042881011963 720.9031982421875 0.5592353940010071 857.0010986328125 0.24582943320274353 0.6881231 6.567124843597412 True -1 5518 30.37456750869751 0.5770595073699951 684.9799194335938 0.45151787996292114 790.5617065429688 0.3135417699813843 0.7559283 1.5987850427627563 True -2 8277 30.579464197158813 0.576500415802002 775.09033203125 0.2958458364009857 777.7361450195312 0.3256610631942749 0.77562577 0.888595461845398 True -3 11036 30.358042001724243 0.5624675750732422 659.662841796875 0.37304389476776123 771.5204467773438 0.3319217264652252 0.7817813 0.6572797298431396 True -4 13795 30.303788661956787 0.5607771873474121 702.5426025390625 0.38348403573036194 768.996826171875 0.33470943570137024 0.78699344 0.6063808798789978 True -5 16554 30.342049598693848 0.5746452808380127 644.4351806640625 0.33595460653305054 766.0721435546875 0.33821746706962585 0.7916676 0.6924340724945068 True -6 19313 30.39574408531189 2.0903658866882324 658.0084228515625 0.3353654742240906 765.9258422851562 0.3381485641002655 0.7946913 0.6712148189544678 True -7 22072 30.364535808563232 0.5695478916168213 636.2678833007812 0.3677392303943634 762.7886962890625 0.34323930740356445 0.79684323 0.5555034279823303 True -8 24831 30.394010305404663 0.5633330345153809 723.5138549804688 0.2893798351287842 760.7166748046875 0.34511566162109375 0.8049108 0.5324458479881287 True -9 27590 30.379751205444336 0.5570523738861084 746.37841796875 0.3750396966934204 759.3086547851562 0.34590867161750793 0.81235576 0.4740946590900421 True -10 30349 30.410545587539673 0.5574653148651123 614.0472412109375 0.3452926278114319 757.070556640625 0.3486165404319763 0.81836295 0.4461892247200012 True -11 33108 30.390233278274536 0.8180642127990723 669.404052734375 0.2967437207698822 755.61376953125 0.3488938510417938 0.8247134 0.4181324243545532 True -12 35867 30.38182783126831 0.5734009742736816 651.0486450195312 0.24431219696998596 753.0602416992188 0.3527393937110901 0.8301428 0.36867886781692505 True -13 38626 30.410959243774414 0.5715758800506592 658.7972412109375 0.2611401677131653 752.5283813476562 0.3522637188434601 0.83892894 0.3301532566547394 True -14 41385 30.361058950424194 0.5613596439361572 688.8858642578125 0.2313811480998993 750.2001342773438 0.35518452525138855 0.8467073 0.2912808656692505 True -15 44144 30.300453901290894 0.5603358745574951 705.8936767578125 0.24274998903274536 748.8917236328125 0.35637545585632324 0.8509266 0.2611490488052368 True -16 46903 30.24708580970764 0.5616481304168701 674.32763671875 0.1766228973865509 748.4451293945312 0.35677632689476013 0.8544016 0.24466562271118164 True -17 49662 29.74540901184082 0.5656054019927979 705.6040649414062 0.1696965992450714 748.834716796875 0.356628954410553 0.8561633 0.2293647825717926 True -18 52421 29.80761170387268 0.8729240894317627 716.9410400390625 0.1993032544851303 747.8449096679688 0.357480525970459 0.8577877 0.2244250327348709 True -19 55180 29.812637090682983 0.561002254486084 551.5919189453125 0.18003825843334198 748.6541748046875 0.35628798604011536 0.85759574 0.2245069146156311 False diff --git a/ENCSR552RKI/cherimoya.fold_3.performance.tsv b/ENCSR552RKI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c05880f2538ea85318db826cd5b196b4fd43d7d7..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -747.8449096679688 0.39550867676734924 0.357480525970459 0.14898768067359924 0.8577877283096313 0.8207379579544067 0.2244250327348709 \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_4.evaluate.json b/ENCSR552RKI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 623374a028a7d4774fb122e879541cc30f2ddbeb..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF260RYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_4.fit.json b/ENCSR552RKI/cherimoya.fold_4.fit.json deleted file mode 100644 index f94d21e5de6fda245885644120e3b6dcb2d7094e..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF260RYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552RKI/cherimoya.fold_4.log b/ENCSR552RKI/cherimoya.fold_4.log deleted file mode 100644 index dc3b0c940d9c4b01cf98ad85c53fc93e5b137828..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2826 35.02067685127258 6.614187955856323 716.122314453125 0.31400346755981445 829.2393798828125 0.23993408679962158 0.68777907 5.182738304138184 True -1 5652 31.070149660110474 0.5766499042510986 716.215087890625 0.36213451623916626 770.3935546875 0.30222851037979126 0.7530614 1.2746771574020386 True -2 8478 31.082364797592163 0.5622866153717041 630.2347412109375 0.30023738741874695 756.770263671875 0.3144959509372711 0.7785484 0.6790834069252014 True -3 11304 31.059420824050903 2.4323956966400146 614.9769287109375 0.3588188886642456 750.1884765625 0.32172542810440063 0.7899634 0.6602063179016113 True -4 14130 31.063690423965454 0.5700743198394775 555.6737670898438 0.323384165763855 750.4390869140625 0.3217605650424957 0.7870225 0.544231116771698 False -5 16956 31.091802835464478 0.5685698986053467 606.6370239257812 0.3483904302120209 749.0319213867188 0.3230189383029938 0.7921337 0.5268995761871338 True -6 19782 31.066511392593384 0.5604748725891113 572.41943359375 0.3663507103919983 745.641845703125 0.32713934779167175 0.80446935 0.4019608199596405 True -7 22608 31.07790470123291 0.5673081874847412 675.302490234375 0.3014366328716278 743.8236083984375 0.3296931982040405 0.8100603 0.37973469495773315 True -8 25434 31.030628204345703 0.5609898567199707 608.357421875 0.2159447968006134 742.038330078125 0.3311603367328644 0.812478 0.38168495893478394 True -9 28260 31.061630487442017 0.5512678623199463 654.029052734375 0.24624142050743103 739.932861328125 0.33381718397140503 0.8163844 0.3545629680156708 True -10 31086 31.042164087295532 1.6791341304779053 637.6806030273438 0.20499175786972046 736.3015747070312 0.3387007713317871 0.82453585 0.3353254795074463 True -11 33912 31.057206630706787 0.5608634948730469 607.479736328125 0.23143038153648376 736.3302612304688 0.33860722184181213 0.8286114 0.3136861026287079 True -12 36738 31.070055961608887 0.562319278717041 546.0608520507812 0.34946057200431824 734.43798828125 0.34052979946136475 0.8354306 0.2812003493309021 True -13 39564 31.140291929244995 0.57041335105896 678.1212158203125 0.19873102009296417 733.333740234375 0.3415946066379547 0.8393096 0.26772746443748474 True -14 42390 31.10150146484375 0.5663230419158936 618.750732421875 0.19629137217998505 732.2020263671875 0.34222978353500366 0.8457596 0.24310456216335297 True -15 45216 30.931891441345215 0.5631239414215088 617.8538818359375 0.17610028386116028 732.1281127929688 0.34272539615631104 0.84931695 0.22521427273750305 True -16 48042 30.4976065158844 0.5598385334014893 697.9092407226562 0.2926064729690552 730.6754760742188 0.34466254711151123 0.85136515 0.2155562937259674 True -17 50868 30.629262447357178 0.55458664894104 637.671875 0.16181379556655884 730.481201171875 0.3450463116168976 0.85192466 0.20955681800842285 True -18 53694 30.72894048690796 2.6223230361938477 631.370849609375 0.1803608238697052 731.6969604492188 0.3435138165950775 0.85262984 0.2077183723449707 True -19 56520 30.650443077087402 0.5749831199645996 575.4677734375 0.1285705268383026 731.9034423828125 0.34308409690856934 0.8535707 0.2071499228477478 True diff --git a/ENCSR552RKI/cherimoya.fold_4.performance.tsv b/ENCSR552RKI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c8c4eabd609d8b76770220e2dfb45ae6a53f18a9..0000000000000000000000000000000000000000 --- a/ENCSR552RKI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -731.9034423828125 0.40435272455215454 0.3430841267108917 0.14220687747001648 0.8535706996917725 0.8091489672660828 0.2071499228477478 \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_0.evaluate.json b/ENCSR552TPH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ef3a5dd0dc2a65ce16627890503f25e5efa628e6..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498SGM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_0.fit.json b/ENCSR552TPH/cherimoya.fold_0.fit.json deleted file mode 100644 index b6cc1b394920e9829d4e61091c1fe79971df0b09..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF498SGM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_0.log b/ENCSR552TPH/cherimoya.fold_0.log deleted file mode 100644 index 4538cb13d66af3d94608832bfeb62e6e18a0f46d..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 34.94050741195679 3.7974891662597656 219.45962524414062 0.5977387428283691 354.1337890625 0.1596752107143402 0.66251034 4.808462142944336 True -1 5506 30.19449806213379 0.6875026226043701 263.00274658203125 0.48411402106285095 311.36962890625 0.2080238312482834 0.7582276 1.8238062858581543 True -2 8259 30.743820190429688 0.5872037410736084 264.3965759277344 0.5067201256752014 306.7350769042969 0.21164236962795258 0.74100924 1.4349064826965332 False -3 11012 29.614872455596924 0.589792013168335 265.4797058105469 0.4468808174133301 301.1248474121094 0.21672403812408447 0.7697945 0.9660437107086182 True -4 13765 29.6459321975708 0.5607655048370361 228.09503173828125 0.762854278087616 297.75238037109375 0.2213934063911438 0.7826885 0.9021412134170532 True -5 16518 29.587602615356445 0.56148362159729 198.9638671875 0.466745525598526 295.9847717285156 0.22376786172389984 0.7918139 0.7591208815574646 True -6 19271 29.647340536117554 0.5655193328857422 298.6666259765625 0.551774263381958 293.89361572265625 0.2252807319164276 0.79735243 0.7355236411094666 True -7 22024 30.009820461273193 0.5642256736755371 240.08187866210938 0.6692843437194824 292.47247314453125 0.22628717124462128 0.8050741 0.6592302918434143 True -8 24777 29.672030210494995 0.5575222969055176 241.54031372070312 0.6316080093383789 290.1686706542969 0.22955822944641113 0.8161792 0.6249362230300903 True -9 27530 29.62730121612549 0.5640525817871094 252.68838500976562 0.4098131060600281 288.4735107421875 0.2320350557565689 0.82096475 0.5460752248764038 True -10 30283 29.60937213897705 0.5654740333557129 251.99232482910156 0.2867693305015564 286.6117248535156 0.23495882749557495 0.8284391 0.496982604265213 True -11 33036 29.646888971328735 0.5620200634002686 176.90371704101562 0.3543160855770111 284.894287109375 0.2371405065059662 0.8339217 0.46165931224823 True -12 35789 30.1904513835907 16.351728439331055 291.95947265625 0.34719979763031006 283.58782958984375 0.23984038829803467 0.83906114 0.4376140236854553 True -13 38542 29.64500379562378 0.9373009204864502 307.14959716796875 0.3393733501434326 282.5260314941406 0.24019747972488403 0.8449952 0.41313081979751587 True -14 41295 29.65604829788208 1.7171413898468018 206.8758544921875 0.3349840044975281 281.976806640625 0.24128767848014832 0.8526519 0.383614182472229 True -15 44048 29.624179363250732 1.3438982963562012 259.3748779296875 0.4714827537536621 281.23590087890625 0.242027148604393 0.85574394 0.36206334829330444 True -16 46801 29.63157892227173 22.774346828460693 243.81077575683594 0.31654292345046997 280.89306640625 0.24232640862464905 0.85949916 0.3485308289527893 True -17 49554 29.819679021835327 0.5992121696472168 196.11654663085938 0.26955074071884155 280.10205078125 0.24410153925418854 0.8618936 0.34200024604797363 True -18 52307 31.238990306854248 0.5639102458953857 216.490234375 0.40638625621795654 280.9560546875 0.24199478328227997 0.8612215 0.3427920937538147 False -19 55060 30.0923752784729 10.357664585113525 283.98016357421875 0.3240759074687958 280.01708984375 0.2448320835828781 0.8594522 0.34607088565826416 False diff --git a/ENCSR552TPH/cherimoya.fold_0.performance.tsv b/ENCSR552TPH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6dd61054fb0ae2b993ee34b32036e656d0339e2f..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -280.10205078125 0.5243868231773376 0.24410152435302734 0.07511567324399948 0.8618935942649841 0.7839200496673584 0.34200024604797363 \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_1.evaluate.json b/ENCSR552TPH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0351917dfa6c5d00440e5e36653301e9a9add54c..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498SGM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_1.fit.json b/ENCSR552TPH/cherimoya.fold_1.fit.json deleted file mode 100644 index ee3d1686bb066c21fb30879e9d1250c224df47fc..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF498SGM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_1.log b/ENCSR552TPH/cherimoya.fold_1.log deleted file mode 100644 index 914fed05af98296bc76789e2832166c90f6d56d6..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2720 34.72363901138306 4.098335266113281 310.64697265625 0.8170209527015686 453.1906433105469 0.1788700819015503 0.6374582 6.395351409912109 True -1 5440 29.899826049804688 0.8292102813720703 271.75433349609375 0.6176857352256775 394.0990295410156 0.238544300198555 0.7329731 2.916107654571533 True -2 8160 29.863311290740967 0.7191054821014404 246.94871520996094 0.6749601364135742 385.3701477050781 0.2435780167579651 0.740652 1.8267436027526855 True -3 10880 29.914474725723267 0.7211337089538574 371.7732849121094 0.6990878582000732 379.2513122558594 0.24876417219638824 0.77034837 1.3429646492004395 True -4 13600 29.890815019607544 0.7103097438812256 233.2584686279297 0.5586801767349243 374.2589416503906 0.2530599534511566 0.78578985 1.1459599733352661 True -5 16320 29.73719310760498 0.7030181884765625 201.1665802001953 0.5520097613334656 371.36370849609375 0.25534749031066895 0.79409367 1.0359628200531006 True -6 19040 29.16516089439392 0.708918571472168 191.30859375 0.4493460953235626 367.1748962402344 0.259535551071167 0.8049335 0.9086816310882568 True -7 21760 29.200419902801514 0.7075355052947998 294.0741271972656 0.5093007683753967 364.6033020019531 0.2617100775241852 0.81204605 0.8932151198387146 True -8 24480 29.20530605316162 0.6931068897247314 273.435302734375 0.3610917925834656 362.6192932128906 0.2639264166355133 0.8187654 0.8451526165008545 True -9 27200 29.248000383377075 0.7167627811431885 281.64739990234375 0.6087612509727478 360.42974853515625 0.26771384477615356 0.82340187 0.8153893351554871 True -10 29920 29.196136713027954 0.8880457878112793 228.91952514648438 0.4529808461666107 357.4728698730469 0.2699526846408844 0.83549505 0.7162106037139893 True -11 32640 29.284783363342285 0.708620548248291 345.8478088378906 0.6241360902786255 354.5182189941406 0.2743006646633148 0.8416435 0.6549134850502014 True -12 35360 29.23464274406433 0.7077133655548096 296.1904296875 0.29401540756225586 352.09423828125 0.2773143947124481 0.84785503 0.6120666861534119 True -13 38080 29.272093057632446 0.6986563205718994 301.91436767578125 0.41256654262542725 350.5977478027344 0.2784864604473114 0.85576886 0.5508675575256348 True -14 40800 29.281181812286377 0.7086918354034424 228.59567260742188 0.2767387330532074 349.4400329589844 0.27792593836784363 0.86250895 0.5017005205154419 True -15 43520 29.24584126472473 0.7011747360229492 205.298828125 0.38736969232559204 347.4748229980469 0.2808595895767212 0.8682738 0.4602286219596863 True -16 46240 29.264787435531616 0.704326868057251 240.92745971679688 0.31413567066192627 347.1286926269531 0.28042739629745483 0.8717233 0.4367195963859558 True -17 48960 29.27626657485962 0.7064511775970459 184.74261474609375 0.3210582733154297 347.21710205078125 0.2799344062805176 0.87253374 0.42078128457069397 True -18 51680 29.434358596801758 7.384847402572632 189.28128051757812 0.26249584555625916 347.35198974609375 0.28041329979896545 0.87109905 0.4177437424659729 False -19 54400 29.327099561691284 0.7162773609161377 217.27151489257812 0.19520433247089386 347.8120422363281 0.27907779812812805 0.87060547 0.4190666377544403 False diff --git a/ENCSR552TPH/cherimoya.fold_1.performance.tsv b/ENCSR552TPH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 37114d14323ee4343ef008afe4adae8151c50da8..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -347.21710205078125 0.4959070682525635 0.27993443608283997 0.09295643121004105 0.8725337386131287 0.8317385315895081 0.42078128457069397 \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_2.evaluate.json b/ENCSR552TPH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 33021496e91ada4b4a86d8d044ea02ec693f59c2..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498SGM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_2.fit.json b/ENCSR552TPH/cherimoya.fold_2.fit.json deleted file mode 100644 index 615c16782df1667a7897784b5da96a427cb9947b..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF498SGM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_2.log b/ENCSR552TPH/cherimoya.fold_2.log deleted file mode 100644 index 469ffd2424c02854178d17613a1b9f97d565ccae..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2904 36.34774470329285 3.429103136062622 236.79278564453125 1.089217185974121 376.75982666015625 0.16553466022014618 0.6368329 5.3265886306762695 True -1 5808 32.14969444274902 0.5852081775665283 199.4327392578125 0.5434339046478271 329.3638000488281 0.21947486698627472 0.7438573 2.087123394012451 True -2 8712 31.97863268852234 0.5742747783660889 223.9010009765625 0.6636335253715515 322.3744201660156 0.22482359409332275 0.7455556 1.2234240770339966 True -3 11616 31.88482666015625 0.5793235301971436 330.83929443359375 0.7052330374717712 319.23175048828125 0.2274625599384308 0.76184016 0.9826004505157471 True -4 14520 31.89559507369995 0.5597045421600342 192.80453491210938 0.39980995655059814 315.27740478515625 0.2305912971496582 0.7756945 0.9540226459503174 True -5 17424 31.787973165512085 0.5674910545349121 228.4645538330078 0.5513529181480408 312.14990234375 0.23527823388576508 0.7827562 0.8981934189796448 True -6 20328 31.783581018447876 0.5523626804351807 211.7852020263672 0.4388406276702881 309.8736877441406 0.23675334453582764 0.79058576 0.8075359463691711 True -7 23232 31.51649498939514 0.5465567111968994 320.397705078125 0.6459107398986816 307.7515563964844 0.24000678956508636 0.7989695 0.7700657248497009 True -8 26136 31.233042240142822 0.5415191650390625 170.62106323242188 0.41387081146240234 305.59844970703125 0.24281634390354156 0.802585 0.6977562308311462 True -9 29040 31.19304895401001 0.5433545112609863 231.90234375 0.3890427350997925 303.8509521484375 0.2445969581604004 0.8096371 0.61876380443573 True -10 31944 31.228118658065796 0.5406036376953125 259.25213623046875 0.5549299120903015 301.9190673828125 0.24790126085281372 0.81519794 0.5780194997787476 True -11 34848 31.294649362564087 0.5475766658782959 281.93316650390625 0.38687631487846375 300.4587707519531 0.24876083433628082 0.8241856 0.5385239720344543 True -12 37752 31.193509101867676 0.549990177154541 250.80886840820312 0.414345920085907 299.4057312011719 0.2493026703596115 0.8318171 0.4956468343734741 True -13 40656 31.24313259124756 0.5352442264556885 216.32571411132812 0.3141520917415619 297.01507568359375 0.25362199544906616 0.84377056 0.4349806010723114 True -14 43560 31.216757774353027 0.5476083755493164 224.46597290039062 0.2798365354537964 296.29791259765625 0.25382035970687866 0.85113347 0.41268864274024963 True -15 46464 31.17677879333496 0.5424892902374268 237.02130126953125 0.41660237312316895 295.7879333496094 0.25335124135017395 0.8566336 0.38520023226737976 True -16 49368 31.30009436607361 0.5493354797363281 237.58209228515625 0.2256690412759781 294.5693359375 0.25566792488098145 0.8611084 0.36734458804130554 True -17 52272 31.312277793884277 0.546497106552124 209.3297119140625 0.3688187003135681 293.8653564453125 0.2571443021297455 0.8615151 0.35914745926856995 True -18 55176 31.21124243736267 0.5728774070739746 272.19195556640625 0.3145397901535034 294.9621887207031 0.25459277629852295 0.8596186 0.3616883456707001 False -19 58080 31.601957082748413 1.448918342590332 221.5079803466797 0.23001092672348022 294.8358154296875 0.2557259500026703 0.86068887 0.3653830289840698 False diff --git a/ENCSR552TPH/cherimoya.fold_2.performance.tsv b/ENCSR552TPH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 913d874851b10ee96d227b7336d75507a9f89087..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -293.8653564453125 0.5151190757751465 0.2571442723274231 0.07845977693796158 0.8615151047706604 0.8015608191490173 0.35914745926856995 \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_3.evaluate.json b/ENCSR552TPH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 77276342a488623ff5a210f3934cd30c2b24fcf7..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498SGM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_3.fit.json b/ENCSR552TPH/cherimoya.fold_3.fit.json deleted file mode 100644 index 15f3090c465c3c15522193e74ce93deb10323fda..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF498SGM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_3.log b/ENCSR552TPH/cherimoya.fold_3.log deleted file mode 100644 index f0df37ccd7b7f511309c88e9308eccaca00f0d99..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 37.40700101852417 1.7085111141204834 234.30715942382812 0.901084303855896 379.4261474609375 0.1742105334997177 0.61700547 5.627931594848633 True -1 5516 30.3243510723114 0.579359769821167 282.4599304199219 0.5877057313919067 334.5115966796875 0.22636553645133972 0.7114745 2.500746726989746 True -2 8274 30.34812092781067 0.496049165725708 285.128662109375 0.7242436408996582 330.2787780761719 0.22715003788471222 0.71763414 1.6108042001724243 True -3 11032 30.241145610809326 0.49568939208984375 283.13946533203125 0.8552107810974121 324.06195068359375 0.2342107743024826 0.7466887 1.1645411252975464 True -4 13790 30.192510843276978 0.5026135444641113 375.41290283203125 0.721113383769989 320.5242004394531 0.2366909235715866 0.76273626 1.0262569189071655 True -5 16548 30.23053503036499 0.47353339195251465 332.6826171875 0.7894279956817627 317.966552734375 0.24084754288196564 0.76848537 0.9855539202690125 True -6 19306 30.24318766593933 0.5648961067199707 287.4186706542969 0.42828118801116943 316.62115478515625 0.2434304654598236 0.7701747 0.9922053217887878 True -7 22064 30.19587278366089 4.273807525634766 236.40213012695312 0.36955907940864563 314.6754150390625 0.2457922250032425 0.78331065 0.9224247932434082 True -8 24822 30.03610372543335 0.5028424263000488 220.029296875 0.4967375695705414 312.9613342285156 0.24950245022773743 0.7834107 0.9398967623710632 True -9 27580 29.66337299346924 0.6433594226837158 251.99130249023438 0.3947020173072815 311.46282958984375 0.25098392367362976 0.79312545 0.8576362133026123 True -10 30338 29.659714698791504 0.48734283447265625 182.15225219726562 0.34074538946151733 309.6693115234375 0.253482460975647 0.8034744 0.7829956412315369 True -11 33096 29.624512195587158 0.48344850540161133 281.9749450683594 0.8659605979919434 307.8108825683594 0.25586652755737305 0.81073767 0.7214553356170654 True -12 35854 29.673200607299805 0.49863529205322266 245.41693115234375 0.48350587487220764 306.7450866699219 0.25576120615005493 0.8173636 0.6519843935966492 True -13 38612 29.647924423217773 0.4928402900695801 180.69955444335938 0.38309717178344727 303.6807861328125 0.2608029544353485 0.8278338 0.5790833234786987 True -14 41370 29.620392084121704 0.4841935634613037 218.65542602539062 0.4402995705604553 302.0377502441406 0.2613529860973358 0.8375497 0.5244023203849792 True -15 44128 29.63386344909668 0.4790232181549072 227.80084228515625 0.2950982451438904 301.62725830078125 0.26095935702323914 0.8436696 0.470735639333725 True -16 46886 29.705981254577637 0.4967622756958008 178.64010620117188 0.3262718915939331 300.8421936035156 0.26173901557922363 0.84892935 0.4415000379085541 True -17 49644 29.661762237548828 0.5113260746002197 234.61776733398438 0.27249085903167725 301.5398254394531 0.25990256667137146 0.8508769 0.4255608320236206 True -18 52402 29.68387246131897 0.5003032684326172 282.1563720703125 0.24387365579605103 300.20367431640625 0.26384076476097107 0.8514808 0.415134072303772 True -19 55160 29.697498321533203 0.50738525390625 215.69369506835938 0.3456120193004608 301.46832275390625 0.2607076168060303 0.8518697 0.4166524410247803 True diff --git a/ENCSR552TPH/cherimoya.fold_3.performance.tsv b/ENCSR552TPH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b7469bd5c7e932a176a8986bd993af416913b273..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -301.46832275390625 0.5119327306747437 0.2607076168060303 0.08411746472120285 0.8518697023391724 0.7955304980278015 0.4166524410247803 \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_4.evaluate.json b/ENCSR552TPH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4898cb267f12897b34c5dfcbfe410a3be08f1552..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498SGM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_4.fit.json b/ENCSR552TPH/cherimoya.fold_4.fit.json deleted file mode 100644 index 6a351a324eae55436bf0dff844a292307958c2a2..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF498SGM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552TPH/cherimoya.fold_4.log b/ENCSR552TPH/cherimoya.fold_4.log deleted file mode 100644 index af02796b110553ae66e3b43c985b1db1b92d742c..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 34.77271318435669 3.5346879959106445 268.022705078125 0.7227209210395813 323.61981201171875 0.15713199973106384 0.6235223 4.500128269195557 True -1 5528 30.347075700759888 0.6027505397796631 257.62835693359375 0.763634443283081 290.244873046875 0.19854742288589478 0.71995944 1.6238080263137817 True -2 8292 30.383081197738647 0.5784406661987305 274.52685546875 1.0166685581207275 285.95343017578125 0.20042437314987183 0.7338741 0.9303492307662964 True -3 11056 30.341119050979614 0.5659809112548828 204.7170867919922 0.6632946729660034 279.9934997558594 0.20872196555137634 0.75332093 0.7635886669158936 True -4 13820 30.394386529922485 0.8291380405426025 254.06231689453125 0.5621280670166016 277.5849609375 0.21170060336589813 0.76755357 0.7305222153663635 True -5 16584 30.373667001724243 0.5727078914642334 304.0328369140625 0.6799218654632568 275.0940246582031 0.21464818716049194 0.77325004 0.7924870848655701 True -6 19348 30.392449140548706 0.5715746879577637 262.32781982421875 0.5005806088447571 272.8804016113281 0.21810859441757202 0.7805542 0.7415192723274231 True -7 22112 30.35263180732727 1.2373197078704834 273.1012268066406 0.458664208650589 270.65167236328125 0.22129370272159576 0.786004 0.683895468711853 True -8 24876 30.448629140853882 0.580603837966919 222.14430236816406 0.48179054260253906 269.3559265136719 0.2238815575838089 0.79386616 0.6711131930351257 True -9 27640 29.9326171875 0.5604283809661865 295.6302795410156 0.4663206934928894 268.16680908203125 0.22470791637897491 0.8012171 0.6092208623886108 True -10 30404 29.74139142036438 1.6266860961914062 235.17654418945312 0.4640187621116638 267.11895751953125 0.2267352193593979 0.80837756 0.5544583201408386 True -11 33168 29.815995693206787 0.5830423831939697 272.6999206542969 0.4838159680366516 266.41680908203125 0.22757983207702637 0.81617504 0.4946881830692291 True -12 35932 29.779008388519287 0.5715591907501221 256.8838195800781 0.49819672107696533 264.9975891113281 0.2294445037841797 0.8236522 0.4495868384838104 True -13 38696 29.77864098548889 0.571861982345581 190.2539520263672 0.34741273522377014 263.8844909667969 0.2314545214176178 0.82529575 0.4317408502101898 True -14 41460 29.74059748649597 0.5931005477905273 243.3944549560547 0.6045226454734802 263.388671875 0.23091541230678558 0.8326273 0.39492955803871155 True -15 44224 29.747336864471436 0.5609395503997803 264.46905517578125 0.34398525953292847 261.8769226074219 0.2336190789937973 0.83940786 0.3682592213153839 True -16 46988 29.855058908462524 0.5731277465820312 206.3935546875 0.2767149806022644 261.84112548828125 0.23354008793830872 0.84308696 0.351913183927536 True -17 49752 29.872495889663696 21.056710720062256 230.60101318359375 0.2913942039012909 261.604736328125 0.2338179498910904 0.8442644 0.34764641523361206 True -18 52516 29.72255253791809 0.597545862197876 180.45364379882812 0.23242343962192535 262.0169372558594 0.23324720561504364 0.84442884 0.34561872482299805 True -19 55280 29.80078887939453 18.600714683532715 221.01185607910156 0.21241256594657898 261.70843505859375 0.23397429287433624 0.84277624 0.3472137153148651 False diff --git a/ENCSR552TPH/cherimoya.fold_4.performance.tsv b/ENCSR552TPH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d4eb7c395b68d2df4f282e9ef618b90d42280327..0000000000000000000000000000000000000000 --- a/ENCSR552TPH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -262.0169372558594 0.5318259596824646 0.23324719071388245 0.06754148006439209 0.8444288372993469 0.763838529586792 0.34561872482299805 \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_0.evaluate.json b/ENCSR552XJI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7ff81da4071be499bcb074bfb672a5da74f66149..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538WXJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_0.fit.json b/ENCSR552XJI/cherimoya.fold_0.fit.json deleted file mode 100644 index 7f61eb256e66035534dd40428eb85e69c0893286..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF538WXJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_0.log b/ENCSR552XJI/cherimoya.fold_0.log deleted file mode 100644 index 127767a90f4b0c71b232fe8ce25ba8c62ebed678..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 34.02254915237427 3.545926332473755 688.2986450195312 0.38458919525146484 966.34716796875 0.23758326470851898 0.66262895 7.114017486572266 True -1 5472 30.132630109786987 1.2406859397888184 684.2060546875 0.4784814417362213 886.57373046875 0.3166022300720215 0.7330752 2.1342244148254395 True -2 8208 30.132680654525757 0.5568113327026367 840.1019287109375 0.5247143507003784 871.8676147460938 0.32879260182380676 0.7554007 0.9477919936180115 True -3 10944 29.62962579727173 1.079005241394043 757.0136108398438 0.4072207510471344 863.82666015625 0.33751723170280457 0.76630074 0.7695808410644531 True -4 13680 29.558491706848145 0.5475692749023438 682.1405639648438 0.2928726077079773 861.60009765625 0.34028828144073486 0.77133155 0.7565321326255798 True -5 16416 29.990842580795288 14.086469888687134 843.7606811523438 0.4111672639846802 859.4678344726562 0.342475026845932 0.77313644 0.6340336799621582 True -6 19152 29.62154269218445 0.5399694442749023 775.4031372070312 0.41361764073371887 856.5823974609375 0.3455701470375061 0.7808018 0.6111117005348206 True -7 21888 29.532912254333496 0.5510637760162354 830.881591796875 0.3536837697029114 855.230712890625 0.3464094400405884 0.78740793 0.5502163171768188 True -8 24624 29.54748249053955 0.5519611835479736 780.7924194335938 0.44918495416641235 853.1851196289062 0.3490901291370392 0.79311836 0.4967663288116455 True -9 27360 29.51455330848694 0.5407168865203857 735.8980712890625 0.3488321304321289 851.6931762695312 0.3500552177429199 0.79668343 0.4781956076622009 True -10 30096 29.565268754959106 0.5343525409698486 786.03076171875 0.2870197296142578 850.1593627929688 0.35097911953926086 0.801982 0.46500885486602783 True -11 32832 29.58561635017395 0.5385665893554688 705.6559448242188 0.3689559996128082 847.5966796875 0.35383379459381104 0.8110633 0.4082746207714081 True -12 35568 29.529717445373535 0.5402669906616211 683.5589599609375 0.25081565976142883 844.3010864257812 0.35726433992385864 0.8146688 0.3829355835914612 True -13 38304 29.54022455215454 0.5311470031738281 700.80322265625 0.2615508735179901 842.955810546875 0.3583393096923828 0.82135063 0.34863731265068054 True -14 41040 29.62900948524475 0.5403468608856201 732.8922119140625 0.285223126411438 841.8694458007812 0.3595796525478363 0.8279324 0.31317073106765747 True -15 43776 29.555023670196533 0.541412353515625 749.4728393554688 0.15627805888652802 840.5185546875 0.36016085743904114 0.8324163 0.284597784280777 True -16 46512 29.551417112350464 0.5422523021697998 654.9185791015625 0.2401220202445984 840.3109130859375 0.3601018190383911 0.83478314 0.27057477831840515 True -17 49248 29.552533864974976 1.1288933753967285 625.64990234375 0.260760635137558 839.419921875 0.3613397777080536 0.83459 0.26286834478378296 False -18 51984 29.57967233657837 0.5374407768249512 801.6207885742188 0.27245843410491943 840.5546264648438 0.3596768379211426 0.835648 0.2600674629211426 True -19 54720 29.523524045944214 0.5415983200073242 688.7643432617188 0.18430016934871674 840.223876953125 0.36013302206993103 0.83603185 0.2590814530849457 True diff --git a/ENCSR552XJI/cherimoya.fold_0.performance.tsv b/ENCSR552XJI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index dcf4a7b2bd0f2621ae1f19152d9f1e47e555de54..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -840.223876953125 0.39311298727989197 0.3601330816745758 0.15340444445610046 0.8360318541526794 0.7962011098861694 0.2590814530849457 \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_1.evaluate.json b/ENCSR552XJI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b542941f19c1ea05011102fe29afcdbe70d6a9ec..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538WXJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_1.fit.json b/ENCSR552XJI/cherimoya.fold_1.fit.json deleted file mode 100644 index d035da73dc53b4ebc4306237990b7c809cfbbefd..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF538WXJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_1.log b/ENCSR552XJI/cherimoya.fold_1.log deleted file mode 100644 index d54e189b0e2bb8c996c31e66049c697156656fa3..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 33.76170587539673 4.2579426765441895 778.7232055664062 0.5221350789070129 1066.896728515625 0.2425968497991562 0.6928306 6.7656755447387695 True -1 5466 30.066028833389282 0.7377259731292725 703.559326171875 0.448849618434906 973.035400390625 0.32875576615333557 0.76573455 1.8090336322784424 True -2 8199 30.07604432106018 0.709052324295044 693.779296875 0.4436144232749939 952.2001342773438 0.34311264753341675 0.78944385 0.7671198844909668 True -3 10932 29.668232440948486 0.692310094833374 677.2412719726562 0.5836620926856995 943.0838623046875 0.35104671120643616 0.79789114 0.6145046353340149 True -4 13665 29.50048851966858 0.698967456817627 761.5324096679688 0.3525846600532532 941.5918579101562 0.3525080978870392 0.80438966 0.7597124576568604 True -5 16398 29.499000310897827 0.6964504718780518 730.1851196289062 0.43848729133605957 941.3980102539062 0.35280290246009827 0.7977153 0.7003124952316284 False -6 19131 29.473846197128296 0.6919987201690674 776.7567138671875 0.42351579666137695 935.8667602539062 0.35739898681640625 0.8128762 0.5471954345703125 True -7 21864 29.492013931274414 0.703005313873291 689.0885009765625 0.3525744080543518 932.9845581054688 0.36069995164871216 0.816952 0.46357110142707825 True -8 24597 29.500493049621582 0.7006902694702148 677.5474853515625 0.3171565532684326 931.5692749023438 0.3609401285648346 0.82505554 0.4491611123085022 True -9 27330 29.535847425460815 0.6936676502227783 622.5125732421875 0.2488316297531128 928.9030151367188 0.362949401140213 0.82986635 0.41495010256767273 True -10 30063 29.462564945220947 2.3829123973846436 727.786376953125 0.3143189549446106 926.048583984375 0.3656442165374756 0.83420974 0.4061078131198883 True -11 32796 29.549328565597534 0.7069070339202881 823.1141967773438 0.2708047330379486 924.421630859375 0.3669685423374176 0.8389016 0.3645666837692261 True -12 35529 29.622331619262695 0.703129768371582 715.9833374023438 0.29928869009017944 922.6132202148438 0.3686470091342926 0.8436021 0.34455636143684387 True -13 38262 29.516035795211792 1.523045301437378 737.0157470703125 0.3013598918914795 921.479248046875 0.3689219355583191 0.85021293 0.32174333930015564 True -14 40995 29.650688409805298 0.7137863636016846 636.8212890625 0.18735456466674805 917.7589721679688 0.37309128046035767 0.8532943 0.29563847184181213 True -15 43728 29.5792498588562 0.7110507488250732 653.438232421875 0.2416630983352661 916.9922485351562 0.37450289726257324 0.85730827 0.27321749925613403 True -16 46461 29.610056161880493 0.7097499370574951 705.8333740234375 0.2787666320800781 915.9652709960938 0.3743256628513336 0.858763 0.2591632604598999 True -17 49194 29.70647358894348 0.692467451095581 595.8489990234375 0.2389034926891327 915.2136840820312 0.3755459487438202 0.8609655 0.24919071793556213 True -18 51927 29.537667989730835 0.7075028419494629 647.7188110351562 0.17567060887813568 916.0241088867188 0.37441393733024597 0.8590322 0.24765929579734802 False -19 54660 29.589862823486328 0.7031598091125488 848.247314453125 0.21016234159469604 916.61962890625 0.3733016848564148 0.8595539 0.24832889437675476 False diff --git a/ENCSR552XJI/cherimoya.fold_1.performance.tsv b/ENCSR552XJI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 96e4abc0db88add89f74ab7453f33e473c4fb728..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -915.2136840820312 0.3797203302383423 0.3755459785461426 0.16864609718322754 0.8609654903411865 0.8364412784576416 0.24919071793556213 \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_2.evaluate.json b/ENCSR552XJI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b4ac68ea81877e32fa80b8ae6a4c5f2168c3a308..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538WXJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_2.fit.json b/ENCSR552XJI/cherimoya.fold_2.fit.json deleted file mode 100644 index d0a16aa7d453aa09c0a96c31eb4602bf1c68aa61..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF538WXJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_2.log b/ENCSR552XJI/cherimoya.fold_2.log deleted file mode 100644 index 37ca572c171d0d3b6745e0cca8f2a4144c84ee21..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 35.35181474685669 3.472069263458252 778.9443359375 0.5538111925125122 1008.486083984375 0.24469050765037537 0.66017216 6.5807623863220215 True -1 5740 31.539008378982544 0.5729455947875977 677.5784912109375 0.35635173320770264 921.2299194335938 0.3253929615020752 0.7362979 1.5425370931625366 True -2 8610 31.620200634002686 0.562819242477417 674.8773193359375 0.38943251967430115 904.9487915039062 0.3362695574760437 0.7621486 0.8792219161987305 True -3 11480 31.639528512954712 1.6361191272735596 749.5220947265625 0.2829488217830658 898.4402465820312 0.3420202434062958 0.7699945 0.6664618849754333 True -4 14350 31.536690711975098 0.5618042945861816 702.7144165039062 0.35454848408699036 894.32861328125 0.34606698155403137 0.7784716 0.6508078575134277 True -5 17220 31.409144639968872 0.5593774318695068 604.7979736328125 0.3425638675689697 892.2554321289062 0.3471933603286743 0.78408647 0.5952028632164001 True -6 20090 30.973044872283936 0.5516989231109619 629.582275390625 0.23575901985168457 890.0557861328125 0.34912383556365967 0.7893928 0.49945276975631714 True -7 22960 30.971890211105347 0.5550274848937988 777.3703002929688 0.4564676582813263 886.7008056640625 0.35369083285331726 0.7922949 0.4946724772453308 True -8 25830 31.05786442756653 1.5189120769500732 661.4986572265625 0.28702324628829956 885.3165283203125 0.35437947511672974 0.7986074 0.4672967493534088 True -9 28700 31.085007190704346 1.4228026866912842 631.6238403320312 0.3274424076080322 882.0402221679688 0.3577059209346771 0.8033872 0.4379730522632599 True -10 31570 31.08231782913208 1.1899006366729736 865.71044921875 0.2885077893733978 880.2783813476562 0.3597695231437683 0.80880904 0.40021032094955444 True -11 34440 31.077959537506104 1.4547834396362305 773.2554931640625 0.2569617033004761 878.4862060546875 0.36201319098472595 0.81388146 0.3883483111858368 True -12 37310 31.079302549362183 18.194029092788696 765.0018310546875 0.22465991973876953 875.89208984375 0.36370256543159485 0.8200903 0.34829655289649963 True -13 40180 31.014498949050903 11.176410675048828 725.4417724609375 0.3775300085544586 874.902587890625 0.3644116222858429 0.8251143 0.3212316334247589 True -14 43050 31.217783212661743 1.608234167098999 835.664794921875 0.3302270174026489 874.34716796875 0.36471158266067505 0.83027285 0.3072655498981476 True -15 45920 31.511122226715088 0.5525259971618652 689.0270385742188 0.2111562192440033 872.4911499023438 0.3665429949760437 0.8338911 0.28944480419158936 True -16 48790 31.124538898468018 0.5586576461791992 692.843017578125 0.2778216302394867 871.8959350585938 0.3664971590042114 0.83820504 0.27257227897644043 True -17 51660 31.04015040397644 0.5560035705566406 692.2459716796875 0.17396429181098938 872.7177734375 0.3661072254180908 0.83925784 0.2652113437652588 True -18 54530 30.997618913650513 0.5601277351379395 772.38037109375 0.25153928995132446 871.3927001953125 0.3682105243206024 0.8385887 0.2648192048072815 False -19 57400 30.98407220840454 0.5485806465148926 686.7041625976562 0.19851499795913696 872.4894409179688 0.36643561720848083 0.8385085 0.26421916484832764 False diff --git a/ENCSR552XJI/cherimoya.fold_2.performance.tsv b/ENCSR552XJI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 000878f655fbbaae5fd33d54782f25f4ee3143b8..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -872.7177734375 0.3876112699508667 0.3661072254180908 0.1556605100631714 0.8392578363418579 0.8064978122711182 0.2652113437652588 \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_3.evaluate.json b/ENCSR552XJI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0c7f30eea6a1755502e453cc68b1e9689aef0e0e..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538WXJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_3.fit.json b/ENCSR552XJI/cherimoya.fold_3.fit.json deleted file mode 100644 index 236ae7985b9889ca40825629c79cbc73406a5afd..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF538WXJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_3.log b/ENCSR552XJI/cherimoya.fold_3.log deleted file mode 100644 index d0f1e04a005c7597b97c2408f8f6d1a077df8a30..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2766 34.72555470466614 9.231818199157715 623.6763916015625 0.7091424465179443 953.515380859375 0.24965639412403107 0.655571 6.919829368591309 True -1 5532 30.444464206695557 1.7644810676574707 707.5078125 0.4554356634616852 875.4969482421875 0.3233286738395691 0.7302748 1.8702267408370972 True -2 8298 30.477693557739258 12.2009596824646 744.9404296875 0.4780999422073364 857.4281005859375 0.33798903226852417 0.75633836 0.9020635485649109 True -3 11064 30.905179262161255 0.5642271041870117 629.1176147460938 0.5378068685531616 850.90625 0.34354016184806824 0.76531076 0.7287583351135254 True -4 13830 29.89397144317627 0.5448813438415527 715.56591796875 0.2872973680496216 847.88232421875 0.3460647165775299 0.76850086 0.6263623237609863 True -5 16596 29.902745008468628 0.5396730899810791 688.5594482421875 0.336419016122818 845.9088134765625 0.3484920561313629 0.7739195 0.6730365753173828 True -6 19362 29.865989208221436 1.1299030780792236 724.6188354492188 0.4163976311683655 846.3699340820312 0.3474683165550232 0.7774592 0.68199622631073 True -7 22128 29.863443851470947 0.5531754493713379 629.96923828125 0.35461264848709106 840.1542358398438 0.3551158308982849 0.78118676 0.6192230582237244 True -8 24894 29.931930780410767 0.5494754314422607 735.9758911132812 0.3525000512599945 839.7710571289062 0.3546138107776642 0.7854731 0.5673320293426514 True -9 27660 29.919870615005493 0.5435817241668701 673.4232177734375 0.2828790247440338 837.3414916992188 0.35743197798728943 0.79244214 0.5291064381599426 True -10 30426 29.888468742370605 0.5484659671783447 690.809326171875 0.2773267924785614 834.5325317382812 0.3602351248264313 0.8006575 0.4943224787712097 True -11 33192 29.875608444213867 14.889432191848755 627.88232421875 0.2846831977367401 832.77294921875 0.3613106906414032 0.80631596 0.4558730721473694 True -12 35958 29.974076747894287 0.5492918491363525 649.2978515625 0.3181488811969757 830.5963745117188 0.3641453981399536 0.81436914 0.3979567587375641 True -13 38724 29.89997124671936 0.5573456287384033 733.103271484375 0.24939274787902832 829.6272583007812 0.3651837408542633 0.8245417 0.35722219944000244 True -14 41490 29.934495210647583 0.5480148792266846 801.280029296875 0.18014028668403625 827.8673706054688 0.36659979820251465 0.82878095 0.3270488381385803 True -15 44256 29.959675312042236 0.5453057289123535 646.1837768554688 0.2685205936431885 826.35791015625 0.36761289834976196 0.8322323 0.3019384443759918 True -16 47022 29.927088737487793 0.5390105247497559 680.438232421875 0.2849157452583313 827.1644287109375 0.36622267961502075 0.8377452 0.2854636311531067 True -17 49788 29.96127223968506 0.5401034355163574 840.5546264648438 0.24049249291419983 825.99951171875 0.36853474378585815 0.8394504 0.2760346531867981 True -18 52554 29.835428953170776 0.533062219619751 734.789306640625 0.3157339096069336 826.1913452148438 0.3682246804237366 0.83971286 0.2696763873100281 True -19 55320 29.855352878570557 0.5395386219024658 692.5045166015625 0.1646333932876587 826.6233520507812 0.36789602041244507 0.8378805 0.27088242769241333 False diff --git a/ENCSR552XJI/cherimoya.fold_3.performance.tsv b/ENCSR552XJI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d0c7108337a94246d59e03c477fd9ae9e9dd51bb..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -826.1913452148438 0.390419065952301 0.3682246804237366 0.15684697031974792 0.8397128582000732 0.7980950474739075 0.2696763873100281 \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_4.evaluate.json b/ENCSR552XJI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bec9978d811ad9de5387d9c47f5a92f3f79ae574..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538WXJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_4.fit.json b/ENCSR552XJI/cherimoya.fold_4.fit.json deleted file mode 100644 index a91fb4f79212cd294f9fce1035148799fb8756b6..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF538WXJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR552XJI/cherimoya.fold_4.log b/ENCSR552XJI/cherimoya.fold_4.log deleted file mode 100644 index ae9111a3bc532cff75e24446290bf28c29a4ce9b..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2804 34.85688018798828 3.8708577156066895 598.0047607421875 0.39222848415374756 903.066650390625 0.23575830459594727 0.65713763 5.844590187072754 True -1 5608 32.85519027709961 10.621575117111206 667.8134765625 0.4708801507949829 828.2076416015625 0.3095032274723053 0.7349726 1.6330641508102417 True -2 8412 30.89087986946106 1.5366299152374268 766.2010498046875 0.46030527353286743 816.5342407226562 0.31799614429473877 0.7626927 0.6940799355506897 True -3 11216 31.01987338066101 28.796274423599243 809.05517578125 0.3330571949481964 807.7293701171875 0.3268747329711914 0.776041 0.5815926194190979 True -4 14020 30.706728219985962 1.1857430934906006 737.3596801757812 0.34838810563087463 807.853271484375 0.32702434062957764 0.7774703 0.7198641896247864 True -5 16824 30.305838108062744 1.4868841171264648 718.9927978515625 0.38167431950569153 804.83447265625 0.3305278420448303 0.78417873 0.5686315298080444 True -6 19628 30.401342391967773 1.879176378250122 822.2020874023438 0.5787332057952881 802.0718383789062 0.3330079913139343 0.7894744 0.4837196171283722 True -7 22432 30.41616725921631 0.5694096088409424 615.6189575195312 0.33943697810173035 800.6190185546875 0.3346247971057892 0.79220766 0.49074968695640564 True -8 25236 30.34200692176819 0.560633659362793 619.8157958984375 0.32342880964279175 798.127685546875 0.3377610445022583 0.7977222 0.476759672164917 True -9 28040 30.369128465652466 0.5614123344421387 565.9097900390625 0.4820736050605774 797.8452758789062 0.3376498222351074 0.80251217 0.4263905882835388 True -10 30844 30.328813552856445 0.568021297454834 626.967529296875 0.41375279426574707 794.5062255859375 0.3408111035823822 0.8088477 0.3875279128551483 True -11 33648 30.357128143310547 0.5612246990203857 702.14892578125 0.3040328919887543 792.7249145507812 0.34269073605537415 0.81448466 0.35780900716781616 True -12 36452 30.371430158615112 0.566382884979248 656.384033203125 0.4476580023765564 790.0010986328125 0.34646573662757874 0.82070994 0.3340796232223511 True -13 39256 30.39082646369934 1.1110870838165283 745.4522705078125 0.46786612272262573 789.3523559570312 0.3466913402080536 0.82681006 0.2991102933883667 True -14 42060 30.42191481590271 0.5627496242523193 587.7467041015625 0.17495685815811157 788.2481079101562 0.3473486602306366 0.83513725 0.27923908829689026 True -15 44864 30.462178707122803 0.5580976009368896 578.9534301757812 0.2155657708644867 787.5308227539062 0.3477497398853302 0.83883166 0.263529896736145 True -16 47668 30.447091817855835 0.5642731189727783 745.8699951171875 0.1498255580663681 787.2462158203125 0.3473568260669708 0.83953446 0.2496352344751358 True -17 50472 30.453015565872192 0.5586032867431641 566.0802612304688 0.3055921196937561 786.8540649414062 0.34871283173561096 0.8402776 0.24257290363311768 True -18 53276 30.449129343032837 0.5585908889770508 650.8214111328125 0.24627500772476196 786.5098876953125 0.34925347566604614 0.84150976 0.2407156527042389 True -19 56080 30.42846441268921 0.5591721534729004 649.214599609375 0.21027061343193054 787.5345458984375 0.34723687171936035 0.8402142 0.2413492500782013 False diff --git a/ENCSR552XJI/cherimoya.fold_4.performance.tsv b/ENCSR552XJI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2a705f79bea5b1cbab1fe3e8474912aeffb8a6dc..0000000000000000000000000000000000000000 --- a/ENCSR552XJI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -786.5098876953125 0.40446069836616516 0.34925344586372375 0.1427154690027237 0.8415097594261169 0.7934153079986572 0.2407156527042389 \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_0.evaluate.json b/ENCSR553LAZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2051f8672908c20d48cf32c69663e80ace42ef92..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF812OAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_0.fit.json b/ENCSR553LAZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 48526a5ee46b030fe142b32f87f01321ad1d8a01..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF812OAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_0.log b/ENCSR553LAZ/cherimoya.fold_0.log deleted file mode 100644 index 8e435410e8acdc20c60057216b7a4cfe1f3f8190..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3790 45.09152626991272 3.681183099746704 815.0804443359375 0.9003987312316895 1233.555419921875 0.727763295173645 0.68493146 7.9980573654174805 True -1 7580 41.43058705329895 0.7917337417602539 990.7330322265625 0.8572629690170288 1029.41845703125 0.8103679418563843 0.6997382 1.7774884700775146 True -2 11370 41.66682410240173 2.5485167503356934 818.9412841796875 1.2013109922409058 1002.775634765625 0.8180360198020935 0.7066617 0.99278324842453 True -3 15160 41.69109749794006 0.7422945499420166 843.4638671875 0.7523365020751953 987.06494140625 0.823376476764679 0.6966471 0.7552258372306824 False -4 18950 41.74972677230835 0.7496123313903809 850.9968872070312 0.7982877492904663 980.086669921875 0.8270576596260071 0.6993209 0.762916624546051 False -5 22740 41.692485094070435 0.7448170185089111 761.1038818359375 1.1111304759979248 972.8877563476562 0.829474925994873 0.7002067 0.7224529981613159 False -6 26530 41.72864127159119 0.7549655437469482 881.239013671875 0.7991179823875427 965.1441040039062 0.8319609761238098 0.70769846 0.6701546907424927 True -7 30320 41.70085692405701 0.7453646659851074 802.1399536132812 0.7613294720649719 960.153076171875 0.8344078063964844 0.7096979 0.6547154784202576 True -8 34110 41.71204686164856 0.7563884258270264 926.585693359375 0.8514431715011597 953.1239624023438 0.8372058272361755 0.71838146 0.6268084645271301 True -9 37900 41.81777572631836 0.7603795528411865 784.3056030273438 0.5829459428787231 947.8055419921875 0.839482307434082 0.72153413 0.6380801796913147 True -10 41690 41.74753975868225 28.94628596305847 811.40771484375 0.8077952265739441 940.3746948242188 0.8418897986412048 0.7264058 0.6242759823799133 True -11 45480 42.68607211112976 0.7531471252441406 769.8906860351562 0.7527143955230713 930.9461669921875 0.844803512096405 0.7341489 0.5898700952529907 True -12 49270 41.797364234924316 0.7575335502624512 709.580810546875 0.7154724597930908 925.6239624023438 0.847532331943512 0.7400044 0.5925844311714172 True -13 53060 41.71058678627014 32.99773335456848 874.1292724609375 0.8929144144058228 919.40771484375 0.8496997952461243 0.7499558 0.5837615728378296 True -14 56850 42.741076946258545 6.237255096435547 674.5504150390625 0.4714764356613159 913.8074951171875 0.8520981073379517 0.75913817 0.5620175004005432 True -15 60640 41.008732080459595 0.7528057098388672 815.5429077148438 0.49006760120391846 908.816162109375 0.8538181781768799 0.76878816 0.5510692000389099 True -16 64430 40.87179255485535 0.7335996627807617 787.6827392578125 0.48509669303894043 908.0396118164062 0.8548551797866821 0.77473736 0.5455663204193115 True -17 68220 40.86975574493408 0.7300593852996826 753.70703125 0.4576859474182129 907.2796020507812 0.8551293015480042 0.77842385 0.5476236939430237 True -18 72010 40.86217975616455 0.7399041652679443 765.7682495117188 0.3318074941635132 907.6956176757812 0.8548533916473389 0.77874845 0.5479567646980286 True -19 75800 40.97343325614929 0.7485346794128418 735.2698974609375 0.3568476140499115 908.4073486328125 0.8546020984649658 0.7759324 0.5503755807876587 False diff --git a/ENCSR553LAZ/cherimoya.fold_0.performance.tsv b/ENCSR553LAZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 342698ea1385d865576da3f1ee6590483f125eb1..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -907.6956176757812 0.12036612629890442 0.8548533916473389 0.5395631194114685 0.7787484526634216 0.7225246429443359 0.5479567646980286 \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_1.evaluate.json b/ENCSR553LAZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e860df21d69aec036fd40cc3440e14913504cfe4..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF812OAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_1.fit.json b/ENCSR553LAZ/cherimoya.fold_1.fit.json deleted file mode 100644 index a800383737521fbcf17585508931c3fc37931269..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF812OAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_1.log b/ENCSR553LAZ/cherimoya.fold_1.log deleted file mode 100644 index 35b6a8c549283de90c7509e6c1f16b16482d3fc5..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3736 46.34114122390747 4.149941921234131 822.5791015625 1.0621662139892578 1397.4471435546875 0.7368794679641724 0.7019735 7.8058390617370605 True -1 7472 41.13968324661255 1.0246620178222656 790.62158203125 0.9056237936019897 1149.231689453125 0.8179836273193359 0.72489876 2.1807680130004883 True -2 11208 41.11851739883423 1.6837272644042969 713.2322998046875 1.5756385326385498 1117.0301513671875 0.826506495475769 0.7241833 1.045976996421814 False -3 14944 41.201783895492554 1.0095670223236084 829.9234619140625 0.7780246138572693 1099.5496826171875 0.830662190914154 0.7255072 0.8268533945083618 True -4 18680 41.26029992103577 2.1027112007141113 673.59765625 0.9139612913131714 1087.3720703125 0.8342494368553162 0.73071796 0.7871897220611572 True -5 22416 41.0779550075531 53.69122910499573 877.666015625 0.7967803478240967 1077.551025390625 0.8368226885795593 0.73292863 0.8166213035583496 True -6 26152 43.33930468559265 1.009023904800415 933.0678100585938 1.0218651294708252 1068.3043212890625 0.8394792675971985 0.7474729 0.6777697205543518 True -7 29888 41.129688024520874 1.035667896270752 753.27294921875 0.6112657785415649 1061.1085205078125 0.8416390419006348 0.74702764 0.6635130047798157 False -8 33624 47.44548487663269 5.56854248046875 837.4188232421875 0.7935400009155273 1052.8802490234375 0.8441645503044128 0.7513485 0.6458879113197327 True -9 37360 41.23296880722046 0.9980258941650391 746.5172119140625 0.5762507915496826 1044.5938720703125 0.8467969298362732 0.75622493 0.6510710716247559 True -10 41096 41.12981128692627 3.1115190982818604 742.5440673828125 0.745394229888916 1036.05078125 0.8492791056632996 0.76316583 0.6235464811325073 True -11 44832 43.46955752372742 23.5555899143219 810.1712036132812 1.0279316902160645 1029.6749267578125 0.8517788648605347 0.7689306 0.6114990711212158 True -12 48568 41.81232476234436 1.0444607734680176 738.7840576171875 0.5133681297302246 1021.32421875 0.8541545867919922 0.7742143 0.6096969842910767 True -13 52304 41.723000288009644 42.37901759147644 721.568603515625 0.53132164478302 1013.0866088867188 0.8569737076759338 0.78354275 0.5815585851669312 True -14 56040 42.55841827392578 43.1192193031311 756.8887939453125 0.5158219337463379 1007.7711791992188 0.85920649766922 0.7907334 0.5768941044807434 True -15 59776 41.47016763687134 1.0354492664337158 727.9011840820312 0.4491279423236847 1002.0599365234375 0.8609451055526733 0.79825264 0.5515086054801941 True -16 63512 41.34642243385315 1.0206832885742188 630.56591796875 0.4695189893245697 1000.9716796875 0.8619175553321838 0.80448025 0.5463414192199707 True -17 67248 42.3485643863678 1.2197527885437012 630.089111328125 0.4622134566307068 1000.6812744140625 0.8622065782546997 0.8056765 0.543272852897644 True -18 70984 43.08760356903076 56.656508445739746 807.4136962890625 0.38172563910484314 1001.5082397460938 0.8619500398635864 0.8052187 0.5486617684364319 False -19 74720 43.893014430999756 54.376270055770874 627.083984375 0.645675778388977 1002.9439697265625 0.861579179763794 0.8036457 0.5476975440979004 False diff --git a/ENCSR553LAZ/cherimoya.fold_1.performance.tsv b/ENCSR553LAZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8bd25984ae6a3054f2f2c513110afa7425665a8b..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1000.6812744140625 0.11049366742372513 0.8622065186500549 0.5756703615188599 0.8056765198707581 0.7678461074829102 0.543272852897644 \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_2.evaluate.json b/ENCSR553LAZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3442e5aae883a8068ba32b2ba84262fa6fbfd8f4..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF812OAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_2.fit.json b/ENCSR553LAZ/cherimoya.fold_2.fit.json deleted file mode 100644 index d5b3ea0ffedb8312d0596fd5f13147fd5174d3e7..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF812OAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_2.log b/ENCSR553LAZ/cherimoya.fold_2.log deleted file mode 100644 index adc01df8ebd5ce8f6602d9b432d565b31b793aaa..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3980 48.596633434295654 8.972116708755493 716.0112915039062 0.8442147374153137 1265.7733154296875 0.7399324774742126 0.69158745 6.362941741943359 True -1 7960 44.076467514038086 7.09618353843689 852.3629150390625 0.7953436374664307 1059.42431640625 0.8167170882225037 0.71387005 1.5719739198684692 True -2 11940 44.0380072593689 16.44706702232361 786.5704345703125 1.16409432888031 1034.5787353515625 0.8226246237754822 0.7143306 0.8056958317756653 True -3 15920 44.074867248535156 0.7872195243835449 778.2379150390625 0.8416321277618408 1027.2745361328125 0.8248127698898315 0.7058695 0.7071326375007629 False -4 19900 44.05343985557556 0.8042347431182861 1073.84228515625 0.8805497884750366 1017.779296875 0.8285312056541443 0.7118605 0.7241352796554565 False -5 23880 44.06008958816528 0.7729454040527344 843.525146484375 0.9031546115875244 1007.141845703125 0.832608699798584 0.7131882 0.7034468054771423 False -6 27860 43.909508228302 0.7742855548858643 1004.1639404296875 0.8667959570884705 999.9703979492188 0.8352577090263367 0.72269166 0.7234269380569458 True -7 31840 43.859238147735596 0.7802760601043701 743.1047973632812 0.9187015295028687 992.59130859375 0.8376032710075378 0.73326457 0.710303783416748 True -8 35820 43.7827467918396 2.583000659942627 859.2913818359375 0.6970340013504028 983.501953125 0.8408134579658508 0.73999596 0.6749789714813232 True -9 39800 43.955666065216064 0.7871494293212891 884.639892578125 0.7071901559829712 976.1582641601562 0.8436827063560486 0.740499 0.6547492742538452 True -10 43780 44.38552737236023 4.523348569869995 744.432861328125 0.7449344396591187 969.0199584960938 0.8461021780967712 0.7462328 0.6494479775428772 True -11 47760 43.90179443359375 0.7811610698699951 806.6060180664062 0.7780632376670837 961.33349609375 0.8484386205673218 0.7559507 0.6264020204544067 True -12 51740 44.00997233390808 0.7851316928863525 691.2369384765625 0.7544206976890564 953.871337890625 0.8511466979980469 0.7633803 0.6073833703994751 True -13 55720 43.95650506019592 2.95205020904541 775.80615234375 0.6629690527915955 948.6296997070312 0.8532181978225708 0.76911217 0.5997975468635559 True -14 59700 43.888630867004395 0.8011441230773926 699.9277954101562 0.7429839372634888 944.37109375 0.8552541136741638 0.7744546 0.5882163047790527 True -15 63680 44.589134216308594 0.7784326076507568 758.1614990234375 0.61823570728302 939.7291870117188 0.8570396304130554 0.7826942 0.5501886010169983 True -16 67660 43.873990535736084 0.7810096740722656 679.88330078125 0.5707880258560181 937.356689453125 0.8579432368278503 0.78627384 0.545985221862793 True -17 71640 43.733068227767944 2.219270944595337 694.6819458007812 0.6536498069763184 938.15625 0.8579649925231934 0.7893441 0.5391236543655396 True -18 75620 43.8623321056366 0.7707498073577881 685.5865478515625 0.40633493661880493 939.523681640625 0.8577008247375488 0.78901523 0.5374230146408081 False -19 79600 43.847283363342285 0.7793211936950684 813.650634765625 0.41344332695007324 939.7243041992188 0.8574615120887756 0.7904088 0.5451961159706116 True diff --git a/ENCSR553LAZ/cherimoya.fold_2.performance.tsv b/ENCSR553LAZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 786833e7b7c98d618c9dfe8bf4d834c528200681..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -939.7243041992188 0.11620383709669113 0.8574614524841309 0.5558155179023743 0.7904087901115417 0.738061785697937 0.5451961159706116 \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_3.evaluate.json b/ENCSR553LAZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1ba16bf25fe1b84d52030266c62abc21485d2044..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF812OAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_3.fit.json b/ENCSR553LAZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 74a801aa3b290fee5b59b19738ddbb77121e2db7..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF812OAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_3.log b/ENCSR553LAZ/cherimoya.fold_3.log deleted file mode 100644 index 8fec36043c34c7011b459d40c59cdcab960a6a1e..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3867 47.21730351448059 5.00933575630188 711.4469604492188 1.2275258302688599 1210.9024658203125 0.7393621802330017 0.6984411 7.799136638641357 True -1 7734 43.311198234558105 0.7537353038787842 914.107666015625 0.8374720215797424 1031.333251953125 0.8126433491706848 0.7060978 2.1165947914123535 True -2 11601 42.469366788864136 1.3940603733062744 847.4840698242188 0.9483003616333008 1006.058837890625 0.8188730478286743 0.70257 1.1050375699996948 False -3 15468 42.52711486816406 2.320188045501709 766.6807861328125 0.8955127596855164 995.8275146484375 0.8218178749084473 0.7055384 0.9644611477851868 False -4 19335 43.13211107254028 15.698975801467896 659.7733764648438 0.7800024151802063 984.7478637695312 0.8258727192878723 0.7056986 0.883817732334137 False -5 23202 42.54797005653381 0.7291429042816162 819.4052734375 0.6761614680290222 976.8839721679688 0.8285530805587769 0.715856 0.8097091317176819 True -6 27069 42.43797302246094 0.7345821857452393 834.24609375 0.8297392129898071 966.2101440429688 0.8318234086036682 0.72229487 0.7351799607276917 True -7 30936 42.45994305610657 0.7550373077392578 713.4370727539062 0.6349483728408813 958.0054931640625 0.8348265886306763 0.7265467 0.669781506061554 True -8 34803 42.450061559677124 0.7282981872558594 670.9768676757812 0.6869820356369019 953.0709838867188 0.8369126915931702 0.73154885 0.6924374103546143 True -9 38670 43.18441605567932 0.7310268878936768 832.8472900390625 0.6890586614608765 947.2645874023438 0.8395376801490784 0.7363336 0.6693575978279114 True -10 42537 42.40308380126953 0.7277321815490723 776.14501953125 1.0081124305725098 939.183349609375 0.8422273397445679 0.73949873 0.6354305148124695 True -11 46404 42.574869871139526 0.7263514995574951 757.4853515625 0.5858434438705444 930.8513793945312 0.8449133634567261 0.75149703 0.6188451647758484 True -12 50271 42.52928066253662 0.7222104072570801 835.9385986328125 0.6615972518920898 925.4669189453125 0.8473370671272278 0.7596223 0.5984023213386536 True -13 54138 42.567973613739014 1.4475696086883545 747.7914428710938 0.8055307269096375 917.7800903320312 0.849670946598053 0.76707923 0.5820868015289307 True -14 58005 42.65083384513855 0.7346627712249756 685.9785766601562 0.5829313397407532 913.4639282226562 0.8517999053001404 0.7745366 0.566504955291748 True -15 61872 42.43688893318176 1.961728572845459 945.8050537109375 0.5645148754119873 908.8843994140625 0.8534935116767883 0.78409266 0.5446935892105103 True -16 65739 42.50442290306091 0.734612226486206 673.6553955078125 0.47281521558761597 906.282470703125 0.8546270728111267 0.79266167 0.5370656847953796 True -17 69606 42.52507734298706 0.7253580093383789 745.9983520507812 0.5407629013061523 906.7398681640625 0.8547378778457642 0.7942811 0.5319815278053284 True -18 73473 42.458094358444214 0.716073751449585 756.200927734375 0.36593201756477356 907.9971313476562 0.8544561266899109 0.7933055 0.532522439956665 False -19 77340 42.569040298461914 0.7306554317474365 731.7119140625 0.4712948203086853 908.71875 0.8541992902755737 0.79237616 0.5370170474052429 False diff --git a/ENCSR553LAZ/cherimoya.fold_3.performance.tsv b/ENCSR553LAZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c3794c9a182b1b18585c94e164e9a9e76c78cec4..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -906.7398681640625 0.12106188386678696 0.8547379374504089 0.5352367758750916 0.7942811250686646 0.7385963201522827 0.5319815278053284 \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_4.evaluate.json b/ENCSR553LAZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 01478b3969e3d5155e9498ac4c5dc4571d20d96b..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF812OAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_4.fit.json b/ENCSR553LAZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 0fe7646003ca910af8e1e98e88d33826c08d49b4..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF812OAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553LAZ/cherimoya.fold_4.log b/ENCSR553LAZ/cherimoya.fold_4.log deleted file mode 100644 index 913129a80d4dfd7eaec5a947e54f8874d1f180bc..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3883 47.72216010093689 4.229830265045166 798.4857177734375 1.4862871170043945 1164.013916015625 0.7294042110443115 0.6730371 7.209832191467285 True -1 7766 42.769333839416504 0.773291826248169 946.9337158203125 1.1591472625732422 983.0689086914062 0.8070728778839111 0.6937166 1.5827947854995728 True -2 11649 42.83660340309143 0.7607893943786621 1050.1614990234375 0.7691852450370789 958.1902465820312 0.8139992952346802 0.68245065 1.0183709859848022 False -3 15532 42.70767259597778 2.4695053100585938 718.4896240234375 0.9799072742462158 945.2509155273438 0.8179377913475037 0.68404835 0.7751677632331848 False -4 19415 42.71948289871216 0.7747604846954346 690.2677001953125 1.096933364868164 936.54736328125 0.8217605948448181 0.68926984 0.6984371542930603 False -5 23298 42.65713095664978 0.7637267112731934 880.097900390625 0.734401285648346 928.837646484375 0.8246024250984192 0.69536644 0.6940447688102722 True -6 27181 42.65893626213074 0.758725643157959 662.6815185546875 1.148934006690979 923.0512084960938 0.8270111680030823 0.69761646 0.6977699398994446 True -7 31064 42.56975793838501 1.7936744689941406 718.1127319335938 0.6518756151199341 917.1006469726562 0.8291788697242737 0.70413923 0.6887167692184448 True -8 34947 42.73154425621033 2.1359758377075195 746.9285278320312 0.6107298135757446 909.8367309570312 0.8324957489967346 0.70846444 0.6668676733970642 True -9 38830 42.65409541130066 0.7620701789855957 791.09033203125 0.6665285229682922 900.9009399414062 0.8355158567428589 0.7133984 0.6409759521484375 True -10 42713 42.70911407470703 0.7561445236206055 820.2498779296875 0.6221622228622437 895.4959716796875 0.8379702568054199 0.7255411 0.6265634298324585 True -11 46596 42.70886182785034 0.7640812397003174 687.4312744140625 0.9838098287582397 887.829833984375 0.8407830595970154 0.72508705 0.6116470098495483 False -12 50479 42.75472092628479 0.7605257034301758 656.5020751953125 0.6226242780685425 882.1229248046875 0.8430727124214172 0.73498416 0.5902702808380127 True -13 54362 42.77589464187622 0.762641191482544 728.8533325195312 0.689800500869751 876.9183959960938 0.845667839050293 0.74740237 0.5738807916641235 True -14 58245 42.795382022857666 1.4964921474456787 755.7901611328125 0.6494563817977905 871.5305786132812 0.8480914235115051 0.7592511 0.5561468601226807 True -15 62128 42.67735171318054 0.757077693939209 748.3289184570312 0.4944472908973694 866.794189453125 0.8498562574386597 0.7684177 0.5412126183509827 True -16 66011 43.103280544281006 0.7704305648803711 655.660400390625 0.4406663179397583 866.4281005859375 0.8506600856781006 0.77412766 0.5265394449234009 True -17 69894 44.085707664489746 0.7601172924041748 704.0780639648438 0.772510826587677 866.0550537109375 0.8508183360099792 0.78025836 0.5184388160705566 True -18 73777 42.829238414764404 0.7656795978546143 659.848388671875 0.42883801460266113 867.0326538085938 0.8506891131401062 0.78053796 0.5128508806228638 True -19 77660 42.83414554595947 0.7663609981536865 677.1256103515625 0.36779123544692993 868.232666015625 0.850530743598938 0.78038245 0.5153524875640869 False diff --git a/ENCSR553LAZ/cherimoya.fold_4.performance.tsv b/ENCSR553LAZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 16129f2c1aead55dd3889ac4736eccf92ac20470..0000000000000000000000000000000000000000 --- a/ENCSR553LAZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -867.0326538085938 0.12467184662818909 0.8506892323493958 0.525398313999176 0.7805379629135132 0.7046005725860596 0.5128508806228638 \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_0.evaluate.json b/ENCSR553WJB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 030f09a203cd1263ba54b6784968a23ca909ae34..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF679BXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_0.fit.json b/ENCSR553WJB/cherimoya.fold_0.fit.json deleted file mode 100644 index 6b12d5e8e1e392c9c1b9c30d50fd51127a637b1c..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF679BXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_0.log b/ENCSR553WJB/cherimoya.fold_0.log deleted file mode 100644 index 7abbbb006a3a0cb1d37640908b0694db3945e8fb..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2011 27.257877826690674 3.9364092350006104 692.7429809570312 0.8605507612228394 1130.48291015625 0.24119757115840912 0.61518985 15.720844268798828 True -1 4022 22.246712684631348 0.5819346904754639 756.312744140625 1.5316908359527588 882.335205078125 0.3791161775588989 0.72790664 7.080935955047607 True -2 6033 22.174264192581177 0.4090127944946289 513.0675048828125 1.3280229568481445 832.036376953125 0.40370973944664 0.74128544 3.450638771057129 True -3 8044 22.106159210205078 0.402538537979126 627.386962890625 1.2916736602783203 809.5863647460938 0.41697371006011963 0.75647867 2.731435775756836 True -4 10055 22.109269857406616 0.4016692638397217 645.3994750976562 1.0806270837783813 794.5662231445312 0.42848169803619385 0.7654072 1.7931574583053589 True -5 12066 22.256297826766968 0.7425916194915771 677.260498046875 0.8963747024536133 789.7615356445312 0.4314987063407898 0.7746634 1.452235221862793 True -6 14077 22.324926614761353 21.214284896850586 621.1956787109375 1.013715147972107 784.5333862304688 0.4349305331707001 0.7836668 1.2752994298934937 True -7 16088 22.392350912094116 0.40703773498535156 516.1940307617188 0.818731427192688 778.8483276367188 0.4379795491695404 0.7883928 1.1624524593353271 True -8 18099 22.235695600509644 0.41526198387145996 541.3297729492188 0.9062515497207642 772.49365234375 0.44272008538246155 0.7912925 1.019651174545288 True -9 20110 22.280776977539062 0.4016389846801758 628.4725341796875 0.6999064683914185 768.0629272460938 0.4433581829071045 0.7969977 0.9473032355308533 True -10 22121 22.42597198486328 0.4082164764404297 518.9954223632812 0.520940899848938 764.8246459960938 0.4475443959236145 0.79958886 0.8771854043006897 True -11 24132 22.20578956604004 0.4129331111907959 623.9000854492188 0.823940634727478 760.0204467773438 0.4509870111942291 0.8057807 0.8465838432312012 True -12 26143 22.727240324020386 10.50341010093689 602.7813720703125 0.8470596075057983 754.252197265625 0.4543623626232147 0.8138979 0.7485373616218567 True -13 28154 21.918394327163696 0.4122500419616699 519.7981567382812 0.7767285108566284 750.943603515625 0.45663824677467346 0.81699085 0.6862989664077759 True -14 30165 21.792776107788086 0.4117727279663086 732.2636108398438 0.6055229306221008 745.6355590820312 0.4590906798839569 0.82288796 0.6599157452583313 True -15 32176 21.753005743026733 0.4099390506744385 646.4260864257812 0.6921133995056152 741.9273071289062 0.4621686637401581 0.8244768 0.6471744775772095 True -16 34187 21.78607487678528 0.3999762535095215 758.8793334960938 0.4993377923965454 743.3807373046875 0.46162623167037964 0.8273647 0.6277428865432739 True -17 36198 21.993492603302002 17.87413716316223 630.0137939453125 0.41633519530296326 743.3488159179688 0.4611762762069702 0.8279629 0.6287967562675476 True -18 38209 22.52241015434265 0.41619205474853516 490.5413818359375 0.7405239939689636 744.8416137695312 0.45979198813438416 0.8273155 0.6323972344398499 False -19 40220 21.765461921691895 0.3985176086425781 644.7283935546875 0.5024152994155884 745.1771240234375 0.4589543640613556 0.8279533 0.6397380232810974 False diff --git a/ENCSR553WJB/cherimoya.fold_0.performance.tsv b/ENCSR553WJB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 728598baec0e0d821b3c994036932d0a3e3ce4b0..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -743.3488159179688 0.3471234142780304 0.4611763060092926 0.20174482464790344 0.8279628753662109 0.77574622631073 0.6287967562675476 \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_1.evaluate.json b/ENCSR553WJB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0666d88b98e26cc44750b50efc05798bb4ed98a6..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF679BXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_1.fit.json b/ENCSR553WJB/cherimoya.fold_1.fit.json deleted file mode 100644 index 100b8b8a3d1b8eed0f9c622da70ec61b4e71999e..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF679BXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_1.log b/ENCSR553WJB/cherimoya.fold_1.log deleted file mode 100644 index af18e970f4eb9c7c594aad78b3d3c1e0c6a795c0..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1953 26.07460045814514 35.58147382736206 749.421630859375 1.6008732318878174 1363.6539306640625 0.24363979697227478 0.59995526 18.59067726135254 True -1 3906 21.616246223449707 0.6092078685760498 576.45166015625 0.9853070378303528 1095.132080078125 0.3755309283733368 0.71707976 8.632265090942383 True -2 5859 21.458999156951904 2.953549385070801 719.461181640625 1.3657057285308838 979.2483520507812 0.4191756844520569 0.7561498 4.227668762207031 True -3 7812 21.522927284240723 0.5651659965515137 702.6499633789062 1.1352676153182983 953.462890625 0.42998814582824707 0.7705805 2.7950916290283203 True -4 9765 21.505066394805908 6.5711023807525635 637.7160034179688 0.9520550966262817 941.2281494140625 0.43832144141197205 0.7753887 2.216413974761963 True -5 11718 21.490769147872925 0.5701477527618408 614.4600830078125 1.142455816268921 932.443115234375 0.4441318213939667 0.7734103 1.890200138092041 False -6 13671 21.461007595062256 0.5690040588378906 622.30615234375 0.9271537065505981 925.3010864257812 0.4481533467769623 0.7813826 1.6288962364196777 True -7 15624 21.476378679275513 0.5584893226623535 557.6486206054688 0.7075456380844116 920.620361328125 0.45071569085121155 0.78620577 1.409744143486023 True -8 17577 21.491490364074707 0.5633049011230469 808.710205078125 0.5976806282997131 912.7208251953125 0.4546823799610138 0.79544497 1.226595401763916 True -9 19530 21.478250980377197 0.6746354103088379 577.940185546875 0.6325392723083496 906.4334716796875 0.4583766758441925 0.801295 1.1039454936981201 True -10 21483 21.455446481704712 0.5698964595794678 595.9000854492188 0.6318742036819458 897.239990234375 0.461740642786026 0.8109684 0.9439345002174377 True -11 23436 21.44392228126526 1.2337830066680908 659.9362182617188 0.7068504095077515 893.3406372070312 0.4621458649635315 0.816721 0.917793869972229 True -12 25389 21.635218858718872 0.5734565258026123 717.3905029296875 0.6939250230789185 885.6359252929688 0.4665638506412506 0.82315046 0.859542191028595 True -13 27342 21.535964250564575 2.1906583309173584 618.1502685546875 0.6377637982368469 881.014404296875 0.46829962730407715 0.8303462 0.7888811230659485 True -14 29295 21.507375240325928 0.6439740657806396 741.3402099609375 0.5721728801727295 873.7733154296875 0.47272729873657227 0.83764786 0.7399780750274658 True -15 31248 21.470957279205322 0.578641414642334 651.4957885742188 0.5384329557418823 869.0101928710938 0.4752591550350189 0.84212196 0.7025899291038513 True -16 33201 21.4681453704834 0.584728479385376 708.426513671875 0.6456741094589233 868.6779174804688 0.47422921657562256 0.846105 0.6811679005622864 True -17 35154 21.483025789260864 0.5662052631378174 480.56451416015625 0.385492205619812 871.0029296875 0.4724578261375427 0.8458161 0.6747269630432129 False -18 37107 21.492794513702393 1.0627708435058594 505.96759033203125 0.4287620782852173 874.0867309570312 0.46981263160705566 0.846129 0.6751749515533447 True -19 39060 21.47425365447998 0.5712108612060547 621.02197265625 0.510208010673523 875.3627319335938 0.469178169965744 0.845244 0.6769596934318542 False diff --git a/ENCSR553WJB/cherimoya.fold_1.performance.tsv b/ENCSR553WJB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a8f08523600cc0793e99d334e94ab71bd84e4108..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -874.0867309570312 0.3321286141872406 0.46981263160705566 0.22849518060684204 0.8461290001869202 0.8141521215438843 0.6751749515533447 \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_2.evaluate.json b/ENCSR553WJB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 38811ea132ab8e6ae26c2ce43b851262df4369a3..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF679BXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_2.fit.json b/ENCSR553WJB/cherimoya.fold_2.fit.json deleted file mode 100644 index 761bda15ccad3bb07b3b3409220bbec6997e97fc..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF679BXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_2.log b/ENCSR553WJB/cherimoya.fold_2.log deleted file mode 100644 index 6e6b15a50334c481143467804fa9c2fe774bbc10..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2112 28.036999940872192 6.305994749069214 820.9002685546875 1.1689295768737793 1179.779296875 0.23704326152801514 0.5729516 16.940975189208984 True -1 4224 22.851723670959473 0.45403432846069336 574.30029296875 0.7261413335800171 919.5839233398438 0.37335771322250366 0.7155267 6.670260906219482 True -2 6336 23.253279209136963 0.4273693561553955 812.2603149414062 0.936324954032898 857.8912963867188 0.39273297786712646 0.7489432 3.2156200408935547 True -3 8448 23.335461378097534 4.407966375350952 670.7651977539062 0.8084425926208496 836.1386108398438 0.4069908857345581 0.7611091 2.518662929534912 True -4 10560 23.28208565711975 0.4270896911621094 690.701171875 0.9288819432258606 819.8331298828125 0.4181627929210663 0.7670004 1.9656498432159424 True -5 12672 23.280015230178833 0.4296596050262451 593.48974609375 1.1581830978393555 809.8345947265625 0.4228511154651642 0.7734505 1.4003583192825317 True -6 14784 23.279927730560303 15.355199813842773 535.5948486328125 0.7664816379547119 804.7044677734375 0.42715877294540405 0.7756979 1.1477537155151367 True -7 16896 24.044918298721313 0.44550347328186035 749.6394653320312 0.9798586368560791 801.95703125 0.4285714328289032 0.77936256 1.0735116004943848 True -8 19008 23.344717264175415 13.01302456855774 684.106201171875 0.699077308177948 796.2185668945312 0.4307733178138733 0.78408563 1.0157489776611328 True -9 21120 23.402562379837036 0.4279305934906006 669.6192626953125 0.9757216572761536 789.9664306640625 0.4354546070098877 0.79032224 0.893278956413269 True -10 23232 23.512775421142578 7.3504319190979 457.6918029785156 0.5994588136672974 785.31982421875 0.4381349980831146 0.793518 0.8177708983421326 True -11 25344 23.28306818008423 0.4302799701690674 583.275146484375 0.5252042412757874 779.7923583984375 0.44104883074760437 0.800057 0.7933731079101562 True -12 27456 23.38166117668152 0.4284946918487549 484.2415466308594 0.9400768280029297 776.0001220703125 0.4434472322463989 0.807242 0.7486923336982727 True -13 29568 23.34287691116333 0.42271971702575684 583.6575317382812 0.6224420666694641 770.863037109375 0.4468882083892822 0.8124289 0.7149127721786499 True -14 31680 23.274441719055176 0.4228966236114502 731.941650390625 0.5643907785415649 767.7857055664062 0.4499353766441345 0.8157531 0.6970610022544861 True -15 33792 23.280090808868408 0.42229199409484863 583.5220947265625 0.8446123003959656 768.5131225585938 0.4483018219470978 0.8190505 0.6844392418861389 True -16 35904 23.261558532714844 0.42402172088623047 459.5946044921875 0.45054489374160767 767.7249145507812 0.45013517141342163 0.8237952 0.6748682260513306 True -17 38016 23.255229711532593 0.4220592975616455 564.236572265625 0.768203616142273 765.5714111328125 0.45180240273475647 0.8230609 0.6705885529518127 False -18 40128 23.26203942298889 0.42740345001220703 586.4812622070312 0.4551432132720947 768.345458984375 0.44969817996025085 0.82260615 0.6754147410392761 False -19 42240 23.27322220802307 0.45320677757263184 499.91259765625 0.3945714235305786 767.4948120117188 0.45096078515052795 0.82167184 0.6789554953575134 False diff --git a/ENCSR553WJB/cherimoya.fold_2.performance.tsv b/ENCSR553WJB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4c4afe517c88811d34bfc54ec44e321b9adc8a50..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -767.7249145507812 0.35034024715423584 0.45013517141342163 0.20696072280406952 0.8237951993942261 0.773111879825592 0.6748682260513306 \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_3.evaluate.json b/ENCSR553WJB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 422ed28a8f16a06963b516d7edd1b0e44c52b26c..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF679BXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_3.fit.json b/ENCSR553WJB/cherimoya.fold_3.fit.json deleted file mode 100644 index 8113521c596402ec5d6669032f66910dbf12695c..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF679BXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_3.log b/ENCSR553WJB/cherimoya.fold_3.log deleted file mode 100644 index 72729a45fecd15395c0ffc64c9afee6895feb8da..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2020 27.277597427368164 3.4689884185791016 638.548828125 1.3455501794815063 1147.6917724609375 0.2550812363624573 0.5974197 16.239988327026367 True -1 4040 22.392308235168457 0.4224965572357178 709.0106811523438 0.8368631601333618 912.0729370117188 0.3820326030254364 0.7260064 6.588616371154785 True -2 6060 22.411540269851685 28.620440006256104 642.1419677734375 1.0198618173599243 855.2214965820312 0.40791085362434387 0.74047863 3.2758400440216064 True -3 8080 24.541021585464478 0.4124305248260498 586.5125732421875 0.6174296140670776 833.3313598632812 0.41973215341567993 0.7526677 2.48688006401062 True -4 10100 22.210569381713867 0.40758752822875977 780.173095703125 0.8410833477973938 822.5800170898438 0.4266664385795593 0.7557085 2.2945470809936523 True -5 12120 21.92647075653076 0.40251660346984863 685.614501953125 0.6407948136329651 815.5350341796875 0.4321618974208832 0.7626309 1.8283716440200806 True -6 14140 21.77634048461914 0.4053072929382324 752.0347900390625 1.1468052864074707 806.9324340820312 0.43803584575653076 0.7719348 1.4911916255950928 True -7 16160 21.728825092315674 0.4048879146575928 763.6904907226562 1.0270057916641235 801.1886596679688 0.4404987692832947 0.77928424 1.298117995262146 True -8 18180 21.7490713596344 0.40630578994750977 614.4468994140625 1.0480263233184814 796.9797973632812 0.4427400231361389 0.7817716 1.1369537115097046 True -9 20200 21.79611587524414 0.4048640727996826 677.1781005859375 0.8653163909912109 787.4006958007812 0.4504886567592621 0.78691757 1.016463279724121 True -10 22220 21.822983980178833 0.40373897552490234 565.4351196289062 0.8622446060180664 783.7801513671875 0.4538496434688568 0.78830606 0.9620726704597473 True -11 24240 21.880681037902832 0.4063131809234619 510.3671875 0.6434905529022217 780.4364624023438 0.4531466066837311 0.7942503 0.9179487228393555 True -12 26260 21.842180728912354 0.40429043769836426 687.614501953125 0.45904892683029175 773.81689453125 0.45749056339263916 0.8036448 0.839699387550354 True -13 28280 21.815675735473633 0.40079617500305176 697.8470458984375 0.6303318738937378 769.659912109375 0.4600571095943451 0.8089271 0.7898994088172913 True -14 30300 22.37899684906006 19.46709632873535 533.1181640625 0.593117356300354 767.6054077148438 0.4609247148036957 0.8157999 0.7564716339111328 True -15 32320 25.672467947006226 21.75681734085083 585.4107666015625 0.6363920569419861 763.2590942382812 0.46466389298439026 0.8215344 0.7220163941383362 True -16 34340 22.048014402389526 18.802310466766357 614.8338623046875 0.5436481237411499 764.5406494140625 0.4626069962978363 0.8250405 0.6987384557723999 True -17 36360 22.55321192741394 0.4165775775909424 613.604736328125 0.5422167778015137 764.776611328125 0.46295419335365295 0.8282669 0.694067656993866 True -18 38380 21.869502544403076 0.4087865352630615 567.3977661132812 0.46913447976112366 765.3870239257812 0.4618460536003113 0.8253341 0.7010360956192017 False -19 40400 21.760097980499268 0.6753735542297363 659.7105712890625 0.4526880085468292 767.2625122070312 0.45997676253318787 0.8259902 0.7028811573982239 False diff --git a/ENCSR553WJB/cherimoya.fold_3.performance.tsv b/ENCSR553WJB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 21eeda289e62df2b159e7954e0536641521a39a6..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -764.776611328125 0.34251055121421814 0.46295425295829773 0.21268630027770996 0.8282669186592102 0.7783902883529663 0.694067656993866 \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_4.evaluate.json b/ENCSR553WJB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 799817ca76176f202e060530e3e5106ffc5fd8cd..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF679BXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_4.fit.json b/ENCSR553WJB/cherimoya.fold_4.fit.json deleted file mode 100644 index a9abf06ac95dc4f7180641d736a34ebd80e145c2..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF679BXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR553WJB/cherimoya.fold_4.log b/ENCSR553WJB/cherimoya.fold_4.log deleted file mode 100644 index e5f99f9ee58a5c2a5ea548d5c65d28033dda2172..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2010 26.471808195114136 3.4872570037841797 579.6686401367188 0.965402364730835 1068.312255859375 0.23788617551326752 0.60616136 15.69108772277832 True -1 4020 22.179216623306274 0.3888404369354248 586.5936279296875 1.2070163488388062 862.3580322265625 0.3670215308666229 0.714564 6.501578330993652 True -2 6030 22.112982034683228 0.38415980339050293 737.180419921875 0.8048397302627563 796.6246948242188 0.4016549289226532 0.7316719 3.132810115814209 True -3 8040 22.105433702468872 0.7728636264801025 811.289306640625 0.961707353591919 770.2474975585938 0.4152008891105652 0.7561373 2.1296496391296387 True -4 10050 22.246909856796265 0.3889164924621582 777.1497192382812 0.800753653049469 761.6302490234375 0.42170748114585876 0.75670457 1.6970794200897217 True -5 12060 22.11154866218567 0.37977051734924316 656.1560668945312 0.912147045135498 753.9548950195312 0.4276260435581207 0.7596013 1.470479130744934 True -6 14070 22.152008056640625 18.270402193069458 619.1505737304688 0.7999445796012878 748.951904296875 0.43014952540397644 0.76837796 1.2188795804977417 True -7 16080 23.391966104507446 0.38475871086120605 538.7214965820312 0.9744378924369812 745.2506713867188 0.4319722652435303 0.7762714 1.0924268960952759 True -8 18090 22.18910312652588 0.3867676258087158 743.74658203125 0.922243595123291 739.31689453125 0.4363600015640259 0.78343076 1.005892276763916 True -9 20100 22.118873119354248 0.37505531311035156 556.910400390625 0.6413609981536865 736.884765625 0.439760684967041 0.78481454 0.9119048118591309 True -10 22110 22.20228147506714 0.38193821907043457 529.5896606445312 1.0970735549926758 732.3646850585938 0.4430265426635742 0.79264563 0.8436169028282166 True -11 24120 22.15871500968933 0.37403368949890137 641.0330810546875 0.7052823305130005 728.2183227539062 0.4451844096183777 0.797857 0.7879805564880371 True -12 26130 22.15347146987915 12.307231903076172 633.7949829101562 0.642457902431488 724.5552368164062 0.44678157567977905 0.80683047 0.7194796204566956 True -13 28140 22.93223547935486 15.919511556625366 804.222412109375 0.6902214288711548 716.5235595703125 0.4525711238384247 0.8102151 0.6763900518417358 True -14 30150 24.423749446868896 27.315112352371216 437.87750244140625 0.5874152779579163 714.5105590820312 0.45336222648620605 0.8185299 0.6451115012168884 True -15 32160 24.095500707626343 15.341530084609985 764.5447387695312 0.6984437108039856 715.195556640625 0.45262840390205383 0.8242478 0.6251470446586609 True -16 34170 21.749005794525146 0.3773365020751953 688.0802001953125 0.27910757064819336 713.59619140625 0.4539073705673218 0.8281916 0.6076568961143494 True -17 36180 21.678574562072754 0.37233495712280273 668.32421875 0.44721683859825134 713.5648803710938 0.453922301530838 0.8289501 0.6023651361465454 True -18 38190 21.70538306236267 0.37465476989746094 474.35577392578125 0.35773032903671265 712.97216796875 0.45511940121650696 0.8298021 0.6048144102096558 True -19 40200 21.710168600082397 0.3731813430786133 504.7201232910156 0.4572024941444397 714.6929321289062 0.4540805518627167 0.8291522 0.6078007817268372 False diff --git a/ENCSR553WJB/cherimoya.fold_4.performance.tsv b/ENCSR553WJB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8642a0d3195424b79d86d0462a9d5c2273719b25..0000000000000000000000000000000000000000 --- a/ENCSR553WJB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -712.97216796875 0.3515508472919464 0.45511940121650696 0.19981759786605835 0.8298020958900452 0.7807335257530212 0.6048144102096558 \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_0.evaluate.json b/ENCSR554WUJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7206a92f466fe2a7553da5b0818b0ba5c5d725a8..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390POS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_0.fit.json b/ENCSR554WUJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 8d6bd59fe4c2ebfd805f5053759209382917e8c3..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF390POS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_0.log b/ENCSR554WUJ/cherimoya.fold_0.log deleted file mode 100644 index 13bd1484da88e691c27d272b264c9136e5f6ad60..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 33.93526649475098 4.6866960525512695 255.06918334960938 0.7093558311462402 372.3889465332031 0.1912030130624771 0.63517636 3.593766927719116 True -1 5490 30.318766355514526 0.5706515312194824 242.06341552734375 0.5627409219741821 349.176513671875 0.27019453048706055 0.68050694 1.2816407680511475 True -2 8235 30.33546257019043 1.2049813270568848 254.59246826171875 0.45230424404144287 342.072265625 0.28844648599624634 0.68480366 0.6959062814712524 True -3 10980 30.375221252441406 1.2065861225128174 259.4571533203125 0.5159989595413208 339.31243896484375 0.29537224769592285 0.69101745 0.7748019099235535 True -4 13725 30.35865592956543 3.030794620513916 283.43267822265625 0.600922703742981 337.219482421875 0.3019065260887146 0.70371974 0.7507375478744507 True -5 16470 30.33751916885376 2.065012216567993 251.3412628173828 0.6401579976081848 336.02777099609375 0.30665820837020874 0.70393413 0.772028923034668 True -6 19215 30.33951210975647 1.5775094032287598 235.59637451171875 1.0187321901321411 335.2255859375 0.30950960516929626 0.7085406 0.720868706703186 True -7 21960 30.25514578819275 1.3905301094055176 229.89593505859375 0.500765323638916 334.4621276855469 0.3114488422870636 0.7082895 0.6747285723686218 False -8 24705 30.244840621948242 1.5908129215240479 274.8000183105469 0.799486517906189 333.3876037597656 0.3160298764705658 0.71345764 0.6211910247802734 True -9 27450 30.217108249664307 2.5387847423553467 233.34629821777344 0.5794405937194824 332.77752685546875 0.3178475797176361 0.7159421 0.6029736995697021 True -10 30195 30.262627601623535 1.115978717803955 291.06243896484375 0.47372502088546753 331.7342834472656 0.32157447934150696 0.7217472 0.5340880155563354 True -11 32940 30.244741916656494 1.43381929397583 244.72149658203125 0.4418675899505615 331.1694030761719 0.322773814201355 0.72518075 0.5181047320365906 True -12 35685 30.263622999191284 1.6641526222229004 203.4696502685547 0.3709416091442108 330.429931640625 0.32546305656433105 0.72839105 0.47739335894584656 True -13 38430 30.334853649139404 1.3352820873260498 271.9949951171875 0.4113956689834595 329.75775146484375 0.32817602157592773 0.73818815 0.444647878408432 True -14 41175 30.30347490310669 22.42698884010315 286.7002258300781 0.5143939256668091 329.01812744140625 0.3306525647640228 0.74521554 0.4085814356803894 True -15 43920 30.322588205337524 21.252654790878296 256.8260498046875 0.4119791090488434 328.77777099609375 0.3309524357318878 0.75225127 0.38246291875839233 True -16 46665 30.40589451789856 0.5714967250823975 255.66737365722656 0.3512763977050781 328.1000061035156 0.33265435695648193 0.75536007 0.3614717125892639 True -17 49410 30.68439555168152 0.5638914108276367 278.8995056152344 0.3960437774658203 327.7191162109375 0.33379870653152466 0.7601311 0.3453088402748108 True -18 52155 30.891032457351685 4.828531980514526 237.91619873046875 0.30000120401382446 327.9315490722656 0.33341726660728455 0.76045245 0.33856290578842163 True -19 54900 30.31873655319214 0.566157341003418 239.3206787109375 0.33322277665138245 327.90606689453125 0.3329051733016968 0.7607432 0.3379174470901489 True diff --git a/ENCSR554WUJ/cherimoya.fold_0.performance.tsv b/ENCSR554WUJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4a950591a325069ee85f73b498a029d6f1824d1e..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -327.90606689453125 0.45965179800987244 0.3329051733016968 0.0930013507604599 0.7607432007789612 0.7058097720146179 0.3379174470901489 \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_1.evaluate.json b/ENCSR554WUJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f2849c06f3a1413289f866b6b13d140b64a189ca..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390POS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_1.fit.json b/ENCSR554WUJ/cherimoya.fold_1.fit.json deleted file mode 100644 index b97b33f7a173d79fdc1a3c1e97a7d5902fd08ba2..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF390POS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_1.log b/ENCSR554WUJ/cherimoya.fold_1.log deleted file mode 100644 index 720f42c29dea9e30e56d17cbd19b6b64caa9db70..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 33.62970423698425 4.250119209289551 264.5868835449219 0.8953399658203125 417.5452575683594 0.1939823478460312 0.6357349 4.056880474090576 True -1 5410 29.902928113937378 0.8838510513305664 262.7212829589844 0.6836756467819214 386.16156005859375 0.2861019968986511 0.694204 1.638521432876587 True -2 8115 29.86795973777771 0.7113983631134033 297.37933349609375 0.4292489290237427 378.7647399902344 0.30308082699775696 0.7000162 0.981957197189331 True -3 10820 29.800420999526978 0.8028967380523682 212.40614318847656 0.737499475479126 375.0498352050781 0.31151920557022095 0.7104725 0.950503945350647 True -4 13525 29.7830331325531 0.7076947689056396 315.89056396484375 0.8118203282356262 373.3841247558594 0.31537699699401855 0.7156945 0.8941807746887207 True -5 16230 29.89622974395752 0.7179872989654541 274.7542724609375 0.8061460852622986 371.49749755859375 0.32193830609321594 0.7229318 0.8414686918258667 True -6 18935 29.790868759155273 0.6930608749389648 243.90774536132812 0.615319013595581 370.72271728515625 0.32347410917282104 0.7235221 0.7813299894332886 True -7 21640 29.734720945358276 1.416835069656372 255.89013671875 0.5164132714271545 369.4560546875 0.32739198207855225 0.7308407 0.7103493809700012 True -8 24345 29.82884907722473 0.712458610534668 271.3746337890625 0.700716495513916 368.9548645019531 0.32826632261276245 0.7319371 0.7307313680648804 True -9 27050 29.746297359466553 1.9725935459136963 255.82110595703125 0.7861965894699097 367.4641418457031 0.3334997892379761 0.7416284 0.5661013126373291 True -10 29755 29.86354947090149 0.7102854251861572 263.66461181640625 0.5746747255325317 366.8553161621094 0.33527910709381104 0.7420564 0.5946464538574219 True -11 32460 29.777694702148438 0.721529483795166 313.41949462890625 0.5294795036315918 365.2184753417969 0.3395204544067383 0.74444884 0.5693954229354858 True -12 35165 29.772974252700806 0.7106525897979736 199.64434814453125 0.5438628792762756 364.6434631347656 0.34117886424064636 0.7523209 0.5181858539581299 True -13 37870 29.808558702468872 0.7033307552337646 211.40447998046875 0.31259363889694214 363.5499572753906 0.34412115812301636 0.76060945 0.4855550229549408 True -14 40575 29.781158685684204 0.7100203037261963 250.16835021972656 0.3392828702926636 363.21844482421875 0.34421369433403015 0.7675289 0.4484938383102417 True -15 43280 29.76200580596924 1.6154119968414307 235.60882568359375 0.38578715920448303 362.19439697265625 0.3463284969329834 0.77375597 0.4255484640598297 True -16 45985 29.855792999267578 0.7150363922119141 271.0614929199219 0.3532812297344208 361.7418212890625 0.3483760952949524 0.7775568 0.4019957184791565 True -17 48690 29.877195596694946 0.7096419334411621 235.2518310546875 0.372671902179718 361.65301513671875 0.3488468825817108 0.7801724 0.3818463981151581 True -18 51395 29.930103063583374 0.711010217666626 249.62677001953125 0.31958243250846863 361.5858459472656 0.3488059937953949 0.78171515 0.3749689757823944 True -19 54100 29.85680603981018 1.582061529159546 245.70388793945312 0.6078492403030396 362.0860595703125 0.34854474663734436 0.7810645 0.3747827410697937 False diff --git a/ENCSR554WUJ/cherimoya.fold_1.performance.tsv b/ENCSR554WUJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 15b86cf4a09a6311ade610a063c7f3cda335ff49..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.5858459472656 0.4450792968273163 0.3488060534000397 0.10794961452484131 0.7817151546478271 0.747340738773346 0.3749689757823944 \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_2.evaluate.json b/ENCSR554WUJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e30d743031f989fce05b99411f7f04f10939f768..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390POS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_2.fit.json b/ENCSR554WUJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 6f3396a0cacb5229e03b15fdb2d350445623a129..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF390POS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_2.log b/ENCSR554WUJ/cherimoya.fold_2.log deleted file mode 100644 index 40fbd72ab82225d5830ac078674a6b309c7188c9..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 37.598350524902344 3.5632436275482178 266.3755187988281 0.8223605155944824 381.4678649902344 0.19389356672763824 0.6196049 3.068695306777954 True -1 5742 31.76724886894226 1.0165221691131592 311.20526123046875 1.0005841255187988 355.4834899902344 0.2772883176803589 0.6656691 1.1800999641418457 True -2 8613 31.891228914260864 0.6202113628387451 284.49774169921875 0.7505616545677185 350.17840576171875 0.29144373536109924 0.68470615 0.9260339736938477 True -3 11484 31.752737522125244 0.5377399921417236 293.0982666015625 0.4667457938194275 346.9794616699219 0.29707425832748413 0.6901381 0.6545854210853577 True -4 14355 31.685255527496338 2.5974111557006836 271.74761962890625 0.8179669976234436 344.2026672363281 0.30714380741119385 0.70018417 0.6350745558738708 True -5 17226 31.711803197860718 0.5516433715820312 303.01806640625 0.7527159452438354 343.32623291015625 0.30886122584342957 0.70521003 0.685598611831665 True -6 20097 31.634533405303955 0.5561738014221191 245.29019165039062 0.6906567811965942 342.6950378417969 0.3106907308101654 0.7072813 0.7041378021240234 True -7 22968 31.772498846054077 0.560309648513794 237.64535522460938 0.4366376996040344 341.5433654785156 0.3149702250957489 0.7124314 0.6674700975418091 True -8 25839 31.850136518478394 0.5858705043792725 280.51336669921875 0.7607145309448242 340.717529296875 0.31722015142440796 0.7122636 0.6584377288818359 False -9 28710 31.752038955688477 0.5494191646575928 252.85171508789062 0.6292982697486877 339.21112060546875 0.32270342111587524 0.714785 0.6714179515838623 True -10 31581 31.765875101089478 1.3277690410614014 299.7695007324219 0.3389219641685486 338.6119079589844 0.3248312175273895 0.7201461 0.6101335883140564 True -11 34452 31.801397562026978 0.675093412399292 259.75201416015625 0.5527368187904358 338.2078552246094 0.3254251182079315 0.7193327 0.5640398859977722 False -12 37323 31.7693452835083 0.5296669006347656 289.2389831542969 0.5076054334640503 337.2757263183594 0.3288393020629883 0.7262943 0.5321671962738037 True -13 40194 31.78746461868286 0.5569107532501221 238.5829620361328 0.5660412311553955 336.2580261230469 0.33136242628097534 0.73351914 0.48640015721321106 True -14 43065 31.660785913467407 0.5301840305328369 281.2322082519531 0.36914050579071045 335.4178466796875 0.3340796232223511 0.7422931 0.433936208486557 True -15 45936 31.653660535812378 18.870333194732666 263.6392822265625 0.30720317363739014 335.1082458496094 0.33499348163604736 0.7491538 0.4048651456832886 True -16 48807 31.80188822746277 16.094505786895752 248.40603637695312 0.4642970561981201 334.7547607421875 0.3363024890422821 0.75262636 0.39046457409858704 True -17 51678 31.679820775985718 0.7467067241668701 288.4360046386719 0.40333980321884155 334.57171630859375 0.3371889591217041 0.75713116 0.3761782646179199 True -18 54549 31.7080020904541 0.5181005001068115 246.38131713867188 0.406396746635437 334.6639709472656 0.33666086196899414 0.7560673 0.37285247445106506 False -19 57420 31.71524429321289 17.687188148498535 263.2391357421875 0.30415770411491394 334.46832275390625 0.3376048803329468 0.7561581 0.3745495080947876 False diff --git a/ENCSR554WUJ/cherimoya.fold_2.performance.tsv b/ENCSR554WUJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6e4d7f2ddc089389cfd39178323dbea529beff6e..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -334.57171630859375 0.45619216561317444 0.3371889591217041 0.09561373293399811 0.7571311593055725 0.7131205797195435 0.3761782646179199 \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_3.evaluate.json b/ENCSR554WUJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5dd5e770d8a3b4fff25a241efdc224fb25cb28a2..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390POS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_3.fit.json b/ENCSR554WUJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 17b4e91aea4f7d4f1de4cde29022ced3434b79a4..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF390POS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_3.log b/ENCSR554WUJ/cherimoya.fold_3.log deleted file mode 100644 index fe508ede4d016d9b8c69c7479288d29544b6ae57..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 34.316575050354004 3.8463516235351562 239.44384765625 0.8356869220733643 392.98681640625 0.19116663932800293 0.6363083 4.264710426330566 True -1 5518 30.497315645217896 0.5692145824432373 248.01268005371094 0.8547189235687256 368.8621826171875 0.2727356255054474 0.6838298 1.8787803649902344 True -2 8277 31.20505690574646 7.108395099639893 269.45635986328125 0.800196647644043 363.2491760253906 0.28665101528167725 0.6863854 1.112196683883667 True -3 11036 30.4930522441864 18.98992896080017 257.1000061035156 0.8095117211341858 359.5066833496094 0.2951310873031616 0.69633865 0.7707683444023132 True -4 13795 30.44933247566223 1.7788877487182617 305.3288879394531 0.8131906986236572 357.52008056640625 0.30122870206832886 0.69749427 0.785248875617981 True -5 16554 30.518077850341797 1.3314564228057861 252.41326904296875 0.8109246492385864 355.83184814453125 0.3067695200443268 0.70188403 0.7358462810516357 True -6 19313 30.50003957748413 1.2988483905792236 221.34503173828125 0.6855859756469727 355.0611267089844 0.30865395069122314 0.707858 0.6632947325706482 True -7 22072 30.438441038131714 1.1198616027832031 283.1546630859375 0.543485701084137 353.65264892578125 0.3133530020713806 0.7134361 0.6901460886001587 True -8 24831 30.437436819076538 1.1038053035736084 218.97479248046875 0.5699983835220337 353.41729736328125 0.31519341468811035 0.71285903 0.6802113652229309 False -9 27590 30.417309999465942 1.0101337432861328 262.411376953125 0.5056339502334595 351.97869873046875 0.32026389241218567 0.7173875 0.6249054670333862 True -10 30349 30.497303009033203 1.9251458644866943 257.3416442871094 0.3935183882713318 351.10296630859375 0.3216959238052368 0.7209576 0.6262848377227783 True -11 33108 30.521270513534546 1.8956756591796875 259.1495666503906 0.44855624437332153 350.88226318359375 0.3226076662540436 0.7260134 0.5862389802932739 True -12 35867 30.51986336708069 1.441962480545044 256.85064697265625 0.34550076723098755 349.70941162109375 0.32686883211135864 0.7378094 0.542332112789154 True -13 38626 30.533799171447754 2.286461114883423 260.1487731933594 0.5292665362358093 349.14056396484375 0.3286842703819275 0.7412693 0.4883309304714203 True -14 41385 30.566698789596558 14.576660871505737 239.5277862548828 0.41067636013031006 348.4837341308594 0.3293214440345764 0.7508806 0.444102942943573 True -15 44144 30.558745622634888 21.9968159198761 259.46685791015625 0.39475545287132263 348.6117248535156 0.32969748973846436 0.76140076 0.40301695466041565 True -16 46903 31.43005061149597 0.5734801292419434 247.23167419433594 0.3297598958015442 347.3917541503906 0.3331177830696106 0.7671418 0.3755119740962982 True -17 49662 30.691550493240356 0.5509905815124512 254.20806884765625 0.3235536217689514 347.5044860839844 0.332854688167572 0.7730496 0.35628148913383484 True -18 52421 30.575595378875732 0.5486690998077393 313.24444580078125 0.2997702956199646 347.3462829589844 0.3314158320426941 0.77400243 0.3524690866470337 True -19 55180 30.543081998825073 0.5530250072479248 227.57168579101562 0.24698561429977417 347.59613037109375 0.3317627012729645 0.77431035 0.3525772988796234 True diff --git a/ENCSR554WUJ/cherimoya.fold_3.performance.tsv b/ENCSR554WUJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fb821c8892ef207cd11837533e1f038cb4aeeaee..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -347.59613037109375 0.4555746614933014 0.33176276087760925 0.09853605926036835 0.7743103504180908 0.7226751446723938 0.3525772988796234 \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_4.evaluate.json b/ENCSR554WUJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fc41dda935d9b8cd583f621c0ed34d1d94d14231..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF390POS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_4.fit.json b/ENCSR554WUJ/cherimoya.fold_4.fit.json deleted file mode 100644 index c162ffd3ffb0ef574b09fcd163433ec1380275b2..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF390POS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR554WUJ/cherimoya.fold_4.log b/ENCSR554WUJ/cherimoya.fold_4.log deleted file mode 100644 index 4bf7c63c649e3829caf1f5b5a6a9083be963f8dd..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2823 34.95054817199707 3.912090539932251 273.50689697265625 0.832138180732727 366.8363037109375 0.18813931941986084 0.6226442 3.119763135910034 True -1 5646 31.161885738372803 0.608130931854248 277.29791259765625 0.9564938545227051 344.4361877441406 0.2647312879562378 0.6683486 0.995257556438446 True -2 8469 31.132249116897583 0.5937323570251465 245.14588928222656 0.6570677161216736 340.3199462890625 0.2759144604206085 0.67894226 0.7566184401512146 True -3 11292 31.110979795455933 0.6295912265777588 283.39373779296875 0.7501673102378845 336.8873596191406 0.28599345684051514 0.6831691 0.6144936680793762 True -4 14115 31.100266695022583 0.6035025119781494 213.30905151367188 0.7225122451782227 335.3892822265625 0.29073694348335266 0.68575495 0.6782187819480896 True -5 16938 31.13440752029419 0.6018567085266113 354.68096923828125 0.43963122367858887 334.4001770019531 0.29375267028808594 0.6874765 0.7896868586540222 True -6 19761 31.069803953170776 0.6066160202026367 277.484375 0.5997470617294312 333.285400390625 0.29875296354293823 0.68754935 0.8728658556938171 True -7 22584 31.03459620475769 0.6075575351715088 234.5316162109375 0.6394774913787842 332.1081237792969 0.3029278814792633 0.6959531 0.8817630410194397 True -8 25407 31.09989356994629 0.6059315204620361 269.2450256347656 0.589255690574646 331.9339599609375 0.3025151491165161 0.6966775 0.8050431609153748 True -9 28230 31.145179748535156 0.6074659824371338 275.0623474121094 0.39093875885009766 330.2225646972656 0.30918824672698975 0.703092 0.8048139214515686 True -10 31053 31.128408193588257 0.6036851406097412 251.07345581054688 0.33873870968818665 329.51873779296875 0.31176504492759705 0.7071453 0.7522242665290833 True -11 33876 31.174827098846436 2.192394733428955 225.8265838623047 0.47106966376304626 329.2532653808594 0.3119138181209564 0.713144 0.6590428948402405 True -12 36699 31.13334321975708 0.6123392581939697 236.76425170898438 0.8183696269989014 328.07818603515625 0.3166896402835846 0.7192603 0.612544059753418 True -13 39522 31.114545345306396 0.60711669921875 252.78485107421875 0.4478551745414734 327.4057922363281 0.3185766339302063 0.72600746 0.5194731950759888 True -14 42345 31.14666175842285 9.71297025680542 315.1918640136719 0.4480361044406891 326.6971130371094 0.3206230103969574 0.7354428 0.44807133078575134 True -15 45168 31.110021352767944 0.6042582988739014 260.6858215332031 0.3512367010116577 326.6605224609375 0.31944993138313293 0.7443138 0.40592801570892334 True -16 47991 31.073732137680054 0.6024620532989502 213.87322998046875 0.43113160133361816 325.78839111328125 0.32435059547424316 0.75262135 0.371947318315506 True -17 50814 31.0921630859375 0.6080887317657471 261.4290466308594 0.35395348072052 326.1546325683594 0.3217920660972595 0.75739175 0.350724458694458 True -18 53637 31.022346258163452 0.6113128662109375 281.11737060546875 0.40503543615341187 326.10736083984375 0.32241272926330566 0.75781834 0.34282615780830383 True -19 56460 31.065940380096436 0.5921993255615234 305.5447998046875 0.43547767400741577 326.088623046875 0.32263806462287903 0.7568154 0.34241804480552673 False diff --git a/ENCSR554WUJ/cherimoya.fold_4.performance.tsv b/ENCSR554WUJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7ee277cb0d0328dfaeeab1c02bfcc7bc0e0cd082..0000000000000000000000000000000000000000 --- a/ENCSR554WUJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.10736083984375 0.46387413144111633 0.32241272926330566 0.0929655209183693 0.757818341255188 0.7056126594543457 0.34282615780830383 \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_0.evaluate.json b/ENCSR559WMK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a7b84c62872c5e24cac98aeb7fc576741782ee3f..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF186JJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_0.fit.json b/ENCSR559WMK/cherimoya.fold_0.fit.json deleted file mode 100644 index 44decff74c121a00bd365e256221601ae987092c..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF186JJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_0.log b/ENCSR559WMK/cherimoya.fold_0.log deleted file mode 100644 index 1b8661cc5ed72679daf488e183f8b5d3267a287d..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.62774968147278 3.8411142826080322 879.1572265625 0.7709641456604004 1368.7978515625 0.2940646708011627 0.54723406 7.287526607513428 True -1 5476 30.158408880233765 0.6508686542510986 901.4342041015625 0.9325746893882751 1175.5675048828125 0.44785645604133606 0.65278256 2.380028009414673 True -2 8214 30.134639739990234 0.590461254119873 813.2056274414062 0.5847931504249573 1152.65380859375 0.46090710163116455 0.65106523 0.8004581332206726 False -3 10952 30.045656442642212 0.8657758235931396 976.8823852539062 0.7637115716934204 1135.215576171875 0.4752209484577179 0.66646 0.5390328168869019 True -4 13690 30.04630994796753 0.7111566066741943 913.111328125 0.6286201477050781 1132.9547119140625 0.47559237480163574 0.6699971 0.5447332859039307 True -5 16428 30.056432962417603 0.582648754119873 876.3366088867188 0.6107045412063599 1125.1942138671875 0.4816587567329407 0.68139875 0.6002151370048523 True -6 19166 30.08721899986267 0.581110954284668 904.6790771484375 0.5829944014549255 1119.910400390625 0.4846462607383728 0.68154055 0.4890498220920563 True -7 21904 30.12390661239624 0.5683739185333252 924.3784790039062 0.5794975757598877 1109.566650390625 0.49411359429359436 0.6834862 0.49569132924079895 True -8 24642 30.168057203292847 0.5797977447509766 920.869140625 0.6471172571182251 1102.616455078125 0.5001019239425659 0.6893314 0.47104746103286743 True -9 27380 30.083020448684692 0.5660061836242676 803.0189208984375 0.6884803771972656 1100.9713134765625 0.4987737238407135 0.6965063 0.46858519315719604 True -10 30118 30.07572078704834 0.6083331108093262 900.5892944335938 0.7853524088859558 1093.439697265625 0.5061603784561157 0.70068586 0.4675460159778595 True -11 32856 29.722965717315674 0.572545051574707 791.091064453125 0.32126176357269287 1090.115234375 0.5072962641716003 0.710104 0.4599972665309906 True -12 35594 29.51666522026062 0.5633499622344971 933.013916015625 0.5366437435150146 1083.3719482421875 0.5134394764900208 0.7190162 0.4485151469707489 True -13 38332 29.499061822891235 0.5540876388549805 936.1312866210938 0.3869445323944092 1079.6168212890625 0.5161519646644592 0.7273959 0.4185362458229065 True -14 41070 29.561742782592773 0.5647263526916504 879.848876953125 0.43566781282424927 1077.125732421875 0.5178776979446411 0.7372657 0.39980050921440125 True -15 43808 29.611639738082886 0.5713202953338623 857.5430908203125 0.39429616928100586 1075.12109375 0.518292248249054 0.74624634 0.37457001209259033 True -16 46546 29.663764476776123 0.5717470645904541 771.7916259765625 0.33374500274658203 1072.2467041015625 0.5203542113304138 0.7528078 0.3576868772506714 True -17 49284 29.633765697479248 0.583890438079834 896.0189208984375 0.35565897822380066 1072.143310546875 0.5196720957756042 0.75741595 0.35084784030914307 True -18 52022 29.626542329788208 0.9334487915039062 904.1025390625 0.39683520793914795 1073.235107421875 0.5186317563056946 0.7590063 0.34942108392715454 True -19 54760 29.653160333633423 0.56730055809021 823.7477416992188 0.3006429374217987 1073.0814208984375 0.519422709941864 0.7572984 0.3476221263408661 False diff --git a/ENCSR559WMK/cherimoya.fold_0.performance.tsv b/ENCSR559WMK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7ec5d6f89424d4a31d388efa543b12a493bb5d23..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1073.235107421875 0.2688859701156616 0.5186317563056946 0.26596659421920776 0.7590063214302063 0.7075216174125671 0.34942108392715454 \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_1.evaluate.json b/ENCSR559WMK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3bc65ef6b480b07d37de06d39f1c7ea1758b4fce..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF186JJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_1.fit.json b/ENCSR559WMK/cherimoya.fold_1.fit.json deleted file mode 100644 index 16a34945559bf5b4dfac6116bc9799975352bf81..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF186JJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_1.log b/ENCSR559WMK/cherimoya.fold_1.log deleted file mode 100644 index 0e4eaa3eb922157d0e35647603af9133a51a0101..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2700 34.681742906570435 4.104224443435669 979.6270751953125 0.8863489627838135 1540.8572998046875 0.2968706488609314 0.5678703 9.879244804382324 True -1 5400 29.720032691955566 2.161909818649292 936.1808471679688 0.9104334712028503 1300.398193359375 0.4622996151447296 0.6740831 2.2510671615600586 True -2 8100 29.22240447998047 0.952561616897583 871.7056884765625 0.8069363832473755 1266.5753173828125 0.4759163558483124 0.65627015 0.7442542314529419 False -3 10800 29.152216911315918 0.6976208686828613 831.6024169921875 0.6129437685012817 1245.980712890625 0.4870489239692688 0.66657877 0.5962505340576172 False -4 13500 29.110264539718628 0.6887626647949219 901.8829345703125 0.6667868494987488 1239.8812255859375 0.4872117042541504 0.6782525 0.567798376083374 True -5 16200 29.150405645370483 0.6908292770385742 806.5391845703125 0.5613561868667603 1229.501708984375 0.49545741081237793 0.6862506 0.5543476939201355 True -6 18900 29.143161058425903 0.6934692859649658 868.28466796875 0.7731709480285645 1219.6998291015625 0.5016824007034302 0.6920245 0.4809374511241913 True -7 21600 29.307459354400635 0.6967940330505371 1161.1907958984375 0.7672004699707031 1211.770263671875 0.506622314453125 0.6971242 0.46655547618865967 True -8 24300 29.146294116973877 0.7009460926055908 1058.8529052734375 0.6319136619567871 1204.1116943359375 0.5120971202850342 0.7037862 0.4477635622024536 True -9 27000 29.144765853881836 0.6828985214233398 790.4805908203125 0.8742474317550659 1200.473876953125 0.5131300091743469 0.70915705 0.4742550253868103 True -10 29700 29.173885822296143 0.6822226047515869 906.3070068359375 0.7041571140289307 1199.97412109375 0.5118597149848938 0.7161772 0.45977768301963806 True -11 32400 29.148767948150635 0.6815299987792969 941.8741455078125 0.38737672567367554 1189.562744140625 0.518980860710144 0.7293707 0.45387086272239685 True -12 35100 29.093870639801025 0.6786937713623047 887.73291015625 0.4166637659072876 1183.868408203125 0.5226430892944336 0.7384892 0.43689143657684326 True -13 37800 29.18700122833252 0.7021903991699219 802.7990112304688 0.47423064708709717 1173.419677734375 0.530312716960907 0.7474541 0.42560675740242004 True -14 40500 29.124797105789185 0.6958274841308594 816.1990966796875 0.5134864449501038 1168.6146240234375 0.5319926142692566 0.75787425 0.40751928091049194 True -15 43200 29.113926649093628 1.3628349304199219 866.306884765625 0.4092521071434021 1166.016357421875 0.5335682034492493 0.76622957 0.39344027638435364 True -16 45900 29.172539234161377 0.6969108581542969 924.1822509765625 0.36220037937164307 1165.951171875 0.5329539775848389 0.77030414 0.3830302953720093 True -17 48600 29.108639240264893 0.6980888843536377 872.671630859375 0.2867277264595032 1167.89306640625 0.530251681804657 0.77246535 0.37882837653160095 True -18 51300 29.21198582649231 26.669330835342407 866.475341796875 0.3500516414642334 1166.484375 0.5322663187980652 0.77427894 0.373792827129364 True -19 54000 29.18675684928894 0.7295222282409668 882.5953979492188 0.30145418643951416 1166.8858642578125 0.5313430428504944 0.7750947 0.3741532862186432 True diff --git a/ENCSR559WMK/cherimoya.fold_1.performance.tsv b/ENCSR559WMK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6d91ad2cfa08bcc526c0287723de016de8dee8ea..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1166.8858642578125 0.25709596276283264 0.5313430428504944 0.2883826196193695 0.7750946879386902 0.7333582043647766 0.3741532862186432 \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_2.evaluate.json b/ENCSR559WMK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6a703972322ddcb7fa7abfaa1de23d5f02b3d70f..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF186JJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_2.fit.json b/ENCSR559WMK/cherimoya.fold_2.fit.json deleted file mode 100644 index ae8f05d1fe1362ebb77af51ba8145fc612259673..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF186JJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_2.log b/ENCSR559WMK/cherimoya.fold_2.log deleted file mode 100644 index 5ed2cefb2b3fe34a01317e75dc856c92ca5f7e82..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.1237678527832 4.35095739364624 1003.0629272460938 0.8224157691001892 1405.48974609375 0.3083384037017822 0.56169444 8.060620307922363 True -1 5744 31.599002838134766 0.5934896469116211 1069.849609375 0.7519087791442871 1185.674072265625 0.4624069035053253 0.63593745 2.1458213329315186 True -2 8616 31.615373611450195 0.5414319038391113 817.8214111328125 0.6230278611183167 1166.8743896484375 0.4714285135269165 0.6381725 0.895965576171875 True -3 11488 31.599393367767334 0.5409061908721924 720.4644775390625 0.8915138244628906 1154.706787109375 0.48126235604286194 0.64387643 0.668407142162323 True -4 14360 31.571920156478882 0.5454742908477783 923.8868408203125 0.785259485244751 1144.3309326171875 0.48680776357650757 0.6527427 0.635316014289856 True -5 17232 31.534268379211426 2.9237585067749023 1011.5347900390625 0.7375972270965576 1137.74560546875 0.4926382005214691 0.65789825 0.6094470024108887 True -6 20104 31.644473791122437 0.5572834014892578 972.5054931640625 0.7022807002067566 1134.1683349609375 0.49334198236465454 0.66098243 0.5417748689651489 True -7 22976 31.601338148117065 1.0209314823150635 880.7269287109375 0.44236883521080017 1125.8470458984375 0.4978240728378296 0.67013466 0.48302748799324036 True -8 25848 31.510415077209473 0.5596215724945068 922.275390625 0.5538127422332764 1122.566162109375 0.5009445548057556 0.67201823 0.5026407837867737 True -9 28720 31.012184858322144 0.5308301448822021 988.4508666992188 0.5572596788406372 1118.1162109375 0.5044438242912292 0.68448985 0.477515310049057 True -10 31592 30.97955560684204 0.5675041675567627 1046.4000244140625 0.44437527656555176 1109.914794921875 0.5092620253562927 0.69681364 0.43581423163414 True -11 34464 31.005807161331177 0.5449514389038086 998.6727294921875 0.49800267815589905 1106.975341796875 0.5112860202789307 0.70339763 0.43631571531295776 True -12 37336 31.00527334213257 0.8896653652191162 1031.6925048828125 0.5181276798248291 1100.67919921875 0.5153381824493408 0.713291 0.4164251387119293 True -13 40208 30.987380266189575 0.6697192192077637 761.3880004882812 0.5406317114830017 1095.1773681640625 0.519382894039154 0.7244606 0.40804651379585266 True -14 43080 30.987587451934814 0.5506148338317871 796.53662109375 0.4351774752140045 1092.917236328125 0.5205215215682983 0.7315019 0.39812377095222473 True -15 45952 31.004896879196167 0.5711760520935059 639.2396240234375 0.3519471287727356 1088.3720703125 0.5252461433410645 0.739762 0.38950952887535095 True -16 48824 31.3561270236969 0.5676023960113525 830.5953369140625 0.38690465688705444 1089.6636962890625 0.5225713849067688 0.7450265 0.38039493560791016 True -17 51696 31.052489042282104 0.5326545238494873 909.9169921875 0.4688984751701355 1088.3416748046875 0.5240771770477295 0.74933165 0.3753422498703003 True -18 54568 31.027528047561646 1.179041862487793 859.405029296875 0.284402459859848 1087.414794921875 0.5256413221359253 0.7509552 0.3736882209777832 True -19 57440 31.042216300964355 0.5612094402313232 770.1263427734375 0.28298282623291016 1090.6182861328125 0.521359920501709 0.74869037 0.37320753931999207 False diff --git a/ENCSR559WMK/cherimoya.fold_2.performance.tsv b/ENCSR559WMK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1f5ad90e594bea22adb2e7696477f55927c82bb6..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1087.414794921875 0.26552000641822815 0.5256413221359253 0.275186151266098 0.7509552240371704 0.7038499712944031 0.3736882209777832 \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_3.evaluate.json b/ENCSR559WMK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1d9a9354b183871ecd2e7d153e2162b16b68b184..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF186JJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_3.fit.json b/ENCSR559WMK/cherimoya.fold_3.fit.json deleted file mode 100644 index c147f2e816730f668aaa130b70ffd6901230318e..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF186JJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_3.log b/ENCSR559WMK/cherimoya.fold_3.log deleted file mode 100644 index fa08a12a984eabb87e9ad4ddb7ee9d86abe7aa4d..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 34.495593309402466 3.978605270385742 987.4524536132812 0.831754207611084 1424.6395263671875 0.2903379201889038 0.58335453 8.582534790039062 True -1 5518 30.32916522026062 0.5747778415679932 1183.6064453125 0.9519056081771851 1226.354248046875 0.4483940303325653 0.6507214 2.492619276046753 True -2 8277 30.270447731018066 1.827094554901123 915.1650390625 0.8100322484970093 1205.7349853515625 0.45890533924102783 0.6477061 0.9260308146476746 False -3 11036 30.164340257644653 0.5413827896118164 1089.3638916015625 0.5780845284461975 1186.931640625 0.46832552552223206 0.6605974 0.7206982374191284 True -4 13795 29.764543533325195 0.5444483757019043 1063.939453125 0.7474296689033508 1176.5628662109375 0.47633856534957886 0.65934193 0.6795036196708679 False -5 16554 29.872223138809204 0.5851147174835205 784.5426025390625 0.8937932848930359 1171.876708984375 0.48074692487716675 0.6635363 0.5944324731826782 True -6 19313 29.826574563980103 0.5463881492614746 882.2615966796875 0.7024171352386475 1163.9134521484375 0.4850555956363678 0.66951346 0.5535703301429749 True -7 22072 29.769744396209717 0.5367927551269531 906.771728515625 0.5881930589675903 1158.489501953125 0.4895470142364502 0.67605686 0.5138617753982544 True -8 24831 29.782193183898926 0.5423550605773926 1094.435791015625 0.5346273183822632 1153.1661376953125 0.49176520109176636 0.68606126 0.48221462965011597 True -9 27590 29.832414865493774 0.5504388809204102 986.49658203125 0.5302956700325012 1150.2218017578125 0.49404606223106384 0.69373274 0.48929843306541443 True -10 30349 29.79258394241333 0.6003596782684326 967.0725708007812 0.57760089635849 1140.716552734375 0.5011157989501953 0.69965816 0.47855544090270996 True -11 33108 29.773415327072144 0.5582165718078613 1078.8968505859375 0.5479300022125244 1135.4471435546875 0.5059838891029358 0.71039724 0.4635668098926544 True -12 35867 29.802934646606445 0.6827056407928467 938.2072143554688 0.5301814079284668 1131.2098388671875 0.5082060694694519 0.7239165 0.44741877913475037 True -13 38626 29.814648151397705 1.5397064685821533 875.494140625 0.39296892285346985 1129.3226318359375 0.5091904401779175 0.73748803 0.4241276979446411 True -14 41385 29.76194739341736 0.5525422096252441 892.4207763671875 0.45962727069854736 1128.1724853515625 0.5080733299255371 0.7473828 0.40573400259017944 True -15 44144 29.80980372428894 0.5495519638061523 1021.46435546875 0.3477686047554016 1123.2216796875 0.5132653117179871 0.7563356 0.38238203525543213 True -16 46903 29.810551643371582 0.5419659614562988 871.5767822265625 0.36042749881744385 1121.027099609375 0.5144254565238953 0.7631227 0.3712759017944336 True -17 49662 29.792787551879883 0.5475754737854004 911.860595703125 0.3397383689880371 1120.797119140625 0.5152258276939392 0.76665276 0.3585011959075928 True -18 52421 29.82068371772766 15.943426370620728 1021.4827880859375 0.3324636220932007 1121.5155029296875 0.5138221383094788 0.7695119 0.35446828603744507 True -19 55180 29.877966165542603 1.458404302597046 911.7055053710938 0.4046531617641449 1121.5787353515625 0.5134724378585815 0.76836437 0.3557378351688385 False diff --git a/ENCSR559WMK/cherimoya.fold_3.performance.tsv b/ENCSR559WMK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 444284e5c9215e9866401d1c3ea538724f29a543..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1121.5155029296875 0.26625967025756836 0.5138221383094788 0.27359095215797424 0.769511878490448 0.7215822339057922 0.35446828603744507 \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_4.evaluate.json b/ENCSR559WMK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1016b3ee0ac86d0d2ac7c6f227fb08dc4155f6aa..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF186JJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_4.fit.json b/ENCSR559WMK/cherimoya.fold_4.fit.json deleted file mode 100644 index 57127ce35cf897ddb1f997cc02dcc8d5949e21f4..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF186JJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR559WMK/cherimoya.fold_4.log b/ENCSR559WMK/cherimoya.fold_4.log deleted file mode 100644 index 0078a59f7a561b72df3c146e7c3ab63979c07cc4..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 36.19438648223877 3.919830560684204 955.9446411132812 0.9282651543617249 1345.6387939453125 0.2995266318321228 0.5621673 7.682718276977539 True -1 5664 31.242493867874146 0.614128589630127 768.0718994140625 1.1293118000030518 1163.1827392578125 0.4490523636341095 0.636021 1.7674105167388916 True -2 8496 31.120320796966553 0.5922231674194336 927.2827758789062 0.6915436387062073 1146.646484375 0.4589657485485077 0.63538754 0.6498656272888184 False -3 11328 31.121534824371338 0.5899829864501953 924.0423583984375 0.6495514512062073 1131.28271484375 0.4688851833343506 0.6443084 0.5546855926513672 True -4 14160 31.130810499191284 0.6056058406829834 897.1142578125 0.5025939345359802 1122.4246826171875 0.47624367475509644 0.647047 0.5608320236206055 True -5 16992 31.19832682609558 0.5977945327758789 721.872314453125 0.5499020218849182 1118.2166748046875 0.48095622658729553 0.6536181 0.5626787543296814 True -6 19824 31.10868215560913 0.6018092632293701 989.4007568359375 0.5504068732261658 1116.45068359375 0.4809993505477905 0.65807796 0.5320680141448975 True -7 22656 31.13332438468933 14.365049600601196 899.5128173828125 0.7894866466522217 1108.51123046875 0.4877801835536957 0.6662781 0.5177742838859558 True -8 25488 31.150587558746338 1.1987051963806152 904.0523071289062 0.5826764702796936 1103.8544921875 0.4915594458580017 0.67072034 0.4788757264614105 True -9 28320 31.220885038375854 1.6336257457733154 905.078857421875 0.49409782886505127 1098.832763671875 0.4952131509780884 0.67537767 0.49353328347206116 True -10 31152 31.164548873901367 5.785673379898071 997.046630859375 0.39303216338157654 1096.971435546875 0.49556076526641846 0.6806354 0.45885464549064636 True -11 33984 31.356476068496704 1.0756783485412598 916.562744140625 0.4486458897590637 1088.5252685546875 0.5032603144645691 0.6925401 0.4368513524532318 True -12 36816 31.220966577529907 0.9684679508209229 780.0087890625 0.5182560086250305 1084.2166748046875 0.5064045786857605 0.7031955 0.41567301750183105 True -13 39648 31.217515230178833 0.7285370826721191 1027.37890625 0.43063807487487793 1079.6710205078125 0.5102941393852234 0.7118434 0.40563344955444336 True -14 42480 31.132806539535522 0.5990731716156006 962.102783203125 0.40591123700141907 1078.333251953125 0.5100153088569641 0.7258894 0.39441415667533875 True -15 45312 31.117034196853638 0.6865084171295166 845.463623046875 0.33914315700531006 1076.56787109375 0.5122776031494141 0.7349964 0.37534087896347046 True -16 48144 31.19623374938965 0.5890088081359863 907.51953125 0.29192134737968445 1072.750244140625 0.5154153108596802 0.74294287 0.3563002347946167 True -17 50976 31.232558250427246 0.5930318832397461 805.9298095703125 0.41470983624458313 1072.7772216796875 0.5161334276199341 0.74811316 0.3520446717739105 True -18 53808 31.324687719345093 0.5833508968353271 886.8973388671875 0.3614034950733185 1073.331787109375 0.5145975351333618 0.7491518 0.3469831049442291 True -19 56640 30.66147255897522 0.5900537967681885 876.7103271484375 0.26969006657600403 1075.251708984375 0.5124266743659973 0.7485403 0.34675130248069763 False diff --git a/ENCSR559WMK/cherimoya.fold_4.performance.tsv b/ENCSR559WMK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 47f40535f05f0cf6a8aad04029b70be1559b28e6..0000000000000000000000000000000000000000 --- a/ENCSR559WMK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1073.331787109375 0.2684074342250824 0.5145975351333618 0.268384724855423 0.7491518259048462 0.6953023672103882 0.3469831049442291 \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_0.evaluate.json b/ENCSR561ZLY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8c0f1d81be3048369f28e4766764d0a51dbe4486..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF710YNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_0.fit.json b/ENCSR561ZLY/cherimoya.fold_0.fit.json deleted file mode 100644 index d4e8afc9cf220f2407ae3bd0776ecf53ac053b7f..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF710YNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_0.log b/ENCSR561ZLY/cherimoya.fold_0.log deleted file mode 100644 index f7568b8e4345d89816f695b0814465aba18ff0d4..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 35.17481470108032 3.6484925746917725 512.2119750976562 0.616276204586029 846.791259765625 0.16222304105758667 0.60193276 6.892093181610107 True -1 5510 30.50239586830139 1.4121098518371582 758.7911376953125 1.0870088338851929 795.1483154296875 0.1866084635257721 0.6596795 2.6674487590789795 True -2 8265 30.48798179626465 0.5900669097900391 537.2913818359375 0.5275586247444153 766.5990600585938 0.19468356668949127 0.691804 1.956700086593628 True -3 11020 30.366172552108765 0.5881197452545166 665.51513671875 0.5538095235824585 742.8682861328125 0.20265543460845947 0.71632016 2.0054047107696533 True -4 13775 30.35719060897827 2.399366617202759 534.5991821289062 0.5176894664764404 728.411865234375 0.20863445103168488 0.72536504 1.2242915630340576 True -5 16530 30.39514470100403 0.5847640037536621 703.4432373046875 0.495888888835907 723.532958984375 0.2085069715976715 0.7458951 1.0518748760223389 True -6 19285 30.36884355545044 0.6005668640136719 484.417236328125 1.011885166168213 714.9931030273438 0.21326202154159546 0.7536401 1.0032978057861328 True -7 22040 30.519760370254517 0.5990493297576904 555.0646362304688 0.5078288912773132 704.1118774414062 0.2185492366552353 0.7635047 0.8292467594146729 True -8 24795 30.502052068710327 0.5846161842346191 607.5909423828125 0.37734174728393555 699.78466796875 0.21846699714660645 0.7754608 0.7166467905044556 True -9 27550 30.592663049697876 0.5794835090637207 702.197509765625 0.7654324173927307 694.0162353515625 0.22166183590888977 0.78666407 0.579399824142456 True -10 30305 30.505556344985962 1.9041335582733154 537.029296875 0.48125797510147095 691.3741455078125 0.22232338786125183 0.7961623 0.5506998300552368 True -11 33060 30.509358882904053 0.5973660945892334 637.958251953125 0.7433658838272095 684.9470825195312 0.22579722106456757 0.80382377 0.4986766278743744 True -12 35815 30.50042986869812 36.42375349998474 568.18603515625 0.47804680466651917 682.7863159179688 0.22570458054542542 0.81410444 0.4551253318786621 True -13 38570 31.055060625076294 0.6306116580963135 539.1959228515625 0.46708792448043823 677.852783203125 0.22941625118255615 0.8195639 0.4277474284172058 True -14 41325 30.557432651519775 0.5944857597351074 577.2918701171875 0.39359837770462036 676.7297973632812 0.22825859487056732 0.8274467 0.39858147501945496 True -15 44080 30.491487741470337 0.5887880325317383 512.9581298828125 0.3958111107349396 670.4644165039062 0.23156104981899261 0.8316311 0.376361221075058 True -16 46835 30.46561074256897 0.578742265701294 590.3416748046875 0.4847051501274109 673.453369140625 0.2288011908531189 0.8361416 0.36652401089668274 True -17 49590 30.102660655975342 0.5636224746704102 496.6626281738281 0.4025772213935852 668.88427734375 0.23186661303043365 0.837879 0.36309900879859924 True -18 52345 30.65554118156433 1.7149310111999512 625.7232666015625 0.47255054116249084 670.9194946289062 0.23025459051132202 0.8371933 0.3607114255428314 False -19 55100 30.261629104614258 0.5774276256561279 518.2758178710938 0.329231858253479 672.03125 0.22938500344753265 0.8372446 0.3629002571105957 False diff --git a/ENCSR561ZLY/cherimoya.fold_0.performance.tsv b/ENCSR561ZLY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 22dfdf180f6f6e93013fd2456ff6a87457656be9..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -668.88427734375 0.4878127872943878 0.23186662793159485 0.09293372184038162 0.8378790020942688 0.7962052226066589 0.36309900879859924 \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_1.evaluate.json b/ENCSR561ZLY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 160e73881b84da2de45525a4f3311aa508c5b061..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF710YNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_1.fit.json b/ENCSR561ZLY/cherimoya.fold_1.fit.json deleted file mode 100644 index fd89129013217bd069a024bef8bdaa646269a09c..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF710YNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_1.log b/ENCSR561ZLY/cherimoya.fold_1.log deleted file mode 100644 index 3bc19d8b3b3b33d6405289692be37f23fa5e0e0b..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2698 34.55715727806091 3.775358200073242 781.027587890625 0.8018288612365723 1051.705078125 0.17530953884124756 0.5861679 8.011434555053711 True -1 5396 29.77350616455078 0.7435650825500488 778.2234497070312 0.7080937623977661 970.3762817382812 0.20893460512161255 0.67198557 3.8554329872131348 True -2 8094 29.76920199394226 0.7098293304443359 486.8953857421875 0.7763049602508545 985.431884765625 0.20627766847610474 0.6568463 3.0212106704711914 False -3 10792 29.737486124038696 0.7089965343475342 574.7501220703125 0.6731717586517334 910.0950927734375 0.22456921637058258 0.7121729 2.1830148696899414 True -4 13490 29.691057920455933 0.7165234088897705 731.6315307617188 0.5313035249710083 878.3831176757812 0.2356923222541809 0.7352467 1.4880255460739136 True -5 16188 29.704716205596924 0.7384774684906006 557.0198974609375 0.43101948499679565 863.4015502929688 0.2402140498161316 0.7497786 1.2391974925994873 True -6 18886 29.738072395324707 0.7268927097320557 626.579833984375 0.4947264790534973 853.0397338867188 0.24352791905403137 0.76116246 1.160062313079834 True -7 21584 29.707348108291626 0.7252674102783203 432.1170959472656 0.3911673426628113 847.18115234375 0.24429191648960114 0.7705523 1.035040259361267 True -8 24282 29.691896677017212 0.708160400390625 595.8642578125 0.875951886177063 837.227294921875 0.24908608198165894 0.7816925 0.871378481388092 True -9 26980 29.770955324172974 1.2514879703521729 614.318603515625 0.5549092292785645 832.6763916015625 0.2515629529953003 0.7840753 0.882255494594574 True -10 29678 30.125503301620483 39.3985333442688 860.80419921875 0.7150161266326904 828.5848999023438 0.2532302141189575 0.7952833 0.7528750896453857 True -11 32376 29.767075061798096 0.7199726104736328 839.821044921875 0.9620200395584106 825.5985717773438 0.2532966136932373 0.804013 0.6410987973213196 True -12 35074 29.73395538330078 0.7370803356170654 556.1058349609375 0.550675630569458 816.8728637695312 0.25664716958999634 0.814177 0.5933229327201843 True -13 37772 29.826838731765747 0.7078280448913574 449.3924560546875 0.4095626175403595 810.4238891601562 0.2590954005718231 0.8230706 0.5599562525749207 True -14 40470 29.804433822631836 0.7020144462585449 553.4581298828125 0.396090567111969 805.6631469726562 0.26038387417793274 0.83477765 0.5138545632362366 True -15 43168 29.752485275268555 0.6983480453491211 616.6494140625 0.49342212080955505 803.5830688476562 0.26103025674819946 0.8408979 0.48476749658584595 True -16 45866 29.75348711013794 0.7130236625671387 584.6550903320312 0.3077210783958435 802.3391723632812 0.2615974545478821 0.84246093 0.4661943316459656 True -17 48564 29.52904963493347 0.7008514404296875 613.0545654296875 0.3218122720718384 800.4130249023438 0.262317031621933 0.8455049 0.44910722970962524 True -18 51262 29.54853343963623 21.45547366142273 540.136962890625 0.2534310817718506 797.66357421875 0.2638542652130127 0.84514785 0.44234418869018555 False -19 53960 29.269913911819458 0.7065002918243408 578.4478149414062 0.3585377633571625 797.1021728515625 0.26423144340515137 0.84623873 0.4435679614543915 True diff --git a/ENCSR561ZLY/cherimoya.fold_1.performance.tsv b/ENCSR561ZLY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 905083cfa735975a385b1e75936980a07b729aab..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -797.1021728515625 0.46290987730026245 0.26423144340515137 0.1163056343793869 0.8462387323379517 0.8275209069252014 0.4435679614543915 \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_2.evaluate.json b/ENCSR561ZLY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3e2737e9fcf53941199970032b2b1caf0b0cc520..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF710YNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_2.fit.json b/ENCSR561ZLY/cherimoya.fold_2.fit.json deleted file mode 100644 index de753f4756572ca5faec2398c046f5451a58fea9..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF710YNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_2.log b/ENCSR561ZLY/cherimoya.fold_2.log deleted file mode 100644 index bd51e093ddad8b4075d206ed243dd36d3d2f45ef..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 36.263062715530396 3.6196401119232178 561.315185546875 0.41548460721969604 866.3442993164062 0.16588783264160156 0.5931763 6.0407209396362305 True -1 5736 31.64177417755127 0.6273777484893799 681.6885986328125 1.048506498336792 796.8111572265625 0.1973734349012375 0.6802159 2.844470977783203 True -2 8604 31.60159134864807 0.6211011409759521 578.969482421875 0.5579590201377869 775.923583984375 0.20158898830413818 0.6945009 1.7789169549942017 True -3 11472 31.76845645904541 0.6149179935455322 425.427734375 0.5116997957229614 748.4725341796875 0.20990855991840363 0.71981883 1.6104826927185059 True -4 14340 31.812685251235962 1.348975658416748 616.646240234375 0.7358715534210205 734.0582275390625 0.21406807005405426 0.7347877 1.2638518810272217 True -5 17208 31.74611783027649 9.459190368652344 747.4026489257812 0.640426754951477 727.7186889648438 0.21459455788135529 0.74274164 1.2202945947647095 True -6 20076 31.835904121398926 18.935168504714966 514.0494995117188 0.47711896896362305 720.15576171875 0.21748735010623932 0.74586844 0.8144305348396301 True -7 22944 31.721906423568726 0.6080169677734375 680.1463623046875 0.5938793420791626 713.2072143554688 0.22087086737155914 0.7466159 0.7393945455551147 True -8 25812 31.61776375770569 0.6126041412353516 558.6067504882812 0.48321089148521423 709.6513671875 0.22321917116641998 0.74767184 0.716014564037323 True -9 28680 31.6335928440094 0.6049275398254395 560.7872314453125 0.5227169394493103 705.6176147460938 0.22484090924263 0.7606509 0.6616310477256775 True -10 31548 31.6336612701416 0.6001060009002686 611.568603515625 0.5690000653266907 701.4856567382812 0.22541382908821106 0.77546877 0.5911527276039124 True -11 34416 31.58825135231018 0.5998802185058594 500.3527526855469 0.3246961236000061 697.201416015625 0.22727160155773163 0.7887138 0.5324592590332031 True -12 37284 31.624592304229736 0.5942466259002686 613.8994140625 0.4167063236236572 691.6270141601562 0.2283119261264801 0.80336523 0.47115200757980347 True -13 40152 31.62398076057434 0.5865538120269775 561.9347534179688 0.5757124423980713 688.7957763671875 0.2296135276556015 0.8101353 0.4432261288166046 True -14 43020 31.70757293701172 0.6064739227294922 406.4686584472656 0.46812134981155396 683.6976318359375 0.23178918659687042 0.8197585 0.41496580839157104 True -15 45888 31.63136100769043 2.640132188796997 473.22637939453125 0.3049270510673523 683.0216064453125 0.23085305094718933 0.8241702 0.39643004536628723 True -16 48756 31.63563561439514 0.5873923301696777 509.3363952636719 0.3584868907928467 678.8836669921875 0.23351003229618073 0.83014035 0.377566933631897 True -17 51624 31.002797842025757 0.5888991355895996 567.273193359375 0.2563745975494385 680.9451904296875 0.2323799431324005 0.83277243 0.3682451844215393 True -18 54492 31.035768747329712 0.602238655090332 454.84967041015625 0.21539828181266785 680.9921875 0.23280638456344604 0.8332453 0.3666571080684662 True -19 57360 31.092711687088013 0.5955910682678223 539.489013671875 0.14904598891735077 680.01611328125 0.23321717977523804 0.8333823 0.367855966091156 True diff --git a/ENCSR561ZLY/cherimoya.fold_2.performance.tsv b/ENCSR561ZLY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2891db44085012d3c551b5018ccc99c456103e59..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -680.01611328125 0.48402106761932373 0.23321717977523804 0.09859413653612137 0.8333823084831238 0.794887363910675 0.367855966091156 \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_3.evaluate.json b/ENCSR561ZLY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 92475d74d5893fe7b885f00da8c37458928102bb..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF710YNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_3.fit.json b/ENCSR561ZLY/cherimoya.fold_3.fit.json deleted file mode 100644 index 5841ef41d7399a21cb94ac7a20c802f26fef0cd8..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF710YNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_3.log b/ENCSR561ZLY/cherimoya.fold_3.log deleted file mode 100644 index bcc6f9e3360a3da81eb338246a79fab30324852a..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 34.59805941581726 4.549548625946045 592.525146484375 0.41030430793762207 911.9004516601562 0.17541982233524323 0.52809286 8.665592193603516 True -1 5468 30.209566593170166 0.5581724643707275 678.14404296875 0.909050703048706 821.7055053710938 0.21025416254997253 0.6426711 3.176880359649658 True -2 8202 30.14087438583374 0.548964262008667 704.372314453125 0.7856130003929138 815.3916015625 0.21174703538417816 0.656774 2.164912700653076 True -3 10936 30.164944648742676 0.5424656867980957 551.7037353515625 0.5764167308807373 788.2852783203125 0.22016802430152893 0.68879217 1.7717982530593872 True -4 13670 30.11852741241455 0.5421109199523926 782.930908203125 0.6652765274047852 774.7347412109375 0.22473350167274475 0.71118915 1.3235783576965332 True -5 16404 30.10369634628296 0.5332930088043213 617.8162841796875 0.7888954877853394 762.0096435546875 0.2285674512386322 0.7247473 1.3157716989517212 True -6 19138 30.207605600357056 0.5417835712432861 577.1385498046875 0.508604884147644 756.6163330078125 0.23016886413097382 0.7282246 1.2466788291931152 True -7 21872 30.183115005493164 0.5444231033325195 470.21295166015625 0.14590786397457123 747.6923217773438 0.23481912910938263 0.7419719 1.0534520149230957 True -8 24606 30.142287015914917 0.5445692539215088 689.418212890625 0.43664830923080444 739.9735107421875 0.23701366782188416 0.7546001 0.8485286235809326 True -9 27340 30.143917083740234 2.4037599563598633 609.4844970703125 0.5396864414215088 738.3740234375 0.23954463005065918 0.75654674 0.8309527039527893 True -10 30074 30.212717533111572 0.5478990077972412 644.3160400390625 0.6330270767211914 732.9917602539062 0.24159540235996246 0.7702452 0.7514410614967346 True -11 32808 30.140212297439575 0.5502405166625977 430.793701171875 0.5128064155578613 729.3483276367188 0.24194060266017914 0.77557194 0.709653377532959 True -12 35542 30.151116371154785 0.5511879920959473 714.7913208007812 0.5558475852012634 724.6290893554688 0.24467334151268005 0.7848654 0.629372775554657 True -13 38276 32.12083435058594 31.145445585250854 592.2581787109375 0.27091774344444275 723.6547241210938 0.2446570098400116 0.7910893 0.5836873650550842 True -14 41010 30.286714792251587 0.550194263458252 541.95654296875 0.5107849836349487 717.5526123046875 0.24690528213977814 0.7999456 0.5322980880737305 True -15 43744 30.216159105300903 0.5417473316192627 646.644775390625 0.433569073677063 715.2886352539062 0.24791011214256287 0.80763245 0.5006024241447449 True -16 46478 30.23435616493225 0.537773847579956 454.8863525390625 0.27914851903915405 711.9742431640625 0.24884307384490967 0.8160099 0.4743078947067261 True -17 49212 29.945266008377075 0.5420277118682861 629.6658935546875 0.37260907888412476 711.3287353515625 0.24931147694587708 0.8202308 0.4582878649234772 True -18 51946 29.6338210105896 1.934790849685669 536.740234375 0.32857584953308105 711.1881103515625 0.24932774901390076 0.819974 0.45224615931510925 False -19 54680 29.61227583885193 0.5427157878875732 533.5443115234375 0.25264155864715576 711.6307373046875 0.249264657497406 0.8199416 0.45057690143585205 False diff --git a/ENCSR561ZLY/cherimoya.fold_3.performance.tsv b/ENCSR561ZLY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 39bcfcd1de1374775071a445f5dfe7d652a3e026..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -711.3287353515625 0.4750182628631592 0.24931150674819946 0.10807953029870987 0.8202307820320129 0.7796201109886169 0.4582878649234772 \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_4.evaluate.json b/ENCSR561ZLY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 882da36db05a7876a03e2d024b294ad0492e94ae..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF710YNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_4.fit.json b/ENCSR561ZLY/cherimoya.fold_4.fit.json deleted file mode 100644 index 839c1af4f458fd386e5693afa3a21b769155cda7..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF710YNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR561ZLY/cherimoya.fold_4.log b/ENCSR561ZLY/cherimoya.fold_4.log deleted file mode 100644 index 069b4dd6541c8fa598834da31f13a1acdb3291d0..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2794 35.52101731300354 3.563720941543579 594.955810546875 0.6261813640594482 757.3907470703125 0.1593399941921234 0.5679141 5.846321105957031 True -1 5588 30.886724948883057 20.906922101974487 667.4205932617188 0.6150815486907959 697.5718383789062 0.18231043219566345 0.65598387 2.5308144092559814 True -2 8382 31.81610631942749 0.6138379573822021 508.6144714355469 0.3494013845920563 687.9498291015625 0.1927158385515213 0.67363876 1.7509677410125732 True -3 11176 30.94428014755249 0.6153666973114014 491.2950439453125 0.566938579082489 670.5894165039062 0.19956021010875702 0.6980186 1.8268316984176636 True -4 13970 30.917930126190186 0.6052689552307129 627.0382690429688 0.8097000122070312 662.1670532226562 0.20167241990566254 0.71264905 0.8966323137283325 True -5 16764 30.897502422332764 0.5962433815002441 771.1749877929688 0.7339308261871338 653.0992431640625 0.20516560971736908 0.71424764 0.9838971495628357 True -6 19558 30.841734647750854 0.9960989952087402 752.6385498046875 0.9314538240432739 650.1328735351562 0.20633992552757263 0.7284985 1.0523053407669067 True -7 22352 30.86242413520813 11.70510983467102 660.2134399414062 0.4725637435913086 650.1022338867188 0.20680387318134308 0.72123367 1.0189698934555054 False -8 25146 30.7950222492218 2.307708263397217 601.2510986328125 0.4920743405818939 639.7647094726562 0.21297790110111237 0.7370562 0.8584738969802856 True -9 27940 30.81737494468689 0.6259276866912842 456.98162841796875 0.44867098331451416 637.9351196289062 0.21225348114967346 0.74758285 0.7636169195175171 True -10 30734 30.86929988861084 0.6095154285430908 607.8243408203125 0.302961140871048 636.2354125976562 0.21314848959445953 0.75799245 0.6864426732063293 True -11 33528 30.900052547454834 0.6033613681793213 531.7586669921875 0.5270305275917053 633.9456787109375 0.21331891417503357 0.77056974 0.6190229058265686 True -12 36322 30.772587299346924 0.6042194366455078 535.0233154296875 0.4142962396144867 629.0408935546875 0.21680667996406555 0.7804687 0.5284006595611572 True -13 39116 30.840367794036865 0.5920679569244385 486.1553955078125 0.4011204242706299 626.5328979492188 0.21851345896720886 0.7887289 0.4831303656101227 True -14 41910 30.820142030715942 0.5968573093414307 480.561279296875 0.3097282648086548 624.2251586914062 0.21853382885456085 0.79974806 0.4314042329788208 True -15 44704 30.810959100723267 0.5931024551391602 559.6502685546875 0.26984333992004395 622.1636352539062 0.2187279611825943 0.8084416 0.391156941652298 True -16 47498 30.812231302261353 0.5936353206634521 496.57470703125 0.23114636540412903 620.2948608398438 0.2190563976764679 0.8121308 0.37182432413101196 True -17 50292 30.54810070991516 0.58736252784729 644.4932861328125 0.43064653873443604 618.8185424804688 0.21989862620830536 0.8161383 0.3587377071380615 True -18 53086 30.250598430633545 0.581305742263794 598.3536376953125 0.17901064455509186 617.5418090820312 0.22137422859668732 0.8180763 0.35517746210098267 True -19 55880 30.234668016433716 0.5887072086334229 629.3236083984375 0.30961546301841736 620.2955932617188 0.21868042647838593 0.81667143 0.35625362396240234 False diff --git a/ENCSR561ZLY/cherimoya.fold_4.performance.tsv b/ENCSR561ZLY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f2c6650a89b5797746faab95f3fab942d47b8066..0000000000000000000000000000000000000000 --- a/ENCSR561ZLY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -617.5418090820312 0.49494266510009766 0.22137422859668732 0.08930221199989319 0.8180763125419617 0.7792668342590332 0.35517746210098267 \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_0.evaluate.json b/ENCSR562FNN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9fec9b867e7901f364e78ae6a1e1b291922787ba..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644UHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_0.fit.json b/ENCSR562FNN/cherimoya.fold_0.fit.json deleted file mode 100644 index ebbd74dc4196305037527ff6df748086f9c5ff41..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF644UHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_0.log b/ENCSR562FNN/cherimoya.fold_0.log deleted file mode 100644 index 012d5aa53e689c95f4cdcc3d76861f33f7cbe707..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.74581456184387 4.878378629684448 619.4531860351562 0.3685052990913391 748.9576416015625 0.2365715652704239 0.7639475 4.519201278686523 True -1 5454 30.341938257217407 0.6113040447235107 601.3958740234375 0.27570974826812744 680.9404907226562 0.2952698767185211 0.81567794 0.9173519611358643 True -2 8181 30.375311374664307 0.598158597946167 504.4732666015625 0.22630102932453156 666.6573486328125 0.3052313029766083 0.8228115 0.5473398566246033 True -3 10908 30.381836652755737 0.6561803817749023 552.42236328125 0.4076501131057739 661.957275390625 0.30879783630371094 0.8292532 0.5526337623596191 True -4 13635 30.386775016784668 0.5585982799530029 678.6575927734375 0.20261909067630768 659.3466796875 0.3120090067386627 0.83714867 0.4657977223396301 True -5 16362 30.37601137161255 0.5584280490875244 522.545654296875 0.30188897252082825 655.7577514648438 0.31556981801986694 0.83928025 0.42372646927833557 True -6 19089 30.312514305114746 0.5695247650146484 503.314453125 0.2432231903076172 654.6996459960938 0.31614741683006287 0.843752 0.4088248610496521 True -7 21816 30.305312871932983 1.135155439376831 519.448974609375 0.25918135046958923 652.4306030273438 0.3183034360408783 0.8491516 0.39893820881843567 True -8 24543 30.376020193099976 0.5766336917877197 517.068603515625 0.4288196563720703 650.4498901367188 0.3207949101924896 0.8546695 0.3770861029624939 True -9 27270 30.363222360610962 0.5660347938537598 543.1275634765625 0.2565479576587677 648.4501342773438 0.32286009192466736 0.8594583 0.35595402121543884 True -10 29997 30.319466590881348 0.5630826950073242 552.7173461914062 0.27708256244659424 647.5453491210938 0.32454627752304077 0.863095 0.32897675037384033 True -11 32724 30.332576990127563 0.5598757266998291 680.080322265625 0.20712420344352722 645.1415405273438 0.3264271914958954 0.86890143 0.296209454536438 True -12 35451 30.349759578704834 0.5766768455505371 626.306884765625 0.33217012882232666 642.49853515625 0.32919156551361084 0.8741135 0.2687581181526184 True -13 38178 30.3845317363739 0.5754215717315674 658.0853881835938 0.34633564949035645 640.482666015625 0.3310793936252594 0.8782839 0.24629558622837067 True -14 40905 30.403973817825317 0.5635161399841309 592.0498046875 0.18586164712905884 637.9550170898438 0.33339375257492065 0.88272655 0.2267076075077057 True -15 43632 30.369214057922363 0.5743749141693115 506.86065673828125 0.20429614186286926 636.97705078125 0.33458784222602844 0.8869881 0.21476532518863678 True -16 46359 30.555765390396118 0.5761809349060059 548.0286865234375 0.18748340010643005 637.8493041992188 0.3332313597202301 0.8887991 0.20506586134433746 True -17 49086 30.408305644989014 0.5762245655059814 617.54638671875 0.19475549459457397 637.1080932617188 0.33475741744041443 0.8884656 0.20118194818496704 False -18 51813 30.430996656417847 1.3048980236053467 486.4571838378906 0.16127143800258636 638.3519287109375 0.3325100541114807 0.8888939 0.20076367259025574 True -19 54540 30.37440800666809 0.5537359714508057 510.3856506347656 0.1536039412021637 638.1470947265625 0.332950234413147 0.88756216 0.20223931968212128 False diff --git a/ENCSR562FNN/cherimoya.fold_0.performance.tsv b/ENCSR562FNN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index eb700954c6c6fccf4fe48024dcd0a77803129fa2..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -638.3519287109375 0.40574488043785095 0.3325100839138031 0.14761501550674438 0.8888939023017883 0.8438611030578613 0.20076367259025574 \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_1.evaluate.json b/ENCSR562FNN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index cb99c5489abea0e98c1cd01e6beb4242b4e22c8c..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644UHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_1.fit.json b/ENCSR562FNN/cherimoya.fold_1.fit.json deleted file mode 100644 index 4ade2f730d5fc188b7dc2485c0d184e85c175f10..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF644UHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_1.log b/ENCSR562FNN/cherimoya.fold_1.log deleted file mode 100644 index d05fe3a96cf97ab22d6a4b573b1d321d7a6779b4..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2726 35.02563977241516 4.085346698760986 550.7490234375 0.5278283357620239 865.3050537109375 0.24440482258796692 0.75856113 5.770143032073975 True -1 5452 30.401501655578613 0.9138822555541992 605.1189575195312 0.44655269384384155 780.438720703125 0.3114229142665863 0.8181766 1.4325071573257446 True -2 8178 30.43273687362671 0.7239010334014893 612.503662109375 0.3293878436088562 763.1453247070312 0.3215460181236267 0.8311168 0.7101843953132629 True -3 10904 30.429142951965332 0.7457835674285889 495.02850341796875 0.28051865100860596 758.183837890625 0.32614535093307495 0.83370566 0.6548247337341309 True -4 13630 30.471571922302246 0.7405149936676025 555.02880859375 0.3033774197101593 755.3416748046875 0.32734107971191406 0.83752114 0.6041030883789062 True -5 16356 30.501140832901 0.727694034576416 580.543701171875 0.43017667531967163 751.1570434570312 0.33194500207901 0.8412911 0.6187617182731628 True -6 19082 30.43298077583313 0.732799768447876 639.7564697265625 0.23865967988967896 747.8319091796875 0.33417555689811707 0.849112 0.48513442277908325 True -7 21808 30.412195205688477 0.7464087009429932 534.7628173828125 0.23838773369789124 743.2595825195312 0.3396375775337219 0.85281837 0.4536551237106323 True -8 24534 30.419967651367188 0.7500941753387451 474.05657958984375 0.25969332456588745 739.1178588867188 0.3435037434101105 0.8595979 0.4281674921512604 True -9 27260 30.451040506362915 0.7611055374145508 457.41973876953125 0.30578285455703735 740.0853881835938 0.3420337736606598 0.8639521 0.4202599823474884 True -10 29986 30.3800528049469 0.7367961406707764 584.6717529296875 0.24913285672664642 736.5189819335938 0.345028281211853 0.87155807 0.36836761236190796 True -11 32712 30.400294065475464 0.7344057559967041 534.85595703125 0.1751987338066101 733.6792602539062 0.3465054929256439 0.8787124 0.34793928265571594 True -12 35438 30.52107882499695 0.7428567409515381 532.7579345703125 0.1665945053100586 730.6633911132812 0.3503423035144806 0.8840787 0.3163996636867523 True -13 38164 32.053155183792114 0.753887414932251 565.869873046875 0.2899043560028076 727.73681640625 0.3527829647064209 0.8877115 0.2881506085395813 True -14 40890 30.50618577003479 0.7414870262145996 476.56561279296875 0.17594803869724274 727.306396484375 0.3520936965942383 0.8920433 0.26491793990135193 True -15 43616 30.45695734024048 0.7420880794525146 468.1773681640625 0.23702305555343628 723.6126708984375 0.35560479760169983 0.89484054 0.2478465437889099 True -16 46342 30.469675540924072 0.7461321353912354 524.9908447265625 0.1573939472436905 723.1115112304688 0.3560338020324707 0.8953909 0.23352974653244019 True -17 49068 30.379324436187744 0.7376465797424316 490.00927734375 0.15391968190670013 723.854736328125 0.3546973466873169 0.89711297 0.22673609852790833 True -18 51794 30.438374757766724 1.26226806640625 482.3548583984375 0.14393673837184906 724.4815673828125 0.3546004295349121 0.8957949 0.22819781303405762 False -19 54520 30.383381605148315 0.7415809631347656 592.9053955078125 0.17871451377868652 725.54833984375 0.3531613051891327 0.8959433 0.22702327370643616 False diff --git a/ENCSR562FNN/cherimoya.fold_1.performance.tsv b/ENCSR562FNN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a667e4dbc4362c7a6ba1a3c243f396d658c4df20..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -723.854736328125 0.3863529860973358 0.3546973466873169 0.16699790954589844 0.8971129655838013 0.8731471300125122 0.22673609852790833 \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_2.evaluate.json b/ENCSR562FNN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b3807640e3c71e3b13e103fb9893a0b30488eee9..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644UHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_2.fit.json b/ENCSR562FNN/cherimoya.fold_2.fit.json deleted file mode 100644 index 2f75dd3995627232c0cf622320363a45312654c1..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF644UHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_2.log b/ENCSR562FNN/cherimoya.fold_2.log deleted file mode 100644 index 058811fdcb60c686bcd875ca016f2c4e1985311d..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 36.468379497528076 4.229774236679077 595.7197265625 0.2830871045589447 775.1467895507812 0.24130311608314514 0.7529929 4.809621334075928 True -1 5752 32.05903387069702 0.8830420970916748 633.2294311523438 0.34590834379196167 711.4605712890625 0.2919083833694458 0.7908804 1.23582124710083 True -2 8628 32.0511269569397 1.3247270584106445 644.0864868164062 0.3760657012462616 693.7947387695312 0.3044556975364685 0.8093563 0.7319579124450684 True -3 11504 32.019001960754395 0.9149012565612793 517.5372314453125 0.24901072680950165 687.2183227539062 0.3081163465976715 0.8270118 0.6738200187683105 True -4 14380 32.00382351875305 0.8189423084259033 542.3612670898438 0.5342370867729187 683.0299682617188 0.31287187337875366 0.8296218 0.4871867001056671 True -5 17256 31.931036710739136 0.8203377723693848 564.27587890625 0.39419424533843994 678.080810546875 0.3178887367248535 0.83476365 0.4170968234539032 True -6 20132 31.95171070098877 0.6371808052062988 619.0601196289062 0.23692505061626434 677.5556640625 0.3169485330581665 0.8412076 0.3927399814128876 True -7 23008 31.997835636138916 0.6418588161468506 568.7159423828125 0.39959001541137695 674.3251342773438 0.3214593231678009 0.84917134 0.38435426354408264 True -8 25884 32.003334045410156 0.5938787460327148 469.69134521484375 0.29083776473999023 672.56201171875 0.3227117657661438 0.8525673 0.36764901876449585 True -9 28760 31.96971845626831 0.5954220294952393 432.1601867675781 0.12080179899930954 670.578369140625 0.32456013560295105 0.85768676 0.35724425315856934 True -10 31636 32.05734419822693 0.5920445919036865 466.9759216308594 0.19682122766971588 667.9291381835938 0.3274088203907013 0.86611277 0.3184453845024109 True -11 34512 32.08761477470398 1.5709009170532227 543.4169311523438 0.2328006625175476 667.2996826171875 0.3277382254600525 0.8703119 0.3028995990753174 True -12 37388 32.01357412338257 0.6235783100128174 625.5114135742188 0.22703251242637634 663.2769165039062 0.33259081840515137 0.87389755 0.2880551517009735 True -13 40264 32.006491899490356 1.2979400157928467 561.8456420898438 0.19101938605308533 662.7276611328125 0.3333297669887543 0.87976736 0.25773996114730835 True -14 43140 32.040295124053955 0.5905873775482178 559.612548828125 0.17033535242080688 661.9210205078125 0.3340558409690857 0.8820764 0.24460051953792572 True -15 46016 32.128418922424316 21.235867261886597 483.434814453125 0.14547771215438843 660.9647827148438 0.33491119742393494 0.8851094 0.22933344542980194 True -16 48892 32.047730445861816 0.6136560440063477 650.28857421875 0.14175619184970856 658.935791015625 0.3367452025413513 0.8879818 0.2168498933315277 True -17 51768 32.09687900543213 0.6100783348083496 510.4978332519531 0.17113631963729858 659.2431640625 0.33707430958747864 0.8869584 0.2124752700328827 False -18 54644 32.087302446365356 0.602736234664917 491.0643310546875 0.1457127034664154 661.2740478515625 0.33391883969306946 0.8869057 0.21201425790786743 False -19 57520 32.04118752479553 0.5993916988372803 590.6073608398438 0.13481396436691284 660.4298706054688 0.3355195224285126 0.8871739 0.2124595046043396 False diff --git a/ENCSR562FNN/cherimoya.fold_2.performance.tsv b/ENCSR562FNN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index eceb237a32549b23004ba2139005496bc46f1244..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -658.935791015625 0.40126219391822815 0.3367452025413513 0.14782337844371796 0.8879817724227905 0.8474807739257812 0.2168498933315277 \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_3.evaluate.json b/ENCSR562FNN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5bca80e37803195944c6c730c21ee37087111303..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644UHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_3.fit.json b/ENCSR562FNN/cherimoya.fold_3.fit.json deleted file mode 100644 index df34f50fdc34d66e3619086783991021ccb25ba9..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF644UHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_3.log b/ENCSR562FNN/cherimoya.fold_3.log deleted file mode 100644 index 32846693194e66ec87ac19891aeb403488c64b31..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2724 34.917102098464966 4.266366004943848 444.8883361816406 0.2634009122848511 721.0347290039062 0.24188905954360962 0.7263834 5.959526062011719 True -1 5448 30.3612539768219 15.898854732513428 610.0488891601562 0.5180062651634216 662.7574462890625 0.29328569769859314 0.78881127 1.1509268283843994 True -2 8172 29.854575634002686 1.4227418899536133 514.4592895507812 0.4480229616165161 652.0698852539062 0.29894959926605225 0.80539554 0.5316538214683533 True -3 10896 29.880404233932495 1.3606958389282227 450.7723388671875 0.27208441495895386 646.6542358398438 0.3054027557373047 0.8107853 0.49683094024658203 True -4 13620 29.77470588684082 9.008058309555054 481.9901428222656 0.1477968692779541 643.544189453125 0.3085387945175171 0.8155218 0.4927009344100952 True -5 16344 29.733070135116577 1.26826810836792 593.31591796875 0.27351683378219604 641.2014770507812 0.31138330698013306 0.81554145 0.49047693610191345 True -6 19068 29.64969253540039 1.7269675731658936 645.6849975585938 0.5125014781951904 640.020751953125 0.3125089704990387 0.81878436 0.5442033410072327 True -7 21792 29.709665060043335 1.6672627925872803 703.3099365234375 0.5406773090362549 638.354736328125 0.31364449858665466 0.82542306 0.40805360674858093 True -8 24516 29.76427698135376 1.1326582431793213 501.2672119140625 0.22060608863830566 636.0147705078125 0.31651541590690613 0.8280626 0.41285181045532227 True -9 27240 29.77430820465088 1.4677057266235352 571.0687866210938 0.30115216970443726 635.3864135742188 0.3169103264808655 0.8328909 0.41114941239356995 True -10 29964 29.710772037506104 1.2000768184661865 540.4383544921875 0.3353923261165619 632.4594116210938 0.3202601969242096 0.8426322 0.38310250639915466 True -11 32688 29.80996012687683 1.0748405456542969 601.0214233398438 0.23291677236557007 629.3958129882812 0.3231864273548126 0.8492677 0.3501167893409729 True -12 35412 29.842100143432617 0.5910828113555908 622.7205200195312 0.2652240991592407 628.6978149414062 0.3243055045604706 0.857051 0.31972309947013855 True -13 38136 29.84628939628601 0.5867772102355957 461.60308837890625 0.17429092526435852 626.460205078125 0.32650986313819885 0.8622206 0.2957867980003357 True -14 40860 29.762569665908813 0.575096607208252 518.7933959960938 0.15550315380096436 624.0559692382812 0.32760652899742126 0.8673343 0.2711205780506134 True -15 43584 29.99673295021057 0.5882999897003174 598.5812377929688 0.2153322696685791 624.19140625 0.3274630308151245 0.8722951 0.25285476446151733 True -16 46308 29.76986026763916 0.5742816925048828 584.8169555664062 0.16451534628868103 623.3341064453125 0.3288111388683319 0.87675154 0.24165314435958862 True -17 49032 29.84085440635681 0.6217548847198486 501.4033203125 0.1263655424118042 623.3004150390625 0.3278523087501526 0.87758404 0.2343904972076416 True -18 51756 29.995023012161255 0.5886297225952148 522.0845947265625 0.22984614968299866 624.2453002929688 0.32612061500549316 0.8762728 0.23458455502986908 False -19 54480 29.99259924888611 2.1632349491119385 665.018798828125 0.10472915321588516 624.0161743164062 0.3273589015007019 0.8758707 0.2354286015033722 False diff --git a/ENCSR562FNN/cherimoya.fold_3.performance.tsv b/ENCSR562FNN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e9d6a02e657e194e88fd2853d58f4faac0d88427..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -623.3004150390625 0.4088746905326843 0.3278523087501526 0.14448027312755585 0.8775840401649475 0.8275333642959595 0.2343904972076416 \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_4.evaluate.json b/ENCSR562FNN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 59c318c7a7c9af4d87731636a1e9359a37a9ea99..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644UHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_4.fit.json b/ENCSR562FNN/cherimoya.fold_4.fit.json deleted file mode 100644 index b7e6c6bd6f05ea6f04b4779b217188bd93b61247..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF644UHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR562FNN/cherimoya.fold_4.log b/ENCSR562FNN/cherimoya.fold_4.log deleted file mode 100644 index af2e279de72bb95c4d1e18fc0aa8dba0287c2626..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2829 36.62422966957092 3.9061777591705322 605.446533203125 0.40446949005126953 662.38525390625 0.23816430568695068 0.75227445 4.709331035614014 True -1 5658 31.586896419525146 0.647383451461792 602.147705078125 0.37711358070373535 618.47607421875 0.28063032031059265 0.79149187 1.0740231275558472 True -2 8487 31.583287477493286 0.6117160320281982 543.84912109375 0.2656542658805847 610.6062622070312 0.2844187617301941 0.80528927 0.5606494545936584 True -3 11316 30.85075092315674 0.6111011505126953 644.403076171875 0.41166770458221436 603.9196166992188 0.2903200685977936 0.8176054 0.5976696610450745 True -4 14145 30.795588493347168 0.6126372814178467 662.3355712890625 0.45565927028656006 600.0870971679688 0.29499584436416626 0.825457 0.42081084847450256 True -5 16974 30.83936095237732 0.6072127819061279 489.8870544433594 0.24868428707122803 597.6094970703125 0.29754266142845154 0.8316475 0.37252864241600037 True -6 19803 30.782211780548096 0.6110048294067383 559.0380249023438 0.3270008862018585 596.135986328125 0.29895931482315063 0.8394819 0.35010024905204773 True -7 22632 30.79381012916565 0.6061539649963379 524.2648315429688 0.3122834265232086 592.9859619140625 0.30274510383605957 0.8445704 0.33403459191322327 True -8 25461 30.782063245773315 0.6117558479309082 627.1033935546875 0.3153263330459595 592.2976684570312 0.30327925086021423 0.8497084 0.31697914004325867 True -9 28290 30.876206398010254 0.6076474189758301 565.8540649414062 0.298136442899704 590.1884155273438 0.3060598075389862 0.8537821 0.2958768308162689 True -10 31119 30.927130699157715 0.6124453544616699 534.3143310546875 0.2592551112174988 587.9136962890625 0.3086201250553131 0.85862446 0.2918579578399658 True -11 33948 30.814199209213257 0.6077840328216553 531.1094970703125 0.2122272104024887 586.2866821289062 0.31015729904174805 0.8649644 0.2664080560207367 True -12 36777 30.870898723602295 0.6107838153839111 527.4613647460938 0.2185012400150299 585.7711181640625 0.3120180070400238 0.86873955 0.24885354936122894 True -13 39606 30.876827478408813 0.6023752689361572 544.7365112304688 0.20689302682876587 585.1210327148438 0.3119231164455414 0.8728161 0.22855718433856964 True -14 42435 30.848087787628174 0.6103370189666748 621.180908203125 0.28162622451782227 583.7120971679688 0.3140365481376648 0.877813 0.2120324969291687 True -15 45264 30.83021354675293 0.613774299621582 496.89605712890625 0.11518434435129166 582.3724975585938 0.3159492015838623 0.88084936 0.19980116188526154 True -16 48093 30.874597311019897 0.6058390140533447 529.0231323242188 0.17956039309501648 582.3504638671875 0.31489408016204834 0.88374615 0.18884308636188507 True -17 50922 30.873159646987915 0.6154847145080566 513.1407470703125 0.14973606169223785 582.8540649414062 0.31378892064094543 0.8833268 0.18428291380405426 False -18 53751 30.94122815132141 0.6141552925109863 565.653564453125 0.19552403688430786 581.4912719726562 0.3163585364818573 0.88516486 0.1835685521364212 True -19 56580 33.43082118034363 7.816009283065796 493.32177734375 0.08730001747608185 582.4990844726562 0.3145982325077057 0.883227 0.184188112616539 False diff --git a/ENCSR562FNN/cherimoya.fold_4.performance.tsv b/ENCSR562FNN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index cf8c06beb2ffe9186b7f8a48ad75ba06cd3a30c1..0000000000000000000000000000000000000000 --- a/ENCSR562FNN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -581.4912719726562 0.419253945350647 0.3163585364818573 0.13228432834148407 0.8851648569107056 0.8197924494743347 0.1835685521364212 \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_0.evaluate.json b/ENCSR563CZB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7e8413984d559c791854590fe7d52f6d900a8207..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF269QBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_0.fit.json b/ENCSR563CZB/cherimoya.fold_0.fit.json deleted file mode 100644 index e5dc1b6d36d37c60f45307bf2fc1f96fee503be5..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF269QBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_0.log b/ENCSR563CZB/cherimoya.fold_0.log deleted file mode 100644 index b5e36fd9b4d5f3870916ce1491eb272780fefa1f..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.40995979309082 4.121796369552612 420.56915283203125 0.28633546829223633 575.11865234375 0.2792622148990631 0.78573525 4.61622428894043 True -1 5516 30.101998567581177 26.345415592193604 422.0447998046875 0.3401039242744446 534.2733764648438 0.3517489433288574 0.8147381 0.9665383696556091 True -2 8274 31.03277063369751 2.2009477615356445 419.7980041503906 0.18300586938858032 525.519287109375 0.3646405041217804 0.83557117 0.3559550344944 True -3 11032 30.023934841156006 0.5730063915252686 477.0722961425781 0.3111226558685303 522.4644165039062 0.36861351132392883 0.8413975 0.33109456300735474 True -4 13790 29.996349573135376 0.5742635726928711 434.10455322265625 0.19308485090732574 520.2525024414062 0.37370410561561584 0.8458085 0.23974968492984772 True -5 16548 30.42036509513855 0.5717525482177734 477.36053466796875 0.20262548327445984 519.7146606445312 0.37357163429260254 0.85070646 0.22285550832748413 True -6 19306 30.085014820098877 0.5635576248168945 448.1772766113281 0.16784581542015076 518.5194091796875 0.3758569359779358 0.85041934 0.2020849883556366 False -7 22064 30.312988758087158 0.5719015598297119 451.29705810546875 0.2647070586681366 517.1079711914062 0.3780248463153839 0.8569824 0.18756498396396637 True -8 24822 30.03589630126953 0.5716328620910645 445.0936279296875 0.20222482085227966 516.77734375 0.37790143489837646 0.8607478 0.17739754915237427 True -9 27580 30.027201175689697 0.5713424682617188 449.8646240234375 0.14084714651107788 515.7372436523438 0.3796306550502777 0.86405194 0.16963782906532288 True -10 30338 29.985677003860474 0.5680851936340332 440.707275390625 0.1552710384130478 515.0758056640625 0.3804442882537842 0.8671989 0.16593235731124878 True -11 33096 29.968721866607666 0.5671811103820801 512.3007202148438 0.1728784739971161 513.6071166992188 0.38319653272628784 0.8702657 0.15557321906089783 True -12 35854 30.029149293899536 0.5737061500549316 462.01251220703125 0.11545848846435547 513.3351440429688 0.3835168480873108 0.87274027 0.14585250616073608 True -13 38612 30.09980058670044 18.239699363708496 417.4596252441406 0.17667125165462494 512.4599609375 0.38562092185020447 0.8773871 0.14397570490837097 True -14 41370 30.179466009140015 34.740986585617065 512.0050659179688 0.16180339455604553 511.92303466796875 0.386030912399292 0.8798457 0.140244260430336 True -15 44128 30.174018144607544 0.6109988689422607 403.38409423828125 0.16676616668701172 511.5122375488281 0.3861828148365021 0.8828596 0.13555565476417542 True -16 46886 30.114432334899902 1.4796154499053955 438.0976867675781 0.2386236935853958 510.5838928222656 0.3881250023841858 0.8841472 0.13272754848003387 True -17 49644 30.153028964996338 0.5722908973693848 400.935302734375 0.13081315159797668 511.0556640625 0.3866369128227234 0.8858534 0.13058005273342133 True -18 52402 30.072436094284058 28.745059728622437 448.7073974609375 0.15039965510368347 510.7625427246094 0.3876596987247467 0.88590276 0.12974558770656586 True -19 55160 30.4338858127594 27.983710050582886 480.8158874511719 0.11184313148260117 510.8987121582031 0.38726314902305603 0.88547057 0.12982356548309326 False diff --git a/ENCSR563CZB/cherimoya.fold_0.performance.tsv b/ENCSR563CZB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index bb3d928df8b8b42e33049ea851fad47f572f3ecc..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -510.7625427246094 0.41016849875450134 0.3876596689224243 0.13197658956050873 0.8859027624130249 0.877583384513855 0.12974558770656586 \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_1.evaluate.json b/ENCSR563CZB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c9040298f16e95edf60d08182cfff8a8ace1f8c0..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF269QBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_1.fit.json b/ENCSR563CZB/cherimoya.fold_1.fit.json deleted file mode 100644 index 9ffd3d8988089e12f6462f13aef805d96af75660..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF269QBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_1.log b/ENCSR563CZB/cherimoya.fold_1.log deleted file mode 100644 index 89b29129b6474fa5fb043bedeed75236658afc7e..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 33.55586004257202 4.451907157897949 402.889892578125 0.24723997712135315 638.5529174804688 0.27267464995384216 0.79229975 4.663457870483398 True -1 5404 29.363709449768066 38.43645906448364 418.02862548828125 0.1725015491247177 585.8802490234375 0.35743311047554016 0.8327266 0.8244814276695251 True -2 8106 29.498863220214844 2.1148264408111572 470.06500244140625 0.32867372035980225 574.7046508789062 0.37126636505126953 0.84964526 0.36897993087768555 True -3 10808 30.353032112121582 26.520697116851807 503.109375 0.22336004674434662 570.6715698242188 0.37735867500305176 0.8555977 0.3360193371772766 True -4 13510 29.498476266860962 0.7102420330047607 447.53125 0.330035924911499 568.6574096679688 0.3802051544189453 0.8604342 0.25050315260887146 True -5 16212 29.415764331817627 0.716731071472168 457.42633056640625 0.17952102422714233 567.5403442382812 0.381489098072052 0.8599477 0.2184380441904068 False -6 18914 29.399375200271606 1.4981939792633057 447.4373779296875 0.21760691702365875 567.297119140625 0.38164782524108887 0.8672286 0.2125106006860733 True -7 21616 29.455905437469482 0.7172272205352783 407.2344970703125 0.31780338287353516 565.4218139648438 0.3838912546634674 0.8678995 0.19121123850345612 True -8 24318 29.377672910690308 0.7022736072540283 444.24468994140625 0.18233606219291687 563.9083862304688 0.38652369379997253 0.87107563 0.19175194203853607 True -9 27020 29.402990341186523 2.20135760307312 414.2150573730469 0.16380053758621216 561.8970336914062 0.38962888717651367 0.87696415 0.1755690723657608 True -10 29722 29.350226163864136 0.7099356651306152 452.0099792480469 0.16538278758525848 561.5220336914062 0.39013344049453735 0.8809697 0.17709797620773315 True -11 32424 29.48997950553894 46.17590141296387 496.8534851074219 0.18629030883312225 560.47314453125 0.391613245010376 0.88218266 0.16904132068157196 True -12 35126 29.640129804611206 0.7413861751556396 474.1314697265625 0.12952503561973572 559.6719360351562 0.392412006855011 0.88539517 0.16382743418216705 True -13 37828 29.4638991355896 20.742919206619263 464.1120910644531 0.20757430791854858 558.8878784179688 0.3933364450931549 0.8875755 0.16074194014072418 True -14 40530 31.17520570755005 2.610703468322754 497.8216247558594 0.2168286144733429 557.8147583007812 0.39571475982666016 0.8905893 0.15268243849277496 True -15 43232 29.50385618209839 0.7131092548370361 492.6641845703125 0.14898709952831268 557.5765991210938 0.3953251838684082 0.8928004 0.1464443951845169 True -16 45934 29.53194522857666 0.7169656753540039 417.8232421875 0.13658297061920166 556.911865234375 0.39636579155921936 0.89502865 0.14125357568264008 True -17 48636 29.45931386947632 1.5289828777313232 435.7287292480469 0.08029694855213165 557.416259765625 0.3953460454940796 0.8963198 0.13917995989322662 True -18 51338 29.420104026794434 0.705066442489624 417.6722106933594 0.15030276775360107 557.097412109375 0.39662182331085205 0.8961718 0.13806065917015076 False -19 54040 29.638656616210938 2.7913715839385986 400.8140869140625 0.11931130290031433 556.7360229492188 0.3973037600517273 0.89699036 0.13822506368160248 True diff --git a/ENCSR563CZB/cherimoya.fold_1.performance.tsv b/ENCSR563CZB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 903761132095662d941531013d58569ee79f2c22..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -556.7360229492188 0.4004029631614685 0.3973037898540497 0.14280323684215546 0.8969903588294983 0.8935965299606323 0.13822506368160248 \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_2.evaluate.json b/ENCSR563CZB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 38cb8e4a8803d9be670961b92826c0dfeb664038..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF269QBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_2.fit.json b/ENCSR563CZB/cherimoya.fold_2.fit.json deleted file mode 100644 index 2546a334f4f736295ff86e98c19048b9b1a91aa6..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF269QBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_2.log b/ENCSR563CZB/cherimoya.fold_2.log deleted file mode 100644 index 0807bbd61b6b869602754fe99330d408f24bc12b..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.775980949401855 3.4141907691955566 454.2051086425781 0.27648138999938965 605.5816650390625 0.2821809649467468 0.7754349 3.6425609588623047 True -1 5744 31.344846963882446 0.5544507503509521 472.76495361328125 0.29874587059020996 557.6118774414062 0.36041101813316345 0.8246727 0.8614420294761658 True -2 8616 31.251489877700806 0.5725448131561279 470.885009765625 0.28234991431236267 550.4404296875 0.3689870238304138 0.8370538 0.32972604036331177 True -3 11488 31.312873601913452 0.5314123630523682 482.1005859375 0.2431856393814087 548.385986328125 0.37282484769821167 0.836288 0.32427260279655457 False -4 14360 31.288186073303223 1.4038007259368896 439.068603515625 0.23399865627288818 545.1119384765625 0.37732547521591187 0.84526604 0.20904216170310974 True -5 17232 31.269171476364136 0.5311408042907715 523.1619873046875 0.2838445007801056 544.167236328125 0.3789431154727936 0.8463862 0.20392607152462006 True -6 20104 31.277101039886475 0.5391912460327148 438.13897705078125 0.21393203735351562 543.2034912109375 0.38021212816238403 0.8480412 0.18461255729198456 True -7 22976 31.366527557373047 18.120529413223267 445.2828674316406 0.20047856867313385 541.5619506835938 0.38329726457595825 0.853063 0.19726777076721191 True -8 25848 30.65331220626831 26.0815167427063 387.6006164550781 0.20527034997940063 541.2468872070312 0.38426458835601807 0.85363567 0.18977530300617218 True -9 28720 30.72200345993042 0.5423943996429443 419.32464599609375 0.24890613555908203 539.9862670898438 0.3866114318370819 0.85584795 0.20663021504878998 True -10 31592 30.68059802055359 11.196616411209106 469.6998596191406 0.1568223536014557 539.0369262695312 0.3877813518047333 0.8602976 0.17400577664375305 True -11 34464 31.558879375457764 0.5370137691497803 511.02069091796875 0.10291968286037445 538.2927856445312 0.38833948969841003 0.8631883 0.16369681060314178 True -12 37336 30.68201470375061 0.532850980758667 439.23516845703125 0.23207299411296844 537.3876953125 0.38960710167884827 0.86768484 0.1617872714996338 True -13 40208 30.699377298355103 0.520005464553833 415.03118896484375 0.1704171895980835 535.627197265625 0.3929368257522583 0.87130994 0.15205331146717072 True -14 43080 30.630443811416626 0.5191550254821777 507.12786865234375 0.14319315552711487 535.9981689453125 0.3916100859642029 0.87404126 0.14944849908351898 True -15 45952 30.6627459526062 0.544795036315918 451.4302978515625 0.15529555082321167 534.9332885742188 0.3940350413322449 0.8759621 0.14579616487026215 True -16 48824 30.653605937957764 0.5290215015411377 463.3746337890625 0.1461997926235199 534.5862426757812 0.394108384847641 0.87861466 0.1414799988269806 True -17 51696 30.598347425460815 15.914671182632446 462.202880859375 0.14504623413085938 534.7255249023438 0.3938194215297699 0.8793853 0.13890118896961212 True -18 54568 30.74217939376831 0.5198473930358887 453.71527099609375 0.19847093522548676 534.7506713867188 0.39377954602241516 0.8803059 0.1397436410188675 True -19 57440 30.62711787223816 0.518824577331543 451.9405822753906 0.10790802538394928 535.0447387695312 0.3932749629020691 0.8788028 0.14036284387111664 False diff --git a/ENCSR563CZB/cherimoya.fold_2.performance.tsv b/ENCSR563CZB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1d6d05404f506e0476e1a25c8dbfd66568c0ff4e..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -534.7506713867188 0.4049050509929657 0.39377957582473755 0.13779254257678986 0.8803058862686157 0.8705857396125793 0.1397436410188675 \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_3.evaluate.json b/ENCSR563CZB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6c9267637fb33f71579d6c44f11e73c41113e340..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF269QBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_3.fit.json b/ENCSR563CZB/cherimoya.fold_3.fit.json deleted file mode 100644 index e1f8ac4ab9d18f62449aa7b8b6d61b2276e18874..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF269QBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_3.log b/ENCSR563CZB/cherimoya.fold_3.log deleted file mode 100644 index 40079bb9399a7a1877eaa3e0e86721a91df2c7fa..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2784 34.85690355300903 3.8894472122192383 533.016845703125 0.22978951036930084 558.638427734375 0.283708781003952 0.77858454 4.377228736877441 True -1 5568 30.28877568244934 0.5033509731292725 427.5067138671875 0.28151482343673706 516.032958984375 0.3572225272655487 0.8238692 0.5884717106819153 True -2 8352 30.303532123565674 0.507072925567627 425.92608642578125 0.3694898188114166 508.6777648925781 0.36835989356040955 0.8429005 0.3014856278896332 True -3 11136 29.828222274780273 0.5026569366455078 472.157958984375 0.14818787574768066 506.11065673828125 0.3732822835445404 0.84741867 0.3331969082355499 True -4 13920 29.955735445022583 0.49639177322387695 494.739990234375 0.18808713555335999 504.78228759765625 0.37457653880119324 0.8544277 0.20626607537269592 True -5 16704 30.015411138534546 0.5020277500152588 457.27862548828125 0.1691340208053589 504.0605163574219 0.37548163533210754 0.8552932 0.1946573704481125 True -6 19488 30.542516708374023 31.2071373462677 465.56658935546875 0.3210231363773346 502.0320129394531 0.3801284432411194 0.85441947 0.20288659632205963 False -7 22272 29.978053092956543 0.5562295913696289 447.4539489746094 0.22715073823928833 501.90753173828125 0.3792741894721985 0.8596215 0.1797742396593094 True -8 25056 30.770795583724976 0.5173006057739258 501.4382629394531 0.2541095018386841 501.0693054199219 0.38041993975639343 0.86135924 0.17699941992759705 True -9 27840 29.90755343437195 0.5001645088195801 426.10211181640625 0.24953967332839966 499.5392150878906 0.3837675452232361 0.8635006 0.16383253037929535 True -10 30624 31.61707878112793 0.5043313503265381 440.2608337402344 0.15986281633377075 498.3219299316406 0.38504254817962646 0.8655297 0.16724923253059387 True -11 33408 33.15596914291382 33.28843879699707 432.476318359375 0.24718481302261353 497.81109619140625 0.3853374719619751 0.871675 0.16075670719146729 True -12 36192 29.82617425918579 1.4816057682037354 445.7003173828125 0.16073624789714813 496.6055603027344 0.387551486492157 0.87491673 0.15383091568946838 True -13 38976 29.75078058242798 25.936235666275024 365.64013671875 0.19716796278953552 496.27850341796875 0.387556254863739 0.8775235 0.1484891027212143 True -14 41760 33.788251876831055 0.49431562423706055 448.04150390625 0.20763345062732697 495.2847900390625 0.3893781304359436 0.8813715 0.1421787440776825 True -15 44544 29.736231803894043 0.4954957962036133 400.4967041015625 0.16524900496006012 494.8197326660156 0.3898886442184448 0.88673687 0.13607971370220184 True -16 47328 29.813725471496582 0.49276208877563477 422.0124816894531 0.1901167929172516 494.5367736816406 0.3894047141075134 0.8896323 0.1325182169675827 True -17 50112 29.818476676940918 27.94436001777649 405.039306640625 0.0912114605307579 494.06207275390625 0.3907894790172577 0.88958395 0.13017863035202026 False -18 52896 29.72674298286438 0.5223159790039062 425.4832458496094 0.10797803848981857 494.16644287109375 0.3903822600841522 0.89041173 0.12918272614479065 True -19 55680 29.733479976654053 0.48412036895751953 443.6219787597656 0.10863712430000305 494.0162048339844 0.3901621401309967 0.8921275 0.12949037551879883 True diff --git a/ENCSR563CZB/cherimoya.fold_3.performance.tsv b/ENCSR563CZB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2700d1a3c35d6bcabb83971f65e273cea63aee17..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -494.0162048339844 0.4106404185295105 0.3901621401309967 0.13192489743232727 0.892127513885498 0.8746380805969238 0.12949037551879883 \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_4.evaluate.json b/ENCSR563CZB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fc561fe65d0e0f3749bdd16eca7cd53cd7377fa9..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF269QBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_4.fit.json b/ENCSR563CZB/cherimoya.fold_4.fit.json deleted file mode 100644 index ce0e41df76cfcd8ccd17790793588cb8c957ae89..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF269QBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563CZB/cherimoya.fold_4.log b/ENCSR563CZB/cherimoya.fold_4.log deleted file mode 100644 index 772d31b1e9c1df8c3fb2d15e821595c0a5f37b38..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2827 36.064597606658936 3.7386066913604736 486.203857421875 0.35171109437942505 525.919189453125 0.2750467360019684 0.78405976 4.082118988037109 True -1 5654 30.88687229156494 0.6004409790039062 475.9991455078125 0.2365226298570633 486.82073974609375 0.3475112020969391 0.8225693 0.6796379089355469 True -2 8481 30.834555625915527 1.127049207687378 516.9757080078125 0.19829528033733368 482.10186767578125 0.3540608286857605 0.84008163 0.27210733294487 True -3 11308 31.229260206222534 9.902891635894775 437.29888916015625 0.2980390191078186 479.4479064941406 0.3580601215362549 0.8490708 0.2610572576522827 True -4 14135 30.851792335510254 16.180914878845215 422.62646484375 0.20894551277160645 477.3859558105469 0.36226150393486023 0.8525344 0.184797465801239 True -5 16962 33.17879056930542 0.6081085205078125 408.3810729980469 0.35226911306381226 476.6912536621094 0.36371904611587524 0.85547876 0.16146670281887054 True -6 19789 32.970388889312744 0.6111462116241455 444.5024108886719 0.3570031523704529 476.52880859375 0.36284753680229187 0.8559748 0.15221042931079865 True -7 22616 31.17062020301819 0.5886485576629639 459.17230224609375 0.17997299134731293 474.7505187988281 0.3671848475933075 0.85962117 0.14566516876220703 True -8 25443 31.410924911499023 0.5874896049499512 452.6723327636719 0.19323433935642242 474.0896911621094 0.36904826760292053 0.8617727 0.14703479409217834 True -9 28270 31.212002754211426 0.5914573669433594 413.96624755859375 0.1956850290298462 473.29290771484375 0.36952507495880127 0.8643101 0.1394953578710556 True -10 31097 31.075028657913208 0.5837557315826416 446.73931884765625 0.3993552625179291 472.42449951171875 0.37059804797172546 0.8669559 0.13508880138397217 True -11 33924 30.97506833076477 0.5821442604064941 412.8790283203125 0.22115597128868103 471.6414794921875 0.3727312684059143 0.8687276 0.13310718536376953 True -12 36751 30.91582465171814 1.378915548324585 457.75506591796875 0.2294735610485077 470.3768005371094 0.3750549256801605 0.8740173 0.13035503029823303 True -13 39578 30.830209732055664 0.5756731033325195 398.7584228515625 0.22021254897117615 470.02728271484375 0.37559452652931213 0.87573904 0.12978872656822205 True -14 42405 30.795151472091675 0.5746674537658691 455.84088134765625 0.10654833912849426 469.79962158203125 0.3760770559310913 0.8802148 0.1253012865781784 True -15 45232 30.797794342041016 0.584326982498169 413.264892578125 0.15202906727790833 469.501953125 0.3766079843044281 0.88405114 0.12145014852285385 True -16 48059 30.797136068344116 0.5683493614196777 462.13043212890625 0.10615266114473343 468.9236755371094 0.37777039408683777 0.8863979 0.11929020285606384 True -17 50886 30.805760860443115 0.5853219032287598 376.9293212890625 0.07877492159605026 468.83843994140625 0.3770601153373718 0.88736534 0.1176626980304718 True -18 53713 30.779473304748535 2.273672580718994 450.2679443359375 0.12788188457489014 468.8717346191406 0.37734276056289673 0.88759 0.11742057651281357 True -19 56540 30.860449075698853 0.5861630439758301 466.0534973144531 0.1315522938966751 468.63299560546875 0.3779817819595337 0.88803536 0.11779122799634933 True diff --git a/ENCSR563CZB/cherimoya.fold_4.performance.tsv b/ENCSR563CZB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1767f2316a088145e13a2eb5289209b01921dd0b..0000000000000000000000000000000000000000 --- a/ENCSR563CZB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -468.63299560546875 0.421130508184433 0.3779817819595337 0.12332558631896973 0.8880353569984436 0.8740918636322021 0.11779122799634933 \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_0.evaluate.json b/ENCSR563XRP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5dd7ebf0d5116d4301be8f850238dbc0bb93451d..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF768HMR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_0.fit.json b/ENCSR563XRP/cherimoya.fold_0.fit.json deleted file mode 100644 index 0c20fcb3eb496cdda76441a752bc83dfd6a9f0e5..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF768HMR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_0.log b/ENCSR563XRP/cherimoya.fold_0.log deleted file mode 100644 index 0a4ac5c4c0d97de3457b8fa349d620cec58a579c..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2651 33.07560348510742 3.7084100246429443 126.97464752197266 0.8760533332824707 154.998046875 0.12599590420722961 0.35923088 2.2197442054748535 True -1 5302 30.069658279418945 14.672079086303711 132.32803344726562 0.7237558364868164 145.11647033691406 0.18537886440753937 0.4936959 1.463054895401001 True -2 7953 29.51564335823059 1.175008773803711 102.22505187988281 0.6664667129516602 142.5082550048828 0.1961352676153183 0.52199376 0.8389773964881897 True -3 10604 29.54738163948059 1.7691059112548828 130.50990295410156 0.643064022064209 141.28155517578125 0.20161783695220947 0.53514284 0.884703516960144 True -4 13255 29.524651527404785 23.00956630706787 121.79959869384766 0.6118576526641846 140.75221252441406 0.2047334909439087 0.5388711 0.8788194060325623 True -5 15906 29.471625566482544 22.37625026702881 109.63602447509766 0.6429017782211304 140.20431518554688 0.20659996569156647 0.5559504 0.7535223960876465 True -6 18557 30.06071639060974 0.5410256385803223 112.279541015625 0.5381749868392944 139.98028564453125 0.2075188308954239 0.5635947 0.7118264436721802 True -7 21208 29.375802755355835 0.5253818035125732 122.8667221069336 0.5923980474472046 139.66213989257812 0.21017681062221527 0.57385963 0.770825982093811 True -8 23859 28.815088987350464 0.5242514610290527 92.91111755371094 0.4310730993747711 139.2174835205078 0.21289296448230743 0.57782596 0.6905512809753418 True -9 26510 28.83490800857544 0.5180573463439941 122.33877563476562 0.6322968006134033 138.96609497070312 0.21488742530345917 0.5834019 0.6675298810005188 True -10 29161 28.810359716415405 0.5217115879058838 93.87381744384766 0.46154165267944336 138.79098510742188 0.2156747281551361 0.5921697 0.6164769530296326 True -11 31812 28.84861421585083 0.5245349407196045 114.96090698242188 0.3623446822166443 138.48583984375 0.2178114354610443 0.60167074 0.5661836266517639 True -12 34463 28.874993324279785 0.5164062976837158 114.38177490234375 0.5900556445121765 137.98971557617188 0.22164948284626007 0.6135968 0.5239182710647583 True -13 37114 28.83017349243164 0.5341672897338867 111.27560424804688 0.8662811517715454 137.91453552246094 0.2212860882282257 0.6251601 0.496555358171463 True -14 39765 28.846651554107666 0.5596652030944824 128.98617553710938 0.520726203918457 137.5819549560547 0.2234257310628891 0.63461006 0.4598667025566101 True -15 42416 28.861053466796875 0.5176358222961426 117.46964263916016 0.2359098345041275 137.42601013183594 0.22420936822891235 0.64464927 0.4320332705974579 True -16 45067 28.87910795211792 0.530846357345581 119.06028747558594 0.3836081027984619 137.2419891357422 0.22594007849693298 0.6492194 0.420743465423584 True -17 47718 28.906078338623047 0.5217299461364746 125.39254760742188 0.344791442155838 137.2249755859375 0.22568707168102264 0.65193105 0.4173091948032379 True -18 50369 28.826624870300293 0.5147912502288818 95.15232849121094 0.459940642118454 137.3271484375 0.22517675161361694 0.6535652 0.4140700101852417 True -19 53020 28.801032543182373 0.5205273628234863 120.28958129882812 0.40930384397506714 137.35733032226562 0.224942147731781 0.6517228 0.4183496832847595 False diff --git a/ENCSR563XRP/cherimoya.fold_0.performance.tsv b/ENCSR563XRP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c47eaffc4a0ddba47cd00e8a8144c1c801457b47..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -137.3271484375 0.5589627027511597 0.22517675161361694 0.03992176055908203 0.6535652279853821 0.6182465553283691 0.4140700101852417 \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_1.evaluate.json b/ENCSR563XRP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a9684b8847875a0c0955935e9c0754ef81e56e55..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF768HMR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_1.fit.json b/ENCSR563XRP/cherimoya.fold_1.fit.json deleted file mode 100644 index cb8fd69ca750e37caf4ef01e86c6f2dcdae63036..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF768HMR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_1.log b/ENCSR563XRP/cherimoya.fold_1.log deleted file mode 100644 index ad5b2c490f32701ec98a848a4956ae3273464ae4..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2666 33.16714692115784 3.527310848236084 113.62806701660156 0.7720118761062622 170.94866943359375 0.13255110383033752 0.37355292 2.20625901222229 True -1 5332 29.593757390975952 0.656247615814209 121.91551971435547 0.906385600566864 159.25906372070312 0.1965651512145996 0.48554265 1.4703394174575806 True -2 7998 29.49479866027832 3.4346282482147217 131.85940551757812 0.6186712980270386 156.3151092529297 0.21093344688415527 0.53169894 0.8758253455162048 True -3 10664 29.591709852218628 0.6766796112060547 111.0634536743164 0.7577527761459351 154.6579132080078 0.21745407581329346 0.5536447 0.7789507508277893 True -4 13330 29.6424880027771 0.6722328662872314 128.25750732421875 0.6454476714134216 153.8512725830078 0.22112210094928741 0.56261873 0.8380071520805359 True -5 15996 29.57513427734375 0.6531248092651367 118.5902099609375 0.5901176929473877 153.28025817871094 0.22362591326236725 0.5733577 0.8198152780532837 True -6 18662 29.586207628250122 0.6410496234893799 106.56613159179688 0.45276302099227905 152.98033142089844 0.22396211326122284 0.5851951 0.7583426833152771 True -7 21328 29.56115484237671 0.6822686195373535 113.170654296875 0.5697284936904907 152.1239013671875 0.23019789159297943 0.5939094 0.7613922953605652 True -8 23994 29.579870223999023 0.6469674110412598 111.08572387695312 0.5287919044494629 151.8013458251953 0.23201721906661987 0.60079336 0.7274064421653748 True -9 26660 29.537057399749756 0.65694260597229 124.10530090332031 0.7470563054084778 151.31622314453125 0.23420436680316925 0.6137582 0.6781420707702637 True -10 29326 29.554298400878906 0.689164400100708 98.18982696533203 0.5247915983200073 151.03103637695312 0.23523032665252686 0.62357706 0.6393367648124695 True -11 31992 29.535048484802246 0.9935574531555176 114.84196472167969 0.5390800833702087 150.93942260742188 0.23475497961044312 0.63163674 0.5766419768333435 True -12 34658 29.595799922943115 1.5962398052215576 106.11138916015625 0.36381351947784424 150.59230041503906 0.23658156394958496 0.64074934 0.5414252877235413 True -13 37324 29.32852792739868 1.0744335651397705 113.94464111328125 0.8138481378555298 150.01783752441406 0.24093423783779144 0.6518041 0.5054312944412231 True -14 39990 28.980835437774658 0.6419808864593506 89.74332427978516 0.4115320146083832 149.96836853027344 0.24059398472309113 0.66224694 0.4677185118198395 True -15 42656 28.960914134979248 0.652318000793457 108.37025451660156 0.46457386016845703 149.54310607910156 0.24325551092624664 0.67131317 0.4479423463344574 True -16 45322 28.927799701690674 0.6444823741912842 101.86538696289062 0.5731410980224609 149.6424560546875 0.2416648417711258 0.6769182 0.4286566376686096 True -17 47988 28.943451166152954 0.6502611637115479 117.13973236083984 0.3437495231628418 149.61375427246094 0.2420574426651001 0.68007255 0.42022162675857544 True -18 50654 28.91951823234558 0.6485280990600586 108.71653747558594 0.40727174282073975 149.5535888671875 0.24269190430641174 0.6788598 0.4217507541179657 False -19 53320 28.933250665664673 0.6502578258514404 95.55638885498047 0.306073933839798 149.61334228515625 0.24232779443264008 0.6775833 0.424998015165329 False diff --git a/ENCSR563XRP/cherimoya.fold_1.performance.tsv b/ENCSR563XRP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2c7e5ecb48c2c10222eb3d1ea30a5f8bd079802b..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -149.61375427246094 0.5471060872077942 0.2420574128627777 0.04653817415237427 0.680072546005249 0.6498991847038269 0.42022162675857544 \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_2.evaluate.json b/ENCSR563XRP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9700acc0dcb3c84ddb7228de6ae6c773cbaa53ba..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF768HMR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_2.fit.json b/ENCSR563XRP/cherimoya.fold_2.fit.json deleted file mode 100644 index 52e0f1935f3dedc6e523e1c0db495fb5d39e8995..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF768HMR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_2.log b/ENCSR563XRP/cherimoya.fold_2.log deleted file mode 100644 index 9f03fdc498491b9c402bb11807705a688743d5bd..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2801 34.33798670768738 3.3997178077697754 118.27154541015625 0.7342662811279297 158.84820556640625 0.12838114798069 0.3510352 1.6345542669296265 True -1 5602 31.073041439056396 0.5166680812835693 125.80670166015625 0.6748839020729065 147.53652954101562 0.19348891079425812 0.5086559 1.0295506715774536 True -2 8403 30.834004640579224 0.5023300647735596 147.0465087890625 0.8727553486824036 144.76918029785156 0.20622515678405762 0.53034836 0.7100074291229248 True -3 11204 30.834182262420654 0.5333304405212402 97.29048156738281 0.6207799315452576 143.56935119628906 0.21127375960350037 0.5541452 0.6866756081581116 True -4 14005 32.91777968406677 0.5213325023651123 118.65074920654297 0.49754244089126587 142.78067016601562 0.21522663533687592 0.56957287 0.6306328177452087 True -5 16806 30.151723861694336 0.5089659690856934 101.77204132080078 0.5525171756744385 142.5341339111328 0.2154378443956375 0.5762173 0.6059460639953613 True -6 19607 30.182469844818115 0.5058519840240479 116.76325988769531 0.6711047887802124 142.08924865722656 0.21784435212612152 0.5861328 0.5688789486885071 True -7 22408 30.23320984840393 0.5025308132171631 126.12515258789062 0.6503745317459106 141.81605529785156 0.22014276683330536 0.5936111 0.5861048102378845 True -8 25209 30.068543910980225 0.4964876174926758 106.71507263183594 0.5758536458015442 141.60537719726562 0.22090762853622437 0.6002087 0.5609894394874573 True -9 28010 30.124022006988525 0.5003714561462402 111.12140655517578 0.565235435962677 141.32485961914062 0.22299295663833618 0.6086832 0.5574434399604797 True -10 30811 30.120233297348022 0.5070152282714844 117.66574096679688 0.46065184473991394 140.90809631347656 0.2255755364894867 0.61856645 0.5181803107261658 True -11 33612 30.13560652732849 0.5048646926879883 110.5958251953125 0.3560502529144287 140.64071655273438 0.2272522747516632 0.62828386 0.4790935814380646 True -12 36413 30.186086654663086 15.044733762741089 92.8699951171875 0.3070864677429199 140.39627075195312 0.22835730016231537 0.6348145 0.4657912850379944 True -13 39214 30.282681703567505 1.361694097518921 113.197265625 0.4487871527671814 140.0486602783203 0.23074786365032196 0.6457301 0.44880667328834534 True -14 42015 30.238162517547607 0.7499246597290039 131.8446807861328 0.4675901532173157 139.80064392089844 0.23214173316955566 0.6568518 0.42108309268951416 True -15 44816 30.116362810134888 0.5039000511169434 115.56239318847656 0.3936275839805603 139.473388671875 0.2346261441707611 0.6608266 0.4140172600746155 True -16 47617 30.101168155670166 1.5596437454223633 131.15118408203125 0.3907091021537781 139.33990478515625 0.23541276156902313 0.66692984 0.4065462648868561 True -17 50418 30.17536425590515 0.5012328624725342 98.77932739257812 0.4407661259174347 139.46542358398438 0.23377785086631775 0.6697878 0.4046763479709625 True -18 53219 30.129117012023926 0.5001113414764404 98.2588882446289 0.34917378425598145 139.48745727539062 0.23351173102855682 0.6696423 0.40419116616249084 False -19 56020 30.127496004104614 0.500800371170044 113.3099365234375 0.2942765951156616 139.5691375732422 0.2327231615781784 0.66861314 0.40820661187171936 False diff --git a/ENCSR563XRP/cherimoya.fold_2.performance.tsv b/ENCSR563XRP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d4ed4159c1d79ec8f1d705d79d68aa2374bbca58..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -139.46542358398438 0.5545433759689331 0.23377785086631775 0.044296734035015106 0.6697878241539001 0.6302399039268494 0.4046763479709625 \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_3.evaluate.json b/ENCSR563XRP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d3f8acdd56661cf4d9e92158df6ece628eee6ed6..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF768HMR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_3.fit.json b/ENCSR563XRP/cherimoya.fold_3.fit.json deleted file mode 100644 index eed57dc878ad464cf6d0ded5ae32c5b9f27396ce..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF768HMR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_3.log b/ENCSR563XRP/cherimoya.fold_3.log deleted file mode 100644 index acfe26b4147021f140ef51206d195205b12b8c52..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 33.5953152179718 3.40556001663208 122.01913452148438 0.6816604137420654 162.03041076660156 0.129512757062912 0.38854966 2.0527544021606445 True -1 5406 30.00429391860962 0.5872373580932617 89.87330627441406 0.946418046951294 151.35096740722656 0.19025038182735443 0.5040569 1.308124303817749 True -2 8109 30.028112173080444 0.5541129112243652 113.97936248779297 0.5184900164604187 148.73304748535156 0.2017400711774826 0.5315857 0.9144815802574158 True -3 10812 30.014385223388672 0.5558891296386719 113.62802124023438 0.5988945960998535 147.5146484375 0.20717571675777435 0.55109674 0.8411729335784912 True -4 13515 29.96317172050476 0.5600943565368652 117.09461212158203 0.53258216381073 146.6531219482422 0.21372662484645844 0.5566179 0.8507260680198669 True -5 16218 29.927196502685547 0.5506598949432373 115.02391052246094 0.6823835968971252 146.21343994140625 0.21602708101272583 0.5720424 0.7964897751808167 True -6 18921 29.906047821044922 0.550868034362793 105.38323211669922 0.593535304069519 145.9178009033203 0.21653415262699127 0.58617336 0.7109124064445496 True -7 21624 29.894782543182373 0.5503606796264648 105.41481018066406 0.49269455671310425 145.59410095214844 0.21907080709934235 0.592502 0.7301765084266663 True -8 24327 29.38047695159912 0.5543224811553955 123.2929916381836 0.5917917490005493 145.37042236328125 0.21969258785247803 0.6028909 0.6680202484130859 True -9 27030 29.338188886642456 0.5496275424957275 100.96900177001953 0.49315887689590454 144.81829833984375 0.22365660965442657 0.61439145 0.63038569688797 True -10 29733 29.339872121810913 0.5556595325469971 102.7171630859375 0.682306170463562 144.71044921875 0.2235531508922577 0.6190305 0.5792514681816101 True -11 32436 29.39533567428589 0.5607442855834961 86.30323791503906 0.4682844281196594 144.38674926757812 0.22566884756088257 0.6280781 0.5719467997550964 True -12 35139 29.343923568725586 0.5526375770568848 110.69818115234375 0.6506387591362 144.171630859375 0.226889505982399 0.63945323 0.539693295955658 True -13 37842 29.368371963500977 0.5536625385284424 92.08966827392578 0.6245219707489014 143.79586791992188 0.2293602079153061 0.6483421 0.502055287361145 True -14 40545 29.467690467834473 0.6398077011108398 105.17756652832031 0.5340560078620911 143.53233337402344 0.2307492345571518 0.65486354 0.4742790162563324 True -15 43248 29.434619903564453 0.5688049793243408 114.49987030029297 0.551587700843811 143.4237823486328 0.23079156875610352 0.66220313 0.4513247013092041 True -16 45951 29.442570447921753 0.5592000484466553 94.73444366455078 0.3964543044567108 143.24832153320312 0.23209083080291748 0.6688803 0.43292996287345886 True -17 48654 29.42259931564331 0.5471658706665039 103.33172607421875 0.39198049902915955 143.34840393066406 0.23118560016155243 0.6713594 0.4216797947883606 True -18 51357 29.410531282424927 0.5531501770019531 116.88898468017578 0.3330489993095398 143.31903076171875 0.2315254509449005 0.6705542 0.42046022415161133 False -19 54060 29.336233377456665 0.5530173778533936 113.87094116210938 0.3261605501174927 143.27366638183594 0.23199307918548584 0.6688498 0.42468008399009705 False diff --git a/ENCSR563XRP/cherimoya.fold_3.performance.tsv b/ENCSR563XRP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ec4f54abcc10d4c5597276d78a50e9d18a971d05..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -143.34840393066406 0.554608941078186 0.23118561506271362 0.04015561193227768 0.6713594198226929 0.6401295065879822 0.4216797947883606 \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_4.evaluate.json b/ENCSR563XRP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index cb1b780a0f09cf6762f0e33c02e722302c88185c..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF768HMR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_4.fit.json b/ENCSR563XRP/cherimoya.fold_4.fit.json deleted file mode 100644 index cf59c59813d49ae4ee2f30fbae7e3b0020f76d38..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF768HMR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR563XRP/cherimoya.fold_4.log b/ENCSR563XRP/cherimoya.fold_4.log deleted file mode 100644 index 1e7d803dfaa38fc56541f15e5c5e5615b4e840be..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2790 34.66898226737976 3.6198363304138184 92.46487426757812 0.6057767271995544 154.3938751220703 0.1262606680393219 0.3533747 1.7640581130981445 True -1 5580 30.94010090827942 0.5600619316101074 110.74795532226562 0.8783650398254395 144.00894165039062 0.18601715564727783 0.514293 1.2294590473175049 True -2 8370 31.06841278076172 0.5470550060272217 104.7706298828125 0.5799170136451721 141.86903381347656 0.19539065659046173 0.5409468 0.7264090180397034 True -3 11160 31.009814977645874 0.5509376525878906 105.6936264038086 0.5838140249252319 141.00857543945312 0.20133239030838013 0.5524293 0.6800406575202942 True -4 13950 30.998430967330933 0.566586971282959 97.00069427490234 0.610420823097229 140.4542236328125 0.20360711216926575 0.5653154 0.6855666637420654 True -5 16740 30.908671617507935 0.5477588176727295 92.91304779052734 0.5204228162765503 139.98275756835938 0.20583821833133698 0.5746842 0.6398419141769409 True -6 19530 30.88569474220276 0.5450708866119385 126.31175231933594 0.545426607131958 139.482177734375 0.2096385657787323 0.58431494 0.618258535861969 True -7 22320 30.853160858154297 0.5487091541290283 125.61377716064453 0.42648082971572876 139.36279296875 0.2096363604068756 0.59069425 0.6024051308631897 True -8 25110 30.90423083305359 0.5523073673248291 107.79796600341797 0.6037814617156982 139.12278747558594 0.21073083579540253 0.60400575 0.5989458560943604 True -9 27900 30.308122396469116 1.278775691986084 118.38681030273438 0.66552734375 139.0047149658203 0.2106451839208603 0.60820866 0.5824952125549316 True -10 30690 30.389729976654053 0.5489366054534912 114.50294494628906 0.6297382116317749 138.4365692138672 0.21548394858837128 0.6133419 0.5637097954750061 True -11 33480 30.355211973190308 0.5508995056152344 108.12062072753906 0.5063719749450684 138.244140625 0.21624340116977692 0.62551546 0.5292142033576965 True -12 36270 30.315433025360107 0.5479989051818848 117.43406677246094 0.606452226638794 138.034912109375 0.21737943589687347 0.6322104 0.4926173686981201 True -13 39060 30.32199454307556 0.5492026805877686 113.92691040039062 0.45670977234840393 137.572021484375 0.2208198457956314 0.6417826 0.46646761894226074 True -14 41850 30.361347913742065 0.54060959815979 97.29229736328125 0.5458252429962158 137.42153930664062 0.22153665125370026 0.6506138 0.4457769989967346 True -15 44640 30.272491693496704 0.5399625301361084 109.91889953613281 0.44575464725494385 137.2693634033203 0.22257128357887268 0.659119 0.4216022491455078 True -16 47430 30.271348476409912 0.5396935939788818 103.52478790283203 0.40083563327789307 137.10667419433594 0.22372615337371826 0.66422707 0.40507617592811584 True -17 50220 30.319379329681396 0.5438990592956543 98.66987609863281 0.3125555217266083 137.09881591796875 0.22366014122962952 0.6670207 0.3992573022842407 True -18 53010 30.35962748527527 0.5388526916503906 113.82508850097656 0.31275659799575806 137.00296020507812 0.22481301426887512 0.6658945 0.398858904838562 False -19 55800 30.32438898086548 0.535609245300293 116.84365844726562 0.38197410106658936 137.13827514648438 0.22328022122383118 0.6652356 0.40335774421691895 False diff --git a/ENCSR563XRP/cherimoya.fold_4.performance.tsv b/ENCSR563XRP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index baa2f18e8e5f444b5ecff902d38cca069a6ed15c..0000000000000000000000000000000000000000 --- a/ENCSR563XRP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -137.09881591796875 0.5595828890800476 0.22366014122962952 0.04035239294171333 0.6670206785202026 0.6297075748443604 0.3992573022842407 \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_0.evaluate.json b/ENCSR564FZH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 26a46c20a6041955a5453101f3a64f4890b656f9..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809YTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_0.fit.json b/ENCSR564FZH/cherimoya.fold_0.fit.json deleted file mode 100644 index 7a33576bf33443bc1680dce0170e5d3409d222f4..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF809YTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_0.log b/ENCSR564FZH/cherimoya.fold_0.log deleted file mode 100644 index ccf1b69d1cc5edf02e83b717795f0eac18c0727a..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.27459907531738 3.495788097381592 530.3709106445312 0.6033128499984741 714.0257568359375 0.26702988147735596 0.61556333 5.043418884277344 True -1 5476 30.28744411468506 0.5829358100891113 565.8981323242188 0.35315072536468506 646.250732421875 0.3606777787208557 0.6797115 1.9699054956436157 True -2 8214 30.352614164352417 0.5691165924072266 692.493896484375 0.6344966888427734 632.3225708007812 0.3728862702846527 0.70137167 0.8995345234870911 True -3 10952 30.342554092407227 0.5950002670288086 578.7913818359375 0.32589131593704224 626.2201538085938 0.3803841769695282 0.71384 0.9460911154747009 True -4 13690 30.277631521224976 0.5578947067260742 546.8302001953125 0.48176708817481995 622.3054809570312 0.38639920949935913 0.7216612 0.7163887619972229 True -5 16428 30.292743682861328 0.558565616607666 516.7978515625 0.22060391306877136 621.8751831054688 0.3868287205696106 0.7269765 0.6657655835151672 True -6 19166 30.306677103042603 0.5716285705566406 517.508544921875 0.3945007920265198 618.4405517578125 0.39179718494415283 0.7378767 0.6292672157287598 True -7 21904 30.354586601257324 0.5588278770446777 511.0395202636719 0.3521834909915924 616.4352416992188 0.3935328722000122 0.74524796 0.6108712553977966 True -8 24642 30.329811573028564 0.5551648139953613 459.38214111328125 0.4106178879737854 614.1690673828125 0.39795365929603577 0.7516474 0.5805763006210327 True -9 27380 30.276824951171875 2.726463556289673 436.99462890625 0.2761651277542114 612.0089111328125 0.4006214439868927 0.75880104 0.574791431427002 True -10 30118 30.300607204437256 0.5597624778747559 468.8844299316406 0.2626831829547882 610.5472412109375 0.40207639336586 0.76577204 0.5091227889060974 True -11 32856 29.689756870269775 0.5590336322784424 475.77630615234375 0.2525593042373657 608.7665405273438 0.4036450684070587 0.7705438 0.4631156325340271 True -12 35594 29.658862590789795 0.5483322143554688 490.94378662109375 0.24076694250106812 606.95703125 0.4064226448535919 0.7816131 0.4204995334148407 True -13 38332 29.80706286430359 0.5910956859588623 536.1634521484375 0.5988321304321289 604.8938598632812 0.40865176916122437 0.78799677 0.3682376742362976 True -14 41070 29.713741779327393 7.342220783233643 495.2452392578125 0.28366005420684814 602.612548828125 0.4115981459617615 0.7913863 0.3361895978450775 True -15 43808 29.720651626586914 0.569364070892334 551.2559814453125 0.310870885848999 603.6904907226562 0.4098528325557709 0.79908633 0.310934454202652 True -16 46546 29.76173162460327 0.5569655895233154 530.7884521484375 0.20716343820095062 602.3720092773438 0.41270479559898376 0.8049644 0.29111114144325256 True -17 49284 29.772124767303467 0.9816827774047852 463.60687255859375 0.21260827779769897 602.04638671875 0.4127401113510132 0.80691206 0.2825844883918762 True -18 52022 29.71916890144348 2.47904372215271 506.3671875 0.21684665977954865 602.9109497070312 0.41138797998428345 0.8056998 0.27872660756111145 False -19 54760 29.699292421340942 0.613278865814209 540.9864501953125 0.2020229697227478 602.83056640625 0.41145074367523193 0.803435 0.2797697186470032 False diff --git a/ENCSR564FZH/cherimoya.fold_0.performance.tsv b/ENCSR564FZH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a1914a324f965936a232d1ae4ff725db1d0fb8e3..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -602.04638671875 0.37317711114883423 0.4127401113510132 0.1674116551876068 0.8069120645523071 0.7636563777923584 0.2825844883918762 \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_1.evaluate.json b/ENCSR564FZH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index be738a2d77f89dda73fb3dc15eb5c1537147d662..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809YTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_1.fit.json b/ENCSR564FZH/cherimoya.fold_1.fit.json deleted file mode 100644 index d80241915365fe2c744fb33045953a521ead62ff..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF809YTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_1.log b/ENCSR564FZH/cherimoya.fold_1.log deleted file mode 100644 index 288448f66b3b7c47339fb0c9f53aea493e6da763..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 33.93533778190613 11.71718144416809 603.8524780273438 0.469298779964447 821.2938842773438 0.27089551091194153 0.6295917 5.510696887969971 True -1 5424 29.523193359375 1.6964304447174072 632.115966796875 0.49210408329963684 732.3810424804688 0.3766362965106964 0.7070593 1.7890337705612183 True -2 8136 29.63324761390686 0.7118287086486816 515.3182373046875 0.5167356133460999 716.6671752929688 0.3934173583984375 0.7216831 1.085992455482483 True -3 10848 29.504367351531982 1.231156587600708 592.535400390625 0.3434796631336212 712.3397827148438 0.3955536484718323 0.73628026 1.0548325777053833 True -4 13560 29.471845388412476 0.7018008232116699 529.9420776367188 0.36408016085624695 706.7740478515625 0.40258628129959106 0.7422867 0.8496593236923218 True -5 16272 29.464600563049316 0.6897056102752686 645.5820922851562 0.46127015352249146 704.718017578125 0.40503019094467163 0.7477361 0.7592694759368896 True -6 18984 29.487276077270508 0.693265438079834 482.1393127441406 0.2527131736278534 699.8516235351562 0.4114856719970703 0.75089383 0.740423858165741 True -7 21696 29.503172874450684 0.6845831871032715 516.2791137695312 0.30759626626968384 697.9439697265625 0.41217154264450073 0.7581189 0.7128028273582458 True -8 24408 29.45779275894165 0.7185385227203369 505.1261291503906 0.37386614084243774 696.0856323242188 0.41337913274765015 0.7641328 0.6750400066375732 True -9 27120 29.45557951927185 0.9510149955749512 580.37109375 0.26757875084877014 691.192626953125 0.42073309421539307 0.7714388 0.6410560011863708 True -10 29832 29.514880418777466 0.6970071792602539 444.828125 0.3110593855381012 689.5150756835938 0.42128807306289673 0.7762832 0.5808050632476807 True -11 32544 29.512900352478027 0.6903102397918701 539.5072021484375 0.3345351815223694 685.67333984375 0.4259875416755676 0.7868752 0.5314303636550903 True -12 35256 29.508488178253174 0.6939127445220947 538.4154052734375 0.3524911403656006 683.949951171875 0.42668595910072327 0.79177344 0.48913732171058655 True -13 37968 29.48669695854187 0.6933939456939697 416.1170349121094 0.25478336215019226 680.1787109375 0.430448442697525 0.8022103 0.43259096145629883 True -14 40680 29.54408860206604 0.7003648281097412 517.3533935546875 0.30774378776550293 679.1659545898438 0.43143677711486816 0.80971545 0.393034428358078 True -15 43392 29.437565326690674 0.6982784271240234 577.6719360351562 0.3516865372657776 677.8026733398438 0.4323740601539612 0.81622624 0.3534461259841919 True -16 46104 29.44559097290039 0.6924521923065186 484.06427001953125 0.269065260887146 675.79638671875 0.4341413676738739 0.8232966 0.3229345977306366 True -17 48816 29.46030879020691 0.6992785930633545 577.5567626953125 0.23853838443756104 677.0550537109375 0.43198803067207336 0.8238231 0.30749955773353577 True -18 51528 29.50294852256775 0.6978340148925781 480.6531677246094 0.22127331793308258 676.4317016601562 0.4331083297729492 0.82302547 0.3001372814178467 False -19 54240 29.46037197113037 0.6974079608917236 617.1575927734375 0.22065772116184235 677.688720703125 0.4302750825881958 0.82174534 0.29978981614112854 False diff --git a/ENCSR564FZH/cherimoya.fold_1.performance.tsv b/ENCSR564FZH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 694ca704fd737514e8c2a0a8fde3193cee996b5e..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -677.0550537109375 0.3559103310108185 0.431988000869751 0.1872410774230957 0.823823094367981 0.8001898527145386 0.30749955773353577 \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_2.evaluate.json b/ENCSR564FZH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3046f1b349a73b5be1d77bb717f43eab0f9b27a7..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809YTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_2.fit.json b/ENCSR564FZH/cherimoya.fold_2.fit.json deleted file mode 100644 index fe4afb91027e8cfa822a003db8eb1f38c51bd352..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF809YTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_2.log b/ENCSR564FZH/cherimoya.fold_2.log deleted file mode 100644 index a4fda88dd12315e232b416e3f34852d8d007e530..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 35.38265943527222 3.5942542552948 527.3463745117188 0.43632838129997253 741.548095703125 0.2645311951637268 0.62018496 4.488104343414307 True -1 5740 32.18214154243469 0.5647971630096436 499.06842041015625 0.3290054202079773 659.9490356445312 0.3698571026325226 0.7089098 1.8026564121246338 True -2 8610 31.9033420085907 0.559424877166748 487.520263671875 0.5040276646614075 651.395751953125 0.3772973418235779 0.7169276 0.9169804453849792 True -3 11480 32.135818004608154 0.5563614368438721 532.9544677734375 0.35121193528175354 647.4918212890625 0.38144248723983765 0.7223221 0.9161129593849182 True -4 14350 31.546874523162842 0.5501680374145508 493.72210693359375 0.4475123882293701 645.1777954101562 0.38254475593566895 0.7307132 0.6821881532669067 True -5 17220 31.231038093566895 0.5439248085021973 561.1751098632812 0.513719916343689 641.0769653320312 0.38938453793525696 0.7396743 0.632756233215332 True -6 20090 31.204102993011475 0.5439367294311523 641.1119384765625 0.5533751249313354 640.9366455078125 0.3880811631679535 0.74295014 0.6136200428009033 True -7 22960 31.210681200027466 0.6654284000396729 501.8808898925781 0.5121329426765442 637.7943725585938 0.39212504029273987 0.7516602 0.5728168487548828 True -8 25830 31.35166049003601 0.5483698844909668 485.7985534667969 0.4622424840927124 636.20263671875 0.3948230743408203 0.7551555 0.5606213212013245 True -9 28700 31.248168230056763 0.5508830547332764 444.1453857421875 0.31405654549598694 633.1663818359375 0.3990025818347931 0.76557696 0.5098464488983154 True -10 31570 31.218221187591553 0.5467767715454102 520.1478271484375 0.27261537313461304 630.0825805664062 0.40303707122802734 0.77309924 0.46698197722435 True -11 34440 31.235143899917603 0.5486578941345215 522.2748413085938 0.21865946054458618 628.52099609375 0.40552785992622375 0.77951515 0.44909486174583435 True -12 37310 31.301401376724243 0.5494439601898193 483.3106994628906 0.3193527162075043 627.6619873046875 0.40534722805023193 0.7849539 0.4178020656108856 True -13 40180 31.26423692703247 0.5491135120391846 548.8905639648438 0.2787104547023773 623.1025390625 0.412940114736557 0.7939026 0.3759695887565613 True -14 43050 31.221097230911255 0.5484817028045654 475.8763732910156 0.15497678518295288 623.82763671875 0.40989112854003906 0.7993102 0.34846699237823486 True -15 45920 31.216660737991333 0.5430846214294434 507.13580322265625 0.28469565510749817 622.7249755859375 0.4113757610321045 0.8046006 0.3195505440235138 True -16 48790 31.211824893951416 0.5494170188903809 555.3648681640625 0.2403404265642166 621.7642211914062 0.4126359522342682 0.8103538 0.29764434695243835 True -17 51660 31.263073444366455 0.5482409000396729 599.6131591796875 0.27338892221450806 621.299560546875 0.41373661160469055 0.81051266 0.287258118391037 True -18 54530 31.36586284637451 0.5485012531280518 514.1312866210938 0.21764278411865234 621.3900146484375 0.41353437304496765 0.81055576 0.2843240797519684 True -19 57400 31.263606786727905 0.5508933067321777 599.820068359375 0.17235620319843292 621.4324951171875 0.4137892723083496 0.8089984 0.2844701111316681 False diff --git a/ENCSR564FZH/cherimoya.fold_2.performance.tsv b/ENCSR564FZH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index fb6ca5c0f2cab26eb3d81f7306af30952befdc7b..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -621.3900146484375 0.37048104405403137 0.4135344326496124 0.1740153580904007 0.8105557560920715 0.7807199954986572 0.2843240797519684 \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_3.evaluate.json b/ENCSR564FZH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ce831b0d7d5d75da65a58d03023d1bb2ff1da64f..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809YTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_3.fit.json b/ENCSR564FZH/cherimoya.fold_3.fit.json deleted file mode 100644 index 7002f33daf77c7d734f71027df66d13aa3a51731..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF809YTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_3.log b/ENCSR564FZH/cherimoya.fold_3.log deleted file mode 100644 index 700498da6d51d4a9f9399f10a4d57ab47c241821..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.25397348403931 3.5077054500579834 523.5750732421875 0.5041473507881165 713.7108764648438 0.2668376863002777 0.62725973 5.002982139587402 True -1 5478 30.415167808532715 0.5850417613983154 631.3092651367188 0.3755410313606262 645.0533447265625 0.3570646047592163 0.6985842 2.1576783657073975 True -2 8217 30.376671075820923 0.5647456645965576 557.6991577148438 0.5398446321487427 632.7258911132812 0.3703189790248871 0.7174832 1.1248950958251953 True -3 10956 30.383870124816895 0.5596387386322021 513.9140625 0.6136825084686279 625.9065551757812 0.3770865499973297 0.73261005 0.8899450302124023 True -4 13695 30.51712918281555 19.35572576522827 586.7470703125 0.4119442105293274 624.7291259765625 0.37747108936309814 0.73500514 0.7858873605728149 True -5 16434 30.496246814727783 0.6021935939788818 549.427734375 0.46944281458854675 619.5669555664062 0.38454490900039673 0.74024695 0.7156929969787598 True -6 19173 30.513548135757446 0.5854859352111816 684.9799194335938 0.36676299571990967 618.9041748046875 0.38455891609191895 0.75201327 0.7339690327644348 True -7 21912 29.91968297958374 0.568347692489624 501.0596923828125 0.34157323837280273 615.821044921875 0.38943421840667725 0.75871825 0.7020873427391052 True -8 24651 29.928661584854126 0.5678167343139648 533.1848754882812 0.2884296774864197 612.7304077148438 0.39366233348846436 0.7666876 0.6305593848228455 True -9 27390 29.839520692825317 0.568702220916748 415.5153503417969 0.37230169773101807 611.4810791015625 0.39505326747894287 0.77266467 0.5974971652030945 True -10 30129 29.81009578704834 0.5598185062408447 531.4910278320312 0.32609471678733826 608.8008422851562 0.39831823110580444 0.778992 0.5489864945411682 True -11 32868 29.838242053985596 0.5570316314697266 539.4354248046875 0.2536546289920807 606.1300048828125 0.4011797308921814 0.78950113 0.4940735399723053 True -12 35607 29.869099855422974 0.5611190795898438 641.9520874023438 0.3350598216056824 603.9882202148438 0.4040357172489166 0.79794747 0.4371989667415619 True -13 38346 30.050771951675415 0.5622763633728027 580.749267578125 0.27907365560531616 601.6119384765625 0.40641558170318604 0.804125 0.3934798836708069 True -14 41085 29.827497720718384 2.2500178813934326 603.167236328125 0.24441587924957275 600.4061889648438 0.407254159450531 0.8097357 0.3677770495414734 True -15 43824 29.819061756134033 0.564016580581665 565.1544799804688 0.25661343336105347 599.3836059570312 0.4081650376319885 0.8159156 0.33031660318374634 True -16 46563 29.868662118911743 0.9006035327911377 434.66064453125 0.24532544612884521 599.0991821289062 0.40853211283683777 0.81987363 0.3067896068096161 True -17 49302 29.84149670600891 0.5617904663085938 527.591552734375 0.18378344178199768 598.90478515625 0.40875697135925293 0.81892186 0.29211196303367615 False -18 52041 29.900910139083862 0.5543003082275391 470.5797119140625 0.3820129632949829 598.7615356445312 0.4090147018432617 0.8190695 0.28941527009010315 False -19 54780 29.87446904182434 0.5640130043029785 502.48345947265625 0.1391393542289734 599.4313354492188 0.40794187784194946 0.8176657 0.2897443175315857 False diff --git a/ENCSR564FZH/cherimoya.fold_3.performance.tsv b/ENCSR564FZH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d87aaa50f814d16de82cfdc7be0fe96eccecb86c..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -599.0991821289062 0.3751494288444519 0.40853211283683777 0.1688641458749771 0.8198736310005188 0.7770377993583679 0.3067896068096161 \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_4.evaluate.json b/ENCSR564FZH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 52823122ba0f1d9ef2441f5e0afd5bb52ccb0f0a..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809YTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_4.fit.json b/ENCSR564FZH/cherimoya.fold_4.fit.json deleted file mode 100644 index 87d98b7135fb8a692bf6cac963bcd4405900f0e5..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF809YTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564FZH/cherimoya.fold_4.log b/ENCSR564FZH/cherimoya.fold_4.log deleted file mode 100644 index 4e099fd9bc21e48479bbe5b9b239cb0143976a72..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2834 35.03824281692505 3.550227642059326 506.007568359375 0.47061634063720703 673.401611328125 0.2652934193611145 0.61359453 4.598158359527588 True -1 5668 30.776190280914307 0.5739965438842773 580.6828002929688 0.3897897005081177 614.8682861328125 0.35291749238967896 0.6868835 1.8147974014282227 True -2 8502 31.171146869659424 1.808750867843628 498.9989013671875 0.44048061966896057 600.246337890625 0.3670715391635895 0.7148068 0.8283555507659912 True -3 11336 31.23054838180542 0.5705931186676025 551.183349609375 0.4307701587677002 595.54248046875 0.3716801404953003 0.722543 0.8853294849395752 True -4 14170 31.164947986602783 0.5799787044525146 556.45458984375 0.4309089779853821 592.2501831054688 0.3763090968132019 0.73035514 0.5543147325515747 True -5 17004 31.117603063583374 0.5720350742340088 559.6927490234375 0.3451458215713501 592.0809326171875 0.37595266103744507 0.73014826 0.5623668432235718 False -6 19838 31.118932723999023 0.5712034702301025 560.5283203125 0.3894292712211609 589.455810546875 0.37911108136177063 0.7435791 0.5205729007720947 True -7 22672 31.1112539768219 0.5750143527984619 520.2003173828125 0.4336262047290802 587.4534301757812 0.3818645775318146 0.74964064 0.519579291343689 True -8 25506 31.061662197113037 0.5759181976318359 554.279296875 0.3217240869998932 585.429443359375 0.38519203662872314 0.75476635 0.485296368598938 True -9 28340 31.058100938796997 0.5742485523223877 452.987060546875 0.32108134031295776 584.9688110351562 0.38607072830200195 0.7606901 0.4823211133480072 True -10 31174 31.2560133934021 0.5780656337738037 582.075439453125 0.30323970317840576 582.42529296875 0.3896828293800354 0.77142245 0.44598811864852905 True -11 34008 31.104808807373047 0.5737471580505371 509.823974609375 0.23184490203857422 580.7411499023438 0.3914359211921692 0.77614444 0.4107125401496887 True -12 36842 31.025667667388916 0.5754430294036865 542.829833984375 0.21458999812602997 578.1591186523438 0.3965364098548889 0.7859828 0.3754061162471771 True -13 39676 31.098796844482422 0.6392536163330078 605.0751953125 0.3228929042816162 577.6865234375 0.3957248330116272 0.7925875 0.3426286280155182 True -14 42510 31.054542779922485 0.571906328201294 523.4666137695312 0.25372907519340515 576.676513671875 0.39735662937164307 0.79739076 0.31262412667274475 True -15 45344 31.131627798080444 0.5744445323944092 461.4941101074219 0.4363943338394165 575.3601684570312 0.39946669340133667 0.8071578 0.2868008315563202 True -16 48178 31.119017601013184 0.5653970241546631 560.4647827148438 0.24878904223442078 576.1476440429688 0.39692947268486023 0.8088218 0.27096879482269287 True -17 51012 31.156657218933105 0.5654091835021973 468.8710021972656 0.11142030358314514 575.8217163085938 0.39806973934173584 0.81255025 0.2606164813041687 True -18 53846 30.582369089126587 0.5629153251647949 529.80859375 0.19489389657974243 576.121337890625 0.39723238348960876 0.811794 0.258190780878067 False -19 56680 30.5549795627594 0.5668210983276367 490.4111022949219 0.14817024767398834 574.995361328125 0.4005289673805237 0.8103431 0.2602013051509857 False diff --git a/ENCSR564FZH/cherimoya.fold_4.performance.tsv b/ENCSR564FZH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index eb2eac6054344e08e323e16aae581a041c562173..0000000000000000000000000000000000000000 --- a/ENCSR564FZH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -575.8217163085938 0.3824371099472046 0.39806970953941345 0.1596219539642334 0.8125502467155457 0.7724560499191284 0.2606164813041687 \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_0.evaluate.json b/ENCSR564JUY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b2f40e9f9feba61b4fba5cbb485edbf4828c46c5..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259KWP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_0.fit.json b/ENCSR564JUY/cherimoya.fold_0.fit.json deleted file mode 100644 index 5d86b9adbef4457e436b0a2203b38b1968dc50fe..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF259KWP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_0.log b/ENCSR564JUY/cherimoya.fold_0.log deleted file mode 100644 index e5c242a2451ed2949b08aedbb85a4bf425a76547..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2718 34.335216760635376 4.3209545612335205 1433.390869140625 1.0854169130325317 2362.3486328125 0.2921030819416046 0.5603133 14.971722602844238 True -1 5436 29.943522930145264 0.5455727577209473 1262.9259033203125 0.8822261095046997 1768.848876953125 0.5006895065307617 0.61725426 8.119662284851074 True -2 8154 29.9639093875885 0.5311603546142578 1419.782470703125 1.1637182235717773 1723.5323486328125 0.5145155191421509 0.63480544 4.427370548248291 True -3 10872 29.39180064201355 0.5057666301727295 1149.571044921875 0.8950040340423584 1677.2379150390625 0.5269471406936646 0.6574289 2.7471158504486084 True -4 13590 29.415123462677002 0.5153756141662598 1295.43896484375 1.0987133979797363 1647.767333984375 0.5355441570281982 0.66722876 1.8775945901870728 True -5 16308 29.417396068572998 0.5149886608123779 1528.7008056640625 0.9888076782226562 1624.8900146484375 0.5447723865509033 0.66918844 1.566011667251587 True -6 19026 29.3456289768219 0.5249910354614258 1040.053466796875 0.8454028367996216 1614.9903564453125 0.5484218597412109 0.66713405 1.5374568700790405 False -7 21744 29.37449049949646 0.5278129577636719 1355.4735107421875 0.7009016275405884 1601.9395751953125 0.5537931323051453 0.6632059 1.451972484588623 False -8 24462 29.364049196243286 0.52463698387146 1073.22802734375 1.0606943368911743 1586.168212890625 0.559727132320404 0.66351986 1.288189172744751 False -9 27180 29.36954140663147 0.5230534076690674 1522.327880859375 0.6648807525634766 1576.169921875 0.5635513663291931 0.66949755 1.2513561248779297 True -10 29898 29.36266541481018 0.5264444351196289 1100.8631591796875 0.9306634664535522 1562.0584716796875 0.5703902840614319 0.66478467 1.0530006885528564 False -11 32616 29.360746383666992 0.524874210357666 1151.2906494140625 0.7245610356330872 1542.6436767578125 0.5756872296333313 0.67967576 0.948694109916687 True -12 35334 29.335869550704956 0.5607974529266357 1014.2421875 0.8407104015350342 1530.8319091796875 0.5792072415351868 0.6910586 0.8125348091125488 True -13 38052 29.353331565856934 0.5262465476989746 1113.611083984375 0.5919492840766907 1519.7215576171875 0.5828580856323242 0.7060525 0.736415445804596 True -14 40770 29.580811977386475 0.5206186771392822 1033.695068359375 0.4213513433933258 1513.524658203125 0.5839897394180298 0.71855664 0.6528447866439819 True -15 43488 29.40799045562744 0.530343770980835 1085.051513671875 0.921218991279602 1499.74560546875 0.5906084775924683 0.7328244 0.5889270305633545 True -16 46206 29.32998561859131 0.601294755935669 1174.544921875 1.046561598777771 1492.4915771484375 0.5925642251968384 0.7433077 0.5574190020561218 True -17 48924 29.388760328292847 0.529198408126831 1400.34619140625 0.3475959300994873 1502.7540283203125 0.5865844488143921 0.74760556 0.5400068163871765 True -18 51642 29.354613065719604 0.5263693332672119 1174.6629638671875 0.4584499001502991 1496.5458984375 0.5897223353385925 0.7503433 0.5339234471321106 True -19 54360 29.62571120262146 0.5415899753570557 1006.2703857421875 0.5620936155319214 1499.2100830078125 0.5886040925979614 0.74940526 0.5318071246147156 False diff --git a/ENCSR564JUY/cherimoya.fold_0.performance.tsv b/ENCSR564JUY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 67aeaa9c916604756e974d86c68c85ee8855f40f..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1496.5458984375 0.24021583795547485 0.5897223353385925 0.325268030166626 0.7503433227539062 0.6997193694114685 0.5339234471321106 \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_1.evaluate.json b/ENCSR564JUY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4a3759429b9e1bd839a1cba1203314e95b77e0df..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259KWP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_1.fit.json b/ENCSR564JUY/cherimoya.fold_1.fit.json deleted file mode 100644 index c2915d4273129d2073bed39a82f7965ff50f6d4b..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF259KWP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_1.log b/ENCSR564JUY/cherimoya.fold_1.log deleted file mode 100644 index e8c9a0520fedaf195fe084229a15dcc7e8a3cbbe..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2715 34.587796211242676 4.4383769035339355 1593.7274169921875 0.8170202374458313 2627.429443359375 0.3059577941894531 0.5626421 15.931239128112793 True -1 5430 29.895298719406128 14.566155672073364 1678.394287109375 1.477830171585083 1962.1619873046875 0.5093631148338318 0.63570434 7.401020526885986 True -2 8145 30.18331503868103 0.7370326519012451 1343.724609375 0.9508585929870605 1913.636474609375 0.518794596195221 0.67107743 3.523531675338745 True -3 10860 29.734923124313354 0.7198326587677002 1721.564453125 0.9597325325012207 1869.2564697265625 0.531340479850769 0.68189377 2.400430202484131 True -4 13575 29.31257724761963 0.7599868774414062 1379.9261474609375 0.9513142108917236 1843.8348388671875 0.5401551723480225 0.6828651 2.4611928462982178 True -5 16290 29.306819915771484 0.7216367721557617 1399.047607421875 0.8072402477264404 1812.8251953125 0.5489967465400696 0.70157474 1.891953945159912 True -6 19005 29.344451189041138 0.7133128643035889 1192.924072265625 0.9160321354866028 1797.860595703125 0.554470419883728 0.69714016 1.6470518112182617 False -7 21720 29.31109046936035 0.725210428237915 1310.6246337890625 0.7006444931030273 1780.456298828125 0.5609655976295471 0.6968436 1.4322787523269653 False -8 24435 29.335290908813477 0.727398157119751 1243.746337890625 0.7116817235946655 1758.8958740234375 0.5674131512641907 0.70610154 1.251432180404663 True -9 27150 29.326374292373657 0.716904878616333 1317.2669677734375 0.954511284828186 1745.7425537109375 0.5708062648773193 0.7025335 1.206269383430481 False -10 29865 29.28161907196045 0.7275760173797607 1245.395263671875 0.9248311519622803 1726.63134765625 0.5757761001586914 0.70569694 1.0197087526321411 False -11 32580 29.313465118408203 0.7188608646392822 1353.961669921875 0.8388781547546387 1720.60791015625 0.5771125555038452 0.71142715 0.9505026340484619 True -12 35295 29.314863204956055 0.7167134284973145 1337.23583984375 0.7789729833602905 1700.997802734375 0.5834387540817261 0.72856236 0.8557411432266235 True -13 38010 29.288496494293213 0.724048376083374 1021.8221435546875 0.6985284686088562 1689.2376708984375 0.5865728259086609 0.73891485 0.7356328964233398 True -14 40725 29.337297439575195 5.276280164718628 1165.99267578125 0.691778302192688 1675.650146484375 0.5886577367782593 0.75148964 0.6645210385322571 True -15 43440 29.3799991607666 0.7377743721008301 1325.36376953125 0.5089492797851562 1666.429931640625 0.5918114185333252 0.7640393 0.6134467720985413 True -16 46155 29.37258553504944 0.7588491439819336 1075.048828125 0.6215317249298096 1656.5889892578125 0.5946575999259949 0.7698219 0.5705317854881287 True -17 48870 29.374810457229614 2.0788066387176514 1104.499755859375 0.5632447004318237 1657.8270263671875 0.5940686464309692 0.7750453 0.5433563590049744 True -18 51585 29.4422767162323 0.7790493965148926 1027.4322509765625 0.5883396863937378 1660.6455078125 0.5929872393608093 0.7758629 0.5340593457221985 True -19 54300 29.351893663406372 0.7372448444366455 1272.344970703125 0.632908821105957 1661.020751953125 0.5927965641021729 0.7769621 0.5300782918930054 True diff --git a/ENCSR564JUY/cherimoya.fold_1.performance.tsv b/ENCSR564JUY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 574e660aad4bae500b926a40cb2f9acd7b4097e4..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1661.020751953125 0.2314811795949936 0.5927965641021729 0.34861132502555847 0.7769621014595032 0.746324896812439 0.5300782918930054 \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_2.evaluate.json b/ENCSR564JUY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a3c9511229639eabc3b04f9f2d634615f9fec432..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259KWP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_2.fit.json b/ENCSR564JUY/cherimoya.fold_2.fit.json deleted file mode 100644 index eaf18774da2d46f3bb511ca70d6564a992b6bd00..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF259KWP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_2.log b/ENCSR564JUY/cherimoya.fold_2.log deleted file mode 100644 index 9b7284495a0fc5601333ebfe1a0c65f7c546e655..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 36.335264444351196 4.362568378448486 1648.52880859375 1.5013505220413208 2395.246337890625 0.3094122111797333 0.5513293 12.635984420776367 True -1 5764 32.14071083068848 4.112334251403809 1284.4522705078125 1.1330878734588623 1825.1856689453125 0.49952149391174316 0.6087097 5.935009956359863 True -2 8646 31.82031559944153 11.712788343429565 1426.734130859375 0.9638785123825073 1783.0125732421875 0.5114176869392395 0.6376851 3.800891160964966 True -3 11528 31.77290916442871 0.7015688419342041 1779.7589111328125 1.2310190200805664 1732.48583984375 0.5235535502433777 0.6581233 2.5681612491607666 True -4 14410 31.727205753326416 0.56026291847229 1563.85546875 0.9466707706451416 1703.7940673828125 0.5334831476211548 0.66764015 2.0428807735443115 True -5 17292 31.274414539337158 0.5504555702209473 1308.838623046875 1.0793817043304443 1679.0169677734375 0.5399848222732544 0.67391527 1.7046560049057007 True -6 20174 31.12826418876648 0.556196928024292 1089.110595703125 1.0411231517791748 1670.72607421875 0.5445144176483154 0.67333525 1.6191294193267822 False -7 23056 31.060643196105957 0.5416150093078613 1373.7579345703125 0.690778374671936 1647.4459228515625 0.5547259449958801 0.67199594 1.7290620803833008 False -8 25938 31.194091320037842 0.535618782043457 1197.7298583984375 0.6775022149085999 1638.8426513671875 0.5597447156906128 0.6718865 1.498343825340271 False -9 28820 31.17011260986328 0.55411696434021 1380.71240234375 0.7350236773490906 1625.2435302734375 0.564069926738739 0.67553514 1.3120887279510498 True -10 31702 31.315414667129517 0.5555403232574463 1045.208251953125 0.7946344614028931 1610.7249755859375 0.5683678388595581 0.68359923 1.2490953207015991 True -11 34584 31.237309455871582 0.6024436950683594 1256.6702880859375 0.659243106842041 1598.18115234375 0.5726245045661926 0.6887179 1.0513083934783936 True -12 37466 31.270628929138184 0.573173999786377 1097.968017578125 0.7048572301864624 1581.516845703125 0.5774733424186707 0.7015694 0.8639710545539856 True -13 40348 31.24979567527771 0.5489017963409424 1174.939208984375 0.8876553773880005 1569.2701416015625 0.5801018476486206 0.7138574 0.7596308588981628 True -14 43230 31.281917333602905 0.5476057529449463 1155.679931640625 0.9846943616867065 1553.8604736328125 0.5862233638763428 0.7235507 0.6753302812576294 True -15 46112 31.347167253494263 0.5419173240661621 1143.57177734375 0.5502951145172119 1550.27001953125 0.586209774017334 0.7344045 0.6290426254272461 True -16 48994 31.261350393295288 0.5365006923675537 1038.9769287109375 0.5322413444519043 1546.3558349609375 0.5881729125976562 0.73997325 0.5886711478233337 True -17 51876 31.268640995025635 0.5450870990753174 1290.944091796875 0.8347851634025574 1550.844970703125 0.5847615003585815 0.7459158 0.5633871555328369 True -18 54758 31.10039258003235 0.5342311859130859 925.0493774414062 0.3157223165035248 1548.54052734375 0.5865658521652222 0.7459058 0.5550603270530701 False -19 57640 31.3010311126709 0.5909483432769775 1210.398193359375 0.5529974699020386 1543.523193359375 0.5903517603874207 0.7454066 0.5563061833381653 False diff --git a/ENCSR564JUY/cherimoya.fold_2.performance.tsv b/ENCSR564JUY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8960795475cb3d2e53f5ebd3c670b8129e168b9a..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1550.844970703125 0.23875120282173157 0.5847615003585815 0.3324302136898041 0.7459157705307007 0.7019484043121338 0.5633871555328369 \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_3.evaluate.json b/ENCSR564JUY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3a8d740d3d36d9a0a5c5d1a40c74b00287524b2e..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259KWP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_3.fit.json b/ENCSR564JUY/cherimoya.fold_3.fit.json deleted file mode 100644 index c35f0f0ca1041e28bad52c550a98bb4041f00305..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF259KWP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_3.log b/ENCSR564JUY/cherimoya.fold_3.log deleted file mode 100644 index 653a29c8bd043a9fca509de6c86321ab0a859c85..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2804 35.47896146774292 3.961468458175659 1281.7392578125 1.5654685497283936 2411.041259765625 0.30648404359817505 0.55234486 15.727148056030273 True -1 5608 30.92957305908203 0.8519330024719238 1491.1611328125 1.136942744255066 1862.29052734375 0.4958184063434601 0.6195259 5.688526153564453 True -2 8412 31.283007860183716 15.374755620956421 1366.789306640625 1.1769156455993652 1817.838134765625 0.5097087621688843 0.6185151 3.770867347717285 False -3 11216 30.92567729949951 0.946403980255127 1387.603271484375 1.128382921218872 1774.2193603515625 0.5239415764808655 0.6367042 3.038635015487671 True -4 14020 30.92665457725525 0.6055572032928467 1393.43115234375 0.884867787361145 1754.139404296875 0.5299676060676575 0.6402185 2.4768142700195312 True -5 16824 30.925168752670288 0.6188006401062012 1390.4366455078125 0.8505355715751648 1738.0328369140625 0.5388830304145813 0.63052 2.2620060443878174 False -6 19628 30.892617225646973 0.5675842761993408 1089.825439453125 1.1714531183242798 1720.3541259765625 0.5437991619110107 0.62945926 2.002685546875 False -7 22432 30.553105115890503 0.5899112224578857 1451.4635009765625 0.8483633995056152 1709.1796875 0.5498148202896118 0.625524 1.9492335319519043 False -8 25236 30.36404824256897 0.5853855609893799 1356.53662109375 0.6543890833854675 1684.023681640625 0.5570588707923889 0.6376802 1.6033450365066528 False -9 28040 30.354406595230103 0.5634875297546387 1392.708740234375 0.7287119626998901 1671.8138427734375 0.5617635250091553 0.6461762 1.5107221603393555 True -10 30844 30.306352853775024 1.0931265354156494 1311.4476318359375 0.7838222980499268 1654.9111328125 0.5663952231407166 0.6596628 1.2003737688064575 True -11 33648 30.361770391464233 0.5316169261932373 1443.487060546875 0.6227061748504639 1639.1953125 0.572697103023529 0.6667718 1.0846368074417114 True -12 36452 30.303982973098755 0.787935733795166 1108.0047607421875 0.9345200657844543 1629.7960205078125 0.574736475944519 0.67699593 0.9501599073410034 True -13 39256 30.299431085586548 0.5390639305114746 1189.9234619140625 0.6151930093765259 1612.725341796875 0.5795179605484009 0.693318 0.8097896575927734 True -14 42060 30.482276678085327 0.5660531520843506 1288.470703125 0.7712591886520386 1611.955322265625 0.578870952129364 0.70882016 0.7463880181312561 True -15 44864 30.327664136886597 0.5444512367248535 1094.4903564453125 0.6217833757400513 1602.8406982421875 0.5817795395851135 0.72104746 0.6772518754005432 True -16 47668 30.343443632125854 0.5644650459289551 1055.11669921875 0.5740072727203369 1598.07861328125 0.5829609036445618 0.72900826 0.644625186920166 True -17 50472 30.332659482955933 0.5384600162506104 1109.817626953125 0.3816235363483429 1591.9952392578125 0.5851938724517822 0.73611087 0.6234263181686401 True -18 53276 30.36595368385315 0.5469820499420166 782.1517333984375 0.6515772342681885 1597.59423828125 0.5821488499641418 0.738942 0.6157103180885315 True -19 56080 30.37728714942932 0.5517866611480713 1255.650146484375 0.517258882522583 1597.794189453125 0.5825160145759583 0.74002415 0.6190081834793091 True diff --git a/ENCSR564JUY/cherimoya.fold_3.performance.tsv b/ENCSR564JUY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e61077e721e1181e400b976a371d9109af404035..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1597.794189453125 0.23937441408634186 0.5825160145759583 0.33105871081352234 0.7400241494178772 0.6936473250389099 0.6190081834793091 \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_4.evaluate.json b/ENCSR564JUY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 630f6b8fd841d02b47634cc7fbb0bd82beddc51b..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259KWP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_4.fit.json b/ENCSR564JUY/cherimoya.fold_4.fit.json deleted file mode 100644 index cb096fb7abdb2e7d478695438478b9cb1c54eb3d..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF259KWP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR564JUY/cherimoya.fold_4.log b/ENCSR564JUY/cherimoya.fold_4.log deleted file mode 100644 index f54082b53a8acb1bdabf5f6e7a09964673856e73..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2821 35.80904841423035 4.39220929145813 1521.822265625 1.138383388519287 2259.806884765625 0.30189868807792664 0.55089104 14.265645980834961 True -1 5642 31.12902522087097 0.5702364444732666 1343.59521484375 1.0838251113891602 1723.1060791015625 0.4942154884338379 0.6169637 5.500245571136475 True -2 8463 31.281853199005127 15.64451265335083 1547.88037109375 1.0633535385131836 1677.990966796875 0.5065814256668091 0.6353183 2.2821550369262695 True -3 11284 31.105125188827515 0.5471265316009521 1523.521728515625 1.0450773239135742 1625.400146484375 0.5214914083480835 0.657334 2.018306016921997 True -4 14105 31.227047204971313 0.5089244842529297 1322.83837890625 1.1091914176940918 1594.62451171875 0.5346858501434326 0.6510133 1.9060014486312866 False -5 16926 31.043877124786377 0.5003776550292969 1285.5517578125 0.8961305618286133 1585.6982421875 0.538653552532196 0.65320086 1.6388273239135742 False -6 19747 31.249786376953125 0.5017504692077637 1333.6209716796875 1.068907380104065 1569.255126953125 0.5455013513565063 0.6433484 1.4033294916152954 False -7 22568 31.166189193725586 0.988396406173706 1112.42431640625 0.6274871826171875 1558.044921875 0.5490366816520691 0.6497203 1.2286337614059448 False -8 25389 31.136112213134766 0.5271155834197998 1246.830810546875 0.7175276279449463 1547.583984375 0.5527957677841187 0.65399665 1.1502001285552979 False -9 28210 30.81553363800049 0.5331916809082031 1478.7552490234375 0.7032716870307922 1535.0897216796875 0.557438313961029 0.6595375 0.967954695224762 True -10 31031 30.676568031311035 0.505012035369873 1345.324951171875 0.5101171731948853 1521.2275390625 0.5622239708900452 0.66412205 0.9177113771438599 True -11 33852 30.54340386390686 0.5022032260894775 1166.8236083984375 0.7139395475387573 1509.169921875 0.5677779912948608 0.67086864 0.8840957880020142 True -12 36673 30.501758813858032 0.5099148750305176 1125.751708984375 0.7068350315093994 1496.4267578125 0.5730524659156799 0.68860054 0.7778245210647583 True -13 39494 30.656683444976807 0.5084238052368164 1039.533203125 0.5531011819839478 1486.516357421875 0.5747594833374023 0.6968586 0.7358972430229187 True -14 42315 30.595727920532227 0.5440983772277832 1148.7598876953125 0.6989209055900574 1477.7484130859375 0.5784359574317932 0.7099022 0.6651044487953186 True -15 45136 30.64877939224243 0.5012240409851074 1069.177978515625 0.567861020565033 1469.620361328125 0.580542266368866 0.72564995 0.6078779101371765 True -16 47957 30.77595615386963 0.5068888664245605 1387.428466796875 0.4815245270729065 1463.300048828125 0.5839210748672485 0.73372245 0.5687462091445923 True -17 50778 30.673715353012085 0.5059115886688232 1106.6068115234375 0.6029341220855713 1456.9974365234375 0.5856844782829285 0.73830366 0.5506253838539124 True -18 53599 30.695061206817627 0.5116875171661377 1065.2562255859375 0.4609789550304413 1466.656982421875 0.5812686085700989 0.74053735 0.5425229668617249 True -19 56420 30.598374366760254 0.4964756965637207 1295.1375732421875 0.619175136089325 1468.038330078125 0.5803132057189941 0.7395776 0.5429465770721436 False diff --git a/ENCSR564JUY/cherimoya.fold_4.performance.tsv b/ENCSR564JUY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index cff519844a72b75f79f8f264bf50dbe9b43b9284..0000000000000000000000000000000000000000 --- a/ENCSR564JUY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1466.656982421875 0.2451644241809845 0.5812686085700989 0.3183857500553131 0.7405373454093933 0.6863349676132202 0.5425229668617249 \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_0.evaluate.json b/ENCSR565DSD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2752109ec3e7a6509484aeec88a2093579e21f4c..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539IPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_0.fit.json b/ENCSR565DSD/cherimoya.fold_0.fit.json deleted file mode 100644 index 8c368248b96f5a4e74e3420bd35253e0d27851a4..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF539IPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_0.log b/ENCSR565DSD/cherimoya.fold_0.log deleted file mode 100644 index d4c67104ba66d904990bbfa54278de69588c4439..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2463 31.89869785308838 3.9458158016204834 500.33502197265625 0.27832555770874023 598.9810791015625 0.6645198464393616 0.7138919 5.597505569458008 True -1 4926 27.48086905479431 0.5148754119873047 476.6944580078125 0.2594665288925171 523.3869018554688 0.7315972447395325 0.7852051 0.8536550402641296 True -2 7389 27.478737831115723 0.5061836242675781 430.9270324707031 0.18956385552883148 510.3993835449219 0.7458993792533875 0.805596 0.30150288343429565 True -3 9852 27.422480821609497 0.5113735198974609 472.3302307128906 0.1798485368490219 506.5062255859375 0.7506937980651855 0.8145603 0.2707354724407196 True -4 12315 27.547940969467163 0.5031461715698242 470.6748046875 0.1430419534444809 505.0117492675781 0.752583920955658 0.8187429 0.16178278625011444 True -5 14778 27.373739004135132 0.5055196285247803 479.549560546875 0.15085899829864502 504.2388916015625 0.7535332441329956 0.8207818 0.16100357472896576 True -6 17241 27.360335111618042 0.5048747062683105 482.0353698730469 0.19098621606826782 503.78643798828125 0.7541416883468628 0.825242 0.16134428977966309 True -7 19704 27.362552404403687 0.5059597492218018 439.3294677734375 0.1077432930469513 502.5437316894531 0.7556838989257812 0.8297441 0.14540134370326996 True -8 22167 27.224046230316162 0.48560357093811035 448.5333251953125 0.18804940581321716 501.7579650878906 0.7565711736679077 0.83310413 0.13698753714561462 True -9 24630 26.862945318222046 0.503676176071167 486.11981201171875 0.1322374939918518 500.84344482421875 0.7576643228530884 0.83530444 0.14022794365882874 True -10 27093 26.851545333862305 0.5034737586975098 441.51776123046875 0.13415907323360443 499.7437744140625 0.7590932250022888 0.8434099 0.13066887855529785 True -11 29556 26.90589213371277 0.49758386611938477 429.6406555175781 0.20771872997283936 499.028564453125 0.760246217250824 0.84553844 0.12553121149539948 True -12 32019 26.86854910850525 0.4968883991241455 461.18817138671875 0.16692602634429932 497.9892578125 0.761530339717865 0.85170543 0.1217518150806427 True -13 34482 26.889381647109985 1.3496756553649902 450.42193603515625 0.17186562716960907 497.3883361816406 0.7624844312667847 0.8581914 0.11728595197200775 True -14 36945 26.902097463607788 0.4995157718658447 432.03363037109375 0.1340421885251999 496.7737731933594 0.7633537650108337 0.8622282 0.11502856761217117 True -15 39408 26.90146017074585 0.9777510166168213 430.462890625 0.10206396877765656 496.4708251953125 0.7638641595840454 0.86535805 0.11255957931280136 True -16 41871 26.934695720672607 0.5070383548736572 439.23162841796875 0.11653536558151245 496.3246154785156 0.7640925049781799 0.865839 0.11255405098199844 True -17 44334 26.89081883430481 0.5105092525482178 410.5587463378906 0.06747311353683472 496.46380615234375 0.7640289664268494 0.868686 0.11151128262281418 True -18 46797 26.950455904006958 0.5048432350158691 455.69293212890625 0.055536434054374695 496.51898193359375 0.7637247443199158 0.86630684 0.11135663837194443 False -19 49260 26.97311806678772 0.49466776847839355 444.2371826171875 0.11338268965482712 496.6871337890625 0.7635542154312134 0.8656881 0.11177818477153778 False diff --git a/ENCSR565DSD/cherimoya.fold_0.performance.tsv b/ENCSR565DSD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 34d7e6996bde4b4ec60695af5be297f77684d3ca..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -496.46380615234375 0.19309760630130768 0.7640289664268494 0.37877920269966125 0.8686860203742981 0.8089446425437927 0.11151128262281418 \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_1.evaluate.json b/ENCSR565DSD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7aa4d47e0df5ef0020dee6711da73ace8efb7a53..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539IPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_1.fit.json b/ENCSR565DSD/cherimoya.fold_1.fit.json deleted file mode 100644 index 6241f1c431abeb3eb665ae443288960372025672..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF539IPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_1.log b/ENCSR565DSD/cherimoya.fold_1.log deleted file mode 100644 index 4398c5395b391ab23160d39acb272769465b5596..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2416 31.782578229904175 4.15074348449707 472.17352294921875 0.17407116293907166 673.7278442382812 0.6719216704368591 0.70730615 6.377910614013672 True -1 4832 26.98543930053711 0.7248117923736572 440.1996154785156 0.20244455337524414 576.1057739257812 0.7456545233726501 0.78811073 1.1051931381225586 True -2 7248 26.945107460021973 0.6949198246002197 428.47149658203125 0.10634104907512665 557.6822509765625 0.7635765075683594 0.8049782 0.3162531554698944 True -3 9664 26.912540435791016 0.667686939239502 486.2565612792969 0.21965593099594116 553.6480712890625 0.7674425840377808 0.8145694 0.24825485050678253 True -4 12080 26.91475009918213 0.6492209434509277 482.8016662597656 0.19346126914024353 551.8869018554688 0.7694108486175537 0.8166155 0.20039570331573486 True -5 14496 26.940016269683838 0.6743264198303223 447.4776611328125 0.0987897664308548 550.978759765625 0.7699400186538696 0.81538194 0.18924902379512787 False -6 16912 26.897746562957764 23.651567220687866 411.908935546875 0.2110501527786255 549.5657348632812 0.7716850638389587 0.8232092 0.17235605418682098 True -7 19328 26.976521253585815 0.6831889152526855 423.82476806640625 0.12993937730789185 549.0691528320312 0.7723367214202881 0.82488966 0.17893101274967194 True -8 21744 26.896036863327026 0.6716663837432861 455.49957275390625 0.15325187146663666 548.142822265625 0.7734737396240234 0.8307793 0.17184782028198242 True -9 24160 26.981375694274902 0.6792705059051514 496.8766174316406 0.17775386571884155 546.453125 0.7750446200370789 0.8370191 0.15934254229068756 True -10 26576 26.893441438674927 0.6791470050811768 413.2395324707031 0.10961516201496124 545.5782470703125 0.7760617136955261 0.8449866 0.15504345297813416 True -11 28992 26.86074995994568 0.6779482364654541 424.7440185546875 0.1221974641084671 544.4702758789062 0.7775129079818726 0.850255 0.15074022114276886 True -12 31408 26.891082048416138 0.6632864475250244 435.9939270019531 0.14351284503936768 543.3748779296875 0.7787051796913147 0.8577314 0.14400307834148407 True -13 33824 26.392942667007446 1.516026496887207 453.93310546875 0.1331052929162979 542.3817749023438 0.779847264289856 0.86414903 0.13936984539031982 True -14 36240 26.404914379119873 0.9484143257141113 455.2493591308594 0.10464845597743988 541.5654296875 0.7806928157806396 0.86864525 0.1348787248134613 True -15 38656 26.359063386917114 0.6623311042785645 450.3306884765625 0.09419809281826019 541.20703125 0.7812547087669373 0.8716879 0.13368076086044312 True -16 41072 26.369234085083008 0.6685078144073486 480.64111328125 0.09663756936788559 540.8782348632812 0.781461238861084 0.87427247 0.12875878810882568 True -17 43488 26.4058940410614 0.6607816219329834 457.255615234375 0.09083350002765656 540.9232788085938 0.7813029885292053 0.87441033 0.12631550431251526 True -18 45904 26.419227123260498 0.6609194278717041 453.5574645996094 0.13860884308815002 541.142822265625 0.781036913394928 0.87344706 0.12549540400505066 False -19 48320 26.397571802139282 0.657970666885376 474.98480224609375 0.06935976445674896 541.3274536132812 0.7807943820953369 0.8708231 0.1250016838312149 False diff --git a/ENCSR565DSD/cherimoya.fold_1.performance.tsv b/ENCSR565DSD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8bef331b14edb1ed44bc7b1c860fa3ccd1b377d6..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -540.9232788085938 0.17909301817417145 0.7813029885292053 0.4084933400154114 0.8744103312492371 0.8452123999595642 0.12631550431251526 \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_2.evaluate.json b/ENCSR565DSD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1fd89824fd33a31b42696d66259cc325670bd53d..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539IPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_2.fit.json b/ENCSR565DSD/cherimoya.fold_2.fit.json deleted file mode 100644 index ee901bf53ae9dd6f4e7729dd0e979295014fa6e9..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF539IPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_2.log b/ENCSR565DSD/cherimoya.fold_2.log deleted file mode 100644 index dc619a98926503fa7fa6ed5136a20cee6364ac82..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2566 34.721683502197266 4.025527477264404 473.21710205078125 0.19005617499351501 614.0403442382812 0.6731224656105042 0.68814296 5.6568922996521 True -1 5132 28.681077003479004 0.7689735889434814 468.6409606933594 0.21510961651802063 541.0247802734375 0.7374828457832336 0.78068894 0.6246724724769592 True -2 7698 28.68512773513794 0.53352952003479 420.9100341796875 0.16080963611602783 526.8543701171875 0.7504040002822876 0.8045352 0.22127042710781097 True -3 10264 28.607088327407837 0.5563795566558838 450.5673828125 0.28138014674186707 522.4837036132812 0.7548424601554871 0.81290823 0.23583443462848663 True -4 12830 28.593570232391357 1.0430946350097656 489.78265380859375 0.22289541363716125 522.0758056640625 0.7557483315467834 0.8144919 0.17062683403491974 True -5 15396 28.574835300445557 0.5393950939178467 435.7741394042969 0.12136493623256683 520.7095947265625 0.7571820020675659 0.81912774 0.16310836374759674 True -6 17962 28.64368438720703 0.5287425518035889 448.1240539550781 0.10703220963478088 519.862548828125 0.7579860687255859 0.8212736 0.15685255825519562 True -7 20528 28.65359401702881 0.5294780731201172 462.97650146484375 0.18836086988449097 519.0969848632812 0.7591122388839722 0.824126 0.1671438217163086 True -8 23094 28.593492031097412 0.5339322090148926 425.4881591796875 0.13041959702968597 517.8806762695312 0.7603139281272888 0.82765085 0.16760949790477753 True -9 25660 28.56341314315796 0.5268661975860596 448.22503662109375 0.15084683895111084 517.2240600585938 0.7612641453742981 0.8334056 0.16540871560573578 True -10 28226 28.584784746170044 0.5276892185211182 430.25238037109375 0.15245455503463745 516.2508544921875 0.7625523805618286 0.83708656 0.1589842587709427 True -11 30792 28.582698345184326 13.51571249961853 449.7352294921875 0.2017015516757965 515.4537353515625 0.7635756134986877 0.84118235 0.15997841954231262 True -12 33358 28.63818049430847 0.5392045974731445 453.46795654296875 0.13900402188301086 514.3289794921875 0.7646005749702454 0.8451534 0.14687256515026093 True -13 35924 28.61675524711609 0.5344579219818115 438.3592529296875 0.11661984771490097 513.605224609375 0.7655554413795471 0.8500888 0.13916641473770142 True -14 38490 28.604599475860596 0.525968074798584 506.381103515625 0.09617552161216736 512.9019165039062 0.766340970993042 0.8537672 0.1359097957611084 True -15 41056 28.6381733417511 0.5278010368347168 447.781494140625 0.09843792021274567 512.6195678710938 0.7668024301528931 0.8575327 0.1325118988752365 True -16 43622 28.550841569900513 0.5339784622192383 444.1425476074219 0.08035339415073395 512.4521484375 0.7669358253479004 0.8591069 0.12841664254665375 True -17 46188 28.306066513061523 0.5272774696350098 409.80389404296875 0.0925140529870987 512.6273193359375 0.7667322158813477 0.858577 0.12745866179466248 False -18 48754 27.963248014450073 0.5271084308624268 469.00164794921875 0.07621466368436813 512.7647705078125 0.7664322257041931 0.85697484 0.12722671031951904 False -19 51320 27.96783137321472 0.5558536052703857 453.14056396484375 0.08108784258365631 512.9780883789062 0.7662810683250427 0.85567075 0.12826058268547058 False diff --git a/ENCSR565DSD/cherimoya.fold_2.performance.tsv b/ENCSR565DSD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c85feac8e8060f19177a0f0537d7d0bb5d78408a..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -512.4521484375 0.1892680525779724 0.7669358849525452 0.3887235224246979 0.8591068983078003 0.8142766952514648 0.12841664254665375 \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_3.evaluate.json b/ENCSR565DSD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b181428e3a3b1e53db2cb34ee0c439adccbc8f72..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539IPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_3.fit.json b/ENCSR565DSD/cherimoya.fold_3.fit.json deleted file mode 100644 index 91a40bf4c19331f139ea4ffc8e3ebcdd5ef3c0d6..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF539IPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_3.log b/ENCSR565DSD/cherimoya.fold_3.log deleted file mode 100644 index 96bc82577f47af9fc563d6ba9d91b19dee53cee5..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2473 32.95136737823486 7.610990762710571 475.9966735839844 0.22541895508766174 599.643798828125 0.6632713079452515 0.6742316 4.776419162750244 True -1 4946 27.604758262634277 0.624547004699707 477.57879638671875 0.258664608001709 524.4235229492188 0.7326252460479736 0.75214213 0.8386658430099487 True -2 7419 27.597999572753906 0.6089727878570557 478.4503173828125 0.2671348452568054 511.25994873046875 0.7454713582992554 0.7724605 0.2534700930118561 True -3 9892 27.547032117843628 0.5183234214782715 487.0223388671875 0.15816493332386017 507.64019775390625 0.7486532330513 0.7850177 0.23352868854999542 True -4 12365 27.561958074569702 1.975447416305542 484.19342041015625 0.16310709714889526 505.5525817871094 0.7509004473686218 0.78963315 0.22492657601833344 True -5 14838 27.570104598999023 0.5201327800750732 473.447021484375 0.15264111757278442 504.2365417480469 0.7532693147659302 0.7935826 0.19391439855098724 True -6 17311 27.591049671173096 0.5335934162139893 443.51971435546875 0.16055959463119507 503.4488220214844 0.7537878155708313 0.7983155 0.19242945313453674 True -7 19784 27.618915796279907 0.5290496349334717 520.7662963867188 0.2274112105369568 502.48980712890625 0.7552122473716736 0.7997587 0.18903759121894836 True -8 22257 27.673552751541138 0.5202269554138184 479.4237365722656 0.15050658583641052 501.6363830566406 0.7565418481826782 0.8048175 0.18118423223495483 True -9 24730 27.65531849861145 0.5183897018432617 463.67041015625 0.18559898436069489 500.7189636230469 0.7576528191566467 0.8090291 0.17542017996311188 True -10 27203 27.633556842803955 0.5161073207855225 460.5169982910156 0.17586946487426758 499.7332458496094 0.7587873935699463 0.81402886 0.17112673819065094 True -11 29676 27.674344778060913 1.023158311843872 439.57244873046875 0.09082931280136108 498.9618835449219 0.7598214149475098 0.8155737 0.17029790580272675 True -12 32149 27.651960372924805 0.5323405265808105 429.76666259765625 0.1968677043914795 498.05816650390625 0.7609570622444153 0.81955165 0.16621772944927216 True -13 34622 27.66870379447937 1.5245859622955322 514.2286987304688 0.17343905568122864 497.36761474609375 0.76192706823349 0.82189447 0.1644633710384369 True -14 37095 27.720003843307495 0.5314583778381348 453.0753173828125 0.06364739686250687 496.88494873046875 0.7627068758010864 0.8264376 0.1601361781358719 True -15 39568 27.664081811904907 0.5294301509857178 428.7893981933594 0.08671733736991882 496.5062255859375 0.7633271813392639 0.8325426 0.15518523752689362 True -16 42041 27.676104068756104 0.5297527313232422 464.45660400390625 0.08432088792324066 496.2995910644531 0.7635123133659363 0.8341639 0.1490485519170761 True -17 44514 27.667922496795654 0.5315320491790771 472.5680847167969 0.07719998806715012 496.2897033691406 0.7634292244911194 0.8348659 0.14653173089027405 True -18 46987 27.668004035949707 0.5303947925567627 410.5614318847656 0.09643502533435822 496.515625 0.7631636261940002 0.8332494 0.14571160078048706 False -19 49460 27.615219116210938 1.2157912254333496 417.7489013671875 0.12279833108186722 496.71173095703125 0.76295405626297 0.83176106 0.14599518477916718 False diff --git a/ENCSR565DSD/cherimoya.fold_3.performance.tsv b/ENCSR565DSD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d68302818bcca58672e47b391701ef63a61ce56a..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -496.2897033691406 0.1935814619064331 0.7634292244911194 0.37510040402412415 0.834865927696228 0.779849112033844 0.14653173089027405 \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_4.evaluate.json b/ENCSR565DSD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 71957692a7a66b5358efc09431dbc7e441cb53ec..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539IPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_4.fit.json b/ENCSR565DSD/cherimoya.fold_4.fit.json deleted file mode 100644 index 617820d009ee2d41b8061ed316935e7c23320e63..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF539IPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR565DSD/cherimoya.fold_4.log b/ENCSR565DSD/cherimoya.fold_4.log deleted file mode 100644 index f4a21e68c8ba08a73a287ffa4a570f326981f269..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2483 32.448179483413696 4.031297445297241 467.00152587890625 0.2071860432624817 583.287109375 0.663011908531189 0.6966595 4.939784049987793 True -1 4966 27.74099111557007 0.5375251770019531 490.5594787597656 0.2828681468963623 514.9031982421875 0.728412389755249 0.7761407 0.6126318573951721 True -2 7449 27.80524706840515 0.6987447738647461 448.98455810546875 0.15339303016662598 505.3848571777344 0.7375958561897278 0.79482865 0.28900593519210815 True -3 9932 27.719687461853027 0.49465370178222656 431.5187072753906 0.24839596450328827 499.5132751464844 0.7449358105659485 0.80580014 0.2430759072303772 True -4 12415 27.6926167011261 0.5030479431152344 427.26654052734375 0.17896845936775208 496.80206298828125 0.7477766871452332 0.8180377 0.16439159214496613 True -5 14898 27.26810073852539 0.4894144535064697 526.3197631835938 0.2970324754714966 495.7864990234375 0.7491499781608582 0.82343584 0.15047496557235718 True -6 17381 27.12733769416809 0.49928998947143555 489.06585693359375 0.1970980018377304 495.5689392089844 0.7497829794883728 0.8234214 0.16403627395629883 False -7 19864 27.076203107833862 0.48843812942504883 489.9195251464844 0.16858482360839844 495.38873291015625 0.7503911256790161 0.8255745 0.18517081439495087 True -8 22347 27.11148238182068 0.49930834770202637 456.563232421875 0.07568755745887756 493.9047546386719 0.7520374059677124 0.8304896 0.16228090226650238 True -9 24830 27.056764841079712 0.48746204376220703 453.7446594238281 0.09800431877374649 492.8708190917969 0.7532607913017273 0.8374943 0.1496620625257492 True -10 27313 27.076368808746338 1.2181870937347412 465.10015869140625 0.1264144480228424 491.7388610839844 0.7546486854553223 0.8412631 0.13703598082065582 True -11 29796 27.320738315582275 23.591872930526733 453.74285888671875 0.15520444512367249 490.90716552734375 0.755867600440979 0.8465568 0.1320415586233139 True -12 32279 27.25735330581665 0.48897242546081543 404.2676696777344 0.1323244869709015 490.24542236328125 0.7567607164382935 0.8495703 0.12516479194164276 True -13 34762 27.13085412979126 0.48755693435668945 443.2004699707031 0.08870019763708115 489.4870910644531 0.7577496767044067 0.8539646 0.12008916586637497 True -14 37245 27.13066339492798 0.4890258312225342 427.5675048828125 0.11577384173870087 489.2060852050781 0.7583727836608887 0.8555013 0.11790743470191956 True -15 39728 27.122644186019897 0.4808075428009033 413.62274169921875 0.06940807402133942 488.8237609863281 0.7588745355606079 0.8590042 0.11473309993743896 True -16 42211 27.11054825782776 0.4947385787963867 441.695068359375 0.09876477718353271 488.73541259765625 0.7590972185134888 0.8612595 0.11285372823476791 True -17 44694 27.06910014152527 0.4873523712158203 399.5232238769531 0.052339740097522736 488.8254699707031 0.7590119242668152 0.86301774 0.1105143278837204 True -18 47177 27.094277381896973 0.5340859889984131 421.1348876953125 0.08199997246265411 488.9322814941406 0.7588450908660889 0.86208886 0.1099749207496643 False -19 49660 27.100555181503296 0.490398645401001 443.7380065917969 0.057357750833034515 488.96337890625 0.7586742639541626 0.8620829 0.11071579903364182 False diff --git a/ENCSR565DSD/cherimoya.fold_4.performance.tsv b/ENCSR565DSD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 172529cf668d692f8a188da8033229cbcba2d650..0000000000000000000000000000000000000000 --- a/ENCSR565DSD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -488.8254699707031 0.19629926979541779 0.7590120434761047 0.3720225989818573 0.863017737865448 0.8015922904014587 0.1105143278837204 \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_0.evaluate.json b/ENCSR567EEO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0fdfbadd86555818a64768c2d11ec9b960870d0c..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF026YCU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_0.fit.json b/ENCSR567EEO/cherimoya.fold_0.fit.json deleted file mode 100644 index 6e908c16f7f17c1b955fa78aba812a657ad53e48..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF026YCU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_0.log b/ENCSR567EEO/cherimoya.fold_0.log deleted file mode 100644 index 1679485abc042b944ba922ad03534cde08c90b14..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2774 35.6659414768219 3.9704320430755615 879.097412109375 0.3452657461166382 1147.355712890625 0.3121523857116699 0.8141931 6.556320667266846 True -1 5548 30.839076280593872 0.622889518737793 979.962646484375 0.30134254693984985 1063.2801513671875 0.3579043447971344 0.8507783 1.212762713432312 True -2 8322 30.83147406578064 0.6175286769866943 966.9306640625 0.48780035972595215 1047.244384765625 0.36189666390419006 0.8661588 0.5510005354881287 True -3 11096 30.826714038848877 0.6222105026245117 945.596923828125 0.3562730848789215 1039.3209228515625 0.3664436340332031 0.8724504 0.4730006754398346 True -4 13870 30.830304622650146 0.6104826927185059 933.3135375976562 0.3255155682563782 1032.5457763671875 0.37054938077926636 0.8762534 0.4572449326515198 True -5 16644 30.89542269706726 0.6273117065429688 914.9019165039062 0.31360846757888794 1030.8963623046875 0.3727174699306488 0.87996286 0.42469605803489685 True -6 19418 30.855342388153076 0.6530938148498535 896.724365234375 0.240260511636734 1028.30126953125 0.3740381598472595 0.8818372 0.3900257647037506 True -7 22192 30.868661165237427 0.6052968502044678 802.4005126953125 0.3374096155166626 1026.045166015625 0.3743312954902649 0.8855327 0.35167109966278076 True -8 24966 30.876096963882446 0.6169767379760742 905.8843994140625 0.2684672474861145 1023.2977905273438 0.37567973136901855 0.8907327 0.3155270218849182 True -9 27740 30.79971957206726 2.8059332370758057 1088.3631591796875 0.2302568256855011 1020.345458984375 0.37799686193466187 0.8936354 0.313527911901474 True -10 30514 30.875696420669556 0.6186881065368652 849.298583984375 0.36472344398498535 1017.279052734375 0.37937772274017334 0.8982273 0.2833808362483978 True -11 33288 30.830103874206543 1.9939074516296387 844.162353515625 0.2634795606136322 1011.85693359375 0.3820381462574005 0.9029165 0.2690015733242035 True -12 36062 30.855449199676514 0.623856782913208 891.8956909179688 0.1802702248096466 1013.6361694335938 0.3803536593914032 0.90590733 0.2550479471683502 True -13 38836 30.87661623954773 0.6181695461273193 888.9857788085938 0.21021488308906555 1010.6298828125 0.38273677229881287 0.90937275 0.2357824146747589 True -14 41610 30.84150719642639 0.6106884479522705 948.1497802734375 0.14204911887645721 1009.2651977539062 0.38256633281707764 0.9131765 0.22122061252593994 True -15 44384 30.843047380447388 1.0273373126983643 788.140625 0.1785069853067398 1002.75537109375 0.3863244354724884 0.91631126 0.2001187652349472 True -16 47158 30.86177396774292 0.6213715076446533 850.0140380859375 0.13161757588386536 1005.2984619140625 0.3845118284225464 0.9184817 0.19076226651668549 True -17 49932 30.871304035186768 0.6156551837921143 939.967041015625 0.2057373821735382 1005.6941528320312 0.38431963324546814 0.91993105 0.1849460005760193 True -18 52706 30.88896369934082 0.6242969036102295 944.5816040039062 0.20089086890220642 1007.909423828125 0.3830384910106659 0.9197282 0.183799609541893 False -19 55480 30.823769092559814 0.6221067905426025 906.0484619140625 0.11811000108718872 1008.3800659179688 0.3828253746032715 0.91887045 0.18372802436351776 False diff --git a/ENCSR567EEO/cherimoya.fold_0.performance.tsv b/ENCSR567EEO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index df16d5970115045b47d00b61a36c97de872561a3..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1005.6941528320312 0.36473920941352844 0.38431960344314575 0.19596518576145172 0.9199310541152954 0.8957521319389343 0.1849460005760193 \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_1.evaluate.json b/ENCSR567EEO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1a13367e8730717ee54285efad1dfd8a547c9e57..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF026YCU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_1.fit.json b/ENCSR567EEO/cherimoya.fold_1.fit.json deleted file mode 100644 index 3a32848f7e672a5f8619a4d556ce92dedcf945e4..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF026YCU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_1.log b/ENCSR567EEO/cherimoya.fold_1.log deleted file mode 100644 index 8a803f98b127bb7382603cfb8765c7aedb7fe76e..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2721 34.27944755554199 4.549539089202881 845.068603515625 0.181208074092865 1449.3497314453125 0.32301363348960876 0.7875131 7.788784503936768 True -1 5442 30.37748408317566 0.7346866130828857 978.4420166015625 0.26264244318008423 1321.5068359375 0.37964990735054016 0.8288228 1.7725204229354858 True -2 8163 30.273464679718018 0.709115743637085 857.3109130859375 0.2180883288383484 1283.88330078125 0.3927849233150482 0.85608006 0.9205600023269653 True -3 10884 30.340721607208252 0.7029173374176025 1033.1826171875 0.3717169165611267 1269.0032958984375 0.39773762226104736 0.8612568 0.6813815236091614 True -4 13605 30.248122692108154 0.6959314346313477 874.9716186523438 0.31902000308036804 1259.1715087890625 0.4005468785762787 0.866125 0.6531694531440735 True -5 16326 30.262990951538086 0.7025434970855713 935.5921630859375 0.2712937295436859 1250.203857421875 0.4037611484527588 0.8734771 0.5358585715293884 True -6 19047 30.28954768180847 0.7030723094940186 853.3663330078125 0.2933948338031769 1254.0506591796875 0.40208664536476135 0.8701159 0.6072382926940918 False -7 21768 30.259292125701904 0.6962363719940186 807.9908447265625 0.3283888101577759 1244.9417724609375 0.40696123242378235 0.8743183 0.5139814019203186 True -8 24489 30.281635761260986 0.693324089050293 798.591064453125 0.14847974479198456 1238.7127685546875 0.4093797504901886 0.87751025 0.5086793899536133 True -9 27210 30.308254957199097 0.6910953521728516 1053.23291015625 0.36344483494758606 1235.4442138671875 0.41070565581321716 0.88436747 0.4926541745662689 True -10 29931 30.35878562927246 0.7058873176574707 960.0160522460938 0.35087352991104126 1229.590087890625 0.41390854120254517 0.8861458 0.4513208866119385 True -11 32652 30.300822496414185 0.6985578536987305 726.5264282226562 0.16839870810508728 1225.3564453125 0.4145427942276001 0.8925772 0.3953501284122467 True -12 35373 30.279918432235718 0.7040910720825195 755.320556640625 0.19925165176391602 1221.411865234375 0.41583913564682007 0.90000135 0.34969234466552734 True -13 38094 30.29100465774536 0.6929383277893066 927.7857055664062 0.2353711724281311 1214.615234375 0.41950780153274536 0.9060602 0.32237645983695984 True -14 40815 30.32715606689453 0.7065842151641846 821.8009033203125 0.3291594386100769 1216.0150146484375 0.418342649936676 0.9098081 0.28049778938293457 True -15 43536 30.527341842651367 0.7299823760986328 725.070068359375 0.21962852776050568 1216.770263671875 0.4183400273323059 0.91588145 0.2538924813270569 True -16 46257 30.375704050064087 0.7286117076873779 800.6070556640625 0.14357498288154602 1216.69482421875 0.41817259788513184 0.92 0.23393984138965607 True -17 48978 30.435583353042603 0.7160611152648926 934.7466430664062 0.1265348196029663 1211.7144775390625 0.42138513922691345 0.9197117 0.22402556240558624 False -18 51699 30.510165691375732 0.7083432674407959 792.1340942382812 0.129032701253891 1210.69970703125 0.4222296476364136 0.9186038 0.2216978669166565 False -19 54420 30.419376611709595 0.7076506614685059 902.3525390625 0.12626422941684723 1213.7545166015625 0.4203667938709259 0.9181619 0.222564697265625 False diff --git a/ENCSR567EEO/cherimoya.fold_1.performance.tsv b/ENCSR567EEO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 235409d4536e2d2e89e8371695e79c37be29eecc..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1216.69482421875 0.3345143795013428 0.41817256808280945 0.235830619931221 0.9200000166893005 0.9106029868125916 0.23393984138965607 \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_2.evaluate.json b/ENCSR567EEO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 41e693243f4396b84e56fbee3da4c60deb292948..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF026YCU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_2.fit.json b/ENCSR567EEO/cherimoya.fold_2.fit.json deleted file mode 100644 index f0020e11bfade64aa2f84e473ea31c75255b7dac..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF026YCU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_2.log b/ENCSR567EEO/cherimoya.fold_2.log deleted file mode 100644 index b9b42319660ba36befaae4ecfc87077c837c6759..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 36.150253772735596 3.5221359729766846 793.598388671875 0.358190655708313 1246.062255859375 0.3148975074291229 0.8040186 5.638011455535889 True -1 5788 32.14486050605774 0.6507127285003662 740.1329956054688 0.1829909384250641 1149.1822509765625 0.3615255355834961 0.8478579 1.5141541957855225 True -2 8682 32.18521189689636 0.7821481227874756 946.0048828125 0.21831797063350677 1128.947021484375 0.3688530921936035 0.8620437 0.6430057883262634 True -3 11576 32.201451778411865 0.6128246784210205 1051.38623046875 0.33837252855300903 1121.9774169921875 0.37094002962112427 0.8693603 0.4915548861026764 True -4 14470 32.20396661758423 0.6181514263153076 819.113525390625 0.2697073221206665 1115.18896484375 0.3760068714618683 0.8701114 0.4512559771537781 True -5 17364 32.15476179122925 0.6165075302124023 747.2293701171875 0.330279678106308 1113.345703125 0.37738358974456787 0.87538564 0.38751667737960815 True -6 20258 32.209535360336304 0.6035172939300537 894.3737182617188 0.3178946077823639 1111.882080078125 0.3770343065261841 0.8778053 0.39097121357917786 True -7 23152 32.21704626083374 0.6056573390960693 915.980712890625 0.297382652759552 1110.4595947265625 0.37762707471847534 0.8796253 0.390500545501709 True -8 26046 32.17600917816162 0.5935840606689453 831.338134765625 0.17791405320167542 1106.0885009765625 0.3801640570163727 0.88175213 0.367527574300766 True -9 28940 32.17781925201416 0.6114418506622314 912.6947021484375 0.36611467599868774 1102.8577880859375 0.38212987780570984 0.8845566 0.33864498138427734 True -10 31834 32.26747918128967 0.6151344776153564 921.6275024414062 0.2449718713760376 1098.9315185546875 0.3837273120880127 0.8882297 0.33125442266464233 True -11 34728 32.37982201576233 9.418162822723389 991.91552734375 0.22199061512947083 1093.9124755859375 0.38643792271614075 0.89376277 0.2989613711833954 True -12 37622 32.59268498420715 2.0456926822662354 900.6005249023438 0.33226367831230164 1091.539306640625 0.3868556022644043 0.8953392 0.2792585790157318 True -13 40516 32.38860201835632 22.288997888565063 755.7078857421875 0.22915256023406982 1088.8521728515625 0.38744813203811646 0.9002494 0.2614036798477173 True -14 43410 32.233789682388306 0.9133577346801758 1046.879150390625 0.2336753010749817 1086.817626953125 0.38824188709259033 0.90551054 0.2354869693517685 True -15 46304 32.2187385559082 10.616458415985107 848.77734375 0.1446908414363861 1084.6336669921875 0.3886822462081909 0.90815157 0.22298972308635712 True -16 49198 32.32465124130249 2.0024478435516357 916.9806518554688 0.20208898186683655 1084.7679443359375 0.38914522528648376 0.9100289 0.215122252702713 True -17 52092 32.270100831985474 1.2709376811981201 975.6295166015625 0.13334596157073975 1083.3717041015625 0.389320433139801 0.908082 0.21419014036655426 False -18 54986 32.24090814590454 2.421527624130249 672.5751953125 0.17322157323360443 1084.672119140625 0.38803204894065857 0.9076559 0.2157256007194519 False -19 57880 32.26918578147888 1.7989819049835205 894.0066528320312 0.11222228407859802 1084.7764892578125 0.3891178369522095 0.90734816 0.2178824543952942 False diff --git a/ENCSR567EEO/cherimoya.fold_2.performance.tsv b/ENCSR567EEO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a31c5c736c4cb90634f06a0d55ad46d987ee9ac6..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1084.7679443359375 0.35556456446647644 0.38914522528648376 0.20864054560661316 0.910028874874115 0.8950323462486267 0.215122252702713 \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_3.evaluate.json b/ENCSR567EEO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4f3201fb11f57ea9128c090ccd9ca825514ecfc5..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF026YCU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_3.fit.json b/ENCSR567EEO/cherimoya.fold_3.fit.json deleted file mode 100644 index d97357f23be186e90a30e5d6688776653dd9ff21..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF026YCU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_3.log b/ENCSR567EEO/cherimoya.fold_3.log deleted file mode 100644 index 8fab8fbac2e53e7669aba73ec993cb3464a1e6ae..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 34.70116186141968 3.5866851806640625 752.3074951171875 0.31891608238220215 1128.81640625 0.3169509768486023 0.78411657 6.111822128295898 True -1 5466 30.374224185943604 0.6240401268005371 874.6639404296875 0.33947861194610596 1037.83154296875 0.36369824409484863 0.8201185 1.4447518587112427 True -2 8199 30.43410849571228 0.608595609664917 818.8414306640625 0.25851333141326904 1025.0123291015625 0.36792799830436707 0.8427543 0.6633961796760559 True -3 10932 30.454227209091187 0.5974998474121094 1048.6463623046875 0.4360223412513733 1016.692138671875 0.3718484342098236 0.8481943 0.5429744720458984 True -4 13665 30.422156810760498 0.5981407165527344 768.8469848632812 0.2826281785964966 1011.6962890625 0.3742677867412567 0.84894365 0.5202134251594543 True -5 16398 30.38182306289673 0.5966384410858154 1052.338134765625 0.22896051406860352 1008.8353881835938 0.3757113218307495 0.8557137 0.53155916929245 True -6 19131 30.406192779541016 0.6137478351593018 958.0550537109375 0.2981546223163605 1004.7694091796875 0.3777710795402527 0.8589667 0.46115419268608093 True -7 21864 30.483463287353516 0.6024637222290039 905.8865966796875 0.21183645725250244 1003.547607421875 0.3776395618915558 0.8638377 0.42434921860694885 True -8 24597 30.434433698654175 0.6207571029663086 875.2742309570312 0.4120476245880127 999.2606811523438 0.3805069923400879 0.8686553 0.4035087823867798 True -9 27330 30.651158809661865 0.6245813369750977 905.55712890625 0.1765952706336975 995.9187622070312 0.3820994794368744 0.8757404 0.38320910930633545 True -10 30063 30.65112614631653 0.6089625358581543 1061.81787109375 0.23518288135528564 990.7683715820312 0.38575637340545654 0.8796213 0.3476843237876892 True -11 32796 30.575093984603882 0.608431339263916 988.4306640625 0.2888157069683075 990.9739379882812 0.38472306728363037 0.884113 0.32527920603752136 True -12 35529 30.606379985809326 0.607036828994751 801.90625 0.18451040983200073 989.7522583007812 0.38626179099082947 0.89020723 0.29982396960258484 True -13 38262 30.574137687683105 0.6101887226104736 935.30859375 0.34598326683044434 986.4812622070312 0.388092964887619 0.89396304 0.2771509885787964 True -14 40995 30.58834195137024 0.6136529445648193 872.341796875 0.1789449006319046 983.8125 0.38909056782722473 0.89868873 0.256252646446228 True -15 43728 30.567226886749268 0.60646653175354 997.031982421875 0.21859055757522583 981.18798828125 0.38991665840148926 0.901702 0.23975087702274323 True -16 46461 30.526897192001343 0.6074650287628174 806.7005004882812 0.2620004117488861 982.0072631835938 0.3897759020328522 0.90537506 0.22574204206466675 True -17 49194 30.51458477973938 0.6111240386962891 964.246337890625 0.11642158776521683 979.2752685546875 0.39196813106536865 0.90515393 0.2212742269039154 False -18 51927 30.60732650756836 0.6068966388702393 999.903076171875 0.14362892508506775 981.8433837890625 0.38954949378967285 0.90575176 0.21732889115810394 True -19 54660 30.44706082344055 0.6075248718261719 880.109375 0.11160113662481308 980.7612915039062 0.39103153347969055 0.90476656 0.21743395924568176 False diff --git a/ENCSR567EEO/cherimoya.fold_3.performance.tsv b/ENCSR567EEO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6a5299622ba5610217fcb6998013e05ec62ae822..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -981.8433837890625 0.36348146200180054 0.38954949378967285 0.19610688090324402 0.9057517647743225 0.8834152817726135 0.21732889115810394 \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_4.evaluate.json b/ENCSR567EEO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 62faad1c9161889545485a1ae352a148d087eb51..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF026YCU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_4.fit.json b/ENCSR567EEO/cherimoya.fold_4.fit.json deleted file mode 100644 index 69fbbcb0a34c7cbf652cfd9aa52dddc5a1715aa3..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF026YCU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567EEO/cherimoya.fold_4.log b/ENCSR567EEO/cherimoya.fold_4.log deleted file mode 100644 index 3f7476657ea25a9b2695c7cf1ee36c6d2e7c9073..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 34.570093393325806 4.898528099060059 929.6721801757812 0.3741856813430786 1059.114501953125 0.30792173743247986 0.79620486 6.846541404724121 True -1 5504 30.623977422714233 3.242210865020752 815.287353515625 0.23770739138126373 989.7378540039062 0.34842145442962646 0.82703716 1.001603364944458 True -2 8256 30.71080780029297 0.6706855297088623 816.735107421875 0.22235724329948425 968.9756469726562 0.35681042075157166 0.8580565 0.5064942836761475 True -3 11008 30.64125347137451 0.6788904666900635 923.482421875 0.2267094999551773 964.960205078125 0.3571651577949524 0.86630744 0.3249954581260681 True -4 13760 30.600611925125122 0.6706938743591309 893.5800170898438 0.23291490972042084 961.4279174804688 0.3595128059387207 0.86818486 0.3103393018245697 True -5 16512 30.668805837631226 0.6595244407653809 856.3878173828125 0.25555747747421265 961.724365234375 0.3590688407421112 0.87377954 0.30504778027534485 True -6 19264 30.678877115249634 0.6571464538574219 1112.491943359375 0.3639300763607025 957.1690673828125 0.360740602016449 0.87763625 0.3121570348739624 True -7 22016 30.66983985900879 0.6629073619842529 988.10205078125 0.22034287452697754 954.5744018554688 0.36313387751579285 0.88082176 0.3137040138244629 True -8 24768 30.7425377368927 0.6597950458526611 911.1083374023438 0.29153019189834595 954.16015625 0.36375561356544495 0.88257366 0.2906962037086487 True -9 27520 30.695215225219727 0.6627769470214844 1069.846435546875 0.24304574728012085 947.1187744140625 0.3687317669391632 0.8854697 0.28136003017425537 True -10 30272 30.683451414108276 0.746570348739624 947.241455078125 0.26117023825645447 947.1429443359375 0.3675649166107178 0.8896334 0.2571128308773041 True -11 33024 30.64707350730896 2.7179629802703857 761.0458984375 0.21907132863998413 947.4953002929688 0.36769458651542664 0.8907452 0.24702873826026917 True -12 35776 30.676756143569946 1.3860633373260498 840.338623046875 0.3184693455696106 943.9898681640625 0.3697238266468048 0.8951329 0.23453812301158905 True -13 38528 30.65175771713257 2.3464436531066895 773.3935546875 0.17836320400238037 945.1834106445312 0.36838701367378235 0.8991959 0.22076599299907684 True -14 41280 30.69388175010681 1.4688291549682617 732.36181640625 0.18227720260620117 943.3116455078125 0.37002065777778625 0.90361935 0.2038436383008957 True -15 44032 30.70713520050049 3.692905902862549 718.5408325195312 0.14205430448055267 940.0887451171875 0.37145134806632996 0.90714324 0.19432982802391052 True -16 46784 30.842227935791016 0.6943850517272949 756.9782104492188 0.10023212432861328 941.3856811523438 0.3712455928325653 0.9107075 0.18206609785556793 True -17 49536 30.814356327056885 0.6807916164398193 896.4505004882812 0.22101864218711853 940.1009521484375 0.37193554639816284 0.91144574 0.1797088235616684 True -18 52288 30.866917848587036 0.6713306903839111 861.9708251953125 0.11223451048135757 939.590087890625 0.3727229833602905 0.9106052 0.1787446290254593 False -19 55040 30.831961393356323 0.6733541488647461 823.2097778320312 0.12000271677970886 940.5092163085938 0.37151655554771423 0.9101794 0.17979758977890015 False diff --git a/ENCSR567EEO/cherimoya.fold_4.performance.tsv b/ENCSR567EEO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index eb285591075f9bda3b92a826f9f5632865444c25..0000000000000000000000000000000000000000 --- a/ENCSR567EEO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -940.1009521484375 0.3737775981426239 0.37193557620048523 0.18589049577713013 0.9114457368850708 0.8911569118499756 0.1797088235616684 \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_0.evaluate.json b/ENCSR567IWT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1a3081c0b2d143dae66c2180fa84fb6d3cc7467a..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF707UNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_0.fit.json b/ENCSR567IWT/cherimoya.fold_0.fit.json deleted file mode 100644 index 7dfa30d7c425eb20ecb1a6f5ec045d9c8810e72f..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF707UNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_0.log b/ENCSR567IWT/cherimoya.fold_0.log deleted file mode 100644 index d3a5370cdcfaf268cdf8e4cf7e52f219ce177023..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1840 25.07760453224182 3.9427576065063477 889.204345703125 1.3214948177337646 2538.951171875 0.20796604454517365 0.5278929 25.719755172729492 True -1 3680 20.528127431869507 0.3709712028503418 1269.7144775390625 2.0167675018310547 1943.3681640625 0.336664080619812 0.6494465 12.00757884979248 True -2 5520 20.52170991897583 0.8409981727600098 1195.285400390625 1.5314825773239136 1703.6173095703125 0.3734785318374634 0.6639252 6.624631404876709 True -3 7360 20.46835994720459 0.3540980815887451 1463.7752685546875 1.021705985069275 1600.8026123046875 0.3865710198879242 0.6908528 4.765055179595947 True -4 9200 20.482041835784912 0.3545389175415039 1277.217041015625 1.6591137647628784 1544.4349365234375 0.39707431197166443 0.7081667 3.3373374938964844 True -5 11040 20.47139072418213 0.37225985527038574 1127.074951171875 1.5228610038757324 1506.7000732421875 0.40553951263427734 0.7135117 2.762193441390991 True -6 12880 20.45501470565796 0.3469369411468506 1054.884765625 1.3005774021148682 1486.326904296875 0.4106758236885071 0.72342753 2.1535332202911377 True -7 14720 20.46900773048401 0.3460071086883545 1409.858642578125 1.9513448476791382 1468.3441162109375 0.414049357175827 0.737738 1.806168794631958 True -8 16560 20.509742259979248 0.3550105094909668 777.119873046875 1.1347483396530151 1453.051513671875 0.41633185744285583 0.74807125 1.4877386093139648 True -9 18400 20.508657932281494 0.34569835662841797 1509.2408447265625 1.343022108078003 1433.6268310546875 0.4231142997741699 0.7528635 1.3275612592697144 True -10 20240 20.565623998641968 0.3521292209625244 1033.33642578125 1.0683646202087402 1412.35205078125 0.4272846579551697 0.7623581 1.2287453413009644 True -11 22080 20.57294511795044 0.36043405532836914 1105.6639404296875 1.3402206897735596 1410.78369140625 0.4265469014644623 0.76523197 1.1317237615585327 True -12 23920 20.47319793701172 0.3630797863006592 911.7304077148438 1.0286381244659424 1395.7484130859375 0.43021222949028015 0.7720756 1.0880019664764404 True -13 25760 20.496232748031616 0.36455607414245605 1145.1121826171875 0.8503456115722656 1381.38671875 0.43299758434295654 0.77799845 1.023889183998108 True -14 27600 20.50969099998474 0.35602855682373047 691.4535522460938 0.9759963750839233 1371.703125 0.434214323759079 0.78468996 0.9849021434783936 True -15 29440 20.51363205909729 0.9281795024871826 1224.5296630859375 0.9125379323959351 1365.7225341796875 0.4347168207168579 0.78980404 0.9520353078842163 True -16 31280 20.487128734588623 0.35434985160827637 904.4232788085938 0.8630896806716919 1360.49169921875 0.43772000074386597 0.7932308 0.9232074618339539 True -17 33120 20.469717264175415 0.35067248344421387 936.6941528320312 0.6888309717178345 1362.6484375 0.43653789162635803 0.7972748 0.9109867215156555 True -18 34960 20.479968309402466 0.3548257350921631 808.75927734375 0.8268061280250549 1364.7347412109375 0.4344063699245453 0.79877204 0.9106464385986328 True -19 36800 20.291212797164917 0.35423970222473145 1167.09912109375 0.5925970077514648 1362.2210693359375 0.43603044748306274 0.79795164 0.9128716588020325 False diff --git a/ENCSR567IWT/cherimoya.fold_0.performance.tsv b/ENCSR567IWT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index de1f20425dc4d38ce8178c20aa068642d9089ca7..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1364.7347412109375 0.35700228810310364 0.4344063401222229 0.21050503849983215 0.7987720370292664 0.7382733821868896 0.9106464385986328 \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_1.evaluate.json b/ENCSR567IWT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 72a357d6213940ac14f1d48c7fb3281a42f5db84..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF707UNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_1.fit.json b/ENCSR567IWT/cherimoya.fold_1.fit.json deleted file mode 100644 index b425f030404a7e30745a74e9bb4c3fb1a199c82c..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF707UNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_1.log b/ENCSR567IWT/cherimoya.fold_1.log deleted file mode 100644 index 1f74da1b903fbc174b7b7249706318eafb26587d..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1789 24.212454080581665 3.9479031562805176 1042.2547607421875 1.7094920873641968 3026.894287109375 0.2118869125843048 0.5024424 26.568313598632812 True -1 3578 19.958296298980713 13.100104331970215 1430.033447265625 1.4694744348526 2270.109619140625 0.3391629457473755 0.6409054 15.057497024536133 True -2 5367 19.59888505935669 0.5340890884399414 1312.4310302734375 1.6590065956115723 1994.7166748046875 0.38369014859199524 0.67394125 7.3650922775268555 True -3 7156 19.513813734054565 0.5205647945404053 1243.71923828125 1.0380523204803467 1854.828857421875 0.4061857759952545 0.71478784 5.1581902503967285 True -4 8945 19.525997400283813 0.5201842784881592 1229.2724609375 1.1918448209762573 1811.9654541015625 0.4167211651802063 0.72003454 4.112576484680176 True -5 10734 19.519829511642456 0.5203547477722168 1494.0101318359375 1.7397791147232056 1792.6195068359375 0.4226713478565216 0.72571695 3.1460378170013428 True -6 12523 19.51771831512451 0.5192532539367676 1439.8779296875 1.5801362991333008 1745.8250732421875 0.43006813526153564 0.7439552 2.5121333599090576 True -7 14312 19.54807448387146 0.5118415355682373 1107.1884765625 1.269595742225647 1716.4903564453125 0.4355067014694214 0.75460994 2.0472044944763184 True -8 16101 19.535731554031372 0.5175342559814453 1179.698974609375 1.2248985767364502 1697.264404296875 0.4395979940891266 0.761337 1.65365469455719 True -9 17890 19.49487328529358 0.5090768337249756 965.3834228515625 0.9834522604942322 1683.8555908203125 0.4421488046646118 0.77133083 1.524154543876648 True -10 19679 19.512925148010254 0.597435474395752 1120.9638671875 1.240246295928955 1654.5799560546875 0.446163535118103 0.7771708 1.326478362083435 True -11 21468 19.51597285270691 0.5182132720947266 1091.6160888671875 1.1205657720565796 1639.54638671875 0.45068445801734924 0.78173274 1.2917962074279785 True -12 23257 19.502012968063354 0.5296289920806885 1039.248046875 0.9967955350875854 1618.2100830078125 0.45368194580078125 0.79154825 1.1409683227539062 True -13 25046 19.543917417526245 0.5232107639312744 1074.705078125 0.7661585807800293 1606.002685546875 0.4562211334705353 0.79588854 1.0671416521072388 True -14 26835 19.529263257980347 1.4780333042144775 1076.42529296875 0.993330180644989 1594.993408203125 0.4556468427181244 0.80005914 1.0519726276397705 True -15 28624 19.5298969745636 0.5165057182312012 920.948486328125 1.162861943244934 1581.2630615234375 0.4595267176628113 0.80570316 1.006177544593811 True -16 30413 19.491171836853027 0.5242776870727539 1055.3770751953125 0.7447092533111572 1576.6220703125 0.45967090129852295 0.80857295 0.9951803684234619 True -17 32202 19.496326208114624 0.5148825645446777 1039.779296875 0.9717531800270081 1584.9317626953125 0.45794451236724854 0.81070054 0.9825348854064941 True -18 33991 19.463972330093384 0.5148875713348389 960.4949340820312 0.8550575971603394 1576.990966796875 0.46188560128211975 0.810773 0.9851815104484558 True -19 35780 19.459638357162476 0.5101947784423828 1217.1619873046875 0.8025866746902466 1580.6708984375 0.4608513414859772 0.8103883 0.9789589643478394 False diff --git a/ENCSR567IWT/cherimoya.fold_1.performance.tsv b/ENCSR567IWT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 381eb27ef33a4dfc5fd91dcb232b4b258046c264..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1576.990966796875 0.33529967069625854 0.46188563108444214 0.23925583064556122 0.8107730150222778 0.7766558527946472 0.9851815104484558 \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_2.evaluate.json b/ENCSR567IWT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 00b78758c5c86040a082b2a620f0541fa6b771c7..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF707UNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_2.fit.json b/ENCSR567IWT/cherimoya.fold_2.fit.json deleted file mode 100644 index 6c469f752c8671a0514fec610c9e607a3a2fb45b..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF707UNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_2.log b/ENCSR567IWT/cherimoya.fold_2.log deleted file mode 100644 index 5c98a75e0afe72f71a2081ffbb81f9d487424801..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1936 25.89888334274292 4.046692132949829 1535.6961669921875 1.74708890914917 2590.111328125 0.20207534730434418 0.47550178 23.5725040435791 True -1 3872 21.63640522956848 0.46060872077941895 1521.374267578125 1.618221402168274 1890.180908203125 0.3387812077999115 0.6538028 11.524768829345703 True -2 5808 21.601949453353882 1.4201076030731201 1363.724609375 1.6998060941696167 1694.1865234375 0.3663751780986786 0.69985545 6.762666702270508 True -3 7744 21.58765697479248 0.39403462409973145 828.5596313476562 1.3093297481536865 1581.7877197265625 0.38265812397003174 0.7191313 4.19780969619751 True -4 9680 21.531826496124268 0.39150452613830566 1138.484375 1.734426736831665 1548.7967529296875 0.39050430059432983 0.7262167 2.983818531036377 True -5 11616 21.545614004135132 0.39252305030822754 1048.942138671875 1.4807069301605225 1523.0126953125 0.39587804675102234 0.73394746 2.28755521774292 True -6 13552 21.516561269760132 0.40770840644836426 1262.5291748046875 1.3145720958709717 1492.0003662109375 0.40194129943847656 0.73868704 1.8446816205978394 True -7 15488 21.503430604934692 1.606590747833252 1256.9888916015625 1.7859859466552734 1477.5213623046875 0.4052046835422516 0.74624157 1.5211400985717773 True -8 17424 21.54368019104004 0.3962061405181885 1221.604736328125 1.0037498474121094 1463.0107421875 0.40721380710601807 0.7555001 1.291635513305664 True -9 19360 21.241461038589478 0.3812727928161621 1194.3873291015625 1.1042959690093994 1446.9385986328125 0.4119163155555725 0.7597551 1.1686302423477173 True -10 21296 21.060794591903687 0.39099550247192383 1351.2833251953125 1.0743122100830078 1435.2659912109375 0.413119375705719 0.7664875 1.1218020915985107 True -11 23232 21.06298542022705 0.385392427444458 1119.662353515625 1.1815111637115479 1406.359619140625 0.41994020342826843 0.7725398 1.087416410446167 True -12 25168 21.067023754119873 0.38467931747436523 906.0654296875 1.1785635948181152 1395.2618408203125 0.4221094846725464 0.77784324 1.0589848756790161 True -13 27104 21.13364863395691 0.38201427459716797 770.3814697265625 1.4768644571304321 1379.5478515625 0.42580509185791016 0.7834445 1.0092438459396362 True -14 29040 21.175997495651245 0.38665270805358887 999.1682739257812 0.7270114421844482 1378.1900634765625 0.4265543520450592 0.7873062 0.9845139384269714 True -15 30976 21.081181049346924 0.3830287456512451 1119.590576171875 0.6010323762893677 1368.8760986328125 0.42719945311546326 0.79096675 0.9690380692481995 True -16 32912 21.114099979400635 0.3861978054046631 1049.46630859375 0.7954142093658447 1366.9923095703125 0.4275675415992737 0.79154897 0.9615151286125183 True -17 34848 21.155983924865723 0.39001035690307617 932.255615234375 0.5825498104095459 1361.1435546875 0.4297040104866028 0.7952744 0.9535219669342041 True -18 36784 21.12729048728943 0.39377880096435547 1168.3743896484375 0.6586204767227173 1361.2095947265625 0.42991992831230164 0.79511964 0.9566402435302734 False -19 38720 21.183985948562622 0.3778512477874756 1043.5899658203125 1.3072035312652588 1373.6405029296875 0.4251042306423187 0.7954088 0.9566857814788818 True diff --git a/ENCSR567IWT/cherimoya.fold_2.performance.tsv b/ENCSR567IWT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c8e343984f1f4865985cba8d5c5cb876ecedca39..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1373.6405029296875 0.36173713207244873 0.4251042306423187 0.2100990116596222 0.7954087853431702 0.7429566979408264 0.9566857814788818 \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_3.evaluate.json b/ENCSR567IWT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cc3ef41e2a71d2e39ed552f362773984d036b5fb..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF707UNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_3.fit.json b/ENCSR567IWT/cherimoya.fold_3.fit.json deleted file mode 100644 index 9f2bc9e6c039d36cd943eb1f094abe6b9371fdc2..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF707UNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_3.log b/ENCSR567IWT/cherimoya.fold_3.log deleted file mode 100644 index 527777cef47fb07484159ec8a202b95db6b9202d..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1844 25.255438327789307 4.692064523696899 1251.567626953125 1.4562270641326904 2526.1220703125 0.22168663144111633 0.49599078 25.430309295654297 True -1 3688 20.811878204345703 0.4057590961456299 1319.947265625 1.6054701805114746 1920.21728515625 0.34948551654815674 0.6642205 12.632847785949707 True -2 5532 20.5514874458313 0.400937557220459 1454.089599609375 2.261333465576172 1707.5640869140625 0.3807786703109741 0.6881764 6.073999404907227 True -3 7376 20.67987823486328 0.3701944351196289 1154.120849609375 1.2825301885604858 1627.66845703125 0.3923303186893463 0.7046483 4.018598556518555 True -4 9220 20.507667779922485 0.37674760818481445 1435.028564453125 1.4898161888122559 1582.272705078125 0.4006477892398834 0.71759194 2.7427878379821777 True -5 11064 20.499758005142212 0.37663960456848145 1215.9476318359375 1.3070335388183594 1563.724853515625 0.4044070243835449 0.7267763 2.1984310150146484 True -6 12908 20.527207851409912 0.37627625465393066 1298.9306640625 1.452019214630127 1533.03466796875 0.4148864448070526 0.7253596 2.199474811553955 False -7 14752 20.51943278312683 0.37393832206726074 1266.0460205078125 1.0444214344024658 1517.11376953125 0.4182738959789276 0.7345395 1.728580117225647 True -8 16596 20.520264863967896 0.3745603561401367 975.17919921875 1.4808626174926758 1509.3306884765625 0.41962602734565735 0.74128425 1.5114582777023315 True -9 18440 20.553051233291626 0.37096095085144043 1137.8204345703125 1.5071587562561035 1486.485107421875 0.4255789518356323 0.74451107 1.393789291381836 True -10 20284 20.517996549606323 13.049249172210693 1217.977783203125 1.165935754776001 1468.9984130859375 0.42999255657196045 0.7524508 1.302136778831482 True -11 22128 20.651639461517334 0.3921675682067871 843.617431640625 0.8935932517051697 1455.41455078125 0.43309536576271057 0.7572715 1.2162278890609741 True -12 23972 20.54478931427002 0.38929128646850586 1183.44677734375 0.8443657159805298 1438.259765625 0.4374544620513916 0.76609486 1.1303898096084595 True -13 25816 20.501632690429688 0.37867116928100586 1208.8858642578125 0.9007772207260132 1423.0126953125 0.44113755226135254 0.77315825 1.0822352170944214 True -14 27660 20.590851545333862 0.37437868118286133 1270.58203125 1.0099279880523682 1418.9110107421875 0.44017982482910156 0.78206736 1.0390853881835938 True -15 29504 20.532740354537964 0.37345004081726074 1029.00439453125 1.165938138961792 1401.3720703125 0.4441903531551361 0.7899572 0.9974939823150635 True -16 31348 20.588074445724487 0.37856388092041016 991.0917358398438 0.7802168130874634 1396.6905517578125 0.44437965750694275 0.79691666 0.968384861946106 True -17 33192 20.523479461669922 5.102818965911865 1104.02099609375 0.9578466415405273 1397.861328125 0.4430752098560333 0.799805 0.9492431879043579 True -18 35036 20.555312871932983 0.3793957233428955 1124.49267578125 0.7418944835662842 1399.0848388671875 0.44190147519111633 0.8012603 0.9477060437202454 True -19 36880 20.5420925617218 1.6158733367919922 811.9197998046875 0.7575535774230957 1406.2603759765625 0.43903183937072754 0.8025388 0.9447129368782043 True diff --git a/ENCSR567IWT/cherimoya.fold_3.performance.tsv b/ENCSR567IWT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7e70ae1090ab54be8f7bd1fb6464c7dac2962ca2..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1406.2603759765625 0.35063862800598145 0.43903183937072754 0.21967492997646332 0.8025388121604919 0.749363124370575 0.9447129368782043 \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_4.evaluate.json b/ENCSR567IWT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 913183eca039f17330a70beb672282acd77e5a80..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF707UNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_4.fit.json b/ENCSR567IWT/cherimoya.fold_4.fit.json deleted file mode 100644 index d31095edc8dc2e42c07fd7d5c5092f21c33b83af..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF707UNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR567IWT/cherimoya.fold_4.log b/ENCSR567IWT/cherimoya.fold_4.log deleted file mode 100644 index 5d590794618c6efa612639e9d04abaca3895bbb6..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1808 25.49427819252014 4.452579736709595 1464.73876953125 1.8834738731384277 2181.231201171875 0.2014276087284088 0.46575406 23.34093475341797 True -1 3616 20.341458559036255 0.3922078609466553 1293.9482421875 1.96039617061615 1651.19970703125 0.3272517919540405 0.66049397 11.112640380859375 True -2 5424 20.12452244758606 7.803319931030273 1524.25439453125 1.6741020679473877 1478.8568115234375 0.3551965057849884 0.6698129 6.087944030761719 True -3 7232 20.135672569274902 0.41164445877075195 1509.94091796875 1.8487292528152466 1412.08740234375 0.3674564063549042 0.6835476 4.649765968322754 True -4 9040 20.15362024307251 0.3644578456878662 1180.9013671875 1.1755948066711426 1372.01953125 0.37249311804771423 0.70657575 3.424734592437744 True -5 10848 20.094740867614746 0.37065863609313965 1217.2724609375 1.6495559215545654 1347.8709716796875 0.3799487352371216 0.71696407 2.6209166049957275 True -6 12656 20.12439751625061 0.3653750419616699 801.5386352539062 1.3190274238586426 1323.7652587890625 0.38719868659973145 0.72996545 1.9291332960128784 True -7 14464 20.095136880874634 0.36679768562316895 1088.58837890625 1.7843188047409058 1308.3035888671875 0.39017170667648315 0.7395553 1.536741018295288 True -8 16272 20.088252544403076 0.36750054359436035 1128.817138671875 1.1980656385421753 1296.1768798828125 0.39382606744766235 0.7457901 1.3693641424179077 True -9 18080 20.098215579986572 0.6649973392486572 1075.1124267578125 1.494500756263733 1283.04052734375 0.39760303497314453 0.7472997 1.2506566047668457 True -10 19888 20.132534503936768 0.3642570972442627 737.5491333007812 1.3743207454681396 1273.2032470703125 0.3985905051231384 0.755856 1.1336655616760254 True -11 21696 20.125311613082886 1.7132072448730469 1126.47607421875 1.0537093877792358 1261.258056640625 0.40265679359436035 0.76070935 1.0855827331542969 True -12 23504 20.11521601676941 0.3717358112335205 1390.8272705078125 0.9612283706665039 1254.3460693359375 0.4032583236694336 0.76911306 1.0186320543289185 True -13 25312 20.140544176101685 0.3724193572998047 706.6898193359375 0.8578510284423828 1240.3150634765625 0.4077775478363037 0.7734306 0.9644013047218323 True -14 27120 20.114975452423096 0.36104583740234375 1147.26123046875 1.2718710899353027 1228.6707763671875 0.4122489094734192 0.77736753 0.9384716153144836 True -15 28928 20.096784353256226 0.36048030853271484 1057.30908203125 0.7268797159194946 1227.892333984375 0.41226261854171753 0.7835812 0.9094213843345642 True -16 30736 20.13629174232483 0.3642594814300537 1386.765869140625 0.9813135266304016 1229.611083984375 0.4106992781162262 0.78856313 0.8904438614845276 True -17 32544 20.12656021118164 0.36542391777038574 845.95654296875 0.836239218711853 1224.80029296875 0.41199713945388794 0.7903193 0.8845857381820679 True -18 34352 20.184372663497925 11.309900999069214 1116.9176025390625 0.7050424814224243 1228.035400390625 0.4102090001106262 0.7933314 0.8771603107452393 True -19 36160 20.209936380386353 0.37333035469055176 866.6354370117188 0.6008696556091309 1233.481689453125 0.40788283944129944 0.7924395 0.8780772089958191 False diff --git a/ENCSR567IWT/cherimoya.fold_4.performance.tsv b/ENCSR567IWT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 70cd4e240501c88cec0bc19160c0b953c9986d6e..0000000000000000000000000000000000000000 --- a/ENCSR567IWT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1228.035400390625 0.37374961376190186 0.41020897030830383 0.19403748214244843 0.7933313846588135 0.7315278649330139 0.8771603107452393 \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_0.evaluate.json b/ENCSR569ATD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 31f4d089fba344f2e3af0a528baa3345721e9eef..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF923GSK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_0.fit.json b/ENCSR569ATD/cherimoya.fold_0.fit.json deleted file mode 100644 index 8421747e90f129dd619c16ba123d6a7c2c4229de..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF923GSK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_0.log b/ENCSR569ATD/cherimoya.fold_0.log deleted file mode 100644 index 4bdec3dfcc1fb14a41c13ab52a38047a159017a5..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1588 22.86742377281189 3.3025717735290527 308.5211486816406 0.9639196395874023 408.98919677734375 0.13149097561836243 0.5410281 10.9000883102417 True -1 3176 17.562790870666504 1.555659294128418 243.86766052246094 1.084040641784668 390.8689270019531 0.19760113954544067 0.6648185 4.036548137664795 True -2 4764 17.54191780090332 0.29219865798950195 271.5950927734375 0.8989817500114441 373.0797119140625 0.2486443817615509 0.7074901 1.4947054386138916 True -3 6352 17.52767014503479 0.2996361255645752 246.5353240966797 0.8550001382827759 366.7245178222656 0.26210176944732666 0.73049873 0.755018413066864 True -4 7940 17.503144025802612 0.2914431095123291 309.1107177734375 0.8191594481468201 363.708251953125 0.26922333240509033 0.7303814 0.6770682334899902 False -5 9528 17.504809856414795 0.2916758060455322 330.054931640625 0.93610018491745 363.1473083496094 0.268533319234848 0.7389436 0.5798333883285522 True -6 11116 17.522169828414917 0.29700660705566406 299.35693359375 0.8795158267021179 362.23516845703125 0.272193968296051 0.7409621 0.5701808929443359 True -7 12704 17.581965684890747 0.36399292945861816 306.9980163574219 0.5909827947616577 360.97723388671875 0.275574654340744 0.74058884 0.5550601482391357 False -8 14292 17.555635452270508 0.29256129264831543 233.73182678222656 0.636001706123352 359.9449462890625 0.2789245545864105 0.74669874 0.5363032221794128 True -9 15880 17.509943962097168 0.29695630073547363 322.56524658203125 0.6404589414596558 359.77972412109375 0.27926281094551086 0.7515202 0.5408619046211243 True -10 17468 17.628468990325928 0.3408675193786621 259.3040771484375 0.8771827220916748 358.68682861328125 0.28246089816093445 0.7523366 0.5392359495162964 True -11 19056 17.63042163848877 0.30814337730407715 254.68008422851562 0.5405148863792419 357.9849853515625 0.28421279788017273 0.7574014 0.5279223322868347 True -12 20644 17.713566064834595 16.320446729660034 302.1441650390625 0.7471702098846436 358.13031005859375 0.2833714485168457 0.76191485 0.5285638570785522 True -13 22232 19.871264219284058 5.740601539611816 280.9749755859375 0.4804989695549011 357.500244140625 0.2849659323692322 0.76482636 0.5231097936630249 True -14 23820 17.55959963798523 0.9427640438079834 283.670166015625 0.34316208958625793 356.6122131347656 0.28742387890815735 0.77055377 0.5116145610809326 True -15 25408 17.57020115852356 0.294400691986084 255.2544403076172 0.420526385307312 357.400390625 0.2846914827823639 0.77137065 0.5175712704658508 True -16 26996 17.576720476150513 0.29810667037963867 254.34490966796875 0.4456180930137634 357.3946228027344 0.28516578674316406 0.7711659 0.5314521789550781 False -17 28584 17.539493083953857 0.2971510887145996 291.05767822265625 0.27544721961021423 356.98773193359375 0.28646722435951233 0.7674755 0.553961992263794 False -18 30172 17.51244282722473 0.47214794158935547 298.4569091796875 0.30967193841934204 357.12786865234375 0.2858762741088867 0.7631105 0.572467029094696 False -19 31760 17.559008598327637 0.2938878536224365 265.3592224121094 0.5529919862747192 357.8731689453125 0.2830095887184143 0.7609763 0.5873805284500122 False diff --git a/ENCSR569ATD/cherimoya.fold_0.performance.tsv b/ENCSR569ATD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 89fbb07acda01d9f2413989cee96dd7dcfe79b57..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -357.400390625 0.47475284337997437 0.2846914529800415 0.09909389168024063 0.7713706493377686 0.7413670420646667 0.5175712704658508 \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_1.evaluate.json b/ENCSR569ATD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index affa32f3b107a28508082813e5bf52f1dd9bf28f..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF923GSK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_1.fit.json b/ENCSR569ATD/cherimoya.fold_1.fit.json deleted file mode 100644 index 731eb2980f77ce1b2cdfab3d116844609a020900..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF923GSK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_1.log b/ENCSR569ATD/cherimoya.fold_1.log deleted file mode 100644 index 61098ec248fa63babaf52fe22dab0cbf91ae0756..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1561 21.87856960296631 28.19719386100769 293.177734375 1.2031848430633545 455.051025390625 0.1426367312669754 0.4927801 11.896449089050293 True -1 3122 17.654541015625 0.5063807964324951 310.3818359375 0.7550264596939087 436.10150146484375 0.20679871737957 0.6356386 4.223473072052002 True -2 4683 17.25024676322937 1.113595724105835 308.25927734375 0.688123345375061 413.12261962890625 0.26485586166381836 0.712973 1.885611653327942 True -3 6244 17.51145839691162 29.747692823410034 287.330810546875 1.000976800918579 405.1994934082031 0.2783302962779999 0.7376878 0.9059461951255798 True -4 7805 17.82618021965027 0.4848332405090332 281.7376708984375 0.9936655163764954 402.140380859375 0.2834704518318176 0.7452567 0.7352067232131958 True -5 9366 17.25577187538147 19.355650663375854 308.9854736328125 0.8076258897781372 400.3846740722656 0.28684309124946594 0.7541629 0.6392649412155151 True -6 10927 17.361960887908936 0.4904670715332031 305.74725341796875 1.0140392780303955 399.5671691894531 0.28818508982658386 0.75793976 0.624521791934967 True -7 12488 17.23408579826355 0.4905984401702881 269.858154296875 0.8421930074691772 398.3540344238281 0.29195636510849 0.75962174 0.591788649559021 True -8 14049 17.294821977615356 0.4820420742034912 270.27630615234375 0.5968174934387207 397.4306335449219 0.2937392294406891 0.7641152 0.5870707631111145 True -9 15610 17.238837242126465 0.47884535789489746 307.549560546875 0.7902523279190063 396.0451354980469 0.2975335121154785 0.7692987 0.5791382193565369 True -10 17171 17.22333812713623 0.4843871593475342 267.1864929199219 0.8930060267448425 396.348388671875 0.29625430703163147 0.77149093 0.5698305368423462 True -11 18732 17.294811487197876 0.47492432594299316 278.17144775390625 0.4790452718734741 395.96905517578125 0.2971942722797394 0.775551 0.5523898601531982 True -12 20293 17.23899245262146 0.48129844665527344 359.8121337890625 0.761224627494812 395.2795715332031 0.29916074872016907 0.7791513 0.5506570935249329 True -13 21854 17.247257947921753 0.4844825267791748 259.8242492675781 0.5978659391403198 394.6258850097656 0.30046460032463074 0.7828533 0.5461931228637695 True -14 23415 17.23739004135132 0.47598910331726074 322.74725341796875 0.4025745391845703 394.45574951171875 0.30100205540657043 0.78449553 0.54941725730896 True -15 24976 17.35145854949951 0.476656436920166 293.54437255859375 0.49527812004089355 394.1747131347656 0.30102384090423584 0.7847026 0.5559603571891785 True -16 26537 17.244694471359253 0.47295165061950684 242.4276580810547 0.45296716690063477 394.83978271484375 0.2989216148853302 0.7837324 0.5710560083389282 False -17 28098 17.296140909194946 0.5092823505401611 323.32855224609375 0.2084205448627472 394.8453674316406 0.2993852496147156 0.7822652 0.5920010209083557 False -18 29659 17.25675106048584 0.4842491149902344 285.8364562988281 0.3216876685619354 395.0129089355469 0.2991858422756195 0.7785829 0.6207128167152405 False -19 31220 17.26150155067444 0.48061609268188477 242.59127807617188 0.3587336540222168 394.9561462402344 0.2992026209831238 0.7767983 0.6396042704582214 False diff --git a/ENCSR569ATD/cherimoya.fold_1.performance.tsv b/ENCSR569ATD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 285115e3bdf1dd7cd85fbeb3e857cef75f574988..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -394.1747131347656 0.4601038694381714 0.30102384090423584 0.10647226870059967 0.7847025990486145 0.7652756571769714 0.5559603571891785 \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_2.evaluate.json b/ENCSR569ATD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 13674aac02d0effcd5e386137ce3bec7231ff0ee..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF923GSK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_2.fit.json b/ENCSR569ATD/cherimoya.fold_2.fit.json deleted file mode 100644 index 137d015c38f699f07623a4addde83e246006cbb0..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF923GSK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_2.log b/ENCSR569ATD/cherimoya.fold_2.log deleted file mode 100644 index 84b015f00f5bee20b0e15007af775055ee7c0f66..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1692 23.16717505455017 3.2960541248321533 314.2819519042969 0.6874130964279175 415.6176452636719 0.13562454283237457 0.49608842 9.737772941589355 True -1 3384 18.69160747528076 0.3799245357513428 340.2114562988281 1.1467573642730713 396.96160888671875 0.19879938662052155 0.6244933 4.325401782989502 True -2 5076 18.687445878982544 0.3134431838989258 330.3055114746094 0.8137190341949463 374.2214660644531 0.26025712490081787 0.70166636 1.7077264785766602 True -3 6768 18.67646861076355 0.3166923522949219 282.57769775390625 0.6497753262519836 368.2507019042969 0.2721051275730133 0.7203521 0.8529923558235168 True -4 8460 18.6648371219635 0.313035249710083 320.59783935546875 0.5204810500144958 366.141357421875 0.27667802572250366 0.7279151 0.7017756700515747 True -5 10152 18.6692955493927 0.3154411315917969 309.35308837890625 0.520047664642334 364.8505554199219 0.27968350052833557 0.73988307 0.633222758769989 True -6 11844 18.7436466217041 0.31720972061157227 274.7321472167969 0.6799279451370239 363.754638671875 0.2829303741455078 0.74475026 0.5561239719390869 True -7 13536 18.69250774383545 0.3186933994293213 292.24066162109375 0.8813604116439819 362.5585021972656 0.2867545485496521 0.74543184 0.5711748003959656 True -8 15228 18.722614526748657 9.113406658172607 321.28009033203125 0.9944704174995422 362.1528625488281 0.28825804591178894 0.74871147 0.5779733657836914 True -9 16920 18.817090272903442 0.32189321517944336 295.872802734375 0.6021400690078735 361.69671630859375 0.28978291153907776 0.7514019 0.5771706104278564 True -10 18612 18.765212774276733 1.7978394031524658 285.19183349609375 0.7479561567306519 361.4454345703125 0.28950661420822144 0.7541997 0.5618706345558167 True -11 20304 18.70708990097046 1.5990753173828125 321.6354064941406 0.7686285972595215 360.34844970703125 0.29251712560653687 0.75699437 0.5544056296348572 True -12 21996 18.71130347251892 0.3082621097564697 324.7851257324219 0.7992284893989563 360.1878967285156 0.29282549023628235 0.7600321 0.5537488460540771 True -13 23688 18.720550537109375 6.489303827285767 307.9388732910156 0.4407534599304199 359.6375427246094 0.29488661885261536 0.7605878 0.5501430630683899 True -14 25380 18.700844526290894 0.3159353733062744 314.2158508300781 0.33946871757507324 359.30224609375 0.2962287962436676 0.7650644 0.5464288592338562 True -15 27072 18.66463851928711 0.30756449699401855 292.7237548828125 0.43961355090141296 358.8076477050781 0.2973395884037018 0.7669007 0.5505470633506775 True -16 28764 18.67340588569641 0.3134267330169678 321.6112060546875 0.33268725872039795 359.1483459472656 0.2959150969982147 0.7640526 0.5608240365982056 False -17 30456 18.66765594482422 0.3112194538116455 285.1380615234375 0.3623741865158081 359.6507568359375 0.294570654630661 0.75996804 0.5809239745140076 False -18 32148 18.714361429214478 8.999553442001343 264.93927001953125 0.34630286693573 359.707275390625 0.2944237291812897 0.75843847 0.5976125597953796 False -19 33840 18.777992248535156 0.3220505714416504 253.3721923828125 0.4566328227519989 360.2792053222656 0.29188331961631775 0.755139 0.6097419261932373 False diff --git a/ENCSR569ATD/cherimoya.fold_2.performance.tsv b/ENCSR569ATD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e709646752015912186cc546ca6c695f8aa79a01..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -358.8076477050781 0.4703061878681183 0.2973395884037018 0.10137340426445007 0.7669007182121277 0.7412006855010986 0.5505470633506775 \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_3.evaluate.json b/ENCSR569ATD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 43b7ed69c686a3d49181db380c6e4bd22c8958c4..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF923GSK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_3.fit.json b/ENCSR569ATD/cherimoya.fold_3.fit.json deleted file mode 100644 index 02b9c3a6393b899874c22db725862e453cb10dba..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF923GSK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_3.log b/ENCSR569ATD/cherimoya.fold_3.log deleted file mode 100644 index 5eca6d7b5916a4ae0da0b206ca9ef61349f78baa..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1623 22.57557201385498 3.2265424728393555 309.72686767578125 1.0436828136444092 444.2892150878906 0.1452239453792572 0.49774775 11.569788932800293 True -1 3246 17.9415340423584 0.35642147064208984 353.74786376953125 1.1529207229614258 425.08251953125 0.20886719226837158 0.63292646 4.972049713134766 True -2 4869 17.96847629547119 0.32920074462890625 258.99700927734375 1.1434106826782227 405.1670227050781 0.2606654167175293 0.6927368 2.061323642730713 True -3 6492 17.944876194000244 0.32872939109802246 326.5806884765625 0.8791103363037109 400.095947265625 0.26977303624153137 0.6929415 1.415464997291565 True -4 8115 17.891196250915527 0.3279991149902344 290.4579162597656 0.6244508028030396 398.2864074707031 0.27453991770744324 0.6895853 1.1376746892929077 False -5 9738 17.918177604675293 0.3326609134674072 254.923095703125 0.6206886172294617 397.4595947265625 0.2762312591075897 0.7007743 1.0482009649276733 True -6 11361 17.956408977508545 0.3309922218322754 337.22802734375 0.5864784717559814 395.63397216796875 0.28167325258255005 0.706486 0.9360288977622986 True -7 12984 17.93440318107605 0.3370382785797119 336.5220642089844 0.7468659281730652 394.9207763671875 0.2824539244174957 0.70891875 0.8333266973495483 True -8 14607 17.913108587265015 0.33109569549560547 245.3792724609375 0.6095939874649048 394.2504577636719 0.28468844294548035 0.7162201 0.7788127064704895 True -9 16230 17.943180084228516 0.328000545501709 254.48390197753906 0.5599460005760193 394.12225341796875 0.2839875817298889 0.7166465 0.7387149333953857 True -10 17853 17.92462992668152 0.32977914810180664 273.7340087890625 0.6337640285491943 393.0000305175781 0.28749969601631165 0.7284366 0.6943610310554504 True -11 19476 17.905272483825684 1.4611148834228516 265.7298583984375 0.6164723634719849 392.3677978515625 0.28895846009254456 0.7338429 0.6771860718727112 True -12 21099 17.918398141860962 0.3346245288848877 289.131103515625 0.5582029223442078 392.4975891113281 0.2885683476924896 0.7382297 0.6483088731765747 True -13 22722 17.932278156280518 0.34377312660217285 233.48825073242188 0.5521941184997559 392.2345886230469 0.2886534631252289 0.7420126 0.6403189301490784 True -14 24345 17.897118091583252 0.34189701080322266 316.239501953125 0.4278357923030853 391.9634704589844 0.2897474765777588 0.7454373 0.6326608657836914 True -15 25968 21.496116161346436 21.436299800872803 266.48785400390625 0.3137058615684509 391.6846923828125 0.2892179787158966 0.75135875 0.6263651847839355 True -16 27591 17.992778539657593 0.33768463134765625 317.82183837890625 0.3590238094329834 391.9021911621094 0.2884993851184845 0.7532605 0.6351182460784912 True -17 29214 18.0040225982666 0.3337666988372803 270.637939453125 0.5180232524871826 392.3025817871094 0.2872483730316162 0.7509393 0.6550407409667969 False -18 30837 17.908155918121338 0.332045316696167 283.8338317871094 0.2686127722263336 392.24761962890625 0.2869260609149933 0.74819297 0.6791536808013916 False -19 32460 17.957447052001953 0.33960390090942383 280.4702453613281 0.2562146782875061 392.5126953125 0.2866458296775818 0.7466078 0.6956058144569397 False diff --git a/ENCSR569ATD/cherimoya.fold_3.performance.tsv b/ENCSR569ATD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7a641cfb3d277f5809ccf2e3c4d5e297eddde29c..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -391.9021911621094 0.46581095457077026 0.2884993553161621 0.10365738719701767 0.7532604932785034 0.7253742814064026 0.6351182460784912 \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_4.evaluate.json b/ENCSR569ATD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 03fa045a079c96b23e5777ab464a8b0e146ea24a..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF923GSK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_4.fit.json b/ENCSR569ATD/cherimoya.fold_4.fit.json deleted file mode 100644 index b126a4a7e91df4081d30aeda0cf6af1bf9ab803f..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF923GSK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR569ATD/cherimoya.fold_4.log b/ENCSR569ATD/cherimoya.fold_4.log deleted file mode 100644 index c799c74219829416591dd01b6023a8e93e55aec9..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1614 22.610779523849487 3.4623260498046875 261.4800720214844 1.1344925165176392 408.55426025390625 0.1372801959514618 0.5159493 10.481672286987305 True -1 3228 18.034576416015625 0.3039708137512207 327.25042724609375 1.0238443613052368 392.48291015625 0.1952841728925705 0.6123647 4.376256465911865 True -2 4842 17.901377201080322 0.286041259765625 341.3341979980469 0.6804775595664978 373.91448974609375 0.24845924973487854 0.6671234 2.0870819091796875 True -3 6456 17.874377727508545 0.28914403915405273 323.40924072265625 0.657503604888916 366.6263732910156 0.2640059292316437 0.694963 0.9757283926010132 True -4 8070 18.682857275009155 18.947164297103882 286.51690673828125 0.826471209526062 364.01971435546875 0.2693141996860504 0.7044571 0.7746707797050476 True -5 9684 18.347859621047974 0.30640697479248047 295.7314453125 0.7268563508987427 362.73675537109375 0.2718868553638458 0.7104092 0.7143927216529846 True -6 11298 17.83379292488098 0.4122142791748047 230.70086669921875 0.6025112867355347 361.92108154296875 0.2743239402770996 0.7192069 0.6787075996398926 True -7 12912 17.861766815185547 0.298292875289917 315.88800048828125 0.7305071353912354 360.8366394042969 0.27777621150016785 0.7201263 0.679509699344635 True -8 14526 18.831074476242065 19.49811887741089 293.729248046875 0.756767749786377 360.71221923828125 0.2781345844268799 0.7223276 0.6607016921043396 True -9 16140 18.61265230178833 0.2991211414337158 278.09600830078125 0.6182389259338379 359.60015869140625 0.28068041801452637 0.7300376 0.6356943845748901 True -10 17754 17.872909545898438 12.74369192123413 270.16217041015625 0.5645784139633179 359.4040222167969 0.28140366077423096 0.73319495 0.6215992569923401 True -11 19368 19.975699424743652 7.288529396057129 236.1070556640625 0.500629186630249 358.5467834472656 0.2844946086406708 0.73303306 0.6235405206680298 False -12 20982 18.012218475341797 0.29538464546203613 224.97235107421875 0.4766058921813965 358.2613525390625 0.28376153111457825 0.734611 0.6003890633583069 True -13 22596 17.85914635658264 0.2896864414215088 311.5055236816406 0.5092121958732605 357.8011474609375 0.28556403517723083 0.7404763 0.5934522747993469 True -14 24210 17.852787494659424 0.29877543449401855 290.051025390625 0.47973698377609253 357.2749328613281 0.28662776947021484 0.74314517 0.586459755897522 True -15 25824 17.83456802368164 0.2919595241546631 277.954345703125 0.4000425338745117 357.3735046386719 0.2864795923233032 0.74379814 0.5863131880760193 True -16 27438 17.832627534866333 15.093297719955444 370.053955078125 0.3970615267753601 357.85662841796875 0.28441351652145386 0.7406502 0.6019331812858582 False -17 29052 17.95352339744568 0.2912766933441162 273.3890686035156 0.21483257412910461 358.2239685058594 0.2837056815624237 0.7382196 0.6236047148704529 False -18 30666 17.834464073181152 0.2868533134460449 320.1191101074219 0.27369940280914307 358.2421875 0.28359904885292053 0.73222584 0.647395670413971 False -19 32280 17.805973291397095 0.29142236709594727 248.9605255126953 0.2148115038871765 358.79150390625 0.2813052833080292 0.7302813 0.661527693271637 False diff --git a/ENCSR569ATD/cherimoya.fold_4.performance.tsv b/ENCSR569ATD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index de19d391825ea512c56fc74b83dac469ffc835d0..0000000000000000000000000000000000000000 --- a/ENCSR569ATD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -357.3735046386719 0.4746473729610443 0.28647956252098083 0.09849721938371658 0.7437981367111206 0.7061591148376465 0.5863131880760193 \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_0.evaluate.json b/ENCSR570BWW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f11b793900d27c9f823cce133fd57ef38724b598..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF394SCJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_0.fit.json b/ENCSR570BWW/cherimoya.fold_0.fit.json deleted file mode 100644 index 896be0206ac59b2f4603781b884c4311335e9a6e..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF394SCJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_0.log b/ENCSR570BWW/cherimoya.fold_0.log deleted file mode 100644 index ec2e950a0e98f2008ae21887e65f9d983f9b0777..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 35.223453521728516 4.223701000213623 649.3002319335938 0.35411226749420166 734.6222534179688 0.2925737500190735 0.7607698 3.8253729343414307 True -1 5536 30.435797929763794 0.6083836555480957 561.2960205078125 0.45035627484321594 679.708740234375 0.3526493012905121 0.81545556 1.0065792798995972 True -2 8304 30.38189673423767 0.6410617828369141 503.74407958984375 0.29686832427978516 668.29541015625 0.3655543029308319 0.83422035 0.4576539099216461 True -3 11072 30.352550745010376 0.6628766059875488 570.7258911132812 0.2468157410621643 664.1482543945312 0.36893174052238464 0.8381456 0.36626043915748596 True -4 13840 30.368303060531616 0.5699071884155273 563.716552734375 0.14857494831085205 662.4856567382812 0.369617223739624 0.8450557 0.291169136762619 True -5 16608 30.466427326202393 0.6084837913513184 738.7144165039062 0.3463112711906433 658.6768798828125 0.3738880753517151 0.8535929 0.25849995017051697 True -6 19376 30.409921169281006 0.5806210041046143 629.7301025390625 0.3265066146850586 654.2467041015625 0.3795822858810425 0.8578486 0.23761893808841705 True -7 22144 30.38971519470215 0.5823519229888916 598.0109252929688 0.27550292015075684 654.362060546875 0.37919384241104126 0.8589525 0.24456827342510223 True -8 24912 30.451892852783203 0.5792267322540283 700.4471435546875 1.0967702865600586 652.6438598632812 0.3814883530139923 0.86297137 0.22359399497509003 True -9 27680 30.43477749824524 0.6015262603759766 557.2938232421875 0.21637222170829773 650.7162475585938 0.3835738003253937 0.868326 0.22242477536201477 True -10 30448 30.395869493484497 0.585679292678833 544.7857666015625 0.33797773718833923 649.3163452148438 0.3842158615589142 0.87353706 0.20604334771633148 True -11 33216 30.395153045654297 0.6003737449645996 578.3546752929688 0.25346678495407104 649.1102905273438 0.3840036392211914 0.8752484 0.20220476388931274 True -12 35984 30.39120864868164 0.583319902420044 528.8992919921875 0.2239111214876175 647.9426879882812 0.38553592562675476 0.87960225 0.19191426038742065 True -13 38752 30.383833646774292 0.6003954410552979 528.1686401367188 0.15572577714920044 645.2357177734375 0.3893163204193115 0.8836602 0.18430617451667786 True -14 41520 30.366954565048218 4.898726463317871 593.8058471679688 0.1373928189277649 644.6004638671875 0.3902454078197479 0.88772 0.17749027907848358 True -15 44288 30.41787099838257 1.9104759693145752 537.500244140625 0.14761795103549957 644.166748046875 0.3901984989643097 0.8917161 0.1723647266626358 True -16 47056 30.093980073928833 0.5709047317504883 517.63623046875 0.14832803606987 643.5824584960938 0.390480101108551 0.8918428 0.16770276427268982 True -17 49824 29.94373106956482 0.5732028484344482 559.40673828125 0.18459981679916382 644.4232788085938 0.3891179859638214 0.89301264 0.1666039079427719 True -18 52592 29.811947345733643 0.5784265995025635 613.0816650390625 0.13547983765602112 643.71044921875 0.39052751660346985 0.8928313 0.16648277640342712 False -19 55360 29.852946758270264 0.5967237949371338 523.8836669921875 0.13739830255508423 643.5001831054688 0.3913304805755615 0.894066 0.16640561819076538 True diff --git a/ENCSR570BWW/cherimoya.fold_0.performance.tsv b/ENCSR570BWW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d8b6903f1286402c04f37683c8c2b2efd0209001..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -643.5001831054688 0.38128048181533813 0.3913304805755615 0.16381095349788666 0.8940659761428833 0.8706685900688171 0.16640561819076538 \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_1.evaluate.json b/ENCSR570BWW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 27bea073e4349f424c99fcb467a6616fde274438..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF394SCJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_1.fit.json b/ENCSR570BWW/cherimoya.fold_1.fit.json deleted file mode 100644 index 7d9126f476f780f3e81f8f95b8af221fbb9fe2d0..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF394SCJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_1.log b/ENCSR570BWW/cherimoya.fold_1.log deleted file mode 100644 index 26a9e02b2e25aea359fb0f802c8fc807721d7284..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2715 34.620102643966675 4.489081621170044 597.1795043945312 0.33392414450645447 838.6428833007812 0.29038500785827637 0.76459795 4.583456993103027 True -1 5430 29.87677311897278 0.881671667098999 502.12432861328125 0.31857240200042725 773.8285522460938 0.356540322303772 0.8141231 1.2734217643737793 True -2 8145 29.851346492767334 0.7122764587402344 699.9329833984375 0.37755513191223145 755.4664916992188 0.3719664514064789 0.83829325 0.5464094281196594 True -3 10860 29.8698091506958 0.7123470306396484 641.1474609375 0.29006531834602356 748.8549194335938 0.3796077370643616 0.84006923 0.44063568115234375 True -4 13575 29.816120624542236 0.703211784362793 691.5135498046875 0.2706615924835205 746.2843017578125 0.38195177912712097 0.84659433 0.3822583854198456 True -5 16290 29.891639232635498 0.7044486999511719 539.1830444335938 0.2302098423242569 742.2261352539062 0.3859494924545288 0.85141665 0.32057011127471924 True -6 19005 29.881398677825928 0.6963305473327637 495.6983947753906 0.2947787046432495 739.243896484375 0.3876853585243225 0.8547538 0.303022176027298 True -7 21720 29.93280053138733 26.323012590408325 564.384765625 0.21375367045402527 736.5462646484375 0.390038400888443 0.859371 0.29759159684181213 True -8 24435 30.571539640426636 0.9945685863494873 521.2777099609375 0.17313481867313385 732.4435424804688 0.3943740427494049 0.86610144 0.26359349489212036 True -9 27150 29.885697603225708 0.6881976127624512 528.851318359375 0.2750656306743622 730.0721435546875 0.39632660150527954 0.8688733 0.2647552788257599 True -10 29865 29.885064840316772 0.6882729530334473 525.2598266601562 0.28569334745407104 727.1128540039062 0.39959409832954407 0.873527 0.2446053922176361 True -11 32580 29.888450145721436 0.6898481845855713 570.1570434570312 0.15381258726119995 726.4820556640625 0.3991679251194 0.87872475 0.2335537225008011 True -12 35295 29.888413667678833 2.9938313961029053 609.5169677734375 0.21479737758636475 722.516845703125 0.40386131405830383 0.8833605 0.22068630158901215 True -13 38010 29.861579656600952 31.266550064086914 500.6960144042969 0.11949409544467926 723.4140014648438 0.40117743611335754 0.88808453 0.2128264158964157 True -14 40725 29.450972318649292 0.7554161548614502 548.1849365234375 0.14936324954032898 721.608642578125 0.402809202671051 0.8952222 0.19818516075611115 True -15 43440 29.279358386993408 0.6935899257659912 575.8270874023438 0.19268673658370972 719.0183715820312 0.40615421533584595 0.89836496 0.19081929326057434 True -16 46155 29.311047554016113 0.7070915699005127 494.55560302734375 0.17018982768058777 719.9502563476562 0.4043072462081909 0.9025147 0.18257738649845123 True -17 48870 29.27158784866333 0.6981353759765625 522.4835815429688 0.1654067188501358 718.7994995117188 0.4060559570789337 0.9036981 0.17721547186374664 True -18 51585 29.257548332214355 0.7017045021057129 485.86016845703125 0.2241765707731247 718.2006225585938 0.40715181827545166 0.90400934 0.17580106854438782 True -19 54300 29.501566171646118 0.7306938171386719 552.0166015625 0.1622927337884903 717.6864624023438 0.4079050123691559 0.90325946 0.1757119745016098 False diff --git a/ENCSR570BWW/cherimoya.fold_1.performance.tsv b/ENCSR570BWW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 02d7138a5f89005a2269857a92d20c1b9dca268d..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -718.2006225585938 0.3674473762512207 0.4071517884731293 0.18161872029304504 0.9040093421936035 0.8959570527076721 0.17580106854438782 \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_2.evaluate.json b/ENCSR570BWW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3506f7aa4ab555cb7e6ca7d2d86973c8ec7bb7fc..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF394SCJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_2.fit.json b/ENCSR570BWW/cherimoya.fold_2.fit.json deleted file mode 100644 index 8f8d6722fe8260ff846bfa8d37ad1d01689bd528..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF394SCJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_2.log b/ENCSR570BWW/cherimoya.fold_2.log deleted file mode 100644 index ea78058c7309fe590b18756f75ac5a2310847662..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 36.29191613197327 4.228216886520386 562.9383544921875 0.2963550388813019 775.5758666992188 0.2973441481590271 0.75524724 3.641845464706421 True -1 5746 31.608072519302368 0.643296480178833 457.5006103515625 0.28263968229293823 715.4879760742188 0.35577768087387085 0.8156957 0.9756957292556763 True -2 8619 31.585675477981567 0.5802412033081055 527.6578369140625 0.33649498224258423 702.3132934570312 0.368434876203537 0.8292181 0.4602733254432678 True -3 11492 31.524559497833252 0.591726541519165 504.3832702636719 0.27995315194129944 697.4417724609375 0.37245458364486694 0.83569884 0.390356183052063 True -4 14365 31.56627655029297 0.632591724395752 554.773681640625 0.2743566036224365 695.2607421875 0.3728480935096741 0.83965373 0.33139824867248535 True -5 17238 31.61777925491333 0.5543999671936035 536.1309814453125 0.2705613076686859 691.9205932617188 0.377936989068985 0.84065425 0.28504079580307007 True -6 20111 31.534525632858276 0.572418212890625 586.619873046875 0.2935487926006317 690.2473754882812 0.3789274990558624 0.8467546 0.26596030592918396 True -7 22984 31.572761058807373 0.5778257846832275 549.6235961914062 0.1783902943134308 687.8045043945312 0.3810688257217407 0.85333157 0.2597384750843048 True -8 25857 31.565324783325195 0.5649240016937256 534.379638671875 0.19827595353126526 685.6605834960938 0.38287535309791565 0.85682684 0.24436438083648682 True -9 28730 31.547132968902588 0.5577819347381592 536.296142578125 0.20144732296466827 684.0204467773438 0.38511723279953003 0.8601318 0.2451300472021103 True -10 31603 31.496683835983276 0.5786533355712891 664.96728515625 0.23381608724594116 681.3984985351562 0.38807299733161926 0.864674 0.22665098309516907 True -11 34476 31.537848472595215 0.5578205585479736 578.924560546875 0.2810312509536743 680.5203857421875 0.38886919617652893 0.8704313 0.22266224026679993 True -12 37349 31.55424165725708 0.564063310623169 575.351318359375 0.2519772946834564 678.195556640625 0.391502320766449 0.87367284 0.2130868136882782 True -13 40222 31.674126863479614 0.5751521587371826 577.923095703125 0.15931735932826996 677.4637451171875 0.3917340934276581 0.8759017 0.20253533124923706 True -14 43095 31.416112899780273 0.5695593357086182 523.4154052734375 0.20320948958396912 675.6187744140625 0.39400431513786316 0.88149494 0.19182927906513214 True -15 45968 30.95647931098938 1.096062183380127 528.9141235351562 0.15367193520069122 675.1456298828125 0.39485475420951843 0.8850487 0.1872575730085373 True -16 48841 30.955596446990967 0.5641684532165527 642.4279174804688 0.1766481250524521 674.6161499023438 0.3953123390674591 0.88694507 0.18154673278331757 True -17 51714 30.96906018257141 9.191232442855835 526.3076171875 0.15594446659088135 674.52490234375 0.3952791392803192 0.88870865 0.1781211942434311 True -18 54587 30.98038077354431 1.5937886238098145 553.500244140625 0.1554562896490097 675.5120239257812 0.3935738503932953 0.88722605 0.17826403677463531 False -19 57460 31.005836486816406 0.5542409420013428 629.4583740234375 0.1275840550661087 674.996337890625 0.39429229497909546 0.88814104 0.17941726744174957 False diff --git a/ENCSR570BWW/cherimoya.fold_2.performance.tsv b/ENCSR570BWW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e95db00a1559ffa2c1643683935171beb1078e86..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -674.52490234375 0.37651777267456055 0.3952791392803192 0.17059022188186646 0.8887086510658264 0.8721498847007751 0.1781211942434311 \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_3.evaluate.json b/ENCSR570BWW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 92b45b4bac6512124be11b995d1281890dd4f8c8..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF394SCJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_3.fit.json b/ENCSR570BWW/cherimoya.fold_3.fit.json deleted file mode 100644 index f94a0a4e1757e73a8cf15bcafcd1f1c6ea9ce2d3..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF394SCJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_3.log b/ENCSR570BWW/cherimoya.fold_3.log deleted file mode 100644 index 1a71d858510e6349436d950cf611ed6e73456a01..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 36.15629005432129 4.0107338428497314 603.0667724609375 0.30990394949913025 716.8582153320312 0.29940226674079895 0.73748857 4.541674613952637 True -1 5520 30.312904834747314 0.529731035232544 663.5445556640625 0.2646309435367584 659.0406494140625 0.3611810803413391 0.81669354 1.134313941001892 True -2 8280 30.32058310508728 2.079406261444092 608.4208984375 0.19059623777866364 646.9283447265625 0.37021124362945557 0.83419585 0.39772987365722656 True -3 11040 30.35571050643921 0.5221395492553711 513.408203125 0.24014416337013245 641.863525390625 0.3747822642326355 0.84011126 0.3425678014755249 True -4 13800 30.349174737930298 0.5168251991271973 525.06982421875 0.3014121651649475 639.9298095703125 0.376794695854187 0.8468324 0.3465758264064789 True -5 16560 30.307341814041138 0.5911750793457031 585.7548828125 0.40329134464263916 638.572998046875 0.37721410393714905 0.8509342 0.27463284134864807 True -6 19320 30.326048135757446 0.5295956134796143 500.45391845703125 0.1897767186164856 635.6154174804688 0.3811243772506714 0.8527616 0.25888293981552124 True -7 22080 30.37395668029785 0.909102201461792 613.8240356445312 0.2595518231391907 635.1088256835938 0.38138243556022644 0.8561299 0.2550050914287567 True -8 24840 30.360394716262817 0.5279555320739746 514.8916625976562 0.2829582691192627 632.9907836914062 0.3831883370876312 0.86032623 0.24201937019824982 True -9 27600 30.361278295516968 0.528651237487793 533.0679931640625 0.49736639857292175 631.2970581054688 0.38595688343048096 0.8637458 0.23971521854400635 True -10 30360 30.37183666229248 1.9799277782440186 516.2916259765625 0.1988646537065506 629.6494140625 0.3872506618499756 0.8658364 0.23033460974693298 True -11 33120 30.383005142211914 0.5460939407348633 583.94580078125 0.24101775884628296 628.3245849609375 0.3883742392063141 0.87161887 0.22979098558425903 True -12 35880 30.305635929107666 0.5294785499572754 574.4680786132812 0.22184976935386658 627.8663940429688 0.3886074721813202 0.876693 0.21420139074325562 True -13 38640 30.291568517684937 0.5182251930236816 628.872802734375 0.14321491122245789 625.4260864257812 0.3914410471916199 0.8781872 0.20568478107452393 True -14 41400 30.166072607040405 0.523435115814209 490.7572021484375 0.2712972164154053 625.2853393554688 0.3916527032852173 0.8840749 0.19666990637779236 True -15 44160 29.719329833984375 0.5167810916900635 576.8182373046875 0.16302260756492615 623.8831176757812 0.3929852545261383 0.8890517 0.18906399607658386 True -16 46920 29.741525888442993 0.5120701789855957 479.29827880859375 0.24341212213039398 624.1898803710938 0.39188024401664734 0.8933643 0.18128758668899536 True -17 49680 29.722607374191284 0.5123264789581299 601.835205078125 0.0991535484790802 622.1378173828125 0.3958304226398468 0.8942297 0.1772889792919159 True -18 52440 29.720890045166016 0.5113394260406494 518.3527221679688 0.11030419170856476 623.037109375 0.3942974805831909 0.8933774 0.17701153457164764 False -19 55200 29.73321771621704 0.5141243934631348 583.6739501953125 0.1159365251660347 622.5684204101562 0.3953630030155182 0.89327854 0.17778219282627106 False diff --git a/ENCSR570BWW/cherimoya.fold_3.performance.tsv b/ENCSR570BWW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1765283ce312c9bdd7f6d8289742d0db75152c6e..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -622.1378173828125 0.38109928369522095 0.3958304822444916 0.16324232518672943 0.8942297101020813 0.868186891078949 0.1772889792919159 \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_4.evaluate.json b/ENCSR570BWW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f8f7b49970572f789d821ba6e41b20a997360628..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF394SCJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_4.fit.json b/ENCSR570BWW/cherimoya.fold_4.fit.json deleted file mode 100644 index 10b22137520de1589b968c8e19a8efb5d340f0ae..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF394SCJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR570BWW/cherimoya.fold_4.log b/ENCSR570BWW/cherimoya.fold_4.log deleted file mode 100644 index 0109ebe53a05ad17586065772790c9eee1eb93ce..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 35.42520833015442 4.478668928146362 597.94287109375 0.4486595392227173 676.9735717773438 0.2835344076156616 0.7474036 4.338325023651123 True -1 5564 30.599901914596558 0.6067278385162354 591.601318359375 0.3888234496116638 627.4031372070312 0.3422988951206207 0.8029104 1.0436327457427979 True -2 8346 30.578961610794067 1.5769908428192139 560.6015014648438 0.22742168605327606 618.1765747070312 0.35174527764320374 0.8249169 0.32983481884002686 True -3 11128 30.551300287246704 0.6304018497467041 596.24365234375 0.306887149810791 612.298095703125 0.35716450214385986 0.8339958 0.3268890678882599 True -4 13910 30.555272579193115 0.6055464744567871 480.4375 0.24928045272827148 610.361083984375 0.35968032479286194 0.83815616 0.26078712940216064 True -5 16692 30.564366340637207 0.6026771068572998 508.27447509765625 0.20667660236358643 607.4443359375 0.36287257075309753 0.847797 0.243833526968956 True -6 19474 30.568493127822876 0.601334810256958 629.3126220703125 0.22155240178108215 606.0868530273438 0.36396822333335876 0.8499184 0.2299545407295227 True -7 22256 30.551751375198364 0.5964765548706055 559.733642578125 0.27937665581703186 605.2861938476562 0.3647068738937378 0.85440046 0.23628586530685425 True -8 25038 30.60728359222412 0.6012077331542969 523.8511962890625 0.25909578800201416 602.3255615234375 0.369016170501709 0.8582126 0.22635145485401154 True -9 27820 30.76193380355835 0.6160268783569336 579.5713500976562 0.2858384847640991 602.991943359375 0.3671707510948181 0.862751 0.2178054302930832 True -10 30602 30.61554503440857 0.6037366390228271 469.6712951660156 0.15289026498794556 600.9662475585938 0.3702147901058197 0.8670073 0.2092696726322174 True -11 33384 30.633496284484863 0.6284940242767334 488.70330810546875 0.134891539812088 599.1659545898438 0.37212517857551575 0.8713639 0.2015971839427948 True -12 36166 31.009217500686646 0.6272280216217041 496.2779541015625 0.2431723028421402 598.5770874023438 0.37287431955337524 0.87623674 0.1897687017917633 True -13 38948 30.549111127853394 0.6049561500549316 503.41796875 0.28829383850097656 597.931640625 0.3738202750682831 0.8781168 0.18281175196170807 True -14 41730 30.115838050842285 0.614734411239624 488.2830810546875 0.170828178524971 597.059326171875 0.37503212690353394 0.8829294 0.1726405918598175 True -15 44512 30.024329662322998 0.614943265914917 692.1112060546875 0.17807430028915405 595.7240600585938 0.3766351640224457 0.8868236 0.16774073243141174 True -16 47294 30.013909578323364 0.6110854148864746 565.5880126953125 0.2295156717300415 595.4108276367188 0.37746843695640564 0.8892413 0.1619080752134323 True -17 50076 30.007789850234985 0.6089653968811035 487.34600830078125 0.24544265866279602 595.8096313476562 0.3760763704776764 0.8927094 0.15906022489070892 True -18 52858 30.051197052001953 23.392032623291016 500.3995361328125 0.11762313544750214 596.134033203125 0.3761741816997528 0.89116514 0.1585133671760559 False -19 55640 30.04166841506958 0.6024627685546875 596.4309692382812 0.13228991627693176 596.0911865234375 0.3761407434940338 0.89124376 0.15834757685661316 False diff --git a/ENCSR570BWW/cherimoya.fold_4.performance.tsv b/ENCSR570BWW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e87a6cab1331e1a7ed719252e29755b2f9ca2257..0000000000000000000000000000000000000000 --- a/ENCSR570BWW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -595.8096313476562 0.39410239458084106 0.3760763108730316 0.15004396438598633 0.8927093744277954 0.8622038960456848 0.15906022489070892 \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_0.evaluate.json b/ENCSR571JFO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5f6b44a361defde48f811c53b63051383f0918bf..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350CRU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_0.fit.json b/ENCSR571JFO/cherimoya.fold_0.fit.json deleted file mode 100644 index 0254ac9d8d32250a0972a78ae8da4d754977c770..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF350CRU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_0.log b/ENCSR571JFO/cherimoya.fold_0.log deleted file mode 100644 index b14f5fbbd0bb3900d644d27ff8e8a99820942b0c..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2931 36.98328232765198 4.024857759475708 491.455078125 0.25744524598121643 639.5108642578125 0.6634337902069092 0.69280416 3.443479537963867 True -1 5862 32.2558798789978 0.6402266025543213 531.7763061523438 0.3679969906806946 562.8541259765625 0.7241775989532471 0.77978927 0.729217529296875 True -2 8793 32.2772114276886 0.5837194919586182 489.66375732421875 0.38820549845695496 548.9060668945312 0.7347022294998169 0.7971183 0.33412620425224304 True -3 11724 32.19422221183777 0.5936028957366943 454.41064453125 0.2244706153869629 544.8494262695312 0.7383683323860168 0.81170577 0.2954224646091461 True -4 14655 32.16356301307678 0.5726165771484375 493.86798095703125 0.3506137728691101 542.6400756835938 0.7395007610321045 0.81475544 0.2609710097312927 True -5 17586 32.21555137634277 0.5775547027587891 459.2181396484375 0.338191956281662 540.9110107421875 0.7420203685760498 0.8191415 0.24773669242858887 True -6 20517 32.222750425338745 0.5776236057281494 520.59765625 0.23153024911880493 539.2405395507812 0.7439019083976746 0.8250243 0.257135272026062 True -7 23448 31.9779052734375 0.5658886432647705 461.6101989746094 0.40356186032295227 537.7630004882812 0.7451757788658142 0.823887 0.24708272516727448 False -8 26379 31.579503297805786 0.669478178024292 438.11627197265625 0.3456023335456848 536.2837524414062 0.7468875646591187 0.8281127 0.250912070274353 True -9 29310 31.574918746948242 0.6038408279418945 395.73529052734375 0.1945158839225769 534.7533569335938 0.7482572793960571 0.8340886 0.24890807271003723 True -10 32241 31.577285766601562 0.5631420612335205 456.4991149902344 0.17279887199401855 533.408203125 0.7494921088218689 0.8368669 0.23842555284500122 True -11 35172 31.59017562866211 0.575650691986084 460.3360290527344 0.23780770599842072 531.7301025390625 0.7509788870811462 0.84296787 0.2186751365661621 True -12 38103 31.662720680236816 0.5750794410705566 523.65283203125 0.2209910750389099 530.4478759765625 0.7521255612373352 0.84585476 0.2086673527956009 True -13 41034 31.63848328590393 0.5773329734802246 442.12420654296875 0.23779016733169556 529.2595825195312 0.753262996673584 0.85047364 0.20095811784267426 True -14 43965 31.71212387084961 0.6274864673614502 475.3980407714844 0.16889284551143646 528.232177734375 0.7544146776199341 0.8542735 0.19436092674732208 True -15 46896 31.736915588378906 0.578239917755127 498.382568359375 0.2348720282316208 527.5497436523438 0.7548852562904358 0.8583133 0.19053207337856293 True -16 49827 31.651678323745728 2.1597726345062256 476.7271728515625 0.12334001064300537 527.4232177734375 0.7551956176757812 0.8606934 0.18700312077999115 True -17 52758 31.710237741470337 0.5785036087036133 454.96258544921875 0.14222034811973572 527.4312133789062 0.7549207806587219 0.85953444 0.18703335523605347 False -18 55689 31.79925775527954 0.5743405818939209 447.3274841308594 0.1710529625415802 527.7678833007812 0.754593551158905 0.8576121 0.18875673413276672 False -19 58620 31.7910578250885 0.573662519454956 452.3418884277344 0.09258309006690979 528.0145263671875 0.7543685436248779 0.8550043 0.18985268473625183 False diff --git a/ENCSR571JFO/cherimoya.fold_0.performance.tsv b/ENCSR571JFO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d0775b387d2589fd817b6f517165ac0098b063cc..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -527.4232177734375 0.19737021625041962 0.7551956176757812 0.3813939690589905 0.8606933951377869 0.7988952994346619 0.18700312077999115 \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_1.evaluate.json b/ENCSR571JFO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1b7e07ad208fe98680123da739d8452632efe699..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350CRU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_1.fit.json b/ENCSR571JFO/cherimoya.fold_1.fit.json deleted file mode 100644 index d9b90cd78ed3ab6e28db5c352dfc5e6a594c95b5..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF350CRU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_1.log b/ENCSR571JFO/cherimoya.fold_1.log deleted file mode 100644 index cc0218732ea5ee407dedd997d4cb3b9e8319be89..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2851 35.922744035720825 4.213541030883789 491.4859313964844 0.6172232031822205 745.1597290039062 0.6732850074768066 0.69693077 4.712048053741455 True -1 5702 31.336881637573242 1.612673282623291 474.38037109375 0.28212958574295044 643.2545776367188 0.7408109903335571 0.7859884 0.9888373613357544 True -2 8553 31.335235834121704 0.7848179340362549 548.0125732421875 0.41159841418266296 623.9505615234375 0.7531896233558655 0.80457497 0.4051991105079651 True -3 11404 31.340351819992065 0.7690987586975098 537.350830078125 0.33059191703796387 616.0929565429688 0.7589026093482971 0.81745213 0.3443578779697418 True -4 14255 31.654104709625244 0.7707812786102295 536.2841796875 0.26952460408210754 614.2780151367188 0.7602279782295227 0.8223925 0.33769920468330383 True -5 17106 31.864962816238403 0.775641679763794 446.0462951660156 0.2368815690279007 612.8244018554688 0.7614336013793945 0.8233588 0.30479538440704346 True -6 19957 31.34980010986328 0.7902686595916748 475.6671142578125 0.22469216585159302 611.0775756835938 0.7630658149719238 0.8269923 0.3221980333328247 True -7 22808 31.357099056243896 0.7889528274536133 470.4422302246094 0.28913432359695435 607.8221435546875 0.7653254866600037 0.8342936 0.30115869641304016 True -8 25659 31.333465814590454 0.7895653247833252 485.80487060546875 0.16185039281845093 606.0991821289062 0.7667877674102783 0.8347925 0.3015151619911194 True -9 28510 31.208064556121826 0.7852871417999268 496.435302734375 0.24171310663223267 603.5437622070312 0.7687742710113525 0.8388614 0.2870711088180542 True -10 31361 30.761833906173706 1.0683214664459229 509.89697265625 0.21014611423015594 601.7180786132812 0.7703260779380798 0.8448168 0.2751307189464569 True -11 34212 30.78081488609314 0.7771003246307373 493.20941162109375 0.3009779751300812 599.6085205078125 0.7719738483428955 0.8474848 0.2562078833580017 True -12 37063 30.794557809829712 0.7628688812255859 410.9479675292969 0.3122673034667969 597.8516845703125 0.7733334898948669 0.85528296 0.24170564115047455 True -13 39914 30.77620029449463 0.7623748779296875 448.75146484375 0.1636512130498886 596.6922607421875 0.7745040655136108 0.86034274 0.2335948348045349 True -14 42765 30.755483627319336 0.7629415988922119 435.62579345703125 0.14928480982780457 595.0560913085938 0.7760354280471802 0.8648174 0.21749037504196167 True -15 45616 30.83961510658264 0.7615201473236084 466.77471923828125 0.16814285516738892 594.209228515625 0.7767751216888428 0.8687938 0.21306075155735016 True -16 48467 30.79021406173706 0.7538340091705322 477.6997985839844 0.1260654777288437 594.2216796875 0.7769485712051392 0.8688582 0.20715004205703735 True -17 51318 30.773411512374878 0.7609250545501709 464.90948486328125 0.13051024079322815 594.4933471679688 0.7767112851142883 0.8692581 0.20620472729206085 True -18 54169 30.78081488609314 0.7827706336975098 462.803466796875 0.10945091396570206 595.031005859375 0.7762942314147949 0.8675205 0.20808760821819305 False -19 57020 30.810408115386963 0.7618598937988281 441.2222900390625 0.1154913455247879 595.4408569335938 0.7760553359985352 0.86759657 0.21058443188667297 False diff --git a/ENCSR571JFO/cherimoya.fold_1.performance.tsv b/ENCSR571JFO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0171a37d83d3e3b5ec648d69eee6e5b06fa0c659..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -594.4933471679688 0.17901791632175446 0.7767112851142883 0.421082466840744 0.8692581057548523 0.8316785097122192 0.20620472729206085 \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_2.evaluate.json b/ENCSR571JFO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index baf5ff35de28a35de962676dc35342700156f8a5..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350CRU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_2.fit.json b/ENCSR571JFO/cherimoya.fold_2.fit.json deleted file mode 100644 index c5f5d163b2b7aa250c209773932e1c5db5cf414b..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF350CRU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_2.log b/ENCSR571JFO/cherimoya.fold_2.log deleted file mode 100644 index 3f586390d04097525aa3eadda4ad2f17d2f8776f..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3043 38.1141996383667 4.134819030761719 548.1021728515625 0.5654792785644531 662.6817016601562 0.6728258728981018 0.6950442 3.1325626373291016 True -1 6086 33.493067502975464 0.6640996932983398 521.56982421875 0.2717183232307434 584.1126708984375 0.7281908392906189 0.77754116 0.6783332824707031 True -2 9129 33.46791195869446 0.6554582118988037 541.08154296875 0.3323194980621338 572.168212890625 0.7379367351531982 0.7983166 0.3216405510902405 True -3 12172 33.500839948654175 0.6266329288482666 439.57366943359375 0.24226245284080505 567.9440307617188 0.7418588399887085 0.81007904 0.3218795359134674 True -4 15215 33.46535849571228 0.6072192192077637 480.96697998046875 0.21444371342658997 566.267822265625 0.7431853413581848 0.81559014 0.26074862480163574 True -5 18258 33.48570156097412 0.6201505661010742 560.5994873046875 0.3084444999694824 563.6425170898438 0.7456449270248413 0.8203566 0.24979984760284424 True -6 21301 33.44437599182129 0.6295969486236572 506.0301818847656 0.19125741720199585 562.514404296875 0.7466715574264526 0.82454515 0.2558128535747528 True -7 24344 33.46313524246216 0.60788893699646 434.25341796875 0.36693012714385986 561.4930419921875 0.74773770570755 0.82491946 0.24626554548740387 True -8 27387 33.469181060791016 1.4798352718353271 507.56304931640625 0.31463107466697693 559.4827880859375 0.7493973970413208 0.8315718 0.23123010993003845 True -9 30430 33.478541135787964 0.6314413547515869 498.4298095703125 0.18446466326713562 557.6654663085938 0.7508549094200134 0.8341684 0.22916314005851746 True -10 33473 33.5114803314209 2.489647626876831 538.6649169921875 0.19479727745056152 555.9254760742188 0.7523255348205566 0.836595 0.2263823300600052 True -11 36516 33.56981921195984 0.6251988410949707 484.68060302734375 0.24682149291038513 554.1307373046875 0.7538787126541138 0.8434067 0.2157607525587082 True -12 39559 32.94446802139282 0.6285462379455566 487.44580078125 0.2658286392688751 552.2930297851562 0.755211353302002 0.84871024 0.20995007455348969 True -13 42602 32.9106969833374 0.6045212745666504 495.94970703125 0.19322505593299866 550.6799926757812 0.756702184677124 0.8516407 0.20843300223350525 True -14 45645 32.89730620384216 0.6064510345458984 423.080322265625 0.14256584644317627 549.3414306640625 0.7579187750816345 0.85829604 0.2024926245212555 True -15 48688 32.84636473655701 0.6167936325073242 478.5870361328125 0.2774580717086792 548.430908203125 0.7586769461631775 0.8587535 0.19580571353435516 True -16 51731 32.83369779586792 0.6064126491546631 477.49542236328125 0.13590504229068756 548.3497924804688 0.759035050868988 0.86123806 0.19252820312976837 True -17 54774 32.85516595840454 0.6940147876739502 483.5997619628906 0.09787173569202423 548.4095458984375 0.7590451836585999 0.85970414 0.19326022267341614 False -18 57817 32.87735939025879 18.28294539451599 532.62841796875 0.1497601866722107 548.7760620117188 0.7586818933486938 0.85905135 0.19396919012069702 False -19 60860 32.83553600311279 0.5969524383544922 504.1530456542969 0.11939647793769836 549.103759765625 0.7584585547447205 0.8581196 0.19558219611644745 False diff --git a/ENCSR571JFO/cherimoya.fold_2.performance.tsv b/ENCSR571JFO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a0001c9082e8b25074eaedea7d31ed38ba473612..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -548.3497924804688 0.19237935543060303 0.759035050868988 0.39524948596954346 0.8612380623817444 0.8024494647979736 0.19252820312976837 \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_3.evaluate.json b/ENCSR571JFO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index af06f7eddf53fc5dc5cf960b2c4ace2eaff70e74..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350CRU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_3.fit.json b/ENCSR571JFO/cherimoya.fold_3.fit.json deleted file mode 100644 index e164d111c937b3bbd983196336689e4d89a9e72f..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF350CRU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_3.log b/ENCSR571JFO/cherimoya.fold_3.log deleted file mode 100644 index dc37f12c215f846cdc7c0a4434a9f241a0dc7fc7..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2937 37.19196557998657 5.651764631271362 459.81292724609375 0.2647915482521057 656.7621459960938 0.6659297943115234 0.6827378 4.563885688781738 True -1 5874 32.32540035247803 0.8052692413330078 440.18426513671875 0.3179263174533844 579.5921630859375 0.7250546216964722 0.7691968 0.7807643413543701 True -2 8811 32.30830240249634 0.6760036945343018 554.89697265625 0.2651446461677551 565.5108642578125 0.7362805604934692 0.78826904 0.40850022435188293 True -3 11748 32.58228325843811 10.441294193267822 473.96697998046875 0.2634400427341461 559.5632934570312 0.7407867312431335 0.79775494 0.3483305871486664 True -4 14685 32.31886172294617 0.5733556747436523 482.853515625 0.2486269474029541 557.374755859375 0.7431942820549011 0.8028232 0.3373006284236908 True -5 17622 32.33583450317383 0.5743348598480225 535.8848266601562 0.3123885989189148 555.47412109375 0.7451038360595703 0.80864257 0.2999047040939331 True -6 20559 32.32086944580078 0.5718863010406494 521.8352661132812 0.1976880431175232 553.9483642578125 0.7465521693229675 0.81457484 0.2747637629508972 True -7 23496 32.26642608642578 0.5723311901092529 574.2811889648438 0.1975950002670288 552.2697143554688 0.7482026815414429 0.81715715 0.28117504715919495 True -8 26433 32.33825445175171 1.5769829750061035 547.868408203125 0.2262180894613266 549.9781494140625 0.7498666048049927 0.82144463 0.26811715960502625 True -9 29370 32.297677993774414 0.5821599960327148 465.2080383300781 0.1968938112258911 549.1620483398438 0.7507929801940918 0.82190317 0.2693045437335968 True -10 32307 32.30434799194336 0.5819618701934814 510.5606994628906 0.20439831912517548 547.1946411132812 0.7524183988571167 0.82634455 0.2666856050491333 True -11 35244 32.419164419174194 0.5756931304931641 465.3421936035156 0.1791674792766571 545.6734008789062 0.7540329694747925 0.83359367 0.2562732696533203 True -12 38181 32.2829806804657 0.5745899677276611 464.96173095703125 0.2149835079908371 545.0690307617188 0.7546732425689697 0.8335075 0.25519266724586487 False -13 41118 31.992334842681885 0.5665614604949951 517.654052734375 0.15088266134262085 543.4962158203125 0.7560601234436035 0.8401512 0.24277980625629425 True -14 44055 31.687061071395874 0.5695078372955322 479.1123352050781 0.13016091287136078 542.57080078125 0.7570667862892151 0.84284717 0.23685157299041748 True -15 46992 31.683856964111328 0.5687744617462158 450.47845458984375 0.12535643577575684 541.47802734375 0.7575838565826416 0.844939 0.23096738755702972 True -16 49929 31.781969785690308 0.5622756481170654 520.2072143554688 0.10355857014656067 541.5006103515625 0.7576988935470581 0.84968615 0.22697703540325165 True -17 52866 31.729222536087036 0.5617148876190186 440.256591796875 0.14839115738868713 541.469482421875 0.75753253698349 0.8476638 0.22528108954429626 False -18 55803 31.76352596282959 0.576585054397583 473.72198486328125 0.11931348592042923 541.9628295898438 0.7570738196372986 0.84472877 0.2280285656452179 False -19 58740 31.80848741531372 0.5857303142547607 412.013916015625 0.102147176861763 542.2151489257812 0.7567611336708069 0.84139985 0.2313281148672104 False diff --git a/ENCSR571JFO/cherimoya.fold_3.performance.tsv b/ENCSR571JFO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index edd5f99b3806eb5b8136ec05337cf0280d5b77e2..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -541.5006103515625 0.1951729953289032 0.7576989531517029 0.3845593333244324 0.8496861457824707 0.78520268201828 0.22697703540325165 \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_4.evaluate.json b/ENCSR571JFO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 90ae32195e8d7c3ea6f89a218011ebc9fa3a9ff4..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350CRU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_4.fit.json b/ENCSR571JFO/cherimoya.fold_4.fit.json deleted file mode 100644 index f02e794ce4e614394586d51c2ff2662b6ad312f1..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF350CRU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR571JFO/cherimoya.fold_4.log b/ENCSR571JFO/cherimoya.fold_4.log deleted file mode 100644 index f44db1d85d529cd2e3fe89631f9bdc4543fa37b3..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2928 36.99080967903137 4.645617961883545 536.7169189453125 0.3974519371986389 619.2698974609375 0.6624659895896912 0.696846 3.653043508529663 True -1 5856 32.214380979537964 0.988591194152832 441.5743103027344 0.3267327547073364 547.2674560546875 0.7192570567131042 0.7774452 0.5790131092071533 True -2 8784 32.19364023208618 1.4379827976226807 460.76531982421875 0.34466540813446045 536.5150146484375 0.7290320992469788 0.79275566 0.29423871636390686 True -3 11712 32.70807909965515 1.0874018669128418 479.75103759765625 0.3341032862663269 532.1871337890625 0.7327578663825989 0.8027416 0.2839897572994232 True -4 14640 32.26641058921814 0.614497184753418 491.9611511230469 0.30025923252105713 530.4596557617188 0.7347153425216675 0.8073788 0.2596409320831299 True -5 17568 32.26905846595764 0.6630806922912598 488.7714538574219 0.20122815668582916 530.2854614257812 0.7356419563293457 0.809175 0.28062704205513 True -6 20496 32.18333339691162 0.6008496284484863 509.8136901855469 0.20301896333694458 528.1536865234375 0.7376670241355896 0.8123771 0.2733793258666992 True -7 23424 32.1674268245697 0.5992345809936523 513.52685546875 0.21345387399196625 526.6454467773438 0.7393102645874023 0.8163796 0.27133840322494507 True -8 26352 32.203779458999634 0.602895975112915 488.5535888671875 0.3124289810657501 524.8380737304688 0.7407649159431458 0.82184744 0.25433146953582764 True -9 29280 32.22804927825928 0.5982213020324707 467.9066162109375 0.1590430587530136 523.1415405273438 0.7425395846366882 0.8288051 0.2437930703163147 True -10 32208 32.14593267440796 0.6129779815673828 434.6384582519531 0.18548086285591125 521.2769165039062 0.7438643574714661 0.833696 0.22295935451984406 True -11 35136 32.155293226242065 0.612501859664917 423.78326416015625 0.25132620334625244 519.7567749023438 0.7451724410057068 0.83983314 0.21524548530578613 True -12 38064 32.14873027801514 0.5938379764556885 494.0394592285156 0.21167832612991333 518.2206420898438 0.7466496229171753 0.84690285 0.20161162316799164 True -13 40992 32.21690917015076 0.6156327724456787 488.8213806152344 0.2105676680803299 517.213134765625 0.7477582693099976 0.8507213 0.19665585458278656 True -14 43920 32.039045572280884 0.6051983833312988 537.4620971679688 0.19888591766357422 516.1724853515625 0.748701810836792 0.8532671 0.1889646351337433 True -15 46848 31.634714365005493 0.5913393497467041 434.78466796875 0.16705834865570068 515.8460083007812 0.7492114305496216 0.8568377 0.1825430542230606 True -16 49776 31.623997688293457 0.5980424880981445 488.2305908203125 0.1745564043521881 515.6328735351562 0.7492546439170837 0.8620684 0.17891483008861542 True -17 52704 31.607598304748535 0.6060876846313477 408.78955078125 0.14757178723812103 515.9513549804688 0.7490990161895752 0.8589537 0.1787378489971161 False -18 55632 31.61748480796814 0.6009247303009033 492.98028564453125 0.09471774101257324 516.3134155273438 0.748799204826355 0.8590452 0.17836706340312958 False -19 58560 31.638503313064575 0.5945978164672852 430.950927734375 0.10341168195009232 516.4290771484375 0.7485957741737366 0.8600226 0.17904530465602875 False diff --git a/ENCSR571JFO/cherimoya.fold_4.performance.tsv b/ENCSR571JFO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9a918f1551c3d588686e45e325c44c7e55083c26..0000000000000000000000000000000000000000 --- a/ENCSR571JFO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -515.6328735351562 0.20135723054409027 0.7492546439170837 0.37313544750213623 0.8620684146881104 0.7855265736579895 0.17891483008861542 \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_0.evaluate.json b/ENCSR572FSS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b98c6b900202b25e32a8e16f607602e5884c0bb7..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF072XYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_0.fit.json b/ENCSR572FSS/cherimoya.fold_0.fit.json deleted file mode 100644 index 643a37a5ede34f8db1a6da316df169b7c6534bba..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF072XYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_0.log b/ENCSR572FSS/cherimoya.fold_0.log deleted file mode 100644 index 05b4758e115c6e77c36a285840320de8f8b2b528..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1802 24.524858474731445 3.532956838607788 239.48910522460938 0.6383611559867859 309.9837646484375 0.143769770860672 0.6480763 7.944287300109863 True -1 3604 19.85753560066223 0.4331674575805664 192.55255126953125 0.573765754699707 282.2308349609375 0.2017715573310852 0.7661275 3.466291666030884 True -2 5406 19.846996307373047 0.35869669914245605 245.65798950195312 0.5784531235694885 264.0837707519531 0.22700564563274384 0.80873203 1.302905797958374 True -3 7208 19.83375334739685 0.371673583984375 269.91180419921875 0.48323825001716614 259.015869140625 0.2322547882795334 0.814583 0.7407481074333191 True -4 9010 19.838762521743774 0.4250359535217285 208.1199493408203 0.4536925256252289 257.54827880859375 0.23411041498184204 0.82330084 0.6099973320960999 True -5 10812 19.825063943862915 0.3597226142883301 257.3418884277344 0.32727640867233276 255.329833984375 0.2390337735414505 0.8331697 0.5425361394882202 True -6 12614 19.804252862930298 0.3605537414550781 246.33285522460938 0.3597702383995056 254.1757049560547 0.24127797782421112 0.83732426 0.5003407001495361 True -7 14416 19.852816820144653 0.3602256774902344 170.80630493164062 0.481315553188324 253.40054321289062 0.24261237680912018 0.842872 0.46960654854774475 True -8 16218 19.87845206260681 0.4101595878601074 174.32147216796875 0.32002508640289307 252.06166076660156 0.2454887330532074 0.8515048 0.43736618757247925 True -9 18020 19.839637994766235 0.3657186031341553 258.12310791015625 0.5794199109077454 251.64956665039062 0.24599145352840424 0.85435545 0.40565773844718933 True -10 19822 19.866766452789307 0.3746628761291504 194.79727172851562 0.2561805248260498 251.2147216796875 0.2469341903924942 0.8604216 0.3850565254688263 True -11 21624 19.805370092391968 0.3665328025817871 211.4923553466797 0.44768714904785156 250.56561279296875 0.24843375384807587 0.8625432 0.39010292291641235 True -12 23426 19.855456829071045 0.3675408363342285 232.01681518554688 0.4214962124824524 249.7454071044922 0.25051602721214294 0.86718994 0.37156760692596436 True -13 25228 19.84308886528015 0.3649742603302002 226.75350952148438 0.28660818934440613 249.48666381835938 0.2517589330673218 0.87095255 0.3509640693664551 True -14 27030 19.848175525665283 0.3745710849761963 246.17337036132812 0.23961366713047028 248.607666015625 0.2532031238079071 0.873377 0.33587366342544556 True -15 28832 19.831373691558838 0.3895871639251709 206.85398864746094 0.33914250135421753 248.0311279296875 0.25484150648117065 0.87629706 0.3245471119880676 True -16 30634 19.872496604919434 0.36948561668395996 241.2001953125 0.27515220642089844 248.021728515625 0.25453487038612366 0.8787571 0.31666940450668335 True -17 32436 19.818074941635132 0.36527490615844727 226.42910766601562 0.3054291605949402 248.0413818359375 0.2548234462738037 0.87912506 0.31432458758354187 True -18 34238 19.815181732177734 0.3662426471710205 196.57894897460938 0.23430664837360382 248.75555419921875 0.2526707947254181 0.87764424 0.3159872591495514 False -19 36040 19.82380962371826 0.3886990547180176 207.50375366210938 0.22888970375061035 248.74984741210938 0.25310006737709045 0.87760925 0.3174119293689728 False diff --git a/ENCSR572FSS/cherimoya.fold_0.performance.tsv b/ENCSR572FSS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d88aa212a5455cb04edc6a81632ee0140edd4941..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -248.0413818359375 0.5184254050254822 0.2548234462738037 0.07201851159334183 0.8791250586509705 0.822599470615387 0.31432458758354187 \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_1.evaluate.json b/ENCSR572FSS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 62b8ac74ec77fbc3116f6c48784ab9de51cfbe26..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF072XYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_1.fit.json b/ENCSR572FSS/cherimoya.fold_1.fit.json deleted file mode 100644 index 3afd35667e24e191fb6459cbc526b9cf1858c6f3..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF072XYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_1.log b/ENCSR572FSS/cherimoya.fold_1.log deleted file mode 100644 index 1a6725c4a973622a617c329277a4fdab3480ba88..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1750 23.87941551208496 3.8269026279449463 256.7987976074219 0.607239305973053 388.21832275390625 0.15779100358486176 0.61727685 9.343644142150879 True -1 3500 19.32479453086853 0.6025652885437012 218.764404296875 0.6377459764480591 354.1365966796875 0.2244991660118103 0.7543258 3.8772809505462646 True -2 5250 19.314712047576904 0.4898948669433594 249.06195068359375 0.6283448338508606 326.9335632324219 0.25689491629600525 0.7996817 1.8860938549041748 True -3 7000 19.283973932266235 0.4919302463531494 132.76251220703125 0.3894329071044922 320.23321533203125 0.2633848786354065 0.8095205 1.3924106359481812 True -4 8750 19.29271125793457 0.4864532947540283 167.3712615966797 0.3065304756164551 316.5825500488281 0.2699574828147888 0.8161872 0.9572739601135254 True -5 10500 19.3015079498291 0.4931046962738037 230.21859741210938 0.5519380569458008 314.4090270996094 0.27317243814468384 0.8263935 0.7716290950775146 True -6 12250 19.29630446434021 2.6794848442077637 257.22955322265625 0.6220370531082153 313.0038146972656 0.27528151869773865 0.8324305 0.7437008619308472 True -7 14000 19.10182476043701 0.49396276473999023 252.06752014160156 0.448385089635849 310.8764343261719 0.28005450963974 0.8441101 0.6488239169120789 True -8 15750 18.90831232070923 0.8232355117797852 225.64443969726562 0.5163958072662354 308.78692626953125 0.28424787521362305 0.85335475 0.5962720513343811 True -9 17500 18.934845685958862 0.49028635025024414 203.0228271484375 0.41825994849205017 308.1357727050781 0.2845053970813751 0.86090666 0.552672266960144 True -10 19250 18.95662832260132 0.48855090141296387 248.7810821533203 0.48148849606513977 305.83831787109375 0.289294958114624 0.86936873 0.4848283529281616 True -11 21000 18.93311905860901 0.4912276268005371 228.83689880371094 0.2940073013305664 305.81549072265625 0.2885136902332306 0.8737089 0.4490358531475067 True -12 22750 18.958014726638794 0.49697327613830566 226.69082641601562 0.39971813559532166 304.8652648925781 0.28966930508613586 0.87930995 0.4128396213054657 True -13 24500 18.965752124786377 0.4814608097076416 189.96902465820312 0.36851248145103455 304.1712646484375 0.29090338945388794 0.8844939 0.39075881242752075 True -14 26250 18.91970729827881 0.49033427238464355 270.91925048828125 0.3037724494934082 303.4412536621094 0.29283928871154785 0.8860773 0.37237754464149475 True -15 28000 18.97206449508667 4.116368532180786 182.9268035888672 0.3133352994918823 302.95513916015625 0.29353055357933044 0.88801163 0.3631022870540619 True -16 29750 19.007771253585815 0.5149710178375244 235.7440185546875 0.2265993058681488 303.4114074707031 0.29252153635025024 0.8892098 0.3625733256340027 True -17 31500 19.01980495452881 0.5111818313598633 256.5313720703125 0.3187369704246521 303.33392333984375 0.2933223247528076 0.8894619 0.3596014976501465 True -18 33250 19.032837629318237 0.5036880970001221 222.5465087890625 0.1940862536430359 303.52337646484375 0.29281482100486755 0.88884586 0.3638766407966614 False -19 35000 18.930439233779907 12.982076168060303 201.20794677734375 0.1758124977350235 304.5909423828125 0.28959518671035767 0.88704944 0.36738547682762146 False diff --git a/ENCSR572FSS/cherimoya.fold_1.performance.tsv b/ENCSR572FSS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index af144ff84b2443649520f46ab1ef8155d41c992c..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -303.33392333984375 0.48866793513298035 0.2933223247528076 0.0917283147573471 0.889461874961853 0.8595482707023621 0.3596014976501465 \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_2.evaluate.json b/ENCSR572FSS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 586e4a1fd91f8d59749777dde35cfdafed6d7898..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF072XYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_2.fit.json b/ENCSR572FSS/cherimoya.fold_2.fit.json deleted file mode 100644 index 8f353797b27d870edd05dd7914e4b2cd624e1d35..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF072XYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_2.log b/ENCSR572FSS/cherimoya.fold_2.log deleted file mode 100644 index 3a159a401ec9782ee4ac19a145acd29410641d2b..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1882 26.702224731445312 3.603647232055664 190.87356567382812 0.5665627121925354 325.45709228515625 0.14619828760623932 0.6036584 7.866033554077148 True -1 3764 21.16965675354004 0.44074463844299316 202.82177734375 0.4897390604019165 293.4603271484375 0.20778299868106842 0.72456616 3.1563425064086914 True -2 5646 20.80243444442749 0.43923044204711914 233.36785888671875 0.4057995080947876 273.44610595703125 0.2326798439025879 0.7929725 1.5024971961975098 True -3 7528 23.978209018707275 9.433802127838135 215.64447021484375 0.5747679471969604 269.0061950683594 0.2373477667570114 0.8099178 0.7585144639015198 True -4 9410 20.771306037902832 0.39870357513427734 225.56280517578125 0.5192570686340332 266.876708984375 0.24058352410793304 0.82116884 0.5881819128990173 True -5 11292 20.84000039100647 0.39358019828796387 194.65536499023438 0.5040311813354492 265.8350524902344 0.24091531336307526 0.8285059 0.5002140998840332 True -6 13174 20.90197253227234 1.7751049995422363 216.56307983398438 0.5830500721931458 264.25335693359375 0.24514076113700867 0.83532953 0.4985714554786682 True -7 15056 20.83199429512024 0.4096488952636719 194.74717712402344 0.3907274603843689 263.1986389160156 0.24762773513793945 0.83891505 0.5067153573036194 True -8 16938 20.843183517456055 0.40291714668273926 192.4039764404297 0.36650604009628296 262.3900451660156 0.24914005398750305 0.8466923 0.46967408061027527 True -9 18820 20.80474591255188 0.4007742404937744 247.30364990234375 0.36331844329833984 260.8929748535156 0.25248652696609497 0.8516927 0.44543179869651794 True -10 20702 20.78599786758423 0.39529848098754883 199.3542022705078 0.39224663376808167 260.7190246582031 0.2525268793106079 0.85565686 0.40930649638175964 True -11 22584 20.756441593170166 0.3990335464477539 210.5519561767578 0.2504029870033264 259.250244140625 0.256075918674469 0.8602431 0.39684468507766724 True -12 24466 20.759392023086548 0.3956871032714844 190.402587890625 0.4361341893672943 258.5484924316406 0.2567982077598572 0.86557317 0.38457411527633667 True -13 26348 20.833576679229736 0.38109469413757324 191.23712158203125 0.2573358118534088 257.3328552246094 0.26012280583381653 0.8695359 0.35897141695022583 True -14 28230 20.8313467502594 0.40846967697143555 180.173583984375 0.4385392367839813 257.59442138671875 0.25805792212486267 0.87322056 0.3424249291419983 True -15 30112 20.822465658187866 0.39459919929504395 221.14431762695312 0.1633813977241516 257.0201721191406 0.25987887382507324 0.8750992 0.3335714340209961 True -16 31994 20.863773584365845 0.4002711772918701 190.9703826904297 0.2734379768371582 256.63421630859375 0.26124829053878784 0.8751648 0.3270718455314636 True -17 33876 20.828659534454346 0.3865518569946289 273.8792724609375 0.2698341906070709 256.5869140625 0.2614489495754242 0.8755857 0.32440581917762756 True -18 35758 20.86428928375244 0.38442087173461914 186.47726440429688 0.2531058192253113 257.6360778808594 0.2579837143421173 0.8764958 0.32698237895965576 True -19 37640 20.837724924087524 0.39670395851135254 225.6393585205078 0.2530931532382965 257.8930358886719 0.2575465440750122 0.8759109 0.3303243815898895 False diff --git a/ENCSR572FSS/cherimoya.fold_2.performance.tsv b/ENCSR572FSS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 38e53ff62c1022a4f120068ef96e00d0cd201e6a..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -257.6360778808594 0.5141881704330444 0.2579837143421173 0.07254888117313385 0.8764957785606384 0.8235201239585876 0.32698237895965576 \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_3.evaluate.json b/ENCSR572FSS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6b902b31ad22b3b6619e266b49cd810b730bc10b..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF072XYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_3.fit.json b/ENCSR572FSS/cherimoya.fold_3.fit.json deleted file mode 100644 index 1ecdcd60d48951a7128ebe05feca11d859dafaa8..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF072XYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_3.log b/ENCSR572FSS/cherimoya.fold_3.log deleted file mode 100644 index 152f2badb484c8b63980e8b2469d1e7d2983681a..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1796 24.366747617721558 3.41839337348938 265.4608154296875 0.7592465281486511 332.5935363769531 0.155969500541687 0.6006556 8.51122760772705 True -1 3592 19.86572790145874 0.4213275909423828 238.2449951171875 0.4293169379234314 303.5932922363281 0.21219860017299652 0.72603583 3.610025644302368 True -2 5388 19.79353928565979 8.565630912780762 241.0093994140625 0.5405336022377014 284.450439453125 0.23929500579833984 0.7763104 1.9562335014343262 True -3 7184 19.49090027809143 6.0007641315460205 187.6460418701172 0.381985068321228 279.84808349609375 0.24626561999320984 0.78278166 1.1361957788467407 True -4 8980 19.430127382278442 0.3691105842590332 272.9385070800781 0.5954955816268921 277.7840270996094 0.24928762018680573 0.797482 0.8663488626480103 True -5 10776 19.434666872024536 1.9252562522888184 214.6822967529297 0.6372969150543213 275.6277160644531 0.2544240355491638 0.8062729 0.863753080368042 True -6 12572 19.442980766296387 0.36171936988830566 158.62628173828125 0.33666014671325684 275.0097351074219 0.25538891553878784 0.8151117 0.7940019965171814 True -7 14368 19.42218041419983 0.3500676155090332 159.69012451171875 0.4571222960948944 273.2307434082031 0.2597704827785492 0.8225534 0.7510637640953064 True -8 16164 19.407987594604492 0.34372901916503906 224.88055419921875 0.4294033646583557 272.23687744140625 0.2614579498767853 0.83013904 0.6718750596046448 True -9 17960 19.40287947654724 0.3399851322174072 206.74546813964844 0.3613048493862152 271.4273681640625 0.26296350359916687 0.83790165 0.6224584579467773 True -10 19756 19.456523180007935 0.3511168956756592 180.97909545898438 0.3608192801475525 270.5111999511719 0.26473468542099 0.8444642 0.546517550945282 True -11 21552 19.40693497657776 0.34296298027038574 266.55377197265625 0.4979596734046936 269.6658935546875 0.26640692353248596 0.8518214 0.48295170068740845 True -12 23348 19.445634126663208 0.35481739044189453 160.12490844726562 0.304193377494812 268.684814453125 0.26770561933517456 0.855352 0.45203065872192383 True -13 25144 19.43334436416626 0.3432152271270752 218.25387573242188 0.4239869713783264 267.5895690917969 0.2703043222427368 0.86016005 0.43793120980262756 True -14 26940 19.432276725769043 0.3563416004180908 276.5843505859375 0.394000768661499 267.2037353515625 0.2712600827217102 0.86494756 0.4090493619441986 True -15 28736 19.417155504226685 0.33994269371032715 156.91949462890625 0.30302178859710693 266.890625 0.2710762023925781 0.8718871 0.3910926282405853 True -16 30532 19.39926791191101 0.351560115814209 173.65309143066406 0.1807960569858551 266.6920166015625 0.27204468846321106 0.8751955 0.36951273679733276 True -17 32328 19.399747133255005 0.6236705780029297 212.9990997314453 0.18410012125968933 267.3285827636719 0.2693834900856018 0.87646323 0.36484187841415405 True -18 34124 19.436688661575317 1.364295244216919 215.3398895263672 0.18317723274230957 267.3724365234375 0.26985159516334534 0.8751058 0.36644598841667175 False -19 35920 19.449917316436768 0.3530707359313965 207.5787353515625 0.27357643842697144 267.45159912109375 0.26990485191345215 0.8736073 0.36693981289863586 False diff --git a/ENCSR572FSS/cherimoya.fold_3.performance.tsv b/ENCSR572FSS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 24129603b6a0f749fe14395d0969c9f11fd78d50..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -267.3285827636719 0.5059531331062317 0.2693834900856018 0.08236046880483627 0.8764632344245911 0.8222600221633911 0.36484187841415405 \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_4.evaluate.json b/ENCSR572FSS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8861cb97f93c55aeb56632d7fa4c36d040acc3f9..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF072XYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_4.fit.json b/ENCSR572FSS/cherimoya.fold_4.fit.json deleted file mode 100644 index 1a3bc83618ad4ab65fa92dbd9be6d1ca5b86dcab..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF072XYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR572FSS/cherimoya.fold_4.log b/ENCSR572FSS/cherimoya.fold_4.log deleted file mode 100644 index 155d6ce2b997f103dd0794e0c0a7191ec0b15552..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1802 24.369048595428467 3.424806594848633 223.36441040039062 0.7503969073295593 282.2934265136719 0.14073675870895386 0.6135266 7.208282470703125 True -1 3604 19.855651140213013 0.54317307472229 210.04379272460938 0.6475900411605835 259.66998291015625 0.19362156093120575 0.73221594 2.65346097946167 True -2 5406 19.874517679214478 0.3820486068725586 210.51431274414062 0.5045185685157776 243.6022491455078 0.21605244278907776 0.79391336 1.299087643623352 True -3 7208 19.877301931381226 0.3818509578704834 203.514404296875 0.5286508798599243 239.44436645507812 0.2203289121389389 0.81095296 0.712440013885498 True -4 9010 19.864070177078247 0.3679807186126709 255.18658447265625 0.459213525056839 237.8387451171875 0.22370627522468567 0.816049 0.5915393233299255 True -5 10812 19.86026668548584 0.3658170700073242 159.14974975585938 0.25247374176979065 237.0198516845703 0.22509033977985382 0.8181413 0.5587272047996521 True -6 12614 19.884206771850586 0.3812241554260254 202.0362548828125 0.6105332374572754 235.90377807617188 0.2271283119916916 0.82680506 0.49496322870254517 True -7 14416 19.84327220916748 0.3824324607849121 201.08840942382812 0.46622154116630554 234.72052001953125 0.22914709150791168 0.83894604 0.4206310212612152 True -8 16218 19.829631090164185 0.36832284927368164 219.85516357421875 0.3934507966041565 234.0067901611328 0.23146702349185944 0.841431 0.3913117051124573 True -9 18020 19.849952220916748 0.36739635467529297 206.15316772460938 0.287091463804245 233.2477264404297 0.2333167940378189 0.8464018 0.3702343702316284 True -10 19822 19.823071479797363 0.368741512298584 185.86785888671875 0.47697222232818604 232.72265625 0.23519210517406464 0.8511265 0.3602364659309387 True -11 21624 20.828803062438965 11.525333642959595 186.80404663085938 0.3732355833053589 232.1564483642578 0.23556269705295563 0.8535754 0.3421444296836853 True -12 23426 19.54402208328247 0.3772575855255127 207.732177734375 0.4459892511367798 231.8271484375 0.23577824234962463 0.85733914 0.3370630145072937 True -13 25228 19.514546871185303 1.1242082118988037 185.66293334960938 0.3546561598777771 230.30738830566406 0.2404700219631195 0.8608472 0.3261885643005371 True -14 27030 19.482823371887207 0.38075947761535645 199.32791137695312 0.5446971654891968 230.32835388183594 0.23927219212055206 0.8647537 0.314544677734375 True -15 28832 19.54912233352661 0.4141349792480469 226.68763732910156 0.3808075487613678 230.1787567138672 0.23934446275234222 0.86627525 0.312531977891922 True -16 30634 19.529539585113525 0.37757301330566406 184.0103759765625 0.19940823316574097 230.44189453125 0.23905371129512787 0.86739635 0.30672967433929443 True -17 32436 19.488574266433716 0.3793950080871582 224.4336395263672 0.19332551956176758 230.42083740234375 0.23947346210479736 0.869082 0.3053268790245056 True -18 34238 19.493725061416626 0.3800947666168213 194.7170867919922 0.1807689070701599 230.89537048339844 0.23825997114181519 0.8676605 0.3077317476272583 False -19 36040 19.49150276184082 0.4581434726715088 196.62454223632812 0.18688303232192993 230.77003479003906 0.23908717930316925 0.86793536 0.30876192450523376 False diff --git a/ENCSR572FSS/cherimoya.fold_4.performance.tsv b/ENCSR572FSS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9d3794bf861585cfcd2e471c4aec9ed9182f52d8..0000000000000000000000000000000000000000 --- a/ENCSR572FSS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -230.42083740234375 0.5288990139961243 0.23947349190711975 0.0690302774310112 0.869081974029541 0.7924033999443054 0.3053268790245056 \ No newline at end of file diff --git a/ENCSR572HUG/cherimoya.fold_0.evaluate.json b/ENCSR572HUG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 123d7ea34a170daf4fee80d36e37591afb783dc6..0000000000000000000000000000000000000000 --- a/ENCSR572HUG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF304JTM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR572HUG/cherimoya.fold_3.fit.json b/ENCSR572HUG/cherimoya.fold_3.fit.json deleted file mode 100644 index 58e2c01b8ddf7bd7e800e874612d449d8b1bb587..0000000000000000000000000000000000000000 --- a/ENCSR572HUG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF304JTM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_0.evaluate.json b/ENCSR576UAF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index dd88a1df653ad230cf4d9318b6730b80b2e7ab51..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863OMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_0.fit.json b/ENCSR576UAF/cherimoya.fold_0.fit.json deleted file mode 100644 index d04d116c819166ec4232dca170f9f1c41e06d0d0..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF863OMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_0.log b/ENCSR576UAF/cherimoya.fold_0.log deleted file mode 100644 index b2301e686579919c6143c1d1f10850d2ff55f177..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.77097201347351 4.535950422286987 947.3529052734375 0.5532872676849365 1120.2918701171875 0.299883097410202 0.66599417 7.601902961730957 True -1 5484 30.791024684906006 0.5903580188751221 876.911376953125 0.48251816630363464 971.7911376953125 0.40364882349967957 0.7106298 2.8008010387420654 True -2 8226 30.398728370666504 0.5589537620544434 857.6842041015625 0.5269137024879456 944.447021484375 0.42429468035697937 0.72239864 1.354429006576538 True -3 10968 30.338794946670532 0.5589272975921631 811.0341796875 0.46632492542266846 934.6843872070312 0.42958375811576843 0.73446053 1.0146139860153198 True -4 13710 30.262497425079346 0.5656273365020752 759.9888916015625 0.5333064794540405 929.81982421875 0.43351060152053833 0.73678565 1.0047500133514404 True -5 16452 30.319727897644043 0.5644736289978027 650.203369140625 0.49722346663475037 925.9049072265625 0.4382346272468567 0.7419004 1.2460086345672607 True -6 19194 30.38655185699463 0.5598318576812744 770.0323486328125 0.41719913482666016 922.03173828125 0.44123464822769165 0.74338937 1.0408482551574707 True -7 21936 30.518017530441284 26.159212827682495 857.06591796875 0.5858598947525024 916.9752197265625 0.444862425327301 0.74864954 0.9553159475326538 True -8 24678 30.016642808914185 0.5507674217224121 634.0891723632812 0.37857478857040405 913.5202026367188 0.44772979617118835 0.7568624 0.879205048084259 True -9 27420 29.661433219909668 0.5420322418212891 790.442138671875 0.4118706285953522 908.0248413085938 0.4513890743255615 0.7640458 0.7529394030570984 True -10 30162 29.630754709243774 0.5463964939117432 828.1932373046875 0.5959389209747314 905.5252075195312 0.45353060960769653 0.7698808 0.6686151027679443 True -11 32904 29.623335599899292 0.7037389278411865 652.5479125976562 0.38816380500793457 900.9530639648438 0.45627808570861816 0.78049 0.6095863580703735 True -12 35646 29.677526712417603 0.5705573558807373 805.7615966796875 0.4730997085571289 895.7932739257812 0.4609156548976898 0.7874525 0.5360077023506165 True -13 38388 29.6439790725708 0.7906248569488525 755.209716796875 0.5231339931488037 890.4307861328125 0.46447181701660156 0.7956135 0.4888414144515991 True -14 41130 29.653864860534668 0.5381124019622803 578.4840087890625 0.4251711964607239 887.8558959960938 0.4657403230667114 0.8031516 0.43460115790367126 True -15 43872 29.618387937545776 0.5336906909942627 894.8192749023438 0.3224390745162964 888.7491455078125 0.46387264132499695 0.80922055 0.39205485582351685 True -16 46614 29.676839351654053 0.5338311195373535 716.31689453125 0.3947415053844452 886.3974609375 0.46579036116600037 0.8126087 0.3677561581134796 True -17 49356 29.62342596054077 0.5721023082733154 688.745361328125 0.3378167152404785 885.2346801757812 0.4663600027561188 0.81184554 0.3585189878940582 False -18 52098 29.644492149353027 0.5365426540374756 622.92431640625 0.4291554093360901 887.619140625 0.4636530578136444 0.8141144 0.353275865316391 True -19 54840 29.673970937728882 0.5560619831085205 671.8646850585938 0.29087501764297485 886.082275390625 0.4665544033050537 0.81379515 0.35263529419898987 False diff --git a/ENCSR576UAF/cherimoya.fold_0.performance.tsv b/ENCSR576UAF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8d4c2409b61dedc5bf5bb061830d0324b9e7d1ff..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -887.619140625 0.3224353492259979 0.4636530578136444 0.2221032828092575 0.8141143918037415 0.7593991756439209 0.353275865316391 \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_1.evaluate.json b/ENCSR576UAF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e4ef0fb55f97419668ff9b684dfcde4f5183b244..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863OMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_1.fit.json b/ENCSR576UAF/cherimoya.fold_1.fit.json deleted file mode 100644 index 4359b97bb28be9b834ba971828b321cbff1bca61..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF863OMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_1.log b/ENCSR576UAF/cherimoya.fold_1.log deleted file mode 100644 index c08e0412906911afa6621d9b48a3e505c8c72f13..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2698 36.13009071350098 4.004831075668335 815.2565307617188 0.8015996217727661 1305.032470703125 0.3030279278755188 0.66499263 8.780399322509766 True -1 5396 29.76797080039978 1.0656700134277344 856.6857299804688 0.7525666952133179 1125.69580078125 0.4165838658809662 0.71859896 2.851045608520508 True -2 8094 29.822765588760376 0.7802495956420898 954.1740112304688 0.477647602558136 1089.4429931640625 0.43981000781059265 0.7331677 1.5186389684677124 True -3 10792 30.33216643333435 0.8053953647613525 981.733154296875 0.8110877871513367 1078.171142578125 0.44737109541893005 0.7374775 1.3260189294815063 True -4 13490 31.224632263183594 12.372606992721558 939.3185424804688 0.4366018772125244 1072.64892578125 0.45007702708244324 0.74474204 1.161432147026062 True -5 16188 29.741986989974976 0.9488472938537598 781.893798828125 0.5873305201530457 1061.448974609375 0.4582689702510834 0.75466156 1.0452008247375488 True -6 18886 29.756572008132935 0.7459499835968018 749.8868408203125 0.5255482196807861 1062.1134033203125 0.45688557624816895 0.7549793 1.1051299571990967 True -7 21584 29.835665225982666 0.7430176734924316 844.617919921875 0.3833434581756592 1054.7496337890625 0.46234747767448425 0.7630243 1.0095936059951782 True -8 24282 29.756359100341797 0.8012833595275879 671.3457641601562 0.49466586112976074 1049.0498046875 0.4661327302455902 0.7692469 0.9525042176246643 True -9 26980 29.670926332473755 0.75225830078125 790.458984375 0.39453554153442383 1045.799072265625 0.4665623903274536 0.77352196 0.8483067750930786 True -10 29678 29.24217176437378 0.7582182884216309 877.1668090820312 0.44778308272361755 1039.3385009765625 0.47110792994499207 0.7830416 0.7684602737426758 True -11 32376 29.25403594970703 0.7696454524993896 728.5778198242188 0.4346054494380951 1034.4349365234375 0.47304046154022217 0.79449815 0.6828290224075317 True -12 35074 29.216003894805908 0.7539701461791992 700.1917724609375 0.4375112056732178 1028.310791015625 0.476139098405838 0.80239266 0.5972275733947754 True -13 37772 29.344989776611328 3.039318084716797 758.9678344726562 0.44559404253959656 1025.7373046875 0.47653019428253174 0.8084531 0.5294597148895264 True -14 40470 29.193082809448242 0.7203314304351807 956.0040893554688 0.3573276996612549 1017.071044921875 0.48407217860221863 0.8150782 0.47054585814476013 True -15 43168 29.272448778152466 0.7116067409515381 768.5101318359375 0.43773412704467773 1016.5404052734375 0.4823649227619171 0.81914085 0.4193231761455536 True -16 45866 29.189964532852173 0.7402217388153076 703.3638305664062 0.3387715816497803 1014.320556640625 0.4840230345726013 0.82486564 0.39312198758125305 True -17 48564 29.180773973464966 1.7581498622894287 764.06982421875 0.15474435687065125 1014.8801879882812 0.48408448696136475 0.8270306 0.37560805678367615 True -18 51262 29.22319507598877 27.007431745529175 717.6278686523438 0.3524143099784851 1014.64599609375 0.4835992157459259 0.8261464 0.3705221712589264 False -19 53960 29.373615503311157 22.461958646774292 796.0286865234375 0.4061722159385681 1015.6127319335938 0.48285534977912903 0.82694036 0.3681471347808838 False diff --git a/ENCSR576UAF/cherimoya.fold_1.performance.tsv b/ENCSR576UAF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 716e844a673820c2997751b0551189cb69f7d947..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1014.8801879882812 0.30176034569740295 0.4840845465660095 0.2523418962955475 0.827030599117279 0.7972508072853088 0.37560805678367615 \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_2.evaluate.json b/ENCSR576UAF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 65ed2c538c5907b3b27b46ea8e711f13fa5e43b3..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863OMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_2.fit.json b/ENCSR576UAF/cherimoya.fold_2.fit.json deleted file mode 100644 index 4f3da8e9ef1fc100304e26955efaa107764c6645..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF863OMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_2.log b/ENCSR576UAF/cherimoya.fold_2.log deleted file mode 100644 index aaaa3ef2a870538f265270fa14b1ebcfa172adc6..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 36.36200761795044 3.9845638275146484 840.0430908203125 0.677864670753479 1185.3345947265625 0.30119022727012634 0.6626368 6.948895454406738 True -1 5776 31.876705408096313 0.5745706558227539 746.901611328125 0.7655749320983887 1022.0225219726562 0.41145753860473633 0.71843183 2.4261107444763184 True -2 8664 31.891915559768677 0.5374095439910889 821.35791015625 0.5245484709739685 999.625732421875 0.42649272084236145 0.72741145 1.2101348638534546 True -3 11552 31.8993923664093 0.5328152179718018 700.3856201171875 0.6186363697052002 989.7753295898438 0.43400707840919495 0.7349064 1.3145161867141724 True -4 14440 31.754391193389893 1.1315932273864746 766.516357421875 0.46136441826820374 982.5745849609375 0.4403518736362457 0.7434107 0.9518815279006958 True -5 17328 31.320177793502808 0.531256914138794 721.4976806640625 0.5830503106117249 979.0799560546875 0.44321244955062866 0.7432361 0.9030570983886719 False -6 20216 31.23731255531311 0.5422995090484619 892.0369873046875 0.44129520654678345 974.1611328125 0.44670310616493225 0.74577314 0.8417975902557373 True -7 23104 31.24963617324829 1.1449861526489258 897.4830322265625 0.5331336855888367 969.8263549804688 0.44873079657554626 0.7577169 0.8051820993423462 True -8 25992 31.28346014022827 1.159048080444336 742.91259765625 0.4757311940193176 964.883056640625 0.45316949486732483 0.7620166 0.7584841847419739 True -9 28880 31.2599196434021 1.5610384941101074 749.328125 0.5234826803207397 959.0717163085938 0.45815396308898926 0.76837087 0.7767503261566162 True -10 31768 31.33384370803833 0.5515730381011963 948.6451416015625 0.45906195044517517 954.9989013671875 0.46052005887031555 0.77716225 0.7022296190261841 True -11 34656 31.264703273773193 0.5534348487854004 817.036376953125 0.42998671531677246 949.4917602539062 0.4635930061340332 0.7813871 0.6354981660842896 True -12 37544 31.221623420715332 0.5304074287414551 808.662841796875 0.432523250579834 947.1353759765625 0.4637296497821808 0.78794473 0.5655291080474854 True -13 40432 31.22472310066223 0.5397045612335205 743.12939453125 0.3512173891067505 942.63623046875 0.4671095013618469 0.7967971 0.5042665600776672 True -14 43320 31.301276922225952 0.5427067279815674 725.5770263671875 0.49759212136268616 941.3755493164062 0.4674917757511139 0.80385536 0.4466632604598999 True -15 46208 31.2679283618927 0.5405685901641846 738.01513671875 0.3546891510486603 936.1923217773438 0.47230345010757446 0.80757695 0.4060477018356323 True -16 49096 31.330713510513306 0.5346946716308594 694.9686279296875 0.4413154721260071 937.639404296875 0.4698108732700348 0.8132217 0.3786144256591797 True -17 51984 31.306310176849365 0.5443985462188721 786.644775390625 0.37495869398117065 934.068115234375 0.47283652424812317 0.8155853 0.36418935656547546 True -18 54872 31.274189233779907 0.5339860916137695 648.7000732421875 0.2975923418998718 938.537841796875 0.468119353055954 0.81573397 0.3606327176094055 True -19 57760 31.263181686401367 0.5357742309570312 871.5616455078125 0.19681572914123535 937.9782104492188 0.4694993495941162 0.8144135 0.36100420355796814 False diff --git a/ENCSR576UAF/cherimoya.fold_2.performance.tsv b/ENCSR576UAF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4f1bfda69a1302a3cce8ae7b2db99e757601fddb..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -938.537841796875 0.3149791359901428 0.46811938285827637 0.23460552096366882 0.8157339692115784 0.7799789905548096 0.3606327176094055 \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_3.evaluate.json b/ENCSR576UAF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c9fa46aaf834ef64011513a9e8534549244590ce..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863OMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_3.fit.json b/ENCSR576UAF/cherimoya.fold_3.fit.json deleted file mode 100644 index a6e7abb7d890deae6c5d47a0aff8127bed3dcf23..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF863OMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_3.log b/ENCSR576UAF/cherimoya.fold_3.log deleted file mode 100644 index 0d8bb79fff34f31f80b3d994ea64d80348c579ba..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2774 35.07184028625488 4.780523777008057 951.97265625 0.6850372552871704 1117.2950439453125 0.31132441759109497 0.664386 6.8080902099609375 True -1 5548 30.646546363830566 1.954336166381836 835.90478515625 0.5700775384902954 973.8488159179688 0.40690746903419495 0.7210469 2.296118974685669 True -2 8322 30.133318662643433 0.5361475944519043 904.329345703125 0.5806219577789307 944.8392944335938 0.4283507764339447 0.7335919 1.3322207927703857 True -3 11096 29.997413158416748 1.6347360610961914 886.535888671875 0.642352819442749 935.2920532226562 0.43324804306030273 0.74246824 1.089600920677185 True -4 13870 30.18524146080017 0.5602779388427734 894.7838745117188 0.5975444316864014 932.5160522460938 0.4361569881439209 0.7440323 1.0925979614257812 True -5 16644 30.02224612236023 0.551337718963623 815.55419921875 0.4655250608921051 926.339599609375 0.4415382742881775 0.7533967 1.1918253898620605 True -6 19418 30.077778100967407 1.1917855739593506 911.2303466796875 0.5081880688667297 922.2601318359375 0.44337329268455505 0.75647056 1.0219062566757202 True -7 22192 30.08426260948181 0.5552501678466797 830.22119140625 0.6442732810974121 916.8588256835938 0.4491196870803833 0.7625752 0.9758697152137756 True -8 24966 30.073257207870483 0.5492312908172607 772.1109008789062 0.5734745860099792 913.9918212890625 0.4515689015388489 0.76741767 0.8855416178703308 True -9 27740 31.90881323814392 15.417114019393921 657.1259765625 0.4547664523124695 909.787353515625 0.4548051357269287 0.7753146 0.8043962717056274 True -10 30514 30.161455154418945 1.6572027206420898 738.711669921875 0.4883376955986023 905.6049194335938 0.4574075937271118 0.7823528 0.7126113772392273 True -11 33288 30.218186378479004 0.554459810256958 747.0234375 0.39397352933883667 901.0426025390625 0.4607558846473694 0.78689045 0.6686930060386658 True -12 36062 30.10908555984497 0.56707763671875 730.838134765625 0.3746488690376282 899.7674560546875 0.4594208896160126 0.7975213 0.5956205725669861 True -13 38836 29.998780250549316 0.559654951095581 790.0030517578125 0.3634626865386963 894.55419921875 0.46431681513786316 0.8039025 0.5177845358848572 True -14 41610 29.97860598564148 0.9469327926635742 937.037841796875 0.46524927020072937 894.2111206054688 0.4639612138271332 0.80844265 0.4587284028530121 True -15 44384 30.05555510520935 0.5812087059020996 667.7786254882812 0.3250104784965515 890.9759521484375 0.4658466577529907 0.81515485 0.42227494716644287 True -16 47158 30.00756049156189 0.5535502433776855 665.9016723632812 0.3595159649848938 888.313232421875 0.4672849774360657 0.8197917 0.39303579926490784 True -17 49932 30.00261425971985 0.556316614151001 785.8368530273438 0.32199597358703613 888.5702514648438 0.46697840094566345 0.82040566 0.3719380497932434 True -18 52706 30.006953477859497 0.5631837844848633 715.22509765625 0.25566184520721436 888.7721557617188 0.46773406863212585 0.82093567 0.36715608835220337 True -19 55480 29.976764917373657 0.5426785945892334 722.488037109375 0.2540489733219147 889.5050048828125 0.4667014181613922 0.8199968 0.3673727512359619 False diff --git a/ENCSR576UAF/cherimoya.fold_3.performance.tsv b/ENCSR576UAF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c7804d28feedfb2f77e7e9ef84a7c0cca4c2cb21..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -888.7721557617188 0.3196104168891907 0.46773406863212585 0.2297411412000656 0.8209356665611267 0.7725681066513062 0.36715608835220337 \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_4.evaluate.json b/ENCSR576UAF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 69e439784ed9fb30d1e32948bbfae0c6a5dff391..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863OMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_4.fit.json b/ENCSR576UAF/cherimoya.fold_4.fit.json deleted file mode 100644 index 34a54872aaca52e2705e8c7fa13dfe98940ba4c6..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF863OMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR576UAF/cherimoya.fold_4.log b/ENCSR576UAF/cherimoya.fold_4.log deleted file mode 100644 index acb4f4ba858bee3c947044bd6e3c24a1f6e54296..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2812 35.81377720832825 4.1649675369262695 769.8092041015625 0.5548613667488098 1046.10302734375 0.3010161817073822 0.6469749 6.369070053100586 True -1 5624 31.039180755615234 1.0391788482666016 836.3765869140625 0.5679165720939636 913.16357421875 0.3991457223892212 0.7017663 2.0575218200683594 True -2 8436 31.078219175338745 0.5590312480926514 893.7528076171875 0.6914640665054321 894.2993774414062 0.41381317377090454 0.71193254 1.1240085363388062 True -3 11248 31.043410301208496 0.5607705116271973 869.5125732421875 0.5759724974632263 881.1857299804688 0.42419669032096863 0.7204085 0.9453311562538147 True -4 14060 31.017422199249268 0.5553526878356934 804.5777587890625 0.6309693455696106 878.95947265625 0.4240669906139374 0.73141176 0.9460371136665344 True -5 16872 31.77470374107361 0.5556235313415527 764.552978515625 0.5848829746246338 873.5904541015625 0.42974454164505005 0.7334944 0.8854296803474426 True -6 19684 31.07058548927307 0.5491409301757812 771.5289306640625 0.3674786686897278 869.1136474609375 0.4335939586162567 0.7435137 0.7377679944038391 True -7 22496 30.999568939208984 0.5572836399078369 844.3876342773438 0.5616576671600342 864.5899658203125 0.43744537234306335 0.7479183 0.6831026673316956 True -8 25308 30.99631667137146 0.5674033164978027 803.15185546875 0.4028451144695282 863.6535034179688 0.43784573674201965 0.7487679 0.6554142236709595 True -9 28120 31.012932777404785 0.5680134296417236 816.732177734375 0.6657565236091614 860.4486694335938 0.44121676683425903 0.75464356 0.6408914923667908 True -10 30932 30.978096961975098 0.5691788196563721 726.6405639648438 0.36249029636383057 855.7374267578125 0.44507431983947754 0.7624218 0.607826292514801 True -11 33744 31.053853750228882 0.5690791606903076 676.8098754882812 0.4092642068862915 853.3129272460938 0.44610273838043213 0.7685148 0.5595918297767639 True -12 36556 31.011765241622925 0.5590648651123047 821.287841796875 0.3056491017341614 848.2289428710938 0.4507220685482025 0.7780566 0.49636587500572205 True -13 39368 30.989436388015747 0.5686607360839844 822.7274780273438 0.37658265233039856 848.8306274414062 0.4498154819011688 0.78746164 0.4531308114528656 True -14 42180 31.02019691467285 1.6506149768829346 688.6576538085938 0.28128546476364136 844.719482421875 0.45221713185310364 0.79601574 0.4149096608161926 True -15 44992 31.118797540664673 0.5703895092010498 650.093505859375 0.4804273247718811 844.59228515625 0.45164528489112854 0.8039235 0.3817013204097748 True -16 47804 31.15439224243164 0.5702524185180664 649.4119262695312 0.3635391592979431 841.5158081054688 0.4551384449005127 0.8094858 0.35180458426475525 True -17 50616 31.08911681175232 0.5577409267425537 707.3487548828125 0.3349512815475464 841.1034545898438 0.45485469698905945 0.81234336 0.3366062045097351 True -18 53428 31.07913112640381 0.5753610134124756 727.8944091796875 0.24557581543922424 840.0634765625 0.4573726952075958 0.8138159 0.3329203426837921 True -19 56240 30.919012784957886 0.5687963962554932 737.4945678710938 0.3298376798629761 841.4129638671875 0.45528444647789 0.8142646 0.333973228931427 True diff --git a/ENCSR576UAF/cherimoya.fold_4.performance.tsv b/ENCSR576UAF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a21e60d788f29c886bd9e094d7fbeff484b2e3dc..0000000000000000000000000000000000000000 --- a/ENCSR576UAF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -841.4129638671875 0.3288740813732147 0.45528444647789 0.21608500182628632 0.8142645955085754 0.7533189654350281 0.333973228931427 \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_0.evaluate.json b/ENCSR577QZP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 948b54b5eec31de0fc357d154d5c20f52f1801fd..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF658ZPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_0.fit.json b/ENCSR577QZP/cherimoya.fold_0.fit.json deleted file mode 100644 index 4b30d61180e81e993ccfdeb837c99e27c7f9e60f..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF658ZPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_0.log b/ENCSR577QZP/cherimoya.fold_0.log deleted file mode 100644 index 5bd200f81aeb2be28482296647370a9975d841e6..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 35.54841089248657 4.921045303344727 361.00115966796875 0.3198707401752472 427.81866455078125 0.23781631886959076 0.79462826 2.9043362140655518 True -1 5522 30.685623168945312 0.6829476356506348 370.2415466308594 0.22540751099586487 407.2151794433594 0.2815181612968445 0.82884634 0.6801742315292358 True -2 8283 30.747209310531616 0.5887985229492188 365.12396240234375 0.18838855624198914 402.7174987792969 0.29036134481430054 0.84749436 0.3776281476020813 True -3 11044 30.741254329681396 0.5917606353759766 396.1983642578125 0.20170769095420837 400.6884765625 0.2943895757198334 0.855033 0.3303122818470001 True -4 13805 30.76662015914917 0.6111164093017578 339.5338134765625 0.20147797465324402 399.55816650390625 0.29631826281547546 0.8616428 0.2096247375011444 True -5 16566 30.784102201461792 0.5856311321258545 362.4654541015625 0.14449763298034668 398.6501770019531 0.29803648591041565 0.8679461 0.19649387896060944 True -6 19327 30.176727056503296 0.5903458595275879 324.747802734375 0.2431298792362213 397.89306640625 0.29985561966896057 0.8712592 0.18887461721897125 True -7 22088 30.164813995361328 0.5924880504608154 358.35626220703125 0.1538945436477661 396.7382507324219 0.30414533615112305 0.8708559 0.1901576966047287 False -8 24849 30.193691968917847 0.5835845470428467 340.2491455078125 0.152461975812912 396.6278076171875 0.30319374799728394 0.8773783 0.16340631246566772 True -9 27610 30.294645071029663 0.6067166328430176 379.0806579589844 0.1804479956626892 395.5383605957031 0.3058733642101288 0.8816191 0.15115782618522644 True -10 30371 30.503283500671387 0.6064417362213135 372.9166259765625 0.18603438138961792 395.1543884277344 0.30611586570739746 0.88426924 0.13826175034046173 True -11 33132 30.15116548538208 0.5970134735107422 357.88519287109375 0.20424142479896545 394.7978515625 0.3063490092754364 0.88631684 0.13135750591754913 True -12 35893 30.229992866516113 0.5960278511047363 321.76263427734375 0.12322612851858139 393.911865234375 0.30865678191185 0.89111197 0.12496396899223328 True -13 38654 30.254034519195557 0.5873775482177734 373.5989990234375 0.1993989646434784 393.365478515625 0.3101324439048767 0.89286155 0.1200655996799469 True -14 41415 30.23656177520752 0.5995526313781738 399.5447998046875 0.10168881714344025 393.0758056640625 0.31015095114707947 0.894595 0.11589088290929794 True -15 44176 30.24276041984558 0.588003396987915 317.42510986328125 0.09140536189079285 392.9043273925781 0.31066447496414185 0.8978272 0.11132457107305527 True -16 46937 30.25355291366577 0.6652519702911377 377.3119201660156 0.10555312782526016 392.63421630859375 0.31111761927604675 0.8992445 0.10804210603237152 True -17 49698 30.196044206619263 1.7226262092590332 294.0588073730469 0.06738023459911346 392.74700927734375 0.31067946553230286 0.8999344 0.10702168196439743 True -18 52459 30.216060161590576 0.9537923336029053 393.92864990234375 0.1156260073184967 393.0218200683594 0.3097129166126251 0.89999473 0.10723009705543518 True -19 55220 30.245367765426636 2.0402848720550537 314.93768310546875 0.12884187698364258 392.6205139160156 0.31122317910194397 0.9002286 0.108188696205616 True diff --git a/ENCSR577QZP/cherimoya.fold_0.performance.tsv b/ENCSR577QZP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index edb1b1b2541554ce0d9284a1f4ed20301a18443a..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -392.6205139160156 0.45402848720550537 0.31122317910194397 0.1041366457939148 0.9002286195755005 0.8882961273193359 0.108188696205616 \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_1.evaluate.json b/ENCSR577QZP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8f238ebda656cfc4886f2e65d98d98ba60e51aca..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF658ZPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_1.fit.json b/ENCSR577QZP/cherimoya.fold_1.fit.json deleted file mode 100644 index 1c3dc9f3500f356ed716a3c6166a59b6faa50e01..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF658ZPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_1.log b/ENCSR577QZP/cherimoya.fold_1.log deleted file mode 100644 index 62dc3ba4ec0b575263b6d6d9bf550e994f266dd5..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2708 34.78528094291687 4.3435378074646 307.98870849609375 0.20938369631767273 475.27655029296875 0.23934563994407654 0.80409044 3.453347682952881 True -1 5416 30.06327247619629 0.7525589466094971 344.4587707519531 0.15953995287418365 450.67822265625 0.28506791591644287 0.83304405 0.853070080280304 True -2 8124 30.095882892608643 0.7034573554992676 360.03350830078125 0.22204278409481049 444.2628173828125 0.29439613223075867 0.8430833 0.34299471974372864 True -3 10832 29.7370183467865 0.6741535663604736 361.1655578613281 0.22746208310127258 439.5483703613281 0.3025774359703064 0.8643602 0.2576325833797455 True -4 13540 29.692609786987305 0.681084394454956 307.9013366699219 0.21066078543663025 437.5713806152344 0.3057979345321655 0.8730098 0.20721788704395294 True -5 16248 29.48600482940674 0.6959092617034912 392.887939453125 0.16578319668769836 436.29296875 0.30810922384262085 0.8775938 0.18550686538219452 True -6 18956 29.51259136199951 0.6839017868041992 317.0367736816406 0.11806722730398178 435.17071533203125 0.3102514445781708 0.8829487 0.17156700789928436 True -7 21664 29.538389205932617 1.1779990196228027 325.04522705078125 0.14624108374118805 434.1331787109375 0.3127218186855316 0.8849213 0.16413868963718414 True -8 24372 29.498537302017212 0.6727578639984131 378.7005310058594 0.13409598171710968 433.4411926269531 0.31335023045539856 0.89079505 0.15460318326950073 True -9 27080 29.480931758880615 0.6868743896484375 423.25982666015625 0.18607088923454285 432.6302185058594 0.31480127573013306 0.8933817 0.14854297041893005 True -10 29788 29.869603157043457 0.701530933380127 361.151123046875 0.15143832564353943 431.77642822265625 0.31642577052116394 0.89694047 0.1389051228761673 True -11 32496 29.500866174697876 0.7016041278839111 333.4200744628906 0.15510113537311554 430.62542724609375 0.3197091221809387 0.89974487 0.13786830008029938 True -12 35204 29.478352546691895 1.9698448181152344 364.23260498046875 0.15384946763515472 430.32086181640625 0.3192805051803589 0.9012123 0.13068287074565887 True -13 37912 29.56002426147461 0.7153348922729492 387.24334716796875 0.26939892768859863 429.5904235839844 0.32104024291038513 0.90392756 0.12842310965061188 True -14 40620 29.47630739212036 0.6916279792785645 317.0854187011719 0.1104997918009758 429.0108642578125 0.3214196562767029 0.9072495 0.12205308675765991 True -15 43328 29.461549520492554 0.7044532299041748 358.1822814941406 0.09381382167339325 429.02606201171875 0.32130900025367737 0.9084836 0.12121065706014633 True -16 46036 29.475592613220215 0.7218315601348877 347.45318603515625 0.2745135724544525 428.7205810546875 0.3216492235660553 0.9125526 0.11802308261394501 True -17 48744 29.462625980377197 0.6993508338928223 362.3323974609375 0.10540656745433807 428.28668212890625 0.32276707887649536 0.9113331 0.11575207859277725 False -18 51452 29.508177042007446 0.7165513038635254 321.6958312988281 0.0976080372929573 428.5614013671875 0.3218192458152771 0.91309553 0.1152699813246727 True -19 54160 29.553003311157227 0.6847057342529297 372.2337646484375 0.10067225992679596 428.51983642578125 0.32218992710113525 0.91243196 0.11474321782588959 False diff --git a/ENCSR577QZP/cherimoya.fold_1.performance.tsv b/ENCSR577QZP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9171b5c8bc8da6131b3b0b758175e86e1735d1d5..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -428.5614013671875 0.4439534544944763 0.3218192458152771 0.11155456304550171 0.9130955338478088 0.9103121757507324 0.1152699813246727 \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_2.evaluate.json b/ENCSR577QZP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4499110f881288c8465666cd562ec98f6ae7882a..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF658ZPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_2.fit.json b/ENCSR577QZP/cherimoya.fold_2.fit.json deleted file mode 100644 index 9384f66d9750276db62e0d73bc76d57a15a4bc4b..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF658ZPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_2.log b/ENCSR577QZP/cherimoya.fold_2.log deleted file mode 100644 index d674c19541b9d746c2392652ee0a26cb3f57ddf5..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2880 36.60967421531677 3.992750644683838 357.73797607421875 0.221742182970047 454.6003723144531 0.24120482802391052 0.7892532 2.5515809059143066 True -1 5760 32.0247220993042 0.5811741352081299 359.30413818359375 0.1852230727672577 433.9327087402344 0.28496503829956055 0.8197055 0.646837055683136 True -2 8640 32.003191232681274 0.5267593860626221 338.6365966796875 0.23061367869377136 428.3822326660156 0.29380688071250916 0.8320908 0.298141747713089 True -3 11520 32.00232720375061 0.520226240158081 352.5997314453125 0.20372547209262848 425.7331237792969 0.2978658974170685 0.84614724 0.2666226327419281 True -4 14400 31.31845188140869 0.5071649551391602 339.976806640625 0.18535934388637543 424.28265380859375 0.30123329162597656 0.8522705 0.18467426300048828 True -5 17280 31.31744647026062 0.5192368030548096 341.03375244140625 0.22869694232940674 423.6059265136719 0.30153730511665344 0.8553246 0.179917111992836 True -6 20160 31.322860717773438 0.5157787799835205 314.54010009765625 0.2139449119567871 422.4432373046875 0.30405911803245544 0.8608213 0.1776277720928192 True -7 23040 31.33246421813965 0.5131218433380127 361.2992858886719 0.1094450056552887 421.6598815917969 0.3051356375217438 0.86535335 0.15763376653194427 True -8 25920 31.33345055580139 0.5205135345458984 358.899658203125 0.14213483035564423 420.7392272949219 0.30660587549209595 0.86922985 0.15407970547676086 True -9 28800 31.395426511764526 0.5198287963867188 335.458251953125 0.13185107707977295 419.9427795410156 0.30852535367012024 0.87312376 0.14022351801395416 True -10 31680 31.34281849861145 0.539461612701416 303.6815185546875 0.16581302881240845 419.2170104980469 0.3098319172859192 0.8773098 0.13493965566158295 True -11 34560 31.529355764389038 1.670391321182251 363.05987548828125 0.2147892415523529 418.7083435058594 0.31101205945014954 0.87914264 0.13347342610359192 True -12 37440 31.499251127243042 0.9995713233947754 329.57049560546875 0.14100980758666992 418.2206115722656 0.31141117215156555 0.88490367 0.12943261861801147 True -13 40320 31.438727617263794 0.5285384654998779 371.6999816894531 0.23692646622657776 417.18133544921875 0.31410685181617737 0.8871856 0.12381093204021454 True -14 43200 31.448371171951294 0.5305464267730713 355.3222961425781 0.14054174721240997 416.9314880371094 0.31429505348205566 0.89022976 0.12190708518028259 True -15 46080 31.448423385620117 0.5224897861480713 397.99359130859375 0.13932761549949646 416.6764831542969 0.31499484181404114 0.8926815 0.1213756799697876 True -16 48960 31.48784065246582 0.5273487567901611 338.14410400390625 0.11779003590345383 416.7305603027344 0.3143388330936432 0.89180315 0.11938013881444931 False -17 51840 31.467930793762207 0.5271320343017578 307.82763671875 0.08557407557964325 416.61505126953125 0.3147889971733093 0.8927252 0.11897292733192444 True -18 54720 31.502630949020386 0.5301251411437988 323.2900695800781 0.1381685733795166 416.40618896484375 0.31586772203445435 0.89301723 0.11855422705411911 True -19 57600 31.45584464073181 0.5204744338989258 320.14208984375 0.1056651771068573 416.7718811035156 0.31458601355552673 0.892025 0.11923041939735413 False diff --git a/ENCSR577QZP/cherimoya.fold_2.performance.tsv b/ENCSR577QZP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index de36adec318b821bd312e38b74adaed27e306161..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -416.40618896484375 0.4482309818267822 0.31586769223213196 0.10409063845872879 0.8930172324180603 0.8858131170272827 0.11855422705411911 \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_3.evaluate.json b/ENCSR577QZP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5e77451fddcaf8a145236597b5b4024a4dff0f06..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF658ZPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_3.fit.json b/ENCSR577QZP/cherimoya.fold_3.fit.json deleted file mode 100644 index ba7a6164c1405365ef9862e851fc0679ce8609e7..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF658ZPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_3.log b/ENCSR577QZP/cherimoya.fold_3.log deleted file mode 100644 index b29da3db1f5aa1dffee1c876402af88164526bc1..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 35.080418825149536 3.9352970123291016 321.14556884765625 0.2721693217754364 421.59832763671875 0.2452227622270584 0.7777265 3.150454521179199 True -1 5510 30.600597381591797 1.4013280868530273 398.730712890625 0.2930184602737427 400.32928466796875 0.2859747111797333 0.8031958 0.6525413393974304 True -2 8265 30.57893943786621 0.5229902267456055 368.01287841796875 0.16058793663978577 396.10003662109375 0.2926839292049408 0.83450335 0.5491858124732971 True -3 11020 30.058891773223877 0.5095596313476562 370.2105712890625 0.1903650015592575 393.48651123046875 0.2968097925186157 0.8434298 0.2667117714881897 True -4 13775 29.91262650489807 0.511491060256958 368.6033020019531 0.3047542870044708 392.3347473144531 0.29969313740730286 0.84483033 0.24233856797218323 True -5 16530 29.900018453598022 0.5200374126434326 372.79681396484375 0.15174001455307007 391.3664855957031 0.3014996647834778 0.85091275 0.25762686133384705 True -6 19285 29.959879398345947 0.5175199508666992 358.4239196777344 0.19779706001281738 390.60797119140625 0.302929550409317 0.85108 0.26008695363998413 True -7 22040 29.922706365585327 0.5321764945983887 364.6435546875 0.23579803109169006 389.3977966308594 0.3051455020904541 0.8617915 0.22504521906375885 True -8 24795 29.895886182785034 0.5094478130340576 395.71441650390625 0.19720223546028137 388.6768798828125 0.3068632483482361 0.8628041 0.205470472574234 True -9 27550 29.95689630508423 0.5171711444854736 280.5206298828125 0.16617214679718018 387.9814758300781 0.30815085768699646 0.8678894 0.19193777441978455 True -10 30305 29.916921615600586 0.5218775272369385 326.87548828125 0.2518869638442993 387.16680908203125 0.310464084148407 0.869727 0.17969878017902374 True -11 33060 29.918819189071655 0.5303895473480225 354.41949462890625 0.13985195755958557 386.6138610839844 0.3116324841976166 0.8763162 0.1652587354183197 True -12 35815 29.906909227371216 0.5181870460510254 366.3974609375 0.15328453481197357 386.2933654785156 0.31172096729278564 0.87995046 0.15380309522151947 True -13 38570 29.96353030204773 0.51690673828125 329.096923828125 0.1235056072473526 385.0774841308594 0.314718097448349 0.8831923 0.14364323019981384 True -14 41325 29.941911935806274 0.5095887184143066 324.6405029296875 0.1897038221359253 385.17724609375 0.31319481134414673 0.8883228 0.13393718004226685 True -15 44080 30.31532621383667 0.5212819576263428 337.6238098144531 0.15110254287719727 384.25042724609375 0.3159295320510864 0.89254135 0.1279693841934204 True -16 46835 30.048881769180298 0.5170698165893555 314.5870666503906 0.11547186970710754 384.3537292480469 0.314618855714798 0.8954052 0.11923209577798843 True -17 49590 29.97125768661499 0.5123937129974365 324.2315673828125 0.1185702458024025 384.0888671875 0.31554970145225525 0.8960678 0.11711399257183075 True -18 52345 30.010255336761475 0.5174217224121094 333.7644958496094 0.11357246339321136 383.9731140136719 0.316383421421051 0.89790493 0.11580055952072144 True -19 55100 29.99262523651123 0.5178501605987549 350.18963623046875 0.09488888829946518 384.3081359863281 0.31497257947921753 0.8968279 0.11509869992733002 False diff --git a/ENCSR577QZP/cherimoya.fold_3.performance.tsv b/ENCSR577QZP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bd92546d56bde0c71b46322d316ef383952b3b96..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -383.9731140136719 0.4530685544013977 0.316383421421051 0.10220247507095337 0.8979049324989319 0.8776225447654724 0.11580055952072144 \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_4.evaluate.json b/ENCSR577QZP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2c733c3bf5a57a8d162045602c4d47763e0bc220..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF658ZPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_4.fit.json b/ENCSR577QZP/cherimoya.fold_4.fit.json deleted file mode 100644 index 6f878234a58792e5750d053017a383360ad4d22e..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF658ZPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR577QZP/cherimoya.fold_4.log b/ENCSR577QZP/cherimoya.fold_4.log deleted file mode 100644 index d2f8d98c66be126d73f614f88e2b93cd4da70935..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2804 36.20161271095276 4.483323335647583 369.5425109863281 0.18546754121780396 388.5228271484375 0.23498933017253876 0.7885345 2.3776962757110596 True -1 5608 31.28061294555664 0.6884722709655762 367.43511962890625 0.23379220068454742 372.7027282714844 0.2712043821811676 0.81321096 0.5556511282920837 True -2 8412 31.404217004776 0.7011466026306152 337.36676025390625 0.17017404735088348 369.122314453125 0.27924826741218567 0.8295998 0.365559458732605 True -3 11216 31.307685136795044 0.6453695297241211 391.9940185546875 0.26167812943458557 366.664306640625 0.28424039483070374 0.8439199 0.2603295147418976 True -4 14020 31.329350471496582 0.6632776260375977 355.23736572265625 0.30514001846313477 365.5461120605469 0.2866845726966858 0.853066 0.19302868843078613 True -5 16824 31.27636170387268 0.7128779888153076 332.32611083984375 0.1334204375743866 364.8003845214844 0.28812873363494873 0.85855126 0.17029668390750885 True -6 19628 31.21022391319275 0.6468155384063721 366.97113037109375 0.18498370051383972 363.5897216796875 0.2913019359111786 0.8633723 0.15205533802509308 True -7 22432 31.312484741210938 0.6459741592407227 289.22186279296875 0.10765460133552551 362.8923034667969 0.2929579019546509 0.86521405 0.14476101100444794 True -8 25236 31.32887864112854 3.5492537021636963 298.57696533203125 0.1802883893251419 362.6622619628906 0.29311156272888184 0.86799717 0.14353439211845398 True -9 28040 30.60072374343872 0.6558928489685059 318.9621276855469 0.1537676453590393 362.6338806152344 0.292222797870636 0.8739759 0.12600326538085938 True -10 30844 30.47607135772705 0.6439166069030762 364.3712158203125 0.13347500562667847 361.77044677734375 0.2941502630710602 0.8799372 0.11508139222860336 True -11 33648 30.550644874572754 0.6392290592193604 341.55145263671875 0.13897831737995148 361.3043212890625 0.29540523886680603 0.8834127 0.1103113442659378 True -12 36452 30.622167587280273 0.6350991725921631 374.19268798828125 0.1521337330341339 360.6291198730469 0.29722025990486145 0.88800156 0.10625344514846802 True -13 39256 30.61081838607788 0.6391415596008301 357.29205322265625 0.20066165924072266 360.1794128417969 0.29808536171913147 0.89150923 0.10237030684947968 True -14 42060 30.613290309906006 0.6396353244781494 295.64227294921875 0.1274520456790924 360.1000671386719 0.2981959283351898 0.8925929 0.09966672211885452 True -15 44864 30.536623239517212 0.6425867080688477 354.5216979980469 0.12159402668476105 359.94659423828125 0.29847732186317444 0.89613235 0.09747077524662018 True -16 47668 30.56502914428711 0.6405808925628662 302.1195373535156 0.10295382142066956 359.8424072265625 0.2983388602733612 0.89752364 0.09471669793128967 True -17 50472 30.661375045776367 0.639136552810669 346.027099609375 0.11847665160894394 359.59417724609375 0.2995437681674957 0.9004225 0.09427327662706375 True -18 53276 30.570913553237915 0.6747002601623535 428.73870849609375 0.07949170470237732 359.6340026855469 0.2996671497821808 0.90048623 0.09425368905067444 True -19 56080 30.65054488182068 0.6577608585357666 349.5191650390625 0.09781540930271149 359.77728271484375 0.2991509735584259 0.8990901 0.09414374828338623 False diff --git a/ENCSR577QZP/cherimoya.fold_4.performance.tsv b/ENCSR577QZP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9263f9323719dc7c60d9f1fcd913bf2771649f02..0000000000000000000000000000000000000000 --- a/ENCSR577QZP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -359.6340026855469 0.4658714234828949 0.2996671795845032 0.09352988004684448 0.9004862308502197 0.8811468482017517 0.09425368905067444 \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_0.evaluate.json b/ENCSR579RVI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e559cb2079914d2160d60cc013d0ac205d985154..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF428BJG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_0.fit.json b/ENCSR579RVI/cherimoya.fold_0.fit.json deleted file mode 100644 index fa1cf853f95cd72c7090c9867594ea800c33832a..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF428BJG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_0.log b/ENCSR579RVI/cherimoya.fold_0.log deleted file mode 100644 index a32114b4b99e1e2f439b2ca23f597092a44ae546..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 35.491289138793945 4.585464715957642 455.7231750488281 0.14184540510177612 557.2177734375 0.28739285469055176 0.8198986 3.557612180709839 True -1 5504 30.67466711997986 0.6486060619354248 411.413330078125 0.23700429499149323 523.7357177734375 0.3456585109233856 0.8431071 0.5313013792037964 True -2 8256 30.618304014205933 0.6057052612304688 550.7203369140625 0.2525952458381653 517.3284912109375 0.35562294721603394 0.86385244 0.2675325572490692 True -3 11008 30.636407136917114 0.5898492336273193 503.3758239746094 0.2073657214641571 513.4139404296875 0.36077189445495605 0.87414306 0.24802429974079132 True -4 13760 30.604753732681274 0.5982260704040527 482.30718994140625 0.14871934056282043 511.1256408691406 0.36580169200897217 0.8783317 0.15522971749305725 True -5 16512 30.312801361083984 0.5883088111877441 438.31170654296875 0.20810683071613312 510.3670654296875 0.3673463463783264 0.8815667 0.15725699067115784 True -6 19264 29.98795986175537 0.584709882736206 476.23614501953125 0.0840190201997757 510.1617431640625 0.3673073649406433 0.88478225 0.1587667316198349 True -7 22016 29.963048696517944 0.5844736099243164 470.3708190917969 0.15991456806659698 509.0597839355469 0.36931219696998596 0.88608706 0.15109111368656158 True -8 24768 29.95323419570923 0.8617515563964844 493.9493713378906 0.2313362956047058 507.57147216796875 0.3722356855869293 0.8917908 0.139383003115654 True -9 27520 30.015164375305176 0.5820484161376953 536.31201171875 0.1622176170349121 506.1468505859375 0.37486112117767334 0.8953876 0.13688188791275024 True -10 30272 29.979323148727417 0.5942113399505615 490.12115478515625 0.15711288154125214 505.9085693359375 0.37516993284225464 0.8967009 0.13099877536296844 True -11 33024 30.04542303085327 1.2296228408813477 391.3861083984375 0.10125568509101868 505.1104736328125 0.3761783242225647 0.8988671 0.12660931050777435 True -12 35776 30.079983949661255 19.459160327911377 403.51507568359375 0.11541889607906342 504.0832214355469 0.37753555178642273 0.90163136 0.12025827914476395 True -13 38528 30.08724284172058 19.25111222267151 442.4593200683594 0.09648355841636658 503.218505859375 0.3794372081756592 0.90470934 0.11737808585166931 True -14 41280 30.08116888999939 0.5930538177490234 465.8974609375 0.1898314356803894 502.94232177734375 0.3795245885848999 0.9066944 0.1134328693151474 True -15 44032 30.104360818862915 0.5932703018188477 396.26025390625 0.13794709742069244 503.061279296875 0.3795666992664337 0.9088072 0.11028387397527695 True -16 46784 30.109020709991455 0.5809614658355713 390.36627197265625 0.1284460723400116 502.4739074707031 0.3801988661289215 0.9104966 0.10613498091697693 True -17 49536 29.962302684783936 0.5912413597106934 453.1687316894531 0.08498632162809372 502.830810546875 0.3793788552284241 0.9108418 0.10430708527565002 True -18 52288 30.106239318847656 0.5918891429901123 514.310546875 0.07439412921667099 502.4695129394531 0.38055312633514404 0.9116629 0.102996326982975 True -19 55040 30.09427809715271 0.5901970863342285 458.1573486328125 0.0900154858827591 502.3493957519531 0.38116419315338135 0.91145885 0.10390394926071167 False diff --git a/ENCSR579RVI/cherimoya.fold_0.performance.tsv b/ENCSR579RVI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6422ebab26bde7477a65a990542376906fa0f85b..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -502.4695129394531 0.4043898284435272 0.38055315613746643 0.13718292117118835 0.9116628766059875 0.8991591334342957 0.102996326982975 \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_1.evaluate.json b/ENCSR579RVI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bbd7e07ff625432b1e7376f654b5c2c4195a5534..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF428BJG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_1.fit.json b/ENCSR579RVI/cherimoya.fold_1.fit.json deleted file mode 100644 index ce788d0ea451c6ec239d4bc2f1fcf7c1495355eb..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF428BJG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_1.log b/ENCSR579RVI/cherimoya.fold_1.log deleted file mode 100644 index c8a8778abf4729c4fbd3370a483654b88fa29a9a..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2714 35.10134243965149 4.307337045669556 458.1289367675781 0.14629994332790375 619.4280395507812 0.2877650558948517 0.8143814 3.7333812713623047 True -1 5428 30.257370948791504 0.7864441871643066 430.66357421875 0.22103488445281982 578.3601684570312 0.35323822498321533 0.84648836 0.7147798538208008 True -2 8142 30.254047393798828 0.6790938377380371 434.76397705078125 0.2568957209587097 569.5817260742188 0.36394956707954407 0.8671525 0.35749906301498413 True -3 10856 30.263957500457764 0.6971330642700195 461.4915771484375 0.1853748857975006 564.755615234375 0.3721054792404175 0.8728541 0.26247093081474304 True -4 13570 30.218034505844116 0.6898512840270996 456.09197998046875 0.19232767820358276 564.0184326171875 0.3706672191619873 0.87863463 0.19751589000225067 True -5 16284 30.22780418395996 0.6971187591552734 469.27838134765625 0.23343601822853088 561.072998046875 0.3754529058933258 0.8821272 0.1793573945760727 True -6 18998 29.7294921875 0.6751410961151123 424.17236328125 0.11563294380903244 559.0209350585938 0.37960219383239746 0.8874912 0.1688135266304016 True -7 21712 29.642391204833984 0.6903963088989258 458.9632263183594 0.1835693120956421 557.5986328125 0.38151445984840393 0.8904498 0.15771572291851044 True -8 24426 29.647738218307495 0.6828510761260986 410.8651428222656 0.15952947735786438 556.0185546875 0.38395628333091736 0.8953877 0.1563451737165451 True -9 27140 29.62782073020935 0.6813867092132568 434.2823791503906 0.1345994472503662 555.2722778320312 0.384512335062027 0.89724827 0.14750631153583527 True -10 29854 29.579259872436523 0.6893250942230225 427.64080810546875 0.2029561996459961 553.9942016601562 0.38630959391593933 0.90003806 0.1428564488887787 True -11 32568 29.588244438171387 0.6888782978057861 439.96063232421875 0.14577530324459076 552.5469360351562 0.38845884799957275 0.9018722 0.1388377547264099 True -12 35282 29.5951406955719 0.68292236328125 388.7249755859375 0.10771341621875763 552.40625 0.3882720470428467 0.90566057 0.1328490823507309 True -13 37996 29.57789969444275 0.6884481906890869 421.55126953125 0.1402776837348938 551.6314086914062 0.38996535539627075 0.90858173 0.1292450726032257 True -14 40710 29.57381772994995 0.6886675357818604 464.39794921875 0.11696143448352814 551.1279907226562 0.3906548321247101 0.9099831 0.1232079342007637 True -15 43424 29.573930501937866 0.7033190727233887 455.92388916015625 0.13045793771743774 550.9524536132812 0.3903749883174896 0.9123307 0.11974633485078812 True -16 46138 29.5626802444458 0.6828408241271973 445.2631530761719 0.08091539144515991 549.8436889648438 0.3918668329715729 0.91608477 0.11586473137140274 True -17 48852 29.642460823059082 1.6161725521087646 440.46258544921875 0.1084398403763771 550.1636962890625 0.3917446434497833 0.9160738 0.11338436603546143 False -18 51566 29.64517855644226 0.6991362571716309 420.7976989746094 0.07629793882369995 550.646728515625 0.3905973732471466 0.9156238 0.1130661591887474 False -19 54280 29.612479209899902 0.6935453414916992 384.26214599609375 0.1758086383342743 550.3507080078125 0.391584575176239 0.91604066 0.11369440704584122 False diff --git a/ENCSR579RVI/cherimoya.fold_1.performance.tsv b/ENCSR579RVI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d4aed8315f41552e176f68ef23b5cbbf7529ef42..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -549.8436889648438 0.3930521011352539 0.39186686277389526 0.15107347071170807 0.9160847663879395 0.9124150276184082 0.11586473137140274 \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_2.evaluate.json b/ENCSR579RVI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e3f9cc82d476f8d55d70d2b50da13bad16c9ac4e..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF428BJG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_2.fit.json b/ENCSR579RVI/cherimoya.fold_2.fit.json deleted file mode 100644 index f5743e565f92aaffcf705629bc7a4e3e911f96ab..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF428BJG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_2.log b/ENCSR579RVI/cherimoya.fold_2.log deleted file mode 100644 index 7229c4c117f157f28fc54ac90352b5ed38dbcf61..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2861 36.52646017074585 4.174090623855591 429.82830810546875 0.16465063393115997 580.55615234375 0.28912290930747986 0.8089343 3.2251241207122803 True -1 5722 31.93994426727295 0.5690462589263916 483.1553955078125 0.2253236174583435 546.334228515625 0.34473368525505066 0.8293733 0.5718951225280762 True -2 8583 31.865932941436768 0.583824634552002 422.89898681640625 0.22988206148147583 536.90576171875 0.35975024104118347 0.8527009 0.21861401200294495 True -3 11444 31.889301538467407 0.5768628120422363 475.0534973144531 0.14448042213916779 534.3043823242188 0.3621833026409149 0.866481 0.19160820543766022 True -4 14305 31.488292455673218 0.6031761169433594 506.4918212890625 0.1521930694580078 532.2421875 0.36608147621154785 0.8681981 0.1659621000289917 True -5 17166 31.180255651474 0.5603823661804199 394.413818359375 0.16164103150367737 531.4874877929688 0.36700308322906494 0.87379515 0.15071304142475128 True -6 20027 31.20392417907715 0.5430948734283447 422.10272216796875 0.24166014790534973 529.4057006835938 0.3713105618953705 0.87785214 0.1525726169347763 True -7 22888 31.16664719581604 0.5472264289855957 447.9332580566406 0.19367903470993042 527.8643188476562 0.37354719638824463 0.8789327 0.16346698999404907 True -8 25749 31.191295623779297 0.5435905456542969 425.0804443359375 0.13142277300357819 527.4486083984375 0.3739163875579834 0.88114285 0.15001268684864044 True -9 28610 31.195371389389038 0.5518810749053955 474.3221435546875 0.14110833406448364 527.261474609375 0.3734048306941986 0.8856989 0.14474928379058838 True -10 31471 31.180707693099976 1.0743837356567383 390.47894287109375 0.1156252846121788 526.3447875976562 0.3752400279045105 0.8881595 0.1447995901107788 True -11 34332 31.86280131340027 0.5513582229614258 412.7154541015625 0.14085766673088074 525.1939697265625 0.3767736256122589 0.89107823 0.13827024400234222 True -12 37193 31.24497413635254 0.5443079471588135 421.91961669921875 0.12815524637699127 524.6466064453125 0.37773996591567993 0.89342177 0.133509561419487 True -13 40054 31.270782470703125 0.556229829788208 428.0693054199219 0.13777247071266174 524.1971435546875 0.37837162613868713 0.89567304 0.12835130095481873 True -14 42915 31.20012879371643 0.5470283031463623 420.06396484375 0.12565748393535614 523.3815307617188 0.38014909625053406 0.897984 0.12442552298307419 True -15 45776 31.189851999282837 0.5544917583465576 403.72406005859375 0.13079720735549927 522.8342895507812 0.3812793493270874 0.900254 0.1195194348692894 True -16 48637 31.195854663848877 1.5086069107055664 454.2843017578125 0.12007063627243042 522.7704467773438 0.38119176030158997 0.90115273 0.11683298647403717 True -17 51498 31.16735291481018 0.5516717433929443 440.22686767578125 0.09341233968734741 522.716064453125 0.38121703267097473 0.90188885 0.11496751010417938 True -18 54359 31.195211172103882 0.5409066677093506 409.338623046875 0.10701118409633636 523.5709838867188 0.37845033407211304 0.9019879 0.11424873024225235 True -19 57220 31.250335454940796 0.5544123649597168 444.2735595703125 0.10262522846460342 522.4715576171875 0.38169774413108826 0.9020686 0.11436128616333008 True diff --git a/ENCSR579RVI/cherimoya.fold_2.performance.tsv b/ENCSR579RVI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c1afc17fd9313d0b4d12ac37c24ed87e7e1ec8b2..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -522.4715576171875 0.4010689854621887 0.38169777393341064 0.14487811923027039 0.9020686149597168 0.8953086733818054 0.11436128616333008 \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_3.evaluate.json b/ENCSR579RVI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 455182ebea3043ba769620c1664cab953809d2c9..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF428BJG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_3.fit.json b/ENCSR579RVI/cherimoya.fold_3.fit.json deleted file mode 100644 index 03fbe01c23bb3eb0faf988069126a897e821d8fc..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF428BJG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_3.log b/ENCSR579RVI/cherimoya.fold_3.log deleted file mode 100644 index 37636cb2f64d3e38e25a4541bbf6da4bf3cbea21..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 35.953978061676025 4.220376253128052 450.76617431640625 0.32652753591537476 544.794189453125 0.2943364083766937 0.8076592 4.108187198638916 True -1 5536 30.87158989906311 0.6061317920684814 465.4156188964844 0.17569123208522797 510.1029968261719 0.35343071818351746 0.84650177 0.7256168723106384 True -2 8304 31.01873230934143 0.5585858821868896 480.2824401855469 0.27281808853149414 504.3501892089844 0.3621087670326233 0.85873693 0.28757190704345703 True -3 11072 30.592113256454468 0.5299029350280762 476.9390869140625 0.27852097153663635 501.3732604980469 0.3669394850730896 0.8642343 0.2486421763896942 True -4 13840 30.207784175872803 0.8159902095794678 446.2214050292969 0.2370934784412384 499.3384094238281 0.3699936866760254 0.8756714 0.21864397823810577 True -5 16608 30.169188022613525 0.5202789306640625 479.121337890625 0.13844504952430725 498.5711669921875 0.37102317810058594 0.87691796 0.2199290245771408 True -6 19376 30.14282250404358 0.5225706100463867 453.0568542480469 0.1688748598098755 497.4490051269531 0.3724857568740845 0.8822628 0.20585128664970398 True -7 22144 30.138200759887695 20.450047969818115 421.34783935546875 0.12211617082357407 496.9549255371094 0.37348589301109314 0.8863042 0.16868817806243896 True -8 24912 30.357614278793335 0.5444564819335938 450.50665283203125 0.15478432178497314 496.03045654296875 0.37489819526672363 0.8878442 0.1645713895559311 True -9 27680 30.24053645133972 1.0413832664489746 441.7268371582031 0.12105454504489899 494.3860778808594 0.3783996105194092 0.8907273 0.1558847725391388 True -10 30448 30.184287309646606 14.508291721343994 465.92193603515625 0.15329471230506897 493.3545837402344 0.37987035512924194 0.8928286 0.14549635350704193 True -11 33216 30.197763681411743 19.81400990486145 403.5721130371094 0.18428269028663635 492.82769775390625 0.3804556727409363 0.8970857 0.13609804213047028 True -12 35984 30.158520936965942 1.5096242427825928 415.018798828125 0.1879355013370514 492.36767578125 0.38114601373672485 0.8994001 0.12927104532718658 True -13 38752 30.288249015808105 1.1896402835845947 446.462890625 0.0996248871088028 491.51055908203125 0.3823285400867462 0.9020275 0.12487448006868362 True -14 41520 30.194807767868042 1.190894365310669 485.74969482421875 0.20778578519821167 491.371826171875 0.3821820020675659 0.9053408 0.11951395869255066 True -15 44288 30.18927764892578 1.5764236450195312 446.28826904296875 0.1419498473405838 490.2501525878906 0.3845835328102112 0.906751 0.11481606960296631 True -16 47056 30.166969537734985 18.18070101737976 404.06585693359375 0.09213891625404358 490.2415771484375 0.3842381536960602 0.9096712 0.11239396780729294 True -17 49824 30.191964387893677 1.2663953304290771 476.48260498046875 0.12908273935317993 489.4666748046875 0.38591820001602173 0.91065454 0.1101284921169281 True -18 52592 30.213120222091675 0.5326292514801025 409.90966796875 0.19191858172416687 490.10833740234375 0.3846098780632019 0.9106621 0.10975990444421768 True -19 55360 30.11318588256836 0.5260848999023438 477.90838623046875 0.11408916860818863 490.625244140625 0.3831981420516968 0.91036093 0.11036482453346252 False diff --git a/ENCSR579RVI/cherimoya.fold_3.performance.tsv b/ENCSR579RVI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 814db38f3aba359874eb905d3a0df3b95364a693..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -490.10833740234375 0.40353450179100037 0.3846098780632019 0.13828518986701965 0.9106621146202087 0.8900681138038635 0.10975990444421768 \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_4.evaluate.json b/ENCSR579RVI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e57f2eafe9836d2a7c2d2a890b8ed45e63129c89..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF428BJG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_4.fit.json b/ENCSR579RVI/cherimoya.fold_4.fit.json deleted file mode 100644 index 3abad22e4ccf2c4a47c7847916c680d0418c4220..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF428BJG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR579RVI/cherimoya.fold_4.log b/ENCSR579RVI/cherimoya.fold_4.log deleted file mode 100644 index 3c5cd81a73333a836cce4f2cd228a1f521e629ba..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2810 36.09962463378906 4.886708974838257 444.9009704589844 0.21521149575710297 513.7769165039062 0.28598588705062866 0.8134325 3.6692001819610596 True -1 5620 31.333592653274536 0.6453461647033691 441.7129821777344 0.34571513533592224 485.4590148925781 0.3367847800254822 0.8290761 0.6038727164268494 True -2 8430 31.257487773895264 2.5865607261657715 468.9913024902344 0.14504235982894897 477.8179016113281 0.3517646789550781 0.8634439 0.2891187369823456 True -3 11240 30.75793218612671 0.6034228801727295 453.08526611328125 0.1596691757440567 475.17041015625 0.3558834493160248 0.8706348 0.17577873170375824 True -4 14050 30.597265243530273 0.613126277923584 440.8327941894531 0.19568796455860138 474.2630615234375 0.35709357261657715 0.87272435 0.13443303108215332 True -5 16860 30.574710369110107 0.5953149795532227 481.32293701171875 0.23463433980941772 474.5829772949219 0.35570645332336426 0.8748868 0.12777896225452423 True -6 19670 30.611688137054443 1.0995311737060547 419.789306640625 0.17106084525585175 472.79833984375 0.35981932282447815 0.88056135 0.1351783275604248 True -7 22480 30.597633838653564 0.5985856056213379 421.989501953125 0.14152875542640686 471.6605224609375 0.36191532015800476 0.8857056 0.12748263776302338 True -8 25290 30.593854188919067 0.6072232723236084 387.9627685546875 0.17325463891029358 471.35418701171875 0.3622143864631653 0.8894194 0.1197328194975853 True -9 28100 30.589648485183716 0.6022441387176514 435.81610107421875 0.1688883900642395 470.35150146484375 0.36394476890563965 0.8926495 0.11184798181056976 True -10 30910 30.562682390213013 0.6191742420196533 500.287353515625 0.2571127414703369 469.7417297363281 0.36567094922065735 0.8967604 0.1085546463727951 True -11 33720 30.552204847335815 0.5938146114349365 489.6861572265625 0.12280671298503876 468.515869140625 0.36800768971443176 0.8979779 0.10608796030282974 True -12 36530 30.533401489257812 0.5862126350402832 458.0926513671875 0.13645532727241516 468.8977355957031 0.36646828055381775 0.9020546 0.10114816576242447 True -13 39340 30.534172534942627 0.5866048336029053 463.1009521484375 0.12921024858951569 468.0526428222656 0.3688316345214844 0.9050996 0.09811143577098846 True -14 42150 30.603256940841675 0.5900173187255859 398.5226135253906 0.1752581000328064 468.13751220703125 0.3673672080039978 0.9073114 0.0955754965543747 True -15 44960 30.645612239837646 0.6048290729522705 390.5553894042969 0.09620580077171326 466.97064208984375 0.37094420194625854 0.9091542 0.0931977778673172 True -16 47770 30.60386610031128 2.0259768962860107 435.43255615234375 0.10297434031963348 466.95806884765625 0.3704150319099426 0.9119349 0.0921054407954216 True -17 50580 31.209853887557983 0.6359236240386963 423.3066101074219 0.10061336308717728 467.0987548828125 0.36965417861938477 0.91143894 0.09130309522151947 False -18 53390 30.742130756378174 15.587751388549805 374.166015625 0.09597061574459076 466.8771057128906 0.37057363986968994 0.912638 0.09111665934324265 True -19 56200 30.626036643981934 0.6319570541381836 394.2967529296875 0.10957834124565125 466.9349670410156 0.3706207573413849 0.91186243 0.09122157841920853 False diff --git a/ENCSR579RVI/cherimoya.fold_4.performance.tsv b/ENCSR579RVI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 38dddb79a5b65fe3f740885fb1da1ab896021b24..0000000000000000000000000000000000000000 --- a/ENCSR579RVI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -466.8771057128906 0.41402244567871094 0.37057361006736755 0.13068176805973053 0.9126380085945129 0.8921446204185486 0.09111665934324265 \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_0.evaluate.json b/ENCSR580JBA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 93baa7c15c93ab8591cd93e87b28db1ed5c6815b..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871DGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_0.fit.json b/ENCSR580JBA/cherimoya.fold_0.fit.json deleted file mode 100644 index e17c3d1da7662943605f7d15f0051b25effa854d..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF871DGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_0.log b/ENCSR580JBA/cherimoya.fold_0.log deleted file mode 100644 index 1b39b12b4ba38d9b9fb20df7d78570d4d53e6c40..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3083 38.06119513511658 4.0224449634552 381.71728515625 0.8076684474945068 527.3408203125 0.5452113747596741 0.49789837 5.572983741760254 True -1 6166 34.10596323013306 1.0022330284118652 323.181884765625 1.0197064876556396 457.7073669433594 0.6502916216850281 0.55960315 1.617155909538269 True -2 9249 34.04677677154541 0.6520116329193115 361.806640625 0.7268677949905396 450.1242370605469 0.6600503325462341 0.5607674 1.3640629053115845 True -3 12332 33.98617219924927 0.6197385787963867 291.2863464355469 0.9534556865692139 445.5858154296875 0.6670144200325012 0.5700658 1.1722097396850586 True -4 15415 34.02431678771973 0.6241238117218018 395.62353515625 1.0597891807556152 442.87469482421875 0.6715206503868103 0.5752143 1.0679137706756592 True -5 18498 34.02441692352295 0.628298282623291 291.59332275390625 0.6660406589508057 441.91485595703125 0.6737897992134094 0.57529044 0.9734072089195251 True -6 21581 34.017152070999146 0.6295461654663086 331.87017822265625 0.7634569406509399 440.1898498535156 0.6761553287506104 0.5853527 0.9401635527610779 True -7 24664 34.24947500228882 0.6232171058654785 361.7104187011719 0.5587834119796753 438.79718017578125 0.6788012385368347 0.5931621 0.851971447467804 True -8 27747 33.39362120628357 0.6280059814453125 376.6994323730469 0.5064555406570435 437.4495849609375 0.6807914972305298 0.5991198 0.8250885009765625 True -9 30830 33.44135046005249 0.6245720386505127 321.1560363769531 0.6135890483856201 435.25677490234375 0.6838977932929993 0.605883 0.7518017888069153 True -10 33913 33.40543985366821 1.0159645080566406 329.935546875 0.8730474710464478 433.43743896484375 0.686204195022583 0.6096067 0.7301360964775085 True -11 36996 33.382545709609985 0.630408763885498 377.7495422363281 0.50993412733078 431.5867004394531 0.6887667775154114 0.616588 0.6677749156951904 True -12 40079 33.33348321914673 0.6230013370513916 353.2615051269531 0.6946042776107788 429.8029479980469 0.6908928751945496 0.62992954 0.6282580494880676 True -13 43162 33.33414959907532 0.619530200958252 343.65802001953125 0.6941037178039551 428.1162414550781 0.6931323409080505 0.6355158 0.6057683229446411 True -14 46245 33.38865280151367 0.616692304611206 305.4962158203125 0.4778074026107788 426.6346130371094 0.6948513388633728 0.64519143 0.578540563583374 True -15 49328 33.41140413284302 0.628298282623291 326.318359375 0.49963873624801636 425.7488098144531 0.6961028575897217 0.65448487 0.5640428066253662 True -16 52411 33.38164019584656 0.6156601905822754 345.131103515625 0.4964381158351898 425.17132568359375 0.6966027617454529 0.6611071 0.5529714822769165 True -17 55494 33.42943024635315 0.6260268688201904 361.74810791015625 0.478701114654541 425.09381103515625 0.6965726613998413 0.6620291 0.5506943464279175 True -18 58577 33.378448486328125 5.308956623077393 261.37030029296875 0.5544943809509277 425.48931884765625 0.6960522532463074 0.65837526 0.5598263144493103 False -19 61660 33.35719275474548 0.6192724704742432 348.61077880859375 0.375119149684906 425.4118347167969 0.6958053708076477 0.65728223 0.5630467534065247 False diff --git a/ENCSR580JBA/cherimoya.fold_0.performance.tsv b/ENCSR580JBA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 22eab7aeec69eb3d47e0886334812789f02bdcfb..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -425.09381103515625 0.2529968321323395 0.6965726613998413 0.28083717823028564 0.6620290875434875 0.6271025538444519 0.5506943464279175 \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_1.evaluate.json b/ENCSR580JBA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0e510c6a7922ece5252e6c03a025f3514dee53b0..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871DGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_1.fit.json b/ENCSR580JBA/cherimoya.fold_1.fit.json deleted file mode 100644 index 46225ec30a21d0f49e7a6043a4d15c1a177ab089..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF871DGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_1.log b/ENCSR580JBA/cherimoya.fold_1.log deleted file mode 100644 index d4749a2fb94480f893bf9f25800d35979145508f..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3177 38.844897508621216 3.6854825019836426 329.6378173828125 0.9692301154136658 504.4819030761719 0.5477696061134338 0.5142751 5.001668930053711 True -1 6354 35.05746102333069 0.8515760898590088 383.5322570800781 0.8098829984664917 447.4395751953125 0.6469270586967468 0.5675047 1.4756428003311157 True -2 9531 35.06151056289673 0.6453428268432617 358.8525390625 0.6971503496170044 439.3702697753906 0.6569934487342834 0.5783547 0.9914112687110901 True -3 12708 35.033992767333984 0.6543395519256592 299.28875732421875 0.8766056299209595 435.6290283203125 0.6618547439575195 0.5905993 0.7903823256492615 True -4 15885 35.07636046409607 0.6476242542266846 360.87762451171875 0.7664896845817566 433.90625 0.6653162837028503 0.59436613 0.7235532402992249 True -5 19062 34.74399709701538 0.6423275470733643 317.1119079589844 0.7019507884979248 432.1588439941406 0.667717456817627 0.6002176 0.7061728239059448 True -6 22239 34.32520055770874 0.6493308544158936 340.6832275390625 0.8699502348899841 431.0471496582031 0.670086681842804 0.6051409 0.7355018854141235 True -7 25416 34.387067794799805 0.6458606719970703 327.43536376953125 0.6271478533744812 429.2721862792969 0.6731751561164856 0.61050165 0.6716105937957764 True -8 28593 34.35642099380493 13.673177242279053 332.6736145019531 0.8446078300476074 428.0500183105469 0.6755226254463196 0.6089355 0.6463547348976135 False -9 31770 34.71686768531799 0.6325669288635254 304.1195373535156 0.5163701176643372 425.78277587890625 0.6787271499633789 0.6235345 0.6079973578453064 True -10 34947 34.32949447631836 0.635256290435791 315.832275390625 0.6574465036392212 424.2052917480469 0.68124920129776 0.6314278 0.5801540613174438 True -11 38124 34.3689386844635 0.6294660568237305 364.18170166015625 0.6225579977035522 422.77471923828125 0.6835077404975891 0.6363422 0.5561016201972961 True -12 41301 34.33054876327515 0.6362655162811279 286.041748046875 0.4943758547306061 421.2845458984375 0.6857958436012268 0.6444639 0.5369378924369812 True -13 44478 34.4145290851593 0.6427891254425049 337.89208984375 0.6717629432678223 419.6853332519531 0.6881407499313354 0.65726507 0.5004879832267761 True -14 47655 34.40338897705078 0.6329197883605957 330.9747619628906 0.34651750326156616 418.71685791015625 0.689568042755127 0.6633315 0.49406489729881287 True -15 50832 34.3789119720459 0.6413364410400391 356.2179260253906 0.42734161019325256 417.9652404785156 0.6907150149345398 0.6684337 0.4897865951061249 True -16 54009 34.39688229560852 0.6533374786376953 330.79730224609375 0.5074954628944397 417.55291748046875 0.6912692785263062 0.67030644 0.48442575335502625 True -17 57186 34.3801794052124 0.6395699977874756 385.8445129394531 0.34620776772499084 417.459228515625 0.6912016272544861 0.6728743 0.485141783952713 True -18 60363 34.38410186767578 0.6523349285125732 340.67962646484375 0.523212194442749 417.6793518066406 0.6906546354293823 0.67105144 0.4896509349346161 False -19 63540 34.38649249076843 0.6337065696716309 287.6395263671875 0.36397138237953186 417.8108215332031 0.6903846263885498 0.670433 0.4956589639186859 False diff --git a/ENCSR580JBA/cherimoya.fold_1.performance.tsv b/ENCSR580JBA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index aea45c98e8d86a0cf7f917f323ce6d5e2d04e4a3..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -417.459228515625 0.2561910152435303 0.6912016868591309 0.27725598216056824 0.6728742718696594 0.6587863564491272 0.485141783952713 \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_2.evaluate.json b/ENCSR580JBA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f36eec185583c4b9e4e884750687a7f5dfdf0ebf..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871DGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_2.fit.json b/ENCSR580JBA/cherimoya.fold_2.fit.json deleted file mode 100644 index 5748ea99c305af303af8e136f21143c46b53cd07..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF871DGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_2.log b/ENCSR580JBA/cherimoya.fold_2.log deleted file mode 100644 index 4a8c8ae6a448888f1d58fdf164863dbef41c3e36..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3261 39.689127683639526 3.4960882663726807 346.13323974609375 0.8405797481536865 512.9866943359375 0.5451991558074951 0.49976265 5.492856979370117 True -1 6522 36.112061500549316 0.6634783744812012 391.84112548828125 0.7889624238014221 448.68927001953125 0.647142767906189 0.5597854 1.607073187828064 True -2 9783 36.169286251068115 0.6016993522644043 350.6776123046875 0.6315059661865234 441.6634216308594 0.6565753817558289 0.58016163 0.9649587869644165 True -3 13044 36.002198934555054 0.6007778644561768 296.4764404296875 0.9372198581695557 438.1778259277344 0.6619434952735901 0.5861303 0.9234331250190735 True -4 16305 35.525710344314575 0.6065888404846191 364.20428466796875 0.9162148237228394 435.7949523925781 0.6652429699897766 0.591983 0.8425676822662354 True -5 19566 35.31139588356018 0.5970268249511719 390.84429931640625 0.9169321656227112 433.9234313964844 0.668418824672699 0.5907141 0.8002429008483887 False -6 22827 35.25399351119995 0.6126718521118164 294.75579833984375 0.6881434917449951 432.3664245605469 0.6708446145057678 0.59545034 0.7321485877037048 True -7 26088 35.28467082977295 2.425997018814087 363.74627685546875 0.6939412355422974 431.1543884277344 0.6732054352760315 0.6046891 0.6964305639266968 True -8 29349 35.28396391868591 0.6057219505310059 361.2708740234375 0.903428316116333 429.81280517578125 0.6750574707984924 0.6078485 0.6784954071044922 True -9 32610 35.30618953704834 0.5971939563751221 368.13134765625 0.5653063654899597 427.7563781738281 0.6778606176376343 0.6122276 0.6400970816612244 True -10 35871 35.26722812652588 0.5889275074005127 296.019775390625 0.5391047596931458 426.1212463378906 0.6802952885627747 0.62068087 0.6114425659179688 True -11 39132 35.330891132354736 0.5985078811645508 324.5280456542969 0.5015063285827637 424.4997863769531 0.6821995973587036 0.627954 0.6032896637916565 True -12 42393 35.40733623504639 0.597872257232666 349.4541015625 0.626766562461853 423.2743225097656 0.6841480731964111 0.6315508 0.5896990299224854 True -13 45654 35.3434112071991 1.0115420818328857 378.09014892578125 0.7055637240409851 421.9193420410156 0.6861657500267029 0.6446538 0.5682581663131714 True -14 48915 35.23667573928833 0.5936334133148193 259.61279296875 0.4195050597190857 420.8753967285156 0.6876937747001648 0.65069264 0.5509719848632812 True -15 52176 35.25753164291382 0.598548412322998 286.0008544921875 0.4259089529514313 419.93450927734375 0.6887409687042236 0.6570494 0.5484804511070251 True -16 55437 35.212053060531616 0.5885560512542725 331.6507568359375 0.3685244023799896 419.5230712890625 0.6891752481460571 0.66270185 0.5397974252700806 True -17 58698 35.19271659851074 0.6507110595703125 292.597900390625 0.4301188588142395 419.4698181152344 0.6892291903495789 0.66219205 0.539305567741394 False -18 61959 35.22448801994324 0.5939998626708984 361.11590576171875 0.6622902154922485 419.62298583984375 0.6889221668243408 0.6602207 0.5458466410636902 False -19 65220 35.25867247581482 0.5947871208190918 302.1842041015625 0.3309924602508545 419.8111877441406 0.6886726021766663 0.65899575 0.549528181552887 False diff --git a/ENCSR580JBA/cherimoya.fold_2.performance.tsv b/ENCSR580JBA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index af2dcadb4d6e5e40c7a0534acd6a108a15b8429f..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -419.5230712890625 0.2566012740135193 0.6891752481460571 0.2794760763645172 0.6627018451690674 0.6303112506866455 0.5397974252700806 \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_3.evaluate.json b/ENCSR580JBA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 360c865f9fd8b041d4cfe5cd5ef412e90a14a931..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871DGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_3.fit.json b/ENCSR580JBA/cherimoya.fold_3.fit.json deleted file mode 100644 index a70ac8d79b4a4a07490aa1507d5a11e39f2d164a..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF871DGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_3.log b/ENCSR580JBA/cherimoya.fold_3.log deleted file mode 100644 index 8916af250b358d910096ae2ba9aded38e64c0256..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3194 39.4623441696167 3.609959840774536 325.9783935546875 1.1755709648132324 526.0540771484375 0.5523424744606018 0.4920625 6.0149664878845215 True -1 6388 35.2824022769928 0.7037553787231445 305.0174865722656 0.6728655099868774 457.84185791015625 0.6543481945991516 0.5520123 1.5010008811950684 True -2 9582 35.25539827346802 0.6925382614135742 331.67327880859375 0.8984516859054565 450.51708984375 0.6647286415100098 0.57869774 1.0433402061462402 True -3 12776 34.81820511817932 0.6732344627380371 339.9093017578125 0.9117542505264282 447.19964599609375 0.6688941121101379 0.5834137 0.9336019158363342 True -4 15970 34.55082106590271 0.6730241775512695 347.9658203125 0.7670458555221558 445.4334716796875 0.6714063286781311 0.5892968 0.9109281897544861 True -5 19164 34.486440658569336 0.6863293647766113 283.10308837890625 0.7782708406448364 443.71392822265625 0.6738253235816956 0.59472865 0.8836966753005981 True -6 22358 34.45703458786011 2.1304047107696533 354.70379638671875 0.5935392379760742 441.4335021972656 0.677154541015625 0.59970826 0.7816745638847351 True -7 25552 34.46380305290222 0.6760063171386719 334.2754821777344 0.5042127966880798 439.0733337402344 0.6800848245620728 0.6061905 0.7201308012008667 True -8 28746 34.44596791267395 0.6655483245849609 278.3802185058594 0.9337741732597351 437.80413818359375 0.6821575164794922 0.6120652 0.6861528158187866 True -9 31940 34.46146631240845 0.6756184101104736 369.9449768066406 0.9959688186645508 435.9981384277344 0.6847025156021118 0.6186233 0.6410976648330688 True -10 35134 34.53747582435608 31.575001001358032 299.4695129394531 0.6311330795288086 434.90283203125 0.6863657236099243 0.625803 0.6191660761833191 True -11 38328 34.83911418914795 0.6710546016693115 349.92071533203125 0.8552544116973877 433.3229064941406 0.6884337663650513 0.63534725 0.6104637980461121 True -12 41522 34.5640971660614 0.6793930530548096 312.895751953125 0.4929094612598419 431.56597900390625 0.6904768347740173 0.6412449 0.5819873809814453 True -13 44716 34.594783306121826 0.6670057773590088 331.89251708984375 0.4371594190597534 430.4162902832031 0.6922284364700317 0.64918935 0.5815436840057373 True -14 47910 34.55366492271423 0.6782569885253906 353.86492919921875 0.45015114545822144 429.1094970703125 0.6938117742538452 0.65665376 0.5554953813552856 True -15 51104 34.49529695510864 0.6711442470550537 333.90594482421875 0.5523406267166138 428.2234191894531 0.6949576139450073 0.66335547 0.5435797572135925 True -16 54298 34.4867582321167 0.6767568588256836 331.29180908203125 0.4215138852596283 427.5366516113281 0.6956764459609985 0.6641804 0.5442465543746948 True -17 57492 34.4959180355072 0.670687198638916 340.98602294921875 0.4134739637374878 427.50994873046875 0.6955472230911255 0.6658837 0.5465377569198608 True -18 60686 34.51989006996155 0.6724872589111328 291.9782409667969 0.3672480583190918 427.59405517578125 0.69521564245224 0.66239625 0.5553461313247681 False -19 63880 34.548726081848145 0.6649007797241211 339.32037353515625 0.4040079712867737 427.6908874511719 0.6949854493141174 0.6592809 0.5592049956321716 False diff --git a/ENCSR580JBA/cherimoya.fold_3.performance.tsv b/ENCSR580JBA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index de4d998fd26c94e9eca983f096159f63074b8317..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -427.50994873046875 0.25238072872161865 0.6955472230911255 0.284414678812027 0.6658837199211121 0.638911783695221 0.5465377569198608 \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_4.evaluate.json b/ENCSR580JBA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1897e167c90470cc4cef64c5ce81f3268babbf42..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871DGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_4.fit.json b/ENCSR580JBA/cherimoya.fold_4.fit.json deleted file mode 100644 index f93ac761e40ac4235f7bb0c90cf8570869f149f7..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF871DGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580JBA/cherimoya.fold_4.log b/ENCSR580JBA/cherimoya.fold_4.log deleted file mode 100644 index bd963dc7fbf6d21c5b1ea127c950a63d7632df2f..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3302 40.272183418273926 27.5999972820282 351.93994140625 0.7259752750396729 526.4754638671875 0.5547739863395691 0.5366229 6.194711208343506 True -1 6604 36.69133710861206 0.6624906063079834 365.74249267578125 0.9783797860145569 461.49505615234375 0.6587062478065491 0.57029766 1.5219953060150146 True -2 9906 36.5632700920105 21.768176555633545 384.00408935546875 0.8373258709907532 454.1116638183594 0.6681891679763794 0.58652806 1.054832935333252 True -3 13208 36.38896822929382 0.8941304683685303 354.3586120605469 0.7624504566192627 450.79278564453125 0.672852098941803 0.59462005 1.0651479959487915 True -4 16510 35.70221018791199 0.63511061668396 409.749755859375 0.9172378182411194 448.7969055175781 0.6761271953582764 0.59757924 0.905139148235321 True -5 19812 35.651718854904175 0.6367654800415039 318.81939697265625 0.6386857032775879 447.89141845703125 0.6783309578895569 0.59900916 0.8442502021789551 True -6 23114 35.817256927490234 1.545278549194336 308.55181884765625 0.6559532880783081 446.27392578125 0.6810929179191589 0.6059993 0.8029257655143738 True -7 26416 35.72178673744202 0.6334412097930908 360.4117736816406 0.8839793801307678 444.358642578125 0.683914303779602 0.60429513 0.7577118873596191 False -8 29718 35.68945908546448 0.641618013381958 304.1533508300781 0.6265860795974731 442.7603759765625 0.6863095760345459 0.61273986 0.7264617085456848 True -9 33020 35.680928230285645 0.6364090442657471 331.7214660644531 0.6509705781936646 440.1623229980469 0.6895710825920105 0.6212959 0.6777625679969788 True -10 36322 35.67172169685364 0.6396763324737549 346.92877197265625 0.6942203044891357 438.28424072265625 0.6922572255134583 0.63152385 0.6246683597564697 True -11 39624 35.73833632469177 0.6358487606048584 347.568115234375 0.5975486636161804 437.064208984375 0.6938933730125427 0.6374357 0.6233174800872803 True -12 42926 35.722766160964966 0.6384432315826416 360.81396484375 0.7093312740325928 435.5914306640625 0.6960874199867249 0.64120924 0.5996475219726562 True -13 46228 35.68062138557434 0.6268064975738525 367.149169921875 0.6007896661758423 433.84027099609375 0.6985086798667908 0.65005916 0.5832111239433289 True -14 49530 35.68446397781372 0.6277334690093994 407.677978515625 0.7624877691268921 432.46551513671875 0.7004434466362 0.6605161 0.5548016428947449 True -15 52832 35.818411350250244 1.084831953048706 366.489990234375 0.5089027881622314 431.54718017578125 0.7015422582626343 0.66562456 0.539752185344696 True -16 56134 35.73181104660034 0.6308238506317139 279.48712158203125 0.45642051100730896 431.07623291015625 0.7020745277404785 0.6704455 0.5345263481140137 True -17 59436 35.701680183410645 0.6329631805419922 336.77020263671875 0.5422546863555908 431.048095703125 0.7019281983375549 0.6712679 0.538306713104248 True -18 62738 35.736071825027466 0.664050817489624 333.68218994140625 0.34724292159080505 431.1414794921875 0.701715350151062 0.6688043 0.5432929396629333 False -19 66040 35.836020946502686 0.6314668655395508 306.6831970214844 0.4940800666809082 431.32281494140625 0.7014249563217163 0.667427 0.5503599643707275 False diff --git a/ENCSR580JBA/cherimoya.fold_4.performance.tsv b/ENCSR580JBA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b5d9b4b40d8fdaf2114abb9f5a198558f0208928..0000000000000000000000000000000000000000 --- a/ENCSR580JBA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -431.048095703125 0.24967136979103088 0.7019281983375549 0.2892172932624817 0.6712679266929626 0.6319419145584106 0.538306713104248 \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_0.evaluate.json b/ENCSR580OAH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 42ac1427d3572aafc39114bf5a5f2377c648fd76..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF914WQA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_0.fit.json b/ENCSR580OAH/cherimoya.fold_0.fit.json deleted file mode 100644 index 7a47980bdecda47c824b71b8bbddf07a592b7f00..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF914WQA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_0.log b/ENCSR580OAH/cherimoya.fold_0.log deleted file mode 100644 index 3ffd9dad963fdc5a0fbeab980fe36d6d620da2a8..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.82403326034546 4.0583343505859375 202.685546875 0.48768338561058044 301.3146667480469 0.1573561728000641 0.73130655 3.2090697288513184 True -1 5510 30.572952032089233 0.6141080856323242 221.17068481445312 0.5123053193092346 282.6804504394531 0.2213941067457199 0.7901897 0.7137280702590942 True -2 8265 30.407771348953247 0.5824997425079346 226.79164123535156 0.829430103302002 278.52655029296875 0.2324024885892868 0.7958998 0.48039737343788147 True -3 11020 30.405853748321533 0.5696744918823242 254.74928283691406 0.668893039226532 275.1787414550781 0.24128639698028564 0.8041052 0.4467463195323944 True -4 13775 30.400318145751953 0.5585403442382812 247.5076141357422 0.43764376640319824 273.6967468261719 0.2471933513879776 0.80639607 0.4008599817752838 True -5 16530 30.30439805984497 0.5631189346313477 235.21420288085938 0.5625104904174805 272.89788818359375 0.25066232681274414 0.8060769 0.41219663619995117 False -6 19285 30.353153467178345 0.6514861583709717 203.40866088867188 0.4002779424190521 271.9091491699219 0.253731906414032 0.80698204 0.4064961075782776 True -7 22040 30.30521512031555 0.562946081161499 176.49366760253906 0.8924285173416138 271.47344970703125 0.2547059953212738 0.8105548 0.40514224767684937 True -8 24795 30.28940773010254 0.5655958652496338 192.5731201171875 0.37953081727027893 271.00970458984375 0.2573355734348297 0.8139664 0.38594502210617065 True -9 27550 30.365355730056763 0.5904741287231445 250.7397918701172 0.3629458546638489 270.358642578125 0.2598949670791626 0.81705874 0.38090193271636963 True -10 30305 30.349915504455566 0.5654559135437012 222.04542541503906 0.40857332944869995 269.66986083984375 0.2626631557941437 0.82184446 0.3861429989337921 True -11 33060 30.39275622367859 0.5771970748901367 179.99581909179688 0.3565278947353363 268.6345520019531 0.2665603458881378 0.8258941 0.38301795721054077 True -12 35815 30.359448671340942 10.800602436065674 214.43618774414062 0.41325587034225464 268.3493347167969 0.26726794242858887 0.8306148 0.36699801683425903 True -13 38570 30.393386363983154 0.5983576774597168 211.4098663330078 0.3585561215877533 268.1018371582031 0.2677469849586487 0.83432937 0.36038121581077576 True -14 41325 30.42429780960083 0.5639123916625977 208.06675720214844 0.4126451313495636 267.6485900878906 0.26865455508232117 0.8403362 0.3301211893558502 True -15 44080 30.43512225151062 0.5969092845916748 174.5286407470703 0.3035816252231598 266.7299499511719 0.2725103199481964 0.8430506 0.30407488346099854 True -16 46835 30.410077571868896 2.088789939880371 237.83737182617188 0.3357126712799072 266.54339599609375 0.27188578248023987 0.84679806 0.29096654057502747 True -17 49590 30.361880779266357 0.5871477127075195 216.38253784179688 0.25887250900268555 266.9027099609375 0.27124446630477905 0.8488185 0.28217852115631104 True -18 52345 30.619155883789062 0.7188913822174072 248.0275421142578 0.3168882131576538 266.6288146972656 0.2727433741092682 0.8484665 0.27900299429893494 False -19 55100 29.84164023399353 0.6318588256835938 220.01971435546875 0.3072270452976227 266.5693054199219 0.27245524525642395 0.8477353 0.28086960315704346 False diff --git a/ENCSR580OAH/cherimoya.fold_0.performance.tsv b/ENCSR580OAH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a9dcf6ce80abd2f213d6cfbfa79691e220e7cd04..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -266.9027099609375 0.5065416097640991 0.27124446630477905 0.06981578469276428 0.8488184809684753 0.7820616960525513 0.28217852115631104 \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_1.evaluate.json b/ENCSR580OAH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3ea33f1ffcdf9c2c5aae6c25ddacfe2ee595c145..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF914WQA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_1.fit.json b/ENCSR580OAH/cherimoya.fold_1.fit.json deleted file mode 100644 index a40992cc5cdf4bc2e2198b0039a60b212fbc823b..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF914WQA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_1.log b/ENCSR580OAH/cherimoya.fold_1.log deleted file mode 100644 index 9a29c214158eb4df42304d53629a00929302312b..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 33.65134859085083 4.282221555709839 241.12753295898438 0.6205592155456543 351.7404479980469 0.1652803272008896 0.7277151 3.273632526397705 True -1 5410 30.051336765289307 0.7183444499969482 201.63601684570312 0.8122762441635132 326.2080993652344 0.24119144678115845 0.79545754 1.2931289672851562 True -2 8115 29.833904266357422 0.7061381340026855 224.12774658203125 0.6106023788452148 320.516357421875 0.256050169467926 0.8093511 0.518480658531189 True -3 10820 29.793840646743774 0.7209835052490234 220.37850952148438 0.525582492351532 317.0370178222656 0.2635027766227722 0.8170116 0.43198034167289734 True -4 13525 29.791123390197754 0.723212718963623 178.90611267089844 0.4074009656906128 315.517822265625 0.2681417167186737 0.8186611 0.4705851078033447 True -5 16230 29.759880542755127 0.759681224822998 212.04684448242188 0.5812666416168213 314.18426513671875 0.27142494916915894 0.8230619 0.4660039246082306 True -6 18935 29.745813369750977 0.7150311470031738 169.32540893554688 0.35425132513046265 314.337158203125 0.27167749404907227 0.8242778 0.5200040936470032 True -7 21640 29.781978130340576 0.6941056251525879 238.197265625 1.0092377662658691 312.8730163574219 0.2753322720527649 0.82804984 0.4860309064388275 True -8 24345 29.759605884552002 0.7055153846740723 238.38107299804688 0.564949095249176 312.7742919921875 0.27492526173591614 0.82822037 0.4774234890937805 True -9 27050 29.795109748840332 0.6910881996154785 243.84474182128906 0.36831188201904297 311.4973449707031 0.2794935405254364 0.83491474 0.47514137625694275 True -10 29755 29.774224758148193 0.7024872303009033 235.30020141601562 0.4890415072441101 310.439453125 0.28310272097587585 0.8378765 0.4697876572608948 True -11 32460 29.772196769714355 0.7063024044036865 200.51296997070312 0.2628721594810486 309.4697570800781 0.28529444336891174 0.8399229 0.4562721848487854 True -12 35165 29.80309820175171 2.290658950805664 176.56422424316406 0.3956618905067444 309.285888671875 0.2852514982223511 0.84277314 0.434832900762558 True -13 37870 29.84255862236023 0.7361361980438232 205.90049743652344 0.3028751611709595 308.43310546875 0.28776809573173523 0.84827477 0.4014454782009125 True -14 40575 29.820658683776855 0.7420480251312256 226.80564880371094 0.4072049856185913 308.0633239746094 0.28813424706459045 0.85510683 0.355636864900589 True -15 43280 29.815356731414795 0.8558323383331299 190.21881103515625 0.32533714175224304 307.6216735839844 0.2899337410926819 0.85698664 0.34554609656333923 True -16 45985 29.798500776290894 0.7091178894042969 204.22915649414062 0.4076375961303711 307.36639404296875 0.2906434237957001 0.8612416 0.3245256245136261 True -17 48690 29.80847692489624 0.7181451320648193 211.98590087890625 0.32199257612228394 307.19134521484375 0.2912490963935852 0.86019117 0.315244197845459 False -18 51395 29.80371379852295 0.7244734764099121 177.77694702148438 0.28512799739837646 306.88885498046875 0.2924787700176239 0.85882896 0.3094414472579956 False -19 54100 29.797730922698975 0.692427396774292 200.21629333496094 0.28533899784088135 307.67779541015625 0.28894829750061035 0.8582754 0.3119954764842987 False diff --git a/ENCSR580OAH/cherimoya.fold_1.performance.tsv b/ENCSR580OAH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 51ca938a4fd48396f1015659aa00cbcf55b0dd07..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -307.36639404296875 0.48794594407081604 0.2906433939933777 0.08191142976284027 0.8612415790557861 0.8212777972221375 0.3245256245136261 \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_2.evaluate.json b/ENCSR580OAH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f690f1dd6576ff895abe2fcbbc9baaf4d04bca34..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF914WQA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_2.fit.json b/ENCSR580OAH/cherimoya.fold_2.fit.json deleted file mode 100644 index 6c98ca0749eb00a06c2e638e4609a6b44caaa383..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF914WQA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_2.log b/ENCSR580OAH/cherimoya.fold_2.log deleted file mode 100644 index c02b7909198862b73ebc29a6ad5a4d32674bad47..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 35.59639024734497 3.8584508895874023 195.27484130859375 0.6998995542526245 313.4501647949219 0.16605748236179352 0.7329344 3.4204611778259277 True -1 5736 31.690834999084473 0.5804572105407715 260.0354309082031 0.5591100454330444 291.9351501464844 0.2308504581451416 0.78974706 1.0979881286621094 True -2 8604 31.631667613983154 0.576160192489624 229.5294189453125 0.42138993740081787 287.3251647949219 0.24317137897014618 0.8032094 0.610093891620636 True -3 11472 31.609443426132202 1.6930444240570068 188.8441925048828 0.5885298848152161 284.91290283203125 0.24893954396247864 0.80909395 0.41571956872940063 True -4 14340 31.736907482147217 0.5502400398254395 193.82962036132812 0.3826271891593933 283.8045654296875 0.2529296278953552 0.8093571 0.45242249965667725 True -5 17208 31.63704776763916 0.8230350017547607 222.0872039794922 0.4386460781097412 282.87261962890625 0.2568976581096649 0.81178737 0.4694822430610657 True -6 20076 31.539058208465576 0.6020622253417969 205.2595977783203 0.36808639764785767 282.6935729980469 0.25692108273506165 0.8164716 0.43976038694381714 True -7 22944 31.54187774658203 0.5572803020477295 225.97756958007812 0.529552161693573 282.22149658203125 0.25778284668922424 0.8191123 0.42501965165138245 True -8 25812 31.52944564819336 0.5549769401550293 220.2543487548828 0.5863612294197083 281.24822998046875 0.2612563371658325 0.8186671 0.4250467121601105 False -9 28680 31.551634073257446 0.5519614219665527 187.78070068359375 0.339812695980072 280.6908264160156 0.26284629106521606 0.8252463 0.3978511393070221 True -10 31548 31.649921894073486 0.5543456077575684 228.19027709960938 0.3853931128978729 279.66302490234375 0.2666909098625183 0.8283038 0.38729485869407654 True -11 34416 31.657848358154297 1.1248090267181396 266.96630859375 0.41970688104629517 279.31243896484375 0.26810193061828613 0.8288502 0.40016135573387146 True -12 37284 31.672733545303345 0.6446232795715332 230.57958984375 0.36808088421821594 278.75152587890625 0.26959291100502014 0.8322062 0.37251579761505127 True -13 40152 31.70296049118042 0.5546090602874756 235.87295532226562 0.34183669090270996 278.07757568359375 0.27109143137931824 0.8372673 0.3492138683795929 True -14 43020 31.623777866363525 0.5392341613769531 234.58135986328125 0.3739197552204132 277.6460266113281 0.27271026372909546 0.8409492 0.33356109261512756 True -15 45888 31.629298210144043 0.5487792491912842 233.3249969482422 0.3382464647293091 277.267822265625 0.27424269914627075 0.8444179 0.310508131980896 True -16 48756 31.62259793281555 0.5540525913238525 195.47955322265625 0.29251694679260254 277.408447265625 0.27353355288505554 0.8467172 0.30126747488975525 True -17 51624 31.717315196990967 0.5725486278533936 250.68426513671875 0.24613842368125916 277.2987060546875 0.2737182676792145 0.8488698 0.29546692967414856 True -18 54492 31.74142813682556 0.8993167877197266 235.89248657226562 0.27534082531929016 277.2972412109375 0.273858904838562 0.84859 0.2949836254119873 False -19 57360 31.69698476791382 1.4905612468719482 175.57736206054688 0.2604212164878845 277.2619323730469 0.2738044559955597 0.84830564 0.29730695486068726 False diff --git a/ENCSR580OAH/cherimoya.fold_2.performance.tsv b/ENCSR580OAH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1b9bc93ff6cd78870335d09fde9cf8f86c7e41ea..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -277.2987060546875 0.5024734735488892 0.2737182378768921 0.0747845321893692 0.848869800567627 0.7947338819503784 0.29546692967414856 \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_3.evaluate.json b/ENCSR580OAH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0632c72e6d228e08c805843006ba69edbb451f18..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF914WQA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_3.fit.json b/ENCSR580OAH/cherimoya.fold_3.fit.json deleted file mode 100644 index 9d421a44596bdbe39c0b02598c39f551e1a3289d..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF914WQA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_3.log b/ENCSR580OAH/cherimoya.fold_3.log deleted file mode 100644 index 5b84f5442acb9f809cb06f4cec0857917b2bf40d..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.79150462150574 27.071934461593628 243.597900390625 0.5765185356140137 305.91876220703125 0.16126146912574768 0.7283301 2.9486284255981445 True -1 5494 30.304527521133423 0.6503982543945312 216.58184814453125 0.5346530079841614 287.7180480957031 0.21945242583751678 0.79022396 1.0732314586639404 True -2 8241 30.888396739959717 0.5480854511260986 218.65260314941406 0.5678129196166992 282.25177001953125 0.235401451587677 0.8027338 0.7119299173355103 True -3 10988 30.32130217552185 0.6019668579101562 197.66455078125 0.5049343109130859 279.43756103515625 0.24404874444007874 0.8088458 0.47518405318260193 True -4 13735 30.381041049957275 0.53898024559021 197.60812377929688 0.3988955616950989 278.5007629394531 0.24610961973667145 0.81061184 0.4576148986816406 True -5 16482 30.32892417907715 0.5459825992584229 238.60357666015625 0.6016602516174316 277.80914306640625 0.24893923103809357 0.81271005 0.47654488682746887 True -6 19229 30.275818586349487 0.5461921691894531 292.749755859375 0.5096292495727539 277.1213073730469 0.25120866298675537 0.8115132 0.4814072251319885 False -7 21976 30.254494428634644 0.5479221343994141 240.66519165039062 0.5185758471488953 276.1987609863281 0.2538498044013977 0.81593746 0.4386358857154846 True -8 24723 30.28512167930603 0.5325155258178711 217.7049560546875 0.3989101052284241 275.39666748046875 0.2571628987789154 0.81647176 0.4373342990875244 True -9 27470 30.279814958572388 9.400476455688477 233.004150390625 0.49186235666275024 274.87762451171875 0.25861656665802 0.8198504 0.44489264488220215 True -10 30217 30.287986040115356 0.5376284122467041 223.44189453125 0.41903674602508545 274.1896667480469 0.26204296946525574 0.8204047 0.432175874710083 True -11 32964 30.28757357597351 0.5408680438995361 189.56793212890625 0.3703358769416809 273.6757507324219 0.26374125480651855 0.8227332 0.41544654965400696 True -12 35711 30.267505407333374 0.5340497493743896 227.6318359375 0.28717225790023804 273.1754455566406 0.2643655240535736 0.83086085 0.3964061737060547 True -13 38458 30.406144857406616 0.5348565578460693 196.0142059326172 0.30239057540893555 272.48211669921875 0.26662617921829224 0.8359513 0.37942731380462646 True -14 41205 30.214457511901855 0.5415389537811279 231.26048278808594 0.35342544317245483 272.3006896972656 0.2669421434402466 0.83932793 0.3488541543483734 True -15 43952 29.716843366622925 0.5381412506103516 219.24972534179688 0.25837600231170654 271.7856750488281 0.26902973651885986 0.84391814 0.3297683596611023 True -16 46699 29.684526443481445 0.5288951396942139 156.62741088867188 0.4616076946258545 271.48565673828125 0.2698993980884552 0.8469805 0.31620392203330994 True -17 49446 29.705507040023804 0.5324413776397705 202.8538818359375 0.4371139109134674 271.6699523925781 0.2689764201641083 0.8482665 0.3103320598602295 True -18 52193 29.741814613342285 0.940453290939331 226.80755615234375 0.27246910333633423 271.4681701660156 0.2701824903488159 0.84801394 0.3103106915950775 False -19 54940 29.786633729934692 0.5409128665924072 228.6707763671875 0.3046872019767761 271.65655517578125 0.2695312798023224 0.8483547 0.3097296953201294 True diff --git a/ENCSR580OAH/cherimoya.fold_3.performance.tsv b/ENCSR580OAH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0c7af7ab5c565317ab246267748657e161cb45aa..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.65655517578125 0.5061131715774536 0.2695312798023224 0.0696333646774292 0.848354697227478 0.7754393815994263 0.3097296953201294 \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_4.evaluate.json b/ENCSR580OAH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2ae962497e31694057acdbd4f23189217e3db09c..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF914WQA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_4.fit.json b/ENCSR580OAH/cherimoya.fold_4.fit.json deleted file mode 100644 index 781377e279ee24b48366abc54ce9874057af1550..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF914WQA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR580OAH/cherimoya.fold_4.log b/ENCSR580OAH/cherimoya.fold_4.log deleted file mode 100644 index f8757ab5c868018044eed45bc0998faea1f0ac0e..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 35.74329972267151 3.784391164779663 193.4808349609375 0.5970686674118042 282.5391845703125 0.1515663117170334 0.72094643 2.8941400051116943 True -1 5612 31.030943393707275 1.2097713947296143 191.8861083984375 0.6743288040161133 265.83251953125 0.21156376600265503 0.7813959 0.7587035894393921 True -2 8418 30.958723068237305 0.6132626533508301 188.9493865966797 0.3943173885345459 261.9293212890625 0.22452354431152344 0.78886414 0.4016411304473877 True -3 11224 30.888291597366333 0.6754245758056641 257.25921630859375 0.3414079546928406 259.4041748046875 0.23096485435962677 0.7954251 0.3963066041469574 True -4 14030 30.90046525001526 0.6171042919158936 223.62310791015625 0.6968653798103333 258.3771667480469 0.23394422233104706 0.79876643 0.42261362075805664 True -5 16836 31.015312671661377 0.6106204986572266 206.23861694335938 0.45116931200027466 257.2328796386719 0.23756550252437592 0.8029643 0.4390159845352173 True -6 19642 30.94328784942627 0.6164629459381104 197.19863891601562 0.5074397921562195 256.73284912109375 0.23996533453464508 0.8064204 0.4243268370628357 True -7 22448 30.928529024124146 0.6176338195800781 183.87176513671875 0.42981016635894775 255.8082275390625 0.24368628859519958 0.80748314 0.4231092631816864 True -8 25254 30.92585515975952 0.6091291904449463 188.29006958007812 0.4479358196258545 255.48367309570312 0.24452243745326996 0.8086929 0.4365955889225006 True -9 28060 30.596935987472534 0.6164443492889404 182.4172821044922 0.40771666169166565 255.45265197753906 0.24488376080989838 0.8117686 0.41501161456108093 True -10 30866 30.318443298339844 1.05224609375 225.36744689941406 0.4668812155723572 254.7078399658203 0.2473333775997162 0.81666094 0.4001215994358063 True -11 33672 30.28005886077881 0.597590446472168 230.124755859375 0.3913416862487793 253.89480590820312 0.25107070803642273 0.8177026 0.3831118047237396 True -12 36478 30.318069458007812 0.6165950298309326 196.68179321289062 0.5274947881698608 253.48211669921875 0.25220173597335815 0.8226774 0.3623116612434387 True -13 39284 30.36829376220703 0.6125392913818359 176.55491638183594 0.311714768409729 252.43263244628906 0.25643911957740784 0.8291392 0.3317684531211853 True -14 42090 30.2844717502594 0.6042270660400391 197.99363708496094 0.2527116537094116 252.55880737304688 0.2552967667579651 0.8344607 0.3043735921382904 True -15 44896 30.271883249282837 0.6227352619171143 165.671875 0.464025616645813 251.99102783203125 0.2574956715106964 0.83912337 0.2920072078704834 True -16 47702 30.284693717956543 0.6371912956237793 183.93319702148438 0.20183105766773224 252.30091857910156 0.25597089529037476 0.8438771 0.28008297085762024 True -17 50508 30.284842252731323 0.6069941520690918 181.7340087890625 0.36569708585739136 251.93255615234375 0.25812503695487976 0.8439492 0.2731480598449707 True -18 53314 30.32931923866272 0.5933363437652588 172.26515197753906 0.21068158745765686 252.22642517089844 0.2564665377140045 0.8446024 0.26878949999809265 True -19 56120 30.359676361083984 1.3299517631530762 250.70388793945312 0.16440774500370026 252.4960479736328 0.2549525797367096 0.84580815 0.2706984579563141 True diff --git a/ENCSR580OAH/cherimoya.fold_4.performance.tsv b/ENCSR580OAH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 42bb5e098808dd7e967eb7d98c62e894bad67ee5..0000000000000000000000000000000000000000 --- a/ENCSR580OAH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -252.4960479736328 0.5167660713195801 0.2549525797367096 0.06873514503240585 0.8458081483840942 0.7715166211128235 0.2706984579563141 \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_0.evaluate.json b/ENCSR582QEW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 031b39a866df3729d75091877c195e113592bd14..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF445FMP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_0.fit.json b/ENCSR582QEW/cherimoya.fold_0.fit.json deleted file mode 100644 index 42e09f7c7d0c0764c7750db7a020b33f467c206a..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF445FMP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_0.log b/ENCSR582QEW/cherimoya.fold_0.log deleted file mode 100644 index 0ec7a6751f980fce3fc441441dfc6c779c42d1db..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2242 31.591184854507446 4.702813386917114 278.17095947265625 1.3296343088150024 469.73248291015625 0.1344374716281891 0.65174824 8.170339584350586 True -1 4484 24.654728412628174 6.8302412033081055 322.0855712890625 0.9430620670318604 417.77874755859375 0.17692026495933533 0.72838026 3.5202388763427734 True -2 6726 24.654466152191162 0.5060737133026123 431.38299560546875 0.8207551836967468 402.6225280761719 0.18785089254379272 0.77118266 1.9364289045333862 True -3 8968 24.648034811019897 0.45460009574890137 279.55596923828125 0.7324129343032837 394.95318603515625 0.1932617872953415 0.78735673 1.3601871728897095 True -4 11210 24.63017725944519 0.4528360366821289 358.3608703613281 0.7012140154838562 390.0552673339844 0.19708676636219025 0.79478943 1.0102884769439697 True -5 13452 24.63376522064209 0.4493696689605713 404.7938232421875 1.3388519287109375 387.9871826171875 0.1983409970998764 0.8067848 0.8863076567649841 True -6 15694 24.654708862304688 0.4982888698577881 296.6907653808594 1.0404964685440063 382.9689025878906 0.20408643782138824 0.8128447 0.7782527208328247 True -7 17936 24.85040545463562 30.233436822891235 193.8233184814453 0.790019154548645 381.1051940917969 0.2066326141357422 0.81710327 0.7859110236167908 True -8 20178 25.102880239486694 0.46497654914855957 236.5724639892578 0.410209596157074 378.6633605957031 0.2079962193965912 0.8266637 0.725249171257019 True -9 22420 24.622567415237427 0.4606635570526123 284.3599853515625 0.5026720762252808 377.2782287597656 0.20952144265174866 0.8336226 0.6810411810874939 True -10 24662 24.6262309551239 0.4558830261230469 308.4309387207031 0.6225823163986206 375.25372314453125 0.21179576218128204 0.83945554 0.6215789318084717 True -11 26904 24.74495840072632 1.2508625984191895 249.13894653320312 0.37128210067749023 372.4263610839844 0.21405193209648132 0.84400004 0.5777220129966736 True -12 29146 24.663887977600098 0.6681890487670898 282.2778625488281 0.4613334536552429 372.6228942871094 0.21404902637004852 0.8513489 0.5389530658721924 True -13 31388 24.640822172164917 1.7805349826812744 291.97412109375 0.45681554079055786 370.6388244628906 0.21504805982112885 0.8556916 0.5031556487083435 True -14 33630 24.695346117019653 0.45577406883239746 254.9501495361328 0.8340343236923218 369.8627014160156 0.2161163091659546 0.8593037 0.48067426681518555 True -15 35872 26.077441215515137 24.814154148101807 408.45574951171875 0.5440713763237 368.1623229980469 0.21792611479759216 0.8642648 0.4592911899089813 True -16 38114 24.77232789993286 0.4527754783630371 267.585205078125 0.33235275745391846 367.618408203125 0.21809418499469757 0.8669988 0.44497302174568176 True -17 40356 24.109582901000977 0.4488048553466797 304.6076354980469 0.2927202880382538 368.468994140625 0.21647757291793823 0.8674613 0.44578346610069275 True -18 42598 24.163206100463867 0.44768381118774414 292.3997497558594 0.3105791509151459 368.5926208496094 0.21704576909542084 0.8670628 0.4480689465999603 False -19 44840 24.200104475021362 24.64040970802307 291.5509948730469 0.2589796185493469 368.0087585449219 0.21811126172542572 0.8642422 0.4530619978904724 False diff --git a/ENCSR582QEW/cherimoya.fold_0.performance.tsv b/ENCSR582QEW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1a64acbbe3f9ad6595dede9f3553d33b47775e52..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -368.468994140625 0.5250113606452942 0.21647754311561584 0.08266254514455795 0.8674613237380981 0.7799709439277649 0.44578346610069275 \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_1.evaluate.json b/ENCSR582QEW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a6714efe34f1f1b6004e1e9e98f98074e4506452..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF445FMP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_1.fit.json b/ENCSR582QEW/cherimoya.fold_1.fit.json deleted file mode 100644 index fb5454c8d82adc46f7807c9bbd5f6791f5e9d7f1..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF445FMP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_1.log b/ENCSR582QEW/cherimoya.fold_1.log deleted file mode 100644 index 2d1233c1503118fafbbb454c54d1e1732999e51f..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2193 28.684184312820435 4.1326024532318115 320.55694580078125 0.6443002223968506 607.2703247070312 0.1532377302646637 0.6119053 9.561202049255371 True -1 4386 24.21217370033264 0.6166636943817139 325.6789245605469 0.9978715777397156 537.2036743164062 0.20564678311347961 0.7249762 4.595396518707275 True -2 6579 24.13755989074707 0.5911362171173096 346.0823974609375 0.9825912714004517 516.6231079101562 0.21610769629478455 0.75731665 3.1939198970794678 True -3 8772 24.08282732963562 0.5839262008666992 333.64361572265625 0.7789440155029297 504.189697265625 0.225320503115654 0.7663419 1.9443671703338623 True -4 10965 24.072184562683105 0.578380823135376 286.6265869140625 0.8557659387588501 496.08551025390625 0.22866782546043396 0.77878684 1.689286470413208 True -5 13158 24.177430868148804 0.5996849536895752 346.03765869140625 0.6424452662467957 490.053955078125 0.23245160281658173 0.79597455 1.3689115047454834 True -6 15351 24.154553413391113 1.1666922569274902 343.57293701171875 0.6905661821365356 484.02886962890625 0.2386157363653183 0.8048186 1.299150824546814 True -7 17544 24.05380368232727 0.5863485336303711 213.398193359375 0.5724313855171204 480.6274108886719 0.24178504943847656 0.8091995 1.1404746770858765 True -8 19737 24.082971334457397 3.8389503955841064 373.9632263183594 0.6899268627166748 477.52667236328125 0.24325406551361084 0.81856155 1.039374589920044 True -9 21930 24.084646463394165 0.6147918701171875 282.8105163574219 0.5747213363647461 474.6082458496094 0.24592037498950958 0.8275431 0.9419882893562317 True -10 24123 24.11927103996277 0.5919344425201416 330.8785400390625 0.8052017688751221 469.6429443359375 0.2507334053516388 0.83356965 0.8650417923927307 True -11 26316 24.14706039428711 0.5979247093200684 287.6605224609375 0.42387473583221436 468.4964904785156 0.25058308243751526 0.84701693 0.7759292125701904 True -12 28509 24.200544595718384 1.089827060699463 283.78424072265625 0.7828724384307861 467.2510681152344 0.2516007125377655 0.8490587 0.7665441632270813 True -13 30702 24.163328647613525 0.6082487106323242 223.22262573242188 0.4852595329284668 463.57806396484375 0.25459131598472595 0.85553616 0.6961329579353333 True -14 32895 25.499074935913086 20.208790063858032 277.66143798828125 0.5956303477287292 464.97662353515625 0.252748042345047 0.85996825 0.6596198678016663 True -15 35088 24.16928744316101 0.5988669395446777 265.9669189453125 0.7270982265472412 460.832763671875 0.2554636299610138 0.8655344 0.6082814335823059 True -16 37281 24.82659411430359 21.35393214225769 294.7773742675781 0.4268175959587097 460.7863464355469 0.2554350793361664 0.8661417 0.5932303667068481 True -17 39474 24.109124422073364 2.1010992527008057 320.88873291015625 0.3806450366973877 460.5142822265625 0.255647212266922 0.86852175 0.5721070170402527 True -18 41667 24.56832790374756 0.670518159866333 284.4228210449219 0.2683582305908203 461.74188232421875 0.25413814187049866 0.8665569 0.5693316459655762 False -19 43860 24.18538761138916 45.65089702606201 280.9415283203125 0.43242955207824707 463.24945068359375 0.25232478976249695 0.86621755 0.5719006061553955 False diff --git a/ENCSR582QEW/cherimoya.fold_1.performance.tsv b/ENCSR582QEW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 99f35dd27713e5ca7e910e7c30d71d461a9ba96a..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -460.5142822265625 0.49443554878234863 0.255647212266922 0.1075524389743805 0.8685217499732971 0.8280523419380188 0.5721070170402527 \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_2.evaluate.json b/ENCSR582QEW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 22428d0add768cb51d6958948e6ffb61ea34aff0..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF445FMP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_2.fit.json b/ENCSR582QEW/cherimoya.fold_2.fit.json deleted file mode 100644 index 5959264eb9fbb62ddbc0303d32cd0e3b1b4eea26..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF445FMP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_2.log b/ENCSR582QEW/cherimoya.fold_2.log deleted file mode 100644 index d9f655a3a67479348c0959c5243b7aacf458fed8..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2338 30.371984243392944 3.4179434776306152 488.50787353515625 0.8681631684303284 494.1826477050781 0.13840392231941223 0.6095819 7.007316589355469 True -1 4676 26.242345571517944 0.4889190196990967 356.82659912109375 0.7897590398788452 441.55609130859375 0.18092450499534607 0.71455073 3.450228214263916 True -2 7014 25.82111644744873 24.644235134124756 291.79705810546875 0.9179674386978149 419.52703857421875 0.19369778037071228 0.74921 2.6101624965667725 True -3 9352 25.523757696151733 0.4932444095611572 389.8310546875 0.7148768305778503 409.7288513183594 0.20012472569942474 0.7684313 1.4664552211761475 True -4 11690 25.181300163269043 29.285873651504517 292.0422668457031 0.5362825393676758 404.8359375 0.2049875408411026 0.7746592 1.3141791820526123 True -5 14028 26.67691707611084 0.49556994438171387 357.67401123046875 0.670458972454071 403.8298645019531 0.20379924774169922 0.7849027 1.2161476612091064 True -6 16366 25.71329402923584 28.102112293243408 308.83428955078125 0.6005311608314514 400.7650146484375 0.20665627717971802 0.788875 1.1157811880111694 True -7 18704 25.21410894393921 0.4716005325317383 301.6986083984375 0.939563512802124 397.5850524902344 0.21035026013851166 0.7975075 1.0223877429962158 True -8 21042 25.188089847564697 0.47327756881713867 434.75341796875 0.6044691801071167 394.51776123046875 0.2117217779159546 0.8108088 0.8670523762702942 True -9 23380 25.352172374725342 1.9838063716888428 298.80859375 0.5162220001220703 390.7698974609375 0.21595259010791779 0.8171939 0.8253085017204285 True -10 25718 25.19670343399048 0.4617152214050293 341.4650573730469 0.7304994463920593 388.5906677246094 0.21774263679981232 0.82427424 0.7369987964630127 True -11 28056 25.193795442581177 0.468799352645874 263.81695556640625 0.5318885445594788 385.9580078125 0.22007262706756592 0.8325053 0.6740737557411194 True -12 30394 25.20116090774536 0.47148585319519043 320.77288818359375 0.47769051790237427 385.00048828125 0.2202938199043274 0.8390913 0.6123515367507935 True -13 32732 25.227105617523193 24.798174142837524 248.86166381835938 0.6474689245223999 382.05523681640625 0.22287505865097046 0.84543097 0.5683207511901855 True -14 35070 26.54473638534546 27.35813546180725 320.10687255859375 0.33519604802131653 381.2980041503906 0.22366957366466522 0.85088074 0.5344604253768921 True -15 37408 25.57498574256897 0.47978782653808594 304.01080322265625 0.6179633736610413 382.15863037109375 0.2224419265985489 0.8544487 0.5136127471923828 True -16 39746 25.252828121185303 0.4640316963195801 337.1651611328125 0.3035767674446106 381.92193603515625 0.2222161442041397 0.85762745 0.49594882130622864 True -17 42084 25.162862300872803 0.4656393527984619 274.7579040527344 0.3386414349079132 382.30645751953125 0.22151385247707367 0.85702896 0.4938010275363922 False -18 44422 25.166194200515747 0.464907169342041 221.4961700439453 0.2517549395561218 382.1919250488281 0.22201348841190338 0.8551912 0.49880334734916687 False -19 46760 25.13503909111023 0.461322546005249 263.5267333984375 0.4082963168621063 382.07489013671875 0.22246378660202026 0.8526898 0.5009979605674744 False diff --git a/ENCSR582QEW/cherimoya.fold_2.performance.tsv b/ENCSR582QEW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c5ae71109d54b99a54cc9238084ada54bfa408da..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -381.92193603515625 0.519554615020752 0.2222161591053009 0.08221086859703064 0.8576274514198303 0.787270188331604 0.49594882130622864 \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_3.evaluate.json b/ENCSR582QEW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2397bdd86c1cc8fc60920e8401e0c4bcdce87164..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF445FMP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_3.fit.json b/ENCSR582QEW/cherimoya.fold_3.fit.json deleted file mode 100644 index 03cf2dd74c9f3299e1c8f962d1488fb2374441de..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF445FMP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_3.log b/ENCSR582QEW/cherimoya.fold_3.log deleted file mode 100644 index 7e2b6db5807b08fb2313586fad2a4a88e1c15e50..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2232 28.941911935806274 3.2769765853881836 335.85968017578125 0.4372347295284271 515.498291015625 0.1485442966222763 0.58632034 8.54941177368164 True -1 4464 24.570499181747437 0.43837428092956543 316.35369873046875 1.0813733339309692 462.31634521484375 0.19571587443351746 0.6633324 3.928514003753662 True -2 6696 24.532056093215942 0.41524744033813477 295.36334228515625 0.8978909254074097 447.62042236328125 0.20114369690418243 0.71587896 2.8175759315490723 True -3 8928 24.572242259979248 21.26923131942749 410.35693359375 0.8127478361129761 435.11181640625 0.2104869931936264 0.75210416 1.5853160619735718 True -4 11160 25.380107164382935 14.394238471984863 338.94830322265625 0.77519690990448 431.3379821777344 0.2110995054244995 0.7640429 1.2527549266815186 True -5 13392 24.157878875732422 0.4182114601135254 283.2290344238281 0.5368559956550598 425.62353515625 0.21632185578346252 0.7748054 1.2115377187728882 True -6 15624 24.03569531440735 0.4157576560974121 247.75979614257812 0.5211164951324463 422.0356140136719 0.22014190256595612 0.7862666 1.117396593093872 True -7 17856 23.93691372871399 0.414414644241333 281.92755126953125 0.4250333309173584 420.3089294433594 0.22063903510570526 0.7936213 1.0145004987716675 True -8 20088 23.994500637054443 0.4210686683654785 297.9912109375 0.721034824848175 416.9857482910156 0.2248625010251999 0.80045986 1.0207624435424805 True -9 22320 23.96104121208191 0.41995811462402344 259.0976867675781 0.4903005063533783 415.3431701660156 0.22613750398159027 0.8082591 0.8988659977912903 True -10 24552 24.034318447113037 0.4224386215209961 282.96441650390625 0.4915708005428314 413.5711669921875 0.22853882610797882 0.80950755 0.8673688769340515 True -11 26784 24.22330379486084 0.4225895404815674 307.9908447265625 0.8792122602462769 412.7786865234375 0.22976449131965637 0.8156903 0.8210040926933289 True -12 29016 24.07923913002014 0.41393566131591797 330.1643371582031 0.4323837161064148 408.8518371582031 0.2333601862192154 0.8233819 0.760385274887085 True -13 31248 24.051239728927612 0.41362953186035156 279.6070556640625 0.48119810223579407 407.7937927246094 0.2334320843219757 0.8282709 0.7175365090370178 True -14 33480 24.13324522972107 0.41943359375 286.5651550292969 0.24843424558639526 406.5859680175781 0.23458042740821838 0.83220655 0.6910464763641357 True -15 35712 24.13072395324707 0.420947790145874 294.1371765136719 0.6638556718826294 405.1849060058594 0.23604725301265717 0.83871484 0.6446274518966675 True -16 37944 24.01859140396118 0.41362714767456055 384.14544677734375 0.26780667901039124 404.62744140625 0.23531579971313477 0.8423704 0.6110164523124695 True -17 40176 24.06565546989441 0.5764973163604736 286.4251708984375 0.575947642326355 404.4754638671875 0.23581157624721527 0.8438953 0.6065797805786133 True -18 42408 24.102609872817993 0.4200935363769531 304.5617980957031 0.5096249580383301 404.57305908203125 0.23536138236522675 0.84288186 0.5981670618057251 False -19 44640 24.146824836730957 0.42089319229125977 300.36114501953125 0.4453941285610199 405.202392578125 0.23473979532718658 0.8439156 0.5988415479660034 True diff --git a/ENCSR582QEW/cherimoya.fold_3.performance.tsv b/ENCSR582QEW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9376020bb54dd51a8488fa4640e08030c3f9d638..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -405.202392578125 0.5104646682739258 0.23473981022834778 0.09271114319562912 0.843915581703186 0.7844281792640686 0.5988415479660034 \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_4.evaluate.json b/ENCSR582QEW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a914721195e3913492bad1c577f00444aee0bbff..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF445FMP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_4.fit.json b/ENCSR582QEW/cherimoya.fold_4.fit.json deleted file mode 100644 index 3a9717218ae3fa36dfbf9ce0808c4c4bcb11e8ad..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF445FMP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR582QEW/cherimoya.fold_4.log b/ENCSR582QEW/cherimoya.fold_4.log deleted file mode 100644 index 657fd3bbc716cd2efa66f45db682ba052199778e..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2202 28.970998525619507 3.4591219425201416 422.905029296875 0.8374329209327698 427.770263671875 0.1326911300420761 0.5954808 7.357090473175049 True -1 4404 23.92215895652771 0.461179256439209 318.92681884765625 0.7841496467590332 382.6733703613281 0.17001965641975403 0.72039014 3.133338451385498 True -2 6606 24.260552644729614 0.45354771614074707 316.77606201171875 0.7946857810020447 372.2852783203125 0.1790599524974823 0.737474 2.095668315887451 True -3 8808 24.244613885879517 1.6010019779205322 279.503173828125 0.5099754333496094 367.5576477050781 0.18335217237472534 0.7406294 1.282468318939209 True -4 11010 24.181119441986084 0.45104026794433594 287.9791259765625 0.5109772086143494 361.233154296875 0.18836581707000732 0.7559447 1.0936768054962158 True -5 13212 24.161094903945923 0.4468693733215332 234.59576416015625 0.6169094443321228 356.7475891113281 0.1918504238128662 0.7647229 1.0056005716323853 True -6 15414 24.312318086624146 17.37066650390625 343.4521179199219 0.6671707630157471 354.0526123046875 0.19557641446590424 0.7717894 0.9877405166625977 True -7 17616 25.277278900146484 6.638534307479858 318.3282470703125 0.8208174705505371 351.9286804199219 0.19686050713062286 0.7839991 0.9023523330688477 True -8 19818 24.16975450515747 0.4535024166107178 314.9068908691406 0.5068789720535278 350.3023376464844 0.19821572303771973 0.7920423 0.8317753672599792 True -9 22020 24.172416925430298 1.9761841297149658 277.2606201171875 0.7130034565925598 347.8317565917969 0.2010997235774994 0.803095 0.7404477000236511 True -10 24222 24.200239419937134 0.4456303119659424 307.91656494140625 0.790802001953125 347.2768859863281 0.2015748769044876 0.8097297 0.6953444480895996 True -11 26424 24.17494225502014 0.44193577766418457 215.78726196289062 0.33566194772720337 346.2063903808594 0.20283059775829315 0.8154499 0.665618896484375 True -12 28626 24.18366003036499 1.0061352252960205 313.00604248046875 0.45416566729545593 344.83544921875 0.20380769670009613 0.82223 0.6066434979438782 True -13 30828 24.19440770149231 0.44927358627319336 345.76220703125 0.48320233821868896 343.0377197265625 0.20532390475273132 0.82786435 0.5712592601776123 True -14 33030 24.151044368743896 0.4569120407104492 252.51544189453125 0.39947250485420227 340.8479309082031 0.2072676569223404 0.8368564 0.5226612687110901 True -15 35232 24.167136430740356 0.446882963180542 360.39544677734375 0.7875592708587646 340.6416320800781 0.20743542909622192 0.83999085 0.5051986575126648 True -16 37434 23.84309673309326 0.43689608573913574 306.0735168457031 0.3169780373573303 340.2826843261719 0.20835502445697784 0.8446334 0.4854849576950073 True -17 39636 23.67503261566162 0.4363856315612793 283.2823486328125 0.5033762454986572 340.3016052246094 0.20802012085914612 0.84494 0.47811946272850037 True -18 41838 23.671902656555176 0.4656980037689209 289.22015380859375 0.5628092885017395 341.0246887207031 0.20734338462352753 0.8444498 0.47808024287223816 False -19 44040 23.721017360687256 0.44556713104248047 417.69573974609375 0.36924606561660767 341.1835632324219 0.20659103989601135 0.8451877 0.47791898250579834 True diff --git a/ENCSR582QEW/cherimoya.fold_4.performance.tsv b/ENCSR582QEW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4f6853dde368cfde732c73533d6e008b966204e1..0000000000000000000000000000000000000000 --- a/ENCSR582QEW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -341.1835632324219 0.5327256917953491 0.20659102499485016 0.07709398120641708 0.8451877236366272 0.761085569858551 0.47791898250579834 \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_0.evaluate.json b/ENCSR584AXZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 83a8a853dd88ab230136220bb41fea0dfc3e7de9..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875BVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_0.fit.json b/ENCSR584AXZ/cherimoya.fold_0.fit.json deleted file mode 100644 index de984f635f55e399d32221cb0bfcde8ba9897c33..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF875BVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_0.log b/ENCSR584AXZ/cherimoya.fold_0.log deleted file mode 100644 index 3ad877d99218d1f3eddc862e6429295c061e71d5..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1145 17.31924295425415 3.1729037761688232 227.04840087890625 0.19646549224853516 332.0097961425781 0.4017024338245392 0.70325553 15.498734474182129 True -1 2290 12.689643383026123 0.24694132804870605 224.93194580078125 0.22185666859149933 278.4576721191406 0.4845789074897766 0.75725085 3.8217196464538574 True -2 3435 12.704280614852905 0.2238302230834961 234.57858276367188 0.19450193643569946 265.4683837890625 0.5156452655792236 0.7820929 0.8589632511138916 True -3 4580 12.505298376083374 0.22588205337524414 239.7659149169922 0.21482589840888977 259.141357421875 0.5303933620452881 0.7988342 0.421591579914093 True -4 5725 12.48799991607666 0.22861170768737793 228.88079833984375 0.1639411747455597 254.6016082763672 0.5419656038284302 0.81745857 0.22928081452846527 True -5 6870 12.477041959762573 0.9493346214294434 228.37033081054688 0.15038952231407166 252.99488830566406 0.5460848808288574 0.82595426 0.19187968969345093 True -6 8015 12.497534990310669 0.22391939163208008 217.8357391357422 0.1672210395336151 252.6333770751953 0.546954870223999 0.828215 0.17877131700515747 True -7 9160 12.486735105514526 0.22998332977294922 219.81436157226562 0.25870057940483093 251.91578674316406 0.5496466159820557 0.8369052 0.16019964218139648 True -8 10305 12.477737665176392 0.22292685508728027 228.5932159423828 0.24102307856082916 252.21823120117188 0.5485228896141052 0.83362657 0.1825045496225357 False -9 11450 12.454800128936768 0.2316455841064453 228.33831787109375 0.21254286170005798 251.4411163330078 0.5514199733734131 0.8445734 0.15054580569267273 True -10 12595 12.448541641235352 0.47801804542541504 215.65443420410156 0.12324701249599457 250.94065856933594 0.5531672835350037 0.85124016 0.13504019379615784 True -11 13740 12.456799507141113 0.22902417182922363 202.4608917236328 0.16435357928276062 250.59767150878906 0.5541757345199585 0.8560447 0.12658704817295074 True -12 14885 12.46342158317566 0.23380637168884277 204.43478393554688 0.13704344630241394 250.25953674316406 0.5552269220352173 0.8576657 0.12247104942798615 True -13 16030 12.480371236801147 0.23948192596435547 246.11305236816406 0.1604549139738083 250.11428833007812 0.5557208061218262 0.85950124 0.12070406973361969 True -14 17175 12.459851026535034 0.2346646785736084 221.91937255859375 0.11087408661842346 250.108154296875 0.5556634068489075 0.8613851 0.11987485736608505 True -15 18320 12.453519821166992 0.2313220500946045 223.78323364257812 0.13342779874801636 250.27862548828125 0.5549545884132385 0.86157525 0.11959780007600784 True -16 19465 12.462898254394531 0.22664260864257812 215.7135009765625 0.1127764880657196 250.51304626464844 0.5540810227394104 0.8615674 0.12241289764642715 False -17 20610 12.45537257194519 0.22079062461853027 206.15139770507812 0.09690634906291962 250.89205932617188 0.5527305603027344 0.8613123 0.1279771775007248 False -18 21755 12.4501211643219 0.3646061420440674 211.8897247314453 0.10346297919750214 251.24099731445312 0.5514621138572693 0.85717183 0.1313818097114563 False -19 22900 12.478729248046875 0.2326037883758545 221.0020751953125 0.0425616055727005 251.46046447753906 0.5504195690155029 0.8567741 0.1343754231929779 False diff --git a/ENCSR584AXZ/cherimoya.fold_0.performance.tsv b/ENCSR584AXZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 76b38a00c04c6a25cce12127e93f9f8f4966a234..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.27862548828125 0.3508854806423187 0.554954469203949 0.17219947278499603 0.8615752458572388 0.8462622165679932 0.11959780007600784 \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_1.evaluate.json b/ENCSR584AXZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 754f71778c22b86085a02427fe260dff579baa2a..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875BVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_1.fit.json b/ENCSR584AXZ/cherimoya.fold_1.fit.json deleted file mode 100644 index aa94464669dee8ca28dddc071272643af4ba6be1..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF875BVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_1.log b/ENCSR584AXZ/cherimoya.fold_1.log deleted file mode 100644 index 58a2b498f1780e73f3b9d1ab0c2d0b69716264b3..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1129 17.084386110305786 14.134145975112915 228.65530395507812 0.29400286078453064 360.0391540527344 0.414918452501297 0.64070153 16.692808151245117 True -1 2258 12.619727373123169 0.32702064514160156 224.06130981445312 0.20640915632247925 301.000732421875 0.4991632401943207 0.70966727 4.207676887512207 True -2 3387 12.55574655532837 0.2998199462890625 205.17764282226562 0.2683820128440857 287.3660888671875 0.5308178067207336 0.7443825 0.9800567030906677 True -3 4516 12.532053232192993 0.29912281036376953 218.85401916503906 0.1783083975315094 276.6560363769531 0.5550158023834229 0.7727951 0.3003089427947998 True -4 5645 12.527003049850464 0.2982480525970459 249.114990234375 0.12357362359762192 273.1165466308594 0.5637202858924866 0.7896394 0.19434930384159088 True -5 6774 12.537553071975708 1.2781078815460205 211.9075164794922 0.13549451529979706 271.8555603027344 0.5670502185821533 0.7987698 0.18448559939861298 True -6 7903 12.544701099395752 0.30405735969543457 227.59750366210938 0.27773967385292053 271.1739807128906 0.5690277814865112 0.8054209 0.18507994711399078 True -7 9032 12.52458119392395 0.3065154552459717 228.3939971923828 0.18644937872886658 271.0015869140625 0.5700722336769104 0.8086993 0.1928432583808899 True -8 10161 12.516783952713013 0.2988135814666748 215.96041870117188 0.18003936111927032 270.0736999511719 0.5727593898773193 0.82168114 0.16254420578479767 True -9 11290 12.594301223754883 0.3101222515106201 198.06488037109375 0.0984702929854393 269.70574951171875 0.5741578936576843 0.8263983 0.15572413802146912 True -10 12419 12.54161262512207 0.3098416328430176 242.82254028320312 0.1727616786956787 269.1412353515625 0.5757890343666077 0.8347012 0.14514972269535065 True -11 13548 12.55512809753418 0.301837682723999 215.58148193359375 0.11090414226055145 268.67144775390625 0.5773327350616455 0.83963186 0.13918960094451904 True -12 14677 12.520366668701172 0.30081677436828613 232.77940368652344 0.17673254013061523 268.378662109375 0.5783369541168213 0.8460142 0.13503317534923553 True -13 15806 12.531749963760376 0.30036091804504395 196.8189239501953 0.11504900455474854 268.12274169921875 0.5791224241256714 0.8487604 0.13191847503185272 True -14 16935 12.520037651062012 0.30098700523376465 199.57427978515625 0.08027654886245728 268.0679626464844 0.5791969895362854 0.85278624 0.12873411178588867 True -15 18064 12.52367377281189 8.98254108428955 223.26803588867188 0.0967477560043335 268.2152404785156 0.5785129070281982 0.85511804 0.12839868664741516 True -16 19193 12.539393663406372 0.30407285690307617 199.54388427734375 0.10508599877357483 268.52880859375 0.5771275162696838 0.85304815 0.1299111396074295 False -17 20322 12.536903142929077 0.3010549545288086 197.13308715820312 0.11539936065673828 268.9844665527344 0.5752958059310913 0.8523831 0.13177424669265747 False -18 21451 12.577824592590332 0.2994983196258545 182.1475372314453 0.09340084344148636 269.421142578125 0.5734865665435791 0.8506047 0.13392490148544312 False -19 22580 12.525433540344238 0.30820131301879883 214.00326538085938 0.0822305679321289 269.7695617675781 0.5723070502281189 0.8499783 0.13501819968223572 False diff --git a/ENCSR584AXZ/cherimoya.fold_1.performance.tsv b/ENCSR584AXZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ed1f249ba65c1836de037ddbfd7d7c98b5a55a87..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -268.2152404785156 0.3340272903442383 0.5785129070281982 0.18577736616134644 0.8551180362701416 0.8520886301994324 0.12839868664741516 \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_2.evaluate.json b/ENCSR584AXZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index fa80207a54a0ddcd3c7d461bb773b926b7f476d7..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875BVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_2.fit.json b/ENCSR584AXZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 325603e9c0ea80d3aa5116c7d319b8cb691b4842..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF875BVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_2.log b/ENCSR584AXZ/cherimoya.fold_2.log deleted file mode 100644 index 29fc659c598eed322b94354aa0575e4e38bb61ef..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1194 17.903460025787354 11.336183547973633 208.74896240234375 0.23462386429309845 341.03997802734375 0.4091544449329376 0.6485078 15.785635948181152 True -1 2388 13.273954391479492 0.2544081211090088 220.2236328125 0.21791061758995056 286.63250732421875 0.4910615086555481 0.71919537 3.576594591140747 True -2 3582 13.2512788772583 0.2434077262878418 233.43702697753906 0.22535279393196106 273.13360595703125 0.525576651096344 0.7678288 1.0279613733291626 True -3 4776 13.107040405273438 0.24409961700439453 228.48101806640625 0.1726793646812439 265.6427917480469 0.5429621338844299 0.79424673 0.44408318400382996 True -4 5970 12.985109806060791 0.22995352745056152 211.83587646484375 0.18674428761005402 262.6739807128906 0.5489823818206787 0.80353886 0.22224149107933044 True -5 7164 13.011767387390137 0.25787854194641113 233.476318359375 0.19148385524749756 261.5016174316406 0.5514008402824402 0.80574155 0.1815667450428009 True -6 8358 13.013898372650146 0.23006939888000488 191.4972686767578 0.1718273162841797 260.5558166503906 0.5540659427642822 0.8155959 0.17621517181396484 True -7 9552 12.994247913360596 0.24216604232788086 210.92335510253906 0.1499919891357422 259.962158203125 0.5562164783477783 0.82233095 0.17126679420471191 True -8 10746 12.98435640335083 0.23084616661071777 212.08078002929688 0.12687361240386963 259.7554931640625 0.5572781562805176 0.81813943 0.19025665521621704 False -9 11940 12.998491048812866 1.334564208984375 219.26519775390625 0.12617997825145721 259.7656555175781 0.5573157072067261 0.8194989 0.1993969976902008 False -10 13134 13.017182350158691 0.2358860969543457 220.1931610107422 0.1736045777797699 258.82916259765625 0.5599117875099182 0.8314011 0.1767393946647644 True -11 14328 12.989418029785156 0.23632311820983887 221.1269989013672 0.13709783554077148 258.2609558105469 0.5616461038589478 0.83728564 0.16186389327049255 True -12 15522 13.006196022033691 0.2366342544555664 227.23692321777344 0.12019497156143188 257.9034729003906 0.5624423623085022 0.84307796 0.1516897827386856 True -13 16716 13.033970594406128 0.23397207260131836 218.5672149658203 0.1434122771024704 257.6011047363281 0.5631805658340454 0.8464016 0.14706026017665863 True -14 17910 12.982775688171387 0.23064589500427246 224.50880432128906 0.11861170828342438 257.532470703125 0.5633583664894104 0.8476178 0.1425604522228241 True -15 19104 13.000613451004028 0.24466967582702637 213.50169372558594 0.1154872328042984 257.5041809082031 0.5630285739898682 0.85008985 0.14125075936317444 True -16 20298 12.98180890083313 0.23670458793640137 215.3853759765625 0.08114410936832428 257.7425842285156 0.562035083770752 0.84803283 0.1417272388935089 False -17 21492 13.00897741317749 0.23618793487548828 218.71038818359375 0.08325575292110443 258.1513977050781 0.5606314539909363 0.8479373 0.14447449147701263 False -18 22686 12.998979806900024 0.2763059139251709 210.92709350585938 0.07083151489496231 258.4756774902344 0.5592528581619263 0.84639764 0.14595361053943634 False -19 23880 12.995789766311646 0.23916029930114746 216.69564819335938 0.0596175454556942 258.71807861328125 0.5583451986312866 0.84366417 0.14700163900852203 False diff --git a/ENCSR584AXZ/cherimoya.fold_2.performance.tsv b/ENCSR584AXZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 652bc3865847f7b02f8b7eb2e8d53c1f27700a0b..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -257.5041809082031 0.34422942996025085 0.5630285739898682 0.17960712313652039 0.8500898480415344 0.8382773995399475 0.14125075936317444 \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_3.evaluate.json b/ENCSR584AXZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8be3f5224489f6f3b48514d3afaac90e2916a526..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875BVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_3.fit.json b/ENCSR584AXZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 0b5ec73f253e1e467d155445c83b93d388180d5a..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF875BVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_3.log b/ENCSR584AXZ/cherimoya.fold_3.log deleted file mode 100644 index 7cdb2a8d094cb9ce4616b30e3cb2605c84cbfd53..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1169 17.854829788208008 3.3209633827209473 212.1619873046875 0.22279298305511475 331.9483337402344 0.4034706652164459 0.6722723 15.279000282287598 True -1 2338 12.984037399291992 0.23485565185546875 230.98570251464844 0.2509537935256958 278.12249755859375 0.48686298727989197 0.73570085 3.325526237487793 True -2 3507 12.959510326385498 0.48587965965270996 222.71463012695312 0.1482427418231964 264.8291931152344 0.5202012658119202 0.7756077 0.6669237613677979 True -3 4676 12.96970248222351 1.2420976161956787 211.76885986328125 0.21634292602539062 256.69427490234375 0.5399113893508911 0.80420065 0.25311988592147827 True -4 5845 12.989798069000244 0.2430555820465088 207.73739624023438 0.13634932041168213 254.26719665527344 0.5453581213951111 0.81540537 0.2566531300544739 True -5 7014 12.994797706604004 0.44611072540283203 215.03793334960938 0.22148698568344116 253.06326293945312 0.5489856600761414 0.8225998 0.19471250474452972 True -6 8183 12.986621141433716 0.22477149963378906 216.09327697753906 0.19296401739120483 252.45245361328125 0.5504589080810547 0.8275655 0.16520170867443085 True -7 9352 12.970329523086548 0.2281322479248047 225.59164428710938 0.5674957036972046 252.39036560058594 0.5512788891792297 0.83043253 0.16573725640773773 True -8 10521 12.984981298446655 0.3203556537628174 227.20535278320312 0.1330849826335907 251.92942810058594 0.5526041388511658 0.83402485 0.164751797914505 True -9 11690 12.97202754020691 0.22901368141174316 214.00697326660156 0.10512220859527588 251.47885131835938 0.5537852048873901 0.8385832 0.15649491548538208 True -10 12859 12.997782707214355 0.22957205772399902 211.81622314453125 0.0940212607383728 250.99603271484375 0.5552211403846741 0.84056133 0.15051120519638062 True -11 14028 13.003557205200195 0.2283027172088623 210.5347442626953 0.1447502076625824 250.61769104003906 0.5563614964485168 0.84358805 0.1457129865884781 True -12 15197 13.015536069869995 0.23097825050354004 229.55862426757812 0.15620124340057373 250.2580108642578 0.5575454831123352 0.8445496 0.14117126166820526 True -13 16366 12.985050916671753 0.2270214557647705 234.390380859375 0.11121930181980133 250.03466796875 0.558357298374176 0.84744895 0.1385861486196518 True -14 17535 12.98703932762146 0.22499561309814453 210.87673950195312 0.09875280410051346 249.9720001220703 0.5586681962013245 0.8472494 0.13814754784107208 False -15 18704 12.952948808670044 0.22387313842773438 206.5344696044922 0.12557458877563477 250.1045379638672 0.558188259601593 0.8474001 0.13829582929611206 False -16 19873 12.970672607421875 0.23508787155151367 185.69009399414062 0.10027216374874115 250.28135681152344 0.55730140209198 0.8475911 0.14050571620464325 True -17 21042 12.99506688117981 0.2252655029296875 200.00558471679688 0.12018609046936035 250.59925842285156 0.5559857487678528 0.8447288 0.14367733895778656 False -18 22211 12.985846042633057 0.23131012916564941 216.13656616210938 0.07736474275588989 250.92666625976562 0.5546222925186157 0.8424133 0.1473763883113861 False -19 23380 12.992512464523315 0.22958636283874512 184.14730834960938 0.08497078716754913 251.1605224609375 0.5537142753601074 0.8400051 0.14971989393234253 False diff --git a/ENCSR584AXZ/cherimoya.fold_3.performance.tsv b/ENCSR584AXZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 80fdc3f197aa5dfb0edf7fcd8d480604b9eb1abb..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.28135681152344 0.3490176796913147 0.55730140209198 0.17499272525310516 0.8475911021232605 0.8341488242149353 0.14050571620464325 \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_4.evaluate.json b/ENCSR584AXZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6b4bb29bda895257651387453d0f48c3812573be..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875BVK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_4.fit.json b/ENCSR584AXZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 0151764e075f278b212a39586be31b87acce311f..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF875BVK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR584AXZ/cherimoya.fold_4.log b/ENCSR584AXZ/cherimoya.fold_4.log deleted file mode 100644 index 94e115e3a72475c8e10c8a62c5cca519bb7b04bd..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1153 17.428571939468384 3.2898058891296387 233.8083038330078 0.29478710889816284 326.8368835449219 0.40127646923065186 0.7026791 15.328842163085938 True -1 2306 12.792747974395752 0.2411806583404541 225.00987243652344 0.1678352952003479 273.9436950683594 0.4844035506248474 0.75745946 3.579968214035034 True -2 3459 12.805925369262695 0.23579978942871094 248.2857666015625 0.3937206268310547 262.21795654296875 0.5137193202972412 0.7790525 0.9278295040130615 True -3 4612 12.834503650665283 0.25559306144714355 226.37515258789062 0.1668788194656372 254.12515258789062 0.5327115654945374 0.80419445 0.32282358407974243 True -4 5765 12.821481943130493 0.23357582092285156 238.67984008789062 0.22371640801429749 251.4154510498047 0.5378197431564331 0.8149727 0.21410128474235535 True -5 6918 12.825572729110718 0.23997759819030762 238.73907470703125 0.15980462729930878 250.27301025390625 0.5416044592857361 0.8219383 0.19534987211227417 True -6 8071 12.693901538848877 0.24925804138183594 211.85519409179688 0.19904117286205292 249.4629669189453 0.5448725819587708 0.8245857 0.19524990022182465 True -7 9224 12.56198000907898 7.516775846481323 225.22772216796875 0.18665504455566406 248.41151428222656 0.547976016998291 0.836465 0.15758047997951508 True -8 10377 13.178805828094482 0.24605894088745117 224.82420349121094 0.17318864166736603 247.93307495117188 0.5496329665184021 0.8417846 0.1497022956609726 True -9 11530 12.55136489868164 0.23916935920715332 215.82061767578125 0.11847011744976044 247.51834106445312 0.550773024559021 0.8495306 0.13702011108398438 True -10 12683 12.602454423904419 0.6053836345672607 199.59613037109375 0.18429453670978546 247.28280639648438 0.5516495704650879 0.8586681 0.127984881401062 True -11 13836 12.589945554733276 0.23179388046264648 210.39773559570312 0.14572632312774658 246.9973907470703 0.5530222058296204 0.8625488 0.12141720950603485 True -12 14989 12.58610463142395 0.22337603569030762 234.53683471679688 0.13832609355449677 246.71835327148438 0.5540122985839844 0.8661202 0.11789067089557648 True -13 16142 13.703282117843628 0.23250126838684082 210.4379425048828 0.08831915259361267 246.49285888671875 0.5545946359634399 0.8688263 0.1150316447019577 True -14 17295 12.59749722480774 0.23742032051086426 236.98208618164062 0.11238517612218857 246.40745544433594 0.5547567009925842 0.87203354 0.1133158951997757 True -15 18448 12.594373941421509 0.23086285591125488 216.76724243164062 0.06787200272083282 246.5681610107422 0.55427086353302 0.87445533 0.11327307671308517 True -16 19601 12.5969717502594 0.23108744621276855 209.2052459716797 0.12891164422035217 246.89637756347656 0.552939236164093 0.8734278 0.11415334790945053 False -17 20754 12.552106857299805 0.2284407615661621 201.1868896484375 0.0916740894317627 247.31222534179688 0.551328182220459 0.8727203 0.1167391836643219 False -18 21907 12.559641599655151 0.22443437576293945 223.6304168701172 0.09364192187786102 247.65211486816406 0.5499060153961182 0.8708737 0.11934665590524673 False -19 23060 12.596648454666138 0.2238774299621582 206.36611938476562 0.059983231127262115 247.91697692871094 0.548937201499939 0.87113047 0.12133070081472397 False diff --git a/ENCSR584AXZ/cherimoya.fold_4.performance.tsv b/ENCSR584AXZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5662df31484c696b7243d3fd39c975e94667c3af..0000000000000000000000000000000000000000 --- a/ENCSR584AXZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -246.5681610107422 0.3521186113357544 0.55427086353302 0.1716134250164032 0.8744553327560425 0.8553856611251831 0.11327307671308517 \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_0.evaluate.json b/ENCSR585CGU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d8a9fd728d434ed7bb6939d72db526554c6a8708..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_0.fit.json b/ENCSR585CGU/cherimoya.fold_0.fit.json deleted file mode 100644 index 4801c8159d0f3fcf1a3dfc609d8fa889255da7fc..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF745OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_0.log b/ENCSR585CGU/cherimoya.fold_0.log deleted file mode 100644 index 58805c2d529aacea7df36bc97e22b6adfbfa2b04..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.05135154724121 3.7921249866485596 207.8743133544922 0.9399234056472778 251.15975952148438 0.157939612865448 0.50869304 3.382570505142212 True -1 5454 30.427826404571533 0.6468074321746826 153.1536865234375 0.6712905764579773 232.49757385253906 0.24137793481349945 0.6169701 1.3362069129943848 True -2 8181 30.421573638916016 0.5775332450866699 153.88099670410156 0.49085766077041626 228.1914825439453 0.25611892342567444 0.6363583 0.7039996981620789 True -3 10908 30.40906310081482 0.568671703338623 205.70654296875 0.526498556137085 226.49246215820312 0.260810524225235 0.64950484 0.6350985169410706 True -4 13635 30.340418338775635 0.571575403213501 165.90496826171875 0.4944024085998535 225.58892822265625 0.26405614614486694 0.64972764 0.6277408599853516 True -5 16362 30.41444182395935 0.5768764019012451 163.36196899414062 0.5097661018371582 224.57289123535156 0.26867929100990295 0.6581408 0.58101886510849 True -6 19089 30.377949237823486 0.5797238349914551 133.90768432617188 0.42180854082107544 223.79458618164062 0.27194342017173767 0.66454834 0.566236138343811 True -7 21816 30.44409680366516 0.5711095333099365 152.89810180664062 0.7000243663787842 223.44937133789062 0.27373209595680237 0.66626 0.514182984828949 True -8 24543 30.43941068649292 0.5733234882354736 193.8018035888672 0.5441904067993164 222.952392578125 0.27629315853118896 0.6756945 0.49207231402397156 True -9 27270 30.480960845947266 0.5853559970855713 159.51202392578125 0.5074814558029175 222.31341552734375 0.279568612575531 0.68116826 0.47290146350860596 True -10 29997 30.443923234939575 0.571826696395874 220.69659423828125 0.5139652490615845 221.84530639648438 0.2813916802406311 0.6888679 0.44021669030189514 True -11 32724 30.436137437820435 0.9898505210876465 179.91445922851562 0.4403006136417389 221.12977600097656 0.2847823202610016 0.6975774 0.43247565627098083 True -12 35451 30.381319522857666 0.5792362689971924 171.52664184570312 0.5424985289573669 220.55429077148438 0.2872297763824463 0.7070165 0.4116065800189972 True -13 38178 30.48775315284729 0.5793676376342773 189.77432250976562 0.6259377002716064 220.03018188476562 0.2894292175769806 0.7139389 0.4100521206855774 True -14 40905 30.38644289970398 0.578514575958252 139.65528869628906 0.3685646653175354 219.61550903320312 0.29155969619750977 0.7234185 0.3949275314807892 True -15 43632 30.423489809036255 0.5872747898101807 195.00946044921875 0.37717267870903015 219.50042724609375 0.2920496165752411 0.72888464 0.38510337471961975 True -16 46359 30.410423755645752 0.5786631107330322 147.0797576904297 0.36426252126693726 219.5349884033203 0.29135406017303467 0.73486036 0.38121873140335083 True -17 49086 30.39708638191223 0.5783443450927734 194.8779754638672 0.36636701226234436 219.6940155029297 0.290162056684494 0.7369738 0.38225457072257996 True -18 51813 30.425761699676514 0.576167106628418 185.93893432617188 0.3564679026603699 219.3643798828125 0.2920629382133484 0.73783904 0.3868875503540039 True -19 54540 30.469454526901245 0.5779359340667725 203.61920166015625 0.2692509889602661 219.41293334960938 0.2914702892303467 0.7361887 0.38932549953460693 False diff --git a/ENCSR585CGU/cherimoya.fold_0.performance.tsv b/ENCSR585CGU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 301c8517186eb78b51e964d8917340c68c9ff4ed..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.3643798828125 0.5069828033447266 0.2920629680156708 0.06733500212430954 0.7378390431404114 0.6737191081047058 0.3868875503540039 \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_1.evaluate.json b/ENCSR585CGU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d604252a8d54c8afeb04bbf1087eede0fb901d79..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_1.fit.json b/ENCSR585CGU/cherimoya.fold_1.fit.json deleted file mode 100644 index 4318815861db97487fd658d36f082aa25dd8a34f..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF745OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_1.log b/ENCSR585CGU/cherimoya.fold_1.log deleted file mode 100644 index 9aaf930a4c0f8e94de0c82a1145f5a7021dda1a1..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2719 34.7612578868866 4.078917980194092 194.55010986328125 0.6806195378303528 280.5804443359375 0.1657162457704544 0.5462603 3.2579872608184814 True -1 5438 30.628634691238403 0.7594201564788818 171.69281005859375 0.711976170539856 256.29486083984375 0.26267847418785095 0.6477441 1.712848424911499 True -2 8157 30.360138654708862 0.7353677749633789 199.44871520996094 0.9493958950042725 252.033935546875 0.2734873294830322 0.66115403 0.7693353891372681 True -3 10876 30.31847095489502 17.739177465438843 179.5277862548828 0.5143970251083374 250.0201873779297 0.2799183428287506 0.6803545 0.6812481880187988 True -4 13595 30.379934549331665 0.6978847980499268 163.59152221679688 0.7574150562286377 249.438232421875 0.28157660365104675 0.69214225 0.6665511131286621 True -5 16314 30.331974029541016 0.7015674114227295 184.9814453125 0.6217107176780701 248.88018798828125 0.28293219208717346 0.6941717 0.6552634835243225 True -6 19033 30.381093502044678 0.6785211563110352 139.52699279785156 0.49569809436798096 248.41549682617188 0.2855234742164612 0.70260096 0.6394246220588684 True -7 21752 30.417365312576294 0.6854445934295654 142.09266662597656 0.4564261734485626 247.050048828125 0.290824830532074 0.7070264 0.6259261965751648 True -8 24471 30.434648752212524 0.6891067028045654 185.48883056640625 0.5998406410217285 247.40049743652344 0.2891013026237488 0.7114323 0.6272457242012024 True -9 27190 30.454331874847412 1.7328851222991943 169.9692840576172 0.6685724854469299 246.66336059570312 0.2920772433280945 0.7208878 0.5882896780967712 True -10 29909 30.408594608306885 4.788718223571777 212.2445526123047 0.7669423818588257 246.00355529785156 0.2951343357563019 0.7248196 0.5851483345031738 True -11 32628 30.394893169403076 0.7461519241333008 143.66836547851562 0.6233570575714111 245.2607421875 0.2981703281402588 0.73007834 0.5467519164085388 True -12 35347 30.330004692077637 0.6854598522186279 147.9718017578125 0.37562447786331177 244.5074005126953 0.30014681816101074 0.73866856 0.5104758143424988 True -13 38066 30.36738872528076 0.6828722953796387 147.0238800048828 0.4129040837287903 244.00868225097656 0.30220943689346313 0.74691206 0.48160985112190247 True -14 40785 30.353928089141846 0.6863119602203369 187.518798828125 0.4400486648082733 243.3832244873047 0.30440831184387207 0.75421906 0.456451952457428 True -15 43504 30.355835676193237 0.6678206920623779 196.41989135742188 0.3782963752746582 243.16192626953125 0.3047848045825958 0.7596973 0.4315984547138214 True -16 46223 30.341305255889893 0.6834113597869873 178.23468017578125 0.3166624903678894 242.95431518554688 0.30583858489990234 0.7656886 0.41341572999954224 True -17 48942 30.37178063392639 0.6618790626525879 151.97137451171875 0.3381645977497101 242.67037963867188 0.3071191906929016 0.76830477 0.4056250751018524 True -18 51661 30.41115665435791 0.6899697780609131 149.56072998046875 0.36109647154808044 242.84715270996094 0.30584946274757385 0.76692516 0.404152512550354 False -19 54380 30.450836658477783 0.6961650848388672 183.6709442138672 0.32491335272789 242.69151306152344 0.30701881647109985 0.76493335 0.4084192216396332 False diff --git a/ENCSR585CGU/cherimoya.fold_1.performance.tsv b/ENCSR585CGU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cd0418a174de7e83650970cb44c1f1730f168acd..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -242.67037963867188 0.49417299032211304 0.307119220495224 0.07429562509059906 0.7683047652244568 0.7242130637168884 0.4056250751018524 \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_2.evaluate.json b/ENCSR585CGU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 68b77930fe6d207dc146da03c14b2334cf470e32..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_2.fit.json b/ENCSR585CGU/cherimoya.fold_2.fit.json deleted file mode 100644 index fbc3aedbc829853218f8dd3c3bc4899df8cefb5d..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF745OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_2.log b/ENCSR585CGU/cherimoya.fold_2.log deleted file mode 100644 index bc60f5bd518b1077e6969f0b0f37a924c58416e1..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 35.889185428619385 4.021726131439209 177.7643585205078 0.9417606592178345 252.9591522216797 0.1608690619468689 0.5235608 2.7278037071228027 True -1 5756 32.141643047332764 2.049299955368042 174.33717346191406 0.655142605304718 232.07754516601562 0.2513170838356018 0.6227394 1.361222267150879 True -2 8634 32.325555086135864 0.7768142223358154 184.0745086669922 1.1119284629821777 228.31951904296875 0.2631634771823883 0.6359766 0.7616499066352844 True -3 11512 32.22751998901367 20.021801471710205 186.02374267578125 0.8706084489822388 226.6660614013672 0.2678473889827728 0.6473571 0.7153723835945129 True -4 14390 32.57741189002991 1.863997459411621 149.00714111328125 0.6202664971351624 225.93539428710938 0.2703414559364319 0.6482108 0.6841532588005066 True -5 17268 32.13687229156494 0.5297362804412842 184.28636169433594 0.62139892578125 224.99310302734375 0.27515676617622375 0.65892017 0.6758723855018616 True -6 20146 32.26998710632324 0.5331978797912598 191.75125122070312 0.6000639200210571 224.6954345703125 0.27563536167144775 0.66359556 0.6399592161178589 True -7 23024 32.16228890419006 0.527144193649292 183.04226684570312 0.6396496295928955 224.16720581054688 0.27781009674072266 0.6667237 0.6327705979347229 True -8 25902 32.092610597610474 0.5235576629638672 186.04519653320312 0.44627463817596436 223.4995574951172 0.2811875343322754 0.6763876 0.5585004091262817 True -9 28780 32.11668276786804 0.5155084133148193 173.40660095214844 0.5043186545372009 222.86181640625 0.2828211784362793 0.68318534 0.5512435436248779 True -10 31658 32.11303663253784 0.5202550888061523 172.35546875 0.42926087975502014 222.19618225097656 0.2857230603694916 0.6903376 0.5160176157951355 True -11 34536 32.126874923706055 0.5247182846069336 203.98916625976562 0.5497017502784729 221.8391876220703 0.28737983107566833 0.6956723 0.4921729266643524 True -12 37414 32.18907141685486 0.5253899097442627 154.47119140625 0.44664207100868225 221.16770935058594 0.2896634638309479 0.7045681 0.4711000621318817 True -13 40292 32.18812322616577 0.5215845108032227 163.73532104492188 0.3407266139984131 220.6988983154297 0.2924935519695282 0.7107712 0.452393114566803 True -14 43170 32.09084343910217 0.5250942707061768 185.67483520507812 0.418212354183197 220.29588317871094 0.29401811957359314 0.71819746 0.43474099040031433 True -15 46048 32.120386600494385 0.6136384010314941 148.3954315185547 0.35751020908355713 219.66409301757812 0.2967253029346466 0.7248202 0.4165790379047394 True -16 48926 32.11432361602783 1.7435829639434814 179.07345581054688 0.3100315034389496 219.75485229492188 0.29657110571861267 0.72936445 0.40985462069511414 True -17 51804 32.14350342750549 0.5181300640106201 229.80056762695312 0.3248911201953888 219.6479949951172 0.2970995604991913 0.73293185 0.40799060463905334 True -18 54682 32.15690016746521 0.5220217704772949 180.27847290039062 0.3763303756713867 219.82217407226562 0.2958168089389801 0.7310401 0.40912407636642456 False -19 57560 32.12878966331482 0.5170562267303467 174.66891479492188 0.27584630250930786 219.79226684570312 0.29632118344306946 0.73221344 0.41129234433174133 False diff --git a/ENCSR585CGU/cherimoya.fold_2.performance.tsv b/ENCSR585CGU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9e78a0c1d4120bb6bba460148e2589b06b20df9a..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.6479949951172 0.5050000548362732 0.29709959030151367 0.0667644739151001 0.7329318523406982 0.6697733402252197 0.40799060463905334 \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_3.evaluate.json b/ENCSR585CGU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b6300123eb88b38a09ca0da6e0d3035c91b8a1c4..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_3.fit.json b/ENCSR585CGU/cherimoya.fold_3.fit.json deleted file mode 100644 index c1e03519297d3a555e5800e2db68863439047ae1..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF745OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_3.log b/ENCSR585CGU/cherimoya.fold_3.log deleted file mode 100644 index 267d0e7aeec70fc353ee22cc21634e7e4a32e6ce..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.196693658828735 3.7526485919952393 194.48403930664062 0.667060375213623 258.3361511230469 0.15853078663349152 0.52949494 3.053257703781128 True -1 5498 30.893986701965332 0.6664714813232422 150.60421752929688 0.8664082288742065 237.38987731933594 0.25188273191452026 0.6292848 1.3512800931930542 True -2 8247 30.628429651260376 0.5604541301727295 136.41195678710938 0.6377561092376709 233.68109130859375 0.2616407871246338 0.63186854 0.7319108247756958 True -3 10996 30.652712106704712 0.6222891807556152 183.21026611328125 0.5966475009918213 231.8207244873047 0.2668795585632324 0.6481402 0.562652587890625 True -4 13745 30.657944202423096 8.250991344451904 163.0482177734375 0.5892172455787659 231.20849609375 0.26951175928115845 0.6518285 0.5485495924949646 True -5 16494 30.64246940612793 0.5993137359619141 195.99594116210938 0.7359225749969482 230.04428100585938 0.2747500538825989 0.65654415 0.5523585677146912 True -6 19243 30.7377290725708 0.590855598449707 156.9068603515625 0.6429636478424072 229.69212341308594 0.27489495277404785 0.6660775 0.5287067890167236 True -7 21992 30.69803261756897 0.6682276725769043 160.53680419921875 0.8109023571014404 229.38223266601562 0.27676820755004883 0.66918343 0.5310083627700806 True -8 24741 30.660797595977783 0.6855125427246094 165.1690673828125 0.6576018929481506 228.97161865234375 0.2781022787094116 0.6772657 0.5272045135498047 True -9 27490 30.69179391860962 0.5781595706939697 156.7476043701172 0.4874131679534912 228.44419860839844 0.28065595030784607 0.6844528 0.5039361715316772 True -10 30239 30.729264497756958 0.6139581203460693 181.6754913330078 0.49401578307151794 227.6391143798828 0.2838501036167145 0.6887291 0.5003708004951477 True -11 32988 30.782472133636475 0.5965769290924072 173.67825317382812 0.4531749188899994 227.22665405273438 0.2861853837966919 0.69919723 0.48604023456573486 True -12 35737 30.699212789535522 0.5883433818817139 193.93185424804688 0.47250479459762573 226.97378540039062 0.2862931787967682 0.7075405 0.4634069502353668 True -13 38486 30.708239793777466 0.5843038558959961 207.59620666503906 0.5193237662315369 226.2770538330078 0.290193110704422 0.7176043 0.4573189914226532 True -14 41235 30.676518440246582 0.5831823348999023 210.19921875 0.43105319142341614 226.02346801757812 0.29064127802848816 0.7261132 0.42763105034828186 True -15 43984 30.695072412490845 0.6141650676727295 180.14669799804688 0.47978681325912476 225.77577209472656 0.2915487587451935 0.7332334 0.4156111478805542 True -16 46733 30.742371320724487 0.6047544479370117 190.8253173828125 0.4550073444843292 225.59593200683594 0.2922789454460144 0.7386585 0.4092305600643158 True -17 49482 30.694441556930542 0.5699989795684814 184.65679931640625 0.28123360872268677 225.50523376464844 0.29274967312812805 0.7413675 0.4079741835594177 True -18 52231 30.652966737747192 0.568687915802002 160.56170654296875 0.3876611590385437 225.677978515625 0.2919348180294037 0.7421214 0.4108229875564575 True -19 54980 30.59789538383484 0.5648417472839355 155.8899383544922 0.32932382822036743 225.53382873535156 0.29292649030685425 0.74206734 0.41292956471443176 False diff --git a/ENCSR585CGU/cherimoya.fold_3.performance.tsv b/ENCSR585CGU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7336748c9a139de387dc6347d4d1d5a804e23b65..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -225.677978515625 0.5055485963821411 0.2919348180294037 0.06598075479269028 0.7421213984489441 0.6843001246452332 0.4108229875564575 \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_4.evaluate.json b/ENCSR585CGU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 83c0efdf665802e62c6ff7b0f6b191cd30fd0a2f..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745OOD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_4.fit.json b/ENCSR585CGU/cherimoya.fold_4.fit.json deleted file mode 100644 index 261995a05dfcd15b27b0f4aa264845364263ef71..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF745OOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR585CGU/cherimoya.fold_4.log b/ENCSR585CGU/cherimoya.fold_4.log deleted file mode 100644 index 1579fe74ba883da1c6f023cc5e4c3d4a40fe8c42..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2836 35.464701414108276 3.744497537612915 229.5421600341797 0.6457673907279968 244.27011108398438 0.1547970324754715 0.50072706 3.334479331970215 True -1 5672 31.63275384902954 0.6196742057800293 214.8402862548828 0.6418070197105408 224.82308959960938 0.24382570385932922 0.60277617 1.3880029916763306 True -2 8508 31.61782479286194 0.6319687366485596 168.5099334716797 0.4381813406944275 221.92605590820312 0.25335368514060974 0.6137534 0.7124935388565063 True -3 11344 31.634568452835083 0.6001121997833252 164.048583984375 0.7854798436164856 220.84164428710938 0.25635582208633423 0.6221544 0.6755832433700562 True -4 14180 31.647498607635498 0.5993411540985107 168.31117248535156 0.5325069427490234 219.84996032714844 0.26060932874679565 0.63347584 0.6016908884048462 True -5 17016 31.713197469711304 1.0848891735076904 160.33993530273438 0.8141846656799316 219.38363647460938 0.263442724943161 0.6368102 0.6485806107521057 True -6 19852 31.7981173992157 0.6087372303009033 208.975830078125 0.8770623207092285 218.90028381347656 0.2658032178878784 0.6431585 0.6655843257904053 True -7 22688 31.773415088653564 0.6117594242095947 174.49221801757812 0.4067224860191345 218.6688995361328 0.2665410339832306 0.6488686 0.6135737895965576 True -8 25524 31.748351335525513 0.7041587829589844 177.90625 0.5251330137252808 217.94827270507812 0.2697513997554779 0.65777314 0.5756422877311707 True -9 28360 31.790555715560913 0.6345226764678955 198.58428955078125 0.6063010096549988 217.5129852294922 0.27205878496170044 0.66364557 0.5508618950843811 True -10 31196 31.750884532928467 0.6193606853485107 203.52703857421875 0.6641724705696106 217.1153564453125 0.2741870582103729 0.6748712 0.5268223285675049 True -11 34032 31.711737871170044 0.618323802947998 176.02108764648438 0.8665193319320679 216.28875732421875 0.2774409353733063 0.68156016 0.49173974990844727 True -12 36868 31.80918526649475 0.6054513454437256 164.88331604003906 0.5918283462524414 215.90489196777344 0.27963176369667053 0.686088 0.48636066913604736 True -13 39704 31.773051500320435 0.6007680892944336 158.26187133789062 0.44685718417167664 215.43988037109375 0.28142446279525757 0.6992152 0.4490582346916199 True -14 42540 31.797715425491333 0.6050646305084229 183.9224853515625 0.35132890939712524 215.02040100097656 0.28342002630233765 0.709454 0.4328836500644684 True -15 45376 31.807817220687866 1.037604808807373 191.43765258789062 0.3581260144710541 214.71920776367188 0.28478386998176575 0.7174958 0.4158259332180023 True -16 48212 31.838587045669556 0.6169562339782715 210.4507293701172 0.40991994738578796 214.81272888183594 0.28329917788505554 0.7223369 0.40823763608932495 True -17 51048 31.806952476501465 0.609386682510376 185.24453735351562 0.3753570318222046 214.74850463867188 0.2838272154331207 0.72702944 0.40041425824165344 True -18 53884 31.788227081298828 0.6132125854492188 155.8234100341797 0.23644663393497467 214.53561401367188 0.2850644290447235 0.72830874 0.39904841780662537 True -19 56720 31.796077489852905 0.6134443283081055 157.06881713867188 0.2135263979434967 214.70062255859375 0.2839178442955017 0.7273026 0.4015964865684509 False diff --git a/ENCSR585CGU/cherimoya.fold_4.performance.tsv b/ENCSR585CGU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3a22163c0fe1fbd4975bb8f38586dcfa94f97b84..0000000000000000000000000000000000000000 --- a/ENCSR585CGU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -214.53561401367188 0.5116603374481201 0.2850643992424011 0.06668820977210999 0.7283087372779846 0.6669420599937439 0.39904841780662537 \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_0.evaluate.json b/ENCSR587HPR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f790a321e88d470b9240e3514411809ee638ff8b..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF016CVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_0.fit.json b/ENCSR587HPR/cherimoya.fold_0.fit.json deleted file mode 100644 index 1f09568041be06fec485051da6b596a2cd381926..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF016CVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_0.log b/ENCSR587HPR/cherimoya.fold_0.log deleted file mode 100644 index 0e645d947ca38a9f4db34a7889e8d82a54c7f99b..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 35.070003509521484 3.6673827171325684 209.08506774902344 0.7026609182357788 315.6684875488281 0.16887535154819489 0.381419 3.72628116607666 True -1 5480 30.735946655273438 20.94925308227539 206.13377380371094 0.6904566287994385 301.1280822753906 0.22835886478424072 0.5202402 1.5328478813171387 True -2 8220 30.54129147529602 0.6383893489837646 239.0521240234375 0.7314749956130981 297.21209716796875 0.24036772549152374 0.5425286 0.8786145448684692 True -3 10960 30.50639247894287 0.6238706111907959 284.6981201171875 1.0711404085159302 295.7558898925781 0.24462904036045074 0.5597381 0.7356475591659546 True -4 13700 30.557142972946167 0.8856427669525146 209.51995849609375 0.5947532057762146 294.8118896484375 0.24877852201461792 0.5685934 0.7884454727172852 True -5 16440 30.501479864120483 0.5902845859527588 227.43453979492188 0.6556330919265747 294.42742919921875 0.2506226897239685 0.5709222 0.840506911277771 True -6 19180 30.154463529586792 0.5754334926605225 217.16920471191406 0.839969277381897 293.6903991699219 0.25348249077796936 0.58644736 0.8051563501358032 True -7 21920 29.898149728775024 0.5889613628387451 204.363525390625 0.9408606886863708 293.1601867675781 0.255751371383667 0.5871287 0.7739629149436951 True -8 24660 30.073947191238403 23.941267251968384 274.3735046386719 0.8157289624214172 292.829833984375 0.25679096579551697 0.5979824 0.7299486994743347 True -9 27400 29.959842920303345 1.3249874114990234 182.95388793945312 0.7483230829238892 292.1922607421875 0.2590222656726837 0.6059737 0.656753659248352 True -10 30140 29.947242736816406 0.6615350246429443 199.5879669189453 0.40381506085395813 292.06915283203125 0.25914812088012695 0.6152632 0.6149696707725525 True -11 32880 29.944594144821167 0.5975604057312012 218.7073974609375 0.4674970507621765 291.1570129394531 0.26285549998283386 0.62624365 0.560943067073822 True -12 35620 29.90475821495056 0.6243562698364258 244.90078735351562 0.4893174171447754 290.74359130859375 0.26463592052459717 0.637162 0.5396297574043274 True -13 38360 29.952329397201538 0.5661687850952148 271.7860107421875 0.5265915393829346 290.455810546875 0.2655046284198761 0.6457993 0.5114523768424988 True -14 41100 29.928626537322998 0.5656383037567139 236.9786376953125 0.3975566327571869 290.20294189453125 0.26607394218444824 0.6559406 0.47789493203163147 True -15 43840 29.931841373443604 0.5788092613220215 247.96511840820312 0.48421040177345276 290.03118896484375 0.2662876844406128 0.6655872 0.4511822760105133 True -16 46580 29.92262554168701 1.0726070404052734 191.87506103515625 0.33250483870506287 289.9528503417969 0.26649779081344604 0.67120206 0.43210336565971375 True -17 49320 30.082700490951538 0.6183204650878906 221.40756225585938 0.3482641875743866 289.866943359375 0.26677632331848145 0.67693293 0.42516207695007324 True -18 52060 29.96832299232483 0.6128084659576416 217.4986572265625 0.4516924023628235 289.92535400390625 0.2664515972137451 0.6768025 0.4290896952152252 False -19 54800 29.92275047302246 0.5909967422485352 208.68246459960938 0.32393479347229004 290.0296630859375 0.26597103476524353 0.67502457 0.43392372131347656 False diff --git a/ENCSR587HPR/cherimoya.fold_0.performance.tsv b/ENCSR587HPR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6aebe0701acbe5542c9dbf92b993afe4144e3b62..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -289.866943359375 0.4986506402492523 0.26677632331848145 0.07617679238319397 0.6769329309463501 0.6506648063659668 0.42516207695007324 \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_1.evaluate.json b/ENCSR587HPR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index be60fea00ef60f514d848a9de1a43c94a1a3b3b7..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF016CVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_1.fit.json b/ENCSR587HPR/cherimoya.fold_1.fit.json deleted file mode 100644 index dacf99de72e3e741110928a7bc26ad1509c314b3..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF016CVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_1.log b/ENCSR587HPR/cherimoya.fold_1.log deleted file mode 100644 index ed7e2bf81ebe839222e5c9eb047a8cd2b14a8599..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.86203622817993 4.581565618515015 241.15164184570312 0.9063515663146973 344.8465881347656 0.17789791524410248 0.42495844 4.194842338562012 True -1 5518 30.973901987075806 13.678488492965698 295.96270751953125 0.7539424896240234 327.5165100097656 0.24314311146736145 0.58548665 1.478310227394104 True -2 8277 30.771486282348633 2.20672607421875 214.720947265625 0.6788920164108276 323.48297119140625 0.25346100330352783 0.6080361 0.7630773782730103 True -3 11036 30.820476770401 20.58722496032715 205.77346801757812 0.9242273569107056 321.553466796875 0.25802144408226013 0.62379324 0.68523108959198 True -4 13795 30.921282529830933 0.6626908779144287 174.9223175048828 0.670264720916748 321.15802001953125 0.2585858404636383 0.63360924 0.6691291332244873 True -5 16554 31.077853679656982 0.6539521217346191 206.47833251953125 0.4588194787502289 320.57122802734375 0.2608324885368347 0.6365829 0.7347238659858704 True -6 19313 30.720425367355347 1.836031436920166 225.09657287597656 0.7149431705474854 319.4940490722656 0.26461726427078247 0.64473873 0.7554656267166138 True -7 22072 30.780760288238525 7.779077053070068 247.17901611328125 0.48333680629730225 318.6520080566406 0.2669873535633087 0.6511449 0.7293076515197754 True -8 24831 30.687369346618652 1.42649245262146 240.0809326171875 0.5831270217895508 318.2643127441406 0.2681482434272766 0.6526037 0.6746284365653992 True -9 27590 30.770086765289307 1.3700149059295654 241.0936279296875 0.5517913103103638 317.62548828125 0.2700797915458679 0.6607557 0.6669490337371826 True -10 30349 30.737040996551514 26.685856103897095 235.42349243164062 0.5897606015205383 316.73553466796875 0.273811399936676 0.66915345 0.6318421363830566 True -11 33108 30.77489399909973 1.3883864879608154 166.187255859375 0.4922854006290436 316.6481018066406 0.2733539342880249 0.67768246 0.5934851765632629 True -12 35867 30.906450271606445 1.9835224151611328 236.42388916015625 0.5896037817001343 315.886474609375 0.27639850974082947 0.68650794 0.5443560481071472 True -13 38626 30.758127450942993 1.4064862728118896 247.0470733642578 0.3722890019416809 315.2933044433594 0.27823179960250854 0.6951468 0.5135387778282166 True -14 41385 30.76152515411377 1.695425033569336 205.39942932128906 0.5911428332328796 315.3965148925781 0.2773422598838806 0.7020042 0.48041582107543945 True -15 44144 30.819058656692505 1.6495604515075684 217.94686889648438 0.31883591413497925 314.6657409667969 0.2800365388393402 0.7108368 0.45537543296813965 True -16 46903 30.777974367141724 0.9406671524047852 248.15072631835938 0.37244778871536255 314.2054748535156 0.2814653515815735 0.71298444 0.44232094287872314 True -17 49662 30.436232566833496 1.312953233718872 298.4369812011719 0.31464242935180664 314.3613586425781 0.2812992334365845 0.71626085 0.43596670031547546 True -18 52421 30.343939781188965 1.4181549549102783 207.6341552734375 0.46919670701026917 314.83709716796875 0.2790403962135315 0.71750164 0.44071099162101746 True -19 55180 30.34592890739441 1.5614509582519531 188.47618103027344 0.436283677816391 314.8859558105469 0.27928081154823303 0.715813 0.44348961114883423 False diff --git a/ENCSR587HPR/cherimoya.fold_1.performance.tsv b/ENCSR587HPR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4e36f98c0d8ae3d7f73645d2265bb76c7ed605c4..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -314.83709716796875 0.4872320592403412 0.2790403664112091 0.08443856984376907 0.7175016403198242 0.696026086807251 0.44071099162101746 \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_2.evaluate.json b/ENCSR587HPR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a31ab9491690e62ffc5071dda39428aedd3ccb50..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF016CVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_2.fit.json b/ENCSR587HPR/cherimoya.fold_2.fit.json deleted file mode 100644 index 2bfeb00013a29c82e6ff8f5d6c32dfeee94a9df7..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF016CVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_2.log b/ENCSR587HPR/cherimoya.fold_2.log deleted file mode 100644 index a05605495c15fee7302a840809cccc76f6aba914..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2904 36.94425892829895 4.1162333488464355 258.795654296875 0.7309181094169617 318.65576171875 0.17699883878231049 0.38619968 3.1921346187591553 True -1 5808 32.37586188316345 2.6359925270080566 217.7687530517578 0.8094249963760376 304.0760803222656 0.2326035499572754 0.52837485 1.452720046043396 True -2 8712 32.46890377998352 0.5366544723510742 179.0045623779297 0.4709717035293579 300.1175231933594 0.24481768906116486 0.5586736 0.7814786434173584 True -3 11616 32.44324970245361 0.5222053527832031 247.12466430664062 0.8639265298843384 298.8334045410156 0.2492988109588623 0.5717985 0.8351691365242004 True -4 14520 32.409693241119385 0.5269627571105957 224.76516723632812 0.8612658977508545 298.3130187988281 0.24971137940883636 0.59219766 0.7865289449691772 True -5 17424 32.391738176345825 0.5278987884521484 234.5865478515625 0.7234768867492676 297.21044921875 0.2545323967933655 0.6030916 0.7495332956314087 True -6 20328 32.363520860672 1.2856168746948242 195.87387084960938 0.7664932012557983 296.88787841796875 0.25593844056129456 0.60793054 0.7746586203575134 True -7 23232 32.43957233428955 0.5275437831878662 256.3685302734375 0.6804295778274536 296.5384521484375 0.256326287984848 0.6146119 0.7056479454040527 True -8 26136 32.31142497062683 0.5153393745422363 268.8502197265625 0.6586838364601135 295.7513427734375 0.2597869634628296 0.62769514 0.7211534976959229 True -9 29040 31.999577283859253 0.5228729248046875 205.64404296875 0.5240423679351807 295.1759033203125 0.26145899295806885 0.63091874 0.7011561989784241 True -10 31944 31.745826482772827 0.5058615207672119 249.54258728027344 0.5389385223388672 295.1029052734375 0.2612980306148529 0.6410191 0.655972957611084 True -11 34848 31.7409610748291 0.5365157127380371 226.71328735351562 0.792050302028656 294.2361755371094 0.2646835148334503 0.64407265 0.6135277152061462 True -12 37752 31.70919108390808 0.5148515701293945 226.3860626220703 0.5374025702476501 293.9942626953125 0.2655465602874756 0.6560717 0.5586345791816711 True -13 40656 31.790692806243896 0.5432636737823486 232.96115112304688 0.31999802589416504 293.3175354003906 0.26862046122550964 0.6636442 0.5418851971626282 True -14 43560 31.786080598831177 0.519646167755127 240.76889038085938 0.4676463007926941 293.226806640625 0.26852157711982727 0.6732193 0.4933110177516937 True -15 46464 31.8031108379364 0.5086605548858643 230.74407958984375 0.49913662672042847 293.1522216796875 0.26891568303108215 0.6806376 0.4729268252849579 True -16 49368 31.895609378814697 0.5407493114471436 226.41311645507812 0.3010426163673401 292.7003479003906 0.27003803849220276 0.6869955 0.4554012417793274 True -17 52272 31.839436054229736 0.5192413330078125 230.07321166992188 0.3641919493675232 292.7013244628906 0.2696424126625061 0.68865347 0.45071548223495483 True -18 55176 31.938722848892212 0.5170769691467285 199.78115844726562 0.40643030405044556 293.01678466796875 0.2676778733730316 0.6877165 0.44927793741226196 False -19 58080 31.905714750289917 0.5180978775024414 227.46829223632812 0.2900766432285309 293.1351013183594 0.2674356997013092 0.6873755 0.4532768130302429 False diff --git a/ENCSR587HPR/cherimoya.fold_2.performance.tsv b/ENCSR587HPR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 81f0289c0339cf13e911c08891a3bd48d59d7583..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -292.7013244628906 0.49658656120300293 0.2696424126625061 0.08063105493783951 0.6886534690856934 0.6685107946395874 0.45071548223495483 \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_3.evaluate.json b/ENCSR587HPR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 78d99d9245d8f979350d8998f6c2d408e328f690..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF016CVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_3.fit.json b/ENCSR587HPR/cherimoya.fold_3.fit.json deleted file mode 100644 index 322bf697df688ee2effd0c07518683923192e2d6..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF016CVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_3.log b/ENCSR587HPR/cherimoya.fold_3.log deleted file mode 100644 index 642c5e37bdf5d811c305adb18e3da61817f9314f..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2783 35.836079120635986 3.938133716583252 199.6175079345703 0.6835839748382568 335.13677978515625 0.17425814270973206 0.42999387 4.712944984436035 True -1 5566 31.017016172409058 0.7420077323913574 252.21823120117188 0.8229728937149048 320.3154602050781 0.23293714225292206 0.5315387 1.5272021293640137 True -2 8349 31.08008885383606 0.6652894020080566 211.7532196044922 0.9419099688529968 317.505859375 0.239897683262825 0.5583201 1.1601450443267822 True -3 11132 30.99830198287964 0.6401965618133545 239.17991638183594 0.7736055850982666 315.7335205078125 0.2461007535457611 0.58229446 1.2002938985824585 True -4 13915 31.060023546218872 0.602482795715332 247.66253662109375 0.6641538143157959 315.30859375 0.24779851734638214 0.5933762 1.1509805917739868 True -5 16698 30.991689920425415 0.6626040935516357 224.8529815673828 0.4869121313095093 314.5060729980469 0.25101396441459656 0.60062104 1.078418493270874 True -6 19481 31.003162622451782 0.654402494430542 210.91506958007812 0.6053370833396912 314.122314453125 0.25208228826522827 0.6003912 1.0697996616363525 False -7 22264 30.968515872955322 0.6025121212005615 192.06375122070312 0.6395671963691711 313.56689453125 0.25383368134498596 0.6090552 1.0060474872589111 True -8 25047 30.991706371307373 1.3104722499847412 273.3741149902344 0.7194736003875732 312.6497802734375 0.25679150223731995 0.623667 0.8576876521110535 True -9 27830 30.970776319503784 0.6244363784790039 193.7618865966797 0.5412722826004028 312.3687438964844 0.2580789625644684 0.63098645 0.8254281282424927 True -10 30613 31.060133934020996 0.5858392715454102 234.23805236816406 0.5544143319129944 311.3876037597656 0.26270216703414917 0.63571674 0.7851089835166931 True -11 33396 30.88447618484497 0.5824618339538574 209.55130004882812 0.668270468711853 311.1363830566406 0.26287412643432617 0.6483938 0.6796502470970154 True -12 36179 30.4118549823761 0.5690841674804688 218.21612548828125 0.5939731597900391 311.0898132324219 0.2622782289981842 0.65718484 0.6351391077041626 True -13 38962 30.395783185958862 0.5840868949890137 203.33157348632812 0.5262755155563354 310.76483154296875 0.2634038031101227 0.6685353 0.5591979622840881 True -14 41745 30.41762685775757 0.5811848640441895 267.52569580078125 0.35168740153312683 310.145751953125 0.2662164568901062 0.67495245 0.5242264270782471 True -15 44528 30.40793204307556 0.576573371887207 234.48544311523438 0.5630673766136169 309.4648742675781 0.2690184712409973 0.6866433 0.48458561301231384 True -16 47311 30.40609908103943 0.5698935985565186 224.12808227539062 0.3497260808944702 309.33319091796875 0.2686757743358612 0.69158304 0.46330884099006653 True -17 50094 30.410737991333008 0.5645501613616943 243.5830841064453 0.24806872010231018 309.7567138671875 0.26677215099334717 0.69304407 0.45351865887641907 True -18 52877 30.430628299713135 0.5803539752960205 240.1055450439453 0.44350582361221313 309.6960754394531 0.26679134368896484 0.6908549 0.45169782638549805 False -19 55660 30.424850463867188 0.5796864032745361 222.8134765625 0.3255448341369629 309.9230651855469 0.26590919494628906 0.68992776 0.4597025215625763 False diff --git a/ENCSR587HPR/cherimoya.fold_3.performance.tsv b/ENCSR587HPR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c4502a9cf99f87929249dad70738ed2cede8fe01..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.7567138671875 0.49311497807502747 0.26677215099334717 0.08136585354804993 0.6930440664291382 0.6648914217948914 0.45351865887641907 \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_4.evaluate.json b/ENCSR587HPR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 774e425afe0fa8c605fd4836087eceae7952933d..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF016CVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_4.fit.json b/ENCSR587HPR/cherimoya.fold_4.fit.json deleted file mode 100644 index 3d13ce220c9be2b98c92b15df15c8e6cea885e9b..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF016CVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587HPR/cherimoya.fold_4.log b/ENCSR587HPR/cherimoya.fold_4.log deleted file mode 100644 index a328fcee9bcc4adbe378571ca97027084d23cba5..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 36.801289558410645 3.52595853805542 211.90655517578125 0.9432156682014465 320.7139892578125 0.1754806935787201 0.4019512 3.61566162109375 True -1 5762 32.06166076660156 0.5555031299591064 246.10745239257812 0.649622917175293 306.34405517578125 0.2322850227355957 0.5245822 1.5501108169555664 True -2 8643 32.14646124839783 0.5449376106262207 234.82122802734375 1.0080974102020264 303.5504455566406 0.24011047184467316 0.5527612 0.8308366537094116 True -3 11524 32.114840507507324 0.5703301429748535 206.87399291992188 0.6335842609405518 302.34210205078125 0.24333225190639496 0.5665828 0.7376106381416321 True -4 14405 32.09470844268799 0.5469896793365479 244.74449157714844 0.6410447359085083 301.4383850097656 0.24708591401576996 0.57381046 0.850034773349762 True -5 17286 32.10807752609253 0.5464890003204346 194.34933471679688 0.47463977336883545 300.6471862792969 0.25109177827835083 0.5810672 0.8468534350395203 True -6 20167 32.02602458000183 0.5454685688018799 224.81834411621094 0.6968272924423218 300.9742126464844 0.24802865087985992 0.5897133 0.8186448812484741 True -7 23048 32.0466947555542 0.5341227054595947 234.11093139648438 0.8432907462120056 299.9288024902344 0.25266870856285095 0.598537 0.7651936411857605 True -8 25929 32.099530935287476 2.361182451248169 267.3179016113281 0.6017111539840698 299.3695983886719 0.2554081678390503 0.60297793 0.7712836861610413 True -9 28810 32.24595618247986 0.5852715969085693 239.7005615234375 0.6608424186706543 298.6633605957031 0.2585882544517517 0.60988086 0.7840167880058289 True -10 31691 31.656636953353882 0.8322405815124512 262.49871826171875 0.7438336610794067 298.411865234375 0.2595117688179016 0.6203048 0.674424946308136 True -11 34572 31.605496883392334 0.5523638725280762 261.8039245605469 0.570331335067749 298.05169677734375 0.26026928424835205 0.6247441 0.634930431842804 True -12 37453 31.521443605422974 13.966381549835205 223.70079040527344 0.602545976638794 297.47991943359375 0.2624053657054901 0.63589007 0.5682812929153442 True -13 40334 31.51492428779602 0.5562169551849365 249.62966918945312 0.46759912371635437 296.9957275390625 0.26425623893737793 0.647624 0.5394638776779175 True -14 43215 31.552446603775024 1.1432468891143799 243.68760681152344 0.5281386375427246 296.72418212890625 0.2650299668312073 0.65571713 0.510627269744873 True -15 46096 31.621118307113647 0.5558931827545166 240.4061279296875 0.4445722699165344 296.4830017089844 0.26599782705307007 0.6618321 0.4818849563598633 True -16 48977 31.511691331863403 0.5692100524902344 207.8022918701172 0.314142644405365 296.6806335449219 0.2645168602466583 0.6636908 0.46546149253845215 True -17 51858 31.47251296043396 0.5396888256072998 196.08570861816406 0.46436455845832825 296.5350341796875 0.26527702808380127 0.66660875 0.45597484707832336 True -18 54739 31.483401775360107 0.5490264892578125 195.27911376953125 0.2981473207473755 296.521240234375 0.2655502259731293 0.66385657 0.46005967259407043 False -19 57620 31.46099591255188 0.5421693325042725 235.17953491210938 0.32260939478874207 296.62359619140625 0.26505252718925476 0.6619263 0.46539637446403503 False diff --git a/ENCSR587HPR/cherimoya.fold_4.performance.tsv b/ENCSR587HPR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7efd48fc3fd0bfe17a7c6878a9daa06f09b34266..0000000000000000000000000000000000000000 --- a/ENCSR587HPR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -296.5350341796875 0.4968831241130829 0.26527702808380127 0.07801013439893723 0.6666087508201599 0.646687924861908 0.45597484707832336 \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_0.evaluate.json b/ENCSR587SZC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 55f23261c8c3e9b72f9e564f117b901b50b65767..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF374TJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_0.fit.json b/ENCSR587SZC/cherimoya.fold_0.fit.json deleted file mode 100644 index b25387a8abed7149bdb5b3ff8d44112b094f68c3..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF374TJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_0.log b/ENCSR587SZC/cherimoya.fold_0.log deleted file mode 100644 index d8538763989337b44383d7b66205740fc863d49c..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 34.98286175727844 4.445425748825073 574.755126953125 0.5238364934921265 776.479248046875 0.23661358654499054 0.7679859 6.7064995765686035 True -1 5496 30.263059854507446 0.5947587490081787 592.8463134765625 0.6613851189613342 711.77587890625 0.30414947867393494 0.8246372 1.4485431909561157 True -2 8244 30.312297105789185 0.5759923458099365 628.5217895507812 0.2567584216594696 700.2364501953125 0.3157142996788025 0.8362151 0.5295365452766418 True -3 10992 30.19509530067444 0.5883710384368896 538.2806396484375 0.5732709169387817 693.5957641601562 0.322994589805603 0.8388758 0.4261009991168976 True -4 13740 29.647735357284546 0.6030974388122559 429.0876159667969 0.22800803184509277 691.5076293945312 0.32448336482048035 0.8428089 0.4429107904434204 True -5 16488 29.69656777381897 0.581871509552002 532.3993530273438 0.4804975688457489 689.81201171875 0.3262270390987396 0.8414966 0.42656660079956055 False -6 19236 29.714784622192383 0.6008830070495605 638.7001342773438 0.5490583181381226 688.372802734375 0.3278665542602539 0.84460545 0.3904244899749756 True -7 21984 29.852046966552734 0.5919177532196045 610.75439453125 0.4172004461288452 686.6263427734375 0.32979974150657654 0.8457244 0.35843291878700256 True -8 24732 29.89769673347473 0.5920126438140869 522.938720703125 0.357748419046402 684.6596069335938 0.3319022059440613 0.8471693 0.36675071716308594 True -9 27480 29.895445823669434 0.588099479675293 611.27294921875 0.3487853407859802 683.1884155273438 0.3339681327342987 0.84925854 0.34073179960250854 True -10 30228 29.937175989151 2.22758150100708 531.9571533203125 0.4674825072288513 681.5307006835938 0.33549174666404724 0.8535794 0.3212841749191284 True -11 32976 29.815040349960327 0.6015205383300781 567.3575439453125 0.3422211706638336 679.3217163085938 0.33788755536079407 0.85845315 0.31270599365234375 True -12 35724 29.80193781852722 0.5801734924316406 471.5229797363281 0.39463913440704346 677.0534057617188 0.340642511844635 0.8629133 0.29265594482421875 True -13 38472 29.822486400604248 0.5942459106445312 582.1487426757812 0.2953086495399475 675.2357177734375 0.3418464958667755 0.868983 0.28086933493614197 True -14 41220 29.750733137130737 1.3068771362304688 579.8651733398438 0.3972732424736023 674.0341796875 0.3429737091064453 0.871875 0.2635659873485565 True -15 43968 29.72797679901123 0.9754939079284668 575.2344970703125 0.27178654074668884 673.0237426757812 0.3446074426174164 0.8753954 0.2599857449531555 True -16 46716 29.779098510742188 0.5911054611206055 533.8199462890625 0.22436317801475525 672.7100830078125 0.3446095585823059 0.8794008 0.25099316239356995 True -17 49464 29.756131887435913 0.5817089080810547 592.1865234375 0.24571211636066437 672.364013671875 0.3450164794921875 0.87894803 0.24917924404144287 False -18 52212 29.689077138900757 0.579246997833252 527.8619384765625 0.2288130223751068 673.6456298828125 0.3438669443130493 0.87843543 0.24971328675746918 False -19 54960 29.73535180091858 0.5708396434783936 527.9091796875 0.2656925320625305 673.9268188476562 0.3436565697193146 0.878908 0.2504980266094208 False diff --git a/ENCSR587SZC/cherimoya.fold_0.performance.tsv b/ENCSR587SZC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 80a1a1862f1cec71fbd03b5d38d4b96d8cab76c3..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -672.7100830078125 0.43837934732437134 0.3446095287799835 0.12359283864498138 0.8794007897377014 0.8445412516593933 0.25099316239356995 \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_1.evaluate.json b/ENCSR587SZC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f1a77f751864f485fe4fedd4740d73b1dd1588ac..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF374TJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_1.fit.json b/ENCSR587SZC/cherimoya.fold_1.fit.json deleted file mode 100644 index 35aa1788d812e14db6e9da4ffa3ecf8c871a43e2..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF374TJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_1.log b/ENCSR587SZC/cherimoya.fold_1.log deleted file mode 100644 index afb378e7d1e5737774947dd4c4d0315be3f26959..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 33.72777342796326 4.703441143035889 564.2260131835938 0.4731494188308716 896.158203125 0.2386903017759323 0.7491561 7.285682201385498 True -1 5404 29.36371421813965 0.7505784034729004 628.9058837890625 0.4418618679046631 819.6219482421875 0.31459924578666687 0.8096698 1.5964325666427612 True -2 8106 29.92137360572815 0.7335829734802246 505.63116455078125 0.4305317997932434 801.8292846679688 0.3287152647972107 0.82615674 0.8034239411354065 True -3 10808 29.75459933280945 0.7026453018188477 624.615234375 0.5238603353500366 792.4916381835938 0.3351815938949585 0.832843 0.5767675638198853 True -4 13510 29.21186637878418 0.7022981643676758 462.6480712890625 0.3980579972267151 789.0188598632812 0.3390001356601715 0.8342596 0.4893878698348999 True -5 16212 29.246822834014893 0.7022526264190674 635.40234375 0.3251207172870636 785.145751953125 0.3422326445579529 0.8370518 0.4952181279659271 True -6 18914 29.244585275650024 0.6975257396697998 576.8040771484375 0.4357147514820099 781.19189453125 0.34573304653167725 0.84079975 0.4605786204338074 True -7 21616 29.21982502937317 0.7078461647033691 533.6239013671875 0.3983575403690338 779.21533203125 0.3476429581642151 0.84497136 0.45104753971099854 True -8 24318 29.24307918548584 0.7022764682769775 615.354248046875 0.4016187787055969 776.617919921875 0.3497416377067566 0.8480826 0.412919282913208 True -9 27020 29.20438551902771 0.694352388381958 552.3648681640625 0.29921334981918335 773.0440063476562 0.3530016541481018 0.85338134 0.3949575424194336 True -10 29722 29.207020044326782 0.7001910209655762 646.1357421875 0.30409446358680725 770.9951782226562 0.3546701669692993 0.8609325 0.3612546920776367 True -11 32424 29.210891008377075 0.699134349822998 519.5902099609375 0.3542520999908447 767.88818359375 0.35736405849456787 0.86473763 0.3346429169178009 True -12 35126 29.23295831680298 0.6945316791534424 482.05572509765625 0.4635363817214966 765.8567504882812 0.35914134979248047 0.8668623 0.322015643119812 True -13 37828 29.259971380233765 0.7007229328155518 497.0935974121094 0.5084566473960876 763.461669921875 0.36171573400497437 0.87282866 0.2991858720779419 True -14 40530 29.235242128372192 1.2655532360076904 574.06591796875 0.3272067904472351 761.5402221679688 0.36305689811706543 0.87911594 0.2833351790904999 True -15 43232 29.219237565994263 0.7082657814025879 551.7973022460938 0.27236467599868774 761.1561889648438 0.3629279136657715 0.88344234 0.27609309554100037 True -16 45934 29.26689600944519 31.100609302520752 611.762939453125 0.2409891039133072 761.4583740234375 0.3628065586090088 0.88539183 0.26978015899658203 True -17 48636 29.576780080795288 0.7102510929107666 497.5090026855469 0.2785067558288574 761.0431518554688 0.3631938099861145 0.8845582 0.26455074548721313 False -18 51338 29.218029975891113 0.7165396213531494 544.304931640625 0.3009745478630066 761.695068359375 0.36310940980911255 0.88523656 0.2659348249435425 False -19 54040 29.19445538520813 2.4988105297088623 548.5891723632812 0.22640858590602875 763.3197021484375 0.36118000745773315 0.88598883 0.2679089307785034 True diff --git a/ENCSR587SZC/cherimoya.fold_1.performance.tsv b/ENCSR587SZC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 10362041e803a0e9b169c2c62c13e46d74da7e10..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -763.3197021484375 0.42149728536605835 0.36117997765541077 0.14568661153316498 0.8859888315200806 0.8648977875709534 0.2679089307785034 \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_2.evaluate.json b/ENCSR587SZC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1d5a775ce2cfb5a60b2c71b1792cbf6c7f52c42e..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF374TJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_2.fit.json b/ENCSR587SZC/cherimoya.fold_2.fit.json deleted file mode 100644 index ac9f28876c7cfcbf00b96ce480bfb5029f14c5e1..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF374TJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_2.log b/ENCSR587SZC/cherimoya.fold_2.log deleted file mode 100644 index c0c2cd3401ca4c1ac18f37090cfd1503f1610180..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 35.50849413871765 3.755178928375244 609.7739868164062 0.3695317208766937 798.3543090820312 0.24046964943408966 0.7478781 5.903401851654053 True -1 5754 31.300535440444946 0.5853650569915771 596.6839599609375 0.4705151915550232 731.5465087890625 0.3090701997280121 0.8108271 1.2017114162445068 True -2 8631 31.728567361831665 0.5651941299438477 547.6034545898438 0.5429843664169312 721.3976440429688 0.3179967999458313 0.82053745 0.843997061252594 True -3 11508 31.753581047058105 0.6425514221191406 579.0150146484375 0.5478302240371704 721.2256469726562 0.31712090969085693 0.81368214 0.6978141069412231 False -4 14385 31.78806781768799 0.5655663013458252 503.36102294921875 0.282916784286499 720.2493286132812 0.31698092818260193 0.8096955 0.6678317189216614 False -5 17262 31.707147359848022 0.5658574104309082 628.2850341796875 0.6851129531860352 713.8469848632812 0.3237822353839874 0.82845974 0.5541588664054871 True -6 20139 31.90735960006714 25.6302227973938 664.593505859375 0.3765275478363037 708.5845336914062 0.33012065291404724 0.83580244 0.46517130732536316 True -7 23016 31.927446365356445 1.5024666786193848 594.3046875 0.28062373399734497 706.4061279296875 0.3319462239742279 0.839408 0.4228428304195404 True -8 25893 31.8756422996521 23.323402643203735 557.2798461914062 0.2568661868572235 705.0755615234375 0.3338874280452728 0.843581 0.41601383686065674 True -9 28770 31.851831674575806 0.583014726638794 500.4557800292969 0.4116272032260895 702.62451171875 0.33642446994781494 0.8447056 0.3861325979232788 True -10 31647 31.966150522232056 0.567448616027832 590.3326416015625 0.3961341381072998 700.0585327148438 0.33930110931396484 0.84973955 0.36157238483428955 True -11 34524 31.855326175689697 0.5733914375305176 478.8618469238281 0.30682775378227234 697.8757934570312 0.34169965982437134 0.85247207 0.33290088176727295 True -12 37401 31.773504495620728 0.5752842426300049 571.158447265625 0.24680407345294952 697.167236328125 0.3420332670211792 0.85719407 0.3037867248058319 True -13 40278 31.798105001449585 0.9514403343200684 531.28173828125 0.33758795261383057 695.6358642578125 0.34329891204833984 0.86240655 0.28353235125541687 True -14 43155 31.88824200630188 0.5661604404449463 563.5226440429688 0.4677389860153198 693.5465698242188 0.3456019163131714 0.8663665 0.2744637131690979 True -15 46032 31.803499221801758 0.5657029151916504 589.7217407226562 0.3668951988220215 692.7561645507812 0.34698110818862915 0.8681548 0.2677745223045349 True -16 48909 31.733991622924805 0.5641157627105713 619.8460693359375 0.19646044075489044 692.2534790039062 0.34669044613838196 0.8716263 0.2600783407688141 True -17 51786 31.751627922058105 0.5573775768280029 602.8190307617188 0.3143099844455719 692.893798828125 0.3462458848953247 0.8721414 0.2601972222328186 True -18 54663 31.710768222808838 0.5611777305603027 564.854736328125 0.22329294681549072 692.70556640625 0.34688782691955566 0.8731127 0.2622160315513611 True -19 57540 31.699362754821777 0.5671947002410889 513.5574340820312 0.38393139839172363 692.6455078125 0.3473265469074249 0.87091357 0.2639756500720978 False diff --git a/ENCSR587SZC/cherimoya.fold_2.performance.tsv b/ENCSR587SZC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 74ffb7e0e07e0d7fa765624424182929f31cb447..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -692.70556640625 0.43510714173316956 0.34688782691955566 0.13108056783676147 0.873112678527832 0.8411157131195068 0.2622160315513611 \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_3.evaluate.json b/ENCSR587SZC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index edc2fcdcf80e52e9905e8e3f89e54ba443f25452..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF374TJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_3.fit.json b/ENCSR587SZC/cherimoya.fold_3.fit.json deleted file mode 100644 index a8355602ab6366449e388528c344344baea3d605..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF374TJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_3.log b/ENCSR587SZC/cherimoya.fold_3.log deleted file mode 100644 index 4e81523bc197576a5e67a9101b36a96d6131ac5d..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2769 34.52469038963318 3.440434694290161 686.7454833984375 0.44916242361068726 759.98974609375 0.24409158527851105 0.7600865 7.773688316345215 True -1 5538 30.531423091888428 0.5294554233551025 609.0980224609375 0.5882595777511597 697.7536010742188 0.3077348470687866 0.8260311 1.4062479734420776 True -2 8307 30.5305073261261 0.5207912921905518 725.6175537109375 0.5209861993789673 687.3580932617188 0.3167262673377991 0.839962 0.5458337068557739 True -3 11076 30.551556825637817 0.526437520980835 594.788330078125 0.5944483280181885 681.847412109375 0.32282280921936035 0.84272355 0.5061693787574768 True -4 13845 30.56044840812683 2.1736879348754883 600.7310791015625 0.32053816318511963 681.0589599609375 0.32361170649528503 0.8439634 0.4330601692199707 True -5 16614 30.517748594284058 0.9492175579071045 524.06005859375 0.37344175577163696 678.8736572265625 0.3272903263568878 0.8476416 0.4480552673339844 True -6 19383 30.60082483291626 0.5215301513671875 604.5372314453125 0.5043073296546936 676.9315795898438 0.3289843201637268 0.84927577 0.4314674735069275 True -7 22152 30.493446111679077 0.5180981159210205 589.4397583007812 0.4269843101501465 675.7310180664062 0.33021578192710876 0.85311073 0.4210299551486969 True -8 24921 30.50378680229187 0.5206778049468994 554.246337890625 0.506954550743103 673.5182495117188 0.33202052116394043 0.8538398 0.3911788761615753 True -9 27690 30.541800022125244 0.5303771495819092 592.762451171875 0.4829231798648834 670.0572509765625 0.33643341064453125 0.85845363 0.3761367201805115 True -10 30459 30.596226930618286 1.401803731918335 550.5877685546875 0.37842339277267456 669.52294921875 0.33674952387809753 0.860406 0.3478083610534668 True -11 33228 30.670878648757935 16.22973895072937 590.668701171875 0.3661559522151947 667.7600708007812 0.3383156657218933 0.865736 0.32780975103378296 True -12 35997 30.567267656326294 29.068180799484253 555.0332641601562 0.39065709710121155 665.1510620117188 0.3404226303100586 0.8706349 0.3032277524471283 True -13 38766 30.732604265213013 1.03975248336792 634.2095336914062 0.37462007999420166 662.884033203125 0.3429551422595978 0.87319815 0.28950363397598267 True -14 41535 30.87820291519165 0.5223944187164307 547.3223876953125 0.4126321077346802 661.849609375 0.34352144598960876 0.87859905 0.2701013684272766 True -15 44304 30.895211219787598 0.5235805511474609 559.0152587890625 0.23785045742988586 660.787353515625 0.3448472023010254 0.88163066 0.25955772399902344 True -16 47073 30.860430240631104 0.5208597183227539 560.5369262695312 0.2614094614982605 659.607421875 0.34650614857673645 0.88356763 0.2523571252822876 True -17 49842 30.855215787887573 25.67804980278015 574.89208984375 0.28252100944519043 660.4708862304688 0.34529373049736023 0.8862704 0.2499779760837555 True -18 52611 30.624164581298828 6.072630405426025 562.425048828125 0.23109179735183716 661.8828735351562 0.3442079722881317 0.8847847 0.2508334517478943 False -19 55380 30.538774013519287 0.5321474075317383 522.1464233398438 0.27960407733917236 661.6527099609375 0.34475839138031006 0.88407683 0.25108641386032104 False diff --git a/ENCSR587SZC/cherimoya.fold_3.performance.tsv b/ENCSR587SZC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 66d775bab0c8544dc8b1466db95c453dbbcec478..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -660.4708862304688 0.43951719999313354 0.34529373049736023 0.12271660566329956 0.8862704038619995 0.8477360010147095 0.2499779760837555 \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_4.evaluate.json b/ENCSR587SZC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 701bfc2a0b31b2d905ff23d80a2d25f2330ff8a2..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF374TJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_4.fit.json b/ENCSR587SZC/cherimoya.fold_4.fit.json deleted file mode 100644 index 35ad2b9b3cf44f82ebcf32744b347eb7d9d64a06..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF374TJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587SZC/cherimoya.fold_4.log b/ENCSR587SZC/cherimoya.fold_4.log deleted file mode 100644 index ae579cf76a8bfdf634c4bb60cb7d68a7d8b8c34b..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2801 34.89323878288269 6.1398890018463135 483.1870422363281 0.5300110578536987 730.3067016601562 0.2327287346124649 0.7553968 5.542803764343262 True -1 5602 30.286178588867188 0.5796647071838379 531.5386962890625 0.5754312872886658 674.1594848632812 0.293527752161026 0.80742043 1.3158694505691528 True -2 8403 30.849944591522217 1.6536118984222412 572.3316650390625 0.3901026248931885 661.52099609375 0.30531907081604004 0.8204841 0.41202643513679504 True -3 11204 30.849010705947876 0.5660979747772217 514.491455078125 0.49316877126693726 658.3302001953125 0.30875062942504883 0.816483 0.4153880774974823 False -4 14005 30.861531496047974 0.5603420734405518 531.9793090820312 0.43275001645088196 654.8834228515625 0.31320706009864807 0.8287222 0.35855725407600403 True -5 16806 30.891265153884888 2.34975528717041 677.8651123046875 0.32238900661468506 653.6015014648438 0.3147502541542053 0.8293663 0.36107388138771057 True -6 19607 31.271958112716675 0.5721020698547363 584.2849731445312 0.40859150886535645 651.187255859375 0.3178907334804535 0.8329796 0.3452979028224945 True -7 22408 30.871771812438965 0.5724210739135742 634.6137084960938 0.49870795011520386 648.7744140625 0.32030972838401794 0.835049 0.34086814522743225 True -8 25209 30.99970817565918 0.5683822631835938 613.3079223632812 0.543061375617981 646.8355712890625 0.32251766324043274 0.8391171 0.3325340747833252 True -9 28010 30.874324798583984 0.570199728012085 525.397705078125 0.36596769094467163 645.2217407226562 0.32449400424957275 0.8425146 0.31381818652153015 True -10 30811 30.961204290390015 0.5593090057373047 542.170654296875 0.3639979362487793 644.6892700195312 0.32430437207221985 0.8421746 0.31352755427360535 False -11 33612 30.956441402435303 0.5710015296936035 631.3031616210938 0.3012354373931885 642.2122802734375 0.3273797035217285 0.84853345 0.292742520570755 True -12 36413 31.01027536392212 0.5758357048034668 555.9321899414062 0.25729548931121826 640.2493286132812 0.3290398120880127 0.85462147 0.27585721015930176 True -13 39214 30.870529174804688 0.5594429969787598 544.6175537109375 0.37111520767211914 639.6622924804688 0.32960614562034607 0.8599641 0.2606663107872009 True -14 42015 30.85404634475708 0.5588555335998535 642.925537109375 0.24445487558841705 637.89990234375 0.33209431171417236 0.8639474 0.2551126480102539 True -15 44816 30.846147537231445 0.5601508617401123 501.2326354980469 0.28370898962020874 637.8222045898438 0.3316333591938019 0.8672903 0.24802184104919434 True -16 47617 30.843554258346558 0.5655503273010254 538.0283203125 0.1687132567167282 637.5828857421875 0.3331246078014374 0.870981 0.2455049604177475 True -17 50418 30.86240530014038 1.4838109016418457 647.1815795898438 0.26389625668525696 636.9899291992188 0.3337940573692322 0.87328696 0.2433842271566391 True -18 53219 30.88222646713257 0.5703780651092529 638.2337646484375 0.20009487867355347 637.7604370117188 0.33235472440719604 0.8717787 0.24370938539505005 False -19 56020 30.826251983642578 0.5702171325683594 609.6627197265625 0.2279876470565796 638.6903076171875 0.33135953545570374 0.8716766 0.2454940229654312 False diff --git a/ENCSR587SZC/cherimoya.fold_4.performance.tsv b/ENCSR587SZC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b584d6e6c9260505a362eb76a797027af97482e2..0000000000000000000000000000000000000000 --- a/ENCSR587SZC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -636.9899291992188 0.44699758291244507 0.3337940573692322 0.11772575974464417 0.8732869625091553 0.8240811228752136 0.2433842271566391 \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_0.evaluate.json b/ENCSR587TRP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d682dc52f1f2d7d1849d6ca4117fa89349ca1217..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF263IAC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_0.fit.json b/ENCSR587TRP/cherimoya.fold_0.fit.json deleted file mode 100644 index e7369c27e49bbf34350bd6d06c5eba7369c0949c..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF263IAC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_0.log b/ENCSR587TRP/cherimoya.fold_0.log deleted file mode 100644 index b7fa19c11bbc66c4fcd99a2c6df8f45ded658f96..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3836 46.19103479385376 3.894664764404297 1072.1884765625 0.9565435647964478 1139.0343017578125 0.7281213402748108 0.6619455 4.335629940032959 True -1 7672 42.341537952423096 0.7732076644897461 837.493408203125 0.9405151605606079 966.7879028320312 0.8142765164375305 0.66074854 1.3119068145751953 False -2 11508 42.416072368621826 0.7942326068878174 805.2820434570312 0.8554891347885132 943.4794921875 0.82060307264328 0.66569704 0.5997464060783386 True -3 15344 43.001792192459106 0.7086796760559082 728.2509765625 0.8611069917678833 928.8386840820312 0.825861930847168 0.67411953 0.5796460509300232 True -4 19180 42.233078479766846 2.2332615852355957 841.068359375 0.7704046964645386 922.8068237304688 0.828534722328186 0.67322433 0.5821702480316162 False -5 23016 42.430158376693726 0.7075326442718506 779.33935546875 0.9418294429779053 916.1529541015625 0.8317731022834778 0.6753076 0.5779910087585449 True -6 26852 42.305142641067505 0.7112321853637695 733.4163818359375 0.597797691822052 909.19970703125 0.8351009488105774 0.6844253 0.5513681173324585 True -7 30688 42.24177670478821 0.7076821327209473 878.1387939453125 0.6281355023384094 902.1044921875 0.838702917098999 0.6777148 0.5636223554611206 False -8 34524 42.323039054870605 0.7285606861114502 749.2499389648438 0.47086238861083984 895.3157348632812 0.8417364954948425 0.6823638 0.5368104577064514 False -9 38360 42.383803367614746 0.7408158779144287 797.030029296875 0.726627767086029 890.76123046875 0.8439236879348755 0.69758326 0.5000063180923462 True -10 42196 42.47652316093445 0.7267601490020752 785.5157470703125 0.5328814387321472 884.7642822265625 0.8464807271957397 0.69795847 0.4952087104320526 True -11 46032 42.42174696922302 1.0859684944152832 753.5299072265625 0.515283465385437 879.7611694335938 0.8488518595695496 0.7101577 0.4835166931152344 True -12 49868 42.31581687927246 0.7115144729614258 700.4935913085938 0.780017614364624 874.2498779296875 0.8512557148933411 0.7169857 0.46859481930732727 True -13 53704 42.33734583854675 0.6965618133544922 759.5413208007812 0.5413767099380493 869.8653564453125 0.8534258008003235 0.7292752 0.4465935230255127 True -14 57540 42.301382064819336 0.7107357978820801 741.905029296875 0.39355307817459106 865.9319458007812 0.855090856552124 0.7327738 0.44628509879112244 True -15 61376 42.28393483161926 0.706655740737915 775.367431640625 0.5986790657043457 863.1293334960938 0.856188952922821 0.7393058 0.4397079050540924 True -16 65212 42.33543372154236 0.7085213661193848 593.3699951171875 0.6765614748001099 862.472900390625 0.8565278649330139 0.7450582 0.43916425108909607 True -17 69048 42.434929847717285 0.7074706554412842 673.84619140625 0.35286855697631836 863.4671020507812 0.8562448024749756 0.7456991 0.44734546542167664 True -18 72884 42.3328583240509 0.7083373069763184 669.46044921875 0.3521527945995331 864.1947631835938 0.8556796312332153 0.7434313 0.4534878730773926 False -19 76720 42.29384112358093 0.7065994739532471 654.1661376953125 0.5432688593864441 864.8533325195312 0.855383574962616 0.74189943 0.46061772108078003 False diff --git a/ENCSR587TRP/cherimoya.fold_0.performance.tsv b/ENCSR587TRP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9133ee06f6ec21ae0787c6a83ead5c1eb5c63e13..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -863.4671020507812 0.1191084235906601 0.8562448024749756 0.5349869728088379 0.7456991076469421 0.7116466164588928 0.44734546542167664 \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_1.evaluate.json b/ENCSR587TRP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4fbb16735f221c9d309c6c355be62baf878bb838..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF263IAC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_1.fit.json b/ENCSR587TRP/cherimoya.fold_1.fit.json deleted file mode 100644 index eafbaab52d1ee4e0ee6eec0bc8c21b2c3ee6175b..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF263IAC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_1.log b/ENCSR587TRP/cherimoya.fold_1.log deleted file mode 100644 index 76e7bdd270145eefdc9c1975a06c2c7f1e962e0b..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3872 46.005128622055054 49.272459268569946 799.7413940429688 0.7990615963935852 1319.059326171875 0.7386312484741211 0.6783987 4.621795177459717 True -1 7744 43.1493239402771 1.0408005714416504 801.9655151367188 0.9733998775482178 1115.1827392578125 0.8206120133399963 0.6632854 1.5575031042099 False -2 11616 43.07044219970703 0.9979281425476074 796.93505859375 0.8691979646682739 1078.6646728515625 0.8306653499603271 0.67273325 0.8451327085494995 False -3 15488 43.15955638885498 1.002058506011963 787.01220703125 0.7014958262443542 1060.0045166015625 0.8352214097976685 0.6797599 0.7156991958618164 True -4 19360 43.14598369598389 0.9921538829803467 793.2325439453125 0.7238717079162598 1054.3079833984375 0.8369556069374084 0.6737406 0.7101911902427673 False -5 23232 43.12005543708801 2.9068925380706787 852.586669921875 1.135746955871582 1048.444091796875 0.838891863822937 0.66975594 0.7577395439147949 False -6 27104 43.212263345718384 0.998133659362793 798.1409912109375 0.8617474436759949 1039.55859375 0.8427734971046448 0.6856051 0.6653332710266113 True -7 30976 43.1527373790741 2.758760690689087 567.56396484375 0.46083757281303406 1032.9696044921875 0.8444132208824158 0.68952465 0.666975736618042 True -8 34848 43.29491567611694 2.0672662258148193 722.6419677734375 0.7169412970542908 1024.802490234375 0.8474183082580566 0.6894104 0.6470881700515747 False -9 38720 43.20992708206177 1.0272064208984375 815.2026977539062 0.6146233677864075 1017.770263671875 0.8498328328132629 0.69991326 0.6292556524276733 True -10 42592 43.141631841659546 1.0063366889953613 793.8353271484375 0.6767377853393555 1008.137451171875 0.8533202409744263 0.7078553 0.6085835695266724 True -11 46464 43.12064456939697 1.0120735168457031 755.9285888671875 0.6190726161003113 1001.4610595703125 0.8556270003318787 0.7168501 0.5961523056030273 True -12 50336 43.24084424972534 1.0202839374542236 604.3692626953125 0.7711957693099976 992.8372192382812 0.8580475449562073 0.72532046 0.5728604197502136 True -13 54208 43.14403223991394 1.0087101459503174 754.3235473632812 0.8098911046981812 985.9161987304688 0.8603680729866028 0.7355624 0.5485016703605652 True -14 58080 43.217647314071655 0.990293025970459 694.9532470703125 0.534318745136261 979.6431884765625 0.8623765110969543 0.74257964 0.5333455204963684 True -15 61952 42.304912090301514 0.9930598735809326 716.9071044921875 0.5596891045570374 976.3231201171875 0.863490104675293 0.7494054 0.5334171652793884 True -16 65824 42.338791370391846 0.9816329479217529 737.755615234375 0.46183234453201294 974.9271850585938 0.8640095591545105 0.75308233 0.5307581424713135 True -17 69696 42.186437129974365 2.5086045265197754 726.5302734375 0.44869300723075867 975.0990600585938 0.8637173175811768 0.75560325 0.5270097851753235 True -18 73568 42.2982177734375 1.0182180404663086 677.9479370117188 0.4922393560409546 976.5912475585938 0.8631857633590698 0.7545364 0.5299102663993835 False -19 77440 42.2401008605957 1.000540018081665 696.2821044921875 0.44564178586006165 977.9060668945312 0.8628897666931152 0.75249505 0.5354674458503723 False diff --git a/ENCSR587TRP/cherimoya.fold_1.performance.tsv b/ENCSR587TRP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b3342c14a685cfc735147e2b17c8495f3a3894a4..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -975.0990600585938 0.10845859348773956 0.8637173175811768 0.5744066834449768 0.7556032538414001 0.7434926629066467 0.5270097851753235 \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_2.evaluate.json b/ENCSR587TRP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d94e2f60b7e0533eae05288837173e1f5a44145a..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF263IAC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_2.fit.json b/ENCSR587TRP/cherimoya.fold_2.fit.json deleted file mode 100644 index 2c551b0259bebfc2103ab88cb8e2a9fd438b7918..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF263IAC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_2.log b/ENCSR587TRP/cherimoya.fold_2.log deleted file mode 100644 index 87960d1707881f53a08ce2613f323d184044aed9..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4039 48.5740692615509 4.701601028442383 900.1805419921875 0.563570499420166 1280.820068359375 0.7448776960372925 0.6256739 4.744264125823975 True -1 8078 44.98285245895386 0.8572995662689209 673.24072265625 1.0757009983062744 1070.15625 0.8224388360977173 0.64629805 1.4704564809799194 True -2 12117 44.86064624786377 0.8306467533111572 874.4091796875 0.8751686811447144 1047.3568115234375 0.8286537528038025 0.64924365 1.0828133821487427 True -3 16156 44.81253671646118 0.845526933670044 856.1817626953125 1.1404216289520264 1033.4158935546875 0.8329688906669617 0.64735895 0.9308918714523315 False -4 20195 45.08012366294861 27.165598392486572 844.21435546875 0.7013577818870544 1024.91748046875 0.8371269106864929 0.6596046 0.896228015422821 True -5 24234 44.966184854507446 0.8546922206878662 822.8258056640625 0.590229868888855 1019.5846557617188 0.8392691016197205 0.65627474 0.9048817157745361 False -6 28273 44.92169952392578 0.8527288436889648 832.6249389648438 0.9338529706001282 1013.5918579101562 0.8411913514137268 0.6560225 0.9088481664657593 False -7 32312 44.97563123703003 11.493446588516235 762.8391723632812 0.5594006180763245 1005.8311157226562 0.843993067741394 0.66067195 0.8693190813064575 True -8 36351 44.12088108062744 0.8323838710784912 756.7324829101562 1.26101815700531 997.4092407226562 0.8466213941574097 0.67348266 0.7940108180046082 True -9 40390 44.011634349823 0.8377101421356201 806.0450439453125 0.48918065428733826 989.9219970703125 0.8487582802772522 0.6757013 0.7620453238487244 True -10 44429 43.93161630630493 6.59340238571167 762.215576171875 0.5565873384475708 981.2899780273438 0.8510710000991821 0.6814289 0.7543282508850098 True -11 48468 44.03630757331848 0.8255593776702881 635.0076904296875 0.6132467985153198 973.3095092773438 0.8532680869102478 0.6921133 0.7267760634422302 True -12 52507 43.866416692733765 0.8304650783538818 800.613037109375 0.4304064214229584 967.6358642578125 0.8553087115287781 0.6985552 0.6907722353935242 True -13 56546 43.92104935646057 24.875202655792236 797.6787109375 0.33003532886505127 961.875732421875 0.8569544553756714 0.7039133 0.6889803409576416 True -14 60585 44.03027868270874 10.301775455474854 802.419677734375 0.48080122470855713 957.3550415039062 0.8587639331817627 0.71240604 0.6839661002159119 True -15 64624 44.09590196609497 17.97280979156494 721.9752807617188 0.541024386882782 954.5863037109375 0.8596911430358887 0.71564204 0.6723561882972717 True -16 68663 44.044262170791626 0.8387763500213623 748.1204833984375 0.3674612045288086 952.6035766601562 0.860142707824707 0.7198893 0.6732007265090942 True -17 72702 44.15801501274109 0.8330998420715332 746.2422485351562 0.2712631821632385 953.1526489257812 0.859634280204773 0.71921927 0.6725891828536987 False -18 76741 43.99483513832092 0.8269450664520264 740.2734985351562 0.4120411276817322 955.2923583984375 0.8591328859329224 0.71996576 0.6738339066505432 True -19 80780 43.985565423965454 0.8370327949523926 688.04150390625 0.391154021024704 955.499267578125 0.8588255047798157 0.7191891 0.6786336898803711 False diff --git a/ENCSR587TRP/cherimoya.fold_2.performance.tsv b/ENCSR587TRP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 700a30b33b4c3b74347558ed464a1f69ca6b52a5..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -955.2923583984375 0.11172845959663391 0.8591330051422119 0.5660347938537598 0.7199657559394836 0.684902548789978 0.6738339066505432 \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_3.evaluate.json b/ENCSR587TRP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 62c5f48195098293c73bd8ed7d3548c79458a1af..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF263IAC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_3.fit.json b/ENCSR587TRP/cherimoya.fold_3.fit.json deleted file mode 100644 index d93e01822e25aee1385ea155a8040a6e9b6ef73d..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF263IAC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_3.log b/ENCSR587TRP/cherimoya.fold_3.log deleted file mode 100644 index 3c6f6e4f4fd6e49d70b87c62a323ca77f95872ab..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4042 49.48618292808533 3.708030939102173 1018.7725830078125 0.7199675440788269 1119.981689453125 0.7391182780265808 0.6608927 3.803605556488037 True -1 8084 47.0545711517334 0.780350923538208 725.5753173828125 0.8784042596817017 967.0638427734375 0.8151432275772095 0.65784365 0.9211291670799255 False -2 12126 45.0433087348938 0.7586290836334229 842.286865234375 0.912609338760376 940.5467529296875 0.8221573233604431 0.6639461 0.7573052644729614 True -3 16168 44.46450614929199 0.7395312786102295 888.8603515625 0.7706336379051208 929.5038452148438 0.8270982503890991 0.6634599 0.7023388743400574 False -4 20210 44.033611536026 0.7404804229736328 787.9742431640625 0.7591145038604736 919.831787109375 0.8307300209999084 0.67376095 0.6006270051002502 True -5 24252 43.98985552787781 0.7446722984313965 680.531982421875 0.7305201888084412 916.8786010742188 0.8324186205863953 0.6702565 0.6079248785972595 False -6 28294 43.94572067260742 0.7396283149719238 857.1984252929688 0.8160183429718018 910.6737670898438 0.8355501294136047 0.6765108 0.6087663173675537 True -7 32336 44.06180024147034 0.7401127815246582 818.8421020507812 0.7359128594398499 905.2899169921875 0.8378011584281921 0.6770733 0.592374861240387 True -8 36378 43.958839893341064 0.7517275810241699 936.980224609375 0.7968424558639526 899.8070678710938 0.8400170803070068 0.6897088 0.5830102562904358 True -9 40420 43.964319467544556 0.7472593784332275 729.5213623046875 0.6876122355461121 894.5729370117188 0.8427452445030212 0.6946092 0.5633906722068787 True -10 44462 43.931917905807495 0.7555391788482666 740.0394287109375 0.9923601746559143 888.25 0.8455373048782349 0.6986272 0.5377220511436462 True -11 48504 44.003533601760864 0.7419805526733398 705.3919067382812 0.6415920257568359 882.8071899414062 0.8480414152145386 0.7042095 0.5256151556968689 True -12 52546 43.987799882888794 0.7570755481719971 673.912109375 0.5229707360267639 877.6170654296875 0.8501212000846863 0.7126414 0.4972671568393707 True -13 56588 44.01705837249756 0.732896089553833 832.260009765625 0.7452958226203918 873.4300537109375 0.8523319363594055 0.7196632 0.49235838651657104 True -14 60630 43.94103264808655 0.7386438846588135 760.264892578125 0.6435192227363586 869.6105346679688 0.8541330099105835 0.73008907 0.47917914390563965 True -15 64672 44.08548140525818 0.7343301773071289 747.965087890625 0.627354621887207 867.1171875 0.8553739786148071 0.73558354 0.46919992566108704 True -16 68714 43.96642708778381 0.7389922142028809 672.6053466796875 0.5066267848014832 867.158935546875 0.8555777668952942 0.7379433 0.4734511375427246 True -17 72756 44.05234909057617 0.7384839057922363 716.3357543945312 0.5499005317687988 867.5369262695312 0.855247437953949 0.7378307 0.4807875454425812 False -18 76798 43.99177527427673 0.7396712303161621 781.8167114257812 0.3703050911426544 869.2838745117188 0.8546635508537292 0.73541933 0.4889863431453705 False -19 80840 44.002989768981934 0.7397916316986084 695.9033203125 0.32041674852371216 869.9431762695312 0.8543753027915955 0.7342622 0.49576327204704285 False diff --git a/ENCSR587TRP/cherimoya.fold_3.performance.tsv b/ENCSR587TRP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8e53ee5da6cc5d6807d1923ff4f43fbe8a2d844e..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -867.158935546875 0.1186968982219696 0.8555777668952942 0.5367826819419861 0.7379432916641235 0.7098608613014221 0.4734511375427246 \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_4.evaluate.json b/ENCSR587TRP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9efff5ae6e00a6e12a40d00a3099f98025b469c3..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF263IAC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_4.fit.json b/ENCSR587TRP/cherimoya.fold_4.fit.json deleted file mode 100644 index b777acfb48965eaef5f9276052b12872c55edcb2..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF263IAC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR587TRP/cherimoya.fold_4.log b/ENCSR587TRP/cherimoya.fold_4.log deleted file mode 100644 index cbec2a5d8f52fa9eb959f7c4e079fa113591a474..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3988 48.07777762413025 5.243592977523804 875.519287109375 0.9438815116882324 1101.4931640625 0.7377416491508484 0.65856284 3.8309977054595947 True -1 7976 44.313493728637695 0.7312006950378418 670.6365966796875 0.8196957111358643 935.3218994140625 0.8183159828186035 0.66382366 1.0345501899719238 True -2 11964 44.384989738464355 0.7138783931732178 815.42529296875 0.8799256086349487 915.6542358398438 0.824833869934082 0.6611375 0.6660768389701843 False -3 15952 44.254441022872925 0.7140603065490723 863.0443115234375 0.8018543720245361 904.6163940429688 0.8296185731887817 0.6706544 0.5914674997329712 True -4 19940 44.23426270484924 0.71083664894104 789.806640625 0.6139967441558838 897.6637573242188 0.8332726955413818 0.6744536 0.581445038318634 True -5 23928 44.203624963760376 0.7150876522064209 833.3690185546875 0.7326111793518066 893.1366577148438 0.8351660370826721 0.6789204 0.5657802820205688 True -6 27916 44.29868698120117 0.7131564617156982 718.0250854492188 0.853510856628418 886.81494140625 0.8380378484725952 0.6866674 0.5437189936637878 True -7 31904 44.30407190322876 0.7145912647247314 776.7406616210938 0.7260689735412598 883.2107543945312 0.839867353439331 0.6911191 0.5215010046958923 True -8 35892 44.32161569595337 0.6973378658294678 726.9397583007812 0.8353773951530457 876.3701171875 0.8430164456367493 0.70199865 0.504503607749939 True -9 39880 44.25628089904785 0.813713550567627 758.4390869140625 0.819623589515686 871.546630859375 0.8452342748641968 0.7118507 0.47800925374031067 True -10 43868 44.296791553497314 1.4431812763214111 781.7947387695312 0.8823916912078857 866.4680786132812 0.8475273847579956 0.71620333 0.47621873021125793 True -11 47856 43.610912561416626 0.7240808010101318 840.9031982421875 0.5574923753738403 862.3760986328125 0.8494699597358704 0.7265942 0.4492631256580353 True -12 51844 43.623939037323 0.7142965793609619 739.4156494140625 0.7090522646903992 857.8408813476562 0.8515945672988892 0.7299591 0.44610756635665894 True -13 55832 43.578176736831665 0.7145931720733643 676.0314331054688 0.6712151169776917 853.204345703125 0.8537548780441284 0.7383482 0.436654657125473 True -14 59820 43.40211820602417 0.7132878303527832 740.0234375 0.5307497978210449 849.8591918945312 0.8551299571990967 0.74413097 0.4299326539039612 True -15 63808 43.46887469291687 14.051620483398438 661.3089599609375 0.6321820020675659 848.1763916015625 0.8560892343521118 0.74760413 0.4239059090614319 True -16 67796 43.86052656173706 0.7046594619750977 730.2030029296875 0.6025776863098145 847.6756591796875 0.8563035130500793 0.7507223 0.4271160066127777 True -17 71784 43.42018389701843 0.7227497100830078 719.958251953125 0.363365113735199 848.537353515625 0.8557987213134766 0.7504572 0.4350774884223938 False -18 75772 43.38370680809021 0.7172248363494873 734.9771118164062 0.4487989842891693 849.9686279296875 0.8551421761512756 0.748289 0.43919050693511963 False -19 79760 43.55267834663391 0.7169723510742188 775.41796875 0.2728898823261261 850.3338623046875 0.8548235893249512 0.74794364 0.44340068101882935 False diff --git a/ENCSR587TRP/cherimoya.fold_4.performance.tsv b/ENCSR587TRP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b4630c26c2b383c666837613d85cb85566f94bd9..0000000000000000000000000000000000000000 --- a/ENCSR587TRP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -847.6756591796875 0.11945630609989166 0.8563035130500793 0.5340765714645386 0.7507222890853882 0.7143579125404358 0.4271160066127777 \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_0.evaluate.json b/ENCSR588JXI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 146cf19ce8007c82486ae52ee6597217214b848b..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF866DRV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_0.fit.json b/ENCSR588JXI/cherimoya.fold_0.fit.json deleted file mode 100644 index b502f982e8bccc8fc82e475defd37a1228b319f9..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF866DRV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_0.log b/ENCSR588JXI/cherimoya.fold_0.log deleted file mode 100644 index 31a9b6f56bf77e03c1f73d0cbe3896d617238620..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 34.31310153007507 3.5362815856933594 274.026611328125 0.8978537321090698 313.548583984375 0.16109515726566315 0.60780907 3.4941835403442383 True -1 5536 30.51042628288269 0.566190242767334 243.47647094726562 0.47249048948287964 306.340576171875 0.1955554038286209 0.6639708 0.9557082653045654 True -2 8304 30.55336570739746 0.5548906326293945 239.65185546875 0.658575177192688 303.81719970703125 0.20545829832553864 0.67922884 0.6238572597503662 True -3 11072 30.498340845108032 0.5546581745147705 239.96351623535156 0.9278661608695984 302.7154846191406 0.2093738615512848 0.6919048 0.5418263077735901 True -4 13840 30.515910148620605 0.5517752170562744 239.691650390625 0.2677516043186188 301.89898681640625 0.21328213810920715 0.692347 0.493243932723999 True -5 16608 30.451338529586792 0.5541660785675049 239.542236328125 0.43838539719581604 301.3937683105469 0.21579031646251678 0.69661033 0.48371562361717224 True -6 19376 30.478699922561646 0.5463366508483887 227.13246154785156 0.7143571376800537 301.166748046875 0.21552906930446625 0.7026243 0.46282708644866943 True -7 22144 30.448357343673706 0.5443108081817627 222.55938720703125 0.8574338555335999 300.68792724609375 0.2177322804927826 0.7069967 0.4602300226688385 True -8 24912 30.296879053115845 0.5505027770996094 254.5005645751953 0.6535028219223022 300.4914245605469 0.21869230270385742 0.70906824 0.4376797378063202 True -9 27680 29.817751169204712 0.5454494953155518 257.3603515625 0.7020254135131836 300.1535949707031 0.21985642611980438 0.7104245 0.43458840250968933 True -10 30448 29.842268705368042 0.5502116680145264 245.2141571044922 0.4250994920730591 299.68597412109375 0.22184069454669952 0.71763635 0.4081132709980011 True -11 33216 29.8285870552063 0.5496518611907959 271.90399169921875 0.6405776739120483 299.43963623046875 0.22322243452072144 0.7215385 0.38160255551338196 True -12 35984 29.841541290283203 0.5498752593994141 198.01754760742188 0.39473867416381836 299.4064636230469 0.2230387181043625 0.72254676 0.37872135639190674 True -13 38752 29.883686542510986 0.5476469993591309 224.82159423828125 0.37882137298583984 298.9241943359375 0.2264210432767868 0.72968584 0.33456888794898987 True -14 41520 29.879738807678223 0.5443334579467773 216.01112365722656 0.3532298803329468 298.8481750488281 0.2263532429933548 0.7355821 0.3169126510620117 True -15 44288 29.846792697906494 0.5490217208862305 248.45962524414062 0.2695936858654022 298.44476318359375 0.2289661169052124 0.7399463 0.29439371824264526 True -16 47056 29.855072498321533 0.5484764575958252 259.091796875 0.39309242367744446 298.76800537109375 0.22692807018756866 0.74141914 0.2850103974342346 True -17 49824 29.866968154907227 0.5451912879943848 232.27365112304688 0.16770793497562408 299.13446044921875 0.22502554953098297 0.74278104 0.27810534834861755 True -18 52592 29.901363611221313 1.3029234409332275 225.66287231445312 0.23443108797073364 299.156494140625 0.2249271422624588 0.7413728 0.27791085839271545 False -19 55360 29.88793420791626 0.5413975715637207 203.74264526367188 0.28380095958709717 298.7617492675781 0.22787855565547943 0.73988485 0.2793198525905609 False diff --git a/ENCSR588JXI/cherimoya.fold_0.performance.tsv b/ENCSR588JXI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 29c220b41860f3783692ce7dd1a74cd542ccebdf..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -299.13446044921875 0.5064117908477783 0.22502554953098297 0.07300175726413727 0.7427810430526733 0.7299554347991943 0.27810534834861755 \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_1.evaluate.json b/ENCSR588JXI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6ce4f95c1d9c9be1ba2b5fedd2311687dba84b34..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF866DRV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_1.fit.json b/ENCSR588JXI/cherimoya.fold_1.fit.json deleted file mode 100644 index dcf546c3ca385088aea84be0823bea0c04ca8dcf..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF866DRV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_1.log b/ENCSR588JXI/cherimoya.fold_1.log deleted file mode 100644 index 3e0eb734f75b97c25c113459853e85f0050d00e9..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.11283016204834 3.8352854251861572 225.17745971679688 0.6569550037384033 349.2464904785156 0.16911889612674713 0.6110449 4.470373153686523 True -1 5488 30.300724029541016 0.7134566307067871 260.28240966796875 0.5430611968040466 340.38470458984375 0.20724445581436157 0.67983377 1.1864354610443115 True -2 8232 30.319045066833496 0.7155947685241699 242.1851806640625 0.5266517400741577 336.9619445800781 0.2198784500360489 0.71888685 0.5515350103378296 True -3 10976 30.319256067276 1.7056748867034912 209.01611328125 0.7405049204826355 335.6305236816406 0.22378861904144287 0.72964555 0.4396205246448517 True -4 13720 30.305039405822754 0.6928982734680176 252.51217651367188 0.5702358484268188 334.88665771484375 0.22624729573726654 0.7321726 0.378341943025589 True -5 16464 30.222583770751953 0.6936435699462891 266.619873046875 0.7303966283798218 334.6450500488281 0.2260681688785553 0.73768 0.4143427014350891 True -6 19208 30.25068497657776 0.693340539932251 204.29244995117188 0.5777243375778198 333.7099609375 0.23013372719287872 0.74197406 0.39669695496559143 True -7 21952 30.246269464492798 0.6933393478393555 251.43649291992188 0.5168194770812988 333.48956298828125 0.2314484715461731 0.743583 0.43744194507598877 True -8 24696 30.223493814468384 0.6941030025482178 284.1661376953125 0.4540269672870636 332.9595947265625 0.2329164743423462 0.7480766 0.440621942281723 True -9 27440 29.74744176864624 0.6912026405334473 221.61618041992188 0.6271302700042725 332.6031494140625 0.23456889390945435 0.7531154 0.4022999405860901 True -10 30184 29.68496346473694 0.6952340602874756 238.12496948242188 0.4043308198451996 332.07257080078125 0.23632057011127472 0.7530351 0.40864670276641846 False -11 32928 29.69569420814514 0.6847407817840576 235.53323364257812 0.2866341769695282 331.6405334472656 0.23841871321201324 0.7576746 0.384828120470047 True -12 35672 29.622464179992676 0.7716453075408936 250.85488891601562 0.3940727412700653 331.53411865234375 0.23831422626972198 0.76142126 0.3677496612071991 True -13 38416 29.903146028518677 1.1099700927734375 272.00946044921875 0.4305238723754883 331.56304931640625 0.2380191683769226 0.76513857 0.34214848279953003 True -14 41160 29.943260669708252 21.123887538909912 236.49627685546875 0.29098042845726013 330.7154846191406 0.24172161519527435 0.7691977 0.32379859685897827 True -15 43904 29.817336320877075 0.6971604824066162 229.4044647216797 0.5392271280288696 330.50592041015625 0.24288995563983917 0.7729323 0.3103851079940796 True -16 46648 29.793608903884888 0.697206974029541 246.39907836914062 0.22546210885047913 330.6041564941406 0.2424183040857315 0.77449507 0.30003535747528076 True -17 49392 29.82538366317749 0.6877074241638184 243.36920166015625 0.3354451060295105 331.0708312988281 0.24105478823184967 0.77694654 0.2965364158153534 True -18 52136 29.692131519317627 0.7139644622802734 257.61236572265625 0.284923791885376 331.1728210449219 0.2404440939426422 0.7758739 0.2952119708061218 False -19 54880 29.773921966552734 0.6966555118560791 269.20947265625 0.3578912615776062 331.3829650878906 0.23948270082473755 0.77494884 0.2983432114124298 False diff --git a/ENCSR588JXI/cherimoya.fold_1.performance.tsv b/ENCSR588JXI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4d357ed485f27c51e0a75f1e8f53b6b4d2077224..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -331.0708312988281 0.49197670817375183 0.24105481803417206 0.08476126939058304 0.7769465446472168 0.7650924921035767 0.2965364158153534 \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_2.evaluate.json b/ENCSR588JXI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 69304120b465c6f2c1742510109352a2ce1bd103..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF866DRV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_2.fit.json b/ENCSR588JXI/cherimoya.fold_2.fit.json deleted file mode 100644 index d74bf64fd90e2fa3ee0587262b31372042103d22..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF866DRV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_2.log b/ENCSR588JXI/cherimoya.fold_2.log deleted file mode 100644 index 3a5b429b4a80f9b98d0606a85a3094d5dd559ea3..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2899 35.88878583908081 3.5276427268981934 260.23486328125 0.6073192358016968 317.7252197265625 0.1652517318725586 0.61599135 2.935086727142334 True -1 5798 31.960413932800293 0.51692795753479 238.10159301757812 0.48953601717948914 310.12005615234375 0.2001483142375946 0.6810057 0.7627344727516174 True -2 8697 31.993958234786987 0.5071377754211426 210.0393524169922 0.6459918022155762 307.32122802734375 0.21047917008399963 0.6967074 0.41663962602615356 True -3 11596 31.99606680870056 0.5065975189208984 205.89828491210938 0.5970873236656189 306.15252685546875 0.21495305001735687 0.7044081 0.36840856075286865 True -4 14495 31.89927387237549 0.5116124153137207 256.3140869140625 0.5742723345756531 306.0684509277344 0.21471445262432098 0.7040029 0.344673216342926 False -5 17394 31.904852628707886 0.5080218315124512 254.1505584716797 0.4961616098880768 305.5160827636719 0.2168034017086029 0.7142279 0.33335331082344055 True -6 20293 31.92405915260315 0.5092356204986572 231.9727325439453 0.5807000398635864 304.92816162109375 0.2194080650806427 0.71962136 0.3283967971801758 True -7 23192 31.98091721534729 0.5121331214904785 234.19871520996094 0.558978796005249 304.51776123046875 0.22129091620445251 0.72209454 0.35338595509529114 True -8 26091 31.34359884262085 0.5105195045471191 279.1380920410156 0.41269880533218384 304.4068603515625 0.22143268585205078 0.72712344 0.3425714075565338 True -9 28990 31.324512481689453 0.5105180740356445 230.66961669921875 0.27674680948257446 303.7295227050781 0.22497709095478058 0.7271998 0.33756154775619507 True -10 31889 31.329694747924805 0.5105535984039307 208.72052001953125 0.39925891160964966 303.2000427246094 0.22726094722747803 0.7291597 0.3384465277194977 True -11 34788 31.33543062210083 0.5095040798187256 251.99871826171875 0.487781822681427 303.17694091796875 0.227070614695549 0.73102653 0.3375520706176758 True -12 37687 31.33856987953186 0.5096325874328613 224.80259704589844 0.3819170892238617 302.9279479980469 0.22835011780261993 0.731897 0.33266204595565796 True -13 40586 31.325615882873535 1.2175369262695312 251.7591552734375 0.3779701888561249 302.77862548828125 0.22842718660831451 0.73569334 0.3191545903682709 True -14 43485 31.361307621002197 0.5051193237304688 243.7777099609375 0.4131080210208893 302.52752685546875 0.2297418713569641 0.7409947 0.30506399273872375 True -15 46384 31.378044366836548 0.5191638469696045 244.88497924804688 0.23031847178936005 302.7154846191406 0.22847376763820648 0.7438041 0.3029156029224396 True -16 49283 31.397156953811646 1.5499942302703857 237.46934509277344 0.30409377813339233 302.4554443359375 0.23049430549144745 0.74615777 0.29952481389045715 True -17 52182 31.366800785064697 2.2806589603424072 212.4849853515625 0.4473124146461487 302.4205627441406 0.2303173989057541 0.7464613 0.29520249366760254 True -18 55081 31.383213996887207 0.511455774307251 231.37210083007812 0.31236255168914795 302.3861389160156 0.23085954785346985 0.74511147 0.29941073060035706 False -19 57980 31.36779260635376 0.5175454616546631 273.77716064453125 0.24065947532653809 302.6498718261719 0.22978977859020233 0.7441161 0.3031783699989319 False diff --git a/ENCSR588JXI/cherimoya.fold_2.performance.tsv b/ENCSR588JXI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f380cbb4dae590bc9a08ac1da6967574ed03209e..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.4205627441406 0.5044325590133667 0.2303173989057541 0.0741671770811081 0.7464612722396851 0.7330613732337952 0.29520249366760254 \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_3.evaluate.json b/ENCSR588JXI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f57cd04a07f7ac1e8a8d19d9a50283fea391c97e..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF866DRV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_3.fit.json b/ENCSR588JXI/cherimoya.fold_3.fit.json deleted file mode 100644 index c380fb441e1a284d667259cdcf523299f3ead1aa..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF866DRV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_3.log b/ENCSR588JXI/cherimoya.fold_3.log deleted file mode 100644 index a21161cbbc0fd765bdcb4a078063f6b60c251867..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2775 34.469995737075806 4.554365873336792 265.561279296875 0.5313284993171692 344.2955017089844 0.16634000837802887 0.61593556 3.9320473670959473 True -1 5550 30.598738431930542 0.5832614898681641 247.0177001953125 0.47780537605285645 335.82958984375 0.2052178680896759 0.69291586 0.9751462936401367 True -2 8325 30.640872478485107 0.5778605937957764 244.77943420410156 0.6129469871520996 333.4046325683594 0.21345384418964386 0.7101413 0.5750340223312378 True -3 11100 30.630056381225586 0.5802843570709229 243.59127807617188 0.5047215223312378 332.7975158691406 0.2146858423948288 0.72091746 0.41891035437583923 True -4 13875 30.66031837463379 0.5821478366851807 227.93772888183594 0.5203606486320496 331.62701416015625 0.2202208787202835 0.7231573 0.40762871503829956 True -5 16650 30.68698215484619 4.019933223724365 250.29287719726562 0.3546580374240875 331.1778869628906 0.22116824984550476 0.72294533 0.40817978978157043 False -6 19425 30.605318546295166 0.5810389518737793 241.86370849609375 0.7799674272537231 330.4792175292969 0.22425182163715363 0.725932 0.45134174823760986 True -7 22200 30.061479568481445 0.5768053531646729 228.0651397705078 0.7621594071388245 330.1512451171875 0.22531498968601227 0.72937137 0.42662176489830017 True -8 24975 29.990006685256958 0.5802557468414307 265.28155517578125 0.6695424914360046 329.86529541015625 0.22655855119228363 0.7270805 0.4562038779258728 False -9 27750 29.978612899780273 0.5914931297302246 241.8181915283203 0.5553079843521118 329.6136779785156 0.22695790231227875 0.7343407 0.4389309585094452 True -10 30525 30.083496570587158 3.276902437210083 267.31658935546875 0.33562910556793213 328.6662902832031 0.2324625849723816 0.739763 0.44042298197746277 True -11 33300 29.992061853408813 0.570117712020874 253.06912231445312 0.5771092176437378 329.01751708984375 0.22980087995529175 0.74135154 0.40798836946487427 True -12 36075 30.040173530578613 0.5655491352081299 230.91616821289062 0.30500784516334534 328.7234802246094 0.23093441128730774 0.7427477 0.3818538784980774 True -13 38850 29.999918937683105 0.5629498958587646 282.8252258300781 0.27666306495666504 328.344482421875 0.23205281794071198 0.7510055 0.3717552721500397 True -14 41625 30.000622034072876 0.5636346340179443 199.58880615234375 0.48194801807403564 328.1439208984375 0.23262760043144226 0.7546836 0.3410840630531311 True -15 44400 29.966412782669067 0.5622155666351318 253.56716918945312 0.3246949315071106 327.8014831542969 0.23452231287956238 0.758045 0.32440385222435 True -16 47175 29.984857320785522 0.5724401473999023 235.23141479492188 0.2702753245830536 327.9502868652344 0.23371560871601105 0.7607913 0.3143148422241211 True -17 49950 30.006057739257812 0.5665981769561768 205.30023193359375 0.25448739528656006 328.17791748046875 0.23280644416809082 0.7644864 0.3032694160938263 True -18 52725 30.001755475997925 0.5724124908447266 242.08416748046875 0.20785534381866455 328.41473388671875 0.2318902164697647 0.7623908 0.3019351363182068 False -19 55500 30.0864896774292 0.5785834789276123 248.0232391357422 0.2403339445590973 328.32672119140625 0.23259781301021576 0.76155514 0.3045956790447235 False diff --git a/ENCSR588JXI/cherimoya.fold_3.performance.tsv b/ENCSR588JXI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7046ac382db5efacf4d44775064b39e747c6f6c6..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -328.17791748046875 0.49594947695732117 0.23280644416809082 0.08338862657546997 0.7644863724708557 0.7482063174247742 0.3032694160938263 \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_4.evaluate.json b/ENCSR588JXI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0c748bdd26f15cc844ba099550d9151e5f318492..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF866DRV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_4.fit.json b/ENCSR588JXI/cherimoya.fold_4.fit.json deleted file mode 100644 index 62030fd8fef3b8c8fbf3d4c9887d2311646c4a93..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF866DRV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR588JXI/cherimoya.fold_4.log b/ENCSR588JXI/cherimoya.fold_4.log deleted file mode 100644 index a85b7583ee7b5ab8b2876b0b993b19e1808f6de7..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2875 35.85973381996155 3.7154972553253174 227.0441436767578 0.8968134522438049 320.0998229980469 0.16698463261127472 0.60647887 2.765730142593384 True -1 5750 31.7212975025177 0.6316771507263184 276.03082275390625 0.7057902216911316 313.84332275390625 0.19732557237148285 0.6581062 0.7550472021102905 True -2 8625 31.774930238723755 0.6107645034790039 302.8310546875 0.4413824677467346 311.8932189941406 0.20428135991096497 0.678722 0.5794646143913269 True -3 11500 31.71167254447937 1.5064477920532227 260.50140380859375 0.5780234336853027 310.3684387207031 0.21055485308170319 0.68866926 0.5130538940429688 True -4 14375 31.762290477752686 1.0372779369354248 223.54489135742188 0.44274911284446716 310.0088195800781 0.2110796421766281 0.69013757 0.4973384737968445 True -5 17250 31.78987169265747 0.6392993927001953 263.67266845703125 0.35481566190719604 309.3982238769531 0.21371032297611237 0.69223076 0.5103708505630493 True -6 20125 31.799432516098022 9.435966730117798 257.3152770996094 0.40400803089141846 309.04547119140625 0.214883953332901 0.69598377 0.5268868803977966 True -7 23000 31.364521980285645 1.8558430671691895 249.3897705078125 0.483081579208374 308.408447265625 0.21800027787685394 0.6981145 0.4860697090625763 True -8 25875 31.065252542495728 19.257964849472046 252.9136505126953 0.5765098333358765 308.10955810546875 0.21957962214946747 0.69930506 0.4667041003704071 True -9 28750 31.332438945770264 0.6085436344146729 252.2843017578125 0.41931024193763733 307.79217529296875 0.22022196650505066 0.705944 0.4444039762020111 True -10 31625 31.12998652458191 1.4546806812286377 242.60073852539062 0.40462857484817505 307.1968688964844 0.22415074706077576 0.70819366 0.40139466524124146 True -11 34500 31.714722394943237 0.6094512939453125 269.1620788574219 0.36724698543548584 307.23529052734375 0.22326251864433289 0.7093168 0.39613068103790283 True -12 37375 31.091786861419678 0.6040418148040771 274.51763916015625 0.4063485860824585 306.89306640625 0.22465834021568298 0.71832156 0.3538414537906647 True -13 40250 31.108453273773193 0.609874963760376 230.29086303710938 0.34086844325065613 306.5970764160156 0.22616086900234222 0.72101414 0.3554478585720062 True -14 43125 31.14998483657837 0.6099772453308105 220.34051513671875 0.5857489109039307 306.5025634765625 0.2263827621936798 0.72744924 0.33138784766197205 True -15 46000 31.23787569999695 0.604790449142456 244.79539489746094 0.27572643756866455 306.39599609375 0.2269340455532074 0.7318375 0.3072999119758606 True -16 48875 31.137829065322876 0.6070907115936279 228.11190795898438 0.2782708406448364 306.4739074707031 0.22725169360637665 0.73820734 0.29373183846473694 True -17 51750 31.09556007385254 20.06429433822632 244.8485870361328 0.4458546042442322 306.7330017089844 0.22536520659923553 0.7388578 0.2901225984096527 True -18 54625 31.08469843864441 1.1466505527496338 253.74844360351562 0.28270453214645386 306.7909240722656 0.22511279582977295 0.7393792 0.29060155153274536 True -19 57500 31.09623694419861 0.6061704158782959 288.22613525390625 0.1416182816028595 306.7704772949219 0.2254585325717926 0.73747474 0.29231002926826477 False diff --git a/ENCSR588JXI/cherimoya.fold_4.performance.tsv b/ENCSR588JXI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 59712dd6105599f69b49a47037a99a4710bc63b5..0000000000000000000000000000000000000000 --- a/ENCSR588JXI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -306.7909240722656 0.5041168332099915 0.22511278092861176 0.07752382010221481 0.7393792271614075 0.7178353667259216 0.29060155153274536 \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_0.evaluate.json b/ENCSR589ROM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5bdbeec7b6aeb9e03f77dbf0b086caaccc3a33a2..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF684OHX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_0.fit.json b/ENCSR589ROM/cherimoya.fold_0.fit.json deleted file mode 100644 index d573a4159b70fe25e38c91b017cdbe0e5da00e03..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF684OHX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_0.log b/ENCSR589ROM/cherimoya.fold_0.log deleted file mode 100644 index 8b62ad7666d4dbb5ee48b2fc7bcfa45d2d0d3ddb..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.566617488861084 21.245614290237427 419.14508056640625 0.4206830859184265 691.8145141601562 0.5481259822845459 0.58365643 7.570318698883057 True -1 5516 30.63855767250061 0.6153388023376465 434.91473388671875 0.44913536310195923 565.4207153320312 0.703619658946991 0.66043454 2.050478935241699 True -2 8274 30.69195318222046 0.6743383407592773 483.8807373046875 0.35858017206192017 546.8902587890625 0.7196401953697205 0.6539685 0.8164263367652893 False -3 11032 30.75242280960083 1.6400532722473145 464.0335693359375 0.42130234837532043 541.1516723632812 0.7250550985336304 0.6579114 0.6156194806098938 False -4 13790 30.59404683113098 1.2071454524993896 479.6754455566406 0.4563395380973816 537.964599609375 0.7276820540428162 0.6615983 0.5515179634094238 True -5 16548 30.116422653198242 11.555026054382324 408.06689453125 0.5156068205833435 535.8643798828125 0.7305970788002014 0.6757601 0.48696643114089966 True -6 19306 30.06869888305664 14.082136392593384 453.2802429199219 0.337427020072937 532.3964233398438 0.7339512705802917 0.68933433 0.44530409574508667 True -7 22064 30.57675051689148 0.5830693244934082 389.6470947265625 0.5651344060897827 531.2432250976562 0.7352811694145203 0.6915035 0.4560149908065796 True -8 24822 30.099642515182495 0.5791444778442383 468.2410888671875 0.37734296917915344 529.38818359375 0.737285315990448 0.69789106 0.43536967039108276 True -9 27580 30.205848693847656 0.5945584774017334 462.6109313964844 0.45530304312705994 527.7459716796875 0.739120364189148 0.70848894 0.4220501184463501 True -10 30338 30.109800100326538 3.5438365936279297 389.4323425292969 0.3915528655052185 525.4216918945312 0.7412168979644775 0.7115251 0.3972189128398895 True -11 33096 30.245866298675537 1.0106699466705322 438.15966796875 0.29200851917266846 523.052978515625 0.7435086369514465 0.72289205 0.38310739398002625 True -12 35854 30.16783308982849 1.6155452728271484 464.82763671875 0.39852285385131836 520.93603515625 0.7454215288162231 0.7299913 0.36798232793807983 True -13 38612 30.062015295028687 1.4279160499572754 396.2599792480469 0.3011525273323059 519.2734375 0.7471368908882141 0.74258786 0.35368573665618896 True -14 41370 30.125051498413086 1.5194692611694336 394.09136962890625 0.288974791765213 517.8417358398438 0.7484822273254395 0.7503242 0.3462250828742981 True -15 44128 30.178797960281372 1.3862457275390625 421.4195861816406 0.29043877124786377 516.8533935546875 0.7494034767150879 0.7578396 0.3377281725406647 True -16 46886 30.059913396835327 1.2578883171081543 493.86920166015625 0.26200735569000244 516.4281005859375 0.7497913837432861 0.76449186 0.3261283040046692 True -17 49644 30.07805371284485 1.2194154262542725 449.6578369140625 0.15503224730491638 516.3109130859375 0.7497185468673706 0.7666116 0.3248496353626251 True -18 52402 30.21179509162903 0.579486608505249 372.4366149902344 0.19670173525810242 516.453125 0.7494246363639832 0.76580983 0.3236507475376129 False -19 55160 30.178686380386353 0.5880346298217773 369.80108642578125 0.2647421956062317 516.7974853515625 0.7491708993911743 0.76628906 0.32722100615501404 False diff --git a/ENCSR589ROM/cherimoya.fold_0.performance.tsv b/ENCSR589ROM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 95e695e2c353c1a453d4b9280e37b36307e7c79e..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -516.3109130859375 0.21403390169143677 0.7497185468673706 0.3371877670288086 0.7666115760803223 0.6997917890548706 0.3248496353626251 \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_1.evaluate.json b/ENCSR589ROM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d4cb4b2c52c39af4e0b34173812b6bc8543fafca..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF684OHX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_1.fit.json b/ENCSR589ROM/cherimoya.fold_1.fit.json deleted file mode 100644 index c61a84b37657d97e2a5f58566967f8ea96fc53ea..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF684OHX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_1.log b/ENCSR589ROM/cherimoya.fold_1.log deleted file mode 100644 index 9414e139f04ba2cb523a8d30919bd309af1af4e5..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 35.61122441291809 4.221698045730591 449.67620849609375 0.588921308517456 717.3104248046875 0.563823938369751 0.6095623 7.649131774902344 True -1 5488 30.55973744392395 0.7897861003875732 471.943115234375 0.5202279090881348 590.9633178710938 0.71248859167099 0.69127244 1.5631804466247559 True -2 8232 30.521522760391235 18.14835834503174 460.13531494140625 0.5486193895339966 574.69921875 0.7278344035148621 0.7010626 0.6144378781318665 True -3 10976 30.827425241470337 0.7559783458709717 408.04638671875 0.3969091475009918 567.4090576171875 0.7342429161071777 0.7094549 0.4878694713115692 True -4 13720 30.6473388671875 1.412461519241333 457.48876953125 0.2868439555168152 564.454345703125 0.7370877861976624 0.71717286 0.48353302478790283 True -5 16464 30.623645782470703 0.72684645652771 460.46197509765625 0.45375096797943115 561.9693603515625 0.7398108839988708 0.70989156 0.4098752439022064 False -6 19208 31.069122314453125 0.7411863803863525 412.94403076171875 0.46571215987205505 559.5698852539062 0.742576003074646 0.72143215 0.39066556096076965 True -7 21952 30.616233110427856 0.7401678562164307 413.13446044921875 0.28526386618614197 557.2650756835938 0.744782567024231 0.7261948 0.3759216368198395 True -8 24696 30.692790746688843 0.7210979461669922 493.1737060546875 0.3116162121295929 554.9537353515625 0.7470400929450989 0.73230475 0.3636998236179352 True -9 27440 29.957390546798706 0.868537187576294 415.43402099609375 0.3870449662208557 553.082763671875 0.7491483688354492 0.7458484 0.3559487760066986 True -10 30184 29.960001230239868 0.7241835594177246 413.2287292480469 0.37854692339897156 550.9041137695312 0.7513037323951721 0.7571256 0.3349757790565491 True -11 32928 29.9891574382782 5.90241813659668 450.57855224609375 0.3278380334377289 548.4418334960938 0.7534374594688416 0.76477575 0.3246270716190338 True -12 35672 30.016242742538452 1.7904839515686035 426.14825439453125 0.33208268880844116 546.1597900390625 0.7555310130119324 0.7782328 0.30632084608078003 True -13 38416 29.984241485595703 1.1380717754364014 367.4452209472656 0.19143372774124146 544.8369750976562 0.7568674683570862 0.7855919 0.2952602505683899 True -14 41160 30.007165670394897 11.511464834213257 406.6609191894531 0.29080718755722046 542.6634521484375 0.7586676478385925 0.79355705 0.2855556011199951 True -15 43904 30.046972274780273 8.61458945274353 435.47235107421875 0.22784960269927979 541.502197265625 0.7596619725227356 0.7996345 0.2766818702220917 True -16 46648 29.98482036590576 0.7772829532623291 411.4007568359375 0.2778233289718628 541.08984375 0.7599427700042725 0.80428797 0.27699995040893555 True -17 49392 29.918081521987915 0.7354354858398438 386.6319274902344 0.1704210788011551 540.7744750976562 0.7599440813064575 0.80345875 0.27647706866264343 False -18 52136 29.846468448638916 0.7261643409729004 375.24346923828125 0.20120209455490112 540.9500122070312 0.7596325278282166 0.802205 0.27812474966049194 False -19 54880 29.84584069252014 0.7292218208312988 416.44354248046875 0.21888107061386108 541.2428588867188 0.7592935562133789 0.80215853 0.2808866798877716 False diff --git a/ENCSR589ROM/cherimoya.fold_1.performance.tsv b/ENCSR589ROM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e41d08ffe1b2444059dd4bff40b0ab338ed5bc22..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -541.08984375 0.20555195212364197 0.7599427700042725 0.35204413533210754 0.8042879700660706 0.7599573135375977 0.27699995040893555 \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_2.evaluate.json b/ENCSR589ROM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 353cf39fc4a2ea712f12b3cde2d2bf246df6029f..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF684OHX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_2.fit.json b/ENCSR589ROM/cherimoya.fold_2.fit.json deleted file mode 100644 index 096fdf6537caf160eb21e6abb8827de69f85c9bd..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF684OHX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_2.log b/ENCSR589ROM/cherimoya.fold_2.log deleted file mode 100644 index 7f3185878df043b281df05f1fa72dfca41468066..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2934 37.527549028396606 3.465362310409546 526.64013671875 0.8534564971923828 691.6062622070312 0.5668076872825623 0.5878994 6.801433086395264 True -1 5868 32.54200839996338 1.235905647277832 461.2672119140625 0.6388814449310303 570.1207885742188 0.7092887163162231 0.68347055 1.1878148317337036 True -2 8802 32.54622936248779 0.6284291744232178 410.0087585449219 0.31975048780441284 558.483154296875 0.7182201743125916 0.67592084 0.7246457934379578 False -3 11736 31.87054705619812 0.5492732524871826 445.1198425292969 0.404252290725708 552.114990234375 0.7242023348808289 0.68993217 0.6059838533401489 True -4 14670 31.944878339767456 0.54976487159729 431.0142517089844 0.42828646302223206 549.5823974609375 0.726767897605896 0.69133604 0.5107887983322144 True -5 17604 31.88427472114563 0.5438477993011475 394.43377685546875 0.35107260942459106 546.9127197265625 0.7299288511276245 0.6956933 0.4644728899002075 True -6 20538 31.86696457862854 0.5482339859008789 410.8319091796875 0.3736979365348816 545.0364990234375 0.7315860390663147 0.7044992 0.4484165906906128 True -7 23472 31.98621702194214 0.5799682140350342 526.78857421875 0.40903177857398987 542.1350708007812 0.7342965006828308 0.7143044 0.43654876947402954 True -8 26406 31.92266058921814 0.5469608306884766 449.7690124511719 0.5397509336471558 540.9110717773438 0.7361076474189758 0.7190364 0.4332793951034546 True -9 29340 32.03209137916565 0.5478482246398926 491.912353515625 0.36766600608825684 537.6620483398438 0.7387813329696655 0.72553116 0.4107969105243683 True -10 32274 31.92850971221924 3.3732821941375732 468.9239501953125 0.3942772150039673 535.2638549804688 0.7407927513122559 0.73637855 0.37940269708633423 True -11 35208 32.004976749420166 0.5668871402740479 446.4810791015625 0.3893347978591919 533.0623779296875 0.7430232763290405 0.7461442 0.3641102612018585 True -12 38142 31.908416032791138 0.5647032260894775 366.40191650390625 0.2154092788696289 531.5289916992188 0.7447558641433716 0.7534342 0.35747435688972473 True -13 41076 31.925039052963257 0.5572881698608398 418.1953125 0.2213256061077118 530.0899047851562 0.7463167309761047 0.7601685 0.3469858169555664 True -14 44010 31.939982414245605 0.5542035102844238 470.7565612792969 0.2169399857521057 528.5487670898438 0.7476418614387512 0.76979357 0.33093804121017456 True -15 46944 31.860042810440063 0.5386373996734619 442.6907043457031 0.2140396237373352 527.550537109375 0.7484688758850098 0.77820873 0.3164912760257721 True -16 49878 31.91043734550476 1.4663798809051514 446.339599609375 0.21237064898014069 527.0907592773438 0.7489392757415771 0.78154856 0.313668817281723 True -17 52812 31.89698839187622 0.8331270217895508 420.1749572753906 0.3089595437049866 527.182861328125 0.7488585114479065 0.78126085 0.31356561183929443 False -18 55746 31.944010496139526 0.5754759311676025 457.3899230957031 0.23530817031860352 527.3135986328125 0.7486485838890076 0.7821363 0.3148781657218933 True -19 58680 31.94514298439026 0.5545244216918945 462.374755859375 0.17355391383171082 527.3367309570312 0.748424232006073 0.78071034 0.3169565796852112 False diff --git a/ENCSR589ROM/cherimoya.fold_2.performance.tsv b/ENCSR589ROM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e157928bfa78747b726fd6572f351f6e831a537e..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -527.3135986328125 0.21273548901081085 0.7486485242843628 0.3430033326148987 0.7821363210678101 0.7270603179931641 0.3148781657218933 \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_3.evaluate.json b/ENCSR589ROM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a7958b8a3cf526597c2fe116def751325c66d46c..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF684OHX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_3.fit.json b/ENCSR589ROM/cherimoya.fold_3.fit.json deleted file mode 100644 index 4762f9f184fc291fec33c2007058ccc3ade47455..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF684OHX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_3.log b/ENCSR589ROM/cherimoya.fold_3.log deleted file mode 100644 index 445f724138a35d6a1ebbf1c51c9bd7f99be04022..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2838 36.02061367034912 3.6315200328826904 536.607177734375 0.5251985192298889 687.9775390625 0.5594445466995239 0.5811893 9.403326034545898 True -1 5676 31.362224102020264 0.7078418731689453 396.660888671875 0.52736896276474 566.81689453125 0.7099767327308655 0.66007066 1.8029173612594604 True -2 8514 31.5389883518219 0.5949482917785645 399.444091796875 0.47338399291038513 552.7264404296875 0.7223210334777832 0.64471805 0.6952800154685974 False -3 11352 31.51163148880005 0.607475757598877 402.28448486328125 0.3083916902542114 547.8546142578125 0.7268974184989929 0.6544959 0.6253089308738708 False -4 14190 31.479334592819214 0.8553867340087891 479.94061279296875 0.39174169301986694 544.3623046875 0.7305248379707336 0.66333824 0.5343006253242493 True -5 17028 31.529914140701294 0.9808182716369629 541.5984497070312 0.445203959941864 542.2153930664062 0.732786238193512 0.6668331 0.5004497766494751 True -6 19866 31.66237473487854 0.5826213359832764 439.2770080566406 0.5234823226928711 539.8657836914062 0.7352287173271179 0.6844332 0.4906768798828125 True -7 22704 31.659892559051514 0.5926504135131836 412.6448974609375 0.23321564495563507 537.537353515625 0.7373864650726318 0.6971087 0.4655671715736389 True -8 25542 31.634997844696045 0.5792059898376465 447.8121337890625 0.38780635595321655 535.5089721679688 0.7394425272941589 0.70361584 0.4458746314048767 True -9 28380 31.692658185958862 0.5789210796356201 479.9375 0.34135523438453674 533.1888427734375 0.7417999505996704 0.7112372 0.4280223846435547 True -10 31218 31.73012614250183 0.5711100101470947 430.8820495605469 0.3448804020881653 531.2576904296875 0.7438159584999084 0.7198497 0.4102316200733185 True -11 34056 31.644424438476562 0.666264533996582 411.585205078125 0.2798529863357544 528.7041015625 0.7459079623222351 0.72985923 0.39526987075805664 True -12 36894 31.600369930267334 26.764835119247437 416.36468505859375 0.42455872893333435 526.8606567382812 0.7477988600730896 0.7432245 0.38036876916885376 True -13 39732 31.93715214729309 17.999752044677734 507.9288330078125 0.2851743698120117 525.0097045898438 0.7497169375419617 0.75343627 0.3607476055622101 True -14 42570 31.620405673980713 0.5808737277984619 391.07183837890625 0.35329198837280273 523.4751586914062 0.7510438561439514 0.7611619 0.34673020243644714 True -15 45408 31.662954568862915 0.5901310443878174 400.54473876953125 0.26909175515174866 522.0368041992188 0.7520352005958557 0.7671363 0.3348597586154938 True -16 48246 31.801011323928833 0.5751161575317383 425.1503601074219 0.34586209058761597 521.4097900390625 0.7525365352630615 0.77201927 0.3266359865665436 True -17 51084 31.667904376983643 0.5853922367095947 370.1373291015625 0.23983630537986755 521.3504638671875 0.7524772882461548 0.77517676 0.32166653871536255 True -18 53922 31.69032120704651 2.2403676509857178 455.4588623046875 0.21811392903327942 521.3434448242188 0.7522024512290955 0.7722436 0.3228418231010437 False -19 56760 31.05570912361145 0.5795061588287354 399.57037353515625 0.19628487527370453 521.7113037109375 0.7518870830535889 0.7708117 0.32454806566238403 False diff --git a/ENCSR589ROM/cherimoya.fold_3.performance.tsv b/ENCSR589ROM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 39841347a46e0d535af41bfef17f1a76bcca1979..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -521.3504638671875 0.2113126665353775 0.75247722864151 0.33954957127571106 0.7751767635345459 0.7198958396911621 0.32166653871536255 \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_4.evaluate.json b/ENCSR589ROM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 560e7ba30af0ca2fe35897aeab02a9eda7afa360..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF684OHX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_4.fit.json b/ENCSR589ROM/cherimoya.fold_4.fit.json deleted file mode 100644 index dec3caee0e40bfaefb175f85695338add9b304c6..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF684OHX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR589ROM/cherimoya.fold_4.log b/ENCSR589ROM/cherimoya.fold_4.log deleted file mode 100644 index b2c43c21eefd7ae7dd966bb7c3bbf6801676ba51..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.577438831329346 4.132826566696167 485.5059814453125 0.544391930103302 680.2728881835938 0.5495082139968872 0.597319 7.401524066925049 True -1 5772 32.08697485923767 1.5339305400848389 484.9224853515625 0.6632592678070068 554.9562377929688 0.7076220512390137 0.68159944 1.3171110153198242 True -2 8658 32.130340814590454 0.607750415802002 436.87359619140625 0.417458713054657 539.7969360351562 0.7195824980735779 0.6780456 0.5579543113708496 False -3 11544 32.22754788398743 0.5744435787200928 466.8025817871094 0.4749535620212555 534.3496704101562 0.7250813841819763 0.69553417 0.5332348942756653 True -4 14430 32.87052774429321 11.331724405288696 380.943603515625 0.38914093375205994 531.16357421875 0.7279080152511597 0.6983749 0.46001091599464417 True -5 17316 32.17054510116577 0.568089485168457 404.25274658203125 0.2945290207862854 529.4072875976562 0.7313465476036072 0.7019921 0.4416961371898651 True -6 20202 32.25700330734253 0.8317792415618896 477.6695556640625 0.41539639234542847 526.7546997070312 0.7338382601737976 0.7107196 0.41201484203338623 True -7 23088 32.19125843048096 0.5745785236358643 502.16339111328125 0.4196619987487793 524.9368896484375 0.7359173893928528 0.71721256 0.3992631137371063 True -8 25974 32.18967080116272 0.5615575313568115 478.1897277832031 0.3069266676902771 522.9708862304688 0.7379350066184998 0.7236424 0.38365063071250916 True -9 28860 32.184332609176636 0.5714163780212402 426.916015625 0.28249722719192505 521.3014526367188 0.7398397326469421 0.7273598 0.37349072098731995 True -10 31746 32.13990521430969 0.5625689029693604 370.44012451171875 0.5064787864685059 519.4254760742188 0.7419034242630005 0.7391216 0.36123019456863403 True -11 34632 32.18593668937683 0.569720983505249 419.90411376953125 0.21665628254413605 517.567138671875 0.7436463236808777 0.7503076 0.3452726900577545 True -12 37518 32.23942446708679 0.5864963531494141 435.88580322265625 0.2727004289627075 515.9290771484375 0.7456050515174866 0.75866294 0.33298325538635254 True -13 40404 32.23287582397461 0.6210892200469971 414.9680480957031 0.33530503511428833 514.3438720703125 0.7472538948059082 0.76569927 0.32539740204811096 True -14 43290 32.17147159576416 0.5603022575378418 444.28955078125 0.32121723890304565 513.31103515625 0.7484766840934753 0.7730504 0.3163966238498688 True -15 46176 32.19156837463379 0.5935742855072021 407.1982421875 0.31133604049682617 512.1995849609375 0.7493773102760315 0.78157324 0.3041762113571167 True -16 49062 32.17139720916748 0.6748805046081543 436.8940124511719 0.34985771775245667 511.8123779296875 0.749767541885376 0.7866858 0.2991744577884674 True -17 51948 32.152052879333496 0.5599145889282227 409.9441223144531 0.22687746584415436 511.9197082519531 0.749548077583313 0.78828007 0.29658180475234985 True -18 54834 32.10185384750366 0.567305326461792 402.5144958496094 0.20660972595214844 511.984375 0.7493433356285095 0.79046965 0.2978680431842804 True -19 57720 32.16649079322815 0.5643453598022461 441.9959716796875 0.18276876211166382 512.3272094726562 0.749127209186554 0.7881416 0.2981444001197815 False diff --git a/ENCSR589ROM/cherimoya.fold_4.performance.tsv b/ENCSR589ROM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3749137f1b2f6cc32f16fa6559117118bbabeab5..0000000000000000000000000000000000000000 --- a/ENCSR589ROM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -511.984375 0.21494996547698975 0.7493433356285095 0.33560293912887573 0.7904696464538574 0.7164812088012695 0.2978680431842804 \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_0.evaluate.json b/ENCSR590EFT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 82c42afbd34720a6f1363c364ff7f70f54d18541..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF934GCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_0.fit.json b/ENCSR590EFT/cherimoya.fold_0.fit.json deleted file mode 100644 index 49832682dbb63ff002eb7995989765848245f156..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF934GCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_0.log b/ENCSR590EFT/cherimoya.fold_0.log deleted file mode 100644 index 29120fbed73615e0975deae701589d3cdefbee2a..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2796 35.88768219947815 3.8574724197387695 395.6407470703125 0.2598596513271332 482.06195068359375 0.24430470168590546 0.8044605 3.041785478591919 True -1 5592 31.026233911514282 0.6197528839111328 401.06719970703125 0.10374198853969574 466.30755615234375 0.27543479204177856 0.833185 0.5567433834075928 True -2 8388 31.026153087615967 0.5692377090454102 406.020751953125 0.13724234700202942 460.6145324707031 0.28463074564933777 0.86211413 0.19290921092033386 True -3 11184 31.03596067428589 1.5594136714935303 397.73236083984375 0.16257542371749878 458.7810363769531 0.2875606119632721 0.8670627 0.15650060772895813 True -4 13980 31.042454719543457 0.5619361400604248 392.9790344238281 0.06515573710203171 458.02606201171875 0.28936290740966797 0.8730838 0.13388586044311523 True -5 16776 31.098948001861572 0.5722522735595703 360.9840087890625 0.17843486368656158 457.0758361816406 0.29087695479393005 0.8765353 0.13965322077274323 True -6 19572 30.985004901885986 0.6470415592193604 356.75103759765625 0.08964784443378448 456.0257568359375 0.29364213347435 0.8825679 0.12974482774734497 True -7 22368 30.992716312408447 0.57244873046875 392.2744445800781 0.13921427726745605 455.8096008300781 0.29354074597358704 0.88740194 0.12029021233320236 True -8 25164 30.98773980140686 0.5528445243835449 406.361328125 0.23021240532398224 455.3360290527344 0.29416126012802124 0.8912813 0.12160750478506088 True -9 27960 30.991896152496338 0.5733704566955566 382.5047607421875 0.18028298020362854 454.0348205566406 0.2968631088733673 0.8954999 0.10943000763654709 True -10 30756 30.920604705810547 0.5649580955505371 414.8935546875 0.0843639001250267 454.0121154785156 0.29725655913352966 0.89782465 0.10369138419628143 True -11 33552 30.408653497695923 0.543144702911377 403.143310546875 0.08516311645507812 453.18756103515625 0.29883068799972534 0.90324295 0.09865578263998032 True -12 36348 30.377652883529663 0.5542736053466797 393.3280334472656 0.1338963508605957 452.6083984375 0.2992940843105316 0.9079347 0.09116409718990326 True -13 39144 30.373759031295776 0.5618345737457275 387.2169189453125 0.10728859156370163 452.02685546875 0.3004869818687439 0.9103703 0.08572451025247574 True -14 41940 30.506407737731934 0.744774580001831 392.1036071777344 0.11605793237686157 451.5721130371094 0.3014064431190491 0.9129084 0.08150560408830643 True -15 44736 30.417341947555542 0.5661964416503906 380.27294921875 0.0941145047545433 451.1662902832031 0.30254030227661133 0.9158792 0.07935789972543716 True -16 47532 30.433412075042725 0.56007981300354 397.8017272949219 0.06105904281139374 450.9592590332031 0.30284690856933594 0.91836256 0.07730576395988464 True -17 50328 30.399227619171143 0.5765511989593506 421.27874755859375 0.05086561664938927 451.0487976074219 0.3022916913032532 0.91771346 0.07598976790904999 False -18 53124 30.417511463165283 0.5686624050140381 409.20013427734375 0.048214737325906754 450.6497802734375 0.3034375309944153 0.91813487 0.0761890858411789 False -19 55920 30.459842920303345 0.5596163272857666 425.407958984375 0.2846154570579529 451.0755310058594 0.3018716871738434 0.9173606 0.07617367804050446 False diff --git a/ENCSR590EFT/cherimoya.fold_0.performance.tsv b/ENCSR590EFT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index bf84af263f868b0e086910c0f414d00fa7c48a82..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -450.9592590332031 0.44494402408599854 0.30284690856933594 0.10715848952531815 0.918362557888031 0.9039835929870605 0.07730576395988464 \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_1.evaluate.json b/ENCSR590EFT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0dedf099c41523687d7fdf5e4996c54537561624..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF934GCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_1.fit.json b/ENCSR590EFT/cherimoya.fold_1.fit.json deleted file mode 100644 index 9ca33322df5fd33ff4a5e3e477f0b775a693ba27..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF934GCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_1.log b/ENCSR590EFT/cherimoya.fold_1.log deleted file mode 100644 index fe0302c92028d42b1ac350f0d422e16c58050eb2..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2775 35.45045709609985 3.73572039604187 351.359375 0.216607928276062 541.5140380859375 0.2475046068429947 0.7946094 2.8385837078094482 True -1 5550 30.761128902435303 0.6872844696044922 388.7052001953125 0.15352247655391693 519.8617553710938 0.2849445343017578 0.8287343 0.6754982471466064 True -2 8325 30.976892948150635 12.486612558364868 386.8924560546875 0.2005384862422943 514.5525512695312 0.29317957162857056 0.85543793 0.31387847661972046 True -3 11100 30.78800892829895 1.597862958908081 477.51806640625 0.15060469508171082 511.1517639160156 0.29635682702064514 0.8710043 0.20920796692371368 True -4 13875 30.838600873947144 1.4404535293579102 373.93609619140625 0.10738930106163025 508.97900390625 0.29979050159454346 0.8746641 0.17852140963077545 True -5 16650 30.799826622009277 1.3685967922210693 440.9685363769531 0.12009691447019577 506.5618591308594 0.30477041006088257 0.8799797 0.17481322586536407 True -6 19425 30.82054591178894 0.6905932426452637 355.6177978515625 0.11947338283061981 506.1177978515625 0.3039538860321045 0.8865315 0.1680346578359604 True -7 22200 30.89318299293518 0.6867427825927734 366.6019287109375 0.18168897926807404 504.6522216796875 0.30663061141967773 0.89423114 0.15252119302749634 True -8 24975 30.93521475791931 0.6682000160217285 429.61083984375 0.0980600118637085 502.875732421875 0.3101048469543457 0.8973836 0.1462068110704422 True -9 27750 30.92842388153076 0.680293083190918 438.979736328125 0.10063744336366653 502.1634216308594 0.31130266189575195 0.901749 0.12968619167804718 True -10 30525 30.898157596588135 0.7025942802429199 355.6754150390625 0.1882447898387909 501.23968505859375 0.3123800456523895 0.9060564 0.1196722686290741 True -11 33300 30.91723942756653 0.6737010478973389 449.94708251953125 0.13195177912712097 500.3673095703125 0.3135790228843689 0.90953755 0.11300992965698242 True -12 36075 30.835352897644043 1.1145813465118408 394.90899658203125 0.12555155158042908 499.2190856933594 0.3155701756477356 0.91338414 0.10425177961587906 True -13 38850 30.844916105270386 1.2514991760253906 377.02154541015625 0.05719145014882088 497.9158020019531 0.3184627890586853 0.915094 0.10090001672506332 True -14 41625 30.952828407287598 0.6625792980194092 421.4488830566406 0.10779242217540741 498.0121154785156 0.31713008880615234 0.92088884 0.09625768661499023 True -15 44400 30.87466812133789 0.705981969833374 420.02728271484375 0.1652047038078308 497.3255310058594 0.31870436668395996 0.92150456 0.09266439825296402 True -16 47175 30.92432427406311 1.5709731578826904 412.59576416015625 0.07832242548465729 497.4093322753906 0.3182004690170288 0.9243654 0.09041914343833923 True -17 49950 30.946548223495483 0.6636204719543457 336.02008056640625 0.05503373593091965 497.026611328125 0.31883737444877625 0.92668253 0.08766317367553711 True -18 52725 30.918878078460693 9.06533169746399 402.42474365234375 0.10847832262516022 496.9395751953125 0.3191920518875122 0.92586625 0.08714843541383743 False -19 55500 30.94508385658264 22.340818881988525 353.22528076171875 0.08381879329681396 497.3419494628906 0.31782472133636475 0.9252132 0.08735726028680801 False diff --git a/ENCSR590EFT/cherimoya.fold_1.performance.tsv b/ENCSR590EFT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b7af780ef5724faa756648171b431f9c44660e47..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -497.026611328125 0.43214136362075806 0.31883740425109863 0.12015902996063232 0.9266825318336487 0.9191759824752808 0.08766317367553711 \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_2.evaluate.json b/ENCSR590EFT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2b1a452a12c6a6848a29e532eff767b037180e52..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF934GCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_2.fit.json b/ENCSR590EFT/cherimoya.fold_2.fit.json deleted file mode 100644 index a845209722fd2d99c083ffa627f0d461d1f5fcb7..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF934GCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_2.log b/ENCSR590EFT/cherimoya.fold_2.log deleted file mode 100644 index 9fafca6f2f212e0131d53cd3339a61549cd90ed7..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2904 37.010387897491455 3.4225940704345703 443.3571472167969 0.23284119367599487 514.9835205078125 0.24784579873085022 0.78555596 2.317836284637451 True -1 5808 32.23808979988098 0.522533655166626 363.32232666015625 0.13852429389953613 497.1465148925781 0.27827274799346924 0.8235953 0.44836145639419556 True -2 8712 32.2429301738739 0.5970005989074707 428.69464111328125 0.12034487724304199 490.3874816894531 0.2877814471721649 0.8508264 0.17459172010421753 True -3 11616 32.25881266593933 0.519923210144043 400.02862548828125 0.16710013151168823 488.04119873046875 0.29184475541114807 0.8593798 0.15876330435276031 True -4 14520 32.17074131965637 0.5199501514434814 400.2061767578125 0.08556763827800751 487.4040222167969 0.2925921380519867 0.8629152 0.14890940487384796 True -5 17424 32.15688705444336 0.5085480213165283 461.927490234375 0.18193022906780243 487.17779541015625 0.2923571765422821 0.861766 0.1594165861606598 False -6 20328 32.151833295822144 0.5209918022155762 467.4200439453125 0.1679578423500061 485.1315612792969 0.2975146174430847 0.86507946 0.1529546082019806 True -7 23232 32.16176223754883 0.5172438621520996 380.25927734375 0.12415117025375366 484.42095947265625 0.2985028028488159 0.8701726 0.1427091807126999 True -8 26136 32.254064321517944 0.5176260471343994 393.1076354980469 0.2950100302696228 483.62261962890625 0.2993505895137787 0.8750568 0.13590127229690552 True -9 29040 32.20825505256653 0.5227651596069336 439.66937255859375 0.09150490164756775 483.2315368652344 0.30034780502319336 0.8815872 0.12389542907476425 True -10 31944 32.22095036506653 0.5195140838623047 410.44500732421875 0.12328613549470901 482.6574401855469 0.3010691702365875 0.8852952 0.12096688151359558 True -11 34848 32.23272657394409 0.5183942317962646 386.9369812011719 0.13410046696662903 481.72845458984375 0.30233776569366455 0.88983774 0.11193609237670898 True -12 37752 32.17844820022583 8.471511602401733 448.7637939453125 0.07767216861248016 481.0378723144531 0.3042195439338684 0.89377654 0.10995709896087646 True -13 40656 32.24594068527222 0.5225214958190918 429.62042236328125 0.11175579577684402 480.77313232421875 0.3041476309299469 0.8983498 0.10397368669509888 True -14 43560 32.26159405708313 1.0335097312927246 435.029541015625 0.05013184994459152 479.63861083984375 0.30661770701408386 0.8998251 0.09949538111686707 True -15 46464 32.2639696598053 0.5234405994415283 404.6893005371094 0.12047939002513885 479.6685485839844 0.3058314025402069 0.9047208 0.09502661228179932 True -16 49368 32.256423234939575 0.5227189064025879 399.82574462890625 0.07896746695041656 479.2181396484375 0.30724036693573 0.9061407 0.09297296404838562 True -17 52272 32.24215602874756 0.5140042304992676 358.2014465332031 0.08314310759305954 479.2808837890625 0.3069753050804138 0.9051816 0.09099265187978745 False -18 55176 32.241302251815796 0.5092480182647705 379.25677490234375 0.061342328786849976 479.3314514160156 0.30659976601600647 0.90555006 0.09020373225212097 False -19 58080 32.18930625915527 0.5180985927581787 361.4791259765625 0.06077185273170471 479.38494873046875 0.3069029450416565 0.9056824 0.09060026705265045 False diff --git a/ENCSR590EFT/cherimoya.fold_2.performance.tsv b/ENCSR590EFT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 580841ef598f6a9dfc9f666af9fb379c43219945..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -479.2181396484375 0.4386066794395447 0.3072403073310852 0.11444777995347977 0.9061406850814819 0.8937841057777405 0.09297296404838562 \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_3.evaluate.json b/ENCSR590EFT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ee8de4736891d0a143659cfe585d0a725c52ea08..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF934GCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_3.fit.json b/ENCSR590EFT/cherimoya.fold_3.fit.json deleted file mode 100644 index 677b779c7347a21bdc673d557f226003bc090711..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF934GCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_3.log b/ENCSR590EFT/cherimoya.fold_3.log deleted file mode 100644 index 0efb0e930f84cc5bebed5aaa43b21075347727e8..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 36.00155806541443 3.435474395751953 427.6314697265625 0.1348879486322403 476.0423278808594 0.24902673065662384 0.77753067 2.629425287246704 True -1 5584 30.98666286468506 0.6865370273590088 461.3338623046875 0.1598273515701294 459.7819519042969 0.2810279428958893 0.8135964 0.5900164246559143 True -2 8376 30.987054347991943 0.5504131317138672 377.30584716796875 0.1290118396282196 456.4593200683594 0.2846730947494507 0.8437587 0.20457957684993744 True -3 11168 30.53002619743347 0.5325429439544678 388.0889892578125 0.20278391242027283 454.6213073730469 0.28851670026779175 0.8546757 0.2300785779953003 True -4 13960 30.413639783859253 0.5233745574951172 339.20391845703125 0.17176294326782227 453.2402038574219 0.2909846305847168 0.8582043 0.14923955500125885 True -5 16752 30.42816734313965 0.5271644592285156 419.18218994140625 0.1665632277727127 452.7880554199219 0.2924467623233795 0.85683274 0.1556297391653061 False -6 19544 30.387718677520752 0.5245926380157471 396.3941650390625 0.12234728783369064 451.68731689453125 0.29504770040512085 0.86305743 0.1470186561346054 True -7 22336 30.42316722869873 0.5350639820098877 401.7334289550781 0.13499650359153748 450.93389892578125 0.29625651240348816 0.8681342 0.14270098507404327 True -8 25128 30.436420440673828 0.526818037033081 375.1976623535156 0.15253007411956787 450.8226318359375 0.2958664894104004 0.87417585 0.1342984288930893 True -9 27920 30.376471996307373 0.512423038482666 402.9079895019531 0.08404286205768585 450.27294921875 0.29718154668807983 0.87901676 0.13882532715797424 True -10 30712 30.4354350566864 0.5285539627075195 383.1064758300781 0.2059827446937561 449.49835205078125 0.2976264953613281 0.88422334 0.1240202859044075 True -11 33504 30.372187614440918 0.5171220302581787 448.2625732421875 0.22788769006729126 448.13348388671875 0.30117589235305786 0.88780266 0.11628483980894089 True -12 36296 30.40366291999817 0.5239169597625732 443.78839111328125 0.09446189552545547 447.70611572265625 0.30152493715286255 0.89350337 0.10652785748243332 True -13 39088 30.348254442214966 0.5169146060943604 449.4703674316406 0.11324901133775711 447.1116943359375 0.302372545003891 0.89650685 0.1033940315246582 True -14 41880 30.34412717819214 0.9060516357421875 349.076416015625 0.10523823648691177 446.52252197265625 0.3030559718608856 0.90117586 0.0962439477443695 True -15 44672 30.484428644180298 0.541085958480835 409.2394714355469 0.08035878837108612 445.8974914550781 0.30474796891212463 0.9030694 0.09328996390104294 True -16 47464 30.396934032440186 0.585430383682251 451.46673583984375 0.1578150987625122 445.8730773925781 0.3041403591632843 0.9049945 0.0910722017288208 True -17 50256 30.34854221343994 0.5191357135772705 395.4127197265625 0.09278964251279831 445.5680847167969 0.3051665127277374 0.9066233 0.08965083956718445 True -18 53048 30.414724111557007 0.5354642868041992 417.997802734375 0.06967414170503616 446.2449951171875 0.30314332246780396 0.9073426 0.0900975689291954 True -19 55840 30.345228910446167 0.6749322414398193 376.1971435546875 0.08402913808822632 446.13665771484375 0.3038019835948944 0.90492296 0.09039679169654846 False diff --git a/ENCSR590EFT/cherimoya.fold_3.performance.tsv b/ENCSR590EFT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4c67784734f6b49ae5f5f3cf065254bd182be719..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -446.2449951171875 0.4448480010032654 0.30314332246780396 0.10875809192657471 0.9073426127433777 0.8907434940338135 0.0900975689291954 \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_4.evaluate.json b/ENCSR590EFT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1d09cae38bbdd53f579d74762a5efdf77b764c25..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF934GCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_4.fit.json b/ENCSR590EFT/cherimoya.fold_4.fit.json deleted file mode 100644 index 3c1fef30cd8459bcbd8bd6814cfce80d21fa1668..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF934GCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR590EFT/cherimoya.fold_4.log b/ENCSR590EFT/cherimoya.fold_4.log deleted file mode 100644 index 122028785e9b2625b9b0e16476917dbdd96138ea..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2823 36.55321764945984 4.906149625778198 384.8663330078125 0.1192273497581482 453.9618225097656 0.24407131969928741 0.8092643 2.311771869659424 True -1 5646 31.300999402999878 0.702988862991333 394.7748107910156 0.17275339365005493 440.71844482421875 0.2707729637622833 0.8400721 0.5020511746406555 True -2 8469 31.37818169593811 0.6362385749816895 376.5648193359375 0.0928410217165947 437.2115173339844 0.27610212564468384 0.8591485 0.3130272328853607 True -3 11292 31.312408208847046 0.6324081420898438 378.6934509277344 0.12578821182250977 434.978759765625 0.28026407957077026 0.8685431 0.14313822984695435 True -4 14115 31.314861059188843 0.6553876399993896 432.7822265625 0.38579124212265015 434.4014587402344 0.2813012897968292 0.872278 0.13034304976463318 True -5 16938 31.32007908821106 1.5094316005706787 376.49017333984375 0.1755918264389038 432.9403076171875 0.28428441286087036 0.87715966 0.1223682314157486 True -6 19761 30.741697072982788 0.8097224235534668 365.22100830078125 0.20188236236572266 432.31805419921875 0.2856152057647705 0.88110256 0.11057422310113907 True -7 22584 30.66126561164856 2.0302274227142334 371.45068359375 0.4166697859764099 431.6874694824219 0.2870391607284546 0.88604134 0.11157447844743729 True -8 25407 30.695924043655396 0.6459922790527344 373.2003479003906 0.11005900800228119 431.3779296875 0.2868567109107971 0.88620025 0.10169760137796402 True -9 28230 30.678824424743652 1.2720072269439697 437.356201171875 0.1308693289756775 430.71417236328125 0.2890324592590332 0.8906121 0.09741593152284622 True -10 31053 30.70774555206299 0.6403305530548096 357.11517333984375 0.09218661487102509 430.1393737792969 0.2896488308906555 0.89690113 0.09256891906261444 True -11 33876 30.741708040237427 11.082064867019653 357.68011474609375 0.10886166989803314 429.4991455078125 0.29104357957839966 0.8999958 0.08751371502876282 True -12 36699 30.7741539478302 11.273635864257812 406.45794677734375 0.07647958397865295 429.0943908691406 0.29185909032821655 0.90272737 0.0840674564242363 True -13 39522 30.75468158721924 15.764957189559937 365.57958984375 0.08193840086460114 428.7456970214844 0.2924038767814636 0.9065241 0.0810622125864029 True -14 42345 31.01643991470337 0.6188304424285889 416.9805908203125 0.14592793583869934 428.09588623046875 0.29381611943244934 0.90932703 0.0779958963394165 True -15 45168 31.20568585395813 0.6141517162322998 396.19805908203125 0.08928835391998291 427.806396484375 0.2944841682910919 0.91393536 0.07610055804252625 True -16 47991 30.77405548095703 1.075202465057373 327.8480224609375 0.19281624257564545 427.4935302734375 0.29508593678474426 0.9138317 0.07373985648155212 False -17 50814 31.120170831680298 0.6296288967132568 393.4285888671875 0.07639415562152863 427.5361633300781 0.29420310258865356 0.9144385 0.07249197363853455 True -18 53637 30.7722749710083 0.6214520931243896 399.80841064453125 0.04709776118397713 427.7421875 0.2939910292625427 0.916222 0.07236605882644653 True -19 56460 30.710046529769897 0.6139678955078125 368.6102294921875 0.06935294717550278 427.6287841796875 0.2944748103618622 0.91573334 0.07253710925579071 False diff --git a/ENCSR590EFT/cherimoya.fold_4.performance.tsv b/ENCSR590EFT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 22e5c10abb4d8c0ab38c379e125c5bf121f77091..0000000000000000000000000000000000000000 --- a/ENCSR590EFT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -427.7421875 0.4530104398727417 0.2939910292625427 0.09898067265748978 0.9162219762802124 0.8998091220855713 0.07236605882644653 \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_0.evaluate.json b/ENCSR591PIX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b39f6d2cc094dc1b4d6cfb59be2690c0d138f5db..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF536CUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_0.fit.json b/ENCSR591PIX/cherimoya.fold_0.fit.json deleted file mode 100644 index b476b513085f6098695748a85fc5509124318dc4..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF536CUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_0.log b/ENCSR591PIX/cherimoya.fold_0.log deleted file mode 100644 index b131ff0445c8c946fe255440b9826cddf5f3ec7c..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2927 36.989908933639526 3.4296457767486572 434.805419921875 0.9570518732070923 610.6068115234375 0.6045980453491211 0.6583988 5.9927568435668945 True -1 5854 32.366605281829834 0.5343976020812988 440.0262756347656 1.0167579650878906 526.7617797851562 0.7006320953369141 0.66849256 1.720332384109497 True -2 8781 32.29102802276611 0.5105698108673096 440.3424377441406 0.7318603992462158 510.9286193847656 0.7137372493743896 0.6775418 0.7934149503707886 True -3 11708 32.25157117843628 1.7128558158874512 353.13946533203125 0.9135112762451172 505.9110107421875 0.7194514274597168 0.67828155 0.721474826335907 True -4 14635 32.04808807373047 1.6957824230194092 454.5859375 0.9031898975372314 502.7744445800781 0.7225424647331238 0.6866795 0.669089138507843 True -5 17562 31.69868040084839 0.5013303756713867 408.347900390625 0.5762498378753662 501.1905212402344 0.724757730960846 0.68880963 0.6636393070220947 True -6 20489 31.700525045394897 2.17441463470459 395.70794677734375 0.7071913480758667 499.8221740722656 0.7261467576026917 0.69430465 0.5990286469459534 True -7 23416 31.645525693893433 0.5088529586791992 450.43975830078125 0.8254151940345764 497.69659423828125 0.7282387018203735 0.6988401 0.5857018232345581 True -8 26343 31.70431351661682 5.009253025054932 387.84307861328125 0.6920761466026306 496.21539306640625 0.729989767074585 0.70322114 0.5693650245666504 True -9 29270 31.789496898651123 0.5055639743804932 430.688232421875 0.46079957485198975 494.1022644042969 0.7320057153701782 0.712117 0.5355279445648193 True -10 32197 31.728987455368042 3.1723473072052 369.2022399902344 0.4861254096031189 492.3807678222656 0.7339479923248291 0.71882993 0.5271535515785217 True -11 35124 31.726415395736694 0.51310133934021 394.4615783691406 0.6413596272468567 491.0028076171875 0.7357676029205322 0.72301346 0.5188887119293213 True -12 38051 31.743760108947754 0.5125963687896729 444.3102111816406 0.7101805210113525 489.18890380859375 0.7375654578208923 0.7300795 0.5031520128250122 True -13 40978 31.69757866859436 0.5216042995452881 412.04144287109375 0.4888337552547455 488.1910705566406 0.7388037443161011 0.73429364 0.49691230058670044 True -14 43905 31.7582950592041 0.5127527713775635 453.7769470214844 0.4275580048561096 487.1907043457031 0.7397671937942505 0.7338868 0.5013639330863953 False -15 46832 31.941527605056763 0.5199148654937744 371.1487121582031 0.3829807937145233 487.09844970703125 0.740139901638031 0.7356769 0.5089449882507324 True -16 49759 31.84041929244995 1.709423303604126 382.102294921875 0.35932785272598267 487.1899108886719 0.7398806214332581 0.7334451 0.5294784903526306 False -17 52686 31.846415758132935 0.5499401092529297 401.71368408203125 0.30736181139945984 487.7893371582031 0.7392911911010742 0.72404844 0.5666700601577759 False -18 55613 31.893473625183105 0.5144999027252197 373.9303894042969 0.43857890367507935 488.2008972167969 0.7387070655822754 0.71706235 0.5959405899047852 False -19 58540 31.751065254211426 0.5229141712188721 418.753173828125 0.31459641456604004 488.3514709472656 0.738564670085907 0.7134322 0.6079179644584656 False diff --git a/ENCSR591PIX/cherimoya.fold_0.performance.tsv b/ENCSR591PIX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5343b641d90aa6e307b5a754a8936529f77be6da..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -487.09844970703125 0.21683597564697266 0.7401400208473206 0.34369367361068726 0.7356768846511841 0.7083660960197449 0.5089449882507324 \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_1.evaluate.json b/ENCSR591PIX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a0c5f8513a88d8312ba7d89747e5d8f47fdd4a58..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF536CUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_1.fit.json b/ENCSR591PIX/cherimoya.fold_1.fit.json deleted file mode 100644 index e8873161f76a95f4982646dd41fd4a2f81c4b69c..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF536CUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_1.log b/ENCSR591PIX/cherimoya.fold_1.log deleted file mode 100644 index a59c85d06beb3337ef101fdb3136a7f3c2111845..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2904 40.754987955093384 17.11885976791382 453.963623046875 0.8078078031539917 673.9653930664062 0.6164421439170837 0.6886433 6.792819499969482 True -1 5808 32.02830386161804 0.882849931716919 429.0891418457031 1.0877705812454224 571.633056640625 0.7163402438163757 0.71305645 1.6626838445663452 True -2 8712 31.987165212631226 0.8390712738037109 470.72772216796875 0.634329617023468 558.586181640625 0.7256751656532288 0.72296005 0.8588099479675293 True -3 11616 31.327304124832153 0.8219766616821289 469.68914794921875 0.6519712209701538 553.159912109375 0.7306066155433655 0.7274162 0.7951819896697998 True -4 14520 31.335273504257202 41.81892514228821 459.92578125 0.5721780061721802 548.128662109375 0.7352230548858643 0.7324464 0.6895110607147217 True -5 17424 32.9674870967865 1.6445019245147705 414.33428955078125 1.1523462533950806 546.6135864257812 0.7373130321502686 0.73634803 0.6564763784408569 True -6 20328 31.364660501480103 0.8322396278381348 396.0223388671875 0.727469265460968 544.4837036132812 0.7389377951622009 0.7394146 0.6078695058822632 True -7 23232 31.356160640716553 0.8554530143737793 424.60504150390625 0.6840744018554688 542.2752685546875 0.7408583760261536 0.7406868 0.5714985728263855 True -8 26136 31.374292850494385 0.8319430351257324 383.9180908203125 0.5745382308959961 540.4180297851562 0.742316722869873 0.7428982 0.5648177862167358 True -9 29040 31.428470134735107 0.8414783477783203 360.81109619140625 0.6980717182159424 538.1068725585938 0.7445276975631714 0.75163865 0.5337510108947754 True -10 31944 32.30447340011597 0.8506519794464111 364.622314453125 0.371075838804245 536.1727294921875 0.7465032339096069 0.7532011 0.5174033045768738 True -11 34848 31.414924383163452 0.8513212203979492 412.3907775878906 0.6571488976478577 534.2156372070312 0.7483861446380615 0.75947493 0.5003570318222046 True -12 37752 31.401654720306396 0.8222582340240479 414.61334228515625 0.5114412307739258 532.5508422851562 0.7500734925270081 0.7675737 0.47474855184555054 True -13 40656 31.419917583465576 0.824547529220581 356.9666748046875 0.7117329835891724 530.7655029296875 0.751522421836853 0.77196515 0.46749311685562134 True -14 43560 31.334260940551758 1.8983466625213623 400.0237121582031 0.4849061369895935 529.8965454101562 0.7523876428604126 0.77374744 0.4652848243713379 True -15 46464 31.384770154953003 0.8348708152770996 384.94500732421875 0.623624861240387 529.7462158203125 0.7527700066566467 0.7747495 0.48261281847953796 True -16 49368 33.193718910217285 32.9660370349884 370.514404296875 0.39140957593917847 529.8110961914062 0.7526229023933411 0.77234477 0.5062066316604614 False -17 52272 32.62119817733765 1.1902635097503662 487.45355224609375 0.2500830590724945 530.3878784179688 0.7520523071289062 0.7659748 0.5396119356155396 False -18 55176 31.41067671775818 31.15977931022644 344.252197265625 0.24034816026687622 530.8389282226562 0.7514837980270386 0.75845987 0.5698660612106323 False -19 58080 31.728784799575806 0.8384854793548584 404.3992919921875 0.27814796566963196 531.1332397460938 0.7511397004127502 0.75479144 0.5897431373596191 False diff --git a/ENCSR591PIX/cherimoya.fold_1.performance.tsv b/ENCSR591PIX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c91f8f3704557ac4a47bc06c49c4310ece9d4cd3..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -529.7462158203125 0.20410838723182678 0.7527700066566467 0.3704833686351776 0.7747495174407959 0.7628701329231262 0.48261281847953796 \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_2.evaluate.json b/ENCSR591PIX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9b44b96abc7b68e6dc4c1e4a5448d02ced22a975..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF536CUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_2.fit.json b/ENCSR591PIX/cherimoya.fold_2.fit.json deleted file mode 100644 index b2595ad6f9ffe27a72a3d02ca20d53059b119e85..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF536CUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_2.log b/ENCSR591PIX/cherimoya.fold_2.log deleted file mode 100644 index 55cc5197ba31cf3171ed350e7f45959aab89ee99..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3015 37.85847282409668 4.1038818359375 446.112548828125 0.5320958495140076 612.62744140625 0.6082925796508789 0.6603282 6.327146530151367 True -1 6030 33.326897382736206 0.6844942569732666 411.8536376953125 0.7906867861747742 526.431884765625 0.7004117965698242 0.7105058 1.2787703275680542 True -2 9045 33.367778301239014 44.64495897293091 412.5718994140625 0.741896390914917 514.9560546875 0.709442675113678 0.70867574 0.696715235710144 False -3 12060 33.181480169296265 0.660811185836792 396.4200134277344 0.5934097766876221 508.148193359375 0.7167816162109375 0.71316475 0.6098871231079102 True -4 15075 33.15953850746155 0.6755750179290771 420.010986328125 1.0963077545166016 505.601806640625 0.7191852927207947 0.7167089 0.5978780388832092 True -5 18090 33.24727511405945 1.6615588665008545 372.04339599609375 0.614119291305542 503.73956298828125 0.7208071947097778 0.7234823 0.5495782494544983 True -6 21105 33.184441804885864 0.669858455657959 386.866943359375 0.4041110575199127 502.1603698730469 0.7228298187255859 0.72760284 0.5394731163978577 True -7 24120 33.19230532646179 0.6821539402008057 310.96051025390625 0.875320553779602 500.51904296875 0.7241913080215454 0.7294083 0.5335135459899902 True -8 27135 33.28687500953674 1.14320707321167 515.232177734375 0.48772692680358887 498.8976135253906 0.7260618209838867 0.734955 0.5093002915382385 True -9 30150 33.351539611816406 0.6687331199645996 425.8385009765625 0.5507999658584595 497.18402099609375 0.7279563546180725 0.73672026 0.5179786682128906 True -10 33165 33.336190700531006 0.672990083694458 361.31402587890625 0.646905779838562 495.69439697265625 0.73012375831604 0.7426571 0.4972165822982788 True -11 36180 33.38181185722351 0.6736483573913574 423.7984619140625 0.5636137127876282 494.138427734375 0.7315670251846313 0.7462885 0.4921081066131592 True -12 39195 32.97280406951904 1.3600537776947021 423.515380859375 0.31590697169303894 492.4826354980469 0.7332428097724915 0.7511447 0.4756840765476227 True -13 42210 35.175787687301636 19.740585327148438 368.78668212890625 0.3455340266227722 491.2724914550781 0.7348609566688538 0.755302 0.4778006076812744 True -14 45225 32.77831673622131 0.6752617359161377 388.56787109375 0.39181727170944214 490.24267578125 0.735685408115387 0.7611626 0.47724470496177673 True -15 48240 32.72210454940796 0.6802783012390137 409.8255310058594 0.7223931550979614 489.88165283203125 0.7364895939826965 0.760614 0.4819566309452057 False -16 51255 33.33500027656555 4.0879411697387695 375.1890869140625 0.5490915775299072 489.9688415527344 0.736291766166687 0.7588157 0.498918354511261 False -17 54270 32.64715886116028 0.6677632331848145 414.07550048828125 0.4181099832057953 490.6504211425781 0.7355583310127258 0.75364107 0.5343876481056213 False -18 57285 32.6222608089447 0.6683981418609619 387.1876220703125 0.3949428200721741 491.08349609375 0.7348931431770325 0.748117 0.5646761059761047 False -19 60300 32.65593338012695 0.6679377555847168 375.27362060546875 0.23859436810016632 491.3613586425781 0.7346365451812744 0.74372363 0.5782673358917236 False diff --git a/ENCSR591PIX/cherimoya.fold_2.performance.tsv b/ENCSR591PIX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e0f64ddf1e2191a54c038e9682320d38e1e94b38..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -490.24267578125 0.2174672782421112 0.735685408115387 0.3450883626937866 0.7611625790596008 0.729566752910614 0.47724470496177673 \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_3.evaluate.json b/ENCSR591PIX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4430c35ecfeb7a714251d95dc698ffc061b831f0..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF536CUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_3.fit.json b/ENCSR591PIX/cherimoya.fold_3.fit.json deleted file mode 100644 index fe9d1beab4cc25fe7d53b77dad268706055c5238..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF536CUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_3.log b/ENCSR591PIX/cherimoya.fold_3.log deleted file mode 100644 index 2a332b4b2d704c7abd75b5dacbc4d470f4a6f28f..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2968 37.26719355583191 3.5614354610443115 482.8215637207031 0.7571738958358765 613.4214477539062 0.605841338634491 0.64500743 5.846687316894531 True -1 5936 32.65028786659241 0.5836806297302246 440.00408935546875 0.8892332315444946 527.6567993164062 0.6969960927963257 0.67812985 1.6430912017822266 True -2 8904 32.65073347091675 0.6021311283111572 326.7005615234375 0.5831460952758789 512.7366333007812 0.7093149423599243 0.686983 0.9733424782752991 True -3 11872 32.60345673561096 0.5935630798339844 411.9727478027344 0.5433343648910522 507.4592590332031 0.7151774764060974 0.6935553 0.8064652681350708 True -4 14840 32.67811679840088 0.6565322875976562 424.0064697265625 0.769199013710022 506.16607666015625 0.7167675495147705 0.6926743 0.7597970366477966 False -5 17808 32.759273290634155 5.904609441757202 364.020751953125 0.6667755246162415 505.30413818359375 0.7186065912246704 0.69686574 0.7519475221633911 True -6 20776 32.42614197731018 0.6616194248199463 407.80975341796875 0.7447463274002075 503.5804138183594 0.7205201983451843 0.70619196 0.6936752200126648 True -7 23744 32.252113819122314 0.5816752910614014 387.1983337402344 1.1174612045288086 502.2288513183594 0.7221238613128662 0.70309937 0.6942877173423767 False -8 26712 32.05790710449219 0.5767714977264404 376.63116455078125 0.951609194278717 500.8692932128906 0.7236482501029968 0.7124168 0.6450271606445312 True -9 29680 32.07472777366638 0.5832479000091553 410.91851806640625 0.7091370820999146 498.97271728515625 0.7254871129989624 0.71742696 0.6245481371879578 True -10 32648 32.121742963790894 0.589113712310791 438.28546142578125 0.4314645528793335 496.7361145019531 0.7277309894561768 0.7210663 0.606574535369873 True -11 35616 32.105305433273315 1.0309863090515137 373.2928466796875 0.5215550661087036 494.5458984375 0.7299795746803284 0.7314853 0.5872231721878052 True -12 38584 32.10764455795288 0.5742144584655762 403.8482971191406 0.5905938148498535 492.4244384765625 0.7319857478141785 0.74392176 0.5507937669754028 True -13 41552 31.994259119033813 0.5707402229309082 386.56060791015625 0.5101988911628723 491.0225830078125 0.733180582523346 0.74779934 0.5327414870262146 True -14 44520 32.0503613948822 1.8023030757904053 373.1557312011719 0.46399134397506714 489.3870544433594 0.7345582842826843 0.7547243 0.527764081954956 True -15 47488 32.043264865875244 0.5660815238952637 410.5546875 0.3895379900932312 489.1834716796875 0.7349438667297363 0.75826323 0.5325870513916016 True -16 50456 32.010164976119995 1.8754384517669678 417.04998779296875 0.5051199793815613 489.0980529785156 0.7346785068511963 0.75703675 0.548332154750824 False -17 53424 32.13837504386902 0.5765395164489746 386.78900146484375 0.31605130434036255 489.52911376953125 0.7341769933700562 0.7525013 0.5744536519050598 False -18 56392 32.04792332649231 0.5741045475006104 422.2742919921875 0.2562211751937866 489.9077453613281 0.7336199879646301 0.7457885 0.6036866903305054 False -19 59360 32.025811195373535 0.5643880367279053 425.65252685546875 0.26819106936454773 490.24871826171875 0.7332671880722046 0.74289924 0.6143516898155212 False diff --git a/ENCSR591PIX/cherimoya.fold_3.performance.tsv b/ENCSR591PIX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d951df5122841a7d861c6e75b276d9292c2ff10d..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -489.1834716796875 0.21847449243068695 0.7349438667297363 0.3396867513656616 0.7582632303237915 0.7313598394393921 0.5325870513916016 \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_4.evaluate.json b/ENCSR591PIX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0e1dda6c41bace246058665231696e7c605badd4..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF536CUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_4.fit.json b/ENCSR591PIX/cherimoya.fold_4.fit.json deleted file mode 100644 index 6d972f52d04eddaf41bda663a0a76b2b8139ca0d..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF536CUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR591PIX/cherimoya.fold_4.log b/ENCSR591PIX/cherimoya.fold_4.log deleted file mode 100644 index 81fb5719dd7c89e5598963179b6c8d9080d55840..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 35.66341495513916 3.5041966438293457 465.6080627441406 0.521465539932251 595.282470703125 0.5989091992378235 0.64234567 7.069770336151123 True -1 5784 31.930588722229004 1.096203327178955 389.05767822265625 0.7977252006530762 506.9015808105469 0.6970890164375305 0.6906585 1.3823556900024414 True -2 8676 31.9238760471344 0.6065869331359863 432.16253662109375 0.7189084887504578 494.1075744628906 0.706662118434906 0.694798 0.7708212733268738 True -3 11568 31.893345832824707 0.5999140739440918 404.2820129394531 0.7865908741950989 489.5393371582031 0.7115043997764587 0.7009432 0.6954857707023621 True -4 14460 31.906450033187866 0.600395917892456 453.3031005859375 0.5920895338058472 486.8207092285156 0.7141674160957336 0.70782506 0.6377831697463989 True -5 17352 31.92639398574829 0.5971875190734863 437.6219177246094 0.7056465744972229 484.81768798828125 0.7164852023124695 0.71345985 0.6200588345527649 True -6 20244 31.887523889541626 0.5933988094329834 366.2731018066406 0.6524832844734192 483.24078369140625 0.7181827425956726 0.71684074 0.5921158790588379 True -7 23136 31.9089834690094 0.5948069095611572 341.3103942871094 0.5883781909942627 481.22808837890625 0.7205530405044556 0.7262998 0.5647755265235901 True -8 26028 31.864481449127197 0.5963144302368164 433.8623962402344 0.4984619617462158 480.3013916015625 0.7217108607292175 0.72660863 0.5656840205192566 True -9 28920 31.872791528701782 0.5958261489868164 418.7728576660156 0.49716833233833313 478.9116516113281 0.7233089208602905 0.7330537 0.5593055486679077 True -10 31812 32.07176351547241 26.790394067764282 355.9019470214844 0.656890332698822 477.1231384277344 0.7253907918930054 0.7348197 0.5590511560440063 True -11 34704 31.953540325164795 0.5982234477996826 448.4581604003906 0.5339837074279785 475.75567626953125 0.7268058657646179 0.74249935 0.5478468537330627 True -12 37596 31.88736915588379 0.6066360473632812 422.1112060546875 0.6618430018424988 474.2649230957031 0.7281277179718018 0.7459453 0.5293564796447754 True -13 40488 31.88870143890381 0.5866966247558594 437.9385070800781 0.7381533980369568 473.2221374511719 0.7293629050254822 0.75230634 0.5138664841651917 True -14 43380 32.123228549957275 24.28035259246826 329.38763427734375 0.35532766580581665 472.4420471191406 0.7303616404533386 0.7572924 0.5080941915512085 True -15 46272 32.15247631072998 15.839762449264526 375.05859375 0.45421189069747925 471.9861145019531 0.7308474183082581 0.75632524 0.5172170996665955 False -16 49164 31.906121015548706 0.5983688831329346 451.3857421875 0.35469263792037964 472.1082763671875 0.7306053638458252 0.75477356 0.5470728278160095 False -17 52056 31.822351217269897 0.5925605297088623 390.486083984375 0.3664323389530182 472.577392578125 0.7301259636878967 0.74904823 0.5734170079231262 False -18 54948 31.81083607673645 0.5978810787200928 411.2856140136719 0.35359296202659607 473.0736083984375 0.7297316193580627 0.7409529 0.6017699837684631 False -19 57840 31.83329463005066 0.594186544418335 370.39093017578125 0.3130149841308594 473.2409973144531 0.7294451594352722 0.7365277 0.6187426447868347 False diff --git a/ENCSR591PIX/cherimoya.fold_4.performance.tsv b/ENCSR591PIX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7d502127d20ab4d213b9473b024fa61f574b2911..0000000000000000000000000000000000000000 --- a/ENCSR591PIX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -472.4420471191406 0.2231181561946869 0.7303617000579834 0.33273741602897644 0.7572923898696899 0.7154277563095093 0.5080941915512085 \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_0.evaluate.json b/ENCSR593LTJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0252641b78c8d0f9f3a0c744dcb89d073cf65202..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388TZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_0.fit.json b/ENCSR593LTJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 7b2045ef0b94a45925bba5c3d394dffdb8ccdd6c..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF388TZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_0.log b/ENCSR593LTJ/cherimoya.fold_0.log deleted file mode 100644 index 13f1c2cc564ad0b35852fb1873a32e55eee99bdd..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2711 34.78243923187256 3.9683990478515625 1529.081787109375 1.0668226480484009 2775.902587890625 0.31834617257118225 0.3161425 18.348421096801758 True -1 5422 30.18817448616028 0.6270937919616699 1530.9677734375 1.2343758344650269 2163.357177734375 0.5503686666488647 0.32301602 6.7253546714782715 True -2 8133 30.214513540267944 0.53511643409729 1472.036865234375 0.6780996322631836 2092.365234375 0.5693174600601196 0.40829718 3.1062819957733154 True -3 10844 30.17879056930542 0.5530328750610352 1695.344970703125 1.266365885734558 2057.606201171875 0.5820754170417786 0.43829668 2.0474984645843506 True -4 13555 30.170081853866577 1.705113410949707 1582.558349609375 0.7048153877258301 2045.096923828125 0.5867077112197876 0.46677563 1.6948643922805786 True -5 16266 30.191617727279663 0.5326223373413086 1589.1505126953125 0.7581167221069336 2028.416259765625 0.5910031199455261 0.47466606 1.5812559127807617 True -6 18977 30.193599939346313 0.5284192562103271 1489.423095703125 1.2864558696746826 2009.8663330078125 0.5971245169639587 0.49558097 1.2660895586013794 True -7 21688 30.107860565185547 0.535038948059082 1637.62890625 0.7166281938552856 2001.05615234375 0.59881991147995 0.50624424 1.0923640727996826 True -8 24399 29.620158433914185 0.5688018798828125 1598.7056884765625 0.5437923669815063 1988.990478515625 0.6019389033317566 0.51552826 0.9447521567344666 True -9 27110 29.580174684524536 0.5236530303955078 1403.32958984375 0.5024588704109192 1977.11328125 0.6065965890884399 0.5282685 0.8104508519172668 True -10 29821 29.52941584587097 0.6619076728820801 1733.65087890625 0.8096727728843689 1970.062744140625 0.6083706021308899 0.53674084 0.7871368527412415 True -11 32532 29.58251976966858 0.5446798801422119 1642.200439453125 0.5858434438705444 1953.3348388671875 0.6141831874847412 0.5472145 0.73626708984375 True -12 35243 29.564850330352783 0.5347683429718018 1484.94140625 0.7470532655715942 1934.526611328125 0.6199302077293396 0.5657989 0.6449437141418457 True -13 37954 29.6123046875 9.585959911346436 1454.7021484375 0.610626757144928 1926.1365966796875 0.6231354475021362 0.5766798 0.5991387963294983 True -14 40665 29.639791011810303 19.168855667114258 1562.8759765625 0.562749445438385 1914.9599609375 0.6259456872940063 0.59646696 0.5429815053939819 True -15 43376 29.743611097335815 0.5494239330291748 1420.7177734375 0.35060250759124756 1914.366943359375 0.6247717142105103 0.6102303 0.48964187502861023 True -16 46087 29.570927381515503 0.5437729358673096 1484.224365234375 0.7150590419769287 1901.774658203125 0.6290568709373474 0.623991 0.44969913363456726 True -17 48798 29.603575944900513 0.5364170074462891 1550.297607421875 0.44120898842811584 1898.2701416015625 0.6297733783721924 0.63206685 0.42124292254447937 True -18 51509 29.55018711090088 0.531083345413208 1447.1197509765625 0.35509243607521057 1901.0277099609375 0.6276991963386536 0.6368425 0.40339067578315735 True -19 54220 29.576975107192993 0.5400600433349609 1346.523681640625 0.31905442476272583 1902.7430419921875 0.6264968514442444 0.6354106 0.40301021933555603 False diff --git a/ENCSR593LTJ/cherimoya.fold_0.performance.tsv b/ENCSR593LTJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c25a916b360ea5466af7297193ed053a11c3be4b..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1901.0277099609375 0.18950532376766205 0.6276991963386536 0.41051623225212097 0.6368424892425537 0.6484960317611694 0.40339067578315735 \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_1.evaluate.json b/ENCSR593LTJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4eed8c30cef7ccde31e7a4302fa70cfe8c6aac44..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388TZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_1.fit.json b/ENCSR593LTJ/cherimoya.fold_1.fit.json deleted file mode 100644 index b073e8be259222027c8fc84700bde10504d239a2..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF388TZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_1.log b/ENCSR593LTJ/cherimoya.fold_1.log deleted file mode 100644 index 03c526778b90be7a396b72be7e6a65833a10b1fd..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 36.7537624835968 4.382050037384033 1754.576904296875 1.06458580493927 2851.6259765625 0.331089586019516 0.3538309 16.732343673706055 True -1 5482 30.547853469848633 0.6729907989501953 1668.964111328125 0.730404257774353 2227.969970703125 0.5529066920280457 0.39631385 6.674304485321045 True -2 8223 30.556318759918213 0.7260420322418213 1563.744873046875 0.86693274974823 2163.757080078125 0.5714598298072815 0.44173363 2.7664835453033447 True -3 10964 30.53593611717224 2.75117564201355 1802.266357421875 0.7199395895004272 2128.751708984375 0.580542266368866 0.4790295 1.7360135316848755 True -4 13705 30.569252490997314 0.680225133895874 1531.7447509765625 0.7680352926254272 2097.892578125 0.5897401571273804 0.49151674 1.3221139907836914 True -5 16446 30.54962182044983 0.7152972221374512 1836.24755859375 0.6831039190292358 2085.4736328125 0.5941495299339294 0.50677866 1.2342407703399658 True -6 19187 30.515434503555298 0.7202236652374268 1511.2724609375 0.7626818418502808 2070.64892578125 0.5983844995498657 0.51546913 1.0329172611236572 True -7 21928 30.55380129814148 0.7109711170196533 1693.149169921875 0.6364282369613647 2055.06787109375 0.6015453934669495 0.52439964 0.847674548625946 True -8 24669 29.93598198890686 0.6902062892913818 1566.4761962890625 0.8150320649147034 2041.9591064453125 0.6052120923995972 0.5319706 0.8027923703193665 True -9 27410 29.925870656967163 0.7006325721740723 1610.6265869140625 0.6972661018371582 2031.1885986328125 0.6100489497184753 0.53624845 0.7958559393882751 True -10 30151 30.042083024978638 0.6825811862945557 1452.4010009765625 0.48426660895347595 2021.3033447265625 0.6128464341163635 0.5430922 0.808137059211731 True -11 32892 29.84793448448181 0.6703348159790039 1651.548828125 0.9362443089485168 2010.6060791015625 0.615195095539093 0.5615065 0.7246240377426147 True -12 35633 29.90052080154419 0.6894586086273193 1551.2578125 0.6883158087730408 1992.842529296875 0.6212497353553772 0.5744571 0.674137532711029 True -13 38374 29.813982248306274 0.6852691173553467 1456.5924072265625 0.6999907493591309 1983.2386474609375 0.6237210035324097 0.5924791 0.6103197336196899 True -14 41115 29.868001699447632 0.6715996265411377 1457.81982421875 0.49680662155151367 1976.6407470703125 0.6251326203346252 0.6062797 0.580922544002533 True -15 43856 29.83681869506836 0.6749966144561768 1228.9482421875 0.5413568019866943 1964.0289306640625 0.6285489797592163 0.6250418 0.5087986588478088 True -16 46597 29.870798349380493 0.6813910007476807 1392.634521484375 0.37547487020492554 1959.702880859375 0.6293278932571411 0.637027 0.4678167998790741 True -17 49338 29.8756046295166 0.6643736362457275 1586.070068359375 0.31954333186149597 1958.1544189453125 0.6290470957756042 0.64583325 0.4316420257091522 True -18 52079 29.854952335357666 0.679567813873291 1601.224853515625 0.3281605839729309 1953.342529296875 0.6315151453018188 0.6507442 0.4167865216732025 True -19 54820 29.854711294174194 0.6883227825164795 1438.62646484375 0.4684082865715027 1954.8018798828125 0.6302260756492615 0.65346885 0.412655770778656 True diff --git a/ENCSR593LTJ/cherimoya.fold_1.performance.tsv b/ENCSR593LTJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e10ac58099e3cf42ffd7c674ad4c5fe5b8fc76b2..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1954.8018798828125 0.18624542653560638 0.6302260756492615 0.4177897870540619 0.6534688472747803 0.6703418493270874 0.412655770778656 \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_2.evaluate.json b/ENCSR593LTJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c88b38d7b11656e5661ef12099ba9d2c8f3ef1f8..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388TZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_2.fit.json b/ENCSR593LTJ/cherimoya.fold_2.fit.json deleted file mode 100644 index ca5c349ff870f70bfe62384214c5e31eeb52dccc..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF388TZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_2.log b/ENCSR593LTJ/cherimoya.fold_2.log deleted file mode 100644 index 18eb0d89374fd3cdbf6f58bdaa51241905b324d3..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 36.75099802017212 3.9493043422698975 1936.026123046875 0.9079181551933289 2771.130126953125 0.3365083932876587 0.3074723 16.952526092529297 True -1 5746 31.991077184677124 0.5731794834136963 1556.031005859375 0.79429030418396 2163.70849609375 0.5545910000801086 0.38807735 5.491477012634277 True -2 8619 31.97040033340454 0.5370595455169678 1599.508056640625 0.8356403112411499 2096.29150390625 0.5727519989013672 0.436914 2.5978660583496094 True -3 11492 32.00962042808533 0.5331871509552002 1464.203857421875 0.8029336929321289 2068.0068359375 0.5815160870552063 0.44884315 1.932997226715088 True -4 14365 31.975494623184204 0.5887079238891602 1676.8392333984375 0.6394544243812561 2051.859375 0.5873711109161377 0.48234192 1.6795319318771362 True -5 17238 31.984068632125854 0.5374081134796143 1730.98388671875 0.9314939975738525 2029.19091796875 0.5953577756881714 0.4878448 1.394792914390564 True -6 20111 32.11333179473877 0.5423390865325928 1719.55419921875 0.8172569274902344 2020.4105224609375 0.5969077944755554 0.4968773 1.1061018705368042 True -7 22984 31.962048053741455 0.5386855602264404 1635.800048828125 0.6434170007705688 2006.3994140625 0.6001129150390625 0.5155344 0.9201744198799133 True -8 25857 31.920090436935425 0.5359053611755371 1670.215087890625 0.7722281217575073 1994.00732421875 0.6056463718414307 0.5190123 0.8665356636047363 True -9 28730 31.3344669342041 0.5419971942901611 1334.524658203125 0.8420619368553162 1986.7236328125 0.6089571714401245 0.5274193 0.8992106914520264 True -10 31603 31.274359464645386 0.5387189388275146 1542.8330078125 0.5466089248657227 1975.5054931640625 0.611582338809967 0.5356556 0.7651864290237427 True -11 34476 31.29584312438965 0.5395610332489014 1769.218017578125 0.5580464005470276 1963.28515625 0.6149542927742004 0.55520535 0.675651490688324 True -12 37349 31.381511211395264 0.5374791622161865 1579.182861328125 0.34719574451446533 1951.9476318359375 0.6185686588287354 0.5669836 0.6641412973403931 True -13 40222 31.36191463470459 0.5523533821105957 1538.278076171875 0.6849323511123657 1935.7447509765625 0.62353515625 0.5792609 0.6058743000030518 True -14 43095 31.335957288742065 0.5386981964111328 1411.7042236328125 0.5046531558036804 1928.394287109375 0.6248151063919067 0.5917331 0.5481245517730713 True -15 45968 31.368825912475586 0.5402450561523438 1741.655029296875 0.42002809047698975 1918.45068359375 0.6275811791419983 0.60668933 0.5084139108657837 True -16 48841 31.328786849975586 0.5382330417633057 1413.51318359375 0.4471076726913452 1910.2537841796875 0.6298159956932068 0.6203303 0.4609210193157196 True -17 51714 31.35902237892151 0.5453293323516846 1409.625732421875 0.4692816734313965 1907.7608642578125 0.6295565962791443 0.6273926 0.4348134696483612 True -18 54587 31.301498889923096 0.5434055328369141 1196.709716796875 0.4482550621032715 1908.2620849609375 0.6287944912910461 0.6331174 0.4214019775390625 True -19 57460 31.30703067779541 1.1957542896270752 1427.726806640625 0.3794102668762207 1907.8482666015625 0.6294874548912048 0.6333335 0.4210789203643799 True diff --git a/ENCSR593LTJ/cherimoya.fold_2.performance.tsv b/ENCSR593LTJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a8b899ad20fd0bd4f060a6d4f1a396adb34251e2..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1907.8482666015625 0.18899594247341156 0.6294874548912048 0.4136660397052765 0.6333335041999817 0.6438954472541809 0.4210789203643799 \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_3.evaluate.json b/ENCSR593LTJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a348bf566e8ba19c4921721f4e6943a92314c48f..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388TZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_3.fit.json b/ENCSR593LTJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 2ba6b728943c507b2673e52464b30634fdc34818..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF388TZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_3.log b/ENCSR593LTJ/cherimoya.fold_3.log deleted file mode 100644 index dc4f62e5d933d24b65afb5181345a398eba93491..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2794 37.083189487457275 3.982248306274414 1582.6019287109375 0.9713169932365417 2780.66650390625 0.3367822766304016 0.3487614 16.286537170410156 True -1 5588 31.127588510513306 0.6863570213317871 1634.003662109375 0.9746705889701843 2176.3837890625 0.5574247241020203 0.37070444 7.455408573150635 True -2 8382 31.153519868850708 0.6327097415924072 1654.8662109375 0.7697091102600098 2126.60986328125 0.5705951452255249 0.42994037 3.4016120433807373 True -3 11176 31.103400945663452 0.6125049591064453 1532.83203125 0.7709043025970459 2102.7421875 0.5779144763946533 0.44873902 2.3108389377593994 True -4 13970 31.080541849136353 3.44832181930542 1440.950927734375 0.87293541431427 2082.74951171875 0.5843629837036133 0.46527377 1.9799554347991943 True -5 16764 31.110417127609253 0.6161191463470459 1605.015380859375 0.493502676486969 2067.908203125 0.5886937379837036 0.4770651 1.7335413694381714 True -6 19558 30.836954355239868 0.591071367263794 1529.116943359375 0.8028573989868164 2058.29248046875 0.5913775563240051 0.4830228 1.605987310409546 True -7 22352 30.420271396636963 0.5823249816894531 1654.948486328125 0.5352336168289185 2054.022216796875 0.5946558117866516 0.4914725 1.3998066186904907 True -8 25146 30.42125368118286 0.5961208343505859 1495.1904296875 0.4585718512535095 2025.3148193359375 0.6023531556129456 0.5038083 1.1098129749298096 True -9 27940 30.46666979789734 2.023016929626465 1457.6611328125 0.5222395658493042 2017.71044921875 0.6045699119567871 0.5167488 0.9818055629730225 True -10 30734 30.48294949531555 0.5760843753814697 1621.450927734375 0.5647896528244019 2003.8050537109375 0.6096580624580383 0.5322804 0.9343076944351196 True -11 33528 30.747009992599487 0.9224820137023926 1536.338134765625 0.6683428287506104 1992.9881591796875 0.6116005182266235 0.5550301 0.7946978807449341 True -12 36322 30.636706113815308 0.5880353450775146 1540.760498046875 0.4981551468372345 1977.45947265625 0.616521954536438 0.57148135 0.7395191192626953 True -13 39116 30.65392804145813 0.589597225189209 1478.0535888671875 0.3027995824813843 1964.292724609375 0.6203705668449402 0.58971936 0.6583389639854431 True -14 41910 30.49352788925171 0.5968413352966309 1534.40478515625 0.38976961374282837 1954.8482666015625 0.6224105954170227 0.6114601 0.5836350321769714 True -15 44704 30.481548070907593 0.5742306709289551 1509.467041015625 0.42493829131126404 1950.511474609375 0.6225923895835876 0.626903 0.5137017369270325 True -16 47498 30.51306915283203 0.6367080211639404 1370.9970703125 0.421579509973526 1938.3958740234375 0.6264829635620117 0.6403188 0.4617745876312256 True -17 50292 30.44132137298584 0.5760252475738525 1519.775146484375 0.35306912660598755 1939.501708984375 0.6247190237045288 0.65289426 0.41582703590393066 True -18 53086 30.446948051452637 0.5859713554382324 1367.92138671875 0.3807030916213989 1935.3021240234375 0.6264635920524597 0.65488815 0.4024071991443634 True -19 55880 30.514545679092407 0.5912182331085205 1524.8292236328125 0.36388590931892395 1939.758056640625 0.6239916086196899 0.65581 0.3963624835014343 True diff --git a/ENCSR593LTJ/cherimoya.fold_3.performance.tsv b/ENCSR593LTJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a86e176015c2b84bce0c2113f9e74a7f1eb66ea1..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1939.758056640625 0.18812011182308197 0.6239916682243347 0.4140622317790985 0.6558099985122681 0.6672394871711731 0.3963624835014343 \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_4.evaluate.json b/ENCSR593LTJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 01ba171c39a3fd0f9e93e7ab7ff5401d8a239634..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388TZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_4.fit.json b/ENCSR593LTJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 351e92c04546ee5d37401b6537a4f814cfdf0cdb..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF388TZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593LTJ/cherimoya.fold_4.log b/ENCSR593LTJ/cherimoya.fold_4.log deleted file mode 100644 index b10ecbbcae0c718fa69772ca0d11134c29c65c11..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2840 36.12437176704407 4.352740526199341 2065.72265625 1.0805070400238037 2711.335693359375 0.3304283022880554 0.3410331 16.66949462890625 True -1 5680 31.3176326751709 0.5840356349945068 1740.0224609375 1.0180015563964844 2119.37548828125 0.5545709729194641 0.38034523 5.607852935791016 True -2 8520 31.67565155029297 1.0954322814941406 1520.486328125 0.766194224357605 2067.058837890625 0.5694082975387573 0.43629277 2.8609721660614014 True -3 11360 31.754308462142944 12.772134780883789 1730.2650146484375 0.9372364282608032 2039.2169189453125 0.5785660147666931 0.4644693 2.057788372039795 True -4 14200 31.322863340377808 1.3634097576141357 1651.6334228515625 0.6747368574142456 2020.8448486328125 0.584143877029419 0.4733982 1.857088327407837 True -5 17040 30.962510347366333 1.6001911163330078 1696.213623046875 0.658539354801178 2005.9189453125 0.5890393257141113 0.48581514 1.416732668876648 True -6 19880 30.984994649887085 1.1278433799743652 1637.826416015625 0.654711902141571 1995.07373046875 0.5929096937179565 0.5007187 1.2206432819366455 True -7 22720 31.02286696434021 0.5792934894561768 1794.994384765625 0.6887528300285339 1984.327392578125 0.5965424180030823 0.5097934 1.0786068439483643 True -8 25560 31.02805233001709 0.5251190662384033 1475.3740234375 0.7021167278289795 1973.8984375 0.6007460951805115 0.50876844 1.0414963960647583 False -9 28400 31.054914951324463 0.5614545345306396 1613.920166015625 0.6763947010040283 1970.9959716796875 0.6022459268569946 0.5224971 0.9820237755775452 True -10 31240 31.258403778076172 0.5518546104431152 1628.175537109375 0.6970838904380798 1954.1802978515625 0.6082453727722168 0.5266862 0.9195486307144165 True -11 34080 31.084572076797485 0.556065559387207 1650.3822021484375 0.4109947085380554 1939.3062744140625 0.612696647644043 0.5447193 0.812080979347229 True -12 36920 31.096344470977783 0.5408449172973633 1558.7637939453125 0.5647981762886047 1932.594970703125 0.6124964952468872 0.565655 0.6856974363327026 True -13 39760 31.042564392089844 0.5671157836914062 1626.931396484375 0.5361493825912476 1915.8214111328125 0.618434727191925 0.5815738 0.6083913445472717 True -14 42600 31.0154972076416 0.5384571552276611 1317.31982421875 0.4942741394042969 1907.5941162109375 0.6204993724822998 0.5987557 0.5254111289978027 True -15 45440 31.007837057113647 0.5329976081848145 1586.433349609375 0.2998405992984772 1892.4410400390625 0.6249440312385559 0.6162209 0.48057547211647034 True -16 48280 31.056347370147705 0.533743143081665 1163.74609375 0.41085368394851685 1884.9766845703125 0.6277781128883362 0.6342661 0.42960402369499207 True -17 51120 31.027286052703857 0.5368285179138184 1483.50732421875 0.46276241540908813 1891.6339111328125 0.624077558517456 0.64054793 0.39955469965934753 True -18 53960 31.005377531051636 0.5500855445861816 1511.7537841796875 0.4505771994590759 1887.9112548828125 0.6252223253250122 0.6462714 0.38509029150009155 True -19 56800 31.386981964111328 9.775081634521484 1535.763427734375 0.3705034554004669 1890.0367431640625 0.6238439083099365 0.6474673 0.3820766806602478 True diff --git a/ENCSR593LTJ/cherimoya.fold_4.performance.tsv b/ENCSR593LTJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9d0b8635a416ae807f443f768c1f997ffcc6e682..0000000000000000000000000000000000000000 --- a/ENCSR593LTJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1890.0367431640625 0.19115932285785675 0.6238438487052917 0.40623927116394043 0.647467315196991 0.6551935076713562 0.3820766806602478 \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_0.evaluate.json b/ENCSR593OUE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ac4091d7a81f40f9a6f27eabebca1d02f84498db..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098TXO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_0.fit.json b/ENCSR593OUE/cherimoya.fold_0.fit.json deleted file mode 100644 index 44b2493e5865d62baef442f1dc217fa108c2f71a..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF098TXO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_0.log b/ENCSR593OUE/cherimoya.fold_0.log deleted file mode 100644 index 87623901b59cdae44773d88e0b14e643f920c2fa..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2783 34.584612131118774 3.499159812927246 832.79296875 1.011696457862854 988.0209350585938 0.23871967196464539 0.6309632 7.696663856506348 True -1 5566 30.916183710098267 0.5790195465087891 673.81640625 0.889896035194397 849.8025512695312 0.29158109426498413 0.71754485 3.3179538249969482 True -2 8349 30.967525720596313 0.5594310760498047 719.65478515625 0.6397397518157959 827.713134765625 0.297715425491333 0.7218329 2.3217132091522217 True -3 11132 30.899569034576416 0.5585019588470459 649.580322265625 0.5545602440834045 796.5552368164062 0.31079837679862976 0.74030775 1.4640815258026123 True -4 13915 30.920541048049927 0.5645854473114014 730.1261596679688 0.5541861057281494 779.4451293945312 0.3152240216732025 0.76006573 1.2545613050460815 True -5 16698 30.91672682762146 0.5612702369689941 693.5645751953125 0.804445207118988 770.3359985351562 0.319237619638443 0.7645324 1.0608148574829102 True -6 19481 30.80435299873352 1.0795645713806152 518.69287109375 0.6460064649581909 760.4495849609375 0.323199987411499 0.7777682 1.022094964981079 True -7 22264 30.82164430618286 19.65532660484314 454.7503662109375 0.49821680784225464 755.7680053710938 0.3228815197944641 0.7876669 0.9114821553230286 True -8 25047 31.31030797958374 0.5626463890075684 716.75244140625 0.59736168384552 745.49462890625 0.3295181393623352 0.7966391 0.8399081230163574 True -9 27830 30.880554676055908 0.5605659484863281 669.2830810546875 0.5216693878173828 742.4066162109375 0.33062759041786194 0.804087 0.751650333404541 True -10 30613 30.80861234664917 8.173501968383789 600.83642578125 0.43057674169540405 739.6412963867188 0.3316030502319336 0.8113493 0.7059419751167297 True -11 33396 30.914536952972412 0.5648729801177979 656.88037109375 0.6152889728546143 732.6488037109375 0.33464309573173523 0.8225012 0.6374817490577698 True -12 36179 30.93018651008606 0.5620560646057129 708.5714111328125 0.6781409978866577 725.9266357421875 0.3374478220939636 0.82895386 0.5855121612548828 True -13 38962 30.877686977386475 0.5562443733215332 427.6219482421875 0.5557041168212891 720.9578857421875 0.3381703794002533 0.83537865 0.5270528197288513 True -14 41745 31.17841935157776 6.731868505477905 628.947265625 0.530414879322052 718.2340698242188 0.33813002705574036 0.84155583 0.4932049512863159 True -15 44528 30.91057801246643 0.9959712028503418 580.653564453125 0.28607189655303955 713.7394409179688 0.340520977973938 0.84835 0.4672410190105438 True -16 47311 30.52806043624878 0.543088436126709 548.4136962890625 0.3528221845626831 712.7583618164062 0.33941319584846497 0.8512632 0.447115033864975 True -17 50094 30.212279081344604 0.5495476722717285 513.5364990234375 0.33914560079574585 709.6058349609375 0.3418971002101898 0.85354936 0.4390519857406616 True -18 52877 30.278430461883545 0.5533833503723145 591.8274536132812 0.170289546251297 710.9391479492188 0.3410087823867798 0.8528524 0.44069838523864746 False -19 55660 30.23411726951599 0.5537691116333008 507.4467468261719 0.3194478452205658 711.7008666992188 0.3410539925098419 0.85292697 0.4407166838645935 False diff --git a/ENCSR593OUE/cherimoya.fold_0.performance.tsv b/ENCSR593OUE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 07fb40ba9fe799bd9dc6e1209220776faf55695b..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -709.6058349609375 0.4177703261375427 0.3418971002101898 0.15360228717327118 0.8535493612289429 0.7894648909568787 0.4390519857406616 \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_1.evaluate.json b/ENCSR593OUE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 234d31d7f7d4dbc2b8af6ddbaeacf1bedb3ec001..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098TXO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_1.fit.json b/ENCSR593OUE/cherimoya.fold_1.fit.json deleted file mode 100644 index 32413d04143b6cd574afb1f62c684797f245cff1..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF098TXO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_1.log b/ENCSR593OUE/cherimoya.fold_1.log deleted file mode 100644 index 9cf2239b47b36de3e83066f885842a73d6dff368..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2686 34.44656443595886 4.676295518875122 754.4658813476562 0.6983938217163086 1240.9285888671875 0.24252809584140778 0.61777496 8.476815223693848 True -1 5372 29.87558889389038 0.7579560279846191 737.6930541992188 0.7298381328582764 1026.9593505859375 0.3186653256416321 0.73116904 4.027824401855469 True -2 8058 29.78857970237732 1.235494613647461 646.26611328125 0.629456102848053 1004.18896484375 0.3242780268192291 0.74142474 2.4307782649993896 True -3 10744 29.845277786254883 19.56285572052002 870.656494140625 0.8974933624267578 978.39892578125 0.3274618089199066 0.74447054 1.9718900918960571 True -4 13430 29.79794979095459 27.196712493896484 534.7982177734375 0.7608352303504944 953.6455078125 0.33690881729125977 0.7662316 1.4666264057159424 True -5 16116 29.851030826568604 0.7468762397766113 532.4064331054688 0.4757795035839081 938.0867919921875 0.34026047587394714 0.7876906 1.34635329246521 True -6 18802 29.806538343429565 0.7454361915588379 849.112548828125 0.9790452718734741 924.6531372070312 0.3459523022174835 0.79168904 1.2287061214447021 True -7 21488 29.75957226753235 0.7262136936187744 787.78857421875 0.8584816455841064 911.7650756835938 0.35041356086730957 0.80659294 1.1148097515106201 True -8 24174 29.79716730117798 0.7455742359161377 601.4384765625 0.3437255620956421 904.3396606445312 0.35170692205429077 0.8160835 1.037412166595459 True -9 26860 29.725024223327637 0.7421238422393799 570.8582153320312 0.5063353180885315 898.2693481445312 0.35470327734947205 0.8209237 0.9499935507774353 True -10 29546 29.71220088005066 0.7461788654327393 550.3212280273438 0.5128858089447021 892.0919189453125 0.3592601716518402 0.82600915 0.8933244347572327 True -11 32232 29.709223747253418 0.7441210746765137 555.8037719726562 0.5263766050338745 882.6849365234375 0.36325451731681824 0.8343746 0.8091878890991211 True -12 34918 29.69436502456665 1.153252363204956 671.7376708984375 0.5313044786453247 872.6834106445312 0.36761215329170227 0.8421875 0.729954183101654 True -13 37604 29.836710453033447 0.7890939712524414 486.9207458496094 0.4247779846191406 868.7857055664062 0.3677249848842621 0.8499443 0.6578612923622131 True -14 40290 29.87080478668213 0.7585070133209229 587.6614379882812 0.6912441253662109 858.2503662109375 0.3720034658908844 0.85746413 0.5948120355606079 True -15 42976 29.96785855293274 0.758389949798584 484.7801513671875 0.44930821657180786 856.2369995117188 0.37042534351348877 0.86461025 0.5412614345550537 True -16 45662 29.959915161132812 0.7562568187713623 601.1574096679688 0.3425954282283783 853.69873046875 0.3708495795726776 0.8678097 0.5106649398803711 True -17 48348 29.547301530838013 0.7443053722381592 424.128173828125 0.3276602625846863 853.4689331054688 0.37029165029525757 0.87154967 0.4928551912307739 True -18 51034 29.336304426193237 0.7480742931365967 619.99169921875 0.4127737283706665 857.3453369140625 0.36853519082069397 0.87129974 0.48335158824920654 False -19 53720 29.263516664505005 0.7463862895965576 632.844970703125 0.2428206503391266 856.5877075195312 0.3698436915874481 0.8721916 0.48435574769973755 True diff --git a/ENCSR593OUE/cherimoya.fold_1.performance.tsv b/ENCSR593OUE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 06fe320f13d2887b6994629971543922df368245..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -856.5877075195312 0.39416059851646423 0.3698436915874481 0.17593280971050262 0.8721916079521179 0.8212311267852783 0.48435574769973755 \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_2.evaluate.json b/ENCSR593OUE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6b4036e408bca3dd25982b38827072687cf72b00..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098TXO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_2.fit.json b/ENCSR593OUE/cherimoya.fold_2.fit.json deleted file mode 100644 index def55929e14382e83a0d6d4c31cd9962d087a84d..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF098TXO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_2.log b/ENCSR593OUE/cherimoya.fold_2.log deleted file mode 100644 index 1ca1da6f8415f5dc73218aca6e72d56b0103a236..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 35.71665072441101 3.5493767261505127 601.210205078125 0.6611485481262207 1003.2566528320312 0.24023006856441498 0.60687333 7.88873815536499 True -1 5772 32.12073802947998 0.6015505790710449 664.1910400390625 0.6447939872741699 847.7584228515625 0.295681893825531 0.7220139 2.3790407180786133 True -2 8658 32.02778244018555 0.5904204845428467 594.365478515625 0.5363681316375732 825.7709350585938 0.2988707721233368 0.7424225 1.645223617553711 True -3 11544 32.02646040916443 2.4386327266693115 696.036376953125 1.0769288539886475 799.9371948242188 0.30404868721961975 0.7606497 1.1141438484191895 True -4 14430 32.22761869430542 13.617571592330933 663.6035766601562 0.567743718624115 779.7627563476562 0.31420302391052246 0.77342784 1.0407332181930542 True -5 17316 32.05774188041687 0.6240737438201904 413.4492492675781 0.5289778709411621 772.5230102539062 0.3164099156856537 0.78436404 1.1331251859664917 True -6 20202 32.02244329452515 0.6051938533782959 753.9984741210938 0.8098208904266357 766.933349609375 0.3193592131137848 0.78921795 1.0690703392028809 True -7 23088 32.18698263168335 0.6109817028045654 858.2374877929688 0.6904824376106262 760.1072998046875 0.3221151828765869 0.7994829 0.9219110608100891 True -8 25974 32.0641233921051 0.6084797382354736 665.025390625 0.7204708456993103 753.62939453125 0.32566553354263306 0.7953209 0.939671516418457 False -9 28860 31.96540665626526 0.5998682975769043 488.45635986328125 0.3363505005836487 749.268798828125 0.32842889428138733 0.80388594 0.7935996651649475 True -10 31746 31.97825598716736 0.5923874378204346 507.27191162109375 0.512936532497406 744.1314086914062 0.3298425078392029 0.8140532 0.6827723383903503 True -11 34632 31.929384231567383 14.395504474639893 600.6719360351562 0.4465286433696747 737.2767333984375 0.3346113860607147 0.818687 0.6380321383476257 True -12 37518 32.22071981430054 0.604572057723999 615.0470581054688 0.5839185118675232 731.7733154296875 0.3372644782066345 0.8258561 0.5862051248550415 True -13 40404 32.162840366363525 0.5933599472045898 491.7677917480469 0.4846353530883789 726.744873046875 0.3391517698764801 0.83578366 0.5207328200340271 True -14 43290 32.10304284095764 0.6219465732574463 522.0006713867188 0.5152515172958374 720.3347778320312 0.34245893359184265 0.84178704 0.48687466979026794 True -15 46176 32.78310966491699 3.1632916927337646 551.3880004882812 0.29691892862319946 719.6144409179688 0.34220337867736816 0.8473297 0.462271124124527 True -16 49062 32.17719388008118 1.7949998378753662 550.9314575195312 0.44825828075408936 719.1510620117188 0.34243854880332947 0.84971577 0.44355252385139465 True -17 51948 32.14670920372009 1.4145052433013916 626.4110717773438 0.4030410349369049 718.3901977539062 0.3418950140476227 0.852498 0.4327647089958191 True -18 54834 31.602919578552246 0.6064465045928955 644.2129516601562 0.32975924015045166 720.7802124023438 0.34088414907455444 0.85366154 0.43306291103363037 True -19 57720 31.400102615356445 0.8805301189422607 533.2203369140625 0.2856224775314331 719.7924194335938 0.3416311740875244 0.85348773 0.43414509296417236 False diff --git a/ENCSR593OUE/cherimoya.fold_2.performance.tsv b/ENCSR593OUE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e7b2daf483f4c7f6a506786bb7cd297d971ee640..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -720.7802124023438 0.41586658358573914 0.34088414907455444 0.15194031596183777 0.8536615371704102 0.7919332981109619 0.43306291103363037 \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_3.evaluate.json b/ENCSR593OUE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1307cb295444af8dd0e1268450637d9c53d34424..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098TXO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_3.fit.json b/ENCSR593OUE/cherimoya.fold_3.fit.json deleted file mode 100644 index 63d473298b7ee5460b41a1ad0e0ea834b9653a5c..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF098TXO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_3.log b/ENCSR593OUE/cherimoya.fold_3.log deleted file mode 100644 index 0b8e305a4a4065afc5babad43f054e2d32ddb224..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 33.91779351234436 3.5805070400238037 681.2979736328125 0.9072548151016235 1060.893310546875 0.2518828809261322 0.5516337 9.819306373596191 True -1 5480 30.470958709716797 0.5316731929779053 580.6451416015625 0.7886095643043518 894.8218994140625 0.31550654768943787 0.6779226 3.0950629711151123 True -2 8220 30.449036598205566 0.5237665176391602 594.5010375976562 0.8301913142204285 880.4388427734375 0.32031726837158203 0.68433005 2.376530647277832 True -3 10960 30.455739974975586 0.9353632926940918 665.3756103515625 0.9149339199066162 853.1068725585938 0.3291126787662506 0.70875597 1.9803866147994995 True -4 13700 30.392964124679565 1.4131379127502441 852.7884521484375 1.0265586376190186 838.32080078125 0.3343634009361267 0.71378493 1.8730156421661377 True -5 16440 30.395036458969116 0.523040771484375 686.078369140625 1.1265392303466797 819.5233764648438 0.3419229984283447 0.7254414 1.4428341388702393 True -6 19180 30.404313802719116 0.5234286785125732 529.015380859375 0.7735302448272705 811.5242309570312 0.3442683219909668 0.73873204 1.3892635107040405 True -7 21920 30.375994205474854 0.5348126888275146 631.6087036132812 0.5146971940994263 805.42236328125 0.3467623293399811 0.75398 1.314563274383545 True -8 24660 30.133445739746094 0.5140688419342041 578.9628295898438 0.6123696565628052 796.598388671875 0.35109415650367737 0.76445186 1.1804536581039429 True -9 27400 30.13487982749939 0.511237621307373 681.6917114257812 0.328790545463562 790.8326416015625 0.35488852858543396 0.7695269 1.1065183877944946 True -10 30140 29.767824172973633 0.5116701126098633 586.5796508789062 0.7372416257858276 789.6844482421875 0.3532246947288513 0.77736056 0.9799649715423584 True -11 32880 29.779224157333374 0.5108075141906738 746.576171875 0.6707479953765869 783.6654663085938 0.3556402623653412 0.78888315 0.877083957195282 True -12 35620 29.864139080047607 0.5094776153564453 558.5958251953125 0.7841768860816956 773.7819213867188 0.36025455594062805 0.8034446 0.7575506567955017 True -13 38360 29.76914644241333 0.5171060562133789 453.9128723144531 0.6088297367095947 770.2875366210938 0.3598965108394623 0.81277764 0.683830976486206 True -14 41100 29.749873161315918 21.12643003463745 533.2603759765625 0.641173243522644 764.5198974609375 0.3630969822406769 0.82103187 0.6360437870025635 True -15 43840 29.965508222579956 0.5282115936279297 567.4111328125 0.49707844853401184 761.2098388671875 0.3640233278274536 0.8305667 0.5958719253540039 True -16 46580 29.789186000823975 0.5258557796478271 444.256591796875 0.2549901604652405 756.9014282226562 0.366699755191803 0.83301693 0.5672490000724792 True -17 49320 29.774460554122925 0.519507884979248 683.30078125 0.369104266166687 758.7100219726562 0.3641841411590576 0.8386834 0.5511347055435181 True -18 52060 29.811354875564575 2.2865471839904785 502.8550720214844 0.4055962562561035 759.0301513671875 0.3643490970134735 0.83812666 0.5439103245735168 False -19 54800 29.8401198387146 0.5216119289398193 587.1820068359375 0.532071053981781 756.39599609375 0.36710378527641296 0.8384867 0.5446070432662964 False diff --git a/ENCSR593OUE/cherimoya.fold_3.performance.tsv b/ENCSR593OUE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a6e5a15c48fd03b94d790f1c361bdbfe5ca9266b..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -758.7100219726562 0.40138131380081177 0.3641841411590576 0.1664026379585266 0.8386834263801575 0.7778475880622864 0.5511347055435181 \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_4.evaluate.json b/ENCSR593OUE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ad52c3e1c63967258c192019ae2c2848b2e32f79..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF098TXO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_4.fit.json b/ENCSR593OUE/cherimoya.fold_4.fit.json deleted file mode 100644 index 9a5a0749bf61e803d66766d60f1f8960282d91f1..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF098TXO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR593OUE/cherimoya.fold_4.log b/ENCSR593OUE/cherimoya.fold_4.log deleted file mode 100644 index 56739d585a154d9f19a48ee9be87edd16fe70465..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 34.15806031227112 1.9534316062927246 653.4937744140625 0.5706110000610352 851.8804931640625 0.23118525743484497 0.59483206 6.925033092498779 True -1 5520 30.652456283569336 0.5431456565856934 900.0974731445312 0.8305371403694153 743.4749145507812 0.28130680322647095 0.67889035 2.797010898590088 True -2 8280 30.638842344284058 0.5196292400360107 688.5252075195312 0.6842906475067139 722.1797485351562 0.2870069146156311 0.6968187 1.6583987474441528 True -3 11040 30.591415643692017 0.529045581817627 589.5811767578125 0.7746691703796387 704.7890625 0.2955591380596161 0.70596254 1.5488295555114746 True -4 13800 30.940762042999268 0.8585240840911865 470.7102966308594 0.4737432599067688 689.6695556640625 0.29852810502052307 0.72995955 1.073413372039795 True -5 16560 30.62089776992798 0.5427100658416748 616.3291015625 0.6203137636184692 679.3050537109375 0.3032204508781433 0.74359983 0.9706889390945435 True -6 19320 30.59249496459961 0.5337893962860107 775.3365478515625 0.592067301273346 670.6707763671875 0.30517998337745667 0.75699687 0.9159149527549744 True -7 22080 30.674577236175537 0.5369431972503662 570.7445678710938 0.5508807897567749 663.380859375 0.30894801020622253 0.76871336 0.8346490263938904 True -8 24840 30.616361618041992 0.5361011028289795 570.5984497070312 0.49403485655784607 657.6162109375 0.31083595752716064 0.78043985 0.7226905226707458 True -9 27600 30.580551624298096 1.179417610168457 615.1233520507812 0.5990533828735352 652.0398559570312 0.3137640058994293 0.78508687 0.6987454891204834 True -10 30360 30.5901358127594 3.655546188354492 568.8921508789062 0.3772176504135132 646.2982788085938 0.31679436564445496 0.7960514 0.6330435276031494 True -11 33120 30.726154327392578 16.3800790309906 615.8131713867188 0.7221617102622986 642.2722778320312 0.3198372423648834 0.80400366 0.5745395421981812 True -12 35880 30.62340784072876 0.5304200649261475 531.4052734375 1.2025072574615479 638.2841186523438 0.3203619420528412 0.8148445 0.5178124904632568 True -13 38640 30.19394326210022 0.5228562355041504 595.1937255859375 0.26478832960128784 636.8408813476562 0.32125452160835266 0.82215565 0.48449522256851196 True -14 41400 30.02721858024597 0.8190302848815918 493.5834045410156 0.49822118878364563 633.3638305664062 0.3225860595703125 0.8299626 0.4524722397327423 True -15 44160 30.059008598327637 0.5347592830657959 481.957275390625 0.49190640449523926 631.5477905273438 0.3250003755092621 0.8359158 0.43048232793807983 True -16 46920 30.012182235717773 0.5373754501342773 551.4274291992188 0.38088127970695496 628.951904296875 0.3257101774215698 0.8430479 0.41498565673828125 True -17 49680 30.029239177703857 0.5349819660186768 430.5728454589844 0.2848837375640869 628.0327758789062 0.32607534527778625 0.84301275 0.408553808927536 False -18 52440 29.990886926651 0.5245256423950195 403.6299133300781 0.24768702685832977 629.8087158203125 0.32471612095832825 0.8429289 0.41183730959892273 False -19 55200 29.984192371368408 0.5307862758636475 411.91668701171875 0.3002671003341675 630.3807983398438 0.3247227966785431 0.8428375 0.4133027195930481 False diff --git a/ENCSR593OUE/cherimoya.fold_4.performance.tsv b/ENCSR593OUE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 02fe9771f56ac65a072d08919ffc4dd6c51250cc..0000000000000000000000000000000000000000 --- a/ENCSR593OUE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -628.951904296875 0.43129926919937134 0.32571014761924744 0.13663792610168457 0.8430479168891907 0.7824008464813232 0.41498565673828125 \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_0.evaluate.json b/ENCSR594NOE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 037532207b7f5a278b2d699b8133b98891e94f39..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772RPD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_0.fit.json b/ENCSR594NOE/cherimoya.fold_0.fit.json deleted file mode 100644 index 947e9174c51921c10d2a55e8b3113df222e4f410..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF772RPD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_0.log b/ENCSR594NOE/cherimoya.fold_0.log deleted file mode 100644 index 63f1540f59663906ecf6bf69e39336bd104120d9..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2686 34.43546772003174 3.5896337032318115 1312.2332763671875 1.2069939374923706 2273.048583984375 0.2757123112678528 0.53375226 12.518112182617188 True -1 5372 30.053399085998535 0.5862817764282227 1459.63818359375 1.0754635334014893 1871.0411376953125 0.4194243252277374 0.6049588 5.279613018035889 True -2 8058 30.014781713485718 0.5516438484191895 1423.363037109375 0.9839053750038147 1805.9217529296875 0.4328674077987671 0.615849 3.9971671104431152 True -3 10744 30.02531385421753 0.5576763153076172 1635.1259765625 1.0363348722457886 1747.0286865234375 0.4480050802230835 0.6326092 2.666147232055664 True -4 13430 29.9864444732666 0.5632646083831787 1327.0208740234375 0.9235965013504028 1723.0125732421875 0.4586728513240814 0.6371924 2.1956543922424316 True -5 16116 29.945250034332275 0.5588059425354004 1480.7353515625 1.3238322734832764 1707.567138671875 0.46445849537849426 0.643324 1.874600887298584 True -6 18802 29.965073347091675 0.5581371784210205 1240.704345703125 0.83535236120224 1692.962890625 0.4690285623073578 0.64699423 1.5928983688354492 True -7 21488 29.918373107910156 1.3729078769683838 1476.00634765625 0.8463081121444702 1681.546875 0.47489073872566223 0.6526017 1.447640061378479 True -8 24174 30.011544227600098 0.5774152278900146 1413.7171630859375 0.7356606721878052 1671.1961669921875 0.47679075598716736 0.6640806 1.302702784538269 True -9 26860 30.146225452423096 0.5702450275421143 1621.772216796875 1.1907788515090942 1659.1063232421875 0.4825235605239868 0.6742004 1.2468798160552979 True -10 29546 30.063446521759033 0.5551795959472656 1279.258056640625 0.9866719245910645 1636.036376953125 0.4915478527545929 0.67827845 1.1006855964660645 True -11 32232 30.661765575408936 36.166250705718994 1107.5540771484375 0.8406575322151184 1622.2244873046875 0.4950660765171051 0.68578506 0.9887489676475525 True -12 34918 30.05018925666809 0.5573246479034424 1166.86474609375 0.5887386202812195 1614.2236328125 0.49722933769226074 0.6930446 0.9539768099784851 True -13 37604 29.581413984298706 0.5509026050567627 1206.495849609375 0.725346565246582 1602.9774169921875 0.5000587105751038 0.70145714 0.8568006157875061 True -14 40290 29.309664011001587 0.5468883514404297 1180.9285888671875 0.7163667678833008 1596.2713623046875 0.50249844789505 0.7079562 0.7904693484306335 True -15 42976 29.312365531921387 0.5568294525146484 1301.9600830078125 0.7065565586090088 1585.9110107421875 0.5051996111869812 0.71678597 0.7453722357749939 True -16 45662 29.356333017349243 10.475839853286743 1405.826416015625 0.7760124206542969 1580.3668212890625 0.506252646446228 0.720387 0.7155845761299133 True -17 48348 29.4195396900177 0.9943430423736572 1396.742431640625 0.6379679441452026 1585.6759033203125 0.5044243931770325 0.72348046 0.6968842148780823 True -18 51034 29.63238763809204 0.5530738830566406 1429.322998046875 0.45438122749328613 1598.49951171875 0.49966904520988464 0.7228564 0.6944804191589355 False -19 53720 29.37030601501465 0.5485010147094727 1260.427001953125 0.5594309568405151 1596.3072509765625 0.5012062788009644 0.7210307 0.6960147023200989 False diff --git a/ENCSR594NOE/cherimoya.fold_0.performance.tsv b/ENCSR594NOE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2b7634392eb731909e82a4cc09d1b942a4b06966..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1585.6759033203125 0.27702823281288147 0.5044243931770325 0.27539193630218506 0.7234804630279541 0.6626905798912048 0.6968842148780823 \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_1.evaluate.json b/ENCSR594NOE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8d8d5f276a076505d409c5c9462bb0f0ab0609af..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772RPD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_1.fit.json b/ENCSR594NOE/cherimoya.fold_1.fit.json deleted file mode 100644 index b8c2fe6e43ddcd80a6cad8d06b90ecb2d194c163..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF772RPD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_1.log b/ENCSR594NOE/cherimoya.fold_1.log deleted file mode 100644 index 11077b13bd4bd52ea214818884f1cf9591b830ef..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 35.074957847595215 4.308494329452515 1537.92724609375 1.562254786491394 2612.7646484375 0.2894759178161621 0.53179455 12.49245834350586 True -1 5482 30.601322174072266 0.7055392265319824 2069.7216796875 1.4716838598251343 2112.711669921875 0.44214680790901184 0.6212574 7.583451271057129 True -2 8223 30.569031953811646 0.6926734447479248 1208.9515380859375 1.5522804260253906 2063.4853515625 0.4521189332008362 0.63217074 4.190950870513916 True -3 10964 30.570961713790894 0.7000131607055664 1951.452392578125 1.3819197416305542 2002.8033447265625 0.4648432731628418 0.6501495 3.082728624343872 True -4 13705 30.54091739654541 0.6881916522979736 1290.5887451171875 1.4032459259033203 1962.984130859375 0.471781849861145 0.65927154 2.423546314239502 True -5 16446 30.592609167099 0.6945524215698242 1227.07958984375 0.7889047265052795 1945.00634765625 0.47680336236953735 0.66907614 2.027923583984375 True -6 19187 30.602426767349243 0.7019851207733154 1738.1959228515625 1.2225263118743896 1933.057373046875 0.47857165336608887 0.6808524 1.6560065746307373 True -7 21928 30.647620916366577 0.7080264091491699 1383.370361328125 0.8025493621826172 1904.4556884765625 0.48848092555999756 0.6868682 1.6294854879379272 True -8 24669 30.561102390289307 35.20810317993164 1056.84130859375 0.8755975365638733 1895.0333251953125 0.49098268151283264 0.69542193 1.5364986658096313 True -9 27410 32.58066391944885 0.7168164253234863 1513.822998046875 0.8277050256729126 1875.399658203125 0.49520593881607056 0.7012739 1.415734052658081 True -10 30151 30.57999849319458 0.7040026187896729 1384.634521484375 0.8085622787475586 1859.35009765625 0.5014074444770813 0.7084879 1.3222330808639526 True -11 32892 30.57169008255005 0.6960797309875488 1297.76171875 0.6899310350418091 1842.0372314453125 0.5049067139625549 0.71802896 1.1223262548446655 True -12 35633 30.545547485351562 0.6947391033172607 1198.1920166015625 0.7563533782958984 1830.1221923828125 0.5069735050201416 0.72925276 1.0065240859985352 True -13 38374 30.103555917739868 0.6906516551971436 1674.113037109375 0.7795193195343018 1812.105224609375 0.5126489996910095 0.7388275 0.9039623141288757 True -14 41115 29.938636541366577 0.6840643882751465 1106.292236328125 0.4071749448776245 1795.12109375 0.515468180179596 0.7452421 0.8359462022781372 True -15 43856 29.89499044418335 0.6905241012573242 1213.067626953125 0.87694251537323 1789.98388671875 0.5173779129981995 0.75160563 0.7480994462966919 True -16 46597 29.935253620147705 23.73777413368225 1158.7431640625 0.638515830039978 1780.1165771484375 0.5196240544319153 0.7606172 0.6963358521461487 True -17 49338 30.374777793884277 0.696242094039917 1316.6300048828125 0.6427034139633179 1774.99462890625 0.5214071869850159 0.76318246 0.6648839712142944 True -18 52079 29.921908617019653 0.6868526935577393 1453.5025634765625 0.5930805206298828 1786.3148193359375 0.5171016454696655 0.7626795 0.6582126617431641 False -19 54820 29.915518045425415 1.8835976123809814 1345.9417724609375 0.6122674942016602 1784.0809326171875 0.5184798240661621 0.76341575 0.656480073928833 True diff --git a/ENCSR594NOE/cherimoya.fold_1.performance.tsv b/ENCSR594NOE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c280cf92cbde4d277b8fa01b746cf50f78a66dbc..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1784.0809326171875 0.26394951343536377 0.5184798240661621 0.3053954243659973 0.7634157538414001 0.7278187274932861 0.656480073928833 \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_2.evaluate.json b/ENCSR594NOE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 96d6e3e84274dc99b04ed71b9c000d9ecccec694..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772RPD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_2.fit.json b/ENCSR594NOE/cherimoya.fold_2.fit.json deleted file mode 100644 index d62adbf7d5b936b57c6c1ad13d0ed9b2aa6c1582..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF772RPD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_2.log b/ENCSR594NOE/cherimoya.fold_2.log deleted file mode 100644 index 1a17c9ec61cfa42466186c53e2a36e4b7b79579e..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 36.69218134880066 2.0563573837280273 1329.522705078125 0.9142689108848572 2326.3173828125 0.2881655991077423 0.4883928 9.104433059692383 True -1 5740 32.02538466453552 0.6037979125976562 1582.3897705078125 0.9216707348823547 1883.2735595703125 0.4249214828014374 0.58371085 6.578944683074951 True -2 8610 31.995824813842773 0.58634352684021 1481.715087890625 0.9376737475395203 1852.6229248046875 0.4296424090862274 0.6025773 5.252414703369141 True -3 11480 31.987483501434326 0.5996732711791992 1281.9609375 1.2346177101135254 1807.5462646484375 0.4379318356513977 0.62203616 3.369145154953003 True -4 14350 32.15409183502197 0.595252275466919 1202.522705078125 0.9524660706520081 1781.3504638671875 0.4452103078365326 0.62590796 2.714670419692993 True -5 17220 32.54754447937012 7.775803565979004 1435.6171875 1.004145622253418 1759.005126953125 0.45304805040359497 0.6360189 2.2446539402008057 True -6 20090 31.99340534210205 1.522414207458496 1346.9000244140625 0.771926999092102 1754.99853515625 0.45347464084625244 0.6461592 2.023010492324829 True -7 22960 32.025041580200195 1.28175687789917 1622.1177978515625 0.6143848299980164 1733.5137939453125 0.4610786736011505 0.653122 1.8137978315353394 True -8 25830 31.967023849487305 0.6328413486480713 1436.5889892578125 0.8347213268280029 1717.0286865234375 0.4668298065662384 0.66168296 1.5695981979370117 True -9 28700 31.9517719745636 0.5981767177581787 1495.083984375 0.8874312043190002 1708.3946533203125 0.46978092193603516 0.6675423 1.3738045692443848 True -10 31570 32.00013017654419 0.6052076816558838 1429.533447265625 0.6726930141448975 1695.7386474609375 0.4726315438747406 0.67296183 1.2725167274475098 True -11 34440 31.972490787506104 0.6026933193206787 1447.644775390625 0.550707221031189 1682.5552978515625 0.4768383204936981 0.6835497 1.2234611511230469 True -12 37310 31.98536515235901 0.5953741073608398 1152.5543212890625 0.7571108341217041 1674.3179931640625 0.4775417149066925 0.69058126 1.1279445886611938 True -13 40180 31.317687273025513 0.5957107543945312 1410.05810546875 0.651652455329895 1657.6317138671875 0.48296117782592773 0.6992877 1.018423318862915 True -14 43050 31.31645154953003 0.6018462181091309 1398.582275390625 0.42969879508018494 1649.563720703125 0.48513656854629517 0.7063699 0.9668789505958557 True -15 45920 31.372637033462524 0.5973119735717773 1226.7989501953125 0.8637877106666565 1640.9359130859375 0.48675212264060974 0.7145389 0.8587186932563782 True -16 48790 31.3753023147583 0.5801422595977783 1165.6396484375 0.6270267963409424 1641.4171142578125 0.4864419400691986 0.7191731 0.8019303679466248 True -17 51660 31.39186143875122 2.5871591567993164 1071.232666015625 0.5602492094039917 1642.9610595703125 0.48642125725746155 0.72132987 0.7617323994636536 True -18 54530 31.32896375656128 0.596923828125 1148.8509521484375 0.4917474389076233 1641.7252197265625 0.48746535181999207 0.7216102 0.7499725818634033 True -19 57400 31.366729736328125 1.5386826992034912 1166.9615478515625 0.44837355613708496 1641.05029296875 0.4883487820625305 0.7216579 0.7506340742111206 True diff --git a/ENCSR594NOE/cherimoya.fold_2.performance.tsv b/ENCSR594NOE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 059e1f50494cfccdd5ca1bb19adc6944879cc794..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1641.05029296875 0.2794308662414551 0.4883487820625305 0.27566686272621155 0.7216578722000122 0.6643213033676147 0.7506340742111206 \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_3.evaluate.json b/ENCSR594NOE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e3acc108c8a5fdafce96bf6e3bb264825a79b02c..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772RPD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_3.fit.json b/ENCSR594NOE/cherimoya.fold_3.fit.json deleted file mode 100644 index 0075765ff9887bcc4874080e9926d3873a32b592..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF772RPD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_3.log b/ENCSR594NOE/cherimoya.fold_3.log deleted file mode 100644 index 270864c733f07a54b88586ac59695420aa6f68c1..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2804 35.85439705848694 3.683915615081787 1372.0155029296875 1.5536317825317383 2356.73388671875 0.2848617434501648 0.53447944 12.940256118774414 True -1 5608 31.212765216827393 0.5831329822540283 1437.975830078125 1.2596842050552368 1983.1968994140625 0.4128580391407013 0.5833273 4.670046806335449 True -2 8412 31.239986419677734 0.5658440589904785 1125.494873046875 0.885871410369873 1935.6060791015625 0.42447689175605774 0.58619267 3.4456653594970703 True -3 11216 31.271392107009888 0.5608389377593994 1427.725341796875 1.2772465944290161 1874.925537109375 0.43863850831985474 0.6056114 2.973360061645508 True -4 14020 31.314828634262085 0.5620813369750977 1126.510498046875 0.9262257814407349 1849.4544677734375 0.4445112943649292 0.62196827 2.5637333393096924 True -5 16824 31.24328351020813 0.5619382858276367 1411.66064453125 1.1931506395339966 1834.5269775390625 0.44943347573280334 0.6150735 2.437803268432617 False -6 19628 31.267229318618774 0.5566542148590088 1342.260986328125 0.7133878469467163 1810.927978515625 0.45699408650398254 0.62831473 2.039093255996704 True -7 22432 31.25615096092224 0.570218563079834 1128.3751220703125 1.0530343055725098 1805.573486328125 0.4577386975288391 0.6385344 2.088740587234497 True -8 25236 31.488818407058716 0.574225664138794 1216.2171630859375 1.009475827217102 1766.6439208984375 0.472433865070343 0.64686006 1.7730581760406494 True -9 28040 31.492890119552612 0.5865919589996338 1250.100830078125 0.7421281933784485 1762.1470947265625 0.47180259227752686 0.6564893 1.557887315750122 True -10 30844 31.56365990638733 24.91826581954956 1295.7735595703125 0.8275530338287354 1745.6099853515625 0.476724237203598 0.6591722 1.392419457435608 True -11 33648 38.56387209892273 0.6166892051696777 1325.0626220703125 0.8838889002799988 1734.1285400390625 0.48004698753356934 0.66778827 1.3489534854888916 True -12 36452 30.816353797912598 0.5852029323577881 1476.088134765625 0.572182297706604 1719.0323486328125 0.48420897126197815 0.671201 1.1978718042373657 True -13 39256 31.028358936309814 0.5654556751251221 1225.167236328125 0.7635037302970886 1705.8135986328125 0.487958163022995 0.6845891 1.1042304039001465 True -14 42060 30.731919527053833 0.5659902095794678 1294.1170654296875 0.7489204406738281 1700.53759765625 0.48820582032203674 0.698203 0.978069543838501 True -15 44864 30.77315902709961 0.5687363147735596 1450.964599609375 0.5175457000732422 1692.2122802734375 0.4898214638233185 0.7076511 0.8829314112663269 True -16 47668 30.8570454120636 0.5704522132873535 1283.059326171875 0.5371748208999634 1686.0782470703125 0.49232280254364014 0.71786004 0.8128059506416321 True -17 50472 30.764296054840088 1.331256628036499 1251.0010986328125 0.6935712099075317 1682.0584716796875 0.49224865436553955 0.7224999 0.778753399848938 True -18 53276 30.840261220932007 0.5639166831970215 1136.182373046875 0.574813723564148 1690.915283203125 0.48863399028778076 0.7254901 0.759942889213562 True -19 56080 30.96317958831787 0.5617623329162598 1108.0372314453125 0.4965260922908783 1684.0921630859375 0.4919528067111969 0.72497493 0.7555640935897827 False diff --git a/ENCSR594NOE/cherimoya.fold_3.performance.tsv b/ENCSR594NOE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1c97fb1ee56f31c1cf492c885dbcc447c7eb5ddb..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1690.915283203125 0.27789777517318726 0.488633930683136 0.27849215269088745 0.7254900932312012 0.673338770866394 0.759942889213562 \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_4.evaluate.json b/ENCSR594NOE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b1ca23af13506aebf71e2ed23e4f2a5d79488962..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772RPD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_4.fit.json b/ENCSR594NOE/cherimoya.fold_4.fit.json deleted file mode 100644 index 26ce2929ed67b8123b345844b9787a02c9989994..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF772RPD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594NOE/cherimoya.fold_4.log b/ENCSR594NOE/cherimoya.fold_4.log deleted file mode 100644 index b173bb142ef09f3713dab20a64d98496f1160817..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 36.369022846221924 3.527719736099243 1343.2928466796875 1.3527898788452148 2037.4261474609375 0.2807796597480774 0.5163272 9.612329483032227 True -1 5564 31.12617039680481 0.5159149169921875 1557.7490234375 1.028062343597412 1688.9097900390625 0.41866692900657654 0.57786214 5.781285285949707 True -2 8346 31.085075855255127 0.5041975975036621 1209.736328125 1.0503478050231934 1643.8662109375 0.4298956096172333 0.59692055 2.946129083633423 True -3 11128 31.047820329666138 0.511817455291748 1404.09228515625 0.9297820925712585 1598.446044921875 0.44214490056037903 0.6083969 1.9196083545684814 True -4 13910 31.05121922492981 0.5024423599243164 1461.30517578125 1.0191123485565186 1579.585693359375 0.44762441515922546 0.61665815 1.5324904918670654 True -5 16692 31.34937596321106 0.5027570724487305 1034.232177734375 0.9531557559967041 1571.059326171875 0.4520159065723419 0.62393105 1.515669584274292 True -6 19474 31.094029188156128 0.5005366802215576 1618.4949951171875 1.1089186668395996 1554.11865234375 0.45818233489990234 0.6302955 1.339189052581787 True -7 22256 31.04374861717224 0.5021038055419922 1410.95166015625 1.177860975265503 1542.031005859375 0.4649749994277954 0.6333943 1.275154948234558 True -8 25038 31.06583571434021 0.5018486976623535 1562.1148681640625 0.9135993719100952 1536.3587646484375 0.4669860303401947 0.64376247 1.2039231061935425 True -9 27820 31.046756505966187 0.5055985450744629 1498.26220703125 1.1018445491790771 1527.1669921875 0.4714219570159912 0.64665145 1.0686451196670532 True -10 30602 31.0288245677948 0.504321813583374 1337.017578125 1.237879753112793 1510.15576171875 0.47826242446899414 0.6513105 0.9799360632896423 True -11 33384 31.00196671485901 0.5068771839141846 1308.89453125 1.007834792137146 1504.0762939453125 0.480032742023468 0.6536831 0.9999691247940063 True -12 36166 30.802162408828735 0.5004065036773682 1671.621337890625 1.0359714031219482 1497.0625 0.4831261932849884 0.6633063 0.923050582408905 True -13 38948 30.384055137634277 0.5013473033905029 1337.4794921875 1.0172710418701172 1485.220703125 0.4880993068218231 0.67217183 0.8323628902435303 True -14 41730 30.398619651794434 0.5050156116485596 1168.280029296875 0.6512657403945923 1477.407958984375 0.48982569575309753 0.6809266 0.7622445225715637 True -15 44512 30.3712100982666 0.5006873607635498 1567.756591796875 0.5211048722267151 1475.0821533203125 0.4908316731452942 0.6919345 0.7252935767173767 True -16 47294 30.33439064025879 0.49579453468322754 1091.5028076171875 0.4857391119003296 1461.5089111328125 0.49692919850349426 0.6980824 0.6943696737289429 True -17 50076 30.390333652496338 2.656611680984497 989.01318359375 0.35969382524490356 1470.96533203125 0.4918944835662842 0.70390296 0.6794368028640747 True -18 52858 30.400176286697388 0.5137832164764404 1758.304443359375 0.9398216009140015 1471.9080810546875 0.49148502945899963 0.7037066 0.6840011477470398 False -19 55640 30.447912454605103 0.5139458179473877 1481.9130859375 0.5450793504714966 1475.1558837890625 0.49001410603523254 0.7040956 0.6862139105796814 True diff --git a/ENCSR594NOE/cherimoya.fold_4.performance.tsv b/ENCSR594NOE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b52e11d0967017fe03ab8433d836d87235ea63ee..0000000000000000000000000000000000000000 --- a/ENCSR594NOE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1475.1558837890625 0.2870187759399414 0.49001407623291016 0.2608351707458496 0.7040956020355225 0.6381396651268005 0.6862139105796814 \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_0.evaluate.json b/ENCSR594OWA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f2c8a60dbada9d7c5a536218356e13efef525d52..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF787HHE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_0.fit.json b/ENCSR594OWA/cherimoya.fold_0.fit.json deleted file mode 100644 index 530a637a8376f7d92fae8a312e81e45fe50399e3..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF787HHE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_0.log b/ENCSR594OWA/cherimoya.fold_0.log deleted file mode 100644 index 92a3868bd29361c28a987a56531162a2982e5321..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 35.19425559043884 3.4899773597717285 119.58695983886719 0.7822558879852295 200.12570190429688 0.14057660102844238 0.39708522 2.6299829483032227 True -1 5492 30.62735915184021 0.5502815246582031 140.197021484375 0.7364417910575867 185.9355010986328 0.2175365388393402 0.5110401 1.5094292163848877 True -2 8238 30.621220350265503 0.5308670997619629 145.93756103515625 0.517303466796875 182.74258422851562 0.22697341442108154 0.5296728 0.9386600255966187 True -3 10984 30.706444263458252 0.5289559364318848 145.02911376953125 0.8837613463401794 181.0521240234375 0.23301440477371216 0.54981595 0.9487115144729614 True -4 13730 30.584608554840088 0.5339128971099854 157.78646850585938 0.6785414218902588 180.0748748779297 0.23814356327056885 0.57341045 0.9668346047401428 True -5 16476 30.714620351791382 0.5341794490814209 147.77903747558594 1.1905012130737305 179.2541046142578 0.24281324446201324 0.5807413 0.9099953770637512 True -6 19222 30.90286660194397 33.66960120201111 146.87619018554688 0.4958355724811554 179.0552215576172 0.24376103281974792 0.5850215 0.9146097302436829 True -7 21968 31.330204725265503 1.3012919425964355 159.5860595703125 0.745712161064148 178.7416229248047 0.24550436437129974 0.5897189 0.8635239005088806 True -8 24714 30.614803075790405 18.800498723983765 122.84313201904297 0.6731894016265869 178.19277954101562 0.24864281713962555 0.595794 0.8065623044967651 True -9 27460 31.883581399917603 1.1481800079345703 132.60694885253906 0.5849385857582092 178.09962463378906 0.24778035283088684 0.60679287 0.7374352216720581 True -10 30206 30.62781310081482 0.5559146404266357 147.59194946289062 0.6717637777328491 177.5048065185547 0.251970499753952 0.6116001 0.7396283149719238 True -11 32952 30.768229722976685 0.5437519550323486 147.72962951660156 0.5794677138328552 177.09779357910156 0.25386810302734375 0.6246075 0.6650488376617432 True -12 35698 30.779282808303833 0.5358757972717285 136.56094360351562 0.7515840530395508 176.7068328857422 0.2556784152984619 0.63320506 0.6333650350570679 True -13 38444 30.53266429901123 26.625126361846924 124.07376861572266 0.5468279123306274 176.44076538085938 0.2567494213581085 0.6423725 0.5896768569946289 True -14 41190 32.24052715301514 32.74985718727112 137.35873413085938 0.5999177098274231 176.02394104003906 0.25910434126853943 0.65346867 0.5461863279342651 True -15 43936 31.585705757141113 0.5285232067108154 144.15982055664062 0.6616394519805908 175.82835388183594 0.26020118594169617 0.66384816 0.5229319334030151 True -16 46682 30.04038667678833 0.5246891975402832 134.18394470214844 0.3116742968559265 175.7179718017578 0.26067614555358887 0.66995996 0.5003206133842468 True -17 49428 30.016996383666992 0.530627965927124 139.28298950195312 0.346558541059494 175.59083557128906 0.26133209466934204 0.67550194 0.48670920729637146 True -18 52174 30.04062819480896 0.5227158069610596 129.614990234375 0.43768808245658875 175.51223754882812 0.2619701325893402 0.6750114 0.4838792383670807 False -19 54920 30.005455493927002 0.5295109748840332 123.7567367553711 0.4167480766773224 175.7803497314453 0.259941428899765 0.67400503 0.4875449240207672 False diff --git a/ENCSR594OWA/cherimoya.fold_0.performance.tsv b/ENCSR594OWA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e7dee9fadfbe4fbb59ec9c68c169fdfb51fa6117..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -175.59083557128906 0.5311998128890991 0.26133212447166443 0.051570672541856766 0.6755019426345825 0.6338702440261841 0.48670920729637146 \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_1.evaluate.json b/ENCSR594OWA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 263b8cede3fdb648397af1493238f9ec9528dd44..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF787HHE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_1.fit.json b/ENCSR594OWA/cherimoya.fold_1.fit.json deleted file mode 100644 index 79c26ced3b4fb99e3c042a1a8295d4ad78b69fdf..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF787HHE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_1.log b/ENCSR594OWA/cherimoya.fold_1.log deleted file mode 100644 index b12ebdd5351403d6a44cb79a601b5b6b67570bbb..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.18184041976929 8.5337073802948 139.66226196289062 0.8284432291984558 220.3776092529297 0.14629672467708588 0.45172432 2.6209139823913574 True -1 5516 30.77308940887451 0.9888865947723389 144.76290893554688 0.8432681560516357 204.50779724121094 0.22559134662151337 0.5416008 1.5907821655273438 True -2 8274 30.774774074554443 0.7063789367675781 138.24578857421875 0.7234843969345093 200.7340545654297 0.23880746960639954 0.57235366 0.9667041301727295 True -3 11032 30.74063539505005 0.7066977024078369 157.68258666992188 0.8177645206451416 198.52442932128906 0.24582625925540924 0.59359753 0.8840901255607605 True -4 13790 30.69481110572815 1.9131088256835938 116.88609313964844 0.7345073223114014 197.53343200683594 0.2495431900024414 0.6099117 0.844176709651947 True -5 16548 31.401427030563354 38.28877639770508 117.26004791259766 0.7154299020767212 196.5968475341797 0.2550038993358612 0.61884934 0.9069460034370422 True -6 19306 30.96410083770752 0.7922158241271973 111.28465270996094 0.8149532079696655 195.97523498535156 0.2567640542984009 0.62663805 0.8741826415061951 True -7 22064 30.154924154281616 0.716158390045166 152.42138671875 0.5744762420654297 195.62562561035156 0.2584123909473419 0.63128364 0.8238368630409241 True -8 24822 30.080091953277588 0.6896438598632812 174.41995239257812 0.5673439502716064 195.1763916015625 0.25976356863975525 0.6434625 0.7626239061355591 True -9 27580 30.210989475250244 0.7049894332885742 144.29391479492188 0.5588169097900391 194.71371459960938 0.2622886896133423 0.651387 0.7384536862373352 True -10 30338 34.65116763114929 31.414369106292725 104.83634948730469 0.6389400959014893 194.17440795898438 0.26478543877601624 0.66032636 0.6779686808586121 True -11 33096 35.981255292892456 16.575105905532837 122.03970336914062 0.44994503259658813 193.72149658203125 0.2670214772224426 0.6687964 0.628189742565155 True -12 35854 30.200308084487915 0.7381362915039062 130.64695739746094 0.5676379203796387 193.6000518798828 0.26626861095428467 0.68089014 0.5944186449050903 True -13 38612 30.48027729988098 0.801377534866333 165.77841186523438 0.6088649034500122 192.95169067382812 0.2698623239994049 0.6913752 0.5494870543479919 True -14 41370 30.402840614318848 0.7201411724090576 126.68785858154297 0.48251432180404663 192.55804443359375 0.27172279357910156 0.70000494 0.5285224318504333 True -15 44128 30.508076906204224 0.7130651473999023 122.64899444580078 0.35960471630096436 192.26353454589844 0.272789865732193 0.706784 0.5175725817680359 True -16 46886 30.355652570724487 0.7291431427001953 132.273193359375 0.5464826822280884 192.29403686523438 0.27220994234085083 0.7118717 0.5009714961051941 True -17 49644 30.409421682357788 3.333909749984741 137.39739990234375 0.4319121241569519 192.01824951171875 0.27356037497520447 0.7164245 0.4896889328956604 True -18 52402 31.68365240097046 26.397646188735962 132.94635009765625 0.34908291697502136 191.92831420898438 0.274174302816391 0.71475446 0.4903832674026489 False -19 55160 32.666430711746216 32.755330324172974 128.9293975830078 0.5278416872024536 191.97569274902344 0.27407532930374146 0.7146019 0.48957890272140503 False diff --git a/ENCSR594OWA/cherimoya.fold_1.performance.tsv b/ENCSR594OWA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 38db53454343ff52b191c6a74460746763dc6159..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -192.01824951171875 0.520865797996521 0.27356037497520447 0.057758621871471405 0.7164245247840881 0.6788792610168457 0.4896889328956604 \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_2.evaluate.json b/ENCSR594OWA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0b387338974eda72c21c65aa112abf2464132be4..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF787HHE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_2.fit.json b/ENCSR594OWA/cherimoya.fold_2.fit.json deleted file mode 100644 index 45934bc78af7737052bca3b76c1718bbda1c870f..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF787HHE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_2.log b/ENCSR594OWA/cherimoya.fold_2.log deleted file mode 100644 index 122e32fcad08552aaa84985885ef587fae6b7bcb..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 36.757007360458374 38.65970039367676 147.39266967773438 0.7850630283355713 204.2305908203125 0.14511820673942566 0.40928584 2.024658441543579 True -1 5782 32.328282833099365 0.5413813591003418 150.27838134765625 0.8464233875274658 189.94972229003906 0.22456060349941254 0.5345008 1.165578842163086 True -2 8673 33.21603083610535 10.67774248123169 144.1031494140625 1.2215994596481323 187.11807250976562 0.23154324293136597 0.55564255 0.8644732236862183 True -3 11564 32.261120080947876 0.5226809978485107 162.50796508789062 0.8888910412788391 184.74697875976562 0.2413984090089798 0.5664805 0.9300158023834229 True -4 14455 32.267701625823975 0.5203390121459961 157.14300537109375 0.7855212092399597 183.70660400390625 0.24475914239883423 0.58421415 0.874860405921936 True -5 17346 32.21455693244934 0.5199618339538574 151.1697235107422 0.8405473232269287 182.9169158935547 0.24964956939220428 0.59374446 0.917672336101532 True -6 20237 33.10770845413208 0.5185556411743164 161.40921020507812 1.0389726161956787 182.4189910888672 0.25263527035713196 0.604621 0.8676917552947998 True -7 23128 32.41909456253052 0.5211637020111084 167.0413818359375 0.5417108535766602 182.3307342529297 0.2521817982196808 0.6063235 0.8371616005897522 True -8 26019 32.23485732078552 0.519695520401001 136.27322387695312 0.6944909691810608 181.85321044921875 0.2548259198665619 0.61215687 0.7813645601272583 True -9 28910 32.416523933410645 0.5174846649169922 129.584228515625 0.7224012613296509 181.28448486328125 0.25828057527542114 0.6194897 0.7610679864883423 True -10 31801 32.33146095275879 0.5195577144622803 121.16785430908203 0.3868247866630554 180.86058044433594 0.26041606068611145 0.6293666 0.7000876069068909 True -11 34692 32.404138803482056 0.5388054847717285 144.62904357910156 0.6707583665847778 180.5294952392578 0.2615974247455597 0.6376734 0.6569147706031799 True -12 37583 32.38455510139465 0.547980785369873 122.09015655517578 0.5853460431098938 180.0181884765625 0.2644288241863251 0.6456411 0.6363081932067871 True -13 40474 32.487571477890015 0.5300378799438477 144.8450469970703 0.6006600856781006 179.64932250976562 0.2662080228328705 0.6532244 0.5929691791534424 True -14 43365 32.311933517456055 0.5126268863677979 142.82345581054688 0.50559401512146 179.2280731201172 0.26866012811660767 0.6652185 0.5517045259475708 True -15 46256 31.694987535476685 0.5118613243103027 108.54399108886719 0.6421677470207214 179.02261352539062 0.2684248089790344 0.67476165 0.514306366443634 True -16 49147 31.651660442352295 0.5192441940307617 136.54112243652344 0.7945404052734375 179.02005004882812 0.2686907947063446 0.6794915 0.49106425046920776 True -17 52038 31.681318998336792 0.5099267959594727 126.62124633789062 0.5333921909332275 179.00547790527344 0.26859256625175476 0.682898 0.48277774453163147 True -18 54929 31.632988929748535 0.5142192840576172 139.77784729003906 0.40222054719924927 179.08871459960938 0.26808446645736694 0.68211496 0.48346805572509766 False -19 57820 31.620665073394775 0.5059020519256592 126.73017883300781 0.3894433081150055 178.9132843017578 0.2693083584308624 0.68267614 0.4874415695667267 False diff --git a/ENCSR594OWA/cherimoya.fold_2.performance.tsv b/ENCSR594OWA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0cee64249ba36af2c7ddea49d7dd721ab631a7f0..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -179.00547790527344 0.526948869228363 0.26859256625175476 0.05421101301908493 0.6828979849815369 0.6467555165290833 0.48277774453163147 \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_3.evaluate.json b/ENCSR594OWA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 38e211b8136c346fc25da147084d7b7a00475795..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF787HHE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_3.fit.json b/ENCSR594OWA/cherimoya.fold_3.fit.json deleted file mode 100644 index 4a6511d673ef2403b26a417cf0e57d4877659a70..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF787HHE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_3.log b/ENCSR594OWA/cherimoya.fold_3.log deleted file mode 100644 index bea65288d7d2c769a01944b457d4c099b41ed0ca..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2805 35.97176241874695 4.1851489543914795 125.00840759277344 0.8037647604942322 213.48538208007812 0.1476237177848816 0.43990457 2.870608329772949 True -1 5610 31.234118700027466 0.5752449035644531 133.1752471923828 0.7574276924133301 198.6253204345703 0.2233772724866867 0.5367602 1.7673354148864746 True -2 8415 31.22380042076111 42.11975073814392 145.6009521484375 0.8247232437133789 195.47573852539062 0.23462624847888947 0.56413704 1.0495858192443848 True -3 11220 31.254684448242188 34.54398322105408 151.91592407226562 0.727683424949646 193.8800048828125 0.24091088771820068 0.57520187 1.0380507707595825 True -4 14025 31.43676781654358 0.607893705368042 134.035400390625 0.8592703342437744 193.03628540039062 0.24438384175300598 0.58451664 1.037061333656311 True -5 16830 31.208537340164185 0.5567255020141602 136.29238891601562 0.8993061780929565 192.61544799804688 0.24566106498241425 0.59513336 0.9414883852005005 True -6 19635 31.271487951278687 0.5551469326019287 140.23248291015625 0.7434474229812622 192.01502990722656 0.24971015751361847 0.6021829 0.8950854539871216 True -7 22440 31.048463106155396 0.5453729629516602 143.23281860351562 0.7076976895332336 191.5435333251953 0.2523793578147888 0.60655975 0.8505330681800842 True -8 25245 30.525995016098022 0.5432617664337158 119.34915161132812 0.7385175824165344 191.5190887451172 0.2514241635799408 0.61573946 0.8293366432189941 True -9 28050 30.522098541259766 0.5445833206176758 124.50555419921875 0.6655237078666687 190.8822021484375 0.25528568029403687 0.6244147 0.7628600001335144 True -10 30855 30.697797298431396 0.5460786819458008 138.45965576171875 0.6706993579864502 190.26126098632812 0.25774863362312317 0.63676625 0.7013523578643799 True -11 33660 30.658649682998657 0.5499529838562012 163.6585693359375 0.7873221635818481 189.84226989746094 0.2602764666080475 0.646964 0.6621488928794861 True -12 36465 30.59945034980774 0.5418627262115479 117.60301971435547 0.5873970985412598 189.42677307128906 0.26278555393218994 0.6546991 0.6207727193832397 True -13 39270 30.680060148239136 0.5463509559631348 154.93284606933594 0.7227199673652649 189.17617797851562 0.263766884803772 0.66502506 0.5630534887313843 True -14 42075 30.623411893844604 0.5471963882446289 154.06365966796875 0.4070952236652374 188.87120056152344 0.26453033089637756 0.67825013 0.5289402008056641 True -15 44880 30.77735447883606 0.5708022117614746 152.98455810546875 0.6923865079879761 188.65261840820312 0.26561400294303894 0.68463576 0.5186842679977417 True -16 47685 30.922477960586548 0.5575616359710693 166.13616943359375 0.45665469765663147 188.33009338378906 0.2676258385181427 0.6926568 0.4965173304080963 True -17 50490 30.787180423736572 0.5560359954833984 132.2421875 0.32971665263175964 188.25244140625 0.2680385112762451 0.69457304 0.49089810252189636 True -18 53295 30.658094882965088 19.863730907440186 133.17514038085938 0.4300427734851837 188.23268127441406 0.26820608973503113 0.6937021 0.49011802673339844 False -19 56100 32.689961433410645 0.5503101348876953 140.2503662109375 0.4845748543739319 188.2327117919922 0.26812076568603516 0.69400734 0.49366167187690735 False diff --git a/ENCSR594OWA/cherimoya.fold_3.performance.tsv b/ENCSR594OWA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c2448775eba1e732feb19a9b276fde35c45793ff..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -188.25244140625 0.5253328084945679 0.2680385112762451 0.05500362813472748 0.6945730447769165 0.6582701802253723 0.49089810252189636 \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_4.evaluate.json b/ENCSR594OWA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b75cf89a0ef5aaebc7a657aedd98351ef3ab320b..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF787HHE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_4.fit.json b/ENCSR594OWA/cherimoya.fold_4.fit.json deleted file mode 100644 index e0c1e15d91262622f379e719851548e7223ea9d3..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF787HHE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594OWA/cherimoya.fold_4.log b/ENCSR594OWA/cherimoya.fold_4.log deleted file mode 100644 index 56a237e261089a5d87f7d29d49dc0147baad6c66..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.693445444107056 5.1842241287231445 137.87350463867188 0.9163910746574402 194.77488708496094 0.14321009814739227 0.41514975 2.5339367389678955 True -1 5772 31.691835641860962 4.0007734298706055 162.77125549316406 0.886528491973877 181.97792053222656 0.21067392826080322 0.54130757 1.1845093965530396 True -2 8658 32.431257486343384 0.5907504558563232 147.0180206298828 0.9717824459075928 178.42942810058594 0.22582532465457916 0.566732 0.8978913426399231 True -3 11544 31.595654726028442 0.5756580829620361 155.23768615722656 0.6812587380409241 177.04287719726562 0.230596125125885 0.5826477 0.8697149753570557 True -4 14430 31.501062154769897 0.5707235336303711 149.689208984375 0.7984099984169006 176.4843292236328 0.2322026640176773 0.59236956 0.8672538995742798 True -5 17316 31.5897696018219 0.5660204887390137 118.54299926757812 1.1412169933319092 175.7881622314453 0.23610414564609528 0.60708773 0.7932751178741455 True -6 20202 31.460743188858032 0.5668361186981201 133.03138732910156 0.9078953266143799 175.241943359375 0.2390674352645874 0.61468065 0.7551338076591492 True -7 23088 35.05511474609375 15.149521589279175 135.12503051757812 0.5566914677619934 175.07814025878906 0.23923593759536743 0.62127984 0.7256665825843811 True -8 25974 31.574946880340576 0.5785033702850342 139.60557556152344 0.7809902429580688 174.67283630371094 0.24205532670021057 0.626454 0.7371706962585449 True -9 28860 31.63769268989563 0.569631814956665 180.0229949951172 0.6549829840660095 174.4164276123047 0.24308264255523682 0.63180816 0.7025288343429565 True -10 31746 31.534220457077026 1.3390507698059082 145.58572387695312 0.8315963745117188 173.9649200439453 0.24592509865760803 0.63988453 0.6343836188316345 True -11 34632 31.553619861602783 1.6148030757904053 132.9626007080078 0.5580670833587646 173.452880859375 0.2481587529182434 0.64856356 0.5967534184455872 True -12 37518 31.476037740707397 0.8476262092590332 109.42505645751953 0.6097044944763184 173.31112670898438 0.24869327247142792 0.6532751 0.5754871368408203 True -13 40404 31.54517126083374 0.5633487701416016 121.18301391601562 0.5320072174072266 172.9353790283203 0.2504618167877197 0.6642499 0.5458937287330627 True -14 43290 31.57923984527588 1.3052842617034912 151.88681030273438 0.46782881021499634 172.77566528320312 0.25152692198753357 0.6726871 0.5272643566131592 True -15 46176 31.60132670402527 0.5773332118988037 145.3540496826172 0.33845341205596924 172.53607177734375 0.2530513405799866 0.6801586 0.5003547072410583 True -16 49062 31.554461240768433 0.5655496120452881 119.90194702148438 0.4540342688560486 172.21810913085938 0.2549743354320526 0.6882428 0.47775328159332275 True -17 51948 31.532154321670532 0.5694704055786133 131.41812133789062 0.4125032126903534 172.22265625 0.2552448809146881 0.6912642 0.47009706497192383 True -18 54834 31.546403646469116 0.5742535591125488 142.65206909179688 0.42683565616607666 172.32168579101562 0.25432446599006653 0.6915867 0.4704291820526123 True -19 57720 36.97951912879944 8.751573085784912 145.34567260742188 0.5326111316680908 172.2296142578125 0.2551974654197693 0.68973476 0.4703407287597656 False diff --git a/ENCSR594OWA/cherimoya.fold_4.performance.tsv b/ENCSR594OWA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ecbbcb4cf7d0f4f51b5ddaad2367d7149bfcadb7..0000000000000000000000000000000000000000 --- a/ENCSR594OWA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -172.32168579101562 0.5355786681175232 0.25432446599006653 0.05226549506187439 0.6915866732597351 0.649952232837677 0.4704291820526123 \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_0.evaluate.json b/ENCSR594TMY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3aa2a358cec76070e7ba8de03ef01af9e3975689..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863SSN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_0.fit.json b/ENCSR594TMY/cherimoya.fold_0.fit.json deleted file mode 100644 index 3bcd41c9a2ba049f8eae207229ad5013db7942a8..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF863SSN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_0.log b/ENCSR594TMY/cherimoya.fold_0.log deleted file mode 100644 index 7c4baaf675f67b3c80572863407beb20ed44ef90..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1848 24.12660837173462 1.9573678970336914 233.35440063476562 0.9529576301574707 438.493408203125 0.41862013936042786 0.56624377 11.59421443939209 True -1 3696 20.5919246673584 0.3457331657409668 291.44635009765625 0.4993496239185333 370.3482666015625 0.5342320799827576 0.65350634 4.34420108795166 True -2 5544 20.6252658367157 0.3423895835876465 277.04852294921875 0.5338096022605896 350.9756774902344 0.5780828595161438 0.6816426 1.1864718198776245 True -3 7392 20.595964670181274 0.3417937755584717 313.14599609375 0.7140535116195679 345.4687805175781 0.5874214172363281 0.68222266 0.7424222826957703 True -4 9240 20.56790280342102 0.96915602684021 270.77392578125 0.5939533710479736 343.539306640625 0.5915695428848267 0.6918058 0.6962783932685852 True -5 11088 20.580142974853516 1.2389910221099854 322.64556884765625 0.6027532815933228 342.2969055175781 0.5945952534675598 0.69811606 0.7009587287902832 True -6 12936 20.583298206329346 1.2157466411590576 307.9503173828125 0.5269584655761719 341.2345886230469 0.5967947244644165 0.70465267 0.6648533940315247 True -7 14784 20.60728406906128 0.3455483913421631 280.33502197265625 0.7122611999511719 340.04718017578125 0.599475622177124 0.709166 0.6088883876800537 True -8 16632 20.507078170776367 0.34394168853759766 210.57110595703125 0.5197835564613342 339.1664123535156 0.6013955473899841 0.71455854 0.5883527994155884 True -9 18480 20.54888343811035 0.340620756149292 253.7144012451172 0.5105105042457581 338.37200927734375 0.603069007396698 0.7247376 0.5499202013015747 True -10 20328 20.551349401474 0.34378767013549805 279.84326171875 0.4488169848918915 337.4097595214844 0.6052556037902832 0.7300227 0.52208411693573 True -11 22176 20.534581184387207 0.3437824249267578 279.5574645996094 0.7704718112945557 336.7575988769531 0.6067151427268982 0.73269296 0.5099860429763794 True -12 24024 20.487375497817993 0.339616060256958 249.02825927734375 0.6574265956878662 335.89630126953125 0.6086850166320801 0.7386897 0.4999387562274933 True -13 25872 20.552822589874268 0.3494584560394287 241.17996215820312 0.32725992798805237 335.2911071777344 0.610136866569519 0.74511474 0.478415846824646 True -14 27720 20.545485973358154 0.3440225124359131 254.80068969726562 0.46056026220321655 334.75958251953125 0.6113011240959167 0.7485232 0.4752523899078369 True -15 29568 20.51640820503235 0.33989453315734863 250.31898498535156 0.38589054346084595 334.6256103515625 0.6112396121025085 0.7496951 0.4766118824481964 True -16 31416 20.52389168739319 0.34852075576782227 267.23443603515625 0.45760995149612427 334.7677307128906 0.6110168695449829 0.75062567 0.48318982124328613 True -17 33264 20.5487642288208 17.283221006393433 231.51986694335938 0.30778634548187256 334.7712097167969 0.610456109046936 0.74797636 0.49406933784484863 False -18 35112 20.94087314605713 0.3544645309448242 279.20330810546875 0.36968183517456055 335.1529846191406 0.6098012924194336 0.74540675 0.5054337978363037 False -19 36960 20.556923627853394 0.3456611633300781 291.5728759765625 0.30573445558547974 335.2583923339844 0.6093106269836426 0.74362224 0.5143797993659973 False diff --git a/ENCSR594TMY/cherimoya.fold_0.performance.tsv b/ENCSR594TMY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 71d427b4f800b1bf4dc0176194a37dd1a3e60873..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -334.7677307128906 0.3146952986717224 0.6110168695449829 0.2169499695301056 0.7506256699562073 0.7012787461280823 0.48318982124328613 \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_1.evaluate.json b/ENCSR594TMY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 16771c016c0f801fed3a3f83f7d9e665d996c613..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863SSN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_1.fit.json b/ENCSR594TMY/cherimoya.fold_1.fit.json deleted file mode 100644 index cd8bd6e2b2e60385985dbf194b9c33c9836ca2d4..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF863SSN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_1.log b/ENCSR594TMY/cherimoya.fold_1.log deleted file mode 100644 index a9ef6b01258363abdd60fa14c22a5907f70a5368..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1881 24.271471977233887 3.404165744781494 236.41737365722656 0.8456190824508667 450.48046875 0.4324217140674591 0.57860583 11.404383659362793 True -1 3762 20.902279138565063 20.257142066955566 258.876220703125 0.8500023484230042 387.27911376953125 0.5377035737037659 0.69029 4.106525421142578 True -2 5643 20.75362515449524 0.44130635261535645 277.81854248046875 0.8915910124778748 369.331787109375 0.575999915599823 0.70121336 1.1266049146652222 True -3 7524 20.722495079040527 0.4448888301849365 260.9494323730469 0.916783332824707 363.63104248046875 0.5877169370651245 0.7156333 0.7092711329460144 True -4 9405 20.71764039993286 0.8117506504058838 229.54383850097656 0.8126185536384583 362.1261901855469 0.5923212170600891 0.71959215 0.6045278310775757 True -5 11286 20.70336151123047 0.44449520111083984 284.66619873046875 0.7378360033035278 360.948486328125 0.5950294137001038 0.7256072 0.5546281337738037 True -6 13167 20.69708752632141 0.43216991424560547 292.7569580078125 0.5726144313812256 359.3292236328125 0.5983163118362427 0.73555946 0.49481144547462463 True -7 15048 20.81533718109131 0.462235689163208 310.7396240234375 0.5958675146102905 358.0966491699219 0.6008970141410828 0.7415877 0.48287349939346313 True -8 16929 20.7955801486969 0.4622528553009033 283.0743408203125 0.5374717712402344 357.2725830078125 0.6026862263679504 0.7459616 0.47867321968078613 True -9 18810 20.75926375389099 0.4501631259918213 254.52786254882812 0.5655289888381958 356.3273010253906 0.6049021482467651 0.7506893 0.47479841113090515 True -10 20691 20.684141159057617 0.44000244140625 240.1083984375 0.48877668380737305 355.39349365234375 0.606817901134491 0.7550505 0.46165716648101807 True -11 22572 20.70431613922119 0.4461193084716797 258.4515380859375 0.4909454882144928 354.6781921386719 0.6084141135215759 0.76292473 0.4383602738380432 True -12 24453 20.6967556476593 0.43697023391723633 300.88446044921875 0.5885709524154663 353.96685791015625 0.6099818348884583 0.7687815 0.43045541644096375 True -13 26334 20.715599536895752 0.4368412494659424 231.65296936035156 0.3743656277656555 353.3310546875 0.6113235354423523 0.7743115 0.42302459478378296 True -14 28215 20.71487808227539 0.44426512718200684 274.262939453125 0.4798479676246643 352.866943359375 0.6119379997253418 0.77726245 0.42051178216934204 True -15 30096 20.697654962539673 0.43451356887817383 248.82760620117188 0.4017244875431061 352.7400207519531 0.612366795539856 0.7803865 0.4167141020298004 True -16 31977 20.689400672912598 0.4402592182159424 252.4681854248047 0.3275672197341919 352.6788635253906 0.6121115684509277 0.78312117 0.41705045104026794 True -17 33858 20.694157361984253 0.4326930046081543 309.8662109375 0.2964111566543579 352.94342041015625 0.6115778088569641 0.78231287 0.42294928431510925 False -18 35739 20.70467758178711 0.43573498725891113 222.32333374023438 0.14671964943408966 353.02252197265625 0.6109078526496887 0.7794293 0.4322734475135803 False -19 37620 20.76675033569336 0.4316365718841553 211.9613494873047 0.25454628467559814 353.1861572265625 0.6106917858123779 0.77518296 0.43791064620018005 False diff --git a/ENCSR594TMY/cherimoya.fold_1.performance.tsv b/ENCSR594TMY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2fe5ac5ea6465a3dbc4e419bbbaa99397609dff0..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -352.6788635253906 0.30973732471466064 0.6121115684509277 0.22512933611869812 0.7831211686134338 0.7553309798240662 0.41705045104026794 \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_2.evaluate.json b/ENCSR594TMY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 87525b5dd499dd970c4034c25d08b3895cce1dfa..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863SSN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_2.fit.json b/ENCSR594TMY/cherimoya.fold_2.fit.json deleted file mode 100644 index 3ca1df5a71aa1cd7ddb2d56b7c7300aa3fb8ff7c..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF863SSN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_2.log b/ENCSR594TMY/cherimoya.fold_2.log deleted file mode 100644 index 3e28b32149af78dc39c7cc548ca0f9b655c5874f..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1969 25.314372539520264 3.8734683990478516 276.62890625 0.8245751857757568 434.158203125 0.4253418743610382 0.5817939 10.481949806213379 True -1 3938 21.67591428756714 0.7601795196533203 237.05560302734375 0.6794270873069763 373.397705078125 0.5341359972953796 0.6926962 3.539703369140625 True -2 5907 21.642404556274414 0.3679227828979492 277.9449462890625 0.5076041221618652 352.8276672363281 0.5767079591751099 0.6913235 1.0772442817687988 False -3 7876 21.74134659767151 0.3714437484741211 240.5677947998047 0.41860267519950867 348.3141784667969 0.5849575400352478 0.70510113 0.8470655083656311 True -4 9845 21.692156553268433 0.371448278427124 293.22259521484375 0.6567510366439819 346.348388671875 0.5889721512794495 0.7120347 0.8154954314231873 True -5 11814 21.694430112838745 0.36560606956481934 226.44456481933594 0.9178127646446228 345.18292236328125 0.5916284918785095 0.7172755 0.7232728600502014 True -6 13783 21.663089275360107 0.3663337230682373 272.7983093261719 0.5293600559234619 343.67266845703125 0.5941521525382996 0.72512364 0.6660725474357605 True -7 15752 21.86518883705139 18.41010594367981 288.55828857421875 0.713784396648407 342.61834716796875 0.596266508102417 0.726786 0.67396080493927 True -8 17721 21.743032217025757 0.3672161102294922 238.16644287109375 0.5176728963851929 342.0076599121094 0.5980023145675659 0.73128366 0.6154942512512207 True -9 19690 21.670976877212524 0.37033700942993164 308.519775390625 0.6548565626144409 340.9070129394531 0.6004794239997864 0.7376528 0.5824353694915771 True -10 21659 21.688597917556763 0.36548614501953125 286.58978271484375 0.6384950876235962 339.8424377441406 0.6027629375457764 0.74112433 0.5497241020202637 True -11 23628 21.654375314712524 0.3650202751159668 268.1785888671875 0.5078930854797363 339.163330078125 0.6043868064880371 0.7448085 0.5190242528915405 True -12 25597 21.962687492370605 0.3636009693145752 287.17425537109375 0.43325671553611755 338.434814453125 0.6060593128204346 0.74937904 0.5042872428894043 True -13 27566 21.627593517303467 0.36689162254333496 303.0190734863281 0.5791178941726685 337.62127685546875 0.6078920364379883 0.755811 0.4803495705127716 True -14 29535 21.680235862731934 0.364668607711792 211.31663513183594 0.3569156229496002 337.1449890136719 0.6086398363113403 0.75896645 0.4770549535751343 True -15 31504 21.62276029586792 0.3654165267944336 267.28131103515625 0.7438596487045288 336.9729309082031 0.6089947819709778 0.7649138 0.46821513772010803 True -16 33473 21.603197813034058 0.35958266258239746 249.556640625 0.28718066215515137 336.9949951171875 0.6085540652275085 0.7644319 0.4677559733390808 False -17 35442 21.71183967590332 0.3658020496368408 242.22760009765625 0.23205986618995667 337.19647216796875 0.6080475449562073 0.763155 0.4750729203224182 False -18 37411 21.622705221176147 0.36467432975769043 264.34014892578125 0.2937012314796448 337.37554931640625 0.6074233651161194 0.75698644 0.48025748133659363 False -19 39380 21.649580001831055 0.357318639755249 243.02157592773438 0.29462990164756775 337.5871276855469 0.607006847858429 0.7558276 0.48689475655555725 False diff --git a/ENCSR594TMY/cherimoya.fold_2.performance.tsv b/ENCSR594TMY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f8647dd13f21cbe3c9184e806de49e81b01c3593..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -336.9729309082031 0.3157888650894165 0.6089949011802673 0.21815013885498047 0.76491379737854 0.7150884866714478 0.46821513772010803 \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_3.evaluate.json b/ENCSR594TMY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index dd271b9383c2af07ed24dc2d8aa57bef0610b087..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863SSN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_3.fit.json b/ENCSR594TMY/cherimoya.fold_3.fit.json deleted file mode 100644 index dc855d4d7aee7aa328c765affa09563d9d051af1..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF863SSN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_3.log b/ENCSR594TMY/cherimoya.fold_3.log deleted file mode 100644 index 8715cc7bb81604927e1207d9a00ac0c40007d4be..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1924 24.939035654067993 3.864405632019043 294.8050537109375 0.9143987894058228 437.54986572265625 0.4282108247280121 0.57189167 10.029326438903809 True -1 3848 21.19763684272766 0.4362916946411133 319.5407409667969 0.9175364971160889 372.85614013671875 0.5392476916313171 0.64707214 4.07540225982666 True -2 5772 21.193504571914673 1.2431704998016357 268.5763244628906 0.6411570906639099 354.62030029296875 0.5824126601219177 0.6488936 1.3232574462890625 True -3 7696 21.212387561798096 0.4015955924987793 261.9704895019531 0.5922107696533203 349.7105712890625 0.5896292328834534 0.6600185 0.9376303553581238 True -4 9620 21.21535849571228 9.353597164154053 235.26223754882812 0.5916719436645508 347.6913757324219 0.5939490795135498 0.6775478 0.8102839589118958 True -5 11544 21.30193781852722 0.5784811973571777 302.6937561035156 0.4328797161579132 346.4698181152344 0.5966105461120605 0.68028843 0.7673792243003845 True -6 13468 21.199034214019775 0.9219176769256592 279.3174133300781 0.5655774474143982 345.8373107910156 0.5988222360610962 0.68390214 0.8027321696281433 True -7 15392 21.194859981536865 0.9957222938537598 240.34300231933594 0.5398306846618652 345.0607604980469 0.6003459095954895 0.6933581 0.7360616326332092 True -8 17316 21.481147527694702 0.41547727584838867 255.43365478515625 0.649604320526123 343.99090576171875 0.6025993227958679 0.7005037 0.6763607263565063 True -9 19240 21.37412166595459 0.4264791011810303 251.7825469970703 0.5116065740585327 343.09295654296875 0.6044453382492065 0.7079429 0.6174899935722351 True -10 21164 21.30136275291443 0.4125187397003174 248.62203979492188 0.4776878356933594 342.1905212402344 0.6063265204429626 0.7159497 0.5768902897834778 True -11 23088 21.26666283607483 0.41634631156921387 251.9410400390625 0.5816450715065002 341.2489929199219 0.6082566380500793 0.7242978 0.544727087020874 True -12 25012 21.258392333984375 0.409470796585083 287.6136169433594 0.35559824109077454 340.48968505859375 0.6098641753196716 0.73070717 0.5320484638214111 True -13 26936 21.274056911468506 0.4126601219177246 257.9286804199219 0.5468592643737793 339.97930908203125 0.61079341173172 0.73538184 0.5124236345291138 True -14 28860 21.28053593635559 0.4079856872558594 220.29818725585938 0.3452446460723877 339.42840576171875 0.6117519736289978 0.740898 0.4997349679470062 True -15 30784 21.22740077972412 0.41667890548706055 249.89443969726562 0.3349781036376953 339.2508850097656 0.6123911142349243 0.7456134 0.49295538663864136 True -16 32708 21.22409224510193 0.42132043838500977 263.4678955078125 0.45461276173591614 339.0848083496094 0.6124508380889893 0.74639773 0.4918982684612274 True -17 34632 21.22710943222046 1.5927391052246094 277.83673095703125 0.2095085084438324 339.28875732421875 0.611942708492279 0.7484596 0.49243199825286865 True -18 36556 21.28410291671753 0.41492247581481934 245.48800659179688 0.3217337131500244 339.2041320800781 0.611445426940918 0.7421166 0.506091833114624 False -19 38480 21.2133846282959 0.42659854888916016 263.6082763671875 0.17100900411605835 339.353515625 0.6109998822212219 0.7408352 0.5144250392913818 False diff --git a/ENCSR594TMY/cherimoya.fold_3.performance.tsv b/ENCSR594TMY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7bb49dd8a22c0ea93b3487276be2284cdf01684c..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -339.28875732421875 0.31264761090278625 0.6119428277015686 0.2191065102815628 0.7484595775604248 0.7049258351325989 0.49243199825286865 \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_4.evaluate.json b/ENCSR594TMY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8687e5216222f0ad8a5089d5be7cd0612b4ad841..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863SSN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_4.fit.json b/ENCSR594TMY/cherimoya.fold_4.fit.json deleted file mode 100644 index 77af90ea8eeb4465e3e18a44c7520404d409cc42..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF863SSN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR594TMY/cherimoya.fold_4.log b/ENCSR594TMY/cherimoya.fold_4.log deleted file mode 100644 index 64c28a3453806afbaeff2e63cfbb9b55d40565b1..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1978 25.767000198364258 3.358410358428955 256.20672607421875 0.6169954538345337 432.4788513183594 0.42645037174224854 0.60396796 10.860696792602539 True -1 3956 21.985464811325073 0.3937957286834717 283.2557373046875 0.6179729104042053 367.9447021484375 0.5438002347946167 0.66061157 3.7764196395874023 True -2 5934 21.92896056175232 0.37824177742004395 270.81658935546875 0.9509629607200623 350.8760681152344 0.5808467268943787 0.69064736 0.9716722965240479 True -3 7912 21.971158266067505 0.38277387619018555 247.58740234375 0.6858481168746948 345.7681884765625 0.5903504490852356 0.7058279 0.6210624575614929 True -4 9890 21.96262812614441 0.3784348964691162 287.1578063964844 0.6516913175582886 343.8955078125 0.5944922566413879 0.71467155 0.5832695960998535 True -5 11868 21.93320107460022 1.9781320095062256 320.04058837890625 0.5750408172607422 342.84765625 0.5970585346221924 0.72209114 0.5867591500282288 True -6 13846 21.946513652801514 1.173884630203247 286.21209716796875 0.49638810753822327 341.4878234863281 0.6000652313232422 0.72838855 0.5574663281440735 True -7 15824 21.927629947662354 0.3728041648864746 261.84991455078125 0.40722936391830444 340.544921875 0.6021789908409119 0.7321811 0.5544416904449463 True -8 17802 21.92873454093933 0.3731389045715332 253.6946258544922 0.5102295875549316 339.59014892578125 0.6040590405464172 0.73345816 0.5352857112884521 True -9 19780 21.92885160446167 0.378063440322876 247.76577758789062 0.6206720471382141 338.74884033203125 0.6061177849769592 0.73660135 0.5207036137580872 True -10 21758 21.92708396911621 0.3777298927307129 253.8968505859375 0.47076553106307983 337.7140808105469 0.608525812625885 0.73904085 0.5182150602340698 True -11 23736 21.962403535842896 0.38173341751098633 257.32769775390625 0.461453914642334 337.0219421386719 0.6101720929145813 0.7432508 0.49584150314331055 True -12 25714 21.976858854293823 0.37837696075439453 275.9704284667969 0.7820583581924438 336.24566650390625 0.6118940114974976 0.74673176 0.4894355535507202 True -13 27692 21.965500116348267 0.3773155212402344 242.32620239257812 0.4904370903968811 335.5880126953125 0.6133049726486206 0.75040746 0.4700225591659546 True -14 29670 21.946897983551025 0.3761758804321289 259.3809814453125 0.33443737030029297 335.299072265625 0.614169180393219 0.7541089 0.4672360122203827 True -15 31648 21.95195984840393 0.3776590824127197 274.90069580078125 0.23846906423568726 334.8266906738281 0.6149815320968628 0.7568322 0.4670664370059967 True -16 33626 21.93417978286743 6.187159299850464 246.3218536376953 0.5131127238273621 334.829833984375 0.6150467395782471 0.7568912 0.4720454812049866 True -17 35604 22.1011164188385 9.399362802505493 242.6380157470703 0.1920170783996582 335.02099609375 0.6145000457763672 0.75652105 0.4773460626602173 False -18 37582 22.028191328048706 0.3788323402404785 259.6839599609375 0.2551724910736084 335.2134704589844 0.6139200329780579 0.7518541 0.49020761251449585 False -19 39560 21.960668563842773 0.37800145149230957 272.1231689453125 0.20756906270980835 335.4256591796875 0.6136239767074585 0.7504433 0.49454858899116516 False diff --git a/ENCSR594TMY/cherimoya.fold_4.performance.tsv b/ENCSR594TMY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 24e90cdc2c6682b252385962deec3129dbadecd5..0000000000000000000000000000000000000000 --- a/ENCSR594TMY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -334.829833984375 0.3138435184955597 0.6150467395782471 0.21729959547519684 0.7568911910057068 0.6926209926605225 0.4720454812049866 \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_0.evaluate.json b/ENCSR595CSH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 473e13dad61bd6a2bc8111347c1f01dca1698237..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969AJS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_0.fit.json b/ENCSR595CSH/cherimoya.fold_0.fit.json deleted file mode 100644 index 1090e8ca0f6f510a681124a037766897a3767bb7..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF969AJS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_0.log b/ENCSR595CSH/cherimoya.fold_0.log deleted file mode 100644 index bc09a65d09c030b560f0f15525073a234f969482..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.51455473899841 4.036211729049683 1561.623779296875 1.0795472860336304 2127.049560546875 0.33526480197906494 0.6044965 11.416702270507812 True -1 5476 30.15536665916443 0.6285712718963623 1273.836181640625 1.1704812049865723 1723.68408203125 0.46123361587524414 0.6954829 3.789773464202881 True -2 8214 30.20540952682495 0.5857410430908203 1346.022705078125 1.2241312265396118 1662.5743408203125 0.48449376225471497 0.71964854 1.5795432329177856 True -3 10952 30.133047103881836 0.5817503929138184 1392.954345703125 0.849010705947876 1627.775390625 0.49531257152557373 0.72612077 1.1830849647521973 True -4 13690 30.105786085128784 0.5841159820556641 1086.680419921875 0.6394445896148682 1607.951171875 0.5054189562797546 0.7321632 0.8817464709281921 True -5 16428 30.199461936950684 0.5825290679931641 1228.722412109375 0.9597976803779602 1605.3226318359375 0.5047261714935303 0.7358297 0.6887999176979065 True -6 19166 30.146746158599854 0.5826117992401123 1549.571533203125 0.7770623564720154 1584.3980712890625 0.5126383900642395 0.7395546 0.5964738130569458 True -7 21904 30.046825647354126 0.5833654403686523 1244.13037109375 0.7492920756340027 1570.5391845703125 0.519463062286377 0.74071854 0.5378671884536743 True -8 24642 30.239363431930542 0.5855386257171631 1195.716552734375 0.99786376953125 1555.6536865234375 0.5241935849189758 0.7469348 0.4962242841720581 True -9 27380 30.127734422683716 0.9527437686920166 1345.3232421875 0.6327452659606934 1556.4288330078125 0.5225455164909363 0.75224304 0.47902682423591614 True -10 30118 30.118815898895264 0.5885460376739502 1133.956787109375 0.5403261184692383 1537.0767822265625 0.5309845209121704 0.7609025 0.460927277803421 True -11 32856 30.13590407371521 0.5871992111206055 1049.03173828125 0.4409722089767456 1530.5811767578125 0.533378005027771 0.7699042 0.44762322306632996 True -12 35594 29.549500226974487 0.5815298557281494 1271.4287109375 0.6208266019821167 1520.6636962890625 0.5353685617446899 0.78019947 0.43658071756362915 True -13 38332 29.496108055114746 0.5715022087097168 1410.0537109375 0.40560513734817505 1510.121337890625 0.54137122631073 0.7894179 0.41696274280548096 True -14 41070 29.490813493728638 0.5799896717071533 1290.4073486328125 0.4159112274646759 1508.2320556640625 0.5393272638320923 0.8021931 0.3981854319572449 True -15 43808 29.559382438659668 0.5806446075439453 1066.724853515625 0.41554802656173706 1503.1656494140625 0.5421684384346008 0.8096704 0.3904171288013458 True -16 46546 29.54133677482605 0.5703790187835693 1088.450439453125 0.36187684535980225 1498.1947021484375 0.5438199043273926 0.8158633 0.38262009620666504 True -17 49284 29.53460454940796 0.5785543918609619 981.7831420898438 0.3774542808532715 1496.573974609375 0.5432318449020386 0.81934136 0.37558624148368835 True -18 52022 29.537822246551514 0.5798182487487793 1015.9955444335938 0.3120211064815521 1494.507080078125 0.5456216931343079 0.82056016 0.3795931339263916 True -19 54760 29.495097875595093 0.5712170600891113 1218.729736328125 0.28360605239868164 1495.558837890625 0.5452630519866943 0.82078224 0.3794708847999573 True diff --git a/ENCSR595CSH/cherimoya.fold_0.performance.tsv b/ENCSR595CSH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2f5f96e4bae04da5cf18fe4aecab948039ffe4a1..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1495.558837890625 0.23539167642593384 0.5452630519866943 0.32425203919410706 0.8207822442054749 0.7782287001609802 0.3794708847999573 \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_1.evaluate.json b/ENCSR595CSH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ee56cfa2fde36ef8c25b541782f95c42a21764e1..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969AJS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_1.fit.json b/ENCSR595CSH/cherimoya.fold_1.fit.json deleted file mode 100644 index f4b2c8d547fcd49e295730d2fbef8130453484f7..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF969AJS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_1.log b/ENCSR595CSH/cherimoya.fold_1.log deleted file mode 100644 index 45d10cf350e5c713164b7ee9b6beb30452d28aca..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2707 34.5112087726593 3.8130366802215576 1245.749267578125 0.9250215888023376 2546.4990234375 0.3323562741279602 0.6289031 10.235918045043945 True -1 5414 29.784228086471558 4.178147554397583 1635.68359375 0.8780418038368225 2031.0302734375 0.468305379152298 0.7075674 3.7199692726135254 True -2 8121 29.756710052490234 0.7221338748931885 1478.8802490234375 1.2370939254760742 1929.169921875 0.4926305115222931 0.73542565 1.3295875787734985 True -3 10828 29.763962745666504 0.6572201251983643 1375.626953125 0.9770285487174988 1888.555908203125 0.5044940114021301 0.7412526 0.808940052986145 True -4 13535 29.803353548049927 0.7658591270446777 1032.683349609375 0.7262754440307617 1851.6444091796875 0.515243649482727 0.74717546 0.7015551328659058 True -5 16242 29.723772764205933 1.6501567363739014 1331.3388671875 0.7270160913467407 1833.3310546875 0.5197568535804749 0.7534897 0.6275430917739868 True -6 18949 30.0141818523407 20.904496908187866 1145.4593505859375 0.6005774140357971 1822.8341064453125 0.5238839387893677 0.749933 0.5639009475708008 False -7 21656 29.822272062301636 12.190279245376587 983.0616455078125 0.6791415810585022 1803.5855712890625 0.5286856293678284 0.760606 0.5338583588600159 True -8 24363 29.826846599578857 1.6117467880249023 1121.869873046875 0.7264914512634277 1789.161376953125 0.5334068536758423 0.7617603 0.5359656810760498 True -9 27070 29.750611782073975 1.4545094966888428 1092.289794921875 0.5121172666549683 1775.7835693359375 0.5376299023628235 0.77133197 0.5257285833358765 True -10 29777 29.79204750061035 1.1736645698547363 1238.61474609375 0.6765251159667969 1760.2652587890625 0.5422103404998779 0.77354795 0.5229854583740234 True -11 32484 29.8250470161438 1.7168631553649902 992.8555908203125 0.6328801512718201 1748.752197265625 0.5480040907859802 0.77719694 0.51151442527771 True -12 35191 29.825098752975464 1.3885619640350342 1231.4566650390625 0.39879506826400757 1740.1944580078125 0.549310564994812 0.7880639 0.48070278763771057 True -13 37898 29.47128677368164 0.6664690971374512 1030.8896484375 0.4239427447319031 1719.009765625 0.5571447014808655 0.79574835 0.47159621119499207 True -14 40605 29.288222312927246 0.678708553314209 1156.45751953125 0.5076528787612915 1714.9739990234375 0.557744562625885 0.8060392 0.4466031491756439 True -15 43312 29.208276987075806 0.6645145416259766 1043.9371337890625 0.5515825152397156 1710.5614013671875 0.5575944781303406 0.81779754 0.4305628836154938 True -16 46019 29.266934871673584 0.6576921939849854 1303.635986328125 0.435760498046875 1703.4346923828125 0.5625486373901367 0.823248 0.4258634150028229 True -17 48726 29.28176236152649 0.6757373809814453 1141.0283203125 0.35221120715141296 1700.1534423828125 0.561136782169342 0.8280831 0.4169088304042816 True -18 51433 29.344122886657715 0.6719787120819092 1292.951904296875 0.4186270534992218 1705.31982421875 0.5585748553276062 0.8319643 0.4165084660053253 True -19 54140 29.260352611541748 23.921448230743408 1109.47607421875 0.3670594096183777 1699.74365234375 0.5628368854522705 0.8311098 0.4161785840988159 False diff --git a/ENCSR595CSH/cherimoya.fold_1.performance.tsv b/ENCSR595CSH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 96d94242aa86f7f35364edeba2acf9c625ca594c..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1705.31982421875 0.2232608199119568 0.5585748553276062 0.34793177247047424 0.8319643139839172 0.8055040836334229 0.4165084660053253 \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_2.evaluate.json b/ENCSR595CSH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index acf0fa18c01dc5f65330d1e5cdaa1975d009d144..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969AJS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_2.fit.json b/ENCSR595CSH/cherimoya.fold_2.fit.json deleted file mode 100644 index 9461027b2cc1b63d32484ad1224aa0d6db2a54a6..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF969AJS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_2.log b/ENCSR595CSH/cherimoya.fold_2.log deleted file mode 100644 index 858e5f0d474f05f465035f00f4f48dc00613e5ab..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2869 36.21564483642578 3.7735800743103027 1501.433837890625 0.9153380393981934 2208.24658203125 0.35126233100891113 0.63220304 8.242045402526855 True -1 5738 31.527602672576904 0.6613173484802246 1454.896728515625 0.8626564145088196 1792.94921875 0.4721786379814148 0.68706626 2.602372646331787 True -2 8607 31.501559734344482 0.548637866973877 1488.5986328125 0.9203781485557556 1743.5814208984375 0.4817778468132019 0.7163149 1.1692612171173096 True -3 11476 31.60052490234375 0.5742001533508301 1257.2481689453125 0.7416087985038757 1691.3421630859375 0.49832406640052795 0.73638546 0.8353762626647949 True -4 14345 31.519636392593384 0.5572617053985596 1254.608642578125 0.6796913146972656 1669.55224609375 0.5045670866966248 0.7404344 0.7918269038200378 True -5 17214 31.4893479347229 0.5726296901702881 1462.36328125 0.7540571093559265 1657.1590576171875 0.5101433992385864 0.74464124 0.6446312665939331 True -6 20083 31.502401113510132 0.5739078521728516 1009.29443359375 0.596998929977417 1645.40576171875 0.5151119828224182 0.746936 0.6203979253768921 True -7 22952 31.53911542892456 0.5898220539093018 1436.285888671875 0.7645356059074402 1629.687255859375 0.5199663043022156 0.74969745 0.5582188367843628 True -8 25821 31.531951904296875 0.5689244270324707 999.9798583984375 0.6480128765106201 1615.980224609375 0.5232625007629395 0.7551126 0.5362591743469238 True -9 28690 31.647740364074707 0.5739033222198486 1336.0439453125 0.4359356760978699 1609.994384765625 0.5260857939720154 0.754942 0.5461230874061584 False -10 31559 31.549599647521973 0.5611264705657959 1067.2572021484375 0.5776145458221436 1590.536865234375 0.5335822701454163 0.76322544 0.5203218460083008 True -11 34428 31.52777624130249 0.5476202964782715 1217.0108642578125 0.49953967332839966 1579.798583984375 0.5382497310638428 0.77306783 0.526691198348999 True -12 37297 31.537993669509888 0.5693521499633789 1152.9857177734375 0.33919763565063477 1570.0982666015625 0.5414047837257385 0.77856517 0.4864647388458252 True -13 40166 31.560770750045776 0.5687239170074463 1146.5057373046875 0.4923091530799866 1556.4725341796875 0.5468131303787231 0.7890332 0.4555465877056122 True -14 43035 30.952812433242798 0.5679380893707275 1228.5035400390625 0.4316748082637787 1555.1807861328125 0.5457127690315247 0.79672694 0.4423375129699707 True -15 45904 30.92711639404297 21.631178379058838 1188.439697265625 0.38943153619766235 1543.2957763671875 0.5512375831604004 0.8027232 0.4270632863044739 True -16 48773 31.015738248825073 18.7602219581604 1050.17138671875 0.38662245869636536 1536.51513671875 0.5533044934272766 0.809308 0.42644527554512024 True -17 51642 30.934980869293213 1.2399187088012695 1086.868408203125 0.3503302335739136 1543.679443359375 0.5502005815505981 0.81352407 0.42360249161720276 True -18 54511 30.959354162216187 0.9374508857727051 1232.0396728515625 0.3347107768058777 1541.8740234375 0.5518335700035095 0.81641066 0.42391645908355713 True -19 57380 31.00543236732483 0.552250862121582 1028.6240234375 0.29539579153060913 1543.9686279296875 0.551048219203949 0.81501126 0.42282265424728394 False diff --git a/ENCSR595CSH/cherimoya.fold_2.performance.tsv b/ENCSR595CSH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7907654ce499f3188461983b829c2138002cf07d..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1541.8740234375 0.23140931129455566 0.5518336296081543 0.33106908202171326 0.8164106607437134 0.7757091522216797 0.42391645908355713 \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_3.evaluate.json b/ENCSR595CSH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0b0d9b9bc1fa564e14b361ae0af42e66d5257a8a..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969AJS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_3.fit.json b/ENCSR595CSH/cherimoya.fold_3.fit.json deleted file mode 100644 index cdb482d21dfe4f2bd063a53b6341a869714d7c9b..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF969AJS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_3.log b/ENCSR595CSH/cherimoya.fold_3.log deleted file mode 100644 index fb5621c80f433553f7815ae94cd279448a28088d..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 35.93986487388611 3.450078248977661 1313.87060546875 0.6237481832504272 2237.6630859375 0.3460893929004669 0.6404039 11.55759334564209 True -1 5510 30.303651571273804 0.6487166881561279 1339.970947265625 0.80506432056427 1839.2501220703125 0.46547460556030273 0.7299748 2.9235877990722656 True -2 8265 30.30989384651184 1.2207787036895752 1602.9564208984375 0.681395411491394 1777.7469482421875 0.4882632791996002 0.73987776 1.2059131860733032 True -3 11020 30.327136278152466 0.5274226665496826 1495.240966796875 0.8384255766868591 1742.8582763671875 0.4971117079257965 0.7481351 0.9058923125267029 True -4 13775 30.323567867279053 0.5223498344421387 1233.732666015625 0.9198764562606812 1721.970703125 0.5018875598907471 0.75000364 0.690847635269165 True -5 16530 30.31889033317566 0.5276453495025635 1322.505126953125 0.8689976930618286 1709.322509765625 0.5057473182678223 0.7527221 0.6346685886383057 True -6 19285 30.311310052871704 0.5260138511657715 1183.9346923828125 0.7491744756698608 1689.867431640625 0.5131399035453796 0.74964184 0.6038565039634705 False -7 22040 30.315326690673828 0.5286781787872314 1418.3240966796875 0.7435183525085449 1673.4293212890625 0.5188115239143372 0.7518298 0.5725006461143494 False -8 24795 30.29818558692932 0.5185484886169434 1186.4459228515625 0.6292788982391357 1669.5850830078125 0.5214182734489441 0.7546922 0.5668711066246033 True -9 27550 30.264405488967896 1.9737460613250732 1072.178466796875 0.5300264358520508 1652.875244140625 0.5263442397117615 0.7578557 0.5317004919052124 True -10 30305 30.32694911956787 0.5359854698181152 1335.2933349609375 0.5836071968078613 1643.17724609375 0.5292286276817322 0.7642056 0.5448213815689087 True -11 33060 30.291353702545166 1.399273157119751 1220.5732421875 0.7118615508079529 1630.0045166015625 0.534584105014801 0.773063 0.5225721597671509 True -12 35815 30.323277235031128 0.5289881229400635 1121.115478515625 0.5985256433486938 1617.2049560546875 0.5385829210281372 0.7838661 0.4940660893917084 True -13 38570 30.31314969062805 0.5317163467407227 1278.4229736328125 0.7589918375015259 1610.361572265625 0.539089560508728 0.7941682 0.46286478638648987 True -14 41325 29.925535202026367 0.5320591926574707 998.6876220703125 0.48081347346305847 1598.9659423828125 0.542827844619751 0.80388516 0.4468596577644348 True -15 44080 29.80078101158142 0.5253543853759766 1354.738037109375 0.6973958015441895 1584.5423583984375 0.548754870891571 0.81237596 0.42369344830513 True -16 46835 29.75185465812683 0.5269227027893066 1040.763671875 0.4926926791667938 1590.67431640625 0.5439391732215881 0.8211688 0.40849944949150085 True -17 49590 29.726778030395508 0.523644208908081 1459.031494140625 0.34095826745033264 1586.5120849609375 0.5472545027732849 0.82394683 0.39885443449020386 True -18 52345 29.72257709503174 1.5289485454559326 1034.784423828125 0.3322635889053345 1582.909912109375 0.5492033958435059 0.82512254 0.39750292897224426 True -19 55100 29.780850887298584 0.5179216861724854 994.5136108398438 0.3559618592262268 1583.66845703125 0.5482999086380005 0.825716 0.4016586244106293 True diff --git a/ENCSR595CSH/cherimoya.fold_3.performance.tsv b/ENCSR595CSH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 78761721bbf0fc5c74e90a19f499266d7c0b7929..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1583.66845703125 0.23256903886795044 0.5482998490333557 0.33028408885002136 0.8257160186767578 0.785770058631897 0.4016586244106293 \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_4.evaluate.json b/ENCSR595CSH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 732454a6044230249dbce278c955ed6c4add48a2..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969AJS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_4.fit.json b/ENCSR595CSH/cherimoya.fold_4.fit.json deleted file mode 100644 index 0bcf0e5b521d88b39cb1e0f8d5f497376f3bdb49..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF969AJS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595CSH/cherimoya.fold_4.log b/ENCSR595CSH/cherimoya.fold_4.log deleted file mode 100644 index 6632845b1b67b15f74968968193447401bab1bba..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2847 35.830517053604126 3.5950300693511963 1286.442626953125 1.0941091775894165 2004.2176513671875 0.34390130639076233 0.63389397 9.416157722473145 True -1 5694 31.320430040359497 0.6323122978210449 1264.86962890625 1.0224487781524658 1664.4952392578125 0.4591524600982666 0.70213133 2.1827118396759033 True -2 8541 31.278484344482422 0.5795564651489258 1127.095458984375 0.8801007270812988 1631.224853515625 0.46900445222854614 0.7177136 0.892421543598175 True -3 11388 31.306142568588257 0.5820541381835938 1115.528076171875 0.6861890554428101 1590.1103515625 0.48436617851257324 0.7303464 0.6937575936317444 True -4 14235 31.325390100479126 0.5931427478790283 1911.17529296875 0.7571935653686523 1565.7369384765625 0.49156951904296875 0.7330325 0.5216732025146484 True -5 17082 31.313926219940186 0.601144552230835 1287.3173828125 0.7043654918670654 1551.5286865234375 0.49755939841270447 0.7378489 0.47922825813293457 True -6 19929 31.2795352935791 0.5851082801818848 1339.978759765625 0.6839613914489746 1527.1812744140625 0.5104069709777832 0.7445862 0.45446935296058655 True -7 22776 31.27781105041504 0.5833854675292969 968.7918701171875 0.7395386695861816 1518.6292724609375 0.5105492472648621 0.7493128 0.4561771750450134 True -8 25623 31.259379863739014 0.5959599018096924 1404.5091552734375 0.5878973007202148 1502.936279296875 0.5178074836730957 0.753392 0.45066016912460327 True -9 28470 31.321682929992676 0.5891087055206299 1168.4971923828125 0.6430011987686157 1498.536376953125 0.5186011791229248 0.7592281 0.4356711208820343 True -10 31317 31.30366802215576 0.5986096858978271 1214.174072265625 0.6966084837913513 1488.212158203125 0.5223087668418884 0.7696482 0.42158403992652893 True -11 34164 32.52751183509827 0.5990235805511475 1242.3291015625 0.5768719911575317 1479.9554443359375 0.5271324515342712 0.7804666 0.40396326780319214 True -12 37011 31.383455514907837 0.5982682704925537 1172.985595703125 0.6018665432929993 1476.9454345703125 0.5276573896408081 0.7873151 0.3932855427265167 True -13 39858 31.411495208740234 0.5943706035614014 1029.6865234375 0.9642784595489502 1465.5633544921875 0.5339066386222839 0.7936984 0.38088279962539673 True -14 42705 31.30659580230713 0.5936572551727295 1146.1676025390625 0.4647143483161926 1461.631103515625 0.5352377891540527 0.80220056 0.3706362247467041 True -15 45552 30.743422746658325 0.6019876003265381 1276.4447021484375 0.5406736135482788 1453.77587890625 0.5386015176773071 0.8113441 0.3576098084449768 True -16 48399 30.79787516593933 0.5954990386962891 1176.4359130859375 0.2538108825683594 1450.01806640625 0.5404098629951477 0.81569517 0.35113540291786194 True -17 51246 30.7054181098938 0.5887420177459717 938.1202392578125 0.37787723541259766 1448.71142578125 0.5403015613555908 0.82033426 0.3482847213745117 True -18 54093 30.746537685394287 0.58355712890625 1079.640869140625 0.32219234108924866 1455.9705810546875 0.5353438258171082 0.82058406 0.3482109010219574 True -19 56940 30.761768102645874 0.5818583965301514 1266.064208984375 0.3282501995563507 1451.675537109375 0.539836049079895 0.8228698 0.34941455721855164 True diff --git a/ENCSR595CSH/cherimoya.fold_4.performance.tsv b/ENCSR595CSH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 636b954b8bfc07d2ff69704a96aae9135165045a..0000000000000000000000000000000000000000 --- a/ENCSR595CSH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1451.675537109375 0.23810286819934845 0.539836049079895 0.3191758990287781 0.8228697776794434 0.7762762308120728 0.34941455721855164 \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_0.evaluate.json b/ENCSR595DQM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 31eff0b5f1b2c438250ce6f5c2434fd0c986e86e..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF833GSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_0.fit.json b/ENCSR595DQM/cherimoya.fold_0.fit.json deleted file mode 100644 index 56c937eeb91f1fa2e035a805a1f16f3f15a48e8a..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF833GSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_0.log b/ENCSR595DQM/cherimoya.fold_0.log deleted file mode 100644 index 0537e91b5e729f953ff10f77ad39d6d9d0433cde..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 35.51871943473816 3.83198881149292 983.950927734375 0.3589882254600525 1041.317138671875 0.2873251140117645 0.8193845 4.868710517883301 True -1 5560 30.944637060165405 1.3880906105041504 791.6121826171875 0.2668033540248871 956.6170654296875 0.33662816882133484 0.8529912 1.0957447290420532 True -2 8340 30.902164936065674 0.602304220199585 892.9072875976562 0.19588643312454224 932.1635131835938 0.3491857051849365 0.8757446 0.4163289964199066 True -3 11120 30.928003072738647 0.6003134250640869 897.57177734375 0.21328745782375336 925.0648193359375 0.35242149233818054 0.88722533 0.30560511350631714 True -4 13900 30.974873542785645 0.5816466808319092 986.9337158203125 0.4141082167625427 920.1297607421875 0.355720579624176 0.8844486 0.3080179989337921 False -5 16680 30.88957405090332 0.5722103118896484 779.7674560546875 0.37059009075164795 918.89990234375 0.3558759391307831 0.8846745 0.3133169114589691 False -6 19460 30.851998329162598 0.6854889392852783 883.5628662109375 0.18216457962989807 915.1319580078125 0.35954955220222473 0.8880375 0.33607950806617737 True -7 22240 30.84803080558777 0.6304492950439453 774.305419921875 0.26453396677970886 911.403076171875 0.36188891530036926 0.8905255 0.30309805274009705 True -8 25020 30.841267824172974 1.2047019004821777 972.27783203125 0.17387832701206207 907.32421875 0.3651033341884613 0.8963089 0.2670658826828003 True -9 27800 30.893735885620117 0.5749683380126953 1023.5328369140625 0.186471626162529 906.2291259765625 0.3648200035095215 0.89883524 0.2546829283237457 True -10 30580 30.868592023849487 1.452214241027832 781.2836303710938 0.17901352047920227 904.993408203125 0.3658246397972107 0.90004665 0.26400938630104065 True -11 33360 30.92259979248047 0.5816214084625244 737.3663330078125 0.11634138971567154 898.4981689453125 0.37040671706199646 0.9066881 0.2220752239227295 True -12 36140 30.94284677505493 0.5758254528045654 705.07958984375 0.2472117841243744 895.7560424804688 0.37141963839530945 0.9111732 0.19589583575725555 True -13 38920 30.987713098526 0.587620735168457 752.7486572265625 0.10271326452493668 892.8896484375 0.37297531962394714 0.9162083 0.17640282213687897 True -14 41700 30.577324390411377 0.5921297073364258 707.5555419921875 0.13748793303966522 892.3604736328125 0.3728291690349579 0.9203862 0.15861617028713226 True -15 44480 30.364357709884644 0.5644927024841309 817.2396240234375 0.12533722817897797 890.6099243164062 0.3738853931427002 0.9223112 0.1443893015384674 True -16 47260 30.42948079109192 0.5802531242370605 771.21826171875 0.1130404844880104 889.394775390625 0.3748297691345215 0.926799 0.13479727506637573 True -17 50040 30.49337339401245 0.5594527721405029 900.7379150390625 0.09195626527070999 891.2559204101562 0.37284722924232483 0.9268883 0.13107086718082428 True -18 52820 30.995259046554565 0.5603547096252441 679.9027709960938 0.13196000456809998 888.7863159179688 0.3753215968608856 0.9265941 0.12987758219242096 False -19 55600 30.468498945236206 0.6011343002319336 735.4469604492188 0.09915399551391602 889.2386474609375 0.37486734986305237 0.9258994 0.12950371205806732 False diff --git a/ENCSR595DQM/cherimoya.fold_0.performance.tsv b/ENCSR595DQM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9ecceec9f79d2259a9f895642561bbc6fadf2f78..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -891.2559204101562 0.3921019732952118 0.37284719944000244 0.16265219449996948 0.9268882870674133 0.914267897605896 0.13107086718082428 \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_1.evaluate.json b/ENCSR595DQM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1ebd56c73ba7137e7d18c66b0f6289e98a5c4846..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF833GSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_1.fit.json b/ENCSR595DQM/cherimoya.fold_1.fit.json deleted file mode 100644 index d2b657b5f7a55518c2f9b521eb2a247e8f5b1dce..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF833GSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_1.log b/ENCSR595DQM/cherimoya.fold_1.log deleted file mode 100644 index 8106f48af96504c821bc4f935b0f7c6151adb557..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 35.05825424194336 7.130007266998291 761.0386962890625 0.2131647914648056 1216.4122314453125 0.29093146324157715 0.8101753 6.071552276611328 True -1 5418 30.149837970733643 25.66052770614624 914.783935546875 0.34307268261909485 1108.650634765625 0.350615918636322 0.8516788 1.2749232053756714 True -2 8127 30.322391510009766 21.845670223236084 713.4779052734375 0.22490820288658142 1080.5128173828125 0.3621482253074646 0.87197334 0.48480990529060364 True -3 10836 30.097400426864624 11.301418781280518 849.451416015625 0.3594282269477844 1064.556396484375 0.37049010396003723 0.8829767 0.37042301893234253 True -4 13545 30.42461371421814 0.7298457622528076 948.9803466796875 0.23817136883735657 1061.733154296875 0.37053602933883667 0.88828844 0.3229891061782837 True -5 16254 30.08551025390625 0.7012264728546143 767.9828491210938 0.27773517370224 1054.1065673828125 0.3766152858734131 0.88981813 0.3356296122074127 True -6 18963 30.07146978378296 0.7051265239715576 631.2531127929688 0.16738773882389069 1052.236572265625 0.37681564688682556 0.8923143 0.29180213809013367 True -7 21672 30.063528299331665 0.7002277374267578 908.4203491210938 0.1309516727924347 1046.47412109375 0.3796543478965759 0.8974895 0.2556227743625641 True -8 24381 29.57052445411682 0.7077429294586182 792.6953735351562 0.21141065657138824 1042.966796875 0.3822217881679535 0.9004824 0.24963420629501343 True -9 27090 29.630109548568726 0.7034928798675537 889.6558837890625 0.18567359447479248 1040.8538818359375 0.38344937562942505 0.8997276 0.2684849202632904 False -10 29799 29.61186981201172 0.6966321468353271 706.1065673828125 0.17315925657749176 1035.12109375 0.38720986247062683 0.90886396 0.25675734877586365 True -11 32508 29.494707345962524 0.6890401840209961 804.1630859375 0.12453094869852066 1033.723876953125 0.38748836517333984 0.9112837 0.24025970697402954 True -12 35217 29.497575759887695 1.9180524349212646 763.1190185546875 0.20363204181194305 1028.1851806640625 0.39116084575653076 0.9160761 0.22010813653469086 True -13 37926 29.602558851242065 0.6802546977996826 783.8987426757812 0.27419236302375793 1023.2874145507812 0.39403489232063293 0.919756 0.1975741684436798 True -14 40635 29.603169918060303 0.6833450794219971 790.0902099609375 0.16487671434879303 1022.7772216796875 0.39356982707977295 0.9247727 0.1820630580186844 True -15 43344 29.58127737045288 0.7151587009429932 781.82958984375 0.18734432756900787 1019.4667358398438 0.3959631025791168 0.92905384 0.16741317510604858 True -16 46053 29.69375514984131 0.7048187255859375 723.5867919921875 0.08431027829647064 1021.6246337890625 0.3932485580444336 0.9297142 0.15538783371448517 True -17 48762 29.51807188987732 0.7307536602020264 701.3728637695312 0.09258981049060822 1017.8627319335938 0.39683279395103455 0.9306421 0.1497666984796524 True -18 51471 29.54971933364868 0.7107326984405518 790.384765625 0.10199455171823502 1022.505859375 0.3928045630455017 0.9319967 0.14669056236743927 True -19 54180 29.623716354370117 27.367035150527954 853.7839965820312 0.15436512231826782 1021.6649780273438 0.39423733949661255 0.93193394 0.14703994989395142 False diff --git a/ENCSR595DQM/cherimoya.fold_1.performance.tsv b/ENCSR595DQM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3a44fa614ff5e6f096c41c869d4c74350d946c6f..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1022.505859375 0.3733786642551422 0.3928045332431793 0.1820380687713623 0.9319967031478882 0.927617609500885 0.14669056236743927 \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_2.evaluate.json b/ENCSR595DQM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4a1d2dc3b9e17e2c147e44bdedeaebfa1f505d94..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF833GSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_2.fit.json b/ENCSR595DQM/cherimoya.fold_2.fit.json deleted file mode 100644 index 8bc55fbf9dcf92d46b3709fe9e89324d5cd1c097..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF833GSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_2.log b/ENCSR595DQM/cherimoya.fold_2.log deleted file mode 100644 index 60e5e62962609ff99dfe1a776b7ab4c30db17cfe..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2899 36.562286615371704 4.063738822937012 970.8381958007812 0.35168150067329407 1118.93701171875 0.2869843542575836 0.80313987 5.1073150634765625 True -1 5798 32.18267869949341 0.6767332553863525 911.95703125 0.4175655245780945 1016.3688354492188 0.34309306740760803 0.8550183 1.0506621599197388 True -2 8697 32.24586272239685 0.593252420425415 839.0661010742188 0.30673345923423767 996.7332763671875 0.35112443566322327 0.8689318 0.4122484028339386 True -3 11596 32.19840741157532 0.5395455360412598 714.5795288085938 0.22473254799842834 991.1986694335938 0.35451769828796387 0.8750538 0.3303817808628082 True -4 14495 32.21953535079956 4.280331373214722 872.7708129882812 0.34598734974861145 982.4863891601562 0.3596307635307312 0.8829326 0.3277370035648346 True -5 17394 32.221410512924194 0.5817711353302002 643.1465454101562 0.15996985137462616 983.3085327148438 0.35927289724349976 0.8834551 0.27641767263412476 True -6 20293 32.16773962974548 0.5960917472839355 794.7685546875 0.184348464012146 979.3548583984375 0.36109820008277893 0.8854327 0.29337480664253235 True -7 23192 32.20064306259155 0.5882933139801025 789.3847045898438 0.24908456206321716 979.4564208984375 0.3613559901714325 0.8855459 0.3025752007961273 True -8 26091 32.23478412628174 0.5470030307769775 805.4166259765625 0.24054688215255737 976.1744995117188 0.3641785979270935 0.88984704 0.29879650473594666 True -9 28990 32.15791320800781 0.9015634059906006 708.2762451171875 0.14293357729911804 969.7317504882812 0.36819547414779663 0.8930093 0.26269248127937317 True -10 31889 32.33303618431091 0.5552840232849121 843.7789916992188 0.2080264389514923 967.6027221679688 0.36917445063591003 0.89974415 0.24910730123519897 True -11 34788 32.396859645843506 0.6292049884796143 763.2169189453125 0.19832316040992737 965.8502197265625 0.3694520592689514 0.9016894 0.2228025645017624 True -12 37687 32.4052677154541 0.5589287281036377 723.332763671875 0.2183513343334198 961.342041015625 0.3733569085597992 0.9044841 0.2048775553703308 True -13 40586 32.36897826194763 0.5709514617919922 847.33203125 0.160475492477417 958.8565673828125 0.3743973672389984 0.90850204 0.1858462393283844 True -14 43485 32.33408713340759 0.5513575077056885 871.8302001953125 0.12750352919101715 957.6697387695312 0.37510859966278076 0.9130416 0.1700100153684616 True -15 46384 31.833568334579468 0.5406138896942139 787.6728515625 0.1687544584274292 956.975830078125 0.3746744692325592 0.9175221 0.15716926753520966 True -16 49283 31.792608737945557 0.5437812805175781 743.1925659179688 0.1184418797492981 953.950927734375 0.377677857875824 0.9200152 0.1497725248336792 True -17 52182 31.766660690307617 1.4429099559783936 893.4541015625 0.09489867836236954 954.3018188476562 0.376418799161911 0.91873026 0.14762166142463684 False -18 55081 31.760343074798584 1.282153606414795 744.715087890625 0.10218799114227295 955.9066772460938 0.3751073479652405 0.9186939 0.14751304686069489 False -19 57980 31.765563249588013 0.5369405746459961 786.3939208984375 0.14383435249328613 955.2467041015625 0.3758816123008728 0.9193331 0.1476295292377472 False diff --git a/ENCSR595DQM/cherimoya.fold_2.performance.tsv b/ENCSR595DQM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index abb2437968d260fee02c31569593e3fca7f10b01..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -953.950927734375 0.38480034470558167 0.37767788767814636 0.16819165647029877 0.9200152158737183 0.9104084372520447 0.1497725248336792 \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_3.evaluate.json b/ENCSR595DQM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c544706aab295cdb17cc14f2560971242f7767c8..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF833GSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_3.fit.json b/ENCSR595DQM/cherimoya.fold_3.fit.json deleted file mode 100644 index 1d592d2e9cc643f0f1d23768187fd86879afeab2..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF833GSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_3.log b/ENCSR595DQM/cherimoya.fold_3.log deleted file mode 100644 index be28b68644e16b62c4e13cd23b3aa0aeb88861ab..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 35.43816804885864 3.8611037731170654 860.4920043945312 0.3323586881160736 1015.0326538085938 0.2920066714286804 0.79277205 5.462815761566162 True -1 5494 30.535987615585327 0.6123652458190918 849.6773681640625 0.33817553520202637 927.3873291015625 0.34535685181617737 0.8512694 1.1698076725006104 True -2 8241 30.538122177124023 0.5580024719238281 901.0098876953125 0.19986023008823395 911.3593139648438 0.3534494936466217 0.8647993 0.5118337273597717 True -3 10988 30.518146991729736 0.5581650733947754 853.8958740234375 0.3498586416244507 902.44189453125 0.3593168258666992 0.8764744 0.332048237323761 True -4 13735 30.490052223205566 0.5554046630859375 938.7867431640625 0.17228630185127258 901.1735229492188 0.35917505621910095 0.8777497 0.3347945511341095 True -5 16482 30.512733936309814 0.5533339977264404 781.5761108398438 0.27940720319747925 900.6483154296875 0.35878676176071167 0.8806528 0.3413236141204834 True -6 19229 30.49881672859192 0.5515906810760498 856.3485717773438 0.21522799134254456 898.1365966796875 0.36119067668914795 0.8799499 0.3263876438140869 False -7 21976 30.472052812576294 0.5413303375244141 766.9537353515625 0.15443238615989685 894.10791015625 0.36416515707969666 0.8843264 0.31163808703422546 True -8 24723 30.54639744758606 0.5549178123474121 843.285400390625 0.20320236682891846 891.6793212890625 0.36514338850975037 0.8893099 0.28886279463768005 True -9 27470 30.558977842330933 0.5718369483947754 949.6185302734375 0.12695446610450745 886.7335205078125 0.36887645721435547 0.8923968 0.28088733553886414 True -10 30217 30.506818532943726 0.5543680191040039 685.4857177734375 0.19864913821220398 883.30615234375 0.3710598945617676 0.8975513 0.2745181620121002 True -11 32964 30.530295610427856 0.5574183464050293 803.3541259765625 0.11905437707901001 881.4260864257812 0.37148016691207886 0.90255606 0.24487018585205078 True -12 35711 30.59858274459839 0.5565571784973145 748.394287109375 0.11797484755516052 877.9119262695312 0.37402352690696716 0.9074885 0.21955975890159607 True -13 38458 29.887044668197632 0.5488877296447754 834.59912109375 0.15734246373176575 876.407470703125 0.37499934434890747 0.91296643 0.197919100522995 True -14 41205 29.95824122428894 0.5424528121948242 784.7152099609375 0.2131081223487854 875.455322265625 0.3746147155761719 0.9169693 0.17422497272491455 True -15 43952 30.020471811294556 0.90384840965271 806.4632568359375 0.05300671607255936 872.29443359375 0.37799015641212463 0.9205891 0.16218651831150055 True -16 46699 29.979959726333618 0.5447485446929932 756.144287109375 0.15416738390922546 872.48193359375 0.376794695854187 0.9203596 0.1505817174911499 False -17 49446 29.932616233825684 0.5477516651153564 727.9908447265625 0.11591381579637527 872.03173828125 0.3769308030605316 0.92202663 0.1456693559885025 True -18 52193 29.900965929031372 0.5413520336151123 721.4814453125 0.12533988058567047 872.5613403320312 0.3766028881072998 0.92241734 0.14362867176532745 True -19 54940 29.89096188545227 0.5363821983337402 652.9244384765625 0.1020350381731987 874.2207641601562 0.37549692392349243 0.9222557 0.14413690567016602 False diff --git a/ENCSR595DQM/cherimoya.fold_3.performance.tsv b/ENCSR595DQM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b7d483768f383ceb0f92274f6d7537e0c3b6c180..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -872.5613403320312 0.3907887935638428 0.3766028881072998 0.16009743511676788 0.9224173426628113 0.9052218198776245 0.14362867176532745 \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_4.evaluate.json b/ENCSR595DQM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5dcf1383e2f03179975adf8f0e9ddca279be98ef..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF833GSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_4.fit.json b/ENCSR595DQM/cherimoya.fold_4.fit.json deleted file mode 100644 index 97b4706111a48ba9fd94440316e2ff428861016e..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF833GSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595DQM/cherimoya.fold_4.log b/ENCSR595DQM/cherimoya.fold_4.log deleted file mode 100644 index 4cb8b8a88a585c115fd752d302d0142d0310a161..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 35.40368342399597 4.03178596496582 828.8818969726562 0.1954866200685501 959.3759765625 0.2846096456050873 0.8094278 4.5063982009887695 True -1 5514 30.622052669525146 0.631608247756958 706.3050537109375 0.24393914639949799 883.93359375 0.33376672863960266 0.846932 0.9298079609870911 True -2 8271 30.66256546974182 0.6263320446014404 841.3773803710938 0.17980381846427917 870.166015625 0.33997848629951477 0.862946 0.3897787034511566 True -3 11028 30.603739500045776 0.6144864559173584 747.5963134765625 0.17949455976486206 862.580810546875 0.34396228194236755 0.8706247 0.2982223927974701 True -4 13785 30.653903484344482 0.6147942543029785 886.251708984375 0.3217327892780304 860.0855712890625 0.3451675474643707 0.87775886 0.24610334634780884 True -5 16542 30.656624794006348 0.6164205074310303 837.8023681640625 0.35054337978363037 856.0845336914062 0.3471333682537079 0.8795087 0.23351338505744934 True -6 19299 30.65393328666687 0.6100664138793945 814.6063232421875 0.2319837212562561 852.4549560546875 0.34996339678764343 0.8854707 0.19868168234825134 True -7 22056 30.598145008087158 0.6063122749328613 771.873779296875 0.19320479035377502 848.2637939453125 0.35343945026397705 0.8868588 0.19703209400177002 True -8 24813 30.534130573272705 0.6092774868011475 1003.9968872070312 0.26883333921432495 846.4292602539062 0.3546646535396576 0.8892194 0.19587142765522003 True -9 27570 29.976940870285034 0.6105897426605225 766.9710693359375 0.15504366159439087 844.4631958007812 0.35607707500457764 0.8950918 0.19394592940807343 True -10 30327 30.028276205062866 1.2009963989257812 774.859619140625 0.1161678358912468 843.5928955078125 0.35651829838752747 0.8928566 0.21915599703788757 False -11 33084 30.019801378250122 0.6083457469940186 704.5587768554688 0.18067339062690735 839.8038940429688 0.359298437833786 0.90380484 0.18674561381340027 True -12 35841 30.097660541534424 0.6207690238952637 734.9730224609375 0.08044229447841644 836.9926147460938 0.36190900206565857 0.9066152 0.17008964717388153 True -13 38598 30.105429649353027 0.61466383934021 820.037109375 0.2034345269203186 834.919189453125 0.36310502886772156 0.9105614 0.15803687274456024 True -14 41355 30.083903551101685 0.6121878623962402 654.6380615234375 0.16688984632492065 834.4317016601562 0.3626457452774048 0.91650116 0.14452597498893738 True -15 44112 30.052714109420776 1.3056566715240479 859.3975219726562 0.15140053629875183 834.2069091796875 0.3622332215309143 0.9185358 0.13536784052848816 True -16 46869 30.059978723526 0.6274738311767578 763.5618896484375 0.13664647936820984 833.13623046875 0.3631720244884491 0.9201021 0.12911510467529297 True -17 49626 30.19255757331848 0.613213062286377 785.3641967773438 0.17035922408103943 832.8162231445312 0.3637327253818512 0.92142165 0.12587100267410278 True -18 52383 30.119840145111084 0.630969762802124 772.9606323242188 0.1333848536014557 834.0086669921875 0.3631304204463959 0.92400736 0.12486926466226578 True -19 55140 30.274428606033325 0.621870756149292 755.74951171875 0.10144615918397903 834.09326171875 0.362978994846344 0.9218188 0.12427577376365662 False diff --git a/ENCSR595DQM/cherimoya.fold_4.performance.tsv b/ENCSR595DQM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 24936d4f4f3b7b4ca7cd78e1f640388a7939761a..0000000000000000000000000000000000000000 --- a/ENCSR595DQM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -834.0086669921875 0.40094661712646484 0.36313045024871826 0.15379038453102112 0.9240073561668396 0.9038755297660828 0.12486926466226578 \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_0.evaluate.json b/ENCSR595HZQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e489994c7aa4c289d3049093a16dc43f6bd7acfd..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF880URC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_0.fit.json b/ENCSR595HZQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 94ac2252c4c9bfc5606fe3dfe620dc430210acfe..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF880URC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_0.log b/ENCSR595HZQ/cherimoya.fold_0.log deleted file mode 100644 index 9200fb81cd59cb2cfbab29ecb3dd72b82ebbbe65..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2284 29.862027406692505 24.033244609832764 207.883544921875 0.5866527557373047 265.9700927734375 0.14580422639846802 0.49219617 3.6235575675964355 True -1 4568 25.295539140701294 0.5708322525024414 214.177734375 0.8436256647109985 249.07667541503906 0.22045354545116425 0.58254707 1.5024665594100952 True -2 6852 25.254859447479248 0.4886910915374756 208.4956817626953 0.6859185695648193 241.6446533203125 0.2421952188014984 0.5933477 1.0475372076034546 True -3 9136 25.234792232513428 0.842644453048706 186.09091186523438 0.5901532173156738 238.81202697753906 0.24690671265125275 0.6079571 0.7243281602859497 True -4 11420 25.769643545150757 1.1443090438842773 214.99456787109375 0.43222761154174805 237.73153686523438 0.24958264827728271 0.60809636 0.6993529200553894 True -5 13704 25.266761541366577 0.493776798248291 188.0450439453125 0.40499383211135864 236.6876220703125 0.2525908052921295 0.61613595 0.7026063203811646 True -6 15988 25.86437225341797 0.495558500289917 179.76248168945312 0.32801353931427 235.57679748535156 0.25728023052215576 0.6237843 0.676105797290802 True -7 18272 25.140493631362915 0.46932339668273926 223.10845947265625 0.4667658805847168 234.83441162109375 0.2592909038066864 0.63123894 0.6400836110115051 True -8 20556 25.23213291168213 1.2375788688659668 188.71728515625 0.41810813546180725 234.2946014404297 0.2611871659755707 0.64035463 0.6328285932540894 True -9 22840 25.20149850845337 0.4852406978607178 183.43296813964844 0.3962368369102478 234.10330200195312 0.2615435719490051 0.6473742 0.5870832204818726 True -10 25124 25.230079889297485 0.7846887111663818 217.4684295654297 0.4414306879043579 233.43789672851562 0.2640562951564789 0.656627 0.5482400059700012 True -11 27408 25.288105964660645 0.508411169052124 216.76669311523438 0.44288477301597595 233.03985595703125 0.2657458484172821 0.66178924 0.5029858946800232 True -12 29692 25.277551412582397 17.769867420196533 198.8819122314453 0.40824830532073975 232.423095703125 0.2676491439342499 0.6668495 0.47774407267570496 True -13 31976 25.17886257171631 0.49842405319213867 212.5134735107422 0.5356942415237427 232.04640197753906 0.2693624496459961 0.6763004 0.4411482512950897 True -14 34260 25.20017671585083 0.8965981006622314 169.42581176757812 0.3339427709579468 231.57826232910156 0.2713446021080017 0.6849305 0.4041091799736023 True -15 36544 25.185298681259155 0.468036413192749 217.14613342285156 0.2943616509437561 231.4599609375 0.2710725665092468 0.6922223 0.3798995614051819 True -16 38828 25.175575017929077 0.4664461612701416 200.1773681640625 0.30820614099502563 231.30215454101562 0.27137815952301025 0.6961044 0.37253209948539734 True -17 41112 25.183659553527832 0.46630191802978516 195.41921997070312 0.2454710602760315 231.17002868652344 0.2727029323577881 0.69492716 0.36948898434638977 False -18 43396 25.18788719177246 0.48827600479125977 184.56092834472656 0.24295923113822937 231.49481201171875 0.2706916630268097 0.69248104 0.3739435076713562 False -19 45680 24.959219455718994 0.47463297843933105 191.42977905273438 0.30750328302383423 231.43060302734375 0.27153709530830383 0.6896082 0.38018444180488586 False diff --git a/ENCSR595HZQ/cherimoya.fold_0.performance.tsv b/ENCSR595HZQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 997d399887f96ac19246f5439451f2148343ebac..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -231.30215454101562 0.510338306427002 0.27137815952301025 0.06513002514839172 0.6961044073104858 0.6240796446800232 0.37253209948539734 \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_1.evaluate.json b/ENCSR595HZQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f14d45cac24a6def3aee482280d036573ed2cbcb..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF880URC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_1.fit.json b/ENCSR595HZQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 3020a52b804ac3616d4bdb78e7195a770ca53577..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF880URC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_1.log b/ENCSR595HZQ/cherimoya.fold_1.log deleted file mode 100644 index 7076d612c403d3ad2d6dcbdab62446bed904ba55..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2270 30.378820657730103 3.978961706161499 196.25543212890625 0.5607505440711975 299.328857421875 0.14969965815544128 0.5158683 4.623764991760254 True -1 4540 25.01287817955017 0.7197730541229248 203.8919677734375 0.6924307346343994 278.78533935546875 0.23590688407421112 0.6006909 2.0707459449768066 True -2 6810 25.024696826934814 0.5959813594818115 199.98895263671875 0.5569876432418823 271.3045349121094 0.2526226043701172 0.61380744 1.5240650177001953 True -3 9080 24.989803075790405 1.6013801097869873 224.32366943359375 0.5777386426925659 266.68798828125 0.2620219886302948 0.6246198 0.9946227669715881 True -4 11350 25.015159368515015 0.5953683853149414 215.68798828125 0.59505695104599 264.85052490234375 0.26579898595809937 0.6328467 0.941830039024353 True -5 13620 25.020346641540527 2.0297157764434814 215.25564575195312 0.5088964700698853 263.464111328125 0.2684028446674347 0.6408447 0.8116472959518433 True -6 15890 25.08192729949951 0.5911014080047607 154.28842163085938 0.4698754847049713 262.6444396972656 0.27082183957099915 0.6489107 0.7186618447303772 True -7 18160 25.05589008331299 2.002624034881592 191.2852020263672 0.49698376655578613 261.6766357421875 0.2745131552219391 0.65314335 0.7093636989593506 True -8 20430 25.062231302261353 0.600914478302002 213.1186065673828 0.6091762781143188 260.9809875488281 0.2766464054584503 0.6584889 0.6411848068237305 True -9 22700 25.075935125350952 0.6082475185394287 168.98391723632812 0.4968600869178772 260.592529296875 0.2781355082988739 0.66537637 0.6428341269493103 True -10 24970 25.063937664031982 0.623521089553833 161.15020751953125 0.3229130208492279 259.78192138671875 0.2808316648006439 0.6719077 0.6284162402153015 True -11 27240 25.084110021591187 0.6055409908294678 192.04815673828125 0.3418737053871155 259.03521728515625 0.28263336420059204 0.6810271 0.5590481758117676 True -12 29510 25.062132596969604 0.6122336387634277 212.52127075195312 0.5185502767562866 258.3988952636719 0.28470346331596375 0.6892814 0.4986492693424225 True -13 31780 25.070329904556274 0.6092417240142822 200.03201293945312 0.3333855867385864 257.5580749511719 0.2873678207397461 0.69850206 0.45871710777282715 True -14 34050 25.033855199813843 1.7637853622436523 180.99807739257812 0.33226898312568665 256.8368835449219 0.2903375029563904 0.71080315 0.4339536428451538 True -15 36320 24.996308088302612 0.5763800144195557 170.946533203125 0.5746630430221558 256.74481201171875 0.2897243797779083 0.7176209 0.4145890176296234 True -16 38590 25.259454488754272 8.928348541259766 188.61111450195312 0.3565511703491211 256.4450988769531 0.2905234098434448 0.72162515 0.39904722571372986 True -17 40860 25.053611278533936 0.5969674587249756 184.45101928710938 0.25909334421157837 256.647216796875 0.2893981337547302 0.7232224 0.3970791697502136 True -18 43130 26.418617963790894 0.6056537628173828 194.7303466796875 0.3702264428138733 256.722412109375 0.289619505405426 0.72086865 0.39903101325035095 False -19 45400 24.703422784805298 0.5919704437255859 174.5303955078125 0.3609067499637604 256.7252197265625 0.2897011637687683 0.7195852 0.40430647134780884 False diff --git a/ENCSR595HZQ/cherimoya.fold_1.performance.tsv b/ENCSR595HZQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bdf31e0749c8a0649ebb17322fa64de5d9a27486..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -256.647216796875 0.49581676721572876 0.2893981337547302 0.07107634842395782 0.7232223749160767 0.6687873005867004 0.3970791697502136 \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_2.evaluate.json b/ENCSR595HZQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9ac60af142636518cf759f08b7387b545f3c74f2..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF880URC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_2.fit.json b/ENCSR595HZQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 58d2927852822548d08b973ff8c870c0bc2796fe..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF880URC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_2.log b/ENCSR595HZQ/cherimoya.fold_2.log deleted file mode 100644 index 85cee4e911a6910b6fa8697e44ce3001a596e79c..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2423 31.54502010345459 3.6682896614074707 246.5298309326172 0.7205454111099243 276.7139587402344 0.1505507230758667 0.49046704 3.6774723529815674 True -1 4846 26.690369367599487 0.5528688430786133 219.5966796875 0.6385973691940308 256.7631530761719 0.22932423651218414 0.5639729 1.4097858667373657 True -2 7269 26.769286155700684 0.9437687397003174 179.45919799804688 0.5357047319412231 250.4802703857422 0.2443273663520813 0.589445 1.1432064771652222 True -3 9692 26.725557327270508 0.484264612197876 240.26461791992188 0.627721905708313 246.88034057617188 0.2551284432411194 0.60643965 0.8063740730285645 True -4 12115 26.803070783615112 0.4581131935119629 197.62062072753906 0.4618324637413025 245.3609619140625 0.25975555181503296 0.6102431 0.7512407898902893 True -5 14538 26.758388996124268 0.45644092559814453 202.4217529296875 0.47314009070396423 244.5747528076172 0.2601310908794403 0.6197343 0.6316714882850647 True -6 16961 26.712289094924927 0.44634270668029785 193.64016723632812 0.5608766078948975 243.5657958984375 0.26495108008384705 0.62597036 0.6155372262001038 True -7 19384 26.686119556427002 0.45209693908691406 207.21144104003906 0.3979721665382385 243.32687377929688 0.26448357105255127 0.6320649 0.5903050303459167 True -8 21807 26.742543697357178 0.6999857425689697 165.77015686035156 0.3668181300163269 242.2335968017578 0.2688515782356262 0.6376188 0.5555364489555359 True -9 24230 26.745401859283447 0.47218847274780273 202.80715942382812 0.49995458126068115 241.51303100585938 0.27167049050331116 0.6449291 0.5355404019355774 True -10 26653 26.69292187690735 0.452193021774292 209.58990478515625 0.49622058868408203 240.96759033203125 0.2735957205295563 0.65233666 0.5355857610702515 True -11 29076 26.702590465545654 0.45241498947143555 187.17129516601562 0.5349112153053284 240.4566192626953 0.2748059332370758 0.6583508 0.5206214189529419 True -12 31499 26.724615812301636 0.4564228057861328 189.58262634277344 0.3432924747467041 240.20164489746094 0.2758602499961853 0.6650701 0.48915913701057434 True -13 33922 26.904101610183716 4.013426303863525 158.066650390625 0.4039561152458191 239.7412567138672 0.2768876552581787 0.66986066 0.47790268063545227 True -14 36345 26.7469379901886 0.8971505165100098 185.9078369140625 0.4156356751918793 238.991455078125 0.2802441120147705 0.67496 0.45458102226257324 True -15 38768 26.75186038017273 0.7629086971282959 171.58901977539062 0.33801162242889404 238.77963256835938 0.2809341847896576 0.6798677 0.4327859580516815 True -16 41191 26.702845335006714 14.63253140449524 196.8578338623047 0.3019799590110779 238.50457763671875 0.2821996808052063 0.68500376 0.4147878885269165 True -17 43614 27.020659685134888 0.45039844512939453 191.11952209472656 0.2685794532299042 238.6444549560547 0.28135934472084045 0.68435436 0.41209620237350464 False -18 46037 26.18537139892578 0.45205259323120117 209.46945190429688 0.1852656602859497 238.64398193359375 0.2817310094833374 0.682064 0.4134610593318939 False -19 48460 26.24867081642151 0.4600856304168701 191.62892150878906 0.30302590131759644 238.7729949951172 0.2808454930782318 0.68141806 0.418109267950058 False diff --git a/ENCSR595HZQ/cherimoya.fold_2.performance.tsv b/ENCSR595HZQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4bb29679237bd5e8b97d1f316b7b45f7eaf9961a..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -238.50457763671875 0.5040683150291443 0.2821996510028839 0.06845936924219131 0.6850037574768066 0.6283591985702515 0.4147878885269165 \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_3.evaluate.json b/ENCSR595HZQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 408dd95e1cbc4ba7031fbc37e0a19cb36910b5dd..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF880URC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_3.fit.json b/ENCSR595HZQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 183f8350ac246805985358d6b4b137d63e543188..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF880URC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_3.log b/ENCSR595HZQ/cherimoya.fold_3.log deleted file mode 100644 index f3bf315efaf0e161b9f7ea59c9557c67a5f5d070..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2324 30.343060731887817 3.990354061126709 201.2130126953125 0.7624096870422363 265.9567565917969 0.14444436132907867 0.5223165 4.110597610473633 True -1 4648 25.621695041656494 0.47670769691467285 199.02566528320312 0.6251657009124756 249.05068969726562 0.21738684177398682 0.59773004 1.523067593574524 True -2 6972 25.626262426376343 0.45041728019714355 187.784912109375 0.37353241443634033 241.28187561035156 0.24016278982162476 0.61847705 1.0333868265151978 True -3 9296 25.63216757774353 0.4598705768585205 227.83811950683594 0.4635613262653351 238.23776245117188 0.247505322098732 0.6319903 0.6726062297821045 True -4 11620 25.806044101715088 0.4590308666229248 204.33349609375 0.4965427815914154 236.8370819091797 0.25169116258621216 0.6336375 0.6869078278541565 True -5 13944 25.631266117095947 1.3332700729370117 191.07518005371094 0.4963228702545166 236.33090209960938 0.2527739703655243 0.64034283 0.663059413433075 True -6 16268 25.693298816680908 0.4706003665924072 205.26583862304688 0.4688211977481842 235.65225219726562 0.25551173090934753 0.64202905 0.6209000945091248 True -7 18592 25.65604543685913 0.4588162899017334 215.01138305664062 0.5843907594680786 235.0281982421875 0.2574874460697174 0.6511931 0.6024246215820312 True -8 20916 25.674272537231445 0.46512818336486816 169.93173217773438 0.5225096344947815 234.4172821044922 0.25985074043273926 0.6525014 0.5629895329475403 True -9 23240 25.671178340911865 1.0646955966949463 196.68414306640625 0.40413084626197815 233.846435546875 0.26124459505081177 0.6639707 0.5071109533309937 True -10 25564 25.732449293136597 0.4660918712615967 181.9860382080078 0.4449276924133301 233.38499450683594 0.26324462890625 0.66987634 0.4866122007369995 True -11 27888 25.612290382385254 0.46541714668273926 199.86277770996094 0.4894730746746063 232.96205139160156 0.2643694579601288 0.6783091 0.47824013233184814 True -12 30212 25.613874197006226 0.46196722984313965 191.4024658203125 0.6175874471664429 232.2290496826172 0.26731303334236145 0.68437314 0.4403725862503052 True -13 32536 25.773373126983643 0.4697248935699463 215.346923828125 0.42133423686027527 231.98074340820312 0.2678009271621704 0.6910135 0.42244794964790344 True -14 34860 25.68431282043457 0.47031426429748535 225.1590118408203 0.406527042388916 231.7638702392578 0.2686438262462616 0.69729525 0.3863598108291626 True -15 37184 25.62160563468933 0.4716176986694336 218.41632080078125 0.41916123032569885 231.3527069091797 0.2706693112850189 0.7031508 0.37379583716392517 True -16 39508 25.398643732070923 0.4650709629058838 184.86355590820312 0.3228566348552704 231.17401123046875 0.27083849906921387 0.70595616 0.36104050278663635 True -17 41832 25.169371366500854 0.458223819732666 202.6761932373047 0.25115424394607544 231.3828887939453 0.2698887884616852 0.7024826 0.36533060669898987 False -18 44156 25.206965684890747 0.45886993408203125 190.73681640625 0.24430257081985474 231.5509490966797 0.26904040575027466 0.6996874 0.36865055561065674 False -19 46480 25.207971811294556 0.44960832595825195 172.2084197998047 0.2831592261791229 231.183349609375 0.27145469188690186 0.6964944 0.37423720955848694 False diff --git a/ENCSR595HZQ/cherimoya.fold_3.performance.tsv b/ENCSR595HZQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 27ec32f34ccbbf2090ae6cfd555dcce756f81e46..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -231.17401123046875 0.5107263326644897 0.27083852887153625 0.06357130408287048 0.7059561610221863 0.6329580545425415 0.36104050278663635 \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_4.evaluate.json b/ENCSR595HZQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c4ade08d07c3e50d2e667de08dbfaea0c4e10d0d..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF880URC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_4.fit.json b/ENCSR595HZQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 09afc7fadfb70fe39c0a01c0a7d8543ac52405f5..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF880URC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR595HZQ/cherimoya.fold_4.log b/ENCSR595HZQ/cherimoya.fold_4.log deleted file mode 100644 index 6a033f9e3d2de5eaabe4ff277fac1ab692905830..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2382 30.98841381072998 20.473345041275024 187.93502807617188 0.5310952663421631 258.1898498535156 0.14324182271957397 0.47190493 3.2542715072631836 True -1 4764 26.55907654762268 0.5854942798614502 184.31027221679688 0.651701807975769 241.6353759765625 0.21892192959785461 0.55730915 1.405130386352539 True -2 7146 26.302039623260498 0.48813486099243164 190.22332763671875 0.45190536975860596 236.04598999023438 0.23441794514656067 0.57536215 0.8802224397659302 True -3 9528 26.29644513130188 0.48501157760620117 204.70469665527344 0.6789517402648926 234.49398803710938 0.23698708415031433 0.5795318 0.7736441493034363 True -4 11910 26.061100721359253 0.4737672805786133 168.74588012695312 0.4489283561706543 232.72410583496094 0.2424229383468628 0.5825759 0.7054386734962463 True -5 14292 25.749955654144287 0.472243070602417 188.89219665527344 0.5861746668815613 231.32382202148438 0.2466953992843628 0.5961677 0.5993244647979736 True -6 16674 25.77806830406189 0.47634410858154297 190.0147247314453 0.5523452758789062 230.610595703125 0.24887622892856598 0.6041504 0.6289723515510559 True -7 19056 25.828356504440308 0.4949982166290283 211.74371337890625 0.4779532849788666 229.89230346679688 0.2519029676914215 0.61172396 0.6184187531471252 True -8 21438 25.788694381713867 0.47069644927978516 190.2470703125 0.48643389344215393 229.12017822265625 0.2551605999469757 0.61428237 0.5903863310813904 True -9 23820 25.78109645843506 1.6963636875152588 201.7816162109375 0.2927716374397278 228.89169311523438 0.25509175658226013 0.6272885 0.5569971799850464 True -10 26202 25.778001070022583 0.4870731830596924 160.52011108398438 0.47248977422714233 228.4511260986328 0.25689253211021423 0.63439196 0.5372747182846069 True -11 28584 25.791438579559326 0.6220736503601074 191.21188354492188 0.584031343460083 228.3258819580078 0.25679975748062134 0.6387761 0.49390166997909546 True -12 30966 25.748830318450928 0.4764561653137207 239.82281494140625 0.5536008477210999 227.41429138183594 0.2611849009990692 0.6473097 0.4558369517326355 True -13 33348 25.81540846824646 0.4698214530944824 191.12835693359375 0.468444287776947 227.24623107910156 0.26163214445114136 0.65363264 0.4401739239692688 True -14 35730 25.757827043533325 0.4696004390716553 211.06227111816406 0.34233352541923523 226.82440185546875 0.26347455382347107 0.66361356 0.4155787527561188 True -15 38112 25.759454250335693 0.47449612617492676 161.53451538085938 0.3792423605918884 226.50421142578125 0.26454460620880127 0.670979 0.3918626606464386 True -16 40494 26.28903317451477 17.374602794647217 188.70555114746094 0.2939804494380951 226.4630126953125 0.2648826837539673 0.67646027 0.3792165517807007 True -17 42876 25.785114526748657 1.6783688068389893 187.30203247070312 0.27853459119796753 226.5553436279297 0.2642049491405487 0.6770267 0.3734578788280487 True -18 45258 25.841458797454834 1.3574144840240479 193.79847717285156 0.2832401692867279 226.52005004882812 0.26419878005981445 0.67513573 0.37517768144607544 False -19 47640 25.776102304458618 0.6476728916168213 198.314697265625 0.2885066568851471 226.73529052734375 0.2630702257156372 0.6722202 0.37789055705070496 False diff --git a/ENCSR595HZQ/cherimoya.fold_4.performance.tsv b/ENCSR595HZQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 04d0d8e35d55b2b0abe4deddf948f38b9dfc4951..0000000000000000000000000000000000000000 --- a/ENCSR595HZQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -226.5553436279297 0.5146200060844421 0.2642049789428711 0.06542021781206131 0.6770266890525818 0.605705201625824 0.3734578788280487 \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_0.evaluate.json b/ENCSR598RRF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2ca0c5b3661f5ad6c2ae2661a42f0fbcc78a2de4..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654RAU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_0.fit.json b/ENCSR598RRF/cherimoya.fold_0.fit.json deleted file mode 100644 index 8fb44ff53f0f0f65b7ac8d7bed65ccad49402c74..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF654RAU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_0.log b/ENCSR598RRF/cherimoya.fold_0.log deleted file mode 100644 index 9f542bdd68f8281ffe8ce0db5d6c018af93dc4a5..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 34.64223837852478 4.533157587051392 641.0071411132812 0.3766948878765106 775.9632568359375 0.2618141770362854 0.69784886 4.987208843231201 True -1 5480 30.393215656280518 0.6242659091949463 683.543701171875 0.4442337155342102 715.6927490234375 0.3272978961467743 0.7618994 1.1872189044952393 True -2 8220 30.468353986740112 0.6102242469787598 639.3194580078125 0.3657236695289612 708.0870361328125 0.3375619947910309 0.76743263 0.48195934295654297 True -3 10960 30.436076879501343 0.6196765899658203 656.4158935546875 0.38597506284713745 695.9977416992188 0.34831562638282776 0.78100616 0.4471118152141571 True -4 13700 30.474263191223145 0.6209919452667236 630.3475341796875 0.3191942572593689 692.9530639648438 0.35185614228248596 0.7846585 0.38629817962646484 True -5 16440 30.474271297454834 0.6212325096130371 610.573974609375 0.40478184819221497 692.1004028320312 0.3523792326450348 0.7872966 0.3798522353172302 True -6 19180 30.52361798286438 0.6220550537109375 536.9590454101562 0.36054039001464844 687.5509643554688 0.35878583788871765 0.79389095 0.32146692276000977 True -7 21920 30.467653274536133 0.6222538948059082 676.3933715820312 0.3337762653827667 684.1812133789062 0.36414849758148193 0.79873246 0.3180015981197357 True -8 24660 30.405799388885498 0.620823860168457 572.9334716796875 0.3270813226699829 683.3082885742188 0.3655535876750946 0.8031576 0.311825156211853 True -9 27400 30.47172999382019 0.6212379932403564 569.8194580078125 0.2654309868812561 680.642578125 0.36885979771614075 0.80875975 0.30615702271461487 True -10 30140 30.435377836227417 0.6250348091125488 644.00341796875 0.31350600719451904 679.5392456054688 0.36991769075393677 0.8102907 0.28142479062080383 True -11 32880 30.458255529403687 0.6155774593353271 588.863037109375 0.3344581723213196 676.8530883789062 0.3739668130874634 0.8161812 0.2680191993713379 True -12 35620 30.529180765151978 0.6233556270599365 566.3172607421875 0.29866155982017517 676.0768432617188 0.374571830034256 0.81999344 0.25429046154022217 True -13 38360 30.517488718032837 0.6229829788208008 615.3242797851562 0.22538918256759644 675.14892578125 0.3747359812259674 0.82642406 0.24680885672569275 True -14 41100 30.802881002426147 0.6235294342041016 613.886474609375 0.22622326016426086 673.3837890625 0.37743082642555237 0.8285873 0.2328459471464157 True -15 43840 30.527087688446045 0.6283774375915527 601.1763916015625 0.3773059546947479 672.7876586914062 0.37828975915908813 0.8354996 0.22607088088989258 True -16 46580 30.494824409484863 0.6237893104553223 591.886962890625 0.24607747793197632 672.1204223632812 0.37829655408859253 0.8390569 0.2202140837907791 True -17 49320 30.4384605884552 0.6175553798675537 488.0648498535156 0.1820383369922638 670.2200927734375 0.38197487592697144 0.8374232 0.21759741008281708 False -18 52060 30.48039197921753 0.9479043483734131 568.954833984375 0.18179026246070862 671.0457763671875 0.3800380527973175 0.83897734 0.21868912875652313 False -19 54800 30.479394912719727 2.307884931564331 558.820068359375 0.24019286036491394 672.1727294921875 0.37736091017723083 0.83715004 0.2197972983121872 False diff --git a/ENCSR598RRF/cherimoya.fold_0.performance.tsv b/ENCSR598RRF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cc95d47fcd56fc236ed2ac0f1670e66522c27c74..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -672.1204223632812 0.37564823031425476 0.37829655408859253 0.1690068542957306 0.8390569090843201 0.7635193467140198 0.2202140837907791 \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_1.evaluate.json b/ENCSR598RRF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 51b2f810f1304d9726b0208e166c261c24bfa595..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654RAU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_1.fit.json b/ENCSR598RRF/cherimoya.fold_1.fit.json deleted file mode 100644 index 6039fd6cad83b6a226dd3b61770b4277518bc1d8..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF654RAU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_1.log b/ENCSR598RRF/cherimoya.fold_1.log deleted file mode 100644 index b956d8a253374d49f5c0538d82eab8c8c7de718a..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 34.40675640106201 3.988661289215088 607.7586669921875 0.30909597873687744 894.5076293945312 0.2696811556816101 0.70027494 5.8526201248168945 True -1 5424 30.162611961364746 0.7225143909454346 647.369873046875 0.3662702739238739 816.1513061523438 0.3486475646495819 0.7626617 1.6656936407089233 True -2 8136 30.88270592689514 20.689697265625 580.0751342773438 0.5239709615707397 798.8644409179688 0.36031997203826904 0.77755183 0.6552821397781372 True -3 10848 30.166500329971313 1.658743143081665 547.0145263671875 0.28516995906829834 787.17822265625 0.3699391484260559 0.7843626 0.6890155673027039 True -4 13560 30.15581774711609 1.2272741794586182 628.5330810546875 0.33068251609802246 783.9498901367188 0.37260112166404724 0.79127383 0.4551476240158081 True -5 16272 30.181371927261353 0.7114841938018799 601.27294921875 0.3002755045890808 778.9791259765625 0.3775823414325714 0.79433393 0.3999366760253906 True -6 18984 30.13277578353882 1.690323829650879 562.9209594726562 0.31267404556274414 776.6162109375 0.379988431930542 0.79904467 0.35678571462631226 True -7 21696 30.197120189666748 0.7153398990631104 540.8181762695312 0.34741389751434326 770.8534545898438 0.38595354557037354 0.8070534 0.3253437876701355 True -8 24408 30.17855429649353 0.7180614471435547 616.75927734375 0.32174962759017944 768.462646484375 0.38821685314178467 0.81400526 0.31195855140686035 True -9 27120 30.27727746963501 1.2579278945922852 575.9573974609375 0.29274576902389526 764.09912109375 0.39285266399383545 0.8200982 0.28418266773223877 True -10 29832 30.289167642593384 0.7216520309448242 598.1857299804688 0.23234379291534424 762.6212768554688 0.39373940229415894 0.82708585 0.27437281608581543 True -11 32544 30.22085952758789 0.7088956832885742 581.9730224609375 0.3333583474159241 759.9161987304688 0.39675867557525635 0.83046454 0.26771897077560425 True -12 35256 30.211519718170166 0.7130591869354248 573.596923828125 0.2693277597427368 757.5692749023438 0.39886474609375 0.83724624 0.256445050239563 True -13 37968 30.21985387802124 0.7211225032806396 582.356689453125 0.2930736541748047 757.2513427734375 0.39893049001693726 0.8431722 0.25343549251556396 True -14 40680 30.18682289123535 1.456766128540039 585.9144897460938 0.23169180750846863 755.33544921875 0.4011472761631012 0.84679073 0.24371398985385895 True -15 43392 30.17509698867798 0.7146060466766357 572.1102294921875 0.195281982421875 752.5338134765625 0.40420809388160706 0.852677 0.23943527042865753 True -16 46104 30.16589593887329 0.7003474235534668 618.788330078125 0.17608383297920227 751.3572998046875 0.4058200418949127 0.85563993 0.2311660647392273 True -17 48816 30.225338220596313 0.7056970596313477 556.2056884765625 0.15261098742485046 751.5281372070312 0.4049190282821655 0.8586255 0.2316872924566269 True -18 51528 30.227117776870728 0.708158016204834 708.0166015625 0.36460745334625244 751.5579833984375 0.4050846993923187 0.8576545 0.23181237280368805 False -19 54240 30.204294443130493 0.7165195941925049 581.9318237304688 0.12423622608184814 752.1564331054688 0.40381762385368347 0.85709375 0.23281976580619812 False diff --git a/ENCSR598RRF/cherimoya.fold_1.performance.tsv b/ENCSR598RRF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ac4200791dd5d23f82fadb1972f07748fe84064c..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -751.5281372070312 0.3559896647930145 0.4049190580844879 0.19119492173194885 0.8586254715919495 0.809229850769043 0.2316872924566269 \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_2.evaluate.json b/ENCSR598RRF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index af5e1dd285ab26c31c0cfcb6b3b5bd9fb2020fe0..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654RAU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_2.fit.json b/ENCSR598RRF/cherimoya.fold_2.fit.json deleted file mode 100644 index 607b7ff3989adad14350380130a5e0baf82ff77d..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF654RAU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_2.log b/ENCSR598RRF/cherimoya.fold_2.log deleted file mode 100644 index d36a0cd3f9c03bfc886eb3f276cde973fa91bd08..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 35.582451820373535 4.416249990463257 660.092041015625 0.4612003266811371 792.6047973632812 0.26764416694641113 0.6984544 4.643782138824463 True -1 5736 31.925604820251465 0.9624953269958496 539.80224609375 0.38258838653564453 727.977294921875 0.33547842502593994 0.7625751 1.0443568229675293 True -2 8604 31.998920917510986 4.449359178543091 587.148193359375 0.37198567390441895 717.6240844726562 0.34351596236228943 0.7704712 0.5027941465377808 True -3 11472 31.994115829467773 0.6078159809112549 546.607421875 0.28420981764793396 711.7506103515625 0.3507520854473114 0.77562606 0.6017148494720459 True -4 14340 31.96472954750061 0.6258494853973389 643.7171630859375 0.4184969961643219 706.6041870117188 0.35708048939704895 0.7834841 0.3647191524505615 True -5 17208 31.909752130508423 0.5982747077941895 599.4815063476562 0.3272790312767029 703.3580932617188 0.36023688316345215 0.784148 0.35575011372566223 True -6 20076 31.888548612594604 0.600635290145874 590.6639404296875 0.3880087435245514 702.2099609375 0.36039653420448303 0.7904481 0.35609757900238037 True -7 22944 31.939570665359497 0.5964131355285645 532.907958984375 0.2483048439025879 698.5181884765625 0.36514440178871155 0.7970538 0.3369896113872528 True -8 25812 31.94991946220398 2.3345324993133545 611.3259887695312 0.2596982717514038 695.854736328125 0.36955708265304565 0.7984553 0.34912416338920593 True -9 28680 32.000558614730835 1.454728603363037 543.9320068359375 0.20842981338500977 693.530029296875 0.3714500665664673 0.8061468 0.3093845844268799 True -10 31548 32.028321266174316 0.6026613712310791 617.4320678710938 0.31390511989593506 691.603515625 0.3740465044975281 0.8115468 0.28298842906951904 True -11 34416 31.905033826828003 0.6036171913146973 584.4736938476562 0.2369372844696045 690.2896118164062 0.3753882646560669 0.81411237 0.26090678572654724 True -12 37284 31.916211128234863 0.5953142642974854 547.4698486328125 0.2725936770439148 687.6668090820312 0.37828823924064636 0.8237742 0.24829290807247162 True -13 40152 31.94162344932556 0.5985226631164551 595.0182495117188 0.2822208106517792 686.3214721679688 0.38010936975479126 0.82961696 0.2344258576631546 True -14 43020 31.924876928329468 0.5968232154846191 589.2423706054688 0.2498743236064911 685.9122314453125 0.3803556561470032 0.8314844 0.2345367670059204 True -15 45888 31.96241593360901 0.5950291156768799 506.74127197265625 0.20703789591789246 683.2959594726562 0.38369888067245483 0.83748144 0.22418801486492157 True -16 48756 32.00236797332764 0.6044516563415527 591.142822265625 0.16296477615833282 683.9115600585938 0.38257235288619995 0.8381033 0.22246509790420532 True -17 51624 31.997973442077637 0.622575044631958 534.5751342773438 0.16085515916347504 682.759765625 0.38366058468818665 0.8405859 0.22162969410419464 True -18 54492 32.00313210487366 15.495875358581543 582.2139892578125 0.18190515041351318 684.517822265625 0.3809696137905121 0.84020805 0.22245919704437256 False -19 57360 32.04288029670715 0.6091768741607666 581.4819946289062 0.14947932958602905 683.3507690429688 0.383389949798584 0.83823395 0.22427618503570557 False diff --git a/ENCSR598RRF/cherimoya.fold_2.performance.tsv b/ENCSR598RRF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e2dcbd37601db04585b72e252bc21ea7752723f2..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -682.759765625 0.3719915747642517 0.38366052508354187 0.17525188624858856 0.8405858874320984 0.7706984281539917 0.22162969410419464 \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_3.evaluate.json b/ENCSR598RRF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e35971da0c78f5e0b9ee0f9f90804ea6eebf8f13..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654RAU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_3.fit.json b/ENCSR598RRF/cherimoya.fold_3.fit.json deleted file mode 100644 index 50b185c51fce9b67426ab0b167e7af528e854883..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF654RAU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_3.log b/ENCSR598RRF/cherimoya.fold_3.log deleted file mode 100644 index a228ba886940e22f818451c9555e0be0af189efc..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 34.728938579559326 3.506314992904663 612.5302124023438 0.5152366161346436 777.3313598632812 0.2687903046607971 0.6997253 5.952876567840576 True -1 5528 30.757861852645874 0.5772073268890381 542.982666015625 0.48519158363342285 715.7158203125 0.3330729007720947 0.76481235 1.1572803258895874 True -2 8292 30.715136528015137 0.5674395561218262 619.1480712890625 0.38542670011520386 706.2726440429688 0.3419094383716583 0.7730117 0.6127620339393616 True -3 11056 30.777409076690674 0.5716631412506104 619.2072143554688 0.44390246272087097 697.1253051757812 0.35189202427864075 0.7847195 0.5367958545684814 True -4 13820 30.77422308921814 0.5724713802337646 539.486572265625 0.33551859855651855 693.3204345703125 0.35443446040153503 0.7892117 0.5353044867515564 True -5 16584 30.712604761123657 0.5642647743225098 561.67626953125 0.24735520780086517 691.2506713867188 0.35636425018310547 0.79511297 0.37886232137680054 True -6 19348 30.787017345428467 0.5680632591247559 470.54058837890625 0.17998987436294556 689.0868530273438 0.35936540365219116 0.7935121 0.3770166039466858 False -7 22112 30.901641607284546 0.5756983757019043 629.0501098632812 0.44440245628356934 684.86962890625 0.3659401535987854 0.8018103 0.3241874575614929 True -8 24876 30.722505807876587 18.461237907409668 581.6727905273438 0.2301173359155655 683.6166381835938 0.36736154556274414 0.8055993 0.3017294704914093 True -9 27640 33.112054109573364 24.09533977508545 598.8968505859375 0.2525545358657837 681.9157104492188 0.3689456880092621 0.809242 0.28806018829345703 True -10 30404 30.833014488220215 1.0368590354919434 463.3387145996094 0.2016766369342804 680.6903076171875 0.3703666925430298 0.8118284 0.2854401171207428 True -11 33168 30.770893573760986 2.0862302780151367 540.64990234375 0.21917778253555298 678.5535278320312 0.3736792802810669 0.81826687 0.26516783237457275 True -12 35932 30.7831289768219 0.5785312652587891 594.173828125 0.23536965250968933 675.9635620117188 0.3769015073776245 0.8201391 0.26290494203567505 True -13 38696 30.796674013137817 0.5713527202606201 508.2808837890625 0.2637328505516052 674.874755859375 0.3767763674259186 0.82539463 0.25305837392807007 True -14 41460 30.7789945602417 0.5789618492126465 587.5647583007812 0.29267188906669617 672.454345703125 0.37963250279426575 0.83212185 0.2457476258277893 True -15 44224 30.789214372634888 0.5791380405426025 575.8982543945312 0.26812833547592163 674.0428466796875 0.3767194151878357 0.83662313 0.23854343593120575 True -16 46988 30.730483770370483 0.5738582611083984 548.9811401367188 0.15253666043281555 671.3267211914062 0.38185688853263855 0.8381374 0.23566016554832458 True -17 49752 30.78507685661316 2.3610079288482666 635.3436279296875 0.20564153790473938 672.5980834960938 0.3787716031074524 0.837997 0.23303189873695374 False -18 52516 30.73035740852356 2.465409278869629 662.132080078125 0.14380677044391632 670.477294921875 0.3823944926261902 0.8398345 0.23344972729682922 True -19 55280 30.75133490562439 0.6114199161529541 554.8250732421875 0.16442522406578064 672.2220458984375 0.3789825439453125 0.8403662 0.23373974859714508 True diff --git a/ENCSR598RRF/cherimoya.fold_3.performance.tsv b/ENCSR598RRF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8456c53ed98da0eb4adef110d022389b6fd7a4cc..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -672.2220458984375 0.3761134743690491 0.3789825439453125 0.17375029623508453 0.8403661847114563 0.759039580821991 0.23373974859714508 \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_4.evaluate.json b/ENCSR598RRF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f1cf39892eb8a813e086c307f0c618f2283264b3..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654RAU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_4.fit.json b/ENCSR598RRF/cherimoya.fold_4.fit.json deleted file mode 100644 index 639c0a4b82efbe48315f0a89e9a2c001446461a4..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF654RAU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RRF/cherimoya.fold_4.log b/ENCSR598RRF/cherimoya.fold_4.log deleted file mode 100644 index 20e1a2b689f080253049b807a3348b6b3490ada5..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2831 35.91551327705383 3.7718515396118164 615.851318359375 0.31324508786201477 748.77734375 0.266891747713089 0.692424 4.8818440437316895 True -1 5662 31.49209237098694 0.6186418533325195 678.0189819335938 0.5626760721206665 699.5517578125 0.32502248883247375 0.74536777 1.0687440633773804 True -2 8493 31.47497868537903 0.6257812976837158 545.094970703125 0.4268959164619446 687.38720703125 0.3390589952468872 0.75402015 0.5254582166671753 True -3 11324 31.531010389328003 0.6147010326385498 642.3202514648438 0.29252126812934875 679.4371337890625 0.34619811177253723 0.76285505 0.47271353006362915 True -4 14155 31.539008855819702 0.618281364440918 544.60546875 0.2823690176010132 677.442138671875 0.34866178035736084 0.7699425 0.41927382349967957 True -5 16986 31.517969131469727 1.204756259918213 586.0403442382812 0.31443601846694946 673.5303344726562 0.3525140881538391 0.77912164 0.3814873993396759 True -6 19817 31.6976797580719 0.6153779029846191 709.7589111328125 0.3894515335559845 670.8955078125 0.3566399812698364 0.78280777 0.38783228397369385 True -7 22648 31.599475860595703 0.6136271953582764 672.3428955078125 0.39386916160583496 668.087646484375 0.3610479533672333 0.78803873 0.3841535151004791 True -8 25479 31.648399591445923 0.6078512668609619 540.70263671875 0.27699339389801025 665.9290771484375 0.364388644695282 0.7915739 0.3680889904499054 True -9 28310 31.662206172943115 0.6240313053131104 569.5874633789062 0.20298819243907928 663.928466796875 0.36698228120803833 0.79689425 0.3338492512702942 True -10 31141 31.652394771575928 0.6131606101989746 623.2966918945312 0.25407785177230835 664.630859375 0.3649648129940033 0.8019726 0.3133562505245209 True -11 33972 31.79070258140564 6.126953125 532.1627197265625 0.2961008548736572 661.926025390625 0.3686114549636841 0.8044912 0.2859058380126953 True -12 36803 31.566393852233887 0.6198830604553223 590.2332763671875 0.1928224265575409 659.1793823242188 0.37310224771499634 0.81286 0.2610728442668915 True -13 39634 31.530296087265015 0.6094136238098145 585.1871337890625 0.15922574698925018 659.5994262695312 0.37172701954841614 0.8199111 0.24719631671905518 True -14 42465 31.501569747924805 0.6075136661529541 567.423095703125 0.3053830564022064 658.5554809570312 0.37330159544944763 0.8253201 0.22874224185943604 True -15 45296 31.584614992141724 0.6036832332611084 547.2472534179688 0.21246524155139923 656.9793701171875 0.375005304813385 0.8306835 0.21947206556797028 True -16 48127 31.59509563446045 0.6163990497589111 566.2730712890625 0.19840165972709656 657.33154296875 0.3736414909362793 0.83388495 0.21152767539024353 True -17 50958 31.56432557106018 0.6178851127624512 563.94140625 0.194522887468338 657.2061767578125 0.3748035430908203 0.83643895 0.20826832950115204 True -18 53789 31.599557876586914 0.6084904670715332 586.7431030273438 0.1661437749862671 657.1881713867188 0.3755612075328827 0.8361941 0.2069990187883377 False -19 56620 31.531409740447998 0.6049561500549316 609.5504150390625 0.20968279242515564 657.1043090820312 0.3755267560482025 0.834534 0.20856024324893951 False diff --git a/ENCSR598RRF/cherimoya.fold_4.performance.tsv b/ENCSR598RRF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7d415058b5ad7e5cc183df0e94debd86fd62d1e7..0000000000000000000000000000000000000000 --- a/ENCSR598RRF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -657.2061767578125 0.37803611159324646 0.3748035728931427 0.1651180237531662 0.8364389538764954 0.7477357387542725 0.20826832950115204 \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_0.evaluate.json b/ENCSR598RVJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8a5afb8582a8c988beb1b2ec722ecb76989ce32b..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF145DWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_0.fit.json b/ENCSR598RVJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 04420a93734d2ddb23113c10225863266cc3e2af..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF145DWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_0.log b/ENCSR598RVJ/cherimoya.fold_0.log deleted file mode 100644 index 36e09215c5a4ed09715b9838ec2214cae757677b..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 35.562288999557495 3.473501443862915 808.2655029296875 0.4251863658428192 961.2510375976562 0.23992328345775604 0.8049537 4.92499303817749 True -1 5520 30.60340142250061 0.7305393218994141 749.739990234375 0.2704997658729553 893.6062622070312 0.2808207869529724 0.846494 1.018723964691162 True -2 8280 30.279810190200806 0.5886318683624268 659.9495239257812 0.3465725779533386 879.7901000976562 0.285430371761322 0.8609963 0.47331494092941284 True -3 11040 30.04602575302124 0.5852291584014893 673.9312744140625 0.2515425980091095 874.4918212890625 0.2884354591369629 0.87107927 0.37804681062698364 True -4 13800 30.081193923950195 0.5764596462249756 809.8997802734375 0.2773582935333252 869.2338256835938 0.29174697399139404 0.8725006 0.3506038784980774 True -5 16560 30.11464238166809 0.6111960411071777 632.016845703125 0.25413766503334045 863.9603881835938 0.2953225076198578 0.8758501 0.34067675471305847 True -6 19320 30.061940908432007 0.5691003799438477 711.7994384765625 0.2014000117778778 863.5596923828125 0.29477596282958984 0.8776512 0.28895604610443115 True -7 22080 30.022325038909912 0.6011543273925781 808.960693359375 0.3445455729961395 857.7801513671875 0.2987845242023468 0.88445145 0.28481757640838623 True -8 24840 30.09685444831848 0.5772793292999268 841.4570922851562 0.43878182768821716 856.7245483398438 0.2984261214733124 0.8868012 0.2758183479309082 True -9 27600 30.105904817581177 0.5902683734893799 749.6463012695312 0.3067905306816101 854.00439453125 0.3000808656215668 0.8925735 0.2649224102497101 True -10 30360 30.078946828842163 0.581106424331665 799.5372314453125 0.39618852734565735 853.66064453125 0.3002781867980957 0.8954321 0.24102307856082916 True -11 33120 30.122922658920288 0.5809879302978516 820.2609252929688 0.21286311745643616 851.6415405273438 0.3015545606613159 0.90034723 0.23816494643688202 True -12 35880 30.094501733779907 0.6226894855499268 736.1337280273438 0.17595425248146057 848.06591796875 0.3041817843914032 0.90262395 0.2258318066596985 True -13 38640 30.084314107894897 0.7562336921691895 649.0204467773438 0.2586638331413269 844.5579833984375 0.30685701966285706 0.9060541 0.20803716778755188 True -14 41400 30.0358943939209 0.5795941352844238 699.874267578125 0.15917694568634033 843.99365234375 0.3067939579486847 0.9102561 0.19027245044708252 True -15 44160 30.040293216705322 0.581045389175415 811.7286376953125 0.2788342833518982 843.6209106445312 0.30718088150024414 0.9148612 0.17706498503684998 True -16 46920 30.01595115661621 0.5805256366729736 771.1240234375 0.16407932341098785 842.3107299804688 0.3081541657447815 0.9176431 0.16641372442245483 True -17 49680 30.051517009735107 0.589637041091919 574.4351806640625 0.1210511103272438 842.7647705078125 0.3071044683456421 0.9172868 0.16327504813671112 False -18 52440 30.064573764801025 0.5782806873321533 768.3994140625 0.11238624155521393 844.116943359375 0.30615437030792236 0.9191866 0.16006730496883392 True -19 55200 30.04849934577942 0.5763030052185059 714.5035400390625 0.12141861021518707 843.0255126953125 0.30794933438301086 0.9180281 0.15982548892498016 False diff --git a/ENCSR598RVJ/cherimoya.fold_0.performance.tsv b/ENCSR598RVJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 053cbac60ca5a7e38595a20551966f5adc18a21a..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -844.116943359375 0.45687147974967957 0.30615437030792236 0.10927342623472214 0.9191865921020508 0.900211751461029 0.16006730496883392 \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_1.evaluate.json b/ENCSR598RVJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index df1ec0f4da4abce79e0cacbaea030ec261b72c65..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF145DWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_1.fit.json b/ENCSR598RVJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 4e521b6862adce9390a114810bda3cdf012ed3ab..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF145DWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_1.log b/ENCSR598RVJ/cherimoya.fold_1.log deleted file mode 100644 index 61dc8f5c2204ff937100f8387da346248c2d0731..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 34.688884258270264 3.9407331943511963 709.2232666015625 0.40318793058395386 1178.14453125 0.24500185251235962 0.78941905 6.657982349395752 True -1 5404 30.002296447753906 0.7320129871368408 706.36083984375 0.31341058015823364 1085.912353515625 0.295220285654068 0.83649546 1.493482232093811 True -2 8106 29.50778031349182 0.7116105556488037 823.4520874023438 0.22504884004592896 1057.116943359375 0.30487799644470215 0.8530667 0.5845720767974854 True -3 10808 29.401278257369995 0.6846387386322021 686.6536254882812 0.28938570618629456 1043.302734375 0.3106165826320648 0.8661653 0.6823498606681824 True -4 13510 29.447295904159546 0.6857163906097412 923.1024780273438 0.5206708908081055 1035.7088623046875 0.3135872185230255 0.876486 0.3996949791908264 True -5 16212 29.439415216445923 0.691429615020752 718.3360595703125 0.1806458830833435 1032.2288818359375 0.31515535712242126 0.8785857 0.3422325849533081 True -6 18914 29.4395534992218 0.6890501976013184 718.3614501953125 0.3996340036392212 1023.0499267578125 0.3205028772354126 0.884093 0.32034027576446533 True -7 21616 29.427931785583496 0.692112922668457 675.9473876953125 0.19565635919570923 1022.8599243164062 0.31932899355888367 0.8885918 0.30196183919906616 True -8 24318 29.42713713645935 0.6931073665618896 687.4140014648438 0.22974826395511627 1020.92236328125 0.3205034136772156 0.8934033 0.3104053735733032 True -9 27020 29.399401664733887 0.6948878765106201 777.3175048828125 0.234638512134552 1015.2991943359375 0.32450932264328003 0.8972893 0.28450143337249756 True -10 29722 29.43827795982361 0.6931917667388916 780.39990234375 0.34173116087913513 1012.0947265625 0.3251548707485199 0.90119 0.2604599595069885 True -11 32424 29.406221628189087 0.6947133541107178 827.9666137695312 0.3006102442741394 1009.1436157226562 0.3272693157196045 0.90685725 0.24643483757972717 True -12 35126 29.41703176498413 0.6818959712982178 800.175537109375 0.19257649779319763 1006.0912475585938 0.3292606472969055 0.90931505 0.233634352684021 True -13 37828 29.441485166549683 0.6928503513336182 644.5447998046875 0.16983720660209656 1002.0587768554688 0.3318480849266052 0.9123921 0.2279982715845108 True -14 40530 29.431706190109253 0.6966164112091064 602.5760498046875 0.19048160314559937 1002.1978149414062 0.3304761052131653 0.91537887 0.21167993545532227 True -15 43232 29.40531635284424 0.6930949687957764 601.2330932617188 0.16999982297420502 999.704345703125 0.3326559364795685 0.91876054 0.19751600921154022 True -16 45934 29.4354567527771 0.6935968399047852 646.9696044921875 0.24112142622470856 998.4482421875 0.3329050540924072 0.9205898 0.18872492015361786 True -17 48636 29.380656480789185 0.9523837566375732 740.6910400390625 0.14240917563438416 997.8178100585938 0.33382874727249146 0.92361385 0.1830519139766693 True -18 51338 29.376758575439453 0.6891872882843018 763.6660766601562 0.15858277678489685 998.443115234375 0.33352088928222656 0.92412317 0.18113937973976135 True -19 54040 29.433815717697144 0.6908104419708252 694.4451904296875 0.12602700293064117 998.876708984375 0.3330095410346985 0.9220472 0.18122808635234833 False diff --git a/ENCSR598RVJ/cherimoya.fold_1.performance.tsv b/ENCSR598RVJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0252431781ed8211247f2926a99f81522b61a294..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -998.443115234375 0.43307387828826904 0.33352088928222656 0.13707436621189117 0.9241231679916382 0.9153380393981934 0.18113937973976135 \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_2.evaluate.json b/ENCSR598RVJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8ede26f1bad1e16ffda5053b9cbd1826e5b881f2..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF145DWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_2.fit.json b/ENCSR598RVJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 9aacfc42f075ac9b501e4fea8ebed7fc43c819e0..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF145DWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_2.log b/ENCSR598RVJ/cherimoya.fold_2.log deleted file mode 100644 index d77dffc8cd6a484c30da525f035371c9322b7a14..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 36.44284653663635 3.8697052001953125 766.2006225585938 0.28773385286331177 1041.8648681640625 0.2360476851463318 0.79652274 5.150004863739014 True -1 5742 32.471498250961304 0.6271038055419922 730.19189453125 0.375643789768219 959.4359741210938 0.28005579113960266 0.843659 1.069758415222168 True -2 8613 31.91596746444702 1.4116895198822021 714.3319091796875 0.25748729705810547 944.5263061523438 0.2841222882270813 0.8564739 0.4340064227581024 True -3 11484 31.905856609344482 0.6060869693756104 726.6019897460938 0.29610559344291687 932.0000610351562 0.2910049855709076 0.87223756 0.36350685358047485 True -4 14355 31.86019468307495 0.5997734069824219 753.6339111328125 0.3034767508506775 927.5108032226562 0.29354506731033325 0.8725654 0.33628636598587036 True -5 17226 31.88265872001648 1.5267784595489502 897.9775390625 0.40810245275497437 924.5850219726562 0.2931903004646301 0.88116056 0.2482888102531433 True -6 20097 31.865824937820435 0.5951852798461914 802.7757568359375 0.3372665345668793 922.90966796875 0.29415443539619446 0.8840439 0.2448270171880722 True -7 22968 31.88385534286499 2.826697826385498 779.9777221679688 0.33454132080078125 918.799072265625 0.2980586290359497 0.8857486 0.26449066400527954 True -8 25839 31.977083206176758 1.291191816329956 787.6055908203125 0.24352112412452698 916.2122802734375 0.29928842186927795 0.88852865 0.269773006439209 True -9 28710 31.909035444259644 0.6067423820495605 754.345458984375 0.2517789602279663 913.4822998046875 0.3006952106952667 0.89136255 0.25551939010620117 True -10 31581 31.8569393157959 0.5782144069671631 856.6607055664062 0.2765646278858185 910.2107543945312 0.3032365143299103 0.89596784 0.24146772921085358 True -11 34452 31.847651720046997 0.5995452404022217 680.41357421875 0.3532126247882843 908.7984008789062 0.3033841550350189 0.8996756 0.22762322425842285 True -12 37323 31.858330965042114 0.5871138572692871 666.964111328125 0.1451016217470169 908.44384765625 0.30283334851264954 0.9031848 0.20838522911071777 True -13 40194 31.89825439453125 0.5964095592498779 638.6490478515625 0.26798999309539795 905.7950439453125 0.304953396320343 0.90451 0.20207975804805756 True -14 43065 31.864785194396973 2.6716208457946777 604.356201171875 0.206324964761734 904.0701904296875 0.30575668811798096 0.90923136 0.1895228624343872 True -15 45936 31.90993881225586 0.5832626819610596 674.5946044921875 0.21996325254440308 901.7423706054688 0.30757835507392883 0.9114133 0.1812460720539093 True -16 48807 31.92665386199951 0.5992293357849121 715.4100952148438 0.1819296032190323 900.94970703125 0.3083186447620392 0.91138166 0.1750633865594864 False -17 51678 31.884413480758667 0.5892136096954346 760.7613525390625 0.14672136306762695 901.598388671875 0.3076155185699463 0.9141935 0.1719617396593094 True -18 54549 31.92272424697876 0.6082344055175781 631.3564453125 0.21828311681747437 902.6093139648438 0.30708423256874084 0.91257626 0.17147885262966156 False -19 57420 31.85034203529358 1.2604146003723145 674.9407958984375 0.13085755705833435 902.2332763671875 0.3074492812156677 0.9124559 0.17185814678668976 False diff --git a/ENCSR598RVJ/cherimoya.fold_2.performance.tsv b/ENCSR598RVJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e0ed9c55aa4e74d115e0321b3d3f7855c3b928e6..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -901.598388671875 0.4518897831439972 0.3076155185699463 0.11337239295244217 0.9141935110092163 0.9002218842506409 0.1719617396593094 \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_3.evaluate.json b/ENCSR598RVJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b27491d14b0a90855d189d4848b85681f699e823..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF145DWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_3.fit.json b/ENCSR598RVJ/cherimoya.fold_3.fit.json deleted file mode 100644 index fd2280c1c05e9504d3c21caecf83cfba7109356c..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF145DWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_3.log b/ENCSR598RVJ/cherimoya.fold_3.log deleted file mode 100644 index de1fb11c79d45b03352b5d8488502a7aa9957326..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.671610832214355 3.3674306869506836 707.3619995117188 0.3182670772075653 948.24462890625 0.23583248257637024 0.78687876 5.286741256713867 True -1 5454 30.043651580810547 0.6717724800109863 915.58984375 0.3310829997062683 873.5928955078125 0.28187358379364014 0.84664464 1.0120265483856201 True -2 8181 30.289815187454224 0.5743775367736816 668.7071533203125 0.6698707342147827 861.8910522460938 0.2867390811443329 0.8562146 0.4104205369949341 True -3 10908 30.264670848846436 0.6765918731689453 748.520751953125 0.2836759090423584 853.2182006835938 0.2941030263900757 0.8652611 0.38226762413978577 True -4 13635 30.231115579605103 0.5475037097930908 724.2203369140625 0.4153938889503479 851.20458984375 0.29353398084640503 0.87166494 0.365610808134079 True -5 16362 30.210654735565186 0.555901050567627 841.9482421875 0.406589150428772 848.97216796875 0.29402682185173035 0.8741686 0.35164666175842285 True -6 19089 30.240126848220825 0.5541605949401855 785.921630859375 0.27053916454315186 845.2879638671875 0.2966972589492798 0.8767845 0.37389999628067017 True -7 21816 30.212613821029663 0.5537278652191162 651.9442749023438 0.18767744302749634 843.5379638671875 0.29725223779678345 0.8796301 0.34142357110977173 True -8 24543 30.214282274246216 0.5523247718811035 810.9217529296875 0.24973544478416443 841.5245971679688 0.2986083924770355 0.88135463 0.3416579067707062 True -9 27270 30.214823961257935 0.5568783283233643 695.4920043945312 0.22943666577339172 838.4976196289062 0.3005566895008087 0.88614935 0.2972770929336548 True -10 29997 32.25527238845825 21.37781858444214 791.4356689453125 0.1365567296743393 835.604736328125 0.3027227222919464 0.8904732 0.28652459383010864 True -11 32724 31.422677040100098 28.297053813934326 693.572998046875 0.17338880896568298 835.10546875 0.3027098774909973 0.89386433 0.27454107999801636 True -12 35451 30.423925399780273 0.7010273933410645 780.8046875 0.19664719700813293 833.8434448242188 0.30273911356925964 0.896173 0.2662842571735382 True -13 38178 30.198322296142578 1.177067756652832 839.5181884765625 0.18490740656852722 830.9380493164062 0.3055659532546997 0.9010743 0.2530348300933838 True -14 40905 30.31807804107666 0.5842342376708984 799.8427734375 0.2552158832550049 831.1376953125 0.30394238233566284 0.90490884 0.2269035130739212 True -15 43632 30.222898721694946 0.561845064163208 613.444580078125 0.16389967501163483 827.8076782226562 0.30725228786468506 0.9100431 0.20395953953266144 True -16 46359 30.290705680847168 0.5650420188903809 920.92626953125 0.1862116903066635 826.28076171875 0.30771490931510925 0.9120133 0.18908412754535675 True -17 49086 30.288609266281128 0.5602011680603027 723.7090454101562 0.15195849537849426 826.765625 0.30823439359664917 0.91431236 0.1800743192434311 True -18 51813 30.282145261764526 0.5661072731018066 695.9215087890625 0.19193099439144135 829.0025634765625 0.30468297004699707 0.9155789 0.1767519861459732 True -19 54540 30.279125928878784 1.3804800510406494 717.5672607421875 0.251930832862854 826.5663452148438 0.3076472282409668 0.9147974 0.17567940056324005 False diff --git a/ENCSR598RVJ/cherimoya.fold_3.performance.tsv b/ENCSR598RVJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 75bb714c9c1996b9420c5a4c758327d535d4446e..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -829.0025634765625 0.45781436562538147 0.3046829104423523 0.11084254086017609 0.9155789017677307 0.8911081552505493 0.1767519861459732 \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_4.evaluate.json b/ENCSR598RVJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f811612903bcb2c6a0e1735b2b138693c632d779..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF145DWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_4.fit.json b/ENCSR598RVJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 5ea3da06f5b7fc331b2e0433efff074c883a91e5..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF145DWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR598RVJ/cherimoya.fold_4.log b/ENCSR598RVJ/cherimoya.fold_4.log deleted file mode 100644 index 6d59ef31d51a8c9af441fd2764008fc08151a256..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2799 35.954193353652954 3.5509824752807617 586.138427734375 0.39281126856803894 903.2936401367188 0.23302814364433289 0.8030539 4.522602558135986 True -1 5598 31.09666872024536 1.078345775604248 735.6770629882812 0.40117835998535156 844.9854736328125 0.27103134989738464 0.83914953 0.763963520526886 True -2 8397 31.117316484451294 0.7001388072967529 882.8726806640625 0.28403374552726746 836.3614501953125 0.2738240659236908 0.8478925 0.42445194721221924 True -3 11196 30.99992871284485 0.6202335357666016 778.8154296875 0.21486100554466248 825.7396850585938 0.2803587317466736 0.85957134 0.33022114634513855 True -4 13995 31.040037631988525 0.6137282848358154 773.16552734375 0.3927086293697357 821.169921875 0.28227224946022034 0.86732394 0.2901102900505066 True -5 16794 31.066566228866577 0.6377809047698975 763.1773681640625 0.22221162915229797 817.3780517578125 0.28421497344970703 0.8734902 0.2588794231414795 True -6 19593 30.519874334335327 0.6172568798065186 789.6119384765625 0.3523145318031311 813.50048828125 0.28701967000961304 0.8787703 0.26548847556114197 True -7 22392 30.449397563934326 0.6165697574615479 615.64892578125 0.29021698236465454 810.9656372070312 0.28865471482276917 0.88242894 0.2466716766357422 True -8 25191 30.39325714111328 22.034404754638672 778.86376953125 0.25670355558395386 809.7221069335938 0.2894859313964844 0.8866929 0.25274568796157837 True -9 27990 30.450994968414307 18.617619514465332 685.1317138671875 0.1620442271232605 806.7277221679688 0.2916947901248932 0.8906692 0.23568148910999298 True -10 30789 30.50069499015808 1.5915250778198242 808.1021118164062 0.1498376578092575 805.0040283203125 0.2927895486354828 0.8949076 0.21558193862438202 True -11 33588 30.506715774536133 1.108769416809082 759.6795654296875 0.26578372716903687 803.4274291992188 0.2937716543674469 0.89824766 0.21150796115398407 True -12 36387 30.472642183303833 0.6025643348693848 755.5133666992188 0.2781412899494171 802.7551879882812 0.29403871297836304 0.9015875 0.19818797707557678 True -13 39186 30.45260787010193 0.6146636009216309 851.906982421875 0.22186031937599182 800.4100952148438 0.2960250973701477 0.90516317 0.18731838464736938 True -14 41985 30.436480045318604 1.706617832183838 619.2470092773438 0.21957272291183472 799.1556396484375 0.2969204783439636 0.90925443 0.17674285173416138 True -15 44784 30.491684436798096 0.6012613773345947 757.9449462890625 0.24005474150180817 797.9437866210938 0.2973960340023041 0.91137516 0.16644853353500366 True -16 47583 30.48834204673767 0.6251211166381836 841.7454223632812 0.169014111161232 797.3987426757812 0.2979554533958435 0.91298944 0.15791021287441254 True -17 50382 30.518176555633545 0.6071138381958008 709.6285400390625 0.1911720633506775 798.0772094726562 0.2971746325492859 0.91665334 0.15345332026481628 True -18 53181 30.470885753631592 0.6115529537200928 705.4215698242188 0.20951610803604126 799.9434814453125 0.2960890233516693 0.91611755 0.15205398201942444 False -19 55980 30.618115425109863 0.6049690246582031 584.1912841796875 0.16689778864383698 798.602783203125 0.2977832555770874 0.91601866 0.1514056921005249 False diff --git a/ENCSR598RVJ/cherimoya.fold_4.performance.tsv b/ENCSR598RVJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b907bbda82e55b3cb84a4f9978fa405e9a7748db..0000000000000000000000000000000000000000 --- a/ENCSR598RVJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -798.0772094726562 0.4649844765663147 0.2971746623516083 0.10399477183818817 0.9166533350944519 0.891524612903595 0.15345332026481628 \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_0.evaluate.json b/ENCSR603LVR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f116ecdbf8ed56eff446779ea442cc9804909bb9..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969NAE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_0.fit.json b/ENCSR603LVR/cherimoya.fold_0.fit.json deleted file mode 100644 index 74dff46c1f924d80151c39e3b45e4b7cdd6c22d6..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF969NAE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_0.log b/ENCSR603LVR/cherimoya.fold_0.log deleted file mode 100644 index 71ae1dd2d71029ad8aaed45658939fcd9a98f892..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1382 18.824612617492676 3.1827335357666016 410.03741455078125 1.7760745286941528 878.9808959960938 0.43704915046691895 0.59205836 23.063119888305664 True -1 2764 15.235016107559204 0.26765871047973633 539.38916015625 1.6402111053466797 633.419189453125 0.5591487884521484 0.64102477 17.186302185058594 True -2 4146 15.243408918380737 0.2613990306854248 448.2149963378906 1.5265306234359741 536.0764770507812 0.6550396084785461 0.64246786 9.642816543579102 True -3 5528 15.058781623840332 0.3006570339202881 379.07427978515625 1.3690906763076782 503.98492431640625 0.6821005940437317 0.63654804 4.071338176727295 False -4 6910 14.939718008041382 0.26184701919555664 475.77728271484375 1.2442384958267212 494.0193176269531 0.6906534433364868 0.66095525 2.349564790725708 True -5 8292 14.956066131591797 0.26652956008911133 375.3094482421875 1.5591225624084473 487.0659484863281 0.6970994472503662 0.66052675 1.8678051233291626 False -6 9674 14.926764249801636 0.26218342781066895 346.6866455078125 1.8554232120513916 482.8898620605469 0.7011775970458984 0.67089653 1.6716505289077759 True -7 11056 14.94144868850708 0.26190876960754395 359.12347412109375 1.3690404891967773 478.6808166503906 0.7055605053901672 0.67425394 1.5749084949493408 True -8 12438 14.91810154914856 0.25833630561828613 344.6468200683594 1.1944234371185303 474.4007873535156 0.7091271877288818 0.679194 1.4317227602005005 True -9 13820 14.926134586334229 0.265735387802124 358.8348388671875 0.9786475896835327 471.8123779296875 0.7126607894897461 0.6952732 1.3219022750854492 True -10 15202 14.938897848129272 0.2575705051422119 439.13726806640625 1.5147411823272705 468.4395751953125 0.7154636383056641 0.7090811 1.1751160621643066 True -11 16584 14.940383434295654 1.1231532096862793 345.49273681640625 1.1067378520965576 465.6205139160156 0.7179980874061584 0.71684116 1.1312346458435059 True -12 17966 14.984177112579346 0.2603778839111328 283.0177917480469 1.053436279296875 462.78985595703125 0.7209282517433167 0.7234917 1.085789680480957 True -13 19348 14.959095478057861 0.2634570598602295 272.6279296875 0.8293094635009766 460.5282287597656 0.7229617238044739 0.72732633 1.0500788688659668 True -14 20730 14.938915967941284 0.2622191905975342 401.5492858886719 1.0000550746917725 459.37322998046875 0.7239075303077698 0.73168904 1.0409616231918335 True -15 22112 14.94810676574707 0.26247477531433105 368.0989074707031 0.6832575798034668 458.980224609375 0.7242482304573059 0.73653525 1.0330898761749268 True -16 23494 14.94603705406189 0.25939130783081055 334.2865295410156 0.7326017022132874 459.1618957519531 0.7236286997795105 0.7369387 1.047663927078247 True -17 24876 14.944504976272583 0.2581906318664551 330.9521789550781 0.45161086320877075 460.3083190917969 0.7225901484489441 0.7349989 1.0759696960449219 False -18 26258 14.963681936264038 0.26973605155944824 252.42669677734375 0.46171170473098755 460.77557373046875 0.7215277552604675 0.73190254 1.1091992855072021 False -19 27640 14.938977003097534 0.2612769603729248 391.7223205566406 0.6187691688537598 461.50189208984375 0.72086101770401 0.72893924 1.1301268339157104 False diff --git a/ENCSR603LVR/cherimoya.fold_0.performance.tsv b/ENCSR603LVR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 67e03c520dc4afb2709d891389e3073c9f83d52f..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.1618957519531 0.2365509420633316 0.7236286997795105 0.3002929091453552 0.7369387149810791 0.7136736512184143 1.047663927078247 \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_1.evaluate.json b/ENCSR603LVR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 40bf6b94de8b43010695dce6f8ba8fe14c86beca..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969NAE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_1.fit.json b/ENCSR603LVR/cherimoya.fold_1.fit.json deleted file mode 100644 index 6f3dd54fa1cfa3189d7767cb07e024f01ae1ead2..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF969NAE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_1.log b/ENCSR603LVR/cherimoya.fold_1.log deleted file mode 100644 index 9402e6413c274997800b757f51b11ca5af876a20..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1353 18.587528467178345 3.7619848251342773 402.38983154296875 2.0024964809417725 997.0496826171875 0.45083197951316833 0.5474748 25.63941192626953 True -1 2706 14.942258834838867 0.4440889358520508 292.9552917480469 2.346871852874756 713.7703247070312 0.5739215612411499 0.6308956 19.157846450805664 True -2 4059 14.980890035629272 1.2203571796417236 395.59381103515625 1.7492119073867798 599.6657104492188 0.6724296808242798 0.6541823 10.479082107543945 True -3 5412 14.936943054199219 0.4296226501464844 328.077392578125 1.752629041671753 560.033447265625 0.7059680819511414 0.6500272 4.621582984924316 False -4 6765 14.973273038864136 1.379945993423462 392.1497802734375 1.918559193611145 547.6392211914062 0.7160266041755676 0.6644145 2.8135125637054443 True -5 8118 14.972270011901855 0.42888307571411133 335.04205322265625 1.4475280046463013 540.103759765625 0.7219933867454529 0.6695665 2.1441903114318848 True -6 9471 14.942071914672852 2.077590227127075 305.1949462890625 1.545677661895752 536.0736694335938 0.725017786026001 0.68667805 1.8795182704925537 True -7 10824 14.931572675704956 0.42938685417175293 462.2734069824219 1.2867835760116577 533.1329345703125 0.72816401720047 0.6920963 1.7000162601470947 True -8 12177 14.95580792427063 1.6078007221221924 345.8202819824219 0.9851603507995605 528.8540649414062 0.7314925789833069 0.6981815 1.5132499933242798 True -9 13530 14.990985870361328 11.377767324447632 351.7293701171875 1.5694642066955566 524.9546508789062 0.7348867654800415 0.70743304 1.4072368144989014 True -10 14883 14.970239639282227 0.43251752853393555 423.2581787109375 1.260483980178833 522.4232788085938 0.7378658652305603 0.7105938 1.3332716226577759 True -11 16236 14.92934799194336 0.4374241828918457 358.82275390625 0.8485655784606934 518.2801513671875 0.7409103512763977 0.7213794 1.2009398937225342 True -12 17589 14.94286060333252 0.4349367618560791 355.4332275390625 1.3565735816955566 515.8878784179688 0.7427452206611633 0.72762424 1.1422139406204224 True -13 18942 14.948063611984253 0.43474602699279785 321.05224609375 0.688481330871582 513.5809936523438 0.7443561553955078 0.73641676 1.0836069583892822 True -14 20295 14.980462074279785 0.42839598655700684 272.0645751953125 1.5172936916351318 511.7958679199219 0.7456395626068115 0.74485147 1.0349115133285522 True -15 21648 14.939870595932007 0.4342527389526367 339.1889343261719 0.6426947712898254 510.9146728515625 0.7462705969810486 0.7531809 1.006287693977356 True -16 23001 14.991326570510864 0.42870497703552246 347.290283203125 0.7263710498809814 510.67236328125 0.7463047504425049 0.7527088 1.0275161266326904 False -17 24354 14.944457769393921 0.4253242015838623 318.4605712890625 0.8579910397529602 511.3654479980469 0.7453368902206421 0.7538205 1.0500715970993042 True -18 25707 14.973508834838867 0.42667555809020996 339.1778869628906 0.37211039662361145 511.5898742675781 0.7444844245910645 0.7504747 1.0693949460983276 False -19 27060 14.93929648399353 0.419384241104126 354.3769226074219 0.549628496170044 512.3184814453125 0.7438918948173523 0.7496731 1.0880297422409058 False diff --git a/ENCSR603LVR/cherimoya.fold_1.performance.tsv b/ENCSR603LVR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ce70a3cb77380df49d9bc2ec96126c126a69df67..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -511.3654479980469 0.21786513924598694 0.7453369498252869 0.32888108491897583 0.7538204789161682 0.7541628479957581 1.0500715970993042 \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_2.evaluate.json b/ENCSR603LVR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 69a71028e7e3eb59d68a5abbeb1719e80e3b3e0e..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969NAE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_2.fit.json b/ENCSR603LVR/cherimoya.fold_2.fit.json deleted file mode 100644 index 98686237a62c62a6008edf476fa48e37decb7800..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF969NAE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_2.log b/ENCSR603LVR/cherimoya.fold_2.log deleted file mode 100644 index 32e5864104b6b31c47045012f3dfd37bfb1b1084..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1458 19.773560762405396 3.2450642585754395 466.996337890625 2.884056568145752 905.0907592773438 0.4450511038303375 0.5691659 23.316211700439453 True -1 2916 16.126689434051514 0.3003685474395752 510.5043640136719 1.768897533416748 657.2076416015625 0.5761978030204773 0.64291525 17.563945770263672 True -2 4374 16.386658906936646 0.30402588844299316 370.206298828125 2.0433876514434814 551.0185546875 0.670714795589447 0.64528704 8.348052024841309 True -3 5832 16.124470233917236 0.30851054191589355 371.3773193359375 1.983323097229004 520.3549194335938 0.6930333375930786 0.6595432 3.8047935962677 True -4 7290 16.116658449172974 0.3042011260986328 398.0435791015625 1.2415152788162231 510.13360595703125 0.7018250823020935 0.6616865 2.528292655944824 True -5 8748 16.09104633331299 0.302213191986084 293.1468505859375 1.7222892045974731 504.3017272949219 0.7066994309425354 0.6805352 1.9290211200714111 True -6 10206 16.10625410079956 0.30002593994140625 341.76922607421875 1.416782259941101 499.955322265625 0.7107942700386047 0.6932456 1.7188178300857544 True -7 11664 16.076725721359253 0.2968437671661377 345.5318298339844 1.8468000888824463 497.2367858886719 0.7144362926483154 0.7002996 1.561396598815918 True -8 13122 16.109618425369263 0.29256534576416016 471.18353271484375 1.5552126169204712 493.3441467285156 0.718174934387207 0.70490575 1.4723479747772217 True -9 14580 16.135275840759277 0.3107428550720215 285.31695556640625 1.1433508396148682 489.6146545410156 0.7220690846443176 0.7094923 1.3976894617080688 True -10 16038 16.110137462615967 0.29567623138427734 332.26287841796875 1.2754333019256592 486.13031005859375 0.7254883050918579 0.721111 1.2710423469543457 True -11 17496 16.155982971191406 0.29950499534606934 384.9898376464844 1.4689737558364868 483.59185791015625 0.7277648448944092 0.72603464 1.22046959400177 True -12 18954 16.086132764816284 0.29646897315979004 398.80010986328125 1.3065932989120483 481.0854187011719 0.729951798915863 0.73026997 1.1381652355194092 True -13 20412 16.08333992958069 0.3032076358795166 287.1639709472656 1.4350255727767944 479.30487060546875 0.7314811944961548 0.734577 1.1033421754837036 True -14 21870 16.10927963256836 0.2992069721221924 343.03985595703125 0.9045665264129639 478.2515563964844 0.7325119972229004 0.7404961 1.0705997943878174 True -15 23328 16.079785108566284 10.415855407714844 288.19561767578125 0.9279407262802124 477.2572021484375 0.7330616116523743 0.7448995 1.0502349138259888 True -16 24786 16.80548596382141 0.30762195587158203 369.3707275390625 0.8876885175704956 477.5877380371094 0.7326834201812744 0.74290335 1.0796693563461304 False -17 26244 16.138545036315918 0.30492186546325684 382.0975341796875 0.564710795879364 477.4565734863281 0.732213020324707 0.7391853 1.107499361038208 False -18 27702 17.070661783218384 14.479615688323975 383.9180908203125 0.4423064589500427 478.1308288574219 0.7313379645347595 0.73997617 1.108397126197815 False -19 29160 16.299763441085815 0.31330442428588867 333.94451904296875 0.5112254619598389 478.3411865234375 0.7307754158973694 0.73795915 1.1207530498504639 False diff --git a/ENCSR603LVR/cherimoya.fold_2.performance.tsv b/ENCSR603LVR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7b4f3ac4cacb17217507c13dd688ad7135663adc..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -477.2572021484375 0.2294234335422516 0.733061671257019 0.312326580286026 0.7448995113372803 0.7334432005882263 1.0502349138259888 \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_3.evaluate.json b/ENCSR603LVR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ff09e123e67ea6f17e75d13baf6832ad5e25fb95..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969NAE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_3.fit.json b/ENCSR603LVR/cherimoya.fold_3.fit.json deleted file mode 100644 index dcd233a55b9b928d252d8da15e3262ef37a41855..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF969NAE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_3.log b/ENCSR603LVR/cherimoya.fold_3.log deleted file mode 100644 index 611a2da397b8a37f0866b21af59d84a99b60be59..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1410 19.12751841545105 3.2303946018218994 444.3975524902344 2.680117607116699 879.437255859375 0.4475894570350647 0.59107596 23.827077865600586 True -1 2820 15.543405294418335 0.30138182640075684 441.7240905761719 2.0150365829467773 635.6201171875 0.5752070546150208 0.6407716 17.40359878540039 True -2 4230 15.622838258743286 0.28916239738464355 422.3913879394531 1.795339822769165 552.919677734375 0.659419596195221 0.6428322 8.348176002502441 True -3 5640 15.552659749984741 0.2880995273590088 404.9840087890625 1.6297742128372192 519.00244140625 0.6862963438034058 0.6417759 3.294314384460449 False -4 7050 15.567455053329468 0.2921919822692871 389.3193054199219 1.147237777709961 508.11431884765625 0.6954612135887146 0.6587119 2.1189334392547607 True -5 8460 15.527468204498291 0.2874729633331299 331.7355651855469 1.427788257598877 502.9783935546875 0.7003504037857056 0.66125554 1.6886533498764038 True -6 9870 15.534698009490967 0.29218626022338867 419.8198547363281 1.248976707458496 498.05438232421875 0.7048258781433105 0.6656247 1.4779247045516968 True -7 11280 15.518762588500977 0.2915828227996826 415.1057434082031 2.1128158569335938 494.7177429199219 0.7081095576286316 0.6756569 1.3606789112091064 True -8 12690 15.559786796569824 0.2913532257080078 362.0810546875 0.9756736755371094 493.22821044921875 0.710973858833313 0.6847513 1.4087905883789062 True -9 14100 15.539644241333008 0.2903721332550049 362.9347839355469 1.068068265914917 489.3921203613281 0.7140557169914246 0.68837893 1.3096367120742798 True -10 15510 15.586064338684082 0.2921907901763916 364.6933288574219 1.7858247756958008 485.5444641113281 0.7172579765319824 0.70678467 1.1985729932785034 True -11 16920 15.602607011795044 0.2961921691894531 362.7915344238281 0.8712464570999146 483.2500305175781 0.7196248173713684 0.71798015 1.1548490524291992 True -12 18330 15.566156148910522 0.29287099838256836 338.2287902832031 1.3145098686218262 481.0740051269531 0.7217217087745667 0.72418135 1.0787867307662964 True -13 19740 15.563493013381958 0.29244089126586914 325.62664794921875 0.8636846542358398 479.1482849121094 0.7236342430114746 0.731748 1.0491563081741333 True -14 21150 15.540383338928223 0.2883617877960205 389.3900146484375 0.963110089302063 477.3807678222656 0.7249827980995178 0.7377594 1.0371500253677368 True -15 22560 15.53507661819458 0.2903313636779785 363.6875915527344 0.7635592222213745 476.1310119628906 0.725462794303894 0.74128443 1.0208053588867188 True -16 23970 15.56456208229065 0.28891587257385254 336.84588623046875 0.6137589812278748 476.5085144042969 0.7252587676048279 0.74393314 1.042810082435608 True -17 25380 15.5552659034729 0.2904655933380127 322.6158142089844 0.5128569602966309 476.7189025878906 0.7246881723403931 0.74410033 1.078011155128479 True -18 26790 15.526268482208252 0.28950929641723633 400.99127197265625 0.4368739724159241 477.4200744628906 0.7238303422927856 0.7404271 1.111291766166687 False -19 28200 15.417704105377197 0.2853660583496094 344.8396301269531 0.4378713369369507 477.579345703125 0.7232913374900818 0.7374204 1.1289241313934326 False diff --git a/ENCSR603LVR/cherimoya.fold_3.performance.tsv b/ENCSR603LVR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9d0a5be9e3447672f9497b6bc284d90289c0efc4..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -476.7189025878906 0.23238135874271393 0.7246882319450378 0.30651870369911194 0.7441003322601318 0.7403746843338013 1.078011155128479 \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_4.evaluate.json b/ENCSR603LVR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e295c32a7b0b604f71581f326929a362fec1de9d..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF969NAE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_4.fit.json b/ENCSR603LVR/cherimoya.fold_4.fit.json deleted file mode 100644 index 90a299d175e3bd526d80c0468797e655734a4d3a..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF969NAE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR603LVR/cherimoya.fold_4.log b/ENCSR603LVR/cherimoya.fold_4.log deleted file mode 100644 index 37cbee1f9a02e42c008a0c6f65d47c51b5af239a..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1389 18.994325399398804 3.234788417816162 378.85748291015625 2.412283420562744 846.2996826171875 0.43816956877708435 0.5710428 22.93218994140625 True -1 2778 15.390864133834839 0.26813220977783203 476.5675354003906 2.28252911567688 605.4432983398438 0.5598796606063843 0.63395756 14.717668533325195 True -2 4167 15.322888612747192 0.2544209957122803 464.4601135253906 1.7724947929382324 525.891357421875 0.6497158408164978 0.6258443 8.6214599609375 False -3 5556 15.067165613174438 0.2495710849761963 377.60162353515625 1.6229082345962524 496.0409240722656 0.6759650111198425 0.63805485 3.787302017211914 True -4 6945 15.030216217041016 0.24802374839782715 421.33746337890625 1.8305671215057373 483.53509521484375 0.6856927275657654 0.6463221 2.4756176471710205 True -5 8334 15.041738510131836 0.24541091918945312 423.90087890625 1.2498610019683838 477.50439453125 0.6916398406028748 0.65998024 1.8740304708480835 True -6 9723 15.00871753692627 0.24711871147155762 297.93243408203125 1.3618979454040527 473.2438659667969 0.6956477761268616 0.6659176 1.6567152738571167 True -7 11112 15.047817707061768 0.2512505054473877 363.3284912109375 0.9955530166625977 470.4626770019531 0.6993973851203918 0.67135894 1.6374545097351074 True -8 12501 15.050719976425171 0.24681591987609863 454.4576110839844 1.5968151092529297 466.24224853515625 0.7034589052200317 0.6860593 1.4241935014724731 True -9 13890 15.067118167877197 0.24952363967895508 391.9927062988281 1.7718344926834106 462.8603515625 0.7061104774475098 0.69856226 1.2656527757644653 True -10 15279 15.151566505432129 0.24791836738586426 344.8866882324219 1.1621356010437012 460.2303771972656 0.7099885940551758 0.70453775 1.2100224494934082 True -11 16668 15.081347703933716 0.24911093711853027 339.1611022949219 0.999062716960907 457.8739318847656 0.7123204469680786 0.7117717 1.1248643398284912 True -12 18057 15.103125095367432 0.24996232986450195 380.13189697265625 1.6274304389953613 455.5022277832031 0.7145062685012817 0.71866286 1.0614770650863647 True -13 19446 15.063523530960083 0.24808669090270996 403.6333923339844 1.0781855583190918 454.3199768066406 0.7162553668022156 0.72428274 1.0414178371429443 True -14 20835 15.107239484786987 0.2531898021697998 371.4780578613281 1.1120175123214722 453.0867004394531 0.7172895073890686 0.7291148 1.0307170152664185 True -15 22224 15.14497709274292 0.2517719268798828 348.7351379394531 0.6962161660194397 452.8067626953125 0.7174555659294128 0.73023444 1.0397214889526367 True -16 23613 15.1014404296875 0.25064730644226074 304.32476806640625 0.7572882175445557 452.8786315917969 0.717255711555481 0.73098564 1.0491224527359009 True -17 25002 15.10399580001831 0.2551760673522949 309.12506103515625 0.5790866017341614 453.1683654785156 0.7163530588150024 0.72665566 1.094929814338684 False -18 26391 15.113543510437012 0.24974846839904785 316.7744140625 0.8584709167480469 453.691650390625 0.7156127095222473 0.72396916 1.1206114292144775 False -19 27780 15.530366897583008 5.876013517379761 329.84429931640625 0.36875802278518677 454.5186767578125 0.7149112224578857 0.72167075 1.1430786848068237 False diff --git a/ENCSR603LVR/cherimoya.fold_4.performance.tsv b/ENCSR603LVR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 47899185dff524fbeb4577b80131ec4e7cf898db..0000000000000000000000000000000000000000 --- a/ENCSR603LVR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -452.8786315917969 0.23997379839420319 0.7172556519508362 0.29725411534309387 0.7309856414794922 0.7073127031326294 1.0491224527359009 \ No newline at end of file diff --git a/ENCSR604FER/cherimoya.fold_0.evaluate.json b/ENCSR604FER/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 02947b000ee19eb3d4c99c2615d1336f53f37c84..0000000000000000000000000000000000000000 --- a/ENCSR604FER/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF170CPH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_0.evaluate.json b/ENCSR604YEQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2cf4499f14ee00016b920108c0a8d7facbb30335..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118YHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_0.fit.json b/ENCSR604YEQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 5b4b7eb460117b80714a32dd86db629542f65d2f..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF118YHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_0.log b/ENCSR604YEQ/cherimoya.fold_0.log deleted file mode 100644 index 8d3c9e31b5c814e010010ea7508015a6c8426e6c..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2205 30.11524224281311 4.309711217880249 249.2804412841797 1.2217085361480713 405.3035583496094 0.44136008620262146 0.47871608 8.877245903015137 True -1 4410 24.468621969223022 0.5226507186889648 229.49072265625 1.127662181854248 344.8674621582031 0.5690262913703918 0.5695011 3.822662830352783 True -2 6615 24.451839208602905 0.4732215404510498 254.49874877929688 0.7175397872924805 332.3855285644531 0.597601592540741 0.5747219 1.5665265321731567 True -3 8820 24.386987447738647 0.45912814140319824 209.55520629882812 1.1129310131072998 329.6424865722656 0.6039389371871948 0.5810251 1.1255571842193604 True -4 11025 24.38974690437317 0.4556846618652344 265.3385009765625 0.5525127649307251 328.4695129394531 0.607292890548706 0.5942938 0.9375518560409546 True -5 13230 24.390872478485107 0.44814133644104004 210.36801147460938 0.901053249835968 326.4236755371094 0.6111729741096497 0.60687226 0.7819317579269409 True -6 15435 24.384105920791626 1.2455694675445557 255.38320922851562 0.5550757646560669 325.6010437011719 0.6138449311256409 0.60747814 0.7639921307563782 True -7 17640 24.410619735717773 0.4652397632598877 281.13079833984375 0.8437648415565491 324.60858154296875 0.6164401769638062 0.6157296 0.704788863658905 True -8 19845 24.45132303237915 0.5175015926361084 265.85009765625 0.6684212684631348 323.4202575683594 0.6191123127937317 0.6190245 0.6893994212150574 True -9 22050 24.400387287139893 0.4596278667449951 250.4951629638672 0.583293080329895 322.26483154296875 0.6215706467628479 0.6253628 0.6576668620109558 True -10 24255 24.420994520187378 0.4650716781616211 203.19203186035156 0.7117478847503662 321.4212646484375 0.6235035061836243 0.62748396 0.6329264044761658 True -11 26460 24.439119338989258 0.4577014446258545 262.388671875 0.64430832862854 320.42852783203125 0.6257339119911194 0.6321496 0.6016852259635925 True -12 28665 24.4002628326416 0.4514937400817871 226.31919860839844 0.660241961479187 319.64215087890625 0.6273427605628967 0.64175916 0.5806847810745239 True -13 30870 24.43688178062439 1.4652900695800781 231.17294311523438 0.6585144996643066 318.75238037109375 0.6294780969619751 0.645956 0.5707430243492126 True -14 33075 24.414594650268555 0.45559000968933105 206.16810607910156 0.685552716255188 318.1438903808594 0.6306253671646118 0.65252095 0.5586281418800354 True -15 35280 24.40044593811035 1.5398674011230469 226.57440185546875 0.5160894989967346 317.79193115234375 0.6313067674636841 0.6576235 0.5571900010108948 True -16 37485 24.41559934616089 0.4603142738342285 233.46055603027344 0.5089818835258484 317.7403259277344 0.6312142610549927 0.6590257 0.5509989261627197 True -17 39690 24.451820850372314 0.4525318145751953 228.7955322265625 0.3225248456001282 317.8556213378906 0.6307823657989502 0.6574246 0.5588172078132629 False -18 41895 24.43943691253662 0.4663822650909424 229.95620727539062 0.329655259847641 317.9539489746094 0.630321204662323 0.6543822 0.5711854696273804 False -19 44100 24.403240442276 1.1031482219696045 231.8073272705078 0.2978394329547882 318.1583251953125 0.6298626661300659 0.652416 0.5823960304260254 False diff --git a/ENCSR604YEQ/cherimoya.fold_0.performance.tsv b/ENCSR604YEQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6d98051ef2d0df54f557ce4386d63d99bda6ab54..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.7403259277344 0.30517810583114624 0.6312142610549927 0.21127210557460785 0.6590257287025452 0.6411770582199097 0.5509989261627197 \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_1.evaluate.json b/ENCSR604YEQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1f30e8a375af250c9caef3bc5dec4de0e947d1aa..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118YHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_1.fit.json b/ENCSR604YEQ/cherimoya.fold_1.fit.json deleted file mode 100644 index cc7048ab956a81179b3e5cd123bab89ce234b1f5..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF118YHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_1.log b/ENCSR604YEQ/cherimoya.fold_1.log deleted file mode 100644 index 31ad0561876a29bd0da1c3a68ef1cd2a96383b0d..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2259 29.848698616027832 3.519253730773926 270.4132080078125 0.9812690019607544 377.1225280761719 0.4404429495334625 0.46635503 7.060770511627197 True -1 4518 25.089906454086304 0.7412903308868408 265.9024353027344 0.8389092683792114 327.8349609375 0.5538039207458496 0.55920154 3.0750818252563477 True -2 6777 25.03764510154724 0.5726068019866943 255.94287109375 0.9606651067733765 318.5660705566406 0.5774360299110413 0.5672166 0.9022152423858643 True -3 9036 25.050769090652466 0.4732096195220947 275.86981201171875 1.1101582050323486 315.02569580078125 0.5850515961647034 0.57629746 0.7577744126319885 True -4 11295 24.859419107437134 0.4748084545135498 217.23660278320312 1.0633740425109863 313.6717224121094 0.5887287855148315 0.57827413 0.7389948964118958 True -5 13554 24.580865383148193 0.4937162399291992 232.0329132080078 0.7088778614997864 312.9289855957031 0.5909594893455505 0.58030117 0.710411787033081 True -6 15813 24.505284786224365 0.4911668300628662 203.33609008789062 0.6176639795303345 312.062744140625 0.5937564969062805 0.58411074 0.6569709181785583 True -7 18072 24.485922813415527 0.4924173355102539 243.5317840576172 0.5777689218521118 310.9119873046875 0.5965633392333984 0.5931791 0.6528990268707275 True -8 20331 24.534003973007202 0.5710783004760742 253.3577423095703 0.7744877934455872 310.1319274902344 0.5988066792488098 0.60056275 0.6161869764328003 True -9 22590 24.49335765838623 0.4688541889190674 223.57205200195312 0.8231322765350342 309.1208190917969 0.6008767485618591 0.6077956 0.588276207447052 True -10 24849 24.55085301399231 0.4761197566986084 245.40371704101562 0.8938342332839966 308.2909851074219 0.603115439414978 0.61549646 0.5713921189308167 True -11 27108 24.53519296646118 0.5017032623291016 221.6162567138672 0.657380223274231 307.3292236328125 0.6052179932594299 0.6253044 0.5388491749763489 True -12 29367 24.457098245620728 0.46949124336242676 207.65785217285156 0.6618102788925171 306.664306640625 0.6070556640625 0.63573414 0.5297685265541077 True -13 31626 24.5118567943573 0.4826774597167969 213.48733520507812 0.5123270750045776 306.0214538574219 0.6086110472679138 0.6426403 0.5095122456550598 True -14 33885 24.479919910430908 0.48522257804870605 201.18621826171875 0.5532351136207581 305.4444580078125 0.6102777123451233 0.6521096 0.49707046151161194 True -15 36144 24.53209948539734 0.48267054557800293 256.3980712890625 0.3953824043273926 304.773681640625 0.6111963987350464 0.66076857 0.48662877082824707 True -16 38403 24.505083322525024 0.5022068023681641 253.44400024414062 0.4823547303676605 304.8216857910156 0.611387312412262 0.664722 0.48017004132270813 True -17 40662 24.543121576309204 0.4959540367126465 223.8427734375 0.4050157070159912 304.76214599609375 0.6110507845878601 0.6666298 0.479454904794693 True -18 42921 24.535231590270996 0.5461258888244629 263.8487854003906 0.32497358322143555 305.0728454589844 0.6106005907058716 0.66668874 0.4850367307662964 True -19 45180 24.548693418502808 0.48334336280822754 248.7740478515625 0.3372698426246643 305.03924560546875 0.6102765202522278 0.6664086 0.491997092962265 False diff --git a/ENCSR604YEQ/cherimoya.fold_1.performance.tsv b/ENCSR604YEQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3635073237ac468193725e1f17811e61d091c4f3..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -305.0728454589844 0.317069411277771 0.6106005311012268 0.19803749024868011 0.6666887402534485 0.6676719188690186 0.4850367307662964 \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_2.evaluate.json b/ENCSR604YEQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4b1a55a3584a863b29566876e9507ca4e7219df9..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118YHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_2.fit.json b/ENCSR604YEQ/cherimoya.fold_2.fit.json deleted file mode 100644 index ea79807b49074511df57eb48cc9eb597872d80ab..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF118YHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_2.log b/ENCSR604YEQ/cherimoya.fold_2.log deleted file mode 100644 index 4cf057165a820529e87efbf63ce0b07309c93bbc..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2343 30.662214040756226 3.4510915279388428 237.80833435058594 1.002497673034668 387.9373474121094 0.44643041491508484 0.4698599 7.671327114105225 True -1 4686 25.960081100463867 0.653564453125 280.89599609375 1.195701241493225 334.91455078125 0.5650141835212708 0.5682066 2.847683906555176 True -2 7029 25.944238901138306 0.43024158477783203 222.96249389648438 0.6478033065795898 324.90869140625 0.5878210067749023 0.5761082 1.260822057723999 True -3 9372 25.97395372390747 0.4297511577606201 254.60076904296875 1.0778961181640625 321.84149169921875 0.594450831413269 0.58940697 0.8953877687454224 True -4 11715 26.028480768203735 0.4226686954498291 256.0168151855469 0.7003901600837708 320.39154052734375 0.5980167388916016 0.59039235 0.8428518176078796 True -5 14058 25.933663606643677 0.4290008544921875 226.790771484375 0.3804795742034912 319.298583984375 0.6008268594741821 0.599062 0.818655252456665 True -6 16401 25.97674870491028 0.4675137996673584 216.06834411621094 0.6013637781143188 318.7742614746094 0.6023877263069153 0.60048825 0.8339038491249084 True -7 18744 25.95581889152527 0.42607617378234863 275.3460388183594 0.8319143056869507 317.47882080078125 0.6048805713653564 0.6057281 0.744547426700592 True -8 21087 25.97250247001648 1.080397367477417 211.5469207763672 0.7916525602340698 316.45672607421875 0.607294499874115 0.6094194 0.7176448702812195 True -9 23430 25.985657691955566 1.2484004497528076 263.021484375 0.9973627328872681 315.7735290527344 0.609092652797699 0.6107268 0.6825284957885742 True -10 25773 25.9735164642334 0.4233114719390869 220.79034423828125 0.8582169413566589 314.8232116699219 0.6112430691719055 0.6201475 0.6646919846534729 True -11 28116 25.967790365219116 0.42584657669067383 229.07838439941406 0.5324690341949463 313.732421875 0.613654375076294 0.6258593 0.6463894248008728 True -12 30459 26.006739854812622 0.4124631881713867 243.65379333496094 0.5125035047531128 313.3152160644531 0.6149803400039673 0.63170373 0.6254276633262634 True -13 32802 26.085469961166382 0.42369866371154785 201.81805419921875 0.6661986708641052 312.4744873046875 0.6164336204528809 0.63598454 0.6173067092895508 True -14 35145 25.45397138595581 0.4165794849395752 244.50344848632812 0.689728856086731 311.5534362792969 0.6183788180351257 0.6441027 0.5841646194458008 True -15 37488 25.432539463043213 0.4176943302154541 279.3528747558594 0.7341052293777466 311.2300720214844 0.6191200017929077 0.64828324 0.5791741609573364 True -16 39831 25.425172567367554 0.4174823760986328 218.20953369140625 0.5198951959609985 310.9864196777344 0.6192255020141602 0.6523101 0.5681287050247192 True -17 42174 25.421411514282227 0.40816831588745117 238.39926147460938 0.5969462394714355 310.9337158203125 0.6189993023872375 0.6537444 0.5648815035820007 True -18 44517 25.44443941116333 0.4195902347564697 218.2686767578125 0.2858321964740753 311.1342468261719 0.6185339093208313 0.65231526 0.5670508742332458 False -19 46860 25.413790702819824 0.4108850955963135 232.89111328125 0.37580668926239014 311.1287536621094 0.6181622743606567 0.64877427 0.5756579637527466 False diff --git a/ENCSR604YEQ/cherimoya.fold_2.performance.tsv b/ENCSR604YEQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 683a778d4b860bdbc78564619e23b7e42bd5cd02..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -310.9337158203125 0.3123033940792084 0.6189992427825928 0.2087395340204239 0.6537443995475769 0.6363497972488403 0.5648815035820007 \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_3.evaluate.json b/ENCSR604YEQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a95c0fe37dd46bd84a7e2ad874279ea982ca7892..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118YHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_3.fit.json b/ENCSR604YEQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 71919c40a72e7f088f4675940c7388db18630eb5..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF118YHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_3.log b/ENCSR604YEQ/cherimoya.fold_3.log deleted file mode 100644 index 615486ad08bca012fd6d99ab1bca9359b34c5de4..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2285 29.959327459335327 3.713365077972412 225.25799560546875 1.4378552436828613 402.9220886230469 0.45212194323539734 0.4879088 8.135553359985352 True -1 4570 25.673380136489868 0.510159969329834 284.6097412109375 0.92470383644104 342.7588806152344 0.5760173797607422 0.55628216 3.3386948108673096 True -2 6855 25.36197066307068 0.4943273067474365 239.50668334960938 0.7262896299362183 333.6068115234375 0.5962550044059753 0.57160014 1.2105120420455933 True -3 9140 25.28348970413208 0.4897911548614502 228.117431640625 1.0275983810424805 329.70892333984375 0.6037302613258362 0.58101976 0.9964741468429565 True -4 11425 25.31444215774536 0.491060733795166 268.7250061035156 0.8629013299942017 328.02203369140625 0.6078692078590393 0.59071624 0.9146499037742615 True -5 13710 25.29742193222046 0.5081546306610107 201.7092742919922 0.7687742710113525 326.8621520996094 0.6098560690879822 0.59561014 0.8728675842285156 True -6 15995 25.273242473602295 0.4844388961791992 253.18592834472656 0.6118226051330566 325.84417724609375 0.612437903881073 0.5967184 0.8341761231422424 True -7 18280 25.3179190158844 2.670156717300415 245.4103546142578 0.6744753122329712 324.5981140136719 0.6149130463600159 0.6029336 0.7706676125526428 True -8 20565 25.350804805755615 0.4814581871032715 220.74267578125 0.7126854658126831 323.96337890625 0.6168595552444458 0.60624623 0.7433298826217651 True -9 22850 25.364057064056396 0.5180792808532715 237.11558532714844 0.5203827619552612 323.2380676269531 0.6187759637832642 0.61063206 0.7362737655639648 True -10 25135 25.327229261398315 0.4989030361175537 248.8769989013672 0.7684611082077026 322.17120361328125 0.6212989091873169 0.62076354 0.6677334308624268 True -11 27420 25.298064470291138 0.4780919551849365 201.53424072265625 0.5385756492614746 321.5010986328125 0.6230372190475464 0.6276152 0.6370101571083069 True -12 29705 25.29162335395813 0.49645185470581055 227.94918823242188 0.45508378744125366 320.47943115234375 0.6247680187225342 0.63497365 0.6079186201095581 True -13 31990 25.32587218284607 0.4920668601989746 220.80728149414062 0.5162665843963623 319.9793395996094 0.6262758374214172 0.6454693 0.5799029469490051 True -14 34275 25.30144691467285 0.4932069778442383 225.89002990722656 0.6364989280700684 318.9549255371094 0.6273806095123291 0.65231866 0.5713155269622803 True -15 36560 25.35659170150757 0.4959218502044678 238.73094177246094 0.4242584705352783 318.5040283203125 0.6283621788024902 0.65866846 0.5555355548858643 True -16 38845 25.38145613670349 0.49305081367492676 196.13922119140625 0.4618876576423645 318.8189392089844 0.6283479332923889 0.66258395 0.5572410225868225 True -17 41130 25.325488805770874 0.4954030513763428 212.61886596679688 0.3895171582698822 318.8821716308594 0.6279444098472595 0.6618519 0.5574078559875488 False -18 43415 25.30637550354004 1.629930019378662 230.5074462890625 0.4043468236923218 319.2095031738281 0.6274685263633728 0.6582218 0.5654285550117493 False -19 45700 25.394845008850098 0.5030138492584229 228.33462524414062 0.44420677423477173 318.91650390625 0.6270890831947327 0.65713173 0.5731914043426514 False diff --git a/ENCSR604YEQ/cherimoya.fold_3.performance.tsv b/ENCSR604YEQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ce2b85a2ee3ef3e66c2a7899e72f3b729bb3ef8f..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -318.8189392089844 0.3051842153072357 0.6283479332923889 0.2138039469718933 0.6625839471817017 0.6529701352119446 0.5572410225868225 \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_4.evaluate.json b/ENCSR604YEQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ed88bd024cde380261d2b8a7e40e8620712547cf..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF118YHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_4.fit.json b/ENCSR604YEQ/cherimoya.fold_4.fit.json deleted file mode 100644 index a82025b4677bc7fbe6506433338c26c7f7387962..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF118YHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR604YEQ/cherimoya.fold_4.log b/ENCSR604YEQ/cherimoya.fold_4.log deleted file mode 100644 index ea768680b789f7a437363a4480f6e8218718f0d3..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2360 31.10209560394287 24.891067504882812 298.1622314453125 1.0978138446807861 401.5132141113281 0.4521133303642273 0.53003913 7.724660873413086 True -1 4720 26.164944410324097 0.47235798835754395 289.2938232421875 0.8157526850700378 345.2669677734375 0.5795704126358032 0.57943976 3.1720855236053467 True -2 7080 26.119535207748413 0.49309873580932617 260.0199890136719 1.2197507619857788 335.33636474609375 0.6011689305305481 0.57071334 1.1480127573013306 False -3 9440 26.178778886795044 0.46082448959350586 251.51724243164062 0.6413028240203857 331.2797546386719 0.6085695028305054 0.58389443 0.9685099720954895 True -4 11800 26.13408589363098 0.4625983238220215 233.3816680908203 0.7483603954315186 329.6666564941406 0.6128342151641846 0.5905643 0.8984473943710327 True -5 14160 26.098652601242065 1.3166019916534424 269.4538879394531 1.093325138092041 328.2313537597656 0.6163498163223267 0.600265 0.8538585305213928 True -6 16520 26.231462478637695 0.47185826301574707 242.87991333007812 0.44737470149993896 327.57232666015625 0.6181204915046692 0.6006723 0.8326165676116943 True -7 18880 26.484609127044678 23.715627670288086 242.116455078125 0.901606559753418 326.79296875 0.620177149772644 0.60463285 0.8154802322387695 True -8 21240 25.744788885116577 0.45832109451293945 243.97769165039062 0.6623822450637817 325.7160949707031 0.6227405667304993 0.61093366 0.7750799655914307 True -9 23600 25.596614837646484 0.45046424865722656 286.53472900390625 0.6846809387207031 324.8426513671875 0.6247166395187378 0.6224373 0.7092031836509705 True -10 25960 25.666298151016235 0.4745352268218994 220.0176544189453 0.6291803121566772 323.5767517089844 0.6271951198577881 0.6229955 0.69745934009552 True -11 28320 25.60734272003174 0.46903419494628906 205.7642364501953 0.7542389631271362 322.8627624511719 0.6290531754493713 0.6304129 0.6539252400398254 True -12 30680 25.618561267852783 0.470278263092041 224.50042724609375 0.4920305013656616 321.9839782714844 0.6310822367668152 0.6400623 0.6418569087982178 True -13 33040 25.594911575317383 0.46369075775146484 246.94200134277344 0.3938433825969696 321.0799865722656 0.6326310038566589 0.6453266 0.61147540807724 True -14 35400 25.696808576583862 0.47518396377563477 245.1941680908203 0.523246705532074 320.49383544921875 0.6341015696525574 0.6533195 0.587099552154541 True -15 37760 25.60979723930359 0.47034358978271484 278.3058166503906 0.639419436454773 320.0395812988281 0.6351778507232666 0.65941817 0.570059597492218 True -16 40120 25.597240686416626 0.46770501136779785 253.7860870361328 0.4230539798736572 319.9695129394531 0.635252833366394 0.6650978 0.5624029636383057 True -17 42480 25.62642765045166 0.46987175941467285 222.69569396972656 0.3475691080093384 320.0128479003906 0.6349247694015503 0.6654053 0.5609578490257263 True -18 44840 25.624024629592896 0.4687650203704834 229.787841796875 0.34101107716560364 320.1869201660156 0.6343620419502258 0.66332835 0.5681938529014587 False -19 47200 25.566064834594727 0.7325439453125 192.71568298339844 0.44280579686164856 320.3250427246094 0.6340082287788391 0.659522 0.5736567974090576 False diff --git a/ENCSR604YEQ/cherimoya.fold_4.performance.tsv b/ENCSR604YEQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 055a4c95121d5d88084f5791955b81202a4f7904..0000000000000000000000000000000000000000 --- a/ENCSR604YEQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -320.0128479003906 0.303511381149292 0.6349247694015503 0.21542304754257202 0.6654052734375 0.6454941630363464 0.5609578490257263 \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_0.evaluate.json b/ENCSR605EGR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 83e2ddaf78f8f3f484dd20e9c52e70fa1bd8567b..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299GQH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_0.fit.json b/ENCSR605EGR/cherimoya.fold_0.fit.json deleted file mode 100644 index 64254335f97a9d25e7e3ef1e3725f131b5ffb443..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF299GQH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_0.log b/ENCSR605EGR/cherimoya.fold_0.log deleted file mode 100644 index d1b26cd1f6f778d97c0d1a9d13079726ebc60e31..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2631 33.564725160598755 3.895467758178711 420.89691162109375 0.9370847344398499 562.8694458007812 0.5046799182891846 0.55901456 7.0788373947143555 True -1 5262 29.019291400909424 0.5829246044158936 335.150146484375 0.6615077257156372 461.2820739746094 0.6670224666595459 0.6415327 1.786005973815918 True -2 7893 29.06126594543457 1.355379581451416 402.9967041015625 0.3503396511077881 447.7696228027344 0.682587206363678 0.63634926 0.6196980476379395 False -3 10524 29.01772403717041 0.568507194519043 336.3611145019531 0.348272442817688 442.4236145019531 0.6897765398025513 0.6556377 0.5248107314109802 True -4 13155 29.336048364639282 9.680337190628052 371.7587890625 0.6623139977455139 439.6277770996094 0.6931745409965515 0.6654999 0.44957032799720764 True -5 15786 29.043846368789673 1.4979937076568604 379.26593017578125 0.4466499388217926 438.07904052734375 0.6956304907798767 0.66463876 0.4535367488861084 False -6 18417 29.000452041625977 0.5694737434387207 401.94586181640625 0.413868248462677 436.0442810058594 0.6981785893440247 0.67997336 0.4243204891681671 True -7 21048 29.046221494674683 0.5638456344604492 378.51776123046875 0.45793846249580383 434.3987731933594 0.7006146907806396 0.68737143 0.4097105860710144 True -8 23679 29.049766540527344 0.5615379810333252 354.914306640625 0.43918490409851074 433.4368896484375 0.7023452520370483 0.69125503 0.40898340940475464 True -9 26310 29.09614610671997 0.5803713798522949 343.489990234375 0.49466508626937866 431.7555236816406 0.7045901417732239 0.7020942 0.39973241090774536 True -10 28941 29.02991271018982 0.5624809265136719 329.64129638671875 0.3864056468009949 429.95599365234375 0.7067943215370178 0.71220064 0.38207459449768066 True -11 31572 29.234625339508057 0.5796878337860107 366.89715576171875 0.3414262533187866 428.5137023925781 0.7087886333465576 0.7192806 0.3749472200870514 True -12 34203 28.513824939727783 0.5725860595703125 347.279541015625 0.23810291290283203 427.08465576171875 0.7106154561042786 0.7315034 0.3599301278591156 True -13 36834 28.49759602546692 0.5710196495056152 310.6883850097656 0.34676700830459595 425.9614562988281 0.7119934558868408 0.7394022 0.35495463013648987 True -14 39465 28.458194494247437 0.5520331859588623 317.53558349609375 0.2124432474374771 425.0530700683594 0.7133477926254272 0.7476959 0.34800416231155396 True -15 42096 28.679588556289673 0.5689098834991455 372.14581298828125 0.3550179600715637 424.11285400390625 0.7143712639808655 0.75344175 0.34238696098327637 True -16 44727 28.56723189353943 0.5743134021759033 333.78033447265625 0.24580436944961548 423.74298095703125 0.7147687077522278 0.75863487 0.34085190296173096 True -17 47358 28.523446559906006 0.5580568313598633 285.55169677734375 0.282046377658844 423.6117858886719 0.7145894765853882 0.75960314 0.34302982687950134 True -18 49989 28.501108407974243 0.569244384765625 363.15838623046875 0.279142290353775 423.76263427734375 0.7142866849899292 0.75950366 0.34463441371917725 False -19 52620 28.55386185646057 1.930175542831421 365.2107849121094 0.28219467401504517 423.9122619628906 0.7140324711799622 0.761668 0.34644535183906555 True diff --git a/ENCSR605EGR/cherimoya.fold_0.performance.tsv b/ENCSR605EGR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c22dd76096e3a12263dcdf6f81243df8f9bc019f..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -423.9122619628906 0.24488495290279388 0.7140325307846069 0.27897417545318604 0.7616680264472961 0.7047543525695801 0.34644535183906555 \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_1.evaluate.json b/ENCSR605EGR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 64fca91f7342f9ab87dc4fa4cec8660cc4a83aa7..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299GQH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_1.fit.json b/ENCSR605EGR/cherimoya.fold_1.fit.json deleted file mode 100644 index d5cb47aa54082e06312f2d33199cb206d1a1312a..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF299GQH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_1.log b/ENCSR605EGR/cherimoya.fold_1.log deleted file mode 100644 index a491b6ea832f921f91161c559acccb0aa132f2ec..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2626 33.48463702201843 4.475511312484741 400.3786926269531 0.6458697319030762 585.4804077148438 0.5124760270118713 0.57978654 6.838613986968994 True -1 5252 29.25403618812561 0.7226111888885498 377.4642333984375 0.623546838760376 481.6803283691406 0.6753121018409729 0.67552245 1.9140512943267822 True -2 7878 28.95516014099121 0.6792130470275879 387.64898681640625 0.3998453915119171 467.6466369628906 0.6903545260429382 0.6736051 0.7010314464569092 False -3 10504 28.930744886398315 0.718496561050415 355.3954772949219 0.5986477732658386 461.6227111816406 0.6980695128440857 0.6734201 0.5420577526092529 False -4 13130 28.93596911430359 0.6693563461303711 327.7513427734375 0.46639779210090637 458.82086181640625 0.7017484903335571 0.68640924 0.46652156114578247 True -5 15756 28.94648504257202 1.4789185523986816 377.3380126953125 0.33951395750045776 456.0191345214844 0.7053463459014893 0.6988133 0.4176765978336334 True -6 18382 28.946531295776367 1.7831907272338867 307.5955505371094 0.4202898144721985 454.5589904785156 0.7075352668762207 0.70656276 0.40304216742515564 True -7 21008 30.544774055480957 0.6844301223754883 362.66851806640625 0.39126235246658325 452.5702819824219 0.7102842330932617 0.710985 0.4008916914463043 True -8 23634 28.981966257095337 18.029019594192505 399.52203369140625 0.46059930324554443 450.22802734375 0.7129366397857666 0.72662365 0.3800216317176819 True -9 26260 28.939125299453735 0.6905138492584229 331.3859558105469 0.3184258043766022 448.48077392578125 0.7152352929115295 0.73378384 0.3624696135520935 True -10 28886 28.98703956604004 0.6706275939941406 311.9689025878906 0.23024240136146545 447.283447265625 0.7171087265014648 0.74313575 0.35252636671066284 True -11 31512 28.939823865890503 0.6985151767730713 334.0400390625 0.27042752504348755 445.8699645996094 0.7190382480621338 0.7532247 0.3391776978969574 True -12 34138 28.9321870803833 0.6865620613098145 310.57421875 0.23763132095336914 443.8893127441406 0.7217049598693848 0.76350105 0.3235003352165222 True -13 36764 28.660577535629272 0.6744422912597656 328.8102722167969 0.2910608649253845 442.4002990722656 0.7234790325164795 0.7725443 0.31240683794021606 True -14 39390 28.407861709594727 0.7561385631561279 333.1243896484375 0.3599865138530731 441.385498046875 0.7248390316963196 0.78250444 0.30346402525901794 True -15 42016 28.379372358322144 0.6683385372161865 360.017333984375 0.2779415547847748 440.75238037109375 0.7256366610527039 0.7874946 0.297853946685791 True -16 44642 28.412387132644653 0.6912853717803955 326.22235107421875 0.29652881622314453 440.347412109375 0.7260842323303223 0.7934261 0.2940165400505066 True -17 47268 28.418978214263916 0.6852138042449951 314.473876953125 0.29880213737487793 440.25836181640625 0.725881040096283 0.7976109 0.2931133806705475 True -18 49894 28.451524257659912 0.7074129581451416 335.4798278808594 0.19812524318695068 440.53790283203125 0.7253170013427734 0.7963535 0.2962307035923004 False -19 52520 28.453603506088257 0.6865024566650391 341.4188232421875 0.2625497579574585 440.83111572265625 0.7250167727470398 0.79681045 0.29853585362434387 False diff --git a/ENCSR605EGR/cherimoya.fold_1.performance.tsv b/ENCSR605EGR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 880f635f4fde80dba77d66d1388812ae45eb0702..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -440.25836181640625 0.23715250194072723 0.7258810997009277 0.2893708050251007 0.797610878944397 0.7587201595306396 0.2931133806705475 \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_2.evaluate.json b/ENCSR605EGR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 876d4af84b33f9dfeb03fd3df8060239b81c5565..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299GQH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_2.fit.json b/ENCSR605EGR/cherimoya.fold_2.fit.json deleted file mode 100644 index d3fedff0b33a1f3a08f826ba125dbc504f573c68..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF299GQH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_2.log b/ENCSR605EGR/cherimoya.fold_2.log deleted file mode 100644 index 7fb96e82496461bf456e602ab8d7ff8dac4a28da..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2809 35.433478593826294 4.060347557067871 409.3992614746094 0.9109947085380554 563.4169311523438 0.5222541093826294 0.57384866 5.71924352645874 True -1 5618 30.990199089050293 0.6910793781280518 328.97723388671875 0.7458306550979614 465.64471435546875 0.6754982471466064 0.66844434 1.3674249649047852 True -2 8427 30.987943172454834 0.5242252349853516 386.9888916015625 0.6011437177658081 456.1159362792969 0.6854916214942932 0.6717681 0.6666819453239441 True -3 11236 30.9716637134552 2.218010663986206 404.5606689453125 0.7165818810462952 451.8457946777344 0.6908649206161499 0.679213 0.4577496349811554 True -4 14045 30.980990409851074 10.984578371047974 384.82232666015625 0.36592400074005127 449.7480163574219 0.6930364966392517 0.67385733 0.4610466957092285 False -5 16854 31.105600833892822 0.529055118560791 342.260986328125 0.41514718532562256 447.00030517578125 0.6973701119422913 0.68427414 0.42977848649024963 True -6 19663 30.99161958694458 0.5297954082489014 399.01690673828125 0.630961537361145 444.3706970214844 0.7003280520439148 0.69058704 0.4183924198150635 True -7 22472 31.305522918701172 17.508615970611572 361.41790771484375 0.5213866829872131 443.5740661621094 0.7015077471733093 0.69771993 0.4165273606777191 True -8 25281 31.136207103729248 0.5250494480133057 310.97686767578125 0.38958078622817993 441.1259460449219 0.7049726247787476 0.7059587 0.40188920497894287 True -9 28090 31.009292364120483 0.5269968509674072 348.6815490722656 0.34733495116233826 439.13189697265625 0.7072010636329651 0.7136038 0.3861803412437439 True -10 30899 31.04883885383606 0.5152583122253418 376.37762451171875 0.36652618646621704 437.5882263183594 0.7095025181770325 0.722448 0.37798449397087097 True -11 33708 31.089144706726074 0.5281662940979004 393.4554138183594 0.5004081726074219 435.83673095703125 0.7120189070701599 0.7369506 0.36159655451774597 True -12 36517 31.07737421989441 0.527456521987915 338.85589599609375 0.30336132645606995 434.55419921875 0.7138460874557495 0.7402572 0.3548584282398224 True -13 39326 30.5481960773468 0.5091776847839355 320.07623291015625 0.42080387473106384 433.0816345214844 0.7155551910400391 0.752155 0.3422859013080597 True -14 42135 30.436877727508545 0.5091121196746826 328.6301574707031 0.25000542402267456 431.96221923828125 0.716977059841156 0.7608003 0.33595824241638184 True -15 44944 30.44809603691101 0.5072152614593506 307.7748718261719 0.26982414722442627 431.4559326171875 0.7178093194961548 0.7677015 0.32920122146606445 True -16 47753 30.388017177581787 0.5006003379821777 394.8746643066406 0.3108760118484497 430.9674072265625 0.7184879183769226 0.7745641 0.32338523864746094 True -17 50562 30.375739574432373 0.5067286491394043 335.94586181640625 0.2747785449028015 430.9966735839844 0.7184016108512878 0.7767445 0.325147807598114 True -18 53371 30.4841091632843 6.024907350540161 331.63525390625 0.13520070910453796 431.199951171875 0.718117356300354 0.77631176 0.32882845401763916 False -19 56180 30.412387371063232 0.5200557708740234 361.9468688964844 0.42132291197776794 431.36187744140625 0.7179092764854431 0.7749646 0.3306535482406616 False diff --git a/ENCSR605EGR/cherimoya.fold_2.performance.tsv b/ENCSR605EGR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index db71b132d3d54c5c08bc56556eb3df0003e7238b..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -430.9966735839844 0.24208280444145203 0.7184016108512878 0.28266584873199463 0.7767444849014282 0.7279535531997681 0.325147807598114 \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_3.evaluate.json b/ENCSR605EGR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 84cd9168c6f2a91b8d784216ab496193f521e228..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299GQH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_3.fit.json b/ENCSR605EGR/cherimoya.fold_3.fit.json deleted file mode 100644 index 33a88f1bc23481086f10ebc43c0a128f47d0345b..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF299GQH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_3.log b/ENCSR605EGR/cherimoya.fold_3.log deleted file mode 100644 index 91f619cbc81541a7be7044dd478b6a28df75871a..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2708 34.28999996185303 4.021036386489868 398.8000183105469 0.6290569305419922 561.145263671875 0.5134488344192505 0.56844574 8.057690620422363 True -1 5416 29.878061771392822 0.7319369316101074 359.9014892578125 0.7356610298156738 461.94482421875 0.6731957197189331 0.65189505 1.7271946668624878 True -2 8124 29.89597487449646 0.5558702945709229 382.12835693359375 0.6641373634338379 449.2308349609375 0.6875923871994019 0.6461711 0.6473567485809326 False -3 10832 29.95299768447876 1.6634252071380615 350.0477294921875 0.5736620426177979 445.1486511230469 0.6920673847198486 0.6418367 0.5580188632011414 False -4 13540 29.863283157348633 0.9658775329589844 441.67626953125 0.5117003917694092 442.4310607910156 0.6961830258369446 0.6491362 0.49080026149749756 False -5 16248 29.888017654418945 0.5601048469543457 379.28411865234375 0.3420642018318176 440.0146484375 0.6995280981063843 0.6619238 0.46053487062454224 True -6 18956 29.794752597808838 0.5474777221679688 426.5456237792969 0.8013372421264648 438.17510986328125 0.7020004391670227 0.6688955 0.44169455766677856 True -7 21664 29.808595180511475 0.5659236907958984 404.71197509765625 0.3275328576564789 436.2784118652344 0.7045961022377014 0.6835662 0.42125487327575684 True -8 24372 29.873889923095703 0.5548176765441895 340.2005920410156 0.6119250059127808 434.8490295410156 0.7065747976303101 0.6907945 0.40822529792785645 True -9 27080 29.88151216506958 0.5421357154846191 321.67578125 0.40056347846984863 433.52557373046875 0.7087792158126831 0.6996437 0.4017144441604614 True -10 29788 29.823344945907593 0.5518066883087158 343.4420166015625 0.29768431186676025 431.8134765625 0.7109373807907104 0.7135345 0.3841671049594879 True -11 32496 29.91093683242798 0.5479483604431152 379.20111083984375 0.3507988750934601 430.2540283203125 0.7128555774688721 0.72030693 0.37793728709220886 True -12 35204 29.90410017967224 0.5460231304168701 302.7693176269531 0.2753714919090271 428.46417236328125 0.7147411704063416 0.73140365 0.3616291880607605 True -13 37912 29.823944330215454 17.76930856704712 329.4710693359375 0.24563974142074585 427.095703125 0.7168309092521667 0.7424106 0.35247984528541565 True -14 40620 29.44934630393982 0.545487642288208 319.4765625 0.3117985129356384 425.9168395996094 0.7184018492698669 0.7521303 0.3407025933265686 True -15 43328 29.32039976119995 0.548952579498291 341.316162109375 0.32366690039634705 425.228271484375 0.7192851305007935 0.7613343 0.3355456590652466 True -16 46036 29.337913274765015 0.5494964122772217 365.4743347167969 0.2733446955680847 424.78485107421875 0.7197044491767883 0.76651675 0.33168864250183105 True -17 48744 29.295130014419556 0.5431821346282959 322.7696533203125 0.33654412627220154 424.7149963378906 0.7197895050048828 0.76956916 0.33495453000068665 True -18 51452 29.287842750549316 0.7837574481964111 332.85308837890625 0.22265705466270447 424.93048095703125 0.7193668484687805 0.7681884 0.33606967329978943 False -19 54160 29.345961093902588 1.0779228210449219 292.8001708984375 0.19132059812545776 425.1668395996094 0.7190255522727966 0.7669438 0.33926281332969666 False diff --git a/ENCSR605EGR/cherimoya.fold_3.performance.tsv b/ENCSR605EGR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2103d01d80d0436f728a8069af5c384c4e054fd0..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -424.7149963378906 0.24151748418807983 0.7197893857955933 0.28006479144096375 0.7695691585540771 0.7219926118850708 0.33495453000068665 \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_4.evaluate.json b/ENCSR605EGR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 63c4c6f0e6b60c3d7b35e9c568849981f4194189..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299GQH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_4.fit.json b/ENCSR605EGR/cherimoya.fold_4.fit.json deleted file mode 100644 index 949aa139f040cad84aa7486264ebff1bd39c960d..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF299GQH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605EGR/cherimoya.fold_4.log b/ENCSR605EGR/cherimoya.fold_4.log deleted file mode 100644 index bd2e439ed066226d0232235aff995ad82ecaa404..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 34.8320894241333 4.316983699798584 460.9925842285156 0.5658894181251526 562.6491088867188 0.511850118637085 0.57767946 6.500154972076416 True -1 5520 30.44402837753296 1.0284371376037598 369.15948486328125 0.4664464592933655 459.2459716796875 0.673438310623169 0.66233885 1.5622612237930298 True -2 8280 30.399227142333984 0.542776346206665 347.0794372558594 0.47961533069610596 448.2774353027344 0.6857492923736572 0.66081905 0.6372411847114563 False -3 11040 30.435425758361816 1.2244858741760254 352.9842529296875 0.5424641370773315 442.61212158203125 0.6924540400505066 0.67419565 0.49131307005882263 True -4 13800 30.439101696014404 22.573105812072754 407.5581359863281 0.6679471731185913 439.8168029785156 0.6961894035339355 0.6632707 0.45276325941085815 False -5 16560 30.465070962905884 0.5640289783477783 357.8227233886719 0.3662158250808716 437.734130859375 0.6987437009811401 0.67300683 0.43595364689826965 False -6 19320 30.39177942276001 0.5372257232666016 351.8653564453125 0.34859004616737366 436.5986022949219 0.7010105848312378 0.6784588 0.43485549092292786 True -7 22080 30.469887495040894 0.5479333400726318 399.895751953125 0.33546414971351624 434.3410339355469 0.7038409113883972 0.6923003 0.4125245213508606 True -8 24840 30.46389365196228 0.5343997478485107 347.6822204589844 0.37013915181159973 432.8619689941406 0.7058059573173523 0.7046314 0.39506807923316956 True -9 27600 30.439631938934326 0.5344188213348389 352.8045654296875 0.3575161099433899 431.3805236816406 0.7077322006225586 0.70663524 0.3916511535644531 True -10 30360 30.432363271713257 0.5406429767608643 324.63848876953125 0.2614656984806061 429.85748291015625 0.7100538611412048 0.7209827 0.37814417481422424 True -11 33120 30.471154928207397 0.5381424427032471 388.09771728515625 0.37233346700668335 428.3866271972656 0.7121806740760803 0.732893 0.36483001708984375 True -12 35880 30.464775323867798 0.5463786125183105 317.61529541015625 0.39958643913269043 427.1050720214844 0.7138761281967163 0.74210906 0.3548658788204193 True -13 38640 30.423802375793457 0.5409829616546631 333.68951416015625 0.2850284278392792 425.93719482421875 0.7155683040618896 0.7520165 0.345983624458313 True -14 41400 29.870136737823486 0.5228447914123535 315.396728515625 0.2379210740327835 424.9814758300781 0.7169495224952698 0.76228184 0.3352138102054596 True -15 44160 29.849323511123657 12.667766332626343 324.64825439453125 0.30173754692077637 424.21240234375 0.7180126309394836 0.76853234 0.33076971769332886 True -16 46920 29.91190791130066 0.5294220447540283 331.2447509765625 0.19841362535953522 423.9508361816406 0.7183458209037781 0.7740387 0.327622652053833 True -17 49680 29.901399850845337 0.5401339530944824 380.8257751464844 0.18120887875556946 423.7747497558594 0.7184579968452454 0.7768386 0.32849201560020447 True -18 52440 29.871265649795532 0.5286126136779785 274.57257080078125 0.14901036024093628 424.04547119140625 0.7178928256034851 0.777165 0.3322874903678894 True -19 55200 29.837199211120605 0.5217263698577881 357.806396484375 0.19787169992923737 424.1671142578125 0.717687726020813 0.77470094 0.3340369164943695 False diff --git a/ENCSR605EGR/cherimoya.fold_4.performance.tsv b/ENCSR605EGR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0a99e424648a97f8a7a1f7d60d9b1c4a89b5fa34..0000000000000000000000000000000000000000 --- a/ENCSR605EGR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -424.04547119140625 0.24339430034160614 0.7178928852081299 0.2800184488296509 0.7771649956703186 0.7179831862449646 0.3322874903678894 \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_0.evaluate.json b/ENCSR605SQL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2febfd27db9deb53e52757e2c84e6df2fd2e4b07..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034XGB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_0.fit.json b/ENCSR605SQL/cherimoya.fold_0.fit.json deleted file mode 100644 index 5e5f532416034cc507e00a83cb7e89bd909fbd7d..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF034XGB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_0.log b/ENCSR605SQL/cherimoya.fold_0.log deleted file mode 100644 index 95416ae6faeea575a9ca2a534af0f46f9afc7a74..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1937 26.328295946121216 4.423946857452393 353.708740234375 0.948756217956543 511.728515625 0.16039736568927765 0.68750876 10.583791732788086 True -1 3874 21.397254467010498 0.4082820415496826 308.0589904785156 0.9140341281890869 438.7477722167969 0.23705288767814636 0.7866064 4.679862976074219 True -2 5811 21.39475679397583 0.38064122200012207 282.65814208984375 0.8532838821411133 407.79388427734375 0.2588038742542267 0.8146405 2.2269604206085205 True -3 7748 21.401329278945923 0.38228368759155273 328.205810546875 1.143136739730835 400.9478759765625 0.26585811376571655 0.8282107 1.364925742149353 True -4 9685 21.39404320716858 0.38841748237609863 344.47259521484375 1.0502679347991943 396.786865234375 0.2720123827457428 0.8311203 1.165937900543213 True -5 11622 21.364181756973267 3.7767975330352783 268.87274169921875 1.072288990020752 394.40533447265625 0.2739064693450928 0.8387417 1.0428259372711182 True -6 13559 21.72545599937439 0.38735055923461914 358.0660095214844 0.8949195146560669 392.10211181640625 0.27664273977279663 0.84247303 0.8926008939743042 True -7 15496 21.350263357162476 17.207701206207275 258.3978576660156 0.7876834869384766 390.5018310546875 0.27902668714523315 0.8467336 0.8398770093917847 True -8 17433 22.349385261535645 0.3839230537414551 305.4483642578125 0.8920122385025024 388.056396484375 0.2812836170196533 0.85408694 0.7724721431732178 True -9 19370 21.374573230743408 0.3963892459869385 376.4034423828125 0.553058385848999 387.4466247558594 0.28185418248176575 0.8574859 0.6946942210197449 True -10 21307 21.387796640396118 16.389063596725464 320.44146728515625 0.679877519607544 385.40777587890625 0.28434741497039795 0.86278325 0.6554079651832581 True -11 23244 22.051464080810547 20.461568593978882 235.5170440673828 0.6793187856674194 382.924560546875 0.28799712657928467 0.86373115 0.6262691020965576 True -12 25181 22.070613861083984 22.24604082107544 389.1230163574219 0.8433644771575928 381.39080810546875 0.28955700993537903 0.8686563 0.6005017757415771 True -13 27118 22.026578664779663 19.208147048950195 315.26123046875 0.5784139037132263 379.7057189941406 0.2912316620349884 0.8717628 0.5737743973731995 True -14 29055 21.511778116226196 0.393902063369751 280.9421691894531 0.41414231061935425 379.91497802734375 0.29190367460250854 0.87638724 0.5508865118026733 True -15 30992 20.95456576347351 0.39281678199768066 229.17495727539062 0.4330603778362274 378.3372497558594 0.292822003364563 0.8768086 0.5385701656341553 True -16 32929 21.037158489227295 0.39153099060058594 253.97589111328125 0.42932724952697754 377.5521240234375 0.29459503293037415 0.87788427 0.5360845327377319 True -17 34866 21.041597604751587 2.024423360824585 223.62326049804688 0.5256177186965942 378.7981872558594 0.2922842800617218 0.87786937 0.5389048457145691 False -18 36803 21.073720455169678 0.3921504020690918 249.3277587890625 0.3863045573234558 379.1580505371094 0.29198864102363586 0.87762284 0.5457475185394287 False -19 38740 21.087133169174194 1.4739265441894531 283.8743591308594 0.264288067817688 379.57257080078125 0.2913634777069092 0.87807804 0.5545148253440857 True diff --git a/ENCSR605SQL/cherimoya.fold_0.performance.tsv b/ENCSR605SQL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 98bd7bf50ddea39abfcbc77dc5bc28ed4fce222e..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -379.57257080078125 0.485501766204834 0.29136350750923157 0.10524598509073257 0.878078043460846 0.8225845694541931 0.5545148253440857 \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_1.evaluate.json b/ENCSR605SQL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3bcd7c2cc1ca35ab8b77048817503be0edf42a36..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034XGB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_1.fit.json b/ENCSR605SQL/cherimoya.fold_1.fit.json deleted file mode 100644 index 353f79e03ddfbd543e21e1c29561e3ab55e6d7b4..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF034XGB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_1.log b/ENCSR605SQL/cherimoya.fold_1.log deleted file mode 100644 index 6fbe5c2e22c25c84c62fc5cd891ae997bf5a8174..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1881 24.969515323638916 3.446591377258301 331.1738586425781 0.8140121698379517 621.9027709960938 0.17349210381507874 0.66772014 13.064082145690918 True -1 3762 20.761454343795776 0.5770952701568604 383.46685791015625 0.7988384962081909 540.979736328125 0.2541009783744812 0.77999073 5.7752509117126465 True -2 5643 20.75046133995056 40.327327728271484 311.05853271484375 1.1078473329544067 502.3078308105469 0.2813025116920471 0.8170464 3.0383989810943604 True -3 7524 21.544654607772827 0.5623340606689453 304.6251220703125 0.7535043954849243 484.8805847167969 0.29259049892425537 0.8280832 1.9977928400039673 True -4 9405 20.75485396385193 0.5669441223144531 336.952392578125 0.7103918194770813 480.9552307128906 0.29578253626823425 0.83441854 1.609230637550354 True -5 11286 20.7546067237854 0.5511794090270996 357.7996520996094 1.0370323657989502 477.6941223144531 0.29932698607444763 0.8371617 1.4854081869125366 True -6 13167 20.756282329559326 0.5586941242218018 364.7416687011719 0.8259992599487305 472.64215087890625 0.3052583336830139 0.8472648 1.3319107294082642 True -7 15048 20.77324867248535 0.5547642707824707 312.5550537109375 0.901295006275177 470.1415100097656 0.30717724561691284 0.85019296 1.2129641771316528 True -8 16929 20.758783102035522 28.462292671203613 291.1512451171875 0.9420735836029053 468.6841125488281 0.30949851870536804 0.85768324 1.100084900856018 True -9 18810 21.59086775779724 0.5649359226226807 308.74774169921875 0.7075302600860596 467.1005859375 0.3114354908466339 0.8610922 1.0132039785385132 True -10 20691 20.770933866500854 0.5656471252441406 446.3377990722656 0.931914210319519 462.56072998046875 0.315348356962204 0.8705399 0.8611669540405273 True -11 22572 20.75856328010559 1.1247873306274414 270.92913818359375 0.5217348337173462 460.2076110839844 0.3172912299633026 0.8763191 0.7773779630661011 True -12 24453 20.829898357391357 0.5500125885009766 223.72154235839844 0.5456295609474182 458.6064147949219 0.3187420964241028 0.8811803 0.7197595238685608 True -13 26334 20.819632291793823 0.5590596199035645 275.5289001464844 0.6739813089370728 455.7193908691406 0.3212205767631531 0.88533175 0.6595172882080078 True -14 28215 20.736728191375732 3.549558639526367 253.2339324951172 0.9093411564826965 454.3674621582031 0.3217821717262268 0.88978416 0.6149027347564697 True -15 30096 20.86057424545288 0.5572748184204102 250.69894409179688 0.4575713872909546 453.1459045410156 0.32325637340545654 0.89291215 0.5907914042472839 True -16 31977 20.74655795097351 0.5526692867279053 330.92803955078125 0.39666828513145447 453.63092041015625 0.32178178429603577 0.89464325 0.5614506006240845 True -17 33858 20.741840362548828 0.5529413223266602 258.954833984375 0.5589662790298462 453.79364013671875 0.3220488131046295 0.8977112 0.5574620366096497 True -18 35739 20.79002356529236 0.5590178966522217 297.47015380859375 0.39260587096214294 453.8504333496094 0.32206010818481445 0.89528537 0.5600128769874573 False -19 37620 20.734557628631592 0.5614547729492188 433.2529602050781 0.31331026554107666 454.9562683105469 0.31992051005363464 0.8948279 0.56489098072052 False diff --git a/ENCSR605SQL/cherimoya.fold_1.performance.tsv b/ENCSR605SQL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 74e32d16904b357d5264981e0cf9d11bcac7c1be..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -453.79364013671875 0.4590619206428528 0.3220488131046295 0.12684175372123718 0.8977112174034119 0.8645191788673401 0.5574620366096497 \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_2.evaluate.json b/ENCSR605SQL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3296637090ef97f6006b2da3b572964f1f1de7d4..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034XGB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_2.fit.json b/ENCSR605SQL/cherimoya.fold_2.fit.json deleted file mode 100644 index 4fbcb1d455ac1de6ea58ea18bbd15fd8c270c53d..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF034XGB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_2.log b/ENCSR605SQL/cherimoya.fold_2.log deleted file mode 100644 index b43f22039a7c6f6aed4b45e6406d851ee096022e..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2036 26.704177141189575 4.5750672817230225 474.740966796875 1.453072190284729 538.0812377929688 0.15919889509677887 0.65993434 10.205519676208496 True -1 4072 22.472044467926025 0.43305301666259766 306.5293273925781 1.004372477531433 451.29718017578125 0.24409955739974976 0.78504926 4.317701816558838 True -2 6108 22.454277753829956 21.76162624359131 257.7403869628906 1.2404041290283203 423.4222412109375 0.2620883584022522 0.81564337 2.3153250217437744 True -3 8144 23.11389946937561 0.4187784194946289 302.67041015625 0.9325811862945557 413.97991943359375 0.26857665181159973 0.8306071 1.3253525495529175 True -4 10180 22.469602346420288 0.4183328151702881 291.143798828125 1.1527833938598633 410.4275817871094 0.2721104025840759 0.8336606 1.0973381996154785 True -5 12216 22.4497230052948 0.41065144538879395 317.8019714355469 0.9784241318702698 408.88873291015625 0.2744833528995514 0.839488 1.0157874822616577 True -6 14252 22.45601224899292 27.181246280670166 337.307861328125 0.8170687556266785 405.9062805175781 0.27871179580688477 0.8463737 0.9435603022575378 True -7 16288 23.4216628074646 8.903855085372925 237.7250518798828 1.0799527168273926 404.74041748046875 0.28011611104011536 0.8492507 0.8813152313232422 True -8 18324 22.582324028015137 0.4207899570465088 330.6612548828125 0.9315259456634521 402.2572326660156 0.28263941407203674 0.85430217 0.7875273823738098 True -9 20360 22.611191034317017 0.4212343692779541 272.909423828125 0.6232297420501709 398.615478515625 0.2880910634994507 0.859236 0.7555999755859375 True -10 22396 22.462397813796997 0.41191625595092773 347.3848876953125 0.7686445713043213 398.120361328125 0.2872101664543152 0.86020976 0.7147237658500671 True -11 24432 22.199760913848877 0.4152534008026123 260.73455810546875 0.7146362066268921 396.489013671875 0.2891674339771271 0.86507696 0.6782378554344177 True -12 26468 23.258437871932983 23.97711753845215 227.77647399902344 0.6619364023208618 394.2607421875 0.2910648286342621 0.86714643 0.6481303572654724 True -13 28504 22.64442491531372 0.42942094802856445 289.5161437988281 0.5831941366195679 392.61627197265625 0.2937968671321869 0.87225324 0.6101900339126587 True -14 30540 22.077088117599487 27.551806449890137 308.9339599609375 0.42622146010398865 391.86785888671875 0.2937266528606415 0.8754705 0.5863734483718872 True -15 32576 22.991203784942627 0.4181060791015625 330.9673156738281 0.5300830602645874 392.8070373535156 0.2927830219268799 0.8762325 0.5659679174423218 True -16 34612 22.042897939682007 0.4179260730743408 235.17417907714844 0.34286531805992126 392.2630615234375 0.29351702332496643 0.8783562 0.5585811734199524 True -17 36648 22.011855840682983 0.4117867946624756 251.66368103027344 0.5543361902236938 391.8061828613281 0.2949813902378082 0.87797827 0.5561219453811646 False -18 38684 22.02591300010681 0.41315460205078125 264.4858093261719 0.302215576171875 393.0526123046875 0.29261139035224915 0.87792593 0.5618703365325928 False -19 40720 22.082200288772583 0.4171793460845947 397.22607421875 0.4473626911640167 392.6818542480469 0.2934924066066742 0.8766697 0.5621793270111084 False diff --git a/ENCSR605SQL/cherimoya.fold_2.performance.tsv b/ENCSR605SQL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 74a77f085bcca1255089915bde58cac199fb2390..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -392.2630615234375 0.481552392244339 0.29351702332496643 0.10770265758037567 0.8783562183380127 0.8286834955215454 0.5585811734199524 \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_3.evaluate.json b/ENCSR605SQL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3e718a37028d5ad961be4c260c65d365a88086f7..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034XGB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_3.fit.json b/ENCSR605SQL/cherimoya.fold_3.fit.json deleted file mode 100644 index c3a6a9275ea12c84aecfbddfffdd5cdf42b87ea9..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF034XGB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_3.log b/ENCSR605SQL/cherimoya.fold_3.log deleted file mode 100644 index abff517575794fae7581a34a8614f1e508a0408e..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1945 26.777734518051147 3.2287540435791016 275.2788391113281 0.9225544929504395 521.8414306640625 0.17310510575771332 0.65211475 10.885811805725098 True -1 3890 21.550095081329346 0.3976104259490967 313.6766357421875 1.1638160943984985 450.1027526855469 0.2478177845478058 0.7599504 4.779816150665283 True -2 5835 21.596574068069458 0.3967733383178711 410.3685607910156 0.8030310273170471 425.1062316894531 0.26330071687698364 0.79266495 2.5799474716186523 True -3 7780 21.45932626724243 2.011502504348755 264.4867248535156 0.6044175624847412 416.5799560546875 0.27287808060646057 0.80398154 1.8576122522354126 True -4 9725 21.510552167892456 0.38823652267456055 286.2044677734375 0.5056089162826538 412.80926513671875 0.2785600423812866 0.80879664 1.571580410003662 True -5 11670 21.493614673614502 0.3916513919830322 356.2576599121094 0.8400682210922241 410.4826354980469 0.28260865807533264 0.815184 1.4464439153671265 True -6 13615 21.582021951675415 27.450865030288696 364.6100769042969 1.0592008829116821 407.75360107421875 0.28545981645584106 0.8263077 1.2323373556137085 True -7 15560 21.774133443832397 0.40072059631347656 362.4396057128906 0.7767738699913025 406.3207702636719 0.28616756200790405 0.8299091 1.1608141660690308 True -8 17505 21.487473249435425 0.4878382682800293 313.57098388671875 0.8341866135597229 403.3689270019531 0.2898983657360077 0.83830047 1.0022156238555908 True -9 19450 21.527905702590942 0.38982582092285156 324.474365234375 0.9059275388717651 401.055419921875 0.29352810978889465 0.84616315 0.9183407425880432 True -10 21395 21.847366333007812 20.765076398849487 251.92172241210938 0.8467131853103638 399.8625793457031 0.29536697268486023 0.8498036 0.8774553537368774 True -11 23340 21.611261129379272 1.4182846546173096 362.0627136230469 0.9068417549133301 398.0826721191406 0.2968384325504303 0.856526 0.7902135848999023 True -12 25285 21.529414176940918 0.39633679389953613 217.68942260742188 0.5348340272903442 397.43536376953125 0.2969065308570862 0.8583612 0.7325660586357117 True -13 27230 21.50776958465576 0.39084577560424805 260.7167053222656 0.6048008799552917 394.4859924316406 0.30060622096061707 0.8650394 0.6864618062973022 True -14 29175 21.484323024749756 0.3919501304626465 283.3602294921875 0.5320106148719788 394.2601623535156 0.3003825545310974 0.8673301 0.6468981504440308 True -15 31120 21.448477506637573 0.38110923767089844 279.1902770996094 0.45433902740478516 393.3237609863281 0.30141353607177734 0.87206954 0.6179205775260925 True -16 33065 21.46394157409668 0.3855476379394531 263.14801025390625 0.5068714022636414 392.7427673339844 0.301815003156662 0.87289524 0.6010677814483643 True -17 35010 21.474980115890503 0.3883368968963623 311.7881774902344 0.5661391019821167 393.7475891113281 0.30016568303108215 0.8731157 0.5971876978874207 True -18 36955 21.481201887130737 0.3900432586669922 267.3583679199219 0.4124118685722351 393.8309020996094 0.30076032876968384 0.8707772 0.6063255071640015 False -19 38900 21.483108043670654 0.4066629409790039 343.7167053222656 0.36272478103637695 393.2034912109375 0.30222809314727783 0.869666 0.6131296753883362 False diff --git a/ENCSR605SQL/cherimoya.fold_3.performance.tsv b/ENCSR605SQL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9230c3e812220623164f1aa6c62a3d0df1b53a24..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -393.7475891113281 0.4764513671398163 0.30016571283340454 0.10840046405792236 0.8731157183647156 0.8259799480438232 0.5971876978874207 \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_4.evaluate.json b/ENCSR605SQL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4c0c363071c2480e063558dd44c3fafee29841cd..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034XGB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_4.fit.json b/ENCSR605SQL/cherimoya.fold_4.fit.json deleted file mode 100644 index c5188b369464b5dee8eba45dc0a5a6c8310b2734..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF034XGB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR605SQL/cherimoya.fold_4.log b/ENCSR605SQL/cherimoya.fold_4.log deleted file mode 100644 index 5393f8d8a8dd187c4fca13e8ccbc823d0b58123e..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1947 25.755459547042847 3.3728880882263184 291.24346923828125 1.039345622062683 465.6128234863281 0.15792173147201538 0.6531253 9.846281051635742 True -1 3894 21.453463315963745 0.3760364055633545 362.65618896484375 1.203943133354187 407.56146240234375 0.22571758925914764 0.77202904 4.219575881958008 True -2 5841 21.45988917350769 1.0983633995056152 322.814208984375 1.26859712600708 381.4812927246094 0.2450254112482071 0.8020917 2.1153976917266846 True -3 7788 21.439345121383667 0.3675968647003174 275.05499267578125 0.9730988144874573 372.4896545410156 0.25319576263427734 0.814907 1.3040881156921387 True -4 9735 21.511877298355103 0.3717060089111328 177.08544921875 0.9019087553024292 368.50213623046875 0.2578967809677124 0.82352495 1.0217742919921875 True -5 11682 21.371115684509277 0.36992311477661133 313.60247802734375 1.0690538883209229 366.91558837890625 0.26026761531829834 0.83164984 0.9878411293029785 True -6 13629 21.01807737350464 0.36818957328796387 259.47979736328125 0.6831972599029541 364.48822021484375 0.2634807527065277 0.83411777 0.9359654784202576 True -7 15576 21.04494285583496 0.3695244789123535 320.2746887207031 0.7530038356781006 363.5599670410156 0.26405251026153564 0.8378913 0.8901317715644836 True -8 17523 21.208545684814453 18.714545249938965 327.9180603027344 0.5318847894668579 362.583740234375 0.2648674249649048 0.8467524 0.7759542465209961 True -9 19470 21.04335594177246 0.3756086826324463 329.5049743652344 0.710690438747406 360.1732177734375 0.2678481340408325 0.85141414 0.6954358816146851 True -10 21417 21.053028106689453 0.36658620834350586 286.8221740722656 0.7031581997871399 358.1606140136719 0.2707330584526062 0.8562578 0.6587374210357666 True -11 23364 21.04534912109375 0.3825836181640625 350.02288818359375 0.7422844171524048 356.70123291015625 0.2718231678009033 0.860674 0.6070702075958252 True -12 25311 21.010368824005127 0.688908576965332 266.5633850097656 0.8772917985916138 354.5756530761719 0.2739141285419464 0.8671548 0.5777862668037415 True -13 27258 21.200780868530273 0.38823533058166504 281.5463562011719 0.6322421431541443 353.7126770019531 0.2754829227924347 0.8700464 0.5442686080932617 True -14 29205 21.050780534744263 0.37976908683776855 282.46929931640625 0.5342403054237366 353.4862365722656 0.2754387855529785 0.87514323 0.5234380960464478 True -15 31152 21.056755542755127 0.3698580265045166 217.3569793701172 0.5494974851608276 352.554443359375 0.277506560087204 0.8772197 0.5110967755317688 True -16 33099 21.13770604133606 0.3772742748260498 316.5223388671875 0.38115638494491577 353.9171447753906 0.2749978005886078 0.8785348 0.5054653286933899 True -17 35046 21.111397743225098 0.3667581081390381 352.303466796875 0.5052555799484253 353.228515625 0.27571985125541687 0.878015 0.5083866715431213 False -18 36993 21.085745096206665 0.3771202564239502 278.0523376464844 0.426678866147995 353.6907043457031 0.27510133385658264 0.8781912 0.5168139338493347 False -19 38940 21.084251642227173 0.37050437927246094 273.33111572265625 0.33663636445999146 354.88372802734375 0.2729554772377014 0.8756144 0.5231497883796692 False diff --git a/ENCSR605SQL/cherimoya.fold_4.performance.tsv b/ENCSR605SQL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8f8a7855223bc30944292070376ad20ff186d324..0000000000000000000000000000000000000000 --- a/ENCSR605SQL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -353.9171447753906 0.49522799253463745 0.2749978005886078 0.0930894985795021 0.8785347938537598 0.8228049874305725 0.5054653286933899 \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_0.evaluate.json b/ENCSR606QDB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2f4dbbf67ae40c2c501f089514e73ee018187148..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336QXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_0.fit.json b/ENCSR606QDB/cherimoya.fold_0.fit.json deleted file mode 100644 index e791620e256f3b133377b4726c696ed815db101f..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF336QXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_0.log b/ENCSR606QDB/cherimoya.fold_0.log deleted file mode 100644 index 20ac3959fefcc3387900ec719d33b3b11f1d0d27..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 34.16710567474365 4.85563063621521 429.9783935546875 0.28461575508117676 525.3529052734375 0.27190983295440674 0.79918194 3.5446128845214844 True -1 5456 30.344035387039185 0.6517083644866943 445.49237060546875 0.28095683455467224 485.5320739746094 0.3433609902858734 0.84094834 0.8898621201515198 True -2 8184 30.40307593345642 0.6389224529266357 382.4602355957031 0.16573643684387207 476.18310546875 0.3562176525592804 0.85865915 0.4100016951560974 True -3 10912 30.41219449043274 1.081057071685791 424.90765380859375 0.15782645344734192 472.4372863769531 0.3614971935749054 0.86309975 0.2649988830089569 True -4 13640 30.406616687774658 0.6601383686065674 476.69842529296875 0.19051051139831543 470.2100830078125 0.3656817376613617 0.8659101 0.22166776657104492 True -5 16368 30.387853622436523 0.6408040523529053 407.11944580078125 0.2895140051841736 470.27886962890625 0.364907830953598 0.8695856 0.18820711970329285 True -6 19096 30.35298252105713 0.6412680149078369 436.6884460449219 0.17936471104621887 468.4659118652344 0.36826127767562866 0.8725665 0.195116326212883 True -7 21824 30.295117139816284 0.635988712310791 514.245361328125 0.2246803641319275 466.881591796875 0.3715568482875824 0.8760603 0.18409162759780884 True -8 24552 30.36298394203186 0.6324150562286377 378.50482177734375 0.19588610529899597 466.1994934082031 0.37324196100234985 0.8793835 0.1809980720281601 True -9 27280 30.390627145767212 0.6312406063079834 431.52520751953125 0.2587871849536896 465.4385681152344 0.37400367856025696 0.88115764 0.1649867296218872 True -10 30008 30.400210857391357 0.6315674781799316 437.85491943359375 0.21634633839130402 464.5115661621094 0.37548330426216125 0.88626295 0.16276878118515015 True -11 32736 30.445377111434937 0.6323063373565674 378.1238708496094 0.18616372346878052 463.86761474609375 0.376632422208786 0.885431 0.15700078010559082 False -12 35464 30.396108388900757 0.6383442878723145 337.13433837890625 0.3874673545360565 462.54644775390625 0.37908050417900085 0.8899687 0.1501966416835785 True -13 38192 30.444249391555786 0.64255690574646 400.86187744140625 0.15178710222244263 461.5288391113281 0.38104039430618286 0.8915464 0.144886776804924 True -14 40920 30.453717947006226 0.6337506771087646 359.6180725097656 0.14621767401695251 461.0658874511719 0.3812539279460907 0.8946086 0.13892214000225067 True -15 43648 30.349550247192383 0.644874095916748 436.5369873046875 0.1666499674320221 460.7188720703125 0.38175493478775024 0.8988043 0.13568350672721863 True -16 46376 30.339747190475464 0.6343750953674316 418.00897216796875 0.15255111455917358 459.8321838378906 0.3834063708782196 0.90129983 0.13191615045070648 True -17 49104 30.346864700317383 0.634951114654541 422.13677978515625 0.18292510509490967 459.644775390625 0.3841705322265625 0.89879507 0.13158589601516724 False -18 51832 30.344100952148438 2.035595178604126 490.1273498535156 0.11519540846347809 460.3624572753906 0.38178354501724243 0.90099746 0.13151578605175018 False -19 54560 30.370954036712646 0.644343376159668 408.94915771484375 0.15357083082199097 460.2943115234375 0.3825531601905823 0.8986946 0.13215205073356628 False diff --git a/ENCSR606QDB/cherimoya.fold_0.performance.tsv b/ENCSR606QDB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7612949f386a9e61b7482960ee3155bee5953e59..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.8321838378906 0.409420371055603 0.3834063708782196 0.13285110890865326 0.9012998342514038 0.8816484212875366 0.13191615045070648 \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_1.evaluate.json b/ENCSR606QDB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ee598c8eb90f476d04b278f98bf81d6d66b6f251..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336QXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_1.fit.json b/ENCSR606QDB/cherimoya.fold_1.fit.json deleted file mode 100644 index 0bee7490edb489b339eafe1d4e1c780c5d3fe88d..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF336QXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_1.log b/ENCSR606QDB/cherimoya.fold_1.log deleted file mode 100644 index eb11f9cb435fffdb6433d15a2032dc2b3f55f8ca..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2693 33.88976502418518 7.943784952163696 368.1856384277344 0.22829915583133698 604.7328491210938 0.27351102232933044 0.78138536 4.717077255249023 True -1 5386 29.922633409500122 20.14868712425232 401.40423583984375 0.2868051528930664 553.9523315429688 0.3536989986896515 0.828331 0.888242244720459 True -2 8079 30.007763624191284 0.7323224544525146 443.67718505859375 0.3894504904747009 544.8788452148438 0.36540600657463074 0.84441483 0.3392767310142517 True -3 10772 29.931880474090576 0.7285714149475098 320.9676818847656 0.32676491141319275 541.3151245117188 0.36805397272109985 0.8460654 0.33456388115882874 True -4 13465 30.000431776046753 25.810601234436035 396.69256591796875 0.2291540801525116 536.3438720703125 0.37643152475357056 0.8589209 0.2543996274471283 True -5 16158 30.545342922210693 0.7299118041992188 384.5429992675781 0.2607629895210266 535.486572265625 0.37738507986068726 0.8635426 0.2837454080581665 True -6 18851 30.02923059463501 0.7478892803192139 350.3768310546875 0.17015865445137024 532.3424682617188 0.3826327323913574 0.8693988 0.24721649289131165 True -7 21544 30.166131019592285 0.7582516670227051 395.2413330078125 0.23583492636680603 529.4461669921875 0.38721421360969543 0.87346566 0.2533985376358032 True -8 24237 30.29979181289673 0.7442653179168701 423.273681640625 0.21957866847515106 527.7240600585938 0.3897397816181183 0.8762421 0.24259765446186066 True -9 26930 30.1370632648468 0.7397453784942627 414.2290344238281 0.28443077206611633 525.7833251953125 0.39298632740974426 0.876858 0.2329866588115692 True -10 29623 30.1824312210083 0.735720157623291 336.821044921875 0.22687827050685883 524.6050415039062 0.3944469392299652 0.8809812 0.20374539494514465 True -11 32316 30.030104637145996 0.735107421875 503.3556823730469 0.18504533171653748 523.4232788085938 0.395938515663147 0.88607866 0.19121864438056946 True -12 35009 30.115047454833984 2.6025519371032715 456.39862060546875 0.24918563663959503 522.5706176757812 0.3966376483440399 0.89153904 0.17654885351657867 True -13 37702 30.040118932724 1.5675055980682373 434.3153076171875 0.12475192546844482 521.2054443359375 0.39852607250213623 0.89204603 0.17039211094379425 True -14 40395 30.050564527511597 0.7262592315673828 375.96978759765625 0.15383125841617584 520.0930786132812 0.40034329891204834 0.89768416 0.16388726234436035 True -15 43088 29.99424386024475 0.7398803234100342 420.0325622558594 0.1301829069852829 519.5294799804688 0.4003218114376068 0.90002036 0.15594017505645752 True -16 45781 30.523316860198975 0.7370684146881104 414.805419921875 0.14996546506881714 518.9384765625 0.4009210467338562 0.90312725 0.14930276572704315 True -17 48474 30.14914608001709 0.7338874340057373 377.0373229980469 0.14479833841323853 518.9654541015625 0.40168800950050354 0.9037522 0.14871537685394287 True -18 51167 30.142762422561646 15.42668890953064 406.81951904296875 0.16306746006011963 518.6543579101562 0.40228310227394104 0.9032764 0.14953702688217163 False -19 53860 30.21905541419983 1.248110294342041 392.2078857421875 0.08184240758419037 518.3856201171875 0.40258654952049255 0.90354943 0.15035733580589294 False diff --git a/ENCSR606QDB/cherimoya.fold_1.performance.tsv b/ENCSR606QDB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 373a2aa9bb6c682af30c9e81914613a804ceb7f9..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -518.9654541015625 0.3931616246700287 0.40168800950050354 0.14878907799720764 0.9037522077560425 0.8958899974822998 0.14871537685394287 \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_2.evaluate.json b/ENCSR606QDB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 31b55bed7f3836296b8b87e799b5cd44cea48d83..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336QXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_2.fit.json b/ENCSR606QDB/cherimoya.fold_2.fit.json deleted file mode 100644 index c9077165621b5387fe668e21b4ea81428f6c8e36..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF336QXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_2.log b/ENCSR606QDB/cherimoya.fold_2.log deleted file mode 100644 index c594289ffb118f55ef235196fee59dfc1dc1e867..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2865 35.4734890460968 3.549123764038086 457.832275390625 0.4300805330276489 544.1685180664062 0.2766191363334656 0.79196995 3.5897436141967773 True -1 5730 31.876221895217896 0.6091015338897705 440.9600524902344 0.22308307886123657 502.8711853027344 0.3473685681819916 0.83431786 0.7584468722343445 True -2 8595 31.830963850021362 0.6009359359741211 389.7574768066406 0.25654393434524536 494.4963073730469 0.35708433389663696 0.8418542 0.3473447263240814 True -3 11460 31.804219007492065 0.5972676277160645 438.27294921875 0.31994935870170593 490.5813903808594 0.3637934923171997 0.85038793 0.3003506362438202 True -4 14325 31.881324529647827 0.5826799869537354 382.4676818847656 0.24196580052375793 488.6598815917969 0.3675617575645447 0.857033 0.256604939699173 True -5 17190 31.90607261657715 0.9085114002227783 399.93572998046875 0.2518407702445984 486.583984375 0.37154877185821533 0.85907215 0.25553277134895325 True -6 20055 31.905811309814453 0.6013278961181641 435.96405029296875 0.1642613708972931 485.5025329589844 0.37309715151786804 0.8647938 0.25352412462234497 True -7 22920 31.851198196411133 0.6099002361297607 377.9601135253906 0.19697339832782745 484.1084289550781 0.3755461573600769 0.86878735 0.23440322279930115 True -8 25785 31.97015905380249 0.6029565334320068 429.0535888671875 0.18360041081905365 482.7695617675781 0.37828418612480164 0.86839545 0.23141367733478546 False -9 28650 32.07473373413086 0.5986955165863037 347.5749206542969 0.1907031536102295 482.09906005859375 0.37910792231559753 0.8746303 0.2121199667453766 True -10 31515 31.906918048858643 0.6080203056335449 397.1203308105469 0.10092677175998688 480.1346130371094 0.38298410177230835 0.8753239 0.19979754090309143 True -11 34380 31.965122938156128 0.6015689373016357 384.9056396484375 0.1815025359392166 479.4676818847656 0.3832350969314575 0.8794786 0.19142380356788635 True -12 37245 31.89445996284485 0.5918540954589844 332.1913757324219 0.24963219463825226 478.333251953125 0.38515135645866394 0.88015115 0.1798820197582245 True -13 40110 31.932878732681274 0.9817783832550049 385.22174072265625 0.18582791090011597 476.7699890136719 0.3881957232952118 0.8837283 0.17030885815620422 True -14 42975 31.9365553855896 20.56050968170166 386.95758056640625 0.10761480033397675 476.39593505859375 0.3876504600048065 0.8859934 0.1620023399591446 True -15 45840 32.09129738807678 0.6034488677978516 455.99993896484375 0.13962893187999725 476.2437744140625 0.38843417167663574 0.88934416 0.1527424156665802 True -16 48705 32.15696620941162 0.605316162109375 436.4447021484375 0.14287589490413666 475.85040283203125 0.38852545619010925 0.8906184 0.1481238603591919 True -17 51570 32.40536165237427 0.5962724685668945 431.04034423828125 0.18838028609752655 474.98931884765625 0.3905535638332367 0.891126 0.14547662436962128 True -18 54435 31.960383415222168 0.5977985858917236 401.040771484375 0.1517578661441803 475.6654357910156 0.3892650604248047 0.8920039 0.14565719664096832 True -19 57300 31.875598669052124 0.5994002819061279 390.693603515625 0.18328449130058289 475.8206787109375 0.38891705870628357 0.89154726 0.14584669470787048 False diff --git a/ENCSR606QDB/cherimoya.fold_2.performance.tsv b/ENCSR606QDB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b297c35fa47384553bbff3bb14413a1227743d43..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.6654357910156 0.40544000267982483 0.3892650604248047 0.13660269975662231 0.8920038938522339 0.8789610266685486 0.14565719664096832 \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_3.evaluate.json b/ENCSR606QDB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 06acd72e8b969e1473dad1c0014bd2b5fa879fe8..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336QXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_3.fit.json b/ENCSR606QDB/cherimoya.fold_3.fit.json deleted file mode 100644 index 192edee4eaea2d6cf53aa79f63ceb235d7dc1c33..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF336QXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_3.log b/ENCSR606QDB/cherimoya.fold_3.log deleted file mode 100644 index d5c9bd11485fb8a7ca2aedc9c06c5793244f990e..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 34.48816418647766 3.535842180252075 405.0992736816406 0.4018433690071106 512.1799926757812 0.28136175870895386 0.787143 3.474539041519165 True -1 5504 30.58769989013672 0.819998025894165 418.29595947265625 0.17103219032287598 472.376953125 0.3485434353351593 0.8330093 0.8404962420463562 True -2 8256 30.59359383583069 0.5764901638031006 434.67425537109375 0.3076683580875397 464.3830261230469 0.3615565896034241 0.8463786 0.320834755897522 True -3 11008 30.59167981147766 1.5532281398773193 436.3648986816406 0.2596340477466583 461.1498107910156 0.36540335416793823 0.8512497 0.2577219307422638 True -4 13760 30.609375476837158 0.5698721408843994 343.6336669921875 0.23337772488594055 459.6565856933594 0.3666732609272003 0.85664654 0.1979435831308365 True -5 16512 30.5923011302948 0.577723503112793 417.3036193847656 0.2135942280292511 458.1085510253906 0.36987853050231934 0.85953575 0.19603846967220306 True -6 19264 30.56280255317688 0.5704035758972168 409.50457763671875 0.22593268752098083 457.0137939453125 0.37171974778175354 0.86271954 0.20601224899291992 True -7 22016 30.593743085861206 0.573577880859375 398.6387023925781 0.18856126070022583 454.6083679199219 0.3762029707431793 0.86919385 0.1979108303785324 True -8 24768 30.67011594772339 0.5759451389312744 435.0880126953125 0.14308223128318787 453.9515075683594 0.3767920434474945 0.872459 0.18761573731899261 True -9 27520 30.650952339172363 0.5817389488220215 468.75738525390625 0.19884678721427917 452.79864501953125 0.3793396055698395 0.8749121 0.1854770928621292 True -10 30272 30.664807558059692 0.5735609531402588 398.0440673828125 0.1961732804775238 452.0321960449219 0.3805118203163147 0.87854177 0.17973874509334564 True -11 33024 30.628499031066895 0.5737688541412354 408.92034912109375 0.2355474829673767 451.1703796386719 0.3816315829753876 0.88398343 0.17109376192092896 True -12 35776 30.648003578186035 0.5744724273681641 448.12994384765625 0.2880978584289551 449.9112243652344 0.3836110234260559 0.8877126 0.15974043309688568 True -13 38528 30.62805151939392 0.5768404006958008 386.2279357910156 0.15506651997566223 448.9857177734375 0.3846557140350342 0.88862354 0.15872274339199066 True -14 41280 30.638269901275635 0.56998610496521 386.3031921386719 0.15846121311187744 447.90087890625 0.38628533482551575 0.8923986 0.1516369879245758 True -15 44032 31.095299005508423 0.5761518478393555 386.0971984863281 0.12279398739337921 448.0811462402344 0.385763943195343 0.892696 0.14724232256412506 True -16 46784 30.629850149154663 0.5756351947784424 421.09014892578125 0.17910034954547882 447.69677734375 0.3856741487979889 0.8971426 0.14390769600868225 True -17 49536 30.650821447372437 1.1267235279083252 369.83294677734375 0.19587138295173645 447.42230224609375 0.3864140510559082 0.8974051 0.141645610332489 True -18 52288 30.64294409751892 0.5864076614379883 401.9736633300781 0.12187787890434265 447.3548889160156 0.3869767487049103 0.89818144 0.14178499579429626 True -19 55040 30.59764528274536 1.1541399955749512 371.265625 0.11749520897865295 446.9657287597656 0.38826417922973633 0.8991171 0.1418912708759308 True diff --git a/ENCSR606QDB/cherimoya.fold_3.performance.tsv b/ENCSR606QDB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 63f9c1208247bf19b1587c257614de814dcde1d7..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -446.9657287597656 0.409355103969574 0.38826417922973633 0.1338197886943817 0.899117112159729 0.8715606927871704 0.1418912708759308 \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_4.evaluate.json b/ENCSR606QDB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9375b91b77e7994fdff5bc44eddbfb3d0136fb08..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336QXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_4.fit.json b/ENCSR606QDB/cherimoya.fold_4.fit.json deleted file mode 100644 index 89b9951851eaa97bc636acce7843ae689e8ab588..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF336QXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606QDB/cherimoya.fold_4.log b/ENCSR606QDB/cherimoya.fold_4.log deleted file mode 100644 index 44ae95ebbfa62fc3de78581e1281a8e010e8f17d..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2858 36.29027533531189 4.459999084472656 397.9864501953125 0.3922058045864105 497.530517578125 0.2742941379547119 0.79520696 2.6120188236236572 True -1 5716 31.783944129943848 0.7431228160858154 386.5650939941406 0.18628042936325073 458.17327880859375 0.3417954444885254 0.8314521 0.7430428862571716 True -2 8574 31.77658700942993 0.6102502346038818 388.003662109375 0.28536906838417053 451.6416320800781 0.3525722026824951 0.8469651 0.2892056703567505 True -3 11432 31.768415927886963 0.6238954067230225 428.048828125 0.31513091921806335 447.82257080078125 0.35882657766342163 0.8568339 0.30184701085090637 True -4 14290 31.78356623649597 0.6194331645965576 356.59710693359375 0.21432876586914062 446.8359680175781 0.36096909642219543 0.8606189 0.2064196765422821 True -5 17148 31.815927982330322 0.6067874431610107 333.0780029296875 0.1380148082971573 445.2314453125 0.3648695945739746 0.86312723 0.19894850254058838 True -6 20006 31.77016568183899 0.6069133281707764 397.08349609375 0.2163819968700409 444.71136474609375 0.36559104919433594 0.8646194 0.18747054040431976 True -7 22864 31.782739639282227 0.6113526821136475 403.4200439453125 0.2700742483139038 443.1501770019531 0.36935046315193176 0.8698726 0.17513592541217804 True -8 25722 31.78610110282898 0.610985279083252 466.21563720703125 0.21381543576717377 443.3321533203125 0.3674963712692261 0.87205726 0.17786002159118652 True -9 28580 31.788668870925903 0.6130311489105225 372.43988037109375 0.237503319978714 442.0891418457031 0.36949726939201355 0.8780855 0.1636018007993698 True -10 31438 31.79302453994751 0.6108593940734863 365.5075378417969 0.13151505589485168 440.9463806152344 0.37178754806518555 0.87888175 0.17411470413208008 True -11 34296 31.801659107208252 0.6112699508666992 362.36334228515625 0.20306402444839478 439.93359375 0.37361401319503784 0.8829259 0.1544790267944336 True -12 37154 31.77684712409973 0.6125872135162354 411.38031005859375 0.182608962059021 439.13916015625 0.3754090964794159 0.8843536 0.14493145048618317 True -13 40012 31.782291412353516 0.613116979598999 390.3375549316406 0.14238399267196655 438.5084228515625 0.3760833144187927 0.8903818 0.14130593836307526 True -14 42870 31.828075647354126 0.6176111698150635 464.73040771484375 0.1268714964389801 437.7580261230469 0.3773285150527954 0.89155775 0.13378223776817322 True -15 45728 31.803964376449585 27.788738012313843 417.63067626953125 0.12549607455730438 438.19329833984375 0.3757658898830414 0.8971106 0.12800748646259308 True -16 48586 31.853256464004517 0.6481490135192871 378.7952880859375 0.11123790591955185 437.3804016113281 0.37769150733947754 0.89764106 0.12360367178916931 True -17 51444 31.800883769989014 0.6284608840942383 353.97271728515625 0.1442262828350067 437.1527404785156 0.37871384620666504 0.89888054 0.12095009535551071 True -18 54302 31.808444023132324 0.6198296546936035 372.05975341796875 0.06876831501722336 437.4028015136719 0.3778795897960663 0.89982927 0.12153957039117813 True -19 57160 31.768721342086792 0.6277832984924316 302.1767272949219 0.12070945650339127 437.805908203125 0.37662890553474426 0.8982598 0.12129439413547516 False diff --git a/ENCSR606QDB/cherimoya.fold_4.performance.tsv b/ENCSR606QDB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index afe68cede31e8fe928368bf6ea9df2b451ead9d5..0000000000000000000000000000000000000000 --- a/ENCSR606QDB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -437.4028015136719 0.41527363657951355 0.3778795897960663 0.12763872742652893 0.8998292684555054 0.8773678541183472 0.12153957039117813 \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_0.evaluate.json b/ENCSR606UAR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4fe83fb2ff0b36435635236175e7928d67bde9d5..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF346JIL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_0.fit.json b/ENCSR606UAR/cherimoya.fold_0.fit.json deleted file mode 100644 index b4fb08173a5a6317d4014cb80ecc36fe52e95dbb..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF346JIL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_0.log b/ENCSR606UAR/cherimoya.fold_0.log deleted file mode 100644 index 8c42829f1f9b46491741c1d2b76ee646aab0aa2b..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 34.15020775794983 4.768420219421387 234.11123657226562 0.689020574092865 313.9927673339844 0.17199355363845825 0.69381 3.614241361618042 True -1 5564 30.700450658798218 0.6201622486114502 264.6813659667969 0.7971708178520203 296.3948669433594 0.24165192246437073 0.74234736 1.2008192539215088 True -2 8346 30.64077353477478 0.5627586841583252 207.10433959960938 0.5677676796913147 291.9156188964844 0.25407668948173523 0.74610543 0.6403298377990723 True -3 11128 31.262336492538452 11.93889307975769 203.32611083984375 0.7228030562400818 290.1795349121094 0.2575278878211975 0.7504323 0.54366534948349 True -4 13910 30.661912441253662 14.96063232421875 212.76156616210938 0.47356435656547546 288.70538330078125 0.26335933804512024 0.75652105 0.5487024188041687 True -5 16692 30.826586484909058 0.5766491889953613 266.9703369140625 0.7315860986709595 287.9298095703125 0.2663518190383911 0.7574719 0.5660527348518372 True -6 19474 30.586994647979736 0.5541417598724365 272.1465759277344 0.4497292637825012 287.1693115234375 0.27038800716400146 0.75910395 0.6026502847671509 True -7 22256 30.602060556411743 0.585698127746582 277.7423095703125 0.47054001688957214 286.65802001953125 0.2718619704246521 0.7650152 0.5553395748138428 True -8 25038 30.65467095375061 0.5585157871246338 211.56320190429688 0.49075913429260254 285.83599853515625 0.2753652334213257 0.7692489 0.5267286896705627 True -9 27820 30.656432628631592 0.5638232231140137 182.08523559570312 0.8034164905548096 285.10552978515625 0.2783145308494568 0.7718797 0.5065499544143677 True -10 30602 30.60969567298889 0.7291064262390137 240.84547424316406 0.633817732334137 284.7846374511719 0.2799483835697174 0.77341086 0.49705949425697327 True -11 33384 30.645030975341797 0.5695703029632568 264.8143615722656 0.3420681059360504 284.11456298828125 0.28267061710357666 0.77575713 0.4783632755279541 True -12 36166 30.636780261993408 0.5641281604766846 264.6540222167969 0.32348179817199707 283.79022216796875 0.2836131155490875 0.7784308 0.44828787446022034 True -13 38948 30.65469241142273 0.5680720806121826 218.90228271484375 0.4398237466812134 283.45574951171875 0.28425103425979614 0.78410316 0.4217112064361572 True -14 41730 30.638845920562744 0.5719704627990723 235.86941528320312 0.3173590302467346 282.8236999511719 0.2866855263710022 0.79143375 0.3817530572414398 True -15 44512 30.634650468826294 0.5683166980743408 232.36614990234375 0.39725711941719055 282.26873779296875 0.2895827293395996 0.7992692 0.3467932641506195 True -16 47294 30.733108282089233 0.5631341934204102 250.10714721679688 0.3001094460487366 282.222900390625 0.2891714870929718 0.80320597 0.33016079664230347 True -17 50076 30.677634954452515 0.5945694446563721 184.62106323242188 0.5399492979049683 282.1358947753906 0.28941240906715393 0.80477875 0.31793490052223206 True -18 52858 30.643552780151367 0.6360971927642822 210.81048583984375 0.4002881646156311 282.0992431640625 0.28977277874946594 0.8064923 0.30854395031929016 True -19 55640 30.662898302078247 1.1139323711395264 242.17041015625 0.2694743573665619 282.382080078125 0.28854256868362427 0.8057387 0.3130355477333069 False diff --git a/ENCSR606UAR/cherimoya.fold_0.performance.tsv b/ENCSR606UAR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f05bc0a9c60a70977d52da04ac412f05d68439b8..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -282.0992431640625 0.49131515622138977 0.28977280855178833 0.0762379914522171 0.8064923286437988 0.7498806715011597 0.30854395031929016 \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_1.evaluate.json b/ENCSR606UAR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d331b35bb998074c3ee2ae7fd1e493614a3dd3a3..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF346JIL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_1.fit.json b/ENCSR606UAR/cherimoya.fold_1.fit.json deleted file mode 100644 index ffaffb06482486f9ed72a1e840a286b280e2b400..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF346JIL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_1.log b/ENCSR606UAR/cherimoya.fold_1.log deleted file mode 100644 index a084fac0967fc9a38820de5a0021f708dfbebf35..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2732 33.75601387023926 4.432880878448486 232.25958251953125 0.627192497253418 362.7243957519531 0.17907854914665222 0.6986206 3.383711576461792 True -1 5464 30.13302779197693 0.7645924091339111 190.58221435546875 0.7375645637512207 340.96209716796875 0.25584676861763 0.7634184 1.1619454622268677 True -2 8196 30.059440851211548 0.7714207172393799 207.22830200195312 0.5274646282196045 335.8846740722656 0.2658917009830475 0.77116674 0.5871487855911255 True -3 10928 30.055397033691406 1.0006976127624512 224.3498077392578 0.4830666482448578 332.6396179199219 0.27395302057266235 0.7763796 0.5011103749275208 True -4 13660 30.337329149246216 10.752247095108032 231.01312255859375 0.5640749931335449 329.8030700683594 0.28273528814315796 0.7753906 0.5593888759613037 False -5 16392 30.15762186050415 0.7350692749023438 209.9227294921875 0.7347967624664307 329.0118713378906 0.2847466468811035 0.774099 0.5738816857337952 False -6 19124 30.248342037200928 0.7366623878479004 226.34152221679688 0.6868637204170227 328.779541015625 0.28436222672462463 0.7788927 0.5373588800430298 True -7 21856 30.426527976989746 0.7757976055145264 270.9154052734375 0.6246998310089111 327.6169738769531 0.2890242338180542 0.7854746 0.5459120273590088 True -8 24588 30.24136257171631 0.7327029705047607 208.53228759765625 0.35941842198371887 326.5780944824219 0.29294946789741516 0.78830814 0.5294813513755798 True -9 27320 30.31381392478943 0.7305862903594971 213.02880859375 0.4062727391719818 325.7994689941406 0.29510125517845154 0.7902109 0.4949658215045929 True -10 30052 30.22774648666382 1.670874834060669 244.66622924804688 0.3940899968147278 325.3158874511719 0.29672881960868835 0.79257065 0.4934943914413452 True -11 32784 30.33505916595459 13.066471576690674 207.4260711669922 0.41916120052337646 324.00164794921875 0.3014148473739624 0.79846925 0.4868762493133545 True -12 35516 30.334840059280396 0.7405202388763428 191.58737182617188 0.7619863748550415 323.4850769042969 0.302450954914093 0.8042525 0.45991411805152893 True -13 38248 30.20671033859253 0.7339379787445068 233.5634765625 0.4535420835018158 323.40087890625 0.3021202087402344 0.8085625 0.4289732575416565 True -14 40980 30.060354709625244 0.713930606842041 193.39913940429688 0.42407259345054626 322.176025390625 0.30716270208358765 0.8142299 0.3982432782649994 True -15 43712 30.069612503051758 0.7225675582885742 221.21151733398438 0.5328404903411865 322.1528015136719 0.30594801902770996 0.81928873 0.37580546736717224 True -16 46444 30.630005359649658 7.953316926956177 236.8827362060547 0.4182284474372864 321.67633056640625 0.30763155221939087 0.82434225 0.35993263125419617 True -17 49176 30.228938579559326 25.83008623123169 232.6831512451172 0.19861485064029694 321.5245666503906 0.30773860216140747 0.82622 0.3523785173892975 True -18 51908 30.183618307113647 12.264170408248901 220.47268676757812 0.42079102993011475 321.87152099609375 0.30613869428634644 0.8274351 0.3455285429954529 True -19 54640 30.24335289001465 0.7577097415924072 231.1561279296875 0.17142891883850098 322.07452392578125 0.30565521121025085 0.8285157 0.34726080298423767 True diff --git a/ENCSR606UAR/cherimoya.fold_1.performance.tsv b/ENCSR606UAR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index fefc403d76eea40c55a390f832748520a26f54c7..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -322.07452392578125 0.4748536944389343 0.30565521121025085 0.09155035018920898 0.8285157084465027 0.790182888507843 0.34726080298423767 \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_2.evaluate.json b/ENCSR606UAR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 54210e15a83b0242c49d5113b82d4831d54bffa8..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF346JIL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_2.fit.json b/ENCSR606UAR/cherimoya.fold_2.fit.json deleted file mode 100644 index f4ce1c629108e671b14784d5ac1a8da545d306aa..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF346JIL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_2.log b/ENCSR606UAR/cherimoya.fold_2.log deleted file mode 100644 index 17317b6f3fd957f0b4de6966744431c422ef60c6..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 35.67778396606445 3.8499977588653564 202.8335723876953 0.7921541929244995 326.4800109863281 0.1766795516014099 0.68475056 3.0079314708709717 True -1 5788 31.905903100967407 0.5750935077667236 242.82723999023438 0.7284849286079407 306.2638244628906 0.24979612231254578 0.7466047 1.078965187072754 True -2 8682 31.834741353988647 0.5417311191558838 205.51036071777344 0.5955371856689453 301.7250061035156 0.2614169120788574 0.7543499 0.7165967226028442 True -3 11576 31.842070817947388 0.5262033939361572 213.1053466796875 0.7389734387397766 298.9659118652344 0.27113857865333557 0.7631797 0.6164475679397583 True -4 14470 31.90740966796875 0.7852776050567627 236.45855712890625 0.6973463296890259 298.80120849609375 0.27134427428245544 0.76485366 0.6871729493141174 True -5 17364 31.94483733177185 0.5531625747680664 240.16453552246094 0.45976290106773376 297.8403015136719 0.2756892442703247 0.76734364 0.6763837933540344 True -6 20258 31.880141019821167 0.5525131225585938 228.95773315429688 0.48586422204971313 297.4520263671875 0.2767809331417084 0.77321404 0.6555184125900269 True -7 23152 31.857908964157104 0.5860521793365479 196.040771484375 0.589050829410553 296.84423828125 0.2792339324951172 0.77577364 0.5911601185798645 True -8 26046 31.899616479873657 0.5412757396697998 235.76756286621094 0.30410417914390564 295.675537109375 0.2840103507041931 0.7781267 0.5565748810768127 True -9 28940 31.862340927124023 0.5275661945343018 226.3656005859375 0.5614331364631653 294.8888244628906 0.28640273213386536 0.7802758 0.5135680437088013 True -10 31834 31.84742784500122 0.8489542007446289 206.9860382080078 0.32681888341903687 294.9150390625 0.28562870621681213 0.78595847 0.4788697063922882 True -11 34728 31.8984797000885 0.5291421413421631 265.8266906738281 0.2977987825870514 294.07183837890625 0.2881244421005249 0.78676254 0.4712894558906555 True -12 37622 31.940586805343628 0.6457080841064453 233.5553436279297 0.6810746192932129 293.21234130859375 0.2911459505558014 0.7917146 0.46576637029647827 True -13 40516 31.883110284805298 0.5341894626617432 206.52639770507812 0.3460432291030884 292.73834228515625 0.29273635149002075 0.7943707 0.41683724522590637 True -14 43410 31.898658752441406 0.5287985801696777 247.11973571777344 0.4600912630558014 292.29595947265625 0.2950889468193054 0.7985454 0.40516218543052673 True -15 46304 31.887465476989746 0.5383005142211914 206.61526489257812 0.3698756694793701 292.2521057128906 0.2946328818798065 0.80527675 0.36787986755371094 True -16 49198 31.89676260948181 0.6948916912078857 268.1510009765625 0.3832331895828247 291.91217041015625 0.29528382420539856 0.8097604 0.35000669956207275 True -17 52092 31.864093780517578 0.5218541622161865 224.2914276123047 0.31454214453697205 291.97576904296875 0.2959398329257965 0.81014466 0.3382691740989685 True -18 54986 31.86168646812439 0.5329091548919678 263.48785400390625 0.25190433859825134 292.0350646972656 0.29553332924842834 0.81106275 0.3335866332054138 True -19 57880 31.850993871688843 0.5227246284484863 239.03529357910156 0.32746776938438416 292.3845520019531 0.29346907138824463 0.80954057 0.33578670024871826 False diff --git a/ENCSR606UAR/cherimoya.fold_2.performance.tsv b/ENCSR606UAR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 56555da63808f6c58c1274bfbaa0122c02adf0d1..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -292.0350646972656 0.48653727769851685 0.29553332924842834 0.08137170225381851 0.811062753200531 0.7609191536903381 0.3335866332054138 \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_3.evaluate.json b/ENCSR606UAR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f675e9927e6d3beee637937c21cace2767c1fab7..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF346JIL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_3.fit.json b/ENCSR606UAR/cherimoya.fold_3.fit.json deleted file mode 100644 index efac9a089721688bc9aadfff5447e563c07a4d2c..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF346JIL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_3.log b/ENCSR606UAR/cherimoya.fold_3.log deleted file mode 100644 index b8b5c3dcad4d193032013cd6adb82db9c57e6969..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2778 34.67657232284546 3.6196348667144775 268.60931396484375 0.9877828359603882 333.8697509765625 0.17281967401504517 0.6965957 3.8059396743774414 True -1 5556 30.69577383995056 0.9335825443267822 250.97125244140625 0.7834035754203796 314.732666015625 0.24481426179409027 0.7511825 1.180422306060791 True -2 8334 30.57709813117981 0.54215407371521 214.06048583984375 0.4677613377571106 311.2680358886719 0.2546549141407013 0.7622985 0.5744161009788513 True -3 11112 30.57606530189514 0.5684530735015869 202.68081665039062 0.5985794067382812 308.95184326171875 0.26149633526802063 0.7627998 0.5348506569862366 True -4 13890 30.644989728927612 0.5511174201965332 245.15518188476562 0.5289703607559204 307.2861022949219 0.26786017417907715 0.77224207 0.4913076162338257 True -5 16668 30.627991199493408 0.5572264194488525 250.66412353515625 0.644501805305481 306.8913879394531 0.26934880018234253 0.7712927 0.5397573113441467 False -6 19446 30.61380124092102 0.5522210597991943 214.6923065185547 0.7695691585540771 306.00140380859375 0.27311480045318604 0.77578187 0.5188981890678406 True -7 22224 30.613219261169434 0.5565025806427002 253.06597900390625 0.800505518913269 305.6842956542969 0.2738586664199829 0.7764189 0.48614880442619324 True -8 25002 30.573960781097412 0.5545985698699951 238.98377990722656 0.5962450504302979 304.98626708984375 0.2765275537967682 0.7777797 0.4755825996398926 True -9 27780 30.620136976242065 1.1410012245178223 233.60565185546875 0.5237528681755066 304.29400634765625 0.2786060571670532 0.78009284 0.443314790725708 True -10 30558 30.645100116729736 0.5590178966522217 187.56887817382812 0.6753437519073486 303.61468505859375 0.2820832431316376 0.78538173 0.42328181862831116 True -11 33336 30.572712659835815 0.5617787837982178 204.315185546875 0.5124295949935913 303.1939392089844 0.2828434407711029 0.7843192 0.43331077694892883 False -12 36114 30.628421306610107 0.5505855083465576 211.87454223632812 0.329007089138031 302.816162109375 0.28541526198387146 0.7890197 0.4267246425151825 True -13 38892 30.583902597427368 0.5528757572174072 208.01329040527344 0.33359962701797485 302.2033996582031 0.28691789507865906 0.79345965 0.4013001322746277 True -14 41670 30.646108627319336 0.5430550575256348 245.1754913330078 0.6017951965332031 302.1417541503906 0.2868027687072754 0.80154693 0.3750118911266327 True -15 44448 30.6107976436615 0.5460548400878906 233.79534912109375 0.5329959988594055 301.738037109375 0.28807324171066284 0.8083152 0.36103442311286926 True -16 47226 30.660816431045532 0.5604941844940186 220.296630859375 0.36577892303466797 301.50726318359375 0.28830793499946594 0.81257117 0.3462879955768585 True -17 50004 30.636914253234863 0.5426225662231445 258.58331298828125 0.3582385778427124 301.38165283203125 0.2896134555339813 0.8126696 0.34531888365745544 True -18 52782 30.64888095855713 0.5572612285614014 221.99533081054688 0.23735715448856354 301.23388671875 0.2904748022556305 0.8136113 0.3364563286304474 True -19 55560 30.64570116996765 0.5512163639068604 236.28982543945312 0.3475736975669861 301.5819091796875 0.28868383169174194 0.8114297 0.3418697714805603 False diff --git a/ENCSR606UAR/cherimoya.fold_3.performance.tsv b/ENCSR606UAR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a70c05b61e18483c9d903033159f32d697c01324..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -301.23388671875 0.486844927072525 0.2904748022556305 0.08267265558242798 0.8136113286018372 0.7561985850334167 0.3364563286304474 \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_4.evaluate.json b/ENCSR606UAR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d1b8bdfade2e179b2f97c2329d6512dcaf78d628..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF346JIL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_4.fit.json b/ENCSR606UAR/cherimoya.fold_4.fit.json deleted file mode 100644 index e27f266d8c291450871e584fe9a29ba573340c75..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF346JIL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR606UAR/cherimoya.fold_4.log b/ENCSR606UAR/cherimoya.fold_4.log deleted file mode 100644 index 3830f1f9e42d3cc0a57fef88716a2884b339921e..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2853 35.36401867866516 5.108791828155518 235.5736083984375 0.9902042150497437 306.40966796875 0.17018750309944153 0.6862971 2.9917004108428955 True -1 5706 31.624961853027344 1.0360639095306396 288.69439697265625 0.7113783359527588 290.5249328613281 0.23653864860534668 0.7346454 1.0975135564804077 True -2 8559 31.48019814491272 0.6205172538757324 224.498779296875 0.5414813160896301 286.9914855957031 0.24463209509849548 0.7455819 0.5131644606590271 True -3 11412 31.477080583572388 0.6304488182067871 199.0154571533203 0.530134379863739 284.69964599609375 0.2531195878982544 0.7549173 0.3953219950199127 True -4 14265 31.47522473335266 0.6317272186279297 202.33409118652344 0.5454005002975464 283.6646728515625 0.25691908597946167 0.7575243 0.4040517210960388 True -5 17118 31.47172474861145 0.6202797889709473 245.4577178955078 0.7502944469451904 282.9460754394531 0.25893184542655945 0.75968164 0.4386589527130127 True -6 19971 31.59459400177002 1.5101218223571777 213.8957977294922 0.46023786067962646 282.19830322265625 0.2616983652114868 0.7610211 0.4554527997970581 True -7 22824 31.51816725730896 0.6544225215911865 252.8650665283203 0.7384300231933594 281.3760986328125 0.2658458650112152 0.7652316 0.4736177921295166 True -8 25677 31.519626140594482 0.6379532814025879 193.55520629882812 0.675460934638977 281.21575927734375 0.2658267915248871 0.7679338 0.4850899279117584 True -9 28530 31.436278581619263 0.634340763092041 248.02020263671875 0.44015395641326904 280.5989685058594 0.2683369219303131 0.7684149 0.4803406000137329 True -10 31383 31.440553188323975 0.6293861865997314 253.90850830078125 0.563954770565033 280.38177490234375 0.2689063549041748 0.7730528 0.45705756545066833 True -11 34236 31.464536905288696 0.6261515617370605 275.92108154296875 0.6130399703979492 279.4186706542969 0.27331092953681946 0.7741134 0.4556891620159149 True -12 37089 32.02836489677429 3.750354051589966 227.34133911132812 0.38310641050338745 279.2969970703125 0.27414530515670776 0.77835685 0.4714897572994232 True -13 39942 31.43798518180847 0.7251381874084473 258.0819396972656 0.47190147638320923 279.03314208984375 0.27542924880981445 0.78436416 0.4373835623264313 True -14 42795 31.435702323913574 0.6282131671905518 205.32028198242188 0.42792341113090515 278.7330017089844 0.2758660912513733 0.79044545 0.3947315216064453 True -15 45648 31.55715250968933 0.6321015357971191 253.80868530273438 0.43576568365097046 278.0869445800781 0.27879592776298523 0.7969217 0.36381232738494873 True -16 48501 31.757405519485474 16.937068223953247 200.85806274414062 0.3760080337524414 277.80487060546875 0.27962368726730347 0.8022788 0.33706510066986084 True -17 51354 31.55090880393982 1.1931562423706055 233.5830535888672 0.33130475878715515 277.85528564453125 0.2799665331840515 0.80350035 0.32693493366241455 True -18 54207 31.659159183502197 0.68343186378479 263.203125 0.30811211466789246 277.9288330078125 0.2788987159729004 0.80326325 0.3184736669063568 False -19 57060 31.55376172065735 0.6398565769195557 233.1603546142578 0.32254642248153687 277.8377380371094 0.2791852653026581 0.80317026 0.32065582275390625 False diff --git a/ENCSR606UAR/cherimoya.fold_4.performance.tsv b/ENCSR606UAR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 752ca8bab09dfbe34065ffd07076c59128f9e723..0000000000000000000000000000000000000000 --- a/ENCSR606UAR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -277.85528564453125 0.4965769052505493 0.2799665629863739 0.07452495396137238 0.8035003542900085 0.742277204990387 0.32693493366241455 \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_0.evaluate.json b/ENCSR607BTF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c21248c6bac2d2edaca3a0874fb779b94ec1e05a..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF358QRW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_0.fit.json b/ENCSR607BTF/cherimoya.fold_0.fit.json deleted file mode 100644 index 915b0b5decc1ebb112a623432d9b75bf1cbd1634..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF358QRW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_0.log b/ENCSR607BTF/cherimoya.fold_0.log deleted file mode 100644 index d4932d4b930508641d3812f525564b3a72427e88..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3558 43.18433427810669 4.844202518463135 701.502685546875 0.8826566338539124 995.6201782226562 0.6791593432426453 0.5443321 8.372369766235352 True -1 7116 39.40638852119446 3.366147756576538 623.605712890625 0.814765214920044 822.62158203125 0.7855402231216431 0.6110205 1.8854503631591797 True -2 10674 39.38125228881836 0.681154727935791 595.7061767578125 0.9161388278007507 800.2308959960938 0.7933807373046875 0.6284418 1.1594738960266113 True -3 14232 39.40751528739929 0.6969549655914307 731.4207763671875 0.6340904235839844 790.7804565429688 0.7979270815849304 0.63070446 0.9512746334075928 True -4 17790 39.324079275131226 0.6860506534576416 710.7195434570312 0.6092364192008972 787.0930786132812 0.7998669743537903 0.6367578 0.9281647205352783 True -5 21348 39.37815546989441 0.6962137222290039 617.5355834960938 1.048043131828308 782.7123413085938 0.8026068806648254 0.6445396 0.841422975063324 True -6 24906 39.4222686290741 1.4130139350891113 703.8323974609375 0.7645450830459595 778.0181274414062 0.8047881722450256 0.64755225 0.76695716381073 True -7 28464 39.45466351509094 0.692927360534668 684.0244140625 0.7397912740707397 776.4843139648438 0.8063552379608154 0.6509184 0.7518646717071533 True -8 32022 39.45296335220337 0.6894581317901611 642.87060546875 0.7618581056594849 771.4449462890625 0.8086164593696594 0.65638065 0.7051596641540527 True -9 35580 40.23961400985718 0.6790072917938232 622.2947998046875 0.5948991775512695 766.8140258789062 0.8109921216964722 0.66475374 0.6607969403266907 True -10 39138 39.434476375579834 0.698350191116333 597.55517578125 0.8242520689964294 763.7884521484375 0.8123894929885864 0.67301965 0.6236393451690674 True -11 42696 39.356597900390625 0.6839590072631836 724.478759765625 0.5063568353652954 759.3233642578125 0.8146504163742065 0.6790863 0.6085322499275208 True -12 46254 39.37323832511902 0.6810939311981201 637.929931640625 0.4312940239906311 755.15087890625 0.816929042339325 0.69067717 0.5885040163993835 True -13 49812 39.365278244018555 20.86760973930359 591.2302856445312 0.6767653226852417 751.3186645507812 0.8192517161369324 0.70345217 0.5650288462638855 True -14 53370 39.56220769882202 0.6865940093994141 593.627197265625 0.5567803978919983 747.3287353515625 0.821088433265686 0.7116309 0.5430063009262085 True -15 56928 39.416271924972534 0.6877357959747314 570.15478515625 0.472789466381073 744.8302612304688 0.8224945664405823 0.7196292 0.5283526182174683 True -16 60486 39.32637643814087 0.6745669841766357 562.42236328125 0.6990668773651123 744.9111328125 0.8231527209281921 0.7250145 0.5223709940910339 True -17 64044 39.454070806503296 0.6893744468688965 584.283935546875 0.3008668124675751 744.7393188476562 0.8231108784675598 0.7287191 0.5216964483261108 True -18 67602 39.350239992141724 2.744434356689453 526.9926147460938 0.38359129428863525 745.6519775390625 0.822784960269928 0.72542816 0.5320586562156677 False -19 71160 39.37894630432129 0.7000870704650879 568.77099609375 0.3394712507724762 746.3106079101562 0.8225243091583252 0.72374016 0.5364617109298706 False diff --git a/ENCSR607BTF/cherimoya.fold_0.performance.tsv b/ENCSR607BTF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 776dbcc6b8b072b3a72497b6292f38c6834f3623..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -744.7393188476562 0.14800409972667694 0.823110818862915 0.4722925126552582 0.7287191152572632 0.6848216652870178 0.5216964483261108 \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_1.evaluate.json b/ENCSR607BTF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e72486de0f8e1daa79540e179b2a7a727838280f..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF358QRW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_1.fit.json b/ENCSR607BTF/cherimoya.fold_1.fit.json deleted file mode 100644 index 22784bc5e4e553c669b7d69d9b6c6141acb1ffe0..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF358QRW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_1.log b/ENCSR607BTF/cherimoya.fold_1.log deleted file mode 100644 index f50c4cf5404b1097e634e37c141fa9ccf96c4d41..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3495 42.598570108413696 3.558558225631714 737.1141357421875 0.8778160810470581 1058.466552734375 0.688125491142273 0.5811578 6.848764896392822 True -1 6990 38.771427392959595 0.8814544677734375 687.8134765625 1.057780146598816 886.6908569335938 0.7844919562339783 0.6384604 2.4187421798706055 True -2 10485 38.605000734329224 0.8535037040710449 671.1025390625 0.722028911113739 862.9573364257812 0.79294753074646 0.64380443 1.5122871398925781 True -3 13980 38.62204122543335 0.8704519271850586 617.5960693359375 0.6642076969146729 852.7515258789062 0.7972976565361023 0.6562105 1.1656895875930786 True -4 17475 38.598063707351685 0.9052670001983643 608.4602661132812 0.5324304103851318 848.3717041015625 0.7993482947349548 0.6557844 1.1550207138061523 False -5 20970 38.678481101989746 0.8567452430725098 603.908203125 0.9403759241104126 842.0469360351562 0.8012726306915283 0.6544405 0.9053639769554138 False -6 24465 38.551384687423706 0.8819141387939453 636.1224975585938 0.835885226726532 838.5769653320312 0.802970290184021 0.66126585 0.8080746531486511 True -7 27960 38.59104585647583 0.852776288986206 647.27734375 0.8259950280189514 832.4118041992188 0.8061899542808533 0.6679309 0.7652862668037415 True -8 31455 38.57379984855652 0.8532171249389648 635.6802978515625 0.8932414054870605 827.1360473632812 0.8088822364807129 0.6817892 0.7496857643127441 True -9 34950 38.590168952941895 1.370025634765625 549.111083984375 0.7068156003952026 821.318359375 0.8109545111656189 0.6897802 0.6712573170661926 True -10 38445 38.65320134162903 2.4894161224365234 603.26806640625 0.8416828513145447 817.8512573242188 0.8133446574211121 0.69219565 0.6666415333747864 True -11 41940 38.562350034713745 0.8736610412597656 581.478515625 0.805118203163147 811.3742065429688 0.8158321976661682 0.7030908 0.6103420257568359 True -12 45435 38.58936953544617 0.8704583644866943 724.2139892578125 0.711762547492981 807.4590454101562 0.8177679181098938 0.7118606 0.591942548751831 True -13 48930 38.670241832733154 7.76947021484375 666.6647338867188 0.43505120277404785 802.4229125976562 0.8203068971633911 0.7200655 0.5744109749794006 True -14 52425 38.6720712184906 0.8568687438964844 626.6698608398438 0.645276665687561 798.3597412109375 0.8223156332969666 0.7311121 0.5487061142921448 True -15 55920 38.62880825996399 0.8577237129211426 584.8858642578125 0.5038728713989258 796.3936767578125 0.8234415650367737 0.7392302 0.5303702354431152 True -16 59415 38.5884644985199 2.3631978034973145 705.841796875 0.4877406358718872 795.1341552734375 0.8242378830909729 0.74753463 0.5250459313392639 True -17 62910 38.66741728782654 0.8714120388031006 570.6814575195312 0.6304900050163269 795.898193359375 0.8241718411445618 0.74849457 0.5273237228393555 True -18 66405 38.673397064208984 1.751704216003418 689.7972412109375 0.4483104944229126 797.0491333007812 0.823805034160614 0.74738276 0.5325016379356384 False -19 69900 38.65763521194458 2.993515968322754 622.8465576171875 0.4688599109649658 797.7579345703125 0.8235263228416443 0.7467429 0.5394237637519836 False diff --git a/ENCSR607BTF/cherimoya.fold_1.performance.tsv b/ENCSR607BTF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c55354ec46cdd18126dcfd2b1184de72f0fc4bb6..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -795.898193359375 0.1418864130973816 0.8241718411445618 0.4963463842868805 0.748494565486908 0.7225233316421509 0.5273237228393555 \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_2.evaluate.json b/ENCSR607BTF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 76a287fb66c83f1b86bbc5188793ee95740bf3e0..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF358QRW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_2.fit.json b/ENCSR607BTF/cherimoya.fold_2.fit.json deleted file mode 100644 index abef932e31811cf26d73796107b3f22ad93cfdf8..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF358QRW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_2.log b/ENCSR607BTF/cherimoya.fold_2.log deleted file mode 100644 index e9de6af3de38b97a73c1a5786e651abdf8a6c937..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3696 44.98586082458496 4.312234163284302 669.373779296875 0.8301244974136353 1014.4390869140625 0.6903318762779236 0.56135225 7.738840103149414 True -1 7392 40.91620373725891 0.7464690208435059 624.0137329101562 0.9047760367393494 861.2311401367188 0.7830692529678345 0.62204224 2.342047929763794 True -2 11088 40.84960722923279 0.7308239936828613 659.97216796875 0.8947324752807617 837.4794311523438 0.7912889719009399 0.6334855 1.2636736631393433 True -3 14784 41.434884548187256 0.7353794574737549 669.0838623046875 0.7595089673995972 825.5882568359375 0.7958676218986511 0.6402561 1.0319700241088867 True -4 18480 40.981833696365356 0.7667155265808105 601.4987182617188 0.7324171662330627 821.2576904296875 0.7976714372634888 0.6415646 0.8687101006507874 True -5 22176 41.05854868888855 0.7594959735870361 642.05859375 0.8236342668533325 812.731689453125 0.8011178374290466 0.655887 0.7415859699249268 True -6 25872 40.84344816207886 0.7296833992004395 729.49658203125 0.5618253946304321 810.3147583007812 0.8030043244361877 0.66030616 0.7558062672615051 True -7 29568 40.965994358062744 0.7407636642456055 691.1754150390625 0.8583464026451111 805.0172119140625 0.8050951361656189 0.66692215 0.6734883785247803 True -8 33264 40.86028838157654 0.7323040962219238 621.3023681640625 0.6620855331420898 800.7091064453125 0.807169497013092 0.67333204 0.6468441486358643 True -9 36960 40.76732516288757 0.7341897487640381 652.72314453125 0.6696301698684692 796.1873779296875 0.8093834519386292 0.6774965 0.6154448986053467 True -10 40656 40.822192430496216 0.7336041927337646 579.767578125 0.3876698315143585 792.3699340820312 0.8117967247962952 0.68401426 0.6208705306053162 True -11 44352 40.73779296875 10.791609287261963 741.5635375976562 0.5317338705062866 787.8902587890625 0.81378173828125 0.6900852 0.5956864356994629 True -12 48048 40.921900033950806 0.7653970718383789 641.2503051757812 0.38296279311180115 783.5916137695312 0.815941572189331 0.6992836 0.5760934948921204 True -13 51744 40.81808567047119 0.7687575817108154 696.185791015625 0.5767394304275513 780.2098999023438 0.8183366656303406 0.70934427 0.5630266070365906 True -14 55440 40.852152824401855 11.462026357650757 680.8035278320312 0.5606937408447266 777.2628784179688 0.8203360438346863 0.71679586 0.5526039600372314 True -15 59136 41.02404975891113 0.7992348670959473 636.27587890625 0.5633383393287659 775.678955078125 0.8217419981956482 0.7232477 0.5426879525184631 True -16 62832 41.029337882995605 0.7515275478363037 588.0654296875 0.5688666105270386 775.2356567382812 0.82257080078125 0.7299663 0.5353859066963196 True -17 66528 40.869112491607666 21.57387065887451 542.8187255859375 0.4032830595970154 775.5633544921875 0.8226391673088074 0.73145896 0.5449129939079285 True -18 70224 41.100417613983154 0.7600762844085693 699.9632568359375 0.6361302733421326 777.156982421875 0.8222222328186035 0.72923183 0.5544001460075378 False -19 73920 41.01543402671814 0.759742021560669 610.5647583007812 0.39545655250549316 777.41259765625 0.8219719529151917 0.7290482 0.5601099729537964 False diff --git a/ENCSR607BTF/cherimoya.fold_2.performance.tsv b/ENCSR607BTF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c0038a6e17389a4ef22290023e5dc9b3285347e1..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -775.5633544921875 0.14436228573322296 0.8226391673088074 0.4880683422088623 0.7314589619636536 0.6984062790870667 0.5449129939079285 \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_3.evaluate.json b/ENCSR607BTF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1fe182c954383433c4f68e03daf717d7e25eb8df..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF358QRW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_3.fit.json b/ENCSR607BTF/cherimoya.fold_3.fit.json deleted file mode 100644 index 7d78e5eb19a5baffa77e0e44f4199602b1e72bb0..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF358QRW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_3.log b/ENCSR607BTF/cherimoya.fold_3.log deleted file mode 100644 index 2d42bfa15cfbdfc8fda02155dfb7222c0545c633..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3611 44.08041286468506 3.6508491039276123 609.5869140625 1.2914881706237793 993.5994873046875 0.6871625185012817 0.57617044 7.201487064361572 True -1 7222 40.03975868225098 1.3542134761810303 699.24462890625 0.8463987112045288 838.56396484375 0.7818444967269897 0.5979007 1.813934326171875 True -2 10833 39.93421292304993 0.6887547969818115 650.5087280273438 1.0019625425338745 816.8109130859375 0.7903244495391846 0.62704575 1.0720219612121582 True -3 14444 39.84315037727356 0.6864404678344727 634.9482421875 0.5672751069068909 805.167236328125 0.795434832572937 0.63044417 0.9787651300430298 True -4 18055 39.86139416694641 0.6763827800750732 677.6434326171875 0.8521852493286133 799.7088623046875 0.7990665435791016 0.6373689 0.8849356174468994 True -5 21666 40.257540225982666 0.6801767349243164 613.2080078125 0.8570367097854614 797.0602416992188 0.8001002073287964 0.6258022 0.766710102558136 False -6 25277 39.843764781951904 7.250149488449097 743.373291015625 0.6663140058517456 792.4031982421875 0.8032130002975464 0.641012 0.7620817422866821 True -7 28888 40.027931928634644 0.7015800476074219 680.172607421875 0.8131829500198364 789.008544921875 0.8040633201599121 0.64273876 0.7084521055221558 True -8 32499 40.000449657440186 0.6849684715270996 617.6256103515625 0.7430887222290039 785.3790893554688 0.8066304326057434 0.6529711 0.6864610910415649 True -9 36110 39.916006326675415 0.6909177303314209 714.4547729492188 0.6679894924163818 780.5711669921875 0.8090565204620361 0.66521394 0.6480693221092224 True -10 39721 39.804526805877686 0.6925268173217773 701.495849609375 0.6086541414260864 775.6568603515625 0.8118349313735962 0.6714735 0.6327176690101624 True -11 43332 39.914146423339844 0.681288480758667 706.39501953125 0.649520754814148 771.7855834960938 0.813538134098053 0.68049353 0.6080729961395264 True -12 46943 39.93380427360535 1.6397507190704346 639.516357421875 0.6675503253936768 766.778564453125 0.8161802291870117 0.68755746 0.6006804704666138 True -13 50554 40.01213455200195 0.6877853870391846 567.0974731445312 0.5014703273773193 762.53857421875 0.8178737163543701 0.6966774 0.5718220472335815 True -14 54165 39.91147446632385 0.6892809867858887 614.2789306640625 0.35287442803382874 759.5936889648438 0.8201122879981995 0.7093676 0.5585491061210632 True -15 57776 39.92998552322388 0.6833484172821045 718.6900634765625 0.29105836153030396 757.1594848632812 0.8214395046234131 0.71854985 0.5450524687767029 True -16 61387 39.89905142784119 0.6811985969543457 657.014404296875 0.5411027669906616 755.2249755859375 0.8222603797912598 0.72221774 0.5393689274787903 True -17 64998 39.920973777770996 0.6900153160095215 604.4857177734375 0.5465946197509766 755.759033203125 0.8222252130508423 0.72369593 0.5483450889587402 True -18 68609 39.89266848564148 1.6257843971252441 609.1309814453125 0.42480605840682983 756.1644897460938 0.8220040798187256 0.723911 0.5583048462867737 True -19 72220 40.35932660102844 0.6830606460571289 627.0463256835938 0.3933265805244446 756.6886596679688 0.8216626048088074 0.7221912 0.5642282366752625 False diff --git a/ENCSR607BTF/cherimoya.fold_3.performance.tsv b/ENCSR607BTF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d2d96003dff392ee51f66e85aa5aa9a3c42d7b01..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -756.1644897460938 0.14716212451457977 0.8220040798187256 0.4758226275444031 0.7239109873771667 0.6891208291053772 0.5583048462867737 \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_4.evaluate.json b/ENCSR607BTF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a09cf9b8d8b9d89234064f53af14337fd0619ff3..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF358QRW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_4.fit.json b/ENCSR607BTF/cherimoya.fold_4.fit.json deleted file mode 100644 index 6abfda5c746930d83c02a5edfae21364d26e16de..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF358QRW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607BTF/cherimoya.fold_4.log b/ENCSR607BTF/cherimoya.fold_4.log deleted file mode 100644 index 315e0aa6aa7167a57b6ce3f7e431f39b4e659055..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3641 44.5041127204895 3.5884227752685547 781.7628173828125 1.1111056804656982 964.2582397460938 0.6839783787727356 0.5279939 10.846978187561035 True -1 7282 40.305041790008545 25.59473204612732 621.4481811523438 0.8175975680351257 804.6338500976562 0.7792679071426392 0.59732556 1.9273667335510254 True -2 10923 40.318480014801025 0.7516956329345703 747.7064208984375 0.8664572238922119 787.0175170898438 0.7883116602897644 0.60261387 0.8957321047782898 True -3 14564 40.213072538375854 0.7394466400146484 611.7435913085938 0.9536099433898926 776.7781982421875 0.7941089868545532 0.60707724 0.8143236041069031 True -4 18205 40.20927953720093 0.7252066135406494 707.728271484375 0.8536763787269592 772.094970703125 0.7973414063453674 0.6192988 0.7538637518882751 True -5 21846 40.19404077529907 27.321318864822388 703.3204345703125 0.929549515247345 766.869384765625 0.7994869351387024 0.61677265 0.7538027167320251 False -6 25487 40.21947431564331 0.7291817665100098 739.3841552734375 0.9164835214614868 763.388916015625 0.8019366264343262 0.62183315 0.7023624777793884 True -7 29128 40.26816654205322 0.7351081371307373 704.5023193359375 0.6831533312797546 760.3187255859375 0.8035884499549866 0.62561136 0.6763259172439575 True -8 32769 40.22630333900452 0.7188930511474609 740.937744140625 0.6854797601699829 755.76123046875 0.8059431910514832 0.6300387 0.6628694534301758 True -9 36410 40.262943983078 0.7240161895751953 779.575927734375 1.2916069030761719 751.5270385742188 0.8080964088439941 0.64214104 0.6301541328430176 True -10 40051 40.42204165458679 0.7211875915527344 615.60693359375 0.6359066963195801 747.4747924804688 0.8104074597358704 0.64842445 0.6282786130905151 True -11 43692 40.291115045547485 0.7268388271331787 646.078369140625 0.6623902320861816 744.5968627929688 0.8119415640830994 0.65710014 0.6120928525924683 True -12 47333 40.25552463531494 4.1659770011901855 657.5205078125 0.699200451374054 740.7360229492188 0.8139315843582153 0.6603423 0.609462320804596 True -13 50974 40.373637437820435 0.7248208522796631 574.1697998046875 0.6752084493637085 737.3521118164062 0.8158628344535828 0.6708732 0.5835843682289124 True -14 54615 40.351983070373535 0.7227814197540283 629.7490234375 0.523693859577179 734.1043090820312 0.8177639245986938 0.68130225 0.5702069401741028 True -15 58256 40.23626375198364 0.7260820865631104 633.5103759765625 0.645160973072052 732.6737670898438 0.8189519643783569 0.68990976 0.5626974105834961 True -16 61897 40.261327505111694 0.729393482208252 576.6112670898438 0.47191303968429565 732.3119506835938 0.8193548917770386 0.6943629 0.560832142829895 True -17 65538 40.415669202804565 11.26050066947937 569.9017333984375 0.3713657855987549 732.7100830078125 0.8192076683044434 0.69588 0.5672188997268677 True -18 69179 40.33444595336914 0.7423429489135742 607.4370727539062 0.4877789318561554 733.7322387695312 0.8186058402061462 0.69748735 0.5698733329772949 True -19 72820 40.20875644683838 0.7237257957458496 617.9857177734375 0.631121039390564 733.990478515625 0.8182434439659119 0.69647837 0.5758088827133179 False diff --git a/ENCSR607BTF/cherimoya.fold_4.performance.tsv b/ENCSR607BTF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1e736b4daba38b20745e478899553bc2b4404704..0000000000000000000000000000000000000000 --- a/ENCSR607BTF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -733.7322387695312 0.15002267062664032 0.8186058402061462 0.46956244111061096 0.6974873542785645 0.6541706919670105 0.5698733329772949 \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_0.evaluate.json b/ENCSR607EJV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5684a18bbc04edb6544030e8bbbd85f3e464b498..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343HOF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_0.fit.json b/ENCSR607EJV/cherimoya.fold_0.fit.json deleted file mode 100644 index ae02be149aa29a766ee3f811528153e645b2b9c3..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF343HOF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_0.log b/ENCSR607EJV/cherimoya.fold_0.log deleted file mode 100644 index 3683abc68f029b1f351f310059ef7c16cb008c3b..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1079 15.86017656326294 6.006012678146362 564.6320190429688 2.1473495960235596 951.52197265625 0.1508910208940506 0.5525568 22.64009666442871 True -1 2158 12.057259798049927 0.23451018333435059 661.7294311523438 1.6571539640426636 862.879150390625 0.2082034796476364 0.6768989 15.960931777954102 True -2 3237 12.040518283843994 0.23138117790222168 474.4833984375 1.4860787391662598 751.5444946289062 0.28007829189300537 0.72647977 10.62378978729248 True -3 4316 12.080956220626831 0.23500370979309082 376.371337890625 1.2798254489898682 668.0372924804688 0.32630693912506104 0.75386363 6.084980010986328 True -4 5395 12.060096263885498 0.2336416244506836 568.9500732421875 1.3229514360427856 637.3280639648438 0.3429057002067566 0.76477194 4.118247032165527 True -5 6474 12.047196626663208 0.22591114044189453 363.2019958496094 0.9350849390029907 625.147705078125 0.3503126800060272 0.77629405 3.0690362453460693 True -6 7553 12.095494985580444 0.2282102108001709 403.4515380859375 0.9348493814468384 618.113037109375 0.3542878329753876 0.78569907 2.3033485412597656 True -7 8632 12.068569660186768 0.23036432266235352 526.3048095703125 0.8848135471343994 610.7268676757812 0.3609219491481781 0.7951546 1.8105939626693726 True -8 9711 12.078593015670776 0.23153281211853027 660.2825927734375 0.9475796222686768 606.495361328125 0.3657248616218567 0.8044203 1.5960735082626343 True -9 10790 12.150948762893677 0.23844599723815918 261.70513916015625 0.8894927501678467 600.9599609375 0.36902183294296265 0.81183493 1.2840079069137573 True -10 11869 12.082810640335083 0.234816312789917 312.3386535644531 0.9855748414993286 598.3895874023438 0.3694780766963959 0.82344264 1.0644421577453613 True -11 12948 12.090105772018433 0.24295282363891602 534.201416015625 0.9146391153335571 594.3772583007812 0.37205708026885986 0.82965386 0.9535064101219177 True -12 14027 12.10745358467102 0.23594880104064941 405.2518005371094 0.9659962058067322 592.4193115234375 0.37349286675453186 0.83622783 0.9043610692024231 True -13 15106 12.105041742324829 0.24090242385864258 404.604248046875 0.990661084651947 589.49658203125 0.37642133235931396 0.8396193 0.8560441136360168 True -14 16185 12.092308521270752 0.23308348655700684 440.8775634765625 0.9633074402809143 586.457275390625 0.37828338146209717 0.844547 0.820102334022522 True -15 17264 12.140672206878662 0.23582124710083008 384.2298583984375 0.7840919494628906 582.9945678710938 0.3811756372451782 0.8492696 0.7934189438819885 True -16 18343 12.090113639831543 0.23276686668395996 390.41802978515625 0.7360315322875977 583.9737548828125 0.3791031539440155 0.8504933 0.7745869755744934 True -17 19422 12.104084968566895 0.2320554256439209 473.90008544921875 0.5984628796577454 585.8285522460938 0.37743905186653137 0.85270816 0.7694529294967651 True -18 20501 12.097587585449219 0.23230600357055664 389.2674255371094 0.6658856868743896 587.3955078125 0.37608474493026733 0.85349244 0.7722018957138062 True -19 21580 12.086772203445435 1.5771653652191162 405.050537109375 0.7265064120292664 588.4619750976562 0.3750791549682617 0.85179585 0.7743627429008484 False diff --git a/ENCSR607EJV/cherimoya.fold_0.performance.tsv b/ENCSR607EJV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6ea74abf203a89af2ad7609526d9c87bc5292547..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -587.3955078125 0.41791078448295593 0.3760848045349121 0.15535968542099 0.8534924387931824 0.8200981020927429 0.7722018957138062 \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_1.evaluate.json b/ENCSR607EJV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0b7589082efb9f4e08010483f7c7b2f892b950df..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343HOF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_1.fit.json b/ENCSR607EJV/cherimoya.fold_1.fit.json deleted file mode 100644 index 8701ee6035f3e07afcfd026a9c69d96fdd8493a8..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF343HOF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_1.log b/ENCSR607EJV/cherimoya.fold_1.log deleted file mode 100644 index ae19dfe90427a69cd69349b4b548f792a3701f24..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1052 15.290571212768555 3.1651713848114014 784.317138671875 1.379351258277893 1187.8414306640625 0.1737898886203766 0.4845401 25.62120819091797 True -1 2104 11.661285161972046 0.3471412658691406 714.8759155273438 1.3805533647537231 1075.108154296875 0.23061539232730865 0.6102127 19.501617431640625 True -2 3156 11.641679048538208 0.3346865177154541 611.1283569335938 1.8748911619186401 934.6777954101562 0.30764836072921753 0.69212997 14.018523216247559 True -3 4208 11.631130456924438 0.33592700958251953 592.3612060546875 1.7406225204467773 811.5824584960938 0.36268743872642517 0.7478669 7.7821574211120605 True -4 5260 11.648059844970703 0.33551621437072754 587.90771484375 1.1532800197601318 773.3919677734375 0.381788969039917 0.7705817 4.801360130310059 True -5 6312 11.632492065429688 0.3355143070220947 626.0537719726562 1.377197504043579 760.92529296875 0.3888015151023865 0.77967113 3.3817269802093506 True -6 7364 11.641252040863037 11.415600061416626 527.2628173828125 1.0159252882003784 752.91748046875 0.3931316137313843 0.792865 2.6597185134887695 True -7 8416 11.684133768081665 1.3094027042388916 415.07037353515625 0.8986389636993408 742.1370239257812 0.4001990854740143 0.80038273 2.235352039337158 True -8 9468 11.652353763580322 1.070589542388916 573.3546752929688 0.9453729391098022 739.9161376953125 0.40112394094467163 0.80716014 1.8292460441589355 True -9 10520 11.671680688858032 10.27007246017456 335.07708740234375 0.8626723289489746 734.0936279296875 0.403664767742157 0.81261533 1.534942626953125 True -10 11572 11.965763330459595 9.00562047958374 515.4307861328125 1.2030748128890991 727.234375 0.4078923463821411 0.8138367 1.4181581735610962 True -11 12624 11.692153215408325 0.34568119049072266 485.9091796875 0.7210937738418579 719.3775024414062 0.41259726881980896 0.8248084 1.1850595474243164 True -12 13676 11.648761510848999 0.33299994468688965 436.32611083984375 1.0561199188232422 715.0518798828125 0.41480857133865356 0.8282676 1.084670901298523 True -13 14728 11.649379253387451 0.3405728340148926 505.11822509765625 1.0100840330123901 709.7350463867188 0.41666746139526367 0.83250713 0.9988134503364563 True -14 15780 11.679545164108276 0.3440513610839844 574.818115234375 0.9468849897384644 706.4257202148438 0.41856053471565247 0.83847624 0.9391578435897827 True -15 16832 11.665212631225586 0.33720970153808594 470.25677490234375 0.597637414932251 704.1092529296875 0.4200959801673889 0.8413412 0.9087867140769958 True -16 17884 11.67221188545227 0.33864355087280273 481.2703857421875 0.4811873435974121 704.3148193359375 0.42006999254226685 0.8441405 0.8960033059120178 True -17 18936 11.637837171554565 0.33995866775512695 513.6023559570312 0.448597252368927 704.4970703125 0.4189785122871399 0.84621286 0.8905475735664368 True -18 19988 11.648998737335205 0.3494405746459961 451.54998779296875 0.46349620819091797 708.1137084960938 0.4147343039512634 0.84536666 0.8988932371139526 False -19 21040 11.638957738876343 0.33852243423461914 335.8251647949219 0.4317420721054077 709.8303833007812 0.41372665762901306 0.844791 0.9063858985900879 False diff --git a/ENCSR607EJV/cherimoya.fold_1.performance.tsv b/ENCSR607EJV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 016373dec380d41245dd9cd8d9fb1cc292bc68c8..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -704.4970703125 0.383188396692276 0.4189785122871399 0.1857147067785263 0.8462128639221191 0.8258460164070129 0.8905475735664368 \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_2.evaluate.json b/ENCSR607EJV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 420d66d01614eff41edec2f7f24c43076917c296..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343HOF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_2.fit.json b/ENCSR607EJV/cherimoya.fold_2.fit.json deleted file mode 100644 index 6095b9475338f8f12586455f0ad0e7923783c9c0..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF343HOF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_2.log b/ENCSR607EJV/cherimoya.fold_2.log deleted file mode 100644 index 982af2901f9bc8990f700350756b9737362dfd83..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1133 16.417129516601562 3.367603063583374 580.7806396484375 2.142036199569702 1003.8477172851562 0.15859323740005493 0.4719552 22.26654052734375 True -1 2266 12.647715330123901 0.2599613666534424 596.8372802734375 1.9866565465927124 893.4772338867188 0.22077827155590057 0.6356303 16.176345825195312 True -2 3399 12.64160943031311 0.24806785583496094 481.49395751953125 1.359594702720642 759.6676025390625 0.2896788716316223 0.70855194 11.188957214355469 True -3 4532 12.634388208389282 0.2472212314605713 556.3575439453125 1.612647294998169 679.8547973632812 0.33188050985336304 0.76361465 5.561983108520508 True -4 5665 12.63105320930481 0.24805641174316406 371.54071044921875 2.016155242919922 648.8014526367188 0.3497294485569 0.7895252 3.383373498916626 True -5 6798 12.63737177848816 0.2558279037475586 620.9993286132812 1.4759089946746826 633.8827514648438 0.3579604923725128 0.8045614 2.463057041168213 True -6 7931 12.637600898742676 0.24989533424377441 491.5097351074219 0.8148399591445923 624.9920654296875 0.36363911628723145 0.81092083 1.900138020515442 True -7 9064 12.645180225372314 7.399444818496704 560.669921875 1.149803876876831 622.0617065429688 0.36532798409461975 0.81484663 1.669529914855957 True -8 10197 12.999868154525757 0.25665974617004395 708.50048828125 1.4029171466827393 617.6343383789062 0.36952462792396545 0.8228941 1.4055474996566772 True -9 11330 12.692411184310913 0.2473289966583252 421.2969665527344 0.9556013941764832 613.749755859375 0.37158235907554626 0.8299353 1.192252516746521 True -10 12463 12.67231822013855 0.8713812828063965 493.28729248046875 1.054332971572876 610.6817016601562 0.3727325201034546 0.8340926 1.0811059474945068 True -11 13596 12.664335012435913 0.25247907638549805 624.612060546875 0.7385363578796387 607.0401000976562 0.3756280541419983 0.838319 0.9460417628288269 True -12 14729 12.65758490562439 0.25034594535827637 359.5029296875 0.8592146635055542 605.0437622070312 0.3766174614429474 0.8423829 0.8779720067977905 True -13 15862 12.647627115249634 0.2588012218475342 398.6532897949219 0.9151819348335266 600.10986328125 0.3803919553756714 0.8449126 0.8333911299705505 True -14 16995 12.642344236373901 0.25254130363464355 410.1759033203125 0.9989621043205261 599.5925903320312 0.38053005933761597 0.84816074 0.8092820048332214 True -15 18128 12.638702154159546 0.2520921230316162 326.5027160644531 0.8580169677734375 595.03955078125 0.38496026396751404 0.8514652 0.7929893732070923 True -16 19261 12.668197631835938 0.24970293045043945 594.8758544921875 0.9600576162338257 596.5996704101562 0.38280314207077026 0.85246325 0.7873254418373108 True -17 20394 12.706357479095459 0.9457674026489258 461.664794921875 0.7595161199569702 598.8893432617188 0.3805865943431854 0.85423464 0.782749354839325 True -18 21527 12.727445125579834 0.24643564224243164 455.35888671875 0.5573687553405762 600.6455078125 0.37925955653190613 0.85308325 0.7907273173332214 False -19 22660 12.667422771453857 0.25113582611083984 425.0273132324219 0.6736912131309509 602.6905517578125 0.3771708309650421 0.8514938 0.7995359301567078 False diff --git a/ENCSR607EJV/cherimoya.fold_2.performance.tsv b/ENCSR607EJV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 400e05920f3b1801e790bac889134f70c32f847f..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -598.8893432617188 0.414072185754776 0.3805865943431854 0.15820056200027466 0.8542346358299255 0.827006995677948 0.782749354839325 \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_3.evaluate.json b/ENCSR607EJV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3b2db241169318d3c9f2bba61da3f8c9169f4d89..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343HOF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_3.fit.json b/ENCSR607EJV/cherimoya.fold_3.fit.json deleted file mode 100644 index 65d0380b65189f94ec8262da49e1fd5ea2438d09..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF343HOF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_3.log b/ENCSR607EJV/cherimoya.fold_3.log deleted file mode 100644 index ac9a8ba2e998ca96c8f7403d90a5fdf59189a6bf..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1089 15.795813798904419 3.096414804458618 350.5082702636719 1.5286914110183716 1026.1475830078125 0.1694810688495636 0.510439 23.942394256591797 True -1 2178 12.168707132339478 0.23566102981567383 581.1642456054688 0.9604522585868835 925.45458984375 0.22817014157772064 0.6242096 18.17829132080078 True -2 3267 12.170466423034668 0.22853469848632812 505.5515441894531 1.957276463508606 801.2417602539062 0.3026506304740906 0.7037339 13.726752281188965 True -3 4356 12.169873237609863 0.22960448265075684 444.07879638671875 1.429323434829712 718.3572387695312 0.3466891944408417 0.73056877 7.590124607086182 True -4 5445 12.177645683288574 0.9837431907653809 564.6565551757812 1.4406111240386963 694.712890625 0.360958993434906 0.7530226 4.464053153991699 True -5 6534 12.158189535140991 0.23919177055358887 667.1693115234375 1.4457063674926758 682.3477783203125 0.3688282072544098 0.7640663 3.2944183349609375 True -6 7623 12.138603210449219 0.6827049255371094 636.4224853515625 1.147953748703003 677.0030517578125 0.37261858582496643 0.77233666 2.6817643642425537 True -7 8712 12.155726909637451 0.2313976287841797 654.823974609375 0.8950580358505249 669.5445556640625 0.37757402658462524 0.7810284 2.1663405895233154 True -8 9801 12.154190301895142 0.22832226753234863 486.78106689453125 0.9746532440185547 663.6115112304688 0.38342106342315674 0.7845562 1.8219958543777466 True -9 10890 12.148339986801147 1.1671099662780762 425.3647155761719 1.0055900812149048 662.8672485351562 0.38419049978256226 0.7888816 1.6176376342773438 True -10 11979 12.180385828018188 0.23355412483215332 544.4473876953125 1.2273606061935425 658.9109497070312 0.38543301820755005 0.7957334 1.4164607524871826 True -11 13068 12.154870510101318 0.23663091659545898 571.7124633789062 1.3165537118911743 654.9882202148438 0.3875316083431244 0.80187327 1.2643346786499023 True -12 14157 12.174862623214722 0.2292473316192627 439.929443359375 1.3870470523834229 649.9581298828125 0.39086994528770447 0.81128544 1.1248884201049805 True -13 15246 12.168021440505981 0.22997784614562988 414.18353271484375 0.9613005518913269 644.1997680664062 0.39391979575157166 0.8170874 1.0403789281845093 True -14 16335 12.164964199066162 0.5059311389923096 585.458740234375 1.1616480350494385 639.3219604492188 0.396731972694397 0.8251088 0.960304856300354 True -15 17424 12.167265176773071 0.23210811614990234 358.1075439453125 0.7370508909225464 636.6618041992188 0.39903590083122253 0.8310192 0.9182002544403076 True -16 18513 12.1760995388031 0.23166108131408691 349.03985595703125 0.5245321989059448 636.1195678710938 0.39790308475494385 0.8334638 0.901469886302948 True -17 19602 12.161959409713745 0.2326192855834961 557.4337158203125 0.8982165455818176 639.2392578125 0.39607954025268555 0.8364981 0.8959535956382751 True -18 20691 12.163975954055786 0.23381924629211426 519.3350830078125 0.5231965780258179 641.2346801757812 0.3938713073730469 0.83603776 0.9048148989677429 False -19 21780 12.153368711471558 0.4596407413482666 406.33050537109375 0.3711245656013489 641.2968139648438 0.39412862062454224 0.8346817 0.9129651784896851 False diff --git a/ENCSR607EJV/cherimoya.fold_3.performance.tsv b/ENCSR607EJV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fec62606b8fdff9fbeece54d604588533944c4b8..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -639.2392578125 0.39882853627204895 0.39607957005500793 0.16877040266990662 0.8364980816841125 0.8117361664772034 0.8959535956382751 \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_4.evaluate.json b/ENCSR607EJV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4155a194dae784b5385a43f1c50cde95f508e7d0..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343HOF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_4.fit.json b/ENCSR607EJV/cherimoya.fold_4.fit.json deleted file mode 100644 index e56518e501a6b39d6d7166dfd19c1ee98575392e..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF343HOF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607EJV/cherimoya.fold_4.log b/ENCSR607EJV/cherimoya.fold_4.log deleted file mode 100644 index e16d624bc9a8247eb4e58a3d7eb9fb94baf84d4f..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1067 15.768210172653198 3.229696035385132 499.5123596191406 1.8804988861083984 889.745361328125 0.15482008457183838 0.5203585 21.90331268310547 True -1 2134 11.917331457138062 0.8882262706756592 616.930419921875 1.882164478302002 807.3508911132812 0.20981216430664062 0.6486108 15.539450645446777 True -2 3201 11.896310567855835 0.22009015083312988 440.8582763671875 1.119443416595459 706.0697021484375 0.2792023718357086 0.6999672 10.339607238769531 True -3 4268 11.900883913040161 0.2198946475982666 522.32666015625 1.3283870220184326 629.1359252929688 0.3207874894142151 0.7459171 5.620729446411133 True -4 5335 11.909136295318604 0.8377902507781982 505.7231750488281 1.3728928565979004 600.9696655273438 0.3362666964530945 0.76117665 3.664980411529541 True -5 6402 11.964266300201416 0.2267928123474121 654.397216796875 1.2628867626190186 588.9036254882812 0.3427201807498932 0.76691514 2.8235678672790527 True -6 7469 11.939413070678711 0.22102856636047363 456.24517822265625 1.6068007946014404 580.4476318359375 0.34784412384033203 0.77304584 2.144261121749878 True -7 8536 11.927801132202148 0.22032713890075684 490.8918151855469 0.9531189799308777 576.8623657226562 0.35075199604034424 0.77537787 1.7561546564102173 True -8 9603 11.922502279281616 0.22064566612243652 486.6387634277344 1.4081707000732422 571.1541748046875 0.35586196184158325 0.78699636 1.4621680974960327 True -9 10670 11.938639163970947 0.22059154510498047 401.23602294921875 1.3362876176834106 566.83056640625 0.3605632781982422 0.79901177 1.3077332973480225 True -10 11737 11.921566724777222 0.22060608863830566 402.91448974609375 1.019312858581543 561.7198486328125 0.3642546236515045 0.8038975 1.14251708984375 True -11 12804 11.92886734008789 0.22060227394104004 512.40869140625 1.5347577333450317 560.1873779296875 0.3640364408493042 0.8107524 1.0312509536743164 True -12 13871 11.901089429855347 0.22064781188964844 410.232666015625 0.991631031036377 557.5869140625 0.36609387397766113 0.81726503 0.9472984671592712 True -13 14938 11.903905630111694 0.22125887870788574 560.8875732421875 0.8368467092514038 554.762939453125 0.3669927418231964 0.8249526 0.8962827324867249 True -14 16005 11.902558326721191 0.22336697578430176 515.9248657226562 0.8676095008850098 552.5838012695312 0.368152379989624 0.8314125 0.8520961403846741 True -15 17072 11.902729988098145 0.2212662696838379 469.3333740234375 0.5985682606697083 550.7857055664062 0.3686867654323578 0.8351185 0.8276577591896057 True -16 18139 11.904907703399658 0.22190260887145996 470.12322998046875 0.45488274097442627 550.8147583007812 0.36964818835258484 0.83778584 0.8121986389160156 True -17 19206 11.902652025222778 0.6889197826385498 320.33770751953125 0.7906244993209839 552.4668579101562 0.3674054443836212 0.8411799 0.7942236661911011 True -18 20273 11.901875495910645 0.22790169715881348 470.07183837890625 0.44744008779525757 554.3519287109375 0.3658272624015808 0.84184843 0.7927485108375549 True -19 21340 11.90910291671753 0.22896027565002441 473.03533935546875 0.5998528003692627 555.9151611328125 0.36370211839675903 0.8423339 0.7964622974395752 True diff --git a/ENCSR607EJV/cherimoya.fold_4.performance.tsv b/ENCSR607EJV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 10b374937cdb2ceb260375509b279dc400dd171a..0000000000000000000000000000000000000000 --- a/ENCSR607EJV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -555.9151611328125 0.42662256956100464 0.36370208859443665 0.15085631608963013 0.8423339128494263 0.7972937226295471 0.7964622974395752 \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_0.evaluate.json b/ENCSR607HIL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ec8afdbc991b54ad42bba16f101e1f216652c43e..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430EXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_0.fit.json b/ENCSR607HIL/cherimoya.fold_0.fit.json deleted file mode 100644 index ce301fb25c0cffb55b60327391676e01fc341782..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF430EXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_0.log b/ENCSR607HIL/cherimoya.fold_0.log deleted file mode 100644 index 1b3f2d4204a0d7402c1469d3acc100466aa67daf..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2553 32.58787250518799 4.3552820682525635 319.55560302734375 0.6038610339164734 428.6657409667969 0.19223085045814514 0.66936415 5.336987018585205 True -1 5106 28.215373754501343 0.6500289440155029 295.5057373046875 0.7565703392028809 385.1901550292969 0.25822004675865173 0.7606909 2.3817760944366455 True -2 7659 28.19784927368164 0.5307583808898926 280.9474792480469 0.7078066468238831 375.4961242675781 0.269137442111969 0.7604992 1.5039753913879395 False -3 10212 28.20495295524597 0.5407764911651611 335.7890319824219 0.6132593750953674 372.111572265625 0.27449145913124084 0.77400583 0.9817442297935486 True -4 12765 28.224198818206787 0.5409743785858154 346.1737976074219 0.6181585788726807 369.8323059082031 0.2785905599594116 0.7890666 0.7937254309654236 True -5 15318 28.181495666503906 0.5559971332550049 298.48626708984375 0.8063580393791199 368.6908264160156 0.28045928478240967 0.80003846 0.6970422863960266 True -6 17871 28.137234210968018 0.5414373874664307 316.51025390625 0.5420488119125366 367.4707336425781 0.28377097845077515 0.80718124 0.671092689037323 True -7 20424 28.155211210250854 0.520247220993042 319.005126953125 0.5127151608467102 366.1704406738281 0.28599539399147034 0.81493825 0.6168824434280396 True -8 22977 28.238818645477295 0.541654109954834 284.6786804199219 0.35560697317123413 364.938720703125 0.28725460171699524 0.8194559 0.569441020488739 True -9 25530 28.213963508605957 0.568382740020752 259.460693359375 0.5633900165557861 364.4962463378906 0.2885276973247528 0.825541 0.5198534727096558 True -10 28083 28.22040820121765 0.5303826332092285 285.2310791015625 0.5079387426376343 364.07269287109375 0.2887958586215973 0.8304035 0.4955297112464905 True -11 30636 28.227006912231445 1.1264002323150635 320.0287780761719 0.427667498588562 363.19805908203125 0.29095011949539185 0.8340755 0.4612223505973816 True -12 33189 28.230263233184814 7.692969083786011 410.6383056640625 0.5388803482055664 361.8203125 0.29287561774253845 0.8387859 0.44521957635879517 True -13 35742 28.168991088867188 0.530773401260376 260.4681396484375 0.3317168951034546 361.062744140625 0.2947952151298523 0.8420886 0.4347616136074066 True -14 38295 28.189981937408447 1.2099792957305908 248.06117248535156 0.4506746530532837 360.8115234375 0.2941705286502838 0.84657794 0.4094182550907135 True -15 40848 28.266242742538452 0.5627527236938477 309.89703369140625 0.49409985542297363 360.00189208984375 0.29547569155693054 0.8490243 0.40237608551979065 True -16 43401 28.164180994033813 0.6306705474853516 208.168212890625 0.4146654009819031 359.47021484375 0.29689013957977295 0.84912694 0.3990078866481781 True -17 45954 27.717154264450073 0.551128625869751 319.998291015625 0.4399857223033905 360.0088806152344 0.2957608997821808 0.8492488 0.3994435667991638 True -18 48507 27.65892744064331 0.540416955947876 319.422607421875 0.35789233446121216 359.6971130371094 0.2969139814376831 0.8481511 0.4020465612411499 False -19 51060 27.699246168136597 0.5521702766418457 317.1885986328125 0.264087975025177 359.8292236328125 0.2962501347064972 0.84696496 0.40286529064178467 False diff --git a/ENCSR607HIL/cherimoya.fold_0.performance.tsv b/ENCSR607HIL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6b3aae1dd8c24d46c261c3811029d5eb9df75db6..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -360.0088806152344 0.47553446888923645 0.2957608699798584 0.09844806790351868 0.8492488265037537 0.7887647747993469 0.3994435667991638 \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_1.evaluate.json b/ENCSR607HIL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 12c270066a7d4678f7538d9a631634cca575b7d1..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430EXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_1.fit.json b/ENCSR607HIL/cherimoya.fold_1.fit.json deleted file mode 100644 index 71674ede7d5b5c8066b16cdb6df4800cc43b3eab..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF430EXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_1.log b/ENCSR607HIL/cherimoya.fold_1.log deleted file mode 100644 index de9d6f7e17f925056ba6843d51de9cbafbd77dec..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2536 32.518919229507446 4.094796419143677 355.77227783203125 0.5973899364471436 523.708251953125 0.20131023228168488 0.68726814 6.777420520782471 True -1 5072 28.072124004364014 0.731896162033081 294.211181640625 0.6507302522659302 462.4266357421875 0.28328239917755127 0.7841553 2.170635938644409 True -2 7608 28.041387796401978 0.7047221660614014 325.98504638671875 0.7414300441741943 453.1263732910156 0.2932188808917999 0.8001348 1.635493516921997 True -3 10144 28.048352003097534 0.7068040370941162 235.8920440673828 0.6734045743942261 447.2473449707031 0.3002130687236786 0.8036975 0.9510436654090881 True -4 12680 27.990272760391235 0.7073719501495361 407.37860107421875 0.7646021842956543 446.17877197265625 0.3006637394428253 0.81195223 0.8928768038749695 True -5 15216 27.976523637771606 0.6969678401947021 261.925048828125 0.5453177690505981 443.2953796386719 0.3048250377178192 0.8203946 0.8154549598693848 True -6 17752 27.984654903411865 0.6978106498718262 283.3764953613281 0.42556267976760864 442.46649169921875 0.30606013536453247 0.8295916 0.7478911280632019 True -7 20288 27.9689724445343 0.7081809043884277 205.09640502929688 0.497860312461853 441.4588928222656 0.3081549406051636 0.83225423 0.7546481490135193 True -8 22824 27.95988702774048 1.2487983703613281 369.7969055175781 0.5916709899902344 439.9969787597656 0.3100219964981079 0.83989704 0.6787497401237488 True -9 25360 28.007551431655884 24.24675154685974 280.95050048828125 0.46462535858154297 438.0643310546875 0.3134496212005615 0.845312 0.6025770306587219 True -10 27896 28.067484378814697 1.580465316772461 331.54718017578125 0.45551246404647827 435.88525390625 0.3166789710521698 0.8513945 0.5566322207450867 True -11 30432 27.97852635383606 0.7148618698120117 297.27490234375 0.31478220224380493 435.2176208496094 0.3179604709148407 0.8560321 0.5252286791801453 True -12 32968 28.06584405899048 0.7166478633880615 240.43972778320312 0.5534359216690063 434.2115783691406 0.31870830059051514 0.8617532 0.4959436058998108 True -13 35504 28.41638445854187 0.7307109832763672 315.453125 0.36939942836761475 432.1585388183594 0.32122865319252014 0.86556077 0.46268361806869507 True -14 38040 28.19767451286316 0.7775576114654541 349.5919189453125 0.4816514253616333 432.0599670410156 0.3219137191772461 0.87086916 0.43555793166160583 True -15 40576 29.197425842285156 1.5350286960601807 349.9444274902344 0.4127500057220459 430.78515625 0.32326391339302063 0.87438434 0.41863813996315 True -16 43112 28.119295120239258 12.840236902236938 345.33929443359375 0.3603261709213257 430.53485107421875 0.3230138421058655 0.87451196 0.4115557074546814 True -17 45648 28.042243242263794 0.730259895324707 232.77005004882812 0.22457173466682434 430.66192626953125 0.3234860301017761 0.8758697 0.41068509221076965 True -18 48184 28.131480932235718 1.248323917388916 294.97259521484375 0.31476032733917236 430.9588623046875 0.3224242329597473 0.87503844 0.41050291061401367 False -19 50720 27.86448574066162 0.7248802185058594 333.5311279296875 0.40635257959365845 430.6302185058594 0.3232046663761139 0.8728808 0.41250449419021606 False diff --git a/ENCSR607HIL/cherimoya.fold_1.performance.tsv b/ENCSR607HIL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f8879f6c2030cfa77140b7d58fd9a46de635b435..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -430.66192626953125 0.44994303584098816 0.3234860301017761 0.11977308988571167 0.8758696913719177 0.839560866355896 0.41068509221076965 \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_2.evaluate.json b/ENCSR607HIL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1e18e5bb489ceb5415298b928a79d0cc3850d165..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430EXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_2.fit.json b/ENCSR607HIL/cherimoya.fold_2.fit.json deleted file mode 100644 index 9237756eba0540ed6ddf0ab3adafc1159392fa20..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF430EXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_2.log b/ENCSR607HIL/cherimoya.fold_2.log deleted file mode 100644 index 2ac6990ccf75b6bb3b24d11a110e3b5084ae3cc6..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 34.497251749038696 3.592587947845459 289.21661376953125 0.8072476983070374 455.17425537109375 0.19451205432415009 0.65856224 6.217618942260742 True -1 5480 30.223748683929443 0.7334036827087402 424.9062805175781 0.7161827087402344 400.3979797363281 0.2654995024204254 0.7723177 1.8316878080368042 True -2 8220 30.257869482040405 0.6281633377075195 259.3305358886719 0.6098229289054871 393.1252136230469 0.2738752067089081 0.78168815 1.1456817388534546 True -3 10960 30.225993871688843 0.5288095474243164 341.81744384765625 0.6013352870941162 389.53704833984375 0.279572457075119 0.7935571 0.8465050458908081 True -4 13700 30.22358727455139 0.5573785305023193 324.9127197265625 0.7368645668029785 387.77618408203125 0.28254449367523193 0.8016082 0.7945045828819275 True -5 16440 30.286295413970947 1.9419806003570557 333.54217529296875 0.4435976445674896 386.9750671386719 0.2840348780155182 0.8077872 0.7421969175338745 True -6 19180 30.34024953842163 0.5876710414886475 304.4322509765625 0.6523691415786743 385.0028076171875 0.2880154550075531 0.8144709 0.7046284675598145 True -7 21920 30.25650453567505 0.5383660793304443 219.7540283203125 0.32535117864608765 383.58935546875 0.29025402665138245 0.8214533 0.64319908618927 True -8 24660 30.25745677947998 0.530350923538208 330.2631530761719 0.6681162118911743 382.6905822753906 0.2914183735847473 0.82584226 0.5902941226959229 True -9 27400 30.269717931747437 0.5617587566375732 283.74176025390625 0.7180144786834717 382.0121765136719 0.29235735535621643 0.8294244 0.541455864906311 True -10 30140 30.297229051589966 0.5328364372253418 259.912353515625 0.6459146738052368 379.9914855957031 0.2964867651462555 0.83418375 0.5139923095703125 True -11 32880 30.23156499862671 0.5417490005493164 299.1864013671875 0.44431594014167786 380.03533935546875 0.295994371175766 0.837304 0.4801708459854126 True -12 35620 30.29047155380249 0.5296039581298828 279.336181640625 0.47589707374572754 378.6467590332031 0.2980862855911255 0.84250665 0.46565207839012146 True -13 38360 30.294957399368286 0.6002485752105713 270.01251220703125 0.5667576193809509 378.24090576171875 0.2988346517086029 0.84564793 0.4366586208343506 True -14 41100 30.28964614868164 0.5332338809967041 263.23583984375 0.45236074924468994 376.1005859375 0.30350688099861145 0.849513 0.4218446612358093 True -15 43840 30.29989266395569 0.5285258293151855 238.6628875732422 0.38383716344833374 376.0996398925781 0.30308306217193604 0.85200423 0.40790843963623047 True -16 46580 30.265283823013306 0.5331907272338867 276.01788330078125 0.40641799569129944 376.447021484375 0.30234527587890625 0.8531092 0.4020586609840393 True -17 49320 30.418423891067505 1.7118592262268066 223.4883575439453 0.4200551509857178 376.9072570800781 0.3011184632778168 0.8521949 0.40472331643104553 False -18 52060 30.461381912231445 16.530311346054077 300.85162353515625 0.34260547161102295 376.6080627441406 0.3016028106212616 0.8508223 0.4077392816543579 False -19 54800 30.33595561981201 0.5398485660552979 268.5625915527344 0.30040809512138367 376.639892578125 0.30153119564056396 0.8482452 0.41142982244491577 False diff --git a/ENCSR607HIL/cherimoya.fold_2.performance.tsv b/ENCSR607HIL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1dc587034b2fe9b020427a395dc34c0fddb5c421..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -376.447021484375 0.4690866768360138 0.30234530568122864 0.10514595359563828 0.8531091809272766 0.8014202117919922 0.4020586609840393 \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_3.evaluate.json b/ENCSR607HIL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 866f37a2ef2d8d820ab6db70e0e624c1c31b8db5..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430EXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_3.fit.json b/ENCSR607HIL/cherimoya.fold_3.fit.json deleted file mode 100644 index 5e487618f6b8bc4ead210351df802d45a2d6b24a..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF430EXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_3.log b/ENCSR607HIL/cherimoya.fold_3.log deleted file mode 100644 index 6962ecb3d008a250738d2b1d8111ce2daf72f8a2..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2599 32.84504985809326 3.6207833290100098 351.032470703125 1.0454095602035522 441.86785888671875 0.19966629147529602 0.65343744 6.038352012634277 True -1 5198 28.694910764694214 0.6274609565734863 336.947021484375 0.7086687684059143 396.0611877441406 0.26499924063682556 0.7550241 1.9066475629806519 True -2 7797 28.73048424720764 0.5659868717193604 307.7225341796875 0.44935280084609985 389.246826171875 0.2722650170326233 0.776587 1.2312439680099487 True -3 10396 28.772889375686646 0.5860133171081543 254.83853149414062 0.620172917842865 387.5445251464844 0.27448907494544983 0.7804969 0.9800165891647339 True -4 12995 28.6985502243042 0.5638020038604736 326.24481201171875 0.6694361567497253 385.1647644042969 0.2797846496105194 0.7863536 0.9136432409286499 True -5 15594 28.756896495819092 0.5575628280639648 295.36944580078125 0.45095548033714294 384.4096374511719 0.28115177154541016 0.7931309 0.8357940912246704 True -6 18193 28.694604635238647 0.5649056434631348 326.564208984375 0.5780601501464844 383.2857360839844 0.2835289239883423 0.7985511 0.7929391264915466 True -7 20792 28.65506625175476 0.5537838935852051 283.06365966796875 0.6790060997009277 381.8680114746094 0.2856377959251404 0.8041435 0.7039626836776733 True -8 23391 28.70318293571472 0.6305954456329346 315.8548583984375 0.4609546959400177 380.5715637207031 0.2889192998409271 0.808653 0.7093454599380493 True -9 25990 28.85653853416443 0.6072397232055664 337.35687255859375 0.4683530926704407 379.7533874511719 0.29008370637893677 0.81550837 0.6587291955947876 True -10 28589 28.83948850631714 0.5854921340942383 367.72442626953125 0.7197926044464111 379.34173583984375 0.2909543216228485 0.8212442 0.6294741630554199 True -11 31188 28.923194885253906 0.5600771903991699 322.341796875 0.8244243860244751 378.3583679199219 0.2932235598564148 0.82607114 0.603477954864502 True -12 33787 28.854560375213623 0.5700232982635498 288.7622375488281 0.4234638512134552 376.7983093261719 0.29558733105659485 0.83277404 0.5513513684272766 True -13 36386 28.879661321640015 0.57377028465271 299.593994140625 0.678213357925415 375.2806396484375 0.2977311313152313 0.8390636 0.5133026242256165 True -14 38985 28.745957374572754 0.549203634262085 245.67030334472656 0.4798213243484497 374.6109924316406 0.29906049370765686 0.84321296 0.48375728726387024 True -15 41584 28.79542589187622 2.842376947402954 295.21124267578125 0.5021569728851318 374.136474609375 0.29983586072921753 0.8474541 0.45553088188171387 True -16 44183 28.86408305168152 0.5696878433227539 344.6339111328125 0.3926530182361603 373.4904479980469 0.29984042048454285 0.851481 0.43467170000076294 True -17 46782 28.84085965156555 0.584075927734375 307.59405517578125 0.32297205924987793 373.44219970703125 0.30026477575302124 0.852732 0.4305417835712433 True -18 49381 28.72668194770813 0.5740396976470947 329.1024475097656 0.24373279511928558 374.2262268066406 0.29857808351516724 0.8506795 0.4288594424724579 False -19 51980 28.864201307296753 0.5540640354156494 306.780029296875 0.3520534932613373 373.1919860839844 0.301213800907135 0.8491742 0.4314281642436981 False diff --git a/ENCSR607HIL/cherimoya.fold_3.performance.tsv b/ENCSR607HIL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c287a3ed756ee3d0e45b7d202d9619e3a558f27f..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -373.44219970703125 0.46930792927742004 0.30026477575302124 0.10681577026844025 0.8527320027351379 0.7968969345092773 0.4305417835712433 \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_4.evaluate.json b/ENCSR607HIL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 33b7eccb5b4434abb27913b060d763a9134e5a12..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430EXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_4.fit.json b/ENCSR607HIL/cherimoya.fold_4.fit.json deleted file mode 100644 index 9da316a9cc1755f109697d6da0cbb4680b991f68..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF430EXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR607HIL/cherimoya.fold_4.log b/ENCSR607HIL/cherimoya.fold_4.log deleted file mode 100644 index 8fb96f62ed48e549de3b0c167678df2b7c965c2d..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2621 33.99085831642151 4.514500617980957 349.29766845703125 0.6042566299438477 405.51617431640625 0.18815915286540985 0.65480024 4.746959686279297 True -1 5242 29.036808967590332 0.5704963207244873 287.6818542480469 0.6206835508346558 366.6753845214844 0.2487555295228958 0.7522146 1.7027539014816284 True -2 7863 28.994831323623657 0.5296037197113037 368.88525390625 0.5948188304901123 358.9156799316406 0.2629363238811493 0.7773132 0.9540285468101501 True -3 10484 28.687102556228638 0.5229611396789551 284.6220703125 0.4793647527694702 355.3030700683594 0.2666189968585968 0.78787476 0.7022913694381714 True -4 13105 28.403207063674927 0.968104362487793 267.5843200683594 0.41065847873687744 353.1958923339844 0.2691569924354553 0.791963 0.6211623549461365 True -5 15726 28.371461629867554 0.5265383720397949 340.89971923828125 0.6886751651763916 351.1103820800781 0.2738867998123169 0.7972431 0.5462725162506104 True -6 18347 28.369012594223022 0.5261900424957275 283.25921630859375 0.5032418966293335 350.58477783203125 0.2746730148792267 0.80441904 0.5416330695152283 True -7 20968 28.450605154037476 0.5213079452514648 275.0020446777344 0.7735801935195923 349.3122863769531 0.27707695960998535 0.8109174 0.4855112135410309 True -8 23589 28.379247665405273 0.5251543521881104 275.739013671875 0.5546454787254333 348.9812316894531 0.27727943658828735 0.8125002 0.4843958616256714 True -9 26210 28.416133880615234 0.5165719985961914 302.3905029296875 0.5288271903991699 347.6173400878906 0.2804773151874542 0.8212469 0.47521090507507324 True -10 28831 28.38283920288086 0.5196070671081543 344.1539611816406 0.5359760522842407 347.9377746582031 0.27993568778038025 0.82670265 0.45850318670272827 True -11 31452 28.42046022415161 0.5156962871551514 309.2663879394531 0.7006990909576416 346.5653991699219 0.2823859751224518 0.8328197 0.428864061832428 True -12 34073 28.40695548057556 0.5171051025390625 286.7202453613281 0.5034486055374146 345.55657958984375 0.2844301462173462 0.83615047 0.41766780614852905 True -13 36694 28.518237590789795 0.5374722480773926 254.3738250732422 0.4717295467853546 344.99945068359375 0.28614071011543274 0.84124404 0.4018988013267517 True -14 39315 28.554824829101562 0.528721809387207 306.4366149902344 0.32384636998176575 345.0616455078125 0.28550368547439575 0.8456178 0.3848612308502197 True -15 41936 28.55398178100586 0.5270605087280273 283.3172912597656 0.2989436388015747 344.9238586425781 0.28599777817726135 0.8501241 0.3725427985191345 True -16 44557 28.689977884292603 0.5175552368164062 267.28973388671875 0.24658843874931335 344.37811279296875 0.2870786786079407 0.8508408 0.36441484093666077 True -17 47178 28.58590817451477 0.528052806854248 271.0425720214844 0.37730318307876587 344.0507507324219 0.2886331081390381 0.8523399 0.36334556341171265 True -18 49799 28.467895030975342 0.5146915912628174 329.203369140625 0.27059510350227356 344.4367980957031 0.2872086465358734 0.8499424 0.3685067594051361 False -19 52420 28.529582738876343 1.6962757110595703 266.86529541015625 0.3334607183933258 344.9162902832031 0.28614506125450134 0.84928423 0.37379294633865356 False diff --git a/ENCSR607HIL/cherimoya.fold_4.performance.tsv b/ENCSR607HIL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 084d38e04f85265b0685b54b60972430d84a21ad..0000000000000000000000000000000000000000 --- a/ENCSR607HIL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -344.0507507324219 0.48068147897720337 0.2886331081390381 0.09585893899202347 0.8523399233818054 0.7952232956886292 0.36334556341171265 \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_0.evaluate.json b/ENCSR608AHQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2c2b77f81b1351da9e8c422d5002cada2c5c0021..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903UAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_0.fit.json b/ENCSR608AHQ/cherimoya.fold_0.fit.json deleted file mode 100644 index f047aa7563ccf3b39235bfe38916b0d1d3dba0ec..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF903UAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_0.log b/ENCSR608AHQ/cherimoya.fold_0.log deleted file mode 100644 index da45866b8f2f4f110b3cf84ec7872d4896b4999c..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2722 34.935298442840576 3.8938424587249756 201.82815551757812 0.4242820739746094 237.7296600341797 0.12333154678344727 0.7272001 2.864999532699585 True -1 5444 30.347855806350708 1.0869996547698975 201.08392333984375 0.5707995891571045 228.26873779296875 0.17147330939769745 0.78606284 0.7516039609909058 True -2 8166 31.16973042488098 17.963772296905518 182.01803588867188 0.547554075717926 225.33447265625 0.18292772769927979 0.7980377 0.4829457998275757 True -3 10888 30.49031162261963 0.6410648822784424 180.83570861816406 0.4613330066204071 223.6614227294922 0.18843090534210205 0.8058529 0.44324684143066406 True -4 13610 30.392741680145264 1.1155462265014648 195.44378662109375 0.4494813084602356 223.2589874267578 0.18902666866779327 0.81140834 0.4266425371170044 True -5 16332 30.455692768096924 0.5859260559082031 157.8871612548828 0.4384782612323761 222.6690673828125 0.19203753769397736 0.8167854 0.3960047662258148 True -6 19054 30.41875386238098 0.5882863998413086 193.22344970703125 0.41365185379981995 222.73768615722656 0.19134573638439178 0.8200597 0.40332841873168945 True -7 21776 30.27901315689087 0.5855765342712402 158.9644775390625 0.38793134689331055 222.0683135986328 0.195232555270195 0.82185525 0.38882485032081604 True -8 24498 30.273590326309204 0.5897970199584961 180.80459594726562 0.46944287419319153 221.66845703125 0.19710451364517212 0.82412213 0.398868203163147 True -9 27220 30.293785095214844 0.5874676704406738 199.2837371826172 0.32566338777542114 221.39759826660156 0.1989160031080246 0.8293539 0.3718894124031067 True -10 29942 30.265342473983765 1.1194579601287842 178.30892944335938 0.34825047850608826 221.02940368652344 0.19947028160095215 0.8341984 0.343303918838501 True -11 32664 30.417543411254883 0.5973572731018066 170.87844848632812 0.44887858629226685 220.70970153808594 0.20134548842906952 0.83621913 0.32657426595687866 True -12 35386 30.28866171836853 0.5881524085998535 194.361572265625 0.3539803922176361 220.55120849609375 0.20255938172340393 0.8401368 0.31131643056869507 True -13 38108 30.31243348121643 0.5767786502838135 188.55824279785156 0.2904818058013916 220.2315216064453 0.20327341556549072 0.84246105 0.2922109365463257 True -14 40830 30.384639024734497 0.5756490230560303 180.92613220214844 0.26794683933258057 219.9241180419922 0.20429834723472595 0.84881246 0.2787943482398987 True -15 43552 30.331780195236206 0.5770580768585205 176.85263061523438 0.24980409443378448 220.0111083984375 0.20383356511592865 0.851858 0.27224817872047424 True -16 46274 30.379966259002686 0.5700991153717041 171.40415954589844 0.16680440306663513 219.9154052734375 0.20475910604000092 0.85283 0.2661812901496887 True -17 48996 30.306296825408936 0.5859987735748291 166.4825439453125 0.23996767401695251 219.8748779296875 0.20520877838134766 0.8524359 0.26476797461509705 False -18 51718 30.293604612350464 0.5893032550811768 180.15203857421875 0.23757962882518768 220.1529083251953 0.20305927097797394 0.8508761 0.26775509119033813 False -19 54440 30.373125791549683 0.5745339393615723 184.78929138183594 0.20270289480686188 220.0675048828125 0.2034941464662552 0.85012704 0.268364816904068 False diff --git a/ENCSR608AHQ/cherimoya.fold_0.performance.tsv b/ENCSR608AHQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 41f2987df9a7e4c440d864b37d9a122ebc34fa86..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.9154052734375 0.5451956391334534 0.20475910604000092 0.05512384697794914 0.8528299927711487 0.7956493496894836 0.2661812901496887 \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_1.evaluate.json b/ENCSR608AHQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 677f924c90416a5835c792d91255c9b0983fc7b9..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903UAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_1.fit.json b/ENCSR608AHQ/cherimoya.fold_1.fit.json deleted file mode 100644 index d2b3508614cef4451d21ac00c0c30b34defe31a9..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF903UAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_1.log b/ENCSR608AHQ/cherimoya.fold_1.log deleted file mode 100644 index 028a8aa9bdcbb8d3644f8e34313d3bc996281565..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2706 34.11012840270996 3.8881173133850098 170.1002197265625 0.5629020929336548 275.568115234375 0.1374470293521881 0.72270715 2.651484966278076 True -1 5412 30.12364649772644 1.6613636016845703 198.77679443359375 0.4336682856082916 263.6416015625 0.19093187153339386 0.78213453 0.8750432729721069 True -2 8118 30.30204963684082 27.615459203720093 187.40924072265625 0.4729101359844208 259.91119384765625 0.20308220386505127 0.8060077 0.535313069820404 True -3 10824 30.138269901275635 20.410871744155884 129.6111297607422 0.45863476395606995 258.3910217285156 0.20759370923042297 0.81267536 0.45375657081604004 True -4 13530 30.775333404541016 0.7664268016815186 166.5351104736328 0.4119611382484436 257.3643493652344 0.2111649215221405 0.81991357 0.43871909379959106 True -5 16236 30.119800567626953 0.7374532222747803 181.44403076171875 0.40199577808380127 256.93048095703125 0.21257762610912323 0.82441205 0.4418848752975464 True -6 18942 30.106403350830078 0.7398676872253418 192.85638427734375 0.5089373588562012 256.56439208984375 0.2141287624835968 0.82852095 0.4408925175666809 True -7 21648 30.11488175392151 1.4161779880523682 168.8681182861328 0.201566681265831 255.59730529785156 0.21843640506267548 0.8350427 0.41232383251190186 True -8 24354 30.120312213897705 0.7401986122131348 218.2353057861328 0.4750429093837738 255.49551391601562 0.21862252056598663 0.83872336 0.4012162685394287 True -9 27060 30.11928105354309 0.8821954727172852 186.65223693847656 0.22780272364616394 255.2292938232422 0.21971026062965393 0.84212726 0.34442293643951416 True -10 29766 30.11652898788452 0.7530779838562012 142.72784423828125 0.5545035600662231 254.891357421875 0.22114013135433197 0.84637 0.32704687118530273 True -11 32472 30.07725167274475 0.7391953468322754 226.0093231201172 0.31171348690986633 254.68919372558594 0.22131527960300446 0.8490057 0.3179667890071869 True -12 35178 30.14248490333557 0.7444519996643066 166.02230834960938 0.2517785429954529 254.19419860839844 0.2238069772720337 0.8519178 0.3083373010158539 True -13 37884 30.197930574417114 0.7474215030670166 161.9119873046875 0.382149338722229 253.9860076904297 0.2243826985359192 0.85521656 0.294760137796402 True -14 40590 30.189108848571777 1.633340835571289 180.28274536132812 0.25226831436157227 253.7736358642578 0.225522980093956 0.8586524 0.28556105494499207 True -15 43296 30.124757051467896 0.7458033561706543 160.54559326171875 0.31457021832466125 253.29454040527344 0.2273433804512024 0.86185837 0.2816990315914154 True -16 46002 30.093758821487427 0.7532815933227539 190.8951416015625 0.2645723819732666 253.4651336669922 0.226498544216156 0.860358 0.2822246849536896 False -17 48708 29.969651699066162 0.7374167442321777 201.07327270507812 0.18509867787361145 253.5282745361328 0.22627507150173187 0.86211526 0.28489574790000916 True -18 51414 29.43078899383545 0.7200334072113037 184.18911743164062 0.17240314185619354 253.61976623535156 0.22562289237976074 0.858421 0.28858789801597595 False -19 54120 29.51264524459839 0.7373001575469971 181.85354614257812 0.18442857265472412 253.74185180664062 0.225129172205925 0.8586806 0.29297903180122375 False diff --git a/ENCSR608AHQ/cherimoya.fold_1.performance.tsv b/ENCSR608AHQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 84dfcf8a6f3fc53e9e4f18893aacda929eba649e..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -253.5282745361328 0.5266615748405457 0.22627507150173187 0.06388499587774277 0.8621152639389038 0.831282377243042 0.28489574790000916 \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_2.evaluate.json b/ENCSR608AHQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 94357ead26d6a69219da6792876338e524316fb1..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903UAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_2.fit.json b/ENCSR608AHQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 65cb1d276b103ec1b784ee0a3721d179884ed7f7..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF903UAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_2.log b/ENCSR608AHQ/cherimoya.fold_2.log deleted file mode 100644 index 097998765546df1c0248a4216e5da07baba5b1ef..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2884 36.65360951423645 4.037115573883057 192.5614013671875 0.4407757818698883 246.4579315185547 0.13101275265216827 0.72527146 1.9557607173919678 True -1 5768 32.181379318237305 1.439892292022705 181.08641052246094 0.3538658022880554 234.94778442382812 0.18470057845115662 0.79073125 0.6451477408409119 True -2 8652 32.14401817321777 0.5644447803497314 160.52438354492188 0.3518059253692627 232.5177764892578 0.19136960804462433 0.80201423 0.47333386540412903 True -3 11536 32.10482430458069 0.5825743675231934 179.4932098388672 0.5594290494918823 231.24063110351562 0.19590544700622559 0.81097364 0.39689958095550537 True -4 14420 32.07112526893616 0.5531542301177979 195.3922882080078 0.26805436611175537 230.30348205566406 0.1997460573911667 0.815484 0.3759818375110626 True -5 17304 32.048816442489624 0.5611743927001953 163.54071044921875 0.3580360412597656 230.02191162109375 0.20029060542583466 0.82047904 0.37728410959243774 True -6 20188 32.0636670589447 1.0672953128814697 177.15469360351562 0.41185352206230164 229.63845825195312 0.20197276771068573 0.8230014 0.35114073753356934 True -7 23072 32.051270961761475 0.5549685955047607 222.96011352539062 0.38691413402557373 229.2283477783203 0.20377536118030548 0.8281397 0.32516908645629883 True -8 25956 32.03025960922241 0.5574488639831543 185.68898010253906 0.3872643709182739 228.74755859375 0.20594066381454468 0.83278257 0.32058611512184143 True -9 28840 32.106409788131714 0.5701851844787598 187.26303100585938 0.36291569471359253 228.6833038330078 0.2062862515449524 0.8340756 0.3050335645675659 True -10 31724 32.09036326408386 0.5733282566070557 199.5648651123047 0.43588003516197205 228.35549926757812 0.20746564865112305 0.83783823 0.29765740036964417 True -11 34608 32.10544276237488 0.5490748882293701 190.02256774902344 0.3044256567955017 228.22219848632812 0.20833830535411835 0.83965224 0.2910654842853546 True -12 37492 32.12875437736511 0.5628345012664795 140.75852966308594 0.3965253233909607 227.73451232910156 0.2109382301568985 0.8418345 0.2847432494163513 True -13 40376 31.584868907928467 0.5475597381591797 189.2220458984375 0.28660789132118225 227.46243286132812 0.2123609036207199 0.8451394 0.2811685800552368 True -14 43260 31.47172451019287 0.54817795753479 150.3126983642578 0.22028908133506775 227.19662475585938 0.2130371779203415 0.849395 0.27190855145454407 True -15 46144 31.528525829315186 0.5475566387176514 145.85513305664062 0.37212833762168884 227.35833740234375 0.2120262086391449 0.8520564 0.26624149084091187 True -16 49028 31.47242259979248 0.5378925800323486 181.85960388183594 0.3224797248840332 227.06973266601562 0.2139519602060318 0.8531902 0.2649051249027252 True -17 51912 31.418617248535156 0.5466451644897461 183.0206298828125 0.27990415692329407 227.0959014892578 0.21376001834869385 0.85366434 0.26754963397979736 True -18 54796 31.456984519958496 0.5497303009033203 174.79061889648438 0.1578579843044281 227.14532470703125 0.2138763815164566 0.85334706 0.27032414078712463 False -19 57680 31.4647536277771 0.5362813472747803 189.75555419921875 0.14095456898212433 227.06993103027344 0.21429584920406342 0.85297716 0.27363571524620056 False diff --git a/ENCSR608AHQ/cherimoya.fold_2.performance.tsv b/ENCSR608AHQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 84d50511e4d2a1c4eedfebecc671cf8ece48d45d..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -227.0959014892578 0.539998471736908 0.21376001834869385 0.058317750692367554 0.8536643385887146 0.8122586607933044 0.26754963397979736 \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_3.evaluate.json b/ENCSR608AHQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d8a1f023ad2d649f42692f0b6f3597ef7291af51..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903UAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_3.fit.json b/ENCSR608AHQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 1832126bec2098e9b9d1e2d4dc8a79ff44dcab34..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF903UAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_3.log b/ENCSR608AHQ/cherimoya.fold_3.log deleted file mode 100644 index deec5ad594e7b16dee103a31b0e7c8bdbea25e94..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 35.2527379989624 4.305356740951538 163.63198852539062 0.5166183710098267 242.6378631591797 0.1280970275402069 0.7336666 2.3384459018707275 True -1 5524 30.731329679489136 0.6777663230895996 192.62530517578125 0.6281507611274719 233.6002197265625 0.1729605495929718 0.80277544 0.7282652854919434 True -2 8286 30.720483541488647 0.6094019412994385 216.37716674804688 0.3256838619709015 231.0083770751953 0.1828918308019638 0.8107962 0.47178199887275696 True -3 11048 30.78249955177307 0.5891985893249512 202.3802490234375 0.32823923230171204 229.6279296875 0.1876271665096283 0.8183458 0.3994005024433136 True -4 13810 30.730680465698242 0.5951540470123291 161.4283447265625 0.4517274796962738 228.566650390625 0.1926289200782776 0.82206666 0.3830360472202301 True -5 16572 30.667237043380737 0.6003515720367432 213.2716522216797 0.4406282603740692 228.43255615234375 0.1930007040500641 0.8272471 0.3969898521900177 True -6 19334 30.680431604385376 0.5757582187652588 190.98703002929688 0.5082190632820129 228.04029846191406 0.1950198858976364 0.82848245 0.37793222069740295 True -7 22096 30.716715097427368 0.5841999053955078 162.091552734375 0.34207168221473694 227.9938507080078 0.19461779296398163 0.8319219 0.3737644851207733 True -8 24858 30.697522163391113 0.5770134925842285 173.86207580566406 0.3773733377456665 227.52467346191406 0.19688434898853302 0.8342675 0.3765234053134918 True -9 27620 30.6988582611084 0.5858533382415771 178.84165954589844 0.46471768617630005 227.36602783203125 0.19761474430561066 0.8379025 0.34160682559013367 True -10 30382 30.62870216369629 0.5801444053649902 190.52444458007812 0.23299092054367065 226.97702026367188 0.19988009333610535 0.8406826 0.3371046185493469 True -11 33144 30.10873532295227 0.5832197666168213 175.2626953125 0.35469943284988403 226.77491760253906 0.1998940259218216 0.84247994 0.3154168725013733 True -12 35906 30.057138681411743 0.5776193141937256 190.36111450195312 0.31364840269088745 226.76905822753906 0.20002853870391846 0.84826344 0.3024800717830658 True -13 38668 30.042296648025513 0.580557107925415 173.358642578125 0.4500511586666107 225.98175048828125 0.2041434794664383 0.8505624 0.302153080701828 True -14 41430 30.067697525024414 0.5762426853179932 173.5479736328125 0.3010816276073456 226.13720703125 0.2034039944410324 0.8535299 0.286943644285202 True -15 44192 30.096933126449585 2.3821887969970703 162.99847412109375 0.4100998342037201 225.79367065429688 0.20519191026687622 0.8569996 0.28105437755584717 True -16 46954 30.13208842277527 0.6049220561981201 157.2784881591797 0.23469401895999908 225.5902099609375 0.2059379667043686 0.85866416 0.2751670181751251 True -17 49716 30.139415502548218 0.6033539772033691 154.60055541992188 0.13661687076091766 225.93885803222656 0.20396101474761963 0.85733837 0.2786285877227783 False -18 52478 30.117427110671997 0.5870535373687744 174.65524291992188 0.18782097101211548 225.7375030517578 0.2050868719816208 0.85550874 0.28200364112854004 False -19 55240 30.09127950668335 0.5812065601348877 154.3872833251953 0.1950436681509018 225.88624572753906 0.2041446715593338 0.85638815 0.2836364507675171 False diff --git a/ENCSR608AHQ/cherimoya.fold_3.performance.tsv b/ENCSR608AHQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f68fab3b51843ec34b5392014631432b6724b2f1..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -225.5902099609375 0.543453574180603 0.20593798160552979 0.053838130086660385 0.8586641550064087 0.8034546971321106 0.2751670181751251 \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_4.evaluate.json b/ENCSR608AHQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 41a1ce148877d31d7bc533942220dc298b49eb82..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903UAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_4.fit.json b/ENCSR608AHQ/cherimoya.fold_4.fit.json deleted file mode 100644 index f3565c666b03eee3f91c48a09a05f6a3b9efc508..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF903UAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608AHQ/cherimoya.fold_4.log b/ENCSR608AHQ/cherimoya.fold_4.log deleted file mode 100644 index 25b3c0ea832b48ef7d0e24507558aca5d86dac87..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2834 36.28456449508667 4.5588531494140625 205.04095458984375 0.5254601836204529 229.56503295898438 0.12203795462846756 0.7233303 2.1696717739105225 True -1 5668 31.70064902305603 0.712268590927124 177.27203369140625 0.5565654039382935 220.2664031982422 0.17014311254024506 0.78545344 0.6080143451690674 True -2 8502 31.582335233688354 0.616051197052002 190.54879760742188 0.4610743522644043 218.39256286621094 0.17571941018104553 0.7962151 0.3904426693916321 True -3 11336 31.56557297706604 0.6053080558776855 176.45889282226562 0.46445921063423157 217.2028045654297 0.18120776116847992 0.8041793 0.33560293912887573 True -4 14170 31.56691288948059 0.606318473815918 215.35696411132812 0.5737496018409729 216.3006591796875 0.18488457798957825 0.81171626 0.3314652740955353 True -5 17004 31.581182956695557 0.6010282039642334 183.69659423828125 0.289044052362442 216.06747436523438 0.18573661148548126 0.8156192 0.3243407905101776 True -6 19838 31.15996026992798 0.6190991401672363 165.0426483154297 0.4975791275501251 215.6965789794922 0.18806461989879608 0.8187735 0.3124657869338989 True -7 22672 31.01263928413391 0.5908105373382568 162.79486083984375 0.2541910409927368 215.32882690429688 0.18953652679920197 0.82209635 0.31115785241127014 True -8 25506 30.98618483543396 0.5928852558135986 213.79443359375 0.45178136229515076 215.1009521484375 0.18995530903339386 0.82823104 0.3044772148132324 True -9 28340 31.091076850891113 0.5930655002593994 151.30364990234375 0.37187886238098145 214.47056579589844 0.1942121535539627 0.83083224 0.3033554255962372 True -10 31174 31.004901885986328 0.5759363174438477 220.9178466796875 0.4876650273799896 214.44041442871094 0.1943581998348236 0.8357336 0.2848542034626007 True -11 34008 31.017341136932373 0.5765342712402344 179.25164794921875 0.233562171459198 213.96351623535156 0.19652238488197327 0.83843 0.2809026539325714 True -12 36842 31.000473976135254 0.5800490379333496 126.27032470703125 0.2843554615974426 213.6256103515625 0.19774848222732544 0.8420311 0.273122638463974 True -13 39676 31.018402814865112 0.5821266174316406 156.37197875976562 0.2473275065422058 213.7660675048828 0.19690953195095062 0.84509706 0.2664070129394531 True -14 42510 30.985939025878906 0.5743064880371094 182.40310668945312 0.420670747756958 213.5543670654297 0.19802148640155792 0.8474656 0.2606699764728546 True -15 45344 30.97750997543335 0.5823140144348145 180.0936279296875 0.356866717338562 213.4496612548828 0.1988622546195984 0.85258275 0.2531121075153351 True -16 48178 30.903611660003662 0.5763759613037109 188.7420654296875 0.2761147916316986 213.34640502929688 0.19917285442352295 0.85270363 0.25067853927612305 True -17 51012 30.94446563720703 0.5826349258422852 173.27586364746094 0.21137335896492004 213.2269287109375 0.19996027648448944 0.85334516 0.2504311501979828 True -18 53846 30.91551971435547 0.577641487121582 188.3382568359375 0.19205045700073242 213.2837371826172 0.1993817687034607 0.85344476 0.2517286241054535 True -19 56680 30.888920545578003 0.6637382507324219 205.56353759765625 0.19092871248722076 213.45101928710938 0.19863739609718323 0.8531405 0.253549724817276 False diff --git a/ENCSR608AHQ/cherimoya.fold_4.performance.tsv b/ENCSR608AHQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b1316f1b325c0ad7e849dbf47fae1daa0a5e0899..0000000000000000000000000000000000000000 --- a/ENCSR608AHQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -213.2837371826172 0.549632728099823 0.1993817538022995 0.05335056781768799 0.8534447550773621 0.7888966202735901 0.2517286241054535 \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_0.evaluate.json b/ENCSR608KJD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9890dd0f6a4b769fbc843ae162413e171382602f..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277DNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_0.fit.json b/ENCSR608KJD/cherimoya.fold_0.fit.json deleted file mode 100644 index 40ff0033c59c1ef28cf50c159fef86df60838c16..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF277DNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_0.log b/ENCSR608KJD/cherimoya.fold_0.log deleted file mode 100644 index c30a9ce4a9f65941b0865c3a663a00a44430947a..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1795 24.28883147239685 3.882873058319092 310.07568359375 0.5515581965446472 455.7731018066406 0.44436129927635193 0.53315383 11.533326148986816 True -1 3590 19.829435348510742 0.41333532333374023 345.9820556640625 0.5953882932662964 396.8558349609375 0.538235604763031 0.6297107 4.624955654144287 True -2 5385 19.809553146362305 0.3762650489807129 295.46075439453125 0.636501669883728 377.85662841796875 0.5830934643745422 0.64253753 1.4090744256973267 True -3 7180 19.80677890777588 0.37228894233703613 303.5826416015625 0.550561785697937 372.9544372558594 0.5932621359825134 0.66418046 0.7575997114181519 True -4 8975 19.809898853302002 0.39124536514282227 314.0893859863281 0.6039243936538696 370.548095703125 0.5985879302024841 0.6822908 0.5886784195899963 True -5 10770 19.91121792793274 0.3724534511566162 321.89337158203125 0.5641089677810669 369.22686767578125 0.6018105745315552 0.6821948 0.48255839943885803 False -6 12565 20.933791399002075 12.800333738327026 312.5093994140625 0.5849827527999878 368.2233581542969 0.6046172976493835 0.6915202 0.45556873083114624 True -7 14360 19.885966062545776 0.3785278797149658 264.5179443359375 0.45358940958976746 367.3557434082031 0.6066916584968567 0.6945144 0.43779438734054565 True -8 16155 19.888306140899658 0.3800182342529297 277.3229064941406 0.4323934316635132 366.8567199707031 0.6079089641571045 0.693769 0.4220529794692993 False -9 17950 19.887343168258667 0.37905430793762207 283.7696533203125 0.26274412870407104 365.99114990234375 0.6097046732902527 0.701657 0.40458595752716064 True -10 19745 19.934600591659546 0.37416648864746094 310.3785095214844 0.5194759368896484 365.5227355957031 0.6109004020690918 0.7049432 0.4036213159561157 True -11 21540 19.846696376800537 0.3658638000488281 345.44195556640625 0.4216381907463074 364.9191589355469 0.6124803423881531 0.7098047 0.39392349123954773 True -12 23335 19.85581064224243 0.38111209869384766 332.95159912109375 0.3731114864349365 364.2279357910156 0.6138170957565308 0.7151905 0.3872304856777191 True -13 25130 19.889788389205933 0.36916327476501465 302.6220703125 0.2589205205440521 363.897705078125 0.6146986484527588 0.71671957 0.3910152316093445 True -14 26925 19.9733464717865 1.5639324188232422 266.1283874511719 0.29931750893592834 363.43292236328125 0.6153610944747925 0.719365 0.39171063899993896 True -15 28720 19.553566694259644 0.36618590354919434 291.8031005859375 0.39394956827163696 363.5975646972656 0.6153523921966553 0.71938413 0.3952176570892334 True -16 30515 19.528512477874756 0.3766810894012451 320.3648681640625 0.39591026306152344 363.5237731933594 0.6150397062301636 0.71839404 0.4015209972858429 False -17 32310 19.515477418899536 0.3699350357055664 344.69500732421875 0.3103019595146179 363.9032897949219 0.6142662763595581 0.71549577 0.4135757088661194 False -18 34105 19.48724102973938 0.37816739082336426 296.751953125 0.23600298166275024 363.9584655761719 0.613531768321991 0.70927685 0.4274061322212219 False -19 35900 19.479001760482788 0.3638148307800293 339.0503234863281 0.20830541849136353 364.18853759765625 0.6131203770637512 0.7055239 0.43505099415779114 False diff --git a/ENCSR608KJD/cherimoya.fold_0.performance.tsv b/ENCSR608KJD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d2343378686931b6eac79e9efe12b9ef55e8b50a..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -363.5975646972656 0.3064613938331604 0.6153524518013 0.23586568236351013 0.7193841338157654 0.6803815960884094 0.3952176570892334 \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_1.evaluate.json b/ENCSR608KJD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4035ffc065c5e3b0e66d840e8c0c9d5d8c97a6a4..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277DNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_1.fit.json b/ENCSR608KJD/cherimoya.fold_1.fit.json deleted file mode 100644 index e786e37c06b4a3d17f53cf7868293cc9a668b781..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF277DNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_1.log b/ENCSR608KJD/cherimoya.fold_1.log deleted file mode 100644 index b878785888775b3b32adef23f5e7f791de4f4e2e..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1803 24.410224199295044 3.6950061321258545 279.72161865234375 0.5884757041931152 476.90826416015625 0.4565677046775818 0.5334325 11.501091957092285 True -1 3606 19.939817905426025 0.6820974349975586 347.91485595703125 0.6189789175987244 417.1109619140625 0.5488131642341614 0.6371215 4.024972438812256 True -2 5409 19.898379802703857 0.9995090961456299 290.5569152832031 0.6230107545852661 402.6874694824219 0.5823706984519958 0.6611436 1.185861587524414 True -3 7212 19.91062045097351 1.553311824798584 306.49798583984375 0.5289681553840637 397.1712646484375 0.5920714735984802 0.6833662 0.6312649846076965 True -4 9015 19.905853748321533 0.483691930770874 348.78912353515625 0.6911420822143555 395.5813903808594 0.5955727696418762 0.70087 0.5241835117340088 True -5 10818 19.905367851257324 1.748033046722412 242.2386016845703 0.5502387285232544 394.4964294433594 0.5983570218086243 0.70596015 0.5000073909759521 True -6 12621 19.899027585983276 0.5486304759979248 289.7271728515625 0.6514641642570496 393.8593444824219 0.6000782251358032 0.7073702 0.49650266766548157 True -7 14424 19.875457286834717 0.4787266254425049 300.05047607421875 0.7746449112892151 392.88165283203125 0.602260172367096 0.7150079 0.46017754077911377 True -8 16227 19.9172306060791 0.4785745143890381 265.4110107421875 0.3617044687271118 392.0636291503906 0.6044077277183533 0.72022325 0.4455433189868927 True -9 18030 19.9245126247406 0.45728135108947754 294.438720703125 0.6285092234611511 390.8658752441406 0.6068899035453796 0.7297525 0.40767237544059753 True -10 19833 19.993056774139404 0.4855926036834717 284.48406982421875 0.5061966180801392 390.1600036621094 0.6087730526924133 0.7338002 0.3879930377006531 True -11 21636 19.98567509651184 0.4651782512664795 277.44635009765625 0.4842149615287781 389.19403076171875 0.610767662525177 0.7362035 0.38534921407699585 True -12 23439 20.06213116645813 0.4770088195800781 240.798095703125 0.49657708406448364 388.72113037109375 0.6117788553237915 0.744491 0.36720776557922363 True -13 25242 20.003563165664673 0.8271684646606445 293.3511962890625 0.23356884717941284 388.10382080078125 0.612838864326477 0.7463599 0.370118647813797 True -14 27045 20.0088369846344 0.4617915153503418 276.72314453125 0.3437577486038208 387.62481689453125 0.6139788627624512 0.7487477 0.37009692192077637 True -15 28848 19.98020052909851 0.46255922317504883 264.5220642089844 0.30401742458343506 387.3912048339844 0.6142494082450867 0.7523591 0.3664008677005768 True -16 30651 19.93136692047119 0.4609534740447998 272.666015625 0.22621911764144897 387.30450439453125 0.6142759323120117 0.75374335 0.36764445900917053 True -17 32454 19.88785457611084 0.4719107151031494 339.75958251953125 0.2289891242980957 387.479248046875 0.6138007044792175 0.7503822 0.3740462064743042 False -18 34257 19.926122188568115 1.7083275318145752 263.3193359375 0.19920067489147186 387.5514221191406 0.6133213639259338 0.74512637 0.38615381717681885 False -19 36060 19.927777528762817 0.45092010498046875 250.52987670898438 0.25530147552490234 387.702392578125 0.6129257082939148 0.7437618 0.39020976424217224 False diff --git a/ENCSR608KJD/cherimoya.fold_1.performance.tsv b/ENCSR608KJD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d2a7d1500fd615712dadeddec08739b50cb1a019..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -387.30450439453125 0.299674391746521 0.6142758727073669 0.24933524429798126 0.7537433505058289 0.73842453956604 0.36764445900917053 \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_2.evaluate.json b/ENCSR608KJD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 525f7c97a51b6d04d8dbd330862263fd3a6dcd27..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277DNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_2.fit.json b/ENCSR608KJD/cherimoya.fold_2.fit.json deleted file mode 100644 index a8cf6eb29e968852f7fc6c4697d2cc276a500db1..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF277DNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_2.log b/ENCSR608KJD/cherimoya.fold_2.log deleted file mode 100644 index e6bf4dd1c844bd02e77164e20a0ee07e7f0bffba..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1897 25.49445343017578 3.4654507637023926 286.1675109863281 0.8469891548156738 451.6944580078125 0.4478203058242798 0.550798 11.132144927978516 True -1 3794 20.998404026031494 0.5181291103363037 301.1982116699219 0.46484023332595825 395.96923828125 0.5449371933937073 0.6466068 4.15342903137207 True -2 5691 20.931782960891724 0.3621988296508789 292.950439453125 0.3847719132900238 381.754638671875 0.5776083469390869 0.66101915 1.0920196771621704 True -3 7588 20.93643069267273 0.3736584186553955 326.6240234375 0.448890745639801 377.0213317871094 0.586308479309082 0.68273586 0.5906170606613159 True -4 9485 20.910057067871094 0.36173367500305176 385.426513671875 0.5678489804267883 374.9177551269531 0.5908946394920349 0.69289 0.5640684366226196 True -5 11382 20.92660403251648 0.3603200912475586 324.3568115234375 0.43579593300819397 374.21441650390625 0.592997133731842 0.69225 0.5418057441711426 False -6 13279 20.85187339782715 0.429945707321167 280.2825622558594 0.39615321159362793 373.34112548828125 0.595043957233429 0.7005426 0.5274178385734558 True -7 15176 20.529314517974854 0.3657538890838623 284.0201721191406 0.5667312145233154 372.673095703125 0.5968993306159973 0.7054761 0.49201008677482605 True -8 17073 20.535601139068604 0.5870761871337891 339.952392578125 0.5238152742385864 371.8026123046875 0.5990629196166992 0.7113594 0.45651882886886597 True -9 18970 20.52931809425354 0.39135289192199707 247.32150268554688 0.7377325296401978 371.1831359863281 0.600542426109314 0.7160183 0.45367249846458435 True -10 20867 20.58403253555298 2.269761085510254 284.2633361816406 0.4830242395401001 370.4864501953125 0.6023019552230835 0.7208102 0.43052276968955994 True -11 22764 20.565431594848633 0.3645472526550293 245.60496520996094 0.5651954412460327 369.62347412109375 0.6038712859153748 0.72333044 0.41917261481285095 True -12 24661 20.579827547073364 0.3669719696044922 301.99481201171875 0.3113590478897095 369.0672607421875 0.6053682565689087 0.7284201 0.40631091594696045 True -13 26558 20.618104457855225 0.37647008895874023 260.21600341796875 0.3260763883590698 368.5455627441406 0.6065114736557007 0.73384315 0.39995113015174866 True -14 28455 20.673245668411255 0.37119603157043457 316.71588134765625 0.22380544245243073 368.1274719238281 0.6074708700180054 0.73681766 0.3904403746128082 True -15 30352 20.601764678955078 1.4050655364990234 236.58157348632812 0.41576147079467773 367.8271179199219 0.6080670356750488 0.73977506 0.3843579590320587 True -16 32249 20.62971568107605 13.978909254074097 258.9632568359375 0.35856136679649353 367.8631896972656 0.6081473231315613 0.74021286 0.38788941502571106 True -17 34146 21.469505548477173 0.4448528289794922 252.74588012695312 0.27896803617477417 368.0028381347656 0.607826828956604 0.7353723 0.393646776676178 False -18 36043 20.65472149848938 1.2866230010986328 317.9322509765625 0.2894163727760315 368.03216552734375 0.6073563098907471 0.7308054 0.40409791469573975 False -19 37940 20.659276485443115 0.35707545280456543 260.5723876953125 0.17343461513519287 368.2468566894531 0.6070489883422852 0.72994685 0.409046471118927 False diff --git a/ENCSR608KJD/cherimoya.fold_2.performance.tsv b/ENCSR608KJD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c38d411db5f5eb8acf16cc8c99163bd74afae011..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -367.8631896972656 0.308010071516037 0.6081473231315613 0.23762109875679016 0.7402128577232361 0.7083931565284729 0.38788941502571106 \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_3.evaluate.json b/ENCSR608KJD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8b2688d14c899c294368d12b5f571012705aa3bd..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277DNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_3.fit.json b/ENCSR608KJD/cherimoya.fold_3.fit.json deleted file mode 100644 index 8e46715e88d3f5711477a5edc0707d97202f7293..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF277DNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_3.log b/ENCSR608KJD/cherimoya.fold_3.log deleted file mode 100644 index 7ea8b282b51b5b0dc9e8342d1275802d57595401..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1840 24.745654344558716 3.4774422645568848 311.3075256347656 0.6777058839797974 463.1848449707031 0.44858434796333313 0.5374117 12.16242504119873 True -1 3680 20.308809757232666 0.5189390182495117 316.72088623046875 0.6004914045333862 400.58831787109375 0.5479863882064819 0.62278056 4.350043296813965 True -2 5520 20.32097363471985 0.4453291893005371 315.91131591796875 0.47287797927856445 385.2066650390625 0.582861602306366 0.6280108 1.2908743619918823 True -3 7360 20.325496435165405 13.42624044418335 286.30938720703125 0.4753347337245941 380.6040344238281 0.592167854309082 0.6302697 0.7344691753387451 True -4 9200 20.311409950256348 0.4412820339202881 310.1180419921875 0.3465724289417267 378.592529296875 0.5960962176322937 0.64785403 0.5591702461242676 True -5 11040 20.29046130180359 0.4367845058441162 327.3380432128906 0.5301660299301147 377.5415954589844 0.598883330821991 0.6567463 0.5445360541343689 True -6 12880 20.294217824935913 0.42888474464416504 281.9701843261719 0.6973628997802734 377.0091247558594 0.60037761926651 0.66199493 0.5428078174591064 True -7 14720 20.37353825569153 0.42542600631713867 296.3465576171875 0.37886184453964233 375.9425354003906 0.6025962233543396 0.6701539 0.5270957946777344 True -8 16560 20.111745357513428 0.4142765998840332 273.73095703125 0.40370774269104004 375.4078674316406 0.604148805141449 0.67954 0.523212194442749 True -9 18400 19.959153175354004 0.3955559730529785 262.7126159667969 0.5218689441680908 374.618896484375 0.6060383319854736 0.68427426 0.48022010922431946 True -10 20240 19.926063060760498 0.40905165672302246 238.53878784179688 0.46184757351875305 373.79815673828125 0.6077883839607239 0.6920827 0.4609975516796112 True -11 22080 19.926762342453003 0.4062943458557129 280.90301513671875 0.37952321767807007 373.14495849609375 0.6093505024909973 0.6942044 0.45913973450660706 True -12 23920 19.92853593826294 0.39548349380493164 323.4421691894531 0.39031684398651123 372.4884033203125 0.6107300519943237 0.7076921 0.43881872296333313 True -13 25760 19.96321177482605 0.4087710380554199 259.405517578125 0.3509681224822998 371.98828125 0.611879825592041 0.7111235 0.4467349350452423 True -14 27600 19.959038972854614 9.494819641113281 325.3747863769531 0.5677194595336914 371.4786682128906 0.6126902103424072 0.71549106 0.44108086824417114 True -15 29440 20.132863998413086 0.4188573360443115 280.7169189453125 0.34184229373931885 371.34625244140625 0.6129393577575684 0.7190737 0.4255525767803192 True -16 31280 20.022791624069214 0.42902088165283203 321.3765869140625 0.2865694761276245 371.27685546875 0.6129553914070129 0.7195947 0.4283793568611145 True -17 33120 20.03908681869507 0.4162790775299072 288.23516845703125 0.3123185634613037 371.33282470703125 0.6124505996704102 0.71887964 0.43239885568618774 False -18 34960 19.95885467529297 0.418651819229126 276.16326904296875 0.27908623218536377 371.4654235839844 0.6118649244308472 0.71315813 0.44229987263679504 False -19 36800 19.970357179641724 0.3970005512237549 273.6740417480469 0.19890263676643372 371.63848876953125 0.6114616990089417 0.70997405 0.4497852623462677 False diff --git a/ENCSR608KJD/cherimoya.fold_3.performance.tsv b/ENCSR608KJD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f4c05a6ab3a9b4c9c94817fa9413e0664561329c..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -371.27685546875 0.3046940863132477 0.6129553914070129 0.2426128387451172 0.7195947170257568 0.6892090439796448 0.4283793568611145 \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_4.evaluate.json b/ENCSR608KJD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7062e1c63ad5548461a091a5b673ae5a18e86514..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277DNX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_4.fit.json b/ENCSR608KJD/cherimoya.fold_4.fit.json deleted file mode 100644 index f90a8f09822c2201ccd85252d629c1a465bf8aa7..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF277DNX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR608KJD/cherimoya.fold_4.log b/ENCSR608KJD/cherimoya.fold_4.log deleted file mode 100644 index 7917ae5568fa7f6a1f0c66f11f4f2060a505da33..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1869 25.32789921760559 3.648155689239502 342.5038757324219 0.6009366512298584 455.47650146484375 0.44744545221328735 0.5456451 10.620911598205566 True -1 3738 20.64622926712036 0.42233991622924805 268.49896240234375 0.7515420317649841 397.4207763671875 0.5447680950164795 0.6133692 4.002643585205078 True -2 5607 20.628071784973145 0.4258146286010742 303.4715576171875 0.5703166127204895 380.2843017578125 0.582558274269104 0.6318214 1.1620759963989258 True -3 7476 21.002081394195557 2.147818088531494 307.23602294921875 0.5955769419670105 375.1275634765625 0.5937434434890747 0.65520954 0.68808513879776 True -4 9345 20.628811836242676 0.38837194442749023 296.0926513671875 0.6237392425537109 373.01708984375 0.5983220934867859 0.6669627 0.5826632380485535 True -5 11214 20.659750938415527 0.37702250480651855 329.71014404296875 0.5990473031997681 371.9587707519531 0.6010528802871704 0.67550576 0.5415913462638855 True -6 13083 20.643420457839966 0.37405967712402344 306.47052001953125 0.7259581089019775 371.0630798339844 0.603158175945282 0.68372774 0.5215184092521667 True -7 14952 20.637284517288208 0.37332987785339355 260.4158935546875 0.3819940984249115 370.02392578125 0.6060773134231567 0.6853454 0.47805091738700867 True -8 16821 20.64116621017456 0.3742811679840088 278.1685791015625 0.5542910099029541 369.3424072265625 0.6075084805488586 0.69259495 0.46696388721466064 True -9 18690 20.600958108901978 0.3744211196899414 348.96905517578125 0.4221837520599365 368.390869140625 0.6097210049629211 0.69781286 0.45537644624710083 True -10 20559 20.60889768600464 0.3662433624267578 284.0285339355469 0.4979771375656128 367.6612548828125 0.6115813255310059 0.703736 0.4347004294395447 True -11 22428 20.608070611953735 1.36195969581604 298.5420837402344 0.48858922719955444 367.090576171875 0.6128460764884949 0.71192837 0.4225398004055023 True -12 24297 20.699226140975952 2.396348714828491 343.9295654296875 0.4234153628349304 366.6712646484375 0.6140398383140564 0.71366763 0.4156591296195984 True -13 26166 20.304238080978394 0.3705787658691406 291.7294921875 0.46165260672569275 366.1834716796875 0.6149756908416748 0.71655345 0.41379550099372864 True -14 28035 20.246395587921143 1.0430986881256104 316.37884521484375 0.25481241941452026 365.7334899902344 0.6160898804664612 0.7197666 0.41229313611984253 True -15 29904 20.239391565322876 0.3696572780609131 289.615478515625 0.3351637125015259 365.675537109375 0.6162636876106262 0.72012556 0.41471579670906067 True -16 31773 20.22010040283203 0.37696313858032227 282.9805908203125 0.3130037188529968 365.71484375 0.6159150004386902 0.7221031 0.41610655188560486 True -17 33642 20.2174813747406 0.5665290355682373 254.4285888671875 0.26162633299827576 365.96405029296875 0.6154152154922485 0.7204225 0.4205993115901947 False -18 35511 20.271454334259033 0.37524843215942383 268.52410888671875 0.3544095456600189 366.1181335449219 0.6148195862770081 0.715647 0.4358818531036377 False -19 37380 20.234216690063477 0.36968445777893066 282.25738525390625 0.24834685027599335 366.2457275390625 0.614528477191925 0.7122511 0.44144633412361145 False diff --git a/ENCSR608KJD/cherimoya.fold_4.performance.tsv b/ENCSR608KJD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b6788fd21527920d2346a8c9a81cc711f541032f..0000000000000000000000000000000000000000 --- a/ENCSR608KJD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -365.71484375 0.3062184154987335 0.6159150004386902 0.23973968625068665 0.7221031188964844 0.6757570505142212 0.41610655188560486 \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_0.evaluate.json b/ENCSR609DDQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3eb6b7cafe82050cbad31487e643ac587f5e2dc4..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF293UAN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_0.fit.json b/ENCSR609DDQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 52cefd0b622495f550df2b6b9ea48b098104bc8f..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF293UAN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_0.log b/ENCSR609DDQ/cherimoya.fold_0.log deleted file mode 100644 index f3aa37e59a031a1ebe3c73aa9d3714c7a4e74342..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1867 25.453043222427368 4.334969520568848 122.76465606689453 0.438315212726593 185.35025024414062 0.08750393986701965 0.58448917 4.52251672744751 True -1 3734 20.553121089935303 0.3794257640838623 158.69285583496094 0.7967594265937805 179.51785278320312 0.12985780835151672 0.6653634 1.7367229461669922 True -2 5601 20.509032487869263 0.350510835647583 144.7739715576172 0.762580156326294 174.0029296875 0.15600310266017914 0.72889555 0.8558049201965332 True -3 7468 20.533385515213013 0.352858304977417 145.44720458984375 0.5785414576530457 172.28675842285156 0.1612236648797989 0.75658536 0.5806896090507507 True -4 9335 20.560871839523315 0.3521566390991211 150.0296630859375 0.6061016321182251 171.30804443359375 0.1654093861579895 0.7620217 0.5197229981422424 True -5 11202 20.561846256256104 0.34642934799194336 157.51817321777344 0.5138254165649414 170.88162231445312 0.16640746593475342 0.77020293 0.5041624307632446 True -6 13069 20.53321671485901 0.3565998077392578 108.56829833984375 0.5233827829360962 170.63223266601562 0.16816802322864532 0.77484095 0.49895399808883667 True -7 14936 20.515311241149902 1.2884702682495117 126.06370544433594 0.43953990936279297 170.21458435058594 0.16947223246097565 0.7931732 0.42245611548423767 True -8 16803 20.494449853897095 0.3462855815887451 167.36302185058594 0.5313255190849304 169.71487426757812 0.17214098572731018 0.7992567 0.4038223624229431 True -9 18670 20.517967224121094 0.35070371627807617 149.8590545654297 0.5048762559890747 169.4699249267578 0.17340372502803802 0.80254453 0.3905779719352722 True -10 20537 20.518505334854126 0.34898924827575684 153.86444091796875 0.48731154203414917 169.3535919189453 0.17393994331359863 0.8077816 0.3805517256259918 True -11 22404 20.56440496444702 10.96709942817688 146.74374389648438 0.41100382804870605 168.88082885742188 0.1766449362039566 0.81064284 0.3774329721927643 True -12 24271 20.53299331665039 0.3731977939605713 178.07110595703125 0.36483392119407654 168.8002166748047 0.17675992846488953 0.81419414 0.36203867197036743 True -13 26138 20.615529537200928 0.36533451080322266 159.40191650390625 0.43779319524765015 168.65103149414062 0.17697535455226898 0.8182655 0.35560503602027893 True -14 28005 20.542645692825317 0.39997339248657227 115.9043960571289 0.42978760600090027 168.47215270996094 0.17818306386470795 0.8202254 0.35432788729667664 True -15 29872 20.515332221984863 0.35042619705200195 147.24835205078125 0.48690539598464966 168.4127960205078 0.17817071080207825 0.82196003 0.3575912415981293 True -16 31739 20.515587329864502 0.355670690536499 153.52822875976562 0.27206164598464966 168.56517028808594 0.1768798530101776 0.8223923 0.35982584953308105 True -17 33606 20.53042960166931 0.35510873794555664 163.6744842529297 0.2346639782190323 168.65451049804688 0.1765211522579193 0.82053673 0.37073269486427307 False -18 35473 20.521709442138672 0.35715723037719727 130.9064178466797 0.2506694793701172 168.70138549804688 0.1765531301498413 0.8169574 0.3836694061756134 False -19 37340 20.522553205490112 0.35112619400024414 157.86643981933594 0.2185167670249939 168.84271240234375 0.17575989663600922 0.81329393 0.39054974913597107 False diff --git a/ENCSR609DDQ/cherimoya.fold_0.performance.tsv b/ENCSR609DDQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e1d810b1b9009dd870839089123502a9a0f71657..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -168.56517028808594 0.5712040066719055 0.1768798679113388 0.04247666522860527 0.8223922848701477 0.7969066500663757 0.35982584953308105 \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_1.evaluate.json b/ENCSR609DDQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0304119801c910148ae04effed4b69e07165bc96..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF293UAN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_1.fit.json b/ENCSR609DDQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 2c14f5f839a37db17f2d6585eb1cb5b7fccef30c..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF293UAN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_1.log b/ENCSR609DDQ/cherimoya.fold_1.log deleted file mode 100644 index 9c0654d0a98df91f9ede24645b522ffbfb388726..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1867 24.94001841545105 3.660033941268921 154.05210876464844 0.8411973714828491 217.8065643310547 0.10067503899335861 0.55247486 5.255774021148682 True -1 3734 20.60313391685486 0.5834779739379883 126.90248107910156 0.5221797227859497 210.0865936279297 0.14728933572769165 0.6877279 1.9690442085266113 True -2 5601 20.557048082351685 0.5468175411224365 144.6661376953125 0.5415669083595276 204.56761169433594 0.17075079679489136 0.7521274 0.9741158485412598 True -3 7468 20.191954374313354 0.5171918869018555 109.29964447021484 0.49143847823143005 201.83946228027344 0.17907215654850006 0.7748439 0.6485297679901123 True -4 9335 20.17147707939148 0.5539419651031494 129.33567810058594 0.6143185496330261 200.71580505371094 0.18213589489459991 0.7832182 0.5966289043426514 True -5 11202 20.17804479598999 0.5166277885437012 154.97113037109375 0.39607053995132446 199.91688537597656 0.1848159283399582 0.7910866 0.5509980916976929 True -6 13069 20.17231011390686 0.5329396724700928 117.87770080566406 0.6445638537406921 199.38784790039062 0.18699713051319122 0.80283904 0.5012723803520203 True -7 14936 20.105926752090454 0.5169241428375244 125.74049377441406 0.5773299932479858 198.77552795410156 0.19001387059688568 0.8081031 0.4882098436355591 True -8 16803 20.16564178466797 0.5349307060241699 167.5865020751953 0.49321556091308594 198.23202514648438 0.19194450974464417 0.81384975 0.45235711336135864 True -9 18670 20.152672290802002 0.5228166580200195 113.87315368652344 0.44243764877319336 198.00411987304688 0.19286678731441498 0.8174531 0.4284464120864868 True -10 20537 20.15069818496704 0.5052273273468018 159.04188537597656 0.6158686280250549 197.78343200683594 0.19358086585998535 0.82202 0.42026329040527344 True -11 22404 20.14806842803955 0.5027306079864502 121.31586456298828 0.5231200456619263 197.59352111816406 0.19433051347732544 0.8255303 0.39691197872161865 True -12 24271 20.13943123817444 0.51413893699646 120.12492370605469 0.38115382194519043 197.48928833007812 0.19437389075756073 0.82866627 0.39130890369415283 True -13 26138 20.14914870262146 0.5292916297912598 154.48403930664062 0.5948532819747925 197.13111877441406 0.19662407040596008 0.8304976 0.3829597532749176 True -14 28005 20.148061752319336 0.517125129699707 153.95428466796875 0.391424298286438 197.0650634765625 0.1965867429971695 0.8316357 0.3801024854183197 True -15 29872 20.146958351135254 0.5354242324829102 137.91293334960938 0.2626931071281433 196.97833251953125 0.19715116918087006 0.8326165 0.38875818252563477 True -16 31739 20.149139165878296 0.5283927917480469 119.7393798828125 0.44729939103126526 197.1866455078125 0.19583208858966827 0.8292942 0.3994203209877014 False -17 33606 20.14115071296692 0.5182175636291504 146.09544372558594 0.14902839064598083 197.19039916992188 0.19613711535930634 0.8255601 0.4164307415485382 False -18 35473 20.146873235702515 0.5152630805969238 146.61981201171875 0.3056010603904724 197.10731506347656 0.1970847249031067 0.82211816 0.4320371150970459 False -19 37340 20.141945838928223 0.520240306854248 130.6177520751953 0.26015105843544006 197.25531005859375 0.1963329315185547 0.81961817 0.44327491521835327 False diff --git a/ENCSR609DDQ/cherimoya.fold_1.performance.tsv b/ENCSR609DDQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c18d224ac50159cfea9f2e146f29c7c8ee00b9f8..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -196.97833251953125 0.5539727210998535 0.19715118408203125 0.043657086789608 0.8326165080070496 0.8150080442428589 0.38875818252563477 \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_2.evaluate.json b/ENCSR609DDQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a0b472ee4c52ce60973ea503346b3088dbbda1ef..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF293UAN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_2.fit.json b/ENCSR609DDQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 3af5fadacaf607dacf8c9a02d710ce60f2cce665..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF293UAN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_2.log b/ENCSR609DDQ/cherimoya.fold_2.log deleted file mode 100644 index 73ba4322e7a3e942cc49a2c1d36a88c692cd402d..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1990 26.322460412979126 4.718939304351807 141.48573303222656 0.5334420204162598 191.82781982421875 0.09567420184612274 0.56392586 4.362807273864746 True -1 3980 21.942538022994995 0.42105865478515625 100.49273681640625 0.6243550777435303 185.11712646484375 0.1392427533864975 0.66157377 1.8524842262268066 True -2 5970 21.905376434326172 0.41179776191711426 113.08810424804688 0.5333030223846436 179.14036560058594 0.16420456767082214 0.73463535 0.8632370829582214 True -3 7960 21.901012182235718 0.41919660568237305 158.54681396484375 0.7922825813293457 177.6284637451172 0.16782812774181366 0.75673455 0.5611655712127686 True -4 9950 21.932594299316406 0.37545299530029297 171.72601318359375 0.6232519745826721 176.9830322265625 0.17009225487709045 0.7684233 0.49745973944664 True -5 11940 21.890870332717896 0.38792943954467773 126.12596130371094 0.3696862459182739 176.43711853027344 0.17147988080978394 0.77566856 0.49023735523223877 True -6 13930 21.879908800125122 0.3935275077819824 164.2467803955078 0.3834347128868103 175.74920654296875 0.17552100121974945 0.7782678 0.513297975063324 True -7 15920 21.878810167312622 0.8865976333618164 153.52041625976562 0.5520938634872437 175.27825927734375 0.17699332535266876 0.79001325 0.4631829559803009 True -8 17910 21.887436151504517 0.3912472724914551 133.52891540527344 0.4614318013191223 175.07711791992188 0.17730742692947388 0.7972702 0.4428171217441559 True -9 19900 21.878265380859375 0.36167216300964355 159.74746704101562 0.5533484220504761 174.74319458007812 0.17939260601997375 0.8018489 0.423284649848938 True -10 21890 21.50346541404724 0.36126708984375 134.27777099609375 0.37769585847854614 174.3575897216797 0.181621253490448 0.80491096 0.41146478056907654 True -11 23880 21.4721040725708 0.36382365226745605 137.66036987304688 0.4655769467353821 174.1177520751953 0.18269497156143188 0.80995363 0.39799341559410095 True -12 25870 21.463194608688354 0.36333799362182617 161.15548706054688 0.5039052963256836 174.13148498535156 0.182310089468956 0.8131535 0.3874424993991852 True -13 27860 21.474737644195557 0.3577587604522705 157.33929443359375 0.5941356420516968 173.82369995117188 0.18416449427604675 0.8176327 0.380698025226593 True -14 29850 21.582740545272827 0.3690783977508545 147.11456298828125 0.2462199181318283 173.79446411132812 0.18402071297168732 0.8171728 0.37963125109672546 False -15 31840 21.51382875442505 0.3754591941833496 126.21479797363281 0.32598677277565 173.57550048828125 0.1852281391620636 0.8188633 0.37751081585884094 True -16 33830 21.518887519836426 0.3636939525604248 142.82479858398438 0.40505450963974 173.64537048339844 0.18499286472797394 0.8179085 0.38183218240737915 False -17 35820 21.568283319473267 0.3645360469818115 156.09326171875 0.2605541944503784 173.75624084472656 0.18428760766983032 0.8147791 0.39133894443511963 False -18 37810 21.55557942390442 0.38957977294921875 143.40841674804688 0.2571589946746826 173.7132110595703 0.18458275496959686 0.8114267 0.40262851119041443 False -19 39800 21.573105096817017 0.38547325134277344 131.54498291015625 0.2982334494590759 173.81411743164062 0.1842486560344696 0.80801004 0.40984711050987244 False diff --git a/ENCSR609DDQ/cherimoya.fold_2.performance.tsv b/ENCSR609DDQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 045c4656b95c4330fedc897050dda099ed281d49..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -173.57550048828125 0.5666999220848083 0.1852281391620636 0.04150622710585594 0.8188632726669312 0.7976531386375427 0.37751081585884094 \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_3.evaluate.json b/ENCSR609DDQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0b8a1096c5b11722c957ec237f362db57c6d00ae..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF293UAN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_3.fit.json b/ENCSR609DDQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 1bb283adb18f26f924b7831b710334faa570df60..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF293UAN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_3.log b/ENCSR609DDQ/cherimoya.fold_3.log deleted file mode 100644 index 69fd9c16058a71417fc0e26a712286e99d21a696..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1918 25.544808864593506 3.5255589485168457 135.32591247558594 0.6889456510543823 200.51519775390625 0.09513942897319794 0.5721209 4.743022918701172 True -1 3836 21.128289699554443 1.5397114753723145 178.23707580566406 0.4373604953289032 194.8469696044922 0.13110972940921783 0.6629294 1.8200713396072388 True -2 5754 21.064733028411865 0.4055764675140381 123.95576477050781 0.555747389793396 189.40625 0.15631268918514252 0.71725935 0.9818243980407715 True -3 7672 21.042977333068848 0.39943552017211914 117.0426025390625 0.5662915110588074 187.91200256347656 0.16078336536884308 0.7339073 0.7226905822753906 True -4 9590 21.045424222946167 0.3983781337738037 144.93922424316406 0.5089678764343262 187.5081787109375 0.1617506891489029 0.7492678 0.6270424723625183 True -5 11508 21.03278923034668 9.775145292282104 151.59393310546875 0.6396619081497192 186.80868530273438 0.1646645963191986 0.7486005 0.6766813397407532 False -6 13426 21.47779107093811 0.6840379238128662 150.09378051757812 0.5739771723747253 185.94044494628906 0.16936138272285461 0.7512736 0.6453308463096619 True -7 15344 21.140393495559692 0.39673280715942383 140.50074768066406 0.4451042413711548 185.85670471191406 0.16950027644634247 0.7630855 0.5915371775627136 True -8 17262 21.042876958847046 0.40403294563293457 110.07291412353516 0.29834455251693726 185.55364990234375 0.17129771411418915 0.7703894 0.582001268863678 True -9 19180 21.087453365325928 0.39766597747802734 155.30056762695312 0.54127037525177 185.284912109375 0.1724623739719391 0.7721264 0.5722324252128601 True -10 21098 21.35270857810974 16.9311683177948 126.01121520996094 0.45072194933891296 184.7487335205078 0.17547327280044556 0.77694434 0.5581148266792297 True -11 23016 21.131370306015015 0.3905918598175049 155.49365234375 0.7035269141197205 184.72386169433594 0.17497345805168152 0.7838465 0.5358628630638123 True -12 24934 21.11640214920044 0.40074849128723145 137.15103149414062 0.42962968349456787 184.28533935546875 0.1777067333459854 0.7922868 0.4978385269641876 True -13 26852 21.099873781204224 2.1121134757995605 123.12969970703125 0.444522500038147 184.072021484375 0.17850500345230103 0.7968526 0.4777609705924988 True -14 28770 21.104845762252808 0.3893163204193115 187.1937255859375 0.3518002927303314 183.95956420898438 0.1785086691379547 0.79992557 0.47501641511917114 True -15 30688 21.079482078552246 0.4010779857635498 130.56753540039062 0.41809579730033875 183.78843688964844 0.17909398674964905 0.8027804 0.4584868848323822 True -16 32606 21.116921424865723 0.5668022632598877 128.2590789794922 0.19547533988952637 183.98483276367188 0.1774800568819046 0.80468714 0.4498247802257538 True -17 34524 21.11301326751709 0.39336705207824707 128.91018676757812 0.317186176776886 184.083251953125 0.17705634236335754 0.80375534 0.4524565041065216 False -18 36442 21.525266647338867 0.3934590816497803 131.80596923828125 0.25318610668182373 184.14427185058594 0.17701157927513123 0.80330384 0.4607601463794708 False -19 38360 21.117006540298462 0.3924746513366699 110.90211486816406 0.3901461660861969 184.1098175048828 0.17760613560676575 0.8005623 0.46394437551498413 False diff --git a/ENCSR609DDQ/cherimoya.fold_3.performance.tsv b/ENCSR609DDQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 456e85abe5b2610842ea3b96c82629d096750593..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -183.98483276367188 0.5666309595108032 0.1774800419807434 0.04566676914691925 0.8046871423721313 0.7915464639663696 0.4498247802257538 \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_4.evaluate.json b/ENCSR609DDQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7296bf9170859736a0a6c71eeab2f7880764dbac..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF293UAN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_4.fit.json b/ENCSR609DDQ/cherimoya.fold_4.fit.json deleted file mode 100644 index a573cef5e1cdc219acfd7274bb5aaaab65363481..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF293UAN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609DDQ/cherimoya.fold_4.log b/ENCSR609DDQ/cherimoya.fold_4.log deleted file mode 100644 index 6d6aed41384a51705214125d13191fd338987a82..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1911 25.36622381210327 3.7938125133514404 176.78262329101562 0.7445100545883179 181.48216247558594 0.08719512075185776 0.5629376 4.194658279418945 True -1 3822 21.1176860332489 0.4302821159362793 123.0994873046875 0.5174955129623413 176.21473693847656 0.12582898139953613 0.6413394 1.8004642724990845 True -2 5733 21.020710468292236 0.34651899337768555 140.06109619140625 0.4278712272644043 171.63156127929688 0.14764092862606049 0.7262751 0.7593724131584167 True -3 7644 20.766767740249634 0.34782886505126953 151.31991577148438 0.5736830830574036 169.5833740234375 0.15543684363365173 0.74327826 0.5413329601287842 True -4 9555 20.637664079666138 0.34073662757873535 150.23348999023438 0.5718476176261902 168.8638916015625 0.1561385691165924 0.7542836 0.5185935497283936 True -5 11466 20.631384134292603 0.341904878616333 137.8811798095703 0.38199079036712646 168.1553955078125 0.15959472954273224 0.76336485 0.5015637278556824 True -6 13377 20.59671950340271 0.34747743606567383 154.2740478515625 0.5960415005683899 167.75341796875 0.1613946259021759 0.77010924 0.47040727734565735 True -7 15288 20.639869689941406 0.3410656452178955 150.25511169433594 0.6456085443496704 167.36573791503906 0.1632387936115265 0.77972084 0.45214152336120605 True -8 17199 20.633240461349487 0.34106993675231934 115.2386245727539 0.5378838181495667 167.0935821533203 0.16463249921798706 0.7851205 0.43829816579818726 True -9 19110 20.73157048225403 0.34834885597229004 172.5903778076172 0.4610826373100281 166.7874755859375 0.16574528813362122 0.7928246 0.41353991627693176 True -10 21021 20.688236951828003 0.34217023849487305 149.83428955078125 0.5563543438911438 166.54263305664062 0.16742463409900665 0.7982121 0.4019974172115326 True -11 22932 20.622384309768677 0.36515259742736816 123.67030334472656 0.46844226121902466 166.31993103027344 0.16855940222740173 0.8005245 0.391830176115036 True -12 24843 20.63428258895874 0.3605060577392578 156.3216552734375 0.45926159620285034 166.1022491455078 0.1693609207868576 0.8047222 0.3861577808856964 True -13 26754 20.62483811378479 0.3514885902404785 139.81704711914062 0.37307095527648926 165.91600036621094 0.1703510731458664 0.80692375 0.37746745347976685 True -14 28665 20.6567485332489 0.37407398223876953 126.54214477539062 0.4656132161617279 165.81076049804688 0.1706271916627884 0.81020755 0.37540873885154724 True -15 30576 20.628087282180786 0.3428215980529785 131.6372528076172 0.4006823003292084 165.7723846435547 0.1712806075811386 0.8124487 0.37496963143348694 True -16 32487 20.65926432609558 0.3611431121826172 142.36172485351562 0.3290691375732422 165.68984985351562 0.17171506583690643 0.811479 0.3799877464771271 False -17 34398 20.63922691345215 0.34966039657592773 119.0046615600586 0.2635940611362457 165.85459899902344 0.17068326473236084 0.80835164 0.3908001780509949 False -18 36309 20.69081687927246 12.740572690963745 108.84557342529297 0.23556259274482727 166.0457763671875 0.16938652098178864 0.8059276 0.39896082878112793 False -19 38220 20.715399026870728 0.36379408836364746 133.46685791015625 0.19665737450122833 165.96730041503906 0.17048314213752747 0.8019409 0.40605777502059937 False diff --git a/ENCSR609DDQ/cherimoya.fold_4.performance.tsv b/ENCSR609DDQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index bb0a5951d62ab3782a883cfeb733c8a48621d811..0000000000000000000000000000000000000000 --- a/ENCSR609DDQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -165.7723846435547 0.575192928314209 0.17128059267997742 0.04237409308552742 0.8124486804008484 0.7838729023933411 0.37496963143348694 \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_0.evaluate.json b/ENCSR609GST/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4244c09942317c4d2353f64d7586d41d002e31d6..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF916IVN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_0.fit.json b/ENCSR609GST/cherimoya.fold_0.fit.json deleted file mode 100644 index f502d2cd595694c6a2a8cc0a79f6b69abed7ccd9..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF916IVN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_0.log b/ENCSR609GST/cherimoya.fold_0.log deleted file mode 100644 index ea22fc3c0388dc7b723e27ef41cb4260a33e8806..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 772 12.098114967346191 2.947589874267578 159.91781616210938 0.2321799397468567 239.63925170898438 0.3116286098957062 0.6562712 14.889693260192871 True -1 1544 8.574518918991089 0.1794450283050537 165.60812377929688 0.2049839198589325 205.43597412109375 0.38392961025238037 0.7009366 7.114892482757568 True -2 2316 8.6068754196167 6.887851238250732 161.23394775390625 0.182814359664917 192.68287658691406 0.42301058769226074 0.73905295 2.5053093433380127 True -3 3088 8.636994123458862 0.8611316680908203 153.50048828125 0.17298483848571777 187.2394256591797 0.4392780363559723 0.7428534 1.019077181816101 True -4 3860 8.58553171157837 0.281477689743042 150.548583984375 0.23176932334899902 182.72486877441406 0.45406487584114075 0.75906926 0.4961608648300171 True -5 4632 8.586049795150757 0.1754014492034912 158.25257873535156 0.17886416614055634 179.9053192138672 0.4645216166973114 0.7702902 0.3824100196361542 True -6 5404 8.581487894058228 0.17563724517822266 162.3162841796875 0.11919444799423218 178.61029052734375 0.46972349286079407 0.77975374 0.28363755345344543 True -7 6176 8.580437421798706 0.17221951484680176 155.0675048828125 0.1073717400431633 177.98573303222656 0.4726041853427887 0.7889021 0.20711944997310638 True -8 6948 8.562793493270874 0.17235493659973145 167.97703552246094 0.19423267245292664 177.5931854248047 0.4745161533355713 0.79711384 0.16428931057453156 True -9 7720 8.5675790309906 0.17598533630371094 161.7566680908203 0.1805180311203003 177.2490234375 0.47621801495552063 0.804278 0.14610399305820465 True -10 8492 8.577026128768921 0.34354519844055176 165.90753173828125 0.19337087869644165 176.97958374023438 0.4776601195335388 0.8132352 0.13094590604305267 True -11 9264 8.577507019042969 0.17662596702575684 158.16859436035156 0.1381017565727234 176.72621154785156 0.47884780168533325 0.8196315 0.12192356586456299 True -12 10036 8.578055620193481 0.17486166954040527 157.1963348388672 0.12326914817094803 176.62173461914062 0.4794258177280426 0.82716596 0.11412165313959122 True -13 10808 8.561826467514038 0.1720738410949707 163.2720947265625 0.1313844472169876 176.52713012695312 0.4795968532562256 0.8303936 0.10830558836460114 True -14 11580 8.581855535507202 0.17251324653625488 152.60305786132812 0.09787198156118393 176.55763244628906 0.4793151021003723 0.83155507 0.10576745867729187 True -15 12352 8.592350721359253 0.17270445823669434 147.42872619628906 0.10108533501625061 176.68507385253906 0.47824177145957947 0.83284134 0.10438966751098633 True -16 13124 8.604378938674927 0.8207535743713379 137.45144653320312 0.09491795301437378 176.95425415039062 0.47673988342285156 0.83159405 0.10538201034069061 False -17 13896 8.606523990631104 0.17372345924377441 149.7093505859375 0.10451401770114899 177.3096466064453 0.4745052456855774 0.8303949 0.10667667537927628 False -18 14668 8.575500726699829 0.17472171783447266 148.21533203125 0.052272215485572815 177.69332885742188 0.47233009338378906 0.8286925 0.1094619482755661 False -19 15440 8.566450357437134 0.17597699165344238 157.1544952392578 0.06240014731884003 177.9679412841797 0.4705447256565094 0.8275211 0.1119721531867981 False diff --git a/ENCSR609GST/cherimoya.fold_0.performance.tsv b/ENCSR609GST/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c4bfd743724190b4ff04aec0b4263018c8046483..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -176.68507385253906 0.4093664586544037 0.47824180126190186 0.11690601706504822 0.8328413367271423 0.8042486310005188 0.10438966751098633 \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_1.evaluate.json b/ENCSR609GST/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ad594bd62454b13ebadd6054b841de5d9f3b8d55..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF916IVN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_1.fit.json b/ENCSR609GST/cherimoya.fold_1.fit.json deleted file mode 100644 index b6e02234b14f7556f0c0c9ca6183c9494df522dc..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF916IVN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_1.log b/ENCSR609GST/cherimoya.fold_1.log deleted file mode 100644 index 018ed606a3f4667a958344323caa08373e1111b4..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 774 12.182188272476196 2.9706826210021973 176.05856323242188 0.38478773832321167 257.1444396972656 0.3223671615123749 0.56167537 15.58134651184082 True -1 1548 8.896095275878906 0.22684001922607422 152.84725952148438 0.2018219232559204 220.30059814453125 0.3970138430595398 0.6399452 7.238786697387695 True -2 2322 8.600762367248535 0.21727585792541504 146.05438232421875 0.1939544975757599 205.98670959472656 0.43719282746315 0.7009667 2.509603500366211 True -3 3096 8.607986450195312 0.2114269733428955 154.4344940185547 0.1752685159444809 199.20889282226562 0.4589895009994507 0.69856423 0.9640073180198669 False -4 3870 8.605606079101562 0.21433067321777344 157.43414306640625 0.23044531047344208 194.6734161376953 0.4741216003894806 0.71187085 0.40549561381340027 True -5 4644 8.58754301071167 0.2114863395690918 170.4548797607422 0.1471382975578308 191.7071075439453 0.48360568284988403 0.739668 0.256692498922348 True -6 5418 8.582248449325562 0.2219407558441162 157.67129516601562 0.159272700548172 190.7932586669922 0.4864606261253357 0.7501368 0.21572580933570862 True -7 6192 8.585835695266724 0.21124911308288574 153.0628662109375 0.13408216834068298 190.2112274169922 0.489001601934433 0.7628227 0.18449808657169342 True -8 6966 8.645111322402954 0.31606602668762207 144.25186157226562 0.1507023274898529 189.66891479492188 0.4909569025039673 0.77381855 0.1690741628408432 True -9 7740 8.599547147750854 0.21262550354003906 161.5447998046875 0.1371450573205948 189.21432495117188 0.49289217591285706 0.78427935 0.15698470175266266 True -10 8514 8.59164309501648 0.2117931842803955 160.82388305664062 0.12102100253105164 188.86563110351562 0.49472203850746155 0.7948988 0.14702677726745605 True -11 9288 8.651170015335083 0.21749019622802734 153.747314453125 0.18561023473739624 188.58218383789062 0.49601781368255615 0.80421066 0.13415510952472687 True -12 10062 8.606022834777832 0.5067214965820312 154.34768676757812 0.15212905406951904 188.40606689453125 0.4967826306819916 0.8119067 0.12658165395259857 True -13 10836 8.601559400558472 0.6651961803436279 150.2276153564453 0.0926467552781105 188.32305908203125 0.4969884157180786 0.8163899 0.12765584886074066 True -14 11610 8.620303392410278 1.0065028667449951 152.03781127929688 0.11462439596652985 188.30621337890625 0.4967588186264038 0.8244847 0.11897235363721848 True -15 12384 8.615602016448975 0.22469258308410645 150.39588928222656 0.09505811333656311 188.4132080078125 0.4956492781639099 0.82567966 0.11605864018201828 True -16 13158 8.61100721359253 0.21931815147399902 151.9638671875 0.12265045940876007 188.7333221435547 0.49333661794662476 0.8297931 0.11381849646568298 True -17 13932 8.697864770889282 0.21556520462036133 135.71058654785156 0.10197959840297699 189.1777801513672 0.4903387725353241 0.82911605 0.11337204277515411 False -18 14706 8.646114587783813 0.2157905101776123 146.31597900390625 0.07654125988483429 189.66883850097656 0.4873458743095398 0.8287687 0.11288999766111374 False -19 15480 8.59791874885559 0.21727347373962402 159.20921325683594 0.08037824928760529 190.0541534423828 0.48497188091278076 0.8282859 0.11239347606897354 False diff --git a/ENCSR609GST/cherimoya.fold_1.performance.tsv b/ENCSR609GST/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 77ce60904b8d81570576574bbfa79b9fa8394b4d..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -188.7333221435547 0.39673998951911926 0.49333661794662476 0.12670475244522095 0.8297930955886841 0.8238585591316223 0.11381849646568298 \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_2.evaluate.json b/ENCSR609GST/cherimoya.fold_2.evaluate.json deleted file mode 100644 index faa2c654b0c77258ed79e07cadd51d20f450ad51..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF916IVN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_2.fit.json b/ENCSR609GST/cherimoya.fold_2.fit.json deleted file mode 100644 index 11d1151894601bc2d4ad1f95de41e51294621a10..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF916IVN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_2.log b/ENCSR609GST/cherimoya.fold_2.log deleted file mode 100644 index d8dfaa0176a7de1e0e3d2e4c1920ab3ccb500aa6..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 808 12.745518922805786 3.0275371074676514 164.5777587890625 0.26790210604667664 244.0814971923828 0.32241955399513245 0.609907 14.98932933807373 True -1 1616 8.96907353401184 0.40322089195251465 155.7753143310547 0.11340471357107162 209.13389587402344 0.39252969622612 0.6620068 6.5001020431518555 True -2 2424 8.971192598342896 0.17329645156860352 166.222900390625 0.15241016447544098 196.60198974609375 0.4307629466056824 0.73607403 2.3901913166046143 True -3 3232 8.989942073822021 0.17595672607421875 163.0531463623047 0.24984237551689148 190.30599975585938 0.4525643587112427 0.749357 0.6117126941680908 True -4 4040 8.98143196105957 0.17235612869262695 147.934814453125 0.13792157173156738 186.3021240234375 0.46407073736190796 0.7523761 0.2821127772331238 True -5 4848 8.972670555114746 0.17252254486083984 161.30618286132812 0.13407444953918457 185.45985412597656 0.4659491181373596 0.75426644 0.2500077486038208 True -6 5656 9.021144390106201 0.17617344856262207 147.16696166992188 0.16785678267478943 183.45228576660156 0.4747624695301056 0.7706655 0.22140151262283325 True -7 6464 8.949392318725586 0.17618680000305176 173.90380859375 0.14319443702697754 182.9617919921875 0.47675827145576477 0.77887475 0.22520367801189423 True -8 7272 8.947635889053345 0.3781118392944336 165.84996032714844 0.12001287192106247 182.57411193847656 0.47854289412498474 0.78744066 0.1896018087863922 True -9 8080 8.967922925949097 0.1757800579071045 148.53713989257812 0.16121527552604675 182.4200897216797 0.480118989944458 0.79386693 0.1652761995792389 True -10 8888 8.97623872756958 0.17690706253051758 155.03781127929688 0.08934357762336731 183.2679443359375 0.47742414474487305 0.80015504 0.15373747050762177 True -11 9696 8.956275701522827 0.1767749786376953 154.9644775390625 0.11404645442962646 182.04254150390625 0.48189976811408997 0.8099678 0.13741564750671387 True -12 10504 8.977636814117432 0.1736457347869873 175.75685119628906 0.1166037917137146 181.4875946044922 0.4846475124359131 0.8154431 0.1314580887556076 True -13 11312 8.968953371047974 0.17220425605773926 154.24586486816406 0.10912750661373138 181.13890075683594 0.4857924282550812 0.8196039 0.12542065978050232 True -14 12120 8.969343423843384 0.17494702339172363 142.9929962158203 0.11707543581724167 181.08924865722656 0.4861358404159546 0.8228228 0.12199755012989044 True -15 12928 8.973434209823608 4.420313358306885 151.78729248046875 0.13374489545822144 181.12435913085938 0.485655277967453 0.82427335 0.12189453840255737 True -16 13736 8.995925188064575 0.17511987686157227 146.04141235351562 0.1196051687002182 181.37100219726562 0.4842403531074524 0.8221502 0.12328892946243286 False -17 14544 8.986214637756348 0.17183136940002441 149.94198608398438 0.06924429535865784 181.6731414794922 0.4823510944843292 0.8214359 0.1257334053516388 False -18 15352 8.986351013183594 0.1721327304840088 157.165283203125 0.12137183547019958 181.95791625976562 0.4802459478378296 0.81746083 0.12703271210193634 False -19 16160 8.98623514175415 0.17275285720825195 153.96998596191406 0.10870136320590973 182.23580932617188 0.4787227213382721 0.8170366 0.12849506735801697 False diff --git a/ENCSR609GST/cherimoya.fold_2.performance.tsv b/ENCSR609GST/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 962db5b68d409b605706a390ab65c059ea936bd8..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -181.12435913085938 0.4050767123699188 0.4856552481651306 0.12026337534189224 0.8242733478546143 0.805708646774292 0.12189453840255737 \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_3.evaluate.json b/ENCSR609GST/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cf56ba6b9b95ccd8ab87a45395499036d9b35630..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF916IVN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_3.fit.json b/ENCSR609GST/cherimoya.fold_3.fit.json deleted file mode 100644 index bde9770823b0353e8b79cb13deabf9da8b6095a1..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF916IVN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_3.log b/ENCSR609GST/cherimoya.fold_3.log deleted file mode 100644 index 6a89b0655bfad928d128a9738fde0cc0d4c08b6b..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 789 12.353480100631714 2.981621503829956 174.90728759765625 0.2076859474182129 241.92013549804688 0.3197181820869446 0.63454324 15.003466606140137 True -1 1578 8.768165588378906 0.2083146572113037 174.61868286132812 0.19444721937179565 207.08248901367188 0.39057859778404236 0.6775077 6.7721662521362305 True -2 2367 8.771399736404419 0.17975616455078125 160.3217010498047 0.18626733124256134 194.34201049804688 0.43041694164276123 0.7295798 2.6188466548919678 True -3 3156 8.770206689834595 0.17664790153503418 174.75323486328125 0.154057115316391 188.18545532226562 0.4510185122489929 0.7355247 0.7636544704437256 True -4 3945 8.758552312850952 0.17681074142456055 147.51406860351562 0.20031660795211792 184.19459533691406 0.4644908607006073 0.7463969 0.3266776502132416 True -5 4734 8.73457670211792 0.17621850967407227 152.8046875 0.15253368020057678 183.79151916503906 0.4629150331020355 0.7544232 0.23240630328655243 True -6 5523 8.732953310012817 0.4142270088195801 147.27996826171875 0.1502992808818817 182.41665649414062 0.46853914856910706 0.7639009 0.2370520979166031 True -7 6312 8.74486756324768 0.1793079376220703 163.76065063476562 0.15766771137714386 181.0461883544922 0.4743645191192627 0.7756386 0.21259553730487823 True -8 7101 8.72713303565979 0.7704284191131592 165.21633911132812 0.1669773906469345 180.5836181640625 0.47696179151535034 0.7828468 0.19036799669265747 True -9 7890 8.757544755935669 0.17965412139892578 165.6788330078125 0.11711819469928741 180.26040649414062 0.47859805822372437 0.7901557 0.18304474651813507 True -10 8679 8.74828028678894 0.18001699447631836 159.1735382080078 0.1243065744638443 179.9162139892578 0.48018017411231995 0.7979504 0.1713542491197586 True -11 9468 8.734100103378296 0.17737030982971191 147.38282775878906 0.1465224325656891 179.57257080078125 0.4819915294647217 0.80111486 0.15702635049819946 True -12 10257 8.77284288406372 0.17738080024719238 133.98007202148438 0.18271508812904358 179.33493041992188 0.48279842734336853 0.8054257 0.1444741189479828 True -13 11046 8.759335994720459 0.180372953414917 155.2095947265625 0.11690499633550644 179.18423461914062 0.48343852162361145 0.8079588 0.13885188102722168 True -14 11835 8.759890079498291 0.1796433925628662 163.49118041992188 0.11149659752845764 179.15499877929688 0.48361051082611084 0.8079407 0.13443510234355927 False -15 12624 8.753397941589355 0.1808621883392334 150.37368774414062 0.09935355186462402 179.2138671875 0.4829532206058502 0.8081245 0.13248217105865479 True -16 13413 8.75651502609253 0.18064332008361816 160.04214477539062 0.09489131718873978 179.41116333007812 0.481624960899353 0.80810034 0.13170233368873596 False -17 14202 8.802414417266846 0.8633313179016113 153.23448181152344 0.1402287483215332 179.7413330078125 0.4795766770839691 0.8074225 0.13323724269866943 False -18 14991 8.784679651260376 0.18340659141540527 149.79791259765625 0.08886084705591202 180.02557373046875 0.4776144027709961 0.80521643 0.13337606191635132 False -19 15780 8.779571294784546 0.1778862476348877 144.06951904296875 0.11989915370941162 180.31922912597656 0.4761711061000824 0.8046152 0.13546499609947205 False diff --git a/ENCSR609GST/cherimoya.fold_3.performance.tsv b/ENCSR609GST/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a80aa562c67af88cc0dd71d5fe2526645347ed18..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -179.2138671875 0.4057251513004303 0.4829532206058502 0.1185663640499115 0.8081244826316833 0.7912890911102295 0.13248217105865479 \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_4.evaluate.json b/ENCSR609GST/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8b31a03c6ece1048d1ea7c718d1c930740a1121d..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF916IVN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_4.fit.json b/ENCSR609GST/cherimoya.fold_4.fit.json deleted file mode 100644 index b0d5d1e04e5164fae119328b14e95ed182f234f5..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF916IVN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR609GST/cherimoya.fold_4.log b/ENCSR609GST/cherimoya.fold_4.log deleted file mode 100644 index e23db1eb0e0f91b78454b6da17506ccede9c47b7..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 810 12.566368103027344 2.9660797119140625 161.840087890625 0.2353055626153946 238.369384765625 0.31699037551879883 0.6697766 14.875336647033691 True -1 1620 8.979817152023315 0.18572402000427246 144.35769653320312 0.15753526985645294 204.3038787841797 0.39054185152053833 0.7095172 6.28957986831665 True -2 2430 9.003857851028442 0.17916488647460938 176.19393920898438 0.1985761821269989 191.9111785888672 0.4283703565597534 0.74610734 2.5848300457000732 True -3 3240 9.023284435272217 0.18452858924865723 168.04779052734375 0.26804161071777344 185.58343505859375 0.449236124753952 0.75530547 0.7098976969718933 True -4 4050 8.993895053863525 0.18019390106201172 143.27383422851562 0.14901085197925568 182.10012817382812 0.4615245759487152 0.7708766 0.3043643832206726 True -5 4860 8.975704193115234 0.179093599319458 150.48959350585938 0.19846588373184204 180.108154296875 0.4682375490665436 0.78739524 0.21055839955806732 True -6 5670 8.9945547580719 0.17990446090698242 159.85647583007812 0.13564112782478333 179.44435119628906 0.4708999991416931 0.79890865 0.1727416068315506 True -7 6480 8.977926969528198 0.17988109588623047 148.65541076660156 0.1738756000995636 179.0010223388672 0.47267547249794006 0.8044806 0.1618514209985733 True -8 7290 8.972768068313599 0.1797025203704834 154.51132202148438 0.1257501244544983 178.50462341308594 0.47508153319358826 0.8119459 0.15652483701705933 True -9 8100 8.982396364212036 0.17882490158081055 147.36004638671875 0.1433466672897339 178.1431884765625 0.47728726267814636 0.81957555 0.13828246295452118 True -10 8910 8.994061708450317 0.18044638633728027 163.96707153320312 0.15869061648845673 177.92376708984375 0.4786466062068939 0.8259631 0.1250966191291809 True -11 9720 8.997383832931519 0.7631864547729492 151.4658203125 0.11932207643985748 177.69898986816406 0.4800189435482025 0.8294334 0.11596737802028656 True -12 10530 8.990512609481812 0.18130731582641602 154.17266845703125 0.15628351271152496 177.52886962890625 0.4807899296283722 0.8372006 0.10697905719280243 True -13 11340 9.004108667373657 0.17891311645507812 160.18788146972656 0.10855994373559952 177.4467010498047 0.4810360372066498 0.8382462 0.10287947952747345 True -14 12150 8.998162746429443 0.17667722702026367 143.76458740234375 0.10787840932607651 177.40943908691406 0.4809325635433197 0.8410293 0.10241539031267166 True -15 12960 9.012890100479126 0.1766800880432129 147.7180938720703 0.10236907005310059 177.51480102539062 0.4800260365009308 0.84104556 0.10091231763362885 True -16 13770 9.049248695373535 4.328125953674316 151.0433349609375 0.08371476829051971 177.76535034179688 0.4784053862094879 0.84125787 0.10128854960203171 True -17 14580 9.043383836746216 0.18178081512451172 132.0831298828125 0.10572493076324463 178.0885467529297 0.4763452708721161 0.83951306 0.10278497636318207 False -18 15390 9.005813360214233 0.35845494270324707 143.55230712890625 0.08389518409967422 178.43374633789062 0.4741975665092468 0.8371925 0.10399358719587326 False -19 16200 9.044156312942505 0.17749857902526855 147.14993286132812 0.0889858603477478 178.71734619140625 0.47243309020996094 0.83693486 0.10560240596532822 False diff --git a/ENCSR609GST/cherimoya.fold_4.performance.tsv b/ENCSR609GST/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 82c27b190b0dbb943916929ca1929088d84d4a57..0000000000000000000000000000000000000000 --- a/ENCSR609GST/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -177.76535034179688 0.408390611410141 0.4784053862094879 0.11572553962469101 0.8412578701972961 0.8120019435882568 0.10128854960203171 \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_0.evaluate.json b/ENCSR611BQR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d4801d31f151194b308be94de233ee34c19e104b..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF061SJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_0.fit.json b/ENCSR611BQR/cherimoya.fold_0.fit.json deleted file mode 100644 index 2ec3200ee8a0845ca4a973fdb610b2220c6ddf62..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF061SJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_0.log b/ENCSR611BQR/cherimoya.fold_0.log deleted file mode 100644 index 25363ce5f81e20e2a4a6b112227724f2275f52aa..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1780 24.189860105514526 3.388359785079956 668.8937377929688 2.864406108856201 1431.2615966796875 0.5102718472480774 0.5600422 24.985599517822266 True -1 3560 19.640268802642822 0.3420121669769287 714.4752807617188 1.6635626554489136 919.8234252929688 0.6776549220085144 0.6601668 12.648953437805176 True -2 5340 19.639416217803955 0.34706711769104004 674.7745361328125 2.015594005584717 788.4343872070312 0.7371933460235596 0.68741 3.0251033306121826 True -3 7120 19.69898796081543 2.3376870155334473 637.6682739257812 1.0239253044128418 757.9884033203125 0.7503700256347656 0.6951915 1.7468225955963135 True -4 8900 19.663882732391357 0.3289790153503418 562.6538696289062 1.1074824333190918 742.64794921875 0.7577797174453735 0.69575655 1.3909190893173218 True -5 10680 19.642364263534546 0.328263521194458 594.585205078125 1.2700875997543335 732.1263427734375 0.7636756300926208 0.69364464 1.3373342752456665 False -6 12460 19.657445192337036 0.32863450050354004 497.5657653808594 0.8203421831130981 724.1634521484375 0.7679342031478882 0.6970653 1.3154391050338745 True -7 14240 19.620054960250854 0.3348531723022461 513.9961547851562 0.9876004457473755 716.2068481445312 0.7712008357048035 0.6973844 1.2040263414382935 True -8 16020 19.696667432785034 0.33062052726745605 555.2982177734375 1.0698761940002441 710.0902099609375 0.7743010520935059 0.69622886 1.1177020072937012 False -9 17800 19.697997570037842 0.3283965587615967 532.3709716796875 1.0124338865280151 703.3339233398438 0.7767764329910278 0.6934177 1.0949726104736328 False -10 19580 19.670514822006226 0.3281991481781006 661.8157958984375 1.478571891784668 697.5245361328125 0.7799475193023682 0.6991043 1.05972421169281 True -11 21360 19.725234985351562 0.3395552635192871 665.313232421875 1.2780779600143433 692.4058837890625 0.7827302813529968 0.7028125 1.0308438539505005 True -12 23140 19.65779399871826 0.33902668952941895 482.8834228515625 0.7829064726829529 685.9155883789062 0.7852581143379211 0.7066359 1.0354090929031372 True -13 24920 19.62486505508423 0.3332810401916504 568.7308959960938 0.8952895402908325 682.0823364257812 0.7873124480247498 0.7176502 0.9873149991035461 True -14 26700 19.690776586532593 0.3368244171142578 500.94073486328125 1.0859490633010864 677.8493041992188 0.7888428568840027 0.72669435 0.9513958096504211 True -15 28480 19.661985158920288 0.33701133728027344 633.3583984375 0.7596359848976135 676.8526611328125 0.78926020860672 0.73088056 0.9436615705490112 True -16 30260 19.690704107284546 0.3342461585998535 488.36749267578125 0.6056100726127625 677.3124389648438 0.7889106869697571 0.73471266 0.9578981399536133 True -17 32040 19.87667155265808 9.829885005950928 522.365966796875 0.5140289068222046 678.3812255859375 0.7881777882575989 0.73518544 0.9690268635749817 True -18 33820 20.50797390937805 0.33148717880249023 522.384033203125 0.4792288541793823 680.1755981445312 0.7871986627578735 0.73516303 0.9857262372970581 False -19 35600 19.708308458328247 1.6822872161865234 554.5870361328125 0.31935837864875793 681.1336669921875 0.7866883873939514 0.7328259 0.9955083727836609 False diff --git a/ENCSR611BQR/cherimoya.fold_0.performance.tsv b/ENCSR611BQR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e174228e3297fbdbfa91411e49c982cd5ec8a2d0..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -678.3812255859375 0.18018725514411926 0.7881777882575989 0.3914598524570465 0.735185444355011 0.6963244676589966 0.9690268635749817 \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_1.evaluate.json b/ENCSR611BQR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a5a533c61a1371c8d41f3785e47be475bee91246..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF061SJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_1.fit.json b/ENCSR611BQR/cherimoya.fold_1.fit.json deleted file mode 100644 index 82483fd2aee30c4cd7a0e56131a0852519276ffb..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF061SJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_1.log b/ENCSR611BQR/cherimoya.fold_1.log deleted file mode 100644 index c2be54ea2ce6e8d8e10e83a7728650978231aabe..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1746 23.78214931488037 4.378812789916992 646.7559204101562 2.3629026412963867 1711.6580810546875 0.5140082240104675 0.52692604 26.135133743286133 True -1 3492 19.395819187164307 0.5446016788482666 748.1124267578125 1.388257622718811 1105.0487060546875 0.6714075803756714 0.6594939 15.222326278686523 True -2 5238 19.28563117980957 0.5140140056610107 660.4022216796875 1.9938607215881348 917.6940307617188 0.7517995834350586 0.6993185 5.718838214874268 True -3 6984 19.256953477859497 0.5146992206573486 531.9251098632812 1.834202527999878 866.9421997070312 0.7683966159820557 0.7092275 2.5909409523010254 True -4 8730 19.264815092086792 0.52301025390625 685.729736328125 1.3941712379455566 846.8484497070312 0.7739887237548828 0.7198438 2.0983071327209473 True -5 10476 19.410472631454468 24.118326425552368 736.8810424804688 1.197718620300293 833.652099609375 0.7805501222610474 0.7214335 1.876539945602417 True -6 12222 19.28042697906494 0.5271995067596436 585.09130859375 1.142669677734375 822.801513671875 0.7841435074806213 0.7209383 1.6372236013412476 False -7 13968 19.282195329666138 0.5221259593963623 505.66058349609375 1.0458989143371582 817.07275390625 0.786638617515564 0.7181316 1.5516821146011353 False -8 15714 19.279693365097046 0.522937536239624 592.9547729492188 1.0853303670883179 806.4437866210938 0.7902021408081055 0.7210587 1.3825300931930542 False -9 17460 19.528627634048462 0.5137650966644287 504.55560302734375 1.4222562313079834 798.7127685546875 0.7939165830612183 0.7272499 1.3690173625946045 True -10 19206 19.332534074783325 26.5438334941864 485.78570556640625 0.9012776613235474 789.5330810546875 0.7970020771026611 0.72742885 1.2656701803207397 True -11 20952 19.315951824188232 0.5291519165039062 523.791259765625 0.9655803442001343 781.6978149414062 0.7993780374526978 0.7366898 1.164795160293579 True -12 22698 19.406260013580322 4.743572235107422 619.5128173828125 1.0650663375854492 773.5521240234375 0.8023158311843872 0.7421317 1.0666985511779785 True -13 24444 19.296072483062744 0.7457208633422852 481.3860778808594 0.7906423211097717 769.65576171875 0.8044022917747498 0.7480275 1.0269907712936401 True -14 26190 19.27108359336853 0.510319709777832 461.92095947265625 0.9431673288345337 765.2911987304688 0.8057781457901001 0.756692 0.98835289478302 True -15 27936 19.2592716217041 7.192448139190674 482.4505310058594 0.875072717666626 761.7057495117188 0.8071736097335815 0.76629084 0.9440924525260925 True -16 29682 19.456905126571655 25.622886419296265 508.9596862792969 0.28187665343284607 761.6455078125 0.8067695498466492 0.77110386 0.9144275784492493 True -17 31428 19.780062198638916 7.432584524154663 582.99267578125 0.5995315313339233 762.57763671875 0.8060387969017029 0.7732826 0.9120311141014099 True -18 33174 19.395971536636353 0.5304934978485107 564.1937866210938 0.6050536632537842 764.39111328125 0.8051949143409729 0.7731688 0.9196377396583557 False -19 34920 19.370129346847534 1.1215364933013916 436.0604248046875 0.5296497941017151 765.8250122070312 0.8045666813850403 0.7711552 0.9189473390579224 False diff --git a/ENCSR611BQR/cherimoya.fold_1.performance.tsv b/ENCSR611BQR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 370a707efbd4954d84994e63df74be6f78640e4b..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -762.57763671875 0.163955956697464 0.8060389161109924 0.4274637699127197 0.7732825875282288 0.7498101592063904 0.9120311141014099 \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_2.evaluate.json b/ENCSR611BQR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0db8e02c5da23f97fe10350f3c8f8d680fe5d90d..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF061SJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_2.fit.json b/ENCSR611BQR/cherimoya.fold_2.fit.json deleted file mode 100644 index d1e1a764d791d38ef8e41f0c6ba55e530a6b8d0f..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF061SJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_2.log b/ENCSR611BQR/cherimoya.fold_2.log deleted file mode 100644 index 611323b69b87a3bf6c4ec7af569dd971f0ca13a5..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1876 26.283347129821777 3.465681314468384 685.0184326171875 1.444488763809204 1500.185546875 0.5229988694190979 0.5324014 24.561065673828125 True -1 3752 20.852728843688965 0.81536865234375 630.58642578125 1.5163781642913818 962.8070678710938 0.6881791949272156 0.66197616 13.430395126342773 True -2 5628 20.75252890586853 0.3603072166442871 637.5760498046875 1.1652659177780151 847.2947998046875 0.7412269711494446 0.6818739 5.5635247230529785 True -3 7504 20.7257399559021 0.36617255210876465 615.516845703125 0.9777991771697998 802.31298828125 0.7572023868560791 0.69462156 2.48144268989563 True -4 9380 20.7832670211792 0.3628222942352295 605.44775390625 1.3836662769317627 786.3760375976562 0.7641360759735107 0.70000434 1.812085509300232 True -5 11256 20.722482919692993 0.36176514625549316 654.1737670898438 1.2902746200561523 771.4583740234375 0.7685373425483704 0.7043369 1.52505624294281 True -6 13132 20.69444489479065 0.36162638664245605 598.1566772460938 1.441963791847229 761.6874389648438 0.7719182968139648 0.70836955 1.3945940732955933 True -7 15008 20.672107696533203 2.4854466915130615 551.43115234375 1.0820176601409912 752.541015625 0.7750370502471924 0.7102029 1.3049730062484741 True -8 16884 20.6564302444458 21.1960666179657 545.864501953125 1.2176645994186401 743.3035888671875 0.7780570387840271 0.7174782 1.1847646236419678 True -9 18760 23.39805507659912 0.3792901039123535 549.380859375 1.5549308061599731 733.7872314453125 0.7810371518135071 0.7231739 1.095066785812378 True -10 20636 20.715336084365845 0.3621690273284912 479.82086181640625 1.72263765335083 727.3757934570312 0.7839169502258301 0.71954376 1.094017744064331 False -11 22512 20.671164989471436 0.36014699935913086 656.4244995117188 1.2037979364395142 722.2564086914062 0.7867697477340698 0.7245604 1.039292812347412 True -12 24388 20.68929123878479 0.3605363368988037 692.9237060546875 1.4936147928237915 716.2994995117188 0.7895540595054626 0.73135245 1.0236101150512695 True -13 26264 20.70230793952942 0.36040687561035156 563.560791015625 1.1013171672821045 712.1380004882812 0.7915442585945129 0.73858845 0.9837598204612732 True -14 28140 20.68068504333496 0.3577718734741211 516.8029174804688 0.8944274187088013 708.1531372070312 0.7935035228729248 0.74441826 0.9645159244537354 True -15 30016 20.68362832069397 0.3571021556854248 529.715576171875 0.7692517638206482 707.4097290039062 0.7943194508552551 0.75284517 0.9531765580177307 True -16 31892 20.694964170455933 0.3581559658050537 505.8122863769531 0.7199260592460632 707.9732055664062 0.7943969964981079 0.7558577 0.9597183465957642 True -17 33768 20.71414089202881 0.3558380603790283 496.90655517578125 0.6662114262580872 709.602783203125 0.7937682867050171 0.75363463 0.9682735800743103 False -18 35644 20.710612535476685 0.3568863868713379 527.9329833984375 0.7126026153564453 711.1251220703125 0.7931411266326904 0.75287974 0.9855424761772156 False -19 37520 20.697821617126465 0.35712504386901855 474.4879455566406 0.630437970161438 711.8202514648438 0.7927336096763611 0.7502835 0.9974352121353149 False diff --git a/ENCSR611BQR/cherimoya.fold_2.performance.tsv b/ENCSR611BQR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d4f48b0a60a451a32fa14cdbef13e689473dcf07..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -707.9732055664062 0.17409877479076385 0.7943970561027527 0.4061468541622162 0.7558577060699463 0.7200954556465149 0.9597183465957642 \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_3.evaluate.json b/ENCSR611BQR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4b698b04989ca4d549ab52ca97c63d4c68e80228..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF061SJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_3.fit.json b/ENCSR611BQR/cherimoya.fold_3.fit.json deleted file mode 100644 index 25371a44f398dee7e691ff9487920ca2c5122987..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF061SJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_3.log b/ENCSR611BQR/cherimoya.fold_3.log deleted file mode 100644 index 3e6904986eec01c0a8cf99dde2ef5baa3534e2f4..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1807 24.61227536201477 3.435476064682007 722.565673828125 1.1606183052062988 1485.982177734375 0.5209983587265015 0.5473179 25.222591400146484 True -1 3614 19.999865531921387 0.3983490467071533 751.7386474609375 1.6658625602722168 972.6360473632812 0.6848276853561401 0.6228281 13.346943855285645 True -2 5421 19.996797800064087 13.986207008361816 837.1854858398438 1.397247314453125 848.6324462890625 0.736841082572937 0.654933 4.615508556365967 True -3 7228 20.849977254867554 0.37967538833618164 721.07666015625 1.3797900676727295 804.3419189453125 0.7533820271492004 0.6675973 2.7324373722076416 True -4 9035 19.975650548934937 14.812853336334229 685.3055419921875 1.2758769989013672 786.955078125 0.7609543204307556 0.666367 1.9035158157348633 False -5 10842 21.898147583007812 0.3703162670135498 716.1470947265625 0.9929435849189758 776.9973754882812 0.7635073661804199 0.6624899 1.5399402379989624 False -6 12649 19.96069884300232 1.283797264099121 673.6823120117188 1.13446843624115 764.2875366210938 0.7687371373176575 0.66470575 1.3559545278549194 False -7 14456 21.81027340888977 15.155571937561035 592.0531005859375 1.399273157119751 759.6043090820312 0.7708966732025146 0.675245 1.259495496749878 True -8 16263 20.001895666122437 1.172095775604248 557.9735717773438 1.2768795490264893 753.9853515625 0.7737733721733093 0.67755425 1.2140971422195435 True -9 18070 20.1128888130188 0.376300573348999 528.199462890625 0.7794605493545532 747.2531127929688 0.7771734595298767 0.6768461 1.1494810581207275 False -10 19877 19.973830699920654 1.5376019477844238 518.4210205078125 1.161182165145874 737.2947387695312 0.78192138671875 0.6848993 1.1166832447052002 True -11 21684 19.956820964813232 0.3661818504333496 569.103271484375 1.1161880493164062 732.0897827148438 0.7846801280975342 0.69312537 1.0794188976287842 True -12 23491 19.942434549331665 0.3689157962799072 606.064453125 0.9157212972640991 726.51806640625 0.7875303626060486 0.699589 1.078128457069397 True -13 25298 19.919535398483276 0.3665652275085449 475.7321472167969 0.7479062080383301 723.6039428710938 0.7893275618553162 0.7075615 1.0584027767181396 True -14 27105 19.918962478637695 0.37209272384643555 532.4568481445312 0.8531316518783569 721.4557495117188 0.7906887531280518 0.71672124 1.0274029970169067 True -15 28912 19.945388078689575 13.389017105102539 512.5775756835938 1.1241326332092285 719.1701049804688 0.7919041514396667 0.7234612 1.0352791547775269 True -16 30719 19.949801445007324 0.37695813179016113 485.674560546875 0.6713782548904419 718.0315551757812 0.7921464443206787 0.7300321 1.0342317819595337 True -17 32526 19.946728706359863 0.37094545364379883 446.74896240234375 0.8314168453216553 718.7382202148438 0.7917104363441467 0.7326701 1.041523814201355 True -18 34333 19.957607984542847 0.3681795597076416 499.0901184082031 0.41465485095977783 720.4750366210938 0.7906274199485779 0.73054457 1.0674744844436646 False -19 36140 19.995399713516235 0.36711645126342773 448.4820556640625 0.5761842131614685 721.5643920898438 0.7901027798652649 0.72944415 1.0830081701278687 False diff --git a/ENCSR611BQR/cherimoya.fold_3.performance.tsv b/ENCSR611BQR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 14bdf5c22cf2ce032aaa625f1fe15bb677a91f5d..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -718.7382202148438 0.1736377328634262 0.7917104363441467 0.4073407053947449 0.7326701283454895 0.7030534744262695 1.041523814201355 \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_4.evaluate.json b/ENCSR611BQR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b372acb9ffc3fae4418e1fed01395e55caa7d436..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF061SJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_4.fit.json b/ENCSR611BQR/cherimoya.fold_4.fit.json deleted file mode 100644 index e0a6a9c7f6b06e9b745c0d64c8b5497be6f02e3e..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF061SJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR611BQR/cherimoya.fold_4.log b/ENCSR611BQR/cherimoya.fold_4.log deleted file mode 100644 index 87c06c24331a70b4d2999c3d80254fc6f7fd1f40..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1787 24.643885850906372 3.257777214050293 681.6751098632812 1.6609703302383423 1406.0360107421875 0.513018786907196 0.5317111 23.231063842773438 True -1 3574 19.785757541656494 2.571702241897583 718.03564453125 1.5314992666244507 918.0302734375 0.671792209148407 0.6327241 10.5748929977417 True -2 5361 19.75697135925293 0.324404239654541 597.1025390625 1.8128825426101685 784.8817749023438 0.7382861375808716 0.6602352 3.630768060684204 True -3 7148 19.742289543151855 1.0951087474822998 520.5344848632812 1.6163419485092163 750.0481567382812 0.7533000707626343 0.6686803 1.672066330909729 True -4 8935 19.706504821777344 0.3219640254974365 562.6258544921875 1.4826152324676514 731.5262451171875 0.7610154747962952 0.67679197 1.2651724815368652 True -5 10722 19.70167064666748 1.2277319431304932 521.0284423828125 0.869350790977478 727.1788330078125 0.7646992206573486 0.681976 1.3236017227172852 True -6 12509 19.793748378753662 16.108280897140503 483.63543701171875 1.2734415531158447 717.3662109375 0.7684807777404785 0.68085575 1.4011030197143555 False -7 14296 23.411678314208984 16.675538063049316 540.6630249023438 1.2356810569763184 709.685791015625 0.7719285488128662 0.6836914 1.2414299249649048 True -8 16083 21.3357515335083 3.1390466690063477 503.59765625 0.9005563855171204 704.7012329101562 0.7746633887290955 0.6868267 1.194960355758667 True -9 17870 19.75759983062744 0.4018871784210205 630.1080932617188 1.0507996082305908 698.1400756835938 0.7773744463920593 0.68605417 1.1876777410507202 False -10 19657 19.82277488708496 0.33793187141418457 556.4407958984375 0.5422427654266357 692.2568359375 0.7800539135932922 0.6903765 1.1166750192642212 True -11 21444 19.79759454727173 0.3199601173400879 649.5479125976562 0.6587648391723633 686.32568359375 0.7828447222709656 0.6958592 1.0776796340942383 True -12 23231 20.4076144695282 14.550684452056885 591.4547119140625 0.8903695344924927 682.0939331054688 0.7848610281944275 0.6996363 1.0455206632614136 True -13 25018 20.755260467529297 0.3924264907836914 550.7913818359375 0.7153327465057373 677.7398681640625 0.7866066694259644 0.70877516 1.0112650394439697 True -14 26805 19.759509325027466 0.3257122039794922 518.514892578125 0.5975172519683838 674.4957885742188 0.7882477045059204 0.7176385 0.9814591407775879 True -15 28592 19.84376335144043 0.32657933235168457 418.83941650390625 0.6652083396911621 672.1665649414062 0.7894142270088196 0.72280955 0.9646086692810059 True -16 30379 19.78448224067688 0.3222370147705078 534.674560546875 0.6732007265090942 672.7097778320312 0.7895619869232178 0.7234841 0.973580539226532 True -17 32166 19.773777723312378 2.516460657119751 410.3865661621094 0.36090490221977234 674.5291748046875 0.7889266610145569 0.72609663 0.9853680729866028 True -18 33953 19.741234302520752 0.326033353805542 429.2049560546875 0.6563352346420288 675.7726440429688 0.7883408069610596 0.72442514 1.005218505859375 False -19 35740 19.75760316848755 7.301231384277344 390.2041320800781 0.6700414419174194 676.795166015625 0.7878558039665222 0.7214874 1.0138057470321655 False diff --git a/ENCSR611BQR/cherimoya.fold_4.performance.tsv b/ENCSR611BQR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ac9488d3bf51b34f6d7cffadaf9016f8f445afd1..0000000000000000000000000000000000000000 --- a/ENCSR611BQR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -674.5291748046875 0.17893432080745697 0.7889266610145569 0.3944421410560608 0.7260966300964355 0.6731563210487366 0.9853680729866028 \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_0.evaluate.json b/ENCSR612IKQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 788bd63dbfade4a3feb1d221b97c388caca576c0..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426QJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_0.fit.json b/ENCSR612IKQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 2c3ef7c4612a953a4520695a651481ecf5086662..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF426QJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_0.log b/ENCSR612IKQ/cherimoya.fold_0.log deleted file mode 100644 index ad13f942e923ee0318299e24228353c7e2b721e4..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 37.83966851234436 3.9564194679260254 407.7459411621094 0.23311804234981537 488.1725769042969 0.2918647825717926 0.72669727 3.1519367694854736 True -1 5502 30.647302389144897 0.60422682762146 370.49237060546875 0.23846101760864258 452.4637145996094 0.358167827129364 0.7855148 0.9224556684494019 True -2 8253 30.66632103919983 0.9860806465148926 384.37152099609375 0.16107827425003052 443.86932373046875 0.37292876839637756 0.8072475 0.5518746972084045 True -3 11004 30.714425086975098 0.7273039817810059 378.5546875 0.20717661082744598 440.8141784667969 0.3776808977127075 0.82023144 0.2517731785774231 True -4 13755 30.62120246887207 0.5883183479309082 376.711669921875 0.20642167329788208 439.0509033203125 0.38084936141967773 0.8271532 0.22474883496761322 True -5 16506 30.675856113433838 0.5805881023406982 381.60162353515625 0.20024672150611877 438.34881591796875 0.3821909427642822 0.83144385 0.22963684797286987 True -6 19257 30.607616186141968 0.570127010345459 346.27471923828125 0.21961387991905212 438.16693115234375 0.38184893131256104 0.8319561 0.25474685430526733 True -7 22008 30.602077960968018 0.5764937400817871 401.37225341796875 0.23575739562511444 436.0198974609375 0.38642147183418274 0.8404234 0.20523743331432343 True -8 24759 30.68626642227173 0.6045017242431641 353.8153076171875 0.15702447295188904 435.1092834472656 0.3877671957015991 0.8458373 0.1792207658290863 True -9 27510 30.66639542579651 1.5751655101776123 342.8313903808594 0.15349915623664856 434.8543395996094 0.3874649703502655 0.84774536 0.17177683115005493 True -10 30261 30.692423582077026 1.2956511974334717 372.5491943359375 0.18662841618061066 433.65679931640625 0.3899432122707367 0.85231996 0.15799441933631897 True -11 33012 30.64140224456787 0.5910990238189697 347.6875305175781 0.150616854429245 433.4744567871094 0.3899230659008026 0.8565912 0.15504440665245056 True -12 35763 30.017635345458984 0.6197893619537354 370.15283203125 0.16172344982624054 432.2062683105469 0.39390504360198975 0.8574351 0.15054510533809662 True -13 38514 30.00106954574585 1.9276864528656006 349.26873779296875 0.1296863853931427 431.4303283691406 0.39441871643066406 0.8613161 0.14292989671230316 True -14 41265 30.05364155769348 0.576287031173706 364.06787109375 0.09112071245908737 430.949462890625 0.3958248496055603 0.86580724 0.13528002798557281 True -15 44016 30.05136203765869 0.5735900402069092 388.06732177734375 0.17853601276874542 429.99774169921875 0.39831238985061646 0.86854374 0.1308528631925583 True -16 46767 30.001139163970947 0.5681519508361816 407.0863342285156 0.15705937147140503 429.58941650390625 0.39894378185272217 0.8717067 0.12877900898456573 True -17 49518 30.01933979988098 10.22641134262085 417.1864013671875 0.14950555562973022 429.51123046875 0.3982771635055542 0.87414855 0.12670564651489258 True -18 52269 30.060564041137695 0.587270975112915 387.5721740722656 0.07573091238737106 430.3648376464844 0.39567720890045166 0.874465 0.12639281153678894 True -19 55020 30.036442518234253 0.5799546241760254 308.1187438964844 0.12374310195446014 429.66424560546875 0.39832377433776855 0.8730018 0.12617473304271698 False diff --git a/ENCSR612IKQ/cherimoya.fold_0.performance.tsv b/ENCSR612IKQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 06df4ec5aac40fc668673f93f362e15608c4bd0b..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -430.3648376464844 0.40546366572380066 0.39567723870277405 0.13547080755233765 0.8744649887084961 0.8621940612792969 0.12639281153678894 \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_1.evaluate.json b/ENCSR612IKQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index dd486d4ae93087ab532a8771a93fdc0c17418242..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426QJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_1.fit.json b/ENCSR612IKQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 972a286703b81e492130f822f80ed9564253bbe8..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF426QJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_1.log b/ENCSR612IKQ/cherimoya.fold_1.log deleted file mode 100644 index 128f98d1bba43d23526f65d13833e87ebaea96cd..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.671908378601074 4.420981168746948 386.84210205078125 0.3548739552497864 539.172607421875 0.29482147097587585 0.73911846 3.609222412109375 True -1 5454 30.260485649108887 0.8018403053283691 417.0464782714844 0.18665072321891785 500.53997802734375 0.364223837852478 0.79341567 1.0895296335220337 True -2 8181 30.254876852035522 0.6675238609313965 386.3200988769531 0.17470741271972656 489.38250732421875 0.380157470703125 0.82029986 0.3740484416484833 True -3 10908 30.536437511444092 0.6652553081512451 367.19140625 0.21228063106536865 485.0184020996094 0.3850500285625458 0.83035 0.42248591780662537 True -4 13635 30.31477999687195 0.6575610637664795 389.68450927734375 0.20503628253936768 484.3231506347656 0.38486161828041077 0.83446735 0.2801634669303894 True -5 16362 30.315307140350342 0.7522082328796387 380.2075500488281 0.16803677380084991 482.0597839355469 0.38974809646606445 0.84117675 0.24005639553070068 True -6 19089 30.279817819595337 0.6564249992370605 388.08709716796875 0.16741204261779785 480.7637634277344 0.39125049114227295 0.8430739 0.23686331510543823 True -7 21816 30.198734283447266 0.6486272811889648 396.3934631347656 0.22255592048168182 478.88922119140625 0.3950401842594147 0.84707373 0.221883162856102 True -8 24543 30.23925542831421 0.6703915596008301 402.84368896484375 0.25436973571777344 477.20159912109375 0.39822566509246826 0.8519354 0.21235769987106323 True -9 27270 30.25544023513794 0.6625754833221436 407.43011474609375 0.11521182954311371 476.32415771484375 0.39945563673973083 0.8545551 0.19776025414466858 True -10 29997 30.199894189834595 0.649564266204834 388.8419494628906 0.11820641160011292 475.0787658691406 0.4016403257846832 0.86032295 0.1896909773349762 True -11 32724 30.2164249420166 1.218135118484497 392.3209533691406 0.23388665914535522 474.6293640136719 0.4018903076648712 0.8635152 0.1784357875585556 True -12 35451 29.82774591445923 8.442567110061646 374.4163818359375 0.13521605730056763 472.6919860839844 0.40560758113861084 0.8688065 0.1697627454996109 True -13 38178 29.649322748184204 0.6791644096374512 327.994873046875 0.16574954986572266 472.77130126953125 0.4041753113269806 0.8734817 0.16647259891033173 True -14 40905 29.68484878540039 1.2130966186523438 393.26885986328125 0.2025630921125412 471.227783203125 0.40746912360191345 0.87740034 0.15465757250785828 True -15 43632 29.717735290527344 1.215266227722168 418.41021728515625 0.08237355947494507 470.7786560058594 0.40793609619140625 0.88256145 0.14466209709644318 True -16 46359 29.62569522857666 0.6633949279785156 401.7904052734375 0.09324511140584946 470.31005859375 0.40806877613067627 0.8836859 0.14031477272510529 True -17 49086 29.672876358032227 0.6744887828826904 403.5216979980469 0.12485721707344055 470.4754333496094 0.40773043036460876 0.88569397 0.13909193873405457 True -18 51813 29.729806900024414 0.6715025901794434 344.2056884765625 0.08292075246572495 470.26666259765625 0.4083024859428406 0.88571566 0.13678400218486786 True -19 54540 29.691442251205444 0.9367363452911377 355.5640869140625 0.11309058964252472 470.2733459472656 0.40868324041366577 0.88675916 0.13663959503173828 True diff --git a/ENCSR612IKQ/cherimoya.fold_1.performance.tsv b/ENCSR612IKQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 66f8b0ec420b143901d19874bde8f8fd9ceb8abd..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -470.2733459472656 0.39568978548049927 0.40868324041366577 0.1459098607301712 0.8867591619491577 0.883846640586853 0.13663959503173828 \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_2.evaluate.json b/ENCSR612IKQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e4ad126f107166a6da93b1d4668d98f733c1244a..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426QJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_2.fit.json b/ENCSR612IKQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 2e6c551254c03b8e3867984d3110a3ef9b345a90..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF426QJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_2.log b/ENCSR612IKQ/cherimoya.fold_2.log deleted file mode 100644 index 0d90f2cbe29b5f4bb16786c5ce9c4bd2ebf5f82a..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 36.37821316719055 4.190990924835205 353.81298828125 0.18791449069976807 510.4735107421875 0.2982654571533203 0.729603 2.582418441772461 True -1 5740 31.5513436794281 0.5431807041168213 390.99383544921875 0.1661267876625061 474.60589599609375 0.3638441264629364 0.78894746 0.8274104595184326 True -2 8610 31.811150312423706 0.5173518657684326 452.3139953613281 0.26664549112319946 465.881591796875 0.377346932888031 0.8117721 0.3524249494075775 True -3 11480 31.277889728546143 12.134749412536621 358.81597900390625 0.19457468390464783 463.8307189941406 0.3791784644126892 0.8144344 0.3408225476741791 True -4 14350 31.209242820739746 0.7980976104736328 357.07379150390625 0.23758694529533386 461.0152893066406 0.38437286019325256 0.82753223 0.20778168737888336 True -5 17220 31.22413969039917 1.1928184032440186 350.9560852050781 0.18657192587852478 461.15911865234375 0.3835688531398773 0.83091503 0.20854264497756958 True -6 20090 31.15860652923584 0.5045595169067383 384.37762451171875 0.13042044639587402 459.2666015625 0.3872322738170624 0.8359189 0.19959980249404907 True -7 22960 31.163076400756836 0.5063166618347168 409.05908203125 0.2032330334186554 458.8507385253906 0.3872663974761963 0.83999556 0.18731772899627686 True -8 25830 31.17317819595337 0.5101749897003174 362.0241394042969 0.1760026067495346 457.1654052734375 0.39129024744033813 0.84547263 0.18339183926582336 True -9 28700 31.125183820724487 0.5175652503967285 414.66754150390625 0.17122095823287964 456.2349853515625 0.39302077889442444 0.8467785 0.17966125905513763 True -10 31570 31.53955340385437 0.5076978206634521 394.6772155761719 0.14815883338451385 455.03692626953125 0.39557647705078125 0.85084057 0.1755482405424118 True -11 34440 31.185345888137817 1.6484863758087158 409.8873291015625 0.21867910027503967 454.5123291015625 0.396203875541687 0.8554219 0.16286148130893707 True -12 37310 31.20863699913025 0.5044310092926025 421.983642578125 0.20905649662017822 454.5162353515625 0.3951408565044403 0.85835236 0.1591954231262207 True -13 40180 31.21892261505127 0.5093872547149658 375.26080322265625 0.16541382670402527 453.330322265625 0.3971899151802063 0.8625592 0.1521769016981125 True -14 43050 31.472428798675537 0.5217795372009277 392.81011962890625 0.13256341218948364 452.4139709472656 0.3997040092945099 0.86520404 0.1447136551141739 True -15 45920 31.213728189468384 0.5224313735961914 405.44085693359375 0.12327469885349274 451.88690185546875 0.4007357656955719 0.86855155 0.13955608010292053 True -16 48790 31.214439868927002 0.5123453140258789 306.9949035644531 0.08469072729349136 451.5930480957031 0.4012734889984131 0.87198514 0.1354673206806183 True -17 51660 31.161768674850464 0.5214500427246094 339.32720947265625 0.12632276117801666 451.98883056640625 0.39967313408851624 0.87225527 0.13343445956707 True -18 54530 31.278277158737183 0.5210676193237305 360.5456848144531 0.09032094478607178 451.9787292480469 0.39954885840415955 0.873365 0.1328018754720688 True -19 57400 31.18730354309082 0.5176360607147217 373.5038146972656 0.08453626930713654 451.7512512207031 0.40099743008613586 0.87222797 0.13331665098667145 False diff --git a/ENCSR612IKQ/cherimoya.fold_2.performance.tsv b/ENCSR612IKQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 03f5ceaf8b143057286420a7119336dcee97b292..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -451.9787292480469 0.400827556848526 0.39954879879951477 0.1412498652935028 0.8733649849891663 0.8654648065567017 0.1328018754720688 \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_3.evaluate.json b/ENCSR612IKQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fc2808d0c76fdf5703608acd0221683f2d973fb9..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426QJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_3.fit.json b/ENCSR612IKQ/cherimoya.fold_3.fit.json deleted file mode 100644 index f1ab8c248d352e4ed1b8851487b3264ca526f253..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF426QJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_3.log b/ENCSR612IKQ/cherimoya.fold_3.log deleted file mode 100644 index a49c53cca1e9bfd6d82a2932ee54b0ced564f4d7..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2769 35.571807622909546 4.343214273452759 418.5015869140625 0.19691875576972961 477.5093078613281 0.29915153980255127 0.7059734 3.018481969833374 True -1 5538 30.70238184928894 0.5248987674713135 383.5338134765625 0.23519985377788544 442.55242919921875 0.36661699414253235 0.7786262 0.901050329208374 True -2 8307 30.76572036743164 0.5334854125976562 359.075439453125 0.18655407428741455 436.1414794921875 0.37543782591819763 0.8006364 0.39786750078201294 True -3 11076 30.67041563987732 0.5223512649536133 327.7235107421875 0.1624210625886917 433.0197448730469 0.38214126229286194 0.80710274 0.33019304275512695 True -4 13845 30.075042963027954 0.5677776336669922 413.2855224609375 0.25637972354888916 431.5771179199219 0.3841695189476013 0.8147541 0.2528303265571594 True -5 16614 30.070774793624878 1.7665393352508545 435.4961242675781 0.1961883008480072 431.2158203125 0.3839355409145355 0.815878 0.24146851897239685 True -6 19383 30.11177706718445 0.5233988761901855 368.17169189453125 0.2067658007144928 429.2738952636719 0.38844653964042664 0.8215438 0.23788459599018097 True -7 22152 30.10532808303833 0.5236854553222656 397.94073486328125 0.13423775136470795 428.8045959472656 0.38772594928741455 0.8279974 0.2263863980770111 True -8 24921 30.069159507751465 1.171870231628418 400.12335205078125 0.18850205838680267 428.2061767578125 0.38836604356765747 0.8336019 0.2131950855255127 True -9 27690 30.042221546173096 0.739971399307251 329.2747802734375 0.16033780574798584 426.6391296386719 0.39155474305152893 0.83553314 0.19556963443756104 True -10 30459 30.03360152244568 0.5237898826599121 381.52044677734375 0.11659698933362961 425.574951171875 0.39404192566871643 0.8407921 0.19388753175735474 True -11 33228 30.04329752922058 0.5171434879302979 376.4929504394531 0.12152734398841858 424.4530029296875 0.396284818649292 0.8450478 0.1833103597164154 True -12 35997 30.130897045135498 13.870009183883667 415.21063232421875 0.15639567375183105 423.8414306640625 0.39674413204193115 0.84906775 0.17320683598518372 True -13 38766 30.10066843032837 1.3008544445037842 376.8472900390625 0.13717526197433472 423.1634521484375 0.3975198566913605 0.8517903 0.1686517745256424 True -14 41535 30.12579655647278 4.855970621109009 399.64019775390625 0.212819442152977 422.0540771484375 0.39962390065193176 0.8585448 0.16142813861370087 True -15 44304 30.455508947372437 0.5224721431732178 391.32537841796875 0.1558346003293991 420.7440185546875 0.4022650718688965 0.8653955 0.15239165723323822 True -16 47073 30.115766763687134 0.5210452079772949 354.98284912109375 0.12696108222007751 420.7306213378906 0.40162959694862366 0.8678852 0.14754942059516907 True -17 49842 30.06915783882141 0.5192174911499023 396.26153564453125 0.14459460973739624 421.10546875 0.4004623591899872 0.869526 0.14520001411437988 True -18 52611 30.08318591117859 0.5207409858703613 377.0994873046875 0.11931540071964264 420.8470458984375 0.4011822044849396 0.87009513 0.14339964091777802 True -19 55380 30.072378635406494 0.5336837768554688 392.01953125 0.10178391635417938 420.7412414550781 0.40178996324539185 0.8710714 0.14316852390766144 True diff --git a/ENCSR612IKQ/cherimoya.fold_3.performance.tsv b/ENCSR612IKQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8164c52d6eb7b752b4dc39da1654f3e8d7b7ce6f..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -420.7412414550781 0.4037012755870819 0.40178996324539185 0.1353498101234436 0.8710713982582092 0.8530500531196594 0.14316852390766144 \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_4.evaluate.json b/ENCSR612IKQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 86394431a751f79b6b321457cf4e2d724a48579b..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426QJQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_4.fit.json b/ENCSR612IKQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 25d03204e6cda1c5f0b32107fc5f4bd4d1c874ce..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF426QJQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR612IKQ/cherimoya.fold_4.log b/ENCSR612IKQ/cherimoya.fold_4.log deleted file mode 100644 index ec8aaff0453cb0c99d57ab903461f0d25a347aca..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 36.1503791809082 4.248824834823608 366.615234375 0.27562254667282104 448.10345458984375 0.2952393889427185 0.7250457 2.823549270629883 True -1 5664 31.39407706260681 0.6479239463806152 395.2744140625 0.21197348833084106 420.2986755371094 0.3538950979709625 0.7840021 0.5123981833457947 True -2 8496 33.01362872123718 13.549139261245728 379.4075927734375 0.2586478590965271 413.7011413574219 0.3639681935310364 0.80687517 0.2555229365825653 True -3 11328 31.371253967285156 0.5946669578552246 413.1138916015625 0.18784360587596893 411.5589294433594 0.36756157875061035 0.82012075 0.2037017047405243 True -4 14160 31.808960914611816 0.6168975830078125 411.5544128417969 0.26208680868148804 410.5625915527344 0.3685583770275116 0.8275047 0.17160895466804504 True -5 16992 31.42320990562439 0.6337220668792725 363.7636413574219 0.18642006814479828 409.3520812988281 0.37153857946395874 0.833107 0.17943094670772552 True -6 19824 31.460980892181396 0.6048333644866943 345.57550048828125 0.17049603164196014 408.27813720703125 0.37399575114250183 0.83784 0.16925540566444397 True -7 22656 31.37187933921814 1.4950628280639648 351.293701171875 0.24397194385528564 408.1590576171875 0.3733727037906647 0.8423561 0.16785463690757751 True -8 25488 31.40423607826233 0.6203293800354004 362.7955017089844 0.18454046547412872 406.5348205566406 0.37771618366241455 0.84688497 0.15683825314044952 True -9 28320 31.402570009231567 0.6105442047119141 365.54498291015625 0.18301142752170563 406.4074401855469 0.3775404691696167 0.8503482 0.15279445052146912 True -10 31152 31.35750651359558 0.5995628833770752 367.44305419921875 0.16317841410636902 404.8660888671875 0.3820953369140625 0.8533614 0.14569608867168427 True -11 33984 31.335129976272583 0.5919806957244873 332.7050476074219 0.2054075002670288 405.2803649902344 0.37958112359046936 0.8592208 0.13791905343532562 True -12 36816 31.655956745147705 1.371150016784668 362.11236572265625 0.13776558637619019 404.34332275390625 0.38184860348701477 0.86252546 0.13275815546512604 True -13 39648 30.89303708076477 0.7690000534057617 349.71173095703125 0.10014118254184723 403.56414794921875 0.38340437412261963 0.8671917 0.1287378966808319 True -14 42480 30.789374113082886 0.5953893661499023 355.99127197265625 0.16129133105278015 403.57659912109375 0.3834914565086365 0.87013245 0.12304811179637909 True -15 45312 30.872441053390503 0.594778299331665 379.908447265625 0.07531717419624329 403.2173767089844 0.3841792643070221 0.87422556 0.11830034106969833 True -16 48144 30.864902019500732 0.601712703704834 351.9621276855469 0.18497900664806366 403.0107421875 0.38443002104759216 0.8765657 0.11575201153755188 True -17 50976 30.73308253288269 0.5883634090423584 380.3845520019531 0.06995216012001038 402.6536560058594 0.3851877450942993 0.880119 0.1133074164390564 True -18 53808 30.73318338394165 0.5886633396148682 369.20623779296875 0.07579825818538666 402.5142517089844 0.3853724002838135 0.87961245 0.11290127784013748 False -19 56640 30.712019205093384 0.6022117137908936 342.8245849609375 0.11990893632173538 402.3069152832031 0.38633620738983154 0.8793491 0.11248497664928436 False diff --git a/ENCSR612IKQ/cherimoya.fold_4.performance.tsv b/ENCSR612IKQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d796c29df2504360d33d411f28337fb7d8f01b6e..0000000000000000000000000000000000000000 --- a/ENCSR612IKQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -402.6536560058594 0.41481414437294006 0.3851877450942993 0.1278291791677475 0.8801190257072449 0.8637052178382874 0.1133074164390564 \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_0.evaluate.json b/ENCSR618HFT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 28139226bbaca03b1d67e320ad27e585e03f2fbd..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672UYD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_0.fit.json b/ENCSR618HFT/cherimoya.fold_0.fit.json deleted file mode 100644 index 7666e1f84a8c217d80361d8d8a6edd832b94eb90..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF672UYD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_0.log b/ENCSR618HFT/cherimoya.fold_0.log deleted file mode 100644 index 8904e71baa8021b7905da736f64c290a07040b28..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2723 33.41982698440552 3.5424869060516357 82.6326904296875 0.3946866989135742 135.32040405273438 0.08899345993995667 0.7081235 2.119497060775757 True -1 5446 29.999149322509766 0.5968739986419678 107.02501678466797 0.411449134349823 129.54257202148438 0.1088939979672432 0.75928473 1.066543698310852 True -2 8169 30.07157325744629 0.5807926654815674 114.84683227539062 0.345429003238678 127.7390365600586 0.11232154071331024 0.7646049 0.5789055824279785 True -3 10892 29.940993547439575 0.5770604610443115 140.20449829101562 0.3964412808418274 126.79246520996094 0.11473498493432999 0.76866543 0.5557907223701477 True -4 13615 29.829155683517456 0.5784382820129395 135.1861572265625 0.3466859459877014 125.63556671142578 0.11669059097766876 0.7883651 0.4955822229385376 True -5 16338 29.861156940460205 0.5790145397186279 107.05529022216797 0.5171938538551331 124.82930755615234 0.11981221288442612 0.79240835 0.4681527614593506 True -6 19061 30.229618072509766 3.8039817810058594 131.31546020507812 0.5440481901168823 124.3153076171875 0.121324323117733 0.7971953 0.4480759799480438 True -7 21784 29.872501850128174 0.59285569190979 85.58843994140625 0.3244456648826599 123.99051666259766 0.12228131294250488 0.8001059 0.39237868785858154 True -8 24507 29.849513053894043 0.6038529872894287 101.45109558105469 0.3340538740158081 123.58292388916016 0.12360271066427231 0.8053015 0.3697901964187622 True -9 27230 30.045997858047485 0.5919735431671143 108.83314514160156 0.4378346800804138 123.17687225341797 0.12515497207641602 0.8127916 0.34109076857566833 True -10 29953 29.971472024917603 0.5845706462860107 124.36872100830078 0.3308076560497284 122.80138397216797 0.1262231469154358 0.8226897 0.3175412118434906 True -11 32676 29.839540004730225 0.5815310478210449 107.27006530761719 0.3169657588005066 122.49478912353516 0.12749271094799042 0.82572985 0.3053950071334839 True -12 35399 29.854877710342407 0.5776517391204834 101.18865966796875 0.31540942192077637 122.30451965332031 0.12778890132904053 0.833963 0.28367748856544495 True -13 38122 29.90298581123352 0.5893692970275879 108.02250671386719 0.35735803842544556 122.10062408447266 0.12862151861190796 0.84119946 0.26847368478775024 True -14 40845 29.936821222305298 0.5795063972473145 101.60757446289062 0.3182166814804077 121.7485122680664 0.1298154890537262 0.84748524 0.2569616436958313 True -15 43568 29.926052808761597 0.5796287059783936 107.47773742675781 0.36351191997528076 121.70362854003906 0.12997430562973022 0.85304505 0.2419406920671463 True -16 46291 29.446527004241943 1.3731706142425537 114.92929077148438 0.323582261800766 121.63440704345703 0.12998118996620178 0.8527459 0.2361152321100235 False -17 49014 29.368497371673584 0.5764071941375732 111.0980453491211 0.5241625905036926 121.35419464111328 0.1314118355512619 0.8557784 0.2328094244003296 True -18 51737 29.327749729156494 0.576563835144043 89.85062408447266 0.32280027866363525 121.46315002441406 0.13072426617145538 0.85544586 0.23336590826511383 False -19 54460 29.276262760162354 0.5839276313781738 108.35114288330078 0.3866407871246338 121.49903869628906 0.1303521990776062 0.8536834 0.23408374190330505 False diff --git a/ENCSR618HFT/cherimoya.fold_0.performance.tsv b/ENCSR618HFT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9b9c1e487e74dac0b1083a65dd5bc90a188b5715..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -121.35419464111328 0.6075777411460876 0.1314118355512619 0.023966791108250618 0.8557783961296082 0.7333008646965027 0.2328094244003296 \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_1.evaluate.json b/ENCSR618HFT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f010dbedbba657a88939bd41cd08542ebbabc2f4..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672UYD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_1.fit.json b/ENCSR618HFT/cherimoya.fold_1.fit.json deleted file mode 100644 index a04efa21d7fd262322569089de9969e03d352227..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF672UYD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_1.log b/ENCSR618HFT/cherimoya.fold_1.log deleted file mode 100644 index 5a8701da77a7f330ae2de4ff4d85bc411d0834fc..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2714 34.632569551467896 3.7178866863250732 81.84187316894531 0.37084656953811646 172.73475646972656 0.1037941426038742 0.68401206 2.3853840827941895 True -1 5428 34.47507190704346 17.9701726436615 104.73229217529297 0.5346179008483887 161.77528381347656 0.13915425539016724 0.7483407 1.3793138265609741 True -2 8142 30.295098304748535 4.371156454086304 77.34627532958984 0.44748353958129883 159.0625457763672 0.14183668792247772 0.7617238 0.8419210314750671 True -3 10856 30.26913094520569 2.5338025093078613 127.96815490722656 0.45274341106414795 157.16488647460938 0.14656876027584076 0.7789791 0.77409827709198 True -4 13570 30.206780433654785 3.117729663848877 97.01049041748047 0.44004470109939575 156.3463134765625 0.14764860272407532 0.79241294 0.6925426721572876 True -5 16284 30.14148783683777 2.245483636856079 126.74232482910156 0.4123470187187195 156.89463806152344 0.14642372727394104 0.79599607 0.7911128997802734 True -6 18998 30.25345253944397 1.6286156177520752 100.88444519042969 0.5877282023429871 155.07705688476562 0.15098491311073303 0.8073947 0.705647885799408 True -7 21712 30.19047784805298 1.779148817062378 105.24300384521484 0.48573964834213257 154.41574096679688 0.15303483605384827 0.810257 0.6652955412864685 True -8 24426 30.23506188392639 3.510658025741577 109.65680694580078 0.3433176875114441 153.9735870361328 0.15417079627513885 0.81311154 0.650329053401947 True -9 27140 30.189260005950928 1.821533203125 108.09418487548828 0.32626432180404663 153.28860473632812 0.15634387731552124 0.8202527 0.5830666422843933 True -10 29854 30.205795288085938 1.803992509841919 113.70368957519531 0.41254231333732605 152.50933837890625 0.15876592695713043 0.8284958 0.5432575941085815 True -11 32568 30.14424204826355 1.9743695259094238 118.3268814086914 0.3018486201763153 152.11654663085938 0.15989071130752563 0.8372528 0.5017402768135071 True -12 35282 30.235249519348145 1.3759076595306396 99.50144958496094 0.4099268913269043 151.72816467285156 0.1609450727701187 0.8421952 0.46829017996788025 True -13 37996 30.370739459991455 3.486086368560791 114.994384765625 0.33638837933540344 151.06381225585938 0.16266633570194244 0.85244006 0.4199691116809845 True -14 40710 30.45252799987793 3.129779100418091 106.35751342773438 0.4720315933227539 150.84927368164062 0.16295382380485535 0.8591588 0.3855685591697693 True -15 43424 30.440014839172363 3.578462839126587 106.76799011230469 0.363258421421051 150.39138793945312 0.16422326862812042 0.862878 0.3532542884349823 True -16 46138 30.8030002117157 0.6752047538757324 92.99269104003906 0.22748321294784546 150.16868591308594 0.16467003524303436 0.8687326 0.3288276791572571 True -17 48852 30.761025190353394 9.396491765975952 80.81383514404297 0.2890966534614563 149.95521545410156 0.16518209874629974 0.87173843 0.306918203830719 True -18 51566 30.87751817703247 0.6825859546661377 119.38600158691406 0.3128553032875061 150.20620727539062 0.1639547049999237 0.87195367 0.29878175258636475 True -19 54280 30.45470666885376 0.6647622585296631 110.9037857055664 0.3167690932750702 150.2561798095703 0.1636197566986084 0.8716903 0.29671159386634827 False diff --git a/ENCSR618HFT/cherimoya.fold_1.performance.tsv b/ENCSR618HFT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1f90f1dfe1327a855b98741411200ade3125420d..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -150.20620727539062 0.5846591591835022 0.1639547049999237 0.03967393934726715 0.8719536662101746 0.7953365445137024 0.29878175258636475 \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_2.evaluate.json b/ENCSR618HFT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 77d5a1be1bf48dea611197ec803b699cc142431b..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672UYD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_2.fit.json b/ENCSR618HFT/cherimoya.fold_2.fit.json deleted file mode 100644 index 73454aec3f48115f862c98b1b812ae295ec4ad64..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF672UYD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_2.log b/ENCSR618HFT/cherimoya.fold_2.log deleted file mode 100644 index 30d4bd70743c3494a5b5df39ab90b7957219b9fe..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 36.31579804420471 3.541032314300537 129.9333038330078 0.38777780532836914 143.75680541992188 0.09401732683181763 0.6796573 1.961867094039917 True -1 5736 31.9258553981781 0.5548644065856934 108.20709228515625 0.6053872108459473 136.06002807617188 0.11987773329019547 0.7494681 1.2291407585144043 True -2 8604 31.91051721572876 0.5483114719390869 112.89480590820312 0.7142813205718994 134.242431640625 0.12097959965467453 0.75514823 0.636459231376648 True -3 11472 31.79487943649292 0.5410497188568115 87.80216217041016 0.26701122522354126 132.39808654785156 0.12570543587207794 0.778019 0.5487986207008362 True -4 14340 31.78630042076111 0.5476605892181396 127.72544860839844 0.3445264399051666 131.46536254882812 0.12766359746456146 0.78869796 0.5113798379898071 True -5 17208 31.86472797393799 0.5607390403747559 93.81735229492188 0.43498289585113525 130.74118041992188 0.12986929714679718 0.7988285 0.4378705322742462 True -6 20076 31.869284629821777 0.5505485534667969 116.89966583251953 0.3997440040111542 130.1353759765625 0.13161076605319977 0.80683005 0.42264020442962646 True -7 22944 31.832072257995605 0.5456736087799072 134.177001953125 0.4449992775917053 130.027587890625 0.13140828907489777 0.8123098 0.4164767861366272 True -8 25812 32.37717056274414 25.38714361190796 96.50438690185547 0.3195168077945709 129.73878479003906 0.13235747814178467 0.8164377 0.3983989655971527 True -9 28680 31.86028289794922 0.5525672435760498 103.78114318847656 0.31161385774612427 129.19198608398438 0.1349131166934967 0.8189551 0.3732653558254242 True -10 31548 31.965548753738403 0.5508160591125488 101.70710754394531 0.40522411465644836 128.86264038085938 0.1360272616147995 0.8239298 0.37065649032592773 True -11 34416 31.901796102523804 0.5504336357116699 100.51751708984375 0.3025099039077759 128.56222534179688 0.13702772557735443 0.83163774 0.34089627861976624 True -12 37284 31.895726442337036 0.5498671531677246 95.57060241699219 0.25538575649261475 128.28611755371094 0.13771605491638184 0.8347418 0.31435543298721313 True -13 40152 32.11625051498413 18.721729278564453 103.66816711425781 0.3171062767505646 127.92681121826172 0.13912980258464813 0.839606 0.3000774383544922 True -14 43020 31.91976261138916 0.5643072128295898 96.2318344116211 0.3243599236011505 127.75667572021484 0.13971388339996338 0.8443266 0.2811959981918335 True -15 45888 32.028393268585205 0.5535562038421631 94.84025573730469 0.2366320639848709 127.69599914550781 0.139673113822937 0.8506145 0.26643505692481995 True -16 48756 31.881027460098267 0.5541484355926514 105.4158935546875 0.3508460521697998 127.35150146484375 0.14138692617416382 0.8507965 0.2591151297092438 True -17 51624 31.938645601272583 33.69542455673218 106.54906463623047 0.40393349528312683 127.37481689453125 0.14117023348808289 0.8518468 0.25438156723976135 True -18 54492 32.2002215385437 0.5535104274749756 103.58741760253906 0.29146063327789307 127.53997802734375 0.14033247530460358 0.8515927 0.2535856068134308 False -19 57360 31.94403100013733 0.5502476692199707 107.69709777832031 0.2626924514770508 127.47727966308594 0.14096000790596008 0.85057086 0.2553178071975708 False diff --git a/ENCSR618HFT/cherimoya.fold_2.performance.tsv b/ENCSR618HFT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a3ebadf474c885c2d3cf2623c8560511c649831f..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -127.37481689453125 0.60112065076828 0.1411702185869217 0.027813371270895004 0.8518468141555786 0.748842179775238 0.25438156723976135 \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_3.evaluate.json b/ENCSR618HFT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7419db22fd33edd3401cfcd93d56b3fb7f4d4de8..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672UYD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_3.fit.json b/ENCSR618HFT/cherimoya.fold_3.fit.json deleted file mode 100644 index b0f52824d3963bdbf6c25c4e096612a8efc341a6..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF672UYD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_3.log b/ENCSR618HFT/cherimoya.fold_3.log deleted file mode 100644 index 36620cc6d1022ff02f01a6e06c05e57c2959e1d2..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 35.58079719543457 3.477384090423584 125.518310546875 0.48487991094589233 140.81553649902344 0.09656376391649246 0.66530377 2.091966152191162 True -1 5488 30.498206615447998 1.635739803314209 110.54153442382812 0.6391597986221313 133.97837829589844 0.11947522312402725 0.7287247 1.1741002798080444 True -2 8232 30.59765338897705 0.5581905841827393 83.43801879882812 0.37054234743118286 132.6731414794922 0.1211538091301918 0.7398882 0.6800699830055237 True -3 10976 30.53532600402832 0.5648667812347412 147.67608642578125 0.5889822840690613 131.63595581054688 0.12375025451183319 0.76084703 0.6015159487724304 True -4 13720 30.43071413040161 0.5641322135925293 108.39631652832031 0.32188063859939575 131.31495666503906 0.12522752583026886 0.7648873 0.6207734942436218 True -5 16464 30.4540798664093 1.1243181228637695 117.99762725830078 0.26457875967025757 130.4678497314453 0.12732839584350586 0.77072465 0.5914230346679688 True -6 19208 30.495279788970947 0.571575403213501 77.69709014892578 0.36918914318084717 129.95553588867188 0.12923693656921387 0.7784561 0.5809122323989868 True -7 21952 30.458980560302734 0.5613353252410889 119.66273498535156 0.4169018268585205 129.43568420410156 0.13079914450645447 0.7835945 0.5485025644302368 True -8 24696 30.52270221710205 0.5670132637023926 121.10050964355469 0.46736592054367065 129.07156372070312 0.13190577924251556 0.7899693 0.5168169736862183 True -9 27440 30.490363597869873 0.5765814781188965 127.81102752685547 0.38243433833122253 128.65017700195312 0.13339027762413025 0.7973263 0.48215675354003906 True -10 30184 30.784169673919678 0.5712711811065674 97.1666488647461 0.3737037777900696 128.4111328125 0.13418173789978027 0.80628186 0.44045108556747437 True -11 32928 30.680256843566895 0.5809371471405029 109.91626739501953 0.3110821843147278 127.97798919677734 0.13561509549617767 0.81303847 0.4133375883102417 True -12 35672 30.64504599571228 0.5704731941223145 97.77848052978516 0.4070185422897339 127.84187316894531 0.13593079149723053 0.8210861 0.38283202052116394 True -13 38416 32.32103896141052 31.49056386947632 136.66168212890625 0.3551309108734131 127.49039459228516 0.1373608261346817 0.82773775 0.344927579164505 True -14 41160 31.0118145942688 0.5733458995819092 125.6136703491211 0.39576101303100586 127.18521881103516 0.1379932314157486 0.836174 0.32473692297935486 True -15 43904 32.07009840011597 0.5773196220397949 92.90629577636719 0.3130739629268646 127.0261459350586 0.13855719566345215 0.8428996 0.3028392493724823 True -16 46648 31.881521701812744 25.20107364654541 126.74946594238281 0.39370793104171753 126.7313232421875 0.13955356180667877 0.8468604 0.2860655188560486 True -17 49392 30.601014614105225 2.3630313873291016 98.91132354736328 0.1960952877998352 126.63316345214844 0.1400211751461029 0.8489931 0.2791551351547241 True -18 52136 30.57651376724243 3.3885862827301025 115.52946472167969 0.3077129125595093 126.69847106933594 0.13945458829402924 0.85089093 0.27494850754737854 True -19 54880 30.586758136749268 3.195415496826172 90.4866943359375 0.25431400537490845 126.69705963134766 0.13948997855186462 0.847731 0.27587300539016724 False diff --git a/ENCSR618HFT/cherimoya.fold_3.performance.tsv b/ENCSR618HFT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 15d5d09c8d3efdcedb9c050d5abe384f0edf5c1d..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -126.69847106933594 0.6025248765945435 0.13945460319519043 0.02957742288708687 0.8508909344673157 0.7436597347259521 0.27494850754737854 \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_4.evaluate.json b/ENCSR618HFT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 25ee7af170ba8f4a7075fdcd97eb4683c30d3471..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672UYD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_4.fit.json b/ENCSR618HFT/cherimoya.fold_4.fit.json deleted file mode 100644 index d106cac4151aeadefb8092682f4d5746ee70186c..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF672UYD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR618HFT/cherimoya.fold_4.log b/ENCSR618HFT/cherimoya.fold_4.log deleted file mode 100644 index 2b522b9883050055055c467cd69a18514e4f737e..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2849 34.828938484191895 3.5574302673339844 99.8787841796875 0.4100201725959778 126.52825164794922 0.08987382799386978 0.663994 1.8313840627670288 True -1 5698 31.37529683113098 0.5945839881896973 84.41207122802734 0.23430263996124268 121.09492492675781 0.10940799862146378 0.71890295 0.7956447601318359 True -2 8547 31.34527850151062 0.58489990234375 119.21769714355469 0.3979695737361908 120.3608169555664 0.11002419143915176 0.72425145 0.5060421228408813 True -3 11396 31.245322227478027 0.5830352306365967 126.11808013916016 0.40812912583351135 119.37178802490234 0.112367644906044 0.75294566 0.4940255284309387 True -4 14245 31.204328060150146 0.5826296806335449 86.23008728027344 0.34062910079956055 118.80098724365234 0.11399730294942856 0.76381564 0.4686271548271179 True -5 17094 31.238931894302368 0.5854930877685547 85.86447143554688 0.5345070958137512 118.15967559814453 0.1160886287689209 0.77278554 0.4334828853607178 True -6 19943 31.296772718429565 0.5858492851257324 100.45326232910156 0.3264871835708618 117.88719940185547 0.11685942113399506 0.77463776 0.3977261781692505 True -7 22792 31.17830777168274 0.5936176776885986 99.09278869628906 0.287054181098938 117.46683502197266 0.11829560250043869 0.7824733 0.38252732157707214 True -8 25641 31.32414698600769 0.6027312278747559 97.44224548339844 0.3115267753601074 117.13803100585938 0.11925183981657028 0.7897971 0.3605106770992279 True -9 28490 31.23347496986389 0.5804548263549805 118.9542236328125 0.6515202522277832 116.93150329589844 0.12005863338708878 0.7932693 0.33870306611061096 True -10 31339 31.336007833480835 0.5867142677307129 85.36583709716797 0.3098646402359009 116.64769744873047 0.12125644832849503 0.80048686 0.32039377093315125 True -11 34188 31.271595001220703 0.5765595436096191 122.90526580810547 0.3421315550804138 116.46798706054688 0.12195178121328354 0.80762607 0.3028678297996521 True -12 37037 31.218225955963135 0.5861012935638428 111.96461486816406 0.31385481357574463 116.12285614013672 0.12322963029146194 0.81423414 0.28741252422332764 True -13 39886 31.246073722839355 0.5791521072387695 95.97357940673828 0.27890443801879883 116.04292297363281 0.12327871471643448 0.81940943 0.27059948444366455 True -14 42735 31.40237855911255 0.5830395221710205 91.93095397949219 0.28690433502197266 115.80706787109375 0.12437520921230316 0.82465005 0.2547839283943176 True -15 45584 31.371501207351685 1.0465900897979736 98.86933898925781 0.3710574507713318 115.72789001464844 0.1244172602891922 0.82959694 0.24371343851089478 True -16 48433 31.283093690872192 0.5892109870910645 80.82524108886719 0.24578912556171417 115.5915756225586 0.12480571120977402 0.8354643 0.23462693393230438 True -17 51282 31.27123212814331 0.5822389125823975 127.01390075683594 0.33588507771492004 115.5273666381836 0.12485376000404358 0.83713263 0.23040156066417694 True -18 54131 31.29323410987854 0.5793347358703613 101.43389892578125 0.33833950757980347 115.58173370361328 0.12443865835666656 0.8387542 0.22848066687583923 True -19 56980 30.68840479850769 0.5788047313690186 76.94158935546875 0.3458317518234253 115.53870391845703 0.12502780556678772 0.8381811 0.22805964946746826 False diff --git a/ENCSR618HFT/cherimoya.fold_4.performance.tsv b/ENCSR618HFT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e8f7677a14cc84b9597f391e13ce1a3980fb19ed..0000000000000000000000000000000000000000 --- a/ENCSR618HFT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -115.58173370361328 0.611754298210144 0.12443865835666656 0.025416133925318718 0.8387541770935059 0.7034337520599365 0.22848066687583923 \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_0.evaluate.json b/ENCSR619BNL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f5d22c368a1d8547b9489c37b8719e94898c39b9..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF453LUU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_0.fit.json b/ENCSR619BNL/cherimoya.fold_0.fit.json deleted file mode 100644 index b54be9d0d068e1e9d84735f4830ecc1d35c620f1..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF453LUU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_0.log b/ENCSR619BNL/cherimoya.fold_0.log deleted file mode 100644 index ba606f6ef314b2fa658befb5dec6d66b3b3d0043..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.62619495391846 4.19049596786499 208.37464904785156 0.716486930847168 264.10906982421875 0.13920031487941742 0.5159646 3.1997289657592773 True -1 5500 30.157975673675537 0.754927396774292 198.38943481445312 0.8539397716522217 255.09512329101562 0.19269968569278717 0.630289 0.7558860182762146 True -2 8250 30.217965126037598 0.6775579452514648 174.91268920898438 0.5613753795623779 252.9119110107422 0.20250098407268524 0.64541835 0.45051416754722595 True -3 11000 29.63488006591797 0.8436434268951416 226.50308227539062 0.5539715886116028 251.97036743164062 0.20528392493724823 0.65055805 0.45370176434516907 True -4 13750 29.60932230949402 0.5744104385375977 221.82791137695312 0.4533163607120514 251.21994018554688 0.20873333513736725 0.6585641 0.5048534870147705 True -5 16500 29.598496675491333 0.5727872848510742 192.51100158691406 0.5269926190376282 250.7005157470703 0.2113252580165863 0.66239274 0.4450499415397644 True -6 19250 29.529096603393555 0.573868989944458 185.8955078125 0.5992293953895569 250.3485107421875 0.2133374959230423 0.6655121 0.4610268175601959 True -7 22000 29.57274580001831 0.5748140811920166 195.6414794921875 0.6843374967575073 249.91773986816406 0.2158481776714325 0.6738031 0.47559893131256104 True -8 24750 29.51653218269348 0.5724997520446777 177.216552734375 0.31430280208587646 249.60853576660156 0.21722349524497986 0.6784282 0.442638099193573 True -9 27500 29.560773849487305 0.564295768737793 224.02426147460938 0.49017834663391113 249.45755004882812 0.2182377129793167 0.68378156 0.4312189817428589 True -10 30250 29.60375452041626 0.5725479125976562 235.09686279296875 0.4937501549720764 249.14205932617188 0.2197873294353485 0.6897993 0.4149450361728668 True -11 33000 29.682698249816895 0.5810017585754395 180.64743041992188 0.3176652193069458 248.7880401611328 0.22172313928604126 0.6966988 0.39999064803123474 True -12 35750 29.683418035507202 0.5754745006561279 199.0654296875 0.3958144783973694 248.6326904296875 0.2227199673652649 0.70195675 0.38138872385025024 True -13 38500 29.683549880981445 0.6142702102661133 196.00863647460938 0.3780047595500946 248.2713623046875 0.22445420920848846 0.70824087 0.3514256477355957 True -14 41250 29.58569836616516 0.5748610496520996 179.92034912109375 0.25566619634628296 248.13302612304688 0.22500628232955933 0.7162268 0.33469393849372864 True -15 44000 29.62336826324463 0.6156413555145264 213.79934692382812 0.45709261298179626 248.00485229492188 0.22644968330860138 0.72411704 0.3213721215724945 True -16 46750 29.565429210662842 1.8408594131469727 195.79757690429688 0.3893584907054901 247.92454528808594 0.22665224969387054 0.7284645 0.314871221780777 True -17 49500 29.679746866226196 0.5948657989501953 204.4417266845703 0.3667554259300232 247.8052215576172 0.22710172832012177 0.7306685 0.3116055727005005 True -18 52250 29.645416975021362 1.6163339614868164 224.80935668945312 0.26071321964263916 247.79049682617188 0.22751444578170776 0.73181504 0.3133850395679474 True -19 55000 29.604654550552368 0.5725188255310059 188.20697021484375 0.24129846692085266 247.87823486328125 0.2265760600566864 0.72991914 0.31741172075271606 False diff --git a/ENCSR619BNL/cherimoya.fold_0.performance.tsv b/ENCSR619BNL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2feaf00d434459ee4651249639487d5d7a80b4ed..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -247.79049682617188 0.5243867039680481 0.22751444578170776 0.06273748725652695 0.7318150401115417 0.7007058262825012 0.3133850395679474 \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_1.evaluate.json b/ENCSR619BNL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5633820d1cd1dfcb4d788bff7ba634609f95a711..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF453LUU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_1.fit.json b/ENCSR619BNL/cherimoya.fold_1.fit.json deleted file mode 100644 index 653d032475fca6a127bdac836df167cc4a4e8d7b..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF453LUU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_1.log b/ENCSR619BNL/cherimoya.fold_1.log deleted file mode 100644 index bc48c10c907f767dbc8a87163bb27be4265da79a..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 34.68035054206848 3.4380862712860107 189.75006103515625 0.6552748680114746 295.7373962402344 0.1477222442626953 0.5743673 3.7287399768829346 True -1 5496 30.125550031661987 1.0117170810699463 188.2562255859375 0.7836867570877075 284.6708068847656 0.20760875940322876 0.67042834 0.8671219944953918 True -2 8244 30.138237953186035 0.707866907119751 233.67874145507812 0.6129734516143799 281.985595703125 0.2157704085111618 0.6859783 0.5030566453933716 True -3 10992 30.112127780914307 0.9284746646881104 210.1786346435547 0.5600247383117676 280.6681213378906 0.22049130499362946 0.69619757 0.48878586292266846 True -4 13740 29.595842599868774 0.8829238414764404 213.04443359375 0.42465925216674805 279.90777587890625 0.22352825105190277 0.70347226 0.44219970703125 True -5 16488 29.65137481689453 0.6939315795898438 201.40347290039062 0.578920841217041 279.31488037109375 0.2260301411151886 0.71816885 0.42117196321487427 True -6 19236 29.63272261619568 0.6953892707824707 217.4615478515625 0.4307953715324402 278.6663513183594 0.22942562401294708 0.7228083 0.45217588543891907 True -7 21984 29.624363660812378 0.6725234985351562 194.4681396484375 0.43335312604904175 278.1242980957031 0.23233337700366974 0.72794825 0.39725667238235474 True -8 24732 29.643181562423706 0.7963535785675049 203.18338012695312 0.7615605592727661 278.03509521484375 0.23277439177036285 0.7300844 0.40141230821609497 True -9 27480 29.57705068588257 0.6818220615386963 225.39947509765625 0.6006020903587341 277.7749938964844 0.2335832417011261 0.7349232 0.368754118680954 True -10 30228 29.61890935897827 0.6739447116851807 199.59243774414062 0.5229682326316833 277.2996520996094 0.236574187874794 0.7419466 0.35606658458709717 True -11 32976 29.616962432861328 0.694495677947998 160.9395294189453 0.625708818435669 277.0848083496094 0.2368142306804657 0.7450527 0.34916967153549194 True -12 35724 29.606676816940308 0.684476375579834 164.28948974609375 0.4564031660556793 276.73138427734375 0.23869405686855316 0.75362945 0.33285990357398987 True -13 38472 29.616407871246338 0.6796925067901611 208.56272888183594 0.3576887249946594 276.3172607421875 0.2409132719039917 0.7611117 0.31926947832107544 True -14 41220 29.775457859039307 0.7060997486114502 228.15725708007812 0.3400779068470001 276.3050537109375 0.24066261947155 0.7671384 0.31125780940055847 True -15 43968 29.709015607833862 0.6920473575592041 195.12222290039062 0.481905996799469 275.8916931152344 0.24316999316215515 0.7721522 0.3070334494113922 True -16 46716 29.631776332855225 0.6952438354492188 202.7143096923828 0.40979743003845215 275.7704772949219 0.24383273720741272 0.7769553 0.3014647364616394 True -17 49464 29.674630641937256 1.117163896560669 186.31382751464844 0.3890282213687897 275.782958984375 0.24358221888542175 0.777907 0.30321580171585083 True -18 52212 29.648436069488525 2.4289114475250244 220.18939208984375 0.2681232690811157 275.6254577636719 0.24465791881084442 0.7799803 0.3079296946525574 True -19 54960 29.572961568832397 0.6799263954162598 198.32667541503906 0.4307655692100525 275.9516296386719 0.24262581765651703 0.77910745 0.31209254264831543 False diff --git a/ENCSR619BNL/cherimoya.fold_1.performance.tsv b/ENCSR619BNL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 49992d96ef589fccdd55f7850fbaac06dc1ea72c..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.6254577636719 0.5097686052322388 0.24465791881084442 0.07027143985033035 0.7799803018569946 0.7629038095474243 0.3079296946525574 \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_2.evaluate.json b/ENCSR619BNL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ad4f77fc8b6e49fe9320303c731a40bf4f5964fb..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF453LUU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_2.fit.json b/ENCSR619BNL/cherimoya.fold_2.fit.json deleted file mode 100644 index 26d9adf672d953f32b78c775ffa2ad056fd279ce..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF453LUU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_2.log b/ENCSR619BNL/cherimoya.fold_2.log deleted file mode 100644 index dea0ac661adee1d4fc5ab8e3f99045a5419ba531..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2911 36.79461717605591 4.261000156402588 238.01039123535156 0.7315444946289062 265.95294189453125 0.1434628665447235 0.5544253 3.0707619190216064 True -1 5822 31.960612535476685 0.5982069969177246 181.94268798828125 0.7364654541015625 256.44097900390625 0.1979239583015442 0.6491916 0.8331871032714844 True -2 8733 31.95778727531433 0.5752205848693848 181.29551696777344 0.46785277128219604 254.47787475585938 0.20481997728347778 0.656502 0.5085832476615906 True -3 11644 31.991854429244995 0.628652811050415 208.36488342285156 0.9391154646873474 253.76683044433594 0.20711718499660492 0.67129135 0.5175508260726929 True -4 14555 31.483142137527466 0.7155265808105469 204.20083618164062 0.8026902079582214 253.1228790283203 0.21108631789684296 0.6739181 0.5451532006263733 True -5 17466 31.3446946144104 0.5545868873596191 195.91192626953125 0.5051093101501465 252.2460174560547 0.2159046232700348 0.6763843 0.524252712726593 True -6 20377 31.318567991256714 0.5362873077392578 210.91107177734375 0.5285664200782776 252.02120971679688 0.21678414940834045 0.6807454 0.4903760850429535 True -7 23288 31.303475379943848 0.5869042873382568 204.00596618652344 0.3836175501346588 251.9459991455078 0.21695329248905182 0.6826385 0.4692792594432831 True -8 26199 31.41027307510376 1.2978954315185547 237.6391143798828 0.4479132294654846 251.33335876464844 0.22037991881370544 0.6880264 0.43326547741889954 True -9 29110 31.38341212272644 0.5330467224121094 212.6243896484375 0.413051962852478 251.0789031982422 0.22151291370391846 0.69503194 0.4123489260673523 True -10 32021 31.368228673934937 0.5329761505126953 228.42608642578125 0.4605613350868225 250.78305053710938 0.22295556962490082 0.6990296 0.3859458565711975 True -11 34932 31.386813640594482 7.579455614089966 211.3524169921875 0.5554031133651733 250.38058471679688 0.2249082326889038 0.7054351 0.3699988126754761 True -12 37843 31.317535877227783 20.073030710220337 212.76461791992188 0.4484604001045227 250.29185485839844 0.22550725936889648 0.7128008 0.36355075240135193 True -13 40754 31.751755714416504 0.5319418907165527 191.71917724609375 0.26762381196022034 249.68914794921875 0.22917300462722778 0.7178688 0.3486725389957428 True -14 43665 31.34848976135254 1.2032454013824463 189.39849853515625 0.5059804916381836 249.50650024414062 0.22989298403263092 0.7259882 0.3371313214302063 True -15 46576 31.459573984146118 1.4025661945343018 200.92831420898438 0.442403644323349 249.32296752929688 0.2308894842863083 0.7318777 0.3282478451728821 True -16 49487 31.33210515975952 28.210947036743164 225.55767822265625 0.34014585614204407 249.179443359375 0.23118190467357635 0.7348345 0.32384976744651794 True -17 52398 31.37468647956848 10.5560302734375 187.9017333984375 0.257571280002594 249.29788208007812 0.2308182269334793 0.73834443 0.3231445550918579 True -18 55309 31.692704439163208 0.5274655818939209 185.09185791015625 0.1909148097038269 249.42677307128906 0.2300427258014679 0.7379392 0.3260570466518402 False -19 58220 31.400375843048096 0.5144140720367432 213.4108428955078 0.26119643449783325 249.26963806152344 0.23073862493038177 0.7380038 0.3295145332813263 False diff --git a/ENCSR619BNL/cherimoya.fold_2.performance.tsv b/ENCSR619BNL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6973f1945528d8d55cbaedcfeb618957513d7c6d..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -249.29788208007812 0.522786557674408 0.2308182269334793 0.06145213916897774 0.7383444309234619 0.7088574767112732 0.3231445550918579 \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_3.evaluate.json b/ENCSR619BNL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0439d63c3b70697f6dc185b7e348ad38c7554ef9..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF453LUU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_3.fit.json b/ENCSR619BNL/cherimoya.fold_3.fit.json deleted file mode 100644 index 510337dd1dd8e498cb0a78b83a86377e97da18a5..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF453LUU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_3.log b/ENCSR619BNL/cherimoya.fold_3.log deleted file mode 100644 index b3198bf16ce0949e041ee6e4baa3b520de9f2bfe..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2774 35.37360858917236 3.591627359390259 228.5848846435547 0.8571361303329468 277.165283203125 0.1426069140434265 0.558173 3.420131206512451 True -1 5548 30.472479104995728 0.6621291637420654 187.8623504638672 0.8723617792129517 268.26507568359375 0.19373719394207 0.6337297 1.247334361076355 True -2 8322 30.495764017105103 0.6633198261260986 213.23153686523438 0.36323660612106323 266.1871643066406 0.20214830338954926 0.646499 0.5345912575721741 True -3 11096 30.41506052017212 0.5869154930114746 187.42276000976562 0.42190006375312805 265.26007080078125 0.20620670914649963 0.6601808 0.4915304183959961 True -4 13870 29.89302086830139 0.5856671333312988 216.5100860595703 0.4472922086715698 264.525390625 0.20951445400714874 0.6684808 0.5273995399475098 True -5 16644 29.925880193710327 9.145018100738525 190.3138427734375 0.4325025677680969 264.2607116699219 0.21054889261722565 0.6751218 0.5110831260681152 True -6 19418 29.873459100723267 0.8639142513275146 194.96334838867188 0.5233062505722046 263.9946594238281 0.212091863155365 0.68286705 0.5274067521095276 True -7 22192 29.933326482772827 0.601959228515625 197.4832763671875 0.4966004192829132 263.6313171386719 0.21418017148971558 0.6867713 0.5153309106826782 True -8 24966 30.035595655441284 0.5949432849884033 186.58189392089844 0.5842950344085693 263.4953918457031 0.21507029235363007 0.69197226 0.48051488399505615 True -9 27740 29.873093605041504 0.6442568302154541 211.8203125 0.3813462257385254 263.4319763183594 0.21506430208683014 0.69520694 0.4374449849128723 True -10 30514 29.860339164733887 0.6050262451171875 191.7578125 0.3991333842277527 262.9432373046875 0.21752199530601501 0.70084095 0.4178393483161926 True -11 33288 29.914769172668457 0.5926868915557861 225.814453125 0.4951825737953186 262.3872985839844 0.22039134800434113 0.7087661 0.39436566829681396 True -12 36062 29.847946643829346 0.6001796722412109 202.24862670898438 0.5402514934539795 262.13323974609375 0.22210480272769928 0.7129666 0.3728857636451721 True -13 38836 29.854280471801758 0.5855565071105957 184.79090881347656 0.3595043420791626 261.96197509765625 0.2224842607975006 0.72098684 0.3564206659793854 True -14 41610 29.83745789527893 0.6010606288909912 169.778076171875 0.3149142265319824 261.609130859375 0.2245277315378189 0.72960633 0.341187059879303 True -15 44384 29.862046003341675 0.6067512035369873 175.26580810546875 0.4006246328353882 261.4639587402344 0.22480688989162445 0.73788714 0.32792937755584717 True -16 47158 29.91442632675171 0.5993196964263916 208.87661743164062 0.31289738416671753 261.4820251464844 0.22475391626358032 0.7422635 0.32122400403022766 True -17 49932 29.825503826141357 0.5982978343963623 207.7141876220703 0.3114674985408783 261.63226318359375 0.22429156303405762 0.7438904 0.32376381754875183 True -18 52706 29.943254947662354 21.37444567680359 176.127685546875 0.29139310121536255 261.5425109863281 0.22476261854171753 0.7431224 0.33148759603500366 False -19 55480 29.890578985214233 0.5924732685089111 179.75637817382812 0.29392004013061523 261.7027893066406 0.2238326072692871 0.741316 0.3368341028690338 False diff --git a/ENCSR619BNL/cherimoya.fold_3.performance.tsv b/ENCSR619BNL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 872fe641e5dcc2245538b63042a48766a907d4f0..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -261.63226318359375 0.5207892656326294 0.22429156303405762 0.06349418312311172 0.7438904047012329 0.7154558300971985 0.32376381754875183 \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_4.evaluate.json b/ENCSR619BNL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8e63f6638d7fe456aab539a77a9e2191a4c6576d..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF453LUU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_4.fit.json b/ENCSR619BNL/cherimoya.fold_4.fit.json deleted file mode 100644 index 2778cd17074f3908247b465e825d0b7a7217649e..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF453LUU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_4.log b/ENCSR619BNL/cherimoya.fold_4.log deleted file mode 100644 index be1cd665ded847d9c64da31b8d4758a4ea97b0b0..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 36.37140488624573 3.457519769668579 216.3102264404297 0.6239327788352966 269.89776611328125 0.14354342222213745 0.5238092 3.1531193256378174 True -1 5752 31.597712516784668 1.9253716468811035 165.82321166992188 0.5050287842750549 261.00714111328125 0.19577400386333466 0.62644607 0.9439689517021179 True -2 8628 31.00999426841736 0.5743649005889893 218.75814819335938 0.5326610803604126 259.1804504394531 0.20222258567810059 0.6431707 0.4595947563648224 True -3 11504 30.940669775009155 0.588517427444458 195.69989013671875 0.4749215841293335 258.20941162109375 0.20661471784114838 0.65459025 0.42000412940979004 True -4 14380 30.939356565475464 0.580491304397583 201.54156494140625 0.5418394804000854 257.5425720214844 0.209867924451828 0.66569114 0.4141187071800232 True -5 17256 30.95396327972412 3.5888774394989014 194.08828735351562 0.6147598624229431 257.2659912109375 0.21065817773342133 0.67190295 0.4136406481266022 True -6 20132 30.991623640060425 0.587310791015625 234.60833740234375 0.34492918848991394 256.8877868652344 0.21303755044937134 0.6730528 0.4386444389820099 True -7 23008 30.99232268333435 0.5921342372894287 193.01547241210938 0.4609715938568115 256.5931701660156 0.21419495344161987 0.67899364 0.427209734916687 True -8 25884 31.020551204681396 0.6074163913726807 197.54380798339844 0.7662167549133301 256.2601318359375 0.21644410490989685 0.6833188 0.46666190028190613 True -9 28760 30.946501970291138 0.5826683044433594 234.63491821289062 0.45007243752479553 255.96705627441406 0.217975914478302 0.6882961 0.4127879738807678 True -10 31636 30.993775129318237 0.5833888053894043 180.85604858398438 0.35622715950012207 255.9085235595703 0.21804754436016083 0.6911511 0.4348319470882416 True -11 34512 31.019620656967163 0.5903899669647217 190.31117248535156 0.39436787366867065 255.3032684326172 0.2212817668914795 0.69973505 0.410020649433136 True -12 37388 31.001458883285522 0.6018469333648682 189.83009338378906 0.3927499055862427 255.21742248535156 0.2216622531414032 0.7057911 0.390045702457428 True -13 40264 30.99332332611084 0.5830743312835693 177.40408325195312 0.29641616344451904 254.82110595703125 0.2243814915418625 0.71272016 0.36150217056274414 True -14 43140 30.99644923210144 0.5815191268920898 212.91488647460938 0.3490142226219177 254.62171936035156 0.22535152733325958 0.7231996 0.3463843762874603 True -15 46016 30.98348641395569 0.5770227909088135 189.48089599609375 0.3636757731437683 254.2273406982422 0.22862638533115387 0.73123205 0.32764774560928345 True -16 48892 31.048468351364136 1.5863254070281982 230.630615234375 0.2877836525440216 254.4661102294922 0.22653409838676453 0.73634094 0.31160035729408264 True -17 51768 31.036344289779663 0.573972225189209 194.2615966796875 0.47280505299568176 254.45680236816406 0.22598348557949066 0.7379332 0.313349187374115 True -18 54644 30.97527837753296 0.5825812816619873 206.5438232421875 0.22182857990264893 254.57525634765625 0.2253241240978241 0.7386629 0.314620703458786 True -19 57520 30.979671955108643 0.5895323753356934 220.42510986328125 0.21706265211105347 254.4779052734375 0.2261410653591156 0.7395072 0.31679484248161316 True diff --git a/ENCSR619BNL/cherimoya.fold_4.performance.tsv b/ENCSR619BNL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7e9de4627fee54acfef5f09725f12e45cb9e38d3..0000000000000000000000000000000000000000 --- a/ENCSR619BNL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -254.4779052734375 0.5225704908370972 0.2261410802602768 0.06205759570002556 0.7395071983337402 0.7053284645080566 0.31679484248161316 \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_0.evaluate.json b/ENCSR619DRM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 57826560a3e3fbb61bb26ab080fe1f012a1a6dfd..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF128JXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_0.fit.json b/ENCSR619DRM/cherimoya.fold_0.fit.json deleted file mode 100644 index c9139e4a0f2397bf9cef7deae9fdbfd07616bc79..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF128JXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_0.log b/ENCSR619DRM/cherimoya.fold_0.log deleted file mode 100644 index c6cb41b426b7040017a7126c3e532afd752b7b2e..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2525 32.288602113723755 3.637477397918701 122.17085266113281 0.49603646993637085 155.3809814453125 0.10631250590085983 0.73428285 2.022005796432495 True -1 5050 27.85729742050171 0.5730633735656738 133.41717529296875 0.30952543020248413 149.27508544921875 0.14874587953090668 0.80173826 0.796095609664917 True -2 7575 27.862154960632324 0.530379056930542 103.54864501953125 0.3747762143611908 146.60430908203125 0.16148988902568817 0.81724876 0.3395286202430725 True -3 10100 27.83636474609375 0.516343355178833 151.19692993164062 0.4291943907737732 145.16690063476562 0.16885797679424286 0.82435256 0.278793066740036 True -4 12625 27.845194339752197 0.5205793380737305 122.925048828125 0.30541712045669556 144.7985382080078 0.1699552834033966 0.8282455 0.26351645588874817 True -5 15150 28.039113521575928 0.5258975028991699 125.98298645019531 0.355053186416626 144.2924346923828 0.17359612882137299 0.8311851 0.25916966795921326 True -6 17675 27.30425763130188 1.1733012199401855 113.08920288085938 0.3466159403324127 144.06979370117188 0.17449885606765747 0.83589345 0.24357964098453522 True -7 20200 27.335906744003296 0.7262849807739258 126.52816772460938 0.33427324891090393 143.81068420410156 0.17643101513385773 0.8356044 0.2484336495399475 False -8 22725 27.347188234329224 0.5295817852020264 114.08822631835938 0.25370731949806213 143.39979553222656 0.17912545800209045 0.8405127 0.24151794612407684 True -9 25250 27.286388635635376 0.5280327796936035 118.29071044921875 0.24031519889831543 143.18316650390625 0.180311918258667 0.84319156 0.23531176149845123 True -10 27775 27.33319902420044 0.5241434574127197 114.65727233886719 0.2804908752441406 143.12814331054688 0.18089964985847473 0.84530306 0.2299748957157135 True -11 30300 27.28073477745056 0.5208415985107422 123.87016296386719 0.36053186655044556 142.78353881835938 0.18275023996829987 0.8493528 0.22907619178295135 True -12 32825 27.298218250274658 0.5269107818603516 103.35597229003906 0.32910001277923584 142.66293334960938 0.18409912288188934 0.8528368 0.22568994760513306 True -13 35350 27.316052675247192 0.516085147857666 129.2877655029297 0.22068503499031067 142.33616638183594 0.18617860972881317 0.8570706 0.2165103405714035 True -14 37875 27.318792819976807 0.5116441249847412 118.09451293945312 0.35955992341041565 142.08157348632812 0.1877109259366989 0.8592192 0.21313904225826263 True -15 40400 27.321036338806152 0.533682107925415 111.55361938476562 0.2643447518348694 142.0055694580078 0.18811166286468506 0.86306393 0.2107250839471817 True -16 42925 27.331148147583008 0.5310158729553223 98.51859283447266 0.22618968784809113 142.09201049804688 0.18707647919654846 0.86792165 0.20381172001361847 True -17 45450 27.517329692840576 1.0745849609375 106.7522201538086 0.22703734040260315 142.0564727783203 0.18715181946754456 0.8665509 0.20244787633419037 False -18 47975 27.541163682937622 7.237151145935059 136.4177703857422 0.16232705116271973 142.10874938964844 0.1865251064300537 0.8660355 0.20170220732688904 False -19 50500 27.64778757095337 0.5339820384979248 121.83505249023438 0.22463536262512207 142.05712890625 0.18719592690467834 0.8662084 0.20295922458171844 False diff --git a/ENCSR619DRM/cherimoya.fold_0.performance.tsv b/ENCSR619DRM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 85a1434915bf1dcc10623c0890a90eeb34bffa5c..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -142.09201049804688 0.5764842629432678 0.18707644939422607 0.03523840010166168 0.8679216504096985 0.7983620762825012 0.20381172001361847 \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_1.evaluate.json b/ENCSR619DRM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c6578316d928e6e62e521a20997e8cb41e30e95a..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF128JXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_1.fit.json b/ENCSR619DRM/cherimoya.fold_1.fit.json deleted file mode 100644 index e37f74b450e06cea798822506b6ce545e0dd1ccc..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF128JXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_1.log b/ENCSR619DRM/cherimoya.fold_1.log deleted file mode 100644 index 04e427361a9df469b8c55d9f78d69c011f272d9d..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2481 32.01983189582825 4.374411344528198 123.14737701416016 0.5181432962417603 183.89126586914062 0.11793835461139679 0.7267321 2.7060461044311523 True -1 4962 27.321976900100708 0.8083095550537109 125.32418823242188 0.42754703760147095 175.5232696533203 0.16772443056106567 0.80378807 0.8192252516746521 True -2 7443 27.430397033691406 0.6671497821807861 124.649658203125 0.40504851937294006 172.17352294921875 0.18239732086658478 0.8209774 0.3791913092136383 True -3 9924 27.377949237823486 0.8067121505737305 116.15353393554688 0.32277023792266846 170.97488403320312 0.18576335906982422 0.8275748 0.3624267578125 True -4 12405 27.0140700340271 1.3667311668395996 102.76079559326172 0.33957234025001526 169.65206909179688 0.19183851778507233 0.8323983 0.3399450480937958 True -5 14886 26.8037531375885 0.7210040092468262 117.28050231933594 0.33210253715515137 169.18438720703125 0.19405823945999146 0.83663934 0.3389759659767151 True -6 17367 26.81397581100464 0.6470880508422852 105.63926696777344 0.26804661750793457 168.657470703125 0.19709466397762299 0.8396141 0.34863510727882385 True -7 19848 26.79077982902527 0.6386828422546387 105.28231811523438 0.23432877659797668 168.29515075683594 0.19911529123783112 0.84432936 0.3466547131538391 True -8 22329 26.811348915100098 1.444176435470581 121.1169662475586 0.35680073499679565 168.00064086914062 0.20082883536815643 0.8468082 0.33085304498672485 True -9 24810 26.884671926498413 0.674116849899292 118.33355712890625 0.363890141248703 167.5506591796875 0.20354759693145752 0.85054326 0.32209229469299316 True -10 27291 26.859752893447876 0.6283042430877686 126.4759521484375 0.37843820452690125 167.3622589111328 0.2045358270406723 0.8556742 0.30761271715164185 True -11 29772 26.885361671447754 0.6474847793579102 134.520751953125 0.17572294175624847 166.98269653320312 0.20668520033359528 0.8593941 0.2962346374988556 True -12 32253 26.86787486076355 1.7934491634368896 127.45968627929688 0.23271028697490692 166.65673828125 0.20835207402706146 0.86228824 0.27560505270957947 True -13 34734 26.846126079559326 0.6578035354614258 108.17042541503906 0.22965949773788452 166.4322967529297 0.20872944593429565 0.8680804 0.2606258988380432 True -14 37215 26.81456184387207 0.6341447830200195 127.28181457519531 0.40587079524993896 166.2087860107422 0.21008211374282837 0.86948806 0.2514902353286743 True -15 39696 26.867392778396606 0.6713724136352539 107.80783081054688 0.2763116657733917 166.2673797607422 0.2090664654970169 0.8721148 0.2385895848274231 True -16 42177 26.82684588432312 1.150763750076294 132.49380493164062 0.22206923365592957 165.95870971679688 0.21108469367027283 0.87301713 0.23372454941272736 True -17 44658 26.858991861343384 17.055590867996216 132.51580810546875 0.2015499472618103 165.98291015625 0.21068428456783295 0.874164 0.2298525720834732 True -18 47139 26.890400171279907 0.6730241775512695 115.93052673339844 0.17620733380317688 166.13768005371094 0.20991764962673187 0.8735544 0.22895321249961853 False -19 49620 26.841654539108276 0.6467804908752441 112.49620056152344 0.20014908909797668 166.36639404296875 0.20846720039844513 0.8728397 0.22935520112514496 False diff --git a/ENCSR619DRM/cherimoya.fold_1.performance.tsv b/ENCSR619DRM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f7c8ab5714818af87ad0f98b4b1ccc93932a1d5a..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -165.98291015625 0.558973491191864 0.21068423986434937 0.0467916876077652 0.8741639852523804 0.8326051831245422 0.2298525720834732 \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_2.evaluate.json b/ENCSR619DRM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 445b4b2e6f72dec734722d5df2a554ccd76db5a4..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF128JXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_2.fit.json b/ENCSR619DRM/cherimoya.fold_2.fit.json deleted file mode 100644 index 934569f297e5e4d19e9ce3dac8910eb2a7c3032e..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF128JXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_2.log b/ENCSR619DRM/cherimoya.fold_2.log deleted file mode 100644 index de870f027d28a8c10579ee9e4bc1b438bee8f4fb..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2642 33.590864181518555 3.8573832511901855 127.25992584228516 0.3373459577560425 159.91102600097656 0.11208982020616531 0.7291075 1.8558868169784546 True -1 5284 29.401151180267334 0.5323734283447266 121.19172668457031 0.27357184886932373 152.8496856689453 0.15712834894657135 0.80166054 0.6665002107620239 True -2 7926 29.124497413635254 0.5093889236450195 98.7371826171875 0.3528771698474884 149.86863708496094 0.1702083796262741 0.8189702 0.3219543695449829 True -3 10568 29.14764165878296 0.4960494041442871 140.12216186523438 0.36997127532958984 148.8391876220703 0.17450310289859772 0.8271218 0.2652817964553833 True -4 13210 29.113163232803345 1.6301801204681396 122.73698425292969 0.3421385884284973 148.4130096435547 0.17644204199314117 0.8313806 0.26211848855018616 True -5 15852 29.18957209587097 0.5074901580810547 130.58473205566406 0.24858331680297852 147.9437713623047 0.17954061925411224 0.83452153 0.2463604062795639 True -6 18494 29.147403717041016 0.5010569095611572 120.68754577636719 0.28744596242904663 147.61679077148438 0.18086159229278564 0.83926547 0.24875852465629578 True -7 21136 29.08874821662903 0.5054371356964111 105.70325469970703 0.288570761680603 147.45933532714844 0.18173328042030334 0.84044665 0.24569463729858398 True -8 23778 29.071592807769775 0.5028824806213379 109.26113891601562 0.19422289729118347 147.08523559570312 0.1842058002948761 0.8441322 0.24478213489055634 True -9 26420 29.071939706802368 0.500917911529541 103.3126220703125 0.41502320766448975 146.8990020751953 0.18503312766551971 0.84544444 0.23800034821033478 True -10 29062 29.128456354141235 0.5044825077056885 116.1157455444336 0.3321102261543274 146.7702178955078 0.18567071855068207 0.8489912 0.23692677915096283 True -11 31704 29.10490131378174 0.5051841735839844 102.5721435546875 0.27323830127716064 146.3282470703125 0.18891391158103943 0.85169375 0.23392213881015778 True -12 34346 29.748506546020508 8.23146653175354 137.57493591308594 0.24733640253543854 146.18862915039062 0.18980619311332703 0.85296607 0.22900889813899994 True -13 36988 29.14694905281067 0.505589485168457 98.23824310302734 0.19042612612247467 145.9838409423828 0.19045011699199677 0.85693276 0.22548523545265198 True -14 39630 29.146329164505005 0.6602077484130859 106.89482879638672 0.24433590471744537 145.9386444091797 0.19065915048122406 0.8585126 0.22217565774917603 True -15 42272 29.162896633148193 1.6015658378601074 127.29145812988281 0.15588274598121643 145.8990020751953 0.191025510430336 0.8605723 0.2184319794178009 True -16 44914 28.642026662826538 0.4911842346191406 113.68734741210938 0.15776154398918152 145.88645935058594 0.19118884205818176 0.86241674 0.21635541319847107 True -17 47556 28.58303689956665 0.5065128803253174 132.4777374267578 0.14247570931911469 145.93222045898438 0.19070033729076385 0.8626659 0.21397018432617188 True -18 50198 28.644110441207886 0.5030243396759033 116.78825378417969 0.1657993197441101 146.0734405517578 0.18957383930683136 0.8628311 0.21623091399669647 True -19 52840 28.765549898147583 0.4985470771789551 95.49258422851562 0.18413762748241425 145.978271484375 0.19035887718200684 0.8606128 0.21793296933174133 False diff --git a/ENCSR619DRM/cherimoya.fold_2.performance.tsv b/ENCSR619DRM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2b0a4dd36d566a58b69eac5b7840b028fcfe9531..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -146.0734405517578 0.5737526416778564 0.18957380950450897 0.03863144293427467 0.8628311157226562 0.8085498809814453 0.21623091399669647 \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_3.evaluate.json b/ENCSR619DRM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d773b896e6881bc364a6f0acef89cb65b6574ea1..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF128JXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_3.fit.json b/ENCSR619DRM/cherimoya.fold_3.fit.json deleted file mode 100644 index 24f443dadaa1ea656959d7fccef317187302d461..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF128JXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_3.log b/ENCSR619DRM/cherimoya.fold_3.log deleted file mode 100644 index 56912183dc2cba7d1d13aa1a29562b0fe585f9f0..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2524 34.558258056640625 3.969825506210327 134.30038452148438 0.5126950740814209 161.9523162841797 0.1128629595041275 0.7195459 2.2642834186553955 True -1 5048 27.804781675338745 0.724398136138916 102.99009704589844 0.34865933656692505 155.11766052246094 0.1570875197649002 0.7986745 0.7881551384925842 True -2 7572 27.879531621932983 1.1722526550292969 134.80987548828125 0.3335089385509491 152.5867156982422 0.16756734251976013 0.81618625 0.4075171947479248 True -3 10096 27.856169939041138 0.5105159282684326 124.91958618164062 0.37322545051574707 151.7424774169922 0.17046219110488892 0.8194354 0.3440755605697632 True -4 12620 27.823969841003418 0.5098690986633301 125.03392028808594 0.2703826427459717 151.2676544189453 0.17297188937664032 0.82361925 0.35462626814842224 True -5 15144 27.819215536117554 1.1090776920318604 118.55337524414062 0.35374850034713745 150.74317932128906 0.17633692920207977 0.8302091 0.31748297810554504 True -6 17668 27.86897301673889 0.5020205974578857 122.00312805175781 0.2802939713001251 150.53668212890625 0.17692497372627258 0.83560896 0.31143420934677124 True -7 20192 27.861348390579224 0.5007214546203613 106.13880920410156 0.329787939786911 150.1941375732422 0.1792406290769577 0.8381506 0.31788498163223267 True -8 22716 27.792232036590576 0.49904489517211914 127.224609375 0.32149577140808105 149.9729766845703 0.18062067031860352 0.8435072 0.2912568151950836 True -9 25240 27.91400694847107 0.5112993717193604 102.6181869506836 0.3617934286594391 149.67831420898438 0.18203744292259216 0.84500766 0.28449124097824097 True -10 27764 27.392356395721436 1.3787479400634766 133.65591430664062 0.39833447337150574 149.3817138671875 0.18472298979759216 0.8489037 0.27579793334007263 True -11 30288 27.34510350227356 0.5106289386749268 131.58639526367188 0.2297143042087555 149.16940307617188 0.1856473833322525 0.8526868 0.26468950510025024 True -12 32812 27.34681534767151 0.4987144470214844 134.54107666015625 0.36373114585876465 149.04808044433594 0.1864890158176422 0.85450155 0.2570793330669403 True -13 35336 27.371583938598633 0.5585298538208008 102.69895935058594 0.38153955340385437 148.79232788085938 0.18762318789958954 0.8593663 0.2547711730003357 True -14 37860 27.47076940536499 0.4903583526611328 119.39170837402344 0.26998963952064514 148.67967224121094 0.1879645437002182 0.86358863 0.23979486525058746 True -15 40384 27.32802677154541 0.5129408836364746 129.78631591796875 0.17720898985862732 148.61692810058594 0.1886344850063324 0.867611 0.23211193084716797 True -16 42908 27.339897871017456 1.6007568836212158 121.06291198730469 0.2664625346660614 148.4678497314453 0.1902836263179779 0.8675214 0.22611552476882935 False -17 45432 27.34673523902893 0.506248950958252 124.55848693847656 0.20416930317878723 148.58770751953125 0.18881286680698395 0.87032187 0.22210101783275604 True -18 47956 27.30448079109192 0.4998607635498047 132.37286376953125 0.18731778860092163 148.675537109375 0.18819798529148102 0.86807 0.22235803306102753 False -19 50480 27.38682246208191 7.402972221374512 99.71485900878906 0.2927333414554596 148.58848571777344 0.18904976546764374 0.86800075 0.2247074842453003 False diff --git a/ENCSR619DRM/cherimoya.fold_3.performance.tsv b/ENCSR619DRM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7c9340bc526fcad09062ac405467e54af7c03ab7..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -148.58770751953125 0.5737398862838745 0.18881285190582275 0.03530236706137657 0.8703218698501587 0.8004369735717773 0.22210101783275604 \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_4.evaluate.json b/ENCSR619DRM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ce477dde56e0b5da1ad4c26c5f7b8a4aba1cf631..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF128JXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_4.fit.json b/ENCSR619DRM/cherimoya.fold_4.fit.json deleted file mode 100644 index f3f79028483553dfdb5d93568336c84b460a8377..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF128JXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619DRM/cherimoya.fold_4.log b/ENCSR619DRM/cherimoya.fold_4.log deleted file mode 100644 index 381499fad71f2da41eeff336a14fd15e1abd5830..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2568 33.08240509033203 4.193660259246826 120.37184143066406 0.3093528151512146 150.0838623046875 0.10841946303844452 0.7200693 2.0486485958099365 True -1 5136 28.24617862701416 0.6051406860351562 131.23670959472656 0.43643903732299805 144.4883270263672 0.14563719928264618 0.7878443 0.6357266306877136 True -2 7704 28.25993299484253 1.7017710208892822 104.27598571777344 0.3805418610572815 142.4205322265625 0.15589484572410583 0.806169 0.28550273180007935 True -3 10272 28.233843326568604 0.5387446880340576 124.36952209472656 0.3488333821296692 141.28286743164062 0.16129370033740997 0.815845 0.23324967920780182 True -4 12840 28.128490686416626 0.538841724395752 130.67999267578125 0.34107816219329834 140.8077850341797 0.16412702202796936 0.8222835 0.22703465819358826 True -5 15408 27.722880601882935 0.5546951293945312 104.77821350097656 0.4185076951980591 140.35018920898438 0.1675858348608017 0.8265887 0.22656650841236115 True -6 17976 27.69043231010437 0.5593881607055664 146.9889678955078 0.41682499647140503 140.04443359375 0.17010390758514404 0.82937187 0.2250746488571167 True -7 20544 27.775505781173706 9.778820037841797 108.18900299072266 0.36455976963043213 139.80752563476562 0.1713482290506363 0.8331006 0.2198859602212906 True -8 23112 27.757218599319458 0.5489301681518555 131.5926971435547 0.37310367822647095 139.7961883544922 0.17137469351291656 0.83451205 0.22780871391296387 True -9 25680 27.71461820602417 0.540452241897583 137.52322387695312 0.3083750009536743 139.3272247314453 0.17450113594532013 0.8368001 0.21815802156925201 True -10 28248 27.699224948883057 0.5499267578125 110.67604064941406 0.24427103996276855 139.2777099609375 0.17467105388641357 0.84403175 0.21314017474651337 True -11 30816 27.763325214385986 0.5662238597869873 117.9678955078125 0.34642109274864197 138.91702270507812 0.1776057630777359 0.8468423 0.21624526381492615 True -12 33384 27.801275968551636 0.5588719844818115 96.25186157226562 0.3073631525039673 138.71298217773438 0.17865779995918274 0.8498283 0.21602851152420044 True -13 35952 27.83017587661743 0.5517003536224365 149.83236694335938 0.18029314279556274 138.60675048828125 0.17931844294071198 0.8509483 0.21446354687213898 True -14 38520 27.85780930519104 0.5468573570251465 92.67820739746094 0.28618597984313965 138.54733276367188 0.17905934154987335 0.8535884 0.2134656012058258 True -15 41088 27.779967546463013 0.55324387550354 109.8866958618164 0.1286858320236206 138.4356231689453 0.17997823655605316 0.858628 0.2038709968328476 True -16 43656 27.78071689605713 0.9701628684997559 112.95645904541016 0.2940727174282074 138.374755859375 0.18051213026046753 0.86194307 0.20236223936080933 True -17 46224 27.870177268981934 9.163371086120605 127.01385498046875 0.19296032190322876 138.37252807617188 0.180670827627182 0.86318344 0.19870486855506897 True -18 48792 27.796133756637573 0.5539548397064209 98.66633605957031 0.21750080585479736 138.5373077392578 0.17953570187091827 0.86238354 0.19853131473064423 False -19 51360 27.7747859954834 0.5378282070159912 102.4803466796875 0.23007455468177795 138.5706329345703 0.17960962653160095 0.8624823 0.19809412956237793 False diff --git a/ENCSR619DRM/cherimoya.fold_4.performance.tsv b/ENCSR619DRM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d2f5a4f19c854ae85255b3bfed7e7e0406fbddbd..0000000000000000000000000000000000000000 --- a/ENCSR619DRM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -138.37252807617188 0.5804300308227539 0.1806708127260208 0.03440267965197563 0.8631834387779236 0.7918103337287903 0.19870486855506897 \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_0.evaluate.json b/ENCSR619LHF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3d4490ba72298a67a69840fc90b3fbfabfd4399a..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF611ADI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_0.fit.json b/ENCSR619LHF/cherimoya.fold_0.fit.json deleted file mode 100644 index 0e3f7e2e256ac4ff36871332b2d8d124cf47da24..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF611ADI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_0.log b/ENCSR619LHF/cherimoya.fold_0.log deleted file mode 100644 index 49f258f2508c207749ed0bc18d173e216ec84492..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2607 34.052979469299316 6.27888035774231 458.8228759765625 0.3498976230621338 689.4322509765625 0.6846351027488708 0.63134056 4.724050045013428 True -1 5214 28.416418313980103 0.559950590133667 527.9861450195312 0.24494865536689758 602.0818481445312 0.7489970326423645 0.7237019 0.7056558132171631 True -2 7821 28.391448497772217 0.5241384506225586 514.2679443359375 0.1870822161436081 580.4701538085938 0.765354335308075 0.7537924 0.24585917592048645 True -3 10428 28.357890367507935 0.5242147445678711 491.9503479003906 0.28868407011032104 576.2730102539062 0.7685688734054565 0.764269 0.2544206380844116 True -4 13035 28.36802315711975 0.5267302989959717 579.7882690429688 0.23518338799476624 574.7702026367188 0.7693220376968384 0.7713992 0.2324819266796112 True -5 15642 28.334176540374756 0.529308557510376 530.734375 0.1924145519733429 573.2507934570312 0.7713373899459839 0.7787194 0.21938161551952362 True -6 18249 28.3924822807312 0.6638162136077881 508.4534912109375 0.16675838828086853 573.2742309570312 0.7723779082298279 0.7740807 0.29585587978363037 False -7 20856 28.412237882614136 0.5297307968139648 552.2066040039062 0.2381039559841156 571.1025390625 0.7748091816902161 0.7850777 0.24643507599830627 True -8 23463 28.47155475616455 0.5339648723602295 519.7967529296875 0.1898484230041504 569.3419189453125 0.7763349413871765 0.78982294 0.22002770006656647 True -9 26070 28.387192249298096 29.220842838287354 517.322265625 0.15856590867042542 567.7870483398438 0.7776076793670654 0.7970477 0.2057826817035675 True -10 28677 29.466217041015625 0.5288610458374023 540.925048828125 0.1580619513988495 566.6950073242188 0.7788456678390503 0.8005641 0.19801108539104462 True -11 31284 28.45453453063965 0.5307199954986572 501.4604797363281 0.1748484969139099 565.4717407226562 0.7800869941711426 0.80669755 0.19352392852306366 True -12 33891 28.74916410446167 2.852354049682617 520.7816162109375 0.1819533109664917 564.60986328125 0.7811001539230347 0.8119193 0.1861158311367035 True -13 36498 28.994609832763672 0.5331974029541016 501.45062255859375 0.12677866220474243 563.7273559570312 0.7820035815238953 0.8152203 0.17812694609165192 True -14 39105 28.338018894195557 0.5294137001037598 455.2706604003906 0.1661618947982788 562.8754272460938 0.783001184463501 0.8206484 0.17403778433799744 True -15 41712 28.491430044174194 0.5331788063049316 480.0323486328125 0.13638092577457428 562.5219116210938 0.7834697365760803 0.82383347 0.16776558756828308 True -16 44319 28.35838484764099 0.5263690948486328 517.9132080078125 0.16771955788135529 562.290283203125 0.7837646007537842 0.82602876 0.1629580557346344 True -17 46926 28.398045301437378 14.818178176879883 502.12322998046875 0.10295869410037994 562.3318481445312 0.7835909128189087 0.82388 0.16127488017082214 False -18 49533 28.42766261100769 0.5234289169311523 503.3271789550781 0.0979699045419693 562.6137084960938 0.7833933234214783 0.8215284 0.16230414807796478 False -19 52140 28.33201575279236 16.63804054260254 522.8204345703125 0.08865383267402649 562.8519897460938 0.7831894755363464 0.81831616 0.16393540799617767 False diff --git a/ENCSR619LHF/cherimoya.fold_0.performance.tsv b/ENCSR619LHF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cc4d881483ad255dc3b7cb3a30314cf986964559..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -562.290283203125 0.17488698661327362 0.7837645411491394 0.4170974791049957 0.8260287642478943 0.7620465755462646 0.1629580557346344 \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_1.evaluate.json b/ENCSR619LHF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a7c5fc29124e678c3686b3f3ae2d2735f6d0982a..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF611ADI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_1.fit.json b/ENCSR619LHF/cherimoya.fold_1.fit.json deleted file mode 100644 index 55423616aab836e24c5b19f589c447282062bb2d..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF611ADI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_1.log b/ENCSR619LHF/cherimoya.fold_1.log deleted file mode 100644 index eb7e8c52e44eba6a86cd24fbc8ddd782867f0353..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2566 32.48835301399231 3.6643271446228027 525.22802734375 0.32934892177581787 796.6590576171875 0.6934200525283813 0.63433796 6.588791370391846 True -1 5132 27.949531316757202 0.6811871528625488 532.3626098632812 0.21840626001358032 677.2112426757812 0.7675755023956299 0.7320327 0.9780329465866089 True -2 7698 27.93983745574951 0.6570043563842773 481.4701232910156 0.22876539826393127 655.8522338867188 0.7824680209159851 0.7527849 0.40564221143722534 True -3 10264 27.948322534561157 0.6529486179351807 503.9604187011719 0.2280065268278122 647.8211059570312 0.78707355260849 0.7668702 0.2960962951183319 True -4 12830 27.924514293670654 0.6671757698059082 456.3531494140625 0.1812599152326584 645.2911376953125 0.7886818051338196 0.77535486 0.3328922688961029 True -5 15396 27.9003803730011 30.777162313461304 557.23828125 0.2832897901535034 642.2814331054688 0.7908830642700195 0.7836112 0.28262457251548767 True -6 17962 33.953978300094604 0.9133970737457275 509.5838623046875 0.2147623598575592 641.1119384765625 0.7920076251029968 0.7860354 0.26830974221229553 True -7 20528 28.096190452575684 12.364577293395996 496.75299072265625 0.20966185629367828 639.1469116210938 0.7939295172691345 0.7900141 0.2611042559146881 True -8 23094 27.972772359848022 0.6750352382659912 461.57598876953125 0.21553179621696472 637.8040161132812 0.7953606843948364 0.79552764 0.25945714116096497 True -9 25660 27.938801527023315 0.6578831672668457 490.50238037109375 0.1944168359041214 635.8916625976562 0.7967633605003357 0.7985452 0.24669483304023743 True -10 28226 27.989248275756836 8.466838598251343 492.6410827636719 0.12385427951812744 634.1181030273438 0.798116147518158 0.80901486 0.2388373613357544 True -11 30792 27.98098874092102 0.6735012531280518 542.4610595703125 0.10705749690532684 632.5195922851562 0.7996408343315125 0.81263614 0.23841674625873566 True -12 33358 28.505094528198242 0.6660764217376709 535.5875854492188 0.12408864498138428 631.0418701171875 0.8007043600082397 0.81946254 0.21743245422840118 True -13 35924 27.91390109062195 3.229682445526123 509.7178039550781 0.11793629825115204 629.8106079101562 0.8018526434898376 0.8266967 0.21409842371940613 True -14 38490 27.95351767539978 0.6628842353820801 486.8044738769531 0.12110382318496704 629.068115234375 0.8025805950164795 0.83113754 0.20517368614673615 True -15 41056 27.957006454467773 0.6526870727539062 532.9393920898438 0.10450237989425659 628.4188842773438 0.8031547665596008 0.83358806 0.1994018852710724 True -16 43622 27.9352068901062 7.386436223983765 487.8647155761719 0.14589400589466095 628.4367065429688 0.8031014204025269 0.83283794 0.19395430386066437 False -17 46188 27.927274227142334 0.6657862663269043 512.541015625 0.10141372680664062 629.0092163085938 0.802645742893219 0.8324869 0.19420921802520752 False -18 48754 27.98570966720581 0.6587677001953125 483.3572998046875 0.0742373988032341 629.5975341796875 0.8022128343582153 0.82801676 0.1958230882883072 False -19 51320 27.995567083358765 47.37875008583069 522.0604248046875 0.14716243743896484 629.7171630859375 0.8019834160804749 0.8254716 0.19761082530021667 False diff --git a/ENCSR619LHF/cherimoya.fold_1.performance.tsv b/ENCSR619LHF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 963c147cee1a86df7529e77a198b92c827040133..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -628.4188842773438 0.15848036110401154 0.8031547665596008 0.4564021825790405 0.8335880637168884 0.7883637547492981 0.1994018852710724 \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_2.evaluate.json b/ENCSR619LHF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1fb7228869b99e7a3964dbd335a674df1695fcd5..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF611ADI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_2.fit.json b/ENCSR619LHF/cherimoya.fold_2.fit.json deleted file mode 100644 index 41b4d444a06850209f693272b92c5aa34f5f6977..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF611ADI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_2.log b/ENCSR619LHF/cherimoya.fold_2.log deleted file mode 100644 index 3cf103ac03662f1cd7548cff85442ce023d30ae2..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 34.25027537345886 3.4410810470581055 541.1590576171875 0.2629082202911377 705.182861328125 0.6942981481552124 0.63213414 4.370562553405762 True -1 5458 29.773476123809814 0.535722017288208 550.8509521484375 0.2769871950149536 615.6375732421875 0.7568297982215881 0.74832594 0.6365770697593689 True -2 8187 29.73877453804016 0.5250627994537354 527.011962890625 0.2455475926399231 600.8116455078125 0.7685890793800354 0.76776874 0.2718683183193207 True -3 10916 29.688032150268555 20.14868187904358 505.19390869140625 0.21535073220729828 595.4505004882812 0.7717239856719971 0.7787658 0.21976806223392487 True -4 13645 33.48506784439087 0.5198957920074463 567.6951293945312 0.2226249724626541 593.6657104492188 0.7730949521064758 0.7865897 0.2502342462539673 True -5 16374 29.7397940158844 0.5298397541046143 590.2334594726562 0.22018861770629883 593.2196655273438 0.772891640663147 0.7882119 0.23219960927963257 True -6 19103 29.98441219329834 0.5194456577301025 557.3742065429688 0.21426637470722198 592.0408935546875 0.7754026055335999 0.7918577 0.23303496837615967 True -7 21832 29.714776754379272 0.5223038196563721 558.2196655273438 0.18909130990505219 590.4785766601562 0.7767193913459778 0.7967229 0.23272067308425903 True -8 24561 29.796082019805908 0.5395417213439941 515.69140625 0.16633890569210052 589.0657958984375 0.7780033349990845 0.79913855 0.2273423969745636 True -9 27290 29.731480836868286 0.5344536304473877 534.437744140625 0.2684350907802582 587.752197265625 0.7789647579193115 0.80182 0.218507319688797 True -10 30019 29.75616145133972 0.5368382930755615 528.7213134765625 0.164727121591568 586.257080078125 0.7801748514175415 0.8058839 0.20387671887874603 True -11 32748 29.68733835220337 0.5123236179351807 511.03826904296875 0.264016330242157 585.2567749023438 0.7811479568481445 0.81255627 0.20560027658939362 True -12 35477 30.516090154647827 3.337212562561035 456.6433410644531 0.08972729742527008 583.869873046875 0.7823147177696228 0.8148308 0.18863262236118317 True -13 38206 29.831876754760742 24.353721380233765 469.8125 0.14116200804710388 582.8653564453125 0.7831956744194031 0.82146627 0.18171928822994232 True -14 40935 31.71828269958496 15.838215351104736 495.44580078125 0.10903167724609375 582.1421508789062 0.7841075658798218 0.82345927 0.18092259764671326 True -15 43664 29.870062112808228 0.5217840671539307 527.7572021484375 0.12605711817741394 581.7910766601562 0.7847608923912048 0.824433 0.17556504905223846 True -16 46393 29.844158172607422 1.1752712726593018 522.9454345703125 0.10896887630224228 581.4448852539062 0.7849660515785217 0.8256596 0.17174355685710907 True -17 49122 29.732221841812134 0.5219943523406982 483.42730712890625 0.14258494973182678 581.7798461914062 0.7848328351974487 0.8239861 0.17199039459228516 False -18 51851 29.73319911956787 2.149553060531616 521.0010375976562 0.09567667543888092 582.2465209960938 0.7844294309616089 0.819115 0.17361755669116974 False -19 54580 29.725085258483887 0.5216162204742432 489.9549255371094 0.0780797004699707 582.4566650390625 0.7843209505081177 0.8189077 0.17487601935863495 False diff --git a/ENCSR619LHF/cherimoya.fold_2.performance.tsv b/ENCSR619LHF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7fa9d7c1013c59b018ef44ea7a1cdeddfce7b230..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -581.4448852539062 0.1715942770242691 0.7849660515785217 0.4291512668132782 0.8256595730781555 0.7619219422340393 0.17174355685710907 \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_3.evaluate.json b/ENCSR619LHF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a5b2e295a0f2aef3307221f93e5fc160ffff1901..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF611ADI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_3.fit.json b/ENCSR619LHF/cherimoya.fold_3.fit.json deleted file mode 100644 index bc7c5fe75c6847e1e7a676fe9ab22ea4ddc28ee1..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF611ADI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_3.log b/ENCSR619LHF/cherimoya.fold_3.log deleted file mode 100644 index bb1c06a0ede9e8f4f7f0b30bfa0af1cfb79ba80d..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2617 33.020169734954834 5.656620740890503 512.5276489257812 0.22735244035720825 707.5965576171875 0.6844879984855652 0.6269014 6.837550640106201 True -1 5234 28.506120920181274 0.5690772533416748 540.1865234375 0.43389788269996643 610.2062377929688 0.7529392838478088 0.7166871 0.9813053607940674 True -2 7851 28.616831064224243 0.5358450412750244 552.3021240234375 0.32141685485839844 593.66015625 0.7661499381065369 0.738787 0.32715103030204773 True -3 10468 28.46140742301941 0.5340197086334229 475.1474914550781 0.19781291484832764 588.6782836914062 0.7698445916175842 0.749018 0.31955400109291077 True -4 13085 28.468849658966064 0.5348780155181885 526.1646728515625 0.24472001194953918 585.8535766601562 0.7723150253295898 0.756956 0.3130212426185608 True -5 15702 28.451788187026978 0.5314640998840332 524.1633911132812 0.24361863732337952 588.0933837890625 0.7691523432731628 0.7575471 0.3272925317287445 True -6 18319 28.451412677764893 2.2078068256378174 557.5283203125 0.3147609829902649 583.6851806640625 0.7742878198623657 0.75987613 0.27045273780822754 True -7 20936 30.353947162628174 22.588184356689453 531.8215942382812 0.24895945191383362 582.39697265625 0.7750373482704163 0.76063216 0.26665183901786804 True -8 23553 28.654115676879883 1.2320587635040283 551.3089599609375 0.13620252907276154 581.0960693359375 0.7771633863449097 0.7700792 0.275576114654541 True -9 26170 28.700940370559692 0.556739330291748 545.7340698242188 0.20524638891220093 579.8560180664062 0.7779720425605774 0.7683805 0.2512326240539551 False -10 28787 28.591776609420776 0.5529665946960449 531.5106201171875 0.15137162804603577 578.6373291015625 0.7794541716575623 0.7683874 0.2543060779571533 False -11 31404 28.47389554977417 1.5797271728515625 513.5689697265625 0.207103431224823 577.2515258789062 0.7810003161430359 0.7780419 0.24801500141620636 True -12 34021 28.56077003479004 0.54593825340271 517.743408203125 0.18970246613025665 576.3031616210938 0.782145619392395 0.7835139 0.23370857536792755 True -13 36638 28.560823440551758 0.5415291786193848 550.8071899414062 0.12622316181659698 575.1920166015625 0.7833335399627686 0.78807324 0.2396090179681778 True -14 39255 28.617862701416016 0.5432660579681396 501.9473571777344 0.16427189111709595 574.17431640625 0.7841573357582092 0.79092807 0.22378510236740112 True -15 41872 29.080129861831665 9.059327125549316 572.1085205078125 0.11055053770542145 573.5048217773438 0.7847168445587158 0.79336876 0.2167051136493683 True -16 44489 28.525923252105713 1.0671465396881104 526.3961181640625 0.14987266063690186 573.441162109375 0.7848907709121704 0.7958169 0.21191732585430145 True -17 47106 28.800044536590576 0.5436358451843262 512.095458984375 0.13543398678302765 573.677001953125 0.7847161293029785 0.7920832 0.20809271931648254 False -18 49723 28.73229169845581 2.423955202102661 483.36181640625 0.11932703852653503 573.8461303710938 0.78444904088974 0.7887665 0.20920774340629578 False -19 52340 28.718449354171753 0.7074465751647949 511.40380859375 0.12268659472465515 573.900390625 0.7842430472373962 0.78740895 0.20958948135375977 False diff --git a/ENCSR619LHF/cherimoya.fold_3.performance.tsv b/ENCSR619LHF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f6bafa3ee6147515e2ad64b4008f3bf45906aac9..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -573.441162109375 0.17332136631011963 0.7848907113075256 0.4204217791557312 0.7958168983459473 0.7325260043144226 0.21191732585430145 \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_4.evaluate.json b/ENCSR619LHF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 13e27200c7b4ef2a60e09b1d2557c7aa4daf715a..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF611ADI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_4.fit.json b/ENCSR619LHF/cherimoya.fold_4.fit.json deleted file mode 100644 index 327dfce98d422f6671399625ebb7e459ffa448e7..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF611ADI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619LHF/cherimoya.fold_4.log b/ENCSR619LHF/cherimoya.fold_4.log deleted file mode 100644 index a6f0ef1e4791361d45aec1dbdb3f1a001112f081..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2646 34.682047605514526 3.4004452228546143 586.6261596679688 0.42210936546325684 675.3386840820312 0.6888329386711121 0.6077466 5.12380313873291 True -1 5292 28.842000246047974 0.5724704265594482 486.7768859863281 0.1723971962928772 589.5133666992188 0.7532214522361755 0.71451306 0.7406130433082581 True -2 7938 28.861884832382202 0.5169696807861328 515.603759765625 0.24149230122566223 574.687744140625 0.7652969360351562 0.74200314 0.2758835554122925 True -3 10584 28.801384925842285 0.5243983268737793 527.2296142578125 0.2292623519897461 570.5638427734375 0.7686113715171814 0.7540277 0.24547088146209717 True -4 13230 28.789957523345947 0.5172102451324463 522.60107421875 0.2359299510717392 568.4906005859375 0.7700533866882324 0.7607248 0.24060316383838654 True -5 15876 28.73963737487793 0.5230069160461426 514.3603515625 0.23003016412258148 567.4033203125 0.7706286311149597 0.7683145 0.20569062232971191 True -6 18522 28.84324860572815 0.52535080909729 518.2523193359375 0.2283259928226471 565.6716918945312 0.7727152705192566 0.7736484 0.19920769333839417 True -7 21168 28.7786648273468 0.5171380043029785 553.4715576171875 0.1878809630870819 564.68408203125 0.773786187171936 0.77847 0.19642305374145508 True -8 23814 28.83623957633972 0.5221455097198486 502.2972717285156 0.2008177489042282 563.468017578125 0.7748963236808777 0.7833324 0.19195055961608887 True -9 26460 28.698147535324097 1.461348533630371 506.8473815917969 0.1603320837020874 562.1659545898438 0.7764043211936951 0.7871834 0.1853136569261551 True -10 29106 28.928466081619263 0.5227680206298828 472.22247314453125 0.19047746062278748 561.2166137695312 0.777511477470398 0.79262245 0.17898166179656982 True -11 31752 28.931456089019775 0.5208616256713867 538.506591796875 0.15297651290893555 560.1373291015625 0.7788292169570923 0.79858035 0.17530439794063568 True -12 34398 28.79035472869873 0.5188674926757812 538.21826171875 0.16456930339336395 559.2252807617188 0.7797738313674927 0.8046022 0.1723421961069107 True -13 37044 28.967238426208496 0.5222046375274658 544.2587890625 0.13135294616222382 558.3032836914062 0.7807204723358154 0.80765146 0.16665714979171753 True -14 39690 28.93309450149536 0.5199451446533203 526.03564453125 0.1770511269569397 557.4771118164062 0.7820203900337219 0.81034386 0.16720867156982422 True -15 42336 29.12226390838623 0.5199840068817139 494.9562072753906 0.10045990347862244 556.881103515625 0.7825576066970825 0.8146682 0.1626027375459671 True -16 44982 30.139578580856323 10.180086135864258 462.99957275390625 0.07439295947551727 556.9544067382812 0.7826511263847351 0.8175489 0.16022469103336334 True -17 47628 29.008235931396484 0.5310940742492676 502.6171875 0.12474745512008667 557.015380859375 0.782555103302002 0.81511456 0.15956932306289673 False -18 50274 28.85574173927307 16.65730595588684 475.10052490234375 0.10529317706823349 557.4605712890625 0.7821512222290039 0.81137127 0.1620839685201645 False -19 52920 29.03348135948181 0.5151731967926025 454.2777099609375 0.06393377482891083 557.7200317382812 0.7819267511367798 0.8118245 0.163563072681427 False diff --git a/ENCSR619LHF/cherimoya.fold_4.performance.tsv b/ENCSR619LHF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d182af3b2ea0325f2343d991a16c064785d0625d..0000000000000000000000000000000000000000 --- a/ENCSR619LHF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -556.9544067382812 0.1758359670639038 0.7826511263847351 0.4147137701511383 0.8175488710403442 0.7404418587684631 0.16022469103336334 \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_0.evaluate.json b/ENCSR620QNS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 136f0ba416db6c6de68b09b71c0575cb5c7b0ccc..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF063KLA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_0.fit.json b/ENCSR620QNS/cherimoya.fold_0.fit.json deleted file mode 100644 index d9db4fea11826a915d3a20b9818cc63b7bc3d267..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF063KLA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_0.log b/ENCSR620QNS/cherimoya.fold_0.log deleted file mode 100644 index eab87fc7faf1bcdefc937e2bd687d0ad3b45e8f9..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.626758337020874 4.0657103061676025 1306.912109375 0.9189895391464233 1798.402587890625 0.23224110901355743 0.38405308 6.9809794425964355 True -1 5476 30.236746072769165 0.6554677486419678 1262.9190673828125 0.5280814170837402 1627.7828369140625 0.33934879302978516 0.48284483 2.7154362201690674 True -2 8214 30.1956889629364 0.5043377876281738 1443.8880615234375 0.5995036363601685 1577.7144775390625 0.35938096046447754 0.5428159 1.5893625020980835 True -3 10952 30.17232847213745 0.49922871589660645 1113.6102294921875 0.41367414593696594 1541.362060546875 0.37172093987464905 0.5641743 1.210539698600769 True -4 13690 30.145087242126465 0.5119779109954834 1192.864990234375 0.5754252672195435 1510.210693359375 0.38523486256599426 0.57172424 0.9210577011108398 True -5 16428 30.174124002456665 0.5085461139678955 1110.8419189453125 0.5561965703964233 1500.7330322265625 0.39081335067749023 0.5821681 0.9025286436080933 True -6 19166 30.132046699523926 0.525618314743042 1109.06201171875 0.6657989621162415 1499.106201171875 0.3918761909008026 0.58517814 0.8617936968803406 True -7 21904 30.21261191368103 0.5140163898468018 1098.205322265625 0.6065014600753784 1484.088623046875 0.39761143922805786 0.59776294 0.7798780202865601 True -8 24642 29.62970733642578 0.4953186511993408 1291.430419921875 0.5662272572517395 1474.547607421875 0.403591126203537 0.6054954 0.7635179758071899 True -9 27380 29.58676528930664 0.5059804916381836 1273.4747314453125 0.4320610761642456 1462.1751708984375 0.40982529520988464 0.60859925 0.6912145614624023 True -10 30118 29.650343418121338 0.5022029876708984 1111.8160400390625 0.5352166891098022 1458.5882568359375 0.41259893774986267 0.6089884 0.6435638070106506 True -11 32856 29.666218280792236 0.4946291446685791 1087.7315673828125 0.49149802327156067 1448.13671875 0.4167199432849884 0.6152038 0.626934289932251 True -12 35594 29.633235692977905 0.5004513263702393 976.050537109375 0.5202903747558594 1434.03125 0.4229492247104645 0.62534016 0.5629794001579285 True -13 38332 29.708665132522583 0.5324633121490479 1063.925048828125 0.3044591546058655 1429.8270263671875 0.42430034279823303 0.6361177 0.53229159116745 True -14 41070 29.631767749786377 0.48926782608032227 997.56982421875 0.3439650535583496 1420.3665771484375 0.42949166893959045 0.64663684 0.4720962345600128 True -15 43808 29.658735752105713 0.5216848850250244 1092.951416015625 0.37134844064712524 1416.3232421875 0.4306001663208008 0.66025877 0.4257744252681732 True -16 46546 29.651756048202515 0.4903757572174072 1171.4580078125 0.43332046270370483 1412.2154541015625 0.43259289860725403 0.6679272 0.40629100799560547 True -17 49284 29.692532777786255 2.8686349391937256 1081.61083984375 0.3584963083267212 1411.5438232421875 0.43244218826293945 0.67258877 0.39595410227775574 True -18 52022 29.662952184677124 0.5107543468475342 1089.79443359375 0.38942670822143555 1410.9344482421875 0.43302100896835327 0.67337984 0.39313414692878723 True -19 54760 29.642159461975098 0.5273697376251221 1053.95458984375 0.3235624432563782 1412.486083984375 0.43212535977363586 0.6728136 0.39362195134162903 False diff --git a/ENCSR620QNS/cherimoya.fold_0.performance.tsv b/ENCSR620QNS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c3755be7eb220846ec17e393a520b7ff62bddf89..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1410.9344482421875 0.33583301305770874 0.4330209791660309 0.2085471749305725 0.6733798384666443 0.6526578664779663 0.39313414692878723 \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_1.evaluate.json b/ENCSR620QNS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 267624caa83f0aa62d8800790a4b747411bc68b0..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF063KLA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_1.fit.json b/ENCSR620QNS/cherimoya.fold_1.fit.json deleted file mode 100644 index 02e3117c5a1921815a18db71dace29d9831a2e80..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF063KLA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_1.log b/ENCSR620QNS/cherimoya.fold_1.log deleted file mode 100644 index 32ea1d2f99ed112e64cd06854a2f6e503c59712d..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2776 35.468981981277466 4.9037580490112305 1237.83251953125 0.36751168966293335 1878.4776611328125 0.25015613436698914 0.45766193 5.587201118469238 True -1 5552 30.666245698928833 13.464211702346802 1356.1689453125 0.6967406868934631 1689.4208984375 0.353299081325531 0.52836347 2.379483699798584 True -2 8328 30.641055822372437 1.0312786102294922 1364.1171875 0.9038846492767334 1644.7640380859375 0.3724834620952606 0.6011309 0.9912619590759277 True -3 11104 30.632808685302734 0.632307767868042 1215.285888671875 0.5334304571151733 1606.470947265625 0.38419896364212036 0.6119465 0.9323787093162537 True -4 13880 30.601105451583862 0.6475174427032471 1071.3466796875 0.414531946182251 1584.5008544921875 0.39322274923324585 0.62488115 0.6718466281890869 True -5 16656 30.541234493255615 0.6971616744995117 1150.0230712890625 0.523048996925354 1572.937255859375 0.3984425961971283 0.6254888 0.7143189311027527 True -6 19432 30.03531575202942 0.6450769901275635 1151.8690185546875 0.43674665689468384 1566.8997802734375 0.40133288502693176 0.6271495 0.6617538928985596 True -7 22208 29.977135181427002 0.640350341796875 1160.40771484375 0.6848617792129517 1548.888671875 0.4098401963710785 0.6397241 0.5914807915687561 True -8 24984 29.987807750701904 0.6396417617797852 1175.861328125 0.5082962512969971 1541.855712890625 0.4127063751220703 0.6478052 0.6037970185279846 True -9 27760 29.99867057800293 0.6394219398498535 1068.3648681640625 0.4041944742202759 1527.917236328125 0.42120084166526794 0.6526147 0.5966678261756897 True -10 30536 30.03651261329651 0.6367900371551514 1055.482666015625 0.4523325562477112 1523.5977783203125 0.4240390956401825 0.6617544 0.5863191485404968 True -11 33312 30.027525663375854 26.57883310317993 1146.958251953125 0.626895546913147 1517.681640625 0.42552754282951355 0.6694051 0.5568287372589111 True -12 36088 30.089377403259277 1.2371790409088135 1278.43017578125 0.7774378657341003 1509.501953125 0.42991605401039124 0.6771333 0.5380959510803223 True -13 38864 30.139448642730713 0.6501708030700684 1207.415283203125 0.6208287477493286 1503.9586181640625 0.43282651901245117 0.6878107 0.5005782842636108 True -14 41640 30.066282033920288 0.6484479904174805 1112.057861328125 0.33574873208999634 1495.30517578125 0.4366146922111511 0.6953071 0.46206656098365784 True -15 44416 30.05737590789795 1.3075039386749268 1207.28955078125 0.3799765706062317 1486.452880859375 0.44202688336372375 0.7068068 0.4267072379589081 True -16 47192 30.06196904182434 0.6358566284179688 1168.321533203125 0.4098847508430481 1483.248046875 0.4430641531944275 0.71467054 0.3952738642692566 True -17 49968 30.106315851211548 0.6311564445495605 1206.173583984375 0.270751416683197 1482.8140869140625 0.44288408756256104 0.7186861 0.3782827854156494 True -18 52744 30.067129611968994 0.6356799602508545 1205.90576171875 0.26317518949508667 1483.6944580078125 0.44208824634552 0.72175086 0.3748203217983246 True -19 55520 30.130239009857178 0.6388888359069824 1026.30126953125 0.2556505799293518 1484.37548828125 0.44196733832359314 0.7198912 0.37165454030036926 False diff --git a/ENCSR620QNS/cherimoya.fold_1.performance.tsv b/ENCSR620QNS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9d2d931eb54ae2509bf12e0e028ec9424043b86e..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1483.6944580078125 0.32623031735420227 0.4420882761478424 0.22165045142173767 0.7217508554458618 0.702475368976593 0.3748203217983246 \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_2.evaluate.json b/ENCSR620QNS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0e09aac89b264d3de2fbd220d888c31493314914..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF063KLA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_2.fit.json b/ENCSR620QNS/cherimoya.fold_2.fit.json deleted file mode 100644 index aea5d5074cc01a1a9c06fb0a7352eb98880dc6ea..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF063KLA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_2.log b/ENCSR620QNS/cherimoya.fold_2.log deleted file mode 100644 index b826056b20a391ca606d445c3e6674cc51596db3..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2841 35.76102066040039 4.6153199672698975 1208.1915283203125 0.5994455814361572 1797.7115478515625 0.2425692230463028 0.37705702 7.094344615936279 True -1 5682 31.306063890457153 0.5319068431854248 1471.4617919921875 0.9837809205055237 1610.8758544921875 0.35453543066978455 0.47258207 2.1781303882598877 True -2 8523 31.354596376419067 0.5663473606109619 1133.293212890625 0.5717145800590515 1572.39453125 0.36699068546295166 0.5291998 1.2842353582382202 True -3 11364 31.33988380432129 0.5407891273498535 1027.264892578125 0.6008352041244507 1530.4447021484375 0.3819166421890259 0.55952716 0.9042191505432129 True -4 14205 31.26484966278076 0.5330395698547363 1119.2744140625 0.5975521206855774 1512.17041015625 0.3893721401691437 0.57592 0.7534606456756592 True -5 17046 31.042991161346436 0.5302679538726807 1190.318359375 0.5014608502388 1498.7025146484375 0.39590078592300415 0.5818564 0.7111882567405701 True -6 19887 30.70939588546753 0.5313122272491455 1323.8759765625 0.6654237508773804 1492.0517578125 0.3995252847671509 0.59373444 0.6758570671081543 True -7 22728 30.724109411239624 0.534433126449585 1198.35205078125 0.5144553184509277 1484.686279296875 0.4038031995296478 0.59571695 0.6441290378570557 True -8 25569 30.73958706855774 0.7790327072143555 1204.69873046875 0.6424717903137207 1474.4119873046875 0.40868109464645386 0.6031054 0.6102498173713684 True -9 28410 30.723976135253906 0.5232577323913574 1236.456298828125 0.5734829306602478 1466.138427734375 0.41317856311798096 0.6145406 0.5691756010055542 True -10 31251 30.72042441368103 0.521268367767334 1177.97998046875 0.5097447633743286 1459.343017578125 0.41659265756607056 0.62182623 0.5437683463096619 True -11 34092 30.735679626464844 0.5222949981689453 1208.355712890625 0.4722832441329956 1456.5352783203125 0.4187765121459961 0.624907 0.5616411566734314 True -12 36933 30.752305030822754 0.531996488571167 1234.837646484375 0.4076415002346039 1453.041259765625 0.4201268255710602 0.6309668 0.5514589548110962 True -13 39774 30.702435970306396 0.5302844047546387 1171.080810546875 0.4739791750907898 1440.9686279296875 0.42690348625183105 0.6491527 0.4973294138908386 True -14 42615 30.760602951049805 0.5077259540557861 1152.55859375 0.33451250195503235 1436.7576904296875 0.42827552556991577 0.6590124 0.4625280201435089 True -15 45456 30.705926656723022 0.5320961475372314 1291.638671875 0.32148125767707825 1430.3233642578125 0.4318063259124756 0.67061615 0.4344709515571594 True -16 48297 30.763380765914917 0.5199012756347656 1101.82958984375 0.33998820185661316 1429.2987060546875 0.4312092959880829 0.6815148 0.4063686430454254 True -17 51138 30.768968105316162 0.5192704200744629 1385.393798828125 0.353709876537323 1429.230224609375 0.4302201569080353 0.6871811 0.39447683095932007 True -18 53979 30.940048694610596 0.7128736972808838 1139.92626953125 0.43376487493515015 1427.5889892578125 0.43143996596336365 0.6885352 0.3952263593673706 True -19 56820 30.75433659553528 0.6014139652252197 1220.705078125 0.2990768551826477 1427.786376953125 0.4313802719116211 0.6884612 0.3949531614780426 False diff --git a/ENCSR620QNS/cherimoya.fold_2.performance.tsv b/ENCSR620QNS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index faa151be486fc78bc19511608dc1bd51a5790370..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1427.5889892578125 0.333507239818573 0.43143996596336365 0.21196523308753967 0.688535213470459 0.6698117256164551 0.3952263593673706 \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_3.evaluate.json b/ENCSR620QNS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5d6e165d985d333acb607ecdd92cbd8ebcdab0fe..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF063KLA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_3.fit.json b/ENCSR620QNS/cherimoya.fold_3.fit.json deleted file mode 100644 index df4fad10382fc89cd408ee591723d493a49b3372..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF063KLA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_3.log b/ENCSR620QNS/cherimoya.fold_3.log deleted file mode 100644 index fc0150e29eeca314928f44f53db84c1d6659df27..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2838 35.701082944869995 4.677384614944458 1287.13134765625 0.683741569519043 1859.0994873046875 0.24754811823368073 0.44622338 7.366294860839844 True -1 5676 31.462587118148804 0.6451187133789062 1363.8193359375 0.7698646783828735 1689.59423828125 0.34991979598999023 0.48956206 2.286466598510742 True -2 8514 31.708202362060547 0.6574857234954834 1287.4111328125 0.7607293128967285 1643.492919921875 0.366819828748703 0.5106425 1.4488379955291748 True -3 11352 31.332967519760132 1.284794569015503 1129.9852294921875 0.854283332824707 1599.240478515625 0.3783155679702759 0.55076385 0.9668757319450378 True -4 14190 31.28466248512268 2.4893109798431396 1180.2467041015625 0.6630526185035706 1582.2510986328125 0.38462400436401367 0.55071324 0.8390806913375854 False -5 17028 31.012373208999634 18.446715831756592 1352.31298828125 0.5541406869888306 1564.7313232421875 0.3929380178451538 0.55854535 0.7761395573616028 True -6 19866 30.63640785217285 2.008085012435913 1367.0697021484375 0.5689871311187744 1555.6597900390625 0.39717531204223633 0.57166237 0.6410790085792542 True -7 22704 30.691210508346558 1.2197842597961426 1069.40185546875 0.3425438404083252 1547.258544921875 0.4013206362724304 0.5818468 0.6324790120124817 True -8 25542 30.704772233963013 1.2297120094299316 1180.0048828125 0.6276775598526001 1540.5770263671875 0.40489262342453003 0.5869635 0.5973716378211975 True -9 28380 30.688778400421143 0.5837607383728027 1279.7415771484375 0.492798388004303 1534.6640625 0.4088023900985718 0.58641267 0.6236857175827026 False -10 31218 30.718525886535645 0.6077027320861816 1286.99609375 0.44967618584632874 1527.256103515625 0.4139796495437622 0.5859698 0.6268858313560486 False -11 34056 30.792964935302734 0.5489988327026367 1180.72265625 0.41012656688690186 1519.477783203125 0.4177894592285156 0.5966715 0.605829656124115 True -12 36894 30.779042720794678 0.5651543140411377 1440.6207275390625 0.45730119943618774 1513.364990234375 0.4205646514892578 0.6092307 0.562698245048523 True -13 39732 30.745912313461304 0.5362579822540283 977.34716796875 0.3009272813796997 1505.18310546875 0.42401203513145447 0.62349826 0.5488560199737549 True -14 42570 30.732197999954224 0.5553464889526367 1283.271728515625 0.3146296739578247 1498.6090087890625 0.4272806942462921 0.6401762 0.5016915798187256 True -15 45408 30.68618130683899 0.6508700847625732 1077.923828125 0.4665335416793823 1491.3507080078125 0.4311355650424957 0.6544711 0.46160033345222473 True -16 48246 30.685114860534668 1.796694278717041 1110.639404296875 0.286960244178772 1489.01318359375 0.43162184953689575 0.6682147 0.42872393131256104 True -17 51084 30.67678999900818 0.632537841796875 1178.5216064453125 0.5470041036605835 1487.9832763671875 0.43173307180404663 0.67634004 0.4112779498100281 True -18 53922 30.71003794670105 0.5484485626220703 1085.1715087890625 0.4966106116771698 1486.951904296875 0.4326167702674866 0.6778613 0.40642035007476807 True -19 56760 30.783557653427124 0.5839641094207764 1307.1280517578125 0.3593074679374695 1488.6300048828125 0.43090084195137024 0.6782712 0.4065839648246765 True diff --git a/ENCSR620QNS/cherimoya.fold_3.performance.tsv b/ENCSR620QNS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3baab379599de931db36c6bc5994522109b5b743..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1488.6300048828125 0.32964226603507996 0.43090084195137024 0.2195468544960022 0.6782711744308472 0.6600727438926697 0.4065839648246765 \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_4.evaluate.json b/ENCSR620QNS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 289ae5831de9981feb140821ccd7409205f27182..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF063KLA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_4.fit.json b/ENCSR620QNS/cherimoya.fold_4.fit.json deleted file mode 100644 index 3a20fa54de86e1d23afbca56146ef3ae95022ac1..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF063KLA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620QNS/cherimoya.fold_4.log b/ENCSR620QNS/cherimoya.fold_4.log deleted file mode 100644 index ffdcd63489cfb8ba5ea587e7b6b890d70ec06d86..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2831 35.70919108390808 4.142422199249268 1305.3504638671875 0.7037551403045654 1780.7860107421875 0.242325559258461 0.40147194 6.312580108642578 True -1 5662 31.2247097492218 0.8193192481994629 1203.6778564453125 0.528881311416626 1611.851806640625 0.3459625244140625 0.4990484 2.165757179260254 True -2 8493 31.262487649917603 0.526679277420044 1267.8597412109375 0.5345442295074463 1567.3563232421875 0.359902024269104 0.542721 1.1809879541397095 True -3 11324 31.213540077209473 0.5076892375946045 1251.998779296875 0.49721962213516235 1543.8919677734375 0.370136022567749 0.56244934 0.8760652542114258 True -4 14155 31.14175844192505 0.5036880970001221 1426.869384765625 0.6981744170188904 1513.091552734375 0.38181790709495544 0.5655199 0.798507809638977 True -5 16986 30.82786798477173 0.5107614994049072 1089.52880859375 0.42755264043807983 1490.1304931640625 0.39270246028900146 0.5714197 0.7499724626541138 True -6 19817 30.57718586921692 0.5362846851348877 1106.982666015625 0.6134920716285706 1480.0 0.3972647190093994 0.5865131 0.6619963645935059 True -7 22648 30.576247930526733 0.5117919445037842 1555.5712890625 0.622728168964386 1473.2210693359375 0.399181604385376 0.59439504 0.6279858946800232 True -8 25479 30.572196006774902 0.5124285221099854 1199.6650390625 0.6583523750305176 1461.8614501953125 0.4050690829753876 0.6079589 0.5636860132217407 True -9 28310 30.594419956207275 0.5033786296844482 1177.503662109375 0.45924633741378784 1455.431396484375 0.4085552394390106 0.6128281 0.5345122814178467 True -10 31141 30.582953453063965 0.5115838050842285 1206.369140625 0.5194203853607178 1445.6707763671875 0.41419801115989685 0.62168133 0.5064762830734253 True -11 33972 30.575156927108765 0.5102267265319824 1151.4952392578125 0.5410041809082031 1438.5823974609375 0.4175676703453064 0.6285777 0.5026341676712036 True -12 36803 30.59590458869934 0.5116291046142578 1177.666015625 0.28883814811706543 1431.96630859375 0.4212977886199951 0.6362721 0.4832453429698944 True -13 39634 30.662102460861206 0.5128765106201172 1150.9342041015625 0.4512995481491089 1425.9937744140625 0.4235914349555969 0.64905226 0.45513179898262024 True -14 42465 30.640652179718018 0.5118365287780762 1266.517578125 0.36267051100730896 1416.4140625 0.42938631772994995 0.66105783 0.4286120533943176 True -15 45296 30.622069358825684 1.5884654521942139 1106.4677734375 0.4025370478630066 1411.0526123046875 0.43118107318878174 0.669972 0.4032406806945801 True -16 48127 30.638938903808594 0.5175282955169678 1110.648193359375 0.3990640640258789 1409.3697509765625 0.43097615242004395 0.6807102 0.38650745153427124 True -17 50958 30.643519163131714 0.5092887878417969 1270.273681640625 0.3406003713607788 1407.7939453125 0.43144434690475464 0.68690896 0.3749324083328247 True -18 53789 30.60760188102722 0.5212550163269043 1179.1080322265625 0.4373897910118103 1405.13916015625 0.4337218701839447 0.69007754 0.37376874685287476 True -19 56620 30.56450343132019 0.5190377235412598 951.9761962890625 0.32845163345336914 1407.3826904296875 0.43157657980918884 0.6895653 0.3736405670642853 False diff --git a/ENCSR620QNS/cherimoya.fold_4.performance.tsv b/ENCSR620QNS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index db9f453df12aba82b4aebb86ad50268963ee4b3e..0000000000000000000000000000000000000000 --- a/ENCSR620QNS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1405.13916015625 0.3357958197593689 0.4337218701839447 0.21169808506965637 0.690077543258667 0.6670604348182678 0.37376874685287476 \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_0.evaluate.json b/ENCSR620WAR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 82e9444697f121a1bc4b98713f2c5e0f349001b5..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074VEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_0.fit.json b/ENCSR620WAR/cherimoya.fold_0.fit.json deleted file mode 100644 index 19d0345f4071ebf77551f623327d41ba2ba16756..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF074VEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_0.log b/ENCSR620WAR/cherimoya.fold_0.log deleted file mode 100644 index 818aac953ab69edabbcff6ffb68556edddcdb1b4..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 33.667150020599365 3.554246664047241 1335.6094970703125 0.958647608757019 1798.6395263671875 0.28863951563835144 0.41279447 9.528162002563477 True -1 5424 29.559520483016968 0.5823063850402832 1233.5316162109375 0.8174580335617065 1602.8731689453125 0.41836103796958923 0.4657705 3.94708251953125 True -2 8136 29.979782819747925 0.5713467597961426 1125.8790283203125 0.7916339635848999 1567.1475830078125 0.43675872683525085 0.47337627 2.2902920246124268 True -3 10848 30.607102870941162 0.5669283866882324 1206.30078125 0.6746185421943665 1546.6600341796875 0.44493547081947327 0.5061757 1.8796836137771606 True -4 13560 29.94093418121338 31.886854887008667 1200.527587890625 0.9849692583084106 1533.2802734375 0.4516777992248535 0.5288495 1.6632065773010254 True -5 16272 29.97234582901001 8.189773559570312 1054.5220947265625 0.6258174777030945 1524.1453857421875 0.45845040678977966 0.53024125 1.5986549854278564 True -6 18984 29.937265396118164 9.554553985595703 990.818603515625 1.0519084930419922 1519.8345947265625 0.4595341384410858 0.5519326 1.498321533203125 True -7 21696 29.95053505897522 7.789874315261841 964.0250244140625 1.2440602779388428 1514.443603515625 0.4625602066516876 0.5590986 1.2759830951690674 True -8 24408 30.0078547000885 28.7515926361084 1246.9364013671875 0.8319613933563232 1509.810302734375 0.46503838896751404 0.567909 1.2132352590560913 True -9 27120 30.416411876678467 0.5770969390869141 1033.875732421875 0.7898461818695068 1501.3173828125 0.46994340419769287 0.57833725 1.0845259428024292 True -10 29832 30.35271406173706 0.5800888538360596 1267.6083984375 0.8743315935134888 1495.5888671875 0.47259846329689026 0.594594 0.956756055355072 True -11 32544 30.47463059425354 18.368976593017578 1098.3251953125 0.6815600991249084 1487.48388671875 0.4775041341781616 0.6009169 0.9077580571174622 True -12 35256 30.34941339492798 0.6294786930084229 1130.1356201171875 0.8483164310455322 1481.805419921875 0.4801184833049774 0.6182429 0.8322610855102539 True -13 37968 29.90326166152954 0.5719857215881348 1087.4188232421875 0.6343046426773071 1475.2760009765625 0.4834224581718445 0.632272 0.7511778473854065 True -14 40680 29.937910556793213 4.6598687171936035 1096.1123046875 0.38990962505340576 1473.8289794921875 0.4817377030849457 0.64183694 0.6925026178359985 True -15 43392 29.94977831840515 0.5746369361877441 1068.028076171875 0.43799734115600586 1469.3782958984375 0.4861113727092743 0.6509424 0.653933584690094 True -16 46104 29.925349950790405 0.5713639259338379 1048.0445556640625 0.8091436624526978 1466.779052734375 0.48776060342788696 0.6551058 0.6303012371063232 True -17 48816 29.928886890411377 0.5853264331817627 1138.354248046875 0.5511472225189209 1467.547607421875 0.486689031124115 0.6578353 0.6195261478424072 True -18 51528 29.91745090484619 0.5714931488037109 1165.360595703125 0.4850759506225586 1473.4251708984375 0.4821990430355072 0.65356225 0.618768036365509 False -19 54240 29.903510570526123 0.5719068050384521 980.5694580078125 0.392598956823349 1474.6622314453125 0.48177558183670044 0.65315855 0.6214808225631714 False diff --git a/ENCSR620WAR/cherimoya.fold_0.performance.tsv b/ENCSR620WAR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2c2433df6423cb308a63f2522968c078b1796659..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1467.547607421875 0.2539409399032593 0.486689031124115 0.31107813119888306 0.6578353047370911 0.6383658647537231 0.6195261478424072 \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_1.evaluate.json b/ENCSR620WAR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5bbee694d94b3bed1cd03ed3f73fb5ccededf109..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074VEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_1.fit.json b/ENCSR620WAR/cherimoya.fold_1.fit.json deleted file mode 100644 index b3189898ec32594e01e9bee84bfbaf5e7bc8b168..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF074VEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_1.log b/ENCSR620WAR/cherimoya.fold_1.log deleted file mode 100644 index a06f9244fb2947af9a29557ece82f328c1c30d44..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2687 33.78192687034607 5.714432239532471 1087.35205078125 1.0785316228866577 1951.3406982421875 0.2909539043903351 0.40894786 10.62338924407959 True -1 5374 29.688107013702393 1.5676674842834473 1394.380859375 1.246704339981079 1731.269775390625 0.4343056082725525 0.40837812 4.52324914932251 False -2 8061 29.74415397644043 1.5815980434417725 1428.939453125 1.0954443216323853 1709.388427734375 0.4372974932193756 0.41316935 2.4533987045288086 True -3 10748 29.640302419662476 0.7818393707275391 1220.8978271484375 0.6608189940452576 1695.874755859375 0.4418044686317444 0.44210467 2.176898956298828 True -4 13435 29.622192859649658 0.7525200843811035 1326.355712890625 1.0110599994659424 1673.3521728515625 0.45418667793273926 0.43783966 2.0146703720092773 False -5 16122 29.592693090438843 0.7503025531768799 1197.837158203125 1.0072765350341797 1665.08837890625 0.4580889940261841 0.43849188 2.0643653869628906 False -6 18809 29.614105463027954 1.7146384716033936 1209.52001953125 1.0658656358718872 1656.6119384765625 0.4634866416454315 0.4516165 1.863040566444397 True -7 21496 29.656108856201172 0.7447586059570312 1121.147216796875 0.6302987337112427 1647.7586669921875 0.46833571791648865 0.45885143 1.7571938037872314 True -8 24183 29.636842489242554 0.7561712265014648 1232.846923828125 0.7861785888671875 1640.2318115234375 0.4716245234012604 0.46108842 1.6165070533752441 True -9 26870 29.651790380477905 0.7342948913574219 1131.276611328125 0.9384791851043701 1638.1708984375 0.4711078107357025 0.4612959 1.4663408994674683 True -10 29557 29.620290279388428 0.7538762092590332 1166.105712890625 0.6720014214515686 1627.73095703125 0.4768489599227905 0.4790801 1.3703433275222778 True -11 32244 29.602128267288208 0.744542121887207 999.0298461914062 0.6607484817504883 1616.242919921875 0.4827097952365875 0.48701146 1.2853319644927979 True -12 34931 29.67983341217041 0.7345194816589355 1165.58251953125 0.778736412525177 1613.3394775390625 0.4830350875854492 0.49981803 1.198464035987854 True -13 37618 29.642576217651367 0.7550406455993652 1063.604736328125 0.5451518893241882 1603.069580078125 0.48747435212135315 0.51015943 1.116939902305603 True -14 40305 29.694403171539307 0.7424774169921875 1210.243896484375 0.4971962571144104 1595.3541259765625 0.4916696846485138 0.52437943 1.059141755104065 True -15 42992 29.595895051956177 0.7325344085693359 1187.7210693359375 0.4269754886627197 1592.2215576171875 0.4922076463699341 0.5322474 1.0302156209945679 True -16 45679 29.632840156555176 0.7339320182800293 970.7074584960938 0.34376728534698486 1592.427490234375 0.4916693866252899 0.53799593 1.0000728368759155 True -17 48366 29.643731355667114 0.7392487525939941 1120.2576904296875 0.4676269292831421 1596.035400390625 0.49011003971099854 0.53896576 0.9853062033653259 True -18 51053 29.594932079315186 0.7333903312683105 1092.415283203125 0.5754157900810242 1596.84619140625 0.4906030595302582 0.53730685 0.9905151128768921 False -19 53740 29.614190340042114 1.2699000835418701 911.1505126953125 0.3443630039691925 1594.17138671875 0.4926239848136902 0.5384608 0.9991111755371094 False diff --git a/ENCSR620WAR/cherimoya.fold_1.performance.tsv b/ENCSR620WAR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e699d5e5a72a5af1cfe7d60707ecd75a56c5331f..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1596.035400390625 0.24182160198688507 0.4901100993156433 0.32508641481399536 0.5389657616615295 0.5595754981040955 0.9853062033653259 \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_2.evaluate.json b/ENCSR620WAR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7bf617a3bb8f8339822c352d9724b5cdd9721a15..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074VEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_2.fit.json b/ENCSR620WAR/cherimoya.fold_2.fit.json deleted file mode 100644 index 10ed0fd5003fefd80eef78a05e13170f14f1b556..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF074VEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_2.log b/ENCSR620WAR/cherimoya.fold_2.log deleted file mode 100644 index 592b6ef6fa0e532d36bd377ff570c2cb13cadd1a..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2884 35.61765789985657 3.446953296661377 1293.6845703125 0.8468328714370728 1751.391357421875 0.30252519249916077 0.4399349 7.811705589294434 True -1 5768 31.81163740158081 0.5333354473114014 1404.02294921875 0.9393713474273682 1564.071533203125 0.4202827513217926 0.49434215 3.270160675048828 True -2 8652 31.767703533172607 0.521399974822998 1191.296630859375 0.9420772790908813 1535.910400390625 0.43524011969566345 0.51959234 1.5531527996063232 True -3 11536 31.737757205963135 0.5212931632995605 1229.030517578125 0.9140198230743408 1521.8125 0.4426308572292328 0.52747166 1.3578945398330688 True -4 14420 31.78293204307556 0.5299084186553955 990.30810546875 0.8206453323364258 1507.7437744140625 0.4493330717086792 0.5497457 1.0952147245407104 True -5 17304 32.09883451461792 3.388615608215332 1271.33056640625 0.8647187948226929 1498.1907958984375 0.45410385727882385 0.5657175 1.016156792640686 True -6 20188 31.78277087211609 0.5286960601806641 1308.8154296875 0.5815050005912781 1494.943115234375 0.45581603050231934 0.5696074 0.9823712706565857 True -7 23072 31.824769973754883 0.5330779552459717 1194.335693359375 0.6020081639289856 1484.79052734375 0.46351850032806396 0.58064425 0.9819152355194092 True -8 25956 31.78099536895752 0.520526647567749 924.5501708984375 0.6084283590316772 1480.6861572265625 0.4648078382015228 0.5864116 0.9613120555877686 True -9 28840 31.835559368133545 0.5194213390350342 1316.2532958984375 0.5980722308158875 1477.263427734375 0.4657105505466461 0.59947485 0.883414626121521 True -10 31724 31.810604095458984 0.5195181369781494 1008.836181640625 0.7313168048858643 1465.890625 0.47365283966064453 0.6186447 0.7941879630088806 True -11 34608 31.732259511947632 0.5271732807159424 952.072265625 1.0197603702545166 1455.715576171875 0.47900667786598206 0.6330018 0.7515163421630859 True -12 37492 31.75562596321106 0.5296258926391602 1086.458251953125 0.8077243566513062 1452.8494873046875 0.48034751415252686 0.64314836 0.7098248600959778 True -13 40376 31.879700660705566 0.5315883159637451 1150.20068359375 0.41584861278533936 1446.826904296875 0.48432105779647827 0.6519715 0.6762392520904541 True -14 43260 31.854959726333618 0.5260941982269287 1183.3970947265625 0.4291455149650574 1443.8045654296875 0.4847971498966217 0.6637728 0.6204431056976318 True -15 46144 31.86599850654602 0.7526988983154297 1066.3145751953125 0.45192548632621765 1445.8155517578125 0.48156508803367615 0.67526263 0.5755180716514587 True -16 49028 31.809659004211426 0.5317368507385254 1139.240478515625 0.38661718368530273 1442.0123291015625 0.4848189055919647 0.67964906 0.5647465586662292 True -17 51912 31.890857696533203 1.576246976852417 1052.3387451171875 0.39382582902908325 1442.6937255859375 0.48360151052474976 0.6790909 0.56360924243927 False -18 54796 31.811380624771118 0.5288083553314209 1079.617919921875 0.25965219736099243 1446.3966064453125 0.48108336329460144 0.67807513 0.5623542070388794 False -19 57680 31.406374216079712 0.5257930755615234 1165.9019775390625 0.28278329968452454 1445.1910400390625 0.4825991690158844 0.6770159 0.5692904591560364 False diff --git a/ENCSR620WAR/cherimoya.fold_2.performance.tsv b/ENCSR620WAR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index fdbbdeee462e717e7c5cc655768cef6bab3ccc5f..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1442.0123291015625 0.2557488977909088 0.4848189055919647 0.311265230178833 0.6796490550041199 0.6649912595748901 0.5647465586662292 \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_3.evaluate.json b/ENCSR620WAR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 43bd5078bdf89a0439671971cfcc47af85e3e1ac..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074VEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_3.fit.json b/ENCSR620WAR/cherimoya.fold_3.fit.json deleted file mode 100644 index 6ae62dbce23febdca3fdbb5a56b305781d5c22b4..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF074VEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_3.log b/ENCSR620WAR/cherimoya.fold_3.log deleted file mode 100644 index 5a6ef7751153709a8575d3eef6102baf3579760b..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 35.04748225212097 3.6781575679779053 1338.72705078125 1.1966112852096558 1824.3809814453125 0.29371216893196106 0.46488443 10.197409629821777 True -1 5500 30.300215005874634 0.5958635807037354 982.964111328125 0.9324238896369934 1631.619873046875 0.4215151071548462 0.49112993 4.618663787841797 True -2 8250 30.29174280166626 0.5961654186248779 1334.912841796875 1.1342942714691162 1596.03369140625 0.4367568790912628 0.50376564 2.1691551208496094 True -3 11000 30.264662504196167 0.5835931301116943 1033.74658203125 1.107635498046875 1576.228759765625 0.44931167364120483 0.5307587 1.7035346031188965 True -4 13750 30.248244762420654 0.5837399959564209 1179.065673828125 1.392580270767212 1568.9599609375 0.4523758888244629 0.53742266 1.5545308589935303 True -5 16500 30.329662799835205 0.592078685760498 1027.8084716796875 0.6504908204078674 1561.156005859375 0.45586323738098145 0.5563988 1.3262372016906738 True -6 19250 30.463547945022583 0.6161031723022461 991.870361328125 0.9693439602851868 1553.0494384765625 0.46112778782844543 0.57600343 1.178620457649231 True -7 22000 30.380643129348755 0.593602180480957 1047.08349609375 0.6696459650993347 1545.3984375 0.46567538380622864 0.5750366 1.0947734117507935 False -8 24750 30.38630509376526 0.5855395793914795 1129.85302734375 0.5200599431991577 1542.7034912109375 0.4678846001625061 0.59000486 1.1491279602050781 True -9 27500 30.348946809768677 0.5877237319946289 1219.9591064453125 0.8202614784240723 1542.538330078125 0.4662292003631592 0.6011454 1.0433690547943115 True -10 30250 30.339922189712524 0.585925817489624 1234.78466796875 0.7917504906654358 1531.632080078125 0.4735020101070404 0.6141767 0.9468034505844116 True -11 33000 30.329625368118286 0.5927629470825195 1200.7513427734375 0.7314677238464355 1521.0211181640625 0.4794783592224121 0.6245926 0.8711271286010742 True -12 35750 30.378956079483032 0.5851938724517822 1169.730712890625 0.6471002101898193 1519.178466796875 0.4785037338733673 0.64277816 0.7884442806243896 True -13 38500 30.32885503768921 1.1604530811309814 1080.2763671875 0.6184643507003784 1514.2459716796875 0.48208922147750854 0.6616914 0.6908391118049622 True -14 41250 30.36586904525757 0.5966358184814453 1055.95849609375 0.6529788970947266 1507.1573486328125 0.48436641693115234 0.67760164 0.6557469367980957 True -15 44000 30.393213272094727 0.6026325225830078 1017.8380737304688 0.5687558650970459 1504.4022216796875 0.485726535320282 0.6876442 0.6089044809341431 True -16 46750 31.45363187789917 0.5966124534606934 1119.79736328125 0.7295390367507935 1502.977294921875 0.48562002182006836 0.6928454 0.5789003968238831 True -17 49500 30.572805404663086 1.0461339950561523 1128.251220703125 0.6245517134666443 1505.29443359375 0.4841974675655365 0.68987507 0.5755318999290466 False -18 52250 30.357534170150757 0.5883145332336426 1294.1932373046875 0.3493526577949524 1506.2283935546875 0.4834184944629669 0.68798757 0.5786850452423096 False -19 55000 29.74172830581665 0.5994257926940918 1054.319091796875 0.3185384273529053 1506.0638427734375 0.48383742570877075 0.68478906 0.5848627686500549 False diff --git a/ENCSR620WAR/cherimoya.fold_3.performance.tsv b/ENCSR620WAR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 70a4d91058a5d6030e5f95c63f9628d1f7bdfaec..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1502.977294921875 0.25056880712509155 0.48562005162239075 0.3157406151294708 0.6928454041481018 0.6832181811332703 0.5789003968238831 \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_4.evaluate.json b/ENCSR620WAR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9dc7dca8e72171e5f4729703a32fe9ee7fcf85e7..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074VEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_4.fit.json b/ENCSR620WAR/cherimoya.fold_4.fit.json deleted file mode 100644 index 7ad90bcdfe28aff1538847ef83337bb412cee49b..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF074VEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR620WAR/cherimoya.fold_4.log b/ENCSR620WAR/cherimoya.fold_4.log deleted file mode 100644 index aaf88baaa626e707ad6695a4b36208c83a21aadb..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2843 35.17916178703308 4.426929712295532 1084.251953125 0.9164641499519348 1732.3975830078125 0.30351343750953674 0.45133403 7.351317405700684 True -1 5686 31.483145713806152 0.5740966796875 1150.0810546875 1.0401735305786133 1544.189453125 0.4282066524028778 0.4914887 4.498928546905518 True -2 8529 31.470889806747437 0.551262378692627 1106.9072265625 0.9847544431686401 1519.623291015625 0.44015541672706604 0.54099447 1.777755618095398 True -3 11372 31.502436637878418 0.5421063899993896 1177.0078125 0.628633975982666 1502.8648681640625 0.44925373792648315 0.55912614 1.467388391494751 True -4 14215 31.51473093032837 0.541938304901123 1277.38720703125 1.0056040287017822 1500.2369384765625 0.4510161876678467 0.57351685 1.3367873430252075 True -5 17058 31.462113618850708 0.5630753040313721 1235.837890625 0.6462559103965759 1491.8345947265625 0.4559605121612549 0.5795844 1.1902823448181152 True -6 19901 31.484664916992188 0.5611734390258789 1114.32861328125 0.8932181000709534 1481.2418212890625 0.4636323153972626 0.5784566 1.2165167331695557 False -7 22744 31.58287525177002 0.5510225296020508 1219.5587158203125 0.8051417469978333 1476.6116943359375 0.46688610315322876 0.5943342 1.092703938484192 True -8 25587 31.47489619255066 0.6779553890228271 1008.76318359375 0.3250511586666107 1470.3184814453125 0.46896129846572876 0.6023429 1.0344977378845215 True -9 28430 31.53957486152649 13.566765785217285 1095.497802734375 0.6997734308242798 1466.54345703125 0.47225984930992126 0.6106614 0.924615204334259 True -10 31273 31.55148220062256 6.05063271522522 1139.42431640625 0.8436854481697083 1462.114501953125 0.4743097424507141 0.6166447 0.8932148814201355 True -11 34116 31.526443481445312 0.7875223159790039 1051.5760498046875 0.6457930207252502 1455.6080322265625 0.477315753698349 0.6293164 0.8066248297691345 True -12 36959 31.486847162246704 2.0799615383148193 1360.958984375 0.6528323292732239 1448.6663818359375 0.48146605491638184 0.64656657 0.7195526361465454 True -13 39802 31.448641300201416 0.5730981826782227 1086.7587890625 0.29582756757736206 1440.9862060546875 0.4851444959640503 0.6606882 0.6593672633171082 True -14 42645 31.492408752441406 9.797403573989868 1165.19189453125 0.42544516921043396 1440.6201171875 0.4847315549850464 0.6728614 0.5961129069328308 True -15 45488 31.44502282142639 0.8902382850646973 1120.352783203125 0.41177278757095337 1437.58447265625 0.4851844906806946 0.68194497 0.5552970170974731 True -16 48331 31.449742794036865 0.7043576240539551 1182.607666015625 0.3670557141304016 1440.375732421875 0.4832209050655365 0.6882324 0.5380239486694336 True -17 51174 31.447221755981445 17.518815755844116 1030.1121826171875 0.48828041553497314 1437.035888671875 0.4863424599170685 0.68507826 0.5317398309707642 False -18 54017 31.613485097885132 0.54982590675354 1122.5697021484375 0.23380887508392334 1439.1690673828125 0.4842960834503174 0.6807981 0.5416865944862366 False -19 56860 30.83048176765442 0.5384690761566162 1079.575439453125 0.3601043224334717 1440.8092041015625 0.4827510714530945 0.67833 0.5472334027290344 False diff --git a/ENCSR620WAR/cherimoya.fold_4.performance.tsv b/ENCSR620WAR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 36f3130c9b6a16e1d76c15954c8f4e18aa8c5249..0000000000000000000000000000000000000000 --- a/ENCSR620WAR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1440.375732421875 0.2553400993347168 0.4832208752632141 0.3080041706562042 0.688232421875 0.6731367707252502 0.5380239486694336 \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_0.evaluate.json b/ENCSR621ENC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4cd174eaa46d644c03f08bd3058a7e7ec35179cd..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672IYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_0.fit.json b/ENCSR621ENC/cherimoya.fold_0.fit.json deleted file mode 100644 index 938256224c5585af987387d1c03387eb3f1fbb3b..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF672IYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_0.log b/ENCSR621ENC/cherimoya.fold_0.log deleted file mode 100644 index 9a85dcbe4bffc614628200f50811fabe9c8cd676..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2794 34.82630920410156 3.5573570728302 1230.45458984375 1.3412132263183594 1963.3321533203125 0.3213343322277069 0.74817324 8.710838317871094 True -1 5588 30.800426721572876 0.5780391693115234 1353.543701171875 0.5786822438240051 1765.727294921875 0.41689950227737427 0.79137766 1.272005558013916 True -2 8382 30.800914525985718 0.5614058971405029 1354.17138671875 0.6775881052017212 1732.7593994140625 0.4282461404800415 0.78663784 0.8163924813270569 False -3 11176 30.737443923950195 0.5644609928131104 1228.2451171875 0.7545784115791321 1726.4287109375 0.43088090419769287 0.7939894 0.6985575556755066 True -4 13970 30.746099710464478 0.5604469776153564 1323.8719482421875 0.5373736619949341 1712.14990234375 0.43820324540138245 0.7984676 0.5859889984130859 True -5 16764 30.71598196029663 0.5609955787658691 1325.715576171875 0.43270352482795715 1705.5081787109375 0.4404720664024353 0.8070501 0.4885387718677521 True -6 19558 30.7329421043396 0.5630345344543457 1486.1220703125 0.6496486067771912 1702.1376953125 0.4403788149356842 0.80854475 0.43992161750793457 True -7 22352 30.79201316833496 0.5718240737915039 1403.090087890625 1.098555326461792 1697.4351806640625 0.4423660635948181 0.81142974 0.42414718866348267 True -8 25146 30.79673719406128 0.5626373291015625 1223.8619384765625 0.43886661529541016 1689.9852294921875 0.4465850591659546 0.8189571 0.38140156865119934 True -9 27940 30.762520790100098 0.5697159767150879 1292.8822021484375 0.4974851608276367 1684.00732421875 0.44879209995269775 0.8210574 0.3651200234889984 True -10 30734 30.71117854118347 1.424889087677002 1455.4560546875 0.517690896987915 1682.6744384765625 0.4485037326812744 0.8258859 0.3372066915035248 True -11 33528 30.73634696006775 0.5627825260162354 1426.7529296875 0.4318951368331909 1672.1114501953125 0.4547009766101837 0.8297213 0.33196884393692017 True -12 36322 30.742424249649048 0.569211483001709 1334.052490234375 0.4259999096393585 1669.5557861328125 0.4547336995601654 0.83745205 0.3206983804702759 True -13 39116 30.748595714569092 0.5585713386535645 1230.3466796875 0.28579676151275635 1664.2255859375 0.45779934525489807 0.8381768 0.30580681562423706 True -14 41910 30.789785385131836 0.5643610954284668 1223.600830078125 0.40811583399772644 1661.1864013671875 0.45700597763061523 0.84542924 0.28806620836257935 True -15 44704 30.533637523651123 0.5621426105499268 1360.25537109375 0.2824072241783142 1659.574462890625 0.4593959152698517 0.848537 0.2828442454338074 True -16 47498 30.171124935150146 0.5484497547149658 1611.0771484375 0.21230527758598328 1662.0968017578125 0.4579654335975647 0.8485564 0.2760492265224457 True -17 50292 30.230576038360596 0.5535273551940918 1429.9541015625 0.4610533118247986 1660.30224609375 0.4587401747703552 0.85003006 0.2788410484790802 True -18 53086 30.153903007507324 0.5608277320861816 1390.55224609375 0.19782589375972748 1661.8590087890625 0.4593358039855957 0.84784985 0.28030917048454285 False -19 55880 30.15553307533264 0.5611724853515625 1400.7640380859375 0.29028791189193726 1664.0986328125 0.45732465386390686 0.8458958 0.2832825779914856 False diff --git a/ENCSR621ENC/cherimoya.fold_0.performance.tsv b/ENCSR621ENC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3c7ff043c41b3629532ce817a7c52de92ad6bee1..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1660.30224609375 0.25790661573410034 0.45874014496803284 0.30090105533599854 0.8500300645828247 0.8240140676498413 0.2788410484790802 \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_1.evaluate.json b/ENCSR621ENC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ddecded07867f0e33121a2163df09df755d33922..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672IYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_1.fit.json b/ENCSR621ENC/cherimoya.fold_1.fit.json deleted file mode 100644 index a661448eb1f41660b6888898aa4946f5f5851ac8..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF672IYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_1.log b/ENCSR621ENC/cherimoya.fold_1.log deleted file mode 100644 index 5e94784bdeec9784ca6cfd72e004f581be5060a8..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 34.154886960983276 5.797809839248657 1356.466796875 0.6929370164871216 2287.302734375 0.3292956054210663 0.71599597 11.592144012451172 True -1 5470 30.52582836151123 0.7425308227539062 1398.5482177734375 0.5827338695526123 2039.0550537109375 0.4298610985279083 0.7851517 1.8400803804397583 True -2 8205 32.18009400367737 0.7540993690490723 1202.0028076171875 0.8754168748855591 1986.6842041015625 0.4447796940803528 0.7967148 0.8992298245429993 True -3 10940 30.284285068511963 0.7313187122344971 1333.4473876953125 0.841317355632782 1977.4974365234375 0.44477298855781555 0.7982443 0.6557077169418335 True -4 13675 30.201812744140625 0.7195181846618652 1362.270751953125 0.46767178177833557 1955.2532958984375 0.453175812959671 0.80314714 0.5353975296020508 True -5 16410 30.187994718551636 0.7250204086303711 1362.959716796875 0.41255611181259155 1944.50341796875 0.45845547318458557 0.804732 0.5293325781822205 True -6 19145 30.425959825515747 0.7217533588409424 1273.7401123046875 0.8741265535354614 1940.9210205078125 0.45868566632270813 0.8065127 0.5065072178840637 True -7 21880 30.252399921417236 2.162609100341797 1467.487548828125 0.5690784454345703 1932.3582763671875 0.4612974226474762 0.8104289 0.4843975007534027 True -8 24615 30.296852827072144 0.7164039611816406 1303.1976318359375 0.4712477922439575 1919.44970703125 0.46699807047843933 0.81521976 0.4639539122581482 True -9 27350 30.258197784423828 21.504851579666138 1420.82958984375 0.5335638523101807 1912.8438720703125 0.46918201446533203 0.8151737 0.44602781534194946 False -10 30085 30.18876314163208 0.7330870628356934 1464.353759765625 0.301131010055542 1900.76513671875 0.474677175283432 0.8245039 0.4142833948135376 True -11 32820 30.179295539855957 0.7186298370361328 1187.20654296875 0.38248348236083984 1898.0771484375 0.47410473227500916 0.8327471 0.3826432228088379 True -12 35555 30.25567388534546 1.3751811981201172 1295.498779296875 0.35408419370651245 1896.6512451171875 0.4740506708621979 0.83892894 0.36748218536376953 True -13 38290 30.21680498123169 8.075990438461304 1248.853515625 0.400371253490448 1887.448486328125 0.4777910113334656 0.84638005 0.3407357335090637 True -14 41025 30.2045578956604 0.7125608921051025 1664.28662109375 0.40566587448120117 1879.9725341796875 0.48077696561813354 0.8512544 0.320360004901886 True -15 43760 30.17907452583313 0.9039027690887451 1545.01806640625 0.5342194437980652 1878.788330078125 0.47894901037216187 0.8556314 0.30301520228385925 True -16 46495 29.559028387069702 0.7037692070007324 1407.9078369140625 0.2632017135620117 1879.5560302734375 0.47870901226997375 0.8579704 0.29682159423828125 True -17 49230 29.537222862243652 0.7084839344024658 1273.9892578125 0.24724294245243073 1879.3055419921875 0.47966310381889343 0.8604906 0.29352474212646484 True -18 51965 29.501774311065674 0.7041230201721191 1404.7523193359375 0.2184804230928421 1883.45947265625 0.47748127579689026 0.85990393 0.29279929399490356 False -19 54700 29.507020711898804 0.703141450881958 1187.4552001953125 0.45952311158180237 1880.1114501953125 0.48073458671569824 0.86114055 0.29297634959220886 True diff --git a/ENCSR621ENC/cherimoya.fold_1.performance.tsv b/ENCSR621ENC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 62b86752a0eda9f95013aac7635c31a9a5a2dac4..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1880.1114501953125 0.2388344258069992 0.48073458671569824 0.32918787002563477 0.8611405491828918 0.8536498546600342 0.29297634959220886 \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_2.evaluate.json b/ENCSR621ENC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b6a2b13cb327af6ee55987933b28c1b518103d3c..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672IYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_2.fit.json b/ENCSR621ENC/cherimoya.fold_2.fit.json deleted file mode 100644 index 703ac14d5b542fe5dc5a8647015a6da649617338..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF672IYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_2.log b/ENCSR621ENC/cherimoya.fold_2.log deleted file mode 100644 index c1de5a11da19563d271c461164a8040734bf2159..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2909 35.66158604621887 3.4488916397094727 1587.974365234375 0.4849895238876343 2035.40380859375 0.3272927701473236 0.7358253 7.664579391479492 True -1 5818 31.939865112304688 0.5546286106109619 1839.66943359375 0.5507872700691223 1821.0548095703125 0.425245076417923 0.7815577 1.734135627746582 True -2 8727 31.967178344726562 0.544691801071167 1294.47021484375 0.5745539665222168 1795.90478515625 0.43431034684181213 0.7922204 0.9066721200942993 True -3 11636 31.945964097976685 0.5533132553100586 1318.06396484375 0.6043813228607178 1787.7081298828125 0.4353141486644745 0.79595214 0.6779730916023254 True -4 14545 32.185394525527954 1.3757553100585938 1494.4947509765625 0.3725079298019409 1774.662109375 0.44129860401153564 0.80162686 0.5733429789543152 True -5 17454 31.988667488098145 0.689171314239502 1468.956787109375 0.7353540658950806 1763.8447265625 0.4475158751010895 0.80317116 0.5327458381652832 True -6 20363 31.98835849761963 0.5485033988952637 1401.86572265625 0.6271063089370728 1762.6435546875 0.44682571291923523 0.80700374 0.4727099537849426 True -7 23272 31.988676071166992 0.5575573444366455 1199.472412109375 0.5018200874328613 1750.6082763671875 0.4528249502182007 0.8141288 0.4778599739074707 True -8 26181 32.01571798324585 0.5502662658691406 1481.4818115234375 0.33964020013809204 1745.5574951171875 0.4551185965538025 0.81671053 0.41100558638572693 True -9 29090 32.02253985404968 0.5584132671356201 1657.507080078125 0.382669061422348 1736.2022705078125 0.45909634232521057 0.8221915 0.38220131397247314 True -10 31999 31.974029302597046 0.54988694190979 1282.678466796875 0.34091490507125854 1735.6640625 0.45825040340423584 0.8302517 0.37258821725845337 True -11 34908 31.9892315864563 0.5560758113861084 1476.4970703125 0.41508689522743225 1733.511962890625 0.45871010422706604 0.83447874 0.35938334465026855 True -12 37817 32.07428979873657 0.548349142074585 1510.3946533203125 0.3139108419418335 1728.712158203125 0.46037963032722473 0.83778936 0.3469528257846832 True -13 40726 31.998629808425903 0.560427188873291 1396.609619140625 0.44711044430732727 1718.8157958984375 0.46554118394851685 0.8408214 0.3205626308917999 True -14 43635 31.59599494934082 1.1384329795837402 1252.4970703125 0.35149532556533813 1716.9990234375 0.4661702513694763 0.84442705 0.30350562930107117 True -15 46544 31.362648725509644 0.5606379508972168 1184.7132568359375 0.3681032061576843 1718.1484375 0.4651660919189453 0.84874535 0.29040515422821045 True -16 49453 31.32568645477295 0.5628969669342041 1293.126953125 0.2689487934112549 1716.271484375 0.46536239981651306 0.8532136 0.28503939509391785 True -17 52362 31.416563510894775 0.5579328536987305 1433.479736328125 0.3962843418121338 1714.2818603515625 0.46733397245407104 0.85465837 0.28165772557258606 True -18 55271 31.411813497543335 0.5466287136077881 1640.2110595703125 0.20823276042938232 1713.5234375 0.46850767731666565 0.85262495 0.285349577665329 False -19 58180 31.34606099128723 0.558387041091919 1129.067626953125 0.1516483873128891 1716.7215576171875 0.4655950665473938 0.85325843 0.28694039583206177 False diff --git a/ENCSR621ENC/cherimoya.fold_2.performance.tsv b/ENCSR621ENC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d4f476cf9cd2083d290fd1dc6141cefb6e438880..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1714.2818603515625 0.2512308657169342 0.46733400225639343 0.31071197986602783 0.8546583652496338 0.8327348232269287 0.28165772557258606 \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_3.evaluate.json b/ENCSR621ENC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 66ef3f902fa52709c111448aa1585aaf6326b58c..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672IYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_3.fit.json b/ENCSR621ENC/cherimoya.fold_3.fit.json deleted file mode 100644 index 1e831cdd3845a16c23e028c9b4cb761a65f5055c..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF672IYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_3.log b/ENCSR621ENC/cherimoya.fold_3.log deleted file mode 100644 index a269a912f9ba009ad42957b0d6919d110ec78d2a..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2788 34.46703338623047 3.5403475761413574 1483.5087890625 0.7353453636169434 2048.899658203125 0.33664730191230774 0.74731284 9.883140563964844 True -1 5576 30.641456604003906 0.5649204254150391 1290.844970703125 0.8537001013755798 1854.9190673828125 0.42422229051589966 0.7893666 1.939314842224121 True -2 8364 30.72070860862732 0.5264608860015869 1111.6263427734375 0.49130871891975403 1820.029541015625 0.43579915165901184 0.7950868 0.8276582956314087 True -3 11152 30.739683866500854 0.5272994041442871 1492.4520263671875 0.517428994178772 1811.6092529296875 0.437549352645874 0.8028489 0.6587491631507874 True -4 13940 30.689509391784668 0.5287079811096191 1415.77685546875 0.5674190521240234 1806.43603515625 0.4408985674381256 0.79753053 0.6273423433303833 False -5 16728 30.640759468078613 0.5298213958740234 1297.2001953125 0.23639477789402008 1803.1019287109375 0.44146910309791565 0.80432767 0.5508837699890137 True -6 19516 30.654431104660034 0.5245351791381836 1254.080078125 0.7444498538970947 1784.675537109375 0.4518003761768341 0.8057696 0.5018675923347473 True -7 22304 30.670132160186768 0.531623363494873 1625.787109375 0.5354886054992676 1783.3822021484375 0.4511951804161072 0.8076516 0.4865528345108032 True -8 25092 30.6698796749115 0.529245138168335 1549.19677734375 0.573776125907898 1778.5657958984375 0.4537166357040405 0.81329757 0.4731456935405731 True -9 27880 30.623133420944214 0.530648946762085 1378.927001953125 0.37008509039878845 1778.732421875 0.45240235328674316 0.82351613 0.4308801293373108 True -10 30668 30.85789966583252 0.5294291973114014 1355.8720703125 0.30923235416412354 1772.704345703125 0.45613983273506165 0.8305675 0.42990919947624207 True -11 33456 30.68116331100464 2.880178689956665 1385.6092529296875 0.9538055658340454 1765.43896484375 0.4596411883831024 0.8338773 0.40958908200263977 True -12 36244 30.781760215759277 0.5325362682342529 1263.9169921875 0.2904428541660309 1755.9488525390625 0.46383094787597656 0.84021044 0.3834960460662842 True -13 39032 30.669219493865967 0.5297884941101074 1116.868408203125 0.4281047582626343 1756.528076171875 0.46194562315940857 0.8446538 0.3510689437389374 True -14 41820 30.346505165100098 0.5237293243408203 1261.786865234375 0.3590696454048157 1749.4620361328125 0.4657804071903229 0.8509171 0.34159886837005615 True -15 44608 30.059981107711792 0.5231847763061523 1341.0479736328125 0.304226279258728 1749.3065185546875 0.46542438864707947 0.8566816 0.31258252263069153 True -16 47396 30.056962728500366 0.5246067047119141 1162.064208984375 0.28272372484207153 1748.9326171875 0.46474090218544006 0.8594807 0.2978951930999756 True -17 50184 30.004022359848022 0.5121440887451172 1197.31494140625 0.2694849371910095 1755.289306640625 0.46065717935562134 0.8600536 0.2941916882991791 True -18 52972 30.049355506896973 0.5225193500518799 1249.9920654296875 0.2711579203605652 1755.8172607421875 0.46047037839889526 0.8602601 0.2927621901035309 True -19 55760 30.0714750289917 0.9452269077301025 1462.1256103515625 0.3780266046524048 1758.8087158203125 0.4595482647418976 0.8572837 0.2965225279331207 False diff --git a/ENCSR621ENC/cherimoya.fold_3.performance.tsv b/ENCSR621ENC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e3c6f4951b6b44274ff7ace02324fa57c2aebc38..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1755.8172607421875 0.25310805439949036 0.46047043800354004 0.3092040419578552 0.8602601289749146 0.8414994478225708 0.2927621901035309 \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_4.evaluate.json b/ENCSR621ENC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2242fa0f2f7283aa7496911989c4425c1a87df72..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF672IYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_4.fit.json b/ENCSR621ENC/cherimoya.fold_4.fit.json deleted file mode 100644 index 75359b90f79327b4c35c849d142fd597a4dc92dc..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF672IYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR621ENC/cherimoya.fold_4.log b/ENCSR621ENC/cherimoya.fold_4.log deleted file mode 100644 index c36b8bc7c9e4c0810cdcfb8e24e0f4f7709d80fb..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2841 36.86849617958069 3.5608749389648438 1431.5634765625 0.6014559864997864 1911.050048828125 0.32762208580970764 0.7490365 7.9619975090026855 True -1 5682 31.710306882858276 0.9175968170166016 1350.638427734375 0.9553534984588623 1730.02783203125 0.41627559065818787 0.7917666 1.7471613883972168 True -2 8523 31.673306226730347 13.268372535705566 1403.494384765625 0.7087253332138062 1703.80224609375 0.4256599545478821 0.7903771 0.885196328163147 False -3 11364 33.153913497924805 0.5918872356414795 1186.8828125 0.5963486433029175 1696.4896240234375 0.42702701687812805 0.79501885 0.6598663330078125 True -4 14205 31.736007928848267 1.4445414543151855 1367.697265625 0.5870200991630554 1687.1029052734375 0.4314234256744385 0.8006183 0.5407249331474304 True -5 17046 31.751750469207764 0.5930814743041992 1432.37841796875 0.8050192594528198 1679.7337646484375 0.43609291315078735 0.8089487 0.4912426471710205 True -6 19887 31.69929313659668 0.6035172939300537 1340.5809326171875 0.7271695137023926 1679.7498779296875 0.434840589761734 0.80858266 0.43850651383399963 False -7 22728 31.655039310455322 0.6011233329772949 1682.2757568359375 0.3664362132549286 1674.58740234375 0.43841633200645447 0.8125843 0.43993088603019714 True -8 25569 31.632673978805542 0.5972774028778076 1408.956787109375 0.47349509596824646 1662.072265625 0.445618212223053 0.8190833 0.3822581171989441 True -9 28410 31.66197681427002 0.6189055442810059 1372.66748046875 0.3397842347621918 1661.0150146484375 0.4456847012042999 0.8218752 0.3397035002708435 True -10 31251 31.77664542198181 0.8376305103302002 1304.5701904296875 0.1842980831861496 1657.098876953125 0.44611218571662903 0.825648 0.3474870026111603 True -11 34092 31.79478359222412 0.5993654727935791 1512.421875 0.6100368499755859 1655.7432861328125 0.4461456537246704 0.83072084 0.3284418284893036 True -12 36933 31.65893006324768 1.2307968139648438 1227.8492431640625 0.6271679401397705 1646.328857421875 0.4517393410205841 0.8364043 0.3144139051437378 True -13 39774 31.703365325927734 0.5983524322509766 1308.009765625 0.389777809381485 1642.0306396484375 0.45318132638931274 0.84262305 0.29234570264816284 True -14 42615 31.762489557266235 0.5997476577758789 1245.713134765625 0.4071093201637268 1640.95654296875 0.4537193775177002 0.84720826 0.282667338848114 True -15 45456 31.70314908027649 1.256559133529663 1140.2470703125 0.41889071464538574 1640.6650390625 0.45381152629852295 0.85042053 0.26945966482162476 True -16 48297 31.762391090393066 0.5922369956970215 1352.65185546875 0.38707926869392395 1640.1478271484375 0.4526546001434326 0.8513482 0.2681288719177246 True -17 51138 31.70078945159912 0.601017951965332 1357.9090576171875 0.3020921051502228 1639.1053466796875 0.45439612865448 0.8530991 0.2675929665565491 True -18 53979 31.978170156478882 0.635732889175415 1345.6175537109375 0.314534068107605 1643.9949951171875 0.4509508013725281 0.85358983 0.2693599462509155 True -19 56820 31.710787773132324 0.5930712223052979 1366.812255859375 0.2489227056503296 1645.1195068359375 0.4503878951072693 0.85141927 0.2730274200439453 False diff --git a/ENCSR621ENC/cherimoya.fold_4.performance.tsv b/ENCSR621ENC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9a9dcd22792a23574389692cc813bda8e3325fef..0000000000000000000000000000000000000000 --- a/ENCSR621ENC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1643.9949951171875 0.25965625047683716 0.4509508013725281 0.29531288146972656 0.8535898327827454 0.8257142901420593 0.2693599462509155 \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_0.evaluate.json b/ENCSR622CAH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index dffd1ff951e14b9aa1453b54a46996ca0805f857..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF340RAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_0.fit.json b/ENCSR622CAH/cherimoya.fold_0.fit.json deleted file mode 100644 index 813a6148d849ead1416063ed0c31b02e26362a45..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF340RAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_0.log b/ENCSR622CAH/cherimoya.fold_0.log deleted file mode 100644 index 6b68e4bd367eb7fd00e3f2947117f4afa97c7eca..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 34.82448744773865 2.1490132808685303 177.16000366210938 0.8405284881591797 244.30210876464844 0.16538222134113312 0.52418727 2.9244606494903564 True -1 5460 30.509042501449585 0.5511970520019531 153.35369873046875 0.8848152160644531 223.22833251953125 0.25512319803237915 0.64122057 1.7993388175964355 True -2 8190 29.88861918449402 0.5324606895446777 173.41163635253906 0.9280901551246643 219.9481201171875 0.26664766669273376 0.6462998 0.8690173029899597 True -3 10920 29.848222732543945 0.5240066051483154 158.59725952148438 0.7858386635780334 218.50990295410156 0.2709246873855591 0.6622917 0.6487594246864319 True -4 13650 30.30370569229126 18.87285804748535 146.46832275390625 1.0727782249450684 217.73829650878906 0.27468428015708923 0.6639254 0.6176773309707642 True -5 16380 29.840044736862183 0.5531330108642578 207.08096313476562 0.9613943099975586 217.12350463867188 0.2770557105541229 0.6660426 0.586279034614563 True -6 19110 30.71744179725647 14.502705812454224 149.045166015625 0.7292203903198242 216.2469940185547 0.2808270752429962 0.67047364 0.5852896571159363 True -7 21840 29.950419425964355 0.5335903167724609 188.8031005859375 0.9955356121063232 215.6427001953125 0.2831379175186157 0.675923 0.5632815361022949 True -8 24570 29.92030358314514 0.5335752964019775 162.76486206054688 0.7948944568634033 215.13290405273438 0.2859881520271301 0.682524 0.5681729316711426 True -9 27300 29.807472944259644 0.5205192565917969 188.2998046875 0.7970243096351624 214.8759002685547 0.2871108055114746 0.68607724 0.5629771947860718 True -10 30030 29.786936283111572 0.5328109264373779 159.45947265625 0.841982364654541 214.44580078125 0.2887682020664215 0.692 0.5598180294036865 True -11 32760 29.770402431488037 0.5139234066009521 194.14453125 0.5625685453414917 213.8354949951172 0.29070213437080383 0.7003871 0.526547908782959 True -12 35490 30.459039449691772 20.327324628829956 175.64993286132812 0.6080141663551331 213.24392700195312 0.2935808300971985 0.7117866 0.509859025478363 True -13 38220 29.859392642974854 5.332902908325195 166.04849243164062 0.39293164014816284 212.6502685546875 0.29576870799064636 0.7198045 0.49592626094818115 True -14 40950 29.828984260559082 0.5351064205169678 187.3879852294922 0.387166827917099 211.96751403808594 0.29929056763648987 0.73046935 0.4763793349266052 True -15 43680 29.808210134506226 0.5322964191436768 188.85479736328125 0.619560956954956 211.9181365966797 0.29901137948036194 0.7371104 0.46776115894317627 True -16 46410 29.92821168899536 0.5430796146392822 191.72373962402344 0.2821645438671112 211.68304443359375 0.2998160123825073 0.7431817 0.4560025632381439 True -17 49140 29.872116565704346 0.5490894317626953 204.8638916015625 0.5725373029708862 211.63082885742188 0.30048561096191406 0.74529487 0.45777177810668945 True -18 51870 30.342085361480713 35.28883337974548 146.44415283203125 0.44662386178970337 211.65469360351562 0.29960429668426514 0.74462676 0.462012380361557 False -19 54600 33.00692343711853 31.143946409225464 162.23129272460938 0.423336386680603 211.53103637695312 0.30044102668762207 0.743554 0.46531951427459717 False diff --git a/ENCSR622CAH/cherimoya.fold_0.performance.tsv b/ENCSR622CAH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 98c149fe24f06555354d20856dd57b51df35f534..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -211.63082885742188 0.5054039359092712 0.30048561096191406 0.06982303410768509 0.7452948689460754 0.6759428381919861 0.45777177810668945 \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_1.evaluate.json b/ENCSR622CAH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9323de11e338327636d2e2e6291bdb99afd8e8f7..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF340RAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_1.fit.json b/ENCSR622CAH/cherimoya.fold_1.fit.json deleted file mode 100644 index 0bf79f3c147db2b3ecafe4adcd17a401c932c87d..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF340RAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_1.log b/ENCSR622CAH/cherimoya.fold_1.log deleted file mode 100644 index 373968495eff8075f1b218016931a76739bf06c2..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2716 34.49074578285217 3.7342147827148438 161.6407012939453 1.0315163135528564 279.6337890625 0.17282544076442719 0.571116 3.7694382667541504 True -1 5432 30.25740909576416 0.6896922588348389 160.91696166992188 0.9104109406471252 254.49996948242188 0.2701643109321594 0.663083 1.5672578811645508 True -2 8148 30.329631805419922 0.6725399494171143 174.46975708007812 0.5635132789611816 249.91488647460938 0.28008460998535156 0.67512846 0.8581969141960144 True -3 10864 29.653725147247314 0.6721901893615723 139.30029296875 0.836127758026123 247.6033935546875 0.28686895966529846 0.6887829 0.6553001403808594 True -4 13580 29.699320793151855 0.6748669147491455 196.13160705566406 0.669488787651062 246.14439392089844 0.29226550459861755 0.6989779 0.6536391377449036 True -5 16296 29.726377964019775 0.6636168956756592 131.200439453125 0.7454611659049988 245.90921020507812 0.29215145111083984 0.7032373 0.6567302346229553 True -6 19012 29.68669581413269 0.6606669425964355 164.91253662109375 0.6260510683059692 245.0706024169922 0.2957014739513397 0.708647 0.6142252087593079 True -7 21728 29.662744283676147 0.6656191349029541 164.9499053955078 0.548900306224823 244.4272918701172 0.296892374753952 0.71576464 0.6055731177330017 True -8 24444 29.68245220184326 0.6557672023773193 253.24368286132812 0.7189550995826721 243.70704650878906 0.29957568645477295 0.7211232 0.5581783652305603 True -9 27160 29.66850757598877 1.518827199935913 224.8836212158203 0.6186921000480652 242.9360809326172 0.3027678430080414 0.72685283 0.5647249221801758 True -10 29876 29.75078010559082 0.6638326644897461 173.73190307617188 0.7051793932914734 242.62103271484375 0.30357539653778076 0.7309775 0.5398510098457336 True -11 32592 29.736324787139893 0.6574139595031738 165.42308044433594 0.7425979375839233 241.97254943847656 0.3050219714641571 0.7380377 0.5309706330299377 True -12 35308 29.86720299720764 0.962562084197998 172.0320281982422 0.5800632834434509 241.02633666992188 0.3094611167907715 0.74611413 0.5077987313270569 True -13 38024 30.425715684890747 0.6615173816680908 157.51177978515625 0.6140937805175781 240.7318572998047 0.3103688955307007 0.7560515 0.4953085482120514 True -14 40740 29.78078055381775 0.6660428047180176 176.15936279296875 0.4553002119064331 240.50218200683594 0.3110356628894806 0.76368153 0.48416879773139954 True -15 43456 32.22245717048645 37.3909592628479 162.69329833984375 0.4334254562854767 240.12362670898438 0.31195303797721863 0.76866233 0.47410184144973755 True -16 46172 29.639817714691162 33.0326874256134 149.97625732421875 0.5215654373168945 239.92845153808594 0.3137207627296448 0.77175564 0.4714967906475067 True -17 48888 31.060526609420776 0.6693587303161621 152.23728942871094 0.5187708139419556 239.9534149169922 0.31385892629623413 0.7732325 0.47701069712638855 True -18 51604 29.875097036361694 0.6823303699493408 182.12130737304688 0.36525189876556396 240.10751342773438 0.312881201505661 0.7725516 0.47921356558799744 False -19 54320 29.786508083343506 0.6703078746795654 164.29315185546875 0.3327409029006958 240.2534637451172 0.31250908970832825 0.7707688 0.4849577844142914 False diff --git a/ENCSR622CAH/cherimoya.fold_1.performance.tsv b/ENCSR622CAH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7e5db76fdebd9032830f5d490227bbefd28a65aa..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -239.9534149169922 0.4917992353439331 0.3138589560985565 0.07658528536558151 0.7732325196266174 0.7297244071960449 0.47701069712638855 \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_2.evaluate.json b/ENCSR622CAH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 65d5dccf4e700b141dcd10598478cccbfb80d3a4..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF340RAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_2.fit.json b/ENCSR622CAH/cherimoya.fold_2.fit.json deleted file mode 100644 index 96a8bca67444c92f353d2002745be3352812315b..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF340RAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_2.log b/ENCSR622CAH/cherimoya.fold_2.log deleted file mode 100644 index 77fe3a1b22fa87c30f41fba3f0601b255c51ae31..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2887 36.807862997055054 4.30446457862854 175.18182373046875 0.8312320113182068 247.6461944580078 0.16728191077709198 0.54905343 2.586332321166992 True -1 5774 32.32059192657471 36.61374497413635 155.63050842285156 1.0798604488372803 226.2591552734375 0.2587440013885498 0.63649315 1.573318600654602 True -2 8661 32.33221697807312 27.532421827316284 166.37646484375 1.0085704326629639 222.6846466064453 0.27051660418510437 0.6386382 0.7051391005516052 True -3 11548 31.60491156578064 14.94467282295227 171.80157470703125 0.7142012715339661 220.7890625 0.2762148380279541 0.6555176 0.6260366439819336 True -4 14435 31.62977409362793 20.15392518043518 182.076416015625 0.5988094210624695 220.0592041015625 0.27944785356521606 0.6603133 0.5770987272262573 True -5 17322 33.361263275146484 0.550856351852417 183.87820434570312 0.7188942432403564 219.37655639648438 0.2812028229236603 0.666478 0.5682758688926697 True -6 20209 31.57825493812561 0.5246968269348145 176.74978637695312 0.5305953025817871 218.65025329589844 0.2838713824748993 0.67434037 0.5906992554664612 True -7 23096 31.715205192565918 0.5244131088256836 174.67721557617188 0.7176439166069031 217.89781188964844 0.2866531312465668 0.67673516 0.5697228908538818 True -8 25983 31.59021759033203 0.5241897106170654 160.81549072265625 0.7002115249633789 217.85888671875 0.2872597277164459 0.67920774 0.5838547348976135 True -9 28870 31.517866849899292 0.5236616134643555 198.4906005859375 0.9530490040779114 217.14759826660156 0.2901476323604584 0.6863231 0.5525947213172913 True -10 31757 31.509637117385864 0.522881031036377 151.72901916503906 0.593431830406189 216.52447509765625 0.2922039330005646 0.6939879 0.541664183139801 True -11 34644 31.65375852584839 0.5193939208984375 184.0620574951172 0.6342482566833496 216.0074462890625 0.294438898563385 0.7024671 0.5298236608505249 True -12 37531 31.575589895248413 0.5264654159545898 202.32102966308594 0.7665740251541138 215.3012237548828 0.2963813543319702 0.7102707 0.5160573720932007 True -13 40418 31.602838039398193 0.5235354900360107 166.94525146484375 0.7333818674087524 214.7952423095703 0.2983842194080353 0.71775913 0.5182440876960754 True -14 43305 31.698250770568848 0.5239048004150391 191.00323486328125 0.5758215188980103 214.3813934326172 0.30035436153411865 0.7275375 0.4893653690814972 True -15 46192 31.594531059265137 0.5295822620391846 164.80453491210938 0.46831315755844116 213.9745330810547 0.30170950293540955 0.7353343 0.47875773906707764 True -16 49079 31.605692863464355 0.5396642684936523 175.28598022460938 0.5495001077651978 213.85589599609375 0.30247506499290466 0.73914105 0.46907925605773926 True -17 51966 31.601760149002075 30.576027870178223 159.9638671875 0.5949009656906128 213.99497985839844 0.3018823564052582 0.7392859 0.47276192903518677 True -18 54853 32.32337713241577 0.5278968811035156 189.44210815429688 0.34913238883018494 214.08811950683594 0.30200138688087463 0.74007756 0.47752001881599426 True -19 57740 31.790355682373047 38.5130410194397 190.51031494140625 0.42809322476387024 214.069580078125 0.30208176374435425 0.7398725 0.4807016849517822 False diff --git a/ENCSR622CAH/cherimoya.fold_2.performance.tsv b/ENCSR622CAH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 14a60f73637afe48cdd6d72cfada13d5b63a510d..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -214.08811950683594 0.5040073990821838 0.30200138688087463 0.0671481043100357 0.740077555179596 0.679699182510376 0.47752001881599426 \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_3.evaluate.json b/ENCSR622CAH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 59290d8f9ef356ecd58c388113629471c4e260b6..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF340RAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_3.fit.json b/ENCSR622CAH/cherimoya.fold_3.fit.json deleted file mode 100644 index 65d7d76fa667dcc45f367f28572edd7675f9e042..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF340RAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_3.log b/ENCSR622CAH/cherimoya.fold_3.log deleted file mode 100644 index d577b3533a61aed3eeffe960b7a031198bfc76b8..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 35.5113251209259 3.716160535812378 162.6162109375 0.7229397296905518 252.0874786376953 0.16355173289775848 0.5485464 3.5094337463378906 True -1 5476 30.664610385894775 0.5836882591247559 162.14175415039062 0.8431380391120911 229.46791076660156 0.2576221227645874 0.6387208 1.6342792510986328 True -2 8214 30.38098454475403 0.5655581951141357 213.56033325195312 0.8243240118026733 225.94229125976562 0.2688642740249634 0.64857227 0.9222710132598877 True -3 10952 29.941240787506104 1.5354297161102295 166.8274383544922 0.741786539554596 224.19847106933594 0.27518948912620544 0.65510255 0.8110275864601135 True -4 13690 30.01453185081482 0.5785329341888428 196.96560668945312 0.8219252824783325 223.4700469970703 0.2779046297073364 0.66285837 0.818199872970581 True -5 16428 29.891690731048584 0.571157693862915 173.33404541015625 0.8370954990386963 222.65953063964844 0.2814941108226776 0.67035276 0.7503359913825989 True -6 19166 29.865841150283813 0.5666534900665283 180.21926879882812 0.637883186340332 222.3992156982422 0.2823437750339508 0.6744122 0.7399380803108215 True -7 21904 29.87493896484375 0.56294846534729 189.49574279785156 0.8590219616889954 221.2718048095703 0.28701215982437134 0.6812414 0.6761078238487244 True -8 24642 29.95159149169922 0.5727925300598145 184.11940002441406 0.6105569005012512 220.86468505859375 0.2889770567417145 0.6876592 0.654378354549408 True -9 27380 30.19827914237976 6.526419162750244 144.00570678710938 0.5111016035079956 220.20799255371094 0.29074472188949585 0.69011503 0.6071900129318237 True -10 30118 29.896581649780273 27.892607927322388 174.28131103515625 0.6236710548400879 219.8836212158203 0.2914026975631714 0.7003743 0.5752519965171814 True -11 32856 30.320212602615356 0.573267936706543 192.62939453125 0.900946855545044 219.31723022460938 0.2933165431022644 0.7120675 0.5412102937698364 True -12 35594 30.545541286468506 27.763386011123657 186.93014526367188 0.567866325378418 218.50146484375 0.2966676652431488 0.72135544 0.5261080265045166 True -13 38332 30.164814233779907 0.5899763107299805 196.71405029296875 0.4745618999004364 217.9219207763672 0.29902854561805725 0.72802323 0.4924854338169098 True -14 41070 29.871281385421753 0.5697994232177734 164.21981811523438 0.5193070769309998 217.38540649414062 0.30113816261291504 0.73591614 0.49006831645965576 True -15 43808 29.88946795463562 0.565251350402832 190.61923217773438 0.6059173345565796 217.16329956054688 0.30277392268180847 0.7407744 0.48078837990760803 True -16 46546 29.937364101409912 0.5646178722381592 199.89010620117188 0.47065240144729614 217.0484619140625 0.30308228731155396 0.7458951 0.4782828390598297 True -17 49284 30.012349605560303 0.8411624431610107 173.53359985351562 0.4384487271308899 217.09759521484375 0.30273938179016113 0.7489031 0.48114272952079773 True -18 52022 29.99781084060669 1.275956153869629 153.54208374023438 0.4930335581302643 216.80023193359375 0.3048226535320282 0.7465573 0.4871392548084259 False -19 54760 30.105116844177246 1.5138235092163086 159.65756225585938 0.49804583191871643 216.91815185546875 0.3038475811481476 0.74532515 0.492916077375412 False diff --git a/ENCSR622CAH/cherimoya.fold_3.performance.tsv b/ENCSR622CAH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 925499c84d06a5166662a709b15e37e0d3fb0214..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -217.09759521484375 0.5023844242095947 0.3027394115924835 0.06831532716751099 0.7489030957221985 0.6863557696342468 0.48114272952079773 \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_4.evaluate.json b/ENCSR622CAH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d88d7710873b0169ce78db54ba64ba746021a361..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF340RAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_4.fit.json b/ENCSR622CAH/cherimoya.fold_4.fit.json deleted file mode 100644 index 1b1a06edbd981efce3cbcc39d10d78e267bc2804..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF340RAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622CAH/cherimoya.fold_4.log b/ENCSR622CAH/cherimoya.fold_4.log deleted file mode 100644 index b7a5fb0f173c08c4f6ca1246027ea52d3363dbb5..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2827 37.114834785461426 4.233802318572998 203.37506103515625 0.7705853581428528 243.539306640625 0.16429613530635834 0.5106537 3.7014198303222656 True -1 5654 31.908618688583374 0.6119105815887451 171.89175415039062 0.91355299949646 222.31858825683594 0.2578262388706207 0.60366255 1.5292574167251587 True -2 8481 31.044663906097412 0.6130235195159912 177.81858825683594 1.2082926034927368 220.20486450195312 0.2642551362514496 0.6164808 0.8198484182357788 True -3 11308 31.004890203475952 0.5995469093322754 158.50201416015625 0.6876583099365234 217.92025756835938 0.2733358144760132 0.6266416 0.713681161403656 True -4 14135 30.84003448486328 1.0719351768493652 164.7384033203125 0.8115497827529907 217.2276153564453 0.27639153599739075 0.63794917 0.7137523293495178 True -5 16962 30.865718841552734 0.5937910079956055 188.882080078125 0.5319257974624634 216.64279174804688 0.27827268838882446 0.64916384 0.6539208292961121 True -6 19789 31.035500288009644 0.5941493511199951 162.11459350585938 0.4762978255748749 216.35650634765625 0.27985405921936035 0.6551467 0.6657071113586426 True -7 22616 30.97111177444458 0.5909585952758789 166.41006469726562 0.993441104888916 215.96133422851562 0.2811513841152191 0.66264695 0.6624141931533813 True -8 25443 30.96676015853882 1.6933550834655762 186.6213836669922 0.4848215878009796 215.0616912841797 0.28517845273017883 0.6710703 0.638111412525177 True -9 28270 31.84810733795166 0.5987560749053955 172.18704223632812 0.7779836654663086 214.6868438720703 0.28711429238319397 0.6750465 0.6238226890563965 True -10 31097 31.0011568069458 0.6061699390411377 164.92169189453125 0.7841397523880005 214.18524169921875 0.2887166440486908 0.6810601 0.5904474258422852 True -11 33924 30.980122804641724 0.5947287082672119 159.52908325195312 0.5194868445396423 213.36273193359375 0.292326420545578 0.68861455 0.571322500705719 True -12 36751 30.8976948261261 0.6003298759460449 171.97763061523438 0.39343035221099854 213.26724243164062 0.2922450006008148 0.6970947 0.5366075038909912 True -13 39578 31.200340509414673 24.682520389556885 178.2886962890625 0.5359833836555481 212.5823974609375 0.2955248951911926 0.7069244 0.5229465365409851 True -14 42405 31.212931394577026 0.5943717956542969 156.40467834472656 0.49793869256973267 212.17092895507812 0.2975492775440216 0.718489 0.4987749457359314 True -15 45232 31.152405977249146 0.5926105976104736 159.69827270507812 0.563167929649353 212.36631774902344 0.29633742570877075 0.7254665 0.4851972758769989 True -16 48059 30.98768901824951 0.5911571979522705 140.65045166015625 0.5049000978469849 211.73342895507812 0.3002154231071472 0.7305837 0.47756004333496094 True -17 50886 32.60897755622864 0.5806751251220703 146.497314453125 0.28619685769081116 211.8249053955078 0.29899299144744873 0.73229194 0.47441190481185913 True -18 53713 30.893590450286865 1.3699367046356201 159.50271606445312 0.3927408456802368 211.6266632080078 0.301029771566391 0.7320145 0.47908714413642883 False -19 56540 30.9229474067688 0.5887832641601562 179.42181396484375 0.4311799108982086 211.7649383544922 0.30004754662513733 0.73173004 0.4831986427307129 False diff --git a/ENCSR622CAH/cherimoya.fold_4.performance.tsv b/ENCSR622CAH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 57e388ca1fc48e681796ba647aa101c320b3c2b4..0000000000000000000000000000000000000000 --- a/ENCSR622CAH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -211.8249053955078 0.505910336971283 0.29899299144744873 0.06731893122196198 0.7322919368743896 0.6699360609054565 0.47441190481185913 \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_0.evaluate.json b/ENCSR622HTS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a49f5e00ba0401eaeccb9fd3fa2222aaec65c815..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020TZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_0.fit.json b/ENCSR622HTS/cherimoya.fold_0.fit.json deleted file mode 100644 index 74e8b77eade6211e14db7e46e22147be97ac89f4..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF020TZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_0.log b/ENCSR622HTS/cherimoya.fold_0.log deleted file mode 100644 index 1137997a42284cc5d6e0f97063aa232a61d03b5a..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 35.07233023643494 4.1486334800720215 665.7570190429688 0.4305098354816437 1046.2713623046875 0.2800903022289276 0.6638639 9.092066764831543 True -1 5522 30.464160442352295 0.5913362503051758 870.1634521484375 0.8321099281311035 878.8511962890625 0.3822714388370514 0.75713426 2.205559015274048 True -2 8283 30.488579988479614 0.6038315296173096 551.5573120117188 0.6512061357498169 854.4839477539062 0.3967887759208679 0.76988345 1.0292959213256836 True -3 11044 30.490257024765015 1.1335489749908447 879.6162109375 1.1024127006530762 848.2935180664062 0.399723082780838 0.77564603 0.9738906025886536 True -4 13805 30.44162082672119 0.5786266326904297 743.6515502929688 0.6370889544487 843.0360717773438 0.4036746621131897 0.78094774 0.8438591957092285 True -5 16566 30.43599557876587 0.5817093849182129 973.7177124023438 0.6697053909301758 837.9175415039062 0.4061642289161682 0.7826862 0.7566017508506775 True -6 19327 30.109426975250244 6.903328895568848 717.93212890625 0.639703631401062 829.8728637695312 0.41333162784576416 0.78970397 0.6207441687583923 True -7 22088 29.979861736297607 0.5726597309112549 828.4854736328125 0.6973468661308289 824.7974853515625 0.41544783115386963 0.79240537 0.5660425424575806 True -8 24849 29.940409660339355 0.6706132888793945 815.8773193359375 0.8036139011383057 823.5634765625 0.4154755771160126 0.7976003 0.5325224995613098 True -9 27610 30.002620220184326 0.5982749462127686 577.2071533203125 0.6188849806785583 817.1871337890625 0.4209573566913605 0.80528575 0.5449482202529907 True -10 30371 30.026751279830933 0.5704617500305176 734.3436279296875 0.5041658878326416 815.5310668945312 0.4211045503616333 0.80929416 0.5127648711204529 True -11 33132 29.90062975883484 0.571965217590332 768.7874755859375 0.9857536554336548 809.9515991210938 0.4250272512435913 0.819343 0.4916844367980957 True -12 35893 29.931870222091675 0.5658314228057861 658.6312255859375 0.6716310381889343 809.9209594726562 0.4245077073574066 0.8233674 0.47163280844688416 True -13 38654 29.823983669281006 0.5598201751708984 732.588134765625 0.46941256523132324 806.517822265625 0.4260888695716858 0.8288204 0.4474835991859436 True -14 41415 29.901310682296753 0.5709667205810547 579.2105102539062 0.4187544584274292 804.1515502929688 0.42613640427589417 0.8348098 0.4276823103427887 True -15 44176 29.907898902893066 0.5693962574005127 778.4086303710938 0.5395257472991943 801.9366455078125 0.4295026957988739 0.8409468 0.41372331976890564 True -16 46937 29.88929581642151 0.5595436096191406 617.3087768554688 0.600598156452179 799.651123046875 0.43085378408432007 0.8443304 0.4042314887046814 True -17 49698 29.891648292541504 0.5716884136199951 654.8862915039062 0.3687058687210083 801.3803100585938 0.42843863368034363 0.8445194 0.39838099479675293 True -18 52459 29.883605003356934 0.5748355388641357 707.5486450195312 0.3814694881439209 801.476806640625 0.4284265339374542 0.8461199 0.3997655510902405 True -19 55220 29.80004072189331 0.55364990234375 622.8721923828125 0.2618717849254608 801.56201171875 0.42793917655944824 0.84437776 0.40121421217918396 False diff --git a/ENCSR622HTS/cherimoya.fold_0.performance.tsv b/ENCSR622HTS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5fe4a98a30bc08a232f240de085f6edaeff68e1b..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -801.476806640625 0.3758239448070526 0.4284265339374542 0.17389564216136932 0.8461198806762695 0.8013386130332947 0.3997655510902405 \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_1.evaluate.json b/ENCSR622HTS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a6e20081a696f0c51dadbec78831b0b96bbe67a8..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020TZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_1.fit.json b/ENCSR622HTS/cherimoya.fold_1.fit.json deleted file mode 100644 index 9b4f06a3482a1914818de47df6ed1a9f0e73e836..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF020TZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_1.log b/ENCSR622HTS/cherimoya.fold_1.log deleted file mode 100644 index f5d8f1c02894860c9156f87e6cc997e7011363fc..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2692 34.54595732688904 4.133031129837036 745.0944213867188 0.8170254230499268 1250.93408203125 0.2848525643348694 0.66473466 8.537516593933105 True -1 5384 29.69943356513977 0.7748227119445801 853.3065185546875 0.6759128570556641 1047.04541015625 0.390750914812088 0.76107574 3.037870168685913 True -2 8076 29.723521947860718 0.7420203685760498 662.9644775390625 0.7441744804382324 1019.6132202148438 0.4024905860424042 0.7812385 1.489058017730713 True -3 10768 29.69287347793579 0.7372379302978516 599.6063842773438 0.6552227139472961 1002.8539428710938 0.41069573163986206 0.7904602 1.198914647102356 True -4 13460 29.69240164756775 0.726682186126709 752.114013671875 0.5309832096099854 998.9313354492188 0.4134637415409088 0.7964974 1.0546422004699707 True -5 16152 29.64396357536316 0.7306985855102539 640.1163330078125 0.6350246071815491 993.0491943359375 0.4158208966255188 0.80168974 0.9227353930473328 True -6 18844 29.144616842269897 0.7229082584381104 641.26318359375 0.365808367729187 986.044677734375 0.4208727478981018 0.8020787 0.9350742697715759 True -7 21536 29.162315368652344 0.7174210548400879 739.177978515625 0.5607978105545044 981.10986328125 0.42338812351226807 0.80851114 0.8215674757957458 True -8 24228 29.17166042327881 0.716101884841919 604.146240234375 0.5624243021011353 975.5763549804688 0.4257729947566986 0.81245375 0.780073881149292 True -9 26920 29.095153093338013 0.7218689918518066 677.4959106445312 0.48776185512542725 969.8594970703125 0.428946852684021 0.82062143 0.7575346231460571 True -10 29612 29.232887744903564 0.7470407485961914 608.721435546875 0.7302393913269043 963.2577514648438 0.4322507977485657 0.82544655 0.6948859691619873 True -11 32304 29.290722608566284 0.7534427642822266 604.9735107421875 0.4085197448730469 959.767578125 0.4337017238140106 0.83308643 0.6078581213951111 True -12 34996 29.26323676109314 0.751375675201416 620.2493896484375 0.7206162810325623 951.739013671875 0.4384274184703827 0.83791685 0.5598663687705994 True -13 37688 29.324823141098022 0.7420408725738525 639.1438598632812 0.31218451261520386 950.0936889648438 0.4377067983150482 0.8437331 0.5189031362533569 True -14 40380 29.29584527015686 0.7489583492279053 615.988525390625 0.5373266935348511 945.606201171875 0.44042760133743286 0.8518895 0.4793495535850525 True -15 43072 29.27825379371643 0.749755859375 657.896240234375 0.47326621413230896 941.6358032226562 0.44213199615478516 0.85654867 0.4592556655406952 True -16 45764 29.19862198829651 0.7408945560455322 614.1648559570312 0.3754563629627228 940.7623291015625 0.44150859117507935 0.8589687 0.43698808550834656 True -17 48456 29.227385997772217 13.770767450332642 654.1006469726562 0.4850352108478546 941.1279907226562 0.4412350654602051 0.86063105 0.4225548505783081 True -18 51148 29.236801624298096 0.7734262943267822 724.2636108398438 0.34504634141921997 940.6594848632812 0.4423699975013733 0.86223185 0.41717639565467834 True -19 53840 29.308765649795532 0.7544715404510498 565.0526123046875 0.4603722393512726 939.826904296875 0.4432356655597687 0.8599336 0.4170099198818207 False diff --git a/ENCSR622HTS/cherimoya.fold_1.performance.tsv b/ENCSR622HTS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 25d3283a6d12ff0b0d8f764078872abb1f89e060..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -940.6594848632812 0.3598082661628723 0.44237005710601807 0.19402295351028442 0.8622318506240845 0.8379051089286804 0.41717639565467834 \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_2.evaluate.json b/ENCSR622HTS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b555d8cd90f7b08a7342e5826608d35df2990220..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020TZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_2.fit.json b/ENCSR622HTS/cherimoya.fold_2.fit.json deleted file mode 100644 index 69070284456888e52dff6958a9f8b467a5587378..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF020TZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_2.log b/ENCSR622HTS/cherimoya.fold_2.log deleted file mode 100644 index 11e79aa0b9e239152003362c2ec6ab1d51135690..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.557368993759155 4.273142576217651 810.2012939453125 0.9082691073417664 1078.7086181640625 0.2820280194282532 0.6570919 6.7135772705078125 True -1 5794 31.96039891242981 0.7440352439880371 625.892333984375 0.619594395160675 913.5266723632812 0.3762325048446655 0.7550849 2.179145336151123 True -2 8691 31.924620151519775 2.352882146835327 598.2534790039062 0.7105977535247803 901.098876953125 0.3826562166213989 0.76300454 1.3028672933578491 True -3 11588 32.02233123779297 0.588510274887085 700.00048828125 0.8546673059463501 889.6936645507812 0.39012816548347473 0.7697349 0.9956499338150024 True -4 14485 31.94085121154785 0.6231672763824463 692.6334838867188 0.5695599913597107 883.6544189453125 0.39330559968948364 0.7755929 0.8639463782310486 True -5 17382 31.791218996047974 0.571725606918335 729.103271484375 0.7070655226707458 878.5538330078125 0.3964761197566986 0.7792345 0.8372082114219666 True -6 20279 31.306795835494995 0.5640435218811035 768.0623779296875 0.49611735343933105 874.8233032226562 0.39891985058784485 0.7831153 0.8586523532867432 True -7 23176 31.36409568786621 0.5733053684234619 776.70556640625 0.8542105555534363 872.6802368164062 0.40160396695137024 0.78782064 0.8402872085571289 True -8 26073 31.317694902420044 0.5709183216094971 636.60546875 0.546600878238678 866.5418090820312 0.4042780101299286 0.7924041 0.786405086517334 True -9 28970 31.286336660385132 0.5701806545257568 715.9593505859375 1.2384594678878784 859.8347778320312 0.40839913487434387 0.7996394 0.6807559132575989 True -10 31867 31.297807931900024 0.6666727066040039 684.329833984375 0.7612902522087097 855.548583984375 0.41094714403152466 0.80468875 0.6773675680160522 True -11 34764 31.28073763847351 0.583991527557373 619.90869140625 0.49707096815109253 852.3207397460938 0.4130881130695343 0.8103048 0.6144289374351501 True -12 37661 31.278189659118652 0.5755364894866943 814.87353515625 0.5374529361724854 849.534423828125 0.41475263237953186 0.8183797 0.5718359351158142 True -13 40558 31.32835865020752 0.5742294788360596 787.3646850585938 0.4899049401283264 845.3259887695312 0.4170590937137604 0.82381696 0.5212880969047546 True -14 43455 31.2726788520813 0.5607407093048096 668.3143920898438 0.3352929353713989 843.3432006835938 0.41774410009384155 0.8293845 0.4746251404285431 True -15 46352 31.281888008117676 0.5600185394287109 576.4865112304688 0.5299500226974487 840.0335083007812 0.4197576642036438 0.8351063 0.4460097849369049 True -16 49249 31.296380758285522 0.5549600124359131 482.8336181640625 0.37525269389152527 838.1753540039062 0.42117640376091003 0.8400675 0.4267849326133728 True -17 52146 31.270501375198364 0.5634751319885254 736.8436279296875 0.3144034147262573 841.043701171875 0.4193735420703888 0.8389312 0.41798311471939087 False -18 55043 31.304301738739014 0.5550870895385742 627.2011108398438 0.2963714599609375 839.576904296875 0.4206105172634125 0.8399683 0.41321665048599243 False -19 57940 31.309390783309937 0.5602574348449707 598.5836181640625 0.3389660120010376 840.2557373046875 0.4201035499572754 0.8410281 0.4158882200717926 True diff --git a/ENCSR622HTS/cherimoya.fold_2.performance.tsv b/ENCSR622HTS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 48bd381b8d5d8d397e30e9d749d033db0a4c4049..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -840.2557373046875 0.3773486614227295 0.42010360956192017 0.17322351038455963 0.841028094291687 0.8085141777992249 0.4158882200717926 \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_3.evaluate.json b/ENCSR622HTS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 051fa08aec8c9191ee16e1485101213ba2712f8d..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020TZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_3.fit.json b/ENCSR622HTS/cherimoya.fold_3.fit.json deleted file mode 100644 index 2b466f9b28d46b833ad4b06d756f93865c8e3ca0..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF020TZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_3.log b/ENCSR622HTS/cherimoya.fold_3.log deleted file mode 100644 index 204ca7820725727b5b38dd5ac48f0a575c21f50f..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.968318700790405 3.624824285507202 543.1834716796875 0.6882875561714172 1029.6241455078125 0.2897748649120331 0.6688727 6.5903472900390625 True -1 5498 30.308000802993774 0.6265044212341309 601.8321533203125 1.1068528890609741 871.8502807617188 0.3821476101875305 0.77227235 3.068453073501587 True -2 8247 30.288049697875977 0.5440242290496826 822.2300415039062 1.0032848119735718 852.6007690429688 0.39564037322998047 0.7855278 1.3672055006027222 True -3 10996 30.322952270507812 0.6126022338867188 855.8677978515625 0.6370943784713745 841.7351684570312 0.39956361055374146 0.7900492 1.1531550884246826 True -4 13745 30.27342987060547 0.5126650333404541 711.76513671875 0.6924939751625061 838.2949829101562 0.4009978771209717 0.79709905 1.15305757522583 True -5 16494 30.32593822479248 0.5137197971343994 759.7235717773438 0.9838130474090576 832.6293334960938 0.4054294526576996 0.7991953 0.9036909341812134 True -6 19243 30.11048460006714 0.5141081809997559 838.03271484375 0.7621368765830994 825.6923217773438 0.41000720858573914 0.8008194 0.9452627301216125 True -7 21992 29.764412879943848 0.5135045051574707 585.5305786132812 0.47496873140335083 821.2894287109375 0.4132258892059326 0.80470747 0.797068178653717 True -8 24741 29.79838252067566 0.516376256942749 625.6061401367188 0.8487343192100525 816.9721069335938 0.4162029027938843 0.80848485 0.7754985690116882 True -9 27490 29.74688148498535 0.5133368968963623 695.7291870117188 0.6219851970672607 812.2752075195312 0.41846784949302673 0.8112642 0.7282518744468689 True -10 30239 29.738964080810547 0.5128498077392578 615.7144165039062 0.4261033535003662 810.3045043945312 0.41904908418655396 0.81705314 0.6906427145004272 True -11 32988 29.746742010116577 0.5117793083190918 579.1192626953125 0.4627915918827057 806.0880737304688 0.4220654368400574 0.82163674 0.677233874797821 True -12 35737 29.776352167129517 0.5037782192230225 809.3377685546875 0.45490390062332153 799.7697143554688 0.4266880750656128 0.8276179 0.5783605575561523 True -13 38486 30.698744297027588 0.5258798599243164 553.041015625 0.5356284379959106 797.5645751953125 0.42644229531288147 0.8322908 0.5376030206680298 True -14 41235 29.833576440811157 0.518510103225708 716.4608154296875 0.7703949213027954 795.2369384765625 0.4281824231147766 0.83897 0.4959070682525635 True -15 43984 29.78621220588684 0.5235710144042969 633.7090454101562 0.35815489292144775 793.306640625 0.4293387830257416 0.84527797 0.4549371004104614 True -16 46733 29.754247903823853 0.5130622386932373 770.46142578125 0.555519163608551 792.631591796875 0.4291236102581024 0.84949553 0.43026599287986755 True -17 49482 29.73205256462097 0.5171875953674316 740.335693359375 0.38086938858032227 788.287109375 0.43354156613349915 0.8501279 0.4169742465019226 True -18 52231 29.758800506591797 0.515143632888794 684.023681640625 0.39006465673446655 792.7322998046875 0.4289780855178833 0.8512979 0.41416895389556885 True -19 54980 29.779935836791992 0.5153393745422363 554.903076171875 0.34676480293273926 792.638671875 0.4294254779815674 0.85112154 0.41494306921958923 False diff --git a/ENCSR622HTS/cherimoya.fold_3.performance.tsv b/ENCSR622HTS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f249e816b49a7ff8d214577dc40da46e6ef86274..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -792.7322998046875 0.3749443590641022 0.4289780855178833 0.17285878956317902 0.851297914981842 0.8075246214866638 0.41416895389556885 \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_4.evaluate.json b/ENCSR622HTS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d8b687c86ed218d6449dd2ec9eb5a754c25719ee..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020TZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_4.fit.json b/ENCSR622HTS/cherimoya.fold_4.fit.json deleted file mode 100644 index be4934dcbe050f414090ed951113e23c12b43c3b..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF020TZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR622HTS/cherimoya.fold_4.log b/ENCSR622HTS/cherimoya.fold_4.log deleted file mode 100644 index 2e68191da76ec4790c64c2fd9d09424eff24b429..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 35.307130336761475 4.1034746170043945 827.0869140625 0.8634099960327148 947.27197265625 0.2781948149204254 0.6470971 6.728936195373535 True -1 5544 30.621114015579224 0.6179277896881104 730.4074096679688 0.576941192150116 805.5611572265625 0.373297780752182 0.7359251 2.236790180206299 True -2 8316 30.609973907470703 0.5950541496276855 806.9315795898438 0.7192302942276001 791.0623779296875 0.3832482695579529 0.74766475 1.3107352256774902 True -3 11088 30.55377769470215 0.5989267826080322 786.664306640625 0.7733985185623169 779.5009155273438 0.3903596103191376 0.76181555 1.0263919830322266 True -4 13860 30.53792405128479 1.6486647129058838 687.0009765625 0.6964304447174072 771.9443969726562 0.39634305238723755 0.76880276 0.8619058728218079 True -5 16632 30.04473066329956 0.5878677368164062 599.2935791015625 0.6024907231330872 769.7909545898438 0.39661121368408203 0.77484304 0.6986687779426575 True -6 19404 29.983516454696655 0.6278398036956787 591.314208984375 0.5977770090103149 765.1688842773438 0.3994385302066803 0.7794444 0.671949028968811 True -7 22176 29.96581220626831 0.6049056053161621 679.1949462890625 0.5692000389099121 761.2071533203125 0.4014952778816223 0.78631574 0.6428725719451904 True -8 24948 30.018810033798218 0.5990095138549805 632.3114013671875 0.5080249905586243 758.2118530273438 0.4044792354106903 0.7889157 0.6231299638748169 True -9 27720 30.02080225944519 0.6024091243743896 701.5076293945312 0.5027139186859131 756.8964233398438 0.40497076511383057 0.7957618 0.623376727104187 True -10 30492 30.03918743133545 0.6613485813140869 766.1986083984375 0.4825247526168823 752.2211303710938 0.40921127796173096 0.79889894 0.5743517875671387 True -11 33264 30.00318956375122 0.6013524532318115 622.869140625 0.6371723413467407 748.063720703125 0.4118660092353821 0.805855 0.5489099025726318 True -12 36036 30.062305688858032 0.5892541408538818 677.123291015625 0.3512438237667084 742.758544921875 0.41639214754104614 0.8139071 0.5193724632263184 True -13 38808 30.019496202468872 0.6508269309997559 715.3968505859375 0.5470706224441528 743.1698608398438 0.4141780436038971 0.81838864 0.4877248704433441 True -14 41580 30.06601572036743 0.6021633148193359 499.783935546875 0.5028955340385437 740.9288940429688 0.41501563787460327 0.8246426 0.45889946818351746 True -15 44352 30.049493074417114 0.6490869522094727 931.06689453125 0.3701804280281067 740.0975952148438 0.4160826802253723 0.8314811 0.43275144696235657 True -16 47124 29.998430490493774 0.6049067974090576 569.98095703125 0.3809244930744171 737.0831298828125 0.41822266578674316 0.8358686 0.41312795877456665 True -17 49896 29.973573684692383 0.5925807952880859 625.6311645507812 0.827293872833252 737.6189575195312 0.41796472668647766 0.8369467 0.4044174253940582 True -18 52668 30.024189233779907 1.1982932090759277 596.1610107421875 0.31453779339790344 737.6088256835938 0.41833245754241943 0.83882415 0.39827921986579895 True -19 55440 30.072617530822754 0.6270549297332764 700.9782104492188 0.3146890103816986 740.6063232421875 0.4154544770717621 0.84147584 0.3975405693054199 True diff --git a/ENCSR622HTS/cherimoya.fold_4.performance.tsv b/ENCSR622HTS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5e24b96e8b06e526d8121ba8f29fe726cee38c9c..0000000000000000000000000000000000000000 --- a/ENCSR622HTS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -740.6063232421875 0.38712072372436523 0.4154544472694397 0.16016417741775513 0.8414758443832397 0.7882192134857178 0.3975405693054199 \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_0.evaluate.json b/ENCSR623PVB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ba6528c9d2f053947e1b8f57f7fc42dbcee2ddb5..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF823TQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_0.fit.json b/ENCSR623PVB/cherimoya.fold_0.fit.json deleted file mode 100644 index 5e577adec57a548c241da8a9aaf305f3a597de69..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF823TQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_0.log b/ENCSR623PVB/cherimoya.fold_0.log deleted file mode 100644 index 77631cfe579e79e724511e5d232af2d901006148..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.333314657211304 3.6778564453125 518.6390380859375 0.4754878580570221 762.4352416992188 0.20464029908180237 0.6950611 7.42583703994751 True -1 5516 30.54904270172119 0.6022281646728516 651.4760131835938 0.6702223420143127 692.927734375 0.2399810403585434 0.7615395 2.0753912925720215 True -2 8274 30.49027395248413 0.5877408981323242 760.7958984375 0.6190153360366821 688.2090454101562 0.24030117690563202 0.7691976 1.3738784790039062 True -3 11032 30.07494068145752 1.1505985260009766 630.959228515625 0.5248610377311707 666.565185546875 0.24741652607917786 0.7935865 0.9825885891914368 True -4 13790 29.82517957687378 0.5801942348480225 461.87060546875 0.30956363677978516 657.2156372070312 0.25173142552375793 0.79691285 0.9624649286270142 True -5 16548 29.777353286743164 0.5863535404205322 627.0955810546875 0.4481654763221741 653.7262573242188 0.2534371614456177 0.7925331 0.8081977963447571 False -6 19306 29.770477294921875 0.8770272731781006 646.5526123046875 0.23947645723819733 649.5280151367188 0.25583845376968384 0.8046962 0.6449236273765564 True -7 22064 29.85145854949951 0.575916051864624 493.4856872558594 0.3263718783855438 647.9356079101562 0.2566324472427368 0.80668706 0.6112692952156067 True -8 24822 29.791561126708984 0.5812406539916992 429.9867858886719 0.32495325803756714 641.2967529296875 0.2607559263706207 0.8160987 0.5507387518882751 True -9 27580 29.74609899520874 0.5884144306182861 446.67803955078125 0.4485939145088196 640.1702880859375 0.25989237427711487 0.8249978 0.4636803865432739 True -10 30338 29.74183678627014 0.5774538516998291 617.7083129882812 0.33098188042640686 635.4533081054688 0.2628881633281708 0.83100384 0.4308808743953705 True -11 33096 29.75202965736389 0.8066751956939697 706.6229858398438 0.21199241280555725 633.3383178710938 0.2632383108139038 0.8449018 0.382744699716568 True -12 35854 29.82138156890869 0.5881619453430176 534.8023681640625 0.320658415555954 629.6004638671875 0.26463577151298523 0.85196096 0.34227001667022705 True -13 38612 29.771379947662354 0.5937511920928955 572.21923828125 0.2827942967414856 626.6258544921875 0.26633450388908386 0.8592811 0.3114522397518158 True -14 41370 29.787472009658813 1.2932469844818115 519.1900024414062 0.25851669907569885 624.274658203125 0.2677960991859436 0.86556375 0.28620201349258423 True -15 44128 30.065421104431152 0.5843944549560547 495.385009765625 0.2461954653263092 624.4325561523438 0.2670891284942627 0.87168604 0.27269110083580017 True -16 46886 29.882093906402588 0.5907692909240723 668.05224609375 0.2638062834739685 622.0994262695312 0.26854926347732544 0.8756183 0.261747270822525 True -17 49644 29.903836965560913 1.41170072555542 520.5638427734375 0.20393598079681396 620.7762451171875 0.26885655522346497 0.8759347 0.2599325180053711 True -18 52402 30.12428307533264 35.098917722702026 527.6578369140625 0.09075461328029633 621.792236328125 0.2679501175880432 0.8748754 0.2610833942890167 False -19 55160 29.83764362335205 34.38828921318054 656.0363159179688 0.20562541484832764 621.47314453125 0.26915526390075684 0.8732176 0.263068825006485 False diff --git a/ENCSR623PVB/cherimoya.fold_0.performance.tsv b/ENCSR623PVB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index af533239288dc22471e3983339643a689ebc4ee8..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -620.7762451171875 0.4538780152797699 0.26885655522346497 0.11431515961885452 0.8759347200393677 0.8364948034286499 0.2599325180053711 \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_1.evaluate.json b/ENCSR623PVB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6f935aa8184f8a63d2b61b346361734156c6ce09..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF823TQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_1.fit.json b/ENCSR623PVB/cherimoya.fold_1.fit.json deleted file mode 100644 index 854dc0f8fd3cf6fe2b5226cc54c58a1bf28ff8f9..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF823TQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_1.log b/ENCSR623PVB/cherimoya.fold_1.log deleted file mode 100644 index c4817310ddd087d7a6bfe3ce0ce55141df7e4c3b..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2704 34.79510045051575 7.088216781616211 805.9966430664062 0.6999498605728149 988.650146484375 0.2183752804994583 0.6705342 7.336280822753906 True -1 5408 29.84696865081787 0.7088067531585693 669.3047485351562 0.38933882117271423 893.232666015625 0.25838571786880493 0.7385635 2.5867581367492676 True -2 8112 29.804489135742188 0.6990878582000732 513.92724609375 0.5351253747940063 885.6687622070312 0.263832151889801 0.7391506 1.913627028465271 True -3 10816 29.851768016815186 1.4396941661834717 495.08721923828125 0.3644089698791504 857.1749267578125 0.2714107930660248 0.76946497 1.3212671279907227 True -4 13520 29.365371465682983 0.688894510269165 514.64697265625 0.4315057694911957 829.6465454101562 0.27881982922554016 0.78777826 1.0978833436965942 True -5 16224 29.250163316726685 0.6868388652801514 636.6149291992188 0.3084942102432251 823.0628051757812 0.2785840332508087 0.7983936 1.016921043395996 True -6 18928 29.223548889160156 0.6965420246124268 593.479248046875 0.4249829947948456 808.4049682617188 0.2851269543170929 0.8134178 0.7359995245933533 True -7 21632 29.21663784980774 0.6940658092498779 534.8492431640625 0.3649701774120331 801.900634765625 0.2896428108215332 0.8182008 0.7353987097740173 True -8 24336 29.176649570465088 1.5601074695587158 581.1224975585938 0.2794058620929718 794.4675903320312 0.29150623083114624 0.8285462 0.650096595287323 True -9 27040 29.317437171936035 0.6943461894989014 450.7459411621094 0.29680246114730835 790.9568481445312 0.2919940650463104 0.83475643 0.6235500574111938 True -10 29744 29.31852674484253 0.7029080390930176 441.03515625 0.24418802559375763 782.9702758789062 0.29640865325927734 0.84407115 0.5624215602874756 True -11 32448 29.20758843421936 0.6876657009124756 665.871337890625 0.27130553126335144 781.27490234375 0.29661497473716736 0.8510496 0.5107303261756897 True -12 35152 29.204368114471436 26.88039779663086 596.1701049804688 0.36536604166030884 776.1993408203125 0.29803186655044556 0.861894 0.45470982789993286 True -13 37856 31.036905765533447 26.173108339309692 531.681640625 0.17030657827854156 769.2005615234375 0.3028968870639801 0.8724029 0.41704002022743225 True -14 40560 34.46574568748474 0.7351775169372559 642.339599609375 0.3456883430480957 765.4187622070312 0.30314305424690247 0.8758811 0.3882846236228943 True -15 43264 29.383366584777832 0.6957414150238037 481.8418273925781 0.2004755735397339 765.366943359375 0.3023776710033417 0.8838808 0.35746511816978455 True -16 45968 29.41932439804077 0.6901638507843018 449.0445556640625 0.15966281294822693 763.3668823242188 0.30285465717315674 0.88626736 0.3376031816005707 True -17 48672 29.322559118270874 0.6907522678375244 499.7059631347656 0.24416851997375488 763.0050048828125 0.30254504084587097 0.8897369 0.3245627284049988 True -18 51376 29.37539553642273 1.1251857280731201 541.1175537109375 0.13901430368423462 761.2318725585938 0.3045496642589569 0.8889266 0.321209192276001 False -19 54080 29.710284948349 0.720578670501709 679.5625610351562 0.2553464472293854 763.2318115234375 0.3029220700263977 0.88947093 0.3220255970954895 False diff --git a/ENCSR623PVB/cherimoya.fold_1.performance.tsv b/ENCSR623PVB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b6dccf79fd98ebc854dd726294dfb0734162c57f..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -763.0050048828125 0.4263589680194855 0.3025450110435486 0.14257977902889252 0.8897368907928467 0.8623862862586975 0.3245627284049988 \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_2.evaluate.json b/ENCSR623PVB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f4249492faa2a2b41abb95c3014a749d7f184d89..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF823TQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_2.fit.json b/ENCSR623PVB/cherimoya.fold_2.fit.json deleted file mode 100644 index cae4d0e801f4b5bc97475be30cc3434a9e9d7d37..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF823TQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_2.log b/ENCSR623PVB/cherimoya.fold_2.log deleted file mode 100644 index 98333c11d027dc02303d8552199cd37eed06a818..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.69760322570801 3.6382431983947754 756.956298828125 0.6455093622207642 824.600341796875 0.21056844294071198 0.65992457 6.71396017074585 True -1 5772 31.8445725440979 23.97286820411682 626.6670532226562 0.4610770344734192 749.5203857421875 0.24454669654369354 0.71492195 2.1040101051330566 True -2 8658 32.24335694313049 0.6237716674804688 650.3911743164062 0.4109770953655243 734.8378295898438 0.24686025083065033 0.7539262 1.1246123313903809 True -3 11544 31.83844256401062 1.0145728588104248 628.02294921875 0.5780808329582214 713.0278930664062 0.2528366148471832 0.7824812 0.8913471102714539 True -4 14430 31.530789613723755 0.582064151763916 583.23681640625 0.4406093955039978 705.6714477539062 0.2555446922779083 0.7957843 0.9024168848991394 True -5 17316 31.230555534362793 0.5754439830780029 616.3123779296875 0.28480595350265503 700.6250610351562 0.2561893165111542 0.80225605 0.7769917249679565 True -6 20202 31.184943675994873 0.5867998600006104 605.3206176757812 0.4727000594139099 691.76708984375 0.25980764627456665 0.8101486 0.6948850750923157 True -7 23088 31.173545360565186 0.5877165794372559 460.8675537109375 0.3423384130001068 685.8032836914062 0.26254764199256897 0.8198975 0.6197959780693054 True -8 25974 31.149173259735107 0.7341749668121338 661.920654296875 0.5284014940261841 679.0460205078125 0.2665918469429016 0.8298437 0.5317155718803406 True -9 28860 31.36957836151123 0.585552453994751 498.32220458984375 0.4625888466835022 676.92041015625 0.2675100564956665 0.83217764 0.4870881140232086 True -10 31746 31.277165412902832 0.587634801864624 487.72137451171875 0.4951839745044708 671.4183349609375 0.27060651779174805 0.83822703 0.4381110668182373 True -11 34632 31.22459578514099 0.595832347869873 589.83447265625 0.3346318006515503 672.5862426757812 0.2693133056163788 0.8421154 0.4058685898780823 True -12 37518 31.26103448867798 0.5883870124816895 472.09613037109375 0.3542783856391907 670.4779663085938 0.26985490322113037 0.8504702 0.3694027364253998 True -13 40404 31.351852416992188 30.349414348602295 550.4896240234375 0.44161257147789 667.388916015625 0.2715909481048584 0.85581106 0.33914151787757874 True -14 43290 31.42582678794861 0.5970737934112549 532.8411865234375 0.23141923546791077 665.6006469726562 0.27319589257240295 0.8612829 0.31633612513542175 True -15 46176 31.376368522644043 0.5848517417907715 629.616455078125 0.2899168133735657 662.483154296875 0.273958683013916 0.86406887 0.30501171946525574 True -16 49062 31.265050411224365 0.5899271965026855 509.6676025390625 0.10903147608041763 661.8858032226562 0.2734505832195282 0.86748564 0.2925315201282501 True -17 51948 31.22759485244751 0.6227903366088867 604.066650390625 0.24463719129562378 661.9524536132812 0.2747113108634949 0.86826915 0.28971320390701294 True -18 54834 31.271816730499268 0.5714547634124756 413.361083984375 0.1692901849746704 661.1713256835938 0.2737528681755066 0.8689239 0.29076963663101196 True -19 57720 31.308614015579224 0.5860013961791992 565.5744018554688 0.16443085670471191 661.7083129882812 0.27406737208366394 0.8680679 0.29235976934432983 False diff --git a/ENCSR623PVB/cherimoya.fold_2.performance.tsv b/ENCSR623PVB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 961c349643ccaeb1467737159f53b40ee7b6acde..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -661.1713256835938 0.445668488740921 0.2737528681755066 0.12157630920410156 0.8689239025115967 0.834820032119751 0.29076963663101196 \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_3.evaluate.json b/ENCSR623PVB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 42dfdacb172db84beee4d6107f466f3f918a4521..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF823TQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_3.fit.json b/ENCSR623PVB/cherimoya.fold_3.fit.json deleted file mode 100644 index 28b98c4ad3c7e4cd224c3b703876900f366f20cc..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF823TQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_3.log b/ENCSR623PVB/cherimoya.fold_3.log deleted file mode 100644 index ff2ef46246d119c3a0d8e687cfa8dae097ce16ce..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2722 34.5881245136261 4.062912464141846 647.5933227539062 0.4813435673713684 809.4205322265625 0.21556533873081207 0.63040334 8.575780868530273 True -1 5444 30.11750054359436 0.5647387504577637 589.3139038085938 0.6150199770927429 751.1079711914062 0.24698051810264587 0.6697482 2.2786948680877686 True -2 8166 30.118446826934814 0.5494067668914795 575.4947509765625 0.47638121247291565 733.1624755859375 0.2546614408493042 0.70985335 1.761411428451538 True -3 10888 30.402157306671143 32.30956268310547 681.5289916992188 0.43316906690597534 711.379638671875 0.25912806391716003 0.72226065 1.4118574857711792 True -4 13610 30.22904682159424 0.560795783996582 641.1998291015625 0.2939792573451996 701.2557373046875 0.26176321506500244 0.7437208 0.946100652217865 True -5 16332 29.427206993103027 0.5567722320556641 538.6575927734375 0.29926812648773193 691.3952026367188 0.26719117164611816 0.7568823 0.9089862108230591 True -6 19054 29.443318367004395 0.5516312122344971 520.7767333984375 0.19024202227592468 688.239013671875 0.26516202092170715 0.77162755 0.766150712966919 True -7 21776 29.427431344985962 0.54931640625 672.7921752929688 0.49126705527305603 681.0359497070312 0.2716219127178192 0.77449024 0.739052951335907 True -8 24498 29.404157161712646 1.133239984512329 505.88623046875 0.4688953161239624 678.2689819335938 0.2715880274772644 0.7861777 0.6750218272209167 True -9 27220 29.39514923095703 0.5486507415771484 714.398681640625 0.45789799094200134 672.7487182617188 0.275176078081131 0.79456294 0.6425058245658875 True -10 29942 29.455129861831665 0.5453243255615234 640.1383056640625 0.22884689271450043 671.5297241210938 0.2759874761104584 0.80067444 0.568849503993988 True -11 32664 29.483914136886597 0.5508930683135986 598.2589111328125 0.42515021562576294 666.302490234375 0.279061883687973 0.8129147 0.5173355340957642 True -12 35386 29.49903392791748 0.5543694496154785 540.3294677734375 0.2980457842350006 665.9364013671875 0.2792915105819702 0.8207811 0.4813917875289917 True -13 38108 29.58609127998352 1.2419955730438232 688.352294921875 0.3003188967704773 661.86962890625 0.280948668718338 0.82903683 0.43517830967903137 True -14 40830 29.75088930130005 31.00088095664978 486.96746826171875 0.27066630125045776 659.2452392578125 0.28299835324287415 0.83667475 0.4117516875267029 True -15 43552 30.360183477401733 31.137606143951416 623.0797729492188 0.3835551142692566 655.6723022460938 0.28456783294677734 0.8438975 0.3850504755973816 True -16 46274 30.456316232681274 12.273642778396606 469.8364562988281 0.3195624351501465 655.3467407226562 0.28305521607398987 0.8484411 0.36558184027671814 True -17 48996 29.57088828086853 0.550814151763916 610.3212280273438 0.2965549826622009 656.047607421875 0.28284651041030884 0.8524331 0.3547017574310303 True -18 51718 29.58231258392334 3.8612380027770996 660.0292358398438 0.18051078915596008 655.507568359375 0.2842634320259094 0.8525072 0.3515336811542511 True -19 54440 29.626874685287476 0.5630898475646973 486.022705078125 0.1621488630771637 657.303955078125 0.2825521230697632 0.8520511 0.3503805100917816 False diff --git a/ENCSR623PVB/cherimoya.fold_3.performance.tsv b/ENCSR623PVB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b86ad2034c67f6001fd53f98121d743d1988e955..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -655.507568359375 0.4431634247303009 0.2842634320259094 0.12676681578159332 0.8525071740150452 0.8115438222885132 0.3515336811542511 \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_4.evaluate.json b/ENCSR623PVB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 027ac4ad8cc3fb462aecf51c3fd34792605742f7..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF823TQX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_4.fit.json b/ENCSR623PVB/cherimoya.fold_4.fit.json deleted file mode 100644 index 50f9439c35e01a3e10ec9330f8f37976c7bb734e..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF823TQX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR623PVB/cherimoya.fold_4.log b/ENCSR623PVB/cherimoya.fold_4.log deleted file mode 100644 index 617463843ed6732e2fc47a157de7f7379f213e64..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2786 35.60389709472656 3.821202278137207 634.8483276367188 0.5868209600448608 689.00048828125 0.20315459370613098 0.63760084 6.435790538787842 True -1 5572 30.79331874847412 2.7871387004852295 533.0047607421875 0.6100884675979614 635.6029663085938 0.23502598702907562 0.7008317 1.8417572975158691 True -2 8358 30.773844957351685 0.6113898754119873 530.074462890625 0.3898696303367615 627.3082885742188 0.2374284416437149 0.7364483 1.342961072921753 True -3 11144 30.826013326644897 0.6636922359466553 566.7838134765625 0.4308866262435913 614.0055541992188 0.24155324697494507 0.7494858 0.9293580055236816 True -4 13930 31.023032188415527 36.18406867980957 662.7584228515625 0.4063798189163208 607.3147583007812 0.24409161508083344 0.75305086 0.8923197984695435 True -5 16716 31.573122262954712 0.6050033569335938 556.9051513671875 0.43936634063720703 603.758544921875 0.24540045857429504 0.7592906 0.8002751469612122 True -6 19502 30.115126848220825 1.0090563297271729 444.8268737792969 0.25716233253479004 596.2659301757812 0.25069621205329895 0.7768382 0.6386460065841675 True -7 22288 30.242638111114502 0.5991384983062744 647.1633911132812 0.5533157587051392 594.1610107421875 0.2513570487499237 0.7858657 0.5924021005630493 True -8 25074 30.200091123580933 0.5958492755889893 515.569091796875 0.35811302065849304 589.9209594726562 0.2555449903011322 0.7919979 0.5226779580116272 True -9 27860 30.095783948898315 0.5825438499450684 535.2037963867188 0.5552494525909424 587.4053344726562 0.2562545835971832 0.8005794 0.4661432206630707 True -10 30646 30.072343349456787 0.5814423561096191 563.511962890625 0.30639755725860596 585.1194458007812 0.25751540064811707 0.80548275 0.4213314354419708 True -11 33432 30.109753370285034 0.586653470993042 759.2222900390625 0.5399770736694336 585.9688720703125 0.2549736201763153 0.81287134 0.3853971064090729 True -12 36218 30.262201070785522 0.5896656513214111 472.3891906738281 0.26273542642593384 584.2579345703125 0.2566404938697815 0.8194083 0.3616376221179962 True -13 39004 30.12876558303833 1.050365686416626 556.2136840820312 0.49499356746673584 581.9691162109375 0.2575690746307373 0.82937336 0.3327184319496155 True -14 41790 30.2968909740448 0.5968945026397705 525.5892333984375 0.3419501483440399 579.024658203125 0.2598257064819336 0.83780193 0.3042129576206207 True -15 44576 30.736035585403442 37.02600121498108 553.71044921875 0.22717654705047607 576.8090209960938 0.26121142506599426 0.84511894 0.2850954532623291 True -16 47362 30.451545000076294 0.6185641288757324 570.47216796875 0.36888107657432556 575.5799560546875 0.2625971734523773 0.85084116 0.27371615171432495 True -17 50148 32.13662528991699 0.6042711734771729 474.6068115234375 0.2055782675743103 575.8827514648438 0.2607579827308655 0.8535188 0.26802539825439453 True -18 52934 30.211642503738403 0.5966668128967285 490.65948486328125 0.17115435004234314 576.7888793945312 0.26018717885017395 0.8535923 0.2677242159843445 True -19 55720 30.14151406288147 1.3878779411315918 589.4713134765625 0.1915281116962433 577.1697387695312 0.26001420617103577 0.85194814 0.2692495286464691 False diff --git a/ENCSR623PVB/cherimoya.fold_4.performance.tsv b/ENCSR623PVB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index cbdaad2b03e95de2e72c58088aa7f29b60f58a09..0000000000000000000000000000000000000000 --- a/ENCSR623PVB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -576.7888793945312 0.4602854251861572 0.26018717885017395 0.10915819555521011 0.8535922765731812 0.8137261867523193 0.2677242159843445 \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_0.evaluate.json b/ENCSR624CTU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ef34edaa32a2edee7c7487d66573667c7e4bb025..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372FVO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_0.fit.json b/ENCSR624CTU/cherimoya.fold_0.fit.json deleted file mode 100644 index cce5b4e6785202a3fb9ff468a66ca8820380f9f1..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF372FVO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_0.log b/ENCSR624CTU/cherimoya.fold_0.log deleted file mode 100644 index ba62ba298ae85924536bb8226617722ea44b792c..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2055 27.261262893676758 2.130603075027466 258.6016845703125 1.2454177141189575 398.5794982910156 0.42728787660598755 0.51847404 8.549036026000977 True -1 4110 22.603105783462524 0.5348262786865234 257.2491455078125 0.7966383695602417 340.0682678222656 0.5467170476913452 0.6112602 2.952010154724121 True -2 6165 22.541152477264404 0.37686824798583984 222.89559936523438 0.5122029781341553 324.7652893066406 0.5831493735313416 0.6283662 0.9616574645042419 True -3 8220 22.615532398223877 0.45115113258361816 283.87591552734375 1.0897490978240967 321.48291015625 0.5903853178024292 0.6326155 0.7387853860855103 True -4 10275 22.496129035949707 0.3728029727935791 303.6478271484375 0.4832611680030823 320.17694091796875 0.5939708948135376 0.6383051 0.7090548276901245 True -5 12330 22.174036502838135 0.37302398681640625 263.06475830078125 0.6948887705802917 319.04150390625 0.5967761874198914 0.64399153 0.6855449080467224 True -6 14385 23.24964928627014 3.265031099319458 221.6054229736328 0.7009721994400024 318.145263671875 0.5990277528762817 0.64852977 0.6889084577560425 True -7 16440 22.198912382125854 13.153168678283691 233.3192901611328 0.46450212597846985 317.5354919433594 0.6008872389793396 0.64932984 0.6805527806282043 True -8 18495 22.441243410110474 0.3813595771789551 222.46484375 0.6404445767402649 316.6005554199219 0.6027435064315796 0.6529292 0.6413885951042175 True -9 20550 22.52433156967163 14.20555853843689 237.03170776367188 0.48310190439224243 315.9173583984375 0.6049384474754333 0.6606824 0.6279953718185425 True -10 22605 22.147521018981934 1.7672080993652344 206.48448181152344 0.4667186141014099 314.618896484375 0.6076504588127136 0.66480464 0.5905742645263672 True -11 24660 22.5426082611084 0.38877058029174805 231.32408142089844 0.37657415866851807 313.9339294433594 0.6094720363616943 0.6690572 0.548690915107727 True -12 26715 22.257595777511597 0.3866894245147705 236.95355224609375 0.5222427845001221 313.2919006347656 0.6109060645103455 0.6789041 0.5291656255722046 True -13 28770 22.161836862564087 0.38944101333618164 250.10154724121094 0.48536986112594604 312.7919616699219 0.6122377514839172 0.68435526 0.5263946056365967 True -14 30825 22.199174404144287 0.3804295063018799 210.6364288330078 0.5023375749588013 312.11053466796875 0.61365807056427 0.69234735 0.5070823431015015 True -15 32880 22.237022876739502 0.38713622093200684 255.14028930664062 0.35636112093925476 311.767822265625 0.6141447424888611 0.6981268 0.49686890840530396 True -16 34935 22.185609102249146 1.1855599880218506 226.74200439453125 0.34339025616645813 311.8258056640625 0.6139457821846008 0.7004409 0.501789391040802 True -17 36990 22.167409420013428 0.3724243640899658 232.09231567382812 0.42794471979141235 311.8985900878906 0.6135194897651672 0.7013214 0.49552440643310547 True -18 39045 22.607271909713745 0.40088534355163574 260.8613586425781 0.3470906913280487 312.08502197265625 0.6128189563751221 0.699881 0.5003966689109802 False -19 41100 22.227158784866333 0.3876824378967285 191.71946716308594 0.26486921310424805 312.2928161621094 0.6123464107513428 0.6989024 0.5037566423416138 False diff --git a/ENCSR624CTU/cherimoya.fold_0.performance.tsv b/ENCSR624CTU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 24f3a7c6896decbeb6fcf4f640e561aab237d840..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -311.8985900878906 0.31682246923446655 0.6135194897651672 0.20507819950580597 0.7013214230537415 0.6640554070472717 0.49552440643310547 \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_1.evaluate.json b/ENCSR624CTU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f63532594309c53adb196abae848b9e6631bda9b..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372FVO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_1.fit.json b/ENCSR624CTU/cherimoya.fold_1.fit.json deleted file mode 100644 index 7fc43b4a8c4ab3f09839a82a147707370f7fb465..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF372FVO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_1.log b/ENCSR624CTU/cherimoya.fold_1.log deleted file mode 100644 index f562ed8c82cb0e9df4842f210d11e270b1a2fcb2..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2098 27.831992864608765 4.038926839828491 279.53466796875 0.6859087347984314 401.90985107421875 0.4393136203289032 0.52425164 8.187799453735352 True -1 4196 23.03967547416687 0.6956994533538818 259.7591552734375 0.565009593963623 348.8709411621094 0.5487288236618042 0.6388681 3.506227731704712 True -2 6294 23.067405223846436 0.463608980178833 247.85440063476562 0.8648145198822021 337.13677978515625 0.577935516834259 0.6507227 0.9793956279754639 True -3 8392 23.113147258758545 0.46604371070861816 270.50433349609375 0.6342201232910156 333.1105651855469 0.5863957405090332 0.66215944 0.7761520147323608 True -4 10490 23.033175706863403 0.45696353912353516 281.06378173828125 0.922728419303894 331.92132568359375 0.5898652672767639 0.667853 0.6702637076377869 True -5 12588 23.084270477294922 0.46781468391418457 232.09835815429688 0.675173282623291 331.0963134765625 0.592395007610321 0.67398757 0.6213446259498596 True -6 14686 23.08979558944702 1.262404441833496 255.75814819335938 0.5702152252197266 329.9455261230469 0.595211923122406 0.676372 0.6004824638366699 True -7 16784 23.1056227684021 0.46997642517089844 266.5709533691406 0.5468641519546509 329.097900390625 0.5975168943405151 0.68184334 0.5724532008171082 True -8 18882 22.992045402526855 0.45967841148376465 246.68931579589844 0.5621304512023926 328.69415283203125 0.5988484621047974 0.68525845 0.5665953159332275 True -9 20980 22.673519611358643 0.46199750900268555 256.9644775390625 0.5396413207054138 327.6055908203125 0.601557195186615 0.6933284 0.5046546459197998 True -10 23078 22.62584114074707 0.4596223831176758 253.5550079345703 0.4568626284599304 326.7120361328125 0.60346519947052 0.6994197 0.4911263585090637 True -11 25176 22.631036281585693 0.4600389003753662 248.30218505859375 0.508758008480072 325.8816833496094 0.6055090427398682 0.7069353 0.4689227342605591 True -12 27274 22.628692150115967 0.4586300849914551 245.60585021972656 0.3699576258659363 325.25213623046875 0.6071327924728394 0.7134571 0.4608304798603058 True -13 29372 22.63907265663147 0.4617123603820801 263.6484375 0.6871559619903564 324.6131286621094 0.6085037589073181 0.71957254 0.43967288732528687 True -14 31470 22.66393494606018 0.459383487701416 229.5736846923828 0.4685630202293396 323.94854736328125 0.6099979281425476 0.7263377 0.43299007415771484 True -15 33568 22.67307949066162 0.45717692375183105 248.21932983398438 0.4646260142326355 323.647216796875 0.6105501651763916 0.72980356 0.4240780472755432 True -16 35666 22.652158975601196 0.46249961853027344 237.80755615234375 0.2913374900817871 323.47412109375 0.6108354330062866 0.7332445 0.42063108086586 True -17 37764 22.66632843017578 0.46276259422302246 213.7978515625 0.37604883313179016 323.5631103515625 0.6103883981704712 0.73380417 0.42275360226631165 True -18 39862 22.68617081642151 0.46408963203430176 223.7874298095703 0.2885967493057251 323.6721496582031 0.6097363233566284 0.7303692 0.42992931604385376 False -19 41960 23.23630666732788 1.2410719394683838 255.34518432617188 0.23822489380836487 323.74969482421875 0.609411358833313 0.7282009 0.4352710545063019 False diff --git a/ENCSR624CTU/cherimoya.fold_1.performance.tsv b/ENCSR624CTU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7bcc686136c3b9e01ebf2fbae5d67573a3d31064..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -323.5631103515625 0.3144591748714447 0.6103883981704712 0.2102498859167099 0.7338041663169861 0.7221289873123169 0.42275360226631165 \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_2.evaluate.json b/ENCSR624CTU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c1a5fc8e7309a1a4d1ccc6b932237d2d8fa866e4..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372FVO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_2.fit.json b/ENCSR624CTU/cherimoya.fold_2.fit.json deleted file mode 100644 index f831ce560c2e90b35864ea2c0e737fd8563d70b8..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF372FVO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_2.log b/ENCSR624CTU/cherimoya.fold_2.log deleted file mode 100644 index 3fad0e97c00b241f6e950d0868393934ba512908..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2196 28.894649505615234 3.598370313644409 290.46759033203125 0.7173267602920532 396.78839111328125 0.44093871116638184 0.5334492 7.655283451080322 True -1 4392 24.169644594192505 0.4229443073272705 265.21966552734375 0.5853270888328552 344.7407531738281 0.5523288249969482 0.6147175 3.1656808853149414 True -2 6588 24.14865016937256 1.1912219524383545 227.7030029296875 0.6394187211990356 331.8189697265625 0.5799890160560608 0.6302639 0.9194689393043518 True -3 8784 24.16994881629944 0.4053311347961426 290.82659912109375 0.6312412023544312 327.9329833984375 0.5877543687820435 0.6489157 0.6523095965385437 True -4 10980 24.15655207633972 0.4057588577270508 248.06988525390625 0.5190566778182983 325.6279296875 0.5927723050117493 0.6609977 0.5685810446739197 True -5 13176 24.115638971328735 0.411099910736084 228.624755859375 0.5937711000442505 324.84625244140625 0.5951319336891174 0.6602424 0.5766326785087585 False -6 15372 24.116788148880005 0.4003593921661377 222.480712890625 0.6528493165969849 323.8339538574219 0.5980515480041504 0.6638653 0.5768123865127563 True -7 17568 24.117642879486084 0.7202067375183105 246.18458557128906 0.9689055681228638 322.8155517578125 0.6004782319068909 0.6707591 0.5408820509910583 True -8 19764 24.12876868247986 0.4046964645385742 267.20880126953125 0.5579046607017517 321.9069519042969 0.602641224861145 0.67532957 0.5387543439865112 True -9 21960 24.148149490356445 0.40210676193237305 243.4853515625 0.5040449500083923 321.0174865722656 0.6047548651695251 0.6782386 0.5325832962989807 True -10 24156 24.100890398025513 0.4000825881958008 203.99343872070312 0.5894685387611389 320.12518310546875 0.6068257689476013 0.6837189 0.5270453095436096 True -11 26352 24.11478042602539 0.40137267112731934 239.04061889648438 0.41084808111190796 319.28887939453125 0.6086252927780151 0.68751484 0.5212971568107605 True -12 28548 24.110323190689087 0.6061477661132812 264.376220703125 0.5349823236465454 318.7508239746094 0.610016942024231 0.69140047 0.5077712535858154 True -13 30744 24.15530252456665 9.568787336349487 268.3955993652344 0.49604272842407227 318.152587890625 0.6118687987327576 0.7003089 0.48854750394821167 True -14 32940 24.677469968795776 0.4202578067779541 276.7301025390625 0.5295295715332031 317.6700744628906 0.6129288673400879 0.70235884 0.4896601736545563 True -15 35136 24.191974401474 0.4025421142578125 237.51141357421875 0.4281770586967468 317.4543762207031 0.6133726835250854 0.70533717 0.4835014343261719 True -16 37332 24.177802562713623 0.42397499084472656 264.4420166015625 0.2937537431716919 317.3193054199219 0.6134083867073059 0.7095785 0.4878097474575043 True -17 39528 24.065326929092407 0.3982963562011719 248.42564392089844 0.30412548780441284 317.4348449707031 0.613213300704956 0.7088649 0.4898120164871216 False -18 41724 23.710840225219727 0.3968355655670166 216.60330200195312 0.37129056453704834 317.635986328125 0.6126704216003418 0.707334 0.49864768981933594 False -19 43920 23.691395044326782 0.3994176387786865 254.51084899902344 0.34304171800613403 317.7295837402344 0.6122792959213257 0.7061755 0.5038735270500183 False diff --git a/ENCSR624CTU/cherimoya.fold_2.performance.tsv b/ENCSR624CTU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c20b037076d94423187bad29c47478c643296061..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.3193054199219 0.3153972923755646 0.6134084463119507 0.2104124277830124 0.7095785140991211 0.6819154024124146 0.4878097474575043 \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_3.evaluate.json b/ENCSR624CTU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c55beebc46e873ca3fee36269617bc77c691a22a..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372FVO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_3.fit.json b/ENCSR624CTU/cherimoya.fold_3.fit.json deleted file mode 100644 index 9c28b42cf1ff28711541281b89ff0f9289a7973b..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF372FVO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_3.log b/ENCSR624CTU/cherimoya.fold_3.log deleted file mode 100644 index f66b74b924d088f1055119c339622d637f49af66..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2139 29.19538187980652 3.6341381072998047 250.32269287109375 0.7777946591377258 402.1155090332031 0.43701204657554626 0.5193126 9.69600772857666 True -1 4278 23.5100200176239 0.687814474105835 292.32012939453125 0.8979451060295105 344.8923645019531 0.5530534386634827 0.6090784 2.8325753211975098 True -2 6417 23.50038981437683 0.46438097953796387 238.09312438964844 0.7491635680198669 331.59857177734375 0.5855387449264526 0.6106722 0.8720366358757019 True -3 8556 23.498604774475098 0.46483778953552246 246.8218536376953 0.7495574951171875 327.3938903808594 0.5930889248847961 0.6257745 0.6433677673339844 True -4 10695 23.468435287475586 0.44957542419433594 311.0135498046875 0.7584588527679443 325.87701416015625 0.596322774887085 0.6363297 0.6590444445610046 True -5 12834 23.510682106018066 0.4718184471130371 204.95870971679688 0.8212113380432129 324.8902893066406 0.5983924865722656 0.64173603 0.6449294686317444 True -6 14973 23.502065658569336 0.46020984649658203 254.00311279296875 0.7565444111824036 323.83001708984375 0.6009430289268494 0.6461998 0.5863320231437683 True -7 17112 23.475332498550415 0.4655497074127197 246.8501434326172 0.39274540543556213 323.1205749511719 0.6029807329177856 0.6531337 0.5728902220726013 True -8 19251 23.48199200630188 0.5111064910888672 229.34014892578125 0.5279334783554077 322.4766540527344 0.6046220660209656 0.6570048 0.5534608960151672 True -9 21390 23.49294900894165 1.4064388275146484 256.4244384765625 0.5636085271835327 321.27008056640625 0.6069207787513733 0.6704231 0.5173550248146057 True -10 23529 23.5141282081604 0.46175074577331543 221.00057983398438 0.4503104090690613 320.6331481933594 0.6086869835853577 0.67873573 0.49709081649780273 True -11 25668 23.489823579788208 0.46135473251342773 257.2321472167969 0.5199449062347412 319.903564453125 0.610312283039093 0.6819227 0.49748194217681885 True -12 27807 23.515952825546265 6.149159908294678 249.7184295654297 0.6068531274795532 319.2616882324219 0.6119649410247803 0.6883273 0.48975762724876404 True -13 29946 23.4998836517334 0.4767298698425293 232.25779724121094 0.5518349409103394 318.4557800292969 0.6132693290710449 0.69659936 0.4817308783531189 True -14 32085 23.521390199661255 0.451352596282959 260.91046142578125 0.3747560977935791 318.1808776855469 0.6144846081733704 0.7052635 0.4742552936077118 True -15 34224 23.487491607666016 0.44865942001342773 256.9214172363281 0.4468861222267151 317.4210205078125 0.6151422262191772 0.71199495 0.46754929423332214 True -16 36363 23.53619647026062 0.475902795791626 250.01959228515625 0.30328160524368286 317.5943908691406 0.6153615713119507 0.71438 0.46923917531967163 True -17 38502 23.54021954536438 0.4977757930755615 197.95697021484375 0.2690378725528717 317.7093505859375 0.6148821115493774 0.7147238 0.47502022981643677 True -18 40641 23.616849422454834 0.49783945083618164 194.2129364013672 0.3068857192993164 317.5304870605469 0.6143861413002014 0.71137995 0.4831794500350952 False -19 42780 23.604970455169678 0.452500581741333 198.88540649414062 0.45384812355041504 317.81341552734375 0.6140745282173157 0.7068204 0.4910564124584198 False diff --git a/ENCSR624CTU/cherimoya.fold_3.performance.tsv b/ENCSR624CTU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bca036437c0e6f18393a103bf4d7120ff428d9c1..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.7093505859375 0.3134068250656128 0.6148821115493774 0.21039454638957977 0.7147238254547119 0.6813176274299622 0.47502022981643677 \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_4.evaluate.json b/ENCSR624CTU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 141a5bd0903409b73c8ef9e42388663ff4409d66..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372FVO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_4.fit.json b/ENCSR624CTU/cherimoya.fold_4.fit.json deleted file mode 100644 index f4c9c32a060af0501417ee024e322c18d65b1782..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF372FVO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624CTU/cherimoya.fold_4.log b/ENCSR624CTU/cherimoya.fold_4.log deleted file mode 100644 index e4b2446476da50b6f3edf33656f5e025194d4dc2..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2192 28.56980538368225 3.914299249649048 240.62936401367188 0.8079892992973328 399.4381408691406 0.4391925036907196 0.56000465 7.643717288970947 True -1 4384 24.07734489440918 0.5169663429260254 249.46139526367188 0.8736218810081482 340.8060607910156 0.5628174543380737 0.60551834 3.093501567840576 True -2 6576 24.22542929649353 0.4394969940185547 232.445556640625 0.7502670288085938 330.2957458496094 0.5871500372886658 0.6353894 0.8075507283210754 True -3 8768 24.115275382995605 1.0981857776641846 254.2501220703125 0.5753611326217651 326.6125183105469 0.594743549823761 0.6430184 0.6543409824371338 True -4 10960 23.836517572402954 0.46454429626464844 226.13270568847656 0.5791497230529785 324.7516784667969 0.5988528728485107 0.65670913 0.6180574893951416 True -5 13152 23.631295919418335 0.4137148857116699 273.0066223144531 0.630152702331543 323.6100158691406 0.602027952671051 0.65540636 0.588317334651947 False -6 15344 23.609947443008423 0.4380958080291748 233.9605712890625 0.5627142190933228 322.4496154785156 0.6048650741577148 0.6628899 0.5672289729118347 True -7 17536 23.655737161636353 0.4135916233062744 291.9732666015625 0.4982374608516693 322.0477294921875 0.6065205931663513 0.66497266 0.5635987520217896 True -8 19728 23.658129930496216 0.41971468925476074 228.6185302734375 0.7621380090713501 321.028076171875 0.6087916493415833 0.6698139 0.5336741805076599 True -9 21920 23.646254539489746 0.4241786003112793 247.89590454101562 0.41632547974586487 320.2655334472656 0.6111319661140442 0.67497265 0.5213421583175659 True -10 24112 23.653157711029053 0.4137997627258301 216.62420654296875 0.5015467405319214 319.2939758300781 0.6134039759635925 0.68127435 0.5217527151107788 True -11 26304 23.624977350234985 1.4385643005371094 232.17108154296875 0.43031594157218933 318.41436767578125 0.6151447892189026 0.6838335 0.501917839050293 True -12 28496 23.619555473327637 0.41524243354797363 243.26300048828125 0.5993505120277405 317.61724853515625 0.6169978976249695 0.6937567 0.49514490365982056 True -13 30688 23.59756088256836 3.0606606006622314 280.4700622558594 0.49845317006111145 316.9079284667969 0.6183815598487854 0.69890255 0.49270933866500854 True -14 32880 23.626011610031128 0.4335968494415283 251.29759216308594 0.4880257844924927 316.3903503417969 0.6194533705711365 0.70216453 0.4904462993144989 True -15 35072 23.62260150909424 0.4200425148010254 263.053955078125 0.4647618234157562 316.00274658203125 0.6203129887580872 0.7077427 0.48018693923950195 True -16 37264 23.61949372291565 0.4115605354309082 266.1793212890625 0.3829275369644165 315.87738037109375 0.620269238948822 0.71107924 0.4838935136795044 True -17 39456 23.617290496826172 1.438978672027588 274.5466003417969 0.43616345524787903 315.9924621582031 0.6196789741516113 0.71003217 0.48845377564430237 False -18 41648 23.64363980293274 0.4164552688598633 268.6754455566406 0.30674704909324646 316.2786560058594 0.6189408898353577 0.7080163 0.49510425329208374 False -19 43840 23.632933378219604 0.4197123050689697 235.46759033203125 0.27308881282806396 316.3058776855469 0.6185954213142395 0.7062537 0.49909594655036926 False diff --git a/ENCSR624CTU/cherimoya.fold_4.performance.tsv b/ENCSR624CTU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a977ff94658ade5255dd683cca00b5b9c793019b..0000000000000000000000000000000000000000 --- a/ENCSR624CTU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -315.87738037109375 0.31269022822380066 0.6202691793441772 0.21076591312885284 0.7110792398452759 0.6688919067382812 0.4838935136795044 \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_0.evaluate.json b/ENCSR624ODL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0deea84bbb5631af0cacd410da41a7c9916eec41..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF382DHA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_0.fit.json b/ENCSR624ODL/cherimoya.fold_0.fit.json deleted file mode 100644 index 04846457cda5a83df43c169be120ab03bb69c9e5..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF382DHA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_0.log b/ENCSR624ODL/cherimoya.fold_0.log deleted file mode 100644 index 7eff78cbfb7652d2982b172d58face4651e3da54..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3854 46.39410638809204 32.38460564613342 1013.3216552734375 0.7419471740722656 1394.8643798828125 0.7293764352798462 0.6296954 10.769950866699219 True -1 7708 42.49678945541382 0.7854552268981934 965.404052734375 1.1389131546020508 1147.3067626953125 0.8182007670402527 0.66332126 1.7842745780944824 True -2 11562 42.375078439712524 0.735692024230957 735.52294921875 1.1165177822113037 1115.021240234375 0.8271169066429138 0.6710237 1.1400865316390991 True -3 15416 41.82117819786072 0.7539973258972168 967.1864013671875 0.8385787010192871 1101.4393310546875 0.8324775695800781 0.6764802 1.0298566818237305 True -4 19270 41.51148557662964 0.7255575656890869 890.3469848632812 1.152004361152649 1094.1451416015625 0.8346154093742371 0.6775555 1.0617032051086426 True -5 23124 41.47349953651428 0.7220532894134521 1092.808349609375 0.8881424069404602 1089.9398193359375 0.8364012241363525 0.670252 0.968413233757019 False -6 26978 41.51836681365967 1.9377171993255615 897.7509765625 1.2589519023895264 1084.6805419921875 0.8382135033607483 0.6756401 0.9596907496452332 False -7 30832 41.49638247489929 0.7324368953704834 993.4300537109375 0.6267886757850647 1073.44384765625 0.8406092524528503 0.68340117 0.7955052256584167 True -8 34686 41.474111795425415 0.7272088527679443 812.6263427734375 0.7689744830131531 1061.02001953125 0.8436981439590454 0.68882537 0.7379733920097351 True -9 38540 41.55498003959656 0.7233195304870605 839.90283203125 1.0893689393997192 1051.302734375 0.845970094203949 0.6968755 0.7257342338562012 True -10 42394 41.57419514656067 1.7841691970825195 862.6280517578125 0.6615469455718994 1042.9378662109375 0.8483512997627258 0.7030186 0.6743550300598145 True -11 46248 41.62239694595337 0.7253203392028809 667.190185546875 0.5622855424880981 1033.8138427734375 0.8510056734085083 0.7156834 0.6516143083572388 True -12 50102 41.490949869155884 0.728447437286377 1013.6036987304688 0.6334674954414368 1026.402099609375 0.8531387448310852 0.72467077 0.6133216619491577 True -13 53956 41.56036901473999 0.7356936931610107 810.4544677734375 0.5926666259765625 1018.4183959960938 0.8555313348770142 0.73445797 0.5907151103019714 True -14 57810 41.50555610656738 1.433690071105957 908.3990478515625 0.851853609085083 1011.7313232421875 0.8577777147293091 0.74343497 0.5702146291732788 True -15 61664 41.59034252166748 0.7274622917175293 841.878662109375 0.6694676876068115 1005.802490234375 0.8592305183410645 0.7537861 0.5520536303520203 True -16 65518 41.5442008972168 0.7202630043029785 816.084716796875 0.7530722618103027 1002.7884521484375 0.8603295683860779 0.75613946 0.5505459308624268 True -17 69372 41.479676961898804 0.7134361267089844 762.397216796875 0.722642183303833 1003.4639282226562 0.8606259226799011 0.75928473 0.5491267442703247 True -18 73226 41.47790837287903 0.7191543579101562 802.83056640625 0.38334453105926514 1004.1254272460938 0.8603705763816833 0.76033294 0.5547633767127991 True -19 77080 41.45964336395264 0.718958854675293 632.3256225585938 0.6277325749397278 1005.2266845703125 0.8600995540618896 0.7602502 0.5602555871009827 False diff --git a/ENCSR624ODL/cherimoya.fold_0.performance.tsv b/ENCSR624ODL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c67876c4698776497cd407ac5737b461b2abe391..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1004.1254272460938 0.11141951382160187 0.8603705763816833 0.5680904984474182 0.7603329420089722 0.7141289114952087 0.5547633767127991 \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_1.evaluate.json b/ENCSR624ODL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8cc51f58ad562f4682bb939390faed0db595082a..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF382DHA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_1.fit.json b/ENCSR624ODL/cherimoya.fold_1.fit.json deleted file mode 100644 index 00b53c89527457e9c1e04b5fcabfcb49c3751733..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF382DHA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_1.log b/ENCSR624ODL/cherimoya.fold_1.log deleted file mode 100644 index a3304987d2a9777e66ad3c37386415836766ec7b..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3795 46.76389670372009 3.982640266418457 838.88525390625 1.416653037071228 1535.8919677734375 0.7336406111717224 0.65373033 11.503047943115234 True -1 7590 41.76416516304016 1.0075726509094238 835.7416381835938 1.125093698501587 1262.972900390625 0.8193771839141846 0.6813381 2.6122019290924072 True -2 11385 41.883110761642456 2.9327309131622314 896.5967407226562 1.0839204788208008 1218.0107421875 0.8277794718742371 0.6925701 1.1409488916397095 True -3 15180 41.80975103378296 1.0095221996307373 856.2735595703125 0.7337920665740967 1195.440673828125 0.8334043025970459 0.6973971 1.1353574991226196 True -4 18975 41.80793046951294 0.997178316116333 1038.44189453125 1.1960972547531128 1184.6856689453125 0.835774838924408 0.7026757 0.9306923747062683 True -5 22770 41.83077788352966 1.0123863220214844 779.266845703125 0.877814531326294 1177.7010498046875 0.8371427059173584 0.7022572 0.9436615705490112 False -6 26565 41.88716244697571 1.0093340873718262 772.8175048828125 1.1000096797943115 1171.8955078125 0.8388621211051941 0.70252204 0.915363609790802 False -7 30360 41.792556047439575 1.0013163089752197 906.0872802734375 0.625391960144043 1159.447265625 0.8423506617546082 0.7054785 0.8281201720237732 True -8 34155 41.761208295822144 0.9819056987762451 1003.0849609375 1.5850114822387695 1146.6925048828125 0.8450031280517578 0.7131952 0.7779514789581299 True -9 37950 41.054255962371826 0.9824113845825195 732.3936767578125 0.7245464324951172 1133.49609375 0.8475459218025208 0.72783613 0.6819729804992676 True -10 41745 40.99759864807129 0.9876480102539062 858.46142578125 0.57338547706604 1124.1065673828125 0.8501471877098083 0.73347735 0.6538950204849243 True -11 45540 40.929787397384644 0.9742119312286377 765.0352172851562 1.0229225158691406 1118.1190185546875 0.8525991439819336 0.74284565 0.6412677764892578 True -12 49335 40.99743962287903 0.9798047542572021 802.7334594726562 0.9129027128219604 1105.409423828125 0.8551610708236694 0.75395316 0.5884727239608765 True -13 53130 40.99496269226074 0.9883298873901367 877.6082153320312 0.8177511096000671 1098.3465576171875 0.857845664024353 0.76092863 0.5746321678161621 True -14 56925 40.98664855957031 3.862293004989624 774.2684936523438 0.5381906628608704 1090.353759765625 0.8601300120353699 0.7690437 0.5591915845870972 True -15 60720 40.97909355163574 0.9877982139587402 848.2434692382812 1.1067830324172974 1084.249755859375 0.8621060252189636 0.7751459 0.5479713082313538 True -16 64515 40.95866847038269 13.846420049667358 697.9932250976562 0.5234068632125854 1081.427978515625 0.863170325756073 0.77936727 0.5422741770744324 True -17 68310 40.90369391441345 0.9719448089599609 878.052490234375 0.8746777176856995 1081.4093017578125 0.8634471297264099 0.7806311 0.5471841096878052 True -18 72105 40.93217706680298 0.978356122970581 896.825927734375 0.458362877368927 1083.568603515625 0.8630584478378296 0.77938956 0.557765781879425 False -19 75900 40.97907781600952 1.668137788772583 819.5186767578125 0.44536322355270386 1084.537109375 0.8628554940223694 0.7784562 0.5621762275695801 False diff --git a/ENCSR624ODL/cherimoya.fold_1.performance.tsv b/ENCSR624ODL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 41f03d05731fe401b4471d9f6aad0a2a969be192..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1081.4093017578125 0.10506581515073776 0.8634471297264099 0.5938451290130615 0.7806311249732971 0.7584894299507141 0.5471841096878052 \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_2.evaluate.json b/ENCSR624ODL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 07231bfdce544b7b5dbba360c9ada48ff979befe..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF382DHA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_2.fit.json b/ENCSR624ODL/cherimoya.fold_2.fit.json deleted file mode 100644 index 4094d80069cb007509bbf2666293059043950231..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF382DHA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_2.log b/ENCSR624ODL/cherimoya.fold_2.log deleted file mode 100644 index d20a8995b5b4e5065a3fa03f84305af7b30f67ec..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4006 47.88198232650757 3.8346309661865234 920.8991088867188 0.9257165193557739 1469.8583984375 0.7393327951431274 0.6316047 12.051261901855469 True -1 8012 44.11440348625183 0.8062779903411865 864.6407470703125 0.7501689791679382 1211.169921875 0.8221612572669983 0.6696323 2.01991605758667 True -2 12018 43.80195641517639 0.7766938209533691 822.093994140625 0.7853138446807861 1187.3349609375 0.8275132775306702 0.67968315 1.5249028205871582 True -3 16024 43.290603160858154 2.1022825241088867 957.7706298828125 0.711271345615387 1161.2178955078125 0.8332802653312683 0.68506825 1.1530020236968994 True -4 20030 43.27136254310608 0.7809767723083496 953.3614501953125 0.9410023093223572 1153.2264404296875 0.8347939848899841 0.6924986 0.9622026681900024 True -5 24036 43.269567012786865 0.7822833061218262 925.8788452148438 0.8001130223274231 1142.7398681640625 0.8384965062141418 0.69453907 0.8422165513038635 True -6 28042 43.55810332298279 17.233914375305176 845.0469360351562 1.256424903869629 1131.11083984375 0.8407607078552246 0.703874 0.724226713180542 True -7 32048 43.336833000183105 0.7827169895172119 837.908447265625 0.7924165725708008 1123.7171630859375 0.8430212140083313 0.7091113 0.7107174396514893 True -8 36054 43.27106738090515 0.7878615856170654 817.2453002929688 1.058394193649292 1112.7222900390625 0.8461609482765198 0.7182863 0.6899636387825012 True -9 40060 43.38090443611145 0.7857489585876465 983.4263916015625 0.5906335115432739 1105.539306640625 0.8482372760772705 0.7224439 0.6605824828147888 True -10 44066 43.73539352416992 0.7891438007354736 902.6876220703125 1.1685395240783691 1094.0169677734375 0.8505471348762512 0.7289621 0.6162143349647522 True -11 48072 43.359254598617554 1.55877685546875 796.1582641601562 0.524488091468811 1085.784423828125 0.8530767560005188 0.73218405 0.6047973036766052 True -12 52078 43.35355997085571 0.7881340980529785 807.0678100585938 0.5684033632278442 1081.18359375 0.8548606038093567 0.7424011 0.5866270661354065 True -13 56084 43.37492871284485 0.7824239730834961 842.5661010742188 0.6331254243850708 1072.9830322265625 0.857263445854187 0.74691665 0.5781799554824829 True -14 60090 43.24563455581665 0.7820286750793457 795.5127563476562 0.664142906665802 1064.2591552734375 0.8593783378601074 0.7547394 0.5652575492858887 True -15 64096 43.246888399124146 1.5421597957611084 842.3827514648438 0.631946861743927 1058.90576171875 0.8610051274299622 0.76003134 0.5633239150047302 True -16 68102 43.25720953941345 0.7853121757507324 815.025634765625 1.0203640460968018 1056.4990234375 0.8618863224983215 0.76217324 0.5631373524665833 True -17 72108 43.3266441822052 0.7731838226318359 737.1055908203125 0.4387756586074829 1057.145751953125 0.8619143962860107 0.7631069 0.5730418562889099 True -18 76114 43.42916464805603 0.8125417232513428 902.934326171875 0.4647262394428253 1059.5443115234375 0.8615744113922119 0.7646008 0.5784608125686646 True -19 80120 43.473591804504395 4.403416156768799 889.726806640625 0.4250236749649048 1061.3128662109375 0.8613880276679993 0.7639303 0.5864465832710266 False diff --git a/ENCSR624ODL/cherimoya.fold_2.performance.tsv b/ENCSR624ODL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6a06de5e292a60287d4dfc2b5e2c4fce7334bd36..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1059.5443115234375 0.10696391016244888 0.8615744113922119 0.5874210596084595 0.7646008133888245 0.7354800701141357 0.5784608125686646 \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_3.evaluate.json b/ENCSR624ODL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 33ef21cc41af0184c04cc2fc3aba82ccd28cd5e5..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF382DHA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_3.fit.json b/ENCSR624ODL/cherimoya.fold_3.fit.json deleted file mode 100644 index b94d0bbaa5a604fbdf903d41aac0efbcbcf77b7c..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF382DHA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_3.log b/ENCSR624ODL/cherimoya.fold_3.log deleted file mode 100644 index 89579a060c5b36ffaa855d53c7c09689b38a7078..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3912 47.11376595497131 4.416548490524292 1020.7108154296875 1.092467188835144 1381.9400634765625 0.733189046382904 0.6405093 10.771167755126953 True -1 7824 43.080339431762695 1.517690658569336 964.8131713867188 1.217145562171936 1143.345703125 0.8168444633483887 0.67170143 2.222946882247925 True -2 11736 43.095396518707275 0.7550475597381592 962.457275390625 0.8787437677383423 1113.845458984375 0.8249034881591797 0.68387884 1.209007740020752 True -3 15648 43.10730028152466 0.7411572933197021 809.018798828125 0.9129461050033569 1100.5145263671875 0.8296337723731995 0.6863137 0.9814139604568481 True -4 19560 43.032543659210205 0.7396981716156006 823.1464233398438 0.9928073287010193 1090.30859375 0.8318244218826294 0.67881155 0.889677882194519 False -5 23472 43.1050341129303 0.7534584999084473 954.8448486328125 1.7049267292022705 1084.75146484375 0.833981990814209 0.6781676 0.8410788178443909 False -6 27384 43.117629289627075 0.7521054744720459 979.5799560546875 1.2815425395965576 1076.082275390625 0.8360356688499451 0.6769945 0.7677555084228516 False -7 31296 43.07556700706482 1.347249984741211 906.648193359375 0.5937879085540771 1069.7755126953125 0.8386527895927429 0.68484133 0.7951629757881165 False -8 35208 43.09816884994507 0.7414326667785645 990.10986328125 0.7326256632804871 1063.2349853515625 0.8410136699676514 0.69796985 0.7545433640480042 True -9 39120 43.05159592628479 0.7473325729370117 840.7056274414062 0.5385745763778687 1051.309326171875 0.8437995314598083 0.7021064 0.6810634136199951 True -10 43032 43.04972743988037 23.360219478607178 853.1898193359375 0.751905083656311 1041.4400634765625 0.8466584086418152 0.7132366 0.6631276607513428 True -11 46944 43.076154470443726 0.7519659996032715 756.5527954101562 0.7969262599945068 1036.677734375 0.8484163284301758 0.7181595 0.6547465324401855 True -12 50856 43.080989837646484 0.753244161605835 885.710205078125 0.6771960258483887 1028.5040283203125 0.8509122133255005 0.73062044 0.6188843250274658 True -13 54768 42.69170928001404 0.7375426292419434 883.707763671875 0.5628747940063477 1017.5286254882812 0.853705644607544 0.74124056 0.5971924066543579 True -14 58680 42.260873556137085 0.7325725555419922 886.2504272460938 0.5809119343757629 1014.1581420898438 0.8558856844902039 0.7487338 0.5920467376708984 True -15 62592 42.22193098068237 0.7409384250640869 893.6090087890625 0.8579994440078735 1008.6218872070312 0.857703447341919 0.75498587 0.5699900984764099 True -16 66504 42.20028209686279 0.7382416725158691 812.4338989257812 0.47641077637672424 1007.1668090820312 0.8585193753242493 0.75919914 0.5614367127418518 True -17 70416 42.2185595035553 1.1207797527313232 874.1021728515625 0.5704747438430786 1006.6382446289062 0.8587433695793152 0.75974286 0.5662807822227478 True -18 74328 42.27633547782898 0.7345411777496338 865.9037475585938 0.5949218273162842 1006.7281494140625 0.8585607409477234 0.7583911 0.5723719596862793 False -19 78240 44.449057817459106 0.7341549396514893 682.808349609375 0.49285051226615906 1008.6934814453125 0.85829097032547 0.7572842 0.5780956745147705 False diff --git a/ENCSR624ODL/cherimoya.fold_3.performance.tsv b/ENCSR624ODL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bf758fa2c1f0dbd3518a27ac99bf8da53474ffd0..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1006.6382446289062 0.11174895614385605 0.8587433695793152 0.565563976764679 0.7597428560256958 0.7250834703445435 0.5662807822227478 \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_4.evaluate.json b/ENCSR624ODL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 337462bf0fbe6dd6c2fa2452f8bca92cd0aec425..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF382DHA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_4.fit.json b/ENCSR624ODL/cherimoya.fold_4.fit.json deleted file mode 100644 index dafb2326d718f39f29424573a6adfc8b7312dd7a..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF382DHA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR624ODL/cherimoya.fold_4.log b/ENCSR624ODL/cherimoya.fold_4.log deleted file mode 100644 index ed93163f565920461398ae131c75d7df2492922d..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3949 48.24011826515198 3.820059061050415 1069.4716796875 0.7561708688735962 1344.6676025390625 0.7335332036018372 0.6142933 10.904572486877441 True -1 7898 43.47074270248413 0.8039066791534424 932.5550537109375 1.200815200805664 1124.689453125 0.8141939043998718 0.6337859 2.582167625427246 True -2 11847 43.37073612213135 0.7842743396759033 964.5363159179688 1.1136687994003296 1092.840087890625 0.824330747127533 0.65127414 1.1623634099960327 True -3 15796 43.34608817100525 0.7867121696472168 1017.546875 0.7808003425598145 1078.1417236328125 0.8282862901687622 0.65778077 0.9448968172073364 True -4 19745 43.48886299133301 0.7843940258026123 871.6318359375 0.8322877883911133 1064.42333984375 0.8320736289024353 0.655925 0.8982048630714417 False -5 23694 43.41363739967346 0.7805259227752686 879.58349609375 0.8180512189865112 1059.9315185546875 0.833878755569458 0.65889156 0.85843825340271 True -6 27643 43.431264877319336 0.7800817489624023 966.3533935546875 0.9532881379127502 1052.4786376953125 0.8365878462791443 0.66130066 0.7988011240959167 True -7 31592 43.472596406936646 29.24016785621643 857.9099731445312 0.6496725678443909 1044.35498046875 0.8387384414672852 0.66480374 0.8163526654243469 True -8 35541 43.249462842941284 0.7956109046936035 781.9777221679688 1.120923638343811 1036.7667236328125 0.8404408097267151 0.67197347 0.7423797249794006 True -9 39490 42.71123147010803 1.796544075012207 889.724609375 0.45602160692214966 1029.424560546875 0.8431185483932495 0.6769652 0.7421504259109497 True -10 43439 42.63031339645386 0.7871816158294678 943.2587280273438 0.9834915399551392 1021.7033081054688 0.845757246017456 0.68316084 0.7170031070709229 True -11 47388 42.66677737236023 0.7863852977752686 681.3734741210938 0.7449716329574585 1013.4205932617188 0.8479195833206177 0.690644 0.6763942837715149 True -12 51337 42.777827978134155 0.7768998146057129 726.5726318359375 0.8042139410972595 1003.9692993164062 0.8507190942764282 0.70068794 0.6398206353187561 True -13 55286 42.8083758354187 29.130929708480835 731.9966430664062 0.5776957273483276 998.98779296875 0.852593719959259 0.70787466 0.6282252669334412 True -14 59235 42.58009171485901 0.7839908599853516 791.9321899414062 0.7018575668334961 993.2304077148438 0.8551425933837891 0.72042716 0.6025388836860657 True -15 63184 42.636788845062256 0.7880394458770752 847.473876953125 0.717590868473053 988.3637084960938 0.8565281629562378 0.7267039 0.5935088396072388 True -16 67133 42.71628928184509 0.7825021743774414 716.9420166015625 0.6113876104354858 986.797119140625 0.8572515845298767 0.7319172 0.5889866948127747 True -17 71082 42.65485692024231 0.7705492973327637 774.624755859375 0.6768779158592224 986.8248901367188 0.857718825340271 0.7344499 0.5938053131103516 True -18 75031 42.55952477455139 0.7675836086273193 651.305908203125 0.8684769868850708 988.2020263671875 0.8572729825973511 0.7343676 0.6001777052879333 False -19 78980 42.70979571342468 0.7785208225250244 728.0922241210938 0.45487478375434875 989.036865234375 0.8570392727851868 0.7318479 0.606414794921875 False diff --git a/ENCSR624ODL/cherimoya.fold_4.performance.tsv b/ENCSR624ODL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0511fff892a689fb22b264eb01e0ea738173a378..0000000000000000000000000000000000000000 --- a/ENCSR624ODL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -986.8248901367188 0.11260711401700974 0.857718825340271 0.5637988448143005 0.7344499230384827 0.6908472180366516 0.5938053131103516 \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_0.evaluate.json b/ENCSR625WLB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 86088f3ed08fe88e6617769f2a432d9678464eb4..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF025LWJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_0.fit.json b/ENCSR625WLB/cherimoya.fold_0.fit.json deleted file mode 100644 index f20f1b8484b5eb7e1e605329a6be033d965137ec..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF025LWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_0.log b/ENCSR625WLB/cherimoya.fold_0.log deleted file mode 100644 index 3a4795729568825dff0e5d6daefa5ab8496b830e..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.025227546691895 3.7468936443328857 351.109130859375 0.603866696357727 437.22235107421875 0.1812090426683426 0.68774366 4.632542133331299 True -1 5492 30.33482551574707 6.439810037612915 285.88531494140625 0.6576297283172607 392.4712219238281 0.22218205034732819 0.7648021 1.7398329973220825 True -2 8238 30.4780912399292 0.5837991237640381 266.33709716796875 0.7145237922668457 387.1983642578125 0.22869791090488434 0.7540316 1.359130859375 False -3 10984 30.33826994895935 0.5816140174865723 341.2951354980469 0.5079439878463745 381.0340881347656 0.23485516011714935 0.7669061 0.8647180199623108 True -4 13730 30.25022315979004 0.5844650268554688 255.592529296875 0.4703451097011566 375.5314636230469 0.23861312866210938 0.79342043 0.8091742992401123 True -5 16476 30.105278491973877 0.5902225971221924 369.2268981933594 0.6216073036193848 372.1048583984375 0.2418084591627121 0.8075273 0.741091787815094 True -6 19222 29.67107582092285 0.5739202499389648 395.13983154296875 0.5281586647033691 370.1239318847656 0.24425359070301056 0.81577235 0.7137889862060547 True -7 21968 29.653676748275757 0.5688474178314209 282.85772705078125 0.39230531454086304 367.9207763671875 0.24743568897247314 0.8253059 0.6385048031806946 True -8 24714 29.61977744102478 0.5666110515594482 271.996826171875 0.5365976691246033 367.14794921875 0.24659599363803864 0.82785887 0.6317164301872253 True -9 27460 29.757017135620117 0.5750851631164551 324.5068359375 0.5824700593948364 365.5380859375 0.2486175149679184 0.8352223 0.6010188460350037 True -10 30206 29.655380964279175 0.5763452053070068 290.98779296875 0.3918742537498474 363.3953857421875 0.2513357996940613 0.8427155 0.5362449288368225 True -11 32952 29.64064335823059 0.5740141868591309 261.4111328125 0.5092471837997437 360.9422302246094 0.253774493932724 0.84984297 0.4781029522418976 True -12 35698 29.660196781158447 0.5747039318084717 393.2484436035156 0.28258073329925537 359.1387634277344 0.25555601716041565 0.8562724 0.43600499629974365 True -13 38444 29.62715220451355 0.5684108734130859 273.4591979980469 0.19158817827701569 357.59942626953125 0.25659263134002686 0.8624212 0.38513997197151184 True -14 41190 29.69695806503296 0.5747208595275879 279.13134765625 0.5668544769287109 357.4864807128906 0.25561079382896423 0.86733556 0.35669273138046265 True -15 43936 29.715285062789917 0.5770368576049805 292.0283203125 0.3830941319465637 355.8084411621094 0.25816240906715393 0.87285924 0.3269170820713043 True -16 46682 29.68968415260315 0.5680556297302246 324.1990661621094 0.3695511221885681 354.8538818359375 0.2597658932209015 0.8750783 0.3125855624675751 True -17 49428 29.63882279396057 0.6648528575897217 276.1587829589844 0.1825660765171051 356.122802734375 0.25784924626350403 0.8742457 0.3105389475822449 False -18 52174 29.85452389717102 0.5758481025695801 346.2276306152344 0.20010092854499817 355.0987243652344 0.2597522437572479 0.8733319 0.3123999536037445 False -19 54920 29.715451955795288 0.5745534896850586 367.6153869628906 0.14227637648582458 355.6302185058594 0.25833243131637573 0.8714569 0.315661758184433 False diff --git a/ENCSR625WLB/cherimoya.fold_0.performance.tsv b/ENCSR625WLB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 03f30f104c6526fe81dfafe87ea57ea4b40743ec..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -354.8538818359375 0.503117024898529 0.2597658932209015 0.0918574184179306 0.8750783205032349 0.8045795559883118 0.3125855624675751 \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_1.evaluate.json b/ENCSR625WLB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1a93d4c7b2ff1ab4df464be717abb1be07b1bf55..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF025LWJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_1.fit.json b/ENCSR625WLB/cherimoya.fold_1.fit.json deleted file mode 100644 index 8650c5db3e978a2a71c43877355e3a5598fa9341..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF025LWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_1.log b/ENCSR625WLB/cherimoya.fold_1.log deleted file mode 100644 index d0dd7f38f6504c553fffdc7b06b1187752e8feaa..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2686 33.469056367874146 4.285243272781372 355.0393981933594 0.37714049220085144 558.9545288085938 0.19510115683078766 0.6611301 7.007651329040527 True -1 5372 29.654693365097046 0.8187642097473145 347.43988037109375 0.5979191064834595 490.464599609375 0.2508622407913208 0.77032226 2.692105293273926 True -2 8058 29.66476583480835 0.7262821197509766 309.53057861328125 0.6690230369567871 483.1226806640625 0.25592240691185 0.7772557 1.6425302028656006 True -3 10744 29.642446279525757 1.5798325538635254 275.561279296875 0.5035040378570557 472.3043212890625 0.2622489333152771 0.79288864 1.0847547054290771 True -4 13430 29.65727472305298 0.8971762657165527 278.724853515625 0.42074620723724365 466.67779541015625 0.2667306661605835 0.8005289 0.9954603910446167 True -5 16116 29.59995126724243 0.7434639930725098 240.11456298828125 0.5378568768501282 461.0284729003906 0.27056336402893066 0.8109911 0.8878414630889893 True -6 18802 29.486363649368286 0.7296390533447266 270.6970520019531 0.4453609585762024 457.6369323730469 0.27362239360809326 0.82271856 0.8143228888511658 True -7 21488 29.00379705429077 0.7161104679107666 300.218017578125 0.2683468759059906 454.53656005859375 0.27568912506103516 0.82627547 0.7718040943145752 True -8 24174 29.052265167236328 0.7200403213500977 438.3785095214844 0.780320942401886 451.3572998046875 0.2800447940826416 0.83325404 0.7196454405784607 True -9 26860 29.215013027191162 0.7224907875061035 268.154296875 0.19291271269321442 448.3758239746094 0.2836184799671173 0.84120846 0.6904337406158447 True -10 29546 28.958749294281006 0.708550214767456 293.49285888671875 0.3414067029953003 447.88714599609375 0.28352758288383484 0.8454679 0.6841123104095459 True -11 32232 28.990681409835815 0.7136211395263672 442.044921875 0.3897339105606079 444.942138671875 0.28684601187705994 0.85534006 0.6046137809753418 True -12 34918 29.05428981781006 0.7187409400939941 299.63153076171875 0.3296540677547455 441.4937744140625 0.2902504503726959 0.8623456 0.5407341122627258 True -13 37604 29.10643243789673 0.7165441513061523 263.9154052734375 0.3530847430229187 440.4494934082031 0.2902405261993408 0.86821735 0.49776002764701843 True -14 40290 29.02734065055847 0.7171342372894287 256.07415771484375 0.3486713767051697 438.9017639160156 0.2918354868888855 0.8762952 0.4495280385017395 True -15 42976 29.0382137298584 0.7200548648834229 408.6339111328125 0.47789424657821655 438.77545166015625 0.2912168800830841 0.8789197 0.4241486191749573 True -16 45662 29.000306606292725 0.7151191234588623 337.5212097167969 0.40892577171325684 436.47332763671875 0.29366081953048706 0.8837266 0.3942766487598419 True -17 48348 29.001542568206787 0.7113909721374512 237.90309143066406 0.417794793844223 435.9975280761719 0.2938973009586334 0.88595706 0.3786528408527374 True -18 51034 28.99113965034485 0.7195608615875244 359.4375 0.22232840955257416 436.1216125488281 0.2935504615306854 0.8854606 0.37811556458473206 False -19 53720 28.992771863937378 0.7177510261535645 350.85186767578125 0.3632231056690216 436.6358642578125 0.29299473762512207 0.88272333 0.37820279598236084 False diff --git a/ENCSR625WLB/cherimoya.fold_1.performance.tsv b/ENCSR625WLB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 609442e0e74c419e43e80431a9e2876031c5c0f5..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -435.9975280761719 0.47508126497268677 0.2938973009586334 0.1096590906381607 0.8859570622444153 0.8400779366493225 0.3786528408527374 \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_2.evaluate.json b/ENCSR625WLB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 658aaa2afef91a7e500362de6de93a08761da314..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF025LWJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_2.fit.json b/ENCSR625WLB/cherimoya.fold_2.fit.json deleted file mode 100644 index 4aa140cf726018f725f960f258d4d4efde514711..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF025LWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_2.log b/ENCSR625WLB/cherimoya.fold_2.log deleted file mode 100644 index cc76014f7be248e07ff48a842d91eb2b1d82d57a..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 35.85845351219177 4.7902820110321045 326.210205078125 0.5429530739784241 464.6310119628906 0.18337111175060272 0.6617406 5.148983955383301 True -1 5776 32.08071303367615 1.0814664363861084 318.061767578125 0.5485923886299133 410.44183349609375 0.2326582670211792 0.7646115 2.2362382411956787 True -2 8664 31.936534881591797 0.593745231628418 290.90283203125 0.40660953521728516 405.4723205566406 0.23572611808776855 0.76897275 1.443569302558899 True -3 11552 31.90069317817688 0.5940396785736084 372.76678466796875 0.4031428098678589 400.11859130859375 0.2390093058347702 0.77687514 0.9499131441116333 True -4 14440 31.802019834518433 0.5927436351776123 311.2769775390625 0.7380965352058411 394.3798828125 0.2437250018119812 0.7955203 0.7962214946746826 True -5 17328 31.804712533950806 1.0661370754241943 288.007568359375 0.5538387298583984 391.0155029296875 0.2468603253364563 0.8028356 0.750823438167572 True -6 20216 31.589107751846313 0.5837192535400391 362.10009765625 0.38868141174316406 388.2998962402344 0.24920907616615295 0.8121542 0.6392583250999451 True -7 23104 31.185925245285034 0.5900468826293945 318.3748779296875 0.5186077356338501 385.40887451171875 0.25170186161994934 0.8196378 0.587121307849884 True -8 25992 31.19166874885559 0.5748791694641113 301.0278625488281 0.4704764485359192 383.95806884765625 0.2527093291282654 0.82769495 0.5273667573928833 True -9 28880 31.198023557662964 0.6157224178314209 317.1815185546875 0.3610405921936035 382.9965515136719 0.253845751285553 0.8292481 0.48888954520225525 True -10 31768 31.285444736480713 1.354764461517334 355.41070556640625 0.4544227123260498 380.463623046875 0.25621017813682556 0.84012014 0.4656278192996979 True -11 34656 31.302704572677612 0.6114749908447266 273.55377197265625 0.4502326250076294 378.7010192871094 0.2591569125652313 0.84896934 0.4210052490234375 True -12 37544 31.284252166748047 0.6033649444580078 292.7244873046875 0.1958806812763214 377.14617919921875 0.2613879442214966 0.8537267 0.3903407156467438 True -13 40432 31.24156379699707 0.5919821262359619 364.76055908203125 0.30567604303359985 376.1487731933594 0.262454628944397 0.86164653 0.3655188977718353 True -14 43320 31.268052339553833 0.5900232791900635 289.3313293457031 0.37186092138290405 374.7030029296875 0.2637413442134857 0.87029743 0.33896157145500183 True -15 46208 31.1907479763031 0.5864498615264893 322.22247314453125 0.33566924929618835 374.90924072265625 0.2627808153629303 0.8736239 0.3266851007938385 True -16 49096 31.202146768569946 1.1744377613067627 241.63095092773438 0.46410423517227173 373.4195861816406 0.2653995156288147 0.87508875 0.32308852672576904 True -17 51984 31.27580976486206 0.5803449153900146 260.0399169921875 0.3157787621021271 373.533935546875 0.2649255394935608 0.8722762 0.3222270905971527 False -18 54872 31.29856777191162 0.5845828056335449 305.8976135253906 0.22499550879001617 374.5031433105469 0.2640925347805023 0.8728877 0.3268451690673828 False -19 57760 31.30177354812622 0.5843973159790039 376.7239990234375 0.153745636343956 374.6322021484375 0.2647751271724701 0.87184185 0.3292185664176941 False diff --git a/ENCSR625WLB/cherimoya.fold_2.performance.tsv b/ENCSR625WLB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 08dbd6e9ef015fe2e2d2c0259820cc2cd90f4a05..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -373.4195861816406 0.4965614080429077 0.2653994858264923 0.08858345448970795 0.8750887513160706 0.8107911944389343 0.32308852672576904 \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_3.evaluate.json b/ENCSR625WLB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cfed18896e8520c9966da6a362e3a8df72cfc2b6..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF025LWJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_3.fit.json b/ENCSR625WLB/cherimoya.fold_3.fit.json deleted file mode 100644 index f70c46f3fe104bc2de7b8bfa53b06b1ac941e191..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF025LWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_3.log b/ENCSR625WLB/cherimoya.fold_3.log deleted file mode 100644 index c81e067c35a9a311f495448ff08c19d9149e88f6..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 34.30785536766052 3.6425716876983643 341.67742919921875 0.7578430771827698 449.66082763671875 0.19456560909748077 0.6309764 5.501711845397949 True -1 5460 30.5723717212677 0.5713839530944824 349.4373779296875 0.8774940967559814 405.02337646484375 0.23891077935695648 0.71595645 2.328273296356201 True -2 8190 30.246074199676514 0.5431275367736816 299.317138671875 0.7933645248413086 399.6803894042969 0.24270130693912506 0.72149134 1.967492699623108 True -3 10920 30.1628839969635 0.5547504425048828 299.0750732421875 0.7219904661178589 392.7370300292969 0.24701426923274994 0.74202526 1.092282772064209 True -4 13650 30.14677906036377 0.5469827651977539 357.7793884277344 0.46815985441207886 390.0097961425781 0.25016874074935913 0.7588379 0.8927507996559143 True -5 16380 30.193320274353027 16.288734197616577 291.516357421875 0.4226030707359314 386.70245361328125 0.2537418007850647 0.7680731 0.8802095055580139 True -6 19110 29.63608169555664 0.8503804206848145 375.255859375 0.3649177551269531 383.06085205078125 0.2575984597206116 0.7773737 0.8454917669296265 True -7 21840 29.602598667144775 0.5662717819213867 348.5350341796875 0.6544696688652039 382.41790771484375 0.2582496106624603 0.7892721 0.8136699795722961 True -8 24570 29.448649883270264 0.5514316558837891 284.4414367675781 0.47091782093048096 379.7842102050781 0.2617013454437256 0.79745096 0.7503880858421326 True -9 27300 29.491047859191895 1.0553407669067383 394.26678466796875 0.6321569085121155 378.82940673828125 0.26278358697891235 0.810059 0.6799367666244507 True -10 30030 29.70598793029785 0.5428993701934814 223.94764709472656 0.5532445907592773 377.27740478515625 0.26472795009613037 0.8169224 0.6156185865402222 True -11 32760 29.479944229125977 0.5375375747680664 338.3600158691406 0.35594886541366577 374.3255310058594 0.26829761266708374 0.82796556 0.560849666595459 True -12 35490 29.487005949020386 1.7219078540802002 331.4700927734375 0.5405901670455933 374.234619140625 0.26613301038742065 0.8348271 0.5066187381744385 True -13 38220 29.531829595565796 0.5445168018341064 300.760986328125 0.37109625339508057 371.23095703125 0.2707686126232147 0.8423992 0.46585214138031006 True -14 40950 29.465470552444458 1.7684543132781982 343.056640625 0.6469295024871826 370.4453125 0.270493745803833 0.851461 0.42144763469696045 True -15 43680 29.620814323425293 0.5336852073669434 290.65179443359375 0.3272547721862793 368.6768798828125 0.2726120948791504 0.8574698 0.3994894027709961 True -16 46410 29.51347041130066 0.5380096435546875 260.7896728515625 0.2848304510116577 368.8406982421875 0.2720644772052765 0.86077416 0.3826291859149933 True -17 49140 29.86592936515808 0.5353124141693115 251.46859741210938 0.23088409006595612 369.6183776855469 0.27087369561195374 0.8622311 0.3737431764602661 True -18 51870 29.602492332458496 0.53861403465271 335.8177490234375 0.2968742847442627 368.9039611816406 0.2720426917076111 0.8638661 0.37128835916519165 True -19 54600 29.529278993606567 0.5388145446777344 275.54779052734375 0.32910555601119995 369.6770324707031 0.27079036831855774 0.86148256 0.3723509609699249 False diff --git a/ENCSR625WLB/cherimoya.fold_3.performance.tsv b/ENCSR625WLB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ea260114fa5be0f76a345f90ea65d9e53d40b8af..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -368.9039611816406 0.4931860864162445 0.2720426321029663 0.09381598979234695 0.8638660907745361 0.7979831099510193 0.37128835916519165 \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_4.evaluate.json b/ENCSR625WLB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d151c3175e4abb9ffcde4a8439b7b63c08cc696b..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF025LWJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_4.fit.json b/ENCSR625WLB/cherimoya.fold_4.fit.json deleted file mode 100644 index 420e3fc2ac76ad02b4a00f0fab1e8ce653dd182a..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF025LWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR625WLB/cherimoya.fold_4.log b/ENCSR625WLB/cherimoya.fold_4.log deleted file mode 100644 index 5df1487d9de77925699512d34f62a4bd38ce2b25..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2802 35.195433139801025 3.724856376647949 388.8349609375 0.5750110149383545 389.154541015625 0.17813770473003387 0.6288948 5.284851551055908 True -1 5604 30.980403900146484 0.6041572093963623 243.04592895507812 0.5146373510360718 356.229736328125 0.21413563191890717 0.7207074 1.6549607515335083 True -2 8406 31.059216022491455 0.8239316940307617 309.354736328125 0.39217454195022583 349.74261474609375 0.22065848112106323 0.7448027 1.2822264432907104 True -3 11208 31.0065016746521 0.5937695503234863 289.3117370605469 0.2946323752403259 346.1965026855469 0.2236955612897873 0.74652153 0.7597636580467224 True -4 14010 30.845532417297363 0.5904452800750732 365.6280212402344 0.6414711475372314 341.35693359375 0.22987641394138336 0.7647559 0.6678906679153442 True -5 16812 30.86326265335083 0.5860545635223389 452.19415283203125 0.6549521684646606 338.0515441894531 0.2321644276380539 0.7752115 0.6264871954917908 True -6 19614 30.898118495941162 0.5964667797088623 410.3188171386719 0.399472177028656 336.60626220703125 0.23345749080181122 0.7897958 0.5630531907081604 True -7 22416 30.934104919433594 0.5765194892883301 311.80316162109375 0.41323035955429077 335.31573486328125 0.23425531387329102 0.79701954 0.5264305472373962 True -8 25218 30.272454738616943 0.5946567058563232 288.6990051269531 0.3331145644187927 334.03289794921875 0.23605677485466003 0.80285764 0.48725655674934387 True -9 28020 30.570874214172363 0.594489336013794 232.67929077148438 0.42834746837615967 331.8096923828125 0.2394399493932724 0.810563 0.45817893743515015 True -10 30822 30.291053295135498 0.5927798748016357 352.458740234375 0.5075768232345581 330.7069091796875 0.24020540714263916 0.82035637 0.4146575927734375 True -11 33624 30.226462602615356 0.5931158065795898 232.88882446289062 0.28333649039268494 329.06427001953125 0.2420598566532135 0.83104455 0.38100939989089966 True -12 36426 30.37972354888916 0.580876350402832 380.57867431640625 0.5430311560630798 328.1116638183594 0.2441556751728058 0.8369563 0.36198508739471436 True -13 39228 30.25477123260498 0.5897424221038818 293.99285888671875 0.38152235746383667 327.383544921875 0.24445509910583496 0.84225357 0.34600529074668884 True -14 42030 30.262954235076904 0.5863852500915527 345.5364990234375 0.2204200178384781 326.4424133300781 0.24634909629821777 0.84825134 0.3268546462059021 True -15 44832 30.60251212120056 0.5864932537078857 349.6631164550781 0.32358628511428833 325.7103271484375 0.24672766029834747 0.85509765 0.3104681074619293 True -16 47634 30.300739526748657 0.5807332992553711 371.7191162109375 0.2798265218734741 325.49365234375 0.2471126765012741 0.8581157 0.30272647738456726 True -17 50436 30.25155758857727 0.5872769355773926 294.4815673828125 0.17179729044437408 326.0719909667969 0.2458115816116333 0.859289 0.30259549617767334 True -18 53238 30.248063564300537 0.5782160758972168 359.6985778808594 0.273790180683136 325.9574279785156 0.2470778226852417 0.8582711 0.30416715145111084 False -19 56040 30.328014373779297 0.5732343196868896 282.9067077636719 0.24617068469524384 325.5026550292969 0.2481134682893753 0.8585309 0.30636656284332275 False diff --git a/ENCSR625WLB/cherimoya.fold_4.performance.tsv b/ENCSR625WLB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 52a1f56972181c6f300267ec752520803b65028a..0000000000000000000000000000000000000000 --- a/ENCSR625WLB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.0719909667969 0.5122096538543701 0.2458115816116333 0.0803980901837349 0.8592889904975891 0.7829681038856506 0.30259549617767334 \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_0.evaluate.json b/ENCSR627NIF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9f3170f5cf580eb71ade1b0957262b0da3e3a804..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF331DXV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_0.fit.json b/ENCSR627NIF/cherimoya.fold_0.fit.json deleted file mode 100644 index 2c2eb37896487d9c17442769a1ffc15c110f5868..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF331DXV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_0.log b/ENCSR627NIF/cherimoya.fold_0.log deleted file mode 100644 index 4835a64bd34544be68a557979214b177f1b3d07d..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.88884902000427 4.210577726364136 1008.3387451171875 0.3970893621444702 1330.0589599609375 0.2767936587333679 0.6382614 7.915853023529053 True -1 5514 30.52068829536438 0.6154837608337402 1000.5733032226562 0.5819021463394165 1197.3402099609375 0.3937705457210541 0.7058129 1.2495664358139038 True -2 8271 30.510178565979004 0.5805695056915283 1057.54345703125 0.5617930293083191 1170.99267578125 0.41385242342948914 0.7132596 0.6072331666946411 True -3 11028 30.48924160003662 2.107189655303955 990.694580078125 0.5364681482315063 1158.8450927734375 0.42252326011657715 0.7191202 0.7136290073394775 True -4 13785 30.542405128479004 0.6074879169464111 811.6314697265625 0.32184308767318726 1154.7685546875 0.4268879294395447 0.72147465 0.6958574056625366 True -5 16542 30.425119638442993 0.5791475772857666 860.8416137695312 0.728472113609314 1149.3751220703125 0.432071328163147 0.7270255 0.5429860949516296 True -6 19299 30.426432847976685 0.5979111194610596 842.3797607421875 0.6150432825088501 1145.5684814453125 0.4365901052951813 0.7320716 0.45306897163391113 True -7 22056 30.431067943572998 0.5931198596954346 977.107666015625 0.3492351472377777 1142.4947509765625 0.43754202127456665 0.73213685 0.4376614987850189 True -8 24813 30.38584852218628 0.5974380970001221 1040.508056640625 0.4404667913913727 1137.61328125 0.44179508090019226 0.7352457 0.41544726490974426 True -9 27570 30.390945434570312 0.5925776958465576 977.283447265625 0.4760339856147766 1134.9716796875 0.44353628158569336 0.7416855 0.40605515241622925 True -10 30327 30.45960307121277 0.6089260578155518 954.0406494140625 0.30862367153167725 1131.90283203125 0.4474099576473236 0.74897325 0.40562909841537476 True -11 33084 30.43216061592102 0.8092019557952881 1023.1860961914062 0.4945302903652191 1126.0633544921875 0.4531782865524292 0.7551547 0.37570858001708984 True -12 35841 30.22705864906311 0.5819706916809082 834.011474609375 0.4854809045791626 1122.2364501953125 0.45691579580307007 0.76389354 0.3398858606815338 True -13 38598 29.886277437210083 0.5887820720672607 810.8311767578125 0.3646155595779419 1121.537353515625 0.4569128155708313 0.7710379 0.315812349319458 True -14 41355 29.85888361930847 0.5747110843658447 968.916259765625 0.25548282265663147 1117.29833984375 0.45967838168144226 0.7796962 0.29438573122024536 True -15 44112 29.92306399345398 0.5629796981811523 906.9190063476562 0.27043670415878296 1113.6373291015625 0.46371638774871826 0.78707546 0.2802512049674988 True -16 46869 29.804057359695435 0.5850784778594971 923.5204467773438 0.2816106081008911 1115.1571044921875 0.46219688653945923 0.7931397 0.262330561876297 True -17 49626 29.926063776016235 0.5835282802581787 834.9059448242188 0.22803637385368347 1113.917236328125 0.4636339247226715 0.7941831 0.25908148288726807 True -18 52383 29.900132179260254 0.5772151947021484 868.7857666015625 0.21388393640518188 1114.092041015625 0.46336039900779724 0.79420424 0.2584421932697296 True -19 55140 29.879640340805054 0.566490888595581 830.3419799804688 0.3003006875514984 1114.70166015625 0.46247202157974243 0.7934449 0.25849393010139465 False diff --git a/ENCSR627NIF/cherimoya.fold_0.performance.tsv b/ENCSR627NIF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ba7378f4c3a542889ca3b490f11436532bdfd33f..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1114.092041015625 0.2775857448577881 0.46336042881011963 0.24434001743793488 0.7942042350769043 0.7269505262374878 0.2584421932697296 \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_1.evaluate.json b/ENCSR627NIF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 93dc3c475ff8c03abab669b39a151733fe21d636..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF331DXV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_1.fit.json b/ENCSR627NIF/cherimoya.fold_1.fit.json deleted file mode 100644 index 182beaca7e0eadc20ce4dd6695ecfcc03daa5cde..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF331DXV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_1.log b/ENCSR627NIF/cherimoya.fold_1.log deleted file mode 100644 index 591b770b66b55d02eab4a505866c3fe893b2944a..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 35.80281329154968 4.139327526092529 1078.16259765625 0.42381617426872253 1513.6170654296875 0.28413325548171997 0.6493885 7.36954402923584 True -1 5486 30.15382981300354 1.4022693634033203 916.9635620117188 0.8476834893226624 1345.6739501953125 0.4075887203216553 0.72449 1.4919122457504272 True -2 8229 30.113097190856934 0.7044773101806641 821.3200073242188 0.5536637306213379 1314.8482666015625 0.4227653443813324 0.744008 0.6720638275146484 True -3 10972 30.903659105300903 18.858815670013428 955.0450439453125 0.3943752646446228 1291.1239013671875 0.43960893154144287 0.7535585 0.5843979120254517 True -4 13715 30.120936393737793 0.7228102684020996 924.69873046875 0.35296887159347534 1287.8284912109375 0.4418625831604004 0.76022387 0.5563978552818298 True -5 16458 30.17113208770752 0.6946687698364258 997.4198608398438 0.5941749811172485 1279.2454833984375 0.4473271369934082 0.7619866 0.5453798174858093 True -6 19201 30.184080600738525 0.7030949592590332 1003.6839599609375 0.539908766746521 1275.864501953125 0.4501195549964905 0.76131946 0.5381060242652893 False -7 21944 30.146498918533325 0.7011823654174805 1016.3505859375 0.31287384033203125 1269.799072265625 0.4554695785045624 0.7758168 0.4825097620487213 True -8 24687 29.67352533340454 0.6913886070251465 1113.30615234375 0.3568427562713623 1265.43017578125 0.4595850110054016 0.77609867 0.4982132613658905 True -9 27430 29.527294158935547 0.6772418022155762 972.666748046875 0.22102664411067963 1261.07958984375 0.4608781635761261 0.7818959 0.49086418747901917 True -10 30173 29.63028597831726 0.6986322402954102 978.360595703125 0.28327468037605286 1256.3328857421875 0.4658282995223999 0.78847224 0.4574916362762451 True -11 32916 29.584062099456787 0.6822795867919922 854.1024169921875 0.3508903980255127 1254.3470458984375 0.4653148055076599 0.7964128 0.434867799282074 True -12 35659 29.53905200958252 0.6632828712463379 935.168212890625 0.2357172966003418 1245.3658447265625 0.47326526045799255 0.80387247 0.3701407015323639 True -13 38402 29.53392744064331 1.1187784671783447 953.7860717773438 0.2810286581516266 1238.4296875 0.4790821075439453 0.808426 0.3397708237171173 True -14 41145 29.601575136184692 0.7070484161376953 894.1456909179688 0.24544358253479004 1237.1910400390625 0.4785003960132599 0.8158962 0.316534161567688 True -15 43888 29.553160667419434 0.6789777278900146 927.72900390625 0.28944453597068787 1237.1324462890625 0.4781474173069 0.823629 0.28818830847740173 True -16 46631 29.583739042282104 3.9733240604400635 877.4671630859375 0.20299386978149414 1233.6614990234375 0.48075777292251587 0.82450885 0.276826411485672 True -17 49374 29.544153451919556 0.6706173419952393 957.8724365234375 0.2657458484172821 1233.3597412109375 0.48113566637039185 0.8275032 0.2698693871498108 True -18 52117 29.5525164604187 0.6842787265777588 859.352783203125 0.309326708316803 1230.4273681640625 0.48384469747543335 0.8266921 0.26632240414619446 False -19 54860 29.535600900650024 0.6855802536010742 941.7509765625 0.25488606095314026 1233.9376220703125 0.47952282428741455 0.8271142 0.2688387930393219 False diff --git a/ENCSR627NIF/cherimoya.fold_1.performance.tsv b/ENCSR627NIF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8be17c1085d48750dfe4249bb4ee2b19f0c9b87c..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1233.3597412109375 0.2626250088214874 0.48113560676574707 0.2693653106689453 0.8275032043457031 0.7833517789840698 0.2698693871498108 \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_2.evaluate.json b/ENCSR627NIF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 200368c9761b509d4cddab1ba4c8e9abc00e0ddb..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF331DXV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_2.fit.json b/ENCSR627NIF/cherimoya.fold_2.fit.json deleted file mode 100644 index 63df93dc0b1730de5132b33c657ecc3349b64dab..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF331DXV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_2.log b/ENCSR627NIF/cherimoya.fold_2.log deleted file mode 100644 index be89f20cf07b2801ed7080ed94a4c68ffa9504cb..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2902 36.555142641067505 3.415306568145752 1015.5975952148438 0.6092586517333984 1371.128173828125 0.2829645276069641 0.61428887 5.5821356773376465 True -1 5804 31.89665126800537 0.5520622730255127 1192.2960205078125 1.1882812976837158 1226.1302490234375 0.40109261870384216 0.7101775 1.2065781354904175 True -2 8706 31.95013117790222 0.6206328868865967 815.095703125 0.5430096387863159 1202.37158203125 0.41576406359672546 0.7161871 0.631990373134613 True -3 11608 31.91910982131958 0.5391697883605957 880.122314453125 0.3135696351528168 1190.3935546875 0.4250929355621338 0.72649634 0.6010688543319702 True -4 14510 31.913068056106567 0.5335640907287598 919.607666015625 0.5046697854995728 1182.1181640625 0.43274813890457153 0.7327229 0.5753014087677002 True -5 17412 31.251428365707397 0.5229663848876953 901.6717529296875 0.3720460832118988 1182.46923828125 0.4327031075954437 0.73307675 0.5763584971427917 True -6 20314 31.20432710647583 0.5238237380981445 992.2131958007812 0.8399344682693481 1178.5047607421875 0.43481990694999695 0.73643523 0.5894634127616882 True -7 23216 31.24472713470459 0.5304958820343018 986.3690185546875 0.39428502321243286 1176.0977783203125 0.43822094798088074 0.7381586 0.5194429159164429 True -8 26118 31.276052713394165 0.5332374572753906 793.9408569335938 0.3684638738632202 1171.376708984375 0.44310134649276733 0.7415339 0.47742605209350586 True -9 29020 31.306194305419922 0.5385940074920654 1037.977294921875 0.35005950927734375 1166.404541015625 0.4475974142551422 0.74993616 0.4740801453590393 True -10 31922 31.304600715637207 0.5327854156494141 1057.8074951171875 0.5773496627807617 1161.0235595703125 0.452900230884552 0.75405926 0.44039079546928406 True -11 34824 31.32934045791626 0.533395528793335 1007.5598754882812 0.28778699040412903 1158.3492431640625 0.45538216829299927 0.7618067 0.4280005693435669 True -12 37726 31.24021625518799 0.5311746597290039 921.42529296875 0.3586096167564392 1153.6197509765625 0.4584604501724243 0.7711528 0.3740462064743042 True -13 40628 31.25680160522461 0.5332205295562744 890.351318359375 0.25469067692756653 1147.056640625 0.46361392736434937 0.776281 0.34968388080596924 True -14 43530 31.24768877029419 0.5346307754516602 887.5131225585938 0.3411039710044861 1143.843994140625 0.4657457768917084 0.7837971 0.3270619511604309 True -15 46432 31.234951496124268 0.534102201461792 982.8142700195312 0.25547677278518677 1142.8670654296875 0.4665561318397522 0.7886322 0.2973836362361908 True -16 49334 31.256832122802734 0.5338349342346191 959.1039428710938 0.2882186472415924 1145.16162109375 0.46357446908950806 0.7938696 0.2873026132583618 True -17 52236 31.318020820617676 0.5289323329925537 1000.4961547851562 0.23944616317749023 1141.9427490234375 0.467489093542099 0.79584765 0.27862611413002014 True -18 55138 31.245860815048218 0.5351157188415527 1038.3876953125 0.2519334554672241 1141.575927734375 0.4678153991699219 0.79954034 0.2743571400642395 True -19 58040 31.293386459350586 0.5330097675323486 934.6607055664062 0.3160396218299866 1142.120361328125 0.466564416885376 0.7990761 0.2750300168991089 False diff --git a/ENCSR627NIF/cherimoya.fold_2.performance.tsv b/ENCSR627NIF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 04405ef392234b21b667fafa8a8c8b822cdff730..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1141.575927734375 0.2739330232143402 0.4678153991699219 0.2525407373905182 0.7995403409004211 0.7390875816345215 0.2743571400642395 \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_3.evaluate.json b/ENCSR627NIF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9bd102e6b4cd7aa37e18c960d4cffd7eb803668f..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF331DXV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_3.fit.json b/ENCSR627NIF/cherimoya.fold_3.fit.json deleted file mode 100644 index 91a439b85e80b335430f41f979ac610e6e3e2fde..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF331DXV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_3.log b/ENCSR627NIF/cherimoya.fold_3.log deleted file mode 100644 index c111e1d0ab9b7ddf9fb73cb2d78e6f99def70bac..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2793 35.51965308189392 5.18201756477356 1001.5555419921875 0.6896783113479614 1371.252197265625 0.28172028064727783 0.6355522 6.731790065765381 True -1 5586 30.721892833709717 1.1063971519470215 1017.7999267578125 0.38464197516441345 1253.16357421875 0.38551944494247437 0.7083457 1.3071932792663574 True -2 8379 30.616821765899658 0.7083830833435059 937.3265991210938 0.531672477722168 1227.4481201171875 0.4031434655189514 0.72045237 0.7485657334327698 True -3 11172 30.046727657318115 0.9749751091003418 885.847412109375 0.47348687052726746 1213.4317626953125 0.4164721667766571 0.7195494 0.5681097507476807 False -4 13965 30.136099815368652 1.0553090572357178 897.3462524414062 0.6129064559936523 1206.80859375 0.422113299369812 0.72296816 0.6101552248001099 True -5 16758 30.16190266609192 2.2899627685546875 905.180419921875 0.28910040855407715 1205.8270263671875 0.4213845431804657 0.71802366 0.5028986930847168 False -6 19551 30.1267991065979 0.5725624561309814 938.7770385742188 0.3627224266529083 1200.82080078125 0.42590001225471497 0.7232193 0.47805550694465637 True -7 22344 30.117754220962524 0.6225388050079346 909.6064453125 0.44512033462524414 1195.559814453125 0.4307905435562134 0.72887504 0.5027470588684082 True -8 25137 30.12271237373352 0.5736308097839355 947.2948608398438 0.38757163286209106 1192.7042236328125 0.4346071779727936 0.7333478 0.4862040579319 True -9 27930 30.077260971069336 0.5865223407745361 982.262451171875 0.48640191555023193 1190.0506591796875 0.43622228503227234 0.7357214 0.4764021039009094 True -10 30723 30.093526363372803 0.5664854049682617 1040.963134765625 0.3418647050857544 1182.642822265625 0.44307583570480347 0.74787664 0.414075642824173 True -11 33516 30.104783296585083 1.3075904846191406 999.228515625 0.23141144216060638 1178.4691162109375 0.4460844397544861 0.7584068 0.4000878930091858 True -12 36309 30.107070207595825 0.5663802623748779 983.7921142578125 0.24513596296310425 1178.9580078125 0.44582492113113403 0.7652379 0.38294753432273865 True -13 39102 30.14392113685608 0.5681688785552979 984.03564453125 0.24460092186927795 1174.427490234375 0.4492676854133606 0.7754071 0.3505752384662628 True -14 41895 30.117725133895874 0.5731170177459717 1011.344482421875 0.21182222664356232 1169.657470703125 0.45424726605415344 0.78552866 0.32117486000061035 True -15 44688 30.09331488609314 0.6033291816711426 834.1697998046875 0.3467909097671509 1168.1165771484375 0.454338014125824 0.7917929 0.30099067091941833 True -16 47481 30.18737816810608 0.57470703125 904.204345703125 0.15147680044174194 1165.984130859375 0.45574524998664856 0.7976194 0.2861892580986023 True -17 50274 30.048216819763184 0.620281457901001 939.43994140625 0.1742798388004303 1167.7701416015625 0.4532527029514313 0.80168563 0.27645164728164673 True -18 53067 30.085646390914917 0.6042191982269287 961.1082153320312 0.4367592930793762 1167.1685791015625 0.45442065596580505 0.8003048 0.27312690019607544 False -19 55860 30.071253061294556 0.5960619449615479 963.4415893554688 0.22779756784439087 1166.76904296875 0.4544665217399597 0.80173653 0.27288195490837097 True diff --git a/ENCSR627NIF/cherimoya.fold_3.performance.tsv b/ENCSR627NIF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8276cab7e0d3fc1f2b50ac72cebec815095f0bbd..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1166.76904296875 0.27452245354652405 0.45446649193763733 0.24870739877223969 0.8017365336418152 0.7415177226066589 0.27288195490837097 \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_4.evaluate.json b/ENCSR627NIF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index eb8c01dda40684da67ae8216dbff7551bbeb7f20..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF331DXV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_4.fit.json b/ENCSR627NIF/cherimoya.fold_4.fit.json deleted file mode 100644 index bea52fab181b51d65b13fa541ef63b565342e811..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF331DXV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627NIF/cherimoya.fold_4.log b/ENCSR627NIF/cherimoya.fold_4.log deleted file mode 100644 index f120c32707f527a17c5fbc9413a400c12dbbe162..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 36.24807643890381 3.5100080966949463 1188.823486328125 0.5709453821182251 1314.5806884765625 0.2737370729446411 0.6411542 6.571610927581787 True -1 5748 31.5968759059906 0.6262242794036865 854.7559814453125 0.982876181602478 1190.334716796875 0.3898811936378479 0.71407557 1.4125093221664429 True -2 8622 31.584085702896118 0.6058969497680664 900.733154296875 0.5511208176612854 1169.0260009765625 0.4038286507129669 0.7214943 0.7760413289070129 True -3 11496 32.56090021133423 0.6055521965026855 984.6118774414062 0.5382149815559387 1157.4599609375 0.41564905643463135 0.7218364 0.6905499696731567 True -4 14370 31.67433190345764 0.6162450313568115 987.8469848632812 0.6413364410400391 1152.2900390625 0.419715017080307 0.7208258 0.7648184895515442 False -5 17244 31.65755534172058 0.586616039276123 906.701416015625 0.2737916111946106 1149.698486328125 0.422566682100296 0.7228875 0.586487889289856 True -6 20118 31.592475414276123 0.5940124988555908 1103.6142578125 0.350761741399765 1145.2159423828125 0.42645999789237976 0.7279914 0.6149360537528992 True -7 22992 31.587573766708374 0.6254847049713135 924.3145751953125 0.47089946269989014 1142.65869140625 0.43052512407302856 0.7352191 0.5824054479598999 True -8 25866 31.590871334075928 0.5845179557800293 864.99951171875 0.22940123081207275 1138.653564453125 0.4338018596172333 0.7380044 0.5677860379219055 True -9 28740 31.59180212020874 0.6018321514129639 825.9497680664062 0.3563039004802704 1134.612060546875 0.43755820393562317 0.7449165 0.48578402400016785 True -10 31614 31.610533475875854 1.053837537765503 916.9662475585938 0.39101511240005493 1129.44775390625 0.44327932596206665 0.75132287 0.45657363533973694 True -11 34488 31.637559175491333 0.5963253974914551 910.7390747070312 0.6255886554718018 1126.8311767578125 0.44539564847946167 0.7600092 0.403009295463562 True -12 37362 31.592464923858643 0.583512544631958 939.2421875 0.1736987978219986 1123.802490234375 0.4469071626663208 0.767756 0.3631468415260315 True -13 40236 31.624005794525146 0.5967977046966553 853.4270629882812 0.26959165930747986 1118.61328125 0.4518689215183258 0.7757346 0.3208729922771454 True -14 43110 31.69678497314453 0.598480224609375 903.977783203125 0.3348415493965149 1117.5245361328125 0.45072275400161743 0.7862999 0.2937101423740387 True -15 45984 31.628292560577393 0.5729033946990967 934.736083984375 0.36219850182533264 1114.1318359375 0.4560547471046448 0.79086226 0.2667231857776642 True -16 48858 31.594412803649902 0.5849194526672363 967.2247314453125 0.2175196409225464 1113.3543701171875 0.45499110221862793 0.79708576 0.25567662715911865 True -17 51732 31.577327966690063 0.5792124271392822 1015.8118896484375 0.18544594943523407 1114.220703125 0.45332902669906616 0.7998666 0.24760276079177856 True -18 54606 31.569069862365723 0.5948567390441895 821.0139770507812 0.2200969010591507 1113.8670654296875 0.4555060565471649 0.7996507 0.24630825221538544 False -19 57480 31.631859064102173 0.6003832817077637 840.0474243164062 0.211188405752182 1113.6700439453125 0.45532628893852234 0.7975994 0.2492782175540924 False diff --git a/ENCSR627NIF/cherimoya.fold_4.performance.tsv b/ENCSR627NIF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e7ee2a45a971202b00702ea92dceaf51487ed27f..0000000000000000000000000000000000000000 --- a/ENCSR627NIF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1114.220703125 0.27879616618156433 0.4533289968967438 0.24124428629875183 0.7998666167259216 0.7344387173652649 0.24760276079177856 \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_0.evaluate.json b/ENCSR627QIA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6b45e1f8318b47cfecc396f43d43c3ec4f165937..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187UXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_0.fit.json b/ENCSR627QIA/cherimoya.fold_0.fit.json deleted file mode 100644 index b93c57190eb03240b0a77eca6003171ebae15359..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF187UXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_0.log b/ENCSR627QIA/cherimoya.fold_0.log deleted file mode 100644 index ac5b58cc70cff53e1c08e12ce9b8bbe9f001b2cf..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1603 22.277862310409546 3.8631882667541504 552.7699584960938 1.9870119094848633 802.32568359375 0.16696281731128693 0.48343605 15.651191711425781 True -1 3206 17.653005361557007 0.33692073822021484 360.3177490234375 1.1567249298095703 661.3263549804688 0.2594236433506012 0.67443323 8.84394645690918 True -2 4809 17.581249952316284 0.3196446895599365 605.841552734375 0.9203475713729858 577.9801025390625 0.3033410906791687 0.72775716 4.41641092300415 True -3 6412 17.584131240844727 0.31791162490844727 605.4451904296875 1.369673490524292 551.68359375 0.31812310218811035 0.73493 2.9483726024627686 True -4 8015 17.598865509033203 0.3228285312652588 409.92779541015625 1.2257004976272583 540.9142456054688 0.32594284415245056 0.7357033 2.2273287773132324 True -5 9618 17.58195924758911 0.32175707817077637 361.66925048828125 0.8648768663406372 533.1298828125 0.33056724071502686 0.74474436 1.9310908317565918 True -6 11221 17.586257219314575 0.8534369468688965 528.60498046875 1.346883773803711 527.694091796875 0.3355140686035156 0.7533896 1.6364372968673706 True -7 12824 17.621842861175537 0.31630802154541016 443.1058654785156 0.7566101551055908 519.9843139648438 0.34062981605529785 0.763825 1.4143670797348022 True -8 14427 17.60660409927368 0.31940603256225586 483.34552001953125 0.8482100963592529 514.2869873046875 0.3441993296146393 0.77576315 1.1759122610092163 True -9 16030 17.58293342590332 0.31294751167297363 380.04376220703125 0.9148551225662231 512.8746948242188 0.3440459966659546 0.7858006 1.0475773811340332 True -10 17633 17.6591534614563 0.31359028816223145 473.9097900390625 1.0059161186218262 507.35430908203125 0.34850338101387024 0.7913669 0.9397436380386353 True -11 19236 17.623578786849976 0.31707000732421875 532.8431396484375 0.8755584955215454 501.636962890625 0.352748304605484 0.8009839 0.8804860711097717 True -12 20839 17.637906551361084 0.3175206184387207 465.607421875 1.4726035594940186 499.2273864746094 0.3541211187839508 0.8094202 0.8287456631660461 True -13 22442 17.603393077850342 0.5788741111755371 467.7135009765625 1.063455581665039 496.4515380859375 0.35698404908180237 0.8141299 0.7989794611930847 True -14 24045 17.633760690689087 0.31496214866638184 335.92449951171875 0.7011251449584961 492.0317687988281 0.36029407382011414 0.8194706 0.7574871182441711 True -15 25648 17.576438188552856 0.3658716678619385 294.3981628417969 0.34424063563346863 490.591552734375 0.36085909605026245 0.8239717 0.7299456000328064 True -16 27251 17.629254579544067 0.32902050018310547 330.3511657714844 0.5586521625518799 487.8298034667969 0.36323586106300354 0.82792044 0.709661602973938 True -17 28854 17.5798761844635 12.251335144042969 461.07757568359375 0.5826228857040405 488.00811767578125 0.362317830324173 0.8307707 0.7013706564903259 True -18 30457 17.9532527923584 0.32587504386901855 439.6925964355469 0.5826274156570435 488.62432861328125 0.3618886470794678 0.8313419 0.7003386616706848 True -19 32060 17.64184331893921 1.2540123462677002 299.5481262207031 0.5817970633506775 489.957275390625 0.36014723777770996 0.82987404 0.7040934562683105 False diff --git a/ENCSR627QIA/cherimoya.fold_0.performance.tsv b/ENCSR627QIA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d4893dfb62a721c3665004f8b4dd82b42587f9c2..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -488.62432861328125 0.4319131374359131 0.3618886470794678 0.134435772895813 0.8313419222831726 0.7851460576057434 0.7003386616706848 \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_1.evaluate.json b/ENCSR627QIA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8241c44846297031183c3a7d2e1000f37c015232..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187UXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_1.fit.json b/ENCSR627QIA/cherimoya.fold_1.fit.json deleted file mode 100644 index bb4ff87ef8947355900202ca12398ab0ca41608a..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF187UXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_1.log b/ENCSR627QIA/cherimoya.fold_1.log deleted file mode 100644 index 7c5bf6e1c8532f883589ee560e06af76fb3d4c17..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1545 21.750235319137573 3.3376376628875732 524.0751953125 1.7016735076904297 993.3416748046875 0.1720363199710846 0.43625915 18.518863677978516 True -1 3090 16.976584911346436 0.51515793800354 484.2065124511719 1.406437873840332 812.02685546875 0.27189525961875916 0.6409144 12.091134071350098 True -2 4635 16.753481149673462 0.4740912914276123 464.0796813964844 1.3118176460266113 714.5425415039062 0.3258729577064514 0.71333027 7.324681282043457 True -3 6180 16.62287425994873 0.45006608963012695 274.846435546875 1.2472668886184692 671.2400512695312 0.3448813557624817 0.73612285 4.823397636413574 True -4 7725 16.644468784332275 0.4945404529571533 429.39385986328125 1.6011559963226318 653.93994140625 0.35063406825065613 0.74798644 3.2559468746185303 True -5 9270 16.621110916137695 1.616532802581787 489.4525451660156 0.7321360111236572 642.6817626953125 0.35566723346710205 0.7622497 2.474874496459961 True -6 10815 16.650464057922363 0.4722435474395752 395.22027587890625 1.3793439865112305 633.6129760742188 0.36078113317489624 0.76813155 2.0234811305999756 True -7 12360 16.590372323989868 0.4700303077697754 366.0068359375 1.041471004486084 627.709716796875 0.36577796936035156 0.7738426 1.7925405502319336 True -8 13905 16.67148780822754 0.44359397888183594 345.96710205078125 1.0204793214797974 619.87451171875 0.36980700492858887 0.7859525 1.4816367626190186 True -9 15450 16.67048978805542 0.45453357696533203 581.33740234375 0.9317615032196045 615.9267578125 0.37243106961250305 0.79017824 1.3414287567138672 True -10 16995 16.653493642807007 0.4528031349182129 473.826416015625 0.730500340461731 608.702392578125 0.3775717318058014 0.7994138 1.1935393810272217 True -11 18540 16.705971002578735 0.45228004455566406 455.90380859375 0.8446052074432373 604.69970703125 0.3795517385005951 0.80806315 1.083333134651184 True -12 20085 16.61956477165222 0.4581291675567627 477.88720703125 0.8791492581367493 594.2845458984375 0.386664479970932 0.8166404 0.9624740481376648 True -13 21630 16.65026545524597 1.4896430969238281 367.14849853515625 0.8186980485916138 591.4515380859375 0.3875814974308014 0.8241183 0.9145528078079224 True -14 23175 16.620524406433105 0.465604305267334 505.4845275878906 0.43244877457618713 587.4271850585938 0.38936570286750793 0.8275186 0.8791500926017761 True -15 24720 16.627837419509888 1.2177250385284424 379.12567138671875 0.5910646319389343 585.8077392578125 0.38926512002944946 0.8335335 0.8344906568527222 True -16 26265 16.63696837425232 0.4525327682495117 487.14996337890625 0.48779934644699097 583.9850463867188 0.3902572989463806 0.8351868 0.8005832433700562 True -17 27810 16.62530255317688 0.455777645111084 344.58880615234375 0.5734134912490845 586.2147216796875 0.3874528408050537 0.8367607 0.7804591655731201 True -18 29355 16.654171466827393 0.4476492404937744 564.1646728515625 0.5356982350349426 586.0140991210938 0.3886924684047699 0.8386138 0.7749046087265015 True -19 30900 16.632741451263428 0.4499497413635254 432.7711486816406 0.5146954655647278 586.8279418945312 0.3879946768283844 0.83826154 0.7745927572250366 False diff --git a/ENCSR627QIA/cherimoya.fold_1.performance.tsv b/ENCSR627QIA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c6e0c039eeac25b8e9b0f8456fcbbe850925a019..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -586.0140991210938 0.4078848361968994 0.3886924684047699 0.15571175515651703 0.8386138081550598 0.8092794418334961 0.7749046087265015 \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_2.evaluate.json b/ENCSR627QIA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a6c567edb7d7d4f399570047e12df9bbd506508d..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187UXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_2.fit.json b/ENCSR627QIA/cherimoya.fold_2.fit.json deleted file mode 100644 index d7eb936956bc367e7ed81279ded29d837cb7ca9c..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF187UXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_2.log b/ENCSR627QIA/cherimoya.fold_2.log deleted file mode 100644 index 38a641c32297bba6891f8da5cc0d0adf8c99d959..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1668 22.900115489959717 4.137027263641357 451.4427795410156 0.9526346921920776 815.2391967773438 0.16587521135807037 0.42323247 14.189598083496094 True -1 3336 18.46796941757202 0.36068272590637207 622.1163330078125 1.5879155397415161 670.2943725585938 0.25472262501716614 0.6403893 9.003425598144531 True -2 5004 18.310691833496094 0.3626594543457031 550.5064697265625 1.3886933326721191 580.1381225585938 0.3017878532409668 0.721 4.594010353088379 True -3 6672 18.329158782958984 0.38332581520080566 667.6416015625 1.2905385494232178 554.2859497070312 0.3111702501773834 0.7402214 2.9990546703338623 True -4 8340 18.319241762161255 0.3495821952819824 350.3006896972656 0.9880538582801819 542.810302734375 0.31757327914237976 0.7460217 2.193002462387085 True -5 10008 18.364662885665894 0.35320568084716797 547.5769653320312 0.9790178537368774 532.3546142578125 0.3247048556804657 0.75603175 1.6113239526748657 True -6 11676 18.31872010231018 0.3551292419433594 374.67315673828125 0.7532225847244263 524.6456298828125 0.328725665807724 0.7691383 1.407993197441101 True -7 13344 18.298816680908203 0.35329103469848633 484.3216552734375 1.040590763092041 519.929931640625 0.3316405117511749 0.77501875 1.2274572849273682 True -8 15012 18.313992977142334 1.1820940971374512 397.6722412109375 0.9643771052360535 514.638671875 0.33518245816230774 0.7850209 1.1089715957641602 True -9 16680 18.326003789901733 0.3434569835662842 369.1492614746094 0.8926545977592468 508.7485656738281 0.3394726812839508 0.79345185 0.9838464260101318 True -10 18348 18.314836025238037 0.34793686866760254 397.68865966796875 0.9368172287940979 505.9923400878906 0.34083086252212524 0.7995133 0.9464817643165588 True -11 20016 18.503612518310547 0.3536348342895508 444.8962097167969 0.8100695610046387 500.41375732421875 0.344670832157135 0.80678874 0.8984196186065674 True -12 21684 18.197025060653687 0.35062313079833984 365.18145751953125 0.6205103993415833 494.90875244140625 0.3498471975326538 0.8139043 0.8150883316993713 True -13 23352 17.96047806739807 0.3487510681152344 499.72979736328125 0.8878971934318542 492.3887023925781 0.35041314363479614 0.81903404 0.7684887051582336 True -14 25020 18.00784206390381 0.3605966567993164 488.7979736328125 0.6410309076309204 487.5552673339844 0.3546338975429535 0.82579976 0.7272876501083374 True -15 26688 18.082540035247803 0.3577730655670166 295.11224365234375 0.5432422161102295 487.4952392578125 0.3541025221347809 0.83045745 0.7083674669265747 True -16 28356 18.02885937690735 0.3523671627044678 310.02569580078125 0.6269928812980652 487.55865478515625 0.3543727397918701 0.83234066 0.6881449818611145 True -17 30024 18.03558087348938 0.37319207191467285 376.6246337890625 0.6189828515052795 486.2802734375 0.3558119535446167 0.833759 0.6802243590354919 True -18 31692 18.095040559768677 0.34898996353149414 363.8045654296875 0.49401164054870605 487.4303894042969 0.3544739782810211 0.8355416 0.6788946390151978 True -19 33360 18.04911184310913 0.3544890880584717 378.6342468261719 0.7177598476409912 489.67138671875 0.3520205318927765 0.83439636 0.6842592358589172 False diff --git a/ENCSR627QIA/cherimoya.fold_2.performance.tsv b/ENCSR627QIA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3afe2a9b4866d3ccaa9b338330cc56163cbdd65f..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -487.4303894042969 0.43588218092918396 0.35447394847869873 0.1313820630311966 0.8355416059494019 0.7902098894119263 0.6788946390151978 \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_3.evaluate.json b/ENCSR627QIA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6e3953d1a2eba8edf001460fb2246933dc731f37..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187UXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_3.fit.json b/ENCSR627QIA/cherimoya.fold_3.fit.json deleted file mode 100644 index fe9753fc3a121a6bd789956f64fdfb0b84e2008d..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF187UXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_3.log b/ENCSR627QIA/cherimoya.fold_3.log deleted file mode 100644 index 27968a9c249283cc03b483a5b51845e39082e16d..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1596 22.0560462474823 3.09828782081604 605.1934814453125 2.0035905838012695 863.4471435546875 0.17779624462127686 0.41652578 15.998346328735352 True -1 3192 17.570634603500366 0.3516409397125244 434.5791015625 1.117862582206726 710.5735473632812 0.27667248249053955 0.62834746 9.883898735046387 True -2 4788 17.57280135154724 0.30011916160583496 635.778076171875 1.0232967138290405 619.3961181640625 0.324303537607193 0.6960534 6.391206741333008 True -3 6384 18.588457345962524 10.231973648071289 386.30682373046875 1.4248385429382324 595.7725219726562 0.3348250389099121 0.710482 3.7876603603363037 True -4 7980 17.54812002182007 0.3427603244781494 559.2689819335938 1.1102986335754395 583.3406982421875 0.33997416496276855 0.72225654 2.67991042137146 True -5 9576 17.84117031097412 15.611372232437134 452.7205505371094 1.0706496238708496 573.5718383789062 0.3474256694316864 0.72751546 2.219031572341919 True -6 11172 17.547220945358276 0.4163064956665039 523.0087890625 1.6716251373291016 568.2727661132812 0.3521677553653717 0.73783004 2.0812814235687256 True -7 12768 17.545815467834473 0.31584668159484863 525.0551147460938 1.0600807666778564 560.4166259765625 0.3576328456401825 0.74551314 1.8411648273468018 True -8 14364 17.562087297439575 0.33232927322387695 412.3173522949219 1.033383846282959 556.24560546875 0.3607535660266876 0.7586552 1.5375490188598633 True -9 15960 17.538591861724854 0.314380407333374 457.8003234863281 0.8405933976173401 548.6876831054688 0.3661523461341858 0.76519287 1.3141473531723022 True -10 17556 17.51225996017456 0.5705752372741699 397.7328186035156 1.3156388998031616 543.4356689453125 0.3694160580635071 0.7723831 1.1789157390594482 True -11 19152 17.607820510864258 0.3196840286254883 332.1714782714844 1.1324386596679688 535.93310546875 0.3741094172000885 0.7841661 1.0394281148910522 True -12 20748 17.558720588684082 0.3301403522491455 405.8103332519531 0.7872925996780396 532.185791015625 0.3763798773288727 0.7900955 0.9774503111839294 True -13 22344 17.56929659843445 0.3173220157623291 453.4615173339844 0.8981233835220337 528.6405029296875 0.37836509943008423 0.8006211 0.9189803004264832 True -14 23940 17.578447818756104 0.31571531295776367 442.80828857421875 0.7946736216545105 524.6892700195312 0.38112685084342957 0.806642 0.8652764558792114 True -15 25536 17.529630184173584 0.3206934928894043 368.2611389160156 0.6298222541809082 523.7647705078125 0.3809182047843933 0.8135977 0.8395261764526367 True -16 27132 17.669008016586304 0.31763458251953125 390.2247009277344 0.5671509504318237 522.3511352539062 0.38150686025619507 0.8163056 0.8167462348937988 True -17 28728 17.556065559387207 0.3172266483306885 451.9384765625 0.5104488730430603 525.7643432617188 0.3774707615375519 0.81846863 0.8108397722244263 True -18 30324 17.51966953277588 0.3175077438354492 321.72637939453125 0.5258638858795166 525.291748046875 0.3788555860519409 0.8196151 0.8109133839607239 True -19 31920 17.509793281555176 0.307999849319458 351.37017822265625 0.3913523256778717 526.0175170898438 0.37847357988357544 0.8188453 0.81289142370224 False diff --git a/ENCSR627QIA/cherimoya.fold_3.performance.tsv b/ENCSR627QIA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 51353ba53ccf921c67ce9c88f2fd08f3679dcfcd..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -525.291748046875 0.41608837246894836 0.3788556158542633 0.1460723578929901 0.8196151256561279 0.7768880128860474 0.8109133839607239 \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_4.evaluate.json b/ENCSR627QIA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f4b7401569a3eafab6a3121315d7066acd5ed128..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187UXD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_4.fit.json b/ENCSR627QIA/cherimoya.fold_4.fit.json deleted file mode 100644 index 5f6e9442c44c3edc0fd7c01389e15e9ea274864a..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF187UXD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627QIA/cherimoya.fold_4.log b/ENCSR627QIA/cherimoya.fold_4.log deleted file mode 100644 index 143e67b0d7d1e818ec384aaa799283ca0f608acb..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1572 21.77616238594055 2.871438980102539 478.4896240234375 1.394804835319519 733.0104370117188 0.16745755076408386 0.42347896 15.6675386428833 True -1 3144 17.26452350616455 0.298933744430542 400.4717102050781 1.3071869611740112 604.7755737304688 0.2584961950778961 0.6249161 9.430940628051758 True -2 4716 17.228386640548706 0.28067946434020996 358.22314453125 1.1777832508087158 546.620849609375 0.2942812144756317 0.6859425 5.094141006469727 True -3 6288 17.231441974639893 0.27478718757629395 454.79791259765625 1.2749509811401367 517.3761596679688 0.30849042534828186 0.70332927 3.4447004795074463 True -4 7860 17.222716569900513 0.6063659191131592 510.4627380371094 0.9359171390533447 505.4799499511719 0.3162837624549866 0.7140597 2.318019151687622 True -5 9432 17.236388444900513 0.2792339324951172 299.6689147949219 0.939429521560669 495.9692687988281 0.32311588525772095 0.7214214 1.6946874856948853 True -6 11004 17.237711191177368 11.047488689422607 334.3795471191406 0.8455628156661987 489.2333679199219 0.32649990916252136 0.73255444 1.4125889539718628 True -7 12576 17.31351590156555 0.2772257328033447 449.33807373046875 1.2830270528793335 485.3394775390625 0.32677358388900757 0.7433817 1.2335535287857056 True -8 14148 16.90514850616455 0.27692365646362305 381.0753479003906 0.9025110006332397 478.63433837890625 0.3342322111129761 0.74543554 1.1187292337417603 True -9 15720 16.904143810272217 1.4595093727111816 467.4139709472656 0.6073347330093384 475.9940185546875 0.3355899453163147 0.7513873 1.0393993854522705 True -10 17292 16.9378662109375 0.276688814163208 380.69769287109375 0.8616806268692017 473.9449462890625 0.33826562762260437 0.7652761 0.9503468871116638 True -11 18864 16.896982669830322 0.2763841152191162 453.5850830078125 1.3398690223693848 470.3971252441406 0.3410341441631317 0.77091503 0.9249807596206665 True -12 20436 16.870968103408813 0.27460646629333496 398.1138916015625 0.7388627529144287 466.7866516113281 0.3434317409992218 0.7831643 0.8738499283790588 True -13 22008 16.89997363090515 0.27985668182373047 336.81475830078125 0.4596511721611023 462.1805725097656 0.3471603989601135 0.7903214 0.8312485218048096 True -14 23580 16.945627689361572 0.2749192714691162 347.48455810546875 0.6082216501235962 459.2514343261719 0.34928417205810547 0.7990461 0.7933091521263123 True -15 25152 16.94587206840515 1.2372581958770752 284.7278747558594 0.6364068388938904 458.26959228515625 0.3494367003440857 0.80552125 0.7590502500534058 True -16 26724 17.038517713546753 0.27951812744140625 495.408203125 0.6523667573928833 457.7167663574219 0.350389689207077 0.8088457 0.7440212965011597 True -17 28296 17.001028299331665 0.2788989543914795 531.8876953125 0.3887394964694977 458.07232666015625 0.34973666071891785 0.8117035 0.7347988486289978 True -18 29868 16.94180679321289 0.27776312828063965 269.26971435546875 0.680972695350647 458.2796630859375 0.34933778643608093 0.8131553 0.7324944734573364 True -19 31440 16.999638557434082 0.27973103523254395 374.5761413574219 0.5861527323722839 457.27752685546875 0.35147860646247864 0.81277055 0.7317962050437927 False diff --git a/ENCSR627QIA/cherimoya.fold_4.performance.tsv b/ENCSR627QIA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8299f9a3c955ca0736dd81f8131200dcdbb919d8..0000000000000000000000000000000000000000 --- a/ENCSR627QIA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -458.2796630859375 0.44016504287719727 0.3493378460407257 0.13040822744369507 0.8131552934646606 0.7568902373313904 0.7324944734573364 \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_0.evaluate.json b/ENCSR627UDJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ee7115fe2fc294517496bca98a5e1e4d2e092226..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539WPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_0.fit.json b/ENCSR627UDJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 8eec20d5bca41a077940b86b8409027931c8c1f4..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF539WPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_0.log b/ENCSR627UDJ/cherimoya.fold_0.log deleted file mode 100644 index fe4f528d3fc348b601b7fba39bef9c85ee0d92be..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2358 30.0542414188385 4.129814624786377 102.23277282714844 0.3320823311805725 151.9720916748047 0.09848206490278244 0.5179524 2.4916861057281494 True -1 4716 26.235329151153564 1.055408239364624 123.49201965332031 0.6180171966552734 144.32968139648438 0.13190560042858124 0.56201977 1.539975881576538 True -2 7074 26.17908811569214 0.5093424320220947 127.38597106933594 0.8688377141952515 141.20828247070312 0.13929735124111176 0.6127236 0.8857107162475586 True -3 9432 26.134538888931274 0.5214483737945557 109.7110595703125 0.5313989520072937 139.43218994140625 0.14356063306331635 0.63164854 0.8581995368003845 True -4 11790 26.117051362991333 0.5100152492523193 123.88160705566406 0.5650665163993835 138.2222900390625 0.14668260514736176 0.62874323 0.8570696115493774 False -5 14148 26.16620635986328 0.5113656520843506 97.28825378417969 0.6013268232345581 136.90220642089844 0.1513817310333252 0.6389571 0.7548322677612305 True -6 16506 26.19335699081421 0.7042787075042725 111.28495025634766 0.44756340980529785 135.9156036376953 0.15508899092674255 0.63313687 0.6741572618484497 False -7 18864 26.185856103897095 0.5212972164154053 131.2953338623047 0.7006721496582031 134.89698791503906 0.15828190743923187 0.64601547 0.6168087720870972 True -8 21222 26.148970365524292 0.5200872421264648 113.0655288696289 0.2666782736778259 134.5701141357422 0.15773944556713104 0.6684858 0.5536346435546875 True -9 23580 26.130457401275635 0.5114700794219971 131.26060485839844 0.495111882686615 133.78237915039062 0.16144372522830963 0.6815823 0.5173459053039551 True -10 25938 26.17535424232483 0.511408805847168 91.68385314941406 0.382268488407135 133.0850372314453 0.1631886065006256 0.69883245 0.4630279839038849 True -11 28296 26.167314291000366 0.9347240924835205 125.21650695800781 0.31230202317237854 132.8045654296875 0.16364458203315735 0.7091282 0.4417538642883301 True -12 30654 26.18684148788452 0.5203096866607666 124.76725769042969 0.5401740074157715 132.17050170898438 0.16617800295352936 0.727912 0.4035629630088806 True -13 33012 26.286179065704346 0.515275239944458 99.94755554199219 0.20308087766170502 131.6132049560547 0.16739436984062195 0.7432465 0.37289687991142273 True -14 35370 26.244006872177124 0.5119771957397461 104.7389907836914 0.21850213408470154 130.93914794921875 0.1695299744606018 0.75601286 0.34075769782066345 True -15 37728 26.24395990371704 0.5104210376739502 118.34585571289062 0.5323648452758789 130.52935791015625 0.16966399550437927 0.76965475 0.31210339069366455 True -16 40086 26.425082445144653 0.5212576389312744 129.33584594726562 0.31471705436706543 130.4215087890625 0.17030605673789978 0.77657187 0.2942224442958832 True -17 42444 26.221654415130615 0.5105690956115723 110.89386749267578 0.30886802077293396 130.16107177734375 0.1726069152355194 0.78121775 0.2870577871799469 True -18 44802 26.217838287353516 1.5525970458984375 123.47856140136719 0.2251240313053131 130.18260192871094 0.1710994392633438 0.78235465 0.2837601602077484 True -19 47160 26.226651430130005 0.5180225372314453 109.38395690917969 0.2065885066986084 130.03558349609375 0.17166903614997864 0.7826914 0.28480294346809387 True diff --git a/ENCSR627UDJ/cherimoya.fold_0.performance.tsv b/ENCSR627UDJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8259fc1b83b1dfec44203c846a61baa1bdfff462..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -130.03558349609375 0.5919691324234009 0.17166903614997864 0.03327690809965134 0.7826914191246033 0.6238722205162048 0.28480294346809387 \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_1.evaluate.json b/ENCSR627UDJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5468b4b48f2decb7b969272fb9fadf7810a8cf42..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539WPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_1.fit.json b/ENCSR627UDJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 83e3a2fa801366f4dd08a81c7bc42ddcc3f52e95..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF539WPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_1.log b/ENCSR627UDJ/cherimoya.fold_1.log deleted file mode 100644 index 4bfa31d0a1dbb604c49be68b7eb32218a098c348..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2372 29.943167209625244 3.5440001487731934 150.23898315429688 0.8029810190200806 216.24588012695312 0.11591816693544388 0.50121987 3.716804027557373 True -1 4744 26.318333625793457 0.6000449657440186 123.91958618164062 0.9741714000701904 200.20504760742188 0.1590825468301773 0.59895283 2.3131375312805176 True -2 7116 26.300549268722534 0.5712347030639648 110.74870300292969 0.4536946713924408 196.5620574951172 0.16444697976112366 0.6167582 1.332269549369812 True -3 9488 26.272116899490356 0.5781230926513672 131.75631713867188 0.5843217372894287 190.4828338623047 0.17429186403751373 0.64535046 1.282991886138916 True -4 11860 26.223413467407227 0.5703411102294922 117.47806549072266 0.539914608001709 187.49710083007812 0.1799786537885666 0.66468096 1.1958794593811035 True -5 14232 26.21598792076111 0.5828166007995605 113.93903350830078 0.5955740213394165 186.36849975585938 0.18220458924770355 0.6678817 1.1991058588027954 True -6 16604 26.211007833480835 0.5762224197387695 109.87812805175781 0.27314865589141846 184.63970947265625 0.1866121143102646 0.6748233 1.0572503805160522 True -7 18976 26.228238821029663 0.575702428817749 123.95407104492188 0.45238858461380005 183.22377014160156 0.18905769288539886 0.6877545 0.9589828848838806 True -8 21348 26.30974531173706 0.5988678932189941 112.15951538085938 0.5765416026115417 182.26406860351562 0.19200016558170319 0.6960949 0.868491530418396 True -9 23720 26.333856344223022 0.5879254341125488 133.45069885253906 0.6094191670417786 181.5767059326172 0.19421856105327606 0.70602643 0.8003042936325073 True -10 26092 26.31485605239868 2.641697645187378 91.07382202148438 0.28444811701774597 180.5951690673828 0.19520211219787598 0.718836 0.7198443412780762 True -11 28464 26.249990224838257 0.591867208480835 108.88211059570312 0.4226847290992737 179.02481079101562 0.19844187796115875 0.7338898 0.6515021324157715 True -12 30836 26.288002014160156 0.5999741554260254 130.79476928710938 0.42921870946884155 178.0887451171875 0.2013835608959198 0.74390537 0.615445613861084 True -13 33208 26.28025507926941 0.8846392631530762 103.58612060546875 0.21417537331581116 176.760498046875 0.2051137387752533 0.7577965 0.589758574962616 True -14 35580 26.33415126800537 0.6658363342285156 91.93331146240234 0.4285479784011841 176.38671875 0.20275112986564636 0.7724477 0.5408316850662231 True -15 37952 26.335230827331543 0.5858962535858154 97.59805297851562 0.203950434923172 175.1903533935547 0.206227108836174 0.78739405 0.49514779448509216 True -16 40324 26.33225965499878 0.5934855937957764 112.23182678222656 0.33087578415870667 174.03086853027344 0.2094765603542328 0.797578 0.46189212799072266 True -17 42696 26.371526956558228 0.592275857925415 100.99102020263672 0.14839884638786316 174.18019104003906 0.2079334706068039 0.8031539 0.4298728108406067 True -18 45068 26.414916038513184 0.591594934463501 102.27021026611328 0.3650003671646118 174.06922912597656 0.20686061680316925 0.8041573 0.42152148485183716 True -19 47440 26.403831720352173 0.5897548198699951 105.02172088623047 0.3464297652244568 173.96072387695312 0.20741049945354462 0.8030641 0.4181695282459259 False diff --git a/ENCSR627UDJ/cherimoya.fold_1.performance.tsv b/ENCSR627UDJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c5c65a67e48e020953c86770bc25aafbdc9b8a5b..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -174.06922912597656 0.5668190121650696 0.20686060190200806 0.04682030901312828 0.8041573166847229 0.7146623134613037 0.42152148485183716 \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_2.evaluate.json b/ENCSR627UDJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 05fd3ebcbd1ccfc83122fe52e0f64f3cdde06f01..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539WPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_2.fit.json b/ENCSR627UDJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 8edade72463b60a2a7bf76df64b09d00c8d55614..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF539WPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_2.log b/ENCSR627UDJ/cherimoya.fold_2.log deleted file mode 100644 index 75d22d125bf41ec17a8a6e449d6941151a3e3b59..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2497 31.393260717391968 3.4013826847076416 132.37271118164062 0.7471367120742798 166.89654541015625 0.10835961252450943 0.51768035 2.6943461894989014 True -1 4994 27.778675079345703 0.46032190322875977 109.04228210449219 0.41966360807418823 156.71788024902344 0.14500457048416138 0.5873736 1.484120488166809 True -2 7491 27.715836763381958 0.45948004722595215 133.3688507080078 0.5514599680900574 152.97735595703125 0.15356285870075226 0.6087483 1.0722402334213257 True -3 9988 27.868319988250732 0.45625734329223633 90.86109924316406 0.354000985622406 151.3434295654297 0.15418125689029694 0.6203725 1.0128103494644165 True -4 12485 27.7165470123291 0.6161141395568848 89.68162536621094 0.4708240032196045 148.95184326171875 0.16064374148845673 0.6341527 0.8224972486495972 True -5 14982 27.7360577583313 0.4525876045227051 119.3773193359375 0.4515399634838104 147.68862915039062 0.1652931272983551 0.6279701 0.794917106628418 False -6 17479 27.67345666885376 0.4539484977722168 152.81866455078125 0.5425882935523987 147.23390197753906 0.16660627722740173 0.62636846 0.7147142291069031 False -7 19976 27.651856660842896 0.4529902935028076 99.77472686767578 0.27258461713790894 146.5570526123047 0.16768090426921844 0.6334236 0.6614241600036621 False -8 22473 27.69113302230835 0.44434475898742676 128.90838623046875 0.4019113779067993 145.84674072265625 0.17114578187465668 0.64261687 0.6177268028259277 True -9 24970 27.675124883651733 0.4534118175506592 104.31546020507812 0.39194226264953613 144.80665588378906 0.17472726106643677 0.6676854 0.5578283071517944 True -10 27467 27.67902159690857 0.4537954330444336 119.96692657470703 0.5141569972038269 144.04827880859375 0.17555801570415497 0.69242966 0.5154539942741394 True -11 29964 27.70367932319641 0.455735445022583 109.89220428466797 0.3736424446105957 143.49781799316406 0.1763034611940384 0.7050093 0.47897323966026306 True -12 32461 27.770177364349365 0.4516007900238037 162.0821990966797 0.8567212820053101 142.29017639160156 0.18088479340076447 0.72465366 0.4411746561527252 True -13 34958 27.74524235725403 0.45392537117004395 104.00709533691406 0.37198126316070557 141.5858154296875 0.1811286211013794 0.744973 0.4063430726528168 True -14 37455 27.722786903381348 0.6077499389648438 118.24638366699219 0.3465515375137329 141.33761596679688 0.17944099009037018 0.75562507 0.38902854919433594 True -15 39952 27.73970913887024 0.4595060348510742 100.35308074951172 0.3980865180492401 140.53607177734375 0.18281367421150208 0.76845074 0.3619711399078369 True -16 42449 27.83523726463318 11.680947065353394 103.86650085449219 0.18423104286193848 140.25279235839844 0.1840461939573288 0.77436745 0.3478798568248749 True -17 44946 27.839720487594604 0.45781922340393066 135.42684936523438 0.2948080003261566 140.26243591308594 0.18394577503204346 0.77716434 0.33890724182128906 True -18 47443 27.859942197799683 0.8360912799835205 113.77478790283203 0.3404886722564697 140.55426025390625 0.18215131759643555 0.77848184 0.33774736523628235 True -19 49940 27.93331217765808 0.463855504989624 92.9290542602539 0.1936667561531067 140.34446716308594 0.18317259848117828 0.7770768 0.33807939291000366 False diff --git a/ENCSR627UDJ/cherimoya.fold_2.performance.tsv b/ENCSR627UDJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bf0c2c2a63dee36193f3a8717eb656a770d270fb..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -140.55426025390625 0.5850359201431274 0.18215131759643555 0.038505762815475464 0.7784818410873413 0.6561957597732544 0.33774736523628235 \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_3.evaluate.json b/ENCSR627UDJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 83cc18dfc32b566260f9e099eff42df40fc84919..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539WPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_3.fit.json b/ENCSR627UDJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 55bec8eb24278ab44f399560fe9c11321d2fa366..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF539WPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_3.log b/ENCSR627UDJ/cherimoya.fold_3.log deleted file mode 100644 index 7813cd1a0dc5d60175a5e1c772818c49b9662b12..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2405 30.420273065567017 3.7326369285583496 94.06935119628906 0.41118061542510986 183.66696166992188 0.10458159446716309 0.5066914 3.27152681350708 True -1 4810 26.69636368751526 0.5385341644287109 123.80471801757812 0.41690513491630554 174.68112182617188 0.14035549759864807 0.44590613 1.7548816204071045 False -2 7215 26.67750835418701 2.0705463886260986 94.73958587646484 0.2841236889362335 171.2384490966797 0.14798016846179962 0.59211534 1.1605584621429443 True -3 9620 26.664482831954956 1.0829229354858398 111.32530212402344 0.49951404333114624 168.11981201171875 0.15454478561878204 0.60684437 1.073923945426941 True -4 12025 26.593849182128906 0.5154266357421875 96.95938110351562 0.34787237644195557 165.23289489746094 0.1584382802248001 0.6302281 0.9719284176826477 True -5 14430 26.624919176101685 0.5183553695678711 109.49249267578125 0.43975111842155457 163.7290496826172 0.16397009789943695 0.6249997 0.9608598351478577 False -6 16835 26.62419843673706 0.5179586410522461 122.08871459960938 0.6013567447662354 162.9646759033203 0.16314834356307983 0.6345751 0.8821403384208679 True -7 19240 26.62783980369568 0.5067894458770752 126.29486083984375 0.4670642018318176 161.77777099609375 0.1675093173980713 0.63318396 0.8497185111045837 False -8 21645 26.71480369567871 0.5211958885192871 127.14207458496094 0.5940190553665161 160.61557006835938 0.17099298536777496 0.64830256 0.8322130441665649 True -9 24050 26.648075580596924 0.5142872333526611 114.2447509765625 0.4073984920978546 159.86062622070312 0.17274345457553864 0.66474324 0.7463322281837463 True -10 26455 26.63187026977539 0.51877760887146 105.96284484863281 0.40050947666168213 158.9271240234375 0.17407076060771942 0.67874694 0.6537122130393982 True -11 28860 26.656827449798584 6.986404895782471 139.38682556152344 0.7731471061706543 157.94845581054688 0.17742624878883362 0.69135374 0.6032642126083374 True -12 31265 26.715524435043335 0.512554407119751 165.4534454345703 0.6213405132293701 157.27378845214844 0.17941905558109283 0.71044564 0.5515563488006592 True -13 33670 26.6540789604187 0.5148153305053711 101.99312591552734 0.5496838092803955 156.34747314453125 0.1819102019071579 0.7281168 0.5145424008369446 True -14 36075 26.698280334472656 0.5141897201538086 132.52725219726562 0.5174837708473206 155.4005889892578 0.1843857765197754 0.7432051 0.48804980516433716 True -15 38480 26.740987062454224 0.5096502304077148 108.35502624511719 0.2601909339427948 154.86941528320312 0.1844530701637268 0.76071143 0.44022709131240845 True -16 40885 26.775475025177002 0.51621413230896 125.70284271240234 0.33361202478408813 154.3794708251953 0.1854015737771988 0.772484 0.4116164743900299 True -17 43290 26.76002264022827 9.521815299987793 97.38423919677734 0.3223809003829956 154.18527221679688 0.18575851619243622 0.7783913 0.39170578122138977 True -18 45695 26.775527715682983 0.5207998752593994 106.81696319580078 0.3022524416446686 153.8562469482422 0.18704187870025635 0.78070945 0.3830720782279968 True -19 48100 26.808260679244995 0.5266420841217041 106.50831604003906 0.2513960599899292 154.1791534423828 0.18541517853736877 0.7809224 0.37963226437568665 True diff --git a/ENCSR627UDJ/cherimoya.fold_3.performance.tsv b/ENCSR627UDJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b4df66da75f5959436e3672eaa77370648df821b..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -154.1791534423828 0.5816988945007324 0.18541516363620758 0.03851761296391487 0.7809224128723145 0.6705123782157898 0.37963226437568665 \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_4.evaluate.json b/ENCSR627UDJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9a9cfed7ff14a2e81673ea128b40f06da48297a0..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539WPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_4.fit.json b/ENCSR627UDJ/cherimoya.fold_4.fit.json deleted file mode 100644 index d9ec521fb77214f2d316a586d0606140e7c3d124..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF539WPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR627UDJ/cherimoya.fold_4.log b/ENCSR627UDJ/cherimoya.fold_4.log deleted file mode 100644 index 6555283634cad69b82a35005d3645520b63dbc0e..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2437 30.813568592071533 3.7568438053131104 102.34603881835938 0.4119173288345337 156.7633819580078 0.09958598762750626 0.48937666 2.346799612045288 True -1 4874 27.132938385009766 0.5156898498535156 101.47999572753906 0.34293586015701294 147.4677734375 0.14175789058208466 0.5748651 1.4418487548828125 True -2 7311 27.12886905670166 0.5089972019195557 115.35470581054688 0.4521135091781616 145.15220642089844 0.14370404183864594 0.5995981 0.8331652879714966 True -3 9748 27.17615056037903 0.5097613334655762 136.50457763671875 0.4979163706302643 143.2752227783203 0.148010715842247 0.61706597 0.8484262228012085 True -4 12185 27.019089698791504 0.5083935260772705 125.02593231201172 0.4056612253189087 142.39059448242188 0.14914143085479736 0.6228149 0.7971927523612976 True -5 14622 27.012537002563477 8.383817434310913 129.8171844482422 0.5357774496078491 140.6993865966797 0.15295648574829102 0.642316 0.6933196187019348 True -6 17059 27.000283241271973 0.5060067176818848 116.41572570800781 0.5809729695320129 139.49029541015625 0.1579338163137436 0.65663975 0.7061688303947449 True -7 19496 26.986442804336548 0.5128309726715088 106.92595672607422 0.3674916625022888 139.3885955810547 0.1571032702922821 0.6565378 0.6944635510444641 False -8 21933 27.12506675720215 0.49951624870300293 93.75228881835938 0.375497043132782 138.27891540527344 0.16130894422531128 0.66845155 0.6128035187721252 True -9 24370 27.04705309867859 0.5131924152374268 136.91604614257812 0.718153178691864 137.590087890625 0.1621924787759781 0.6783711 0.5795720219612122 True -10 26807 27.0694260597229 0.5117571353912354 113.6464614868164 0.3420596718788147 136.65237426757812 0.16439653933048248 0.70172334 0.5114436745643616 True -11 29244 27.055719137191772 8.68331789970398 104.6188735961914 0.4128189980983734 136.10340881347656 0.16638676822185516 0.711871 0.46143364906311035 True -12 31681 27.11427116394043 0.5116264820098877 82.286376953125 0.13794651627540588 135.39791870117188 0.16837655007839203 0.73162574 0.40711894631385803 True -13 34118 27.035439014434814 0.513016939163208 126.93107604980469 0.3713015615940094 134.96316528320312 0.168884739279747 0.7460921 0.3796507716178894 True -14 36555 27.021276473999023 0.4989442825317383 119.96935272216797 0.474323034286499 134.24462890625 0.17200340330600739 0.75656456 0.3521258234977722 True -15 38992 27.1308434009552 0.5104119777679443 89.34811401367188 0.22494381666183472 133.84945678710938 0.17250946164131165 0.76649266 0.33651602268218994 True -16 41429 27.06796646118164 1.2807574272155762 89.88119506835938 0.3412015438079834 133.82252502441406 0.1719842106103897 0.7717825 0.3246835172176361 True -17 43866 27.07766318321228 0.5120134353637695 142.7796630859375 0.3810989260673523 133.5251007080078 0.17303721606731415 0.771886 0.31773847341537476 True -18 46303 27.211597204208374 0.5056407451629639 88.10517883300781 0.22603918612003326 133.68313598632812 0.17119638621807098 0.7729714 0.3155202269554138 True -19 48740 27.071909189224243 0.5102479457855225 102.79411315917969 0.18271195888519287 133.654296875 0.17183637619018555 0.77119654 0.3155093789100647 False diff --git a/ENCSR627UDJ/cherimoya.fold_4.performance.tsv b/ENCSR627UDJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f45021b8fe8dbb52502f58a33974679f6420e9dc..0000000000000000000000000000000000000000 --- a/ENCSR627UDJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -133.68313598632812 0.5915937423706055 0.17119638621807098 0.034269172698259354 0.7729713916778564 0.6236976385116577 0.3155202269554138 \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_0.evaluate.json b/ENCSR628GQE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5b31902a18989451196d87b6f08c1ac78e590761..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF437YYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_0.fit.json b/ENCSR628GQE/cherimoya.fold_0.fit.json deleted file mode 100644 index 4f539d49464727d38c2cc51593d4679f2067b336..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF437YYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_0.log b/ENCSR628GQE/cherimoya.fold_0.log deleted file mode 100644 index fe55e6407acd95c34a2313b0c0128b1289bc1543..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.115774631500244 3.621736764907837 421.3195495605469 0.13720513880252838 539.1354370117188 0.31772124767303467 0.8480298 3.2993109226226807 True -1 5516 30.362380266189575 1.9439120292663574 494.1805419921875 0.21385949850082397 505.24554443359375 0.37620893120765686 0.87525976 0.5724366307258606 True -2 8274 30.283325672149658 24.64622735977173 433.2483825683594 0.16298907995224 497.3419189453125 0.3874734342098236 0.8983028 0.22503562271595 True -3 11032 32.921674489974976 0.5987701416015625 469.2794189453125 0.09698624908924103 494.91583251953125 0.39102521538734436 0.9038174 0.21294791996479034 True -4 13790 30.315741539001465 0.5990769863128662 393.68408203125 0.22847551107406616 493.8901062011719 0.3931910991668701 0.90864795 0.14003680646419525 True -5 16548 30.378060817718506 0.5854156017303467 399.9443359375 0.15656965970993042 492.2198791503906 0.3968517482280731 0.90987355 0.12129943072795868 True -6 19306 30.36728072166443 0.5876834392547607 441.81854248046875 0.13217277824878693 490.9659118652344 0.39795565605163574 0.9153415 0.11025836318731308 True -7 22064 30.32614278793335 0.5844235420227051 410.9625549316406 0.08070989698171616 490.4366455078125 0.3982997238636017 0.91818196 0.10970797389745712 True -8 24822 29.762178897857666 0.5763645172119141 428.652587890625 0.10383646190166473 489.5560302734375 0.39952975511550903 0.9217706 0.10531271249055862 True -9 27580 29.82691788673401 0.6517066955566406 489.01263427734375 0.0855182483792305 488.11712646484375 0.4022931158542633 0.9241774 0.09671101719141006 True -10 30338 29.860033988952637 0.5955774784088135 480.2679748535156 0.1666163206100464 487.1338195800781 0.4040679633617401 0.9278745 0.09076126664876938 True -11 33096 31.117771863937378 33.109615325927734 420.2929382324219 0.11421974003314972 486.43988037109375 0.40542200207710266 0.9298995 0.08801992982625961 True -12 35854 29.945648431777954 0.5942540168762207 431.043701171875 0.07714919000864029 486.3855285644531 0.40453431010246277 0.93073547 0.08684197068214417 True -13 38612 29.871984481811523 0.5979564189910889 411.87994384765625 0.09731930494308472 485.8429870605469 0.40499985218048096 0.9332701 0.08217721432447433 True -14 41370 29.916553258895874 0.5808279514312744 392.8836669921875 0.07056733220815659 485.1727294921875 0.405630886554718 0.9349432 0.07919550687074661 True -15 44128 29.859345197677612 0.5929744243621826 389.2548522949219 0.10193681716918945 484.84381103515625 0.406354695558548 0.9375257 0.0763118714094162 True -16 46886 29.905786752700806 1.5527729988098145 474.9912109375 0.0633014440536499 484.08135986328125 0.40779560804367065 0.9381996 0.07404716312885284 True -17 49644 29.837533712387085 18.454647541046143 470.75604248046875 0.06583932042121887 484.8017578125 0.4062844216823578 0.9393219 0.07287696748971939 True -18 52402 30.380316019058228 0.5847718715667725 388.5032043457031 0.15360501408576965 484.16302490234375 0.4083302319049835 0.9398449 0.07335838675498962 True -19 55160 29.919161319732666 0.5928547382354736 483.1160583496094 0.05039658397436142 484.86553955078125 0.40641364455223083 0.94067895 0.07329516857862473 True diff --git a/ENCSR628GQE/cherimoya.fold_0.performance.tsv b/ENCSR628GQE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6fed1925b5f3c9179a8da4ce7f247b3d5bdd6b2c..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -484.86553955078125 0.389595091342926 0.4064136743545532 0.14577406644821167 0.9406789541244507 0.9274060130119324 0.07329516857862473 \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_1.evaluate.json b/ENCSR628GQE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index cdf185428256047d6cf721f896e1ce0463da56ab..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF437YYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_1.fit.json b/ENCSR628GQE/cherimoya.fold_1.fit.json deleted file mode 100644 index c0f3eafe892d822f8a9e7bbf4f684c2983e534d6..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF437YYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_1.log b/ENCSR628GQE/cherimoya.fold_1.log deleted file mode 100644 index 259cdc2747f0151c3ae8b37a3cd40e5ae0b307a4..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2725 34.77511525154114 4.497720003128052 478.388916015625 0.10679261386394501 605.1080322265625 0.3169449269771576 0.84786433 3.9584672451019287 True -1 5450 29.99207592010498 0.6817595958709717 473.3584899902344 0.1415155827999115 562.4351196289062 0.3865388333797455 0.87825155 0.6281306743621826 True -2 8175 30.358233213424683 0.6719651222229004 412.7568359375 0.16161641478538513 553.3999633789062 0.39736685156822205 0.8999646 0.2236330360174179 True -3 10900 29.996237754821777 0.6786000728607178 431.6148681640625 0.08361517637968063 550.2018432617188 0.4023793935775757 0.8988461 0.1764049381017685 False -4 13625 29.952833890914917 0.6728742122650146 467.6662292480469 0.13053253293037415 548.1963500976562 0.4054730534553528 0.90701145 0.16020849347114563 True -5 16350 29.978477239608765 0.6719300746917725 431.329345703125 0.16295118629932404 547.5869750976562 0.40610116720199585 0.90854156 0.13746976852416992 True -6 19075 29.962536811828613 0.6564085483551025 403.98626708984375 0.19047504663467407 545.6792602539062 0.4090210497379303 0.91089964 0.13416163623332977 True -7 21800 29.997724533081055 0.6718013286590576 472.04302978515625 0.11446940898895264 543.620849609375 0.41272372007369995 0.91606754 0.12201898545026779 True -8 24525 30.00348138809204 0.673832893371582 382.9207458496094 0.09906178712844849 542.9959716796875 0.41309288144111633 0.92041284 0.116114541888237 True -9 27250 30.005906105041504 0.6737806797027588 439.64422607421875 0.12353449314832687 541.3611450195312 0.4156205654144287 0.92172545 0.11223471909761429 True -10 29975 29.996121644973755 0.672152042388916 409.3983459472656 0.1097666472196579 540.4658203125 0.41557613015174866 0.927145 0.10240239650011063 True -11 32700 29.737968683242798 0.6580483913421631 364.10772705078125 0.09239139407873154 539.6282958984375 0.4166688919067383 0.9293003 0.10263922810554504 True -12 35425 29.274271965026855 1.4919180870056152 467.9557189941406 0.07906690239906311 538.3634643554688 0.4184552729129791 0.93236375 0.10120555758476257 True -13 38150 29.699240684509277 31.411606550216675 422.94970703125 0.04958202689886093 536.4779052734375 0.4213007092475891 0.93399394 0.09497080743312836 True -14 40875 29.395323514938354 0.6781566143035889 439.0374755859375 0.11387234926223755 536.3726196289062 0.4210570454597473 0.93650365 0.09034271538257599 True -15 43600 29.313318014144897 0.6710889339447021 431.5946044921875 0.08924181014299393 535.7427368164062 0.4215952157974243 0.9400033 0.08460018783807755 True -16 46325 29.509498357772827 38.95638656616211 437.99383544921875 0.10654640942811966 535.3898315429688 0.42249831557273865 0.94017345 0.08198145031929016 True -17 49050 29.331812381744385 0.6635739803314209 432.1230163574219 0.06485970318317413 535.3889770507812 0.4226677119731903 0.9411614 0.08126848191022873 True -18 51775 29.97644805908203 13.3392915725708 453.02581787109375 0.08837208151817322 535.5768432617188 0.42254289984703064 0.9431486 0.08014386147260666 True -19 54500 29.35888695716858 0.6658360958099365 404.9091491699219 0.060890551656484604 535.9757690429688 0.42187559604644775 0.94287926 0.08072470873594284 False diff --git a/ENCSR628GQE/cherimoya.fold_1.performance.tsv b/ENCSR628GQE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 539b1eeccd9b8fcde9d56030570a83c690b09fd5..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -535.5768432617188 0.3765907883644104 0.42254287004470825 0.16168488562107086 0.9431486129760742 0.9378117918968201 0.08014386147260666 \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_2.evaluate.json b/ENCSR628GQE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0788e964910f2a4c5ee0be72d90ce574942f171c..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF437YYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_2.fit.json b/ENCSR628GQE/cherimoya.fold_2.fit.json deleted file mode 100644 index faf394a884eb391e2a682455067d419dacc1197c..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF437YYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_2.log b/ENCSR628GQE/cherimoya.fold_2.log deleted file mode 100644 index c1e84278cd0fa5bad2c391c545a3e4e2177b8e60..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2880 36.63666343688965 4.295477628707886 476.6360168457031 0.21135160326957703 564.0953979492188 0.3217071294784546 0.85381347 3.5079193115234375 True -1 5760 31.688623189926147 0.5600941181182861 407.5561218261719 0.11894527077674866 530.5236206054688 0.37947767972946167 0.87458545 0.506454348564148 True -2 8640 31.639116764068604 0.5497701168060303 478.22637939453125 0.10086850076913834 521.5562744140625 0.392705500125885 0.89384747 0.2581615447998047 True -3 11520 31.561046361923218 0.5272433757781982 435.9444885253906 0.07997609674930573 519.1505737304688 0.39560753107070923 0.8990099 0.20661300420761108 True -4 14400 31.098806858062744 0.5597102642059326 497.12432861328125 0.12364141643047333 516.97607421875 0.39914047718048096 0.90581524 0.1453891098499298 True -5 17280 31.066516160964966 0.5353522300720215 472.80096435546875 0.07733356952667236 516.3421020507812 0.39967381954193115 0.90888816 0.14134974777698517 True -6 20160 30.984240531921387 0.5309450626373291 433.001220703125 0.14976367354393005 514.8209228515625 0.4026241600513458 0.9105536 0.12938277423381805 True -7 23040 30.948967933654785 0.5286211967468262 429.3656921386719 0.12034902721643448 514.9400634765625 0.4012835919857025 0.9114427 0.1289597898721695 True -8 25920 30.94596529006958 0.5491268634796143 417.5128479003906 0.29627907276153564 513.1591796875 0.4047839641571045 0.91504174 0.12078718096017838 True -9 28800 30.951597452163696 19.89353370666504 428.342529296875 0.0980430319905281 512.1248779296875 0.4061729609966278 0.9174841 0.11452576518058777 True -10 31680 31.758391618728638 0.5490767955780029 438.29620361328125 0.24246519804000854 512.5337524414062 0.4045814275741577 0.9206877 0.11026961356401443 True -11 34560 31.09282350540161 0.5548491477966309 406.34234619140625 0.12401841580867767 510.50079345703125 0.4090522229671478 0.92443424 0.10454582422971725 True -12 37440 31.136390447616577 20.18016767501831 427.9804382324219 0.059912752360105515 510.88897705078125 0.4070371687412262 0.927277 0.09781406074762344 True -13 40320 31.877495050430298 0.5377480983734131 455.92852783203125 0.22737464308738708 509.77691650390625 0.40869367122650146 0.92951924 0.09150096029043198 True -14 43200 31.08626103401184 0.538071870803833 375.6375732421875 0.053116217255592346 508.9546203613281 0.41041818261146545 0.9298549 0.08779176324605942 True -15 46080 30.985788106918335 0.5385644435882568 400.5588073730469 0.15652133524417877 508.54022216796875 0.41092780232429504 0.9334225 0.084940604865551 True -16 48960 31.0763738155365 0.5317542552947998 401.79986572265625 0.07874513417482376 508.2460021972656 0.4111095666885376 0.9328814 0.08342260122299194 False -17 51840 30.965393543243408 0.5325226783752441 441.6993713378906 0.2819157540798187 508.29205322265625 0.4117254912853241 0.9329977 0.08208047598600388 False -18 54720 30.96919894218445 0.5374021530151367 410.5935974121094 0.0855187252163887 508.2865295410156 0.41161590814590454 0.9335536 0.08243595063686371 True -19 57600 30.91599464416504 0.6322710514068604 419.0479736328125 0.10654504597187042 508.76165771484375 0.41061583161354065 0.93318856 0.08195656538009644 False diff --git a/ENCSR628GQE/cherimoya.fold_2.performance.tsv b/ENCSR628GQE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6dbc934e82d7e01ed392b45483cab688b4b8d50f..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -508.2865295410156 0.3848362863063812 0.41161587834358215 0.1534852534532547 0.9335535764694214 0.92754065990448 0.08243595063686371 \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_3.evaluate.json b/ENCSR628GQE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c2c6584a0d5f3effafb4d4c2bd42f43c86eb9583..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF437YYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_3.fit.json b/ENCSR628GQE/cherimoya.fold_3.fit.json deleted file mode 100644 index a72929de4e77b621c237f7c37f2c74a1f3b5b72a..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF437YYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_3.log b/ENCSR628GQE/cherimoya.fold_3.log deleted file mode 100644 index 306bb4ae5fd070c7d822481d38fc12116ec23070..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.928051471710205 3.5333049297332764 381.30499267578125 0.09697285294532776 521.5177612304688 0.3267291784286499 0.83759993 3.888807773590088 True -1 5494 30.234018802642822 10.420645475387573 516.8449096679688 0.15083463490009308 489.6951599121094 0.38242074847221375 0.8642588 0.7182930707931519 True -2 8241 30.32882046699524 0.5446336269378662 412.330078125 0.17767268419265747 483.3964538574219 0.3907964527606964 0.8917302 0.25508299469947815 True -3 10988 30.577925443649292 0.5433626174926758 445.391845703125 0.22083163261413574 480.8212890625 0.3951926827430725 0.89533454 0.16328129172325134 True -4 13735 30.665015697479248 33.62716746330261 389.3699645996094 0.18122947216033936 478.0939636230469 0.3999917209148407 0.9050942 0.13529187440872192 True -5 16482 30.864133596420288 32.31413984298706 498.4693603515625 0.19514498114585876 477.6295471191406 0.4006139039993286 0.9092299 0.13496701419353485 True -6 19229 30.458627462387085 0.5519576072692871 432.92694091796875 0.07745186984539032 476.7491149902344 0.4012124836444855 0.91134876 0.12741731107234955 True -7 21976 30.540459871292114 0.546518087387085 436.90771484375 0.1601516157388687 475.6565856933594 0.4041280150413513 0.9151907 0.12272831052541733 True -8 24723 30.214221954345703 0.553950309753418 452.37823486328125 0.12563540041446686 474.02056884765625 0.40632426738739014 0.91634214 0.11412803828716278 True -9 27470 30.40475082397461 0.5488462448120117 468.8450012207031 0.09208424389362335 473.83770751953125 0.406583696603775 0.91851723 0.10685650259256363 True -10 30217 30.448103666305542 0.5559897422790527 420.7764892578125 0.11196377128362656 474.12030029296875 0.40484386682510376 0.9215096 0.10057473182678223 True -11 32964 30.326817989349365 0.5368788242340088 382.67645263671875 0.11702077090740204 472.641357421875 0.408042848110199 0.92553735 0.09819985926151276 True -12 35711 30.21455955505371 20.723292589187622 442.526123046875 0.08142338693141937 471.630615234375 0.4096381366252899 0.92898667 0.09012757241725922 True -13 38458 30.115448474884033 0.5406994819641113 447.49017333984375 0.08532363176345825 471.1448974609375 0.4107390344142914 0.9307104 0.08621736615896225 True -14 41205 29.583028316497803 0.5462849140167236 492.2612609863281 0.0835660845041275 470.3199462890625 0.4120723307132721 0.93254864 0.08430641889572144 True -15 43952 29.551888704299927 0.5390372276306152 474.23052978515625 0.10449712723493576 470.3077087402344 0.4115397334098816 0.9347481 0.08074384182691574 True -16 46699 29.572028160095215 21.412872076034546 378.6464538574219 0.09334889054298401 470.3009338378906 0.4108150601387024 0.93733037 0.07810354977846146 True -17 49446 30.377553462982178 10.323009729385376 462.5328369140625 0.08319418132305145 469.59808349609375 0.41302990913391113 0.93802345 0.07666336745023727 True -18 52193 29.57704782485962 0.5580651760101318 477.1676330566406 0.05936058610677719 469.92547607421875 0.4117852449417114 0.938345 0.07637714594602585 True -19 54940 29.544342279434204 0.5451533794403076 483.1693115234375 0.05039040371775627 469.77685546875 0.41254881024360657 0.93850756 0.07636605203151703 True diff --git a/ENCSR628GQE/cherimoya.fold_3.performance.tsv b/ENCSR628GQE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 46faeae214e355a53f425e2ce0849171bbe92073..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -469.77685546875 0.38813507556915283 0.41254881024360657 0.1469256728887558 0.9385075569152832 0.9223315119743347 0.07636605203151703 \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_4.evaluate.json b/ENCSR628GQE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3daa2a4f59294a08943cd23d01dc22d0e93cfbef..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF437YYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_4.fit.json b/ENCSR628GQE/cherimoya.fold_4.fit.json deleted file mode 100644 index 1e5e55dbdcf2d29cc22625be2a2a97a8eb8ac1d0..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF437YYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628GQE/cherimoya.fold_4.log b/ENCSR628GQE/cherimoya.fold_4.log deleted file mode 100644 index 968b02b61d34646e5f47ba4058f8cdf069bb9a25..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2791 36.03950619697571 4.011418581008911 377.38153076171875 0.14049285650253296 499.189208984375 0.31696367263793945 0.8551929 2.9588944911956787 True -1 5582 31.11023712158203 0.6508517265319824 503.1331481933594 0.13401369750499725 470.36578369140625 0.3724251091480255 0.88091844 0.5805395841598511 True -2 8373 31.139182329177856 0.622943639755249 437.3380432128906 0.14186879992485046 464.74090576171875 0.38004809617996216 0.898393 0.2033340185880661 True -3 11164 31.171042680740356 0.6303002834320068 387.9560546875 0.13559028506278992 462.2492980957031 0.38362249732017517 0.9051173 0.16475239396095276 True -4 13955 31.179553270339966 0.6255629062652588 364.2366027832031 0.10900124907493591 460.3169860839844 0.38764044642448425 0.9099595 0.10718818753957748 True -5 16746 32.76767539978027 26.22106146812439 463.1509094238281 0.10055661201477051 458.4694519042969 0.3916393220424652 0.9145676 0.09289886057376862 True -6 19537 31.782122135162354 37.799049615859985 462.89129638671875 0.09013448655605316 457.0311279296875 0.39365047216415405 0.9206547 0.08699295669794083 True -7 22328 30.572200059890747 1.1289191246032715 438.81756591796875 0.09073451161384583 457.04583740234375 0.39331600069999695 0.92293835 0.08560498803853989 True -8 25119 30.738176107406616 0.6203250885009766 399.4605407714844 0.12136828899383545 456.6946105957031 0.39298224449157715 0.9246549 0.08314856886863708 True -9 27910 30.508124828338623 0.6329822540283203 438.2490539550781 0.13022220134735107 455.7430725097656 0.39517080783843994 0.926634 0.08046436309814453 True -10 30701 30.528733730316162 0.6139752864837646 397.147216796875 0.14161008596420288 454.7674560546875 0.3967157304286957 0.9274535 0.08013810962438583 True -11 33492 30.49784231185913 0.6132755279541016 430.8973388671875 0.05713164061307907 454.129150390625 0.3980426788330078 0.9305671 0.07796596735715866 True -12 36283 30.476459503173828 0.6125915050506592 403.63983154296875 0.07856445014476776 453.86273193359375 0.39819279313087463 0.93512625 0.0727035254240036 True -13 39074 30.460795879364014 0.6100418567657471 434.11187744140625 0.06580539047718048 452.3873596191406 0.4015234112739563 0.9369808 0.07067345827817917 True -14 41865 30.461178064346313 0.6102941036224365 442.3887939453125 0.10191002488136292 452.5849609375 0.4006170928478241 0.9394068 0.06749462336301804 True -15 44656 30.521081686019897 0.6162540912628174 395.4730529785156 0.09406585246324539 452.3081970214844 0.40061527490615845 0.9406272 0.06502187252044678 True -16 47447 30.49224042892456 0.6176965236663818 449.3287353515625 0.05295910686254501 452.7623596191406 0.3996769189834595 0.9397876 0.063555046916008 False -17 50238 30.47580599784851 0.6152853965759277 421.7234191894531 0.1344340741634369 452.0966796875 0.4011576175689697 0.9432662 0.06228488311171532 True -18 53029 30.62031602859497 0.6180629730224609 435.34405517578125 0.08587253093719482 452.6022033691406 0.4002138376235962 0.9415429 0.06274274736642838 False -19 55820 30.494582414627075 0.6193933486938477 386.3980407714844 0.06967105716466904 452.63897705078125 0.39991503953933716 0.9414753 0.06289830803871155 False diff --git a/ENCSR628GQE/cherimoya.fold_4.performance.tsv b/ENCSR628GQE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7371ed9c7971c0961049b9a653147a3c63771a9d..0000000000000000000000000000000000000000 --- a/ENCSR628GQE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -452.0966796875 0.39712339639663696 0.4011576175689697 0.13955886662006378 0.9432662129402161 0.9280303120613098 0.06228488311171532 \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_0.evaluate.json b/ENCSR628IRM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ba21ba9f3928eb3b8742e026811e05e6623a98b6..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF952BQU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_0.fit.json b/ENCSR628IRM/cherimoya.fold_0.fit.json deleted file mode 100644 index 5f7ec90454caec55049078ca3468e0f90ae507de..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF952BQU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_0.log b/ENCSR628IRM/cherimoya.fold_0.log deleted file mode 100644 index ff29fbba3efe53150f4b614c4fcda685a18577fd..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1653 23.032814502716064 6.022271633148193 1076.948486328125 1.7300728559494019 2642.55810546875 0.20220144093036652 0.5200484 28.019838333129883 True -1 3306 18.216382265090942 0.3794436454772949 1294.5859375 1.1082916259765625 2123.436767578125 0.360848605632782 0.6491582 17.795486450195312 True -2 4959 18.196056127548218 0.31987810134887695 1220.1358642578125 1.2317290306091309 1823.487548828125 0.4257311224937439 0.6614837 9.55783748626709 True -3 6612 18.1403911113739 0.3320279121398926 969.9256591796875 1.5785746574401855 1691.78955078125 0.45989763736724854 0.67106193 5.429691791534424 True -4 8265 18.162222146987915 0.3295598030090332 1437.607666015625 1.063814640045166 1646.4227294921875 0.47149407863616943 0.6779249 3.819976568222046 True -5 9918 17.943497896194458 0.3371584415435791 1364.398193359375 1.4199576377868652 1622.544921875 0.47639405727386475 0.6811245 2.9004929065704346 True -6 11571 17.85004425048828 0.34873294830322266 1208.85400390625 1.1218010187149048 1603.9852294921875 0.47964799404144287 0.6880661 2.342567205429077 True -7 13224 17.834789037704468 7.328892230987549 1330.3743896484375 1.0946438312530518 1571.637939453125 0.4888765513896942 0.6917885 1.9895099401474 True -8 14877 18.278998613357544 0.32205677032470703 1396.90234375 0.9545409083366394 1550.48828125 0.4958942234516144 0.7013802 1.706408143043518 True -9 16530 17.81428623199463 0.30698704719543457 957.8484497070312 1.6298341751098633 1531.101318359375 0.5014654397964478 0.70889854 1.5594873428344727 True -10 18183 17.876106023788452 0.3122720718383789 1487.2498779296875 1.2264511585235596 1512.765380859375 0.5057752728462219 0.7127518 1.2455978393554688 True -11 19836 17.779993534088135 0.31056690216064453 1223.859619140625 0.8868750333786011 1494.2193603515625 0.5117332339286804 0.7167807 1.1809781789779663 True -12 21489 17.810283184051514 0.310150146484375 1338.10498046875 0.9628546237945557 1489.4666748046875 0.5130380988121033 0.7240971 1.1177424192428589 True -13 23142 17.826282501220703 0.30893969535827637 1406.010009765625 1.1302781105041504 1471.077392578125 0.5168265104293823 0.73362726 1.0460623502731323 True -14 24795 17.833008766174316 0.3105947971343994 1029.943359375 1.0178897380828857 1468.8092041015625 0.5168775320053101 0.7403802 1.0184011459350586 True -15 26448 17.915345430374146 0.30961108207702637 1062.667724609375 0.9019381999969482 1456.7132568359375 0.5214016437530518 0.74732244 0.9656899571418762 True -16 28101 17.878552675247192 0.3132176399230957 1547.26318359375 0.869392991065979 1452.369384765625 0.5213372707366943 0.7528605 0.9359882473945618 True -17 29754 18.304105281829834 0.31252121925354004 976.7015380859375 1.011549711227417 1455.896240234375 0.5190768241882324 0.75553316 0.9268739223480225 True -18 31407 17.83087134361267 0.6645393371582031 1009.708740234375 0.5986461639404297 1451.63134765625 0.5205346941947937 0.7557236 0.9253300428390503 True -19 33060 18.099067449569702 10.013113975524902 1000.7310180664062 1.2412747144699097 1456.873779296875 0.517353892326355 0.75610846 0.9258522391319275 True diff --git a/ENCSR628IRM/cherimoya.fold_0.performance.tsv b/ENCSR628IRM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index de81a6a4a2a1206ec45c36ad3ce47da326559a3f..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1456.873779296875 0.2758505642414093 0.517353892326355 0.2834322154521942 0.7561084628105164 0.6905732154846191 0.9258522391319275 \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_1.evaluate.json b/ENCSR628IRM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5ff452990acbd1ead4e7c4c56ef71dfba8a14baf..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF952BQU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_1.fit.json b/ENCSR628IRM/cherimoya.fold_1.fit.json deleted file mode 100644 index cc3bff2c67c6d7819d487fea2c185919cf82005b..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF952BQU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_1.log b/ENCSR628IRM/cherimoya.fold_1.log deleted file mode 100644 index 3f62a2b409c79e8e71acc7e64c1c15988be56165..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1632 22.575148105621338 2.0009968280792236 1302.84814453125 2.5532724857330322 3047.70068359375 0.20909135043621063 0.46378383 28.96343231201172 True -1 3264 18.018649101257324 0.4736175537109375 1212.0888671875 1.6420499086380005 2477.819580078125 0.35937070846557617 0.6203969 13.260354995727539 True -2 4896 17.943208932876587 1.0745680332183838 1575.0242919921875 1.6160824298858643 2094.289794921875 0.4348086714744568 0.67288595 6.241098880767822 True -3 6528 17.931899070739746 0.4358670711517334 1332.2236328125 1.7653862237930298 1969.37158203125 0.45445436239242554 0.6821911 4.0033063888549805 True -4 8160 17.65049958229065 0.429868221282959 1531.864013671875 2.006674289703369 1873.587158203125 0.4702572226524353 0.696711 2.683112144470215 True -5 9792 17.627676963806152 0.4316112995147705 1256.3621826171875 1.2285611629486084 1825.720947265625 0.4794614613056183 0.7089561 2.191729784011841 True -6 11424 17.621029376983643 0.47199034690856934 1360.182861328125 1.7102264165878296 1787.55078125 0.49055004119873047 0.7176617 1.9994370937347412 True -7 13056 17.587667226791382 0.4337270259857178 884.3507080078125 1.0269379615783691 1760.7647705078125 0.49443569779396057 0.726255 1.6568764448165894 True -8 14688 17.617565870285034 0.4566683769226074 1306.60791015625 1.391251564025879 1755.974853515625 0.4955940544605255 0.73341644 1.4582810401916504 True -9 16320 17.552908897399902 0.4436969757080078 1130.27880859375 1.2082102298736572 1733.1993408203125 0.501228928565979 0.7379798 1.230272650718689 True -10 17952 17.60103487968445 0.44859886169433594 1126.5570068359375 1.039440393447876 1721.831787109375 0.504693865776062 0.7418384 1.1663031578063965 True -11 19584 17.588692665100098 0.4316868782043457 1363.452392578125 1.1013193130493164 1705.742919921875 0.5095421671867371 0.7452042 1.0979868173599243 True -12 21216 17.650350332260132 0.45171236991882324 1390.311279296875 1.5082296133041382 1690.590087890625 0.5139703750610352 0.74828464 1.054552435874939 True -13 22848 17.60075616836548 0.4292716979980469 1083.181640625 1.0202265977859497 1678.8443603515625 0.5171447992324829 0.7536988 1.0276633501052856 True -14 24480 17.70802116394043 0.4568297863006592 1158.3564453125 0.9099379777908325 1663.5968017578125 0.5199397802352905 0.7592311 0.9986314177513123 True -15 26112 17.578144073486328 0.47301220893859863 1028.966064453125 0.6945743560791016 1654.1614990234375 0.5209803581237793 0.7643951 0.9693976044654846 True -16 27744 17.565186262130737 0.4581773281097412 1049.757568359375 0.9662914872169495 1646.4088134765625 0.5242583751678467 0.76832235 0.9547654986381531 True -17 29376 17.56363606452942 0.41992712020874023 1039.486083984375 0.599686324596405 1650.0552978515625 0.5214772820472717 0.7711526 0.9528279900550842 True -18 31008 17.60957956314087 0.4479854106903076 1173.55859375 0.486237108707428 1662.9923095703125 0.5166493058204651 0.77121943 0.9560168385505676 True -19 32640 17.563772916793823 0.41872739791870117 1019.86328125 0.6104851365089417 1655.5721435546875 0.5205708146095276 0.7717418 0.9601243138313293 True diff --git a/ENCSR628IRM/cherimoya.fold_1.performance.tsv b/ENCSR628IRM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 35a4788f927378b5a3a42c1430266491aa01e121..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1655.5721435546875 0.2656101584434509 0.5205708146095276 0.3086695671081543 0.7717418074607849 0.727493941783905 0.9601243138313293 \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_2.evaluate.json b/ENCSR628IRM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index fa6e8f7855a5f0ffa1d890c8e6f209818a55abc0..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF952BQU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_2.fit.json b/ENCSR628IRM/cherimoya.fold_2.fit.json deleted file mode 100644 index 3c6844bdec905bc247c59c6739a2e1c8fd13b9c0..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF952BQU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_2.log b/ENCSR628IRM/cherimoya.fold_2.log deleted file mode 100644 index dd7a503c6f81d928bc94ed7d50b38615d6e13293..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1755 23.88467788696289 3.4524924755096436 1699.087158203125 2.410398483276367 2686.65771484375 0.20731119811534882 0.45807478 27.74345588684082 True -1 3510 19.692086219787598 13.423050165176392 1863.762939453125 2.1075620651245117 2021.601806640625 0.39064645767211914 0.61283356 17.198984146118164 True -2 5265 19.37083911895752 0.35318660736083984 1219.33203125 1.5132490396499634 1749.4229736328125 0.4465458393096924 0.6556146 8.070385932922363 True -3 7020 19.271247625350952 0.33179235458374023 1368.96435546875 2.0697638988494873 1679.708984375 0.45984914898872375 0.66588783 4.864169120788574 True -4 8775 19.306921005249023 0.34916043281555176 880.7706298828125 1.523988127708435 1635.12109375 0.4732234477996826 0.6678222 3.926722288131714 True -5 10530 19.38675332069397 0.3388650417327881 1427.2919921875 0.9957934617996216 1615.378173828125 0.4768475294113159 0.67645717 3.4383907318115234 True -6 12285 19.30394148826599 4.27431321144104 1493.4324951171875 1.347635269165039 1592.748291015625 0.4805598556995392 0.6871948 2.3872885704040527 True -7 14040 19.11042594909668 0.33521056175231934 1436.0694580078125 1.0612643957138062 1582.460693359375 0.48305633664131165 0.6994254 2.0513103008270264 True -8 15795 18.94107413291931 0.3306291103363037 1382.29638671875 1.1886703968048096 1563.44921875 0.48752734065055847 0.7031022 1.7678815126419067 True -9 17550 18.9480299949646 0.3346831798553467 1303.5159912109375 1.6905696392059326 1543.703369140625 0.49290549755096436 0.70888627 1.4747816324234009 True -10 19305 18.94519543647766 0.327404260635376 1110.9981689453125 1.4003489017486572 1536.567626953125 0.4950968325138092 0.7133018 1.340067744255066 True -11 21060 18.977601051330566 0.3352186679840088 917.4364013671875 1.5456510782241821 1527.490478515625 0.497707724571228 0.7173457 1.2342451810836792 True -12 22815 18.95608901977539 0.32770705223083496 1318.05712890625 0.8841803073883057 1507.54541015625 0.5017099380493164 0.72721535 1.12794029712677 True -13 24570 18.965070247650146 2.0891385078430176 1071.8634033203125 0.9357461333274841 1485.1949462890625 0.5090718865394592 0.73435104 1.068308711051941 True -14 26325 18.978359699249268 0.33198046684265137 1232.5064697265625 0.9066611528396606 1478.7655029296875 0.5084066987037659 0.74199384 1.0093473196029663 True -15 28080 18.963252544403076 0.320936918258667 984.9887084960938 1.0985749959945679 1467.240966796875 0.5125006437301636 0.74789685 0.9793728590011597 True -16 29835 19.126625299453735 0.34051084518432617 1050.409912109375 0.7148988246917725 1467.9942626953125 0.5113641023635864 0.7498446 0.9569790959358215 True -17 31590 18.958707332611084 0.32549381256103516 1201.051513671875 1.1343533992767334 1467.6580810546875 0.5115802884101868 0.75111794 0.9560772180557251 True -18 33345 18.95324206352234 0.3271212577819824 1098.71142578125 0.5684612989425659 1466.1751708984375 0.5122972726821899 0.74970615 0.96699059009552 False -19 35100 18.977652549743652 0.3295431137084961 1213.84716796875 0.8058800101280212 1467.3812255859375 0.5123584866523743 0.7477305 0.9732520580291748 False diff --git a/ENCSR628IRM/cherimoya.fold_2.performance.tsv b/ENCSR628IRM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b31b62bdeaa0067a85eb4d919f28fd6f714aa4ee..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1467.6580810546875 0.2785647511482239 0.511580228805542 0.28465911746025085 0.7511179447174072 0.6944329738616943 0.9560772180557251 \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_3.evaluate.json b/ENCSR628IRM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f8dd5269db24901c0b18290742f22ef1890b98b2..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF952BQU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_3.fit.json b/ENCSR628IRM/cherimoya.fold_3.fit.json deleted file mode 100644 index abbeec8f90e8b1f1e2da6b1c0f8e7e252fb57a80..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF952BQU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_3.log b/ENCSR628IRM/cherimoya.fold_3.log deleted file mode 100644 index 0c0033d25444dcc2673612e095a6bb95f24928fa..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1684 23.018156051635742 3.2295939922332764 2335.3720703125 1.3123188018798828 2687.890380859375 0.2132757306098938 0.48618236 30.95474624633789 True -1 3368 18.500690698623657 0.43425512313842773 1689.13427734375 1.751887321472168 2174.388427734375 0.3696264624595642 0.6219063 16.24161720275879 True -2 5052 18.515180826187134 0.3441305160522461 1711.57177734375 1.8944772481918335 1888.0863037109375 0.43532267212867737 0.64543253 7.881683349609375 True -3 6736 18.479434967041016 0.34541964530944824 1196.172607421875 1.6241061687469482 1786.7279052734375 0.45676273107528687 0.6593447 5.513761520385742 True -4 8420 18.46824884414673 0.34334778785705566 1294.2120361328125 1.1386091709136963 1750.2926025390625 0.4650411903858185 0.67202574 4.373094081878662 True -5 10104 18.47828960418701 0.3730659484863281 1299.609130859375 1.4690430164337158 1724.4351806640625 0.47491928935050964 0.6723935 3.7585654258728027 True -6 11788 18.504271507263184 0.35565829277038574 956.8846435546875 1.165783166885376 1698.193603515625 0.4819450080394745 0.67401034 2.948363780975342 True -7 13472 18.535156726837158 0.3516197204589844 1480.97265625 1.0278223752975464 1677.0714111328125 0.4870825707912445 0.6809229 2.3692493438720703 True -8 15156 18.522539854049683 0.34903526306152344 1837.302001953125 1.3101320266723633 1661.4013671875 0.4924521744251251 0.6855579 1.9603179693222046 True -9 16840 18.37793231010437 0.351637601852417 1418.7076416015625 0.9299112558364868 1643.6375732421875 0.4993216395378113 0.68491155 1.705151081085205 False -10 18524 18.136412382125854 0.3758127689361572 1284.7696533203125 0.9746588468551636 1627.7613525390625 0.5016829967498779 0.6956234 1.511983036994934 True -11 20208 18.153587341308594 0.5541565418243408 1059.5657958984375 1.1183390617370605 1606.810791015625 0.5073289275169373 0.70535934 1.4403613805770874 True -12 21892 18.15517234802246 0.37685465812683105 1001.174560546875 1.010446310043335 1596.81005859375 0.5103603005409241 0.70974785 1.324073314666748 True -13 23576 18.176438093185425 0.3590240478515625 1195.0797119140625 1.2406518459320068 1592.5411376953125 0.5096229314804077 0.7172045 1.216480016708374 True -14 25260 18.19208812713623 0.3577597141265869 1024.8580322265625 1.0323867797851562 1579.142333984375 0.5131709575653076 0.73026294 1.142913818359375 True -15 26944 18.24064612388611 0.3539128303527832 942.1068115234375 0.9037793874740601 1578.1378173828125 0.5115357637405396 0.7405056 1.0730847120285034 True -16 28628 18.303333282470703 0.3829662799835205 1157.4742431640625 0.6440298557281494 1566.951171875 0.5126199126243591 0.7457367 1.0273690223693848 True -17 30312 18.213183641433716 0.338207483291626 812.8323364257812 0.7679107189178467 1563.3961181640625 0.5145668387413025 0.7491034 1.0104577541351318 True -18 31996 18.181148052215576 0.39553070068359375 1049.04248046875 0.8944863080978394 1566.912353515625 0.5135239958763123 0.7499024 0.9968330264091492 True -19 33680 18.177175045013428 0.35419559478759766 1007.3431396484375 0.7033160924911499 1566.42626953125 0.5144467353820801 0.74800515 0.9984109401702881 False diff --git a/ENCSR628IRM/cherimoya.fold_3.performance.tsv b/ENCSR628IRM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ee89ed6ac7817245b3068e9b24ae8419bcd925bc..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1566.912353515625 0.271333783864975 0.5135239958763123 0.29263806343078613 0.7499024271965027 0.6949976682662964 0.9968330264091492 \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_4.evaluate.json b/ENCSR628IRM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c23a31e8b78842151335752fdb5b987c6143d84e..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF952BQU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_4.fit.json b/ENCSR628IRM/cherimoya.fold_4.fit.json deleted file mode 100644 index 65d1cf0039d903d0aecb762862ef4f4f57f7ce86..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF952BQU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628IRM/cherimoya.fold_4.log b/ENCSR628IRM/cherimoya.fold_4.log deleted file mode 100644 index 27ff856414f3ea51ee966d68e2eb2a1c787fa8d2..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1671 22.872912406921387 3.249908447265625 1630.426513671875 2.1758151054382324 2488.657470703125 0.204426109790802 0.47631714 28.982709884643555 True -1 3342 18.392661094665527 0.40392160415649414 1121.3748779296875 1.0177541971206665 2039.25732421875 0.3646013140678406 0.59465504 14.633848190307617 True -2 5013 18.386165618896484 1.074817180633545 1296.788330078125 1.1669166088104248 1754.5330810546875 0.42694878578186035 0.6243448 6.702914237976074 True -3 6684 18.339073419570923 0.30177950859069824 1051.7298583984375 1.378000259399414 1629.32373046875 0.455115407705307 0.6205064 5.611110687255859 False -4 8355 18.315150022506714 0.2968790531158447 1331.486083984375 1.2854359149932861 1564.882568359375 0.4722127318382263 0.6420589 3.5135388374328613 True -5 10026 18.316639184951782 0.8902854919433594 1445.781005859375 1.7786967754364014 1536.68603515625 0.4796540439128876 0.64924777 2.699019432067871 True -6 11697 18.407955169677734 0.29624390602111816 933.8575439453125 1.0666816234588623 1515.081787109375 0.4862276613712311 0.64993876 2.319579601287842 True -7 13368 18.324066400527954 0.32465600967407227 1393.195556640625 1.7022597789764404 1500.1666259765625 0.4917033910751343 0.6615414 1.98738694190979 True -8 15039 18.337085247039795 0.3091137409210205 1169.093994140625 0.9940590858459473 1487.6339111328125 0.49541816115379333 0.6703259 1.7378602027893066 True -9 16710 18.34086775779724 0.3084523677825928 1185.06201171875 1.4906222820281982 1473.6864013671875 0.5003076195716858 0.67033446 1.6248341798782349 True -10 18381 18.350489854812622 1.276522159576416 1398.0606689453125 1.1492928266525269 1458.4290771484375 0.5052432417869568 0.67908597 1.4217394590377808 True -11 20052 18.197495937347412 0.3167870044708252 1120.97412109375 1.1200578212738037 1443.09228515625 0.5083990097045898 0.6823995 1.2761447429656982 True -12 21723 17.989908695220947 0.3150312900543213 1216.8536376953125 1.0825700759887695 1431.1956787109375 0.5119483470916748 0.6927184 1.148375391960144 True -13 23394 17.98440146446228 0.3012349605560303 1017.62744140625 0.7730247974395752 1421.7132568359375 0.5143613219261169 0.6998109 1.101701259613037 True -14 25065 17.993446111679077 0.2907297611236572 1038.2847900390625 0.7971811890602112 1416.531494140625 0.515038013458252 0.70894796 1.0639439821243286 True -15 26736 18.026062726974487 0.3194141387939453 1187.63037109375 1.1485623121261597 1405.4437255859375 0.5182033777236938 0.7174871 1.0127090215682983 True -16 28407 18.109662294387817 0.29984521865844727 1152.5714111328125 0.7758665680885315 1404.1251220703125 0.5176030993461609 0.72194296 0.9907006025314331 True -17 30078 18.005574464797974 1.036156177520752 1071.4627685546875 0.7077434062957764 1412.8402099609375 0.5126457810401917 0.72660255 0.9837865829467773 True -18 31749 18.01629948616028 0.29825878143310547 750.0440673828125 1.0325018167495728 1415.2115478515625 0.5107795596122742 0.72750497 0.9809809327125549 True -19 33420 17.99048399925232 0.2937750816345215 1117.8607177734375 0.6840267777442932 1415.02587890625 0.5113365054130554 0.7277813 0.9841665029525757 True diff --git a/ENCSR628IRM/cherimoya.fold_4.performance.tsv b/ENCSR628IRM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a8fb25084ac50eb4af783921b67eeb5bd209928a..0000000000000000000000000000000000000000 --- a/ENCSR628IRM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1415.02587890625 0.2770223915576935 0.5113365054130554 0.2840401530265808 0.7277812957763672 0.6588424444198608 0.9841665029525757 \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_0.evaluate.json b/ENCSR628PLS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index fbb1c05d65a43628e3377e50564160c2c85679e9..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653NLM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_0.fit.json b/ENCSR628PLS/cherimoya.fold_0.fit.json deleted file mode 100644 index 9cc132deefb835b69f206a8d68f6a4a5343321cc..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF653NLM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_0.log b/ENCSR628PLS/cherimoya.fold_0.log deleted file mode 100644 index 87fa0fa0e93e3f6ad959ae4a3a0de5b485867a10..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2094 27.95687961578369 3.5643844604492188 297.7500305175781 0.6295133233070374 438.54205322265625 0.44033026695251465 0.44677925 9.884272575378418 True -1 4188 23.308470249176025 9.883297204971313 249.3900146484375 0.8606007695198059 372.185302734375 0.5709104537963867 0.5427609 4.059168815612793 True -2 6282 23.377689361572266 0.43421053886413574 202.12496948242188 0.7090805172920227 357.6604919433594 0.600681483745575 0.5473545 1.2286067008972168 True -3 8376 23.342265129089355 0.48522496223449707 287.89739990234375 0.8259789347648621 352.9125061035156 0.6107463240623474 0.5613577 0.8172516226768494 True -4 10470 23.372758626937866 0.44176149368286133 267.36737060546875 0.6196542978286743 351.0970153808594 0.6151036024093628 0.5847265 0.699049711227417 True -5 12564 23.34499740600586 0.45198512077331543 274.03656005859375 0.8074550628662109 350.6263122558594 0.6164336204528809 0.5956786 0.6724171042442322 True -6 14658 23.342312812805176 0.43981480598449707 265.79119873046875 0.587912917137146 349.558349609375 0.6189067959785461 0.5992569 0.64632248878479 True -7 16752 23.342257738113403 0.921755313873291 304.66668701171875 0.6782773733139038 348.1260986328125 0.622230589389801 0.6024882 0.6032661199569702 True -8 18846 23.07735300064087 0.5953202247619629 267.54876708984375 0.7681480646133423 347.0006408691406 0.6248059868812561 0.6065534 0.6235040426254272 True -9 20940 22.83113121986389 0.4411900043487549 254.96087646484375 0.7712630033493042 345.9413146972656 0.627098798751831 0.61102444 0.5959282517433167 True -10 23034 22.858747005462646 0.42310214042663574 254.12020874023438 0.4892670810222626 344.72064208984375 0.6295113563537598 0.61844605 0.589730978012085 True -11 25128 22.81022024154663 10.986040830612183 249.67819213867188 0.7128664255142212 344.0198974609375 0.6313313841819763 0.6231163 0.5856683254241943 True -12 27222 22.85014319419861 0.4379880428314209 300.63623046875 0.47085338830947876 342.91217041015625 0.6335529088973999 0.62849075 0.5633838772773743 True -13 29316 22.831592559814453 0.43181943893432617 269.52056884765625 0.5731375217437744 342.2298278808594 0.635155439376831 0.6352214 0.5563608407974243 True -14 31410 22.838167190551758 0.43639039993286133 323.50140380859375 0.32511937618255615 341.30950927734375 0.6371538043022156 0.6445497 0.5240699648857117 True -15 33504 22.863130569458008 1.2485027313232422 254.87342834472656 0.2607852518558502 341.0126953125 0.6375950574874878 0.6506385 0.5168545842170715 True -16 35598 22.872702598571777 0.42650651931762695 302.577880859375 0.4548643231391907 340.8024597167969 0.6380574107170105 0.6525914 0.5162907838821411 True -17 37692 22.82621693611145 0.434924840927124 257.3257141113281 0.3284955620765686 340.9609375 0.6376582384109497 0.65240633 0.5153360366821289 False -18 39786 22.874504566192627 0.4385395050048828 241.32177734375 0.2849482595920563 341.08331298828125 0.6369953751564026 0.65038455 0.519734799861908 False -19 41880 22.87226939201355 1.91865873336792 265.79705810546875 0.3229745626449585 341.2519836425781 0.6365751028060913 0.6478862 0.5244693756103516 False diff --git a/ENCSR628PLS/cherimoya.fold_0.performance.tsv b/ENCSR628PLS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e85008f300f871286a55c762cb9949a5973baf4d..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -340.8024597167969 0.29903048276901245 0.6380574107170105 0.22081653773784637 0.6525914072990417 0.6212798357009888 0.5162907838821411 \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_1.evaluate.json b/ENCSR628PLS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 364643281b23cc42650e29b601c7384ac8b3de96..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653NLM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_1.fit.json b/ENCSR628PLS/cherimoya.fold_1.fit.json deleted file mode 100644 index 18c5c7b0eb2b1f0639416ba1f5fa6c0358c45999..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF653NLM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_1.log b/ENCSR628PLS/cherimoya.fold_1.log deleted file mode 100644 index 6b76bc5d3ca6ca750cabca827d5c1e4277194044..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2136 28.358285665512085 3.611530065536499 287.6865539550781 0.8365308046340942 431.75152587890625 0.4446139633655548 0.44917727 7.461675643920898 True -1 4272 23.809923887252808 0.5215623378753662 281.9091796875 0.8777991533279419 374.4575500488281 0.5618525147438049 0.5670184 2.6574718952178955 True -2 6408 23.751042366027832 0.5315210819244385 320.10968017578125 0.8056678771972656 362.20916748046875 0.5896070599555969 0.5875479 0.7962368726730347 True -3 8544 23.33571481704712 0.6800251007080078 303.8497619628906 0.5162309408187866 358.4193115234375 0.5975860357284546 0.6023013 0.6063346862792969 True -4 10680 23.44316077232361 1.1640708446502686 262.3333740234375 0.5781234502792358 356.603759765625 0.6022376418113708 0.61045116 0.5518082976341248 True -5 12816 23.334792137145996 0.5318965911865234 264.5245666503906 0.5614004731178284 355.796630859375 0.6044375896453857 0.6159699 0.51604163646698 True -6 14952 23.29445242881775 0.5043272972106934 297.56494140625 0.44154664874076843 354.8095397949219 0.6071203947067261 0.6203063 0.5132472515106201 True -7 17088 23.29547905921936 0.9247801303863525 310.6033935546875 0.7887623906135559 353.873779296875 0.6093927621841431 0.6200309 0.5050984621047974 False -8 19224 23.328693389892578 0.52339768409729 245.47909545898438 0.37964439392089844 352.6794738769531 0.6118143200874329 0.62848663 0.4911472201347351 True -9 21360 23.2766215801239 0.5005192756652832 314.03302001953125 0.4966379404067993 351.7467956542969 0.6141027808189392 0.63713783 0.47866466641426086 True -10 23496 23.323613166809082 1.600212812423706 247.82748413085938 0.7135607004165649 351.0780944824219 0.6159247159957886 0.64233583 0.4679461717605591 True -11 25632 23.330759048461914 0.5082075595855713 292.1372985839844 0.5218892097473145 350.19091796875 0.6179816722869873 0.64624244 0.4645713269710541 True -12 27768 23.30329990386963 0.49814605712890625 249.8565216064453 0.5065908432006836 349.2768859863281 0.6199774146080017 0.65598464 0.4494272768497467 True -13 29904 23.327735900878906 0.506065845489502 284.05828857421875 0.42000240087509155 348.5794677734375 0.6213744282722473 0.6574592 0.45584821701049805 True -14 32040 23.35346221923828 0.5100512504577637 269.14337158203125 0.43604326248168945 348.08599853515625 0.6224112510681152 0.6634345 0.45278629660606384 True -15 34176 23.30174970626831 0.5010604858398438 304.79931640625 0.27656763792037964 347.51385498046875 0.6234262585639954 0.66783124 0.4501838982105255 True -16 36312 23.327279806137085 0.4962577819824219 242.89849853515625 0.3617814779281616 347.1922607421875 0.6241147518157959 0.6716633 0.4440005421638489 True -17 38448 23.57628607749939 0.503765344619751 273.17352294921875 0.3253352642059326 347.1097106933594 0.6239185929298401 0.67011005 0.44763144850730896 False -18 40584 23.321502923965454 0.503509521484375 294.1181640625 0.3521442711353302 347.3096923828125 0.6235358715057373 0.6678922 0.45911240577697754 False -19 42720 23.3205509185791 0.5085601806640625 239.78900146484375 0.30647605657577515 347.3680419921875 0.6233102679252625 0.66556543 0.4629947543144226 False diff --git a/ENCSR628PLS/cherimoya.fold_1.performance.tsv b/ENCSR628PLS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 293424f961a7cb8ae37a3bfd69cc64d72037c113..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -347.1922607421875 0.3019584119319916 0.6241147518157959 0.22017577290534973 0.6716632843017578 0.6539928913116455 0.4440005421638489 \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_2.evaluate.json b/ENCSR628PLS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d7ec90459c001f6fdef6f886a7e7aa0174cf52df..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653NLM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_2.fit.json b/ENCSR628PLS/cherimoya.fold_2.fit.json deleted file mode 100644 index 1cf5c9436582486e6f72d5354a82fa7493f16944..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF653NLM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_2.log b/ENCSR628PLS/cherimoya.fold_2.log deleted file mode 100644 index 5e830f36b7622b33c08e5975b941b0c9fd718a1f..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2236 29.701185941696167 3.9377927780151367 258.408447265625 0.991671085357666 425.318359375 0.4457935094833374 0.45826685 8.139774322509766 True -1 4472 24.98184108734131 0.43972253799438477 246.17283630371094 0.6912407279014587 366.5226745605469 0.5662176012992859 0.53544456 3.2728750705718994 True -2 6708 24.91866183280945 0.4215667247772217 258.2567443847656 0.9457705616950989 354.2881164550781 0.5928885340690613 0.5496731 1.2580453157424927 True -3 8944 24.8806254863739 0.739539623260498 261.58856201171875 0.5299901962280273 350.2779235839844 0.6000936031341553 0.57781035 0.8514868021011353 True -4 11180 24.897313117980957 17.432781219482422 294.7731628417969 0.552778422832489 348.4428405761719 0.6041086316108704 0.58352506 0.7390034198760986 True -5 13416 25.17824149131775 0.4247281551361084 284.4066162109375 0.5640425682067871 347.1084899902344 0.6073389053344727 0.59370244 0.6718279123306274 True -6 15652 24.979878902435303 0.4221320152282715 285.7620849609375 0.7929413914680481 345.290283203125 0.6112885475158691 0.60082877 0.6023471355438232 True -7 17888 24.924000024795532 0.4153752326965332 289.0323791503906 0.6036074161529541 344.4239501953125 0.6129441857337952 0.6037445 0.6016061902046204 True -8 20124 24.880460739135742 0.9187166690826416 273.7037353515625 0.6991479992866516 343.57220458984375 0.6151596307754517 0.60952914 0.5837897062301636 True -9 22360 25.006482124328613 0.42450833320617676 325.4132080078125 0.528221070766449 342.668212890625 0.6172555088996887 0.6105189 0.5689553618431091 True -10 24596 24.882408142089844 0.4224698543548584 251.74404907226562 0.5426210165023804 341.7738952636719 0.6197214722633362 0.6184264 0.5596660375595093 True -11 26832 24.914541006088257 0.42598438262939453 258.92840576171875 0.5004024505615234 340.6751708984375 0.6223556995391846 0.62554777 0.5422255992889404 True -12 29068 24.85998249053955 0.41473889350891113 230.65777587890625 0.4344080984592438 339.99005126953125 0.6239686012268066 0.63207686 0.5294156670570374 True -13 31304 24.444721937179565 0.41054487228393555 279.14501953125 0.5432298183441162 339.0326843261719 0.6259730458259583 0.6401427 0.5130960941314697 True -14 33540 24.357173681259155 1.2675888538360596 252.83319091796875 0.4376155734062195 338.4028625488281 0.62725430727005 0.64915305 0.49968546628952026 True -15 35776 24.40217900276184 0.4055464267730713 290.43670654296875 0.5703170299530029 337.9833068847656 0.6282137632369995 0.6537172 0.4936193525791168 True -16 38012 24.37163257598877 0.40456366539001465 279.18743896484375 0.3664553165435791 337.7618103027344 0.6285130977630615 0.65762377 0.4870505630970001 True -17 40248 24.380861043930054 0.4135727882385254 282.2893371582031 0.34872952103614807 337.8003845214844 0.6283652782440186 0.6563922 0.49472248554229736 False -18 42484 24.362361192703247 0.4140636920928955 309.7814025878906 0.32177525758743286 337.88079833984375 0.627816379070282 0.65549195 0.49963971972465515 False -19 44720 24.37565016746521 0.41873741149902344 297.90185546875 0.3148142695426941 338.0613708496094 0.6275306344032288 0.655312 0.5005630850791931 False diff --git a/ENCSR628PLS/cherimoya.fold_2.performance.tsv b/ENCSR628PLS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 508e8c52eef6851bdc3214784d87340fa453f99e..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -337.7618103027344 0.303584486246109 0.6285130977630615 0.22128206491470337 0.6576237678527832 0.633205235004425 0.4870505630970001 \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_3.evaluate.json b/ENCSR628PLS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 22242fb47cee4d123fb11d2c9ae1545f40436e79..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653NLM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_3.fit.json b/ENCSR628PLS/cherimoya.fold_3.fit.json deleted file mode 100644 index 65f031d7eb32e0d8d2570cb3657e55c0dbd860f5..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF653NLM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_3.log b/ENCSR628PLS/cherimoya.fold_3.log deleted file mode 100644 index f9256337c3b199fcf7fde2201f07e90fee665caa..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2181 29.233350038528442 3.672823429107666 254.07736206054688 0.6635379791259766 441.3229675292969 0.44692063331604004 0.45617032 8.684357643127441 True -1 4362 24.327943801879883 0.6819922924041748 267.92486572265625 0.680526614189148 376.1319580078125 0.5732595920562744 0.5388521 3.1587576866149902 True -2 6543 24.36708664894104 0.4947793483734131 266.07794189453125 0.763733446598053 363.3123474121094 0.5995491743087769 0.53346944 1.1090002059936523 False -3 8724 24.35423445701599 0.481431245803833 260.3699951171875 0.7123515605926514 358.26409912109375 0.608638346195221 0.5611386 0.8990430235862732 True -4 10905 24.305630922317505 0.5072877407073975 254.08580017089844 0.6076569557189941 356.53863525390625 0.6131383776664734 0.580769 0.7220811247825623 True -5 13086 24.32100510597229 19.23932981491089 289.4826965332031 0.5690956711769104 355.08856201171875 0.6164481043815613 0.5975197 0.6568924784660339 True -6 15267 24.947795152664185 0.5008640289306641 248.9697265625 0.7137680053710938 354.1665344238281 0.6187185645103455 0.59457177 0.6651331782341003 False -7 17448 24.368059635162354 0.4884946346282959 256.1892395019531 0.7970448732376099 353.04095458984375 0.6210582256317139 0.59990925 0.6185836791992188 True -8 19629 24.369812965393066 0.4803183078765869 321.5821533203125 0.49873223900794983 352.20587158203125 0.6230468153953552 0.606683 0.6015726327896118 True -9 21810 24.33120036125183 0.5023455619812012 260.10650634765625 0.4918244481086731 351.4084167480469 0.6246501803398132 0.6134374 0.6142767667770386 True -10 23991 24.33047604560852 0.48004603385925293 241.88137817382812 0.4062691926956177 350.5189208984375 0.6266032457351685 0.6221566 0.5784895420074463 True -11 26172 24.280215740203857 0.4920623302459717 242.09121704101562 0.5037065744400024 349.318115234375 0.6291205286979675 0.6275775 0.5546299815177917 True -12 28353 24.87238621711731 0.49996232986450195 250.50424194335938 0.4246937334537506 348.2976989746094 0.6307424902915955 0.6361033 0.5510697960853577 True -13 30534 24.263265132904053 0.4851570129394531 234.23648071289062 0.3300440311431885 347.44866943359375 0.6327166557312012 0.64551073 0.5390043258666992 True -14 32715 24.300865411758423 0.4793393611907959 244.00381469726562 0.5088311433792114 346.6701965332031 0.6339896321296692 0.6518294 0.5268452763557434 True -15 34896 24.863483905792236 8.876307964324951 218.72373962402344 0.410945862531662 346.1300048828125 0.6347094774246216 0.65865606 0.5167509913444519 True -16 37077 24.37156057357788 1.197988748550415 286.5215759277344 0.3569101393222809 345.8968505859375 0.63499915599823 0.6607093 0.5056630373001099 True -17 39258 24.295246839523315 0.48551511764526367 252.97943115234375 0.3154372274875641 345.9723205566406 0.6346789002418518 0.6610232 0.5014716982841492 True -18 41439 24.304356575012207 0.4765286445617676 240.19805908203125 0.31499895453453064 346.03619384765625 0.634390652179718 0.6598424 0.5071815848350525 False -19 43620 24.305667400360107 0.48965024948120117 269.3672790527344 0.34261029958724976 346.0906677246094 0.6340582370758057 0.6571153 0.5128070712089539 False diff --git a/ENCSR628PLS/cherimoya.fold_3.performance.tsv b/ENCSR628PLS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a3cb6082c679c702798fb024ce401ba50c8e2258..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -345.9723205566406 0.29834866523742676 0.6346789002418518 0.22405913472175598 0.6610231995582581 0.6381810307502747 0.5014716982841492 \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_4.evaluate.json b/ENCSR628PLS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 28e3610e38b11324ccd693301de3048242d5a2fb..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653NLM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_4.fit.json b/ENCSR628PLS/cherimoya.fold_4.fit.json deleted file mode 100644 index 14eb7180eb522ae43ddbb37708082e66ee167976..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF653NLM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628PLS/cherimoya.fold_4.log b/ENCSR628PLS/cherimoya.fold_4.log deleted file mode 100644 index 1cd4188a8b431eb6f81a82b99aff59645c145e02..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2227 29.635340690612793 3.601104259490967 313.1142578125 1.003331184387207 435.0316162109375 0.4470768868923187 0.47065106 7.374389171600342 True -1 4454 24.76894974708557 0.4460256099700928 301.161865234375 0.757836639881134 370.0344543457031 0.5760394930839539 0.54573333 2.6978671550750732 True -2 6681 24.787307024002075 0.4335794448852539 259.0884094238281 0.8239423036575317 358.89642333984375 0.6035757660865784 0.54512405 1.270574688911438 False -3 8908 24.7796311378479 0.48909783363342285 284.91595458984375 0.782730221748352 354.4312438964844 0.6121543049812317 0.55127805 0.9678117632865906 True -4 11135 24.763951778411865 0.43087077140808105 228.18972778320312 0.5778177976608276 352.1556701660156 0.6171888113021851 0.5619201 0.8425500392913818 True -5 13362 24.765426635742188 1.326141119003296 257.7171936035156 0.6609890460968018 350.8727111816406 0.6200351715087891 0.5742972 0.7408061027526855 True -6 15589 24.8311710357666 0.4446256160736084 275.43109130859375 0.6998794078826904 349.6214904785156 0.6230831742286682 0.5862016 0.6970426440238953 True -7 17816 24.85206651687622 0.4426417350769043 239.58062744140625 0.5964483022689819 348.69775390625 0.6252925395965576 0.59579587 0.6376498937606812 True -8 20043 24.78247857093811 0.444530725479126 317.37042236328125 0.665668785572052 347.7486877441406 0.6273916363716125 0.600856 0.6181448698043823 True -9 22270 24.794591188430786 0.43030381202697754 288.3506164550781 0.46900928020477295 346.6431884765625 0.6297265291213989 0.6074696 0.5853405594825745 True -10 24497 24.775253534317017 1.2117199897766113 289.87310791015625 0.6544212102890015 345.58343505859375 0.6321254968643188 0.62128043 0.533831000328064 True -11 26724 24.83424139022827 0.43363213539123535 236.05987548828125 0.5166056156158447 344.6463317871094 0.634289562702179 0.6251757 0.5259103178977966 True -12 28951 24.798973560333252 0.428973913192749 262.5998229980469 0.6349168419837952 343.5569763183594 0.6365307569503784 0.6317746 0.5137420892715454 True -13 31178 24.765499114990234 0.4298882484436035 264.16357421875 0.3331192433834076 342.9483337402344 0.6379774212837219 0.63916653 0.504000186920166 True -14 33405 24.791377782821655 0.43939924240112305 221.97140502929688 0.33129072189331055 342.2712707519531 0.6393882632255554 0.64814126 0.48889634013175964 True -15 35632 24.77190852165222 0.45017576217651367 253.82595825195312 0.4207087457180023 341.8544616699219 0.6400720477104187 0.6533723 0.4896547198295593 True -16 37859 24.874617099761963 0.4420027732849121 291.27972412109375 0.36379194259643555 341.7205505371094 0.6404048204421997 0.6589828 0.484559565782547 True -17 40086 24.90392804145813 0.4381105899810791 244.19168090820312 0.32148802280426025 341.83819580078125 0.6401626467704773 0.65938026 0.48739928007125854 True -18 42313 24.828938484191895 0.46392130851745605 231.065185546875 0.23354202508926392 341.86126708984375 0.639477014541626 0.65565467 0.5010908842086792 False -19 44540 24.88229250907898 1.6546998023986816 227.25770568847656 0.3202383816242218 342.15924072265625 0.639178991317749 0.6540087 0.5061498880386353 False diff --git a/ENCSR628PLS/cherimoya.fold_4.performance.tsv b/ENCSR628PLS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b360a2a90d5905e52d8cec74581fe92c1463b5ca..0000000000000000000000000000000000000000 --- a/ENCSR628PLS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -341.83819580078125 0.29779863357543945 0.6401625871658325 0.22543296217918396 0.6593802571296692 0.6241169571876526 0.48739928007125854 \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_0.evaluate.json b/ENCSR628SXX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e963e9d9c2297f3b871851facfac3bf42d6755ed..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350KPW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_0.fit.json b/ENCSR628SXX/cherimoya.fold_0.fit.json deleted file mode 100644 index ced0e9241bc41c8c978a89106b38f3af4e43cf69..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF350KPW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_0.log b/ENCSR628SXX/cherimoya.fold_0.log deleted file mode 100644 index fdc0b790602820d1e545ffeed994b336ec7537a8..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1678 23.154314279556274 3.5956804752349854 264.9486999511719 0.46511054039001465 348.7741394042969 0.38674741983413696 0.584933 10.212095260620117 True -1 3356 18.51847529411316 0.6018779277801514 252.1373291015625 0.3862858712673187 304.7582092285156 0.4844067692756653 0.6382969 2.4351251125335693 True -2 5034 18.532968997955322 0.3847625255584717 250.73704528808594 0.35178500413894653 286.4097595214844 0.5465422868728638 0.6894934 0.7989141941070557 True -3 6712 18.501351356506348 0.3850891590118408 226.3983154296875 0.3851143717765808 280.67401123046875 0.562061607837677 0.7025636 0.5119348764419556 True -4 8390 18.513408422470093 0.3725261688232422 215.65826416015625 0.326501727104187 278.49713134765625 0.5679784417152405 0.7048462 0.33363252878189087 True -5 10068 18.549004793167114 0.3592817783355713 249.37930297851562 0.3294268548488617 277.22491455078125 0.5717223882675171 0.7073347 0.28958189487457275 True -6 11746 18.575052976608276 0.3594324588775635 234.99215698242188 0.2414594143629074 276.6020812988281 0.5737771987915039 0.7126189 0.2717050313949585 True -7 13424 18.537423849105835 0.6420538425445557 231.81077575683594 0.35282111167907715 276.01312255859375 0.5755080580711365 0.71569425 0.257842093706131 True -8 15102 18.518494844436646 0.3675556182861328 257.74017333984375 0.335207998752594 275.1131591796875 0.5780166387557983 0.72600937 0.24413533508777618 True -9 16780 18.507789850234985 0.37979722023010254 215.0513458251953 0.26256823539733887 274.4109191894531 0.5802187323570251 0.72926617 0.2406340390443802 True -10 18458 18.518392086029053 0.3592512607574463 256.2966613769531 0.18638303875923157 273.7601623535156 0.5819013118743896 0.74332786 0.229256734251976 True -11 20136 18.532015323638916 0.3594064712524414 229.59347534179688 0.24496054649353027 273.17620849609375 0.5837539434432983 0.7508718 0.22555239498615265 True -12 21814 18.508419036865234 0.3599672317504883 220.2493896484375 0.17754939198493958 272.7961120605469 0.5850149989128113 0.7561054 0.22160547971725464 True -13 23492 18.504317045211792 0.673163652420044 213.8576202392578 0.20143313705921173 272.3728332519531 0.5863018035888672 0.7660688 0.21568244695663452 True -14 25170 18.528188943862915 0.3638124465942383 241.20407104492188 0.20543555915355682 272.0224914550781 0.5870340466499329 0.77279156 0.21198664605617523 True -15 26848 18.57685136795044 0.37595272064208984 243.8468017578125 0.19413265585899353 271.810546875 0.5875447988510132 0.7781219 0.20969606935977936 True -16 28526 18.540322303771973 13.086864471435547 220.60337829589844 0.18911784887313843 271.8158264160156 0.5875272750854492 0.7839688 0.20878930389881134 True -17 30204 18.847635746002197 0.3682572841644287 225.1062774658203 0.1603061407804489 271.8758544921875 0.5871544480323792 0.78609896 0.20985615253448486 True -18 31882 18.16618275642395 0.3651883602142334 220.55458068847656 0.1951347291469574 272.0049743652344 0.5866161584854126 0.78602916 0.21247164905071259 False -19 33560 18.216711044311523 0.361255407333374 241.361572265625 0.16554850339889526 272.1103820800781 0.5862264037132263 0.7848265 0.21268817782402039 False diff --git a/ENCSR628SXX/cherimoya.fold_0.performance.tsv b/ENCSR628SXX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 14f54e8b99129b9da1e555624cc44292c1e8fca3..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.8758544921875 0.33787593245506287 0.5871544480323792 0.17479291558265686 0.7860989570617676 0.7487284541130066 0.20985615253448486 \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_1.evaluate.json b/ENCSR628SXX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a942e965145c428eb4ea745588ffd78a8d0d8cd4..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350KPW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_1.fit.json b/ENCSR628SXX/cherimoya.fold_1.fit.json deleted file mode 100644 index 50698bf3c9f278e95fd82edaee6e989fbb875a52..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF350KPW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_1.log b/ENCSR628SXX/cherimoya.fold_1.log deleted file mode 100644 index b997cd23ce9f34f4d6f3f5da5037ff661943bd77..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1664 23.000881910324097 3.6873526573181152 235.1741943359375 0.42192894220352173 356.180908203125 0.39210453629493713 0.56064874 10.728466987609863 True -1 3328 18.358933925628662 0.6419880390167236 236.84457397460938 0.310920774936676 314.1729431152344 0.48277923464775085 0.6245985 2.82895565032959 True -2 4992 18.382371187210083 0.44959139823913574 236.283935546875 0.26175928115844727 295.4895935058594 0.5491364002227783 0.668726 0.8155097365379333 True -3 6656 18.371499061584473 0.43294835090637207 219.76651000976562 0.31145888566970825 289.29583740234375 0.5646921992301941 0.69131476 0.4440762400627136 True -4 8320 18.362804651260376 0.4425501823425293 235.42498779296875 0.26746541261672974 287.1634216308594 0.5706353783607483 0.7003121 0.31096750497817993 True -5 9984 18.398494482040405 14.317656755447388 234.60494995117188 0.28311818838119507 285.80731201171875 0.5745589733123779 0.70755166 0.26912638545036316 True -6 11648 18.35761284828186 0.44486212730407715 236.92547607421875 0.2769985795021057 284.9779052734375 0.5773874521255493 0.7152822 0.2486492544412613 True -7 13312 18.372679948806763 0.45284605026245117 218.26727294921875 0.22122395038604736 284.32196044921875 0.5795660018920898 0.7203795 0.24013562500476837 True -8 14976 18.33651638031006 0.4410979747772217 236.642822265625 0.24001507461071014 283.5820617675781 0.5817415118217468 0.7306951 0.23306824266910553 True -9 16640 18.384045839309692 0.44005537033081055 216.563720703125 0.27537935972213745 282.9676818847656 0.5836085081100464 0.7413572 0.22372151911258698 True -10 18304 18.35324215888977 0.452099084854126 229.28103637695312 0.22833853960037231 282.3031005859375 0.585769772529602 0.7503587 0.2191232144832611 True -11 19968 18.341102361679077 0.4552915096282959 238.38392639160156 0.28962600231170654 281.6269226074219 0.5874670147895813 0.76111186 0.21159546077251434 True -12 21632 18.3391170501709 0.44825243949890137 237.58462524414062 0.12767118215560913 280.9346923828125 0.5893097519874573 0.76806104 0.20540717244148254 True -13 23296 18.334516286849976 0.4477884769439697 214.2013702392578 0.16865020990371704 280.38714599609375 0.5908666849136353 0.77294886 0.2019471526145935 True -14 24960 18.328376531600952 0.44820308685302734 195.25575256347656 0.20838923752307892 280.04229736328125 0.5917515158653259 0.7786622 0.19982179999351501 True -15 26624 18.327106475830078 0.44806647300720215 233.07229614257812 0.20202532410621643 279.8474426269531 0.5923566818237305 0.7835408 0.19789578020572662 True -16 28288 18.33436155319214 0.45464038848876953 226.86688232421875 0.15836262702941895 279.7796325683594 0.5923371315002441 0.78476954 0.1982538104057312 True -17 29952 18.010913610458374 9.133541107177734 251.41836547851562 0.16042982041835785 279.8517761230469 0.5918688774108887 0.7885898 0.19949331879615784 True -18 31616 17.991450786590576 0.44103097915649414 215.23794555664062 0.17192406952381134 279.918212890625 0.5912759304046631 0.78722906 0.20031973719596863 False -19 33280 17.99939799308777 0.4343898296356201 235.82154846191406 0.1661359965801239 280.06109619140625 0.5908860564231873 0.78811777 0.20228439569473267 False diff --git a/ENCSR628SXX/cherimoya.fold_1.performance.tsv b/ENCSR628SXX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d1a3d7ed7eba8398c4ba55c203fd2712e27c49ae..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -279.8517761230469 0.3331068158149719 0.5918688774108887 0.17883507907390594 0.7885897755622864 0.7639755606651306 0.19949331879615784 \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_2.evaluate.json b/ENCSR628SXX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cc47cddd0dc0fa8eb473002620bf7732f3bcc564..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350KPW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_2.fit.json b/ENCSR628SXX/cherimoya.fold_2.fit.json deleted file mode 100644 index 852caefa92ad7fbed178a91358b1dc707d6661dc..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF350KPW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_2.log b/ENCSR628SXX/cherimoya.fold_2.log deleted file mode 100644 index 6179136987e6f98ebdbb55fc01e0ac7457501e28..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1785 23.973215103149414 3.7172327041625977 209.11083984375 0.39733055233955383 350.01190185546875 0.39502862095832825 0.5553253 9.683557510375977 True -1 3570 19.725838899612427 0.703840970993042 212.87606811523438 0.3699488639831543 307.85650634765625 0.490991473197937 0.64130247 2.4883291721343994 True -2 5355 19.695985794067383 0.3899986743927002 214.9322509765625 0.3328865170478821 291.9631042480469 0.5453569889068604 0.68713844 0.7642205357551575 True -3 7140 19.706594944000244 0.3816499710083008 221.71481323242188 0.22785134613513947 285.9256896972656 0.5610175132751465 0.7118281 0.518582820892334 True -4 8925 19.694051265716553 0.38100266456604004 256.30523681640625 0.2663675546646118 283.7557678222656 0.5665181279182434 0.7251428 0.3201214671134949 True -5 10710 19.687780141830444 0.34644150733947754 228.65386962890625 0.250531405210495 282.63763427734375 0.5700705647468567 0.7257451 0.2767692804336548 True -6 12495 19.710524797439575 8.938597917556763 246.45216369628906 0.3080129027366638 281.336669921875 0.5734096169471741 0.73335 0.25927063822746277 True -7 14280 19.746578454971313 0.38333892822265625 228.090576171875 0.22319842875003815 280.6272277832031 0.5756502151489258 0.73503846 0.2525279223918915 True -8 16065 19.69835877418518 0.3674652576446533 224.19313049316406 0.22112709283828735 279.87530517578125 0.5778083205223083 0.74261343 0.24090127646923065 True -9 17850 19.706995725631714 0.38195323944091797 214.21604919433594 0.20298680663108826 279.4364318847656 0.5792607665061951 0.75246066 0.23356105387210846 True -10 19635 19.71743106842041 0.35419154167175293 237.20095825195312 0.27436429262161255 278.9971923828125 0.5804938673973083 0.7562114 0.23028813302516937 True -11 21420 19.679092407226562 0.3634469509124756 218.04348754882812 0.28270986676216125 278.33587646484375 0.5826504826545715 0.76488566 0.22305794060230255 True -12 23205 19.668163537979126 0.35514092445373535 193.81944274902344 0.20082101225852966 277.8233947753906 0.5840086936950684 0.7693341 0.21772664785385132 True -13 24990 19.657447576522827 0.3411595821380615 241.6336212158203 0.19128714501857758 277.4098815917969 0.5850731730461121 0.7764046 0.21171528100967407 True -14 26775 19.691415786743164 0.36510133743286133 245.85491943359375 0.18098433315753937 277.1563720703125 0.5857948064804077 0.78359836 0.20919305086135864 True -15 28560 19.800849437713623 0.3709087371826172 232.48736572265625 0.12623117864131927 276.9067077636719 0.5863661170005798 0.7881512 0.20570775866508484 True -16 30345 19.809125423431396 0.35704612731933594 222.195556640625 0.15837383270263672 276.8485412597656 0.5867053270339966 0.7911392 0.20624388754367828 True -17 32130 19.7801411151886 0.3682708740234375 229.17967224121094 0.1020720973610878 276.90283203125 0.5863679051399231 0.79480994 0.20632293820381165 True -18 33915 19.722049474716187 0.34105944633483887 209.63815307617188 0.1356193572282791 277.0290832519531 0.5859145522117615 0.7940432 0.2087981253862381 False -19 35700 19.687129497528076 0.35355234146118164 228.5881805419922 0.14390848577022552 277.1123046875 0.5856180787086487 0.793089 0.2108764350414276 False diff --git a/ENCSR628SXX/cherimoya.fold_2.performance.tsv b/ENCSR628SXX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 162142d6e5134df478c5abc9430524ec75467eda..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -276.90283203125 0.3365332782268524 0.5863678455352783 0.17609938979148865 0.7948099374771118 0.7664362788200378 0.20632293820381165 \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_3.evaluate.json b/ENCSR628SXX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f1969bfb39e1b6c4ff0573777dbd96cc329283cb..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350KPW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_3.fit.json b/ENCSR628SXX/cherimoya.fold_3.fit.json deleted file mode 100644 index 0be7e332042970342e8fc25482730af57efc0fc5..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF350KPW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_3.log b/ENCSR628SXX/cherimoya.fold_3.log deleted file mode 100644 index b0aa9e7ab20ec1f8454061e1d4e06b2df846564f..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1724 24.44193172454834 3.614243745803833 233.01658630371094 0.47502732276916504 346.6401062011719 0.39215144515037537 0.5623137 10.21638298034668 True -1 3448 19.032910346984863 0.4411163330078125 219.91232299804688 0.2450076937675476 303.38458251953125 0.48630890250205994 0.6357473 2.672973394393921 True -2 5172 19.04899263381958 1.0548255443572998 232.47384643554688 0.28573179244995117 287.4023132324219 0.5447344779968262 0.66881305 0.9749086499214172 True -3 6896 19.101867198944092 0.3735783100128174 236.982666015625 0.28308695554733276 281.2113952636719 0.5602774024009705 0.67105246 0.5370292067527771 True -4 8620 19.032335996627808 0.36754631996154785 270.5640563964844 0.3176841735839844 279.19036865234375 0.5658499002456665 0.67928416 0.3799034357070923 True -5 10344 19.002715587615967 0.3657832145690918 240.04286193847656 0.26225799322128296 277.9239807128906 0.5696988105773926 0.6883126 0.33298203349113464 True -6 12068 19.005814790725708 0.8312020301818848 232.7763671875 0.27677106857299805 277.0059509277344 0.5720216631889343 0.6928174 0.3184282183647156 True -7 13792 18.92230772972107 0.3712191581726074 269.64166259765625 0.3343883156776428 276.31103515625 0.5745628476142883 0.69816047 0.299112468957901 True -8 15516 18.667911767959595 0.3691902160644531 244.2188720703125 0.3609171509742737 275.2362976074219 0.5776370167732239 0.7105712 0.283508837223053 True -9 17240 18.64951777458191 0.3614532947540283 211.15103149414062 0.21422114968299866 274.43524169921875 0.5799219608306885 0.71987253 0.267825186252594 True -10 18964 18.65825057029724 0.35963916778564453 250.31031799316406 0.2284528911113739 273.90789794921875 0.5813937783241272 0.7292577 0.2541838586330414 True -11 20688 18.640733242034912 0.35463929176330566 239.7077178955078 0.1558179259300232 273.25177001953125 0.5833082795143127 0.7354566 0.2492658644914627 True -12 22412 18.64271640777588 0.3589470386505127 208.35943603515625 0.2902933955192566 272.6783142089844 0.5849390625953674 0.74450016 0.23792076110839844 True -13 24136 18.645580768585205 0.36226940155029297 227.72177124023438 0.2548423409461975 272.1058654785156 0.586451530456543 0.7529173 0.23076799511909485 True -14 25860 18.668210983276367 0.3607320785522461 218.78448486328125 0.1849946677684784 271.79156494140625 0.5871749520301819 0.7592614 0.22641266882419586 True -15 27584 18.67396092414856 0.3542776107788086 212.24847412109375 0.17909836769104004 271.51751708984375 0.5878632664680481 0.7672138 0.22410626709461212 True -16 29308 18.660572052001953 0.35288071632385254 225.56968688964844 0.27087438106536865 271.387451171875 0.5879942774772644 0.76841664 0.2229568064212799 True -17 31032 18.71090865135193 0.3585216999053955 219.18783569335938 0.16451039910316467 271.4442138671875 0.5877175331115723 0.770265 0.22526925802230835 True -18 32756 18.696306467056274 7.987921953201294 243.3777313232422 0.1237698569893837 271.5709533691406 0.587104082107544 0.77055275 0.22696465253829956 True -19 34480 18.71419906616211 0.371532678604126 216.57493591308594 0.11965728551149368 271.679443359375 0.5867051482200623 0.76911026 0.22858121991157532 False diff --git a/ENCSR628SXX/cherimoya.fold_3.performance.tsv b/ENCSR628SXX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 77103785a0f3007293a927217103588930feddf2..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.5709533691406 0.33704984188079834 0.587104082107544 0.17278751730918884 0.7705527544021606 0.7337687015533447 0.22696465253829956 \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_4.evaluate.json b/ENCSR628SXX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b2ab4f647d88029ed016661b6f4e91ba4b3ef610..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350KPW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_4.fit.json b/ENCSR628SXX/cherimoya.fold_4.fit.json deleted file mode 100644 index c16a1cc72c0e268675507f91f2ac75adfac29345..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF350KPW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR628SXX/cherimoya.fold_4.log b/ENCSR628SXX/cherimoya.fold_4.log deleted file mode 100644 index ab75538ddc46651f6e25692df77f2062f3af6eb2..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1738 23.799299001693726 3.609912157058716 263.75042724609375 0.5940306186676025 344.4606018066406 0.3886958062648773 0.60205466 9.90385913848877 True -1 3476 19.1948721408844 0.4094200134277344 231.1953887939453 0.3765084147453308 301.2110290527344 0.4901626706123352 0.66451544 2.7322542667388916 True -2 5214 19.23188066482544 0.36440443992614746 227.4064178466797 0.27998507022857666 283.34814453125 0.5513166785240173 0.72060627 0.8144311308860779 True -3 6952 19.217551469802856 1.703449010848999 262.0681457519531 0.3285616636276245 277.9244689941406 0.5644481182098389 0.7357139 0.4616285264492035 True -4 8690 19.231724977493286 0.3646202087402344 241.5477294921875 0.2874014377593994 276.0732116699219 0.5692200660705566 0.7378949 0.27098312973976135 True -5 10428 19.22300100326538 0.36856532096862793 227.69786071777344 0.27172377705574036 274.9753723144531 0.5721878409385681 0.7423734 0.2472902536392212 True -6 12166 19.17683458328247 0.37406015396118164 262.51104736328125 0.28509896993637085 274.0560607910156 0.5751200318336487 0.75190574 0.24524939060211182 True -7 13904 19.228909254074097 0.38977599143981934 214.92593383789062 0.26089560985565186 273.3466796875 0.5774136781692505 0.75232476 0.2337563931941986 True -8 15642 19.361740827560425 16.02919101715088 222.2574462890625 0.29538822174072266 272.7864990234375 0.5789035558700562 0.76078814 0.22393681108951569 True -9 17380 19.489004373550415 0.36567234992980957 234.01522827148438 0.25795772671699524 272.2050476074219 0.5806417465209961 0.76390046 0.22126716375350952 True -10 19118 19.22263193130493 0.48587608337402344 225.5810546875 0.19260995090007782 271.6973571777344 0.5822356939315796 0.7703482 0.21511965990066528 True -11 20856 19.228965997695923 0.3606250286102295 208.9849853515625 0.29479479789733887 271.1551208496094 0.5838794112205505 0.7758188 0.21031567454338074 True -12 22594 19.20584535598755 0.36055994033813477 223.8001708984375 0.2049957811832428 270.6432189941406 0.5853114128112793 0.781311 0.20558983087539673 True -13 24332 19.2211172580719 0.3631138801574707 226.23577880859375 0.20130345225334167 270.2276611328125 0.5866203904151917 0.7872642 0.2016344964504242 True -14 26070 19.22330617904663 0.3509039878845215 229.751220703125 0.20679166913032532 269.92724609375 0.587384819984436 0.7916803 0.2008158564567566 True -15 27808 19.226757526397705 0.35852694511413574 205.00604248046875 0.21372860670089722 269.80517578125 0.5877707004547119 0.7961262 0.19918404519557953 True -16 29546 19.23157000541687 0.35494256019592285 213.7244873046875 0.16824445128440857 269.74041748046875 0.587795078754425 0.7989075 0.19847753643989563 True -17 31284 19.23735761642456 0.35411620140075684 229.98074340820312 0.17486967146396637 269.8279724121094 0.587381899356842 0.8001142 0.19994598627090454 True -18 33022 19.21009850502014 0.35130810737609863 200.96365356445312 0.13213877379894257 269.9502868652344 0.586810290813446 0.80134505 0.20098978281021118 True -19 34760 19.198235750198364 0.3471651077270508 254.1851043701172 0.2294091284275055 270.0708923339844 0.5864527821540833 0.8011154 0.20320172607898712 False diff --git a/ENCSR628SXX/cherimoya.fold_4.performance.tsv b/ENCSR628SXX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0f36ba203913784c220fd0613f6a641ad8433026..0000000000000000000000000000000000000000 --- a/ENCSR628SXX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -269.9502868652344 0.33876746892929077 0.586810290813446 0.1741388440132141 0.8013450503349304 0.7562417387962341 0.20098978281021118 \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_0.evaluate.json b/ENCSR630XDN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0b1f7e1cb9385d6d6f60be0ceeb963ad664b6875..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF998YFX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_0.fit.json b/ENCSR630XDN/cherimoya.fold_0.fit.json deleted file mode 100644 index add39c3ce41dcd1740b9ff8305dcd22c251ea727..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF998YFX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_0.log b/ENCSR630XDN/cherimoya.fold_0.log deleted file mode 100644 index bbc5405b6b516fd650d9112101afb715cb84a3ca..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2795 35.628018617630005 3.8694376945495605 195.71539306640625 0.31749051809310913 331.2719421386719 0.16128720343112946 0.7051731 4.166439056396484 True -1 5590 30.87396740913391 1.3383533954620361 199.14804077148438 0.2629697918891907 305.1950378417969 0.19230075180530548 0.7859932 1.8447141647338867 True -2 8385 30.87799072265625 0.5485706329345703 224.66546630859375 0.24361896514892578 298.9554748535156 0.1962968111038208 0.786911 1.1415834426879883 True -3 11180 30.79963970184326 1.8297603130340576 220.5941925048828 0.31831246614456177 292.5509948730469 0.20202822983264923 0.80336803 0.6544394493103027 True -4 13975 30.79564905166626 0.6426796913146973 338.0103759765625 0.7827539443969727 288.8215637207031 0.20684932172298431 0.81525105 0.5189333558082581 True -5 16770 30.81603217124939 0.5881764888763428 216.28372192382812 0.334261953830719 286.957763671875 0.20801576972007751 0.8203585 0.5215217471122742 True -6 19565 30.81422519683838 0.5720646381378174 172.26504516601562 0.2849351763725281 283.98223876953125 0.2124864012002945 0.8264522 0.45463594794273376 True -7 22360 30.81383514404297 0.5631942749023438 216.29246520996094 0.2563847303390503 283.2697448730469 0.21306145191192627 0.82734597 0.46236908435821533 True -8 25155 30.71846652030945 1.8448522090911865 263.39813232421875 0.3322923481464386 283.02252197265625 0.2121109962463379 0.83094627 0.4446938633918762 True -9 27950 30.795886754989624 0.5657422542572021 228.677001953125 0.3815021812915802 280.8839111328125 0.21727369725704193 0.83598936 0.40029701590538025 True -10 30745 30.7648024559021 0.5775914192199707 202.24847412109375 0.2828202545642853 280.1159362792969 0.21842800080776215 0.83801097 0.3690858781337738 True -11 33540 30.819217443466187 3.2736496925354004 245.83773803710938 0.28977230191230774 278.93060302734375 0.22072140872478485 0.8456844 0.3515690565109253 True -12 36335 30.84890651702881 0.5882000923156738 275.1080322265625 0.2813795804977417 278.59136962890625 0.2211650311946869 0.849022 0.34472450613975525 True -13 39130 30.964335918426514 0.562227725982666 199.6903533935547 0.2688679099082947 276.14495849609375 0.22423097491264343 0.858201 0.30831965804100037 True -14 41925 30.938169717788696 0.5690231323242188 201.59169006347656 0.40215563774108887 276.0197448730469 0.22395475208759308 0.8650083 0.2848707437515259 True -15 44720 31.81403112411499 9.516528129577637 230.07135009765625 0.5146018266677856 275.1527099609375 0.22575466334819794 0.86871624 0.2746393084526062 True -16 47515 30.47364354133606 1.557264804840088 234.5436248779297 0.3085141181945801 273.8518371582031 0.22637955844402313 0.8723158 0.2653743028640747 True -17 50310 30.424525022506714 1.3854701519012451 249.64129638671875 0.20468613505363464 274.5446472167969 0.22511647641658783 0.8713622 0.2635953426361084 False -18 53105 30.518108367919922 1.319227933883667 201.29071044921875 0.25615620613098145 274.39208984375 0.22495248913764954 0.8730786 0.26219987869262695 True -19 55900 30.408296585083008 0.5588183403015137 189.37281799316406 0.1376969963312149 274.92095947265625 0.2240781933069229 0.8735136 0.2624560296535492 True diff --git a/ENCSR630XDN/cherimoya.fold_0.performance.tsv b/ENCSR630XDN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9e526364544500484c67368f8297f5fdeee6b152..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -274.92095947265625 0.5320568680763245 0.22407817840576172 0.06748878210783005 0.8735135793685913 0.8150624632835388 0.2624560296535492 \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_1.evaluate.json b/ENCSR630XDN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9612bb6d7f89616e549a522f659764fbd4d12a81..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF998YFX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_1.fit.json b/ENCSR630XDN/cherimoya.fold_1.fit.json deleted file mode 100644 index 6c5f54f462bc1b0e2567c66f54d4fd35b96b8246..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF998YFX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_1.log b/ENCSR630XDN/cherimoya.fold_1.log deleted file mode 100644 index a41e1faaecd35619bef7e71fba26ccc0840b1c48..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 34.48660969734192 4.781578063964844 184.43540954589844 0.4437176287174225 397.3730163574219 0.1720077097415924 0.70252645 4.322105884552002 True -1 5406 29.837371826171875 2.3630385398864746 237.34959411621094 0.6502310037612915 363.3880920410156 0.21266356110572815 0.7657539 2.064439535140991 True -2 8109 29.914204120635986 0.6989517211914062 205.88714599609375 0.7180619835853577 357.2655334472656 0.2155560702085495 0.7575321 2.0185587406158447 False -3 10812 29.805761098861694 0.7099695205688477 210.47264099121094 0.49211785197257996 347.42950439453125 0.22363930940628052 0.7933288 1.0989947319030762 True -4 13515 29.805624961853027 0.7690057754516602 276.99066162109375 0.543231725692749 342.0791931152344 0.22890520095825195 0.8042676 0.878373920917511 True -5 16218 29.80273127555847 0.7561688423156738 216.1258087158203 0.40641123056411743 338.9156494140625 0.23177434504032135 0.8092701 0.8766708970069885 True -6 18921 29.77523112297058 0.72041916847229 252.12509155273438 0.5338547229766846 336.08087158203125 0.2348271757364273 0.8174948 0.8033507466316223 True -7 21624 29.772756576538086 0.7184560298919678 252.24057006835938 0.5872804522514343 332.73004150390625 0.23885630071163177 0.8273097 0.679076075553894 True -8 24327 29.798330307006836 0.7254698276519775 309.88787841796875 0.6015019416809082 332.0108947753906 0.2370380014181137 0.83482 0.6081486344337463 True -9 27030 29.770118713378906 0.8439943790435791 198.3437042236328 0.3327368199825287 330.10736083984375 0.2400890737771988 0.8388069 0.5865351557731628 True -10 29733 29.753663539886475 2.1195273399353027 251.4445037841797 0.2547968327999115 327.98162841796875 0.2432989627122879 0.8466494 0.5152125358581543 True -11 32436 29.940600872039795 1.1882245540618896 199.65415954589844 0.28919804096221924 325.8829040527344 0.24500033259391785 0.8536314 0.46177828311920166 True -12 35139 29.823436975479126 0.7861363887786865 221.76585388183594 0.403164803981781 324.7134094238281 0.2461107224225998 0.86155397 0.4133453369140625 True -13 37842 30.018585443496704 0.758735179901123 224.4038543701172 0.20769628882408142 323.7205505371094 0.24724218249320984 0.8697345 0.3836437165737152 True -14 40545 29.980116605758667 10.16193151473999 210.5199432373047 0.38009709119796753 322.5650939941406 0.24813960492610931 0.8763673 0.36020103096961975 True -15 43248 29.475351810455322 0.7847559452056885 210.09654235839844 0.23152339458465576 320.982666015625 0.2502727508544922 0.8813515 0.3383008539676666 True -16 45951 29.446779012680054 0.7553074359893799 159.18496704101562 0.2485150545835495 320.1542663574219 0.24974526464939117 0.88198453 0.32503339648246765 True -17 48654 29.34012007713318 0.7672929763793945 252.38265991210938 0.16088411211967468 320.1064147949219 0.2506202757358551 0.8829505 0.31698110699653625 True -18 51357 29.355178833007812 0.7947797775268555 213.61709594726562 0.20577627420425415 320.1507568359375 0.25118744373321533 0.881771 0.3171200156211853 False -19 54060 29.378310680389404 0.7414717674255371 265.739990234375 0.23680642247200012 320.4527893066406 0.2505122423171997 0.88179636 0.317678302526474 False diff --git a/ENCSR630XDN/cherimoya.fold_1.performance.tsv b/ENCSR630XDN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8940ce6b47bb9cb6b8a3e0f5e6605283f85516dd..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -320.1064147949219 0.5127266049385071 0.2506203055381775 0.08228477835655212 0.882950484752655 0.8514007329940796 0.31698110699653625 \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_2.evaluate.json b/ENCSR630XDN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c570d28f31196977c4b4830c12f8547b3d68d34a..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF998YFX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_2.fit.json b/ENCSR630XDN/cherimoya.fold_2.fit.json deleted file mode 100644 index 60374847931261d21d4ce2a93b9d28753adb4846..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF998YFX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_2.log b/ENCSR630XDN/cherimoya.fold_2.log deleted file mode 100644 index 1cf7b97bcf592ada40c38554dfaddcb6bc8793a4..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2910 36.65614676475525 3.847989559173584 268.4493713378906 0.5106695890426636 353.5423583984375 0.16703084111213684 0.68226635 3.7317519187927246 True -1 5820 32.30670499801636 0.717012882232666 275.5146484375 0.7942796349525452 323.5450439453125 0.2042711228132248 0.7456887 1.8233020305633545 True -2 8730 32.0604190826416 0.5780248641967773 265.6837158203125 0.7076084613800049 319.2367858886719 0.20545683801174164 0.74449575 1.2627545595169067 False -3 11640 32.02256751060486 0.5295023918151855 247.36997985839844 0.3336196839809418 314.06024169921875 0.2083570510149002 0.77030164 0.9089721441268921 True -4 14550 32.05973958969116 0.5990612506866455 239.32339477539062 0.3316541612148285 309.245849609375 0.21392464637756348 0.78972423 0.7768806219100952 True -5 17460 32.04863524436951 0.7918918132781982 214.557373046875 0.38150835037231445 305.57086181640625 0.21687152981758118 0.8035403 0.6420484185218811 True -6 20370 32.080750942230225 0.5673482418060303 197.97720336914062 0.25948023796081543 302.9606018066406 0.21857862174510956 0.81081927 0.6299734711647034 True -7 23280 32.019675970077515 0.5770759582519531 251.3859100341797 0.6208232641220093 301.77447509765625 0.21880827844142914 0.81509876 0.5520665049552917 True -8 26190 32.00948977470398 0.8930544853210449 215.30328369140625 0.450843870639801 299.0812683105469 0.22322973608970642 0.8194743 0.5160523056983948 True -9 29100 32.05978345870972 0.54085373878479 273.7493591308594 0.4288499355316162 298.5416564941406 0.22365348041057587 0.8220302 0.4956498146057129 True -10 32010 32.029667377471924 0.5461549758911133 228.81178283691406 0.3147946000099182 296.9049377441406 0.22684712707996368 0.8270228 0.49080002307891846 True -11 34920 32.04061031341553 0.543175458908081 261.49603271484375 0.25741058588027954 294.2205505371094 0.23124095797538757 0.83568496 0.4256868064403534 True -12 37830 32.09144973754883 0.5643248558044434 223.48403930664062 0.5200161933898926 294.1698303222656 0.23016352951526642 0.84234375 0.39520263671875 True -13 40740 32.059938192367554 0.5340948104858398 277.72967529296875 0.4073900878429413 293.1125793457031 0.2314155399799347 0.84908897 0.36552199721336365 True -14 43650 32.098878145217896 9.07842493057251 181.13021850585938 0.39345985651016235 291.6061096191406 0.23329904675483704 0.85659486 0.3294365704059601 True -15 46560 31.725359678268433 0.5737910270690918 182.7598876953125 0.2914184331893921 290.6540832519531 0.23384085297584534 0.8623464 0.3113437294960022 True -16 49470 31.497138500213623 0.5493566989898682 213.89163208007812 0.2011595368385315 290.34130859375 0.23457683622837067 0.8666029 0.2933509945869446 True -17 52380 31.573932647705078 0.5565659999847412 279.6099548339844 0.22947219014167786 289.89471435546875 0.234650120139122 0.8689562 0.28496232628822327 True -18 55290 31.57241702079773 0.5529887676239014 222.8874053955078 0.20978796482086182 290.1648254394531 0.23463831841945648 0.87091714 0.2830164432525635 True -19 58200 31.480547428131104 0.7012686729431152 227.47691345214844 0.20005206763744354 290.09674072265625 0.23495768010616302 0.8699543 0.28453436493873596 False diff --git a/ENCSR630XDN/cherimoya.fold_2.performance.tsv b/ENCSR630XDN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9d52aa287f3c6569f7180d448a5167eebd798952..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -290.1648254394531 0.523763120174408 0.23463833332061768 0.07230474799871445 0.8709171414375305 0.8290762305259705 0.2830164432525635 \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_3.evaluate.json b/ENCSR630XDN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 913692cc91fd11bc295ef1121038eecac3d361b0..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF998YFX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_3.fit.json b/ENCSR630XDN/cherimoya.fold_3.fit.json deleted file mode 100644 index ecdd5473445d9a87735bba07db614646697acf4b..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF998YFX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_3.log b/ENCSR630XDN/cherimoya.fold_3.log deleted file mode 100644 index de0134824cc9f701be9479124ce8d2f586c302bb..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 35.476401567459106 4.255733251571655 240.82806396484375 0.35679662227630615 351.1234130859375 0.17249663174152374 0.6537256 4.495459079742432 True -1 5526 30.480448007583618 0.5399789810180664 224.53839111328125 0.38700148463249207 323.262939453125 0.2080080360174179 0.7282566 1.9255297183990479 True -2 8289 30.475025415420532 0.513981819152832 285.86163330078125 0.40949252247810364 319.1812438964844 0.20876803994178772 0.70838827 1.7186205387115479 False -3 11052 30.487227201461792 0.5112481117248535 247.9342041015625 0.41261711716651917 313.74078369140625 0.21470460295677185 0.7412593 1.1724082231521606 True -4 13815 30.464624166488647 0.5084569454193115 208.2989501953125 0.3848796486854553 309.8040466308594 0.22063274681568146 0.7572142 1.0148053169250488 True -5 16578 30.431992769241333 0.5367567539215088 214.30386352539062 0.38990047574043274 305.04327392578125 0.2245614379644394 0.7818152 0.8856807351112366 True -6 19341 30.386629581451416 0.5095117092132568 229.62649536132812 0.33927708864212036 303.3643493652344 0.22616730630397797 0.78826994 0.8345993757247925 True -7 22104 30.415172815322876 0.5115785598754883 278.7279968261719 0.51014643907547 301.37237548828125 0.22828710079193115 0.7944889 0.7653538584709167 True -8 24867 30.44372868537903 0.532048225402832 261.7187805175781 0.4159485697746277 300.43048095703125 0.22852109372615814 0.7992405 0.7350969910621643 True -9 27630 30.400657176971436 0.5110960006713867 228.492919921875 0.5183688998222351 298.6641540527344 0.2319198101758957 0.80507094 0.6407684683799744 True -10 30393 30.45052695274353 0.5092198848724365 244.7578887939453 0.4511428475379944 297.5462646484375 0.23342019319534302 0.81315047 0.6029818654060364 True -11 33156 30.437953233718872 0.4995265007019043 273.2445068359375 0.5234360694885254 296.6930847167969 0.2341069132089615 0.81987953 0.5294069647789001 True -12 35919 30.42834496498108 0.4995872974395752 222.21621704101562 0.384310245513916 295.2501220703125 0.23676647245883942 0.8259313 0.508236825466156 True -13 38682 30.43211269378662 0.5053746700286865 300.7552795410156 0.45670872926712036 293.8614196777344 0.2383420467376709 0.8339316 0.45869749784469604 True -14 41445 29.990585565567017 0.49686670303344727 211.2156219482422 0.22027936577796936 293.1033020019531 0.23908132314682007 0.84325397 0.4167248010635376 True -15 44208 29.893447875976562 0.49790000915527344 218.09625244140625 0.40918147563934326 291.5404357910156 0.240385964512825 0.85126776 0.37740954756736755 True -16 46971 29.905215740203857 0.5075581073760986 206.77822875976562 0.2359098494052887 290.644287109375 0.24087053537368774 0.8566396 0.34933871030807495 True -17 49734 29.963271856307983 0.50673508644104 221.37904357910156 0.33478787541389465 290.9841003417969 0.24008427560329437 0.8584143 0.33668479323387146 True -18 52497 29.86095643043518 0.5080382823944092 278.63555908203125 0.24064771831035614 290.302734375 0.24198126792907715 0.8573614 0.3324272632598877 False -19 55260 29.898855924606323 0.5045080184936523 161.55323791503906 0.18210065364837646 291.5213317871094 0.23828347027301788 0.85837346 0.33266007900238037 False diff --git a/ENCSR630XDN/cherimoya.fold_3.performance.tsv b/ENCSR630XDN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2e84ddf46259da12b7af11b53950ea24a33b5659..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -290.9841003417969 0.5212960243225098 0.24008429050445557 0.07007167488336563 0.8584142923355103 0.8112161755561829 0.33668479323387146 \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_4.evaluate.json b/ENCSR630XDN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8edbaf70990e0634ebf887217b30a21770bba63a..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF998YFX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_4.fit.json b/ENCSR630XDN/cherimoya.fold_4.fit.json deleted file mode 100644 index f209ae98a3c56f8e24d57d2b3d036064fdc33f55..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF998YFX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR630XDN/cherimoya.fold_4.log b/ENCSR630XDN/cherimoya.fold_4.log deleted file mode 100644 index b0704dd97e3a6c56bae94f4ec3818a677462ce33..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 35.016459226608276 4.805781364440918 199.9792938232422 0.531580924987793 283.17315673828125 0.15587441623210907 0.6798229 3.9517154693603516 True -1 5472 30.22373676300049 1.7802529335021973 270.5820007324219 0.4802095592021942 262.82904052734375 0.1863500475883484 0.7418793 1.2501366138458252 True -2 8208 30.21678352355957 0.6939270496368408 249.7127227783203 0.6299828290939331 261.5132141113281 0.18479789793491364 0.7367235 0.8275584578514099 False -3 10944 30.1064612865448 0.6564347743988037 227.42588806152344 0.29109832644462585 256.5975341796875 0.18833820521831512 0.7758419 0.6083590984344482 True -4 13680 30.13526225090027 0.6775810718536377 267.698974609375 0.512191653251648 252.65087890625 0.19304250180721283 0.79185706 0.5380997061729431 True -5 16416 30.0858051776886 0.729196310043335 208.52166748046875 0.46485739946365356 249.79971313476562 0.19692720472812653 0.80417836 0.48053455352783203 True -6 19152 30.0892333984375 0.771066427230835 262.1297912597656 0.41109922528266907 249.1573944091797 0.19924229383468628 0.80588347 0.4845212697982788 True -7 21888 30.13129448890686 0.6398704051971436 222.7707977294922 0.46504783630371094 248.1890411376953 0.20047685503959656 0.8123709 0.48949265480041504 True -8 24624 30.08905601501465 0.639042854309082 297.9950866699219 0.368533194065094 247.19871520996094 0.19998110830783844 0.8215286 0.40632206201553345 True -9 27360 30.187284231185913 0.6374328136444092 298.55419921875 0.40452271699905396 245.77377319335938 0.20349471271038055 0.82506776 0.3734143376350403 True -10 30096 30.22501254081726 0.6355550289154053 239.38259887695312 0.22323650121688843 244.89553833007812 0.2050561010837555 0.8314787 0.35875236988067627 True -11 32832 30.218379735946655 0.6376128196716309 233.1979217529297 0.3593633770942688 244.17373657226562 0.20683355629444122 0.8321297 0.3300955295562744 True -12 35568 30.244041442871094 0.6253833770751953 260.62103271484375 0.29848766326904297 244.1699676513672 0.2065275013446808 0.8391022 0.30375778675079346 True -13 38304 30.265798568725586 1.481062412261963 161.29095458984375 0.25394850969314575 243.6231231689453 0.20683233439922333 0.8452611 0.2850989103317261 True -14 41040 29.767603874206543 0.6443886756896973 221.52565002441406 0.39189770817756653 243.0744171142578 0.2073454111814499 0.85308594 0.26067715883255005 True -15 43776 29.73536729812622 0.6451828479766846 196.08355712890625 0.25311151146888733 242.27639770507812 0.20849978923797607 0.85454905 0.253277063369751 True -16 46512 29.767643451690674 0.6356046199798584 189.02920532226562 0.29395657777786255 241.7175750732422 0.20924785733222961 0.8603206 0.24030113220214844 True -17 49248 29.753015279769897 0.6169288158416748 186.39852905273438 0.22561661899089813 241.5673065185547 0.20931924879550934 0.8620375 0.23471993207931519 True -18 51984 29.706682920455933 0.6376702785491943 207.30335998535156 0.2754061818122864 241.83421325683594 0.20818601548671722 0.8630911 0.23380132019519806 True -19 54720 29.80136251449585 1.0490055084228516 260.5419921875 0.14263208210468292 242.19618225097656 0.20734632015228271 0.8641136 0.2328127920627594 True diff --git a/ENCSR630XDN/cherimoya.fold_4.performance.tsv b/ENCSR630XDN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c883206fcbd3271e1cced5fa1b2ebd7876f5b5af..0000000000000000000000000000000000000000 --- a/ENCSR630XDN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -242.19618225097656 0.5454163551330566 0.2073463350534439 0.06313444674015045 0.8641136288642883 0.7957341074943542 0.2328127920627594 \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_0.evaluate.json b/ENCSR634WYX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 46e65f1461bc30604ea89157437ff937ec909115..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF803SMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_0.fit.json b/ENCSR634WYX/cherimoya.fold_0.fit.json deleted file mode 100644 index af7325b84723ac568f25d23f9b7a300dd6e6fdab..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF803SMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_0.log b/ENCSR634WYX/cherimoya.fold_0.log deleted file mode 100644 index 1f4c485290ee5337d5c210d000d000260453f541..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3260 40.42151689529419 3.5419459342956543 693.0578002929688 1.351076364517212 1016.2731323242188 0.6920885443687439 0.70846426 9.23070240020752 True -1 6520 35.947877168655396 8.817990779876709 529.57470703125 1.349104404449463 845.5226440429688 0.7599904537200928 0.73523897 2.136240005493164 True -2 9780 35.97200846672058 1.054938793182373 701.080322265625 1.060258150100708 819.689453125 0.7711648344993591 0.73502827 1.1892532110214233 False -3 13040 35.936813831329346 0.6970999240875244 550.4962768554688 1.184928297996521 805.26708984375 0.7794211506843567 0.7462924 0.996398389339447 True -4 16300 35.485047578811646 0.6677262783050537 675.3388671875 1.3397185802459717 796.6626586914062 0.7842206358909607 0.74685663 0.8596462607383728 True -5 19560 35.289005756378174 0.6964120864868164 504.415771484375 1.074735403060913 792.5828857421875 0.7865442633628845 0.7522176 0.7996235489845276 True -6 22820 35.18907809257507 1.5636405944824219 600.957275390625 0.9963176250457764 786.14111328125 0.789979100227356 0.75316566 0.7674462199211121 True -7 26080 35.266684770584106 0.7611870765686035 637.8654174804688 1.16848623752594 781.7605590820312 0.7924073934555054 0.7583011 0.7481806874275208 True -8 29340 35.169676303863525 0.6803014278411865 695.7274169921875 0.9557907581329346 776.8798828125 0.7950555086135864 0.7564624 0.7790193557739258 False -9 32600 35.288262367248535 0.6698622703552246 461.01544189453125 0.9431384801864624 767.5609130859375 0.7987819314002991 0.7658056 0.7546338438987732 True -10 35860 37.12906217575073 0.6730916500091553 643.6466064453125 1.0792056322097778 762.9498291015625 0.8015247583389282 0.7690873 0.7344384789466858 True -11 39120 36.248331785202026 22.38113021850586 738.4888305664062 0.8844259977340698 757.4305419921875 0.8038296699523926 0.77432543 0.7094099521636963 True -12 42380 35.20467400550842 0.6855745315551758 554.05615234375 0.8365485668182373 751.8089599609375 0.8066899180412292 0.7827383 0.6744958162307739 True -13 45640 35.21862745285034 0.6763951778411865 592.248046875 0.6332674026489258 746.473876953125 0.809087336063385 0.7906942 0.6527035236358643 True -14 48900 35.250497579574585 0.6833083629608154 538.585205078125 1.2602189779281616 741.81103515625 0.810942530632019 0.79770595 0.6282827258110046 True -15 52160 35.17117428779602 0.6633062362670898 526.596923828125 0.6809677481651306 739.3589477539062 0.8123242259025574 0.8049323 0.6266235709190369 True -16 55420 35.19858646392822 0.6797668933868408 511.14501953125 0.5633012056350708 737.8220825195312 0.8130520582199097 0.8083886 0.6213682889938354 True -17 58680 35.18685603141785 0.6659116744995117 563.3203125 0.5891808271408081 738.8051147460938 0.8132175207138062 0.8102605 0.6254234910011292 True -18 61940 35.21057057380676 0.6583113670349121 466.6499938964844 0.7206106185913086 739.2799682617188 0.8129419088363647 0.80895 0.626923143863678 False -19 65200 35.14503312110901 0.6721663475036621 542.1531982421875 0.7102823257446289 739.3486938476562 0.8127966523170471 0.8084848 0.6291428208351135 False diff --git a/ENCSR634WYX/cherimoya.fold_0.performance.tsv b/ENCSR634WYX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8b3cfedbb2154ca70193e6a310bd6775b0b61183..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -738.8051147460938 0.15705515444278717 0.8132174611091614 0.4461182951927185 0.8102604746818542 0.7627153992652893 0.6254234910011292 \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_1.evaluate.json b/ENCSR634WYX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b625b60d3585d61ab1764ccee6c60a7a7d96b2d5..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF803SMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_1.fit.json b/ENCSR634WYX/cherimoya.fold_1.fit.json deleted file mode 100644 index 6d04796e999a1f40a8acc54cd7761bd40a3e6cde..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF803SMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_1.log b/ENCSR634WYX/cherimoya.fold_1.log deleted file mode 100644 index e517513211449bcad2e419ae1719a92b7271b956..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3246 40.579121351242065 4.101284742355347 789.7805786132812 2.18966007232666 1225.41552734375 0.7045775055885315 0.705691 9.25348949432373 True -1 6492 35.665619134902954 1.1213140487670898 708.6739501953125 1.279471516609192 997.4862060546875 0.7769330739974976 0.75823766 2.5663633346557617 True -2 9738 35.6701545715332 0.8382251262664795 829.9641723632812 1.116276502609253 968.6592407226562 0.7869860529899597 0.76233727 1.1875054836273193 True -3 12984 35.49477005004883 0.7963969707489014 561.8053588867188 1.0961428880691528 953.1829223632812 0.7926769256591797 0.7616714 1.03078293800354 False -4 16230 34.98555064201355 0.7985992431640625 632.0723876953125 0.9538581371307373 938.4636840820312 0.7981780767440796 0.7661623 0.9031773805618286 True -5 19476 34.949342489242554 0.7969589233398438 710.9656982421875 1.0803320407867432 931.5985717773438 0.8006777167320251 0.77656054 0.8285706639289856 True -6 22722 34.97420811653137 0.8160107135772705 628.9962768554688 1.1097216606140137 926.9603271484375 0.8020427227020264 0.7757615 0.7898387908935547 False -7 25968 34.94914627075195 0.8030107021331787 741.1209716796875 1.134132981300354 916.7567749023438 0.8053849935531616 0.78076977 0.7362471222877502 True -8 29214 34.95055937767029 0.8159446716308594 693.1715087890625 0.8717962503433228 910.2754516601562 0.8072949051856995 0.78499985 0.7180781960487366 True -9 32460 34.975879192352295 0.8138136863708496 537.268798828125 1.0224004983901978 901.0173950195312 0.8105159401893616 0.78912383 0.6984758377075195 True -10 35706 34.97671365737915 0.8161320686340332 787.0675048828125 0.8838279843330383 894.9781494140625 0.8125454783439636 0.79536986 0.6779566407203674 True -11 38952 35.00200414657593 0.8051824569702148 666.3819580078125 1.3020973205566406 885.606689453125 0.8156136870384216 0.79961616 0.6652142405509949 True -12 42198 34.8884220123291 1.8846242427825928 549.5618896484375 0.7662870287895203 879.8116455078125 0.8179574012756348 0.8074282 0.646253228187561 True -13 45444 34.931458711624146 1.5268664360046387 591.537841796875 0.8949499130249023 873.5558471679688 0.8204054236412048 0.8151304 0.6435288190841675 True -14 48690 35.0571026802063 0.8154819011688232 565.5765991210938 0.6481812596321106 868.9231567382812 0.8222432732582092 0.821303 0.6164571642875671 True -15 51936 35.1335346698761 0.8658850193023682 619.767333984375 0.6500833034515381 866.4780883789062 0.8237050175666809 0.8238608 0.6068019866943359 True -16 55182 35.1372709274292 0.8433036804199219 595.4556884765625 0.6993144750595093 863.8065795898438 0.8243968486785889 0.8291167 0.60685133934021 True -17 58428 35.24303698539734 1.4550118446350098 499.9765319824219 0.8942480087280273 863.9129638671875 0.8245863914489746 0.8298092 0.6076626181602478 True -18 61674 35.147653341293335 0.8420345783233643 534.7800903320312 0.5706632137298584 865.2077026367188 0.8242840766906738 0.8281335 0.6199647188186646 False -19 64920 35.1328182220459 0.8132283687591553 654.992431640625 0.48949605226516724 865.4697875976562 0.824009895324707 0.8289948 0.6251018643379211 False diff --git a/ENCSR634WYX/cherimoya.fold_1.performance.tsv b/ENCSR634WYX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index aeb275f7727dadafa9dd7e755a3a6e180dcc49ed..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -863.9129638671875 0.14184542000293732 0.8245863318443298 0.49779051542282104 0.8298091888427734 0.8104984164237976 0.6076626181602478 \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_2.evaluate.json b/ENCSR634WYX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index aa233644d906b9c3f260295e71442f420c9cce4d..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF803SMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_2.fit.json b/ENCSR634WYX/cherimoya.fold_2.fit.json deleted file mode 100644 index a58347e504fe67f69bc62e28bc582a67691ed300..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF803SMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_2.log b/ENCSR634WYX/cherimoya.fold_2.log deleted file mode 100644 index 400cc279d8fddfa67094a089eb8d287e889bdb9d..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3495 43.10237383842468 3.5390613079071045 666.4619750976562 1.4254438877105713 1075.2227783203125 0.7044421434402466 0.7082477 9.116044998168945 True -1 6990 38.568936586380005 0.7601318359375 636.9566040039062 1.3132688999176025 907.1657104492188 0.766197919845581 0.7575254 2.326969623565674 True -2 10485 38.483691453933716 0.6652095317840576 687.4443969726562 1.2238619327545166 883.4948120117188 0.7756356596946716 0.76126075 1.2612041234970093 True -3 13980 38.44325637817383 0.9421951770782471 654.8427124023438 1.0794081687927246 866.6121215820312 0.7825312614440918 0.76263374 1.0744425058364868 True -4 17475 37.67518496513367 0.8434889316558838 671.0321044921875 1.428128957748413 856.5353393554688 0.7861799597740173 0.7656667 0.8075787425041199 True -5 20970 37.64586615562439 0.6533870697021484 459.3905029296875 1.2688772678375244 850.5296020507812 0.7889004945755005 0.7690876 0.7885403633117676 True -6 24465 37.67610764503479 0.6496362686157227 579.3196411132812 1.1970807313919067 841.2207641601562 0.7918112277984619 0.77382696 0.7543832659721375 True -7 27960 37.58901810646057 1.425605058670044 757.4794921875 1.1820275783538818 833.4217529296875 0.7944948077201843 0.7765921 0.7270848155021667 True -8 31455 37.6631875038147 0.6391491889953613 677.688232421875 0.9429289102554321 826.4336547851562 0.7972208857536316 0.7818516 0.6930049657821655 True -9 34950 37.772812366485596 0.6855552196502686 720.6217041015625 1.0419480800628662 819.9266357421875 0.7998044490814209 0.782958 0.6898142099380493 True -10 38445 37.730997800827026 0.6624202728271484 598.3796997070312 1.0995874404907227 813.6448364257812 0.8020303845405579 0.7841496 0.6741742491722107 True -11 41940 37.79052710533142 0.663642168045044 506.6129150390625 1.405448317527771 808.197998046875 0.8045626282691956 0.7932022 0.6572009325027466 True -12 45435 37.75077795982361 1.221276044845581 590.931396484375 0.790306031703949 801.8148803710938 0.8070179224014282 0.8000034 0.6420759558677673 True -13 48930 37.802258014678955 0.6646349430084229 468.5450134277344 1.063429355621338 795.7012329101562 0.8097205758094788 0.80642545 0.6297264695167542 True -14 52425 37.820637941360474 2.5510292053222656 515.5966186523438 0.8460142612457275 791.9564819335938 0.8116062879562378 0.8126361 0.6119756698608398 True -15 55920 37.91723036766052 0.6544358730316162 572.9454345703125 0.7190102934837341 788.551025390625 0.8130826354026794 0.8185248 0.5968702435493469 True -16 59415 37.94898700714111 0.6465070247650146 593.3187866210938 0.5825831890106201 786.6512451171875 0.8140060901641846 0.82150865 0.5993935465812683 True -17 62910 37.80372190475464 0.6556315422058105 530.5416870117188 0.6833568811416626 786.7014770507812 0.8143671154975891 0.8237078 0.597861647605896 True -18 66405 37.85970664024353 0.6322526931762695 596.751953125 0.769333004951477 787.7042236328125 0.8141160011291504 0.823141 0.6027500033378601 False -19 69900 37.850364208221436 0.6502416133880615 515.4188232421875 0.6117703914642334 788.2155151367188 0.8138446807861328 0.8217085 0.6107046604156494 False diff --git a/ENCSR634WYX/cherimoya.fold_2.performance.tsv b/ENCSR634WYX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1506861791dc5d090306a924280a306154876151..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -786.7014770507812 0.15330316126346588 0.8143670558929443 0.4643382728099823 0.8237078189849854 0.788677990436554 0.597861647605896 \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_3.evaluate.json b/ENCSR634WYX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3091d8f888d641b36e7b4462738e83d5ac4ec1c6..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF803SMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_3.fit.json b/ENCSR634WYX/cherimoya.fold_3.fit.json deleted file mode 100644 index 71ba329d3eea019ec679e787c7aa7015879b70a9..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF803SMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_3.log b/ENCSR634WYX/cherimoya.fold_3.log deleted file mode 100644 index 779add56cde2d0440b78a315da354f3e5ad3cb59..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3336 41.31605887413025 3.599642276763916 705.4759521484375 1.1517103910446167 1014.6200561523438 0.6972859501838684 0.7026274 9.684196472167969 True -1 6672 36.56518793106079 0.83437180519104 668.2640380859375 0.9692702293395996 839.3811645507812 0.7638437151908875 0.7386902 2.001115083694458 True -2 10008 36.56346106529236 0.6174037456512451 679.6958618164062 1.40897798538208 818.9212646484375 0.7734125852584839 0.74306816 1.277325987815857 True -3 13344 35.964099645614624 2.711270332336426 631.3191528320312 0.8349785208702087 805.4459838867188 0.7797871828079224 0.74741393 1.0674989223480225 True -4 16680 35.91137957572937 4.399822473526001 636.4759521484375 1.1083638668060303 796.9807739257812 0.7854923605918884 0.7520719 0.9090935587882996 True -5 20016 35.96386647224426 0.6643967628479004 698.3741455078125 1.0531704425811768 791.64111328125 0.7887007594108582 0.749023 0.8761789202690125 False -6 23352 35.87633395195007 1.2966852188110352 660.703125 0.8584034442901611 788.2951049804688 0.7909641265869141 0.7490325 0.8750647306442261 False -7 26688 35.888943910598755 0.6417319774627686 543.4847412109375 0.9104759693145752 780.273681640625 0.7939439415931702 0.7507567 0.8062891364097595 False -8 30024 35.95978760719299 20.524144411087036 657.4486083984375 0.7526000738143921 773.2838134765625 0.796895444393158 0.7528818 0.7830464839935303 True -9 33360 36.20715618133545 11.488967180252075 578.6506958007812 1.1740162372589111 770.2291870117188 0.7988221645355225 0.75588024 0.7673084139823914 True -10 36696 36.05833077430725 0.6303238868713379 692.9635009765625 1.1573216915130615 764.6129760742188 0.8019246459007263 0.7577658 0.755526602268219 True -11 40032 36.00054168701172 0.6206717491149902 660.9712524414062 1.056240439414978 760.846435546875 0.8038004636764526 0.76321054 0.7558334469795227 True -12 43368 35.9647696018219 0.6295127868652344 563.559326171875 1.0890686511993408 753.9623413085938 0.8065376281738281 0.77301455 0.7357496619224548 True -13 46704 35.93721914291382 0.6201374530792236 496.773193359375 0.4743499755859375 750.8944702148438 0.8083676099777222 0.78198665 0.7142752408981323 True -14 50040 35.98761510848999 0.6234257221221924 629.4744262695312 0.9463479518890381 746.5555419921875 0.8104347586631775 0.7905142 0.688494086265564 True -15 53376 35.96501541137695 0.6299810409545898 626.7490234375 0.8501602411270142 744.0958862304688 0.8114041686058044 0.796225 0.675920844078064 True -16 56712 35.96064615249634 0.6282923221588135 610.3367919921875 0.4797658920288086 742.9733276367188 0.8120672702789307 0.8013003 0.6701121926307678 True -17 60048 36.028478384017944 0.6294112205505371 568.5348510742188 0.799684464931488 743.359619140625 0.812078058719635 0.80604136 0.6653013229370117 True -18 63384 35.98483967781067 0.6257545948028564 599.9268798828125 0.47262299060821533 743.6127319335938 0.8117390275001526 0.8055665 0.6736326813697815 False -19 66720 35.96941661834717 0.622429370880127 605.5651245117188 0.5607525706291199 744.3670654296875 0.8115274310112 0.8048663 0.6755262017250061 False diff --git a/ENCSR634WYX/cherimoya.fold_3.performance.tsv b/ENCSR634WYX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 33fef8c1725a26d810764a5345eb8d0d16a34520..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -743.359619140625 0.15719416737556458 0.8120781183242798 0.4411625862121582 0.8060413599014282 0.7490388751029968 0.6653013229370117 \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_4.evaluate.json b/ENCSR634WYX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9a5508f23882462fe70d869d676d05558d3bedf7..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF803SMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_4.fit.json b/ENCSR634WYX/cherimoya.fold_4.fit.json deleted file mode 100644 index cc0dde54f799257f7a7ec52a1be1f4837a963421..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF803SMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634WYX/cherimoya.fold_4.log b/ENCSR634WYX/cherimoya.fold_4.log deleted file mode 100644 index f0bace51657d2cd4cec8b4325ca41a4c80734689..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3363 41.63911437988281 4.7327611446380615 564.419677734375 1.669579267501831 954.4542236328125 0.6940575242042542 0.70409817 8.40938663482666 True -1 6726 36.91207432746887 1.2265064716339111 703.5765380859375 1.7958892583847046 807.4403076171875 0.7624873518943787 0.74117213 2.301992654800415 True -2 10089 36.34545660018921 0.6680424213409424 718.1476440429688 1.4123659133911133 784.3941650390625 0.7733475565910339 0.74589545 1.2781078815460205 True -3 13452 36.223183155059814 1.1817588806152344 732.737060546875 1.503666877746582 770.9197387695312 0.781146228313446 0.7493225 0.8445739150047302 True -4 16815 36.17453670501709 0.6669623851776123 725.94384765625 1.4742586612701416 764.031982421875 0.7846259474754333 0.75412333 0.8388814926147461 True -5 20178 36.18951392173767 0.6727027893066406 751.8168334960938 0.976335346698761 758.8678588867188 0.7874109745025635 0.75763524 0.7759568691253662 True -6 23541 36.195436000823975 0.6860904693603516 671.6102294921875 1.1231544017791748 754.6430053710938 0.7897778749465942 0.7617653 0.7419304847717285 True -7 26904 36.24844408035278 0.682807445526123 679.1829223632812 1.0125528573989868 747.1528930664062 0.7927913665771484 0.7644192 0.7098658084869385 True -8 30267 36.203041553497314 0.7079968452453613 594.5321044921875 1.0107744932174683 742.0814208984375 0.7955897450447083 0.7696856 0.6620048880577087 True -9 33630 36.20543050765991 0.68255615234375 775.9364013671875 0.8220481872558594 736.8866577148438 0.7982516884803772 0.7713145 0.6575378179550171 True -10 36993 36.16458606719971 0.6602175235748291 575.945556640625 0.7801705598831177 732.9293212890625 0.8003881573677063 0.7744807 0.6499962210655212 True -11 40356 36.26442909240723 0.6837151050567627 531.2780151367188 1.2599745988845825 728.2144165039062 0.8028231263160706 0.7792661 0.6496315598487854 True -12 43719 36.29701280593872 0.6717453002929688 550.646240234375 0.792299747467041 723.0078735351562 0.8054144382476807 0.78480625 0.6141944527626038 True -13 47082 36.15015625953674 0.6655259132385254 521.9954223632812 0.8052190542221069 718.159912109375 0.8080907464027405 0.7916833 0.5980748534202576 True -14 50445 36.15444302558899 22.452037572860718 597.4302368164062 0.6640515327453613 715.5364379882812 0.8098457455635071 0.79636407 0.5884889960289001 True -15 53808 36.53017258644104 12.582596778869629 495.58123779296875 0.7221400141716003 711.7644653320312 0.8113750219345093 0.8015697 0.58110511302948 True -16 57171 36.27869629859924 0.7008178234100342 492.6296081542969 0.6897238492965698 710.2183227539062 0.8124621510505676 0.80759484 0.5759055614471436 True -17 60534 36.28533363342285 1.6603260040283203 469.0450439453125 0.3511459231376648 709.7772216796875 0.8126586675643921 0.80880594 0.5749920606613159 True -18 63897 36.25543165206909 0.6856682300567627 550.6682739257812 0.6850578784942627 709.8502197265625 0.8124927282333374 0.8082547 0.5821384191513062 False -19 67260 36.23617172241211 0.6728050708770752 454.5400085449219 0.48388874530792236 709.89306640625 0.8122140169143677 0.80642724 0.5890078544616699 False diff --git a/ENCSR634WYX/cherimoya.fold_4.performance.tsv b/ENCSR634WYX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8c7be27ccb96729d470882fb2d8f1828a6354675..0000000000000000000000000000000000000000 --- a/ENCSR634WYX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -709.7772216796875 0.1587059497833252 0.8126585483551025 0.43727874755859375 0.8088059425354004 0.75777667760849 0.5749920606613159 \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_0.evaluate.json b/ENCSR634YVQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8af9b6c6596fccac9337bd64f9c1285936094b8c..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF030URW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_0.fit.json b/ENCSR634YVQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 3e0b5919e66d36e762bba7cc139984927c177010..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF030URW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_0.log b/ENCSR634YVQ/cherimoya.fold_0.log deleted file mode 100644 index 4139196ea8a321d8247d0601899910d2f07423f9..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2663 33.25021505355835 3.6701157093048096 403.9957275390625 0.8529449701309204 687.0712280273438 0.23086997866630554 0.6565384 7.237107276916504 True -1 5326 29.041125535964966 0.6146883964538574 467.171142578125 0.7504377365112305 617.6256713867188 0.31829026341438293 0.71867675 2.7613346576690674 True -2 7989 29.566775798797607 0.5839087963104248 510.9709167480469 0.6697381138801575 605.7467041015625 0.3313625752925873 0.71702385 1.7628456354141235 False -3 10652 29.60965657234192 0.594510555267334 554.9163818359375 0.9605178833007812 602.1455078125 0.3340550363063812 0.72498614 1.4216285943984985 True -4 13315 29.535823106765747 0.581413984298706 572.1065673828125 1.2450226545333862 600.4263305664062 0.33654940128326416 0.72683376 1.3745251893997192 True -5 15978 29.55150032043457 0.5915141105651855 531.6585083007812 0.6327347755432129 597.31884765625 0.3408252000808716 0.7348476 1.2325249910354614 True -6 18641 29.503052949905396 0.5754806995391846 506.82415771484375 0.8807917833328247 595.8436279296875 0.3421902656555176 0.7419415 1.262315034866333 True -7 21304 29.89004111289978 0.8151423931121826 394.91864013671875 0.8535469770431519 595.33935546875 0.343208372592926 0.74493927 1.1653121709823608 True -8 23967 29.568389177322388 25.271652221679688 525.394287109375 0.7984886765480042 593.5576782226562 0.34534752368927 0.7535341 1.09481942653656 True -9 26630 29.627185106277466 0.6099598407745361 480.24505615234375 0.7643767595291138 590.3270874023438 0.3502962589263916 0.7575474 1.0039706230163574 True -10 29293 29.754716396331787 0.5956106185913086 569.68359375 1.0005227327346802 586.4830932617188 0.3555707633495331 0.7649399 0.9269285202026367 True -11 31956 29.739439964294434 0.5867574214935303 491.86962890625 0.5706331133842468 586.21435546875 0.3543343245983124 0.769182 0.8591331839561462 True -12 34619 29.636215448379517 0.592233419418335 566.1943969726562 0.5949801206588745 585.4077758789062 0.35587450861930847 0.77621716 0.8100098371505737 True -13 37282 29.610742807388306 0.6011371612548828 592.6138916015625 0.758745551109314 583.6674194335938 0.35729852318763733 0.78250426 0.7692469358444214 True -14 39945 29.720197200775146 0.5878200531005859 452.20928955078125 0.4510567784309387 582.8796997070312 0.3591478765010834 0.78801167 0.7286927700042725 True -15 42608 29.63703942298889 0.6008744239807129 428.91729736328125 0.5262198448181152 582.907470703125 0.3578869104385376 0.7917945 0.7048448324203491 True -16 45271 29.70486354827881 1.2614762783050537 388.7276306152344 0.458606481552124 581.0154418945312 0.3609939217567444 0.7922574 0.6923398375511169 True -17 47934 29.630358695983887 0.608375072479248 479.3248596191406 0.48796582221984863 582.9443359375 0.35765162110328674 0.7903531 0.6873838305473328 False -18 50597 29.65281319618225 0.5777373313903809 430.50872802734375 0.5514169931411743 582.6005859375 0.35852038860321045 0.78893524 0.6952870488166809 False -19 53260 29.11057758331299 0.5708940029144287 436.20947265625 0.42420095205307007 583.39697265625 0.3572603762149811 0.7857883 0.7013811469078064 False diff --git a/ENCSR634YVQ/cherimoya.fold_0.performance.tsv b/ENCSR634YVQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 95452aefb21c3a4bef4f251d1f1f3c7c78b6904b..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -581.0154418945312 0.40675416588783264 0.3609939217567444 0.15370726585388184 0.7922574281692505 0.748309850692749 0.6923398375511169 \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_1.evaluate.json b/ENCSR634YVQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 94f2ab0616244b8c52c3d1b3b765b50c54b803b3..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF030URW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_1.fit.json b/ENCSR634YVQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 5db79427535662b3815412dbfba9394ee89273e9..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF030URW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_1.log b/ENCSR634YVQ/cherimoya.fold_1.log deleted file mode 100644 index f4f9bd447a0e26134cb5012df36badbb0dea57a0..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2700 33.59598660469055 3.786353588104248 434.21337890625 0.9233814477920532 789.8958740234375 0.24302570521831512 0.68501794 7.104079723358154 True -1 5400 29.73840880393982 0.7543768882751465 478.92193603515625 1.1849123239517212 715.0165405273438 0.3314797580242157 0.7463937 2.554258346557617 True -2 8100 29.708616256713867 2.024909734725952 399.3023376464844 0.9989460706710815 702.3764038085938 0.34532079100608826 0.7590082 1.856938362121582 True -3 10800 29.68570590019226 0.7580912113189697 586.577880859375 1.2040432691574097 691.9815063476562 0.35545405745506287 0.7670454 1.5819988250732422 True -4 13500 29.73471736907959 0.7389490604400635 383.6617431640625 1.1412534713745117 690.2413940429688 0.3567858338356018 0.7688713 1.3837974071502686 True -5 16200 29.7303729057312 2.0835623741149902 497.9912414550781 0.8238336443901062 689.4352416992188 0.35768142342567444 0.7779905 1.286320447921753 True -6 18900 29.673961639404297 0.7497129440307617 501.7854309082031 0.6714333891868591 686.3750610351562 0.3606664836406708 0.7814093 1.2274802923202515 True -7 21600 29.676892042160034 0.7577197551727295 401.7247314453125 0.5385004281997681 682.821533203125 0.3642047047615051 0.79070914 1.0447622537612915 True -8 24300 29.69598913192749 0.7484099864959717 530.5626220703125 0.8020424842834473 679.5906982421875 0.36822381615638733 0.79655856 0.9794275760650635 True -9 27000 29.702685356140137 0.7546501159667969 444.5221252441406 0.6589500904083252 678.586669921875 0.36958688497543335 0.7987653 0.9264671206474304 True -10 29700 29.35881233215332 0.744835615158081 460.80914306640625 0.7437331676483154 675.201171875 0.37274107336997986 0.80690217 0.861770510673523 True -11 32400 29.144633769989014 0.7476141452789307 400.3492431640625 0.6603238582611084 673.1929931640625 0.3747282326221466 0.8140015 0.7609090805053711 True -12 35100 29.19489812850952 0.7384567260742188 426.00921630859375 0.756193995475769 671.0502319335938 0.37763240933418274 0.8190669 0.7074422836303711 True -13 37800 29.215739965438843 0.7472760677337646 330.8397216796875 0.691913366317749 670.4882202148438 0.3771342635154724 0.8241972 0.6812195777893066 True -14 40500 29.182936906814575 0.738100528717041 441.8408203125 0.6915620565414429 670.0394897460938 0.3773961067199707 0.83025324 0.638846218585968 True -15 43200 29.300623178482056 0.744675874710083 504.50970458984375 0.9810290336608887 668.7711181640625 0.37896740436553955 0.83476186 0.6152014136314392 True -16 45900 29.273534059524536 1.8151969909667969 403.5694274902344 0.6508687734603882 669.344482421875 0.3781700134277344 0.83708435 0.5987606048583984 True -17 48600 29.21788454055786 0.7536327838897705 493.4882507324219 0.5418875813484192 669.1701049804688 0.37799984216690063 0.83437014 0.6017734408378601 False -18 51300 29.13730239868164 0.7516717910766602 365.6273193359375 0.5801847577095032 669.9760131835938 0.37746763229370117 0.8329231 0.6063477396965027 False -19 54000 29.183013200759888 0.7388534545898438 444.8403625488281 0.27163439989089966 669.8016967773438 0.3778059184551239 0.83051425 0.6164624094963074 False diff --git a/ENCSR634YVQ/cherimoya.fold_1.performance.tsv b/ENCSR634YVQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index dd934bd29ac9f13404504a9849a9afda3eea1124..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -669.344482421875 0.38770273327827454 0.3781700134277344 0.1751405894756317 0.8370843529701233 0.8112103343009949 0.5987606048583984 \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_2.evaluate.json b/ENCSR634YVQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 56b4fdbe054629f7d74bb12b82d4bb22868a4178..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF030URW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_2.fit.json b/ENCSR634YVQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 0c77619699349b7493a5f2ea57618d7350f5522c..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF030URW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_2.log b/ENCSR634YVQ/cherimoya.fold_2.log deleted file mode 100644 index e36d763f712cfa707c2163be0be3cda615c18147..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2908 36.09703779220581 4.123990297317505 557.4970703125 1.222847819328308 709.4609985351562 0.24275638163089752 0.67550194 6.232642650604248 True -1 5816 31.898752450942993 0.5847337245941162 499.72161865234375 0.9020708799362183 641.255859375 0.320997416973114 0.73764545 2.396334648132324 True -2 8724 32.04341197013855 1.1146061420440674 497.55767822265625 1.4184529781341553 631.6441650390625 0.33280712366104126 0.75035346 1.5637582540512085 True -3 11632 31.596128463745117 16.110686779022217 476.13677978515625 1.1282180547714233 627.5481567382812 0.3376171588897705 0.75431395 1.325592041015625 True -4 14540 31.38250756263733 0.5670368671417236 369.95648193359375 1.2592449188232422 624.658203125 0.3425114154815674 0.7516318 1.2792267799377441 False -5 17448 31.405768394470215 0.5619971752166748 406.27618408203125 0.8010323643684387 621.9583740234375 0.3459487855434418 0.76283276 1.090678095817566 True -6 20356 31.33381223678589 0.5534539222717285 473.2232666015625 0.7052731513977051 620.1923217773438 0.3473384380340576 0.7694004 1.0573546886444092 True -7 23264 31.29520535469055 0.5598347187042236 483.7464599609375 0.9407398104667664 620.0424194335938 0.3477783799171448 0.77294564 0.9844755530357361 True -8 26172 31.512539863586426 0.5589892864227295 448.6703796386719 0.7898380756378174 617.5715942382812 0.35116294026374817 0.7791782 0.8975217938423157 True -9 29080 31.323869705200195 0.5644948482513428 546.222412109375 0.6919490694999695 615.5230102539062 0.35373663902282715 0.78266466 0.8702342510223389 True -10 31988 31.32254385948181 0.5587785243988037 461.5534362792969 0.8376443982124329 613.5350952148438 0.3564859628677368 0.78465736 0.7985568046569824 True -11 34896 31.39196014404297 0.5622210502624512 484.44476318359375 0.524711012840271 611.9055786132812 0.35789501667022705 0.79380405 0.7470933198928833 True -12 37804 31.35139560699463 1.109116554260254 425.0690002441406 0.8093966841697693 609.870361328125 0.36071720719337463 0.79772747 0.7063326239585876 True -13 40712 31.378755569458008 1.4164988994598389 555.0855712890625 0.5191576480865479 609.8406372070312 0.36052122712135315 0.8033531 0.662377655506134 True -14 43620 31.302862644195557 0.6743407249450684 404.67022705078125 0.8367478847503662 608.7808837890625 0.36183324456214905 0.80833495 0.6330760717391968 True -15 46528 31.376419067382812 0.5635724067687988 382.9808349609375 0.5655263066291809 607.0909423828125 0.3639243543148041 0.8124944 0.6081525683403015 True -16 49436 31.339322805404663 0.5653929710388184 363.55108642578125 0.5881768465042114 608.0777587890625 0.3622368276119232 0.8161611 0.5949246883392334 True -17 52344 31.35189175605774 0.577871561050415 367.41412353515625 0.6305099129676819 606.1851196289062 0.36545825004577637 0.8134491 0.6002241969108582 False -18 55252 31.47352623939514 0.5622007846832275 540.9141845703125 0.3131723403930664 607.6868286132812 0.36323338747024536 0.81313527 0.6063796281814575 False -19 58160 31.397749423980713 0.5603179931640625 456.2569885253906 0.43083667755126953 607.5119018554688 0.36351844668388367 0.81056386 0.6126068830490112 False diff --git a/ENCSR634YVQ/cherimoya.fold_2.performance.tsv b/ENCSR634YVQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 31e1b44df492e0c9d45fb6c15ef726bb22b17517..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -608.0777587890625 0.40251755714416504 0.362236887216568 0.15982584655284882 0.8161610960960388 0.7788761258125305 0.5949246883392334 \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_3.evaluate.json b/ENCSR634YVQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9eda783cc7a1ab9a903b157c9b8c2c006fe03cc0..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF030URW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_3.fit.json b/ENCSR634YVQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 163f75c4625986ee133125410a0df21b9823a9b4..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF030URW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_3.log b/ENCSR634YVQ/cherimoya.fold_3.log deleted file mode 100644 index 4e227d6908fe0e6b3c4aa04a5327b80b65691950..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.005332469940186 3.490403175354004 493.0662841796875 0.8302760124206543 676.0868530273438 0.24826647341251373 0.6824808 6.524255275726318 True -1 5596 31.08409547805786 0.531965970993042 498.9173583984375 0.9933004975318909 618.6275634765625 0.32310426235198975 0.7416673 1.9826741218566895 True -2 8394 31.070443868637085 0.5187780857086182 464.488037109375 0.8580837249755859 608.7003784179688 0.3346349000930786 0.7477477 1.3221718072891235 True -3 11192 31.02705144882202 2.7430505752563477 561.7313232421875 0.9505013823509216 605.399169921875 0.3373996317386627 0.7581031 1.1564704179763794 True -4 13990 31.07378077507019 0.5223321914672852 505.1689453125 0.6844209432601929 602.3618774414062 0.34298235177993774 0.7593507 1.1297616958618164 True -5 16788 31.060965299606323 0.5155606269836426 592.851806640625 0.9105970859527588 598.918212890625 0.3472789227962494 0.7606369 1.0456598997116089 True -6 19586 31.114128351211548 5.012872219085693 597.9783935546875 1.4264516830444336 597.0150146484375 0.35025715827941895 0.7699315 0.9583072066307068 True -7 22384 30.50144934654236 0.5157418251037598 399.07354736328125 0.7819318771362305 595.2361450195312 0.353854775428772 0.7727711 0.9182144999504089 True -8 25182 30.596413373947144 0.5276312828063965 450.48626708984375 0.6717491149902344 592.69873046875 0.35648196935653687 0.7810285 0.8628456592559814 True -9 27980 30.5237557888031 1.147601842880249 443.51849365234375 0.6085479259490967 591.1264038085938 0.35866275429725647 0.7856928 0.8183356523513794 True -10 30778 30.553675174713135 0.750239372253418 448.21185302734375 0.9102263450622559 590.850830078125 0.3587810695171356 0.7895358 0.7828682661056519 True -11 33576 30.544978380203247 0.5213868618011475 447.42987060546875 0.7100188732147217 589.69775390625 0.3610130250453949 0.79757845 0.7334824204444885 True -12 36374 30.49381399154663 0.8598322868347168 396.9795227050781 0.504002034664154 587.9426879882812 0.363599568605423 0.8057388 0.6997115015983582 True -13 39172 30.546079397201538 0.8025338649749756 478.2723693847656 0.5021179914474487 586.81689453125 0.3647647500038147 0.8125004 0.6631444096565247 True -14 41970 30.589381456375122 0.5234496593475342 373.409912109375 0.5106208324432373 584.7698364257812 0.367742121219635 0.81911314 0.6202986836433411 True -15 44768 30.488117694854736 0.5238935947418213 485.15386962890625 0.788011372089386 584.7996826171875 0.3671043813228607 0.82685316 0.5778098106384277 True -16 47566 30.573463678359985 0.5228233337402344 483.846923828125 0.5896663069725037 584.7222900390625 0.3664698004722595 0.8283573 0.5608105659484863 True -17 50364 30.57139825820923 0.5219902992248535 400.648681640625 0.36811697483062744 583.4484252929688 0.3689757287502289 0.8285978 0.5598739981651306 True -18 53162 31.27395987510681 0.5233221054077148 427.70294189453125 0.5198509693145752 583.6351318359375 0.3679785430431366 0.824362 0.5736361145973206 False -19 55960 30.66007399559021 0.5255835056304932 460.7850341796875 0.4204100966453552 584.2239379882812 0.3671397864818573 0.8216724 0.5756744146347046 False diff --git a/ENCSR634YVQ/cherimoya.fold_3.performance.tsv b/ENCSR634YVQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d56ec3c581c1a0708a7aee5d59180f41f64625e2..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -583.4484252929688 0.40274927020072937 0.36897575855255127 0.1585974395275116 0.8285977840423584 0.7881657481193542 0.5598739981651306 \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_4.evaluate.json b/ENCSR634YVQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index da605f79f2f6bb8be5bf447f1f80646e9b215c43..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF030URW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_4.fit.json b/ENCSR634YVQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 16c715b03ce0e33ca31a9067cce2afb564c8d659..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF030URW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634YVQ/cherimoya.fold_4.log b/ENCSR634YVQ/cherimoya.fold_4.log deleted file mode 100644 index d0eba38b1893b8b7e33aaa1f7ebb6f7972fe9074..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2817 35.27416777610779 3.460143804550171 485.9021301269531 1.1529849767684937 639.9778442382812 0.2323201596736908 0.66213286 5.297548294067383 True -1 5634 31.22791886329651 0.564838171005249 539.174072265625 1.108886480331421 585.9979858398438 0.30678102374076843 0.71760255 2.21671724319458 True -2 8451 30.830273866653442 0.5465347766876221 460.0050048828125 0.9088997840881348 575.8902587890625 0.318970650434494 0.73473203 1.3489811420440674 True -3 11268 30.674991607666016 0.5479474067687988 450.482177734375 0.9100842475891113 571.5774536132812 0.3231828808784485 0.74333346 1.2448042631149292 True -4 14085 30.628950357437134 0.5535070896148682 395.8864440917969 0.9099484086036682 567.9452514648438 0.32783493399620056 0.75011176 1.111899495124817 True -5 16902 30.616072416305542 0.5465757846832275 471.803466796875 0.5842515230178833 565.7472534179688 0.33140692114830017 0.75607985 0.9887000322341919 True -6 19719 30.65952777862549 0.545602560043335 514.6591796875 1.0495843887329102 562.9789428710938 0.33462488651275635 0.7634943 0.894104540348053 True -7 22536 30.657643795013428 0.5483791828155518 398.77569580078125 0.7548000812530518 562.5733642578125 0.33494502305984497 0.7714775 0.8176169991493225 True -8 25353 30.65016198158264 0.5464568138122559 373.1512756347656 0.711034893989563 559.4857788085938 0.33977875113487244 0.7779093 0.8018823862075806 True -9 28170 30.658653497695923 0.5472738742828369 462.66070556640625 0.7139809131622314 558.3145751953125 0.3413843810558319 0.78388536 0.7651734948158264 True -10 30987 30.60885262489319 0.5455708503723145 452.753173828125 0.7703509330749512 557.1629638671875 0.34168535470962524 0.78678924 0.7190449833869934 True -11 33804 30.620718240737915 0.5475187301635742 437.4428405761719 0.4413580894470215 555.404296875 0.345540314912796 0.7934358 0.6787962317466736 True -12 36621 30.66241979598999 0.5456292629241943 395.29754638671875 0.7763240337371826 554.72265625 0.345353364944458 0.800674 0.6383627653121948 True -13 39438 30.67828130722046 0.5478403568267822 387.2750244140625 0.794718861579895 553.5671997070312 0.3470116853713989 0.8046169 0.618735134601593 True -14 42255 30.721282243728638 0.545015811920166 339.85772705078125 0.8768656253814697 552.468017578125 0.3485531806945801 0.8114886 0.5920385718345642 True -15 45072 30.67471480369568 0.5523891448974609 465.00299072265625 0.5019533634185791 553.21142578125 0.34799104928970337 0.81440336 0.5824138522148132 True -16 47889 30.654898643493652 0.5476741790771484 565.5714721679688 0.6118531823158264 552.622314453125 0.34848546981811523 0.8155396 0.5655737519264221 True -17 50706 30.650858402252197 0.5483081340789795 419.96954345703125 0.4893435537815094 552.1607666015625 0.3494820296764374 0.8154629 0.5670493841171265 False -18 53523 30.662222623825073 0.5505714416503906 414.5457763671875 0.42178696393966675 553.0762329101562 0.3486346900463104 0.8106132 0.5791404843330383 False -19 56340 30.63687491416931 0.5478808879852295 475.875244140625 0.3815477788448334 552.4479370117188 0.3497202694416046 0.8082639 0.5892217755317688 False diff --git a/ENCSR634YVQ/cherimoya.fold_4.performance.tsv b/ENCSR634YVQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c33184a9fb2ceafba1a3f7899e11f27d7ada890f..0000000000000000000000000000000000000000 --- a/ENCSR634YVQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -552.622314453125 0.4166676998138428 0.34848544001579285 0.14841358363628387 0.8155395984649658 0.7710946798324585 0.5655737519264221 \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_0.evaluate.json b/ENCSR634ZYB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index dd79e430f97ad152b4dd342be8f1d4c4dc7aa8dc..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586XTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_0.fit.json b/ENCSR634ZYB/cherimoya.fold_0.fit.json deleted file mode 100644 index f2ca0d25599df9f2e64f0ad77b1ec8a330ce0ded..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF586XTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_0.log b/ENCSR634ZYB/cherimoya.fold_0.log deleted file mode 100644 index 131aa766369cc8d7ac5ea28b7715f676398f4058..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1820 24.63765859603882 3.568288803100586 411.9034423828125 0.772092342376709 372.1000671386719 0.12899817526340485 0.6335237 8.305556297302246 True -1 3640 19.937188625335693 1.3460948467254639 264.63885498046875 0.8701143264770508 332.70819091796875 0.20522911846637726 0.7216945 4.211493015289307 True -2 5460 20.13068437576294 0.7663860321044922 247.51898193359375 0.8816262483596802 308.397216796875 0.2339017242193222 0.74781954 2.392881155014038 True -3 7280 20.052736282348633 10.900195121765137 232.11550903320312 0.7328135967254639 302.6951599121094 0.24182100594043732 0.7741571 1.3002359867095947 True -4 9100 20.836605310440063 0.37026429176330566 222.47979736328125 0.6504900455474854 300.1455993652344 0.24644862115383148 0.7845899 1.0099103450775146 True -5 10920 20.08884882926941 0.3602879047393799 253.30856323242188 0.6081534624099731 298.5852355957031 0.24997639656066895 0.7903723 0.892978310585022 True -6 12740 20.45979928970337 0.363933801651001 289.08721923828125 0.5571562051773071 297.55029296875 0.2515678405761719 0.8045919 0.8005942106246948 True -7 14560 20.079484701156616 0.36518406867980957 194.93667602539062 0.6194444894790649 296.306396484375 0.25412583351135254 0.81259865 0.7843314409255981 True -8 16380 20.042804718017578 0.349229097366333 231.45269775390625 0.6174682974815369 293.85906982421875 0.2587786316871643 0.8212465 0.6765212416648865 True -9 18200 20.04646062850952 0.3547823429107666 200.41415405273438 0.7740036249160767 293.8637390136719 0.2577337622642517 0.82284945 0.6420948505401611 True -10 20020 20.04458212852478 0.3606297969818115 221.26048278808594 0.5320727229118347 292.68109130859375 0.2600144147872925 0.8298297 0.6082652807235718 True -11 21840 20.07747530937195 0.36154794692993164 273.206298828125 0.39641645550727844 291.8597717285156 0.26211071014404297 0.8342793 0.5928633809089661 True -12 23660 20.125863313674927 0.36628079414367676 246.51390075683594 0.43892019987106323 290.7513427734375 0.2642185389995575 0.8375805 0.5689516067504883 True -13 25480 20.114283323287964 0.368821382522583 213.47869873046875 0.7661114931106567 290.0624084472656 0.26488620042800903 0.84068114 0.537711501121521 True -14 27300 20.099229335784912 0.3619108200073242 244.93954467773438 0.6004210710525513 289.33001708984375 0.26588377356529236 0.84605086 0.5144177675247192 True -15 29120 20.07963538169861 0.3626837730407715 268.44635009765625 0.5182885527610779 289.2684020996094 0.2660021185874939 0.846839 0.5033753514289856 True -16 30940 20.10592293739319 0.3565826416015625 281.9014892578125 0.39585256576538086 289.5715026855469 0.26439526677131653 0.84964913 0.4951149523258209 True -17 32760 20.10109853744507 0.3611137866973877 246.06301879882812 0.380344033241272 289.07843017578125 0.26600557565689087 0.8489166 0.4905396103858948 False -18 34580 20.060006380081177 0.36238932609558105 240.32113647460938 0.4496687650680542 289.187744140625 0.2655010223388672 0.8460367 0.49562689661979675 False -19 36400 20.05536699295044 0.35660576820373535 209.81785583496094 0.4471961259841919 289.7528076171875 0.2639998197555542 0.8468832 0.4976079761981964 False diff --git a/ENCSR634ZYB/cherimoya.fold_0.performance.tsv b/ENCSR634ZYB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2ffd28f4f5cade293aec5c23eaa2bd7d807a3d27..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -289.5715026855469 0.5064477920532227 0.26439520716667175 0.08016405254602432 0.8496491312980652 0.7985682487487793 0.4951149523258209 \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_1.evaluate.json b/ENCSR634ZYB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 12a18443d6be3b251a03b68a4cbf51b418843b16..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586XTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_1.fit.json b/ENCSR634ZYB/cherimoya.fold_1.fit.json deleted file mode 100644 index 58feaf5e52737e804cb87f2b0213cd40c91ad45d..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF586XTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_1.log b/ENCSR634ZYB/cherimoya.fold_1.log deleted file mode 100644 index 639eeb9866636275c4b40a3c0102bb175fb6b2f4..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1801 24.591191291809082 4.427933931350708 235.03712463378906 0.7671912908554077 456.4724426269531 0.14454546570777893 0.60858244 10.480642318725586 True -1 3602 19.880651712417603 0.5961377620697021 228.79420471191406 0.8826353549957275 412.53118896484375 0.2180512696504593 0.7229434 4.869776725769043 True -2 5403 19.89531922340393 0.505638837814331 334.30810546875 0.6335968375205994 377.3742370605469 0.25828710198402405 0.78503126 2.5050151348114014 True -3 7204 19.847594499588013 0.6647181510925293 248.90777587890625 0.7127784490585327 367.576171875 0.2685491740703583 0.802789 1.5051382780075073 True -4 9005 19.852707624435425 0.5166232585906982 263.38037109375 0.7804268598556519 363.4420471191406 0.27497225999832153 0.8085915 1.1035537719726562 True -5 10806 19.86024045944214 1.4935507774353027 211.93014526367188 0.4840283989906311 360.26165771484375 0.280303418636322 0.8169522 0.9263436198234558 True -6 12607 19.868975400924683 0.5261037349700928 182.64834594726562 0.8995943069458008 358.681884765625 0.2820913791656494 0.8275609 0.8030647039413452 True -7 14408 19.857080698013306 0.5126638412475586 308.6375732421875 0.7440059185028076 357.7225036621094 0.2843981981277466 0.8327126 0.7297101020812988 True -8 16209 19.849928617477417 0.5024533271789551 299.4451904296875 0.8241208791732788 357.827880859375 0.2842790484428406 0.8401809 0.6390480995178223 True -9 18010 20.29179310798645 0.5363690853118896 221.03533935546875 0.5429021120071411 355.6666564941406 0.2875182330608368 0.8453372 0.5944987535476685 True -10 19811 19.868269443511963 0.5094339847564697 361.38934326171875 0.6428041458129883 353.8724060058594 0.29100504517555237 0.8476645 0.5660561323165894 True -11 21612 19.85207486152649 0.5086181163787842 202.38876342773438 0.32272282242774963 352.8703308105469 0.29212042689323425 0.85294205 0.5424479246139526 True -12 23413 19.88097310066223 1.0823898315429688 191.51962280273438 0.35865411162376404 351.0505065917969 0.29546794295310974 0.8563332 0.5340434908866882 True -13 25214 19.871346950531006 0.519303560256958 211.6822052001953 0.42737603187561035 349.6064453125 0.2980242967605591 0.86281747 0.5231560468673706 True -14 27015 19.838008403778076 0.5194592475891113 224.6124725341797 0.382802814245224 348.99755859375 0.2983333468437195 0.86504203 0.5182367563247681 True -15 28816 19.825122356414795 0.5076243877410889 265.0068054199219 0.5068037509918213 347.97515869140625 0.3001350462436676 0.86833763 0.5034059882164001 True -16 30617 19.876725912094116 0.5185463428497314 159.21490478515625 0.29911190271377563 348.14501953125 0.29889994859695435 0.87063295 0.5001524090766907 True -17 32418 19.669482946395874 0.514742374420166 260.99658203125 0.5727298259735107 347.8992919921875 0.299527108669281 0.8690685 0.5053526759147644 False -18 34219 19.471834659576416 0.5083432197570801 214.75778198242188 0.4419628381729126 348.2603454589844 0.2982248067855835 0.8687045 0.5145167708396912 False -19 36020 19.475488424301147 0.5008101463317871 253.9311065673828 0.3362905979156494 348.30126953125 0.2986149489879608 0.86625063 0.5203268527984619 False diff --git a/ENCSR634ZYB/cherimoya.fold_1.performance.tsv b/ENCSR634ZYB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7ab422d762d8fd2dd63aabeb6b3d06e7ca792249..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -348.14501953125 0.478825181722641 0.29889988899230957 0.09844774752855301 0.8706329464912415 0.8437911868095398 0.5001524090766907 \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_2.evaluate.json b/ENCSR634ZYB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 469f8908ecf45038863f61e06cfa953f9e7eb62e..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586XTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_2.fit.json b/ENCSR634ZYB/cherimoya.fold_2.fit.json deleted file mode 100644 index 1f166229a605316a64d963d0e0959650a0ccaf9e..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF586XTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_2.log b/ENCSR634ZYB/cherimoya.fold_2.log deleted file mode 100644 index e34d09c5d7c380fce41fb2b54e38fa61d72ac109..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1944 26.577051877975464 3.5145444869995117 267.5960693359375 1.0924944877624512 388.5494689941406 0.13658639788627625 0.60757077 8.337206840515137 True -1 3888 21.496156454086304 0.38123488426208496 263.0814208984375 0.9571660757064819 344.984130859375 0.21328207850456238 0.7242503 3.803554058074951 True -2 5832 21.50312852859497 0.37871742248535156 272.0301513671875 0.5959861278533936 319.64788818359375 0.2424188107252121 0.7764196 1.9529160261154175 True -3 7776 21.46392011642456 0.6906673908233643 265.1304016113281 0.7255035638809204 313.8919677734375 0.24804601073265076 0.79430497 1.1116678714752197 True -4 9720 21.416065216064453 0.36493587493896484 223.2040252685547 0.5953938961029053 310.30072021484375 0.25471407175064087 0.79975986 0.9262685179710388 True -5 11664 21.46409511566162 0.5620408058166504 270.022705078125 0.4825980067253113 308.1423034667969 0.2589641213417053 0.80925065 0.8887699842453003 True -6 13608 21.49090027809143 6.835348606109619 224.21826171875 0.6557152271270752 306.9296569824219 0.26139697432518005 0.81552196 0.7911171317100525 True -7 15552 21.48290181159973 0.6309950351715088 228.29246520996094 1.0325589179992676 305.81597900390625 0.26307836174964905 0.8253795 0.6880552768707275 True -8 17496 21.461110830307007 0.366788387298584 232.68115234375 0.6272966861724854 304.71771240234375 0.26555147767066956 0.83036435 0.6507467031478882 True -9 19440 21.424001693725586 0.3666689395904541 248.18508911132812 0.4908505976200104 304.2330322265625 0.26656314730644226 0.8316024 0.6096150875091553 True -10 21384 21.428412437438965 0.3617360591888428 248.96017456054688 0.6826742887496948 303.29962158203125 0.2680542469024658 0.84002674 0.5672817826271057 True -11 23328 21.43968105316162 1.8047082424163818 230.56130981445312 0.4110507071018219 301.8154602050781 0.27055373787879944 0.8416756 0.5514934062957764 True -12 25272 21.025542974472046 0.3645505905151367 253.95941162109375 0.6917304992675781 301.2268981933594 0.27175620198249817 0.8464302 0.525058388710022 True -13 27216 21.073435306549072 0.3658738136291504 272.0859375 0.5011631846427917 299.9839172363281 0.2738124430179596 0.85134387 0.5083494186401367 True -14 29160 21.04105019569397 0.3680696487426758 221.07098388671875 0.29051363468170166 298.9332580566406 0.27668431401252747 0.8540966 0.48789364099502563 True -15 31104 21.045888662338257 0.3851604461669922 274.5433044433594 0.5263810157775879 298.69110107421875 0.2753974199295044 0.8555386 0.4787629246711731 True -16 33048 21.044614553451538 0.3606891632080078 295.53192138671875 0.5785600543022156 298.64764404296875 0.27590247988700867 0.8563739 0.4699821174144745 True -17 34992 21.041524410247803 0.6116523742675781 268.0838623046875 0.382663369178772 299.0426940917969 0.2752697169780731 0.85584563 0.4741361141204834 False -18 36936 21.08547616004944 0.3607609272003174 238.8307647705078 0.3477325439453125 299.2464599609375 0.27458399534225464 0.855131 0.48102208971977234 False -19 38880 21.057411193847656 0.3664264678955078 249.08267211914062 0.39207732677459717 299.6115417480469 0.27412015199661255 0.8540484 0.4854196608066559 False diff --git a/ENCSR634ZYB/cherimoya.fold_2.performance.tsv b/ENCSR634ZYB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d9f48fc755588b1f5501f13f3bfd30ad1f829ed7..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -298.64764404296875 0.4993910789489746 0.27590247988700867 0.08424142748117447 0.8563739061355591 0.8208604454994202 0.4699821174144745 \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_3.evaluate.json b/ENCSR634ZYB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 72d7c0d7ea2f6d039c6e130bb24a4cb27b359ba7..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586XTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_3.fit.json b/ENCSR634ZYB/cherimoya.fold_3.fit.json deleted file mode 100644 index 4a8a504ddd7c16e3220a1d9088bc048228d1b0c2..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF586XTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_3.log b/ENCSR634ZYB/cherimoya.fold_3.log deleted file mode 100644 index ce9178649c4ca5eedfe5496b53ad19ef72997b58..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1854 25.050533294677734 4.039212226867676 315.26220703125 0.9381885528564453 388.9660339355469 0.14264245331287384 0.60487664 9.133585929870605 True -1 3708 20.415342330932617 0.6213791370391846 247.93496704101562 1.1861774921417236 352.5363464355469 0.2119651734828949 0.7102001 4.270169258117676 True -2 5562 20.408239603042603 0.3867380619049072 231.5514678955078 0.6782933473587036 330.56695556640625 0.2390737533569336 0.74435025 2.4082558155059814 True -3 7416 20.411078453063965 0.44365477561950684 202.38011169433594 0.5551726222038269 324.9852600097656 0.24617016315460205 0.76060236 1.5888229608535767 True -4 9270 20.445244550704956 0.38793301582336426 230.25540161132812 0.743797779083252 323.22381591796875 0.24869880080223083 0.7738611 1.3017631769180298 True -5 11124 20.461732387542725 0.38631582260131836 235.64541625976562 0.7130927443504333 321.1680908203125 0.25290149450302124 0.7832201 1.141133427619934 True -6 12978 20.415523767471313 0.3867170810699463 254.0175323486328 0.9630177617073059 319.9031677246094 0.2546404004096985 0.7998229 0.9975711107254028 True -7 14832 20.450682163238525 0.42879176139831543 222.806640625 0.882510781288147 318.4505615234375 0.25712233781814575 0.80699676 0.8164472579956055 True -8 16686 20.24270725250244 0.39398956298828125 224.68246459960938 0.6132571697235107 316.4282531738281 0.2617661654949188 0.81131846 0.7333372831344604 True -9 18540 20.143684148788452 0.38604164123535156 250.51315307617188 0.64293372631073 315.7823486328125 0.2632894515991211 0.81481194 0.6874292492866516 True -10 20394 20.051462650299072 0.3788938522338867 259.6763000488281 0.6129938364028931 314.4761657714844 0.2647216022014618 0.81830204 0.6370604634284973 True -11 22248 20.06646180152893 0.37957072257995605 255.05581665039062 0.39965587854385376 314.1799011230469 0.2649606168270111 0.8220543 0.6267688870429993 True -12 24102 20.12300705909729 0.394972562789917 139.98419189453125 0.45680221915245056 312.6812744140625 0.26741936802864075 0.8268835 0.5925602316856384 True -13 25956 20.152775764465332 0.39061737060546875 210.70523071289062 0.7725988626480103 311.27252197265625 0.2691161036491394 0.8323154 0.5619280338287354 True -14 27810 20.24345827102661 0.39223217964172363 210.29299926757812 0.6453266143798828 309.9631042480469 0.271206796169281 0.83657867 0.5469335317611694 True -15 29664 20.342230319976807 0.3892514705657959 237.46414184570312 0.3441360890865326 309.51385498046875 0.2718392610549927 0.84263784 0.533984363079071 True -16 31518 20.15998601913452 0.3880496025085449 266.07244873046875 0.42750003933906555 309.20550537109375 0.27200132608413696 0.84506994 0.5284439325332642 True -17 33372 20.16396737098694 0.8201549053192139 230.62010192871094 0.39719605445861816 308.9472961425781 0.27210310101509094 0.8460914 0.5336278676986694 True -18 35226 20.13193392753601 0.3850667476654053 194.01358032226562 0.39837947487831116 310.12493896484375 0.26879173517227173 0.8443248 0.5423533916473389 False -19 37080 20.18268632888794 0.6050891876220703 265.14471435546875 0.33041805028915405 310.15081787109375 0.26926812529563904 0.8433012 0.5470981001853943 False diff --git a/ENCSR634ZYB/cherimoya.fold_3.performance.tsv b/ENCSR634ZYB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a5cfa0d120c230fde53bdff13315e43abf132b46..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.9472961425781 0.4988013505935669 0.27210313081741333 0.08952118456363678 0.8460913896560669 0.8043920993804932 0.5336278676986694 \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_4.evaluate.json b/ENCSR634ZYB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6beb11b2d16734ed7d713f565d3f16e770799592..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586XTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_4.fit.json b/ENCSR634ZYB/cherimoya.fold_4.fit.json deleted file mode 100644 index 9e2491cd28c3d3d74356057299c54010303ca3e5..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF586XTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR634ZYB/cherimoya.fold_4.log b/ENCSR634ZYB/cherimoya.fold_4.log deleted file mode 100644 index 3dd5f381898e537f7da7dfa5962ef7059955b864..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1842 24.80682396888733 3.6779191493988037 242.26351928710938 0.8200149536132812 346.01239013671875 0.12931714951992035 0.6128062 8.398670196533203 True -1 3684 20.337881088256836 0.3947329521179199 219.5729217529297 0.6808785200119019 313.13238525390625 0.19678808748722076 0.73356307 3.377946615219116 True -2 5526 20.3054301738739 0.766568660736084 238.21868896484375 0.9310122728347778 293.6357116699219 0.22188922762870789 0.764865 1.958424687385559 True -3 7368 20.33232808113098 0.35826802253723145 265.8914794921875 0.824701726436615 287.8219299316406 0.23086199164390564 0.78497213 1.2671260833740234 True -4 9210 20.297176361083984 0.3622171878814697 245.900634765625 0.9535583853721619 285.54852294921875 0.23505541682243347 0.79302084 0.9583319425582886 True -5 11052 20.3044650554657 1.402569055557251 200.10873413085938 0.6150202751159668 283.7873840332031 0.23764467239379883 0.7988136 0.8942673802375793 True -6 12894 20.05910348892212 0.39714646339416504 210.37257385253906 0.7907742857933044 282.2817077636719 0.24195046722888947 0.8033037 0.8452517986297607 True -7 14736 19.957468271255493 0.35953402519226074 232.2194061279297 0.5723352432250977 281.2408142089844 0.2445080578327179 0.80997866 0.7825642824172974 True -8 16578 19.95575785636902 1.754002332687378 231.78866577148438 0.6793707013130188 280.5948181152344 0.24619831144809723 0.8170137 0.670708417892456 True -9 18420 19.945782899856567 0.3499166965484619 292.20281982421875 0.5948031544685364 280.1515197753906 0.2468108981847763 0.8184636 0.6345553994178772 True -10 20262 19.91506004333496 0.353259801864624 218.6956787109375 0.4741995632648468 278.67938232421875 0.2493584156036377 0.827047 0.5829473733901978 True -11 22104 19.926393508911133 0.35373854637145996 211.64564514160156 0.4705269932746887 277.9794006347656 0.25047168135643005 0.83114725 0.5270059704780579 True -12 23946 19.93382716178894 0.3497781753540039 284.07147216796875 0.4066214859485626 277.3194274902344 0.25116536021232605 0.8341516 0.5003409385681152 True -13 25788 19.954179525375366 0.35640621185302734 202.50411987304688 0.4491956830024719 276.10205078125 0.2534525692462921 0.83945626 0.479631632566452 True -14 27630 19.929691076278687 0.3490257263183594 178.23208618164062 0.4805286228656769 276.0444030761719 0.2540791928768158 0.8425245 0.4687900245189667 True -15 29472 19.89847183227539 0.36084508895874023 225.94879150390625 0.3163154125213623 275.3367004394531 0.2552488446235657 0.8454328 0.45949697494506836 True -16 31314 19.921581268310547 0.3513004779815674 174.73269653320312 0.3583635687828064 275.1032409667969 0.25624629855155945 0.84770495 0.4565708339214325 True -17 33156 19.981327295303345 0.35573554039001465 180.66778564453125 0.35188961029052734 275.48809814453125 0.2552805244922638 0.84832174 0.4555417001247406 True -18 34998 19.958019971847534 0.3688507080078125 237.51638793945312 0.4078720808029175 275.7729797363281 0.2546200156211853 0.8467726 0.4590223729610443 False -19 36840 19.924891233444214 0.3513193130493164 199.50872802734375 0.48717963695526123 275.3570556640625 0.256111741065979 0.8460655 0.4626731872558594 False diff --git a/ENCSR634ZYB/cherimoya.fold_4.performance.tsv b/ENCSR634ZYB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index eb2fffa8f3802c23b9c76aeff732d081d653fc4a..0000000000000000000000000000000000000000 --- a/ENCSR634ZYB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.48809814453125 0.5135315656661987 0.2552805244922638 0.0740966722369194 0.8483217358589172 0.8017783164978027 0.4555417001247406 \ No newline at end of file diff --git a/ENCSR635AIF/cherimoya.fold_3.fit.json b/ENCSR635AIF/cherimoya.fold_3.fit.json deleted file mode 100644 index f9d19f521509361c8b47d38ec7706bcd5a3eb80c..0000000000000000000000000000000000000000 --- a/ENCSR635AIF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF110UZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635AIF/cherimoya.fold_4.log b/ENCSR635AIF/cherimoya.fold_4.log deleted file mode 100644 index 462ac7edca74f7c082ec819031ad9aa18543be59..0000000000000000000000000000000000000000 --- a/ENCSR635AIF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1276 17.752639770507812 3.8479795455932617 117.66664123535156 0.6600984334945679 164.2349090576172 0.24462853372097015 0.53319806 8.841336250305176 True -1 2552 14.035725831985474 0.26830434799194336 107.50936126708984 0.7743600606918335 145.68798828125 0.3072868287563324 0.5605476 4.329068660736084 True -2 3828 14.055353879928589 0.26157116889953613 117.64912414550781 1.1059167385101318 138.34596252441406 0.35413506627082825 0.62317926 2.1767618656158447 True -3 5104 14.038535118103027 0.2604939937591553 101.04815673828125 0.45452064275741577 134.59278869628906 0.3762160539627075 0.6395926 1.0997563600540161 True -4 6380 14.042327880859375 0.2596609592437744 95.08821868896484 0.74779212474823 133.02239990234375 0.3833998441696167 0.66522694 0.6967047452926636 True -5 7656 14.064316511154175 0.2614479064941406 105.63691711425781 0.7470235824584961 132.08885192871094 0.38797879219055176 0.6742111 0.5822296738624573 True -6 8932 14.064993381500244 0.262286901473999 108.95397186279297 0.526223361492157 131.5135040283203 0.3915737569332123 0.6888817 0.5194863080978394 True -7 10208 14.04737663269043 0.2617785930633545 88.64460754394531 0.6242884993553162 131.18450927734375 0.39366868138313293 0.6929031 0.5007759928703308 True -8 11484 14.036831617355347 0.27524876594543457 101.23956298828125 0.7137764692306519 130.89698791503906 0.3955575227737427 0.7009373 0.47366565465927124 True -9 12760 14.052185535430908 0.2716958522796631 98.70901489257812 0.5224059820175171 130.63014221191406 0.3971301019191742 0.7044941 0.45038720965385437 True -10 14036 14.074368000030518 0.25975918769836426 105.1920166015625 0.3833397328853607 130.33682250976562 0.39912572503089905 0.7088541 0.4424988925457001 True -11 15312 14.100708723068237 0.26146745681762695 97.45276641845703 0.41506868600845337 130.06837463378906 0.40081900358200073 0.7109432 0.4358260929584503 True -12 16588 14.025699138641357 0.26106834411621094 138.43545532226562 0.4058656096458435 129.78350830078125 0.40221717953681946 0.7174797 0.4191431403160095 True -13 17864 14.028434038162231 0.2614707946777344 100.87556457519531 0.5572336316108704 129.63755798339844 0.4031270742416382 0.72000414 0.41680121421813965 True -14 19140 14.072437047958374 0.2614452838897705 95.563720703125 0.35987377166748047 129.48580932617188 0.4038419723510742 0.7256384 0.4165467619895935 True -15 20416 14.084805965423584 0.25989389419555664 111.18172454833984 0.39964550733566284 129.43576049804688 0.4040590524673462 0.72830695 0.4193938672542572 True -16 21692 14.087218284606934 0.2622551918029785 103.00556182861328 0.2844873070716858 129.46315002441406 0.403497576713562 0.728424 0.42137086391448975 True -17 22968 14.082494258880615 0.2592809200286865 102.7109375 0.4175906777381897 129.58404541015625 0.40248391032218933 0.72965264 0.42816707491874695 True -18 24244 14.026873111724854 0.26378846168518066 93.35055541992188 0.425889253616333 129.72535705566406 0.4015856981277466 0.72912437 0.4352148771286011 False -19 25520 14.052944421768188 0.26103663444519043 101.78247833251953 0.21548782289028168 129.77975463867188 0.4009495973587036 0.72610074 0.44089820981025696 False diff --git a/ENCSR635CAC/cherimoya.fold_0.evaluate.json b/ENCSR635CAC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7f6347d153a537d86cd0c47bc434805455212e14..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF849MLS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_0.fit.json b/ENCSR635CAC/cherimoya.fold_0.fit.json deleted file mode 100644 index a64bc3ddcc66af45c490006fde577e8813933a88..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF849MLS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_0.log b/ENCSR635CAC/cherimoya.fold_0.log deleted file mode 100644 index 7e1e170828d76764bda756b553c813fe1bbaa49c..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1901 25.624877452850342 3.943262815475464 338.78216552734375 0.6310225129127502 447.5743408203125 0.4394916892051697 0.5386247 11.491607666015625 True -1 3802 21.133687734603882 0.40915656089782715 267.1163330078125 0.7234876155853271 383.58154296875 0.551748514175415 0.63716656 3.969968318939209 True -2 5703 21.09256672859192 0.39011096954345703 282.5253601074219 0.797687292098999 365.8049011230469 0.5950047373771667 0.64244115 1.0712178945541382 True -3 7604 21.10269808769226 0.38881635665893555 247.18453979492188 0.47172561287879944 360.37274169921875 0.6052739024162292 0.6520229 0.6469281315803528 True -4 9505 21.09618377685547 2.4278385639190674 282.64190673828125 0.7097407579421997 358.0910949707031 0.6099599599838257 0.6575568 0.5618302226066589 True -5 11406 21.1195011138916 0.388507604598999 310.503173828125 0.4471821188926697 356.8503112792969 0.6132323145866394 0.6608314 0.5171323418617249 True -6 13307 21.330317735671997 0.6604018211364746 263.0181579589844 0.5989987850189209 355.7759704589844 0.6154808402061462 0.6692185 0.5007470846176147 True -7 15208 21.58495831489563 18.101259231567383 303.8021240234375 0.4358827471733093 355.3050231933594 0.6173751354217529 0.6678679 0.49993830919265747 False -8 17109 24.80630588531494 8.772650957107544 287.2841796875 0.4189842939376831 354.3060302734375 0.6196631193161011 0.671792 0.48054760694503784 True -9 19010 21.128309965133667 2.3135311603546143 259.385498046875 0.369576096534729 353.0841979980469 0.622235119342804 0.679748 0.4632396399974823 True -10 20911 21.15014958381653 1.7005345821380615 299.89898681640625 0.4128706157207489 352.0235900878906 0.6244245767593384 0.6857214 0.4448482096195221 True -11 22812 21.143213272094727 1.2383217811584473 270.2937316894531 0.40369606018066406 351.3181457519531 0.6262335777282715 0.6921856 0.42928412556648254 True -12 24713 21.16407012939453 1.3924436569213867 274.158203125 0.38335293531417847 350.4839782714844 0.6281901597976685 0.7000388 0.41578131914138794 True -13 26614 21.12183952331543 1.1899826526641846 261.02227783203125 0.509295642375946 349.973388671875 0.6294637322425842 0.70402217 0.41508913040161133 True -14 28515 21.166276693344116 2.3622066974639893 281.7564697265625 0.29141154885292053 349.2804260253906 0.6303998231887817 0.71120685 0.413186639547348 True -15 30416 21.097488403320312 29.414451360702515 277.23284912109375 0.29280567169189453 349.1716003417969 0.630831241607666 0.7146799 0.4107721149921417 True -16 32317 23.739745616912842 0.4090735912322998 297.5031433105469 0.3280588984489441 349.1242370605469 0.6304827332496643 0.7098052 0.42138680815696716 False -17 34218 21.061298370361328 0.391035795211792 231.26907348632812 0.2932445704936981 349.3854675292969 0.6298487186431885 0.70827615 0.4322592318058014 False -18 36119 26.11549949645996 20.401052236557007 287.47515869140625 0.22487790882587433 349.5021057128906 0.6290920972824097 0.7047648 0.445701539516449 False -19 38020 21.168725728988647 1.083014965057373 296.4466552734375 0.164139986038208 349.62420654296875 0.6286289095878601 0.69961286 0.4543934166431427 False diff --git a/ENCSR635CAC/cherimoya.fold_0.performance.tsv b/ENCSR635CAC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b8b549118e332eeb20abeb6bd03f5846e341acd6..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -349.1716003417969 0.3007899522781372 0.630831241607666 0.23057420551776886 0.7146798968315125 0.6666041612625122 0.4107721149921417 \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_1.evaluate.json b/ENCSR635CAC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b93b96e1accc944284d6363357b89f4060991425..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF849MLS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_1.fit.json b/ENCSR635CAC/cherimoya.fold_1.fit.json deleted file mode 100644 index 3490090ed7c2bfca974da64f510f923091d616b7..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF849MLS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_1.log b/ENCSR635CAC/cherimoya.fold_1.log deleted file mode 100644 index 9a33615b5e9bee05859cf3b6f2a137733c90aa7e..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1930 25.97576928138733 3.3943233489990234 352.0042724609375 0.7850491404533386 450.5368957519531 0.45015621185302734 0.523235 9.642742156982422 True -1 3860 21.444901943206787 0.45035672187805176 285.3074035644531 0.6898261308670044 390.1199645996094 0.5589076280593872 0.64028573 3.1519935131073 True -2 5790 21.46562933921814 0.44809436798095703 287.3653869628906 0.6422767639160156 375.7365417480469 0.5916560292243958 0.6559703 0.9598336815834045 True -3 7720 21.45939564704895 1.3822720050811768 286.004638671875 0.4993816614151001 371.8656921386719 0.5998429656028748 0.6560826 0.7112740874290466 True -4 9650 21.3310809135437 0.4483156204223633 279.32904052734375 0.8062976598739624 370.033935546875 0.6037681698799133 0.66863406 0.6055969595909119 True -5 11580 21.035717010498047 0.45424652099609375 287.83416748046875 0.3684571087360382 369.1041564941406 0.6063466668128967 0.6751781 0.580016016960144 True -6 13510 21.021262407302856 12.729912042617798 282.25872802734375 0.7570573091506958 367.9619445800781 0.6088815331459045 0.67805284 0.5290476679801941 True -7 15440 24.57422137260437 0.4775571823120117 233.2455291748047 0.5092841386795044 367.2260437011719 0.6108651161193848 0.6820043 0.513999342918396 True -8 17370 21.028671741485596 0.45342040061950684 304.7850341796875 0.39571672677993774 366.3389892578125 0.6128926873207092 0.6882246 0.49535492062568665 True -9 19300 21.191956043243408 0.4478023052215576 256.06585693359375 0.3503609597682953 365.3163757324219 0.6151740550994873 0.6938944 0.46793317794799805 True -10 21230 21.223140001296997 32.94452214241028 258.1679992675781 0.4275926947593689 364.6597595214844 0.6168206334114075 0.7002699 0.4410323202610016 True -11 23160 21.32735276222229 0.4554128646850586 262.77044677734375 0.406022310256958 363.7591552734375 0.6184829473495483 0.7068765 0.4375869929790497 True -12 25090 21.060292720794678 19.37653422355652 242.03012084960938 0.41896533966064453 363.1412048339844 0.6198426485061646 0.7149924 0.41266167163848877 True -13 27020 21.341245889663696 0.7106258869171143 283.20562744140625 0.4915482997894287 362.4296875 0.6214523911476135 0.722622 0.39975836873054504 True -14 28950 21.277495861053467 32.34462356567383 265.16973876953125 0.2990162968635559 361.9216613769531 0.6223896145820618 0.72840613 0.3981298506259918 True -15 30880 24.27396249771118 0.44362664222717285 279.34619140625 0.406286358833313 361.7105712890625 0.6229454278945923 0.7317698 0.3905060887336731 True -16 32810 21.03808903694153 0.4617917537689209 245.96429443359375 0.2676430940628052 361.455322265625 0.6230307817459106 0.7320047 0.3895954191684723 True -17 34740 21.180535554885864 0.4825117588043213 251.42138671875 0.2627216577529907 361.5791320800781 0.6226779222488403 0.73090434 0.3934805691242218 False -18 36670 21.202309370040894 0.44172215461730957 273.8133544921875 0.2638704180717468 361.6107482910156 0.6221270561218262 0.72809154 0.3963806927204132 False -19 38600 21.164660692214966 0.44467663764953613 278.0621337890625 0.23896387219429016 361.6827697753906 0.621973991394043 0.72543985 0.3992851674556732 False diff --git a/ENCSR635CAC/cherimoya.fold_1.performance.tsv b/ENCSR635CAC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 87085e27681a85e6f30ea4709c3539fe30f3eaee..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.455322265625 0.30093351006507874 0.6230307817459106 0.23398378491401672 0.732004702091217 0.7152982950210571 0.3895954191684723 \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_2.evaluate.json b/ENCSR635CAC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5fee081d70513daa618a1659cef794069d7a3990..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF849MLS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_2.fit.json b/ENCSR635CAC/cherimoya.fold_2.fit.json deleted file mode 100644 index ec23e4bdf2fd24f6d204adb1888a4b671729eaf1..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF849MLS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_2.log b/ENCSR635CAC/cherimoya.fold_2.log deleted file mode 100644 index c4506a10f531bc98d499f57b5383eaabfce31226..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2027 26.95379137992859 3.3287978172302246 285.18878173828125 0.6385387182235718 444.0312805175781 0.44743582606315613 0.5443588 10.00322151184082 True -1 4054 22.54940104484558 0.3800034523010254 326.6263427734375 0.54859459400177 383.3066101074219 0.5592330098152161 0.65150815 3.1898343563079834 True -2 6081 22.525280475616455 0.3680455684661865 298.7856750488281 0.6388835906982422 368.7491455078125 0.5930966138839722 0.6541439 1.1296674013137817 True -3 8108 22.502341508865356 2.0776844024658203 231.9445037841797 0.5990219712257385 364.37713623046875 0.601466715335846 0.6710701 0.7431342601776123 True -4 10135 22.535792589187622 0.3638758659362793 282.5027160644531 0.5475836396217346 362.01763916015625 0.606610119342804 0.6761299 0.6114417314529419 True -5 12162 22.512025356292725 0.3629343509674072 288.2880859375 0.717522144317627 360.8648986816406 0.6093369722366333 0.67642003 0.583464503288269 True -6 14189 22.53658413887024 0.3688313961029053 311.70794677734375 0.5115150213241577 359.6199951171875 0.612015962600708 0.68289953 0.5732145309448242 True -7 16216 22.552237033843994 20.28730869293213 324.52850341796875 0.4320174753665924 358.5570983886719 0.614692747592926 0.687511 0.5488693118095398 True -8 18243 23.9725501537323 0.3776676654815674 261.24957275390625 0.36527714133262634 357.5595703125 0.6164563298225403 0.6903903 0.5193255543708801 True -9 20270 22.525623321533203 0.36654186248779297 265.7627868652344 0.563042402267456 356.9560546875 0.6181783080101013 0.695746 0.5030136108398438 True -10 22297 22.55685043334961 0.36522817611694336 285.56622314453125 0.33331042528152466 356.13409423828125 0.6199116706848145 0.7022988 0.47196096181869507 True -11 24324 22.5118145942688 0.3635122776031494 297.3153991699219 0.6520719528198242 355.5014953613281 0.6213417649269104 0.7041522 0.46958670020103455 True -12 26351 22.04446268081665 0.3623533248901367 282.0871276855469 0.3756011426448822 354.9530334472656 0.6225903034210205 0.7087063 0.4622894823551178 True -13 28378 22.064090967178345 0.36690711975097656 242.66207885742188 0.4189751148223877 354.4653625488281 0.6237974762916565 0.71300685 0.44685691595077515 True -14 30405 22.06425189971924 0.3644394874572754 237.63864135742188 0.537506639957428 353.8907470703125 0.6246814131736755 0.71851915 0.43917837738990784 True -15 32432 22.052197456359863 0.3652365207672119 303.8027038574219 0.2662472724914551 353.9130554199219 0.6250292658805847 0.7204224 0.435869425535202 True -16 34459 22.081972122192383 0.37733960151672363 320.2761535644531 0.3390793800354004 353.81463623046875 0.6248704791069031 0.72265065 0.4294275641441345 True -17 36486 22.0479519367218 0.3735032081604004 262.4207458496094 0.19941477477550507 353.9022216796875 0.6246272921562195 0.72152597 0.4288260042667389 False -18 38513 22.036580801010132 0.36953067779541016 254.0733642578125 0.2065393626689911 354.0657958984375 0.624045729637146 0.7171173 0.4327462315559387 False -19 40540 23.59228777885437 10.747240543365479 227.44906616210938 0.31984424591064453 354.1427001953125 0.623719334602356 0.71560895 0.44200241565704346 False diff --git a/ENCSR635CAC/cherimoya.fold_2.performance.tsv b/ENCSR635CAC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 673b6eaa6c537ec0012849a85820c3a30df58ca2..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -353.81463623046875 0.30268293619155884 0.6248704791069031 0.23206739127635956 0.7226506471633911 0.6898376941680908 0.4294275641441345 \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_3.evaluate.json b/ENCSR635CAC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4c147500bc21405aba5514f64d9449b8ef39a1ca..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF849MLS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_3.fit.json b/ENCSR635CAC/cherimoya.fold_3.fit.json deleted file mode 100644 index 9802aba28f4dfaaf6359c4e5bfce1bc43a254bcb..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF849MLS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_3.log b/ENCSR635CAC/cherimoya.fold_3.log deleted file mode 100644 index 45013aa7cd0b40cf5c605d122164e46804b0d4b3..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1965 26.5151309967041 3.346874952316284 267.30621337890625 0.8729395866394043 454.3324279785156 0.44772273302078247 0.5328746 10.569440841674805 True -1 3930 21.968849897384644 0.4209632873535156 272.6827697753906 0.6995274424552917 389.6558837890625 0.5591698884963989 0.61555415 4.003565311431885 True -2 5895 21.867936611175537 0.41153573989868164 331.30902099609375 0.599501371383667 371.3451843261719 0.6004314422607422 0.6118956 1.3112494945526123 False -3 7860 21.815083980560303 0.41324687004089355 254.7646942138672 0.5555462837219238 366.65509033203125 0.6089837551116943 0.6264527 0.8005675673484802 True -4 9825 22.16916823387146 0.41727113723754883 284.34063720703125 0.4028345048427582 365.52142333984375 0.6112569570541382 0.640626 0.6969681978225708 True -5 11790 21.844254732131958 0.41704320907592773 295.1568603515625 0.579505205154419 364.5147399902344 0.6141324639320374 0.64743704 0.6558818221092224 True -6 13755 21.856935024261475 0.41950201988220215 283.3784484863281 0.44941872358322144 363.7099609375 0.6159637570381165 0.6509743 0.6104726195335388 True -7 15720 21.901070594787598 0.419086217880249 284.509765625 0.3215104341506958 362.7350769042969 0.618460476398468 0.6583271 0.5626642107963562 True -8 17685 21.878655910491943 0.40967464447021484 251.32310485839844 0.4305723309516907 361.685302734375 0.6207329034805298 0.663323 0.5280708074569702 True -9 19650 21.846984148025513 0.41225743293762207 259.0466613769531 0.36321255564689636 360.6927490234375 0.6229174137115479 0.6747096 0.4954455494880676 True -10 21615 21.876360416412354 0.4071385860443115 270.1718444824219 0.43841445446014404 359.9684143066406 0.6248633861541748 0.6793446 0.48456206917762756 True -11 23580 21.811774492263794 0.41692042350769043 305.00994873046875 0.40242868661880493 359.2743225097656 0.6261837482452393 0.68431246 0.46947532892227173 True -12 25545 21.83725380897522 0.41165947914123535 253.82398986816406 0.4430762827396393 358.4980163574219 0.6281790733337402 0.695733 0.45124703645706177 True -13 27510 21.90070652961731 17.458512544631958 316.54046630859375 0.34519246220588684 357.5630187988281 0.6297622919082642 0.7007471 0.4372490346431732 True -14 29475 21.871598720550537 0.4280064105987549 244.97927856445312 0.5403614640235901 357.1110534667969 0.6306201815605164 0.7063103 0.43006402254104614 True -15 31440 21.837316036224365 0.419036865234375 292.16748046875 0.2893027067184448 356.82452392578125 0.6312462687492371 0.71092594 0.4246656596660614 True -16 33405 21.825214624404907 0.41583824157714844 254.27171325683594 0.38884615898132324 356.7260437011719 0.6311438679695129 0.7128869 0.4258072078227997 True -17 35370 21.877933263778687 0.41997456550598145 232.41900634765625 0.2079777717590332 356.9361267089844 0.6304885149002075 0.71117616 0.43636947870254517 False -18 37335 21.86790132522583 14.108040571212769 231.13925170898438 0.19492009282112122 357.1363220214844 0.6298227310180664 0.70779717 0.4485510289669037 False -19 39300 22.091131925582886 9.177126169204712 251.90383911132812 0.24604937434196472 357.3447570800781 0.6293179392814636 0.7053115 0.46093904972076416 False diff --git a/ENCSR635CAC/cherimoya.fold_3.performance.tsv b/ENCSR635CAC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9e28f7f8828faf48e00e2f0ea7159ac892adb46d..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -356.7260437011719 0.29829028248786926 0.6311439275741577 0.23551878333091736 0.7128869295120239 0.6797081828117371 0.4258072078227997 \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_4.evaluate.json b/ENCSR635CAC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1606a91374e1d2cd92e67a8f849e0c2df1e7576d..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF849MLS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_4.fit.json b/ENCSR635CAC/cherimoya.fold_4.fit.json deleted file mode 100644 index 4b25b040d5dda02fda5c9bb7c31f629bdc4f770d..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF849MLS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635CAC/cherimoya.fold_4.log b/ENCSR635CAC/cherimoya.fold_4.log deleted file mode 100644 index 7a349367b2533e25acf87263cd8077a592444172..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2000 25.681171417236328 3.6959452629089355 301.1318359375 0.8771580457687378 441.50732421875 0.44507429003715515 0.55849993 10.092307090759277 True -1 4000 22.02027702331543 0.4128108024597168 279.038818359375 0.8279780149459839 380.8446960449219 0.5587598085403442 0.6253225 3.4972081184387207 True -2 6000 22.003839015960693 0.3813896179199219 241.51852416992188 0.5453199148178101 363.5718078613281 0.599594235420227 0.6260304 1.0174084901809692 True -3 8000 22.008239030838013 0.38593077659606934 278.7357177734375 0.6655992269515991 359.0359802246094 0.6076982617378235 0.64967537 0.6368050575256348 True -4 10000 21.995760679244995 0.3866863250732422 316.28204345703125 0.6769819855690002 357.658203125 0.6107212901115417 0.65332645 0.6085370182991028 True -5 12000 21.995596647262573 0.4137227535247803 247.4261474609375 0.5394465327262878 356.3703918457031 0.6141077876091003 0.6623659 0.5716798305511475 True -6 14000 21.934500217437744 0.3897979259490967 272.0820007324219 0.4702715277671814 355.4809265136719 0.6162332892417908 0.66472083 0.5523908138275146 True -7 16000 21.99281668663025 0.3842465877532959 327.93310546875 0.45202094316482544 354.4796447753906 0.6183841824531555 0.67405057 0.5278629064559937 True -8 18000 21.935014486312866 0.39176297187805176 271.52655029296875 0.61102294921875 353.6253662109375 0.6200652122497559 0.6843016 0.4728674292564392 True -9 20000 21.939078092575073 0.39362430572509766 291.38482666015625 0.40179771184921265 352.88397216796875 0.6216909885406494 0.6910751 0.46648091077804565 True -10 22000 21.934200763702393 0.38710737228393555 290.4186096191406 0.5521562099456787 352.1282958984375 0.6235933303833008 0.6918143 0.4639569818973541 True -11 24000 22.017980098724365 0.38272666931152344 296.963623046875 0.5633941888809204 351.4500732421875 0.6253101229667664 0.7027036 0.4299687147140503 True -12 26000 21.97156262397766 0.38303637504577637 277.367431640625 0.4446081519126892 350.4367980957031 0.6274347901344299 0.7036254 0.43394142389297485 True -13 28000 21.933876752853394 0.3846323490142822 295.0182800292969 0.43078458309173584 349.8851318359375 0.6287978887557983 0.712087 0.42002251744270325 True -14 30000 21.752259969711304 0.6748919486999512 237.53443908691406 0.4169444143772125 349.3641052246094 0.6296834945678711 0.71900403 0.41095808148384094 True -15 32000 21.60191512107849 0.9972612857818604 291.17218017578125 0.2814255356788635 348.91748046875 0.630695104598999 0.72594935 0.40690600872039795 True -16 34000 21.563905954360962 0.654644250869751 309.7100524902344 0.2858278751373291 348.9795837402344 0.6306908130645752 0.7253673 0.4049448072910309 False -17 36000 21.579817533493042 1.6017520427703857 289.4737548828125 0.20322373509407043 349.04290771484375 0.6302670836448669 0.7261258 0.41499942541122437 True -18 38000 21.615058183670044 1.250715732574463 280.49444580078125 0.26995202898979187 349.29815673828125 0.6297688484191895 0.7215461 0.42589977383613586 False -19 40000 21.625582456588745 0.8741662502288818 268.209228515625 0.3105531334877014 349.35662841796875 0.6294628977775574 0.7203185 0.4293524920940399 False diff --git a/ENCSR635CAC/cherimoya.fold_4.performance.tsv b/ENCSR635CAC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 650c166c42b593bd49f20c5dafcce89b60e5fcc8..0000000000000000000000000000000000000000 --- a/ENCSR635CAC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -349.04290771484375 0.301602303981781 0.6302669644355774 0.23069000244140625 0.7261257767677307 0.671865701675415 0.41499942541122437 \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_0.evaluate.json b/ENCSR635GDW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 08b2ab1e5239edb9dff98d433eaa6f2155395a8d..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF734WMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_0.fit.json b/ENCSR635GDW/cherimoya.fold_0.fit.json deleted file mode 100644 index df4238119d1e4ae9f939d2ada472f4a2acd5f166..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF734WMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_0.log b/ENCSR635GDW/cherimoya.fold_0.log deleted file mode 100644 index b86c78238474f0484540e31e2e1a1d4083865391..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 36.33695387840271 3.6821322441101074 477.85491943359375 0.45925846695899963 684.9873046875 0.2933180034160614 0.76401687 6.127043724060059 True -1 5526 30.310521364212036 0.5806479454040527 537.567626953125 0.5642331838607788 618.31298828125 0.35765495896339417 0.80846405 1.5689953565597534 True -2 8289 30.333333492279053 0.5663723945617676 468.57293701171875 0.558509886264801 605.1085815429688 0.36986038088798523 0.8190672 0.7074769139289856 True -3 11052 30.348368644714355 0.5662989616394043 530.4808959960938 0.4588622450828552 599.9249267578125 0.3747904598712921 0.8287988 0.632459819316864 True -4 13815 29.95575499534607 0.7446203231811523 374.6141357421875 0.3337588906288147 594.498779296875 0.37789952754974365 0.83508074 0.5373954176902771 True -5 16578 29.7849760055542 0.5616822242736816 568.1549072265625 0.5310827493667603 590.6148071289062 0.3826025724411011 0.841817 0.43120846152305603 True -6 19341 29.754956007003784 0.5749657154083252 439.6942138671875 0.33605825901031494 588.8150634765625 0.38384008407592773 0.8448118 0.45320209860801697 True -7 22104 29.75138282775879 0.568626880645752 496.52655029296875 0.32730215787887573 586.2864990234375 0.38724756240844727 0.8470925 0.4328237771987915 True -8 24867 29.899031162261963 0.5710041522979736 468.925048828125 0.34890806674957275 584.8157348632812 0.3890804350376129 0.8510508 0.4044487476348877 True -9 27630 31.07323718070984 9.025741338729858 438.03179931640625 0.3287341594696045 580.33544921875 0.3942946791648865 0.8555618 0.36177927255630493 True -10 30393 29.804152011871338 25.774109840393066 448.3291931152344 0.27813175320625305 576.575927734375 0.397981733083725 0.86223835 0.342442125082016 True -11 33156 30.566762924194336 0.5893464088439941 474.19775390625 0.5669686198234558 574.9338989257812 0.3994050920009613 0.866069 0.3363213837146759 True -12 35919 29.838427782058716 0.5765321254730225 436.8065185546875 0.43602272868156433 571.94384765625 0.4027680456638336 0.87128323 0.3179876208305359 True -13 38682 34.00420522689819 4.24727988243103 384.6717529296875 0.2969357967376709 572.0269165039062 0.40201839804649353 0.8763484 0.298129677772522 True -14 41445 29.75405764579773 1.0594666004180908 577.7294921875 0.28308746218681335 571.1310424804688 0.4032459259033203 0.8815069 0.2835935950279236 True -15 44208 29.799517393112183 0.9228231906890869 520.352294921875 0.4007764160633087 568.4619140625 0.40500736236572266 0.88499045 0.27028563618659973 True -16 46971 29.796253442764282 0.5633697509765625 382.89727783203125 0.2196805477142334 567.8512573242188 0.4067845642566681 0.886133 0.2635888159275055 True -17 49734 29.678045749664307 0.562427282333374 440.15228271484375 0.13072672486305237 568.0078735351562 0.4058021008968353 0.88639873 0.260964572429657 True -18 52497 29.87231206893921 0.5667343139648438 471.55084228515625 0.23490828275680542 568.7314453125 0.4047674834728241 0.8860517 0.25921735167503357 False -19 55260 29.8302264213562 0.5663144588470459 382.61920166015625 0.17738047242164612 568.202880859375 0.4057515561580658 0.8861277 0.2606741786003113 False diff --git a/ENCSR635GDW/cherimoya.fold_0.performance.tsv b/ENCSR635GDW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b1d5ba4beaa350f2a0cd25bfbc0a459d6097d41d..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -568.0078735351562 0.38412773609161377 0.40580207109451294 0.16129782795906067 0.8863987326622009 0.8525099754333496 0.260964572429657 \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_1.evaluate.json b/ENCSR635GDW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 755bd48743dc9678a7ff88326aa6252b8610dd58..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF734WMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_1.fit.json b/ENCSR635GDW/cherimoya.fold_1.fit.json deleted file mode 100644 index 8592b4a1bcea71fbf4af08df5beea72194d0ef5e..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF734WMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_1.log b/ENCSR635GDW/cherimoya.fold_1.log deleted file mode 100644 index 72feff87a2ccbae7aa9c5629a7d2018066e3ad20..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2713 34.55259346961975 3.8116705417633057 498.49267578125 0.4490078091621399 803.080322265625 0.29471829533576965 0.7525006 6.117141246795654 True -1 5426 29.902436017990112 0.7070205211639404 562.468994140625 0.4898237884044647 711.9833374023438 0.36942288279533386 0.8122617 1.6757004261016846 True -2 8139 29.857550382614136 0.6963725090026855 413.5097351074219 0.47552329301834106 694.4463500976562 0.3780808448791504 0.82452095 0.798595666885376 True -3 10852 29.778372764587402 0.6970973014831543 433.78515625 0.3413488268852234 685.3156127929688 0.38585832715034485 0.83044803 0.6252782344818115 True -4 13565 29.855058908462524 3.029676675796509 545.0869140625 0.6007353663444519 679.8844604492188 0.38990867137908936 0.83704627 0.6560268998146057 True -5 16278 29.268885850906372 0.7054338455200195 498.7659606933594 0.3855209946632385 673.7569580078125 0.3954830467700958 0.84118295 0.634766697883606 True -6 18991 29.18045663833618 0.6789450645446777 586.678466796875 0.5398823022842407 672.6236572265625 0.3953593671321869 0.8480886 0.5260331630706787 True -7 21704 29.26362109184265 0.6914253234863281 558.8668823242188 0.3289461135864258 667.2461547851562 0.40103256702423096 0.8540226 0.5172526836395264 True -8 24417 29.260011911392212 38.08412289619446 427.0437316894531 0.4940580725669861 664.4006958007812 0.4043464660644531 0.8562284 0.508479118347168 True -9 27130 29.643231868743896 0.6914947032928467 483.70941162109375 0.31564533710479736 660.9775390625 0.40636301040649414 0.863444 0.46633848547935486 True -10 29843 29.170181274414062 6.672308683395386 412.1289978027344 0.2500043511390686 657.1256713867188 0.41113221645355225 0.8655598 0.4492129981517792 True -11 32556 29.16828989982605 0.7109687328338623 443.5018005371094 0.29975855350494385 651.4892578125 0.41594019532203674 0.8748924 0.38555678725242615 True -12 35269 29.60299062728882 0.6920497417449951 543.5588989257812 0.2433207929134369 651.0556030273438 0.41538310050964355 0.8795471 0.36643725633621216 True -13 37982 29.482364416122437 42.26523995399475 462.07781982421875 0.2550908327102661 648.0594482421875 0.4184615910053253 0.8827457 0.33374178409576416 True -14 40695 29.285115480422974 0.7060844898223877 382.7047424316406 0.24176976084709167 645.391845703125 0.42029502987861633 0.8871813 0.3189248740673065 True -15 43408 29.189313173294067 0.7096250057220459 459.63214111328125 0.15640951693058014 646.098388671875 0.4187639653682709 0.8911522 0.30261364579200745 True -16 46121 30.093626022338867 31.501065969467163 436.5638427734375 0.27567148208618164 643.4641723632812 0.42236822843551636 0.89326805 0.2934868633747101 True -17 48834 29.326119899749756 0.7117018699645996 381.6656494140625 0.29767924547195435 643.04150390625 0.4221944510936737 0.8930816 0.28597259521484375 False -18 51547 29.294141054153442 0.9195587635040283 453.00927734375 0.18216654658317566 644.0706176757812 0.4216160774230957 0.8922362 0.2852340638637543 False -19 54260 29.189866542816162 30.671138763427734 403.89056396484375 0.25302308797836304 645.3673706054688 0.4195343554019928 0.8918596 0.2863946855068207 False diff --git a/ENCSR635GDW/cherimoya.fold_1.performance.tsv b/ENCSR635GDW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4135dec50585ad2ac59ac68133b162c8e7436f83..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -643.4641723632812 0.36946046352386475 0.42236825823783875 0.1815563440322876 0.8932680487632751 0.8771935105323792 0.2934868633747101 \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_2.evaluate.json b/ENCSR635GDW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5382d1f28cd1de9f336f774049cefaac6d06231d..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF734WMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_2.fit.json b/ENCSR635GDW/cherimoya.fold_2.fit.json deleted file mode 100644 index d8a12167de2bae8cb811c0683d8f46b51a997c8e..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF734WMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_2.log b/ENCSR635GDW/cherimoya.fold_2.log deleted file mode 100644 index f46b0cbd386284b01b20092e2252131270185913..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2875 36.078434467315674 3.5619826316833496 551.1630859375 0.5627387166023254 711.535888671875 0.2901726961135864 0.7559019 5.629395008087158 True -1 5750 31.710991144180298 1.4822227954864502 510.8589782714844 0.3033257722854614 634.2494506835938 0.3580407500267029 0.80636996 1.312882423400879 True -2 8625 31.624372482299805 0.5710844993591309 496.3332214355469 0.7975307703018188 622.812255859375 0.3681676983833313 0.81840175 0.7268505692481995 True -3 11500 31.60851502418518 0.5627520084381104 523.08447265625 0.3876301646232605 616.04541015625 0.3730393946170807 0.8278399 0.6069557666778564 True -4 14375 31.659931898117065 0.5732390880584717 401.9142761230469 0.5243526697158813 610.3103637695312 0.3785015940666199 0.83659273 0.49734383821487427 True -5 17250 31.7011878490448 1.0088701248168945 523.73291015625 0.4124141037464142 608.8023681640625 0.3794204890727997 0.8385744 0.4698972702026367 True -6 20125 30.995973348617554 28.34621262550354 458.94219970703125 0.3254661560058594 603.9231567382812 0.385383278131485 0.84182954 0.4737109839916229 True -7 23000 30.947999954223633 18.52963423728943 480.53985595703125 0.3937912881374359 602.5072021484375 0.3861396610736847 0.8476075 0.4527888298034668 True -8 25875 31.008769989013672 2.79943585395813 421.5732421875 0.4913223385810852 599.6834716796875 0.38935601711273193 0.85177505 0.41480204463005066 True -9 28750 31.43029236793518 0.5657453536987305 437.78314208984375 0.3664274215698242 595.8546142578125 0.3930591940879822 0.85641736 0.3986913561820984 True -10 31625 30.99159002304077 0.5589780807495117 344.32696533203125 0.3776403069496155 593.2410278320312 0.3963344395160675 0.85897267 0.38321956992149353 True -11 34500 30.95969009399414 0.5596706867218018 376.7615966796875 0.22632922232151031 589.751708984375 0.3997352719306946 0.8658087 0.3493541181087494 True -12 37375 30.9040744304657 0.5592727661132812 426.6798095703125 0.33751124143600464 588.9828491210938 0.4002934694290161 0.8689697 0.33775100111961365 True -13 40250 30.937001943588257 0.5533301830291748 441.4867248535156 0.2725733518600464 587.2778930664062 0.4020029604434967 0.87587357 0.32033079862594604 True -14 43125 30.899320363998413 0.5613024234771729 525.7161865234375 0.31280645728111267 585.3344116210938 0.40416598320007324 0.87760574 0.29869866371154785 True -15 46000 30.846792697906494 0.5596864223480225 445.45367431640625 0.28064703941345215 584.9351806640625 0.40472909808158875 0.8817228 0.28294768929481506 True -16 48875 30.828917026519775 0.560981273651123 453.94677734375 0.210580974817276 585.1709594726562 0.4036083221435547 0.88361514 0.2729656994342804 True -17 51750 30.87432336807251 0.5549006462097168 458.9608154296875 0.2576657831668854 584.2477416992188 0.40512189269065857 0.8855892 0.2685459852218628 True -18 54625 30.954031944274902 0.5599603652954102 474.0993957519531 0.20143981277942657 585.10986328125 0.40443840622901917 0.88405174 0.2688305974006653 False -19 57500 30.875591039657593 0.5568881034851074 406.73370361328125 0.2747228741645813 585.5618286132812 0.40426573157310486 0.88427925 0.2701459228992462 False diff --git a/ENCSR635GDW/cherimoya.fold_2.performance.tsv b/ENCSR635GDW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bd428f5ddaeea4824cc89d5eed9842803d8fa340..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -584.2477416992188 0.3828444480895996 0.40512189269065857 0.1670682728290558 0.8855891823768616 0.8601112961769104 0.2685459852218628 \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_3.evaluate.json b/ENCSR635GDW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8830cc92558be51b976e93df06408d68536ceb70..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF734WMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_3.fit.json b/ENCSR635GDW/cherimoya.fold_3.fit.json deleted file mode 100644 index 178446700e7640cd0358065dd31f2d0d3dc7a538..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF734WMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_3.log b/ENCSR635GDW/cherimoya.fold_3.log deleted file mode 100644 index 36e55f83d51c95e50c77af94cbfe2f05d55a493e..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 34.935387134552 3.5478811264038086 416.5744323730469 0.5516220331192017 657.1717529296875 0.30139103531837463 0.7440695 6.704751968383789 True -1 5480 30.08476948738098 0.5377631187438965 522.5335693359375 0.5497246384620667 593.616943359375 0.36222946643829346 0.7998732 1.3435276746749878 True -2 8220 30.060547351837158 0.8821868896484375 474.40692138671875 0.4828195571899414 585.5755615234375 0.3697616457939148 0.81214225 0.7694097757339478 True -3 10960 29.88825559616089 0.5503458976745605 586.8671264648438 0.6204090118408203 578.9140014648438 0.3743276596069336 0.8222404 0.6452186107635498 True -4 13700 29.435805082321167 0.5323302745819092 527.5907592773438 0.49127405881881714 573.6480712890625 0.3761238157749176 0.83151394 0.5831182599067688 True -5 16440 29.390416383743286 0.5286762714385986 584.5308837890625 0.3319002687931061 567.5838623046875 0.38320639729499817 0.83628565 0.4904978275299072 True -6 19180 29.390024423599243 0.5210833549499512 483.15252685546875 0.34405946731567383 563.743408203125 0.3869697153568268 0.84323585 0.42744749784469604 True -7 21920 29.41339874267578 0.530975341796875 604.5668334960938 0.631547749042511 562.5794067382812 0.3875373601913452 0.8465515 0.43033474683761597 True -8 24660 29.454426288604736 0.5306077003479004 586.73388671875 0.3816182613372803 560.0125732421875 0.388660728931427 0.8525451 0.4045253098011017 True -9 27400 29.70148205757141 25.873706102371216 416.32720947265625 0.3332429528236389 555.9506225585938 0.3948577046394348 0.856387 0.388659805059433 True -10 30140 29.61890172958374 0.5350360870361328 499.3450012207031 0.2597208619117737 556.1956787109375 0.3933326303958893 0.86011434 0.36494913697242737 True -11 32880 30.21301531791687 0.5313820838928223 441.456787109375 0.28385525941848755 552.6448974609375 0.39710450172424316 0.8663076 0.3440052568912506 True -12 35620 29.43268060684204 32.53410768508911 538.3890991210938 0.38238027691841125 550.4531860351562 0.39941737055778503 0.8714793 0.3213638365268707 True -13 38360 30.33060884475708 0.5363051891326904 556.9807739257812 0.33419889211654663 547.4304809570312 0.4034998118877411 0.8744155 0.3132566809654236 True -14 41100 29.912392139434814 0.5218710899353027 515.8714599609375 0.2942574620246887 545.1521606445312 0.4039132595062256 0.8792652 0.2973025441169739 True -15 43840 29.639020442962646 28.270549535751343 407.24407958984375 0.4375874102115631 544.2633666992188 0.4062667489051819 0.8808141 0.288473904132843 True -16 46580 29.60299015045166 0.5320167541503906 507.1395263671875 0.21407251060009003 543.96826171875 0.4056042432785034 0.88401735 0.2839283049106598 True -17 49320 30.031776905059814 1.1883525848388672 487.0372314453125 0.363534152507782 544.660400390625 0.40385156869888306 0.8857889 0.28082042932510376 True -18 52060 29.527775049209595 0.6793277263641357 411.0913391113281 0.2104293406009674 543.8029174804688 0.40622150897979736 0.8847881 0.28034505248069763 False -19 54800 29.456438541412354 0.5280630588531494 425.433349609375 0.24303263425827026 544.4926147460938 0.40422752499580383 0.88473076 0.2815622091293335 False diff --git a/ENCSR635GDW/cherimoya.fold_3.performance.tsv b/ENCSR635GDW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index be2216fa8420351cc70240cbaa39a1a7f2a320f2..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -544.660400390625 0.38771530985832214 0.40385156869888306 0.1603173315525055 0.8857889175415039 0.8461160659790039 0.28082042932510376 \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_4.evaluate.json b/ENCSR635GDW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f15c310816b450903abfb157be901da84f58493c..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF734WMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_4.fit.json b/ENCSR635GDW/cherimoya.fold_4.fit.json deleted file mode 100644 index 30c9d88054e7d232004505f3f94f08c61cd8c194..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF734WMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635GDW/cherimoya.fold_4.log b/ENCSR635GDW/cherimoya.fold_4.log deleted file mode 100644 index e4e1b8d275b191655685a1894b092c148dd5a0b0..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2794 35.59582161903381 5.4335198402404785 489.31158447265625 0.7313060760498047 624.7302856445312 0.28768038749694824 0.74822235 5.776172161102295 True -1 5588 30.83822512626648 3.9187984466552734 428.28125 0.36899101734161377 563.0751342773438 0.3539871275424957 0.797163 1.5874311923980713 True -2 8382 30.72213578224182 1.5350914001464844 420.78912353515625 0.3734355866909027 555.263427734375 0.3597416281700134 0.80830073 0.9983534812927246 True -3 11176 31.049441814422607 0.6018509864807129 477.1995849609375 0.6050288081169128 550.7673950195312 0.36260759830474854 0.814562 0.6070610284805298 True -4 13970 31.407787322998047 0.59490966796875 555.5848388671875 0.4866373538970947 547.3406372070312 0.36514392495155334 0.81828445 0.5709202289581299 True -5 16764 30.125617504119873 0.5929512977600098 578.372314453125 0.475541889667511 541.58837890625 0.37129732966423035 0.8308846 0.4998827874660492 True -6 19558 30.104363203048706 5.708232402801514 481.68780517578125 0.4897143244743347 538.8158569335938 0.3741927742958069 0.83844066 0.4256284832954407 True -7 22352 30.085460424423218 0.6069033145904541 493.4848937988281 0.37982404232025146 536.1089477539062 0.37739697098731995 0.84604824 0.4286481440067291 True -8 25146 30.136847257614136 0.5923671722412109 465.33685302734375 0.3823583126068115 535.0370483398438 0.377753347158432 0.84866077 0.3988189101219177 True -9 27940 31.278011798858643 18.389715909957886 475.3438720703125 0.410381555557251 532.20458984375 0.3818458020687103 0.8522608 0.3943786323070526 True -10 30734 30.148533821105957 0.6042182445526123 386.6026611328125 0.34452417492866516 530.1739501953125 0.3849659264087677 0.85793906 0.3541177213191986 True -11 33528 30.201560258865356 0.5974586009979248 564.588134765625 0.43390148878097534 527.7117309570312 0.38789448142051697 0.86319846 0.3364489674568176 True -12 36322 30.071878910064697 0.5978696346282959 448.2010498046875 0.30516868829727173 526.4800415039062 0.3886561095714569 0.8683697 0.302988737821579 True -13 39116 30.49296498298645 39.237409591674805 455.435302734375 0.33849889039993286 524.6046752929688 0.39107251167297363 0.8725736 0.28958389163017273 True -14 41910 30.330036163330078 34.733742475509644 461.2252197265625 0.37650418281555176 525.160400390625 0.38984543085098267 0.87662554 0.269217312335968 True -15 44704 30.882411241531372 0.6220042705535889 376.62664794921875 0.22755952179431915 523.77734375 0.3920315206050873 0.8816732 0.2586907148361206 True -16 47498 30.238773345947266 0.621192216873169 565.0406494140625 0.26039206981658936 521.4580078125 0.39566701650619507 0.8832632 0.2518061399459839 True -17 50292 30.08741593360901 0.6022076606750488 391.42926025390625 0.220342755317688 521.688232421875 0.3950955271720886 0.884715 0.24810467660427094 True -18 53086 30.065603971481323 0.6111791133880615 502.7488708496094 0.1758628785610199 523.2161865234375 0.39270931482315063 0.88321227 0.24933017790317535 False -19 55880 30.123538732528687 0.6081233024597168 444.2416076660156 0.2106405645608902 522.9180908203125 0.39309120178222656 0.88463145 0.24990589916706085 False diff --git a/ENCSR635GDW/cherimoya.fold_4.performance.tsv b/ENCSR635GDW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b05371546b79b256de7330982df65303144d3219..0000000000000000000000000000000000000000 --- a/ENCSR635GDW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -521.688232421875 0.3951817452907562 0.3950955271720886 0.15410169959068298 0.8847150206565857 0.8446117639541626 0.24810467660427094 \ No newline at end of file diff --git a/ENCSR635URJ/cherimoya.fold_0.evaluate.json b/ENCSR635URJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 824ba02eca268271a140bb53427098926e17be39..0000000000000000000000000000000000000000 --- a/ENCSR635URJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF758CSY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635URJ/cherimoya.fold_0.performance.tsv b/ENCSR635URJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d442e81330f09e037257017b41f6d33c2990fdec..0000000000000000000000000000000000000000 --- a/ENCSR635URJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -337.7461853027344 0.49159112572669983 0.28228288888931274 0.09713772684335709 0.8707073330879211 0.822209894657135 0.487633615732193 \ No newline at end of file diff --git a/ENCSR635URJ/cherimoya.fold_3.performance.tsv b/ENCSR635URJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2504bc9e57a4793e4db766276fd6623e000e64eb..0000000000000000000000000000000000000000 --- a/ENCSR635URJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -356.9551696777344 0.4779171347618103 0.29910239577293396 0.10103313624858856 0.856124758720398 0.8211716413497925 0.5672261118888855 \ No newline at end of file diff --git a/ENCSR635URJ/cherimoya.fold_4.performance.tsv b/ENCSR635URJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index de21d555b2b6d9343e8f720b7fee9d6d0a1e2ca3..0000000000000000000000000000000000000000 --- a/ENCSR635URJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.7318115234375 0.5011825561523438 0.2703758776187897 0.09079030156135559 0.8630942106246948 0.8068674206733704 0.4860619008541107 \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_0.evaluate.json b/ENCSR635VQU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index afb66f1c95bbc473b41783af3a05e0bc39072ada..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551BKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_0.fit.json b/ENCSR635VQU/cherimoya.fold_0.fit.json deleted file mode 100644 index 37bc5937c718eaec0a7847c6b38ae0063e88a407..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF551BKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_0.log b/ENCSR635VQU/cherimoya.fold_0.log deleted file mode 100644 index ff034317a346047251522c68fd7ce4bb656bebfb..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1854 24.487203121185303 3.5455117225646973 516.5626831054688 0.8770392537117004 964.5413818359375 0.17735108733177185 0.519746 14.568755149841309 True -1 3708 20.709070920944214 0.5620336532592773 665.2368774414062 1.0552895069122314 841.5911254882812 0.2822500169277191 0.63595545 5.439746379852295 True -2 5562 20.66914653778076 0.45409202575683594 743.9559326171875 0.849201500415802 775.5698852539062 0.3266834318637848 0.65451664 3.2818665504455566 True -3 7416 20.6550931930542 0.41614341735839844 475.976806640625 0.8094732761383057 738.9083251953125 0.3428734242916107 0.67352945 2.5278899669647217 True -4 9270 20.659810781478882 0.3827352523803711 594.969970703125 1.0261995792388916 718.8816528320312 0.35613495111465454 0.6883964 2.0295987129211426 True -5 11124 20.607454538345337 0.3806750774383545 562.8994140625 0.8534910678863525 706.6015625 0.36321747303009033 0.70145583 1.5919824838638306 True -6 12978 20.658373832702637 0.3696584701538086 595.0891723632812 0.9568842649459839 698.4878540039062 0.3690865635871887 0.70889986 1.34811270236969 True -7 14832 20.629337310791016 0.3747704029083252 546.759521484375 1.0418226718902588 691.744873046875 0.3713829517364502 0.7184806 1.1582688093185425 True -8 16686 20.632732152938843 0.38865113258361816 728.5809326171875 1.4950594902038574 688.2945556640625 0.3755410611629486 0.722044 1.1193950176239014 True -9 18540 20.6452898979187 0.853356122970581 587.533447265625 0.9961487650871277 683.6956787109375 0.3772696256637573 0.72848046 0.9489630460739136 True -10 20394 20.630606174468994 1.4595649242401123 549.386962890625 0.840933620929718 680.0349731445312 0.3799283802509308 0.7333858 0.8502224683761597 True -11 22248 20.67454171180725 0.7072267532348633 558.331787109375 0.6654766201972961 675.8611450195312 0.38387617468833923 0.7419284 0.7774086594581604 True -12 24102 20.661255598068237 0.3870067596435547 491.0664367675781 0.69498610496521 669.0463256835938 0.38876762986183167 0.7448064 0.7334492206573486 True -13 25956 20.615172386169434 0.6026525497436523 593.4423217773438 0.9156639575958252 664.994873046875 0.3910047709941864 0.7527059 0.6911472082138062 True -14 27810 20.656585693359375 0.3765861988067627 633.9879760742188 0.7909137010574341 664.3763427734375 0.39149630069732666 0.7592411 0.6590891480445862 True -15 29664 20.641632318496704 0.4031529426574707 510.25799560546875 0.699090838432312 661.7938842773438 0.39273637533187866 0.76380426 0.6217778325080872 True -16 31518 20.660896062850952 0.677201509475708 457.0972900390625 0.6782634258270264 659.1782836914062 0.3938958942890167 0.7682139 0.6094337105751038 True -17 33372 20.616974592208862 0.375598669052124 569.0247192382812 0.6747784614562988 659.2612915039062 0.39226940274238586 0.7688937 0.6000899076461792 True -18 35226 20.666617393493652 0.3701615333557129 370.85333251953125 0.5736433267593384 658.311279296875 0.3924734890460968 0.7680777 0.5981521010398865 False -19 37080 20.65950918197632 0.3712594509124756 625.4564208984375 0.7069270610809326 658.2581176757812 0.3929764926433563 0.7670803 0.6004719138145447 False diff --git a/ENCSR635VQU/cherimoya.fold_0.performance.tsv b/ENCSR635VQU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 81a2bbe02fda158a638419bc1e66b8a4db75fd5e..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -659.2612915039062 0.39800509810447693 0.39226943254470825 0.16106925904750824 0.7688937187194824 0.719848096370697 0.6000899076461792 \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_1.evaluate.json b/ENCSR635VQU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 75e30dfc46ee467396c593e7a71ba95f08ab9292..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551BKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_1.fit.json b/ENCSR635VQU/cherimoya.fold_1.fit.json deleted file mode 100644 index 09ff0128ea997382fab5a833a4a2842924164f48..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF551BKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_1.log b/ENCSR635VQU/cherimoya.fold_1.log deleted file mode 100644 index 086a9928a90b778f2e571c701c19a8d98c142eaa..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1859 24.411593914031982 3.661501407623291 577.9622192382812 1.0252680778503418 1185.4056396484375 0.18736594915390015 0.4760874 16.573448181152344 True -1 3718 20.749953985214233 0.5376207828521729 567.0692138671875 0.8500679135322571 1010.5737915039062 0.30773305892944336 0.60026795 7.5149922370910645 True -2 5577 21.007561922073364 0.5135388374328613 540.8955688476562 0.6586936116218567 953.9199829101562 0.34224560856819153 0.6127937 5.364173412322998 True -3 7436 20.69801092147827 0.5097250938415527 576.1241455078125 0.6924518346786499 892.1197509765625 0.36767613887786865 0.63891834 4.201634407043457 True -4 9295 20.685526371002197 0.8654346466064453 636.0721435546875 1.0107474327087402 859.1483154296875 0.3798779547214508 0.65986836 2.9758059978485107 True -5 11154 20.729078769683838 0.5217702388763428 567.7301635742188 0.8055509328842163 837.2747802734375 0.3889960050582886 0.6733251 2.159806489944458 True -6 13013 20.749006032943726 0.5070631504058838 513.942626953125 1.0098484754562378 825.9775390625 0.39429372549057007 0.68672025 1.8776768445968628 True -7 14872 20.892744779586792 0.5080521106719971 641.7691040039062 0.8471808433532715 815.6029663085938 0.40251919627189636 0.6949669 1.7031177282333374 True -8 16731 20.701923847198486 0.5055563449859619 602.7080078125 0.8091322779655457 814.4957275390625 0.4032360911369324 0.7039802 1.5332545042037964 True -9 18590 20.757490396499634 0.510859489440918 455.6907958984375 0.8922335505485535 806.7389526367188 0.4087825119495392 0.70934373 1.431151032447815 True -10 20449 20.726578950881958 0.5190567970275879 576.3966064453125 1.2724430561065674 798.1300048828125 0.413138747215271 0.72135717 1.1993985176086426 True -11 22308 20.69936490058899 0.5229616165161133 474.9141845703125 0.8434593677520752 793.804443359375 0.4144456088542938 0.7262279 1.1779570579528809 True -12 24167 20.785645961761475 0.7142517566680908 468.1230163574219 0.8556085824966431 787.1962890625 0.4176875650882721 0.7333846 1.0530619621276855 True -13 26026 20.71135449409485 0.5054442882537842 627.01611328125 0.598400354385376 780.674560546875 0.42051637172698975 0.74020714 0.9422057867050171 True -14 27885 20.744009494781494 0.5195643901824951 694.85546875 0.6756377220153809 773.6119384765625 0.4231809973716736 0.74742794 0.8514361381530762 True -15 29744 20.6954288482666 0.5169863700866699 567.4061889648438 0.4958626925945282 769.3927001953125 0.4261031150817871 0.75456077 0.7909242510795593 True -16 31603 20.765701293945312 0.5085382461547852 450.3921813964844 0.5116994380950928 766.9996948242188 0.42603105306625366 0.76017785 0.7600302696228027 True -17 33462 20.73064374923706 0.5004658699035645 597.33251953125 0.6314351558685303 765.0758666992188 0.4271755516529083 0.7635766 0.7338125705718994 True -18 35321 20.73081660270691 1.5221147537231445 504.9261474609375 0.5002678036689758 766.6879272460938 0.42488154768943787 0.7638336 0.722061276435852 True -19 37180 20.743708610534668 0.5167970657348633 492.27764892578125 0.3531387448310852 767.1221923828125 0.4243728518486023 0.76495564 0.7202171683311462 True diff --git a/ENCSR635VQU/cherimoya.fold_1.performance.tsv b/ENCSR635VQU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6871cc492f66898b355d5e68c73d9b502b544939..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -767.1221923828125 0.372780442237854 0.4243727922439575 0.18650802969932556 0.7649556398391724 0.7229064106941223 0.7202171683311462 \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_2.evaluate.json b/ENCSR635VQU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 64292ce1bf56851713efd8c0eeb0f3c73333857c..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551BKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_2.fit.json b/ENCSR635VQU/cherimoya.fold_2.fit.json deleted file mode 100644 index 6731ce4c6cfc446976b209397534a1714fb953d6..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF551BKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_2.log b/ENCSR635VQU/cherimoya.fold_2.log deleted file mode 100644 index 4b740ead583609cf6ddc130a0058a545accbb4da..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1989 25.770988702774048 3.683168888092041 610.33935546875 1.0091145038604736 1026.4906005859375 0.1844734102487564 0.5172984 12.801721572875977 True -1 3978 22.177507400512695 0.3885011672973633 567.5555419921875 0.9333339333534241 865.4584350585938 0.30806559324264526 0.62431 6.805900573730469 True -2 5967 22.177100658416748 0.3665463924407959 566.583740234375 0.9811535477638245 811.3429565429688 0.3392200171947479 0.64447427 4.7042460441589355 True -3 7956 22.14025855064392 0.3603024482727051 680.092529296875 1.0050641298294067 772.2296142578125 0.3539094030857086 0.6584017 3.103341579437256 True -4 9945 22.1358904838562 0.36154818534851074 871.607666015625 1.0652519464492798 755.2078857421875 0.36420196294784546 0.6678777 2.2154266834259033 True -5 11934 22.09627604484558 0.4163055419921875 681.7847900390625 1.0672669410705566 745.4039916992188 0.3694787621498108 0.6782866 1.8887118101119995 True -6 13923 22.10302472114563 0.42159366607666016 715.7099609375 0.8766037225723267 734.0008544921875 0.37997323274612427 0.6832497 1.7354947328567505 True -7 15912 22.12625026702881 0.35950803756713867 644.6922607421875 1.1062052249908447 724.0914916992188 0.384026437997818 0.7001223 1.3016541004180908 True -8 17901 22.128894805908203 0.3642697334289551 589.056884765625 0.8815478086471558 718.2941284179688 0.3880676329135895 0.70767695 1.1799598932266235 True -9 19890 22.197840452194214 0.362748384475708 531.8944702148438 0.4268294870853424 713.2020874023438 0.391095370054245 0.71781784 1.0295772552490234 True -10 21879 22.126276969909668 0.3591325283050537 704.4794921875 0.8108062744140625 708.4426879882812 0.39424020051956177 0.72657955 0.9748443365097046 True -11 23868 22.16925597190857 0.36327457427978516 652.5422973632812 0.8654829263687134 701.0850219726562 0.3987322747707367 0.73129684 0.9096745252609253 True -12 25857 22.181483268737793 0.35172533988952637 557.0535888671875 0.9704888463020325 697.2013549804688 0.40087470412254333 0.73608327 0.8479424118995667 True -13 27846 22.140297412872314 0.3645145893096924 512.365966796875 0.44623273611068726 691.8750610351562 0.40268197655677795 0.74140507 0.7799403071403503 True -14 29835 22.118237495422363 0.35950422286987305 611.253173828125 0.4957817792892456 685.8541259765625 0.40686774253845215 0.75127685 0.7259039282798767 True -15 31824 22.1527042388916 0.36464548110961914 515.04248046875 0.6970199346542358 685.9186401367188 0.40563979744911194 0.75549364 0.6897217631340027 True -16 33813 22.188233137130737 0.3654041290283203 482.9912109375 0.4430573880672455 683.1472778320312 0.40624797344207764 0.7595068 0.6694355010986328 True -17 35802 22.229496955871582 0.35979437828063965 492.7014465332031 0.49195176362991333 682.4845581054688 0.40634214878082275 0.7613263 0.656324028968811 True -18 37791 22.187143087387085 0.3600795269012451 457.41229248046875 0.571405827999115 683.8831176757812 0.406293660402298 0.7620222 0.6550329923629761 True -19 39780 22.227699756622314 0.36502623558044434 604.2450561523438 0.39529287815093994 684.9756469726562 0.4047066867351532 0.76223224 0.6544710397720337 True diff --git a/ENCSR635VQU/cherimoya.fold_2.performance.tsv b/ENCSR635VQU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 42ca3efe7fabcdf6de3be0b1a232fc2089c51ef4..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -684.9756469726562 0.3898637890815735 0.4047066569328308 0.16958436369895935 0.76223224401474 0.7149524092674255 0.6544710397720337 \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_3.evaluate.json b/ENCSR635VQU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a784e5cbeca929ab73ecd3a7c957b9d4085aed9d..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551BKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_3.fit.json b/ENCSR635VQU/cherimoya.fold_3.fit.json deleted file mode 100644 index 6e540511531cd6fc9dc91ba3cc5bc0baea8b4a26..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF551BKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_3.log b/ENCSR635VQU/cherimoya.fold_3.log deleted file mode 100644 index e08febc21474cef99f9c2a4b852908d98b428a6a..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1902 26.441023111343384 6.843594074249268 703.325439453125 1.271988868713379 1014.6058959960938 0.17944452166557312 0.49602082 14.006134033203125 True -1 3804 21.19254779815674 0.3783249855041504 613.5873413085938 1.1315524578094482 887.9616088867188 0.29075631499290466 0.60317713 6.223045349121094 True -2 5706 21.66938066482544 9.004803657531738 522.30224609375 0.8084653615951538 829.9325561523438 0.326304167509079 0.6134738 4.034536838531494 True -3 7608 21.2230703830719 0.4004089832305908 568.873046875 0.8816965222358704 792.3875122070312 0.3428192734718323 0.6353566 3.1853580474853516 True -4 9510 21.6428439617157 0.3738222122192383 450.7841491699219 0.6350081562995911 776.604736328125 0.35317105054855347 0.6404989 2.533756732940674 True -5 11412 21.156896352767944 0.38474249839782715 609.603271484375 0.9617780447006226 763.5159301757812 0.3595592677593231 0.66414803 2.2396466732025146 True -6 13314 23.153114080429077 7.540015697479248 600.1876220703125 0.9207953214645386 751.2415771484375 0.36687901616096497 0.6739382 1.6027153730392456 True -7 15216 21.272289514541626 0.38661837577819824 556.8324584960938 0.7851921319961548 746.4873046875 0.37124958634376526 0.67592806 1.5356085300445557 True -8 17118 21.196648836135864 0.3758277893066406 505.7388000488281 0.8683137893676758 736.3289794921875 0.37684735655784607 0.6937035 1.3211309909820557 True -9 19020 21.159149885177612 0.37221264839172363 470.7789611816406 0.651653528213501 732.2636108398438 0.3798520565032959 0.7015505 1.170344352722168 True -10 20922 21.15151333808899 0.3771705627441406 479.877197265625 0.7150776982307434 728.5729370117188 0.3818691372871399 0.7085933 1.038753628730774 True -11 22824 21.200995683670044 0.3734114170074463 617.67138671875 0.584991455078125 722.7155151367188 0.38479891419410706 0.7175315 0.990568995475769 True -12 24726 21.209067344665527 0.3714866638183594 513.1351318359375 0.515943706035614 716.2921752929688 0.38917598128318787 0.7225594 0.9409913420677185 True -13 26628 21.15454387664795 0.37151288986206055 674.0159912109375 0.6764288544654846 714.8616943359375 0.3883942663669586 0.7312251 0.8750353455543518 True -14 28530 21.22067904472351 0.3838081359863281 521.6932373046875 0.45612868666648865 709.09765625 0.3908820152282715 0.74110496 0.7967352867126465 True -15 30432 21.218005418777466 0.4409604072570801 613.9629516601562 0.9673313498497009 701.3299560546875 0.3963364064693451 0.74984473 0.7415880560874939 True -16 32334 21.271013498306274 0.4056284427642822 453.0863037109375 0.6379822492599487 700.897705078125 0.3937165141105652 0.7552182 0.69638991355896 True -17 34236 21.22610092163086 0.38997936248779297 545.017333984375 0.7432191967964172 701.1257934570312 0.39350560307502747 0.75713164 0.6817681193351746 True -18 36138 21.196733236312866 0.3898804187774658 554.6170654296875 0.48240360617637634 702.106689453125 0.3926194906234741 0.756319 0.6756875514984131 False -19 38040 21.22572350502014 0.3643219470977783 499.6983337402344 0.37924593687057495 701.1907958984375 0.3934149146080017 0.7565205 0.67710280418396 False diff --git a/ENCSR635VQU/cherimoya.fold_3.performance.tsv b/ENCSR635VQU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f476132dad12ae788bbffb037c5455675f3849d3..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -701.1257934570312 0.39467233419418335 0.39350560307502747 0.16562959551811218 0.7571316361427307 0.7115902900695801 0.6817681193351746 \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_4.evaluate.json b/ENCSR635VQU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 63f1e31fd5dd2a156dba92351322b99903694276..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF551BKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_4.fit.json b/ENCSR635VQU/cherimoya.fold_4.fit.json deleted file mode 100644 index d8d072986a1d2b1d0ca160154e855af061b5e6f5..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF551BKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR635VQU/cherimoya.fold_4.log b/ENCSR635VQU/cherimoya.fold_4.log deleted file mode 100644 index 82f409fb9101d5e746657449b8005b0402eb5865..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1951 25.238731384277344 4.112468719482422 649.417236328125 1.0712993144989014 943.0845336914062 0.17813289165496826 0.49864376 12.657259941101074 True -1 3902 21.759913682937622 3.6566121578216553 573.912841796875 1.1504478454589844 822.5365600585938 0.2872750461101532 0.61807066 5.609464168548584 True -2 5853 21.76740026473999 0.3829946517944336 655.6939697265625 1.1645368337631226 777.547607421875 0.31671011447906494 0.61872053 3.5624818801879883 True -3 7804 21.790070295333862 0.4873485565185547 534.631591796875 0.6164364218711853 738.6336669921875 0.3355172574520111 0.6378017 2.604403257369995 True -4 9755 21.750147819519043 1.3470723628997803 533.7791137695312 0.6107420921325684 715.6458740234375 0.34753429889678955 0.65721565 1.8326358795166016 True -5 11706 21.752461910247803 0.38321471214294434 434.8668518066406 0.6342060565948486 703.0693969726562 0.35628408193588257 0.6667357 1.7516627311706543 True -6 13657 21.7135808467865 0.3642251491546631 722.9788818359375 1.1679633855819702 695.1627807617188 0.35969963669776917 0.675098 1.4452160596847534 True -7 15608 21.725236415863037 0.37799978256225586 583.923583984375 0.9738338589668274 688.458251953125 0.36393752694129944 0.686724 1.1976221799850464 True -8 17559 21.73762536048889 0.36544346809387207 552.4063110351562 0.8079873323440552 683.8224487304688 0.36836037039756775 0.69187224 1.0743242502212524 True -9 19510 21.702049016952515 0.3579437732696533 455.8918151855469 0.6708526611328125 675.6180419921875 0.3750913441181183 0.70068926 0.9633487462997437 True -10 21461 21.68551278114319 0.376145601272583 547.912353515625 0.7513308525085449 672.91943359375 0.37851107120513916 0.7047128 0.9375460147857666 True -11 23412 21.726879596710205 0.3842172622680664 524.0648803710938 1.233940839767456 671.028564453125 0.378937691450119 0.7076585 0.8820012211799622 True -12 25363 21.713762283325195 0.36354494094848633 480.3051452636719 0.511676013469696 665.5150146484375 0.38200879096984863 0.71633863 0.8068733215332031 True -13 27314 21.731178283691406 0.3667325973510742 657.8436889648438 0.8614863753318787 662.4929809570312 0.38325178623199463 0.7244631 0.748785138130188 True -14 29265 21.75126361846924 1.219794750213623 523.0720825195312 0.4112366735935211 661.6405029296875 0.3839920163154602 0.7273665 0.7263203263282776 True -15 31216 21.789384126663208 0.35837411880493164 525.9558715820312 0.4514427185058594 657.6653442382812 0.3875006437301636 0.73587203 0.695112943649292 True -16 33167 21.70140027999878 0.3659360408782959 534.578125 0.4869358241558075 656.5569458007812 0.3866594731807709 0.74178976 0.6691541075706482 True -17 35118 21.777647733688354 0.9160490036010742 635.9136352539062 0.2918253540992737 656.7932739257812 0.38625237345695496 0.74564433 0.6563864350318909 True -18 37069 21.756089210510254 0.3757650852203369 542.4482421875 0.6089540123939514 657.305419921875 0.3860829174518585 0.74362916 0.6554749608039856 False -19 39020 21.7475323677063 0.38251543045043945 541.5106201171875 0.33004653453826904 658.475341796875 0.3850770592689514 0.7429495 0.6591119766235352 False diff --git a/ENCSR635VQU/cherimoya.fold_4.performance.tsv b/ENCSR635VQU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fb66e06f379d7a6ae5bdb75185e02bea20d80c99..0000000000000000000000000000000000000000 --- a/ENCSR635VQU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -656.7932739257812 0.40144091844558716 0.38625234365463257 0.16071484982967377 0.7456443309783936 0.6995195746421814 0.6563864350318909 \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_0.evaluate.json b/ENCSR637OPZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6270e76b7e12f9922c3ffa3f47b38a04f21ac973..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF525TVD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_0.fit.json b/ENCSR637OPZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 8ec07e13163c0ae186341d43aefdfe0ad5c527fc..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF525TVD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_0.log b/ENCSR637OPZ/cherimoya.fold_0.log deleted file mode 100644 index 96803bcbdbd3f6cfcc881cf6cd737e7af4db6dc7..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2928 36.16687059402466 3.823354482650757 499.0738830566406 1.203215479850769 766.5292358398438 0.6063197255134583 0.5580033 7.76753568649292 True -1 5856 32.28331255912781 0.5867788791656494 531.80078125 1.2649706602096558 614.2031860351562 0.7156739830970764 0.6712277 2.1612250804901123 True -2 8784 32.17653012275696 0.5727095603942871 481.2902526855469 0.8390803337097168 597.10693359375 0.7248549461364746 0.69398403 1.1069697141647339 True -3 11712 32.138633012771606 1.5374317169189453 590.966552734375 1.7195783853530884 588.7996215820312 0.7300649881362915 0.7020456 1.0791289806365967 True -4 14640 32.178001165390015 14.339693307876587 526.3687133789062 0.8914799094200134 583.40087890625 0.734574556350708 0.70421416 0.9935130476951599 True -5 17568 32.287445068359375 0.578068733215332 573.3257446289062 1.0552873611450195 579.0281982421875 0.7369521260261536 0.71064746 0.8881736993789673 True -6 20496 32.21583914756775 0.5946071147918701 457.6083984375 1.0060274600982666 575.468994140625 0.7406985759735107 0.7133588 0.8155571222305298 True -7 23424 32.369138956069946 0.581416130065918 490.0480041503906 0.8198462128639221 572.580322265625 0.7427785992622375 0.71770257 0.7982507348060608 True -8 26352 32.40956902503967 0.5871813297271729 442.6836242675781 0.7387963533401489 568.3251953125 0.7463529109954834 0.7239067 0.7707388997077942 True -9 29280 32.33821654319763 0.580258846282959 465.568603515625 0.8508278727531433 564.4834594726562 0.74867844581604 0.7303552 0.7169755101203918 True -10 32208 32.29831528663635 1.5750017166137695 471.02490234375 0.7195703387260437 561.059326171875 0.7513957023620605 0.7357341 0.7073329091072083 True -11 35136 32.456835985183716 0.5808517932891846 425.48089599609375 0.6704263687133789 557.58154296875 0.7542009949684143 0.742436 0.6749858260154724 True -12 38064 32.28342866897583 0.568474531173706 419.2087707519531 0.7943286895751953 554.5855102539062 0.7563959360122681 0.7523058 0.6395573616027832 True -13 40992 32.299870014190674 0.581709623336792 455.5675048828125 0.5982507467269897 551.9509887695312 0.7584341168403625 0.76021355 0.6086711287498474 True -14 43920 32.34184455871582 0.5790860652923584 438.841796875 0.5465315580368042 549.9790649414062 0.7600840330123901 0.7675006 0.5914493799209595 True -15 46848 32.361592054367065 0.5771405696868896 453.772705078125 0.4487380385398865 548.3351440429688 0.7610043287277222 0.7723681 0.574018120765686 True -16 49776 32.306464433670044 0.5669131278991699 481.822509765625 0.46100521087646484 547.9022216796875 0.7612563967704773 0.77277464 0.5778254270553589 True -17 52704 31.98707890510559 0.5563437938690186 389.61614990234375 0.431846559047699 548.2155151367188 0.7609831690788269 0.77459276 0.5811819434165955 True -18 55632 31.673691511154175 0.8890507221221924 396.9552001953125 0.36151620745658875 549.1424560546875 0.7603906989097595 0.769522 0.5962194204330444 False -19 58560 31.700170278549194 0.5857601165771484 473.731689453125 0.371202290058136 549.5330200195312 0.7600658535957336 0.76846504 0.6046929359436035 False diff --git a/ENCSR637OPZ/cherimoya.fold_0.performance.tsv b/ENCSR637OPZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6192f9d4b4c926b3dfafabbf8899c196d34cd007..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -548.2155151367188 0.20057673752307892 0.7609831690788269 0.3570133149623871 0.7745927572250366 0.7298287749290466 0.5811819434165955 \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_1.evaluate.json b/ENCSR637OPZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3f85d11c8c335376213b635d7a68cf9eb5f067d9..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF525TVD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_1.fit.json b/ENCSR637OPZ/cherimoya.fold_1.fit.json deleted file mode 100644 index e2549b399a20ed01177a330247276fef128293b8..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF525TVD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_1.log b/ENCSR637OPZ/cherimoya.fold_1.log deleted file mode 100644 index cf2d5ab5ca37c566c5e8fd7820b0b5af812e6569..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 36.212560415267944 3.9771037101745605 564.3131103515625 0.8395957350730896 902.3758544921875 0.6179413199424744 0.5761934 8.42782974243164 True -1 5784 31.947136640548706 0.7917554378509521 567.1736450195312 0.8072613477706909 715.0541381835938 0.7315487265586853 0.675547 2.8583719730377197 True -2 8676 31.88709568977356 0.7622435092926025 496.87066650390625 0.6183745861053467 686.791748046875 0.7441675066947937 0.6999748 1.6146135330200195 True -3 11568 31.86453914642334 0.754525899887085 370.3052673339844 0.7695921659469604 678.2396850585938 0.7510396838188171 0.7038016 1.4429247379302979 True -4 14460 31.901597261428833 1.5244860649108887 414.31982421875 0.8865083456039429 670.7929077148438 0.7562585473060608 0.7057246 1.311418890953064 True -5 17352 31.975926637649536 0.7528367042541504 451.67059326171875 0.9598901867866516 663.932861328125 0.7603881359100342 0.71144456 1.1195099353790283 True -6 20244 31.87647032737732 0.7582528591156006 501.36700439453125 1.1210147142410278 659.5245971679688 0.7632805109024048 0.71982455 1.0247390270233154 True -7 23136 31.901346683502197 0.7510981559753418 394.23773193359375 1.0487029552459717 653.3937377929688 0.7666164636611938 0.727959 0.9635365009307861 True -8 26028 31.95337152481079 0.7613129615783691 481.17742919921875 0.8115420341491699 647.646728515625 0.7701655030250549 0.7347099 0.8516708612442017 True -9 28920 32.00517272949219 0.756812334060669 451.32843017578125 0.7287893295288086 643.2931518554688 0.772702693939209 0.7437676 0.8062783479690552 True -10 31812 32.25973963737488 0.7646808624267578 394.4109802246094 0.8518579006195068 638.4334716796875 0.7759260535240173 0.74404925 0.8063621520996094 True -11 34704 31.939624786376953 0.7585506439208984 409.31787109375 0.6729493737220764 633.7716064453125 0.7790062427520752 0.75647426 0.7553613185882568 True -12 37596 31.833879947662354 0.8466246128082275 405.6866760253906 0.6193846464157104 630.8570556640625 0.7812968492507935 0.7617843 0.7360798120498657 True -13 40488 31.811011791229248 0.7637412548065186 467.85528564453125 0.8058009147644043 626.6184692382812 0.7837343215942383 0.76933056 0.693449079990387 True -14 43380 31.817463397979736 0.762864351272583 380.11962890625 0.43746864795684814 623.291259765625 0.7854864597320557 0.7780365 0.6548832654953003 True -15 46272 31.828402042388916 0.7560651302337646 435.14361572265625 0.5795570611953735 622.1795043945312 0.7860792875289917 0.78297526 0.6347661018371582 True -16 49164 31.78231644630432 0.7424702644348145 357.41259765625 0.40643757581710815 621.8469848632812 0.7860401272773743 0.7840688 0.6175224184989929 True -17 52056 31.500471830368042 0.7471725940704346 403.0423583984375 0.508613646030426 622.174072265625 0.7856059074401855 0.781197 0.6306833028793335 False -18 54948 31.289379358291626 0.7499957084655762 427.0909423828125 0.28859224915504456 623.5816040039062 0.7847329378128052 0.7778428 0.641279399394989 False -19 57840 31.189337968826294 0.7457423210144043 396.25164794921875 0.468521386384964 624.1853637695312 0.7842533588409424 0.7742983 0.647676408290863 False diff --git a/ENCSR637OPZ/cherimoya.fold_1.performance.tsv b/ENCSR637OPZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 16b10877b5984ede19289133542cc78da462e09c..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -621.8469848632812 0.18018299341201782 0.786040186882019 0.3971143662929535 0.7840688228607178 0.7603769898414612 0.6175224184989929 \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_2.evaluate.json b/ENCSR637OPZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0e7e068e04b589a5748463b6795b4eb2cc83fdf7..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF525TVD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_2.fit.json b/ENCSR637OPZ/cherimoya.fold_2.fit.json deleted file mode 100644 index ac3707ec69503f42dbf55cc09a71350bcd9813ea..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF525TVD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_2.log b/ENCSR637OPZ/cherimoya.fold_2.log deleted file mode 100644 index 9389b7406edda878609acf8c36d6c1fb27d13c12..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3073 38.00605344772339 3.6621177196502686 601.413818359375 0.945238471031189 774.4711303710938 0.6159118413925171 0.55304885 5.803828239440918 True -1 6146 33.905670404434204 0.6232848167419434 555.2295532226562 1.2149499654769897 633.9829711914062 0.7102128267288208 0.69095093 2.759521007537842 True -2 9219 33.979652881622314 0.6189987659454346 446.823974609375 0.8860180974006653 617.80712890625 0.7208321690559387 0.70003587 1.6915208101272583 True -3 12292 33.84207797050476 1.6649117469787598 490.8662109375 0.8808494806289673 608.9962768554688 0.7259914875030518 0.710446 1.3413476943969727 True -4 15365 33.89062833786011 0.6031994819641113 462.53521728515625 0.97455894947052 603.459228515625 0.7298461198806763 0.7140152 1.2406960725784302 True -5 18438 33.792439222335815 0.6084578037261963 380.97784423828125 0.8332136869430542 599.63671875 0.7325615882873535 0.7141024 1.168090581893921 True -6 21511 33.75287437438965 1.3771016597747803 514.408935546875 0.9285524487495422 594.554443359375 0.7355098128318787 0.72167283 1.0722923278808594 True -7 24584 33.92418909072876 0.6113791465759277 480.41839599609375 0.6254044771194458 589.5914306640625 0.7382090091705322 0.73299253 0.9712120294570923 True -8 27657 33.94553875923157 0.6198928356170654 410.0797119140625 0.865602970123291 587.5009765625 0.7407965064048767 0.73229927 0.9293420910835266 False -9 30730 33.87115502357483 0.9017858505249023 414.13128662109375 0.9041714072227478 580.9600219726562 0.7444341778755188 0.7428104 0.8116232752799988 True -10 33803 33.59674668312073 0.626223087310791 470.5123291015625 0.7996202111244202 576.67333984375 0.7466950416564941 0.74903756 0.7540042996406555 True -11 36876 33.297999143600464 0.6192843914031982 452.70947265625 0.957030177116394 573.0343017578125 0.7489298582077026 0.7544848 0.7069692611694336 True -12 39949 33.39089775085449 1.7805583477020264 392.71575927734375 0.4458605647087097 569.2909545898438 0.7513322234153748 0.7626134 0.6703526973724365 True -13 43022 33.4083616733551 0.6133952140808105 522.0608520507812 0.4691036343574524 565.9506225585938 0.7534026503562927 0.77133924 0.6366239786148071 True -14 46095 33.35668063163757 1.7362613677978516 430.90557861328125 0.499686598777771 563.6080322265625 0.7550658583641052 0.775484 0.6109092831611633 True -15 49168 33.32112741470337 0.6067945957183838 392.6087646484375 0.4505654573440552 561.748291015625 0.7561323642730713 0.7800374 0.5943397283554077 True -16 52241 33.323583364486694 0.6044342517852783 429.6829833984375 0.3577548861503601 560.5369873046875 0.756560742855072 0.7820385 0.5797938704490662 True -17 55314 33.289008378982544 0.6052200794219971 466.7790222167969 0.536038875579834 560.9522094726562 0.7562125325202942 0.77923375 0.5888087153434753 False -18 58387 33.11460828781128 0.5975136756896973 412.14495849609375 0.3291490077972412 562.0152587890625 0.7555273771286011 0.7760922 0.6072764992713928 False -19 61460 33.11858868598938 0.6003143787384033 428.9168701171875 0.3683631122112274 562.06298828125 0.7552120685577393 0.7752282 0.6104488372802734 False diff --git a/ENCSR637OPZ/cherimoya.fold_2.performance.tsv b/ENCSR637OPZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e78042e6c7e0a35111d5ec4632e1b1fa3c93a801..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -560.5369873046875 0.20062781870365143 0.7565606832504272 0.3649790287017822 0.7820385098457336 0.7367600202560425 0.5797938704490662 \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_3.evaluate.json b/ENCSR637OPZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 77e1dbdaa75abaceb0c52bce1cadceb59a947fe5..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF525TVD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_3.fit.json b/ENCSR637OPZ/cherimoya.fold_3.fit.json deleted file mode 100644 index b9ddeefb5454ab7b578b0d240544f8d91e7c2ee8..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF525TVD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_3.log b/ENCSR637OPZ/cherimoya.fold_3.log deleted file mode 100644 index 9f1860a955db033b6b4c0f1d9059a4630c708ced..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2988 36.80013108253479 3.5116827487945557 520.7750244140625 0.8846198320388794 778.9812622070312 0.6205573081970215 0.5423007 7.945461273193359 True -1 5976 33.35981750488281 3.0127930641174316 498.7503356933594 1.0929577350616455 633.3320922851562 0.7202543616294861 0.6494071 2.862401008605957 True -2 8964 32.94319534301758 0.5903005599975586 495.59857177734375 0.9702638387680054 613.185546875 0.730726957321167 0.6603033 1.7216825485229492 True -3 11952 32.54685401916504 0.574188232421875 497.0369873046875 1.3075551986694336 602.605712890625 0.7373248934745789 0.67352307 1.3414419889450073 True -4 14940 32.2473726272583 0.5854222774505615 449.960205078125 0.6405154466629028 599.1265869140625 0.7402950525283813 0.6767728 1.2452244758605957 True -5 17928 32.142493724823 0.5773723125457764 450.2884216308594 0.916192889213562 595.9412231445312 0.7431002855300903 0.6740848 1.2033473253250122 False -6 20916 32.141539335250854 0.5723228454589844 506.7487487792969 0.763888955116272 592.8763427734375 0.745725154876709 0.6844419 1.0910372734069824 True -7 23904 32.151464223861694 0.5845956802368164 480.6641540527344 0.8276350498199463 588.4507446289062 0.7486598491668701 0.68901354 1.0348618030548096 True -8 26892 32.19572567939758 1.2491350173950195 489.2399597167969 0.8816145658493042 585.0159912109375 0.7513359785079956 0.6984191 0.9514978528022766 True -9 29880 32.24859571456909 0.5898227691650391 495.391845703125 0.5714153051376343 581.5396728515625 0.7541497349739075 0.7040096 0.9078302383422852 True -10 32868 32.19584798812866 21.855356216430664 433.7922668457031 1.0427883863449097 578.1913452148438 0.7570543885231018 0.71173793 0.8565516471862793 True -11 35856 32.33311629295349 0.8913400173187256 430.0615539550781 0.47804489731788635 574.8106689453125 0.7591807246208191 0.72169536 0.817882239818573 True -12 38844 32.31475520133972 0.5957155227661133 416.42596435546875 0.6431348919868469 570.4703369140625 0.7622435688972473 0.73627967 0.7639138102531433 True -13 41832 32.163147926330566 0.5715558528900146 524.12744140625 0.8038196563720703 566.6036987304688 0.7646552324295044 0.74677896 0.719932496547699 True -14 44820 32.22733974456787 0.5870332717895508 433.8453369140625 0.4670809209346771 564.835693359375 0.7663816809654236 0.7509208 0.7101910710334778 True -15 47808 32.27158761024475 0.581627368927002 378.47576904296875 0.389446496963501 562.8113403320312 0.7676929831504822 0.7609066 0.6769586205482483 True -16 50796 32.30804395675659 0.5838277339935303 398.70758056640625 0.3716017007827759 561.8197021484375 0.7680428624153137 0.7641055 0.6603110432624817 True -17 53784 32.22464847564697 0.5739293098449707 412.5848388671875 0.6326602101325989 561.9008178710938 0.7679533362388611 0.76729536 0.6518151760101318 True -18 56772 32.18514823913574 0.5826332569122314 371.15643310546875 0.4060162305831909 562.5028686523438 0.7675361037254333 0.76372933 0.66683030128479 False -19 59760 32.19763231277466 0.5829370021820068 402.1476745605469 0.23124632239341736 563.1622314453125 0.7671664357185364 0.7646068 0.6686513423919678 False diff --git a/ENCSR637OPZ/cherimoya.fold_3.performance.tsv b/ENCSR637OPZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b66657ba84c484161de6dfa8e8fc2926da7390ae..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -561.9008178710938 0.194607213139534 0.7679533362388611 0.3642740547657013 0.7672953605651855 0.7317284941673279 0.6518151760101318 \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_4.evaluate.json b/ENCSR637OPZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index dc1f41e185cc5392d8b5299d0159fe09b2a84984..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF525TVD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_4.fit.json b/ENCSR637OPZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 0dc34d06532025b20a5571f5df4ae99a9a07afc0..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF525TVD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637OPZ/cherimoya.fold_4.log b/ENCSR637OPZ/cherimoya.fold_4.log deleted file mode 100644 index b32ce752e022652dceb294e8d73b94e0e7a95982..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2978 38.1789493560791 4.437916994094849 487.0914611816406 0.8547759056091309 721.3383178710938 0.605506181716919 0.52097803 7.003910541534424 True -1 5956 34.61869525909424 1.896958827972412 494.06927490234375 0.8907736539840698 584.3385009765625 0.7034381628036499 0.66349655 2.290743112564087 True -2 8934 34.51741075515747 5.221075057983398 475.5511474609375 1.1186542510986328 569.9080810546875 0.7102762460708618 0.68439054 1.1597039699554443 True -3 11912 33.32727098464966 0.5706052780151367 478.1310119628906 0.849277138710022 564.4149169921875 0.7149778008460999 0.69320333 1.0344654321670532 True -4 14890 33.209288120269775 0.5748739242553711 548.0531005859375 1.4279484748840332 559.4016723632812 0.7193582057952881 0.6992316 0.9399201273918152 True -5 17868 33.2592236995697 0.5703492164611816 400.9267578125 0.7963719964027405 555.3711547851562 0.7219653129577637 0.7086284 0.8420087099075317 True -6 20846 33.18217706680298 2.268968105316162 536.7938842773438 1.026294231414795 550.7466430664062 0.7243547439575195 0.71345603 0.758356511592865 True -7 23824 33.15226650238037 0.5941078662872314 417.81256103515625 0.900672435760498 547.8681030273438 0.7263675332069397 0.71767664 0.7346731424331665 True -8 26802 33.16106462478638 0.5584673881530762 533.2279663085938 0.6995631456375122 543.8516235351562 0.7296832799911499 0.7247738 0.7159547209739685 True -9 29780 33.27877926826477 0.5707147121429443 463.5976257324219 0.8433226346969604 540.7427978515625 0.7325974702835083 0.7298502 0.6921643018722534 True -10 32758 33.189855098724365 0.5744457244873047 484.3058166503906 0.7568458318710327 537.0015258789062 0.7360057830810547 0.73538417 0.668346107006073 True -11 35736 33.21327209472656 0.5672070980072021 515.4484252929688 0.6617513298988342 533.5789794921875 0.7383992075920105 0.74461275 0.6406059861183167 True -12 38714 33.225119829177856 3.1011555194854736 472.0055847167969 0.5114558339118958 530.3638916015625 0.7409777045249939 0.7509434 0.6251261830329895 True -13 41692 33.239410400390625 0.6255621910095215 485.3580322265625 0.7032701969146729 527.5436401367188 0.7431237697601318 0.76055783 0.5923029184341431 True -14 44670 33.15424394607544 33.66012716293335 385.46234130859375 0.5023869276046753 526.1903686523438 0.7447361350059509 0.7665233 0.5754266381263733 True -15 47648 33.30981969833374 0.5639984607696533 474.1842041015625 0.4436405301094055 524.9476318359375 0.7460622191429138 0.77287805 0.5722223520278931 True -16 50626 32.5818932056427 0.563063383102417 408.4405517578125 0.3099968433380127 524.8348388671875 0.746366560459137 0.7736336 0.5648012757301331 True -17 53604 32.54819083213806 0.5670139789581299 342.00982666015625 0.5807454586029053 525.421875 0.7461574673652649 0.77429163 0.5716984868049622 True -18 56582 33.12128758430481 0.5617001056671143 447.32989501953125 0.419200599193573 526.2527465820312 0.7456645965576172 0.77278864 0.5792051553726196 False -19 59560 32.53829503059387 0.5625417232513428 422.97900390625 0.36080995202064514 526.5897216796875 0.7453597784042358 0.76953715 0.5880633592605591 False diff --git a/ENCSR637OPZ/cherimoya.fold_4.performance.tsv b/ENCSR637OPZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 125ed309366b0341128eb9e2e4efad794e27d189..0000000000000000000000000000000000000000 --- a/ENCSR637OPZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -525.421875 0.20976075530052185 0.7461574673652649 0.34435608983039856 0.7742916345596313 0.7185657620429993 0.5716984868049622 \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_0.evaluate.json b/ENCSR637XSC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 595314c6aaff19347eb702914c92264bca1720a7..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF180XQC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_0.fit.json b/ENCSR637XSC/cherimoya.fold_0.fit.json deleted file mode 100644 index 0c7153d45cd07a7c4a045b35053f2606001f914e..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF180XQC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_0.log b/ENCSR637XSC/cherimoya.fold_0.log deleted file mode 100644 index 6312b7d6a3dc0f3299d74389d1d2d6edee1cf5fa..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3772 46.11023783683777 4.0109641551971436 927.5689086914062 1.0408787727355957 1412.648681640625 0.7390103340148926 0.59439856 10.164299964904785 True -1 7544 41.63543343544006 1.8112034797668457 969.48583984375 0.9567481279373169 1146.952880859375 0.8338788151741028 0.58537495 2.7829983234405518 False -2 11316 41.716389656066895 0.8166263103485107 1031.7679443359375 1.021270513534546 1118.0633544921875 0.8426503539085388 0.5910691 1.6908904314041138 False -3 15088 41.649624824523926 0.7457764148712158 758.6337890625 1.2472211122512817 1099.9755859375 0.8482303023338318 0.60390055 1.5113790035247803 True -4 18860 41.59423637390137 0.8175103664398193 931.167236328125 1.2530901432037354 1086.8558349609375 0.8519362211227417 0.60691094 1.409438967704773 True -5 22632 41.559000968933105 1.962571144104004 980.1371459960938 0.7228094935417175 1084.50537109375 0.8536992073059082 0.6095604 1.4897462129592896 True -6 26404 41.71697545051575 0.763685941696167 792.7633056640625 0.5708141922950745 1079.3370361328125 0.8557085990905762 0.6163762 1.328662633895874 True -7 30176 41.57090473175049 0.7531263828277588 738.8792724609375 0.9346542954444885 1069.0030517578125 0.8583555817604065 0.61824006 1.2468990087509155 True -8 33948 42.097591400146484 0.748126745223999 841.8505859375 1.237028956413269 1057.85009765625 0.8613311648368835 0.6245162 1.1261039972305298 True -9 37720 41.5341362953186 0.7543785572052002 798.6292724609375 1.1205973625183105 1049.2576904296875 0.8639575242996216 0.63594764 1.0504281520843506 True -10 41492 41.55032777786255 0.7522387504577637 950.2012329101562 1.0753200054168701 1040.5750732421875 0.8668552041053772 0.6400089 1.0228595733642578 True -11 45264 41.22620940208435 0.7441294193267822 790.0635986328125 0.721422553062439 1030.193603515625 0.8691862225532532 0.6531436 0.9321469664573669 True -12 49036 40.901264905929565 0.7452821731567383 873.8216552734375 0.7487415671348572 1022.3164672851562 0.8715465068817139 0.66340697 0.8369619250297546 True -13 52808 40.81425857543945 0.7460107803344727 827.5621948242188 0.8039878010749817 1013.0157470703125 0.8738676309585571 0.6717524 0.8115538954734802 True -14 56580 40.72506308555603 0.7450952529907227 862.5101318359375 0.6010593771934509 1005.7380981445312 0.8757765889167786 0.6799303 0.755003035068512 True -15 60352 40.80736064910889 0.7450385093688965 789.814208984375 0.663478672504425 1001.182861328125 0.8766550421714783 0.68945277 0.7254510521888733 True -16 64124 40.813339710235596 0.7531471252441406 778.2066650390625 0.9277834892272949 998.6055908203125 0.877355694770813 0.69371355 0.6999036073684692 True -17 67896 40.77902007102966 0.7305269241333008 697.8322143554688 0.40432003140449524 997.6458129882812 0.8772071003913879 0.6946292 0.6924822926521301 True -18 71668 40.78793382644653 0.7445504665374756 829.1206665039062 0.6695151329040527 998.588623046875 0.8769142031669617 0.6950734 0.6901566386222839 True -19 75440 40.848081827163696 0.7445220947265625 783.0914306640625 0.48972705006599426 999.1637573242188 0.8766927123069763 0.69358873 0.6941360831260681 False diff --git a/ENCSR637XSC/cherimoya.fold_0.performance.tsv b/ENCSR637XSC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 00c78bb33008d2dd3e1e5f9a86402b87974b322e..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -998.588623046875 0.10381750762462616 0.8769142031669617 0.5686777234077454 0.6950734257698059 0.6584590673446655 0.6901566386222839 \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_1.evaluate.json b/ENCSR637XSC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index dbaef187a64a058c2bbbc0732f15512247e9154c..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF180XQC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_1.fit.json b/ENCSR637XSC/cherimoya.fold_1.fit.json deleted file mode 100644 index 13f7d6232850abf4fbaae8097fb5594618071b6a..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF180XQC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_1.log b/ENCSR637XSC/cherimoya.fold_1.log deleted file mode 100644 index c22e5fcd8df8defecae357adced2dba6bb1b7604..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3806 47.06945204734802 4.771178960800171 1114.80029296875 1.3797502517700195 1586.1993408203125 0.7397063970565796 0.60571206 10.276933670043945 True -1 7612 41.992910385131836 1.097522258758545 837.179931640625 1.0732042789459229 1273.188232421875 0.8385301232337952 0.61499083 2.378936529159546 True -2 11418 41.646095514297485 0.9891347885131836 981.3388061523438 1.3665162324905396 1228.726806640625 0.8478966355323792 0.6314354 1.3337211608886719 True -3 15224 41.226749420166016 1.006601333618164 1009.4413452148438 1.0114991664886475 1207.1978759765625 0.8533992171287537 0.6382096 1.1907459497451782 True -4 19030 41.09571027755737 0.9699616432189941 1007.10791015625 1.2031455039978027 1196.6495361328125 0.8566737174987793 0.6448025 1.1808912754058838 True -5 22836 41.148218870162964 1.409541368484497 880.935302734375 1.2541409730911255 1186.7064208984375 0.8593974113464355 0.64413285 1.2251836061477661 False -6 26642 41.15627145767212 0.9565153121948242 818.310791015625 1.0882952213287354 1180.5908203125 0.8617311716079712 0.64071834 1.1723244190216064 False -7 30448 41.15166211128235 0.9574873447418213 764.2498779296875 1.030919075012207 1167.696533203125 0.8647820949554443 0.65281945 1.003738522529602 True -8 34254 41.145371437072754 0.9526982307434082 930.86669921875 0.9904947280883789 1157.366943359375 0.8675553202629089 0.65683913 0.9533718228340149 True -9 38060 41.122045040130615 0.9719398021697998 792.44287109375 0.9548442363739014 1145.038330078125 0.8699943423271179 0.66506684 0.8578172326087952 True -10 41866 41.16659688949585 0.9555177688598633 968.7120971679688 0.537599503993988 1135.6827392578125 0.8726112246513367 0.6683917 0.8889686465263367 True -11 45672 41.06640887260437 0.9575788974761963 740.001220703125 0.8363527059555054 1124.3348388671875 0.8750705122947693 0.6743864 0.8259110450744629 True -12 49478 41.06851029396057 0.9510071277618408 874.7862548828125 0.8289350271224976 1114.5076904296875 0.8773821592330933 0.68329215 0.7664824724197388 True -13 53284 41.07954001426697 0.9502367973327637 750.5460205078125 0.972447395324707 1105.2027587890625 0.8796022534370422 0.69317967 0.7350534796714783 True -14 57090 41.15240979194641 31.687288284301758 823.7581787109375 0.8268144130706787 1095.9697265625 0.8815469145774841 0.70004237 0.709213376045227 True -15 60896 41.78651523590088 27.882651805877686 732.9213256835938 0.5714444518089294 1091.3363037109375 0.8824419975280762 0.7086985 0.6949175000190735 True -16 64702 41.84408950805664 0.9801926612854004 779.0049438476562 0.5266069173812866 1088.916259765625 0.8829489350318909 0.71410114 0.6750057339668274 True -17 68508 41.32656788825989 1.0231602191925049 937.451416015625 0.5741811990737915 1087.9920654296875 0.8829021453857422 0.7186079 0.6573001146316528 True -18 72314 41.36857795715332 0.9952614307403564 770.3408813476562 0.5318925380706787 1089.2913818359375 0.8822879791259766 0.7211491 0.6543858647346497 True -19 76120 41.29039001464844 0.9732692241668701 857.3488159179688 0.5188418626785278 1091.5694580078125 0.8819499015808105 0.72066927 0.6545504331588745 False diff --git a/ENCSR637XSC/cherimoya.fold_1.performance.tsv b/ENCSR637XSC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cdcd7e899db9d0c2dda2de0b13af1ed8955ae124..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1089.2913818359375 0.0958215743303299 0.8822880983352661 0.6001962423324585 0.7211490869522095 0.7084627747535706 0.6543858647346497 \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_2.evaluate.json b/ENCSR637XSC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f890a00fe15248751cbe76157c9201904aa48b07..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF180XQC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_2.fit.json b/ENCSR637XSC/cherimoya.fold_2.fit.json deleted file mode 100644 index 43f286244f66d352c0a99b72d10b09f17b00e9d8..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF180XQC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_2.log b/ENCSR637XSC/cherimoya.fold_2.log deleted file mode 100644 index b44f17939f28e03c18e33e1e0b52cd8149ca1565..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3995 48.671982765197754 2.948147773742676 951.8516845703125 1.3987977504730225 1430.990966796875 0.75108802318573 0.62354 10.68190860748291 True -1 7990 44.02797079086304 0.8676340579986572 959.0943603515625 1.4089317321777344 1189.223388671875 0.8368073105812073 0.61770415 2.876957893371582 False -2 11985 44.0549898147583 0.6890826225280762 992.2189331054688 1.0704489946365356 1157.88427734375 0.8443322777748108 0.63066685 1.8669965267181396 True -3 15980 44.050265073776245 0.671823263168335 949.580078125 1.3035439252853394 1138.0030517578125 0.8499215841293335 0.6320655 1.6440201997756958 True -4 19975 44.11500668525696 0.6731564998626709 913.9912109375 0.7309841513633728 1122.24658203125 0.8538631200790405 0.63905734 1.3413625955581665 True -5 23970 44.02788162231445 2.620445728302002 822.727294921875 0.9458328485488892 1116.9417724609375 0.8560773134231567 0.64139766 1.3826279640197754 True -6 27965 44.11064434051514 0.6758620738983154 788.4771728515625 0.9358744621276855 1109.560302734375 0.8583319783210754 0.6455132 1.241833209991455 True -7 31960 43.98397469520569 0.6841447353363037 942.4719848632812 0.6436642408370972 1099.092041015625 0.8608354330062866 0.6505296 1.086725115776062 True -8 35955 43.23387289047241 0.7750401496887207 823.660888671875 0.9395081400871277 1090.0372314453125 0.8632699847221375 0.6519162 1.0680553913116455 True -9 39950 43.3807156085968 0.6906106472015381 886.568359375 1.1197459697723389 1079.820068359375 0.8659322261810303 0.6554259 0.9584904313087463 True -10 43945 43.14825677871704 0.6637058258056641 777.1302490234375 0.8174294233322144 1071.9969482421875 0.8680694699287415 0.6677265 0.9300380945205688 True -11 47940 43.12660813331604 0.6749207973480225 887.4161376953125 0.5208441615104675 1061.8204345703125 0.8703994154930115 0.67029506 0.8756874799728394 True -12 51935 43.18938422203064 0.6796777248382568 834.5364990234375 0.8003314733505249 1051.26171875 0.8731201887130737 0.68182635 0.8082525134086609 True -13 55930 43.166049003601074 1.2902581691741943 811.6843872070312 0.9569872617721558 1041.9715576171875 0.8752394914627075 0.68953985 0.7708324193954468 True -14 59925 43.369953870773315 0.6665480136871338 896.2081298828125 0.792289137840271 1035.76025390625 0.8769728541374207 0.69654715 0.7396953105926514 True -15 63920 43.123921394348145 0.6645281314849854 837.5687255859375 1.0140595436096191 1029.920166015625 0.878178060054779 0.702673 0.7107152938842773 True -16 67915 43.3420946598053 3.1968905925750732 819.7634887695312 0.7512626647949219 1027.2886962890625 0.8787219524383545 0.7062812 0.699545681476593 True -17 71910 43.17408204078674 0.6661207675933838 863.597900390625 0.6748049259185791 1027.25830078125 0.8785714507102966 0.7106232 0.6889233589172363 True -18 75905 43.07471680641174 0.6663239002227783 851.8280639648438 0.6126227378845215 1027.4683837890625 0.8782846331596375 0.7095889 0.6826452016830444 False -19 79900 43.11880159378052 0.6601212024688721 779.918701171875 0.5471579432487488 1029.432861328125 0.8779775500297546 0.7099969 0.6833280920982361 False diff --git a/ENCSR637XSC/cherimoya.fold_2.performance.tsv b/ENCSR637XSC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7ebfca66693535540164d2fb54760e2b55358a72..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1027.25830078125 0.1012699231505394 0.8785714507102966 0.5799081921577454 0.7106232047080994 0.675442636013031 0.6889233589172363 \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_3.evaluate.json b/ENCSR637XSC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0843fd95fe418ce0485fcf393280380ccdc106e7..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF180XQC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_3.fit.json b/ENCSR637XSC/cherimoya.fold_3.fit.json deleted file mode 100644 index 5a006506952ac04036980b527e7a930f5cb73171..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF180XQC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_3.log b/ENCSR637XSC/cherimoya.fold_3.log deleted file mode 100644 index d06e6d0d1923d5e24b533b3d125af09a3b7aed96..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3868 47.53524160385132 4.147722244262695 1042.994140625 0.875519871711731 1397.9134521484375 0.7505239844322205 0.58363336 9.785021781921387 True -1 7736 42.64780807495117 3.4165844917297363 983.9017944335938 0.7270945310592651 1159.3094482421875 0.8387650847434998 0.5781037 3.2601265907287598 False -2 11604 42.71403527259827 0.8840241432189941 1001.4022216796875 1.0455727577209473 1129.555419921875 0.847183883190155 0.5768251 1.6417877674102783 False -3 15472 42.73994708061218 0.8416268825531006 903.1312866210938 1.6248500347137451 1104.9351806640625 0.8527588248252869 0.59042305 1.5517350435256958 True -4 19340 42.66897892951965 0.8040585517883301 1013.919189453125 1.0443274974822998 1097.6854248046875 0.8548785448074341 0.59229434 1.402134656906128 True -5 23208 42.646955251693726 0.8086655139923096 889.9476318359375 1.150803804397583 1095.0111083984375 0.8565573692321777 0.59376323 1.5022727251052856 True -6 27076 42.61185812950134 0.8046650886535645 854.56201171875 1.1420555114746094 1087.375 0.8587321043014526 0.5956623 1.281079888343811 True -7 30944 42.605650663375854 0.8040475845336914 857.8896484375 1.2079310417175293 1076.1187744140625 0.8617557883262634 0.59458417 1.0932470560073853 False -8 34812 42.6606228351593 0.9228172302246094 780.1673583984375 0.8759380578994751 1068.4610595703125 0.8637398481369019 0.6067096 1.0181386470794678 True -9 38680 42.65313172340393 0.8165407180786133 850.4482421875 0.9364551305770874 1059.69140625 0.8664163947105408 0.6115167 0.9635012745857239 True -10 42548 42.616448402404785 0.8108925819396973 978.1434326171875 0.7676796913146973 1051.492431640625 0.8684870600700378 0.62176174 0.940578281879425 True -11 46416 42.70117926597595 0.8210239410400391 905.427978515625 0.772254467010498 1042.79541015625 0.8707007169723511 0.6341273 0.9136182069778442 True -12 50284 41.95026206970215 0.8131484985351562 744.856201171875 1.0064496994018555 1035.9512939453125 0.8727515935897827 0.63737243 0.912563681602478 True -13 54152 41.776209115982056 0.7977852821350098 843.9600219726562 0.6536951661109924 1028.0643310546875 0.8744901418685913 0.64749974 0.8845593333244324 True -14 58020 41.76199746131897 0.8144750595092773 756.639404296875 0.5796703100204468 1021.8431396484375 0.8762115836143494 0.65953594 0.8529709577560425 True -15 61888 41.83421778678894 0.8189680576324463 714.2505493164062 0.4082634449005127 1016.2403564453125 0.8775573372840881 0.6723151 0.7934248447418213 True -16 65756 41.82549071311951 0.8267340660095215 741.1549072265625 0.6280040740966797 1012.2019653320312 0.8781285881996155 0.6794888 0.7556467652320862 True -17 69624 41.87371850013733 0.8109557628631592 692.1737060546875 0.6146921515464783 1012.4981079101562 0.8781245350837708 0.6843641 0.7420281767845154 True -18 73492 41.979522466659546 0.8420586585998535 684.2198486328125 0.6870937347412109 1012.8333129882812 0.8778366446495056 0.68505335 0.7370175123214722 True -19 77360 41.98813819885254 2.9707396030426025 690.47216796875 0.5888462066650391 1013.51611328125 0.877598762512207 0.68346316 0.735275149345398 False diff --git a/ENCSR637XSC/cherimoya.fold_3.performance.tsv b/ENCSR637XSC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e74c96110cafd9eb2df03ddff62e616646b57838..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1012.8333129882812 0.101835697889328 0.8778367042541504 0.5753732919692993 0.6850533485412598 0.648701548576355 0.7370175123214722 \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_4.evaluate.json b/ENCSR637XSC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index dae68246dcc82034b9beb8f91ed92448be064c04..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF180XQC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_4.fit.json b/ENCSR637XSC/cherimoya.fold_4.fit.json deleted file mode 100644 index 19ed605a0a44d5d6f552280b45791f25a5c61a71..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF180XQC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637XSC/cherimoya.fold_4.log b/ENCSR637XSC/cherimoya.fold_4.log deleted file mode 100644 index 09c76fb4e1707ac9032a58edff42e7810ec9d602..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3954 48.38598108291626 4.075282573699951 1063.544189453125 1.1961727142333984 1359.2100830078125 0.7432149648666382 0.5712865 10.395124435424805 True -1 7908 43.535430908203125 0.7702393531799316 1011.049072265625 1.220131516456604 1107.1121826171875 0.8366308808326721 0.5784297 2.5680792331695557 True -2 11862 43.631717920303345 0.9521255493164062 912.9126586914062 1.4947412014007568 1074.093994140625 0.8463178277015686 0.5699329 1.8993312120437622 False -3 15816 43.56252479553223 0.7824611663818359 937.9129638671875 1.0998539924621582 1060.11669921875 0.8504955172538757 0.5752703 1.608328938484192 False -4 19770 43.61839747428894 0.7738523483276367 1059.5478515625 0.6777593493461609 1048.8857421875 0.8534661531448364 0.5894791 1.4214050769805908 True -5 23724 43.60807824134827 0.7737655639648438 934.02734375 1.1165390014648438 1044.9931640625 0.8550892472267151 0.5940697 1.4436858892440796 True -6 27678 43.619224071502686 0.7687225341796875 850.9575805664062 1.405646562576294 1038.553466796875 0.8576516509056091 0.593962 1.2449501752853394 False -7 31632 42.806721448898315 0.7375102043151855 754.055419921875 0.9740498065948486 1027.1787109375 0.8602519631385803 0.61013794 1.1278599500656128 True -8 35586 42.64557123184204 0.7407557964324951 760.7822265625 0.587510347366333 1019.480712890625 0.8627305030822754 0.61696935 1.0517518520355225 True -9 39540 42.638850688934326 0.751800537109375 833.3850708007812 1.0168100595474243 1015.640625 0.8643760681152344 0.61419255 1.0198071002960205 False -10 43494 42.72072792053223 0.7528901100158691 924.5551147460938 0.9126923084259033 1006.9762573242188 0.8671422004699707 0.62483335 0.9347153306007385 True -11 47448 42.64889430999756 17.625165224075317 845.27783203125 1.040042519569397 999.9710083007812 0.8692948818206787 0.6293598 0.9281678795814514 True -12 51402 42.70545172691345 0.8368206024169922 788.3046264648438 0.5737711787223816 991.2471313476562 0.871635913848877 0.63688606 0.8672757148742676 True -13 55356 42.711909770965576 0.7559225559234619 908.793212890625 0.5889909267425537 984.344482421875 0.8735979199409485 0.64714473 0.817253053188324 True -14 59310 42.74564027786255 0.7515103816986084 774.755859375 1.0041425228118896 978.4515991210938 0.8749374151229858 0.65669584 0.7866567373275757 True -15 63264 42.708338499069214 0.7829477787017822 683.3139038085938 0.793262243270874 974.1494750976562 0.8762595653533936 0.6647599 0.7569532990455627 True -16 67218 42.7142608165741 0.7657201290130615 784.3427124023438 0.6596218347549438 971.6746826171875 0.8767678141593933 0.6730391 0.7272109985351562 True -17 71172 42.676960468292236 0.7530951499938965 809.8222045898438 0.6594573259353638 970.8350219726562 0.8765615820884705 0.67253107 0.719801127910614 False -18 75126 42.63326907157898 0.9046528339385986 723.0463256835938 0.6382178068161011 972.1051025390625 0.8761419653892517 0.6757043 0.713499128818512 True -19 79080 42.66486597061157 0.754033088684082 732.543212890625 0.5628836750984192 973.2294311523438 0.8759099245071411 0.6746533 0.7164719104766846 False diff --git a/ENCSR637XSC/cherimoya.fold_4.performance.tsv b/ENCSR637XSC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d3c8bb900fec1f0f779effa9b46512dcd525feae..0000000000000000000000000000000000000000 --- a/ENCSR637XSC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -972.1051025390625 0.1050504744052887 0.8761419653892517 0.5627360939979553 0.675704300403595 0.6292561292648315 0.713499128818512 \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_0.evaluate.json b/ENCSR637ZLM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d442ccf780abbddf700c05d71e7f55eedf6a8df3..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF144PIF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_0.fit.json b/ENCSR637ZLM/cherimoya.fold_0.fit.json deleted file mode 100644 index 9ef6f8ed833d913eb02510f83c0b94fd10b1b935..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF144PIF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_0.log b/ENCSR637ZLM/cherimoya.fold_0.log deleted file mode 100644 index 09d95dff19404794dc0c5791a4b785ca9314f612..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.293564796447754 4.168702125549316 605.230712890625 0.5241833925247192 622.7272338867188 0.2722429633140564 0.78579223 5.632774353027344 True -1 5518 30.431280374526978 0.896963357925415 511.27880859375 0.38071393966674805 560.700439453125 0.3403938412666321 0.8395792 1.2861342430114746 True -2 8277 30.416041374206543 0.5804355144500732 435.63818359375 0.3849521279335022 551.6511840820312 0.34922274947166443 0.8442527 0.6082000732421875 True -3 11036 30.34478783607483 0.6459341049194336 535.474365234375 0.2891848683357239 546.22314453125 0.35459810495376587 0.8507882 0.4694453179836273 True -4 13795 30.306787967681885 0.5751473903656006 440.5357360839844 0.44735345244407654 544.5476684570312 0.35703158378601074 0.8527758 0.38604429364204407 True -5 16554 30.35174798965454 0.5820071697235107 388.6981201171875 0.3818386197090149 540.0842895507812 0.36381348967552185 0.86024487 0.3574429750442505 True -6 19313 30.327327251434326 0.5688581466674805 441.7862548828125 0.3286861181259155 539.5969848632812 0.3637910485267639 0.8607099 0.35015869140625 True -7 22072 30.245802402496338 0.5716953277587891 467.9007568359375 0.27236488461494446 537.3250122070312 0.3666369616985321 0.86713654 0.344500869512558 True -8 24831 29.63120436668396 0.5714807510375977 436.91497802734375 0.31899091601371765 534.7615356445312 0.3699879050254822 0.8697041 0.29831764101982117 True -9 27590 29.6755690574646 0.636376142501831 488.61395263671875 0.2604585587978363 532.6132202148438 0.37271130084991455 0.87139875 0.2850949168205261 True -10 30349 29.642719984054565 0.5644233226776123 325.04974365234375 0.278880774974823 531.3685302734375 0.37417036294937134 0.87608075 0.2678634822368622 True -11 33108 29.72591757774353 0.5664749145507812 535.4989013671875 0.24837259948253632 530.7500610351562 0.3743680417537689 0.87830603 0.2663176953792572 True -12 35867 29.86702847480774 0.5566315650939941 419.6694030761719 0.22946986556053162 528.2281494140625 0.3777771592140198 0.8840137 0.24270780384540558 True -13 38626 29.685420751571655 0.568138837814331 457.97210693359375 0.21250292658805847 525.5870971679688 0.3809753954410553 0.88921344 0.22306405007839203 True -14 41385 29.67183208465576 0.5731053352355957 525.2344970703125 0.22160586714744568 524.8944091796875 0.3814648985862732 0.8921102 0.21058961749076843 True -15 44144 29.72052240371704 0.9279119968414307 410.965576171875 0.15665210783481598 523.7662963867188 0.3830421566963196 0.8941588 0.20374959707260132 True -16 46903 29.661855220794678 0.554771900177002 512.5450439453125 0.1867678016424179 522.7902221679688 0.383839875459671 0.896557 0.1962708979845047 True -17 49662 29.678775787353516 0.5749883651733398 380.74285888671875 0.17525792121887207 522.9945068359375 0.38325387239456177 0.8976306 0.19496025145053864 True -18 52421 29.658637285232544 0.553250789642334 449.61248779296875 0.2714536190032959 523.0496215820312 0.38307875394821167 0.89655995 0.19612742960453033 False -19 55180 29.675416231155396 0.5614173412322998 428.2703857421875 0.15106557309627533 522.9984741210938 0.3840164244174957 0.89650756 0.19631163775920868 False diff --git a/ENCSR637ZLM/cherimoya.fold_0.performance.tsv b/ENCSR637ZLM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 274f3fac9b1e6e0d43a51b795d82e23b29b22735..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -522.9945068359375 0.40579986572265625 0.38325387239456177 0.14010941982269287 0.8976305723190308 0.8700359463691711 0.19496025145053864 \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_1.evaluate.json b/ENCSR637ZLM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 26718687270f185c4d3ca5dd00e1bb500239cbc1..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF144PIF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_1.fit.json b/ENCSR637ZLM/cherimoya.fold_1.fit.json deleted file mode 100644 index d999e2f45937e04b508f4ad0850b443d6017d9cd..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF144PIF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_1.log b/ENCSR637ZLM/cherimoya.fold_1.log deleted file mode 100644 index 644ab6f4787c179057209f03d76b43323a5aa284..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2701 34.3882474899292 3.767063856124878 508.2978820800781 0.37508004903793335 720.5823364257812 0.2678498327732086 0.7732015 5.248267650604248 True -1 5402 29.757333517074585 3.2735979557037354 437.8248291015625 0.3963969945907593 642.9689331054688 0.3459920883178711 0.82815427 1.6473978757858276 True -2 8103 29.684118032455444 0.7070231437683105 531.9324951171875 0.5150727033615112 627.5899047851562 0.35836824774742126 0.83982974 0.781313419342041 True -3 10804 29.73990535736084 0.7080292701721191 468.3577880859375 0.45666369795799255 617.1032104492188 0.36752626299858093 0.84995055 0.5410001277923584 True -4 13505 29.97549295425415 40.536383628845215 423.98004150390625 0.25795310735702515 613.6974487304688 0.369553804397583 0.85288656 0.4071495831012726 True -5 16206 29.71109652519226 0.7274069786071777 461.667724609375 0.23515045642852783 610.8880615234375 0.37429094314575195 0.8578113 0.4000779688358307 True -6 18907 29.73335886001587 0.707256555557251 501.8736877441406 0.29586872458457947 605.8864135742188 0.3782300055027008 0.86596537 0.3483911156654358 True -7 21608 29.671766757965088 0.7027888298034668 424.36480712890625 0.3103436231613159 603.5430297851562 0.38065096735954285 0.8676953 0.34353169798851013 True -8 24309 29.44003963470459 0.692246675491333 548.9691162109375 0.4118039608001709 600.761474609375 0.3837331235408783 0.87292635 0.3165857791900635 True -9 27010 29.10332679748535 0.734647274017334 394.2386474609375 0.22509916126728058 597.8283081054688 0.38587531447410583 0.8772905 0.2943529784679413 True -10 29711 29.07604956626892 0.68817138671875 362.4991760253906 0.28637534379959106 594.673828125 0.39017507433891296 0.88059276 0.28473252058029175 True -11 32412 29.123945951461792 0.6976890563964844 364.7430419921875 0.24400144815444946 592.77294921875 0.39186805486679077 0.8869745 0.2768191993236542 True -12 35113 29.1476571559906 1.5468707084655762 456.0870361328125 0.1962299942970276 590.2980346679688 0.39496585726737976 0.8907231 0.25789347290992737 True -13 37814 29.117804765701294 0.7596611976623535 478.22979736328125 0.2822762131690979 588.10986328125 0.3963448703289032 0.8959474 0.23886169493198395 True -14 40515 29.114074230194092 0.732041597366333 521.999755859375 0.26923877000808716 586.3382568359375 0.39860764145851135 0.8972802 0.22947679460048676 True -15 43216 29.224963188171387 0.703458309173584 431.2310791015625 0.19285978376865387 585.4874267578125 0.3988521695137024 0.9004873 0.2213025540113449 True -16 45917 29.255350589752197 0.7129769325256348 447.8477783203125 0.19116021692752838 583.1277465820312 0.40176621079444885 0.90373355 0.21508511900901794 True -17 48618 29.20455527305603 0.7030363082885742 458.66729736328125 0.31653475761413574 584.3601684570312 0.3994470536708832 0.90316427 0.21145504713058472 False -18 51319 29.492862224578857 44.60669684410095 406.69879150390625 0.22782570123672485 585.1268310546875 0.39923807978630066 0.9056848 0.21093861758708954 True -19 54020 29.085750818252563 0.7364847660064697 464.7349853515625 0.16685637831687927 583.3426513671875 0.4019758105278015 0.90484035 0.2116163671016693 False diff --git a/ENCSR637ZLM/cherimoya.fold_1.performance.tsv b/ENCSR637ZLM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index aca8374bc0a45b360dab631c224c91d651da9638..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -585.1268310546875 0.3917611837387085 0.39923804998397827 0.15708406269550323 0.9056848287582397 0.8931859731674194 0.21093861758708954 \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_2.evaluate.json b/ENCSR637ZLM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d0ed95442262856bee8fb96a973a0e37e1008427..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF144PIF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_2.fit.json b/ENCSR637ZLM/cherimoya.fold_2.fit.json deleted file mode 100644 index 807b1d65e292a5aacef40b95724828d2b1251ac7..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF144PIF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_2.log b/ENCSR637ZLM/cherimoya.fold_2.log deleted file mode 100644 index fb6801da24a3cb7eedb5236d29bb8283ce3370e8..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 36.67197895050049 10.188565731048584 381.8662109375 0.2147812694311142 661.9548950195312 0.26873454451560974 0.76834905 5.15533971786499 True -1 5756 31.718722581863403 1.4116344451904297 504.2215270996094 0.34674781560897827 591.5709838867188 0.34671589732170105 0.8341069 1.0986642837524414 True -2 8634 31.634434700012207 0.54506516456604 482.9441223144531 0.37215596437454224 583.8994140625 0.35018211603164673 0.83209336 0.5430582165718079 False -3 11512 31.619866609573364 0.5507168769836426 583.7879638671875 0.4199793338775635 574.9295043945312 0.36208757758140564 0.83987117 0.4490810036659241 True -4 14390 31.600724697113037 0.8507280349731445 574.3485107421875 0.3660699129104614 570.6831665039062 0.36599063873291016 0.8489795 0.39892247319221497 True -5 17268 31.69055461883545 0.5413937568664551 456.2395324707031 0.3873109519481659 568.3409423828125 0.3673250675201416 0.8519453 0.32829537987709045 True -6 20146 31.641384601593018 1.12034273147583 383.5587158203125 0.2995147705078125 565.1674194335938 0.3705262541770935 0.8548193 0.31426435708999634 True -7 23024 31.63960313796997 0.5414626598358154 524.9641723632812 0.3491111695766449 564.06298828125 0.371155709028244 0.8591753 0.30838385224342346 True -8 25902 31.370117902755737 0.5394287109375 489.02923583984375 0.3102651834487915 561.1925048828125 0.37525615096092224 0.8633109 0.31691956520080566 True -9 28780 31.02173376083374 1.1682510375976562 455.62750244140625 0.2177850902080536 558.7739868164062 0.3780844807624817 0.866675 0.2986297607421875 True -10 31658 31.017553329467773 0.5435068607330322 513.5687866210938 0.2783917188644409 557.3525390625 0.37901240587234497 0.870745 0.2871605157852173 True -11 34536 30.993627548217773 0.5430443286895752 454.6685791015625 0.2729882299900055 554.4418334960938 0.3834526836872101 0.8741569 0.2710653841495514 True -12 37414 30.977434158325195 0.5464210510253906 426.03387451171875 0.25543490052223206 552.6442260742188 0.385480135679245 0.8804726 0.24681149423122406 True -13 40292 31.095709562301636 0.5425479412078857 506.75567626953125 0.21475058794021606 550.7979736328125 0.387530118227005 0.8824852 0.23330999910831451 True -14 43170 31.157907724380493 0.5430333614349365 529.4723510742188 0.18053875863552094 549.4839477539062 0.388783723115921 0.88663334 0.2225787490606308 True -15 46048 31.149161100387573 0.5408275127410889 435.1111755371094 0.1851138472557068 548.1519775390625 0.39081183075904846 0.88760155 0.21406809985637665 True -16 48926 31.152282238006592 0.5415947437286377 359.8001708984375 0.19417977333068848 547.6163330078125 0.39126092195510864 0.890734 0.2074277251958847 True -17 51804 33.128023862838745 21.42598843574524 516.0477905273438 0.2397773414850235 547.890625 0.39025330543518066 0.89263004 0.20642365515232086 True -18 54682 31.058160066604614 29.578104972839355 442.56903076171875 0.115321084856987 547.89501953125 0.39088019728660583 0.89063615 0.20613394677639008 False -19 57560 34.47972345352173 0.5450780391693115 479.8697814941406 0.12392395734786987 548.3577880859375 0.39003986120224 0.891817 0.20628675818443298 False diff --git a/ENCSR637ZLM/cherimoya.fold_2.performance.tsv b/ENCSR637ZLM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b223e3f16729aaafea5f670b3f45de99bc46f708..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -547.890625 0.3984454274177551 0.39025333523750305 0.14635983109474182 0.8926300406455994 0.8740788102149963 0.20642365515232086 \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_3.evaluate.json b/ENCSR637ZLM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d7fb0a9d978e65186dff782fe9220d6657c742d1..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF144PIF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_3.fit.json b/ENCSR637ZLM/cherimoya.fold_3.fit.json deleted file mode 100644 index 0d12fd8862ddc0e40ea6b8e40c102de08eb40f99..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF144PIF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_3.log b/ENCSR637ZLM/cherimoya.fold_3.log deleted file mode 100644 index 2ea10cdd7995bed0eeaa0f248251f7dcbc37d943..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 34.86575889587402 3.7308266162872314 526.5567626953125 0.38130101561546326 623.9342651367188 0.2819150388240814 0.7724707 4.998373985290527 True -1 5534 31.06614065170288 2.7024924755096436 410.2040100097656 0.42055177688598633 561.8786010742188 0.34795719385147095 0.83071977 1.1619791984558105 True -2 8301 30.42515230178833 1.0096688270568848 441.5751953125 0.36930274963378906 550.3900756835938 0.3588141202926636 0.8403553 0.6428006887435913 True -3 11068 30.4647159576416 0.6757378578186035 394.13629150390625 0.40139785408973694 544.7703857421875 0.36469247937202454 0.84961206 0.6370134353637695 True -4 13835 30.521671295166016 0.83418869972229 482.2796325683594 0.28236791491508484 543.2594604492188 0.36581456661224365 0.8527925 0.4543015956878662 True -5 16602 30.721395254135132 3.4276742935180664 413.6401672363281 0.3648349344730377 539.7161254882812 0.36988598108291626 0.8575976 0.38656628131866455 True -6 19369 30.800002098083496 0.5501599311828613 508.48358154296875 0.3563746213912964 539.0177001953125 0.37101706862449646 0.8596238 0.3590086102485657 True -7 22136 30.569510221481323 0.5285990238189697 461.73260498046875 0.18464019894599915 536.3555908203125 0.37366634607315063 0.8652537 0.3390629291534424 True -8 24903 30.46616530418396 0.5239379405975342 502.5547790527344 0.3504025936126709 532.9181518554688 0.3777047395706177 0.86647224 0.322133332490921 True -9 27670 30.216020345687866 1.7024860382080078 367.72113037109375 0.29847633838653564 532.28173828125 0.37803027033805847 0.86922574 0.3082980811595917 True -10 30437 29.893504858016968 1.9904983043670654 441.97027587890625 0.18176063895225525 529.7767333984375 0.38142821192741394 0.87348664 0.3005581200122833 True -11 33204 29.961989641189575 2.1221425533294678 464.9840087890625 0.33869725465774536 528.3402099609375 0.3830525577068329 0.8779987 0.2887336313724518 True -12 35971 30.105891466140747 1.8596117496490479 453.1920166015625 0.30673861503601074 526.2376708984375 0.3859787881374359 0.8827972 0.2727995216846466 True -13 38738 29.99949860572815 0.5105044841766357 521.59228515625 0.17871111631393433 524.5702514648438 0.3877640664577484 0.8846374 0.2552625238895416 True -14 41505 29.80633544921875 0.5122599601745605 349.3365173339844 0.19245308637619019 522.5518188476562 0.3904283046722412 0.8878294 0.24465297162532806 True -15 44272 29.819496870040894 0.5083253383636475 430.3805236816406 0.266476035118103 521.5310668945312 0.3906773030757904 0.8914892 0.23087266087532043 True -16 47039 29.79621720314026 16.82455039024353 450.95574951171875 0.1636512279510498 520.6434936523438 0.39207229018211365 0.89537317 0.22111740708351135 True -17 49806 29.943735599517822 0.514620304107666 433.46868896484375 0.1710701286792755 520.743896484375 0.39187929034233093 0.89468974 0.21723486483097076 False -18 52573 35.9005446434021 5.385989427566528 490.05072021484375 0.19646872580051422 520.2406005859375 0.3929438292980194 0.8955635 0.21543295681476593 True -19 55340 29.962519645690918 0.566868782043457 453.21881103515625 0.20083758234977722 521.0774536132812 0.39130181074142456 0.8948731 0.21506059169769287 False diff --git a/ENCSR637ZLM/cherimoya.fold_3.performance.tsv b/ENCSR637ZLM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d633aac1e7f093f518db2f4d39336d911fcff914..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -520.2406005859375 0.40078964829444885 0.3929438292980194 0.14771994948387146 0.8955634832382202 0.8642057180404663 0.21543295681476593 \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_4.evaluate.json b/ENCSR637ZLM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 80084145665c050ee959f20b748a30fbd4f63e55..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF144PIF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_4.fit.json b/ENCSR637ZLM/cherimoya.fold_4.fit.json deleted file mode 100644 index 9e00e5011c4d2dc684b4db8e31c704bf6178fd54..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF144PIF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR637ZLM/cherimoya.fold_4.log b/ENCSR637ZLM/cherimoya.fold_4.log deleted file mode 100644 index a6c183e23e64a9d30221d69034667a8a8b53d309..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 35.58238649368286 4.98470664024353 423.55145263671875 0.3641301691532135 575.287841796875 0.2662952244281769 0.77472687 5.075141906738281 True -1 5612 30.908730030059814 0.6178061962127686 467.6544189453125 0.5952243208885193 520.3816528320312 0.33314505219459534 0.82850033 1.044206142425537 True -2 8418 30.865890979766846 0.6032164096832275 508.60247802734375 0.36151522397994995 510.623291015625 0.34128621220588684 0.8343694 0.48114290833473206 True -3 11224 30.88401699066162 0.6025204658508301 433.81036376953125 0.4120326638221741 508.1846923828125 0.34367772936820984 0.83955365 0.4692690670490265 True -4 14030 30.896655082702637 0.5990891456604004 507.0790100097656 0.28075557947158813 505.0065612792969 0.3468240797519684 0.84754544 0.35552874207496643 True -5 16836 30.85870885848999 0.5982778072357178 460.84185791015625 0.3193022608757019 501.3002624511719 0.3518368899822235 0.85326487 0.32412105798721313 True -6 19642 31.093448877334595 29.450774908065796 440.6194152832031 0.36695778369903564 498.94677734375 0.35468244552612305 0.8574082 0.3115655481815338 True -7 22448 31.05307698249817 0.6048274040222168 398.03826904296875 0.3015804588794708 497.3732604980469 0.35633957386016846 0.860834 0.2971566319465637 True -8 25254 30.82959485054016 0.6074597835540771 469.73004150390625 0.3295973539352417 495.040771484375 0.35983920097351074 0.8674793 0.28062933683395386 True -9 28060 30.637802124023438 0.6001796722412109 473.1104736328125 0.21251150965690613 494.05902099609375 0.3605000078678131 0.8704283 0.27682793140411377 True -10 30866 30.236681938171387 2.0401530265808105 515.7223510742188 0.22028237581253052 492.09051513671875 0.3635631203651428 0.8731162 0.2686549425125122 True -11 33672 30.296205520629883 0.6058285236358643 497.39337158203125 0.2335510551929474 490.276611328125 0.3659990131855011 0.88060117 0.2411513775587082 True -12 36478 30.241057872772217 0.5935776233673096 490.23779296875 0.2274542897939682 488.8977355957031 0.3675226867198944 0.88442963 0.22171947360038757 True -13 39284 30.333549976348877 0.5898041725158691 491.3131103515625 0.21240980923175812 487.6242370605469 0.3688596189022064 0.8902359 0.20870673656463623 True -14 42090 30.269667148590088 0.5973706245422363 423.90240478515625 0.17460192739963531 486.135498046875 0.3703891336917877 0.8913409 0.19662430882453918 True -15 44896 30.27790927886963 0.600414514541626 507.3466796875 0.1835774928331375 485.43939208984375 0.371835321187973 0.8938533 0.19061589241027832 True -16 47702 30.280983448028564 0.5996484756469727 425.4483337402344 0.21579070389270782 484.67291259765625 0.37264004349708557 0.896232 0.18466627597808838 True -17 50508 30.275267124176025 3.5097155570983887 410.7953186035156 0.14178144931793213 484.3689880371094 0.37369218468666077 0.8966443 0.18174520134925842 True -18 53314 30.29099988937378 0.6017022132873535 446.3786315917969 0.15098151564598083 485.1245422363281 0.3721889853477478 0.89750063 0.18362805247306824 True -19 56120 30.208831548690796 0.5979714393615723 456.741943359375 0.21964581310749054 485.3999328613281 0.3717851936817169 0.8972428 0.18394999206066132 False diff --git a/ENCSR637ZLM/cherimoya.fold_4.performance.tsv b/ENCSR637ZLM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index aa4d1752daaf16dd0a951333996c50249a01f0c0..0000000000000000000000000000000000000000 --- a/ENCSR637ZLM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -485.1245422363281 0.4157724380493164 0.3721890151500702 0.13264937698841095 0.8975006341934204 0.8661782741546631 0.18362805247306824 \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_0.evaluate.json b/ENCSR639ZJI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8cea24293b00f361c21604ca19c456b8726349d6..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF172NYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_0.fit.json b/ENCSR639ZJI/cherimoya.fold_0.fit.json deleted file mode 100644 index 98c95be75378e688c3b65bb66ff27328002371fc..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF172NYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_0.log b/ENCSR639ZJI/cherimoya.fold_0.log deleted file mode 100644 index a675f0cd69c144592da646a17f6171b66b6a6471..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1614 22.290913820266724 3.76806378364563 185.46737670898438 1.1253281831741333 277.4256591796875 0.139432892203331 0.34921846 8.817268371582031 True -1 3228 17.77753233909607 0.40429115295410156 217.60531616210938 1.6279536485671997 249.67018127441406 0.23318108916282654 0.4787138 6.227936267852783 True -2 4842 17.790491342544556 0.3272578716278076 255.97552490234375 1.2975854873657227 229.7728271484375 0.29814136028289795 0.50073546 4.949809551239014 True -3 6456 17.7688307762146 0.3268616199493408 126.23846435546875 1.0950052738189697 222.41488647460938 0.3116033673286438 0.50758034 3.417553663253784 True -4 8070 17.847447872161865 0.32877039909362793 160.67784118652344 1.055063009262085 219.19529724121094 0.3201552927494049 0.5207638 2.9096333980560303 True -5 9684 17.81160569190979 0.32915163040161133 166.98849487304688 0.8876478672027588 216.64817810058594 0.3279808759689331 0.5312983 2.3700051307678223 True -6 11298 17.803512811660767 0.32135987281799316 180.77322387695312 0.7107774615287781 215.20294189453125 0.3321196138858795 0.5441831 1.8840770721435547 True -7 12912 17.794522523880005 0.3297281265258789 157.81820678710938 0.9203475117683411 213.6022491455078 0.3358399569988251 0.57201415 1.574033260345459 True -8 14526 17.790619134902954 0.3307058811187744 188.1038055419922 0.8431112766265869 212.62631225585938 0.3388391137123108 0.58297956 1.3894950151443481 True -9 16140 17.808106184005737 0.3480257987976074 152.20028686523438 0.7952755689620972 211.85853576660156 0.34114351868629456 0.598416 1.2091931104660034 True -10 17754 17.793875694274902 0.3573427200317383 174.75929260253906 0.9395601749420166 210.6407470703125 0.3452083170413971 0.61284995 1.0848485231399536 True -11 19368 17.793742656707764 0.3477451801300049 186.76869201660156 0.6152327656745911 210.24636840820312 0.3451679050922394 0.62223816 1.0117038488388062 True -12 20982 17.792503833770752 0.3489413261413574 169.0107421875 0.7198625802993774 209.21714782714844 0.35014837980270386 0.6332626 0.9040335416793823 True -13 22596 17.772774696350098 0.7263646125793457 185.52545166015625 0.8594732284545898 207.99423217773438 0.35428544878959656 0.64652646 0.8067229986190796 True -14 24210 17.81180500984192 1.2337806224822998 143.75283813476562 0.7084313631057739 207.7432098388672 0.35347476601600647 0.65771157 0.740597665309906 True -15 25824 17.812482595443726 0.3696444034576416 138.7149658203125 0.6782500147819519 207.3546600341797 0.35359612107276917 0.6691448 0.6807935237884521 True -16 27438 17.81549596786499 0.3445773124694824 159.38174438476562 0.5870194435119629 206.83120727539062 0.3550474941730499 0.6725137 0.6496505737304688 True -17 29052 17.8111355304718 0.3407285213470459 169.14260864257812 0.5493583679199219 206.99887084960938 0.3542217016220093 0.6746523 0.6375830769538879 True -18 30666 17.843961477279663 0.34917330741882324 145.5321044921875 0.5232874751091003 207.3275146484375 0.3525369167327881 0.67485607 0.6347155570983887 True -19 32280 17.8350989818573 0.33931756019592285 164.63319396972656 0.42304307222366333 207.43275451660156 0.3520907163619995 0.6729512 0.6381295919418335 False diff --git a/ENCSR639ZJI/cherimoya.fold_0.performance.tsv b/ENCSR639ZJI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e3c1573932d654984ffc692f88293bd1deeb022b..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -207.3275146484375 0.4819560945034027 0.3525369167327881 0.07449754327535629 0.6748560667037964 0.6181619763374329 0.6347155570983887 \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_1.evaluate.json b/ENCSR639ZJI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2a63546aad41ef8082ea93172506839bdf4644a4..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF172NYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_1.fit.json b/ENCSR639ZJI/cherimoya.fold_1.fit.json deleted file mode 100644 index 4878c8744a82734290542791e8f3db5915ab99b2..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF172NYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_1.log b/ENCSR639ZJI/cherimoya.fold_1.log deleted file mode 100644 index 29ec30c83e30ceeeb310a321a708199ce9bd4b75..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1617 22.356547355651855 3.721803665161133 168.15969848632812 0.8437436819076538 335.0528564453125 0.1444166898727417 0.34050784 10.112384796142578 True -1 3234 17.808549404144287 0.5310356616973877 223.15045166015625 1.3449087142944336 300.04638671875 0.24258637428283691 0.5047805 7.364069938659668 True -2 4851 17.82410955429077 0.45004963874816895 180.39816284179688 1.1777400970458984 276.8354187011719 0.29930052161216736 0.56261885 4.71126127243042 True -3 6468 17.839534997940063 0.4862403869628906 142.50973510742188 0.8601430654525757 266.0715026855469 0.3213658928871155 0.57110083 3.3385214805603027 True -4 8085 17.78859806060791 0.44634222984313965 213.50726318359375 0.886663019657135 261.4673767089844 0.3342495858669281 0.5713132 2.8897998332977295 True -5 9702 17.827452421188354 0.45876407623291016 165.832763671875 0.9776608347892761 258.690185546875 0.34006574749946594 0.585498 2.509031057357788 True -6 11319 17.702869415283203 0.46613264083862305 215.3592529296875 0.9446794986724854 256.12939453125 0.34666767716407776 0.5973683 2.1512250900268555 True -7 12936 17.475768327713013 0.47921037673950195 197.2257080078125 0.5687723159790039 254.98817443847656 0.34991687536239624 0.61211044 1.7825238704681396 True -8 14553 17.47394609451294 0.46909260749816895 192.95751953125 0.6503838300704956 253.1218719482422 0.3531801700592041 0.6394175 1.3649312257766724 True -9 16170 17.5128755569458 0.4582211971282959 196.49729919433594 0.8501238822937012 251.98873901367188 0.3568083345890045 0.64625216 1.2910248041152954 True -10 17787 17.50713014602661 0.4610259532928467 239.93936157226562 0.9588384628295898 251.2481689453125 0.35738828778266907 0.6624255 1.1477540731430054 True -11 19404 17.534708738327026 0.48323750495910645 168.86172485351562 1.0498673915863037 249.7295379638672 0.36045050621032715 0.6739987 1.0160273313522339 True -12 21021 17.519291639328003 0.4844214916229248 182.28631591796875 0.7342491745948792 248.87655639648438 0.36160072684288025 0.6860694 0.9202510714530945 True -13 22638 17.58843493461609 1.8764495849609375 149.9017333984375 0.6740958094596863 247.9061737060547 0.3643314838409424 0.6988441 0.8315441012382507 True -14 24255 17.59301233291626 0.492063045501709 179.58343505859375 0.5971003770828247 246.605224609375 0.36835163831710815 0.7131759 0.7818111181259155 True -15 25872 17.658862590789795 0.4848978519439697 135.00177001953125 0.646001935005188 246.3578643798828 0.36791113018989563 0.7232376 0.7204523086547852 True -16 27489 17.58390474319458 1.4628942012786865 122.55226135253906 0.5443640947341919 245.9593505859375 0.367872416973114 0.7311866 0.6745696663856506 True -17 29106 17.584201335906982 0.48451900482177734 154.74928283691406 0.48336082696914673 246.30184936523438 0.3673474192619324 0.73138267 0.6592890620231628 True -18 30723 17.579941272735596 1.2559149265289307 137.350341796875 0.3534141778945923 246.54469299316406 0.3658409118652344 0.7304425 0.6546860933303833 False -19 32340 17.584838151931763 0.48667120933532715 194.1414794921875 0.4369529187679291 246.8589324951172 0.3653408885002136 0.72838676 0.6573701500892639 False diff --git a/ENCSR639ZJI/cherimoya.fold_1.performance.tsv b/ENCSR639ZJI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index dae5f209a9343ca6d85c8c6e538a5ede10b6ffeb..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -246.30184936523438 0.4669007956981659 0.3673473298549652 0.08495434373617172 0.7313826680183411 0.6637691855430603 0.6592890620231628 \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_2.evaluate.json b/ENCSR639ZJI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index be4f0e40071a416db47a585d18ca06971a4b748c..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF172NYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_2.fit.json b/ENCSR639ZJI/cherimoya.fold_2.fit.json deleted file mode 100644 index 5ce13cd7f9d4c4b383456eb2e0817b78dca62dd4..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF172NYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_2.log b/ENCSR639ZJI/cherimoya.fold_2.log deleted file mode 100644 index c0c60230fef80147a62b01171c8f419d2378a809..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1717 24.235210418701172 13.324453830718994 186.9275360107422 1.0016793012619019 290.583984375 0.1439172327518463 0.3426715 8.154973030090332 True -1 3434 18.937522649765015 0.37856459617614746 181.93951416015625 1.170150637626648 257.55133056640625 0.25088703632354736 0.4623395 6.394939422607422 True -2 5151 18.951158046722412 0.32414793968200684 259.52008056640625 1.0553600788116455 239.27159118652344 0.30154919624328613 0.52280325 3.9647774696350098 True -3 6868 19.006025791168213 0.3362898826599121 162.68612670898438 1.007608413696289 232.44607543945312 0.31412357091903687 0.5338772 3.32177472114563 True -4 8585 18.89296007156372 1.3112492561340332 198.90725708007812 0.9098773002624512 227.79397583007812 0.32528412342071533 0.54583246 2.6246984004974365 True -5 10302 18.981321573257446 0.3344392776489258 193.1503448486328 0.8967015743255615 225.95277404785156 0.3286310136318207 0.5633255 2.2023797035217285 True -6 12019 18.966195344924927 0.3335235118865967 163.43240356445312 1.1113091707229614 223.5580596923828 0.3371908962726593 0.5787724 1.9424831867218018 True -7 13736 18.995426893234253 0.33568835258483887 197.03170776367188 0.8181155920028687 222.30397033691406 0.3400193452835083 0.5901625 1.6938529014587402 True -8 15453 18.9046573638916 0.33579134941101074 186.14447021484375 1.0516729354858398 221.8459930419922 0.34074631333351135 0.59979033 1.4229470491409302 True -9 17170 18.950133562088013 0.3432931900024414 128.40756225585938 0.5993726849555969 220.55332946777344 0.34335339069366455 0.61612916 1.2563714981079102 True -10 18887 19.016895532608032 0.33043360710144043 173.81500244140625 0.9310274124145508 219.16941833496094 0.349195271730423 0.62393546 1.1162225008010864 True -11 20604 19.007878065109253 0.3310861587524414 143.65757751464844 0.8999032974243164 218.6375274658203 0.35018807649612427 0.63648176 0.975883424282074 True -12 22321 19.021737575531006 0.33087635040283203 175.08860778808594 0.7567600011825562 217.92457580566406 0.3526836633682251 0.64349675 0.9015190005302429 True -13 24038 19.042502880096436 1.72222900390625 130.27328491210938 0.6907657384872437 216.5146484375 0.357794851064682 0.6530631 0.824176549911499 True -14 25755 19.01352596282959 0.34142494201660156 160.7506561279297 0.448641836643219 216.04884338378906 0.3570190370082855 0.66992164 0.7358938455581665 True -15 27472 19.04301929473877 0.34389567375183105 218.52297973632812 0.626790463924408 215.76571655273438 0.35794442892074585 0.6831447 0.67451411485672 True -16 29189 19.048466444015503 0.3323080539703369 175.0008544921875 0.680404007434845 215.4183807373047 0.35825175046920776 0.6913206 0.6439416408538818 True -17 30906 18.78415846824646 0.33579182624816895 151.37274169921875 0.43583858013153076 215.59141540527344 0.35829031467437744 0.6939679 0.638484537601471 True -18 32623 18.712982654571533 1.6790683269500732 163.7138671875 0.36927998065948486 215.36822509765625 0.35985758900642395 0.6919065 0.6444845199584961 False -19 34340 18.690349340438843 0.32929444313049316 126.56817626953125 0.3739561140537262 215.67918395996094 0.3578319847583771 0.69097894 0.6506384015083313 False diff --git a/ENCSR639ZJI/cherimoya.fold_2.performance.tsv b/ENCSR639ZJI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1087c1a9c9c45de57ae8dc2c4c4d1f6a059e9034..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -215.59141540527344 0.4781544804573059 0.35829031467437744 0.07575879991054535 0.693967878818512 0.6224136352539062 0.638484537601471 \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_3.evaluate.json b/ENCSR639ZJI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cda98a43f5a46162705691dc3174f1ea46132967..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF172NYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_3.fit.json b/ENCSR639ZJI/cherimoya.fold_3.fit.json deleted file mode 100644 index 06b010a54ae5c649390ec884268bf96f0a742dcf..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF172NYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_3.log b/ENCSR639ZJI/cherimoya.fold_3.log deleted file mode 100644 index 2db7ccf7e664d024f3e35a840ac98e4e1a48a47a..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1658 22.837677478790283 5.036991596221924 183.3807830810547 1.37665593624115 305.93414306640625 0.14787429571151733 0.38815138 9.311304092407227 True -1 3316 18.29555344581604 1.329132080078125 201.2963104248047 1.4489511251449585 275.6796569824219 0.24142879247665405 0.5213071 5.919620037078857 True -2 4974 18.324914693832397 0.394773006439209 215.7960662841797 1.0325533151626587 255.9834747314453 0.2979656755924225 0.5488497 4.369134902954102 True -3 6632 18.29043984413147 0.6399219036102295 170.0701904296875 0.6980189681053162 247.96954345703125 0.31585901975631714 0.5334395 3.3904714584350586 False -4 8290 18.310593843460083 0.3536794185638428 177.4683380126953 1.090785264968872 243.6072540283203 0.3273671269416809 0.51898676 2.907637596130371 False -5 9948 18.297516107559204 0.3458836078643799 148.2044677734375 0.7544049620628357 241.28775024414062 0.333080530166626 0.52844816 2.3314218521118164 False -6 11606 18.33250904083252 1.0219628810882568 193.52149963378906 0.600348949432373 239.66476440429688 0.3378124237060547 0.54490966 1.9328997135162354 False -7 13264 18.31245517730713 0.33950138092041016 260.21173095703125 0.706440806388855 237.94473266601562 0.34227514266967773 0.55969447 1.7039461135864258 True -8 14922 18.313024520874023 0.3397824764251709 137.26895141601562 0.7666603922843933 236.7169647216797 0.3454854488372803 0.5706993 1.5115495920181274 True -9 16580 18.32231068611145 0.33498048782348633 159.11956787109375 0.8862941861152649 234.98065185546875 0.34997186064720154 0.592714 1.3113477230072021 True -10 18238 18.31819725036621 0.3373453617095947 181.8695831298828 1.0126430988311768 234.23690795898438 0.3503924310207367 0.611924 1.0883032083511353 True -11 19896 18.342578172683716 0.33988213539123535 184.26319885253906 0.6133627891540527 233.19073486328125 0.3530462980270386 0.63074017 0.9742417931556702 True -12 21554 18.2951762676239 0.3438832759857178 193.78402709960938 0.6410487294197083 232.05178833007812 0.35636475682258606 0.64417845 0.8992069363594055 True -13 23212 18.726542234420776 0.341998815536499 151.21896362304688 0.5048642158508301 230.7002716064453 0.3597402274608612 0.65975493 0.8313767910003662 True -14 24870 18.307565927505493 0.34235048294067383 159.5613250732422 0.6265001893043518 230.05386352539062 0.36106178164482117 0.67594534 0.7513814568519592 True -15 26528 18.32302951812744 0.341677188873291 163.50819396972656 0.5966062545776367 230.01058959960938 0.35998231172561646 0.68764645 0.7117863893508911 True -16 28186 18.29746150970459 0.33992528915405273 168.26449584960938 0.4892708957195282 230.4689178466797 0.35711538791656494 0.69804716 0.6833082437515259 True -17 29844 18.326898097991943 0.3428483009338379 180.9877166748047 0.565044641494751 230.2165069580078 0.35797378420829773 0.70143616 0.6639906764030457 True -18 31502 18.322348594665527 0.3430979251861572 119.48148345947266 0.6465815305709839 230.10211181640625 0.3590991795063019 0.7027304 0.6668838262557983 True -19 33160 18.302281856536865 0.3376436233520508 178.54974365234375 0.44264063239097595 230.23985290527344 0.3587180972099304 0.70164573 0.6716665029525757 False diff --git a/ENCSR639ZJI/cherimoya.fold_3.performance.tsv b/ENCSR639ZJI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f257f2c8d17ffe8affbd58271fbabccd25dbf591..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -230.10211181640625 0.47538650035858154 0.35909920930862427 0.0793953612446785 0.7027304172515869 0.6352073550224304 0.6668838262557983 \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_4.evaluate.json b/ENCSR639ZJI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0b8f19330cc5a636d5db5939020ab506f9665d13..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF172NYP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_4.fit.json b/ENCSR639ZJI/cherimoya.fold_4.fit.json deleted file mode 100644 index 209948d18709f89f70d30337a390b9552fe9d250..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF172NYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR639ZJI/cherimoya.fold_4.log b/ENCSR639ZJI/cherimoya.fold_4.log deleted file mode 100644 index 5bf2e9588848f2aed0cdf431c1fa07564d224428..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1663 23.427229166030884 3.5889651775360107 236.85040283203125 1.3666877746582031 281.3562316894531 0.13660186529159546 0.36794955 8.66186237335205 True -1 3326 18.308720588684082 0.385695219039917 172.25424194335938 0.7689350843429565 252.7335968017578 0.2351521998643875 0.47372714 6.142195224761963 True -2 4989 18.323451280593872 0.33711743354797363 133.87606811523438 0.9813365936279297 233.6262969970703 0.2911721467971802 0.4813741 4.4518938064575195 True -3 6652 18.304543256759644 1.3255653381347656 155.20733642578125 1.2384604215621948 225.96273803710938 0.31098267436027527 0.49125478 3.2527542114257812 True -4 8315 18.315813064575195 0.3166537284851074 190.45065307617188 1.0812287330627441 221.73416137695312 0.3214663565158844 0.48957616 2.798957347869873 False -5 9978 18.295318603515625 0.3142702579498291 161.3873748779297 0.6493265628814697 218.88633728027344 0.3289330303668976 0.5160386 2.2941486835479736 True -6 11641 18.305476665496826 0.311931848526001 168.0655517578125 0.819137692451477 217.53469848632812 0.33100369572639465 0.5317086 2.056047201156616 True -7 13304 18.064870357513428 1.519655704498291 147.212646484375 0.9708705544471741 216.17181396484375 0.33595743775367737 0.54937524 1.722550392150879 True -8 14967 18.01067066192627 0.32271647453308105 170.3607177734375 0.9617246389389038 215.29769897460938 0.33637455105781555 0.5679305 1.5199074745178223 True -9 16630 18.022777318954468 0.30936241149902344 172.27142333984375 0.8637056946754456 214.14718627929688 0.34012478590011597 0.58355933 1.3183640241622925 True -10 18293 18.025152444839478 0.31691837310791016 146.14639282226562 0.6682863831520081 213.2483367919922 0.3429962396621704 0.60227334 1.2042322158813477 True -11 19956 18.020488500595093 0.3091394901275635 153.53933715820312 0.6930592656135559 211.86392211914062 0.3478703200817108 0.6185428 1.0329240560531616 True -12 21619 17.960097789764404 0.30911970138549805 160.5174560546875 0.6974728107452393 211.22906494140625 0.34833264350891113 0.6307833 0.8798340559005737 True -13 23282 17.99027991294861 0.3256344795227051 155.48861694335938 0.5959678888320923 210.85055541992188 0.34868595004081726 0.6493316 0.7945919632911682 True -14 24945 18.015103816986084 0.32922983169555664 185.10829162597656 0.4783363342285156 209.72132873535156 0.35330745577812195 0.661826 0.7366527915000916 True -15 26608 18.100606203079224 0.3320043087005615 158.05517578125 0.501201868057251 209.5511474609375 0.35111644864082336 0.6718657 0.6842422485351562 True -16 28271 18.07258129119873 0.3312983512878418 155.68670654296875 0.5886011123657227 209.4551544189453 0.3527362644672394 0.67739195 0.6503939032554626 True -17 29934 18.042425870895386 0.3275320529937744 151.34010314941406 0.5275816917419434 209.68893432617188 0.3511929512023926 0.6801461 0.6444100141525269 True -18 31597 18.211612939834595 12.33909821510315 172.49411010742188 0.5193237066268921 210.03831481933594 0.3489135205745697 0.6783391 0.6424086093902588 False -19 33260 18.088390588760376 0.33383941650390625 188.90078735351562 0.46520403027534485 209.8234100341797 0.35043400526046753 0.6770183 0.6446258425712585 False diff --git a/ENCSR639ZJI/cherimoya.fold_4.performance.tsv b/ENCSR639ZJI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a1bff0ea4b45f5c6139a2405837793f5712d69fe..0000000000000000000000000000000000000000 --- a/ENCSR639ZJI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -209.68893432617188 0.48278337717056274 0.3511929512023926 0.07399684190750122 0.6801460981369019 0.6046749353408813 0.6444100141525269 \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_0.evaluate.json b/ENCSR641KNU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b9e643f9dee3d05485da85ef408b551cf137ea1d..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF712DMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_0.fit.json b/ENCSR641KNU/cherimoya.fold_0.fit.json deleted file mode 100644 index a75a3e56629de5e04216d346336525cfc29348ea..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF712DMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_0.log b/ENCSR641KNU/cherimoya.fold_0.log deleted file mode 100644 index 3946e19c1bb014f121866dab90b37d94380345d1..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2076 26.55967402458191 5.1083595752716064 373.45458984375 1.1614457368850708 492.3313293457031 0.4671587646007538 0.5392036 11.086124420166016 True -1 4152 22.83326554298401 0.4307734966278076 313.285888671875 0.7539994120597839 421.4912414550781 0.5807508826255798 0.6272898 3.9674887657165527 True -2 6228 22.843571662902832 0.4195389747619629 335.6116943359375 0.5811939239501953 405.9169921875 0.6112887263298035 0.6285429 1.0718340873718262 True -3 8304 22.78813648223877 1.1900238990783691 291.5216369628906 0.9875189065933228 400.5823059082031 0.6200113296508789 0.64345956 0.76425701379776 True -4 10380 22.804368019104004 0.40601229667663574 308.95550537109375 0.8127678632736206 398.5246276855469 0.6250556707382202 0.6445018 0.8350100517272949 True -5 12456 22.800574779510498 1.5795323848724365 283.0782165527344 0.8195748329162598 396.9541015625 0.6281087398529053 0.6538486 0.7901737093925476 True -6 14532 23.54567313194275 0.40056777000427246 309.67987060546875 0.6426953077316284 396.36834716796875 0.630092203617096 0.6575381 0.771145224571228 True -7 16608 22.391615867614746 0.40691590309143066 295.5028076171875 0.41674211621284485 395.0391540527344 0.6323952078819275 0.6658931 0.7096397280693054 True -8 18684 22.7815682888031 0.40473318099975586 292.7576904296875 0.528591513633728 393.8453369140625 0.6345210075378418 0.6664938 0.679684579372406 True -9 20760 22.42443561553955 16.936747550964355 294.52471923828125 0.42304927110671997 392.79864501953125 0.6368882060050964 0.67508674 0.6294199228286743 True -10 22836 22.39559841156006 0.4163532257080078 359.38409423828125 0.6386852264404297 391.5145263671875 0.6389598846435547 0.67816365 0.5877904891967773 True -11 24912 22.361860990524292 0.419191837310791 344.54815673828125 0.59546959400177 391.1274108886719 0.6409530639648438 0.68619853 0.5517850518226624 True -12 26988 22.347999811172485 0.4103281497955322 281.93707275390625 0.6637719869613647 389.3739013671875 0.642511248588562 0.69539845 0.5265776515007019 True -13 29064 22.333675384521484 0.4152224063873291 319.4893493652344 0.530653715133667 388.6153259277344 0.6438067555427551 0.7015562 0.5239677429199219 True -14 31140 22.34633445739746 0.4094419479370117 336.7775573730469 0.3533754050731659 388.4951171875 0.6448678374290466 0.70875376 0.5023760795593262 True -15 33216 22.3882315158844 0.41261839866638184 332.00360107421875 0.4839654564857483 388.15643310546875 0.6454987525939941 0.7155556 0.4942508637905121 True -16 35292 22.409137725830078 0.4130527973175049 342.36785888671875 0.38892075419425964 388.5395812988281 0.6453266739845276 0.71553487 0.4914983808994293 False -17 37368 22.40646243095398 0.4097743034362793 289.34185791015625 0.2235732525587082 387.8453063964844 0.6448323130607605 0.71454555 0.499458372592926 False -18 39444 22.35333800315857 0.4094831943511963 357.67181396484375 0.23782220482826233 388.7882080078125 0.6442194581031799 0.7095079 0.507343590259552 False -19 41520 22.342815160751343 0.40615010261535645 324.81256103515625 0.18067947030067444 388.2967834472656 0.6438090205192566 0.7068148 0.5142464637756348 False diff --git a/ENCSR641KNU/cherimoya.fold_0.performance.tsv b/ENCSR641KNU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index dfa82d58be490e2c174f05e21b4c31c4b01a411e..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -388.15643310546875 0.28790023922920227 0.6454987525939941 0.2524935305118561 0.7155556082725525 0.6768421530723572 0.4942508637905121 \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_1.evaluate.json b/ENCSR641KNU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6e8234d0b67a33af020ed8baf6a4236965fde66e..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF712DMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_1.fit.json b/ENCSR641KNU/cherimoya.fold_1.fit.json deleted file mode 100644 index b3fcd8c7c4fbe0c2915333916c49a0c67983e319..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF712DMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_1.log b/ENCSR641KNU/cherimoya.fold_1.log deleted file mode 100644 index 8cbf4712c9b1d1f32ae7d59fc502a0c5e08084ef..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2095 27.044142961502075 3.8612308502197266 352.8925476074219 0.621453046798706 503.9071960449219 0.47890475392341614 0.5445799 8.72596263885498 True -1 4190 22.99151921272278 0.5157718658447266 358.0054931640625 0.859728991985321 438.7097473144531 0.5846701264381409 0.6504005 3.6532390117645264 True -2 6285 23.040846586227417 0.5063104629516602 312.15325927734375 0.6425660252571106 424.8010559082031 0.613168478012085 0.6663574 1.1539241075515747 True -3 8380 23.022255659103394 1.2094087600708008 342.22705078125 0.8300567865371704 419.34613037109375 0.6215994954109192 0.6791094 0.6811955571174622 True -4 10475 23.064746618270874 0.507622480392456 320.61962890625 0.8986244201660156 418.62725830078125 0.6233516335487366 0.6825592 0.6567386388778687 True -5 12570 23.069462299346924 0.5145153999328613 278.5277404785156 0.8930302262306213 417.630615234375 0.6256818771362305 0.685728 0.6237478852272034 True -6 14665 23.047803163528442 0.5072619915008545 331.94970703125 0.4790284037590027 416.6941223144531 0.6276628375053406 0.69086134 0.5966662168502808 True -7 16760 23.052307605743408 0.4981398582458496 311.50714111328125 0.7036596536636353 415.5226745605469 0.6300781965255737 0.697076 0.5716702342033386 True -8 18855 23.04046893119812 0.5106296539306641 322.3182067871094 0.5823394656181335 414.48565673828125 0.6321300864219666 0.70428264 0.5270035266876221 True -9 20950 23.05677819252014 1.0195817947387695 325.28948974609375 0.7139752507209778 412.58721923828125 0.6352136135101318 0.71034074 0.4851765036582947 True -10 23045 23.03585147857666 0.525780200958252 302.1497802734375 0.7310320138931274 411.8484191894531 0.6368152499198914 0.7142115 0.47064101696014404 True -11 25140 22.97652268409729 0.5048582553863525 339.7210693359375 0.4581868052482605 410.96954345703125 0.6386796832084656 0.7204271 0.4572627544403076 True -12 27235 22.995280504226685 2.283818483352661 272.46112060546875 0.6003057956695557 410.06134033203125 0.6401562690734863 0.7253379 0.44385114312171936 True -13 29330 23.138178825378418 0.5120751857757568 276.7563171386719 0.7525277733802795 409.3490905761719 0.6415507793426514 0.7311385 0.439718097448349 True -14 31425 25.13190531730652 10.270277976989746 323.4409484863281 0.5461922883987427 408.7601623535156 0.6425304412841797 0.7361758 0.42776498198509216 True -15 33520 23.065279722213745 0.5039694309234619 321.0694580078125 0.37567993998527527 408.447509765625 0.6430814862251282 0.738224 0.4274982213973999 True -16 35615 23.20553421974182 0.498638391494751 337.9776306152344 0.319909006357193 408.3987731933594 0.6430968642234802 0.73771745 0.43190035223960876 False -17 37710 23.121586084365845 0.4995546340942383 279.28582763671875 0.30102020502090454 408.4150390625 0.6429080963134766 0.73540825 0.4404962360858917 False -18 39805 23.005197048187256 19.028704166412354 245.5811767578125 0.2775387763977051 408.6129455566406 0.6424801349639893 0.73022604 0.4523676931858063 False -19 41900 23.58301091194153 0.512181282043457 277.5387268066406 0.24088338017463684 408.69287109375 0.6420744061470032 0.72767365 0.4646031856536865 False diff --git a/ENCSR641KNU/cherimoya.fold_1.performance.tsv b/ENCSR641KNU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 747a56bf37130be8cf6ce1ba3f1c5059ed6b3547..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -408.447509765625 0.2827669382095337 0.643081545829773 0.2630713880062103 0.7382240295410156 0.7242658734321594 0.4274982213973999 \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_2.evaluate.json b/ENCSR641KNU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 539a03f1986826c6a6eb3138973dc26237452666..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF712DMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_2.fit.json b/ENCSR641KNU/cherimoya.fold_2.fit.json deleted file mode 100644 index 91cc318a25153518c5ff22b7d1466c602b4c2178..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF712DMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_2.log b/ENCSR641KNU/cherimoya.fold_2.log deleted file mode 100644 index 55eabcac0f8e38593185e7fec18489a16effa57f..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2210 28.623865127563477 3.890841245651245 417.06243896484375 0.8557162284851074 487.5635986328125 0.47257187962532043 0.5492771 8.483275413513184 True -1 4420 24.36514711380005 0.43020129203796387 327.7677307128906 0.4473295211791992 420.4919128417969 0.5865418910980225 0.64511466 2.642552137374878 True -2 6630 24.33922052383423 0.4151644706726074 359.63409423828125 0.8430148959159851 406.85614013671875 0.6093112826347351 0.64572877 1.0617966651916504 True -3 8840 24.38155484199524 0.4104914665222168 310.0760498046875 0.6533632278442383 402.77294921875 0.6157670021057129 0.6646145 0.8248965740203857 True -4 11050 24.42362880706787 0.4082517623901367 306.14801025390625 0.8900492787361145 401.3130187988281 0.6185490489006042 0.6635522 0.7820510864257812 False -5 13260 24.316264390945435 1.4684627056121826 263.5452575683594 0.6200230717658997 400.298095703125 0.62110435962677 0.6658527 0.8241490721702576 True -6 15470 24.3857159614563 0.4049379825592041 316.73724365234375 0.5094166398048401 399.2381591796875 0.6229642033576965 0.67438513 0.7414840459823608 True -7 17680 24.39369773864746 0.6360149383544922 307.6906433105469 0.6129739880561829 398.0040588378906 0.6254194378852844 0.6759481 0.6935487389564514 True -8 19890 24.27590274810791 0.4018235206604004 299.0145263671875 0.49112871289253235 396.8104248046875 0.6277106404304504 0.68058556 0.6314616799354553 True -9 22100 24.982840538024902 7.9898436069488525 356.52362060546875 0.5929979681968689 395.86895751953125 0.6297758221626282 0.6846185 0.5930584073066711 True -10 24310 24.376338481903076 0.4179878234863281 286.8375549316406 0.5155918598175049 394.7105712890625 0.6316113471984863 0.69021237 0.5358639359474182 True -11 26520 24.436941862106323 0.4084033966064453 283.70257568359375 0.5307274460792542 393.8304748535156 0.6335356831550598 0.6926553 0.5333841443061829 True -12 28730 24.34330463409424 0.8096749782562256 331.4444885253906 0.480864942073822 393.0412902832031 0.6349800825119019 0.7022764 0.512265145778656 True -13 30940 24.331243753433228 0.3960134983062744 315.24884033203125 0.5045850276947021 392.3212890625 0.6363441944122314 0.7058685 0.5033831000328064 True -14 33150 24.269067525863647 0.44317054748535156 313.52593994140625 0.46310973167419434 391.748046875 0.6373904347419739 0.7104769 0.49017664790153503 True -15 35360 24.22955322265625 0.4056973457336426 363.378173828125 0.43473923206329346 391.5795593261719 0.6378624439239502 0.7183603 0.4839853048324585 True -16 37570 24.28218722343445 0.40004754066467285 267.2322998046875 0.3464139699935913 391.4948425292969 0.6379243731498718 0.7217044 0.4814010560512543 True -17 39780 24.295802116394043 0.4004683494567871 340.64263916015625 0.28970691561698914 391.79486083984375 0.637268602848053 0.71892726 0.48929110169410706 False -18 41990 24.37158203125 0.4029388427734375 254.8126983642578 0.2692486047744751 392.02716064453125 0.6366791129112244 0.7157411 0.4999009370803833 False -19 44200 24.352638959884644 0.41073131561279297 261.2421569824219 0.2620796263217926 392.11383056640625 0.6363077163696289 0.7133095 0.5087597966194153 False diff --git a/ENCSR641KNU/cherimoya.fold_2.performance.tsv b/ENCSR641KNU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4b2b661075ca157bd77b2b4fb17df46db8b26b42..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -391.4948425292969 0.2903025150299072 0.6379243731498718 0.2552267611026764 0.7217044234275818 0.6906092166900635 0.4814010560512543 \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_3.evaluate.json b/ENCSR641KNU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 166c57000397a26292be4d07e06de548c50dca6f..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF712DMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_3.fit.json b/ENCSR641KNU/cherimoya.fold_3.fit.json deleted file mode 100644 index c01662be73a5014edce61a6e0cc86b66b9590805..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF712DMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_3.log b/ENCSR641KNU/cherimoya.fold_3.log deleted file mode 100644 index fc58e3e2af56e4b078c5031f36c29c107e7ed9da..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2136 27.056272268295288 3.423428773880005 385.7996826171875 0.8386020660400391 499.0187072753906 0.4746776819229126 0.547012 8.891225814819336 True -1 4272 23.50980806350708 0.46344685554504395 269.4390563964844 0.6729339957237244 428.01666259765625 0.5886560082435608 0.61329234 3.6017634868621826 True -2 6408 23.524564027786255 0.899061918258667 318.56646728515625 0.7713634967803955 413.2234802246094 0.6142595410346985 0.61106163 1.1962673664093018 False -3 8544 23.52611780166626 0.45229530334472656 304.2412109375 0.6521105766296387 408.30316162109375 0.6226270794868469 0.6371164 0.9198991060256958 True -4 10680 23.504412174224854 0.4517548084259033 340.7738342285156 0.7842333912849426 406.4771728515625 0.626592755317688 0.64745855 0.9222710728645325 True -5 12816 23.252548217773438 0.45274996757507324 284.1922912597656 0.8100110292434692 404.7779235839844 0.6292561292648315 0.65803355 0.8325003981590271 True -6 14952 23.06661820411682 0.45792722702026367 288.7176513671875 0.5065619349479675 403.70159912109375 0.6314041018486023 0.6645406 0.7470751404762268 True -7 17088 23.04280161857605 0.44777989387512207 357.3921813964844 0.8628299236297607 402.80963134765625 0.6331319212913513 0.66717875 0.7141460180282593 True -8 19224 23.03911542892456 0.4467329978942871 320.8515625 0.43910083174705505 401.41131591796875 0.6354390978813171 0.67356133 0.6457394361495972 True -9 21360 23.016332864761353 0.4761233329772949 325.1458435058594 0.537002682685852 400.6636047363281 0.6371734142303467 0.67986023 0.6350144147872925 True -10 23496 23.112862825393677 0.4466590881347656 339.2208251953125 0.6024701595306396 400.0426940917969 0.6385754942893982 0.68573713 0.6038631796836853 True -11 25632 23.023019790649414 0.4482433795928955 294.8541259765625 0.5445834398269653 399.0924377441406 0.6402437686920166 0.69337124 0.5742404460906982 True -12 27768 23.06700611114502 0.4504711627960205 336.74481201171875 0.3664878010749817 398.3654479980469 0.6418455243110657 0.6971499 0.550566554069519 True -13 29904 23.043985605239868 0.4501063823699951 275.5743408203125 0.4693862795829773 397.3724670410156 0.6434800624847412 0.7032529 0.5243978500366211 True -14 32040 23.071038246154785 0.45230746269226074 378.99462890625 0.47970011830329895 396.8059387207031 0.6444215774536133 0.70935315 0.5233471393585205 True -15 34176 23.044906616210938 0.4461824893951416 336.7948303222656 0.5026425123214722 396.3945617675781 0.6450641751289368 0.71414465 0.5151419043540955 True -16 36312 23.02658748626709 0.9175691604614258 293.56622314453125 0.36896371841430664 396.32110595703125 0.6451402306556702 0.71695185 0.5063309073448181 True -17 38448 23.063846349716187 0.44376039505004883 319.99481201171875 0.2734387218952179 396.4389953613281 0.6445293426513672 0.7171805 0.5108439326286316 True -18 40584 23.050701379776 0.4443981647491455 282.92425537109375 0.39344337582588196 396.609130859375 0.6442447304725647 0.71407413 0.5180293917655945 False -19 42720 23.04007077217102 0.44664669036865234 266.5372009277344 0.269564151763916 396.7167663574219 0.6438810229301453 0.7111757 0.5217905044555664 False diff --git a/ENCSR641KNU/cherimoya.fold_3.performance.tsv b/ENCSR641KNU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 56ea5d1facaa197f25cf2f086183fdb529c86220..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -396.4389953613281 0.28546637296676636 0.6445292830467224 0.2580510079860687 0.7171804904937744 0.6838703155517578 0.5108439326286316 \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_4.evaluate.json b/ENCSR641KNU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 521c1d7280a85764345411959b5ca805bed2e540..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF712DMW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_4.fit.json b/ENCSR641KNU/cherimoya.fold_4.fit.json deleted file mode 100644 index 711f1831d3a320dde8f4e2276e0b042070c143fb..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF712DMW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR641KNU/cherimoya.fold_4.log b/ENCSR641KNU/cherimoya.fold_4.log deleted file mode 100644 index 94048fe87bcb9763b948a30c885a72001261d322..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2175 27.65425705909729 3.3390305042266846 326.0223388671875 1.1575285196304321 491.392822265625 0.47308143973350525 0.5593416 8.182308197021484 True -1 4350 23.95205783843994 0.43576502799987793 351.83154296875 0.6380050182342529 423.4696044921875 0.5842885971069336 0.6211284 2.6630232334136963 True -2 6525 24.000476837158203 0.42334914207458496 298.739501953125 0.7731409072875977 408.4308776855469 0.613985002040863 0.6329533 0.9154434204101562 True -3 8700 23.984013319015503 0.41965794563293457 277.20538330078125 0.6443421244621277 403.18780517578125 0.6219956874847412 0.64937586 0.7063934803009033 True -4 10875 23.919387340545654 0.4152703285217285 353.01580810546875 0.4476690888404846 401.1996154785156 0.626042366027832 0.66237575 0.630073070526123 True -5 13050 23.948657989501953 1.782515525817871 326.82281494140625 0.5317442417144775 399.46881103515625 0.6293186545372009 0.66397923 0.591694176197052 True -6 15225 23.970122814178467 0.4167642593383789 339.45660400390625 0.7519986033439636 398.4444580078125 0.6318660974502563 0.6670106 0.569500744342804 True -7 17400 23.962260961532593 0.42256903648376465 340.96356201171875 0.5686246156692505 397.68890380859375 0.6335265040397644 0.6720851 0.5687044858932495 True -8 19575 23.94101572036743 0.41711902618408203 266.676513671875 0.6046205759048462 396.602783203125 0.6360002160072327 0.6807653 0.5587022304534912 True -9 21750 23.945316314697266 0.42464423179626465 345.82275390625 0.8797918558120728 395.6717224121094 0.6380623579025269 0.6807816 0.5459684133529663 True -10 23925 23.92583656311035 0.4174683094024658 252.59999084472656 0.7375441789627075 394.80914306640625 0.6397053599357605 0.6878514 0.5244802236557007 True -11 26100 23.904054880142212 0.41719961166381836 302.67974853515625 0.5650867223739624 393.9292907714844 0.6417195200920105 0.6948205 0.512834370136261 True -12 28275 23.819894790649414 0.406994104385376 327.52215576171875 0.3894135653972626 392.84747314453125 0.6434170603752136 0.69972533 0.4997698962688446 True -13 30450 23.4651300907135 0.41252589225769043 329.936279296875 0.5507403612136841 392.19879150390625 0.6448901295661926 0.70704097 0.5002908110618591 True -14 32625 23.47560691833496 0.41668009757995605 326.5101318359375 0.2944377660751343 391.6252746582031 0.6457083821296692 0.71367425 0.49252817034721375 True -15 34800 23.45815658569336 2.1913414001464844 342.619873046875 0.38283395767211914 391.3834533691406 0.646192193031311 0.719991 0.47501620650291443 True -16 36975 23.481485605239868 0.4190819263458252 337.5108642578125 0.2226456105709076 391.3315124511719 0.646060585975647 0.7194231 0.48430657386779785 False -17 39150 23.50515866279602 0.4187891483306885 284.14776611328125 0.5594971179962158 391.366455078125 0.6456742286682129 0.72053087 0.49063849449157715 True -18 41325 23.596580028533936 0.41002917289733887 283.60833740234375 0.32453593611717224 391.5071105957031 0.6451656818389893 0.7172903 0.5036094188690186 False -19 43500 23.478718996047974 0.4193284511566162 284.8004455566406 0.28771209716796875 391.6772766113281 0.6448410749435425 0.71314746 0.5140998363494873 False diff --git a/ENCSR641KNU/cherimoya.fold_4.performance.tsv b/ENCSR641KNU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index dfcf8c45557824a3099c0209ce9ece098b80865d..0000000000000000000000000000000000000000 --- a/ENCSR641KNU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -391.366455078125 0.2873552739620209 0.6456741690635681 0.25772762298583984 0.7205308675765991 0.6727939248085022 0.49063849449157715 \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_0.evaluate.json b/ENCSR645HET/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 93910ea9d5e94f6759810bf41896aa3a5d7f8028..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133NHP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_0.fit.json b/ENCSR645HET/cherimoya.fold_0.fit.json deleted file mode 100644 index ef84036cad74e41dcd52233c90af61d94251f740..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF133NHP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_0.log b/ENCSR645HET/cherimoya.fold_0.log deleted file mode 100644 index 276223e954ba04e6a432c6b05caf7eb67e9343f3..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 34.392394065856934 3.6678614616394043 440.9710998535156 0.336240291595459 625.6685180664062 0.3002931475639343 0.70828223 4.350006580352783 True -1 5462 30.046066761016846 0.7992331981658936 442.10894775390625 0.254048228263855 572.2693481445312 0.3725346326828003 0.7718164 1.0804404020309448 True -2 8193 30.13752770423889 0.6474676132202148 545.388427734375 0.35779476165771484 561.6529541015625 0.3853110671043396 0.7871877 0.5020720362663269 True -3 10924 30.075227975845337 0.6205830574035645 449.64300537109375 0.47855818271636963 555.8290405273438 0.39017635583877563 0.79536533 0.4204806387424469 True -4 13655 29.636879682540894 1.3672518730163574 478.4499816894531 0.3077375888824463 553.18212890625 0.3941724896430969 0.802265 0.3703572154045105 True -5 16386 29.61248540878296 0.6722729206085205 457.5050048828125 0.33609604835510254 551.6061401367188 0.3956161141395569 0.8124621 0.29486289620399475 True -6 19117 29.453998565673828 0.6292064189910889 465.53680419921875 0.24819029867649078 548.961181640625 0.3996466398239136 0.81490254 0.2933630347251892 True -7 21848 29.475540161132812 0.6141481399536133 465.18084716796875 0.27048641443252563 547.4339599609375 0.4019831418991089 0.822352 0.28852882981300354 True -8 24579 29.437464952468872 0.607680082321167 586.077880859375 0.19499212503433228 546.1925048828125 0.40422287583351135 0.824774 0.2770829200744629 True -9 27310 29.446253776550293 0.6078596115112305 543.15771484375 0.236715629696846 543.9911499023438 0.40713781118392944 0.8317364 0.27024996280670166 True -10 30041 29.368776082992554 0.6148741245269775 496.60797119140625 0.3591628670692444 542.5379028320312 0.4091714918613434 0.83242816 0.2634730637073517 True -11 32772 29.410259246826172 1.9268732070922852 607.2620239257812 0.38864943385124207 540.978271484375 0.4114088714122772 0.8402252 0.23932909965515137 True -12 35503 29.549198865890503 0.6430377960205078 501.34027099609375 0.2609587609767914 539.8731079101562 0.4128671884536743 0.8445266 0.22502315044403076 True -13 38234 29.523078203201294 0.5995943546295166 475.36114501953125 0.1831350475549698 538.4710693359375 0.4148118495941162 0.8493513 0.20860397815704346 True -14 40965 29.468713521957397 0.5970461368560791 426.7481689453125 0.15334497392177582 537.4708251953125 0.4155659079551697 0.8561362 0.19773094356060028 True -15 43696 29.461055040359497 0.6215231418609619 485.09100341796875 0.24675674736499786 536.1107788085938 0.4181285500526428 0.85988396 0.18927714228630066 True -16 46427 29.486616134643555 0.5815126895904541 464.69287109375 0.15949448943138123 536.73193359375 0.4163459837436676 0.8609089 0.18394771218299866 True -17 49158 29.400942087173462 0.6029813289642334 471.6251525878906 0.14046210050582886 535.5909423828125 0.4179849922657013 0.86264837 0.17982931435108185 True -18 51889 29.340656280517578 0.6194314956665039 456.1391906738281 0.1353512406349182 536.127197265625 0.41775044798851013 0.8619313 0.1795409768819809 False -19 54620 29.32344889640808 0.6004335880279541 436.1324462890625 0.17413823306560516 536.2666625976562 0.4173031449317932 0.86302376 0.18058091402053833 True diff --git a/ENCSR645HET/cherimoya.fold_0.performance.tsv b/ENCSR645HET/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 87993b987aa1b5334d0f64ed3042a5d5f18a056a..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -536.2666625976562 0.3727283775806427 0.4173031747341156 0.16470444202423096 0.8630237579345703 0.8348283767700195 0.18058091402053833 \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_1.evaluate.json b/ENCSR645HET/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 848f64f545f0f8f4568225592c4297ee13132258..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133NHP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_1.fit.json b/ENCSR645HET/cherimoya.fold_1.fit.json deleted file mode 100644 index 50192f777b6cba4e68cb43a822125a5d2df3941c..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF133NHP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_1.log b/ENCSR645HET/cherimoya.fold_1.log deleted file mode 100644 index ebede899e8c5df52ea9c0e7575e3ebf2ac224814..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2699 34.53353214263916 4.001936197280884 512.3203125 0.4091449975967407 726.6746215820312 0.30342260003089905 0.7073795 4.300902843475342 True -1 5398 29.679681062698364 1.4869616031646729 495.40435791015625 0.47289854288101196 655.373046875 0.38581839203834534 0.775061 1.3317774534225464 True -2 8097 29.20675802230835 0.791637659072876 446.4263916015625 0.38019227981567383 642.2484741210938 0.40005743503570557 0.78776616 0.6823537349700928 True -3 10796 29.27521014213562 0.7215511798858643 480.7806396484375 0.25881385803222656 634.9172973632812 0.40813136100769043 0.7915775 0.5743525624275208 True -4 13495 29.127639770507812 1.3558168411254883 417.09283447265625 0.3670991063117981 632.8967895507812 0.4093155264854431 0.7963646 0.4255583584308624 True -5 16194 29.125985383987427 0.6830809116363525 497.3687438964844 0.22069740295410156 628.391845703125 0.4164912700653076 0.8039514 0.371522456407547 True -6 18893 29.027550220489502 0.6845517158508301 530.911376953125 0.3411218822002411 626.12890625 0.41905778646469116 0.80837387 0.343161016702652 True -7 21592 28.99070978164673 0.6757488250732422 447.2264099121094 0.22376708686351776 623.47314453125 0.4213758409023285 0.81730705 0.3155701756477356 True -8 24291 29.009798288345337 0.6582770347595215 538.7037353515625 0.33069485425949097 620.3810424804688 0.42518869042396545 0.8237234 0.3013668656349182 True -9 26990 29.025726318359375 0.6812844276428223 568.0778198242188 0.25550606846809387 618.7373046875 0.42665642499923706 0.83016586 0.278772234916687 True -10 29689 29.19062900543213 0.6879017353057861 485.6573486328125 0.2722724676132202 616.14794921875 0.4290465712547302 0.83363396 0.26421475410461426 True -11 32388 29.049720764160156 0.6909470558166504 432.76324462890625 0.3377472758293152 615.8359375 0.4280044138431549 0.83610576 0.2538597881793976 True -12 35087 29.148531913757324 0.7178454399108887 507.6073913574219 0.22687962651252747 611.9078979492188 0.4333776831626892 0.8434953 0.2357737272977829 True -13 37786 31.2151358127594 0.6908881664276123 434.6759033203125 0.18080571293830872 611.0032958984375 0.4339342713356018 0.84947544 0.22599640488624573 True -14 40485 29.37680435180664 0.687870979309082 442.65667724609375 0.19126340746879578 609.3379516601562 0.4354284405708313 0.856472 0.2218163013458252 True -15 43184 29.430219411849976 0.6771330833435059 567.8153076171875 0.21662572026252747 607.6553955078125 0.438227117061615 0.86055005 0.2128373384475708 True -16 45883 29.526134967803955 0.6807143688201904 498.1365966796875 0.21695610880851746 606.9334106445312 0.4391530454158783 0.8655197 0.20640550553798676 True -17 48582 29.23693537712097 0.6829574108123779 409.69183349609375 0.18035884201526642 607.4876098632812 0.43759045004844666 0.86691225 0.20248495042324066 True -18 51281 29.187864542007446 1.1106226444244385 426.50189208984375 0.19491595029830933 607.8713989257812 0.43762338161468506 0.86822397 0.2013772428035736 True -19 53980 29.20519995689392 0.6821210384368896 486.8927307128906 0.18903306126594543 606.4600830078125 0.4403953552246094 0.86743087 0.20133018493652344 False diff --git a/ENCSR645HET/cherimoya.fold_1.performance.tsv b/ENCSR645HET/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6475e0101a56611095beaa98a23e95819f50be56..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -607.8713989257812 0.35526004433631897 0.43762338161468506 0.1817614883184433 0.8682239651679993 0.8508715033531189 0.2013772428035736 \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_2.evaluate.json b/ENCSR645HET/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3f1191f2f947696b84c2d8c48e1482293005ee08..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133NHP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_2.fit.json b/ENCSR645HET/cherimoya.fold_2.fit.json deleted file mode 100644 index 07f1da7a085a4813c04ac06e8a0d71b3a5fbffb1..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF133NHP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_2.log b/ENCSR645HET/cherimoya.fold_2.log deleted file mode 100644 index 1b1d80d303e8c6e89c02949410bcb4393c052afd..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2869 36.002660274505615 3.4342708587646484 483.51715087890625 0.2615019381046295 651.0430908203125 0.29970118403434753 0.70173794 3.3503265380859375 True -1 5738 31.51136875152588 0.6325597763061523 503.7924499511719 0.2907071113586426 592.64306640625 0.37668853998184204 0.7718732 0.915759265422821 True -2 8607 31.505795001983643 0.564734935760498 437.1932678222656 0.26866358518600464 583.22265625 0.3859699070453644 0.7824459 0.530287504196167 True -3 11476 30.856043815612793 0.5505239963531494 507.47265625 0.28531989455223083 577.300048828125 0.39163488149642944 0.79176414 0.4082231819629669 True -4 14345 30.859004259109497 0.5608618259429932 567.51318359375 0.3307434320449829 574.2252197265625 0.3952789902687073 0.80004036 0.3420264720916748 True -5 17214 30.866087436676025 0.5530056953430176 514.4662475585938 0.35304492712020874 571.6348876953125 0.3987482190132141 0.8065524 0.32278040051460266 True -6 20083 30.849366188049316 0.5617613792419434 454.0635070800781 0.2166433334350586 569.993896484375 0.40161046385765076 0.8103943 0.3280579745769501 True -7 22952 30.847750663757324 0.5510103702545166 471.83819580078125 0.19243721663951874 566.98828125 0.40657827258110046 0.8151355 0.31557101011276245 True -8 25821 30.807852745056152 0.9240837097167969 562.561767578125 0.3570232391357422 566.1260375976562 0.4072646200656891 0.81892043 0.315713495016098 True -9 28690 30.89231824874878 23.6978497505188 478.3470458984375 0.34448927640914917 565.9473876953125 0.4065980911254883 0.82271194 0.2984600365161896 True -10 31559 31.28147029876709 0.5988738536834717 527.5093994140625 0.2707672119140625 563.142333984375 0.41087228059768677 0.8274503 0.28620538115501404 True -11 34428 30.962238311767578 0.5793135166168213 467.6039123535156 0.15905511379241943 561.681884765625 0.41277047991752625 0.83224314 0.25487446784973145 True -12 37297 30.96452236175537 0.5571668148040771 469.8299865722656 0.2441423535346985 560.3931274414062 0.41432371735572815 0.83779 0.23739664256572723 True -13 40166 30.956929206848145 18.396838665008545 401.4911804199219 0.3759303390979767 558.7553100585938 0.4171381890773773 0.8431762 0.22562511265277863 True -14 43035 31.461429595947266 0.5669643878936768 483.1186218261719 0.13652920722961426 557.4459228515625 0.4186165928840637 0.8458415 0.20976926386356354 True -15 45904 30.948867559432983 1.1004550457000732 444.19464111328125 0.149960458278656 555.7860717773438 0.4212161898612976 0.852648 0.2043202966451645 True -16 48773 30.92331600189209 0.5548763275146484 455.3408203125 0.1044328436255455 556.243408203125 0.41965824365615845 0.8539377 0.19596052169799805 True -17 51642 30.841448545455933 0.5550603866577148 487.22943115234375 0.19745467603206635 556.4385986328125 0.41933199763298035 0.8568907 0.19478239119052887 True -18 54511 30.9137179851532 0.5568227767944336 498.03466796875 0.21641722321510315 556.0885620117188 0.42000406980514526 0.85652465 0.19477479159832 False -19 57380 30.867228269577026 0.5465989112854004 441.76031494140625 0.16700807213783264 555.8475952148438 0.4209178388118744 0.85439414 0.1953778713941574 False diff --git a/ENCSR645HET/cherimoya.fold_2.performance.tsv b/ENCSR645HET/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 041864457f8dd3a4203aef8c76014a49326c433f..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -556.4385986328125 0.3689417243003845 0.41933199763298035 0.1714804470539093 0.8568906784057617 0.8344487547874451 0.19478239119052887 \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_3.evaluate.json b/ENCSR645HET/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f703c1eed5c03f3654b9ebc4c56b9195896aee6c..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133NHP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_3.fit.json b/ENCSR645HET/cherimoya.fold_3.fit.json deleted file mode 100644 index 4a747df550e1f40bee45e41e5b867c39b136f1fa..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF133NHP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_3.log b/ENCSR645HET/cherimoya.fold_3.log deleted file mode 100644 index ef0276f654f96eced648254e8e9c5166fadcdae3..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 36.09904766082764 3.525529384613037 441.8896484375 0.3854677677154541 613.4236450195312 0.3069238066673279 0.69836634 4.058009624481201 True -1 5492 30.23011589050293 0.5759894847869873 522.6275634765625 0.41528603434562683 555.6327514648438 0.38216322660446167 0.7695315 0.9092684388160706 True -2 8238 30.252094507217407 0.5524284839630127 514.6124267578125 0.541571319103241 546.2828979492188 0.39186936616897583 0.78572786 0.46528515219688416 True -3 10984 30.14384889602661 1.897322177886963 552.3951416015625 0.31277719140052795 543.3348999023438 0.3957808017730713 0.79516584 0.5552894473075867 True -4 13730 29.57415270805359 0.5717239379882812 565.3184204101562 0.3251097798347473 539.558349609375 0.39845266938209534 0.8062034 0.4425526261329651 True -5 16476 29.554547786712646 0.5263204574584961 461.9734191894531 0.23310400545597076 537.5659790039062 0.40062347054481506 0.8092146 0.3668050169944763 True -6 19222 29.644810676574707 0.5410711765289307 435.46173095703125 0.2983912229537964 537.640625 0.40022146701812744 0.8139542 0.4512101709842682 True -7 21968 29.58145785331726 0.5399558544158936 476.3841247558594 0.23868271708488464 535.2210083007812 0.402832955121994 0.8194823 0.3354780972003937 True -8 24714 29.552438020706177 0.5385491847991943 546.6982421875 0.2295711487531662 534.478515625 0.40430334210395813 0.8182144 0.3658089339733124 False -9 27460 29.59091329574585 0.5395534038543701 442.98541259765625 0.30426299571990967 532.4115600585938 0.407328724861145 0.82193387 0.31954532861709595 True -10 30206 29.58890724182129 0.5471835136413574 442.4776916503906 0.18767786026000977 530.0784912109375 0.41134777665138245 0.82614136 0.28071722388267517 True -11 32952 29.628307580947876 0.6099202632904053 585.8492431640625 0.2887088656425476 528.2138671875 0.41373324394226074 0.8346361 0.2658672630786896 True -12 35698 29.611947774887085 0.5242371559143066 586.131591796875 0.1761091947555542 527.3680419921875 0.41417789459228516 0.8393071 0.25067198276519775 True -13 38444 29.578218460083008 0.5472793579101562 443.000732421875 0.12821030616760254 526.050048828125 0.41587334871292114 0.8461968 0.23345762491226196 True -14 41190 29.59700655937195 0.5464160442352295 530.3031616210938 0.17692725360393524 524.5027465820312 0.41853010654449463 0.8530307 0.2200470268726349 True -15 43936 29.550615310668945 0.5444092750549316 453.60595703125 0.28096431493759155 523.4037475585938 0.41929081082344055 0.85840744 0.20763422548770905 True -16 46682 29.560865879058838 1.223586082458496 419.0437927246094 0.17142407596111298 522.0209350585938 0.421219140291214 0.8627395 0.2003721296787262 True -17 49428 29.639036417007446 0.5409471988677979 528.8675537109375 0.1573064625263214 522.7933959960938 0.4199833571910858 0.8621289 0.19832047820091248 False -18 52174 29.551828861236572 0.5484514236450195 492.53167724609375 0.3607723116874695 522.4635009765625 0.4208987057209015 0.8614208 0.19705908000469208 False -19 54920 29.528623819351196 0.544243335723877 463.3343505859375 0.19610600173473358 522.6673583984375 0.4201648235321045 0.863633 0.19787125289440155 True diff --git a/ENCSR645HET/cherimoya.fold_3.performance.tsv b/ENCSR645HET/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2ad1049a4085687304723f8eacf9f40d4183de65..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -522.6673583984375 0.37297001481056213 0.4201648235321045 0.1662745475769043 0.8636329770088196 0.831460177898407 0.19787125289440155 \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_4.evaluate.json b/ENCSR645HET/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6d4f3a7eb90cff703cfba38259e50a3911abae6a..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133NHP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_4.fit.json b/ENCSR645HET/cherimoya.fold_4.fit.json deleted file mode 100644 index 0c889711a41b2dd9feb400dd08c173ee33e1aa1e..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF133NHP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR645HET/cherimoya.fold_4.log b/ENCSR645HET/cherimoya.fold_4.log deleted file mode 100644 index 489c76e3c8448eabf30347948768bdfe41f27c60..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2856 36.3405065536499 4.431775093078613 489.6427001953125 0.309600830078125 594.927734375 0.29666656255722046 0.689951 3.294865369796753 True -1 5712 31.30817413330078 0.6252868175506592 435.96783447265625 0.4169197678565979 544.7416381835938 0.36891764402389526 0.7524169 0.840110719203949 True -2 8568 31.32507872581482 0.6136205196380615 499.23297119140625 0.33732402324676514 537.0780029296875 0.37903186678886414 0.7645216 0.4733242690563202 True -3 11424 31.39618182182312 0.5735893249511719 571.614990234375 0.32297855615615845 531.217041015625 0.3847543001174927 0.7789501 0.4429093599319458 True -4 14280 30.7100350856781 0.5781736373901367 404.45367431640625 0.2719522714614868 528.4168701171875 0.38888242840766907 0.78755504 0.3429446220397949 True -5 17136 30.693129301071167 0.5760180950164795 523.826416015625 0.2563531696796417 526.055908203125 0.3915967047214508 0.7956841 0.2738255560398102 True -6 19992 30.701733350753784 0.5611281394958496 455.61187744140625 0.24977725744247437 524.4010009765625 0.39345458149909973 0.80185026 0.2570478022098541 True -7 22848 30.768512725830078 0.5761778354644775 452.0369873046875 0.22728709876537323 522.2319946289062 0.3965857923030853 0.80837125 0.242413729429245 True -8 25704 30.65452551841736 0.5783154964447021 453.72613525390625 0.21808567643165588 520.394775390625 0.3999972939491272 0.8126364 0.23608586192131042 True -9 28560 30.732102394104004 3.10434889793396 450.259521484375 0.2633497416973114 520.1895141601562 0.39945557713508606 0.8181721 0.22613932192325592 True -10 31416 30.859294891357422 0.5712428092956543 414.84893798828125 0.2352132499217987 519.1546020507812 0.40091243386268616 0.8229395 0.22025316953659058 True -11 34272 30.707707405090332 0.5688607692718506 454.3201904296875 0.21361210942268372 517.2809448242188 0.40458205342292786 0.8297745 0.20655614137649536 True -12 37128 30.765129327774048 0.5755531787872314 565.2269287109375 0.21494752168655396 516.7099609375 0.40453144907951355 0.8329697 0.19795691967010498 True -13 39984 30.736608028411865 0.5692992210388184 501.0755920410156 0.17819300293922424 516.3839111328125 0.40465596318244934 0.8403886 0.19094668328762054 True -14 42840 30.662782907485962 0.5816450119018555 442.4173889160156 0.15787772834300995 514.4912109375 0.4074437618255615 0.84546244 0.18538756668567657 True -15 45696 30.710795402526855 0.569512128829956 454.7334289550781 0.22551590204238892 514.515380859375 0.40746578574180603 0.85009956 0.18085360527038574 True -16 48552 30.652783155441284 0.5628607273101807 477.2606201171875 0.23364034295082092 513.3643798828125 0.4105992913246155 0.8537272 0.17660057544708252 True -17 51408 30.75308108329773 0.5826880931854248 448.41107177734375 0.14124508202075958 513.5717163085938 0.4101790189743042 0.8557317 0.17535367608070374 True -18 54264 30.72647213935852 0.5671563148498535 479.13092041015625 0.1480039805173874 513.4669799804688 0.41038334369659424 0.856466 0.17457245290279388 True -19 57120 30.738869428634644 0.5745456218719482 391.2527160644531 0.16862444579601288 513.4591064453125 0.41011714935302734 0.8554784 0.1745016723871231 False diff --git a/ENCSR645HET/cherimoya.fold_4.performance.tsv b/ENCSR645HET/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b8347805b098acf59ee22803b6ade2417bc1d92a..0000000000000000000000000000000000000000 --- a/ENCSR645HET/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -513.4669799804688 0.3786781132221222 0.41038331389427185 0.1605885773897171 0.8564659953117371 0.823611855506897 0.17457245290279388 \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_0.evaluate.json b/ENCSR648GDP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 44f791ea6e8b353e8deaac4192be75b8e9e0f5a4..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF271GWL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_0.fit.json b/ENCSR648GDP/cherimoya.fold_0.fit.json deleted file mode 100644 index 91a7670830e71d17c61b4a6b56d9f6f8cd11d81e..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF271GWL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_0.log b/ENCSR648GDP/cherimoya.fold_0.log deleted file mode 100644 index 9f02a11a125d8a23ba0b3acbf6e07bfbc9668cc0..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2561 32.994691371917725 3.712740421295166 210.60299682617188 1.272024154663086 275.1558532714844 0.1482844352722168 0.30499998 4.582729339599609 True -1 5122 28.46479034423828 0.5736222267150879 164.08847045898438 1.0648531913757324 240.31434631347656 0.2661479413509369 0.42672697 3.2511749267578125 True -2 7683 28.41588592529297 0.5446765422821045 193.17300415039062 0.9685258865356445 233.95188903808594 0.28216883540153503 0.4540679 1.6812762022018433 True -3 10244 28.43646788597107 0.6240077018737793 166.33934020996094 1.5792871713638306 229.61831665039062 0.2954350411891937 0.48322368 1.4488639831542969 True -4 12805 28.57603359222412 0.549536943435669 183.3180389404297 1.3171745538711548 228.66494750976562 0.2981763184070587 0.49330115 1.3061912059783936 True -5 15366 28.532591581344604 0.5499968528747559 152.484619140625 1.0476727485656738 226.27833557128906 0.30717790126800537 0.5081563 1.3033818006515503 True -6 17927 28.435357332229614 0.5551128387451172 174.83509826660156 0.8481765985488892 225.24615478515625 0.3098873794078827 0.5203287 1.094349980354309 True -7 20488 28.373147010803223 0.5403587818145752 132.09246826171875 1.0960876941680908 224.2093963623047 0.31334713101387024 0.53261024 0.9754363298416138 True -8 23049 28.4461350440979 0.5582985877990723 142.55104064941406 0.6158594489097595 223.58734130859375 0.31443288922309875 0.54078823 0.9001650214195251 True -9 25610 28.4052414894104 0.5820019245147705 141.1676025390625 0.7530719041824341 222.4112548828125 0.3195386826992035 0.55265623 0.9187270402908325 True -10 28171 28.371344327926636 0.5381255149841309 173.26727294921875 0.8022134304046631 221.93438720703125 0.32116231322288513 0.5591276 0.900081217288971 True -11 30732 28.410619735717773 0.5438780784606934 198.05923461914062 0.9698206782341003 220.77975463867188 0.32520246505737305 0.5721657 0.8649622201919556 True -12 33293 28.38983154296875 0.5331640243530273 165.11126708984375 0.8695070743560791 220.3632354736328 0.3267703652381897 0.58613735 0.800844669342041 True -13 35854 28.388158082962036 0.5333127975463867 175.86575317382812 0.8759192228317261 219.7696533203125 0.32837793231010437 0.59704405 0.7800828218460083 True -14 38415 28.01294183731079 0.5426099300384521 152.80615234375 0.8248922824859619 219.6152801513672 0.3275669515132904 0.60933167 0.750505268573761 True -15 40976 27.879963874816895 0.5299029350280762 172.63583374023438 0.5571515560150146 218.8656463623047 0.33046698570251465 0.616881 0.717979907989502 True -16 43537 27.795649528503418 0.5443358421325684 159.75906372070312 0.47361379861831665 218.57205200195312 0.3312581777572632 0.6224566 0.7089803814888 True -17 46098 27.828933238983154 0.542210578918457 152.83023071289062 0.45923441648483276 218.08148193359375 0.33372369408607483 0.62516135 0.7021501660346985 True -18 48659 27.91566777229309 0.5406317710876465 172.59378051757812 0.8372941017150879 218.4429473876953 0.3317827582359314 0.6247269 0.7035230994224548 False -19 51220 28.0128493309021 0.5546998977661133 164.71633911132812 0.3691254258155823 218.58596801757812 0.3311174213886261 0.62457263 0.7080597281455994 False diff --git a/ENCSR648GDP/cherimoya.fold_0.performance.tsv b/ENCSR648GDP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 629949a716ea6b4dc6081928ad9c4195b70a2d67..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -218.08148193359375 0.4818464517593384 0.33372369408607483 0.07911132276058197 0.625161349773407 0.5872524976730347 0.7021501660346985 \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_1.evaluate.json b/ENCSR648GDP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2f1ac78f4809168177e24d8861eb0ae929f8ebdb..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF271GWL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_1.fit.json b/ENCSR648GDP/cherimoya.fold_1.fit.json deleted file mode 100644 index b55935d1b48b9b1f15820e85535eb43f9a31c639..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF271GWL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_1.log b/ENCSR648GDP/cherimoya.fold_1.log deleted file mode 100644 index a2aca9d08bf7232e9b6b7f8bed7f68e5f4fae713..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2602 33.239999532699585 3.9929049015045166 197.6804962158203 1.6393064260482788 296.47857666015625 0.15789291262626648 0.3335902 4.40448522567749 True -1 5204 28.90281343460083 0.7454004287719727 215.73492431640625 1.364004373550415 259.2907409667969 0.2832614779472351 0.46736157 3.7846059799194336 True -2 7806 28.90861415863037 0.955981969833374 231.862060546875 1.5948225259780884 251.29518127441406 0.30172425508499146 0.48787513 1.6233099699020386 True -3 10408 28.885143518447876 0.7060532569885254 161.3251953125 1.4836950302124023 248.03538513183594 0.30906689167022705 0.50833005 1.5421284437179565 True -4 13010 28.893064498901367 0.6112077236175537 196.50814819335938 1.2843492031097412 246.7834930419922 0.3121325671672821 0.5237952 1.4679440259933472 True -5 15612 28.833593606948853 0.6092829704284668 159.7391357421875 0.8456102609634399 245.59600830078125 0.3156633675098419 0.53942174 1.3177382946014404 True -6 18214 28.78524112701416 0.6134655475616455 169.83242797851562 0.9659690260887146 244.30718994140625 0.3197994530200958 0.54177094 1.3204121589660645 True -7 20816 28.77348828315735 0.6103968620300293 188.5768280029297 0.9132450819015503 243.38157653808594 0.3225906789302826 0.5511347 1.3033629655838013 True -8 23418 28.772384643554688 0.6193161010742188 162.587646484375 0.9843988418579102 242.8732452392578 0.32346320152282715 0.5631809 1.2540819644927979 True -9 26020 28.77348780632019 0.647702693939209 227.93569946289062 1.0236653089523315 241.7802734375 0.32732805609703064 0.5733816 1.1921511888504028 True -10 28622 28.834266662597656 0.6110694408416748 164.32237243652344 0.811948299407959 241.30943298339844 0.3277691900730133 0.57764906 1.1809720993041992 True -11 31224 28.82943630218506 0.6290438175201416 161.9213104248047 0.9099648594856262 240.05868530273438 0.3310430347919464 0.59438246 1.0685948133468628 True -12 33826 28.809484720230103 1.636061429977417 202.27529907226562 0.7281961441040039 238.86508178710938 0.33475083112716675 0.6075823 1.0045747756958008 True -13 36428 28.90686345100403 0.6631371974945068 149.71603393554688 1.0166974067687988 238.31146240234375 0.33548450469970703 0.6223094 0.9083433151245117 True -14 39030 28.92534899711609 0.6280055046081543 178.4727783203125 0.7154480218887329 237.49298095703125 0.33820876479148865 0.6365084 0.8334967494010925 True -15 41632 28.445318460464478 1.7261602878570557 173.68540954589844 0.549161434173584 236.97215270996094 0.33911868929862976 0.6481868 0.771851658821106 True -16 44234 28.31608247756958 0.625239372253418 179.86993408203125 0.7927911281585693 236.72390747070312 0.34002211689949036 0.6558544 0.743730902671814 True -17 46836 28.452849864959717 0.6240620613098145 215.65338134765625 0.4460026025772095 236.48936462402344 0.34039250016212463 0.6584883 0.7215704321861267 True -18 49438 28.304919004440308 0.6293654441833496 146.09384155273438 0.5736569166183472 236.32925415039062 0.3412933349609375 0.65993834 0.7154273986816406 True -19 52040 28.35459589958191 0.6462118625640869 192.610595703125 0.40962374210357666 236.69700622558594 0.3395971953868866 0.6608263 0.7168297171592712 True diff --git a/ENCSR648GDP/cherimoya.fold_1.performance.tsv b/ENCSR648GDP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 60b6b2dd7e3e54d6307e7bbfc9a17614062997ec..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -236.69700622558594 0.47409936785697937 0.339597225189209 0.08404668420553207 0.6608263254165649 0.6241380572319031 0.7168297171592712 \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_2.evaluate.json b/ENCSR648GDP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 77fd80d457f03454d55c2e18e4b575661cc102b3..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF271GWL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_2.fit.json b/ENCSR648GDP/cherimoya.fold_2.fit.json deleted file mode 100644 index 915f3d9f5af74f99dafe60aff6ca20090ceea1c3..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF271GWL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_2.log b/ENCSR648GDP/cherimoya.fold_2.log deleted file mode 100644 index 48ddc60d02fc574dcf91b7c72be53decffccc354..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 35.0160117149353 4.274437189102173 204.5579071044922 1.1489715576171875 273.5762634277344 0.15341655910015106 0.30582327 3.892967700958252 True -1 5458 30.31531596183777 0.6078598499298096 149.3846435546875 1.386559009552002 236.91079711914062 0.27794772386550903 0.46531567 3.0319013595581055 True -2 8187 30.355047702789307 0.5014815330505371 187.61077880859375 1.3744136095046997 230.48565673828125 0.29455941915512085 0.4771623 1.8055366277694702 True -3 10916 30.97779941558838 14.403085708618164 227.39846801757812 1.2706341743469238 228.21212768554688 0.30075886845588684 0.48838112 1.3838391304016113 True -4 13645 30.485055685043335 1.588526725769043 200.35711669921875 0.838792085647583 225.9702606201172 0.3078096807003021 0.5062903 1.4111051559448242 True -5 16374 30.402124881744385 1.5859324932098389 179.757568359375 1.0682952404022217 225.0990753173828 0.310610830783844 0.518856 1.2794570922851562 True -6 19103 30.42551827430725 1.109581470489502 169.5516357421875 0.9645090103149414 224.23594665527344 0.3121168613433838 0.53160566 1.1622692346572876 True -7 21832 30.261438608169556 1.0288503170013428 191.01959228515625 1.0973457098007202 223.15098571777344 0.3164796829223633 0.54321086 1.2190978527069092 True -8 24561 30.263074159622192 1.7950668334960938 196.17083740234375 0.8608652353286743 222.4506072998047 0.3179321885108948 0.5576318 1.0635627508163452 True -9 27290 30.405208587646484 0.7264518737792969 176.51980590820312 0.8267769813537598 221.2792205810547 0.3227398991584778 0.5656309 1.009291172027588 True -10 30019 30.22236728668213 0.7354514598846436 188.6162109375 1.0210182666778564 221.14846801757812 0.3233245611190796 0.5772688 0.9219548106193542 True -11 32748 30.226200580596924 0.47049713134765625 170.41604614257812 1.0478641986846924 219.82550048828125 0.3267351984977722 0.5894746 0.9074267148971558 True -12 35477 30.2304368019104 0.502342939376831 170.87083435058594 1.0947833061218262 219.24281311035156 0.32835331559181213 0.6023827 0.8393226861953735 True -13 38206 30.19517469406128 0.5107264518737793 169.97857666015625 0.6745607852935791 219.1952362060547 0.32801565527915955 0.6116549 0.8004617094993591 True -14 40935 30.288334846496582 0.8034429550170898 178.06924438476562 0.8724868297576904 218.1565704345703 0.33175212144851685 0.6254299 0.7608475089073181 True -15 43664 29.708019971847534 0.46926379203796387 143.79641723632812 0.6985376477241516 217.58978271484375 0.332366943359375 0.6352253 0.7277008295059204 True -16 46393 29.634231090545654 0.48293209075927734 148.5592041015625 0.505478024482727 217.2953338623047 0.33329659700393677 0.64215916 0.7075170874595642 True -17 49122 29.603451013565063 0.4618721008300781 162.06210327148438 0.7019259333610535 217.5319366455078 0.33177945017814636 0.64405644 0.6957281827926636 True -18 51851 29.646965742111206 0.4654703140258789 212.55718994140625 0.4496382772922516 217.277587890625 0.3327164649963379 0.6437292 0.693576455116272 False -19 54580 29.664742469787598 0.47880101203918457 177.52426147460938 0.9079508781433105 217.49630737304688 0.3325503468513489 0.6420091 0.702529788017273 False diff --git a/ENCSR648GDP/cherimoya.fold_2.performance.tsv b/ENCSR648GDP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 88af5c051ebb794fc1603c1c36df10b4682934cd..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -217.5319366455078 0.482578307390213 0.33177945017814636 0.07833938300609589 0.6440564393997192 0.603069007396698 0.6957281827926636 \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_3.evaluate.json b/ENCSR648GDP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0d321886bfc25a256006891bad017ba4ba56a119..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF271GWL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_3.fit.json b/ENCSR648GDP/cherimoya.fold_3.fit.json deleted file mode 100644 index 76131aa751b4ec9792ab3a69745d77ab9040f175..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF271GWL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_3.log b/ENCSR648GDP/cherimoya.fold_3.log deleted file mode 100644 index b1375b25d68be5ddb7a5adfdca8fb96d581bf7eb..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2629 33.558268547058105 3.880366325378418 187.770751953125 1.643763542175293 288.0471496582031 0.15870879590511322 0.3042916 4.973621368408203 True -1 5258 29.253928899765015 0.5996026992797852 184.97500610351562 1.244118094444275 251.2236328125 0.2791796624660492 0.45093843 3.784716844558716 True -2 7887 29.25308895111084 0.5795855522155762 174.45956420898438 1.5514726638793945 246.0048065185547 0.29330217838287354 0.44752637 2.1552891731262207 False -3 10516 29.189996242523193 0.5845136642456055 180.28045654296875 1.0382459163665771 242.99940490722656 0.29961681365966797 0.4912965 1.3962420225143433 True -4 13145 29.183098793029785 0.5657579898834229 137.66700744628906 1.0009562969207764 240.39971923828125 0.3073830306529999 0.50937325 1.3216840028762817 True -5 15774 29.2767915725708 14.129420280456543 149.53005981445312 0.8616427779197693 239.09449768066406 0.31127166748046875 0.52101475 1.2246103286743164 True -6 18403 29.198923349380493 0.5879838466644287 173.7645263671875 1.1088827848434448 238.04922485351562 0.31415125727653503 0.53445524 1.2264251708984375 True -7 21032 29.294906616210938 0.5690910816192627 169.81141662597656 0.8463725447654724 237.5183563232422 0.3164963722229004 0.537217 1.262621283531189 True -8 23661 29.285130262374878 0.5780489444732666 167.42616271972656 0.7429919242858887 236.45169067382812 0.32030636072158813 0.54739016 1.2354933023452759 True -9 26290 29.17279815673828 0.5790896415710449 167.20433044433594 1.168755292892456 235.61471557617188 0.32294508814811707 0.55856013 1.2129626274108887 True -10 28919 29.15968608856201 0.5795083045959473 191.16098022460938 1.2317078113555908 234.57147216796875 0.32619181275367737 0.569905 1.1671653985977173 True -11 31548 29.180057048797607 0.5731160640716553 183.27008056640625 1.028398036956787 233.64071655273438 0.32970768213272095 0.58286047 1.0972230434417725 True -12 34177 29.18526840209961 0.5599358081817627 164.23141479492188 0.8550216555595398 233.18255615234375 0.32991746068000793 0.59711367 0.9472531080245972 True -13 36806 29.16842031478882 0.5762522220611572 164.58663940429688 0.5821918845176697 232.33560180664062 0.3323231637477875 0.6075369 0.8920652866363525 True -14 39435 29.19918441772461 0.5766146183013916 178.592529296875 0.9335454702377319 232.2106475830078 0.3313440680503845 0.621432 0.8346675634384155 True -15 42064 29.166222095489502 0.5658595561981201 189.61444091796875 0.7491036653518677 231.69325256347656 0.332796573638916 0.63195676 0.7981743216514587 True -16 44693 28.602254629135132 0.5528659820556641 167.57476806640625 0.4918353259563446 231.0161590576172 0.3349887430667877 0.64058405 0.7426705956459045 True -17 47322 28.618267059326172 0.5661051273345947 163.37567138671875 0.5906835198402405 231.1163787841797 0.33405497670173645 0.644089 0.7252851128578186 True -18 49951 28.593799829483032 0.5657846927642822 162.85935974121094 0.8960949778556824 230.8038787841797 0.3354003429412842 0.6435801 0.7181432247161865 False -19 52580 28.551788091659546 0.5628745555877686 169.19857788085938 0.6157890558242798 231.126708984375 0.3332076370716095 0.6430159 0.7239392995834351 False diff --git a/ENCSR648GDP/cherimoya.fold_3.performance.tsv b/ENCSR648GDP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index aa676ccebc8a2cc9d6c222defe0f0d14a05bbd32..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -231.1163787841797 0.4776296615600586 0.33405497670173645 0.08345258235931396 0.6440889835357666 0.6075618267059326 0.7252851128578186 \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_4.evaluate.json b/ENCSR648GDP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 52acdc0d8a25b47aec516923e17ebcd4dae26961..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF271GWL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_4.fit.json b/ENCSR648GDP/cherimoya.fold_4.fit.json deleted file mode 100644 index 2b3fb7dc02fed4bfd823774337d6a7ad1cbe41e5..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF271GWL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648GDP/cherimoya.fold_4.log b/ENCSR648GDP/cherimoya.fold_4.log deleted file mode 100644 index 2bb77bacd628ebe53b9ef82cd6734feab4f77ccf..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.90398025512695 3.745666027069092 139.75335693359375 1.3144177198410034 278.552490234375 0.15028224885463715 0.30648223 4.917910575866699 True -1 5500 30.446632862091064 0.6264700889587402 212.55923461914062 1.5284929275512695 244.02703857421875 0.2712183892726898 0.43512937 3.2377336025238037 True -2 8250 30.45824098587036 0.5737783908843994 165.70407104492188 1.0452113151550293 237.2223663330078 0.2899966537952423 0.46900624 1.8695486783981323 True -3 11000 30.508610248565674 0.551058292388916 186.81582641601562 1.0098689794540405 233.9575653076172 0.2988462746143341 0.4917959 1.6077897548675537 True -4 13750 30.49451732635498 0.5325901508331299 210.28663635253906 1.179271936416626 232.8986358642578 0.30169689655303955 0.49630967 1.6343616247177124 True -5 16500 30.55342173576355 0.5408895015716553 196.52603149414062 1.1479990482330322 231.6209259033203 0.306799054145813 0.50230265 1.5397127866744995 True -6 19250 30.503039360046387 1.6157686710357666 146.0030517578125 0.7362106442451477 230.0117645263672 0.31222328543663025 0.5213871 1.2624017000198364 True -7 22000 30.47209119796753 0.5360958576202393 192.4060821533203 1.4993464946746826 229.2550506591797 0.3142054080963135 0.52945626 1.3173798322677612 True -8 24750 30.490427494049072 0.5494587421417236 152.27920532226562 1.023742437362671 228.23045349121094 0.3184814155101776 0.5381349 1.234621286392212 True -9 27500 30.546546936035156 0.5349974632263184 149.3165740966797 1.1269445419311523 227.74021911621094 0.31971117854118347 0.5503757 1.2018860578536987 True -10 30250 30.491933822631836 0.5495257377624512 134.96514892578125 0.8713635802268982 226.91946411132812 0.32171136140823364 0.5614788 1.064153790473938 True -11 33000 30.510334014892578 0.5371158123016357 135.61605834960938 0.7328306436538696 225.97116088867188 0.3245731592178345 0.5741487 1.0164144039154053 True -12 35750 30.51237177848816 0.5422377586364746 178.36842346191406 0.9943745136260986 225.36761474609375 0.3255895674228668 0.58984584 0.907090425491333 True -13 38500 30.54949975013733 0.5443813800811768 200.61666870117188 0.8310372829437256 224.28121948242188 0.3295988440513611 0.6026159 0.8453488349914551 True -14 41250 30.528026580810547 0.5405991077423096 174.23037719726562 0.8524401187896729 224.19371032714844 0.3284051716327667 0.61425334 0.7876108884811401 True -15 44000 30.44656538963318 0.5399219989776611 171.80816650390625 0.6233941316604614 223.01950073242188 0.3329579532146454 0.624891 0.7378401756286621 True -16 46750 30.358689546585083 0.53387451171875 166.99850463867188 0.5995311737060547 222.90988159179688 0.33246442675590515 0.63399976 0.7121814489364624 True -17 49500 29.791903257369995 0.5319249629974365 148.74143981933594 0.6565905809402466 222.88612365722656 0.33184194564819336 0.63515574 0.6978206038475037 True -18 52250 29.784664630889893 0.6771717071533203 170.15077209472656 0.6359187960624695 222.5425567626953 0.3340259790420532 0.63415164 0.6985666155815125 False -19 55000 29.886840343475342 0.5541293621063232 153.08975219726562 0.6531725525856018 223.15431213378906 0.3305008113384247 0.63404477 0.702306866645813 False diff --git a/ENCSR648GDP/cherimoya.fold_4.performance.tsv b/ENCSR648GDP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 79df4d81717148d22b3c16efcc4800df30c0927c..0000000000000000000000000000000000000000 --- a/ENCSR648GDP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -222.88612365722656 0.4810495674610138 0.3318418860435486 0.076572947204113 0.6351557374000549 0.5948996543884277 0.6978206038475037 \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_0.evaluate.json b/ENCSR648JJT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index dbb313c0ec0d829e185a67375341cb49722c25ea..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925LAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_0.fit.json b/ENCSR648JJT/cherimoya.fold_0.fit.json deleted file mode 100644 index ff74cf9c55fe93543f8cd089b18300b5b164e7dd..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF925LAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_0.log b/ENCSR648JJT/cherimoya.fold_0.log deleted file mode 100644 index 10622319a7efa7833c2840b6cd26821dbb8932df..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2917 36.89368796348572 4.120401620864868 500.549072265625 0.5979388952255249 671.6796875 0.5366257429122925 0.581439 8.13147258758545 True -1 5834 32.51703977584839 2.3909730911254883 389.8565368652344 0.5009831786155701 538.3901977539062 0.7109184861183167 0.6121246 1.7210112810134888 True -2 8751 32.496878147125244 0.6364362239837646 415.7547912597656 0.6593429446220398 525.2468872070312 0.7214381694793701 0.6250271 0.7821546196937561 True -3 11668 32.458617210388184 0.6149570941925049 378.3236999511719 0.5306931734085083 519.4910888671875 0.726125180721283 0.6266446 0.5377568602561951 True -4 14585 32.535465240478516 0.592968225479126 426.59381103515625 0.579119086265564 516.1077880859375 0.7305309176445007 0.64057356 0.5066898465156555 True -5 17502 32.43169808387756 0.607083797454834 452.2044677734375 0.5741960406303406 513.0953979492188 0.7333468794822693 0.654989 0.4997532367706299 True -6 20419 32.41753101348877 0.595757246017456 394.70794677734375 0.6540449857711792 510.8576354980469 0.7358371019363403 0.6674872 0.4789029061794281 True -7 23336 32.45571851730347 0.6027319431304932 431.869384765625 0.45480671525001526 509.1228942871094 0.7377372980117798 0.66888607 0.476936936378479 True -8 26253 32.44286847114563 0.6166577339172363 418.3086242675781 0.4633667469024658 507.45355224609375 0.7398196458816528 0.6814089 0.466195672750473 True -9 29170 32.52566432952881 0.594456672668457 414.829345703125 0.4003840386867523 505.2872619628906 0.7422817349433899 0.69645554 0.4430723190307617 True -10 32087 32.46285915374756 0.9541001319885254 380.6231689453125 0.31891411542892456 502.7695617675781 0.7446404695510864 0.71066093 0.4187052547931671 True -11 35004 32.48286032676697 0.614534854888916 402.8578796386719 0.4587293863296509 500.4681091308594 0.7469092607498169 0.7173499 0.4094597399234772 True -12 37921 32.44800019264221 1.8937888145446777 384.11212158203125 0.4064466953277588 498.5770263671875 0.7487861514091492 0.72758454 0.40567925572395325 True -13 40838 32.50887632369995 0.8411564826965332 442.63250732421875 0.36048129200935364 496.8547668457031 0.7505707740783691 0.741092 0.3881712257862091 True -14 43755 32.647765159606934 8.38735818862915 417.6654968261719 0.3903810381889343 495.272705078125 0.7519373893737793 0.7513812 0.3751455545425415 True -15 46672 32.27790284156799 0.6191303730010986 373.2044677734375 0.3587762415409088 494.2925720214844 0.7527492046356201 0.76145464 0.3683995008468628 True -16 49589 31.783779859542847 0.6185846328735352 442.19769287109375 0.31948941946029663 493.81170654296875 0.7531383037567139 0.7665737 0.3616796135902405 True -17 52506 31.748109102249146 1.160862684249878 384.3525085449219 0.29228001832962036 493.60028076171875 0.753185510635376 0.7697424 0.3611331582069397 True -18 55423 31.743237018585205 1.125546932220459 343.3230285644531 0.21428793668746948 493.7857666015625 0.7528436779975891 0.76831925 0.3650214672088623 False -19 58340 31.803674936294556 0.6292092800140381 331.70819091796875 0.26714420318603516 494.0561218261719 0.7525976300239563 0.7686639 0.3672846853733063 False diff --git a/ENCSR648JJT/cherimoya.fold_0.performance.tsv b/ENCSR648JJT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 20a8515bee8bd735b3b34dd6da0928a0fd810d6a..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -493.60028076171875 0.21514613926410675 0.7531855702400208 0.3181755244731903 0.7697424292564392 0.7088732123374939 0.3611331582069397 \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_1.evaluate.json b/ENCSR648JJT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8ca3cc16fd773ea0f08e119d14fa458beba0e532..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925LAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_1.fit.json b/ENCSR648JJT/cherimoya.fold_1.fit.json deleted file mode 100644 index 1f3dc1a20309d2768b67afb9fadf67c89bb8f25f..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF925LAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_1.log b/ENCSR648JJT/cherimoya.fold_1.log deleted file mode 100644 index 3a1e8ccd31906f336122b94a3959b73c8018beab..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2906 37.350046157836914 4.63942289352417 485.4167175292969 0.8386940956115723 707.39208984375 0.5408942103385925 0.5921813 8.077759742736816 True -1 5812 32.590144634246826 1.0367851257324219 404.8418273925781 0.603873610496521 570.8909301757812 0.7113840579986572 0.6432714 1.8126716613769531 True -2 8718 32.96549034118652 21.95872664451599 356.5363464355469 0.7923980951309204 554.6736450195312 0.7245722413063049 0.64520186 0.7707512974739075 True -3 11624 32.376070499420166 0.7878508567810059 389.7080383300781 0.33743637800216675 545.444580078125 0.7329409718513489 0.6796658 0.5204532742500305 True -4 14530 32.4439857006073 1.794287919998169 399.51373291015625 0.56645268201828 541.4961547851562 0.7369769811630249 0.69507384 0.4726038873195648 True -5 17436 32.35689163208008 0.8391585350036621 401.37255859375 0.5307449102401733 539.5206909179688 0.7393181324005127 0.69447947 0.48849281668663025 False -6 20342 32.393763065338135 0.7819545269012451 424.5446472167969 0.5175244212150574 537.865234375 0.74135822057724 0.70456636 0.47091007232666016 True -7 23248 32.362715005874634 0.8123316764831543 440.6258544921875 0.5226713418960571 534.41748046875 0.744052529335022 0.711932 0.4508919417858124 True -8 26154 32.29252743721008 1.2007472515106201 370.4989929199219 0.674396812915802 531.269775390625 0.7471716403961182 0.72633904 0.4262775182723999 True -9 29060 32.00501108169556 0.7574107646942139 360.2081298828125 0.46275949478149414 529.2098999023438 0.7494806051254272 0.73427856 0.41262781620025635 True -10 31966 31.67178702354431 0.7721569538116455 422.6930847167969 0.3675941526889801 526.2935180664062 0.7523004412651062 0.7446255 0.39714905619621277 True -11 34872 31.67802095413208 0.7418437004089355 380.33135986328125 0.33740127086639404 523.945068359375 0.7544036507606506 0.75353926 0.388176828622818 True -12 37778 33.78686761856079 0.7566537857055664 371.5598449707031 0.3775075674057007 521.8840942382812 0.7565382122993469 0.764786 0.37908196449279785 True -13 40684 31.657777786254883 0.7579164505004883 396.4840087890625 0.3587610125541687 519.8705444335938 0.7583417892456055 0.77628124 0.36271512508392334 True -14 43590 31.711382627487183 0.7553451061248779 361.995361328125 0.4051407277584076 517.9360961914062 0.7601128220558167 0.7863601 0.34465640783309937 True -15 46496 31.86840558052063 1.7636690139770508 408.52691650390625 0.4187049865722656 516.4420776367188 0.7615202069282532 0.7968128 0.3319438099861145 True -16 49402 31.9558687210083 0.7785956859588623 397.5974426269531 0.32189124822616577 515.4718017578125 0.7623928189277649 0.80012405 0.32528379559516907 True -17 52308 31.852109909057617 0.7646298408508301 388.1597900390625 0.2210882306098938 515.4229736328125 0.7623718976974487 0.80370194 0.3224576413631439 True -18 55214 31.823518991470337 0.7630593776702881 339.16790771484375 0.2116200029850006 515.6136474609375 0.7620167136192322 0.80329734 0.32241901755332947 False -19 58120 31.823055028915405 1.8988897800445557 403.1220703125 0.35295021533966064 515.77197265625 0.7618666887283325 0.8022994 0.32312944531440735 False diff --git a/ENCSR648JJT/cherimoya.fold_1.performance.tsv b/ENCSR648JJT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 23bd55009141459aace56cb3fe06be8e97ec6178..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -515.4229736328125 0.20840725302696228 0.7623718976974487 0.3339318335056305 0.8037019371986389 0.7618486881256104 0.3224576413631439 \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_2.evaluate.json b/ENCSR648JJT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7c2f45973e0dd11a1995427a1f9ed83b36a6ccff..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925LAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_2.fit.json b/ENCSR648JJT/cherimoya.fold_2.fit.json deleted file mode 100644 index 825ecc7f997715da3ec11f1b1af7bbb2d1f3b220..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF925LAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_2.log b/ENCSR648JJT/cherimoya.fold_2.log deleted file mode 100644 index 123742f0f2ce6ab186e7ebbdbbb3f671c327ade2..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3103 39.26039958000183 4.052254915237427 423.8774108886719 0.5720967054367065 683.7882080078125 0.5490877628326416 0.5873155 6.04036283493042 True -1 6206 34.67245697975159 1.610417127609253 393.0313720703125 0.5273927450180054 555.423583984375 0.7103903889656067 0.6436601 1.7205517292022705 True -2 9309 34.604081869125366 0.5689945220947266 472.29193115234375 0.527861475944519 543.9111938476562 0.718283474445343 0.63235676 0.9295434355735779 False -3 12412 34.35201549530029 0.5511424541473389 484.77410888671875 0.6489354372024536 535.169921875 0.7257664799690247 0.6578196 0.6696213483810425 True -4 15515 33.82959175109863 0.5474457740783691 391.6022644042969 0.2993786334991455 530.0247192382812 0.7306389808654785 0.6673919 0.5666921138763428 True -5 18618 33.79231572151184 0.5606355667114258 407.6212158203125 0.5277633666992188 526.5888671875 0.73421710729599 0.68047595 0.5164012312889099 True -6 21721 33.809098958969116 0.5624418258666992 400.3255310058594 0.5320010185241699 525.2149658203125 0.7357296943664551 0.68757766 0.49236464500427246 True -7 24824 33.812331438064575 0.5626678466796875 415.2403259277344 0.4694528579711914 523.4547119140625 0.7376155853271484 0.6912553 0.5001542568206787 True -8 27927 33.968321800231934 0.5918188095092773 422.4520568847656 0.4822593033313751 519.3562622070312 0.7412353157997131 0.71031 0.4554646909236908 True -9 31030 33.79656529426575 0.5596754550933838 385.88433837890625 0.2726566195487976 517.4978637695312 0.7434354424476624 0.7147961 0.4499598741531372 True -10 34133 33.845503091812134 0.5625979900360107 396.2574462890625 0.42043066024780273 515.4109497070312 0.74537593126297 0.72178304 0.4375303387641907 True -11 37236 33.82565975189209 0.5606615543365479 400.64288330078125 0.3225199580192566 513.3563842773438 0.7476039528846741 0.73235023 0.4212898015975952 True -12 40339 33.78326225280762 0.5618228912353516 415.3327941894531 0.4063608646392822 511.2293701171875 0.7496394515037537 0.74459827 0.40760666131973267 True -13 43442 33.74480319023132 0.5621070861816406 404.4526062011719 0.36878111958503723 509.04486083984375 0.7517645359039307 0.7558889 0.3981909155845642 True -14 46545 33.93249988555908 0.5618031024932861 351.65069580078125 0.3513590693473816 507.5688781738281 0.7531047463417053 0.76342213 0.3841516077518463 True -15 49648 34.16118049621582 0.5492024421691895 436.2276306152344 0.26299849152565 506.40728759765625 0.7541338801383972 0.7689429 0.3728788495063782 True -16 52751 33.81007766723633 0.5543270111083984 403.24029541015625 0.4009559750556946 505.6776428222656 0.7547339797019958 0.7763272 0.36501508951187134 True -17 55854 33.86535453796387 0.5608711242675781 389.02325439453125 0.310838520526886 505.565185546875 0.7547591924667358 0.77691895 0.36509910225868225 True -18 58957 33.794639587402344 0.5609502792358398 412.95233154296875 0.3036506175994873 506.0801696777344 0.7542600035667419 0.7767213 0.36957600712776184 False -19 62060 33.838202476501465 0.5594990253448486 387.8245544433594 0.264242559671402 506.3413391113281 0.7540225386619568 0.7761748 0.3726906180381775 False diff --git a/ENCSR648JJT/cherimoya.fold_2.performance.tsv b/ENCSR648JJT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d94ad13bb7947aa40968ce5a4215f6832637aa75..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -505.565185546875 0.21294714510440826 0.7547591924667358 0.326837420463562 0.7769189476966858 0.7275152206420898 0.36509910225868225 \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_3.evaluate.json b/ENCSR648JJT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 92bad5396787193fc3d099af33254ccaa8862ec8..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925LAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_3.fit.json b/ENCSR648JJT/cherimoya.fold_3.fit.json deleted file mode 100644 index b0fe7ff7eb82d9fa7e134b981278e944ad7dd868..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF925LAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_3.log b/ENCSR648JJT/cherimoya.fold_3.log deleted file mode 100644 index dddf3121169abeb1c5962df4e97e7cbe99ae5a88..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3004 39.656877756118774 4.32041597366333 460.91912841796875 0.749502420425415 673.9505615234375 0.5533127784729004 0.58990073 7.923105716705322 True -1 6008 33.43665385246277 0.6700360774993896 446.398681640625 0.6723192930221558 548.7772827148438 0.7139025926589966 0.6192865 1.8551791906356812 True -2 9012 33.45087909698486 1.23270583152771 466.0753479003906 0.43714985251426697 536.1270141601562 0.7233082056045532 0.6168695 0.7987516522407532 False -3 12016 33.48200011253357 0.660773515701294 388.4416198730469 0.48061007261276245 529.1943359375 0.7302318215370178 0.6292851 0.678516685962677 True -4 15020 33.49117612838745 0.6047070026397705 464.87969970703125 0.5998471975326538 525.3553466796875 0.7340630292892456 0.6320148 0.5763145089149475 True -5 18024 33.39795923233032 0.9370396137237549 394.1222229003906 0.7212607264518738 523.5305786132812 0.736107587814331 0.63494015 0.5621338486671448 True -6 21028 33.46309280395508 0.5966637134552002 426.3369140625 0.44582223892211914 521.2068481445312 0.738280177116394 0.6372154 0.5617833733558655 True -7 24032 33.388086795806885 0.8694248199462891 473.575927734375 0.47897598147392273 518.4429321289062 0.7408109903335571 0.6586855 0.5361762046813965 True -8 27036 33.372411489486694 1.260552167892456 439.48028564453125 0.4722602069377899 516.3894653320312 0.7429296970367432 0.6613547 0.5190654993057251 True -9 30040 33.404369831085205 0.6042830944061279 395.7703857421875 0.5386127829551697 514.1640625 0.7453839778900146 0.6752027 0.4907030463218689 True -10 33044 33.38832950592041 0.6196784973144531 386.33380126953125 0.5647270679473877 511.54876708984375 0.7478710412979126 0.68992525 0.4679490923881531 True -11 36048 33.42866325378418 0.6046209335327148 417.50799560546875 0.34638309478759766 509.85418701171875 0.7496386170387268 0.7064715 0.45377597212791443 True -12 39052 33.46899175643921 1.393054485321045 377.47698974609375 0.33387428522109985 507.88897705078125 0.7516971230506897 0.7199511 0.4377172589302063 True -13 42056 33.429147243499756 0.5982015132904053 449.18212890625 0.5727876424789429 506.0221252441406 0.7535164952278137 0.73045045 0.42542317509651184 True -14 45060 33.439143896102905 1.3908474445343018 393.23297119140625 0.3787750005722046 503.9671325683594 0.755122721195221 0.7471046 0.39822420477867126 True -15 48064 32.97341966629028 1.1213014125823975 370.9921875 0.2860335111618042 502.7929992675781 0.7561918497085571 0.75698715 0.39026880264282227 True -16 51068 32.91703701019287 0.6232953071594238 328.5912780761719 0.3692690134048462 502.2316589355469 0.7566863298416138 0.76639473 0.3804488480091095 True -17 54072 33.017956495285034 15.648792028427124 396.6246337890625 0.2996067702770233 501.94329833984375 0.7565560340881348 0.76875764 0.38185378909111023 True -18 57076 32.925782918930054 0.6168830394744873 402.6714172363281 0.20168471336364746 502.217529296875 0.7561966776847839 0.76915604 0.38475728034973145 True -19 60080 32.9178204536438 0.6027092933654785 371.7204895019531 0.28334808349609375 502.53436279296875 0.7559397220611572 0.76851034 0.3872370421886444 False diff --git a/ENCSR648JJT/cherimoya.fold_3.performance.tsv b/ENCSR648JJT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index aef8226ca9567eaf4bc7389ebc03320a37f4cded..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -502.217529296875 0.21196424961090088 0.7561967968940735 0.32498347759246826 0.7691560387611389 0.7204738855361938 0.38475728034973145 \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_4.evaluate.json b/ENCSR648JJT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 290d59f41c0da155c66e0c21dd6f58d4a6a856aa..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925LAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_4.fit.json b/ENCSR648JJT/cherimoya.fold_4.fit.json deleted file mode 100644 index 3bde892755e7360848718b23ee0f47c13f5c221a..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF925LAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648JJT/cherimoya.fold_4.log b/ENCSR648JJT/cherimoya.fold_4.log deleted file mode 100644 index 2a7bd36493a30c44b1238e10aaa09516ceb279f2..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3055 38.79047989845276 4.722841024398804 433.40753173828125 0.540989100933075 671.3919067382812 0.5433229804039001 0.59979266 7.295475959777832 True -1 6110 34.00592398643494 0.8500978946685791 420.068359375 0.4726766049861908 541.0479736328125 0.7110979557037354 0.6359015 1.3179432153701782 True -2 9165 34.027955770492554 0.6130936145782471 414.505615234375 0.862868070602417 529.31787109375 0.7207028865814209 0.6286305 0.616341233253479 False -3 12220 34.03225636482239 0.809394359588623 385.3263854980469 0.5002409219741821 520.8385620117188 0.7293410897254944 0.6396517 0.6158634424209595 True -4 15275 33.97793221473694 0.5937819480895996 488.3657531738281 0.7214740514755249 518.6546630859375 0.7317296862602234 0.6451032 0.5264747738838196 True -5 18330 33.98312330245972 0.5881092548370361 461.1932067871094 0.6649883985519409 516.1632080078125 0.7345905303955078 0.6474555 0.5111648440361023 True -6 21385 34.02756118774414 0.606297492980957 424.79327392578125 0.4841338098049164 513.160400390625 0.7373363375663757 0.66209286 0.48752453923225403 True -7 24440 34.01303315162659 0.6007728576660156 430.8642883300781 0.5251730680465698 511.2210998535156 0.7395007610321045 0.6690125 0.48046183586120605 True -8 27495 33.92839527130127 0.6123077869415283 436.4449157714844 0.4606282114982605 508.9268798828125 0.7418229579925537 0.6823064 0.463433176279068 True -9 30550 33.966928005218506 0.593235969543457 435.381591796875 0.4333125948905945 507.6470642089844 0.7435543537139893 0.6928753 0.4524097442626953 True -10 33605 33.8342182636261 1.4409475326538086 409.5550537109375 0.4381996691226959 505.4341735839844 0.7459206581115723 0.70580876 0.43638166785240173 True -11 36660 33.30270767211914 0.5742688179016113 415.73095703125 0.41961297392845154 503.1282958984375 0.7481583952903748 0.7250932 0.4122406542301178 True -12 39715 33.335479736328125 0.587409496307373 400.2412109375 0.3828161954879761 501.2734375 0.7498269081115723 0.7372319 0.39975476264953613 True -13 42770 33.304563760757446 0.5797624588012695 417.12542724609375 0.26623737812042236 499.5213928222656 0.7516023516654968 0.7519588 0.38363540172576904 True -14 45825 33.257803440093994 1.2505605220794678 428.078857421875 0.2766894996166229 497.80963134765625 0.7530933618545532 0.7638942 0.3667204678058624 True -15 48880 33.30416917800903 1.1734747886657715 410.72509765625 0.2577262818813324 497.0347595214844 0.7540022134780884 0.77082396 0.3623391389846802 True -16 51935 33.279776096343994 0.5922305583953857 398.10150146484375 0.35319089889526367 496.2507019042969 0.7545950412750244 0.77733517 0.35821768641471863 True -17 54990 33.29902482032776 0.5734767913818359 403.9425048828125 0.31567710638046265 496.1881408691406 0.7545103430747986 0.78233474 0.35090696811676025 True -18 58045 33.292906761169434 0.5833964347839355 416.42889404296875 0.3569331169128418 496.3851318359375 0.7542467713356018 0.78131527 0.3537288308143616 False -19 61100 33.273491621017456 0.6018092632293701 350.412109375 0.2861891984939575 496.508544921875 0.7540631294250488 0.78302294 0.356819212436676 True diff --git a/ENCSR648JJT/cherimoya.fold_4.performance.tsv b/ENCSR648JJT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2f2da9d95f6fd266fbbd03cb427af794eec45f2f..0000000000000000000000000000000000000000 --- a/ENCSR648JJT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -496.508544921875 0.21479642391204834 0.7540631294250488 0.32252827286720276 0.783022940158844 0.714838445186615 0.356819212436676 \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_0.evaluate.json b/ENCSR648RAX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4e9b41e99ae023fe0a524a2455acbd239e64e1be..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF686FPN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_0.fit.json b/ENCSR648RAX/cherimoya.fold_0.fit.json deleted file mode 100644 index 944e22352988252db4cb4ef2dfde6c87878bc573..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF686FPN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_0.log b/ENCSR648RAX/cherimoya.fold_0.log deleted file mode 100644 index 5c69ca94c48fe5ed2ad54d473d26916646cda076..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 34.26867198944092 3.544412612915039 188.03091430664062 1.2161834239959717 301.4078063964844 0.16814051568508148 0.379283 4.774780750274658 True -1 5404 29.86609649658203 0.5567073822021484 183.7746124267578 0.9502692818641663 268.55767822265625 0.2900129556655884 0.47944322 2.9530863761901855 True -2 8106 29.80767798423767 1.3677000999450684 195.88516235351562 0.7989746928215027 263.6096496582031 0.30204424262046814 0.5046122 1.6634104251861572 True -3 10808 30.187445878982544 0.539024829864502 224.6554718017578 0.7965786457061768 261.7703552246094 0.3088005483150482 0.5239938 1.6132019758224487 True -4 13510 29.818621158599854 0.5434234142303467 176.90115356445312 1.0433547496795654 260.4084777832031 0.3133815824985504 0.5338835 1.557407259941101 True -5 16212 29.82028579711914 0.5519912242889404 208.87103271484375 0.6049432158470154 259.4539794921875 0.31701788306236267 0.5419483 1.520653247833252 True -6 18914 29.82138967514038 0.5486538410186768 225.86776733398438 0.9138673543930054 258.2038879394531 0.3220394551753998 0.5426036 1.4874787330627441 True -7 21616 29.815026998519897 0.5512270927429199 146.68972778320312 0.735879123210907 258.17913818359375 0.3209681808948517 0.5489295 1.3062433004379272 True -8 24318 29.9291729927063 1.487107515335083 221.81668090820312 0.8609118461608887 257.45135498046875 0.32440710067749023 0.55536306 1.2547826766967773 True -9 27020 29.83370018005371 0.5394859313964844 202.26348876953125 0.637200653553009 256.27117919921875 0.32782724499702454 0.56448835 1.1458256244659424 True -10 29722 29.874915838241577 2.7182562351226807 214.54879760742188 0.7050172090530396 255.6985321044922 0.33022069931030273 0.5777026 1.0164669752120972 True -11 32424 29.85860276222229 0.5466632843017578 137.92361450195312 0.80536288022995 254.96363830566406 0.3323942720890045 0.58841395 0.9249840378761292 True -12 35126 29.918231964111328 6.158733606338501 195.7796630859375 0.6769939661026001 254.30357360839844 0.3345143496990204 0.598277 0.8606379628181458 True -13 37828 32.38984656333923 0.5535910129547119 193.0641632080078 0.5459030866622925 253.70590209960938 0.3365432024002075 0.6084826 0.8099856972694397 True -14 40530 30.127901077270508 0.5442342758178711 183.27784729003906 0.6458309888839722 253.0633544921875 0.3389361500740051 0.6226168 0.7425528764724731 True -15 43232 30.07143259048462 0.5473523139953613 174.58596801757812 0.5672851800918579 252.4736328125 0.34149372577667236 0.6322368 0.6780250072479248 True -16 45934 30.332721710205078 0.5462315082550049 220.74513244628906 0.6762697696685791 252.2884521484375 0.3411657214164734 0.64006126 0.6416550874710083 True -17 48636 30.108869552612305 0.5416858196258545 189.27154541015625 0.4381922483444214 252.00299072265625 0.34222638607025146 0.6427613 0.6222219467163086 True -18 51338 30.06876850128174 0.5420143604278564 207.54901123046875 0.5128899812698364 252.42112731933594 0.33963221311569214 0.6418913 0.6102201342582703 False -19 54040 29.9959659576416 11.7132568359375 198.39105224609375 0.4454941153526306 252.3610076904297 0.34019434452056885 0.64072233 0.6102705597877502 False diff --git a/ENCSR648RAX/cherimoya.fold_0.performance.tsv b/ENCSR648RAX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a54abc9917c4080bcabe7dc60c2e274046bd9c42..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -252.00299072265625 0.47276410460472107 0.34222638607025146 0.08621803671121597 0.6427612900733948 0.611952543258667 0.6222219467163086 \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_1.evaluate.json b/ENCSR648RAX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 36cb99b0a31697791f50bc14c5e20e73d1d65006..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF686FPN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_1.fit.json b/ENCSR648RAX/cherimoya.fold_1.fit.json deleted file mode 100644 index a4915449fd6fc4f991d6c11092eba0df77f94a13..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF686FPN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_1.log b/ENCSR648RAX/cherimoya.fold_1.log deleted file mode 100644 index f64dde1e3e245a53690a59d678aebac957272949..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 34.632811069488525 4.231668472290039 173.62208557128906 0.9347141981124878 317.17596435546875 0.1713465005159378 0.41166118 5.308769226074219 True -1 5480 29.96880793571472 3.399257183074951 233.21002197265625 1.1780869960784912 282.9091796875 0.2950044274330139 0.52359545 3.2137393951416016 True -2 8220 30.180704355239868 0.69264817237854 166.80230712890625 1.0162887573242188 278.02862548828125 0.30646148324012756 0.5435352 1.802568793296814 True -3 10960 29.629716396331787 0.9686233997344971 230.8594512939453 0.8662681579589844 275.883056640625 0.3120499551296234 0.56778723 1.3522186279296875 True -4 13700 29.637393712997437 0.6769893169403076 224.0631103515625 1.050749659538269 273.9511413574219 0.31817489862442017 0.58379817 1.0857958793640137 True -5 16440 29.629241228103638 0.8494431972503662 209.88082885742188 0.9467666149139404 272.306640625 0.325162410736084 0.5872386 1.152352213859558 True -6 19180 29.742168426513672 0.6667590141296387 192.53103637695312 0.7827804088592529 271.59613037109375 0.3269396424293518 0.59614104 1.121707797050476 True -7 21920 29.68123745918274 21.34405517578125 221.6366424560547 0.7260386943817139 270.8577880859375 0.32978948950767517 0.6048361 1.0533201694488525 True -8 24660 30.830177068710327 0.6868789196014404 156.1564483642578 0.8123593926429749 270.4588928222656 0.3307643234729767 0.61269444 1.0542396306991577 True -9 27400 29.706580877304077 0.671783447265625 196.68978881835938 0.6879831552505493 269.3825378417969 0.3349033296108246 0.6202038 0.9857351779937744 True -10 30140 29.627765417099 0.6746923923492432 210.18423461914062 0.8418307304382324 268.9812927246094 0.3362073004245758 0.6254397 0.9618712663650513 True -11 32880 29.577974319458008 0.6684520244598389 195.9114990234375 1.0048882961273193 267.4712219238281 0.3413034677505493 0.6352016 0.8541412949562073 True -12 35620 29.649950981140137 1.3281323909759521 205.16696166992188 0.4615972638130188 267.3706970214844 0.34101366996765137 0.6463482 0.8004496097564697 True -13 38360 29.673872470855713 0.6592922210693359 216.989990234375 0.8385130763053894 266.5996398925781 0.3432602882385254 0.6544398 0.74732506275177 True -14 41100 29.65625810623169 0.653245210647583 191.7768096923828 0.8327426910400391 265.8326721191406 0.34574970602989197 0.66485935 0.6890460252761841 True -15 43840 29.8650860786438 0.6762688159942627 224.8706817626953 0.9641347527503967 265.6060485839844 0.3464333713054657 0.6719387 0.6365644335746765 True -16 46580 29.712502002716064 0.6729044914245605 225.30320739746094 0.3802366852760315 265.046142578125 0.3482029139995575 0.6770457 0.6043871641159058 True -17 49320 32.11898159980774 25.665804147720337 197.93972778320312 0.5243733525276184 265.2489929199219 0.3478316366672516 0.67995876 0.5794756412506104 True -18 52060 29.712904691696167 7.5221107006073 213.34027099609375 0.7532981634140015 265.4286804199219 0.34655192494392395 0.6805137 0.5740514397621155 True -19 54800 29.635308742523193 9.664483308792114 170.3970489501953 0.6397430300712585 265.43963623046875 0.3460882902145386 0.67991227 0.5768725872039795 False diff --git a/ENCSR648RAX/cherimoya.fold_1.performance.tsv b/ENCSR648RAX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 64cb1fdbafc986d964b7883bad79e9b763474dc7..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -265.4286804199219 0.46677976846694946 0.34655192494392395 0.08781098574399948 0.6805136799812317 0.6570502519607544 0.5740514397621155 \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_2.evaluate.json b/ENCSR648RAX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8327c469c94e29eaa0518131379535410250c6eb..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF686FPN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_2.fit.json b/ENCSR648RAX/cherimoya.fold_2.fit.json deleted file mode 100644 index eb0da4ab437d77fdf22507e8c1bd8f7f7a2b1f1c..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF686FPN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_2.log b/ENCSR648RAX/cherimoya.fold_2.log deleted file mode 100644 index f73ad6db75bb24d3811aca1e38a4f254b4fcb2bb..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2880 36.178818702697754 3.5751664638519287 252.28994750976562 0.886772632598877 303.3150329589844 0.17445987462997437 0.384128 5.809505939483643 True -1 5760 31.75594186782837 0.5512185096740723 200.2147216796875 1.2721450328826904 268.865966796875 0.2963264286518097 0.49719465 2.66178035736084 True -2 8640 31.808210849761963 0.5441412925720215 211.45074462890625 0.9049456715583801 266.06365966796875 0.301464706659317 0.5231704 1.491015076637268 True -3 11520 33.38183403015137 5.304215669631958 227.81063842773438 0.907474935054779 263.67901611328125 0.3097164034843445 0.5307411 1.3072532415390015 True -4 14400 31.230772495269775 2.1748952865600586 233.34681701660156 1.0952019691467285 262.25152587890625 0.31477880477905273 0.54739136 1.211507797241211 True -5 17280 31.204866886138916 0.8174459934234619 199.1354217529297 0.9534515142440796 261.6240234375 0.3171144723892212 0.5535782 1.1783534288406372 True -6 20160 31.202162742614746 0.5599074363708496 241.38429260253906 0.7642436027526855 261.03948974609375 0.31903788447380066 0.5613729 1.199773907661438 True -7 23040 31.407979726791382 0.5504653453826904 197.62197875976562 0.8675827980041504 260.4218444824219 0.3211349844932556 0.570595 1.1453368663787842 True -8 25920 31.570064306259155 0.5417153835296631 190.4788055419922 0.5877606868743896 259.7163391113281 0.3229788541793823 0.57770425 1.0762226581573486 True -9 28800 31.20451068878174 0.541555643081665 161.72300720214844 0.7483747005462646 258.7582092285156 0.3267160952091217 0.5903457 0.9713468551635742 True -10 31680 31.212543725967407 0.535118818283081 244.64422607421875 0.7890667915344238 257.6291198730469 0.3316383957862854 0.59838706 0.8879425525665283 True -11 34560 31.287053108215332 2.603811025619507 181.43954467773438 0.6887553334236145 257.1802673339844 0.333053320646286 0.6042523 0.8505658507347107 True -12 37440 31.22747778892517 0.5583548545837402 209.40774536132812 0.7718852758407593 256.2207946777344 0.3366237282752991 0.6130853 0.827928364276886 True -13 40320 31.239902019500732 0.5412712097167969 179.17520141601562 0.5733587741851807 255.75775146484375 0.33731159567832947 0.6223195 0.7823880910873413 True -14 43200 31.221120595932007 0.5582170486450195 176.59925842285156 0.6137953996658325 254.7700958251953 0.3412608206272125 0.6333357 0.7009177207946777 True -15 46080 31.343916177749634 0.5479249954223633 215.60086059570312 0.5750924348831177 254.5987548828125 0.3412071466445923 0.6437777 0.6729179620742798 True -16 48960 31.43788480758667 1.141965627670288 194.07217407226562 0.44057348370552063 254.0763397216797 0.343392014503479 0.65135753 0.6290414929389954 True -17 51840 31.363796949386597 0.542382001876831 156.97048950195312 0.6161950826644897 254.35885620117188 0.34118199348449707 0.653601 0.6119654178619385 True -18 54720 31.422573804855347 0.562342643737793 200.23883056640625 0.6404802799224854 253.85745239257812 0.3441781997680664 0.6552464 0.6004272103309631 True -19 57600 31.490198850631714 0.5540690422058105 157.2921905517578 0.5124267935752869 254.02691650390625 0.3434058129787445 0.6556557 0.6009961366653442 True diff --git a/ENCSR648RAX/cherimoya.fold_2.performance.tsv b/ENCSR648RAX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 80836d951a5e5075e18e9cfaa8cdb0bead6f4c8b..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -254.02691650390625 0.47206372022628784 0.3434057831764221 0.08233410120010376 0.6556556820869446 0.6245485544204712 0.6009961366653442 \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_3.evaluate.json b/ENCSR648RAX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b4c85036e5305784cda1f899518c6638d94a595b..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF686FPN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_3.fit.json b/ENCSR648RAX/cherimoya.fold_3.fit.json deleted file mode 100644 index 2ad229a51a47ecc0f7a91986b461e25a76393153..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF686FPN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_3.log b/ENCSR648RAX/cherimoya.fold_3.log deleted file mode 100644 index e3e02944ef234ec1670cec19e1aca352a5f53620..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2790 38.04090189933777 10.601831674575806 231.31182861328125 1.164404273033142 306.96917724609375 0.16911529004573822 0.4003687 5.435179710388184 True -1 5580 30.767536878585815 0.9587817192077637 230.64251708984375 0.8731033802032471 274.9980163574219 0.29242727160453796 0.48631057 2.6721017360687256 True -2 8370 30.804485082626343 1.2148828506469727 204.55882263183594 1.1153204441070557 270.3686828613281 0.3028205931186676 0.51216584 1.8843624591827393 True -3 11160 30.816720962524414 0.5770058631896973 216.43072509765625 0.6675761342048645 268.1031799316406 0.30887725949287415 0.54507995 1.4074584245681763 True -4 13950 30.407745361328125 0.5761020183563232 151.1015625 0.7854933738708496 266.33624267578125 0.31565797328948975 0.56243515 1.15547513961792 True -5 16740 30.123456954956055 0.6079461574554443 209.11366271972656 0.8247403502464294 264.9715881347656 0.32093533873558044 0.5707518 1.1244056224822998 True -6 19530 30.164608478546143 0.5730071067810059 212.87417602539062 0.8805074691772461 264.5780944824219 0.32178688049316406 0.578015 1.1020041704177856 True -7 22320 30.140908241271973 0.5745091438293457 220.85894775390625 0.7065021991729736 263.82305908203125 0.32479387521743774 0.5827067 1.0832315683364868 True -8 25110 30.146360397338867 0.5738706588745117 200.04916381835938 0.7999147772789001 263.3250427246094 0.3257769048213959 0.59331197 1.0316863059997559 True -9 27900 31.149672985076904 29.197219848632812 184.33651733398438 0.9648086428642273 262.2594909667969 0.33038780093193054 0.60143566 0.911753237247467 True -10 30690 30.245417833328247 0.5905165672302246 193.96914672851562 0.6257528066635132 261.896728515625 0.33072447776794434 0.6057901 0.9090214371681213 True -11 33480 30.168678522109985 1.6037061214447021 159.59075927734375 0.6635875701904297 261.25762939453125 0.3332197368144989 0.61627704 0.8373623490333557 True -12 36270 30.210689783096313 0.5751841068267822 202.53924560546875 0.7658047676086426 260.3616943359375 0.3368019461631775 0.62397105 0.8030912280082703 True -13 39060 30.140319108963013 0.571429967880249 180.16644287109375 0.6667150855064392 260.1244201660156 0.3361419439315796 0.6312381 0.7581703066825867 True -14 41850 30.866135120391846 0.5733885765075684 218.14578247070312 0.6374276876449585 259.5345458984375 0.3380317687988281 0.64155126 0.6948173642158508 True -15 44640 30.507236003875732 41.04939413070679 175.42506408691406 0.6892778873443604 259.087890625 0.3395706117153168 0.6544779 0.6515148878097534 True -16 47430 30.16562056541443 25.944234609603882 242.40591430664062 0.34987935423851013 258.57696533203125 0.3417901396751404 0.6611765 0.6201525926589966 True -17 50220 31.28507113456726 0.576512336730957 183.1005096435547 0.5134116411209106 258.1539306640625 0.3432503044605255 0.6644734 0.6022899150848389 True -18 53010 30.28413224220276 0.5654420852661133 177.76625061035156 0.424514502286911 258.43341064453125 0.34143808484077454 0.6622743 0.5947446823120117 False -19 55800 30.16032314300537 1.289720058441162 177.63214111328125 0.43599948287010193 258.6116638183594 0.3406592905521393 0.66085106 0.593597948551178 False diff --git a/ENCSR648RAX/cherimoya.fold_3.performance.tsv b/ENCSR648RAX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f069bde9ae28c759072cd46b1db78e77a8e8df1a..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -258.1539306640625 0.4703860580921173 0.3432502746582031 0.0829099714756012 0.6644734144210815 0.6402319073677063 0.6022899150848389 \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_4.evaluate.json b/ENCSR648RAX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bce8b79c23eb5cd16d9f899d9577de4269045f2c..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF686FPN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_4.fit.json b/ENCSR648RAX/cherimoya.fold_4.fit.json deleted file mode 100644 index 3ab7beac94bb559fcc989f2d9101c17e49c85f33..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF686FPN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR648RAX/cherimoya.fold_4.log b/ENCSR648RAX/cherimoya.fold_4.log deleted file mode 100644 index a20d7c74396f34a004c4919d84e7f84f62213f21..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2827 35.68123531341553 3.6224653720855713 192.88015747070312 0.8526327610015869 294.76123046875 0.16897916793823242 0.39550787 4.737353324890137 True -1 5654 32.96193242073059 0.5643866062164307 211.05169677734375 0.9687162041664124 263.13299560546875 0.2870975136756897 0.4964219 2.7482874393463135 True -2 8481 31.246668100357056 0.5650064945220947 208.0907745361328 0.8069990873336792 258.76995849609375 0.3000255227088928 0.5120738 2.010485887527466 True -3 11308 31.27015781402588 0.5406026840209961 223.055908203125 0.9808093309402466 256.6562805175781 0.3057766556739807 0.53386486 1.6714799404144287 True -4 14135 31.206663846969604 0.8255884647369385 248.10386657714844 0.6923866271972656 255.4634246826172 0.30977556109428406 0.5452493 1.5461976528167725 True -5 16962 31.177861213684082 0.5184848308563232 215.0983428955078 0.86974036693573 254.76596069335938 0.3138102889060974 0.5475588 1.5193389654159546 True -6 19789 30.708380699157715 0.5225708484649658 186.45501708984375 0.7760240435600281 254.281982421875 0.31553661823272705 0.5533177 1.4451887607574463 True -7 22616 30.6627995967865 0.515172004699707 201.51251220703125 1.0294694900512695 253.3689422607422 0.31966352462768555 0.5637049 1.2809512615203857 True -8 25443 30.526877880096436 0.53285813331604 213.4619140625 0.8541902303695679 252.666259765625 0.3226344585418701 0.56939304 1.1574933528900146 True -9 28270 30.560381650924683 0.5215809345245361 204.876220703125 0.7925904989242554 252.04803466796875 0.32379069924354553 0.5746047 1.0424636602401733 True -10 31097 30.88680648803711 0.5250580310821533 155.2111053466797 0.7707619667053223 251.653564453125 0.3255099952220917 0.5833784 0.9942089915275574 True -11 33924 30.609843730926514 0.5240993499755859 262.4753723144531 0.7469664216041565 250.6084747314453 0.3294050693511963 0.594055 0.8906400799751282 True -12 36751 30.59769344329834 0.5241250991821289 189.4094696044922 0.9248110055923462 249.6574249267578 0.33222511410713196 0.60978407 0.7844256162643433 True -13 39578 30.509064435958862 1.4003825187683105 205.95233154296875 0.5728992223739624 249.26930236816406 0.3327428996562958 0.62369424 0.7108877301216125 True -14 42405 30.56829285621643 0.5234596729278564 211.99111938476562 0.49357953667640686 248.7369842529297 0.3350277245044708 0.6352869 0.6663050651550293 True -15 45232 30.728066444396973 0.524550199508667 162.95184326171875 0.5987995862960815 248.41592407226562 0.33601999282836914 0.6485818 0.6346933841705322 True -16 48059 30.59892511367798 0.5169241428375244 166.85240173339844 0.5755705833435059 247.8748779296875 0.33783572912216187 0.6547435 0.5950475335121155 True -17 50886 30.61644458770752 0.5175154209136963 185.31076049804688 0.41784557700157166 247.85853576660156 0.3369769752025604 0.65910757 0.577987790107727 True -18 53713 30.61591076850891 1.6922719478607178 192.37664794921875 0.4380190968513489 247.85948181152344 0.33830738067626953 0.65916663 0.5740756392478943 True -19 56540 30.663056135177612 0.5268950462341309 178.90625 0.6275784969329834 247.8382568359375 0.33803117275238037 0.65962934 0.5788393616676331 True diff --git a/ENCSR648RAX/cherimoya.fold_4.performance.tsv b/ENCSR648RAX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 216997944250498301bef1e7eaa2835a0505c109..0000000000000000000000000000000000000000 --- a/ENCSR648RAX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -247.8382568359375 0.476004421710968 0.33803117275238037 0.08370981365442276 0.6596293449401855 0.6270054578781128 0.5788393616676331 \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_0.evaluate.json b/ENCSR649XRC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2dffe9aecce7c4cb66430803bc799d596e6d395c..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430ZZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_0.fit.json b/ENCSR649XRC/cherimoya.fold_0.fit.json deleted file mode 100644 index d01dd92ba71d814b01562793b782f89ff840f988..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF430ZZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_0.log b/ENCSR649XRC/cherimoya.fold_0.log deleted file mode 100644 index edb8d5cd6c39a41c24ac5051d32ebf1c232548ab..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2350 29.78504204750061 3.3883156776428223 125.34986877441406 0.6789788603782654 174.19119262695312 0.09451694786548615 0.68268657 3.336925506591797 True -1 4700 26.19731330871582 0.50498366355896 162.0029296875 0.9406115412712097 162.61444091796875 0.13684244453907013 0.7514804 1.7291346788406372 True -2 7050 26.134682178497314 0.4787015914916992 112.19715881347656 0.5393877029418945 158.61521911621094 0.14340634644031525 0.757299 0.9075345993041992 True -3 9400 26.135130643844604 2.766035795211792 126.39279174804688 0.37356334924697876 156.78135681152344 0.14798246324062347 0.7781561 0.7319774627685547 True -4 11750 26.11405873298645 0.48542094230651855 135.698974609375 0.6089112758636475 155.43568420410156 0.15227927267551422 0.7939929 0.573427140712738 True -5 14100 26.10621976852417 0.4873485565185547 99.22958374023438 0.2361818552017212 154.7822723388672 0.15387742221355438 0.8081557 0.4776732325553894 True -6 16450 26.15764355659485 0.480665922164917 111.77462768554688 0.5741937756538391 154.08676147460938 0.1565113067626953 0.81745285 0.43123480677604675 True -7 18800 26.15663456916809 0.4868471622467041 125.23782348632812 0.6978485584259033 153.89248657226562 0.15636438131332397 0.8266516 0.4027876555919647 True -8 21150 26.120535373687744 0.48960208892822266 174.51455688476562 0.5981545448303223 153.3157501220703 0.1590053290128708 0.8337462 0.3875686824321747 True -9 23500 26.141918659210205 0.4913468360900879 137.77517700195312 0.5601080656051636 153.02342224121094 0.16012805700302124 0.8381742 0.37949538230895996 True -10 25850 26.04836940765381 0.4780864715576172 130.20870971679688 0.6248689293861389 152.54965209960938 0.16101878881454468 0.8474272 0.34418365359306335 True -11 28200 25.692038774490356 0.4904017448425293 91.96697998046875 0.6519967317581177 152.426513671875 0.16157521307468414 0.8512373 0.32851460576057434 True -12 30550 25.710402250289917 0.4882659912109375 115.36210632324219 0.2750728726387024 152.1120147705078 0.16269880533218384 0.8536651 0.3202267289161682 True -13 32900 25.759755849838257 0.49062252044677734 111.4822006225586 0.367791086435318 151.79803466796875 0.16384157538414001 0.8587394 0.3083750605583191 True -14 35250 25.743313550949097 0.4755442142486572 157.80224609375 0.4401826858520508 151.5306854248047 0.16497914493083954 0.860269 0.3002079725265503 True -15 37600 25.697233200073242 0.47458696365356445 102.54762268066406 0.3184739649295807 151.34921264648438 0.16550317406654358 0.86334157 0.29351523518562317 True -16 39950 25.631633043289185 0.4772963523864746 122.65287780761719 0.2619941830635071 151.38641357421875 0.1650315225124359 0.8637638 0.29191672801971436 True -17 42300 25.679588079452515 0.4752037525177002 127.9485855102539 0.3904632031917572 151.473876953125 0.16416482627391815 0.86396736 0.29199227690696716 True -18 44650 25.65248131752014 0.47471094131469727 173.68289184570312 0.23553702235221863 151.26792907714844 0.16590429842472076 0.86406 0.29450657963752747 True -19 47000 25.601807355880737 0.4792768955230713 126.86991882324219 0.398062527179718 151.49168395996094 0.1647145301103592 0.8621251 0.2981337606906891 False diff --git a/ENCSR649XRC/cherimoya.fold_0.performance.tsv b/ENCSR649XRC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c82d53855a116ccd8912f0e990ebeca7a35e2b46..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -151.26792907714844 0.5830125212669373 0.16590429842472076 0.03919600695371628 0.8640599846839905 0.7517369389533997 0.29450657963752747 \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_1.evaluate.json b/ENCSR649XRC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2af35ba0fed8a90be47997aaabb8c99fb7c271c9..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430ZZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_1.fit.json b/ENCSR649XRC/cherimoya.fold_1.fit.json deleted file mode 100644 index 357b0bd345610e54bf729bd16b1af6bc2e1d33d3..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF430ZZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_1.log b/ENCSR649XRC/cherimoya.fold_1.log deleted file mode 100644 index cb6b0e09022cda0569ec12dc90183dc028565d22..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2339 30.2563738822937 3.437596082687378 120.7616958618164 0.7211534976959229 225.39466857910156 0.11461389064788818 0.657867 4.6424336433410645 True -1 4678 25.78019881248474 0.6021103858947754 145.67098999023438 0.5199114084243774 208.25674438476562 0.17010542750358582 0.74160457 2.109802484512329 True -2 7017 25.69510531425476 0.5847516059875488 138.0126953125 0.5160822868347168 205.12124633789062 0.1750665009021759 0.74855113 1.406125783920288 True -3 9356 25.644216537475586 0.5807266235351562 129.37625122070312 0.5125036239624023 200.71286010742188 0.1848868429660797 0.7691105 1.041333794593811 True -4 11695 25.686097383499146 1.2723987102508545 133.21728515625 0.549042284488678 198.99484252929688 0.1877659559249878 0.785759 0.9123117923736572 True -5 14034 25.64818549156189 0.6082768440246582 155.6681365966797 0.4681892395019531 197.61752319335938 0.19161216914653778 0.8022634 0.8142621517181396 True -6 16373 25.657039403915405 0.5994551181793213 150.97906494140625 0.4819318354129791 196.3558807373047 0.19515183568000793 0.81616735 0.7024433612823486 True -7 18712 25.68966817855835 0.6007065773010254 110.4560546875 0.4232436418533325 196.0518035888672 0.19625376164913177 0.81340736 0.7259196639060974 False -8 21051 25.675628900527954 0.5927512645721436 178.5734405517578 0.6164196729660034 195.26708984375 0.19826073944568634 0.826451 0.6338158249855042 True -9 23390 25.711796760559082 3.7460989952087402 97.86626434326172 0.3473885655403137 194.7615509033203 0.20025040209293365 0.8335556 0.5956342220306396 True -10 25729 25.67039942741394 0.6008415222167969 162.85684204101562 0.5337804555892944 194.25619506835938 0.2015203982591629 0.844521 0.5278694033622742 True -11 28068 25.684767246246338 0.5935566425323486 133.77609252929688 0.45179039239883423 193.83084106445312 0.20208172500133514 0.851052 0.4745836853981018 True -12 30407 25.69076180458069 0.5922071933746338 153.26719665527344 0.49785587191581726 193.1223907470703 0.20460359752178192 0.8581879 0.45509767532348633 True -13 32746 25.759449243545532 0.6154358386993408 124.92704010009766 0.43480491638183594 192.79379272460938 0.20487599074840546 0.86434627 0.421362966299057 True -14 35085 25.615883588790894 1.535430908203125 102.53887939453125 0.43991556763648987 192.61619567871094 0.20509833097457886 0.8677952 0.39784669876098633 True -15 37424 25.23749041557312 0.5975275039672852 105.23694610595703 0.4242854118347168 192.361083984375 0.20595742762088776 0.8705091 0.3854706585407257 True -16 39763 25.281128644943237 0.6069839000701904 93.21112060546875 0.4268479347229004 192.31541442871094 0.20587942004203796 0.8704498 0.37689223885536194 False -17 42102 25.165701150894165 0.5887608528137207 125.4584732055664 0.34571942687034607 192.42666625976562 0.20530645549297333 0.870951 0.3763268291950226 True -18 44441 25.317364931106567 0.594721794128418 151.70106506347656 0.3068698048591614 192.31341552734375 0.2059481143951416 0.8677638 0.37833371758461 False -19 46780 25.199632167816162 0.5871503353118896 98.45494079589844 0.31404757499694824 192.3801727294922 0.20563775300979614 0.86663365 0.3808382749557495 False diff --git a/ENCSR649XRC/cherimoya.fold_1.performance.tsv b/ENCSR649XRC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3e5128c6c4116692ec23aa06d71910d5292ec49a..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -192.42666625976562 0.5537890195846558 0.20530644059181213 0.04771055653691292 0.8709509968757629 0.8099752068519592 0.3763268291950226 \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_2.evaluate.json b/ENCSR649XRC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e462e536a6eb5e0eca1a018cc8c37f562227b2f9..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430ZZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_2.fit.json b/ENCSR649XRC/cherimoya.fold_2.fit.json deleted file mode 100644 index e1ded29600a755b78f73d7189649d0caae0e3ead..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF430ZZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_2.log b/ENCSR649XRC/cherimoya.fold_2.log deleted file mode 100644 index fef70aa0ce767295cbbbf7d1ca7a28b253da4060..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2485 31.287543296813965 3.386841297149658 135.30393981933594 0.5056610107421875 186.03294372558594 0.1048145592212677 0.6630319 3.1516735553741455 True -1 4970 27.574723720550537 0.4791851043701172 129.02102661132812 0.5123956203460693 171.99082946777344 0.1512593924999237 0.75647026 1.5410107374191284 True -2 7455 27.541165828704834 0.47495412826538086 99.98294067382812 0.7175444960594177 169.43748474121094 0.15586519241333008 0.7556848 0.9130659699440002 False -3 9940 27.513022899627686 0.45630741119384766 122.26527404785156 0.6327506303787231 166.90797424316406 0.1625547856092453 0.7624199 0.7502815127372742 True -4 12425 27.537774562835693 0.4623579978942871 91.00106811523438 0.48686593770980835 165.1996307373047 0.1663103699684143 0.78563195 0.6186037659645081 True -5 14910 27.486489057540894 0.4613034725189209 180.8477783203125 0.5577996969223022 164.44204711914062 0.16859278082847595 0.7945928 0.5817285776138306 True -6 17395 27.475929498672485 0.46268296241760254 149.23716735839844 0.632123589515686 163.60133361816406 0.17144906520843506 0.8085152 0.514292299747467 True -7 19880 27.484414100646973 0.46208834648132324 118.14717864990234 0.4830167293548584 163.36241149902344 0.1715196669101715 0.81711817 0.49771496653556824 True -8 22365 27.4816312789917 0.4618985652923584 132.12660217285156 0.6787564754486084 162.6859893798828 0.17381097376346588 0.824938 0.4467565417289734 True -9 24850 27.507522583007812 0.46525120735168457 124.64692687988281 0.5112909078598022 162.26255798339844 0.17485938966274261 0.8329348 0.41810545325279236 True -10 27335 27.546112775802612 0.462937593460083 140.13632202148438 0.5231142044067383 161.93209838867188 0.17586369812488556 0.8389334 0.39977461099624634 True -11 29820 27.55029058456421 14.415523767471313 132.7484588623047 0.5740524530410767 161.3424072265625 0.1780777871608734 0.84516126 0.3711879849433899 True -12 32305 27.6230309009552 0.49434995651245117 118.61624145507812 0.3457423448562622 161.06846618652344 0.17877495288848877 0.8496481 0.35004904866218567 True -13 34790 27.69853687286377 0.4718928337097168 123.17677307128906 0.3610602021217346 160.73793029785156 0.17954924702644348 0.8520491 0.34312230348587036 True -14 37275 27.552137851715088 0.4770939350128174 123.74382781982422 0.36231115460395813 160.659423828125 0.17976753413677216 0.8545896 0.33537930250167847 True -15 39760 27.419117212295532 0.4679384231567383 138.15562438964844 0.43150222301483154 160.0959014892578 0.1821441948413849 0.85658205 0.3300066590309143 True -16 42245 26.94502329826355 0.4690585136413574 142.39816284179688 0.32585638761520386 160.4799346923828 0.1805681586265564 0.85910046 0.32619577646255493 True -17 44730 26.98175048828125 0.4661118984222412 109.77339935302734 0.19578522443771362 160.31317138671875 0.1818159520626068 0.8576377 0.32897457480430603 False -18 47215 27.015716314315796 0.46169257164001465 136.07540893554688 0.23878657817840576 160.51856994628906 0.18083308637142181 0.85715324 0.3337995707988739 False -19 49700 27.04286003112793 1.905102014541626 146.33428955078125 0.27965468168258667 160.51644897460938 0.1807532161474228 0.8561884 0.3372255563735962 False diff --git a/ENCSR649XRC/cherimoya.fold_2.performance.tsv b/ENCSR649XRC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 00b4f0a387ee2fd7529f6f68e2169f6e2761d677..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -160.4799346923828 0.5734039545059204 0.1805681437253952 0.046093232929706573 0.8591004610061646 0.7691552639007568 0.32619577646255493 \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_3.evaluate.json b/ENCSR649XRC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6bf4c5df198948d288c369a7778e1f46d4132841..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430ZZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_3.fit.json b/ENCSR649XRC/cherimoya.fold_3.fit.json deleted file mode 100644 index 5df5e28ec96251455a30acff58965f80b0474d4f..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF430ZZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_3.log b/ENCSR649XRC/cherimoya.fold_3.log deleted file mode 100644 index 1ee902a0d9b4481482243f46ae7c02539b9ef663..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2386 30.064046382904053 4.248706817626953 140.57814025878906 0.4947018027305603 187.82501220703125 0.10483437031507492 0.6653788 3.678957939147949 True -1 4772 26.33798909187317 0.5017571449279785 137.9163360595703 0.2931438386440277 176.48585510253906 0.14485237002372742 0.7193342 2.1500043869018555 True -2 7158 26.265372037887573 0.47202205657958984 120.68497467041016 0.6893674731254578 171.69129943847656 0.15590405464172363 0.748664 1.0474799871444702 True -3 9544 26.19429326057434 0.46604442596435547 137.0511474609375 0.5535104274749756 170.30886840820312 0.16059806942939758 0.7636135 0.9019173383712769 True -4 11930 26.24781560897827 0.4765360355377197 136.17672729492188 0.4786764979362488 170.0221405029297 0.1607649028301239 0.7681058 0.9130284190177917 True -5 14316 26.212671756744385 0.4801056385040283 153.84500122070312 0.7092083692550659 168.8411407470703 0.16476987302303314 0.78058416 0.8379451036453247 True -6 16702 26.225709676742554 0.47643351554870605 107.50216674804688 0.5068387985229492 168.30462646484375 0.16618523001670837 0.79092455 0.6948788166046143 True -7 19088 26.20027756690979 0.4710662364959717 123.67003631591797 0.45061051845550537 167.38143920898438 0.1700514405965805 0.79814535 0.6556335687637329 True -8 21474 26.22769784927368 0.47769713401794434 123.2491455078125 0.3746933341026306 167.09410095214844 0.17016030848026276 0.8134439 0.5961914658546448 True -9 23860 26.237765312194824 0.47355198860168457 140.11642456054688 0.3563213348388672 166.83583068847656 0.17108924686908722 0.81892914 0.5702025890350342 True -10 26246 26.27143907546997 0.48268556594848633 137.09854125976562 0.6264944672584534 166.401123046875 0.17307111620903015 0.82654005 0.5307444930076599 True -11 28632 26.229094982147217 3.1896002292633057 119.6523666381836 0.4069921374320984 165.8915557861328 0.17430277168750763 0.834497 0.47717779874801636 True -12 31018 26.264993906021118 0.4828479290008545 116.53706359863281 0.3306548297405243 165.4684295654297 0.1757817268371582 0.84033304 0.43911534547805786 True -13 33404 26.287648916244507 0.4728212356567383 144.3370361328125 0.5585691928863525 165.15939331054688 0.17662997543811798 0.84635866 0.41985443234443665 True -14 35790 26.38416814804077 1.276421070098877 162.97071838378906 0.38227832317352295 164.7530975341797 0.1782100945711136 0.8490007 0.3998337388038635 True -15 38176 26.327959775924683 0.4849832057952881 130.7038116455078 0.47246241569519043 164.68447875976562 0.17789006233215332 0.8532517 0.37588781118392944 True -16 40562 26.306244611740112 0.4703514575958252 129.21578979492188 0.33559519052505493 164.6942138671875 0.17750141024589539 0.85924506 0.3576377332210541 True -17 42948 26.305591583251953 1.807821273803711 93.46186065673828 0.44902580976486206 164.52523803710938 0.17824093997478485 0.8593459 0.3541896343231201 True -18 45334 26.164625644683838 0.4717378616333008 136.1337127685547 0.2421121895313263 164.76547241210938 0.17709645628929138 0.85819894 0.35252347588539124 False -19 47720 25.848684787750244 0.46513795852661133 131.8521728515625 0.26407527923583984 164.71954345703125 0.17716263234615326 0.85807395 0.35330742597579956 False diff --git a/ENCSR649XRC/cherimoya.fold_3.performance.tsv b/ENCSR649XRC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 67befe11e89fb2624857dfca827bf3b046473e2a..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -164.52523803710938 0.5742567181587219 0.17824093997478485 0.04672091826796532 0.8593459129333496 0.7767952084541321 0.3541896343231201 \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_4.evaluate.json b/ENCSR649XRC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 37483bf1f9f5c4f3f2ae8c93ca498d2190e9f06d..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF430ZZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_4.fit.json b/ENCSR649XRC/cherimoya.fold_4.fit.json deleted file mode 100644 index 5d8bdc844087250c6f9bcb8ba3c719664ce05889..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF430ZZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_4.log b/ENCSR649XRC/cherimoya.fold_4.log deleted file mode 100644 index 5f0aaf3a9e7a43750a841f96b89e24aa251e42ad..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2387 29.940213441848755 5.5650153160095215 181.36114501953125 0.700809121131897 164.74449157714844 0.09559563547372818 0.6573331 2.953233003616333 True -1 4774 26.26516079902649 0.5064048767089844 136.36343383789062 0.5175105333328247 154.99497985839844 0.13280870020389557 0.7308238 1.6067012548446655 True -2 7161 26.16196632385254 0.49782228469848633 157.41537475585938 0.6723747253417969 151.54681396484375 0.14058972895145416 0.75467104 0.7749248743057251 True -3 9548 26.14341425895691 0.48754215240478516 152.72286987304688 0.4769841134548187 149.81092834472656 0.1442548930644989 0.7796923 0.5909601449966431 True -4 11935 26.30688452720642 0.486339807510376 129.15505981445312 0.6727209091186523 148.76654052734375 0.14858005940914154 0.7873324 0.5788002610206604 True -5 14322 26.195533752441406 0.4873535633087158 113.7659912109375 0.5696514844894409 148.17771911621094 0.14965473115444183 0.7939416 0.5756526589393616 True -6 16709 26.135668516159058 0.48577094078063965 129.2227783203125 0.5908811092376709 147.7509307861328 0.1512593924999237 0.7988957 0.5557966828346252 True -7 19096 26.36461877822876 0.4884073734283447 130.81109619140625 0.8423103094100952 147.3189239501953 0.152295783162117 0.81169116 0.5000655055046082 True -8 21483 26.767923831939697 15.74201250076294 130.90931701660156 0.41192594170570374 146.96163940429688 0.1536034494638443 0.81675786 0.4703333079814911 True -9 23870 26.305498123168945 0.4878876209259033 122.03475189208984 0.34229856729507446 146.4906005859375 0.15544606745243073 0.8277825 0.4118126332759857 True -10 26257 26.305113315582275 0.4881408214569092 125.56343078613281 0.39076048135757446 146.4559783935547 0.15461860597133636 0.8331112 0.38503679633140564 True -11 28644 26.232680320739746 0.478198766708374 120.27055358886719 0.36758291721343994 146.10549926757812 0.15625905990600586 0.84125465 0.3529561758041382 True -12 31031 26.198261499404907 0.47701382637023926 127.54765319824219 0.3794083595275879 145.8188018798828 0.15742181241512299 0.844656 0.33564889430999756 True -13 33418 26.235968112945557 0.4910562038421631 140.47833251953125 0.3804509937763214 145.53359985351562 0.15826909244060516 0.8490114 0.3152577579021454 True -14 35805 26.1925208568573 0.48537588119506836 111.99183654785156 0.40345537662506104 145.4419403076172 0.15842367708683014 0.85396415 0.30393949151039124 True -15 38192 26.19692349433899 0.49022650718688965 124.19921112060547 0.36743152141571045 145.33477783203125 0.15829771757125854 0.8551753 0.2971245050430298 True -16 40579 26.18877601623535 0.5989594459533691 96.9539794921875 0.38653820753097534 145.3219451904297 0.15875183045864105 0.857149 0.29172083735466003 True -17 42966 26.18680715560913 1.3460841178894043 78.4998550415039 0.28104662895202637 145.4428253173828 0.15824027359485626 0.85629267 0.2930898368358612 False -18 45353 26.293727159500122 0.4877140522003174 105.10597229003906 0.3296416997909546 145.41407775878906 0.15830543637275696 0.85503423 0.29318955540657043 False -19 47740 26.149201154708862 0.47452545166015625 133.494384765625 0.2412956953048706 145.3759765625 0.15860997140407562 0.85635 0.29416170716285706 False diff --git a/ENCSR649XRC/cherimoya.fold_4.performance.tsv b/ENCSR649XRC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fe74a25ca8a99c8633cf2bb947110a7059a2d6d6..0000000000000000000000000000000000000000 --- a/ENCSR649XRC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -145.3219451904297 0.5871028304100037 0.15875183045864105 0.0372958667576313 0.8571490049362183 0.7393954396247864 0.29172083735466003 \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_0.evaluate.json b/ENCSR650FLQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 103f906ca8c1c2768e724d5ab0b6a7d0ff0ee038..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF095BJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_0.fit.json b/ENCSR650FLQ/cherimoya.fold_0.fit.json deleted file mode 100644 index f6f8e5b37640ae1c6501036b99b0cb5816eac5f3..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF095BJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_0.log b/ENCSR650FLQ/cherimoya.fold_0.log deleted file mode 100644 index 9a95219ba7db6b44344a638c0339a97823c6457b..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2706 34.14430212974548 5.565260410308838 564.4119873046875 0.37896203994750977 678.8236083984375 0.3016184866428375 0.69248116 4.888695240020752 True -1 5412 29.7512845993042 0.6352705955505371 509.162353515625 0.5345056056976318 600.2764892578125 0.39248159527778625 0.7520144 1.759637713432312 True -2 8118 29.983629941940308 2.3680906295776367 465.0452575683594 0.30802953243255615 585.7175903320312 0.4070827066898346 0.76359797 0.9093154668807983 True -3 10824 29.750906944274902 0.5733475685119629 581.9739990234375 0.4173075556755066 579.5146484375 0.41355594992637634 0.7727005 0.9003065228462219 True -4 13530 29.718137979507446 19.6659836769104 504.02398681640625 0.3995267450809479 575.8856201171875 0.41740456223487854 0.78132623 0.6272715926170349 True -5 16236 29.967430114746094 21.598325729370117 540.2406005859375 0.3673827350139618 573.6602783203125 0.42053231596946716 0.7840086 0.5619597434997559 True -6 18942 30.449100732803345 0.5704398155212402 483.54217529296875 0.313266396522522 570.3529663085938 0.4252086579799652 0.7891307 0.5054884552955627 True -7 21648 29.748749256134033 0.5747885704040527 465.5804443359375 0.2928171157836914 567.8333740234375 0.4280383586883545 0.7950935 0.47414812445640564 True -8 24354 29.72862219810486 0.563774824142456 647.8589477539062 0.24155426025390625 565.9384155273438 0.4309176802635193 0.8017711 0.48290708661079407 True -9 27060 29.67179012298584 0.5699868202209473 521.681640625 0.29664283990859985 565.0104370117188 0.4305202066898346 0.8057693 0.46310779452323914 True -10 29766 29.697670221328735 21.530508995056152 563.6739501953125 0.3397752344608307 563.405029296875 0.43362802267074585 0.8082974 0.4434807598590851 True -11 32472 30.806443214416504 11.126659154891968 503.9492492675781 0.3506373167037964 561.4636840820312 0.4352087676525116 0.81265277 0.3834623694419861 True -12 35178 29.775645971298218 0.5855042934417725 467.57196044921875 0.3981660306453705 558.7792358398438 0.439370334148407 0.82116354 0.3492436707019806 True -13 37884 29.777490377426147 0.5630767345428467 531.9326171875 0.27007901668548584 557.4832153320312 0.4412349760532379 0.82485473 0.31678974628448486 True -14 40590 29.675882816314697 0.5715053081512451 478.05072021484375 0.2645607590675354 556.5709838867188 0.4417261481285095 0.83243537 0.2744119465351105 True -15 43296 29.702576160430908 0.5653860569000244 574.2242431640625 0.22708731889724731 555.45751953125 0.4427250027656555 0.837381 0.2536980211734772 True -16 46002 29.7113618850708 12.479036331176758 436.06793212890625 0.24262362718582153 554.66259765625 0.443637490272522 0.83848953 0.23604780435562134 True -17 48708 29.720196962356567 0.5636937618255615 459.4468994140625 0.19725078344345093 554.1626586914062 0.44472745060920715 0.8415664 0.2271462231874466 True -18 51414 29.831130504608154 0.5705916881561279 485.36163330078125 0.1897348165512085 554.0757446289062 0.44518783688545227 0.84005034 0.22378510236740112 False -19 54120 29.70975637435913 0.5704762935638428 436.0970458984375 0.2978270947933197 554.4482421875 0.4443325102329254 0.841044 0.22405458986759186 False diff --git a/ENCSR650FLQ/cherimoya.fold_0.performance.tsv b/ENCSR650FLQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8f2410d3c265614e86585933b4fc9a5a4e120bfc..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -554.1626586914062 0.36413127183914185 0.44472748041152954 0.17192593216896057 0.8415663838386536 0.8188884854316711 0.2271462231874466 \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_1.evaluate.json b/ENCSR650FLQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 20be85d3fe638029a2dda5d1bbefb5ec52c718b0..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF095BJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_1.fit.json b/ENCSR650FLQ/cherimoya.fold_1.fit.json deleted file mode 100644 index bf298324f7a518d0596c0104b8cddfd080c8099a..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF095BJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_1.log b/ENCSR650FLQ/cherimoya.fold_1.log deleted file mode 100644 index 94797ddb184150732ad17f189981a99f635d8c32..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2707 34.98331308364868 26.52230668067932 576.8160400390625 0.2942827343940735 794.4541625976562 0.3004470765590668 0.7039108 5.370567321777344 True -1 5414 30.301517009735107 0.7360024452209473 478.5351867675781 0.28320616483688354 696.1852416992188 0.40868523716926575 0.7665048 1.6079347133636475 True -2 8121 29.86750316619873 0.6861922740936279 471.8843994140625 0.3634084463119507 677.9962158203125 0.4245931804180145 0.7739147 0.9121859073638916 True -3 10828 30.62306547164917 16.824267148971558 551.0562133789062 0.5052809119224548 672.4325561523438 0.4286481440067291 0.7831051 0.7982263565063477 True -4 13535 29.85196089744568 17.187119007110596 506.975830078125 0.5110620260238647 667.7884521484375 0.43313729763031006 0.7905721 0.6855069994926453 True -5 16242 30.0506591796875 0.6994385719299316 434.82257080078125 0.33821195363998413 663.9552001953125 0.43843334913253784 0.7930282 0.7149349451065063 True -6 18949 29.809178113937378 0.685809850692749 443.7586364746094 0.30767202377319336 662.6123046875 0.43971994519233704 0.798248 0.685849130153656 True -7 21656 29.880980491638184 1.7555615901947021 532.0733642578125 0.4714224338531494 659.4581298828125 0.44339466094970703 0.8032858 0.6631122827529907 True -8 24363 29.812273263931274 0.6888070106506348 478.48382568359375 0.3220660984516144 655.8651123046875 0.4477585554122925 0.8042201 0.597766101360321 True -9 27070 30.475189447402954 41.637556076049805 440.0431823730469 0.2615935206413269 653.6773681640625 0.45158520340919495 0.80349994 0.6157490611076355 False -10 29777 29.84102177619934 0.7010316848754883 592.9349365234375 0.47684305906295776 650.6729736328125 0.4539978802204132 0.81096804 0.5320017337799072 True -11 32484 29.787177324295044 0.6920561790466309 580.762451171875 0.3393402695655823 647.911865234375 0.45685631036758423 0.8170763 0.46796703338623047 True -12 35191 29.88129496574402 0.7051751613616943 475.89154052734375 0.24006995558738708 643.8125610351562 0.4610207676887512 0.82414836 0.42397043108940125 True -13 37898 29.877480506896973 0.7131726741790771 448.5902099609375 0.19115649163722992 644.021484375 0.4590992033481598 0.83116853 0.37168145179748535 True -14 40605 29.826936721801758 0.6921284198760986 450.839111328125 0.3087539076805115 640.29541015625 0.4641902446746826 0.83840084 0.3336809277534485 True -15 43312 29.79657292366028 0.6944217681884766 443.43890380859375 0.2797859013080597 638.5018310546875 0.46501651406288147 0.8452752 0.290742963552475 True -16 46019 29.73866057395935 0.6957492828369141 518.0186767578125 0.20377418398857117 637.96044921875 0.46568867564201355 0.8489174 0.26991429924964905 True -17 48726 29.750757455825806 2.352501392364502 480.60931396484375 0.2496708184480667 637.9235229492188 0.46583959460258484 0.8515758 0.2527351677417755 True -18 51433 29.78949761390686 0.6857903003692627 451.0704345703125 0.16319411993026733 637.2691650390625 0.4666856825351715 0.8520496 0.24357344210147858 True -19 54140 29.81983757019043 0.7028543949127197 409.86785888671875 0.3043249249458313 637.3653564453125 0.46584010124206543 0.8507978 0.24164997041225433 False diff --git a/ENCSR650FLQ/cherimoya.fold_1.performance.tsv b/ENCSR650FLQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 219553c5d4d80f75ca27939b17305f9daa84b7f9..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -637.2691650390625 0.3454880118370056 0.4666856825351715 0.19516126811504364 0.8520495891571045 0.8394110202789307 0.24357344210147858 \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_2.evaluate.json b/ENCSR650FLQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 996c2cd7bcc5698a1be8a7b681e98a870c392169..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF095BJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_2.fit.json b/ENCSR650FLQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 8f033f0e8a5807b18f94e4e6c68c25bf0b414f1e..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF095BJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_2.log b/ENCSR650FLQ/cherimoya.fold_2.log deleted file mode 100644 index 62f87bfa04e8af877cacc2b9bf6486eabdd18d47..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 36.432793855667114 4.045849561691284 510.992431640625 0.34122276306152344 712.0765380859375 0.3056763708591461 0.7042904 3.851411819458008 True -1 5770 31.716642379760742 0.5568490028381348 589.0137939453125 0.5018153190612793 629.6315307617188 0.40186476707458496 0.7622694 1.6524213552474976 True -2 8655 32.03079581260681 0.5268065929412842 517.8885498046875 0.5492569804191589 617.3125 0.4122282564640045 0.7718951 0.7436290979385376 True -3 11540 31.675323963165283 0.5310628414154053 546.0350341796875 0.38488662242889404 610.9829711914062 0.4181607663631439 0.78205675 0.7264414429664612 True -4 14425 31.686267614364624 0.5298669338226318 392.8154296875 0.33730438351631165 608.8986206054688 0.4204016625881195 0.78617877 0.6254647374153137 True -5 17310 31.720324993133545 0.5300064086914062 475.0164489746094 0.32164430618286133 606.298828125 0.4225878119468689 0.79052365 0.578197717666626 True -6 20195 31.647242069244385 0.5324149131774902 460.50946044921875 0.3776957392692566 602.6592407226562 0.42707791924476624 0.7963998 0.5016990900039673 True -7 23080 31.650503396987915 0.5246944427490234 572.5385131835938 0.32087117433547974 600.868408203125 0.429083913564682 0.80073404 0.47730159759521484 True -8 25965 31.670892477035522 0.5218274593353271 483.39068603515625 0.18960975110530853 598.77685546875 0.43185219168663025 0.804714 0.4591729938983917 True -9 28850 31.658494472503662 0.531489372253418 439.32086181640625 0.18311676383018494 596.8970947265625 0.4337500333786011 0.80894667 0.4282388389110565 True -10 31735 31.653950691223145 0.5349249839782715 499.56439208984375 0.2884971797466278 593.9034423828125 0.43860456347465515 0.81473386 0.41045308113098145 True -11 34620 31.67666482925415 0.5380563735961914 524.703369140625 0.2139786183834076 592.9053955078125 0.43844345211982727 0.8216907 0.36275559663772583 True -12 37505 31.694648265838623 0.5415165424346924 492.42669677734375 0.24500766396522522 590.1763916015625 0.4426981210708618 0.824801 0.34672775864601135 True -13 40390 31.810895681381226 5.853863000869751 503.84375 0.22573629021644592 588.9498291015625 0.4436489939689636 0.8311755 0.30757734179496765 True -14 43275 31.77246928215027 0.5522089004516602 498.5362243652344 0.25885307788848877 587.5712890625 0.4456701874732971 0.832085 0.27532076835632324 True -15 46160 31.73429560661316 0.5471222400665283 590.0518798828125 0.24314528703689575 586.0701904296875 0.44774335622787476 0.83726 0.25538384914398193 True -16 49045 31.838276863098145 0.5444297790527344 467.38616943359375 0.2786257266998291 585.8077392578125 0.44782721996307373 0.84048235 0.23930929601192474 True -17 51930 31.797327756881714 0.5436949729919434 441.23516845703125 0.32033848762512207 584.3224487304688 0.4506273865699768 0.8445189 0.22988012433052063 True -18 54815 31.84878921508789 0.5328323841094971 467.45928955078125 0.16442640125751495 585.8225708007812 0.44750872254371643 0.8434717 0.22711069881916046 False -19 57700 31.701481819152832 1.1264026165008545 486.484619140625 0.1792881041765213 586.115234375 0.44663557410240173 0.8443893 0.22747381031513214 False diff --git a/ENCSR650FLQ/cherimoya.fold_2.performance.tsv b/ENCSR650FLQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a24c1f3222204f30292f4012b5a153a3d5da10ea..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -584.3224487304688 0.35861673951148987 0.4506273865699768 0.17762143909931183 0.8445188999176025 0.8276800513267517 0.22988012433052063 \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_3.evaluate.json b/ENCSR650FLQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5db26b47c174b161a5dbf3d21009de97625e6cb1..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF095BJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_3.fit.json b/ENCSR650FLQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 7f2a96e850476fd9d709294d2bf99e814d38440c..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF095BJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_3.log b/ENCSR650FLQ/cherimoya.fold_3.log deleted file mode 100644 index 2b5b2263bd936bb60e42a6865a1feb55b18b22a8..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 35.001412868499756 3.5704874992370605 490.8719482421875 0.4222497344017029 668.6464233398438 0.3121650815010071 0.6899782 5.375906944274902 True -1 5498 30.226478338241577 0.5967292785644531 527.212890625 0.4660021662712097 596.4436645507812 0.3944438099861145 0.74423015 1.4439548254013062 True -2 8247 30.436704635620117 0.5876960754394531 503.5162353515625 0.30861467123031616 583.4298706054688 0.41012731194496155 0.76587725 0.8692429661750793 True -3 10996 30.33023715019226 0.5845401287078857 587.33251953125 0.481212854385376 579.0194702148438 0.41422635316848755 0.77270365 0.7841019630432129 True -4 13745 30.451398611068726 0.5961885452270508 461.05438232421875 0.3770661950111389 574.1600952148438 0.42225003242492676 0.77786493 0.6745212078094482 True -5 16494 30.432862758636475 0.6080336570739746 528.088623046875 0.2991505265235901 572.07666015625 0.4243118464946747 0.7804168 0.7380070686340332 True -6 19243 30.379178762435913 0.5875320434570312 501.8544006347656 0.28930574655532837 569.44091796875 0.4267010986804962 0.7864526 0.6362459063529968 True -7 21992 30.512431621551514 0.5906813144683838 541.5438232421875 0.35529130697250366 568.51806640625 0.4278355538845062 0.790516 0.6844078302383423 True -8 24741 30.401487827301025 0.5855271816253662 479.1893615722656 0.3886887729167938 566.4501953125 0.43091338872909546 0.7940379 0.6364398002624512 True -9 27490 30.461089611053467 0.5778236389160156 629.82568359375 0.4115598797798157 564.3247680664062 0.43274301290512085 0.8014341 0.5475175380706787 True -10 30239 30.375432014465332 26.817811250686646 486.2226867675781 0.4006873071193695 561.5400390625 0.43610456585884094 0.80421335 0.5107349753379822 True -11 32988 30.525333642959595 0.5810060501098633 614.0155029296875 0.34635430574417114 560.4654541015625 0.43724626302719116 0.81065893 0.46860331296920776 True -12 35737 30.350724935531616 0.5933363437652588 606.2828369140625 0.18946301937103271 557.4431762695312 0.4410361051559448 0.8173441 0.40031030774116516 True -13 38486 30.285234451293945 0.5870649814605713 470.6710205078125 0.31644579768180847 556.4503173828125 0.44157737493515015 0.82240593 0.34948721528053284 True -14 41235 30.306330680847168 0.5802059173583984 514.666259765625 0.2522968649864197 555.3421020507812 0.44216814637184143 0.83045614 0.30345985293388367 True -15 43984 30.367694854736328 0.5787508487701416 518.1362915039062 0.3066486120223999 553.7190551757812 0.44493550062179565 0.8363033 0.2767249345779419 True -16 46733 30.38317370414734 0.5797712802886963 491.21734619140625 0.19859297573566437 552.6773071289062 0.44527217745780945 0.83931226 0.2546209692955017 True -17 49482 30.303841590881348 0.5796101093292236 522.68359375 0.2833278179168701 552.2952880859375 0.4460899531841278 0.84065115 0.24631954729557037 True -18 52231 30.25390934944153 0.5736229419708252 494.1000061035156 0.1824030578136444 552.2110595703125 0.4462946057319641 0.8420104 0.24025306105613708 True -19 54980 30.299375295639038 0.5789649486541748 462.6513366699219 0.287521094083786 552.3981323242188 0.445956289768219 0.84052944 0.23919229209423065 False diff --git a/ENCSR650FLQ/cherimoya.fold_3.performance.tsv b/ENCSR650FLQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 31a8de8bad204ebac381220ed2c0282bb8bb41b7..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -552.2110595703125 0.36250829696655273 0.4462946057319641 0.1716526597738266 0.8420103788375854 0.81609708070755 0.24025306105613708 \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_4.evaluate.json b/ENCSR650FLQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d9ff77a6b1e395e4b1437ee9d5ad56ae6fbe3da4..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF095BJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_4.fit.json b/ENCSR650FLQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 2c2cfaf111d7ccda1e01df020977503855b067a9..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF095BJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR650FLQ/cherimoya.fold_4.log b/ENCSR650FLQ/cherimoya.fold_4.log deleted file mode 100644 index c87991d2d232ea6c588fdc85def5dc7527c088ee..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2847 36.10661339759827 27.69708013534546 519.634521484375 0.4275996685028076 639.7297973632812 0.3065551817417145 0.6853513 4.257220268249512 True -1 5694 35.55284905433655 0.5974037647247314 505.1854248046875 0.416159451007843 575.0061645507812 0.3884417414665222 0.7425713 1.493883728981018 True -2 8541 31.395259141921997 0.5860841274261475 519.6571655273438 0.27715620398521423 561.2781372070312 0.40562841296195984 0.7571879 0.6839125156402588 True -3 11388 31.426592588424683 2.214597463607788 524.738037109375 0.4064989686012268 558.9159545898438 0.4065854847431183 0.76510453 0.8232696652412415 True -4 14235 31.45626139640808 0.9948399066925049 540.9818115234375 0.3146299421787262 554.4008178710938 0.410657674074173 0.7737011 0.4909253418445587 True -5 17082 31.413652420043945 0.6032571792602539 484.309326171875 0.365242063999176 552.035400390625 0.41391536593437195 0.7815736 0.5051762461662292 True -6 19929 31.36585831642151 0.5958256721496582 484.40338134765625 0.38515108823776245 549.640869140625 0.4180126488208771 0.7854242 0.5194525718688965 True -7 22776 31.357997179031372 0.5954437255859375 568.2000732421875 0.28621935844421387 547.6491088867188 0.41907209157943726 0.7904889 0.4804782271385193 True -8 25623 31.50528383255005 0.5992751121520996 529.0596923828125 0.41283535957336426 545.376220703125 0.42313724756240845 0.7966713 0.4244476556777954 True -9 28470 31.694181203842163 0.5857388973236084 469.92132568359375 0.25267988443374634 543.5639038085938 0.42525991797447205 0.7997789 0.41124463081359863 True -10 31317 31.882845878601074 28.997838497161865 542.882568359375 0.4271663427352905 542.7987060546875 0.4263583719730377 0.802385 0.4019710123538971 True -11 34164 32.92441987991333 0.5886545181274414 454.185302734375 0.2319955676794052 540.237548828125 0.4308847486972809 0.80678695 0.36016079783439636 True -12 37011 31.48496437072754 0.5952885150909424 404.14324951171875 0.34072452783584595 539.30712890625 0.4307585060596466 0.81620187 0.31714609265327454 True -13 39858 31.471237421035767 0.5851099491119385 530.8699951171875 0.25914546847343445 537.7049560546875 0.43341904878616333 0.8222403 0.28109997510910034 True -14 42705 31.448030710220337 0.6029415130615234 586.8567504882812 0.40839624404907227 535.4532470703125 0.4363965690135956 0.8270131 0.25662535429000854 True -15 45552 31.52324104309082 0.6002748012542725 400.97589111328125 0.21035553514957428 534.6743774414062 0.4365689158439636 0.8331582 0.23314733803272247 True -16 48399 31.491103887557983 0.5952498912811279 527.045654296875 0.26196375489234924 534.1166381835938 0.4376305937767029 0.8358222 0.2237834334373474 True -17 51246 31.41036057472229 1.0114026069641113 475.767822265625 0.20171040296554565 534.71875 0.43610966205596924 0.83881277 0.21481963992118835 True -18 54093 31.516431093215942 29.853862762451172 444.4987487792969 0.15764233469963074 534.2639770507812 0.4379366636276245 0.83862233 0.2131340205669403 False -19 56940 32.93547582626343 0.5972621440887451 486.7026672363281 0.19452139735221863 534.5105590820312 0.43709394335746765 0.84025514 0.2123914361000061 True diff --git a/ENCSR650FLQ/cherimoya.fold_4.performance.tsv b/ENCSR650FLQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9a1f2ef1a3d6d86d3f789399fe7e11493eb014a5..0000000000000000000000000000000000000000 --- a/ENCSR650FLQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -534.5105590820312 0.36989840865135193 0.43709391355514526 0.16619744896888733 0.8402551412582397 0.8149893879890442 0.2123914361000061 \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_0.evaluate.json b/ENCSR651SOJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9a002c872fc0571f14d6d153ebff8915d2ebdd88..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF310VZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_0.fit.json b/ENCSR651SOJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 3d28bcd3413c7e261b2a882e03825cb6f13a51cd..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF310VZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_0.log b/ENCSR651SOJ/cherimoya.fold_0.log deleted file mode 100644 index 29cb6bc7e2a4ccb5e24c86011f4a4237e43f55ef..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3838 48.36658310890198 4.000489950180054 876.7007446289062 1.2932791709899902 1086.1917724609375 0.7032214999198914 0.74096256 7.9282708168029785 True -1 7676 42.23857641220093 1.8531816005706787 692.2545776367188 0.7487841844558716 907.310302734375 0.7904388308525085 0.73759866 1.2646881341934204 False -2 11514 42.20071196556091 0.762275218963623 824.0272216796875 1.188140630722046 894.9754028320312 0.796089231967926 0.748951 0.8474413752555847 True -3 15352 42.182716608047485 0.7690622806549072 900.7122802734375 0.7580929398536682 878.948486328125 0.8035066723823547 0.74050856 0.7122117877006531 False -4 19190 42.21154975891113 23.660381078720093 722.4388427734375 1.1135940551757812 870.549560546875 0.8077791333198547 0.74370056 0.7303704023361206 False -5 23028 43.389681339263916 0.7853848934173584 726.4892578125 1.280773401260376 865.3339233398438 0.8097066283226013 0.7463009 0.6722025871276855 False -6 26866 42.25111103057861 0.7812106609344482 661.3020629882812 1.3877778053283691 857.07568359375 0.8131833076477051 0.7539205 0.6587386131286621 True -7 30704 41.58140254020691 0.7732129096984863 618.8636474609375 0.6825757026672363 849.53271484375 0.8164849281311035 0.75257486 0.6573714017868042 False -8 34542 41.34589147567749 48.500365257263184 696.492919921875 1.2907538414001465 840.6167602539062 0.8197164535522461 0.75866896 0.6334264278411865 True -9 38380 41.52531838417053 0.7857048511505127 815.1901245117188 1.057878017425537 835.6486206054688 0.8222182393074036 0.7611077 0.6286256313323975 True -10 42218 41.29758548736572 0.7691552639007568 568.539794921875 0.9092974662780762 829.5086669921875 0.825408935546875 0.7689965 0.6122847199440002 True -11 46056 41.29102826118469 1.59940767288208 599.88623046875 0.9333713054656982 820.6943969726562 0.8292955756187439 0.7755765 0.5883504152297974 True -12 49894 41.33499097824097 0.7505841255187988 743.3782958984375 0.7500362396240234 814.5128784179688 0.8326290845870972 0.7861615 0.5707105994224548 True -13 53732 42.08451747894287 9.725987434387207 555.2567138671875 0.8987970948219299 808.548828125 0.8355602622032166 0.7908559 0.5579432249069214 True -14 57570 41.321688413619995 1.5343029499053955 822.3770751953125 0.6877627372741699 803.9364624023438 0.8381303548812866 0.7972618 0.5484041571617126 True -15 61408 41.50377345085144 39.24694204330444 646.435791015625 0.5687573552131653 801.4910278320312 0.8396974802017212 0.8038885 0.5494144558906555 True -16 65246 41.36992168426514 0.7782907485961914 689.1717529296875 0.6877307891845703 800.0037841796875 0.840662956237793 0.80661064 0.5483990907669067 True -17 69084 41.35835528373718 0.786677360534668 632.2312622070312 0.5576483011245728 798.9010620117188 0.8410035371780396 0.811061 0.5479736328125 True -18 72922 41.312613010406494 0.7484312057495117 638.5311279296875 0.6297140121459961 800.060791015625 0.8408687710762024 0.8103342 0.5545053482055664 False -19 76760 41.86896014213562 0.74318528175354 582.8740234375 0.7059382200241089 799.9710083007812 0.840714693069458 0.81029904 0.5584393739700317 False diff --git a/ENCSR651SOJ/cherimoya.fold_0.performance.tsv b/ENCSR651SOJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2e3a6995ba41e6325c43fa423371f3af5211c3bd..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -798.9010620117188 0.13759469985961914 0.8410036563873291 0.4774681031703949 0.8110610246658325 0.7541577816009521 0.5479736328125 \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_1.evaluate.json b/ENCSR651SOJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 13de5b16fa2e70125857ebd47525ac1d7b6fbb52..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF310VZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_1.fit.json b/ENCSR651SOJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 271c2c81754324cace40313e235b22bb08bb143d..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF310VZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_1.log b/ENCSR651SOJ/cherimoya.fold_1.log deleted file mode 100644 index 9e478796244c4dd2fc2350ac62797e30a844af95..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3778 46.048529863357544 4.338543891906738 725.13623046875 1.3356807231903076 1242.5574951171875 0.7107192873954773 0.74975646 10.030243873596191 True -1 7556 41.60134816169739 1.0251593589782715 599.1278076171875 1.7108607292175293 1024.7237548828125 0.8038632869720459 0.76363605 1.9490375518798828 True -2 11334 41.517494916915894 1.6612904071807861 689.09814453125 1.0264371633529663 1007.1674194335938 0.8084569573402405 0.7675897 1.0996254682540894 True -3 15112 41.540345907211304 2.089327573776245 725.2325439453125 0.9798608422279358 985.268310546875 0.8157936930656433 0.77331066 0.8801933526992798 True -4 18890 41.51399540901184 1.0301880836486816 595.1700439453125 1.2206593751907349 973.4990234375 0.8200995922088623 0.77883035 0.7890727519989014 True -5 22668 41.58352017402649 44.94521474838257 700.144775390625 1.0569151639938354 967.8919677734375 0.8219881057739258 0.7797282 0.7635679244995117 True -6 26446 41.427433490753174 1.1015830039978027 595.681884765625 1.0623507499694824 960.7411499023438 0.8241721987724304 0.77995837 0.7252044081687927 True -7 30224 40.6351273059845 1.0246796607971191 690.6414794921875 0.864060640335083 952.2163696289062 0.8278611302375793 0.7871026 0.6725733280181885 True -8 34002 40.65835165977478 1.0091588497161865 638.3429565429688 1.2776668071746826 946.3975219726562 0.8298133015632629 0.7921293 0.6446838974952698 True -9 37780 40.655105113983154 1.0176563262939453 649.9210205078125 0.8532537817955017 936.4352416992188 0.8331507444381714 0.79612786 0.6066059470176697 True -10 41558 40.64122748374939 1.0134313106536865 715.5858154296875 1.0145397186279297 930.0284423828125 0.8359012603759766 0.79703 0.6016319990158081 True -11 45336 41.64278745651245 9.74010443687439 746.0448608398438 0.85868901014328 922.2080688476562 0.8388587832450867 0.80666614 0.5838392376899719 True -12 49114 40.648587465286255 1.0374927520751953 695.246826171875 0.663800060749054 914.458251953125 0.8421033620834351 0.81713057 0.5599877238273621 True -13 52892 41.651132583618164 39.866514921188354 707.8987426757812 0.5180758237838745 907.8523559570312 0.8445266485214233 0.8223308 0.5616892576217651 True -14 56670 41.93833684921265 30.46092391014099 699.1945190429688 0.9324181079864502 901.4542846679688 0.8471142649650574 0.8297276 0.5526929497718811 True -15 60448 42.46392798423767 1.0433883666992188 414.5652160644531 0.8526079058647156 896.8819580078125 0.8489351868629456 0.8316808 0.5481084585189819 True -16 64226 40.93573784828186 1.0254015922546387 572.9015502929688 0.4645853638648987 894.1780395507812 0.8501325249671936 0.83649254 0.5520329475402832 True -17 68004 40.76260304450989 1.0494134426116943 546.481201171875 0.6230483055114746 892.88623046875 0.8505539298057556 0.8372402 0.548424243927002 True -18 71782 40.81926465034485 1.0455033779144287 668.3831787109375 0.4716745615005493 894.2304077148438 0.8502966165542603 0.836398 0.5474337935447693 False -19 75560 40.93137860298157 1.0280139446258545 491.0150146484375 0.6000494360923767 894.5263061523438 0.850047767162323 0.8351712 0.546894371509552 False diff --git a/ENCSR651SOJ/cherimoya.fold_1.performance.tsv b/ENCSR651SOJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 77a71596526803569873358943c4ff5e5c2280de..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -892.88623046875 0.12553560733795166 0.8505538702011108 0.5186587572097778 0.8372402191162109 0.8044137358665466 0.548424243927002 \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_2.evaluate.json b/ENCSR651SOJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5559fede81702bc3ce3de9801f4519df86210490..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF310VZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_2.fit.json b/ENCSR651SOJ/cherimoya.fold_2.fit.json deleted file mode 100644 index a31ce1a2337ce169883d04b98e2ef9fd8efea0ac..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF310VZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_2.log b/ENCSR651SOJ/cherimoya.fold_2.log deleted file mode 100644 index 1f19f59448826101c06b27668c6ee1dee4339247..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4046 49.26081299781799 3.922224760055542 719.3695678710938 1.4187853336334229 1131.2059326171875 0.7154858708381653 0.7442175 6.222690105438232 True -1 8092 44.5330548286438 0.8131923675537109 879.8359375 1.3251062631607056 972.8295288085938 0.7942131757736206 0.75168616 2.2152881622314453 True -2 12138 44.45781087875366 1.9507720470428467 705.6485595703125 1.1942873001098633 944.6585693359375 0.8017688989639282 0.75569856 1.3736780881881714 True -3 16184 44.57789850234985 1.2891199588775635 765.3072509765625 1.0242862701416016 933.0336303710938 0.8077820539474487 0.7546366 1.2223087549209595 False -4 20230 44.476200342178345 0.7810714244842529 788.3643798828125 0.9084566235542297 925.0875854492188 0.8116316795349121 0.7564277 0.9612815976142883 True -5 24276 44.040849924087524 0.7699382305145264 744.030517578125 0.7654682993888855 916.9603881835938 0.8152585029602051 0.7579885 0.8242899179458618 True -6 28322 43.506773948669434 0.7746145725250244 572.5545043945312 1.3931465148925781 907.0825805664062 0.8188767433166504 0.7662907 0.800475537776947 True -7 32368 43.62570571899414 0.7854812145233154 696.8619995117188 0.8428092002868652 901.2508544921875 0.8214837312698364 0.76938933 0.7397556304931641 True -8 36414 44.780176639556885 0.7843191623687744 848.590087890625 0.8156168460845947 890.4420166015625 0.8251656293869019 0.7711841 0.7372565865516663 True -9 40460 43.556732177734375 41.82437872886658 779.9261474609375 0.6975581645965576 880.1658935546875 0.8289234042167664 0.778517 0.6906964182853699 True -10 44506 45.45285964012146 0.7849628925323486 712.833251953125 0.7830823659896851 874.0711669921875 0.8316685557365417 0.7844552 0.678682267665863 True -11 48552 49.32184052467346 0.7937467098236084 617.2769775390625 0.8287225365638733 865.7730712890625 0.8350945711135864 0.7891468 0.6403167843818665 True -12 52598 43.71927094459534 0.7826220989227295 696.6026611328125 0.5740965604782104 859.3697509765625 0.8381979465484619 0.79837805 0.6175353527069092 True -13 56644 43.959192991256714 1.5205824375152588 647.4195556640625 0.7098620533943176 852.511474609375 0.8409472107887268 0.80502915 0.6053324937820435 True -14 60690 43.83863663673401 0.77174973487854 672.9053955078125 0.9205824136734009 846.7449340820312 0.8432603478431702 0.8097805 0.5749922394752502 True -15 64736 43.58944535255432 0.7856261730194092 640.7144165039062 0.7885161638259888 843.8253173828125 0.8447349667549133 0.8137178 0.5722852945327759 True -16 68782 43.52738857269287 0.7688455581665039 564.9054565429688 0.604079008102417 840.832763671875 0.8457291126251221 0.81771547 0.5632935166358948 True -17 72828 43.60427451133728 1.916642189025879 525.65673828125 0.7835074663162231 840.7229614257812 0.8460730910301208 0.82015747 0.5574738383293152 True -18 76874 43.566428422927856 1.5658185482025146 556.1724853515625 0.671183705329895 841.5438232421875 0.8459193706512451 0.8196088 0.5544970631599426 False -19 80920 43.490928411483765 0.9905245304107666 601.9810791015625 0.6193986535072327 841.9223022460938 0.8458749055862427 0.81903374 0.5598683953285217 False diff --git a/ENCSR651SOJ/cherimoya.fold_2.performance.tsv b/ENCSR651SOJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ef51df5012c75269fe2d42c5e233cb7f5224f1c5..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -840.7229614257812 0.13164719939231873 0.8460730910301208 0.49850499629974365 0.8201574683189392 0.7747352123260498 0.5574738383293152 \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_3.evaluate.json b/ENCSR651SOJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 24e82ea570a39d1e958b80c20858551056b824d1..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF310VZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_3.fit.json b/ENCSR651SOJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 9ec12fd5755b387b783838ed0b3afb0e54cc2a14..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF310VZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_3.log b/ENCSR651SOJ/cherimoya.fold_3.log deleted file mode 100644 index 5f35424f21e9eb2e6198993bf8af8b2499713c0f..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3912 47.92767310142517 4.18033242225647 686.89892578125 1.4530131816864014 1061.62353515625 0.6963359117507935 0.73676354 8.352160453796387 True -1 7824 42.94684600830078 1.323582649230957 719.375 1.199735403060913 895.5938720703125 0.7840942740440369 0.7438024 1.7253230810165405 True -2 11736 42.26745104789734 37.18008732795715 649.4708251953125 0.8286193013191223 871.59521484375 0.7931809425354004 0.7453299 0.8890536427497864 True -3 15648 42.65960192680359 0.7261602878570557 657.2359619140625 0.937830924987793 861.2593994140625 0.7986442446708679 0.73559254 0.8527742624282837 False -4 19560 42.479374170303345 14.394800186157227 733.33349609375 1.312425971031189 853.09912109375 0.8017323613166809 0.7413751 0.7323213815689087 False -5 23472 42.15587496757507 1.996805191040039 684.5826416015625 1.070016622543335 848.7548828125 0.8035477995872498 0.74055403 0.7663331627845764 False -6 27384 42.19836378097534 0.7309174537658691 663.2532958984375 0.68874192237854 840.4088745117188 0.8082031011581421 0.74467546 0.7254064679145813 False -7 31296 42.32922434806824 12.72777009010315 736.2299194335938 0.8154646158218384 835.0481567382812 0.8099968433380127 0.75245816 0.7014137506484985 True -8 35208 42.08101844787598 0.7237465381622314 606.1282958984375 0.6055639982223511 828.0964965820312 0.8126852512359619 0.75125825 0.7054387927055359 False -9 39120 44.876219034194946 32.46683406829834 656.724609375 0.8786050081253052 820.476318359375 0.8162196278572083 0.75534266 0.6798799633979797 True -10 43032 42.12397050857544 0.7160937786102295 621.0362548828125 0.7104156017303467 814.3269653320312 0.8195939660072327 0.7635653 0.670910656452179 True -11 46944 42.02316427230835 0.7136368751525879 657.4147338867188 0.9043962955474854 807.3509521484375 0.823373019695282 0.7742011 0.6489041447639465 True -12 50856 42.00628328323364 0.7038397789001465 703.4164428710938 0.8974454402923584 799.4642333984375 0.8267382383346558 0.7849383 0.6212477684020996 True -13 54768 42.04475235939026 2.4332821369171143 694.3743286132812 0.7700344324111938 792.7766723632812 0.8295301198959351 0.7936725 0.6030504107475281 True -14 58680 42.02026581764221 0.7195098400115967 620.5145263671875 0.8295781016349792 786.5418701171875 0.832225501537323 0.80177414 0.5901517271995544 True -15 62592 45.9560866355896 25.870609998703003 609.3487548828125 0.9313542246818542 783.8345336914062 0.8341590762138367 0.8060013 0.5745830535888672 True -16 66504 43.130784034729004 0.7144780158996582 648.52099609375 0.5906224846839905 780.5128173828125 0.8353089094161987 0.80947584 0.5701644420623779 True -17 70416 42.029566287994385 0.7191054821014404 706.1241455078125 0.7309237718582153 779.657470703125 0.835844874382019 0.81276226 0.5615085959434509 True -18 74328 42.23940062522888 6.469072341918945 659.8126220703125 0.6086769700050354 780.4050903320312 0.8356183767318726 0.8116052 0.5664103627204895 False -19 78240 42.08670473098755 14.301906824111938 638.35986328125 0.7590606212615967 780.559814453125 0.8354752659797668 0.8121241 0.568733274936676 False diff --git a/ENCSR651SOJ/cherimoya.fold_3.performance.tsv b/ENCSR651SOJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 586163baaea200b3dbcb9d5be454e89414b9d5af..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -779.657470703125 0.14150729775428772 0.835844874382019 0.4642222821712494 0.8127622604370117 0.7519400715827942 0.5615085959434509 \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_4.evaluate.json b/ENCSR651SOJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4ad554006ffa2ee3e8a65e8568f6e98393021204..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF310VZK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_4.fit.json b/ENCSR651SOJ/cherimoya.fold_4.fit.json deleted file mode 100644 index e6833148825b3da8e65c02ea9d1348fe869b9fea..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF310VZK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR651SOJ/cherimoya.fold_4.log b/ENCSR651SOJ/cherimoya.fold_4.log deleted file mode 100644 index d7b113e9c2f9e57f3058791131f0f4994af88a9b..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3891 48.66533708572388 9.469691038131714 712.552734375 1.210174798965454 1006.6132202148438 0.6937216520309448 0.72063464 8.192873001098633 True -1 7782 42.97494053840637 0.8004598617553711 736.642822265625 0.7445862889289856 844.4161987304688 0.7883589267730713 0.722929 1.564788818359375 True -2 11673 42.735060930252075 48.59492206573486 768.3716430664062 1.0873401165008545 831.1232299804688 0.7950443625450134 0.7181082 1.0468693971633911 False -3 15564 42.91766381263733 0.7686660289764404 643.8363037109375 0.9163638949394226 818.14990234375 0.8014993667602539 0.7236377 0.8348033428192139 True -4 19455 42.78995752334595 2.745774507522583 627.0438842773438 1.1198819875717163 812.603515625 0.8050462603569031 0.7234966 0.8698773384094238 False -5 23346 42.76360487937927 0.7524361610412598 797.7883911132812 0.8868889808654785 805.66943359375 0.8073542714118958 0.7267802 0.8274109959602356 True -6 27237 42.679505348205566 36.99547100067139 573.76953125 1.0464073419570923 800.2449340820312 0.8101487755775452 0.72869307 0.7393149733543396 True -7 31128 43.53890419006348 0.7706508636474609 742.972900390625 0.8686608076095581 793.9137573242188 0.8139545917510986 0.7288218 0.735858678817749 True -8 35019 43.365562915802 1.0795440673828125 772.8592529296875 0.8204754590988159 787.661865234375 0.816771924495697 0.734945 0.7145283818244934 True -9 38910 42.863959312438965 0.7750675678253174 650.7943725585938 0.9079242944717407 781.5714111328125 0.8199031352996826 0.7412761 0.6901630759239197 True -10 42801 42.877686500549316 0.7760696411132812 550.6754150390625 1.4453932046890259 775.8456420898438 0.8231669664382935 0.7457581 0.6716251969337463 True -11 46692 42.86152625083923 0.7857773303985596 572.2169189453125 0.7550641298294067 770.2103271484375 0.8265080451965332 0.7522483 0.658053457736969 True -12 50583 43.83890652656555 0.7740297317504883 631.6700439453125 1.0919606685638428 764.2247314453125 0.8300291895866394 0.76441234 0.6187888383865356 True -13 54474 43.4653377532959 33.321579694747925 817.2678833007812 0.5044568777084351 760.2767944335938 0.8324158191680908 0.7734563 0.6027002930641174 True -14 58365 43.54840970039368 0.7750916481018066 589.48876953125 0.6669071912765503 756.1127319335938 0.8347742557525635 0.78010964 0.5864222645759583 True -15 62256 42.187230587005615 0.7648718357086182 615.8565063476562 0.722771167755127 753.066162109375 0.8362317681312561 0.78618056 0.5596066117286682 True -16 66147 42.09780740737915 0.7693171501159668 662.22802734375 0.5554871559143066 751.6358032226562 0.8371880650520325 0.79048806 0.5499241948127747 True -17 70038 42.04695200920105 0.7572345733642578 671.2862548828125 0.6608340740203857 751.3822021484375 0.8373433351516724 0.7934215 0.5405465364456177 True -18 73929 42.02145767211914 0.7691211700439453 568.4534912109375 0.4526234269142151 752.310791015625 0.8372218012809753 0.79493934 0.5417982935905457 True -19 77820 42.00813174247742 3.390951633453369 631.52880859375 0.5834692716598511 752.4955444335938 0.8370417356491089 0.7936982 0.5415679216384888 False diff --git a/ENCSR651SOJ/cherimoya.fold_4.performance.tsv b/ENCSR651SOJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ac61ede91a275f662418b4f47b0e5c2cd7863baa..0000000000000000000000000000000000000000 --- a/ENCSR651SOJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -752.310791015625 0.14197933673858643 0.8372219204902649 0.46079450845718384 0.7949393391609192 0.7270181775093079 0.5417982935905457 \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_0.evaluate.json b/ENCSR652IZW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5a6de7eb5cb83e372beabbcc2a3a878846332ed1..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155SVA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_0.fit.json b/ENCSR652IZW/cherimoya.fold_0.fit.json deleted file mode 100644 index a58b045a4bd98ee3fe6d61b373736832aad642d9..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF155SVA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_0.log b/ENCSR652IZW/cherimoya.fold_0.log deleted file mode 100644 index ddef8301825cfdd2a15ce9bf7de155cb5f645284..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 35.83734178543091 3.7157442569732666 356.11431884765625 0.25847384333610535 523.5303955078125 0.27333134412765503 0.7837959 4.401881694793701 True -1 5554 30.96404528617859 0.6380553245544434 452.1767883300781 0.249627947807312 487.75885009765625 0.32316508889198303 0.82393646 0.8794261813163757 True -2 8331 30.92935585975647 0.5958735942840576 384.15643310546875 0.41052162647247314 478.67529296875 0.33512747287750244 0.8442766 0.5428357124328613 True -3 11108 30.916277647018433 0.8813846111297607 469.06475830078125 0.2749975919723511 473.8724060058594 0.3419294059276581 0.8485685 0.36788833141326904 True -4 13885 30.956449031829834 0.5973410606384277 411.5003662109375 0.3246367275714874 471.38360595703125 0.34411001205444336 0.85588455 0.29951587319374084 True -5 16662 30.929136991500854 0.5969560146331787 382.76763916015625 0.27014756202697754 470.32928466796875 0.34480300545692444 0.8624741 0.26490098237991333 True -6 19439 30.943243265151978 0.5957167148590088 419.4771728515625 0.35766899585723877 468.9553527832031 0.3460879623889923 0.8668241 0.25759533047676086 True -7 22216 30.980451822280884 0.5962011814117432 386.41339111328125 0.2214939445257187 467.54248046875 0.3486013114452362 0.87153184 0.2425747662782669 True -8 24993 30.98033833503723 0.5963296890258789 354.70745849609375 0.27344179153442383 466.34173583984375 0.3501506447792053 0.8736936 0.22822466492652893 True -9 27770 30.4336838722229 1.3797497749328613 425.18035888671875 0.24697552621364594 465.1289367675781 0.3518221378326416 0.88086194 0.21560075879096985 True -10 30547 30.30235481262207 0.5824306011199951 450.4936218261719 0.3111146092414856 464.19921875 0.3522002398967743 0.88290906 0.20929288864135742 True -11 33324 30.37917137145996 0.5877957344055176 428.55523681640625 0.25680094957351685 463.19134521484375 0.3540143370628357 0.88825554 0.20294052362442017 True -12 36101 30.350452423095703 0.5900452136993408 382.81268310546875 0.22104895114898682 462.1230773925781 0.3554283082485199 0.88987327 0.19939175248146057 True -13 38878 30.372435331344604 0.5853569507598877 451.969482421875 0.20272615551948547 460.7628479003906 0.3577110469341278 0.8942697 0.1909562647342682 True -14 41655 30.344654321670532 0.5845141410827637 368.9644775390625 0.20510312914848328 459.7696533203125 0.3581415116786957 0.89887977 0.18508173525333405 True -15 44432 30.361069917678833 0.5793366432189941 383.28472900390625 0.18795587122440338 459.45684814453125 0.3588377833366394 0.90110856 0.17961986362934113 True -16 47209 30.33961772918701 0.5858848094940186 360.55694580078125 0.19881989061832428 459.59222412109375 0.35882827639579773 0.9027553 0.17535623908042908 True -17 49986 30.30660891532898 0.5727429389953613 377.18365478515625 0.10753566026687622 459.181640625 0.3595221936702728 0.9017972 0.17514458298683167 False -18 52763 30.33803367614746 0.5742688179016113 418.3272399902344 0.23072198033332825 459.8047790527344 0.3580697178840637 0.90318793 0.17373114824295044 True -19 55540 30.330273628234863 0.5739972591400146 343.1939697265625 0.15856586396694183 460.3289794921875 0.35683757066726685 0.902168 0.17461472749710083 False diff --git a/ENCSR652IZW/cherimoya.fold_0.performance.tsv b/ENCSR652IZW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 19b0f144413fc6d261e3098087f93afb63661f8f..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.8047790527344 0.42675045132637024 0.35806965827941895 0.1215185821056366 0.9031879305839539 0.8886714577674866 0.17373114824295044 \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_1.evaluate.json b/ENCSR652IZW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 875878836dbf47899ab681259fcb9283a260e394..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155SVA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_1.fit.json b/ENCSR652IZW/cherimoya.fold_1.fit.json deleted file mode 100644 index 1540c205ca99f046b45a2bb1dd3b2e4bb0219fed..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF155SVA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_1.log b/ENCSR652IZW/cherimoya.fold_1.log deleted file mode 100644 index 4d9d6ab4b30236b7ed1f6780526553d925db21e7..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2710 34.596930742263794 4.093632221221924 422.3471374511719 0.29530882835388184 616.9689331054688 0.2765549123287201 0.7725834 4.728793621063232 True -1 5420 30.214593410491943 27.713300943374634 396.9942626953125 0.35932937264442444 567.5906982421875 0.3340175747871399 0.81592196 0.9448238611221313 True -2 8130 30.174098014831543 0.6982829570770264 396.2803649902344 0.3928356468677521 555.3230590820312 0.3464423716068268 0.8338377 0.5250962376594543 True -3 10840 30.312055826187134 0.7763288021087646 348.35516357421875 0.5068289637565613 550.7862548828125 0.3510044515132904 0.84799296 0.49368417263031006 True -4 13550 30.356886863708496 0.6913783550262451 460.1031494140625 0.4470345377922058 545.9127807617188 0.35692763328552246 0.8558124 0.32773059606552124 True -5 16260 30.242854595184326 0.6789462566375732 397.9139404296875 0.2958790361881256 543.3567504882812 0.3608647286891937 0.86176896 0.280764102935791 True -6 18970 30.308908939361572 0.7008728981018066 393.23748779296875 0.24384455382823944 541.597412109375 0.3612825870513916 0.8659036 0.278164267539978 True -7 21680 29.667205572128296 0.664149284362793 376.38922119140625 0.4098355174064636 539.2798461914062 0.36382433772087097 0.8726466 0.2542020082473755 True -8 24390 29.682902812957764 0.6617081165313721 429.8680419921875 0.2691473960876465 539.198486328125 0.3625376224517822 0.87774634 0.2407432645559311 True -9 27100 29.616981029510498 0.6743762493133545 395.17926025390625 0.25015151500701904 536.200927734375 0.3668200373649597 0.8802033 0.23734711110591888 True -10 29810 29.62220048904419 0.6837542057037354 433.47088623046875 0.18929439783096313 535.1276245117188 0.367693692445755 0.8835038 0.23364825546741486 True -11 32520 29.584010362625122 0.6737329959869385 371.1414794921875 0.20935720205307007 533.3717041015625 0.3698490560054779 0.88907206 0.22501397132873535 True -12 35230 29.579827308654785 0.6670148372650146 378.14556884765625 0.23020517826080322 531.9901123046875 0.3715938329696655 0.8935978 0.21520084142684937 True -13 37940 29.88846707344055 28.099793910980225 435.8824462890625 0.40461716055870056 530.7740478515625 0.3732397258281708 0.8965286 0.20993492007255554 True -14 40650 29.69058871269226 1.1569342613220215 419.99993896484375 0.14714395999908447 529.6573486328125 0.37458112835884094 0.90026563 0.19934645295143127 True -15 43360 29.680866241455078 0.6774239540100098 391.7289733886719 0.22360670566558838 528.5473022460938 0.37553870677948 0.90360576 0.1942785084247589 True -16 46070 29.71095585823059 0.6893727779388428 449.6231689453125 0.15522165596485138 527.6940307617188 0.3771366775035858 0.9057527 0.18998900055885315 True -17 48780 29.636507749557495 0.6721503734588623 421.9949951171875 0.18804123997688293 526.9826049804688 0.3781324326992035 0.9073619 0.18812187016010284 True -18 51490 29.598994970321655 0.6604692935943604 315.43060302734375 0.1374933123588562 527.932861328125 0.3760073184967041 0.90812236 0.18608760833740234 True -19 54200 29.7448947429657 0.6863415241241455 376.4822082519531 0.19295671582221985 528.4960327148438 0.37488076090812683 0.90860075 0.1861855536699295 True diff --git a/ENCSR652IZW/cherimoya.fold_1.performance.tsv b/ENCSR652IZW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d71a90d0c54c821c4d8b76bd4e42eba18c7101e7..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -528.4960327148438 0.41079118847846985 0.37488070130348206 0.14350514113903046 0.9086007475852966 0.9025510549545288 0.1861855536699295 \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_2.evaluate.json b/ENCSR652IZW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4da712da7fee7459f03cca4f6cad3d7026c17c90..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155SVA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_2.fit.json b/ENCSR652IZW/cherimoya.fold_2.fit.json deleted file mode 100644 index ff081db1683babe357379648ffa015be8821c869..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF155SVA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_2.log b/ENCSR652IZW/cherimoya.fold_2.log deleted file mode 100644 index ebf7576783014e362dd036a61d73745cd78ecf1e..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.563300132751465 4.0557568073272705 383.8845520019531 0.5512096285820007 552.2562255859375 0.27871912717819214 0.7818667 3.1641204357147217 True -1 5754 32.74990153312683 9.413663864135742 337.29534912109375 0.24882671236991882 514.2020874023438 0.32819586992263794 0.81749123 0.9315034747123718 True -2 8631 32.14941072463989 0.6333155632019043 413.8321533203125 0.2515392005443573 504.2035217285156 0.33908578753471375 0.8406304 0.43301263451576233 True -3 11508 32.10125803947449 0.5892972946166992 398.54180908203125 0.41698285937309265 501.6706848144531 0.3403973877429962 0.85284024 0.3211803436279297 True -4 14385 32.1563982963562 0.5806910991668701 370.74774169921875 0.1603575050830841 498.3923034667969 0.34445756673812866 0.85769665 0.2540338933467865 True -5 17262 32.12199831008911 0.5715439319610596 398.7508544921875 0.31458187103271484 497.269287109375 0.34489110112190247 0.86290735 0.25404229760169983 True -6 20139 31.902472734451294 0.5635826587677002 374.885009765625 0.20980873703956604 495.8657531738281 0.3467230498790741 0.86656296 0.23245973885059357 True -7 23016 31.459086418151855 0.5535078048706055 397.27203369140625 0.318549245595932 494.839111328125 0.347547322511673 0.8734255 0.22598983347415924 True -8 25893 31.468164682388306 0.594012975692749 477.4033203125 0.3023981750011444 493.4369812011719 0.3496237099170685 0.8754295 0.2245548963546753 True -9 28770 31.534903049468994 0.5669491291046143 418.14105224609375 0.31205758452415466 491.17413330078125 0.3535461723804474 0.8793012 0.21332640945911407 True -10 31647 31.480350255966187 0.5574963092803955 464.04931640625 0.15031296014785767 491.24566650390625 0.35197708010673523 0.8805648 0.20359715819358826 True -11 34524 31.510562896728516 0.564378023147583 407.0383605957031 0.22738513350486755 490.180908203125 0.3537159860134125 0.88445324 0.20007438957691193 True -12 37401 31.569591999053955 0.5679864883422852 420.054443359375 0.19343653321266174 488.66009521484375 0.35602548718452454 0.8864634 0.19536124169826508 True -13 40278 31.53740882873535 0.5579571723937988 350.0909423828125 0.19103112816810608 487.0195617675781 0.35872018337249756 0.8895945 0.19282926619052887 True -14 43155 31.477848768234253 0.5542421340942383 419.1684875488281 0.26060086488723755 486.1107177734375 0.36049148440361023 0.89305323 0.188469797372818 True -15 46032 31.53349232673645 0.5651798248291016 370.843994140625 0.20800447463989258 485.47271728515625 0.36101654171943665 0.8932329 0.18716217577457428 True -16 48909 31.600693225860596 0.5532529354095459 348.470458984375 0.17453131079673767 486.4393310546875 0.35880279541015625 0.89552194 0.1835780292749405 True -17 51786 31.501996755599976 0.5500068664550781 350.43927001953125 0.24630258977413177 485.3301696777344 0.36194613575935364 0.8962577 0.18240498006343842 True -18 54663 31.472534894943237 0.5629017353057861 463.15234375 0.20015498995780945 485.9582824707031 0.3606715202331543 0.8975055 0.18181416392326355 True -19 57540 31.4603214263916 0.5667858123779297 354.4891357421875 0.15418463945388794 485.8857421875 0.3608867824077606 0.89616215 0.1837967038154602 False diff --git a/ENCSR652IZW/cherimoya.fold_2.performance.tsv b/ENCSR652IZW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2db0118914aed90d7d43a36011a8ffae167a672f..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -485.9582824707031 0.4229142963886261 0.3606715202331543 0.13070666790008545 0.897505521774292 0.8875410556793213 0.18181416392326355 \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_3.evaluate.json b/ENCSR652IZW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ecf2d1c7bbe333ace479b946a4b5e1e859160dd1..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155SVA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_3.fit.json b/ENCSR652IZW/cherimoya.fold_3.fit.json deleted file mode 100644 index 8717a1528919f008d8221f92dda5fce2af3115d3..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF155SVA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_3.log b/ENCSR652IZW/cherimoya.fold_3.log deleted file mode 100644 index 87b9799de84a8600dbc6f75a5d5970de540ea9b3..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.096325159072876 3.846975326538086 366.8985595703125 0.2151884138584137 506.6306457519531 0.28077298402786255 0.7677918 3.6872992515563965 True -1 5518 30.755128622055054 0.6365795135498047 450.63018798828125 0.37378597259521484 469.3791198730469 0.3298929035663605 0.8300013 1.0794010162353516 True -2 8277 30.877206325531006 0.5293030738830566 458.94970703125 0.2707350254058838 459.89105224609375 0.33924952149391174 0.8505464 0.3717763125896454 True -3 11036 30.741567134857178 0.5557379722595215 411.15533447265625 0.20751306414604187 457.29229736328125 0.3428083062171936 0.8584086 0.302548885345459 True -4 13795 30.862075567245483 0.538902759552002 424.0054626464844 0.42384064197540283 455.7806396484375 0.34402912855148315 0.86336315 0.26353874802589417 True -5 16554 30.789029359817505 0.5256936550140381 405.74420166015625 0.3024928867816925 454.421875 0.34564200043678284 0.86828595 0.24352237582206726 True -6 19313 30.783976316452026 2.588986396789551 395.19403076171875 0.20930975675582886 453.3828125 0.347380131483078 0.86888915 0.22644619643688202 True -7 22072 30.77877902984619 0.5919721126556396 423.3557434082031 0.3835754990577698 452.1264953613281 0.34854379296302795 0.87279814 0.22283709049224854 True -8 24831 30.13067388534546 1.3893382549285889 445.12579345703125 0.4501935839653015 450.97393798828125 0.35022976994514465 0.8775189 0.21988821029663086 True -9 27590 30.247503519058228 1.0890052318572998 362.0418701171875 0.324275940656662 450.12786865234375 0.3509971797466278 0.8802045 0.21754106879234314 True -10 30349 30.258211612701416 0.6479504108428955 341.1458435058594 0.33874475955963135 448.7484436035156 0.35359838604927063 0.8828273 0.2157507985830307 True -11 33108 30.226197481155396 0.546626091003418 450.8005065917969 0.25900864601135254 446.7092590332031 0.35677003860473633 0.88846815 0.20363113284111023 True -12 35867 30.159832000732422 0.5259952545166016 415.47100830078125 0.19776029884815216 446.3724365234375 0.3563373386859894 0.89073694 0.19918407499790192 True -13 38626 30.142088890075684 0.5485684871673584 404.9246520996094 0.1890714317560196 445.3710632324219 0.35768741369247437 0.8932515 0.19516439735889435 True -14 41385 30.246962785720825 0.565565824508667 444.00506591796875 0.1548602133989334 444.9186706542969 0.3580411970615387 0.8971639 0.1885196417570114 True -15 44144 30.257140636444092 0.5447285175323486 378.8665771484375 0.24566884338855743 444.4692687988281 0.35815152525901794 0.9005209 0.18183201551437378 True -16 46903 30.21721363067627 0.5287413597106934 424.0135803222656 0.21515381336212158 443.948974609375 0.35877376794815063 0.904771 0.1771399974822998 True -17 49662 30.170175790786743 0.5260927677154541 360.94622802734375 0.26059669256210327 444.5050048828125 0.3577258288860321 0.9043295 0.1760386973619461 False -18 52421 30.24028778076172 0.5195150375366211 393.94427490234375 0.10791563987731934 443.7832946777344 0.35925817489624023 0.90548515 0.17524601519107819 True -19 55180 30.221763134002686 0.5692248344421387 370.1316833496094 0.1707787662744522 444.10528564453125 0.35875725746154785 0.90497047 0.1749720573425293 False diff --git a/ENCSR652IZW/cherimoya.fold_3.performance.tsv b/ENCSR652IZW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1fd4db4bebb546e3d89fa7254a82aa1dbcca3390..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -443.7832946777344 0.4276190400123596 0.359258234500885 0.12253008037805557 0.9054851531982422 0.8816498517990112 0.17524601519107819 \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_4.evaluate.json b/ENCSR652IZW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 04255f5894f3fb52d7716085ba0c4466c877a7d2..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF155SVA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_4.fit.json b/ENCSR652IZW/cherimoya.fold_4.fit.json deleted file mode 100644 index 3de153d94345db1ff07a07f14383457dcfa0e6fa..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF155SVA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR652IZW/cherimoya.fold_4.log b/ENCSR652IZW/cherimoya.fold_4.log deleted file mode 100644 index 547b8ba776fa8e58f5704be143073a8d3bbeae3c..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2778 35.32416868209839 4.252035140991211 441.1716003417969 0.3763478100299835 484.3824157714844 0.2716679573059082 0.7694174 3.1081628799438477 True -1 5556 30.9582097530365 0.8756327629089355 379.15399169921875 0.2192520797252655 451.65618896484375 0.31881099939346313 0.8173734 0.8095020055770874 True -2 8334 30.982072591781616 0.6211328506469727 338.88580322265625 0.20046204328536987 444.3232116699219 0.3273240625858307 0.839639 0.34352394938468933 True -3 11112 31.006513118743896 0.5876460075378418 402.40472412109375 0.3623538911342621 441.1416015625 0.3311525583267212 0.84832567 0.31449583172798157 True -4 13890 31.045284271240234 0.6015229225158691 430.63372802734375 0.30232930183410645 439.7330322265625 0.3326963186264038 0.85461897 0.2612851560115814 True -5 16668 30.598495721817017 0.5933775901794434 441.276611328125 0.3621304929256439 438.4355773925781 0.33347517251968384 0.85877335 0.24517717957496643 True -6 19446 30.47163987159729 0.5932528972625732 387.42529296875 0.3580162525177002 436.48651123046875 0.3368283212184906 0.8618804 0.23415334522724152 True -7 22224 30.380401611328125 0.5929796695709229 338.5967102050781 0.4495944380760193 436.09991455078125 0.33653557300567627 0.86641455 0.23378106951713562 True -8 25002 30.312259435653687 0.5920898914337158 399.79925537109375 0.21349206566810608 435.2093811035156 0.33829793334007263 0.8690384 0.2263641208410263 True -9 27780 30.344921112060547 0.5913877487182617 399.40228271484375 0.23364850878715515 433.3087463378906 0.34201088547706604 0.87207556 0.21711531281471252 True -10 30558 30.338056802749634 1.4562230110168457 374.4491882324219 0.2620629668235779 433.2633972167969 0.34142065048217773 0.8764457 0.2193061113357544 True -11 33336 30.41367244720459 0.6150968074798584 394.0164489746094 0.14228634536266327 431.93609619140625 0.3438575565814972 0.8820853 0.20477189123630524 True -12 36114 30.40310788154602 0.6202654838562012 384.72076416015625 0.1311001032590866 430.9143981933594 0.3450334370136261 0.8854967 0.19492776691913605 True -13 38892 30.39698839187622 0.6095497608184814 350.67333984375 0.1252925544977188 430.7930908203125 0.34457165002822876 0.8891419 0.1838316172361374 True -14 41670 30.36989450454712 0.5945703983306885 412.03802490234375 0.21993093192577362 429.8905944824219 0.3463735282421112 0.8933179 0.17574049532413483 True -15 44448 30.35031008720398 0.5947830677032471 368.62432861328125 0.1059017926454544 428.7269592285156 0.348183274269104 0.8966668 0.16860410571098328 True -16 47226 30.37544298171997 0.9686808586120605 421.3271789550781 0.1684795618057251 428.9318542480469 0.34785178303718567 0.90116817 0.16172385215759277 True -17 50004 30.372580528259277 0.5851407051086426 404.5135498046875 0.25401604175567627 429.46978759765625 0.3465338349342346 0.90275866 0.15707449615001678 True -18 52782 30.388736963272095 0.6013336181640625 394.4912109375 0.1455739140510559 428.88824462890625 0.34841135144233704 0.9028273 0.15631864964962006 True -19 55560 30.37586736679077 0.5899083614349365 362.59423828125 0.11144725978374481 429.5535583496094 0.34658190608024597 0.90279996 0.155978262424469 False diff --git a/ENCSR652IZW/cherimoya.fold_4.performance.tsv b/ENCSR652IZW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 983faaa03977b21258c54850848344bfe6a88ab6..0000000000000000000000000000000000000000 --- a/ENCSR652IZW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -428.88824462890625 0.4358184337615967 0.34841135144233704 0.11540903151035309 0.9028273224830627 0.8816548585891724 0.15631864964962006 \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_0.evaluate.json b/ENCSR653ISV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e5f10f0fd0e84842f56675ce5e12bd4f7aa23f1d..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF166RFN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_0.fit.json b/ENCSR653ISV/cherimoya.fold_0.fit.json deleted file mode 100644 index 5697fa6b77a41407c64fe6b78781a6fdfc3b795e..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF166RFN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_0.log b/ENCSR653ISV/cherimoya.fold_0.log deleted file mode 100644 index 3810981b2c20507f6767bb3b08a7a8c785a5e87b..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 35.88882923126221 4.404909610748291 677.5730590820312 0.42276912927627563 972.9011840820312 0.28574299812316895 0.72998327 6.8191447257995605 True -1 5488 30.511415243148804 2.8961267471313477 586.086669921875 0.451635479927063 892.0004272460938 0.34411537647247314 0.7922226 1.462814450263977 True -2 8232 30.211538553237915 20.96878433227539 798.6832885742188 0.37733280658721924 879.671875 0.3508247137069702 0.80619633 0.7249109745025635 True -3 10976 30.655936002731323 12.907076597213745 671.674072265625 0.3771246671676636 872.101318359375 0.35774877667427063 0.8200513 0.587610125541687 True -4 13720 30.19425892829895 22.537087440490723 849.4507446289062 0.49468207359313965 866.749267578125 0.36182302236557007 0.8244698 0.6558552980422974 True -5 16464 30.29848551750183 6.726626634597778 642.821044921875 0.47001251578330994 865.5802612304688 0.3625316917896271 0.8292577 0.5290718078613281 True -6 19208 30.152573585510254 0.5356190204620361 690.0482177734375 0.2690281867980957 861.4567260742188 0.3665609061717987 0.83600533 0.4783709645271301 True -7 21952 30.227834463119507 0.5238029956817627 706.9117431640625 0.577743411064148 861.6145629882812 0.3646549582481384 0.8435459 0.42271292209625244 True -8 24696 30.18601417541504 0.5782084465026855 733.4246215820312 0.3473528325557709 857.595703125 0.36835819482803345 0.8477208 0.40142565965652466 True -9 27440 30.184381008148193 1.3557579517364502 695.6072387695312 0.3997637927532196 855.5235595703125 0.36998286843299866 0.8515481 0.3820345997810364 True -10 30184 30.163318157196045 0.5239989757537842 772.469970703125 0.2219085395336151 853.5709228515625 0.37183240056037903 0.8542516 0.370369553565979 True -11 32928 30.653948307037354 0.5368423461914062 676.0960083007812 0.31401586532592773 852.3405151367188 0.3728748559951782 0.8588062 0.3535221815109253 True -12 35672 30.257107257843018 0.5299699306488037 820.4241333007812 0.49959224462509155 850.276611328125 0.3746225833892822 0.86025846 0.34547823667526245 True -13 38416 30.225284814834595 0.5201442241668701 837.8328247070312 0.24992609024047852 848.3402099609375 0.37623879313468933 0.8641801 0.325695663690567 True -14 41160 30.189298152923584 0.5361831188201904 697.792236328125 0.31829458475112915 849.4910278320312 0.3746948540210724 0.86721927 0.3181712031364441 True -15 43904 30.275591611862183 0.5278947353363037 806.745361328125 0.26534050703048706 846.0128173828125 0.379183828830719 0.8705513 0.3083537220954895 True -16 46648 30.179800748825073 0.5196852684020996 643.4720458984375 0.3450673222541809 845.9378051757812 0.3784342110157013 0.8707148 0.3053409159183502 True -17 49392 30.243700981140137 0.5169637203216553 769.0450439453125 0.22626088559627533 846.835205078125 0.377716988325119 0.8702272 0.30719390511512756 False -18 52136 30.250093460083008 0.5265240669250488 690.511474609375 0.16163179278373718 849.0169677734375 0.37567338347435 0.86781245 0.31042754650115967 False -19 54880 30.22493839263916 0.5260658264160156 692.4302978515625 0.22568073868751526 847.8016967773438 0.3772399127483368 0.8673559 0.3134397268295288 False diff --git a/ENCSR653ISV/cherimoya.fold_0.performance.tsv b/ENCSR653ISV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5f2ee902d1d5ba09e9140872ca5440466968ab2d..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -845.9378051757812 0.35636866092681885 0.3784342110157013 0.20274516940116882 0.8707147836685181 0.8342764973640442 0.3053409159183502 \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_1.evaluate.json b/ENCSR653ISV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a2c328628f5bbb012c5bb5c1c7e86e52eef4eddb..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF166RFN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_1.fit.json b/ENCSR653ISV/cherimoya.fold_1.fit.json deleted file mode 100644 index e2e40079761016b8c00c77c31440b61fd8e40333..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF166RFN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_1.log b/ENCSR653ISV/cherimoya.fold_1.log deleted file mode 100644 index 94741ae2bef627d9f3c4e7c671b1db0186b1507b..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 34.188074588775635 4.434478282928467 793.9990234375 0.4195810556411743 1123.333251953125 0.30023863911628723 0.75674456 7.237594127655029 True -1 5418 29.92372179031372 0.7677047252655029 649.70703125 0.6252082586288452 1029.2861328125 0.36228418350219727 0.81632775 1.7562671899795532 True -2 8127 29.85614323616028 0.7787714004516602 728.768310546875 0.453390896320343 1011.4734497070312 0.37019607424736023 0.8360689 0.8616451025009155 True -3 10836 29.81226420402527 0.7410519123077393 853.167236328125 0.5915314555168152 999.75390625 0.378958135843277 0.8410568 0.7336899638175964 True -4 13545 29.801939487457275 0.7544207572937012 829.4555053710938 0.8088647723197937 996.8755493164062 0.3798617720603943 0.84977263 0.6507681012153625 True -5 16254 30.87138342857361 0.7559983730316162 706.5336303710938 0.4400339424610138 993.2227783203125 0.38284069299697876 0.8548982 0.5931186079978943 True -6 18963 29.836552143096924 0.7589869499206543 659.37353515625 0.35122305154800415 993.5586547851562 0.3821652829647064 0.85734755 0.5634577870368958 True -7 21672 29.79060435295105 0.7575418949127197 707.0374145507812 0.4229013919830322 989.670166015625 0.38585731387138367 0.8632464 0.49622994661331177 True -8 24381 29.77653193473816 0.7492494583129883 866.8953857421875 0.38499727845191956 986.8673095703125 0.38771533966064453 0.8680158 0.4766756296157837 True -9 27090 29.79976511001587 0.7589209079742432 669.3568725585938 0.4753763675689697 984.1019287109375 0.38869503140449524 0.86992973 0.4428562521934509 True -10 29799 29.765750408172607 0.7589225769042969 653.65380859375 0.48267605900764465 980.00244140625 0.3928389549255371 0.87478656 0.4100955128669739 True -11 32508 29.80854892730713 0.7485909461975098 844.6859130859375 0.37884098291397095 976.0474243164062 0.39624011516571045 0.8778434 0.3812124729156494 True -12 35217 29.83655309677124 0.7566647529602051 721.5721435546875 0.38605567812919617 975.7125244140625 0.39550158381462097 0.8816235 0.3617522418498993 True -13 37926 29.819135904312134 0.7571432590484619 895.9400634765625 0.37772172689437866 974.5646362304688 0.39594677090644836 0.8845604 0.3510489761829376 True -14 40635 29.835126161575317 0.770207405090332 721.7469482421875 0.2147296965122223 972.4124145507812 0.39729467034339905 0.88653016 0.3380756974220276 True -15 43344 29.87590527534485 0.7564184665679932 568.523681640625 0.3102763295173645 972.6668090820312 0.39636537432670593 0.8895051 0.3306693136692047 True -16 46053 29.864786386489868 0.7659523487091064 605.2166137695312 0.25496503710746765 969.7617797851562 0.39955565333366394 0.88750416 0.33068111538887024 False -17 48762 29.803393125534058 1.0533912181854248 693.4844970703125 0.2054305076599121 972.0983276367188 0.3967265784740448 0.8876029 0.3308091163635254 False -18 51471 29.829148054122925 1.5718598365783691 794.6676025390625 0.1939716935157776 974.2836303710938 0.39444029331207275 0.886574 0.3353990614414215 False -19 54180 29.802006721496582 25.96857714653015 655.4622802734375 0.1509987711906433 972.4456787109375 0.39722874760627747 0.8852144 0.3360810875892639 False diff --git a/ENCSR653ISV/cherimoya.fold_1.performance.tsv b/ENCSR653ISV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3cdc9bf436723b4447add1408b51b4a52c19ffc5..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -972.6668090820312 0.33559051156044006 0.39636534452438354 0.22850430011749268 0.8895050883293152 0.8740932941436768 0.3306693136692047 \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_2.evaluate.json b/ENCSR653ISV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bfdf6929624a06d558e0ae1dc347e4748870bbec..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF166RFN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_2.fit.json b/ENCSR653ISV/cherimoya.fold_2.fit.json deleted file mode 100644 index 3f526b5d31eaad8abcefb150d3cd1110bb6723d5..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF166RFN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_2.log b/ENCSR653ISV/cherimoya.fold_2.log deleted file mode 100644 index 0ac3414572399850e25c7e1fff179f1041bfcc3f..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2917 36.40099334716797 3.841658115386963 798.803955078125 0.5929478406906128 1044.7666015625 0.29791921377182007 0.72706866 6.3695526123046875 True -1 5834 32.16951608657837 0.6006443500518799 681.8765869140625 0.36434513330459595 958.3743286132812 0.35182881355285645 0.79002047 1.356329083442688 True -2 8751 32.2243218421936 0.5563459396362305 916.01904296875 0.5504945516586304 941.0859985351562 0.3616678714752197 0.80575806 0.7503580451011658 True -3 11668 32.13037824630737 0.5486562252044678 610.0453491210938 0.3068860173225403 937.3338012695312 0.36350879073143005 0.81503004 0.6132639646530151 True -4 14585 32.192264795303345 0.5538320541381836 774.1898803710938 0.3917672634124756 934.0658569335938 0.36536791920661926 0.82155305 0.6263247728347778 True -5 17502 32.2242648601532 0.9775204658508301 730.050048828125 0.36359065771102905 928.1270751953125 0.37177032232284546 0.8251535 0.5932446122169495 True -6 20419 32.199142932891846 0.6540429592132568 753.5159301757812 0.23273807764053345 927.9495239257812 0.3715747594833374 0.83077484 0.5379247069358826 True -7 23336 32.22316598892212 0.5500848293304443 633.5596313476562 0.3251844644546509 924.83349609375 0.37395185232162476 0.83456916 0.5211185812950134 True -8 26253 32.16716170310974 0.5502610206604004 799.4177856445312 0.44453415274620056 924.7059936523438 0.37338539958000183 0.8428086 0.4670804738998413 True -9 29170 32.17836356163025 0.5656006336212158 797.0821533203125 0.5651230812072754 920.2019653320312 0.37779349088668823 0.84693795 0.43354615569114685 True -10 32087 32.22555112838745 0.5527927875518799 711.9646606445312 0.2753598093986511 917.6369018554688 0.37886178493499756 0.8500436 0.4115065336227417 True -11 35004 32.16271090507507 6.240376949310303 795.6773071289062 0.394594669342041 916.4357299804688 0.38027721643447876 0.8520984 0.4004739820957184 True -12 37921 32.22366428375244 2.8486523628234863 666.4497680664062 0.41314896941185 912.5362548828125 0.38281577825546265 0.855906 0.3852347135543823 True -13 40838 32.18332624435425 0.5589923858642578 694.25927734375 0.2671205401420593 911.6509399414062 0.383182555437088 0.8590971 0.3640076518058777 True -14 43755 32.20836901664734 0.5468544960021973 699.5034790039062 0.36181023716926575 913.0369873046875 0.3814149498939514 0.8608572 0.3516353368759155 True -15 46672 32.175352811813354 0.5546369552612305 803.010986328125 0.13513487577438354 909.99853515625 0.38471752405166626 0.8631879 0.34375646710395813 True -16 49589 32.184338092803955 0.5476367473602295 690.8687744140625 0.24854077398777008 909.4783935546875 0.38470372557640076 0.861803 0.3416261374950409 False -17 52506 32.23236441612244 0.5475714206695557 647.662353515625 0.2898150086402893 911.2472534179688 0.3825402855873108 0.8608689 0.3461516201496124 False -18 55423 32.18462586402893 0.5405948162078857 699.9000244140625 0.200394868850708 911.8446044921875 0.3823243975639343 0.85826606 0.3513929545879364 False -19 58340 32.186856746673584 0.5468080043792725 692.049072265625 0.22294113039970398 911.6174926757812 0.3826218247413635 0.857302 0.3555629551410675 False diff --git a/ENCSR653ISV/cherimoya.fold_2.performance.tsv b/ENCSR653ISV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0d592f089a5efa1ba0426d2c9fefb2d03b968a9d..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -909.99853515625 0.3458954095840454 0.38471752405166626 0.21538189053535461 0.8631879091262817 0.8390615582466125 0.34375646710395813 \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_3.evaluate.json b/ENCSR653ISV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e7d7da2c881a458c9045fc9b47177b9faa034d5f..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF166RFN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_3.fit.json b/ENCSR653ISV/cherimoya.fold_3.fit.json deleted file mode 100644 index 531e6ed5626abf2559934fa51ae4db704b587f79..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF166RFN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_3.log b/ENCSR653ISV/cherimoya.fold_3.log deleted file mode 100644 index 8e9b3fd2e7065d8aa5548f9133f3a449b51266ee..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 35.15004801750183 5.0443503856658936 741.1707763671875 0.4900951087474823 955.8047485351562 0.3004402220249176 0.7104358 6.370381832122803 True -1 5530 30.256078004837036 0.6564846038818359 685.782958984375 0.4368175268173218 881.703125 0.35375410318374634 0.775967 1.650368571281433 True -2 8295 30.394339561462402 0.5804638862609863 964.9583740234375 0.4845718741416931 867.0127563476562 0.3627367913722992 0.80046284 0.8859157562255859 True -3 11060 30.424926042556763 1.3517796993255615 689.89599609375 0.5809809565544128 864.2281494140625 0.3633936047554016 0.80781597 0.8119251132011414 True -4 13825 30.482449531555176 0.6033787727355957 734.9556884765625 0.47021234035491943 863.6098022460938 0.362236887216568 0.8111432 0.7578561305999756 True -5 16590 30.508400678634644 0.5714001655578613 799.07470703125 0.4423618018627167 860.74951171875 0.3667231500148773 0.811925 0.7310770153999329 True -6 19355 30.45247983932495 0.5724685192108154 787.4834594726562 0.5749772787094116 857.07958984375 0.3709578514099121 0.81559664 0.6779845356941223 True -7 22120 30.433857202529907 0.57769775390625 934.43017578125 0.45223408937454224 857.4091186523438 0.3691771328449249 0.82179165 0.5773559212684631 True -8 24885 30.40270185470581 0.6033487319946289 791.262939453125 0.26588723063468933 854.3385009765625 0.37184372544288635 0.82677263 0.5489659309387207 True -9 27650 30.447858810424805 0.5836381912231445 736.0499877929688 0.5913668870925903 853.3115844726562 0.3723292946815491 0.8287758 0.5475212335586548 True -10 30415 30.415082693099976 0.616436243057251 658.8905029296875 0.2749113440513611 851.6871948242188 0.3731650114059448 0.8344612 0.4991138279438019 True -11 33180 30.462363481521606 0.5686085224151611 700.0018310546875 0.28567999601364136 848.8295288085938 0.37582406401634216 0.83886784 0.48186567425727844 True -12 35945 30.487658977508545 0.5803134441375732 756.8973388671875 0.31260213255882263 845.7070922851562 0.3791404962539673 0.8429658 0.45935577154159546 True -13 38710 30.442415714263916 0.6126291751861572 571.0655517578125 0.1963970959186554 846.5260620117188 0.37732914090156555 0.84840137 0.4254438281059265 True -14 41475 30.606858491897583 0.6171290874481201 830.1046142578125 0.24769432842731476 842.51220703125 0.38122472167015076 0.85363376 0.4012259840965271 True -15 44240 30.4971604347229 2.389732837677002 766.1710205078125 0.34332364797592163 842.4376831054688 0.378963828086853 0.85708016 0.3809395730495453 True -16 47005 30.40686345100403 2.4840662479400635 759.8055419921875 0.2521766126155853 842.6051025390625 0.37945982813835144 0.86080897 0.362542986869812 True -17 49770 30.409528017044067 1.9050984382629395 678.4417724609375 0.17648354172706604 841.2786865234375 0.38116490840911865 0.86109567 0.35790207982063293 True -18 52535 30.522940397262573 1.49015474319458 580.1307373046875 0.21222063899040222 842.4908447265625 0.37917107343673706 0.86105746 0.3562678098678589 False -19 55300 30.50921893119812 1.2646074295043945 717.6737060546875 0.20880278944969177 842.97119140625 0.37913259863853455 0.859389 0.3561772108078003 False diff --git a/ENCSR653ISV/cherimoya.fold_3.performance.tsv b/ENCSR653ISV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 86fde36693e4499e060ba4cb36e719fac00fac17..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -841.2786865234375 0.3545769155025482 0.38116493821144104 0.20529484748840332 0.861095666885376 0.817794919013977 0.35790207982063293 \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_4.evaluate.json b/ENCSR653ISV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1e290d38033ee710893de16fe2ad00e8e84b3ae9..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF166RFN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_4.fit.json b/ENCSR653ISV/cherimoya.fold_4.fit.json deleted file mode 100644 index 3857fb13a57545a5b9e097ea9ad0a808dbe5343a..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF166RFN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ISV/cherimoya.fold_4.log b/ENCSR653ISV/cherimoya.fold_4.log deleted file mode 100644 index e6aa9fbf8965dcf42be3cb4a2f6964976936ce22..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2769 36.624030113220215 4.065011739730835 735.350341796875 0.5899093151092529 876.2589721679688 0.2783292829990387 0.7258768 6.907739639282227 True -1 5538 30.00994873046875 0.5966730117797852 836.3026123046875 0.49059316515922546 809.0551147460938 0.33255913853645325 0.7841861 1.4064991474151611 True -2 8307 30.42930507659912 1.3082613945007324 680.7304077148438 0.43921607732772827 796.2064819335938 0.34011417627334595 0.80261904 0.6992859840393066 True -3 11076 30.46072268486023 0.760460615158081 793.233154296875 0.511238694190979 790.974853515625 0.3434695899486542 0.8105506 0.59087735414505 True -4 13845 30.480865001678467 0.5520317554473877 785.0895385742188 0.49518024921417236 788.8681030273438 0.34586983919143677 0.81818753 0.5498691201210022 True -5 16614 30.435108423233032 0.5506618022918701 792.6519775390625 0.6006504893302917 786.0838012695312 0.3484695255756378 0.82513636 0.5144458413124084 True -6 19383 30.384598970413208 0.5513181686401367 755.5694580078125 0.503839373588562 782.83349609375 0.3507128655910492 0.8314536 0.43072015047073364 True -7 22152 30.429134368896484 0.5499355792999268 820.9744873046875 0.47079020738601685 779.8988647460938 0.35403305292129517 0.83687913 0.3917464017868042 True -8 24921 30.496937036514282 0.5642585754394531 737.9862670898438 0.3414303660392761 780.4915771484375 0.3534347414970398 0.8418523 0.37394970655441284 True -9 27690 30.44798731803894 0.5619673728942871 724.9398803710938 0.26821643114089966 777.2265014648438 0.35585924983024597 0.84663546 0.3550558090209961 True -10 30459 30.437086820602417 0.5558285713195801 872.1511840820312 0.32830214500427246 775.6148681640625 0.35699179768562317 0.8503806 0.3355657756328583 True -11 33228 30.475593090057373 0.5587751865386963 622.3275146484375 0.3359445333480835 774.5809326171875 0.3572824001312256 0.85397106 0.32366159558296204 True -12 35997 30.449198722839355 0.5903403759002686 718.869384765625 0.2652967870235443 774.4351196289062 0.35767388343811035 0.86004966 0.314710408449173 True -13 38766 30.411438941955566 0.5632426738739014 703.5106201171875 0.27269503474235535 773.7792358398438 0.35775744915008545 0.86369646 0.30250275135040283 True -14 41535 30.41191339492798 0.5642764568328857 700.4078369140625 0.1952088475227356 770.0052490234375 0.36170318722724915 0.8677136 0.2951546311378479 True -15 44304 30.452935695648193 0.5947351455688477 760.213134765625 0.28520822525024414 771.293212890625 0.3596748113632202 0.86978316 0.2874247133731842 True -16 47073 30.44939088821411 0.5668659210205078 715.2401123046875 0.17208829522132874 770.1884155273438 0.3608308434486389 0.8723756 0.28220123052597046 True -17 49842 30.4089298248291 1.4398999214172363 639.4971923828125 0.364778071641922 772.2799072265625 0.3580400049686432 0.8727904 0.2830926775932312 True -18 52611 30.418961763381958 0.5680348873138428 720.9541015625 0.2735275626182556 770.7669677734375 0.3605712950229645 0.8706309 0.28649505972862244 False -19 55380 30.395993947982788 0.5562751293182373 535.5740356445312 0.2291349470615387 771.4656372070312 0.35998013615608215 0.86932963 0.2891122102737427 False diff --git a/ENCSR653ISV/cherimoya.fold_4.performance.tsv b/ENCSR653ISV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 976188e024dce2e6d38ba32b7aecbf061971c3e0..0000000000000000000000000000000000000000 --- a/ENCSR653ISV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -772.2799072265625 0.3732703626155853 0.3580400049686432 0.18617062270641327 0.8727903962135315 0.8275769948959351 0.2830926775932312 \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_0.evaluate.json b/ENCSR653ZWW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9ef0fbd6a42ee14bd529242206f920186b8d81f7..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654KWF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_0.fit.json b/ENCSR653ZWW/cherimoya.fold_0.fit.json deleted file mode 100644 index f0b7dc0dce0a8cf60a121db1740a0157a4039ec3..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF654KWF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_0.log b/ENCSR653ZWW/cherimoya.fold_0.log deleted file mode 100644 index 366b4ebbe89a67e65f943cd4b0bf018bfd9edd57..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2277 30.670285940170288 3.7970504760742188 481.2757568359375 0.4366014003753662 630.0738525390625 0.6253231763839722 0.6314577 7.910933017730713 True -1 4554 25.054713249206543 16.43580150604248 404.1707458496094 0.22792652249336243 528.4489135742188 0.7129583954811096 0.74275166 1.138600468635559 True -2 6831 25.024110555648804 0.45380330085754395 399.01568603515625 0.21528145670890808 507.6603698730469 0.734053909778595 0.7650897 0.43234938383102417 True -3 9108 25.10730242729187 0.45058155059814453 431.52191162109375 0.2116779386997223 499.7174072265625 0.7418955564498901 0.7827187 0.3410564661026001 True -4 11385 27.08042335510254 18.245067596435547 433.4404296875 0.19599103927612305 498.9915466308594 0.7429604530334473 0.78413546 0.31441178917884827 True -5 13662 25.07059383392334 0.4527881145477295 414.9809265136719 0.2474241554737091 497.01202392578125 0.74574214220047 0.79238945 0.28600752353668213 True -6 15939 25.071470737457275 0.4502389430999756 468.041015625 0.3001711964607239 495.1387939453125 0.7477361559867859 0.8003295 0.25704425573349 True -7 18216 25.076756715774536 0.44807887077331543 438.679931640625 0.2214348018169403 493.36468505859375 0.749298095703125 0.8033445 0.2585034966468811 True -8 20493 25.08369779586792 0.48042774200439453 465.554443359375 0.24093568325042725 492.2449645996094 0.7511696219444275 0.80753314 0.2532057464122772 True -9 22770 25.08908438682556 12.947376489639282 498.80096435546875 0.19550953805446625 491.1831359863281 0.7525578141212463 0.81065804 0.2538144290447235 True -10 25047 25.027523517608643 0.4470236301422119 438.13092041015625 0.17790281772613525 489.73828125 0.7543015480041504 0.8172699 0.23700051009655 True -11 27324 25.175774097442627 0.4522366523742676 460.7288818359375 0.16532811522483826 488.6778259277344 0.7554455399513245 0.8184593 0.23723112046718597 True -12 29601 25.04453444480896 0.4500865936279297 487.59735107421875 0.18141323328018188 487.52166748046875 0.7567886710166931 0.8237533 0.22077049314975739 True -13 31878 25.07944416999817 0.4533195495605469 434.47821044921875 0.11446715891361237 486.5978088378906 0.7578251361846924 0.8317855 0.20347003638744354 True -14 34155 25.0276837348938 12.605578184127808 417.93206787109375 0.208784818649292 485.7232971191406 0.7586753368377686 0.83600676 0.18808874487876892 True -15 36432 25.11112880706787 0.4679427146911621 417.5555114746094 0.1516883373260498 485.61669921875 0.758966863155365 0.83878833 0.17709773778915405 True -16 38709 26.62131905555725 21.122363805770874 438.57464599609375 0.1573181003332138 485.40948486328125 0.7589914202690125 0.8418392 0.1661406308412552 True -17 40986 25.090825080871582 1.610142707824707 453.21307373046875 0.061854876577854156 485.6676025390625 0.7586209177970886 0.83998334 0.16289374232292175 False -18 43263 25.057571411132812 0.4570753574371338 416.878173828125 0.05651209130883217 485.99627685546875 0.7582511901855469 0.8421402 0.16171571612358093 True -19 45540 25.005494594573975 0.44745349884033203 469.80511474609375 0.09237030148506165 486.18267822265625 0.7579901218414307 0.8386496 0.1628267467021942 False diff --git a/ENCSR653ZWW/cherimoya.fold_0.performance.tsv b/ENCSR653ZWW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 046b5436a41fb9509df87cf66e5fcd3087e6adba..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -485.99627685546875 0.19956551492214203 0.7582511901855469 0.36162465810775757 0.8421401977539062 0.7802749276161194 0.16171571612358093 \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_1.evaluate.json b/ENCSR653ZWW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 923df406982aad6718d8607a9579bb243c664bf5..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654KWF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_1.fit.json b/ENCSR653ZWW/cherimoya.fold_1.fit.json deleted file mode 100644 index bf6f14b571a9e3f29865662f4c918f9f9e7b3dcf..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF654KWF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_1.log b/ENCSR653ZWW/cherimoya.fold_1.log deleted file mode 100644 index 267c26edc55d3439226f25c084aaa4a746f0f57d..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2230 31.97805404663086 3.5752828121185303 490.66015625 0.3261713683605194 714.3886108398438 0.6308044195175171 0.6207423 8.386306762695312 True -1 4460 24.532143115997314 1.7078680992126465 453.03985595703125 0.4282921254634857 585.6604614257812 0.7263752818107605 0.71361643 1.4056456089019775 True -2 6690 24.822872638702393 0.5963282585144043 487.93017578125 0.3411598801612854 562.4486694335938 0.7487127184867859 0.7365824 0.7029903531074524 True -3 8920 24.477320194244385 0.5954627990722656 400.87158203125 0.2091616839170456 556.4603881835938 0.7540282011032104 0.75481933 0.535723090171814 True -4 11150 24.570463180541992 0.59818434715271 540.680908203125 0.3514517843723297 551.1097412109375 0.7602564692497253 0.7683716 0.5298706293106079 True -5 13380 24.517335653305054 2.00116229057312 465.4520568847656 0.2800428867340088 548.8287963867188 0.7627118825912476 0.7782967 0.40552622079849243 True -6 15610 24.532685041427612 0.5945992469787598 436.4869384765625 0.25368595123291016 546.6721801757812 0.7642107009887695 0.7850505 0.38245707750320435 True -7 17840 24.517802000045776 0.5907471179962158 450.57177734375 0.2379080057144165 545.084228515625 0.7659790515899658 0.7863189 0.3736349642276764 True -8 20070 24.57569646835327 0.6030645370483398 419.585205078125 0.18553988635540009 543.591064453125 0.7675982713699341 0.7921414 0.35921964049339294 True -9 22300 24.54722809791565 0.5927608013153076 417.73779296875 0.16203127801418304 540.9125366210938 0.7701626420021057 0.802211 0.31463000178337097 True -10 24530 24.581063270568848 0.5952186584472656 424.52960205078125 0.1685284972190857 539.5704345703125 0.7718941569328308 0.8071963 0.29646360874176025 True -11 26760 24.514671325683594 0.5906331539154053 441.7886962890625 0.1713554412126541 538.1336059570312 0.7731037139892578 0.8168065 0.2792746424674988 True -12 28990 24.463693380355835 2.712585210800171 450.1162414550781 0.18407630920410156 536.5870971679688 0.7747052311897278 0.8212302 0.26867255568504333 True -13 31220 24.53835701942444 0.5898253917694092 448.54302978515625 0.19342118501663208 535.3643188476562 0.7758983969688416 0.8292311 0.24346350133419037 True -14 33450 24.52017307281494 0.5918021202087402 456.736083984375 0.1350807547569275 534.0758056640625 0.7771936058998108 0.83484876 0.23319324851036072 True -15 35680 24.51827883720398 1.2731542587280273 433.6715087890625 0.09026089310646057 533.4136962890625 0.7779659032821655 0.83830655 0.2144857794046402 True -16 37910 24.548314332962036 0.5881807804107666 424.129150390625 0.11242738366127014 533.24072265625 0.7781767249107361 0.84388274 0.19773924350738525 True -17 40140 24.546347856521606 0.5890243053436279 402.8248291015625 0.09632724523544312 533.3507690429688 0.7780455350875854 0.8431858 0.18823829293251038 False -18 42370 24.476583003997803 0.5875780582427979 442.2071533203125 0.07510201632976532 533.5213623046875 0.7776523232460022 0.84172857 0.18362614512443542 False -19 44600 24.521616458892822 0.5971753597259521 434.120849609375 0.071929931640625 533.7042846679688 0.7773400545120239 0.8404582 0.18395094573497772 False diff --git a/ENCSR653ZWW/cherimoya.fold_1.performance.tsv b/ENCSR653ZWW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 56eb498d3efc4faf0cfbafcac66b780e5e12bfb8..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -533.24072265625 0.18403542041778564 0.7781767249107361 0.39328092336654663 0.8438827395439148 0.8053740859031677 0.19773924350738525 \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_2.evaluate.json b/ENCSR653ZWW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 48f88f2c31137d963c153ea74dc305e9c6c7823a..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654KWF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_2.fit.json b/ENCSR653ZWW/cherimoya.fold_2.fit.json deleted file mode 100644 index 957af4e24ed21aa80fa9f64c9452aad64221255b..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF654KWF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_2.log b/ENCSR653ZWW/cherimoya.fold_2.log deleted file mode 100644 index 260195f6a8ce64b58b4249971e78f258fca548a2..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2362 30.662083864212036 4.058484077453613 477.7908020019531 0.2642843723297119 643.4608764648438 0.636055052280426 0.62346184 7.0946526527404785 True -1 4724 25.970317363739014 0.48744654655456543 427.0981140136719 0.19522731006145477 546.8008422851562 0.7158045172691345 0.73136616 1.095670461654663 True -2 7086 26.12496304512024 27.643481016159058 464.7945556640625 0.18619728088378906 523.3463745117188 0.7397312521934509 0.7692415 0.4953758716583252 True -3 9448 26.75631356239319 0.48808979988098145 464.022216796875 0.15908873081207275 516.8237915039062 0.7454003691673279 0.78261167 0.32599660754203796 True -4 11810 25.999895334243774 0.48009562492370605 486.4126281738281 0.2494533658027649 514.5232543945312 0.7473985552787781 0.7890604 0.39282405376434326 True -5 14172 25.661139011383057 1.6386101245880127 449.43017578125 0.27080947160720825 513.9205932617188 0.7482603192329407 0.7864712 0.26055487990379333 False -6 16534 25.502901077270508 1.488692045211792 419.0618896484375 0.16788934171199799 511.2739562988281 0.7513728141784668 0.7971966 0.26357704401016235 True -7 18896 26.418590545654297 1.9209108352661133 421.5427551269531 0.2622568905353546 510.0130615234375 0.752816379070282 0.80373436 0.2545919716358185 True -8 21258 25.527631282806396 12.907963752746582 443.3063049316406 0.17887327075004578 508.9908142089844 0.7540084719657898 0.8047019 0.27020394802093506 True -9 23620 30.470247745513916 3.1484081745147705 456.0762939453125 0.15328125655651093 507.1025085449219 0.755962073802948 0.813009 0.2518649101257324 True -10 25982 25.4827401638031 2.0704147815704346 474.47900390625 0.17301997542381287 505.7119140625 0.7574429512023926 0.8169841 0.23558638989925385 True -11 28344 25.52621054649353 0.7366929054260254 417.95703125 0.13443973660469055 504.3711853027344 0.7588786482810974 0.8192104 0.23015061020851135 True -12 30706 25.697505235671997 24.848710536956787 440.40802001953125 0.2377239167690277 503.51763916015625 0.760040283203125 0.8236564 0.2209671586751938 True -13 33068 25.64822483062744 0.4682283401489258 432.8240661621094 0.15459492802619934 502.4776306152344 0.7610588669776917 0.8300955 0.20590604841709137 True -14 35430 25.710881233215332 0.4618668556213379 455.2615966796875 0.17590506374835968 501.7845153808594 0.7619274854660034 0.83293015 0.19898022711277008 True -15 37792 25.543154001235962 0.4598863124847412 462.44207763671875 0.1450113207101822 501.3074645996094 0.7623730897903442 0.8348606 0.1903059184551239 True -16 40154 25.46799659729004 0.462982177734375 430.2391357421875 0.13153153657913208 501.15582275390625 0.7626258730888367 0.8375259 0.18229283392429352 True -17 42516 25.389228343963623 0.4588296413421631 433.50274658203125 0.09998995065689087 501.16558837890625 0.7624949812889099 0.8381734 0.1769859790802002 True -18 44878 25.383230447769165 0.4533045291900635 405.1781005859375 0.08954158425331116 501.4649658203125 0.7620770931243896 0.83582747 0.17788571119308472 False -19 47240 25.424245357513428 0.4582688808441162 421.9192199707031 0.05631233751773834 501.7005310058594 0.7618438601493835 0.8335109 0.17871558666229248 False diff --git a/ENCSR653ZWW/cherimoya.fold_2.performance.tsv b/ENCSR653ZWW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 74bc79f1972e5568e753ebaaf86837c6524fdc99..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -501.16558837890625 0.19543638825416565 0.7624951004981995 0.37197715044021606 0.8381733894348145 0.7820514440536499 0.1769859790802002 \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_3.evaluate.json b/ENCSR653ZWW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 66b17e63acd22e6341e9cbe4972a9874d97ba7cc..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654KWF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_3.fit.json b/ENCSR653ZWW/cherimoya.fold_3.fit.json deleted file mode 100644 index f599cc58beb7da64889c4c09ed3149c9db58d5b9..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF654KWF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_3.log b/ENCSR653ZWW/cherimoya.fold_3.log deleted file mode 100644 index 83253a3f3016e04227666b54a0ad77d49fe6311d..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2306 30.002782344818115 3.8074095249176025 425.0965270996094 0.3437434732913971 650.886474609375 0.6271141171455383 0.60889924 7.9767913818359375 True -1 4612 25.42650532722473 0.45711803436279297 420.39154052734375 0.29421621561050415 541.6755981445312 0.7205808758735657 0.6934282 1.1860978603363037 True -2 6918 25.400474309921265 0.4499979019165039 461.11712646484375 0.2679149806499481 520.535400390625 0.7398069500923157 0.71595544 0.49766111373901367 True -3 9224 25.414947748184204 21.97710871696472 452.31939697265625 0.32555562257766724 514.9148559570312 0.7454887628555298 0.7314435 0.5114316344261169 True -4 11530 30.669015645980835 5.162899971008301 439.9874267578125 0.20274588465690613 511.8774719238281 0.7493751645088196 0.74233526 0.37294483184814453 True -5 13836 25.567208766937256 1.3178801536560059 441.81695556640625 0.1865328848361969 511.00360107421875 0.7496219873428345 0.7462635 0.36289697885513306 True -6 16142 25.383026838302612 0.6004765033721924 434.68609619140625 0.16274231672286987 510.2294006347656 0.7509968280792236 0.7503544 0.4125118553638458 True -7 18448 25.3995144367218 0.44751548767089844 431.4360046386719 0.1740761548280716 508.7717590332031 0.753598153591156 0.75549537 0.36048248410224915 True -8 20754 25.395726203918457 0.4460117816925049 432.0973815917969 0.18152260780334473 506.7245178222656 0.7561666369438171 0.7609316 0.32580941915512085 True -9 23060 26.849154472351074 20.55466341972351 447.58135986328125 0.2245379090309143 505.0854797363281 0.7577008605003357 0.7642661 0.32161831855773926 True -10 25366 25.463041305541992 0.8568379878997803 444.7057800292969 0.1655624806880951 504.0132751464844 0.7593291997909546 0.7684878 0.30733996629714966 True -11 27672 30.136330604553223 16.316157579421997 436.11407470703125 0.14313772320747375 503.0991516113281 0.7603020668029785 0.7674581 0.2982557415962219 False -12 29978 24.915355443954468 0.9000678062438965 473.568115234375 0.21431812644004822 501.8269348144531 0.7617174386978149 0.77423304 0.2947281301021576 True -13 32284 24.89302110671997 0.9644927978515625 423.0041198730469 0.13258154690265656 501.243408203125 0.7626853585243225 0.7781958 0.2780397832393646 True -14 34590 24.920108795166016 0.44390439987182617 477.81402587890625 0.1259366124868393 500.0885009765625 0.763557493686676 0.7857759 0.26146867871284485 True -15 36896 24.880234003067017 0.436687707901001 412.34063720703125 0.13743971288204193 499.2506103515625 0.7642095685005188 0.79160726 0.24432218074798584 True -16 39202 25.047343254089355 0.4373948574066162 402.6614074707031 0.10290707647800446 499.0956726074219 0.7644158601760864 0.7930477 0.23468391597270966 True -17 41508 24.908839464187622 17.761393308639526 439.19586181640625 0.07881167531013489 499.3415222167969 0.7641327977180481 0.7912849 0.2299043834209442 False -18 43814 24.906140089035034 0.4360806941986084 433.4667053222656 0.13400444388389587 499.4721374511719 0.7638428211212158 0.7914726 0.22772395610809326 False -19 46120 25.27090549468994 0.45044827461242676 421.04022216796875 0.07224057614803314 499.65673828125 0.7636598348617554 0.7887954 0.22724486887454987 False diff --git a/ENCSR653ZWW/cherimoya.fold_3.performance.tsv b/ENCSR653ZWW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d8748bf7a0e3351919a8ca2f98d79e7cb9bcaa95..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -499.0956726074219 0.19524067640304565 0.7644158601760864 0.36662352085113525 0.7930477261543274 0.7341771721839905 0.23468391597270966 \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_4.evaluate.json b/ENCSR653ZWW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c79f713b8a8efa53367428a3d4c58744ea3af906..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF654KWF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_4.fit.json b/ENCSR653ZWW/cherimoya.fold_4.fit.json deleted file mode 100644 index 541656e632c1f7da2228abf0fb9fbde1e847b6e2..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF654KWF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR653ZWW/cherimoya.fold_4.log b/ENCSR653ZWW/cherimoya.fold_4.log deleted file mode 100644 index 2f394f2e3bde524afb1343e17b8a8c4a22c2f510..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2288 30.001044511795044 3.407357931137085 482.0467529296875 0.31830063462257385 621.5465698242188 0.6218777894973755 0.61304957 8.374597549438477 True -1 4576 25.194058895111084 0.4609341621398926 422.74005126953125 0.18531055748462677 524.602294921875 0.7107509970664978 0.7226743 1.1561208963394165 True -2 6864 25.22981572151184 21.007384777069092 524.8280029296875 0.258628249168396 504.6014404296875 0.7311738133430481 0.75035983 0.46600550413131714 True -3 9152 27.555662870407104 0.4562962055206299 456.57275390625 0.22156038880348206 496.11712646484375 0.7399476766586304 0.7729199 0.3877834677696228 True -4 11440 25.327728748321533 0.4495868682861328 477.86920166015625 0.22124551236629486 496.92633056640625 0.7387017607688904 0.7671703 0.3398797810077667 False -5 13728 25.32084822654724 0.534576416015625 437.5477600097656 0.20801421999931335 492.55792236328125 0.7443548440933228 0.786143 0.27260830998420715 True -6 16016 25.255035638809204 4.241041660308838 459.40167236328125 0.14611798524856567 490.7619323730469 0.7463127970695496 0.7925242 0.26977524161338806 True -7 18304 25.334527015686035 0.44629788398742676 435.9652099609375 0.27200138568878174 489.36273193359375 0.7477456331253052 0.79510653 0.266714870929718 True -8 20592 25.195921421051025 0.44301629066467285 423.444091796875 0.21793532371520996 488.56298828125 0.7490328550338745 0.80013573 0.26251471042633057 True -9 22880 25.23502016067505 0.44226622581481934 410.37579345703125 0.1446957290172577 487.64532470703125 0.7501475214958191 0.8035197 0.261372447013855 True -10 25168 25.520552396774292 25.041298151016235 425.126708984375 0.16297394037246704 485.86041259765625 0.7521557807922363 0.8118642 0.2452317327260971 True -11 27456 25.485049724578857 0.46122241020202637 428.39398193359375 0.24006542563438416 485.19256591796875 0.7533267736434937 0.81327564 0.24086244404315948 True -12 29744 25.182957887649536 0.44988369941711426 447.2120361328125 0.14756079018115997 483.7644958496094 0.7548494935035706 0.8161389 0.2187386304140091 True -13 32032 25.185638666152954 0.4411888122558594 425.1920166015625 0.18988850712776184 482.3756408691406 0.7562088966369629 0.8233733 0.20194567739963531 True -14 34320 25.24544858932495 17.029877424240112 404.2789611816406 0.11923869699239731 481.8822937011719 0.7570142149925232 0.8271499 0.19270652532577515 True -15 36608 25.71705722808838 0.44596171379089355 471.7944641113281 0.10306552797555923 481.3858947753906 0.7575435638427734 0.82903135 0.18378400802612305 True -16 38896 25.314340829849243 0.44040775299072266 400.473876953125 0.13014674186706543 481.1457214355469 0.7578069567680359 0.83237815 0.17364299297332764 True -17 41184 25.219407081604004 0.4452550411224365 450.00927734375 0.12182224541902542 481.25201416015625 0.7576401829719543 0.83164674 0.16880549490451813 False -18 43472 24.889286994934082 0.4395866394042969 415.7017822265625 0.08403339236974716 481.343017578125 0.7573010921478271 0.8291251 0.16762016713619232 False -19 45760 24.650784015655518 0.43320584297180176 384.488037109375 0.08385248482227325 481.4623718261719 0.7571064233779907 0.82893974 0.1679370403289795 False diff --git a/ENCSR653ZWW/cherimoya.fold_4.performance.tsv b/ENCSR653ZWW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 405d6351b3f7489619f30eeeb66419861b9b3f2e..0000000000000000000000000000000000000000 --- a/ENCSR653ZWW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -481.1457214355469 0.2002379298210144 0.7578069567680359 0.35819974541664124 0.8323781490325928 0.7682400345802307 0.17364299297332764 \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_0.evaluate.json b/ENCSR654GSG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0e93daf30cc7b024f0d86770ee98fb05c41b0929..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF677PDT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_0.fit.json b/ENCSR654GSG/cherimoya.fold_0.fit.json deleted file mode 100644 index ae8de5082f81578b4deb410dc16c3a3b2bd843df..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF677PDT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_0.log b/ENCSR654GSG/cherimoya.fold_0.log deleted file mode 100644 index e273ee7c5553dbe198dc3d016da477231c1e732b..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.49626851081848 3.985349178314209 435.1909484863281 0.49656060338020325 622.5556030273438 0.24091997742652893 0.7376621 5.069674491882324 True -1 5494 30.480020761489868 0.664942741394043 435.7262268066406 0.5983520150184631 561.658203125 0.3109252452850342 0.79994404 1.4825855493545532 True -2 8241 30.482959032058716 0.6126577854156494 492.49102783203125 0.48490607738494873 550.946533203125 0.3233267068862915 0.81309247 0.6314108967781067 True -3 10988 30.532182455062866 0.66632080078125 499.8812255859375 0.5558314323425293 544.3343505859375 0.3312009871006012 0.8152045 0.5229328274726868 True -4 13735 30.50706911087036 0.9510047435760498 491.25628662109375 0.4393134117126465 543.0509643554688 0.3322541117668152 0.8158948 0.4273492097854614 True -5 16482 30.4789297580719 0.6064417362213135 492.8315734863281 0.4489697813987732 540.2068481445312 0.3345256447792053 0.8218915 0.3561386168003082 True -6 19229 30.474377155303955 0.6170158386230469 479.6027526855469 0.29347431659698486 538.2091674804688 0.3372664749622345 0.824365 0.3462367355823517 True -7 21976 30.526745080947876 0.6281745433807373 482.20513916015625 0.3664938807487488 536.4208984375 0.3389800190925598 0.8302879 0.3397412896156311 True -8 24723 30.815082788467407 0.6364264488220215 422.59979248046875 0.6117312908172607 534.2813720703125 0.3418630063533783 0.83223575 0.3181704580783844 True -9 27470 30.55508327484131 0.6209256649017334 420.13177490234375 0.38167840242385864 532.87158203125 0.342791348695755 0.8381746 0.3009805977344513 True -10 30217 30.486069202423096 0.6189169883728027 569.4114990234375 0.4387648105621338 531.4713134765625 0.34474968910217285 0.8422208 0.30209431052207947 True -11 32964 30.526236057281494 0.6323409080505371 358.49639892578125 0.513309121131897 530.2843627929688 0.3458097577095032 0.8468251 0.29172006249427795 True -12 35711 30.48260736465454 0.6321277618408203 412.2116394042969 0.40390467643737793 528.0279541015625 0.3490646481513977 0.85090774 0.28077253699302673 True -13 38458 30.543987035751343 0.6513702869415283 441.02728271484375 0.37631869316101074 526.8618774414062 0.35060086846351624 0.85389686 0.2740975022315979 True -14 41205 30.545095443725586 0.6774263381958008 450.545654296875 0.48889240622520447 524.4701538085938 0.3536856174468994 0.8581836 0.2655014991760254 True -15 43952 30.56229066848755 0.6381378173828125 507.729248046875 0.3825598359107971 523.8173828125 0.3546757698059082 0.8608405 0.2615106701850891 True -16 46699 30.51302194595337 0.684295654296875 477.1540832519531 0.37626343965530396 523.3368530273438 0.3546333611011505 0.86444193 0.2571674883365631 True -17 49446 30.54196548461914 0.6825611591339111 468.6361999511719 0.16483014822006226 523.384521484375 0.35439392924308777 0.8656428 0.2583291232585907 True -18 52193 30.585935831069946 0.633073091506958 471.50311279296875 0.2339046597480774 523.5927124023438 0.35428667068481445 0.8652476 0.2610527575016022 False -19 54940 30.51223587989807 0.6559643745422363 461.43487548828125 0.19743117690086365 523.825439453125 0.3538787364959717 0.8640228 0.2633626461029053 False diff --git a/ENCSR654GSG/cherimoya.fold_0.performance.tsv b/ENCSR654GSG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c45bea78e92b5e182a1365768c60e6fb91ca3d88..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -523.384521484375 0.4218394160270691 0.35439392924308777 0.13061940670013428 0.865642786026001 0.8286263346672058 0.2583291232585907 \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_1.evaluate.json b/ENCSR654GSG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index da082726ed57299de0c5f61c2e47085f8ab725cb..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF677PDT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_1.fit.json b/ENCSR654GSG/cherimoya.fold_1.fit.json deleted file mode 100644 index 4861c7cbeae59b7c6eddc6988f11378f8432ce2e..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF677PDT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_1.log b/ENCSR654GSG/cherimoya.fold_1.log deleted file mode 100644 index f7421a2f7c78194eba03340df1ab7099abd253ba..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2681 33.33612060546875 4.115670204162598 422.7916259765625 0.5485110282897949 727.2688598632812 0.2431611269712448 0.73044485 4.677395820617676 True -1 5362 29.806432008743286 1.2518560886383057 441.6097412109375 0.5744352340698242 651.7340087890625 0.3213598132133484 0.80203056 1.381523609161377 True -2 8043 29.845020294189453 0.750255823135376 413.92730712890625 0.48893147706985474 632.0083618164062 0.3386891186237335 0.81434524 0.81089186668396 True -3 10724 29.813678979873657 0.7588284015655518 458.27911376953125 0.48017388582229614 624.43994140625 0.3443441390991211 0.813676 0.7552067041397095 False -4 13405 30.09708595275879 0.7586445808410645 493.19439697265625 0.4250546097755432 620.6133422851562 0.34667086601257324 0.827481 0.5076838135719299 True -5 16086 29.95117425918579 0.7578344345092773 519.363037109375 0.5983439683914185 616.9392700195312 0.35094064474105835 0.83158016 0.4361600875854492 True -6 18767 29.881012201309204 0.758533239364624 349.95318603515625 0.4368388056755066 613.3519287109375 0.35459253191947937 0.8343029 0.4225243031978607 True -7 21448 29.900382041931152 0.7649214267730713 500.930419921875 0.38133561611175537 611.1595458984375 0.3567626178264618 0.8414892 0.3757467567920685 True -8 24129 29.878654718399048 0.7607359886169434 462.66357421875 0.31260693073272705 608.083984375 0.36076241731643677 0.8452836 0.36732175946235657 True -9 26810 29.88264513015747 0.7641887664794922 442.19805908203125 0.5537000298500061 604.9517211914062 0.363961786031723 0.8482105 0.34359872341156006 True -10 29491 29.810712575912476 0.7627174854278564 427.28375244140625 0.3569697439670563 603.8890991210938 0.36395886540412903 0.8532066 0.34554100036621094 True -11 32172 29.852445602416992 0.7552869319915771 495.5755310058594 0.32482197880744934 601.2785034179688 0.3677110970020294 0.8556605 0.33075904846191406 True -12 34853 29.816779613494873 0.7644572257995605 415.431884765625 0.42013412714004517 601.3848266601562 0.3664546310901642 0.8583626 0.3190407156944275 True -13 37534 29.78293776512146 0.7627665996551514 416.73944091796875 0.3171055316925049 598.1881103515625 0.3700593113899231 0.8665219 0.30089396238327026 True -14 40215 29.83450436592102 1.0534510612487793 413.2162780761719 0.2385643571615219 596.0768432617188 0.3727327287197113 0.8714729 0.29115015268325806 True -15 42896 29.935139179229736 3.3449182510375977 433.69744873046875 0.3594009280204773 595.2691650390625 0.3729369640350342 0.87420255 0.28505226969718933 True -16 45577 30.070539712905884 0.7683131694793701 454.24249267578125 0.2647942900657654 594.879150390625 0.3728083670139313 0.8766365 0.28066176176071167 True -17 48258 29.986459255218506 0.7746970653533936 385.50653076171875 0.22207416594028473 594.5873413085938 0.3727365732192993 0.87711936 0.27708059549331665 True -18 50939 30.002633810043335 0.7625555992126465 455.78948974609375 0.2764286994934082 594.8171997070312 0.372568279504776 0.87852126 0.27997592091560364 True -19 53620 29.96912980079651 0.7617607116699219 389.04058837890625 0.2539832890033722 595.5513916015625 0.3714524209499359 0.879429 0.2795793116092682 True diff --git a/ENCSR654GSG/cherimoya.fold_1.performance.tsv b/ENCSR654GSG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 40cf4902c8ac14550cf244441706398a32549783..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -595.5513916015625 0.40559351444244385 0.3714524209499359 0.1475370228290558 0.8794289827346802 0.8582450151443481 0.2795793116092682 \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_2.evaluate.json b/ENCSR654GSG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a5d1013f8ba0aab234a0cabd909c720321164196..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF677PDT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_2.fit.json b/ENCSR654GSG/cherimoya.fold_2.fit.json deleted file mode 100644 index 3b387f4b1969c3b36c006de870437ed39773e12f..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF677PDT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_2.log b/ENCSR654GSG/cherimoya.fold_2.log deleted file mode 100644 index d29638c1169c4a52644b076c33bdcef1a2e4b774..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 35.973299980163574 3.662564992904663 545.142822265625 0.5112137794494629 658.2761840820312 0.24925464391708374 0.7335784 5.053458213806152 True -1 5752 31.947691917419434 0.6247613430023193 403.50994873046875 0.5051397085189819 591.4625244140625 0.3198429048061371 0.7971714 1.0381823778152466 True -2 8628 31.99492645263672 0.6326265335083008 467.3604431152344 0.48298877477645874 578.07568359375 0.331451416015625 0.8047518 0.6286119222640991 True -3 11504 31.955675840377808 0.594475269317627 412.9022216796875 0.4490136206150055 572.3636474609375 0.33496853709220886 0.81205446 0.42166948318481445 True -4 14380 31.939352989196777 1.327880620956421 466.41033935546875 0.38745880126953125 568.4113159179688 0.3399302661418915 0.8169346 0.350381463766098 True -5 17256 31.99807333946228 0.5798799991607666 367.488037109375 0.5884909629821777 565.0798950195312 0.3440837264060974 0.82132506 0.3558123707771301 True -6 20132 31.94099497795105 0.6069836616516113 407.69189453125 0.48727816343307495 563.5091552734375 0.34450700879096985 0.82388717 0.3310836851596832 True -7 23008 31.939502239227295 0.5822467803955078 460.5411071777344 0.41228336095809937 561.3606567382812 0.34817126393318176 0.8258239 0.3275563418865204 True -8 25884 32.01678490638733 0.6102433204650879 364.9786376953125 0.4067080616950989 560.2257080078125 0.34815800189971924 0.832706 0.3091329038143158 True -9 28760 32.00893449783325 0.5821778774261475 487.01025390625 0.25408101081848145 557.5646362304688 0.3518344461917877 0.83708054 0.30215057730674744 True -10 31636 32.03902769088745 0.6070094108581543 484.4872741699219 0.4808877110481262 555.190185546875 0.35531923174858093 0.8401911 0.2964824140071869 True -11 34512 31.98158049583435 0.6011953353881836 445.7235107421875 0.536648690700531 553.7488403320312 0.35697752237319946 0.84404474 0.292997270822525 True -12 37388 32.01430940628052 1.4205684661865234 415.83819580078125 0.4471418261528015 552.54248046875 0.3581441044807434 0.84638774 0.2882521152496338 True -13 40264 31.954849004745483 0.5961933135986328 467.6051330566406 0.3309868574142456 552.0814819335938 0.35767367482185364 0.85155267 0.2781977951526642 True -14 43140 32.03072905540466 1.139678955078125 438.2513427734375 0.3083665072917938 550.5350341796875 0.35961437225341797 0.85679793 0.27114805579185486 True -15 46016 31.994558095932007 21.74940776824951 401.1102294921875 0.19421367347240448 548.5123291015625 0.36229175329208374 0.85971093 0.26981958746910095 True -16 48892 32.00832557678223 0.6103439331054688 464.2210693359375 0.29630929231643677 549.521240234375 0.36127912998199463 0.8629159 0.26820147037506104 True -17 51768 31.983376264572144 0.5920021533966064 419.8086242675781 0.1522255539894104 548.8111572265625 0.3615998327732086 0.8619792 0.26936882734298706 False -18 54644 31.99629521369934 0.5967340469360352 399.88714599609375 0.24669282138347626 548.5700073242188 0.3623276948928833 0.86256707 0.27243462204933167 False -19 57520 32.02736520767212 0.5898702144622803 371.2894287109375 0.21437333524227142 548.3577880859375 0.36311057209968567 0.8619947 0.27532288432121277 False diff --git a/ENCSR654GSG/cherimoya.fold_2.performance.tsv b/ENCSR654GSG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4d434c3d4ff067d599476ffef7feb2ef6a70a518..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -549.521240234375 0.4144708216190338 0.361279159784317 0.13985496759414673 0.8629158735275269 0.8307976722717285 0.26820147037506104 \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_3.evaluate.json b/ENCSR654GSG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c27f198086492ff0daf36b602347bd92097d3c5b..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF677PDT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_3.fit.json b/ENCSR654GSG/cherimoya.fold_3.fit.json deleted file mode 100644 index f5dd59bb27ce950d786f4ed99496d74d3ad3c3cd..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF677PDT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_3.log b/ENCSR654GSG/cherimoya.fold_3.log deleted file mode 100644 index e6877a05ca397dca1592572ed56a983170ae97d2..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 34.54675793647766 3.724997043609619 448.24652099609375 0.4645320177078247 633.9085693359375 0.2555292248725891 0.73867726 4.416065692901611 True -1 5522 30.637149572372437 1.136826992034912 512.8734741210938 0.48629075288772583 573.3458862304688 0.32260778546333313 0.8029247 1.117119550704956 True -2 8283 30.716395378112793 0.5502805709838867 458.9698181152344 0.5463560223579407 558.943359375 0.3363631069660187 0.81612235 0.6136403679847717 True -3 11044 30.653809070587158 0.5496261119842529 414.47216796875 0.4728112518787384 552.481689453125 0.3402863144874573 0.82547516 0.5093520283699036 True -4 13805 30.65405011177063 0.5514822006225586 445.4111328125 0.4689154624938965 548.9169921875 0.34529945254325867 0.829535 0.4449024498462677 True -5 16566 30.654701948165894 0.5406081676483154 465.05712890625 0.4616042673587799 546.75390625 0.34662532806396484 0.83437604 0.4211868643760681 True -6 19327 30.65296959877014 0.5574820041656494 473.7937316894531 0.35462069511413574 545.3904418945312 0.3482551574707031 0.8330868 0.4280557930469513 False -7 22088 30.671414136886597 0.5524885654449463 450.19952392578125 0.4242129921913147 543.3001098632812 0.3510373830795288 0.8364193 0.38309723138809204 True -8 24849 30.691166400909424 0.5438194274902344 480.36676025390625 0.2992412745952606 541.3173828125 0.3544142544269562 0.8387459 0.3766588270664215 True -9 27610 30.707629919052124 0.5592756271362305 496.0947570800781 0.60303795337677 540.6509399414062 0.35373759269714355 0.8402333 0.3748261034488678 True -10 30371 30.75366711616516 0.5492508411407471 373.007568359375 0.3537883758544922 538.486328125 0.35694432258605957 0.8447786 0.35478171706199646 True -11 33132 30.71451497077942 0.5329558849334717 390.75909423828125 0.4564446210861206 536.52294921875 0.3585401773452759 0.8470725 0.34369200468063354 True -12 35893 30.68331265449524 0.5550286769866943 469.9302978515625 0.32737839221954346 534.51220703125 0.3611082434654236 0.8525852 0.3267071843147278 True -13 38654 30.72489833831787 0.5400576591491699 473.6937561035156 0.25982147455215454 533.6537475585938 0.3610423803329468 0.8578494 0.306922048330307 True -14 41415 30.685286283493042 0.5331225395202637 423.67333984375 0.3187752366065979 532.477783203125 0.36230552196502686 0.8618748 0.2933484613895416 True -15 44176 30.696857929229736 0.5453650951385498 494.14166259765625 0.27970096468925476 531.380126953125 0.3634088635444641 0.8673904 0.2795700430870056 True -16 46937 30.66276717185974 0.550555944442749 509.0230712890625 0.23216181993484497 529.2080078125 0.36603718996047974 0.87054837 0.273208886384964 True -17 49698 30.715632915496826 0.5512757301330566 429.17926025390625 0.19737514853477478 530.2681274414062 0.36414504051208496 0.87384194 0.2696245610713959 True -18 52459 30.707805395126343 2.062363386154175 442.4800720214844 0.468569278717041 529.4879150390625 0.3655499815940857 0.87286526 0.2698107361793518 False -19 55220 30.72466802597046 0.5641031265258789 493.93310546875 0.1919233798980713 530.2376708984375 0.36386364698410034 0.87253636 0.2713533341884613 False diff --git a/ENCSR654GSG/cherimoya.fold_3.performance.tsv b/ENCSR654GSG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ec5a7638f76f8e23e20125065327cb4f01e4e398..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -530.2681274414062 0.4157509207725525 0.36414504051208496 0.13662636280059814 0.8738419413566589 0.8374274969100952 0.2696245610713959 \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_4.evaluate.json b/ENCSR654GSG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fb137d579f64fb7d063aae397eb1e236d6a025f6..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF677PDT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_4.fit.json b/ENCSR654GSG/cherimoya.fold_4.fit.json deleted file mode 100644 index 45bda7ef0e287bbc6485352cf576086e36ce13cd..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF677PDT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654GSG/cherimoya.fold_4.log b/ENCSR654GSG/cherimoya.fold_4.log deleted file mode 100644 index a1030c8eab3b97d1deab80504eebd8871c34f5df..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2834 35.46232581138611 4.185901165008545 509.1441650390625 0.5455803871154785 576.5326538085938 0.24087578058242798 0.735801 4.453505039215088 True -1 5668 31.548457622528076 0.6888692378997803 455.5875549316406 0.42478689551353455 521.6805419921875 0.3028842508792877 0.7922832 0.9112838506698608 True -2 8502 31.599663972854614 0.6427288055419922 429.208251953125 0.6116244792938232 513.3087768554688 0.3151445686817169 0.80516243 0.5496219396591187 True -3 11336 31.546571254730225 2.0326435565948486 466.44940185546875 0.6107525825500488 509.1136169433594 0.31902554631233215 0.80750144 0.43484431505203247 True -4 14170 31.54005742073059 0.6456422805786133 418.36175537109375 0.38507604598999023 506.3814392089844 0.32179170846939087 0.81516975 0.360076904296875 True -5 17004 31.49603581428528 0.639676570892334 445.9774169921875 0.3814004361629486 503.7562561035156 0.3242041766643524 0.8220399 0.3224981129169464 True -6 19838 31.650983095169067 0.6317577362060547 426.3045349121094 0.3708517253398895 503.2889099121094 0.3232918977737427 0.82600945 0.3333158493041992 True -7 22672 31.656710624694824 0.6318511962890625 530.0347900390625 0.2201504111289978 500.741943359375 0.3279480040073395 0.8324611 0.3234862685203552 True -8 25506 31.662065505981445 0.6482033729553223 517.8593139648438 0.41829627752304077 499.1485290527344 0.3306305706501007 0.83570826 0.30327466130256653 True -9 28340 31.60636591911316 0.6268813610076904 466.2684326171875 0.31942200660705566 497.6178283691406 0.33261778950691223 0.83940476 0.2975744307041168 True -10 31174 31.52840232849121 0.6279029846191406 456.4576416015625 0.4466361999511719 496.5488586425781 0.3337782621383667 0.8442484 0.27963346242904663 True -11 34008 31.550965309143066 0.644538402557373 505.80950927734375 0.3973473012447357 494.7388000488281 0.3360980451107025 0.84756064 0.27444666624069214 True -12 36842 31.55515217781067 0.6312825679779053 375.6012878417969 0.32958561182022095 493.7904052734375 0.33698755502700806 0.8525531 0.26419776678085327 True -13 39676 32.059576749801636 2.5046193599700928 443.06146240234375 0.42981019616127014 492.3541259765625 0.3388712704181671 0.8555029 0.2545284032821655 True -14 42510 31.680522441864014 0.6440670490264893 437.3023681640625 0.3317704200744629 490.7465515136719 0.34135162830352783 0.8603334 0.24876254796981812 True -15 45344 31.706727266311646 0.6518566608428955 478.75006103515625 0.18578577041625977 490.4866027832031 0.3416669964790344 0.86497974 0.24247866868972778 True -16 48178 31.618384838104248 0.6478536128997803 485.50048828125 0.2751685082912445 490.9229736328125 0.34076982736587524 0.867359 0.24074687063694 True -17 51012 31.511930465698242 1.7937724590301514 496.88372802734375 0.34900379180908203 490.1826477050781 0.34191182255744934 0.86670226 0.24043956398963928 False -18 53846 31.56891965866089 0.63456130027771 401.31024169921875 0.2798178195953369 489.62445068359375 0.34309664368629456 0.86799145 0.239919051527977 True -19 56680 31.56167697906494 0.6313118934631348 428.7343444824219 0.20542371273040771 490.06573486328125 0.3422428071498871 0.8679382 0.24201317131519318 False diff --git a/ENCSR654GSG/cherimoya.fold_4.performance.tsv b/ENCSR654GSG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f04fc138bdfc1cc48766f1f040d5f5d7c1caa635..0000000000000000000000000000000000000000 --- a/ENCSR654GSG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -489.62445068359375 0.43203336000442505 0.34309667348861694 0.12556684017181396 0.8679914474487305 0.8244625926017761 0.239919051527977 \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_0.evaluate.json b/ENCSR654UYP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e2243c6ddf92bb6d3fc06e631c07b4085906544f..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF886PTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_0.fit.json b/ENCSR654UYP/cherimoya.fold_0.fit.json deleted file mode 100644 index 2e93539e093735580b519dc3a4d13bf05f9d29cf..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF886PTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_0.log b/ENCSR654UYP/cherimoya.fold_0.log deleted file mode 100644 index 646236936b9430ff43c745e30a27e85dc771aaa2..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1735 23.683303117752075 5.052940845489502 271.209228515625 0.34146052598953247 409.8206787109375 0.482308954000473 0.69839895 11.481208801269531 True -1 3470 19.110066413879395 1.1640872955322266 283.24908447265625 0.31879162788391113 350.07147216796875 0.5717200040817261 0.7490608 1.9611765146255493 True -2 5205 19.117583751678467 0.3452439308166504 273.87225341796875 0.326026976108551 334.0340270996094 0.606613039970398 0.7805446 0.48020532727241516 True -3 6940 19.08534026145935 0.3431694507598877 266.812255859375 0.2628942131996155 327.00592041015625 0.6178476810455322 0.79913616 0.3577362298965454 True -4 8675 19.05778980255127 0.8329248428344727 284.52947998046875 0.19917121529579163 325.1773376464844 0.6210242509841919 0.8066051 0.2877979874610901 True -5 10410 19.102747440338135 0.3432776927947998 279.1344909667969 0.3223036527633667 323.9961242675781 0.6238497495651245 0.80786294 0.22269763052463531 True -6 12145 19.057589530944824 0.3418412208557129 299.00640869140625 0.2601057291030884 323.1571044921875 0.6260998845100403 0.8110311 0.21103155612945557 True -7 13880 19.084473848342896 0.3408479690551758 278.14794921875 0.25081345438957214 322.6372985839844 0.6272441744804382 0.81212425 0.19441533088684082 True -8 15615 19.191211223602295 16.65414810180664 257.4134521484375 0.22608217597007751 321.8106384277344 0.6295213103294373 0.8171937 0.18718069791793823 True -9 17350 19.10068941116333 0.3666996955871582 266.8584289550781 0.35599732398986816 320.9327392578125 0.6317732930183411 0.82114536 0.205900177359581 True -10 19085 19.078925848007202 7.2785022258758545 285.39874267578125 0.20084160566329956 320.0318603515625 0.6336177587509155 0.82393396 0.18653105199337006 True -11 20820 19.236067295074463 0.3462357521057129 246.64010620117188 0.17253096401691437 319.225830078125 0.6353242993354797 0.82843906 0.17142745852470398 True -12 22555 19.113929510116577 12.489206790924072 273.04150390625 0.21912004053592682 318.77587890625 0.6365523338317871 0.8308245 0.17181751132011414 True -13 24290 19.180116891860962 0.3520655632019043 255.3040008544922 0.1686118245124817 318.39453125 0.6374728083610535 0.8335092 0.16852213442325592 True -14 26025 18.8721764087677 0.3390364646911621 293.00830078125 0.32446080446243286 318.1917419433594 0.6380701065063477 0.8362734 0.16805651783943176 True -15 27760 18.720672130584717 0.3446662425994873 280.9225158691406 0.1911011040210724 318.2234191894531 0.6384499073028564 0.83662134 0.1683456003665924 True -16 29495 18.713658332824707 14.149970531463623 264.6457214355469 0.18261799216270447 318.3800964355469 0.6380559206008911 0.8348272 0.17193150520324707 False -17 31230 18.770161390304565 0.34838271141052246 252.37237548828125 0.1501043438911438 318.6212158203125 0.6371390223503113 0.8348528 0.17486153542995453 False -18 32965 18.704604148864746 0.3469066619873047 260.4393310546875 0.12399926781654358 318.9458923339844 0.6364798545837402 0.82990205 0.17889530956745148 False -19 34700 18.72654151916504 0.33892345428466797 281.198486328125 0.2551811933517456 319.1981201171875 0.6360275745391846 0.8264932 0.18263337016105652 False diff --git a/ENCSR654UYP/cherimoya.fold_0.performance.tsv b/ENCSR654UYP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 20b728fe19fb8c188930ddc44aadfd05b8e25729..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -318.2234191894531 0.29519620537757874 0.6384499669075012 0.22599762678146362 0.8366213440895081 0.7751797437667847 0.1683456003665924 \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_1.evaluate.json b/ENCSR654UYP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index cbabd7dcebd4dcc4b792f9492d650a67a600d3ac..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF886PTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_1.fit.json b/ENCSR654UYP/cherimoya.fold_1.fit.json deleted file mode 100644 index 68e9da2de1257706e7030ebe536ace6e7f9066f8..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF886PTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_1.log b/ENCSR654UYP/cherimoya.fold_1.log deleted file mode 100644 index 50a3da820ef25f5d7153e2e6bc45de41afa87b4d..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1714 22.56301712989807 3.393646240234375 265.84075927734375 0.25846201181411743 439.4749450683594 0.49191272258758545 0.60996205 11.744848251342773 True -1 3428 18.860442399978638 0.44797706604003906 294.50872802734375 0.24126484990119934 375.5627136230469 0.586891770362854 0.6883208 2.0189528465270996 True -2 5142 18.845072031021118 0.43043088912963867 254.14503479003906 0.26518502831459045 357.6446533203125 0.6219562292098999 0.7202021 0.6784821152687073 True -3 6856 18.863219499588013 0.4266693592071533 279.3087158203125 0.25565025210380554 349.2289123535156 0.6367304921150208 0.7536243 0.38283398747444153 True -4 8570 18.817711353302002 0.42182302474975586 284.5308837890625 0.3150598704814911 349.2611083984375 0.6352865695953369 0.7453284 0.3670617640018463 False -5 10284 18.82963275909424 1.265657663345337 277.3721618652344 0.21113157272338867 347.9042663574219 0.6380284428596497 0.7503429 0.32213401794433594 False -6 11998 18.846863269805908 0.4295227527618408 275.1424255371094 0.23283880949020386 345.43951416015625 0.6450334787368774 0.77029306 0.2597520649433136 True -7 13712 18.836018323898315 0.42989253997802734 258.535888671875 0.1708890050649643 344.4450378417969 0.6474305987358093 0.7807084 0.2317449301481247 True -8 15426 18.82291603088379 0.4337599277496338 266.5687255859375 0.3372519612312317 343.2955322265625 0.6496725678443909 0.78906184 0.21052083373069763 True -9 17140 18.810991764068604 0.4320201873779297 270.6547546386719 0.15394312143325806 342.54095458984375 0.6514332294464111 0.7929386 0.20244476199150085 True -10 18854 18.83485174179077 0.4367809295654297 243.16940307617188 0.16973942518234253 341.6268005371094 0.6536880731582642 0.8002413 0.19295042753219604 True -11 20568 18.456023693084717 0.4218785762786865 264.5077819824219 0.163899227976799 340.99615478515625 0.6552519202232361 0.8061103 0.1940959095954895 True -12 22282 18.576404333114624 0.4205820560455322 263.704833984375 0.148782417178154 340.3306884765625 0.6566712260246277 0.8095456 0.18885308504104614 True -13 23996 18.517661333084106 0.49372172355651855 261.760986328125 0.19379708170890808 339.84527587890625 0.6576730012893677 0.8149169 0.18640612065792084 True -14 25710 18.51526427268982 0.42218899726867676 273.21295166015625 0.13087403774261475 339.537353515625 0.6580585241317749 0.81704926 0.18453852832317352 True -15 27424 18.49865984916687 0.41986536979675293 263.45751953125 0.11102885007858276 339.4105224609375 0.6580989360809326 0.8183005 0.18214665353298187 True -16 29138 18.490280866622925 0.42166590690612793 258.96917724609375 0.12700264155864716 339.4895935058594 0.6576374769210815 0.8186075 0.1826574206352234 True -17 30852 18.50725483894348 0.7891438007354736 261.2132568359375 0.09954681247472763 339.81170654296875 0.6566362380981445 0.8164151 0.18513965606689453 False -18 32566 18.451798677444458 0.42395520210266113 276.80548095703125 0.11500106751918793 340.1601867675781 0.6556956768035889 0.815147 0.18711219727993011 False -19 34280 18.640110731124878 15.515160322189331 263.0122985839844 0.08163441717624664 340.3923645019531 0.6550830006599426 0.81224966 0.18946769833564758 False diff --git a/ENCSR654UYP/cherimoya.fold_1.performance.tsv b/ENCSR654UYP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 85263e8565f89a8e2bc3c58de06eebb8e39605f5..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -339.4895935058594 0.28160256147384644 0.6576375365257263 0.2406221330165863 0.8186075091362 0.8001310229301453 0.1826574206352234 \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_2.evaluate.json b/ENCSR654UYP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2842113c1fabd57e08b9c64bbdd32ac653382b75..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF886PTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_2.fit.json b/ENCSR654UYP/cherimoya.fold_2.fit.json deleted file mode 100644 index e253832de21561068a01ae95c0d2fa4a1f1b523a..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF886PTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_2.log b/ENCSR654UYP/cherimoya.fold_2.log deleted file mode 100644 index 9eb11d2b144f1d3c3e271f1758a9ad2806ce1a0d..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1804 23.549309730529785 3.2818915843963623 296.5811462402344 0.4572601914405823 416.8191223144531 0.48813217878341675 0.63798326 9.824661254882812 True -1 3608 19.819185972213745 1.0756895542144775 284.98126220703125 0.3639417290687561 356.6029968261719 0.5816201567649841 0.71657467 1.5821826457977295 True -2 5412 19.862560510635376 0.34117555618286133 262.1991882324219 0.2580752372741699 339.4698791503906 0.61472088098526 0.74811393 0.5335355401039124 True -3 7216 19.82103705406189 0.331226110458374 241.8910369873047 0.21387013792991638 332.9633483886719 0.625921368598938 0.77036136 0.30574676394462585 True -4 9020 19.822264432907104 0.3337900638580322 228.650634765625 0.17198118567466736 330.8549499511719 0.6297340989112854 0.7775124 0.2867005169391632 True -5 10824 19.856379985809326 0.3334023952484131 300.10675048828125 0.30312520265579224 330.1054382324219 0.6314523816108704 0.777063 0.2796710729598999 False -6 12628 19.808652877807617 0.3387596607208252 275.783935546875 0.27628839015960693 328.88861083984375 0.6346727609634399 0.7865611 0.23279862105846405 True -7 14432 19.813854455947876 0.34091997146606445 270.9051818847656 0.19280993938446045 328.2694091796875 0.6363162398338318 0.78985417 0.2259015440940857 True -8 16236 19.81196427345276 0.33145976066589355 277.58563232421875 0.2087305188179016 327.6743469238281 0.6379063129425049 0.7926268 0.2206525355577469 True -9 18040 19.807632446289062 0.6396729946136475 271.8909912109375 0.23380625247955322 326.9462585449219 0.6395075917243958 0.79573804 0.2145577073097229 True -10 19844 19.85085964202881 0.3385753631591797 298.4178771972656 0.16406048834323883 326.31756591796875 0.641027569770813 0.79792875 0.21372893452644348 True -11 21648 19.844865322113037 0.3345463275909424 290.24383544921875 0.19013908505439758 325.52294921875 0.6428662538528442 0.8036447 0.20598874986171722 True -12 23452 19.814956426620483 0.3336446285247803 251.20782470703125 0.20150189101696014 325.0605773925781 0.6438966989517212 0.80452967 0.20443940162658691 True -13 25256 20.95896315574646 10.132777452468872 272.39788818359375 0.2930441200733185 324.6966247558594 0.6445719003677368 0.8073976 0.19702765345573425 True -14 27060 19.9514377117157 0.9381237030029297 258.1615295410156 0.18592259287834167 324.4820556640625 0.6452167630195618 0.81037194 0.2001308798789978 True -15 28864 19.85825276374817 1.2272615432739258 249.72195434570312 0.13279294967651367 324.40985107421875 0.6452818512916565 0.81108904 0.19612213969230652 True -16 30668 19.86086630821228 0.334136962890625 284.4392395019531 0.09912601113319397 324.6051330566406 0.6446033120155334 0.813058 0.19655165076255798 True -17 32472 19.687377452850342 1.2538373470306396 246.30015563964844 0.1447008103132248 325.0231628417969 0.6433908343315125 0.8108635 0.19728338718414307 False -18 34276 19.48936891555786 0.33730292320251465 242.9971160888672 0.08213281631469727 325.3961181640625 0.642471194267273 0.8080731 0.19891634583473206 False -19 36080 19.488754749298096 0.33686184883117676 282.007568359375 0.12231577187776566 325.5817565917969 0.6419712901115417 0.8067634 0.20012825727462769 False diff --git a/ENCSR654UYP/cherimoya.fold_2.performance.tsv b/ENCSR654UYP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9e3a614664376785ac7f613e5bc273816d271fd0..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.6051330566406 0.2909741997718811 0.6446032524108887 0.23026606440544128 0.8130580186843872 0.7736029028892517 0.19655165076255798 \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_3.evaluate.json b/ENCSR654UYP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 51135617f695893a0ad21f05b325f00f1cabed16..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF886PTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_3.fit.json b/ENCSR654UYP/cherimoya.fold_3.fit.json deleted file mode 100644 index 98b565b246ae3a570442aa4ff3f896b4f295a2dc..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF886PTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_3.log b/ENCSR654UYP/cherimoya.fold_3.log deleted file mode 100644 index 1d36e7a9829bc126eab54916b71bf193edecd9c7..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1765 23.17475652694702 3.2836291790008545 275.68133544921875 0.32947811484336853 406.7233581542969 0.4834303557872772 0.67517394 10.4965238571167 True -1 3530 19.44598913192749 0.3708536624908447 299.94342041015625 0.25592952966690063 349.0419006347656 0.5746297240257263 0.7397917 1.7846651077270508 True -2 5295 19.446710109710693 0.3686397075653076 265.84332275390625 0.2388748973608017 333.078125 0.6032335162162781 0.76499724 0.6559340357780457 True -3 7060 19.414092779159546 0.35368967056274414 270.73309326171875 0.2082885503768921 326.356201171875 0.6168093681335449 0.787438 0.3294907808303833 True -4 8825 19.36192011833191 0.3532447814941406 253.57412719726562 0.21285364031791687 324.5472412109375 0.6208577752113342 0.790414 0.2963912785053253 True -5 10590 19.402590036392212 0.3606581687927246 287.6143798828125 0.19812870025634766 323.8179931640625 0.622573733329773 0.7967299 0.23428355157375336 True -6 12355 19.3703830242157 0.35292935371398926 287.61181640625 0.19236770272254944 323.0276184082031 0.6250932812690735 0.7980049 0.21794982254505157 True -7 14120 19.40654492378235 0.3751828670501709 269.26031494140625 0.22913199663162231 322.2154541015625 0.6273286938667297 0.80242074 0.20987428724765778 True -8 15885 19.402751207351685 0.35753488540649414 254.3220672607422 0.2423478662967682 321.765380859375 0.6290403604507446 0.80118597 0.2105141580104828 False -9 17650 19.39369249343872 0.3610091209411621 286.89666748046875 0.16840267181396484 321.0607604980469 0.6305001378059387 0.80481577 0.2027949094772339 True -10 19415 19.35774517059326 3.35512638092041 256.1793212890625 0.2436864823102951 320.4272766113281 0.6319690942764282 0.8083737 0.196277916431427 True -11 21180 19.43894076347351 0.3668031692504883 250.49981689453125 0.16211538016796112 319.76318359375 0.633614718914032 0.8098881 0.1953999549150467 True -12 22945 19.417160749435425 0.3605802059173584 299.3832092285156 0.1583741456270218 319.3638610839844 0.6346094608306885 0.8136046 0.1897754669189453 True -13 24710 19.403265476226807 0.5166671276092529 233.11688232421875 0.15505684912204742 318.8305969238281 0.6359113454818726 0.81660706 0.1862124800682068 True -14 26475 19.423946619033813 0.3615531921386719 264.2559509277344 0.16880512237548828 318.52874755859375 0.6367033123970032 0.81927186 0.18560302257537842 True -15 28240 19.459532260894775 0.364591121673584 268.1901550292969 0.1389712393283844 318.42108154296875 0.6369712352752686 0.8210436 0.18693768978118896 True -16 30005 19.435605764389038 0.3591742515563965 278.81585693359375 0.12783774733543396 318.51513671875 0.636527419090271 0.82303303 0.18250209093093872 True -17 31770 19.41042447090149 0.35337352752685547 256.5442810058594 0.1648768186569214 318.7882080078125 0.635807991027832 0.8228368 0.1859203428030014 False -18 33535 19.38555908203125 0.36461567878723145 272.0162353515625 0.07242441177368164 319.02789306640625 0.635150671005249 0.81763077 0.18917788565158844 False -19 35300 19.43011975288391 0.3579401969909668 266.40814208984375 0.080692358314991 319.2864685058594 0.6345228552818298 0.816351 0.19034554064273834 False diff --git a/ENCSR654UYP/cherimoya.fold_3.performance.tsv b/ENCSR654UYP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 53213a312747b8eb15e81120ab6956db5e7cee57..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -318.51513671875 0.29485058784484863 0.6365274786949158 0.22714866697788239 0.8230330348014832 0.7842992544174194 0.18250209093093872 \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_4.evaluate.json b/ENCSR654UYP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 07863efc9055443387c3de5a1894af80d30fcb98..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF886PTG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_4.fit.json b/ENCSR654UYP/cherimoya.fold_4.fit.json deleted file mode 100644 index ac409bfda9d74d75bcfeaafce482c28d4fb9e767..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF886PTG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654UYP/cherimoya.fold_4.log b/ENCSR654UYP/cherimoya.fold_4.log deleted file mode 100644 index 2b69324de0a15e47774190ae28219dbc86c31c2b..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1783 23.22154188156128 3.3861052989959717 279.46490478515625 0.2744465470314026 396.5486145019531 0.4836743175983429 0.6813534 10.24170207977295 True -1 3566 19.59234046936035 0.3466217517852783 312.6728515625 0.22884967923164368 340.62139892578125 0.5751330852508545 0.73012865 1.3984981775283813 True -2 5349 19.676477432250977 0.33306241035461426 246.0057373046875 0.20276887714862823 327.3597717285156 0.6039193868637085 0.76965463 0.4301666021347046 True -3 7132 19.30760645866394 0.3280766010284424 313.76519775390625 0.2765983045101166 321.81353759765625 0.6117185354232788 0.77828825 0.3133283853530884 True -4 8915 19.205353498458862 0.3225069046020508 266.8548583984375 0.2213531881570816 319.502197265625 0.6186647415161133 0.7917532 0.2654965817928314 True -5 10698 19.222646951675415 17.381641626358032 268.55133056640625 0.1946212351322174 318.3404846191406 0.6220300793647766 0.79839575 0.2387564778327942 True -6 12481 19.51800775527954 0.33153462409973145 277.2172546386719 0.227231964468956 317.73492431640625 0.6233143210411072 0.79850775 0.25280940532684326 True -7 14264 19.210460662841797 0.6617200374603271 260.74627685546875 0.24190112948417664 316.83245849609375 0.6257616281509399 0.80703336 0.22509415447711945 True -8 16047 19.25357985496521 0.3286135196685791 256.1830749511719 0.22886624932289124 316.0582580566406 0.6276171803474426 0.81135255 0.21524299681186676 True -9 17830 19.25639533996582 0.3328084945678711 271.381591796875 0.17760208249092102 315.2731018066406 0.6296256184577942 0.8146232 0.1999102532863617 True -10 19613 19.250613927841187 0.3247535228729248 277.71954345703125 0.190110981464386 314.6338806152344 0.6314689517021179 0.8199264 0.18955543637275696 True -11 21396 19.209221124649048 0.324413537979126 261.9652099609375 0.19246041774749756 314.02471923828125 0.6329390406608582 0.82572323 0.18369519710540771 True -12 23179 19.18411087989807 0.3274683952331543 258.50958251953125 0.1669827401638031 313.56268310546875 0.6340163350105286 0.8295732 0.17314644157886505 True -13 24962 19.227556228637695 0.32704925537109375 263.607177734375 0.111579030752182 313.21112060546875 0.634989321231842 0.83152086 0.1707858145236969 True -14 26745 19.241681575775146 0.3273029327392578 268.887939453125 0.15748143196105957 313.02288818359375 0.6354191899299622 0.83440435 0.16924799978733063 True -15 28528 19.236574172973633 0.32869768142700195 254.88705444335938 0.13676294684410095 313.01080322265625 0.6354823708534241 0.83523273 0.163848415017128 True -16 30311 19.175641298294067 0.32315659523010254 274.9986572265625 0.10313907265663147 313.1280822753906 0.6351292133331299 0.8336966 0.16415899991989136 False -17 32094 19.20372486114502 0.850440502166748 275.4830627441406 0.12908054888248444 313.5024719238281 0.6340925097465515 0.829998 0.16567398607730865 False -18 33877 19.223913431167603 0.33564186096191406 269.9201354980469 0.08162404596805573 313.7295837402344 0.6334160566329956 0.828851 0.1661209613084793 False -19 35660 19.191210508346558 0.33102917671203613 246.87789916992188 0.12842285633087158 313.9284362792969 0.6328457593917847 0.8260667 0.16643209755420685 False diff --git a/ENCSR654UYP/cherimoya.fold_4.performance.tsv b/ENCSR654UYP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2bfe528ea6b65f224aae6bcc3c30b670b73c0ebc..0000000000000000000000000000000000000000 --- a/ENCSR654UYP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -313.01080322265625 0.2976883351802826 0.6354823708534241 0.22316357493400574 0.8352327346801758 0.7777877449989319 0.163848415017128 \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_0.evaluate.json b/ENCSR654WXX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1d7d02afcf614d3cbf167a2b95417c39e889fc48..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF623NNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_0.fit.json b/ENCSR654WXX/cherimoya.fold_0.fit.json deleted file mode 100644 index 2d56d17ccf6052e1034c95762f07c12a03e3c041..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF623NNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_0.log b/ENCSR654WXX/cherimoya.fold_0.log deleted file mode 100644 index 5e2891baf0d0a9d2997b533b822524bad1fb3e84..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1801 24.356321334838867 29.690293073654175 262.1369323730469 1.1969783306121826 239.01275634765625 0.10507276654243469 0.6273521 6.480930805206299 True -1 3602 20.997538328170776 0.38275647163391113 127.90080261230469 0.629575252532959 216.31272888183594 0.15350210666656494 0.73790956 3.2980759143829346 True -2 5403 20.876845121383667 28.560842275619507 155.1720733642578 0.9602961540222168 202.08718872070312 0.17633475363254547 0.7502094 2.0623109340667725 True -3 7204 20.32210683822632 0.3694875240325928 222.73092651367188 0.9613059759140015 197.4292755126953 0.1820356845855713 0.76650286 1.2285690307617188 True -4 9005 20.20706033706665 0.37793493270874023 169.14166259765625 0.9035217761993408 193.97628784179688 0.1861315369606018 0.7918147 0.9944564700126648 True -5 10806 20.202261209487915 0.3717334270477295 203.3109588623047 0.905865490436554 192.16490173339844 0.18955199420452118 0.80172044 0.9160199761390686 True -6 12607 20.24864172935486 0.37402963638305664 132.6291046142578 1.1400458812713623 190.50526428222656 0.19370590150356293 0.8094312 0.815065860748291 True -7 14408 20.3929500579834 0.3775811195373535 156.46414184570312 0.7110440135002136 189.19895935058594 0.19691161811351776 0.8171345 0.743981122970581 True -8 16209 20.251142263412476 0.3735544681549072 177.75872802734375 0.9627068042755127 188.43504333496094 0.1987091600894928 0.8256285 0.6392360925674438 True -9 18010 20.205374240875244 0.6966438293457031 201.9662322998047 0.6321417689323425 187.86737060546875 0.19897443056106567 0.8349181 0.5847648978233337 True -10 19811 20.3576500415802 0.3776533603668213 156.66970825195312 0.699876070022583 187.01840209960938 0.20117251574993134 0.83698696 0.5311657190322876 True -11 21612 19.847254753112793 0.3735005855560303 179.90615844726562 0.8487950563430786 186.13323974609375 0.20306716859340668 0.8429205 0.5007148385047913 True -12 23413 19.79216194152832 0.37480950355529785 223.56649780273438 0.8779857754707336 185.0497589111328 0.20552177727222443 0.8482544 0.4837472438812256 True -13 25214 19.815402507781982 0.42697644233703613 111.10458374023438 0.6550347805023193 185.02490234375 0.20539580285549164 0.85050803 0.4731656610965729 True -14 27015 19.793493509292603 0.37052345275878906 129.34344482421875 0.5328178405761719 184.4198455810547 0.20691591501235962 0.8526168 0.46511855721473694 True -15 28816 19.718876838684082 0.3697397708892822 173.00387573242188 0.3729180097579956 184.00265502929688 0.2071579247713089 0.8547701 0.4556342661380768 True -16 30617 19.773553609848022 0.36913180351257324 178.9516143798828 0.40421465039253235 183.9137725830078 0.20757032930850983 0.85701114 0.45052453875541687 True -17 32418 19.708765983581543 0.37033581733703613 138.62680053710938 0.3876534700393677 184.05709838867188 0.2071145474910736 0.8579433 0.45298099517822266 True -18 34219 19.67203164100647 0.3674349784851074 124.26766967773438 0.8119045495986938 184.18643188476562 0.20737531781196594 0.856007 0.45910200476646423 False -19 36020 19.682352304458618 0.36997079849243164 136.9823455810547 0.33169832825660706 184.44671630859375 0.20679309964179993 0.8567012 0.46143069863319397 False diff --git a/ENCSR654WXX/cherimoya.fold_0.performance.tsv b/ENCSR654WXX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7321422711f68cdb76a568d3e03865e56279c001..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -184.05709838867188 0.5547291040420532 0.2071145623922348 0.059398822486400604 0.8579432964324951 0.7879918217658997 0.45298099517822266 \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_1.evaluate.json b/ENCSR654WXX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7afb3ece8ae48b9b0e7f1c29730efb48d582e651..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF623NNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_1.fit.json b/ENCSR654WXX/cherimoya.fold_1.fit.json deleted file mode 100644 index 6493b490e6dff7b3369fe391e8dac77e0e2b638b..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF623NNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_1.log b/ENCSR654WXX/cherimoya.fold_1.log deleted file mode 100644 index 963ba08dc1cf54fff6a024cd8c84cd5a35061c67..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1760 24.13459801673889 3.42895770072937 196.22190856933594 0.7422788143157959 313.2418518066406 0.11743800342082977 0.5882152 8.549592018127441 True -1 3520 19.65085482597351 1.3075652122497559 192.94973754882812 0.6912668943405151 279.9486999511719 0.18254120647907257 0.71345234 5.166454315185547 True -2 5280 19.716480016708374 0.4914844036102295 166.707763671875 0.6277472376823425 258.8768310546875 0.21120962500572205 0.7449389 2.8317341804504395 True -3 7040 19.620042324066162 0.4906444549560547 207.29913330078125 0.897593080997467 251.15625 0.21865881979465485 0.767714 1.7731815576553345 True -4 8800 19.606162786483765 0.48446011543273926 191.5513916015625 0.897291362285614 247.1678009033203 0.22406142950057983 0.7877941 1.4110225439071655 True -5 10560 19.625789642333984 0.507502555847168 236.3126678466797 0.7591620683670044 244.96673583984375 0.22875794768333435 0.79479414 1.2927675247192383 True -6 12320 19.611714601516724 0.47957587242126465 234.96224975585938 1.2515220642089844 243.18017578125 0.23183652758598328 0.80310625 1.1646548509597778 True -7 14080 19.64081311225891 1.0350563526153564 160.6964874267578 0.6529589295387268 241.431640625 0.23499538004398346 0.81178015 1.0481388568878174 True -8 15840 19.65152335166931 0.4820735454559326 186.9189453125 0.4691912531852722 240.26011657714844 0.23696327209472656 0.8258968 0.9030243754386902 True -9 17600 19.653128385543823 1.2389445304870605 157.72244262695312 0.5919535160064697 238.8226318359375 0.2395477443933487 0.83475566 0.8281893134117126 True -10 19360 19.66207504272461 0.5019810199737549 131.88018798828125 0.5550061464309692 237.5413055419922 0.24156713485717773 0.8418325 0.7496563792228699 True -11 21120 19.696632623672485 0.4953882694244385 190.61483764648438 0.8203490972518921 236.44097900390625 0.243111714720726 0.8500625 0.651136040687561 True -12 22880 19.65204644203186 0.494964599609375 162.156982421875 0.3986859917640686 235.32168579101562 0.24489983916282654 0.8540511 0.6075983047485352 True -13 24640 19.623153924942017 0.49376487731933594 167.6465606689453 0.42022937536239624 234.55824279785156 0.24640077352523804 0.86018974 0.578726589679718 True -14 26400 19.652244567871094 0.48703455924987793 144.6924591064453 0.41955214738845825 233.81736755371094 0.24761523306369781 0.8626922 0.5531378984451294 True -15 28160 19.639254093170166 0.4784352779388428 156.40093994140625 0.3606392741203308 233.27845764160156 0.24844522774219513 0.8671386 0.5492169260978699 True -16 29920 19.686999320983887 0.48621034622192383 135.25814819335938 0.6045712232589722 233.57525634765625 0.24698027968406677 0.8672238 0.5347676873207092 True -17 31680 19.62363886833191 2.2147579193115234 154.10516357421875 0.3879210948944092 233.04312133789062 0.24829919636249542 0.86905175 0.5341798663139343 True -18 33440 19.653818607330322 2.327946424484253 128.2980499267578 0.538628876209259 233.11019897460938 0.24839210510253906 0.86885566 0.5353125929832458 False -19 35200 19.659645080566406 0.4915339946746826 194.72100830078125 0.36287668347358704 233.42385864257812 0.24800601601600647 0.8694058 0.5394367575645447 True diff --git a/ENCSR654WXX/cherimoya.fold_1.performance.tsv b/ENCSR654WXX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 414d8dfa5ed8d08ad18a61894612999a016418e4..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -233.42385864257812 0.5245332717895508 0.24800601601600647 0.076781265437603 0.8694058060646057 0.8313271999359131 0.5394367575645447 \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_2.evaluate.json b/ENCSR654WXX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0185312e59b9b20784e5f048f1f05bf97dcfe3bc..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF623NNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_2.fit.json b/ENCSR654WXX/cherimoya.fold_2.fit.json deleted file mode 100644 index e0cfea3d4a6f884f803a145fc4323b80f50fa5d1..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF623NNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_2.log b/ENCSR654WXX/cherimoya.fold_2.log deleted file mode 100644 index 1f5dc0f9d8a5c3d1f00ff31b367a232b85e0eb69..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1896 25.488189697265625 3.418753147125244 160.35552978515625 0.644093930721283 261.55523681640625 0.11014103144407272 0.59325486 6.670833110809326 True -1 3792 21.78938055038452 0.45227837562561035 166.21253967285156 0.7889801859855652 231.54510498046875 0.16928648948669434 0.7236727 3.69062876701355 True -2 5688 21.006263494491577 0.3643608093261719 141.20562744140625 0.7197710275650024 214.77882385253906 0.19113509356975555 0.77391243 1.8643324375152588 True -3 7584 20.831949949264526 0.987356424331665 145.62637329101562 0.9356287717819214 210.22409057617188 0.197706937789917 0.7883038 1.1537699699401855 True -4 9480 20.752331733703613 2.0805249214172363 152.76727294921875 0.5257382988929749 208.53302001953125 0.19959129393100739 0.7956677 1.004905104637146 True -5 11376 20.743505239486694 0.3659639358520508 165.1635284423828 0.963492751121521 206.24839782714844 0.20359905064105988 0.80803037 0.8479264974594116 True -6 13272 20.724337339401245 1.4728593826293945 166.2238006591797 0.9452892541885376 204.7626190185547 0.20738226175308228 0.81283814 0.8122830986976624 True -7 15168 20.745997667312622 2.0096657276153564 140.24130249023438 0.40648871660232544 203.6869354248047 0.20904186367988586 0.82209796 0.7279829382896423 True -8 17064 20.734368324279785 0.3668086528778076 132.37696838378906 0.5721487998962402 202.67568969726562 0.21123282611370087 0.8270487 0.6725510358810425 True -9 18960 20.733744144439697 0.3685591220855713 157.57398986816406 0.6585038900375366 201.16136169433594 0.21455588936805725 0.8353111 0.5914278626441956 True -10 20856 20.74255609512329 0.36057162284851074 225.3546142578125 0.6543592214584351 200.0909881591797 0.2167997807264328 0.8403493 0.5572983026504517 True -11 22752 20.729654550552368 24.764519691467285 174.19479370117188 0.36967095732688904 199.28106689453125 0.21810442209243774 0.8434548 0.5416614413261414 True -12 24648 21.48897075653076 0.36752891540527344 206.55311584472656 0.5650840401649475 199.0416717529297 0.2182663232088089 0.8478238 0.5212799310684204 True -13 26544 20.757797956466675 0.36353445053100586 118.98341369628906 0.4707421064376831 197.6463165283203 0.22107245028018951 0.85264593 0.503723680973053 True -14 28440 20.753292560577393 0.3661625385284424 172.81936645507812 0.5456124544143677 197.62660217285156 0.22093786299228668 0.8552451 0.4890749454498291 True -15 30336 20.710691213607788 0.361738920211792 178.80300903320312 0.6202529668807983 197.3866729736328 0.2214861661195755 0.85813904 0.4791889190673828 True -16 32232 20.765769958496094 0.369356632232666 210.8291015625 0.35711240768432617 197.27658081054688 0.22193391621112823 0.861245 0.4713493883609772 True -17 34128 20.725739002227783 0.4033546447753906 149.65773010253906 0.4057542681694031 197.22442626953125 0.22205600142478943 0.85953945 0.47452065348625183 False -18 36024 20.831713676452637 0.3593747615814209 107.47119140625 0.394363671541214 197.1201629638672 0.22290730476379395 0.8587455 0.4804699420928955 False -19 37920 20.725569009780884 0.3637521266937256 165.8912353515625 0.5200240015983582 197.72496032714844 0.2209959626197815 0.85732216 0.48487985134124756 False diff --git a/ENCSR654WXX/cherimoya.fold_2.performance.tsv b/ENCSR654WXX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index df6840702ad3d61fcc0fe99a024b493e3180aff2..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -197.27658081054688 0.5441580414772034 0.22193388640880585 0.06436262279748917 0.8612449765205383 0.8006163239479065 0.4713493883609772 \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_3.evaluate.json b/ENCSR654WXX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 542dd0dae7ba2223252a3c515ec095ccc5e9cd1c..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF623NNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_3.fit.json b/ENCSR654WXX/cherimoya.fold_3.fit.json deleted file mode 100644 index 12f3e0f84e569fd771c80b39c87fe59a98c4a1b9..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF623NNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_3.log b/ENCSR654WXX/cherimoya.fold_3.log deleted file mode 100644 index 58b285f0192f1ef292878f8b056616e0418a3181..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1811 25.188136339187622 3.3220815658569336 141.31527709960938 0.8500191569328308 267.4003601074219 0.11733866482973099 0.60142326 6.872674465179443 True -1 3622 20.239470958709717 0.35196685791015625 197.31607055664062 0.5580317378044128 239.93255615234375 0.1734488606452942 0.7172629 4.115321636199951 True -2 5433 20.20448136329651 0.3388686180114746 166.4982147216797 0.955620527267456 226.93792724609375 0.19131684303283691 0.7430005 2.2383906841278076 True -3 7244 20.211015939712524 0.3376600742340088 186.10629272460938 0.6563795804977417 220.96725463867188 0.20098260045051575 0.76517016 1.5838639736175537 True -4 9055 20.1537983417511 0.3331272602081299 225.40769958496094 0.9824894666671753 219.35047912597656 0.2030722200870514 0.776977 1.3058944940567017 True -5 10866 20.137993812561035 0.3683292865753174 155.34219360351562 0.8882880210876465 216.41244506835938 0.20810605585575104 0.7940893 1.1548504829406738 True -6 12677 20.166303634643555 0.334796667098999 176.61680603027344 0.5880513787269592 214.2958221435547 0.21300764381885529 0.79495895 1.054727554321289 True -7 14488 20.130703449249268 0.33743834495544434 155.7939910888672 0.8296617269515991 213.18896484375 0.21475383639335632 0.8064386 0.92564457654953 True -8 16299 20.157697200775146 0.3412208557128906 145.7125701904297 0.6300437450408936 212.07398986816406 0.21740780770778656 0.81538343 0.8117998838424683 True -9 18110 20.11962914466858 1.5867383480072021 184.50302124023438 0.7454961538314819 210.80032348632812 0.2193855494260788 0.82668155 0.6954032778739929 True -10 19921 20.185829401016235 0.3488914966583252 139.26629638671875 0.8803573846817017 209.84384155273438 0.2209606170654297 0.83692914 0.6312727928161621 True -11 21732 20.176023721694946 0.33973145484924316 121.00728607177734 0.8743338584899902 208.95091247558594 0.22339388728141785 0.84097093 0.6011629700660706 True -12 23543 20.17615795135498 2.1425037384033203 182.91799926757812 0.7353500127792358 207.8262176513672 0.2255091816186905 0.84636915 0.5770659446716309 True -13 25354 20.184943675994873 12.591386318206787 220.94976806640625 0.7418711185455322 207.60250854492188 0.22626887261867523 0.8512058 0.5552878975868225 True -14 27165 20.882185459136963 13.734398603439331 190.00912475585938 0.4810163974761963 207.13621520996094 0.22637657821178436 0.8553068 0.5376132130622864 True -15 28976 20.208109855651855 0.4808218479156494 169.10208129882812 0.3877473473548889 206.28384399414062 0.22812597453594208 0.8598017 0.514143705368042 True -16 30787 20.191637992858887 1.461583137512207 149.69903564453125 0.31801992654800415 205.63943481445312 0.22919198870658875 0.8633904 0.5029275417327881 True -17 32598 20.208919048309326 0.38924551010131836 150.48667907714844 0.41978028416633606 205.72634887695312 0.22876282036304474 0.8632394 0.49918001890182495 False -18 34409 20.21208620071411 1.8668358325958252 140.0441436767578 0.3631556034088135 206.26231384277344 0.22768568992614746 0.8622186 0.5036866664886475 False -19 36220 20.35238218307495 18.649736404418945 165.27761840820312 0.34837645292282104 206.159912109375 0.2283020317554474 0.86123514 0.5058320760726929 False diff --git a/ENCSR654WXX/cherimoya.fold_3.performance.tsv b/ENCSR654WXX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 179acf5006078047b7674d26c71c8aa2b170cb50..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -205.63943481445312 0.5382312536239624 0.22919200360774994 0.0649930015206337 0.8633903861045837 0.8199586868286133 0.5029275417327881 \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_4.evaluate.json b/ENCSR654WXX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 063ac994bc5f1d9e6bcb743eea0b8d9e4edafc43..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF623NNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_4.fit.json b/ENCSR654WXX/cherimoya.fold_4.fit.json deleted file mode 100644 index d3d13cb6c17c6745ae741be47365a5e8cdad6472..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF623NNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR654WXX/cherimoya.fold_4.log b/ENCSR654WXX/cherimoya.fold_4.log deleted file mode 100644 index 8540448f06bc790112e4afb0178b30c407fd37a9..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1789 24.471094846725464 4.289016246795654 199.6347198486328 0.8523436784744263 221.61683654785156 0.10400617122650146 0.5973784 5.735121250152588 True -1 3578 19.61533212661743 0.37964701652526855 188.90499877929688 1.0182291269302368 201.86944580078125 0.15114203095436096 0.71204185 3.508610486984253 True -2 5367 19.963841438293457 12.755719184875488 172.69480895996094 1.0294156074523926 189.674560546875 0.17022940516471863 0.7494459 2.1329424381256104 True -3 7156 20.962002277374268 10.589239597320557 128.98681640625 0.6930657625198364 184.32518005371094 0.17688357830047607 0.7696046 1.1812857389450073 True -4 8945 19.920095682144165 0.3616292476654053 135.9041748046875 0.8163334131240845 182.13507080078125 0.17961348593235016 0.7815049 1.02497398853302 True -5 10734 19.928579092025757 0.36301493644714355 178.84873962402344 0.7908320426940918 181.0167999267578 0.18041664361953735 0.79305714 0.978156328201294 True -6 12523 19.92362904548645 0.35422825813293457 209.66696166992188 0.8322509527206421 179.8135223388672 0.18413804471492767 0.7917732 0.9143733978271484 False -7 14312 19.94120979309082 0.35921359062194824 112.20193481445312 0.4937896728515625 178.75965881347656 0.186630979180336 0.80049884 0.8127667903900146 True -8 16101 19.95454478263855 0.3606283664703369 203.67457580566406 0.6101933717727661 177.43972778320312 0.18949171900749207 0.8143144 0.6787751913070679 True -9 17890 19.9492506980896 0.5057826042175293 179.21495056152344 0.6918578147888184 176.82496643066406 0.1905742883682251 0.8231401 0.5808554291725159 True -10 19679 19.932183742523193 0.3579280376434326 200.4786376953125 0.44742733240127563 176.17556762695312 0.1918668895959854 0.8301283 0.5211953520774841 True -11 21468 19.92635941505432 1.3287303447723389 193.3976287841797 0.6080173850059509 175.95947265625 0.19197964668273926 0.8340761 0.4953248202800751 True -12 23257 19.990087747573853 0.35864996910095215 156.63438415527344 0.40978527069091797 175.40707397460938 0.19340740144252777 0.8367427 0.47919225692749023 True -13 25046 20.032543182373047 0.36066341400146484 136.32620239257812 0.6007559299468994 174.89588928222656 0.19451768696308136 0.8413844 0.46924519538879395 True -14 26835 19.98195743560791 0.3532743453979492 177.99127197265625 0.5873971581459045 174.447509765625 0.19559699296951294 0.84486884 0.45754387974739075 True -15 28624 19.908037900924683 0.973874568939209 152.74209594726562 0.49223101139068604 174.07994079589844 0.1960243433713913 0.8468171 0.44485780596733093 True -16 30413 19.92188310623169 0.3559725284576416 158.445068359375 0.4321615993976593 173.66159057617188 0.19737635552883148 0.8499589 0.43996843695640564 True -17 32202 19.968268156051636 0.35196447372436523 151.6280975341797 0.35511648654937744 173.7299041748047 0.196975976228714 0.85058504 0.4400058686733246 True -18 33991 19.9160737991333 0.359804630279541 93.93083953857422 0.3069612979888916 174.141845703125 0.19605852663516998 0.8507674 0.44342169165611267 True -19 35780 19.90487551689148 0.35384225845336914 136.84986877441406 0.5090498924255371 174.1466064453125 0.1965918391942978 0.85141295 0.44580695033073425 True diff --git a/ENCSR654WXX/cherimoya.fold_4.performance.tsv b/ENCSR654WXX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3487199b0407710286a4b3f016624486251fa800..0000000000000000000000000000000000000000 --- a/ENCSR654WXX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -174.1466064453125 0.5621721744537354 0.1965918242931366 0.0512654185295105 0.8514129519462585 0.776235818862915 0.44580695033073425 \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_0.evaluate.json b/ENCSR656KLT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 79e69fd8e45cfabf62c408e3965d1e99c25600e9..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124YLB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_0.fit.json b/ENCSR656KLT/cherimoya.fold_0.fit.json deleted file mode 100644 index be8b3823e75064a275b31bab1b0ca3b5e3db3735..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF124YLB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_0.log b/ENCSR656KLT/cherimoya.fold_0.log deleted file mode 100644 index 32bccfb2409bc39c5ccfc36e9c9711e8ddd3e087..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 35.220635414123535 3.870433807373047 990.51123046875 1.3679882287979126 1266.8885498046875 0.3056600093841553 0.4717083 13.331842422485352 True -1 5526 29.84176540374756 0.6111264228820801 743.9996337890625 0.9302011132240295 985.9135131835938 0.4395892024040222 0.5875089 7.411647319793701 True -2 8289 30.362067699432373 0.5685234069824219 563.162353515625 0.7851136326789856 967.4124145507812 0.4489961266517639 0.5986821 4.598911285400391 True -3 11052 30.09333610534668 0.6399710178375244 891.025390625 1.431635856628418 948.9180908203125 0.4574888348579407 0.6158141 3.7533931732177734 True -4 13815 29.6898455619812 0.5370502471923828 733.538330078125 0.8862903118133545 938.2899169921875 0.461470365524292 0.62093055 2.9142417907714844 True -5 16578 29.73023271560669 0.5365655422210693 931.7677612304688 1.2409937381744385 923.046630859375 0.47077780961990356 0.6310505 2.6220688819885254 True -6 19341 29.748814821243286 0.5488128662109375 699.32861328125 0.8359691500663757 917.2054443359375 0.473094642162323 0.6371285 2.214832067489624 True -7 22104 29.763763904571533 0.5250563621520996 582.487060546875 1.0029315948486328 911.6854248046875 0.4763427674770355 0.6430151 2.1009347438812256 True -8 24867 29.768988847732544 0.5391044616699219 667.6085815429688 0.7082322835922241 903.40234375 0.48143184185028076 0.6543505 2.0233986377716064 True -9 27630 29.721975326538086 0.5353977680206299 724.2259521484375 1.0519919395446777 897.63330078125 0.48578599095344543 0.66318774 1.775253176689148 True -10 30393 29.693256855010986 0.5379915237426758 647.8472290039062 0.7214037775993347 893.7002563476562 0.48612308502197266 0.67082113 1.5922902822494507 True -11 33156 29.69713282585144 0.5435352325439453 899.904296875 0.8126881718635559 886.5892333984375 0.4899967312812805 0.6817319 1.3841698169708252 True -12 35919 29.758301258087158 0.534630298614502 608.5103759765625 0.8583016395568848 877.7741088867188 0.4942881166934967 0.6863297 1.2945644855499268 True -13 38682 29.695587635040283 0.5371742248535156 718.7169189453125 0.5942854881286621 867.0494384765625 0.4997807443141937 0.70459145 1.085316777229309 True -14 41445 29.743919610977173 0.533374547958374 608.6741943359375 0.63621985912323 861.0184936523438 0.5009348392486572 0.7151686 0.9588927030563354 True -15 44208 29.72173261642456 0.5352921485900879 563.4053955078125 0.6675440669059753 859.292724609375 0.5002090930938721 0.7252111 0.8560918569564819 True -16 46971 29.73565411567688 0.5415482521057129 645.868896484375 0.6409623622894287 854.6300048828125 0.5049602389335632 0.73077494 0.7950077056884766 True -17 49734 29.812889099121094 0.5383424758911133 639.0866088867188 0.6274884343147278 855.4199829101562 0.50423663854599 0.73513544 0.7469149231910706 True -18 52497 29.78177523612976 0.5391445159912109 686.4844970703125 0.5928809642791748 853.9385375976562 0.5047678351402283 0.73561233 0.729990541934967 True -19 55260 29.79077410697937 0.5296876430511475 637.46337890625 0.47723421454429626 854.3153076171875 0.5052458643913269 0.7341136 0.7293738126754761 False diff --git a/ENCSR656KLT/cherimoya.fold_0.performance.tsv b/ENCSR656KLT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ac786d2bc3a8d24a121ea497e039381f2acc885b..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -853.9385375976562 0.3138919174671173 0.5047678351402283 0.22607135772705078 0.7356123328208923 0.6875855922698975 0.729990541934967 \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_1.evaluate.json b/ENCSR656KLT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9e4b7f97538cae7ca8eafb3f1025b1cdbeb977b9..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124YLB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_1.fit.json b/ENCSR656KLT/cherimoya.fold_1.fit.json deleted file mode 100644 index 2576abee55b252e35e22cc0fec6b96995f59bc7d..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF124YLB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_1.log b/ENCSR656KLT/cherimoya.fold_1.log deleted file mode 100644 index 63dc3aae0a075669863f12b5860b6e5261c51afa..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2722 34.69866132736206 5.004868030548096 848.5247802734375 2.106661319732666 1453.6552734375 0.30053040385246277 0.507149 14.372130393981934 True -1 5444 29.85239291191101 0.9274556636810303 829.2215576171875 1.3147835731506348 1148.931884765625 0.43694695830345154 0.62543315 8.739654541015625 True -2 8166 29.840484142303467 0.7173893451690674 766.6747436523438 1.1836713552474976 1131.531982421875 0.4426902234554291 0.6396161 4.946253776550293 True -3 10888 29.985770225524902 2.104337692260742 613.684814453125 0.8853667378425598 1089.1859130859375 0.4611513614654541 0.6601117 3.4610934257507324 True -4 13610 29.84917187690735 0.7232623100280762 631.28955078125 0.7749960422515869 1085.223388671875 0.4644452929496765 0.66414726 3.3218417167663574 True -5 16332 29.839483976364136 0.7293016910552979 651.5931396484375 1.0250893831253052 1076.65283203125 0.46913567185401917 0.66765887 3.2888431549072266 True -6 19054 29.84887146949768 0.7020502090454102 698.0518798828125 0.9115759134292603 1067.4791259765625 0.4742787480354309 0.67123425 2.7218949794769287 True -7 21776 29.788443088531494 0.7087633609771729 870.267333984375 1.1343472003936768 1059.05224609375 0.47715502977371216 0.67973316 2.5555636882781982 True -8 24498 29.283318281173706 0.7260138988494873 634.68994140625 0.7565149068832397 1045.07861328125 0.4846237599849701 0.6920801 2.0832417011260986 True -9 27220 29.27402424812317 0.7033171653747559 765.2463989257812 0.6200791597366333 1033.057861328125 0.4900682866573334 0.70101804 1.885918140411377 True -10 29942 29.47703218460083 0.9044959545135498 792.3119506835938 0.9217427968978882 1024.890380859375 0.4928966462612152 0.70749235 1.7083547115325928 True -11 32664 29.300801515579224 0.7279901504516602 571.762451171875 0.5886900424957275 1016.4769287109375 0.4954912066459656 0.72254103 1.5173324346542358 True -12 35386 29.517468690872192 0.7419488430023193 758.0291748046875 0.8527330756187439 1001.4540405273438 0.5005301237106323 0.7317541 1.2915210723876953 True -13 38108 29.249608755111694 16.29074716567993 758.966064453125 0.8730553388595581 993.2056274414062 0.5027885437011719 0.7475446 1.0703794956207275 True -14 40830 29.36117959022522 0.7082643508911133 517.4995727539062 0.6358678936958313 985.4812622070312 0.503970742225647 0.7594974 0.92511385679245 True -15 43552 29.280570030212402 0.7056334018707275 588.108154296875 0.5770014524459839 973.653564453125 0.5106739401817322 0.76942134 0.805656373500824 True -16 46274 29.274160861968994 1.2369866371154785 716.0924682617188 0.444715678691864 971.61376953125 0.5095251202583313 0.7730017 0.7330834269523621 True -17 48996 29.33120894432068 0.703927755355835 797.718505859375 0.794655442237854 968.7208251953125 0.5111967921257019 0.77686924 0.6904711723327637 True -18 51718 29.343055486679077 0.6890754699707031 651.0335693359375 0.45366159081459045 969.3674926757812 0.5112316012382507 0.777576 0.6726033687591553 True -19 54440 29.279757499694824 0.6954140663146973 643.042236328125 0.3981305956840515 970.0072631835938 0.5105487108230591 0.77652895 0.673095166683197 False diff --git a/ENCSR656KLT/cherimoya.fold_1.performance.tsv b/ENCSR656KLT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f6e94a585563874d1016cce9f0edd1429240fc49..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -969.3674926757812 0.30330485105514526 0.511231541633606 0.24565880000591278 0.7775760293006897 0.7420267462730408 0.6726033687591553 \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_2.evaluate.json b/ENCSR656KLT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cd43429a9b4cce5093dba49c5d67aa7fa970eaff..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124YLB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_2.fit.json b/ENCSR656KLT/cherimoya.fold_2.fit.json deleted file mode 100644 index 33143a440f9328a9cac3507967d9e945d5634808..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF124YLB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_2.log b/ENCSR656KLT/cherimoya.fold_2.log deleted file mode 100644 index 2a4ec63806cb17f2d0eb98fac71f542691c6dfa2..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.39448595046997 4.123625993728638 830.7664184570312 1.3499655723571777 1300.7376708984375 0.30519264936447144 0.46255362 12.486212730407715 True -1 5772 31.829606294631958 9.131540060043335 684.221923828125 0.948241114616394 1031.2967529296875 0.4248082637786865 0.59159786 6.488165855407715 True -2 8658 31.446383953094482 0.5948801040649414 708.0841064453125 0.8711305856704712 1016.8994140625 0.43159112334251404 0.600762 3.266127586364746 True -3 11544 31.043930053710938 0.896141529083252 915.221435546875 1.1738243103027344 994.554931640625 0.44192391633987427 0.61885923 4.269761085510254 True -4 14430 31.15393853187561 21.793365716934204 728.8189697265625 0.8743806481361389 975.5242309570312 0.4508063495159149 0.63753045 2.4051027297973633 True -5 17316 31.213768005371094 0.8051013946533203 748.6724853515625 1.1699929237365723 963.7778930664062 0.45756766200065613 0.64973843 2.1544783115386963 True -6 20202 31.10593032836914 0.6118850708007812 814.16796875 1.1675947904586792 958.5579833984375 0.4630126655101776 0.654029 2.1529955863952637 True -7 23088 31.1021511554718 0.5992286205291748 739.4035034179688 1.1339975595474243 948.1553955078125 0.4667976200580597 0.66457766 1.9613360166549683 True -8 25974 31.091944456100464 0.9416613578796387 531.6187133789062 0.8417314291000366 938.4661254882812 0.47056373953819275 0.6754656 1.8150752782821655 True -9 28860 31.04914689064026 0.5917911529541016 678.553466796875 0.6364222168922424 934.1165161132812 0.47422248125076294 0.6850883 1.66077721118927 True -10 31746 31.096781969070435 0.591965913772583 549.5957641601562 1.0098950862884521 926.6603393554688 0.4786085784435272 0.6938111 1.4864009618759155 True -11 34632 31.07128667831421 0.5873830318450928 771.0679931640625 0.5761042237281799 917.5738525390625 0.4815063774585724 0.7032927 1.2869715690612793 True -12 37518 31.030706644058228 1.0449614524841309 741.5506591796875 0.6943637132644653 912.5546875 0.4825596213340759 0.7122815 1.116283655166626 True -13 40404 31.092756271362305 0.5804588794708252 662.2557373046875 0.7024490833282471 901.5870971679688 0.4880898892879486 0.72051316 0.9796642661094666 True -14 43290 31.084943532943726 0.5933253765106201 619.6646728515625 0.7801780700683594 898.7310791015625 0.4884745180606842 0.72781044 0.8835002779960632 True -15 46176 31.089935064315796 0.5887892246246338 690.5283203125 0.48414987325668335 891.646484375 0.4914207458496094 0.7357562 0.7968160510063171 True -16 49062 31.16714572906494 5.736370086669922 706.7662353515625 0.6057642698287964 886.4599609375 0.4945952892303467 0.74107885 0.7480782866477966 True -17 51948 31.112085103988647 7.975612640380859 573.35693359375 0.7430409789085388 886.4573364257812 0.49451667070388794 0.7428022 0.724558413028717 True -18 54834 31.144376754760742 0.587343692779541 625.9525146484375 0.5516189336776733 888.6365966796875 0.4920908212661743 0.74144644 0.7175465226173401 False -19 57720 31.11078977584839 1.202946662902832 614.4356689453125 0.45576751232147217 885.9434204101562 0.494830459356308 0.741683 0.7190966606140137 False diff --git a/ENCSR656KLT/cherimoya.fold_2.performance.tsv b/ENCSR656KLT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ac340d4815f7e138acf15565a63e704537a20786..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -886.4573364257812 0.31662115454673767 0.4945165812969208 0.22875872254371643 0.7428022027015686 0.7005229592323303 0.724558413028717 \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_3.evaluate.json b/ENCSR656KLT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 55f13988e9f783636eb5891b503eb64be5d0806a..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124YLB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_3.fit.json b/ENCSR656KLT/cherimoya.fold_3.fit.json deleted file mode 100644 index 0ebdeecf2c67704d1d8a1a3a2a2b1cc4d315bec8..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF124YLB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_3.log b/ENCSR656KLT/cherimoya.fold_3.log deleted file mode 100644 index 7278a02682edcf0c7d69290fde6c80da11fc1cd6..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2781 35.375351905822754 3.8152568340301514 678.6005859375 0.9479397535324097 1215.856689453125 0.3158501386642456 0.45644152 13.196734428405762 True -1 5562 30.562209367752075 0.7347283363342285 663.7216796875 1.118727684020996 978.5774536132812 0.438586562871933 0.5870561 7.237987995147705 True -2 8343 30.649139642715454 0.5573415756225586 748.2945556640625 1.0465465784072876 950.4313354492188 0.45295706391334534 0.6061231 5.006518840789795 True -3 11124 30.500574827194214 0.5574078559875488 964.3223876953125 1.767256259918213 930.0807495117188 0.4604024589061737 0.6258132 4.220715522766113 True -4 13905 30.74347949028015 0.5849878787994385 772.5611572265625 0.9268072843551636 921.452880859375 0.467245876789093 0.6329903 3.2417166233062744 True -5 16686 30.509074687957764 0.5590014457702637 881.5113525390625 0.6771721839904785 912.2685546875 0.46993592381477356 0.63804233 2.9365968704223633 True -6 19467 30.52601909637451 0.5529580116271973 679.4857177734375 0.766564130783081 897.5028076171875 0.4792579710483551 0.648747 2.616048574447632 True -7 22248 30.64422607421875 13.047772407531738 678.5689697265625 0.8994559645652771 889.69580078125 0.4813394248485565 0.6535268 2.3950247764587402 True -8 25029 30.616597175598145 1.0800228118896484 645.9735717773438 1.0625684261322021 882.6832275390625 0.48571425676345825 0.66683125 2.0519001483917236 True -9 27810 30.466586351394653 0.5438320636749268 981.4510498046875 0.7344068884849548 874.9190673828125 0.48944079875946045 0.675127 1.9446775913238525 True -10 30591 30.071995735168457 0.5583930015563965 715.5819091796875 1.0469826459884644 866.046875 0.49459314346313477 0.6846131 1.6694320440292358 True -11 33372 30.01486039161682 0.5529229640960693 903.4667358398438 0.8454666137695312 858.1080322265625 0.49757635593414307 0.69435537 1.3996143341064453 True -12 36153 30.060899019241333 0.5529389381408691 726.1326904296875 0.7442185878753662 849.400146484375 0.502618670463562 0.70389336 1.2592796087265015 True -13 38934 29.993185997009277 0.537388801574707 643.17041015625 0.5729320645332336 841.3128662109375 0.5062867403030396 0.7157633 1.0985941886901855 True -14 41715 30.071234941482544 0.5803730487823486 738.1925659179688 1.0350797176361084 836.6968383789062 0.5066700577735901 0.72547275 0.9473084807395935 True -15 44496 30.010898113250732 0.5349102020263672 529.2337646484375 0.5235011577606201 833.5953369140625 0.5078118443489075 0.7325619 0.8536856174468994 True -16 47277 29.967817783355713 0.5527925491333008 695.287353515625 0.6244131326675415 830.5823364257812 0.5103487968444824 0.74053705 0.7701608538627625 True -17 50058 30.04953646659851 0.5476851463317871 664.031005859375 0.7433489561080933 828.9891357421875 0.5116347074508667 0.7430196 0.7337902188301086 True -18 52839 29.99914312362671 0.9435310363769531 669.855224609375 0.6454439759254456 830.16796875 0.5108088254928589 0.7421883 0.7186803221702576 False -19 55620 29.975169897079468 0.5395071506500244 621.4736938476562 0.3906432092189789 829.8556518554688 0.5113113522529602 0.74199724 0.7173451781272888 False diff --git a/ENCSR656KLT/cherimoya.fold_3.performance.tsv b/ENCSR656KLT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 344da817a8426acd4356ea343b9304cfb1262724..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -828.9891357421875 0.3093874156475067 0.5116346478462219 0.22898373007774353 0.7430195808410645 0.6924989223480225 0.7337902188301086 \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_4.evaluate.json b/ENCSR656KLT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d9f0fadf4c4cfa0d78a07fcb2b83149df12b29dc..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124YLB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_4.fit.json b/ENCSR656KLT/cherimoya.fold_4.fit.json deleted file mode 100644 index 27ee8b7402d961e46c6bb308da0fdd3545dfbce5..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF124YLB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR656KLT/cherimoya.fold_4.log b/ENCSR656KLT/cherimoya.fold_4.log deleted file mode 100644 index 87d5b8473f59732ce6bebb1562eb961d736d705f..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.25864791870117 3.8467648029327393 745.064208984375 0.9793213605880737 1148.5714111328125 0.3034817576408386 0.4502648 12.532848358154297 True -1 5518 30.313952207565308 0.649371862411499 809.7662353515625 0.8755849599838257 914.6437377929688 0.42441314458847046 0.57746077 7.228645324707031 True -2 8277 30.27694010734558 0.5639348030090332 783.8795776367188 1.1879918575286865 900.0481567382812 0.4299779534339905 0.5865318 4.250120162963867 True -3 11036 30.169018983840942 0.5471031665802002 850.58154296875 1.4642078876495361 880.8807373046875 0.4408998489379883 0.60404897 3.3487305641174316 True -4 13795 29.670989990234375 0.5475249290466309 836.2369995117188 1.0904760360717773 868.9352416992188 0.4466942250728607 0.6190989 2.8759050369262695 True -5 16554 29.66648507118225 0.545041561126709 789.234375 1.0436885356903076 859.4680786132812 0.4518565237522125 0.6278076 2.7490127086639404 True -6 19313 29.696344137191772 0.5467522144317627 873.1647338867188 1.011501669883728 852.2567749023438 0.4556402266025543 0.6373919 2.3365912437438965 True -7 22072 29.819339990615845 0.5431108474731445 715.43017578125 0.8724338412284851 844.5967407226562 0.45931726694107056 0.64292264 2.0006468296051025 True -8 24831 29.709353923797607 18.737773418426514 624.0709228515625 1.1640291213989258 837.41650390625 0.4624484181404114 0.6551052 1.7265111207962036 True -9 27590 29.82711100578308 10.719924688339233 866.8983154296875 0.7539347410202026 828.4197998046875 0.4696361720561981 0.6700681 1.566850185394287 True -10 30349 29.752068519592285 0.9820520877838135 623.5062255859375 1.1409279108047485 822.1785278320312 0.4722990393638611 0.67401534 1.4123014211654663 True -11 33108 29.7023286819458 0.549994707107544 844.3489990234375 0.9505256414413452 816.9495239257812 0.47690075635910034 0.68229365 1.2696889638900757 True -12 35867 29.70328378677368 0.5817856788635254 790.3746337890625 0.7747601866722107 807.8969116210938 0.4813816547393799 0.69577485 1.1071761846542358 True -13 38626 29.663115739822388 0.5415468215942383 749.8890380859375 0.7809292674064636 803.7012329101562 0.48246487975120544 0.70546293 0.9745123386383057 True -14 41385 29.669523000717163 0.5472583770751953 571.879638671875 0.6419810056686401 799.0836791992188 0.48505473136901855 0.71449953 0.8808931112289429 True -15 44144 29.71459197998047 0.5449652671813965 656.3031005859375 0.6745103597640991 794.7116088867188 0.4883387088775635 0.72562796 0.7855570316314697 True -16 46903 29.69671368598938 0.5280277729034424 741.2947387695312 0.5345728993415833 796.7177734375 0.48551079630851746 0.73338383 0.7317941188812256 True -17 49662 29.674084186553955 0.5357208251953125 691.16259765625 0.9388102293014526 794.8125610351562 0.4848365783691406 0.73789996 0.7024681568145752 True -18 52421 29.734523057937622 0.5358960628509521 686.42626953125 0.6711163520812988 795.4794311523438 0.4849694073200226 0.7375902 0.6964803338050842 False -19 55180 29.734743118286133 0.5398023128509521 578.5849609375 0.436933308839798 792.2526245117188 0.4886346757411957 0.73781615 0.6936548948287964 False diff --git a/ENCSR656KLT/cherimoya.fold_4.performance.tsv b/ENCSR656KLT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fac98be42985e4ab246bc74b5721458290b11ba0..0000000000000000000000000000000000000000 --- a/ENCSR656KLT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -794.8125610351562 0.3257235586643219 0.484836608171463 0.21493622660636902 0.7378999590873718 0.6797261834144592 0.7024681568145752 \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_0.evaluate.json b/ENCSR658UBE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 13f3e6defe3af93fe8ea43e82e7f544ac3121031..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF926FGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_0.fit.json b/ENCSR658UBE/cherimoya.fold_0.fit.json deleted file mode 100644 index 35e838ada6ced763c713a5d3d528bd3bce851b3e..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF926FGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_0.log b/ENCSR658UBE/cherimoya.fold_0.log deleted file mode 100644 index 3d7596b682ab96e7ae0da259b1d773a3b22479b0..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 34.279003620147705 3.5686800479888916 547.9390258789062 0.5138492584228516 774.3392333984375 0.28966134786605835 0.7358577 4.980748176574707 True -1 5468 30.44080424308777 0.6319248676300049 599.4029541015625 0.638785719871521 695.5196533203125 0.35852548480033875 0.79668975 1.9009344577789307 True -2 8202 30.349940299987793 0.5952146053314209 535.5523071289062 0.28469783067703247 680.2893676757812 0.3718683421611786 0.80740845 0.7458812594413757 True -3 10936 30.308404445648193 0.6134531497955322 589.03564453125 0.454338014125824 674.6475830078125 0.3769669532775879 0.8167308 0.5894202589988708 True -4 13670 30.42208456993103 0.6202595233917236 583.7646484375 0.32198160886764526 669.384521484375 0.3806159794330597 0.82171214 0.4907972514629364 True -5 16404 30.525623321533203 1.134091854095459 524.727783203125 0.4148966670036316 664.4666137695312 0.3879890739917755 0.8276077 0.45696794986724854 True -6 19138 30.445549964904785 0.6153826713562012 589.014404296875 0.3862774968147278 663.6424560546875 0.38899993896484375 0.83125764 0.44582727551460266 True -7 21872 30.56104612350464 0.611534833908081 526.5709228515625 0.23791079223155975 660.9884643554688 0.39122438430786133 0.8364539 0.4284674823284149 True -8 24606 30.506763219833374 0.6110954284667969 679.710205078125 0.4160451292991638 658.402099609375 0.39340269565582275 0.84152836 0.37718069553375244 True -9 27340 30.520646810531616 0.6396393775939941 495.34033203125 0.585514485836029 655.3475952148438 0.3957503139972687 0.8468645 0.35772573947906494 True -10 30074 30.48165249824524 0.6100490093231201 518.8236694335938 0.23795339465141296 653.2228393554688 0.3990938365459442 0.85050356 0.35685017704963684 True -11 32808 30.437713861465454 0.6107845306396484 526.3865966796875 0.2035413682460785 650.7615356445312 0.40049606561660767 0.85259604 0.3468111753463745 True -12 35542 30.51767063140869 0.608330488204956 660.20361328125 0.33922597765922546 649.8660888671875 0.4002847969532013 0.85739857 0.3349939286708832 True -13 38276 30.52065134048462 0.6081116199493408 547.0008544921875 0.34493452310562134 648.1475219726562 0.4024254083633423 0.86470467 0.3051557242870331 True -14 41010 30.458281993865967 0.6095690727233887 555.6110229492188 0.24980410933494568 644.6881103515625 0.40615785121917725 0.87002033 0.27521148324012756 True -15 43744 30.478872776031494 0.6143972873687744 503.9364929199219 0.2404269576072693 643.7125244140625 0.4066976010799408 0.8735825 0.25776606798171997 True -16 46478 30.483625173568726 0.6092562675476074 653.968994140625 0.30360350012779236 644.6383666992188 0.40543559193611145 0.8749887 0.2485928237438202 True -17 49212 30.45435643196106 0.6082236766815186 596.541259765625 0.2644405663013458 642.8731689453125 0.40814208984375 0.8777747 0.2405211180448532 True -18 51946 30.46967101097107 0.6097543239593506 580.70068359375 0.17763888835906982 642.6255493164062 0.40807053446769714 0.8776223 0.23955217003822327 False -19 54680 30.491492748260498 0.6114122867584229 563.8342895507812 0.18424299359321594 643.8220825195312 0.40614232420921326 0.87581563 0.23934689164161682 False diff --git a/ENCSR658UBE/cherimoya.fold_0.performance.tsv b/ENCSR658UBE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e13c9eb87d4a6b44bc26cad2d4051f728978c09e..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -642.8731689453125 0.37715062499046326 0.4081420600414276 0.17016690969467163 0.877774715423584 0.8332520723342896 0.2405211180448532 \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_1.evaluate.json b/ENCSR658UBE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bed86788d73d41d101d31340bf68d13957ffa81c..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF926FGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_1.fit.json b/ENCSR658UBE/cherimoya.fold_1.fit.json deleted file mode 100644 index ecf07c13b3a2596b663a44b62184e9b7d66816f5..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF926FGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_1.log b/ENCSR658UBE/cherimoya.fold_1.log deleted file mode 100644 index a46cf24ad16354062c8814a165119890fcd5eb8e..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 33.81011748313904 4.727443695068359 652.3592529296875 0.37162643671035767 937.2322387695312 0.29080042243003845 0.73419344 5.976014137268066 True -1 5410 29.939045667648315 0.7646493911743164 613.8410034179688 0.41005080938339233 828.9112548828125 0.3785398602485657 0.7976493 2.043320417404175 True -2 8115 29.92959690093994 0.7274322509765625 563.324462890625 0.6671439409255981 804.9139404296875 0.39732447266578674 0.8149261 0.9047150611877441 True -3 10820 29.9600932598114 0.766735315322876 647.8110961914062 0.4058568477630615 798.0548706054688 0.4009576737880707 0.8213849 0.749384343624115 True -4 13525 29.95006775856018 0.7408039569854736 621.0194091796875 0.45476436614990234 793.8226928710938 0.40605783462524414 0.8229288 0.7465970516204834 True -5 16230 29.911368131637573 0.7371609210968018 543.3797607421875 0.49026310443878174 790.46142578125 0.4090505838394165 0.8286444 0.7151683568954468 True -6 18935 29.961124658584595 1.195793628692627 499.349365234375 0.509121298789978 791.2455444335938 0.4074348211288452 0.83193237 0.6529145240783691 True -7 21640 30.012247800827026 0.7454962730407715 485.1724548339844 0.26389890909194946 785.6963500976562 0.4111464023590088 0.83695173 0.5902849435806274 True -8 24345 29.99447464942932 0.7473578453063965 526.911376953125 0.28305622935295105 781.1927490234375 0.41590553522109985 0.84075505 0.5996387004852295 True -9 27050 30.42392587661743 0.7411506175994873 630.66748046875 0.3139101564884186 777.2598876953125 0.4187670350074768 0.84770185 0.536149799823761 True -10 29755 29.942602396011353 0.7439343929290771 553.5077514648438 0.21079964935779572 772.2899780273438 0.4238339364528656 0.8508384 0.4929982125759125 True -11 32460 30.019604206085205 0.7270307540893555 568.6865234375 0.26005515456199646 771.1123657226562 0.4238130748271942 0.85435873 0.4532262980937958 True -12 35165 29.919836282730103 3.2371826171875 523.2518920898438 0.30305275321006775 766.78271484375 0.42754995822906494 0.8628261 0.40240439772605896 True -13 37870 29.912432193756104 0.7357420921325684 575.4267578125 0.3840734362602234 763.7499389648438 0.42941391468048096 0.8650678 0.3765502870082855 True -14 40575 29.927873611450195 0.7444858551025391 458.4678955078125 0.2478279024362564 762.4918823242188 0.43089786171913147 0.87050533 0.34836772084236145 True -15 43280 29.916001319885254 0.7364790439605713 548.8850708007812 0.22499120235443115 759.9674072265625 0.43282660841941833 0.87681097 0.3109547793865204 True -16 45985 29.93915319442749 0.735032320022583 608.8282470703125 0.18251971900463104 758.104248046875 0.4345638155937195 0.8814611 0.2846505641937256 True -17 48690 29.932623863220215 0.7482964992523193 505.3380432128906 0.37064844369888306 760.25927734375 0.4322117865085602 0.88298357 0.27206718921661377 True -18 51395 29.989943027496338 0.7381184101104736 570.322998046875 0.20756828784942627 759.7539672851562 0.43265315890312195 0.88426757 0.26688051223754883 True -19 54100 29.913976430892944 0.7451224327087402 474.56768798828125 0.22601160407066345 759.9456787109375 0.4324243366718292 0.8846306 0.26681193709373474 True diff --git a/ENCSR658UBE/cherimoya.fold_1.performance.tsv b/ENCSR658UBE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 95bd16d1a60bd7f25004aa1c6ce09b5f7e2f45b5..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -759.9456787109375 0.35422471165657043 0.4324243366718292 0.1964767426252365 0.8846306204795837 0.8621917963027954 0.26681193709373474 \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_2.evaluate.json b/ENCSR658UBE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 474d2a62c2513eac1af7ec114f47f11fb52b17fe..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF926FGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_2.fit.json b/ENCSR658UBE/cherimoya.fold_2.fit.json deleted file mode 100644 index 9f57cb7fe46bfbf2ec74a598187b68fc52020933..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF926FGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_2.log b/ENCSR658UBE/cherimoya.fold_2.log deleted file mode 100644 index da7e03ac432c9b0dfb3c87567d4ad1fe7ddbfc6d..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2901 35.80706739425659 3.40415096282959 578.5360107421875 0.48660212755203247 821.701171875 0.29238006472587585 0.7306489 4.668433666229248 True -1 5802 32.36409640312195 25.770261764526367 682.29736328125 0.42992550134658813 740.99853515625 0.3628557026386261 0.7996562 1.571205735206604 True -2 8703 32.202245235443115 2.241189956665039 663.31494140625 0.36890023946762085 726.5745849609375 0.3720501661300659 0.8049906 0.6602133512496948 True -3 11604 32.15968060493469 0.5760526657104492 662.734375 0.6607871055603027 719.3804321289062 0.37896105647087097 0.81281143 0.6064537763595581 True -4 14505 32.148311614990234 0.579986572265625 538.298095703125 0.3541852831840515 713.8882446289062 0.38279691338539124 0.8179414 0.6155836582183838 True -5 17406 32.097203969955444 0.5668656826019287 630.1888427734375 0.30622512102127075 712.6163330078125 0.38492220640182495 0.821154 0.5424516797065735 True -6 20307 32.14452886581421 0.5794730186462402 670.0653076171875 0.28973907232284546 709.0662841796875 0.38881203532218933 0.8247438 0.5196549296379089 True -7 23208 32.11757802963257 0.5726358890533447 425.63372802734375 0.27022188901901245 706.7039794921875 0.3906000554561615 0.8285326 0.4885258078575134 True -8 26109 32.17384672164917 0.5810091495513916 497.4787902832031 0.5372228622436523 704.9230346679688 0.39189401268959045 0.83347183 0.4697071611881256 True -9 29010 32.27689170837402 22.267979621887207 651.841064453125 0.4004385769367218 701.9279174804688 0.3954966366291046 0.8381912 0.4458424150943756 True -10 31911 32.14045000076294 0.5798959732055664 558.8287963867188 0.32264283299446106 698.9844970703125 0.3974127471446991 0.84483117 0.3956652581691742 True -11 34812 32.15743803977966 0.5770699977874756 610.58447265625 0.2773110866546631 695.521484375 0.40143606066703796 0.84837496 0.3818322718143463 True -12 37713 32.145516872406006 0.574284553527832 530.88427734375 0.282595694065094 691.5503540039062 0.40483298897743225 0.853393 0.34995439648628235 True -13 40614 32.11456847190857 0.5735447406768799 536.2679443359375 0.27428728342056274 691.2025756835938 0.4048115313053131 0.8568366 0.3293468654155731 True -14 43515 32.1366662979126 0.5766019821166992 487.1183776855469 0.24214714765548706 688.6052856445312 0.40748050808906555 0.86035836 0.30272695422172546 True -15 46416 32.10043549537659 0.5765604972839355 633.6939697265625 0.19787544012069702 687.7822875976562 0.4075063169002533 0.86593854 0.28257831931114197 True -16 49317 32.08752775192261 0.5704751014709473 467.83221435546875 0.22472098469734192 686.25146484375 0.41058096289634705 0.8690851 0.2687390446662903 True -17 52218 32.087575912475586 0.5776886940002441 522.4172973632812 0.2571324110031128 685.7590942382812 0.41052746772766113 0.8703726 0.26132744550704956 True -18 55119 32.085259437561035 0.5722103118896484 584.0909423828125 0.2097214162349701 687.2035522460938 0.40914466977119446 0.87025684 0.2577091157436371 False -19 58020 32.108561754226685 1.2612111568450928 507.9532470703125 0.18683061003684998 687.1378173828125 0.40984979271888733 0.86842096 0.2589241862297058 False diff --git a/ENCSR658UBE/cherimoya.fold_2.performance.tsv b/ENCSR658UBE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3bbc2adf072cab94ee43a81af6e0e543942cd59b..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -685.7590942382812 0.3716857433319092 0.41052746772766113 0.1735263168811798 0.8703725934028625 0.8407984972000122 0.26132744550704956 \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_3.evaluate.json b/ENCSR658UBE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 99592ac3b56e098f8c47d09444d1689ada46dca7..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF926FGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_3.fit.json b/ENCSR658UBE/cherimoya.fold_3.fit.json deleted file mode 100644 index 959c8d592b411fa34662bef84f62f769556d0a5e..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF926FGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_3.log b/ENCSR658UBE/cherimoya.fold_3.log deleted file mode 100644 index 841d9f3efa73b4f8a1587d5ce774252fa71f518b..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.08946657180786 4.333943605422974 732.380615234375 0.5054519772529602 759.2186889648438 0.29537099599838257 0.7171261 5.202589511871338 True -1 5498 30.447041273117065 1.8763771057128906 574.8506469726562 0.4601908326148987 679.257568359375 0.36689209938049316 0.79185474 1.4015462398529053 True -2 8247 30.481366634368896 0.5919415950775146 603.6721801757812 0.5268540382385254 664.7233276367188 0.37714117765426636 0.80658567 0.7422714233398438 True -3 10996 30.559611082077026 0.5847640037536621 573.4404296875 0.4616449475288391 655.978515625 0.3865826725959778 0.81442356 0.7049350738525391 True -4 13745 30.491140127182007 0.6040258407592773 638.2042236328125 0.3655703067779541 651.2760009765625 0.3917427957057953 0.81796247 0.5711260437965393 True -5 16494 30.492682933807373 0.5949060916900635 578.09716796875 0.4084700345993042 649.0903930664062 0.3934704065322876 0.8220389 0.5525742173194885 True -6 19243 30.415342092514038 0.5944185256958008 465.043212890625 0.5216740369796753 647.4789428710938 0.3952008783817291 0.82706267 0.5548101663589478 True -7 21992 30.440552711486816 0.5925946235656738 577.7000732421875 0.24638482928276062 645.5692749023438 0.39642593264579773 0.8290219 0.5467706322669983 True -8 24741 30.478934288024902 0.5920114517211914 515.9119262695312 0.37973904609680176 643.4697875976562 0.3981880247592926 0.83151865 0.5351076722145081 True -9 27490 30.5295352935791 0.5982072353363037 600.2180786132812 0.21742334961891174 640.9828491210938 0.4014376997947693 0.83606404 0.5170386433601379 True -10 30239 30.465935230255127 0.5928807258605957 634.165283203125 0.3385894000530243 639.701171875 0.40216127038002014 0.8387454 0.48884084820747375 True -11 32988 30.475252151489258 0.593895435333252 741.13525390625 0.43905171751976013 637.0379028320312 0.40446048974990845 0.8441455 0.44955936074256897 True -12 35737 30.54708743095398 0.5941405296325684 595.1781005859375 0.34500575065612793 634.4736938476562 0.40773341059684753 0.8489507 0.40691080689430237 True -13 38486 30.58795428276062 0.5902788639068604 524.7948608398438 0.3118797540664673 631.2857055664062 0.41069766879081726 0.8552832 0.363763689994812 True -14 41235 30.519387006759644 0.6012654304504395 663.9649047851562 0.31575024127960205 630.3261108398438 0.41122716665267944 0.8620208 0.32972782850265503 True -15 43984 30.49469804763794 0.5878751277923584 531.0385131835938 0.19356732070446014 629.0419921875 0.4123145639896393 0.8675073 0.3024716079235077 True -16 46733 30.510846376419067 0.5956380367279053 594.3104248046875 0.20627419650554657 627.7740478515625 0.4144226014614105 0.8698479 0.2817002236843109 True -17 49482 30.48042345046997 0.592381477355957 566.6630859375 0.23558655381202698 627.1478881835938 0.41490980982780457 0.87160856 0.26803910732269287 True -18 52231 30.471641063690186 0.5835568904876709 505.8345031738281 0.2970905005931854 627.0127563476562 0.41489797830581665 0.87338346 0.2629340589046478 True -19 54980 30.48784899711609 1.4043066501617432 567.193603515625 0.14136666059494019 628.2880859375 0.41321200132369995 0.87187964 0.2628130316734314 False diff --git a/ENCSR658UBE/cherimoya.fold_3.performance.tsv b/ENCSR658UBE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6d03baee9b38464193918c44e095458d844246dc..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -627.0127563476562 0.37476837635040283 0.41489797830581665 0.17002475261688232 0.8733834624290466 0.827186107635498 0.2629340589046478 \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_4.evaluate.json b/ENCSR658UBE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 97a5680f7d6bbaa3c7573f5107b808ceda256429..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF926FGI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_4.fit.json b/ENCSR658UBE/cherimoya.fold_4.fit.json deleted file mode 100644 index db31b97b4f47c5a5cb420635f01d8618bd21ede6..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF926FGI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR658UBE/cherimoya.fold_4.log b/ENCSR658UBE/cherimoya.fold_4.log deleted file mode 100644 index 207d5bf9421100dacd5a310412bca2ca83f73c56..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2795 34.946205377578735 3.58683180809021 609.4076538085938 0.34314483404159546 726.9981689453125 0.28858286142349243 0.7172717 4.8420233726501465 True -1 5590 30.957874059677124 0.6346135139465332 577.9044189453125 0.5284512042999268 655.4827270507812 0.35557329654693604 0.7825841 1.2938750982284546 True -2 8385 30.99873113632202 4.562074184417725 523.08837890625 0.41045069694519043 642.9149169921875 0.36714065074920654 0.7942106 0.6757410764694214 True -3 11180 31.069623947143555 0.6190121173858643 457.05767822265625 0.3993108868598938 637.359619140625 0.37285712361335754 0.8009017 0.5868029594421387 True -4 13975 31.05253839492798 0.6190037727355957 561.071044921875 0.31672367453575134 634.6450805664062 0.37696805596351624 0.80519676 0.547579824924469 True -5 16770 31.056434631347656 0.621722936630249 535.0697021484375 0.4120854139328003 631.9375610351562 0.3773598372936249 0.8127389 0.5383461117744446 True -6 19565 30.949270009994507 0.6276335716247559 491.6515808105469 0.3751944601535797 629.1489868164062 0.38075509667396545 0.8179543 0.5336989760398865 True -7 22360 30.968692779541016 1.19981050491333 496.2681579589844 0.2520982623100281 624.8560791015625 0.3872087001800537 0.8221038 0.5362148284912109 True -8 25155 31.002815008163452 2.10561466217041 596.6767578125 0.3943120241165161 623.7880249023438 0.3872917592525482 0.8309567 0.510192334651947 True -9 27950 30.982632398605347 0.6102497577667236 546.813720703125 0.3307545781135559 621.1378173828125 0.3902827501296997 0.8363278 0.4398759603500366 True -10 30745 30.955689907073975 0.6169540882110596 501.90283203125 0.2406010627746582 620.1451416015625 0.39044389128685 0.8393967 0.41553226113319397 True -11 33540 30.945178985595703 0.6164147853851318 633.7049560546875 0.32374170422554016 618.771240234375 0.3921683728694916 0.8429787 0.40747135877609253 True -12 36335 30.95364236831665 0.6100442409515381 539.9383544921875 0.2625085413455963 617.5712890625 0.393302321434021 0.8469909 0.366696834564209 True -13 39130 31.016336679458618 2.714867115020752 605.7521362304688 0.3721678555011749 616.156494140625 0.39499688148498535 0.85299855 0.338147908449173 True -14 41925 31.028996229171753 25.429425477981567 618.7994384765625 0.20862257480621338 614.050537109375 0.3960585296154022 0.8597354 0.2968449592590332 True -15 44720 30.9982807636261 0.6369976997375488 536.04150390625 0.23115912079811096 612.8479614257812 0.3985249400138855 0.86560416 0.26372581720352173 True -16 47515 30.944552183151245 0.6263253688812256 548.658203125 0.19599580764770508 613.059326171875 0.3968322277069092 0.8705462 0.2444152534008026 True -17 50310 31.00890803337097 0.619473934173584 600.013916015625 0.1820639669895172 612.65478515625 0.39778393507003784 0.87158555 0.23465681076049805 True -18 53105 30.958667993545532 0.6089777946472168 439.0534362792969 0.1919979304075241 612.280029296875 0.39850184321403503 0.8735372 0.22931642830371857 True -19 55900 30.994014501571655 0.6219987869262695 500.24200439453125 0.16127659380435944 611.8115844726562 0.3993370831012726 0.87326294 0.2292889952659607 False diff --git a/ENCSR658UBE/cherimoya.fold_4.performance.tsv b/ENCSR658UBE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 68be16443c859e3de5cb4e600029e7a78ce368fc..0000000000000000000000000000000000000000 --- a/ENCSR658UBE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -612.280029296875 0.38426175713539124 0.39850181341171265 0.1629210114479065 0.8735371828079224 0.8263702392578125 0.22931642830371857 \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_0.evaluate.json b/ENCSR660FSU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9b15698c2dc802358dfee4fb866bb6518409d0bf..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426LBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_0.fit.json b/ENCSR660FSU/cherimoya.fold_0.fit.json deleted file mode 100644 index da4b37f516e89467c5527cbd8e00c59fb44aa33f..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF426LBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_0.log b/ENCSR660FSU/cherimoya.fold_0.log deleted file mode 100644 index ced69df3018146c7bf180f4800a3a0404e784300..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1648 22.060360193252563 4.158726930618286 465.1259765625 1.0556784868240356 542.5833129882812 0.16058385372161865 0.5840499 12.552932739257812 True -1 3296 18.10439157485962 0.3237111568450928 488.28759765625 0.7391872406005859 488.94757080078125 0.2255229502916336 0.7212165 6.309462547302246 True -2 4944 18.113343000411987 1.0425341129302979 373.38409423828125 0.8523015975952148 441.516845703125 0.2706564664840698 0.7578637 3.532437801361084 True -3 6592 18.159152507781982 0.31217026710510254 351.699462890625 0.5433363318443298 427.7801818847656 0.28011655807495117 0.76674986 2.365391969680786 True -4 8240 18.083714485168457 0.31348156929016113 400.12646484375 0.6830825805664062 422.45172119140625 0.28559184074401855 0.77222663 1.5547178983688354 True -5 9888 18.083844900131226 1.0018205642700195 381.3087158203125 0.625001847743988 418.10357666015625 0.29090502858161926 0.78347766 1.2169276475906372 True -6 11536 18.1084201335907 0.32097887992858887 365.436767578125 0.6945987939834595 415.16119384765625 0.294901579618454 0.79181 1.07027006149292 True -7 13184 18.179928064346313 0.3216235637664795 368.96856689453125 0.8208403587341309 414.0343322753906 0.29593902826309204 0.80240244 0.9357385635375977 True -8 14832 18.16592836380005 0.31688952445983887 256.954833984375 0.7355043888092041 409.3804931640625 0.30198049545288086 0.8139612 0.8029906153678894 True -9 16480 18.118300437927246 0.32280731201171875 279.39703369140625 0.9781593680381775 409.028076171875 0.3012758493423462 0.8216173 0.7415556311607361 True -10 18128 18.08394169807434 0.3220963478088379 322.8016357421875 0.6565781831741333 407.038330078125 0.30531078577041626 0.82660705 0.7001188397407532 True -11 19776 18.091575384140015 0.3213658332824707 386.66619873046875 0.47412002086639404 405.2977600097656 0.30618444085121155 0.8289885 0.6453140377998352 True -12 21424 18.15205717086792 0.3207533359527588 314.8265075683594 0.5793384313583374 404.69012451171875 0.30541324615478516 0.8374398 0.5869858264923096 True -13 23072 19.31269121170044 8.938283205032349 288.4185485839844 0.5776970386505127 403.2969665527344 0.3077930510044098 0.8418621 0.563115119934082 True -14 24720 18.07882857322693 0.3876018524169922 392.9788818359375 0.44010627269744873 401.6382141113281 0.30937185883522034 0.84635556 0.5364612936973572 True -15 26368 18.10667634010315 0.31955790519714355 372.8174743652344 0.4827784299850464 401.5667419433594 0.3083622455596924 0.8502836 0.5193593502044678 True -16 28016 18.072104454040527 0.31882452964782715 278.04931640625 0.5274949073791504 400.6007995605469 0.3100537955760956 0.8523732 0.5047102570533752 True -17 29664 18.10693097114563 0.3216841220855713 340.39337158203125 0.4044853150844574 400.7664794921875 0.3093404173851013 0.85256714 0.5029389262199402 True -18 31312 18.124014616012573 0.3177666664123535 291.13800048828125 0.26474398374557495 401.2538757324219 0.3087901473045349 0.85149264 0.5056578516960144 False -19 32960 18.142239570617676 0.3341677188873291 300.9052734375 0.4675374925136566 402.2637634277344 0.3073198199272156 0.8508038 0.5072076916694641 False diff --git a/ENCSR660FSU/cherimoya.fold_0.performance.tsv b/ENCSR660FSU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e51c4be6edd4ba40d39a16601a1a72c986c02c88..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -400.7664794921875 0.46573829650878906 0.3093404173851013 0.11452638357877731 0.8525671362876892 0.7916631102561951 0.5029389262199402 \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_1.evaluate.json b/ENCSR660FSU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f76fe0fe6ea8da3349104c696d1b5589e3881083..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426LBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_1.fit.json b/ENCSR660FSU/cherimoya.fold_1.fit.json deleted file mode 100644 index 512296b557701e6c30e5642524551b0eb5a75ba4..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF426LBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_1.log b/ENCSR660FSU/cherimoya.fold_1.log deleted file mode 100644 index 1f5e519f9abf5261ca0090a6aba34d6b81530dec..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1606 23.123046159744263 3.4749104976654053 338.66888427734375 0.6342349052429199 655.285400390625 0.1678149402141571 0.55901295 15.183029174804688 True -1 3212 17.693788766860962 0.4791417121887207 372.9005126953125 0.7680237889289856 584.5330200195312 0.24831031262874603 0.71663785 7.024311065673828 True -2 4818 17.688124656677246 0.46921730041503906 325.3740234375 0.6593912839889526 527.6460571289062 0.29432517290115356 0.76942414 3.051520824432373 True -3 6424 17.48497748374939 0.4701375961303711 366.5567626953125 0.9556443691253662 508.1288757324219 0.30635204911231995 0.79289764 1.9122596979141235 True -4 8030 17.315911769866943 0.4694216251373291 346.44012451171875 0.8570014238357544 502.35089111328125 0.3102969527244568 0.80639786 1.435407280921936 True -5 9636 17.31677746772766 0.47966647148132324 342.5709228515625 0.6320394277572632 498.3262023925781 0.3144703805446625 0.8122497 1.1653094291687012 True -6 11242 17.305338859558105 0.46297168731689453 288.43536376953125 0.7699504494667053 493.9233703613281 0.3194712996482849 0.8213632 0.9734892249107361 True -7 12848 17.32260751724243 1.1399099826812744 343.8662109375 0.6135783195495605 490.08551025390625 0.32305705547332764 0.82947624 0.8278700113296509 True -8 14454 17.420371532440186 0.4958188533782959 238.51278686523438 0.8864776492118835 487.57891845703125 0.32575440406799316 0.8345929 0.7563201785087585 True -9 16060 17.381099462509155 0.4893214702606201 256.611328125 1.017401933670044 485.82208251953125 0.3274343013763428 0.84107226 0.7208399772644043 True -10 17666 17.398108959197998 1.6292102336883545 405.6146240234375 0.9140670299530029 484.9061584472656 0.3286546468734741 0.84795046 0.6680407524108887 True -11 19272 17.411453247070312 0.4882664680480957 294.7734375 0.5390943884849548 482.13214111328125 0.33082446455955505 0.85044336 0.6230427622795105 True -12 20878 17.41127920150757 0.490398645401001 390.8535461425781 0.5779458284378052 480.10919189453125 0.33336907625198364 0.85534865 0.5911967754364014 True -13 22484 17.441359281539917 1.1347219944000244 344.53839111328125 0.35684579610824585 477.967041015625 0.3348532021045685 0.85932976 0.5708369016647339 True -14 24090 17.386513233184814 0.489330530166626 320.4695739746094 0.6851533651351929 475.4862976074219 0.3364262580871582 0.8638819 0.5453698635101318 True -15 25696 17.373785734176636 0.6326744556427002 408.6495361328125 0.6158333420753479 475.4819030761719 0.33558377623558044 0.8667193 0.53154057264328 True -16 27302 17.392889261245728 0.4801950454711914 320.5552062988281 0.23058193922042847 475.3526306152344 0.33515721559524536 0.86867565 0.522778332233429 True -17 28908 17.392189264297485 0.48637890815734863 275.53759765625 0.31723612546920776 474.64697265625 0.3367144465446472 0.8688551 0.5249866247177124 True -18 30514 17.38648295402527 0.4732203483581543 304.3884582519531 0.29906246066093445 475.861083984375 0.334989458322525 0.868014 0.5351165533065796 False -19 32120 17.87687587738037 3.8297579288482666 391.092041015625 0.3353646993637085 475.50115966796875 0.3355681300163269 0.8670453 0.5412197709083557 False diff --git a/ENCSR660FSU/cherimoya.fold_1.performance.tsv b/ENCSR660FSU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f5526ebdb484b959291553cd984d98c94883423b..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -474.64697265625 0.441662073135376 0.3367144465446472 0.1349584013223648 0.8688551187515259 0.829719603061676 0.5249866247177124 \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_2.evaluate.json b/ENCSR660FSU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7375015bab3c165d46905d066c4386372293dba8..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426LBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_2.fit.json b/ENCSR660FSU/cherimoya.fold_2.fit.json deleted file mode 100644 index 3be8cd5b9a270d75510d661572d0fdadd0535b12..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF426LBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_2.log b/ENCSR660FSU/cherimoya.fold_2.log deleted file mode 100644 index 980b93bf7473b21ab08de95a18824d7ec711a4a0..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1739 22.731306314468384 3.421846389770508 468.6290283203125 0.6916074752807617 562.946044921875 0.1611778736114502 0.5532318 12.136533737182617 True -1 3478 19.15034294128418 0.36149144172668457 424.8095703125 0.9393978118896484 494.8196105957031 0.2347790151834488 0.7347123 5.440048694610596 True -2 5217 19.12412166595459 0.35309481620788574 365.77520751953125 0.9027772545814514 449.0336608886719 0.27023881673812866 0.7851098 2.0903162956237793 True -3 6956 19.1195285320282 0.3522820472717285 310.80999755859375 0.5340240597724915 436.62506103515625 0.27852314710617065 0.7944828 1.437720537185669 True -4 8695 19.08719778060913 0.34777140617370605 403.10113525390625 0.8005483746528625 432.2361145019531 0.2835688889026642 0.79807967 1.3689773082733154 True -5 10434 19.123430490493774 0.3495302200317383 407.89129638671875 0.7865283489227295 427.6636962890625 0.2883365750312805 0.80924827 0.9840264916419983 True -6 12173 19.1332950592041 0.344318151473999 412.837646484375 0.6059470176696777 425.39129638671875 0.2914991080760956 0.8186687 0.8326424956321716 True -7 13912 19.13728380203247 0.3466019630432129 371.88409423828125 0.596872866153717 422.6549987792969 0.29576000571250916 0.82504046 0.7699102163314819 True -8 15651 19.12948727607727 0.3399953842163086 356.3319091796875 0.6204819679260254 420.71075439453125 0.29840055108070374 0.8295825 0.7118778228759766 True -9 17390 19.113877773284912 0.34287428855895996 323.216064453125 0.44761350750923157 419.4465026855469 0.2994411885738373 0.83553034 0.6319019794464111 True -10 19129 19.155783653259277 0.8823254108428955 329.498291015625 0.6098740696907043 417.9101257324219 0.3012244701385498 0.8392979 0.5741136074066162 True -11 20868 19.15606379508972 1.3666646480560303 350.98095703125 0.4336475133895874 415.199462890625 0.30474376678466797 0.8433312 0.550920307636261 True -12 22607 19.11558246612549 1.2382214069366455 303.7287292480469 0.4528619647026062 413.2154235839844 0.30744534730911255 0.8447796 0.5375677347183228 True -13 24346 19.097799062728882 0.3488035202026367 273.7655029296875 0.5791987180709839 413.17462158203125 0.3069344162940979 0.84857404 0.518505334854126 True -14 26085 19.047950744628906 0.34470343589782715 338.3853759765625 0.2892567813396454 412.21173095703125 0.30761417746543884 0.8527035 0.5037596821784973 True -15 27824 18.806180477142334 0.3445909023284912 351.9185791015625 0.450953871011734 411.87060546875 0.3072371184825897 0.854514 0.49597489833831787 True -16 29563 18.750359058380127 0.3449540138244629 346.12103271484375 0.35383620858192444 412.0405578613281 0.3066926896572113 0.85610545 0.49201199412345886 True -17 31302 18.725564002990723 0.33840084075927734 303.9354248046875 0.3594481647014618 411.0769348144531 0.30920732021331787 0.8568597 0.49158501625061035 True -18 33041 18.7138352394104 0.33960413932800293 346.47772216796875 0.42532581090927124 411.93084716796875 0.3081235885620117 0.8552153 0.4959070682525635 False -19 34780 18.674270629882812 0.3417494297027588 273.08062744140625 0.36789074540138245 412.18963623046875 0.3078506886959076 0.8544574 0.5005047917366028 False diff --git a/ENCSR660FSU/cherimoya.fold_2.performance.tsv b/ENCSR660FSU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e6a8608f701ca64dd620a350de9b24d60c7ffe00..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -411.0769348144531 0.46472397446632385 0.30920732021331787 0.12161362171173096 0.8568596839904785 0.7978183031082153 0.49158501625061035 \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_3.evaluate.json b/ENCSR660FSU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 92cbc145bd4299326d0ef7f4c3b9d94d8bb530bb..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426LBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_3.fit.json b/ENCSR660FSU/cherimoya.fold_3.fit.json deleted file mode 100644 index b662e74fb01c51dcbf9862bfa9424bcb1c5eb9f1..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF426LBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_3.log b/ENCSR660FSU/cherimoya.fold_3.log deleted file mode 100644 index 199ce7e92363af6d6fea27e44f0103b89c6a9a2c..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1658 21.85391592979431 3.296783447265625 393.65399169921875 1.0969728231430054 572.236572265625 0.17167574167251587 0.53509825 13.620341300964355 True -1 3316 18.22441840171814 0.34400367736816406 334.33538818359375 0.6602276563644409 509.77288818359375 0.2429802119731903 0.68767375 6.128990173339844 True -2 4974 18.23668622970581 1.1089212894439697 377.0174865722656 0.7803312540054321 467.2618408203125 0.2805195152759552 0.74380654 2.6644232273101807 True -3 6632 18.228338956832886 0.32856297492980957 395.745849609375 0.6910688877105713 455.80029296875 0.2907337248325348 0.7617314 2.2595531940460205 True -4 8290 18.238040685653687 0.33311986923217773 591.6338500976562 0.5360681414604187 449.4913635253906 0.2974889576435089 0.77628225 1.5824192762374878 True -5 9948 18.222763776779175 0.3316457271575928 407.08935546875 0.6754928827285767 447.46270751953125 0.29883095622062683 0.7873643 1.3071640729904175 True -6 11606 18.486064672470093 0.3329904079437256 308.33892822265625 0.4727402329444885 443.5764465332031 0.3046998083591461 0.7979912 1.1079305410385132 True -7 13264 18.203543663024902 0.3295564651489258 335.07000732421875 0.6162493824958801 441.6959533691406 0.30754828453063965 0.79950064 1.0440372228622437 True -8 14922 18.205268383026123 0.3289206027984619 327.5004577636719 0.751570463180542 438.9272155761719 0.31030163168907166 0.80800027 0.921444833278656 True -9 16580 18.2173593044281 0.3355884552001953 300.12359619140625 0.6984039545059204 436.32855224609375 0.3138359487056732 0.81380785 0.8289679288864136 True -10 18238 18.25213599205017 0.33458971977233887 383.290283203125 0.7601997256278992 434.1228942871094 0.31594040989875793 0.8216213 0.7421842217445374 True -11 19896 18.23711895942688 0.33042192459106445 324.82244873046875 0.5201882123947144 432.7369689941406 0.31708863377571106 0.82643414 0.6837670803070068 True -12 21554 18.230496168136597 0.33072733879089355 300.4224853515625 0.6325806379318237 429.974853515625 0.32069844007492065 0.83267826 0.6495218873023987 True -13 23212 18.209858417510986 0.3293335437774658 355.6209716796875 0.43308770656585693 428.5838317871094 0.32063090801239014 0.8353627 0.6333492398262024 True -14 24870 18.243051528930664 0.33685731887817383 355.91094970703125 0.5705641508102417 427.9186096191406 0.3214772045612335 0.84252626 0.598274290561676 True -15 26528 18.261316776275635 0.8982553482055664 264.1061096191406 0.3967859148979187 426.6254577636719 0.3237190544605255 0.8473762 0.5781362652778625 True -16 28186 18.20547914505005 1.4379360675811768 285.364501953125 0.2916419506072998 426.7229919433594 0.32333338260650635 0.84953725 0.5621188282966614 True -17 29844 18.514255046844482 0.3309142589569092 226.97662353515625 0.5346029996871948 425.8175964355469 0.32434144616127014 0.84841 0.5582808256149292 False -18 31502 18.26751446723938 0.32860422134399414 360.7052001953125 0.32689401507377625 427.0784606933594 0.3225485682487488 0.8484538 0.5628927946090698 False -19 33160 18.251281023025513 0.33273983001708984 351.8045959472656 0.3943564295768738 427.13909912109375 0.32273542881011963 0.84698796 0.5645768642425537 False diff --git a/ENCSR660FSU/cherimoya.fold_3.performance.tsv b/ENCSR660FSU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ce075b1d0e38c52d9f2224720fb1c6785a4a9087..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -426.7229919433594 0.4522678852081299 0.32333338260650635 0.12371782213449478 0.8495372533798218 0.7936074733734131 0.5621188282966614 \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_4.evaluate.json b/ENCSR660FSU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 68f67ae391d3df20c1e05b8c77bb1b10b51dffe1..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF426LBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_4.fit.json b/ENCSR660FSU/cherimoya.fold_4.fit.json deleted file mode 100644 index 6a5de13911aaad9bd956bcd827740ab0d2fe34ed..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF426LBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR660FSU/cherimoya.fold_4.log b/ENCSR660FSU/cherimoya.fold_4.log deleted file mode 100644 index 2f622ae5d01a70cd307523ac85b95231ef0ba6d8..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1630 21.903862237930298 3.235696315765381 384.0516357421875 1.186821699142456 511.0866394042969 0.15833722054958344 0.5572642 12.081830978393555 True -1 3260 17.927119493484497 2.2377145290374756 398.5023193359375 0.620167076587677 460.52215576171875 0.22438332438468933 0.726444 5.60195255279541 True -2 4890 17.926355838775635 0.3091166019439697 255.21469116210938 0.6666874885559082 422.4927978515625 0.2595604956150055 0.7742987 2.121422052383423 True -3 6520 17.899327278137207 0.30947232246398926 317.534423828125 1.2386457920074463 409.3048095703125 0.2709822356700897 0.78724635 1.3398045301437378 True -4 8150 17.889024019241333 0.31644463539123535 367.475830078125 1.1867607831954956 404.84576416015625 0.27483493089675903 0.790982 1.0976492166519165 True -5 9780 17.923856735229492 0.3131828308105469 408.5276794433594 0.7518578767776489 401.298828125 0.27940136194229126 0.7969474 0.8601146340370178 True -6 11410 17.88615083694458 0.30977773666381836 285.8113098144531 0.8919403553009033 400.0138244628906 0.2805234491825104 0.80257934 0.7726656794548035 True -7 13040 17.908766508102417 0.3144078254699707 367.7972412109375 0.6456125974655151 397.1498718261719 0.2836543917655945 0.81075126 0.7065059542655945 True -8 14670 17.718587160110474 0.30991077423095703 341.69952392578125 0.7269972562789917 394.1583251953125 0.28741857409477234 0.8217279 0.6770296692848206 True -9 16300 17.536647081375122 0.3107943534851074 265.02276611328125 0.5033219456672668 392.8973083496094 0.2893088757991791 0.8241845 0.6158629059791565 True -10 17930 17.593353748321533 0.3130011558532715 388.57269287109375 0.4463115334510803 391.83953857421875 0.290611207485199 0.82866573 0.5877318978309631 True -11 19560 17.592504501342773 0.31066346168518066 256.368408203125 0.3643566966056824 390.2980041503906 0.2924826443195343 0.8328069 0.5654267072677612 True -12 21190 17.5985209941864 0.3142576217651367 292.02923583984375 0.508307158946991 388.6280212402344 0.29482293128967285 0.8379638 0.5444697737693787 True -13 22820 17.541290760040283 0.31203126907348633 303.8606872558594 0.5777692794799805 387.5942077636719 0.29538097977638245 0.8432371 0.5202145576477051 True -14 24450 17.550213098526 0.31238293647766113 300.11669921875 0.42097458243370056 386.51751708984375 0.2970397472381592 0.84855616 0.49497613310813904 True -15 26080 17.580759048461914 0.3093996047973633 342.239501953125 0.4719281792640686 386.03094482421875 0.2976074516773224 0.85098064 0.4839094281196594 True -16 27710 17.59797954559326 0.3063323497772217 320.8057861328125 0.3349658250808716 385.6275939941406 0.2983553111553192 0.8532853 0.47399115562438965 True -17 29340 17.535157203674316 0.3085014820098877 324.634765625 0.3433208465576172 386.3497619628906 0.29733768105506897 0.8540523 0.47519776225090027 True -18 30970 17.531184434890747 0.30878257751464844 318.02655029296875 0.2882513403892517 386.8885803222656 0.29690566658973694 0.8541421 0.4782978296279907 True -19 32600 17.568869829177856 0.3098022937774658 334.63433837890625 0.22527331113815308 387.4785461425781 0.29616475105285645 0.853162 0.4820101261138916 False diff --git a/ENCSR660FSU/cherimoya.fold_4.performance.tsv b/ENCSR660FSU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 441687d1b61267ce8d1cdf9ce2fff150b9e69482..0000000000000000000000000000000000000000 --- a/ENCSR660FSU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -386.8885803222656 0.4743506610393524 0.29690563678741455 0.10541488975286484 0.8541421294212341 0.7902619242668152 0.4782978296279907 \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_0.evaluate.json b/ENCSR661AMM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ec228b42d07301582abea1ce0defcead72da4378..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF989SAK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_0.fit.json b/ENCSR661AMM/cherimoya.fold_0.fit.json deleted file mode 100644 index c6d2b1304647ebbbde4222b7f2dc7e8ccb4d27a3..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF989SAK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_0.log b/ENCSR661AMM/cherimoya.fold_0.log deleted file mode 100644 index e531bb9ab861c8c5ff43793a8867444516391ced..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 35.06655478477478 4.4806413650512695 460.24945068359375 0.2550029158592224 528.0497436523438 0.27990013360977173 0.7742513 3.711599111557007 True -1 5480 30.441818237304688 0.7147963047027588 426.26470947265625 0.2550464868545532 498.71441650390625 0.3244158625602722 0.803792 0.8299422860145569 True -2 8220 30.301910638809204 0.646291971206665 506.8210754394531 0.29435497522354126 494.0706481933594 0.3315674960613251 0.82509506 0.3408985435962677 True -3 10960 29.86458468437195 4.4115166664123535 459.59722900390625 0.1973578929901123 490.5498046875 0.33632993698120117 0.8422814 0.32137230038642883 True -4 13700 29.680670261383057 0.6567032337188721 402.2158508300781 0.14017848670482635 488.3638610839844 0.3391769826412201 0.85010374 0.20846118032932281 True -5 16440 29.697160243988037 0.612299919128418 412.96429443359375 0.11215900629758835 488.2311096191406 0.33948594331741333 0.8537239 0.20939303934574127 True -6 19180 29.626506090164185 0.6152529716491699 451.44293212890625 0.19140923023223877 486.8915710449219 0.34166184067726135 0.857389 0.2049756646156311 True -7 21920 29.69870352745056 0.6171278953552246 414.6038818359375 0.15412360429763794 485.7004089355469 0.3432464599609375 0.86721367 0.17437249422073364 True -8 24660 29.663039922714233 0.612330436706543 447.0821228027344 0.17167231440544128 485.5834045410156 0.3429579436779022 0.86866057 0.16887333989143372 True -9 27400 29.70499277114868 1.5214359760284424 377.9495849609375 0.1120745986700058 485.0284423828125 0.3439197242259979 0.8710535 0.16579006612300873 True -10 30140 29.739858865737915 0.6219651699066162 421.91632080078125 0.2420547604560852 483.1794128417969 0.3482808470726013 0.87454695 0.15872663259506226 True -11 32880 29.733052015304565 0.5932998657226562 436.0764465332031 0.11048751324415207 482.277587890625 0.3491430878639221 0.8777077 0.14963996410369873 True -12 35620 29.657139539718628 0.6112220287322998 390.50445556640625 0.08776786923408508 482.34466552734375 0.3483080267906189 0.8813779 0.13384081423282623 True -13 38360 29.709908485412598 0.5899808406829834 474.8941650390625 0.13277852535247803 481.5735168457031 0.34897753596305847 0.88475084 0.12701217830181122 True -14 41100 29.637839317321777 0.6054854393005371 439.1072998046875 0.09236696362495422 481.38818359375 0.3494614064693451 0.88779217 0.11784593760967255 True -15 43840 29.765183925628662 0.6122989654541016 431.10028076171875 0.0957082062959671 480.92437744140625 0.3501507639884949 0.89132833 0.11496094614267349 True -16 46580 29.67065739631653 0.6076931953430176 393.8885192871094 0.14813172817230225 480.7052917480469 0.351042240858078 0.8916902 0.11024992913007736 True -17 49320 29.67400336265564 0.6120531558990479 462.01593017578125 0.1168660968542099 481.00177001953125 0.3500252366065979 0.89304274 0.10914801806211472 True -18 52060 29.744075059890747 0.6049337387084961 411.6402587890625 0.043457839637994766 480.7794189453125 0.35067319869995117 0.8931088 0.10845600813627243 True -19 54800 29.72564148902893 0.6119420528411865 442.7025451660156 0.10458921641111374 480.7724609375 0.35090765357017517 0.89226276 0.10910940915346146 False diff --git a/ENCSR661AMM/cherimoya.fold_0.performance.tsv b/ENCSR661AMM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 0b127b744acfcf6a58758a3c00845d566c2d7a07..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -480.7794189453125 0.4203236401081085 0.35067319869995117 0.1285780817270279 0.8931087851524353 0.8853169083595276 0.10845600813627243 \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_1.evaluate.json b/ENCSR661AMM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0b5c8f95c0ebe31d7e824ade7c669179592f070d..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF989SAK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_1.fit.json b/ENCSR661AMM/cherimoya.fold_1.fit.json deleted file mode 100644 index e3629104c0ea68a03286cc138998fbe0710a425a..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF989SAK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_1.log b/ENCSR661AMM/cherimoya.fold_1.log deleted file mode 100644 index bc8a380e0442dd6586ce6865b1858f7732d8b8a0..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 35.20755624771118 4.3663716316223145 486.2332458496094 0.21355581283569336 617.2088012695312 0.2832527756690979 0.76757866 3.48730206489563 True -1 5504 30.405763864517212 0.8558766841888428 387.36669921875 0.14859983325004578 581.9657592773438 0.33587825298309326 0.8022741 0.9020577073097229 True -2 8256 30.378826379776 0.6331784725189209 446.56964111328125 0.18900145590305328 573.2774047851562 0.3454184830188751 0.8184577 0.4911692440509796 True -3 11008 30.33212637901306 0.6434712409973145 449.66766357421875 0.17594486474990845 568.8570556640625 0.3497208058834076 0.83222586 0.4020646810531616 True -4 13760 30.327444314956665 0.6197552680969238 410.03472900390625 0.13920998573303223 565.7208251953125 0.35366424918174744 0.8419905 0.28967708349227905 True -5 16512 30.3399178981781 0.6279294490814209 349.70440673828125 0.16612467169761658 563.0226440429688 0.3578755557537079 0.8475788 0.2615414559841156 True -6 19264 30.347593784332275 0.6211974620819092 450.259765625 0.19014912843704224 561.9866333007812 0.3585461974143982 0.8543888 0.2559834420681 True -7 22016 30.356226682662964 0.6589217185974121 386.5582275390625 0.1900743693113327 559.778564453125 0.36184293031692505 0.8605793 0.23443517088890076 True -8 24768 30.3441002368927 0.6179535388946533 444.76116943359375 0.19506116211414337 558.9210815429688 0.36226126551628113 0.8635914 0.22885766625404358 True -9 27520 30.360290050506592 0.634514331817627 407.958740234375 0.14230340719223022 557.28271484375 0.36562350392341614 0.86693853 0.21386180818080902 True -10 30272 30.347626447677612 0.6256942749023438 486.96588134765625 0.16510115563869476 556.3364868164062 0.36544549465179443 0.8724161 0.20078502595424652 True -11 33024 30.35031795501709 0.6228606700897217 406.69775390625 0.13356924057006836 556.0435180664062 0.3656872808933258 0.87559295 0.19161784648895264 True -12 35776 30.32822275161743 0.9651198387145996 394.0593566894531 0.18895743787288666 554.052490234375 0.3687267303466797 0.8820648 0.17595553398132324 True -13 38528 30.319371700286865 0.6258552074432373 430.1396484375 0.12904970347881317 553.7710571289062 0.3686314821243286 0.8868835 0.16338816285133362 True -14 41280 30.053266286849976 0.6207723617553711 445.80108642578125 0.1399913728237152 552.6934204101562 0.3698682188987732 0.88990676 0.1524941325187683 True -15 44032 29.732290029525757 0.6183514595031738 434.75506591796875 0.16537439823150635 551.543701171875 0.3713720738887787 0.89203817 0.1451071947813034 True -16 46784 29.739353895187378 1.7874329090118408 452.3231201171875 0.06521854549646378 551.1459350585938 0.3722634017467499 0.89651054 0.13856056332588196 True -17 49536 29.83290982246399 1.9776883125305176 408.18353271484375 0.10846266150474548 551.277587890625 0.3714123070240021 0.8955984 0.1340922862291336 False -18 52288 29.814711093902588 14.044860363006592 412.8909606933594 0.1172223836183548 551.6097412109375 0.3714193105697632 0.8965704 0.13150905072689056 True -19 55040 29.85645055770874 1.4094619750976562 418.455078125 0.11568194627761841 551.3785400390625 0.37189793586730957 0.89825904 0.1321420818567276 True diff --git a/ENCSR661AMM/cherimoya.fold_1.performance.tsv b/ENCSR661AMM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7f93a848c0464387acc6073b39df3ba154a47fa7..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -551.3785400390625 0.40218549966812134 0.37189793586730957 0.14461378753185272 0.8982590436935425 0.8995817303657532 0.1321420818567276 \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_2.evaluate.json b/ENCSR661AMM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 62e8ef91905d5fa1773b056db3e74f7f8112bc86..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF989SAK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_2.fit.json b/ENCSR661AMM/cherimoya.fold_2.fit.json deleted file mode 100644 index 79f1018310ad7df7ccb33ff021bec5c909d63dd1..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF989SAK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_2.log b/ENCSR661AMM/cherimoya.fold_2.log deleted file mode 100644 index cc6f4d1d0e6ec8c7a1854d0a295828b47a184fe8..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2884 36.5285108089447 20.863981246948242 465.30828857421875 0.16823363304138184 553.5670166015625 0.2813083827495575 0.7658799 2.7581169605255127 True -1 5768 31.788410902023315 19.53485631942749 406.1535949707031 0.18437610566616058 526.20166015625 0.32404133677482605 0.79786557 0.8254846930503845 True -2 8652 32.18356943130493 0.5833277702331543 441.54229736328125 0.29413527250289917 518.1558837890625 0.33603614568710327 0.8203494 0.3078215718269348 True -3 11536 32.495758295059204 0.5445396900177002 421.0804138183594 0.2021859884262085 514.9496459960938 0.34049636125564575 0.8306927 0.296505868434906 True -4 14420 31.863152027130127 0.5594754219055176 429.6632080078125 0.13949397206306458 514.4053344726562 0.34098920226097107 0.83126754 0.24578338861465454 True -5 17304 31.80326223373413 1.0179710388183594 446.6744689941406 0.19072118401527405 512.9215698242188 0.3423282504081726 0.841347 0.23877042531967163 True -6 20188 31.893829584121704 5.321088075637817 428.6148681640625 0.281246155500412 510.92529296875 0.3450464606285095 0.84959495 0.2141585797071457 True -7 23072 31.832748651504517 0.5466022491455078 471.18865966796875 0.2094440460205078 510.3537292480469 0.3453323543071747 0.8515958 0.20789816975593567 True -8 25956 31.96452045440674 0.5895950794219971 412.0631103515625 0.2189846932888031 508.51251220703125 0.34873244166374207 0.85932845 0.19614610075950623 True -9 28840 31.845457315444946 0.546579122543335 456.3668212890625 0.20423798263072968 508.4726867675781 0.34813523292541504 0.8587342 0.2079872339963913 False -10 31724 31.82006287574768 0.5596706867218018 425.1940002441406 0.2012542337179184 507.1625671386719 0.3497588038444519 0.8660543 0.16914309561252594 True -11 34608 31.81047797203064 0.5589563846588135 408.9610595703125 0.11220219731330872 506.4853820800781 0.3504199981689453 0.8710957 0.1575416475534439 True -12 37492 31.824284076690674 0.5463833808898926 468.11773681640625 0.07884806394577026 506.10125732421875 0.350862592458725 0.8746592 0.1505011022090912 True -13 40376 31.825594663619995 0.9589107036590576 419.1357421875 0.09442270547151566 504.96270751953125 0.35257619619369507 0.8768389 0.14440493285655975 True -14 43260 31.532077312469482 0.5511875152587891 443.2964782714844 0.1330229938030243 504.2799987792969 0.3541014790534973 0.8801525 0.13643327355384827 True -15 46144 31.314263105392456 0.5385885238647461 409.50909423828125 0.11233174055814743 504.1558532714844 0.35386890172958374 0.88311917 0.13117773830890656 True -16 49028 31.236473083496094 0.5336432456970215 410.5621337890625 0.10252529382705688 503.388427734375 0.356359601020813 0.8846678 0.1278846561908722 True -17 51912 31.213476181030273 0.5388715267181396 405.6585693359375 0.12412568181753159 503.8470458984375 0.3546931743621826 0.88550496 0.12476345896720886 True -18 54796 31.192766427993774 0.5362040996551514 465.9822082519531 0.09724699705839157 503.9853210449219 0.35439619421958923 0.8841413 0.12611255049705505 False -19 57680 31.19018578529358 0.5434730052947998 433.37835693359375 0.09761758148670197 504.75299072265625 0.3524772524833679 0.8831379 0.12676306068897247 False diff --git a/ENCSR661AMM/cherimoya.fold_2.performance.tsv b/ENCSR661AMM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 38ce63f4dcadc2262d0ecdc1d75ecf62ad5b3ee2..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -503.8470458984375 0.4157804250717163 0.35469314455986023 0.13470962643623352 0.885504961013794 0.8815199732780457 0.12476345896720886 \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_3.evaluate.json b/ENCSR661AMM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 69e90c76f43a0474f682b2e7b702b101e7836f77..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF989SAK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_3.fit.json b/ENCSR661AMM/cherimoya.fold_3.fit.json deleted file mode 100644 index 8fc89124d8a9302e215b0d409640b5ee0c03d7a5..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF989SAK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_3.log b/ENCSR661AMM/cherimoya.fold_3.log deleted file mode 100644 index c9db8d7f33bd8f6918fc13f72f8ecd274ef34690..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 35.04203462600708 3.917825222015381 362.73809814453125 0.17057228088378906 518.2871704101562 0.2856760621070862 0.7409183 2.9741365909576416 True -1 5500 30.4540696144104 0.6478462219238281 460.9109191894531 0.1946668177843094 491.4261779785156 0.3263895511627197 0.78279847 0.8595232963562012 True -2 8250 30.379390478134155 0.6254425048828125 433.26788330078125 0.3007184565067291 484.6103820800781 0.3362249732017517 0.80684394 0.4455362856388092 True -3 11000 30.43538999557495 1.43247652053833 461.49298095703125 0.14519613981246948 481.97308349609375 0.3409479856491089 0.82260925 0.3016323447227478 True -4 13750 30.6051664352417 0.9428720474243164 446.194091796875 0.17801529169082642 480.73504638671875 0.34205952286720276 0.82904714 0.22577466070652008 True -5 16500 30.45766854286194 24.298390865325928 437.0587158203125 0.09970487654209137 479.81268310546875 0.3434741795063019 0.83110774 0.23176586627960205 True -6 19250 30.547386169433594 28.8134982585907 502.5016174316406 0.33620622754096985 478.9239807128906 0.34408921003341675 0.8377611 0.2249041348695755 True -7 22000 30.372507333755493 15.970817804336548 427.6513671875 0.1107977107167244 477.93975830078125 0.3448852002620697 0.84560883 0.20422764122486115 True -8 24750 30.807912588119507 0.6256940364837646 472.65570068359375 0.1747691035270691 476.7166748046875 0.3471469283103943 0.851318 0.2012193202972412 True -9 27500 30.449804306030273 0.6235830783843994 413.85614013671875 0.14767131209373474 475.7309265136719 0.34847551584243774 0.8558004 0.19482862949371338 True -10 30250 30.418269395828247 0.6128675937652588 470.2506103515625 0.11824492365121841 475.2291564941406 0.34909307956695557 0.8592855 0.18300729990005493 True -11 33000 30.40924596786499 0.615969181060791 418.87164306640625 0.1100011095404625 473.86724853515625 0.3518528938293457 0.8629535 0.17523932456970215 True -12 35750 30.39169955253601 0.6019647121429443 415.92120361328125 0.12149979919195175 473.0865783691406 0.35310524702072144 0.865935 0.16263078153133392 True -13 38500 30.39993381500244 0.59549880027771 378.4617919921875 0.1359694004058838 472.7223815917969 0.35331639647483826 0.87092215 0.15389303863048553 True -14 41250 30.355912446975708 0.6106569766998291 345.74346923828125 0.09680912643671036 472.8341979980469 0.3527776002883911 0.8729696 0.1427699476480484 True -15 44000 30.22289776802063 0.6007330417633057 448.90386962890625 0.12173185497522354 472.2508850097656 0.35362502932548523 0.8755038 0.13666577637195587 True -16 46750 29.845614433288574 0.5915541648864746 384.9083251953125 0.1113193929195404 471.3181457519531 0.35558581352233887 0.87762433 0.13063842058181763 True -17 49500 29.856382608413696 0.7780804634094238 417.0111083984375 0.0710090845823288 472.535400390625 0.3523675501346588 0.8793094 0.1279902309179306 True -18 52250 29.862018585205078 1.4475083351135254 438.88079833984375 0.18031254410743713 471.51177978515625 0.35556045174598694 0.87882143 0.12697453796863556 False -19 55000 29.763713598251343 0.6812310218811035 471.4837646484375 0.08631156384944916 471.6827697753906 0.355260968208313 0.8787767 0.1274130940437317 False diff --git a/ENCSR661AMM/cherimoya.fold_3.performance.tsv b/ENCSR661AMM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c6ebaaa13e4de0b7368b667756b8c5973653b3cc..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -472.535400390625 0.41944485902786255 0.3523675799369812 0.13075850903987885 0.8793094158172607 0.8658985495567322 0.1279902309179306 \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_4.evaluate.json b/ENCSR661AMM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index af5789845c21d37d003fa4b72cf2485ec7734f41..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF989SAK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_4.fit.json b/ENCSR661AMM/cherimoya.fold_4.fit.json deleted file mode 100644 index c7bcef49f66ab9e09f298fc108a14d20816db9db..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF989SAK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR661AMM/cherimoya.fold_4.log b/ENCSR661AMM/cherimoya.fold_4.log deleted file mode 100644 index 8cee87aad917b79716ede9b0db2cc7c1669c8555..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2818 35.81628370285034 2.2443759441375732 397.40802001953125 0.13293194770812988 511.4002685546875 0.2822352945804596 0.7578813 3.129464626312256 True -1 5636 31.100683450698853 0.7201051712036133 480.6018981933594 0.19289609789848328 486.35040283203125 0.32223930954933167 0.7760651 0.903961718082428 True -2 8454 31.162553310394287 0.5435402393341064 433.01416015625 0.1430206596851349 479.8597106933594 0.332715779542923 0.81086004 0.34646928310394287 True -3 11272 31.16233777999878 0.5577340126037598 466.1077880859375 0.31795579195022583 477.3451232910156 0.3348096013069153 0.82574683 0.3168312609195709 True -4 14090 31.183104515075684 0.559389591217041 478.321044921875 0.21333181858062744 477.1893615722656 0.33587291836738586 0.82547057 0.23898892104625702 False -5 16908 31.15777611732483 0.570288896560669 412.9665832519531 0.22137901186943054 474.7796325683594 0.33958229422569275 0.8372711 0.2040594220161438 True -6 19726 31.098147869110107 0.5288619995117188 456.2513427734375 0.1646164208650589 474.45050048828125 0.33970195055007935 0.8450159 0.2014472633600235 True -7 22544 31.092013120651245 0.5516724586486816 433.7314453125 0.10148777067661285 472.9732360839844 0.3432164490222931 0.8475186 0.21153654158115387 True -8 25362 31.064910173416138 0.5315690040588379 386.79815673828125 0.12326426804065704 472.419189453125 0.3429890275001526 0.85287935 0.19645516574382782 True -9 28180 31.081945180892944 0.5528891086578369 426.3189392089844 0.1136055439710617 472.5635070800781 0.3418339192867279 0.85739547 0.18282495439052582 True -10 30998 31.05495548248291 0.5751473903656006 477.16668701171875 0.16453474760055542 471.24774169921875 0.34467726945877075 0.86367714 0.16795849800109863 True -11 33816 31.083693742752075 0.5235888957977295 378.155029296875 0.10583755373954773 470.8084411621094 0.34524640440940857 0.8669565 0.15453235805034637 True -12 36634 31.1364266872406 0.5474188327789307 479.29571533203125 0.17538611590862274 470.32257080078125 0.34541064500808716 0.8694462 0.14299537241458893 True -13 39452 31.14825177192688 0.5413579940795898 375.76416015625 0.10480885207653046 469.3752746582031 0.3474215567111969 0.8744616 0.13198038935661316 True -14 42270 30.846560955047607 3.4210169315338135 441.88995361328125 0.1544663906097412 469.15264892578125 0.34719035029411316 0.879914 0.1209414005279541 True -15 45088 30.568139791488647 0.5493757724761963 401.4332275390625 0.09156370162963867 468.780029296875 0.3476350009441376 0.88266295 0.11495156586170197 True -16 47906 30.572762966156006 0.5700576305389404 460.0772705078125 0.10404674708843231 469.1074523925781 0.3472127318382263 0.8856678 0.10917201638221741 True -17 50724 30.572325706481934 0.5426640510559082 381.00238037109375 0.09433147311210632 468.6183166503906 0.34881591796875 0.88548756 0.10704688727855682 False -18 53542 30.566014528274536 0.5314922332763672 480.58319091796875 0.07064610719680786 468.9888916015625 0.34764549136161804 0.8844478 0.10692363232374191 False -19 56360 30.544780731201172 0.5364201068878174 400.94976806640625 0.07288466393947601 468.7140197753906 0.3485078513622284 0.8847025 0.10673249512910843 False diff --git a/ENCSR661AMM/cherimoya.fold_4.performance.tsv b/ENCSR661AMM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 38b5c4eb7dfa47b6f4185bdaf9f0d54632eb62a4..0000000000000000000000000000000000000000 --- a/ENCSR661AMM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -469.1074523925781 0.4229457378387451 0.3472127318382263 0.1249546930193901 0.8856678009033203 0.8754729628562927 0.10917201638221741 \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_0.evaluate.json b/ENCSR662HMO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8bd4eff55da5952d49c33a920a5437d7abd0530b..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF587FEV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_0.fit.json b/ENCSR662HMO/cherimoya.fold_0.fit.json deleted file mode 100644 index 5eacedeec2d931cd4b76d62bb56a1792a31e9d92..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF587FEV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_0.log b/ENCSR662HMO/cherimoya.fold_0.log deleted file mode 100644 index f8d0ae22a7f92a45c7b584bcfa9b3f3463fe10fa..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2804 34.87281680107117 3.3163137435913086 1506.523193359375 0.7757084369659424 2163.229248046875 0.302250474691391 0.5663006 8.638991355895996 True -1 5608 31.096792459487915 0.4427945613861084 1735.791015625 0.9497511386871338 1839.137939453125 0.4333917498588562 0.5636437 3.83081316947937 False -2 8412 31.011162996292114 0.4313805103302002 1664.068115234375 1.0739942789077759 1823.1077880859375 0.43569958209991455 0.61877465 2.501995086669922 True -3 11216 30.963417053222656 0.4286363124847412 1242.7989501953125 0.7450421452522278 1755.1253662109375 0.45626160502433777 0.6380367 2.254390239715576 True -4 14020 31.112189531326294 16.30576777458191 1249.634521484375 0.7364985942840576 1725.125732421875 0.4631081819534302 0.65999717 1.8017761707305908 True -5 16824 31.074719190597534 1.5764858722686768 1240.2279052734375 1.045234203338623 1707.0059814453125 0.469979852437973 0.6641071 1.5049352645874023 True -6 19628 31.056965351104736 2.271474838256836 1276.596923828125 1.0228692293167114 1687.8638916015625 0.4794508218765259 0.6728879 1.3487991094589233 True -7 22432 31.065446376800537 1.2272160053253174 1426.6856689453125 0.7186994552612305 1670.97265625 0.48700639605522156 0.67667466 1.2316241264343262 True -8 25236 30.701495885849 1.6851706504821777 1306.343017578125 0.916912317276001 1663.27392578125 0.49130529165267944 0.67608887 1.196588397026062 False -9 28040 30.514448881149292 1.1963210105895996 1484.560302734375 0.6586602926254272 1649.196044921875 0.49717170000076294 0.6802524 1.126854419708252 True -10 30844 30.43916130065918 0.5495429039001465 1373.14599609375 0.6320046782493591 1650.4881591796875 0.496724933385849 0.68318844 1.040890097618103 True -11 33648 30.380821704864502 0.4330861568450928 1172.769775390625 0.3904900848865509 1628.8040771484375 0.5054110288619995 0.686222 0.9422058463096619 True -12 36452 30.330384731292725 0.4317460060119629 1073.6624755859375 0.44983595609664917 1621.983642578125 0.5076021552085876 0.6948017 0.8530559539794922 True -13 39256 30.348995447158813 0.43148303031921387 1573.163818359375 1.133509874343872 1610.1304931640625 0.5110884308815002 0.7033466 0.7764305472373962 True -14 42060 30.33070969581604 0.4328653812408447 1308.021484375 0.39067521691322327 1599.2529296875 0.5145316123962402 0.7125345 0.6986706256866455 True -15 44864 30.675392866134644 0.43270444869995117 1387.91552734375 0.7736420035362244 1590.2618408203125 0.5160974860191345 0.7242467 0.639752984046936 True -16 47668 30.366090059280396 0.42909669876098633 1226.82666015625 0.29038572311401367 1581.3118896484375 0.5197308659553528 0.7316254 0.6085875630378723 True -17 50472 30.30342411994934 0.42838215827941895 1264.3173828125 0.3318743109703064 1579.896240234375 0.5187156796455383 0.7340564 0.5947327613830566 True -18 53276 30.30525231361389 0.4276747703552246 1299.8953857421875 0.3330473303794861 1580.6949462890625 0.5193766951560974 0.7347657 0.5925303101539612 True -19 56080 30.314043283462524 11.720192432403564 1272.364990234375 0.2688862681388855 1587.6478271484375 0.5146830081939697 0.7344327 0.5958755016326904 False diff --git a/ENCSR662HMO/cherimoya.fold_0.performance.tsv b/ENCSR662HMO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 18d985a6e488780a5bb84e21f7d134abc4110031..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1580.6949462890625 0.23512741923332214 0.5193766951560974 0.3209548592567444 0.7347657084465027 0.6612833142280579 0.5925303101539612 \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_1.evaluate.json b/ENCSR662HMO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 094bfe1dd4e74bafb62ed931dadcc8079dc4d88f..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF587FEV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_1.fit.json b/ENCSR662HMO/cherimoya.fold_1.fit.json deleted file mode 100644 index e5e9c2aee59d79b2e5a8ad6312de93c14e52bd2d..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF587FEV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_1.log b/ENCSR662HMO/cherimoya.fold_1.log deleted file mode 100644 index 5ac5f136efd4c57e06aa676fe3fc179453a896cb..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2842 35.19510531425476 22.988986253738403 1260.823486328125 0.8187160491943359 2468.210205078125 0.3061605393886566 0.55749154 10.932039260864258 True -1 5684 31.546748876571655 0.7698867321014404 1694.392333984375 0.7976824045181274 2135.803955078125 0.41442805528640747 0.60919726 4.472342491149902 True -2 8526 31.47840118408203 0.7699368000030518 1531.1737060546875 0.6366551518440247 2081.457763671875 0.4219890832901001 0.6449274 2.921424627304077 True -3 11368 31.542173385620117 21.377461910247803 1328.9007568359375 0.7158373594284058 2001.661376953125 0.43803200125694275 0.6736728 2.2238965034484863 True -4 14210 31.18835997581482 0.7575719356536865 1568.28125 0.8213642239570618 1942.5087890625 0.4566830098628998 0.6875614 1.8653302192687988 True -5 17052 30.988611459732056 0.7277572154998779 1555.337646484375 0.9276466369628906 1915.6258544921875 0.4646714925765991 0.6908999 1.955005407333374 True -6 19894 30.857361316680908 0.7236340045928955 1441.223876953125 0.8524184823036194 1893.6641845703125 0.47167259454727173 0.7011517 1.5453624725341797 True -7 22736 30.816073894500732 0.7119176387786865 1219.318359375 0.5471923351287842 1886.578125 0.4722466766834259 0.706741 1.5213900804519653 True -8 25578 30.885735034942627 0.7095892429351807 1636.036865234375 1.1080753803253174 1871.9915771484375 0.4797319173812866 0.7132948 1.394477128982544 True -9 28420 30.808422803878784 0.7221879959106445 1162.2225341796875 0.681289792060852 1862.3187255859375 0.48335692286491394 0.7144968 1.388648271560669 True -10 31262 30.839786767959595 0.9433083534240723 1245.92724609375 0.6813347339630127 1852.6754150390625 0.4844256043434143 0.7225778 1.190626859664917 True -11 34104 30.901177644729614 14.696823120117188 1373.844482421875 0.7659671902656555 1841.4847412109375 0.49051526188850403 0.7279708 1.1129060983657837 True -12 36946 30.915550470352173 1.0372953414916992 1069.736572265625 0.812395453453064 1829.5482177734375 0.49135082960128784 0.7379483 0.9907941222190857 True -13 39788 30.912056922912598 0.7148177623748779 1101.8724365234375 0.5371754169464111 1813.8668212890625 0.4945234954357147 0.74684834 0.8668071627616882 True -14 42630 31.473099946975708 0.7173745632171631 1359.736328125 0.4177105128765106 1791.7213134765625 0.5016688704490662 0.7543986 0.7784398198127747 True -15 45472 30.904568433761597 0.7152976989746094 1273.643798828125 0.6032443642616272 1791.6663818359375 0.5000156164169312 0.76559836 0.7083739638328552 True -16 48314 30.8614559173584 2.097566604614258 1020.67041015625 0.5186759829521179 1785.8375244140625 0.5001959204673767 0.777345 0.6404286623001099 True -17 51156 30.912009477615356 0.7147204875946045 1129.741943359375 0.4236975908279419 1789.0233154296875 0.4984802007675171 0.7804391 0.6009376645088196 True -18 53998 30.805654525756836 0.7187018394470215 1232.2872314453125 0.6481565237045288 1785.5106201171875 0.4995480179786682 0.7819832 0.5883848071098328 True -19 56840 30.84242582321167 2.791995048522949 1354.08544921875 0.3781817555427551 1779.8858642578125 0.5018982887268066 0.7811198 0.5882903337478638 False diff --git a/ENCSR662HMO/cherimoya.fold_1.performance.tsv b/ENCSR662HMO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 52cec8bce43a077a463c5845ea0a4bd7c7b1d03c..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1785.5106201171875 0.23373164236545563 0.4995479881763458 0.3286803364753723 0.7819831967353821 0.7250070571899414 0.5883848071098328 \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_2.evaluate.json b/ENCSR662HMO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3e943cf01c8eb6ce26f255db3764bd85d1c73968..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF587FEV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_2.fit.json b/ENCSR662HMO/cherimoya.fold_2.fit.json deleted file mode 100644 index 79bb62467a5854c6cad61a3852be8e1cb5571bba..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF587FEV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_2.log b/ENCSR662HMO/cherimoya.fold_2.log deleted file mode 100644 index 4594c052571ded38e19d5610c80aade12bc118a0..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2786 34.545156955718994 3.961477041244507 1627.1083984375 0.5767134428024292 1968.75732421875 0.2728292644023895 0.5607181 9.786389350891113 True -1 5572 30.279921770095825 0.909071683883667 1260.4088134765625 0.8700994253158569 1688.3199462890625 0.3610251545906067 0.6769504 3.485137939453125 True -2 8358 30.99579930305481 0.894749641418457 1493.6961669921875 0.8504753112792969 1659.754150390625 0.367001473903656 0.683278 2.0654094219207764 True -3 11144 30.9964919090271 0.9041934013366699 1462.265625 0.7663853764533997 1615.6439208984375 0.38042426109313965 0.6928798 1.6698284149169922 True -4 13930 30.98770809173584 0.9051392078399658 1686.823486328125 1.0822765827178955 1585.204833984375 0.3872886300086975 0.71074 1.4874805212020874 True -5 16716 30.977494478225708 1.7641029357910156 1541.038330078125 0.8798234462738037 1574.91748046875 0.38995328545570374 0.7164429 1.4055521488189697 True -6 19502 32.88145184516907 0.9018795490264893 1232.73779296875 1.1734066009521484 1561.2369384765625 0.39499226212501526 0.72319704 1.310021162033081 True -7 22288 30.976744174957275 1.6289942264556885 1269.523681640625 0.7322059869766235 1542.5052490234375 0.4031873941421509 0.73434 1.1858776807785034 True -8 25074 30.911762952804565 0.893587589263916 1296.88525390625 1.1196664571762085 1534.2677001953125 0.40546914935112 0.7422089 1.229382038116455 True -9 27860 30.923986673355103 0.8906445503234863 1329.0062255859375 0.5182478427886963 1519.7998046875 0.41144344210624695 0.7506194 1.1686958074569702 True -10 30646 30.842263221740723 0.8914775848388672 1287.1502685546875 0.7213401794433594 1518.2896728515625 0.4104951322078705 0.75559604 1.1258167028427124 True -11 33432 30.86637282371521 25.040334939956665 1247.2659912109375 0.6267731189727783 1502.8680419921875 0.4151836335659027 0.76006806 0.9859697818756104 True -12 36218 30.846519708633423 1.435227394104004 1379.7392578125 0.7336617708206177 1497.0015869140625 0.416287899017334 0.7654806 0.9621664881706238 True -13 39004 30.79532551765442 0.8953108787536621 1287.1038818359375 0.7864946126937866 1483.698974609375 0.4209235608577728 0.7736176 0.8151295781135559 True -14 41790 30.8055419921875 0.9007539749145508 1290.6376953125 0.4307611584663391 1470.9822998046875 0.42295897006988525 0.78399044 0.7114976644515991 True -15 44576 30.703879833221436 0.8840029239654541 1248.791259765625 0.5698438882827759 1469.8314208984375 0.423473596572876 0.7856035 0.6456055641174316 True -16 47362 30.693745374679565 0.8734853267669678 1108.6009521484375 0.478395015001297 1465.85693359375 0.42313265800476074 0.7899002 0.5854637026786804 True -17 50148 31.70239567756653 0.8818178176879883 1212.835693359375 0.30481255054473877 1462.8551025390625 0.4239518642425537 0.7901612 0.5452314019203186 True -18 52934 30.773392915725708 1.5401840209960938 1298.4818115234375 0.35967928171157837 1463.267822265625 0.4233967959880829 0.787691 0.537041187286377 False -19 55720 30.73374629020691 1.6645565032958984 1104.81689453125 0.3546442985534668 1471.0413818359375 0.41799598932266235 0.78583425 0.5325740575790405 False diff --git a/ENCSR662HMO/cherimoya.fold_2.performance.tsv b/ENCSR662HMO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 522d1afb7cc3e36e65d4d7d2824cf84675e66f0b..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1462.8551025390625 0.2698236405849457 0.4239518642425537 0.2639579176902771 0.7901611924171448 0.6932082176208496 0.5452314019203186 \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_3.evaluate.json b/ENCSR662HMO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ee0d2f2060295f175071b8fac7da4edd1d29999b..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF587FEV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_3.fit.json b/ENCSR662HMO/cherimoya.fold_3.fit.json deleted file mode 100644 index fd7b7ec36d9b4cc61c10b5c0ad7312b3de31f96e..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF587FEV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_3.log b/ENCSR662HMO/cherimoya.fold_3.log deleted file mode 100644 index 35965746197878a436410ba41d3df331aafe8690..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2903 35.766345262527466 4.169808387756348 1888.249755859375 0.9618875980377197 2338.885498046875 0.3002490997314453 0.57554644 9.593148231506348 True -1 5806 32.06680178642273 0.5554494857788086 1346.08203125 0.9837629795074463 1995.7730712890625 0.4237074851989746 0.59626126 3.9484102725982666 True -2 8709 32.07033944129944 0.5120573043823242 1509.61279296875 0.6321485638618469 1987.9359130859375 0.4231339395046234 0.62815267 3.3492281436920166 True -3 11612 32.055795192718506 0.5167069435119629 1288.3870849609375 0.5563809275627136 1911.2593994140625 0.4386458396911621 0.66842395 2.365138292312622 True -4 14515 32.00990295410156 0.5190608501434326 1438.70654296875 1.0891493558883667 1887.1710205078125 0.44896548986434937 0.6678609 2.1891822814941406 False -5 17418 31.966543912887573 0.5047130584716797 1085.5177001953125 0.6711758971214294 1855.6190185546875 0.4613683521747589 0.6723023 1.8524500131607056 True -6 20321 31.952805042266846 0.5092177391052246 1626.751220703125 0.8825274705886841 1836.68017578125 0.46766915917396545 0.67549855 1.6842645406723022 True -7 23224 31.958556413650513 0.7449607849121094 1442.6046142578125 0.6579568982124329 1838.2744140625 0.46570974588394165 0.6757336 1.4969525337219238 True -8 26127 32.01261782646179 0.511786937713623 1385.12646484375 0.6935770511627197 1829.231689453125 0.4713016450405121 0.67978764 1.471961498260498 True -9 29030 32.05399465560913 8.273825407028198 1231.1630859375 0.768126368522644 1811.7415771484375 0.4777202010154724 0.68503636 1.3485246896743774 True -10 31933 32.3342022895813 1.0326838493347168 1223.795654296875 0.5513110756874084 1804.14892578125 0.4790274500846863 0.6937979 1.1920188665390015 True -11 34836 32.03313875198364 0.5064871311187744 1267.7496337890625 0.5927239060401917 1791.7449951171875 0.48615801334381104 0.70238703 1.090189814567566 True -12 37739 32.007779598236084 0.5247178077697754 1436.81494140625 0.5168650150299072 1787.59375 0.48681455850601196 0.7122241 0.999685525894165 True -13 40642 32.0713427066803 0.5149729251861572 1412.4248046875 0.6912065744400024 1774.5560302734375 0.49117860198020935 0.71775085 0.9424197673797607 True -14 43545 32.036959648132324 0.5110538005828857 1265.2216796875 0.4474935531616211 1762.853515625 0.49297577142715454 0.73200643 0.8176004886627197 True -15 46448 31.590934991836548 0.5046095848083496 1077.8895263671875 0.6311702728271484 1752.0628662109375 0.495185911655426 0.7390779 0.7609211802482605 True -16 49351 31.500794172286987 0.501467227935791 1310.48876953125 0.5644877552986145 1744.8050537109375 0.49805939197540283 0.74813807 0.7032579779624939 True -17 52254 31.394556283950806 1.6226482391357422 1249.017822265625 0.6685717701911926 1748.1416015625 0.4973936378955841 0.75280464 0.6638193726539612 True -18 55157 31.40529179573059 0.5062417984008789 1471.800537109375 0.6312452554702759 1738.6978759765625 0.5013845562934875 0.75056326 0.6536884903907776 False -19 58060 31.534401655197144 0.5040194988250732 1518.204345703125 0.3173863887786865 1745.55322265625 0.4971632957458496 0.75047207 0.6503320932388306 False diff --git a/ENCSR662HMO/cherimoya.fold_3.performance.tsv b/ENCSR662HMO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 95d8bc8ec48ad6a91145a65f71ce991cfee2ee6e..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1748.1416015625 0.236925408244133 0.4973936378955841 0.32123687863349915 0.7528046369552612 0.6725784540176392 0.6638193726539612 \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_4.evaluate.json b/ENCSR662HMO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 34cd727590031ca25152c26b3823e82e9b363578..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF587FEV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_4.fit.json b/ENCSR662HMO/cherimoya.fold_4.fit.json deleted file mode 100644 index 6e93872a1563ebdb05f0f5a86341b5866f5cdc73..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF587FEV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662HMO/cherimoya.fold_4.log b/ENCSR662HMO/cherimoya.fold_4.log deleted file mode 100644 index 4c5b7382e0d1a7f9f5413ed5e0ffa13a7f251d55..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2683 33.62937307357788 2.019465208053589 1417.73095703125 0.7432793378829956 2127.0166015625 0.2868153154850006 0.54647744 9.72751522064209 True -1 5366 29.755411386489868 1.1290199756622314 1422.9725341796875 0.722225546836853 1803.7745361328125 0.4157160818576813 0.6156057 3.99688982963562 True -2 8049 29.640892505645752 0.43977904319763184 1992.8687744140625 1.0364623069763184 1770.4718017578125 0.4208362102508545 0.630159 2.519958734512329 True -3 10732 29.57704782485962 0.4309389591217041 1501.7850341796875 1.0876307487487793 1731.119384765625 0.43183770775794983 0.6491594 1.8240817785263062 True -4 13415 29.593307733535767 13.100061178207397 970.2801513671875 0.6512213945388794 1687.9234619140625 0.44821855425834656 0.66438437 1.4591636657714844 True -5 16098 30.00363779067993 0.42847752571105957 1456.1534423828125 0.9614551067352295 1669.7529296875 0.4516327679157257 0.6755279 1.5571045875549316 True -6 18781 29.578924655914307 1.4406230449676514 1376.2216796875 0.8995949625968933 1656.30810546875 0.45589959621429443 0.6834062 1.3326610326766968 True -7 21464 29.71839165687561 0.4437427520751953 1283.1292724609375 0.6793439984321594 1637.4083251953125 0.464508980512619 0.6882504 1.1590684652328491 True -8 24147 29.72041153907776 0.43459606170654297 1214.659912109375 1.0296396017074585 1633.2811279296875 0.46386945247650146 0.6915563 1.097272276878357 True -9 26830 29.696356296539307 0.42937421798706055 1509.991943359375 0.8423056602478027 1615.458740234375 0.47246256470680237 0.69490284 0.9859711527824402 True -10 29513 29.653175115585327 0.4325063228607178 1253.8031005859375 0.7812339067459106 1605.6923828125 0.4764917492866516 0.6942553 0.9558960199356079 False -11 32196 29.765132188796997 0.42922091484069824 1474.0419921875 0.3508182764053345 1589.535888671875 0.4816385507583618 0.7052619 0.8764556646347046 True -12 34879 29.51209855079651 0.4315221309661865 1321.5281982421875 0.5873074531555176 1585.0963134765625 0.48131024837493896 0.7100355 0.7881513833999634 True -13 37562 29.065536975860596 0.42989158630371094 1773.0001220703125 0.6290901899337769 1571.36669921875 0.4870186150074005 0.7160972 0.7367715239524841 True -14 40245 29.044973850250244 1.1968047618865967 1144.2938232421875 0.4541577696800232 1565.27734375 0.4893971383571625 0.7203394 0.7026400566101074 True -15 42928 29.11457848548889 0.4252007007598877 1483.785888671875 0.45550471544265747 1554.8173828125 0.4919753968715668 0.73200715 0.6433008909225464 True -16 45611 29.093306064605713 0.4215362071990967 1366.904052734375 0.5831130743026733 1550.52294921875 0.4925633370876312 0.73890185 0.605796217918396 True -17 48294 29.059568405151367 0.4185781478881836 1228.75537109375 0.6323851346969604 1548.8258056640625 0.4925946593284607 0.7431793 0.5824702382087708 True -18 50977 29.15252113342285 0.4297032356262207 1277.5953369140625 0.4443918466567993 1548.5438232421875 0.49382442235946655 0.7430238 0.5813004970550537 False -19 53660 29.181898593902588 0.4421350955963135 1116.69189453125 0.3843111991882324 1552.631591796875 0.4916304051876068 0.7414321 0.5821464657783508 False diff --git a/ENCSR662HMO/cherimoya.fold_4.performance.tsv b/ENCSR662HMO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 123eec0bdae27065bd9a59373cca7a9bfd8a49fd..0000000000000000000000000000000000000000 --- a/ENCSR662HMO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1548.8258056640625 0.24457590281963348 0.4925945997238159 0.30383503437042236 0.7431793212890625 0.6688063144683838 0.5824702382087708 \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_0.evaluate.json b/ENCSR662IRS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c3fd7b3450e799be1db756de2924ec7b817bc436..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF730RCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_0.fit.json b/ENCSR662IRS/cherimoya.fold_0.fit.json deleted file mode 100644 index 5eb97d2408eb8f3637cafb7d6d2e4fe898a2a656..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF730RCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_0.log b/ENCSR662IRS/cherimoya.fold_0.log deleted file mode 100644 index 1b1c23d9092ab7d6748f049da06453f9424da392..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2583 33.02073264122009 4.32804274559021 475.922119140625 0.9738582372665405 985.0970458984375 0.2172752320766449 0.58238256 8.95908260345459 True -1 5166 28.433427572250366 0.9178454875946045 446.764892578125 0.7359890937805176 804.11865234375 0.2935221195220947 0.7316884 3.119072914123535 True -2 7749 27.99759578704834 0.49291324615478516 637.8035278320312 1.0019848346710205 794.488525390625 0.2931838929653168 0.73741335 2.3373448848724365 True -3 10332 27.87509822845459 0.5194394588470459 605.374755859375 1.0721001625061035 772.3809204101562 0.30087292194366455 0.7438101 1.763162612915039 True -4 12915 27.904403686523438 0.49524688720703125 669.8283081054688 1.0168302059173584 759.5905151367188 0.3060026168823242 0.75028914 1.1822090148925781 True -5 15498 27.900996685028076 0.4930903911590576 434.6385498046875 0.7029436826705933 750.1943359375 0.30884355306625366 0.76456916 1.0112481117248535 True -6 18081 27.92482900619507 0.510084867477417 701.208740234375 0.9640889167785645 742.80078125 0.3138691484928131 0.7725358 0.9365205764770508 True -7 20664 27.905041217803955 0.49829912185668945 575.2169189453125 0.48265907168388367 732.7175903320312 0.31788820028305054 0.7833338 0.8243627548217773 True -8 23247 27.880541563034058 0.5312168598175049 556.2935791015625 0.6039735078811646 729.7456665039062 0.3185688257217407 0.79032135 0.7725246548652649 True -9 25830 27.971452474594116 0.9777500629425049 551.1727294921875 0.5871341228485107 727.80517578125 0.31978878378868103 0.7956933 0.6946514248847961 True -10 28413 27.946198225021362 0.563549280166626 659.271240234375 0.4854077100753784 720.303955078125 0.3241872489452362 0.8040544 0.6561629176139832 True -11 30996 27.953749418258667 0.5119476318359375 724.294189453125 0.683807373046875 716.1275024414062 0.3262315094470978 0.8126625 0.6193612813949585 True -12 33579 28.039191484451294 0.6217947006225586 561.9674072265625 0.5709723234176636 714.02099609375 0.3271409869194031 0.818671 0.5772265791893005 True -13 36162 28.053818702697754 0.516756534576416 518.4937133789062 0.4574333131313324 711.9861450195312 0.3275162875652313 0.82449347 0.5418479442596436 True -14 38745 28.117234230041504 0.5117175579071045 645.5843505859375 0.6169394254684448 707.5305786132812 0.33034613728523254 0.82950383 0.5235797762870789 True -15 41328 28.160144090652466 0.5068767070770264 578.2996826171875 0.5397449731826782 704.53466796875 0.3323662579059601 0.8332328 0.5118461847305298 True -16 43911 28.06945490837097 0.5005462169647217 539.162353515625 0.7755996584892273 702.478271484375 0.33376219868659973 0.83470213 0.5009145140647888 True -17 46494 28.09796142578125 0.8086223602294922 561.6466674804688 0.371884286403656 705.0005493164062 0.33100903034210205 0.8369431 0.49783968925476074 True -18 49077 28.036001443862915 2.597490072250366 745.3287353515625 0.3675464391708374 704.0782470703125 0.33159053325653076 0.8363035 0.5004590749740601 False -19 51660 28.037043571472168 0.5098707675933838 543.0403442382812 0.44887176156044006 706.317138671875 0.33018818497657776 0.8350493 0.5044481158256531 False diff --git a/ENCSR662IRS/cherimoya.fold_0.performance.tsv b/ENCSR662IRS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e48b3730470d3dd567ac0c16698898b5bf1ab91f..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -705.0005493164062 0.4218084514141083 0.33100903034210205 0.1496639847755432 0.8369430899620056 0.756635844707489 0.49783968925476074 \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_1.evaluate.json b/ENCSR662IRS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f82c2ed9a077d5f1a399bdf3aca162c89f0cbb71..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF730RCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_1.fit.json b/ENCSR662IRS/cherimoya.fold_1.fit.json deleted file mode 100644 index cbbc010e025fcc71d9819e96d31e83d3dde1f095..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF730RCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_1.log b/ENCSR662IRS/cherimoya.fold_1.log deleted file mode 100644 index 8538e11fbadd034cae234d665cff30f71d2b2bb2..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2505 32.13627791404724 4.477041721343994 777.7704467773438 1.233266830444336 1202.9114990234375 0.2269519418478012 0.5726367 10.570840835571289 True -1 5010 27.760401010513306 0.7095131874084473 752.0335083007812 1.3340275287628174 986.9419555664062 0.30675312876701355 0.71617717 3.983098268508911 True -2 7515 27.670403957366943 0.708488941192627 595.5693359375 0.9910119771957397 962.143798828125 0.31207704544067383 0.7391473 4.269653797149658 True -3 10020 27.64294981956482 2.396552801132202 445.47235107421875 0.568444013595581 927.6707763671875 0.32412612438201904 0.7427934 2.1246888637542725 True -4 12525 27.650792598724365 0.6912786960601807 631.64501953125 0.7177691459655762 909.8934936523438 0.3289896845817566 0.7650338 1.3013982772827148 True -5 15030 27.620192289352417 4.907188415527344 623.4552612304688 0.6080235838890076 894.295166015625 0.33398449420928955 0.7736988 1.0800492763519287 True -6 17535 27.21447467803955 0.7098391056060791 578.88525390625 0.870137631893158 887.2379150390625 0.33611854910850525 0.7786602 1.0236155986785889 True -7 20040 27.09335684776306 0.7001762390136719 770.160888671875 0.7530337572097778 877.6217041015625 0.3405035436153412 0.79012674 0.9811695218086243 True -8 22545 27.102015495300293 0.6917784214019775 808.9080200195312 0.7814450263977051 867.9537963867188 0.34584280848503113 0.7974078 0.8966971635818481 True -9 25050 27.330052852630615 0.7071318626403809 657.4303588867188 0.48957955837249756 863.4954223632812 0.3477725386619568 0.80515116 0.829367995262146 True -10 27555 27.23301672935486 0.7053985595703125 436.5279846191406 0.5284347534179688 858.946044921875 0.34839221835136414 0.81515366 0.749884307384491 True -11 30060 27.21074652671814 0.7077622413635254 468.81103515625 0.5916090607643127 854.7068481445312 0.35109496116638184 0.82199895 0.7307913899421692 True -12 32565 27.140005588531494 0.7055165767669678 497.1388854980469 0.7294808626174927 848.9073486328125 0.3531525433063507 0.83202565 0.6597826480865479 True -13 35070 27.238094806671143 0.7029330730438232 472.19500732421875 0.2668304741382599 840.5735473632812 0.3564631938934326 0.8397931 0.6236793994903564 True -14 37575 27.233105659484863 1.5274724960327148 518.907470703125 0.4239673912525177 837.1054077148438 0.3562133014202118 0.84764373 0.5936278700828552 True -15 40080 27.190131187438965 0.7118926048278809 515.55517578125 0.40305936336517334 833.3195190429688 0.3589151203632355 0.85138696 0.5691149830818176 True -16 42585 27.156898260116577 0.7090883255004883 734.623291015625 0.4945724308490753 833.3003540039062 0.3578275144100189 0.85247666 0.5547777414321899 True -17 45090 27.120206117630005 0.7028138637542725 522.69287109375 0.3417642116546631 832.3770141601562 0.35882166028022766 0.85353786 0.5452896356582642 True -18 47595 27.32840847969055 0.6943004131317139 632.4000854492188 0.4981723427772522 831.426513671875 0.36009299755096436 0.8523816 0.5459713935852051 False -19 50100 27.233455181121826 0.7183237075805664 640.3619384765625 0.33187681436538696 832.73681640625 0.3595374822616577 0.85204375 0.5526179671287537 False diff --git a/ENCSR662IRS/cherimoya.fold_1.performance.tsv b/ENCSR662IRS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8bda7ce118a6baad6ffae6e0f953c048cfd2ba91..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -832.3770141601562 0.3970649540424347 0.35882169008255005 0.17599090933799744 0.8535378575325012 0.8013468384742737 0.5452896356582642 \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_2.evaluate.json b/ENCSR662IRS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f43145e23c3571a5e82726a4f0ac1491463e248f..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF730RCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_2.fit.json b/ENCSR662IRS/cherimoya.fold_2.fit.json deleted file mode 100644 index 1f0270d415b8994f24836ba70695a56b2030e202..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF730RCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_2.log b/ENCSR662IRS/cherimoya.fold_2.log deleted file mode 100644 index 2b8ed366f0574d55f52b4b408d8cfaf845766836..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2690 34.13756990432739 4.396525859832764 517.562744140625 0.5261072516441345 995.39501953125 0.21961340308189392 0.5482981 8.267980575561523 True -1 5380 29.661189317703247 1.186697006225586 565.7111206054688 0.8313498497009277 816.0140380859375 0.2847164273262024 0.71156985 3.071467876434326 True -2 8070 29.7168710231781 0.6014111042022705 917.187744140625 1.044448971748352 795.8901977539062 0.29314395785331726 0.7215287 2.430222749710083 True -3 10760 29.661123037338257 1.104914903640747 631.1455688476562 0.612499475479126 774.7268676757812 0.2993558645248413 0.73801655 1.6895484924316406 True -4 13450 29.688066720962524 0.5887837409973145 498.022705078125 0.5496000647544861 763.9111328125 0.30304667353630066 0.7469676 1.0404261350631714 True -5 16140 29.628090858459473 0.5806543827056885 596.7689208984375 0.6376603841781616 757.9070434570312 0.30459216237068176 0.75442183 0.915222704410553 True -6 18830 29.64808464050293 0.59084153175354 488.26409912109375 0.7073025703430176 748.8140258789062 0.3090808093547821 0.7650365 0.8206983804702759 True -7 21520 29.602055549621582 0.6166150569915771 766.38427734375 0.6734006404876709 745.0784912109375 0.3096678555011749 0.76945716 0.8288737535476685 True -8 24210 29.616960763931274 0.5956978797912598 616.4471435546875 1.0324941873550415 734.6796875 0.3177178204059601 0.7851602 0.7310822010040283 True -9 26900 29.63045024871826 1.3718228340148926 554.351806640625 0.4692535996437073 733.5363159179688 0.315668523311615 0.79591167 0.657597541809082 True -10 29590 29.660011529922485 0.5773055553436279 591.2044677734375 0.703239917755127 724.0470581054688 0.3216628432273865 0.8050624 0.6196603178977966 True -11 32280 29.056938886642456 0.5740656852722168 573.7208862304688 0.7558383345603943 721.4511108398438 0.3219112455844879 0.8114714 0.5865663290023804 True -12 34970 29.060195446014404 0.5762670040130615 697.141845703125 0.4966478943824768 714.2523193359375 0.32585859298706055 0.81686723 0.5673574805259705 True -13 37660 29.094797134399414 0.5866279602050781 698.20263671875 0.7458906173706055 711.1766357421875 0.32715389132499695 0.823719 0.5404086709022522 True -14 40350 29.142582654953003 0.5938055515289307 439.48419189453125 0.5422901511192322 710.0115966796875 0.32623183727264404 0.8289082 0.5214492082595825 True -15 43040 29.20309543609619 0.5976378917694092 469.1120910644531 0.42631426453590393 708.354736328125 0.3270453214645386 0.8345627 0.505926787853241 True -16 45730 29.209911108016968 0.57615065574646 558.3911743164062 0.33224165439605713 705.5393676757812 0.3297017812728882 0.83554024 0.4974617660045624 True -17 48420 29.28972029685974 0.5808074474334717 559.5021362304688 0.38258251547813416 705.1806030273438 0.33006277680397034 0.83594877 0.4944750964641571 True -18 51110 29.217931032180786 0.5873608589172363 577.4424438476562 0.24114608764648438 708.0037231445312 0.32791659235954285 0.83411455 0.49814262986183167 False -19 53800 29.205500602722168 1.2790746688842773 681.2618408203125 0.34100496768951416 707.4667358398438 0.32896173000335693 0.8364407 0.4983442723751068 True diff --git a/ENCSR662IRS/cherimoya.fold_2.performance.tsv b/ENCSR662IRS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7d1a38c9daa8b52d02802a6fc90e406150e45586..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -707.4667358398438 0.42039984464645386 0.32896173000335693 0.153648242354393 0.8364406824111938 0.7515668869018555 0.4983442723751068 \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_3.evaluate.json b/ENCSR662IRS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7acf89c6ac257912f50c0c42fb2be1144aff1d5b..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF730RCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_3.fit.json b/ENCSR662IRS/cherimoya.fold_3.fit.json deleted file mode 100644 index d5b96b45910510a332c5ecdabeae516541a0659e..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF730RCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_3.log b/ENCSR662IRS/cherimoya.fold_3.log deleted file mode 100644 index d279ed4cd86feff7956ae1f42888562470c3fea1..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2562 33.107526779174805 3.9658925533294678 628.6446533203125 0.8292138576507568 1016.0296630859375 0.23113276064395905 0.53391165 11.850343704223633 True -1 5124 28.27921414375305 0.5389230251312256 706.58154296875 1.2722305059432983 845.6387939453125 0.30145853757858276 0.6929835 3.5908923149108887 True -2 7686 28.28608226776123 0.5280134677886963 740.5245971679688 0.8630586266517639 823.5536499023438 0.3079400956630707 0.7126809 3.0971357822418213 True -3 10248 28.247685432434082 0.5198378562927246 749.1351318359375 0.6968754529953003 811.5753173828125 0.31109699606895447 0.71835566 1.9866528511047363 True -4 12810 28.235238313674927 0.49530816078186035 690.0794067382812 1.0110337734222412 799.0890502929688 0.31645748019218445 0.74041903 1.2954007387161255 True -5 15372 28.217040061950684 0.5038530826568604 889.6998291015625 1.0004034042358398 789.781494140625 0.3217109143733978 0.75053525 1.146682858467102 True -6 17934 28.217613458633423 12.875575542449951 503.301025390625 0.8706116676330566 782.4701538085938 0.32543495297431946 0.7546866 1.088931679725647 True -7 20496 28.274179458618164 0.5208122730255127 486.39227294921875 0.48034632205963135 775.1240234375 0.3311762809753418 0.76028967 1.0616633892059326 True -8 23058 28.25170612335205 0.49346113204956055 523.6444091796875 0.4980318546295166 768.8908081054688 0.3343857228755951 0.7680315 0.9862564206123352 True -9 25620 28.297444343566895 0.5185973644256592 493.1233825683594 0.5411297678947449 766.1085205078125 0.33506834506988525 0.7771116 0.9064285755157471 True -10 28182 28.245770692825317 0.511150598526001 650.603515625 0.6306928396224976 762.550048828125 0.33732324838638306 0.7814624 0.8813658952713013 True -11 30744 28.485848903656006 0.5139784812927246 604.68017578125 0.5417832136154175 756.6387939453125 0.34049752354621887 0.78723 0.816804826259613 True -12 33306 27.978839635849 0.519127607345581 690.1029052734375 0.35803326964378357 749.085693359375 0.3440166413784027 0.7978342 0.75002521276474 True -13 35868 27.785468816757202 0.5073039531707764 538.4627685546875 0.49066275358200073 744.7477416992188 0.3448246717453003 0.804729 0.718892514705658 True -14 38430 27.892277717590332 0.5170774459838867 643.837158203125 0.5074402093887329 741.9342041015625 0.34593480825424194 0.81227547 0.662213921546936 True -15 40992 27.81967043876648 0.4956026077270508 593.753662109375 0.5665355920791626 739.259521484375 0.34599554538726807 0.8184331 0.6209762096405029 True -16 43554 27.86915922164917 0.5010952949523926 674.4672241210938 0.4548889994621277 739.265869140625 0.3448350429534912 0.8223061 0.5928949117660522 True -17 46116 28.257588148117065 22.612295150756836 648.9161376953125 0.4829903841018677 734.0693969726562 0.34959208965301514 0.8244243 0.5774080753326416 True -18 48678 27.89444613456726 1.268381118774414 558.7539672851562 0.2892649173736572 737.2644653320312 0.34635862708091736 0.8271309 0.5747655630111694 True -19 51240 27.939337015151978 0.5089023113250732 550.804443359375 0.4643089771270752 739.007568359375 0.34509849548339844 0.8250476 0.5728614330291748 False diff --git a/ENCSR662IRS/cherimoya.fold_3.performance.tsv b/ENCSR662IRS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7fc68465195a79060b13c10ce923cfe1c2cd68f7..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -737.2644653320312 0.4103887379169464 0.34635862708091736 0.1619979441165924 0.827130913734436 0.7511802911758423 0.5747655630111694 \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_4.evaluate.json b/ENCSR662IRS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 95fc59cb215464b526e83ff43034eb01e4bbec75..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF730RCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_4.fit.json b/ENCSR662IRS/cherimoya.fold_4.fit.json deleted file mode 100644 index bf3845fbb7a41d9d17ce159ae21b5ab692785994..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF730RCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662IRS/cherimoya.fold_4.log b/ENCSR662IRS/cherimoya.fold_4.log deleted file mode 100644 index c6ca5b319bb724e456f8ee2bd1b0d221f71eefbb..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2525 32.659947872161865 4.17466926574707 650.402099609375 0.7826198935508728 871.4990844726562 0.21430476009845734 0.5192951 9.034791946411133 True -1 5050 27.819645643234253 0.7070889472961426 478.110107421875 0.6667057275772095 735.7281494140625 0.27977630496025085 0.68840384 2.9848458766937256 True -2 7575 27.858372449874878 0.5111339092254639 802.458984375 1.003704309463501 726.9444580078125 0.28332793712615967 0.6863115 2.0925514698028564 False -3 10100 27.878966331481934 0.5015349388122559 636.6834716796875 0.9175190329551697 700.6520385742188 0.29270362854003906 0.7184309 1.9681702852249146 True -4 12625 27.79129958152771 1.8510494232177734 591.6927490234375 0.8658668994903564 688.0188598632812 0.2975020110607147 0.7219936 1.4306082725524902 True -5 15150 27.815380096435547 0.5222647190093994 566.94140625 0.722809374332428 679.7021484375 0.30016228556632996 0.7431776 0.9374393224716187 True -6 17675 27.874833583831787 1.0821378231048584 758.6522216796875 0.850875973701477 675.1220092773438 0.30315548181533813 0.7498413 0.8455787301063538 True -7 20200 27.832248210906982 0.5061376094818115 419.5509033203125 0.5751208662986755 670.56884765625 0.3060826361179352 0.75286806 0.7829329371452332 True -8 22725 27.80747961997986 0.5072553157806396 615.2486572265625 0.6587097644805908 667.445068359375 0.3071829378604889 0.7571271 0.7656811475753784 True -9 25250 27.85788869857788 0.5239224433898926 599.0079345703125 0.4482278525829315 662.4334106445312 0.3099709451198578 0.76955694 0.7052439451217651 True -10 27775 27.874401330947876 0.5138883590698242 639.4229125976562 0.5743980407714844 658.757568359375 0.31286105513572693 0.7813171 0.6489537954330444 True -11 30300 27.84799289703369 1.1820166110992432 529.2191162109375 0.5999108552932739 654.9495849609375 0.31498420238494873 0.7888693 0.6246294379234314 True -12 32825 27.899332761764526 0.5035648345947266 487.28533935546875 0.7037505507469177 650.6318969726562 0.31621289253234863 0.7952322 0.5952563881874084 True -13 35350 27.816943168640137 0.5081424713134766 527.8896484375 0.3522934019565582 648.4439697265625 0.3170921802520752 0.8060954 0.5521302819252014 True -14 37875 27.847996950149536 0.49784421920776367 455.9500732421875 0.3981963098049164 644.8998413085938 0.32064902782440186 0.81162375 0.5274715423583984 True -15 40400 27.512657642364502 0.4880096912384033 533.46875 0.4009554088115692 643.7589111328125 0.31991803646087646 0.81956106 0.5035263895988464 True -16 42925 27.314815044403076 0.501014232635498 450.445068359375 0.4137713313102722 645.567626953125 0.31776756048202515 0.82292056 0.492698073387146 True -17 45450 27.325535774230957 0.5016789436340332 456.49505615234375 0.4279518127441406 645.2869873046875 0.31949353218078613 0.82459515 0.48691365122795105 True -18 47975 27.332969903945923 0.5079128742218018 612.364013671875 0.5065478086471558 645.3321533203125 0.3201160430908203 0.8247959 0.48739129304885864 True -19 50500 27.335973024368286 0.4980347156524658 496.9459533691406 0.4595377743244171 646.1864624023438 0.319253534078598 0.8232314 0.4897976815700531 False diff --git a/ENCSR662IRS/cherimoya.fold_4.performance.tsv b/ENCSR662IRS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6619d4db668eb2ce636678e395e282b827e71ef7..0000000000000000000000000000000000000000 --- a/ENCSR662IRS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -645.3321533203125 0.4310666024684906 0.3201160430908203 0.14041221141815186 0.8247959017753601 0.7388664484024048 0.48739129304885864 \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_0.evaluate.json b/ENCSR662RIZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 643e5a00b9a38281551c5ae30bf69f4322b8c878..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF870XOC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_0.fit.json b/ENCSR662RIZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 35b6e9f939514e31399f16745c57332e3313d15f..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF870XOC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_0.log b/ENCSR662RIZ/cherimoya.fold_0.log deleted file mode 100644 index 6ba8b028bd2483f0ecb4458ce199e5854a09290d..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2766 40.738943099975586 7.212686061859131 529.0438232421875 0.6868476867675781 803.7151489257812 0.33690589666366577 0.77494603 7.220475196838379 True -1 5532 30.082289218902588 39.8455548286438 510.22216796875 0.47487595677375793 687.7532348632812 0.4507121741771698 0.8270733 1.4786159992218018 True -2 8298 30.608977794647217 0.5590589046478271 636.4752807617188 0.435788094997406 673.0255126953125 0.46756112575531006 0.83349836 0.7331190705299377 True -3 11064 29.482910633087158 0.5612969398498535 535.1101684570312 0.36630624532699585 663.8048706054688 0.47791022062301636 0.8429576 0.4762471914291382 True -4 13830 29.50922703742981 0.5543060302734375 530.6768798828125 0.3832855224609375 659.8673706054688 0.48167234659194946 0.85351586 0.4226331412792206 True -5 16596 29.50613522529602 0.5546143054962158 544.2412719726562 0.6295913457870483 655.2237548828125 0.4880857765674591 0.85590535 0.35680091381073 True -6 19362 29.52157688140869 0.5512263774871826 473.72784423828125 0.3018295466899872 654.8603515625 0.48700112104415894 0.85992783 0.32363760471343994 True -7 22128 29.572168588638306 0.5588464736938477 583.0704345703125 0.5024489164352417 650.586181640625 0.4923902750015259 0.86349547 0.3056687116622925 True -8 24894 29.54401993751526 0.5510189533233643 545.54541015625 0.35396808385849 647.4337158203125 0.496243417263031 0.86714005 0.29890286922454834 True -9 27660 29.509866952896118 0.5494050979614258 538.0142822265625 0.29197925329208374 643.4127807617188 0.5012465119361877 0.87092704 0.2817455232143402 True -10 30426 32.22647023200989 32.437917709350586 552.4035034179688 0.525989294052124 642.6790161132812 0.5008821487426758 0.87658674 0.26006457209587097 True -11 33192 29.487268209457397 1.1049268245697021 518.0551147460938 0.23718567192554474 639.810791015625 0.5041161775588989 0.8814128 0.2496435046195984 True -12 35958 29.613885641098022 40.26296877861023 543.209716796875 0.3145613670349121 638.2946166992188 0.5047562122344971 0.8837989 0.23685015738010406 True -13 38724 29.907291889190674 0.5775711536407471 569.4303588867188 0.25087276101112366 636.4838256835938 0.507053792476654 0.8906259 0.22737611830234528 True -14 41490 29.552934646606445 0.549196720123291 484.9217834472656 0.3240025043487549 635.3779907226562 0.5084975361824036 0.89263636 0.21995782852172852 True -15 44256 29.53288960456848 0.5472939014434814 553.2718505859375 0.26065924763679504 632.4100952148438 0.5118352770805359 0.89587086 0.21418577432632446 True -16 47022 29.53322148323059 0.5583219528198242 482.3500061035156 0.18962329626083374 632.5982666015625 0.5118931531906128 0.8984209 0.2064904421567917 True -17 49788 29.53493571281433 9.609529256820679 515.8165893554688 0.2161518782377243 633.9666137695312 0.5094845294952393 0.8992884 0.20624351501464844 True -18 52554 29.589245557785034 0.5705676078796387 538.043701171875 0.31880125403404236 630.7940673828125 0.5148082971572876 0.8991695 0.20892241597175598 False -19 55320 29.672804832458496 0.5689847469329834 553.29296875 0.25861603021621704 630.8590087890625 0.5138705372810364 0.89978606 0.20927707850933075 True diff --git a/ENCSR662RIZ/cherimoya.fold_0.performance.tsv b/ENCSR662RIZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 278347c654b3bfcaafd2689788cd692093ffdd0a..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -630.8590087890625 0.3215046525001526 0.5138705372810364 0.205448716878891 0.8997860550880432 0.8771657943725586 0.20927707850933075 \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_1.evaluate.json b/ENCSR662RIZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index eea2e1b384356cc3014fcec0c4b01cc448e83f13..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF870XOC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_1.fit.json b/ENCSR662RIZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 04550a4e1e7e68186a6baeef36b826645ee0b1fd..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF870XOC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_1.log b/ENCSR662RIZ/cherimoya.fold_1.log deleted file mode 100644 index e5b2b3bfd49eec3f9ed36e11be51867422a6fa05..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 34.15661549568176 3.6392784118652344 617.8184814453125 0.468156635761261 935.6814575195312 0.3353031873703003 0.7672317 8.801531791687012 True -1 5418 29.473585844039917 0.8050432205200195 559.7274169921875 0.7134798765182495 796.146728515625 0.4566606879234314 0.83191574 1.6910580396652222 True -2 8127 29.525657892227173 0.7124073505401611 475.74615478515625 0.4940398335456848 774.7191162109375 0.4773852527141571 0.84931487 0.5413600206375122 True -3 10836 29.60154938697815 0.7149455547332764 590.8150024414062 0.41250380873680115 763.6797485351562 0.48799705505371094 0.8557842 0.4459885358810425 True -4 13545 29.547290086746216 1.728593349456787 479.7862854003906 0.3677363693714142 757.993896484375 0.49459439516067505 0.85843885 0.3572019040584564 True -5 16254 29.474207162857056 1.4691987037658691 546.7501220703125 0.5537161231040955 756.3341674804688 0.49549540877342224 0.86120194 0.34988152980804443 True -6 18963 30.027653694152832 5.299564361572266 603.010009765625 0.27737587690353394 751.9102172851562 0.4993806481361389 0.8645761 0.3121342360973358 True -7 21672 29.53179907798767 29.089168071746826 485.597412109375 0.41829314827919006 748.5945434570312 0.5015637278556824 0.87147117 0.29277586936950684 True -8 24381 29.529149293899536 0.7445564270019531 435.3642883300781 0.499131977558136 746.2257080078125 0.504037082195282 0.87609667 0.2767364978790283 True -9 27090 29.529320240020752 29.04789423942566 488.54498291015625 0.37062105536460876 742.2393798828125 0.5084272623062134 0.8776992 0.2682603895664215 True -10 29799 29.731410264968872 0.7239294052124023 525.157958984375 0.298423707485199 739.9168701171875 0.5101571083068848 0.88117445 0.260381281375885 True -11 32508 29.372320652008057 0.750342845916748 532.089599609375 0.2664991617202759 737.8887329101562 0.5116989612579346 0.8834207 0.2526763081550598 True -12 35217 28.972399950027466 0.7115254402160645 501.68658447265625 0.3627333641052246 735.1862182617188 0.5136595368385315 0.88914967 0.23687654733657837 True -13 37926 28.903807163238525 1.3215246200561523 518.442138671875 0.44168707728385925 732.642822265625 0.5167954564094543 0.8945667 0.22689679265022278 True -14 40635 28.945712089538574 0.716278076171875 487.5785827636719 0.2202741801738739 730.01513671875 0.5187473893165588 0.89870965 0.21966862678527832 True -15 43344 28.916783094406128 0.7033112049102783 454.46685791015625 0.22074034810066223 727.7507934570312 0.5218859314918518 0.9001308 0.21634826064109802 True -16 46053 29.198147296905518 8.239493370056152 553.879150390625 0.29130667448043823 728.9342041015625 0.519430935382843 0.9021865 0.21468253433704376 True -17 48762 28.99185538291931 0.7212107181549072 498.2623596191406 0.19637124240398407 727.6691284179688 0.5200885534286499 0.9034693 0.2122136801481247 True -18 51471 28.957930326461792 0.7114577293395996 470.449462890625 0.2194298505783081 726.7986450195312 0.5216692090034485 0.9050992 0.215023934841156 True -19 54180 28.963115453720093 1.2395095825195312 584.4862060546875 0.18756204843521118 727.6607666015625 0.5200845003128052 0.90294003 0.21603386104106903 False diff --git a/ENCSR662RIZ/cherimoya.fold_1.performance.tsv b/ENCSR662RIZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 014b27d117cd7ed1780f16b943f33bac6c799247..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -726.7986450195312 0.3071512281894684 0.5216691493988037 0.22839964926242828 0.9050992131233215 0.8977654576301575 0.215023934841156 \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_2.evaluate.json b/ENCSR662RIZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 508a78c35fbdf02c374ff5ff75af7e5802c96eb3..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF870XOC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_2.fit.json b/ENCSR662RIZ/cherimoya.fold_2.fit.json deleted file mode 100644 index c33af8bb41953e3b03bd76b30fd94df09f1875d9..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF870XOC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_2.log b/ENCSR662RIZ/cherimoya.fold_2.log deleted file mode 100644 index 4fddbdddbdcf88a758144753ac14db609f281fba..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 35.703147411346436 3.639492988586426 519.6870727539062 0.4276890456676483 839.429443359375 0.33704203367233276 0.7584681 7.4736552238464355 True -1 5758 31.419435262680054 0.6525046825408936 458.2132568359375 0.41023847460746765 718.3114624023438 0.4511580169200897 0.8246041 1.1262946128845215 True -2 8637 31.403756856918335 0.5833091735839844 590.709716796875 0.3760993778705597 703.0628051757812 0.46670377254486084 0.8322087 0.6151106953620911 True -3 11516 31.406134128570557 0.5674948692321777 550.5198364257812 0.3797891139984131 693.302978515625 0.4782535433769226 0.84414655 0.4469699263572693 True -4 14395 31.36399006843567 34.503504037857056 517.1746826171875 0.3919913172721863 689.4221801757812 0.48185718059539795 0.8509675 0.3822522759437561 True -5 17274 32.56030297279358 0.9930460453033447 484.0351867675781 0.37511003017425537 685.532958984375 0.487165629863739 0.8531735 0.37118417024612427 True -6 20153 30.771604537963867 7.467223644256592 552.5234985351562 0.43522781133651733 683.627685546875 0.48956534266471863 0.85540944 0.34788715839385986 True -7 23032 30.76844048500061 0.5675837993621826 552.1771240234375 0.4455115795135498 682.3366088867188 0.49009770154953003 0.85682124 0.3342655599117279 True -8 25911 31.68366837501526 0.5733983516693115 524.687255859375 0.3065117597579956 680.2540893554688 0.49212774634361267 0.86216986 0.3075060546398163 True -9 28790 32.62943196296692 36.63456177711487 613.4063110351562 0.26329341530799866 677.5003662109375 0.4947633445262909 0.86511 0.28402653336524963 True -10 31669 30.788729667663574 0.8324074745178223 454.36737060546875 0.39413130283355713 672.7783203125 0.501541018486023 0.86899936 0.27130720019340515 True -11 34548 30.783428192138672 32.360225439071655 624.1551513671875 0.3234770894050598 670.6094360351562 0.5021440982818604 0.8730884 0.25763681530952454 True -12 37427 33.0666446685791 0.6169281005859375 567.2811279296875 0.3076859414577484 668.6486206054688 0.504321813583374 0.87678343 0.25056448578834534 True -13 40306 30.76942276954651 0.5686047077178955 539.607421875 0.33170005679130554 666.7030639648438 0.5064069628715515 0.8805721 0.2404298186302185 True -14 43185 30.99077296257019 1.0878770351409912 467.702880859375 0.24816206097602844 664.8760375976562 0.5087205171585083 0.8846949 0.23505084216594696 True -15 46064 32.9802508354187 15.167349576950073 570.5443115234375 0.2917672395706177 664.0315551757812 0.5092940330505371 0.887409 0.23027582466602325 True -16 48943 30.76270866394043 0.5624709129333496 444.35614013671875 0.22780974209308624 663.7487182617188 0.5087246894836426 0.89037585 0.223476842045784 True -17 51822 30.886892080307007 0.5916938781738281 443.09295654296875 0.18467940390110016 663.2301025390625 0.5100655555725098 0.8910716 0.22281727194786072 True -18 54701 30.870908737182617 0.5622985363006592 499.3910217285156 0.26752448081970215 663.0167846679688 0.5098064541816711 0.8917069 0.2244107574224472 True -19 57580 30.800071001052856 0.5896406173706055 526.1676025390625 0.3764941096305847 664.10400390625 0.5082422494888306 0.8919115 0.225259467959404 True diff --git a/ENCSR662RIZ/cherimoya.fold_2.performance.tsv b/ENCSR662RIZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6cf61b3abd2a79b9dab6c44095045838e0a2bfa1..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -664.10400390625 0.3195430636405945 0.5082422494888306 0.20873701572418213 0.891911506652832 0.8730060458183289 0.225259467959404 \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_3.evaluate.json b/ENCSR662RIZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b4beee19d2ce3d900a98fc57488c13b882396d1c..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF870XOC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_3.fit.json b/ENCSR662RIZ/cherimoya.fold_3.fit.json deleted file mode 100644 index de4361687c52b65a946271bcb321b5264b9e9ffe..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF870XOC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_3.log b/ENCSR662RIZ/cherimoya.fold_3.log deleted file mode 100644 index c7ee617fd8621c5ff6c43918e80a6d851eab90f0..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2775 34.57553791999817 4.0843353271484375 574.2936401367188 0.950658917427063 785.7490234375 0.34510287642478943 0.7681595 8.09490966796875 True -1 5550 29.930304050445557 10.1970796585083 710.2117309570312 0.5228512287139893 676.45068359375 0.45475271344184875 0.8266547 1.560424566268921 True -2 8325 30.283132076263428 21.627944946289062 661.5546875 0.4535759687423706 662.4639892578125 0.4723871052265167 0.8358507 0.6575044989585876 True -3 11100 30.953531742095947 1.3517744541168213 660.1348266601562 0.25594931840896606 655.184814453125 0.4812784194946289 0.8422883 0.5159925222396851 True -4 13875 32.606823682785034 2.3531336784362793 583.5899658203125 0.39921340346336365 651.0826416015625 0.48609718680381775 0.8414314 0.4617311656475067 False -5 16650 30.32024621963501 10.068239450454712 631.2440185546875 0.4602971076965332 649.026123046875 0.4882897436618805 0.8496392 0.4027453362941742 True -6 19425 30.1746928691864 1.6383633613586426 498.5870056152344 0.599370002746582 647.155029296875 0.49145564436912537 0.8489454 0.40699639916419983 False -7 22200 30.244762182235718 1.8455066680908203 455.236328125 0.32793956995010376 644.0886840820312 0.49492865800857544 0.8510108 0.38956138491630554 True -8 24975 30.229960680007935 1.2069807052612305 565.0725708007812 0.4111652374267578 642.7655639648438 0.49556684494018555 0.85828626 0.34845247864723206 True -9 27750 30.214207887649536 1.2037250995635986 495.0478515625 0.34129393100738525 639.6979370117188 0.4994174838066101 0.86141986 0.3246663212776184 True -10 30525 30.23026156425476 0.9377400875091553 531.5157470703125 0.3383449912071228 637.5338745117188 0.5015794634819031 0.8668339 0.3013707101345062 True -11 33300 30.21208167076111 0.5205483436584473 445.611328125 0.3625115156173706 636.4954223632812 0.5009528398513794 0.870029 0.28602221608161926 True -12 36075 30.218841075897217 0.5227227210998535 555.1077880859375 0.2219027578830719 633.6406860351562 0.5044645071029663 0.8763297 0.2746656537055969 True -13 38850 30.209439277648926 0.5145926475524902 544.9495239257812 0.42913222312927246 631.7479858398438 0.5073451399803162 0.8817894 0.26015862822532654 True -14 41625 30.215818166732788 0.5225591659545898 503.23681640625 0.3348783850669861 629.4826049804688 0.5089590549468994 0.88761926 0.24196551740169525 True -15 44400 30.231547117233276 0.5205862522125244 531.4019775390625 0.19978629052639008 626.2975463867188 0.5133621692657471 0.8927027 0.2289130985736847 True -16 47175 30.316993236541748 0.5127508640289307 536.9150390625 0.28010332584381104 628.1950073242188 0.5093768835067749 0.8977355 0.2191045880317688 True -17 49950 30.263145446777344 21.450963973999023 452.024169921875 0.28854531049728394 626.0472412109375 0.5129309296607971 0.8992352 0.2152501493692398 True -18 52725 30.296138048171997 0.5253605842590332 475.5849304199219 0.21591012179851532 626.708740234375 0.5120391845703125 0.9019695 0.21466168761253357 True -19 55500 30.247376441955566 0.519829511642456 548.1959838867188 0.17160825431346893 628.5625610351562 0.50934898853302 0.9014897 0.21170735359191895 False diff --git a/ENCSR662RIZ/cherimoya.fold_3.performance.tsv b/ENCSR662RIZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2f1b1d085be017ba6daa24f72bd85a79d4962e41..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -626.708740234375 0.32032307982444763 0.5120391845703125 0.2020314484834671 0.9019694924354553 0.875991940498352 0.21466168761253357 \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_4.evaluate.json b/ENCSR662RIZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 122674f80f02c7094ebaeb01ff926715cb07bf28..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF870XOC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_4.fit.json b/ENCSR662RIZ/cherimoya.fold_4.fit.json deleted file mode 100644 index df78aa07599bc303ce64c10ab52e999484893b95..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF870XOC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR662RIZ/cherimoya.fold_4.log b/ENCSR662RIZ/cherimoya.fold_4.log deleted file mode 100644 index 4a404f28ea6fafcfc22d07a0d573f60e375f29fb..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2785 34.60672903060913 3.610682487487793 518.4110717773438 0.4000245928764343 732.6317749023438 0.33814388513565063 0.76007134 7.207036972045898 True -1 5570 30.401382446289062 0.5898253917694092 518.8082275390625 0.5101056098937988 633.0313720703125 0.4430747926235199 0.81765205 1.0744301080703735 True -2 8355 30.30353879928589 0.577075719833374 569.794921875 0.5350440740585327 621.6390380859375 0.4564281702041626 0.826862 0.6274095773696899 True -3 11140 30.299213409423828 0.5719707012176514 466.0037841796875 0.3744472861289978 612.8580932617188 0.46732544898986816 0.8417999 0.4740561842918396 True -4 13925 30.30465078353882 0.5673599243164062 490.25189208984375 0.45484742522239685 610.2068481445312 0.47089913487434387 0.84666026 0.4602007269859314 True -5 16710 30.539445877075195 30.500287294387817 563.016357421875 0.33884018659591675 606.5857543945312 0.4760248064994812 0.85015523 0.38284391164779663 True -6 19495 30.60637855529785 0.5654346942901611 540.2700805664062 0.4283444583415985 605.0191650390625 0.4773189127445221 0.8512578 0.3694905638694763 True -7 22280 32.594539403915405 1.0977704524993896 571.8353271484375 0.39527928829193115 601.8500366210938 0.4814554750919342 0.8567718 0.3113696873188019 True -8 25065 30.47938346862793 42.40158486366272 578.3680419921875 0.3745524287223816 600.6265258789062 0.48259568214416504 0.86064106 0.2982473075389862 True -9 27850 30.43055486679077 0.5833351612091064 526.4945068359375 0.43146073818206787 597.529541015625 0.4867108166217804 0.86464685 0.2809992730617523 True -10 30635 30.749457597732544 0.5720758438110352 523.7334594726562 0.21524403989315033 594.0291137695312 0.49079811573028564 0.8682301 0.26773929595947266 True -11 33420 32.922895431518555 13.619186401367188 544.279296875 0.2981358766555786 593.207275390625 0.4910843074321747 0.8734826 0.2498074322938919 True -12 36205 30.35219931602478 14.124783039093018 523.1746826171875 0.2597305178642273 591.5537719726562 0.49321305751800537 0.8771988 0.23538365960121155 True -13 38990 30.474737405776978 0.6069726943969727 499.84222412109375 0.24319276213645935 589.4660034179688 0.49568507075309753 0.8823726 0.2242341935634613 True -14 41775 30.410738229751587 0.5756077766418457 619.2488403320312 0.14645373821258545 587.9492797851562 0.49732643365859985 0.8865246 0.2186242789030075 True -15 44560 30.317641496658325 0.5785257816314697 483.2637939453125 0.27244633436203003 587.2028198242188 0.4977857768535614 0.8904247 0.2093304544687271 True -16 47345 30.326046466827393 0.7669711112976074 410.5318908691406 0.16988399624824524 587.3001708984375 0.49740496277809143 0.89419776 0.20288516581058502 True -17 50130 30.31514000892639 2.9496734142303467 560.3668823242188 0.17086350917816162 586.0511474609375 0.5004690289497375 0.8952965 0.20070026814937592 True -18 52915 30.330185890197754 0.5850050449371338 636.4239501953125 0.24921637773513794 587.3598022460938 0.4975379407405853 0.8950638 0.2010996788740158 False -19 55700 30.33136558532715 1.9476726055145264 474.7994689941406 0.21796058118343353 587.1359252929688 0.49807316064834595 0.894651 0.201382577419281 False diff --git a/ENCSR662RIZ/cherimoya.fold_4.performance.tsv b/ENCSR662RIZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 952c47520429f4f18b93123552127a070e5057d3..0000000000000000000000000000000000000000 --- a/ENCSR662RIZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -586.0511474609375 0.3320551812648773 0.5004690885543823 0.190913587808609 0.8952965140342712 0.8652564883232117 0.20070026814937592 \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_0.evaluate.json b/ENCSR663MNQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2ef8aa4c1c8e8ca1cf3f8fd6389ae983676cd614..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131YSB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_0.fit.json b/ENCSR663MNQ/cherimoya.fold_0.fit.json deleted file mode 100644 index c4a47595ea6b33974cbd9b4d1b68ae0a9f0e04df..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF131YSB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_0.log b/ENCSR663MNQ/cherimoya.fold_0.log deleted file mode 100644 index 4d66bbe128d4c25d5823b1843416dd7e76ce295a..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 35.675050497055054 3.667189836502075 613.5029296875 0.4975018799304962 702.0751342773438 0.24122320115566254 0.74364597 5.739814281463623 True -1 5488 30.317952156066895 1.6766705513000488 606.4454956054688 0.5864943861961365 650.37109375 0.3082156777381897 0.78419185 0.9976420998573303 True -2 8232 30.363953351974487 0.5789046287536621 551.6500244140625 0.37681275606155396 640.8035278320312 0.3190363347530365 0.797071 0.4715364873409271 True -3 10976 30.26420760154724 0.5741469860076904 594.8911743164062 0.32779693603515625 636.1415405273438 0.32319778203964233 0.80390084 0.4784834086894989 True -4 13720 30.24534034729004 2.6319234371185303 577.167236328125 0.45031797885894775 632.3193969726562 0.3287269175052643 0.807217 0.3771326541900635 True -5 16464 30.558706998825073 0.5830883979797363 556.280029296875 0.31471726298332214 631.0839233398438 0.33013179898262024 0.8102975 0.369632750749588 True -6 19208 30.323085069656372 0.5703606605529785 486.1961669921875 0.2842593491077423 626.781982421875 0.33669766783714294 0.8138742 0.39446741342544556 True -7 21952 30.32780361175537 0.5691778659820557 544.7737426757812 0.29045361280441284 626.0165405273438 0.33759281039237976 0.8191066 0.357207328081131 True -8 24696 30.268290758132935 0.5786714553833008 483.62200927734375 0.19166876375675201 623.236572265625 0.3418439030647278 0.8261264 0.3348948359489441 True -9 27440 30.316805124282837 0.5638337135314941 494.7647399902344 0.2438918650150299 621.1194458007812 0.3443851172924042 0.8279573 0.3006038963794708 True -10 30184 30.338273525238037 0.573340654373169 544.4051513671875 0.24408480525016785 619.8995971679688 0.34561416506767273 0.8325951 0.28133440017700195 True -11 32928 30.30949640274048 0.5786902904510498 632.29345703125 0.2205790877342224 618.0220947265625 0.3473077118396759 0.8392717 0.24560217559337616 True -12 35672 30.294024229049683 0.5791134834289551 606.611572265625 0.21100805699825287 615.8233032226562 0.3506615161895752 0.8419232 0.23776543140411377 True -13 38416 30.30466866493225 0.5708637237548828 460.1563720703125 0.29793351888656616 614.2523803710938 0.35306763648986816 0.84577024 0.22118039429187775 True -14 41160 30.307450532913208 6.382940769195557 519.511962890625 0.2715841233730316 613.6317138671875 0.35351502895355225 0.8486452 0.21268434822559357 True -15 43904 30.3522789478302 28.630783319473267 560.7674560546875 0.29144829511642456 611.6079711914062 0.35628485679626465 0.8537418 0.20532740652561188 True -16 46648 32.20129323005676 0.5798749923706055 575.82763671875 0.2315739393234253 612.0103149414062 0.35524335503578186 0.8561056 0.20291352272033691 True -17 49392 30.35501718521118 0.5955851078033447 534.9092407226562 0.1692512035369873 612.0098876953125 0.3548373579978943 0.85665244 0.19977405667304993 True -18 52136 30.338934659957886 2.0682082176208496 511.09112548828125 0.30706286430358887 612.3294067382812 0.35510262846946716 0.8552812 0.20083041489124298 False -19 54880 34.2814679145813 31.124833345413208 532.5943603515625 0.17114165425300598 611.628173828125 0.35653063654899597 0.8547341 0.20192165672779083 False diff --git a/ENCSR663MNQ/cherimoya.fold_0.performance.tsv b/ENCSR663MNQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 038a6f8a80731b4d62ea6af72dd40c963e395eef..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -612.0098876953125 0.4207460284233093 0.3548373281955719 0.1355239301919937 0.8566524386405945 0.8190144896507263 0.19977405667304993 \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_1.evaluate.json b/ENCSR663MNQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4b0643548a5b0eaf446490afac55e2ea24b667f7..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131YSB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_1.fit.json b/ENCSR663MNQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 884f482fe75d3d346cf29915dc1f02a00a70053b..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF131YSB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_1.log b/ENCSR663MNQ/cherimoya.fold_1.log deleted file mode 100644 index 0c2d7373fc31bff93225f9d8d99b59d06ed53e77..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2711 35.307910203933716 6.277043581008911 546.6867065429688 0.4353369474411011 801.3976440429688 0.2497594654560089 0.72862893 5.42437219619751 True -1 5422 29.710447072982788 0.7390975952148438 519.04541015625 0.3883090615272522 738.263671875 0.32129281759262085 0.78186864 1.5436859130859375 True -2 8133 29.928056716918945 0.7017204761505127 561.05810546875 0.553200364112854 723.8446655273438 0.33230888843536377 0.7944596 0.6314663887023926 True -3 10844 30.060114860534668 0.6877565383911133 598.634765625 0.33361101150512695 715.54052734375 0.3409421443939209 0.79788625 0.6492843627929688 True -4 13555 29.903566598892212 0.6918470859527588 496.30670166015625 0.39652350544929504 710.734375 0.34710660576820374 0.80274224 0.4543249309062958 True -5 16266 29.80986189842224 0.6880984306335449 552.0748291015625 0.33447349071502686 706.20703125 0.35229918360710144 0.8088074 0.38017264008522034 True -6 18977 29.81260395050049 2.3379383087158203 624.9684448242188 0.3878304362297058 702.9925537109375 0.3550461530685425 0.81171644 0.3390381932258606 True -7 21688 29.82460308074951 0.693936824798584 477.846923828125 0.36370357871055603 700.4727172851562 0.3581048250198364 0.8237417 0.33085840940475464 True -8 24399 33.65957689285278 11.855401039123535 570.1375732421875 0.28788402676582336 695.9561157226562 0.3638140857219696 0.8303498 0.2984035015106201 True -9 27110 29.87915563583374 3.008267402648926 503.108642578125 0.3535624146461487 694.7534790039062 0.36477231979370117 0.83552 0.28138571977615356 True -10 29821 29.90672540664673 0.7927472591400146 455.25811767578125 0.16803216934204102 691.7572631835938 0.36774662137031555 0.8392144 0.25536495447158813 True -11 32532 29.927743673324585 0.6909537315368652 480.11102294921875 0.3214256465435028 690.8941650390625 0.368047297000885 0.8454204 0.24599605798721313 True -12 35243 29.93458342552185 36.869075298309326 524.366455078125 0.20882250368595123 687.6765747070312 0.37211620807647705 0.84802115 0.24298089742660522 True -13 37954 31.584867000579834 0.7123844623565674 459.73614501953125 0.2297256737947464 686.2639770507812 0.3733246624469757 0.8527609 0.23986966907978058 True -14 40665 29.854488611221313 1.3096826076507568 538.8096923828125 0.21701940894126892 685.117431640625 0.37407031655311584 0.85801953 0.2292994111776352 True -15 43376 29.840866804122925 1.803748607635498 531.7576904296875 0.24925489723682404 683.7918701171875 0.37504440546035767 0.8615056 0.22277793288230896 True -16 46087 29.784259557724 2.398270845413208 518.2054443359375 0.13376618921756744 683.1041259765625 0.3756053149700165 0.8631557 0.2204938679933548 True -17 48798 29.769808292388916 1.5157458782196045 478.8830261230469 0.23967789113521576 682.7911376953125 0.3763001561164856 0.8666452 0.21952757239341736 True -18 51509 29.894216537475586 4.634815692901611 441.2369384765625 0.09973812848329544 682.9642944335938 0.37643763422966003 0.86535275 0.2193775773048401 False -19 54220 29.918930292129517 0.6935169696807861 468.7764587402344 0.176824152469635 683.6641845703125 0.3754110634326935 0.8654554 0.22114615142345428 False diff --git a/ENCSR663MNQ/cherimoya.fold_1.performance.tsv b/ENCSR663MNQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e12c365b1bc2d3d1d4fb29c5c7c3de7859da3981..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -682.7911376953125 0.4031321108341217 0.3763001561164856 0.15261441469192505 0.8666452169418335 0.8426196575164795 0.21952757239341736 \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_2.evaluate.json b/ENCSR663MNQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e6fbbf7b19b1ca9fb0d2dec885dbd214a8c581de..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131YSB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_2.fit.json b/ENCSR663MNQ/cherimoya.fold_2.fit.json deleted file mode 100644 index b6d30f31ffb9bed0fd3aab6532c3156d033b4f75..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF131YSB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_2.log b/ENCSR663MNQ/cherimoya.fold_2.log deleted file mode 100644 index d1ae4163db93ab530e03efb32d7a0a1783c6b64f..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 36.028908014297485 3.4789867401123047 487.6711120605469 0.44340425729751587 719.3916625976562 0.24888655543327332 0.7312989 4.84473991394043 True -1 5746 31.75007939338684 0.5790016651153564 539.676025390625 0.39180973172187805 663.3525390625 0.31850460171699524 0.7820317 1.1676926612854004 True -2 8619 31.79122042655945 0.5551142692565918 572.1099853515625 0.3541826605796814 653.5489501953125 0.327675998210907 0.7894955 0.6495715379714966 True -3 11492 31.725584030151367 1.5771923065185547 616.436279296875 0.3403497636318207 650.2015991210938 0.3288254141807556 0.7966021 0.49125340580940247 True -4 14365 31.696682929992676 0.5564208030700684 537.822509765625 0.27782440185546875 646.4889526367188 0.3337233066558838 0.7995775 0.45861950516700745 True -5 17238 31.72386074066162 0.5591421127319336 553.5206298828125 0.31089115142822266 643.603759765625 0.33802542090415955 0.8048094 0.4435700476169586 True -6 20111 31.68167495727539 0.5579588413238525 490.7035827636719 0.34888792037963867 640.0164184570312 0.34215274453163147 0.8145884 0.40789249539375305 True -7 22984 31.721274614334106 0.5549650192260742 551.73291015625 0.3778056204319 638.0379638671875 0.34512096643447876 0.81492954 0.4027853310108185 True -8 25857 31.737988233566284 0.5544936656951904 461.8519592285156 0.4424731135368347 635.4638671875 0.34839433431625366 0.8223431 0.3408908247947693 True -9 28730 31.716353178024292 0.5536403656005859 496.83221435546875 0.31646257638931274 634.3192749023438 0.34979116916656494 0.8250597 0.3130304515361786 True -10 31603 31.713107347488403 0.5590908527374268 498.52642822265625 0.34366822242736816 632.086669921875 0.3521752655506134 0.82935995 0.28665363788604736 True -11 34476 35.40548586845398 6.727040767669678 464.9931945800781 0.3027350604534149 630.3427734375 0.35442981123924255 0.8348196 0.263344407081604 True -12 37349 31.791253328323364 0.7337729930877686 450.76654052734375 0.25498151779174805 627.8225708007812 0.3581905663013458 0.83607334 0.2469479888677597 True -13 40222 31.756913423538208 0.5542395114898682 474.9571533203125 0.24207989871501923 626.3512573242188 0.35968121886253357 0.8429685 0.23436252772808075 True -14 43095 31.970458269119263 13.90648341178894 459.5087890625 0.27264994382858276 625.6251220703125 0.35996270179748535 0.84851444 0.2252611517906189 True -15 45968 31.740582942962646 3.8705637454986572 575.0086669921875 0.16366034746170044 624.5515747070312 0.3617441952228546 0.84890205 0.21842125058174133 True -16 48841 31.78185772895813 16.842636108398438 509.8035888671875 0.201976016163826 623.1087036132812 0.3628833591938019 0.85319203 0.21097354590892792 True -17 51714 31.689271211624146 0.5588994026184082 503.64312744140625 0.14908960461616516 624.4120483398438 0.36126527190208435 0.8521277 0.20939283072948456 False -18 54587 34.062784910202026 23.13305354118347 532.6550903320312 0.1337852030992508 624.7474975585938 0.36049583554267883 0.85107046 0.20899099111557007 False -19 57460 31.854300260543823 0.6711490154266357 559.872314453125 0.15898776054382324 625.2987670898438 0.35975298285484314 0.850473 0.20972096920013428 False diff --git a/ENCSR663MNQ/cherimoya.fold_2.performance.tsv b/ENCSR663MNQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3593a4f55c05016621fa91b9d382cf11be060cd0..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -623.1087036132812 0.41577789187431335 0.3628833591938019 0.1385982781648636 0.8531920313835144 0.8173918724060059 0.21097354590892792 \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_3.evaluate.json b/ENCSR663MNQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a657037e004c014aa3ccb238a8f2a7f858016684..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131YSB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_3.fit.json b/ENCSR663MNQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 50909713d1d884695d2e8a132b38a8adf33b8c76..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF131YSB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_3.log b/ENCSR663MNQ/cherimoya.fold_3.log deleted file mode 100644 index d9295f60ecd152349ce67a6211c49fbd1a3a1891..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 34.80518817901611 4.686380624771118 553.366943359375 0.4420357942581177 708.4198608398438 0.2543223798274994 0.74927366 5.13608455657959 True -1 5520 30.450982332229614 26.575695753097534 532.6145629882812 0.4206281900405884 655.4788818359375 0.3141084611415863 0.8018467 1.0171289443969727 True -2 8280 30.69103455543518 28.987707376480103 519.6636352539062 0.3557782769203186 644.1098022460938 0.32623985409736633 0.81198 0.5470155477523804 True -3 11040 30.94250178337097 0.5256829261779785 621.798828125 0.334306001663208 638.431640625 0.3331630527973175 0.8191123 0.5480104684829712 True -4 13800 31.219929695129395 25.63638186454773 623.1018676757812 0.27049458026885986 634.7509155273438 0.3374733328819275 0.8233766 0.3921944200992584 True -5 16560 30.48814845085144 10.444757223129272 604.611083984375 0.3650025725364685 632.8905639648438 0.3393213152885437 0.8275872 0.3601802885532379 True -6 19320 30.40518355369568 3.119753122329712 593.71044921875 0.3320322334766388 630.4928588867188 0.3427155017852783 0.832528 0.3314155042171478 True -7 22080 30.473856687545776 27.898003101348877 530.0540771484375 0.3536093235015869 629.133544921875 0.3447094261646271 0.8335815 0.32709982991218567 True -8 24840 31.11992597579956 0.5353076457977295 615.3694458007812 0.24181151390075684 626.7423095703125 0.34768661856651306 0.83974284 0.3087347149848938 True -9 27600 30.415284395217896 0.5249655246734619 524.3622436523438 0.19387808442115784 624.4218139648438 0.35091912746429443 0.8427726 0.2960975170135498 True -10 30360 30.842963933944702 35.005786418914795 525.51416015625 0.2472887933254242 621.9334716796875 0.3541417419910431 0.8456314 0.2793774902820587 True -11 33120 30.54823136329651 6.778121471405029 481.15594482421875 0.1696595549583435 621.2344970703125 0.35454270243644714 0.851771 0.2605917155742645 True -12 35880 30.529372930526733 19.40869903564453 549.4284057617188 0.25322508811950684 620.3896484375 0.35499629378318787 0.85380185 0.24688762426376343 True -13 38640 30.43106698989868 29.443040132522583 531.7402954101562 0.26392823457717896 617.698974609375 0.3583962321281433 0.8600149 0.23532956838607788 True -14 41400 30.826156854629517 0.5403854846954346 456.80596923828125 0.28698021173477173 616.552001953125 0.35943296551704407 0.863107 0.22175364196300507 True -15 44160 30.525470972061157 0.5292232036590576 527.0538330078125 0.18386240303516388 615.6627807617188 0.36080750823020935 0.86665696 0.21135292947292328 True -16 46920 30.471309900283813 0.5244121551513672 488.3172912597656 0.1277504563331604 615.4777221679688 0.360958456993103 0.86705726 0.20710113644599915 True -17 49680 31.040222644805908 0.5294344425201416 491.87139892578125 0.2057548612356186 615.2322998046875 0.3609094023704529 0.86755836 0.20340010523796082 True -18 52440 30.51456069946289 0.5238900184631348 557.51708984375 0.17347951233386993 615.291015625 0.36115777492523193 0.8678191 0.20202505588531494 True -19 55200 30.84688663482666 0.5312283039093018 520.9044189453125 0.14150100946426392 614.697509765625 0.3617750406265259 0.86761874 0.2030588537454605 False diff --git a/ENCSR663MNQ/cherimoya.fold_3.performance.tsv b/ENCSR663MNQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1d34b56cddfd5c6deb1387fd08dea5e8e691f5f1..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -615.291015625 0.41822129487991333 0.36115777492523193 0.13970902562141418 0.86781907081604 0.8322725892066956 0.20202505588531494 \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_4.evaluate.json b/ENCSR663MNQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9d6a9bf208cabca41b15caed38a5f8ba9b252617..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131YSB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_4.fit.json b/ENCSR663MNQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 346516e4c988f0553b71a86e9b7ad1b83a66bea4..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF131YSB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR663MNQ/cherimoya.fold_4.log b/ENCSR663MNQ/cherimoya.fold_4.log deleted file mode 100644 index d328049ebcd253c0e912d6c86f026c1f6030d17e..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2820 35.395519733428955 3.5753824710845947 602.5301513671875 0.3363242447376251 657.021240234375 0.24166326224803925 0.72965527 3.989314556121826 True -1 5640 30.881471157073975 0.6107091903686523 558.800537109375 0.40643733739852905 612.947998046875 0.2983763813972473 0.769898 1.1545881032943726 True -2 8460 30.84986162185669 0.5874288082122803 625.8887939453125 0.375863254070282 602.2144165039062 0.31295716762542725 0.784305 0.6635425090789795 True -3 11280 31.218417167663574 21.177971839904785 553.538330078125 0.39388900995254517 599.0819702148438 0.3159429132938385 0.7921893 0.41405171155929565 True -4 14100 30.847721099853516 15.294618844985962 549.3173828125 0.30738359689712524 595.6876220703125 0.3211219608783722 0.79877794 0.337610125541687 True -5 16920 30.924068212509155 0.5970511436462402 589.31982421875 0.39968597888946533 594.7061767578125 0.3217862546443939 0.8011527 0.3341917395591736 True -6 19740 30.869153261184692 0.9319987297058105 489.7625427246094 0.23638328909873962 592.8660278320312 0.3245316445827484 0.8073212 0.3261496424674988 True -7 22560 30.871027946472168 42.36771035194397 469.742919921875 0.32311946153640747 590.8009643554688 0.32800689339637756 0.80505455 0.3235333561897278 False -8 25380 31.026150703430176 0.5983695983886719 459.3236083984375 0.27806544303894043 587.7294921875 0.33247238397598267 0.8210889 0.27117520570755005 True -9 28200 30.889552354812622 21.046711206436157 493.36224365234375 0.2905340790748596 587.4505004882812 0.33248400688171387 0.8240708 0.25843197107315063 True -10 31020 31.08120846748352 0.7380838394165039 530.3736572265625 0.2785763740539551 584.4696044921875 0.3365035653114319 0.8283977 0.23331117630004883 True -11 33840 30.88893222808838 0.659156322479248 474.524169921875 0.1612440049648285 584.0653686523438 0.33701106905937195 0.83383155 0.219724640250206 True -12 36660 30.820744276046753 1.1059401035308838 494.13201904296875 0.23557327687740326 582.7874145507812 0.3386426866054535 0.8387105 0.2122393548488617 True -13 39480 30.879621744155884 0.5896809101104736 595.0958862304688 0.2878556549549103 580.2960205078125 0.3427523672580719 0.84165484 0.20626835525035858 True -14 42300 30.801188707351685 0.5926735401153564 522.7643432617188 0.21577352285385132 579.9342651367188 0.342519611120224 0.8460889 0.20257049798965454 True -15 45120 30.867767333984375 0.5925197601318359 591.9722290039062 0.20595648884773254 579.4935302734375 0.34344977140426636 0.852317 0.19714777171611786 True -16 47940 30.84419059753418 0.5888509750366211 529.0947265625 0.20145834982395172 579.5656127929688 0.3428880274295807 0.85375583 0.19151625037193298 True -17 50760 30.83044958114624 0.5957474708557129 457.6925964355469 0.308113694190979 579.3837890625 0.34327661991119385 0.8567002 0.18862004578113556 True -18 53580 31.577277421951294 34.025304079055786 517.4464111328125 0.16655907034873962 580.0032348632812 0.34216541051864624 0.8569316 0.18883268535137177 True -19 56400 31.614829540252686 14.900997877120972 550.4334716796875 0.11000915616750717 580.2587280273438 0.3420577645301819 0.85528266 0.18957865238189697 False diff --git a/ENCSR663MNQ/cherimoya.fold_4.performance.tsv b/ENCSR663MNQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 809607d287e508d61b535acb3884a16e0cb4d7f3..0000000000000000000000000000000000000000 --- a/ENCSR663MNQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -580.0032348632812 0.43050065636634827 0.34216538071632385 0.12889547646045685 0.8569316267967224 0.8154670000076294 0.18883268535137177 \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_0.evaluate.json b/ENCSR664PKM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c6eab39b7aa53878b5be0080cac8b7a5e2a1b3ec..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF669XAX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_0.fit.json b/ENCSR664PKM/cherimoya.fold_0.fit.json deleted file mode 100644 index 9841e0bf43633b2d088184bd5d8418483ba9a5f1..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF669XAX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_0.log b/ENCSR664PKM/cherimoya.fold_0.log deleted file mode 100644 index dce799b02806762578c25710cac9295d92dfafbb..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 33.92065978050232 3.5930988788604736 1519.115966796875 0.956770658493042 2403.959228515625 0.37802737951278687 0.5485925 10.370973587036133 True -1 5482 30.176307201385498 0.5698153972625732 1598.582275390625 0.982599675655365 2103.04736328125 0.48592880368232727 0.56016445 2.138185739517212 True -2 8223 30.24967050552368 7.527261257171631 1730.5416259765625 0.6985717415809631 2055.2333984375 0.5001522898674011 0.57998353 1.1606472730636597 True -3 10964 30.217746019363403 0.5615332126617432 1549.634033203125 1.1423168182373047 2023.217041015625 0.5125027298927307 0.5744006 0.9103721976280212 False -4 13705 30.238994359970093 0.5558621883392334 1735.5250244140625 0.6404622793197632 2010.3402099609375 0.5162743330001831 0.59105486 0.6622404456138611 True -5 16446 30.199625253677368 0.5546226501464844 1654.91455078125 0.6708189249038696 2005.3828125 0.5178666114807129 0.5911193 0.6225659251213074 True -6 19187 30.184444904327393 0.5532872676849365 1592.6884765625 0.6471399068832397 2005.50634765625 0.5177640914916992 0.59501725 0.6017517447471619 True -7 21928 30.233667850494385 0.557420015335083 1614.48046875 0.5467407703399658 1996.8118896484375 0.5203279256820679 0.6026642 0.5477057099342346 True -8 24669 30.18404507637024 0.5504446029663086 1550.107666015625 0.9158031344413757 1987.0633544921875 0.524972677230835 0.61110735 0.5004925727844238 True -9 27410 30.57033944129944 26.760116577148438 1638.13818359375 0.6303367018699646 1979.704833984375 0.5279640555381775 0.6115374 0.48508405685424805 True -10 30151 30.22519588470459 0.5555610656738281 1624.755859375 0.6231208443641663 1978.1138916015625 0.5274266004562378 0.61819166 0.46990373730659485 True -11 32892 30.05987524986267 0.5519092082977295 1457.721435546875 0.6438131928443909 1966.5887451171875 0.5325379371643066 0.6280753 0.47454947233200073 True -12 35633 29.652254104614258 0.5502767562866211 1469.5540771484375 0.5916248559951782 1963.021240234375 0.5327357053756714 0.63843083 0.4689091742038727 True -13 38374 29.61878204345703 0.551532506942749 1546.6373291015625 0.4669329524040222 1958.8931884765625 0.5342043042182922 0.6486736 0.45233163237571716 True -14 41115 29.66473960876465 5.609463691711426 1685.64404296875 0.4918701648712158 1947.4190673828125 0.5397612452507019 0.66123885 0.43111997842788696 True -15 43856 29.651845693588257 1.2120373249053955 1600.057373046875 0.5940418243408203 1945.2628173828125 0.5404070019721985 0.676686 0.4028671681880951 True -16 46597 29.7624089717865 25.030283212661743 1667.8853759765625 0.3889015018939972 1940.102294921875 0.5421809554100037 0.68504095 0.3877253234386444 True -17 49338 29.729079961776733 0.5555522441864014 1509.1180419921875 0.43144065141677856 1946.4501953125 0.5394472479820251 0.6929957 0.3739030957221985 True -18 52079 29.711129188537598 0.5525376796722412 1672.769287109375 0.3613153100013733 1946.5560302734375 0.5394493341445923 0.6967964 0.36719757318496704 True -19 54820 29.641676902770996 0.5486564636230469 1520.2833251953125 0.4914933443069458 1942.4835205078125 0.5410985350608826 0.695646 0.36918652057647705 False diff --git a/ENCSR664PKM/cherimoya.fold_0.performance.tsv b/ENCSR664PKM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d543f166690b0c0880fe506a96eb1ea8b605e58e..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1946.5560302734375 0.2363291084766388 0.5394494533538818 0.3606615960597992 0.6967964172363281 0.6614136099815369 0.36719757318496704 \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_1.evaluate.json b/ENCSR664PKM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 521aa1e34ed7fcfd1f955238e6330452c7a1ccb7..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF669XAX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_1.fit.json b/ENCSR664PKM/cherimoya.fold_1.fit.json deleted file mode 100644 index 38dc456309e775ca39abfdaaee889f57efb34104..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF669XAX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_1.log b/ENCSR664PKM/cherimoya.fold_1.log deleted file mode 100644 index 102657ccb0f22ae75c6853e537d46ba68ca89ab7..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 34.18596124649048 5.758497714996338 1565.6583251953125 0.7886216044425964 2720.439208984375 0.3897384703159332 0.57224905 12.19079875946045 True -1 5518 30.3601496219635 0.7297887802124023 1827.812255859375 1.1181986331939697 2359.00341796875 0.49854886531829834 0.58215946 2.7336764335632324 True -2 8277 30.36966824531555 0.6823601722717285 1315.03271484375 0.7182390689849854 2310.80517578125 0.5092973709106445 0.60235345 1.2574082612991333 True -3 11036 30.376342296600342 0.6857106685638428 1492.6109619140625 0.976642370223999 2270.186767578125 0.5192441344261169 0.6269749 0.9736983180046082 True -4 13795 30.481796264648438 0.6844818592071533 1600.51953125 0.5264483690261841 2248.648193359375 0.5268003344535828 0.63656604 0.8372747898101807 True -5 16554 30.531314611434937 3.2613706588745117 1799.812744140625 0.685021162033081 2239.16845703125 0.5287334322929382 0.6413728 0.747381865978241 True -6 19313 30.451910734176636 1.5493199825286865 1449.8507080078125 0.7318912148475647 2226.772216796875 0.5324782133102417 0.64975333 0.6948768496513367 True -7 22072 30.452980518341064 1.9160161018371582 1687.4871826171875 0.6498177647590637 2221.931884765625 0.5322656035423279 0.6561755 0.6211679577827454 True -8 24831 30.457759857177734 1.795644998550415 1692.779541015625 0.5614256262779236 2212.27001953125 0.5357961058616638 0.6640228 0.6392688751220703 True -9 27590 30.56363534927368 1.2358980178833008 1507.041015625 0.978832483291626 2202.56201171875 0.5384166836738586 0.6734632 0.5664759278297424 True -10 30349 29.995875120162964 3.279160737991333 1380.98046875 0.45794376730918884 2193.809814453125 0.539944052696228 0.68351483 0.5276789665222168 True -11 33108 29.942742586135864 1.6765646934509277 1561.9818115234375 0.4874979555606842 2187.49755859375 0.5419649481773376 0.69342905 0.4918418526649475 True -12 35867 30.096486806869507 1.587186336517334 1577.2239990234375 0.5371284484863281 2174.344482421875 0.5464741587638855 0.7036743 0.4884248673915863 True -13 38626 29.95214557647705 1.8354744911193848 1580.3974609375 0.4732767343521118 2162.762451171875 0.5498248934745789 0.7195017 0.4548588693141937 True -14 41385 29.955684900283813 26.85982608795166 1656.943603515625 0.3312866687774658 2153.809326171875 0.5526533722877502 0.7277345 0.41300252079963684 True -15 44144 30.71821904182434 0.7403035163879395 1691.3179931640625 0.43109723925590515 2148.409423828125 0.5541710257530212 0.73678535 0.39260759949684143 True -16 46903 30.17416763305664 0.6953334808349609 1692.6927490234375 0.49882760643959045 2147.893310546875 0.5532280206680298 0.7417617 0.3800543546676636 True -17 49662 29.97301745414734 0.6883325576782227 1572.801025390625 0.36753755807876587 2146.035888671875 0.5539059638977051 0.7433849 0.37402984499931335 True -18 52421 30.063626527786255 0.7069215774536133 1435.6170654296875 0.34743204712867737 2145.82421875 0.5540192127227783 0.7461049 0.369183212518692 True -19 55180 30.047973155975342 0.6940200328826904 1565.434326171875 0.21652261912822723 2149.567626953125 0.5516307353973389 0.7443936 0.37134867906570435 False diff --git a/ENCSR664PKM/cherimoya.fold_1.performance.tsv b/ENCSR664PKM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ba47bf33ec8f4ac9897ee94a6addd7eb13e92c28..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2145.82421875 0.22419553995132446 0.5540191531181335 0.38364461064338684 0.746104896068573 0.7198164463043213 0.369183212518692 \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_2.evaluate.json b/ENCSR664PKM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 195e2752249df92a2d1e17343c9dfa333c2e58d0..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF669XAX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_2.fit.json b/ENCSR664PKM/cherimoya.fold_2.fit.json deleted file mode 100644 index 6394814480f0c1bc53a536791d4b27356bd6dfad..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF669XAX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_2.log b/ENCSR664PKM/cherimoya.fold_2.log deleted file mode 100644 index 65c68b2f9cd05dd3bf22c05299f048a0cbad1764..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2890 36.123167753219604 16.373103618621826 1772.5562744140625 0.9333148002624512 2420.201416015625 0.3927985727787018 0.5653321 9.065572738647461 True -1 5780 31.991826057434082 0.5677118301391602 1465.3084716796875 1.1708859205245972 2132.05810546875 0.4908648133277893 0.54987776 2.027937412261963 False -2 8670 31.859759092330933 0.5544164180755615 1757.5986328125 0.8033486604690552 2083.6748046875 0.50634765625 0.59098524 0.8895376324653625 True -3 11560 31.981868505477905 0.5380873680114746 1829.13330078125 0.7330276966094971 2051.7529296875 0.5150063633918762 0.5985793 0.6335998177528381 True -4 14450 31.9203519821167 0.5492784976959229 1467.2791748046875 0.6090458035469055 2041.8646240234375 0.5197685956954956 0.5963301 0.6264184713363647 False -5 17340 31.931204080581665 0.5494303703308105 1417.9078369140625 0.9962396025657654 2035.1048583984375 0.5210923552513123 0.5962189 0.6276147961616516 False -6 20230 31.861443758010864 0.5326974391937256 1627.77685546875 0.8236750364303589 2030.044189453125 0.523102343082428 0.6056579 0.5898134112358093 True -7 23120 31.84140110015869 0.5461173057556152 1518.644287109375 0.9474308490753174 2025.724365234375 0.524444043636322 0.60763764 0.5425750613212585 True -8 26010 31.830429315567017 0.532665491104126 1756.794921875 0.4196225702762604 2016.1844482421875 0.5276162624359131 0.61700046 0.5390874743461609 True -9 28900 31.580030918121338 0.5195138454437256 1616.400390625 0.6424206495285034 2013.6361083984375 0.5283140540122986 0.6170707 0.5087975859642029 True -10 31790 31.254024982452393 0.5383555889129639 1609.5029296875 0.7558892369270325 2003.8199462890625 0.5323026776313782 0.6237726 0.5044060945510864 True -11 34680 31.564373254776 0.5459115505218506 1964.516357421875 0.4132743775844574 1993.309814453125 0.5357915759086609 0.6378817 0.4569815695285797 True -12 37570 31.50246262550354 1.2216997146606445 1739.3043212890625 0.4486699104309082 1988.271240234375 0.5367823839187622 0.6473188 0.4562113285064697 True -13 40460 31.666125535964966 0.5649402141571045 1572.650390625 0.5314974784851074 1979.0179443359375 0.5403522253036499 0.6641535 0.4249878227710724 True -14 43350 31.457749843597412 1.412733793258667 1619.22607421875 0.6613965630531311 1971.4046630859375 0.5437811017036438 0.67112786 0.4224769175052643 True -15 46240 31.472480535507202 0.536435604095459 1428.700927734375 0.3856339454650879 1966.2093505859375 0.5449002385139465 0.6833705 0.40105539560317993 True -16 49130 31.394882202148438 0.5321197509765625 1541.357177734375 0.5298540592193604 1966.7716064453125 0.5437536835670471 0.691669 0.39324286580085754 True -17 52020 31.852901220321655 23.929715633392334 1475.698974609375 0.3310605585575104 1972.330322265625 0.5411547422409058 0.6939774 0.39037731289863586 True -18 54910 31.363024473190308 2.07667875289917 1491.54833984375 0.592229425907135 1972.0662841796875 0.5408411026000977 0.6954951 0.3870867192745209 True -19 57800 31.358031511306763 0.7532849311828613 1478.785888671875 0.5983756184577942 1969.8558349609375 0.542384147644043 0.6960772 0.38753780722618103 True diff --git a/ENCSR664PKM/cherimoya.fold_2.performance.tsv b/ENCSR664PKM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8299f50820bf271530d62c1b09394fcdfd8062f8..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1969.8558349609375 0.2342219054698944 0.542384147644043 0.3653113842010498 0.6960772275924683 0.6599530577659607 0.38753780722618103 \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_3.evaluate.json b/ENCSR664PKM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 03b4aaed23078d00eb4dc1842d3b4bfc50048f91..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF669XAX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_3.fit.json b/ENCSR664PKM/cherimoya.fold_3.fit.json deleted file mode 100644 index d98063c6b25c095f2919e7155609b36d7f0eca4b..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF669XAX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_3.log b/ENCSR664PKM/cherimoya.fold_3.log deleted file mode 100644 index 78ab4e1ee849e15dc3db789ad6a945a5f7062fac..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 35.23366570472717 3.6198461055755615 1602.4561767578125 1.0518994331359863 2492.536376953125 0.39445963501930237 0.57040024 9.923977851867676 True -1 5606 31.02668523788452 0.5877604484558105 1733.3472900390625 0.9545900821685791 2215.608642578125 0.4878452718257904 0.58033293 2.6677098274230957 True -2 8409 30.96108365058899 0.5801396369934082 1733.61865234375 0.5887185335159302 2163.1181640625 0.5017645955085754 0.60263866 1.0243512392044067 True -3 11212 30.907134532928467 0.5651962757110596 1291.035888671875 0.6392784714698792 2146.3681640625 0.5053538084030151 0.59989077 0.6759588122367859 False -4 14015 30.898022413253784 0.5596692562103271 1729.033447265625 0.7625079154968262 2134.115234375 0.5100902318954468 0.59425044 0.6538764834403992 False -5 16818 30.927101135253906 0.5609936714172363 1650.1953125 1.530541181564331 2117.95751953125 0.5167735815048218 0.60658693 0.6737133860588074 True -6 19621 30.99515986442566 2.737571954727173 1566.822021484375 0.7962206602096558 2116.98974609375 0.5158506631851196 0.6087784 0.6598409414291382 True -7 22424 31.039090633392334 0.5809628963470459 1561.41748046875 0.5024386644363403 2118.765380859375 0.514850914478302 0.61862314 0.6429017186164856 True -8 25227 30.43678879737854 0.5817267894744873 1716.4853515625 0.9121087789535522 2108.3017578125 0.5189316272735596 0.6186313 0.5822085738182068 True -9 28030 30.458101272583008 0.5763773918151855 1391.2698974609375 0.34658968448638916 2095.715087890625 0.5230873823165894 0.6255641 0.5632346868515015 True -10 30833 30.52327799797058 0.5683634281158447 1797.161376953125 0.7004333734512329 2086.66357421875 0.5270907282829285 0.63814723 0.5355786085128784 True -11 33636 30.45102620124817 0.5744147300720215 1715.74853515625 0.38277536630630493 2079.611572265625 0.5295411348342896 0.64661235 0.502284049987793 True -12 36439 30.470314264297485 0.5689451694488525 1761.717041015625 0.4269408583641052 2077.199951171875 0.5303486585617065 0.6563706 0.5065835118293762 True -13 39242 30.496903896331787 0.5712649822235107 1823.0146484375 0.41475802659988403 2077.91015625 0.5283716320991516 0.67422646 0.46966418623924255 True -14 42045 30.49921727180481 0.5628867149353027 1474.0272216796875 0.5222373008728027 2066.330810546875 0.5321550369262695 0.68491876 0.4415742754936218 True -15 44848 30.407424449920654 0.5658061504364014 1535.858154296875 0.3810548484325409 2056.235107421875 0.5362439155578613 0.6985293 0.417898565530777 True -16 47651 30.423489570617676 0.5652408599853516 1724.22802734375 0.41357845067977905 2050.022705078125 0.5373374223709106 0.70613533 0.39802461862564087 True -17 50454 30.457833290100098 0.5741379261016846 1449.12353515625 0.2504568099975586 2052.886474609375 0.5355829000473022 0.70997775 0.3889460265636444 True -18 53257 30.476786613464355 0.5674691200256348 1592.2227783203125 0.4477953612804413 2048.659423828125 0.5377452373504639 0.71234584 0.38295596837997437 True -19 56060 30.482824325561523 0.5676627159118652 1350.676513671875 0.3973456025123596 2047.59326171875 0.5380059480667114 0.71184087 0.3867192268371582 False diff --git a/ENCSR664PKM/cherimoya.fold_3.performance.tsv b/ENCSR664PKM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4661d7834cd762f543a262ac93892d88c49bdddf..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2048.659423828125 0.2334868609905243 0.5377452373504639 0.3689345121383667 0.7123458385467529 0.6745740175247192 0.38295596837997437 \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_4.evaluate.json b/ENCSR664PKM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d400001ebb828fdee26acff3660125536a3433e7..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF669XAX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_4.fit.json b/ENCSR664PKM/cherimoya.fold_4.fit.json deleted file mode 100644 index 70ff07f6e5f6a9a2384cd38e6f0b84f66cd69d58..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF669XAX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR664PKM/cherimoya.fold_4.log b/ENCSR664PKM/cherimoya.fold_4.log deleted file mode 100644 index f09491c05d6224f8b384e49f1e0281fbbf721efe..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 36.113338470458984 3.740729331970215 1650.1502685546875 0.9480798244476318 2391.50732421875 0.39808207750320435 0.5514069 7.714905738830566 True -1 5776 31.992380380630493 0.5895648002624512 1658.1593017578125 1.107155680656433 2123.5751953125 0.49104052782058716 0.5524521 2.3673622608184814 True -2 8664 31.88183903694153 0.5772473812103271 1896.69140625 1.2236526012420654 2072.975341796875 0.5043051838874817 0.5604124 1.0570111274719238 True -3 11552 31.850860834121704 0.5771148204803467 2033.0330810546875 1.1806013584136963 2062.046142578125 0.5063669681549072 0.5711773 0.7802280783653259 True -4 14440 32.73539876937866 0.5701334476470947 1670.3072509765625 0.5176825523376465 2051.56787109375 0.5106486678123474 0.57207996 0.7742760181427002 True -5 17328 31.86100149154663 0.5795671939849854 1556.5263671875 0.4086560904979706 2044.5623779296875 0.5130921602249146 0.5779882 0.7011353373527527 True -6 20216 31.866770029067993 0.5755980014801025 1464.810791015625 0.8474466800689697 2036.5040283203125 0.5158827900886536 0.585591 0.6240719556808472 True -7 23104 31.700026273727417 0.5711760520935059 1849.670166015625 0.695530891418457 2035.4345703125 0.51636803150177 0.59789085 0.623410701751709 True -8 25992 31.241843461990356 0.5711936950683594 1603.9654541015625 0.6490448713302612 2025.525634765625 0.5196594595909119 0.6055784 0.5430628061294556 True -9 28880 31.20753502845764 0.5660254955291748 1727.092529296875 0.6109582185745239 2016.171630859375 0.5228571891784668 0.61739165 0.5268608331680298 True -10 31768 31.194436073303223 0.5718643665313721 1645.645751953125 0.4969402551651001 2007.947509765625 0.5255060195922852 0.6285005 0.4771600663661957 True -11 34656 31.175193071365356 0.5677804946899414 1557.189208984375 0.4352926015853882 2007.163818359375 0.5251132845878601 0.6405499 0.4628225862979889 True -12 37544 31.180484533309937 1.0253825187683105 1543.682861328125 0.6933807730674744 1999.480712890625 0.5288965106010437 0.65288883 0.4338890016078949 True -13 40432 31.25365686416626 0.5675797462463379 1636.855224609375 0.4876633286476135 1985.644775390625 0.5355228781700134 0.66187215 0.41761577129364014 True -14 43320 31.24177312850952 0.5701797008514404 1607.88720703125 0.2741967439651489 1979.48876953125 0.5369914770126343 0.6724711 0.3982290029525757 True -15 46208 31.215922117233276 0.5635747909545898 1723.7664794921875 0.3633185923099518 1979.327880859375 0.5370544195175171 0.67800266 0.40273046493530273 True -16 49096 31.17348051071167 0.5695955753326416 1522.764892578125 0.5395050048828125 1974.6669921875 0.5383153557777405 0.6833005 0.3898199498653412 True -17 51984 31.12502408027649 0.5623738765716553 1588.75927734375 0.40318799018859863 1982.2242431640625 0.5360496640205383 0.6908136 0.3794315755367279 True -18 54872 31.152519702911377 0.5708446502685547 1513.3067626953125 0.3783394694328308 1980.9180908203125 0.536155641078949 0.69277924 0.37668731808662415 True -19 57760 31.150516033172607 0.5695686340332031 1221.7890625 0.32100483775138855 1979.699951171875 0.5371385812759399 0.69195724 0.37838709354400635 False diff --git a/ENCSR664PKM/cherimoya.fold_4.performance.tsv b/ENCSR664PKM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ed895e86d01257b65ed92f777aedba90a7142b66..0000000000000000000000000000000000000000 --- a/ENCSR664PKM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1980.9180908203125 0.23469853401184082 0.536155641078949 0.36506786942481995 0.6927792429924011 0.6580356359481812 0.37668731808662415 \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_0.evaluate.json b/ENCSR666YVE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6e11e9fb0bee21b97c6d8d8449733f1a286a31ee..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836NVQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_0.fit.json b/ENCSR666YVE/cherimoya.fold_0.fit.json deleted file mode 100644 index fdbe6229fd493243198322bb9198b26c294de758..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF836NVQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_0.log b/ENCSR666YVE/cherimoya.fold_0.log deleted file mode 100644 index 5a12560faf20bf04ddeb0a18d030d03365c6b04b..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.712148904800415 3.6604886054992676 235.81549072265625 0.5645191669464111 265.8590393066406 0.14471815526485443 0.5139452 3.0313291549682617 True -1 5478 30.217794179916382 1.524986982345581 216.86300659179688 0.7056048512458801 259.6635437011719 0.17777107656002045 0.5810463 0.8335092663764954 True -2 8217 30.212741136550903 18.59066653251648 191.56048583984375 0.6575779914855957 257.5040283203125 0.18653419613838196 0.60624117 0.5973769426345825 True -3 10956 30.16144609451294 0.5273969173431396 220.44122314453125 0.5801870822906494 256.7177429199219 0.18869183957576752 0.6264403 0.5277200937271118 True -4 13695 30.208656787872314 0.5269477367401123 212.53134155273438 0.48147881031036377 256.1468200683594 0.19130583107471466 0.6325515 0.49004510045051575 True -5 16434 30.17021942138672 0.53643798828125 220.12222290039062 0.5522599816322327 255.54579162597656 0.19498269259929657 0.64259213 0.4849177300930023 True -6 19173 30.206035375595093 0.5582444667816162 253.4748077392578 0.5515379309654236 255.45375061035156 0.19420170783996582 0.6498314 0.4576823115348816 True -7 21912 30.15051555633545 0.5362365245819092 229.96218872070312 0.6446843147277832 255.1495361328125 0.19606122374534607 0.65520614 0.4614753723144531 True -8 24651 30.397949695587158 0.5581076145172119 197.74530029296875 0.4448152184486389 254.81539916992188 0.19802002608776093 0.6553954 0.47313371300697327 True -9 27390 30.264777898788452 0.5922431945800781 199.37135314941406 0.4786560833454132 254.58192443847656 0.19870121777057648 0.66035336 0.4358426332473755 True -10 30129 30.203575611114502 0.529533863067627 215.59317016601562 0.28941646218299866 253.91319274902344 0.20279917120933533 0.66941005 0.4086396396160126 True -11 32868 30.18557834625244 0.5231077671051025 225.8263397216797 0.37805628776550293 253.54428100585938 0.20488809049129486 0.6760916 0.3659111559391022 True -12 35607 30.19457745552063 0.5249924659729004 185.95281982421875 0.34685182571411133 253.4853973388672 0.20472875237464905 0.6820377 0.354256272315979 True -13 38346 30.266964435577393 0.530808687210083 206.6708984375 0.31627851724624634 253.326416015625 0.20542392134666443 0.6911681 0.33048105239868164 True -14 41085 30.275843620300293 1.4786226749420166 208.65908813476562 0.4220902919769287 253.1943359375 0.20614299178123474 0.6988254 0.32295581698417664 True -15 43824 30.212870121002197 0.526287317276001 218.62933349609375 0.4138451814651489 252.9925994873047 0.20723608136177063 0.7042292 0.3152258098125458 True -16 46563 30.183735370635986 0.5265400409698486 209.5478973388672 0.25140172243118286 253.0786895751953 0.2065742313861847 0.70943904 0.31750455498695374 True -17 49302 29.868128061294556 0.5432186126708984 228.548583984375 0.2942866384983063 253.04666137695312 0.20695948600769043 0.7112677 0.31733280420303345 True -18 52041 29.622278213500977 0.5336427688598633 199.9593963623047 0.2132914662361145 253.2826385498047 0.20540158450603485 0.7093412 0.31933701038360596 False -19 54780 29.63394069671631 0.5214715003967285 231.81838989257812 0.27551034092903137 253.23016357421875 0.20606407523155212 0.70988744 0.32161760330200195 False diff --git a/ENCSR666YVE/cherimoya.fold_0.performance.tsv b/ENCSR666YVE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 874ccbc7cade7bf05b9d06243eb88aac1e3236e8..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -253.04666137695312 0.5289241075515747 0.20695948600769043 0.06097235530614853 0.7112677097320557 0.6793980002403259 0.31733280420303345 \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_1.evaluate.json b/ENCSR666YVE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 49787eaa6f0ef4e44d512eb730544e47b3e959dd..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836NVQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_1.fit.json b/ENCSR666YVE/cherimoya.fold_1.fit.json deleted file mode 100644 index 736506a4f3a4884d47688267e3d19657f303002d..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF836NVQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_1.log b/ENCSR666YVE/cherimoya.fold_1.log deleted file mode 100644 index 0c2d78280068210f63c4eef719a2b0bff0a478b4..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 34.71053767204285 4.177668333053589 203.1470947265625 0.6425348520278931 295.6875915527344 0.14583909511566162 0.531175 3.3293728828430176 True -1 5502 30.46861505508423 0.7282974720001221 221.84738159179688 0.726614236831665 286.9776916503906 0.1900925636291504 0.6108508 1.0649839639663696 True -2 8253 30.370673894882202 1.021611213684082 196.0271453857422 0.6274105310440063 284.8664855957031 0.19923141598701477 0.6435943 0.5923415422439575 True -3 11004 30.335971117019653 0.7173075675964355 197.0783233642578 0.509640097618103 283.6123352050781 0.20306386053562164 0.6556336 0.5365104079246521 True -4 13755 30.350837230682373 0.7152493000030518 218.48239135742188 0.7952958345413208 283.0907287597656 0.20440888404846191 0.65986335 0.6035244464874268 True -5 16506 30.29842448234558 0.7176587581634521 202.46047973632812 0.7510234713554382 282.56427001953125 0.2070266604423523 0.6682226 0.6161575317382812 True -6 19257 30.29369330406189 19.289931774139404 228.17520141601562 0.4742608666419983 282.07672119140625 0.20918726921081543 0.677654 0.6111333966255188 True -7 22008 30.761988162994385 0.7606992721557617 181.47500610351562 0.5994672775268555 282.0869445800781 0.20900247991085052 0.6805051 0.5998702049255371 True -8 24759 30.31502056121826 0.7311015129089355 221.73365783691406 0.4541725218296051 281.36376953125 0.21262747049331665 0.69073886 0.5852816700935364 True -9 27510 30.36702823638916 0.7199227809906006 165.86944580078125 0.6595557928085327 281.0401611328125 0.21379056572914124 0.7009455 0.5037064552307129 True -10 30261 30.346510887145996 0.7111625671386719 187.6934814453125 0.4202851951122284 280.51171875 0.21613560616970062 0.7080234 0.47893521189689636 True -11 33012 30.338895320892334 0.7171306610107422 208.73171997070312 0.29992419481277466 280.1891174316406 0.21730388700962067 0.7184774 0.4233243763446808 True -12 35763 30.34734082221985 0.7136478424072266 181.2503662109375 0.5623236894607544 280.0539245605469 0.21730177104473114 0.7238288 0.3906625807285309 True -13 38514 30.328301668167114 29.30470323562622 210.82235717773438 0.41969090700149536 279.4662170410156 0.2205035239458084 0.7302202 0.36372318863868713 True -14 41265 30.365310192108154 1.9837253093719482 209.70179748535156 0.440114825963974 279.344482421875 0.22091220319271088 0.738975 0.3465452790260315 True -15 44016 30.370005130767822 0.8913562297821045 223.66915893554688 0.28011322021484375 279.1798400878906 0.22187839448451996 0.7479726 0.3249160051345825 True -16 46767 30.393382787704468 0.7231791019439697 213.35997009277344 0.3531457185745239 279.5619201660156 0.2196916788816452 0.75082666 0.31745409965515137 True -17 49518 29.930449962615967 1.4627900123596191 207.04312133789062 0.20108520984649658 279.2163391113281 0.22213226556777954 0.7531077 0.31515809893608093 True -18 52269 29.779043674468994 0.7272157669067383 207.98507690429688 0.5424273014068604 279.4837341308594 0.22068296372890472 0.7515702 0.3196437954902649 False -19 55020 29.71556782722473 0.7141833305358887 212.60064697265625 0.32809048891067505 279.7120056152344 0.21898871660232544 0.7502107 0.32403305172920227 False diff --git a/ENCSR666YVE/cherimoya.fold_1.performance.tsv b/ENCSR666YVE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a14a353c387d5e84891633d3b5679234996c570e..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -279.2163391113281 0.5150676369667053 0.22213225066661835 0.06680452823638916 0.7531077265739441 0.7315783500671387 0.31515809893608093 \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_2.evaluate.json b/ENCSR666YVE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 43955c186d5222e0bca93c9211b56db0794eaf29..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836NVQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_2.fit.json b/ENCSR666YVE/cherimoya.fold_2.fit.json deleted file mode 100644 index 52875d1612e7f191569713732d6966b068d7fedf..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF836NVQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_2.log b/ENCSR666YVE/cherimoya.fold_2.log deleted file mode 100644 index 6d3a20cfe81945fb87a4e683bd5482f34ab9e298..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 36.804869651794434 4.231058835983276 191.87307739257812 0.6850766539573669 272.6837463378906 0.14746704697608948 0.54308563 2.381251096725464 True -1 5784 31.905569553375244 0.6445026397705078 181.8900146484375 0.6750674247741699 265.65032958984375 0.18535687029361725 0.6064588 1.0834935903549194 True -2 8676 31.896668434143066 0.5217268466949463 221.9009552001953 0.4731312394142151 264.0175476074219 0.1908019632101059 0.61604786 0.7051661014556885 True -3 11568 31.85695219039917 0.5163514614105225 204.2754364013672 0.3945360779762268 263.01190185546875 0.19425912201404572 0.6454853 0.6483502984046936 True -4 14460 31.90122961997986 0.5224010944366455 211.47265625 0.5293914675712585 262.424560546875 0.19693829119205475 0.655459 0.6566685438156128 True -5 17352 32.42759943008423 0.5158529281616211 182.2672119140625 0.3977605104446411 261.7168273925781 0.2010631114244461 0.6648328 0.590644121170044 True -6 20244 31.91181182861328 0.5220420360565186 228.12603759765625 0.5274063944816589 261.2713928222656 0.20268401503562927 0.67443377 0.5808232426643372 True -7 23136 32.861409187316895 10.639201164245605 219.01031494140625 0.5887386798858643 261.1147155761719 0.20314444601535797 0.68211806 0.507946252822876 True -8 26028 31.892755270004272 9.56479787826538 175.34158325195312 0.43965643644332886 260.81256103515625 0.2043895423412323 0.6839632 0.4752592146396637 True -9 28920 31.880929470062256 0.5180258750915527 225.5797119140625 0.6939228773117065 260.2313537597656 0.20770345628261566 0.6894458 0.4303559958934784 True -10 31812 31.939402103424072 0.5119900703430176 186.44679260253906 0.35286447405815125 259.9976806640625 0.20877040922641754 0.6922474 0.4083783030509949 True -11 34704 32.084433794021606 0.5091879367828369 199.6243133544922 0.40593621134757996 259.50372314453125 0.21142980456352234 0.6977077 0.3860660195350647 True -12 37596 31.947830200195312 0.5237016677856445 203.6195068359375 0.43822360038757324 259.4541320800781 0.21106767654418945 0.7058183 0.3576114773750305 True -13 40488 31.901850700378418 0.5193402767181396 211.6969757080078 0.4394303262233734 259.2631530761719 0.21212179958820343 0.7095273 0.3362017869949341 True -14 43380 32.35196137428284 16.74431562423706 223.14352416992188 0.37079596519470215 258.99249267578125 0.21329651772975922 0.71716255 0.32584717869758606 True -15 46272 31.92180061340332 6.864182949066162 152.3482208251953 0.3719608187675476 258.9676513671875 0.21351124346256256 0.71939427 0.32262516021728516 True -16 49164 31.958441495895386 0.5416123867034912 221.34841918945312 0.3087082505226135 258.8629150390625 0.21395739912986755 0.7229425 0.311700701713562 True -17 52056 31.488784790039062 0.5096354484558105 198.2717742919922 0.29408910870552063 259.01898193359375 0.212919682264328 0.7252735 0.30969128012657166 True -18 54948 31.381420612335205 0.5066618919372559 199.83346557617188 0.1887558400630951 259.12359619140625 0.2119503617286682 0.7251105 0.3128843903541565 False -19 57840 31.261720180511475 0.509835958480835 212.67494201660156 0.3173713982105255 259.1239318847656 0.21201589703559875 0.7239185 0.3173848092556 False diff --git a/ENCSR666YVE/cherimoya.fold_2.performance.tsv b/ENCSR666YVE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e21844a483d7e282c413a94ad9089814a8bcb481..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -259.01898193359375 0.5246990323066711 0.21291965246200562 0.06256317347288132 0.7252734899520874 0.7000619769096375 0.30969128012657166 \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_3.evaluate.json b/ENCSR666YVE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fc30b0883055b1ac1186e4113435c574a6eb02d1..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836NVQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_3.fit.json b/ENCSR666YVE/cherimoya.fold_3.fit.json deleted file mode 100644 index 37c43617f951fd5580a11f85a81eb672b5827035..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF836NVQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_3.log b/ENCSR666YVE/cherimoya.fold_3.log deleted file mode 100644 index 1e75a08618e2169b51074f3d1c7237faa423c7b9..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2802 35.918750286102295 4.031529903411865 205.13687133789062 0.8537182807922363 285.31182861328125 0.14916054904460907 0.55800575 3.352597713470459 True -1 5604 30.913182973861694 1.163957118988037 205.3728485107422 0.9396368861198425 278.82623291015625 0.1826980710029602 0.62091786 1.1192731857299805 True -2 8406 30.94632601737976 0.6046152114868164 238.3018341064453 0.7412819862365723 276.75921630859375 0.18953415751457214 0.6296527 0.6464318037033081 True -3 11208 30.891246795654297 0.59476637840271 201.56390380859375 0.4845314621925354 275.70184326171875 0.19355516135692596 0.65602744 0.5415298938751221 True -4 14010 30.9261474609375 0.5991024971008301 256.63385009765625 0.322902649641037 274.9438171386719 0.19723989069461823 0.6631777 0.5933182239532471 True -5 16812 30.927979707717896 0.5919506549835205 209.66519165039062 0.48377296328544617 274.862060546875 0.19737166166305542 0.6809544 0.5301287174224854 True -6 19614 30.92555594444275 0.59147047996521 214.9749755859375 0.6461108922958374 274.5869445800781 0.19860850274562836 0.6795645 0.5576958656311035 False -7 22416 30.913777112960815 0.6025726795196533 197.42381286621094 0.4775201082229614 274.05230712890625 0.2020108848810196 0.6837494 0.5553621053695679 True -8 25218 30.89592170715332 1.0282912254333496 209.48577880859375 0.4762309491634369 273.42425537109375 0.20484395325183868 0.6931149 0.500393807888031 True -9 28020 31.010610580444336 0.6319968700408936 181.6876220703125 0.38401323556900024 273.1033935546875 0.20664988458156586 0.704033 0.4714225232601166 True -10 30822 30.892191886901855 0.590585470199585 196.50355529785156 0.4587196111679077 272.78131103515625 0.2080601006746292 0.70625687 0.4362892806529999 True -11 33624 30.88062572479248 0.5889453887939453 182.2294464111328 0.4268561601638794 272.4395446777344 0.20965179800987244 0.718409 0.3972185552120209 True -12 36426 30.930774211883545 0.6022076606750488 201.7838592529297 0.5064831376075745 272.3199768066406 0.20982863008975983 0.72551 0.3797593116760254 True -13 39228 30.91498565673828 0.6035275459289551 242.50576782226562 0.5675113797187805 272.1739501953125 0.2104206383228302 0.7323524 0.363077849149704 True -14 42030 30.871442317962646 0.5913577079772949 207.84677124023438 0.3845210075378418 271.9720153808594 0.21121081709861755 0.7352688 0.3413258492946625 True -15 44832 30.873446464538574 0.5805091857910156 196.91017150878906 0.2991970181465149 272.0388488769531 0.2110501229763031 0.7426598 0.32730814814567566 True -16 47634 30.700106620788574 0.5937373638153076 177.89614868164062 0.4020732343196869 271.8964538574219 0.21190562844276428 0.743085 0.3195294439792633 True -17 50436 30.27018165588379 0.5713717937469482 215.12548828125 0.19000153243541718 271.9542541503906 0.21128666400909424 0.7430966 0.3193301558494568 True -18 53238 30.213828563690186 0.5724024772644043 205.35952758789062 0.28643953800201416 272.2325134277344 0.2096318155527115 0.7414487 0.32233932614326477 False -19 56040 30.25566077232361 0.5969679355621338 210.45321655273438 0.29636213183403015 272.13934326171875 0.210617333650589 0.737264 0.33026283979415894 False diff --git a/ENCSR666YVE/cherimoya.fold_3.performance.tsv b/ENCSR666YVE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3e4a732c744baa58b3078a80cf80b1e01d10546d..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.9542541503906 0.5215357542037964 0.21128664910793304 0.06298146396875381 0.7430965900421143 0.7163708209991455 0.3193301558494568 \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_4.evaluate.json b/ENCSR666YVE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9363789a7c1d7d1dd6722edc9ad51f49a14d649c..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836NVQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_4.fit.json b/ENCSR666YVE/cherimoya.fold_4.fit.json deleted file mode 100644 index b6d39b3185cbb69614903302c0a4238b4b52611c..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF836NVQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR666YVE/cherimoya.fold_4.log b/ENCSR666YVE/cherimoya.fold_4.log deleted file mode 100644 index d5bf05ab87d54e0cefccad519849b0243e20e810..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2903 36.86104679107666 3.9216880798339844 220.59471130371094 0.5625038146972656 267.70904541015625 0.14426708221435547 0.53556013 1.9835268259048462 True -1 5806 31.95764994621277 0.7848436832427979 240.131103515625 0.7392047643661499 261.63201904296875 0.17849884927272797 0.6084474 0.8422209620475769 True -2 8709 32.03226017951965 0.579246997833252 220.77304077148438 0.5357080698013306 259.4732666015625 0.1868295967578888 0.63759315 0.6226254105567932 True -3 11612 32.000739336013794 0.557417631149292 224.3392333984375 0.5333552360534668 258.6431579589844 0.19031892716884613 0.650609 0.5434333086013794 True -4 14515 32.02549147605896 0.553431510925293 196.45547485351562 0.5126027464866638 258.15289306640625 0.19215059280395508 0.6554237 0.528308629989624 True -5 17418 31.990119695663452 0.5537536144256592 173.45602416992188 0.3875601887702942 258.0948486328125 0.19252100586891174 0.6618017 0.5565614700317383 True -6 20321 31.981709957122803 3.2447853088378906 184.5243377685547 0.3855455815792084 257.6474914550781 0.1946135014295578 0.66840196 0.546524167060852 True -7 23224 32.01990056037903 0.5615925788879395 195.69369506835938 0.41092225909233093 257.4153747558594 0.1958359330892563 0.6687907 0.5178526639938354 True -8 26127 32.06750750541687 0.5725359916687012 211.08657836914062 0.6420021057128906 256.9247741699219 0.19807226955890656 0.67757726 0.4681435823440552 True -9 29030 32.05880880355835 0.5801715850830078 203.9068603515625 0.5604271292686462 256.64385986328125 0.19939444959163666 0.68749136 0.4370287358760834 True -10 31933 32.18311047554016 0.586097240447998 192.68963623046875 0.4263121485710144 256.40472412109375 0.20066913962364197 0.6926289 0.3767056465148926 True -11 34836 32.17464733123779 0.575082540512085 196.90243530273438 0.5817538499832153 255.89508056640625 0.20371805131435394 0.7010499 0.35626161098480225 True -12 37739 32.2077260017395 1.2081496715545654 207.5294189453125 0.5155285596847534 255.77471923828125 0.20404215157032013 0.703746 0.355035662651062 True -13 40642 32.15954351425171 0.5633423328399658 203.11404418945312 0.39121213555336 255.56126403808594 0.20491495728492737 0.71207696 0.3435558080673218 True -14 43545 32.19106650352478 0.5641415119171143 199.4876708984375 0.3383725881576538 255.42649841308594 0.20521150529384613 0.71684587 0.3320259153842926 True -15 46448 32.190757274627686 0.5627977848052979 216.12184143066406 0.32120198011398315 255.1745147705078 0.20682601630687714 0.7228558 0.3165266513824463 True -16 49351 32.149741888046265 0.5731267929077148 223.4582061767578 0.27125856280326843 255.10765075683594 0.2073901891708374 0.72504073 0.3087261915206909 True -17 52254 32.075982332229614 0.5761566162109375 187.79415893554688 0.2986535429954529 255.09971618652344 0.20735874772071838 0.72861826 0.3060929477214813 True -18 55157 31.525588989257812 0.5591185092926025 210.59750366210938 0.29353538155555725 255.2212677001953 0.20657901465892792 0.7268574 0.3077070713043213 False -19 58060 31.47279977798462 0.5578773021697998 201.40597534179688 0.23571787774562836 255.26266479492188 0.20658299326896667 0.7251175 0.31436488032341003 False diff --git a/ENCSR666YVE/cherimoya.fold_4.performance.tsv b/ENCSR666YVE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6604fa578786fd6100fce2ba92f32261c78a3641..0000000000000000000000000000000000000000 --- a/ENCSR666YVE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -255.09971618652344 0.5283955931663513 0.20735874772071838 0.05920543521642685 0.7286182641983032 0.6952610611915588 0.3060929477214813 \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_0.evaluate.json b/ENCSR669NQZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6eac8481dff5c16d8b4e3f459c8a505c21202ef5..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387HGR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_0.fit.json b/ENCSR669NQZ/cherimoya.fold_0.fit.json deleted file mode 100644 index fb20c77f13d8ff8f68be3d997723310d0f04e4f3..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF387HGR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_0.log b/ENCSR669NQZ/cherimoya.fold_0.log deleted file mode 100644 index 97a7c38575cccc4a48ec3842dac9a61151e98e3f..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1585 21.29302167892456 3.721722364425659 335.9791259765625 1.2151522636413574 615.6331787109375 0.16535469889640808 0.58362246 14.052464485168457 True -1 3170 17.440387725830078 0.36443519592285156 343.8089599609375 0.8230891227722168 535.5664672851562 0.23971125483512878 0.7341755 6.910070896148682 True -2 4755 17.474587440490723 0.3224194049835205 423.18792724609375 1.0052766799926758 480.4541015625 0.28779804706573486 0.7725283 3.331850528717041 True -3 6340 17.458221197128296 0.33176612854003906 362.5002136230469 1.0889863967895508 467.3054504394531 0.3001517951488495 0.7800489 2.3194684982299805 True -4 7925 17.454581022262573 0.3389713764190674 484.69451904296875 0.8272312879562378 462.59423828125 0.30421504378318787 0.7930543 1.556483507156372 True -5 9510 17.442229747772217 0.30892229080200195 427.400146484375 0.6984308958053589 457.7719421386719 0.309701532125473 0.80233806 1.2065961360931396 True -6 11095 17.47114133834839 0.30904340744018555 332.0716247558594 0.5177494287490845 454.2004699707031 0.3115750551223755 0.81015986 1.0799719095230103 True -7 12680 17.476133346557617 1.1038997173309326 318.88250732421875 0.8336483836174011 450.3511047363281 0.31568557024002075 0.81572545 0.9253436326980591 True -8 14265 17.471176624298096 0.3127453327178955 428.4805908203125 0.30748802423477173 448.3260803222656 0.3186216652393341 0.82590777 0.8512821793556213 True -9 15850 17.463889122009277 0.306302547454834 309.79986572265625 0.5047013163566589 445.6590576171875 0.32190823554992676 0.82792044 0.788861870765686 True -10 17435 17.436862468719482 0.31975650787353516 415.93475341796875 0.6690347194671631 441.71685791015625 0.3256947100162506 0.8339288 0.7253937721252441 True -11 19020 17.424538135528564 0.30638861656188965 306.09564208984375 0.8516107797622681 441.4193420410156 0.32496511936187744 0.8424473 0.6613745093345642 True -12 20605 17.43791961669922 0.31110525131225586 355.752685546875 0.4184147119522095 440.22705078125 0.32556450366973877 0.8469944 0.6310322284698486 True -13 22190 17.442768812179565 0.30582571029663086 346.3465270996094 0.5563121438026428 437.7929382324219 0.3285420536994934 0.8516819 0.5981106758117676 True -14 23775 17.44624900817871 0.3123457431793213 451.96685791015625 0.43207985162734985 437.10235595703125 0.32909876108169556 0.85611737 0.5818001627922058 True -15 25360 17.439711570739746 0.3067028522491455 371.8093566894531 0.2893787622451782 436.75408935546875 0.3294525742530823 0.85927176 0.5588148236274719 True -16 26945 17.44449806213379 0.3054234981536865 329.72723388671875 0.3517243564128876 436.542236328125 0.329222708940506 0.8607852 0.5435148477554321 True -17 28530 17.44479537010193 0.3141937255859375 400.5536193847656 0.4208417236804962 436.1297912597656 0.3303281366825104 0.86157614 0.539215087890625 True -18 30115 17.41746187210083 0.30552196502685547 321.79644775390625 0.554417610168457 437.5538330078125 0.3286072909832001 0.8613642 0.5421628952026367 False -19 31700 17.43331027030945 0.3099181652069092 340.3438415527344 0.3245825171470642 438.2375793457031 0.32738369703292847 0.8609692 0.5454713702201843 False diff --git a/ENCSR669NQZ/cherimoya.fold_0.performance.tsv b/ENCSR669NQZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ed98fa6b676ea3a1e71473479695ae35e44d5cfa..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -436.1297912597656 0.45177459716796875 0.330328106880188 0.12613917887210846 0.8615761399269104 0.8025117516517639 0.539215087890625 \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_1.evaluate.json b/ENCSR669NQZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d779f121f609f490df9b9cd91e7aedd0b5275e33..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387HGR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_1.fit.json b/ENCSR669NQZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 9fdcbdb3215d45a680b8b94ffd25c7a2260563b7..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF387HGR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_1.log b/ENCSR669NQZ/cherimoya.fold_1.log deleted file mode 100644 index cc597fc4b371707787ee1b872a7518429ab99e87..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1527 20.612507104873657 4.052425384521484 314.18524169921875 0.850960373878479 753.7003784179688 0.17672424018383026 0.5524258 16.35541534423828 True -1 3054 16.815122604370117 1.3256309032440186 315.5791015625 0.9982165694236755 669.1771850585938 0.2541693449020386 0.70632863 10.292774200439453 True -2 4581 16.852121114730835 0.4615190029144287 330.71197509765625 0.6499998569488525 591.6419067382812 0.31046733260154724 0.76270884 5.455537796020508 True -3 6108 16.82238745689392 0.4623987674713135 447.47076416015625 1.0105081796646118 562.4165649414062 0.32895317673683167 0.7932297 3.046286106109619 True -4 7635 16.827802658081055 0.463392972946167 408.183349609375 0.861676037311554 552.3009643554688 0.33787834644317627 0.8063516 2.1763088703155518 True -5 9162 16.82584309577942 0.4600558280944824 374.044921875 1.2397699356079102 545.865478515625 0.3434934914112091 0.8116857 1.712704062461853 True -6 10689 16.786487817764282 0.45832180976867676 341.394287109375 0.5530535578727722 541.4498291015625 0.3477533757686615 0.820992 1.3368844985961914 True -7 12216 16.832574367523193 0.49330663681030273 373.0924987792969 0.8594626188278198 537.212158203125 0.3521389961242676 0.8282561 1.1509886980056763 True -8 13743 16.868704080581665 0.46094655990600586 330.8160095214844 0.8270390629768372 536.5125122070312 0.35203608870506287 0.8355622 0.9952297806739807 True -9 15270 16.811118125915527 1.2170100212097168 355.21484375 0.581281304359436 533.1865234375 0.3542773723602295 0.84101194 0.8821360468864441 True -10 16797 16.828887224197388 0.9279918670654297 332.75494384765625 0.643315315246582 529.0169677734375 0.3577747344970703 0.84443426 0.8271780014038086 True -11 18324 16.783844709396362 0.4737584590911865 440.30523681640625 0.47786954045295715 526.099365234375 0.3606731593608856 0.85030115 0.7532976865768433 True -12 19851 16.828195810317993 0.4978814125061035 282.86505126953125 0.5757958889007568 522.3507080078125 0.36442655324935913 0.8567973 0.6815950870513916 True -13 21378 16.84388279914856 0.4745352268218994 370.60772705078125 0.5015532970428467 520.0941162109375 0.36570996046066284 0.8616361 0.6589955687522888 True -14 22905 16.798274040222168 0.47281765937805176 222.1462860107422 0.5900068283081055 519.544189453125 0.36544039845466614 0.86342853 0.6353561878204346 True -15 24432 16.82531452178955 0.4731757640838623 327.81878662109375 0.4809883236885071 519.2415161132812 0.3651098608970642 0.86828536 0.6092841625213623 True -16 25959 16.80311632156372 1.0212559700012207 314.27301025390625 0.41171178221702576 518.1110229492188 0.3672775328159332 0.86863005 0.5954938530921936 True -17 27486 16.83845019340515 0.4668548107147217 359.6042175292969 0.34803593158721924 519.209228515625 0.3656192421913147 0.8698151 0.5919219255447388 True -18 29013 16.84524369239807 0.47419285774230957 320.19921875 0.2792952060699463 520.0581665039062 0.3652395009994507 0.86924785 0.5943832397460938 False -19 30540 16.80853009223938 0.4643402099609375 364.5255432128906 0.4026833176612854 520.3483276367188 0.36501139402389526 0.86797535 0.5998913049697876 False diff --git a/ENCSR669NQZ/cherimoya.fold_1.performance.tsv b/ENCSR669NQZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 353468d23b26326e7cce10570506dcaabcfc9b08..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -519.209228515625 0.4228830933570862 0.3656192421913147 0.14587728679180145 0.8698151111602783 0.8300223350524902 0.5919219255447388 \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_2.evaluate.json b/ENCSR669NQZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7481f55cbb22c755323ec6456865a381340a7a34..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387HGR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_2.fit.json b/ENCSR669NQZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 2ca5e0d5b2ab9a7ab2fc80123e5a35fe0dd1be22..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF387HGR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_2.log b/ENCSR669NQZ/cherimoya.fold_2.log deleted file mode 100644 index f37b4d5a675c17f88e655ee9704b5beb3b569b69..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1651 21.841283559799194 3.6909773349761963 366.3445129394531 0.9959940314292908 633.4174194335938 0.16507117450237274 0.53806007 14.440130233764648 True -1 3302 18.20069408416748 0.37795567512512207 362.9017333984375 0.9430342316627502 550.7398681640625 0.23754999041557312 0.7040274 6.478168487548828 True -2 4953 18.29179358482361 0.3455367088317871 270.52081298828125 0.8558365702629089 495.64569091796875 0.2815825939178467 0.7650756 3.2219924926757812 True -3 6604 18.209752082824707 0.34452247619628906 339.076416015625 0.6337758302688599 479.2725524902344 0.2943476736545563 0.78459156 2.338277578353882 True -4 8255 18.23642373085022 0.342252254486084 320.3759460449219 0.7163223028182983 469.9384765625 0.30309566855430603 0.7945307 1.6963459253311157 True -5 9906 18.22400212287903 0.34505534172058105 457.8809509277344 0.6843413710594177 464.6308288574219 0.3087201416492462 0.8040106 1.348830223083496 True -6 11557 18.208722591400146 0.34176158905029297 315.0235900878906 0.7575357556343079 462.7797546386719 0.31074392795562744 0.81312984 1.2140872478485107 True -7 13208 18.214839220046997 0.34207797050476074 332.244384765625 0.7987685203552246 458.3576965332031 0.31321707367897034 0.8216139 0.9726134538650513 True -8 14859 18.17506742477417 0.3484220504760742 477.30633544921875 0.8464182615280151 455.12603759765625 0.3165765106678009 0.82835394 0.8726790547370911 True -9 16510 18.2169406414032 0.34203457832336426 309.51605224609375 0.5891026258468628 453.4115295410156 0.3181176483631134 0.8322828 0.7785715460777283 True -10 18161 18.20421266555786 0.3416707515716553 368.16357421875 0.6031975746154785 451.73162841796875 0.3200383186340332 0.83883667 0.7220552563667297 True -11 19812 18.205520629882812 0.3419187068939209 432.011474609375 0.4846504032611847 449.04974365234375 0.32266688346862793 0.8425855 0.65675288438797 True -12 21463 18.215407609939575 1.1833000183105469 367.1352844238281 0.6662347316741943 446.7899169921875 0.3248015344142914 0.84775096 0.6260380148887634 True -13 23114 18.212372541427612 0.3392446041107178 338.7255859375 0.40204015374183655 445.6850280761719 0.3269403576850891 0.8503798 0.6064876317977905 True -14 24765 18.219031810760498 0.34757089614868164 353.78546142578125 0.41242337226867676 444.2966613769531 0.3280014991760254 0.8536265 0.5859071016311646 True -15 26416 18.20276379585266 0.3518095016479492 276.65875244140625 0.4336135983467102 443.2817687988281 0.3291078805923462 0.854818 0.5670844316482544 True -16 28067 18.18973422050476 0.33831024169921875 416.35906982421875 0.5617005825042725 443.6184997558594 0.32833731174468994 0.85979086 0.5511453151702881 True -17 29718 18.161603212356567 0.34134745597839355 364.7540283203125 0.4117490351200104 444.0835876464844 0.32874593138694763 0.858254 0.5489320755004883 False -18 31369 18.219733476638794 0.6819417476654053 360.29083251953125 0.5303399562835693 444.2979736328125 0.328552782535553 0.85804135 0.5550943613052368 False -19 33020 18.176258087158203 0.3409137725830078 357.948486328125 0.37235695123672485 443.4806213378906 0.32991650700569153 0.8558942 0.5596997737884521 False diff --git a/ENCSR669NQZ/cherimoya.fold_2.performance.tsv b/ENCSR669NQZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a5d2d0ed54d55360ba02228f05367746b6da8d76..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -443.6184997558594 0.45160940289497375 0.32833728194236755 0.12923353910446167 0.8597908616065979 0.802645206451416 0.5511453151702881 \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_3.evaluate.json b/ENCSR669NQZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6c9b25be244f972f008cfc44112bd21089dfc1ae..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387HGR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_3.fit.json b/ENCSR669NQZ/cherimoya.fold_3.fit.json deleted file mode 100644 index d38fa20b3317e29584b175a6a3d8ef49b2cac855..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF387HGR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_3.log b/ENCSR669NQZ/cherimoya.fold_3.log deleted file mode 100644 index ac7b921dfd8ed2b4b09d71a7844e2eec8c16c4fb..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1582 21.257725477218628 3.520015001296997 457.0813293457031 1.2131714820861816 649.3418579101562 0.18330372869968414 0.5578433 15.100730895996094 True -1 3164 17.450194120407104 0.3824937343597412 334.58856201171875 1.7437167167663574 568.1488037109375 0.2621271312236786 0.71050686 8.037056922912598 True -2 4746 17.443278074264526 0.35481762886047363 383.4438171386719 1.421194076538086 512.8404541015625 0.30723148584365845 0.7627159 3.7030489444732666 True -3 6328 17.429316997528076 0.3354623317718506 392.5744934082031 0.9195244312286377 493.2720031738281 0.3221531808376312 0.7823548 2.2932562828063965 True -4 7910 17.42755389213562 0.3070411682128906 432.160400390625 0.9641458988189697 485.02862548828125 0.3298739790916443 0.7866029 1.7549612522125244 True -5 9492 17.432116508483887 0.29900527000427246 425.0599365234375 0.8451055288314819 482.05926513671875 0.3327215909957886 0.7912086 1.4611362218856812 True -6 11074 17.41442561149597 0.2998316287994385 389.27374267578125 0.7770935893058777 479.8357849121094 0.33463922142982483 0.79887444 1.1939060688018799 True -7 12656 17.456111192703247 0.31714725494384766 356.93878173828125 1.2610805034637451 476.2895202636719 0.3391178548336029 0.80532664 1.1782127618789673 True -8 14238 17.47175431251526 0.3391246795654297 426.034423828125 0.896305501461029 474.201416015625 0.34037941694259644 0.8108914 1.0577116012573242 True -9 15820 17.41827392578125 0.30536890029907227 273.0849914550781 0.7536047101020813 471.5502624511719 0.34342098236083984 0.81679046 0.9911828637123108 True -10 17402 17.412959337234497 0.30904722213745117 315.610107421875 0.7982376217842102 469.57098388671875 0.3450978696346283 0.82490325 0.9065290093421936 True -11 18984 17.412801265716553 0.2985646724700928 295.15557861328125 0.6352999210357666 467.69158935546875 0.34663116931915283 0.8307788 0.8464081287384033 True -12 20566 17.39060115814209 0.6614944934844971 332.0469055175781 0.47080475091934204 465.4611511230469 0.34903326630592346 0.8366555 0.7753336429595947 True -13 22148 17.387861013412476 0.332672119140625 385.83453369140625 0.9636463522911072 463.2501220703125 0.35065773129463196 0.8416939 0.7250024676322937 True -14 23730 17.389122486114502 0.3177628517150879 280.4089050292969 0.7102006673812866 461.44232177734375 0.3531094193458557 0.8491997 0.6746174693107605 True -15 25312 17.418802499771118 0.30426955223083496 330.650146484375 0.4358678460121155 460.82794189453125 0.35354888439178467 0.853402 0.6570860743522644 True -16 26894 17.394143104553223 0.30768632888793945 367.7283935546875 0.543687105178833 460.5773620605469 0.3527626693248749 0.8548489 0.6284031271934509 True -17 28476 17.3940486907959 0.3110837936401367 400.20135498046875 0.3144042491912842 459.98004150390625 0.354093998670578 0.85448295 0.6228390336036682 False -18 30058 17.392512559890747 0.33530235290527344 378.8218078613281 0.47555315494537354 461.62310791015625 0.35201382637023926 0.85395426 0.6219384670257568 False -19 31640 17.391077280044556 0.32413673400878906 321.88726806640625 0.34980887174606323 463.1944885253906 0.35038816928863525 0.8537051 0.6273770928382874 False diff --git a/ENCSR669NQZ/cherimoya.fold_3.performance.tsv b/ENCSR669NQZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 882d93a86421c818e0bf108e45d63b4e3063bbf2..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -460.5773620605469 0.4345457851886749 0.3527626395225525 0.13763785362243652 0.8548489212989807 0.8045435547828674 0.6284031271934509 \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_4.evaluate.json b/ENCSR669NQZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 19d304b83dfa585bcc0c6708bcfcc2b90510cf79..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387HGR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_4.fit.json b/ENCSR669NQZ/cherimoya.fold_4.fit.json deleted file mode 100644 index fa65f4154535da216edb49c3edc7dad93ed97a1a..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF387HGR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR669NQZ/cherimoya.fold_4.log b/ENCSR669NQZ/cherimoya.fold_4.log deleted file mode 100644 index 796c6b4ca0c3828851ded44dc32e07aa8c99c9e4..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1547 20.687453031539917 3.4300692081451416 385.7911071777344 2.2207891941070557 576.2447509765625 0.16669534146785736 0.55704254 14.15396785736084 True -1 3094 17.037028312683105 0.3427436351776123 394.329345703125 0.6951630115509033 515.2631225585938 0.23205162584781647 0.68688464 6.808209419250488 True -2 4641 17.013370037078857 0.29325151443481445 401.535400390625 0.743571400642395 458.4955139160156 0.2808031439781189 0.7629712 3.539069890975952 True -3 6188 17.020912885665894 0.2921473979949951 528.8955078125 0.9127335548400879 440.9028015136719 0.2938603460788727 0.7819614 2.2454938888549805 True -4 7735 17.045103073120117 0.30501604080200195 371.23876953125 1.067608118057251 433.3627624511719 0.30126404762268066 0.79206085 1.3860561847686768 True -5 9282 17.00579071044922 0.2955198287963867 368.2677307128906 0.9633587598800659 430.8766174316406 0.3033584952354431 0.79642546 1.1560020446777344 True -6 10829 16.994120359420776 0.2928314208984375 294.8412780761719 0.7967414855957031 427.6271057128906 0.3077651262283325 0.80650353 1.0390613079071045 True -7 12376 17.005666255950928 0.2919628620147705 389.76373291015625 0.6804141402244568 425.04949951171875 0.3103243112564087 0.81353146 0.9132428169250488 True -8 13923 17.053415775299072 0.29285669326782227 383.66552734375 0.7417702078819275 421.9945373535156 0.314373254776001 0.8211844 0.8414316773414612 True -9 15470 17.022021055221558 0.7102048397064209 402.335693359375 0.6270833015441895 421.14056396484375 0.3147599399089813 0.82496256 0.7727733254432678 True -10 17017 17.02655005455017 0.29636216163635254 402.16259765625 0.785862147808075 419.53216552734375 0.31639233231544495 0.82949185 0.6854602098464966 True -11 18564 17.072750568389893 0.29383039474487305 291.57220458984375 0.591341495513916 417.3582763671875 0.3199501931667328 0.8332436 0.6566689610481262 True -12 20111 17.035722255706787 0.2970774173736572 349.70855712890625 0.7694627046585083 415.2422790527344 0.32196277379989624 0.8379323 0.6278144121170044 True -13 21658 17.036073207855225 0.29489707946777344 376.91009521484375 0.6275242567062378 415.22442626953125 0.32186436653137207 0.84433687 0.599639356136322 True -14 23205 17.01177191734314 0.2951219081878662 446.9457702636719 0.5952157974243164 414.975341796875 0.3220248520374298 0.8482315 0.5693597197532654 True -15 24752 17.003344774246216 0.29047226905822754 381.69842529296875 0.5281875133514404 413.7038879394531 0.3240494430065155 0.85208964 0.5511415600776672 True -16 26299 17.01071858406067 0.2888760566711426 351.8084716796875 0.4247782826423645 413.4100341796875 0.3248465061187744 0.85206413 0.5436025857925415 False -17 27846 17.023645401000977 0.2891678810119629 359.5931091308594 0.42441055178642273 414.2325134277344 0.32411909103393555 0.85325235 0.5424938797950745 True -18 29393 17.056556701660156 1.2090983390808105 372.2619323730469 0.42396435141563416 414.5232238769531 0.32275307178497314 0.85285884 0.5470806956291199 False -19 30940 17.056829690933228 0.30048370361328125 376.6440734863281 0.46772462129592896 414.3930358886719 0.3237493634223938 0.85229146 0.5494945049285889 False diff --git a/ENCSR669NQZ/cherimoya.fold_4.performance.tsv b/ENCSR669NQZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fc4e2fb59c8c40ce4afef338c8cc199177347184..0000000000000000000000000000000000000000 --- a/ENCSR669NQZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -414.2325134277344 0.4565633237361908 0.32411909103393555 0.11935392767190933 0.8532523512840271 0.7889001965522766 0.5424938797950745 \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_0.evaluate.json b/ENCSR670BGI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9d749f9ea0f7c8a8f817ab1c924f9847198c24de..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693QHW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_0.fit.json b/ENCSR670BGI/cherimoya.fold_0.fit.json deleted file mode 100644 index b59f178467dab0f96d22b851255c01b1422d4a1b..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF693QHW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_0.log b/ENCSR670BGI/cherimoya.fold_0.log deleted file mode 100644 index 684aef13ebe8326b26542a501797344588fefb3a..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2779 34.523589849472046 3.842116355895996 366.5852966308594 0.2581271231174469 539.7620849609375 0.29425787925720215 0.81543475 3.851165771484375 True -1 5558 30.867026329040527 0.6776058673858643 438.2508239746094 0.25320425629615784 505.5012512207031 0.3460182547569275 0.8665322 0.8602967262268066 True -2 8337 30.95119881629944 0.7108244895935059 345.94873046875 0.15351790189743042 499.4833679199219 0.3524339199066162 0.87352633 0.32995784282684326 True -3 11116 30.863880157470703 0.6633694171905518 383.8149108886719 0.13242533802986145 496.49725341796875 0.35637539625167847 0.87697357 0.2632409334182739 True -4 13895 30.864404678344727 0.6089334487915039 457.7682800292969 0.13654181361198425 493.6050720214844 0.3612818717956543 0.88720876 0.24568243324756622 True -5 16674 30.89631676673889 1.3511648178100586 397.3026428222656 0.1429261863231659 491.26190185546875 0.3643623888492584 0.8902855 0.20916055142879486 True -6 19453 30.85832905769348 17.510706901550293 433.494384765625 0.27653753757476807 490.0212097167969 0.3657841384410858 0.8973949 0.19267083704471588 True -7 22232 30.932273626327515 0.6266977787017822 427.5223083496094 0.24120652675628662 488.3537902832031 0.3683822453022003 0.901176 0.18258289992809296 True -8 25011 30.91766357421875 0.6436655521392822 501.30035400390625 0.11226122081279755 487.32244873046875 0.3700731098651886 0.9028499 0.1868903487920761 True -9 27790 30.942143201828003 0.6382267475128174 395.0961608886719 0.1547592282295227 486.3185119628906 0.3710487186908722 0.9064122 0.17360906302928925 True -10 30569 30.896524906158447 0.9425218105316162 435.6871337890625 0.23966233432292938 485.0355529785156 0.37372979521751404 0.90698856 0.1655283123254776 True -11 33348 30.89199447631836 1.1899781227111816 451.28155517578125 0.20519010722637177 484.1214599609375 0.3742436170578003 0.9134486 0.15823838114738464 True -12 36127 30.882876873016357 0.6275269985198975 429.70416259765625 0.12264296412467957 483.63031005859375 0.37519729137420654 0.9168137 0.14567101001739502 True -13 38906 30.88630700111389 0.6452414989471436 385.9924011230469 0.17214588820934296 482.3786926269531 0.37718313932418823 0.91900414 0.1381542682647705 True -14 41685 30.936741828918457 0.640479564666748 410.9624328613281 0.08833721280097961 482.0547790527344 0.37776899337768555 0.9212006 0.12984609603881836 True -15 44464 30.917821407318115 0.6119551658630371 467.3547058105469 0.1282249391078949 481.4732360839844 0.3786218762397766 0.9236623 0.12341559678316116 True -16 47243 31.01730179786682 0.639672040939331 410.4217834472656 0.10250262171030045 481.662109375 0.3783963918685913 0.92331386 0.12078215926885605 False -17 50022 31.070970058441162 0.6465952396392822 378.9501647949219 0.10448981821537018 481.1562805175781 0.37947455048561096 0.92618036 0.1177130863070488 True -18 52801 30.96888279914856 0.6315891742706299 406.69970703125 0.12051203101873398 481.2662353515625 0.3785088360309601 0.9246502 0.11767825484275818 False -19 55580 31.010701417922974 0.6409401893615723 476.3887939453125 0.06748730689287186 480.94915771484375 0.37991654872894287 0.92552745 0.11838687211275101 False diff --git a/ENCSR670BGI/cherimoya.fold_0.performance.tsv b/ENCSR670BGI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 36717bdfd851ca1e84e9aff6b0be5d1a89fff6e6..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -481.1562805175781 0.4018048346042633 0.37947455048561096 0.14095117151737213 0.926180362701416 0.9081690907478333 0.1177130863070488 \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_1.evaluate.json b/ENCSR670BGI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 62894eabf580557571e52caa04f98909ce7bbbe8..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693QHW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_1.fit.json b/ENCSR670BGI/cherimoya.fold_1.fit.json deleted file mode 100644 index c78738652c420b0e15629ecd8bfb52fc1fecd7d0..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF693QHW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_1.log b/ENCSR670BGI/cherimoya.fold_1.log deleted file mode 100644 index bcbef8052faf1294e907833963f60e738448b804..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2725 34.17238140106201 22.8564875125885 441.2333984375 0.26041698455810547 613.4843139648438 0.2944824993610382 0.7955081 4.678642749786377 True -1 5450 30.63507580757141 0.860821008682251 355.7747802734375 0.40711700916290283 570.242919921875 0.3557716906070709 0.8508672 0.9456196427345276 True -2 8175 30.331097841262817 1.2980644702911377 359.11724853515625 0.17012012004852295 559.5037841796875 0.3667990267276764 0.86744195 0.3565399646759033 True -3 10900 30.31701159477234 0.7392778396606445 476.44287109375 0.32312512397766113 554.65234375 0.3717724084854126 0.87393194 0.30814942717552185 True -4 13625 30.297542572021484 0.7295470237731934 400.0334167480469 0.21703413128852844 552.742431640625 0.3736140727996826 0.87502235 0.30644845962524414 True -5 16350 30.317884922027588 0.7441198825836182 422.74969482421875 0.1713377833366394 549.7716064453125 0.37692520022392273 0.8821505 0.25596657395362854 True -6 19075 30.335307121276855 0.7465674877166748 410.62078857421875 0.1670341193675995 546.895263671875 0.3812294900417328 0.8875175 0.23627831041812897 True -7 21800 30.3298659324646 0.741178035736084 433.33538818359375 0.21804654598236084 545.5390625 0.38291627168655396 0.89166445 0.25139120221138 True -8 24525 30.399898767471313 0.7342085838317871 422.6565856933594 0.12995122373104095 544.3688354492188 0.3835117816925049 0.89683706 0.22241371870040894 True -9 27250 30.303860425949097 0.7456154823303223 412.93988037109375 0.1388079673051834 542.3806762695312 0.3867931663990021 0.90184766 0.21238331496715546 True -10 29975 30.31434392929077 0.7381155490875244 399.075439453125 0.21164730191230774 540.929931640625 0.38835522532463074 0.9045145 0.19588959217071533 True -11 32700 30.36168932914734 0.7381439208984375 391.9308776855469 0.13119591772556305 539.9066162109375 0.38953083753585815 0.9089025 0.1826055347919464 True -12 35425 30.32491636276245 0.7346792221069336 367.53070068359375 0.15003877878189087 538.3020629882812 0.3916744589805603 0.912562 0.1725698560476303 True -13 38150 30.42775797843933 0.7390015125274658 418.05694580078125 0.20262935757637024 536.7858276367188 0.393342524766922 0.91628444 0.1631060093641281 True -14 40875 30.421466827392578 1.788356065750122 442.9171142578125 0.09758606553077698 535.510498046875 0.3945615589618683 0.91856515 0.153432697057724 True -15 43600 30.602940797805786 0.7507994174957275 416.21197509765625 0.13159386813640594 535.3350830078125 0.39451438188552856 0.92272 0.14428934454917908 True -16 46325 30.355689525604248 0.746056318283081 425.4741516113281 0.09883800148963928 534.7837524414062 0.394608736038208 0.9237588 0.13830848038196564 True -17 49050 30.476763486862183 0.7573881149291992 445.32421875 0.10267147421836853 534.2349243164062 0.3962153196334839 0.9252616 0.1356322169303894 True -18 51775 30.434020042419434 0.7427728176116943 428.4075927734375 0.08859414607286453 535.07861328125 0.39408499002456665 0.92509305 0.13552893698215485 False -19 54500 30.417365074157715 0.7505204677581787 417.000244140625 0.13375058770179749 534.9774169921875 0.39540213346481323 0.9246116 0.1354958564043045 False diff --git a/ENCSR670BGI/cherimoya.fold_1.performance.tsv b/ENCSR670BGI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 24014cd135e6b8675f5d0f8efae4fe5cbb5b4f57..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -534.2349243164062 0.38776081800460815 0.3962153196334839 0.1587747186422348 0.9252616167068481 0.9181361794471741 0.1356322169303894 \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_2.evaluate.json b/ENCSR670BGI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 469517da36b59c3cb4b627d8210e25a532614289..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693QHW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_2.fit.json b/ENCSR670BGI/cherimoya.fold_2.fit.json deleted file mode 100644 index dfd5bda16fb02e21518bfb29bc40a73903e3d3b4..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF693QHW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_2.log b/ENCSR670BGI/cherimoya.fold_2.log deleted file mode 100644 index cb031283d02046d51f2f6ff4574a4a3e8b03bb85..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 35.49148106575012 3.4074857234954834 455.234130859375 0.41176894307136536 574.1095581054688 0.2897273302078247 0.7962268 3.483617067337036 True -1 5754 31.949594259262085 0.679673433303833 418.45574951171875 0.20260146260261536 535.47900390625 0.3481143116950989 0.8495047 0.761834979057312 True -2 8631 31.956560850143433 0.61350417137146 392.6943359375 0.17389360070228577 529.2142944335938 0.35741716623306274 0.85461414 0.35825255513191223 True -3 11508 32.030386209487915 0.6047961711883545 359.17840576171875 0.14205604791641235 525.8890380859375 0.35986825823783875 0.8605459 0.3121214509010315 True -4 14385 32.034568309783936 0.6009159088134766 443.28778076171875 0.1307814121246338 525.9940185546875 0.35921710729599 0.8609342 0.24892887473106384 True -5 17262 32.01219868659973 0.6282870769500732 403.44464111328125 0.26610636711120605 522.8842163085938 0.3640356659889221 0.8672215 0.2416478395462036 True -6 20139 32.071515798568726 0.6019620895385742 403.1723937988281 0.18584293127059937 521.1835327148438 0.3659874200820923 0.87132794 0.23268358409404755 True -7 23016 32.00555944442749 0.6045022010803223 382.89398193359375 0.14746740460395813 520.0325927734375 0.3676474988460541 0.87315184 0.2344406247138977 True -8 25893 32.05262589454651 0.6059374809265137 409.9436340332031 0.1722179353237152 517.83154296875 0.3714475631713867 0.87983954 0.22172124683856964 True -9 28770 32.054012060165405 0.9887750148773193 400.01239013671875 0.1443471908569336 516.72802734375 0.3714686632156372 0.8843679 0.20958280563354492 True -10 31647 32.065680503845215 0.6020793914794922 392.8022155761719 0.1793881058692932 514.7139282226562 0.37485241889953613 0.8889569 0.19488345086574554 True -11 34524 32.06490230560303 1.703453540802002 412.97686767578125 0.20094811916351318 513.4614868164062 0.3758421540260315 0.89460087 0.18490153551101685 True -12 37401 32.04435849189758 15.404245853424072 386.781494140625 0.09848706424236298 512.728271484375 0.3761770725250244 0.89795345 0.1682611107826233 True -13 40278 32.00023651123047 0.6052701473236084 419.4187316894531 0.14966365694999695 511.085693359375 0.3782205283641815 0.9012914 0.1577840894460678 True -14 43155 32.072486877441406 0.6199281215667725 407.67596435546875 0.13673892617225647 509.46197509765625 0.38173919916152954 0.9060292 0.1507991999387741 True -15 46032 31.976877689361572 2.260221004486084 411.156982421875 0.12899792194366455 509.32720947265625 0.3805675804615021 0.90773606 0.14500005543231964 True -16 48909 32.15032625198364 0.6216945648193359 377.44415283203125 0.11085842549800873 509.65948486328125 0.37977784872055054 0.90983474 0.13916867971420288 True -17 51786 32.18491077423096 0.6165268421173096 381.54638671875 0.11102034151554108 509.342041015625 0.3804131746292114 0.9105477 0.1368679255247116 True -18 54663 32.204373359680176 0.6270084381103516 432.2032470703125 0.0886676162481308 509.64117431640625 0.379914790391922 0.9110488 0.1369277387857437 True -19 57540 32.15108323097229 1.324373483657837 433.62005615234375 0.14289018511772156 509.4200439453125 0.38104909658432007 0.9117074 0.1371939331293106 True diff --git a/ENCSR670BGI/cherimoya.fold_2.performance.tsv b/ENCSR670BGI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c7691c579060a5f4d0604cbaf222e8931ec83efc..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -509.4200439453125 0.39659422636032104 0.38104909658432007 0.1498572826385498 0.9117074012756348 0.8998662829399109 0.1371939331293106 \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_3.evaluate.json b/ENCSR670BGI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b2424718ba02c21923384daca81fc68353e58aa3..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693QHW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_3.fit.json b/ENCSR670BGI/cherimoya.fold_3.fit.json deleted file mode 100644 index 48f8e48ca257a29dc3369c01967a580d83608053..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF693QHW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_3.log b/ENCSR670BGI/cherimoya.fold_3.log deleted file mode 100644 index 035b756987492b94f55e08fa29f4e9f3e82bc7c2..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 34.06434178352356 4.2015674114227295 418.4823303222656 0.19376477599143982 529.6004638671875 0.3005790710449219 0.7887412 3.7378876209259033 True -1 5502 30.599221229553223 0.5957238674163818 394.20989990234375 0.32144877314567566 495.88433837890625 0.35121840238571167 0.85197204 0.7263474464416504 True -2 8253 30.691107749938965 0.5832417011260986 429.1842041015625 0.4065966308116913 490.00018310546875 0.35903117060661316 0.86059713 0.29389411211013794 True -3 11004 30.563825368881226 0.6210241317749023 453.4114074707031 0.3384917378425598 485.3183898925781 0.36512601375579834 0.868575 0.2823033034801483 True -4 13755 30.579946994781494 0.5936880111694336 418.670166015625 0.14193303883075714 482.6999206542969 0.3678058683872223 0.87322545 0.23223714530467987 True -5 16506 30.551506280899048 0.9648103713989258 418.3528747558594 0.1893739104270935 481.0441589355469 0.37006497383117676 0.87610483 0.2380567342042923 True -6 19257 30.585856676101685 0.5707366466522217 454.48638916015625 0.19661788642406464 481.0038146972656 0.3685244023799896 0.8782215 0.2131720334291458 True -7 22008 30.535454273223877 0.5667726993560791 458.5181884765625 0.3419664204120636 479.468994140625 0.37069442868232727 0.8819007 0.20691178739070892 True -8 24759 30.545106172561646 0.5765297412872314 374.27081298828125 0.16462993621826172 478.057373046875 0.37291696667671204 0.88587385 0.19550882279872894 True -9 27510 30.555426359176636 0.6230127811431885 381.3297119140625 0.20597994327545166 476.396728515625 0.3758707642555237 0.8897818 0.1899823248386383 True -10 30261 30.588069200515747 0.603630781173706 447.9593505859375 0.18799330294132233 476.5988464355469 0.37438586354255676 0.89467996 0.1838936060667038 True -11 33012 30.55900263786316 0.5572748184204102 450.8309020996094 0.13048556447029114 474.7455749511719 0.3785848021507263 0.89789337 0.17501594126224518 True -12 35763 30.59505581855774 0.6562862396240234 386.6855163574219 0.24599620699882507 474.26904296875 0.3780408799648285 0.90050316 0.16536077857017517 True -13 38514 30.584136247634888 1.255669355392456 374.21746826171875 0.11382929980754852 472.8314208984375 0.3805828392505646 0.9059633 0.15951676666736603 True -14 41265 30.59497570991516 0.5583016872406006 452.80523681640625 0.10568267852067947 471.76312255859375 0.38242316246032715 0.9091474 0.15286339819431305 True -15 44016 30.563512325286865 0.6833498477935791 419.90142822265625 0.2074720859527588 471.3945007324219 0.38290244340896606 0.9131516 0.14450904726982117 True -16 46767 30.659432649612427 1.1961195468902588 479.02685546875 0.09397553652524948 471.5792541503906 0.3820979595184326 0.9146024 0.1406211107969284 True -17 49518 30.660036325454712 0.7424697875976562 426.5266418457031 0.12980282306671143 471.4899597167969 0.38218194246292114 0.9166858 0.13814722001552582 True -18 52269 30.6412353515625 0.5624949932098389 444.867431640625 0.13638216257095337 470.9568176269531 0.38370412588119507 0.91647214 0.13796617090702057 False -19 55020 30.629061698913574 0.56852126121521 396.8072204589844 0.09253432601690292 471.3024597167969 0.382611483335495 0.9153075 0.13880503177642822 False diff --git a/ENCSR670BGI/cherimoya.fold_3.performance.tsv b/ENCSR670BGI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index cbd9d876bbd45c4813407a134a3a52841147d6e9..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -471.4899597167969 0.40071535110473633 0.38218194246292114 0.14454440772533417 0.9166858196258545 0.8943701982498169 0.13814722001552582 \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_4.evaluate.json b/ENCSR670BGI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index abccc6c8aad97397528d221d2a30ac5d133d77ef..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF693QHW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_4.fit.json b/ENCSR670BGI/cherimoya.fold_4.fit.json deleted file mode 100644 index 4897faf5f0a4155d8da1cd10cb6e196c2a1e8c21..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF693QHW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670BGI/cherimoya.fold_4.log b/ENCSR670BGI/cherimoya.fold_4.log deleted file mode 100644 index 327f948cf36c83c5bec62d4307e5131840d7021e..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 46.87001395225525 61.276185750961304 476.22845458984375 0.3321719169616699 497.447265625 0.2880440056324005 0.8116544 2.9629616737365723 True -1 5508 30.80207633972168 0.6235427856445312 407.3426208496094 0.15555019676685333 467.13446044921875 0.3370357155799866 0.8610411 0.7430387139320374 True -2 8262 30.815857887268066 0.6077814102172852 450.69989013671875 0.19457414746284485 460.6663513183594 0.3459244966506958 0.8711507 0.2902858257293701 True -3 11016 30.794227838516235 0.6105875968933105 406.2430114746094 0.25598248839378357 458.9130554199219 0.34735947847366333 0.8738777 0.19848471879959106 True -4 13770 30.789234161376953 0.6029932498931885 412.2749328613281 0.2481674998998642 456.9976501464844 0.3487160801887512 0.88209707 0.16933779418468475 True -5 16524 30.796263694763184 0.6034762859344482 392.75311279296875 0.16730722784996033 455.2098388671875 0.35183605551719666 0.8865198 0.1591821014881134 True -6 19278 30.781100273132324 0.6020359992980957 470.3116455078125 0.16674871742725372 453.8888854980469 0.3540843427181244 0.888876 0.15706738829612732 True -7 22032 30.77525782585144 0.6075749397277832 413.7282409667969 0.20327377319335938 453.5108642578125 0.35367777943611145 0.89511853 0.15481312572956085 True -8 24786 30.8680260181427 0.607344388961792 398.0320129394531 0.1941855251789093 452.10809326171875 0.35663101077079773 0.89991915 0.14376062154769897 True -9 27540 30.824779510498047 0.5984439849853516 439.1361083984375 0.1888081431388855 451.3221740722656 0.35821300745010376 0.90061593 0.14209002256393433 True -10 30294 30.811805963516235 2.165334701538086 428.19122314453125 0.1690095067024231 449.8417053222656 0.3611893057823181 0.90702826 0.13918529450893402 True -11 33048 30.86503314971924 0.6104741096496582 467.9590148925781 0.10773121565580368 448.7769775390625 0.3633905053138733 0.9076228 0.13409505784511566 True -12 35802 30.863438367843628 0.6072640419006348 423.6295471191406 0.10254599153995514 448.2919006347656 0.36379697918891907 0.9124257 0.1288834512233734 True -13 38556 30.853434324264526 0.6117627620697021 513.1061401367188 0.14529743790626526 447.42181396484375 0.36442604660987854 0.91520613 0.12454423308372498 True -14 41310 30.82428741455078 0.6154320240020752 413.62811279296875 0.06653892993927002 446.9197998046875 0.3658836781978607 0.91758466 0.12015033513307571 True -15 44064 30.826685190200806 0.6111898422241211 410.5622863769531 0.1805187612771988 446.7846984863281 0.36547771096229553 0.920554 0.11625790596008301 True -16 46818 30.81415843963623 1.375840187072754 400.1256103515625 0.16101309657096863 446.4403991699219 0.3663954734802246 0.9219297 0.11311393231153488 True -17 49572 30.81800413131714 0.6204140186309814 358.38397216796875 0.11838211119174957 446.1628112792969 0.36784154176712036 0.9227945 0.11200906336307526 True -18 52326 30.839778661727905 0.6095423698425293 447.8964538574219 0.1468493491411209 446.6051330566406 0.3665645718574524 0.922961 0.1116948127746582 True -19 55080 30.882019758224487 0.6148281097412109 392.71875 0.07896587997674942 446.3669128417969 0.36760497093200684 0.9231525 0.11195740848779678 True diff --git a/ENCSR670BGI/cherimoya.fold_4.performance.tsv b/ENCSR670BGI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 14c71ff1283c5dde3d287dbd5f0d97a43d5eee71..0000000000000000000000000000000000000000 --- a/ENCSR670BGI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -446.3669128417969 0.4128885269165039 0.36760497093200684 0.13519364595413208 0.923152506351471 0.9034619331359863 0.11195740848779678 \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_0.evaluate.json b/ENCSR670VQZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index fe4d6e921aef8402e573ccabbbdf8f00ac1f8a14..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444ZNA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_0.fit.json b/ENCSR670VQZ/cherimoya.fold_0.fit.json deleted file mode 100644 index e735735b35d6597c712dcf140394e18ec425385e..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF444ZNA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_0.log b/ENCSR670VQZ/cherimoya.fold_0.log deleted file mode 100644 index 9decdb21500dc5dbbcf506b612ae3aadf7b432d9..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2548 31.56053352355957 3.8969593048095703 170.36038208007812 1.6426335573196411 241.21502685546875 0.1472964733839035 0.2583032 3.833817481994629 True -1 5096 28.282299757003784 0.5689167976379395 140.453125 1.0111083984375 210.37835693359375 0.26624348759651184 0.4150842 3.1431937217712402 True -2 7644 28.05041003227234 0.5586867332458496 158.10977172851562 0.8881507515907288 204.26077270507812 0.282162070274353 0.43857706 1.7668802738189697 True -3 10192 28.04096555709839 0.5400598049163818 166.26797485351562 0.8884727954864502 201.34585571289062 0.292135626077652 0.46793815 1.4613745212554932 True -4 12740 28.02258586883545 0.5280516147613525 150.7093963623047 0.9610855579376221 200.11306762695312 0.29690131545066833 0.46833423 1.2067838907241821 True -5 15288 28.069743633270264 1.4914753437042236 172.73388671875 1.0486024618148804 198.78219604492188 0.30032646656036377 0.48383865 1.071110486984253 True -6 17836 28.081877946853638 0.537398099899292 119.00672912597656 0.6881454586982727 198.28778076171875 0.3031708002090454 0.48852494 1.0736031532287598 True -7 20384 28.073190689086914 0.5398604869842529 177.24671936035156 1.048380732536316 197.3570556640625 0.3053189516067505 0.5077204 0.99193274974823 True -8 22932 28.015541553497314 0.5392096042633057 151.93212890625 0.862897515296936 196.51637268066406 0.3103887438774109 0.5158055 0.9147819876670837 True -9 25480 28.043129682540894 0.7264790534973145 157.56594848632812 0.743238091468811 195.760986328125 0.311755895614624 0.53556275 0.8722261190414429 True -10 28028 28.094736576080322 1.271287441253662 168.20199584960938 0.9308544993400574 195.4103240966797 0.3131285607814789 0.54399586 0.8468047380447388 True -11 30576 28.10294818878174 0.5402421951293945 98.45288848876953 0.6991314888000488 194.8369140625 0.3147939145565033 0.55902976 0.7890334725379944 True -12 33124 28.02830410003662 0.5236446857452393 149.70843505859375 0.7387071847915649 194.4609375 0.31572580337524414 0.57069814 0.7663841247558594 True -13 35672 28.019664764404297 0.5590229034423828 144.98150634765625 0.5893916487693787 193.41598510742188 0.3205145597457886 0.58792245 0.6962457299232483 True -14 38220 28.092156410217285 0.5408139228820801 132.07687377929688 0.5096501111984253 193.302001953125 0.32004228234291077 0.60080993 0.6565454602241516 True -15 40768 28.11833429336548 0.5382254123687744 109.0931396484375 0.5503674149513245 192.77859497070312 0.3205925226211548 0.6120391 0.6314780712127686 True -16 43316 28.099762201309204 0.9962406158447266 138.90670776367188 0.6383910775184631 192.65428161621094 0.3205235004425049 0.6215258 0.6096208095550537 True -17 45864 28.070048570632935 0.5403344631195068 163.0034942626953 0.6789239048957825 192.4324188232422 0.3219367563724518 0.623526 0.6074870824813843 True -18 48412 28.077946662902832 0.5426568984985352 160.52593994140625 0.4404633939266205 192.30653381347656 0.32336175441741943 0.6243307 0.6108083724975586 True -19 50960 28.084657669067383 0.5513772964477539 151.68777465820312 0.4302900433540344 192.50526428222656 0.3208276927471161 0.62312335 0.6150315999984741 False diff --git a/ENCSR670VQZ/cherimoya.fold_0.performance.tsv b/ENCSR670VQZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c2af67ea901455346b1283bfc131ae4cb25a8b98..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -192.30653381347656 0.4919601082801819 0.32336172461509705 0.06714020669460297 0.6243306994438171 0.5860650539398193 0.6108083724975586 \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_1.evaluate.json b/ENCSR670VQZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a761c6328bb29349fcf2bf5d7eed4aceac673685..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444ZNA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_1.fit.json b/ENCSR670VQZ/cherimoya.fold_1.fit.json deleted file mode 100644 index dbdb135eb657a0a2648e6b895150e66654b1f7b0..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF444ZNA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_1.log b/ENCSR670VQZ/cherimoya.fold_1.log deleted file mode 100644 index 139f43ad65381254dd70f12c5d707272975af7ee..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2589 33.73102831840515 3.7943732738494873 176.685546875 1.1787432432174683 259.5916748046875 0.14817692339420319 0.29820138 4.057065963745117 True -1 5178 28.6207332611084 0.676661491394043 196.28128051757812 1.0981745719909668 227.45838928222656 0.27192798256874084 0.45344582 3.4852166175842285 True -2 7767 28.636134386062622 0.9083800315856934 139.97244262695312 0.7754561901092529 220.69956970214844 0.2907152771949768 0.47287974 1.6284486055374146 True -3 10356 28.648550271987915 0.5920963287353516 197.90887451171875 1.3512146472930908 217.7077178955078 0.298657089471817 0.48953936 1.0968607664108276 True -4 12945 28.52105212211609 0.607736349105835 147.50538635253906 0.5540487170219421 216.25001525878906 0.3035317659378052 0.5049383 1.136552095413208 True -5 15534 28.5076584815979 0.6036415100097656 133.2368621826172 0.8270572423934937 215.12025451660156 0.306673526763916 0.5158498 1.0926555395126343 True -6 18123 28.60519552230835 0.6103305816650391 169.01980590820312 1.1647753715515137 213.82896423339844 0.3115982413291931 0.5279942 1.1555607318878174 True -7 20712 28.51777720451355 0.5957925319671631 139.18096923828125 0.5902187824249268 212.9307098388672 0.31443101167678833 0.53897446 1.0270806550979614 True -8 23301 28.511187076568604 0.6008033752441406 139.9595489501953 0.8506893515586853 211.8190460205078 0.31820589303970337 0.54874235 1.0174767971038818 True -9 25890 28.564319610595703 0.6006209850311279 146.1155548095703 1.1927367448806763 211.15391540527344 0.32069042325019836 0.5580243 0.9286560416221619 True -10 28479 28.589902877807617 0.5967249870300293 134.1649627685547 0.7782394886016846 210.01852416992188 0.32454556226730347 0.5748813 0.9067559242248535 True -11 31068 28.562567949295044 0.6058714389801025 152.60604858398438 0.8105326890945435 209.2589874267578 0.32658055424690247 0.5890225 0.8552873730659485 True -12 33657 28.52164602279663 0.6076679229736328 145.07957458496094 0.7155256867408752 208.75540161132812 0.3276665508747101 0.59887916 0.8238024115562439 True -13 36246 28.51576828956604 0.6060378551483154 158.7036895751953 0.7985721826553345 208.3227996826172 0.3286288380622864 0.6144685 0.7702193856239319 True -14 38835 28.5443012714386 0.6122405529022217 133.1063690185547 0.6090689897537231 207.7112274169922 0.3309202492237091 0.6281591 0.7182952165603638 True -15 41424 28.585778951644897 1.159041404724121 128.35340881347656 0.6668834686279297 207.26495361328125 0.33203279972076416 0.63727194 0.6792483925819397 True -16 44013 28.59572720527649 0.7015295028686523 163.93325805664062 0.578277587890625 207.27561950683594 0.33060380816459656 0.64774615 0.6485007405281067 True -17 46602 28.575326681137085 0.6012167930603027 138.14114379882812 0.6118283867835999 207.01039123535156 0.33223646879196167 0.652273 0.6323217153549194 True -18 49191 28.599026679992676 0.6113510131835938 146.4860382080078 0.5609121918678284 207.1144561767578 0.332070529460907 0.6539505 0.6246973276138306 True -19 51780 28.52026057243347 0.609696626663208 133.43731689453125 0.4719047546386719 207.29017639160156 0.3307965099811554 0.6541296 0.629936695098877 True diff --git a/ENCSR670VQZ/cherimoya.fold_1.performance.tsv b/ENCSR670VQZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0710dd7dd99553cd2fa36c636348c6589fcf9bbd..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -207.29017639160156 0.48395875096321106 0.3307965397834778 0.07642510533332825 0.6541296243667603 0.6175321936607361 0.629936695098877 \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_2.evaluate.json b/ENCSR670VQZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a95412b7498aa56f807f50556f04facb4237bfdb..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444ZNA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_2.fit.json b/ENCSR670VQZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 4db8948773f25a21e439192751e9fe724f7d51d3..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF444ZNA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_2.log b/ENCSR670VQZ/cherimoya.fold_2.log deleted file mode 100644 index 1c8116e44b15b1fb8a0f016a24ccfde98fbcfa4e..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2716 34.037702322006226 3.7865352630615234 218.55995178222656 1.2672371864318848 241.867431640625 0.15095482766628265 0.25725955 4.069261074066162 True -1 5432 29.89578914642334 0.7118875980377197 130.54981994628906 1.1319994926452637 209.64869689941406 0.2731209099292755 0.42734784 3.762225389480591 True -2 8148 29.96262240409851 0.464463472366333 149.68655395507812 0.967510461807251 204.23826599121094 0.2894022464752197 0.44931614 2.0088422298431396 True -3 10864 29.937780141830444 0.4645657539367676 137.66281127929688 1.169734239578247 201.9485626220703 0.29623445868492126 0.48096403 1.4015443325042725 True -4 13580 29.963441133499146 0.464083194732666 133.9396209716797 0.8165359497070312 200.2932891845703 0.30064839124679565 0.50088525 1.2261093854904175 True -5 16296 29.9092800617218 0.46412086486816406 162.52932739257812 1.0548782348632812 199.78192138671875 0.302091121673584 0.5173542 1.0435278415679932 True -6 19012 29.879390954971313 1.0279479026794434 191.05844116210938 1.0117006301879883 198.86082458496094 0.30592694878578186 0.52679205 1.0682213306427002 True -7 21728 29.920251846313477 0.47400784492492676 144.65872192382812 1.307032823562622 197.94837951660156 0.3094950318336487 0.5394664 0.9480099678039551 True -8 24444 29.934134483337402 0.46296215057373047 155.96661376953125 0.7932045459747314 197.38027954101562 0.31152960658073425 0.5520472 0.9390751719474792 True -9 27160 29.929870128631592 0.758803129196167 154.63916015625 0.8461911678314209 196.49618530273438 0.31587520241737366 0.5633108 0.8686274886131287 True -10 29876 29.92388129234314 0.46751952171325684 158.02597045898438 0.7439103126525879 195.94168090820312 0.31831932067871094 0.57297194 0.8517508506774902 True -11 32592 29.957737922668457 0.4625887870788574 128.50514221191406 0.663048267364502 195.30612182617188 0.3199617862701416 0.5877649 0.769405722618103 True -12 35308 29.877454042434692 0.4707484245300293 203.37977600097656 0.8814722895622253 194.8013916015625 0.3210059404373169 0.5998659 0.7321974635124207 True -13 38024 29.920992851257324 0.46798205375671387 200.32125854492188 0.67174232006073 194.22525024414062 0.32343217730522156 0.61048675 0.6837319135665894 True -14 40740 29.871794939041138 0.4640932083129883 132.47218322753906 0.5158761739730835 193.61846923828125 0.32510414719581604 0.6207362 0.6628991961479187 True -15 43456 29.96855902671814 0.46837496757507324 164.6359405517578 0.5183829665184021 193.48619079589844 0.3244962990283966 0.63291526 0.6310155391693115 True -16 46172 29.961917638778687 0.4651041030883789 145.89935302734375 0.5656232833862305 193.23025512695312 0.32588866353034973 0.6392332 0.6224862933158875 True -17 48888 29.9477481842041 1.2941875457763672 158.44375610351562 0.5942060947418213 193.17538452148438 0.32570573687553406 0.6424199 0.6106687784194946 True -18 51604 29.947170972824097 0.47033047676086426 150.4707794189453 0.5217170715332031 193.08604431152344 0.3262796998023987 0.64374655 0.6091147661209106 True -19 54320 29.911746501922607 0.46019887924194336 140.065673828125 0.5609477162361145 193.06817626953125 0.32613036036491394 0.6417353 0.6165633201599121 False diff --git a/ENCSR670VQZ/cherimoya.fold_2.performance.tsv b/ENCSR670VQZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index dbf1df7a2e9533a8a974b1ceea406f936514be83..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -193.08604431152344 0.49052107334136963 0.32627972960472107 0.06866926699876785 0.643746554851532 0.607130229473114 0.6091147661209106 \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_3.evaluate.json b/ENCSR670VQZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7c8bf7aa118c8dda5637eef33ee22095791c5ec5..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444ZNA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_3.fit.json b/ENCSR670VQZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 6faaa064d68fc6a40cbec175be96f4f3f7e9516d..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF444ZNA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_3.log b/ENCSR670VQZ/cherimoya.fold_3.log deleted file mode 100644 index 44a01a20f6bf365bb422e04c851642c2111229bd..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2621 34.8958694934845 3.5588715076446533 182.76486206054688 1.0912888050079346 251.99493408203125 0.14880196750164032 0.27301762 4.325206756591797 True -1 5242 28.84490728378296 0.8519289493560791 140.3271484375 1.1822384595870972 219.52761840820312 0.27499836683273315 0.43457398 3.862039089202881 True -2 7863 28.865303993225098 1.1105010509490967 160.9534912109375 1.1350266933441162 213.69566345214844 0.2886272668838501 0.4501864 2.070960283279419 True -3 10484 28.849661111831665 0.567171573638916 206.78321838378906 1.2135013341903687 211.07870483398438 0.29701557755470276 0.46757132 1.6024309396743774 True -4 13105 28.928566455841064 0.6326184272766113 135.33694458007812 0.7921919822692871 209.44906616210938 0.30086982250213623 0.48550707 1.3007307052612305 True -5 15726 28.96911907196045 0.5615005493164062 164.1876220703125 1.0271551609039307 208.0825958251953 0.3064579665660858 0.49709934 1.2736670970916748 True -6 18347 28.866626501083374 0.5663306713104248 162.9879608154297 0.7398145198822021 207.51492309570312 0.308093786239624 0.5080786 1.1272175312042236 True -7 20968 28.881593704223633 0.5626394748687744 211.42080688476562 1.2069101333618164 206.6664276123047 0.31160128116607666 0.51587903 1.125195860862732 True -8 23589 28.850471019744873 0.5996890068054199 173.55438232421875 0.9785250425338745 206.09559631347656 0.31268370151519775 0.52668554 1.0548161268234253 True -9 26210 28.923312664031982 21.675891876220703 143.63003540039062 0.8534294366836548 205.090576171875 0.3176451325416565 0.5393614 0.9964326620101929 True -10 28831 28.98674511909485 1.134826421737671 162.047119140625 1.0275554656982422 204.1759033203125 0.31989431381225586 0.55069983 0.8851962089538574 True -11 31452 28.91425323486328 0.561112642288208 140.47642517089844 0.6347770094871521 203.35202026367188 0.3229835629463196 0.5670402 0.8340635895729065 True -12 34073 29.606605529785156 0.556952953338623 127.13658905029297 0.6117466688156128 202.74737548828125 0.3240428864955902 0.5827069 0.7436749339103699 True -13 36694 28.89029884338379 0.5614986419677734 143.00607299804688 0.5803107619285583 201.767333984375 0.3279520273208618 0.5951157 0.7507182359695435 True -14 39315 28.97110652923584 0.5909099578857422 129.75289916992188 0.6278013586997986 201.77842712402344 0.3278449773788452 0.6100459 0.6968697905540466 True -15 41936 29.04524302482605 0.5911767482757568 188.00863647460938 0.7645630836486816 201.4568634033203 0.32752928137779236 0.6204739 0.672274112701416 True -16 44557 29.056506156921387 0.5670502185821533 146.67056274414062 0.7661266326904297 201.0782928466797 0.32927843928337097 0.6279757 0.6441558003425598 True -17 47178 29.098735332489014 15.432847261428833 161.4683074951172 0.6817196011543274 200.85850524902344 0.33006832003593445 0.63301045 0.6359286904335022 True -18 49799 28.996063470840454 0.5588321685791016 170.90733337402344 0.39149656891822815 200.6717987060547 0.33120495080947876 0.63574773 0.6325668096542358 True -19 52420 29.04507613182068 0.5609922409057617 162.94027709960938 0.4581630527973175 201.0459442138672 0.32809823751449585 0.6341615 0.6360504627227783 False diff --git a/ENCSR670VQZ/cherimoya.fold_3.performance.tsv b/ENCSR670VQZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fc1b4b648a631953b7befee01414335c0265d98d..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -200.6717987060547 0.4861360788345337 0.33120495080947876 0.0745048075914383 0.6357477307319641 0.6023672819137573 0.6325668096542358 \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_4.evaluate.json b/ENCSR670VQZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 153d56badefdebced1bd1b9653f29e85632b7fe5..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444ZNA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_4.fit.json b/ENCSR670VQZ/cherimoya.fold_4.fit.json deleted file mode 100644 index c6cca13d98970d3c47abbebe775268c0a26ce9ff..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF444ZNA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670VQZ/cherimoya.fold_4.log b/ENCSR670VQZ/cherimoya.fold_4.log deleted file mode 100644 index a3404778ee0f96fcdacbd8bdc047d82c86741d23..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 33.75380802154541 3.730329751968384 179.99658203125 1.1659146547317505 244.89950561523438 0.15557527542114258 0.26888925 4.253842353820801 True -1 5482 30.194910764694214 0.6270146369934082 196.447265625 0.9721680283546448 212.26881408691406 0.277539998292923 0.43112996 3.0473062992095947 True -2 8223 30.1871337890625 0.529541015625 204.72030639648438 1.2274186611175537 207.90794372558594 0.28814026713371277 0.4546551 1.8362879753112793 True -3 10964 30.164539098739624 0.5292327404022217 155.87716674804688 0.8064079284667969 205.8143768310547 0.29481470584869385 0.46977973 1.4981037378311157 True -4 13705 30.176517248153687 0.5300760269165039 174.62924194335938 0.9162862300872803 204.24913024902344 0.3002900779247284 0.4812229 1.3368216753005981 True -5 16446 30.15370535850525 0.5312514305114746 145.0953369140625 0.6728730201721191 203.5246124267578 0.3028777241706848 0.4908811 1.28292715549469 True -6 19187 30.14013957977295 0.53031325340271 197.87677001953125 0.6760725975036621 202.371826171875 0.30674296617507935 0.51105165 1.0317414999008179 True -7 21928 30.177497148513794 0.5474197864532471 139.65211486816406 0.8023938536643982 201.88002014160156 0.30776163935661316 0.5203136 0.9917348027229309 True -8 24669 30.16927433013916 0.530198335647583 130.072998046875 0.8936697244644165 200.9191131591797 0.31177273392677307 0.5343073 0.8944498896598816 True -9 27410 30.19388747215271 0.5286116600036621 115.75377655029297 0.6082078218460083 200.34449768066406 0.313699871301651 0.5426405 0.8685028553009033 True -10 30151 30.311707496643066 0.5369894504547119 158.58978271484375 0.6489947438240051 199.572021484375 0.3164798319339752 0.5551538 0.8093600273132324 True -11 32892 30.223824501037598 0.5314829349517822 153.91026306152344 0.5441100597381592 198.81765747070312 0.31929486989974976 0.5667721 0.768259584903717 True -12 35633 30.172505855560303 0.5289440155029297 155.583740234375 0.7142497301101685 197.97848510742188 0.32224559783935547 0.5791919 0.7067928910255432 True -13 38374 30.16961359977722 0.5337066650390625 162.2344207763672 0.8471075296401978 197.54966735839844 0.3230958878993988 0.5934993 0.6804516315460205 True -14 41115 30.225639581680298 0.5259203910827637 154.48898315429688 0.7303692102432251 197.2461395263672 0.3240351974964142 0.60485446 0.6616630554199219 True -15 43856 30.213576316833496 0.5342750549316406 189.6621551513672 0.6638810634613037 196.9207763671875 0.3246585428714752 0.61446214 0.6427319645881653 True -16 46597 30.218812704086304 1.6859097480773926 209.372314453125 0.6470328569412231 196.189208984375 0.3289894163608551 0.6232934 0.630669891834259 True -17 49338 30.240267992019653 0.5355055332183838 174.9636993408203 0.6739100217819214 196.5215301513672 0.32652944326400757 0.6274446 0.6205487847328186 True -18 52079 30.173635482788086 0.5237634181976318 139.70150756835938 0.4633920192718506 196.3013153076172 0.32782551646232605 0.6284576 0.621722400188446 True -19 54820 30.176258325576782 0.5357398986816406 184.48782348632812 0.38389867544174194 196.3843536376953 0.32714730501174927 0.62617564 0.6261649131774902 False diff --git a/ENCSR670VQZ/cherimoya.fold_4.performance.tsv b/ENCSR670VQZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 261f382dcfeaae58d12f960bbc26508da9dbd09b..0000000000000000000000000000000000000000 --- a/ENCSR670VQZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -196.3013153076172 0.4889434576034546 0.32782551646232605 0.06994006782770157 0.6284576058387756 0.5837897658348083 0.621722400188446 \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_0.evaluate.json b/ENCSR670ZSA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6940e91eb0aa466e6cb9bb76a2b40ff1eb9c6c2e..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038GZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_0.fit.json b/ENCSR670ZSA/cherimoya.fold_0.fit.json deleted file mode 100644 index f31ab1824be8d50c2bc2666c3ccd1b0b63cb556b..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF038GZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_0.log b/ENCSR670ZSA/cherimoya.fold_0.log deleted file mode 100644 index d29f65cb2f447bb7dadd96ab6d78692b93f91b48..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 35.38805389404297 3.4083921909332275 181.4096221923828 0.48232144117355347 289.0130920410156 0.15173770487308502 0.68907976 2.864849805831909 True -1 5536 30.689342498779297 1.2115485668182373 217.09320068359375 0.4335556626319885 281.5439758300781 0.1894696056842804 0.75206196 0.6885272860527039 True -2 8304 30.711565017700195 0.5888550281524658 213.235107421875 0.35964304208755493 279.1941223144531 0.1964278668165207 0.7681915 0.4569820463657379 True -3 11072 30.70360279083252 0.562915563583374 225.77297973632812 0.5181443691253662 278.0014343261719 0.20147472620010376 0.77127004 0.4766187369823456 True -4 13840 30.702998638153076 0.5693025588989258 227.9178466796875 0.4497556686401367 276.67596435546875 0.20879696309566498 0.7704252 0.5271542072296143 False -5 16608 30.81092596054077 0.5644428730010986 262.3162536621094 0.42470037937164307 276.2718505859375 0.2099926918745041 0.7699425 0.5047808289527893 False -6 19376 30.70184063911438 0.5868961811065674 280.1506042480469 0.4933715760707855 275.77313232421875 0.21203568577766418 0.7733887 0.5488593578338623 True -7 22144 30.685285091400146 0.5655968189239502 205.64907836914062 0.5372896790504456 275.4105224609375 0.21421408653259277 0.7747406 0.532655656337738 True -8 24912 30.709511518478394 0.6137690544128418 217.33544921875 0.44141885638237 274.9384765625 0.21625755727291107 0.77546203 0.5239527225494385 True -9 27680 30.71634006500244 0.5535123348236084 212.16661071777344 0.6762776970863342 274.33599853515625 0.21874788403511047 0.78024805 0.4623115062713623 True -10 30448 30.090656995773315 0.5447378158569336 186.3089599609375 0.5241974592208862 274.2770080566406 0.21929287910461426 0.7861164 0.46015089750289917 True -11 33216 30.12571954727173 0.5609982013702393 203.62347412109375 0.35625508427619934 274.009521484375 0.22081820666790009 0.78646725 0.42955732345581055 True -12 35984 30.127640962600708 0.5552926063537598 209.3873291015625 0.2878338396549225 273.7648010253906 0.2210424244403839 0.79367423 0.36595168709754944 True -13 38752 30.114081144332886 1.393303632736206 267.0845947265625 0.41767269372940063 273.3889465332031 0.22268539667129517 0.79774797 0.33904269337654114 True -14 41520 30.100192308425903 0.5411617755889893 230.50515747070312 0.37550944089889526 273.1907653808594 0.22417892515659332 0.80411655 0.3138701915740967 True -15 44288 30.087377786636353 1.64518141746521 213.39236450195312 0.39210304617881775 272.6941833496094 0.22743690013885498 0.80523556 0.2759924829006195 True -16 47056 30.147639513015747 0.5519416332244873 212.1763458251953 0.2548558712005615 272.8843688964844 0.22607849538326263 0.81297517 0.25297272205352783 True -17 49824 30.128297090530396 0.5579719543457031 205.92198181152344 0.2210635542869568 272.99981689453125 0.2249613255262375 0.8137576 0.24359971284866333 True -18 52592 30.214325666427612 0.5592935085296631 225.8430633544922 0.22256040573120117 273.3327331542969 0.2232883870601654 0.8117733 0.2383698672056198 False -19 55360 30.124799013137817 0.5509514808654785 204.83445739746094 0.22076134383678436 273.102783203125 0.2249443084001541 0.81136024 0.24043910205364227 False diff --git a/ENCSR670ZSA/cherimoya.fold_0.performance.tsv b/ENCSR670ZSA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 331868ab43971b8d23deca16d42fd4fab5ac6e09..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -272.99981689453125 0.5166429877281189 0.22496137022972107 0.07107198983430862 0.813757598400116 0.7728241086006165 0.24359971284866333 \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_1.evaluate.json b/ENCSR670ZSA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9773a8e34703b3272d126d3b294160303a01b483..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038GZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_1.fit.json b/ENCSR670ZSA/cherimoya.fold_1.fit.json deleted file mode 100644 index 950e978026a44d907600089d34fa7de42104ed11..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF038GZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_1.log b/ENCSR670ZSA/cherimoya.fold_1.log deleted file mode 100644 index 09db594abc4d0288e81c899a38820d5d4bd133e5..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 34.85804986953735 3.5028553009033203 236.61563110351562 0.7238601446151733 330.08184814453125 0.15940193831920624 0.6820782 2.9073386192321777 True -1 5470 30.429834842681885 0.9841518402099609 204.73670959472656 0.48123064637184143 319.82598876953125 0.20670682191848755 0.75022787 0.8567105531692505 True -2 8205 30.487075090408325 0.7329144477844238 212.9361572265625 0.5237621068954468 317.0242614746094 0.21521927416324615 0.7737164 0.533176839351654 True -3 10940 30.4375958442688 1.0064442157745361 214.64016723632812 0.3403489589691162 315.3818664550781 0.22081685066223145 0.78094184 0.38826724886894226 True -4 13675 30.369070768356323 0.8308196067810059 201.98046875 0.5143215656280518 314.61187744140625 0.2230411022901535 0.7873432 0.4040662348270416 True -5 16410 30.347159147262573 0.7259955406188965 262.96490478515625 0.4623146057128906 313.37664794921875 0.22856856882572174 0.78196895 0.4483770430088043 False -6 19145 30.36875629425049 0.7263607978820801 221.72885131835938 0.5498992204666138 313.10479736328125 0.22898291051387787 0.7868744 0.4402175545692444 False -7 21880 30.332212448120117 0.7296011447906494 190.07461547851562 0.5147161483764648 312.5942687988281 0.23064754903316498 0.78871787 0.4496229887008667 True -8 24615 30.37288808822632 0.7282364368438721 200.27671813964844 0.5290240049362183 311.7254638671875 0.23423346877098083 0.7952754 0.4462299346923828 True -9 27350 30.360839366912842 2.0559139251708984 210.78433227539062 0.3570447564125061 311.0796203613281 0.237580806016922 0.7989145 0.41636475920677185 True -10 30085 30.084957361221313 0.7188911437988281 209.05767822265625 0.4858666658401489 310.8275451660156 0.23817220330238342 0.8067424 0.41682863235473633 True -11 32820 29.938989639282227 0.7632415294647217 195.5279541015625 0.3482387661933899 310.8045349121094 0.2378503382205963 0.81077474 0.3667275607585907 True -12 35555 30.061229705810547 0.7495071887969971 266.66448974609375 0.2752830386161804 310.39959716796875 0.2389020025730133 0.81612265 0.3456967771053314 True -13 38290 29.99311399459839 0.7410693168640137 249.04388427734375 0.2535482943058014 309.9554443359375 0.24083872139453888 0.8194354 0.3197554051876068 True -14 41025 29.9004909992218 0.7355124950408936 232.51158142089844 0.2869933247566223 310.07366943359375 0.24043364822864532 0.8210644 0.3081563413143158 True -15 43760 30.013758420944214 0.7335500717163086 239.27044677734375 0.3608601689338684 310.02740478515625 0.2408323734998703 0.82462037 0.285942941904068 True -16 46495 29.966763019561768 1.0099713802337646 240.65565490722656 0.24602070450782776 309.446044921875 0.24354423582553864 0.8290971 0.27045050263404846 True -17 49230 29.978464603424072 0.7168757915496826 178.12857055664062 0.2150731384754181 309.9003601074219 0.24147340655326843 0.828397 0.2662621736526489 False -18 51965 29.987678289413452 0.7194581031799316 230.0736541748047 0.23324339091777802 309.5236511230469 0.24347853660583496 0.82761866 0.2654976546764374 False -19 54700 29.988944053649902 0.7259242534637451 200.25914001464844 0.209134042263031 310.0351867675781 0.24072076380252838 0.8262034 0.26638948917388916 False diff --git a/ENCSR670ZSA/cherimoya.fold_1.performance.tsv b/ENCSR670ZSA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 54d59547a19fcd06f9a236840330758100a114fe..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.446044921875 0.49919965863227844 0.24354423582553864 0.0770530179142952 0.8290970921516418 0.8056492805480957 0.27045050263404846 \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_2.evaluate.json b/ENCSR670ZSA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2943d6d19dd3353f6fd1ec4a9f5d2afe352663f7..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038GZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_2.fit.json b/ENCSR670ZSA/cherimoya.fold_2.fit.json deleted file mode 100644 index 2754d335e439334a8b6cdd7f12f70d37181ecfe9..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF038GZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_2.log b/ENCSR670ZSA/cherimoya.fold_2.log deleted file mode 100644 index e1a91d35e663850792fce93f6bb32772d88a8614..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2902 37.57707333564758 3.9450252056121826 264.57440185546875 0.86226487159729 295.4941711425781 0.1587161421775818 0.68904036 1.8689218759536743 True -1 5804 32.25769639015198 0.6347160339355469 228.5615234375 0.7602278590202332 286.8890686035156 0.20030343532562256 0.746897 0.7689873576164246 True -2 8706 32.24100923538208 0.5588812828063965 186.00897216796875 0.517741322517395 284.8356628417969 0.2057686299085617 0.75967324 0.47534114122390747 True -3 11608 32.266931772232056 0.5937764644622803 214.1992645263672 0.4199214577674866 283.82989501953125 0.20801696181297302 0.7656014 0.4549826979637146 True -4 14510 32.47443604469299 0.7669243812561035 229.1636199951172 0.4437847137451172 283.1729431152344 0.21139468252658844 0.7699569 0.4824242889881134 True -5 17412 32.33856272697449 0.5653684139251709 225.60006713867188 0.523258626461029 282.58489990234375 0.21441438794136047 0.77106327 0.5008866190910339 True -6 20314 32.34305024147034 0.5550475120544434 188.9145050048828 0.49439260363578796 282.17730712890625 0.21670949459075928 0.7750348 0.519879162311554 True -7 23216 32.2876980304718 0.5639734268188477 194.08877563476562 0.5278559923171997 282.1203918457031 0.2165914624929428 0.777996 0.49314549565315247 True -8 26118 32.22339129447937 0.5732851028442383 190.61444091796875 0.24669542908668518 281.5362548828125 0.21959288418293 0.77935153 0.4791710376739502 True -9 29020 31.69522523880005 0.5434789657592773 209.11785888671875 0.31346595287323 280.9801330566406 0.22239942848682404 0.781695 0.4599197208881378 True -10 31922 31.801610469818115 0.564556360244751 215.8307342529297 0.3229031562805176 280.6968688964844 0.22363826632499695 0.78464526 0.44066908955574036 True -11 34824 31.749396800994873 0.565925121307373 207.49771118164062 0.2870839834213257 280.1861877441406 0.22561462223529816 0.78935677 0.40819796919822693 True -12 37726 31.730136394500732 0.5556178092956543 238.74154663085938 0.47603389620780945 279.85791015625 0.22748294472694397 0.7920575 0.3808830976486206 True -13 40628 31.751399278640747 0.5281362533569336 237.1399383544922 0.23143194615840912 279.5561828613281 0.22856514155864716 0.79457074 0.3394039273262024 True -14 43530 31.76826310157776 0.5483429431915283 216.45120239257812 0.3124763071537018 279.65692138671875 0.22764626145362854 0.8003171 0.3157360851764679 True -15 46432 31.75570559501648 0.5546653270721436 263.0152587890625 0.4176366329193115 279.2632141113281 0.229730024933815 0.803724 0.29365992546081543 True -16 49334 31.770342588424683 0.5321733951568604 217.728271484375 0.22845354676246643 279.50146484375 0.22796465456485748 0.80520034 0.2750667929649353 True -17 52236 31.74293541908264 0.5953412055969238 240.48521423339844 0.1856318563222885 279.37994384765625 0.2286371886730194 0.806504 0.263933002948761 True -18 55138 31.756344318389893 0.5282821655273438 183.53494262695312 0.23971760272979736 279.0462951660156 0.23055389523506165 0.80691123 0.26476630568504333 True -19 58040 31.78529191017151 0.5468540191650391 199.36141967773438 0.25740331411361694 279.2814025878906 0.2288033664226532 0.80478454 0.26579979062080383 False diff --git a/ENCSR670ZSA/cherimoya.fold_2.performance.tsv b/ENCSR670ZSA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f25d2ddb6d8d446f63acce2e6e100faf71722ec6..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -279.0462951660156 0.513167142868042 0.23055389523506165 0.06972422450780869 0.8069112300872803 0.7723836302757263 0.26476630568504333 \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_3.evaluate.json b/ENCSR670ZSA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 39778ac30c37f355a867226de617fc273c409cf1..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038GZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_3.fit.json b/ENCSR670ZSA/cherimoya.fold_3.fit.json deleted file mode 100644 index 1c5d912b1cee65f2cf8d7577d5c8b170d141f28f..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF038GZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_3.log b/ENCSR670ZSA/cherimoya.fold_3.log deleted file mode 100644 index b8f87775fa8b32c283a7336cf3ba9742b81e3f60..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2786 35.625606536865234 5.418280601501465 200.30142211914062 0.4182159900665283 309.4576416015625 0.15708111226558685 0.6765537 3.078083038330078 True -1 5572 30.936388969421387 0.6314725875854492 213.38148498535156 0.5677433609962463 301.0010070800781 0.19832387566566467 0.74074787 0.795399010181427 True -2 8358 30.915369510650635 0.5688674449920654 231.357421875 0.5176420211791992 298.64801025390625 0.20592822134494781 0.7612503 0.5037260055541992 True -3 11144 30.5084445476532 0.5548267364501953 196.65646362304688 0.42805734276771545 297.5684509277344 0.20898659527301788 0.7762048 0.42066946625709534 True -4 13930 30.320792198181152 1.095780611038208 223.95986938476562 0.43307214975357056 296.71575927734375 0.2122800350189209 0.7712154 0.4746723473072052 False -5 16716 30.37639808654785 0.565037727355957 238.697021484375 0.6095155477523804 296.791015625 0.21151286363601685 0.7686464 0.4899064898490906 False -6 19502 30.3621563911438 0.5721142292022705 215.50762939453125 0.4837256968021393 296.1837463378906 0.21397671103477478 0.77103865 0.5005368590354919 False -7 22288 30.349363327026367 0.8522510528564453 227.7744140625 0.33130940794944763 295.5406799316406 0.21655260026454926 0.7709801 0.4910724461078644 False -8 25074 30.33465313911438 0.5597984790802002 220.4132080078125 0.3329005539417267 295.5206604003906 0.21669700741767883 0.77906835 0.5104066133499146 True -9 27860 30.313839435577393 0.553962230682373 191.23104858398438 0.3034866452217102 295.0343933105469 0.21904031932353973 0.78085554 0.4815658926963806 True -10 30646 30.37118911743164 0.5596492290496826 235.06820678710938 0.4091893434524536 294.78729248046875 0.22009612619876862 0.7829335 0.4308376908302307 True -11 33432 30.358519554138184 0.5604109764099121 232.63980102539062 0.35425835847854614 294.2640686035156 0.22262908518314362 0.7878278 0.4207212030887604 True -12 36218 30.314378023147583 0.5555050373077393 180.451171875 0.5075631141662598 293.90435791015625 0.22442707419395447 0.7927556 0.3811921179294586 True -13 39004 30.332570791244507 0.5503361225128174 205.56219482421875 0.24353569746017456 293.5456848144531 0.22582532465457916 0.79891986 0.3471057713031769 True -14 41790 30.36632990837097 0.5576698780059814 185.80206298828125 0.41062724590301514 293.6571044921875 0.22498495876789093 0.80402064 0.3226783871650696 True -15 44576 30.349695920944214 0.6004719734191895 259.9222412109375 0.3742527365684509 293.5696716308594 0.22541970014572144 0.8071932 0.3073166608810425 True -16 47362 30.425185680389404 0.562363862991333 228.47848510742188 0.33078688383102417 293.3260803222656 0.2263036072254181 0.810896 0.2857724726200104 True -17 50148 30.3478262424469 0.5542798042297363 247.45457458496094 0.24158547818660736 293.4362487792969 0.22559823095798492 0.8092071 0.28118467330932617 False -18 52934 30.3742892742157 0.5600440502166748 221.07943725585938 0.27050456404685974 293.7282409667969 0.22406570613384247 0.8106108 0.2800242006778717 False -19 55720 30.405627489089966 0.5569350719451904 198.0377960205078 0.2371416836977005 293.7586669921875 0.22407762706279755 0.809946 0.2815442383289337 False diff --git a/ENCSR670ZSA/cherimoya.fold_3.performance.tsv b/ENCSR670ZSA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a712f660eed9765d6cc090805a0590297358b671..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -293.3260803222656 0.5103878974914551 0.22630362212657928 0.07229850441217422 0.8108959794044495 0.7737389802932739 0.2857724726200104 \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_4.evaluate.json b/ENCSR670ZSA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6f467d0b10f0d417a0e5d551e3e293d80e912c31..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038GZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_4.fit.json b/ENCSR670ZSA/cherimoya.fold_4.fit.json deleted file mode 100644 index 615f3588c6b62ea4bf1fea934ba7d887d7b9e61b..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF038GZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR670ZSA/cherimoya.fold_4.log b/ENCSR670ZSA/cherimoya.fold_4.log deleted file mode 100644 index 0765bee7a301f01a1cab8d53e9374619b3ab3812..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2866 36.481898069381714 3.8063459396362305 284.1440124511719 0.4621850252151489 288.0592346191406 0.15385837852954865 0.6750204 2.825374126434326 True -1 5732 31.887025594711304 0.6189045906066895 207.00079345703125 0.5232840776443481 280.7670593261719 0.19047822058200836 0.7451454 0.5771420001983643 True -2 8598 31.826311111450195 0.6054303646087646 267.034912109375 0.5642377138137817 278.70880126953125 0.19669291377067566 0.75624603 0.40796172618865967 True -3 11464 31.85734486579895 0.6180200576782227 248.033447265625 0.5137437582015991 277.2064208984375 0.2037244439125061 0.7621476 0.3487796485424042 True -4 14330 31.87341046333313 0.6071739196777344 190.033203125 0.6047029495239258 276.66888427734375 0.2053932100534439 0.76471245 0.338506817817688 True -5 17196 31.738457679748535 0.6157920360565186 246.76638793945312 0.5080713629722595 276.1667785644531 0.20729999244213104 0.7644339 0.3540300130844116 False -6 20062 31.24805235862732 25.292996883392334 244.8220672607422 0.4268157482147217 275.75103759765625 0.20951297879219055 0.7682025 0.36312630772590637 True -7 22928 31.820303916931152 1.475243091583252 241.38975524902344 0.3433592915534973 275.5400085449219 0.210281103849411 0.7739669 0.3685687482357025 True -8 25794 31.34791350364685 1.580143928527832 252.17933654785156 0.37094706296920776 274.81829833984375 0.2142064869403839 0.7768309 0.3574437201023102 True -9 28660 31.31150794029236 0.6061134338378906 271.95428466796875 0.3043683171272278 274.52032470703125 0.21515026688575745 0.7753899 0.357832133769989 False -10 31526 31.258597373962402 0.6011316776275635 236.36578369140625 0.3469482362270355 274.2810974121094 0.21582013368606567 0.78394526 0.3200048804283142 True -11 34392 31.359459161758423 0.6038501262664795 247.56228637695312 0.45669710636138916 274.02337646484375 0.21723686158657074 0.7875516 0.31925931572914124 True -12 37258 31.246060371398926 0.6100575923919678 230.79534912109375 0.21741659939289093 273.7546081542969 0.2183060199022293 0.7888878 0.3053252398967743 True -13 40124 31.250675916671753 0.6024303436279297 253.27845764160156 0.43382641673088074 273.58251953125 0.21963265538215637 0.79273117 0.30154523253440857 True -14 42990 31.397095441818237 1.1426692008972168 194.38697814941406 0.2573598027229309 273.1871032714844 0.22124804556369781 0.80038595 0.27486154437065125 True -15 45856 31.414782762527466 0.6083245277404785 230.67327880859375 0.24154475331306458 273.4275207519531 0.21962568163871765 0.80545694 0.26029133796691895 True -16 48722 31.438941478729248 0.6026806831359863 190.0234375 0.27476704120635986 273.06610107421875 0.2218027114868164 0.8060995 0.25443336367607117 True -17 51588 31.43524432182312 0.6178314685821533 213.35513305664062 0.22562015056610107 273.2276306152344 0.22124862670898438 0.8072701 0.24657858908176422 True -18 54454 31.273775339126587 0.5876851081848145 225.97216796875 0.20535914599895477 273.3609619140625 0.2207108438014984 0.80463773 0.24530240893363953 False -19 57320 31.28675603866577 0.5873367786407471 211.80691528320312 0.2011088877916336 273.42999267578125 0.22002418339252472 0.80456364 0.24306830763816833 False diff --git a/ENCSR670ZSA/cherimoya.fold_4.performance.tsv b/ENCSR670ZSA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 26eb3089dc7809af1abbc27035713a3a43858021..0000000000000000000000000000000000000000 --- a/ENCSR670ZSA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -273.2276306152344 0.5177898406982422 0.221248596906662 0.06741049885749817 0.8072701096534729 0.7610186338424683 0.24657858908176422 \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_0.evaluate.json b/ENCSR671YPX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 06c7378688deef2b37a366db76a9960dc46bcce6..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF647FBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_0.fit.json b/ENCSR671YPX/cherimoya.fold_0.fit.json deleted file mode 100644 index 57de6005a1c8b67bcd4f16c6e701d036ad2907b9..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF647FBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_0.log b/ENCSR671YPX/cherimoya.fold_0.log deleted file mode 100644 index 854e9792c4ffda77839bf2a40fcf89c8f55cdbb0..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 35.38913631439209 3.558223009109497 511.66876220703125 0.2090461552143097 584.7772216796875 0.27284419536590576 0.79850036 4.232893943786621 True -1 5492 30.494742393493652 0.9532971382141113 500.1241455078125 0.23074112832546234 541.7327270507812 0.3350655138492584 0.8431836 0.7256803512573242 True -2 8238 30.47282099723816 0.6006708145141602 433.5314636230469 0.20748913288116455 533.5967407226562 0.3426980674266815 0.8518583 0.3955586552619934 True -3 10984 30.413815021514893 0.601097822189331 397.85302734375 0.14124014973640442 527.3587036132812 0.3526571989059448 0.8640307 0.31228190660476685 True -4 13730 30.427777767181396 0.5987906455993652 444.9455261230469 0.27543017268180847 525.7622680664062 0.35435906052589417 0.86573344 0.3012833893299103 True -5 16476 29.927372217178345 1.9077136516571045 517.18798828125 0.22984102368354797 523.6417846679688 0.3576216995716095 0.8745964 0.21329815685749054 True -6 19222 29.78527808189392 0.6009430885314941 370.41192626953125 0.18389859795570374 522.6055297851562 0.35908225178718567 0.8761183 0.21538908779621124 True -7 21968 29.766167402267456 0.5842447280883789 460.60821533203125 0.16263195872306824 520.677001953125 0.36195969581604004 0.8827332 0.2054196149110794 True -8 24714 29.755232334136963 0.5954201221466064 457.510986328125 0.3101242184638977 520.0337524414062 0.36283648014068604 0.88055336 0.2267899066209793 False -9 27460 29.77710270881653 0.5772111415863037 485.3479309082031 0.2706475853919983 518.3523559570312 0.365792840719223 0.88520175 0.1967398226261139 True -10 30206 29.758878469467163 0.5956614017486572 417.66363525390625 0.203743115067482 517.6134033203125 0.36656758189201355 0.8911531 0.19072845578193665 True -11 32952 29.788650274276733 0.5966353416442871 475.13629150390625 0.22125573456287384 516.8800659179688 0.3670680820941925 0.89017344 0.18657048046588898 False -12 35698 29.758118867874146 0.5928645133972168 460.34423828125 0.17916466295719147 515.0498046875 0.3703988492488861 0.8952627 0.17559553682804108 True -13 38444 29.749611139297485 0.5827562808990479 439.1673889160156 0.2008131444454193 514.693359375 0.3705207407474518 0.8986632 0.16450956463813782 True -14 41190 29.744964122772217 0.5741755962371826 427.03265380859375 0.14574140310287476 514.0759887695312 0.3715828061103821 0.9007403 0.15656563639640808 True -15 43936 29.796329975128174 0.5961618423461914 433.3600158691406 0.11244536936283112 513.1138305664062 0.3736688196659088 0.9018659 0.14853990077972412 True -16 46682 29.7665057182312 0.5818524360656738 380.332275390625 0.1929406374692917 512.228515625 0.3749832510948181 0.9049676 0.14225149154663086 True -17 49428 29.754741191864014 0.5707461833953857 430.66180419921875 0.12361003458499908 512.450927734375 0.3739888370037079 0.9059153 0.1411074846982956 True -18 52174 29.76539635658264 0.5862312316894531 464.4658203125 0.12661771476268768 512.09326171875 0.37523239850997925 0.90560824 0.14082030951976776 False -19 54920 29.785493850708008 0.5828256607055664 448.6109924316406 0.18951892852783203 512.2789306640625 0.3744031488895416 0.9045988 0.14122144877910614 False diff --git a/ENCSR671YPX/cherimoya.fold_0.performance.tsv b/ENCSR671YPX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ef9da83af222dbfda75676b16764ef63f68b9771..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -512.450927734375 0.4020683169364929 0.3739888370037079 0.1452404260635376 0.9059153199195862 0.8765659332275391 0.1411074846982956 \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_1.evaluate.json b/ENCSR671YPX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a710a0c9744ef23e7baebf551596b70dd136f923..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF647FBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_1.fit.json b/ENCSR671YPX/cherimoya.fold_1.fit.json deleted file mode 100644 index 3dee8700728919225444bb483efd4dc803e670eb..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF647FBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_1.log b/ENCSR671YPX/cherimoya.fold_1.log deleted file mode 100644 index e7aa9a2329a7d5946186804f37283676b21f6325..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 35.024540185928345 3.5558176040649414 518.0936279296875 0.33430537581443787 693.9996337890625 0.27531781792640686 0.78993505 4.899075031280518 True -1 5424 29.81230401992798 0.708928108215332 430.5422668457031 0.33539751172065735 633.9403076171875 0.3505118787288666 0.83970326 1.093801498413086 True -2 8136 30.082225799560547 0.6726062297821045 495.68035888671875 0.2397388070821762 619.1491088867188 0.36602774262428284 0.853236 0.46571609377861023 True -3 10848 30.02683186531067 0.6630513668060303 374.4742126464844 0.2225695103406906 614.6574096679688 0.37028029561042786 0.8571904 0.40414637327194214 True -4 13560 30.055129528045654 0.6439929008483887 448.7975769042969 0.24005967378616333 611.6757202148438 0.3739582598209381 0.8650648 0.30477380752563477 True -5 16272 30.153442859649658 0.664158821105957 438.9940185546875 0.1808762401342392 608.4161376953125 0.37830978631973267 0.8693037 0.2615143656730652 True -6 18984 30.00391411781311 0.6613647937774658 460.32745361328125 0.21715688705444336 607.0985717773438 0.3802308738231659 0.8742823 0.25078415870666504 True -7 21696 29.515278100967407 0.651019811630249 520.5651245117188 0.18998223543167114 604.80615234375 0.3823048770427704 0.87931275 0.23155005276203156 True -8 24408 29.42790150642395 0.6522138118743896 475.37469482421875 0.18318739533424377 602.1596069335938 0.3865004777908325 0.8814413 0.23626306653022766 True -9 27120 29.41416835784912 0.653782844543457 431.8106384277344 0.1746198832988739 601.3126220703125 0.38739997148513794 0.8843633 0.2294228971004486 True -10 29832 29.45941472053528 0.6407802104949951 462.3703918457031 0.17076584696769714 599.5135498046875 0.3889724612236023 0.89107203 0.2066735178232193 True -11 32544 29.47469997406006 0.6332089900970459 501.93280029296875 0.24121876060962677 596.4647827148438 0.3941650092601776 0.89202696 0.2063300907611847 True -12 35256 29.40713334083557 0.6498105525970459 433.0308532714844 0.1788146197795868 595.90380859375 0.3934885263442993 0.8951756 0.19435563683509827 True -13 37968 29.371309757232666 0.6473724842071533 425.1741943359375 0.20198780298233032 593.7427978515625 0.3968193531036377 0.8976676 0.18663617968559265 True -14 40680 29.367600440979004 0.6673882007598877 447.21600341796875 0.12870904803276062 593.104248046875 0.3968981206417084 0.90248734 0.1779794991016388 True -15 43392 29.68381428718567 30.83620309829712 425.32049560546875 0.14711397886276245 592.9843139648438 0.3967429995536804 0.90326715 0.1721816509962082 True -16 46104 29.52432632446289 22.094735145568848 419.12322998046875 0.16573533415794373 591.0740356445312 0.399808794260025 0.90496254 0.16665689647197723 True -17 48816 29.609689950942993 26.28127646446228 438.174560546875 0.08273238688707352 591.1409301757812 0.3994198143482208 0.90640396 0.16647574305534363 True -18 51528 29.58555579185486 1.2825069427490234 434.8590087890625 0.09041550010442734 592.3797607421875 0.3970600664615631 0.9057725 0.16538949310779572 False -19 54240 29.591020107269287 0.6773393154144287 483.6061096191406 0.09793645143508911 591.7938232421875 0.39860376715660095 0.90663916 0.16727648675441742 True diff --git a/ENCSR671YPX/cherimoya.fold_1.performance.tsv b/ENCSR671YPX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0c9c1f5f6360837815f639448ca1b02d3470d43f..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -591.7938232421875 0.38050737977027893 0.39860373735427856 0.16594207286834717 0.9066391587257385 0.8966732621192932 0.16727648675441742 \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_2.evaluate.json b/ENCSR671YPX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 63a0d5103ddfb81a365b4dfd3e6f4a01b12c4b2c..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF647FBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_2.fit.json b/ENCSR671YPX/cherimoya.fold_2.fit.json deleted file mode 100644 index 236b6c225693db25d62676a6afc92a1f8f9f5bef..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF647FBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_2.log b/ENCSR671YPX/cherimoya.fold_2.log deleted file mode 100644 index 93383ad29954a68829e3df777ee1152058fca12c..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2890 36.83325147628784 3.563565492630005 451.4720458984375 0.36885809898376465 614.3766479492188 0.27393004298210144 0.79317355 4.008760452270508 True -1 5780 32.05019545555115 0.5752005577087402 580.5575561523438 0.29038161039352417 565.4859008789062 0.33989834785461426 0.8412272 0.9084760546684265 True -2 8670 31.461883068084717 0.7403926849365234 498.16400146484375 0.276567667722702 555.3441162109375 0.3529721200466156 0.85234416 0.4097312092781067 True -3 11560 31.412245750427246 0.6017532348632812 505.6230773925781 0.22066183388233185 550.837158203125 0.3581279218196869 0.8569544 0.35417798161506653 True -4 14450 31.35142683982849 0.5967590808868408 541.70556640625 0.2303057163953781 549.617919921875 0.3603259325027466 0.8585449 0.2581828236579895 True -5 17340 31.30785369873047 1.3649952411651611 461.97509765625 0.2843223214149475 548.0870361328125 0.3623816668987274 0.8656746 0.24407042562961578 True -6 20230 31.330485820770264 0.6691899299621582 496.1820373535156 0.15323063731193542 546.621337890625 0.36478808522224426 0.8675687 0.24261097609996796 True -7 23120 31.34304141998291 0.5573272705078125 437.65521240234375 0.19102464616298676 544.3975830078125 0.36739155650138855 0.8737728 0.21326054632663727 True -8 26010 31.357574701309204 0.5486948490142822 418.3442077636719 0.18761710822582245 542.5379028320312 0.3711148798465729 0.87617296 0.23560868203639984 True -9 28900 31.340949535369873 0.5617012977600098 485.8200378417969 0.11901214718818665 541.902587890625 0.3704240620136261 0.8818359 0.20137467980384827 True -10 31790 31.342341661453247 1.631744384765625 505.4520263671875 0.21188358962535858 540.549072265625 0.3723694980144501 0.88470423 0.19497714936733246 True -11 34680 31.39087748527527 0.5992059707641602 430.8544616699219 0.1293562948703766 539.583251953125 0.37425222992897034 0.8878591 0.18493372201919556 True -12 37570 31.35405445098877 0.56951904296875 372.891845703125 0.13561514019966125 537.1815185546875 0.3784421980381012 0.88935596 0.1802646964788437 True -13 40460 31.36723279953003 0.594296932220459 391.2708740234375 0.16167522966861725 535.6480712890625 0.3798350691795349 0.8912079 0.17102795839309692 True -14 43350 31.3907790184021 0.5871396064758301 457.099609375 0.14066237211227417 535.0711059570312 0.3802684247493744 0.89305735 0.16686001420021057 True -15 46240 31.413268089294434 0.5811872482299805 446.52557373046875 0.13762250542640686 534.5570678710938 0.3806123733520508 0.8978893 0.15790314972400665 True -16 49130 31.408157348632812 0.5707533359527588 433.78411865234375 0.17325086891651154 533.6995849609375 0.38333627581596375 0.8990316 0.1557673215866089 True -17 52020 31.394437074661255 0.9193744659423828 483.3060607910156 0.15267036855220795 534.4517822265625 0.38130906224250793 0.8980131 0.15453287959098816 False -18 54910 31.40979552268982 0.5826497077941895 423.4700012207031 0.12717467546463013 533.7714233398438 0.3830975592136383 0.89969134 0.1549621820449829 True -19 57800 31.388071298599243 0.5573153495788574 457.0699768066406 0.15542927384376526 534.69970703125 0.3808761537075043 0.89910257 0.15561096370220184 False diff --git a/ENCSR671YPX/cherimoya.fold_2.performance.tsv b/ENCSR671YPX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8c0cd2eb32e133f34dd7cecf1fdecd0d9facb39b..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -533.7714233398438 0.39541491866111755 0.3830975890159607 0.1456640064716339 0.8996913433074951 0.8778224587440491 0.1549621820449829 \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_3.evaluate.json b/ENCSR671YPX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 092c16aba9d12832d5de0e8e289ef6f5a7aa5e59..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF647FBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_3.fit.json b/ENCSR671YPX/cherimoya.fold_3.fit.json deleted file mode 100644 index 8bdf3471da7b398c10016c6f723c9415d690e3b0..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF647FBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_3.log b/ENCSR671YPX/cherimoya.fold_3.log deleted file mode 100644 index a46239ac35b97292f7ee9ab39861ab71727d5242..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 35.137107133865356 3.395306348800659 478.5043640136719 0.2956885099411011 579.0198974609375 0.2829521894454956 0.7891392 5.235849857330322 True -1 5502 30.51847267150879 0.7272317409515381 403.961669921875 0.3628431260585785 534.999267578125 0.343512624502182 0.838497 0.7284839153289795 True -2 8253 30.50154209136963 0.6639032363891602 479.20318603515625 0.2364751696586609 527.4779052734375 0.35313680768013 0.85392714 0.3740944266319275 True -3 11004 29.909534454345703 0.5491867065429688 470.42657470703125 0.28000912070274353 523.6520385742188 0.3599475622177124 0.86189437 0.32868096232414246 True -4 13755 29.950286626815796 1.2831957340240479 475.2678527832031 0.22984039783477783 522.2133178710938 0.3603980541229248 0.8644281 0.23726169764995575 True -5 16506 29.89941644668579 0.5599172115325928 401.9515380859375 0.3265039920806885 521.29931640625 0.36183974146842957 0.8680093 0.22745738923549652 True -6 19257 29.88570785522461 0.5480389595031738 501.0345458984375 0.2755684554576874 519.8299560546875 0.3641916513442993 0.8697949 0.21607568860054016 True -7 22008 29.80534315109253 0.5420753955841064 504.2043151855469 0.3166903257369995 517.4196166992188 0.36815571784973145 0.8732857 0.2067801058292389 True -8 24759 29.77912449836731 0.5444331169128418 406.19122314453125 0.1990768313407898 516.3535766601562 0.36959776282310486 0.8764936 0.20322725176811218 True -9 27510 29.934980392456055 0.5548560619354248 440.489501953125 0.25437259674072266 515.2051391601562 0.3721988797187805 0.87977844 0.2006189376115799 True -10 30261 29.840340614318848 0.5382590293884277 448.7107238769531 0.22933022677898407 513.9429321289062 0.373744398355484 0.88269484 0.19401927292346954 True -11 33012 29.817623615264893 0.5438156127929688 489.1619873046875 0.15099692344665527 512.8389282226562 0.37452268600463867 0.8866567 0.18984651565551758 True -12 35763 29.808779001235962 0.5336546897888184 505.04644775390625 0.2043341100215912 511.5715637207031 0.37678879499435425 0.88922703 0.18384084105491638 True -13 38514 29.828693151474 0.8975493907928467 449.6678466796875 0.16501419246196747 510.7225646972656 0.37775149941444397 0.89271635 0.177571102976799 True -14 41265 29.837764263153076 1.4426794052124023 430.1605529785156 0.18551334738731384 509.3564453125 0.3800574839115143 0.89323586 0.17087028920650482 True -15 44016 29.8487708568573 0.5433070659637451 485.55816650390625 0.1719592660665512 508.74212646484375 0.3798901438713074 0.89684343 0.16632896661758423 True -16 46767 29.84957504272461 0.5420467853546143 469.807861328125 0.09885770082473755 508.2094421386719 0.38061627745628357 0.8975433 0.16220657527446747 True -17 49518 29.838085889816284 0.5553488731384277 432.5506591796875 0.1688656210899353 507.4284362792969 0.38272029161453247 0.89992326 0.15867088735103607 True -18 52269 29.836756229400635 0.5446271896362305 468.29705810546875 0.1253383457660675 508.5572814941406 0.37944433093070984 0.89839214 0.15915566682815552 False -19 55020 29.828848361968994 0.5545132160186768 417.17742919921875 0.16004137694835663 508.30279541015625 0.38073354959487915 0.8982584 0.15979930758476257 False diff --git a/ENCSR671YPX/cherimoya.fold_3.performance.tsv b/ENCSR671YPX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 30314e424c81c02135cd470177abe5f73f22c9a5..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -507.4284362792969 0.3989125192165375 0.38272029161453247 0.14516513049602509 0.8999232649803162 0.8657624125480652 0.15867088735103607 \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_4.evaluate.json b/ENCSR671YPX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f33252434d666aa53b5d8e0549f24952e8c98256..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF647FBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_4.fit.json b/ENCSR671YPX/cherimoya.fold_4.fit.json deleted file mode 100644 index f957157bb362b0388370e3280afeea6ae686cc2f..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF647FBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR671YPX/cherimoya.fold_4.log b/ENCSR671YPX/cherimoya.fold_4.log deleted file mode 100644 index ffdd54dfdd8ea5f80d277c5b309634139bd8843f..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2805 35.87085795402527 3.4632017612457275 425.8872985839844 0.23314625024795532 558.8734741210938 0.2754354178905487 0.7965915 3.7546958923339844 True -1 5610 31.075815677642822 0.6791338920593262 478.75946044921875 0.22921131551265717 518.9738159179688 0.33483636379241943 0.83418417 0.7514199018478394 True -2 8415 30.866363525390625 13.636391639709473 443.22991943359375 0.49114468693733215 513.2485961914062 0.3419651985168457 0.84631443 0.3432881534099579 True -3 11220 30.510933876037598 21.19854164123535 475.83197021484375 0.26605501770973206 508.7386779785156 0.34752321243286133 0.85559446 0.27444925904273987 True -4 14025 30.387582778930664 0.6122610569000244 460.0093994140625 0.4584980010986328 508.0604248046875 0.34875139594078064 0.8573224 0.22773145139217377 True -5 16830 30.40483331680298 0.6320536136627197 546.4493408203125 0.30004483461380005 503.642822265625 0.3562083840370178 0.8669714 0.2004513293504715 True -6 19635 30.379582166671753 0.5789198875427246 475.2665710449219 0.4499616324901581 502.57025146484375 0.3575856685638428 0.8712222 0.21508516371250153 True -7 22440 30.398689031600952 0.6062040328979492 465.06488037109375 0.19838684797286987 501.406005859375 0.3588728606700897 0.8780507 0.20240338146686554 True -8 25245 30.364431142807007 0.6038763523101807 484.18731689453125 0.16418683528900146 499.6453857421875 0.3621082603931427 0.8815524 0.1873190551996231 True -9 28050 30.434635877609253 1.601393699645996 463.45318603515625 0.17128129303455353 498.0065002441406 0.36486002802848816 0.88604337 0.1774541735649109 True -10 30855 30.48591160774231 0.5946159362792969 446.3531494140625 0.15199434757232666 497.6530456542969 0.3659383952617645 0.8848491 0.17470091581344604 False -11 33660 30.49368715286255 0.5817162990570068 485.4451599121094 0.21006816625595093 497.8438415527344 0.3642675280570984 0.8887112 0.17266327142715454 True -12 36465 30.421574592590332 0.5984127521514893 472.51513671875 0.19224978983402252 496.4391174316406 0.36659425497055054 0.8919101 0.16296181082725525 True -13 39270 30.46482491493225 0.622229814529419 491.124267578125 0.16829462349414825 495.3890075683594 0.368625283241272 0.89575064 0.1542518436908722 True -14 42075 30.435412168502808 0.6986029148101807 447.466064453125 0.2044215053319931 494.4471435546875 0.3706865608692169 0.89882976 0.14624331891536713 True -15 44880 30.467385292053223 0.5929441452026367 432.8194580078125 0.0818190947175026 493.90960693359375 0.371698796749115 0.89997643 0.1418655663728714 True -16 47685 30.50372076034546 0.5924637317657471 451.9326171875 0.11555828154087067 493.78521728515625 0.3717230558395386 0.9012607 0.13756121695041656 True -17 50490 30.43923044204712 0.5837550163269043 408.0290222167969 0.1353427618741989 494.6184997558594 0.3696950376033783 0.903551 0.1354074478149414 True -18 53295 31.949223041534424 0.5948491096496582 386.02520751953125 0.12112142890691757 494.3005676269531 0.36979833245277405 0.9043292 0.134796142578125 True -19 56100 30.43890380859375 0.5942282676696777 411.21978759765625 0.13114990293979645 494.10552978515625 0.3705650269985199 0.9026726 0.13545873761177063 False diff --git a/ENCSR671YPX/cherimoya.fold_4.performance.tsv b/ENCSR671YPX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5411d50540aeead0ae3032dab7d2e340ea32f959..0000000000000000000000000000000000000000 --- a/ENCSR671YPX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -494.3005676269531 0.40616941452026367 0.3697982728481293 0.14080572128295898 0.9043291807174683 0.8708312511444092 0.134796142578125 \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_0.evaluate.json b/ENCSR672EWY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a59a25573bd934cc2096e0c391243632fffe3d51..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF815QLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_0.fit.json b/ENCSR672EWY/cherimoya.fold_0.fit.json deleted file mode 100644 index fd6f88563dedd4bf9f80b2e3f48e00e633880f0c..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF815QLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_0.log b/ENCSR672EWY/cherimoya.fold_0.log deleted file mode 100644 index 3a342de7983ffeac6467903bb830046d997e86ad..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2695 34.35474920272827 4.201400518417358 1362.718017578125 1.0109742879867554 1779.35009765625 0.27259135246276855 0.35318112 8.732391357421875 True -1 5390 30.052884340286255 0.8639230728149414 1060.649169921875 0.820722222328186 1443.9814453125 0.4352276921272278 0.46565717 4.261223793029785 True -2 8085 30.073256254196167 0.6875126361846924 1224.53076171875 0.6501743793487549 1395.589111328125 0.4496150612831116 0.47401583 1.8229376077651978 True -3 10780 30.028263807296753 3.3549137115478516 1066.439208984375 0.8408151865005493 1349.1895751953125 0.46681883931159973 0.5070077 1.3194900751113892 True -4 13475 30.025699377059937 0.7117526531219482 1094.7603759765625 0.7203855514526367 1332.9776611328125 0.47258460521698 0.52457964 1.528207778930664 True -5 16170 29.978955268859863 2.548921585083008 1341.4515380859375 1.0160468816757202 1319.7742919921875 0.4800630509853363 0.53375185 1.1171976327896118 True -6 18865 30.060510635375977 0.5561153888702393 983.5777587890625 0.5835257768630981 1312.885498046875 0.48070818185806274 0.54444844 1.0424516201019287 True -7 21560 29.95272397994995 0.571894645690918 1034.9798583984375 0.537216305732727 1302.3731689453125 0.4867404103279114 0.55004185 0.9814451932907104 True -8 24255 29.964919328689575 0.5687973499298096 977.782470703125 0.44634753465652466 1288.800537109375 0.4946707487106323 0.56593883 0.8872575163841248 True -9 26950 30.008578300476074 0.5719449520111084 1350.111083984375 0.7099453210830688 1279.2685546875 0.49980199337005615 0.5803356 0.8438358306884766 True -10 29645 29.99493908882141 0.5756270885467529 1008.7181396484375 0.5047420263290405 1274.068359375 0.5002456903457642 0.5935316 0.7889565825462341 True -11 32340 29.98291850090027 0.5637743473052979 1151.5308837890625 0.7380994558334351 1267.4212646484375 0.5031529068946838 0.6057846 0.7964048981666565 True -12 35035 29.98174810409546 0.5803055763244629 1105.135009765625 0.40920931100845337 1262.32958984375 0.5041334629058838 0.619965 0.6770381331443787 True -13 37730 29.962453842163086 0.5782747268676758 1015.736083984375 0.5554778575897217 1255.115478515625 0.5073136687278748 0.6310789 0.6567817330360413 True -14 40425 29.960627555847168 0.5702729225158691 1116.4276123046875 0.5102010369300842 1247.6761474609375 0.5115284323692322 0.643664 0.6312604546546936 True -15 43120 29.99525237083435 2.1193995475769043 1008.7647705078125 0.6769778728485107 1243.722900390625 0.5117934346199036 0.655232 0.5923048257827759 True -16 45815 30.03500461578369 0.5667097568511963 1081.640380859375 0.5155059099197388 1243.4649658203125 0.5107096433639526 0.6611311 0.568206250667572 True -17 48510 29.973904132843018 0.571101188659668 1017.3841552734375 0.6485776305198669 1239.98193359375 0.512693464756012 0.66561383 0.5540561079978943 True -18 51205 29.971839904785156 1.1343138217926025 946.63134765625 0.6079121828079224 1238.9947509765625 0.513787031173706 0.66588485 0.5494565367698669 True -19 53900 29.986589431762695 0.5850450992584229 998.243896484375 0.4396865963935852 1240.896240234375 0.512091875076294 0.66576505 0.5492546558380127 False diff --git a/ENCSR672EWY/cherimoya.fold_0.performance.tsv b/ENCSR672EWY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 428934187bf59d9224932f26b00f3039ef834ed2..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1238.9947509765625 0.2941873073577881 0.513787031173706 0.25441354513168335 0.6658848524093628 0.6238440275192261 0.5494565367698669 \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_1.evaluate.json b/ENCSR672EWY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 03b981d1589afbc7ce1854974e07c8be775dc104..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF815QLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_1.fit.json b/ENCSR672EWY/cherimoya.fold_1.fit.json deleted file mode 100644 index 451a93f14408dfac3340e7a5c3bb2e717de22b78..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF815QLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_1.log b/ENCSR672EWY/cherimoya.fold_1.log deleted file mode 100644 index 987fd045fae9f00cb3f3c1bcc8686a631c8b237f..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2717 34.856650590896606 6.064882755279541 1187.353759765625 0.7872055172920227 1914.8441162109375 0.2665799558162689 0.37379393 8.901873588562012 True -1 5434 30.340726613998413 1.7540502548217773 1107.0556640625 0.9049007296562195 1568.23388671875 0.43632084131240845 0.4688893 5.212717056274414 True -2 8151 30.319023370742798 0.7481362819671631 953.7374267578125 0.5564212799072266 1516.2744140625 0.4544796347618103 0.49099204 2.233602523803711 True -3 10868 30.333781003952026 1.9800782203674316 974.7835083007812 0.5934514403343201 1468.4097900390625 0.46521931886672974 0.50716555 1.3624705076217651 True -4 13585 30.235433101654053 1.5475256443023682 1065.94287109375 0.5895299911499023 1454.533935546875 0.47193631529808044 0.511627 1.3409944772720337 True -5 16302 30.33986210823059 0.7289819717407227 1133.8824462890625 0.7913186550140381 1428.5345458984375 0.4826495051383972 0.53193325 1.1373249292373657 True -6 19019 30.280664682388306 0.7115609645843506 1016.8976440429688 0.4945714771747589 1416.7506103515625 0.48722267150878906 0.5445442 1.087309718132019 True -7 21736 30.30557680130005 0.74220871925354 1214.2138671875 0.859143853187561 1403.96630859375 0.49242907762527466 0.56129295 0.948891818523407 True -8 24453 30.222455978393555 0.7179267406463623 1209.563232421875 0.7291551828384399 1392.6798095703125 0.49734246730804443 0.5711112 0.8549484014511108 True -9 27170 30.2338924407959 0.9307520389556885 1188.208251953125 0.6823236346244812 1382.0185546875 0.5013585090637207 0.5834099 0.8480311632156372 True -10 29887 30.304274797439575 0.7173547744750977 1017.84765625 0.589479923248291 1367.577392578125 0.5078610181808472 0.59932023 0.810823917388916 True -11 32604 30.264167308807373 0.7069535255432129 1044.955810546875 0.6363719701766968 1358.3804931640625 0.5101327300071716 0.61616385 0.771957516670227 True -12 35321 30.244565963745117 0.714214563369751 1209.212646484375 0.44923943281173706 1347.9390869140625 0.5133591294288635 0.62760013 0.7308805584907532 True -13 38038 30.3013813495636 0.7152841091156006 1003.736328125 0.5096933841705322 1338.6212158203125 0.5173546671867371 0.6436301 0.7024076581001282 True -14 40755 30.251168489456177 0.6979551315307617 987.546875 0.5924780964851379 1329.1470947265625 0.5204993486404419 0.66234094 0.6504265069961548 True -15 43472 30.271647453308105 0.6957011222839355 1003.7254028320312 0.8461607694625854 1324.700439453125 0.5218124985694885 0.6734674 0.6096314787864685 True -16 46189 30.253808975219727 0.7010388374328613 793.9493408203125 0.3258175253868103 1317.6754150390625 0.5240989327430725 0.68169177 0.5868545174598694 True -17 48906 30.254857778549194 2.4585204124450684 892.3451538085938 0.42951443791389465 1319.8155517578125 0.5214072465896606 0.68652606 0.5650916695594788 True -18 51623 30.26024103164673 0.7104556560516357 1177.97412109375 0.5472475290298462 1320.495361328125 0.5206606388092041 0.6873136 0.5594157576560974 True -19 54340 30.304006576538086 0.7358109951019287 859.279052734375 0.5080313682556152 1321.597412109375 0.5200225114822388 0.6882885 0.5558532476425171 True diff --git a/ENCSR672EWY/cherimoya.fold_1.performance.tsv b/ENCSR672EWY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 013594f378a93daa2cd7efe7c6cca362359c99a6..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1321.597412109375 0.28623491525650024 0.520022451877594 0.2668832540512085 0.6882885098457336 0.650340735912323 0.5558532476425171 \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_2.evaluate.json b/ENCSR672EWY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 195e587077d41d3418361026ff59a421aa6084cc..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF815QLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_2.fit.json b/ENCSR672EWY/cherimoya.fold_2.fit.json deleted file mode 100644 index b8c051a6d04b8b0171d048150e7c16829f360f97..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF815QLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_2.log b/ENCSR672EWY/cherimoya.fold_2.log deleted file mode 100644 index 70143f978ca60fc042e5f6b9ba9aa174d56841ea..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2865 35.83309578895569 4.002920627593994 1306.71826171875 1.0708621740341187 1787.8402099609375 0.2790117561817169 0.3611454 8.29751205444336 True -1 5730 31.93653130531311 0.5752108097076416 1019.0249633789062 1.0460069179534912 1437.628662109375 0.4458422362804413 0.45683113 3.8810999393463135 True -2 8595 31.960675954818726 0.5505685806274414 1088.768310546875 0.4644292891025543 1395.2996826171875 0.4550609588623047 0.5035365 2.329514741897583 True -3 11460 31.8726704120636 0.5245065689086914 1114.34326171875 0.5815372467041016 1363.442138671875 0.4650633633136749 0.51356435 1.6586432456970215 True -4 14325 31.857741832733154 0.52414870262146 1299.488037109375 0.7738763093948364 1342.566650390625 0.4731360673904419 0.5321265 1.4147975444793701 True -5 17190 31.849338054656982 0.5224628448486328 1274.2689208984375 0.7997561693191528 1329.021484375 0.4779675006866455 0.54608977 1.1913472414016724 True -6 20055 31.83453106880188 0.5134222507476807 1180.356201171875 0.8138450384140015 1312.41455078125 0.4870266318321228 0.5592256 1.379512071609497 True -7 22920 31.914586305618286 0.5518243312835693 1130.755126953125 0.7999918460845947 1308.111328125 0.48726117610931396 0.5736546 1.1533808708190918 True -8 25785 31.902653455734253 0.5228691101074219 963.9761352539062 0.7737330794334412 1297.4964599609375 0.49173304438591003 0.5862094 0.9762418866157532 True -9 28650 31.920936107635498 0.5251290798187256 966.2032470703125 0.7519557476043701 1288.593505859375 0.4968477189540863 0.5944785 0.9447018504142761 True -10 31515 31.941148042678833 0.5189356803894043 824.9779663085938 0.5454144477844238 1281.2276611328125 0.5000718832015991 0.60472226 0.8547642230987549 True -11 34380 31.92817497253418 0.5227062702178955 957.740478515625 0.5656594038009644 1275.512939453125 0.5025594234466553 0.6117944 0.8218446373939514 True -12 37245 31.945045232772827 0.521198034286499 956.244384765625 0.7447424530982971 1266.502685546875 0.5063173770904541 0.6285005 0.737617552280426 True -13 40110 31.988902807235718 0.5331768989562988 946.927490234375 0.668183445930481 1260.9478759765625 0.5077626705169678 0.64298767 0.7019468545913696 True -14 42975 31.892809867858887 0.5221104621887207 1010.0380859375 0.4822242856025696 1254.8255615234375 0.5095047354698181 0.6531065 0.649925172328949 True -15 45840 31.89021587371826 0.51242995262146 1128.39501953125 0.4401368498802185 1248.27294921875 0.5132582783699036 0.66272855 0.609129786491394 True -16 48705 31.876894235610962 0.5228745937347412 935.3226318359375 0.4463721513748169 1245.3402099609375 0.5140823721885681 0.67099226 0.5705803632736206 True -17 51570 31.948601961135864 0.5252182483673096 889.451171875 0.5323797464370728 1246.8045654296875 0.5119906663894653 0.675885 0.5504159927368164 True -18 54435 31.94061255455017 0.5220956802368164 1118.559814453125 0.48963484168052673 1242.557861328125 0.5149599313735962 0.67548305 0.5494595170021057 False -19 57300 31.899284839630127 11.92416000366211 1032.0426025390625 0.4136021137237549 1244.776611328125 0.5132513642311096 0.6767199 0.5501409769058228 True diff --git a/ENCSR672EWY/cherimoya.fold_2.performance.tsv b/ENCSR672EWY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index aa2f27250869d4726e1f9d4087867a65bba315d1..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1244.776611328125 0.2939678728580475 0.5132513642311096 0.2558175325393677 0.6767199039459229 0.6290913820266724 0.5501409769058228 \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_3.evaluate.json b/ENCSR672EWY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index be3a823f9bc70affcd874ed326c0b70ed0ffc40d..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF815QLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_3.fit.json b/ENCSR672EWY/cherimoya.fold_3.fit.json deleted file mode 100644 index 779dd8db3b98a390d6a73a577ac238338d43de40..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF815QLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_3.log b/ENCSR672EWY/cherimoya.fold_3.log deleted file mode 100644 index 622d381dd59088fdffa3e20fa1090219cdcaa546..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2808 35.75929379463196 4.230385780334473 1039.4573974609375 0.8724349737167358 1806.8216552734375 0.2796805500984192 0.38719735 7.772366046905518 True -1 5616 31.3108332157135 0.5866601467132568 1112.944091796875 0.5742801427841187 1475.0001220703125 0.4425271153450012 0.47715965 4.2887983322143555 True -2 8424 31.36800765991211 6.665143966674805 1107.064697265625 0.7338266372680664 1439.8572998046875 0.4513648748397827 0.48074922 2.1211838722229004 True -3 11232 31.82274889945984 0.5896313190460205 1119.64892578125 1.1552629470825195 1403.2349853515625 0.4620187282562256 0.5084977 1.5064505338668823 True -4 14040 32.05760931968689 0.584963321685791 1028.366455078125 1.0327337980270386 1386.1361083984375 0.4698638916015625 0.5244415 1.732096552848816 True -5 16848 31.297817945480347 0.5796689987182617 1127.58349609375 0.7610856294631958 1374.0294189453125 0.4760280251502991 0.53484255 1.3885794878005981 True -6 19656 31.300015926361084 0.5775940418243408 1132.62158203125 1.0006685256958008 1364.5106201171875 0.4779653549194336 0.5490418 1.1569937467575073 True -7 22464 31.3068106174469 0.5756337642669678 911.8296508789062 0.5340093374252319 1356.7178955078125 0.48323488235473633 0.5558637 1.1800380945205688 True -8 25272 31.245883226394653 0.5747275352478027 1143.1390380859375 0.9343476295471191 1339.8179931640625 0.4919625222682953 0.5685494 1.1115583181381226 True -9 28080 31.246037244796753 0.5705335140228271 997.0322265625 0.6898622512817383 1331.2193603515625 0.49408963322639465 0.58645684 1.0407729148864746 True -10 30888 31.295121431350708 0.5772342681884766 761.90087890625 0.6942121386528015 1323.9189453125 0.49700844287872314 0.5988792 0.998009204864502 True -11 33696 31.291912078857422 0.580514669418335 1018.1107177734375 0.4204332232475281 1317.474365234375 0.49878236651420593 0.60558635 0.9049500226974487 True -12 36504 31.35732674598694 0.5910534858703613 1048.5604248046875 0.5267940759658813 1309.90283203125 0.5017029643058777 0.619961 0.8443079590797424 True -13 39312 31.266079664230347 0.5818188190460205 1096.301025390625 0.7093222141265869 1299.73486328125 0.507559597492218 0.63285536 0.7861882448196411 True -14 42120 31.31580638885498 0.5872178077697754 978.234130859375 0.5353402495384216 1295.1524658203125 0.5068743824958801 0.6449447 0.7256124019622803 True -15 44928 31.31841230392456 9.314224481582642 904.6054077148438 0.3473179042339325 1288.1004638671875 0.5094178318977356 0.662786 0.6436799764633179 True -16 47736 31.325534343719482 0.6554274559020996 862.1595458984375 0.48464885354042053 1285.406494140625 0.5089612603187561 0.67034686 0.6034952402114868 True -17 50544 31.325655698776245 0.6019597053527832 1053.4017333984375 0.4218180477619171 1278.1492919921875 0.5149524211883545 0.6741427 0.5770093202590942 True -18 53352 31.17745590209961 0.9679181575775146 889.221923828125 0.27439630031585693 1282.0006103515625 0.5119159817695618 0.67585063 0.5657689571380615 True -19 56160 30.744343519210815 0.5821428298950195 890.8388061523438 0.43484604358673096 1286.022705078125 0.5090001821517944 0.67652607 0.5638109445571899 True diff --git a/ENCSR672EWY/cherimoya.fold_3.performance.tsv b/ENCSR672EWY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 850f4365b3821f3cdff38115485d4ed00f22b654..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1286.022705078125 0.29457220435142517 0.5090001821517944 0.2560502290725708 0.6765260696411133 0.6358634233474731 0.5638109445571899 \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_4.evaluate.json b/ENCSR672EWY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ce9f632a6a426651de04faee75e2f8bfd40cca51..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF815QLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_4.fit.json b/ENCSR672EWY/cherimoya.fold_4.fit.json deleted file mode 100644 index 958dc2f1fbcd235f6d0af6426d525b5cb3a2ce7c..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF815QLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672EWY/cherimoya.fold_4.log b/ENCSR672EWY/cherimoya.fold_4.log deleted file mode 100644 index a5586a39ace2f61dfdfba5e39c2af9dd693c4c03..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 36.494755268096924 4.198971271514893 1328.04248046875 0.6637277603149414 1756.749267578125 0.2710237503051758 0.3552656 8.763047218322754 True -1 5752 32.11453866958618 0.7223711013793945 1150.6568603515625 0.960465133190155 1412.59912109375 0.4425947964191437 0.45820192 4.410741329193115 True -2 8628 32.12419390678406 0.5833370685577393 1306.3525390625 0.8982478380203247 1397.385498046875 0.4457997977733612 0.47311768 2.1071839332580566 True -3 11504 32.09158778190613 0.5561051368713379 1346.415283203125 1.1084659099578857 1357.798828125 0.45909589529037476 0.51290023 1.6890546083450317 True -4 14380 32.00554847717285 0.5787127017974854 1099.8896484375 0.9291547536849976 1334.74267578125 0.46839481592178345 0.5320188 1.3014285564422607 True -5 17256 31.99302101135254 0.5540115833282471 1080.57421875 0.7444294095039368 1323.6873779296875 0.4744502007961273 0.53448236 1.0421385765075684 True -6 20132 31.99678349494934 0.5712013244628906 1201.0877685546875 0.9123992919921875 1310.001953125 0.48057520389556885 0.54604256 1.003182053565979 True -7 23008 31.996403217315674 0.5763838291168213 1090.5595703125 0.7586773633956909 1296.1175537109375 0.48722463846206665 0.55849034 0.8958563208580017 True -8 25884 32.00872230529785 0.5559720993041992 929.70166015625 0.6640830039978027 1293.48095703125 0.4871242344379425 0.5682823 0.8896085023880005 True -9 28760 32.04678821563721 0.5889468193054199 842.6234130859375 0.5701069831848145 1280.11083984375 0.4947856664657593 0.5786177 0.8550991415977478 True -10 31636 32.06917858123779 1.0641953945159912 871.19287109375 0.493145227432251 1270.4166259765625 0.4988700747489929 0.58824646 0.7804352045059204 True -11 34512 32.04014825820923 0.5805273056030273 1205.073486328125 0.8084527850151062 1261.803955078125 0.5022262334823608 0.6040145 0.7297084927558899 True -12 37388 32.017866134643555 0.5612280368804932 1062.7906494140625 0.5837848782539368 1252.721923828125 0.5061492919921875 0.61338884 0.7034456729888916 True -13 40264 32.024794816970825 0.574847936630249 1119.0518798828125 0.3952319622039795 1248.5682373046875 0.5070376992225647 0.62489843 0.6426506638526917 True -14 43140 32.03847813606262 0.575920581817627 918.980712890625 0.5787956714630127 1239.4361572265625 0.5126012563705444 0.6401401 0.6092092394828796 True -15 46016 32.1053409576416 0.5762457847595215 1024.89501953125 0.45435476303100586 1239.760009765625 0.5103285312652588 0.65082824 0.5850969552993774 True -16 48892 31.437240600585938 0.5681090354919434 1170.047607421875 0.5739058256149292 1235.291259765625 0.5124852061271667 0.6596386 0.5607452392578125 True -17 51768 31.45491909980774 0.5661141872406006 845.178955078125 0.5254327058792114 1237.819091796875 0.510120689868927 0.6641673 0.5483930706977844 True -18 54644 31.370510578155518 0.5616095066070557 941.5595703125 0.4413420259952545 1235.4134521484375 0.5119034647941589 0.6663244 0.542534589767456 True -19 57520 31.33189105987549 0.5567350387573242 1022.4222412109375 0.3377994894981384 1236.5943603515625 0.5115689039230347 0.66616553 0.5439543724060059 False diff --git a/ENCSR672EWY/cherimoya.fold_4.performance.tsv b/ENCSR672EWY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e4052192a73c0342fdc6fe604af47c546c1d0cba..0000000000000000000000000000000000000000 --- a/ENCSR672EWY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1235.4134521484375 0.29568642377853394 0.5119035840034485 0.2531626522541046 0.6663243770599365 0.6237220168113708 0.542534589767456 \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_0.evaluate.json b/ENCSR672MOG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 42f2fe33d470f8dae808c79f0dde4c2c4b19e47a..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF869KNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_0.fit.json b/ENCSR672MOG/cherimoya.fold_0.fit.json deleted file mode 100644 index 53ad3b042c157b2b747c76ff664c7c9edb117df3..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF869KNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_0.log b/ENCSR672MOG/cherimoya.fold_0.log deleted file mode 100644 index c1ae09571acac961831e7e8152fcc1409ffffabc..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 35.15010857582092 3.5497968196868896 497.27490234375 0.6377789378166199 816.6431274414062 0.31218424439430237 0.7865961 4.453988075256348 True -1 5534 30.555309057235718 1.1194941997528076 668.7346801757812 0.273526668548584 740.7125854492188 0.38484662771224976 0.837631 1.2014715671539307 True -2 8301 30.639100313186646 2.515852928161621 659.88037109375 0.29210329055786133 729.8908081054688 0.3926514983177185 0.83858234 0.3957776427268982 True -3 11068 30.57729172706604 2.915337562561035 545.9044189453125 0.3525322675704956 720.5250854492188 0.40092554688453674 0.85271615 0.3735784590244293 True -4 13835 30.570724964141846 0.5582222938537598 705.078369140625 0.3766028881072998 718.6829223632812 0.4017425775527954 0.8571817 0.36108139157295227 True -5 16602 31.081387281417847 31.936039209365845 579.353759765625 0.26745301485061646 714.59619140625 0.40671783685684204 0.8621275 0.33472391963005066 True -6 19369 30.554189682006836 0.5543591976165771 783.6060791015625 0.345126748085022 712.093505859375 0.4091707766056061 0.86669904 0.31499090790748596 True -7 22136 30.52565574645996 0.5742361545562744 561.9534912109375 0.2634696662425995 711.9882202148438 0.4095505475997925 0.87142044 0.3082747459411621 True -8 24903 30.530195951461792 0.5602226257324219 603.7958984375 0.2584405541419983 709.0255737304688 0.4127691686153412 0.87507856 0.3146902322769165 True -9 27670 30.52844762802124 0.5474488735198975 714.6959838867188 0.24877670407295227 706.9764404296875 0.4147647023200989 0.8799354 0.2884471118450165 True -10 30437 30.485373497009277 0.5540616512298584 679.2271118164062 0.2165093570947647 703.8507690429688 0.41714659333229065 0.88312197 0.27367493510246277 True -11 33204 30.541337966918945 0.557234525680542 628.8262939453125 0.18602226674556732 702.4011840820312 0.4176720380783081 0.8878806 0.25185665488243103 True -12 35971 30.744219541549683 0.5589532852172852 651.32373046875 0.3881096839904785 700.4058837890625 0.4196930527687073 0.8907209 0.23755566775798798 True -13 38738 30.51751160621643 13.443044662475586 656.0971069335938 0.17233997583389282 697.5725708007812 0.42186957597732544 0.8943874 0.2209455370903015 True -14 41505 31.53830599784851 11.805395603179932 523.5916137695312 0.23216435313224792 696.5814208984375 0.42288634181022644 0.89749444 0.20436784625053406 True -15 44272 30.600454330444336 0.563866138458252 556.384521484375 0.14034634828567505 696.0706787109375 0.42337578535079956 0.9005661 0.1856360137462616 True -16 47039 30.450311183929443 2.5560083389282227 584.3033447265625 0.08615981042385101 692.810546875 0.4254954755306244 0.9048357 0.17455659806728363 True -17 49806 29.992477416992188 0.5575413703918457 598.6475830078125 0.1729917824268341 693.8746948242188 0.42541393637657166 0.9057668 0.16789954900741577 True -18 52573 30.066179037094116 0.5598070621490479 554.9820556640625 0.11762425303459167 693.8446655273438 0.4247102737426758 0.9043496 0.16694490611553192 False -19 55340 29.896761655807495 0.5485091209411621 592.7613525390625 0.08865104615688324 693.98876953125 0.4247201979160309 0.90403867 0.1665342152118683 False diff --git a/ENCSR672MOG/cherimoya.fold_0.performance.tsv b/ENCSR672MOG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f87d0d3887fefcd99e755c5c37d4fa40743bd3e9..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -693.8746948242188 0.35825079679489136 0.42541390657424927 0.18843144178390503 0.9057667851448059 0.8828456997871399 0.16789954900741577 \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_1.evaluate.json b/ENCSR672MOG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1e381a000b3ec85588237e891445bb36b2819c05..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF869KNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_1.fit.json b/ENCSR672MOG/cherimoya.fold_1.fit.json deleted file mode 100644 index a8793f1c5491620fe3adf00ba48b1eb2bb43d712..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF869KNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_1.log b/ENCSR672MOG/cherimoya.fold_1.log deleted file mode 100644 index 1d80755d02ff6010a0a131eda1986a74fefbf31c..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2699 34.39262247085571 5.397659063339233 638.015625 0.280961275100708 962.1652221679688 0.3134861886501312 0.77926505 5.1129045486450195 True -1 5398 29.867916107177734 0.7364888191223145 635.3046875 0.23683561384677887 865.2191772460938 0.3935941755771637 0.83005625 1.624299168586731 True -2 8097 29.833873748779297 1.8268406391143799 647.7003173828125 0.27346915006637573 842.2130126953125 0.40534093976020813 0.8546209 0.608162522315979 True -3 10796 29.994717597961426 0.7690660953521729 612.461669921875 0.2531335949897766 833.1951293945312 0.41247960925102234 0.8630304 0.48068398237228394 True -4 13495 29.96323299407959 0.7434883117675781 617.6571044921875 0.2699710726737976 827.88818359375 0.41763195395469666 0.86548674 0.45921260118484497 True -5 16194 29.845414876937866 0.7495207786560059 610.142333984375 0.2898755371570587 825.6506958007812 0.41778847575187683 0.87004083 0.3423829674720764 True -6 18893 31.978851556777954 11.453368902206421 727.1820068359375 0.2117728292942047 823.6182861328125 0.4201522767543793 0.8729958 0.33182212710380554 True -7 21592 29.794730186462402 17.75893521308899 622.423095703125 0.5843780040740967 818.940185546875 0.42479315400123596 0.87683535 0.34401294589042664 True -8 24291 32.616894483566284 3.2401859760284424 588.6593017578125 0.23239754140377045 817.17138671875 0.4258876144886017 0.87777585 0.34667953848838806 True -9 26990 29.842166900634766 1.556697130203247 561.4020385742188 0.18358856439590454 812.1329956054688 0.4308265447616577 0.88432837 0.3357422649860382 True -10 29689 29.859311819076538 0.7293105125427246 655.40234375 0.3718176484107971 812.1310424804688 0.4304661154747009 0.8858588 0.3654405176639557 True -11 32388 29.803875207901 0.7255380153656006 627.3762817382812 0.23188820481300354 808.7022094726562 0.4330006539821625 0.8935544 0.30866295099258423 True -12 35087 29.824495553970337 0.7271506786346436 593.6332397460938 0.17516586184501648 806.4287719726562 0.4343000650405884 0.8965767 0.27510377764701843 True -13 37786 29.90554451942444 36.272900342941284 537.9752197265625 0.21631404757499695 801.6898193359375 0.43836066126823425 0.9027054 0.25673767924308777 True -14 40485 30.216591358184814 1.6069178581237793 607.5045166015625 0.1688556969165802 798.9072265625 0.43989190459251404 0.9039734 0.2343415915966034 True -15 43184 30.125147342681885 1.121753215789795 560.8214111328125 0.1209724023938179 799.3820190429688 0.4384767711162567 0.91029465 0.21247722208499908 True -16 45883 29.839123010635376 0.7176401615142822 610.740234375 0.15043576061725616 799.1243896484375 0.4397653043270111 0.91121125 0.1981438398361206 True -17 48582 29.908229112625122 0.719151496887207 682.100341796875 0.14959846436977386 797.7396850585938 0.4408237636089325 0.91436595 0.18973787128925323 True -18 51281 29.824498653411865 0.760228157043457 553.5806884765625 0.17530608177185059 799.11279296875 0.4393284022808075 0.9143586 0.1874273419380188 False -19 53980 29.739777326583862 17.22149109840393 551.9176025390625 0.18497326970100403 799.5782470703125 0.43918275833129883 0.9146876 0.18639184534549713 True diff --git a/ENCSR672MOG/cherimoya.fold_1.performance.tsv b/ENCSR672MOG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index fa316cbf22814d4a446dd41223dfa87300292410..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -799.5782470703125 0.34103819727897644 0.4391828179359436 0.20996323227882385 0.9146875739097595 0.9056657552719116 0.18639184534549713 \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_2.evaluate.json b/ENCSR672MOG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 11bee0f8d27ea0a76298c3db5280ecbaca56ca3f..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF869KNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_2.fit.json b/ENCSR672MOG/cherimoya.fold_2.fit.json deleted file mode 100644 index 773d09163d2058d9a863e5fb73f2bef1a8c5b317..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF869KNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_2.log b/ENCSR672MOG/cherimoya.fold_2.log deleted file mode 100644 index d6db7edb421c14d330ac0a286afce2b9d0079c75..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 38.56368088722229 3.5237457752227783 658.7742919921875 0.3615775406360626 872.9920654296875 0.3123474419116974 0.77374405 4.422605037689209 True -1 5794 32.278183937072754 0.555121660232544 586.6046142578125 0.2687937021255493 778.1614990234375 0.39243513345718384 0.836148 1.253531813621521 True -2 8691 32.08727836608887 0.9340500831604004 615.8587036132812 0.2460322380065918 772.6909790039062 0.39666786789894104 0.8371395 0.5161834359169006 True -3 11588 31.974311351776123 2.490063428878784 676.95166015625 0.1962004005908966 762.3695068359375 0.401827871799469 0.85229135 0.37868085503578186 True -4 14485 32.02012825012207 0.5616445541381836 526.06689453125 0.1517508327960968 759.9760131835938 0.404331237077713 0.8518135 0.33519962430000305 False -5 17382 31.99378514289856 0.5530931949615479 650.5506591796875 0.3140987157821655 757.7338256835938 0.4051588475704193 0.8558104 0.28628480434417725 True -6 20279 31.913273811340332 0.5356323719024658 512.952880859375 0.2967810034751892 756.0628051757812 0.4069935977458954 0.8631946 0.3015938401222229 True -7 23176 31.904882192611694 0.5466823577880859 548.33447265625 0.22069770097732544 754.0790405273438 0.4087508022785187 0.86935693 0.295411616563797 True -8 26073 31.896313667297363 0.553865909576416 620.8447875976562 0.18476445972919464 752.1580810546875 0.4099445343017578 0.87021357 0.28727471828460693 True -9 28970 31.943011045455933 0.5488355159759521 638.046875 0.16153274476528168 748.9759521484375 0.41254061460494995 0.8761069 0.2667296826839447 True -10 31867 31.987523078918457 0.5379645824432373 591.2713012695312 0.1417735069990158 746.7601318359375 0.41626670956611633 0.8776148 0.2678503692150116 True -11 34764 31.99741220474243 9.128461837768555 686.0849609375 0.1395784616470337 743.5458374023438 0.4191133379936218 0.882938 0.25578051805496216 True -12 37661 32.15789866447449 0.5835621356964111 557.55078125 0.21158552169799805 742.400146484375 0.4185725748538971 0.8871006 0.23060405254364014 True -13 40558 32.181337118148804 22.82861852645874 575.8889770507812 0.15598750114440918 739.524169921875 0.4226030707359314 0.8873672 0.221106618642807 True -14 43455 37.16062068939209 0.5626006126403809 639.57958984375 0.14798948168754578 738.2509155273438 0.42340779304504395 0.89067936 0.20873452723026276 True -15 46352 32.502471923828125 29.728408813476562 468.869140625 0.23930159211158752 738.0682373046875 0.4234485626220703 0.89534086 0.19714562594890594 True -16 49249 32.081796169281006 0.559149980545044 609.06494140625 0.1803622841835022 736.4939575195312 0.4259602129459381 0.8958035 0.18792803585529327 True -17 52146 31.976168155670166 0.5484580993652344 500.95184326171875 0.1567087471485138 737.3363037109375 0.4240778386592865 0.89736915 0.18360793590545654 True -18 55043 32.282007694244385 27.931941270828247 604.9959716796875 0.19572365283966064 736.9072875976562 0.42490798234939575 0.8970178 0.18342016637325287 False -19 57940 32.56120800971985 0.5533649921417236 639.217529296875 0.11916609853506088 737.4790649414062 0.42444559931755066 0.8975718 0.1838495284318924 True diff --git a/ENCSR672MOG/cherimoya.fold_2.performance.tsv b/ENCSR672MOG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 12cb635db092b36e1f37438f4ca699bab713c0af..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -737.4790649414062 0.35320231318473816 0.42444559931755066 0.19059891998767853 0.8975718021392822 0.8812196254730225 0.1838495284318924 \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_3.evaluate.json b/ENCSR672MOG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2252d3b5be101e5f08cbc704f4d431f14164e771..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF869KNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_3.fit.json b/ENCSR672MOG/cherimoya.fold_3.fit.json deleted file mode 100644 index 5a84225de19979fbe54d18bd730af1b5f9465a48..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF869KNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_3.log b/ENCSR672MOG/cherimoya.fold_3.log deleted file mode 100644 index 794246279ff9850d64c491379b2c574fc49f811e..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 35.09959435462952 42.33879780769348 625.3432006835938 0.38783079385757446 807.678955078125 0.31555989384651184 0.7637192 5.21441125869751 True -1 5476 29.880265712738037 28.56077480316162 638.395263671875 0.3240974545478821 728.7053833007812 0.3913763761520386 0.8244656 1.2047899961471558 True -2 8214 30.2226619720459 0.5721728801727295 751.703857421875 0.2864793539047241 718.4483642578125 0.39746570587158203 0.83522236 0.5402936339378357 True -3 10952 31.88993811607361 0.5386672019958496 640.314453125 0.22135581076145172 708.6167602539062 0.4067137539386749 0.8478192 0.40174025297164917 True -4 13690 31.34920024871826 23.606940031051636 668.6510009765625 0.3594285845756531 706.20751953125 0.40737658739089966 0.853201 0.360860675573349 True -5 16428 29.736252069473267 1.1395082473754883 578.5494384765625 0.2519897520542145 702.9386596679688 0.4100870192050934 0.85821587 0.3334631323814392 True -6 19166 29.833369731903076 0.545708417892456 651.6387939453125 0.4280111491680145 699.951416015625 0.41378504037857056 0.86240494 0.3246505856513977 True -7 21904 29.71734642982483 0.543968677520752 591.25390625 0.1823769211769104 698.4115600585938 0.4146866202354431 0.8671953 0.3059285581111908 True -8 24642 29.637023210525513 0.5455546379089355 551.6732177734375 0.18715590238571167 697.9530029296875 0.41383096575737 0.8711685 0.30702146887779236 True -9 27380 29.607545852661133 0.5428845882415771 650.56884765625 0.22770580649375916 694.5512084960938 0.4179816246032715 0.87564826 0.31660452485084534 True -10 30118 29.6138117313385 7.828585386276245 577.9056396484375 0.20157553255558014 692.50439453125 0.4201929569244385 0.8791411 0.3117353320121765 True -11 32856 29.667662620544434 0.5456387996673584 745.4813232421875 0.17959274351596832 690.6681518554688 0.4220242202281952 0.8819843 0.2864045798778534 True -12 35594 29.650023698806763 0.5368902683258057 573.7039184570312 0.15168866515159607 688.48681640625 0.4230440855026245 0.8861854 0.2634026110172272 True -13 38332 29.75007915496826 0.5433871746063232 592.5857543945312 0.12508364021778107 686.1380004882812 0.42554354667663574 0.88893396 0.24258770048618317 True -14 41070 29.842179536819458 0.5581789016723633 629.7236328125 0.13810129463672638 686.2232666015625 0.42448970675468445 0.8913071 0.22152996063232422 True -15 43808 29.88092064857483 0.5674922466278076 521.395263671875 0.17898890376091003 683.790771484375 0.42806631326675415 0.8957594 0.2065594345331192 True -16 46546 30.009225368499756 0.5498497486114502 642.520263671875 0.11432483792304993 683.0828247070312 0.4287915527820587 0.8974555 0.1945076882839203 True -17 49284 30.131865739822388 32.247194051742554 622.703857421875 0.18095889687538147 683.3580932617188 0.42814627289772034 0.89899284 0.18747080862522125 True -18 52022 30.21184253692627 0.5982978343963623 561.1536865234375 0.1144593209028244 682.915283203125 0.4284658133983612 0.8999043 0.1869284063577652 True -19 54760 29.923761129379272 40.76007270812988 508.6209716796875 0.1701437383890152 684.4442749023438 0.42617079615592957 0.9000951 0.1874043345451355 True diff --git a/ENCSR672MOG/cherimoya.fold_3.performance.tsv b/ENCSR672MOG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9df8c1b34fed9acf9c83add205c6b8779d2e8eaf..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -684.4442749023438 0.3569185733795166 0.4261707663536072 0.1881331205368042 0.9000951051712036 0.8722480535507202 0.1874043345451355 \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_4.evaluate.json b/ENCSR672MOG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2152c046a0c5d675ef40ecf73331c8214d5c697d..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF869KNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_4.fit.json b/ENCSR672MOG/cherimoya.fold_4.fit.json deleted file mode 100644 index 2f3508b6931d00c5a93e01fe4e793ed4fc19fc05..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF869KNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR672MOG/cherimoya.fold_4.log b/ENCSR672MOG/cherimoya.fold_4.log deleted file mode 100644 index de2db9d7fe67ebb4a8be4f6b694e508b3434b37f..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2773 34.328675985336304 3.705376148223877 729.3284912109375 0.5331554412841797 746.849365234375 0.30594393610954285 0.7722204 4.927389144897461 True -1 5546 30.485442399978638 1.5818407535552979 754.1795654296875 0.45444455742836 681.5185546875 0.3754551410675049 0.8217894 1.2233561277389526 True -2 8319 30.562348127365112 0.6272170543670654 580.777587890625 0.2111055701971054 669.8511352539062 0.382610946893692 0.8355087 0.47280463576316833 True -3 11092 30.452390432357788 0.6176447868347168 574.433837890625 0.22479301691055298 661.5371704101562 0.3897956907749176 0.8420101 0.384217768907547 True -4 13865 30.44032621383667 0.6258947849273682 616.1265258789062 0.2055829018354416 658.5953979492188 0.39434173703193665 0.85157615 0.3708515167236328 True -5 16638 30.494283199310303 0.5943582057952881 472.760009765625 0.13083818554878235 656.0711059570312 0.39629897475242615 0.85696954 0.3017463982105255 True -6 19411 30.500921726226807 0.6043558120727539 648.6165161132812 0.15729331970214844 654.8413696289062 0.3959563076496124 0.85881364 0.30491992831230164 True -7 22184 30.587743997573853 0.6006712913513184 720.65771484375 0.303730845451355 651.1575927734375 0.4007425308227539 0.8672443 0.29614096879959106 True -8 24957 30.560381412506104 0.6011059284210205 536.8715209960938 0.2198333442211151 650.9732666015625 0.4014887809753418 0.8709063 0.2720988988876343 True -9 27730 30.610515117645264 3.427079439163208 567.36474609375 0.2176172435283661 648.522216796875 0.4039023518562317 0.87517726 0.2718595564365387 True -10 30503 30.67180109024048 0.6142501831054688 674.4806518554688 0.20232588052749634 647.5597534179688 0.4042356014251709 0.8794879 0.25201064348220825 True -11 33276 30.689954042434692 0.6290633678436279 588.269775390625 0.18732815980911255 645.745361328125 0.4064303934574127 0.8835401 0.24510905146598816 True -12 36049 30.63496994972229 0.6123394966125488 653.4987182617188 0.13849923014640808 643.870361328125 0.40816858410835266 0.8863526 0.21539726853370667 True -13 38822 30.606562614440918 0.6142921447753906 619.4716186523438 0.12686361372470856 641.6688232421875 0.4115326702594757 0.89121664 0.20273025333881378 True -14 41595 30.472328662872314 0.601630449295044 523.0319213867188 0.1301860213279724 639.3569946289062 0.4137532413005829 0.89272135 0.18612302839756012 True -15 44368 29.99782633781433 0.620131254196167 560.133056640625 0.12795299291610718 640.2095947265625 0.41173210740089417 0.8964313 0.17118047177791595 True -16 47141 29.99987292289734 0.6076724529266357 637.2422485351562 0.1231328547000885 639.7568359375 0.41180408000946045 0.8991269 0.16171841323375702 True -17 49914 30.043997764587402 0.6119503974914551 495.1066589355469 0.1563566029071808 639.2548217773438 0.41299915313720703 0.90169877 0.15785259008407593 True -18 52687 29.99106788635254 0.6136445999145508 568.0276489257812 0.13053864240646362 639.9144287109375 0.41113168001174927 0.90249544 0.1558079719543457 True -19 55460 29.968616485595703 0.6081829071044922 524.8810424804688 0.11719827353954315 640.8472290039062 0.4094785153865814 0.90224767 0.1555021107196808 False diff --git a/ENCSR672MOG/cherimoya.fold_4.performance.tsv b/ENCSR672MOG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6d92aec85a4cc8d8d953cbc9624e330cdeed3dec..0000000000000000000000000000000000000000 --- a/ENCSR672MOG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -639.9144287109375 0.3695005774497986 0.4111316502094269 0.1738206148147583 0.9024954438209534 0.8728702068328857 0.1558079719543457 \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_0.evaluate.json b/ENCSR673ZMQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index bf7e77eb418b9e9442b4940c60a9ee7c67a7b7d5..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF503YRJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_0.fit.json b/ENCSR673ZMQ/cherimoya.fold_0.fit.json deleted file mode 100644 index c9ce414eaf14a84a938aa681cebe4c998ddfcd0c..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF503YRJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_0.log b/ENCSR673ZMQ/cherimoya.fold_0.log deleted file mode 100644 index 88debfe7ba9ab850c8f398517d86d9b66c0c1932..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1830 25.29272484779358 3.5304055213928223 245.9036865234375 0.6544505953788757 379.5185241699219 0.41292762756347656 0.57785076 10.498841285705566 True -1 3660 20.17322611808777 0.38744401931762695 227.43731689453125 0.5777068138122559 329.918212890625 0.5130977630615234 0.6681374 3.7124454975128174 True -2 5490 20.3273446559906 14.194903373718262 234.76353454589844 0.5577726364135742 314.4375915527344 0.5549497604370117 0.6671463 1.0149145126342773 False -3 7320 20.232100248336792 0.3698146343231201 272.18365478515625 0.6415271759033203 310.4207458496094 0.5649111270904541 0.6803414 0.5886527895927429 True -4 9150 20.22102689743042 0.37381863594055176 228.5446014404297 0.3523513078689575 309.1980895996094 0.5680838227272034 0.69099 0.5050039291381836 True -5 10980 20.181795835494995 0.36383986473083496 251.19483947753906 0.5371901988983154 308.1763610839844 0.5710580348968506 0.7065015 0.4794858694076538 True -6 12810 20.17555332183838 0.3677968978881836 219.57199096679688 0.3512347638607025 307.3098449707031 0.5731163024902344 0.7106158 0.467014342546463 True -7 14640 20.216274976730347 0.3667480945587158 259.53216552734375 0.4667898714542389 306.6636657714844 0.575141191482544 0.7172628 0.43041667342185974 True -8 16470 20.15740156173706 0.3624238967895508 222.95443725585938 0.4427559971809387 305.8715515136719 0.5772165656089783 0.7203415 0.4331130087375641 True -9 18300 20.539769887924194 18.61849331855774 247.12278747558594 0.3898429870605469 305.2808532714844 0.5788723230361938 0.7226192 0.42815282940864563 True -10 20130 20.18626570701599 0.8349659442901611 280.06256103515625 0.3550606966018677 304.6334228515625 0.5805654525756836 0.7320719 0.40262073278427124 True -11 21960 20.237342834472656 0.5764684677124023 254.87661743164062 0.49534112215042114 304.10418701171875 0.5821638107299805 0.7339106 0.3938707411289215 True -12 23790 20.19755482673645 0.36455416679382324 203.3817138671875 0.37479180097579956 303.73248291015625 0.5834081768989563 0.7393947 0.3858421742916107 True -13 25620 20.251773834228516 0.3642864227294922 234.04635620117188 0.29735296964645386 303.1821594238281 0.5846282839775085 0.74423546 0.370350182056427 True -14 27450 20.161563634872437 0.3632323741912842 238.21446228027344 0.3150436282157898 302.9283752441406 0.5852829217910767 0.7494246 0.3640497028827667 True -15 29280 20.14503836631775 0.36289262771606445 211.72821044921875 0.2963367700576782 302.7877502441406 0.5855552554130554 0.75094324 0.36839377880096436 True -16 31110 20.207226514816284 0.3597598075866699 245.32135009765625 0.2945903539657593 303.0989685058594 0.5848654508590698 0.7494873 0.37528759241104126 False -17 32940 20.203640460968018 0.3640153408050537 239.76156616210938 0.23520435392856598 303.343505859375 0.5839223861694336 0.7478635 0.3797338902950287 False -18 34770 20.227629899978638 3.0294034481048584 212.15045166015625 0.3828134536743164 303.6546630859375 0.5829879641532898 0.7421074 0.3908657431602478 False -19 36600 20.229828119277954 0.3702232837677002 229.13099670410156 0.15972886979579926 303.7629699707031 0.5823718905448914 0.73812807 0.3980027437210083 False diff --git a/ENCSR673ZMQ/cherimoya.fold_0.performance.tsv b/ENCSR673ZMQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 32921f0fd8721cb3ab4db6a51ab0b494ad51e03b..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.7877502441406 0.33269837498664856 0.5855553150177002 0.19595034420490265 0.7509432435035706 0.7135811448097229 0.36839377880096436 \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_1.evaluate.json b/ENCSR673ZMQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5a9a064d173d4370c4948b817bfd38a48f7ef74c..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF503YRJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_1.fit.json b/ENCSR673ZMQ/cherimoya.fold_1.fit.json deleted file mode 100644 index ca7986ac84ab8b448d70b36a1c9f4d1348844410..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF503YRJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_1.log b/ENCSR673ZMQ/cherimoya.fold_1.log deleted file mode 100644 index d6af30e19a2656d8a22eafa06a105ad43d480124..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1864 24.925726890563965 3.362532615661621 266.18072509765625 0.6921332478523254 385.5777282714844 0.42155393958091736 0.5402757 10.095746040344238 True -1 3728 20.580060243606567 0.4294886589050293 243.982421875 0.5250765085220337 338.7581481933594 0.5172216892242432 0.6613794 3.2943532466888428 True -2 5592 20.327243089675903 0.41056036949157715 238.84722900390625 0.5054802298545837 326.7891845703125 0.5509545803070068 0.6780027 1.025967001914978 True -3 7456 20.14346694946289 0.8304812908172607 220.26675415039062 0.46793580055236816 323.4162292480469 0.5589317083358765 0.6963914 0.4926120340824127 True -4 9320 20.16277289390564 0.42084717750549316 262.10247802734375 0.6102205514907837 322.11865234375 0.562231183052063 0.70587355 0.41132017970085144 True -5 11184 21.57374620437622 25.806076288223267 225.62606811523438 0.4758933484554291 321.2218017578125 0.564476490020752 0.7097124 0.3935207724571228 True -6 13048 20.84884524345398 0.41795802116394043 254.13275146484375 0.4464137554168701 320.4131774902344 0.566760778427124 0.71955544 0.37624606490135193 True -7 14912 20.25286054611206 0.42214155197143555 239.82110595703125 0.6546089053153992 319.9517822265625 0.5680857300758362 0.72356075 0.3678416311740875 True -8 16776 20.285377264022827 0.4159839153289795 253.16482543945312 0.47939980030059814 319.5502014160156 0.5695976614952087 0.72656375 0.3675606846809387 True -9 18640 20.230639934539795 0.41753339767456055 225.8533172607422 0.4109339714050293 318.7043762207031 0.5715551376342773 0.7341084 0.3517722189426422 True -10 20504 20.202553749084473 0.4160802364349365 248.54544067382812 0.3569071292877197 318.2268981933594 0.5729526877403259 0.73649436 0.3476466238498688 True -11 22368 20.17635750770569 0.414614200592041 243.02471923828125 0.3363052010536194 317.9959411621094 0.5741202235221863 0.73978055 0.342788428068161 True -12 24232 20.147890329360962 0.40767478942871094 248.41470336914062 0.49355730414390564 317.5110168457031 0.5753465294837952 0.7439511 0.3415360450744629 True -13 26096 20.197723388671875 0.4173600673675537 204.55435180664062 0.32915568351745605 317.0284118652344 0.5764217972755432 0.7503537 0.3382423520088196 True -14 27960 20.208978414535522 0.42027783393859863 255.0200958251953 0.2956482768058777 316.7796325683594 0.5770991444587708 0.75551057 0.3346019387245178 True -15 29824 20.159404754638672 0.4184422492980957 215.04306030273438 0.3569851219654083 316.6594543457031 0.5771885514259338 0.7581478 0.3335210382938385 True -16 31688 20.20466160774231 1.5318450927734375 232.51895141601562 0.2766123116016388 316.8565673828125 0.5767984986305237 0.7597763 0.3357904851436615 True -17 33552 20.16433548927307 0.40401506423950195 273.6712951660156 0.20973794162273407 317.0296936035156 0.5760690569877625 0.7604231 0.3400576710700989 True -18 35416 20.178661346435547 0.4115641117095947 260.20489501953125 0.1764587014913559 317.2192687988281 0.5753318667411804 0.7581611 0.3482702076435089 False -19 37280 20.169349431991577 1.808445930480957 220.599609375 0.2466428577899933 317.34149169921875 0.5749065279960632 0.7551704 0.35168179869651794 False diff --git a/ENCSR673ZMQ/cherimoya.fold_1.performance.tsv b/ENCSR673ZMQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index def3d9fe6f43d0ad0aacf13610cec6f78bd055b1..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.0296936035156 0.3317321240901947 0.5760691165924072 0.20130324363708496 0.7604231238365173 0.7546133399009705 0.3400576710700989 \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_2.evaluate.json b/ENCSR673ZMQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d4639510643c7676bddf519055dfbc089c259dc0..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF503YRJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_2.fit.json b/ENCSR673ZMQ/cherimoya.fold_2.fit.json deleted file mode 100644 index fecff5efa4d1206141f550e9c0e9bf97694e382a..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF503YRJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_2.log b/ENCSR673ZMQ/cherimoya.fold_2.log deleted file mode 100644 index 8ef437cb93410996c166b843409a7eb440a2d9c9..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1950 26.147987127304077 3.80051851272583 258.9459533691406 0.5887083411216736 381.6478576660156 0.42034509778022766 0.56339866 9.027059555053711 True -1 3900 21.516275644302368 0.3960530757904053 262.2738037109375 0.4303169846534729 334.57257080078125 0.5153844952583313 0.6534351 3.479623794555664 True -2 5850 21.529027700424194 0.3602871894836426 255.58914184570312 0.47847747802734375 320.2352294921875 0.5539478659629822 0.6772995 0.9123848080635071 True -3 7800 21.55332922935486 0.35624217987060547 226.80870056152344 0.7480448484420776 316.0243225097656 0.5621719360351562 0.6883101 0.643305242061615 True -4 9750 21.51028823852539 0.352170467376709 228.75730895996094 0.3548905849456787 314.61553955078125 0.5656211972236633 0.6980677 0.5365500450134277 True -5 11700 21.511064529418945 1.117676019668579 230.3572235107422 0.4739518463611603 313.3995666503906 0.5685340166091919 0.6995934 0.508165180683136 True -6 13650 21.533716917037964 0.3518543243408203 282.94891357421875 0.50146484375 312.9367980957031 0.5697545409202576 0.70450145 0.4617060124874115 True -7 15600 21.590457677841187 0.5186824798583984 271.4610290527344 0.5519551634788513 312.4566955566406 0.5707776546478271 0.7049942 0.45686212182044983 True -8 17550 21.58972430229187 0.3492927551269531 249.11195373535156 0.3546750247478485 311.8558654785156 0.5724446177482605 0.71081257 0.44523441791534424 True -9 19500 21.561316967010498 0.3514077663421631 292.04669189453125 0.3603326380252838 311.1365051269531 0.5742782950401306 0.71442306 0.4351889193058014 True -10 21450 21.412540912628174 0.34415578842163086 287.30291748046875 0.5167316198348999 310.381103515625 0.576248824596405 0.716897 0.4223060607910156 True -11 23400 21.117412328720093 0.3490011692047119 227.33750915527344 0.5264142155647278 309.7251281738281 0.5780389904975891 0.720714 0.4177635610103607 True -12 25350 21.68169140815735 24.67278742790222 227.91384887695312 0.4309759736061096 309.27362060546875 0.5793123245239258 0.7268949 0.40473493933677673 True -13 27300 21.102907419204712 0.35256099700927734 273.8165588378906 0.3310908079147339 308.9654846191406 0.5804656744003296 0.73177916 0.39159634709358215 True -14 29250 21.14435386657715 0.34716796875 230.31556701660156 0.32865533232688904 308.61383056640625 0.5811884999275208 0.7349125 0.39108872413635254 True -15 31200 21.062974452972412 0.34771156311035156 270.8033447265625 0.33355557918548584 308.59185791015625 0.5813146829605103 0.7366004 0.3966723680496216 True -16 33150 21.12288188934326 0.3407902717590332 201.6505126953125 0.2936163544654846 308.64398193359375 0.58100825548172 0.73827803 0.3955529034137726 True -17 35100 21.0899920463562 0.3410978317260742 231.0131378173828 0.22132925689220428 308.85748291015625 0.5802726149559021 0.73823553 0.4017415940761566 False -18 37050 21.06839656829834 0.3449723720550537 212.81875610351562 0.2132921814918518 309.2637634277344 0.5792162418365479 0.7350917 0.4107744097709656 False -19 39000 21.114039659500122 0.34563541412353516 270.5419006347656 0.1717146933078766 309.3517761230469 0.578738272190094 0.7334323 0.4129840135574341 False diff --git a/ENCSR673ZMQ/cherimoya.fold_2.performance.tsv b/ENCSR673ZMQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 08e4dca0b74087bb143d8c6987e907c439ea7b51..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.64398193359375 0.33289864659309387 0.5810083746910095 0.2019430547952652 0.7382780313491821 0.7133780717849731 0.3955529034137726 \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_3.evaluate.json b/ENCSR673ZMQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bfedad8667cc6a93ad3d1b31d7c00de7156ecee8..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF503YRJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_3.fit.json b/ENCSR673ZMQ/cherimoya.fold_3.fit.json deleted file mode 100644 index efc2fd7e2d338f52320cca2eeed8cde29cd30c02..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF503YRJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_3.log b/ENCSR673ZMQ/cherimoya.fold_3.log deleted file mode 100644 index a6e5122bccc16e93f870f19c0fc975a5d633e337..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1907 25.284881353378296 3.3018181324005127 222.43026733398438 0.6962122321128845 382.4731750488281 0.42106330394744873 0.5547465 9.563746452331543 True -1 3814 21.025543212890625 0.4142296314239502 231.81591796875 0.5297250747680664 331.7740478515625 0.5244784951210022 0.66029847 3.2501704692840576 True -2 5721 21.030065298080444 0.3910176753997803 274.8368835449219 0.5343040227890015 318.1292724609375 0.5606012344360352 0.6661866 0.9500067830085754 True -3 7628 21.035147190093994 1.739961862564087 235.0247344970703 0.2668013572692871 313.9365234375 0.5689895749092102 0.67199844 0.5677903294563293 True -4 9535 21.04971981048584 0.41167545318603516 218.63626098632812 0.3889768719673157 312.46514892578125 0.5722327828407288 0.6734885 0.5124035477638245 True -5 11442 21.000683307647705 1.0827116966247559 234.66151428222656 0.5188342928886414 311.852294921875 0.5744876861572266 0.682895 0.4891672432422638 True -6 13349 21.050726413726807 0.39570140838623047 257.2924499511719 0.4837559461593628 311.00543212890625 0.5762041211128235 0.688769 0.47468724846839905 True -7 15256 21.033238172531128 6.881045579910278 240.0808868408203 0.4068700075149536 310.1507263183594 0.5785039067268372 0.6926399 0.45647281408309937 True -8 17163 21.66281223297119 24.288444757461548 234.66123962402344 0.38240891695022583 309.57958984375 0.580136239528656 0.6969341 0.44467705488204956 True -9 19070 21.207864999771118 0.39850401878356934 244.71705627441406 0.3504621386528015 309.0318298339844 0.5815041065216064 0.70533204 0.41953033208847046 True -10 20977 21.03597855567932 0.4009430408477783 217.7095947265625 0.43422579765319824 308.3950500488281 0.5832223296165466 0.7126744 0.40532833337783813 True -11 22884 21.040234088897705 0.39568257331848145 243.04873657226562 0.27449023723602295 307.94329833984375 0.5845614075660706 0.7140195 0.40587887167930603 True -12 24791 21.053943395614624 0.40140485763549805 226.42520141601562 0.5058304071426392 307.26495361328125 0.5862550139427185 0.7222758 0.3961375951766968 True -13 26698 21.03288173675537 0.400346040725708 223.5923614501953 0.39419516921043396 306.8877258300781 0.587499737739563 0.72735804 0.38612091541290283 True -14 28605 21.099515438079834 0.3956105709075928 264.9942321777344 0.4831625819206238 306.7166748046875 0.5881027579307556 0.73403007 0.38195741176605225 True -15 30512 21.085912227630615 2.0241687297821045 239.1720733642578 0.2907121777534485 306.5065612792969 0.5885009765625 0.7379149 0.3789750933647156 True -16 32419 21.112587690353394 0.393599271774292 244.5749053955078 0.2278660535812378 306.69219970703125 0.5880628228187561 0.73825485 0.3852478265762329 True -17 34326 21.05123519897461 0.39463281631469727 230.80502319335938 0.19927872717380524 306.908203125 0.5873804688453674 0.7354134 0.39676427841186523 False -18 36233 20.922508001327515 0.39511561393737793 267.22406005859375 0.22925865650177002 307.07403564453125 0.5867979526519775 0.7327632 0.4056456983089447 False -19 38140 20.606391668319702 0.39337921142578125 241.00823974609375 0.1435973346233368 307.2568359375 0.5863609313964844 0.7293889 0.4153512120246887 False diff --git a/ENCSR673ZMQ/cherimoya.fold_3.performance.tsv b/ENCSR673ZMQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0061989c09941e462779a5197ef821ff3c40456c..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -306.69219970703125 0.32978224754333496 0.5880628228187561 0.20123541355133057 0.7382548451423645 0.7134148478507996 0.3852478265762329 \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_4.evaluate.json b/ENCSR673ZMQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 355df0d2fa96096fb778ada84a7cf6768beb0b69..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF503YRJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_4.fit.json b/ENCSR673ZMQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 08195962454a9c51b418e687928828f1b56d6b72..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF503YRJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR673ZMQ/cherimoya.fold_4.log b/ENCSR673ZMQ/cherimoya.fold_4.log deleted file mode 100644 index 008b86345940f35103c5fcd4575e6cf68378d2e9..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1943 25.649250268936157 3.5803415775299072 284.504150390625 0.5698550939559937 379.3984375 0.4191863238811493 0.6164772 8.91352367401123 True -1 3886 21.448872804641724 0.3823978900909424 234.82156372070312 0.5954419374465942 332.54595947265625 0.5222119688987732 0.64870423 3.216063976287842 True -2 5829 21.45588755607605 0.36148858070373535 237.44393920898438 1.0252220630645752 319.90008544921875 0.5564723014831543 0.65408856 0.9691682457923889 True -3 7772 21.44866442680359 0.3549778461456299 230.43128967285156 0.5400602221488953 315.0182800292969 0.5674065351486206 0.68625957 0.5754854679107666 True -4 9715 21.418251991271973 0.3603246212005615 255.71377563476562 0.6513018608093262 313.4832458496094 0.5713489055633545 0.6971769 0.5184227824211121 True -5 11658 21.413958311080933 0.4249587059020996 213.8902587890625 0.4337121844291687 312.2720642089844 0.5750859379768372 0.7024646 0.48154616355895996 True -6 13601 21.44143533706665 0.37004542350769043 233.6476593017578 0.4279745817184448 311.58489990234375 0.5770313143730164 0.70828444 0.4735499918460846 True -7 15544 21.483798265457153 1.2785866260528564 235.1320343017578 0.39308714866638184 310.6877746582031 0.5795417428016663 0.71616966 0.45165568590164185 True -8 17487 21.42697310447693 0.36607956886291504 238.08929443359375 0.24503061175346375 310.0777282714844 0.5811769962310791 0.72338194 0.43607693910598755 True -9 19430 21.416285514831543 7.142168045043945 249.83547973632812 0.40862834453582764 309.5970153808594 0.5828337669372559 0.7286831 0.4202747642993927 True -10 21373 21.48999333381653 0.36619043350219727 249.0697479248047 0.4017474055290222 309.0809631347656 0.5841177701950073 0.7282521 0.41870978474617004 False -11 23316 21.49168634414673 0.39745521545410156 253.55642700195312 0.2680770754814148 308.52337646484375 0.585698127746582 0.73112804 0.41665199398994446 True -12 25259 21.510857105255127 0.36070680618286133 264.379638671875 0.29255616664886475 308.0086975097656 0.5870636701583862 0.7375078 0.40530335903167725 True -13 27202 21.58993172645569 0.3620603084564209 201.13015747070312 0.4185512065887451 307.6688232421875 0.5879849791526794 0.74100655 0.39282724261283875 True -14 29145 21.454096794128418 0.35866355895996094 231.99063110351562 0.3323030173778534 307.3272399902344 0.5887020230293274 0.74565285 0.38629966974258423 True -15 31088 21.460789918899536 0.36197876930236816 248.7371826171875 0.23207688331604004 307.3206481933594 0.5887852311134338 0.74887896 0.38459187746047974 True -16 33031 21.44516372680664 7.853872537612915 250.9764404296875 0.2395854890346527 307.4079895019531 0.5882673263549805 0.75087816 0.381824791431427 True -17 34974 21.520496368408203 0.3642449378967285 258.7226867675781 0.21396097540855408 307.6573486328125 0.5876426100730896 0.7511704 0.3810916841030121 True -18 36917 21.477787256240845 0.3695206642150879 223.6307373046875 0.1348053514957428 307.8159484863281 0.5869215130805969 0.7501738 0.3866041898727417 False -19 38860 21.46841311454773 0.3594241142272949 228.35780334472656 0.13837194442749023 307.9975280761719 0.5862438082695007 0.7471562 0.3919215202331543 False diff --git a/ENCSR673ZMQ/cherimoya.fold_4.performance.tsv b/ENCSR673ZMQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0d19eef04d5a9f058043c34635270ffe06f4e591..0000000000000000000000000000000000000000 --- a/ENCSR673ZMQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -307.6573486328125 0.3311372995376587 0.5876425504684448 0.19995476305484772 0.7511703968048096 0.7066029906272888 0.3810916841030121 \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_0.evaluate.json b/ENCSR674JIL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8c215a05f922ec2f1d3299ce31fd1c24250270fe..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF996HIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_0.fit.json b/ENCSR674JIL/cherimoya.fold_0.fit.json deleted file mode 100644 index 26a30a13cc6ca33a285207022b5a45f09b6d48b6..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF996HIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_0.log b/ENCSR674JIL/cherimoya.fold_0.log deleted file mode 100644 index 884d787e5c81721c520d4e7eb085c085ff693b3a..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1757 23.882026433944702 4.218585014343262 137.53790283203125 0.9201546907424927 247.26409912109375 0.11411599069833755 0.2528349 7.224381923675537 True -1 3514 19.530312538146973 1.061448097229004 152.52987670898438 0.674017071723938 217.1932830810547 0.22037163376808167 0.4733584 5.444841384887695 True -2 5271 19.52245855331421 0.40137672424316406 165.82070922851562 1.1467007398605347 199.83282470703125 0.26268771290779114 0.55661464 3.030646562576294 True -3 7028 19.51602554321289 0.38308048248291016 151.6082305908203 1.2482831478118896 195.710205078125 0.27354133129119873 0.5790303 2.1216020584106445 True -4 8785 19.441558361053467 0.37930893898010254 156.4204559326172 0.6618801355361938 193.6607666015625 0.27820974588394165 0.5962994 1.6786104440689087 True -5 10542 19.442591905593872 0.4547550678253174 150.52821350097656 1.0435419082641602 192.4451904296875 0.2815300524234772 0.6054012 1.4655925035476685 True -6 12299 19.452338695526123 0.3795783519744873 155.83631896972656 1.2939563989639282 191.1846160888672 0.2843533456325531 0.6136081 1.2604843378067017 True -7 14056 19.46777105331421 0.37421250343322754 120.1605224609375 0.7440524101257324 190.6486358642578 0.285235196352005 0.62444544 1.1606435775756836 True -8 15813 19.9326229095459 0.9506456851959229 200.97000122070312 1.0239380598068237 189.90963745117188 0.2876613736152649 0.63597125 1.0377596616744995 True -9 17570 19.502722024917603 0.45746421813964844 114.62875366210938 0.9385409355163574 189.02850341796875 0.29012995958328247 0.64833105 0.9460702538490295 True -10 19327 19.507084369659424 0.40039634704589844 127.59814453125 0.7787629961967468 188.6064453125 0.29073747992515564 0.6580391 0.8612549304962158 True -11 21084 19.555009126663208 9.63284969329834 122.33297729492188 0.8099344968795776 187.9488067626953 0.2931109368801117 0.67201865 0.786860466003418 True -12 22841 19.467591762542725 0.37495923042297363 142.2518768310547 0.5527797341346741 187.33314514160156 0.29515790939331055 0.6814088 0.7524501085281372 True -13 24598 19.482916116714478 0.40264129638671875 147.60812377929688 0.891340970993042 187.01185607910156 0.295143723487854 0.6943892 0.7066681385040283 True -14 26355 19.464592456817627 0.3938870429992676 138.3653106689453 0.7581087350845337 186.3328094482422 0.29785090684890747 0.70504606 0.6758376359939575 True -15 28112 19.430599212646484 0.3755197525024414 162.78961181640625 0.47773921489715576 186.29965209960938 0.2974487245082855 0.7100516 0.6592023968696594 True -16 29869 19.47763442993164 0.38515162467956543 132.33840942382812 0.47032177448272705 186.26394653320312 0.2977560758590698 0.7135232 0.6575942039489746 True -17 31626 19.46948266029358 0.36797308921813965 153.61929321289062 0.618502140045166 186.31857299804688 0.2975773811340332 0.71322757 0.6682408452033997 False -18 33383 19.471314191818237 0.3839132785797119 131.77859497070312 0.3038214147090912 186.49034118652344 0.2968531847000122 0.708791 0.6818432807922363 False -19 35140 19.37582516670227 0.37250685691833496 155.22085571289062 0.48069635033607483 186.46136474609375 0.2974373400211334 0.70752907 0.6911271810531616 False diff --git a/ENCSR674JIL/cherimoya.fold_0.performance.tsv b/ENCSR674JIL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 29be104177ec20cc24f6cf63d3b1d7a1f6d590b3..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -186.26394653320312 0.5075218677520752 0.2977560758590698 0.06806140393018723 0.7135232090950012 0.6869258880615234 0.6575942039489746 \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_1.evaluate.json b/ENCSR674JIL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ada780f4d4b106471b6add2b7a6ba6e9d5f93d61..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF996HIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_1.fit.json b/ENCSR674JIL/cherimoya.fold_1.fit.json deleted file mode 100644 index 49fa94329d15967ea3705d6dc14c28045dacf3cd..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF996HIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_1.log b/ENCSR674JIL/cherimoya.fold_1.log deleted file mode 100644 index 448c4437da26a6db304deb9471227bc933f9cbff..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1756 23.799373388290405 4.3818604946136475 125.61817169189453 1.0182908773422241 270.8793029785156 0.11403809487819672 0.25394306 7.715698719024658 True -1 3512 19.506232738494873 0.6039936542510986 133.4490203857422 0.8407171964645386 238.28298950195312 0.23213247954845428 0.4594974 6.724843502044678 True -2 5268 19.452937841415405 0.48657989501953125 146.7853240966797 1.0555391311645508 220.13723754882812 0.2774781286716461 0.5516701 3.0340003967285156 True -3 7024 19.451303958892822 0.481952428817749 163.42208862304688 1.0818455219268799 214.91119384765625 0.28845375776290894 0.5749112 1.9182143211364746 True -4 8780 19.43937849998474 20.543166160583496 192.15899658203125 0.7430409789085388 213.6964874267578 0.290997177362442 0.5828499 1.7025032043457031 True -5 10536 20.223587036132812 0.49259042739868164 142.24942016601562 0.79188072681427 211.48777770996094 0.29613029956817627 0.5960707 1.4988912343978882 True -6 12292 19.45024561882019 0.5015401840209961 133.82635498046875 0.633243978023529 210.2462615966797 0.30088934302330017 0.6007442 1.4702796936035156 True -7 14048 19.408705234527588 13.944111347198486 153.98141479492188 0.6311378479003906 209.4078826904297 0.3021751046180725 0.61482257 1.335782766342163 True -8 15804 19.421119928359985 0.504645586013794 166.77304077148438 0.8136157989501953 208.18716430664062 0.3059791922569275 0.63031673 1.2088016271591187 True -9 17560 19.438323736190796 0.5041909217834473 148.26315307617188 0.6667996644973755 207.1090545654297 0.3073780834674835 0.6464491 1.0152219533920288 True -10 19316 19.4847092628479 0.8867661952972412 155.53297424316406 0.6734892725944519 205.94786071777344 0.31074047088623047 0.6639619 0.9310025572776794 True -11 21072 19.434351205825806 0.49013733863830566 139.273681640625 0.6811518669128418 205.13311767578125 0.31197813153266907 0.68015075 0.8338262438774109 True -12 22828 19.458631992340088 1.5751731395721436 132.184326171875 0.8702254891395569 204.2215576171875 0.31385156512260437 0.69368774 0.7735335230827332 True -13 24584 19.431466341018677 0.4988369941711426 120.88794708251953 0.5155415534973145 203.8092041015625 0.3146851658821106 0.7046406 0.740411639213562 True -14 26340 19.4921395778656 0.5087966918945312 147.64749145507812 0.54051274061203 203.328857421875 0.315406858921051 0.71646136 0.7031349539756775 True -15 28096 19.462350130081177 0.5020768642425537 141.34368896484375 0.5911266803741455 203.09230041503906 0.3143863379955292 0.7249803 0.6716216206550598 True -16 29852 19.445847511291504 0.5046446323394775 135.85238647460938 0.6221493482589722 202.7542724609375 0.31625786423683167 0.7337599 0.6491603851318359 True -17 31608 19.448184967041016 0.5005426406860352 154.961181640625 0.5034235715866089 202.7530517578125 0.315811425447464 0.73693097 0.6436001658439636 True -18 33364 19.411659002304077 0.5002436637878418 137.32705688476562 0.44679245352745056 203.23043823242188 0.3136345446109772 0.7355449 0.6530380249023438 False -19 35120 19.422457218170166 0.5006470680236816 125.35721588134766 0.6117259860038757 203.26365661621094 0.31323373317718506 0.73435104 0.6592920422554016 False diff --git a/ENCSR674JIL/cherimoya.fold_1.performance.tsv b/ENCSR674JIL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8387db6010f7bb56f21a2287dfb58e185c2c9e46..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -202.7530517578125 0.49450626969337463 0.315811425447464 0.07177074253559113 0.7369309663772583 0.7052571773529053 0.6436001658439636 \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_2.evaluate.json b/ENCSR674JIL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 140c43fac8005485848f2d12eb6c7ee2393300a0..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF996HIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_2.fit.json b/ENCSR674JIL/cherimoya.fold_2.fit.json deleted file mode 100644 index a7422a999dd77f62dc2865649bf0bd6e34fd06e8..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF996HIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_2.log b/ENCSR674JIL/cherimoya.fold_2.log deleted file mode 100644 index 9ef574b5f204deb47f975f41d1b35b00cfbd6ca1..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1893 25.31714916229248 4.733731508255005 156.5869140625 1.3287707567214966 250.61724853515625 0.11766891926527023 0.25750142 6.396067142486572 True -1 3786 21.091246366500854 0.39104509353637695 128.37979125976562 0.9399933815002441 217.06446838378906 0.23220117390155792 0.4793839 5.482056140899658 True -2 5679 21.01431894302368 0.3410487174987793 132.0925750732422 0.7713636755943298 202.23944091796875 0.2655993402004242 0.5774938 2.1577343940734863 True -3 7572 20.968406915664673 0.34586334228515625 168.79592895507812 0.9255853891372681 198.9036407470703 0.2759505808353424 0.6036273 1.507013201713562 True -4 9465 20.942022562026978 0.34401726722717285 166.84906005859375 0.7526432275772095 197.52427673339844 0.281442791223526 0.614316 1.3490568399429321 True -5 11358 20.95452570915222 0.3305206298828125 159.61895751953125 1.304640531539917 196.442138671875 0.2843717634677887 0.6246227 1.2379611730575562 True -6 13251 20.855010271072388 0.7500796318054199 169.82632446289062 1.232295274734497 195.47010803222656 0.28787127137184143 0.6392443 1.100640892982483 True -7 15144 20.582517623901367 0.3469581604003906 145.60409545898438 0.6692126989364624 195.23153686523438 0.2882855236530304 0.64616 1.0559639930725098 True -8 17037 20.539260387420654 0.35039472579956055 138.3452606201172 0.43651843070983887 194.0526580810547 0.29193437099456787 0.6557535 0.9753371477127075 True -9 18930 20.534985780715942 0.3495748043060303 138.14935302734375 0.762334942817688 193.82403564453125 0.2920513153076172 0.6639707 0.9399302005767822 True -10 20823 20.561115503311157 0.3373386859893799 158.6072540283203 0.8307250738143921 192.6855926513672 0.2955644428730011 0.6749319 0.8730456829071045 True -11 22716 20.55907964706421 0.35300731658935547 147.20639038085938 0.777660608291626 191.99610900878906 0.296062707901001 0.68364847 0.807865560054779 True -12 24609 20.575732469558716 0.3522047996520996 134.13980102539062 0.7505890130996704 191.39727783203125 0.2975253462791443 0.69547635 0.7566855549812317 True -13 26502 20.544859409332275 0.33830690383911133 144.44863891601562 0.5700994729995728 190.64834594726562 0.30079084634780884 0.70421505 0.7253257632255554 True -14 28395 20.57192635536194 0.32990550994873047 149.9450225830078 0.7276259660720825 190.7672882080078 0.2980457544326782 0.7119848 0.6961850523948669 True -15 30288 20.560412645339966 0.3494374752044678 139.65420532226562 0.7110841274261475 190.51878356933594 0.29858100414276123 0.7197732 0.6665370464324951 True -16 32181 20.53024458885193 1.3645508289337158 132.98904418945312 0.6763852834701538 189.89938354492188 0.3019798994064331 0.72559094 0.6572105884552002 True -17 34074 20.549531936645508 0.3383619785308838 143.52430725097656 0.47221606969833374 190.236328125 0.29941263794898987 0.72392106 0.6595979928970337 False -18 35967 20.538795948028564 0.33750081062316895 129.0940704345703 0.5789469480514526 190.2060546875 0.29987940192222595 0.72264045 0.6677560210227966 False -19 37860 20.572124242782593 0.9817016124725342 119.90934753417969 0.3605220913887024 190.40423583984375 0.29929956793785095 0.7210217 0.6758700013160706 False diff --git a/ENCSR674JIL/cherimoya.fold_2.performance.tsv b/ENCSR674JIL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6504fdc2c952c693ab6db0f4f8dce4f412862695..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -189.89938354492188 0.5053822994232178 0.3019798994064331 0.06825936585664749 0.7255909442901611 0.6943567395210266 0.6572105884552002 \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_3.evaluate.json b/ENCSR674JIL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fb71348b5f5b285294604ae88801e7c956f13e6d..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF996HIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_3.fit.json b/ENCSR674JIL/cherimoya.fold_3.fit.json deleted file mode 100644 index 7cc5b700d55a2cb65c6e79a427f53edc5a4e9f1c..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF996HIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_3.log b/ENCSR674JIL/cherimoya.fold_3.log deleted file mode 100644 index 031820d3d12b8828b326e7246f05744a84109750..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1814 24.283098697662354 3.7159550189971924 172.88406372070312 1.3699039220809937 259.7760925292969 0.12214679270982742 0.26026413 7.70942497253418 True -1 3628 20.0943443775177 0.8381612300872803 148.77940368652344 0.9193389415740967 229.8000030517578 0.22754991054534912 0.45797843 6.540037155151367 True -2 5442 19.66644859313965 0.3769710063934326 184.98867797851562 1.0941399335861206 212.5306396484375 0.27182674407958984 0.53271496 3.3407142162323 True -3 7256 19.687711000442505 0.38553404808044434 177.29220581054688 1.0131078958511353 206.79193115234375 0.2826637923717499 0.5699395 1.8147271871566772 True -4 9070 19.659599542617798 0.36622095108032227 174.7073974609375 0.7843027114868164 205.05209350585938 0.2878112494945526 0.5810888 1.56514310836792 True -5 10884 19.682666063308716 0.36632347106933594 120.23783874511719 0.7630903720855713 203.81980895996094 0.2921806275844574 0.5856184 1.4879645109176636 True -6 12698 19.688207149505615 1.301316499710083 124.96591186523438 0.8475518226623535 202.9143524169922 0.29402467608451843 0.5932952 1.3651121854782104 True -7 14512 19.696876049041748 0.3741443157196045 115.27684020996094 0.9135403633117676 202.49008178710938 0.2938520312309265 0.60743123 1.2454527616500854 True -8 16326 19.678917407989502 0.37882280349731445 144.76251220703125 0.9009816646575928 201.16893005371094 0.2973123788833618 0.62021226 1.1684107780456543 True -9 18140 19.639835596084595 8.641103744506836 146.74404907226562 0.7233010530471802 200.13426208496094 0.29986104369163513 0.6363487 1.085750937461853 True -10 19954 21.137530088424683 0.38282203674316406 126.40984344482422 0.5857693552970886 198.95921325683594 0.3041200041770935 0.6465023 1.01942777633667 True -11 21768 19.721113204956055 0.38337111473083496 149.10121154785156 0.6781439781188965 198.2998046875 0.3053759038448334 0.65841347 0.9207649230957031 True -12 23582 19.750368356704712 0.38490748405456543 110.37425994873047 0.5816026926040649 197.5137481689453 0.30706918239593506 0.67136157 0.8784153461456299 True -13 25396 19.715922594070435 0.3756682872772217 145.63259887695312 0.5812667608261108 197.19195556640625 0.3064229488372803 0.68349135 0.8132253289222717 True -14 27210 19.665013074874878 0.3737032413482666 149.97183227539062 0.8249724507331848 196.71319580078125 0.30777543783187866 0.6962897 0.7595350742340088 True -15 29024 19.655495643615723 1.070258617401123 182.27517700195312 0.6023858785629272 196.5841522216797 0.3068433701992035 0.70523196 0.7183111906051636 True -16 30838 19.697174310684204 0.3661050796508789 147.918212890625 0.4028278589248657 196.71218872070312 0.3062674403190613 0.7114821 0.7122446298599243 True -17 32652 19.68905282020569 0.6721482276916504 152.59361267089844 0.4598115086555481 196.3507080078125 0.3086914122104645 0.710149 0.7101033926010132 False -18 34466 19.703210592269897 0.3796098232269287 195.98153686523438 0.3136628270149231 196.638916015625 0.30689212679862976 0.7075561 0.7214528322219849 False -19 36280 19.698334455490112 9.265995502471924 180.6013946533203 0.5860097408294678 196.47421264648438 0.308534175157547 0.7061468 0.7278841137886047 False diff --git a/ENCSR674JIL/cherimoya.fold_3.performance.tsv b/ENCSR674JIL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 638528c3b991f430557b40b74fd04ae55ad1d941..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -196.71218872070312 0.5012961626052856 0.3062674403190613 0.07017353922128677 0.7114821076393127 0.6791712045669556 0.7122446298599243 \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_4.evaluate.json b/ENCSR674JIL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c95c50ef82e29cd97f28934221e4e0c3b8f954b8..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF996HIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_4.fit.json b/ENCSR674JIL/cherimoya.fold_4.fit.json deleted file mode 100644 index 1296c13805f4e97f8bbe950d86c86ef2665ddec4..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF996HIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR674JIL/cherimoya.fold_4.log b/ENCSR674JIL/cherimoya.fold_4.log deleted file mode 100644 index b3205f955be838bce13e1645762911e2e98d38e6..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1850 24.869606971740723 3.692401647567749 169.10491943359375 0.9102929830551147 236.09161376953125 0.1146634891629219 0.25086236 6.565495014190674 True -1 3700 20.490596055984497 0.44631505012512207 138.75857543945312 1.3736212253570557 205.08837890625 0.22702006995677948 0.47105172 5.337604999542236 True -2 5550 20.470797777175903 0.34806108474731445 150.93026733398438 0.7617199420928955 191.81422424316406 0.257713258266449 0.5499258 2.570500135421753 True -3 7400 20.454838037490845 0.3577263355255127 177.06076049804688 1.072364091873169 188.15484619140625 0.26738306879997253 0.5759333 1.7058175802230835 True -4 9250 20.466228723526 0.6551175117492676 177.9704132080078 1.145965576171875 186.77740478515625 0.2719413936138153 0.5874658 1.5308235883712769 True -5 11100 20.465317010879517 0.37386226654052734 130.2187042236328 0.706004798412323 185.576904296875 0.2743496596813202 0.595401 1.3718575239181519 True -6 12950 20.452280521392822 0.36586666107177734 159.94802856445312 0.7673259973526001 185.01785278320312 0.2751724421977997 0.6111459 1.2406154870986938 True -7 14800 20.42744016647339 0.36168694496154785 129.5387725830078 0.824658989906311 183.99002075195312 0.2781682312488556 0.6235755 1.1147496700286865 True -8 16650 20.46171498298645 0.36426687240600586 127.595947265625 0.6569185256958008 183.39297485351562 0.2804376482963562 0.6250232 1.0549548864364624 True -9 18500 20.477325916290283 0.3625195026397705 136.31967163085938 0.743849515914917 182.66458129882812 0.28248006105422974 0.63610923 0.9497658610343933 True -10 20350 20.49132513999939 0.36155271530151367 160.7694091796875 0.872667670249939 182.0547332763672 0.28398990631103516 0.6494494 0.883610725402832 True -11 22200 20.802642107009888 0.3613321781158447 173.99432373046875 0.666128933429718 181.10899353027344 0.28770798444747925 0.6661997 0.8161348104476929 True -12 24050 20.046083450317383 0.4785759449005127 169.6786346435547 1.0644023418426514 180.73568725585938 0.28776228427886963 0.67627895 0.7648111581802368 True -13 25900 20.119025707244873 0.36115479469299316 159.74771118164062 0.7231341600418091 180.1582489013672 0.2899409234523773 0.6878234 0.7137174010276794 True -14 27750 20.072875261306763 0.358428955078125 127.89374542236328 0.8157201409339905 180.01223754882812 0.2890405058860779 0.6966557 0.677665114402771 True -15 29600 20.052528619766235 0.3507575988769531 124.66886138916016 0.7102789878845215 179.33673095703125 0.2918180227279663 0.70347613 0.6571212410926819 True -16 31450 20.067124366760254 0.35522913932800293 144.85252380371094 0.63663649559021 179.27581787109375 0.29164204001426697 0.7062362 0.6551353931427002 True -17 33300 20.01947283744812 0.36237168312072754 146.46585083007812 0.49972909688949585 179.59312438964844 0.28975144028663635 0.7047647 0.6626843214035034 False -18 35150 20.096636056900024 0.9842655658721924 137.58282470703125 0.515324592590332 179.776611328125 0.28904709219932556 0.70287913 0.6744612455368042 False -19 37000 20.038014888763428 0.36775898933410645 133.21780395507812 0.5214196443557739 179.72763061523438 0.2896449863910675 0.7005838 0.6855323910713196 False diff --git a/ENCSR674JIL/cherimoya.fold_4.performance.tsv b/ENCSR674JIL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 33371345bfa0d0db22a1879243885b63a831f7e3..0000000000000000000000000000000000000000 --- a/ENCSR674JIL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -179.27581787109375 0.512739896774292 0.29164204001426697 0.06388580054044724 0.7062361836433411 0.6779476404190063 0.6551353931427002 \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_0.evaluate.json b/ENCSR678PDD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 996461a6d0311171a424c3bd7a48c7c81a9cf81a..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF400ATH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_0.fit.json b/ENCSR678PDD/cherimoya.fold_0.fit.json deleted file mode 100644 index 6022bb573841f7de8d41c87b8f89e66dd9249f9e..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF400ATH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_0.log b/ENCSR678PDD/cherimoya.fold_0.log deleted file mode 100644 index 77168fbac0a2f3db47b561e3b0529c7a41fd3ae4..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2717 34.15485191345215 3.662606716156006 1056.843994140625 0.5184760093688965 1427.296875 0.30720871686935425 0.62997913 9.147186279296875 True -1 5434 29.300203561782837 0.674612283706665 850.5615844726562 0.7052516937255859 1227.4315185546875 0.4607725739479065 0.7066061 1.4506654739379883 True -2 8151 29.84011960029602 0.6298503875732422 1087.4658203125 0.6460181474685669 1201.646484375 0.4748551547527313 0.7081604 0.5871074199676514 True -3 10868 29.910401582717896 0.6204020977020264 969.4042358398438 0.5310370326042175 1186.72705078125 0.4821757376194 0.7109545 0.4815951883792877 True -4 13585 29.826127529144287 0.5876603126525879 953.93017578125 0.6710038781166077 1173.9656982421875 0.49125322699546814 0.71522784 0.4164569079875946 True -5 16302 29.835774660110474 0.677509069442749 909.57080078125 0.3378380537033081 1170.38916015625 0.49337252974510193 0.712016 0.4144001603126526 False -6 19019 29.785435438156128 0.5810256004333496 1037.225341796875 0.41787129640579224 1163.1226806640625 0.4977962374687195 0.71384907 0.3675183355808258 False -7 21736 29.77239227294922 0.7749860286712646 1200.335205078125 0.39464980363845825 1159.475830078125 0.49868083000183105 0.72392875 0.3568355143070221 True -8 24453 29.88912558555603 0.6032743453979492 1004.131591796875 0.5607373714447021 1153.8699951171875 0.5042092800140381 0.733955 0.34093308448791504 True -9 27170 29.825013399124146 0.5843021869659424 884.8071899414062 0.41496074199676514 1149.77294921875 0.5070368647575378 0.7425023 0.3376181721687317 True -10 29887 29.883305311203003 0.5898182392120361 910.74853515625 0.33302295207977295 1145.3717041015625 0.5106568932533264 0.7518765 0.3227798640727997 True -11 32604 29.834235668182373 0.5875210762023926 839.38525390625 0.368161141872406 1141.6588134765625 0.5112345218658447 0.75833 0.3152172863483429 True -12 35321 29.807049036026 0.590918779373169 922.8488159179688 0.37315917015075684 1133.35498046875 0.5192672610282898 0.7686553 0.30688047409057617 True -13 38038 29.817468643188477 0.5899844169616699 978.4756469726562 0.5256814956665039 1131.3211669921875 0.5200080871582031 0.78303933 0.29128238558769226 True -14 40755 29.82576894760132 0.5842616558074951 923.970458984375 0.3669479489326477 1127.2327880859375 0.5228555798530579 0.7931773 0.2830704152584076 True -15 43472 29.884504795074463 0.5910308361053467 926.1617431640625 0.2830856740474701 1124.2288818359375 0.5251067876815796 0.80245274 0.27410614490509033 True -16 46189 29.931591272354126 0.6172082424163818 773.546630859375 0.30905523896217346 1124.8463134765625 0.5237230062484741 0.8101659 0.26540127396583557 True -17 48906 29.840986013412476 0.5779509544372559 799.409423828125 0.306458055973053 1123.95068359375 0.5250587463378906 0.8119766 0.26577162742614746 True -18 51623 29.841200828552246 0.5801963806152344 838.8197631835938 0.43971312046051025 1124.668701171875 0.5236048698425293 0.8125183 0.26854339241981506 True -19 54340 29.860707759857178 0.5908422470092773 938.6971435546875 0.29053816199302673 1125.6177978515625 0.5236767530441284 0.8142497 0.26803094148635864 True diff --git a/ENCSR678PDD/cherimoya.fold_0.performance.tsv b/ENCSR678PDD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8bfa0e1c597070999a372f046a8c29dc418f8596..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1125.6177978515625 0.2621298134326935 0.5236768126487732 0.27860140800476074 0.8142496943473816 0.7616763114929199 0.26803094148635864 \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_1.evaluate.json b/ENCSR678PDD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ebcc8afc6e04de921ddce5cf33407fe90f6db8ad..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF400ATH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_1.fit.json b/ENCSR678PDD/cherimoya.fold_1.fit.json deleted file mode 100644 index 45a02f11a636d46c4998ff01436d8a99322ad2ed..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF400ATH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_1.log b/ENCSR678PDD/cherimoya.fold_1.log deleted file mode 100644 index 4d8ee255e5f490ffd8e739cd462e57b0c6367645..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2708 34.40683341026306 4.610039472579956 1172.601806640625 0.7700533866882324 1636.17724609375 0.3051411211490631 0.6445426 7.872000217437744 True -1 5416 29.798074960708618 2.1991167068481445 1092.40576171875 0.8405461311340332 1394.8272705078125 0.46590331196784973 0.7089576 1.7701917886734009 True -2 8124 29.373062133789062 0.7368133068084717 939.523193359375 0.6225529909133911 1349.697509765625 0.4854018986225128 0.7028687 0.6533350348472595 False -3 10832 29.195109605789185 0.6798560619354248 1082.09716796875 0.8380107879638672 1325.65625 0.4937680959701538 0.722334 0.5666444897651672 True -4 13540 29.199708223342896 0.6612973213195801 850.644775390625 0.7959127426147461 1314.0899658203125 0.49869194626808167 0.73310196 0.5032315850257874 True -5 16248 29.248024225234985 2.576666831970215 890.09326171875 0.6432468295097351 1301.4686279296875 0.5081800818443298 0.72993493 0.48746538162231445 False -6 18956 29.203439950942993 0.6537919044494629 920.5020751953125 0.35386157035827637 1300.5059814453125 0.5077228546142578 0.73078555 0.43103688955307007 False -7 21664 29.194369077682495 0.6641232967376709 899.75244140625 0.5117790699005127 1291.730224609375 0.5115148425102234 0.73778313 0.41744476556777954 True -8 24372 29.170067310333252 0.6798403263092041 869.1103515625 0.641708493232727 1281.7105712890625 0.5179333090782166 0.7473111 0.38867947459220886 True -9 27080 29.152090549468994 0.6637189388275146 919.1318359375 0.41813382506370544 1278.8270263671875 0.5193592309951782 0.75580484 0.3739210069179535 True -10 29788 29.142069339752197 0.6749992370605469 974.1231079101562 0.3746911883354187 1271.053466796875 0.5229896306991577 0.76893926 0.35735243558883667 True -11 32496 29.146620512008667 0.6659126281738281 868.457275390625 0.4562634825706482 1268.6910400390625 0.5228697061538696 0.77590317 0.345924973487854 True -12 35204 29.203243255615234 0.6649465560913086 1019.6912231445312 0.45828020572662354 1258.9227294921875 0.5294581055641174 0.7883176 0.327249139547348 True -13 37912 29.143840789794922 0.6845698356628418 874.861328125 0.3239429295063019 1258.301025390625 0.5288715958595276 0.798572 0.31561461091041565 True -14 40620 29.185152530670166 2.129517078399658 860.0064697265625 0.3743934631347656 1249.5196533203125 0.5335796475410461 0.8079206 0.3060108721256256 True -15 43328 29.207854747772217 0.6750659942626953 997.53662109375 0.4531340003013611 1248.1737060546875 0.5340421795845032 0.8136909 0.30358654260635376 True -16 46036 29.19388771057129 0.7748901844024658 952.7362060546875 0.34824123978614807 1245.891845703125 0.5343135595321655 0.8201865 0.29914671182632446 True -17 48744 29.231826305389404 0.6697311401367188 820.3848876953125 0.24863827228546143 1241.3636474609375 0.5389948487281799 0.8256549 0.29430800676345825 True -18 51452 29.21770477294922 0.6410245895385742 895.0477294921875 0.26967573165893555 1239.912109375 0.5391618609428406 0.8268608 0.29568079113960266 True -19 54160 29.219510316848755 0.6584343910217285 959.0623779296875 0.22274474799633026 1243.941650390625 0.5349109768867493 0.826582 0.297568678855896 False diff --git a/ENCSR678PDD/cherimoya.fold_1.performance.tsv b/ENCSR678PDD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 484a673b273ee39e6434c07b2ace60ca9577fa75..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1239.912109375 0.24979275465011597 0.5391618609428406 0.30130237340927124 0.826860785484314 0.7964131236076355 0.29568079113960266 \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_2.evaluate.json b/ENCSR678PDD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bde2d4a9c6622ba5b9090abc34b3f4ebb0365a22..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF400ATH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_2.fit.json b/ENCSR678PDD/cherimoya.fold_2.fit.json deleted file mode 100644 index 8a655130dcbbd71c4b90c7c5892cc9a07448b171..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF400ATH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_2.log b/ENCSR678PDD/cherimoya.fold_2.log deleted file mode 100644 index bfb4a8ab458de5246a7bdf17296f45db4c64306d..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 35.86197638511658 3.817786455154419 1113.8291015625 0.5532281398773193 1485.9503173828125 0.3138231933116913 0.6427717 7.072404384613037 True -1 5746 31.598636627197266 0.6193480491638184 1078.807373046875 0.7632782459259033 1262.764404296875 0.47092899680137634 0.69887066 1.8158116340637207 True -2 8619 31.341304302215576 0.560293436050415 1081.08154296875 0.5048996806144714 1239.2672119140625 0.4825889468193054 0.7012241 0.6786636114120483 True -3 11492 30.957359552383423 0.9816365242004395 966.6261596679688 0.6419664025306702 1226.1339111328125 0.48824554681777954 0.71415013 0.5795185565948486 True -4 14365 31.035674333572388 0.5587255954742432 850.9279174804688 0.5627079606056213 1216.741943359375 0.49254879355430603 0.719383 0.49314919114112854 True -5 17238 31.155789852142334 0.5429186820983887 997.4715576171875 0.5209032893180847 1206.7718505859375 0.4990789294242859 0.7257255 0.4746719300746918 True -6 20111 31.03731656074524 0.5384421348571777 1049.6671142578125 0.4971274733543396 1202.4361572265625 0.5024824142456055 0.73141825 0.4329826533794403 True -7 22984 31.10734796524048 0.5400381088256836 851.8946533203125 0.2203781008720398 1197.558837890625 0.5042969584465027 0.73225087 0.4089512825012207 True -8 25857 31.07086753845215 0.5396287441253662 877.7978515625 0.3639131188392639 1191.125 0.5080950856208801 0.7426157 0.39251357316970825 True -9 28730 31.12033224105835 0.5387790203094482 1002.6041870117188 0.6081844568252563 1185.2418212890625 0.5126169919967651 0.7475825 0.36820852756500244 True -10 31603 31.07798171043396 0.5357329845428467 840.9871826171875 0.4982881546020508 1176.6190185546875 0.5180648565292358 0.759862 0.35364413261413574 True -11 34476 31.06386923789978 0.5388839244842529 841.7568359375 0.4692274332046509 1173.992919921875 0.5192914009094238 0.76811135 0.3514191210269928 True -12 37349 31.03856086730957 0.536686897277832 846.6072998046875 0.29091495275497437 1169.2020263671875 0.5215167999267578 0.7791501 0.34333565831184387 True -13 40222 31.038914442062378 1.707221508026123 820.1444702148438 0.3519822359085083 1164.8319091796875 0.526226818561554 0.78426254 0.32685473561286926 True -14 43095 31.072901248931885 2.9759140014648438 994.7525024414062 0.2897629737854004 1163.3780517578125 0.526709258556366 0.79609734 0.3094726502895355 True -15 45968 31.168691396713257 1.758000135421753 968.766845703125 0.33633914589881897 1159.8779296875 0.5278522968292236 0.8012057 0.305049329996109 True -16 48841 31.1113383769989 23.355319023132324 825.3285522460938 0.3229595124721527 1155.7764892578125 0.531258761882782 0.80522096 0.3007294535636902 True -17 51714 31.170812606811523 0.5535333156585693 854.8314208984375 0.2585987448692322 1156.960205078125 0.530938982963562 0.80980617 0.2975773811340332 True -18 54587 31.04278016090393 0.5401270389556885 900.692138671875 0.2081427276134491 1158.8475341796875 0.5283032059669495 0.8108999 0.295021653175354 True -19 57460 31.105807304382324 0.5557975769042969 990.3090209960938 0.2754938006401062 1154.70068359375 0.5331346392631531 0.80868953 0.2964737117290497 False diff --git a/ENCSR678PDD/cherimoya.fold_2.performance.tsv b/ENCSR678PDD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9616deec826c790c9dceea798a5c65772c45879c..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1158.8475341796875 0.2586085796356201 0.5283032059669495 0.2869880497455597 0.8108999133110046 0.7697583436965942 0.295021653175354 \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_3.evaluate.json b/ENCSR678PDD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 734e67f0e299b54ab7dfae52fef7d7b530c3bb4e..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF400ATH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_3.fit.json b/ENCSR678PDD/cherimoya.fold_3.fit.json deleted file mode 100644 index 1d1d2be3f6c01f84309211f3694ccd229d190948..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF400ATH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_3.log b/ENCSR678PDD/cherimoya.fold_3.log deleted file mode 100644 index 52e1e50f144c81c7a88877fb63ae3cffa637dbda..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.53306198120117 3.7494425773620605 1023.623046875 0.6741195917129517 1499.4498291015625 0.30722323060035706 0.6410324 9.100590705871582 True -1 5514 30.289714097976685 0.534543514251709 992.6566162109375 0.5932408571243286 1291.41943359375 0.46507665514945984 0.7156037 1.535101056098938 True -2 8271 30.00981378555298 0.5866022109985352 1026.97900390625 0.6941040754318237 1260.189208984375 0.4817856550216675 0.7065409 0.6900944113731384 False -3 11028 29.67119002342224 0.5713684558868408 907.7966918945312 0.45188480615615845 1250.2144775390625 0.48379379510879517 0.71233577 0.5524342060089111 False -4 13785 29.703036069869995 0.5641210079193115 998.6578369140625 0.5219210386276245 1240.550048828125 0.4884759485721588 0.716826 0.5323070883750916 True -5 16542 29.713002681732178 0.5462131500244141 947.9197998046875 0.380916029214859 1234.3389892578125 0.49159035086631775 0.71662635 0.5130755305290222 False -6 19299 29.654964208602905 1.1652259826660156 948.5300903320312 0.4133131504058838 1228.857177734375 0.4955197870731354 0.7260858 0.44743719696998596 True -7 22056 29.76609468460083 0.5489470958709717 1266.669677734375 0.6239649057388306 1221.822509765625 0.4996475577354431 0.72690535 0.43383872509002686 True -8 24813 29.706390619277954 1.330953598022461 877.68505859375 0.404834121465683 1222.029296875 0.49910974502563477 0.72974247 0.4159401059150696 True -9 27570 29.6883385181427 0.5679342746734619 1050.8436279296875 0.37416183948516846 1211.8834228515625 0.5059008598327637 0.7375948 0.38751962780952454 True -10 30327 29.73870825767517 0.575434684753418 902.2764892578125 0.4773397743701935 1206.24658203125 0.5100769996643066 0.7445426 0.3711759150028229 True -11 33084 29.877272605895996 0.5539968013763428 987.87353515625 0.38577234745025635 1202.5875244140625 0.5104888081550598 0.76077193 0.3583233654499054 True -12 35841 29.744351625442505 0.5657496452331543 1162.92041015625 0.4026865065097809 1196.8497314453125 0.5155438184738159 0.77369136 0.34807056188583374 True -13 38598 29.82987403869629 0.5628526210784912 907.12744140625 0.4826728105545044 1191.1790771484375 0.5180678367614746 0.78615093 0.32260245084762573 True -14 41355 29.837491512298584 0.5579378604888916 1009.1426391601562 0.30410856008529663 1187.9351806640625 0.521672785282135 0.7945614 0.31582459807395935 True -15 44112 29.72961163520813 0.5777254104614258 882.0321044921875 0.3029976785182953 1183.547607421875 0.5224341154098511 0.8069646 0.299267053604126 True -16 46869 29.696489095687866 1.1066858768463135 947.2615356445312 0.3686089515686035 1179.7176513671875 0.5249277949333191 0.813673 0.29476749897003174 True -17 49626 29.764788150787354 1.9285621643066406 1027.0677490234375 0.27536430954933167 1181.0810546875 0.5239879488945007 0.81658214 0.2939017415046692 True -18 52383 29.694379329681396 21.784790754318237 896.2545776367188 0.2601061463356018 1178.556640625 0.5265887379646301 0.8180028 0.2921118140220642 True -19 55140 29.751206874847412 0.5579686164855957 1107.3076171875 0.22281873226165771 1183.1065673828125 0.5225157737731934 0.8201749 0.29298579692840576 True diff --git a/ENCSR678PDD/cherimoya.fold_3.performance.tsv b/ENCSR678PDD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6a74d6805dcb57915c0a680ff78381e15cea565b..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1183.1065673828125 0.25960618257522583 0.5225158333778381 0.2842444181442261 0.8201748728752136 0.7717374563217163 0.29298579692840576 \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_4.evaluate.json b/ENCSR678PDD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9e2576e9970ab09f16d224e9fe75c78d255af9dd..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF400ATH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_4.fit.json b/ENCSR678PDD/cherimoya.fold_4.fit.json deleted file mode 100644 index e5c880134548f3c3ce624e55158438b080f9627d..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF400ATH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_4.log b/ENCSR678PDD/cherimoya.fold_4.log deleted file mode 100644 index 4057fd040fb4d87e81fffe20dcad277706cefa43..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2856 36.14880394935608 4.5414814949035645 1013.375 0.9544016122817993 1389.999755859375 0.30616867542266846 0.6353667 6.925800323486328 True -1 5712 31.186248302459717 0.8923783302307129 928.44580078125 0.651508092880249 1200.9278564453125 0.46085280179977417 0.6853355 1.2040215730667114 True -2 8568 31.419564962387085 0.5882718563079834 1093.5235595703125 0.6036536693572998 1181.134765625 0.47156810760498047 0.693375 0.6739857792854309 True -3 11424 31.28202986717224 0.5621011257171631 1032.2349853515625 0.803492546081543 1168.4139404296875 0.4792560338973999 0.69812757 0.6308251619338989 True -4 14280 30.69952368736267 21.772866249084473 1077.406982421875 0.4895145893096924 1162.590087890625 0.4829385578632355 0.69318044 0.46849024295806885 False -5 17136 30.833001375198364 0.5714693069458008 951.4073486328125 0.4179169833660126 1155.631591796875 0.48791801929473877 0.7016672 0.42465710639953613 True -6 19992 39.17110276222229 6.847887754440308 842.9321899414062 0.48307257890701294 1150.642333984375 0.49099001288414 0.7129053 0.39776283502578735 True -7 22848 30.89811944961548 0.5782599449157715 931.5757446289062 0.6280975341796875 1146.7249755859375 0.49331244826316833 0.7159787 0.3785198926925659 True -8 25704 30.797464609146118 0.5742738246917725 996.086181640625 0.4510464668273926 1142.37646484375 0.4971030056476593 0.7227779 0.3697049915790558 True -9 28560 31.007253646850586 0.5659394264221191 839.4685668945312 0.3221651315689087 1135.176025390625 0.5023000240325928 0.72878927 0.35802286863327026 True -10 31416 30.946925401687622 0.5723435878753662 802.008544921875 0.4135971963405609 1131.102294921875 0.5043314099311829 0.73759544 0.35128024220466614 True -11 34272 31.633047342300415 35.27102041244507 741.8024291992188 0.39306795597076416 1126.3856201171875 0.5093557238578796 0.7470214 0.3435216546058655 True -12 37128 30.895315408706665 6.319931983947754 1062.30029296875 0.36820465326309204 1120.2196044921875 0.5128911137580872 0.7591054 0.31795400381088257 True -13 39984 30.9679114818573 0.5833845138549805 1073.718994140625 0.3170420527458191 1115.2720947265625 0.5163818597793579 0.7693196 0.30771636962890625 True -14 42840 31.096911907196045 0.5696465969085693 1023.1621704101562 0.2824298143386841 1110.6890869140625 0.5206652283668518 0.779241 0.2965705394744873 True -15 45696 30.76975917816162 0.5652437210083008 843.5670776367188 0.24988187849521637 1109.9261474609375 0.5209957361221313 0.7879177 0.289342999458313 True -16 48552 30.909220933914185 0.5653200149536133 1080.7308349609375 0.2525918483734131 1110.397705078125 0.5195052623748779 0.79609823 0.27886441349983215 True -17 51408 30.910691022872925 0.5726978778839111 928.8348388671875 0.2701631188392639 1110.783203125 0.5192002654075623 0.8006211 0.27445581555366516 True -18 54264 32.4084632396698 34.005518436431885 863.3033447265625 0.2506139576435089 1110.0863037109375 0.5198201537132263 0.8014452 0.2732005715370178 True -19 57120 30.883885622024536 0.5700232982635498 786.2611083984375 0.2994609475135803 1110.5950927734375 0.5195552110671997 0.80061793 0.2723158597946167 False diff --git a/ENCSR678PDD/cherimoya.fold_4.performance.tsv b/ENCSR678PDD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 13c0141fb92c6073b4b42047dbf8c908e527e5f4..0000000000000000000000000000000000000000 --- a/ENCSR678PDD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1110.0863037109375 0.26377177238464355 0.5198201537132263 0.2769334614276886 0.8014451861381531 0.7503060102462769 0.2732005715370178 \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_0.evaluate.json b/ENCSR679EFH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c0606de20fc3d98d27e51a7d477f6d7595ba7dda..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF522ORI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_0.fit.json b/ENCSR679EFH/cherimoya.fold_0.fit.json deleted file mode 100644 index 73aa70c11c73bbae0bc4e41193aa24c48297d867..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF522ORI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_0.log b/ENCSR679EFH/cherimoya.fold_0.log deleted file mode 100644 index b100b574a1c6e2b7eb05e6dff5feeeb05aa7e1a9..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 34.91256523132324 3.990051507949829 138.92108154296875 0.6016526222229004 230.20310974121094 0.1236545592546463 0.6669824 4.179355621337891 True -1 5534 30.567013025283813 0.8431165218353271 156.04776000976562 0.657899796962738 206.4022674560547 0.17707042396068573 0.7540982 2.129210948944092 True -2 8301 30.60995101928711 0.6564154624938965 174.49842834472656 0.6142153739929199 203.7986297607422 0.1799802929162979 0.7611892 1.1927874088287354 True -3 11068 30.564432621002197 0.5494465827941895 139.10861206054688 0.6678715348243713 200.81407165527344 0.18600992858409882 0.7795255 1.0120681524276733 True -4 13835 30.53989815711975 1.858104944229126 175.01837158203125 0.6667983531951904 199.31639099121094 0.1898849904537201 0.7896498 0.8511250615119934 True -5 16602 30.56365966796875 0.5507891178131104 138.5219268798828 0.6494518518447876 198.5603485107422 0.1919274926185608 0.796703 0.8268303871154785 True -6 19369 30.53791117668152 0.76611328125 141.0873260498047 0.4815707504749298 198.09645080566406 0.1929357647895813 0.8031851 0.7529160976409912 True -7 22136 30.508443355560303 1.3754103183746338 187.52809143066406 0.7062238454818726 197.40509033203125 0.19440464675426483 0.80731004 0.7556141018867493 True -8 24903 30.455913066864014 0.5447697639465332 107.20149230957031 0.5983664989471436 196.09463500976562 0.19881445169448853 0.8203341 0.666083574295044 True -9 27670 30.494251251220703 0.5415036678314209 146.83114624023438 0.4390277862548828 195.9571533203125 0.19873899221420288 0.8285885 0.5973812341690063 True -10 30437 30.48502826690674 0.5413310527801514 136.48863220214844 0.3104008436203003 195.37550354003906 0.1998293697834015 0.83529776 0.5486968159675598 True -11 33204 30.469285249710083 0.5475096702575684 170.29364013671875 0.4586886763572693 194.783935546875 0.20175801217556 0.84025186 0.5150005221366882 True -12 35971 30.50782299041748 2.085400342941284 129.19180297851562 0.5482922792434692 194.25303649902344 0.20274776220321655 0.84717035 0.4831322729587555 True -13 38738 30.54825186729431 0.5409984588623047 122.92451477050781 0.3816452622413635 193.711181640625 0.20366324484348297 0.85176575 0.4559054672718048 True -14 41505 30.211060047149658 0.5402629375457764 137.30252075195312 0.45068594813346863 193.16966247558594 0.20512525737285614 0.855758 0.4375881254673004 True -15 44272 29.98286747932434 0.5323810577392578 167.0167236328125 0.5120836496353149 192.85284423828125 0.206281840801239 0.8589115 0.42104536294937134 True -16 47039 30.03967833518982 0.5350673198699951 153.64093017578125 0.3478985130786896 192.67391967773438 0.2064128816127777 0.8621508 0.4095289409160614 True -17 49806 29.992746591567993 0.5090579986572266 113.19528198242188 0.3437739908695221 192.50894165039062 0.20720450580120087 0.8609623 0.4054812490940094 False -18 52573 29.941476345062256 0.5354759693145752 127.64369201660156 0.4309483766555786 192.735595703125 0.2055366039276123 0.8600218 0.4076288938522339 False -19 55340 29.988362073898315 0.5008103847503662 168.88845825195312 0.39278143644332886 192.8956298828125 0.20485959947109222 0.8592886 0.4086068272590637 False diff --git a/ENCSR679EFH/cherimoya.fold_0.performance.tsv b/ENCSR679EFH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 37aa39360fd0d895a6cf2c0d9d03983fd1569c3e..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -192.67391967773438 0.5560297966003418 0.2064128816127777 0.05404677614569664 0.8621507883071899 0.7877437472343445 0.4095289409160614 \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_1.evaluate.json b/ENCSR679EFH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9b6c1f83d0f13f361cdd74071e6440f737f0e5db..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF522ORI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_1.fit.json b/ENCSR679EFH/cherimoya.fold_1.fit.json deleted file mode 100644 index 4b6ea789b528d115e44d30f2d93db33f4d682fbe..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF522ORI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_1.log b/ENCSR679EFH/cherimoya.fold_1.log deleted file mode 100644 index 3c6b4a137a4ea3c3f6b85a582def3af8c1003ed7..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.95283651351929 4.059342622756958 170.324951171875 0.46642088890075684 262.35101318359375 0.1298317313194275 0.6943892 4.1320648193359375 True -1 5484 30.296637535095215 1.0820960998535156 123.76376342773438 0.5912626385688782 237.52490234375 0.18526260554790497 0.75842774 2.0960566997528076 True -2 8226 30.267303943634033 1.549424409866333 150.9266357421875 0.758336067199707 232.07736206054688 0.1921454817056656 0.77310294 1.1577327251434326 True -3 10968 30.250107049942017 0.8172955513000488 137.92872619628906 0.5675373673439026 229.40647888183594 0.195764422416687 0.79633445 0.9964631199836731 True -4 13710 30.257161617279053 0.7481093406677246 213.97705078125 0.6900454163551331 226.74778747558594 0.2014104723930359 0.80566347 0.8515886068344116 True -5 16452 30.252756595611572 0.7551164627075195 115.83353424072266 0.7095764875411987 225.8257293701172 0.2042207568883896 0.81143993 0.8326609134674072 True -6 19194 30.251640796661377 2.213068723678589 150.77113342285156 0.6327474117279053 224.49740600585938 0.20716290175914764 0.8222774 0.8178958296775818 True -7 21936 30.198951959609985 0.7843005657196045 126.66313171386719 0.5362280607223511 223.7421112060547 0.2082296758890152 0.8289966 0.7851622104644775 True -8 24678 30.174173593521118 0.7620487213134766 101.22529602050781 0.701806902885437 222.7921905517578 0.21050570905208588 0.83426946 0.752363383769989 True -9 27420 29.67642903327942 0.7983002662658691 99.862548828125 0.49064838886260986 221.77392578125 0.2135208696126938 0.8417616 0.6823678016662598 True -10 30162 29.62665891647339 1.693986415863037 129.7827606201172 0.5237475633621216 221.1116180419922 0.214473158121109 0.85067356 0.6116409301757812 True -11 32904 29.6526620388031 1.418431043624878 125.26929473876953 0.6227985620498657 220.48434448242188 0.2154812216758728 0.85913736 0.5628397464752197 True -12 35646 29.700518369674683 2.0656657218933105 205.47482299804688 0.43396204710006714 219.91928100585938 0.21683605015277863 0.8653971 0.5250276923179626 True -13 38388 29.663490056991577 0.7814407348632812 209.22938537597656 0.40701454877853394 219.2544403076172 0.21794040501117706 0.86786306 0.5003401041030884 True -14 41130 29.686466455459595 0.7614574432373047 172.9822998046875 0.4596191346645355 218.46583557128906 0.2195754051208496 0.87157744 0.48180636763572693 True -15 43872 29.72573757171631 0.7709593772888184 129.6393280029297 0.5047907829284668 218.2067108154297 0.22016595304012299 0.874358 0.45110535621643066 True -16 46614 29.704190969467163 1.9087860584259033 153.02566528320312 0.43006429076194763 217.74159240722656 0.2206002175807953 0.8774298 0.4370833933353424 True -17 49356 29.709694623947144 0.7226452827453613 143.900634765625 0.5531954765319824 217.87933349609375 0.22059094905853271 0.8786068 0.43218284845352173 True -18 52098 29.64594078063965 0.7906873226165771 168.26719665527344 0.4301120638847351 218.0010986328125 0.2204969972372055 0.8776512 0.43321046233177185 False -19 54840 29.645472526550293 1.2780797481536865 135.2899932861328 0.45431196689605713 218.2970428466797 0.21898174285888672 0.876966 0.4366587698459625 False diff --git a/ENCSR679EFH/cherimoya.fold_1.performance.tsv b/ENCSR679EFH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 09c391a210c6dfff3de0f0d85ab4e4801e98dac9..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -217.87933349609375 0.5445480942726135 0.22059093415737152 0.06037523224949837 0.8786067962646484 0.8253076672554016 0.43218284845352173 \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_2.evaluate.json b/ENCSR679EFH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index aa60a4ef621ceaf0335d7e1d3a7d3ad2d6539f32..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF522ORI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_2.fit.json b/ENCSR679EFH/cherimoya.fold_2.fit.json deleted file mode 100644 index 24dcc543819bfaf0b30925607f668be7ba63db17..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF522ORI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_2.log b/ENCSR679EFH/cherimoya.fold_2.log deleted file mode 100644 index 63018aaba32a88d072ce2879b561430caf948a28..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.37607979774475 4.671045780181885 181.3252410888672 0.6170852184295654 251.5908966064453 0.13450133800506592 0.6508604 3.8872458934783936 True -1 5794 31.982150554656982 0.5399761199951172 162.2361297607422 0.6386069655418396 224.41082763671875 0.19147169589996338 0.76331156 1.9023380279541016 True -2 8691 32.00619912147522 2.3083813190460205 196.83941650390625 0.8308610916137695 219.3328399658203 0.19705337285995483 0.77619404 0.9519757032394409 True -3 11588 31.529787063598633 0.5052847862243652 124.15406036376953 0.6130723357200623 218.27513122558594 0.1983521431684494 0.7804096 0.8960063457489014 True -4 14485 31.27940845489502 0.5007035732269287 176.4476776123047 0.6980801820755005 216.46434020996094 0.20278716087341309 0.7887445 0.8433257937431335 True -5 17382 31.31468415260315 0.5301017761230469 176.5321502685547 0.7574462890625 214.66058349609375 0.20711998641490936 0.801582 0.8176882266998291 True -6 20279 31.348137378692627 0.48439979553222656 218.62071228027344 0.6165378093719482 214.10479736328125 0.20783793926239014 0.80737716 0.8052679300308228 True -7 23176 31.27745032310486 0.494565486907959 126.23005676269531 0.49059173464775085 213.59059143066406 0.20970086753368378 0.81615824 0.7599093914031982 True -8 26073 31.340981245040894 0.47585201263427734 163.20144653320312 0.49873507022857666 212.311767578125 0.2129998356103897 0.8222468 0.6942607760429382 True -9 28970 31.343735218048096 0.4881467819213867 184.09988403320312 0.6409605145454407 211.84722900390625 0.21415084600448608 0.8295263 0.6357114315032959 True -10 31867 31.355777263641357 1.3054900169372559 135.98081970214844 0.5179077386856079 210.9337615966797 0.2166270911693573 0.833795 0.5858831405639648 True -11 34764 31.323298931121826 0.6297550201416016 153.71304321289062 0.6727594137191772 210.63742065429688 0.21781231462955475 0.83643305 0.5495467782020569 True -12 37661 31.508357524871826 0.4918501377105713 183.0587615966797 0.6135562658309937 209.87203979492188 0.2193320393562317 0.8439558 0.5235936045646667 True -13 40558 31.443525791168213 0.5054116249084473 142.61294555664062 0.29011034965515137 209.2406005859375 0.22080670297145844 0.84653646 0.5077015161514282 True -14 43455 31.42965030670166 0.5051953792572021 163.03521728515625 0.4133671224117279 208.66952514648438 0.22216354310512543 0.8514194 0.48539969325065613 True -15 46352 31.34358549118042 0.4922139644622803 179.29470825195312 0.48848867416381836 208.40562438964844 0.2226496785879135 0.8542796 0.4658855199813843 True -16 49249 31.377220630645752 0.48635220527648926 139.72689819335938 0.8298158049583435 208.3599090576172 0.22309280931949615 0.8556076 0.45320165157318115 True -17 52146 31.459219932556152 1.2197771072387695 165.28179931640625 0.39071714878082275 208.3566131591797 0.22279973328113556 0.8547467 0.44891834259033203 False -18 55043 31.462104558944702 0.49195051193237305 194.65084838867188 0.5009958744049072 208.28985595703125 0.22322513163089752 0.8557887 0.4488644599914551 True -19 57940 31.362436294555664 0.4875457286834717 154.0608673095703 0.4785521626472473 208.5002899169922 0.22238789498806 0.8552808 0.4503389894962311 False diff --git a/ENCSR679EFH/cherimoya.fold_2.performance.tsv b/ENCSR679EFH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 700b1d5c9bdeeb9f11c1b24259167cc8f58d6116..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -208.28985595703125 0.5448182821273804 0.22322513163089752 0.058730386197566986 0.8557887077331543 0.7971594929695129 0.4488644599914551 \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_3.evaluate.json b/ENCSR679EFH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2acab3d1e460a9c3d5e3dddecc055a90daf0ec43..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF522ORI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_3.fit.json b/ENCSR679EFH/cherimoya.fold_3.fit.json deleted file mode 100644 index 89f93e0a7d6afae2f846a779521dd5cfbb344b4f..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF522ORI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_3.log b/ENCSR679EFH/cherimoya.fold_3.log deleted file mode 100644 index 0423819ba6e3ca2e2f94ef064735d837c74816da..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 35.43207502365112 3.684238910675049 156.80609130859375 0.595267653465271 254.78428649902344 0.13805581629276276 0.64636797 3.9484758377075195 True -1 5540 30.611379623413086 1.1527180671691895 189.47503662109375 0.6970062255859375 231.7925567626953 0.18816755712032318 0.7239928 2.40224289894104 True -2 8310 30.607258081436157 1.6900813579559326 189.3985595703125 0.47397753596305847 229.9490966796875 0.19108429551124573 0.7262101 1.6168626546859741 True -3 11080 30.498727560043335 0.7562999725341797 126.99153900146484 0.6101599335670471 226.54995727539062 0.19699034094810486 0.7477515 1.3218008279800415 True -4 13850 30.479037284851074 9.425959825515747 174.815673828125 0.6227399110794067 224.9989471435547 0.20100656151771545 0.76956946 1.1474663019180298 True -5 16620 30.51574444770813 13.206981658935547 177.24923706054688 0.7576625943183899 223.89735412597656 0.20381517708301544 0.77558035 1.1488206386566162 True -6 19390 30.526955366134644 0.8444309234619141 125.82476806640625 0.3980867862701416 222.29794311523438 0.20820289850234985 0.7892368 1.0442569255828857 True -7 22160 30.450273036956787 0.513404130935669 193.4307403564453 0.868994951248169 221.18258666992188 0.2110556662082672 0.7984637 0.9793271422386169 True -8 24930 30.477409601211548 0.517711877822876 103.75118255615234 0.9176809191703796 220.92311096191406 0.21224826574325562 0.80140114 0.9595823884010315 True -9 27700 30.471062898635864 0.5177609920501709 135.6531219482422 0.6244596242904663 220.18507385253906 0.21412362158298492 0.8098436 0.8690477609634399 True -10 30470 30.572096586227417 0.5147218704223633 91.62640380859375 0.5931558609008789 219.41781616210938 0.21514910459518433 0.8229884 0.7427616119384766 True -11 33240 30.561354637145996 0.5050060749053955 129.20074462890625 0.38621896505355835 218.95130920410156 0.21633018553256989 0.8278612 0.7067946791648865 True -12 36010 30.555498838424683 0.5206015110015869 160.24620056152344 0.4920397400856018 218.76333618164062 0.21648912131786346 0.8292082 0.6964405179023743 True -13 38780 30.888095140457153 14.69090485572815 162.11672973632812 0.5148663520812988 218.00831604003906 0.21826307475566864 0.838047 0.6326884031295776 True -14 41550 30.77124810218811 15.49428415298462 157.22549438476562 0.49362656474113464 216.8481903076172 0.22109252214431763 0.8443805 0.5835692286491394 True -15 44320 30.862134218215942 0.5474987030029297 183.43829345703125 0.5547631978988647 216.2957305908203 0.2221595048904419 0.8490769 0.5405539870262146 True -16 47090 30.721537351608276 0.5206298828125 120.68914031982422 0.2810608744621277 215.832275390625 0.2232624739408493 0.85376185 0.5160605311393738 True -17 49860 30.649003982543945 0.5139045715332031 180.4132843017578 0.19794884324073792 216.03919982910156 0.22151462733745575 0.8533275 0.49793773889541626 False -18 52630 30.12683415412903 0.5123043060302734 110.54704284667969 0.5097941756248474 216.18869018554688 0.22148297727108002 0.852787 0.49720248579978943 False -19 55400 30.036075115203857 0.5113823413848877 116.50732421875 0.5120940208435059 215.8819122314453 0.22297309339046478 0.85218644 0.49936601519584656 False diff --git a/ENCSR679EFH/cherimoya.fold_3.performance.tsv b/ENCSR679EFH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b2d92fb68f5902808f1c1657f66e8dccbdc84334..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -215.832275390625 0.5430238842964172 0.2232624590396881 0.05842314288020134 0.8537618517875671 0.7992215156555176 0.5160605311393738 \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_4.evaluate.json b/ENCSR679EFH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3f834fa7f6adba3394991709a365e723bec2bec7..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF522ORI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_4.fit.json b/ENCSR679EFH/cherimoya.fold_4.fit.json deleted file mode 100644 index 718d8c06f81cedbc4bcb3fba61a9ba1b40365647..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF522ORI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679EFH/cherimoya.fold_4.log b/ENCSR679EFH/cherimoya.fold_4.log deleted file mode 100644 index d801f975589beb7253087fb34d76f61fb75a2f53..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2807 35.90646481513977 4.068254709243774 178.75332641601562 0.629830002784729 189.05303955078125 0.11125148832798004 0.6480544 3.1577847003936768 True -1 5614 31.05791926383972 0.7529349327087402 136.436279296875 0.6921921968460083 173.19915771484375 0.15178154408931732 0.75263846 1.4858160018920898 True -2 8421 30.98954701423645 10.096145153045654 157.92225646972656 0.734890878200531 170.7605743408203 0.15529286861419678 0.7699718 0.7877525091171265 True -3 11228 31.02782440185547 0.6407177448272705 127.56192779541016 0.5638866424560547 169.32521057128906 0.1582736074924469 0.7798564 0.7311360836029053 True -4 14035 31.112040042877197 0.6365141868591309 152.62574768066406 0.9138930439949036 168.38552856445312 0.16104881465435028 0.7824145 0.7155735492706299 True -5 16842 31.058749437332153 0.8229036331176758 127.24081420898438 0.5006152391433716 167.22067260742188 0.16418609023094177 0.788203 0.7102212309837341 True -6 19649 31.087825059890747 0.6183059215545654 156.6597442626953 0.4453439712524414 166.54722595214844 0.1666625440120697 0.79819673 0.6701235175132751 True -7 22456 30.990811347961426 0.6175322532653809 113.73141479492188 0.46336251497268677 166.23475646972656 0.16648530960083008 0.80348134 0.6097291111946106 True -8 25263 30.933023691177368 0.611915111541748 147.93841552734375 0.6338897943496704 165.55221557617188 0.1688266545534134 0.8173736 0.53755122423172 True -9 28070 30.92408561706543 0.6100313663482666 149.6475830078125 0.636340856552124 165.38055419921875 0.16920237243175507 0.8243146 0.5160918831825256 True -10 30877 30.9766263961792 0.6216318607330322 124.00859069824219 0.4265197217464447 164.6627960205078 0.17160014808177948 0.8289302 0.4698891341686249 True -11 33684 30.934643983840942 0.6167278289794922 131.0213165283203 0.48314839601516724 164.33590698242188 0.17229236662387848 0.83427244 0.46038928627967834 True -12 36491 30.9409236907959 0.6049637794494629 177.72503662109375 0.4081295132637024 164.47671508789062 0.1711602807044983 0.8386056 0.4292675256729126 True -13 39298 30.97730326652527 1.1318409442901611 150.71070861816406 0.521356463432312 163.6338653564453 0.17410728335380554 0.84711695 0.3951256275177002 True -14 42105 30.916817665100098 0.6266653537750244 136.83102416992188 0.43687641620635986 163.2763214111328 0.175564706325531 0.85176796 0.38078227639198303 True -15 44912 30.475016832351685 0.6185495853424072 156.55523681640625 0.30705660581588745 163.05117797851562 0.17579896748065948 0.85331196 0.3672012686729431 True -16 47719 30.477288961410522 0.6256988048553467 136.7420654296875 0.3374844193458557 163.08251953125 0.1755935698747635 0.8566222 0.35947683453559875 True -17 50526 30.439997911453247 0.6078927516937256 143.14942932128906 0.49832314252853394 162.8677520751953 0.17676441371440887 0.859015 0.35641324520111084 True -18 53333 30.420896291732788 0.6139407157897949 141.63449096679688 0.4288657307624817 163.14393615722656 0.17598335444927216 0.85540676 0.36014464497566223 False -19 56140 30.37584662437439 0.6294944286346436 138.46047973632812 0.24806815385818481 163.1260986328125 0.17618079483509064 0.85672504 0.36196523904800415 False diff --git a/ENCSR679EFH/cherimoya.fold_4.performance.tsv b/ENCSR679EFH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6a188d44ce91fb4050c0287de075b3553370ac11..0000000000000000000000000000000000000000 --- a/ENCSR679EFH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -162.8677520751953 0.5773571133613586 0.17676442861557007 0.04483840987086296 0.8590149879455566 0.7692427635192871 0.35641324520111084 \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_0.evaluate.json b/ENCSR679IFH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3be881f5835d5b9e0097986caeef5c03e86d37e9..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846BJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_0.fit.json b/ENCSR679IFH/cherimoya.fold_0.fit.json deleted file mode 100644 index 9c29ad108a5cbde84011c272eba5834fa409ff35..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF846BJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_0.log b/ENCSR679IFH/cherimoya.fold_0.log deleted file mode 100644 index 1b30fcdb10b3d3ec6ebea93ef188b95cd2f85f67..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 34.61633014678955 3.752562999725342 187.2939453125 0.8244109153747559 207.93093872070312 0.13183949887752533 0.5267435 2.481428384780884 True -1 5458 29.992440462112427 0.7303309440612793 189.58404541015625 0.7267129421234131 199.16685485839844 0.1844635009765625 0.63224864 0.9565661549568176 True -2 8187 29.970134258270264 0.5614955425262451 165.0390167236328 0.6334863305091858 196.32684326171875 0.19472874701023102 0.6393871 0.5534095764160156 True -3 10916 29.38893961906433 1.0069611072540283 173.41375732421875 0.5443196892738342 194.90406799316406 0.2005508840084076 0.645122 0.4591592848300934 True -4 13645 29.493616104125977 0.5642561912536621 145.68504333496094 0.5541983842849731 194.26449584960938 0.20387889444828033 0.6454705 0.5111284255981445 True -5 16374 29.450067043304443 0.5610594749450684 163.9645538330078 0.4031386077404022 193.9583282470703 0.2056306004524231 0.65139735 0.5287484526634216 True -6 19103 29.39266347885132 0.5625898838043213 155.892822265625 0.48057466745376587 193.4102783203125 0.20918749272823334 0.6583218 0.5073064565658569 True -7 21832 29.37514615058899 1.8816897869110107 157.984375 0.40497255325317383 193.21524047851562 0.21024084091186523 0.6627445 0.46614885330200195 True -8 24561 29.50246524810791 0.5886242389678955 134.39768981933594 0.4068710207939148 192.86280822753906 0.2121124565601349 0.6701114 0.4435200095176697 True -9 27290 29.475980281829834 0.5597567558288574 167.31195068359375 0.49892595410346985 192.48214721679688 0.21425825357437134 0.67604584 0.41971880197525024 True -10 30019 29.414470195770264 0.5600817203521729 147.1240997314453 0.39350542426109314 192.28433227539062 0.21524417400360107 0.6806747 0.40017732977867126 True -11 32748 29.398296356201172 0.5559618473052979 143.21121215820312 0.5308964252471924 191.7548828125 0.21873515844345093 0.6864251 0.3928622007369995 True -12 35477 29.422352075576782 1.8406593799591064 147.75621032714844 0.606769323348999 191.55030822753906 0.21931248903274536 0.6928615 0.3796115815639496 True -13 38206 29.418145656585693 0.5694534778594971 145.11990356445312 0.3014407753944397 191.51739501953125 0.21877063810825348 0.69871074 0.3594527244567871 True -14 40935 29.424859523773193 0.561448335647583 173.4153594970703 0.4826687276363373 191.08499145507812 0.2216511070728302 0.70595926 0.3424866199493408 True -15 43664 29.453011989593506 0.5604434013366699 154.20852661132812 0.4054814279079437 191.0217742919922 0.22203443944454193 0.7118763 0.33644044399261475 True -16 46393 30.5057315826416 0.5615229606628418 156.45504760742188 0.3114352226257324 190.92669677734375 0.22225236892700195 0.71859914 0.32717087864875793 True -17 49122 29.42438316345215 21.046332597732544 148.30862426757812 0.29742008447647095 190.7902374267578 0.22355937957763672 0.7205793 0.32072871923446655 True -18 51851 29.508230686187744 0.5704078674316406 171.916259765625 0.294864296913147 191.03009033203125 0.22158245742321014 0.7215708 0.322338730096817 True -19 54580 29.396127700805664 0.570279598236084 165.45462036132812 0.32952529191970825 191.05213928222656 0.22160381078720093 0.720527 0.32201364636421204 False diff --git a/ENCSR679IFH/cherimoya.fold_0.performance.tsv b/ENCSR679IFH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fdd1ebc6b40feadc4c2bed3f31590caea19fdbdb..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -191.03009033203125 0.5447981357574463 0.22158245742321014 0.04714028537273407 0.7215707898139954 0.6575404405593872 0.322338730096817 \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_1.evaluate.json b/ENCSR679IFH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b3fea1948d2bb1bf19f0338c73dc5197ae97275a..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846BJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_1.fit.json b/ENCSR679IFH/cherimoya.fold_1.fit.json deleted file mode 100644 index 134ae97f2f7bccfd38ee1b9b2a065411f0a46e8e..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF846BJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_1.log b/ENCSR679IFH/cherimoya.fold_1.log deleted file mode 100644 index 337976a1b726cc441c0b7dfc231c78c3d823d24e..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 34.8949294090271 3.9648804664611816 156.68661499023438 0.5061944723129272 239.92982482910156 0.14204299449920654 0.54492915 2.8208401203155518 True -1 5486 30.19458270072937 1.574105978012085 143.66433715820312 0.6616126894950867 227.45745849609375 0.20485931634902954 0.68282384 0.9729439616203308 True -2 8229 30.196334838867188 0.7232990264892578 173.78094482421875 0.7523034811019897 224.30557250976562 0.21620842814445496 0.69687027 0.4990012049674988 True -3 10972 30.160914659500122 0.7192752361297607 138.49017333984375 0.5716843008995056 222.51995849609375 0.22230111062526703 0.7040826 0.5196070671081543 True -4 13715 30.204018592834473 0.7604122161865234 185.1189727783203 0.6988140344619751 221.98785400390625 0.22377651929855347 0.7065332 0.5321362614631653 True -5 16458 30.080718994140625 0.6994287967681885 136.72213745117188 0.32050013542175293 221.84375 0.22392503917217255 0.7103644 0.5351380109786987 True -6 19201 29.599824905395508 1.3763453960418701 138.13790893554688 0.6319037675857544 221.18434143066406 0.22700077295303345 0.71331584 0.5374327898025513 True -7 21944 29.621349096298218 0.7217504978179932 143.31369018554688 0.32100367546081543 220.64244079589844 0.2296169400215149 0.7168836 0.5061734914779663 True -8 24687 29.579529523849487 0.7188990116119385 165.1091766357422 0.41023075580596924 220.27430725097656 0.23136363923549652 0.72027224 0.48920485377311707 True -9 27430 29.58251690864563 0.6991183757781982 138.35693359375 0.5231344103813171 219.76666259765625 0.23419861495494843 0.7238398 0.4606856107711792 True -10 30173 29.76246404647827 0.7263081073760986 157.55734252929688 0.6258121132850647 219.15855407714844 0.23725098371505737 0.7286403 0.4456199109554291 True -11 32916 29.717471837997437 0.7109758853912354 147.38844299316406 0.5799888372421265 218.74514770507812 0.2388405054807663 0.73550224 0.4172397255897522 True -12 35659 29.713122844696045 0.732567548751831 129.2488555908203 0.3638988733291626 218.32290649414062 0.24031932651996613 0.739996 0.3922361135482788 True -13 38402 29.718391180038452 2.7860701084136963 135.90293884277344 0.3791126608848572 218.2681884765625 0.23993739485740662 0.7499699 0.3699283301830292 True -14 41145 29.785604000091553 0.9608757495880127 188.20623779296875 0.5887813568115234 217.78114318847656 0.2426336705684662 0.75366485 0.3673160672187805 True -15 43888 29.72693634033203 0.7136967182159424 141.77197265625 0.32900235056877136 217.68231201171875 0.24307677149772644 0.75962573 0.3608994483947754 True -16 46631 29.769290447235107 0.711855411529541 136.64488220214844 0.3244234025478363 217.2623748779297 0.24531713128089905 0.7653542 0.34984830021858215 True -17 49374 29.796655893325806 0.7217772006988525 171.75389099121094 0.268209844827652 217.5076904296875 0.24337565898895264 0.7690444 0.34226855635643005 True -18 52117 29.847317695617676 0.7823431491851807 136.9058837890625 0.2908218502998352 217.41152954101562 0.2438499927520752 0.7673322 0.3445257544517517 False -19 54860 29.830177545547485 0.7193393707275391 130.4753875732422 0.25173649191856384 217.46864318847656 0.24375085532665253 0.76626426 0.3453418016433716 False diff --git a/ENCSR679IFH/cherimoya.fold_1.performance.tsv b/ENCSR679IFH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 86937ae353ceb373c5ee77660ac3fb0370fd0671..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -217.5076904296875 0.5279299020767212 0.24337562918663025 0.057440806180238724 0.7690443992614746 0.7108743786811829 0.34226855635643005 \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_2.evaluate.json b/ENCSR679IFH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 945118684b4641cc0f8f8cfebde9dce382952917..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846BJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_2.fit.json b/ENCSR679IFH/cherimoya.fold_2.fit.json deleted file mode 100644 index e92883b266ef49b9ba06f76d3706fec1c0d66ec0..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF846BJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_2.log b/ENCSR679IFH/cherimoya.fold_2.log deleted file mode 100644 index b0e547232165530599d35e90238c1e789d41dbab..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2916 36.82667660713196 3.7995238304138184 142.59011840820312 0.588037371635437 212.24522399902344 0.13755197823047638 0.5402984 2.116366386413574 True -1 5832 32.1134135723114 0.5667417049407959 172.6693115234375 1.1941243410110474 202.2490692138672 0.19298720359802246 0.6591842 0.8150999546051025 True -2 8748 32.1424400806427 0.5457401275634766 174.41444396972656 0.6564333438873291 199.19692993164062 0.20615778863430023 0.66952854 0.6298245787620544 True -3 11664 32.06450939178467 0.8831148147583008 157.0262451171875 0.5259652137756348 198.0854034423828 0.21022774279117584 0.6769574 0.5658204555511475 True -4 14580 32.07765173912048 1.0742146968841553 171.80209350585938 0.6553401947021484 197.5203399658203 0.2125588208436966 0.67670316 0.5182888507843018 False -5 17496 32.18754053115845 0.527824878692627 167.408203125 0.7477332949638367 197.22650146484375 0.21333549916744232 0.6810717 0.5096309185028076 True -6 20412 31.991565704345703 0.5366232395172119 178.0244140625 0.4037659764289856 196.7996368408203 0.21562600135803223 0.683943 0.49493667483329773 True -7 23328 31.87044858932495 0.5144171714782715 157.8550567626953 0.4024660587310791 196.36497497558594 0.21866971254348755 0.6851089 0.47491079568862915 True -8 26244 31.350629568099976 1.060513973236084 154.38589477539062 0.5429865121841431 196.1172637939453 0.219188392162323 0.6901016 0.45895805954933167 True -9 29160 31.44350504875183 0.515693187713623 124.42230224609375 0.44069355726242065 195.5599365234375 0.22228413820266724 0.69492555 0.44391053915023804 True -10 32076 31.41987943649292 1.0736191272735596 168.06536865234375 0.42193615436553955 195.40501403808594 0.22275897860527039 0.69668174 0.4241447150707245 True -11 34992 31.488511323928833 0.5286080837249756 141.77691650390625 0.5033794045448303 194.96987915039062 0.22553592920303345 0.7051617 0.38841038942337036 True -12 37908 31.716023683547974 1.7183706760406494 145.3892059326172 0.5599426031112671 194.89639282226562 0.22485697269439697 0.70901453 0.3748362958431244 True -13 40824 31.574442386627197 1.427656888961792 146.04745483398438 0.48898348212242126 194.35182189941406 0.22875386476516724 0.71580386 0.3592578172683716 True -14 43740 31.514668464660645 0.5120961666107178 163.27015686035156 0.24713614583015442 194.169189453125 0.22873881459236145 0.72051024 0.3508451581001282 True -15 46656 31.58393955230713 0.5178065299987793 171.96249389648438 0.32788288593292236 194.02523803710938 0.22964103519916534 0.724325 0.33938220143318176 True -16 49572 31.632703065872192 0.5452446937561035 130.79994201660156 0.3523329496383667 194.01271057128906 0.22946865856647491 0.73253566 0.33624517917633057 True -17 52488 31.638309240341187 0.5211939811706543 143.02313232421875 0.3369191884994507 194.07838439941406 0.22927382588386536 0.7350315 0.331695020198822 True -18 55404 31.586411476135254 1.8943548202514648 169.1082763671875 0.2523835599422455 193.91796875 0.23016230762004852 0.7345996 0.33083030581474304 False -19 58320 31.59505295753479 0.5364797115325928 152.72052001953125 0.21504145860671997 194.02987670898438 0.22946657240390778 0.7347771 0.3319874405860901 False diff --git a/ENCSR679IFH/cherimoya.fold_2.performance.tsv b/ENCSR679IFH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 218ec1140c1481e88d844e893a9c25d641a0f10c..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -194.07838439941406 0.540665328502655 0.22927384078502655 0.051502663642168045 0.7350314855575562 0.6686841249465942 0.331695020198822 \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_3.evaluate.json b/ENCSR679IFH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4c854928cfc630b9b9d7fdd9a03e0e0d2f6ae348..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846BJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_3.fit.json b/ENCSR679IFH/cherimoya.fold_3.fit.json deleted file mode 100644 index 2ea0260fcb87b6127701b373a3490abe44d32433..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF846BJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_3.log b/ENCSR679IFH/cherimoya.fold_3.log deleted file mode 100644 index bbf472c86a0d5d4d4fd91cc9954268f623c5b8ba..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 35.35511374473572 4.2723166942596436 167.55511474609375 0.5775055289268494 226.51202392578125 0.13522763550281525 0.54461706 2.7816665172576904 True -1 5584 30.701679468154907 0.596879243850708 150.8910675048828 0.5048213601112366 216.26194763183594 0.1907225102186203 0.65588313 1.0186285972595215 True -2 8376 30.65694522857666 0.58241868019104 161.28964233398438 0.751543402671814 213.88258361816406 0.20132461190223694 0.68489194 0.5327852964401245 True -3 11168 30.657814264297485 0.5816023349761963 165.7320556640625 0.4706750512123108 212.74830627441406 0.2049117237329483 0.6911861 0.5083274841308594 True -4 13960 30.60174560546875 0.5767076015472412 123.84841918945312 0.4425196647644043 212.0709228515625 0.20760470628738403 0.69478816 0.5064275860786438 True -5 16752 30.653144359588623 0.5847797393798828 176.09088134765625 0.39471012353897095 211.66873168945312 0.20892928540706635 0.7020571 0.5252059698104858 True -6 19544 30.632025480270386 0.5841598510742188 153.32086181640625 0.4789852797985077 211.2115478515625 0.21066062152385712 0.6997208 0.5033095479011536 False -7 22336 30.093072175979614 0.5784761905670166 158.70680236816406 0.4796198308467865 210.7911834716797 0.21331940591335297 0.6984594 0.46773388981819153 False -8 25128 30.052303552627563 0.5809381008148193 135.48971557617188 0.49249139428138733 210.5655975341797 0.21495796740055084 0.7004669 0.466976523399353 False -9 27920 30.044497966766357 0.5795764923095703 137.824462890625 0.3349250257015228 210.27069091796875 0.2162359356880188 0.7046355 0.4609259068965912 True -10 30712 30.07545566558838 0.5810542106628418 172.83253479003906 0.42538323998451233 209.9813995361328 0.2177160382270813 0.7073329 0.4516209065914154 True -11 33504 30.069843292236328 0.5774593353271484 151.88290405273438 0.4756431579589844 209.59169006347656 0.21954159438610077 0.7144577 0.42674383521080017 True -12 36296 30.122737884521484 0.5766472816467285 129.9739227294922 0.37068378925323486 209.2018280029297 0.2216750979423523 0.71830606 0.41875505447387695 True -13 39088 30.13779044151306 0.5754868984222412 161.68849182128906 0.45609840750694275 208.9736785888672 0.2231130748987198 0.72324413 0.40702617168426514 True -14 41880 30.10657501220703 0.5699291229248047 145.2283935546875 0.2860150635242462 208.54306030273438 0.22492970526218414 0.73542106 0.38531774282455444 True -15 44672 30.10065269470215 0.57692551612854 187.02035522460938 0.28790414333343506 208.55043029785156 0.2245822548866272 0.74095154 0.3689819574356079 True -16 47464 30.16428279876709 0.5774803161621094 134.2255859375 0.566806435585022 208.46334838867188 0.2253386676311493 0.7459563 0.35376691818237305 True -17 50256 30.160614728927612 0.5770440101623535 156.43109130859375 0.32375892996788025 208.40377807617188 0.22548940777778625 0.74927604 0.35028716921806335 True -18 53048 30.159958839416504 0.5786135196685791 157.2561798095703 0.35694238543510437 208.3699951171875 0.22520510852336884 0.7502277 0.3489977717399597 True -19 55840 30.15768051147461 0.6011579036712646 183.30194091796875 0.21695664525032043 208.4363250732422 0.22487397491931915 0.74777895 0.3494287133216858 False diff --git a/ENCSR679IFH/cherimoya.fold_3.performance.tsv b/ENCSR679IFH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e6061b7ba91d75ac937e21898dda59d8d84092c6..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -208.3699951171875 0.5386444926261902 0.22520510852336884 0.05181935057044029 0.750227689743042 0.6867050528526306 0.3489977717399597 \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_4.evaluate.json b/ENCSR679IFH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ca66477d58ac5e3f93cf91cb73754faf50ca6ab8..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846BJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_4.fit.json b/ENCSR679IFH/cherimoya.fold_4.fit.json deleted file mode 100644 index 0414de150d11b827c97c923d771a2a0b8fd11f96..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF846BJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679IFH/cherimoya.fold_4.log b/ENCSR679IFH/cherimoya.fold_4.log deleted file mode 100644 index 6f10863f9ad1d40774722f80f507bc0149a1c5f1..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 36.36695623397827 4.2319722175598145 131.62985229492188 1.1155736446380615 208.9065399169922 0.1322876662015915 0.5269624 2.1958699226379395 True -1 5752 31.628899574279785 0.5835864543914795 157.2722625732422 0.5441878437995911 199.91995239257812 0.1855720728635788 0.6213274 0.8955628275871277 True -2 8628 31.629916191101074 0.5637662410736084 142.33514404296875 0.5034096837043762 198.0559539794922 0.19307518005371094 0.6457265 0.4917523264884949 True -3 11504 31.64029359817505 1.2869648933410645 139.3555908203125 0.5396156907081604 196.20323181152344 0.20193952322006226 0.6549208 0.42264649271965027 True -4 14380 31.556390523910522 0.5924427509307861 168.8309326171875 0.5041241645812988 195.9039306640625 0.20268011093139648 0.6584519 0.4167563319206238 True -5 17256 31.548990488052368 0.5625545978546143 145.37548828125 0.619655430316925 195.26235961914062 0.20667892694473267 0.65999085 0.4614143967628479 True -6 20132 31.29447317123413 0.5585446357727051 177.41534423828125 0.4830246865749359 194.77879333496094 0.20939980447292328 0.66272944 0.4656449258327484 True -7 23008 30.990004539489746 0.5895166397094727 144.778076171875 0.42611387372016907 194.67333984375 0.20948460698127747 0.66731656 0.44646361470222473 True -8 25884 31.04993987083435 1.278475284576416 171.3373565673828 0.695904016494751 194.4030303955078 0.21078935265541077 0.6700665 0.41251257061958313 True -9 28760 31.07896900177002 0.5663740634918213 163.53726196289062 0.5854260921478271 194.1362762451172 0.21201564371585846 0.6759261 0.3910219669342041 True -10 31636 31.002371788024902 0.5633914470672607 183.03765869140625 0.33782845735549927 193.82424926757812 0.21406741440296173 0.68184996 0.37630128860473633 True -11 34512 31.111610412597656 0.5737340450286865 184.93357849121094 0.32068932056427 193.5549774169922 0.21508289873600006 0.6857646 0.35785973072052 True -12 37388 31.07351803779602 0.5665872097015381 144.7198944091797 0.29015180468559265 193.28416442871094 0.21670985221862793 0.690589 0.3536435663700104 True -13 40264 31.087013244628906 0.5707721710205078 148.8621063232422 0.4021536111831665 192.9513397216797 0.2184818536043167 0.69592744 0.35185760259628296 True -14 43140 31.012702226638794 0.5699596405029297 153.55386352539062 0.3458971381187439 192.74388122558594 0.21939218044281006 0.70289797 0.33651649951934814 True -15 46016 31.09769320487976 0.5680320262908936 139.49658203125 0.30708885192871094 192.56768798828125 0.2202920913696289 0.70947504 0.3259556293487549 True -16 48892 31.04828929901123 0.5705745220184326 160.11264038085938 0.328672856092453 192.593994140625 0.21950259804725647 0.7141973 0.3253452181816101 True -17 51768 31.03284978866577 0.5643877983093262 161.19912719726562 0.2727474570274353 192.60008239746094 0.2197309285402298 0.7170134 0.32532793283462524 True -18 54644 31.073980569839478 0.5736713409423828 175.23843383789062 0.36117294430732727 192.65859985351562 0.2191993147134781 0.71684057 0.3264710605144501 False -19 57520 31.041529178619385 0.5525345802307129 138.55520629882812 0.21480299532413483 192.65464782714844 0.21950289607048035 0.71591836 0.3278428912162781 False diff --git a/ENCSR679IFH/cherimoya.fold_4.performance.tsv b/ENCSR679IFH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 219dca7ba5f6b7de255e0b023c5bf335f7f12c6a..0000000000000000000000000000000000000000 --- a/ENCSR679IFH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -192.60008239746094 0.5449874997138977 0.2197309285402298 0.04705352708697319 0.717013418674469 0.6479377746582031 0.32532793283462524 \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_0.evaluate.json b/ENCSR679NRJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3c24f005a0cd32afdfca217ee300acfb87c25e0d..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF311DYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_0.fit.json b/ENCSR679NRJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 9be48e54f89e5e794ccae09627f62f4d062f5e4b..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF311DYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_0.log b/ENCSR679NRJ/cherimoya.fold_0.log deleted file mode 100644 index bb49472631b6dce30d4356d7a2699ff43587d26b..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1570 21.123267650604248 21.901992559432983 154.17970275878906 0.6890902519226074 252.57186889648438 0.32203933596611023 0.55715954 9.56807804107666 True -1 3140 17.954273462295532 2.2525672912597656 190.86474609375 0.634213387966156 221.76998901367188 0.40196478366851807 0.61984146 3.901801347732544 True -2 4710 17.35349178314209 0.33170318603515625 153.59805297851562 0.4850495457649231 206.50572204589844 0.4717923104763031 0.6825927 1.5356444120407104 True -3 6280 17.317025661468506 0.3271141052246094 177.68890380859375 0.5082730054855347 201.80010986328125 0.4861176908016205 0.7039415 0.6996752023696899 True -4 7850 17.347548961639404 0.3311271667480469 156.1983184814453 0.4978305697441101 200.01412963867188 0.49125364422798157 0.7111288 0.5189286470413208 True -5 9420 17.361100673675537 0.32604336738586426 181.86956787109375 0.5818236470222473 199.206787109375 0.4937931299209595 0.71787935 0.45888030529022217 True -6 10990 17.208014249801636 0.3229091167449951 161.44168090820312 0.40308141708374023 198.58575439453125 0.49647048115730286 0.71781725 0.4434356689453125 False -7 12560 17.169418334960938 0.48044753074645996 159.68875122070312 0.51708984375 197.8181610107422 0.49926090240478516 0.72689617 0.4142967462539673 True -8 14130 17.065325498580933 0.3260009288787842 158.5374755859375 0.43436306715011597 197.3023223876953 0.5015597343444824 0.7330814 0.395534485578537 True -9 15700 17.111602067947388 0.32392358779907227 166.77076721191406 0.39505910873413086 196.79908752441406 0.5036430358886719 0.7399055 0.37821969389915466 True -10 17270 17.106306791305542 0.32387375831604004 178.27699279785156 0.4633745551109314 196.20651245117188 0.5058057904243469 0.74401504 0.3693890869617462 True -11 18840 17.140194416046143 0.3361847400665283 140.5415496826172 0.4577324390411377 195.6887664794922 0.5072932839393616 0.7489737 0.3598504066467285 True -12 20410 17.040439128875732 0.3411571979522705 154.1162872314453 0.28505080938339233 195.264404296875 0.5087649822235107 0.75873065 0.3528293967247009 True -13 21980 17.166898012161255 0.33822107315063477 148.923828125 0.3034767210483551 194.88839721679688 0.5100138187408447 0.76593244 0.3434350788593292 True -14 23550 17.10282254219055 0.331712007522583 160.87509155273438 0.3349578380584717 194.68580627441406 0.5107669830322266 0.7687511 0.34227851033210754 True -15 25120 17.095191478729248 0.3359944820404053 143.23052978515625 0.3065439760684967 194.61721801757812 0.510948121547699 0.7715174 0.3447856903076172 True -16 26690 17.100582122802734 0.3388526439666748 152.7423553466797 0.29241806268692017 194.57435607910156 0.5109320878982544 0.7743576 0.34146884083747864 True -17 28260 17.087392330169678 0.3344252109527588 169.6059112548828 0.25500041246414185 194.73492431640625 0.5102283954620361 0.7742875 0.34766319394111633 False -18 29830 17.10503053665161 0.3367621898651123 142.40232849121094 0.22842994332313538 194.8916473388672 0.5093759298324585 0.7747071 0.3523658812046051 True -19 31400 17.08436131477356 0.3352062702178955 142.70407104492188 0.23040485382080078 194.9967041015625 0.5088485479354858 0.7743462 0.35664474964141846 False diff --git a/ENCSR679NRJ/cherimoya.fold_0.performance.tsv b/ENCSR679NRJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 49e7a0e060d8544233011f4aa6502295e17aad47..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -194.8916473388672 0.3936469554901123 0.5093759894371033 0.12234032899141312 0.7747070789337158 0.7488359808921814 0.3523658812046051 \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_1.evaluate.json b/ENCSR679NRJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a90deeb3728a520b59f2832918f0a4152425a092..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF311DYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_1.fit.json b/ENCSR679NRJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 1fa73cb6a6c8828ba506e4dd266b6a230992c7ab..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF311DYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_1.log b/ENCSR679NRJ/cherimoya.fold_1.log deleted file mode 100644 index 23bd312a2dbdf921f3cb73c1a6830a314d4af387..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1572 21.19656777381897 3.3185222148895264 156.372802734375 0.5313894152641296 251.25804138183594 0.3249533176422119 0.57223076 9.034403800964355 True -1 3144 17.314953804016113 0.4920670986175537 165.81375122070312 0.610038161277771 221.56683349609375 0.4101097285747528 0.6387293 3.3546066284179688 True -2 4716 17.36222505569458 0.38747119903564453 141.53448486328125 0.5459151268005371 210.33578491210938 0.46204525232315063 0.6980456 1.2517883777618408 True -3 6288 17.35442852973938 0.38095736503601074 170.8428955078125 0.5113539695739746 206.33726501464844 0.47582730650901794 0.7083821 0.6254539489746094 True -4 7860 17.375157833099365 0.3837893009185791 153.83709716796875 0.43229803442955017 204.5907440185547 0.4818582534790039 0.71403784 0.48852217197418213 True -5 9432 17.33185863494873 0.3821732997894287 160.05352783203125 0.6565351486206055 203.65000915527344 0.48558899760246277 0.7278908 0.43123260140419006 True -6 11004 17.329067945480347 0.3818073272705078 134.4304962158203 0.4361143708229065 202.9290008544922 0.4885147511959076 0.73918396 0.37559622526168823 True -7 12576 17.33150887489319 0.3805720806121826 143.86770629882812 0.498803049325943 202.3062286376953 0.4911252558231354 0.75041527 0.34946152567863464 True -8 14148 17.33244800567627 0.38607120513916016 158.1075439453125 0.49704402685165405 201.57513427734375 0.4939437806606293 0.75775385 0.33546561002731323 True -9 15720 17.378362894058228 0.38039112091064453 136.92416381835938 0.5617740154266357 201.1529083251953 0.4956730604171753 0.7616049 0.3308398723602295 True -10 17292 17.393320560455322 11.16758418083191 148.82835388183594 0.38292527198791504 200.567626953125 0.4979791045188904 0.7675218 0.32492825388908386 True -11 18864 17.486574172973633 0.3977799415588379 150.31640625 0.36433956027030945 200.02548217773438 0.5000410079956055 0.7734104 0.3166450262069702 True -12 20436 17.32326889038086 0.38808465003967285 140.56036376953125 0.4885271191596985 199.50094604492188 0.5019709467887878 0.777704 0.3084013760089874 True -13 22008 17.418937921524048 0.3891725540161133 145.05728149414062 0.39082077145576477 199.07884216308594 0.5033625364303589 0.7840227 0.30113205313682556 True -14 23580 17.353373050689697 0.9921810626983643 162.60369873046875 0.22698554396629333 198.81146240234375 0.5043281316757202 0.7871858 0.2996603846549988 True -15 25152 17.393598079681396 0.39422607421875 144.6223907470703 0.26657211780548096 198.6862335205078 0.5045630931854248 0.79253525 0.29452964663505554 True -16 26724 17.40396022796631 0.39176487922668457 127.7220458984375 0.25066855549812317 198.6551971435547 0.5043701529502869 0.79279506 0.2978648245334625 True -17 28296 17.365631580352783 0.3927023410797119 142.96939086914062 0.27550095319747925 198.72413635253906 0.5038663744926453 0.7930946 0.3003635108470917 True -18 29868 17.370330095291138 0.3915395736694336 156.55850219726562 0.31508710980415344 198.8450469970703 0.5031813383102417 0.7928004 0.3043418824672699 False -19 31440 17.36962366104126 0.3936614990234375 158.26394653320312 0.34003889560699463 198.93582153320312 0.5027219653129578 0.79097027 0.3080833852291107 False diff --git a/ENCSR679NRJ/cherimoya.fold_1.performance.tsv b/ENCSR679NRJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 548119d0dedbdb7b6bb09ee7d7f3989f69782778..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -198.72413635253906 0.39515867829322815 0.5038663744926453 0.12055660784244537 0.7930945754051208 0.7842983603477478 0.3003635108470917 \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_2.evaluate.json b/ENCSR679NRJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2b1baacd9319e690dfb1ee00435962646aa35be2..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF311DYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_2.fit.json b/ENCSR679NRJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 632900b63b24942539bfde495bdcd6be8bba8bb6..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF311DYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_2.log b/ENCSR679NRJ/cherimoya.fold_2.log deleted file mode 100644 index 00f67d8e2e9ba7b73e03bc65f5d1cca350d1619c..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1667 22.260709285736084 3.309617757797241 171.40652465820312 0.6799591183662415 256.83612060546875 0.33142346143722534 0.5486972 8.219971656799316 True -1 3334 18.397006034851074 0.32103919982910156 153.17379760742188 0.5111217498779297 225.3323974609375 0.41844287514686584 0.62940913 3.399221658706665 True -2 5001 18.4224910736084 0.3152132034301758 144.6201934814453 0.49142494797706604 212.95729064941406 0.4728916883468628 0.6888026 1.3382928371429443 True -3 6668 18.053829669952393 0.3049190044403076 162.26797485351562 0.7795547246932983 208.31268310546875 0.4874797761440277 0.706899 0.7321501970291138 True -4 8335 18.073450803756714 0.3569645881652832 160.82797241210938 0.4001736640930176 206.99232482910156 0.4911787509918213 0.7065109 0.5263456106185913 False -5 10002 18.065768718719482 0.30523133277893066 156.40194702148438 0.6030563116073608 205.8352508544922 0.49511536955833435 0.7146382 0.49860909581184387 True -6 11669 18.070910215377808 0.31158018112182617 167.25616455078125 0.4839969575405121 205.2623291015625 0.4972662329673767 0.723554 0.48109138011932373 True -7 13336 18.047635316848755 0.3054463863372803 132.50637817382812 0.42831772565841675 204.5438690185547 0.49977588653564453 0.7303277 0.444097101688385 True -8 15003 18.054409980773926 0.30873942375183105 128.78378295898438 0.4095783829689026 203.832763671875 0.5023302435874939 0.73575103 0.42334842681884766 True -9 16670 18.04048728942871 0.30534887313842773 166.13571166992188 0.38446587324142456 203.519775390625 0.5036760568618774 0.74148625 0.40965020656585693 True -10 18337 18.058169841766357 0.30700182914733887 182.97720336914062 0.30713027715682983 202.84347534179688 0.5059179067611694 0.7513776 0.39085713028907776 True -11 20004 18.072360515594482 0.31558656692504883 164.06109619140625 0.3375418782234192 202.2982940673828 0.5077303647994995 0.75815356 0.37335577607154846 True -12 21671 18.136074781417847 0.3106865882873535 182.6300048828125 0.3037973642349243 201.87037658691406 0.5090221166610718 0.76858705 0.3639473021030426 True -13 23338 18.09489870071411 0.3054947853088379 149.31629943847656 0.3408783972263336 201.42117309570312 0.5105341672897339 0.7757249 0.35319656133651733 True -14 25005 18.08614754676819 0.3119838237762451 183.1422882080078 0.325481653213501 201.1605224609375 0.5115424394607544 0.7811267 0.3454665541648865 True -15 26672 18.093827962875366 0.30922937393188477 176.89334106445312 0.29000240564346313 200.96348571777344 0.5120322704315186 0.7834957 0.3415215015411377 True -16 28339 18.087021589279175 0.30719780921936035 159.5167236328125 0.32488465309143066 200.9071044921875 0.5120793581008911 0.78658307 0.3393302857875824 True -17 30006 18.091788291931152 0.31256961822509766 131.77999877929688 0.27488455176353455 200.99119567871094 0.5113776922225952 0.7887744 0.33964842557907104 True -18 31673 18.063390731811523 0.33905935287475586 140.81210327148438 0.19032056629657745 201.1328125 0.5107715129852295 0.78621614 0.34347298741340637 False -19 33340 18.09298062324524 0.3056478500366211 133.22576904296875 0.2492816150188446 201.21829223632812 0.5103855729103088 0.7868522 0.34640005230903625 False diff --git a/ENCSR679NRJ/cherimoya.fold_2.performance.tsv b/ENCSR679NRJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9347145cd65260c8c5edb69a55d71b9096aaaa8c..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -200.99119567871094 0.391582727432251 0.51137775182724 0.12617875635623932 0.7887743711471558 0.7755217552185059 0.33964842557907104 \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_3.evaluate.json b/ENCSR679NRJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 82e904d992d9c61aae8760eebe3b7f2f3e2120d2..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF311DYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_3.fit.json b/ENCSR679NRJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 7185192627a9d233ad8fbd13181341e8daebe008..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF311DYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_3.log b/ENCSR679NRJ/cherimoya.fold_3.log deleted file mode 100644 index cdf63a176426aa03f4fffc28b906b43943019ab5..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1606 22.122944593429565 3.3230626583099365 144.75311279296875 0.619907021522522 247.67352294921875 0.32345879077911377 0.5552558 8.820490837097168 True -1 3212 17.784464836120605 0.3453693389892578 146.32672119140625 0.36776235699653625 215.88076782226562 0.41069522500038147 0.6388179 3.580587863922119 True -2 4818 17.802297353744507 0.3409123420715332 171.02743530273438 0.7222244739532471 203.15786743164062 0.4673726260662079 0.6936402 1.2759759426116943 True -3 6424 17.82565665245056 0.33791565895080566 135.8448486328125 0.4591546356678009 198.43414306640625 0.4829370081424713 0.7068283 0.6535766124725342 True -4 8030 17.804487705230713 0.3374814987182617 156.16221618652344 0.5372189879417419 196.9031219482422 0.4876735508441925 0.7167979 0.5021534562110901 True -5 9636 17.811054944992065 0.3342924118041992 177.545654296875 0.4893435835838318 196.01087951660156 0.490386962890625 0.72403 0.44093555212020874 True -6 11242 17.749889373779297 1.5159845352172852 136.60919189453125 0.2744843363761902 195.5010986328125 0.49261197447776794 0.73208755 0.41531243920326233 True -7 12848 18.26569366455078 19.77674698829651 153.72264099121094 0.4482337534427643 195.06607055664062 0.4944211542606354 0.7320568 0.41674911975860596 False -8 14454 17.82546901702881 0.39069342613220215 169.04998779296875 0.35953208804130554 194.59657287597656 0.4964416027069092 0.73702097 0.40782684087753296 True -9 16060 17.79461646080017 0.3296523094177246 145.0668182373047 0.39089348912239075 194.1096954345703 0.49803903698921204 0.7437279 0.39908331632614136 True -10 17666 17.81857204437256 0.3446202278137207 158.70806884765625 0.37929868698120117 193.6649169921875 0.4995938837528229 0.7495646 0.3844050467014313 True -11 19272 17.803104639053345 0.34236860275268555 147.8509521484375 0.36911576986312866 193.2112274169922 0.5013999342918396 0.75304085 0.37876567244529724 True -12 20878 17.741726875305176 0.4777534008026123 161.70098876953125 0.3398088216781616 192.88998413085938 0.5027488470077515 0.7609485 0.36339887976646423 True -13 22484 17.79056692123413 0.3469357490539551 167.6881103515625 0.299494206905365 192.5164794921875 0.5041647553443909 0.7659044 0.35322490334510803 True -14 24090 17.83052897453308 0.33336448669433594 143.77783203125 0.37449172139167786 192.3997039794922 0.5045943260192871 0.7708695 0.34995487332344055 True -15 25696 17.833675622940063 0.34143781661987305 163.10110473632812 0.27868375182151794 192.23199462890625 0.5049901008605957 0.7741533 0.34938719868659973 True -16 27302 17.836026430130005 0.6724545955657959 158.749267578125 0.2491844743490219 192.24560546875 0.5050110220909119 0.7767138 0.3527661859989166 True -17 28908 17.818213939666748 0.3278203010559082 141.9109649658203 0.2634550929069519 192.33680725097656 0.5044838190078735 0.7767903 0.35925087332725525 True -18 30514 17.629181385040283 0.3398451805114746 156.7294464111328 0.24013248085975647 192.51324462890625 0.5036629438400269 0.7754579 0.36793237924575806 False -19 32120 17.48723793029785 0.3240971565246582 127.95848083496094 0.2311234176158905 192.6002960205078 0.5031888484954834 0.77403194 0.37461137771606445 False diff --git a/ENCSR679NRJ/cherimoya.fold_3.performance.tsv b/ENCSR679NRJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e77454c71f907e35f5f9899053045c158fb284f8..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -192.33680725097656 0.3959600031375885 0.5044838190078735 0.11934391409158707 0.7767903208732605 0.7554841041564941 0.35925087332725525 \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_4.evaluate.json b/ENCSR679NRJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 30b700653f597b171d8537e18ffff5e7e081d2e0..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF311DYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_4.fit.json b/ENCSR679NRJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 13f351e243d20c4a404b7271fedb5d5a0c2320cb..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF311DYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR679NRJ/cherimoya.fold_4.log b/ENCSR679NRJ/cherimoya.fold_4.log deleted file mode 100644 index 3f1160441d6801fcc07a351b1df19a6f9ea0cddd..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1626 21.644737720489502 3.2256767749786377 176.72299194335938 0.45627743005752563 251.60055541992188 0.32011541724205017 0.58716905 8.994956970214844 True -1 3252 17.926979064941406 0.7101767063140869 154.91351318359375 0.5621885061264038 220.94296264648438 0.4039660096168518 0.65170765 3.5192134380340576 True -2 4878 18.023092031478882 0.3268246650695801 171.5417938232422 0.63192218542099 206.95458984375 0.46499213576316833 0.71390355 1.438492774963379 True -3 6504 18.012531995773315 13.14542841911316 182.72665405273438 0.5690373778343201 202.1388702392578 0.4806881546974182 0.72295684 0.7083129286766052 True -4 8130 18.048924207687378 0.3397030830383301 160.06910705566406 0.5328981876373291 200.41246032714844 0.4865781366825104 0.7347205 0.471015602350235 True -5 9756 17.937524795532227 0.333111047744751 138.9914093017578 0.3696274161338806 199.5912322998047 0.48939070105552673 0.7445775 0.41638830304145813 True -6 11382 17.92991805076599 0.3324122428894043 166.7864990234375 0.49799245595932007 198.62454223632812 0.49283072352409363 0.7564964 0.38382503390312195 True -7 13008 17.95084810256958 0.32776761054992676 163.3116455078125 0.4429621398448944 198.04293823242188 0.49480777978897095 0.76172423 0.37245050072669983 True -8 14634 17.969191551208496 0.3295912742614746 148.3155059814453 0.45759183168411255 197.58651733398438 0.49681130051612854 0.76144964 0.37116071581840515 False -9 16260 17.99139380455017 0.5228936672210693 160.08013916015625 0.3335897922515869 197.01199340820312 0.4986383020877838 0.76870906 0.3587598204612732 True -10 17886 17.95069909095764 0.32550740242004395 161.9214630126953 0.33907508850097656 196.46499633789062 0.5008180141448975 0.7743866 0.3552006483078003 True -11 19512 17.957285404205322 0.33408379554748535 124.54931640625 0.43875211477279663 195.91592407226562 0.5024259686470032 0.7835442 0.3381277620792389 True -12 21138 17.959479570388794 0.32492756843566895 155.7909393310547 0.4013972282409668 195.45062255859375 0.5041027665138245 0.78663635 0.33679884672164917 True -13 22764 17.975556135177612 0.32831335067749023 149.70587158203125 0.2697465121746063 195.14712524414062 0.5054244995117188 0.7915668 0.33142590522766113 True -14 24390 17.950315237045288 0.5752134323120117 166.74755859375 0.32173675298690796 194.95916748046875 0.5061431527137756 0.79854333 0.3249311149120331 True -15 26016 17.943219900131226 1.67679762840271 151.391357421875 0.3276403248310089 194.822998046875 0.5063824653625488 0.8003087 0.3248383104801178 True -16 27642 18.0035719871521 0.3277103900909424 167.24752807617188 0.35279586911201477 194.81588745117188 0.506234884262085 0.8042092 0.3251728415489197 True -17 29268 17.948286056518555 0.3274500370025635 170.52923583984375 0.2388867437839508 194.92227172851562 0.5056621432304382 0.8073321 0.3256693184375763 True -18 30894 17.956124782562256 0.33375978469848633 130.51486206054688 0.3114987313747406 195.08074951171875 0.5050891041755676 0.8062434 0.33247023820877075 False -19 32520 17.95410656929016 0.32812070846557617 135.0345458984375 0.2470429539680481 195.16070556640625 0.5046405792236328 0.80500257 0.33796703815460205 False diff --git a/ENCSR679NRJ/cherimoya.fold_4.performance.tsv b/ENCSR679NRJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 325bda5ad192fc1728cab9d29de9477859cc8510..0000000000000000000000000000000000000000 --- a/ENCSR679NRJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -194.92227172851562 0.39636045694351196 0.5056621432304382 0.12472973763942719 0.8073320984840393 0.7802414894104004 0.3256693184375763 \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_0.evaluate.json b/ENCSR682PKY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5873408323115d1818aa2e80b00c020b88d98bd1..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538UOS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_0.fit.json b/ENCSR682PKY/cherimoya.fold_0.fit.json deleted file mode 100644 index bcbb2f731b990947693c32f70e5de78d0533000a..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF538UOS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_0.log b/ENCSR682PKY/cherimoya.fold_0.log deleted file mode 100644 index 9dc584e8e92361d5a04323654ff1d7f87dcabb89..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1717 23.96456527709961 3.3028156757354736 209.5692596435547 1.0465984344482422 296.975830078125 0.12710587680339813 0.56804717 7.337226390838623 True -1 3434 18.867119312286377 0.36976075172424316 217.9614715576172 1.10484778881073 280.1211853027344 0.19637072086334229 0.65136945 2.781728982925415 True -2 5151 18.84792733192444 0.35578489303588867 232.75840759277344 0.6817973852157593 263.1473388671875 0.24354219436645508 0.68827236 0.9871062636375427 True -3 6868 18.838972330093384 0.8101391792297363 256.1270751953125 0.6890733242034912 258.296630859375 0.25462618470191956 0.72382706 0.6904413104057312 True -4 8585 18.877418518066406 0.3460824489593506 221.56541442871094 0.7109755873680115 256.198974609375 0.2602557837963104 0.73296607 0.5937973856925964 True -5 10302 18.841006755828857 0.342914342880249 208.6948699951172 1.032815933227539 255.3412628173828 0.2628384530544281 0.73901427 0.5647251605987549 True -6 12019 18.850553274154663 0.33585405349731445 222.74795532226562 0.49042558670043945 254.74681091308594 0.26494988799095154 0.74054325 0.545414388179779 True -7 13736 18.868857383728027 0.9676105976104736 185.8019256591797 0.5833715796470642 253.3972930908203 0.2689812481403351 0.7404683 0.5452169179916382 False -8 15453 18.86391854286194 0.3437178134918213 274.8450927734375 0.6292264461517334 252.78919982910156 0.2718193233013153 0.74397904 0.5401439070701599 True -9 17170 18.876649618148804 0.3325178623199463 215.9319305419922 0.5456416010856628 252.9479217529297 0.27028390765190125 0.74433094 0.5391892790794373 True -10 18887 18.86439061164856 0.3494255542755127 192.41635131835938 0.6340586543083191 251.7353515625 0.2746472954750061 0.75313836 0.5300168991088867 True -11 20604 18.855776071548462 0.34462499618530273 219.19805908203125 0.5959948301315308 251.0710906982422 0.2765803337097168 0.7573708 0.521641731262207 True -12 22321 18.87100911140442 0.33770322799682617 154.83132934570312 0.6191900968551636 250.32998657226562 0.27918770909309387 0.76775515 0.511597752571106 True -13 24038 18.86066699028015 0.3421638011932373 210.92343139648438 0.48388150334358215 250.4029998779297 0.27825725078582764 0.76877075 0.5112237930297852 True -14 25755 18.838313102722168 0.34652256965637207 208.4793701171875 0.5047863721847534 249.6646728515625 0.2802537977695465 0.7771575 0.5015976428985596 True -15 27472 18.83290457725525 0.33948707580566406 181.55123901367188 0.3385228216648102 249.359619140625 0.2809930145740509 0.78108084 0.4974979758262634 True -16 29189 18.85349726676941 0.33842968940734863 229.85775756835938 0.35439300537109375 249.2482147216797 0.28121113777160645 0.78311783 0.4964314103126526 True -17 30906 18.878151893615723 0.339505672454834 202.62208557128906 0.3278113007545471 249.39793395996094 0.280306875705719 0.7829185 0.5078638195991516 False -18 32623 18.940890550613403 10.622207403182983 198.21633911132812 0.3278452157974243 249.61135864257812 0.27987799048423767 0.7808635 0.5162009000778198 False -19 34340 18.87646245956421 0.3397040367126465 194.1382598876953 0.31803059577941895 249.81610107421875 0.2787342369556427 0.7789904 0.5262691974639893 False diff --git a/ENCSR682PKY/cherimoya.fold_0.performance.tsv b/ENCSR682PKY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b97d03ad18829c6114d5c6ba7bf06ad1c9c11faa..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -249.2482147216797 0.5055442452430725 0.28121116757392883 0.07882706820964813 0.7831178307533264 0.7222530841827393 0.4964314103126526 \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_1.evaluate.json b/ENCSR682PKY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8e0e5ee7acd46223dbf1f168761771bfd521e7ac..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538UOS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_1.fit.json b/ENCSR682PKY/cherimoya.fold_1.fit.json deleted file mode 100644 index 93b726aec242f856007d1cacfac0b1d5b5758018..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF538UOS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_1.log b/ENCSR682PKY/cherimoya.fold_1.log deleted file mode 100644 index 45508ee67722a27cf9a19c4e976722ca151f6568..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1711 23.547611474990845 3.3683645725250244 245.84213256835938 1.099064826965332 364.1160888671875 0.14073224365711212 0.5326774 9.47474193572998 True -1 3422 18.85239267349243 0.677940845489502 181.79286193847656 0.7371756434440613 341.31439208984375 0.22155316174030304 0.6024354 4.3993821144104 True -2 5133 18.861191511154175 0.47956347465515137 180.3443603515625 1.089526653289795 318.13323974609375 0.2745654881000519 0.6845642 2.2166647911071777 True -3 6844 18.856807947158813 0.4773581027984619 206.33956909179688 0.5394254922866821 311.97705078125 0.28559502959251404 0.6951092 1.1254184246063232 True -4 8555 18.823790311813354 0.4809548854827881 184.12925720214844 0.6714212894439697 309.4755554199219 0.29054784774780273 0.7238633 0.8040606379508972 True -5 10266 18.823792934417725 0.4847910404205322 227.26693725585938 0.6778631210327148 308.1065673828125 0.2931327223777771 0.731061 0.7185807228088379 True -6 11977 18.856717824935913 0.505983829498291 202.4069366455078 0.9814810752868652 306.17626953125 0.2988134026527405 0.74548244 0.6378170847892761 True -7 13688 18.842145442962646 0.47701001167297363 191.0299072265625 0.6561315059661865 305.139404296875 0.3015705943107605 0.74878776 0.6190605163574219 True -8 15399 18.861498832702637 0.8201358318328857 198.5675506591797 0.6662046313285828 303.9730529785156 0.3050309717655182 0.75794184 0.6033211946487427 True -9 17110 18.419145584106445 0.46680712699890137 191.7508544921875 0.6403077840805054 303.5310363769531 0.3046179413795471 0.761886 0.581519365310669 True -10 18821 18.43366837501526 13.039706707000732 171.42333984375 0.5482107996940613 303.04266357421875 0.3062255382537842 0.7676574 0.5737202167510986 True -11 20532 18.44016981124878 0.4777498245239258 220.24942016601562 0.7965594530105591 302.0430908203125 0.30891939997673035 0.77100843 0.5665189027786255 True -12 22243 18.420637369155884 0.4714212417602539 195.3840789794922 0.6375710964202881 301.11614990234375 0.3114376962184906 0.7773775 0.5496729016304016 True -13 23954 18.454220056533813 0.47150683403015137 207.10025024414062 0.7468576431274414 300.5462341308594 0.3122437298297882 0.781451 0.5437349081039429 True -14 25665 18.474172830581665 0.4789774417877197 252.30935668945312 0.5364658832550049 299.62078857421875 0.31544995307922363 0.7887777 0.5431424975395203 True -15 27376 18.46134328842163 0.47187185287475586 216.6024169921875 0.41960299015045166 299.4463195800781 0.315462589263916 0.7916944 0.54306960105896 True -16 29087 18.468390226364136 0.47989964485168457 223.3434295654297 0.39729902148246765 299.77154541015625 0.31437692046165466 0.7922784 0.5600645542144775 True -17 30798 18.44567561149597 0.47440195083618164 187.1856689453125 0.46370548009872437 299.46783447265625 0.3160358965396881 0.79150265 0.5756465196609497 False -18 32509 18.456862449645996 0.4634406566619873 186.21005249023438 0.3139519691467285 300.2339172363281 0.3126259744167328 0.7895668 0.5959079265594482 False -19 34220 18.4236741065979 0.4684131145477295 177.92929077148438 0.27102935314178467 300.55755615234375 0.31200286746025085 0.7873341 0.6051381230354309 False diff --git a/ENCSR682PKY/cherimoya.fold_1.performance.tsv b/ENCSR682PKY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 13d2e56c3836c859a4bfc4f22dc475a3fa25ebdb..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -299.77154541015625 0.4782869815826416 0.3143768906593323 0.0892077311873436 0.7922784090042114 0.745248019695282 0.5600645542144775 \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_2.evaluate.json b/ENCSR682PKY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 59f2228f3423049bfd3fca31d11a26c2c447d62b..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538UOS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_2.fit.json b/ENCSR682PKY/cherimoya.fold_2.fit.json deleted file mode 100644 index 1f81bd3b2b343f2b392664752d6fbfeefd2605b3..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF538UOS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_2.log b/ENCSR682PKY/cherimoya.fold_2.log deleted file mode 100644 index 110825ad35e0b4ec10fffaf1033b65d15917cf80..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1831 24.592490434646606 4.198773622512817 238.19027709960938 0.9710394740104675 308.5461730957031 0.1304284781217575 0.52951753 7.337258815765381 True -1 3662 20.12616777420044 0.3999342918395996 231.74549865722656 1.0888805389404297 289.28118896484375 0.20572392642498016 0.62953913 2.6897330284118652 True -2 5493 20.120192527770996 0.3803901672363281 193.64349365234375 0.7996333241462708 269.6744384765625 0.2539660632610321 0.68781567 1.296849250793457 True -3 7324 20.07908034324646 11.763771295547485 200.08914184570312 1.077934741973877 264.3392333984375 0.26469364762306213 0.7191138 0.796454131603241 True -4 9155 20.088860273361206 0.3533623218536377 165.220458984375 0.7952894568443298 262.89971923828125 0.26736071705818176 0.7290834 0.7064427137374878 True -5 10986 20.095330476760864 0.3661918640136719 270.96356201171875 0.9808714389801025 261.7656555175781 0.27080851793289185 0.73235184 0.6573203802108765 True -6 12817 20.135782957077026 0.33994054794311523 230.64837646484375 1.0745329856872559 260.5707702636719 0.27553263306617737 0.738474 0.6182881593704224 True -7 14648 20.09707808494568 0.35347938537597656 278.633544921875 0.7363573312759399 259.4844970703125 0.27930769324302673 0.7418118 0.594607949256897 True -8 16479 20.101115942001343 0.3459937572479248 157.3968048095703 0.5816347599029541 258.5901184082031 0.28186938166618347 0.74452674 0.5666686296463013 True -9 18310 20.131576776504517 0.3388097286224365 228.59197998046875 0.7851029634475708 258.13677978515625 0.28241297602653503 0.7482193 0.5523878931999207 True -10 20141 20.09699559211731 0.3385946750640869 182.2494659423828 0.4976198077201843 257.8780517578125 0.28301143646240234 0.75666034 0.5511027574539185 True -11 21972 20.11450695991516 0.33853626251220703 197.5950927734375 0.6766929030418396 257.26666259765625 0.2851494550704956 0.75989276 0.5431108474731445 True -12 23803 20.14192795753479 0.338550329208374 238.03565979003906 0.3962026834487915 256.2388000488281 0.2890079915523529 0.76755464 0.5386935472488403 True -13 25634 20.127290964126587 0.3487510681152344 198.85696411132812 0.7574751377105713 256.6919860839844 0.28657135367393494 0.7729966 0.5280522704124451 True -14 27465 20.131092309951782 0.379375696182251 249.450927734375 0.36658167839050293 256.0467224121094 0.2891048789024353 0.7765741 0.5211730003356934 True -15 29296 20.112242937088013 0.366513729095459 201.3896942138672 0.3396255373954773 255.76651000976562 0.29046592116355896 0.78074664 0.5167756676673889 True -16 31127 20.071933031082153 0.3526291847229004 218.13156127929688 0.33580735325813293 255.97157287597656 0.29010000824928284 0.7841838 0.5217183828353882 True -17 32958 19.75225830078125 0.33765411376953125 187.01222229003906 0.46071872115135193 256.108154296875 0.2890879511833191 0.7826436 0.5322670936584473 False -18 34789 19.715233325958252 0.33724474906921387 170.36251831054688 0.32437700033187866 256.069091796875 0.2902383506298065 0.77978426 0.5439611077308655 False -19 36620 19.72859287261963 0.34557580947875977 206.28384399414062 0.2955709397792816 256.4397277832031 0.2882738709449768 0.7785015 0.5540184378623962 False diff --git a/ENCSR682PKY/cherimoya.fold_2.performance.tsv b/ENCSR682PKY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 593a596c06b14a30e341e30f1e6da3ee39044898..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -255.97157287597656 0.5000312328338623 0.29010000824928284 0.07995899021625519 0.7841838002204895 0.7269030809402466 0.5217183828353882 \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_3.evaluate.json b/ENCSR682PKY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 93daba1500440596c69dbeb964f94efce11ebbef..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538UOS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_3.fit.json b/ENCSR682PKY/cherimoya.fold_3.fit.json deleted file mode 100644 index 5cea9cdf2bad3f3a7eb602645f20198da5f924c6..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF538UOS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_3.log b/ENCSR682PKY/cherimoya.fold_3.log deleted file mode 100644 index 39ee602e5d73ced6f0889f11af017e734f2e9f60..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1750 23.428250074386597 3.3437581062316895 217.6826171875 0.6894271969795227 327.6684875488281 0.13228480517864227 0.56030685 8.456558227539062 True -1 3500 19.214893102645874 0.44568824768066406 232.44424438476562 0.5565158128738403 309.97528076171875 0.20093299448490143 0.6472278 3.351388692855835 True -2 5250 19.258957386016846 0.3661355972290039 257.02252197265625 0.9704564809799194 291.190673828125 0.2488459348678589 0.6757784 1.403639554977417 True -3 7000 19.24118661880493 0.36539244651794434 199.17138671875 0.9249436855316162 286.0603942871094 0.2629154622554779 0.6994832 1.0032978057861328 True -4 8750 19.22528600692749 0.36513757705688477 187.01068115234375 0.7822580337524414 283.58966064453125 0.269027978181839 0.7119601 0.83525151014328 True -5 10500 19.19972562789917 0.3652219772338867 185.11065673828125 0.8505256175994873 282.620361328125 0.2711089253425598 0.72051835 0.8248810768127441 True -6 12250 19.205800771713257 0.7389051914215088 222.3213348388672 0.8723165988922119 281.52166748046875 0.27437958121299744 0.72917765 0.7525495886802673 True -7 14000 19.253862142562866 0.372053861618042 240.1984100341797 0.7775949835777283 280.5824279785156 0.2765965163707733 0.7361425 0.705186128616333 True -8 15750 19.25008726119995 0.36768388748168945 156.99026489257812 0.5360774993896484 279.3887023925781 0.27980348467826843 0.736957 0.6544674634933472 True -9 17500 19.254502534866333 1.762439489364624 236.19839477539062 0.5483617186546326 278.7664489746094 0.28136199712753296 0.7469988 0.626079797744751 True -10 19250 19.217786073684692 0.3759446144104004 202.650634765625 0.7209709882736206 278.2624816894531 0.2832454442977905 0.7479629 0.6194301247596741 True -11 21000 19.22574210166931 0.37387990951538086 178.95510864257812 0.6514002084732056 277.60498046875 0.28415071964263916 0.7575593 0.5977928042411804 True -12 22750 19.218069791793823 0.6925411224365234 245.98321533203125 0.6980129480361938 276.84991455078125 0.28611284494400024 0.7674198 0.5778985619544983 True -13 24500 19.199511289596558 0.36351656913757324 175.3748779296875 0.4880678057670593 276.1470642089844 0.2875789403915405 0.77559495 0.55741947889328 True -14 26250 19.23086667060852 0.37293124198913574 169.502197265625 0.4314500689506531 275.8914794921875 0.28795039653778076 0.7816809 0.5475315451622009 True -15 28000 19.186498880386353 0.3701045513153076 192.5172882080078 0.48237329721450806 275.39141845703125 0.2897288501262665 0.7872083 0.5418661832809448 True -16 29750 19.200773239135742 0.35437870025634766 199.90025329589844 0.3395901918411255 275.512451171875 0.2891930639743805 0.79280484 0.5399755239486694 True -17 31500 19.205843925476074 0.36359715461730957 175.74050903320312 0.4995109438896179 275.858154296875 0.2866484820842743 0.79097986 0.5455759763717651 False -18 33250 19.244542598724365 0.36275362968444824 237.0699920654297 0.2716771066188812 275.9839172363281 0.28652551770210266 0.79111314 0.5549875497817993 False -19 35000 19.219467878341675 0.3650379180908203 237.56900024414062 0.2277548611164093 276.2510986328125 0.28619009256362915 0.79041183 0.5623385906219482 False diff --git a/ENCSR682PKY/cherimoya.fold_3.performance.tsv b/ENCSR682PKY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fbeb654ac4921fb7010612343fe49c5fe7beaa7b..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.512451171875 0.4969242215156555 0.2891930937767029 0.08011452108621597 0.7928048372268677 0.7428382039070129 0.5399755239486694 \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_4.evaluate.json b/ENCSR682PKY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d20bef44eecf02c7be802d3962113054d133e50e..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF538UOS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_4.fit.json b/ENCSR682PKY/cherimoya.fold_4.fit.json deleted file mode 100644 index 84c1eec05bfe6ec728e52aeb9725c87a2e7cf5c5..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF538UOS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682PKY/cherimoya.fold_4.log b/ENCSR682PKY/cherimoya.fold_4.log deleted file mode 100644 index f9cdf1a39bc1a50dbd58b4493aa4597f402e2c66..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1780 24.043367862701416 3.181764602661133 215.91156005859375 1.1145718097686768 292.00537109375 0.125265434384346 0.5468214 7.596761226654053 True -1 3560 19.564932107925415 0.37499570846557617 181.26516723632812 0.7103915214538574 274.2035827636719 0.200325608253479 0.6285192 3.2233965396881104 True -2 5340 19.62318706512451 0.37297654151916504 216.72671508789062 0.6839132308959961 258.3416442871094 0.24248006939888 0.6840168 1.159959316253662 True -3 7120 19.629862785339355 0.33257007598876953 180.9082489013672 0.6961164474487305 254.13807678222656 0.2516706883907318 0.7100483 0.6964687705039978 True -4 8900 19.645735263824463 0.3769810199737549 194.20431518554688 0.5070326328277588 252.95608520507812 0.2553061544895172 0.71506375 0.6284646987915039 True -5 10680 19.645657062530518 0.32670116424560547 191.43951416015625 0.8265931606292725 252.01426696777344 0.25897160172462463 0.72024417 0.5974313020706177 True -6 12460 19.669390439987183 0.33322787284851074 214.99501037597656 0.8248899579048157 250.7519989013672 0.26290807127952576 0.7270851 0.588890016078949 True -7 14240 19.299466848373413 10.850652694702148 177.01705932617188 0.5279245376586914 249.7451171875 0.26677846908569336 0.73343533 0.5529583096504211 True -8 16020 19.386306762695312 0.327667236328125 202.60281372070312 0.8848373293876648 249.86109924316406 0.2657742500305176 0.73812294 0.5440248250961304 True -9 17800 19.281803369522095 0.3322322368621826 191.68487548828125 0.6392936110496521 249.34262084960938 0.26650455594062805 0.74615574 0.5295719504356384 True -10 19580 19.28704309463501 0.32544398307800293 175.21054077148438 0.6450085043907166 248.8946533203125 0.2689059376716614 0.75201595 0.5212773084640503 True -11 21360 19.304607629776 0.32091474533081055 190.61849975585938 0.4906422793865204 248.0970001220703 0.2706708312034607 0.75907 0.5084018111228943 True -12 23140 19.27966547012329 0.3227832317352295 272.2366943359375 0.551689863204956 248.05276489257812 0.2711425721645355 0.76286083 0.5050123333930969 True -13 24920 19.269943952560425 0.3129427433013916 247.4781951904297 0.3194226026535034 247.19760131835938 0.27461662888526917 0.7651026 0.5042023062705994 True -14 26700 19.24886202812195 0.4876437187194824 159.4058837890625 0.5361539125442505 247.0201416015625 0.2746288776397705 0.77120775 0.49568048119544983 True -15 28480 19.18615221977234 0.336550235748291 195.85552978515625 0.834452748298645 247.0597381591797 0.27475109696388245 0.7771422 0.49343574047088623 True -16 30260 19.170727252960205 0.3268260955810547 225.00865173339844 0.40001147985458374 247.16941833496094 0.27477774024009705 0.7812158 0.4965168833732605 True -17 32040 19.21990656852722 0.31298160552978516 191.2714385986328 0.4384676218032837 247.13656616210938 0.2750089466571808 0.78023225 0.5083930492401123 False -18 33820 19.21124768257141 0.31785058975219727 186.9661865234375 0.2956787049770355 247.5732879638672 0.27299764752388 0.7762497 0.5264054536819458 False -19 35600 19.22331666946411 0.3049318790435791 162.821044921875 0.28342247009277344 247.6728057861328 0.27335214614868164 0.7754904 0.5327745079994202 False diff --git a/ENCSR682PKY/cherimoya.fold_4.performance.tsv b/ENCSR682PKY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ead9bbe314ddda28e9b1f8fd03342b380fde3443..0000000000000000000000000000000000000000 --- a/ENCSR682PKY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -247.16941833496094 0.5087382197380066 0.27477774024009705 0.0733959823846817 0.7812157869338989 0.7194415926933289 0.4965168833732605 \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_0.evaluate.json b/ENCSR682ZZT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5efffb0066adaf7856a2626d5f2cca597f256ab7..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF531SKB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_0.fit.json b/ENCSR682ZZT/cherimoya.fold_0.fit.json deleted file mode 100644 index fa10ab0a2101261a1cf1fa364c17c7763d20bb33..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF531SKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_0.log b/ENCSR682ZZT/cherimoya.fold_0.log deleted file mode 100644 index 1a17bf73be5c2446f9718f23d08f8817c3edc703..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 33.74838614463806 26.978660345077515 541.626708984375 0.3935549557209015 791.9026489257812 0.27060186862945557 0.65218484 5.62482213973999 True -1 5476 31.034175872802734 1.1453967094421387 522.9091186523438 0.562649130821228 713.1702880859375 0.35879045724868774 0.71259767 1.7568638324737549 True -2 8214 30.182682275772095 0.563969612121582 585.3135986328125 0.5278800129890442 697.9019775390625 0.37692949175834656 0.7211249 0.9149481058120728 True -3 10952 29.506980180740356 1.346648931503296 620.44287109375 0.532153308391571 690.77685546875 0.38440659642219543 0.7229931 0.7089564800262451 True -4 13690 29.532471895217896 0.5677037239074707 516.20849609375 0.5275356769561768 687.7728881835938 0.3890794515609741 0.72468626 0.6591470837593079 True -5 16428 29.492546558380127 0.5505654811859131 601.0530395507812 0.5715068578720093 684.1036987304688 0.39467954635620117 0.73182523 0.5681421756744385 True -6 19166 29.510408401489258 0.5512387752532959 522.38427734375 0.40649598836898804 682.0151977539062 0.3970819413661957 0.7388139 0.43703851103782654 True -7 21904 29.552359580993652 0.5587449073791504 554.2836303710938 0.44219112396240234 680.4375610351562 0.39808499813079834 0.74100655 0.42171239852905273 True -8 24642 29.53536558151245 0.5607821941375732 564.89208984375 0.4462569057941437 678.8861083984375 0.39967018365859985 0.74045414 0.4061899781227112 False -9 27380 29.923659801483154 22.773409366607666 565.1740112304688 0.3824790120124817 674.7679443359375 0.4049184322357178 0.750559 0.3711532652378082 True -10 30118 29.550761938095093 0.5562865734100342 595.6036987304688 0.488303005695343 672.9310913085938 0.4078041613101959 0.7559447 0.35819384455680847 True -11 32856 29.701295137405396 0.580085039138794 581.66064453125 0.5785681009292603 670.3775634765625 0.4117363691329956 0.76314294 0.3490585386753082 True -12 35594 29.752525568008423 0.5759174823760986 451.37939453125 0.4443668723106384 669.5404663085938 0.4124239981174469 0.7719522 0.3381037414073944 True -13 38332 29.723893880844116 0.5712454319000244 496.343994140625 0.34758448600769043 667.0454711914062 0.4157566726207733 0.7769671 0.32571732997894287 True -14 41070 29.718604564666748 0.5727286338806152 504.4924621582031 0.31805554032325745 665.2769165039062 0.417559951543808 0.78468996 0.31688690185546875 True -15 43808 29.68157720565796 0.5708024501800537 564.5826416015625 0.21909740567207336 664.2198486328125 0.41941097378730774 0.79151917 0.30107054114341736 True -16 46546 29.62946081161499 0.5700118541717529 552.093994140625 0.27931246161460876 663.939208984375 0.4197078049182892 0.7989881 0.29538437724113464 True -17 49284 29.664435148239136 0.5714154243469238 506.9030456542969 0.26474684476852417 662.1805419921875 0.42172113060951233 0.8004872 0.29474547505378723 True -18 52022 29.666249990463257 0.5696854591369629 601.1724853515625 0.2388351410627365 663.2230224609375 0.419828861951828 0.80066013 0.2954331040382385 True -19 54760 29.592976570129395 0.5618228912353516 489.3562316894531 0.20946207642555237 663.1023559570312 0.4199073612689972 0.797727 0.2973456382751465 False diff --git a/ENCSR682ZZT/cherimoya.fold_0.performance.tsv b/ENCSR682ZZT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c13f01f5e6f7cc7552131ab2ea5fa4b3bf22c0dc..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -663.2230224609375 0.36111217737197876 0.419828861951828 0.18221451342105865 0.8006601333618164 0.7450594305992126 0.2954331040382385 \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_1.evaluate.json b/ENCSR682ZZT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2f4b82c10625239a124c49813f1fea29f1e722a6..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF531SKB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_1.fit.json b/ENCSR682ZZT/cherimoya.fold_1.fit.json deleted file mode 100644 index 4fc90b7d344cb212a6f02fc8dd766960f9c93f00..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF531SKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_1.log b/ENCSR682ZZT/cherimoya.fold_1.log deleted file mode 100644 index 32780c3f3624db80765c3d06866988152fdf375f..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2723 34.772427558898926 6.884843111038208 549.9417724609375 0.6689381003379822 889.8753051757812 0.2711680829524994 0.6576716 5.943587303161621 True -1 5446 29.974063396453857 0.7138891220092773 637.210693359375 0.8146979808807373 790.242919921875 0.37136176228523254 0.7208702 1.7941436767578125 True -2 8169 29.961713552474976 0.6900689601898193 626.240478515625 0.7261545062065125 771.9869384765625 0.3867097795009613 0.72874385 0.6409299373626709 True -3 10892 29.911500930786133 0.6856932640075684 629.783203125 0.6160077452659607 763.07568359375 0.39430874586105347 0.737101 0.7472125291824341 True -4 13615 29.936901330947876 0.6964361667633057 547.7343139648438 0.5248339772224426 758.18359375 0.4007017910480499 0.74104846 0.5095785856246948 True -5 16338 29.952157735824585 1.8211205005645752 523.4674072265625 0.4206387996673584 756.1337280273438 0.4036967158317566 0.7387389 0.44598570466041565 False -6 19061 29.959874391555786 0.6884822845458984 599.5774536132812 0.48903849720954895 751.8778076171875 0.407800555229187 0.74929446 0.4615686237812042 True -7 21784 29.9693865776062 0.6838922500610352 553.5322875976562 0.4786759316921234 750.2908935546875 0.40897849202156067 0.74907935 0.3987640142440796 False -8 24507 29.917845964431763 0.6739387512207031 574.0103759765625 0.5188374519348145 744.6312866210938 0.4156510829925537 0.76025456 0.38655078411102295 True -9 27230 29.892959356307983 0.672504186630249 558.2042236328125 0.410477876663208 741.1122436523438 0.4189424514770508 0.7621551 0.38414350152015686 True -10 29953 29.90452265739441 0.677454948425293 542.239501953125 0.4300609230995178 738.6510620117188 0.4208424985408783 0.77431756 0.3639349341392517 True -11 32676 29.924449920654297 0.6824309825897217 533.915771484375 0.2800941467285156 735.826171875 0.42383313179016113 0.77761984 0.3653821647167206 True -12 35399 29.619043350219727 0.6809120178222656 533.4227294921875 0.302760511636734 732.132568359375 0.4267047047615051 0.78776276 0.3490695655345917 True -13 38122 29.34504532814026 0.668433666229248 558.3062133789062 0.32652899622917175 729.9849853515625 0.42884814739227295 0.79436994 0.3447129726409912 True -14 40845 29.346063375473022 1.4845473766326904 550.2149658203125 0.30218642950057983 726.6997680664062 0.432451993227005 0.80453545 0.32760411500930786 True -15 43568 29.394874334335327 0.6827771663665771 602.7199096679688 0.43415701389312744 725.7979736328125 0.4331781268119812 0.80999863 0.3211572468280792 True -16 46291 29.35181736946106 0.6741011142730713 546.9793090820312 0.21751615405082703 725.0730590820312 0.43463683128356934 0.8146772 0.31296268105506897 True -17 49014 29.362833738327026 0.6804783344268799 454.88824462890625 0.3121049702167511 725.8958740234375 0.4326208531856537 0.81757057 0.3102741241455078 True -18 51737 29.32089066505432 0.6843664646148682 456.316650390625 0.37419798970222473 724.968017578125 0.43359795212745667 0.81891793 0.31179067492485046 True -19 54460 29.432968378067017 0.6797354221343994 512.5696411132812 0.2912196218967438 725.347900390625 0.43349188566207886 0.81844145 0.31250613927841187 False diff --git a/ENCSR682ZZT/cherimoya.fold_1.performance.tsv b/ENCSR682ZZT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3c1e4754dba96d5ed5d0ac18d8ebbc088524e496..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -724.968017578125 0.3492993116378784 0.43359798192977905 0.19271710515022278 0.8189179301261902 0.7787887454032898 0.31179067492485046 \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_2.evaluate.json b/ENCSR682ZZT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6afd74a959751b446ffe492d118268c22045be4c..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF531SKB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_2.fit.json b/ENCSR682ZZT/cherimoya.fold_2.fit.json deleted file mode 100644 index 7d04bc6e2f15e2027b84c0cd03159626630c20c8..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF531SKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_2.log b/ENCSR682ZZT/cherimoya.fold_2.log deleted file mode 100644 index c56e71340db5ad738974084110a06ce4d9fff5d0..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2862 35.10615515708923 3.49831485748291 462.3148193359375 0.45585891604423523 802.3673095703125 0.2755386531352997 0.6456676 5.590190410614014 True -1 5724 31.404014110565186 0.5960047245025635 663.8282470703125 0.5098358392715454 720.7412109375 0.3628670275211334 0.7169365 1.5954174995422363 True -2 8586 31.700401782989502 0.5762162208557129 646.4095458984375 0.720226526260376 706.4354248046875 0.37873488664627075 0.7116071 0.6925274729728699 False -3 11448 31.565598487854004 0.5596520900726318 566.026123046875 0.6499503254890442 696.8268432617188 0.38922715187072754 0.72546875 0.6955803632736206 True -4 14310 31.496230363845825 0.5686883926391602 614.2447509765625 0.5746339559555054 693.4723510742188 0.39259085059165955 0.7291034 0.42097601294517517 True -5 17172 30.874065160751343 0.5443716049194336 621.6307373046875 0.47261351346969604 689.9378051757812 0.39704063534736633 0.73444605 0.40474966168403625 True -6 20034 30.921457767486572 0.5568244457244873 576.77587890625 0.3959175944328308 688.1552124023438 0.399086594581604 0.7377624 0.39454299211502075 True -7 22896 30.956137657165527 0.562952995300293 626.54443359375 0.306013286113739 683.4783935546875 0.4057310223579407 0.74077326 0.37320205569267273 True -8 25758 31.109360694885254 0.5592231750488281 615.542236328125 0.32651466131210327 682.5225219726562 0.40610459446907043 0.74899507 0.3669876158237457 True -9 28620 31.05525493621826 0.559981107711792 536.4737548828125 0.62339186668396 679.5838012695312 0.4101499915122986 0.75344527 0.3671719431877136 True -10 31482 30.96133303642273 0.5520682334899902 565.3466186523438 0.3162345886230469 679.5007934570312 0.40854790806770325 0.754368 0.35234972834587097 True -11 34344 30.94174885749817 1.7960467338562012 513.1474609375 0.2589530944824219 675.6801147460938 0.4144764840602875 0.76162803 0.33926475048065186 True -12 37206 30.92477035522461 0.5601058006286621 487.037109375 0.4235019385814667 673.6046142578125 0.41678643226623535 0.77087086 0.3309647738933563 True -13 40068 31.053778886795044 0.9966189861297607 542.35693359375 0.37376973032951355 671.0458374023438 0.4196285605430603 0.7766924 0.32029879093170166 True -14 42930 31.48049020767212 13.147448301315308 542.18603515625 0.42229223251342773 669.404296875 0.4214657247066498 0.78268933 0.31325989961624146 True -15 45792 30.95045018196106 0.5614504814147949 676.8099365234375 0.41489654779434204 670.5340576171875 0.4194972813129425 0.79018384 0.30712059140205383 True -16 48654 30.889535427093506 0.965266227722168 566.231689453125 0.23473888635635376 667.7952270507812 0.42343437671661377 0.79250443 0.30369195342063904 True -17 51516 30.883747339248657 0.5442922115325928 515.5172119140625 0.2706579267978668 667.7537841796875 0.4232516884803772 0.7961091 0.3019210994243622 True -18 54378 30.87915825843811 0.5505950450897217 490.97027587890625 0.31698518991470337 667.9210815429688 0.4229848086833954 0.7956404 0.3031213879585266 False -19 57240 30.864486694335938 0.5482838153839111 465.3273010253906 0.2879878580570221 668.468017578125 0.42208319902420044 0.7973064 0.3044711947441101 True diff --git a/ENCSR682ZZT/cherimoya.fold_2.performance.tsv b/ENCSR682ZZT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ef6945dc02f05f14f7e4c82ce0ea6e0e5b582691..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -668.468017578125 0.3594553768634796 0.42208319902420044 0.18105484545230865 0.7973064184188843 0.7456632852554321 0.3044711947441101 \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_3.evaluate.json b/ENCSR682ZZT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bd091dfb4b6b29ea080de376d04fa6c2a94f693f..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF531SKB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_3.fit.json b/ENCSR682ZZT/cherimoya.fold_3.fit.json deleted file mode 100644 index f1a10a024fa806fb7f120227226562c71fc7b731..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF531SKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_3.log b/ENCSR682ZZT/cherimoya.fold_3.log deleted file mode 100644 index 145ffa077656ea3a8a4080dc38939ca9d4483876..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 34.75782656669617 4.000481128692627 531.1005859375 0.5501374006271362 783.6011352539062 0.2788171172142029 0.6689556 5.377648830413818 True -1 5534 30.476285219192505 1.8485422134399414 561.0790405273438 0.5813467502593994 707.1962280273438 0.36645179986953735 0.7296397 1.6990611553192139 True -2 8301 30.572311401367188 0.5343244075775146 527.0888671875 0.5008342266082764 697.509765625 0.3761554956436157 0.7346749 0.7266812324523926 True -3 11068 30.445788860321045 0.527498722076416 629.802490234375 0.5145043730735779 688.4938354492188 0.38525107502937317 0.7386998 0.5802651643753052 True -4 13835 30.456514835357666 0.5359671115875244 614.13427734375 0.6696324348449707 683.2767333984375 0.39109283685684204 0.7429733 0.6321215033531189 True -5 16602 30.495623111724854 0.5335214138031006 490.6097717285156 0.44480812549591064 681.6554565429688 0.3937465250492096 0.7396845 0.5251075625419617 False -6 19369 30.461896419525146 0.6778116226196289 520.4940185546875 0.44091886281967163 676.4707641601562 0.40002670884132385 0.7511304 0.5480265021324158 True -7 22136 30.420419931411743 0.5321056842803955 594.8693237304688 0.4289957582950592 674.9503784179688 0.4012070298194885 0.7495713 0.4818912446498871 False -8 24903 30.35555911064148 13.757478475570679 523.2394409179688 0.7520579695701599 672.37060546875 0.4040929079055786 0.7510939 0.4454667270183563 False -9 27670 30.108403205871582 0.6191761493682861 476.3907470703125 0.5242817401885986 670.5138549804688 0.40598806738853455 0.759963 0.4315956234931946 True -10 30437 29.950390815734863 0.529850959777832 600.9945678710938 0.4402482509613037 666.819580078125 0.41148167848587036 0.76492786 0.40431928634643555 True -11 33204 30.013672590255737 0.5280990600585938 533.6612548828125 0.3573217988014221 665.849853515625 0.41090142726898193 0.7773489 0.3659452795982361 True -12 35971 30.083030700683594 0.5351271629333496 672.61328125 0.4180365800857544 663.0897216796875 0.4137516915798187 0.7855295 0.35669487714767456 True -13 38738 30.06890058517456 0.546684741973877 513.9437255859375 0.4910449981689453 660.2128295898438 0.4179728627204895 0.79385215 0.3410148322582245 True -14 41505 30.051578521728516 0.5334212779998779 569.7659301757812 0.2774011492729187 658.2081909179688 0.41923296451568604 0.79942286 0.32160884141921997 True -15 44272 30.095919609069824 0.5345399379730225 579.6978149414062 0.40183818340301514 656.1616821289062 0.42138803005218506 0.8074162 0.312254935503006 True -16 47039 30.023804426193237 0.5339038372039795 479.89154052734375 0.26166725158691406 656.923828125 0.4199387729167938 0.81325686 0.3038385212421417 True -17 49806 29.923208236694336 0.9689247608184814 571.55224609375 0.2261497974395752 655.7340087890625 0.42207881808280945 0.81582606 0.2988714277744293 True -18 52573 30.05063033103943 0.5330410003662109 527.9279174804688 0.3605087995529175 655.9580688476562 0.42191722989082336 0.8158347 0.2997042238712311 True -19 55340 30.112777948379517 1.670046329498291 533.444580078125 0.24745595455169678 655.473388671875 0.42278939485549927 0.81363124 0.3012411594390869 False diff --git a/ENCSR682ZZT/cherimoya.fold_3.performance.tsv b/ENCSR682ZZT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0cd898f0bdb33b593c20a66d48eb5f9cfbda4a03..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -655.9580688476562 0.3610008955001831 0.4219171702861786 0.18116344511508942 0.8158347010612488 0.7635238170623779 0.2997042238712311 \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_4.evaluate.json b/ENCSR682ZZT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4bc5f68090429fd9279bdc8011f75ca4cdb516de..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF531SKB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_4.fit.json b/ENCSR682ZZT/cherimoya.fold_4.fit.json deleted file mode 100644 index 282b54b65287f6dd86c37f7a75c69112f77c33a3..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF531SKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR682ZZT/cherimoya.fold_4.log b/ENCSR682ZZT/cherimoya.fold_4.log deleted file mode 100644 index adb20559ea5b3addb0bcb0fa296f1cb4dbf5678c..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2828 34.23486304283142 3.5125107765197754 611.4305419921875 0.6513535976409912 748.7369995117188 0.27105003595352173 0.6412425 5.402970790863037 True -1 5656 30.952637195587158 0.6208081245422363 668.3515625 0.6226550340652466 679.6049194335938 0.3524172604084015 0.6992632 1.3967199325561523 True -2 8484 31.14152479171753 0.5980851650238037 532.3796997070312 0.7592881917953491 668.395263671875 0.3668501675128937 0.7038663 0.6597788333892822 True -3 11312 31.172470569610596 0.5921399593353271 587.8132934570312 0.5542465448379517 661.1380004882812 0.37391218543052673 0.71631104 0.6262059807777405 True -4 14140 31.130179166793823 0.5872344970703125 483.4979248046875 0.46468621492385864 655.927978515625 0.3813636600971222 0.72276074 0.6171025633811951 True -5 16968 32.22445297241211 0.6031525135040283 442.9512634277344 0.48906949162483215 653.7469482421875 0.38388168811798096 0.7260769 0.5371313691139221 True -6 19796 31.259572982788086 0.5933308601379395 557.0947265625 0.34972137212753296 651.620361328125 0.3874872326850891 0.72762775 0.5320317149162292 True -7 22624 31.29647445678711 0.574364423751831 448.32916259765625 0.45468127727508545 647.0186767578125 0.39313870668411255 0.73135537 0.4434486925601959 True -8 25452 31.329509496688843 0.5710210800170898 563.0614013671875 0.36227887868881226 645.597900390625 0.39511096477508545 0.7391685 0.42234691977500916 True -9 28280 31.224456310272217 0.5711138248443604 506.957763671875 0.5899261832237244 643.8829345703125 0.39758437871932983 0.7462641 0.38728198409080505 True -10 31108 31.21869659423828 1.195706844329834 528.1251220703125 0.31276577711105347 641.6144409179688 0.40078380703926086 0.74711466 0.39266350865364075 True -11 33936 31.340203523635864 13.224200963973999 499.41925048828125 0.4236043095588684 639.6404418945312 0.4015074074268341 0.7534047 0.3552551567554474 True -12 36764 31.21881341934204 0.6011786460876465 544.8801879882812 0.35419756174087524 637.5615844726562 0.4047802984714508 0.76179427 0.3368110656738281 True -13 39592 30.853695392608643 0.5816535949707031 498.0541687011719 0.26030758023262024 636.257568359375 0.40659719705581665 0.7727121 0.319148987531662 True -14 42420 30.617342472076416 0.5719819068908691 624.8687133789062 0.21689070761203766 634.4676513671875 0.4087618887424469 0.77885836 0.30475789308547974 True -15 45248 30.68034052848816 0.5645308494567871 518.9027709960938 0.3345373272895813 633.6907348632812 0.40945735573768616 0.7868084 0.3000904619693756 True -16 48076 30.700053930282593 0.5706419944763184 502.35833740234375 0.2936561703681946 632.6653442382812 0.4110149145126343 0.78914386 0.2918430268764496 True -17 50904 30.669814586639404 0.5726852416992188 578.3514404296875 0.2533252239227295 632.8319091796875 0.4110695421695709 0.7912328 0.291210412979126 True -18 53732 30.623786687850952 0.5637726783752441 479.47723388671875 0.29511895775794983 632.9071044921875 0.4114404320716858 0.7939862 0.28937849402427673 True -19 56560 30.617557764053345 0.567962646484375 612.568603515625 0.21675264835357666 633.8672485351562 0.4094235599040985 0.7923235 0.28973183035850525 False diff --git a/ENCSR682ZZT/cherimoya.fold_4.performance.tsv b/ENCSR682ZZT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c1953a66a17aa79d7cda8cf7944b56ae408505c1..0000000000000000000000000000000000000000 --- a/ENCSR682ZZT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -632.9071044921875 0.3679981231689453 0.4114404320716858 0.17462410032749176 0.7939862012863159 0.7370702028274536 0.28937849402427673 \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_0.evaluate.json b/ENCSR683QJJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 56eab8abbd6fd679662423b66bb184131448f800..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917XZD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_0.fit.json b/ENCSR683QJJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 226d8f50709574e1f135b03e9c3083375606dc33..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF917XZD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_0.log b/ENCSR683QJJ/cherimoya.fold_0.log deleted file mode 100644 index 793e57d4e5f52e394fe5bedf65e4a8f7a9af58b6..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1822 24.80189609527588 3.361802339553833 1471.423828125 1.5434749126434326 2682.12451171875 0.2269521951675415 0.5752588 26.39100456237793 True -1 3644 20.312127828598022 0.3661057949066162 1094.8760986328125 1.7100247144699097 2050.43359375 0.3878130316734314 0.7038219 13.979482650756836 True -2 5466 20.29800510406494 0.36072444915771484 1122.81982421875 1.8265037536621094 1840.66064453125 0.4398557245731354 0.7171349 7.849393844604492 True -3 7288 20.342089414596558 0.35866665840148926 909.8001708984375 1.0434339046478271 1736.3201904296875 0.4563959836959839 0.7281446 4.181122779846191 True -4 9110 20.281025648117065 0.35639238357543945 1064.7491455078125 1.0752856731414795 1688.6207275390625 0.4709470570087433 0.72850287 3.3241019248962402 True -5 10932 20.293092489242554 1.2430622577667236 1444.586181640625 1.3336114883422852 1646.7447509765625 0.48252955079078674 0.73186827 2.9447269439697266 True -6 12754 20.298237800598145 0.3643612861633301 1499.378662109375 0.7601267099380493 1623.8184814453125 0.49259790778160095 0.7315762 2.4980123043060303 False -7 14576 20.504082441329956 0.3657665252685547 1534.469970703125 1.2157156467437744 1605.936279296875 0.49589627981185913 0.7362076 1.9123176336288452 True -8 16398 20.37977695465088 0.36000919342041016 1127.4964599609375 1.0775690078735352 1596.9775390625 0.49877485632896423 0.73695225 1.652772068977356 True -9 18220 20.36040449142456 0.3939552307128906 1555.260498046875 1.549954891204834 1570.779541015625 0.5066279172897339 0.7392234 1.4402376413345337 True -10 20042 20.35428237915039 0.3683178424835205 1232.50830078125 1.2728575468063354 1549.0086669921875 0.5096762776374817 0.74221516 1.2211130857467651 True -11 21864 20.41613793373108 0.3648498058319092 942.8408813476562 1.078434705734253 1536.25927734375 0.5136249661445618 0.74949855 1.128377914428711 True -12 23686 20.198994159698486 0.36217331886291504 1175.8173828125 0.9754817485809326 1522.2530517578125 0.5197950005531311 0.75588983 1.0152307748794556 True -13 25508 19.8966007232666 0.363006591796875 1134.900146484375 0.981717050075531 1513.8050537109375 0.5209713578224182 0.76560515 0.9469389319419861 True -14 27330 20.51886534690857 2.728499412536621 1284.208740234375 1.2599862813949585 1499.410888671875 0.524907648563385 0.7726447 0.8948192596435547 True -15 29152 19.964134216308594 0.35799264907836914 886.3154296875 0.7392133474349976 1492.5826416015625 0.5259495973587036 0.7788999 0.8593527674674988 True -16 30974 19.961004734039307 0.3541724681854248 1083.2828369140625 0.6897246837615967 1487.337890625 0.526207447052002 0.78452426 0.822695255279541 True -17 32796 19.864599466323853 0.35765504837036133 1135.74560546875 0.7582370042800903 1499.9393310546875 0.521905779838562 0.78641206 0.8053355813026428 True -18 34618 19.925304412841797 1.0637435913085938 1134.8668212890625 0.7936419248580933 1500.759765625 0.5231075882911682 0.7877518 0.7998136878013611 True -19 36440 19.884829998016357 0.8154757022857666 1487.3948974609375 0.7096514701843262 1496.2628173828125 0.5264007449150085 0.78896654 0.8006940484046936 True diff --git a/ENCSR683QJJ/cherimoya.fold_0.performance.tsv b/ENCSR683QJJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 78be48d7328b6efbfa75fb64b364efcb89e5a9bc..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1496.2628173828125 0.27148663997650146 0.5264007449150085 0.2893618941307068 0.7889665365219116 0.700133204460144 0.8006940484046936 \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_1.evaluate.json b/ENCSR683QJJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5020364b790ed2ecc6cb500f1c339b6609467f07..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917XZD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_1.fit.json b/ENCSR683QJJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 2bd8aba082c64bd41673bf739c2d555fa9a6e8bb..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF917XZD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_1.log b/ENCSR683QJJ/cherimoya.fold_1.log deleted file mode 100644 index 753763557f71cd4a6f791ab7855beb29a91cfdf2..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1799 24.301185369491577 3.559279680252075 2128.71630859375 1.75667405128479 3268.73876953125 0.23101669549942017 0.5337867 28.56024932861328 True -1 3598 20.04719877243042 0.5573282241821289 1354.9166259765625 1.7590246200561523 2502.53125 0.3984070420265198 0.68451107 16.856143951416016 True -2 5397 20.088499069213867 0.5327448844909668 1493.423095703125 1.3990153074264526 2178.751220703125 0.45368048548698425 0.7200747 6.378877639770508 True -3 7196 20.008296251296997 0.5323548316955566 1218.3349609375 1.373779535293579 2064.787109375 0.47327080368995667 0.7292301 4.209349632263184 True -4 8995 20.061803102493286 0.5369696617126465 1018.977294921875 1.3164513111114502 2005.1466064453125 0.4863930940628052 0.7363703 3.067993402481079 True -5 10794 20.014436960220337 0.5306136608123779 1575.4468994140625 1.4429049491882324 1966.6568603515625 0.4954456388950348 0.7474326 2.591641664505005 True -6 12593 20.005131721496582 0.8198220729827881 1456.677001953125 0.9940586090087891 1933.9725341796875 0.5023792386054993 0.75151765 2.3199551105499268 True -7 14392 20.0590500831604 0.5438110828399658 1320.003662109375 1.1388328075408936 1910.0745849609375 0.5051577091217041 0.7586934 1.9593521356582642 True -8 16191 20.037174701690674 0.5392704010009766 1446.631103515625 1.0059220790863037 1892.3721923828125 0.5118415951728821 0.7651793 1.7069737911224365 True -9 17990 20.070316076278687 1.297677993774414 1638.30908203125 1.2218084335327148 1881.0882568359375 0.5146177411079407 0.7652389 1.6576522588729858 True -10 19789 20.073413372039795 0.5409221649169922 1511.171142578125 1.0367090702056885 1856.8310546875 0.521498441696167 0.7721154 1.491331696510315 True -11 21588 20.00856041908264 0.5298902988433838 975.5062255859375 0.7936567068099976 1842.3487548828125 0.5242329835891724 0.77618027 1.3283578157424927 True -12 23387 20.010713815689087 0.5286552906036377 1289.24755859375 0.914614737033844 1821.6717529296875 0.5288131833076477 0.7803392 1.154691457748413 True -13 25186 21.614696502685547 37.306474447250366 1048.6298828125 0.8657575845718384 1799.020751953125 0.5317513942718506 0.78678554 1.027101993560791 True -14 26985 21.478949069976807 0.5347607135772705 1003.2818603515625 0.712598443031311 1791.279052734375 0.5317490696907043 0.7923593 0.9518789052963257 True -15 28784 19.635798692703247 10.458224058151245 977.6368408203125 0.8714414834976196 1771.94091796875 0.5367593765258789 0.79688084 0.9060502648353577 True -16 30583 19.713669300079346 0.5347175598144531 1248.10205078125 0.6789473295211792 1773.139404296875 0.5346211791038513 0.8024127 0.8664745688438416 True -17 32382 19.663113832473755 0.5439181327819824 860.9974365234375 0.657977819442749 1764.2303466796875 0.5391075611114502 0.80458206 0.8467931747436523 True -18 34181 19.620615243911743 0.5209560394287109 1099.337646484375 1.0465846061706543 1772.9625244140625 0.5371161103248596 0.8058519 0.8397508859634399 True -19 35980 19.672309637069702 0.5267314910888672 1221.6336669921875 0.9447276592254639 1776.15087890625 0.5362265110015869 0.8038523 0.8394858241081238 False diff --git a/ENCSR683QJJ/cherimoya.fold_1.performance.tsv b/ENCSR683QJJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 19c399121e7471e3d9c01e3ae5eebc155ccf6edb..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1772.9625244140625 0.25560420751571655 0.5371161103248596 0.31892555952072144 0.8058518767356873 0.7456439137458801 0.8397508859634399 \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_2.evaluate.json b/ENCSR683QJJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 51160914c6394231e71376f5b84dd52002f45d30..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917XZD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_2.fit.json b/ENCSR683QJJ/cherimoya.fold_2.fit.json deleted file mode 100644 index b118c041bc8623332203a5b8fa75a2130316e89a..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF917XZD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_2.log b/ENCSR683QJJ/cherimoya.fold_2.log deleted file mode 100644 index 555eecb3719e01c4094b62b71140ad74bc2d36da..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1941 25.849862098693848 3.282656192779541 1486.6949462890625 1.241675615310669 2915.067138671875 0.2345743477344513 0.5323523 25.75514030456543 True -1 3882 21.626544713974 0.37417101860046387 1047.0654296875 1.0649256706237793 2155.21337890625 0.4104178547859192 0.67292726 15.330808639526367 True -2 5823 21.666053295135498 0.3657262325286865 1500.7198486328125 1.6949260234832764 1935.7545166015625 0.45360952615737915 0.6940907 9.325379371643066 True -3 7764 21.64518404006958 0.3654313087463379 1728.3974609375 1.2042282819747925 1848.7828369140625 0.4720257520675659 0.70039916 5.248917579650879 True -4 9705 21.656848192214966 0.36342692375183105 1646.078125 1.4723780155181885 1802.579345703125 0.48180684447288513 0.7063997 3.619068145751953 True -5 11646 21.67263436317444 0.36147284507751465 1001.869384765625 0.9629530906677246 1764.8040771484375 0.4895111620426178 0.7131866 3.4676549434661865 True -6 13587 21.63507056236267 0.7740838527679443 1235.9173583984375 1.3564729690551758 1740.43994140625 0.49283546209335327 0.71731454 2.8934671878814697 True -7 15528 21.6302752494812 2.5783889293670654 730.1258544921875 1.141286849975586 1717.7095947265625 0.4980950951576233 0.7253144 2.512223958969116 True -8 17469 21.73114800453186 0.3654913902282715 1330.654052734375 0.942172646522522 1684.4854736328125 0.5049054622650146 0.7318122 1.8661516904830933 True -9 19410 21.644282341003418 0.9518337249755859 1896.7255859375 1.119572401046753 1672.06298828125 0.5104913711547852 0.7400085 1.5565345287322998 True -10 21351 21.643700122833252 0.36126112937927246 1062.6470947265625 1.1136680841445923 1651.3782958984375 0.5126171112060547 0.74758816 1.3371117115020752 True -11 23292 21.60968780517578 1.8983118534088135 861.776611328125 0.9371873736381531 1634.677978515625 0.5168641805648804 0.7525345 1.2039114236831665 True -12 25233 21.694212436676025 0.36659789085388184 1074.1231689453125 0.8347845077514648 1621.0888671875 0.5202692747116089 0.75785595 1.0935826301574707 True -13 27174 21.30280327796936 0.3598756790161133 1131.380859375 0.6773365139961243 1602.9364013671875 0.5252944231033325 0.7637948 1.0112428665161133 True -14 29115 21.15501379966736 0.3551054000854492 1036.173095703125 0.8917537927627563 1584.9766845703125 0.5300523042678833 0.77128816 0.9268956184387207 True -15 31056 21.243110418319702 16.557785511016846 995.036865234375 0.6039393544197083 1578.9180908203125 0.5310352444648743 0.776533 0.8890308737754822 True -16 32997 23.337515354156494 0.3876657485961914 1059.9287109375 0.7091580629348755 1582.8834228515625 0.5299279689788818 0.77936405 0.8691825866699219 True -17 34938 21.29963707923889 0.37413787841796875 1222.0677490234375 0.9817851185798645 1586.9705810546875 0.5272547602653503 0.7833551 0.8561975359916687 True -18 36879 22.924734830856323 14.963682651519775 870.6116943359375 0.8272266983985901 1576.7294921875 0.5324199795722961 0.78184044 0.8521916270256042 False -19 38820 21.202545881271362 0.36293864250183105 1280.481689453125 0.7128159403800964 1573.9844970703125 0.5334854125976562 0.78390896 0.8547881245613098 True diff --git a/ENCSR683QJJ/cherimoya.fold_2.performance.tsv b/ENCSR683QJJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2c53455bf9fd0a9d1ac383ddb20cc4c10e22c292..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1573.9844970703125 0.26553991436958313 0.5334854125976562 0.29988184571266174 0.7839089632034302 0.7097193598747253 0.8547881245613098 \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_3.evaluate.json b/ENCSR683QJJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index dc524b77dab7ce01c26a7b55dda76efa9d1c2140..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917XZD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_3.fit.json b/ENCSR683QJJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 147fce2469d05880b4e892c6d479e0282030dfc9..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF917XZD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_3.log b/ENCSR683QJJ/cherimoya.fold_3.log deleted file mode 100644 index 741f67934e6b1fabfe395a4087e2dbbf69a65ce8..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1859 24.978114128112793 3.4721546173095703 1399.7041015625 1.2175021171569824 2755.762939453125 0.24224725365638733 0.5433534 27.985109329223633 True -1 3718 20.759753942489624 0.3948345184326172 1752.3480224609375 1.4199111461639404 2159.66015625 0.3905227780342102 0.6637366 14.727807998657227 True -2 5577 20.725301265716553 0.39000582695007324 1904.009033203125 1.7517869472503662 1952.1793212890625 0.43763503432273865 0.68389434 8.085684776306152 True -3 7436 20.687439441680908 0.3793015480041504 1341.93505859375 1.695818543434143 1851.3087158203125 0.4613071084022522 0.69616 5.613293647766113 True -4 9295 20.751248121261597 0.39122581481933594 1469.4613037109375 1.265561819076538 1802.881591796875 0.4700351655483246 0.70498276 4.520247459411621 True -5 11154 20.694785594940186 0.38509392738342285 1597.1260986328125 1.4541206359863281 1755.064453125 0.4873652458190918 0.7096429 3.5543439388275146 True -6 13013 20.837082862854004 15.67725157737732 1235.87353515625 1.2884236574172974 1739.9378662109375 0.49053454399108887 0.7116777 2.961376667022705 True -7 14872 21.1902756690979 0.42526984214782715 1037.8980712890625 1.274311900138855 1716.1937255859375 0.4935028851032257 0.7201035 2.21260142326355 True -8 16731 20.74651002883911 0.389676570892334 1097.5848388671875 1.1796942949295044 1703.5880126953125 0.4982897937297821 0.72911215 1.802411675453186 True -9 18590 20.737693786621094 0.3828434944152832 1200.09521484375 0.9312841296195984 1691.2235107421875 0.5018999576568604 0.7300568 1.618271827697754 True -10 20449 20.74854016304016 0.38776063919067383 1057.9991455078125 0.7750252485275269 1659.0030517578125 0.5104842782020569 0.7405937 1.3149667978286743 True -11 22308 20.69411849975586 13.182199001312256 1482.46630859375 0.8742647171020508 1647.545654296875 0.5122538208961487 0.74753016 1.182821273803711 True -12 24167 24.228134632110596 0.40819358825683594 1520.581298828125 0.825737476348877 1632.186767578125 0.5171194672584534 0.7535975 1.1147061586380005 True -13 26026 20.29740071296692 0.37718915939331055 1146.3067626953125 0.9232677221298218 1618.3682861328125 0.5205091238021851 0.75840443 1.0288143157958984 True -14 27885 20.34538698196411 0.38298606872558594 1483.0185546875 0.8303095102310181 1600.5743408203125 0.5243828296661377 0.7676066 0.9638307690620422 True -15 29744 20.279304027557373 1.3507890701293945 972.095458984375 0.9056234359741211 1595.931640625 0.5269207954406738 0.772603 0.9371887445449829 True -16 31603 20.348230600357056 0.3848881721496582 1079.22314453125 0.7560944557189941 1589.5006103515625 0.5279248952865601 0.779984 0.9128455519676208 True -17 33462 20.253952741622925 0.37645840644836426 1319.1837158203125 0.6918623447418213 1581.3466796875 0.5298451781272888 0.7817815 0.8984199166297913 True -18 35321 20.2692928314209 0.3842482566833496 951.937744140625 0.8006673455238342 1585.90478515625 0.5275462865829468 0.7840272 0.8828552961349487 True -19 37180 20.337281227111816 16.19166874885559 1048.75927734375 0.713492751121521 1587.39501953125 0.5275077223777771 0.7835975 0.881096363067627 False diff --git a/ENCSR683QJJ/cherimoya.fold_3.performance.tsv b/ENCSR683QJJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a257affdb01c005ae3511d1c3b4a69b9c7254e49..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1585.90478515625 0.266357958316803 0.5275462865829468 0.2974749505519867 0.7840272188186646 0.710318922996521 0.8828552961349487 \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_4.evaluate.json b/ENCSR683QJJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index dd8110b426a75db25775cc4ceefa14fe1df92b26..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917XZD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_4.fit.json b/ENCSR683QJJ/cherimoya.fold_4.fit.json deleted file mode 100644 index d5320c2cd8fd82139f745fac6d4dfe34ecbd1526..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF917XZD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683QJJ/cherimoya.fold_4.log b/ENCSR683QJJ/cherimoya.fold_4.log deleted file mode 100644 index d96d833291471cbc7deaef885b7d1bfd5b4699fb..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1859 25.22873878479004 15.996790170669556 1139.5516357421875 2.007005214691162 2526.1650390625 0.2229960411787033 0.53117794 25.059741973876953 True -1 3718 20.746551275253296 0.357633113861084 1358.5191650390625 1.43770170211792 1959.1083984375 0.39505401253700256 0.6596791 11.002768516540527 True -2 5577 20.7071635723114 0.35140132904052734 1249.7181396484375 1.2493996620178223 1774.3836669921875 0.42668208479881287 0.66875964 5.865786075592041 True -3 7436 20.69979500770569 9.404842376708984 1269.6099853515625 1.3572118282318115 1677.7889404296875 0.4521511197090149 0.6697421 4.684564113616943 True -4 9295 21.215217351913452 0.40000343322753906 1009.2743530273438 1.4528740644454956 1625.1746826171875 0.4696711599826813 0.68373823 3.614961624145508 True -5 11154 20.75352954864502 0.34101128578186035 1238.6380615234375 1.3115098476409912 1585.8594970703125 0.4834290146827698 0.69413835 2.7476603984832764 True -6 13013 20.689153909683228 0.3431239128112793 1202.5167236328125 1.289318561553955 1564.8426513671875 0.49077755212783813 0.6927147 2.595543622970581 False -7 14872 20.853349685668945 22.314135313034058 1400.97509765625 0.9091059565544128 1556.9815673828125 0.4925922751426697 0.7003629 2.064120292663574 True -8 16731 23.61196994781494 0.3509244918823242 1607.623291015625 1.1601684093475342 1539.9276123046875 0.4968431890010834 0.7053547 1.608340859413147 True -9 18590 20.65716862678528 0.4074833393096924 1066.7120361328125 0.825391411781311 1524.6142578125 0.5024357438087463 0.7118434 1.415482521057129 True -10 20449 23.06976628303528 6.5873517990112305 985.8350219726562 0.8975187540054321 1511.177978515625 0.5056302547454834 0.72065717 1.269797682762146 True -11 22308 20.717093467712402 0.3447399139404297 937.7832641601562 1.213133692741394 1482.8931884765625 0.5155431628227234 0.7275283 1.1501089334487915 True -12 24167 20.762850761413574 0.33980703353881836 1275.9061279296875 1.1420340538024902 1485.3907470703125 0.5120179057121277 0.7321396 1.0367671251296997 True -13 26026 20.738759994506836 1.2565994262695312 1579.988525390625 1.1775169372558594 1476.6978759765625 0.51528400182724 0.73740774 0.975310206413269 True -14 27885 20.73916745185852 0.3429279327392578 1185.9453125 0.8173388242721558 1465.432861328125 0.5191868543624878 0.74359775 0.925547182559967 True -15 29744 20.710615634918213 0.33791065216064453 891.765380859375 0.8128631711006165 1453.4857177734375 0.5228910446166992 0.75110286 0.9102546572685242 True -16 31603 20.748472452163696 0.3371589183807373 1148.217529296875 0.7759754657745361 1445.8270263671875 0.5242279767990112 0.75381815 0.8897404670715332 True -17 33462 20.701111793518066 0.3461484909057617 1076.44140625 0.6138159036636353 1446.649658203125 0.5233461260795593 0.7575165 0.8728631734848022 True -18 35321 21.939399242401123 18.97498655319214 992.114501953125 0.7901092767715454 1455.09130859375 0.5202968120574951 0.7595507 0.8674310445785522 True -19 37180 20.91801381111145 0.3461618423461914 894.5736083984375 0.8374875783920288 1457.1710205078125 0.5207319855690002 0.7577397 0.8713832497596741 False diff --git a/ENCSR683QJJ/cherimoya.fold_4.performance.tsv b/ENCSR683QJJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5e9cb1a907f65fc1affa5a8bf489db5929f45037..0000000000000000000000000000000000000000 --- a/ENCSR683QJJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1455.09130859375 0.27344244718551636 0.5202968120574951 0.282549649477005 0.7595506906509399 0.669255256652832 0.8674310445785522 \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_0.evaluate.json b/ENCSR683YLO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ac20b729c5dbd5598f964427db5a9e93af225368..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420QIQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_0.fit.json b/ENCSR683YLO/cherimoya.fold_0.fit.json deleted file mode 100644 index aee1de33d9f28a60fa623b381d58314ff32fb658..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF420QIQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_0.log b/ENCSR683YLO/cherimoya.fold_0.log deleted file mode 100644 index f1894d7a883ad0eb699fdf9e717bf0e435481940..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.21622920036316 4.350516080856323 247.1702880859375 0.6359821557998657 392.98822021484375 0.17211027443408966 0.6941381 3.5687732696533203 True -1 5516 30.769073724746704 0.5928962230682373 255.510986328125 0.6044138669967651 370.5337829589844 0.2460644543170929 0.7558422 0.9571898579597473 True -2 8274 30.780444860458374 0.9749526977539062 276.71026611328125 0.5171954035758972 365.154052734375 0.2581325173377991 0.76058555 0.5791006088256836 True -3 11032 30.766798734664917 1.7647101879119873 277.5042419433594 0.37923747301101685 363.3070983886719 0.26326149702072144 0.76387036 0.43521609902381897 True -4 13790 30.7389874458313 2.030242681503296 284.112060546875 0.4190707504749298 362.0533447265625 0.2666946351528168 0.77047294 0.3692903518676758 True -5 16548 30.78189516067505 11.386350154876709 325.431640625 0.27500125765800476 360.5464782714844 0.2716010510921478 0.77708995 0.3461446762084961 True -6 19306 30.732683658599854 0.5635905265808105 285.177001953125 0.5174640417098999 359.8733825683594 0.2738588750362396 0.77949446 0.35850250720977783 True -7 22064 30.82551884651184 0.9410755634307861 315.5328369140625 0.3771288990974426 359.09014892578125 0.27670279145240784 0.7813933 0.34013649821281433 True -8 24822 30.869524240493774 0.5543134212493896 320.153564453125 0.358481228351593 358.7191162109375 0.27816832065582275 0.7845198 0.3470061719417572 True -9 27580 31.007533073425293 1.0274410247802734 318.50811767578125 0.3290455937385559 358.07977294921875 0.28078222274780273 0.7861504 0.33263444900512695 True -10 30338 30.855826377868652 3.6338508129119873 228.2349853515625 0.3383910059928894 357.4958801269531 0.28160780668258667 0.79033 0.3297167718410492 True -11 33096 30.488252639770508 2.195681095123291 256.4222412109375 0.38352644443511963 356.52734375 0.285982221364975 0.7931948 0.32573285698890686 True -12 35854 30.350815296173096 0.784801721572876 364.80938720703125 0.30540257692337036 356.3087463378906 0.2864106297492981 0.7958225 0.31688570976257324 True -13 38612 30.24921727180481 0.5611364841461182 250.44412231445312 0.44630593061447144 355.72796630859375 0.28761813044548035 0.79918665 0.3159686028957367 True -14 41370 30.17025589942932 0.5377483367919922 292.2562561035156 0.3913947343826294 355.42315673828125 0.28898096084594727 0.8048406 0.3078787624835968 True -15 44128 30.14529013633728 0.5437347888946533 286.78021240234375 0.3131338953971863 355.3642272949219 0.29030704498291016 0.812246 0.28775668144226074 True -16 46886 30.124650955200195 0.545814037322998 305.4666748046875 0.46282994747161865 355.41461181640625 0.28963688015937805 0.81485707 0.27578282356262207 True -17 49644 30.146960496902466 0.5935482978820801 289.4459533691406 0.19845184683799744 355.0812072753906 0.29168254137039185 0.8175694 0.2744358479976654 True -18 52402 30.182827472686768 0.6494982242584229 307.2430419921875 0.2658860683441162 355.5681457519531 0.2891748249530792 0.81835794 0.2747535705566406 True -19 55160 30.227128505706787 0.5471878051757812 288.5726318359375 0.37797582149505615 355.0712890625 0.2904092073440552 0.8169238 0.2764355540275574 False diff --git a/ENCSR683YLO/cherimoya.fold_0.performance.tsv b/ENCSR683YLO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a6945e635447b763859117e3e049cb95f7017b4b..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -355.5681457519531 0.47181299328804016 0.2891748249530792 0.09034483134746552 0.8183579444885254 0.7516517639160156 0.2747535705566406 \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_1.evaluate.json b/ENCSR683YLO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2face975eb930e0bb9403ee0cf31192feae453b3..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420QIQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_1.fit.json b/ENCSR683YLO/cherimoya.fold_1.fit.json deleted file mode 100644 index 461abe7a2b42939686396e8ebbc38ecd82e22301..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF420QIQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_1.log b/ENCSR683YLO/cherimoya.fold_1.log deleted file mode 100644 index 8a4b9e2c6f2f95a133622766efcef17509c678df..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 35.007699728012085 4.000060081481934 273.468505859375 0.6502165794372559 442.271240234375 0.1793576180934906 0.68566227 3.7378618717193604 True -1 5486 30.869238138198853 0.8280534744262695 325.9627380371094 0.6450616717338562 415.39691162109375 0.2607184648513794 0.75692075 1.045129656791687 True -2 8229 30.559490442276 0.7234559059143066 294.19757080078125 0.36525577306747437 409.4107360839844 0.27227064967155457 0.7723827 0.5506360530853271 True -3 10972 30.535040616989136 0.7195470333099365 304.719482421875 0.6595880389213562 405.2702941894531 0.28124937415122986 0.7826116 0.5024588108062744 True -4 13715 30.573517084121704 2.5939395427703857 273.89227294921875 0.6269963979721069 403.08343505859375 0.2858559489250183 0.78886366 0.5104497075080872 True -5 16458 30.572043895721436 0.8136811256408691 318.658447265625 0.42607027292251587 402.7175598144531 0.2861933708190918 0.79488987 0.46147188544273376 True -6 19201 30.60287833213806 0.9351887702941895 247.23793029785156 0.46904081106185913 402.1509704589844 0.28730931878089905 0.79821324 0.446961909532547 True -7 21944 30.650633335113525 0.7465078830718994 291.8302001953125 0.3498544991016388 400.222900390625 0.2939811646938324 0.79856753 0.4235171973705292 True -8 24687 30.55711841583252 0.7231311798095703 343.4461669921875 0.5300236940383911 399.6731262207031 0.2943834364414215 0.8039064 0.3859235942363739 True -9 27430 30.552507877349854 0.7208719253540039 276.0929260253906 0.33548471331596375 399.2787170410156 0.296720415353775 0.8064387 0.4031270146369934 True -10 30173 30.617919921875 0.736553430557251 287.85107421875 0.47467297315597534 398.7095031738281 0.29784154891967773 0.8105771 0.3741912543773651 True -11 32916 30.570738792419434 0.7232275009155273 310.40606689453125 0.30211174488067627 397.8885803222656 0.3003360331058502 0.81526124 0.35418906807899475 True -12 35659 30.19027543067932 0.7078382968902588 243.03033447265625 0.3391945958137512 397.3885803222656 0.30128780007362366 0.81884444 0.34535956382751465 True -13 38402 29.98461890220642 0.7084531784057617 248.77345275878906 0.4671262502670288 396.3129577636719 0.3049907088279724 0.8227694 0.33039915561676025 True -14 41145 30.013001203536987 0.7029006481170654 269.1089782714844 0.2517068386077881 396.0350036621094 0.30564752221107483 0.8280912 0.3219141662120819 True -15 43888 29.983715057373047 0.7088987827301025 270.6922607421875 0.2744448781013489 395.55413818359375 0.30650264024734497 0.83245873 0.3085353374481201 True -16 46631 29.952106952667236 0.7063131332397461 249.04847717285156 0.19859431684017181 395.2354431152344 0.3081020712852478 0.8361514 0.29537102580070496 True -17 49374 30.017292976379395 0.7110815048217773 348.2752990722656 0.40645551681518555 395.66009521484375 0.3060248792171478 0.8379661 0.28915199637413025 True -18 52117 30.00462055206299 0.7290828227996826 331.99267578125 0.2278786599636078 395.4149169921875 0.3077183961868286 0.8376722 0.29284149408340454 False -19 54860 29.979485750198364 0.7203502655029297 304.0550231933594 0.24281467497348785 395.7830810546875 0.30558067560195923 0.836616 0.2964463531970978 False diff --git a/ENCSR683YLO/cherimoya.fold_1.performance.tsv b/ENCSR683YLO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6527d1e80db54d16e5e1a0b8220be47b4e6048fd..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -395.66009521484375 0.4560873210430145 0.30602484941482544 0.10600367188453674 0.8379660844802856 0.7958309054374695 0.28915199637413025 \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_2.evaluate.json b/ENCSR683YLO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c218d0c7621dcaf18c4187d2ebf77fb5cd59ead4..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420QIQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_2.fit.json b/ENCSR683YLO/cherimoya.fold_2.fit.json deleted file mode 100644 index 4a14fce29184393ca5d7d64acd15c4af2b94e9d5..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF420QIQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_2.log b/ENCSR683YLO/cherimoya.fold_2.log deleted file mode 100644 index d83d7bb33ad3f324eff63e4ed2d71b2d1e5549cd..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2911 37.18429255485535 4.135600328445435 304.7919921875 0.7430325746536255 404.9765319824219 0.178817480802536 0.68802935 3.5825233459472656 True -1 5822 32.530519247055054 0.6539380550384521 270.7173767089844 0.9423490762710571 380.6809387207031 0.25623026490211487 0.7593354 0.7245703935623169 True -2 8733 32.45354604721069 0.576439380645752 283.648681640625 0.46143126487731934 375.55120849609375 0.26662909984588623 0.76998883 0.4107482433319092 True -3 11644 32.42506456375122 0.659980058670044 283.76654052734375 0.5855239629745483 373.0346984863281 0.27087876200675964 0.7747633 0.409643292427063 True -4 14555 32.457024335861206 0.5198540687561035 317.7193603515625 0.621372401714325 371.50579833984375 0.27539175748825073 0.7781682 0.42318034172058105 True -5 17466 32.432095766067505 0.5255606174468994 238.1348876953125 0.45604413747787476 370.8822937011719 0.27668917179107666 0.7796413 0.423019140958786 True -6 20377 32.46268558502197 0.5321915149688721 264.8750305175781 0.6301283240318298 369.8426818847656 0.2802381217479706 0.78502834 0.390572726726532 True -7 23288 32.431370973587036 0.5316414833068848 257.35296630859375 0.6089269518852234 369.8877258300781 0.2809210419654846 0.7856969 0.3826623260974884 True -8 26199 32.434685945510864 0.5208945274353027 341.32708740234375 0.33852100372314453 368.4457702636719 0.28631478548049927 0.78613335 0.36763089895248413 True -9 29110 32.43652153015137 0.5336477756500244 305.54144287109375 0.4687115252017975 368.33905029296875 0.28644639253616333 0.78906995 0.36425769329071045 True -10 32021 32.45497918128967 0.5282187461853027 320.8624267578125 0.3911476731300354 367.7790222167969 0.2881982624530792 0.7924193 0.3624708950519562 True -11 34932 32.50456142425537 0.5368514060974121 321.74700927734375 0.49251043796539307 366.7205505371094 0.29041188955307007 0.7967653 0.3619978427886963 True -12 37843 32.432936668395996 0.5308494567871094 273.4085388183594 0.4057525098323822 366.7279357910156 0.2909091114997864 0.8015446 0.34325823187828064 True -13 40754 31.900686025619507 0.5254964828491211 300.575439453125 0.35563918948173523 365.6106262207031 0.2940993309020996 0.8048772 0.32709550857543945 True -14 43665 31.788296461105347 0.5245637893676758 241.4252166748047 0.38236239552497864 365.5361022949219 0.29291415214538574 0.80801344 0.31602001190185547 True -15 46576 31.819357872009277 0.5519261360168457 318.4920959472656 0.2625837028026581 364.5743408203125 0.2967625558376312 0.8124082 0.3015255033969879 True -16 49487 32.90198087692261 2.974898338317871 270.86627197265625 0.2651134729385376 364.54473876953125 0.2975537180900574 0.81714594 0.2893599569797516 True -17 52398 31.910155534744263 9.117270946502686 298.61553955078125 0.3103262782096863 364.8617858886719 0.2974046468734741 0.81683624 0.28549036383628845 False -18 55309 31.87917399406433 1.3361153602600098 317.0782165527344 0.21827565133571625 365.1388244628906 0.2960013151168823 0.81846327 0.2864423990249634 True -19 58220 31.814383268356323 0.7693028450012207 292.822998046875 0.26127272844314575 364.9725646972656 0.2952120900154114 0.81654006 0.2907527983188629 False diff --git a/ENCSR683YLO/cherimoya.fold_2.performance.tsv b/ENCSR683YLO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a1931f8f14263267b6302695601a301f16988469..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -365.1388244628906 0.46705999970436096 0.2960013151168823 0.09280966967344284 0.8184632658958435 0.766339898109436 0.2864423990249634 \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_3.evaluate.json b/ENCSR683YLO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7b231023de4f99615dc30a7ddfbe290beb8a3405..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420QIQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_3.fit.json b/ENCSR683YLO/cherimoya.fold_3.fit.json deleted file mode 100644 index 789163c3eefb2a2cd6632eab2d04c491b56a02d7..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF420QIQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_3.log b/ENCSR683YLO/cherimoya.fold_3.log deleted file mode 100644 index c7065806911aa07a7bf104734563d6e00329e221..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2801 36.06768202781677 12.225181341171265 311.09564208984375 0.49918997287750244 411.3999328613281 0.1741076558828354 0.7029394 3.8896522521972656 True -1 5602 31.296222686767578 0.6308832168579102 309.95068359375 0.5859248638153076 388.9418640136719 0.24660280346870422 0.75846857 0.8937246799468994 True -2 8403 31.2630615234375 0.6547732353210449 257.1265563964844 0.56495600938797 384.3106689453125 0.25881287455558777 0.771093 0.5003262162208557 True -3 11204 31.246835708618164 2.093916416168213 270.4893798828125 0.6806296110153198 382.83526611328125 0.26089969277381897 0.7830321 0.42233628034591675 True -4 14005 31.334854125976562 0.6416060924530029 276.1950378417969 0.5849815607070923 381.1750793457031 0.26500964164733887 0.78431094 0.4207373559474945 True -5 16806 31.30142092704773 1.3343985080718994 333.10931396484375 0.9225735068321228 379.7828063964844 0.269538551568985 0.7889952 0.4038483500480652 True -6 19607 31.334124326705933 0.5719954967498779 293.5609436035156 0.3848383128643036 379.73284912109375 0.2697417736053467 0.7916956 0.44576701521873474 True -7 22408 31.363404035568237 0.562706708908081 310.26483154296875 0.7916240096092224 379.34637451171875 0.2705092430114746 0.79545593 0.4081040918827057 True -8 25209 31.31962823867798 0.5709354877471924 292.0560302734375 0.2815590798854828 378.0589599609375 0.27531591057777405 0.795943 0.39743727445602417 True -9 28010 31.321297883987427 0.5865490436553955 305.28155517578125 0.33206605911254883 377.76531982421875 0.27626192569732666 0.79945457 0.40160301327705383 True -10 30811 31.323020458221436 0.5689527988433838 306.143798828125 0.3696986436843872 377.1416320800781 0.2788299322128296 0.80425286 0.38747137784957886 True -11 33612 31.234296083450317 0.5642969608306885 293.67974853515625 0.47783851623535156 377.1973571777344 0.2792092561721802 0.80537647 0.3848241865634918 True -12 36413 31.245519399642944 0.5723419189453125 298.114501953125 0.1910552680492401 376.07769775390625 0.28211718797683716 0.8101878 0.37887924909591675 True -13 39214 30.919440269470215 0.5622484683990479 264.9588623046875 0.34957191348075867 375.7900695800781 0.2826816439628601 0.8159815 0.3541930019855499 True -14 42015 30.608179092407227 0.5541741847991943 289.8382568359375 0.2478252649307251 375.1914978027344 0.2837492823600769 0.8218962 0.3352680504322052 True -15 44816 30.645970106124878 2.4217376708984375 267.5788879394531 0.265377402305603 374.2049255371094 0.28741106390953064 0.82748324 0.30984899401664734 True -16 47617 30.82962465286255 0.5916152000427246 275.6419982910156 0.5491538047790527 375.1096496582031 0.2846469283103943 0.8306539 0.2970205545425415 True -17 50418 30.756178855895996 0.5788323879241943 277.21514892578125 0.22940894961357117 374.4151306152344 0.28621864318847656 0.8309623 0.289125919342041 True -18 53219 30.675795555114746 0.5925357341766357 267.8211364746094 0.3264350891113281 374.7124328613281 0.2860012352466583 0.8306429 0.2885887622833252 False -19 56020 30.63744592666626 0.5743656158447266 288.9710693359375 0.18737220764160156 374.55841064453125 0.28604593873023987 0.829869 0.2883390486240387 False diff --git a/ENCSR683YLO/cherimoya.fold_3.performance.tsv b/ENCSR683YLO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d75b5befde0d16285afed8f8b457ec7c9085cf5f..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -374.4151306152344 0.4686359763145447 0.28621864318847656 0.09805622696876526 0.8309623003005981 0.7704249024391174 0.289125919342041 \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_4.evaluate.json b/ENCSR683YLO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 506ef0a69801895a028c24248d28099f2720166b..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF420QIQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_4.fit.json b/ENCSR683YLO/cherimoya.fold_4.fit.json deleted file mode 100644 index 5efe80be2bd02b0384c6e9341d75d2a82d9b7bd8..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF420QIQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR683YLO/cherimoya.fold_4.log b/ENCSR683YLO/cherimoya.fold_4.log deleted file mode 100644 index 18a1c36054d179cb525acf56f3910fca21cf749b..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2864 36.63026690483093 4.820337772369385 265.73968505859375 0.50548255443573 377.8401184082031 0.16858848929405212 0.6981327 3.233576536178589 True -1 5728 31.971482515335083 0.618255615234375 327.14727783203125 0.7048810720443726 359.1598205566406 0.2365531176328659 0.75313914 0.7892835736274719 True -2 8592 31.98529076576233 2.563300132751465 252.16790771484375 0.5710809826850891 353.5434875488281 0.24870117008686066 0.7653697 0.4307820498943329 True -3 11456 31.93491220474243 0.5596230030059814 344.604736328125 0.6221011281013489 352.0924072265625 0.2517388164997101 0.76788557 0.4034722149372101 True -4 14320 31.88840126991272 0.56996750831604 312.6465759277344 0.3769530951976776 350.5553283691406 0.25627607107162476 0.7773422 0.3761191666126251 True -5 17184 31.938417196273804 0.5747761726379395 287.1762390136719 0.5372918844223022 350.35333251953125 0.2564881145954132 0.7803997 0.3675471544265747 True -6 20048 31.88589096069336 0.5684044361114502 316.6729431152344 0.4564893841743469 348.95794677734375 0.26152151823043823 0.7831778 0.3570455312728882 True -7 22912 31.893182516098022 0.5629680156707764 283.21490478515625 0.362085223197937 348.79400634765625 0.2630687355995178 0.78045386 0.3649418354034424 False -8 25776 31.850906372070312 3.0667285919189453 278.406982421875 0.4992445707321167 347.80126953125 0.26615825295448303 0.7837496 0.3386065363883972 True -9 28640 31.418983697891235 0.5618317127227783 271.4624328613281 0.38066866993904114 347.4145202636719 0.26785168051719666 0.78882307 0.3446267247200012 True -10 31504 31.343637466430664 0.5569851398468018 261.952880859375 0.49307572841644287 346.2663269042969 0.27188003063201904 0.78941196 0.3375622630119324 True -11 34368 31.27646780014038 0.5711078643798828 294.05670166015625 0.3354111611843109 346.1750793457031 0.2716420292854309 0.79368037 0.32529935240745544 True -12 37232 31.310421228408813 0.5733771324157715 272.7000732421875 0.4061259627342224 346.0124816894531 0.27255862951278687 0.7973711 0.3164796829223633 True -13 40096 31.33807945251465 0.5707581043243408 286.9404296875 0.31334057450294495 345.4556884765625 0.27452486753463745 0.8019327 0.3048061430454254 True -14 42960 31.432207822799683 1.3041350841522217 271.9610595703125 0.23969689011573792 345.1750183105469 0.2748241722583771 0.80759513 0.2928255498409271 True -15 45824 31.47976016998291 0.5781934261322021 360.1313781738281 0.3248329162597656 344.8215637207031 0.2761053442955017 0.81249726 0.27952712774276733 True -16 48688 31.61032485961914 0.5630888938903809 248.3142852783203 0.2734641432762146 344.7765197753906 0.2764803171157837 0.8173763 0.26876184344291687 True -17 51552 31.469998598098755 0.600128173828125 279.7456359863281 0.29699867963790894 344.9470520019531 0.2758246958255768 0.8191372 0.2643462121486664 True -18 54416 31.461943864822388 0.5782263278961182 301.93389892578125 0.25821632146835327 344.7372741699219 0.2781079411506653 0.8187354 0.26466837525367737 False -19 57280 31.423508405685425 0.5694270133972168 307.9649353027344 0.29165512323379517 344.7279357910156 0.27663904428482056 0.81886554 0.2662733793258667 False diff --git a/ENCSR683YLO/cherimoya.fold_4.performance.tsv b/ENCSR683YLO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index bb0f952467e3da1dd9c2a1e89d9f9d54ce489080..0000000000000000000000000000000000000000 --- a/ENCSR683YLO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -344.9470520019531 0.4794989228248596 0.27582472562789917 0.08568063378334045 0.8191372156143188 0.752543568611145 0.2643462121486664 \ No newline at end of file diff --git a/ENCSR684KUG/cherimoya.fold_0.log b/ENCSR684KUG/cherimoya.fold_0.log deleted file mode 100644 index 341833e79a208d8857816cdef828f8280b8500d5..0000000000000000000000000000000000000000 --- a/ENCSR684KUG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2240 28.925700902938843 4.290265083312988 286.8954162597656 0.6603677868843079 398.3144836425781 0.4435915946960449 0.41122845 8.067306518554688 True -1 4480 24.825177669525146 0.4855823516845703 285.8326416015625 0.76370769739151 344.8854064941406 0.5598066449165344 0.5093753 2.6672563552856445 True -2 6720 24.740896940231323 0.45072269439697266 248.47129821777344 0.545869767665863 334.2193908691406 0.5841608047485352 0.5324555 1.1507123708724976 True -3 8960 24.723930835723877 0.4486267566680908 279.97723388671875 0.5287570953369141 331.2294921875 0.5909810662269592 0.54290134 0.8662064075469971 True -4 11200 24.687864065170288 0.49010682106018066 225.9138641357422 0.5391805171966553 329.6210632324219 0.5947972536087036 0.5505261 0.7731668949127197 True -5 13440 24.64745569229126 12.498610734939575 241.6453857421875 0.4832831025123596 328.66534423828125 0.5976920127868652 0.5586313 0.6321609616279602 True -6 15680 24.750537395477295 0.45558929443359375 241.09783935546875 0.34844642877578735 327.60797119140625 0.6004042625427246 0.5631473 0.6134518980979919 True -7 17920 24.73211359977722 0.4516317844390869 254.23129272460938 0.3797726035118103 326.61920166015625 0.6030663847923279 0.57106376 0.5519763827323914 True -8 20160 24.759114027023315 0.4513988494873047 231.9117889404297 0.7387230396270752 325.73980712890625 0.6057631373405457 0.5813192 0.5216705799102783 True -9 22400 24.72455334663391 0.45020103454589844 261.84088134765625 0.42495661973953247 324.9529724121094 0.6078251004219055 0.58678925 0.5010260939598083 True -10 24640 24.746821641921997 0.45325326919555664 230.31907653808594 0.4642390012741089 324.038330078125 0.6099381446838379 0.59497213 0.48190924525260925 True -11 26880 24.69600486755371 0.4507889747619629 229.64599609375 0.41037315130233765 323.234130859375 0.6122631430625916 0.6024284 0.47027745842933655 True -12 29120 24.680281162261963 0.4502718448638916 272.794921875 0.5243217349052429 322.26141357421875 0.6136380434036255 0.60842127 0.46120619773864746 True -13 31360 24.691232919692993 0.4519636631011963 231.5272216796875 0.5008798241615295 321.7517395019531 0.6151345372200012 0.6138834 0.4567279517650604 True -14 33600 24.724871158599854 0.5314245223999023 242.59634399414062 0.46291327476501465 321.17291259765625 0.61662358045578 0.6206955 0.4461793601512909 True -15 35840 24.69313359260559 0.4550604820251465 233.21054077148438 0.4006000757217407 320.759033203125 0.6172890067100525 0.6275576 0.43694064021110535 True -16 38080 24.691481828689575 0.44556713104248047 255.44126892089844 0.289315402507782 320.7748718261719 0.6173483729362488 0.63045645 0.43401381373405457 True -17 40320 24.658643007278442 0.45058417320251465 260.81689453125 0.37213224172592163 320.7674560546875 0.6169707775115967 0.63148314 0.43549689650535583 True -18 42560 24.684065341949463 0.44628477096557617 246.68890380859375 0.24943171441555023 320.9427185058594 0.6163985133171082 0.62588495 0.44337549805641174 False -19 44800 24.67119288444519 0.5083849430084229 237.13638305664062 0.29842376708984375 321.0093994140625 0.6159634590148926 0.62241256 0.44789397716522217 False diff --git a/ENCSR684KUG/cherimoya.fold_1.evaluate.json b/ENCSR684KUG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5d5b9fe53f1bd73e3c10f96cedb8fd69b9f4d0cf..0000000000000000000000000000000000000000 --- a/ENCSR684KUG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF745DCO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR684KUG/cherimoya.fold_1.log b/ENCSR684KUG/cherimoya.fold_1.log deleted file mode 100644 index ab52c65bc735e844145531c02467e70da5fb65f1..0000000000000000000000000000000000000000 --- a/ENCSR684KUG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2300 29.51709222793579 3.437466621398926 232.7999267578125 0.42235714197158813 388.3297119140625 0.44721993803977966 0.4107924 7.1601738929748535 True -1 4600 25.35242486000061 0.9175832271575928 247.8521270751953 0.48619210720062256 343.03741455078125 0.5515013933181763 0.50799894 2.249263286590576 True -2 6900 25.386899948120117 0.4793534278869629 218.35693359375 0.7282264232635498 336.19659423828125 0.5692045092582703 0.54577065 0.8071308135986328 True -3 9200 25.403010606765747 0.4766366481781006 272.65948486328125 0.7373611927032471 333.5722351074219 0.5756803154945374 0.5603232 0.5940123796463013 True -4 11500 25.33208179473877 0.4762134552001953 268.083251953125 0.6941205859184265 332.14532470703125 0.5798969268798828 0.5683 0.5542175769805908 True -5 13800 25.3468120098114 1.8043570518493652 274.1107177734375 0.6073839068412781 331.2117919921875 0.582461953163147 0.5751906 0.5296651721000671 True -6 16100 25.388575792312622 0.4802122116088867 212.4490203857422 0.49337878823280334 330.6058044433594 0.5848425030708313 0.58002794 0.5008081197738647 True -7 18400 25.349932432174683 0.47823238372802734 261.76348876953125 0.5312873125076294 329.8635559082031 0.5870946645736694 0.5874821 0.5002400279045105 True -8 20700 25.42260766029358 0.4792768955230713 256.1432800292969 0.4231569170951843 329.0906677246094 0.5892114639282227 0.59099627 0.47429051995277405 True -9 23000 25.41192078590393 0.48648977279663086 289.55218505859375 0.543914794921875 328.6091613769531 0.5906695127487183 0.5944146 0.47407734394073486 True -10 25300 25.305155754089355 3.4632463455200195 263.65985107421875 0.5506018996238708 327.7359619140625 0.592869758605957 0.60434747 0.459340363740921 True -11 27600 25.41509222984314 0.48438358306884766 261.12579345703125 0.49074599146842957 326.94366455078125 0.5949176549911499 0.6146483 0.43727096915245056 True -12 29900 25.307635068893433 0.48244595527648926 258.52532958984375 0.4188781976699829 326.4410705566406 0.5963708758354187 0.62115926 0.41880524158477783 True -13 32200 25.299996614456177 21.26261067390442 260.86737060546875 0.42464691400527954 325.8337707519531 0.5977486968040466 0.6305295 0.40754684805870056 True -14 34500 26.7404842376709 0.49071478843688965 240.78146362304688 0.42208799719810486 324.9337463378906 0.5992797017097473 0.6375422 0.3973127007484436 True -15 36800 25.341005086898804 0.4959123134613037 241.31491088867188 0.34849703311920166 324.525146484375 0.600255012512207 0.64611953 0.38724496960639954 True -16 39100 25.32016110420227 0.4874534606933594 232.749267578125 0.24996647238731384 324.34405517578125 0.6006435751914978 0.64995307 0.38225701451301575 True -17 41400 25.310630083084106 0.47388601303100586 239.90805053710938 0.27792492508888245 324.1297912597656 0.6003014445304871 0.65011334 0.3856605291366577 True -18 43700 25.378382444381714 0.4774656295776367 245.2900390625 0.35179460048675537 324.42962646484375 0.5998121500015259 0.6485411 0.39279088377952576 False -19 46000 25.3410542011261 0.4794807434082031 259.21044921875 0.2758966088294983 324.3545837402344 0.5995053052902222 0.64583 0.39799052476882935 False diff --git a/ENCSR684KUG/cherimoya.fold_2.fit.json b/ENCSR684KUG/cherimoya.fold_2.fit.json deleted file mode 100644 index b50a53da78d6d757ae1183dcd952e53fdfe89331..0000000000000000000000000000000000000000 --- a/ENCSR684KUG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF745DCO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR684KUG/cherimoya.fold_4.performance.tsv b/ENCSR684KUG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3a1817aed24b1884e0fae0476b7da5da7656b5fb..0000000000000000000000000000000000000000 --- a/ENCSR684KUG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -316.97088623046875 0.3134075701236725 0.6160497665405273 0.2080475091934204 0.6477465629577637 0.6215923428535461 0.41047754883766174 \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_0.evaluate.json b/ENCSR685OFR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6b34ce1b906eaa6d998695be2d58aea4da7a6261..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576HTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_0.fit.json b/ENCSR685OFR/cherimoya.fold_0.fit.json deleted file mode 100644 index 2079aebc01d5211fbb4ebbbe0c884658fc376588..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF576HTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_0.log b/ENCSR685OFR/cherimoya.fold_0.log deleted file mode 100644 index 4dee5d8a39e316a7fb9a11a5f84788af982c9829..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1669 23.090240240097046 21.48810601234436 562.1345825195312 2.2253966331481934 1312.9559326171875 0.46425411105155945 0.5385432 24.883255004882812 True -1 3338 18.65648102760315 11.39135193824768 589.379638671875 2.1989006996154785 879.2672119140625 0.6380062103271484 0.61476755 17.124202728271484 True -2 5007 18.510982275009155 0.3375234603881836 527.1956787109375 2.462632417678833 740.927734375 0.7232741117477417 0.62318283 6.954319477081299 True -3 6676 18.14509129524231 0.3132596015930176 510.96405029296875 1.6550869941711426 702.3639526367188 0.743310809135437 0.6053816 4.152072429656982 False -4 8345 18.15791130065918 0.3199479579925537 554.1572875976562 1.3228704929351807 687.3618774414062 0.7514122724533081 0.62066644 3.0068297386169434 False -5 10014 18.14510154724121 0.31238269805908203 446.94970703125 1.716409683227539 676.6039428710938 0.7570033669471741 0.63271374 2.6698102951049805 True -6 11683 18.169074773788452 0.3180506229400635 526.092529296875 1.7685738801956177 666.9150390625 0.7627710103988647 0.63786924 2.278599977493286 True -7 13352 18.13654899597168 0.3110377788543701 377.27142333984375 2.5142037868499756 658.876708984375 0.7680230140686035 0.63900846 2.088958978652954 True -8 15021 18.169678449630737 0.9669809341430664 553.1473999023438 1.8384513854980469 650.5049438476562 0.7721750736236572 0.64798546 1.8886947631835938 True -9 16690 18.28002429008484 8.8258695602417 474.78955078125 1.3119781017303467 644.2503051757812 0.7752828001976013 0.6542332 1.7007182836532593 True -10 18359 18.166250228881836 0.3215670585632324 589.144287109375 0.8539643287658691 636.2271118164062 0.7797425985336304 0.66598016 1.55680513381958 True -11 20028 18.22458267211914 0.31870484352111816 445.5261535644531 1.024186372756958 630.7927856445312 0.7830201983451843 0.6784878 1.4368691444396973 True -12 21697 18.19566774368286 0.47799062728881836 405.0599670410156 1.2009375095367432 624.888427734375 0.785858154296875 0.69097745 1.268929123878479 True -13 23366 18.75818109512329 8.208863496780396 485.7454528808594 1.2914856672286987 619.1812133789062 0.7881609201431274 0.6984463 1.2070616483688354 True -14 25035 18.61041522026062 0.3241400718688965 566.5050048828125 0.9982710480690002 616.6179809570312 0.7893837690353394 0.7101028 1.1512434482574463 True -15 26704 18.200488328933716 0.471787691116333 431.4415588378906 1.0139758586883545 615.7117309570312 0.7898733615875244 0.71703696 1.116969108581543 True -16 28373 18.197473526000977 0.3217301368713379 473.5281066894531 0.7424527406692505 615.0305786132812 0.7899262309074402 0.71968716 1.0860508680343628 True -17 30042 18.18307328224182 0.31869006156921387 407.621337890625 0.8773319721221924 616.379150390625 0.7892540693283081 0.7218294 1.0843380689620972 True -18 31711 18.211273670196533 0.31830883026123047 452.7230224609375 0.7551112771034241 617.0599365234375 0.7881803512573242 0.72082305 1.0935391187667847 False -19 33380 18.229784727096558 0.323697566986084 482.04345703125 0.742587149143219 618.5709838867188 0.7873606085777283 0.71891373 1.1064791679382324 False diff --git a/ENCSR685OFR/cherimoya.fold_0.performance.tsv b/ENCSR685OFR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8a3e4163ba66a651cb3faee4fee85904dff94988..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -616.379150390625 0.1852715015411377 0.7892540693283081 0.35875725746154785 0.7218294143676758 0.7043812870979309 1.0843380689620972 \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_1.evaluate.json b/ENCSR685OFR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2a414fd8d1542e2dd061036cc385042057115a42..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576HTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_1.fit.json b/ENCSR685OFR/cherimoya.fold_1.fit.json deleted file mode 100644 index 5fa68db8322b1aa73de40519a10748afa4c1b8e8..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF576HTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_1.log b/ENCSR685OFR/cherimoya.fold_1.log deleted file mode 100644 index d18d2cb2932cc990a80405b071399db483de5b5d..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1636 22.330482006072998 3.5136070251464844 668.2935791015625 2.464785575866699 1511.0533447265625 0.46814200282096863 0.5102708 27.521305084228516 True -1 3272 17.822377920150757 0.5284931659698486 667.3599853515625 1.9748444557189941 1002.7269897460938 0.6390700936317444 0.6121433 19.1279354095459 True -2 4908 17.816330194473267 2.1484522819519043 577.02978515625 1.9750256538391113 844.2781982421875 0.7309291362762451 0.6403671 8.73591423034668 True -3 6544 17.56823754310608 0.4872620105743408 534.95849609375 2.517810821533203 795.1582641601562 0.751884400844574 0.6436067 4.351866245269775 True -4 8180 17.49604892730713 0.4861025810241699 399.0064697265625 1.9245736598968506 772.3609008789062 0.7621949315071106 0.653115 3.0282695293426514 True -5 9816 17.47177290916443 0.4819927215576172 546.0842895507812 1.3200790882110596 759.9353637695312 0.7695075273513794 0.65951335 2.698976516723633 True -6 11452 17.585339784622192 0.5124599933624268 466.7626647949219 1.4565306901931763 749.354736328125 0.7748005986213684 0.66555196 2.3273990154266357 True -7 13088 17.455698490142822 0.4765479564666748 440.49884033203125 1.2279489040374756 737.9461669921875 0.7802450656890869 0.6812387 2.0459396839141846 True -8 14724 17.534088373184204 0.48768067359924316 393.3011779785156 1.9155243635177612 728.102294921875 0.7843576073646545 0.6825616 1.7603158950805664 True -9 16360 17.488517999649048 34.171016454696655 515.2603759765625 1.0269312858581543 718.4362182617188 0.7888066172599792 0.68406606 1.6231011152267456 True -10 17996 17.892383575439453 0.4827077388763428 596.1651611328125 1.0337088108062744 710.4783325195312 0.7927278280258179 0.69553035 1.5221139192581177 True -11 19632 17.484018802642822 0.5029592514038086 455.4179992675781 1.3004684448242188 702.8509521484375 0.7961429953575134 0.70801693 1.298406720161438 True -12 21268 18.174850702285767 32.92565035820007 499.53509521484375 1.9572327136993408 697.6196899414062 0.7991206645965576 0.71479446 1.2405816316604614 True -13 22904 18.321818828582764 0.50579833984375 373.58038330078125 0.9496015906333923 691.9818725585938 0.801690936088562 0.72340536 1.1655625104904175 True -14 24540 17.608309507369995 0.5062508583068848 442.5718994140625 0.8554023504257202 687.7401733398438 0.8033697009086609 0.7334719 1.097609281539917 True -15 26176 17.574082374572754 0.4954047203063965 392.32611083984375 0.8487906455993652 684.9805297851562 0.8046714067459106 0.7400325 1.0700299739837646 True -16 27812 17.797919034957886 0.4896249771118164 453.64947509765625 0.903080940246582 684.8568115234375 0.8046523332595825 0.7443357 1.0624914169311523 True -17 29448 17.567280769348145 25.85558533668518 431.2988586425781 0.7693289518356323 686.4271240234375 0.8037598729133606 0.74586165 1.0602571964263916 True -18 31084 19.209113597869873 0.5087399482727051 431.971923828125 0.5154821276664734 687.9208374023438 0.802813708782196 0.743683 1.0782501697540283 False -19 32720 17.503793716430664 0.49121761322021484 450.069091796875 0.4534836411476135 689.1420288085938 0.8021101951599121 0.7420556 1.0881457328796387 False diff --git a/ENCSR685OFR/cherimoya.fold_1.performance.tsv b/ENCSR685OFR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 94364fc6dd9e99ce72db9714f6c1a678c0e6ebb1..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -686.4271240234375 0.17081646621227264 0.8037598133087158 0.3899836242198944 0.7458616495132446 0.7463017106056213 1.0602571964263916 \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_2.evaluate.json b/ENCSR685OFR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b8264d398707c57c23fcb3cb5f8c8ca6707d73a4..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576HTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_2.fit.json b/ENCSR685OFR/cherimoya.fold_2.fit.json deleted file mode 100644 index 95461d9f5d74625cc7680dc8d7c2283d551ef929..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF576HTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_2.log b/ENCSR685OFR/cherimoya.fold_2.log deleted file mode 100644 index 97fd4cecd65d359d501f05e7df5da22c6f5248d4..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1763 27.428056001663208 21.733152866363525 464.0510559082031 2.171677827835083 1368.4991455078125 0.47535496950149536 0.5231497 23.73561668395996 True -1 3526 19.344643354415894 0.3787200450897217 699.4783935546875 1.7887272834777832 904.1578369140625 0.6645103096961975 0.6244882 17.338760375976562 True -2 5289 19.236783504486084 0.35578417778015137 503.5569152832031 1.7120320796966553 776.0709228515625 0.7373078465461731 0.65282804 6.446455478668213 True -3 7052 19.24119520187378 0.3537287712097168 635.849365234375 1.515395164489746 733.8995361328125 0.7530288100242615 0.6615932 3.20576548576355 True -4 8815 19.20510458946228 0.3484151363372803 670.63671875 2.194157123565674 719.2161254882812 0.7608644962310791 0.66533166 2.3826704025268555 True -5 10578 19.157288074493408 0.3474581241607666 559.8853759765625 2.0964465141296387 708.9828491210938 0.7670160531997681 0.6704953 2.2442686557769775 True -6 12341 19.179993867874146 0.7632620334625244 447.11328125 1.8740642070770264 699.2245483398438 0.7728750109672546 0.67022383 2.1519532203674316 False -7 14104 19.27114701271057 0.5847628116607666 465.922119140625 1.3261359930038452 688.5736083984375 0.7778863310813904 0.6784708 1.858016014099121 True -8 15867 19.168415784835815 0.34970784187316895 532.087890625 2.1131370067596436 682.18896484375 0.7810401320457458 0.68253607 1.6564512252807617 True -9 17630 19.251709699630737 1.9181082248687744 484.8602294921875 1.615849494934082 675.3946533203125 0.7854591608047485 0.68817675 1.4824129343032837 True -10 19393 19.243645906448364 11.148190259933472 479.3433532714844 1.2150495052337646 668.3600463867188 0.7892718315124512 0.6951488 1.3925145864486694 True -11 21156 21.74131727218628 15.573297500610352 488.9879150390625 1.1496158838272095 659.1578979492188 0.7928070425987244 0.70505494 1.2609976530075073 True -12 22919 19.40340518951416 0.35870361328125 601.0061645507812 1.1217129230499268 652.8990478515625 0.7961136698722839 0.7131451 1.177198052406311 True -13 24682 19.191924571990967 0.34670329093933105 476.97637939453125 0.8421149253845215 648.159912109375 0.7981158494949341 0.71826065 1.1384183168411255 True -14 26445 19.21115016937256 0.3492317199707031 464.21539306640625 0.9671930074691772 644.8385620117188 0.799344003200531 0.7275861 1.0824344158172607 True -15 28208 19.238277912139893 0.3473536968231201 434.00653076171875 0.9181841611862183 643.4904174804688 0.7999653816223145 0.73339105 1.075343132019043 True -16 29971 19.54654884338379 2.7914116382598877 329.539306640625 1.0851397514343262 642.8203125 0.7999928593635559 0.73490775 1.0620851516723633 True -17 31734 19.230974435806274 0.34781932830810547 463.9064025878906 0.6779234409332275 643.99462890625 0.7993558049201965 0.7353826 1.0744671821594238 True -18 33497 20.214123249053955 22.49963402748108 462.0614318847656 0.7154837250709534 645.3077392578125 0.7983614802360535 0.7328483 1.09246826171875 False -19 35260 19.701693296432495 0.3483853340148926 453.5329895019531 0.6374143958091736 646.3372802734375 0.797703206539154 0.72996837 1.1049259901046753 False diff --git a/ENCSR685OFR/cherimoya.fold_2.performance.tsv b/ENCSR685OFR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 27741a84552f13f057c5ecac53b4819ff84a76ed..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -643.99462890625 0.17768427729606628 0.7993558049201965 0.3770567774772644 0.735382616519928 0.7266531586647034 1.0744671821594238 \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_3.evaluate.json b/ENCSR685OFR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 48787352e62eb778d576339c8df47c7720d71c4a..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576HTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_3.fit.json b/ENCSR685OFR/cherimoya.fold_3.fit.json deleted file mode 100644 index 11188d41581eab22dac8e2a89c49763657625db1..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF576HTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_3.log b/ENCSR685OFR/cherimoya.fold_3.log deleted file mode 100644 index e4c92cf364d61210ab9c33913d6661997afaf18f..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1704 23.922919750213623 3.3199260234832764 710.6353149414062 2.051739454269409 1379.7705078125 0.47370514273643494 0.5382495 27.072492599487305 True -1 3408 18.535134077072144 0.3717021942138672 645.193115234375 1.800278663635254 909.6868286132812 0.6494221687316895 0.59768033 18.572914123535156 True -2 5112 18.56707739830017 0.3600621223449707 599.5816650390625 1.5975489616394043 774.7890014648438 0.7293897271156311 0.60984665 5.63535737991333 True -3 6816 18.550369024276733 0.34900474548339844 638.882080078125 1.883220911026001 738.8159790039062 0.7460492849349976 0.6202183 2.7893290519714355 True -4 8520 18.5565402507782 0.7090151309967041 572.12841796875 1.4237122535705566 725.3932495117188 0.7546749711036682 0.62288785 2.5492911338806152 True -5 10224 18.543826580047607 0.3557014465332031 436.5110778808594 1.658743143081665 716.7513427734375 0.7609911561012268 0.63304913 2.4474456310272217 True -6 11928 18.500847101211548 0.3566460609436035 559.1399536132812 1.254260540008545 706.8712768554688 0.7660302519798279 0.6408344 2.220959186553955 True -7 13632 18.479945182800293 0.3483772277832031 498.83380126953125 1.6039135456085205 700.6219482421875 0.7704821825027466 0.64872324 2.1484358310699463 True -8 15336 18.490989446640015 0.35298657417297363 438.73931884765625 1.613401174545288 692.0635986328125 0.7743381857872009 0.6588893 1.9086405038833618 True -9 17040 18.555469274520874 0.36068105697631836 518.8598022460938 0.7757513523101807 684.2576904296875 0.7779226303100586 0.65807956 1.7364469766616821 False -10 18744 18.590429544448853 0.3635594844818115 435.66717529296875 1.4947258234024048 678.8590087890625 0.7816312909126282 0.6664695 1.594530463218689 True -11 20448 18.55426287651062 0.36074256896972656 467.79547119140625 1.2180883884429932 672.1712036132812 0.784905731678009 0.67695564 1.5419228076934814 True -12 22152 18.543662786483765 0.3549685478210449 533.5403442382812 1.203041911125183 664.5463256835938 0.7882774472236633 0.6893235 1.4058090448379517 True -13 23856 18.544874668121338 0.3583688735961914 451.33465576171875 1.413069725036621 659.57373046875 0.7909291982650757 0.69476104 1.3145006895065308 True -14 25560 18.564701795578003 15.74033784866333 362.03131103515625 0.9001812934875488 657.083251953125 0.7926052212715149 0.7057611 1.2532265186309814 True -15 27264 19.72130274772644 17.449087858200073 444.2174072265625 0.8324707746505737 654.1422119140625 0.7936210036277771 0.7151009 1.2096389532089233 True -16 28968 18.551563501358032 0.36516666412353516 507.0227966308594 1.0766373872756958 654.3343505859375 0.7932612299919128 0.71834433 1.2022849321365356 True -17 30672 18.51548933982849 0.3578979969024658 534.864013671875 0.737453281879425 653.7340698242188 0.7926992177963257 0.71947074 1.2010772228240967 True -18 32376 18.50335454940796 0.3542144298553467 430.796875 0.7693109512329102 655.0496215820312 0.7919013500213623 0.7185676 1.2184053659439087 False -19 34080 18.8507239818573 0.35794949531555176 474.3033447265625 0.4908705949783325 656.1124877929688 0.7912929654121399 0.71897453 1.2243918180465698 False diff --git a/ENCSR685OFR/cherimoya.fold_3.performance.tsv b/ENCSR685OFR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9086c9b7db9e04935cf8096f052a7e56a33b51ab..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -653.7340698242188 0.17945674061775208 0.7926991581916809 0.3722544312477112 0.719470739364624 0.7178453803062439 1.2010772228240967 \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_4.evaluate.json b/ENCSR685OFR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6fb7582e70e116f1c7872256129dcf6d9c1824e0..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576HTN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_4.fit.json b/ENCSR685OFR/cherimoya.fold_4.fit.json deleted file mode 100644 index 6a3e99e264d299e75a85c0ef38660fb32ba8d1ab..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF576HTN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR685OFR/cherimoya.fold_4.log b/ENCSR685OFR/cherimoya.fold_4.log deleted file mode 100644 index dfe1c756a74cc0e8f0564c26b7bb4249633fd6b5..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1672 22.696505784988403 1.6298487186431885 652.3235473632812 3.0238423347473145 1314.4439697265625 0.46097642183303833 0.52747506 25.279104232788086 True -1 3344 18.25684142112732 0.28269028663635254 570.5567626953125 2.115891218185425 860.8418579101562 0.6453744769096375 0.6102134 17.248157501220703 True -2 5016 18.232784271240234 0.2677135467529297 629.8893432617188 1.2144520282745361 731.9143676757812 0.7276420593261719 0.6228971 5.941593647003174 True -3 6688 18.203976154327393 0.2649803161621094 672.9779052734375 1.3120330572128296 691.5179443359375 0.744565486907959 0.62363136 3.0706868171691895 True -4 8360 18.233696460723877 0.2723653316497803 570.38818359375 1.9352688789367676 673.6602172851562 0.7538322806358337 0.6356843 2.3327982425689697 True -5 10032 18.222559928894043 0.27130746841430664 499.2496337890625 1.6241302490234375 663.5857543945312 0.7602333426475525 0.6291247 2.3469979763031006 False -6 11704 20.143190383911133 18.457311868667603 567.5210571289062 1.7494754791259766 656.2412109375 0.7640454769134521 0.63391703 2.0760738849639893 False -7 13376 18.555668115615845 0.2698678970336914 457.6062927246094 1.6171462535858154 649.4335327148438 0.7674334049224854 0.6374651 1.8324719667434692 True -8 15048 18.208253145217896 0.27482032775878906 491.92584228515625 0.8531534075737 643.4788208007812 0.770466148853302 0.6423271 1.6820403337478638 True -9 16720 18.244840383529663 0.26859593391418457 456.0825500488281 1.275721788406372 637.74609375 0.7739614844322205 0.65824336 1.5184316635131836 True -10 18392 18.415757656097412 0.27444028854370117 335.9034423828125 1.227013349533081 632.1796875 0.777046263217926 0.66076696 1.377785086631775 True -11 20064 18.30051612854004 0.2726325988769531 424.976318359375 1.182342529296875 626.8116455078125 0.7802892923355103 0.6696609 1.2589858770370483 True -12 21736 18.308405876159668 0.9682168960571289 399.4338073730469 1.5475800037384033 621.1055908203125 0.7834909558296204 0.68390155 1.1884305477142334 True -13 23408 18.02840495109558 0.26683640480041504 472.2474365234375 1.306188941001892 616.811279296875 0.7858335375785828 0.69416696 1.1247004270553589 True -14 25080 17.926966428756714 0.27449488639831543 450.60418701171875 0.7317643165588379 613.27783203125 0.787555456161499 0.69985 1.11528480052948 True -15 26752 22.334978580474854 17.978403568267822 465.88177490234375 1.1021523475646973 612.1396484375 0.7881764769554138 0.70827293 1.0909513235092163 True -16 28424 18.46175789833069 0.2661561965942383 398.4700012207031 0.6470131874084473 612.3448486328125 0.7882968187332153 0.71183133 1.0967501401901245 True -17 30096 17.953307390213013 0.275127649307251 406.5650634765625 0.8899239301681519 613.16064453125 0.7876253724098206 0.7123 1.1047301292419434 True -18 31768 17.85715913772583 1.2898385524749756 441.5857238769531 0.5337769985198975 614.6864013671875 0.7867133021354675 0.7109645 1.1273093223571777 False -19 33440 17.982494354248047 0.27005767822265625 521.2567749023438 0.5624743700027466 615.933837890625 0.7860139608383179 0.70993054 1.1341794729232788 False diff --git a/ENCSR685OFR/cherimoya.fold_4.performance.tsv b/ENCSR685OFR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 95e60f0fab2f6fb42e2bf674cfce148719e6a961..0000000000000000000000000000000000000000 --- a/ENCSR685OFR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -613.16064453125 0.18588431179523468 0.7876253128051758 0.35832661390304565 0.7123000025749207 0.6902952194213867 1.1047301292419434 \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_0.evaluate.json b/ENCSR686WJL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 275c173d6fdd3bdbb78ca3a5a22dda48fea3b21a..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF389LCL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_0.fit.json b/ENCSR686WJL/cherimoya.fold_0.fit.json deleted file mode 100644 index ec26971f11b1d197c148f10fc946fe03f1d7589a..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF389LCL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_0.log b/ENCSR686WJL/cherimoya.fold_0.log deleted file mode 100644 index f162ada354da9c22c24699cc1832bc67c5764930..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 34.96560287475586 24.969895124435425 681.6785278320312 0.5769340991973877 908.1666259765625 0.2132234424352646 0.6280931 5.217860698699951 True -1 5462 30.54880928993225 0.6511416435241699 594.977294921875 0.5110592842102051 841.5990600585938 0.2584836483001709 0.69045097 2.0822951793670654 True -2 8193 30.38785696029663 0.7016630172729492 795.1104125976562 0.439922571182251 833.5546875 0.2615658938884735 0.7001224 1.109169840812683 True -3 10924 30.352842330932617 0.5967824459075928 725.4727172851562 0.5420864820480347 818.8567504882812 0.27098870277404785 0.7200061 0.9564478993415833 True -4 13655 30.394304513931274 0.5882093906402588 657.9492797851562 0.3368683457374573 819.2710571289062 0.27126654982566833 0.7160186 0.8823407888412476 False -5 16386 30.344838857650757 0.5631768703460693 741.7530517578125 0.5171610713005066 812.5277709960938 0.27516818046569824 0.7317591 0.7277889847755432 True -6 19117 30.340121269226074 0.8733165264129639 691.0496826171875 0.33613866567611694 807.8015747070312 0.2777039408683777 0.7441545 0.782158374786377 True -7 21848 30.392212629318237 1.0526015758514404 853.3944091796875 0.33585911989212036 805.7823486328125 0.27819108963012695 0.7496603 0.7746806740760803 True -8 24579 30.361948013305664 0.5885493755340576 812.4246826171875 0.49662941694259644 801.4908447265625 0.2810126543045044 0.76074713 0.6915683150291443 True -9 27310 30.372395753860474 0.5758116245269775 781.78564453125 0.7445221543312073 797.6319580078125 0.2854968309402466 0.764166 0.6479113101959229 True -10 30041 30.437898874282837 0.597611665725708 723.3807373046875 0.3030771315097809 796.2476196289062 0.2842475175857544 0.7741005 0.5471184253692627 True -11 32772 30.31025195121765 0.5761725902557373 708.6326904296875 0.30599379539489746 792.677490234375 0.28669407963752747 0.78158665 0.47417140007019043 True -12 35503 30.269648790359497 0.5668182373046875 580.4607543945312 0.3570120334625244 788.7073974609375 0.2892383933067322 0.78818834 0.4359319508075714 True -13 38234 30.332085609436035 0.5896797180175781 682.762451171875 0.277576744556427 785.654052734375 0.29148879647254944 0.79232335 0.3990273177623749 True -14 40965 30.24664878845215 0.5660214424133301 617.9041748046875 0.4060525596141815 783.6749877929688 0.2927684783935547 0.7976312 0.3631243109703064 True -15 43696 30.316678762435913 0.7872636318206787 764.206787109375 0.33528202772140503 783.2416381835938 0.2921206057071686 0.80160254 0.33472663164138794 True -16 46427 29.861305952072144 0.6006591320037842 682.7120361328125 0.2572568655014038 782.250732421875 0.2923494279384613 0.80630237 0.3122783899307251 True -17 49158 29.8905987739563 0.5754058361053467 655.7833251953125 0.26101434230804443 782.1148071289062 0.2921440601348877 0.80654234 0.30212831497192383 True -18 51889 29.78993558883667 2.3509488105773926 743.5382080078125 0.24195575714111328 781.5775146484375 0.2930034101009369 0.8059606 0.29985904693603516 False -19 54620 29.90229606628418 0.5804116725921631 677.5172119140625 0.23336388170719147 781.7113647460938 0.29329437017440796 0.8066502 0.30065837502479553 True diff --git a/ENCSR686WJL/cherimoya.fold_0.performance.tsv b/ENCSR686WJL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ee434e4634a1f55afb0221d55f2ea77e835c1e78..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -781.7113647460938 0.4642263352870941 0.29329437017440796 0.10943799465894699 0.8066502213478088 0.7873834371566772 0.30065837502479553 \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_1.evaluate.json b/ENCSR686WJL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4cab0a9b4be9a2a01c7a99d8bc67ec781c3cce7c..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF389LCL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_1.fit.json b/ENCSR686WJL/cherimoya.fold_1.fit.json deleted file mode 100644 index b511fba74b52c439cb6d01294605369d60f28d96..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF389LCL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_1.log b/ENCSR686WJL/cherimoya.fold_1.log deleted file mode 100644 index ccb932220b2ca86699177a613edad16a03816b41..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2720 35.11306357383728 4.0516345500946045 663.7216186523438 0.3987509608268738 1078.47607421875 0.22355066239833832 0.63498145 4.974656581878662 True -1 5440 30.190096139907837 0.7320065498352051 628.3458862304688 0.41358911991119385 1000.0879516601562 0.2718781530857086 0.69313174 2.3295586109161377 True -2 8160 30.176517486572266 0.7179999351501465 767.9248657226562 0.5450117588043213 984.609130859375 0.2801622748374939 0.7020299 1.3774577379226685 True -3 10880 30.16462016105652 0.6714377403259277 708.76025390625 0.48127174377441406 971.3938598632812 0.28692862391471863 0.7168794 1.467090368270874 True -4 13600 30.158544540405273 0.6655299663543701 592.3958740234375 0.5790258646011353 958.2984008789062 0.293824702501297 0.72930384 0.966021716594696 True -5 16320 30.20123815536499 0.6718971729278564 785.1231689453125 0.6723033785820007 954.66650390625 0.2942979335784912 0.73742914 0.9820515513420105 True -6 19040 30.15221881866455 0.6672823429107666 700.2650146484375 0.33626553416252136 948.230224609375 0.29855048656463623 0.7442711 0.9201228022575378 True -7 21760 30.10255193710327 0.6704311370849609 794.3269653320312 0.5057919025421143 940.7838134765625 0.302418977022171 0.75283045 0.8885299563407898 True -8 24480 30.086382627487183 0.6640410423278809 818.6075439453125 0.46644118428230286 937.9481811523438 0.3037041127681732 0.7569517 0.8354475498199463 True -9 27200 30.138901233673096 0.676415205001831 681.44580078125 0.517670750617981 931.3475952148438 0.3075805604457855 0.76626885 0.7367748618125916 True -10 29920 30.128693103790283 0.7558619976043701 662.2630004882812 0.41913920640945435 928.0065307617188 0.30862846970558167 0.7726053 0.6878993511199951 True -11 32640 30.25312638282776 0.6592824459075928 571.8645629882812 0.27966004610061646 923.2208862304688 0.31105929613113403 0.780549 0.5971423387527466 True -12 35360 30.21373224258423 25.22867441177368 697.86376953125 0.386263370513916 919.9893188476562 0.3123573660850525 0.7875787 0.5465432405471802 True -13 38080 30.509716510772705 0.687877893447876 673.267822265625 0.27998679876327515 917.7020263671875 0.31275519728660583 0.79507893 0.4870203137397766 True -14 40800 30.26583695411682 0.6810054779052734 612.5262451171875 0.17835015058517456 914.4114990234375 0.3144386410713196 0.802196 0.4450240731239319 True -15 43520 30.535401344299316 12.961750745773315 599.4773559570312 0.30425289273262024 911.0465698242188 0.31578007340431213 0.80762464 0.39754483103752136 True -16 46240 30.2563796043396 0.718125581741333 583.9685668945312 0.23657815158367157 907.311767578125 0.3187924921512604 0.81282294 0.37160658836364746 True -17 48960 29.819854497909546 1.1950433254241943 580.9815673828125 0.23033928871154785 907.2835693359375 0.3189072608947754 0.81502837 0.3547428250312805 True -18 51680 29.695986032485962 0.6766719818115234 598.2405395507812 0.21954023838043213 906.9570922851562 0.3190418481826782 0.8147669 0.3508647084236145 False -19 54400 29.65544319152832 0.6684780120849609 641.9012451171875 0.3929430842399597 908.8936767578125 0.3173736035823822 0.81388074 0.34811797738075256 False diff --git a/ENCSR686WJL/cherimoya.fold_1.performance.tsv b/ENCSR686WJL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 113607f8a02375895fa9008b5e5a25636ebd219c..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -907.2835693359375 0.44269227981567383 0.3189072608947754 0.12628890573978424 0.8150283694267273 0.8064857721328735 0.3547428250312805 \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_2.evaluate.json b/ENCSR686WJL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6c172c68d49b122cc491729a016b35e7a33ba2e8..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF389LCL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_2.fit.json b/ENCSR686WJL/cherimoya.fold_2.fit.json deleted file mode 100644 index cc395f3295911b87bb5c6e6c42c8f15c5f8667ff..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF389LCL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_2.log b/ENCSR686WJL/cherimoya.fold_2.log deleted file mode 100644 index 0c6730091c5445a9a9613d1a384a8f59fcb7963d..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 36.584096908569336 4.1618735790252686 666.9765014648438 0.4547768831253052 957.09716796875 0.21603305637836456 0.62476957 3.974929094314575 True -1 5782 32.197028398513794 0.6410760879516602 679.6859741210938 0.41775447130203247 889.1096801757812 0.2603878378868103 0.6900791 2.0550544261932373 True -2 8673 32.1401789188385 0.5470151901245117 772.962890625 0.6627826690673828 872.786865234375 0.26718923449516296 0.70320284 1.2019124031066895 True -3 11564 32.193557262420654 0.5730457305908203 798.783203125 0.520730197429657 862.4324340820312 0.272204726934433 0.7146982 0.8416794538497925 True -4 14455 32.05600881576538 0.5443894863128662 806.2716064453125 0.42290574312210083 856.8618774414062 0.275236040353775 0.7273399 0.7264320850372314 True -5 17346 32.071552753448486 0.5446293354034424 627.955078125 0.4346614480018616 850.3150024414062 0.278723806142807 0.7379859 0.688831627368927 True -6 20237 32.10173034667969 0.5509366989135742 718.6177978515625 0.35080045461654663 845.9624633789062 0.28148353099823 0.746562 0.6637328863143921 True -7 23128 32.14087104797363 0.5463857650756836 704.5892944335938 0.33933115005493164 842.8512573242188 0.28509530425071716 0.75070965 0.6441081762313843 True -8 26019 32.06102776527405 0.5496788024902344 797.3067626953125 0.38675007224082947 840.628662109375 0.2852976620197296 0.754748 0.6432125568389893 True -9 28910 32.05163884162903 0.5373368263244629 588.5599365234375 0.3861500024795532 836.7857055664062 0.28656330704689026 0.7661187 0.5464414954185486 True -10 31801 32.08444309234619 0.5446226596832275 755.204345703125 0.4430834650993347 833.7322998046875 0.28935593366622925 0.77354497 0.5067577958106995 True -11 34692 32.015703439712524 0.5508177280426025 778.8754272460938 0.40579789876937866 831.83447265625 0.29021793603897095 0.77579486 0.4789738357067108 True -12 37583 32.11258673667908 14.131608963012695 636.862548828125 0.32054176926612854 827.6578979492188 0.29252198338508606 0.7803831 0.4450088441371918 True -13 40474 32.17756533622742 0.5581259727478027 750.2208251953125 0.4145106077194214 824.421142578125 0.2956586182117462 0.787043 0.396232545375824 True -14 43365 32.155922412872314 0.550337553024292 763.1412353515625 0.34394675493240356 823.2099609375 0.29551059007644653 0.7948672 0.3703993558883667 True -15 46256 32.162381172180176 0.5389988422393799 682.105712890625 0.3224831223487854 820.9277954101562 0.2961259186267853 0.7973717 0.3447001576423645 True -16 49147 32.051164627075195 1.2055928707122803 773.1278686523438 0.32005947828292847 820.266845703125 0.2960742712020874 0.80032253 0.33167093992233276 True -17 52038 31.537772178649902 3.9321656227111816 561.6370849609375 0.29747307300567627 819.926025390625 0.2969813942909241 0.80149084 0.3224775493144989 True -18 54929 31.479568004608154 0.5597529411315918 792.9205322265625 0.20587682723999023 820.1412963867188 0.29612961411476135 0.80129546 0.3218618929386139 False -19 57820 31.458723068237305 0.5467009544372559 848.5385131835938 0.26036515831947327 820.1090698242188 0.29657408595085144 0.8008728 0.32132670283317566 False diff --git a/ENCSR686WJL/cherimoya.fold_2.performance.tsv b/ENCSR686WJL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 68cc4266abd68de857e9559c8077d99ef16fbf8e..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -819.926025390625 0.45912250876426697 0.2969813942909241 0.1130448654294014 0.801490843296051 0.7896455526351929 0.3224775493144989 \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_3.evaluate.json b/ENCSR686WJL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ba1afa1b799d68323733e0383a90e9ef9e348708..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF389LCL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_3.fit.json b/ENCSR686WJL/cherimoya.fold_3.fit.json deleted file mode 100644 index 8b68d70be1b588cd7dbf966855c4664d592454b9..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF389LCL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_3.log b/ENCSR686WJL/cherimoya.fold_3.log deleted file mode 100644 index 1d7fd94f9a74228f8f08f4bea95ede82ab5cd6f8..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 34.9446861743927 3.854914665222168 785.8267211914062 0.43870988488197327 885.1904296875 0.2189522385597229 0.6026502 4.967474937438965 True -1 5486 30.449918270111084 9.234567403793335 805.9830932617188 0.5253204703330994 825.8617553710938 0.26115694642066956 0.6681414 2.092468023300171 True -2 8229 30.552818059921265 0.6047337055206299 666.6416625976562 0.2908589243888855 808.8259887695312 0.27137425541877747 0.6838643 1.145820140838623 True -3 10972 30.459104299545288 0.5917913913726807 765.35595703125 0.33707505464553833 799.3107299804688 0.2760589122772217 0.69720334 1.6080482006072998 True -4 13715 30.55618977546692 0.5985109806060791 816.470458984375 0.7734955549240112 792.8145751953125 0.2794645130634308 0.7143402 0.846112847328186 True -5 16458 30.45579504966736 1.1891930103302002 670.1559448242188 0.5078429579734802 787.6621704101562 0.2823171317577362 0.7285962 0.8136144876480103 True -6 19201 30.46991801261902 2.5552542209625244 635.6266479492188 0.35882943868637085 784.4160766601562 0.2843661606311798 0.7331626 0.7588803172111511 True -7 21944 30.505549430847168 0.58658766746521 697.872314453125 0.6712244749069214 781.5724487304688 0.2855461537837982 0.7406998 0.7291956543922424 True -8 24687 30.404600381851196 0.5727508068084717 744.8229370117188 0.42690393328666687 776.14892578125 0.28947824239730835 0.75103456 0.6473737359046936 True -9 27430 30.404187440872192 0.5629150867462158 786.5343017578125 0.37470245361328125 774.4293212890625 0.2898626923561096 0.7579269 0.6170434355735779 True -10 30173 30.767019510269165 0.5774505138397217 752.06689453125 0.4920963644981384 770.9619140625 0.29269254207611084 0.76293683 0.5462151169776917 True -11 32916 30.469061374664307 0.5708625316619873 609.050048828125 0.3859047591686249 768.6660766601562 0.29385241866111755 0.7701516 0.5117151141166687 True -12 35659 30.485549449920654 0.578326940536499 701.4751586914062 0.40855151414871216 766.2874145507812 0.2948879301548004 0.7772335 0.4519214928150177 True -13 38402 29.878971338272095 2.242438554763794 720.310546875 0.35894137620925903 763.9766845703125 0.29621997475624084 0.7823391 0.4082198441028595 True -14 41145 30.125337600708008 14.653083801269531 657.17919921875 0.3480445444583893 761.83203125 0.29778167605400085 0.78982735 0.378438800573349 True -15 43888 29.88883066177368 1.5038552284240723 671.250244140625 0.2610175609588623 761.59912109375 0.2970351576805115 0.7927765 0.35108184814453125 True -16 46631 30.093889236450195 1.3586373329162598 647.7364501953125 0.3084430694580078 760.4522094726562 0.2978838086128235 0.79453003 0.33298659324645996 True -17 49374 30.114192724227905 1.291092872619629 686.0558471679688 0.39166468381881714 758.9694213867188 0.2994794547557831 0.79648 0.32388028502464294 True -18 52117 30.000200033187866 1.8318438529968262 628.2636108398438 0.31425607204437256 758.5894775390625 0.30020901560783386 0.7968816 0.3203073740005493 True -19 54860 30.060431957244873 1.6888234615325928 586.6375732421875 0.19360709190368652 759.4329833984375 0.29913586378097534 0.79535586 0.3214951157569885 False diff --git a/ENCSR686WJL/cherimoya.fold_3.performance.tsv b/ENCSR686WJL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e68914de5719dc9a6756697d1094a302a3f52ddd..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -758.5894775390625 0.46221765875816345 0.3002089560031891 0.10794001817703247 0.7968816161155701 0.769367516040802 0.3203073740005493 \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_4.evaluate.json b/ENCSR686WJL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7641511d871584cefc9c17665e9ee24f59fff519..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF389LCL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_4.fit.json b/ENCSR686WJL/cherimoya.fold_4.fit.json deleted file mode 100644 index 76305571d7b8ca25a819778bb0d840a08ef24ab0..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF389LCL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR686WJL/cherimoya.fold_4.log b/ENCSR686WJL/cherimoya.fold_4.log deleted file mode 100644 index 83a777195b8e0f270cdcf9d539f6dbac395a0cc3..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2813 36.173152923583984 4.119117736816406 697.2052001953125 0.5173836946487427 879.8919677734375 0.21285396814346313 0.588716 4.510435104370117 True -1 5626 31.22607660293579 0.6770899295806885 764.5150146484375 0.5721962451934814 822.461181640625 0.2543056011199951 0.6500236 2.238996744155884 True -2 8439 31.236450910568237 0.591111421585083 705.5439453125 0.5160385370254517 806.3495483398438 0.2639981508255005 0.6664131 0.9495258927345276 True -3 11252 31.196234226226807 0.6002955436706543 518.360595703125 0.36363309621810913 795.153076171875 0.268873006105423 0.68577313 0.7635456919670105 True -4 14065 31.281081676483154 0.5918130874633789 636.9815673828125 0.43891453742980957 790.6047973632812 0.27245354652404785 0.6947472 0.6718695163726807 True -5 16878 31.22848105430603 0.6678600311279297 696.185546875 0.3460609018802643 788.6254272460938 0.27281156182289124 0.6999237 0.6358229517936707 True -6 19691 31.222266674041748 0.6130931377410889 641.173583984375 0.39894911646842957 781.42431640625 0.2769503891468048 0.7156157 0.6153436899185181 True -7 22504 31.173928260803223 0.602454423904419 679.3948974609375 0.2702087163925171 778.6426391601562 0.27769485116004944 0.72944564 0.5860802531242371 True -8 25317 31.26634192466736 0.5976095199584961 776.365966796875 0.4114782214164734 776.4251708984375 0.27890294790267944 0.7352017 0.5584614276885986 True -9 28130 31.273844957351685 0.69830322265625 747.86865234375 0.37546831369400024 774.3497924804688 0.2791403532028198 0.74391466 0.5135489106178284 True -10 30943 31.24724578857422 2.3894145488739014 654.400390625 0.37430500984191895 772.2039794921875 0.28189805150032043 0.7513863 0.5244425535202026 True -11 33756 31.255874395370483 1.4713621139526367 662.2333374023438 0.40091508626937866 770.46435546875 0.2824527621269226 0.75864977 0.4736882150173187 True -12 36569 31.281219244003296 0.6056475639343262 646.3220825195312 0.31639760732650757 766.0470581054688 0.28618088364601135 0.7673223 0.41592028737068176 True -13 39382 31.253273963928223 0.5810894966125488 626.537353515625 0.26277732849121094 764.9338989257812 0.28682413697242737 0.7748759 0.3821107745170593 True -14 42195 30.638619422912598 0.5930790901184082 713.904296875 0.44606757164001465 763.4127807617188 0.2875303030014038 0.7795655 0.3566962480545044 True -15 45008 30.629600048065186 0.5894880294799805 721.8951416015625 0.3000195026397705 761.9937744140625 0.2881484031677246 0.7836344 0.3277856409549713 True -16 47821 30.667025327682495 0.5897860527038574 613.3509521484375 0.24282698333263397 760.8486328125 0.2893676161766052 0.78968644 0.31271862983703613 True -17 50634 30.58904242515564 0.5909116268157959 730.4609375 0.3440525233745575 760.76806640625 0.2890372574329376 0.7886371 0.3044564127922058 False -18 53447 30.65535593032837 0.5911448001861572 618.3848876953125 0.2344212532043457 762.470703125 0.28723254799842834 0.78763247 0.30268409848213196 False -19 56260 30.633483409881592 0.5832643508911133 663.4960327148438 0.3831363320350647 761.7664794921875 0.2884657084941864 0.7879872 0.30276623368263245 False diff --git a/ENCSR686WJL/cherimoya.fold_4.performance.tsv b/ENCSR686WJL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9ee342e7d4c28645d122035e57aa45b18455edae..0000000000000000000000000000000000000000 --- a/ENCSR686WJL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -760.8486328125 0.46717172861099243 0.2893676161766052 0.10328515619039536 0.7896864414215088 0.7704158425331116 0.31271862983703613 \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_0.evaluate.json b/ENCSR688DKY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9bcd4f61a0902f5a6066e92320b2c6dc4bf2af77..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF607PBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_0.fit.json b/ENCSR688DKY/cherimoya.fold_0.fit.json deleted file mode 100644 index e13f177607b79b5de962fa4302e3294b7005d52b..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF607PBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_0.log b/ENCSR688DKY/cherimoya.fold_0.log deleted file mode 100644 index c067c7378be570ebc68d829d65c2241645340167..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2704 33.84741401672363 3.7503914833068848 224.9015655517578 0.7467341423034668 198.00851440429688 0.11619213968515396 0.71823484 3.3115315437316895 True -1 5408 29.572351694107056 0.5966732501983643 124.17236328125 0.5355709791183472 176.80442810058594 0.15307265520095825 0.8035579 1.52064049243927 True -2 8112 29.567708492279053 0.5590784549713135 197.1728057861328 0.5525146722793579 174.9833984375 0.15594038367271423 0.80547667 0.9911483526229858 True -3 10816 29.476358890533447 0.5647614002227783 179.15138244628906 0.6947329044342041 173.1681365966797 0.15910287201404572 0.8206573 0.7430983185768127 True -4 13520 29.67902159690857 20.251375436782837 161.9368438720703 0.6190951466560364 172.49774169921875 0.16040575504302979 0.8286345 0.6806854605674744 True -5 16224 29.476920127868652 0.5721275806427002 151.39813232421875 0.4810665547847748 171.62301635742188 0.16153965890407562 0.8354223 0.60943204164505 True -6 18928 29.47002100944519 0.5739955902099609 174.8624267578125 0.8350419998168945 170.5355682373047 0.16462500393390656 0.8416446 0.5611445307731628 True -7 21632 29.47925090789795 26.1822350025177 148.3040771484375 0.49767953157424927 169.83993530273438 0.16577742993831635 0.8479749 0.5052968859672546 True -8 24336 29.921961307525635 0.5659499168395996 171.36236572265625 0.37938520312309265 169.28860473632812 0.16701580584049225 0.85375124 0.47309112548828125 True -9 27040 29.487417459487915 0.578812837600708 179.56881713867188 0.48790374398231506 168.5215606689453 0.16933001577854156 0.859363 0.4303712844848633 True -10 29744 29.506420135498047 0.572138786315918 123.70849609375 0.5852375030517578 168.2324981689453 0.16996917128562927 0.8664999 0.3990759253501892 True -11 32448 29.429084062576294 0.5669922828674316 140.12840270996094 0.36917173862457275 167.4644012451172 0.172260582447052 0.86939794 0.38066428899765015 True -12 35152 29.45000147819519 0.5684795379638672 106.85342407226562 0.5533654093742371 167.0117645263672 0.17357034981250763 0.8754169 0.3432677984237671 True -13 37856 29.7994487285614 6.787621974945068 140.45779418945312 0.4187597334384918 166.79078674316406 0.17385238409042358 0.8776805 0.31848567724227905 True -14 40560 29.503373622894287 0.5885603427886963 159.1968536376953 0.5298972725868225 166.5269775390625 0.17504902184009552 0.8822808 0.3039742708206177 True -15 43264 29.550695419311523 1.2728519439697266 127.24317932128906 0.3620568513870239 166.08627319335938 0.17557087540626526 0.8843588 0.2965852618217468 True -16 45968 29.560755968093872 0.5654058456420898 127.0226058959961 0.4661031663417816 166.095458984375 0.1748514324426651 0.8857116 0.2894197702407837 True -17 48672 29.48024296760559 0.5642368793487549 177.83250427246094 0.30071282386779785 166.07618713378906 0.17547041177749634 0.8855909 0.2883674204349518 False -18 51376 29.540926218032837 0.5695207118988037 133.3202667236328 0.2784336805343628 166.32005310058594 0.17486482858657837 0.8871892 0.2894051671028137 True -19 54080 29.56380820274353 35.50555181503296 215.6147003173828 0.1900193691253662 166.09925842285156 0.175749734044075 0.88541305 0.2899117171764374 False diff --git a/ENCSR688DKY/cherimoya.fold_0.performance.tsv b/ENCSR688DKY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 40ce963ae8144b3923e560ca36f33566fc385676..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -166.32005310058594 0.5761401057243347 0.17486482858657837 0.04559028148651123 0.8871892094612122 0.765409529209137 0.2894051671028137 \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_1.evaluate.json b/ENCSR688DKY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c3a0ed7e936af0110fc5de0f9618b7f527fb0b40..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF607PBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_1.fit.json b/ENCSR688DKY/cherimoya.fold_1.fit.json deleted file mode 100644 index 851290dbccb913d3f56b46242b2c466523079ca8..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF607PBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_1.log b/ENCSR688DKY/cherimoya.fold_1.log deleted file mode 100644 index 4cc0804a4bc207bb358005e5876091b0011f936c..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2677 34.025282859802246 5.2317445278167725 149.91354370117188 0.5162330269813538 270.65753173828125 0.1353936791419983 0.69891864 4.845665454864502 True -1 5354 29.69208002090454 3.162114143371582 144.90179443359375 0.45361918210983276 242.49037170410156 0.18143890798091888 0.78100914 2.4548773765563965 True -2 8031 30.260308980941772 35.75244188308716 178.17730712890625 0.594425618648529 237.16311645507812 0.18600159883499146 0.8054581 1.4563387632369995 True -3 10708 29.552844047546387 37.7220938205719 192.64439392089844 0.5766105651855469 233.33152770996094 0.19184733927249908 0.8213767 1.1864149570465088 True -4 13385 29.857258796691895 0.6835532188415527 167.72206115722656 0.4575701653957367 231.05316162109375 0.19642452895641327 0.82831323 1.167496681213379 True -5 16062 30.870631217956543 0.7082457542419434 142.08908081054688 0.7515226006507874 229.34817504882812 0.19821575284004211 0.8412224 0.9872027635574341 True -6 18739 29.8224995136261 0.7286138534545898 123.823486328125 0.5364962816238403 228.28228759765625 0.20025353133678436 0.8463198 0.9243455529212952 True -7 21416 29.671476364135742 40.903868198394775 172.6568145751953 0.5220357775688171 226.65689086914062 0.20393085479736328 0.8551198 0.7858522534370422 True -8 24093 32.32590460777283 0.6917731761932373 162.607177734375 0.36914461851119995 225.9296417236328 0.20434246957302094 0.8638374 0.6784659624099731 True -9 26770 29.52669596672058 0.6905689239501953 89.46437072753906 0.2883172035217285 224.69900512695312 0.20702463388442993 0.870977 0.6141974329948425 True -10 29447 30.08916187286377 36.13571643829346 137.8519744873047 0.6018937826156616 223.9123992919922 0.2084251046180725 0.8775814 0.5541451573371887 True -11 32124 29.903076171875 1.4015698432922363 114.47130584716797 0.4590015113353729 222.65145874023438 0.21085961163043976 0.880016 0.5254988074302673 True -12 34801 29.802552700042725 2.6508123874664307 110.73306274414062 0.6140404939651489 221.83209228515625 0.21224677562713623 0.8875919 0.46609237790107727 True -13 37478 29.534876108169556 0.6863934993743896 166.83847045898438 0.42620283365249634 221.42868041992188 0.21283723413944244 0.891556 0.4348047375679016 True -14 40155 29.55570363998413 0.7069976329803467 157.72308349609375 0.3459036946296692 220.51089477539062 0.21443603932857513 0.8978622 0.4035777449607849 True -15 42832 29.66875433921814 0.7076327800750732 129.04354858398438 0.3463984727859497 220.19981384277344 0.21485990285873413 0.89918643 0.385873407125473 True -16 45509 29.537801504135132 2.0053162574768066 89.15858459472656 0.36102303862571716 219.64073181152344 0.21584933996200562 0.9001205 0.3693860173225403 True -17 48186 29.548503637313843 0.6980335712432861 100.06944274902344 0.23727761209011078 219.41310119628906 0.21610768139362335 0.90067184 0.36301183700561523 True -18 50863 29.57894778251648 0.6829049587249756 130.03012084960938 0.18532249331474304 219.5144500732422 0.21603694558143616 0.90080225 0.363164484500885 True -19 53540 29.515779972076416 40.240145683288574 144.8518524169922 0.17423078417778015 219.75279235839844 0.21531224250793457 0.8999858 0.3602558672428131 False diff --git a/ENCSR688DKY/cherimoya.fold_1.performance.tsv b/ENCSR688DKY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8e47233a28ea3aa8a9d091c3867dfff51202f542..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.5144500732422 0.5452918410301208 0.21603697538375854 0.06526624411344528 0.9008022546768188 0.8258335590362549 0.363164484500885 \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_2.evaluate.json b/ENCSR688DKY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 569fa36b0ab36b68b34913acdcd74b6ad1c842ea..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF607PBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_2.fit.json b/ENCSR688DKY/cherimoya.fold_2.fit.json deleted file mode 100644 index 8a4a4f84ce8902e835184e6901201bb480dbf84e..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF607PBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_2.log b/ENCSR688DKY/cherimoya.fold_2.log deleted file mode 100644 index 94a791a6b9e4fd34ab165575b5567e70ef5d3d63..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2857 35.37971210479736 3.5810506343841553 109.67402648925781 1.0804169178009033 219.87681579589844 0.12277611345052719 0.7002346 3.477957010269165 True -1 5714 31.692798614501953 0.5542407035827637 182.5902862548828 0.599390983581543 196.01052856445312 0.16347476840019226 0.79996306 1.5860356092453003 True -2 8571 31.619181632995605 0.5452063083648682 138.8888397216797 0.51423579454422 192.79493713378906 0.16816860437393188 0.8011525 1.052528738975525 True -3 11428 31.636289358139038 0.5407822132110596 173.7821044921875 0.7329012751579285 191.06243896484375 0.1688302755355835 0.81776685 0.8421988487243652 True -4 14285 31.55859112739563 0.5547802448272705 126.8128890991211 0.31074970960617065 189.32427978515625 0.17196229100227356 0.8303461 0.7327573299407959 True -5 17142 31.334235668182373 0.5391783714294434 146.86846923828125 0.39630717039108276 187.92666625976562 0.1749507635831833 0.8384771 0.6604363322257996 True -6 19999 30.94806408882141 0.5385723114013672 130.0787353515625 0.5129923224449158 186.9471435546875 0.17713117599487305 0.8425477 0.60040283203125 True -7 22856 30.910478591918945 0.5390026569366455 142.28680419921875 0.5982909202575684 186.1473388671875 0.17903344333171844 0.848348 0.5590965747833252 True -8 25713 30.9000301361084 1.9465913772583008 193.20663452148438 0.395748496055603 185.93276977539062 0.1789686679840088 0.8546629 0.5502668023109436 True -9 28570 31.028398990631104 0.5458602905273438 126.1720199584961 0.47735947370529175 185.42532348632812 0.18034395575523376 0.85909915 0.4978860020637512 True -10 31427 31.068813800811768 0.5401806831359863 130.50978088378906 0.35454511642456055 184.54835510253906 0.1819239854812622 0.8665057 0.4457637667655945 True -11 34284 31.060133934020996 0.5414717197418213 131.37481689453125 0.3430117964744568 184.0814666748047 0.1831052452325821 0.8697122 0.4096483886241913 True -12 37141 31.007447481155396 0.53548264503479 163.72946166992188 0.39730045199394226 183.16632080078125 0.18571114540100098 0.87390685 0.39151138067245483 True -13 39998 31.061814308166504 0.5451512336730957 117.02314758300781 0.4270186424255371 182.65638732910156 0.18644756078720093 0.8775052 0.3598923683166504 True -14 42855 31.196354389190674 0.545079231262207 139.63401794433594 0.3895138204097748 182.4061279296875 0.1868031919002533 0.880001 0.3402939736843109 True -15 45712 31.025378465652466 0.9045331478118896 85.69418334960938 0.3175973892211914 181.77999877929688 0.1883697211742401 0.8843599 0.32665106654167175 True -16 48569 31.145630836486816 1.2557451725006104 175.61358642578125 0.40548068284988403 181.787353515625 0.18787793815135956 0.8881556 0.3166850507259369 True -17 51426 31.128754138946533 0.5507526397705078 186.5545654296875 0.389288067817688 181.5421905517578 0.18878525495529175 0.88647807 0.31443148851394653 False -18 54283 31.08065104484558 1.0186097621917725 143.8052978515625 0.3635009825229645 181.6754608154297 0.1885928511619568 0.8871282 0.31512126326560974 False -19 57140 31.093093395233154 1.726433515548706 105.16766357421875 0.37946391105651855 181.9306182861328 0.187694251537323 0.8876863 0.31704801321029663 False diff --git a/ENCSR688DKY/cherimoya.fold_2.performance.tsv b/ENCSR688DKY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d3b4ab4be03ef60e2247a5b1e020324e50f8fd88..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -181.787353515625 0.5659917593002319 0.18787795305252075 0.05160195380449295 0.8881555795669556 0.78731769323349 0.3166850507259369 \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_3.evaluate.json b/ENCSR688DKY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 16eeb1743a74ac3f8c6d1e4d64fccccd5e739561..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF607PBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_3.fit.json b/ENCSR688DKY/cherimoya.fold_3.fit.json deleted file mode 100644 index 16047e421e698f190425156ea0075add544b0259..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF607PBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_3.log b/ENCSR688DKY/cherimoya.fold_3.log deleted file mode 100644 index f8aed27f3bde3e0e5bc3f6f2eca69ea9a16dba72..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2724 33.553237199783325 12.520947456359863 103.02522277832031 0.394247442483902 213.18585205078125 0.12608203291893005 0.68870217 3.7289953231811523 True -1 5448 29.928551197052002 0.5063900947570801 107.17718505859375 0.45338040590286255 193.88995361328125 0.16322292387485504 0.77225757 1.7239627838134766 True -2 8172 29.550929307937622 0.4974491596221924 175.0807342529297 0.4551498293876648 191.74656677246094 0.16549494862556458 0.7619663 1.0848366022109985 False -3 10896 29.231083869934082 0.489915132522583 188.84771728515625 0.40914249420166016 188.66322326660156 0.16855280101299286 0.79411733 0.8759720325469971 True -4 13620 29.20420241355896 0.5575911998748779 120.02972412109375 0.3685111403465271 187.30860900878906 0.17026983201503754 0.80313385 0.8271510004997253 True -5 16344 29.267383813858032 0.4909188747406006 179.89828491210938 0.5729573965072632 185.8307647705078 0.17331188917160034 0.81613463 0.7596773505210876 True -6 19068 29.261985778808594 0.4937114715576172 163.54122924804688 0.5884099006652832 185.5170135498047 0.17417961359024048 0.82213056 0.7461608648300171 True -7 21792 29.30269694328308 0.4928553104400635 176.88697814941406 0.4615449905395508 183.89109802246094 0.17796137928962708 0.8313575 0.6465725302696228 True -8 24516 29.325079441070557 0.4924159049987793 220.68331909179688 0.3976694941520691 183.58126831054688 0.17932523787021637 0.83506054 0.6330244541168213 True -9 27240 29.33126974105835 0.49236059188842773 121.07244110107422 0.4322561025619507 182.40744018554688 0.18193086981773376 0.8439146 0.5805225372314453 True -10 29964 29.367403745651245 2.923149585723877 132.5966796875 0.511599063873291 181.7898712158203 0.18297222256660461 0.8513962 0.521307647228241 True -11 32688 29.40938448905945 0.511324405670166 170.57980346679688 0.29491856694221497 181.35028076171875 0.18433967232704163 0.85425293 0.4875861704349518 True -12 35412 29.438497304916382 0.552152156829834 128.75457763671875 0.326634019613266 180.8482666015625 0.18536503612995148 0.85975844 0.4640023112297058 True -13 38136 29.402761936187744 0.4897329807281494 143.84060668945312 0.44896626472473145 180.32711791992188 0.1863469034433365 0.8653642 0.42320650815963745 True -14 40860 29.326499700546265 0.490386962890625 173.8349609375 0.4187442660331726 179.8802490234375 0.1871916800737381 0.8702193 0.39950451254844666 True -15 43584 29.345311641693115 0.5058803558349609 151.84512329101562 0.4648284912109375 179.3253631591797 0.18847160041332245 0.8772118 0.37431707978248596 True -16 46308 29.95671319961548 0.4900827407836914 129.0196990966797 0.5061492323875427 179.17868041992188 0.18848377466201782 0.8792563 0.35773956775665283 True -17 49032 29.32806158065796 0.49045443534851074 127.79466247558594 0.24442178010940552 178.90890502929688 0.18915824592113495 0.8847266 0.34304141998291016 True -18 51756 29.268332958221436 0.49027466773986816 130.15130615234375 0.36513030529022217 179.1029052734375 0.18862469494342804 0.8844723 0.3390171229839325 False -19 54480 29.3780460357666 0.48977136611938477 177.0947723388672 0.31592318415641785 179.2022705078125 0.18836690485477448 0.8829391 0.33891525864601135 False diff --git a/ENCSR688DKY/cherimoya.fold_3.performance.tsv b/ENCSR688DKY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d23d98703fd667c50407f69ef55db16c6be422f3..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -178.90890502929688 0.566811740398407 0.18915823101997375 0.054227136075496674 0.8847265839576721 0.7780237793922424 0.34304141998291016 \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_4.evaluate.json b/ENCSR688DKY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 525bfd7299c5cf678a751bbf99893d5a278d5f76..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF607PBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_4.fit.json b/ENCSR688DKY/cherimoya.fold_4.fit.json deleted file mode 100644 index c8d907d14d7cdd936d7068ada44ba3b29f669655..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF607PBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688DKY/cherimoya.fold_4.log b/ENCSR688DKY/cherimoya.fold_4.log deleted file mode 100644 index 222eb7bd8fa314f0761e4879fea8c7e60fb06c57..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2810 34.51315522193909 3.447202205657959 212.77684020996094 0.5400024652481079 183.23550415039062 0.11630403995513916 0.69719774 2.824406385421753 True -1 5620 31.02454662322998 0.5978922843933105 118.90229797363281 0.6374036073684692 167.1627960205078 0.1480621099472046 0.7672538 1.429147481918335 True -2 8430 31.03572106361389 0.5740020275115967 169.5174560546875 0.6449037194252014 166.02931213378906 0.14894452691078186 0.75625944 0.8661410212516785 False -3 11240 30.74312114715576 0.5699002742767334 148.3320770263672 0.5266080498695374 163.75833129882812 0.15091870725154877 0.7987469 0.6776538491249084 True -4 14050 30.404160499572754 0.8501460552215576 192.74630737304688 0.6272871494293213 162.73666381835938 0.1522998958826065 0.8091852 0.5545507073402405 True -5 16860 30.298238515853882 0.5679059028625488 149.48956298828125 0.4237109422683716 161.56747436523438 0.1546729952096939 0.8174017 0.5471509099006653 True -6 19670 30.181931495666504 0.5710396766662598 161.76080322265625 0.39191552996635437 160.6533660888672 0.15759915113449097 0.82023627 0.535620391368866 True -7 22480 30.17578935623169 0.5682213306427002 174.52406311035156 0.6754325032234192 159.913818359375 0.15923042595386505 0.8287824 0.485501766204834 True -8 25290 30.16368842124939 0.5684823989868164 170.5969696044922 0.7705492377281189 159.25424194335938 0.16024015843868256 0.8395342 0.43853673338890076 True -9 28100 30.170202255249023 0.5617811679840088 155.90463256835938 0.8181217908859253 158.9303741455078 0.1611802726984024 0.8455704 0.41475820541381836 True -10 30910 30.25164484977722 0.5664069652557373 122.61046600341797 0.3832758069038391 158.1473388671875 0.16328486800193787 0.85054094 0.39110246300697327 True -11 33720 30.222636222839355 0.5621137619018555 139.60134887695312 0.38873475790023804 157.8278350830078 0.1639152616262436 0.8555941 0.3624550998210907 True -12 36530 30.182518005371094 0.5614907741546631 126.9112777709961 0.5417271852493286 157.59449768066406 0.16435019671916962 0.86270696 0.33966967463493347 True -13 39340 30.176798582077026 0.5603890419006348 128.64389038085938 0.2982912063598633 156.9434356689453 0.16612203419208527 0.8658806 0.3212088942527771 True -14 42150 30.326112031936646 0.5708768367767334 129.7436065673828 0.26847487688064575 156.5350799560547 0.16734148561954498 0.8697841 0.3082795739173889 True -15 44960 30.242037534713745 0.5706520080566406 131.17625427246094 0.25890785455703735 156.21437072753906 0.16827139258384705 0.8720245 0.29533883929252625 True -16 47770 30.324345588684082 1.1768314838409424 141.59957885742188 0.16475000977516174 156.49281311035156 0.16671399772167206 0.87601817 0.28361696004867554 True -17 50580 30.321303844451904 0.576563835144043 126.78824615478516 0.3485400080680847 156.2079315185547 0.16757290065288544 0.8777524 0.28003236651420593 True -18 53390 30.285065174102783 0.5883541107177734 143.57272338867188 0.19541101157665253 156.12017822265625 0.16782715916633606 0.8779682 0.2789512574672699 True -19 56200 30.323753118515015 0.5674500465393066 128.8273162841797 0.23139774799346924 156.5789031982422 0.16640876233577728 0.87736034 0.27966275811195374 False diff --git a/ENCSR688DKY/cherimoya.fold_4.performance.tsv b/ENCSR688DKY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c1fa43a9c6045da0e6f6e1d3e58ff560c9801477..0000000000000000000000000000000000000000 --- a/ENCSR688DKY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -156.12017822265625 0.5819590091705322 0.16782715916633606 0.04436653479933739 0.8779681921005249 0.7404335737228394 0.2789512574672699 \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_0.evaluate.json b/ENCSR688OIJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 92a131ef0009afabbad296027509468e3061dd3f..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF854OYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_0.fit.json b/ENCSR688OIJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 621bc2e2511492b97e19e0087fd61b450ed01c26..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF854OYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_0.log b/ENCSR688OIJ/cherimoya.fold_0.log deleted file mode 100644 index bd421e27cc9f0426a09e80aeae543f483ec9599a..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2239 28.440710306167603 3.716886520385742 179.56629943847656 0.8313500881195068 264.6625061035156 0.15287631750106812 0.6943473 5.665470600128174 True -1 4478 24.727717876434326 0.7457127571105957 164.96774291992188 0.6743817329406738 239.25347900390625 0.21456366777420044 0.7840829 2.539926290512085 True -2 6717 24.6881206035614 0.44669294357299805 181.9210968017578 0.6661574244499207 231.06809997558594 0.23024289309978485 0.80206954 1.423350214958191 True -3 8956 24.640279293060303 0.4476163387298584 232.37445068359375 0.5623493194580078 227.7559356689453 0.23623748123645782 0.8148334 0.8985444903373718 True -4 11195 24.66425919532776 0.4460911750793457 221.14529418945312 0.5361839532852173 225.37667846679688 0.24287107586860657 0.8236802 0.8477156162261963 True -5 13434 24.655367612838745 0.4483790397644043 163.4340057373047 0.6842937469482422 225.01956176757812 0.2422214299440384 0.83723414 0.7446228861808777 True -6 15673 24.645522356033325 0.4406619071960449 231.94400024414062 0.652665913105011 224.01095581054688 0.24546290934085846 0.84334064 0.6984829902648926 True -7 17912 24.61338996887207 1.756631851196289 197.42691040039062 0.6647378206253052 223.34938049316406 0.24657657742500305 0.84564525 0.6797109842300415 True -8 20151 24.77661108970642 0.45465898513793945 165.479248046875 0.47676995396614075 222.83486938476562 0.24742387235164642 0.85380787 0.5997084379196167 True -9 22390 24.68577003479004 14.670632123947144 228.41729736328125 0.5978844165802002 221.8052215576172 0.25053027272224426 0.858879 0.5523373484611511 True -10 24629 25.000826835632324 0.45139384269714355 145.28927612304688 0.8658049702644348 221.23776245117188 0.2516191303730011 0.86118907 0.5093732476234436 True -11 26868 25.097808599472046 0.448993444442749 171.52554321289062 0.5578019618988037 221.14744567871094 0.25149357318878174 0.8666881 0.4854946434497833 True -12 29107 24.74912166595459 0.4536092281341553 197.81529235839844 0.514187216758728 220.30799865722656 0.2538038194179535 0.8685711 0.45510584115982056 True -13 31346 24.801678895950317 0.4454028606414795 178.13064575195312 0.5303799510002136 219.73680114746094 0.2560008764266968 0.87414074 0.43337273597717285 True -14 33585 24.69018840789795 0.45119309425354004 182.74649047851562 0.3560863733291626 219.2808837890625 0.2574765086174011 0.8744612 0.4217389225959778 True -15 35824 24.667545318603516 0.4458744525909424 137.45053100585938 0.35938340425491333 219.09080505371094 0.2574755549430847 0.8781725 0.41468214988708496 True -16 38063 24.66130805015564 0.4453246593475342 189.5210418701172 0.5019984245300293 218.6265106201172 0.25831732153892517 0.87995815 0.40734344720840454 True -17 40302 24.67004632949829 0.446763277053833 191.09005737304688 0.28785765171051025 219.40786743164062 0.25617220997810364 0.87935364 0.4043041467666626 False -18 42541 24.74864888191223 0.4507148265838623 148.8870849609375 0.36120468378067017 219.5391387939453 0.2560119926929474 0.87847686 0.4106811285018921 False -19 44780 24.602762460708618 0.45194458961486816 128.10533142089844 0.2626294493675232 219.24217224121094 0.2575991153717041 0.8755091 0.41479170322418213 False diff --git a/ENCSR688OIJ/cherimoya.fold_0.performance.tsv b/ENCSR688OIJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 258bf154ad6778c589f47d67c8c51bc80adee1b1..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -218.6265106201172 0.5254749059677124 0.25831735134124756 0.06788285076618195 0.8799581527709961 0.8298264741897583 0.40734344720840454 \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_1.evaluate.json b/ENCSR688OIJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2eeaf5a55b4514a4fe080241e3b1fb2bbdad445e..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF854OYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_1.fit.json b/ENCSR688OIJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 790845d3fbd03062670f1ec0b0067eeb691cc420..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF854OYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_1.log b/ENCSR688OIJ/cherimoya.fold_1.log deleted file mode 100644 index cb5e8f20c7bfc3a835751f985c02cd8e328a2778..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2196 27.66490864753723 4.642416000366211 155.3925018310547 0.6490798592567444 327.3960266113281 0.16294826567173004 0.6848815 7.314453601837158 True -1 4392 24.219377756118774 1.537933588027954 232.75497436523438 0.8444874286651611 294.3659362792969 0.2354007363319397 0.79067236 2.992302894592285 True -2 6588 24.268584489822388 0.6264333724975586 192.88096618652344 0.6584397554397583 282.5699768066406 0.2524532377719879 0.8156731 1.7113523483276367 True -3 8784 24.290447235107422 0.6107122898101807 195.22756958007812 0.6380456686019897 278.111083984375 0.2597082853317261 0.81966865 1.2507375478744507 True -4 10980 24.258724689483643 0.5992646217346191 171.20751953125 0.6493101716041565 275.7068786621094 0.2637861669063568 0.8303011 1.1417756080627441 True -5 13176 24.18447256088257 0.6083972454071045 164.9439697265625 0.4298185110092163 273.4841613769531 0.2687299847602844 0.83891344 0.9778081178665161 True -6 15372 24.159704208374023 1.8363652229309082 181.5793914794922 0.6984655857086182 272.5911865234375 0.27052417397499084 0.8470103 0.9052922129631042 True -7 17568 24.246941804885864 0.6147773265838623 160.99163818359375 0.6694867610931396 271.8948059082031 0.27225661277770996 0.85158974 0.842695951461792 True -8 19764 24.16269302368164 0.6122162342071533 222.2525177001953 0.2857493758201599 271.2372741699219 0.27331286668777466 0.8617371 0.7444691061973572 True -9 21960 24.178183555603027 0.6103618144989014 219.92013549804688 0.5276726484298706 269.63092041015625 0.27724623680114746 0.8658678 0.705649733543396 True -10 24156 24.21112823486328 12.62680435180664 176.60317993164062 0.6017552614212036 268.90386962890625 0.27872392535209656 0.87293166 0.6153754591941833 True -11 26352 24.252976417541504 0.6186182498931885 175.25453186035156 0.35121649503707886 267.97088623046875 0.280264288187027 0.87893605 0.5583522915840149 True -12 28548 24.264822483062744 0.6204171180725098 192.02084350585938 0.4217298626899719 267.56866455078125 0.2812575399875641 0.88034195 0.5333559513092041 True -13 30744 24.220492839813232 0.5983829498291016 149.95811462402344 0.4784384071826935 266.43634033203125 0.2845170795917511 0.8846587 0.48185691237449646 True -14 32940 24.175628423690796 0.622899055480957 161.98391723632812 0.5581241846084595 266.5438232421875 0.28421255946159363 0.8892727 0.45965471863746643 True -15 35136 24.259331464767456 0.6013715267181396 181.57559204101562 0.49658918380737305 266.1513977050781 0.2846662700176239 0.8897923 0.44344407320022583 True -16 37332 24.214878797531128 0.5865025520324707 191.9739227294922 0.35856112837791443 266.26318359375 0.2846977710723877 0.8921477 0.43449854850769043 True -17 39528 24.226289749145508 0.5956985950469971 172.24395751953125 0.2288120687007904 266.2506103515625 0.28444674611091614 0.8920426 0.43972480297088623 False -18 41724 24.20987319946289 0.5986182689666748 141.3186798095703 0.4690997004508972 266.4803771972656 0.28411757946014404 0.88966435 0.44895249605178833 False -19 43920 24.244202613830566 31.498834133148193 210.7108154296875 0.35599178075790405 266.54541015625 0.2839556634426117 0.8879571 0.45399245619773865 False diff --git a/ENCSR688OIJ/cherimoya.fold_1.performance.tsv b/ENCSR688OIJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a58b3bdd65db407e6977ebbfa5c893d65d18b9f1..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -266.26318359375 0.5019822120666504 0.2846977710723877 0.08302286267280579 0.8921477198600769 0.8631632924079895 0.43449854850769043 \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_2.evaluate.json b/ENCSR688OIJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index dc2dda5db5d0fffb5d47a00579dc402ae8c0e398..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF854OYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_2.fit.json b/ENCSR688OIJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 21cdb07a6715161d2e06bb64229a3e3f6680691b..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF854OYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_2.log b/ENCSR688OIJ/cherimoya.fold_2.log deleted file mode 100644 index daea9a072e446af228960b7083a4a5cecbfa9290..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2360 29.855193376541138 21.790753602981567 134.092041015625 0.803787887096405 279.2688903808594 0.15531092882156372 0.6736182 5.540765285491943 True -1 4720 26.083287954330444 0.4780242443084717 198.13401794433594 0.6052634119987488 249.0821990966797 0.22137747704982758 0.7917054 2.4937851428985596 True -2 7080 25.920276880264282 0.48921656608581543 194.45986938476562 0.4841696619987488 242.04904174804688 0.23274005949497223 0.8157097 1.17625892162323 True -3 9440 25.953441381454468 0.4729301929473877 235.09210205078125 0.47514665126800537 238.00567626953125 0.2422865927219391 0.82072604 0.8532952666282654 True -4 11800 25.977794408798218 0.47258567810058594 205.00698852539062 0.4943969249725342 237.22621154785156 0.24280592799186707 0.82777536 0.780646562576294 True -5 14160 26.07201910018921 0.4687488079071045 167.10116577148438 0.6881016492843628 235.84617614746094 0.24522341787815094 0.83416593 0.6619408130645752 True -6 16520 26.03139591217041 0.46323561668395996 229.177978515625 0.5517171621322632 234.96934509277344 0.24748103320598602 0.8413858 0.6166858077049255 True -7 18880 26.47843360900879 0.4847412109375 193.88299560546875 0.5823445916175842 233.8939971923828 0.24991093575954437 0.8508808 0.5778045058250427 True -8 21240 26.088769674301147 0.7482001781463623 171.06997680664062 0.5743918418884277 232.7793426513672 0.2527647316455841 0.85599023 0.5595149397850037 True -9 23600 26.124908685684204 0.48174595832824707 189.0369873046875 0.6789168119430542 232.3106689453125 0.2535702884197235 0.8589881 0.5491424798965454 True -10 25960 26.136699199676514 0.47890591621398926 160.08306884765625 0.3353229761123657 231.37557983398438 0.25622010231018066 0.86438566 0.49074509739875793 True -11 28320 26.176795959472656 0.47640013694763184 252.57611083984375 0.29606640338897705 230.71620178222656 0.2578034996986389 0.86900985 0.4831320345401764 True -12 30680 26.149598360061646 0.4800426959991455 190.77557373046875 0.4616580605506897 230.7114715576172 0.25729578733444214 0.8724062 0.4546235501766205 True -13 33040 26.16520357131958 0.47237396240234375 197.32162475585938 0.3238404095172882 229.63417053222656 0.26047295331954956 0.87813175 0.44098442792892456 True -14 35400 26.131464958190918 0.4792969226837158 222.341064453125 0.4256042242050171 229.3352508544922 0.2613251209259033 0.8794904 0.421368271112442 True -15 37760 26.13347029685974 0.48119473457336426 181.18902587890625 0.3087393343448639 229.39285278320312 0.2604745924472809 0.88208693 0.4141990840435028 True -16 40120 26.129506587982178 0.47690844535827637 173.25204467773438 0.5121850371360779 229.42987060546875 0.2607894539833069 0.8830949 0.4020133912563324 True -17 42480 26.1189386844635 1.4160957336425781 151.9138946533203 0.31027406454086304 229.32716369628906 0.2613593339920044 0.88396364 0.4002866744995117 True -18 44840 26.104429244995117 0.48319363594055176 184.34854125976562 0.2585000991821289 229.5914764404297 0.26079481840133667 0.8848177 0.4030817151069641 True -19 47200 26.131237030029297 0.469482421875 190.4312744140625 0.275045245885849 229.2886962890625 0.26193326711654663 0.88355947 0.4077824056148529 False diff --git a/ENCSR688OIJ/cherimoya.fold_2.performance.tsv b/ENCSR688OIJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 43aee2419d9b94a6ccf5e873be784c28c7e9b522..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -229.5914764404297 0.522814154624939 0.2607947885990143 0.07292857021093369 0.8848177194595337 0.8391124606132507 0.4030817151069641 \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_3.evaluate.json b/ENCSR688OIJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index df7243deb56f64456dfda980bca837733193652c..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF854OYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_3.fit.json b/ENCSR688OIJ/cherimoya.fold_3.fit.json deleted file mode 100644 index bbd7c6d3e2e2519a794825faf7796e996c88d0b1..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF854OYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_3.log b/ENCSR688OIJ/cherimoya.fold_3.log deleted file mode 100644 index c1155535123c09b1fede404768c5cbf862fd732d..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2254 28.73564076423645 4.931893825531006 211.50682067871094 0.7104748487472534 270.8574523925781 0.16281995177268982 0.66667324 5.658261299133301 True -1 4508 24.912189960479736 0.5058169364929199 194.67086791992188 0.7849801778793335 245.1298065185547 0.22346580028533936 0.7693851 2.5559983253479004 True -2 6762 24.895265102386475 0.44408082962036133 151.60476684570312 1.1971149444580078 236.88711547851562 0.2391601800918579 0.79273814 1.4604796171188354 True -3 9016 24.859315633773804 0.44993066787719727 183.48358154296875 0.868013322353363 234.22543334960938 0.24394671618938446 0.8051171 1.043555736541748 True -4 11270 24.926705837249756 0.44225645065307617 229.739501953125 0.6214555501937866 233.0618133544922 0.2457437962293625 0.8124163 1.0105968713760376 True -5 13524 24.837645530700684 0.44806361198425293 254.1781005859375 0.766477644443512 232.5383758544922 0.2476755976676941 0.81611365 0.924442708492279 True -6 15778 24.841371774673462 0.44022345542907715 173.1068115234375 0.3823868930339813 231.66429138183594 0.25038862228393555 0.8262988 0.875331461429596 True -7 18032 24.87338352203369 0.5904519557952881 230.14578247070312 0.600529670715332 230.43780517578125 0.25429171323776245 0.8310741 0.8170098066329956 True -8 20286 24.90310788154602 0.4386281967163086 151.36651611328125 0.8384566903114319 230.19631958007812 0.254581481218338 0.837165 0.7314215302467346 True -9 22540 24.8829128742218 0.4438002109527588 225.67922973632812 0.53029865026474 229.27822875976562 0.2574308514595032 0.83922154 0.7365153431892395 True -10 24794 24.876792669296265 0.4362521171569824 166.4073486328125 0.630841851234436 228.81674194335938 0.25801414251327515 0.84426177 0.6675392985343933 True -11 27048 24.877315282821655 0.4353954792022705 227.38790893554688 0.49588364362716675 228.11550903320312 0.26010429859161377 0.8515292 0.6184422373771667 True -12 29302 24.97603988647461 7.302493333816528 163.58840942382812 0.5057991743087769 228.0414276123047 0.260639488697052 0.8551388 0.595418393611908 True -13 31556 25.032808780670166 0.4491593837738037 205.13107299804688 0.4470863938331604 227.33096313476562 0.2628822326660156 0.8632801 0.5506261587142944 True -14 33810 24.94643545150757 1.8589913845062256 178.5310516357422 0.5346987247467041 226.61529541015625 0.2643987536430359 0.86696565 0.5112160444259644 True -15 36064 25.036861896514893 0.4535214900970459 222.2303466796875 0.4753872752189636 226.1433563232422 0.2650998532772064 0.8709888 0.47234880924224854 True -16 38318 24.81417989730835 0.4372251033782959 201.4893798828125 0.3999270498752594 226.4065399169922 0.26382893323898315 0.87457615 0.4550583064556122 True -17 40572 24.836963176727295 0.43731236457824707 203.53602600097656 0.34912487864494324 226.6909942626953 0.26332902908325195 0.875115 0.4457077383995056 True -18 42826 24.893483877182007 0.4311075210571289 181.9183349609375 0.48984962701797485 226.57830810546875 0.26439982652664185 0.874468 0.4498094320297241 False -19 45080 24.854642629623413 0.437852144241333 218.04208374023438 0.29906412959098816 226.43368530273438 0.26402172446250916 0.874205 0.45052847266197205 False diff --git a/ENCSR688OIJ/cherimoya.fold_3.performance.tsv b/ENCSR688OIJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 76c46d0a1c8d90dc5f60d7f63c591777d3326905..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -226.6909942626953 0.5200038552284241 0.26332899928092957 0.07342325150966644 0.8751149773597717 0.8339025974273682 0.4457077383995056 \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_4.evaluate.json b/ENCSR688OIJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3fa6752e399efc55f8a9b1c15735c804a693306d..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF854OYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_4.fit.json b/ENCSR688OIJ/cherimoya.fold_4.fit.json deleted file mode 100644 index cbe3f84c76ba2b99df4d4b630a7da7cec448b75f..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF854OYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR688OIJ/cherimoya.fold_4.log b/ENCSR688OIJ/cherimoya.fold_4.log deleted file mode 100644 index fbbff36a1cabd05a04354f1e7deea71da4ae1cb6..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2234 28.177561283111572 3.897712230682373 160.09478759765625 0.47188103199005127 247.15672302246094 0.148946151137352 0.67711294 5.328254222869873 True -1 4468 24.694921255111694 0.5031142234802246 161.7664337158203 0.5178278684616089 223.9220428466797 0.2062799483537674 0.77988803 2.3103139400482178 True -2 6702 24.641178369522095 0.6043665409088135 178.33731079101562 0.8941031694412231 216.9960479736328 0.2204754501581192 0.8026874 1.118014931678772 True -3 8936 24.63492226600647 0.44326114654541016 127.32183837890625 0.623591959476471 214.22357177734375 0.22476325929164886 0.814487 0.846526026725769 True -4 11170 24.6021089553833 0.4541330337524414 139.71897888183594 0.8308892250061035 212.54954528808594 0.22901228070259094 0.8253121 0.7322683930397034 True -5 13404 24.635116815567017 0.44580936431884766 201.78182983398438 1.3481788635253906 211.5989532470703 0.2315874993801117 0.8322668 0.7262380719184875 True -6 15638 24.55108904838562 0.4497396945953369 151.71078491210938 0.634861946105957 210.88568115234375 0.2326490730047226 0.8389112 0.6637424826622009 True -7 17872 24.62001609802246 0.44682931900024414 195.80865478515625 0.6166815757751465 209.96261596679688 0.2352982610464096 0.8468359 0.6060823202133179 True -8 20106 24.716963529586792 15.408083438873291 192.88717651367188 0.5355792045593262 209.26202392578125 0.2373356819152832 0.8512303 0.5583984851837158 True -9 22340 24.798503637313843 0.4582390785217285 161.2300262451172 0.636457622051239 208.65504455566406 0.23891454935073853 0.85510355 0.5213773846626282 True -10 24574 24.61334466934204 0.44347143173217773 182.77767944335938 0.5692585110664368 207.9026641845703 0.24145838618278503 0.8561544 0.4938444197177887 True -11 26808 24.610166311264038 0.4429945945739746 157.35610961914062 0.5809696316719055 207.7237091064453 0.24160613119602203 0.86136013 0.47636687755584717 True -12 29042 24.659624099731445 0.4509613513946533 172.52716064453125 0.5228976011276245 207.2413330078125 0.24227328598499298 0.86713934 0.44880399107933044 True -13 31276 24.66459584236145 0.45149874687194824 177.41326904296875 0.29663053154945374 206.9476318359375 0.2436402589082718 0.8703292 0.42219823598861694 True -14 33510 24.649613857269287 0.4501936435699463 176.09878540039062 0.3566311299800873 206.46437072753906 0.2446674257516861 0.8736243 0.409664511680603 True -15 35744 24.56107759475708 0.4419238567352295 150.22537231445312 0.3760637640953064 206.36837768554688 0.24521306157112122 0.8759672 0.4001011252403259 True -16 37978 24.63406753540039 0.4535503387451172 174.5093994140625 0.41735970973968506 206.2930908203125 0.2465912103652954 0.87495255 0.39477673172950745 False -17 40212 24.65795373916626 0.45446324348449707 159.9136505126953 0.35091209411621094 206.5138702392578 0.24603106081485748 0.8747577 0.39840707182884216 False -18 42446 24.608315467834473 15.239844560623169 147.2797088623047 0.3909158706665039 206.92764282226562 0.24480663239955902 0.8729979 0.4031267762184143 False -19 44680 24.751842260360718 0.4868943691253662 158.21630859375 0.31237196922302246 206.93807983398438 0.24444690346717834 0.8719157 0.40724077820777893 False diff --git a/ENCSR688OIJ/cherimoya.fold_4.performance.tsv b/ENCSR688OIJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6de14cccbd86bc6f8a64d26a51139703802b7608..0000000000000000000000000000000000000000 --- a/ENCSR688OIJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -206.36837768554688 0.533867359161377 0.24521306157112122 0.062296025454998016 0.8759672045707703 0.8266766667366028 0.4001011252403259 \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_0.evaluate.json b/ENCSR689DSM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 59278e03c4f374ad991e9228331ff88d4066c58e..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907ZRZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_0.fit.json b/ENCSR689DSM/cherimoya.fold_0.fit.json deleted file mode 100644 index a15a01409fbaa8bff2b7f13119221f4c3bf57996..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF907ZRZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_0.log b/ENCSR689DSM/cherimoya.fold_0.log deleted file mode 100644 index 042db16b7f57382d67759df796596625202baeae..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.67935299873352 3.6225621700286865 840.1604614257812 0.664360523223877 1192.0865478515625 0.31608885526657104 0.66885823 7.656132221221924 True -1 5476 30.243105173110962 0.5914962291717529 722.1265258789062 0.499855637550354 999.110595703125 0.40860259532928467 0.7383037 3.11667537689209 True -2 8214 30.323593854904175 0.5838210582733154 961.1854248046875 0.7470003366470337 968.1591186523438 0.42396581172943115 0.74847394 1.6777771711349487 True -3 10952 30.224090576171875 0.8393256664276123 874.7674560546875 0.6048633456230164 953.7551879882812 0.43329232931137085 0.74884164 1.5266358852386475 True -4 13690 30.243523597717285 0.5625925064086914 691.9777221679688 0.5353682041168213 946.8030395507812 0.43669581413269043 0.7528545 1.4247199296951294 True -5 16428 30.221010208129883 0.5483601093292236 733.3870849609375 0.7730674147605896 936.5986938476562 0.4435083270072937 0.7543655 1.2611122131347656 True -6 19166 30.238117456436157 0.5526697635650635 726.1007080078125 0.5851441621780396 927.18408203125 0.4482428729534149 0.76630867 0.985971212387085 True -7 21904 30.243852138519287 0.5625824928283691 721.2591552734375 0.51914381980896 922.5000610351562 0.4517562985420227 0.7661143 0.985924243927002 False -8 24642 30.236441612243652 0.836402177810669 651.2195434570312 0.6541956663131714 917.4581298828125 0.45396316051483154 0.7734703 0.8967778086662292 True -9 27380 30.256147146224976 0.5565760135650635 726.7081298828125 0.49557188153266907 910.72509765625 0.45875129103660583 0.7808002 0.7492583394050598 True -10 30118 30.2659592628479 0.553138256072998 860.49853515625 0.7045167684555054 904.479736328125 0.4621986746788025 0.78718746 0.6701170802116394 True -11 32856 30.209757328033447 0.5617458820343018 860.39501953125 0.3742053210735321 894.7420043945312 0.46793484687805176 0.7953322 0.5842936038970947 True -12 35594 30.235119819641113 0.5608415603637695 759.6448974609375 0.4820295572280884 890.3158569335938 0.4713684022426605 0.80175257 0.5301700234413147 True -13 38332 30.334643363952637 8.444834232330322 820.9745483398438 0.3856913447380066 883.2216796875 0.4742685556411743 0.8108022 0.47309550642967224 True -14 41070 30.295626878738403 0.5738592147827148 791.4307861328125 0.32565370202064514 877.7041625976562 0.47845837473869324 0.81866586 0.4213108718395233 True -15 43808 31.391121864318848 15.913520812988281 741.8504638671875 0.309112548828125 877.4254760742188 0.47760075330734253 0.8264773 0.39530810713768005 True -16 46546 30.271507024765015 33.94357967376709 713.219482421875 0.3154633045196533 872.9735107421875 0.48125043511390686 0.83031213 0.37627559900283813 True -17 49284 33.40787672996521 0.56111741065979 826.79443359375 0.3352329730987549 876.6708374023438 0.47836121916770935 0.8323877 0.3641960322856903 True -18 52022 30.351682424545288 0.5626246929168701 780.6241455078125 0.3231890797615051 876.531005859375 0.4785996079444885 0.8343725 0.3603754937648773 True -19 54760 30.367116928100586 0.5603973865509033 920.5005493164062 0.2348322570323944 878.8421020507812 0.4765629768371582 0.8342332 0.3611306846141815 False diff --git a/ENCSR689DSM/cherimoya.fold_0.performance.tsv b/ENCSR689DSM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index aa6a08fddb15ba6d506d156a1b9e264a0ddb774f..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -876.531005859375 0.32072389125823975 0.47859957814216614 0.22473959624767303 0.8343725204467773 0.7764832377433777 0.3603754937648773 \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_1.evaluate.json b/ENCSR689DSM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 82da4d012f3c1ddc66154a9204f5a15abea3cc53..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907ZRZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_1.fit.json b/ENCSR689DSM/cherimoya.fold_1.fit.json deleted file mode 100644 index bb48b3d8365a9690b0fe8dc96039b30595bf86b7..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF907ZRZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_1.log b/ENCSR689DSM/cherimoya.fold_1.log deleted file mode 100644 index 09cbd1fa9bb1c0b782fa6375871a929803ebdf8a..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2699 34.508657455444336 3.765536069869995 889.34521484375 0.8594000339508057 1434.6561279296875 0.3155127465724945 0.67054826 9.306375503540039 True -1 5398 29.76704168319702 0.7361814975738525 1121.5625 1.2488009929656982 1190.6434326171875 0.4211094081401825 0.7515825 3.4332516193389893 True -2 8097 29.779099464416504 0.7232983112335205 838.0191650390625 0.5308756828308105 1151.617431640625 0.43819260597229004 0.76252663 2.054450511932373 True -3 10796 29.77977418899536 2.5380187034606934 853.7516479492188 0.5932536125183105 1124.88232421875 0.4472527503967285 0.7683776 1.7875226736068726 True -4 13495 29.833893060684204 0.7509398460388184 642.2542724609375 0.5734619498252869 1111.1636962890625 0.4544301927089691 0.77100366 1.6642721891403198 True -5 16194 29.733495950698853 0.7359728813171387 974.81298828125 0.5346574783325195 1099.227294921875 0.458434522151947 0.78032917 1.2461355924606323 True -6 18893 29.762738943099976 0.7387781143188477 678.9071655273438 0.6801825165748596 1086.1171875 0.4672021269798279 0.78586596 1.2017474174499512 True -7 21592 29.756033658981323 0.7288527488708496 801.489013671875 0.726303219795227 1077.0045166015625 0.4711710512638092 0.7902205 1.0611058473587036 True -8 24291 29.73023772239685 0.7366652488708496 740.76806640625 0.4186345338821411 1069.6932373046875 0.4754161834716797 0.7978764 0.9950616359710693 True -9 26990 30.122918844223022 2.3783938884735107 808.2090454101562 0.514257550239563 1064.9139404296875 0.4786584675312042 0.80148435 0.9848094582557678 True -10 29689 29.858944416046143 0.813248872756958 766.0580444335938 0.46890512108802795 1056.386474609375 0.4842005670070648 0.80694205 0.9201842546463013 True -11 32388 30.341299057006836 0.7462897300720215 691.73291015625 0.3701359033584595 1052.2786865234375 0.4853673279285431 0.8148457 0.8154870867729187 True -12 35087 29.819908618927002 0.7389135360717773 802.1695556640625 0.39699244499206543 1042.9873046875 0.4901897609233856 0.8219189 0.7271217107772827 True -13 37786 29.847162008285522 0.7479438781738281 749.6988525390625 0.33336377143859863 1032.9290771484375 0.4949597120285034 0.82966834 0.6274969577789307 True -14 40485 30.030477046966553 0.738621711730957 748.9517822265625 0.5219944715499878 1029.7060546875 0.4950658082962036 0.8353931 0.5455447435379028 True -15 43184 29.95951509475708 0.7370030879974365 772.5738525390625 0.40344542264938354 1025.030517578125 0.4979226887226105 0.8444051 0.4729669988155365 True -16 45883 30.04940676689148 1.2132377624511719 747.8426513671875 0.4229404926300049 1022.04736328125 0.49813634157180786 0.84706765 0.4210678040981293 True -17 48582 30.04513669013977 0.7402908802032471 707.38232421875 0.35152849555015564 1021.0099487304688 0.49795952439308167 0.8495911 0.39150381088256836 True -18 51281 30.393064737319946 5.61150336265564 832.20458984375 0.3505908250808716 1021.9024658203125 0.4978179633617401 0.85274774 0.37957605719566345 True -19 53980 29.913596630096436 0.7332909107208252 748.5440673828125 0.39284008741378784 1021.500244140625 0.4984564781188965 0.85154194 0.37536829710006714 False diff --git a/ENCSR689DSM/cherimoya.fold_1.performance.tsv b/ENCSR689DSM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 12d4bdee8c02b91bf4c0323a8829f45c70016b0b..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1021.9024658203125 0.30232974886894226 0.4978180229663849 0.254763126373291 0.8527477383613586 0.8189989328384399 0.37957605719566345 \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_2.evaluate.json b/ENCSR689DSM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4e735b5b1fcbee64d237cee37775c673be049679..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907ZRZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_2.fit.json b/ENCSR689DSM/cherimoya.fold_2.fit.json deleted file mode 100644 index d5c1713819754b217441af6dfb1a26b23af8c02e..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF907ZRZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_2.log b/ENCSR689DSM/cherimoya.fold_2.log deleted file mode 100644 index 5f47a9d1d14eb23b29e720c6b004d5adf6f8a1a1..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 36.743459939956665 3.684805393218994 797.7865600585938 0.4440953731536865 1271.8238525390625 0.3197161555290222 0.6661105 7.179152965545654 True -1 5788 32.001784801483154 1.358872413635254 877.0245971679688 0.5929862260818481 1054.873046875 0.4113077223300934 0.7514003 2.7312419414520264 True -2 8682 31.987544775009155 0.9632089138031006 1113.341552734375 0.5450233817100525 1031.20166015625 0.4253888428211212 0.76111984 1.7122795581817627 True -3 11576 31.93006706237793 0.5493996143341064 892.27685546875 0.62366783618927 1013.2611694335938 0.4326428472995758 0.7677872 1.3346303701400757 True -4 14470 32.03660702705383 0.5615415573120117 733.6791381835938 0.5497648119926453 995.3922119140625 0.4424256980419159 0.77556247 1.087850570678711 True -5 17364 31.90098738670349 0.5550780296325684 786.2489013671875 0.4694518446922302 990.6329345703125 0.44624900817871094 0.7824418 1.1490439176559448 True -6 20258 31.90877628326416 2.091628313064575 747.483154296875 0.4941439628601074 979.91259765625 0.45211032032966614 0.7882488 0.9002030491828918 True -7 23152 31.978482961654663 0.5610575675964355 744.24560546875 0.5067270398139954 975.8042602539062 0.45381924510002136 0.7911207 0.8573583364486694 True -8 26046 32.00505709648132 0.5548498630523682 643.4326171875 0.4002898633480072 965.5715942382812 0.45982569456100464 0.79779685 0.7297207117080688 True -9 28940 31.90586280822754 0.5533323287963867 949.6859130859375 0.42912930250167847 958.227294921875 0.46399208903312683 0.8062739 0.692236602306366 True -10 31834 31.887662410736084 0.5527975559234619 732.1282958984375 0.2715362012386322 954.3204345703125 0.4665117859840393 0.81049293 0.6324604153633118 True -11 34728 32.19661498069763 0.5502691268920898 676.728759765625 0.4862576723098755 950.5177612304688 0.4689502716064453 0.8140237 0.6255576610565186 True -12 37622 31.94210433959961 0.5493907928466797 765.5607299804688 0.34120607376098633 944.3977661132812 0.4728153944015503 0.82090986 0.5452642440795898 True -13 40516 31.960248708724976 0.5618033409118652 829.8348999023438 0.40334466099739075 935.4273681640625 0.4785028100013733 0.8247472 0.49038586020469666 True -14 43410 32.007376194000244 0.5612332820892334 665.775146484375 0.28862154483795166 934.4580078125 0.47740069031715393 0.8316829 0.4431653618812561 True -15 46304 31.995487451553345 0.5424489974975586 915.9645385742188 0.42788392305374146 929.2972412109375 0.4815373718738556 0.83553445 0.40052834153175354 True -16 49198 31.97898530960083 1.5609774589538574 830.2273559570312 0.3302410840988159 931.5882568359375 0.47888296842575073 0.8376359 0.3817027807235718 True -17 52092 32.04021191596985 0.5665156841278076 627.1770629882812 0.32779863476753235 930.0570678710938 0.4801059663295746 0.8385264 0.3690931797027588 True -18 54986 32.15820670127869 0.5637302398681641 879.24853515625 0.3712400496006012 929.2062377929688 0.48140695691108704 0.83821124 0.36579805612564087 False -19 57880 32.01822257041931 0.5512433052062988 791.0340576171875 0.32037585973739624 927.6266479492188 0.4828675389289856 0.8369593 0.3653716742992401 False diff --git a/ENCSR689DSM/cherimoya.fold_2.performance.tsv b/ENCSR689DSM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f873b37436e52d43007723c8f167009eef718cfd..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -930.0570678710938 0.31586578488349915 0.48010602593421936 0.23547153174877167 0.8385264277458191 0.7946462631225586 0.3690931797027588 \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_3.evaluate.json b/ENCSR689DSM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 77f90ecbe9860d6f08ed715fe892d2e9e84e1f14..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907ZRZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_3.fit.json b/ENCSR689DSM/cherimoya.fold_3.fit.json deleted file mode 100644 index 5417a8ff770a4cc68110c1a9134c1414bdf16d8e..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF907ZRZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_3.log b/ENCSR689DSM/cherimoya.fold_3.log deleted file mode 100644 index 1dca2f63df524a8016b5c5e42e1ae6f5d2f41ee1..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 35.10844564437866 3.666261911392212 947.083251953125 0.8327605128288269 1188.0206298828125 0.3235000967979431 0.66015124 7.856628894805908 True -1 5498 30.3095965385437 0.5711979866027832 923.4735107421875 0.50599205493927 998.2404174804688 0.41553905606269836 0.73845243 3.2930684089660645 True -2 8247 30.45331072807312 0.5605325698852539 703.0950927734375 0.8658394813537598 976.2233276367188 0.4255324602127075 0.74801576 1.8868848085403442 True -3 10996 30.355146646499634 0.5628867149353027 885.9722290039062 0.44980472326278687 951.3200073242188 0.4375822842121124 0.7564092 1.6371411085128784 True -4 13745 32.29735040664673 5.126869201660156 748.9452514648438 0.7255164384841919 940.5048828125 0.44283488392829895 0.7653538 1.4514896869659424 True -5 16494 30.401538133621216 1.5801067352294922 723.2737426757812 0.48472970724105835 931.064208984375 0.44586533308029175 0.77038246 1.1984732151031494 True -6 19243 30.40424370765686 1.9832472801208496 776.17041015625 0.7751468420028687 922.6655883789062 0.4527604877948761 0.7732317 1.251744270324707 True -7 21992 30.46308207511902 0.8630824089050293 738.6914672851562 0.6372346878051758 918.1937866210938 0.45553550124168396 0.777626 1.0410822629928589 True -8 24741 30.329313278198242 1.0602588653564453 797.1204833984375 0.6433194875717163 914.984619140625 0.45731833577156067 0.7784786 0.9443469047546387 True -9 27490 30.41077446937561 1.7886431217193604 850.8626708984375 0.5250650644302368 908.4249267578125 0.4619764983654022 0.78615427 0.8756757378578186 True -10 30239 30.359599828720093 1.5367686748504639 652.4156494140625 0.395992249250412 905.3377685546875 0.4636424481868744 0.79169875 0.8074559569358826 True -11 32988 30.85895323753357 1.7689728736877441 869.662353515625 0.549772322177887 893.9453735351562 0.4732153117656708 0.79954135 0.7186288833618164 True -12 35737 30.35463833808899 0.5680477619171143 760.7869873046875 0.3630697727203369 891.4895629882812 0.471905916929245 0.8083184 0.6282482147216797 True -13 38486 30.359586000442505 0.5616581439971924 659.6812133789062 0.39268043637275696 882.9540405273438 0.476234495639801 0.8143751 0.5478353500366211 True -14 41235 30.378761291503906 2.0077011585235596 751.3024291992188 0.3850173354148865 879.1298217773438 0.4795093238353729 0.8216578 0.514895498752594 True -15 43984 30.69314408302307 0.5714445114135742 532.719970703125 0.3414396345615387 875.6174926757812 0.4815067946910858 0.82807684 0.4572239816188812 True -16 46733 30.397773027420044 2.1733603477478027 755.3764038085938 0.4383462965488434 871.9177856445312 0.48348039388656616 0.83167374 0.42580747604370117 True -17 49482 30.379422187805176 0.6130495071411133 868.2567138671875 0.39302778244018555 872.9019775390625 0.4825079143047333 0.8353154 0.40306487679481506 True -18 52231 30.342175483703613 0.5682823657989502 786.319580078125 0.20583978295326233 874.3775634765625 0.4813070595264435 0.8367534 0.39223647117614746 True -19 54980 30.368753671646118 0.5620524883270264 767.971923828125 0.2145509421825409 874.2487182617188 0.48177728056907654 0.83793396 0.3898311257362366 True diff --git a/ENCSR689DSM/cherimoya.fold_3.performance.tsv b/ENCSR689DSM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2f0e54cf3eff68519f4fd02a786609f388dea09d..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -874.2487182617188 0.3196694254875183 0.48177728056907654 0.22820109128952026 0.8379339575767517 0.7844383716583252 0.3898311257362366 \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_4.evaluate.json b/ENCSR689DSM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 42aaec7233cddc0cca3425840f9ea1e49914a139..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907ZRZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_4.fit.json b/ENCSR689DSM/cherimoya.fold_4.fit.json deleted file mode 100644 index ea3d8b7baa54df5aa120089f1033040ed160d961..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF907ZRZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR689DSM/cherimoya.fold_4.log b/ENCSR689DSM/cherimoya.fold_4.log deleted file mode 100644 index ffa9f8c3e6f72f6f2e7c2ce600d9282cbaf28f19..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2796 36.173758029937744 6.04465913772583 662.1373291015625 0.8825751543045044 1077.859375 0.31455501914024353 0.6468248 5.515220642089844 True -1 5592 30.889198064804077 0.5964276790618896 819.2169189453125 0.5527049899101257 909.6959838867188 0.40110674500465393 0.7278202 2.4795641899108887 True -2 8388 30.87126851081848 0.5799779891967773 855.1783447265625 0.5643576383590698 884.4328002929688 0.4172154366970062 0.7369221 1.3134812116622925 True -3 11184 30.95778489112854 0.5715973377227783 867.5875854492188 0.7074780464172363 869.9299926757812 0.424496054649353 0.7456572 1.108079433441162 True -4 13980 30.823601007461548 0.5808351039886475 749.2694091796875 0.8448771834373474 860.9970703125 0.4299372732639313 0.7504959 0.9037695527076721 True -5 16776 30.81930446624756 0.5736725330352783 771.5791015625 0.6217817068099976 857.0330810546875 0.4307548701763153 0.75775766 0.9389500617980957 True -6 19572 30.856412649154663 0.5770511627197266 808.5382080078125 0.5658469200134277 846.1747436523438 0.44007667899131775 0.761459 0.8573599457740784 True -7 22368 30.915560007095337 0.5815513134002686 1053.901611328125 0.4116453230381012 841.4140625 0.4430069029331207 0.76852924 0.7497417330741882 True -8 25164 31.33858895301819 28.270307064056396 739.9783935546875 0.4567030072212219 838.2711181640625 0.44660285115242004 0.77158767 0.7251365184783936 True -9 27960 30.93611431121826 5.473835706710815 693.8978271484375 0.5388966798782349 834.8033447265625 0.4471380412578583 0.77479345 0.6156504154205322 True -10 30756 30.9613196849823 19.076318740844727 695.2271728515625 0.5844630002975464 831.5579223632812 0.4493446350097656 0.78079057 0.6112374663352966 True -11 33552 32.127445459365845 7.0667405128479 779.0364990234375 0.4053165912628174 824.7416381835938 0.45466703176498413 0.78882384 0.5488865971565247 True -12 36348 30.969677209854126 2.5968496799468994 907.9107055664062 0.36487245559692383 818.8853759765625 0.45928701758384705 0.79584897 0.5098934173583984 True -13 39144 30.889063835144043 0.6029617786407471 921.7861328125 0.3937404155731201 815.5293579101562 0.4603365957736969 0.80313486 0.4558199644088745 True -14 41940 30.829785585403442 0.5760424137115479 762.9580078125 0.33857476711273193 811.2992553710938 0.4625643193721771 0.8114263 0.41621509194374084 True -15 44736 30.86490225791931 0.5795314311981201 600.9032592773438 0.3256223201751709 810.2129516601562 0.46265965700149536 0.81835127 0.38811439275741577 True -16 47532 30.867734670639038 0.5784478187561035 725.4947509765625 0.33278894424438477 809.3893432617188 0.46486446261405945 0.82368904 0.368098646402359 True -17 50328 30.882751941680908 18.43708086013794 704.9998779296875 0.3402080535888672 806.1193237304688 0.46778103709220886 0.82693774 0.35429078340530396 True -18 53124 30.935489416122437 0.5910317897796631 744.259521484375 0.29236188530921936 808.167236328125 0.4642674922943115 0.8290154 0.3499416708946228 True -19 55920 30.864289045333862 0.5738651752471924 749.928466796875 0.2012856900691986 809.2108154296875 0.46430546045303345 0.8279879 0.3497906029224396 False diff --git a/ENCSR689DSM/cherimoya.fold_4.performance.tsv b/ENCSR689DSM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d2f7b4890905a048e24ace5e1b9a32568d2cdc5c..0000000000000000000000000000000000000000 --- a/ENCSR689DSM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -808.167236328125 0.33182889223098755 0.4642674922943115 0.21202661097049713 0.8290153741836548 0.7628465294837952 0.3499416708946228 \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_0.evaluate.json b/ENCSR691MQJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 157f526ffbf1f6799361582ef5f0f611f7678fa2..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_0.fit.json b/ENCSR691MQJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 5614b2a98e4278751a8fd41f8a139c05766a7c1b..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF215GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_0.log b/ENCSR691MQJ/cherimoya.fold_0.log deleted file mode 100644 index b15d94b25918a5a01c7e9d56c4618a9f0c0293ce..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 34.32760143280029 3.8604178428649902 1326.9117431640625 1.4127047061920166 1783.2288818359375 0.28431302309036255 0.41626757 11.215999603271484 True -1 5424 30.606507539749146 18.609394073486328 1409.799072265625 1.243398904800415 1377.7374267578125 0.4960089921951294 0.5166405 6.2064409255981445 True -2 8136 30.068239450454712 0.5935766696929932 1371.92333984375 1.4581596851348877 1332.1514892578125 0.5138406753540039 0.52088416 3.95086407661438 True -3 10848 29.890228509902954 0.6114566326141357 904.0833129882812 0.6693500280380249 1296.231201171875 0.5251888632774353 0.55197746 2.290160655975342 True -4 13560 29.815557956695557 0.6808314323425293 1139.8203125 0.9313054084777832 1274.1776123046875 0.5376733541488647 0.56410974 1.995944619178772 True -5 16272 29.418394804000854 0.5833134651184082 898.83984375 0.8136390447616577 1265.889892578125 0.5419973731040955 0.5756475 2.1638503074645996 True -6 18984 29.232015132904053 1.2454679012298584 849.1373901367188 0.9734987616539001 1254.839599609375 0.5488731265068054 0.5791637 1.9090062379837036 True -7 21696 29.255561113357544 0.5811319351196289 1021.1610107421875 1.063293695449829 1243.6798095703125 0.5556349754333496 0.58536386 1.764348030090332 True -8 24408 29.35612440109253 0.5622920989990234 982.310302734375 0.6848726272583008 1241.4649658203125 0.5551362633705139 0.589372 1.6794440746307373 True -9 27120 29.23798656463623 0.589836835861206 761.0992431640625 0.8669453263282776 1227.0684814453125 0.5611523389816284 0.61476445 1.3616551160812378 True -10 29832 29.264201164245605 0.5941188335418701 1048.9879150390625 0.8096308708190918 1216.3282470703125 0.5665817856788635 0.62171817 1.2676827907562256 True -11 32544 29.289082527160645 0.5768470764160156 924.80029296875 0.8985220193862915 1210.3243408203125 0.5670874118804932 0.63839966 1.1545252799987793 True -12 35256 29.266358375549316 0.5894327163696289 837.4991455078125 0.9804672002792358 1193.1239013671875 0.5764651298522949 0.6539757 1.0099290609359741 True -13 37968 29.327346086502075 0.5802977085113525 1026.4725341796875 0.7994766235351562 1191.5325927734375 0.5748294591903687 0.66573405 0.9410174489021301 True -14 40680 29.28473949432373 2.780670166015625 1095.25146484375 1.0512416362762451 1185.3896484375 0.5770562887191772 0.68242604 0.8622174263000488 True -15 43392 29.315130710601807 0.6436038017272949 926.8034057617188 0.7194378972053528 1174.5748291015625 0.582855761051178 0.6957214 0.7663650512695312 True -16 46104 29.354938745498657 0.6056265830993652 824.13330078125 1.0618833303451538 1174.9329833984375 0.5800167322158813 0.70362175 0.7235544323921204 True -17 48816 29.35593557357788 0.5883419513702393 809.6124267578125 0.6730632185935974 1171.8643798828125 0.5813510417938232 0.70825934 0.6895772218704224 True -18 51528 29.284053325653076 0.6040694713592529 816.076416015625 0.7719674110412598 1166.162109375 0.5862624645233154 0.70868975 0.6793712973594666 True -19 54240 29.265652656555176 0.6098699569702148 899.7688598632812 0.6224684119224548 1170.1982421875 0.582756519317627 0.7100255 0.6783839464187622 True diff --git a/ENCSR691MQJ/cherimoya.fold_0.performance.tsv b/ENCSR691MQJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a0de189ed8eb588d800e506ef73351c7d4175aa6..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1170.1982421875 0.24554872512817383 0.5827564597129822 0.3165583908557892 0.7100254893302917 0.6732794642448425 0.6783839464187622 \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_1.evaluate.json b/ENCSR691MQJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 50f15e63dca5864c32a286e085f0d1b987e95feb..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_1.fit.json b/ENCSR691MQJ/cherimoya.fold_1.fit.json deleted file mode 100644 index b9285b602d150ecb94aca382174de4013cefe667..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF215GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_1.log b/ENCSR691MQJ/cherimoya.fold_1.log deleted file mode 100644 index 00e5837b5efa95f798a3c88fae0c833e6406468e..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 35.19199013710022 4.689451694488525 914.5587158203125 0.7958143353462219 1968.262451171875 0.2793242037296295 0.4510941 9.819877624511719 True -1 5482 30.24506664276123 11.563182592391968 1218.5478515625 1.2019612789154053 1550.5145263671875 0.48623624444007874 0.5612739 5.861210823059082 True -2 8223 30.30124282836914 0.7620704174041748 855.482666015625 0.8793195486068726 1483.88232421875 0.5119728446006775 0.5801927 2.846550703048706 True -3 10964 30.204578161239624 0.7320010662078857 1039.683349609375 0.9041236639022827 1446.6571044921875 0.5262047648429871 0.5958691 2.02843976020813 True -4 13705 30.163631439208984 0.7334775924682617 1244.5123291015625 1.0537724494934082 1427.7960205078125 0.5360040664672852 0.5958866 1.9212102890014648 True -5 16446 29.800858736038208 0.729785680770874 931.3245239257812 0.7763420343399048 1415.81640625 0.5403287410736084 0.60259277 1.8373359441757202 True -6 19187 29.67599320411682 0.7244617938995361 1000.432373046875 1.1431951522827148 1398.13916015625 0.5488935112953186 0.6162359 1.7859431505203247 True -7 21928 29.70739221572876 0.7371153831481934 1039.63720703125 1.058326244354248 1382.6951904296875 0.5553148984909058 0.63067025 1.5690523386001587 True -8 24669 29.60386824607849 0.7244541645050049 863.890380859375 0.7703642845153809 1373.3818359375 0.5579182505607605 0.6388604 1.542523741722107 True -9 27410 29.714166164398193 0.7427911758422852 1017.7489624023438 1.0576056241989136 1353.0245361328125 0.5657040476799011 0.6521616 1.3069528341293335 True -10 30151 29.90666651725769 0.7614398002624512 745.2913818359375 0.7505683302879333 1342.1669921875 0.568862795829773 0.66290486 1.1623930931091309 True -11 32892 29.856972694396973 0.7620701789855957 927.9826049804688 0.9785047173500061 1326.9716796875 0.5757442116737366 0.674147 1.0710936784744263 True -12 35633 29.88188886642456 0.7345123291015625 968.5806884765625 0.5775887966156006 1317.103271484375 0.5784063339233398 0.68761367 0.9890658855438232 True -13 38374 29.84846591949463 0.7305929660797119 800.1526489257812 0.7454653382301331 1310.2718505859375 0.5796955227851868 0.70033383 0.8787692785263062 True -14 41115 29.724424362182617 0.758298397064209 805.7260131835938 0.9660413265228271 1299.46240234375 0.5854749083518982 0.712826 0.7983593940734863 True -15 43856 29.660218715667725 0.7504303455352783 901.3928833007812 0.5968425273895264 1296.37890625 0.5856369137763977 0.7194813 0.7574676275253296 True -16 46597 29.683200359344482 0.7273480892181396 1028.578369140625 0.5932506322860718 1294.8900146484375 0.5835340619087219 0.73144466 0.7054415941238403 True -17 49338 29.62598991394043 0.7123095989227295 794.6058349609375 0.41191595792770386 1294.8577880859375 0.5848982930183411 0.7347469 0.6784284710884094 True -18 52079 29.627851724624634 0.7375295162200928 873.2882080078125 0.7043040990829468 1288.3746337890625 0.5885070562362671 0.73758125 0.6718971729278564 True -19 54820 29.648136377334595 0.843029260635376 1042.23681640625 0.6926437020301819 1286.74609375 0.5890647172927856 0.7361661 0.6726574897766113 False diff --git a/ENCSR691MQJ/cherimoya.fold_1.performance.tsv b/ENCSR691MQJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 47e382e2c6d42afacb36558a3ec50669c6803aee..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1288.3746337890625 0.237538143992424 0.5885069966316223 0.3292178213596344 0.7375812530517578 0.7063676714897156 0.6718971729278564 \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_2.evaluate.json b/ENCSR691MQJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 28cc81fe8874561c6fb1d83f3588b0d854f7ad7c..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_2.fit.json b/ENCSR691MQJ/cherimoya.fold_2.fit.json deleted file mode 100644 index dbd7378abecd263145dfe4ee3b3d6992438acd73..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF215GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_2.log b/ENCSR691MQJ/cherimoya.fold_2.log deleted file mode 100644 index 01f88eb2fc9401d36576b71b1e4749f4a37aa604..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2913 36.555543661117554 3.583169460296631 1019.493896484375 0.9474363923072815 1725.4849853515625 0.2947528064250946 0.42308593 10.317915916442871 True -1 5826 32.09329533576965 0.6395840644836426 969.634033203125 1.1081650257110596 1332.6846923828125 0.5050039887428284 0.51833093 5.470879554748535 True -2 8739 32.11507487297058 0.5581579208374023 1050.1807861328125 1.1367506980895996 1293.9278564453125 0.5191773772239685 0.5446336 2.6293721199035645 True -3 11652 31.981996536254883 0.5540516376495361 955.9847412109375 1.338292121887207 1264.1605224609375 0.532252848148346 0.56690675 1.8771661520004272 True -4 14565 31.495675563812256 2.7093327045440674 1077.5439453125 1.4052281379699707 1257.15185546875 0.5343418717384338 0.5808794 1.9410760402679443 True -5 17478 31.562100887298584 0.6085162162780762 998.050048828125 1.1857191324234009 1251.7567138671875 0.5379438996315002 0.5834371 1.9406636953353882 True -6 20391 31.55029010772705 0.5482156276702881 931.3233642578125 0.7721765041351318 1240.220947265625 0.5436170697212219 0.5907685 1.712735652923584 True -7 23304 31.45131754875183 0.5412735939025879 994.2843017578125 0.7518836259841919 1220.5904541015625 0.5523257851600647 0.60632503 1.5690052509307861 True -8 26217 31.523046731948853 0.5600478649139404 874.3225708007812 1.1754801273345947 1217.2353515625 0.555895984172821 0.6122037 1.5155459642410278 True -9 29130 31.61380386352539 0.5364663600921631 1095.164306640625 0.7943984270095825 1206.7154541015625 0.5600274205207825 0.6224722 1.3562921285629272 True -10 32043 31.54296088218689 0.5478765964508057 948.809814453125 0.7253050804138184 1201.025634765625 0.5613346695899963 0.63511634 1.2024418115615845 True -11 34956 31.469691276550293 0.5289957523345947 864.0580444335938 0.7192916870117188 1189.85595703125 0.5668200254440308 0.6443377 1.1157022714614868 True -12 37869 31.518465995788574 0.5386900901794434 970.5806274414062 0.9211717247962952 1178.3233642578125 0.5718251466751099 0.6582255 1.0028139352798462 True -13 40782 31.47215485572815 0.522658109664917 1088.341552734375 1.1778630018234253 1172.2081298828125 0.5718851685523987 0.6728423 0.894851803779602 True -14 43695 31.539665937423706 0.5289621353149414 926.4673461914062 0.586505651473999 1160.9661865234375 0.5777098536491394 0.6844764 0.8018031120300293 True -15 46608 31.51944923400879 0.5338959693908691 863.0306396484375 1.0033291578292847 1157.707275390625 0.5782004594802856 0.69635195 0.7313602566719055 True -16 49521 31.536799907684326 0.850555419921875 916.97998046875 0.6324132680892944 1150.5582275390625 0.5819683074951172 0.7055124 0.6872755289077759 True -17 52434 31.538125038146973 0.5363929271697998 1105.4608154296875 0.5743923187255859 1152.6610107421875 0.5806095004081726 0.71177834 0.6631372570991516 True -18 55347 31.515362977981567 0.5162200927734375 851.4202270507812 0.7825435400009155 1148.4871826171875 0.5831676125526428 0.711679 0.659183144569397 False -19 58260 31.52577781677246 0.5341451168060303 1090.152099609375 0.4942944049835205 1151.289794921875 0.5799639225006104 0.7112944 0.6591435074806213 False diff --git a/ENCSR691MQJ/cherimoya.fold_2.performance.tsv b/ENCSR691MQJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f3bfdcb3f7b41709517ab8152aaa6e14fbf43dce..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1152.6610107421875 0.24781033396720886 0.5806095004081726 0.312259703874588 0.7117783427238464 0.6753809452056885 0.6631372570991516 \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_3.evaluate.json b/ENCSR691MQJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c35cb0ee4be5838c1dea1629ce345668519162b3..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_3.fit.json b/ENCSR691MQJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 3724d47ce1ff744ce5a50291c20d13fed4345d98..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF215GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_3.log b/ENCSR691MQJ/cherimoya.fold_3.log deleted file mode 100644 index 7862724a986658fcdc19dc59db27b87f83742f90..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2820 35.604135036468506 4.05443811416626 1116.5521240234375 1.493272304534912 1795.5238037109375 0.29644015431404114 0.43994308 10.997909545898438 True -1 5640 31.196504831314087 0.7451841831207275 927.7772827148438 1.5070698261260986 1393.81689453125 0.505034327507019 0.53747743 5.984272003173828 True -2 8460 31.13706660270691 0.6291735172271729 928.0938110351562 0.8198214769363403 1360.7381591796875 0.5183789134025574 0.5373296 4.022062301635742 False -3 11280 30.916885137557983 0.5952041149139404 1050.32373046875 1.034997820854187 1333.7081298828125 0.5272276401519775 0.56885964 2.7406561374664307 True -4 14100 30.552948713302612 0.5996196269989014 1025.8211669921875 1.021756649017334 1312.265869140625 0.5392611026763916 0.5773988 2.3555262088775635 True -5 16920 30.529850482940674 0.6127221584320068 977.0584716796875 0.990442156791687 1305.575927734375 0.5413631200790405 0.5885258 2.020169258117676 True -6 19740 30.54142951965332 0.6211373805999756 1075.72412109375 0.9889727234840393 1293.733154296875 0.5473071336746216 0.5992678 1.8863214254379272 True -7 22560 30.509080410003662 0.6142017841339111 781.4459228515625 0.7527253031730652 1285.396728515625 0.5526175498962402 0.60285974 1.6015545129776 True -8 25380 30.54065227508545 1.0799705982208252 941.6647338867188 0.9587323665618896 1274.6715087890625 0.5569614768028259 0.6135375 1.551812767982483 True -9 28200 30.591309309005737 0.6063628196716309 944.239013671875 0.6542155742645264 1269.5479736328125 0.55849689245224 0.62277293 1.4254626035690308 True -10 31020 30.64177370071411 0.6203427314758301 990.9512939453125 0.9731777906417847 1260.249267578125 0.562233567237854 0.63554937 1.3425787687301636 True -11 33840 30.737060070037842 0.6018750667572021 935.1268310546875 0.8990455865859985 1247.9295654296875 0.5677211284637451 0.643831 1.1900556087493896 True -12 36660 30.639944314956665 0.6002006530761719 860.3792724609375 0.910770833492279 1237.437255859375 0.5716855525970459 0.6617684 1.0713534355163574 True -13 39480 30.644803285598755 0.6070144176483154 891.290283203125 0.6956335306167603 1228.453857421875 0.5762838125228882 0.67476803 0.9607117772102356 True -14 42300 30.63145661354065 0.6016395092010498 834.16259765625 0.8052334785461426 1223.5587158203125 0.5771684050559998 0.6909102 0.880359947681427 True -15 45120 30.728817224502563 0.6015875339508057 778.4207153320312 0.895203709602356 1222.6656494140625 0.5750653743743896 0.7016449 0.8064436912536621 True -16 47940 32.45000863075256 5.511465549468994 836.8263549804688 0.519966185092926 1217.2362060546875 0.5788609981536865 0.710825 0.7581548690795898 True -17 50760 30.71312642097473 1.4257090091705322 764.5733642578125 0.45355552434921265 1209.53759765625 0.583050012588501 0.71754324 0.7191124558448792 True -18 53580 30.720908641815186 1.8341352939605713 837.6140747070312 0.9340949058532715 1211.641845703125 0.5800466537475586 0.7177081 0.7070028781890869 True -19 56400 30.635111093521118 1.3087873458862305 981.025146484375 0.5798555612564087 1212.7000732421875 0.5796138644218445 0.71725553 0.7005904316902161 False diff --git a/ENCSR691MQJ/cherimoya.fold_3.performance.tsv b/ENCSR691MQJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d713d38ab3a88edf153387a3ff8fa06fbd309f3f..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1211.641845703125 0.2445351481437683 0.5800467133522034 0.31823965907096863 0.7177081108093262 0.6874651908874512 0.7070028781890869 \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_4.evaluate.json b/ENCSR691MQJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b850ecb24a1a0545a320743e8de3ee9971fc56ea..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_4.fit.json b/ENCSR691MQJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 83c2263402aaef8ee6e6ac536742054ba5a8b8e4..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF215GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR691MQJ/cherimoya.fold_4.log b/ENCSR691MQJ/cherimoya.fold_4.log deleted file mode 100644 index cda477d4fef62e39e35aa3a77d531339a7d326da..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2910 36.545549154281616 4.086576461791992 1243.9581298828125 1.6423306465148926 1718.5927734375 0.2826070189476013 0.41636756 10.501392364501953 True -1 5820 32.10149812698364 0.580317497253418 1408.30517578125 1.2978527545928955 1335.3887939453125 0.49897104501724243 0.52704275 5.081717491149902 True -2 8730 32.091180086135864 0.5514051914215088 1036.651611328125 1.0965070724487305 1298.458251953125 0.5096826553344727 0.54514366 2.615558385848999 True -3 11640 31.68945002555847 0.5474109649658203 898.16748046875 0.9236869215965271 1256.4837646484375 0.5270401835441589 0.5751232 1.7859463691711426 True -4 14550 31.438772201538086 0.5385842323303223 904.235107421875 0.908191442489624 1238.7056884765625 0.5347430109977722 0.5870492 1.5769926309585571 True -5 17460 31.45968770980835 0.5392615795135498 993.262451171875 1.0211944580078125 1231.7730712890625 0.5399377942085266 0.5880568 1.583818793296814 True -6 20370 31.395305156707764 0.5364377498626709 1104.500244140625 0.7050656676292419 1212.6744384765625 0.5504639744758606 0.5991205 1.3864705562591553 True -7 23280 31.422781705856323 0.5460309982299805 987.45166015625 0.9595441818237305 1206.2510986328125 0.5526834726333618 0.6113413 1.2193623781204224 True -8 26190 31.483436822891235 0.5418462753295898 907.530029296875 1.1149544715881348 1198.76904296875 0.5578442811965942 0.6189816 1.253200888633728 True -9 29100 31.407449960708618 0.5419621467590332 1033.5264892578125 0.8196512460708618 1194.825927734375 0.5573811531066895 0.6271969 1.1273194551467896 True -10 32010 31.43161678314209 0.5430059432983398 745.131103515625 0.7594375610351562 1178.7254638671875 0.5682868361473083 0.6352031 1.0591967105865479 True -11 34920 31.40704083442688 1.2620675563812256 1042.739990234375 0.8514229655265808 1169.180419921875 0.5731810331344604 0.64859897 1.0066560506820679 True -12 37830 31.474924564361572 0.5468394756317139 1087.3892822265625 1.037015438079834 1164.6370849609375 0.5740214586257935 0.66024995 0.9339028596878052 True -13 40740 31.475756645202637 0.5446734428405762 1001.7218627929688 0.6114276647567749 1158.0726318359375 0.5775555968284607 0.67219114 0.8676052093505859 True -14 43650 31.476519346237183 0.5632507801055908 969.711669921875 0.8628522157669067 1150.9732666015625 0.5804190039634705 0.686516 0.783417284488678 True -15 46560 31.47779130935669 0.5718963146209717 1022.894287109375 0.8119020462036133 1147.6688232421875 0.5808057188987732 0.69912046 0.7214533686637878 True -16 49470 31.66997456550598 14.089439392089844 907.7327880859375 0.7032318711280823 1143.4384765625 0.5825483202934265 0.7093341 0.672283411026001 True -17 52380 31.576314210891724 0.5529770851135254 710.4369506835938 0.39748334884643555 1139.348388671875 0.585387647151947 0.7131585 0.6516966819763184 True -18 55290 31.589860200881958 0.5670685768127441 914.69384765625 0.4361279606819153 1141.416015625 0.5840675234794617 0.71411854 0.6449966430664062 True -19 58200 31.578723430633545 0.5733339786529541 908.4501342773438 0.47153240442276 1140.9769287109375 0.5840218663215637 0.7152079 0.643267810344696 True diff --git a/ENCSR691MQJ/cherimoya.fold_4.performance.tsv b/ENCSR691MQJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ac5270e6600e01a6778de4d95260c18d34a9ab65..0000000000000000000000000000000000000000 --- a/ENCSR691MQJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1140.9769287109375 0.24655060470104218 0.5840219259262085 0.3131667971611023 0.7152078747749329 0.675847053527832 0.643267810344696 \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_0.evaluate.json b/ENCSR693UHT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 27476f7559f62398dae3c4ba3f82bbfd6a590272..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OMI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_0.fit.json b/ENCSR693UHT/cherimoya.fold_0.fit.json deleted file mode 100644 index a6108eb1bd27d02630f8264c91005507dc4cbc1d..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF378OMI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_0.log b/ENCSR693UHT/cherimoya.fold_0.log deleted file mode 100644 index a96fac3744a2156eb393c09b1ce5d2aec4473597..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.94574451446533 4.126864433288574 359.82220458984375 0.24664804339408875 475.6787109375 0.1975230574607849 0.7681753 3.9463553428649902 True -1 5484 30.433833837509155 0.613433837890625 344.73907470703125 0.2563951015472412 443.28485107421875 0.2489173859357834 0.81453884 0.8523852825164795 True -2 8226 30.511353969573975 0.574420690536499 393.80328369140625 0.29115742444992065 437.36767578125 0.2563525438308716 0.8368114 0.5278599262237549 True -3 10968 30.713674783706665 11.852926015853882 433.2222900390625 0.3720109164714813 434.56170654296875 0.26006919145584106 0.84671444 0.29889434576034546 True -4 13710 30.460912227630615 0.8822650909423828 370.9764404296875 0.29273897409439087 433.7696838378906 0.2621465027332306 0.85011894 0.2888740599155426 True -5 16452 30.472261667251587 0.5740129947662354 428.29522705078125 0.19194266200065613 432.3817443847656 0.2641686797142029 0.8525348 0.2767278850078583 True -6 19194 30.508334636688232 0.5976006984710693 362.14208984375 0.2934091091156006 431.7631530761719 0.2653118073940277 0.8566013 0.2870665490627289 True -7 21936 30.59762406349182 0.5876224040985107 348.98529052734375 0.2283944934606552 430.9583740234375 0.26640886068344116 0.85670376 0.2859734892845154 True -8 24678 30.48698139190674 0.5881240367889404 355.89794921875 0.3156690001487732 430.55462646484375 0.2667176425457001 0.8632894 0.26183438301086426 True -9 27420 30.522428274154663 0.5882952213287354 359.07666015625 0.1807064414024353 429.098388671875 0.2700333595275879 0.865661 0.25406748056411743 True -10 30162 30.462631225585938 0.5821077823638916 385.9317626953125 0.2632533311843872 428.7715148925781 0.2702246308326721 0.8680204 0.23256780207157135 True -11 32904 30.480612754821777 0.5846226215362549 464.8130187988281 0.22586624324321747 427.82147216796875 0.2721484303474426 0.8720322 0.21771851181983948 True -12 35646 30.58305025100708 0.5789830684661865 360.8740234375 0.1900670826435089 427.1039733886719 0.2727375030517578 0.8767369 0.19811224937438965 True -13 38388 30.46178126335144 0.5857853889465332 388.2235107421875 0.23253394663333893 426.5700988769531 0.2738475501537323 0.8777367 0.18055173754692078 True -14 41130 30.56993794441223 0.575709342956543 337.202880859375 0.2187981903553009 425.62322998046875 0.27605774998664856 0.8822051 0.16308066248893738 True -15 43872 30.5626482963562 0.581510066986084 377.86590576171875 0.16716229915618896 425.1294860839844 0.27664926648139954 0.88468933 0.15433833003044128 True -16 46614 30.533416509628296 0.5674431324005127 391.655029296875 0.22078385949134827 425.4194641113281 0.27536770701408386 0.8859228 0.14589552581310272 True -17 49356 30.541024446487427 0.5804164409637451 398.2388916015625 0.2666778862476349 425.61236572265625 0.2750687003135681 0.8864574 0.14291739463806152 True -18 52098 30.50328540802002 0.5627529621124268 320.46405029296875 0.12668678164482117 425.2222900390625 0.2765205204486847 0.8869014 0.14111807942390442 True -19 54840 30.472965002059937 0.559830904006958 380.7320556640625 0.1694391667842865 425.45068359375 0.275566965341568 0.88618 0.1413467675447464 False diff --git a/ENCSR693UHT/cherimoya.fold_0.performance.tsv b/ENCSR693UHT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 30f7d3cb84ca99120a82db5e51293095b0c18ef5..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -425.2222900390625 0.4933145046234131 0.2765205502510071 0.07948482036590576 0.8869013786315918 0.8599541783332825 0.14111807942390442 \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_1.evaluate.json b/ENCSR693UHT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 65c91be8ff155d931487a09fc07535f090496fcc..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OMI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_1.fit.json b/ENCSR693UHT/cherimoya.fold_1.fit.json deleted file mode 100644 index bddf8c0a396953ce090f60cf8a7eeb874b909654..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF378OMI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_1.log b/ENCSR693UHT/cherimoya.fold_1.log deleted file mode 100644 index 3ee83c56b07a90e81044b7a70c1843bc75414559..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2724 35.12062859535217 5.375959873199463 431.0765686035156 0.30372893810272217 534.7842407226562 0.20331688225269318 0.7808456 3.981091022491455 True -1 5448 30.240596055984497 0.7653663158416748 352.735107421875 0.3244357705116272 500.11773681640625 0.2537693679332733 0.8273653 0.9428106546401978 True -2 8172 31.046529054641724 0.7070279121398926 381.61224365234375 0.24130752682685852 491.2820739746094 0.26566845178604126 0.8505123 0.46378007531166077 True -3 10896 30.345794200897217 2.1426873207092285 386.87042236328125 0.31376349925994873 486.62847900390625 0.2718411684036255 0.8632632 0.36343273520469666 True -4 13620 30.24541139602661 0.742302656173706 386.2588806152344 0.32631218433380127 484.7479248046875 0.27409300208091736 0.8685305 0.32710444927215576 True -5 16344 30.205700397491455 0.7178208827972412 411.298828125 0.29947108030319214 483.8155822753906 0.2758752703666687 0.8694979 0.30650395154953003 True -6 19068 30.364392042160034 2.481458902359009 372.0678405761719 0.3070552945137024 482.79241943359375 0.2775627672672272 0.87448037 0.29696404933929443 True -7 21792 30.30212712287903 0.7066586017608643 350.922119140625 0.14288565516471863 481.3122253417969 0.2800388038158417 0.8745029 0.2862190008163452 True -8 24516 30.22334909439087 0.7068014144897461 378.4737548828125 0.22323670983314514 480.664306640625 0.28072571754455566 0.8766647 0.25734859704971313 True -9 27240 30.258187294006348 0.7327253818511963 383.26416015625 0.18537090718746185 479.62396240234375 0.2829079031944275 0.8801327 0.2518581748008728 True -10 29964 30.196624517440796 1.410926103591919 340.916748046875 0.1758420765399933 478.76995849609375 0.2836202383041382 0.8848669 0.2241956889629364 True -11 32688 30.349588871002197 0.7303981781005859 384.6800231933594 0.16196079552173615 477.4939880371094 0.28595253825187683 0.887832 0.20181132853031158 True -12 35412 30.28446102142334 0.7480180263519287 348.4573669433594 0.17792551219463348 477.2867736816406 0.2859359681606293 0.8911156 0.19256021082401276 True -13 38136 30.243303775787354 0.704754114151001 343.3025817871094 0.22245457768440247 475.6445617675781 0.28879600763320923 0.894475 0.18370458483695984 True -14 40860 30.238651990890503 0.7460136413574219 334.6031494140625 0.1753096878528595 474.9261474609375 0.289867103099823 0.8995987 0.17204630374908447 True -15 43584 30.254363298416138 0.724785327911377 320.7515563964844 0.29670923948287964 474.79498291015625 0.29043281078338623 0.9009987 0.15906134247779846 True -16 46308 30.227572917938232 0.707890510559082 355.0328674316406 0.2008379101753235 474.444580078125 0.2903818190097809 0.90528286 0.15056633949279785 True -17 49032 30.249475240707397 2.2057268619537354 340.0658264160156 0.16578233242034912 474.3348083496094 0.2904498279094696 0.9057587 0.14513812959194183 True -18 51756 30.293732404708862 0.7429323196411133 340.2123718261719 0.13403531908988953 475.10009765625 0.2888486981391907 0.9055308 0.14325189590454102 False -19 54480 30.2403347492218 4.474757432937622 400.94586181640625 0.118763267993927 475.1925964355469 0.288901686668396 0.9042998 0.14334160089492798 False diff --git a/ENCSR693UHT/cherimoya.fold_1.performance.tsv b/ENCSR693UHT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 022055fbd29276403c1a213a4076afbaec571dc3..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -474.3348083496094 0.4801660180091858 0.2904498279094696 0.09269680827856064 0.9057586789131165 0.8912169337272644 0.14513812959194183 \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_2.evaluate.json b/ENCSR693UHT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 98ddc9fd3feb87c8434cec76ca5b24747416c3ea..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OMI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_2.fit.json b/ENCSR693UHT/cherimoya.fold_2.fit.json deleted file mode 100644 index f5a47b49bd117152a0abf884c50f968caba6a99f..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF378OMI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_2.log b/ENCSR693UHT/cherimoya.fold_2.log deleted file mode 100644 index a776100eee0b9966412943568c9414291ea7e1d7..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 36.547430753707886 4.141108274459839 393.3953552246094 0.22741079330444336 496.23492431640625 0.2010851800441742 0.76370597 3.147812843322754 True -1 5764 31.98269748687744 0.5841164588928223 406.4036865234375 0.19586385786533356 462.5841369628906 0.25126829743385315 0.81902254 0.6520035862922668 True -2 8646 32.027156829833984 0.5775246620178223 380.95648193359375 0.2580929696559906 455.4332580566406 0.25968706607818604 0.84211576 0.4180986285209656 True -3 11528 32.00064468383789 0.5352604389190674 364.2236328125 0.20361657440662384 453.2932434082031 0.26289379596710205 0.8468855 0.2779269516468048 True -4 14410 32.104891300201416 0.5164761543273926 364.55712890625 0.41982194781303406 451.4635925292969 0.26617231965065 0.84970844 0.25634607672691345 True -5 17292 32.000755310058594 0.5161483287811279 366.1266784667969 0.21955859661102295 450.0506286621094 0.26846104860305786 0.8553966 0.25654926896095276 True -6 20174 32.016666412353516 0.5281853675842285 408.77520751953125 0.3001359701156616 449.00518798828125 0.2703329920768738 0.86005497 0.23887570202350616 True -7 23056 31.95183253288269 0.5429713726043701 413.1043701171875 0.32373982667922974 448.0304260253906 0.27198028564453125 0.86434555 0.21408632397651672 True -8 25938 31.936073541641235 0.5151653289794922 460.2190856933594 0.24845853447914124 448.0221862792969 0.27212172746658325 0.86738366 0.20983198285102844 True -9 28820 31.96205973625183 0.5425076484680176 382.42449951171875 0.2396940141916275 446.66839599609375 0.27454355359077454 0.8697941 0.19028252363204956 True -10 31702 31.97098422050476 0.5266022682189941 346.8504638671875 0.24563920497894287 446.66021728515625 0.2741493284702301 0.8725201 0.17834784090518951 True -11 34584 31.976521015167236 17.5890052318573 364.08428955078125 0.14995795488357544 446.43243408203125 0.2738678753376007 0.87235385 0.17673495411872864 False -12 37466 32.056217432022095 1.2919821739196777 422.63189697265625 0.18825355172157288 445.4188537597656 0.2766316533088684 0.87713784 0.16874442994594574 True -13 40348 31.993433237075806 0.5455183982849121 380.86492919921875 0.12334930896759033 445.0670166015625 0.27650031447410583 0.8802782 0.16278481483459473 True -14 43230 31.972723722457886 1.4612810611724854 353.0364990234375 0.1795751005411148 444.69317626953125 0.2770485281944275 0.8826604 0.1579204648733139 True -15 46112 31.947967052459717 0.5304014682769775 416.53662109375 0.261724591255188 443.945556640625 0.27810266613960266 0.88399017 0.15117456018924713 True -16 48994 31.939950227737427 0.5458130836486816 357.1921081542969 0.17616713047027588 443.72918701171875 0.27849674224853516 0.887191 0.14655601978302002 True -17 51876 31.90606689453125 0.538428783416748 343.468994140625 0.25164511799812317 443.45062255859375 0.279145210981369 0.8879341 0.14438267052173615 True -18 54758 31.90384531021118 1.072350263595581 420.93438720703125 0.11482629179954529 443.32061767578125 0.27988094091415405 0.8872901 0.1440872997045517 False -19 57640 32.03004240989685 0.5142014026641846 368.0446472167969 0.21442478895187378 443.8479309082031 0.2784762382507324 0.8885616 0.14466385543346405 True diff --git a/ENCSR693UHT/cherimoya.fold_2.performance.tsv b/ENCSR693UHT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 39c711290864eda99362ffe2a66dd3a3a3f1c5a4..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -443.8479309082031 0.48951172828674316 0.2784762382507324 0.08667396008968353 0.8885616064071655 0.8673853278160095 0.14466385543346405 \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_3.evaluate.json b/ENCSR693UHT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c7481d2d4ff72f575f10606ff55323da3a87f44c..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OMI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_3.fit.json b/ENCSR693UHT/cherimoya.fold_3.fit.json deleted file mode 100644 index 1307a75d4638235d18d29e201179c96a7132743f..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF378OMI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_3.log b/ENCSR693UHT/cherimoya.fold_3.log deleted file mode 100644 index 10a161cff1833221048cfef6a5b7c98b85c123a3..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 35.500184535980225 3.989424228668213 366.44940185546875 0.2406826913356781 473.5082702636719 0.2030724138021469 0.7500246 4.075372219085693 True -1 5540 30.781217575073242 0.7128036022186279 415.58135986328125 0.19434380531311035 443.0713195800781 0.24958762526512146 0.81015134 0.859618067741394 True -2 8310 30.76321315765381 0.5630919933319092 377.0503234863281 0.36114081740379333 436.6690979003906 0.2592017650604248 0.83780575 0.4128889739513397 True -3 11080 30.818569898605347 0.5433800220489502 434.03179931640625 0.16809342801570892 434.9906311035156 0.2613726556301117 0.8471662 0.46972978115081787 True -4 13850 30.75689196586609 0.5452756881713867 321.7823791503906 0.22426506876945496 432.89068603515625 0.2652139365673065 0.8522782 0.27464208006858826 True -5 16620 30.75990867614746 0.5445101261138916 406.58489990234375 0.1735629141330719 431.6291809082031 0.26760348677635193 0.8545957 0.25367650389671326 True -6 19390 30.709429025650024 0.5447201728820801 367.029296875 0.20360568165779114 431.03033447265625 0.2680678069591522 0.857213 0.25884443521499634 True -7 22160 30.697351932525635 0.5457041263580322 407.9147644042969 0.20609547197818756 429.8760986328125 0.27045005559921265 0.86117303 0.24632351100444794 True -8 24930 30.72478222846985 0.5365324020385742 301.7528381347656 0.20318184792995453 429.406982421875 0.2714622914791107 0.8659643 0.23552517592906952 True -9 27700 30.685821771621704 0.6476268768310547 376.98541259765625 0.2491166889667511 428.3208312988281 0.27313870191574097 0.86749494 0.23366869986057281 True -10 30470 30.836655855178833 0.5814967155456543 362.41571044921875 0.15278053283691406 427.86578369140625 0.27382439374923706 0.8721665 0.21853359043598175 True -11 33240 30.82876491546631 0.5546467304229736 419.73779296875 0.1651022583246231 426.5622253417969 0.2760208249092102 0.876062 0.2091803252696991 True -12 36010 30.742064714431763 0.5585458278656006 340.8138732910156 0.31218793988227844 426.1046142578125 0.2766397297382355 0.8798116 0.19630053639411926 True -13 38780 30.741771459579468 0.5472943782806396 348.0142822265625 0.159183531999588 425.2437744140625 0.2780725061893463 0.88221306 0.18480385839939117 True -14 41550 30.721212148666382 1.1690990924835205 383.56512451171875 0.1460587978363037 424.6993713378906 0.2793174684047699 0.88525367 0.17442983388900757 True -15 44320 30.78835940361023 0.5515716075897217 376.0452880859375 0.1371707171201706 425.01397705078125 0.27863577008247375 0.8898239 0.16022580862045288 True -16 47090 30.810291290283203 1.190648078918457 335.9344482421875 0.13141736388206482 424.629638671875 0.2786805033683777 0.89041644 0.15419286489486694 True -17 49860 30.855161666870117 0.5616340637207031 428.6130065917969 0.08846857398748398 424.1108093261719 0.2799084186553955 0.8914609 0.1490880399942398 True -18 52630 31.458011388778687 0.5691847801208496 385.9670715332031 0.14667503535747528 424.31927490234375 0.2792106866836548 0.8931716 0.14694641530513763 True -19 55400 30.79697585105896 1.1390831470489502 291.5161437988281 0.1047254130244255 424.2545166015625 0.27944669127464294 0.8900711 0.14653265476226807 False diff --git a/ENCSR693UHT/cherimoya.fold_3.performance.tsv b/ENCSR693UHT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a22d11e68adfd6c67f4831c704f21da030e55fe8..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -424.31927490234375 0.48994526267051697 0.2792106866836548 0.08273984491825104 0.8931716084480286 0.8563847541809082 0.14694641530513763 \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_4.evaluate.json b/ENCSR693UHT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d0596002e77a095329e567531346cd0569bf0c70..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OMI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_4.fit.json b/ENCSR693UHT/cherimoya.fold_4.fit.json deleted file mode 100644 index a5ce9988bd91e78536e4e835ee2f599f2d93b656..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF378OMI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR693UHT/cherimoya.fold_4.log b/ENCSR693UHT/cherimoya.fold_4.log deleted file mode 100644 index c2061e1cc5d0e18d385ea86aa53fe6ed78202f09..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2791 35.63993859291077 3.927051544189453 349.329345703125 0.2621459364891052 436.7362365722656 0.1954617202281952 0.7546568 3.3298070430755615 True -1 5582 31.013814210891724 0.610485315322876 382.9136962890625 0.33206072449684143 410.0722351074219 0.24042004346847534 0.8047777 0.7163012623786926 True -2 8373 31.07641625404358 0.6312103271484375 419.7726745605469 0.1961001753807068 405.48675537109375 0.24623000621795654 0.8319819 0.3278457224369049 True -3 11164 31.040095806121826 0.5870378017425537 416.401123046875 0.12858250737190247 403.3377380371094 0.2497599869966507 0.83805686 0.2632136642932892 True -4 13955 31.062145471572876 1.138638973236084 445.20770263671875 0.3164152503013611 401.9742431640625 0.25190043449401855 0.8471855 0.23470495641231537 True -5 16746 31.026485919952393 0.6110439300537109 364.05731201171875 0.2647528052330017 401.3196105957031 0.25274720788002014 0.8513975 0.22532683610916138 True -6 19537 31.02243208885193 0.6056914329528809 345.11083984375 0.21980249881744385 400.726318359375 0.25366026163101196 0.85545844 0.2246668040752411 True -7 22328 31.337825298309326 0.6074931621551514 399.64923095703125 0.27188631892204285 399.3614501953125 0.2567724287509918 0.85533077 0.21089068055152893 False -8 25119 31.043712854385376 0.6120991706848145 356.6307373046875 0.17345520853996277 399.2509765625 0.2568250000476837 0.8583782 0.1926410049200058 True -9 27910 30.994417190551758 0.5910887718200684 363.62908935546875 0.1518332064151764 398.7460021972656 0.2577532231807709 0.86175185 0.18542665243148804 True -10 30701 31.040295600891113 0.598430871963501 353.9442443847656 0.23815447092056274 398.1798400878906 0.25869402289390564 0.86511934 0.17491188645362854 True -11 33492 30.97084951400757 0.6007976531982422 288.18170166015625 0.09835365414619446 397.1901550292969 0.2606865465641022 0.86846876 0.16783690452575684 True -12 36283 30.973557949066162 0.581489086151123 348.97698974609375 0.31493449211120605 396.8130798339844 0.2608148455619812 0.8733207 0.1572141945362091 True -13 39074 30.986383199691772 20.593259811401367 356.15985107421875 0.2483363002538681 396.096923828125 0.2624376118183136 0.87607914 0.14836567640304565 True -14 41865 31.164304494857788 0.5950922966003418 345.42755126953125 0.1990172415971756 396.00537109375 0.26219525933265686 0.87950397 0.14026518166065216 True -15 44656 30.986724138259888 0.5893068313598633 401.2260437011719 0.18993821740150452 396.0987854003906 0.26210907101631165 0.8829862 0.1359245926141739 True -16 47447 31.00018882751465 1.3233487606048584 378.9449462890625 0.14636628329753876 395.5375671386719 0.2641545534133911 0.88544375 0.13012686371803284 True -17 50238 31.08414626121521 0.641167402267456 353.65692138671875 0.1406300961971283 395.2531433105469 0.2641945779323578 0.8862982 0.12887130677700043 True -18 53029 31.132238388061523 0.6445376873016357 378.7112121582031 0.15578991174697876 395.1783752441406 0.2643619179725647 0.8866895 0.1275763064622879 True -19 55820 31.065941333770752 0.6436824798583984 408.0939636230469 0.1650235652923584 395.72039794921875 0.2626625895500183 0.8868638 0.12779991328716278 True diff --git a/ENCSR693UHT/cherimoya.fold_4.performance.tsv b/ENCSR693UHT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2565ec4226ab9a21f825b5f321e8906e031e6eef..0000000000000000000000000000000000000000 --- a/ENCSR693UHT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -395.72039794921875 0.5034257173538208 0.2626625895500183 0.07695909589529037 0.8868638277053833 0.8470746278762817 0.12779991328716278 \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_0.evaluate.json b/ENCSR694OWY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ae8d635120bb101f2ccd7efc363f28041c3d1acd..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259UMJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_0.fit.json b/ENCSR694OWY/cherimoya.fold_0.fit.json deleted file mode 100644 index 5b1aa3507b5c0cc0e2799c6eaa53012b1109c8ed..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF259UMJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_0.log b/ENCSR694OWY/cherimoya.fold_0.log deleted file mode 100644 index 3ede322618cf64e4cef66d7c8d4240cf9e6ee4d8..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2838 35.96064352989197 4.1011271476745605 363.2541198730469 0.11537951976060867 453.2041320800781 0.6620280742645264 0.798741 3.5199615955352783 True -1 5676 31.06900906562805 0.7755465507507324 364.1073913574219 0.12713034451007843 426.06475830078125 0.7061699032783508 0.7954615 0.12035118788480759 False -2 8514 31.489891529083252 0.7091078758239746 359.76605224609375 0.13641899824142456 419.8370666503906 0.7164131999015808 0.812232 0.05580597743391991 True -3 11352 31.469861268997192 0.9397897720336914 363.7373046875 0.19015111029148102 417.4541931152344 0.7200593948364258 0.8177009 0.051063422113657 True -4 14190 31.49266529083252 1.5920860767364502 372.3557434082031 0.0882355347275734 416.3638000488281 0.7225432395935059 0.82051957 0.054814763367176056 True -5 17028 31.495194911956787 1.1400642395019531 358.10479736328125 0.07465432584285736 415.3674621582031 0.7245380878448486 0.8221586 0.060538213700056076 True -6 19866 31.485738039016724 0.6316630840301514 350.0123291015625 0.10357498377561569 414.87640380859375 0.7255251407623291 0.82163256 0.0616564005613327 False -7 22704 31.459895372390747 0.6415195465087891 362.5706787109375 0.08365722745656967 413.9943542480469 0.7274012565612793 0.8269737 0.05715078115463257 True -8 25542 31.43123173713684 1.275899887084961 355.0667419433594 0.09060591459274292 413.2882995605469 0.7288508415222168 0.8299137 0.05600956082344055 True -9 28380 31.458664655685425 0.6396334171295166 352.3119201660156 0.09093914926052094 412.5633850097656 0.7304248809814453 0.8332517 0.05580460652709007 True -10 31218 31.490959882736206 0.6398377418518066 336.48150634765625 0.1155843734741211 411.9811096191406 0.7319280505180359 0.8364029 0.0506158210337162 True -11 34056 31.424566984176636 0.6303167343139648 364.42529296875 0.05948808789253235 411.2225646972656 0.7334690690040588 0.83974445 0.049224548041820526 True -12 36894 31.533581733703613 1.7500431537628174 365.0379943847656 0.09037135541439056 410.4497985839844 0.735228955745697 0.8420934 0.047111812978982925 True -13 39732 31.438525915145874 0.8295912742614746 346.8734130859375 0.0568435974419117 409.7716979980469 0.7367818355560303 0.8453906 0.04463357478380203 True -14 42570 31.420204877853394 0.6426122188568115 376.5574035644531 0.054259900003671646 409.3572082519531 0.7377885580062866 0.8464415 0.04370588809251785 True -15 45408 31.528984785079956 0.639467716217041 344.46759033203125 0.1497625857591629 408.946533203125 0.7385766506195068 0.8469765 0.043240129947662354 True -16 48246 31.438170671463013 0.627610445022583 349.7801818847656 0.058474354445934296 408.70806884765625 0.7391752600669861 0.847066 0.04385948181152344 True -17 51084 31.466580390930176 0.6387355327606201 375.4878845214844 0.065005823969841 408.5726318359375 0.739361047744751 0.8467899 0.045033711940050125 False -18 53922 31.540679693222046 0.6555185317993164 339.236572265625 0.07814845442771912 408.5466613769531 0.7391741871833801 0.84442675 0.046152543276548386 False -19 56760 31.488443613052368 0.6385657787322998 361.93359375 0.09001834690570831 408.6263122558594 0.7390693426132202 0.8419934 0.047054875642061234 False diff --git a/ENCSR694OWY/cherimoya.fold_0.performance.tsv b/ENCSR694OWY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 899fdd9bbdcbdc905342b4facc9382e4a9f04f2b..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -408.70806884765625 0.2160109132528305 0.7391752600669861 0.3118347227573395 0.8470659852027893 0.8621985912322998 0.04385948181152344 \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_1.evaluate.json b/ENCSR694OWY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 89ffa019761117a114feb0f80716324d0cdfc4de..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259UMJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_1.fit.json b/ENCSR694OWY/cherimoya.fold_1.fit.json deleted file mode 100644 index f2b90c42194e4b57ca208e1f7d016a107d11f20b..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF259UMJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_1.log b/ENCSR694OWY/cherimoya.fold_1.log deleted file mode 100644 index ee6c70e852fc62adee4c8645cdf98db5c3178d29..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 35.783714056015015 3.92122483253479 376.4964599609375 0.1798522174358368 457.5267333984375 0.6459080576896667 0.7769709 3.670896291732788 True -1 5584 31.0168354511261 1.1076123714447021 368.2101745605469 0.1050424724817276 428.1120910644531 0.6945871710777283 0.78080565 0.14729608595371246 True -2 8376 31.334627151489258 0.6853861808776855 363.9708251953125 0.20267362892627716 420.5800476074219 0.7076480984687805 0.7923689 0.06849435716867447 True -3 11168 30.872076988220215 0.685396671295166 384.69183349609375 0.10808487236499786 416.4731750488281 0.7150779962539673 0.80027217 0.05873318761587143 True -4 13960 30.325071811676025 0.6201901435852051 350.1904296875 0.1607653796672821 414.8382263183594 0.7183277606964111 0.79907113 0.06589733064174652 False -5 16752 30.34962034225464 0.6213729381561279 369.70953369140625 0.08997943997383118 413.7011413574219 0.7202075123786926 0.80521494 0.0662669837474823 True -6 19544 30.364105463027954 0.6195871829986572 375.9114074707031 0.07235301285982132 412.4764404296875 0.7226110100746155 0.80863005 0.06448239833116531 True -7 22336 30.435935735702515 0.6338057518005371 368.8548583984375 0.08691714704036713 411.4924621582031 0.7247121930122375 0.81242454 0.06303751468658447 True -8 25128 30.377045154571533 0.6391851902008057 361.29229736328125 0.11841970682144165 410.5329895019531 0.726557731628418 0.81964934 0.06101100891828537 True -9 27920 30.571675300598145 0.6492292881011963 357.4052734375 0.09131905436515808 409.6731262207031 0.7285609245300293 0.821614 0.05890290066599846 True -10 30712 30.359302759170532 0.6319727897644043 393.78704833984375 0.08047646284103394 408.4949951171875 0.7311100363731384 0.82688826 0.05499975383281708 True -11 33504 30.309658527374268 0.6341884136199951 357.508544921875 0.125448077917099 407.6207580566406 0.7330413460731506 0.8341098 0.053033649921417236 True -12 36296 30.447400331497192 0.6590976715087891 357.22271728515625 0.1342664211988449 406.5051574707031 0.7353737950325012 0.840357 0.05079502612352371 True -13 39088 30.327292442321777 1.1467618942260742 352.687255859375 0.05053316801786423 405.6077575683594 0.7373241782188416 0.8423336 0.04866829514503479 True -14 41880 30.49943232536316 0.6271374225616455 327.10247802734375 0.1419905126094818 404.9669189453125 0.7387917041778564 0.84657013 0.046938683837652206 True -15 44672 30.328871488571167 0.6188645362854004 348.6224365234375 0.07893244177103043 404.4306945800781 0.7399209141731262 0.84914064 0.04584227129817009 True -16 47464 30.40410876274109 4.240673065185547 340.01605224609375 0.09586648643016815 404.0306091308594 0.7407430410385132 0.84796184 0.046045105904340744 False -17 50256 30.36523723602295 0.6240847110748291 375.36859130859375 0.06915488839149475 403.8858642578125 0.7408899068832397 0.85037935 0.04657610505819321 True -18 53048 30.313016891479492 0.6253118515014648 345.53851318359375 0.04550908878445625 403.8664855957031 0.7409042716026306 0.84838444 0.0477796345949173 False -19 55840 30.30707359313965 0.6070668697357178 336.9634094238281 0.048922598361968994 403.8752746582031 0.7408229112625122 0.84675115 0.04804038628935814 False diff --git a/ENCSR694OWY/cherimoya.fold_1.performance.tsv b/ENCSR694OWY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 264db5c0e42fcde68ff8fd6f819d0d80fece653e..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -403.8858642578125 0.21693582832813263 0.740889847278595 0.30608153343200684 0.8503793478012085 0.8527818322181702 0.04657610505819321 \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_2.evaluate.json b/ENCSR694OWY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index fdde9fcde44b431931b4a6880c663a348711661c..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259UMJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_2.fit.json b/ENCSR694OWY/cherimoya.fold_2.fit.json deleted file mode 100644 index 4ffcae68b3ced958fa06871003bdfe0a50bb15b6..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF259UMJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_2.log b/ENCSR694OWY/cherimoya.fold_2.log deleted file mode 100644 index 7281951e8fc81b59455f54792b7fc70f4f1f33f4..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2947 37.32554912567139 4.176738739013672 336.3519592285156 0.09419582784175873 466.9057922363281 0.6636542081832886 0.7925201 2.999586820602417 True -1 5894 32.652754068374634 0.7169263362884521 349.88616943359375 0.19218310713768005 440.6563720703125 0.7058723568916321 0.7810965 0.11443006247282028 False -2 8841 32.672985553741455 0.6167135238647461 368.75445556640625 0.13107404112815857 433.4598388671875 0.7162846326828003 0.7953116 0.06311778724193573 True -3 11788 32.673622131347656 0.6016170978546143 387.21923828125 0.060698360204696655 430.7877197265625 0.7213596105575562 0.79806316 0.060475632548332214 True -4 14735 32.731399059295654 0.5786385536193848 350.82012939453125 0.1771605908870697 429.6180114746094 0.7235280275344849 0.8017387 0.06946671009063721 True -5 17682 32.53743863105774 0.5781714916229248 363.47015380859375 0.08396274596452713 428.7851257324219 0.7250069975852966 0.803377 0.06921364367008209 True -6 20629 31.964932680130005 0.5900511741638184 383.42803955078125 0.0572444386780262 427.713134765625 0.7271882891654968 0.80773586 0.0672207698225975 True -7 23576 31.9711172580719 0.5710692405700684 358.50457763671875 0.05662639066576958 426.9079284667969 0.7288220524787903 0.811879 0.06721022725105286 True -8 26523 32.032896757125854 0.5888526439666748 343.49237060546875 0.0852850079536438 426.02978515625 0.7305866479873657 0.8120663 0.06454233825206757 True -9 29470 32.06391978263855 0.5856776237487793 369.5635986328125 0.059842243790626526 425.19757080078125 0.7325586080551147 0.8142796 0.06312660872936249 True -10 32417 32.00516080856323 0.5842108726501465 385.8211975097656 0.07855691015720367 424.435791015625 0.7340130805969238 0.81767666 0.06289102137088776 True -11 35364 32.03136205673218 0.5874781608581543 378.452392578125 0.06555788964033127 423.57415771484375 0.735884964466095 0.8227508 0.0588887482881546 True -12 38311 31.964364051818848 0.585284948348999 362.01318359375 0.05324468016624451 422.70745849609375 0.737549364566803 0.8257519 0.05528721213340759 True -13 41258 32.034974575042725 0.5927584171295166 339.3934631347656 0.1621893346309662 421.9355163574219 0.7391980886459351 0.82902884 0.05269351229071617 True -14 44205 32.145105600357056 0.6189935207366943 333.578857421875 0.06561292707920074 421.3096008300781 0.7405407428741455 0.8312717 0.051630742847919464 True -15 47152 32.22120141983032 0.5818390846252441 346.8759460449219 0.045488785952329636 420.7290954589844 0.741538405418396 0.83410054 0.051100436598062515 True -16 50099 32.12844204902649 0.5912148952484131 351.0531311035156 0.11939053237438202 420.4814453125 0.7420211434364319 0.83412343 0.051437221467494965 True -17 53046 32.113831758499146 0.5834314823150635 345.9131774902344 0.0487995371222496 420.4157409667969 0.7422161102294922 0.8348693 0.052584052085876465 True -18 55993 32.28773260116577 0.591439962387085 370.4751281738281 0.03879208117723465 420.3663635253906 0.74212646484375 0.83295953 0.05424661934375763 False -19 58940 32.10248398780823 0.5797955989837646 334.5574951171875 0.0670875832438469 420.4291687011719 0.7420141696929932 0.8337182 0.05442392826080322 False diff --git a/ENCSR694OWY/cherimoya.fold_2.performance.tsv b/ENCSR694OWY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index abf65c3d9d96391eee40457c4d6addfb5abf1dfc..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -420.4157409667969 0.21254472434520721 0.7422160506248474 0.3208547532558441 0.8348693251609802 0.8492333292961121 0.052584052085876465 \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_3.evaluate.json b/ENCSR694OWY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 45809a806fbef979844a9ea456b73079248e4514..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259UMJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_3.fit.json b/ENCSR694OWY/cherimoya.fold_3.fit.json deleted file mode 100644 index 8f076af9dc5e4fe509ac103413b866a59644e178..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF259UMJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_3.log b/ENCSR694OWY/cherimoya.fold_3.log deleted file mode 100644 index 70b84bc01b602e666f4beef01a6817638c65730f..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 35.76957178115845 4.303350210189819 351.0511474609375 0.1170276403427124 444.1316223144531 0.6515468955039978 0.75536597 3.6876797676086426 True -1 5584 31.27361035346985 0.5698661804199219 370.85321044921875 0.10767203569412231 415.58984375 0.6984715461730957 0.73853594 0.11816581338644028 False -2 8376 31.14484977722168 0.5994970798492432 355.3789978027344 0.0938258022069931 408.0220031738281 0.7107082605361938 0.7578399 0.07196076214313507 True -3 11168 31.137532949447632 0.5629873275756836 359.54327392578125 0.10278278589248657 405.7172546386719 0.7152561545372009 0.7627401 0.06957068294286728 True -4 13960 31.111510515213013 0.5559031963348389 354.938232421875 0.11670169234275818 404.6891784667969 0.7175129055976868 0.76128954 0.0767202377319336 False -5 16752 31.04409885406494 0.5554466247558594 361.3873291015625 0.049084000289440155 404.1175842285156 0.7186748385429382 0.7647935 0.07777827233076096 True -6 19544 30.822383880615234 0.5478918552398682 366.10467529296875 0.07260435819625854 403.353271484375 0.7201316356658936 0.76992524 0.07081997394561768 True -7 22336 30.45376944541931 0.5792007446289062 334.3792419433594 0.06805206090211868 402.7819519042969 0.7212174534797668 0.7693196 0.0716727003455162 False -8 25128 30.510905265808105 1.0541045665740967 328.156005859375 0.12922942638397217 402.30194091796875 0.7227965593338013 0.770289 0.07213207334280014 True -9 27920 30.69236469268799 0.5763475894927979 355.49981689453125 0.095210000872612 401.811767578125 0.724729597568512 0.77598953 0.06927851587533951 True -10 30712 30.502150774002075 0.8298559188842773 365.707763671875 0.061498355120420456 401.2560119628906 0.7268375754356384 0.77966183 0.06586660444736481 True -11 33504 30.49940061569214 0.5530307292938232 372.5666198730469 0.07875928282737732 400.3608703613281 0.7283986806869507 0.7812242 0.06469181925058365 True -12 36296 30.51701521873474 0.5544531345367432 335.74371337890625 0.08222635090351105 399.7403564453125 0.7300886511802673 0.7867823 0.062320858240127563 True -13 39088 30.43313479423523 0.5545814037322998 355.1162109375 0.06366485357284546 399.06719970703125 0.7316648364067078 0.7842868 0.062367916107177734 False -14 41880 30.41218852996826 24.221665382385254 362.4593811035156 0.06777181476354599 398.6900939941406 0.732757568359375 0.786755 0.061529114842414856 False -15 44672 30.69689393043518 0.5551095008850098 359.4712829589844 0.10148884356021881 398.2454528808594 0.7336889505386353 0.78756183 0.061471126973629 True -16 47464 30.59400463104248 0.5597424507141113 332.708740234375 0.09051421284675598 398.10357666015625 0.7341706156730652 0.7873646 0.0615670382976532 False -17 50256 30.47510838508606 0.548365592956543 353.9161376953125 0.03879067301750183 397.9799499511719 0.7342435121536255 0.7847267 0.06318578124046326 False -18 53048 30.473166465759277 0.5544736385345459 358.1557312011719 0.08084851503372192 397.9647216796875 0.7342332005500793 0.78359234 0.06461825221776962 False -19 55840 30.460640907287598 0.5612847805023193 356.57855224609375 0.0389004647731781 397.9835205078125 0.7341210842132568 0.78554314 0.06456603109836578 False diff --git a/ENCSR694OWY/cherimoya.fold_3.performance.tsv b/ENCSR694OWY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ec3256af1339edc2b9ab21d6bc6d7afae9dc127a..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -398.2454528808594 0.22097903490066528 0.7336889505386353 0.3012191951274872 0.78756183385849 0.8407106995582581 0.061471126973629 \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_4.evaluate.json b/ENCSR694OWY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 90dc91a6671527cf8c881423f83c7c115ab16e2f..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF259UMJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_4.fit.json b/ENCSR694OWY/cherimoya.fold_4.fit.json deleted file mode 100644 index 3ae19392303615c3d1203b1567966dc53ea62b94..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF259UMJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR694OWY/cherimoya.fold_4.log b/ENCSR694OWY/cherimoya.fold_4.log deleted file mode 100644 index 4cf0107ef66b1df75919ead19ea7de457fc5e562..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2957 37.833024978637695 4.634565114974976 351.6664733886719 0.07440268993377686 451.5786437988281 0.6707311868667603 0.82923394 2.9252681732177734 True -1 5914 32.831908226013184 1.2073912620544434 375.30902099609375 0.10117325186729431 427.36962890625 0.7106921076774597 0.83270085 0.10407387465238571 True -2 8871 32.799564838409424 1.367499589920044 368.7967834472656 0.08096132427453995 422.5362548828125 0.7188287377357483 0.84124243 0.052814073860645294 True -3 11828 32.80265283584595 3.2341949939727783 357.22332763671875 0.10105032473802567 420.6986083984375 0.7220984697341919 0.843086 0.046966977417469025 True -4 14785 32.215803146362305 1.2553410530090332 352.7196044921875 0.08664900809526443 419.52911376953125 0.7243807315826416 0.8449904 0.049377165734767914 True -5 17742 32.105518102645874 0.7008812427520752 351.8193359375 0.1128690242767334 419.0854797363281 0.7254327535629272 0.8465092 0.04668022319674492 True -6 20699 32.06175422668457 0.6647040843963623 360.09759521484375 0.11364774405956268 418.4906921386719 0.7265265583992004 0.8494857 0.045348577201366425 True -7 23656 32.06691360473633 0.7741203308105469 364.21588134765625 0.042582444846630096 417.86334228515625 0.7278158664703369 0.8498695 0.046075254678726196 True -8 26613 32.111106395721436 0.6961746215820312 359.674560546875 0.1343468725681305 417.1737060546875 0.7294072508811951 0.8526042 0.04653508961200714 True -9 29570 32.099783182144165 0.7244303226470947 355.65802001953125 0.14762750267982483 416.4785461425781 0.7309926748275757 0.8579449 0.045963630080223083 True -10 32527 32.10528612136841 0.6971359252929688 332.3099365234375 0.09358449280261993 415.8541564941406 0.7324308753013611 0.8606511 0.04445508122444153 True -11 35484 32.25521922111511 0.6964607238769531 339.5555419921875 0.0884619876742363 415.1667175292969 0.7340856790542603 0.86386 0.04231042042374611 True -12 38441 32.235410928726196 0.6966793537139893 356.2120361328125 0.05120417848229408 414.4919738769531 0.7355263233184814 0.8679136 0.040379296988248825 True -13 41398 32.2441668510437 1.5848805904388428 359.4629211425781 0.046567726880311966 414.1031799316406 0.7365272641181946 0.8673715 0.039055775851011276 False -14 44355 32.28225564956665 0.7024493217468262 346.0130615234375 0.07369843125343323 413.7037048339844 0.7374892830848694 0.86966664 0.03762231767177582 True -15 47312 32.3380184173584 20.307158946990967 361.60723876953125 0.05586625635623932 413.3005065917969 0.7383331656455994 0.87193346 0.03749365732073784 True -16 50269 32.20341229438782 0.6913352012634277 345.5756530761719 0.055909663438797 413.09197998046875 0.7388748526573181 0.8737016 0.0377177931368351 True -17 53226 32.2892279624939 0.7137882709503174 342.9298095703125 0.07395903766155243 413.0343322753906 0.738917887210846 0.87306666 0.03853506222367287 False -18 56183 32.17936611175537 0.6945381164550781 372.9268493652344 0.02876078337430954 413.082275390625 0.7388468980789185 0.87083334 0.04021960124373436 False -19 59140 32.178892374038696 0.7036070823669434 342.592041015625 0.06698178499937057 413.1075744628906 0.7386828064918518 0.871441 0.040696658194065094 False diff --git a/ENCSR694OWY/cherimoya.fold_4.performance.tsv b/ENCSR694OWY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5b5aca5d314c45f9fa6bea8534ab83ac3f84e0af..0000000000000000000000000000000000000000 --- a/ENCSR694OWY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -413.09197998046875 0.21503856778144836 0.7388748526573181 0.3152056634426117 0.8737015724182129 0.8839884400367737 0.0377177931368351 \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_0.evaluate.json b/ENCSR695AUY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3511bf17a682bb1af056fab7ab9644c0e8c2bb28..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF377KFT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_0.fit.json b/ENCSR695AUY/cherimoya.fold_0.fit.json deleted file mode 100644 index ea28c683b438cebefb536095e75c1d09e0763c07..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF377KFT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_0.log b/ENCSR695AUY/cherimoya.fold_0.log deleted file mode 100644 index 2d92e71f644d6ac1e4d95b8c7c62278bf559d0dc..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1567 21.62742304801941 2.5649259090423584 143.5926513671875 0.9164480566978455 236.99362182617188 0.11535771936178207 0.3321969 8.078015327453613 True -1 3134 17.038389205932617 0.3014500141143799 169.59661865234375 1.1056060791015625 218.39028930664062 0.1958150863647461 0.46025175 5.811280727386475 True -2 4701 17.034015655517578 0.30230283737182617 147.35205078125 0.9755454063415527 200.62161254882812 0.245221808552742 0.59986454 3.0072226524353027 True -3 6268 17.00741696357727 0.2972450256347656 147.07650756835938 0.697291374206543 195.57443237304688 0.25662755966186523 0.63310665 1.5097779035568237 True -4 7835 17.042903900146484 0.2965219020843506 150.58653259277344 0.9418559074401855 193.42872619628906 0.2623562216758728 0.6517168 1.1298294067382812 True -5 9402 17.043447732925415 3.0993692874908447 128.8822479248047 0.650518536567688 192.02822875976562 0.26676198840141296 0.66651785 1.0190001726150513 True -6 10969 17.08694362640381 0.30530643463134766 174.5146484375 0.5026369094848633 191.18898010253906 0.2681361138820648 0.67677784 0.8898241519927979 True -7 12536 17.04013967514038 0.30664825439453125 144.9449462890625 0.7128772735595703 190.90480041503906 0.26860320568084717 0.68131554 0.8700928688049316 True -8 14103 17.04096508026123 0.29922962188720703 152.1478271484375 0.6687760353088379 190.0373077392578 0.2714756429195404 0.6894661 0.7834789156913757 True -9 15670 17.08413577079773 0.2951805591583252 165.26544189453125 0.8129878044128418 189.622802734375 0.2718270421028137 0.6977545 0.7370980978012085 True -10 17237 17.020787000656128 0.30322885513305664 154.161865234375 0.5685776472091675 188.6614990234375 0.2758346199989319 0.70622265 0.7057750225067139 True -11 18804 17.02210569381714 0.2988860607147217 137.58155822753906 0.7280924320220947 188.12184143066406 0.27749061584472656 0.71370167 0.6708293557167053 True -12 20371 17.00294303894043 0.3027963638305664 98.233642578125 0.5986781120300293 187.93600463867188 0.27679842710494995 0.7224104 0.6473300457000732 True -13 21938 17.006532430648804 0.2971208095550537 161.79800415039062 0.5843620896339417 187.4965362548828 0.27803000807762146 0.73019767 0.6214056611061096 True -14 23505 17.07376718521118 0.3038480281829834 139.829833984375 0.40842241048812866 187.41587829589844 0.2781064510345459 0.73639554 0.60965895652771 True -15 25072 17.048354148864746 0.8413181304931641 136.61631774902344 0.5472546815872192 187.2767791748047 0.2784213125705719 0.73910403 0.6059412360191345 True -16 26639 17.075632095336914 0.30785179138183594 132.68844604492188 0.44896334409713745 187.25340270996094 0.27907148003578186 0.73905295 0.6129636168479919 False -17 28206 17.197161436080933 14.503587245941162 132.45541381835938 0.3922004997730255 187.18890380859375 0.28003478050231934 0.73560154 0.6262286901473999 False -18 29773 18.584830284118652 6.571606397628784 142.56463623046875 0.303720086812973 187.44265747070312 0.2789361774921417 0.73233175 0.6454654932022095 False -19 31340 17.060697555541992 0.3063337802886963 169.81085205078125 0.41674721240997314 187.58558654785156 0.278171569108963 0.7304657 0.6578006148338318 False diff --git a/ENCSR695AUY/cherimoya.fold_0.performance.tsv b/ENCSR695AUY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f354d7e7be836cb6112651ed95673d5a49ef864f..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -187.2767791748047 0.5170589089393616 0.2784213423728943 0.06583110988140106 0.7391040325164795 0.7229228615760803 0.6059412360191345 \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_1.evaluate.json b/ENCSR695AUY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f32832ef524f2241d34b0e764ee86166f1cd27ed..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF377KFT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_1.fit.json b/ENCSR695AUY/cherimoya.fold_1.fit.json deleted file mode 100644 index 1989756c6a13f917ecb079c5507511957c56ced5..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF377KFT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_1.log b/ENCSR695AUY/cherimoya.fold_1.log deleted file mode 100644 index 354088146e779c3500a136b80cdf9335c43756de..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1556 21.419098138809204 3.7516093254089355 165.3909149169922 1.0258550643920898 262.3246765136719 0.12441857159137726 0.3311824 8.810946464538574 True -1 3112 16.949076890945435 0.4509410858154297 156.98492431640625 0.9686751365661621 243.06729125976562 0.20466908812522888 0.45776168 5.093591213226318 True -2 4668 17.052145957946777 0.43855834007263184 158.73138427734375 1.118760585784912 223.1770782470703 0.26581573486328125 0.56361264 3.271381139755249 True -3 6224 16.97851538658142 0.43792128562927246 152.4691162109375 0.7760016918182373 215.98263549804688 0.2807292342185974 0.6091422 1.843998670578003 True -4 7780 16.929473400115967 0.43749260902404785 190.30970764160156 0.9058939814567566 213.27078247070312 0.285542368888855 0.62799037 1.3558204174041748 True -5 9336 16.952889680862427 0.4322481155395508 155.4046630859375 0.7268773317337036 211.86839294433594 0.28927281498908997 0.6430939 1.1868013143539429 True -6 10892 16.949656009674072 5.096089601516724 154.9466094970703 0.924132227897644 210.8382110595703 0.29171091318130493 0.6553668 1.0688003301620483 True -7 12448 17.7660813331604 27.03119683265686 153.42611694335938 0.6711879372596741 210.17691040039062 0.29310065507888794 0.66155756 1.0040998458862305 True -8 14004 17.44147825241089 0.43784022331237793 119.08351135253906 0.5825451016426086 209.14382934570312 0.2980506122112274 0.6747479 0.9487207531929016 True -9 15560 16.97854995727539 0.4456291198730469 135.75033569335938 0.6530443429946899 208.6615753173828 0.29877814650535583 0.6848015 0.8915094137191772 True -10 17116 16.99472975730896 0.43543052673339844 161.62857055664062 0.6905688047409058 208.2790985107422 0.2990272045135498 0.6931652 0.8360993266105652 True -11 18672 17.106815099716187 0.4503951072692871 177.0343780517578 0.5121482610702515 207.81396484375 0.29991838335990906 0.7050436 0.7894546985626221 True -12 20228 17.046685934066772 0.45346784591674805 142.3498077392578 0.4762302339076996 206.74786376953125 0.303907185792923 0.71544397 0.7267215251922607 True -13 21784 17.0352041721344 0.4492475986480713 119.68609619140625 0.4726783037185669 206.450439453125 0.3047330379486084 0.72305864 0.6831181645393372 True -14 23340 17.002029180526733 0.44815802574157715 131.71511840820312 0.3698444366455078 206.35023498535156 0.3047133684158325 0.733966 0.6496345400810242 True -15 24896 17.060950756072998 0.4455130100250244 162.25103759765625 0.6248228549957275 206.55648803710938 0.3034014403820038 0.74005234 0.6343091726303101 True -16 26452 17.00998044013977 0.45049190521240234 144.15296936035156 0.5804431438446045 206.56689453125 0.30336856842041016 0.7420948 0.6293153762817383 True -17 28008 17.014408588409424 0.44687843322753906 152.59747314453125 0.4451799690723419 206.35037231445312 0.30525442957878113 0.74203885 0.627515435218811 False -18 29564 17.014923334121704 0.44063663482666016 140.11117553710938 0.252926230430603 206.892333984375 0.30241429805755615 0.74004453 0.637638509273529 False -19 31120 17.024332523345947 0.9917111396789551 129.046142578125 0.31833308935165405 207.1468505859375 0.3010116517543793 0.74007744 0.6445584297180176 False diff --git a/ENCSR695AUY/cherimoya.fold_1.performance.tsv b/ENCSR695AUY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6dc95592b09d00441027db220924d1fbf6e39eab..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -206.56689453125 0.5006586313247681 0.30336853861808777 0.06934652477502823 0.7420948147773743 0.7184506058692932 0.6293153762817383 \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_2.evaluate.json b/ENCSR695AUY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b150ee74a6cb3bdbf8453aaa02cb64dcc97a0140..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF377KFT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_2.fit.json b/ENCSR695AUY/cherimoya.fold_2.fit.json deleted file mode 100644 index cc231fc7665507f161dcd59274f0be180f440ad9..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF377KFT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_2.log b/ENCSR695AUY/cherimoya.fold_2.log deleted file mode 100644 index 7bdc93b71dc7ea516d8fbc7d01d3b346a3b5429d..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1680 22.604592323303223 3.331763505935669 157.4585723876953 1.0672249794006348 239.7384796142578 0.1183144673705101 0.31354892 7.484393119812012 True -1 3360 18.27185034751892 0.31775856018066406 151.37200927734375 1.0710783004760742 221.17982482910156 0.1916254609823227 0.458612 4.526801109313965 True -2 5040 18.193847179412842 0.3098440170288086 129.17449951171875 0.6407948732376099 202.41717529296875 0.24617469310760498 0.58967197 2.274775266647339 True -3 6720 17.960418224334717 0.30666661262512207 163.10601806640625 0.7697755098342896 197.0003204345703 0.26063108444213867 0.633244 1.4076822996139526 True -4 8400 17.94951629638672 0.29613280296325684 141.99790954589844 0.8112624287605286 195.7364501953125 0.26365500688552856 0.6456342 1.2084797620773315 True -5 10080 18.00576162338257 0.3006772994995117 172.07562255859375 0.8901406526565552 194.38209533691406 0.2682676911354065 0.659873 1.020875334739685 True -6 11760 17.98676061630249 0.3066558837890625 151.22628784179688 0.6630022525787354 193.89654541015625 0.26879024505615234 0.66567916 1.0144755840301514 True -7 13440 17.904017686843872 0.31099867820739746 135.60589599609375 0.6754592657089233 193.09259033203125 0.2709248661994934 0.6820168 0.9136794209480286 True -8 15120 17.981390714645386 0.30679988861083984 127.92727661132812 0.922431468963623 192.4423370361328 0.2720372676849365 0.69250053 0.8237378001213074 True -9 16800 18.008481979370117 0.3064451217651367 137.189697265625 0.7866471409797668 191.64088439941406 0.27480560541152954 0.6993033 0.7802996039390564 True -10 18480 17.9546320438385 0.31203603744506836 185.20811462402344 0.8996835947036743 191.18568420410156 0.275760293006897 0.7120971 0.7421474456787109 True -11 20160 17.905853271484375 12.835798501968384 134.92315673828125 0.5577559471130371 190.36212158203125 0.27872252464294434 0.7232237 0.6958429217338562 True -12 21840 20.522693872451782 10.18678593635559 149.94863891601562 0.503166913986206 189.84912109375 0.2805543839931488 0.7335189 0.6499983072280884 True -13 23520 17.933812856674194 0.3239762783050537 153.21676635742188 0.629730761051178 189.69558715820312 0.2797382175922394 0.7402694 0.622550904750824 True -14 25200 17.91549587249756 0.303800106048584 170.1165313720703 0.5449920892715454 189.40086364746094 0.2799101769924164 0.7462527 0.6024610996246338 True -15 26880 17.92240023612976 0.30188536643981934 142.7263946533203 0.6358733177185059 188.96572875976562 0.28164857625961304 0.7496105 0.5919468402862549 True -16 28560 17.981278657913208 0.3040130138397217 152.93490600585938 0.5335320830345154 189.25686645507812 0.2792726457118988 0.7537709 0.5863661170005798 True -17 30240 17.98194932937622 0.3143181800842285 129.6403350830078 0.4084765613079071 189.01675415039062 0.28101155161857605 0.7532534 0.5926774144172668 False -18 31920 17.929083824157715 0.30953240394592285 153.02110290527344 0.34929776191711426 189.15223693847656 0.2804867625236511 0.7507389 0.601753830909729 False -19 33600 18.0108003616333 0.72823166847229 127.01461791992188 0.428999125957489 189.22457885742188 0.28029564023017883 0.747789 0.6118856072425842 False diff --git a/ENCSR695AUY/cherimoya.fold_2.performance.tsv b/ENCSR695AUY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a0813e114b0faac4d9dacf88023a62d63ade659e..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -189.25686645507812 0.5164361000061035 0.2792726457118988 0.06745303422212601 0.7537708878517151 0.7326726317405701 0.5863661170005798 \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_3.evaluate.json b/ENCSR695AUY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9d60115df0ce9f465a87565e49338595668c8902..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF377KFT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_3.fit.json b/ENCSR695AUY/cherimoya.fold_3.fit.json deleted file mode 100644 index 6edbdb5cdaa23f0e1e5732b9360ed53a73b965e2..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF377KFT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_3.log b/ENCSR695AUY/cherimoya.fold_3.log deleted file mode 100644 index 4bdcdcfe02b34c39440690445f8beea159f80704..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1604 21.99429488182068 3.283668279647827 169.5023193359375 1.0227553844451904 246.18605041503906 0.11937325447797775 0.32315505 8.052891731262207 True -1 3208 17.45582675933838 0.33932042121887207 139.42025756835938 0.9164850115776062 226.34117126464844 0.2016405612230301 0.46180317 5.117061138153076 True -2 4812 17.495858430862427 0.32881903648376465 150.67816162109375 1.260885238647461 207.96044921875 0.25483545660972595 0.60055166 3.0044641494750977 True -3 6416 17.43449068069458 19.660478830337524 124.34385681152344 0.6677893400192261 203.47767639160156 0.26674988865852356 0.6194677 1.8079818487167358 True -4 8020 22.04099988937378 4.191356658935547 148.4241485595703 0.538786768913269 201.95411682128906 0.27196070551872253 0.63198245 1.568292498588562 True -5 9624 17.500521183013916 1.3113245964050293 155.56192016601562 0.7438706159591675 201.39683532714844 0.2726876437664032 0.6363552 1.440286636352539 True -6 11228 17.496214866638184 0.33126330375671387 152.9271697998047 0.7419066429138184 200.0236358642578 0.2783786654472351 0.64081365 1.297267198562622 True -7 12832 17.462223052978516 0.32605409622192383 145.87222290039062 0.6441760063171387 199.35736083984375 0.2796172797679901 0.6510385 1.197187900543213 True -8 14436 17.451000213623047 0.3297562599182129 155.7607879638672 0.570761501789093 199.1485595703125 0.27881523966789246 0.660277 1.0711606740951538 True -9 16040 17.485227346420288 0.38451433181762695 134.83975219726562 0.8273641467094421 198.17367553710938 0.28241485357284546 0.6725353 0.997530996799469 True -10 17644 17.47909188270569 0.33280158042907715 173.1562042236328 0.6966619491577148 197.3314971923828 0.2852146625518799 0.682456 0.9109616279602051 True -11 19248 17.468584060668945 0.3248617649078369 143.0462646484375 1.0000361204147339 196.64166259765625 0.287174254655838 0.69094676 0.8441506624221802 True -12 20852 17.46727967262268 0.32791924476623535 181.88607788085938 0.6639605760574341 196.15325927734375 0.2887687683105469 0.70274186 0.7843005657196045 True -13 22456 17.49898910522461 0.33865976333618164 132.16696166992188 0.6414781212806702 196.02769470214844 0.2881779968738556 0.7138653 0.7297416925430298 True -14 24060 17.46539878845215 0.3302140235900879 166.5970916748047 0.47628334164619446 195.37469482421875 0.2904816269874573 0.72189766 0.701752781867981 True -15 25664 18.24335241317749 11.352342367172241 165.63604736328125 0.5960486531257629 195.39779663085938 0.28967317938804626 0.727707 0.674924910068512 True -16 27268 17.451873779296875 0.35160160064697266 116.75298309326172 0.5540744066238403 195.3402862548828 0.28963834047317505 0.7328578 0.6607480049133301 True -17 28872 17.460343599319458 0.32449984550476074 120.12812805175781 0.3545042872428894 195.36085510253906 0.2899547219276428 0.73304564 0.6609251499176025 True -18 30476 17.46409010887146 0.3307168483734131 136.25473022460938 0.3476386070251465 195.32046508789062 0.2904917597770691 0.73098296 0.670458197593689 False -19 32080 17.478165864944458 0.332197904586792 145.79483032226562 0.21957527101039886 195.4811248779297 0.28963392972946167 0.7296774 0.6763216257095337 False diff --git a/ENCSR695AUY/cherimoya.fold_3.performance.tsv b/ENCSR695AUY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9d7b86764644b4289e323c549c9837db13fe9e3c..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -195.36085510253906 0.511210024356842 0.2899547219276428 0.06775202602148056 0.7330456376075745 0.7089654803276062 0.6609251499176025 \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_4.evaluate.json b/ENCSR695AUY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d4b8ec16c6e6191d85e9c4f79568e6d331ab30d5..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF377KFT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_4.fit.json b/ENCSR695AUY/cherimoya.fold_4.fit.json deleted file mode 100644 index 255ef337814e8835303e3254d3f54375ef7a85a9..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF377KFT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR695AUY/cherimoya.fold_4.log b/ENCSR695AUY/cherimoya.fold_4.log deleted file mode 100644 index e2609d50b042c307442f9c39c8b915beb33d9f60..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1613 22.289799690246582 3.4453787803649902 180.84567260742188 1.2299447059631348 223.0540313720703 0.1113242655992508 0.30436394 6.929841041564941 True -1 3226 18.0104341506958 0.37706875801086426 172.92941284179688 0.8398926258087158 207.0497283935547 0.18405096232891083 0.43755993 5.138072967529297 True -2 4839 17.59459924697876 0.8064415454864502 196.10479736328125 1.0841083526611328 190.0277557373047 0.2400263398885727 0.59592474 2.706303834915161 True -3 6452 17.57467222213745 0.31418323516845703 196.90147399902344 1.1393258571624756 185.1421356201172 0.2493564486503601 0.630372 1.4207292795181274 True -4 8065 17.747501134872437 13.464590072631836 155.23141479492188 0.8310203552246094 183.68362426757812 0.25239962339401245 0.64766824 1.1763314008712769 True -5 9678 17.618261098861694 0.31998300552368164 119.62052917480469 0.6101263761520386 182.3501739501953 0.2580431401729584 0.65427685 1.0254154205322266 True -6 11291 17.544238805770874 0.6950287818908691 171.99533081054688 0.8425347805023193 181.51348876953125 0.2602998614311218 0.66489494 0.9328458905220032 True -7 12904 17.546306848526 2.0447497367858887 115.96238708496094 0.7301068902015686 181.20921325683594 0.26084205508232117 0.6648179 0.9124335646629333 False -8 14517 17.605376482009888 0.31988072395324707 105.35659790039062 0.6707742214202881 180.38877868652344 0.2628716230392456 0.6747157 0.8524549007415771 True -9 16130 17.6258385181427 1.0258140563964844 155.10836791992188 0.7146356105804443 179.84654235839844 0.26417088508605957 0.69182175 0.7550071477890015 True -10 17743 17.636664390563965 0.32152295112609863 131.90652465820312 0.5183001756668091 179.59982299804688 0.2643611431121826 0.70112246 0.7234678864479065 True -11 19356 17.560328722000122 0.3193950653076172 136.46615600585938 0.5080188512802124 179.24061584472656 0.265669584274292 0.7090836 0.6734111309051514 True -12 20969 17.535221099853516 0.31807398796081543 152.63914489746094 0.7123645544052124 179.020263671875 0.265802800655365 0.71919394 0.6401515603065491 True -13 22582 17.56222629547119 0.3139503002166748 141.0321044921875 0.5436210632324219 178.52040100097656 0.26772692799568176 0.72784704 0.6141656637191772 True -14 24195 17.573262214660645 0.3170738220214844 142.31100463867188 0.6577620506286621 178.08566284179688 0.27004435658454895 0.73405105 0.5985194444656372 True -15 25808 17.57373857498169 0.31532788276672363 154.40615844726562 0.6001635193824768 178.1036376953125 0.26895254850387573 0.7403403 0.5804247856140137 True -16 27421 17.556108951568604 0.3160102367401123 137.738037109375 0.28686174750328064 178.1248016357422 0.26863551139831543 0.7449502 0.5798507332801819 True -17 29034 17.553316354751587 0.31307291984558105 127.38029479980469 0.41551268100738525 178.13583374023438 0.26879528164863586 0.7440201 0.5828889012336731 False -18 30647 17.60429358482361 0.31925034523010254 139.51451110839844 0.5047817230224609 178.2719268798828 0.2687932550907135 0.7409456 0.5955183506011963 False -19 32260 17.559252500534058 0.31911754608154297 152.39923095703125 0.28631746768951416 178.1890869140625 0.2698166072368622 0.7376678 0.6060269474983215 False diff --git a/ENCSR695AUY/cherimoya.fold_4.performance.tsv b/ENCSR695AUY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d00535057ce39c431d37f36ee8dfc49fbdf151d3..0000000000000000000000000000000000000000 --- a/ENCSR695AUY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -178.1248016357422 0.5242694020271301 0.26863551139831543 0.06301840394735336 0.7449501752853394 0.7222597599029541 0.5798507332801819 \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_0.evaluate.json b/ENCSR697FME/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c06721b795292d8224e99e4a76551d80c7c9e6aa..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695GCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_0.fit.json b/ENCSR697FME/cherimoya.fold_0.fit.json deleted file mode 100644 index 80e463b0f758a81a73505ffd22a5a1a723c06131..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF695GCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_0.log b/ENCSR697FME/cherimoya.fold_0.log deleted file mode 100644 index 5d450730fe311c33b106bfe7830110afb7d8883e..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2236 32.24879240989685 3.840959310531616 213.21990966796875 0.7495840191841125 366.9372253417969 0.13209058344364166 0.6432832 7.290038108825684 True -1 4472 24.829461097717285 0.6112320423126221 320.18804931640625 1.070930004119873 313.0496826171875 0.18591751158237457 0.7528405 3.4271433353424072 True -2 6708 24.83683705329895 0.501204252243042 246.29440307617188 0.9907158017158508 300.1622619628906 0.19500504434108734 0.7603912 2.018662214279175 True -3 8944 24.805646896362305 0.47914576530456543 226.98477172851562 0.7324652671813965 294.4496765136719 0.19856904447078705 0.7691709 1.4552178382873535 True -4 11180 24.75021457672119 0.48509955406188965 173.10279846191406 0.5856853723526001 290.3492736816406 0.20150648057460785 0.7896433 1.1592166423797607 True -5 13416 24.754297018051147 0.4835031032562256 232.51788330078125 0.8740211725234985 286.3031005859375 0.20426662266254425 0.7965591 0.9632655382156372 True -6 15652 24.755815505981445 0.4760301113128662 269.1289367675781 0.8205373883247375 284.1454162597656 0.20745861530303955 0.80679053 0.918881893157959 True -7 17888 24.769518852233887 0.47467851638793945 215.9227294921875 0.4380175769329071 281.5379943847656 0.20942148566246033 0.8170703 0.7826546430587769 True -8 20124 24.746328830718994 0.4733269214630127 314.44140625 0.9259442090988159 279.0709228515625 0.21267034113407135 0.82492787 0.6921784281730652 True -9 22360 24.733832597732544 1.1725540161132812 257.8732604980469 0.7894027829170227 278.12994384765625 0.21387822926044464 0.8262877 0.6936732530593872 True -10 24596 24.72393274307251 0.4728882312774658 253.17422485351562 0.6637868285179138 276.9031982421875 0.2153608649969101 0.8344779 0.6270227432250977 True -11 26832 24.745290994644165 0.47823476791381836 202.84329223632812 0.5048094391822815 275.141845703125 0.2181725651025772 0.83844286 0.5808800458908081 True -12 29068 24.737878799438477 0.4769139289855957 231.66983032226562 0.420261412858963 274.7017822265625 0.2176826149225235 0.84528255 0.552276074886322 True -13 31304 24.74846625328064 0.5038526058197021 204.05169677734375 0.46153128147125244 273.4409484863281 0.21921761333942413 0.8476036 0.5274466872215271 True -14 33540 24.824503183364868 0.47169017791748047 202.0458221435547 0.5381906628608704 271.9914245605469 0.2211998552083969 0.8537636 0.5098938345909119 True -15 35776 24.825055599212646 0.5167434215545654 269.92218017578125 1.0218642950057983 270.5424499511719 0.2231503129005432 0.85538363 0.49598971009254456 True -16 38012 24.78952980041504 0.5535080432891846 219.62405395507812 0.37538474798202515 270.63458251953125 0.22250738739967346 0.8607362 0.4824278652667999 True -17 40248 24.769323110580444 0.46953916549682617 222.98666381835938 0.5584436058998108 270.5888671875 0.22219498455524445 0.8590419 0.47642213106155396 False -18 42484 24.4502010345459 0.4689621925354004 206.98684692382812 0.4349559247493744 270.9550476074219 0.22169286012649536 0.85974926 0.4751192629337311 False -19 44720 24.29105520248413 0.4745364189147949 185.95489501953125 0.4255984425544739 271.1029968261719 0.2215714156627655 0.85952926 0.4779072105884552 False diff --git a/ENCSR697FME/cherimoya.fold_0.performance.tsv b/ENCSR697FME/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f7df002b6525174db7cc797b2f0d8b80f644ef7b..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -270.63458251953125 0.5347625017166138 0.22250738739967346 0.06826300173997879 0.8607361912727356 0.7857027649879456 0.4824278652667999 \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_1.evaluate.json b/ENCSR697FME/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9bfa3af011bd18c66376b14611d4ba4a6c400201..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695GCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_1.fit.json b/ENCSR697FME/cherimoya.fold_1.fit.json deleted file mode 100644 index ad069609cbc329c9e4896ee4fa9506d24f2b6ae3..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF695GCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_1.log b/ENCSR697FME/cherimoya.fold_1.log deleted file mode 100644 index 944439e5cd9dfd23c2fb9d52eac803890e937e1f..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2189 28.58830428123474 3.491061210632324 257.79205322265625 1.205114483833313 479.29815673828125 0.1463957130908966 0.62301666 8.608980178833008 True -1 4378 24.35613465309143 0.6036655902862549 283.27130126953125 1.1100447177886963 408.062255859375 0.2105449140071869 0.73315006 4.947064399719238 True -2 6567 24.321699619293213 0.6556065082550049 322.649169921875 0.938805341720581 394.24859619140625 0.21828605234622955 0.7404055 3.1769049167633057 True -3 8756 24.299046754837036 0.604191780090332 189.38905334472656 0.8126448392868042 377.7890625 0.22701974213123322 0.7840473 1.633512258529663 True -4 10945 24.272918462753296 0.6062450408935547 250.32652282714844 0.9700305461883545 371.0830078125 0.23282083868980408 0.7996964 1.276532769203186 True -5 13134 24.280624389648438 0.5939741134643555 234.6442108154297 0.8222023248672485 364.14990234375 0.23899023234844208 0.81217116 1.213395118713379 True -6 15323 24.26712989807129 0.603663444519043 211.93235778808594 0.9514432549476624 359.7309875488281 0.24414919316768646 0.8176124 1.1362131834030151 True -7 17512 24.32393527030945 0.6076710224151611 305.7711486816406 0.799769401550293 357.6800231933594 0.24594558775424957 0.8250717 1.0871405601501465 True -8 19701 24.244972467422485 2.252882480621338 147.0209197998047 0.8732973337173462 354.3671875 0.24905379116535187 0.8326409 0.9488087296485901 True -9 21890 24.321961402893066 1.5623462200164795 242.7294158935547 0.577675461769104 351.5223693847656 0.2515663206577301 0.8385057 0.8871763348579407 True -10 24079 24.291316032409668 0.6346426010131836 294.3487548828125 0.9677774310112 348.24371337890625 0.25539112091064453 0.8461617 0.7743097543716431 True -11 26268 24.251838445663452 0.6092181205749512 206.77354431152344 0.8927525281906128 347.0677795410156 0.2555367052555084 0.8513749 0.7208351492881775 True -12 28457 24.293678283691406 0.5929980278015137 187.15911865234375 0.5875828862190247 345.30572509765625 0.2573707103729248 0.8556016 0.6729297637939453 True -13 30646 24.281524419784546 0.6013631820678711 189.20565795898438 0.39765554666519165 344.6187744140625 0.257245272397995 0.86143106 0.6130516529083252 True -14 32835 24.258683443069458 0.6142430305480957 244.47459411621094 0.8705981373786926 342.4517517089844 0.2595473527908325 0.865601 0.5956581234931946 True -15 35024 24.24514675140381 0.6121373176574707 220.72576904296875 0.6199297904968262 340.1908874511719 0.2611680030822754 0.8693131 0.5839312672615051 True -16 37213 24.315566778182983 0.6107845306396484 181.0670166015625 0.5728791356086731 340.62823486328125 0.26090043783187866 0.8719503 0.5741333961486816 True -17 39402 24.298527002334595 0.6121633052825928 223.2452392578125 0.3726346790790558 339.5482482910156 0.2619327902793884 0.8723401 0.5676153302192688 True -18 41591 24.272095203399658 0.6077256202697754 215.798583984375 0.4137924313545227 341.01806640625 0.260047972202301 0.87106603 0.572782039642334 False -19 43780 24.262883186340332 0.6242995262145996 273.1390380859375 0.3339531421661377 341.3844299316406 0.26006796956062317 0.87136906 0.5706454515457153 False diff --git a/ENCSR697FME/cherimoya.fold_1.performance.tsv b/ENCSR697FME/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 06f7454dcecb2d573117c52e71fcd96a7af670cf..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -339.5482482910156 0.5049912333488464 0.2619328796863556 0.09283578395843506 0.8723400831222534 0.8311980366706848 0.5676153302192688 \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_2.evaluate.json b/ENCSR697FME/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f6a207feba9dd53012d45bb57383da2cc2992eac..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695GCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_2.fit.json b/ENCSR697FME/cherimoya.fold_2.fit.json deleted file mode 100644 index 919053c0d096f8688564f6716a1e1a52b75880e7..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF695GCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_2.log b/ENCSR697FME/cherimoya.fold_2.log deleted file mode 100644 index 9334d804e5f61085bc683eeec72e39f6ea73947a..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2352 30.719284772872925 3.366184711456299 156.14288330078125 0.8022213578224182 391.7334289550781 0.13467293977737427 0.6145995 7.039223670959473 True -1 4704 25.792473316192627 0.5029220581054688 280.61004638671875 0.7658077478408813 333.34259033203125 0.19380980730056763 0.7446635 3.0918407440185547 True -2 7056 26.17071008682251 0.4640064239501953 379.7279968261719 0.8557554483413696 322.673828125 0.1980189085006714 0.75641334 2.129718780517578 True -3 9408 26.11396813392639 0.4798727035522461 161.17489624023438 0.8402999043464661 313.10235595703125 0.2060919851064682 0.769818 1.4307702779769897 True -4 11760 26.075631141662598 0.47751760482788086 238.10205078125 1.0649083852767944 307.7746276855469 0.20975901186466217 0.78262186 1.203849196434021 True -5 14112 26.056889057159424 0.4693176746368408 281.251220703125 1.1020209789276123 304.6501159667969 0.21054798364639282 0.7879193 1.116044044494629 True -6 16464 26.057140111923218 0.7618672847747803 264.6831970214844 0.9199920892715454 300.28680419921875 0.21481190621852875 0.8028451 0.892508864402771 True -7 18816 26.000353813171387 0.4757208824157715 276.3711242675781 0.8734924793243408 297.1268615722656 0.21703538298606873 0.81452334 0.779382586479187 True -8 21168 25.550710916519165 0.47519564628601074 237.37255859375 0.7163954377174377 294.8017578125 0.21898731589317322 0.8213976 0.7123783230781555 True -9 23520 25.561617851257324 0.4723653793334961 269.65106201171875 0.7524773478507996 292.91839599609375 0.22116726636886597 0.8283121 0.6512565612792969 True -10 25872 25.548197984695435 0.47362756729125977 228.680419921875 0.5564639568328857 291.3419189453125 0.22289824485778809 0.83446676 0.6457228660583496 True -11 28224 25.560393571853638 0.46818971633911133 250.14248657226562 0.5696675181388855 289.3778991699219 0.22517050802707672 0.84190524 0.585479199886322 True -12 30576 25.604296445846558 0.4737093448638916 335.5289306640625 0.8645616769790649 287.9211730957031 0.22679856419563293 0.8451096 0.5631768107414246 True -13 32928 25.5262508392334 0.4643669128417969 344.7655029296875 0.5864778757095337 286.1819152832031 0.22972479462623596 0.8494118 0.5408212542533875 True -14 35280 25.55895233154297 0.46736836433410645 240.63409423828125 0.7148243188858032 285.5447998046875 0.22961543500423431 0.8511732 0.5300202965736389 True -15 37632 25.541628122329712 0.4749178886413574 206.3920135498047 0.4275433123111725 285.01995849609375 0.22959445416927338 0.8542485 0.5182003378868103 True -16 39984 25.566814422607422 0.4735133647918701 298.1431884765625 0.4440861940383911 284.6380615234375 0.23042920231819153 0.85524565 0.5101089477539062 True -17 42336 25.553014278411865 0.4727325439453125 180.91958618164062 0.4660225808620453 285.3181457519531 0.23009973764419556 0.854419 0.5105317831039429 False -18 44688 25.598353385925293 1.8870365619659424 242.14280700683594 0.4208110272884369 285.5284423828125 0.22952421009540558 0.85351956 0.5144085884094238 False -19 47040 25.662739515304565 0.4758610725402832 218.56382751464844 0.42800670862197876 285.1346740722656 0.23075945675373077 0.8548959 0.5166215896606445 False diff --git a/ENCSR697FME/cherimoya.fold_2.performance.tsv b/ENCSR697FME/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5a0771387b566e3b54d10e32585e4f6d96236249..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -284.6380615234375 0.5279960632324219 0.23042918741703033 0.0773279219865799 0.8552456498146057 0.8028483986854553 0.5101089477539062 \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_3.evaluate.json b/ENCSR697FME/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6ad3af71ecb5b5b5029abdfb93d508536dfebe2b..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695GCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_3.fit.json b/ENCSR697FME/cherimoya.fold_3.fit.json deleted file mode 100644 index 60d2fcbfbf90c63441acc2dfdfb12518de874ee9..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF695GCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_3.log b/ENCSR697FME/cherimoya.fold_3.log deleted file mode 100644 index 82c37070bdf149fcf4f6c20ff7c09f52ae3484f9..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2237 29.3158597946167 3.3832106590270996 195.721435546875 0.7579135894775391 402.646484375 0.1453937292098999 0.6078032 7.659980773925781 True -1 4474 24.80958080291748 0.434309720993042 202.2620391845703 0.8329294323921204 343.68878173828125 0.20362965762615204 0.74156874 4.012620449066162 True -2 6711 24.857620000839233 0.43421435356140137 318.29193115234375 0.8719382286071777 330.6986999511719 0.21419662237167358 0.74370426 2.9517877101898193 True -3 8948 24.779093980789185 10.189963340759277 322.4410400390625 0.7795116901397705 323.9560241699219 0.2193879634141922 0.7574489 1.7985877990722656 True -4 11185 24.832889080047607 0.4469609260559082 307.20220947265625 0.8951371908187866 318.3388366699219 0.2248174250125885 0.77437425 1.4954416751861572 True -5 13422 24.82120156288147 0.43456339836120605 329.36376953125 1.1807074546813965 313.7626953125 0.22956296801567078 0.7860438 1.3753958940505981 True -6 15659 24.78434944152832 0.6285698413848877 255.29002380371094 0.8713474273681641 312.8026428222656 0.23002448678016663 0.7868182 1.33928382396698 True -7 17896 24.830978631973267 0.4357950687408447 187.7146453857422 0.6988493800163269 309.98187255859375 0.23255489766597748 0.8032328 1.063827395439148 True -8 20133 24.58454442024231 1.989652395248413 206.47113037109375 0.6090124249458313 308.2959289550781 0.2345142364501953 0.81272566 0.9262010455131531 True -9 22370 24.277010202407837 0.43814730644226074 193.4439239501953 0.8050699830055237 307.47613525390625 0.23463210463523865 0.8178267 0.8462299108505249 True -10 24607 24.394020318984985 0.4687221050262451 215.17745971679688 0.5846465826034546 304.95361328125 0.23835308849811554 0.8266565 0.7657696604728699 True -11 26844 24.292351961135864 0.4561738967895508 284.6805419921875 0.5997531414031982 303.0054626464844 0.23968704044818878 0.8342269 0.7323933839797974 True -12 29081 24.31440544128418 0.46419644355773926 259.06207275390625 1.134357213973999 301.43231201171875 0.2417011559009552 0.8411669 0.6902858018875122 True -13 31318 24.326104402542114 0.4512805938720703 268.6182861328125 0.7531732320785522 299.7154541015625 0.24322205781936646 0.8461364 0.6452920436859131 True -14 33555 24.315255880355835 0.442535400390625 201.97007751464844 0.46111828088760376 298.1536865234375 0.24451622366905212 0.8508654 0.616493821144104 True -15 35792 24.327648162841797 0.45160484313964844 238.71170043945312 0.520697295665741 296.8078308105469 0.24625174701213837 0.8569239 0.5845909714698792 True -16 38029 24.32073950767517 0.4424300193786621 244.84373474121094 0.6321597695350647 296.6514587402344 0.24584481120109558 0.8604098 0.5603889226913452 True -17 40266 24.408036470413208 0.4663105010986328 181.02000427246094 0.5638909339904785 297.0906066894531 0.24489840865135193 0.86029613 0.5488659739494324 False -18 42503 24.437417030334473 0.4428212642669678 185.4808349609375 0.3847903907299042 297.8990478515625 0.2434433400630951 0.8599805 0.5472555160522461 False -19 44740 24.43739628791809 0.4504060745239258 277.7176208496094 0.34579998254776 297.1725769042969 0.2457166463136673 0.8622608 0.5464382767677307 True diff --git a/ENCSR697FME/cherimoya.fold_3.performance.tsv b/ENCSR697FME/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c8eaa2134f496fa535923c2b0072b460e18a9a71..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -297.1725769042969 0.519298255443573 0.2457166463136673 0.08032111078500748 0.8622608184814453 0.800484299659729 0.5464382767677307 \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_4.evaluate.json b/ENCSR697FME/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 32fd6851d078a3deca345794cb0987cbd3ab5bf7..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695GCN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_4.fit.json b/ENCSR697FME/cherimoya.fold_4.fit.json deleted file mode 100644 index 20c19118734e3d618762cf2db6c8326ce75d3b86..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF695GCN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR697FME/cherimoya.fold_4.log b/ENCSR697FME/cherimoya.fold_4.log deleted file mode 100644 index e5acb9f8138034cec0fa1656bf7d78bdd54e4b64..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2271 30.452178239822388 3.4732792377471924 238.7882080078125 0.794460654258728 327.82403564453125 0.1304997056722641 0.61932 6.9222893714904785 True -1 4542 25.189090967178345 0.5006711483001709 381.3652038574219 1.3374783992767334 287.6688537597656 0.17272375524044037 0.7331175 3.186591625213623 True -2 6813 25.192559957504272 0.5380403995513916 222.11624145507812 1.2579939365386963 279.3863220214844 0.1796198934316635 0.7440248 2.1671979427337646 True -3 9084 25.15005111694336 0.47476863861083984 223.8453369140625 0.8272421360015869 271.384033203125 0.18653619289398193 0.76224285 1.2271608114242554 True -4 11355 25.153244018554688 0.4691319465637207 206.3310546875 0.5775174498558044 267.1268005371094 0.19243896007537842 0.7727108 1.036527156829834 True -5 13626 25.14850425720215 0.47990870475769043 248.60487365722656 0.7597315311431885 263.3900146484375 0.19376268982887268 0.78761876 0.9086988568305969 True -6 15897 25.153369426727295 0.4678382873535156 209.82081604003906 0.7341876029968262 260.4267272949219 0.19660694897174835 0.7927979 0.930379331111908 True -7 18168 25.15288996696472 0.467073917388916 252.94281005859375 0.6644841432571411 258.55078125 0.19772687554359436 0.80174655 0.8484176397323608 True -8 20439 25.179429054260254 0.4735088348388672 192.65744018554688 1.3858107328414917 256.4549865722656 0.20095692574977875 0.8066569 0.7523866891860962 True -9 22710 25.11910891532898 0.4800705909729004 172.9047088623047 0.5756940841674805 255.08221435546875 0.20228685438632965 0.8149258 0.6545024514198303 True -10 24981 25.169278621673584 0.4653325080871582 262.4864807128906 0.6063640713691711 255.04696655273438 0.20160344243049622 0.82381207 0.5814073085784912 True -11 27252 25.164785623550415 0.4660305976867676 193.76536560058594 0.48128992319107056 252.5872802734375 0.2056470513343811 0.8318095 0.5226011872291565 True -12 29523 25.15948987007141 0.46964359283447266 298.4505615234375 0.3963664472103119 252.0164794921875 0.2059495896100998 0.83560705 0.4970167577266693 True -13 31794 25.134522199630737 2.577881097793579 165.68475341796875 0.41589289903640747 250.80897521972656 0.20869892835617065 0.8397257 0.4781453609466553 True -14 34065 25.247171878814697 0.49489879608154297 257.3065490722656 0.46275582909584045 250.68055725097656 0.20832960307598114 0.84428275 0.4709523618221283 True -15 36336 24.983081340789795 0.463778018951416 242.2839813232422 0.36197665333747864 249.2998046875 0.2099366933107376 0.8506402 0.45872676372528076 True -16 38607 24.699218034744263 0.46538376808166504 285.07275390625 0.5612831115722656 249.9586944580078 0.20888464152812958 0.8525072 0.4520609974861145 True -17 40878 24.744624376296997 0.4742100238800049 222.51345825195312 0.4733428359031677 249.6471405029297 0.20902398228645325 0.8540052 0.4490891396999359 True -18 43149 24.722705602645874 0.4651949405670166 145.06814575195312 0.377998024225235 250.11544799804688 0.2083558738231659 0.85322165 0.45349669456481934 False -19 45420 24.79793620109558 0.4557938575744629 291.987060546875 0.5318027138710022 250.52606201171875 0.20822186768054962 0.85056156 0.45507538318634033 False diff --git a/ENCSR697FME/cherimoya.fold_4.performance.tsv b/ENCSR697FME/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c0e3c80085f5f382ad1138e1f3bc83743ee48d3e..0000000000000000000000000000000000000000 --- a/ENCSR697FME/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -249.6471405029297 0.5443689823150635 0.20902398228645325 0.06839270144701004 0.8540052175521851 0.7686429619789124 0.4490891396999359 \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_0.evaluate.json b/ENCSR698CUE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d4d78c728f3ba3e9955047872364ffd73c640388..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_0.fit.json b/ENCSR698CUE/cherimoya.fold_0.fit.json deleted file mode 100644 index 21d28d85eef6c862f6f8b8aa9b4c99f928f8eaff..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF006JUS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_0.log b/ENCSR698CUE/cherimoya.fold_0.log deleted file mode 100644 index 2d591868661d0890c901685f851cfede792f0acb..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 35.13741588592529 3.8938522338867188 189.98793029785156 0.5483691692352295 236.23431396484375 0.1360056847333908 0.49160394 3.8224074840545654 True -1 5496 30.947134971618652 0.6405088901519775 157.18511962890625 0.4231296181678772 227.70494079589844 0.18758368492126465 0.6046483 0.9726385474205017 True -2 8244 30.677533864974976 0.6018078327178955 161.6698760986328 0.7307900786399841 225.11578369140625 0.1992121934890747 0.61928993 0.5508607625961304 True -3 10992 30.61496591567993 0.628575325012207 144.45425415039062 0.5205446481704712 223.7396697998047 0.2043634057044983 0.6363064 0.5730810761451721 True -4 13740 30.411408185958862 0.6120741367340088 187.5830078125 0.49830999970436096 223.4193572998047 0.20553193986415863 0.64368856 0.5203345417976379 True -5 16488 29.964579105377197 0.6276130676269531 166.6446075439453 0.5780792832374573 223.18394470214844 0.20678181946277618 0.6441349 0.5595507025718689 True -6 19236 29.91839361190796 0.5900144577026367 164.31097412109375 0.5120749473571777 222.78240966796875 0.2097303867340088 0.651958 0.6132431030273438 True -7 21984 30.009713888168335 0.6142537593841553 172.27523803710938 0.5583773255348206 222.45895385742188 0.21176254749298096 0.6560233 0.6377659440040588 True -8 24732 30.021233797073364 17.008009672164917 158.4481201171875 0.43316400051116943 222.08216857910156 0.21392914652824402 0.660436 0.6009596586227417 True -9 27480 29.969824075698853 14.313305854797363 186.65936279296875 0.6723853349685669 222.1221923828125 0.21283911168575287 0.6651082 0.5640270113945007 True -10 30228 30.129978895187378 18.564238786697388 144.2203369140625 0.354489266872406 221.52133178710938 0.21709273755550385 0.6700454 0.5203884243965149 True -11 32976 30.093148469924927 11.662818431854248 189.85205078125 0.33123278617858887 221.50408935546875 0.21637964248657227 0.67827255 0.48627737164497375 True -12 35724 30.142627000808716 1.6565337181091309 184.26177978515625 0.35934436321258545 221.0204315185547 0.21933786571025848 0.6859455 0.46606096625328064 True -13 38472 30.10320544242859 2.7550644874572754 183.49380493164062 0.40187889337539673 220.90621948242188 0.2194678783416748 0.69549876 0.4228222072124481 True -14 41220 30.075931787490845 1.5494799613952637 179.17376708984375 0.4513234496116638 220.7934112548828 0.2198142409324646 0.7022659 0.4000861644744873 True -15 43968 30.080894947052002 1.4944922924041748 175.1182861328125 0.39955127239227295 220.36593627929688 0.2224275767803192 0.7105764 0.3843890130519867 True -16 46716 30.158281564712524 1.4793684482574463 166.2723846435547 0.6414382457733154 220.17214965820312 0.2232222557067871 0.71232146 0.3788612186908722 True -17 49464 30.25353980064392 1.3357532024383545 155.44158935546875 0.4031256437301636 220.34022521972656 0.2222043126821518 0.7139867 0.38200926780700684 True -18 52212 30.158584117889404 2.712109327316284 168.87953186035156 0.34143292903900146 220.3392333984375 0.22246260941028595 0.71407133 0.38512110710144043 True -19 54960 30.13840341567993 1.4946134090423584 197.5203094482422 0.2859994173049927 220.5162353515625 0.2209806591272354 0.7103596 0.39419257640838623 False diff --git a/ENCSR698CUE/cherimoya.fold_0.performance.tsv b/ENCSR698CUE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e276bf8ec6eac0de0c6630a7ecb88005b513c39e..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -220.3392333984375 0.536546528339386 0.22246260941028595 0.056840647011995316 0.7140713334083557 0.6673287749290466 0.38512110710144043 \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_1.evaluate.json b/ENCSR698CUE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a544914dccc0fba63be4aee7a38e38d535b0955d..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_1.fit.json b/ENCSR698CUE/cherimoya.fold_1.fit.json deleted file mode 100644 index a7b86400e4601307e3b9af112ada12792674cbb4..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF006JUS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_1.log b/ENCSR698CUE/cherimoya.fold_1.log deleted file mode 100644 index 0ee9573158bdf743599c4ef16a685a4cd2ad7950..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 35.34099197387695 4.0644731521606445 207.156005859375 1.1817162036895752 264.8040771484375 0.14393039047718048 0.5476377 3.398345470428467 True -1 5506 30.67956042289734 0.8249025344848633 190.9958038330078 0.9407169818878174 253.8931884765625 0.20254717767238617 0.6541337 1.1920279264450073 True -2 8259 30.679277420043945 2.2340707778930664 197.76718139648438 0.5791255235671997 250.14169311523438 0.21599221229553223 0.6833308 0.6303160190582275 True -3 11012 30.717219829559326 0.7506623268127441 180.28819274902344 0.5608037710189819 248.99452209472656 0.2195868343114853 0.6920175 0.62139493227005 True -4 13765 30.785945177078247 1.8456354141235352 164.38919067382812 0.5829696655273438 248.365478515625 0.2221505045890808 0.699114 0.6452201008796692 True -5 16518 30.576714038848877 0.8637957572937012 168.6082763671875 0.6757770776748657 247.97134399414062 0.223808154463768 0.69980174 0.625678539276123 True -6 19271 30.06006360054016 0.7082433700561523 168.02090454101562 0.6012873649597168 247.8486785888672 0.22477753460407257 0.70277244 0.6536217331886292 True -7 22024 30.068906784057617 0.696213960647583 149.2392120361328 0.5372486114501953 247.29563903808594 0.22704735398292542 0.71231306 0.5845783352851868 True -8 24777 30.023632287979126 0.7101602554321289 175.9300537109375 1.0335183143615723 246.98733520507812 0.2284696251153946 0.71453816 0.5847993493080139 True -9 27530 29.969401836395264 0.7202460765838623 202.60916137695312 0.5977163314819336 246.6408233642578 0.23022541403770447 0.7184484 0.5412763357162476 True -10 30283 30.061367750167847 0.7028281688690186 172.53445434570312 0.4611353874206543 246.0594024658203 0.2320210486650467 0.72800833 0.5240090489387512 True -11 33036 30.112276315689087 1.004995584487915 165.5581817626953 0.5646780133247375 245.7963409423828 0.23338532447814941 0.73328567 0.5021201968193054 True -12 35789 30.10714054107666 0.8152475357055664 213.73362731933594 0.49733516573905945 245.65721130371094 0.23384013772010803 0.7412564 0.4757935702800751 True -13 38542 30.045324325561523 1.3216862678527832 213.9095001220703 0.5178424715995789 245.36073303222656 0.2351536899805069 0.74731916 0.4362116754055023 True -14 41295 30.052876472473145 0.7154285907745361 213.07028198242188 0.2501201033592224 244.99575805664062 0.23703131079673767 0.7553923 0.4061599373817444 True -15 44048 29.996668338775635 0.7035820484161377 184.76010131835938 0.41853800415992737 244.7418975830078 0.23875032365322113 0.7623433 0.39032188057899475 True -16 46801 30.005781412124634 0.6923491954803467 182.37429809570312 0.42288175225257874 244.87615966796875 0.23761899769306183 0.76703256 0.379207044839859 True -17 49554 30.092499256134033 0.7425365447998047 153.07235717773438 0.36226192116737366 244.9454803466797 0.23723426461219788 0.76696146 0.3755013644695282 False -18 52307 30.138105392456055 0.7067251205444336 199.793212890625 0.22681190073490143 244.95115661621094 0.23695477843284607 0.7673477 0.375742644071579 True -19 55060 30.13085699081421 0.732224702835083 165.44271850585938 0.36479097604751587 244.88748168945312 0.23784855008125305 0.7669269 0.3776242136955261 False diff --git a/ENCSR698CUE/cherimoya.fold_1.performance.tsv b/ENCSR698CUE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6df536ec63d71216c6c8f279a48f62699bfcf334..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -244.95115661621094 0.5232052803039551 0.23695477843284607 0.06342413276433945 0.7673476934432983 0.7341395616531372 0.375742644071579 \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_2.evaluate.json b/ENCSR698CUE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d9312dc88ccfb5b6ac0e9c56fe4b9bc49b8e6891..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_2.fit.json b/ENCSR698CUE/cherimoya.fold_2.fit.json deleted file mode 100644 index d4a62498d5e1911069398f0295b7f0971dce4739..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF006JUS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_2.log b/ENCSR698CUE/cherimoya.fold_2.log deleted file mode 100644 index 6151b586bb3afd413318dec1731212a03411283a..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2914 37.14207196235657 3.920377492904663 189.74395751953125 0.8719843029975891 239.09568786621094 0.137374609708786 0.5162011 3.184129476547241 True -1 5828 32.53469181060791 0.7395734786987305 193.75234985351562 0.6586688756942749 229.19004821777344 0.19448278844356537 0.6279612 1.0828579664230347 True -2 8742 32.5274121761322 0.5395927429199219 208.7815704345703 0.7485266923904419 226.63502502441406 0.2038603127002716 0.6451445 0.5907295942306519 True -3 11656 32.4331169128418 0.619077205657959 196.47438049316406 0.5448967218399048 225.6134796142578 0.2072245478630066 0.65631694 0.5381495952606201 True -4 14570 32.465837240219116 0.5331306457519531 171.52499389648438 0.6617742776870728 225.09710693359375 0.20965449512004852 0.6596977 0.5375682711601257 True -5 17484 32.55533051490784 0.5752747058868408 163.56182861328125 0.6225183010101318 224.3220672607422 0.21446524560451508 0.6655995 0.5504413843154907 True -6 20398 32.34008717536926 0.5533304214477539 213.60714721679688 0.453756719827652 224.3515167236328 0.21405905485153198 0.6690247 0.5542309880256653 True -7 23312 31.771731853485107 0.5257556438446045 203.80792236328125 0.8047890663146973 224.1148681640625 0.21474117040634155 0.67281353 0.5252490639686584 True -8 26226 31.72195267677307 1.1510319709777832 177.15176391601562 0.8904054164886475 223.67483520507812 0.21781300008296967 0.67856604 0.528054416179657 True -9 29140 31.877102851867676 0.5360777378082275 162.862060546875 0.5976153612136841 223.275634765625 0.21982255578041077 0.68171805 0.4969061613082886 True -10 32054 31.852982759475708 0.5346155166625977 152.61044311523438 0.40176644921302795 223.0155029296875 0.22060494124889374 0.6862765 0.48013338446617126 True -11 34968 31.772999048233032 0.5245020389556885 192.31390380859375 0.423801451921463 223.0250244140625 0.2208346128463745 0.6915623 0.47266241908073425 True -12 37882 31.92087173461914 0.5399575233459473 196.271240234375 0.3535442352294922 222.40431213378906 0.22405396401882172 0.70040643 0.43777987360954285 True -13 40796 31.797420501708984 0.5313770771026611 182.697021484375 0.682347297668457 222.06060791015625 0.2260339856147766 0.70911485 0.42107248306274414 True -14 43710 31.776166677474976 0.5520937442779541 143.53207397460938 0.575218677520752 221.87939453125 0.22629545629024506 0.71391493 0.40715858340263367 True -15 46624 31.756232261657715 0.5254995822906494 185.7021942138672 0.45887115597724915 221.66668701171875 0.22803914546966553 0.7211657 0.3875715136528015 True -16 49538 31.734293222427368 0.979755163192749 171.3229522705078 0.41833606362342834 221.47991943359375 0.229108527302742 0.7243715 0.3835175335407257 True -17 52452 31.74387240409851 1.8803143501281738 185.14382934570312 0.25828564167022705 221.5790557861328 0.22837531566619873 0.7264266 0.38516154885292053 True -18 55366 31.745492696762085 0.52335524559021 182.59542846679688 0.30711108446121216 221.6894989013672 0.2268880158662796 0.7269686 0.3908551037311554 True -19 58280 31.734316110610962 0.5220081806182861 195.9220733642578 0.22688448429107666 221.85877990722656 0.2262047380208969 0.72429955 0.39643576741218567 False diff --git a/ENCSR698CUE/cherimoya.fold_2.performance.tsv b/ENCSR698CUE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 125a281feb9fdc824dc5b20782c958110bf75805..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -221.6894989013672 0.5344036817550659 0.2268880009651184 0.05716656520962715 0.7269685864448547 0.6812109351158142 0.3908551037311554 \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_3.evaluate.json b/ENCSR698CUE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index da49c37a2d4a98bc5613479d55ea0b1acaff2513..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_3.fit.json b/ENCSR698CUE/cherimoya.fold_3.fit.json deleted file mode 100644 index bdb4827b02206909472e9c36a4d5524abf01f103..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF006JUS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_3.log b/ENCSR698CUE/cherimoya.fold_3.log deleted file mode 100644 index afb315a28c94892513f84bb81aebc8a7767a7d90..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 35.47661876678467 4.799454689025879 177.84304809570312 0.7771115303039551 251.8197021484375 0.13625651597976685 0.52419496 3.420379638671875 True -1 5540 30.868977785110474 17.259636163711548 145.3660430908203 0.7294961214065552 242.32308959960938 0.19154036045074463 0.6091674 0.9913811683654785 True -2 8310 30.93591070175171 0.7195990085601807 194.33108520507812 0.6545835733413696 240.2233123779297 0.19893276691436768 0.639387 0.596798837184906 True -3 11080 30.825695514678955 0.6279456615447998 195.66432189941406 0.5527197122573853 239.1348114013672 0.20370177924633026 0.647487 0.5273321866989136 True -4 13850 30.862292289733887 0.6469883918762207 145.35765075683594 0.6977649927139282 238.57748413085938 0.20570051670074463 0.6564475 0.6441648602485657 True -5 16620 31.434348106384277 0.614997386932373 196.6173095703125 0.6555650234222412 237.91091918945312 0.20913609862327576 0.6647856 0.644960880279541 True -6 19390 30.81447410583496 0.622802734375 215.33737182617188 0.6565526127815247 237.8202362060547 0.21019169688224792 0.6650461 0.6199238896369934 True -7 22160 30.86665439605713 0.6138343811035156 164.59442138671875 0.5714753866195679 237.60769653320312 0.21094739437103271 0.6743465 0.563190221786499 True -8 24930 30.156450510025024 0.5993616580963135 175.55291748046875 0.5186818838119507 237.32518005371094 0.2125658541917801 0.6786218 0.5587605237960815 True -9 27700 30.154043912887573 0.628978967666626 148.68572998046875 0.5185211300849915 237.23001098632812 0.21313293278217316 0.680469 0.5348427295684814 True -10 30470 30.173392295837402 0.6168923377990723 164.5487060546875 0.5447502136230469 236.77967834472656 0.21540981531143188 0.6857491 0.5248021483421326 True -11 33240 30.19875407218933 0.6230940818786621 180.44589233398438 0.5259387493133545 236.41793823242188 0.21727250516414642 0.6934671 0.5017106533050537 True -12 36010 30.1978440284729 0.6073765754699707 182.85394287109375 0.4933719038963318 236.1024627685547 0.21919050812721252 0.69959587 0.47266414761543274 True -13 38780 30.238770723342896 0.616220235824585 161.9813232421875 0.4593770503997803 235.87582397460938 0.22014188766479492 0.70954466 0.43598562479019165 True -14 41550 30.195125341415405 0.619879961013794 200.11361694335938 0.5558289885520935 235.53038024902344 0.22220441699028015 0.7120523 0.43209701776504517 True -15 44320 30.206827878952026 1.5752620697021484 174.37762451171875 0.4287567734718323 235.5814666748047 0.22210635244846344 0.7199333 0.41392815113067627 True -16 47090 30.243783712387085 0.6119987964630127 159.54632568359375 0.5423141717910767 235.3316650390625 0.223288893699646 0.72214156 0.40871524810791016 True -17 49860 30.27470564842224 0.6225206851959229 163.19732666015625 0.3060917258262634 235.36489868164062 0.22342750430107117 0.72330725 0.4089581370353699 True -18 52630 30.27298641204834 0.6078684329986572 164.88491821289062 0.3091435730457306 235.3037567138672 0.22258360683918 0.7227329 0.4129892885684967 False -19 55400 30.4847674369812 0.6172754764556885 196.0124969482422 0.35456764698028564 235.52891540527344 0.22143803536891937 0.71876055 0.41694602370262146 False diff --git a/ENCSR698CUE/cherimoya.fold_3.performance.tsv b/ENCSR698CUE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2d3d2a69c66f5230286db1ef5ab06b65725e0c47..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -235.36489868164062 0.5311709046363831 0.22342748939990997 0.055234696716070175 0.7233072519302368 0.6823641657829285 0.4089581370353699 \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_4.evaluate.json b/ENCSR698CUE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 386aa60ddfccfe828aefa3385f5a001cc8ee0421..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF006JUS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_4.fit.json b/ENCSR698CUE/cherimoya.fold_4.fit.json deleted file mode 100644 index 0640e70cfaf0b90906d3fc137ee55062d868e69d..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF006JUS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698CUE/cherimoya.fold_4.log b/ENCSR698CUE/cherimoya.fold_4.log deleted file mode 100644 index 8a2284657895789859215e36ceddab3614915e72..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 36.735806941986084 3.996248722076416 155.61248779296875 0.8291068077087402 240.30206298828125 0.13525710999965668 0.50059336 3.293811798095703 True -1 5746 32.708672523498535 0.6928369998931885 158.48782348632812 0.932280421257019 230.9541778564453 0.19205935299396515 0.599843 0.8374125361442566 True -2 8619 31.985523223876953 0.6502234935760498 198.85891723632812 0.8272737264633179 229.00070190429688 0.19916585087776184 0.6262865 0.4287247955799103 True -3 11492 32.04431962966919 0.620004415512085 170.9569091796875 0.8610154390335083 227.94859313964844 0.20283593237400055 0.637178 0.4551067054271698 True -4 14365 31.981040239334106 0.6218321323394775 190.30116271972656 0.590351939201355 227.64952087402344 0.20345327258110046 0.64279556 0.4500078856945038 True -5 17238 32.09570550918579 0.6167185306549072 213.94517517089844 0.3736477196216583 227.18328857421875 0.2068481743335724 0.6460603 0.48459523916244507 True -6 20111 31.80711078643799 1.5966641902923584 194.8332977294922 0.7510495185852051 227.04074096679688 0.20694047212600708 0.6529872 0.5292812585830688 True -7 22984 31.403563737869263 0.6171104907989502 189.5047607421875 0.5121643543243408 226.6932373046875 0.20933955907821655 0.65293103 0.5333362817764282 False -8 25857 31.319650411605835 0.6138455867767334 163.70626831054688 0.4319462776184082 226.29627990722656 0.2116207480430603 0.6564854 0.5256340503692627 True -9 28730 31.351539373397827 0.6134116649627686 187.07855224609375 0.5097839832305908 226.19166564941406 0.21172238886356354 0.6619371 0.5056166052818298 True -10 31603 31.3109233379364 0.6147341728210449 169.2761688232422 0.5504355430603027 225.9814910888672 0.21277952194213867 0.6707683 0.4818475842475891 True -11 34476 31.309443950653076 0.6122393608093262 190.73428344726562 0.44969287514686584 225.4872283935547 0.21604490280151367 0.6772926 0.45142078399658203 True -12 37349 31.41535711288452 0.6133387088775635 160.29275512695312 0.3845266103744507 225.32424926757812 0.21634507179260254 0.68336624 0.43554508686065674 True -13 40222 31.366776943206787 0.6238365173339844 173.6973876953125 0.5573201179504395 225.0436553955078 0.21791675686836243 0.69485223 0.41100719571113586 True -14 43095 31.347870111465454 0.6156463623046875 163.5306396484375 0.37352481484413147 224.79164123535156 0.21944274008274078 0.7026113 0.39916253089904785 True -15 45968 31.344077348709106 0.6151366233825684 213.47857666015625 0.4604354500770569 224.74618530273438 0.21936185657978058 0.71088105 0.38173332810401917 True -16 48841 31.372175931930542 0.6259415149688721 168.98544311523438 0.45029813051223755 224.68878173828125 0.2198306918144226 0.7172618 0.37566420435905457 True -17 51714 31.36376976966858 0.6079728603363037 182.509033203125 0.2987654209136963 224.64761352539062 0.2202494889497757 0.72146887 0.37604981660842896 True -18 54587 31.328385829925537 0.6123731136322021 179.50502014160156 0.2196972668170929 224.71298217773438 0.2196485549211502 0.7222686 0.3797813653945923 True -19 57460 31.380706310272217 0.613093376159668 176.8623504638672 0.4355727732181549 224.8392791748047 0.21879985928535461 0.72086 0.38364335894584656 False diff --git a/ENCSR698CUE/cherimoya.fold_4.performance.tsv b/ENCSR698CUE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e1a05a4302324a33f3e8dddb651026c0c3f6c0e8..0000000000000000000000000000000000000000 --- a/ENCSR698CUE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -224.71298217773438 0.5355928540229797 0.2196485549211502 0.055616237223148346 0.7222685813903809 0.6779606938362122 0.3797813653945923 \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_0.evaluate.json b/ENCSR698VDM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d889695965f3e0a2a45379d66f9a0cd174c885c8..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034IAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_0.fit.json b/ENCSR698VDM/cherimoya.fold_0.fit.json deleted file mode 100644 index 3f2f6a4094ac2f9927214c21f92a1defd888a0d7..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF034IAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_0.log b/ENCSR698VDM/cherimoya.fold_0.log deleted file mode 100644 index 3ab41f0d877d341719ac3275d0d613392910bc4e..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2277 28.907637357711792 3.478015184402466 293.97845458984375 0.7785993218421936 643.1338500976562 0.1613885909318924 0.5943731 9.627470016479492 True -1 4554 25.11780071258545 0.4814944267272949 442.90496826171875 0.8730030059814453 526.0811157226562 0.2358606904745102 0.74643505 4.093689918518066 True -2 6831 25.02859616279602 0.45774245262145996 424.4583740234375 0.6959609985351562 510.3690185546875 0.24444130063056946 0.742975 3.1192445755004883 False -3 9108 25.01182985305786 0.45974183082580566 502.9620361328125 1.1555838584899902 499.7762756347656 0.24852681159973145 0.74992955 1.7783161401748657 True -4 11385 24.75901460647583 0.4635508060455322 498.81781005859375 1.1641244888305664 491.2033386230469 0.25561821460723877 0.7667521 1.4316461086273193 True -5 13662 24.548054456710815 0.9842166900634766 467.62664794921875 0.9205229878425598 488.06683349609375 0.25915828347206116 0.76909876 1.2472153902053833 True -6 15939 24.520577907562256 0.45462894439697266 435.6588134765625 0.7930154800415039 484.8501892089844 0.2607431709766388 0.7762044 1.1996389627456665 True -7 18216 24.5191330909729 0.4549129009246826 442.97906494140625 0.6742548942565918 479.3697509765625 0.26406922936439514 0.78143907 1.0744597911834717 True -8 20493 24.514353275299072 0.45302462577819824 418.191162109375 1.1870734691619873 473.4126892089844 0.2684863805770874 0.79637617 0.9245300889015198 True -9 22770 24.575185537338257 0.45256471633911133 384.1177673339844 0.5967060327529907 469.9438781738281 0.2707268297672272 0.8059537 0.8882411122322083 True -10 25047 24.561305046081543 0.4536476135253906 376.4995422363281 1.0205225944519043 464.51470947265625 0.27481088042259216 0.8148908 0.8115982413291931 True -11 27324 24.549034595489502 0.45439600944519043 596.2391357421875 0.43737858533859253 463.02252197265625 0.2748597264289856 0.8240337 0.718998908996582 True -12 29601 24.54600429534912 0.4539070129394531 478.02783203125 0.6648547649383545 460.00341796875 0.277422696352005 0.83250356 0.6639681458473206 True -13 31878 24.540274143218994 0.46132588386535645 381.21942138671875 0.6010133028030396 459.1947326660156 0.2770986258983612 0.83884156 0.6075133681297302 True -14 34155 24.532701015472412 0.4513742923736572 325.44769287109375 0.5483251810073853 455.59246826171875 0.28035134077072144 0.8475032 0.5690746903419495 True -15 36432 24.503498315811157 0.6874668598175049 387.6594543457031 0.6502758264541626 452.34210205078125 0.28258824348449707 0.8511437 0.5445494055747986 True -16 38709 24.492405891418457 0.45842719078063965 356.69879150390625 0.4894025921821594 453.33782958984375 0.2804725766181946 0.8538964 0.5256327390670776 True -17 40986 24.55816674232483 0.4568352699279785 343.82489013671875 0.37615811824798584 454.5032958984375 0.27949461340904236 0.85644746 0.5178235769271851 True -18 43263 24.546480178833008 0.4728360176086426 389.8958435058594 0.307730495929718 454.6645202636719 0.27922365069389343 0.856407 0.518564760684967 False -19 45540 24.562902212142944 0.4712059497833252 407.92059326171875 0.44867730140686035 455.3288269042969 0.2789844870567322 0.85405576 0.5198443531990051 False diff --git a/ENCSR698VDM/cherimoya.fold_0.performance.tsv b/ENCSR698VDM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 76a0579a8df04938ea3717f25ebdfe1f6467c069..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -454.5032958984375 0.4840447008609772 0.27949461340904236 0.10649582743644714 0.8564474582672119 0.7895849943161011 0.5178235769271851 \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_1.evaluate.json b/ENCSR698VDM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 50a5be7dc27df3470846d7e669fa8c99cf9f986e..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034IAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_1.fit.json b/ENCSR698VDM/cherimoya.fold_1.fit.json deleted file mode 100644 index ab2c8edb7e2df288258e50946b8557e8106f3fc6..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF034IAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_1.log b/ENCSR698VDM/cherimoya.fold_1.log deleted file mode 100644 index 6f3c9ce517e8e15f21b384a85846ca23d535e5a8..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2209 28.178709983825684 3.6243858337402344 440.8478088378906 1.1861375570297241 819.450439453125 0.17351534962654114 0.57459444 11.803338050842285 True -1 4418 24.311540842056274 0.6630856990814209 282.4510192871094 0.5852227210998535 678.6854858398438 0.25405460596084595 0.73360366 5.470948696136475 True -2 6627 24.256682634353638 0.6499927043914795 582.0609130859375 1.4308671951293945 647.671630859375 0.26789548993110657 0.7283602 3.8233938217163086 False -3 8836 24.217283487319946 0.6369109153747559 364.57330322265625 0.5674934387207031 630.26171875 0.2752932012081146 0.7546108 2.2024073600769043 True -4 11045 24.402435064315796 0.6614124774932861 258.3164978027344 1.0369350910186768 622.6605224609375 0.2794611155986786 0.75361973 1.9852112531661987 False -5 13254 25.112542629241943 18.772656679153442 379.58648681640625 0.9431480169296265 608.93359375 0.28850027918815613 0.7806457 1.7249329090118408 True -6 15463 24.307745695114136 0.6574115753173828 400.7559814453125 0.8139746189117432 602.9927368164062 0.29095685482025146 0.79676574 1.4451724290847778 True -7 17672 23.94740056991577 0.6291506290435791 501.3340148925781 0.6542563438415527 591.8452758789062 0.2978569567203522 0.8158019 1.2509808540344238 True -8 19881 23.805996417999268 0.64817214012146 377.3770751953125 0.6508557200431824 587.6366577148438 0.30010297894477844 0.82095516 1.2293701171875 True -9 22090 23.81140112876892 0.6257615089416504 346.2506103515625 0.8716375827789307 583.3380737304688 0.302654504776001 0.8276762 1.090368628501892 True -10 24299 23.77785015106201 0.6351680755615234 310.98907470703125 0.6612025499343872 576.6178588867188 0.3070793151855469 0.8388824 0.9371167421340942 True -11 26508 23.838423252105713 0.642622709274292 345.9658203125 0.9010591506958008 574.6464233398438 0.3079046308994293 0.8449924 0.8507987260818481 True -12 28717 23.817725896835327 1.5562584400177002 398.9500732421875 0.6634024381637573 572.1843872070312 0.3094746768474579 0.85246253 0.7678670883178711 True -13 30926 23.852821350097656 0.6412327289581299 365.0733642578125 0.48795923590660095 567.1867065429688 0.31180548667907715 0.8593862 0.7162061929702759 True -14 33135 23.840914964675903 0.65525221824646 345.1456298828125 0.6289606094360352 565.0033569335938 0.31249070167541504 0.86823344 0.6334216594696045 True -15 35344 23.896982192993164 0.6387722492218018 356.30328369140625 0.44472742080688477 561.2760009765625 0.3146596848964691 0.8718227 0.5987483263015747 True -16 37553 23.788461446762085 1.116851806640625 376.0889892578125 0.7332347631454468 558.7385864257812 0.3162045478820801 0.87469834 0.5708286762237549 True -17 39762 23.758779764175415 0.6413314342498779 392.732177734375 0.5540989637374878 559.110595703125 0.31492772698402405 0.875055 0.5601987242698669 True -18 41971 23.780481815338135 0.6318106651306152 317.22259521484375 0.37707656621932983 558.1381225585938 0.31679049134254456 0.8760512 0.5537286996841431 True -19 44180 23.760297536849976 0.6304645538330078 359.26922607421875 0.24684442579746246 561.296875 0.3140682280063629 0.87547684 0.5546032786369324 False diff --git a/ENCSR698VDM/cherimoya.fold_1.performance.tsv b/ENCSR698VDM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9081eacb1c8b8224a5b58cbc120f92c032f938bf..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -558.1381225585938 0.45574402809143066 0.31679046154022217 0.13090209662914276 0.8760511875152588 0.8323515057563782 0.5537286996841431 \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_2.evaluate.json b/ENCSR698VDM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ead19aeb3e744bd5d1c2fa6e10817a66243f10f9..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034IAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_2.fit.json b/ENCSR698VDM/cherimoya.fold_2.fit.json deleted file mode 100644 index d526929593cf11c1c2a79bc43d94ff6a0a4d2efc..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF034IAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_2.log b/ENCSR698VDM/cherimoya.fold_2.log deleted file mode 100644 index 4e362dc333fcdb669b05783a7b6b185731dccfaf..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2388 29.916080951690674 3.7139382362365723 418.304443359375 0.8233237862586975 664.8951416015625 0.16744011640548706 0.56489897 7.919552326202393 True -1 4776 26.353501319885254 0.5024065971374512 475.876220703125 0.9892388582229614 547.457763671875 0.23670797049999237 0.75111544 3.9716484546661377 True -2 7164 26.260613441467285 0.48550915718078613 643.7006225585938 0.5382946133613586 529.1683349609375 0.24167025089263916 0.76817966 2.4622931480407715 True -3 9552 26.21997570991516 0.48781681060791016 481.25579833984375 1.026869297027588 512.9104614257812 0.25017672777175903 0.7827607 1.4865490198135376 True -4 11940 26.28610134124756 0.48793959617614746 539.2542114257812 1.2203764915466309 509.3265686035156 0.2512538731098175 0.79071957 1.3299033641815186 True -5 14328 26.19848132133484 0.48355865478515625 408.03411865234375 1.2839243412017822 499.7684020996094 0.2567596733570099 0.8022858 1.1519025564193726 True -6 16716 26.2558171749115 3.3139231204986572 458.5325927734375 0.771138072013855 493.5352478027344 0.2621239721775055 0.8104101 1.0821746587753296 True -7 19104 26.465821266174316 0.673065185546875 422.0548095703125 0.7891641855239868 490.4926452636719 0.2646477222442627 0.8134879 0.995733916759491 True -8 21492 26.2210054397583 0.49153661727905273 379.07135009765625 0.6584738492965698 486.3904113769531 0.2671124339103699 0.81927836 0.953376054763794 True -9 23880 26.23452663421631 0.5058267116546631 405.775146484375 1.0181273221969604 484.84954833984375 0.268672913312912 0.82821065 0.8137378096580505 True -10 26268 26.20792865753174 0.49592089653015137 457.4761657714844 0.7161108255386353 481.1325988769531 0.2718312740325928 0.83173776 0.7869974970817566 True -11 28656 25.994215488433838 0.49015092849731445 382.97271728515625 0.5375671982765198 477.5770263671875 0.27430424094200134 0.83770514 0.7074739933013916 True -12 31044 25.756758213043213 0.4862086772918701 410.71441650390625 0.5068870186805725 475.3965759277344 0.27470308542251587 0.8436381 0.6463334560394287 True -13 33432 25.748647689819336 0.4860646724700928 410.06402587890625 0.707773745059967 472.26812744140625 0.27623409032821655 0.84879017 0.5930691957473755 True -14 35820 25.765819787979126 0.4855766296386719 260.99322509765625 0.6049506664276123 468.3623352050781 0.2794097363948822 0.85580534 0.5436478853225708 True -15 38208 25.799249410629272 17.355437517166138 304.822265625 0.590228796005249 466.6327209472656 0.2805629372596741 0.8586902 0.5191031694412231 True -16 40596 28.02966594696045 0.4885852336883545 365.5923156738281 0.37115970253944397 467.08184814453125 0.2806956171989441 0.86264783 0.5062232613563538 True -17 42984 25.737634897232056 0.4768688678741455 580.0404052734375 0.6290807723999023 466.11480712890625 0.2808423638343811 0.8613901 0.49668198823928833 False -18 45372 25.768585681915283 0.4868428707122803 465.53302001953125 0.5643604397773743 466.8708801269531 0.27932989597320557 0.8623446 0.4952954947948456 False -19 47760 25.716060638427734 0.4803886413574219 375.39093017578125 0.32379060983657837 467.2829284667969 0.2792380750179291 0.8598716 0.4979233145713806 False diff --git a/ENCSR698VDM/cherimoya.fold_2.performance.tsv b/ENCSR698VDM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 52eaa84acd0d3b9af833786b5504e186fd3c20ef..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -467.08184814453125 0.4827257990837097 0.2806956470012665 0.10601956397294998 0.8626478314399719 0.7957311868667603 0.5062232613563538 \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_3.evaluate.json b/ENCSR698VDM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 601a90f589f23128aa612fe71249c7adba82014c..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034IAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_3.fit.json b/ENCSR698VDM/cherimoya.fold_3.fit.json deleted file mode 100644 index 5febbc8878e19ae3a8fc01e091bac4f8bf63eae1..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF034IAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_3.log b/ENCSR698VDM/cherimoya.fold_3.log deleted file mode 100644 index 3ed9106b38419c7aa7c6f0b1e4771b7686101e10..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2278 29.268152713775635 3.600735664367676 448.9788818359375 0.8511815667152405 714.5870971679688 0.1837267130613327 0.54566395 11.296414375305176 True -1 4556 25.087141275405884 0.4586191177368164 503.4671630859375 0.7501519918441772 593.0261840820312 0.2577086389064789 0.7141238 4.476274013519287 True -2 6834 24.9793541431427 0.4379274845123291 369.38385009765625 0.7723496556282043 572.294189453125 0.26645514369010925 0.7501991 2.967677593231201 True -3 9112 25.034717321395874 0.43742847442626953 579.569091796875 0.7789989113807678 563.2799072265625 0.2705380618572235 0.7546367 2.1639113426208496 True -4 11390 24.99262499809265 0.43990039825439453 424.74627685546875 0.7169995903968811 548.8428955078125 0.2792222797870636 0.76766086 1.698582410812378 True -5 13668 24.966928243637085 0.4390838146209717 425.17523193359375 0.5785223245620728 539.6552734375 0.28495514392852783 0.78017825 1.48226797580719 True -6 15946 24.98996615409851 0.441819429397583 260.65606689453125 0.7018082737922668 535.2568969726562 0.288459837436676 0.78899086 1.3183168172836304 True -7 18224 25.052003622055054 0.4379889965057373 506.1500244140625 0.809795618057251 534.5336303710938 0.2877961993217468 0.79354584 1.2230583429336548 True -8 20502 24.996373176574707 0.4377148151397705 394.19952392578125 0.5861657857894897 528.1383666992188 0.29360634088516235 0.79953986 1.210516095161438 True -9 22780 25.03072452545166 0.44288015365600586 504.8781433105469 0.7620793581008911 522.80029296875 0.2978079915046692 0.8087918 1.0529314279556274 True -10 25058 25.077659130096436 0.4431273937225342 561.9573974609375 0.5980258584022522 518.4223022460938 0.30103081464767456 0.8162279 0.9565761685371399 True -11 27336 25.013261556625366 0.43788671493530273 399.56219482421875 0.4006419777870178 516.2997436523438 0.30134764313697815 0.8211595 0.9247147440910339 True -12 29614 25.00955581665039 0.43730926513671875 398.875732421875 0.791806697845459 512.2407836914062 0.3046007752418518 0.82777244 0.8249056935310364 True -13 31892 24.99877119064331 0.44271278381347656 428.9034423828125 0.37903621792793274 506.83306884765625 0.3083142936229706 0.83599424 0.7545778751373291 True -14 34170 25.054738998413086 0.44353818893432617 250.13841247558594 0.747788667678833 506.4122314453125 0.3071264922618866 0.84295803 0.701275646686554 True -15 36448 24.991256713867188 0.43891072273254395 375.4857177734375 0.5599356889724731 503.41717529296875 0.3097119927406311 0.8481552 0.6605193614959717 True -16 38726 25.075509548187256 0.44269251823425293 423.2845458984375 0.3615545630455017 503.64178466796875 0.30913302302360535 0.8542362 0.6130104064941406 True -17 41004 25.08228635787964 0.9763867855072021 377.15899658203125 0.48700422048568726 503.03033447265625 0.31091782450675964 0.8542716 0.6028385162353516 True -18 43282 25.017856121063232 0.43871378898620605 578.5348510742188 0.3879077434539795 505.391357421875 0.3083382248878479 0.8565071 0.596710205078125 True -19 45560 25.020259380340576 0.4326057434082031 318.87078857421875 0.3521956205368042 504.5419006347656 0.30949610471725464 0.85581005 0.5960200428962708 False diff --git a/ENCSR698VDM/cherimoya.fold_3.performance.tsv b/ENCSR698VDM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 81e903e2fba160bb5472abccc0b85e23b0b89974..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -505.391357421875 0.46327075362205505 0.3083382248878479 0.1217631846666336 0.8565071225166321 0.7944641709327698 0.596710205078125 \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_4.evaluate.json b/ENCSR698VDM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f8b29be9bace2c25f11cada2af9813057251062b..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034IAL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_4.fit.json b/ENCSR698VDM/cherimoya.fold_4.fit.json deleted file mode 100644 index 3f3080aec9e7ea7386bf7374de14fefbdb8b46f1..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF034IAL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR698VDM/cherimoya.fold_4.log b/ENCSR698VDM/cherimoya.fold_4.log deleted file mode 100644 index 2d517157ba82aa8cf11bb39140afb6a848f79982..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2281 28.981587171554565 3.3580353260040283 460.10186767578125 1.108003854751587 603.231689453125 0.1625727117061615 0.5630172 9.107691764831543 True -1 4562 25.07810664176941 0.48737144470214844 362.53173828125 0.850795567035675 505.2243347167969 0.2295342981815338 0.7155962 3.868652820587158 True -2 6843 25.131617069244385 0.44535374641418457 322.19921875 0.6583670377731323 493.2307434082031 0.23262740671634674 0.7263934 2.7812612056732178 True -3 9124 25.086058378219604 0.6049656867980957 350.197021484375 0.6242899894714355 481.6175231933594 0.24066400527954102 0.7406627 1.743415355682373 True -4 11405 25.113399267196655 0.4542109966278076 392.30126953125 0.7510095834732056 470.78826904296875 0.24718151986598969 0.76030225 1.3637620210647583 True -5 13686 24.693286180496216 0.4394032955169678 488.5491027832031 0.9653223752975464 466.7919921875 0.2491128146648407 0.767386 1.2012498378753662 True -6 15967 24.516355276107788 0.4439418315887451 344.7023010253906 0.6140434145927429 459.42059326171875 0.2551310956478119 0.7772123 1.035524606704712 True -7 18248 24.534451723098755 0.45307087898254395 317.8525390625 0.6169447898864746 455.7209777832031 0.2579978406429291 0.78642946 0.9240710139274597 True -8 20529 24.572992086410522 2.059022903442383 393.630126953125 0.6624618768692017 451.027587890625 0.26124441623687744 0.7946627 0.8397737741470337 True -9 22810 24.66369605064392 0.4538102149963379 770.738037109375 0.9701763391494751 447.7314453125 0.26365232467651367 0.8024421 0.7688565254211426 True -10 25091 24.683961868286133 0.45008301734924316 393.7923583984375 0.8513914346694946 444.3363952636719 0.2657524347305298 0.81211907 0.693487823009491 True -11 27372 24.589351177215576 0.4473574161529541 312.1936340332031 0.4975115954875946 441.8562316894531 0.2685355246067047 0.81967384 0.646917998790741 True -12 29653 24.593975067138672 0.4531214237213135 360.1751708984375 0.6958029270172119 440.4015197753906 0.2689777910709381 0.8282207 0.6013895273208618 True -13 31934 24.56217360496521 0.445284366607666 324.1134338378906 0.46404343843460083 437.5162048339844 0.27151796221733093 0.8323128 0.5747645497322083 True -14 34215 24.608668327331543 0.45085835456848145 422.5044860839844 0.46898722648620605 436.9604797363281 0.27110907435417175 0.8379474 0.552582323551178 True -15 36496 24.63516139984131 0.45004868507385254 438.3079833984375 0.8910785913467407 434.4839172363281 0.2732582688331604 0.8443253 0.5310591459274292 True -16 38777 24.542132139205933 0.44444751739501953 353.39361572265625 0.250316858291626 434.7904968261719 0.272600919008255 0.84710616 0.5183872580528259 True -17 41058 24.561249256134033 0.45040082931518555 272.0249938964844 0.4281116724014282 434.7992858886719 0.2722557485103607 0.84960294 0.5120680332183838 True -18 43339 24.529903650283813 0.4466066360473633 452.04229736328125 0.39393800497055054 436.0234375 0.2709723711013794 0.84903485 0.512512743473053 False -19 45620 24.586313247680664 0.4478108882904053 358.5133361816406 0.4541443884372711 435.0975036621094 0.27191632986068726 0.8475883 0.514893651008606 False diff --git a/ENCSR698VDM/cherimoya.fold_4.performance.tsv b/ENCSR698VDM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1b9a4176521eb5977dcd18373b82c5758c34eab4..0000000000000000000000000000000000000000 --- a/ENCSR698VDM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -434.7992858886719 0.4900023341178894 0.2722557485103607 0.10125619173049927 0.8496029376983643 0.7750885486602783 0.5120680332183838 \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_0.evaluate.json b/ENCSR702DPD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4dab29587c241f4dcd39adfe1e2d9f4d2dce6e76..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF127WYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_0.fit.json b/ENCSR702DPD/cherimoya.fold_0.fit.json deleted file mode 100644 index 6d44456b3ae38f78f4ab99a02e1a76460755c8e3..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF127WYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_0.log b/ENCSR702DPD/cherimoya.fold_0.log deleted file mode 100644 index 25aaa97ed381f36a86b6ad089e5e16303e438851..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 35.67120146751404 25.670052528381348 421.19122314453125 0.20942947268486023 628.01025390625 0.3387822210788727 0.78956544 4.454168319702148 True -1 5468 31.09659743309021 0.7763214111328125 485.9315185546875 0.31611788272857666 576.4886474609375 0.4027121067047119 0.8269978 0.9925678968429565 True -2 8202 30.374393463134766 0.6527683734893799 503.839111328125 0.24997586011886597 566.8179321289062 0.4149647057056427 0.83932936 0.41184163093566895 True -3 10936 30.298388719558716 0.8866913318634033 499.1297607421875 0.32816028594970703 560.9008178710938 0.42231979966163635 0.8512084 0.3568216562271118 True -4 13670 30.297643661499023 0.6084890365600586 488.400146484375 0.23686078190803528 557.6829223632812 0.4263024628162384 0.8595034 0.33053290843963623 True -5 16404 29.85084843635559 0.5929703712463379 495.43719482421875 0.38907575607299805 556.8594360351562 0.4269879162311554 0.86082655 0.2701292037963867 True -6 19138 29.643371105194092 0.5852067470550537 532.2225952148438 0.23128007352352142 556.3251342773438 0.42779868841171265 0.8645767 0.26159587502479553 True -7 21872 29.69444727897644 0.5922539234161377 535.1385498046875 0.2110523283481598 555.0459594726562 0.4287157356739044 0.8678789 0.2636740505695343 True -8 24606 29.640869855880737 0.5941472053527832 505.1114501953125 0.2454644739627838 552.4810180664062 0.43346551060676575 0.87227243 0.26245763897895813 True -9 27340 29.689758777618408 0.6522679328918457 502.3680419921875 0.2707177698612213 551.7457885742188 0.433727890253067 0.87530684 0.24545705318450928 True -10 30074 29.63497233390808 0.5889418125152588 461.48919677734375 0.15361478924751282 549.3761596679688 0.4383198916912079 0.879073 0.23720990121364594 True -11 32808 29.637014627456665 1.7926709651947021 489.3977966308594 0.285065233707428 548.2078247070312 0.4402032494544983 0.88210684 0.22092221677303314 True -12 35542 29.681215286254883 0.5862715244293213 505.56390380859375 0.22096146643161774 547.494140625 0.4406430125236511 0.8845622 0.2095666229724884 True -13 38276 29.761365175247192 0.612839937210083 496.5975341796875 0.20980140566825867 547.0106811523438 0.44112956523895264 0.88879013 0.19757632911205292 True -14 41010 29.858680248260498 0.5945711135864258 527.870361328125 0.2068989872932434 547.1964721679688 0.43951085209846497 0.89202076 0.18284524977207184 True -15 43744 29.786200284957886 0.5989043712615967 513.7783203125 0.2128230333328247 545.9334106445312 0.4420902132987976 0.89609104 0.17097900807857513 True -16 46478 29.777698278427124 0.6035914421081543 504.48773193359375 0.14080652594566345 545.328369140625 0.44199323654174805 0.8984725 0.15767301619052887 True -17 49212 29.775466918945312 0.5926716327667236 553.777587890625 0.11435996741056442 545.8724365234375 0.4415651559829712 0.90024763 0.15132656693458557 True -18 51946 29.830875158309937 0.6062717437744141 509.8434143066406 0.08805084973573685 545.8603515625 0.4416652321815491 0.8999671 0.1501401662826538 False -19 54680 29.785573959350586 0.594419002532959 500.7369384765625 0.13474906980991364 545.53759765625 0.44249463081359863 0.898154 0.15036578476428986 False diff --git a/ENCSR702DPD/cherimoya.fold_0.performance.tsv b/ENCSR702DPD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 09a2d073cb11e4a765363c8a7ae385b96464a2e9..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -545.8724365234375 0.36458784341812134 0.4415651559829712 0.17762726545333862 0.9002476334571838 0.8775448799133301 0.15132656693458557 \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_1.evaluate.json b/ENCSR702DPD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 015e8c593f5d3beeb0b30f0dcd8e8602a7aafab5..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF127WYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_1.fit.json b/ENCSR702DPD/cherimoya.fold_1.fit.json deleted file mode 100644 index 5fa25f189b0e82b50f8155f703d4185b07c67303..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF127WYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_1.log b/ENCSR702DPD/cherimoya.fold_1.log deleted file mode 100644 index f909cf6f63dccde748ebc3e5736592d67a377145..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2715 34.81750822067261 4.2182862758636475 514.9463500976562 0.2353729009628296 745.449462890625 0.3385525047779083 0.7921012 5.625180721282959 True -1 5430 29.98668122291565 1.082327127456665 401.58990478515625 0.1980452537536621 678.1983642578125 0.4154870808124542 0.83089846 1.096934199333191 True -2 8145 29.901690006256104 0.8586468696594238 448.70428466796875 0.19848251342773438 660.8506469726562 0.4355649948120117 0.8502704 0.5203097462654114 True -3 10860 29.395307779312134 0.8462793827056885 484.9122619628906 0.31017059087753296 656.5466918945312 0.43741774559020996 0.85653126 0.44909635186195374 True -4 13575 29.432759284973145 0.7355625629425049 482.26324462890625 0.18600338697433472 652.5126342773438 0.44292327761650085 0.86229706 0.3669585883617401 True -5 16290 29.435919761657715 0.7190062999725342 529.66748046875 0.2899262011051178 651.03173828125 0.44572341442108154 0.86547697 0.33385080099105835 True -6 19005 29.39560866355896 0.7970435619354248 428.385009765625 0.17533521354198456 649.259521484375 0.4466129243373871 0.8693677 0.3238770365715027 True -7 21720 29.40687370300293 0.716928243637085 516.8177490234375 0.19938528537750244 647.0661010742188 0.44999468326568604 0.8705741 0.32020634412765503 True -8 24435 29.377926111221313 0.7398278713226318 548.9193115234375 0.24930556118488312 644.4361572265625 0.4536821246147156 0.8737477 0.3022494316101074 True -9 27150 29.422996282577515 0.7435247898101807 575.2881469726562 0.2988736033439636 644.0604248046875 0.4532761871814728 0.8785383 0.2955422103404999 True -10 29865 29.422380924224854 0.7408673763275146 501.4309387207031 0.18909481167793274 642.276611328125 0.4558500051498413 0.88268375 0.2774529457092285 True -11 32580 29.35295605659485 0.7182962894439697 473.5716552734375 0.13815411925315857 640.6251220703125 0.45806241035461426 0.8827981 0.2823200821876526 True -12 35295 29.37725019454956 0.7196557521820068 476.9261474609375 0.16541653871536255 638.5338134765625 0.46078523993492126 0.88736016 0.2681536078453064 True -13 38010 29.41247820854187 2.931652784347534 560.4947509765625 0.201157808303833 636.1698608398438 0.46321338415145874 0.8911871 0.23715661466121674 True -14 40725 29.823548793792725 0.7262828350067139 532.0758056640625 0.15703493356704712 636.4641723632812 0.46152928471565247 0.8972465 0.21346114575862885 True -15 43440 29.352313995361328 19.307654857635498 438.08905029296875 0.15534526109695435 636.309814453125 0.4617021381855011 0.90023136 0.19728344678878784 True -16 46155 29.383115768432617 10.930569887161255 466.7071228027344 0.17123498022556305 635.0862426757812 0.46322697401046753 0.9027918 0.18176324665546417 True -17 48870 29.86724019050598 0.746286153793335 480.0090026855469 0.20997056365013123 635.2726440429688 0.46342623233795166 0.9040113 0.1729191690683365 True -18 51585 29.513360023498535 0.7112135887145996 416.7748107910156 0.16554924845695496 636.0947875976562 0.4611392319202423 0.90578127 0.1704014092683792 True -19 54300 29.55723762512207 0.7597405910491943 523.28857421875 0.18793927133083344 637.5169067382812 0.4584738314151764 0.90398353 0.16811370849609375 False diff --git a/ENCSR702DPD/cherimoya.fold_1.performance.tsv b/ENCSR702DPD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 85030d0ba063ddcddef27a70054711f5fc1bec1d..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -636.0947875976562 0.34447693824768066 0.4611392319202423 0.20554612576961517 0.9057812690734863 0.8977455496788025 0.1704014092683792 \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_2.evaluate.json b/ENCSR702DPD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index df5b80416ff09ace8cd5c72af1fafd5226f1cfd0..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF127WYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_2.fit.json b/ENCSR702DPD/cherimoya.fold_2.fit.json deleted file mode 100644 index 988923d537a0626f1d68718623bbec90f9b64141..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF127WYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_2.log b/ENCSR702DPD/cherimoya.fold_2.log deleted file mode 100644 index a9c486c88b9ba915c00a714f83a681631d28475a..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.79350256919861 3.9869000911712646 545.032470703125 0.2538036108016968 670.217041015625 0.33903977274894714 0.78561276 4.050563812255859 True -1 5794 31.995392322540283 0.598447322845459 473.3392333984375 0.34824782609939575 612.4094848632812 0.4116305708885193 0.8353265 1.0327993631362915 True -2 8691 31.661231517791748 0.5347938537597656 487.7095642089844 0.2721024751663208 601.220947265625 0.4222954511642456 0.8490373 0.36154770851135254 True -3 11588 31.47343921661377 0.5343542098999023 592.4027099609375 0.278848260641098 598.267333984375 0.42528241872787476 0.8577576 0.34113892912864685 True -4 14485 31.433227062225342 0.6595964431762695 499.5508117675781 0.18310391902923584 594.9622802734375 0.43018046021461487 0.8599346 0.30832335352897644 True -5 17382 31.434533834457397 0.5511887073516846 486.75042724609375 0.2160908728837967 594.7042236328125 0.4304814040660858 0.8630418 0.28416746854782104 True -6 20279 31.492766618728638 0.5484437942504883 511.96417236328125 0.2847355604171753 592.7713623046875 0.4326782822608948 0.8643594 0.27452352643013 True -7 23176 31.510411500930786 0.5490808486938477 452.7922058105469 0.2752927243709564 591.7839965820312 0.4333585202693939 0.868785 0.26912662386894226 True -8 26073 31.752559423446655 0.5377874374389648 480.6585693359375 0.2545764744281769 591.1273193359375 0.43438538908958435 0.8698237 0.26038146018981934 True -9 28970 31.47700262069702 0.5694313049316406 362.6741027832031 0.20982222259044647 587.9884643554688 0.439052939414978 0.87503093 0.24499155580997467 True -10 31867 31.536340475082397 0.5557897090911865 503.7738952636719 0.17714571952819824 587.1265258789062 0.44017964601516724 0.8792238 0.24274814128875732 True -11 34764 31.499710083007812 11.172941446304321 499.0406799316406 0.11929848045110703 587.0560913085938 0.4390261173248291 0.8823015 0.23213528096675873 True -12 37661 31.540680408477783 0.5768647193908691 481.9510803222656 0.10386843979358673 585.66748046875 0.44161713123321533 0.8841419 0.21352121233940125 True -13 40558 32.171995401382446 0.5507853031158447 468.4031677246094 0.13904011249542236 585.6069946289062 0.4404354691505432 0.8864981 0.2008960247039795 True -14 43455 31.436004638671875 0.5513389110565186 498.955078125 0.1516544371843338 583.2247924804688 0.444444864988327 0.8892777 0.1893596351146698 True -15 46352 31.501580953598022 0.5827019214630127 534.7413940429688 0.26128101348876953 583.7355346679688 0.44272056221961975 0.892953 0.1777879148721695 True -16 49249 31.489715576171875 0.544501781463623 437.86871337890625 0.13459229469299316 582.7199096679688 0.4434852600097656 0.8954989 0.1686336249113083 True -17 52146 31.47141718864441 0.5527644157409668 513.474609375 0.08844593912363052 583.380859375 0.4439258575439453 0.8967899 0.1643342524766922 True -18 55043 31.469809770584106 0.5530595779418945 527.3370361328125 0.10420513898134232 582.4089965820312 0.4450894594192505 0.8950544 0.16186760365962982 False -19 57940 31.376289129257202 0.5454072952270508 429.20477294921875 0.11847343295812607 583.2118530273438 0.4432852268218994 0.89737093 0.16194571554660797 True diff --git a/ENCSR702DPD/cherimoya.fold_2.performance.tsv b/ENCSR702DPD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a45900f09d5d434d534e2abc2c073e6eacfbb4df..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -583.2118530273438 0.35922133922576904 0.4432852566242218 0.18507638573646545 0.8973709344863892 0.8826872110366821 0.16194571554660797 \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_3.evaluate.json b/ENCSR702DPD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 27c2daa7149b2f26462f4c20ecad1474d08190cc..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF127WYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_3.fit.json b/ENCSR702DPD/cherimoya.fold_3.fit.json deleted file mode 100644 index 6159ef0e84282b74faf7105407cb6a15ff67176e..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF127WYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_3.log b/ENCSR702DPD/cherimoya.fold_3.log deleted file mode 100644 index 87896afe8a8bd2206befcd05b6d7038b7ebf71f0..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.092395544052124 3.4710264205932617 472.802001953125 0.21980804204940796 612.7423095703125 0.3447762131690979 0.77273035 4.795180797576904 True -1 5508 30.43336272239685 0.6322107315063477 528.8914184570312 0.2321995496749878 561.4746704101562 0.41367587447166443 0.82432216 1.0846991539001465 True -2 8262 30.374845266342163 0.6822707653045654 513.5288696289062 0.3031754493713379 554.1929321289062 0.4213870167732239 0.83756095 0.512480616569519 True -3 11016 30.192604303359985 0.525209903717041 428.00482177734375 0.2934877872467041 549.6005859375 0.42570993304252625 0.8453484 0.5386103391647339 True -4 13770 29.840113639831543 17.587528944015503 500.5283203125 0.30745112895965576 547.0631713867188 0.42979857325553894 0.8484801 0.3651778995990753 True -5 16524 29.85304856300354 0.729240894317627 513.9678955078125 0.11101046204566956 546.7037353515625 0.4290662109851837 0.8522181 0.3398439884185791 True -6 19278 29.851163864135742 0.5354468822479248 520.3438720703125 0.24835273623466492 544.5870361328125 0.43321725726127625 0.8552582 0.35215944051742554 True -7 22032 29.924051523208618 0.557330846786499 519.9584350585938 0.2536904811859131 543.0582885742188 0.43429210782051086 0.8597961 0.35744285583496094 True -8 24786 29.890254020690918 0.5712137222290039 466.8657531738281 0.27397167682647705 540.6216430664062 0.4383142590522766 0.8652123 0.32389962673187256 True -9 27540 29.96391224861145 0.5520334243774414 382.6053466796875 0.12626245617866516 540.460205078125 0.4386267364025116 0.8698777 0.32423949241638184 True -10 30294 29.9170925617218 0.5463674068450928 524.8199462890625 0.17917025089263916 539.20556640625 0.4391038715839386 0.87322277 0.307900071144104 True -11 33048 29.87557625770569 0.541419506072998 559.2277221679688 0.12329578399658203 537.3980102539062 0.44221559166908264 0.87719476 0.2816371023654938 True -12 35802 29.99487590789795 0.5371711254119873 508.82464599609375 0.20881564915180206 537.4762573242188 0.4411185681819916 0.87985575 0.2572392523288727 True -13 38556 29.828975200653076 0.5321245193481445 446.7061462402344 0.13962224125862122 536.422119140625 0.4421580135822296 0.8816371 0.22977201640605927 True -14 41310 29.784459352493286 0.5463416576385498 506.20672607421875 0.16201148927211761 535.8013916015625 0.44324585795402527 0.887428 0.20496296882629395 True -15 44064 29.87490725517273 0.5240981578826904 433.93536376953125 0.1325942873954773 534.1075439453125 0.44583576917648315 0.89106804 0.1905939131975174 True -16 46818 29.86683940887451 0.5430097579956055 420.9551696777344 0.11910507827997208 534.4546508789062 0.44459810853004456 0.8927206 0.17423135042190552 True -17 49572 29.89248752593994 0.5360407829284668 496.2867431640625 0.07617161422967911 535.2451171875 0.44319605827331543 0.8931185 0.1673445850610733 True -18 52326 29.956754207611084 12.594358205795288 498.86114501953125 0.08926577866077423 535.25390625 0.44466492533683777 0.8941914 0.1654832810163498 True -19 55080 29.899986028671265 0.5451889038085938 469.61358642578125 0.13987645506858826 535.2402954101562 0.44410279393196106 0.89279276 0.16415077447891235 False diff --git a/ENCSR702DPD/cherimoya.fold_3.performance.tsv b/ENCSR702DPD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 45fbdc1cebc74b0e13314195cb2ea6ea76d90681..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -535.25390625 0.3630467653274536 0.44466495513916016 0.17866814136505127 0.8941913843154907 0.866194486618042 0.1654832810163498 \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_4.evaluate.json b/ENCSR702DPD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 827c1a2286acf6331103037175cbc2b2f90c6304..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF127WYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_4.fit.json b/ENCSR702DPD/cherimoya.fold_4.fit.json deleted file mode 100644 index ccd4d7c8546158700b8981a46921a010a7038ddd..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF127WYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR702DPD/cherimoya.fold_4.log b/ENCSR702DPD/cherimoya.fold_4.log deleted file mode 100644 index e0bc66caac8ce1ee44f1bb253b52a003559bbd2b..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.50740051269531 3.001793146133423 606.1082763671875 0.29963505268096924 589.2406616210938 0.3394305109977722 0.7723086 4.3966965675354 True -1 5596 30.933797359466553 0.5633690357208252 502.63885498046875 0.3042561411857605 543.5017700195312 0.4025636911392212 0.81878185 1.0010818243026733 True -2 8394 30.9052951335907 0.5595090389251709 518.727783203125 0.30437421798706055 534.393310546875 0.4140583574771881 0.83863264 0.4060632884502411 True -3 11192 30.360370635986328 0.524808406829834 530.3802490234375 0.19507241249084473 530.47314453125 0.41920095682144165 0.84527063 0.36676111817359924 True -4 13990 30.245295524597168 0.5387983322143555 470.133056640625 0.19419166445732117 530.49658203125 0.41830021142959595 0.8433166 0.3252665400505066 False -5 16788 30.285086393356323 0.5390639305114746 455.720703125 0.2507088780403137 528.0350341796875 0.42208704352378845 0.8523897 0.2741129696369171 True -6 19586 30.324852466583252 0.524519681930542 504.70068359375 0.2097383290529251 525.092041015625 0.4276009202003479 0.857387 0.25678750872612 True -7 22384 30.52618408203125 0.5234665870666504 470.7342529296875 0.24322645366191864 524.5817260742188 0.42744484543800354 0.8604092 0.24050267040729523 True -8 25182 30.71038794517517 0.5152719020843506 432.0427551269531 0.17972305417060852 524.758544921875 0.4262535274028778 0.8655813 0.23456953465938568 True -9 27980 30.2833149433136 0.5371592044830322 483.91278076171875 0.23564976453781128 522.8593139648438 0.43026548624038696 0.8685972 0.23116359114646912 True -10 30778 30.264309883117676 0.7538104057312012 468.69024658203125 0.20316022634506226 521.3681640625 0.4326263666152954 0.87066215 0.22089043259620667 True -11 33576 30.29645872116089 0.5242655277252197 554.7166748046875 0.19281208515167236 520.4390869140625 0.434166818857193 0.8767789 0.20410151779651642 True -12 36374 30.249823808670044 0.5216400623321533 480.8158264160156 0.14079704880714417 520.253173828125 0.4327772557735443 0.87837034 0.19740347564220428 True -13 39172 30.23981022834778 0.550086498260498 482.27166748046875 0.10219024121761322 518.8110961914062 0.43626469373703003 0.8842717 0.182149276137352 True -14 41970 30.30670166015625 0.5231287479400635 483.8702392578125 0.1206025779247284 518.5289916992188 0.4352470934391022 0.8881016 0.16980071365833282 True -15 44768 30.298166751861572 0.9912898540496826 543.3984375 0.18893776834011078 518.2588500976562 0.43530339002609253 0.8913466 0.1588921844959259 True -16 47566 30.284071445465088 0.53839111328125 548.7529296875 0.17524659633636475 517.6893310546875 0.4354996085166931 0.8925661 0.14922063052654266 True -17 50364 30.265851497650146 1.5693845748901367 425.68121337890625 0.17414413392543793 518.0325927734375 0.43627551198005676 0.89427185 0.14411243796348572 True -18 53162 30.275039672851562 0.5447671413421631 499.4823913574219 0.12025735527276993 518.0716552734375 0.43641677498817444 0.89408004 0.1424499750137329 False -19 55960 30.27409529685974 0.5328309535980225 507.95977783203125 0.13327933847904205 518.3822631835938 0.4355972707271576 0.8945792 0.14201469719409943 True diff --git a/ENCSR702DPD/cherimoya.fold_4.performance.tsv b/ENCSR702DPD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2ac11dd6b32fbe15fa3ec79c9e0644f9a559a386..0000000000000000000000000000000000000000 --- a/ENCSR702DPD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -518.3822631835938 0.3700648546218872 0.4355972409248352 0.1720750629901886 0.8945791721343994 0.8678337335586548 0.14201469719409943 \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_0.evaluate.json b/ENCSR703VGI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2bfc8b69c915fa6cf0a0f6e91a1ebc6e298d2e40..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF140ONW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_0.fit.json b/ENCSR703VGI/cherimoya.fold_0.fit.json deleted file mode 100644 index 58820fd6d63a955647e1c50521c1363b9b597776..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF140ONW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_0.log b/ENCSR703VGI/cherimoya.fold_0.log deleted file mode 100644 index 8a9d1a648dd120db9f7e616e0536536f63674654..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 37.96902251243591 3.67620587348938 618.93505859375 0.7218227982521057 733.4848022460938 0.13435471057891846 0.62111944 5.679950714111328 True -1 5512 31.195574522018433 1.4940595626831055 751.3165283203125 1.0066308975219727 669.1687622070312 0.1714501529932022 0.7219327 3.76540207862854 True -2 8268 30.30506730079651 17.02188801765442 553.5809936523438 0.9452903270721436 662.9765625 0.17085908353328705 0.70686376 2.405722141265869 False -3 11024 29.686444520950317 0.5509557723999023 671.3768920898438 1.197990894317627 639.9880981445312 0.1806204468011856 0.7201978 1.64382803440094 False -4 13780 29.68373394012451 0.5425641536712646 375.5928955078125 0.376467227935791 628.2775268554688 0.18406851589679718 0.74588704 1.330069661140442 True -5 16536 31.776689291000366 0.5366318225860596 535.3350830078125 0.5652147531509399 618.3340454101562 0.19010983407497406 0.76081073 1.1811997890472412 True -6 19292 29.724279165267944 0.5421233177185059 503.16705322265625 0.5069211721420288 615.18505859375 0.19180041551589966 0.7662781 1.0976606607437134 True -7 22048 29.754249811172485 0.5371582508087158 611.5604248046875 0.7223036885261536 610.9947509765625 0.19306491315364838 0.77907133 1.0032285451889038 True -8 24804 29.843629360198975 0.5381917953491211 500.7378234863281 0.5798778533935547 606.8173828125 0.195866197347641 0.79014474 0.8536344766616821 True -9 27560 29.80494475364685 0.5355572700500488 573.7347412109375 0.6720520853996277 600.7020263671875 0.20012328028678894 0.78943664 0.8112519383430481 False -10 30316 29.712630033493042 0.5371072292327881 661.0249633789062 1.0806150436401367 598.9332275390625 0.2005615085363388 0.79760003 0.7180008292198181 True -11 33072 29.695719242095947 1.6653954982757568 373.52532958984375 0.6334089040756226 595.6205444335938 0.20252305269241333 0.8110247 0.6404962539672852 True -12 35828 29.858046770095825 0.5499792098999023 641.767333984375 0.6818336248397827 592.0527954101562 0.2031383067369461 0.8184708 0.5610219240188599 True -13 38584 29.68713879585266 0.5431454181671143 379.6275329589844 0.9240260720252991 588.2136840820312 0.20474311709403992 0.8273781 0.5256667137145996 True -14 41340 34.295673847198486 29.17568874359131 543.83935546875 0.5256037712097168 585.72021484375 0.20585933327674866 0.8308565 0.49803656339645386 True -15 44096 29.945406675338745 0.5493409633636475 523.8265991210938 0.44305264949798584 584.7128295898438 0.20625342428684235 0.8370011 0.4778493046760559 True -16 46852 29.78197479248047 0.994255542755127 424.40875244140625 0.45867568254470825 580.9978637695312 0.2077736109495163 0.84133404 0.4600953161716461 True -17 49608 29.80228352546692 0.5382850170135498 422.3153991699219 0.3282555341720581 580.8982543945312 0.208176851272583 0.8410633 0.45557886362075806 False -18 52364 29.75690722465515 0.8674542903900146 455.7563171386719 0.5476240515708923 580.973388671875 0.20804233849048615 0.8423362 0.45476388931274414 True -19 55120 29.799391984939575 0.5413658618927002 468.6351318359375 0.3670111894607544 580.0733032226562 0.20870770514011383 0.8408765 0.45661938190460205 False diff --git a/ENCSR703VGI/cherimoya.fold_0.performance.tsv b/ENCSR703VGI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 93ebe2143b28c7a12867d1d11fdc63f5d1c35910..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -580.973388671875 0.5202747583389282 0.20804233849048615 0.08395808190107346 0.8423361778259277 0.7842524647712708 0.45476388931274414 \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_1.evaluate.json b/ENCSR703VGI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3fbab39a377f35fa8cbb35003d61e1865f7ff41d..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF140ONW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_1.fit.json b/ENCSR703VGI/cherimoya.fold_1.fit.json deleted file mode 100644 index 56ce7fd18434415673d3a80390410f2d9fd42167..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF140ONW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_1.log b/ENCSR703VGI/cherimoya.fold_1.log deleted file mode 100644 index 682230c5360533229c7ae2d45b4aa8df0843d22f..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2704 34.2961266040802 3.768010377883911 468.38238525390625 0.6686834692955017 894.27294921875 0.14537717401981354 0.5948583 8.653054237365723 True -1 5408 29.682159900665283 0.7604176998138428 545.3209228515625 1.1558122634887695 799.7771606445312 0.1955064833164215 0.70249486 3.7588891983032227 True -2 8112 35.25226044654846 0.7534325122833252 394.6065979003906 0.4142911732196808 786.8380737304688 0.19666530191898346 0.7054445 2.8442459106445312 True -3 10816 29.890833854675293 0.7660713195800781 736.026611328125 1.1191269159317017 759.8687744140625 0.20784704387187958 0.73160547 2.040006637573242 True -4 13520 29.71053123474121 0.7563588619232178 513.2706298828125 0.5749874114990234 751.9528198242188 0.21072670817375183 0.7374551 1.7039158344268799 True -5 16224 29.734464645385742 0.7576642036437988 416.31671142578125 0.44012337923049927 734.5860595703125 0.21634028851985931 0.7638174 1.3886874914169312 True -6 18928 29.79154896736145 1.570695161819458 548.3836669921875 0.9963946342468262 727.4769897460938 0.21951529383659363 0.7776722 1.230696439743042 True -7 21632 29.755568981170654 0.7639095783233643 702.0511474609375 0.7795325517654419 720.653076171875 0.22149305045604706 0.7900683 0.9909324049949646 True -8 24336 29.79320001602173 1.6084949970245361 468.3497619628906 0.6312779188156128 715.5570678710938 0.22498776018619537 0.79628396 0.9082880616188049 True -9 27040 29.71911597251892 0.7582502365112305 402.12310791015625 0.554012656211853 714.9572143554688 0.22512361407279968 0.80378115 0.8704075813293457 True -10 29744 29.70237708091736 1.1248281002044678 533.4285888671875 0.5696448087692261 710.5104370117188 0.2287561595439911 0.8068369 0.8591877818107605 True -11 32448 29.715380907058716 0.7531311511993408 462.68218994140625 0.41176092624664307 707.0760498046875 0.23033910989761353 0.8146527 0.7681413292884827 True -12 35152 29.73694634437561 7.2450361251831055 510.3804626464844 0.37475040555000305 702.8950805664062 0.23327407240867615 0.8178777 0.7398016452789307 True -13 37856 29.710487127304077 0.7403650283813477 441.70452880859375 0.5178571343421936 699.4926147460938 0.23444071412086487 0.82476556 0.712679922580719 True -14 40560 32.09016561508179 34.120408058166504 389.8744812011719 0.6174442768096924 694.7373657226562 0.23644819855690002 0.83428645 0.6454480886459351 True -15 43264 30.19425106048584 0.7588984966278076 392.50457763671875 0.6461975574493408 691.8981323242188 0.2368474155664444 0.8436694 0.5751173496246338 True -16 45968 29.780807733535767 0.7436060905456543 454.05572509765625 0.31435972452163696 688.4136352539062 0.23789362609386444 0.8478533 0.5415816307067871 True -17 48672 29.731257677078247 1.2570502758026123 495.87738037109375 0.24931694567203522 684.83544921875 0.2399464100599289 0.8484159 0.5242459177970886 True -18 51376 29.812925100326538 0.7483477592468262 426.629150390625 0.41340482234954834 688.3605346679688 0.23688241839408875 0.8498074 0.516261100769043 True -19 54080 29.320587396621704 0.7459943294525146 449.0906982421875 0.22760649025440216 688.4754028320312 0.2371038794517517 0.8477066 0.5153205990791321 False diff --git a/ENCSR703VGI/cherimoya.fold_1.performance.tsv b/ENCSR703VGI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5a58179c00a38e2e9147a57c5614b51e06fb2e71..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -688.3605346679688 0.4961257874965668 0.23688244819641113 0.10205566138029099 0.8498073816299438 0.8176499009132385 0.516261100769043 \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_2.evaluate.json b/ENCSR703VGI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f59fd69ccddad6b3c0b40d849d6292385b7d24e4..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF140ONW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_2.fit.json b/ENCSR703VGI/cherimoya.fold_2.fit.json deleted file mode 100644 index 6e3ce809d1d5d38f9665b2a1a42d6671c6d515f6..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF140ONW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_2.log b/ENCSR703VGI/cherimoya.fold_2.log deleted file mode 100644 index e7fafb1307b2a166e7b9d1ebf95b57c557fd5d78..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2861 36.09582161903381 3.6137847900390625 495.28240966796875 0.8577097654342651 738.5076904296875 0.13263742625713348 0.5878408 6.464548110961914 True -1 5722 31.44189190864563 0.6232426166534424 575.3172607421875 1.3657268285751343 660.2637329101562 0.17364464700222015 0.714642 3.1113240718841553 True -2 8583 31.65066695213318 0.5931241512298584 397.6901550292969 0.49385374784469604 656.1179809570312 0.17315581440925598 0.7018478 2.3679327964782715 False -3 11444 31.487709522247314 0.5958852767944336 527.367919921875 0.9441239237785339 633.601318359375 0.18199269473552704 0.73878455 1.5625941753387451 True -4 14305 31.3865065574646 19.844597816467285 689.7257690429688 1.1167105436325073 620.623779296875 0.18643474578857422 0.75582117 1.3650059700012207 True -5 17166 31.367565155029297 0.6237523555755615 516.26513671875 0.8691288232803345 613.6316528320312 0.1898043155670166 0.76300746 1.1339445114135742 True -6 20027 31.805312156677246 0.6187515258789062 448.02581787109375 0.6795869469642639 610.4408569335938 0.19199128448963165 0.7702816 1.0577728748321533 True -7 22888 31.470410346984863 23.523921728134155 532.3831787109375 0.5698749423027039 605.7052612304688 0.1947358101606369 0.778695 0.9848816990852356 True -8 25749 31.5612735748291 0.6115016937255859 541.6160888671875 0.7808982133865356 602.4874877929688 0.1962074488401413 0.7888541 0.8148379921913147 True -9 28610 31.637264013290405 0.6169254779815674 550.6553955078125 0.5676872730255127 598.4762573242188 0.19931745529174805 0.7966363 0.7590250372886658 True -10 31471 31.57845115661621 0.6152148246765137 577.419677734375 0.5138712525367737 597.3778076171875 0.1999794840812683 0.7996805 0.7380973100662231 True -11 34332 31.66022801399231 0.6127550601959229 555.510986328125 0.5989336967468262 593.0186157226562 0.2029694765806198 0.8081223 0.671808660030365 True -12 37193 31.160120248794556 0.9071667194366455 663.335693359375 0.7967379093170166 588.9132690429688 0.2047925591468811 0.81549996 0.6049574017524719 True -13 40054 31.021024703979492 21.93149757385254 360.3328857421875 0.5315155982971191 585.6580810546875 0.20723022520542145 0.82417506 0.5481705069541931 True -14 42915 30.99501085281372 0.6002514362335205 408.53436279296875 0.5497552156448364 584.2073364257812 0.2071109265089035 0.8288724 0.5147254467010498 True -15 45776 30.946561574935913 0.8699691295623779 497.8251647949219 0.6771764755249023 579.1189575195312 0.21048381924629211 0.83700943 0.4744490683078766 True -16 48637 30.929351806640625 0.601179838180542 516.6421508789062 0.43000197410583496 578.926025390625 0.2095128893852234 0.8403218 0.45084279775619507 True -17 51498 30.979254484176636 27.415496349334717 439.99407958984375 0.42130136489868164 579.2810668945312 0.20855192840099335 0.84178793 0.4342344403266907 True -18 54359 31.803560256958008 0.6048128604888916 413.0162353515625 0.46302491426467896 580.0577392578125 0.20813371241092682 0.8431781 0.4302217960357666 True -19 57220 30.964648485183716 0.6000974178314209 405.15093994140625 0.42321261763572693 577.9609375 0.21061448752880096 0.84244025 0.4311581254005432 False diff --git a/ENCSR703VGI/cherimoya.fold_2.performance.tsv b/ENCSR703VGI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3e4fde230b623afbcbeb7810bd96809a7e7bf1d1..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -580.0577392578125 0.518333911895752 0.20813369750976562 0.0817963182926178 0.8431780934333801 0.787159264087677 0.4302217960357666 \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_3.evaluate.json b/ENCSR703VGI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 758f2fde9d6def0caafe77c4d06f1307501bc65f..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF140ONW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_3.fit.json b/ENCSR703VGI/cherimoya.fold_3.fit.json deleted file mode 100644 index 552597409ab0afcd75dbb01f961a5a1d1167d52b..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF140ONW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_3.log b/ENCSR703VGI/cherimoya.fold_3.log deleted file mode 100644 index dede7ef8dd5358b5467dfb7f52666dd84bd55f46..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 34.297788858413696 3.4911551475524902 553.818115234375 0.6021281480789185 794.4329833984375 0.14383547008037567 0.5856295 6.898862838745117 True -1 5528 30.59335994720459 0.6783361434936523 521.5830078125 0.8859937191009521 725.0087280273438 0.18319550156593323 0.659774 4.465768337249756 True -2 8292 30.42763900756836 0.5268850326538086 429.3188781738281 0.6587067246437073 716.9920043945312 0.18623173236846924 0.65969294 2.9560341835021973 False -3 11056 30.41458225250244 0.5469050407409668 559.8659057617188 0.9585676193237305 696.8240356445312 0.19365282356739044 0.7013859 2.2034528255462646 True -4 13820 30.44280171394348 2.538217306137085 494.476318359375 0.6848499774932861 678.36083984375 0.20248883962631226 0.7148368 1.866593599319458 True -5 16584 30.498006343841553 0.5310978889465332 405.87384033203125 0.9324629306793213 668.0478515625 0.20580486953258514 0.73418367 1.5824182033538818 True -6 19348 30.51759362220764 0.5454199314117432 385.3855285644531 0.3994653820991516 664.9091186523438 0.2063763439655304 0.75151414 1.4248950481414795 True -7 22112 30.420251607894897 0.5299434661865234 480.89447021484375 0.8389617800712585 659.5883178710938 0.20911100506782532 0.7605602 1.2633241415023804 True -8 24876 30.427861213684082 1.6149308681488037 573.8130493164062 0.5734492540359497 654.1729125976562 0.21184256672859192 0.76682556 1.1625993251800537 True -9 27640 30.417956590652466 0.5455484390258789 527.0865478515625 0.7801350951194763 651.584716796875 0.2128017693758011 0.7723967 1.0698386430740356 True -10 30404 30.426313638687134 0.539024829864502 570.4480590820312 0.49795934557914734 645.8720703125 0.21559827029705048 0.78169703 0.9260761141777039 True -11 33168 30.548364400863647 0.5429871082305908 408.7342529296875 0.47981855273246765 641.406494140625 0.21893149614334106 0.7860261 0.8779590129852295 True -12 35932 30.472668170928955 0.5411896705627441 563.512939453125 0.4102175235748291 639.3019409179688 0.22054268419742584 0.79081976 0.8056021332740784 True -13 38696 30.474803924560547 0.5438840389251709 499.07269287109375 0.7699868679046631 637.333740234375 0.22128987312316895 0.7952455 0.7888320088386536 True -14 41460 30.433000326156616 0.5424327850341797 434.072265625 0.34933120012283325 632.9147338867188 0.22371257841587067 0.80211705 0.7204799652099609 True -15 44224 30.554041862487793 0.8248183727264404 562.5722045898438 0.47691580653190613 627.9072875976562 0.226629376411438 0.80917853 0.665606677532196 True -16 46988 32.79430389404297 4.642773151397705 385.1468505859375 0.503096342086792 628.656005859375 0.22547665238380432 0.8162965 0.6176366806030273 True -17 49752 30.594216346740723 0.560114860534668 367.6222839355469 0.5701711177825928 626.54931640625 0.22619736194610596 0.82067287 0.5853216648101807 True -18 52516 30.638854503631592 0.541572093963623 500.0926513671875 0.4441079795360565 625.98388671875 0.2263191044330597 0.82279885 0.5739063024520874 True -19 55280 30.529690742492676 0.5507190227508545 485.3848571777344 0.4772558808326721 629.1661376953125 0.22341112792491913 0.8219889 0.5717198252677917 False diff --git a/ENCSR703VGI/cherimoya.fold_3.performance.tsv b/ENCSR703VGI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6fa6ec367fdc64ee54bf557bf20ed3b8e2deefe9..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -625.98388671875 0.5084338784217834 0.2263191193342209 0.09110073745250702 0.8227988481521606 0.7846145629882812 0.5739063024520874 \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_4.evaluate.json b/ENCSR703VGI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4c0fd2f14d43e1498c2860bcf0421017553cbf6a..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF140ONW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_4.fit.json b/ENCSR703VGI/cherimoya.fold_4.fit.json deleted file mode 100644 index 52c7a17ddc5937a9dcb1af443ec9f251e710dcbd..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF140ONW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR703VGI/cherimoya.fold_4.log b/ENCSR703VGI/cherimoya.fold_4.log deleted file mode 100644 index e97b6943959e51521f37e69950d834df25afcda5..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2781 35.43445658683777 3.8760986328125 548.5306396484375 0.8278806209564209 644.2095336914062 0.12373559176921844 0.58783555 5.581831455230713 True -1 5562 30.800705671310425 2.924635410308838 414.2786560058594 0.8631871938705444 590.4798583984375 0.15843415260314941 0.68388176 2.614865779876709 True -2 8343 32.67549180984497 2.506354808807373 554.0277709960938 0.8394314050674438 583.9769287109375 0.16059820353984833 0.6650783 2.264334201812744 False -3 11124 30.304081916809082 0.584437370300293 487.250732421875 0.6738312244415283 566.857177734375 0.16885094344615936 0.6855713 1.3509783744812012 True -4 13905 29.941974639892578 0.5790905952453613 565.1109619140625 1.0046508312225342 558.4829711914062 0.17097821831703186 0.7126853 1.2139742374420166 True -5 16686 29.922180652618408 0.8034582138061523 443.7984924316406 0.7066975831985474 548.2626342773438 0.17699578404426575 0.7267893 1.0125805139541626 True -6 19467 29.98747444152832 0.5718989372253418 377.8250427246094 0.6517521739006042 544.2964477539062 0.17748767137527466 0.7425103 0.899925708770752 True -7 22248 30.013697862625122 0.5774590969085693 417.185791015625 0.4558703899383545 537.3619384765625 0.18215012550354004 0.754313 0.7869606614112854 True -8 25029 30.02928066253662 0.5799059867858887 543.8431396484375 0.6280478835105896 534.8511962890625 0.18293894827365875 0.7618818 0.6936975717544556 True -9 27810 29.960355520248413 3.5990936756134033 596.125 0.544854462146759 533.2113037109375 0.18397298455238342 0.77136976 0.6445732116699219 True -10 30591 30.292948961257935 27.743945837020874 408.3656005859375 0.4441660940647125 531.1422729492188 0.18587304651737213 0.77418005 0.6109078526496887 True -11 33372 30.935152769088745 0.5739140510559082 481.2330322265625 0.4554600715637207 529.7011108398438 0.18686705827713013 0.7815225 0.5811766386032104 True -12 36153 30.107661485671997 0.5790402889251709 547.718994140625 0.36213478446006775 527.5454711914062 0.18798097968101501 0.79135156 0.5420136451721191 True -13 38934 30.21031641960144 0.5776863098144531 642.6136474609375 0.4481559991836548 525.8396606445312 0.18882285058498383 0.80135727 0.5099290013313293 True -14 41715 30.108050107955933 0.5656206607818604 409.16455078125 0.3694630563259125 523.3037719726562 0.19070225954055786 0.8093027 0.4782331585884094 True -15 44496 30.165700912475586 0.5697112083435059 426.3703308105469 0.3227938413619995 521.426025390625 0.19122718274593353 0.81494975 0.4625239670276642 True -16 47277 30.353199005126953 40.73656249046326 421.53948974609375 0.34074079990386963 521.104736328125 0.19120289385318756 0.8209324 0.4466733932495117 True -17 50058 30.073877573013306 30.178351163864136 525.6541748046875 0.430885374546051 520.335693359375 0.19219021499156952 0.8222605 0.44218239188194275 True -18 52839 30.73150062561035 0.5782575607299805 448.10418701171875 0.2535570561885834 519.6185913085938 0.19243845343589783 0.8229299 0.4432162940502167 True -19 55620 30.52854299545288 27.221807718276978 454.2052001953125 0.2781056761741638 521.0513916015625 0.19121141731739044 0.820368 0.4452812969684601 False diff --git a/ENCSR703VGI/cherimoya.fold_4.performance.tsv b/ENCSR703VGI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 19988b3979832b93a2ca6a26433b59890b719708..0000000000000000000000000000000000000000 --- a/ENCSR703VGI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -519.6185913085938 0.533147394657135 0.19243846833705902 0.07168393582105637 0.8229299187660217 0.7653989791870117 0.4432162940502167 \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_0.evaluate.json b/ENCSR704HNG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index fd8c75782127a5eec995ad90bc4997a69951c822..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF039IBG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_0.fit.json b/ENCSR704HNG/cherimoya.fold_0.fit.json deleted file mode 100644 index 74f878a06640666f97f092d3e7f0ba36a99f6fff..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF039IBG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_0.log b/ENCSR704HNG/cherimoya.fold_0.log deleted file mode 100644 index e936d42d626134d1ad81279f80e33adfa252272b..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1763 24.0979905128479 3.7455098628997803 3090.39453125 2.5489001274108887 5023.8408203125 0.23919525742530823 0.51064664 35.566688537597656 True -1 3526 19.393930673599243 0.33549952507019043 2747.87109375 1.7549189329147339 3755.504150390625 0.41899749636650085 0.65145373 19.173707962036133 True -2 5289 19.405152082443237 0.33263492584228516 2174.21533203125 1.526465892791748 3222.351806640625 0.47686466574668884 0.6698842 8.232131958007812 True -3 7052 19.3772451877594 0.34209370613098145 2527.609130859375 1.6012864112854004 3015.366943359375 0.4980359375476837 0.68076736 5.31264591217041 True -4 8815 19.33773183822632 0.3395545482635498 2116.48876953125 1.7712430953979492 2922.212646484375 0.5011820197105408 0.6952079 3.2605836391448975 True -5 10578 19.33266806602478 10.070176601409912 2264.876953125 1.176851511001587 2823.839599609375 0.5145587921142578 0.7051119 2.6288814544677734 True -6 12341 19.362314224243164 0.3438847064971924 2863.86474609375 1.8132002353668213 2770.732177734375 0.5213802456855774 0.7089255 2.2327523231506348 True -7 14104 19.383811235427856 0.3413515090942383 2131.78515625 1.1647231578826904 2739.178466796875 0.5266970992088318 0.71329 1.9227803945541382 True -8 15867 19.344088792800903 0.3383619785308838 2281.095703125 1.3637473583221436 2696.939453125 0.5358055233955383 0.7139392 1.7841079235076904 True -9 17630 19.388975620269775 0.3432025909423828 2744.366943359375 1.101407766342163 2668.419921875 0.54061359167099 0.7206572 1.5887119770050049 True -10 19393 19.348938703536987 0.6114988327026367 1932.74560546875 1.502378225326538 2622.843994140625 0.5489111542701721 0.72298443 1.4452669620513916 True -11 21156 19.358027458190918 0.34127354621887207 2673.85888671875 1.3673415184020996 2589.150146484375 0.5528351664543152 0.72891515 1.2507110834121704 True -12 22919 19.3700590133667 0.3485240936279297 1824.957763671875 0.9529726505279541 2554.056396484375 0.5565770864486694 0.7381781 1.1276743412017822 True -13 24682 19.33765745162964 0.3369019031524658 1920.2667236328125 1.01986563205719 2539.893310546875 0.5594426989555359 0.74447936 1.0563124418258667 True -14 26445 19.347330331802368 0.3381385803222656 2278.480712890625 0.8300299644470215 2513.69091796875 0.5633690357208252 0.7470169 1.0092285871505737 True -15 28208 19.365554809570312 0.3449995517730713 1390.4554443359375 1.3161602020263672 2492.6572265625 0.5642979741096497 0.75192696 0.9761137962341309 True -16 29971 19.35428786277771 0.35174131393432617 1823.496337890625 1.1771140098571777 2494.48388671875 0.5646854043006897 0.7567539 0.9459781646728516 True -17 31734 19.37134313583374 0.3389906883239746 1406.06640625 0.8971270322799683 2475.933837890625 0.5682594776153564 0.7589538 0.9381052255630493 True -18 33497 19.36785912513733 0.3396596908569336 2047.7581787109375 0.8637074828147888 2479.643310546875 0.5683061480522156 0.7596494 0.9329561591148376 True -19 35260 19.349883556365967 0.34641194343566895 1680.20458984375 0.8815996050834656 2494.094970703125 0.5650227069854736 0.7589092 0.9330703616142273 False diff --git a/ENCSR704HNG/cherimoya.fold_0.performance.tsv b/ENCSR704HNG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 0af7e4becc3c631948a934dab95004385add61c9..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2479.643310546875 0.21944813430309296 0.5683060884475708 0.3640254735946655 0.759649395942688 0.688622236251831 0.9329561591148376 \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_1.evaluate.json b/ENCSR704HNG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 97bc03d11e3e8fd42b9e70eb8a971e6fab3e1370..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF039IBG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_1.fit.json b/ENCSR704HNG/cherimoya.fold_1.fit.json deleted file mode 100644 index 6b7c1d26edd26c858f2f66113de25df774f7939a..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF039IBG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_1.log b/ENCSR704HNG/cherimoya.fold_1.log deleted file mode 100644 index 14990cc02a090d8eede1348a9e0c448eb8930089..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1734 23.734199047088623 4.021259784698486 2837.6572265625 2.667635440826416 6040.361328125 0.23520958423614502 0.4698077 39.650108337402344 True -1 3468 18.79404854774475 0.547461986541748 2560.5419921875 1.252908706665039 4573.74365234375 0.41756537556648254 0.6212639 15.437039375305176 True -2 5202 19.048492908477783 0.5230941772460938 2558.748046875 1.2909770011901855 3857.978515625 0.4798397421836853 0.6741546 8.007104873657227 True -3 6936 19.07112145423889 0.5380470752716064 1617.6287841796875 1.0750389099121094 3587.72314453125 0.5007758140563965 0.6887713 4.390691757202148 True -4 8670 19.065752267837524 0.5380454063415527 2376.721435546875 1.347982406616211 3458.427490234375 0.5139716267585754 0.6979455 3.371644973754883 True -5 10404 19.03070616722107 1.6401185989379883 2677.917236328125 1.468898892402649 3341.61572265625 0.5286626219749451 0.7068071 2.8067541122436523 True -6 12138 19.07579016685486 0.5264501571655273 2400.25634765625 1.4518177509307861 3260.84765625 0.5380278825759888 0.7141557 2.440887928009033 True -7 13872 19.085962772369385 0.5411355495452881 1905.90283203125 1.2524664402008057 3254.994384765625 0.536641538143158 0.7181635 2.187607765197754 True -8 15606 19.083354949951172 0.5218427181243896 2088.717041015625 1.2622390985488892 3193.546875 0.5433393120765686 0.7253708 1.904975414276123 True -9 17340 19.087483882904053 0.5160081386566162 1730.082275390625 1.1151896715164185 3140.561279296875 0.5516029000282288 0.738414 1.6998121738433838 True -10 19074 18.78081464767456 0.5200443267822266 2879.76611328125 0.9445819854736328 3099.4189453125 0.5564569234848022 0.7424591 1.5705549716949463 True -11 20808 18.678988695144653 0.5359053611755371 1893.006103515625 1.6240352392196655 3075.53759765625 0.5582373142242432 0.7500958 1.422429084777832 True -12 22542 20.092877864837646 5.8364338874816895 2253.708251953125 1.3184192180633545 3045.6240234375 0.5602383613586426 0.75621706 1.303710699081421 True -13 24276 18.71242928504944 0.5177221298217773 2251.840576171875 0.8235268592834473 2991.8037109375 0.5671047568321228 0.75910336 1.2646139860153198 True -14 26010 18.802627563476562 0.5232164859771729 2193.402099609375 0.7386614680290222 2943.1953125 0.5712059736251831 0.7650886 1.1471891403198242 True -15 27744 18.724722862243652 1.0158474445343018 2067.837646484375 0.9993240237236023 2929.26318359375 0.5715499520301819 0.77104425 1.0621076822280884 True -16 29478 18.83210277557373 0.5160019397735596 2079.769775390625 0.7238600254058838 2926.71044921875 0.5701212286949158 0.77410156 0.9965870976448059 True -17 31212 18.770925998687744 0.5303952693939209 1574.6722412109375 0.5951158404350281 2926.638916015625 0.5693207383155823 0.7770918 0.9727497696876526 True -18 32946 18.71078372001648 0.5227217674255371 1512.7177734375 0.8636224269866943 2920.453125 0.5711846947669983 0.77769536 0.9567069411277771 True -19 34680 18.7928409576416 0.5249497890472412 2187.05810546875 0.5954649448394775 2914.619140625 0.5718812942504883 0.7776701 0.9515711069107056 False diff --git a/ENCSR704HNG/cherimoya.fold_1.performance.tsv b/ENCSR704HNG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7efd54b0a20b5dade3c27053da742c89fe6269ae..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2920.453125 0.20810748636722565 0.5711846947669983 0.3917425572872162 0.77769535779953 0.7351261377334595 0.9567069411277771 \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_2.evaluate.json b/ENCSR704HNG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2b269fbb34ad64096901d0fcc217378747faf787..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF039IBG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_2.fit.json b/ENCSR704HNG/cherimoya.fold_2.fit.json deleted file mode 100644 index 91dfa184b809b471523025ce8d88386bdec6e291..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF039IBG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_2.log b/ENCSR704HNG/cherimoya.fold_2.log deleted file mode 100644 index 2635e496ba426f9d6f64dfceee341d6e383f1bd6..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1865 25.640727281570435 3.7800557613372803 2788.385009765625 1.6538997888565063 5135.84912109375 0.24203196167945862 0.4651083 30.21259880065918 True -1 3730 20.55286145210266 0.43673014640808105 3570.91162109375 1.9359524250030518 3666.727783203125 0.4251949191093445 0.61201274 16.055171966552734 True -2 5595 20.539209365844727 21.27551245689392 2273.3896484375 1.204190969467163 3241.486572265625 0.46979206800460815 0.65455264 5.542850971221924 True -3 7460 20.698708534240723 0.39930105209350586 2012.553466796875 1.4309910535812378 3018.4853515625 0.4927220642566681 0.6701203 3.604731798171997 True -4 9325 20.514551877975464 0.3662707805633545 2451.171142578125 1.1932694911956787 2938.231201171875 0.5063067078590393 0.6783998 3.125723123550415 True -5 11190 20.49435520172119 1.2779326438903809 2062.3251953125 1.1268388032913208 2865.96875 0.5128400921821594 0.68253607 2.336193561553955 True -6 13055 20.484326362609863 0.3597433567047119 2479.70849609375 1.3383731842041016 2785.06640625 0.5257163643836975 0.6883401 2.214053153991699 True -7 14920 20.478898763656616 0.3613433837890625 2381.84814453125 1.8017771244049072 2741.6826171875 0.5305325984954834 0.70013285 1.823014497756958 True -8 16785 20.542049884796143 1.02968430519104 1716.1922607421875 1.0206024646759033 2696.531005859375 0.5378314852714539 0.70645225 1.6989526748657227 True -9 18650 20.56837224960327 1.3493504524230957 1360.126953125 1.032908320426941 2676.07421875 0.5391548871994019 0.71648306 1.5021179914474487 True -10 20515 20.54061985015869 0.3594050407409668 2054.73193359375 1.27420973777771 2636.555419921875 0.5442696213722229 0.72359073 1.3946925401687622 True -11 22380 20.4958016872406 0.36492013931274414 1706.08642578125 1.040583848953247 2606.54638671875 0.5500255823135376 0.72791576 1.2967324256896973 True -12 24245 20.50897526741028 0.3757913112640381 2692.68701171875 0.8871985673904419 2579.47998046875 0.553428590297699 0.73092455 1.2173471450805664 True -13 26110 20.52730369567871 0.3558766841888428 1707.1376953125 1.2285101413726807 2548.25439453125 0.5560398697853088 0.73603404 1.1272457838058472 True -14 27975 20.46576690673828 0.34851574897766113 1680.3251953125 1.2577108144760132 2534.808837890625 0.5576767921447754 0.74157816 1.062187910079956 True -15 29840 20.148563623428345 0.3693230152130127 1660.5166015625 0.9785583019256592 2511.949462890625 0.5626190304756165 0.74464595 1.0145461559295654 True -16 31705 20.203068256378174 6.598164796829224 2579.27978515625 0.8614659309387207 2495.0341796875 0.5645321607589722 0.7455599 0.9923220276832581 True -17 33570 20.16426181793213 0.37685179710388184 1934.73095703125 0.7643980383872986 2492.059814453125 0.5656653642654419 0.7478806 0.982069730758667 True -18 35435 20.152072429656982 0.35840916633605957 2013.652099609375 0.5151998996734619 2503.493408203125 0.5634022951126099 0.74843884 0.978431761264801 True -19 37300 20.1983380317688 0.3577237129211426 1705.7774658203125 1.0739588737487793 2518.5361328125 0.5604696869850159 0.747933 0.9791669249534607 False diff --git a/ENCSR704HNG/cherimoya.fold_2.performance.tsv b/ENCSR704HNG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ab1fceec0ce39e2b6bf43eb8a073abcff9dbff91..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2503.493408203125 0.21974752843379974 0.5634023547172546 0.36639633774757385 0.748438835144043 0.6889187097549438 0.978431761264801 \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_3.evaluate.json b/ENCSR704HNG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8e29c51ee5b8e07f24b7eccfa3d905461079014b..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF039IBG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_3.fit.json b/ENCSR704HNG/cherimoya.fold_3.fit.json deleted file mode 100644 index dfef5f9a599f64c3578d12504f77d4442436afe3..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF039IBG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_3.log b/ENCSR704HNG/cherimoya.fold_3.log deleted file mode 100644 index c9b4540e9eb38dcf2576a5b74399ddcaf0fe93ff..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1793 24.42691159248352 3.844135046005249 2485.71826171875 1.2198939323425293 5131.16357421875 0.24575138092041016 0.4778732 35.60578918457031 True -1 3586 19.700331687927246 0.3927648067474365 2902.07763671875 1.5593867301940918 3927.462890625 0.418009489774704 0.6188675 17.801525115966797 True -2 5379 19.712145566940308 0.37438535690307617 2517.3935546875 1.5067384243011475 3416.65380859375 0.4760305881500244 0.64817196 7.920233726501465 True -3 7172 19.700622081756592 0.3596811294555664 2518.248046875 1.3691232204437256 3191.24462890625 0.5023193955421448 0.6563538 4.706130027770996 True -4 8965 19.719101190567017 0.3586099147796631 2446.8720703125 1.409485101699829 3108.54931640625 0.5112848877906799 0.67723995 3.660682439804077 True -5 10758 19.72937798500061 0.7822146415710449 2002.3372802734375 1.4261572360992432 3044.959228515625 0.5143162608146667 0.6866533 2.8908157348632812 True -6 12551 19.682432651519775 0.3595893383026123 2973.054931640625 1.410947561264038 2979.685546875 0.524315357208252 0.6948262 2.4195611476898193 True -7 14344 19.686707258224487 0.3596055507659912 1875.6630859375 1.5861406326293945 2955.115234375 0.5283042788505554 0.69724673 2.213510513305664 True -8 16137 19.72052001953125 0.3788321018218994 1564.964111328125 1.492323875427246 2909.795166015625 0.5386359691619873 0.6951846 2.257300615310669 False -9 17930 19.729812622070312 0.3646829128265381 1775.99951171875 1.361794114112854 2864.36962890625 0.5439198017120361 0.7012542 1.79863703250885 True -10 19723 19.70274329185486 0.35860443115234375 2834.62158203125 1.083406686782837 2846.976318359375 0.5421496629714966 0.70910275 1.5601236820220947 True -11 21516 19.738958597183228 0.3589916229248047 1700.874755859375 0.7421897649765015 2821.72216796875 0.5471264719963074 0.71489525 1.4680262804031372 True -12 23309 19.722116231918335 0.368027925491333 2023.6077880859375 1.141801357269287 2773.385986328125 0.5531137585639954 0.7182746 1.3188731670379639 True -13 25102 19.723535299301147 0.3733377456665039 1719.8612060546875 1.0262278318405151 2734.0546875 0.5586530566215515 0.7255623 1.2288479804992676 True -14 26895 19.710675716400146 0.3662397861480713 2453.41650390625 0.7160404920578003 2727.47412109375 0.5562684535980225 0.7319433 1.1732659339904785 True -15 28688 19.735872507095337 0.3582267761230469 2128.4453125 0.7981347441673279 2692.479736328125 0.5624337792396545 0.7377171 1.1048778295516968 True -16 30481 19.72402858734131 0.36716413497924805 2430.47900390625 0.7777906060218811 2681.636962890625 0.5628896355628967 0.7447419 1.0489381551742554 True -17 32274 19.764020204544067 1.5295321941375732 1910.006591796875 1.0844874382019043 2669.761962890625 0.5656460523605347 0.74857855 1.0163861513137817 True -18 34067 19.74999451637268 0.36637115478515625 1860.63330078125 0.6149787902832031 2679.45263671875 0.5623148083686829 0.74977773 1.0035369396209717 True -19 35860 19.72902226448059 0.3935887813568115 1770.1234130859375 0.7945942282676697 2697.216552734375 0.5572356581687927 0.75012076 1.0035579204559326 True diff --git a/ENCSR704HNG/cherimoya.fold_3.performance.tsv b/ENCSR704HNG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9ea07fca8474eab12bd3270e879ee48a5b3f3d17..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2697.216552734375 0.2164011150598526 0.5572356581687927 0.3732891380786896 0.7501207590103149 0.6927481889724731 1.0035579204559326 \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_4.evaluate.json b/ENCSR704HNG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 814c900ba71a7fddabed9aea28ebcc15008f00ec..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF039IBG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_4.fit.json b/ENCSR704HNG/cherimoya.fold_4.fit.json deleted file mode 100644 index beb14a1322aac10c4fd244222d0cdb89d710ab99..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF039IBG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704HNG/cherimoya.fold_4.log b/ENCSR704HNG/cherimoya.fold_4.log deleted file mode 100644 index 9fbdb2da3acc174c881bba6a2020971b94d9c313..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1778 24.169675827026367 13.583620071411133 2272.84521484375 1.338623285293579 4740.85888671875 0.23793552815914154 0.47438505 34.7703742980957 True -1 3556 19.498385667800903 0.3391454219818115 2658.126953125 1.7460970878601074 3495.44189453125 0.4361658990383148 0.60398996 21.108793258666992 True -2 5334 19.52940058708191 0.33136844635009766 2577.46923828125 2.1745691299438477 3123.646484375 0.46939152479171753 0.6199555 7.961524486541748 True -3 7112 19.50132155418396 0.3275618553161621 1629.7613525390625 1.509242296218872 2921.741943359375 0.49526509642601013 0.631469 4.292344570159912 True -4 8890 19.479660034179688 0.68149733543396 2287.024169921875 1.526731252670288 2824.26416015625 0.5102854371070862 0.6431135 3.1288297176361084 True -5 10668 19.551567316055298 0.3371286392211914 2165.094482421875 1.163626790046692 2755.83740234375 0.5167379975318909 0.6544413 2.6281397342681885 True -6 12446 19.599982500076294 0.3512136936187744 2113.373291015625 1.8620866537094116 2684.349853515625 0.5277286767959595 0.65909535 2.460597515106201 True -7 14224 19.55343723297119 0.35589170455932617 2586.016357421875 1.2357017993927002 2638.6083984375 0.534278154373169 0.6677906 2.289383888244629 True -8 16002 19.55937123298645 0.3392672538757324 2697.95654296875 1.2837539911270142 2597.01513671875 0.5412446856498718 0.6724669 1.9761395454406738 True -9 17780 19.529315948486328 1.0559585094451904 2248.16015625 1.1521761417388916 2562.38818359375 0.5472516417503357 0.67581624 1.7814713716506958 True -10 19558 19.477258682250977 0.33662939071655273 1829.55810546875 1.1231213808059692 2541.81884765625 0.5498207211494446 0.68052995 1.670609712600708 True -11 21336 19.191263914108276 0.35204291343688965 2285.88134765625 0.876225471496582 2505.89794921875 0.5556741952896118 0.68532 1.5116058588027954 True -12 23114 19.31809711456299 0.3385181427001953 1466.125732421875 1.3879725933074951 2476.75439453125 0.5602759122848511 0.6903001 1.378206491470337 True -13 24892 19.301624536514282 0.33683276176452637 1652.7724609375 0.8767378330230713 2455.94873046875 0.5628259778022766 0.6986873 1.245954155921936 True -14 26670 19.263352632522583 0.33154988288879395 1755.441162109375 1.087177038192749 2430.677978515625 0.5659347772598267 0.70564574 1.1556143760681152 True -15 28448 19.281750917434692 0.3337867259979248 2036.7034912109375 0.5528583526611328 2433.717041015625 0.5629899501800537 0.7125897 1.0943580865859985 True -16 30226 19.28078556060791 0.34119391441345215 1704.49755859375 0.49764764308929443 2418.3662109375 0.5675160884857178 0.7183805 1.0484604835510254 True -17 32004 19.265853881835938 0.32416868209838867 1689.2509765625 0.9780280590057373 2426.419189453125 0.5635942816734314 0.7223195 1.016360878944397 True -18 33782 19.288095474243164 0.32269811630249023 1467.7464599609375 1.2425568103790283 2427.881591796875 0.5630256533622742 0.72451353 1.0071282386779785 True -19 35560 19.31037974357605 0.32940196990966797 1912.51025390625 0.8048993349075317 2437.35400390625 0.5617104768753052 0.72391325 1.0075945854187012 False diff --git a/ENCSR704HNG/cherimoya.fold_4.performance.tsv b/ENCSR704HNG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 84ce56a6577a1785a6554d01dcc2ded0e885f12c..0000000000000000000000000000000000000000 --- a/ENCSR704HNG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2427.881591796875 0.21866099536418915 0.5630255937576294 0.3635813593864441 0.7245135307312012 0.6478167772293091 1.0071282386779785 \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_0.evaluate.json b/ENCSR704VZY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index edf2875b3d6deb34f0ea7077fda6beb060327117..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444GRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_0.fit.json b/ENCSR704VZY/cherimoya.fold_0.fit.json deleted file mode 100644 index 406f92b16095994839e22d16e2e8f3348f09d282..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF444GRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_0.log b/ENCSR704VZY/cherimoya.fold_0.log deleted file mode 100644 index 701ebdad57f666fd56c98acda86a83c03099240f..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3654 44.57048773765564 3.668163299560547 759.6754760742188 1.0259990692138672 1119.85888671875 0.6960456371307373 0.7236416 8.372550964355469 True -1 7308 40.15166997909546 0.7622168064117432 778.8949584960938 1.7589529752731323 940.6163940429688 0.7623279094696045 0.75812006 2.0121350288391113 True -2 10962 40.0450963973999 29.58337378501892 723.9105224609375 1.1578096151351929 923.487060546875 0.7681847810745239 0.7635533 1.3588091135025024 True -3 14616 40.18220591545105 0.7475042343139648 817.5341796875 1.161978006362915 910.554931640625 0.7747834324836731 0.76716685 0.9371710419654846 True -4 18270 40.1938591003418 0.7368721961975098 846.3253173828125 0.8931407332420349 901.5353393554688 0.7784686088562012 0.76915866 0.8160265684127808 True -5 21924 40.141501903533936 0.741957426071167 747.62646484375 1.2418690919876099 889.5648803710938 0.7819916605949402 0.77091736 0.7167516350746155 True -6 25578 40.04295372962952 0.7331788539886475 679.3177490234375 1.088160514831543 881.3356323242188 0.7844587564468384 0.7774761 0.7104892730712891 True -7 29232 40.021321058273315 0.8075382709503174 843.8272094726562 0.7213649749755859 872.1649780273438 0.7874931693077087 0.7824978 0.6787176728248596 True -8 32886 39.96052575111389 0.7348041534423828 544.419189453125 0.7067265510559082 865.2911376953125 0.7905157804489136 0.7811675 0.6952332258224487 False -9 36540 39.30839514732361 1.133805274963379 533.4117431640625 0.9521746635437012 856.5621948242188 0.7931350469589233 0.78547114 0.6750453114509583 True -10 40194 39.47868800163269 1.8034374713897705 608.8411865234375 0.4645668566226959 850.2105102539062 0.7954367995262146 0.79009056 0.6465818285942078 True -11 43848 39.34023690223694 0.7300989627838135 751.2647705078125 1.2544184923171997 845.390380859375 0.7982152700424194 0.79337573 0.6379285454750061 True -12 47502 39.422521114349365 0.7396378517150879 819.5665283203125 0.6161618232727051 838.264892578125 0.8009156584739685 0.8029018 0.6201885342597961 True -13 51156 39.380481243133545 0.7384943962097168 771.7471923828125 0.5909531116485596 830.5692749023438 0.8041843771934509 0.808085 0.6064558625221252 True -14 54810 39.34033560752869 0.7235598564147949 743.9759521484375 0.8207604885101318 824.7899169921875 0.8068408966064453 0.81546885 0.5945026874542236 True -15 58464 39.32714009284973 0.731060266494751 645.6002197265625 0.6845575571060181 820.5906982421875 0.8087612390518188 0.8215242 0.5829678177833557 True -16 62118 39.35795021057129 0.7302193641662598 681.3550415039062 0.7817568778991699 819.3092651367188 0.8100256323814392 0.82432383 0.5834646224975586 True -17 65772 39.3287672996521 0.7283234596252441 605.4293212890625 0.6025158166885376 818.7139282226562 0.8100743889808655 0.8250895 0.5889774560928345 True -18 69426 39.276577949523926 34.7352614402771 701.018798828125 0.7394120693206787 819.947021484375 0.8098548650741577 0.8240171 0.6024738550186157 False -19 73080 39.528693199157715 0.7410998344421387 530.0579833984375 0.8406781554222107 819.6539306640625 0.809723973274231 0.8243353 0.6093366146087646 False diff --git a/ENCSR704VZY/cherimoya.fold_0.performance.tsv b/ENCSR704VZY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index efa7e021872ceeaf3e7ea0c868d2a74960e9237b..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -818.7139282226562 0.15581963956356049 0.8100743293762207 0.46178436279296875 0.8250895142555237 0.7567530274391174 0.5889774560928345 \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_1.evaluate.json b/ENCSR704VZY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 521da5eaa07bfc2fdf961b93b3769a7b9c776840..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444GRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_1.fit.json b/ENCSR704VZY/cherimoya.fold_1.fit.json deleted file mode 100644 index 8b36c4180b8b5f6cbb7112452f322fcaf28674ce..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF444GRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_1.log b/ENCSR704VZY/cherimoya.fold_1.log deleted file mode 100644 index a88b8df5af01b8befbf803af6e055f4de7fc794f..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3642 44.31695580482483 5.408468008041382 656.18701171875 1.8916127681732178 1355.5675048828125 0.7151554226875305 0.7393716 9.88574504852295 True -1 7284 40.172706604003906 0.8964159488677979 738.616455078125 1.2883220911026 1148.884765625 0.7730197310447693 0.7751607 1.6934608221054077 True -2 10926 40.16916346549988 0.9114468097686768 582.0519409179688 1.4359993934631348 1119.524658203125 0.7788068056106567 0.7824632 1.183760404586792 True -3 14568 40.14733695983887 0.9631209373474121 874.6943359375 1.6114476919174194 1101.0015869140625 0.784665584564209 0.78318137 0.9082051515579224 True -4 18210 40.0012640953064 1.1441688537597656 892.3145141601562 1.5840566158294678 1085.9207763671875 0.787784993648529 0.7861281 0.8584010601043701 True -5 21852 39.9808886051178 0.8856120109558105 776.2552490234375 0.8525632619857788 1078.37060546875 0.7909924983978271 0.7833956 0.833420991897583 False -6 25494 39.984039306640625 22.31264877319336 888.7027587890625 1.0017023086547852 1061.188232421875 0.7942206859588623 0.7892013 0.7799953818321228 True -7 29136 40.069244384765625 1.8485097885131836 625.5353393554688 1.5372812747955322 1046.968017578125 0.7971579432487488 0.7922762 0.7661551237106323 True -8 32778 40.10550379753113 1.4882404804229736 556.2733154296875 1.6638270616531372 1037.1961669921875 0.7994402647018433 0.7980287 0.7124942541122437 True -9 36420 39.32664489746094 0.8728764057159424 624.1231689453125 0.9049383401870728 1025.4815673828125 0.8024464249610901 0.80090433 0.6999402046203613 True -10 40062 39.2329626083374 12.217550039291382 660.9028930664062 1.0695586204528809 1013.0477905273438 0.8058733344078064 0.8087248 0.6926112174987793 True -11 43704 39.27737498283386 0.8785808086395264 635.1796875 1.1217808723449707 1006.160400390625 0.8080930113792419 0.8090931 0.6847122311592102 True -12 47346 39.20439028739929 0.8668961524963379 674.8070068359375 0.7890548706054688 994.7596435546875 0.8115229606628418 0.8190127 0.6575626134872437 True -13 50988 39.14755940437317 0.8686292171478271 649.0830688476562 1.0430046319961548 985.304931640625 0.8148033618927002 0.8287825 0.6430310010910034 True -14 54630 39.20605182647705 0.8569967746734619 692.3143310546875 0.8312702178955078 976.51904296875 0.8174116611480713 0.83466965 0.6223607063293457 True -15 58272 39.23125743865967 0.8692383766174316 719.87646484375 0.6602365970611572 972.6404418945312 0.8192367553710938 0.84037197 0.6109499335289001 True -16 61914 39.235302209854126 0.8633697032928467 656.6649169921875 0.80552077293396 969.7119750976562 0.8204500675201416 0.8436556 0.6121046543121338 True -17 65556 39.215351581573486 0.8714375495910645 690.6923217773438 0.6792705059051514 969.5698852539062 0.8208282589912415 0.84645724 0.611807107925415 True -18 69198 39.191781997680664 0.8642041683197021 538.3497924804688 0.6160703897476196 970.4378662109375 0.8207359313964844 0.84647477 0.6176018118858337 True -19 72840 39.30035090446472 0.8730816841125488 546.9847412109375 0.46082496643066406 971.0882568359375 0.8205763697624207 0.8458715 0.6202144622802734 False diff --git a/ENCSR704VZY/cherimoya.fold_1.performance.tsv b/ENCSR704VZY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0c5c094b1906fd122604ca26f18e557c1e431ae8..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -970.4378662109375 0.14180991053581238 0.82073575258255 0.5111595392227173 0.8464747667312622 0.8085606694221497 0.6176018118858337 \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_2.evaluate.json b/ENCSR704VZY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 048598e8c82d402913aecd45afc34e570d3cf63d..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444GRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_2.fit.json b/ENCSR704VZY/cherimoya.fold_2.fit.json deleted file mode 100644 index e0a4543ad500c8126f512646604a68b66ee3991a..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF444GRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_2.log b/ENCSR704VZY/cherimoya.fold_2.log deleted file mode 100644 index b71ca59951bf63dac51d7d16c9a07009d9ca0ee3..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3900 46.983811140060425 3.6943752765655518 727.2549438476562 1.560896873474121 1205.4915771484375 0.7107347846031189 0.73915845 7.959939002990723 True -1 7800 42.87816381454468 0.7402069568634033 766.7149658203125 1.346147894859314 1041.51025390625 0.760275661945343 0.77453685 2.6476008892059326 True -2 11700 42.9134464263916 0.705925464630127 801.8544921875 1.2912709712982178 1020.3809204101562 0.7681004405021667 0.77688205 1.207557201385498 True -3 15600 42.75112700462341 0.7023093700408936 747.350830078125 0.9204471707344055 990.6301879882812 0.7763915657997131 0.78221315 0.8510513305664062 True -4 19500 42.767658710479736 0.702263593673706 635.2258911132812 1.6535475254058838 982.8011474609375 0.7801042795181274 0.7862758 0.7839097380638123 True -5 23400 42.716970682144165 0.6994028091430664 758.7733154296875 1.4981462955474854 964.5785522460938 0.7841681241989136 0.79097766 0.7014063000679016 True -6 27300 42.758378982543945 0.6994316577911377 728.760009765625 1.04317045211792 955.1278076171875 0.7864556312561035 0.79277503 0.6956839561462402 True -7 31200 42.758580446243286 0.7073755264282227 796.9403686523438 0.929495096206665 946.372802734375 0.7891273498535156 0.79590523 0.6939889788627625 True -8 35100 42.809122800827026 0.7005727291107178 701.560546875 0.9177257418632507 936.8156127929688 0.7911695837974548 0.80156434 0.6770132184028625 True -9 39000 42.28217911720276 0.6969823837280273 729.5838623046875 0.8047640323638916 926.8211669921875 0.7948821783065796 0.80336255 0.6733766794204712 True -10 42900 41.9596962928772 0.6977710723876953 555.1400756835938 1.0441017150878906 916.552001953125 0.7975075244903564 0.807405 0.653818666934967 True -11 46800 41.957218647003174 0.6948826313018799 545.4944458007812 0.7614387273788452 908.9384765625 0.7999712824821472 0.81208926 0.6445962190628052 True -12 50700 41.982136964797974 0.6944396495819092 678.0078125 1.4775967597961426 900.9440307617188 0.8026880621910095 0.8183896 0.6243520379066467 True -13 54600 41.939674377441406 0.6920485496520996 601.7657470703125 0.6256910562515259 893.7462768554688 0.8053401708602905 0.82741123 0.6044793128967285 True -14 58500 42.01000189781189 0.6919732093811035 632.0664672851562 0.658976674079895 887.626220703125 0.8072724938392639 0.8307062 0.5986233353614807 True -15 62400 41.97132420539856 0.6928510665893555 547.126220703125 0.8657376766204834 881.7598876953125 0.8098682761192322 0.83678347 0.5863076448440552 True -16 66300 41.99529576301575 0.6943614482879639 626.28955078125 0.5147041082382202 879.1187133789062 0.8109865784645081 0.8406961 0.5811527371406555 True -17 70200 41.98662757873535 0.6919193267822266 583.1812744140625 0.510964035987854 877.8937377929688 0.8114091753959656 0.84373343 0.5764164328575134 True -18 74100 41.96351623535156 0.6929826736450195 578.18505859375 0.8344557285308838 878.0631713867188 0.8113271594047546 0.84225476 0.5824674367904663 False -19 78000 42.0024778842926 0.6906156539916992 668.7630615234375 0.492561012506485 879.39697265625 0.811145544052124 0.84271944 0.5830582976341248 False diff --git a/ENCSR704VZY/cherimoya.fold_2.performance.tsv b/ENCSR704VZY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2506c3e134a85b697e63dec0a9b7f6a310584b6e..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -877.8937377929688 0.15179027616977692 0.8114091157913208 0.4812864363193512 0.8437334299087524 0.7865611910820007 0.5764164328575134 \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_3.evaluate.json b/ENCSR704VZY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3e0e2b84a0a526cee7a082df6c22a7329f0b94b5..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444GRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_3.fit.json b/ENCSR704VZY/cherimoya.fold_3.fit.json deleted file mode 100644 index af0a3803ab97ff7cfed8cdaeb2fad9a63950e4a0..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF444GRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_3.log b/ENCSR704VZY/cherimoya.fold_3.log deleted file mode 100644 index d181a6300fcc74a6b234098376f10f51985abc4f..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3736 45.56934905052185 3.779111862182617 680.537353515625 1.597689151763916 1092.66943359375 0.706367015838623 0.7304496 10.32907772064209 True -1 7472 41.52699685096741 0.7088875770568848 679.7852172851562 1.373842477798462 941.93359375 0.759592592716217 0.758183 2.440204381942749 True -2 11208 41.526891231536865 0.6810450553894043 570.8028564453125 0.8952925205230713 921.4027709960938 0.7670288681983948 0.7560911 1.5276132822036743 False -3 14944 41.4529664516449 0.6866781711578369 740.8865966796875 1.3760645389556885 903.2130737304688 0.7742682695388794 0.7626002 1.0513039827346802 True -4 18680 41.538734436035156 0.6788365840911865 623.7362060546875 1.290975570678711 895.5699462890625 0.7776772975921631 0.7550216 0.944235622882843 False -5 22416 41.39563608169556 1.6881957054138184 676.5159912109375 1.1608803272247314 888.2260131835938 0.7802201509475708 0.7553852 0.8150961399078369 False -6 26152 41.46060490608215 0.6749081611633301 761.7784423828125 0.9113042950630188 878.5608520507812 0.7825583815574646 0.7619205 0.7887904644012451 False -7 29888 41.36663603782654 1.3566629886627197 571.904052734375 1.0986067056655884 872.1553955078125 0.785044252872467 0.76472586 0.7550420165061951 True -8 33624 41.41995668411255 0.6815733909606934 600.7941284179688 0.9396225214004517 862.2111206054688 0.7887352108955383 0.7700207 0.7241543531417847 True -9 37360 41.47504186630249 0.6834213733673096 718.25830078125 0.8498711585998535 854.7911987304688 0.7913312315940857 0.77235013 0.7378033995628357 True -10 41096 41.3893940448761 0.6762087345123291 748.6343994140625 0.8026609420776367 847.6614990234375 0.7943832874298096 0.7764157 0.7169278264045715 True -11 44832 41.45312261581421 0.6862194538116455 544.818115234375 0.9135034680366516 841.798828125 0.7968388199806213 0.78443533 0.6984626054763794 True -12 48568 41.456355571746826 3.2094826698303223 725.6312255859375 0.9316893219947815 834.5745239257812 0.7991749048233032 0.79063547 0.692446768283844 True -13 52304 41.48328423500061 0.6767449378967285 683.9063110351562 0.747162938117981 828.1571655273438 0.8015298843383789 0.80074376 0.6696289777755737 True -14 56040 41.952417612075806 0.6926143169403076 765.5828857421875 0.6720454692840576 822.4749145507812 0.8038713335990906 0.8056641 0.6537758708000183 True -15 59776 41.425092458724976 0.6789658069610596 656.7406005859375 0.5490052103996277 818.3348999023438 0.8060450553894043 0.81310904 0.6411906480789185 True -16 63512 41.410677433013916 0.6772556304931641 554.676513671875 0.7404938340187073 814.139892578125 0.807831346988678 0.8168362 0.6347767114639282 True -17 67248 41.506123781204224 0.6727478504180908 659.3977661132812 0.4664897918701172 813.4580688476562 0.8082695007324219 0.82050586 0.6272359490394592 True -18 70984 41.44170379638672 0.6885230541229248 575.08837890625 0.9668763279914856 814.6937255859375 0.8081541657447815 0.8202507 0.6309587955474854 False -19 74720 41.438958168029785 0.6769261360168457 740.5145263671875 0.9206085205078125 814.7030639648438 0.8081028461456299 0.81942064 0.6376664042472839 False diff --git a/ENCSR704VZY/cherimoya.fold_3.performance.tsv b/ENCSR704VZY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e7dd05c8964ed21d1dfa3b8ef991f546374dbca3..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -813.4580688476562 0.157059445977211 0.8082695603370667 0.4563292860984802 0.8205058574676514 0.749005138874054 0.6272359490394592 \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_4.evaluate.json b/ENCSR704VZY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bf9d94a35431273f49a530bd9f39db7e1d08aebf..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF444GRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_4.fit.json b/ENCSR704VZY/cherimoya.fold_4.fit.json deleted file mode 100644 index 3decd334aba3a7e090711b355af3269faf1c8121..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF444GRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR704VZY/cherimoya.fold_4.log b/ENCSR704VZY/cherimoya.fold_4.log deleted file mode 100644 index 1b188802bd0208e535df96f7b09207722c2bb6b9..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3784 46.01452970504761 3.732105255126953 672.5668334960938 1.4091297388076782 1039.830322265625 0.7012982368469238 0.7241276 7.88808012008667 True -1 7568 42.05970525741577 0.8116624355316162 583.1654052734375 1.0939124822616577 898.3896484375 0.7584091424942017 0.7541648 2.331787347793579 True -2 11352 42.1496684551239 0.7771148681640625 793.182373046875 1.190244197845459 877.7424926757812 0.7654505968093872 0.7615828 1.145040512084961 True -3 15136 41.93604350090027 0.7659730911254883 762.254638671875 0.7765283584594727 865.1362915039062 0.7715722322463989 0.7608727 0.893769383430481 False -4 18920 41.89122223854065 0.7760202884674072 607.6669921875 1.524991512298584 854.9338989257812 0.776390016078949 0.7622439 0.7078864574432373 True -5 22704 41.866586685180664 2.015141487121582 659.5570068359375 0.8894449472427368 846.9527587890625 0.7783511877059937 0.7658625 0.7088863253593445 True -6 26488 41.93008279800415 0.774956226348877 767.9488525390625 0.9859070777893066 839.2936401367188 0.7805426716804504 0.7674625 0.6885265111923218 True -7 30272 42.00739765167236 0.7721366882324219 810.938232421875 1.3837149143218994 830.5614624023438 0.7851325273513794 0.7707739 0.6737042665481567 True -8 34056 41.98288893699646 0.7666265964508057 656.2543334960938 0.9167613387107849 822.64599609375 0.7887586951255798 0.77552795 0.6631304025650024 True -9 37840 41.96252179145813 1.0113608837127686 583.498779296875 1.3048136234283447 816.6474609375 0.7910763621330261 0.7785437 0.6460773944854736 True -10 41624 41.930429220199585 0.7723653316497803 701.919921875 0.7228872776031494 810.3308715820312 0.7943511605262756 0.78371537 0.6296298503875732 True -11 45408 41.97758221626282 0.7676610946655273 807.5443725585938 0.9728401899337769 802.0119018554688 0.7976359128952026 0.7867082 0.6213093400001526 True -12 49192 41.92740345001221 0.7668154239654541 683.4366455078125 0.7460702657699585 795.8447265625 0.8001878261566162 0.7937513 0.6031893491744995 True -13 52976 41.90939450263977 0.7691657543182373 781.6288452148438 0.781562089920044 791.3006591796875 0.8029685020446777 0.8025416 0.5883541703224182 True -14 56760 41.89201784133911 0.7669827938079834 731.8621215820312 0.589015007019043 784.7894287109375 0.8061220049858093 0.8095419 0.5705108046531677 True -15 60544 41.951796531677246 0.765887975692749 544.6863403320312 0.6972911357879639 782.3287353515625 0.808003842830658 0.81648475 0.562019407749176 True -16 64328 41.90438914299011 0.7658987045288086 723.445068359375 0.5643391013145447 779.576416015625 0.8094476461410522 0.82008 0.5542011260986328 True -17 68112 41.964670181274414 0.7677586078643799 583.6580200195312 0.9132111072540283 779.0447998046875 0.810044527053833 0.8243843 0.5487850308418274 True -18 71896 41.917596101760864 0.76747727394104 641.5799560546875 0.9102725386619568 779.3467407226562 0.8099423050880432 0.8238824 0.5499110817909241 False -19 75680 41.92814087867737 0.7688493728637695 600.3232421875 0.6242297291755676 780.7075805664062 0.8097130656242371 0.8230925 0.5540228486061096 False diff --git a/ENCSR704VZY/cherimoya.fold_4.performance.tsv b/ENCSR704VZY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5f51ef1461eb9804c8d71325ccbaed9984d32198..0000000000000000000000000000000000000000 --- a/ENCSR704VZY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -779.0447998046875 0.15820658206939697 0.810044527053833 0.45091408491134644 0.8243842720985413 0.747016429901123 0.5487850308418274 \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_0.evaluate.json b/ENCSR705CNJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 81fb3886a648eacf9fec26dc17361a4aa25e74f5..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126QXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_0.fit.json b/ENCSR705CNJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 6ead55ff79bc5d81ecfcef8ac61043421580a784..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF126QXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_0.log b/ENCSR705CNJ/cherimoya.fold_0.log deleted file mode 100644 index 410f6171a30ff47fdb9a43324d3bc9a6c9d88f8f..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 33.77145195007324 3.534287452697754 1110.742919921875 0.7930678129196167 1774.903076171875 0.31058797240257263 0.56806594 9.240519523620605 True -1 5486 30.40570878982544 0.57828688621521 1104.091064453125 0.7839255332946777 1522.9193115234375 0.46121010184288025 0.61573565 2.163968324661255 True -2 8229 30.276561737060547 0.5590300559997559 1306.960205078125 0.5348961353302002 1494.8468017578125 0.4739263355731964 0.5976248 0.800331175327301 False -3 10972 30.21984577178955 0.5408718585968018 1192.2935791015625 0.7133009433746338 1475.438232421875 0.481597900390625 0.6164127 0.6277291178703308 True -4 13715 30.195723295211792 0.5396790504455566 1232.2484130859375 0.9277085065841675 1467.8477783203125 0.4850427508354187 0.6278583 0.5583708882331848 True -5 16458 30.17186164855957 0.5366644859313965 1011.1134643554688 0.9438372850418091 1458.3675537109375 0.4908740818500519 0.6389159 0.5731722116470337 True -6 19201 30.179089546203613 0.5457944869995117 1335.592529296875 0.5801482200622559 1450.158935546875 0.495011568069458 0.64667803 0.5467862486839294 True -7 21944 30.186819076538086 1.1762616634368896 1247.7779541015625 0.6754082441329956 1444.306396484375 0.49976590275764465 0.64991146 0.5190609097480774 True -8 24687 30.16901683807373 0.5816779136657715 1153.80419921875 0.6004451513290405 1436.930419921875 0.5030791759490967 0.6571973 0.5113052725791931 True -9 27430 30.135058403015137 0.5436551570892334 1177.2037353515625 0.60956871509552 1435.0574951171875 0.5039827227592468 0.6620701 0.483954519033432 True -10 30173 30.11639928817749 0.5438225269317627 1083.030029296875 0.4132445156574249 1426.6329345703125 0.5099377036094666 0.66743386 0.4682883024215698 True -11 32916 30.134782552719116 0.5484304428100586 1027.2777099609375 0.5112964510917664 1417.648193359375 0.5146710276603699 0.6791185 0.4413278102874756 True -12 35659 30.183768033981323 2.619385242462158 972.4826049804688 0.6972311735153198 1414.7906494140625 0.5161644816398621 0.6875514 0.42983362078666687 True -13 38402 30.338112592697144 22.228416681289673 1054.578857421875 0.4011133313179016 1406.533447265625 0.5221662521362305 0.6999076 0.402436226606369 True -14 41145 30.391146421432495 0.5538952350616455 1051.6434326171875 0.3316155970096588 1399.6802978515625 0.5274130702018738 0.70806205 0.3951753079891205 True -15 43888 30.15835976600647 0.548105001449585 1157.423095703125 0.43177303671836853 1396.462646484375 0.528502881526947 0.71589404 0.3839021623134613 True -16 46631 30.216424226760864 0.5489566326141357 1084.8896484375 0.39913541078567505 1395.690673828125 0.5293749570846558 0.7212677 0.37391576170921326 True -17 49374 30.17688012123108 0.5413722991943359 1098.83544921875 0.4078827500343323 1396.7501220703125 0.5277056694030762 0.7235346 0.37476110458374023 True -18 52117 30.18489170074463 0.5447814464569092 1056.6953125 0.2752314805984497 1395.6253662109375 0.5290824174880981 0.72394663 0.3744707405567169 True -19 54860 30.18909764289856 0.5495016574859619 1071.064208984375 0.2802637815475464 1397.4075927734375 0.5277085900306702 0.7230809 0.3745739161968231 False diff --git a/ENCSR705CNJ/cherimoya.fold_0.performance.tsv b/ENCSR705CNJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c0516328aac659fc3973d9271e984a12159fcae5..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1395.6253662109375 0.23884381353855133 0.5290824174880981 0.3103456497192383 0.7239466309547424 0.6604685187339783 0.3744707405567169 \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_1.evaluate.json b/ENCSR705CNJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 737e9bc2a0c3874b24e53520b68d31cc9e108d58..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126QXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_1.fit.json b/ENCSR705CNJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 25a3ee52aececf70806b85e67e77c9a34c49cd17..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF126QXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_1.log b/ENCSR705CNJ/cherimoya.fold_1.log deleted file mode 100644 index 2e3415c82cf0be1d2478051a196707fa5ae573bd..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 34.209346771240234 3.7583749294281006 1479.162109375 0.5129705667495728 2026.806884765625 0.3193804621696472 0.58671117 8.20056438446045 True -1 5522 30.429805994033813 0.6978347301483154 1330.4755859375 0.6251213550567627 1729.6650390625 0.46483588218688965 0.62477875 2.0147740840911865 True -2 8283 30.48889446258545 0.683391809463501 1257.43798828125 0.7159756422042847 1687.4398193359375 0.48119091987609863 0.6423973 0.8794086575508118 True -3 11044 30.33117985725403 2.334528684616089 1140.1083984375 0.7986515760421753 1655.3037109375 0.4953490197658539 0.6617608 0.6640609502792358 True -4 13805 30.419716358184814 0.6789400577545166 1300.6905517578125 0.7201876640319824 1649.9215087890625 0.4949054419994354 0.6725692 0.6151136755943298 True -5 16566 30.342623710632324 0.6795101165771484 1160.9530029296875 0.44915470480918884 1639.55810546875 0.5003491640090942 0.67176586 0.6227748394012451 False -6 19327 30.356526374816895 0.682293176651001 1292.077880859375 0.5731587409973145 1632.46435546875 0.5034272074699402 0.6811381 0.5888751745223999 True -7 22088 31.153681755065918 1.383873701095581 1428.271240234375 1.0912736654281616 1619.494873046875 0.5090492963790894 0.68337125 0.5670855641365051 True -8 24849 30.35463237762451 0.6870989799499512 1093.0057373046875 0.6074732542037964 1608.0225830078125 0.5163561701774597 0.6942327 0.5447593331336975 True -9 27610 30.331536769866943 0.6823482513427734 1240.6729736328125 0.5486763715744019 1597.1636962890625 0.5202774405479431 0.7093444 0.4940774738788605 True -10 30371 30.35676407814026 0.6826908588409424 1359.7113037109375 0.42316514253616333 1587.6929931640625 0.5243920683860779 0.71035326 0.4875141382217407 True -11 33132 30.41773533821106 0.6812338829040527 1330.1513671875 0.3640788197517395 1577.3934326171875 0.5291831493377686 0.71874577 0.4659299850463867 True -12 35893 30.3819100856781 0.6870942115783691 1116.60986328125 0.8347582221031189 1568.783203125 0.5326334238052368 0.73371845 0.4507054090499878 True -13 38654 30.318400859832764 0.6805262565612793 1588.246337890625 0.5674476027488708 1561.0035400390625 0.535754382610321 0.74297816 0.4241085350513458 True -14 41415 30.323351621627808 0.6687653064727783 1096.4619140625 0.4127412438392639 1562.4918212890625 0.5341273546218872 0.7539459 0.4100606441497803 True -15 44176 30.384413480758667 0.6699473857879639 1218.095703125 0.3498334586620331 1555.5 0.5394055247306824 0.7633652 0.39106133580207825 True -16 46937 30.369280576705933 0.6708204746246338 1045.068359375 0.5192503333091736 1547.22509765625 0.5428881645202637 0.7711206 0.3776721656322479 True -17 49698 30.404253005981445 1.742431402206421 1029.100341796875 0.38198626041412354 1544.764892578125 0.5439850091934204 0.7730287 0.37246954441070557 True -18 52459 30.359449863433838 0.6717801094055176 1052.714111328125 0.35507693886756897 1554.5577392578125 0.5371344089508057 0.77659225 0.3686985671520233 True -19 55220 30.37520742416382 0.6816627979278564 1166.995849609375 0.3751433789730072 1552.140625 0.539568305015564 0.7763104 0.3722139000892639 False diff --git a/ENCSR705CNJ/cherimoya.fold_1.performance.tsv b/ENCSR705CNJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8c0bee6a6f655163064d1460da69e70ae71cbc94..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1554.5577392578125 0.22781415283679962 0.5371344089508057 0.33356809616088867 0.7765922546386719 0.7333282828330994 0.3686985671520233 \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_2.evaluate.json b/ENCSR705CNJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 77429e9307639308f6f67ae6e16444062bcce8d4..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126QXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_2.fit.json b/ENCSR705CNJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 0b18a99ee516a58ccb7e6706c344db5333e89466..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF126QXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_2.log b/ENCSR705CNJ/cherimoya.fold_2.log deleted file mode 100644 index 1f84d98329ff3978ff84d850fa78091966fc2742..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2889 35.66118240356445 3.7700705528259277 1457.303466796875 0.7120742797851562 1822.05615234375 0.3255188465118408 0.559737 9.147955894470215 True -1 5778 31.855634927749634 1.0911552906036377 1437.564208984375 0.5976321697235107 1549.0040283203125 0.4724155068397522 0.61103964 1.936689853668213 True -2 8667 31.816565990447998 0.8001358509063721 1097.652099609375 0.7029765844345093 1526.9912109375 0.478974848985672 0.628558 0.7426123023033142 True -3 11556 31.983298301696777 7.835934400558472 1261.84716796875 0.8253809213638306 1504.1412353515625 0.4884791672229767 0.6447244 0.6099594235420227 True -4 14445 31.89427638053894 0.5534923076629639 1234.182373046875 0.632054328918457 1495.6380615234375 0.49345773458480835 0.65091103 0.5576814413070679 True -5 17334 31.839848041534424 0.5345089435577393 1244.0224609375 0.6282126307487488 1484.4927978515625 0.5005447268486023 0.65833557 0.5732817053794861 True -6 20223 31.851346015930176 0.5448403358459473 1205.24853515625 0.8064742088317871 1481.0408935546875 0.5016809701919556 0.6535679 0.5817340612411499 False -7 23112 31.76541829109192 0.5322208404541016 1278.12353515625 0.6674614548683167 1473.2227783203125 0.5062342286109924 0.6671931 0.49231815338134766 True -8 26001 31.852449893951416 1.1764702796936035 1091.9063720703125 0.5986233353614807 1464.6827392578125 0.5113815665245056 0.6680145 0.48043036460876465 True -9 28890 31.888103008270264 12.818793058395386 1215.949462890625 0.9606927633285522 1460.1942138671875 0.5125737190246582 0.67637885 0.4647524952888489 True -10 31779 31.888283491134644 0.5520298480987549 1183.4683837890625 0.535906195640564 1447.7515869140625 0.5202217698097229 0.6812738 0.4559729993343353 True -11 34668 31.838302850723267 0.537604570388794 977.9197387695312 0.37555891275405884 1443.9447021484375 0.5224616527557373 0.68627745 0.4463823139667511 True -12 37557 31.88788652420044 0.563586950302124 1130.1717529296875 0.3765678405761719 1436.4647216796875 0.5266289114952087 0.6991104 0.4392942488193512 True -13 40446 31.920497179031372 0.5396287441253662 1149.442626953125 0.4752127230167389 1434.9554443359375 0.5258955955505371 0.7086342 0.426408588886261 True -14 43335 32.03386831283569 0.5562143325805664 1195.7967529296875 0.6250636577606201 1430.7174072265625 0.5291040539741516 0.71702474 0.4086785316467285 True -15 46224 31.81640076637268 0.5595879554748535 1360.2918701171875 0.5891559720039368 1424.9959716796875 0.532726526260376 0.7255009 0.3955936133861542 True -16 49113 31.89999508857727 0.5430967807769775 1183.9771728515625 0.6765493154525757 1423.63671875 0.5323659181594849 0.73223555 0.3877086043357849 True -17 52002 31.878514766693115 0.5595753192901611 1110.723876953125 0.3731124997138977 1418.9886474609375 0.5355046987533569 0.7354839 0.3838036358356476 True -18 54891 31.989813089370728 0.5586447715759277 1227.8621826171875 0.4060460925102234 1419.872802734375 0.5344177484512329 0.7353267 0.3865363597869873 False -19 57780 31.87549352645874 0.5472147464752197 1034.5941162109375 0.35331904888153076 1420.002685546875 0.5345610976219177 0.73526573 0.387896865606308 False diff --git a/ENCSR705CNJ/cherimoya.fold_2.performance.tsv b/ENCSR705CNJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index fb202fe581ef65f640ec71f929459f1a29d605e5..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1418.9886474609375 0.2356698364019394 0.5355046987533569 0.3171078860759735 0.7354838848114014 0.6750218868255615 0.3838036358356476 \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_3.evaluate.json b/ENCSR705CNJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f22d9dadf7add25398dc510d0ba8c8f662a79466..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126QXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_3.fit.json b/ENCSR705CNJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 1b83df07e0831b4290559e47144010776c053fdb..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF126QXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_3.log b/ENCSR705CNJ/cherimoya.fold_3.log deleted file mode 100644 index f7472ced8530d32fe572584d1fdcc2f4a6b4f1f1..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2802 34.84040665626526 3.4973647594451904 1118.1806640625 0.5666531324386597 1830.4552001953125 0.32094606757164 0.5892142 8.672574996948242 True -1 5604 30.900600910186768 0.5612778663635254 1233.2374267578125 0.8329101800918579 1579.8765869140625 0.4560392200946808 0.61914015 2.4225568771362305 True -2 8406 30.890178680419922 0.5555047988891602 1178.4400634765625 0.7843846082687378 1558.626220703125 0.4672856628894806 0.6109529 1.042816162109375 False -3 11208 30.900694131851196 0.5536296367645264 1545.752685546875 0.7106373310089111 1533.539306640625 0.4808785319328308 0.6285463 0.8166093230247498 True -4 14010 30.895594835281372 0.5517723560333252 1204.4111328125 0.7968503832817078 1521.1361083984375 0.4865702688694 0.64281285 0.6868048310279846 True -5 16812 30.87502908706665 0.5592901706695557 1057.55517578125 0.6849917769432068 1515.9893798828125 0.49155160784721375 0.6400691 0.7453762292861938 False -6 19614 30.849673748016357 0.5543928146362305 1160.729736328125 0.4379260540008545 1513.016845703125 0.4926169514656067 0.65292364 0.7023125886917114 True -7 22416 30.810692071914673 0.9203512668609619 1314.89794921875 0.6301690340042114 1503.982177734375 0.4971589148044586 0.656064 0.68998122215271 True -8 25218 30.837197065353394 0.5615968704223633 1155.258544921875 0.48320233821868896 1499.947509765625 0.5009662508964539 0.66373104 0.6339858770370483 True -9 28020 30.80711269378662 0.5650427341461182 1004.0986328125 0.7337948083877563 1491.4459228515625 0.5036633014678955 0.6767335 0.5905394554138184 True -10 30822 30.816604614257812 0.5567283630371094 1221.4949951171875 0.6648025512695312 1486.9676513671875 0.5060052275657654 0.6864401 0.5371045470237732 True -11 33624 30.76184058189392 2.43408465385437 1010.0274658203125 0.45607244968414307 1480.4429931640625 0.5103734731674194 0.69635296 0.524025559425354 True -12 36426 31.005767345428467 0.5828995704650879 1087.648681640625 0.5784622430801392 1470.240234375 0.5168021321296692 0.7106976 0.47389015555381775 True -13 39228 30.872564792633057 0.5886099338531494 1232.599609375 0.680942177772522 1467.65380859375 0.5154960751533508 0.7189595 0.4441084563732147 True -14 42030 31.038050174713135 0.5667605400085449 1285.15283203125 0.3251749575138092 1459.056884765625 0.5220568776130676 0.73059595 0.40939652919769287 True -15 44832 30.875922441482544 0.5747060775756836 1157.981201171875 0.42050862312316895 1454.5452880859375 0.5241764187812805 0.7361926 0.39062654972076416 True -16 47634 30.868113040924072 0.5654330253601074 1124.783447265625 0.5378400087356567 1452.3466796875 0.5255349278450012 0.74333715 0.3768725097179413 True -17 50436 30.86903405189514 1.2942276000976562 1093.029296875 0.4165828227996826 1455.4093017578125 0.5228416323661804 0.745323 0.3728907108306885 True -18 53238 30.872031927108765 0.6753323078155518 1105.260009765625 0.4370589554309845 1449.6630859375 0.5268442630767822 0.74683243 0.37340524792671204 True -19 56040 30.857802391052246 0.5591554641723633 1208.23828125 0.4700563848018646 1453.722900390625 0.5233991742134094 0.7461082 0.37211787700653076 False diff --git a/ENCSR705CNJ/cherimoya.fold_3.performance.tsv b/ENCSR705CNJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0dd2f0aa7d3a163ee0d52639fac99f625c0a917b..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1449.6630859375 0.23553155362606049 0.5268442034721375 0.3173448145389557 0.7468324303627014 0.6860825419425964 0.37340524792671204 \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_4.evaluate.json b/ENCSR705CNJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b12fcb87fc00ac77f81ec3ea35583d1d841ba357..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126QXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_4.fit.json b/ENCSR705CNJ/cherimoya.fold_4.fit.json deleted file mode 100644 index ad0a4007d85fdc23444989918cc6fe7b18a700af..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF126QXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705CNJ/cherimoya.fold_4.log b/ENCSR705CNJ/cherimoya.fold_4.log deleted file mode 100644 index ec23422e7d99c7902e38943c1134511b7c223e8d..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2889 35.85517501831055 3.740849256515503 1226.543701171875 0.8330846428871155 1762.007568359375 0.3231937289237976 0.5686001 8.497533798217773 True -1 5778 31.927119255065918 0.6035552024841309 1196.088134765625 1.383885383605957 1520.812744140625 0.4611751437187195 0.5830106 1.8915866613388062 True -2 8667 31.9985830783844 0.5815596580505371 1329.205322265625 0.7306903004646301 1496.319091796875 0.4689590036869049 0.61461437 0.7436999082565308 True -3 11556 31.92830777168274 0.5744030475616455 995.753173828125 0.7140375971794128 1482.6737060546875 0.4758661985397339 0.6334829 0.534656822681427 True -4 14445 31.860727071762085 0.5785562992095947 1079.7490234375 0.7898916006088257 1470.4249267578125 0.4838823676109314 0.6394912 0.5717832446098328 True -5 17334 31.89844822883606 0.5779542922973633 1339.29638671875 0.4225578308105469 1466.817138671875 0.48436278104782104 0.64556915 0.5660237073898315 True -6 20223 32.020243406295776 0.5787866115570068 1206.072021484375 0.7323588132858276 1455.654541015625 0.49149709939956665 0.64797384 0.4521227180957794 True -7 23112 31.868629217147827 1.7108228206634521 1129.1488037109375 0.41465315222740173 1449.685791015625 0.494460791349411 0.6481177 0.4640734791755676 True -8 26001 31.954216718673706 4.12471604347229 1099.201171875 0.6108109951019287 1438.564208984375 0.5020024180412292 0.6603364 0.4632352888584137 True -9 28890 32.0370032787323 0.6098031997680664 1052.29443359375 0.5041079521179199 1436.1478271484375 0.5036218166351318 0.66600436 0.4496593475341797 True -10 31779 31.962740182876587 0.5867104530334473 1083.3544921875 0.5656222105026245 1428.9683837890625 0.5087450742721558 0.67198545 0.4472905397415161 True -11 34668 31.988209009170532 0.5877907276153564 1177.27978515625 0.4897267520427704 1424.7113037109375 0.5106825232505798 0.6824837 0.4332822561264038 True -12 37557 31.925339460372925 0.5877590179443359 1122.2431640625 0.5005360245704651 1413.8680419921875 0.5186437964439392 0.68779224 0.43581750988960266 True -13 40446 31.896393537521362 0.5878098011016846 1039.9503173828125 0.4803794026374817 1411.43212890625 0.5180726051330566 0.6998228 0.420794278383255 True -14 43335 31.87434196472168 0.5752453804016113 1078.23193359375 0.4799959063529968 1408.439697265625 0.5200514197349548 0.710446 0.3941051661968231 True -15 46224 31.935994863510132 0.5960190296173096 933.3172607421875 0.5708376169204712 1403.1138916015625 0.5244749784469604 0.7178068 0.38013097643852234 True -16 49113 31.92048692703247 0.5913572311401367 1040.141845703125 0.7269896268844604 1403.3272705078125 0.5229923725128174 0.7259555 0.3727514445781708 True -17 52002 31.917593240737915 0.6017758846282959 1276.5921630859375 0.28713178634643555 1399.7564697265625 0.5258430242538452 0.72917855 0.3705665171146393 True -18 54891 32.69253730773926 0.5911386013031006 1060.186279296875 0.24792861938476562 1406.9736328125 0.520173966884613 0.730578 0.37056243419647217 True -19 57780 31.97727108001709 0.5868511199951172 1036.7021484375 0.22315478324890137 1404.0020751953125 0.5228732228279114 0.7302847 0.37395110726356506 False diff --git a/ENCSR705CNJ/cherimoya.fold_4.performance.tsv b/ENCSR705CNJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9d2be0937b3437432dd6c9807b978bac6b5e59dc..0000000000000000000000000000000000000000 --- a/ENCSR705CNJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1406.9736328125 0.2394517958164215 0.520173966884613 0.3096359074115753 0.7305780053138733 0.6669532656669617 0.37056243419647217 \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_0.evaluate.json b/ENCSR705GCU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 928255a0f0315575aaaa1eca6924658453ffdd34..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506CBL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_0.fit.json b/ENCSR705GCU/cherimoya.fold_0.fit.json deleted file mode 100644 index 6017d7d4bc8010ab048c1e5188802058dad4216c..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF506CBL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_0.log b/ENCSR705GCU/cherimoya.fold_0.log deleted file mode 100644 index e1f82b87d7c5f20443c027092183087dde1fba14..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 34.07677912712097 4.379418134689331 945.0220336914062 0.7199740409851074 1205.5562744140625 0.1810762882232666 0.63085043 8.714189529418945 True -1 5530 30.453994274139404 1.2104012966156006 768.1712036132812 0.8186334371566772 1077.9013671875 0.22131192684173584 0.7070279 3.7072527408599854 True -2 8295 30.4684054851532 0.8831779956817627 940.11181640625 0.7042319178581238 1071.8583984375 0.2178826481103897 0.715596 2.1270647048950195 True -3 11060 30.350508451461792 0.5846571922302246 1075.94140625 1.3693430423736572 1037.7750244140625 0.22584949433803558 0.7351444 1.7838674783706665 True -4 13825 30.304900884628296 0.6002116203308105 911.1857299804688 0.8304700255393982 1012.4166870117188 0.23057301342487335 0.7498545 1.2014226913452148 True -5 16590 30.35273003578186 0.5816535949707031 920.865234375 0.8894781470298767 996.5491943359375 0.23431077599525452 0.7556441 1.1298867464065552 True -6 19355 30.366238117218018 0.6270439624786377 740.4425048828125 0.7675947546958923 983.9044799804688 0.23599110543727875 0.7704874 0.9765837788581848 True -7 22120 30.303101301193237 0.6889269351959229 941.0624389648438 0.7408781051635742 970.7737426757812 0.24201591312885284 0.77726126 0.9540761113166809 True -8 24885 30.336658716201782 0.5930385589599609 792.537353515625 0.3511849641799927 967.30859375 0.24209634959697723 0.78627026 0.8261997699737549 True -9 27650 30.263167142868042 0.5894744396209717 860.7175903320312 0.5680602192878723 961.8854370117188 0.24242259562015533 0.79736835 0.7265430688858032 True -10 30415 30.416755199432373 0.5851571559906006 1018.1646728515625 0.6509267687797546 954.2523803710938 0.2446494698524475 0.8083533 0.617845892906189 True -11 33180 30.425085306167603 0.599834680557251 634.7605590820312 0.5229568481445312 946.1617431640625 0.24813705682754517 0.8174425 0.5819689035415649 True -12 35945 30.36193609237671 0.5957117080688477 743.7064208984375 0.6000868082046509 940.5476684570312 0.24855901300907135 0.82604164 0.5243438482284546 True -13 38710 30.346322536468506 0.581718921661377 808.6064453125 0.4450540542602539 935.951904296875 0.2502088248729706 0.83510846 0.4888828694820404 True -14 41475 30.335440397262573 0.593860387802124 761.6636962890625 0.7345743179321289 931.0416870117188 0.25181901454925537 0.84136856 0.45303022861480713 True -15 44240 30.38896632194519 0.6251485347747803 709.981689453125 0.3574121594429016 928.6007080078125 0.25196573138237 0.8453484 0.43373897671699524 True -16 47005 30.388129234313965 0.5847296714782715 950.7932739257812 0.37311312556266785 927.0327758789062 0.2521458566188812 0.8505113 0.4070366322994232 True -17 49770 30.418006896972656 0.5949704647064209 491.53314208984375 0.3472529351711273 924.1703491210938 0.253690630197525 0.8526836 0.39416632056236267 True -18 52535 30.36352014541626 1.878065824508667 902.3991088867188 0.32768651843070984 924.5628051757812 0.2527279257774353 0.85307425 0.38930726051330566 True -19 55300 30.46852159500122 0.586174726486206 785.76220703125 0.4096369445323944 927.8080444335938 0.25098541378974915 0.854085 0.3909745216369629 True diff --git a/ENCSR705GCU/cherimoya.fold_0.performance.tsv b/ENCSR705GCU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6307aac24df7813a18fc90c46b7996e3c63aa090..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -927.8080444335938 0.4911814033985138 0.25098538398742676 0.1022145077586174 0.8540850281715393 0.8068268299102783 0.3909745216369629 \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_1.evaluate.json b/ENCSR705GCU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 89d823abe2b8f75ae6d218a0407318ce70bee5c8..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506CBL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_1.fit.json b/ENCSR705GCU/cherimoya.fold_1.fit.json deleted file mode 100644 index 60c7e2c59399ea8eaedc50356d6792361f20925d..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF506CBL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_1.log b/ENCSR705GCU/cherimoya.fold_1.log deleted file mode 100644 index 270db922b7e8ba20b30272eb10ecda167dd3df65..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2692 33.8892183303833 4.399040937423706 768.1171264648438 0.6024827361106873 1543.6011962890625 0.1930341124534607 0.5992555 9.71735954284668 True -1 5384 29.685328245162964 0.7665472030639648 701.2900390625 0.494241327047348 1376.48193359375 0.2391117513179779 0.6776 4.820636749267578 True -2 8076 29.654524087905884 22.552340507507324 974.1416625976562 0.7536784410476685 1344.0009765625 0.24338115751743317 0.7052182 3.8763222694396973 True -3 10768 29.57300591468811 0.7498970031738281 680.0028686523438 0.5046562552452087 1275.7996826171875 0.2540278136730194 0.74445903 2.7034432888031006 True -4 13460 29.595876455307007 0.7307665348052979 921.927490234375 0.795272946357727 1252.901611328125 0.2568332850933075 0.7588058 2.284884214401245 True -5 16152 29.552131414413452 1.5634281635284424 745.904296875 0.45257261395454407 1231.9893798828125 0.2630596458911896 0.7663879 1.9993664026260376 True -6 18844 29.641465187072754 0.7536420822143555 1013.8392333984375 0.605105459690094 1212.1669921875 0.26559290289878845 0.7804071 1.6339812278747559 True -7 21536 29.494240760803223 0.7318356037139893 649.07958984375 0.8046152591705322 1200.27880859375 0.2687494158744812 0.78863376 1.4117963314056396 True -8 24228 29.56760573387146 0.7482244968414307 816.9223022460938 0.5893135666847229 1190.2991943359375 0.2698570489883423 0.7912446 1.1048303842544556 True -9 26920 29.56455111503601 0.7649576663970947 1065.711669921875 0.7037689089775085 1176.74658203125 0.27348098158836365 0.8038291 0.9918715953826904 True -10 29612 29.543203592300415 0.7529549598693848 741.790283203125 0.6895402669906616 1165.5361328125 0.27642756700515747 0.81181747 0.8703198432922363 True -11 32304 29.560853242874146 0.7315409183502197 907.4598999023438 0.6877709031105042 1157.5638427734375 0.27957797050476074 0.819242 0.8098283410072327 True -12 34996 29.615296363830566 0.7400891780853271 684.8430786132812 0.6100702881813049 1155.2061767578125 0.27945205569267273 0.83062077 0.7200409173965454 True -13 37688 29.665597200393677 0.7805099487304688 957.9428100585938 0.3662083148956299 1142.560302734375 0.2819097638130188 0.83736235 0.6660885810852051 True -14 40380 29.68584156036377 0.7387745380401611 772.88037109375 0.4450078010559082 1141.494384765625 0.2815813422203064 0.84682065 0.5934671759605408 True -15 43072 29.66622805595398 0.7412683963775635 682.766357421875 0.29958027601242065 1134.111572265625 0.2825242578983307 0.8532071 0.5402572154998779 True -16 45764 29.720316648483276 0.7512004375457764 758.4290771484375 0.46215885877609253 1130.6500244140625 0.2833716571331024 0.8595096 0.5034450888633728 True -17 48456 29.724803686141968 1.318425178527832 730.81884765625 0.34060436487197876 1127.6617431640625 0.28438860177993774 0.8611133 0.4822946786880493 True -18 51148 29.605791330337524 0.7604451179504395 553.53173828125 0.5233327150344849 1125.8343505859375 0.28588369488716125 0.86149687 0.47394612431526184 True -19 53840 29.674834728240967 2.295128345489502 664.0638427734375 0.47429734468460083 1126.922607421875 0.28533637523651123 0.86293066 0.4695855975151062 True diff --git a/ENCSR705GCU/cherimoya.fold_1.performance.tsv b/ENCSR705GCU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4c6d8ba9727eb92222b06f8e6b41624d63c0f08a..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1126.922607421875 0.464331716299057 0.28533634543418884 0.127946674823761 0.8629306554794312 0.8299556374549866 0.4695855975151062 \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_2.evaluate.json b/ENCSR705GCU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d9ce154ad3315449c1ef57829389d719812cf710..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506CBL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_2.fit.json b/ENCSR705GCU/cherimoya.fold_2.fit.json deleted file mode 100644 index 7b81cbb917bddbf8b32489fb9da65347ca056310..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF506CBL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_2.log b/ENCSR705GCU/cherimoya.fold_2.log deleted file mode 100644 index 91b03edef58ad5c820449dac4db5982860b281aa..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 35.44734311103821 6.737358093261719 882.5513305664062 0.6598588228225708 1233.551513671875 0.1818389892578125 0.60484535 7.913290500640869 True -1 5758 31.819011211395264 0.659949779510498 933.6005859375 0.9485082626342773 1118.8857421875 0.2164226770401001 0.6824326 3.3578779697418213 True -2 8637 31.67890167236328 0.619382381439209 971.8692626953125 0.5903379917144775 1097.2685546875 0.21788246929645538 0.70525986 2.7006783485412598 True -3 11516 31.682686805725098 0.6129250526428223 802.6983032226562 0.8617775440216064 1051.708251953125 0.227872833609581 0.7316204 2.846672534942627 True -4 14395 31.65784478187561 0.6088709831237793 886.9277954101562 0.6652271747589111 1036.6309814453125 0.23055337369441986 0.7377488 1.4762483835220337 True -5 17274 31.648633241653442 0.6156136989593506 993.6725463867188 0.7505635023117065 1018.807861328125 0.23513562977313995 0.7532654 1.2200740575790405 True -6 20153 31.627533197402954 0.6441733837127686 901.7259521484375 0.48654159903526306 1002.3681640625 0.23706680536270142 0.7709773 1.085821270942688 True -7 23032 31.704865217208862 0.6173725128173828 1220.630126953125 1.014162302017212 991.0905151367188 0.2384018748998642 0.7790063 0.9449989199638367 True -8 25911 31.77855896949768 1.6040515899658203 805.69384765625 0.4368492066860199 986.0682983398438 0.24015958607196808 0.78334135 0.8497852683067322 True -9 28790 31.780014276504517 0.6412656307220459 688.9212036132812 0.399496853351593 977.8290405273438 0.24409878253936768 0.7911263 0.7179728150367737 True -10 31669 31.86436915397644 0.6353228092193604 886.5882568359375 0.6139929890632629 976.816162109375 0.24302995204925537 0.7930297 0.6921711564064026 True -11 34548 31.841954469680786 0.6260991096496582 859.683837890625 0.6120792031288147 969.8959350585938 0.24570798873901367 0.8038453 0.6180657148361206 True -12 37427 31.669958353042603 0.6227388381958008 724.3944091796875 0.497047483921051 963.7614135742188 0.24694307148456573 0.8123262 0.5593929886817932 True -13 40306 31.61419701576233 2.1416094303131104 811.8526611328125 0.3511934280395508 957.64599609375 0.24836856126785278 0.8233029 0.5052182674407959 True -14 43185 31.6950101852417 0.624657154083252 1043.3154296875 0.7268166542053223 952.5277099609375 0.2511015236377716 0.83471316 0.45073574781417847 True -15 46064 31.732064485549927 0.6112017631530762 749.162841796875 0.5370885133743286 947.987548828125 0.25307226181030273 0.84000605 0.423010915517807 True -16 48943 31.790499687194824 0.6331198215484619 1090.470703125 0.682496964931488 945.8963623046875 0.2527577877044678 0.8422475 0.40649843215942383 True -17 51822 31.885868787765503 1.5004069805145264 807.0836791992188 0.30756086111068726 944.44873046875 0.25275135040283203 0.84596944 0.3973895311355591 True -18 54701 31.750449419021606 0.6150977611541748 889.891845703125 0.3965100049972534 946.0911865234375 0.25138071179389954 0.8458453 0.39721354842185974 False -19 57580 31.729235887527466 2.4409420490264893 979.1727905273438 0.3722805976867676 948.949462890625 0.2500201463699341 0.8441858 0.39971092343330383 False diff --git a/ENCSR705GCU/cherimoya.fold_2.performance.tsv b/ENCSR705GCU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6d1ad16b1f57c266e6a719cf31372fdb9e717dc5..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -944.44873046875 0.48707205057144165 0.25275135040283203 0.10522279888391495 0.8459694385528564 0.8061264157295227 0.3973895311355591 \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_3.evaluate.json b/ENCSR705GCU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 36ce2fb0e0664c6dff19ba9ef4b1625e2cc5e0ca..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506CBL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_3.fit.json b/ENCSR705GCU/cherimoya.fold_3.fit.json deleted file mode 100644 index c7a5a37e00a25dd6ae0777c757abfbc26066edd6..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF506CBL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_3.log b/ENCSR705GCU/cherimoya.fold_3.log deleted file mode 100644 index 3d19de1a0fc5446eff507d7cd079850f0ca8a8c4..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 34.116098403930664 3.6348206996917725 842.3464965820312 0.4184824228286743 1310.7222900390625 0.19121167063713074 0.5612094 9.582528114318848 True -1 5472 30.11313557624817 0.5449063777923584 1049.5516357421875 0.8119497299194336 1167.1435546875 0.23296061158180237 0.64190525 3.7430968284606934 True -2 8208 30.104676485061646 1.4727287292480469 687.3946533203125 0.6533915996551514 1151.947998046875 0.2331269234418869 0.6759654 2.5514488220214844 True -3 10944 30.140835762023926 0.532447338104248 721.7232666015625 0.48130613565444946 1102.223388671875 0.24530017375946045 0.7038406 2.2353153228759766 True -4 13680 30.023565530776978 0.5831680297851562 602.135498046875 0.48047810792922974 1075.158935546875 0.2500452697277069 0.7249476 1.4161070585250854 True -5 16416 30.045817375183105 0.5359430313110352 648.6202392578125 0.7223111987113953 1066.1981201171875 0.2501087784767151 0.73084795 1.3063193559646606 True -6 19152 30.03695511817932 0.5366504192352295 712.4130859375 0.7897510528564453 1056.3250732421875 0.2542882561683655 0.73703206 1.2945016622543335 True -7 21888 30.038676261901855 0.5370852947235107 793.1874389648438 0.3934999406337738 1050.86083984375 0.2533736824989319 0.74981356 1.1111044883728027 True -8 24624 30.05743932723999 0.5377814769744873 905.6173095703125 0.48004043102264404 1041.888671875 0.25635358691215515 0.7492433 1.0266036987304688 False -9 27360 30.29825448989868 13.938800573348999 989.41357421875 0.8770718574523926 1033.38720703125 0.26147499680519104 0.7581435 1.038787841796875 True -10 30096 30.104083776474 0.9530208110809326 847.6326904296875 0.44270843267440796 1028.7515869140625 0.2632230818271637 0.7714767 0.9210762977600098 True -11 32832 30.096304416656494 14.036307573318481 556.9796142578125 0.29561716318130493 1021.8831787109375 0.26564547419548035 0.78057426 0.8754897117614746 True -12 35568 30.10075330734253 0.5446724891662598 1137.5662841796875 0.7627404928207397 1011.6889038085938 0.26869910955429077 0.7932027 0.7735242247581482 True -13 38304 30.14525270462036 0.5393466949462891 935.0994873046875 0.318522572517395 1007.0499877929688 0.26988181471824646 0.8007205 0.7218676209449768 True -14 41040 30.17654252052307 0.5387911796569824 1133.6285400390625 0.7040461301803589 996.4539184570312 0.2724764943122864 0.8129883 0.6334333419799805 True -15 43776 30.127628087997437 0.5278165340423584 744.0784912109375 0.5998636484146118 993.963623046875 0.27234992384910583 0.82222265 0.5855472683906555 True -16 46512 30.13266086578369 0.5324327945709229 786.9925537109375 0.22657528519630432 992.7427978515625 0.2721215486526489 0.8296563 0.5343137979507446 True -17 49248 31.62945032119751 0.533566951751709 855.8900146484375 0.28691303730010986 992.5609130859375 0.2721453309059143 0.8349435 0.5046328902244568 True -18 51984 30.132687091827393 0.5318019390106201 856.4654541015625 0.2246033400297165 992.1546630859375 0.2714099884033203 0.83646214 0.49686750769615173 True -19 54720 30.18091320991516 0.5379137992858887 585.0842895507812 0.3491750955581665 992.2449340820312 0.271544486284256 0.838173 0.4934680163860321 True diff --git a/ENCSR705GCU/cherimoya.fold_3.performance.tsv b/ENCSR705GCU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7becdff91997c20a168f6622efd8eafc64b81987..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -992.2449340820312 0.4769864082336426 0.271544486284256 0.11018985509872437 0.838172972202301 0.7998708486557007 0.4934680163860321 \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_4.evaluate.json b/ENCSR705GCU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b00ae9598d0475ff02a6b2c064775c61e1563d82..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506CBL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_4.fit.json b/ENCSR705GCU/cherimoya.fold_4.fit.json deleted file mode 100644 index eecab31343c095d039d487ffee99aa99c59a5312..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF506CBL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705GCU/cherimoya.fold_4.log b/ENCSR705GCU/cherimoya.fold_4.log deleted file mode 100644 index 37e7ea29286ca9699f5c08b465d6168f2e8b2374..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2774 34.31220555305481 3.6540205478668213 838.7652587890625 0.7142190933227539 1083.9200439453125 0.17639675736427307 0.5928344 8.276080131530762 True -1 5548 30.513734340667725 0.6079964637756348 638.29150390625 0.46750393509864807 982.1027221679688 0.21193408966064453 0.68267846 3.2184982299804688 True -2 8322 30.609631061553955 0.5881659984588623 729.4898681640625 0.9255892038345337 977.638916015625 0.21250200271606445 0.67830646 2.278404951095581 False -3 11096 30.57650589942932 0.5905003547668457 656.571533203125 0.6319553256034851 941.2611083984375 0.2188524752855301 0.7094212 1.5074388980865479 True -4 13870 30.555646419525146 0.5839836597442627 794.16748046875 0.5012821555137634 920.4618530273438 0.22554892301559448 0.6982977 1.3337795734405518 False -5 16644 30.522923946380615 0.5949854850769043 825.8092041015625 0.8911374807357788 908.6387939453125 0.22778350114822388 0.71145976 0.9915282130241394 True -6 19418 30.51270294189453 0.5860164165496826 801.6826171875 0.5375760793685913 902.2403564453125 0.229820117354393 0.72999024 1.0677192211151123 True -7 22192 30.48179030418396 0.585435152053833 823.6171875 0.6619742512702942 892.9276733398438 0.23178744316101074 0.73938173 1.0651689767837524 True -8 24966 30.435383796691895 0.5860326290130615 846.7572021484375 0.34947192668914795 878.9402465820312 0.23660805821418762 0.7581627 0.976350724697113 True -9 27740 30.451896905899048 2.0424864292144775 963.3525390625 0.4207439720630646 876.8546752929688 0.23687589168548584 0.7648813 0.8950194716453552 True -10 30514 30.5293288230896 0.6045753955841064 725.4677734375 0.4243161678314209 873.0430297851562 0.2376466989517212 0.7747498 0.7410919070243835 True -11 33288 30.551112413406372 0.6376192569732666 861.2999267578125 0.6604568958282471 867.3175048828125 0.24015213549137115 0.7844173 0.6494482755661011 True -12 36062 30.533324241638184 0.6055850982666016 774.558837890625 0.4793710708618164 863.6795654296875 0.24113695323467255 0.796845 0.5625739097595215 True -13 38836 30.559428930282593 0.5957491397857666 833.1861572265625 0.6415514349937439 858.9439086914062 0.2423071265220642 0.80759585 0.49576449394226074 True -14 41610 30.501118659973145 0.585759162902832 633.83203125 0.3281766474246979 856.6972045898438 0.24215196073055267 0.8170674 0.46149811148643494 True -15 44384 30.562249898910522 0.585099458694458 881.5792236328125 0.4174787998199463 851.4254150390625 0.24404853582382202 0.8245027 0.43314453959465027 True -16 47158 30.647966623306274 0.5887291431427002 905.5651245117188 0.3833808898925781 850.2726440429688 0.24501347541809082 0.8279356 0.40911585092544556 True -17 49932 30.53535485267639 1.8878865242004395 839.933837890625 0.262790709733963 850.4511108398438 0.2451869398355484 0.83286333 0.39782434701919556 True -18 52706 30.610932111740112 0.6344707012176514 880.0501708984375 0.49941274523735046 850.9925537109375 0.24478812515735626 0.83340186 0.39582186937332153 True -19 55480 30.64095902442932 1.252765417098999 871.1212158203125 0.20538856089115143 852.8419799804688 0.24380731582641602 0.83298355 0.3973323702812195 False diff --git a/ENCSR705GCU/cherimoya.fold_4.performance.tsv b/ENCSR705GCU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e376bab5ffdf514e19ad460a0c6243dabd664d21..0000000000000000000000000000000000000000 --- a/ENCSR705GCU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -850.9925537109375 0.4986094534397125 0.24478811025619507 0.0966825783252716 0.8334018588066101 0.7864714860916138 0.39582186937332153 \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_0.evaluate.json b/ENCSR705RZX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index cd812b268cb156091b422da365dcae29bbd9e025..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372BIB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_0.fit.json b/ENCSR705RZX/cherimoya.fold_0.fit.json deleted file mode 100644 index 9ce7db759fccb1e67e9cda05ed0c8c0f57e7fc1f..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF372BIB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_0.log b/ENCSR705RZX/cherimoya.fold_0.log deleted file mode 100644 index 876418e5806cd9c17a36e37e8b207f151d3000a7..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1918 25.566269636154175 4.519333600997925 380.35284423828125 0.15144045650959015 498.69171142578125 0.5924310088157654 0.6930049 8.962507247924805 True -1 3836 21.135319471359253 0.4278080463409424 370.04205322265625 0.15134498476982117 423.95440673828125 0.6801446676254272 0.7760151 0.7698690891265869 True -2 5754 21.14394474029541 0.48725104331970215 375.03619384765625 0.1597021371126175 409.07598876953125 0.6992926597595215 0.7935237 0.3024710416793823 True -3 7672 21.175705909729004 0.3944673538208008 405.72332763671875 0.19029152393341064 404.6098937988281 0.7042573690414429 0.7981021 0.15528687834739685 True -4 9590 21.205618858337402 0.3975403308868408 376.68597412109375 0.10979874432086945 403.5865478515625 0.7046335339546204 0.8045809 0.15739840269088745 True -5 11508 21.179680585861206 0.38825488090515137 363.69219970703125 0.17586404085159302 402.6209716796875 0.7070565819740295 0.80759794 0.12242086231708527 True -6 13426 21.162352800369263 0.3869471549987793 378.4779968261719 0.07928505539894104 401.2252502441406 0.7093732953071594 0.8139199 0.1132090836763382 True -7 15344 21.177904844284058 0.390596866607666 385.49114990234375 0.10212403535842896 401.62408447265625 0.708954930305481 0.81308216 0.1217595785856247 False -8 17262 21.247281312942505 0.38602256774902344 369.2814636230469 0.16621536016464233 400.54071044921875 0.7107149362564087 0.81915945 0.11180080473423004 True -9 19180 21.20682954788208 1.1226897239685059 378.5025329589844 0.1562836766242981 399.8154602050781 0.7119937539100647 0.8236799 0.10886142402887344 True -10 21098 21.263057231903076 0.39690375328063965 355.301025390625 0.1078280657529831 399.2724304199219 0.7130883932113647 0.82538426 0.10668400675058365 True -11 23016 21.21622323989868 0.3837285041809082 378.35467529296875 0.11574183404445648 398.63629150390625 0.7140311598777771 0.82936573 0.10523177683353424 True -12 24934 20.853341341018677 0.3894338607788086 329.5056457519531 0.10581877827644348 398.005859375 0.7153682112693787 0.8344513 0.10382172465324402 True -13 26852 20.855960607528687 0.3847980499267578 376.6831970214844 0.10943323373794556 397.7156677246094 0.7161200046539307 0.835733 0.1028391495347023 True -14 28770 20.850167989730835 0.3945631980895996 384.5003356933594 0.11447998881340027 397.4842224121094 0.716738760471344 0.8380237 0.10121321678161621 True -15 30688 20.851886510849 0.38391923904418945 327.73150634765625 0.08053454756736755 397.2564392089844 0.7170643210411072 0.84073395 0.10134576261043549 True -16 32606 20.829060077667236 0.4190673828125 367.2259216308594 0.11533349752426147 397.3699951171875 0.7170493006706238 0.8396485 0.10254843533039093 False -17 34524 20.86103916168213 0.3824641704559326 337.2499084472656 0.06819203495979309 397.4737854003906 0.7166705131530762 0.83916163 0.1049363985657692 False -18 36442 20.857788562774658 0.37769198417663574 356.87042236328125 0.05494288355112076 397.7928771972656 0.7162584066390991 0.8385837 0.1057494580745697 False -19 38360 20.82812237739563 1.598193645477295 364.82537841796875 0.06991586089134216 397.938232421875 0.7159938812255859 0.8364851 0.1077008917927742 False diff --git a/ENCSR705RZX/cherimoya.fold_0.performance.tsv b/ENCSR705RZX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c3f09c82c82052f6af5114bdf468ab01142358db..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -397.2564392089844 0.23255202174186707 0.717064380645752 0.305166095495224 0.8407339453697205 0.7805827856063843 0.10134576261043549 \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_1.evaluate.json b/ENCSR705RZX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index dde7942bba71cb72e868a83dbc8ef26d54bd7001..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372BIB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_1.fit.json b/ENCSR705RZX/cherimoya.fold_1.fit.json deleted file mode 100644 index 8daf17eb065141c6e6e66caf70424ea683701024..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF372BIB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_1.log b/ENCSR705RZX/cherimoya.fold_1.log deleted file mode 100644 index de43d012a3c27f333a4de80ee9470e6ce79e8abd..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1900 25.361398696899414 3.740232467651367 340.63775634765625 0.15109795331954956 561.3985595703125 0.6013104319572449 0.654959 10.509400367736816 True -1 3800 20.912718057632446 0.5209214687347412 324.78570556640625 0.148380845785141 468.3785705566406 0.6955551505088806 0.76882356 0.9922340512275696 True -2 5700 20.946110248565674 0.735945463180542 346.9857177734375 0.12185841053724289 449.97064208984375 0.7176126837730408 0.7855629 0.5207234621047974 True -3 7600 20.979371070861816 0.4726574420928955 379.64593505859375 0.12985925376415253 450.76727294921875 0.714858889579773 0.7781708 0.30864888429641724 False -4 9500 20.913673877716064 0.46858811378479004 376.1268310546875 0.18069131672382355 443.59674072265625 0.7247170805931091 0.80053097 0.19038523733615875 True -5 11400 20.93523383140564 0.4606783390045166 350.68475341796875 0.11510641872882843 442.5152893066406 0.7273964285850525 0.798515 0.1762835532426834 False -6 13300 20.915764331817627 0.46823692321777344 371.46185302734375 0.12672418355941772 440.64117431640625 0.7306305766105652 0.81329715 0.15220794081687927 True -7 15200 20.922258615493774 2.178539276123047 355.3070983886719 0.08790023624897003 439.52008056640625 0.732500433921814 0.82128525 0.1400831788778305 True -8 17100 20.91485047340393 0.7695944309234619 347.9658203125 0.10342559218406677 438.6662292480469 0.7341062426567078 0.8294366 0.13012608885765076 True -9 19000 20.925531148910522 0.45871448516845703 359.6725769042969 0.11799821257591248 437.7981262207031 0.7353661060333252 0.8386187 0.12328427284955978 True -10 20900 20.938024759292603 0.4622976779937744 413.43878173828125 0.09929855167865753 436.8641052246094 0.7368481159210205 0.8436629 0.11927367746829987 True -11 22800 20.94886612892151 0.47289013862609863 367.8675231933594 0.10023584216833115 436.2673034667969 0.738051176071167 0.84957975 0.11465515941381454 True -12 24700 20.922074556350708 1.730989933013916 342.37799072265625 0.06111687794327736 435.55682373046875 0.7389631271362305 0.8523123 0.11059828102588654 True -13 26600 20.967324256896973 0.5271716117858887 345.29150390625 0.0989207923412323 435.12579345703125 0.7397418022155762 0.8581193 0.10760795325040817 True -14 28500 20.97253656387329 0.47687649726867676 349.6074523925781 0.0702899694442749 434.6339111328125 0.7403717637062073 0.86210847 0.10392589867115021 True -15 30400 20.944877862930298 0.49011898040771484 356.1335144042969 0.06497730314731598 434.4808654785156 0.740584135055542 0.8625939 0.10468067973852158 True -16 32300 20.948813676834106 0.46725940704345703 369.918701171875 0.07389285415410995 434.51470947265625 0.740325927734375 0.86426055 0.10400579124689102 True -17 34200 20.944979429244995 0.46489572525024414 355.3555603027344 0.08423607796430588 434.6875915527344 0.7397778034210205 0.86217487 0.10535155981779099 False -18 36100 20.94318199157715 0.46097326278686523 335.90386962890625 0.03235652297735214 435.25616455078125 0.7392293214797974 0.8583951 0.10747235268354416 False -19 38000 20.947092533111572 0.46945881843566895 352.0429992675781 0.0827198177576065 435.28424072265625 0.7389057874679565 0.8577822 0.10815726220607758 False diff --git a/ENCSR705RZX/cherimoya.fold_1.performance.tsv b/ENCSR705RZX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bd39047988030e2811a826c77e3a3e0ff7bacf5f..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -434.51470947265625 0.21590104699134827 0.740325927734375 0.3324875235557556 0.8642605543136597 0.8386756181716919 0.10400579124689102 \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_2.evaluate.json b/ENCSR705RZX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 88fe061c37bce88308fa84550e22e45224d91580..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372BIB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_2.fit.json b/ENCSR705RZX/cherimoya.fold_2.fit.json deleted file mode 100644 index c0685a02b643f0e5d651d44e05db6c9bb69621a8..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF372BIB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_2.log b/ENCSR705RZX/cherimoya.fold_2.log deleted file mode 100644 index 4fb407674edea55118aa17e02ee32f632193d3e2..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1999 26.593482971191406 4.003719091415405 405.70074462890625 0.14903903007507324 507.45880126953125 0.603924036026001 0.65849024 8.47404670715332 True -1 3998 22.032374620437622 0.4281959533691406 349.6719970703125 0.1933276653289795 433.2790222167969 0.6882314085960388 0.765873 0.8207955956459045 True -2 5997 22.04185199737549 0.3935973644256592 346.89776611328125 0.12456218153238297 422.8748779296875 0.7029823064804077 0.77573574 0.22345563769340515 True -3 7996 22.007364749908447 0.38410282135009766 342.673583984375 0.14780069887638092 417.7783508300781 0.7094590663909912 0.7842441 0.17657291889190674 True -4 9995 21.704967737197876 0.38282275199890137 369.1725158691406 0.1316373348236084 416.6939392089844 0.7104130983352661 0.79689246 0.20319975912570953 True -5 11994 21.5918972492218 0.3825647830963135 378.0023498535156 0.14003869891166687 415.43316650390625 0.7135862112045288 0.80018497 0.16270452737808228 True -6 13993 21.625742197036743 0.38289618492126465 338.25018310546875 0.14840102195739746 414.4958801269531 0.715264081954956 0.80391383 0.146646186709404 True -7 15992 21.58465576171875 0.4033932685852051 401.527587890625 0.10717039555311203 414.0938720703125 0.7159515023231506 0.8122063 0.1433034986257553 True -8 17991 21.59325408935547 1.834876298904419 369.0086669921875 0.20841729640960693 413.2333068847656 0.7173720598220825 0.8165745 0.13221603631973267 True -9 19990 21.604015111923218 0.40985107421875 384.465576171875 0.1881849616765976 412.7982482910156 0.7179867029190063 0.8219528 0.12690414488315582 True -10 21989 21.644156217575073 0.3816492557525635 349.5479736328125 0.09566017985343933 411.7212219238281 0.7199113368988037 0.82883793 0.11845745891332626 True -11 23988 21.659759283065796 0.3823723793029785 350.85772705078125 0.10693755745887756 411.1599426269531 0.7207927107810974 0.83122355 0.11419229209423065 True -12 25987 21.682490587234497 0.3833127021789551 362.0371398925781 0.08979631960391998 410.643310546875 0.7217012643814087 0.8341055 0.11331012845039368 True -13 27986 21.686439275741577 0.3749568462371826 373.34710693359375 0.09378834068775177 410.18609619140625 0.7223449945449829 0.83453214 0.11273670196533203 True -14 29985 22.280213832855225 0.38970351219177246 360.64178466796875 0.055779434740543365 409.9658508300781 0.7228397130966187 0.8371727 0.11227864772081375 True -15 31984 21.61039137840271 0.38966846466064453 347.2005615234375 0.09331691265106201 409.7278747558594 0.7232800722122192 0.8387575 0.11319060623645782 True -16 33983 21.737159490585327 0.38292503356933594 359.336181640625 0.05634685978293419 409.78546142578125 0.7232187986373901 0.8402954 0.11387864500284195 True -17 35982 21.760801315307617 0.38182902336120605 361.7718505859375 0.07243463397026062 409.94146728515625 0.7228609323501587 0.8393912 0.11445873230695724 False -18 37981 21.669360876083374 0.3807382583618164 370.0709533691406 0.06543820351362228 410.1690673828125 0.7223436236381531 0.8374727 0.11661679297685623 False -19 39980 21.67799139022827 0.3813798427581787 364.2835998535156 0.07445904612541199 410.33575439453125 0.7220537662506104 0.8358514 0.11812656372785568 False diff --git a/ENCSR705RZX/cherimoya.fold_2.performance.tsv b/ENCSR705RZX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 047d3e8542aac46aee96524b4cc0ee057de1cd6d..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -409.78546142578125 0.22722606360912323 0.7232187390327454 0.31514087319374084 0.8402953743934631 0.7864137887954712 0.11387864500284195 \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_3.evaluate.json b/ENCSR705RZX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d3523b08a1ff898101d574cff0cdd4edfbc08648..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372BIB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_3.fit.json b/ENCSR705RZX/cherimoya.fold_3.fit.json deleted file mode 100644 index 5dcb8412bcdc503ac2b153a788c60fbabd106ccf..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF372BIB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_3.log b/ENCSR705RZX/cherimoya.fold_3.log deleted file mode 100644 index 7d4757d0ca36d595ea3b010a0f76109816b8c851..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1949 26.05597710609436 3.595174551010132 384.34259033203125 0.21200448274612427 505.3204345703125 0.5920420289039612 0.63828814 9.824808120727539 True -1 3898 21.459357023239136 0.47440171241760254 378.43682861328125 0.1349780559539795 427.7646179199219 0.680947482585907 0.73424125 0.945051908493042 True -2 5847 21.472252130508423 0.42247843742370605 374.3074035644531 0.17053920030593872 414.0011901855469 0.6998142600059509 0.7433476 0.2643373906612396 True -3 7796 21.48378038406372 0.4032914638519287 374.36859130859375 0.13763800263404846 410.4254150390625 0.7038784027099609 0.7534873 0.21840345859527588 True -4 9745 21.505727767944336 0.40397095680236816 358.7992248535156 0.14621785283088684 408.381103515625 0.7078669667243958 0.7600992 0.18571707606315613 True -5 11694 21.484065055847168 0.397230863571167 377.05621337890625 0.15924543142318726 408.1594543457031 0.7093186974525452 0.7698437 0.1830974519252777 True -6 13643 21.464964389801025 0.5765647888183594 352.3938293457031 0.16237036883831024 407.7055969238281 0.7105107307434082 0.7773913 0.1883634626865387 True -7 15592 21.480281591415405 0.4257664680480957 378.8582458496094 0.1857592761516571 406.9834899902344 0.711665153503418 0.781654 0.17920467257499695 True -8 17541 21.49404501914978 0.4294090270996094 381.53009033203125 0.13960812985897064 406.831787109375 0.7126810550689697 0.78694254 0.17586858570575714 True -9 19490 21.250840425491333 0.39498353004455566 361.3614196777344 0.11381465196609497 406.1488952636719 0.7137813568115234 0.7863566 0.1698438823223114 False -10 21439 21.110976934432983 0.390002965927124 368.4180603027344 0.10510977357625961 405.35443115234375 0.7146242260932922 0.7857955 0.1663723737001419 False -11 23388 21.10492515563965 0.39319849014282227 362.88665771484375 0.12499892711639404 404.5492858886719 0.7157570123672485 0.78812915 0.1669936329126358 True -12 25337 21.10355305671692 0.39736294746398926 338.23541259765625 0.0968635231256485 403.7535705566406 0.7166389226913452 0.7910799 0.15858374536037445 True -13 27286 21.262062549591064 16.953386783599854 383.1280212402344 0.1310025006532669 403.6047668457031 0.7172293066978455 0.7908544 0.15556995570659637 False -14 29235 21.100991010665894 0.40869832038879395 365.09771728515625 0.07224474102258682 403.29766845703125 0.717757523059845 0.7928148 0.1531554013490677 True -15 31184 21.083590507507324 0.39952945709228516 361.9720764160156 0.08922962844371796 403.53350830078125 0.7181240916252136 0.79657155 0.1532909870147705 True -16 33133 21.064364433288574 0.3987090587615967 380.0411071777344 0.08044679462909698 402.917236328125 0.7182201743125916 0.7943108 0.15158750116825104 False -17 35082 21.03978705406189 10.504317283630371 368.8078308105469 0.06200602650642395 402.76422119140625 0.7178792357444763 0.7911968 0.15245521068572998 False -18 37031 21.206034421920776 0.39345312118530273 355.59332275390625 0.047393057495355606 402.8933410644531 0.7174306511878967 0.7861938 0.15457385778427124 False -19 38980 21.149418115615845 0.40577077865600586 353.9974670410156 0.11371117830276489 403.015869140625 0.717140793800354 0.78496045 0.15600448846817017 False diff --git a/ENCSR705RZX/cherimoya.fold_3.performance.tsv b/ENCSR705RZX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7f039c0bcf19d55cd0e50ad647e5ae335dc8dd3d..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -403.53350830078125 0.23113735020160675 0.7181240916252136 0.30617576837539673 0.7965715527534485 0.7715046405792236 0.1532909870147705 \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_4.evaluate.json b/ENCSR705RZX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 773013c56a8e1d1c4ab69be162c933e2c92414c1..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF372BIB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_4.fit.json b/ENCSR705RZX/cherimoya.fold_4.fit.json deleted file mode 100644 index 48ee83f6d6d5978de87d4e85d5158494d204db6e..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF372BIB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR705RZX/cherimoya.fold_4.log b/ENCSR705RZX/cherimoya.fold_4.log deleted file mode 100644 index 65c28b95873349686a02c7a59994cc1fd01a7315..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1951 26.881070852279663 6.071098804473877 347.8740234375 0.17626602947711945 487.2193908691406 0.5948552489280701 0.67434174 9.233925819396973 True -1 3902 21.543535947799683 0.4278111457824707 356.0055847167969 0.22673973441123962 416.5931396484375 0.6809461116790771 0.7619031 0.719603419303894 True -2 5853 22.271738290786743 0.40042662620544434 357.70489501953125 0.15870338678359985 403.7347106933594 0.6986310482025146 0.7879538 0.24086937308311462 True -3 7804 21.53648090362549 0.4197075366973877 370.00042724609375 0.12026411294937134 399.4078674316406 0.7029727697372437 0.7969329 0.12508012354373932 True -4 9755 21.610402822494507 0.3837006092071533 365.2471923828125 0.18010568618774414 397.8777770996094 0.7061219215393066 0.8092839 0.12640464305877686 True -5 11706 21.601229190826416 1.5505571365356445 326.1340637207031 0.18514615297317505 397.0060729980469 0.7077170610427856 0.81644493 0.11264003813266754 True -6 13657 21.574113368988037 1.1738972663879395 381.0325927734375 0.12076947093009949 396.4974365234375 0.7087070345878601 0.81673723 0.111166812479496 True -7 15608 21.586852312088013 0.37286877632141113 366.3553466796875 0.150436669588089 395.7779235839844 0.7097599506378174 0.8265764 0.10594360530376434 True -8 17559 21.57966661453247 0.37280750274658203 355.87042236328125 0.16340771317481995 395.36907958984375 0.7106183767318726 0.832798 0.1006200760602951 True -9 19510 21.540055513381958 0.3755495548248291 346.48004150390625 0.16130641102790833 394.87542724609375 0.7112787365913391 0.83645105 0.09588820487260818 True -10 21461 21.505236387252808 0.3771779537200928 352.08526611328125 0.1299915909767151 394.3449401855469 0.7121235728263855 0.84061533 0.09355364739894867 True -11 23412 21.57236647605896 0.37428855895996094 338.80560302734375 0.13520918786525726 394.0233154296875 0.7126985788345337 0.84541947 0.09135454893112183 True -12 25363 21.566337823867798 0.3836948871612549 360.16546630859375 0.0663687214255333 393.41290283203125 0.7136357426643372 0.84913296 0.08934131264686584 True -13 27314 21.563172817230225 0.38298797607421875 344.29205322265625 0.11589516699314117 393.17523193359375 0.7143638134002686 0.8520291 0.08720904588699341 True -14 29265 21.566469192504883 0.3819913864135742 347.4718017578125 0.06539435684680939 392.7484436035156 0.7149761319160461 0.85267925 0.08767713606357574 True -15 31216 21.503182411193848 0.37549495697021484 346.42376708984375 0.08330123871564865 392.58551025390625 0.7153497338294983 0.8541696 0.08811204135417938 True -16 33167 21.48760485649109 0.36833858489990234 354.53173828125 0.051572494208812714 392.661865234375 0.7153196334838867 0.8544928 0.09025005996227264 True -17 35118 21.55265712738037 0.3780062198638916 348.9507141113281 0.04901218041777611 392.89508056640625 0.7149584293365479 0.85283154 0.09259498119354248 False -18 37069 21.65378499031067 0.3768942356109619 344.2047119140625 0.06342919170856476 393.087646484375 0.714553713798523 0.8517857 0.09507851302623749 False -19 39020 21.377702474594116 0.3715198040008545 341.9282531738281 0.04618555307388306 392.9942932128906 0.7142302393913269 0.84922284 0.0964922085404396 False diff --git a/ENCSR705RZX/cherimoya.fold_4.performance.tsv b/ENCSR705RZX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ec56747b1350fd18d40248bb244a583c8eb3d073..0000000000000000000000000000000000000000 --- a/ENCSR705RZX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -392.661865234375 0.23430033028125763 0.7153196334838867 0.3020152449607849 0.8544927835464478 0.7923682928085327 0.09025005996227264 \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_0.evaluate.json b/ENCSR706GDQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 97d0d492593090cd309766f6522ea5d461a69eb6..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF010SUI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_0.fit.json b/ENCSR706GDQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 6099664c4dd4de8a003c2914310cf0bf12f6fdd7..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF010SUI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_0.log b/ENCSR706GDQ/cherimoya.fold_0.log deleted file mode 100644 index feb15a7d46b34a212325f24b7e7ff039d33e54e8..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1959 25.762253761291504 25.80882954597473 321.393310546875 0.7148535251617432 454.0517272949219 0.44585371017456055 0.5592293 10.604260444641113 True -1 3918 23.004971265792847 0.4064362049102783 271.7491760253906 0.6607360243797302 390.3102722167969 0.5542056560516357 0.6483976 3.9779248237609863 True -2 5877 21.349694967269897 0.40397167205810547 292.480224609375 0.6461293697357178 372.1349792480469 0.5932770371437073 0.6344307 1.2152974605560303 False -3 7836 21.31176471710205 0.4033334255218506 272.69659423828125 0.6592085957527161 366.0409240722656 0.6039994359016418 0.6419372 0.8617986440658569 False -4 9795 21.31616520881653 0.39627528190612793 290.07110595703125 0.6088799238204956 364.22479248046875 0.607771635055542 0.64830697 0.8588984608650208 False -5 11754 21.885749340057373 27.099178791046143 346.348876953125 0.5591033697128296 362.9215393066406 0.6102900505065918 0.6563706 0.8056085705757141 True -6 13713 22.271982192993164 0.3951849937438965 258.061279296875 0.5189154148101807 361.1849670410156 0.6139487624168396 0.6671813 0.7156491279602051 True -7 15672 21.363166093826294 18.226865530014038 256.8787536621094 0.6261435747146606 360.418701171875 0.6158512830734253 0.67210865 0.6848922371864319 True -8 17631 22.81662893295288 0.6462492942810059 292.9864807128906 0.584579586982727 359.6328125 0.6176398992538452 0.6778556 0.6513017416000366 True -9 19590 21.416339635849 0.39410972595214844 268.2644958496094 0.6190081834793091 358.5316467285156 0.6196759343147278 0.68246454 0.6343200206756592 True -10 21549 21.31894302368164 0.40026164054870605 270.73016357421875 0.4844236671924591 357.6201171875 0.6215777397155762 0.69013137 0.5941069722175598 True -11 23508 21.314457416534424 0.39507484436035156 247.199462890625 0.5215367674827576 356.81085205078125 0.6235435605049133 0.6952975 0.5736652612686157 True -12 25467 21.305161952972412 1.332094430923462 275.0434265136719 0.5030761957168579 355.830322265625 0.6252057552337646 0.70419383 0.5400801301002502 True -13 27426 21.372400283813477 0.392444372177124 315.82427978515625 0.343533992767334 355.3596496582031 0.626035213470459 0.7069093 0.5298948287963867 True -14 29385 21.064050674438477 0.3922150135040283 259.1400146484375 0.5601097345352173 354.8616638183594 0.6267075538635254 0.7086819 0.5241349935531616 True -15 31344 20.93710494041443 0.3914928436279297 269.2676696777344 0.4131771922111511 354.8531494140625 0.6271234750747681 0.7113381 0.5207651853561401 True -16 33303 20.92506980895996 0.3899202346801758 243.62997436523438 0.5093163251876831 354.8653259277344 0.6267170906066895 0.708288 0.5299957394599915 False -17 35262 20.93491291999817 0.3868281841278076 319.0749206542969 0.23974423110485077 355.3362731933594 0.6258766055107117 0.70448387 0.5451051592826843 False -18 37221 20.926907062530518 0.39296627044677734 291.6539001464844 0.35631632804870605 355.6343688964844 0.6250981092453003 0.69863206 0.5614517331123352 False -19 39180 20.934448957443237 0.3973710536956787 239.69349670410156 0.3121412694454193 355.5452880859375 0.6246594190597534 0.6946352 0.5684438943862915 False diff --git a/ENCSR706GDQ/cherimoya.fold_0.performance.tsv b/ENCSR706GDQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8d8cb3c7a11f80c8440f0a3c6ab4c5fcc40d5966..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -354.8531494140625 0.30181726813316345 0.6271234154701233 0.23540115356445312 0.7113381028175354 0.6788367033004761 0.5207651853561401 \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_1.evaluate.json b/ENCSR706GDQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 636c1caa74992faadaa92bc135e74c8237d79d03..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF010SUI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_1.fit.json b/ENCSR706GDQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 3045d3879eaefa5d7a581cf7054b3beb681ce6bc..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF010SUI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_1.log b/ENCSR706GDQ/cherimoya.fold_1.log deleted file mode 100644 index 9260dadb06e967b0d6424824c1b84996db279681..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1987 26.082066297531128 3.398993968963623 208.24679565429688 1.1136665344238281 450.6961669921875 0.4571821391582489 0.54619473 10.614757537841797 True -1 3974 21.622928380966187 1.6380608081817627 294.7352294921875 0.7212331295013428 391.4625244140625 0.5600700974464417 0.649874 3.833704948425293 True -2 5961 21.65318012237549 0.47394466400146484 287.8783874511719 0.7138359546661377 377.1116027832031 0.5927587747573853 0.6610382 1.2109524011611938 True -3 7948 21.64867091178894 0.4742298126220703 245.48312377929688 0.7220621705055237 372.1793212890625 0.6018280982971191 0.67048883 0.7373313903808594 True -4 9935 21.622313737869263 0.4626033306121826 274.42767333984375 0.6082028150558472 370.273681640625 0.6059243083000183 0.6832739 0.625841498374939 True -5 11922 21.65461540222168 0.46471500396728516 268.28448486328125 0.6181745529174805 368.4897766113281 0.6099889278411865 0.6850377 0.6069642305374146 True -6 13909 21.642834186553955 25.08488655090332 254.72747802734375 0.6576067805290222 367.2430725097656 0.6128169298171997 0.69106704 0.5590171813964844 True -7 15896 22.788794994354248 0.470170259475708 269.73577880859375 0.35542532801628113 366.75775146484375 0.6139670014381409 0.69590485 0.5350327491760254 True -8 17883 21.650437116622925 1.3758587837219238 295.526123046875 0.7100914716720581 365.71148681640625 0.6160170435905457 0.7024522 0.5183594822883606 True -9 19870 21.677101850509644 0.4751718044281006 254.72027587890625 0.5162314772605896 364.8495178222656 0.6179602146148682 0.70375735 0.5018593072891235 True -10 21857 21.65890073776245 23.892021894454956 325.35205078125 0.7291945219039917 364.1902770996094 0.6194862127304077 0.7079584 0.48768287897109985 True -11 23844 25.245388746261597 0.46957826614379883 271.6610107421875 0.5072848796844482 363.51971435546875 0.6211571097373962 0.71555364 0.46616265177726746 True -12 25831 21.678837060928345 0.4621291160583496 285.39324951171875 0.5089923739433289 362.85028076171875 0.6227244138717651 0.7186293 0.46028804779052734 True -13 27818 21.676242351531982 0.46540260314941406 225.9029541015625 0.5470556020736694 361.9939270019531 0.6241497993469238 0.72592086 0.4455359876155853 True -14 29805 21.695652723312378 0.8738651275634766 298.82806396484375 0.41236624121665955 361.6019592285156 0.6249395608901978 0.7302228 0.4343743920326233 True -15 31792 21.72316026687622 1.3553783893585205 275.8331298828125 0.2685713768005371 361.2309265136719 0.625403642654419 0.7313478 0.43625226616859436 True -16 33779 21.685040712356567 0.45900702476501465 297.28997802734375 0.3659181594848633 361.31292724609375 0.6252739429473877 0.7311207 0.4419916272163391 False -17 35766 21.640472650527954 0.4622983932495117 264.67742919921875 0.3150351047515869 361.5498046875 0.6246256232261658 0.728603 0.4505956470966339 False -18 37753 21.650731086730957 0.4679698944091797 273.791015625 0.3087266981601715 361.7587585449219 0.6239438056945801 0.7259041 0.46151283383369446 False -19 39740 21.638665437698364 0.4670219421386719 258.78277587890625 0.20402199029922485 361.8917236328125 0.6234312057495117 0.7234074 0.469545841217041 False diff --git a/ENCSR706GDQ/cherimoya.fold_1.performance.tsv b/ENCSR706GDQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b61085f7b81ab85a21d2144e305bd259fdcf2d1f..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.2309265136719 0.29930809140205383 0.625403642654419 0.23852448165416718 0.7313477993011475 0.7321068644523621 0.43625226616859436 \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_2.evaluate.json b/ENCSR706GDQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 35935dd3f42176dbce05f509cd62419c86d9db6a..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF010SUI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_2.fit.json b/ENCSR706GDQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 2b8daa06328ca5a28af0210e6c1a4918156282b0..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF010SUI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_2.log b/ENCSR706GDQ/cherimoya.fold_2.log deleted file mode 100644 index 902f6f35709dcf6b84d91896f108114f7526d5aa..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2081 27.384642362594604 3.288414239883423 308.3775939941406 0.6049638986587524 445.966064453125 0.4531378149986267 0.57165223 8.688962936401367 True -1 4162 22.7902410030365 0.7438139915466309 281.76422119140625 0.893799901008606 387.2107849121094 0.557719886302948 0.6514844 3.3955230712890625 True -2 6243 22.236531496047974 0.38274550437927246 270.7856750488281 0.753559947013855 370.5230712890625 0.5930172204971313 0.6516718 0.9537316560745239 True -3 8324 22.253482580184937 0.3978137969970703 271.4560241699219 0.5750690698623657 366.5044860839844 0.5994517207145691 0.6717431 0.6763073801994324 True -4 10405 22.209367990493774 0.39020848274230957 316.20135498046875 0.6800901889801025 364.66064453125 0.6028885245323181 0.67444474 0.6123608350753784 True -5 12486 22.94236731529236 0.3893880844116211 284.0816345214844 0.6065807938575745 363.5274963378906 0.6051157712936401 0.6759186 0.6025091409683228 True -6 14567 22.27916717529297 6.999881267547607 250.938232421875 0.7226197123527527 362.91156005859375 0.6065819263458252 0.6781794 0.6133413910865784 True -7 16648 22.263767957687378 0.3900644779205322 323.35675048828125 0.4929123818874359 361.8040771484375 0.6087093353271484 0.6838741 0.5895493030548096 True -8 18729 25.420148849487305 26.534878969192505 264.7564392089844 0.7801206111907959 360.74981689453125 0.6111438870429993 0.68488383 0.5720419883728027 True -9 20810 26.00883674621582 17.953145265579224 229.484130859375 0.703839898109436 359.7007141113281 0.6132721900939941 0.6927693 0.5511304140090942 True -10 22891 29.706345558166504 6.533414125442505 262.205078125 0.5782907009124756 358.9588623046875 0.615168035030365 0.6987017 0.531692624092102 True -11 24972 22.265631437301636 0.3855607509613037 282.88018798828125 0.5687475204467773 358.1277160644531 0.6171077489852905 0.705819 0.5209596157073975 True -12 27053 22.273847103118896 8.77371072769165 272.4533996582031 0.436698853969574 357.1730651855469 0.6182026267051697 0.7074985 0.5117763876914978 True -13 29134 22.25137424468994 0.3911609649658203 276.00494384765625 0.5545529127120972 356.69451904296875 0.619354784488678 0.7098133 0.49574917554855347 True -14 31215 22.266700983047485 0.4078373908996582 273.21929931640625 0.3519473671913147 356.4963684082031 0.6203813552856445 0.71345097 0.5004516839981079 True -15 33296 22.251275777816772 0.396195650100708 270.8944091796875 0.3431575298309326 356.2735900878906 0.6205357313156128 0.71611315 0.4950491189956665 True -16 35377 22.39292883872986 2.53954815864563 291.9604187011719 0.44901981949806213 356.36151123046875 0.6202945709228516 0.7179203 0.5055486559867859 True -17 37458 22.230701446533203 0.3957815170288086 248.330810546875 0.3402593731880188 356.65203857421875 0.619572103023529 0.7133584 0.5242910385131836 False -18 39539 22.19917869567871 0.3895885944366455 277.6741027832031 0.2603961229324341 356.757080078125 0.6188697218894958 0.7083104 0.5374066829681396 False -19 41620 22.54073429107666 21.03051996231079 316.7607421875 0.2815586030483246 356.8844909667969 0.6184502840042114 0.7065422 0.5497209429740906 False diff --git a/ENCSR706GDQ/cherimoya.fold_2.performance.tsv b/ENCSR706GDQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4c883850f418888b72687dca122be3f991b9f91b..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -356.36151123046875 0.30425024032592773 0.6202945113182068 0.23396003246307373 0.7179203033447266 0.6966368556022644 0.5055486559867859 \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_3.evaluate.json b/ENCSR706GDQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 83bfd1c97d88ae1ec767a229fda8a2680aaf6176..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF010SUI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_3.fit.json b/ENCSR706GDQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 10341fa37067ed2f5fe2a04aacf95d89892a6ffa..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF010SUI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_3.log b/ENCSR706GDQ/cherimoya.fold_3.log deleted file mode 100644 index 34be58312ae87b54b9fd2c85c451631fd9ddae76..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2038 26.971560955047607 4.109602689743042 320.5986328125 0.7489326000213623 456.3567810058594 0.45541590452194214 0.57663864 10.274624824523926 True -1 4076 22.499319314956665 0.43904614448547363 276.48504638671875 0.7385641932487488 391.9222106933594 0.5642120242118835 0.63613117 3.6874871253967285 True -2 6114 22.476807594299316 22.910621643066406 325.1250915527344 1.127378225326538 375.09576416015625 0.5972377061843872 0.6463656 1.2623893022537231 True -3 8152 24.849170684814453 14.158436059951782 291.91339111328125 0.7469859719276428 370.15594482421875 0.6053553223609924 0.6563341 0.7943422198295593 True -4 10190 22.503350734710693 0.43310976028442383 274.94415283203125 0.7985607385635376 368.7260437011719 0.60804682970047 0.6610558 0.7999833822250366 True -5 12228 22.521109342575073 0.4332246780395508 274.90667724609375 0.4754576086997986 367.2991027832031 0.6107701659202576 0.6615738 0.7957445979118347 True -6 14266 22.499294757843018 0.42456698417663574 301.30670166015625 0.7120440006256104 366.23284912109375 0.6129397749900818 0.664782 0.7581284642219543 True -7 16304 22.48491621017456 0.4246037006378174 270.76556396484375 0.5602999925613403 365.653076171875 0.6147251725196838 0.671987 0.715630829334259 True -8 18342 22.499199628829956 1.2676222324371338 286.1714782714844 0.5770083665847778 364.37237548828125 0.616876482963562 0.67278856 0.6886555552482605 True -9 20380 22.303430318832397 0.4253580570220947 276.9849548339844 0.5353748798370361 363.8470764160156 0.6181978583335876 0.68087006 0.6810469031333923 True -10 22418 22.086894035339355 0.412808895111084 294.434326171875 0.5290389060974121 363.1031799316406 0.6199505925178528 0.6837112 0.644739031791687 True -11 24456 22.1432945728302 0.41796064376831055 256.7388000488281 0.3889339566230774 362.3645935058594 0.6215070486068726 0.68918043 0.6102080345153809 True -12 26494 22.10148000717163 0.4238626956939697 313.109619140625 0.4097011983394623 361.4617004394531 0.6232393980026245 0.69338894 0.5769067406654358 True -13 28532 22.107959508895874 0.4268491268157959 325.9014892578125 0.3579632043838501 360.749267578125 0.624420166015625 0.69994986 0.5523788928985596 True -14 30570 22.076158046722412 0.42485594749450684 240.99981689453125 0.7308416366577148 360.35223388671875 0.625292956829071 0.70732397 0.534376859664917 True -15 32608 22.119027376174927 0.42653846740722656 246.23062133789062 0.3839675188064575 360.2133483886719 0.6254690289497375 0.70922023 0.534572184085846 True -16 34646 22.131431579589844 0.4266362190246582 306.726318359375 0.4044784903526306 360.3703918457031 0.6249969005584717 0.709363 0.5440992712974548 True -17 36684 22.557689428329468 30.57466411590576 271.5674133300781 0.33356973528862 360.6036376953125 0.6242032051086426 0.705681 0.5610699653625488 False -18 38722 22.4919855594635 0.43491196632385254 283.61651611328125 0.20067501068115234 360.8932800292969 0.6234905123710632 0.6995301 0.57790607213974 False -19 40760 27.028961420059204 24.03665018081665 292.50750732421875 0.24897484481334686 361.0813293457031 0.6230294704437256 0.6967002 0.5832571387290955 False diff --git a/ENCSR706GDQ/cherimoya.fold_3.performance.tsv b/ENCSR706GDQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0848efae037a98561801679975469522f49e3d18..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -360.3703918457031 0.3008806109428406 0.6249968409538269 0.23743340373039246 0.7093629837036133 0.6846354603767395 0.5440992712974548 \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_4.evaluate.json b/ENCSR706GDQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bbc2ed6b41194ad539155e604410239030230979..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF010SUI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_4.fit.json b/ENCSR706GDQ/cherimoya.fold_4.fit.json deleted file mode 100644 index f815d51919b5dbbb36639bc036c48117c21c608f..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF010SUI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706GDQ/cherimoya.fold_4.log b/ENCSR706GDQ/cherimoya.fold_4.log deleted file mode 100644 index e63b05e0d01b5960bd88c56a45b2472142148a06..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2090 28.393603086471558 4.1167380809783936 299.3617248535156 0.9969236254692078 458.64984130859375 0.4551010727882385 0.6148427 9.887297630310059 True -1 4180 23.128535509109497 0.40648698806762695 329.3377380371094 0.508445143699646 395.6893615722656 0.5700941681861877 0.6466238 3.80141019821167 True -2 6270 23.041346073150635 0.4000511169433594 283.27996826171875 0.6648563146591187 379.4276428222656 0.6013408899307251 0.6631465 0.9522435069084167 True -3 8360 23.11673855781555 0.39389753341674805 230.7944793701172 0.847274899482727 373.53900146484375 0.611081600189209 0.6749694 0.7383208870887756 True -4 10450 23.10098624229431 0.39476871490478516 300.20220947265625 0.8308438658714294 371.8627014160156 0.6146742701530457 0.67783415 0.6787133812904358 True -5 12540 23.011637687683105 0.3935678005218506 260.5803527832031 0.6251875162124634 370.34564208984375 0.6180256605148315 0.679326 0.6836442947387695 True -6 14630 23.011354684829712 0.3951592445373535 221.03802490234375 0.5895108580589294 369.3868103027344 0.6196577548980713 0.6871961 0.6251068711280823 True -7 16720 23.03333353996277 0.390056848526001 281.2720031738281 0.40939706563949585 368.7514953613281 0.6212679743766785 0.69071084 0.6091873049736023 True -8 18810 23.025477409362793 0.392958402633667 257.05059814453125 0.44787412881851196 367.8939514160156 0.6232209801673889 0.69731766 0.5886742472648621 True -9 20900 23.01833176612854 0.39173078536987305 311.67205810546875 0.6088924407958984 366.9555969238281 0.6251251697540283 0.7029043 0.5397492051124573 True -10 22990 23.06860327720642 0.7979781627655029 278.74566650390625 0.5477123260498047 366.0358581542969 0.6268452405929565 0.7112757 0.5292490720748901 True -11 25080 23.055763483047485 0.38870978355407715 289.97772216796875 0.6573224663734436 365.3536682128906 0.628275454044342 0.7131187 0.509731650352478 True -12 27170 23.07499623298645 2.0545315742492676 247.54092407226562 0.6388216018676758 364.5726623535156 0.6296316385269165 0.72092426 0.4904785752296448 True -13 29260 23.04444456100464 0.39562368392944336 256.61383056640625 0.40093162655830383 364.14910888671875 0.6307329535484314 0.7272486 0.4774104952812195 True -14 31350 23.19075870513916 0.40231990814208984 254.28945922851562 0.4359282851219177 363.7834777832031 0.6312050223350525 0.7313328 0.47448351979255676 True -15 33440 23.113611936569214 0.39321112632751465 298.36956787109375 0.4497441053390503 363.8344421386719 0.6311055421829224 0.73331124 0.47665920853614807 True -16 35530 22.733574628829956 0.39373230934143066 293.2840881347656 0.26536110043525696 363.83837890625 0.6310414671897888 0.73174477 0.49063900113105774 False -17 37620 22.72045636177063 2.3619582653045654 261.7100524902344 0.2754075527191162 364.3155517578125 0.6300022006034851 0.72898936 0.507522463798523 False -18 39710 22.68878436088562 0.3919975757598877 254.8924102783203 0.2474232167005539 364.5425109863281 0.6291208267211914 0.7234738 0.5282552242279053 False -19 41800 22.65393900871277 0.3929288387298584 257.65081787109375 0.23982028663158417 364.7198791503906 0.6285701990127563 0.71912503 0.5413581728935242 False diff --git a/ENCSR706GDQ/cherimoya.fold_4.performance.tsv b/ENCSR706GDQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 16ae0d3c029b80e2f815936cb3410ae0494709f4..0000000000000000000000000000000000000000 --- a/ENCSR706GDQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -363.8344421386719 0.29784879088401794 0.6311054825782776 0.24338299036026 0.7333112359046936 0.7000112533569336 0.47665920853614807 \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_0.evaluate.json b/ENCSR706IDL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d164437df6192056eca52762ce9b683ddb6e4ae9..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF489ZRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_0.fit.json b/ENCSR706IDL/cherimoya.fold_0.fit.json deleted file mode 100644 index bc7f9da270a8d43b44e33ae4d8ebd56db17949d5..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF489ZRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_0.log b/ENCSR706IDL/cherimoya.fold_0.log deleted file mode 100644 index 603774a4d4b6dc3fb56c462750aa82125b1b6122..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.29689383506775 3.4648642539978027 1925.72509765625 0.7879418134689331 2298.900146484375 0.2755519151687622 0.43304956 10.05367660522461 True -1 5488 30.661523580551147 0.5904078483581543 1924.24609375 1.0077106952667236 2138.940673828125 0.3520902097225189 0.50545114 2.0197510719299316 True -2 8232 30.6725332736969 0.5780205726623535 1736.341552734375 0.5646795630455017 2113.60302734375 0.3608962893486023 0.5375232 0.5182551741600037 True -3 10976 30.936484336853027 16.17505431175232 1863.56005859375 0.613176167011261 2097.247314453125 0.36760932207107544 0.54801786 0.39971986413002014 True -4 13720 30.612233877182007 0.5975637435913086 1620.7333984375 0.8034689426422119 2087.80859375 0.3722077012062073 0.55270493 0.4290083646774292 True -5 16464 30.674076795578003 0.5681033134460449 1628.1220703125 0.5338369011878967 2087.9677734375 0.3708961009979248 0.5611944 0.3847777545452118 True -6 19208 30.676051139831543 0.571082592010498 1771.263671875 0.4744154214859009 2084.607177734375 0.37246575951576233 0.5730988 0.4031340479850769 True -7 21952 30.6674747467041 0.5696492195129395 1719.517822265625 0.4556693434715271 2071.753662109375 0.3801896870136261 0.58018017 0.3982263207435608 True -8 24696 30.70761775970459 0.5754635334014893 1543.8707275390625 0.4027572274208069 2068.53466796875 0.38180112838745117 0.5797387 0.35900798439979553 False -9 27440 30.67057156562805 0.5715172290802002 1725.240234375 0.4119177460670471 2069.8037109375 0.38003993034362793 0.5887621 0.34754446148872375 True -10 30184 30.659282445907593 0.5752408504486084 1603.393310546875 0.5232078433036804 2062.29541015625 0.3840389847755432 0.5941961 0.336298406124115 True -11 32928 30.653422594070435 0.5803360939025879 1851.4219970703125 0.47661423683166504 2058.616455078125 0.3865348994731903 0.60595304 0.32611283659935 True -12 35672 30.67396354675293 0.5758993625640869 1962.529052734375 0.4695517420768738 2056.832275390625 0.38727083802223206 0.61477053 0.3188782036304474 True -13 38416 30.657273054122925 0.57515549659729 1738.563232421875 0.37947848439216614 2054.197998046875 0.3875582218170166 0.61958945 0.3097541332244873 True -14 41160 30.662514209747314 0.5711154937744141 1807.5716552734375 0.3972983956336975 2050.652099609375 0.38925671577453613 0.63268304 0.3023312985897064 True -15 43904 30.657976150512695 0.5765457153320312 1735.8614501953125 0.4297586679458618 2044.9822998046875 0.3925354778766632 0.6376712 0.2987518310546875 True -16 46648 30.71576428413391 0.5744614601135254 1606.744140625 0.4856577217578888 2047.57275390625 0.3909880816936493 0.64344287 0.2978719472885132 True -17 49392 30.8066565990448 0.5773305892944336 1731.045166015625 0.3342093229293823 2046.5565185546875 0.3909992575645447 0.6450466 0.30040499567985535 True -18 52136 30.645509004592896 0.5696718692779541 1721.534423828125 0.243139386177063 2047.4307861328125 0.39122408628463745 0.6416016 0.30775126814842224 False -19 54880 30.677709341049194 0.577451229095459 1722.769775390625 0.4591416120529175 2047.4208984375 0.3910970091819763 0.6410619 0.3116138279438019 False diff --git a/ENCSR706IDL/cherimoya.fold_0.performance.tsv b/ENCSR706IDL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index de769df4a40cbe77b8d96993def3eae0e078eb6e..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2046.5565185546875 0.28570836782455444 0.3909991681575775 0.2701648771762848 0.645046591758728 0.620084822177887 0.30040499567985535 \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_1.evaluate.json b/ENCSR706IDL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 05531d45f932135fb1f9a2b3d8b5c5343d3f8df0..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF489ZRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_1.fit.json b/ENCSR706IDL/cherimoya.fold_1.fit.json deleted file mode 100644 index 963c464712a6ea1459498ff41865b77ffb5c0132..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF489ZRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_1.log b/ENCSR706IDL/cherimoya.fold_1.log deleted file mode 100644 index 266c04d8794b540bf454194df4774a96827ccecf..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 34.4211950302124 3.960773468017578 1640.754150390625 0.5609411597251892 2447.40380859375 0.2800184190273285 0.48059776 9.647247314453125 True -1 5528 30.581122159957886 0.7126162052154541 1803.59326171875 1.270483136177063 2255.67041015625 0.3652971088886261 0.52473724 1.9414784908294678 True -2 8292 31.138856410980225 0.7161726951599121 1776.2960205078125 1.3326115608215332 2229.085693359375 0.37473100423812866 0.54615796 0.5581413507461548 True -3 11056 32.395179986953735 18.97961735725403 1724.145751953125 0.6657294631004333 2206.20751953125 0.3833920657634735 0.55740774 0.45576587319374084 True -4 13820 30.605098485946655 1.0579617023468018 1577.001953125 0.8164219856262207 2194.517822265625 0.3871769905090332 0.5806694 0.44698864221572876 True -5 16584 30.65731692314148 0.7249586582183838 1975.2760009765625 0.620193362236023 2192.089111328125 0.3884828984737396 0.5824278 0.42119303345680237 True -6 19348 30.59489154815674 0.7238550186157227 1717.41650390625 0.38165634870529175 2185.006591796875 0.3908146917819977 0.5941834 0.41079139709472656 True -7 22112 30.548370361328125 0.7103047370910645 1823.645263671875 0.5068058967590332 2183.09765625 0.39079588651657104 0.61036146 0.39066314697265625 True -8 24876 30.598486185073853 0.7208335399627686 1896.4974365234375 0.6393610239028931 2178.154296875 0.3922586441040039 0.62449956 0.3715113401412964 True -9 27640 30.590357303619385 0.7206954956054688 2002.561279296875 0.4352452754974365 2166.729248046875 0.398586243391037 0.6323397 0.3577721118927002 True -10 30404 30.629995584487915 1.3627574443817139 1775.25341796875 0.5463945865631104 2164.375 0.3988364040851593 0.64419293 0.33767926692962646 True -11 33168 30.638684034347534 0.7235653400421143 1794.4107666015625 0.42356178164482117 2158.103271484375 0.4015468955039978 0.651117 0.33833810687065125 True -12 35932 30.59138822555542 0.7132754325866699 1828.506103515625 0.44095784425735474 2150.81982421875 0.40495407581329346 0.66215605 0.32936224341392517 True -13 38696 30.658526182174683 0.7084133625030518 1651.95556640625 0.4155495762825012 2143.67333984375 0.4084427058696747 0.6720053 0.3086835443973541 True -14 41460 30.6528377532959 0.7171013355255127 1704.885986328125 0.3996650278568268 2148.318603515625 0.40508440136909485 0.68354714 0.3039717972278595 True -15 44224 30.602511882781982 0.7089581489562988 1721.5367431640625 0.32014673948287964 2142.0087890625 0.40787777304649353 0.6867209 0.3036111891269684 True -16 46988 30.62034797668457 0.7087671756744385 1890.232421875 0.27183640003204346 2141.67236328125 0.40874361991882324 0.6922683 0.30062901973724365 True -17 49752 30.57746648788452 0.7162139415740967 1747.9483642578125 0.25977662205696106 2138.210205078125 0.4111422896385193 0.69159895 0.30682727694511414 False -18 52516 30.6211359500885 0.7065258026123047 1483.2314453125 0.26416394114494324 2143.670166015625 0.4070724844932556 0.6917693 0.31469061970710754 False -19 55280 30.58215641975403 0.7194318771362305 1636.201171875 0.2501929998397827 2139.9736328125 0.4095771610736847 0.68969566 0.31890633702278137 False diff --git a/ENCSR706IDL/cherimoya.fold_1.performance.tsv b/ENCSR706IDL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6ec2add32fc06555b837d864734bfdd333f3ce94..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2141.67236328125 0.27450835704803467 0.40874364972114563 0.283967524766922 0.6922683119773865 0.6672878265380859 0.30062901973724365 \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_2.evaluate.json b/ENCSR706IDL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index fba57f92b8f76640f3ec524da623231293377b92..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF489ZRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_2.fit.json b/ENCSR706IDL/cherimoya.fold_2.fit.json deleted file mode 100644 index 4cdb78819ce2dcc2e0058b8c67d917bbf396cce3..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF489ZRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_2.log b/ENCSR706IDL/cherimoya.fold_2.log deleted file mode 100644 index 77fafd4caf8d200ec66c0e43d01d8927b3edbd6f..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 36.25368356704712 4.259789228439331 1977.30908203125 0.5255236625671387 2307.106689453125 0.27719882130622864 0.44354272 6.873144149780273 True -1 5788 32.38036131858826 0.5885577201843262 1628.3919677734375 0.7594404816627502 2144.713623046875 0.3558523952960968 0.5248579 1.237654209136963 True -2 8682 32.404544830322266 0.5769484043121338 1669.0723876953125 0.385933518409729 2116.013427734375 0.3652864098548889 0.54754436 0.5283219218254089 True -3 11576 32.36507797241211 0.5786252021789551 1724.352294921875 0.7289124131202698 2098.702880859375 0.37299925088882446 0.5655037 0.4533282220363617 True -4 14470 32.33583068847656 1.6146860122680664 1847.92236328125 0.597119927406311 2095.5947265625 0.3737708330154419 0.56158525 0.4252759516239166 False -5 17364 32.39009475708008 28.177902460098267 2105.74658203125 0.29568690061569214 2087.812744140625 0.3768070936203003 0.5666713 0.41954323649406433 True -6 20258 32.443010568618774 15.59125304222107 1798.6234130859375 0.6347923874855042 2085.895263671875 0.3775350749492645 0.5688729 0.41630539298057556 True -7 23152 32.32022547721863 0.5692915916442871 1506.0565185546875 0.7717587351799011 2078.760009765625 0.3811158537864685 0.58469915 0.43160611391067505 True -8 26046 32.34656548500061 0.5742340087890625 1724.34716796875 0.604709267616272 2074.1572265625 0.383057564496994 0.59241027 0.41115453839302063 True -9 28940 32.3139431476593 0.6791646480560303 2005.24755859375 0.4448965787887573 2072.13818359375 0.38436657190322876 0.59481615 0.39639049768447876 True -10 31834 32.33512592315674 0.5699782371520996 1788.280517578125 0.35351359844207764 2065.30517578125 0.3873617351055145 0.600921 0.36895087361335754 True -11 34728 32.347163438797 12.743793487548828 1658.0439453125 0.6056370735168457 2060.1376953125 0.389782190322876 0.61738974 0.3465334177017212 True -12 37622 32.363563776016235 0.5765366554260254 1775.4451904296875 0.36600059270858765 2057.152099609375 0.39129865169525146 0.6229123 0.3410777449607849 True -13 40516 32.42790079116821 0.5755109786987305 1757.669677734375 0.4595724046230316 2049.76171875 0.3946070373058319 0.63282984 0.32694011926651 True -14 43410 32.4446964263916 0.5752978324890137 1694.1884765625 0.2552058696746826 2048.23876953125 0.39485687017440796 0.6393391 0.322327196598053 True -15 46304 32.40162539482117 0.5773189067840576 1777.4375 0.29159778356552124 2044.8466796875 0.3969702124595642 0.64566725 0.3139244318008423 True -16 49198 32.3541362285614 0.5778789520263672 1643.687744140625 0.3546023964881897 2044.5743408203125 0.3973762094974518 0.651766 0.31312739849090576 True -17 52092 32.35348129272461 0.5696611404418945 1652.8359375 0.30454882979393005 2043.4190673828125 0.3976304829120636 0.65053666 0.3157833516597748 False -18 54986 32.3779981136322 0.5677988529205322 1790.0948486328125 0.2561483085155487 2051.138916015625 0.3923923075199127 0.6481327 0.3235304057598114 False -19 57880 32.38471436500549 0.5681700706481934 1631.914306640625 0.2795324921607971 2047.014404296875 0.39559227228164673 0.6472421 0.3244069814682007 False diff --git a/ENCSR706IDL/cherimoya.fold_2.performance.tsv b/ENCSR706IDL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7760bc386b37f35a115ecce0abcf94712120af06..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2044.5743408203125 0.28375017642974854 0.3973762094974518 0.2719070613384247 0.6517660021781921 0.6261448264122009 0.31312739849090576 \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_3.evaluate.json b/ENCSR706IDL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3faba6a56442aee130557fc5204df669f10dcff6..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF489ZRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_3.fit.json b/ENCSR706IDL/cherimoya.fold_3.fit.json deleted file mode 100644 index 16efb5dcb57fc678f30eb9792752b3405e27a21f..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF489ZRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_3.log b/ENCSR706IDL/cherimoya.fold_3.log deleted file mode 100644 index 171f0dff2bde069699d195db4070e64ea03dd034..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2797 34.92441534996033 3.7674856185913086 1826.216064453125 0.7580620050430298 2422.99755859375 0.2847520112991333 0.45060313 8.290366172790527 True -1 5594 31.01832127571106 0.6279373168945312 1713.4639892578125 0.4953523576259613 2265.44091796875 0.35638102889060974 0.51860285 1.3177330493927002 True -2 8391 31.01086926460266 0.6079306602478027 1952.964111328125 0.500668466091156 2237.560302734375 0.3675757646560669 0.5308305 0.5379114151000977 True -3 11188 31.02910828590393 2.2880699634552 1886.697021484375 1.1596825122833252 2223.193115234375 0.3730555772781372 0.5461006 0.42952054738998413 True -4 13985 31.12639832496643 0.6494390964508057 1596.051513671875 1.073720932006836 2222.459228515625 0.3716244697570801 0.5559603 0.43207475543022156 True -5 16782 31.034871101379395 0.6286780834197998 1875.387451171875 0.44415760040283203 2213.71533203125 0.37716910243034363 0.55884796 0.4684225618839264 True -6 19579 31.08638072013855 1.5191733837127686 1935.92138671875 0.4767293930053711 2215.250244140625 0.3754865825176239 0.55746657 0.39694395661354065 False -7 22376 30.94154691696167 0.6358497142791748 1788.5931396484375 0.4029476046562195 2206.18603515625 0.38070446252822876 0.5737444 0.39465659856796265 True -8 25173 31.26888680458069 0.6257543563842773 1465.128173828125 0.5784701108932495 2204.1494140625 0.38123685121536255 0.5773823 0.407023161649704 True -9 27970 33.194554805755615 0.6427857875823975 1780.234130859375 0.4365149140357971 2198.3818359375 0.3837074041366577 0.58871573 0.3792365491390228 True -10 30767 31.235053062438965 27.400065898895264 1833.9996337890625 0.3668403923511505 2196.172607421875 0.3846130073070526 0.5948482 0.3708135187625885 True -11 33564 30.986438751220703 0.6229720115661621 1726.648681640625 0.6801151037216187 2189.313720703125 0.38759538531303406 0.60376817 0.3707042932510376 True -12 36361 30.977787733078003 0.6252615451812744 1720.3653564453125 0.37681183218955994 2186.428466796875 0.38872987031936646 0.612944 0.36637082695961 True -13 39158 30.942846298217773 0.8016140460968018 1553.758056640625 0.31794634461402893 2182.896484375 0.39004090428352356 0.6211196 0.3576512336730957 True -14 41955 30.939425230026245 0.6293332576751709 1852.426025390625 0.3158480226993561 2172.327880859375 0.3960467576980591 0.6327637 0.34014859795570374 True -15 44752 30.94408369064331 0.6096696853637695 1482.478515625 0.3793413043022156 2174.823974609375 0.3937475383281708 0.63890755 0.3324551582336426 True -16 47549 30.973721504211426 0.6078181266784668 1769.792724609375 0.32601165771484375 2175.874755859375 0.3926512598991394 0.6455357 0.32438549399375916 True -17 50346 30.91133975982666 1.1888015270233154 1687.965576171875 0.34386470913887024 2173.456787109375 0.39455336332321167 0.64875406 0.324897825717926 True -18 53143 30.967942476272583 2.248244524002075 1892.480712890625 0.4178205132484436 2171.0390625 0.3957309424877167 0.645667 0.33209675550460815 False -19 55940 30.96862244606018 11.051059007644653 1743.455810546875 0.33361101150512695 2170.484619140625 0.39655858278274536 0.6434838 0.33810967206954956 False diff --git a/ENCSR706IDL/cherimoya.fold_3.performance.tsv b/ENCSR706IDL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 518f0061d73650e5af19fbc585ffb854f89902f0..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2173.456787109375 0.27792254090309143 0.39455336332321167 0.28098270297050476 0.6487540602684021 0.6275855898857117 0.324897825717926 \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_4.evaluate.json b/ENCSR706IDL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 31e99906a674dd614b94a7f137acc18c8f4157f3..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF489ZRA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_4.fit.json b/ENCSR706IDL/cherimoya.fold_4.fit.json deleted file mode 100644 index ab94f4ca7e241aafc22e894d58c579c065df010d..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF489ZRA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR706IDL/cherimoya.fold_4.log b/ENCSR706IDL/cherimoya.fold_4.log deleted file mode 100644 index b54fcd70e33ec73553a37bee7c8c0d2ae32ca2d9..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2903 36.37806415557861 1.8974063396453857 1617.92724609375 0.5315776467323303 2320.10791015625 0.28501924872398376 0.44819954 7.2507123947143555 True -1 5806 32.45319104194641 0.554023265838623 1735.464111328125 0.7124530673027039 2173.7890625 0.3539656400680542 0.50170255 1.243964672088623 True -2 8709 32.41981053352356 0.5503382682800293 1902.1649169921875 0.6938761472702026 2147.634033203125 0.36445796489715576 0.5291987 0.4676838517189026 True -3 11612 32.42514085769653 1.1115872859954834 1970.5850830078125 0.49572181701660156 2140.291259765625 0.365273118019104 0.5504294 0.3682268261909485 True -4 14515 32.509438276290894 0.5469579696655273 2134.155029296875 0.7118769884109497 2126.3291015625 0.3723685145378113 0.55476254 0.3895350694656372 True -5 17418 32.47179460525513 0.6576790809631348 1664.088134765625 0.27580487728118896 2123.682373046875 0.3736814558506012 0.56120807 0.36337217688560486 True -6 20321 32.46867537498474 0.540480375289917 1788.648193359375 0.4890148639678955 2118.263916015625 0.3756844699382782 0.56773853 0.3552229106426239 True -7 23224 32.40902328491211 0.5370121002197266 1520.9901123046875 0.41941046714782715 2111.3203125 0.3797239363193512 0.57706136 0.33353814482688904 True -8 26127 32.42068839073181 1.187337875366211 1607.264404296875 0.3939948081970215 2108.3359375 0.3816598653793335 0.58180326 0.3243650496006012 True -9 29030 32.50558400154114 0.5491313934326172 1752.4453125 0.38974884152412415 2105.366455078125 0.3827282786369324 0.59141374 0.3296894431114197 True -10 31933 32.509841203689575 0.5536017417907715 1707.57568359375 0.5253324508666992 2104.236572265625 0.3831334114074707 0.5943199 0.32414889335632324 True -11 34836 32.45690584182739 0.5521278381347656 1638.456787109375 0.38591623306274414 2101.511474609375 0.38410693407058716 0.60250026 0.31167393922805786 True -12 37739 32.45436978340149 0.5477838516235352 1755.477783203125 0.48429638147354126 2099.401123046875 0.38547977805137634 0.6092135 0.31497278809547424 True -13 40642 32.49703669548035 26.576894521713257 1743.57177734375 0.5857023000717163 2094.564697265625 0.3879638612270355 0.6178667 0.3067223131656647 True -14 43545 32.524235248565674 0.5498390197753906 1609.5791015625 0.2649143636226654 2088.362548828125 0.39153262972831726 0.62929356 0.302828311920166 True -15 46448 32.64175295829773 1.760094165802002 1605.976806640625 0.24556830525398254 2088.593505859375 0.3908253610134125 0.63615257 0.30157700181007385 True -16 49351 32.54237127304077 0.5594065189361572 1769.960693359375 0.1911047101020813 2089.462158203125 0.39036524295806885 0.6370847 0.30343782901763916 True -17 52254 32.517192125320435 0.5483365058898926 1725.42138671875 0.18530020117759705 2088.356689453125 0.39037978649139404 0.6374026 0.3099856972694397 True -18 55157 32.501752853393555 0.5532779693603516 1441.40380859375 0.327727347612381 2086.81640625 0.3922925293445587 0.63694 0.31511190533638 False -19 58060 32.48111367225647 0.5485744476318359 1558.087646484375 0.5204178690910339 2091.427001953125 0.389236718416214 0.63527185 0.31865477561950684 False diff --git a/ENCSR706IDL/cherimoya.fold_4.performance.tsv b/ENCSR706IDL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3a93e1dd95897ba790d1ce015a408dd02cb6cd7e..0000000000000000000000000000000000000000 --- a/ENCSR706IDL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2088.356689453125 0.2826021909713745 0.39037981629371643 0.27491167187690735 0.6374025940895081 0.6146900057792664 0.3099856972694397 \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_0.evaluate.json b/ENCSR709PZI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2959f8c74f25d518fb213f250a57438f956982fa..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF225EQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_0.fit.json b/ENCSR709PZI/cherimoya.fold_0.fit.json deleted file mode 100644 index f0936283b0fbcd817f619dfc9826816af3d1f87b..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF225EQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_0.log b/ENCSR709PZI/cherimoya.fold_0.log deleted file mode 100644 index 7cd6192ff9ea7aa8d34cc0d1a02cad95623637a4..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 35.91871380805969 3.6382553577423096 633.202392578125 0.35393452644348145 760.6245727539062 0.21453414857387543 0.79474896 4.034035682678223 True -1 5484 30.765419006347656 34.048887968063354 599.6158447265625 0.21444788575172424 712.4010009765625 0.2606984078884125 0.84606034 0.9153339266777039 True -2 8226 30.67555046081543 26.15624165534973 564.7622680664062 0.2983645796775818 702.440673828125 0.2667427957057953 0.8574668 0.38438737392425537 True -3 10968 30.818331718444824 0.5756092071533203 729.3819580078125 0.35893216729164124 697.4002075195312 0.2711673974990845 0.8654656 0.27992361783981323 True -4 13710 30.439167022705078 0.5768704414367676 653.5135498046875 0.31153854727745056 695.3955688476562 0.2731519639492035 0.86938834 0.2882251739501953 True -5 16452 30.420154809951782 0.7020308971405029 642.7713012695312 0.2699841260910034 693.38037109375 0.2748020589351654 0.87376606 0.23972328007221222 True -6 19194 30.488377809524536 0.5788059234619141 495.26300048828125 0.2854016125202179 690.9286499023438 0.27778899669647217 0.87880594 0.21062390506267548 True -7 21936 30.13639259338379 0.9092855453491211 641.1088256835938 0.19639982283115387 688.3778076171875 0.2804305851459503 0.8832647 0.18916165828704834 True -8 24678 29.8679621219635 11.31725549697876 592.3109130859375 0.279928982257843 688.1073608398438 0.2806025743484497 0.8863722 0.19853079319000244 True -9 27420 29.956941843032837 0.5682613849639893 660.4048461914062 0.13967107236385345 685.9888916015625 0.2826716899871826 0.8907328 0.1894696056842804 True -10 30162 29.83769392967224 0.5702259540557861 575.2086791992188 0.18208125233650208 684.3265991210938 0.28467509150505066 0.89206934 0.18291838467121124 True -11 32904 29.873626470565796 13.547055721282959 608.9158935546875 0.15284961462020874 683.544189453125 0.2846170663833618 0.89517903 0.1751498281955719 True -12 35646 30.66711115837097 0.8338301181793213 611.7586669921875 0.19350379705429077 681.5413818359375 0.2875071167945862 0.89820087 0.17159520089626312 True -13 38388 29.924317836761475 0.5763115882873535 530.1356811523438 0.16463318467140198 680.7294311523438 0.2880411446094513 0.9026131 0.15949201583862305 True -14 41130 29.88982844352722 0.5800721645355225 619.9147338867188 0.16738981008529663 679.3934326171875 0.2890094518661499 0.9031433 0.15219266712665558 True -15 43872 29.853172063827515 0.5799527168273926 675.409423828125 0.23981651663780212 678.730712890625 0.2895963788032532 0.90642214 0.14805923402309418 True -16 46614 29.855053901672363 21.675492763519287 602.558349609375 0.1746312975883484 677.70166015625 0.2908378541469574 0.90777975 0.14303182065486908 True -17 49356 29.899391651153564 39.29956316947937 610.548095703125 0.10445813834667206 677.4558715820312 0.29101797938346863 0.9077692 0.14130261540412903 False -18 52098 29.956523180007935 1.4506232738494873 621.280517578125 0.30507397651672363 678.004150390625 0.29043760895729065 0.9093954 0.14025932550430298 True -19 54840 29.91309666633606 29.865154266357422 536.960693359375 0.11509174108505249 677.9835205078125 0.2904907166957855 0.9075931 0.14166297018527985 False diff --git a/ENCSR709PZI/cherimoya.fold_0.performance.tsv b/ENCSR709PZI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ff3ad30e1884113f807cadd48745883c399fae81..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -678.004150390625 0.4576531648635864 0.29043760895729065 0.11356934905052185 0.9093953967094421 0.8871607184410095 0.14025932550430298 \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_1.evaluate.json b/ENCSR709PZI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 618755041342b06c697672d3a93892cf8ede9f15..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF225EQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_1.fit.json b/ENCSR709PZI/cherimoya.fold_1.fit.json deleted file mode 100644 index 96f2d21d593018a4e257fac92b5150c01c8763aa..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF225EQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_1.log b/ENCSR709PZI/cherimoya.fold_1.log deleted file mode 100644 index db7a19facc32cb062ef23260315340e4de517b5f..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2706 34.26205396652222 4.38505482673645 720.3577270507812 0.4032447040081024 865.1705322265625 0.21714374423027039 0.8008773 4.615553855895996 True -1 5412 30.30891180038452 0.7975833415985107 597.4344482421875 0.28541865944862366 811.6017456054688 0.2657700777053833 0.8439111 0.8211187720298767 True -2 8118 30.345252752304077 0.7326061725616455 550.94482421875 0.44250959157943726 795.8199462890625 0.278227835893631 0.8586021 0.3714936077594757 True -3 10824 30.281902551651 1.4915528297424316 629.2596435546875 0.3515956401824951 784.5369262695312 0.28553980588912964 0.86779153 0.3489944338798523 True -4 13530 30.27391767501831 14.296355485916138 612.1993408203125 0.2543303370475769 781.4223022460938 0.28783056139945984 0.87205255 0.2806050479412079 True -5 16236 30.30153799057007 0.7381448745727539 656.5528564453125 0.2132669985294342 778.2903442382812 0.29019564390182495 0.8777703 0.2599196434020996 True -6 18942 30.391232013702393 0.7383418083190918 531.79443359375 0.34701651334762573 774.7692260742188 0.29358211159706116 0.8828518 0.2530045509338379 True -7 21648 30.321189165115356 0.7279503345489502 640.6951293945312 0.33107054233551025 771.0784301757812 0.29709944128990173 0.88737655 0.24510404467582703 True -8 24354 30.32914423942566 0.7255020141601562 661.12744140625 0.19483323395252228 768.9970092773438 0.29855814576148987 0.89085925 0.24056358635425568 True -9 27060 30.313547611236572 0.7328770160675049 527.1557006835938 0.25376179814338684 766.460205078125 0.3008531630039215 0.89397514 0.22155140340328217 True -10 29766 30.308125019073486 0.7322676181793213 646.6747436523438 0.22944973409175873 763.434326171875 0.3031310439109802 0.89743936 0.19994106888771057 True -11 32472 30.263429164886475 0.7174649238586426 651.9627685546875 0.1986914873123169 762.3525390625 0.30348390340805054 0.9002107 0.18927663564682007 True -12 35178 30.27837347984314 0.7257006168365479 597.734375 0.22443389892578125 759.8047485351562 0.30592817068099976 0.9044882 0.183762326836586 True -13 37884 30.30927300453186 0.7329714298248291 556.8563232421875 0.17089349031448364 758.3279418945312 0.30710646510124207 0.907208 0.17331871390342712 True -14 40590 30.274983406066895 0.7363998889923096 556.3219604492188 0.18880636990070343 757.4529418945312 0.307223379611969 0.90948945 0.16673652827739716 True -15 43296 30.287514448165894 0.7249813079833984 522.9119262695312 0.14301878213882446 756.038330078125 0.3086611032485962 0.91375697 0.1597249060869217 True -16 46002 30.264750957489014 0.7295842170715332 645.4886474609375 0.17853495478630066 755.921875 0.30801817774772644 0.91562515 0.15530945360660553 True -17 48708 30.86067819595337 19.041885375976562 596.4522705078125 0.1322033852338791 755.4050903320312 0.30874818563461304 0.91698235 0.1521809846162796 True -18 51414 30.30291748046875 15.498883485794067 608.8499145507812 0.1376785933971405 754.5198974609375 0.3101727366447449 0.9171302 0.1508346050977707 True -19 54120 30.30464744567871 14.257002592086792 679.0554809570312 0.18701595067977905 755.5557250976562 0.3082003593444824 0.91684794 0.15101610124111176 False diff --git a/ENCSR709PZI/cherimoya.fold_1.performance.tsv b/ENCSR709PZI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8a1fcb0c7411c1002c55bb70348ab3f31bb8aa7d..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -754.5198974609375 0.4408639967441559 0.3101726770401001 0.12626560032367706 0.917130172252655 0.908994197845459 0.1508346050977707 \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_2.evaluate.json b/ENCSR709PZI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 35c1863fd8a740dcc1e79ff4ff75e9fc8492d78a..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF225EQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_2.fit.json b/ENCSR709PZI/cherimoya.fold_2.fit.json deleted file mode 100644 index ce792e1b304997e221b32f6930964aa4e6acbfae..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF225EQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_2.log b/ENCSR709PZI/cherimoya.fold_2.log deleted file mode 100644 index b28069e82aa51540fab7dab893ad21577b7e1153..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 35.7946298122406 3.8909859657287598 656.3715209960938 0.44280412793159485 806.094482421875 0.21850167214870453 0.7925513 3.328585624694824 True -1 5788 32.092013120651245 0.5869801044464111 606.1912841796875 0.20237097144126892 756.2736206054688 0.2646101415157318 0.843805 0.7130674123764038 True -2 8682 32.129390001297 0.5764906406402588 637.1650390625 0.22637814283370972 747.0203857421875 0.2704288959503174 0.8432467 0.40144526958465576 False -3 11576 32.184908866882324 0.5693297386169434 628.6495361328125 0.2941504716873169 739.7168579101562 0.2752978205680847 0.8547257 0.372714102268219 True -4 14470 32.27785110473633 0.5860347747802734 500.9776611328125 0.16298159956932068 733.6893920898438 0.2811751663684845 0.86719394 0.24142897129058838 True -5 17364 32.19306659698486 0.5658149719238281 501.2647705078125 0.15872491896152496 732.1762084960938 0.28300386667251587 0.8685037 0.2613638639450073 True -6 20258 32.076802253723145 0.565859317779541 674.9161376953125 0.2865273058414459 731.4063110351562 0.2829807996749878 0.872295 0.23266761004924774 True -7 23152 32.563199520111084 0.5653784275054932 580.4241943359375 0.17855751514434814 728.6289672851562 0.2849828004837036 0.8792934 0.22165507078170776 True -8 26046 32.07371926307678 1.2131884098052979 551.5969848632812 0.1519782841205597 724.9683837890625 0.2892879545688629 0.8814301 0.20465417206287384 True -9 28940 32.07185196876526 0.5705957412719727 731.4080200195312 0.25009122490882874 723.2830810546875 0.2909446358680725 0.8884785 0.18822641670703888 True -10 31834 32.14753246307373 0.574213981628418 648.6691284179688 0.2356327623128891 721.121337890625 0.2928081452846527 0.8897349 0.18941083550453186 True -11 34728 32.09524655342102 0.567209005355835 616.93212890625 0.15914666652679443 720.1567993164062 0.2930280864238739 0.89316624 0.1747882068157196 True -12 37622 32.06109666824341 0.5607578754425049 583.678955078125 0.09849105775356293 718.7462768554688 0.29471489787101746 0.89533186 0.17017817497253418 True -13 40516 32.07775115966797 0.5602052211761475 610.3914794921875 0.1739630401134491 716.527587890625 0.29697710275650024 0.9003781 0.16388759016990662 True -14 43410 32.0643105506897 0.5621521472930908 548.1842041015625 0.150339275598526 716.2882080078125 0.2969610393047333 0.9032168 0.15724503993988037 True -15 46304 32.17063617706299 0.5631833076477051 649.782470703125 0.2026921510696411 715.7356567382812 0.29678449034690857 0.90376157 0.15131880342960358 True -16 49198 32.10043501853943 0.5699405670166016 548.5503540039062 0.19002090394496918 714.4255981445312 0.29899004101753235 0.9056991 0.1468561440706253 True -17 52092 32.15675902366638 21.4530611038208 620.1876220703125 0.17190364003181458 714.9105834960938 0.29769623279571533 0.9056464 0.14547790586948395 False -18 54986 32.226778507232666 0.5739104747772217 568.3416748046875 0.13514173030853271 714.9105224609375 0.29808419942855835 0.9073091 0.14518055319786072 True -19 57880 32.16692876815796 0.5642437934875488 495.8481140136719 0.12297002971172333 714.9981079101562 0.297970712184906 0.90774775 0.1455288678407669 True diff --git a/ENCSR709PZI/cherimoya.fold_2.performance.tsv b/ENCSR709PZI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b403341fe60e0e4273ec0c6a94fd7ab9752bd88f..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -714.9981079101562 0.44968608021736145 0.297970712184906 0.12052005529403687 0.907747745513916 0.893144428730011 0.1455288678407669 \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_3.evaluate.json b/ENCSR709PZI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3896188ec9398bf99fa20e4fd8dc528321d810bd..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF225EQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_3.fit.json b/ENCSR709PZI/cherimoya.fold_3.fit.json deleted file mode 100644 index b45f4baaa449889d235293af2915c46603449508..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF225EQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_3.log b/ENCSR709PZI/cherimoya.fold_3.log deleted file mode 100644 index 11775d28c39a9f5126d6fd1e29e6ae49c6c65074..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 35.10867166519165 4.434805870056152 571.237060546875 0.36429259181022644 747.4305419921875 0.22009585797786713 0.7792309 4.180325508117676 True -1 5526 30.86400294303894 0.6009585857391357 682.5205078125 0.22544479370117188 701.7706298828125 0.2635042071342468 0.827298 0.8714153170585632 True -2 8289 30.929518699645996 1.4331417083740234 629.9185791015625 0.20903509855270386 691.0828857421875 0.2719968855381012 0.84573823 0.3366234302520752 True -3 11052 30.937039613723755 2.0304481983184814 617.669189453125 0.23952260613441467 683.9075317382812 0.27771326899528503 0.85820895 0.26375070214271545 True -4 13815 31.023106575012207 7.979139804840088 653.182861328125 0.2293878197669983 682.635009765625 0.2782385051250458 0.8638151 0.28670376539230347 True -5 16578 30.872084856033325 4.649656057357788 592.890625 0.27547699213027954 680.4619750976562 0.2806009352207184 0.8711034 0.2279217690229416 True -6 19341 30.921156406402588 0.5664258003234863 660.6324462890625 0.2845457196235657 677.1123657226562 0.2839357852935791 0.87605774 0.22858834266662598 True -7 22104 31.01418948173523 25.838900089263916 681.9224853515625 0.21560120582580566 676.2760009765625 0.2845475375652313 0.8779939 0.22383178770542145 True -8 24867 31.148043394088745 2.206615447998047 655.8922119140625 0.18321919441223145 674.0220336914062 0.2870852053165436 0.88028175 0.21352209150791168 True -9 27630 30.926368951797485 0.5653274059295654 528.81787109375 0.17311188578605652 672.8643798828125 0.2875729501247406 0.8834618 0.2089095115661621 True -10 30393 30.926913261413574 2.2554311752319336 638.4259643554688 0.18012450635433197 671.851318359375 0.2885165214538574 0.8877347 0.1914222240447998 True -11 33156 30.919424057006836 0.5876574516296387 592.0355834960938 0.14487150311470032 670.4484252929688 0.28980880975723267 0.89200664 0.18042026460170746 True -12 35919 30.899128675460815 0.5493779182434082 618.8016357421875 0.28261837363243103 668.5344848632812 0.2914024889469147 0.8951431 0.17845246195793152 True -13 38682 30.916911125183105 0.5538172721862793 608.203369140625 0.18765133619308472 666.7168579101562 0.2934291362762451 0.8988426 0.16983667016029358 True -14 41445 30.860783338546753 0.5636608600616455 530.6240234375 0.15720276534557343 666.2866821289062 0.29305168986320496 0.90083903 0.16314062476158142 True -15 44208 30.837976455688477 0.5660960674285889 547.705322265625 0.13189904391765594 664.8211059570312 0.29472729563713074 0.9033494 0.15860877931118011 True -16 46971 30.882391214370728 0.5427474975585938 502.7813720703125 0.17175494134426117 664.1807861328125 0.29522705078125 0.9058351 0.15226036310195923 True -17 49734 30.927287578582764 0.5480556488037109 563.9885864257812 0.10567820072174072 664.1507568359375 0.29503124952316284 0.9074767 0.15124335885047913 True -18 52497 30.907820224761963 0.549229621887207 671.7269897460938 0.2242555171251297 664.1312255859375 0.29510894417762756 0.90458053 0.15121012926101685 False -19 55260 30.87284517288208 1.3613781929016113 517.1497802734375 0.14694413542747498 664.8668823242188 0.29395490884780884 0.90571004 0.15118034183979034 False diff --git a/ENCSR709PZI/cherimoya.fold_3.performance.tsv b/ENCSR709PZI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 82442042eee6d87b4aecfaa7b6fce2d8b8c849b0..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -664.1507568359375 0.4563388228416443 0.29503127932548523 0.11254141479730606 0.9074767231941223 0.8816421627998352 0.15124335885047913 \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_4.evaluate.json b/ENCSR709PZI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7ed2ed17eaf9df93f61447d225bbbc381e9d95db..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF225EQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_4.fit.json b/ENCSR709PZI/cherimoya.fold_4.fit.json deleted file mode 100644 index 9d8e910666f63d7094e78490547eb325867bd409..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF225EQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709PZI/cherimoya.fold_4.log b/ENCSR709PZI/cherimoya.fold_4.log deleted file mode 100644 index fa628b460c2e9395700158ededeb78bea837fd91..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2815 35.46478295326233 3.5418429374694824 735.7100830078125 0.35592037439346313 703.7579956054688 0.21109293401241302 0.78550583 4.0859456062316895 True -1 5630 31.41438341140747 0.646925687789917 607.85693359375 0.22363446652889252 662.879150390625 0.25241953134536743 0.8379825 0.7629215121269226 True -2 8445 31.421810388565063 0.6415772438049316 483.0722351074219 0.18197715282440186 655.009765625 0.2590561807155609 0.8483328 0.2662793695926666 True -3 11260 31.39068341255188 19.643374919891357 623.4033203125 0.2695087492465973 651.0438232421875 0.26286211609840393 0.8578869 0.2877230942249298 True -4 14075 31.62982988357544 0.6460304260253906 666.009765625 0.1629938781261444 648.0471801757812 0.2661225497722626 0.85898876 0.2292802780866623 True -5 16890 31.389086723327637 0.634329080581665 671.8378295898438 0.21475958824157715 646.2318115234375 0.2675796449184418 0.8659735 0.20835404098033905 True -6 19705 31.451560735702515 0.6458194255828857 653.5374755859375 0.22362573444843292 644.6032104492188 0.2680272161960602 0.87301743 0.20155549049377441 True -7 22520 31.45641851425171 18.81758141517639 541.133544921875 0.23516440391540527 643.1422119140625 0.2700466811656952 0.87491643 0.19505393505096436 True -8 25335 31.59910798072815 0.6574475765228271 569.662353515625 0.291769802570343 640.8978271484375 0.2725275754928589 0.87813556 0.18477189540863037 True -9 28150 31.39372730255127 0.6310358047485352 606.0992431640625 0.2037520706653595 639.990234375 0.2731568217277527 0.8849457 0.18518134951591492 True -10 30965 31.436108112335205 0.6466398239135742 621.6549072265625 0.1801302134990692 638.2565307617188 0.27523717284202576 0.8863037 0.17428669333457947 True -11 33780 31.42656135559082 2.1882853507995605 568.7221069335938 0.19865673780441284 637.9411010742188 0.2754517197608948 0.8893586 0.16420622169971466 True -12 36595 31.45050024986267 0.6494553089141846 517.4358520507812 0.1391907036304474 635.9608764648438 0.2777615785598755 0.892127 0.1595100462436676 True -13 39410 31.438555002212524 0.6463289260864258 592.7818603515625 0.2219390720129013 635.437255859375 0.2778213322162628 0.895922 0.15418581664562225 True -14 42225 31.439599990844727 0.6804752349853516 553.5824584960938 0.1753944605588913 634.1522216796875 0.27988314628601074 0.9007086 0.14369143545627594 True -15 45040 31.489853143692017 0.6434662342071533 554.53271484375 0.15774068236351013 633.9829711914062 0.279261976480484 0.9017326 0.13716481626033783 True -16 47855 31.48085904121399 0.6434121131896973 645.1939697265625 0.19623348116874695 634.2920532226562 0.2785394489765167 0.90542036 0.13377709686756134 True -17 50670 31.447672605514526 0.640958309173584 640.9354858398438 0.15294760465621948 633.2645263671875 0.28042328357696533 0.90719336 0.13048005104064941 True -18 53485 31.41551113128662 0.6366534233093262 585.1103515625 0.1548624187707901 633.6897583007812 0.28001895546913147 0.9062144 0.12978117167949677 False -19 56300 31.445590496063232 0.6481115818023682 565.1837158203125 0.12179353088140488 633.96826171875 0.27953827381134033 0.90787375 0.12983566522598267 True diff --git a/ENCSR709PZI/cherimoya.fold_4.performance.tsv b/ENCSR709PZI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a78bab1d26d85bebc5f04a7f2b155033daab68c5..0000000000000000000000000000000000000000 --- a/ENCSR709PZI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -633.96826171875 0.46785542368888855 0.2795383036136627 0.10530739277601242 0.9078737497329712 0.8807352781295776 0.12983566522598267 \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_0.evaluate.json b/ENCSR709QRD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 847c0184485c96a4a4682021ae63a4d67603f06b..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203PBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_0.fit.json b/ENCSR709QRD/cherimoya.fold_0.fit.json deleted file mode 100644 index 24371b9b5bebb507cdb04f15e472fab1661d34b5..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF203PBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_0.log b/ENCSR709QRD/cherimoya.fold_0.log deleted file mode 100644 index e1c69aa3acf93204bf70b3bf936c5046bc3230dd..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3372 41.62662220001221 4.387020826339722 565.6463623046875 0.8496992588043213 889.2357788085938 0.6537864208221436 0.72982675 7.540804862976074 True -1 6744 37.19700288772583 0.7808208465576172 724.6767578125 0.8666685819625854 775.5939331054688 0.7135602831840515 0.7759978 1.548633098602295 True -2 10116 37.25295925140381 1.008108139038086 595.262451171875 0.6262458562850952 760.5604248046875 0.7212803363800049 0.7859664 0.8810609579086304 True -3 13488 37.262287855148315 1.4447708129882812 596.904052734375 0.8865625262260437 752.2579345703125 0.7263248562812805 0.7910506 0.6958515644073486 True -4 16860 37.2234787940979 0.721264123916626 646.1143798828125 0.8396255970001221 748.48291015625 0.7297554612159729 0.7881142 0.6752879619598389 False -5 20232 37.25091290473938 0.7424285411834717 515.41357421875 0.670650839805603 743.4710083007812 0.7325748205184937 0.7897194 0.5794849395751953 False -6 23604 37.27136468887329 0.7271208763122559 645.4312744140625 0.6667758226394653 739.4453735351562 0.7346795797348022 0.79552644 0.5226966142654419 True -7 26976 37.22040629386902 0.7279465198516846 580.021484375 0.9419828057289124 733.172119140625 0.7376065850257874 0.79822767 0.500664234161377 True -8 30348 37.27353811264038 0.7245333194732666 609.5820922851562 0.4772038757801056 727.9705200195312 0.7402176856994629 0.8045097 0.48711568117141724 True -9 33720 37.25809574127197 0.7084677219390869 568.786865234375 0.611376941204071 722.960693359375 0.742141604423523 0.81066406 0.4728791415691376 True -10 37092 37.72948217391968 0.9483187198638916 563.9627685546875 0.7289004325866699 718.9951171875 0.7447881102561951 0.8122102 0.46591153740882874 True -11 40464 37.31902313232422 0.7201571464538574 672.6932983398438 0.5711943507194519 713.8426513671875 0.7484368085861206 0.8220614 0.4460718333721161 True -12 43836 37.37680435180664 0.7249982357025146 632.0347290039062 0.3970767557621002 710.535888671875 0.750650942325592 0.8312976 0.4250321686267853 True -13 47208 37.33871865272522 1.082007646560669 578.9347534179688 0.523908257484436 706.8563232421875 0.7524786591529846 0.8384441 0.4096132814884186 True -14 50580 36.85348343849182 0.7105638980865479 539.5173950195312 0.5000514388084412 704.019775390625 0.754608154296875 0.8425104 0.40375816822052 True -15 53952 36.50549840927124 0.7120473384857178 502.86712646484375 0.25198787450790405 702.2383422851562 0.7554932236671448 0.84659654 0.40410375595092773 True -16 57324 36.55666661262512 1.8975844383239746 483.86773681640625 0.28808706998825073 701.061767578125 0.7561025619506836 0.8491609 0.40548211336135864 True -17 60696 36.61800789833069 0.7123620510101318 488.81591796875 0.4087924659252167 701.2095336914062 0.7561395764350891 0.8488135 0.41390159726142883 False -18 64068 36.500091552734375 0.7098901271820068 617.5070190429688 0.4333611726760864 701.7235107421875 0.7559048533439636 0.84630144 0.4248150587081909 False -19 67440 36.54014015197754 0.7099912166595459 503.20245361328125 0.3363102376461029 702.0159301757812 0.7556431889533997 0.8468858 0.4298176169395447 False diff --git a/ENCSR709QRD/cherimoya.fold_0.performance.tsv b/ENCSR709QRD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1b9df3836edafe84faae35243dd7292653092802..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -701.061767578125 0.19563943147659302 0.7561026215553284 0.40309861302375793 0.84916090965271 0.775692880153656 0.40548211336135864 \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_1.evaluate.json b/ENCSR709QRD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c0208843b64bfd34d99b819a8faaa5a8d2336ec5..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203PBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_1.fit.json b/ENCSR709QRD/cherimoya.fold_1.fit.json deleted file mode 100644 index 2bd7c5c30da335591915f17ad578cd048393455d..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF203PBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_1.log b/ENCSR709QRD/cherimoya.fold_1.log deleted file mode 100644 index f912516a9c6b1f3c157d4e1cbbc88186cfffac38..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3351 42.628448724746704 21.307072401046753 667.610595703125 0.8993681073188782 1058.697021484375 0.6641367673873901 0.72609663 7.067967414855957 True -1 6702 37.042662620544434 1.146118402481079 565.7215576171875 1.0309486389160156 915.9761962890625 0.7202237248420715 0.78404796 1.6163792610168457 True -2 10053 37.04008960723877 0.9066011905670166 650.358642578125 0.9926264882087708 892.6712646484375 0.7293704152107239 0.79235923 0.8331649303436279 True -3 13404 37.00495433807373 0.9034895896911621 544.17626953125 0.6954227089881897 880.6361083984375 0.734927773475647 0.7962563 0.7325572371482849 True -4 16755 37.02358150482178 0.9064815044403076 668.5372924804688 0.7653213143348694 871.7600708007812 0.7380144596099854 0.8000314 0.7323195338249207 True -5 20106 36.96426844596863 1.0472095012664795 607.9788818359375 0.9271137118339539 862.87158203125 0.7416962385177612 0.8026373 0.6253259181976318 True -6 23457 37.020606994628906 1.7121152877807617 545.3615112304688 0.6656348705291748 857.9273071289062 0.7437652945518494 0.8082183 0.6118860840797424 True -7 26808 37.00164079666138 0.9153389930725098 723.96826171875 1.5585763454437256 850.3831787109375 0.7464435696601868 0.8094872 0.590155839920044 True -8 30159 36.93450975418091 0.9060313701629639 533.0820922851562 0.6712902784347534 845.2632446289062 0.7484955191612244 0.8098275 0.5699422359466553 True -9 33510 37.084129095077515 0.9106688499450684 688.198486328125 0.7112252712249756 837.2730712890625 0.7513383626937866 0.8215864 0.5285247564315796 True -10 36861 37.057997703552246 1.186143398284912 495.60125732421875 0.5603029727935791 830.688232421875 0.7539891004562378 0.8279727 0.5175920128822327 True -11 40212 37.03555750846863 0.9003467559814453 598.9656982421875 0.8313165903091431 826.2825927734375 0.755939245223999 0.8345908 0.4957527220249176 True -12 43563 36.31001377105713 0.8987939357757568 667.330078125 0.5882415771484375 821.079833984375 0.7581393718719482 0.83875287 0.4792056381702423 True -13 46914 36.55477213859558 11.557232856750488 557.1212158203125 0.5959712266921997 817.1991577148438 0.7602899670600891 0.84684944 0.46096888184547424 True -14 50265 36.30911040306091 0.9082269668579102 530.3356323242188 0.646515965461731 812.9398193359375 0.7623931765556335 0.85205925 0.4485975503921509 True -15 53616 36.36378002166748 0.9186341762542725 581.946044921875 0.6864640712738037 809.0269775390625 0.7645690441131592 0.8576815 0.44188356399536133 True -16 56967 36.417319774627686 1.592367172241211 604.6520385742188 0.47163546085357666 807.1594848632812 0.7657568454742432 0.8607539 0.433807909488678 True -17 60318 36.46969962120056 0.9145691394805908 524.3219604492188 0.41551610827445984 806.9984741210938 0.7660815715789795 0.8621361 0.43698644638061523 True -18 63669 36.45980191230774 0.9105830192565918 482.7012023925781 0.4369184970855713 808.1062622070312 0.7659556269645691 0.858285 0.44606608152389526 False -19 67020 36.4798047542572 0.9103701114654541 528.164794921875 0.21020551025867462 807.787353515625 0.7658734917640686 0.85761166 0.45134738087654114 False diff --git a/ENCSR709QRD/cherimoya.fold_1.performance.tsv b/ENCSR709QRD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c7e8d7719f73962f32f3cc547ef1f7ecb5ae8b1b..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -806.9984741210938 0.18162180483341217 0.7660815119743347 0.4471494257450104 0.8621361255645752 0.8102782368659973 0.43698644638061523 \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_2.evaluate.json b/ENCSR709QRD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bccc6a9e3a59e543e5daefa1471e411e5ca6996f..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203PBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_2.fit.json b/ENCSR709QRD/cherimoya.fold_2.fit.json deleted file mode 100644 index 5316a27df3e868b7d7daf8e11aff2885920638c1..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF203PBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_2.log b/ENCSR709QRD/cherimoya.fold_2.log deleted file mode 100644 index 35d8e305cbb6f13604734234e37f21e2f5eba584..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3592 44.36671686172485 5.2451887130737305 594.134765625 0.8299935460090637 942.0008544921875 0.6598867774009705 0.71347946 5.024789333343506 True -1 7184 39.65009260177612 0.8364427089691162 663.51416015625 0.9088730216026306 820.2847900390625 0.7118681073188782 0.7902915 1.3098104000091553 True -2 10776 39.5829975605011 0.803926944732666 602.8533935546875 0.5988867282867432 808.26953125 0.7177450060844421 0.7977857 0.9052072763442993 True -3 14368 39.63873553276062 0.7407519817352295 525.5077514648438 0.785137414932251 798.4329223632812 0.7232435941696167 0.80630845 0.6473948955535889 True -4 17960 39.65329360961914 0.7306880950927734 602.7127685546875 0.7471383810043335 793.424560546875 0.7249885201454163 0.81058735 0.5459335446357727 True -5 21552 39.63980221748352 0.7391364574432373 657.601806640625 0.7131240367889404 787.8150024414062 0.7286059856414795 0.81106055 0.5221889019012451 True -6 25144 39.67385482788086 0.7323014736175537 472.3744201660156 0.8639873266220093 783.0968017578125 0.7307502031326294 0.814888 0.5019407272338867 True -7 28736 39.34323501586914 0.7274060249328613 664.459228515625 0.6248558759689331 778.545166015625 0.7324168086051941 0.81768566 0.48862725496292114 True -8 32328 38.87686729431152 0.7222223281860352 569.7550048828125 0.6792703866958618 772.8153076171875 0.7347855567932129 0.81865144 0.4849334955215454 True -9 35920 38.86690282821655 0.7252140045166016 647.77392578125 0.7364816665649414 767.3944091796875 0.7374752759933472 0.8234187 0.4758576452732086 True -10 39512 38.88444900512695 0.7229750156402588 583.0941162109375 0.5123480558395386 762.3841552734375 0.7397245764732361 0.8273787 0.4654119312763214 True -11 43104 38.87968707084656 0.72579026222229 585.4569091796875 0.4965250492095947 757.766845703125 0.7417113780975342 0.8339726 0.4541005492210388 True -12 46696 38.84421944618225 0.7236998081207275 557.0540771484375 0.6189236640930176 752.6144409179688 0.7449632287025452 0.83882195 0.44021227955818176 True -13 50288 39.714330434799194 0.736461877822876 605.2689208984375 0.4175642728805542 748.2846069335938 0.747683048248291 0.8455186 0.4244884252548218 True -14 53880 38.87389326095581 0.7237529754638672 543.2064208984375 0.4787321090698242 744.6049194335938 0.749637246131897 0.84976923 0.41432082653045654 True -15 57472 38.85913443565369 0.737591028213501 568.4774780273438 0.414817214012146 742.3974609375 0.7512788772583008 0.85575324 0.40381672978401184 True -16 61064 38.93721604347229 25.25434637069702 510.28021240234375 0.4260258674621582 740.9691162109375 0.7518967390060425 0.85818994 0.4003869593143463 True -17 64656 38.951714515686035 0.7421178817749023 597.084716796875 0.3858296275138855 740.5692138671875 0.752251148223877 0.8595791 0.40079545974731445 True -18 68248 38.92964720726013 0.7406566143035889 557.74658203125 0.3136070966720581 741.1073608398438 0.7520596981048584 0.8570334 0.40687260031700134 False -19 71840 39.54413080215454 0.7384302616119385 565.5767822265625 0.37080344557762146 740.9717407226562 0.7519160509109497 0.8576221 0.4090074300765991 False diff --git a/ENCSR709QRD/cherimoya.fold_2.performance.tsv b/ENCSR709QRD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8516adf2f1dcbfaa2c7306a153166f3e99e94ec6..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -740.5692138671875 0.19381476938724518 0.7522510886192322 0.4189991354942322 0.8595790863037109 0.7926596403121948 0.40079545974731445 \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_3.evaluate.json b/ENCSR709QRD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 23a0adf66b051465f0b7903ebdaabf2d4709ff30..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203PBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_3.fit.json b/ENCSR709QRD/cherimoya.fold_3.fit.json deleted file mode 100644 index e9d6e2e5755f917313bbc5c5d27ba1b5310894ac..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF203PBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_3.log b/ENCSR709QRD/cherimoya.fold_3.log deleted file mode 100644 index d6ef56762b59dac907ee59a52a8cb13151d54bc6..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3463 42.942697525024414 4.747230768203735 622.4069213867188 0.7524000406265259 892.295166015625 0.6623950004577637 0.7341788 8.332521438598633 True -1 6926 38.2582848072052 0.7330994606018066 603.1749267578125 0.8020012974739075 782.96875 0.7121961712837219 0.78280026 1.5748273134231567 True -2 10389 38.2069730758667 1.0110273361206055 536.44580078125 0.8375783562660217 769.449951171875 0.7215263843536377 0.78954923 0.8961682915687561 True -3 13852 38.20978045463562 0.6461915969848633 643.4722900390625 0.6958103179931641 761.5150756835938 0.7275153994560242 0.78759205 0.6953254342079163 False -4 17315 37.485700845718384 0.628612756729126 575.8366088867188 1.0448760986328125 756.1060791015625 0.7304428219795227 0.7917978 0.6525896191596985 True -5 20778 37.488359451293945 0.6421940326690674 716.4326171875 0.7673335075378418 750.538330078125 0.7340534329414368 0.7979705 0.6039196848869324 True -6 24241 37.486708879470825 0.6488394737243652 636.2300415039062 0.5940214395523071 747.1610107421875 0.7360022068023682 0.795084 0.6050388216972351 False -7 27704 37.444171667099 0.6354587078094482 551.6273803710938 0.7019537687301636 742.968994140625 0.7384060621261597 0.7956474 0.5797876119613647 False -8 31167 37.516676902770996 0.6352648735046387 681.9122924804688 0.5832000374794006 735.6025390625 0.7419023513793945 0.8004595 0.5737273693084717 True -9 34630 37.484705686569214 0.6257307529449463 560.698486328125 0.9188913106918335 731.5204467773438 0.744632363319397 0.80330056 0.5594529509544373 True -10 38093 37.46633529663086 0.6260290145874023 652.559814453125 0.6524437665939331 727.5816650390625 0.7467634677886963 0.8094594 0.5453140735626221 True -11 41556 37.431289196014404 0.6263828277587891 516.99853515625 0.5090080499649048 723.3709716796875 0.7493317723274231 0.8128368 0.5287911295890808 True -12 45019 37.45165729522705 13.641571044921875 627.6124877929688 0.9443496465682983 719.0717163085938 0.7516276240348816 0.82079494 0.5118868947029114 True -13 48482 37.48982048034668 0.6302447319030762 562.6993408203125 0.6074185371398926 715.2734375 0.7536402344703674 0.8272274 0.4852248728275299 True -14 51945 37.43604350090027 0.620826005935669 660.0230712890625 0.5459834337234497 712.3264770507812 0.7552602887153625 0.8329844 0.46994608640670776 True -15 55408 37.42121505737305 0.6115334033966064 545.16943359375 0.38918691873550415 709.912353515625 0.7566681504249573 0.8421874 0.44839921593666077 True -16 58871 37.463587284088135 0.6329221725463867 552.748046875 0.403963565826416 710.1790771484375 0.7571978569030762 0.8426237 0.4452102482318878 True -17 62334 37.50716733932495 0.6272604465484619 574.76904296875 0.5007538199424744 709.6904296875 0.757229745388031 0.845605 0.4439358711242676 True -18 65797 37.55954313278198 0.6533865928649902 475.09954833984375 0.2422616183757782 710.4298095703125 0.7570571899414062 0.8438706 0.4471697211265564 False -19 69260 37.629616498947144 0.6210179328918457 567.8780517578125 0.24906623363494873 710.8355712890625 0.7567301392555237 0.8440373 0.4516650140285492 False diff --git a/ENCSR709QRD/cherimoya.fold_3.performance.tsv b/ENCSR709QRD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 21ac40e3017d820c52370c90ebf4732c04350d74..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -709.6904296875 0.1947501301765442 0.757229745388031 0.4030013084411621 0.8456050157546997 0.767827033996582 0.4439358711242676 \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_4.evaluate.json b/ENCSR709QRD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1c3bffd5ccce68329170d8267b5e2d5b74badb88..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203PBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_4.fit.json b/ENCSR709QRD/cherimoya.fold_4.fit.json deleted file mode 100644 index 71b862156336b0d1ea4ddd0e71e7f6093902c617..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF203PBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709QRD/cherimoya.fold_4.log b/ENCSR709QRD/cherimoya.fold_4.log deleted file mode 100644 index 19ce76dae8390f6a976c4d23b5a99afac4535633..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3475 43.33881187438965 4.633936405181885 451.84625244140625 0.6324136257171631 836.6508178710938 0.6543823480606079 0.73331875 6.123498916625977 True -1 6950 38.37204313278198 0.827622652053833 588.607177734375 1.3411245346069336 739.904541015625 0.7083418369293213 0.7810971 1.2381671667099 True -2 10425 38.03466486930847 0.7655167579650879 573.863037109375 0.8142110109329224 731.2994384765625 0.7140148878097534 0.77577025 0.8618450164794922 False -3 13900 37.618252754211426 1.2032990455627441 603.613525390625 0.8060443997383118 720.46435546875 0.7189117670059204 0.7793274 0.6491539478302002 False -4 17375 37.57474899291992 0.7155106067657471 580.0455322265625 0.5797834396362305 713.6815795898438 0.723400354385376 0.7841661 0.5498030185699463 True -5 20850 37.563695192337036 0.7256569862365723 528.1292724609375 0.9732499122619629 708.4467163085938 0.7267394065856934 0.78863335 0.5024417042732239 True -6 24325 37.55441379547119 0.7089695930480957 488.71722412109375 0.6043534874916077 703.9900512695312 0.7291461229324341 0.79290116 0.4965253174304962 True -7 27800 37.550530195236206 0.7225167751312256 585.1566772460938 0.6693688631057739 700.1821899414062 0.7316584587097168 0.7943345 0.4929623305797577 True -8 31275 37.59618091583252 0.7094371318817139 467.0238037109375 0.6413900852203369 695.1224365234375 0.734851598739624 0.8018992 0.4792121648788452 True -9 34750 37.79278802871704 29.90164589881897 498.5596618652344 0.5353171229362488 691.8204956054688 0.736607015132904 0.8054795 0.47192636132240295 True -10 38225 37.58209824562073 0.718252420425415 654.9970703125 0.4791635274887085 687.5089721679688 0.7399845719337463 0.81106573 0.45693153142929077 True -11 41700 37.64181923866272 0.7319095134735107 684.1766967773438 0.406740665435791 683.176025390625 0.7430116534233093 0.8155952 0.4430904984474182 True -12 45175 37.63442540168762 0.7281301021575928 678.06494140625 0.5066931247711182 679.421875 0.7456258535385132 0.8237932 0.42973318696022034 True -13 48650 37.6688129901886 1.5461301803588867 588.284423828125 0.8121223449707031 676.4805297851562 0.7477565407752991 0.8287817 0.4157361090183258 True -14 52125 37.649819135665894 0.7285540103912354 557.93212890625 0.4220415949821472 674.6256713867188 0.749302327632904 0.8355575 0.40549781918525696 True -15 55600 38.40815329551697 14.433188915252686 636.4108276367188 0.3849804401397705 672.5994873046875 0.7507970929145813 0.84175557 0.3955535888671875 True -16 59075 37.60530090332031 0.7139806747436523 591.7160034179688 0.33874499797821045 672.3243408203125 0.7516565322875977 0.84266305 0.39166250824928284 True -17 62550 37.64101719856262 0.7294957637786865 498.3363952636719 0.31714463233947754 672.2376098632812 0.7517547607421875 0.8459046 0.39058223366737366 True -18 66025 37.654927253723145 0.7251088619232178 485.2730712890625 0.45581746101379395 672.3983764648438 0.7516064047813416 0.84336823 0.3968971371650696 False -19 69500 37.65264701843262 1.6262118816375732 511.54949951171875 0.3356474041938782 672.613525390625 0.7515149116516113 0.8424292 0.3993501365184784 False diff --git a/ENCSR709QRD/cherimoya.fold_4.performance.tsv b/ENCSR709QRD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 68b06bc48c9a1b4758ace6ce61d6bb42fa5a90ad..0000000000000000000000000000000000000000 --- a/ENCSR709QRD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -672.2376098632812 0.20031966269016266 0.751754879951477 0.39271944761276245 0.8459045886993408 0.7630005478858948 0.39058223366737366 \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_0.evaluate.json b/ENCSR709YRE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1fbb9dc558ccfeede6139bc2454e83c8f96d1620..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF457AIU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_0.fit.json b/ENCSR709YRE/cherimoya.fold_0.fit.json deleted file mode 100644 index 134b7e293dfcfd9d30d2c5c67e0c5273fbe97c32..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF457AIU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_0.log b/ENCSR709YRE/cherimoya.fold_0.log deleted file mode 100644 index 8b9ed980e99a1cd3a67469471620f6f54064e3ec..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 34.79202485084534 3.6926376819610596 205.94161987304688 0.5296754837036133 259.80224609375 0.1317838579416275 0.69068545 3.033729314804077 True -1 5512 30.352330446243286 0.6418559551239014 239.51397705078125 0.5349301099777222 242.62950134277344 0.17077751457691193 0.7544871 1.14888334274292 True -2 8268 30.23306655883789 0.558380126953125 209.6641845703125 0.630173921585083 240.29122924804688 0.17313198745250702 0.76163375 0.7799550294876099 True -3 11024 30.26887536048889 0.5339462757110596 152.7266082763672 0.36835014820098877 238.60646057128906 0.17572906613349915 0.77075416 0.6111676096916199 True -4 13780 30.207632541656494 0.6916189193725586 190.7860565185547 0.36726850271224976 236.73387145996094 0.1798984408378601 0.77827984 0.5547032952308655 True -5 16536 30.253021001815796 0.5234506130218506 184.6317138671875 0.4476638734340668 235.86984252929688 0.18141978979110718 0.79176044 0.5273130536079407 True -6 19292 30.255003690719604 0.5256478786468506 178.10202026367188 0.4954677224159241 235.28140258789062 0.18368247151374817 0.79514736 0.5391802787780762 True -7 22048 30.223108053207397 0.5207901000976562 203.2676239013672 0.4687899947166443 234.6554718017578 0.18511758744716644 0.80047226 0.5021402835845947 True -8 24804 30.255096197128296 0.5194740295410156 174.96249389648438 0.273540735244751 233.96865844726562 0.1869480013847351 0.8047657 0.4792713224887848 True -9 27560 30.212235689163208 0.5259654521942139 167.495361328125 0.3658110499382019 233.51670837402344 0.18812799453735352 0.8096941 0.45300111174583435 True -10 30316 30.381017208099365 22.923980236053467 177.6580047607422 0.36752426624298096 233.6415252685547 0.18752191960811615 0.81239116 0.4417762756347656 True -11 33072 29.93198275566101 0.5327582359313965 232.52227783203125 0.4596943259239197 232.76417541503906 0.18956005573272705 0.82177085 0.4104984998703003 True -12 35828 29.677958011627197 0.5244390964508057 147.0712890625 0.2956165075302124 232.14723205566406 0.1910925954580307 0.82893217 0.38271617889404297 True -13 38584 29.74668860435486 0.5272488594055176 176.41732788085938 0.2903808355331421 231.4137725830078 0.19239233434200287 0.8390623 0.35260993242263794 True -14 41340 29.748056173324585 0.5172557830810547 170.6855926513672 0.430759459733963 231.1176300048828 0.19305899739265442 0.844564 0.32829469442367554 True -15 44096 29.68989133834839 0.5330934524536133 174.33108520507812 0.22197392582893372 230.91139221191406 0.19351737201213837 0.85166544 0.30875101685523987 True -16 46852 29.665814638137817 0.760486364364624 178.91407775878906 0.3224228024482727 230.635009765625 0.19395680725574493 0.85650116 0.2918200194835663 True -17 49608 29.787965297698975 0.531834602355957 164.45608520507812 0.21457871794700623 230.10670471191406 0.19576001167297363 0.85800606 0.28593873977661133 True -18 52364 29.811044692993164 0.5308263301849365 148.47930908203125 0.3707889914512634 230.59201049804688 0.1937410682439804 0.85672146 0.2828850746154785 False -19 55120 29.7434983253479 0.5202045440673828 192.9972381591797 0.25695839524269104 230.61392211914062 0.1939592957496643 0.8565633 0.2834404706954956 False diff --git a/ENCSR709YRE/cherimoya.fold_0.performance.tsv b/ENCSR709YRE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8f6af4724747c0848626de6dfcc3be324a50cf0b..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -230.10670471191406 0.5536342859268188 0.19576001167297363 0.0544905886054039 0.8580060601234436 0.7712196111679077 0.28593873977661133 \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_1.evaluate.json b/ENCSR709YRE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 74aa8816fbcfceb24709ae80fdac4aac4ada446d..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF457AIU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_1.fit.json b/ENCSR709YRE/cherimoya.fold_1.fit.json deleted file mode 100644 index 84e634e2704a48a8201d17975996d4b7041769a9..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF457AIU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_1.log b/ENCSR709YRE/cherimoya.fold_1.log deleted file mode 100644 index 2bd4af4b5192667f6b8bea8b1dca58f5c95ce4fd..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2732 34.59950399398804 5.2687437534332275 215.33639526367188 0.36577802896499634 293.24066162109375 0.13605542480945587 0.68155617 3.734754800796509 True -1 5464 30.296515941619873 0.7319040298461914 194.90945434570312 0.3593606948852539 271.9855041503906 0.17827193439006805 0.76213115 1.6028573513031006 True -2 8196 30.08507513999939 0.7260055541992188 148.23080444335938 0.642142117023468 270.00103759765625 0.18050551414489746 0.7659289 0.9157031774520874 True -3 10928 30.020848751068115 1.8486101627349854 242.25625610351562 0.6045207977294922 267.51336669921875 0.18430466949939728 0.78071815 0.7810011506080627 True -4 13660 30.014657974243164 0.7300021648406982 194.46627807617188 0.32171469926834106 265.2743225097656 0.18958252668380737 0.79016936 0.6962345242500305 True -5 16392 29.95611596107483 1.5878913402557373 176.4512939453125 0.33686235547065735 262.8519592285156 0.19499796628952026 0.8023923 0.6192147135734558 True -6 19124 30.02828073501587 0.7231760025024414 160.14407348632812 0.26866891980171204 261.5030517578125 0.19756504893302917 0.8148626 0.557700514793396 True -7 21856 30.02683448791504 0.7297763824462891 215.997314453125 0.5740814805030823 260.82666015625 0.1991778314113617 0.8173241 0.56241774559021 True -8 24588 30.141340494155884 0.7306258678436279 166.03636169433594 0.27624252438545227 260.0992126464844 0.20053733885288239 0.8277566 0.5115153789520264 True -9 27320 30.01451849937439 0.9977197647094727 163.49102783203125 0.41733846068382263 259.83746337890625 0.20082764327526093 0.8328972 0.4960213899612427 True -10 30052 30.040943145751953 0.7286827564239502 182.8857421875 0.3770173192024231 258.832275390625 0.2033172845840454 0.8375794 0.4661588966846466 True -11 32784 30.023303508758545 0.7186837196350098 205.0712890625 0.3247251510620117 258.5328063964844 0.2038516253232956 0.84143066 0.4465906620025635 True -12 35516 29.90258526802063 1.1174249649047852 181.30752563476562 0.2831805944442749 257.3348388671875 0.20678623020648956 0.8519549 0.4069104790687561 True -13 38248 29.469606161117554 0.7196338176727295 153.669921875 0.3367740213871002 256.6263427734375 0.20839005708694458 0.85874957 0.37249380350112915 True -14 40980 29.977152347564697 14.443799495697021 203.20553588867188 0.2895207405090332 256.3486328125 0.20859472453594208 0.8634041 0.36390790343284607 True -15 43712 29.545307397842407 0.7174818515777588 179.30642700195312 0.3065834045410156 255.56939697265625 0.21042558550834656 0.86795795 0.3355918228626251 True -16 46444 29.465904235839844 0.7137904167175293 151.87722778320312 0.18034955859184265 255.2063446044922 0.21076159179210663 0.8728626 0.322263240814209 True -17 49176 29.50826120376587 0.7293782234191895 151.99110412597656 0.23922517895698547 254.94407653808594 0.21058662235736847 0.8752595 0.3080404996871948 True -18 51908 29.521217823028564 0.7103683948516846 189.11904907226562 0.2767341136932373 255.5635528564453 0.20903056859970093 0.87309957 0.30454808473587036 False -19 54640 29.422836542129517 0.707819938659668 197.20883178710938 0.2898268699645996 255.32337951660156 0.20991748571395874 0.87439984 0.30373620986938477 False diff --git a/ENCSR709YRE/cherimoya.fold_1.performance.tsv b/ENCSR709YRE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index aa9eb504eeaa5655ddb2fecf4ee27bb750cfb6a9..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -254.94407653808594 0.5414811968803406 0.21058662235736847 0.06138131394982338 0.875259518623352 0.8175886273384094 0.3080404996871948 \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_2.evaluate.json b/ENCSR709YRE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5596d354d57c0aa9e64bcc16f17662ec14697641..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF457AIU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_2.fit.json b/ENCSR709YRE/cherimoya.fold_2.fit.json deleted file mode 100644 index 6edaf14b4a6516f7dc71ff636b3389f780e1f6c1..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF457AIU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_2.log b/ENCSR709YRE/cherimoya.fold_2.log deleted file mode 100644 index 8493cda194ca50265563e50dbf0406d29e124ad4..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2845 35.74395704269409 4.038295030593872 149.54046630859375 0.3327277898788452 274.2157287597656 0.13321088254451752 0.6651688 3.2888965606689453 True -1 5690 31.263842821121216 0.5982635021209717 198.82470703125 0.5263806581497192 252.7030029296875 0.17977754771709442 0.7486661 1.3002458810806274 True -2 8535 31.26972508430481 0.49971914291381836 225.82310485839844 0.5647569894790649 250.43287658691406 0.18213072419166565 0.75208443 0.842989444732666 True -3 11380 31.22964119911194 0.49823808670043945 182.44070434570312 0.42192313075065613 247.999267578125 0.18588662147521973 0.766319 0.673628568649292 True -4 14225 31.28596067428589 0.6954343318939209 229.72073364257812 0.40852105617523193 246.11923217773438 0.19016669690608978 0.78317195 0.5814166069030762 True -5 17070 31.413278579711914 0.51259446144104 187.1505889892578 0.5610519647598267 245.90786743164062 0.19076600670814514 0.7814228 0.5946720838546753 False -6 19915 31.241462469100952 0.5134024620056152 226.71910095214844 0.3925805389881134 244.5910186767578 0.193788081407547 0.79205 0.559280514717102 True -7 22760 31.21456217765808 0.5469436645507812 190.44656372070312 0.35226166248321533 244.39044189453125 0.19395220279693604 0.7974872 0.5472949147224426 True -8 25605 31.16913652420044 0.5102620124816895 197.68832397460938 0.26605209708213806 243.9842529296875 0.19483979046344757 0.8023496 0.5263827443122864 True -9 28450 31.171107292175293 0.5136752128601074 217.257080078125 0.37322384119033813 242.92111206054688 0.19787439703941345 0.80988234 0.4948674440383911 True -10 31295 31.163474798202515 0.5118756294250488 214.25479125976562 0.3195488750934601 242.37583923339844 0.19937793910503387 0.82041913 0.4499456584453583 True -11 34140 31.172300338745117 0.5003314018249512 232.14927673339844 0.364178329706192 241.72129821777344 0.2006455957889557 0.82864946 0.4129091501235962 True -12 36985 31.16706871986389 0.5091128349304199 188.65408325195312 0.3676748275756836 241.3590850830078 0.20142005383968353 0.8343728 0.38369736075401306 True -13 39830 30.879124641418457 0.4987602233886719 199.23843383789062 0.26486289501190186 240.8514862060547 0.20241840183734894 0.840638 0.35961759090423584 True -14 42675 30.60681986808777 0.5063884258270264 197.85079956054688 0.31154870986938477 240.06118774414062 0.2047104686498642 0.8458578 0.33527377247810364 True -15 45520 30.657489776611328 0.5013327598571777 190.87103271484375 0.30449143052101135 240.05514526367188 0.20402328670024872 0.8529007 0.3156372010707855 True -16 48365 30.66763162612915 0.49812984466552734 228.92123413085938 0.3294755518436432 239.8396453857422 0.20474372804164886 0.8548908 0.30577361583709717 True -17 51210 30.791035175323486 0.4965367317199707 204.95639038085938 0.3285520672798157 239.6935577392578 0.204594224691391 0.85561025 0.2991461753845215 True -18 54055 30.65556812286377 0.49257969856262207 163.0956573486328 0.22844423353672028 239.7477264404297 0.20454950630664825 0.8529847 0.30100372433662415 False -19 56900 30.676522731781006 0.5039575099945068 193.5238037109375 0.16200609505176544 239.77525329589844 0.20485106110572815 0.85221124 0.3026942312717438 False diff --git a/ENCSR709YRE/cherimoya.fold_2.performance.tsv b/ENCSR709YRE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 146b3c0303f8b6f29c3c5bac3e846abe64c68000..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -239.6935577392578 0.5468371510505676 0.20459425449371338 0.057112351059913635 0.8556102514266968 0.7842340469360352 0.2991461753845215 \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_3.evaluate.json b/ENCSR709YRE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d7cb0e8d8f65db9f6e3ea954619378c40fe15565..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF457AIU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_3.fit.json b/ENCSR709YRE/cherimoya.fold_3.fit.json deleted file mode 100644 index bb11a4f338b088a732cb292358b6c2c54f840366..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF457AIU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_3.log b/ENCSR709YRE/cherimoya.fold_3.log deleted file mode 100644 index 52324c44a1160b7e29c9c32ea14b2d62a29f37c7..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 35.064924478530884 4.739270925521851 195.83441162109375 0.393724262714386 278.8556213378906 0.14082016050815582 0.6397633 3.53466796875 True -1 5522 30.464964151382446 1.186316728591919 167.1693572998047 0.32968929409980774 261.1895446777344 0.177891343832016 0.70564264 1.6737579107284546 True -2 8283 30.39578127861023 0.5110845565795898 193.76959228515625 0.38032227754592896 259.9299621582031 0.17917950451374054 0.6906317 1.2391891479492188 False -3 11044 30.36116600036621 0.5119025707244873 233.72988891601562 0.48599421977996826 256.85858154296875 0.1856345683336258 0.7223006 0.879380464553833 True -4 13805 30.36321783065796 0.5073015689849854 163.4683074951172 0.19761022925376892 255.06930541992188 0.18933288753032684 0.7436154 0.7858002781867981 True -5 16566 30.34040856361389 0.5144932270050049 193.49148559570312 0.4111209213733673 253.8876953125 0.19285830855369568 0.7512411 0.7262923121452332 True -6 19327 30.28774380683899 0.5149290561676025 245.93124389648438 0.32327401638031006 253.062744140625 0.1945134401321411 0.7628887 0.6657540798187256 True -7 22088 30.312933683395386 0.511709451675415 186.062744140625 0.22890257835388184 252.10350036621094 0.1979655623435974 0.7684933 0.6518799066543579 True -8 24849 30.2901291847229 0.5037679672241211 195.53872680664062 0.6870149374008179 251.89154052734375 0.19729562103748322 0.7782883 0.6333133578300476 True -9 27610 30.33580732345581 0.5521814823150635 185.2047119140625 0.37179189920425415 251.38519287109375 0.19965356588363647 0.77856725 0.5996559262275696 True -10 30371 30.29742121696472 0.5149779319763184 182.28953552246094 0.2834228277206421 250.8013916015625 0.20139770209789276 0.78687876 0.5774557590484619 True -11 33132 30.313493967056274 0.5150022506713867 140.90362548828125 0.4426257014274597 250.44805908203125 0.20195959508419037 0.7978699 0.5438705682754517 True -12 35893 30.33290982246399 0.5053091049194336 203.83822631835938 0.295027494430542 249.57684326171875 0.20409685373306274 0.80693287 0.5034304261207581 True -13 38654 30.34219527244568 0.5156979560852051 204.4927978515625 0.4393211007118225 249.1700897216797 0.20392794907093048 0.81753105 0.45526543259620667 True -14 41415 30.194716930389404 0.5110468864440918 156.31578063964844 0.18303282558918 248.31890869140625 0.20627865195274353 0.8261681 0.4276411533355713 True -15 44176 29.83600926399231 0.5102331638336182 186.68040466308594 0.3088706433773041 247.78887939453125 0.20666882395744324 0.83325607 0.3962863087654114 True -16 46937 29.844412326812744 0.5022644996643066 238.5494384765625 0.42960551381111145 247.3956298828125 0.2081025093793869 0.839289 0.37562888860702515 True -17 49698 29.80523991584778 0.5016701221466064 166.18624877929688 0.16870063543319702 247.24229431152344 0.20771963894367218 0.8409592 0.3654247224330902 True -18 52459 29.7879319190979 0.5161561965942383 178.5633544921875 0.1837742030620575 247.46469116210938 0.20737724006175995 0.83985305 0.3644388020038605 False -19 55220 29.840450525283813 0.5025773048400879 162.53457641601562 0.2525099813938141 247.70196533203125 0.20635460317134857 0.8384207 0.36512911319732666 False diff --git a/ENCSR709YRE/cherimoya.fold_3.performance.tsv b/ENCSR709YRE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e9ac301b83e3c165b61ea13747a7b7fff9127a9b..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -247.24229431152344 0.543514609336853 0.207719624042511 0.057291459292173386 0.8409591913223267 0.7821459174156189 0.3654247224330902 \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_4.evaluate.json b/ENCSR709YRE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0b363f312dd64bb095d1c0d3467b8369a2aff194..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF457AIU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_4.fit.json b/ENCSR709YRE/cherimoya.fold_4.fit.json deleted file mode 100644 index c4c9df5f1e7aced760033efa03ae476ca901c0a9..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF457AIU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR709YRE/cherimoya.fold_4.log b/ENCSR709YRE/cherimoya.fold_4.log deleted file mode 100644 index 42bd0166cb3f3fdee296f7b58d5fd58c2d6d58d2..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2838 35.98411464691162 4.235597133636475 219.0590057373047 0.41066765785217285 221.00318908691406 0.12180636823177338 0.6528564 2.4859812259674072 True -1 5676 31.253830432891846 0.6745040416717529 151.21343994140625 0.41761642694473267 209.7503204345703 0.14917516708374023 0.725792 1.0653351545333862 True -2 8514 31.19004535675049 0.6332337856292725 182.02044677734375 0.2923247814178467 207.12783813476562 0.15349626541137695 0.7400055 0.5372097492218018 True -3 11352 31.167896270751953 0.6265201568603516 199.66107177734375 0.35254722833633423 205.6874542236328 0.1566610187292099 0.75531137 0.4661206007003784 True -4 14190 31.13553500175476 0.626641035079956 199.3507843017578 0.4646194279193878 204.9140625 0.1589738130569458 0.76015645 0.48194876313209534 True -5 17028 31.151370525360107 22.041358947753906 208.2134246826172 0.4628656506538391 204.44126892089844 0.15938173234462738 0.77187884 0.45454469323158264 True -6 19866 31.13118076324463 2.1531429290771484 158.3500213623047 0.35148799419403076 203.9168701171875 0.16071461141109467 0.7732799 0.43910205364227295 True -7 22704 31.213040590286255 1.158757209777832 210.5582275390625 0.6392366886138916 203.380859375 0.16268259286880493 0.78378636 0.4056287705898285 True -8 25542 31.19435739517212 0.6546754837036133 231.19863891601562 0.3428454101085663 203.2119903564453 0.16263198852539062 0.79329437 0.3707371652126312 True -9 28380 31.182223320007324 0.6305248737335205 191.9072265625 0.26553577184677124 202.80393981933594 0.1639709323644638 0.8005919 0.3557795286178589 True -10 31218 31.165177583694458 0.6442930698394775 208.83840942382812 0.4044662415981293 202.17822265625 0.16619989275932312 0.80799645 0.3331778049468994 True -11 34056 31.252012968063354 0.6458816528320312 163.3343963623047 0.33783379197120667 201.8040771484375 0.167091965675354 0.81337243 0.31675124168395996 True -12 36894 31.21279001235962 0.6408686637878418 143.00732421875 0.2522679567337036 201.75946044921875 0.16621722280979156 0.8212931 0.3026634156703949 True -13 39732 31.453959465026855 20.17967391014099 204.34902954101562 0.36451756954193115 201.1230010986328 0.16852067410945892 0.827397 0.2864114046096802 True -14 42570 30.669409036636353 1.128359317779541 150.32058715820312 0.2645217776298523 200.90374755859375 0.16878294944763184 0.8334005 0.27382948994636536 True -15 45408 30.602017641067505 1.4057722091674805 224.1538543701172 0.3218991756439209 200.7758026123047 0.16946980357170105 0.8359051 0.2668009400367737 True -16 48246 30.663079261779785 0.6282830238342285 196.70977783203125 0.23627017438411713 200.41661071777344 0.17057645320892334 0.8384255 0.2604607939720154 True -17 51084 30.64231014251709 0.6288483142852783 181.5447998046875 0.2377585619688034 200.3450164794922 0.17065246403217316 0.8401458 0.2571474611759186 True -18 53922 30.614287614822388 0.6250269412994385 164.03610229492188 0.4236254394054413 200.49681091308594 0.16978314518928528 0.84073234 0.25803589820861816 True -19 56760 30.563932418823242 0.6352207660675049 216.61660766601562 0.2067565768957138 200.39910888671875 0.1704060286283493 0.83752465 0.25908124446868896 False diff --git a/ENCSR709YRE/cherimoya.fold_4.performance.tsv b/ENCSR709YRE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index dcc48325d3dad089c2e268d1ad2835cc0e0657ea..0000000000000000000000000000000000000000 --- a/ENCSR709YRE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -200.49681091308594 0.5714686512947083 0.16978313028812408 0.04082181304693222 0.8407323360443115 0.7330011129379272 0.25803589820861816 \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_0.evaluate.json b/ENCSR712PYJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ef666a82c2ea7c5bc7775aa56d2b7f76d9387d79..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF119KBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_0.fit.json b/ENCSR712PYJ/cherimoya.fold_0.fit.json deleted file mode 100644 index bb72dc395cf9e87468c38d52eb45f7ddbc18e8c7..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF119KBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_0.log b/ENCSR712PYJ/cherimoya.fold_0.log deleted file mode 100644 index 4a0e79d6630497618e56aeb7d97ad33fd8a302d7..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2230 29.43790888786316 3.6347477436065674 217.12777709960938 0.6434653401374817 311.6992492675781 0.1568683236837387 0.521427 6.2552809715271 True -1 4460 24.82030963897705 0.6076207160949707 247.7378387451172 0.48864370584487915 288.7777404785156 0.24608102440834045 0.6154889 1.5628657341003418 True -2 6690 24.842778205871582 0.46219491958618164 259.5338439941406 0.7801239490509033 279.73822021484375 0.2682761549949646 0.64692587 0.8762039542198181 True -3 8920 24.826385259628296 0.4997715950012207 242.34658813476562 0.7738288640975952 277.241455078125 0.27354180812835693 0.65947354 0.5979074239730835 True -4 11150 24.289166927337646 0.4525127410888672 234.03350830078125 0.4080193340778351 275.7607116699219 0.27738386392593384 0.66850483 0.5069431066513062 True -5 13380 24.328330039978027 0.47317004203796387 220.84381103515625 0.6215159893035889 274.7191467285156 0.2808234691619873 0.67156535 0.46182703971862793 True -6 15610 24.268413066864014 0.4698677062988281 212.72731018066406 0.8436771631240845 274.22894287109375 0.28156834840774536 0.6776172 0.45189782977104187 True -7 17840 24.271557569503784 0.4575779438018799 216.28822326660156 0.6018326282501221 273.2596435546875 0.2854314148426056 0.67760354 0.45670780539512634 False -8 20070 24.300326585769653 0.4599273204803467 216.5858917236328 0.7642004489898682 273.07232666015625 0.2852388024330139 0.6819956 0.4407733380794525 True -9 22300 24.31994938850403 0.4662477970123291 242.95870971679688 0.5098295211791992 272.4803771972656 0.2876632511615753 0.68874955 0.4594678580760956 True -10 24530 24.32730460166931 0.47022438049316406 199.3416290283203 0.4815710783004761 271.79217529296875 0.2912636697292328 0.68944615 0.455812931060791 True -11 26760 24.29566764831543 0.4694488048553467 214.02505493164062 0.5789000988006592 271.6496887207031 0.29097774624824524 0.6967375 0.4415661096572876 True -12 28990 24.271491050720215 0.4609866142272949 208.9575653076172 0.46280089020729065 270.8384094238281 0.29380783438682556 0.70074475 0.44898873567581177 True -13 31220 24.269184827804565 0.46671175956726074 277.9708557128906 0.8522073030471802 270.1847839355469 0.29651516675949097 0.70760864 0.4468640983104706 True -14 33450 24.328277587890625 0.47674131393432617 254.90365600585938 0.6195048689842224 269.9191589355469 0.2970472276210785 0.70844775 0.43324777483940125 True -15 35680 24.257478713989258 1.2450308799743652 212.02978515625 0.4230881333351135 269.25958251953125 0.2993646562099457 0.71579754 0.41206392645835876 True -16 37910 24.339396715164185 1.4691109657287598 281.5650634765625 0.3872162103652954 269.4692077636719 0.29748156666755676 0.7171005 0.40574055910110474 True -17 40140 24.35929226875305 0.46617960929870605 234.39572143554688 0.2955476641654968 269.59979248046875 0.29777926206588745 0.7190109 0.4055534899234772 True -18 42370 24.355706930160522 0.4601287841796875 214.07672119140625 0.3927203416824341 269.6125793457031 0.29806873202323914 0.7183037 0.4092021584510803 False -19 44600 25.040533781051636 17.80513906478882 184.21841430664062 0.29814398288726807 269.7301940917969 0.2972903251647949 0.7155179 0.4137163460254669 False diff --git a/ENCSR712PYJ/cherimoya.fold_0.performance.tsv b/ENCSR712PYJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f148d65cc4912dec9122ca95e5115c1d1db0e4c3..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -269.59979248046875 0.4914013147354126 0.29777926206588745 0.0837344154715538 0.7190108895301819 0.6516391038894653 0.4055534899234772 \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_1.evaluate.json b/ENCSR712PYJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5937f39f0e2097630e42e53f1719c6b2248f7bb1..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF119KBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_1.fit.json b/ENCSR712PYJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 4f8cbdfc9d648c4bfa86c061f799bcec51efc717..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF119KBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_1.log b/ENCSR712PYJ/cherimoya.fold_1.log deleted file mode 100644 index ab056d4b0e2652891dcfefe081c72a53c12e655e..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2213 29.115529537200928 4.124622821807861 251.7887725830078 0.9056081175804138 363.994384765625 0.16190887987613678 0.52535826 6.236478805541992 True -1 4426 25.029686450958252 0.709291934967041 266.32830810546875 0.8589109182357788 334.30767822265625 0.2597355544567108 0.63452184 2.3913331031799316 True -2 6639 24.681910753250122 0.612612247467041 249.5211944580078 0.5884417295455933 324.1312561035156 0.2827387750148773 0.66454 1.1496555805206299 True -3 8852 24.67306423187256 0.6366961002349854 231.46051025390625 0.6267044544219971 318.9240417480469 0.2922973930835724 0.67894703 0.6812461018562317 True -4 11065 25.23688554763794 6.723753213882446 279.3355712890625 0.8733632564544678 317.5130310058594 0.2944336235523224 0.6866394 0.6275711059570312 True -5 13278 24.68497586250305 1.1529083251953125 227.0283203125 0.5886223316192627 315.67230224609375 0.299894779920578 0.6975474 0.6002508401870728 True -6 15491 24.638840913772583 0.652698278427124 207.52297973632812 0.5209766626358032 315.3853759765625 0.30100390315055847 0.7032432 0.5578227639198303 True -7 17704 24.657041549682617 0.6177084445953369 206.15455627441406 0.5285942554473877 313.6875915527344 0.30636897683143616 0.7109563 0.54123455286026 True -8 19917 24.624565601348877 1.233144760131836 187.41806030273438 0.3725491762161255 313.205078125 0.30698901414871216 0.71703494 0.5146306753158569 True -9 22130 24.651739597320557 1.7737879753112793 223.4278564453125 0.3809197247028351 312.3262634277344 0.3086636960506439 0.7240438 0.4871062934398651 True -10 24343 24.218721389770508 0.6091372966766357 253.84036254882812 0.5718064308166504 310.9651794433594 0.31326034665107727 0.72847885 0.4617602229118347 True -11 26556 24.150517463684082 0.6107363700866699 240.29022216796875 0.5200812220573425 310.79327392578125 0.31286847591400146 0.73620415 0.4501589238643646 True -12 28769 24.25853157043457 0.5975220203399658 185.35342407226562 0.47756168246269226 310.2260437011719 0.31430336833000183 0.74339455 0.44140997529029846 True -13 30982 24.181618690490723 0.6218416690826416 234.75253295898438 0.4859045147895813 309.12176513671875 0.3182464838027954 0.7486968 0.4283618927001953 True -14 33195 24.23305344581604 0.6120040416717529 193.43370056152344 0.3431115448474884 308.4878234863281 0.3190424144268036 0.75429744 0.4177345037460327 True -15 35408 24.151219606399536 0.6137499809265137 223.11827087402344 0.36492058634757996 308.1492919921875 0.31971475481987 0.75982785 0.41436198353767395 True -16 37621 24.221923828125 0.6194005012512207 258.71954345703125 0.31295764446258545 307.9683837890625 0.3200632333755493 0.7614195 0.4147499203681946 True -17 39834 24.203195810317993 0.6139864921569824 206.01222229003906 0.40951651334762573 308.3006286621094 0.31769615411758423 0.7595638 0.42320817708969116 False -18 42047 24.25546908378601 0.6330394744873047 235.7845001220703 0.28572309017181396 308.148193359375 0.31852054595947266 0.7582872 0.4293085038661957 False -19 44260 24.219013929367065 0.6059134006500244 192.65118408203125 0.3113250136375427 308.3636779785156 0.3181038796901703 0.75722474 0.43620291352272034 False diff --git a/ENCSR712PYJ/cherimoya.fold_1.performance.tsv b/ENCSR712PYJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 54b9adf2c8566161d0f5f6a4fbbde4f57b4b6082..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -307.9683837890625 0.4727274775505066 0.3200632333755493 0.09454058855772018 0.7614194750785828 0.7093186974525452 0.4147499203681946 \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_2.evaluate.json b/ENCSR712PYJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a63f22025824d2a16970e47773a50c0cbaf7c6ef..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF119KBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_2.fit.json b/ENCSR712PYJ/cherimoya.fold_2.fit.json deleted file mode 100644 index c1934a42e7c0997062e86ccb5272bfae5f0ad02b..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF119KBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_2.log b/ENCSR712PYJ/cherimoya.fold_2.log deleted file mode 100644 index e7186486ae49387c8f634768d50f8ffe72935157..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2367 31.091001272201538 3.7096669673919678 186.1238555908203 1.0211524963378906 320.6413269042969 0.16225475072860718 0.50772876 4.744565486907959 True -1 4734 26.390183210372925 0.5418860912322998 216.4676513671875 0.6160613298416138 294.0597839355469 0.255772203207016 0.6265998 1.6984719038009644 True -2 7101 26.414504051208496 0.4470505714416504 270.7252197265625 0.7270448207855225 286.5220947265625 0.27163001894950867 0.65744776 0.9154401421546936 True -3 9468 26.43703579902649 0.4421072006225586 230.32244873046875 0.6824324727058411 283.7489929199219 0.2783295810222626 0.67155266 0.5757164359092712 True -4 11835 26.38518524169922 0.4361000061035156 257.59197998046875 1.0326471328735352 282.25128173828125 0.2823328673839569 0.6794307 0.49853771924972534 True -5 14202 26.36619520187378 0.4473390579223633 210.44436645507812 0.747079074382782 280.8267822265625 0.28715217113494873 0.6871009 0.5064358711242676 True -6 16569 26.383362293243408 0.7632369995117188 213.03079223632812 0.4728030264377594 280.7868347167969 0.2868359684944153 0.6910339 0.5238226056098938 True -7 18936 26.430605173110962 0.5018184185028076 241.85450744628906 0.8213337063789368 279.5886535644531 0.2918236553668976 0.69466096 0.5075973272323608 True -8 21303 26.39468765258789 0.6370790004730225 215.35467529296875 0.5755727291107178 278.4767761230469 0.29530641436576843 0.6999472 0.48060378432273865 True -9 23670 26.41405749320984 2.3670034408569336 252.8233642578125 0.7619222402572632 278.2574157714844 0.2956424355506897 0.70509017 0.46206894516944885 True -10 26037 26.435627222061157 0.45606493949890137 231.589599609375 0.5394043922424316 277.9739990234375 0.2962736189365387 0.7112349 0.44926145672798157 True -11 28404 26.35163640975952 0.45568346977233887 230.29617309570312 0.5383337736129761 277.1772155761719 0.2989150285720825 0.71657974 0.4266619086265564 True -12 30771 26.364850759506226 0.4492950439453125 208.32632446289062 0.49434587359428406 276.38067626953125 0.30103600025177 0.7206865 0.42386394739151 True -13 33138 26.39332604408264 0.44779515266418457 228.86209106445312 0.3231602907180786 275.8167419433594 0.30247536301612854 0.726103 0.409784197807312 True -14 35505 26.471710920333862 0.47020959854125977 233.9075927734375 0.5668354034423828 275.72222900390625 0.3022761344909668 0.73120624 0.4075162410736084 True -15 37872 26.506958723068237 0.4679131507873535 224.29786682128906 0.45581069588661194 275.105712890625 0.30512505769729614 0.7339807 0.40374353528022766 True -16 40239 26.47837996482849 1.5824906826019287 216.04421997070312 0.22716429829597473 274.6761474609375 0.3062315881252289 0.7352807 0.403043270111084 True -17 42606 26.03511381149292 0.45095086097717285 262.306640625 0.2909998595714569 274.6537780761719 0.3065345585346222 0.7353364 0.40535274147987366 True -18 44973 25.937002897262573 0.47081470489501953 203.2115020751953 0.2862745225429535 274.680419921875 0.30595871806144714 0.73397785 0.41380926966667175 False -19 47340 25.95110821723938 0.4987635612487793 220.04013061523438 0.34893518686294556 274.9935302734375 0.30473431944847107 0.73183465 0.41830092668533325 False diff --git a/ENCSR712PYJ/cherimoya.fold_2.performance.tsv b/ENCSR712PYJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ea5fbd07fa1a72ab09f120799d6da206c1d7e4b7..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -274.6537780761719 0.48719310760498047 0.3065345883369446 0.086976557970047 0.735336422920227 0.6689706444740295 0.40535274147987366 \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_3.evaluate.json b/ENCSR712PYJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5e0adb171b2c4da9558aeb94d8b5d7b7806d0152..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF119KBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_3.fit.json b/ENCSR712PYJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 744f29c142980242cfac1df139ac96e0ba4fab91..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF119KBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_3.log b/ENCSR712PYJ/cherimoya.fold_3.log deleted file mode 100644 index c7467832fcd0fa9ebd7e192eea26816a86a4ff8f..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2262 30.3131206035614 3.5925421714782715 266.6148681640625 0.6195437908172607 315.70123291015625 0.15940244495868683 0.53066576 5.60251522064209 True -1 4524 25.234671115875244 0.6501741409301758 275.7801513671875 1.074634313583374 294.01434326171875 0.24487225711345673 0.6337184 1.8138549327850342 True -2 6786 25.305533409118652 0.5321576595306396 248.2801055908203 0.8784806728363037 285.8835144042969 0.266509473323822 0.65661204 0.7449206113815308 True -3 9048 25.337349891662598 0.5126638412475586 191.20640563964844 0.4244126081466675 281.9193115234375 0.27454712986946106 0.66568273 0.4714740514755249 True -4 11310 25.515686511993408 0.5075535774230957 266.34637451171875 0.6052496433258057 280.2962951660156 0.2786325514316559 0.66928035 0.459534615278244 True -5 13572 25.259934902191162 0.49796175956726074 226.89865112304688 0.680391252040863 279.04351806640625 0.2821032702922821 0.67276007 0.4484648108482361 True -6 15834 25.385977506637573 0.4977896213531494 218.3822021484375 0.8020926713943481 278.7498474121094 0.2823241055011749 0.68127114 0.45567938685417175 True -7 18096 26.31283926963806 0.4856691360473633 235.37020874023438 0.5420089364051819 277.5201110839844 0.2874392569065094 0.6875042 0.4357891082763672 True -8 20358 25.329663038253784 0.49871230125427246 233.56027221679688 0.5834378004074097 276.99407958984375 0.28802913427352905 0.69163394 0.44695067405700684 True -9 22620 25.298799514770508 0.47603440284729004 234.5960693359375 0.5561661124229431 276.85125732421875 0.28869831562042236 0.6981952 0.43729475140571594 True -10 24882 25.37836241722107 0.48612475395202637 222.58978271484375 0.43070635199546814 275.78790283203125 0.2927459478378296 0.7042226 0.4408770203590393 True -11 27144 25.33298945426941 0.48381543159484863 240.483154296875 0.32399678230285645 275.5648193359375 0.2933221757411957 0.7045109 0.4298323690891266 True -12 29406 25.310741424560547 0.4891185760498047 253.30210876464844 0.5407886505126953 274.9268798828125 0.29514509439468384 0.7093997 0.4249204993247986 True -13 31668 25.299756050109863 0.5026454925537109 206.42263793945312 0.3769657611846924 274.5802917480469 0.2948746979236603 0.7174579 0.41536059975624084 True -14 33930 25.30559206008911 0.5590090751647949 213.5323028564453 0.4119051694869995 274.0124816894531 0.29654383659362793 0.72289914 0.40616586804389954 True -15 36192 25.24368143081665 0.5110077857971191 207.853759765625 0.2870505750179291 273.78228759765625 0.29774779081344604 0.73039615 0.400582879781723 True -16 38454 25.267457962036133 0.4938061237335205 224.8506622314453 0.4890275299549103 273.4618225097656 0.29922372102737427 0.73250926 0.3917573094367981 True -17 40716 25.2629554271698 0.49985671043395996 221.98672485351562 0.2858666479587555 273.8531494140625 0.2973073720932007 0.73453236 0.391920804977417 True -18 42978 25.241888284683228 0.49187779426574707 181.69915771484375 0.2810175120830536 273.9016418457031 0.2970638573169708 0.73135537 0.39536726474761963 False -19 45240 25.203524589538574 0.4902827739715576 205.42425537109375 0.3963538408279419 274.0474853515625 0.2962110638618469 0.73008215 0.4001429080963135 False diff --git a/ENCSR712PYJ/cherimoya.fold_3.performance.tsv b/ENCSR712PYJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index afc4fc1a61c3ec56c1bd4740ec3b69ba1bc85c22..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -273.8531494140625 0.4908638000488281 0.2973073720932007 0.08032781630754471 0.734532356262207 0.6687737703323364 0.391920804977417 \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_4.evaluate.json b/ENCSR712PYJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ec72c3cfa60cadffc0818c6f48b1f8e7e70aa380..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF119KBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_4.fit.json b/ENCSR712PYJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 59f16ca01c49570afa05242f207479fdc84ee0d0..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF119KBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR712PYJ/cherimoya.fold_4.log b/ENCSR712PYJ/cherimoya.fold_4.log deleted file mode 100644 index e10db3a5155afee40db724b3629af25a0a81e5a6..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2321 30.385531187057495 3.8355352878570557 219.0731201171875 0.6566495299339294 310.5111999511719 0.15724396705627441 0.5155544 4.980799198150635 True -1 4642 25.853715419769287 1.2795944213867188 213.6763916015625 0.7902504205703735 287.5050048828125 0.24994459748268127 0.60848266 1.8243521451950073 True -2 6963 25.903523683547974 0.5570950508117676 216.3709716796875 0.7819874882698059 279.5858459472656 0.26825934648513794 0.6337301 0.8706591725349426 True -3 9284 25.866594791412354 0.5077567100524902 273.6551513671875 0.8716166019439697 276.4779357910156 0.277616024017334 0.6421784 0.5441518425941467 True -4 11605 25.83017086982727 0.5331041812896729 239.9905548095703 0.7368344068527222 275.8471984863281 0.27713948488235474 0.6456808 0.5283181071281433 True -5 13926 25.83768320083618 0.49274444580078125 220.25473022460938 0.6036062836647034 274.9081726074219 0.2794705629348755 0.65701437 0.515052855014801 True -6 16247 25.80197262763977 11.460238218307495 231.04901123046875 0.4757802188396454 274.18536376953125 0.2826041877269745 0.66255033 0.5269331932067871 True -7 18568 25.8978168964386 0.5009567737579346 232.24191284179688 0.4455220699310303 273.55426025390625 0.28464382886886597 0.6643315 0.5333774089813232 True -8 20889 25.879689931869507 0.5082342624664307 204.61801147460938 0.4880465269088745 273.3582458496094 0.28564879298210144 0.6667592 0.5218855738639832 True -9 23210 25.91452407836914 0.4999821186065674 222.99237060546875 0.4169046878814697 272.40362548828125 0.2892400026321411 0.6792476 0.497222363948822 True -10 25531 25.8516845703125 0.4897153377532959 181.56333923339844 0.5260733366012573 271.86602783203125 0.29081133008003235 0.6843463 0.4739623963832855 True -11 27852 25.88183903694153 1.7830123901367188 226.6859130859375 0.836480975151062 271.4542236328125 0.29150745272636414 0.6880971 0.46548566222190857 True -12 30173 25.940858840942383 0.502647876739502 210.6278533935547 0.48145791888237 270.5486145019531 0.295312762260437 0.6965836 0.4459657073020935 True -13 32494 25.915749311447144 0.49155116081237793 223.21041870117188 0.39849039912223816 270.3951110839844 0.2952040135860443 0.699512 0.4310372769832611 True -14 34815 25.890515089035034 1.5809605121612549 223.857421875 0.28197425603866577 270.11572265625 0.2960999310016632 0.706919 0.41573765873908997 True -15 37136 25.923502206802368 0.4923686981201172 223.81832885742188 0.501845121383667 270.1169738769531 0.2961214482784271 0.7123798 0.4036407172679901 True -16 39457 25.89320135116577 0.4894535541534424 236.2910919189453 0.4149785339832306 269.7948913574219 0.297230988740921 0.7139166 0.3968072831630707 True -17 41778 25.835800170898438 15.373972654342651 209.39083862304688 0.3416506052017212 270.1290588378906 0.29537439346313477 0.7138317 0.39797836542129517 False -18 44099 25.898932933807373 0.488584041595459 192.35711669921875 0.2548229396343231 269.8421630859375 0.29724934697151184 0.7120032 0.40252599120140076 False -19 46420 25.849780797958374 0.49640965461730957 204.42086791992188 0.3276398777961731 270.0179443359375 0.29596155881881714 0.7115079 0.4059121608734131 False diff --git a/ENCSR712PYJ/cherimoya.fold_4.performance.tsv b/ENCSR712PYJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 52924c56d7eeaf3f51699195166d54a7e0a44611..0000000000000000000000000000000000000000 --- a/ENCSR712PYJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -269.7948913574219 0.4907134771347046 0.297230988740921 0.08262748271226883 0.7139165997505188 0.6513365507125854 0.3968072831630707 \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_0.evaluate.json b/ENCSR713KNQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 12d3c72c4b49dc909f6c3859c3d29e63153fa160..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF678ODJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_0.fit.json b/ENCSR713KNQ/cherimoya.fold_0.fit.json deleted file mode 100644 index f43a21fb8a7f23492f09dd5c832e617bfc299e07..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF678ODJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_0.log b/ENCSR713KNQ/cherimoya.fold_0.log deleted file mode 100644 index 46f1da20d52afc66863e89397327c11d4ff33040..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 34.956143617630005 4.221360921859741 824.78759765625 0.4560398459434509 1049.8065185546875 0.271232008934021 0.7078787 6.855729579925537 True -1 5506 30.32507348060608 2.582463264465332 814.023193359375 0.5416267514228821 928.93603515625 0.34415099024772644 0.7817144 1.7166227102279663 True -2 8259 30.308568239212036 0.6555318832397461 750.6329345703125 0.4883197546005249 905.5243530273438 0.35388368368148804 0.799549 0.9100737571716309 True -3 11012 30.340765476226807 0.7379233837127686 779.544189453125 0.48112544417381287 903.9163818359375 0.35294145345687866 0.80468726 0.6901147961616516 True -4 13765 30.351304292678833 1.7758431434631348 700.7289428710938 0.47176626324653625 895.2769775390625 0.35880541801452637 0.81403714 0.5802306532859802 True -5 16518 30.30900526046753 0.5807244777679443 765.6356201171875 0.3108161389827728 889.9231567382812 0.36332812905311584 0.8149745 0.5312885642051697 True -6 19271 30.309362649917603 0.5738446712493896 767.6802978515625 0.4497872591018677 888.9130859375 0.3635586202144623 0.82199 0.52983158826828 True -7 22024 30.411412477493286 0.5817606449127197 783.9034423828125 0.42978113889694214 882.3470458984375 0.3671945333480835 0.82915735 0.4708040952682495 True -8 24777 30.304097175598145 0.5856678485870361 740.19970703125 0.46339988708496094 877.6121826171875 0.37082910537719727 0.8323386 0.4765252470970154 True -9 27530 30.300910234451294 0.5816850662231445 785.3975830078125 0.38034355640411377 875.8525390625 0.3708425462245941 0.8386432 0.4567577838897705 True -10 30283 30.48836851119995 0.565298318862915 715.0128173828125 0.42478030920028687 869.8466186523438 0.3765680491924286 0.84233385 0.41963863372802734 True -11 33036 30.31303095817566 0.5722160339355469 718.5728149414062 0.31507551670074463 867.2587890625 0.3788430690765381 0.84792143 0.3840555250644684 True -12 35789 30.275094747543335 0.5708198547363281 716.4471435546875 0.3390522003173828 866.1354370117188 0.3772776424884796 0.850329 0.36238279938697815 True -13 38542 30.334850072860718 0.5662379264831543 710.4860229492188 0.4396495819091797 863.552001953125 0.38017839193344116 0.857477 0.3318692445755005 True -14 41295 30.35592746734619 0.5566973686218262 839.5690307617188 0.4381566643714905 860.0628051757812 0.382394015789032 0.8619963 0.3093487322330475 True -15 44048 30.244011640548706 0.5662834644317627 756.9790649414062 0.2430194467306137 858.7754516601562 0.3831881284713745 0.8670316 0.29201844334602356 True -16 46801 29.723198890686035 0.5606305599212646 686.2975463867188 0.260364830493927 856.7965087890625 0.3841354548931122 0.86821485 0.2793581187725067 True -17 49554 29.7029128074646 0.5505063533782959 713.852294921875 0.18058137595653534 855.593505859375 0.38590750098228455 0.87065 0.27177664637565613 True -18 52307 29.7516667842865 0.5743415355682373 810.428466796875 0.21338914334774017 858.4308471679688 0.38261717557907104 0.87047523 0.2708146274089813 False -19 55060 29.754748582839966 0.5531997680664062 888.3304443359375 0.15281563997268677 858.0325317382812 0.38335439562797546 0.87001985 0.27175018191337585 False diff --git a/ENCSR713KNQ/cherimoya.fold_0.performance.tsv b/ENCSR713KNQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f50796a93895b0af178fd6c7bfddd56b4603e165..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -855.593505859375 0.39700624346733093 0.38590747117996216 0.15822674334049225 0.8706499934196472 0.8362917304039001 0.27177664637565613 \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_1.evaluate.json b/ENCSR713KNQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 58c3bbfdc13b9422c5a08a9eb0a3fab57e1703fa..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF678ODJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_1.fit.json b/ENCSR713KNQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 3b9bf0ec626a00fa3fecd040d89d04980236e031..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF678ODJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_1.log b/ENCSR713KNQ/cherimoya.fold_1.log deleted file mode 100644 index 69d6bf8a8695cfcf643600d446c8a023ab4ede30..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2698 34.6159303188324 4.4127891063690186 763.643798828125 0.7116611003875732 1275.3570556640625 0.2794167101383209 0.70472276 6.458693981170654 True -1 5396 29.641374588012695 0.7555766105651855 857.5665283203125 0.5136722326278687 1118.0045166015625 0.3587796986103058 0.78327876 2.2073545455932617 True -2 8094 29.6672945022583 0.7285401821136475 664.6139526367188 0.28097814321517944 1088.546630859375 0.37121012806892395 0.80408907 1.078923225402832 True -3 10792 29.63015079498291 0.7254304885864258 805.6876220703125 0.47868308424949646 1071.4468994140625 0.3797867000102997 0.81422985 0.8177663683891296 True -4 13490 29.71368956565857 0.7282359600067139 805.6799926757812 0.3164622485637665 1066.317626953125 0.3829895853996277 0.8190916 0.8141914010047913 True -5 16188 29.7185115814209 2.0907227993011475 817.4580688476562 0.5167819261550903 1061.326904296875 0.3848874270915985 0.82626474 0.7988771200180054 True -6 18886 29.70979332923889 0.729992151260376 793.5311279296875 0.2999838888645172 1055.608642578125 0.387734055519104 0.8308955 0.7341751456260681 True -7 21584 29.70777988433838 0.7285540103912354 661.1375732421875 0.5213589668273926 1050.134033203125 0.3914633095264435 0.836975 0.7266352772712708 True -8 24282 29.75029158592224 19.550954580307007 598.6868896484375 0.4657796025276184 1046.150146484375 0.3926096558570862 0.8383758 0.6914846897125244 True -9 26980 31.325817346572876 0.8129334449768066 590.7916259765625 0.27046269178390503 1043.875 0.39227455854415894 0.8462211 0.6362779140472412 True -10 29678 29.673351287841797 0.7720720767974854 640.3123779296875 0.2310502976179123 1034.6380615234375 0.39969509840011597 0.851812 0.5832542181015015 True -11 32376 30.25085186958313 3.1764583587646484 748.8995361328125 0.4693029224872589 1030.2457275390625 0.4011392593383789 0.85534936 0.5566301345825195 True -12 35074 29.69080948829651 0.7447788715362549 704.831787109375 0.3321242928504944 1024.150390625 0.4043280780315399 0.866131 0.4494738280773163 True -13 37772 29.755101680755615 0.7406208515167236 757.626220703125 0.32035645842552185 1020.7449951171875 0.4059315323829651 0.87173724 0.39189451932907104 True -14 40470 29.692851305007935 0.73703932762146 800.2481689453125 0.42933231592178345 1018.65625 0.40584030747413635 0.8761734 0.3706672489643097 True -15 43168 29.728979110717773 0.7370650768280029 747.7196044921875 0.20082363486289978 1014.7697143554688 0.40825143456459045 0.8801195 0.33129796385765076 True -16 45866 29.230801820755005 0.7799692153930664 670.0178833007812 0.20435625314712524 1011.8018798828125 0.4101943373680115 0.8842485 0.3079867959022522 True -17 48564 29.214892387390137 1.1991512775421143 597.05615234375 0.25745293498039246 1013.1729125976562 0.4096861779689789 0.8858529 0.29423412680625916 True -18 51262 29.185917854309082 19.70748734474182 739.6455078125 0.19128751754760742 1011.7406616210938 0.4118104577064514 0.8859843 0.28812453150749207 True -19 53960 29.213361024856567 0.8490715026855469 802.9400634765625 0.24518004059791565 1017.1416625976562 0.4062550961971283 0.8849619 0.28714510798454285 False diff --git a/ENCSR713KNQ/cherimoya.fold_1.performance.tsv b/ENCSR713KNQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 87b252e13fa3bee118069e2ab9db4ecac7d5390d..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1011.7406616210938 0.3742750883102417 0.4118104577064514 0.18427583575248718 0.8859843015670776 0.8675687313079834 0.28812453150749207 \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_2.evaluate.json b/ENCSR713KNQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3c45ef2a1254eaf216977970fdc746080f6f47a0..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF678ODJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_2.fit.json b/ENCSR713KNQ/cherimoya.fold_2.fit.json deleted file mode 100644 index ec0dd2dab97591101ad09130a3bf46252561c6e8..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF678ODJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_2.log b/ENCSR713KNQ/cherimoya.fold_2.log deleted file mode 100644 index 691aae64a0eb24c33f7d113a96465a87c43b7d52..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 36.44086217880249 4.176890134811401 784.3428344726562 0.5542550683021545 1118.0277099609375 0.2758820354938507 0.70143676 4.723472595214844 True -1 5800 31.975993871688843 0.6228618621826172 784.1328735351562 0.36844271421432495 998.9557495117188 0.34472742676734924 0.7734091 1.8441493511199951 True -2 8700 31.91382598876953 0.5475914478302002 760.3824462890625 0.4197945296764374 974.9105834960938 0.35654217004776 0.79167414 0.877190113067627 True -3 11600 31.845242738723755 0.5474715232849121 701.6314697265625 0.3044188618659973 967.5291748046875 0.35917750000953674 0.79719216 0.8326034545898438 True -4 14500 32.613401651382446 0.544661283493042 747.5936279296875 0.36778780817985535 962.443115234375 0.3618429899215698 0.803218 0.8340844511985779 True -5 17400 31.826383590698242 0.5471556186676025 759.1578979492188 0.34957581758499146 956.6002197265625 0.3652842342853546 0.81013936 0.6393298506736755 True -6 20300 31.882694005966187 17.852206230163574 746.4017333984375 0.5254768133163452 953.1865234375 0.3670653700828552 0.815037 0.6014103293418884 True -7 23200 31.93244695663452 0.5709939002990723 762.1629638671875 0.4175655245780945 947.55419921875 0.3694576919078827 0.8188085 0.5645012259483337 True -8 26100 31.90490746498108 0.5505161285400391 675.01708984375 0.4030711352825165 942.8096313476562 0.3720262348651886 0.82784635 0.5250561833381653 True -9 29000 31.859201192855835 0.5490353107452393 770.8072509765625 0.3536030054092407 939.9544677734375 0.3729930520057678 0.83439946 0.48725301027297974 True -10 31900 31.813508987426758 0.5385289192199707 797.631591796875 0.3804754912853241 934.6590576171875 0.3769857585430145 0.8392229 0.461521178483963 True -11 34800 31.825750827789307 0.5484228134155273 788.996337890625 0.3605954945087433 930.428955078125 0.379116952419281 0.84373367 0.41640371084213257 True -12 37700 31.884612798690796 0.5412826538085938 782.96044921875 0.3740687370300293 926.83203125 0.38121557235717773 0.84833074 0.39796894788742065 True -13 40600 31.58447551727295 0.5441350936889648 661.5790405273438 0.33681249618530273 925.3344116210938 0.3825700283050537 0.852392 0.36090779304504395 True -14 43500 31.198684692382812 0.5380725860595703 621.9454345703125 0.2771359086036682 923.5769653320312 0.3827553689479828 0.85925204 0.3292279541492462 True -15 46400 31.201350212097168 0.5341567993164062 633.1937255859375 0.2617003321647644 921.1024169921875 0.384871244430542 0.86185426 0.31085091829299927 True -16 49300 31.21449065208435 0.5423898696899414 717.9193115234375 0.35469257831573486 917.8220825195312 0.3868558704853058 0.8635829 0.2934911549091339 True -17 52200 31.231075763702393 0.5278820991516113 715.1173095703125 0.19334815442562103 920.3082885742188 0.3847629129886627 0.8652411 0.2860257625579834 True -18 55100 31.21248435974121 0.5424699783325195 832.134521484375 0.26356440782546997 918.5333251953125 0.3868359327316284 0.86622334 0.28513336181640625 True -19 58000 31.24732780456543 0.5443100929260254 735.31298828125 0.22790133953094482 917.9381103515625 0.38698631525039673 0.8655277 0.2861763834953308 False diff --git a/ENCSR713KNQ/cherimoya.fold_2.performance.tsv b/ENCSR713KNQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 225166e7db18c921881d0bfe77ac9408aba904aa..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -918.5333251953125 0.39184918999671936 0.3868359625339508 0.16473674774169922 0.8662233352661133 0.8412829637527466 0.28513336181640625 \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_3.evaluate.json b/ENCSR713KNQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index df9dc0de9d58592f1662072ac4960d597d3f7144..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF678ODJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_3.fit.json b/ENCSR713KNQ/cherimoya.fold_3.fit.json deleted file mode 100644 index fb0e31fed186186307783632e66c07fe86304cee..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF678ODJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_3.log b/ENCSR713KNQ/cherimoya.fold_3.log deleted file mode 100644 index f6a92a93e1f6ebb4299896c046d55c5e95503abf..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 36.27395820617676 4.898979902267456 714.9937744140625 0.4794396758079529 1039.35107421875 0.2778822183609009 0.6916224 5.57239294052124 True -1 5508 30.27433204650879 0.6488549709320068 836.9097900390625 0.4713594317436218 922.1260986328125 0.3460216522216797 0.77894807 2.107428550720215 True -2 8262 30.26391100883484 0.5447704792022705 781.776123046875 0.4180588722229004 898.87255859375 0.35868531465530396 0.79742783 1.158958077430725 True -3 11016 30.2626473903656 23.64320969581604 764.134033203125 0.5377621650695801 889.0690307617188 0.3641090989112854 0.8028682 0.8082247376441956 True -4 13770 30.447705030441284 0.5527641773223877 897.8792724609375 0.4455885887145996 885.8011474609375 0.3661734163761139 0.8070754 0.8115600943565369 True -5 16524 30.261001110076904 0.5692660808563232 693.8298950195312 0.4736436605453491 881.14208984375 0.36791425943374634 0.8150221 0.6307376623153687 True -6 19278 30.227203130722046 1.4514567852020264 755.5672607421875 0.3588063418865204 874.1634521484375 0.37250185012817383 0.82342815 0.5507661700248718 True -7 22032 30.247671127319336 0.5598759651184082 653.6094970703125 0.5843372941017151 870.8043823242188 0.3743026852607727 0.828347 0.5450015068054199 True -8 24786 30.195252895355225 0.548234224319458 877.6539306640625 0.4406597912311554 865.2212524414062 0.37755343317985535 0.83100206 0.5033280253410339 True -9 27540 30.26793670654297 12.311901330947876 826.3726196289062 0.3675593137741089 864.5379028320312 0.3772733509540558 0.8384176 0.48235031962394714 True -10 30294 31.195210456848145 0.617438554763794 648.373291015625 0.34896132349967957 859.5081176757812 0.38121363520622253 0.8434401 0.4359864592552185 True -11 33048 30.38020968437195 0.5680587291717529 815.7530517578125 0.47420376539230347 857.7390747070312 0.3821484446525574 0.84490526 0.4116070568561554 True -12 35802 30.994881629943848 0.5538737773895264 839.213134765625 0.39320892095565796 853.2493896484375 0.38482603430747986 0.8516658 0.3795258402824402 True -13 38556 30.295436143875122 1.1479392051696777 615.9140625 0.4384804368019104 851.6489868164062 0.3847733736038208 0.85627466 0.3598412573337555 True -14 41310 29.73807382583618 0.547391414642334 720.2728881835938 0.2142985314130783 848.7777099609375 0.38776877522468567 0.86129355 0.3364136219024658 True -15 44064 29.76328682899475 0.5546932220458984 819.1693725585938 0.38507169485092163 846.914306640625 0.3875614404678345 0.866451 0.3193137049674988 True -16 46818 29.67125630378723 0.5587553977966309 636.2584838867188 0.18044990301132202 847.2229614257812 0.38742393255233765 0.8681942 0.30427923798561096 True -17 49572 29.746514081954956 0.5704679489135742 740.0709228515625 0.1984289586544037 847.9646606445312 0.387234091758728 0.87021315 0.293991357088089 True -18 52326 29.83345079421997 0.6827681064605713 696.385009765625 0.27175426483154297 845.4417114257812 0.39001283049583435 0.87123775 0.29083722829818726 True -19 55080 29.884506702423096 0.5647625923156738 842.2647094726562 0.24838252365589142 847.3253784179688 0.3883545994758606 0.8688391 0.2905546724796295 False diff --git a/ENCSR713KNQ/cherimoya.fold_3.performance.tsv b/ENCSR713KNQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e45455b227d01518d0761d4b4941454bb2eaaa6a..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -845.4417114257812 0.39403727650642395 0.3900127708911896 0.15791703760623932 0.8712377548217773 0.8349208235740662 0.29083722829818726 \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_4.evaluate.json b/ENCSR713KNQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f28e975a0b69f3010288c274f67d4a0dfbf02bbf..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF678ODJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_4.fit.json b/ENCSR713KNQ/cherimoya.fold_4.fit.json deleted file mode 100644 index bef292a5695782c1d4e2e5994f846b734dc4a4e0..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF678ODJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR713KNQ/cherimoya.fold_4.log b/ENCSR713KNQ/cherimoya.fold_4.log deleted file mode 100644 index c27430568bb8c751703b9f631d8da27435b687b1..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2786 35.544755935668945 3.8911545276641846 821.80126953125 0.802829921245575 1006.8118896484375 0.2715838849544525 0.68353343 5.394436836242676 True -1 5572 30.648871660232544 0.8060235977172852 668.4772338867188 0.44387561082839966 894.6787109375 0.34265467524528503 0.76365066 1.294409990310669 True -2 8358 30.61049509048462 0.5739891529083252 655.7282104492188 0.24917353689670563 874.802734375 0.35161253809928894 0.7806318 0.7886186242103577 True -3 11144 30.547760486602783 0.5791304111480713 728.962890625 0.5235785245895386 866.294677734375 0.3574259281158447 0.78710425 0.6831840872764587 True -4 13930 30.539427042007446 0.572678804397583 897.5596313476562 0.3824305534362793 859.77685546875 0.3608892858028412 0.79255486 0.68447345495224 True -5 16716 30.54390811920166 0.6747946739196777 585.257568359375 0.4537610113620758 855.9804077148438 0.3637580871582031 0.7994046 0.5822616219520569 True -6 19502 30.529813528060913 0.579932689666748 689.1102905273438 0.48423153162002563 856.257080078125 0.362138956785202 0.7992431 0.5832527875900269 False -7 22288 30.55153226852417 0.5844841003417969 884.0426635742188 0.45977240800857544 849.494384765625 0.3681028485298157 0.8109059 0.5425428748130798 True -8 25074 30.551456212997437 0.5845162868499756 827.4876708984375 0.28172922134399414 852.494873046875 0.36454612016677856 0.8079032 0.702075719833374 False -9 27860 30.826671838760376 8.485228061676025 654.7161254882812 0.38813602924346924 843.5618896484375 0.3723020553588867 0.8214923 0.5514495968818665 True -10 30646 30.672218799591064 0.6217873096466064 835.9454956054688 0.2859451174736023 839.9668579101562 0.37390100955963135 0.8290965 0.4819807708263397 True -11 33432 30.547966480255127 0.6033680438995361 552.77001953125 0.24184785783290863 836.0131225585938 0.3767584264278412 0.8337616 0.4439105689525604 True -12 36218 30.546427965164185 0.6557202339172363 745.4877319335938 0.2451559454202652 837.2000122070312 0.3747832477092743 0.8386198 0.41798558831214905 True -13 39004 30.577322483062744 1.373206377029419 684.439453125 0.5024440288543701 831.572021484375 0.37920865416526794 0.8469792 0.3623269498348236 True -14 41790 30.08118748664856 0.6492960453033447 641.6953125 0.2069062888622284 830.3062744140625 0.3800541162490845 0.8521364 0.3272700309753418 True -15 44576 29.95712447166443 0.596482515335083 683.9422607421875 0.2676003873348236 827.1756591796875 0.3830820620059967 0.85723454 0.3085269629955292 True -16 47362 30.03138256072998 0.6232752799987793 679.0834350585938 0.3465383052825928 828.1528930664062 0.38202038407325745 0.8595417 0.2884729206562042 True -17 50148 30.057371854782104 0.5921428203582764 709.8736572265625 0.22171255946159363 826.9432373046875 0.3842432498931885 0.8626561 0.2748030424118042 True -18 52934 30.045706033706665 0.5719459056854248 761.9765625 0.19058245420455933 827.727783203125 0.3822803199291229 0.86319786 0.2704332172870636 True -19 55720 30.022798776626587 0.5957541465759277 788.4730224609375 0.2496827095746994 827.0787353515625 0.3836231231689453 0.86364996 0.2708752453327179 True diff --git a/ENCSR713KNQ/cherimoya.fold_4.performance.tsv b/ENCSR713KNQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d4f236c1002d80e6787d11b90ec9406955e1bedc..0000000000000000000000000000000000000000 --- a/ENCSR713KNQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -827.0787353515625 0.3997056782245636 0.3836231231689453 0.15526311099529266 0.8636499643325806 0.8208930492401123 0.2708752453327179 \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_0.evaluate.json b/ENCSR714DIF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a4f52f539059bb1c27bba64ab1747dc81467d53f..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737KEW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_0.fit.json b/ENCSR714DIF/cherimoya.fold_0.fit.json deleted file mode 100644 index e8a7e99b30695db6d9d29a07c54ebc9efada56b3..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF737KEW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_0.log b/ENCSR714DIF/cherimoya.fold_0.log deleted file mode 100644 index 84f5f409416a82f11317428021d6d77e3d05014e..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2722 34.76310753822327 3.7990779876708984 813.1403198242188 0.9314019680023193 1229.6395263671875 0.3142907917499542 0.55613476 9.442217826843262 True -1 5444 30.342443704605103 0.7492766380310059 986.1956787109375 0.9984015822410583 1039.162109375 0.47351038455963135 0.6169125 3.2270913124084473 True -2 8166 30.352434635162354 0.6449644565582275 863.4895629882812 1.006084680557251 1016.5796508789062 0.4889838695526123 0.63191265 1.3924087285995483 True -3 10888 30.497236490249634 0.9774389266967773 794.8738403320312 0.9544546604156494 1004.9490356445312 0.4961671829223633 0.6428721 1.0489412546157837 True -4 13610 30.392178297042847 0.9586865901947021 781.1136474609375 0.6635850071907043 997.4850463867188 0.5000134110450745 0.6481069 0.9115869402885437 True -5 16332 30.365933418273926 0.6123135089874268 683.93505859375 0.7329808473587036 989.0028076171875 0.5069753527641296 0.6474158 0.8924241065979004 False -6 19054 30.331229209899902 0.9050168991088867 708.8955688476562 0.7287272214889526 982.203857421875 0.5138526558876038 0.6437816 0.8926916718482971 False -7 21776 30.355380058288574 0.5898020267486572 797.3547973632812 0.6534604430198669 980.1421508789062 0.5140278339385986 0.6511552 0.7910171747207642 True -8 24498 30.342206239700317 2.34236216545105 812.8717041015625 0.8215300440788269 969.4631958007812 0.5243224501609802 0.66396785 0.7035359740257263 True -9 27220 29.83783483505249 0.6116645336151123 851.9884643554688 0.657821536064148 964.4699096679688 0.5293054580688477 0.66540015 0.6694769859313965 True -10 29942 29.76490807533264 0.6035025119781494 790.8228149414062 0.4267715811729431 961.538330078125 0.5308645963668823 0.6703503 0.6143165826797485 True -11 32664 29.746363878250122 0.5725908279418945 761.6974487304688 0.5544675588607788 957.9369506835938 0.5340219736099243 0.6877021 0.5615391135215759 True -12 35386 29.729084968566895 0.5925467014312744 815.4884033203125 0.42272597551345825 953.16748046875 0.5383086800575256 0.70097995 0.5273780822753906 True -13 38108 29.65210795402527 0.6254901885986328 691.6619262695312 0.5009418725967407 950.7071533203125 0.5396788120269775 0.71102136 0.4879491329193115 True -14 40830 29.641517400741577 0.5636072158813477 755.408935546875 0.3266405761241913 945.1946411132812 0.5436443090438843 0.72316015 0.46321383118629456 True -15 43552 29.654651165008545 0.568917989730835 676.9969482421875 0.3117201030254364 943.3816528320312 0.5446686148643494 0.7356247 0.4232235252857208 True -16 46274 29.66720700263977 0.5809352397918701 727.0202026367188 0.3131650686264038 943.0623779296875 0.5428849458694458 0.7438994 0.4001292288303375 True -17 48996 29.649078607559204 0.603541374206543 737.1315307617188 0.24282166361808777 944.3346557617188 0.5415646433830261 0.74864423 0.38666483759880066 True -18 51718 29.760308027267456 0.5727660655975342 613.0965576171875 0.31257960200309753 943.5084838867188 0.5421479940414429 0.75132835 0.38088247179985046 True -19 54440 29.75775146484375 0.586728572845459 750.6160278320312 0.3319815397262573 941.769775390625 0.5446926951408386 0.7505306 0.3797014057636261 False diff --git a/ENCSR714DIF/cherimoya.fold_0.performance.tsv b/ENCSR714DIF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index dd2a7565db0bdabd4f2e3e1c490d2234e2b7be77..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -943.5084838867188 0.27146580815315247 0.5421480536460876 0.2664528489112854 0.7513283491134644 0.7145641446113586 0.38088247179985046 \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_1.evaluate.json b/ENCSR714DIF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9bffa5109da2ad759f48e7a4facb0d7bb2fe0c20..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737KEW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_1.fit.json b/ENCSR714DIF/cherimoya.fold_1.fit.json deleted file mode 100644 index c4e08c8945e534742f657bdc97c5b47abd0a81ff..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF737KEW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_1.log b/ENCSR714DIF/cherimoya.fold_1.log deleted file mode 100644 index b6cf3d40640276022a90c6c1e4b21314cfbcee29..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 35.229106187820435 4.13334321975708 889.253173828125 1.1826846599578857 1398.439453125 0.32026222348213196 0.5914519 7.153181076049805 True -1 5462 30.500780820846558 0.7818336486816406 819.432373046875 1.0873138904571533 1170.0048828125 0.4791586697101593 0.6455426 4.21290397644043 True -2 8193 30.42688751220703 0.6958794593811035 689.8225708007812 0.6902095079421997 1145.455810546875 0.4904564321041107 0.64307004 2.1418471336364746 False -3 10924 30.378795623779297 1.411759853363037 736.1322021484375 0.755038857460022 1125.862548828125 0.5045688152313232 0.65499383 1.5976366996765137 True -4 13655 30.440966606140137 22.257248401641846 851.9693603515625 0.8060644268989563 1117.096923828125 0.5124228596687317 0.66102546 1.4832849502563477 True -5 16386 30.45746922492981 0.7013959884643555 975.9363403320312 0.7930371165275574 1110.1944580078125 0.514215886592865 0.66544366 1.282932996749878 True -6 19117 30.409733295440674 0.7032217979431152 883.978759765625 0.5675874948501587 1103.2755126953125 0.5201813578605652 0.6713481 1.129815936088562 True -7 21848 30.487057209014893 0.6908221244812012 820.1826171875 0.6405824422836304 1095.8851318359375 0.5246443152427673 0.6823764 0.9305037260055542 True -8 24579 29.764241933822632 0.6899702548980713 706.8594970703125 0.7349363565444946 1089.3154296875 0.5285776257514954 0.68695134 0.786177933216095 True -9 27310 29.769941091537476 1.1227161884307861 773.0950927734375 0.590076208114624 1086.214111328125 0.5298159718513489 0.68929654 0.7317420244216919 True -10 30041 29.842299699783325 0.6868915557861328 853.3618774414062 0.7556295990943909 1076.90087890625 0.5374354720115662 0.70444906 0.6472997665405273 True -11 32772 29.789164304733276 0.69999098777771 757.8023681640625 0.869191586971283 1071.69873046875 0.5413188338279724 0.70793813 0.6226053237915039 True -12 35503 29.774101972579956 1.7650108337402344 858.099365234375 0.5347040295600891 1066.7584228515625 0.5429109334945679 0.7215267 0.5844563245773315 True -13 38234 29.850512742996216 0.677623987197876 726.0003662109375 0.5138526558876038 1063.760986328125 0.5444786548614502 0.7358127 0.514997661113739 True -14 40965 29.759027242660522 0.6784212589263916 785.3316650390625 0.30361998081207275 1056.5595703125 0.5496737360954285 0.7461329 0.4807836711406708 True -15 43696 29.79755711555481 0.6806247234344482 656.4442138671875 0.43482011556625366 1052.1829833984375 0.5533851385116577 0.7566955 0.45412495732307434 True -16 46427 29.82704210281372 0.6960632801055908 789.6325073242188 0.361926794052124 1049.5831298828125 0.5537310838699341 0.7645979 0.42439141869544983 True -17 49158 29.771684408187866 1.2689623832702637 822.1119384765625 0.4266607165336609 1049.0965576171875 0.5537979602813721 0.7717812 0.40833476185798645 True -18 51889 29.98085927963257 0.6869652271270752 681.2318115234375 0.41281411051750183 1051.6195068359375 0.5509243607521057 0.7724643 0.40073445439338684 True -19 54620 29.812115907669067 0.6887028217315674 728.211669921875 0.2796388864517212 1050.25341796875 0.5521224141120911 0.77376914 0.3986559510231018 True diff --git a/ENCSR714DIF/cherimoya.fold_1.performance.tsv b/ENCSR714DIF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6da15b553cbf1efd317c24c17b188a8e9b58d484..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1050.25341796875 0.26008543372154236 0.5521223545074463 0.286149799823761 0.7737691402435303 0.750239908695221 0.3986559510231018 \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_2.evaluate.json b/ENCSR714DIF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6236c0c72ed079066120af4ce80111aab69db6db..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737KEW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_2.fit.json b/ENCSR714DIF/cherimoya.fold_2.fit.json deleted file mode 100644 index 3d880a345a9f388d1f87b10efcb0f8d6c5608474..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF737KEW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_2.log b/ENCSR714DIF/cherimoya.fold_2.log deleted file mode 100644 index 9dd84d81f74940591f7263d3f7c4a60bd7255680..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2859 36.36524176597595 4.090591192245483 790.0026245117188 0.5579746961593628 1256.060546875 0.32104843854904175 0.5639715 8.086976051330566 True -1 5718 31.866517066955566 0.9868566989898682 734.5015869140625 0.7886101007461548 1051.2747802734375 0.4793603718280792 0.6015368 3.4643242359161377 True -2 8577 31.901714324951172 0.5692911148071289 782.7949829101562 0.8160640597343445 1039.2020263671875 0.48531556129455566 0.6173755 1.6820919513702393 True -3 11436 31.886184453964233 0.6005606651306152 718.7842407226562 0.6589858531951904 1022.6831665039062 0.4965277314186096 0.64370304 1.1779389381408691 True -4 14295 31.803006172180176 0.5589642524719238 845.3458251953125 0.6129286289215088 1013.561279296875 0.50386643409729 0.6556099 0.9983104467391968 True -5 17154 31.807066917419434 0.5613701343536377 686.9833984375 0.8319360613822937 1006.3500366210938 0.5092500448226929 0.65783453 0.9152738451957703 True -6 20013 31.543789863586426 0.5731704235076904 823.2685546875 0.44659844040870667 1001.8491821289062 0.5123634934425354 0.6548899 0.7559667825698853 False -7 22872 31.218656301498413 0.5444788932800293 839.0372314453125 0.9242704510688782 996.243896484375 0.5193172693252563 0.65647596 0.7791018486022949 False -8 25731 31.169013500213623 0.5419125556945801 1034.012939453125 0.5448982119560242 991.6744384765625 0.5226607322692871 0.6598231 0.7027978301048279 True -9 28590 31.15066170692444 0.5488326549530029 654.9830932617188 0.5871772766113281 989.6469116210938 0.5220947861671448 0.66851526 0.6711234450340271 True -10 31449 31.311203479766846 0.5339534282684326 892.1055908203125 0.6710293889045715 980.8052368164062 0.5312222838401794 0.67602986 0.6263933777809143 True -11 34308 31.242997646331787 0.5464997291564941 860.7509765625 0.7301533818244934 976.2989501953125 0.5326776504516602 0.6837615 0.5699341893196106 True -12 37167 31.226289987564087 0.5418260097503662 753.65576171875 0.47661423683166504 972.6361083984375 0.5360651612281799 0.6972737 0.5340298414230347 True -13 40026 31.280677318572998 0.5372037887573242 736.0485229492188 0.46291953325271606 967.9278564453125 0.5382303595542908 0.7048388 0.514131486415863 True -14 42885 31.21496820449829 0.5449776649475098 859.2228393554688 0.45501309633255005 962.5807495117188 0.5426033735275269 0.7204115 0.46724700927734375 True -15 45744 31.167694568634033 0.5381131172180176 980.2510986328125 0.48626917600631714 963.332763671875 0.5407587885856628 0.7303322 0.4408728778362274 True -16 48603 31.184386730194092 0.5432744026184082 874.637939453125 0.42337459325790405 960.2958374023438 0.5423470735549927 0.736479 0.42394018173217773 True -17 51462 31.673985242843628 21.42221212387085 693.7661743164062 0.22298529744148254 959.57958984375 0.5422051548957825 0.7429965 0.4100845456123352 True -18 54321 31.29959487915039 0.5505936145782471 796.9900512695312 0.4973171353340149 957.130859375 0.5461633801460266 0.7442265 0.40903404355049133 True -19 57180 31.234418630599976 0.5826842784881592 853.73681640625 0.38054558634757996 957.5130004882812 0.5454336404800415 0.745797 0.40803325176239014 True diff --git a/ENCSR714DIF/cherimoya.fold_2.performance.tsv b/ENCSR714DIF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b507ce7c9438677ffb5ec66df0a7dcd610504c8b..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -957.5130004882812 0.2711479365825653 0.545433521270752 0.26814398169517517 0.7457969784736633 0.7108638882637024 0.40803325176239014 \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_3.evaluate.json b/ENCSR714DIF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0146c20a80d6c04e96de393da9db337e3d111aba..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737KEW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_3.fit.json b/ENCSR714DIF/cherimoya.fold_3.fit.json deleted file mode 100644 index 0c0b8d089e36d30603f535dda18a903f7482260b..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF737KEW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_3.log b/ENCSR714DIF/cherimoya.fold_3.log deleted file mode 100644 index 0b248d8fb4366a8500836a1bff9cba333034d107..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2784 35.856208086013794 5.3167948722839355 819.9059448242188 0.8720338344573975 1274.3262939453125 0.32473376393318176 0.5782813 8.28113079071045 True -1 5568 31.06304907798767 0.5714826583862305 611.1243896484375 1.011436939239502 1086.48876953125 0.4731723368167877 0.60116696 2.6421401500701904 True -2 8352 31.019883394241333 0.5695457458496094 751.721923828125 1.0968492031097412 1068.61181640625 0.4834749102592468 0.6272292 1.1626468896865845 True -3 11136 30.38747787475586 0.554424524307251 759.930908203125 0.46052202582359314 1056.2352294921875 0.49315157532691956 0.6441379 0.9336569905281067 True -4 13920 30.343246459960938 0.5405330657958984 818.7777099609375 0.7348182201385498 1049.84814453125 0.4986133873462677 0.63918906 0.8256630897521973 False -5 16704 30.33993434906006 0.5570495128631592 731.8032836914062 0.7250843048095703 1037.7373046875 0.5085535645484924 0.6493979 0.805114209651947 True -6 19488 30.86346745491028 0.553433895111084 846.627685546875 0.5389731526374817 1034.1090087890625 0.5109405517578125 0.6498496 0.7081387042999268 True -7 22272 30.407395839691162 0.5586447715759277 728.6544189453125 0.778195321559906 1026.5880126953125 0.5177715420722961 0.66186947 0.6864408254623413 True -8 25056 30.43332290649414 0.5522520542144775 786.845703125 0.7740359306335449 1026.867919921875 0.5160645842552185 0.66914254 0.6608381271362305 True -9 27840 30.447917461395264 0.539604902267456 736.0830078125 0.6510556936264038 1017.9541625976562 0.5255969762802124 0.67346156 0.592612624168396 True -10 30624 30.437524557113647 1.1594860553741455 811.508544921875 0.47682565450668335 1013.8068237304688 0.5266351103782654 0.6773495 0.5620867013931274 True -11 33408 30.45860195159912 0.579775333404541 813.2763671875 0.5268268585205078 1010.8706665039062 0.5299001336097717 0.6841755 0.5612283945083618 True -12 36192 30.464404106140137 0.5533819198608398 728.9387817382812 0.5210530757904053 1003.747314453125 0.5360742807388306 0.6949336 0.5362497568130493 True -13 38976 30.452821493148804 11.788740158081055 823.3543090820312 0.33993327617645264 999.976318359375 0.5376969575881958 0.70276004 0.49667394161224365 True -14 41760 30.430424690246582 0.5572221279144287 685.2271728515625 0.265861839056015 998.2067260742188 0.5377918481826782 0.72174615 0.46783971786499023 True -15 44544 30.454921007156372 0.5569024085998535 691.0291748046875 0.47301822900772095 997.8638305664062 0.5378116369247437 0.73419714 0.45413801074028015 True -16 47328 30.407482147216797 1.143951654434204 768.4910888671875 0.38775983452796936 992.2583618164062 0.5426862835884094 0.7437339 0.4332134425640106 True -17 50112 30.429197788238525 0.5515336990356445 668.8473510742188 0.30137208104133606 991.8790283203125 0.543488085269928 0.74732095 0.4221987724304199 True -18 52896 30.460042476654053 0.5542490482330322 765.4915161132812 0.4455621838569641 991.9408569335938 0.5429893732070923 0.7523524 0.4107617139816284 True -19 55680 30.450764894485474 2.2035465240478516 776.2305908203125 0.2861191928386688 990.969482421875 0.5441398024559021 0.75212514 0.4063991606235504 False diff --git a/ENCSR714DIF/cherimoya.fold_3.performance.tsv b/ENCSR714DIF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bcd6b448c12c2a5acf4ab31ffb25fc94926d8ee0..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -991.9408569335938 0.2695864140987396 0.5429894328117371 0.26662519574165344 0.7523524165153503 0.7189126014709473 0.4107617139816284 \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_4.evaluate.json b/ENCSR714DIF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fac653d83c6a0a051cc1fc44da960861723977f7..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737KEW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_4.fit.json b/ENCSR714DIF/cherimoya.fold_4.fit.json deleted file mode 100644 index 8d43ad935a3c1917d740ed57a6185c299d575a60..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF737KEW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR714DIF/cherimoya.fold_4.log b/ENCSR714DIF/cherimoya.fold_4.log deleted file mode 100644 index 86a6751be0351482fea1296bdf1a00325f110ebb..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2842 37.226990699768066 3.8222782611846924 996.776611328125 1.0539088249206543 1223.939697265625 0.3250003159046173 0.5470511 8.071663856506348 True -1 5684 31.651631832122803 1.9899678230285645 924.3090209960938 0.8141576051712036 1045.7984619140625 0.4658987522125244 0.6124485 3.005566120147705 True -2 8526 31.075693607330322 0.5802416801452637 774.9878540039062 0.8257725834846497 1020.2380981445312 0.4843239188194275 0.61074924 1.3189302682876587 False -3 11368 30.985884189605713 0.5744028091430664 857.1967163085938 0.6493749618530273 1001.9067993164062 0.4976156949996948 0.6303615 0.901264488697052 True -4 14210 31.030863285064697 0.5748739242553711 801.0675048828125 0.7383624315261841 995.1451416015625 0.501691997051239 0.6432433 0.7227551341056824 True -5 17052 31.014745950698853 0.5744342803955078 748.5938720703125 0.9174475073814392 989.5842895507812 0.5059523582458496 0.63933253 0.7494301795959473 False -6 19894 31.031813383102417 0.5678613185882568 902.70361328125 0.554602324962616 985.2123413085938 0.5085257887840271 0.6481676 0.6907666921615601 True -7 22736 30.960854053497314 0.5750210285186768 711.7537841796875 0.6287500262260437 976.789306640625 0.5186405181884766 0.65592116 0.6631162166595459 True -8 25578 31.004679203033447 0.5708012580871582 805.7861328125 0.61307293176651 973.10986328125 0.5206469893455505 0.6663099 0.623909056186676 True -9 28420 30.942930221557617 0.5668160915374756 708.5863037109375 0.6137789487838745 968.3668823242188 0.5239915251731873 0.6715809 0.527854859828949 True -10 31262 31.141358375549316 0.5922977924346924 724.3909912109375 0.31281670928001404 959.70556640625 0.5313131809234619 0.68022454 0.5078844428062439 True -11 34104 31.4107506275177 0.5662133693695068 817.72607421875 0.5602157115936279 957.57763671875 0.5330871939659119 0.6882533 0.4866425096988678 True -12 36946 30.951966285705566 0.5753779411315918 939.061279296875 0.5027334094047546 953.7740478515625 0.5357916951179504 0.69973767 0.46268925070762634 True -13 39788 31.050849676132202 0.5759844779968262 715.9532470703125 0.3648453950881958 950.4955444335938 0.5378301739692688 0.71106535 0.4357921779155731 True -14 42630 31.024707794189453 0.5726401805877686 669.44580078125 0.4381392300128937 945.677490234375 0.5418925881385803 0.71726054 0.43267032504081726 True -15 45472 30.993746042251587 0.565821647644043 697.082275390625 0.43237534165382385 946.190673828125 0.5400243401527405 0.72797406 0.4100761115550995 True -16 48314 30.969424962997437 0.5782184600830078 813.9568481445312 0.36298954486846924 945.6648559570312 0.5410082340240479 0.7360226 0.3956071436405182 True -17 51156 31.041417837142944 0.5717477798461914 800.4696044921875 0.31149667501449585 942.9007568359375 0.5435708165168762 0.74009204 0.38848668336868286 True -18 53998 30.99493932723999 0.5795834064483643 779.84912109375 0.43322616815567017 943.150634765625 0.5431995987892151 0.7440821 0.38354700803756714 True -19 56840 31.00850749015808 0.57071852684021 803.5205078125 0.2858976423740387 943.1653442382812 0.5440096855163574 0.7420839 0.3855988383293152 False diff --git a/ENCSR714DIF/cherimoya.fold_4.performance.tsv b/ENCSR714DIF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5273e9bc8cfc07cebd6d34c7ce33bd078bb4c67f..0000000000000000000000000000000000000000 --- a/ENCSR714DIF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -943.150634765625 0.27212032675743103 0.5431995987892151 0.2646287977695465 0.7440820932388306 0.7110874652862549 0.38354700803756714 \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_0.evaluate.json b/ENCSR717BBR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 14dc7b1162c2c068a83389319408b472242ffd53..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343NGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_0.fit.json b/ENCSR717BBR/cherimoya.fold_0.fit.json deleted file mode 100644 index a2de452c1142c7b7a00e6ea219d56833383ca494..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF343NGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_0.log b/ENCSR717BBR/cherimoya.fold_0.log deleted file mode 100644 index 5698ab0df5b1f16179fc084df00734a8485915f2..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 33.96009063720703 3.9511914253234863 664.7589111328125 0.5273608565330505 943.0551147460938 0.28094735741615295 0.6385042 5.862653732299805 True -1 5476 30.109270334243774 0.5758130550384521 698.2001953125 0.6677464246749878 818.4777221679688 0.3816779851913452 0.717736 2.0063211917877197 True -2 8214 29.924314498901367 0.5521705150604248 654.4923095703125 0.8530513644218445 803.5220336914062 0.38951194286346436 0.7288638 1.1177129745483398 True -3 10952 29.52048397064209 0.5521631240844727 511.21533203125 0.5952156782150269 791.2429809570312 0.3974650204181671 0.7357974 1.3891865015029907 True -4 13690 29.468292713165283 0.5654356479644775 596.644775390625 0.6192741990089417 779.9968872070312 0.406283974647522 0.7382532 0.8137152791023254 True -5 16428 29.46464443206787 2.00187087059021 689.05615234375 0.6695210933685303 775.6419067382812 0.41096603870391846 0.7437815 0.6116048097610474 True -6 19166 29.524634838104248 0.5670769214630127 695.7991333007812 0.5912283658981323 770.4492797851562 0.41534146666526794 0.74653095 0.5433567762374878 True -7 21904 29.410552501678467 0.5628039836883545 604.0545654296875 0.5423417091369629 767.9124755859375 0.41949784755706787 0.7492481 0.5427852869033813 True -8 24642 29.458488702774048 0.563645601272583 601.82568359375 0.5574989318847656 765.0689697265625 0.4213334321975708 0.7507662 0.5343748927116394 True -9 27380 29.54137086868286 0.5549111366271973 684.9155883789062 0.5283358097076416 761.5775146484375 0.4250423014163971 0.75409687 0.5317574143409729 True -10 30118 29.485159397125244 0.5549252033233643 517.7119750976562 0.3587441146373749 757.0003662109375 0.43103882670402527 0.76172376 0.4834051728248596 True -11 32856 29.49666428565979 0.5623996257781982 712.9564208984375 0.4110695421695709 753.0645751953125 0.4344404637813568 0.7647246 0.4715200960636139 True -12 35594 29.510745525360107 0.5634775161743164 543.835205078125 0.49203407764434814 748.5535888671875 0.4390956163406372 0.77452505 0.4314648509025574 True -13 38332 29.539828538894653 0.5780210494995117 734.5170288085938 0.6559504270553589 746.1978149414062 0.44103506207466125 0.78101903 0.4018600583076477 True -14 41070 29.47960591316223 0.5749430656433105 676.9534301757812 0.4048789143562317 743.1470947265625 0.44334912300109863 0.78620505 0.3965999484062195 True -15 43808 29.499103307724 0.5634326934814453 605.2869873046875 0.5132419466972351 742.2638549804688 0.44339796900749207 0.7897692 0.3861311972141266 True -16 46546 29.583563089370728 0.5639212131500244 633.3903198242188 0.3711729049682617 741.1437377929688 0.4448833465576172 0.7928768 0.3781537711620331 True -17 49284 29.4693284034729 0.8453288078308105 615.7717895507812 0.3499178886413574 741.1326293945312 0.44583263993263245 0.79646516 0.3709762990474701 True -18 52022 29.74210810661316 0.5682692527770996 632.6295776367188 0.5692545175552368 740.9939575195312 0.4452899992465973 0.7963948 0.37138405442237854 False -19 54760 29.442895650863647 0.6006793975830078 601.3372802734375 0.44078344106674194 741.37109375 0.4456118941307068 0.7945507 0.3714771866798401 False diff --git a/ENCSR717BBR/cherimoya.fold_0.performance.tsv b/ENCSR717BBR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5f5de6101b1c92a128c5bf7a176585526047262b..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -741.1326293945312 0.33867183327674866 0.44583263993263245 0.20350728929042816 0.7964651584625244 0.7240618467330933 0.3709762990474701 \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_1.evaluate.json b/ENCSR717BBR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e2dc0983aed0ed436b7e558c54c02dc5118dba7f..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343NGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_1.fit.json b/ENCSR717BBR/cherimoya.fold_1.fit.json deleted file mode 100644 index f97fe28a9296efa74f1f601d3df97b2a3f3289b6..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF343NGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_1.log b/ENCSR717BBR/cherimoya.fold_1.log deleted file mode 100644 index bc7026ca74ab90c17e06fcda64eacdd79a0e427c..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2715 33.755281925201416 3.7599544525146484 584.1414794921875 0.6949607133865356 1086.2237548828125 0.2853875756263733 0.6390832 7.253457069396973 True -1 5430 29.81059503555298 0.6781840324401855 687.4603271484375 0.8378364443778992 923.3544311523438 0.3927713930606842 0.72440195 2.2922346591949463 True -2 8145 30.062739849090576 0.6884334087371826 707.4468383789062 0.8487423062324524 901.3819580078125 0.406765341758728 0.731707 1.1668283939361572 True -3 10860 29.88647747039795 0.6851367950439453 817.8597412109375 0.829553484916687 883.6135864257812 0.41676756739616394 0.74009997 0.9535818696022034 True -4 13575 29.408838033676147 0.6633079051971436 706.812255859375 0.7144892811775208 872.7523803710938 0.42535194754600525 0.7500101 0.7553123831748962 True -5 16290 29.189972400665283 0.6738436222076416 697.4555053710938 0.7782778739929199 866.298095703125 0.43134605884552 0.75602585 0.5959323644638062 True -6 19005 29.196741104125977 0.6760334968566895 645.8504638671875 0.6220719814300537 861.72216796875 0.4344812035560608 0.76186186 0.5312910676002502 True -7 21720 29.183776140213013 0.6722602844238281 622.6596069335938 0.530820369720459 855.92578125 0.4409705102443695 0.7633128 0.5521615147590637 True -8 24435 29.192596435546875 0.6720409393310547 617.4093627929688 0.6047806739807129 854.0590209960938 0.4421458840370178 0.7658072 0.535308301448822 True -9 27150 29.196466207504272 0.671649694442749 524.978759765625 0.5668837428092957 848.802490234375 0.4464702308177948 0.77281064 0.5172260999679565 True -10 29865 29.203055143356323 0.6756675243377686 570.5826416015625 0.37739092111587524 845.6212768554688 0.4491073787212372 0.7736003 0.5097267627716064 True -11 32580 29.179195642471313 0.6693387031555176 713.158203125 0.5933572053909302 841.8168334960938 0.45087239146232605 0.78172106 0.4729170799255371 True -12 35295 29.20608925819397 0.6749060153961182 644.1390991210938 0.47143587470054626 835.9741821289062 0.4568944573402405 0.7865927 0.45783358812332153 True -13 38010 29.296942949295044 1.9238386154174805 589.024658203125 0.46490660309791565 833.8094482421875 0.457843542098999 0.7942 0.44387468695640564 True -14 40725 29.349138975143433 0.7031373977661133 709.280517578125 0.3736235201358795 829.788818359375 0.46061447262763977 0.799685 0.4238709509372711 True -15 43440 29.31956648826599 0.6909830570220947 595.08984375 0.3184845447540283 827.6087646484375 0.46265944838523865 0.8066941 0.4098438322544098 True -16 46155 29.286279678344727 0.684539794921875 599.2027587890625 0.33247628808021545 825.6275024414062 0.4636809825897217 0.810588 0.4022318422794342 True -17 48870 29.268004417419434 14.336092948913574 551.8635864257812 0.26550862193107605 826.2769775390625 0.4630471169948578 0.8125357 0.3992525339126587 True -18 51585 29.287386655807495 1.1030523777008057 515.3236083984375 0.36239421367645264 824.8148803710938 0.46526941657066345 0.81379884 0.3986250162124634 True -19 54300 29.286924600601196 0.6836268901824951 489.9149169921875 0.2919020354747772 825.983154296875 0.46379607915878296 0.81173253 0.39956408739089966 False diff --git a/ENCSR717BBR/cherimoya.fold_1.performance.tsv b/ENCSR717BBR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1cf8a5313d88f53c4a4c285bb6e0eb21bb677cb8..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -824.8148803710938 0.3236725628376007 0.46526941657066345 0.2223997563123703 0.8137988448143005 0.7636494040489197 0.3986250162124634 \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_2.evaluate.json b/ENCSR717BBR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 59474f1be154079df5848291bc87893cb30607c0..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343NGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_2.fit.json b/ENCSR717BBR/cherimoya.fold_2.fit.json deleted file mode 100644 index 04aba25ba9e3824fca59802a1daaba5d114f1cdd..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF343NGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_2.log b/ENCSR717BBR/cherimoya.fold_2.log deleted file mode 100644 index 08e17aca218e24b77468a452052147345fe39966..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2866 35.230361223220825 3.870182991027832 675.93212890625 0.6399970054626465 951.3400268554688 0.29330745339393616 0.644097 6.349416732788086 True -1 5732 31.580514192581177 0.5822136402130127 578.2128295898438 0.6125519275665283 827.1825561523438 0.3861776888370514 0.71803665 1.847165584564209 True -2 8598 31.563643217086792 0.561389684677124 683.305419921875 0.7826489210128784 809.8287353515625 0.3980769217014313 0.7230911 0.9538742303848267 True -3 11464 31.50105309486389 0.5586175918579102 693.3844604492188 0.511357307434082 801.4632568359375 0.3997783660888672 0.73478484 0.7943000793457031 True -4 14330 31.29639220237732 0.5541400909423828 580.358642578125 0.4853208661079407 787.8408813476562 0.41022875905036926 0.74868906 0.678800642490387 True -5 17196 30.898365259170532 0.5487675666809082 674.157958984375 0.8092074394226074 781.6386108398438 0.41518282890319824 0.7483137 0.6181567907333374 False -6 20062 30.87875247001648 0.5512559413909912 719.7636108398438 0.5880625247955322 775.2239379882812 0.4232943058013916 0.74987906 0.5685610771179199 True -7 22928 30.86874294281006 0.5516901016235352 573.761962890625 0.7352718114852905 772.6260986328125 0.42331230640411377 0.75109154 0.5433793663978577 True -8 25794 30.882537364959717 0.5482099056243896 453.34417724609375 0.576869010925293 768.3896484375 0.42796453833580017 0.7541428 0.5082115530967712 True -9 28660 30.902169466018677 0.547682523727417 628.4353637695312 0.4152751564979553 763.90087890625 0.43157249689102173 0.7562772 0.5055387616157532 True -10 31526 30.89291024208069 0.549013614654541 703.5211791992188 0.5875425934791565 762.449462890625 0.4337227940559387 0.76342654 0.5019588470458984 True -11 34392 30.92007541656494 0.5461475849151611 661.3081665039062 0.4354848265647888 759.9559936523438 0.43576154112815857 0.7644559 0.460382342338562 True -12 37258 30.85949397087097 0.5449845790863037 695.877685546875 0.3738895058631897 756.1859130859375 0.4390559494495392 0.7732588 0.4345449209213257 True -13 40124 30.94886541366577 0.5537092685699463 604.4769287109375 0.46553492546081543 751.337890625 0.44447392225265503 0.78190994 0.4178304672241211 True -14 42990 30.886472940444946 0.5531585216522217 440.70050048828125 0.38071975111961365 749.5008544921875 0.4459684193134308 0.7859757 0.40623772144317627 True -15 45856 30.87789797782898 0.5507280826568604 542.538818359375 0.3421277403831482 747.3374633789062 0.4476848542690277 0.79223925 0.38990339636802673 True -16 48722 30.920900106430054 0.5907113552093506 568.61962890625 0.34370356798171997 747.2161865234375 0.44844329357147217 0.7953358 0.3846066892147064 True -17 51588 30.91676378250122 1.1638555526733398 453.4072265625 0.5002045035362244 747.5311279296875 0.4480958878993988 0.79574394 0.38371387124061584 True -18 54454 30.96825933456421 0.5805065631866455 674.224365234375 0.31746387481689453 746.6237182617188 0.4494965970516205 0.7956537 0.3823758661746979 False -19 57320 30.88995909690857 0.5514190196990967 639.4426879882812 0.29421231150627136 747.42578125 0.44801273941993713 0.7950744 0.38564354181289673 False diff --git a/ENCSR717BBR/cherimoya.fold_2.performance.tsv b/ENCSR717BBR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3f6f334dce678abe9600f7807b8ffd2673b91057..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -747.5311279296875 0.33701977133750916 0.4480958580970764 0.2048875093460083 0.7957439422607422 0.7287359833717346 0.38371387124061584 \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_3.evaluate.json b/ENCSR717BBR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d302621c044fedf70e4af0e26b19240b5affdc4d..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343NGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_3.fit.json b/ENCSR717BBR/cherimoya.fold_3.fit.json deleted file mode 100644 index 1d35ffc1ff58b8d4f1cb2a4f31cfaae0fa4f2f8a..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF343NGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_3.log b/ENCSR717BBR/cherimoya.fold_3.log deleted file mode 100644 index 3438efbda4aeb63963fd48ac929cc57679a3cc0f..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2766 34.4595148563385 3.5611796379089355 660.038330078125 0.7361319661140442 937.3297119140625 0.29559338092803955 0.6627047 6.537014484405518 True -1 5532 30.394471168518066 0.5458948612213135 600.9883422851562 0.8223776817321777 829.9417724609375 0.375405490398407 0.7257287 2.2262563705444336 True -2 8298 30.412879705429077 0.6137747764587402 729.5232543945312 0.6269708871841431 811.85009765625 0.38737952709198 0.731373 0.9327090978622437 True -3 11064 30.19005250930786 0.5212628841400146 584.8316650390625 0.6113549470901489 796.2100219726562 0.39861243963241577 0.74339753 0.8616990447044373 True -4 13830 29.82740831375122 0.5302152633666992 713.9259643554688 0.5324525237083435 781.8051147460938 0.4107564091682434 0.7520916 0.9491602182388306 True -5 16596 29.819907188415527 0.5437295436859131 610.4988403320312 0.7583265900611877 775.9700317382812 0.41799017786979675 0.7513814 0.7417828440666199 False -6 19362 29.806998014450073 0.5218665599822998 723.5161743164062 0.6073320508003235 770.58056640625 0.4233332574367523 0.75372887 0.6958084106445312 True -7 22128 29.867761373519897 0.5411262512207031 701.6552124023438 0.5914390087127686 764.8353271484375 0.42870447039604187 0.7573372 0.6444828510284424 True -8 24894 29.88871693611145 0.5417733192443848 631.6073608398438 0.5323174595832825 763.05712890625 0.42991122603416443 0.7622464 0.6367241144180298 True -9 27660 29.87126922607422 0.536613941192627 681.1148681640625 0.5977054238319397 759.5391235351562 0.4330044090747833 0.76668286 0.610396683216095 True -10 30426 29.886404991149902 0.5340392589569092 512.2326049804688 0.4435153901576996 755.890380859375 0.43553879857063293 0.77083236 0.5647217631340027 True -11 33192 29.91024613380432 0.5346581935882568 583.01611328125 0.5312454700469971 752.1809692382812 0.43900272250175476 0.7768882 0.5207501649856567 True -12 35958 29.8915274143219 0.5411717891693115 701.8762817382812 0.5696691870689392 749.44384765625 0.44144970178604126 0.78149205 0.4967673122882843 True -13 38724 30.19091296195984 0.5473270416259766 569.9327392578125 0.4225439429283142 744.7271728515625 0.4439665675163269 0.78856045 0.4594610631465912 True -14 41490 29.931141138076782 0.5308637619018555 588.8261108398438 0.3826467990875244 742.362060546875 0.44613122940063477 0.7918251 0.43076103925704956 True -15 44256 30.01488494873047 0.5388469696044922 610.6537475585938 0.41019362211227417 740.145263671875 0.44760605692863464 0.7978669 0.409538596868515 True -16 47022 30.03877353668213 1.5940601825714111 581.8779296875 0.7669573426246643 738.6199951171875 0.44886964559555054 0.80431366 0.3924797475337982 True -17 49788 30.067155122756958 0.5293772220611572 644.3250122070312 0.28723984956741333 738.485107421875 0.44929319620132446 0.80536455 0.38898980617523193 True -18 52554 29.984266757965088 0.5330252647399902 673.8389892578125 0.29999858140945435 738.8253173828125 0.4491262137889862 0.8037707 0.39014577865600586 False -19 55320 30.001301288604736 0.5484695434570312 721.3491821289062 0.419893741607666 739.7045288085938 0.44785982370376587 0.8049993 0.3890146315097809 False diff --git a/ENCSR717BBR/cherimoya.fold_3.performance.tsv b/ENCSR717BBR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 91f15b56a622bc06ff7523c0c3c7847846e9746f..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -738.485107421875 0.3376719355583191 0.44929319620132446 0.20585890114307404 0.8053645491600037 0.7387845516204834 0.38898980617523193 \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_4.evaluate.json b/ENCSR717BBR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9200dd9509701add20322a397d62946f3622e8d2..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF343NGK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_4.fit.json b/ENCSR717BBR/cherimoya.fold_4.fit.json deleted file mode 100644 index c278b17bb549536dffaf69c1edb5a06e1d1babb2..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF343NGK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR717BBR/cherimoya.fold_4.log b/ENCSR717BBR/cherimoya.fold_4.log deleted file mode 100644 index 3207853dc64a750a49574d8346e8ec1ae1000751..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2837 35.23760533332825 2.3138785362243652 991.6041870117188 0.9116957187652588 903.087646484375 0.2935373783111572 0.6369882 6.153390407562256 True -1 5674 31.237292766571045 0.546278715133667 538.2875366210938 0.6637204885482788 792.2317504882812 0.3804522454738617 0.69845665 2.000370502471924 True -2 8511 31.27492928504944 0.5142180919647217 656.379150390625 0.85236656665802 778.4609375 0.38934949040412903 0.7009746 1.0878958702087402 True -3 11348 31.01802968978882 0.5934360027313232 772.2073974609375 0.7026969790458679 768.097412109375 0.3968336284160614 0.71480435 0.960831344127655 True -4 14185 30.59157085418701 0.5104961395263672 597.7344970703125 0.5954214930534363 759.2198486328125 0.40473106503486633 0.71993506 0.7691433429718018 True -5 17022 30.615676403045654 0.5174250602722168 641.5477294921875 0.588487446308136 753.0520629882812 0.4118979275226593 0.72322977 0.6314489841461182 True -6 19859 30.636521816253662 0.5023798942565918 761.3665771484375 0.5563721060752869 749.7757568359375 0.4147144556045532 0.72933215 0.5944858193397522 True -7 22696 30.590522289276123 0.5135736465454102 604.7816162109375 0.4346768856048584 747.9057006835938 0.4157593548297882 0.7327681 0.5357886552810669 True -8 25533 30.55951237678528 0.5107486248016357 584.8004150390625 0.5466750860214233 744.0362548828125 0.4204898774623871 0.7402107 0.533847987651825 True -9 28370 30.610903024673462 0.5191638469696045 672.8482055664062 0.7032190561294556 740.2133178710938 0.42486003041267395 0.7476896 0.4915083944797516 True -10 31207 30.676477670669556 0.52362060546875 596.5025634765625 0.40500205755233765 734.9341430664062 0.4309306740760803 0.753956 0.4860838055610657 True -11 34044 30.711018562316895 14.604662895202637 559.548828125 0.6505129337310791 733.6663818359375 0.4320526719093323 0.7600782 0.4641283452510834 True -12 36881 30.833914041519165 1.6797525882720947 578.8600463867188 0.5729308128356934 730.436279296875 0.43455737829208374 0.76715046 0.43771040439605713 True -13 39718 30.729729652404785 0.6836097240447998 611.2664184570312 0.5925005674362183 726.6548461914062 0.4386458694934845 0.77206445 0.40404871106147766 True -14 42555 30.757288694381714 16.244352102279663 645.927490234375 0.394037127494812 725.6983032226562 0.43945610523223877 0.7774636 0.3950112760066986 True -15 45392 30.796918153762817 0.9211959838867188 461.24945068359375 0.4231037497520447 722.7951049804688 0.44315454363822937 0.7836367 0.3773808479309082 True -16 48229 30.7837872505188 1.3223628997802734 580.4788208007812 0.4397786855697632 722.4843139648438 0.44273728132247925 0.78761846 0.3737798035144806 True -17 51066 30.72167181968689 0.5355954170227051 568.44677734375 0.405254065990448 723.2169189453125 0.44243916869163513 0.7898669 0.3704482614994049 True -18 53903 30.741771697998047 0.5099263191223145 456.24176025390625 0.40797534584999084 722.1021728515625 0.4435035288333893 0.79107004 0.3669179379940033 True -19 56740 30.693307638168335 0.5113728046417236 522.8673095703125 0.27138185501098633 722.1473999023438 0.4438060522079468 0.79043996 0.36719977855682373 False diff --git a/ENCSR717BBR/cherimoya.fold_4.performance.tsv b/ENCSR717BBR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 399fadc21f8d3497c7ab565f99074918584fda85..0000000000000000000000000000000000000000 --- a/ENCSR717BBR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -722.1021728515625 0.3403221070766449 0.4435035288333893 0.2015470415353775 0.7910700440406799 0.7200466394424438 0.3669179379940033 \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_0.evaluate.json b/ENCSR718AAB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8ac2f1ef92d3df6e1f9d32ffcd5a55ea19f8905a..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF922MLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_0.fit.json b/ENCSR718AAB/cherimoya.fold_0.fit.json deleted file mode 100644 index a1daa424669b20a7afe609390008f33b4ad0948c..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF922MLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_0.log b/ENCSR718AAB/cherimoya.fold_0.log deleted file mode 100644 index f2e1dcfd02b3934fed26b3cd444c6fdc9dda5086..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1542 20.833077669143677 3.248549699783325 152.76165771484375 0.7296494841575623 223.08506774902344 0.09440674632787704 0.55204916 7.420083522796631 True -1 3084 17.034159660339355 0.3116786479949951 179.11923217773438 0.5319826006889343 215.86158752441406 0.14156107604503632 0.64474833 2.5537707805633545 True -2 4626 17.002872705459595 0.30082154273986816 182.9581756591797 0.7742031812667847 206.83245849609375 0.18454019725322723 0.70825493 1.3859097957611084 True -3 6168 17.043365001678467 0.31218481063842773 146.8784942626953 0.3894484043121338 203.2971649169922 0.19585566222667694 0.7521683 0.6953569054603577 True -4 7710 16.98505663871765 0.29992079734802246 168.25250244140625 0.46429044008255005 202.19883728027344 0.19698067009449005 0.7638308 0.5093181729316711 True -5 9252 16.930226802825928 0.30058717727661133 188.75277709960938 0.7035410404205322 201.33187866210938 0.2002057582139969 0.7716633 0.4492119550704956 True -6 10794 16.9406795501709 0.29827189445495605 181.8983154296875 0.5769860148429871 201.02098083496094 0.20106101036071777 0.77609736 0.4349038004875183 True -7 12336 16.973307609558105 0.29952335357666016 176.76600646972656 0.590855598449707 200.57455444335938 0.20294980704784393 0.78078324 0.431033730506897 True -8 13878 16.914846658706665 0.31432294845581055 193.54071044921875 0.6375514268875122 200.06869506835938 0.2055727243423462 0.78341377 0.423514723777771 True -9 15420 17.021002769470215 0.3012831211090088 162.94989013671875 0.8022152185440063 199.54568481445312 0.20819628238677979 0.7908514 0.39009949564933777 True -10 16962 16.972726583480835 0.3001537322998047 162.4187774658203 0.47848933935165405 199.09767150878906 0.2109578400850296 0.7941293 0.36588335037231445 True -11 18504 16.957663536071777 0.30402350425720215 162.8428955078125 0.28509002923965454 198.897216796875 0.21170464158058167 0.7968989 0.3508864939212799 True -12 20046 16.937828302383423 0.301039457321167 150.74441528320312 0.648400068283081 198.42575073242188 0.2137034684419632 0.8008506 0.3414434790611267 True -13 21588 16.972814559936523 0.3006613254547119 145.18357849121094 0.3696171045303345 198.41407775878906 0.21313023567199707 0.8056397 0.33010655641555786 True -14 23130 16.988266706466675 10.01900839805603 188.57382202148438 0.37921062111854553 198.02767944335938 0.21564188599586487 0.8061708 0.332459419965744 True -15 24672 16.972553491592407 0.3037838935852051 174.39981079101562 0.22144515812397003 198.28399658203125 0.21356497704982758 0.8088466 0.3282321095466614 True -16 26214 16.956923723220825 0.2987692356109619 179.15676879882812 0.3292579650878906 198.33734130859375 0.21303720772266388 0.8108815 0.3281668722629547 True -17 27756 16.93380618095398 1.0467252731323242 141.85269165039062 0.3444240093231201 198.27944946289062 0.21367017924785614 0.8088423 0.33674272894859314 False -18 29298 16.988335847854614 0.3050706386566162 144.38735961914062 0.22982646524906158 198.54330444335938 0.21208803355693817 0.8063327 0.34793129563331604 False -19 30840 16.938610076904297 0.3003213405609131 174.96029663085938 0.42315736413002014 198.7176513671875 0.21125482022762299 0.8062106 0.35476866364479065 False diff --git a/ENCSR718AAB/cherimoya.fold_0.performance.tsv b/ENCSR718AAB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9a5c90599fc5d531b47c2a0e214ccd0cd6aa9cca..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -198.33734130859375 0.5463508367538452 0.21303722262382507 0.045086342841386795 0.810881495475769 0.7854529619216919 0.3281668722629547 \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_1.evaluate.json b/ENCSR718AAB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 48633e47733bd4c856e26d738fbf0638c4fef5c3..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF922MLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_1.fit.json b/ENCSR718AAB/cherimoya.fold_1.fit.json deleted file mode 100644 index 28e32c88aa139b041944205680adb82000ba4026..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF922MLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_1.log b/ENCSR718AAB/cherimoya.fold_1.log deleted file mode 100644 index 0522903f09fdd09529021ebc39dd4bb6c4159ff9..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1533 20.6624538898468 3.382359266281128 182.6451416015625 0.6380467414855957 272.0762023925781 0.10802841931581497 0.5031686 8.590126037597656 True -1 3066 17.030293226242065 0.46158337593078613 204.86135864257812 0.6315550804138184 262.4952087402344 0.15801255404949188 0.6348614 3.4545211791992188 True -2 4599 17.041592121124268 0.4532935619354248 167.04769897460938 0.7728585004806519 251.2931671142578 0.2039819061756134 0.72728395 1.4398075342178345 True -3 6132 17.009991884231567 0.443361759185791 156.2103271484375 0.5916013717651367 246.52003479003906 0.2162446677684784 0.7572505 0.8297724723815918 True -4 7665 17.014842987060547 0.4326295852661133 199.35809326171875 0.5371396541595459 244.96978759765625 0.21939204633235931 0.7712923 0.6365616917610168 True -5 9198 16.95534110069275 0.4511444568634033 125.75248718261719 0.33750665187835693 243.24761962890625 0.2269124537706375 0.7808447 0.5513373017311096 True -6 10731 17.01520586013794 0.44280028343200684 215.76724243164062 0.49090999364852905 243.06272888183594 0.22616752982139587 0.78774947 0.5128805637359619 True -7 12264 16.978226900100708 0.44235920906066895 174.63226318359375 0.5516672730445862 242.52464294433594 0.22845950722694397 0.7933689 0.46031975746154785 True -8 13797 16.906446933746338 0.4401724338531494 175.016845703125 0.5207417011260986 242.04598999023438 0.22958944737911224 0.796088 0.4263075590133667 True -9 15330 16.642274141311646 0.42998242378234863 157.36642456054688 0.37819480895996094 241.48667907714844 0.2321442812681198 0.8016847 0.40048426389694214 True -10 16863 16.654067039489746 0.4368410110473633 170.1018829345703 0.5082822442054749 240.9456024169922 0.23509250581264496 0.80583036 0.393195778131485 True -11 18396 16.740049362182617 19.808701038360596 158.87586975097656 0.4010886251926422 240.4322052001953 0.23719114065170288 0.80879176 0.38759559392929077 True -12 19929 16.73781967163086 0.49215197563171387 199.30235290527344 0.4512377083301544 239.91824340820312 0.23883801698684692 0.8177849 0.3735048472881317 True -13 21462 16.718596696853638 0.44690895080566406 201.531005859375 0.3986610770225525 239.6307373046875 0.23952117562294006 0.821603 0.36660146713256836 True -14 22995 16.6840341091156 0.44281697273254395 138.399658203125 0.2616654634475708 239.46263122558594 0.23950570821762085 0.8246719 0.36696943640708923 True -15 24528 16.697535276412964 2.356919527053833 148.2828826904297 0.5055942535400391 239.2392120361328 0.24134473502635956 0.8260608 0.3645035922527313 True -16 26061 16.695155382156372 0.4449903964996338 137.42832946777344 0.3019673526287079 239.63352966308594 0.23907893896102905 0.82650554 0.37355175614356995 True -17 27594 16.669173002243042 0.4471395015716553 207.73617553710938 0.23656734824180603 239.603271484375 0.23929718136787415 0.8237506 0.39249682426452637 False -18 29127 16.632404088974 0.44768619537353516 128.86703491210938 0.2665649652481079 240.0320587158203 0.23725581169128418 0.8210833 0.40941092371940613 False -19 30660 16.65047550201416 0.44668054580688477 200.37277221679688 0.1518624722957611 240.24403381347656 0.23638996481895447 0.818711 0.4216441214084625 False diff --git a/ENCSR718AAB/cherimoya.fold_1.performance.tsv b/ENCSR718AAB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cdbfd5d8f1b31345043e69c499ac073e3ae68468..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -239.63352966308594 0.5236120820045471 0.23907889425754547 0.06084897369146347 0.8265055418014526 0.805908739566803 0.37355175614356995 \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_2.evaluate.json b/ENCSR718AAB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 432479ee6ac9c64723039b06db79ed4603f2ae4b..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF922MLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_2.fit.json b/ENCSR718AAB/cherimoya.fold_2.fit.json deleted file mode 100644 index 9b73ebe1ba225376c0a29fd5268bfb32d0ec98ce..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF922MLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_2.log b/ENCSR718AAB/cherimoya.fold_2.log deleted file mode 100644 index ee38e5ad8dc04887ad8aed6284038c79f4de176d..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1643 21.795782327651978 3.1998472213745117 180.80055236816406 0.8934842348098755 233.82200622558594 0.10168863087892532 0.5207559 6.767275333404541 True -1 3286 18.059903383255005 0.3209547996520996 151.59091186523438 0.8578776717185974 226.4147186279297 0.14559116959571838 0.6016198 2.587545394897461 True -2 4929 18.041702032089233 1.6433351039886475 190.16708374023438 0.5761687159538269 215.70907592773438 0.19209393858909607 0.7019403 1.2129939794540405 True -3 6572 18.066423892974854 0.32093048095703125 155.13534545898438 0.44084182381629944 212.92010498046875 0.20011483132839203 0.7196345 0.803840696811676 True -4 8215 18.056285619735718 0.3101813793182373 174.80030822753906 0.5788980722427368 210.79287719726562 0.2067132145166397 0.74272704 0.5041009783744812 True -5 9858 18.05632472038269 0.8126256465911865 146.91761779785156 0.3645612597465515 209.70848083496094 0.2114594578742981 0.753829 0.46069055795669556 True -6 11501 18.018377542495728 0.30432748794555664 180.15756225585938 0.6495987772941589 209.26654052734375 0.21243201196193695 0.7665153 0.4272298216819763 True -7 13144 18.189769506454468 0.3091776371002197 179.80023193359375 0.41281163692474365 208.81134033203125 0.21487756073474884 0.7750898 0.40158671140670776 True -8 14787 18.024173498153687 0.30597805976867676 163.56552124023438 0.4043687582015991 208.39515686035156 0.2154332846403122 0.78032243 0.3749600052833557 True -9 16430 18.106727600097656 0.3108482360839844 194.4044647216797 0.7530850172042847 207.81246948242188 0.21851801872253418 0.785331 0.3624715507030487 True -10 18073 17.991806268692017 0.305767297744751 182.4658203125 0.352211058139801 207.24118041992188 0.22071100771427155 0.7888362 0.3585645258426666 True -11 19716 17.99240779876709 0.3103451728820801 185.1147003173828 0.5315096378326416 207.16563415527344 0.22091691195964813 0.7931232 0.35210081934928894 True -12 21359 18.010517835617065 7.3792948722839355 149.7193145751953 0.387420654296875 206.979248046875 0.22082124650478363 0.7970176 0.34858188033103943 True -13 23002 19.975454092025757 3.163095235824585 160.6470947265625 0.3438781797885895 206.6785888671875 0.2221791297197342 0.80138576 0.3454214632511139 True -14 24645 18.099357843399048 1.2529244422912598 153.6414337158203 0.35884279012680054 206.4638214111328 0.223272442817688 0.80321515 0.34579500555992126 True -15 26288 18.11966347694397 0.3111143112182617 143.27056884765625 0.43865588307380676 206.44053649902344 0.2233128547668457 0.8058572 0.34568801522254944 True -16 27931 17.98061513900757 0.30625271797180176 177.65078735351562 0.35606592893600464 206.52130126953125 0.2224128544330597 0.8064737 0.3504195809364319 True -17 29574 18.03459858894348 0.30592966079711914 194.0353240966797 0.28255972266197205 206.4503936767578 0.22324298322200775 0.8054529 0.3611604869365692 False -18 31217 18.03465175628662 1.526421308517456 143.9105224609375 0.2291267216205597 206.8267364501953 0.22087495028972626 0.80056846 0.3734554350376129 False -19 32860 18.053109645843506 0.30852222442626953 174.78433227539062 0.23345908522605896 206.69131469726562 0.22189287841320038 0.79915327 0.38345324993133545 False diff --git a/ENCSR718AAB/cherimoya.fold_2.performance.tsv b/ENCSR718AAB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 81a9a1c1e9b3a12ea8bf96fb1eaf99d9357cb196..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -206.52130126953125 0.5402648448944092 0.2224128693342209 0.0522753968834877 0.8064736723899841 0.7819390892982483 0.3504195809364319 \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_3.evaluate.json b/ENCSR718AAB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c6cd6308d1bc4fb9b80fa46a7bd594a057cf9836..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF922MLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_3.fit.json b/ENCSR718AAB/cherimoya.fold_3.fit.json deleted file mode 100644 index 0de383b67dee18ae6423b949329eeaf04bc6403f..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF922MLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_3.log b/ENCSR718AAB/cherimoya.fold_3.log deleted file mode 100644 index 879b47205adc0e971429be500498aa9bd9877dc3..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1579 21.190940618515015 3.673771858215332 139.88134765625 0.5891144275665283 248.9566192626953 0.10173815488815308 0.5270291 7.737152099609375 True -1 3158 17.226178884506226 0.33084583282470703 164.76312255859375 0.8388434052467346 241.54151916503906 0.14480990171432495 0.63069296 3.0208263397216797 True -2 4737 17.574283123016357 0.32588863372802734 178.6896209716797 0.5961939096450806 232.2649688720703 0.18674427270889282 0.682972 1.697117805480957 True -3 6316 17.572211027145386 0.3236565589904785 165.2808837890625 0.5330564975738525 228.84426879882812 0.19626137614250183 0.71054196 0.9844791889190674 True -4 7895 17.53329610824585 0.32781410217285156 196.92428588867188 0.6652959585189819 227.68711853027344 0.19943705201148987 0.72667295 0.7730430960655212 True -5 9474 17.215755462646484 0.33438801765441895 153.62899780273438 0.5860617160797119 227.03253173828125 0.2018256038427353 0.7335744 0.6972647905349731 True -6 11053 17.14524793624878 0.3556399345397949 155.8680419921875 0.44616252183914185 226.74021911621094 0.2034897655248642 0.73597574 0.6255509853363037 True -7 12632 17.172691345214844 0.31601977348327637 167.46905517578125 0.49461421370506287 225.77980041503906 0.20742259919643402 0.75049514 0.5486484169960022 True -8 14211 17.170981407165527 0.31665945053100586 171.5018310546875 0.407841295003891 225.7769012451172 0.20732107758522034 0.75100607 0.5691944360733032 True -9 15790 17.197787284851074 0.322479248046875 194.840576171875 0.38895976543426514 225.13902282714844 0.20947390794754028 0.76599514 0.4865626394748688 True -10 17369 17.18845248222351 0.32700395584106445 157.65704345703125 0.5229345560073853 224.84756469726562 0.20993536710739136 0.77500236 0.4556589424610138 True -11 18948 17.309550523757935 1.2329797744750977 168.4499969482422 0.5279347896575928 224.15750122070312 0.21298976242542267 0.7794453 0.4429943859577179 True -12 20527 17.250106811523438 0.3167541027069092 179.29946899414062 0.46971404552459717 223.61325073242188 0.21429674327373505 0.7912364 0.4107779562473297 True -13 22106 17.154804229736328 0.3212273120880127 193.6304931640625 0.5170470476150513 223.31741333007812 0.2157624512910843 0.80034506 0.4065370559692383 True -14 23685 17.138392448425293 0.6935057640075684 188.3712158203125 0.3063517212867737 222.93556213378906 0.2173159271478653 0.8042643 0.39094066619873047 True -15 25264 17.174434185028076 0.3209974765777588 161.6912384033203 0.392148494720459 222.884765625 0.21699850261211395 0.8090296 0.3816244304180145 True -16 26843 17.18923854827881 0.317075252532959 151.13919067382812 0.3670383095741272 223.10275268554688 0.21547085046768188 0.8111973 0.384255588054657 True -17 28422 17.170504331588745 0.3183867931365967 183.956787109375 0.2854403257369995 223.042724609375 0.21561028063297272 0.8118249 0.3853999972343445 True -18 30001 17.161890506744385 0.3231210708618164 127.44557189941406 0.2706772983074188 223.16065979003906 0.2146577388048172 0.81094235 0.3919650912284851 False -19 31580 17.140169858932495 0.3174293041229248 151.31320190429688 0.2518933415412903 223.11489868164062 0.2152307778596878 0.81097275 0.3968072235584259 False diff --git a/ENCSR718AAB/cherimoya.fold_3.performance.tsv b/ENCSR718AAB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9e816542fe195da7898fd79107fcd79feb9219a7..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.042724609375 0.5388429760932922 0.2156102955341339 0.056624166667461395 0.8118249177932739 0.7952033877372742 0.3853999972343445 \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_4.evaluate.json b/ENCSR718AAB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a7bb88f8dd1fd6fc3d7e24b2f4ed758cb2cf26cd..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF922MLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_4.fit.json b/ENCSR718AAB/cherimoya.fold_4.fit.json deleted file mode 100644 index 0677fc2488b104d5d13b49328afbdc354ca57a3a..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF922MLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR718AAB/cherimoya.fold_4.log b/ENCSR718AAB/cherimoya.fold_4.log deleted file mode 100644 index 4d174e8297517e58766bfcb19c7fe79450896adc..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1602 21.38736605644226 3.655954599380493 168.0667724609375 0.6108663082122803 224.9086456298828 0.09471380710601807 0.5270725 6.829507827758789 True -1 3204 17.845213174819946 0.31459617614746094 176.4398956298828 0.8223080635070801 217.3661346435547 0.14272305369377136 0.6173695 2.657975435256958 True -2 4806 19.25373601913452 11.850859642028809 162.12661743164062 0.41502752900123596 209.92308044433594 0.17787863314151764 0.69910073 1.510745882987976 True -3 6408 17.780304431915283 0.3055384159088135 201.46791076660156 0.5518320202827454 206.83665466308594 0.1882583200931549 0.73425823 0.5673457980155945 True -4 8010 17.833110809326172 0.30425190925598145 151.42877197265625 0.5001975893974304 204.77163696289062 0.19625607132911682 0.7487078 0.44393423199653625 True -5 9612 17.73740839958191 0.3041388988494873 183.62547302246094 0.46255776286125183 204.22682189941406 0.197166308760643 0.75954115 0.4051590859889984 True -6 11214 17.726438283920288 0.2985968589782715 185.914306640625 0.7561874389648438 203.9465789794922 0.19674833118915558 0.76420313 0.3905086815357208 True -7 12816 17.74423885345459 0.5583021640777588 184.03945922851562 0.5282886624336243 203.21942138671875 0.20065583288669586 0.765531 0.38501545786857605 True -8 14418 17.777428150177002 0.3003201484680176 173.9751739501953 0.363799124956131 202.78604125976562 0.20176415145397186 0.77211887 0.3711218237876892 True -9 16020 18.432727336883545 16.038989782333374 192.1938018798828 0.45663881301879883 202.178955078125 0.20544642210006714 0.77601504 0.36517709493637085 True -10 17622 17.943474292755127 0.8064324855804443 179.51219177246094 0.6229735016822815 202.13768005371094 0.2054751217365265 0.7797465 0.3596895635128021 True -11 19224 17.806428909301758 0.3004024028778076 142.7843017578125 0.49469223618507385 201.88951110839844 0.20618441700935364 0.78492737 0.3546100854873657 True -12 20826 17.78175926208496 0.3068716526031494 156.04840087890625 0.4280180037021637 201.4365997314453 0.2084292769432068 0.7836493 0.3561463952064514 False -13 22428 17.790034770965576 0.2971360683441162 160.14706420898438 0.4407205283641815 201.287109375 0.20845608413219452 0.78895897 0.35123270750045776 True -14 24030 17.761207580566406 0.2971007823944092 158.04559326171875 0.41390734910964966 201.13397216796875 0.20885366201400757 0.7917347 0.35232996940612793 True -15 25632 17.813595294952393 0.29587769508361816 172.41387939453125 0.5241403579711914 201.1182403564453 0.20942629873752594 0.79239917 0.3565632104873657 True -16 27234 17.790231943130493 0.2981858253479004 158.41664123535156 0.2982635796070099 201.0978546142578 0.2091173231601715 0.79303885 0.3638312816619873 True -17 28836 17.747142791748047 0.30005550384521484 152.08714294433594 0.19693726301193237 201.49765014648438 0.20657271146774292 0.7894794 0.37799271941185 False -18 30438 17.750407695770264 1.0288772583007812 163.28033447265625 0.16726353764533997 201.42864990234375 0.20760872960090637 0.7866481 0.39178499579429626 False -19 32040 17.51019811630249 0.2991354465484619 164.99974060058594 0.2441898137331009 201.48167419433594 0.20730091631412506 0.78366894 0.39968186616897583 False diff --git a/ENCSR718AAB/cherimoya.fold_4.performance.tsv b/ENCSR718AAB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2a31abc233e9e2dc62f148d9d05a3b2af15e8757..0000000000000000000000000000000000000000 --- a/ENCSR718AAB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.0978546142578 0.5475459098815918 0.2091173380613327 0.05555202439427376 0.7930388450622559 0.767936110496521 0.3638312816619873 \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_0.evaluate.json b/ENCSR718HWW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 88a407fe2f97004db6495b1650027bf23e70a486..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737AXP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_0.performance.tsv b/ENCSR718HWW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 69c10c02285cf9af1b0f339d8c27fc7a677a02f7..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -420.96624755859375 0.24010606110095978 0.7212379574775696 0.2875724136829376 0.7006004452705383 0.6781706809997559 0.8889700770378113 \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_1.evaluate.json b/ENCSR718HWW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 311d82e667ec02f83d952831b7c523578ec45488..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737AXP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_1.log b/ENCSR718HWW/cherimoya.fold_1.log deleted file mode 100644 index 6a9d82654a0b2015a22473752b7e3c0b659243c4..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2260 29.697530269622803 3.6427650451660156 390.09674072265625 2.0476088523864746 703.2814331054688 0.5243206024169922 0.56412494 12.863000869750977 True -1 4520 24.62694001197815 2.8239238262176514 389.28741455078125 1.579736590385437 545.9078979492188 0.670561671257019 0.64433813 7.801551818847656 True -2 6780 24.577805519104004 0.6423912048339844 333.5730285644531 1.8362104892730713 512.3890991210938 0.6997472047805786 0.6367586 2.6169657707214355 False -3 9040 25.116708993911743 11.213545799255371 343.73065185546875 1.8638917207717896 503.55755615234375 0.7095164656639099 0.6424419 1.9775538444519043 False -4 11300 24.22242307662964 0.6446118354797363 342.8232116699219 1.3090037107467651 499.4186096191406 0.7135846018791199 0.6442683 1.758210301399231 False -5 13560 24.25552725791931 18.786267518997192 369.1391906738281 1.3910579681396484 496.7970886230469 0.7167980670928955 0.6533478 1.6185542345046997 True -6 15820 26.440704822540283 0.638817310333252 320.5848388671875 1.7905064821243286 494.1213684082031 0.720072865486145 0.64924246 1.4904613494873047 False -7 18080 24.312639713287354 0.6512670516967773 430.4456481933594 1.6070423126220703 490.5939636230469 0.7232271432876587 0.66252095 1.3536241054534912 True -8 20340 24.172234058380127 0.640134334564209 304.68267822265625 1.4219083786010742 488.02838134765625 0.7261906862258911 0.6682146 1.1942776441574097 True -9 22600 25.91370177268982 0.6355831623077393 344.18524169921875 0.8282513618469238 485.7242736816406 0.7286005020141602 0.6809246 1.103476643562317 True -10 24860 24.15685248374939 33.60837769508362 283.0576171875 1.0470445156097412 481.9333190917969 0.7319729328155518 0.692591 1.0168931484222412 True -11 27120 24.343326568603516 0.631091833114624 240.93939208984375 1.1503310203552246 479.21875 0.7343852519989014 0.69606376 0.9578886032104492 True -12 29380 24.20676898956299 0.6380090713500977 254.29019165039062 1.5686771869659424 476.3343200683594 0.736906111240387 0.706125 0.9297019243240356 True -13 31640 24.163957118988037 0.6403775215148926 315.1370544433594 0.8483455181121826 474.2362976074219 0.7391862869262695 0.71524805 0.892935037612915 True -14 33900 24.197855472564697 10.413432836532593 323.319091796875 0.9812016487121582 472.42474365234375 0.7405636310577393 0.7215316 0.8884315490722656 True -15 36160 24.1738224029541 0.637312650680542 263.4919128417969 0.7024667263031006 470.4049072265625 0.7418099641799927 0.7303589 0.8610615730285645 True -16 38420 24.190104484558105 0.6366362571716309 219.17393493652344 0.6807856559753418 469.91162109375 0.741973340511322 0.736895 0.8556587100028992 True -17 40680 24.18290424346924 0.6401612758636475 340.7707824707031 0.6502535939216614 470.1434631347656 0.741651177406311 0.7356898 0.8746991157531738 False -18 42940 24.314750909805298 2.8622007369995117 293.17236328125 0.8008272647857666 470.4666442871094 0.7410523891448975 0.73231393 0.889495849609375 False -19 45200 24.327829599380493 32.95804572105408 281.68505859375 0.6299761533737183 470.71002197265625 0.7407843470573425 0.73143196 0.9080716371536255 False diff --git a/ENCSR718HWW/cherimoya.fold_1.performance.tsv b/ENCSR718HWW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 10eeacc6dc22979c058e7e1cb3a4434c8bd82296..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -469.91162109375 0.22169682383537292 0.7419734001159668 0.3181335926055908 0.7368950247764587 0.7313334941864014 0.8556587100028992 \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_2.fit.json b/ENCSR718HWW/cherimoya.fold_2.fit.json deleted file mode 100644 index 026f90fe569af93ff62e3b8910a6f84cd6a89614..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF737AXP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_3.evaluate.json b/ENCSR718HWW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3056c33e295c78b95cf43e3aebaa8c53bdd9cf79..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737AXP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_3.performance.tsv b/ENCSR718HWW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 094a65c6fa992891c3561569ce8f586c05620443..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -431.4703063964844 0.23576965928077698 0.7239054441452026 0.2966819107532501 0.6992622017860413 0.6819552779197693 0.9564449191093445 \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_4.evaluate.json b/ENCSR718HWW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8c6e93240ffb6fce7ce0a5643f92d1d01f42a948..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF737AXP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_4.fit.json b/ENCSR718HWW/cherimoya.fold_4.fit.json deleted file mode 100644 index 3fdabc1118cb15bfd5927c8c4c7a98dcd88300e2..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF737AXP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR718HWW/cherimoya.fold_4.log b/ENCSR718HWW/cherimoya.fold_4.log deleted file mode 100644 index 5f5f304c1a69dc5578aa858e50d6f05ad20f95c5..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2331 30.18987536430359 3.4439644813537598 331.0504150390625 1.4224849939346313 600.4796752929688 0.5144796967506409 0.53614837 13.1671724319458 True -1 4662 25.443190813064575 0.4348866939544678 359.21429443359375 1.530452847480774 465.5159606933594 0.6613869071006775 0.5804669 6.00262451171875 True -2 6993 25.482391357421875 0.42575740814208984 439.12896728515625 1.584145426750183 448.0455322265625 0.6783263087272644 0.58536345 1.7135565280914307 True -3 9324 25.382318019866943 0.4244520664215088 409.3616638183594 1.2946009635925293 442.07281494140625 0.6863420605659485 0.5890191 1.3945553302764893 True -4 11655 25.43208932876587 0.507136344909668 376.7232666015625 1.1607985496520996 437.7178649902344 0.692261815071106 0.5915315 1.3192617893218994 True -5 13986 25.385746955871582 0.4342613220214844 344.5157775878906 1.1625523567199707 435.4079284667969 0.6954858899116516 0.5948996 1.221571683883667 True -6 16317 25.446861028671265 0.4279038906097412 322.1689453125 1.2635828256607056 433.640625 0.6987494230270386 0.6052253 1.1024624109268188 True -7 18648 25.405900239944458 1.6500775814056396 287.93475341796875 1.490560531616211 432.0208435058594 0.7014248371124268 0.60915154 1.1121182441711426 True -8 20979 25.473546743392944 0.42522215843200684 280.535400390625 1.1114671230316162 428.8097229003906 0.7049157023429871 0.61933607 1.0312551259994507 True -9 23310 25.409699201583862 0.4295036792755127 359.4256591796875 1.2226219177246094 426.1965637207031 0.7079302072525024 0.63126165 0.981304407119751 True -10 25641 25.359114170074463 0.4248929023742676 319.4551696777344 1.5054723024368286 424.064208984375 0.7106372117996216 0.64020437 0.9442771077156067 True -11 27972 25.478239059448242 20.026265382766724 341.3478698730469 1.5265699625015259 422.14312744140625 0.713131844997406 0.64663965 0.9385421276092529 True -12 30303 26.071155548095703 0.4344043731689453 355.51812744140625 0.8956148624420166 420.07940673828125 0.7153576016426086 0.65883595 0.9097239375114441 True -13 32634 26.505580186843872 3.2113614082336426 376.59564208984375 1.5502376556396484 418.6528625488281 0.7166762351989746 0.6700064 0.8800936937332153 True -14 34965 25.52575945854187 0.8765969276428223 385.9077453613281 0.9319936037063599 417.1148376464844 0.7183317542076111 0.677263 0.8721184134483337 True -15 37296 25.467196941375732 0.42197155952453613 301.81982421875 0.9645889401435852 416.5192565917969 0.7189596891403198 0.6821804 0.8750700354576111 True -16 39627 25.48859930038452 0.4217715263366699 284.23699951171875 1.27874755859375 416.0081787109375 0.7192818522453308 0.6866979 0.887256920337677 True -17 41958 25.50472116470337 0.42266178131103516 325.3304443359375 0.5608611106872559 415.76885986328125 0.7192105650901794 0.6886054 0.8903260231018066 True -18 44289 25.370587587356567 0.41762638092041016 358.48980712890625 0.688309371471405 415.9458923339844 0.7185947299003601 0.68635255 0.9160190224647522 False -19 46620 24.901841640472412 0.42084431648254395 250.34397888183594 0.6182568073272705 416.4516906738281 0.7180792689323425 0.68469083 0.9360160827636719 False diff --git a/ENCSR718HWW/cherimoya.fold_4.performance.tsv b/ENCSR718HWW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c7b4d2286e9d20df2dddf4472bb630fe0b6076f0..0000000000000000000000000000000000000000 --- a/ENCSR718HWW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -415.76885986328125 0.24142493307590485 0.7192105650901794 0.2866058051586151 0.6886054277420044 0.6606391668319702 0.8903260231018066 \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_0.evaluate.json b/ENCSR721DFB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ad3348a996bbdfd6ba51a657c82c602ca9326502..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF403ZYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_0.fit.json b/ENCSR721DFB/cherimoya.fold_0.fit.json deleted file mode 100644 index 7d30049d1204001375203597ba4fca06be3464f1..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF403ZYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_0.log b/ENCSR721DFB/cherimoya.fold_0.log deleted file mode 100644 index 65905b2dd757cffd820053d5efa9118224ef5452..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 37.513263463974 7.590968132019043 645.8931884765625 0.5247448682785034 884.570068359375 0.2794210612773895 0.716325 7.365837574005127 True -1 5482 29.871695041656494 1.040684461593628 696.5081787109375 0.6497598886489868 776.6783447265625 0.3690859377384186 0.7850039 1.9085780382156372 True -2 8223 30.35589909553528 0.6043558120727539 708.8836669921875 0.5139032602310181 759.2421264648438 0.3820359706878662 0.7892064 0.7590809464454651 True -3 10964 30.025399208068848 0.5664107799530029 572.349853515625 0.46653223037719727 750.2046508789062 0.3911511301994324 0.792659 0.6359359622001648 True -4 13705 29.51954674720764 0.5911900997161865 646.972412109375 0.4028172492980957 748.4529418945312 0.39235812425613403 0.7945574 0.5706453919410706 True -5 16446 29.551770448684692 0.5745887756347656 793.1070556640625 0.38266459107398987 742.7760009765625 0.3968106806278229 0.7994862 0.4966963231563568 True -6 19187 29.525397300720215 0.5757040977478027 596.8974609375 0.5953193306922913 742.0841064453125 0.3982883393764496 0.8033273 0.462845116853714 True -7 21928 29.537800312042236 0.5765364170074463 504.2435607910156 0.749859631061554 738.5606689453125 0.40259474515914917 0.80544174 0.44810283184051514 True -8 24669 29.470044136047363 1.971116065979004 657.7844848632812 0.3543109893798828 733.5519409179688 0.4083167016506195 0.80935454 0.41460874676704407 True -9 27410 29.52186632156372 1.0128774642944336 555.1380615234375 0.3541557788848877 729.6110229492188 0.4128718674182892 0.8141678 0.38883155584335327 True -10 30151 29.602747201919556 0.5873086452484131 691.1815185546875 0.39718735218048096 727.3583984375 0.41481244564056396 0.81899863 0.39529913663864136 True -11 32892 29.583216428756714 0.6241905689239502 674.4467163085938 0.288454532623291 724.5798950195312 0.41803011298179626 0.8216309 0.3684385120868683 True -12 35633 29.67236351966858 0.5839834213256836 614.460693359375 0.44320160150527954 721.31396484375 0.4215991199016571 0.8256796 0.35182297229766846 True -13 38374 29.74605441093445 0.5977940559387207 628.44921875 0.38363346457481384 720.1600952148438 0.4212510585784912 0.8331941 0.33169126510620117 True -14 41115 29.6425142288208 0.5881872177124023 567.8214721679688 0.3588976263999939 715.9461059570312 0.42513635754585266 0.83814037 0.3235006034374237 True -15 43856 29.63495659828186 0.5968735218048096 542.4803466796875 0.30183565616607666 715.6796875 0.4244668483734131 0.8427845 0.30796608328819275 True -16 46597 29.77580237388611 30.26325798034668 601.44921875 0.29388728737831116 714.8485107421875 0.42439913749694824 0.847061 0.300135999917984 True -17 49338 29.572697162628174 0.5897696018218994 573.9371948242188 0.2660219073295593 715.4541625976562 0.42438074946403503 0.8481237 0.2956902086734772 True -18 52079 29.499114274978638 21.410526037216187 669.2623291015625 0.2654455006122589 716.2438354492188 0.4237925410270691 0.8470569 0.29698383808135986 False -19 54820 29.565945863723755 0.5883448123931885 550.3087768554688 0.23468515276908875 714.5347900390625 0.4269866645336151 0.8460023 0.2976844012737274 False diff --git a/ENCSR721DFB/cherimoya.fold_0.performance.tsv b/ENCSR721DFB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f6f9519b1fcbf21617b8f65ca42b062804d2661b..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -715.4541625976562 0.3578210473060608 0.42438074946403503 0.1853102594614029 0.8481237292289734 0.7957345247268677 0.2956902086734772 \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_1.evaluate.json b/ENCSR721DFB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index cfa76c2b2781bee794bf9a26bee2756ecd9cfbfe..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF403ZYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_1.fit.json b/ENCSR721DFB/cherimoya.fold_1.fit.json deleted file mode 100644 index 1ee0db56a7751ff8a3af10700eb1b46f806fdebe..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF403ZYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_1.log b/ENCSR721DFB/cherimoya.fold_1.log deleted file mode 100644 index 34ecfcee09c70c219ca3b2396934a24dd3258ae3..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 34.901729583740234 4.451305389404297 809.48291015625 0.6034981608390808 1057.8076171875 0.28070002794265747 0.707045 7.402696132659912 True -1 5418 30.145185947418213 0.6989836692810059 725.4454345703125 0.6243838667869568 919.62060546875 0.38180533051490784 0.7691406 1.9745744466781616 True -2 8127 32.457310914993286 0.7103300094604492 573.5792236328125 0.6642080545425415 897.8544311523438 0.39577019214630127 0.7782295 1.0853155851364136 True -3 10836 30.247057914733887 0.7158734798431396 456.1129455566406 0.6216878890991211 882.0422973632812 0.403192400932312 0.7902614 0.7525403499603271 True -4 13545 30.18014359474182 0.6979906558990479 564.1807250976562 0.5611251592636108 872.1226806640625 0.4117262363433838 0.79787916 0.6446062922477722 True -5 16254 30.17253589630127 1.6561784744262695 705.05615234375 0.35170674324035645 867.2984008789062 0.4148012101650238 0.8037804 0.5461450219154358 True -6 18963 30.20444083213806 1.2378692626953125 572.7828369140625 0.4441276788711548 862.1430053710938 0.418812096118927 0.8106598 0.5076841115951538 True -7 21672 30.190881967544556 11.633841037750244 499.119384765625 0.3042575418949127 857.1510620117188 0.4233790338039398 0.8132377 0.4726974666118622 True -8 24381 29.695494174957275 17.019312381744385 710.1370849609375 0.4745941758155823 853.3305053710938 0.42642742395401 0.8203162 0.47915351390838623 True -9 27090 29.67496657371521 0.7026429176330566 545.8607177734375 0.3768719732761383 849.1766357421875 0.42985326051712036 0.82659656 0.4526115655899048 True -10 29799 29.586847066879272 0.6971917152404785 514.3854370117188 0.368377149105072 844.2077026367188 0.4345265328884125 0.8276478 0.43917882442474365 True -11 32508 29.604560613632202 0.6974859237670898 720.4354858398438 0.2687222361564636 841.449462890625 0.43559548258781433 0.8307973 0.4187189042568207 True -12 35217 29.531731367111206 4.080652236938477 639.7540283203125 0.4003330171108246 837.6636962890625 0.43897491693496704 0.83820885 0.38765770196914673 True -13 37926 29.597179651260376 1.2421667575836182 711.8487548828125 0.3482986092567444 829.7529907226562 0.44563812017440796 0.84325933 0.3748675286769867 True -14 40635 29.59358859062195 1.8414487838745117 484.1063232421875 0.38454118371009827 827.3413696289062 0.4466080367565155 0.8514511 0.35164400935173035 True -15 43344 29.59085464477539 1.9199788570404053 677.0330810546875 0.3440459966659546 825.9588012695312 0.44620850682258606 0.85514796 0.33329054713249207 True -16 46053 29.679268836975098 1.9669792652130127 630.3671875 0.32371801137924194 825.4057006835938 0.4471353590488434 0.8597109 0.32022929191589355 True -17 48762 29.658304452896118 1.795156717300415 739.763671875 0.3113173246383667 824.6276245117188 0.44701361656188965 0.8627112 0.31620943546295166 True -18 51471 29.69137668609619 1.6128623485565186 638.2750244140625 0.29362499713897705 824.0773315429688 0.44814643263816833 0.86214083 0.3160671293735504 False -19 54180 29.699651956558228 1.5602943897247314 579.4273681640625 0.22955048084259033 824.5878295898438 0.44689083099365234 0.8619492 0.31616389751434326 False diff --git a/ENCSR721DFB/cherimoya.fold_1.performance.tsv b/ENCSR721DFB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6436e636d3bfc8ef71a3b004509ad6e69ae2cb7f..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -824.6276245117188 0.33750829100608826 0.44701364636421204 0.21038949489593506 0.8627111911773682 0.8337638974189758 0.31620943546295166 \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_2.evaluate.json b/ENCSR721DFB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 55f79f9365fefcf0db4650b7c4eea47992a6367e..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF403ZYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_2.fit.json b/ENCSR721DFB/cherimoya.fold_2.fit.json deleted file mode 100644 index f4f143a6274d4ef95c40ab67139b36370da2bdc7..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF403ZYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_2.log b/ENCSR721DFB/cherimoya.fold_2.log deleted file mode 100644 index f79ad04a5feaa206ade6906f3cf698180ccaf064..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 37.85198998451233 3.4709107875823975 663.8545532226562 0.4030005931854248 919.2388916015625 0.2824080288410187 0.7132848 6.301180362701416 True -1 5756 31.99387788772583 0.6206924915313721 500.14630126953125 0.5604113340377808 808.7396850585938 0.3693102300167084 0.77561957 1.781626582145691 True -2 8634 32.048269510269165 16.271113634109497 575.5172119140625 0.5199236273765564 791.555419921875 0.3813319206237793 0.78066856 1.036920428276062 True -3 11512 32.229379177093506 0.5836977958679199 654.0234985351562 0.4093123972415924 780.2159423828125 0.39002829790115356 0.7883282 0.9168673157691956 True -4 14390 31.957457542419434 1.270400047302246 481.48309326171875 0.5166921019554138 774.38818359375 0.3950240910053253 0.7878761 0.608911395072937 False -5 17268 32.03044509887695 0.5953218936920166 648.1377563476562 0.4404211938381195 770.6569213867188 0.3981502950191498 0.7926736 0.5619338750839233 True -6 20146 32.22824239730835 0.558845043182373 571.6849365234375 0.40909963846206665 766.6517944335938 0.40192490816116333 0.79599494 0.5095363259315491 True -7 23024 31.956634759902954 0.5759902000427246 552.7515869140625 0.42461708188056946 759.7355346679688 0.4088197648525238 0.8046345 0.44929519295692444 True -8 25902 31.730482816696167 0.5674610137939453 591.7757568359375 0.4357895851135254 756.4818115234375 0.4112907946109772 0.81068885 0.4220772981643677 True -9 28780 31.377403497695923 0.5713236331939697 669.923583984375 0.5137835741043091 752.1619262695312 0.4156284034252167 0.8150569 0.3963976204395294 True -10 31658 31.58850884437561 0.5874431133270264 568.8060302734375 0.4228847026824951 749.6072998046875 0.41849130392074585 0.8196477 0.3986347019672394 True -11 34536 31.6828191280365 0.5754392147064209 617.80322265625 0.3932459354400635 745.9697875976562 0.4215950071811676 0.8232188 0.38730043172836304 True -12 37414 31.42621612548828 0.5695614814758301 575.73291015625 0.26884669065475464 745.01806640625 0.42151397466659546 0.8276595 0.3497762382030487 True -13 40292 31.382333040237427 0.5603742599487305 528.3942260742188 0.25939470529556274 739.9454956054688 0.42600521445274353 0.83256346 0.345661461353302 True -14 43170 31.775567531585693 5.691120386123657 450.70086669921875 0.2172553837299347 739.5369262695312 0.4259742200374603 0.8361989 0.33119383454322815 True -15 46048 31.501342296600342 7.921813249588013 604.4140014648438 0.3359813690185547 736.9734497070312 0.4283948540687561 0.8424961 0.3197062909603119 True -16 48926 31.39677095413208 0.5638899803161621 555.0594482421875 0.33449989557266235 736.6723022460938 0.4285561144351959 0.84345514 0.31110507249832153 True -17 51804 31.34347677230835 0.5595448017120361 589.380859375 0.2745109796524048 736.0753173828125 0.42949536442756653 0.8458746 0.3070463538169861 True -18 54682 31.35444188117981 0.5535759925842285 765.4139404296875 0.2600807547569275 736.1563720703125 0.42811381816864014 0.8448966 0.30911681056022644 False -19 57560 31.380740880966187 0.569061279296875 552.7423095703125 0.3329498767852783 736.0930786132812 0.42880740761756897 0.8431268 0.3100484013557434 False diff --git a/ENCSR721DFB/cherimoya.fold_2.performance.tsv b/ENCSR721DFB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c750071209fab9c477102ad52af1b362b20d3b1b..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -736.0753173828125 0.3537233769893646 0.42949533462524414 0.19011373817920685 0.8458746075630188 0.8012955188751221 0.3070463538169861 \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_3.evaluate.json b/ENCSR721DFB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2a3c131c9755a5b27e8cddce2adae8929de5129d..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF403ZYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_3.fit.json b/ENCSR721DFB/cherimoya.fold_3.fit.json deleted file mode 100644 index 6ebc2ad9568406d56b2e6d69e78aaf7136c4b83c..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF403ZYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_3.log b/ENCSR721DFB/cherimoya.fold_3.log deleted file mode 100644 index db3cd82364bb0edd2334a03a9853e8cc4613b4e3..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 35.57498550415039 3.670980930328369 942.43994140625 0.7495651245117188 878.8346557617188 0.2904088497161865 0.7217801 6.524420738220215 True -1 5512 30.623961448669434 2.382451057434082 655.1875 0.5424478054046631 780.9130249023438 0.37228548526763916 0.7852459 1.8760128021240234 True -2 8268 30.594239950180054 0.5984644889831543 527.0448608398438 0.46045446395874023 766.460205078125 0.3842028081417084 0.7910312 1.1500637531280518 True -3 11024 30.610109567642212 0.5594542026519775 551.0726318359375 0.44050154089927673 751.3280639648438 0.39586713910102844 0.80102444 0.9145947694778442 True -4 13780 30.609517812728882 0.5540635585784912 630.2442626953125 0.46406763792037964 746.119873046875 0.39917421340942383 0.8067044 0.7134000062942505 True -5 16536 30.58860754966736 0.5483736991882324 658.6505126953125 0.46311867237091064 740.8345336914062 0.40382689237594604 0.80470383 0.6672256588935852 False -6 19292 30.61003303527832 1.289959192276001 581.29736328125 0.6210614442825317 738.05078125 0.40626096725463867 0.80823034 0.549094557762146 True -7 22048 30.644238471984863 0.530081033706665 731.689208984375 0.44445332884788513 735.0489501953125 0.4097653925418854 0.8083887 0.5502663850784302 True -8 24804 30.65639305114746 0.5538806915283203 595.6597900390625 0.4299129843711853 731.2655639648438 0.41300296783447266 0.81361204 0.5128850936889648 True -9 27560 30.392006158828735 0.549189567565918 666.7134399414062 0.2747846841812134 728.3803100585938 0.41600194573402405 0.819717 0.5185162425041199 True -10 30316 30.023394346237183 0.5383400917053223 638.4378662109375 0.37559419870376587 724.3602294921875 0.41975700855255127 0.8240777 0.47255057096481323 True -11 33072 29.97108554840088 0.5290029048919678 590.2550048828125 0.3733972907066345 723.6732788085938 0.419452041387558 0.82846504 0.4322010576725006 True -12 35828 29.99740242958069 0.5484304428100586 548.1744384765625 0.41686177253723145 719.8106079101562 0.42265650629997253 0.83373505 0.3998834490776062 True -13 38584 30.04435110092163 1.751239538192749 626.0316162109375 0.4008537530899048 717.3878173828125 0.4246784746646881 0.8402377 0.37935516238212585 True -14 41340 30.054763555526733 0.5464537143707275 607.086181640625 0.3122168779373169 712.928466796875 0.42879220843315125 0.84678674 0.3528471291065216 True -15 44096 30.07807683944702 0.5378928184509277 558.7477416992188 0.3362792730331421 713.267822265625 0.4269343316555023 0.8508577 0.3339132070541382 True -16 46852 30.10625910758972 0.5396392345428467 490.41790771484375 0.24100768566131592 712.9783935546875 0.4280737042427063 0.8550927 0.3191072940826416 True -17 49608 30.285728693008423 0.536766767501831 574.93017578125 0.2814353406429291 710.5252075195312 0.43133604526519775 0.85589725 0.3152913749217987 True -18 52364 30.19724988937378 0.538017988204956 572.56005859375 0.24980930984020233 710.9035034179688 0.42940765619277954 0.85620815 0.3129662573337555 True -19 55120 30.186468839645386 0.5638155937194824 730.3863525390625 0.27126866579055786 711.474365234375 0.42929792404174805 0.85695153 0.3128610849380493 True diff --git a/ENCSR721DFB/cherimoya.fold_3.performance.tsv b/ENCSR721DFB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 210f57df70e07a7e8941749db66b7f94d255f2c0..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -711.474365234375 0.3564284145832062 0.42929792404174805 0.18784154951572418 0.8569515347480774 0.809319794178009 0.3128610849380493 \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_4.evaluate.json b/ENCSR721DFB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 17525a194f72924743fcf6a8be5140d0aafd0881..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF403ZYE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_4.fit.json b/ENCSR721DFB/cherimoya.fold_4.fit.json deleted file mode 100644 index f26e99a967a2512f865948736b12e7326591e29a..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF403ZYE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR721DFB/cherimoya.fold_4.log b/ENCSR721DFB/cherimoya.fold_4.log deleted file mode 100644 index 644efd2b9849fa17eb5f47110285c26691d0cb62..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2816 36.09742259979248 3.806645631790161 619.5855712890625 0.840293824672699 837.3576049804688 0.2811737358570099 0.69970155 5.437384128570557 True -1 5632 31.267818689346313 0.6159422397613525 492.7181396484375 0.44848793745040894 743.7991943359375 0.36418020725250244 0.76287866 1.8390886783599854 True -2 8448 31.228681325912476 0.5812408924102783 691.3890380859375 0.49723953008651733 727.667724609375 0.3787696659564972 0.769272 0.8304182887077332 True -3 11264 31.219602584838867 0.5730807781219482 675.637939453125 0.41994279623031616 719.31005859375 0.38567960262298584 0.7752341 0.7739114165306091 True -4 14080 31.220868587493896 0.5782861709594727 710.360595703125 0.5913493633270264 712.8466796875 0.38970667123794556 0.7862134 0.5519526600837708 True -5 16896 31.294086933135986 0.5753157138824463 625.0553588867188 0.4738405644893646 711.646728515625 0.3919236958026886 0.78923166 0.5117179155349731 True -6 19712 30.803395986557007 0.577765941619873 532.3311157226562 0.4279901385307312 708.4280395507812 0.39458125829696655 0.7909781 0.4440460801124573 True -7 22528 30.66886830329895 0.5737559795379639 601.3036499023438 0.48995959758758545 704.1454467773438 0.3996032476425171 0.79518306 0.43836545944213867 True -8 25344 30.65084958076477 0.5680549144744873 622.4494018554688 0.4750967025756836 701.3316040039062 0.4022265076637268 0.79964244 0.3961639702320099 True -9 28160 30.69394588470459 0.5728764533996582 623.7061157226562 0.29572874307632446 696.7763671875 0.40667545795440674 0.8091255 0.3843457102775574 True -10 30976 30.666956186294556 0.5805830955505371 686.364501953125 0.42751896381378174 694.3716430664062 0.4095485806465149 0.81285506 0.3555426597595215 True -11 33792 30.679168939590454 0.6284050941467285 586.3677368164062 0.2747664451599121 692.7839965820312 0.4118782877922058 0.81729835 0.3471367657184601 True -12 36608 30.68363642692566 27.546156406402588 570.549560546875 0.3677270710468292 690.2899169921875 0.4134913980960846 0.8214233 0.3278355002403259 True -13 39424 30.794087171554565 17.577532529830933 608.2095336914062 0.3455697298049927 688.0304565429688 0.4154241979122162 0.8279329 0.3177505135536194 True -14 42240 30.711897611618042 0.5759005546569824 690.2664794921875 0.3981238603591919 688.3695068359375 0.41417980194091797 0.83291245 0.3040057420730591 True -15 45056 30.75402069091797 0.5657331943511963 588.517578125 0.35165834426879883 685.9395751953125 0.41683244705200195 0.83794713 0.29705971479415894 True -16 47872 30.75011968612671 1.442246437072754 511.6414489746094 0.2733631134033203 685.7059936523438 0.4177669882774353 0.8414668 0.290966659784317 True -17 50688 30.697017192840576 0.5654890537261963 639.0673828125 0.25383496284484863 686.2049560546875 0.4172646999359131 0.8439237 0.2884746491909027 True -18 53504 30.785341024398804 0.5760154724121094 695.8851318359375 0.2419237643480301 685.1276245117188 0.4189892113208771 0.84475154 0.2893337905406952 True -19 56320 30.69396448135376 0.5758190155029297 505.5635986328125 0.3231693506240845 685.69482421875 0.41853630542755127 0.8428797 0.2912551164627075 False diff --git a/ENCSR721DFB/cherimoya.fold_4.performance.tsv b/ENCSR721DFB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ce8b1685df1317c8a4ae5a6aded4197896471de3..0000000000000000000000000000000000000000 --- a/ENCSR721DFB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -685.1276245117188 0.3623885214328766 0.4189891517162323 0.18293927609920502 0.8447515368461609 0.788330614566803 0.2893337905406952 \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_0.evaluate.json b/ENCSR722HJG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c690f09fbfc7dbe98954f2d88d773ffec0d8d898..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_0.fit.json b/ENCSR722HJG/cherimoya.fold_0.fit.json deleted file mode 100644 index 1cc6a06d00102e69751ef7447638d0cc5b4d4776..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF955VFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_0.log b/ENCSR722HJG/cherimoya.fold_0.log deleted file mode 100644 index b574eeeba59f8395d5a4e65d51e9a7e18835d195..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.96462368965149 3.9267795085906982 428.80859375 0.4566148817539215 534.368408203125 0.24864500761032104 0.75783443 4.329753398895264 True -1 5514 30.325087308883667 0.5878374576568604 398.6954345703125 0.47117531299591064 488.5492858886719 0.30998125672340393 0.8023372 1.2590081691741943 True -2 8271 30.28908109664917 0.6092069149017334 432.5877990722656 0.5160753130912781 478.275146484375 0.322323739528656 0.81542104 0.5562169551849365 True -3 11028 30.366393089294434 0.6630129814147949 379.2315673828125 0.42812615633010864 476.9598693847656 0.3236086070537567 0.82411176 0.5398394465446472 True -4 13785 30.369274616241455 0.6881401538848877 390.44146728515625 0.43750810623168945 474.72125244140625 0.32713204622268677 0.827477 0.521254301071167 True -5 16542 30.265984773635864 0.5939998626708984 400.19476318359375 0.44836363196372986 472.04266357421875 0.33137524127960205 0.8354266 0.4669991135597229 True -6 19299 30.26152753829956 0.5922441482543945 380.4293212890625 0.38221368193626404 469.296142578125 0.33626866340637207 0.8412203 0.43114688992500305 True -7 22056 30.266328811645508 0.5920319557189941 441.07989501953125 0.45649927854537964 467.8004455566406 0.3385612666606903 0.84679466 0.4102781116962433 True -8 24813 30.299670219421387 0.593949556350708 396.50927734375 0.36584001779556274 466.5936279296875 0.34152495861053467 0.8513125 0.3801710605621338 True -9 27570 30.28371572494507 1.5332345962524414 340.1767883300781 0.2840728163719177 465.06329345703125 0.3434183895587921 0.8538375 0.3471943736076355 True -10 30327 30.29465889930725 2.3248214721679688 362.40130615234375 0.38851428031921387 463.2838439941406 0.34579145908355713 0.85638607 0.34674814343452454 True -11 33084 30.325567483901978 1.195511817932129 435.4512634277344 0.4241052269935608 461.43695068359375 0.34898483753204346 0.8589628 0.3130840063095093 True -12 35841 30.326586961746216 0.5997180938720703 367.391845703125 0.33781492710113525 460.35906982421875 0.3497175872325897 0.863761 0.3109898269176483 True -13 38598 29.884869813919067 0.5929474830627441 356.59967041015625 0.37547406554222107 457.93115234375 0.354155033826828 0.8686256 0.2876918911933899 True -14 41355 29.74014925956726 0.5883522033691406 371.2215270996094 0.2738685607910156 458.1259765625 0.3532204031944275 0.87225246 0.2743258476257324 True -15 44112 29.748477935791016 0.5942423343658447 368.7746887207031 0.2737981081008911 456.95281982421875 0.35525962710380554 0.8745996 0.264909565448761 True -16 46869 29.752615690231323 0.5855193138122559 477.70703125 0.269944965839386 457.1840515136719 0.3546978831291199 0.8767746 0.25890475511550903 True -17 49626 29.738605737686157 0.5904827117919922 342.69708251953125 0.23936912417411804 456.6449890136719 0.35572564601898193 0.87726796 0.2540174722671509 True -18 52383 29.72514772415161 0.5887343883514404 348.21929931640625 0.3742453455924988 457.1183166503906 0.3547329902648926 0.87661624 0.25190743803977966 False -19 55140 29.762258291244507 0.585991621017456 384.80133056640625 0.2609172463417053 456.6815185546875 0.3567289412021637 0.87618375 0.2544751763343811 False diff --git a/ENCSR722HJG/cherimoya.fold_0.performance.tsv b/ENCSR722HJG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 671869c35e9380056b6fd6f627fda22f4af108f0..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -456.6449890136719 0.43149882555007935 0.35572564601898193 0.12291906774044037 0.8772679567337036 0.8524268865585327 0.2540174722671509 \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_1.evaluate.json b/ENCSR722HJG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 69b63cc7e16319632e805400e879bdc783e9613e..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_1.fit.json b/ENCSR722HJG/cherimoya.fold_1.fit.json deleted file mode 100644 index 6b4eee04a6170a661e8c8d3fc9ddc0f24425079c..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF955VFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_1.log b/ENCSR722HJG/cherimoya.fold_1.log deleted file mode 100644 index 04a88df30fac2cbd7ea4747de45f49d0eeb30850..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2707 34.224562883377075 30.365720987319946 474.5955810546875 0.594565749168396 641.9017944335938 0.25151610374450684 0.74848545 5.389604091644287 True -1 5414 29.93618106842041 1.4079599380493164 402.243896484375 0.7283893823623657 585.1709594726562 0.32206660509109497 0.8061334 1.5798183679580688 True -2 8121 29.738808393478394 0.7165977954864502 336.53631591796875 0.4563571810722351 572.3051147460938 0.3324671685695648 0.8124805 0.8529953956604004 True -3 10828 29.874640941619873 0.6909933090209961 343.44580078125 0.47184091806411743 563.4915771484375 0.34220317006111145 0.82167035 0.7606631517410278 True -4 13535 29.778115034103394 0.6804094314575195 307.0099792480469 0.40302297472953796 558.4884643554688 0.34940531849861145 0.8268065 0.586404025554657 True -5 16242 29.795138120651245 2.2284903526306152 401.43408203125 0.3841097354888916 555.42431640625 0.35220691561698914 0.83443993 0.5168853998184204 True -6 18949 29.797046899795532 0.6810197830200195 442.55706787109375 0.419755220413208 554.2014770507812 0.35353270173072815 0.84243095 0.47553133964538574 True -7 21656 29.72388982772827 0.6937940120697021 407.1197204589844 0.30039137601852417 551.1075439453125 0.3579651415348053 0.848342 0.420957088470459 True -8 24363 29.77566885948181 0.6749742031097412 336.1019592285156 0.31789523363113403 547.8111572265625 0.3630162179470062 0.854083 0.38825881481170654 True -9 27070 29.760446786880493 1.0232374668121338 383.48089599609375 0.3929997980594635 546.8671264648438 0.3630552589893341 0.8582336 0.36564627289772034 True -10 29777 29.772003889083862 0.7062366008758545 322.69744873046875 0.3781822621822357 544.6611328125 0.36720502376556396 0.86370337 0.35498058795928955 True -11 32484 29.718844652175903 0.7092299461364746 408.31298828125 0.5094316005706787 543.1294555664062 0.3680135905742645 0.8652699 0.3287024199962616 True -12 35191 29.768489122390747 0.7077012062072754 371.8887634277344 0.35177239775657654 541.49853515625 0.36982542276382446 0.87035483 0.31308943033218384 True -13 37898 29.735217094421387 0.6833014488220215 331.2964172363281 0.3812313377857208 539.509033203125 0.37233564257621765 0.872214 0.3012734055519104 True -14 40605 29.81514596939087 1.3024065494537354 438.07135009765625 0.27686768770217896 537.6317749023438 0.37431246042251587 0.8762007 0.29028794169425964 True -15 43312 29.1766140460968 0.7624847888946533 381.2977294921875 0.26742807030677795 536.2640991210938 0.375985711812973 0.8827087 0.27729639410972595 True -16 46019 29.162280082702637 0.6722686290740967 357.3302001953125 0.29257720708847046 535.6358642578125 0.3764569163322449 0.8845241 0.2693404257297516 True -17 48726 29.174367427825928 0.7074384689331055 437.9740905761719 0.18771536648273468 535.0472412109375 0.3766597807407379 0.88464797 0.2682800590991974 True -18 51433 29.19992423057556 1.6270487308502197 343.53173828125 0.18269366025924683 535.3837280273438 0.3752766251564026 0.88339216 0.2696009576320648 False -19 54140 29.251250505447388 0.7034413814544678 364.06787109375 0.20441915094852448 534.9598999023438 0.3767772614955902 0.88422865 0.2710093855857849 False diff --git a/ENCSR722HJG/cherimoya.fold_1.performance.tsv b/ENCSR722HJG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 30c572f49025d4b00c82a30954d6b058521cb970..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -535.0472412109375 0.4112074077129364 0.3766597509384155 0.14288786053657532 0.8846479654312134 0.8712642192840576 0.2682800590991974 \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_2.evaluate.json b/ENCSR722HJG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2295e570fc4aaf1cc27f22fe945817a5a2903b0b..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_2.fit.json b/ENCSR722HJG/cherimoya.fold_2.fit.json deleted file mode 100644 index f901bb8187edf1149cb3a3f6e2a7b04c7a944c2e..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF955VFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_2.log b/ENCSR722HJG/cherimoya.fold_2.log deleted file mode 100644 index 8a45997adbaca44840e606a4163782081832422f..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2880 36.076603412628174 3.3565053939819336 399.6568908691406 0.410408616065979 561.9632568359375 0.2545996308326721 0.74739987 4.476293563842773 True -1 5760 31.673800230026245 0.6210319995880127 413.76043701171875 0.4869785010814667 514.9164428710938 0.31252071261405945 0.79533005 1.2090195417404175 True -2 8640 31.669390439987183 0.5745484828948975 417.55364990234375 0.4219967722892761 504.6799621582031 0.3251288831233978 0.81225944 0.621105968952179 True -3 11520 31.668652296066284 0.5752038955688477 454.1059265136719 0.5754007697105408 502.5967712402344 0.3264238238334656 0.8110564 0.5360374450683594 False -4 14400 31.701619148254395 0.55133056640625 385.47467041015625 0.3827478289604187 498.4790344238281 0.3320150375366211 0.8194625 0.4958609938621521 True -5 17280 31.700611114501953 0.5918126106262207 418.17230224609375 0.3050071597099304 495.90875244140625 0.3353131115436554 0.8238724 0.46265318989753723 True -6 20160 31.688309907913208 0.5715363025665283 391.4183349609375 0.5277501940727234 493.09930419921875 0.33891773223876953 0.83220273 0.4772632420063019 True -7 23040 31.698644638061523 0.6212096214294434 439.8618469238281 0.5578413009643555 489.9188232421875 0.34397900104522705 0.83950883 0.45577070116996765 True -8 25920 31.64318323135376 0.5762772560119629 452.05328369140625 0.46449029445648193 487.9483337402344 0.3468536138534546 0.846422 0.3763376474380493 True -9 28800 31.698328733444214 0.5745787620544434 480.21368408203125 0.33957695960998535 486.7630310058594 0.3485061824321747 0.8476065 0.37429478764533997 True -10 31680 31.687031984329224 0.5653529167175293 431.8339538574219 0.25414934754371643 485.5276184082031 0.3503691852092743 0.8499262 0.3501967787742615 True -11 34560 31.713479042053223 0.5756931304931641 340.55078125 0.31255561113357544 484.1068420410156 0.35241109132766724 0.85597783 0.32665878534317017 True -12 37440 31.654884576797485 0.8735473155975342 352.314697265625 0.2954981029033661 482.3752746582031 0.355268269777298 0.85934114 0.31064435839653015 True -13 40320 31.713000059127808 0.5728714466094971 385.4140930175781 0.3104756474494934 480.88671875 0.35719984769821167 0.86325485 0.29722291231155396 True -14 43200 31.737979412078857 0.5740742683410645 350.0317077636719 0.4492911100387573 480.794189453125 0.35592108964920044 0.8651308 0.28467217087745667 True -15 46080 31.681527853012085 0.5786614418029785 374.1314697265625 0.33555006980895996 479.5586242675781 0.35843658447265625 0.86861295 0.27584129571914673 True -16 48960 31.16372561454773 14.607487440109253 384.06451416015625 0.29997897148132324 479.2319641113281 0.3586268126964569 0.8716453 0.2660357356071472 True -17 51840 31.211997985839844 0.5736157894134521 387.20635986328125 0.5305428504943848 479.6139831542969 0.3576256334781647 0.87165576 0.2633281648159027 True -18 54720 31.21034860610962 0.5578632354736328 387.9547424316406 0.18527525663375854 479.527587890625 0.35802584886550903 0.8720779 0.26332029700279236 True -19 57600 31.081525802612305 0.5629673004150391 376.0686340332031 0.29916995763778687 478.9499816894531 0.35973918437957764 0.8709796 0.2647387385368347 False diff --git a/ENCSR722HJG/cherimoya.fold_2.performance.tsv b/ENCSR722HJG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2be18494258c94af00efbb6afe047c186adfb2a9..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -479.527587890625 0.42691877484321594 0.3580258786678314 0.12764552235603333 0.8720778822898865 0.849854588508606 0.26332029700279236 \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_3.evaluate.json b/ENCSR722HJG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 998c5bdecd9310aa73157548328681e9b8beb4d7..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_3.fit.json b/ENCSR722HJG/cherimoya.fold_3.fit.json deleted file mode 100644 index 9537e36644e0a41d95e4b8d961aa1499ce54b414..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF955VFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_3.log b/ENCSR722HJG/cherimoya.fold_3.log deleted file mode 100644 index 8a9dcccccc717f1c579b0c173299700b6ccc6ef8..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 34.68020439147949 3.3973257541656494 460.211669921875 0.5417486429214478 532.6343994140625 0.25653374195098877 0.7415153 5.370223045349121 True -1 5504 30.358936309814453 0.5662591457366943 478.1387939453125 0.7040958404541016 485.29583740234375 0.31816980242729187 0.8087553 1.2251579761505127 True -2 8256 30.303948879241943 0.5534918308258057 372.7909240722656 0.7046297788619995 477.21405029296875 0.3266022205352783 0.81560975 0.8242208361625671 True -3 11008 30.28781533241272 0.5302107334136963 422.26751708984375 0.5514340400695801 472.71661376953125 0.33278295397758484 0.8214806 0.6464492082595825 True -4 13760 30.35060405731201 0.5319344997406006 409.8820495605469 0.3869435787200928 471.10003662109375 0.3346092402935028 0.82844526 0.5210022330284119 True -5 16512 30.258323907852173 0.5316762924194336 403.073486328125 0.5224319696426392 469.6112976074219 0.33583056926727295 0.8362078 0.5244814157485962 True -6 19264 30.239397287368774 0.5307393074035645 424.2174377441406 0.5209318995475769 466.42864990234375 0.3413892686367035 0.83879346 0.4841408431529999 True -7 22016 30.236757516860962 1.5819308757781982 401.85467529296875 0.4006164073944092 464.93212890625 0.3428007960319519 0.84502125 0.4524610638618469 True -8 24768 30.268736124038696 0.5441699028015137 477.4217834472656 0.37730035185813904 463.4211120605469 0.3458986282348633 0.8492658 0.43084970116615295 True -9 27520 30.253475189208984 15.013100862503052 401.249755859375 0.34134626388549805 461.4599609375 0.349334716796875 0.8540212 0.4030531644821167 True -10 30272 30.282402276992798 18.489172220230103 351.51153564453125 0.40113019943237305 459.793212890625 0.35143160820007324 0.8579234 0.37700095772743225 True -11 33024 30.45898127555847 0.7014565467834473 313.8103332519531 0.31414300203323364 460.138916015625 0.34968310594558716 0.8626101 0.3535800576210022 True -12 35776 30.28960156440735 0.5443103313446045 331.3433837890625 0.25256866216659546 457.2255554199219 0.35439202189445496 0.86676294 0.3224506378173828 True -13 38528 30.24063467979431 0.5396585464477539 411.5873718261719 0.2815505564212799 456.19085693359375 0.35536977648735046 0.871969 0.3100891709327698 True -14 41280 30.245190143585205 0.5393080711364746 317.56378173828125 0.3883632719516754 454.59771728515625 0.3582228422164917 0.8744935 0.2890942692756653 True -15 44032 30.296252012252808 14.916861534118652 331.01318359375 0.26834726333618164 453.89508056640625 0.35873162746429443 0.8778507 0.2793162167072296 True -16 46784 30.41936755180359 0.5353574752807617 355.7545166015625 0.2207442969083786 453.5911865234375 0.358416885137558 0.88025683 0.26792994141578674 True -17 49536 30.30421471595764 0.5377397537231445 424.108642578125 0.23975379765033722 453.25567626953125 0.3595969080924988 0.8813573 0.2635326385498047 True -18 52288 29.701043605804443 0.5141091346740723 346.29046630859375 0.23684877157211304 453.56842041015625 0.35878250002861023 0.8816087 0.2617024779319763 True -19 55040 29.676908493041992 0.5274996757507324 381.02606201171875 0.25002321600914 453.2803649902344 0.3594035804271698 0.8810941 0.26227718591690063 False diff --git a/ENCSR722HJG/cherimoya.fold_3.performance.tsv b/ENCSR722HJG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5491e6ff10961d763acdf60bc464f7aded36aa8e..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -453.56842041015625 0.42930227518081665 0.35878250002861023 0.12694749236106873 0.8816087245941162 0.8517191410064697 0.2617024779319763 \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_4.evaluate.json b/ENCSR722HJG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e475da4058f0de7739b05185bee941d7e2ad87e9..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF955VFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_4.fit.json b/ENCSR722HJG/cherimoya.fold_4.fit.json deleted file mode 100644 index 9c83ff40a42502e64334a5421f9e5a3a3acedb73..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF955VFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR722HJG/cherimoya.fold_4.log b/ENCSR722HJG/cherimoya.fold_4.log deleted file mode 100644 index 31dc379bfbd2714c1523c37b04ffc8c7cc436e84..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2797 35.46569061279297 4.00463080406189 340.15704345703125 0.4938591718673706 498.3344421386719 0.24609284102916718 0.7424661 4.258392810821533 True -1 5594 30.82938051223755 1.1231427192687988 458.46478271484375 0.4732196629047394 460.2020263671875 0.30082565546035767 0.7860916 1.1350884437561035 True -2 8391 30.801594734191895 1.3956818580627441 325.7283020019531 0.38683798909187317 451.8514709472656 0.31299370527267456 0.7981842 0.5598244071006775 True -3 11188 30.802769899368286 1.6051387786865234 378.85406494140625 0.5227052569389343 447.5338134765625 0.31818887591362 0.8097612 0.38899630308151245 True -4 13985 30.81467342376709 1.483748197555542 430.6736755371094 0.37655460834503174 446.1336364746094 0.3188004195690155 0.8194051 0.35490691661834717 True -5 16782 30.72011137008667 0.6136348247528076 369.4761962890625 0.42491859197616577 442.9944763183594 0.32466045022010803 0.82081044 0.3639679253101349 True -6 19579 30.764989852905273 0.6149051189422607 444.83160400390625 0.6486085057258606 442.6084899902344 0.32485881447792053 0.8270046 0.37230032682418823 True -7 22376 30.80004119873047 0.5945956707000732 358.56414794921875 0.526102602481842 439.7105407714844 0.32919466495513916 0.8353321 0.35195866227149963 True -8 25173 30.780739545822144 0.5921890735626221 336.85589599609375 0.29864540696144104 438.14691162109375 0.3320253789424896 0.83963364 0.32647904753685 True -9 27970 30.72934651374817 0.599353551864624 430.76275634765625 0.4152226746082306 436.5959167480469 0.33478590846061707 0.8448348 0.33177947998046875 True -10 30767 30.721487760543823 0.6065430641174316 432.95428466796875 0.3621349632740021 435.5855712890625 0.3368099629878998 0.8483052 0.3091306984424591 True -11 33564 30.795818328857422 0.6052646636962891 368.45526123046875 0.3157438635826111 434.3339538574219 0.3385423719882965 0.8540973 0.30986639857292175 True -12 36361 30.902177333831787 0.6129803657531738 373.234619140625 0.3410232663154602 432.7120056152344 0.3414512574672699 0.8590784 0.29499244689941406 True -13 39158 30.837995529174805 0.6262261867523193 411.49908447265625 0.29352766275405884 432.2514953613281 0.3411887586116791 0.86296415 0.2734018564224243 True -14 41955 30.987110137939453 0.6171677112579346 401.1015625 0.2841469943523407 431.48455810546875 0.3428552448749542 0.8666654 0.26021677255630493 True -15 44752 31.022626876831055 17.406039237976074 312.17291259765625 0.3198743462562561 431.3946533203125 0.3427633047103882 0.8698338 0.24778050184249878 True -16 47549 30.9428927898407 0.6120762825012207 431.0385437011719 0.20840895175933838 430.43756103515625 0.3450147211551666 0.872443 0.24464817345142365 True -17 50346 30.954546451568604 0.6718456745147705 403.26324462890625 0.256359726190567 430.3768310546875 0.3450986444950104 0.8724295 0.24166569113731384 False -18 53143 30.953964948654175 0.6139018535614014 329.9164733886719 0.15166383981704712 430.9857482910156 0.3437418043613434 0.8720303 0.23935826122760773 False -19 55940 30.94705629348755 0.6096534729003906 328.4625244140625 0.2382698357105255 431.234375 0.34342890977859497 0.8718313 0.24108478426933289 False diff --git a/ENCSR722HJG/cherimoya.fold_4.performance.tsv b/ENCSR722HJG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e4b4bbb6d3b9003a9942aefe1d651b5f2e4ede61..0000000000000000000000000000000000000000 --- a/ENCSR722HJG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -430.43756103515625 0.4394803047180176 0.34501469135284424 0.11571262776851654 0.8724430203437805 0.8379402160644531 0.24464817345142365 \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_0.evaluate.json b/ENCSR723JLG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3bfd59d7a8181dfb8d7a4e65d81eb107383e2bae..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537TVG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_0.fit.json b/ENCSR723JLG/cherimoya.fold_0.fit.json deleted file mode 100644 index 00adccc111a8d9a3eb378a35acea0095462a8b24..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF537TVG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_0.log b/ENCSR723JLG/cherimoya.fold_0.log deleted file mode 100644 index f96977b59dc529fc31fb61ac8d08ae13946367e7..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2210 28.737172842025757 4.26932168006897 259.35113525390625 0.9817217588424683 299.6097412109375 0.1315460503101349 0.48906106 5.825835704803467 True -1 4420 24.352880001068115 0.451371431350708 197.61097717285156 0.7759827375411987 285.7709045410156 0.19031672179698944 0.6094627 2.1572818756103516 True -2 6630 24.38217854499817 26.76469373703003 224.4248046875 0.6431215405464172 280.8379821777344 0.20471780002117157 0.6754723 0.8043161034584045 True -3 8840 26.93331027030945 0.43311357498168945 216.135009765625 0.6656781435012817 278.37701416015625 0.21184736490249634 0.7059439 0.4900074005126953 True -4 11050 24.340763330459595 1.9313650131225586 210.56814575195312 0.6194161176681519 277.2513122558594 0.21530109643936157 0.710439 0.48225224018096924 True -5 13260 24.211385250091553 0.41712045669555664 247.06678771972656 0.8016852736473083 276.2764892578125 0.21783806383609772 0.7213563 0.4512467086315155 True -6 15470 23.855900049209595 0.42066359519958496 242.25941467285156 0.7730103731155396 275.3847351074219 0.2211558073759079 0.7259969 0.4527885317802429 True -7 17680 23.8450665473938 0.490558385848999 226.521484375 0.6065577268600464 275.03106689453125 0.222237691283226 0.7312264 0.4484598636627197 True -8 19890 23.828068256378174 1.4392383098602295 170.05908203125 0.5005123615264893 274.59393310546875 0.22302588820457458 0.7348896 0.43901512026786804 True -9 22100 23.825594663619995 0.6225559711456299 272.5485534667969 0.44138088822364807 274.1536865234375 0.22499080002307892 0.74397546 0.4321432411670685 True -10 24310 23.88583540916443 3.703516960144043 206.07464599609375 0.6977798938751221 273.5592041015625 0.22685366868972778 0.7504172 0.42289257049560547 True -11 26520 23.82947564125061 0.4197850227355957 190.08889770507812 0.44678372144699097 273.3177795410156 0.2278292030096054 0.7535479 0.42001891136169434 True -12 28730 23.76216197013855 0.41460537910461426 197.32354736328125 0.478586345911026 273.2584228515625 0.22796942293643951 0.7585021 0.4155430197715759 True -13 30940 23.853509426116943 0.42014408111572266 232.47451782226562 0.5404236316680908 272.839111328125 0.2299645096063614 0.7634222 0.41366398334503174 True -14 33150 23.826531648635864 0.4155426025390625 227.04510498046875 0.5274471044540405 272.55780029296875 0.23101255297660828 0.7669885 0.41473644971847534 True -15 35360 23.867552042007446 0.4135873317718506 206.52867126464844 0.45321452617645264 272.5822448730469 0.23077383637428284 0.76805186 0.41453173756599426 True -16 37570 23.896438360214233 0.4095752239227295 207.4637451171875 0.3780101537704468 272.63177490234375 0.2312944084405899 0.7695834 0.42542558908462524 True -17 39780 23.849120378494263 0.415802001953125 206.97390747070312 0.35757240653038025 273.272705078125 0.2278621345758438 0.7664391 0.4429647922515869 False -18 41990 23.825028657913208 0.4133288860321045 211.64248657226562 0.419482946395874 273.5347900390625 0.22681204974651337 0.7626574 0.45966488122940063 False -19 44200 23.76508665084839 0.4076261520385742 239.79052734375 0.25801870226860046 273.5559997558594 0.22686204314231873 0.7600037 0.46964770555496216 False diff --git a/ENCSR723JLG/cherimoya.fold_0.performance.tsv b/ENCSR723JLG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3331d7808eebfa4f883eec48fccded9d29ed606f..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -272.63177490234375 0.517874538898468 0.2312944233417511 0.07412252575159073 0.7695834040641785 0.7505201697349548 0.42542558908462524 \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_1.evaluate.json b/ENCSR723JLG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 558bea78323eff98a891c784bc08f8da4e78de87..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537TVG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_1.fit.json b/ENCSR723JLG/cherimoya.fold_1.fit.json deleted file mode 100644 index 66d099aff7d19b70411e1fa42e5273e08d69a8cb..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF537TVG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_1.log b/ENCSR723JLG/cherimoya.fold_1.log deleted file mode 100644 index a82f02cf277e88e8c4c8d9a7b2e9b064a86d73f7..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2201 28.751229286193848 3.6305785179138184 250.49859619140625 0.9303679466247559 341.4934387207031 0.1436186134815216 0.49528593 5.68491792678833 True -1 4402 24.230553150177002 0.6367020606994629 265.87847900390625 0.7286874651908875 326.2176208496094 0.20118729770183563 0.64554703 2.2958414554595947 True -2 6603 24.203514337539673 0.6340560913085938 224.2156524658203 0.8628820180892944 318.093505859375 0.22528867423534393 0.71805036 0.9175693988800049 True -3 8804 24.190548181533813 1.4907209873199463 233.5515899658203 0.4940471053123474 315.7828674316406 0.23024673759937286 0.73838055 0.595930278301239 True -4 11005 24.25980806350708 3.1298820972442627 184.76431274414062 0.6937496066093445 313.875732421875 0.23599879443645477 0.7497051 0.5133631825447083 True -5 13206 24.24141788482666 0.6243228912353516 241.48089599609375 1.1112451553344727 313.697509765625 0.2341645061969757 0.75350136 0.47693920135498047 True -6 15407 24.292040824890137 0.6237492561340332 188.56427001953125 0.4508935809135437 312.30096435546875 0.23943795263767242 0.7586754 0.4614832103252411 True -7 17608 25.177835941314697 32.566704988479614 173.90484619140625 0.5422554016113281 311.59930419921875 0.24107930064201355 0.7619123 0.4489300549030304 True -8 19809 24.219990253448486 2.7539587020874023 245.6527557373047 0.3883683979511261 311.583984375 0.2402641326189041 0.7633911 0.4392020106315613 True -9 22010 24.224727153778076 0.624946117401123 212.21995544433594 0.4688652753829956 311.007568359375 0.2417937070131302 0.7713715 0.42962759733200073 True -10 24211 23.759816646575928 0.6151213645935059 166.88424682617188 0.7118102312088013 309.9334411621094 0.24531589448451996 0.77528965 0.42002472281455994 True -11 26412 23.83481001853943 0.6219451427459717 164.0556640625 0.685401439666748 309.36883544921875 0.24703501164913177 0.77720165 0.41445496678352356 True -12 28613 23.71759343147278 0.6117644309997559 231.61119079589844 0.3983236253261566 309.1890563964844 0.2475271224975586 0.78274304 0.4121628403663635 True -13 30814 23.81727886199951 0.6869242191314697 198.92572021484375 0.5730910301208496 308.95098876953125 0.24853529036045074 0.7872618 0.4103599786758423 True -14 33015 23.852569341659546 0.6333427429199219 253.43898010253906 0.3439754247665405 308.2433776855469 0.250898540019989 0.7908417 0.4110140800476074 True -15 35216 23.721944332122803 0.6189508438110352 224.883056640625 0.2651602625846863 308.3229064941406 0.25056126713752747 0.7948834 0.41289374232292175 True -16 37417 23.800257205963135 0.6117007732391357 192.32200622558594 0.31897488236427307 308.8303527832031 0.24924704432487488 0.7922096 0.42879393696784973 False -17 39618 23.791340827941895 27.271990060806274 211.74285888671875 0.2895864248275757 308.9061279296875 0.24848997592926025 0.7927341 0.4480768144130707 False -18 41819 24.1088809967041 0.6311726570129395 235.74713134765625 0.30911362171173096 309.5571594238281 0.24591144919395447 0.7896561 0.4690427780151367 False -19 44020 23.785263061523438 0.6244077682495117 218.12908935546875 0.2666130065917969 309.40362548828125 0.24704045057296753 0.7862304 0.47756296396255493 False diff --git a/ENCSR723JLG/cherimoya.fold_1.performance.tsv b/ENCSR723JLG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 548d991569a5fc33b1cef9d7bbb582f51a9cd574..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.3229064941406 0.5006235837936401 0.25056126713752747 0.08055508881807327 0.7948833703994751 0.7766003012657166 0.41289374232292175 \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_2.evaluate.json b/ENCSR723JLG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1b0b8a3f820f370723c71e2b06a4770948c03397..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537TVG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_2.fit.json b/ENCSR723JLG/cherimoya.fold_2.fit.json deleted file mode 100644 index 1b804c93d44d8b0460941ab6cfc8d2b1331683e4..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF537TVG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_2.log b/ENCSR723JLG/cherimoya.fold_2.log deleted file mode 100644 index cbaaaa28609e8110f1ed93ead8b3061a66a3097d..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2364 30.69025206565857 3.056837320327759 296.1957092285156 0.8698817491531372 306.83770751953125 0.14180178940296173 0.50478274 4.525886058807373 True -1 4728 26.046963214874268 1.5813977718353271 216.06385803222656 0.9973124861717224 292.99951171875 0.19646400213241577 0.643123 1.685850739479065 True -2 7092 25.992515563964844 0.39639854431152344 212.63595581054688 0.5914407968521118 287.7467956542969 0.21265915036201477 0.69244444 0.6177058219909668 True -3 9456 25.44022488594055 0.44640302658081055 242.8377685546875 0.7564592361450195 285.1728820800781 0.2198229879140854 0.7154208 0.5080097913742065 True -4 11820 25.448691844940186 0.3853740692138672 222.48240661621094 0.43175068497657776 283.1722412109375 0.22631870210170746 0.7262555 0.4621686637401581 True -5 14184 25.423243522644043 0.38527917861938477 200.08331298828125 0.735817551612854 282.7965087890625 0.22645416855812073 0.7323447 0.466778039932251 True -6 16548 25.475476503372192 0.4009883403778076 164.08738708496094 0.5629256963729858 282.7550964355469 0.22564338147640228 0.7348443 0.4617433547973633 True -7 18912 25.557698488235474 0.37947940826416016 198.10009765625 0.4467817544937134 281.6289978027344 0.2299576997756958 0.73955864 0.4448508024215698 True -8 21276 25.73712944984436 1.2132835388183594 266.32757568359375 0.8270134925842285 281.0758972167969 0.23136760294437408 0.7434128 0.4383690357208252 True -9 23640 25.602457284927368 0.3856048583984375 258.6962890625 0.613918662071228 280.094970703125 0.23516882956027985 0.74851876 0.4313477575778961 True -10 26004 25.613107204437256 0.8627810478210449 214.29885864257812 0.6389796137809753 280.208251953125 0.23465557396411896 0.75237125 0.42602482438087463 True -11 28368 25.727828979492188 0.3839693069458008 231.7524871826172 0.42717456817626953 279.8089904785156 0.23619161546230316 0.7548842 0.4265673756599426 True -12 30732 25.45473575592041 17.919312238693237 188.26864624023438 0.5338049530982971 279.4474182128906 0.2369358092546463 0.75781304 0.42598748207092285 True -13 33096 26.139360189437866 0.38643980026245117 234.78851318359375 0.4331292510032654 278.9620361328125 0.2398570328950882 0.7617092 0.42271876335144043 True -14 35460 25.51950716972351 0.3929452896118164 267.9564514160156 0.32470208406448364 279.3276062011719 0.23776094615459442 0.76423854 0.4251839518547058 True -15 37824 25.901487827301025 25.85881519317627 202.32168579101562 0.4481225609779358 279.11737060546875 0.23876546323299408 0.76604205 0.4326719343662262 True -16 40188 25.51181149482727 0.3878164291381836 207.40771484375 0.4000733494758606 278.471435546875 0.24156233668327332 0.7651439 0.44245535135269165 False -17 42552 28.751537799835205 6.019504070281982 194.529541015625 0.23331227898597717 279.2564697265625 0.238095223903656 0.76078826 0.4615621864795685 False -18 44916 25.513970136642456 1.3304619789123535 212.09915161132812 0.35686933994293213 279.3426818847656 0.23762613534927368 0.7586545 0.47576501965522766 False -19 47280 25.61599850654602 0.37795042991638184 223.9453125 0.33168846368789673 279.728271484375 0.23591504991054535 0.7560026 0.48559659719467163 False diff --git a/ENCSR723JLG/cherimoya.fold_2.performance.tsv b/ENCSR723JLG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index befecf5e77ee608e586d4bb0ec95d28e2523a930..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -279.11737060546875 0.5129121541976929 0.23876544833183289 0.07050319761037827 0.7660420536994934 0.7471308708190918 0.4326719343662262 \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_3.evaluate.json b/ENCSR723JLG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2e2dce64f885661b1352eef4f0205f9877b39829..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537TVG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_3.fit.json b/ENCSR723JLG/cherimoya.fold_3.fit.json deleted file mode 100644 index d67fd663b1821807800683375687a4149e94c6bd..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF537TVG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_3.log b/ENCSR723JLG/cherimoya.fold_3.log deleted file mode 100644 index 62c6e228ea7b6c92bcc78532337cb02aad41d1c0..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2272 29.464998960494995 3.3426809310913086 218.518798828125 0.7952432036399841 334.13885498046875 0.14324940741062164 0.49962494 6.208663463592529 True -1 4544 25.59754252433777 0.917137861251831 304.376708984375 0.689773678779602 319.6603698730469 0.20016200840473175 0.65841156 1.707426905632019 True -2 6816 24.994526863098145 0.45990920066833496 209.65480041503906 0.5145537853240967 314.9090270996094 0.21433912217617035 0.692798 0.793228268623352 True -3 9088 25.00400471687317 0.4551887512207031 291.6309509277344 0.7226632833480835 312.60150146484375 0.21868132054805756 0.71340734 0.560469388961792 True -4 11360 25.30662703514099 18.493116855621338 196.09768676757812 0.5345478057861328 310.92205810546875 0.22424043715000153 0.7225813 0.5245651006698608 True -5 13632 25.01341438293457 0.7145764827728271 244.2809600830078 1.0311224460601807 309.8898620605469 0.22783201932907104 0.73184067 0.5188682079315186 True -6 15904 25.00509214401245 1.5072379112243652 220.0425262451172 0.7327165603637695 309.09674072265625 0.2295726239681244 0.7380028 0.5171316266059875 True -7 18176 25.018258571624756 0.5985069274902344 235.92662048339844 0.6301599740982056 309.136962890625 0.22904649376869202 0.7379257 0.4905807375907898 False -8 20448 25.020769834518433 0.4573242664337158 249.50418090820312 0.5772472620010376 308.3290710449219 0.23138317465782166 0.74221814 0.48176419734954834 True -9 22720 25.298131465911865 12.662711143493652 229.9464111328125 0.754703938961029 307.5313415527344 0.2343500405550003 0.74301445 0.4729621410369873 True -10 24992 25.007612466812134 0.4690699577331543 241.67007446289062 0.39967602491378784 307.4986267089844 0.23410947620868683 0.7446441 0.47283488512039185 True -11 27264 24.954615354537964 0.45729589462280273 259.6794128417969 0.3957575559616089 307.11700439453125 0.23558010160923004 0.74951905 0.45989346504211426 True -12 29536 24.711084127426147 0.4822664260864258 261.38433837890625 0.45512688159942627 306.9109191894531 0.23602856695652008 0.7534993 0.45413845777511597 True -13 31808 24.45722007751465 0.45503902435302734 212.81002807617188 0.4263637959957123 306.77142333984375 0.2354288101196289 0.7564968 0.4525163173675537 True -14 34080 24.450380563735962 1.2805652618408203 225.26715087890625 0.40991729497909546 306.6890563964844 0.23628905415534973 0.7602149 0.4540017545223236 True -15 36352 24.497886896133423 0.4519932270050049 212.9305419921875 0.36621642112731934 306.2533874511719 0.23766444623470306 0.7652164 0.46065187454223633 True -16 38624 24.46775507926941 0.4608643054962158 187.49530029296875 0.44491860270500183 305.9789123535156 0.23854097723960876 0.76790744 0.47204363346099854 True -17 40896 24.45390033721924 0.45989036560058594 214.61404418945312 0.3069112002849579 306.8958435058594 0.23462067544460297 0.76350385 0.5048815608024597 False -18 43168 24.460322380065918 0.45747923851013184 212.50479125976562 0.2960321307182312 307.10601806640625 0.23440438508987427 0.75845134 0.5310093760490417 False -19 45440 24.45662808418274 0.4655342102050781 189.43264770507812 0.27128928899765015 307.0746154785156 0.23475061357021332 0.75710034 0.5457317233085632 False diff --git a/ENCSR723JLG/cherimoya.fold_3.performance.tsv b/ENCSR723JLG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1dcf8062212f749183aae9ace7b0020a23c12cc3..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -305.9789123535156 0.5069361329078674 0.23854097723960876 0.07708986103534698 0.767907440662384 0.7471665740013123 0.47204363346099854 \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_4.evaluate.json b/ENCSR723JLG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b4a54cef523afcdd86359441fb0578cea3f3be69..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537TVG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_4.fit.json b/ENCSR723JLG/cherimoya.fold_4.fit.json deleted file mode 100644 index b452bd646922b4c6087a308f2d358631db759bd1..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF537TVG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR723JLG/cherimoya.fold_4.log b/ENCSR723JLG/cherimoya.fold_4.log deleted file mode 100644 index c8bd08d44b912a7f72124dcb5301690bc94abc3a..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2282 29.651384830474854 4.664207935333252 241.19302368164062 1.1722453832626343 303.00323486328125 0.13900409638881683 0.49955922 4.771843910217285 True -1 4564 25.14906120300293 13.267869710922241 234.5148162841797 0.701539158821106 291.3755187988281 0.18878085911273956 0.62009424 2.075348377227783 True -2 6846 25.112674951553345 0.423842191696167 316.62713623046875 0.8310250043869019 285.52532958984375 0.20548191666603088 0.6842998 0.7861713171005249 True -3 9128 25.163850784301758 1.9426791667938232 209.84356689453125 0.533311128616333 282.8370666503906 0.2121959626674652 0.70112884 0.5473058223724365 True -4 11410 25.134952783584595 0.4342982769012451 248.3905029296875 0.5202322006225586 281.30633544921875 0.21726185083389282 0.71170664 0.4919922649860382 True -5 13692 24.604037284851074 0.4258382320404053 249.47203063964844 0.707852840423584 280.5712890625 0.21933113038539886 0.71305716 0.488677442073822 True -6 15974 24.578589916229248 0.41538262367248535 209.51844787597656 0.8050726652145386 280.4794006347656 0.21907225251197815 0.7157336 0.48005321621894836 True -7 18256 24.549341201782227 3.3704817295074463 220.26358032226562 0.6529152393341064 279.7457275390625 0.22189968824386597 0.7195877 0.4808136224746704 True -8 20538 24.63940191268921 0.4351520538330078 191.56951904296875 0.6813308000564575 279.2615661621094 0.2233046144247055 0.72513396 0.4670940339565277 True -9 22820 24.685314893722534 0.4215877056121826 201.21121215820312 0.3156314790248871 278.7285461425781 0.22492873668670654 0.7279191 0.46235305070877075 True -10 25102 24.6374728679657 0.4128577709197998 197.67510986328125 0.40540987253189087 278.52325439453125 0.22574780881404877 0.7307502 0.460505872964859 True -11 27384 24.58854579925537 0.41485095024108887 224.71426391601562 0.42122331261634827 278.2408447265625 0.22629570960998535 0.7353168 0.46080532670021057 True -12 29666 24.57336711883545 10.902844429016113 201.1846466064453 0.6073399782180786 277.9346923828125 0.22759270668029785 0.7397336 0.4618358016014099 True -13 31948 24.759198904037476 0.42584705352783203 227.4290313720703 0.3298789858818054 277.2864990234375 0.2307479977607727 0.74247944 0.4606517255306244 True -14 34230 24.760913848876953 0.4365205764770508 218.31105041503906 0.4984110891819 277.4742126464844 0.22890503704547882 0.7475217 0.45731601119041443 True -15 36512 24.786362171173096 5.529140472412109 169.7346649169922 0.5361262559890747 277.301513671875 0.2299298793077469 0.74740684 0.46550896763801575 False -16 38794 25.791757345199585 0.4213380813598633 223.76678466796875 0.35081201791763306 277.61773681640625 0.2287668138742447 0.7476132 0.47808659076690674 True -17 41076 24.77485156059265 0.4213893413543701 185.42919921875 0.2136663794517517 278.009765625 0.22741779685020447 0.7448764 0.4968516528606415 False -18 43358 26.080435752868652 16.918736934661865 200.3648223876953 0.3966062664985657 278.021728515625 0.22721141576766968 0.73846036 0.5167470574378967 False -19 45640 25.424208879470825 1.7661421298980713 182.270263671875 0.29087838530540466 278.21075439453125 0.2264089733362198 0.7365479 0.5300971865653992 False diff --git a/ENCSR723JLG/cherimoya.fold_4.performance.tsv b/ENCSR723JLG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 576df312378e8d889569fb1e5af34929fd52fc23..0000000000000000000000000000000000000000 --- a/ENCSR723JLG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -277.61773681640625 0.5176889300346375 0.2287668138742447 0.07450775057077408 0.7476131916046143 0.7281767725944519 0.47808659076690674 \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_0.evaluate.json b/ENCSR726YMS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8155851b92eeda41831f718f1c1d405111370c06..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF113VOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_0.fit.json b/ENCSR726YMS/cherimoya.fold_0.fit.json deleted file mode 100644 index 07fecde14d3733dac917941889dab8621a037317..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF113VOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_0.log b/ENCSR726YMS/cherimoya.fold_0.log deleted file mode 100644 index 985a7f0e2575c7142e24d54e5cb06b735dc012ef..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.37680244445801 3.5694141387939453 154.6524658203125 0.6373182535171509 249.44158935546875 0.13875725865364075 0.675792 3.3997292518615723 True -1 5494 30.72046399116516 0.6134302616119385 222.62905883789062 0.650166392326355 236.0640411376953 0.20552366971969604 0.74035853 0.9883715510368347 True -2 8241 30.723814249038696 0.587428092956543 180.7549285888672 0.8372493982315063 232.26974487304688 0.21942582726478577 0.74754864 0.5376064777374268 True -3 10988 30.71452808380127 0.5858192443847656 157.55474853515625 0.6220201253890991 231.34640502929688 0.22130972146987915 0.7574562 0.42553460597991943 True -4 13735 30.69442391395569 0.597235918045044 186.75830078125 0.7788996696472168 230.9675750732422 0.2225828915834427 0.7560067 0.42072588205337524 False -5 16482 31.75625777244568 0.8955230712890625 188.47779846191406 0.5203425884246826 230.2653045654297 0.22634083032608032 0.7628982 0.46667155623435974 True -6 19229 30.689445972442627 0.5961658954620361 177.33160400390625 0.5506711602210999 229.8447265625 0.22803349792957306 0.7624445 0.4863511621952057 False -7 21976 30.714228868484497 0.5961859226226807 182.78915405273438 0.5173847675323486 229.48065185546875 0.2303100824356079 0.7648524 0.47342267632484436 True -8 24723 30.712886571884155 0.5908844470977783 120.04219818115234 0.5297702550888062 228.9235382080078 0.2330094575881958 0.7692341 0.49338778853416443 True -9 27470 30.712236881256104 0.6065735816955566 181.77796936035156 0.29454708099365234 228.63900756835938 0.23422099649906158 0.76950383 0.4654592275619507 True -10 30217 32.31460499763489 0.613715648651123 185.59664916992188 0.6945585012435913 228.43496704101562 0.2356361299753189 0.77265894 0.43569472432136536 True -11 32964 30.776700973510742 0.5984244346618652 152.02627563476562 0.5174418687820435 227.6779022216797 0.24012650549411774 0.7771949 0.43186575174331665 True -12 35711 30.769714832305908 0.5939486026763916 175.23919677734375 0.5589621067047119 227.45945739746094 0.2398686558008194 0.7846832 0.39390477538108826 True -13 38458 30.775788068771362 0.598822832107544 153.31838989257812 0.4485499858856201 227.0750274658203 0.24218106269836426 0.79187125 0.3549424409866333 True -14 41205 30.784303188323975 20.254061460494995 192.16024780273438 0.37050676345825195 226.58799743652344 0.24460469186306 0.7978195 0.3357350528240204 True -15 43952 30.746923208236694 0.5920450687408447 172.3394317626953 0.27534618973731995 226.45225524902344 0.24504448473453522 0.80335575 0.31427913904190063 True -16 46699 30.76800513267517 0.9384207725524902 144.99807739257812 0.417080819606781 226.35867309570312 0.24534054100513458 0.80731887 0.3052235543727875 True -17 49446 30.72800636291504 0.5968692302703857 214.39456176757812 0.24611631035804749 226.53977966308594 0.24436672031879425 0.810628 0.29845374822616577 True -18 52193 30.727404356002808 0.594724178314209 187.84280395507812 0.44070497155189514 226.20925903320312 0.2465546727180481 0.80904 0.3012084364891052 False -19 54940 30.78083300590515 0.6208975315093994 159.17086791992188 0.38462889194488525 226.1787872314453 0.24663802981376648 0.80865204 0.3015492856502533 False diff --git a/ENCSR726YMS/cherimoya.fold_0.performance.tsv b/ENCSR726YMS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e72cc1dd618694bbdefbf99d3dd9f0a9f5f650fc..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -226.53977966308594 0.5265809893608093 0.24436673521995544 0.05830571800470352 0.8106279969215393 0.7373749613761902 0.29845374822616577 \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_1.evaluate.json b/ENCSR726YMS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7fe22fe9f05ac6ea3f6bb9bade7502c1fc0bcbe7..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF113VOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_1.fit.json b/ENCSR726YMS/cherimoya.fold_1.fit.json deleted file mode 100644 index fccaa692060efec418289a27ebbaf5bbcb7fa79f..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF113VOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_1.log b/ENCSR726YMS/cherimoya.fold_1.log deleted file mode 100644 index 852304140e3073a91bc1c849cf09a51f556f35df..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.427570104599 4.586855173110962 177.0753173828125 0.8108378648757935 290.03857421875 0.15661460161209106 0.6766705 3.3837358951568604 True -1 5494 30.81339454650879 0.7446897029876709 167.10494995117188 0.7927272319793701 274.9074401855469 0.22186237573623657 0.7404576 1.214166522026062 True -2 8241 31.126602172851562 1.223482608795166 151.44517517089844 0.4752799868583679 269.60968017578125 0.23778483271598816 0.76444614 0.6642532348632812 True -3 10988 30.840670824050903 0.7411563396453857 146.6434326171875 0.46335577964782715 267.6814880371094 0.24167320132255554 0.76652455 0.6259092092514038 True -4 13735 30.767674922943115 0.736912727355957 196.45579528808594 0.3495667278766632 266.8091125488281 0.24524028599262238 0.7666279 0.6395573616027832 True -5 16482 30.718099117279053 0.7520203590393066 152.54933166503906 0.6018300652503967 266.32769775390625 0.24682453274726868 0.77215165 0.6129220128059387 True -6 19229 30.876389265060425 2.62093186378479 171.12966918945312 0.5954558253288269 265.46783447265625 0.2505759000778198 0.7808581 0.5524428486824036 True -7 21976 30.82438039779663 1.1244726181030273 155.91387939453125 0.5870668888092041 264.6625061035156 0.2534789741039276 0.7841522 0.5322298407554626 True -8 24723 30.843716859817505 0.763920783996582 206.234130859375 0.47129958868026733 264.6621398925781 0.25353047251701355 0.78913903 0.4785550534725189 True -9 27470 30.891170501708984 0.9368538856506348 215.28472900390625 0.5261996388435364 264.01055908203125 0.2559196352958679 0.7908175 0.4861307740211487 True -10 30217 30.928043365478516 0.7402682304382324 172.836181640625 0.5142655968666077 263.4888000488281 0.258586049079895 0.7966507 0.4504753649234772 True -11 32964 30.96633243560791 2.2900643348693848 169.02664184570312 0.43360987305641174 263.1212463378906 0.25914859771728516 0.80239266 0.41782718896865845 True -12 35711 30.93933939933777 0.7501320838928223 167.53057861328125 0.46819233894348145 262.2467041015625 0.26319947838783264 0.8062937 0.40488964319229126 True -13 38458 31.04410171508789 1.0828666687011719 159.4322509765625 0.3405829668045044 261.6610107421875 0.26478704810142517 0.81381214 0.39413484930992126 True -14 41205 30.778223037719727 0.738062858581543 208.7374267578125 0.3021678924560547 261.3628234863281 0.26583331823349 0.820967 0.3556636869907379 True -15 43952 30.790001392364502 0.7406954765319824 236.76507568359375 0.3054180145263672 261.12530517578125 0.2673645615577698 0.8277103 0.3372535705566406 True -16 46699 30.782857656478882 0.7330262660980225 220.0581817626953 0.3203471302986145 261.0003356933594 0.26715415716171265 0.82984185 0.3244643211364746 True -17 49446 31.011489868164062 5.590814590454102 186.91677856445312 0.25499457120895386 260.5257263183594 0.2697332203388214 0.8310663 0.3209035098552704 True -18 52193 31.199872493743896 1.129284143447876 167.52333068847656 0.25881797075271606 261.2635192871094 0.26601627469062805 0.8325114 0.31870660185813904 True -19 54940 30.811142444610596 0.7294430732727051 174.58920288085938 0.27256113290786743 261.3219909667969 0.2658149302005768 0.8302157 0.32165369391441345 False diff --git a/ENCSR726YMS/cherimoya.fold_1.performance.tsv b/ENCSR726YMS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 66b109056c274f5339f05d6838d8fe8436ee3cd6..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -261.2635192871094 0.5078731775283813 0.26601624488830566 0.07265259325504303 0.8325114250183105 0.7826265692710876 0.31870660185813904 \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_2.evaluate.json b/ENCSR726YMS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3959d48a02057827e3433af126ad1d5f811278cf..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF113VOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_2.fit.json b/ENCSR726YMS/cherimoya.fold_2.fit.json deleted file mode 100644 index be7f23e05c9b7e6f669cf1ff7800718face8e9fa..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF113VOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_2.log b/ENCSR726YMS/cherimoya.fold_2.log deleted file mode 100644 index 5ff501b50764d81b4cf62f9053085bd070ac8cfe..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2901 36.30308151245117 3.6054913997650146 209.25094604492188 0.7345221042633057 253.7981719970703 0.14543592929840088 0.6796391 2.2735557556152344 True -1 5802 32.5502495765686 1.4288814067840576 158.35989379882812 0.39714938402175903 239.21824645996094 0.21380864083766937 0.7418519 0.8504299521446228 True -2 8703 32.50429844856262 0.5800056457519531 207.56210327148438 0.643854022026062 235.90171813964844 0.22523900866508484 0.7590485 0.5254780650138855 True -3 11604 32.505218744277954 0.5709738731384277 177.30352783203125 0.6823890209197998 234.56365966796875 0.22944119572639465 0.7582662 0.39693424105644226 False -4 14505 32.51874876022339 0.5681405067443848 212.31321716308594 0.6827983856201172 233.69703674316406 0.2331317663192749 0.76307297 0.40327319502830505 True -5 17406 32.54708385467529 8.615254163742065 172.07569885253906 0.3922434449195862 233.29188537597656 0.23397140204906464 0.7679586 0.3739570081233978 True -6 20307 32.49440121650696 2.424067974090576 187.7888946533203 0.5208318829536438 232.89280700683594 0.23589205741882324 0.76761264 0.40769582986831665 False -7 23208 32.456624269485474 0.7389914989471436 169.61265563964844 0.556950569152832 232.32949829101562 0.2383454442024231 0.7725509 0.39440619945526123 True -8 26109 32.48655819892883 0.5740478038787842 196.63038635253906 0.46817752718925476 232.00572204589844 0.23959699273109436 0.77431494 0.409942626953125 True -9 29010 32.50349712371826 0.5723922252655029 201.92730712890625 0.5276483297348022 231.96690368652344 0.23970094323158264 0.7773815 0.4207901954650879 True -10 31911 32.58710741996765 0.572258472442627 210.03768920898438 0.5246094465255737 231.46380615234375 0.2422349900007248 0.77884877 0.4292345345020294 True -11 34812 32.514490604400635 0.5627667903900146 185.7154998779297 0.4222400188446045 231.4967041015625 0.24149785935878754 0.78088236 0.427202969789505 True -12 37713 32.521554470062256 0.574143648147583 173.46932983398438 0.3969959318637848 230.78794860839844 0.24544157087802887 0.78640527 0.40356773138046265 True -13 40614 32.51348900794983 0.5638363361358643 177.14317321777344 0.27172744274139404 229.9580535888672 0.24899329245090485 0.794982 0.36965978145599365 True -14 43515 32.49961519241333 0.5620508193969727 219.71835327148438 0.30090996623039246 229.79441833496094 0.2498084455728531 0.8049499 0.33335983753204346 True -15 46416 32.503018379211426 0.5700256824493408 178.5748291015625 0.38751915097236633 229.4224090576172 0.2511083781719208 0.80970764 0.32095474004745483 True -16 49317 32.519070625305176 0.5870270729064941 173.3985595703125 0.35619911551475525 229.12806701660156 0.2523910403251648 0.81299156 0.31145256757736206 True -17 52218 32.589699268341064 0.572012186050415 159.03256225585938 0.257159024477005 229.00860595703125 0.2537371516227722 0.8136466 0.3054755926132202 True -18 55119 32.52619028091431 0.5691499710083008 206.62977600097656 0.384391188621521 229.2277069091797 0.25197672843933105 0.8140172 0.3056994676589966 True -19 58020 32.518277645111084 0.5773766040802002 182.6743621826172 0.19475659728050232 229.31983947753906 0.2513124346733093 0.8123721 0.3084075152873993 False diff --git a/ENCSR726YMS/cherimoya.fold_2.performance.tsv b/ENCSR726YMS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f85c60fd8e54abe494687f37af3f32b86992799d..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -229.2277069091797 0.5229270458221436 0.25197675824165344 0.06522911041975021 0.8140171766281128 0.7510567307472229 0.3056994676589966 \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_3.evaluate.json b/ENCSR726YMS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ec8a3987dbc6229d4f6bbbfd807b029396804f5d..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF113VOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_3.fit.json b/ENCSR726YMS/cherimoya.fold_3.fit.json deleted file mode 100644 index 1ec372aae9e2adf293a8c5cf6940a99f1287cd64..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF113VOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_3.log b/ENCSR726YMS/cherimoya.fold_3.log deleted file mode 100644 index 0b6d86b545b5883e9a878f56833abe9e55313b2e..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2788 35.235172510147095 3.636971950531006 206.49758911132812 0.6962769627571106 259.36212158203125 0.14357073605060577 0.6859382 3.3436129093170166 True -1 5576 31.16897749900818 0.6217043399810791 172.13778686523438 0.543840229511261 245.51882934570312 0.20757311582565308 0.74478745 1.0109540224075317 True -2 8364 31.235143899917603 1.0259239673614502 196.25631713867188 0.8407654762268066 242.70960998535156 0.21598224341869354 0.76106304 0.5829344391822815 True -3 11152 31.213191509246826 0.6292159557342529 197.91189575195312 0.985657811164856 241.1298828125 0.2218887358903885 0.77047366 0.48605889081954956 True -4 13940 31.225834608078003 0.6198303699493408 182.09039306640625 0.44601160287857056 240.55555725097656 0.22352898120880127 0.7733441 0.4703865945339203 True -5 16728 31.211342573165894 2.8262417316436768 184.38223266601562 0.4318896532058716 240.180419921875 0.22466903924942017 0.7825536 0.42153528332710266 True -6 19516 31.236517429351807 4.930680990219116 201.25611877441406 0.36781203746795654 240.1707763671875 0.22483308613300323 0.7829098 0.4098748564720154 True -7 22304 31.173660278320312 1.4356908798217773 161.66421508789062 0.4341390132904053 239.611328125 0.22747083008289337 0.78295743 0.3910168707370758 True -8 25092 31.26040005683899 1.0300464630126953 186.0166015625 0.42963945865631104 239.15516662597656 0.2302645593881607 0.78471774 0.3819093108177185 True -9 27880 31.22769546508789 2.426265239715576 170.45028686523438 0.5363645553588867 238.71055603027344 0.23263117671012878 0.78837144 0.38269761204719543 True -10 30668 31.182226181030273 17.666545152664185 170.62283325195312 0.44408202171325684 238.60850524902344 0.2325623482465744 0.7902677 0.3870878219604492 True -11 33456 31.44200110435486 0.6131420135498047 210.9005126953125 0.38404324650764465 237.9482421875 0.23624423146247864 0.79348207 0.386524498462677 True -12 36244 31.216776132583618 0.6087119579315186 182.88516235351562 0.45444542169570923 237.59942626953125 0.2377835512161255 0.7983715 0.36915692687034607 True -13 39032 31.227647304534912 0.6022064685821533 153.72256469726562 0.453654021024704 237.09620666503906 0.24022908508777618 0.804774 0.3558906614780426 True -14 41820 31.24003314971924 0.6233232021331787 151.6417236328125 0.5763844847679138 237.1412353515625 0.23970206081867218 0.81157357 0.34361767768859863 True -15 44608 31.20004630088806 0.6112368106842041 176.21170043945312 0.31734809279441833 236.52635192871094 0.2426927089691162 0.81858325 0.3171495199203491 True -16 47396 31.171875476837158 0.6182115077972412 160.529052734375 0.3239240050315857 236.76634216308594 0.24118904769420624 0.8207012 0.313801646232605 True -17 50184 31.2132465839386 0.6172261238098145 166.02853393554688 0.35477566719055176 236.343994140625 0.24291560053825378 0.8217636 0.3139309287071228 True -18 52972 31.195003032684326 0.6175949573516846 167.21498107910156 0.28252890706062317 236.50315856933594 0.24271874129772186 0.8205834 0.3122027516365051 False -19 55760 31.16627335548401 0.6898624897003174 173.39190673828125 0.45789629220962524 236.6471710205078 0.24193748831748962 0.82138723 0.31422582268714905 False diff --git a/ENCSR726YMS/cherimoya.fold_3.performance.tsv b/ENCSR726YMS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e450fdabf95f5620fcd594e208d959483960ed3f..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -236.343994140625 0.5247516632080078 0.2429155856370926 0.06077181175351143 0.8217635750770569 0.7529866695404053 0.3139309287071228 \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_4.evaluate.json b/ENCSR726YMS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 66777e94abc37f4abf4bfedd88cb6e0082058020..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF113VOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_4.fit.json b/ENCSR726YMS/cherimoya.fold_4.fit.json deleted file mode 100644 index 8bf3bd237c6fe97ebd5c012101b1d724a2cccec9..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF113VOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR726YMS/cherimoya.fold_4.log b/ENCSR726YMS/cherimoya.fold_4.log deleted file mode 100644 index ebf94f59c4ad5f3079104bd2910f1555b582fd87..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 36.04588222503662 3.5758769512176514 189.58187866210938 0.5872862339019775 245.0429229736328 0.1406150907278061 0.67413944 2.2913196086883545 True -1 5756 32.21350145339966 7.245380163192749 228.33119201660156 0.6486846804618835 233.14752197265625 0.20295342803001404 0.72979945 0.9588701725006104 True -2 8634 32.209752321243286 1.716871976852417 175.96609497070312 0.6291645765304565 229.8909149169922 0.21370725333690643 0.74049735 0.5054370760917664 True -3 11512 32.177634477615356 20.294543266296387 197.1595916748047 0.6473756432533264 228.45855712890625 0.2180853635072708 0.7506402 0.44901522994041443 True -4 14390 32.27335476875305 2.438774824142456 168.77471923828125 0.6285126209259033 227.70945739746094 0.22068774700164795 0.752367 0.43471717834472656 True -5 17268 32.20326042175293 32.39219355583191 174.33456420898438 0.5066062211990356 227.0172882080078 0.2242969572544098 0.75840116 0.40815895795822144 True -6 20146 32.26068592071533 0.6106228828430176 218.52801513671875 0.5051839351654053 226.90745544433594 0.22448153793811798 0.7595045 0.42434731125831604 True -7 23024 32.444969177246094 0.6110234260559082 190.53919982910156 0.43062183260917664 226.32896423339844 0.22815853357315063 0.76384294 0.4052855670452118 True -8 25902 32.158677101135254 0.6019103527069092 171.8529052734375 0.5505192875862122 226.3203125 0.22761988639831543 0.76568854 0.4032120704650879 True -9 28780 32.20978236198425 0.591639518737793 192.48150634765625 0.45991870760917664 225.71112060546875 0.23109817504882812 0.7684152 0.3892573118209839 True -10 31658 32.18669009208679 0.5984010696411133 159.3632354736328 0.3500857651233673 225.4990234375 0.23171022534370422 0.7727185 0.3758242726325989 True -11 34536 32.3036105632782 0.5977027416229248 183.4036865234375 0.4640306234359741 225.2012481689453 0.23370186984539032 0.7748507 0.384676069021225 True -12 37414 32.24296307563782 8.875139951705933 178.17581176757812 0.5711401104927063 224.533447265625 0.23666693270206451 0.78034157 0.36223310232162476 True -13 40292 32.16967558860779 1.336195945739746 176.53530883789062 0.37788066267967224 224.4146728515625 0.23735414445400238 0.7899315 0.3378274738788605 True -14 43170 32.263468742370605 25.128772735595703 158.3787078857422 0.3246551752090454 223.84844970703125 0.240312859416008 0.7975601 0.3094700574874878 True -15 46048 32.91055083274841 0.6241991519927979 148.87368774414062 0.35434627532958984 223.5733184814453 0.24198628962039948 0.8009684 0.30445703864097595 True -16 48926 32.51634621620178 0.6197092533111572 165.6339874267578 0.31212669610977173 223.79319763183594 0.24009093642234802 0.80621386 0.2938026189804077 True -17 51804 32.29650640487671 0.6094753742218018 216.2034454345703 0.19381782412528992 223.51783752441406 0.24217212200164795 0.8081333 0.2912825644016266 True -18 54682 32.29353332519531 1.5837786197662354 195.85321044921875 0.17531853914260864 223.63133239746094 0.24139010906219482 0.8085 0.2894120216369629 True -19 57560 32.305864572525024 0.6278491020202637 161.68966674804688 0.2644278407096863 223.8441162109375 0.24012430012226105 0.80920106 0.29201754927635193 True diff --git a/ENCSR726YMS/cherimoya.fold_4.performance.tsv b/ENCSR726YMS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4e21b9d67db627cd8cf606f3f4b0c32a8a340549..0000000000000000000000000000000000000000 --- a/ENCSR726YMS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.8441162109375 0.5292190313339233 0.24012431502342224 0.05951694771647453 0.8092010617256165 0.7334514856338501 0.29201754927635193 \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_0.evaluate.json b/ENCSR728BAD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 28ad6b1c173118e606c0201f68d3509db5b56724..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF838SOK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_0.fit.json b/ENCSR728BAD/cherimoya.fold_0.fit.json deleted file mode 100644 index baab16ae8a6341c5792dff151d61f6f74579b262..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF838SOK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_0.log b/ENCSR728BAD/cherimoya.fold_0.log deleted file mode 100644 index 30d16d0f2563fc1d28e2be897588f95bc7af5a47..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2613 34.2480046749115 6.1491570472717285 171.86544799804688 0.45185935497283936 216.62106323242188 0.125102698802948 0.6836417 2.8584158420562744 True -1 5226 28.403292894363403 0.6144990921020508 158.62680053710938 0.5278211236000061 206.7074737548828 0.18655912578105927 0.7417237 0.875345766544342 True -2 7839 29.596572637557983 0.5599949359893799 207.2073974609375 0.42387017607688904 203.33377075195312 0.19897596538066864 0.759972 0.4322494566440582 True -3 10452 28.917587518692017 0.5994155406951904 151.88702392578125 0.3514433801174164 202.08322143554688 0.20193752646446228 0.7665417 0.34022167325019836 True -4 13065 28.952908277511597 0.5540821552276611 161.54318237304688 0.3948560059070587 201.0450439453125 0.20683838427066803 0.76886666 0.3483951687812805 True -5 15678 29.002769470214844 0.559685468673706 154.05657958984375 0.4676635265350342 200.67710876464844 0.2090105265378952 0.76949745 0.3535115420818329 True -6 18291 28.975370168685913 11.696409702301025 179.30978393554688 0.470405638217926 200.15521240234375 0.211607426404953 0.7733269 0.3332962095737457 True -7 20904 28.998790502548218 0.5592741966247559 140.60275268554688 0.448932945728302 199.6388702392578 0.2136678695678711 0.7776202 0.32888102531433105 True -8 23517 29.368973970413208 0.5637884140014648 163.97625732421875 0.5014439821243286 199.3563690185547 0.214781254529953 0.7801214 0.32492363452911377 True -9 26130 28.95277690887451 0.5635941028594971 152.05462646484375 0.4939926266670227 198.8223876953125 0.21702522039413452 0.7854314 0.3128160834312439 True -10 28743 28.97549557685852 0.5576176643371582 184.22418212890625 0.2999887466430664 198.41722106933594 0.21905550360679626 0.7904344 0.30341583490371704 True -11 31356 29.0809268951416 8.75933313369751 131.27957153320312 0.3694755434989929 197.98867797851562 0.22170080244541168 0.7925494 0.30213138461112976 True -12 33969 28.998379707336426 0.5554656982421875 135.77040100097656 0.3605455756187439 197.67799377441406 0.2231038361787796 0.7959069 0.2998201549053192 True -13 36582 28.971471071243286 0.5496830940246582 154.84591674804688 0.307555615901947 197.28497314453125 0.2246915102005005 0.8051226 0.28617244958877563 True -14 39195 28.904987573623657 0.5584714412689209 166.69418334960938 0.37584882974624634 197.1680450439453 0.22485044598579407 0.8070613 0.2822969853878021 True -15 41808 28.91291379928589 1.0878753662109375 134.01986694335938 0.27699995040893555 197.00143432617188 0.22568586468696594 0.8118934 0.27833500504493713 True -16 44421 28.953717470169067 0.5482897758483887 222.85791015625 0.16748055815696716 197.21319580078125 0.22412550449371338 0.8130284 0.2797509729862213 True -17 47034 28.92203402519226 0.552556037902832 155.07058715820312 0.2379831075668335 197.05770874023438 0.2248355746269226 0.8165432 0.2832174301147461 True -18 49647 28.951184511184692 0.5580587387084961 155.623046875 0.20093075931072235 197.37435913085938 0.2235543578863144 0.8128669 0.2888582944869995 False -19 52260 28.91440224647522 0.5495679378509521 148.5281219482422 0.18810461461544037 197.3218994140625 0.22416578233242035 0.81443 0.2916659712791443 False diff --git a/ENCSR728BAD/cherimoya.fold_0.performance.tsv b/ENCSR728BAD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c721eeb45b9e160d5ed3467dee4c90f4ec16babf..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -197.05770874023438 0.5415050387382507 0.2248355746269226 0.05072825402021408 0.8165432214736938 0.7425144910812378 0.2832174301147461 \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_1.evaluate.json b/ENCSR728BAD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6987468963e3f846ebcf0d92e81835a98a6f0cf8..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF838SOK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_1.fit.json b/ENCSR728BAD/cherimoya.fold_1.fit.json deleted file mode 100644 index 5503022a8c72718fbe24a81ba75120ad040bfeed..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF838SOK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_1.log b/ENCSR728BAD/cherimoya.fold_1.log deleted file mode 100644 index 8d35fdeef76d748c19b211c6563a3ef0fa5c2b8e..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2603 33.48196625709534 3.9152352809906006 192.79489135742188 0.43121635913848877 244.04568481445312 0.13281062245368958 0.6701651 3.1219840049743652 True -1 5206 28.87238645553589 1.5142951011657715 196.96368408203125 0.6138947010040283 231.673583984375 0.20010097324848175 0.73506856 1.1375600099563599 True -2 7809 28.924715757369995 0.9928808212280273 174.8343505859375 0.4888513684272766 227.84671020507812 0.21138811111450195 0.7635178 0.4628239572048187 True -3 10412 28.884037256240845 0.6977846622467041 172.65322875976562 0.5314527750015259 225.9645538330078 0.2192080020904541 0.7744067 0.37595614790916443 True -4 13015 28.658884525299072 0.6664025783538818 155.31292724609375 0.35919344425201416 224.83815002441406 0.2234250158071518 0.7783232 0.36919063329696655 True -5 15618 28.254796504974365 2.013308525085449 124.44477081298828 0.3594393730163574 223.99290466308594 0.22681747376918793 0.7830431 0.3458995223045349 True -6 18221 28.244398832321167 0.6627695560455322 168.9393768310547 0.4087331295013428 223.34596252441406 0.22932662069797516 0.78723836 0.33600372076034546 True -7 20824 28.24119257926941 0.6655552387237549 155.5478515625 0.7049923539161682 222.6218719482422 0.2324519008398056 0.7946357 0.32050278782844543 True -8 23427 28.2087824344635 0.653393030166626 145.10858154296875 0.4730720520019531 222.16355895996094 0.23388084769248962 0.79984826 0.312937468290329 True -9 26030 28.219002723693848 0.6502771377563477 144.88088989257812 0.36722487211227417 221.4706268310547 0.23729361593723297 0.8039942 0.3104671835899353 True -10 28633 28.245235919952393 0.6514637470245361 169.71778869628906 0.2091781049966812 221.45809936523438 0.23662519454956055 0.8098181 0.29751014709472656 True -11 31236 28.240673303604126 2.111088275909424 145.10446166992188 0.32679885625839233 220.69651794433594 0.2406495064496994 0.8123403 0.29348182678222656 True -12 33839 28.29820466041565 0.6830675601959229 151.8499755859375 0.3463171124458313 220.5313262939453 0.24125739932060242 0.8180507 0.2884179949760437 True -13 36442 28.540236711502075 0.6918644905090332 131.16726684570312 0.37446916103363037 220.04148864746094 0.243519127368927 0.821775 0.283174604177475 True -14 39045 28.344181537628174 0.7034420967102051 114.09052276611328 0.2683295011520386 220.06707763671875 0.242787167429924 0.8261118 0.2809668183326721 True -15 41648 28.625909566879272 0.6799895763397217 149.33926391601562 0.2578975558280945 220.0023193359375 0.24328140914440155 0.8295294 0.28389406204223633 True -16 44251 28.469884872436523 0.7153546810150146 143.44808959960938 0.3153805136680603 219.823486328125 0.24407222867012024 0.8315309 0.2881365418434143 True -17 46854 28.4371919631958 0.6821770668029785 155.7517547607422 0.26165497303009033 219.7475128173828 0.24474266171455383 0.83035797 0.2961989939212799 False -18 49457 28.41210961341858 1.9436473846435547 174.38241577148438 0.2955933213233948 220.0833282470703 0.24290917813777924 0.82896787 0.3079163730144501 False -19 52060 28.55022406578064 0.6891584396362305 147.2624969482422 0.2755439877510071 220.09765625 0.24320317804813385 0.8282705 0.3131955564022064 False diff --git a/ENCSR728BAD/cherimoya.fold_1.performance.tsv b/ENCSR728BAD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 31b915bfebf3d8f167b90b5906b439da0f67f6e2..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.823486328125 0.5266788601875305 0.24407222867012024 0.05696497857570648 0.8315309286117554 0.7802655696868896 0.2881365418434143 \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_2.evaluate.json b/ENCSR728BAD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0997c4df984b8d04c6652384fb79ce953d226d63..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF838SOK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_2.fit.json b/ENCSR728BAD/cherimoya.fold_2.fit.json deleted file mode 100644 index c39892d90b55a4a62de6825a5730c396a29d186c..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF838SOK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_2.log b/ENCSR728BAD/cherimoya.fold_2.log deleted file mode 100644 index 0e53dff9037e5afbec5dead701e367ff49c8587e..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.04527258872986 4.30413031578064 169.29739379882812 0.6608088612556458 223.7523956298828 0.13135220110416412 0.6599067 2.8204033374786377 True -1 5508 30.574973344802856 0.5811042785644531 191.4222412109375 0.4869686961174011 212.45254516601562 0.19280989468097687 0.73383117 0.8513742685317993 True -2 8262 30.518834829330444 0.5293021202087402 140.29579162597656 0.5745033025741577 209.23641967773438 0.20456410944461823 0.7528743 0.4289298951625824 True -3 11016 30.530882835388184 0.5360698699951172 189.45668029785156 0.8197464942932129 207.74147033691406 0.20952224731445312 0.7590162 0.449838250875473 True -4 13770 30.0331289768219 0.5371825695037842 181.55868530273438 0.6635769009590149 206.84654235839844 0.2126844972372055 0.7679288 0.394589900970459 True -5 16524 29.844929456710815 0.5323119163513184 155.3753662109375 0.4500916004180908 206.10995483398438 0.2157662957906723 0.77084935 0.3843575417995453 True -6 19278 29.847747325897217 0.5150220394134521 157.42581176757812 0.310555100440979 205.3566131591797 0.2192697823047638 0.77795553 0.3685358166694641 True -7 22032 29.86447286605835 0.5233650207519531 161.47882080078125 0.34087327122688293 205.04139709472656 0.22077244520187378 0.7797513 0.3472701609134674 True -8 24786 29.815308570861816 0.5325205326080322 148.94821166992188 0.45129168033599854 204.6300048828125 0.2224406599998474 0.78126764 0.3399406969547272 True -9 27540 29.889726400375366 1.8412630558013916 156.13934326171875 0.4215873181819916 204.2088623046875 0.22411757707595825 0.7877513 0.32722318172454834 True -10 30294 29.84448218345642 0.5381379127502441 172.57342529296875 0.4089760184288025 203.85401916503906 0.22583051025867462 0.7898183 0.31995514035224915 True -11 33048 29.827343463897705 0.5181899070739746 165.58631896972656 0.44899192452430725 203.5114288330078 0.2267877459526062 0.7950604 0.3176426887512207 True -12 35802 29.924872636795044 0.516535758972168 166.3590087890625 0.3740551471710205 203.25643920898438 0.2281637340784073 0.7982672 0.31275299191474915 True -13 38556 29.844454050064087 0.5370132923126221 139.41261291503906 0.26850438117980957 202.89198303222656 0.22978752851486206 0.80292606 0.3009496331214905 True -14 41310 29.90256977081299 0.5240187644958496 145.68931579589844 0.5289953351020813 202.78335571289062 0.23014897108078003 0.8088752 0.29200977087020874 True -15 44064 29.929376125335693 0.5406482219696045 139.92855834960938 0.3133520483970642 202.60708618164062 0.23081408441066742 0.81305754 0.2891130745410919 True -16 46818 29.87763285636902 0.5166418552398682 137.5115966796875 0.25913286209106445 202.55938720703125 0.23115314543247223 0.8170002 0.28678515553474426 True -17 49572 29.872865438461304 0.5157713890075684 158.99542236328125 0.324168860912323 202.6615447998047 0.23071151971817017 0.81626993 0.2918989658355713 False -18 52326 29.85070252418518 0.5034511089324951 139.7806396484375 0.23075443506240845 202.73326110839844 0.23028990626335144 0.8169044 0.2950489819049835 False -19 55080 29.910388708114624 0.518498420715332 164.52828979492188 0.2795140743255615 202.94708251953125 0.22914659976959229 0.8168113 0.2983511686325073 False diff --git a/ENCSR728BAD/cherimoya.fold_2.performance.tsv b/ENCSR728BAD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e1ec3a7df01f136d75bb118281103eb5ad9120c3..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -202.55938720703125 0.5370100736618042 0.23115314543247223 0.05478428676724434 0.8170002102851868 0.7507773041725159 0.28678515553474426 \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_3.evaluate.json b/ENCSR728BAD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index aeeab6784fc712586bb263368d7d3794be89771f..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF838SOK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_3.fit.json b/ENCSR728BAD/cherimoya.fold_3.fit.json deleted file mode 100644 index 04120c9adc201d8738fa327836138b29ded2ffbc..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF838SOK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_3.log b/ENCSR728BAD/cherimoya.fold_3.log deleted file mode 100644 index b01ccbeecdf47631764eeec00120702ca4fd0814..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2662 34.04437518119812 3.8109030723571777 192.38400268554688 0.4982795715332031 223.76638793945312 0.12541159987449646 0.68488246 2.6588709354400635 True -1 5324 29.532564878463745 0.8539395332336426 180.5223388671875 0.5467873215675354 212.95376586914062 0.18672090768814087 0.7577142 0.8745697140693665 True -2 7986 29.50332760810852 0.5338983535766602 154.8941650390625 0.5408821702003479 209.9562530517578 0.19824984669685364 0.7725723 0.40709078311920166 True -3 10648 29.5178005695343 1.0122456550598145 185.5700225830078 0.49795106053352356 208.99154663085938 0.20140768587589264 0.7738349 0.34298011660575867 True -4 13310 29.534793376922607 0.5239753723144531 163.53445434570312 0.45462512969970703 208.23724365234375 0.20607410371303558 0.7760216 0.3523634076118469 True -5 15972 29.50481629371643 0.5227546691894531 162.81861877441406 0.49891096353530884 207.84646606445312 0.208139106631279 0.78053063 0.3385525047779083 True -6 18634 29.476664543151855 19.435198545455933 186.3690643310547 0.3207031488418579 207.48504638671875 0.20908640325069427 0.7826444 0.3236981928348541 True -7 21296 29.219784021377563 1.1997711658477783 177.62538146972656 0.44248083233833313 206.91583251953125 0.21221007406711578 0.7912282 0.3179032802581787 True -8 23958 28.95967674255371 0.5081667900085449 204.209228515625 0.6488165855407715 206.70240783691406 0.21363893151283264 0.7935662 0.32587626576423645 True -9 26620 28.932817697525024 0.5836336612701416 132.0721435546875 0.3280467987060547 206.3142852783203 0.21493041515350342 0.79659337 0.32355713844299316 True -10 29282 28.908379077911377 0.5156054496765137 136.89686584472656 0.3494603633880615 205.77455139160156 0.21711495518684387 0.79880315 0.31459543108940125 True -11 31944 28.935834407806396 1.061967134475708 183.58193969726562 0.3400930166244507 205.54966735839844 0.218220055103302 0.8054483 0.3050425946712494 True -12 34606 28.905396223068237 0.5195655822753906 179.25619506835938 0.42289841175079346 205.11463928222656 0.22002777457237244 0.81447697 0.2935100793838501 True -13 37268 28.90679621696472 0.5334389209747314 191.02911376953125 0.40348803997039795 204.8521270751953 0.22133462131023407 0.8189625 0.2853735387325287 True -14 39930 28.905938148498535 1.668555498123169 190.06971740722656 0.2310866117477417 204.4560546875 0.22340184450149536 0.8247854 0.27742433547973633 True -15 42592 29.008312225341797 0.534050703048706 185.64013671875 0.254641056060791 204.41287231445312 0.22300103306770325 0.82838696 0.2709941267967224 True -16 45254 29.05004644393921 0.5291130542755127 156.41754150390625 0.2628478407859802 204.39869689941406 0.22325818240642548 0.83360785 0.2693667411804199 True -17 47916 29.112744331359863 0.5159866809844971 153.57565307617188 0.20645034313201904 204.6954345703125 0.22149939835071564 0.83333594 0.2730967700481415 False -18 50578 29.07866382598877 0.513861894607544 144.47267150878906 0.4014834761619568 204.70030212402344 0.22140257060527802 0.8318975 0.2754315137863159 False -19 53240 29.00574541091919 0.5223009586334229 175.97225952148438 0.23748865723609924 204.82357788085938 0.22095239162445068 0.8311049 0.2781906723976135 False diff --git a/ENCSR728BAD/cherimoya.fold_3.performance.tsv b/ENCSR728BAD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2e8d425ef3552fc2228c3d6d2603fa87bdf4b196..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -204.39869689941406 0.5403563380241394 0.22325818240642548 0.04942570626735687 0.8336078524589539 0.7669315338134766 0.2693667411804199 \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_4.evaluate.json b/ENCSR728BAD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 858e3216c7e6abc92b0bc51712558961861e7956..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF838SOK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_4.fit.json b/ENCSR728BAD/cherimoya.fold_4.fit.json deleted file mode 100644 index 304eb88e97f12688f686aa859cbfa45a2187a137..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF838SOK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR728BAD/cherimoya.fold_4.log b/ENCSR728BAD/cherimoya.fold_4.log deleted file mode 100644 index 6eb5c13b66f47d65f16a7a5470751ea00b20dbe4..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2720 35.9042444229126 3.9393198490142822 138.39674377441406 0.4713638424873352 211.86572265625 0.12276679277420044 0.66339755 2.47776460647583 True -1 5440 30.19728922843933 0.727938175201416 146.07469177246094 0.6633192300796509 201.79788208007812 0.183689147233963 0.7398384 0.7560496926307678 True -2 8160 30.289364099502563 0.55552077293396 178.13619995117188 0.3780721127986908 199.350341796875 0.1924300640821457 0.75022864 0.36752116680145264 True -3 10880 30.206594228744507 0.5630297660827637 147.15167236328125 0.3541297912597656 198.31077575683594 0.19425083696842194 0.75608814 0.3610995411872864 True -4 13600 30.21495485305786 0.5262918472290039 156.19833374023438 0.3471214175224304 197.3009490966797 0.19920122623443604 0.7583706 0.3566839396953583 True -5 16320 30.219048738479614 0.5529186725616455 146.723388671875 0.6406533718109131 196.87930297851562 0.20091082155704498 0.75888294 0.3651605248451233 True -6 19040 30.225099802017212 0.9704515933990479 160.90585327148438 0.3923646807670593 196.4038543701172 0.20364968478679657 0.76596755 0.3463909327983856 True -7 21760 30.206682920455933 0.5554547309875488 154.54087829589844 0.37054261565208435 195.6283721923828 0.20787101984024048 0.7758376 0.3275437653064728 True -8 24480 30.244537830352783 0.5588622093200684 186.188232421875 0.39719119668006897 195.3052978515625 0.20934590697288513 0.78086823 0.32803091406822205 True -9 27200 30.1955246925354 0.5460832118988037 158.7685546875 0.3785088062286377 194.9463348388672 0.21139812469482422 0.7840629 0.3175385296344757 True -10 29920 30.187242031097412 0.5289239883422852 144.0268096923828 0.4144519865512848 194.6042938232422 0.21293266117572784 0.7937469 0.3055049777030945 True -11 32640 30.220221042633057 0.5451934337615967 167.61795043945312 0.3644116520881653 194.18785095214844 0.21542476117610931 0.7969095 0.2980336844921112 True -12 35360 30.07480788230896 0.5998172760009766 125.56472778320312 0.3229759931564331 194.20217895507812 0.2146029770374298 0.8047105 0.28897836804389954 True -13 38080 29.63624620437622 0.5425446033477783 157.8600311279297 0.22021490335464478 193.73828125 0.21743687987327576 0.8084007 0.2863481640815735 True -14 40800 29.603317975997925 11.21044111251831 152.32672119140625 0.35507363080978394 193.42803955078125 0.21916161477565765 0.81377095 0.2776053845882416 True -15 43520 29.668445348739624 0.5487377643585205 173.00576782226562 0.282833456993103 193.24806213378906 0.21993553638458252 0.81725997 0.2698631286621094 True -16 46240 29.66845989227295 0.53920578956604 146.48973083496094 0.300662636756897 193.37583923339844 0.21896806359291077 0.82181376 0.2683325409889221 True -17 48960 29.586688995361328 0.5382463932037354 172.650634765625 0.218057319521904 193.3886260986328 0.21956767141819 0.82326275 0.26864123344421387 True -18 51680 29.677229404449463 0.5264027118682861 120.05906677246094 0.2077944278717041 193.6991424560547 0.21724312007427216 0.82278687 0.2719302773475647 False -19 54400 29.603575468063354 0.5650203227996826 150.32455444335938 0.2085176408290863 193.8256378173828 0.21636177599430084 0.81921923 0.2755398154258728 False diff --git a/ENCSR728BAD/cherimoya.fold_4.performance.tsv b/ENCSR728BAD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d2ac598936ea5fb612ded2bd91a7f857d08cefee..0000000000000000000000000000000000000000 --- a/ENCSR728BAD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -193.3886260986328 0.5448567867279053 0.21956764161586761 0.04914750158786774 0.8232627511024475 0.749115526676178 0.26864123344421387 \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_0.evaluate.json b/ENCSR729DRB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ce34e0bdcb589a6ff80901d514044b1cf80774cb..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029OEN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_0.fit.json b/ENCSR729DRB/cherimoya.fold_0.fit.json deleted file mode 100644 index f51498c7d8f32bd9b24ecea737afa944c8e0d9f9..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF029OEN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_0.log b/ENCSR729DRB/cherimoya.fold_0.log deleted file mode 100644 index 564bf6f63c753bb2de4c8adb1aba2839b645da65..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.807068824768066 19.93977117538452 261.01129150390625 0.6553475856781006 333.06536865234375 0.16745130717754364 0.6653085 3.185656785964966 True -1 5510 31.0160174369812 0.5934834480285645 280.143310546875 0.6292483806610107 311.0541076660156 0.2519631087779999 0.7254192 1.148209571838379 True -2 8265 30.37474489212036 0.5812816619873047 210.66481018066406 0.6316299438476562 306.6593017578125 0.26238536834716797 0.7376624 0.6199027895927429 True -3 11020 30.41112780570984 1.18796706199646 240.10934448242188 0.469383180141449 305.29949951171875 0.26655876636505127 0.74755895 0.4604682922363281 True -4 13775 30.36298966407776 0.5768883228302002 221.6416015625 0.956238865852356 303.7835998535156 0.2729165256023407 0.7533265 0.5009328126907349 True -5 16530 34.91403555870056 6.170411825180054 238.17169189453125 0.6283566951751709 303.365966796875 0.2742810845375061 0.7606921 0.5304185152053833 True -6 19285 30.363569736480713 0.5708720684051514 266.6800231933594 0.48237013816833496 302.6392822265625 0.2764747738838196 0.7589151 0.5208373665809631 False -7 22040 36.235063314437866 21.94278335571289 188.41110229492188 0.6348055601119995 302.4671325683594 0.27652138471603394 0.76453537 0.4909883439540863 True -8 24795 29.8402681350708 0.5841221809387207 222.0894775390625 0.3744734823703766 301.6026916503906 0.280457079410553 0.7683551 0.49116790294647217 True -9 27550 29.76758074760437 1.3315925598144531 260.56097412109375 0.440795361995697 300.9967956542969 0.28208431601524353 0.76979196 0.47233685851097107 True -10 30305 29.766366243362427 20.88030982017517 267.364013671875 0.5158659219741821 300.5564880371094 0.2832319140434265 0.77442384 0.4434334933757782 True -11 33060 31.38541865348816 0.56597900390625 249.4046173095703 0.41436076164245605 299.8462219238281 0.28585922718048096 0.77741975 0.43143364787101746 True -12 35815 29.795339584350586 0.5812821388244629 264.59832763671875 0.38611823320388794 299.2726745605469 0.28802478313446045 0.781141 0.4230313003063202 True -13 38570 29.78280282020569 0.5658271312713623 255.21742248535156 0.4768673777580261 298.5135498046875 0.2910933196544647 0.7845881 0.4015215039253235 True -14 41325 29.95363712310791 0.5640461444854736 255.6263427734375 0.37941038608551025 298.530029296875 0.29107865691185 0.7902031 0.3736410439014435 True -15 44080 29.77312731742859 0.5630362033843994 258.20703125 0.5036628842353821 298.13873291015625 0.29124507308006287 0.7971254 0.3574417233467102 True -16 46835 29.842873334884644 0.5684380531311035 259.9372253417969 0.2586187422275543 297.48065185546875 0.2938777506351471 0.8004085 0.34738075733184814 True -17 49590 29.802480459213257 0.579503059387207 312.45098876953125 0.3430648446083069 298.16607666015625 0.291251003742218 0.8028482 0.3461526930332184 True -18 52345 29.71358847618103 0.5631256103515625 233.71463012695312 0.2439785599708557 298.00335693359375 0.2921093702316284 0.80096537 0.3487960398197174 False -19 55100 29.657617568969727 0.5563273429870605 212.3572998046875 0.2846693992614746 298.2724304199219 0.2919989228248596 0.80037445 0.3506535589694977 False diff --git a/ENCSR729DRB/cherimoya.fold_0.performance.tsv b/ENCSR729DRB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 45aba09cac1aca07ba7b67298a9b6ad8d0c15e14..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -298.16607666015625 0.48788660764694214 0.291251003742218 0.07926252484321594 0.802848219871521 0.7352904081344604 0.3461526930332184 \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_1.evaluate.json b/ENCSR729DRB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 67b3b70d392b9dd2630d92009fcb7bebd7dc97b6..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029OEN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_1.fit.json b/ENCSR729DRB/cherimoya.fold_1.fit.json deleted file mode 100644 index 39fba8651f54414f1d0d5516e662ecc90cc26225..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF029OEN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_1.log b/ENCSR729DRB/cherimoya.fold_1.log deleted file mode 100644 index 70b86cf1305b7af245c527215562de6ea1bccf3b..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 34.93728542327881 2.170220136642456 210.08544921875 0.622808575630188 386.8831787109375 0.17902015149593353 0.6665434 3.865689992904663 True -1 5490 30.206748485565186 0.6268937587738037 277.71044921875 0.7915865778923035 360.78277587890625 0.26614540815353394 0.73503345 1.2841745615005493 True -2 8235 30.287565231323242 3.0813193321228027 271.0752868652344 0.6546617746353149 353.5057678222656 0.28110042214393616 0.75329375 0.6241093277931213 True -3 10980 30.257508754730225 2.604240894317627 216.71963500976562 0.7614885568618774 350.59063720703125 0.28819331526756287 0.762651 0.5166367292404175 True -4 13725 30.47597360610962 36.45444440841675 276.03912353515625 1.057698130607605 348.5303955078125 0.2925996780395508 0.77390456 0.47662055492401123 True -5 16470 30.238539934158325 0.645606279373169 193.56272888183594 0.5281732082366943 347.535400390625 0.295194536447525 0.77928346 0.468966007232666 True -6 19215 30.241118669509888 0.6243062019348145 280.455322265625 0.4366876184940338 346.63543701171875 0.2982022762298584 0.7831512 0.44272881746292114 True -7 21960 30.210992097854614 0.6211624145507812 241.26670837402344 0.549231767654419 346.7259216308594 0.2972571849822998 0.78308594 0.47142842411994934 False -8 24705 29.544421195983887 0.6149888038635254 256.16680908203125 0.3877550959587097 345.83868408203125 0.30022838711738586 0.7861671 0.4555394649505615 True -9 27450 29.609658241271973 0.6129553318023682 218.8952178955078 0.5893127918243408 344.8414306640625 0.30343347787857056 0.7886293 0.4650394022464752 True -10 30195 29.58186912536621 0.6298415660858154 235.715576171875 0.32288140058517456 344.7689514160156 0.3038615882396698 0.79253584 0.42723461985588074 True -11 32940 29.54356050491333 3.6830005645751953 237.80905151367188 0.469838410615921 342.87017822265625 0.309087336063385 0.79763603 0.415675550699234 True -12 35685 29.636005640029907 37.740140199661255 218.26756286621094 0.4663728177547455 343.2213134765625 0.3074631989002228 0.80298704 0.3989010155200958 True -13 38430 32.706111669540405 0.6748034954071045 225.93226623535156 0.4653918743133545 341.78009033203125 0.3119511306285858 0.80945283 0.3857671022415161 True -14 41175 29.716484785079956 4.826519250869751 236.98095703125 0.3751027584075928 341.895263671875 0.31177929043769836 0.81370145 0.37719234824180603 True -15 43920 29.60758137702942 0.6187646389007568 236.22964477539062 0.2975844740867615 341.4211120605469 0.31282708048820496 0.82031775 0.36369088292121887 True -16 46665 29.663222312927246 0.6269197463989258 204.10577392578125 0.2678542733192444 341.35919189453125 0.31247177720069885 0.8239273 0.35802826285362244 True -17 49410 29.73260736465454 0.6260595321655273 210.71578979492188 0.47370800375938416 341.4283142089844 0.31307002902030945 0.823525 0.3592051565647125 False -18 52155 29.821866750717163 1.334684133529663 255.86624145507812 0.2403406798839569 341.7496643066406 0.31214290857315063 0.8231639 0.3589397966861725 False -19 54900 29.750248908996582 0.6223554611206055 285.82861328125 0.3620634078979492 341.5534362792969 0.3127875030040741 0.82529867 0.3632020652294159 True diff --git a/ENCSR729DRB/cherimoya.fold_1.performance.tsv b/ENCSR729DRB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7903247327fc3620ff0b7f881333dbb44f658a6d..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -341.5534362792969 0.46913570165634155 0.3127875030040741 0.09458055347204208 0.8252986669540405 0.7803923487663269 0.3632020652294159 \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_2.evaluate.json b/ENCSR729DRB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 00232a47c3c18be3cd3cbc45449f9926ebe00b84..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029OEN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_2.fit.json b/ENCSR729DRB/cherimoya.fold_2.fit.json deleted file mode 100644 index 57d4de8de1cae2a2a8a1830166241bb63f71f9e5..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF029OEN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_2.log b/ENCSR729DRB/cherimoya.fold_2.log deleted file mode 100644 index 558418dd5f95e1020ce979cf01e99ea39feda041..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2910 36.75931406021118 37.24290728569031 225.06483459472656 0.7374370098114014 344.6830749511719 0.17681607604026794 0.677572 2.982738733291626 True -1 5820 32.583693504333496 0.5489578247070312 294.8592529296875 0.7029485702514648 320.96038818359375 0.2598128318786621 0.7431357 0.937013566493988 True -2 8730 32.038031339645386 0.5260336399078369 188.9619140625 0.37914401292800903 316.9526062011719 0.267586886882782 0.75417066 0.48811134696006775 True -3 11640 32.10304403305054 24.58932900428772 305.050537109375 0.4787566065788269 315.1855163574219 0.2727009952068329 0.7589578 0.44871270656585693 True -4 14550 32.46500325202942 0.5238955020904541 201.14443969726562 0.5366705656051636 313.83612060546875 0.2769228518009186 0.7602321 0.4144488573074341 True -5 17460 31.98969316482544 0.5288758277893066 221.17762756347656 0.5627086758613586 312.5009765625 0.2816454768180847 0.7645373 0.4288478493690491 True -6 20370 31.973644971847534 0.5367200374603271 181.95840454101562 0.6824407577514648 312.2423400878906 0.2822856605052948 0.76678413 0.42280715703964233 True -7 23280 31.4617600440979 0.5264322757720947 247.012939453125 0.6270484328269958 311.65460205078125 0.28402385115623474 0.7727408 0.42485731840133667 True -8 26190 31.249372243881226 0.511620283126831 266.6924133300781 0.5059139728546143 311.0248107910156 0.28601884841918945 0.77560616 0.4134937524795532 True -9 29100 31.3017840385437 1.3089139461517334 229.2159423828125 0.49236300587654114 310.69195556640625 0.28605592250823975 0.7788953 0.4024023115634918 True -10 32010 31.450298309326172 0.5258123874664307 212.2398223876953 0.39722326397895813 309.74542236328125 0.2900351583957672 0.78005546 0.38849735260009766 True -11 34920 31.33347988128662 19.857982635498047 262.2356262207031 0.47636356949806213 308.874755859375 0.29328858852386475 0.78408325 0.3917679786682129 True -12 37830 32.9783673286438 0.5278143882751465 243.02529907226562 0.5253514647483826 308.00372314453125 0.29579710960388184 0.7920682 0.3734545111656189 True -13 40740 31.34834933280945 0.5516073703765869 225.8294677734375 0.4399333596229553 307.8751525878906 0.2962932884693146 0.79442126 0.3676735758781433 True -14 43650 31.32323718070984 0.5373938083648682 241.0959014892578 0.6379758715629578 307.1836242675781 0.29867053031921387 0.8021648 0.35603898763656616 True -15 46560 31.312324047088623 0.5224356651306152 222.0470733642578 0.4457353353500366 307.38385009765625 0.29751554131507874 0.807235 0.3468431234359741 True -16 49470 31.262956142425537 0.5208699703216553 225.5563507080078 0.4652152955532074 307.2373962402344 0.2988872230052948 0.808838 0.344549298286438 True -17 52380 31.3523530960083 0.5245373249053955 209.08038330078125 0.29298925399780273 306.9872131347656 0.29901155829429626 0.8117384 0.34476667642593384 True -18 55290 31.390846967697144 0.5379185676574707 324.9931640625 0.22548344731330872 307.1136779785156 0.2983905076980591 0.81113726 0.34828808903694153 False -19 58200 31.331846237182617 0.5303010940551758 234.8797149658203 0.28881314396858215 307.2882995605469 0.29808884859085083 0.8101214 0.34937846660614014 False diff --git a/ENCSR729DRB/cherimoya.fold_2.performance.tsv b/ENCSR729DRB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f3908a37a4e3a536accd26156eab8c5a4e48b207..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -306.9872131347656 0.4829130172729492 0.2990115284919739 0.0892985388636589 0.8117383718490601 0.7517344355583191 0.34476667642593384 \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_3.evaluate.json b/ENCSR729DRB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 62590bcd9fe97030d7c349b696e95e2433666eab..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029OEN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_3.fit.json b/ENCSR729DRB/cherimoya.fold_3.fit.json deleted file mode 100644 index ebb082d3563a701b01603493c04efe1c0f3d1ec0..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF029OEN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_3.log b/ENCSR729DRB/cherimoya.fold_3.log deleted file mode 100644 index e75d065e510c83058d038f805eed3cc279b4c234..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 35.69865131378174 3.609839677810669 216.45086669921875 0.8322268724441528 351.3843994140625 0.1709900200366974 0.68806386 3.5918211936950684 True -1 5612 30.891015768051147 1.3429853916168213 242.48196411132812 0.7651354670524597 329.69964599609375 0.25179988145828247 0.75340384 0.9891023635864258 True -2 8418 30.8624324798584 0.5549654960632324 205.59194946289062 0.819594144821167 325.2812194824219 0.26233604550361633 0.7660357 0.4753468334674835 True -3 11224 30.897162437438965 1.333103895187378 233.443603515625 0.6396352052688599 323.3307800292969 0.2675894498825073 0.7708296 0.42538174986839294 True -4 14030 30.930048942565918 0.5540146827697754 194.7430419921875 0.4482460916042328 322.7000732421875 0.26917362213134766 0.774707 0.4351317286491394 True -5 16836 30.878693103790283 0.5436365604400635 234.39273071289062 0.4672335982322693 322.1905212402344 0.2706131935119629 0.77483803 0.45369258522987366 True -6 19642 31.077264547348022 1.6431660652160645 224.0382080078125 0.6445053815841675 321.1237487792969 0.2748309075832367 0.77932316 0.45390549302101135 True -7 22448 30.374374866485596 0.548250675201416 256.37237548828125 0.6492391228675842 320.5823974609375 0.27700886130332947 0.77886856 0.44455790519714355 False -8 25254 30.301122188568115 0.541318416595459 244.40188598632812 0.7077463269233704 320.6554870605469 0.2767426371574402 0.7822565 0.43255919218063354 True -9 28060 30.23440170288086 0.5456271171569824 238.16973876953125 0.6295499801635742 319.533935546875 0.28059592843055725 0.78764033 0.4305972158908844 True -10 30866 30.29478645324707 0.5478310585021973 225.64920043945312 0.537721574306488 318.90509033203125 0.2831055521965027 0.79089195 0.42630720138549805 True -11 33672 30.24459981918335 0.5402059555053711 292.10821533203125 0.4554414749145508 318.74066162109375 0.28309062123298645 0.7960621 0.4151541590690613 True -12 36478 30.22863507270813 0.569211483001709 294.064697265625 0.4875888526439667 317.7685241699219 0.2859433591365814 0.79944706 0.407103031873703 True -13 39284 30.50840187072754 0.540116548538208 247.95266723632812 0.5216138958930969 317.3706359863281 0.28743723034858704 0.8062508 0.38065046072006226 True -14 42090 30.301758766174316 0.559636116027832 277.5627746582031 0.3534996509552002 317.21441650390625 0.28717178106307983 0.8081942 0.3663829565048218 True -15 44896 30.351182222366333 0.5448906421661377 208.59658813476562 0.5323911309242249 316.49053955078125 0.2895791828632355 0.8159612 0.3592821955680847 True -16 47702 30.26214027404785 0.5425701141357422 214.355224609375 0.3888353109359741 316.4761962890625 0.2896251976490021 0.8203858 0.3377808630466461 True -17 50508 30.322048664093018 0.5641324520111084 247.3096923828125 0.3150032162666321 316.6597595214844 0.2888331711292267 0.8229644 0.3367384970188141 True -18 53314 30.404733657836914 0.551053524017334 254.62388610839844 0.38616102933883667 316.484375 0.28939783573150635 0.82187533 0.33902162313461304 False -19 56120 31.452685594558716 38.617080211639404 263.21826171875 0.23854950070381165 316.4147644042969 0.289738267660141 0.82176524 0.3433764576911926 False diff --git a/ENCSR729DRB/cherimoya.fold_3.performance.tsv b/ENCSR729DRB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index baff2229ae8881d359d482aaebbc87bf20417ff8..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -316.6597595214844 0.4845382869243622 0.2888331413269043 0.08292665332555771 0.8229643702507019 0.7651586532592773 0.3367384970188141 \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_4.evaluate.json b/ENCSR729DRB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index faf8d4a5f50d21b4532f1090e94b77fa4f35878c..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029OEN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_4.fit.json b/ENCSR729DRB/cherimoya.fold_4.fit.json deleted file mode 100644 index dcc832b9709153d1e880aeb0791275b682297ff6..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF029OEN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729DRB/cherimoya.fold_4.log b/ENCSR729DRB/cherimoya.fold_4.log deleted file mode 100644 index 62a449ba13fd05d0cd77dd93782bc6a52e300d91..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2867 36.73377251625061 3.4940154552459717 231.37258911132812 0.6729848384857178 334.0334777832031 0.17202386260032654 0.68486965 3.5454540252685547 True -1 5734 31.508558750152588 0.585709810256958 210.48719787597656 0.7300281524658203 313.84661865234375 0.24713611602783203 0.746042 0.9212238788604736 True -2 8601 31.48915958404541 0.5740265846252441 222.18675231933594 0.4928051829338074 309.6131286621094 0.25800904631614685 0.7520438 0.5498340725898743 True -3 11468 31.45769190788269 0.5738177299499512 312.6856384277344 0.6689891219139099 307.783203125 0.26320409774780273 0.7590203 0.43447333574295044 True -4 14335 31.516580820083618 0.573357105255127 251.19261169433594 0.560248076915741 306.3076171875 0.26712146401405334 0.7625394 0.4218366742134094 True -5 17202 31.17640972137451 0.5649063587188721 210.1578369140625 0.5853328704833984 305.8854064941406 0.2683316469192505 0.76601595 0.42673158645629883 True -6 20069 30.887479305267334 0.5704345703125 259.9071044921875 0.5989992618560791 305.7158203125 0.26905927062034607 0.7652725 0.4145635962486267 False -7 22936 30.853232383728027 1.7159104347229004 229.66677856445312 0.6932291388511658 305.48272705078125 0.2703683376312256 0.7671356 0.4152839481830597 True -8 25803 30.902952671051025 0.5742197036743164 228.686767578125 0.3377772271633148 304.06195068359375 0.2758082151412964 0.7697349 0.40963247418403625 True -9 28670 31.16710901260376 1.7588236331939697 287.77569580078125 0.4710274338722229 303.72998046875 0.2773962616920471 0.7755988 0.3759736120700836 True -10 31537 30.8723464012146 0.5734298229217529 254.82241821289062 0.4805343747138977 303.08709716796875 0.27983102202415466 0.7761106 0.3717224597930908 True -11 34404 30.8697612285614 0.5736374855041504 241.9441375732422 0.6547822952270508 302.6108093261719 0.2809043228626251 0.78060293 0.3616277575492859 True -12 37271 30.885859727859497 0.5713860988616943 251.04351806640625 0.409192830324173 301.635009765625 0.28503096103668213 0.7864668 0.35869845747947693 True -13 40138 30.979838609695435 0.5740089416503906 249.83023071289062 0.3817219138145447 301.3367919921875 0.2859348654747009 0.7905146 0.35170406103134155 True -14 43005 30.925381660461426 0.5729901790618896 246.286865234375 0.33424079418182373 301.1470031738281 0.2854931950569153 0.79409057 0.350686639547348 True -15 45872 30.909289598464966 0.5775485038757324 216.96839904785156 0.3254886865615845 300.5592956542969 0.28877580165863037 0.8001465 0.3475244343280792 True -16 48739 31.49811363220215 20.925384283065796 255.57064819335938 0.37468504905700684 300.75445556640625 0.28761425614356995 0.8025823 0.3438303768634796 True -17 51606 30.916590452194214 2.4767367839813232 206.69638061523438 0.3465529680252075 300.7772216796875 0.2870158851146698 0.80539995 0.34201350808143616 True -18 54473 31.07823371887207 30.13636302947998 201.13629150390625 0.27419015765190125 300.6336364746094 0.2875520884990692 0.80390203 0.3412650227546692 False -19 57340 32.18663263320923 0.5816607475280762 210.40199279785156 0.30947232246398926 301.1482238769531 0.2850169241428375 0.8037281 0.34376347064971924 False diff --git a/ENCSR729DRB/cherimoya.fold_4.performance.tsv b/ENCSR729DRB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f32ed1c2afca434d815c7aa2c91a5e147e66af20..0000000000000000000000000000000000000000 --- a/ENCSR729DRB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -300.7772216796875 0.4894183874130249 0.2870159149169922 0.08199172466993332 0.8053999543190002 0.7355945110321045 0.34201350808143616 \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_0.evaluate.json b/ENCSR729TYE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d899e66d78e11f7da00d28934a60db62ed5a76ba..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF160ZNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_0.fit.json b/ENCSR729TYE/cherimoya.fold_0.fit.json deleted file mode 100644 index 5ace5e8a4b97ac171877c87c3ca31af59c3470fd..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF160ZNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_0.log b/ENCSR729TYE/cherimoya.fold_0.log deleted file mode 100644 index ac523eb2f3c1dd293677fb578330c1030493b7d5..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 36.694501638412476 3.915286064147949 438.9863586425781 0.21820153295993805 561.1057739257812 0.2796039283275604 0.8147732 3.9310226440429688 True -1 5474 30.601903200149536 0.6173863410949707 492.17474365234375 0.25769057869911194 516.5797729492188 0.3390084207057953 0.8641715 1.062726378440857 True -2 8211 30.53726840019226 0.5960626602172852 464.09429931640625 0.2661563456058502 507.6670837402344 0.3486632704734802 0.8693927 0.42913818359375 True -3 10948 30.45659303665161 36.59121513366699 430.7916564941406 0.32446134090423584 505.1696472167969 0.35009315609931946 0.8773837 0.3406068682670593 True -4 13685 30.773994207382202 0.5987544059753418 373.0756530761719 0.2021927535533905 501.94512939453125 0.3559142053127289 0.8827391 0.2496795505285263 True -5 16422 31.18182110786438 16.380004405975342 485.0618896484375 0.20198889076709747 500.5777282714844 0.3575011193752289 0.88531816 0.2112204134464264 True -6 19159 30.605873823165894 0.5978305339813232 407.7567138671875 0.2218213826417923 498.7583923339844 0.360074520111084 0.8885582 0.20167525112628937 True -7 21896 30.501863718032837 0.6040260791778564 521.5875244140625 0.22724927961826324 497.9031982421875 0.36108309030532837 0.8911689 0.2009291797876358 True -8 24633 30.55765652656555 0.5877118110656738 487.28582763671875 0.28319787979125977 497.4814758300781 0.3609519898891449 0.89508307 0.1976369321346283 True -9 27370 30.49437952041626 0.5963356494903564 442.5508117675781 0.1601470410823822 496.7999267578125 0.3620144724845886 0.8993899 0.18274684250354767 True -10 30107 30.478439569473267 2.630579710006714 422.91156005859375 0.3669469654560089 495.51373291015625 0.36420688033103943 0.9024596 0.17476779222488403 True -11 32844 30.495851278305054 1.1246275901794434 485.38238525390625 0.14373311400413513 493.95343017578125 0.36689212918281555 0.90587944 0.1707768589258194 True -12 35581 30.508166551589966 1.0800468921661377 427.2162170410156 0.25053662061691284 492.6496887207031 0.368757426738739 0.90746176 0.16169306635856628 True -13 38318 30.55279779434204 0.5882019996643066 485.3202209472656 0.1847560703754425 491.6139831542969 0.36991578340530396 0.9093715 0.15235354006290436 True -14 41055 30.57707953453064 0.5951001644134521 442.29046630859375 0.13216672837734222 491.5086364746094 0.3695433437824249 0.9135491 0.14410150051116943 True -15 43792 30.619200706481934 10.234490871429443 493.08734130859375 0.12843845784664154 490.712646484375 0.3704666197299957 0.91634804 0.13718657195568085 True -16 46529 30.594669818878174 0.5950610637664795 374.7186584472656 0.12438014894723892 490.63983154296875 0.3706449270248413 0.9170694 0.13186810910701752 True -17 49266 30.498071432113647 0.607257604598999 373.2816162109375 0.11874136328697205 489.7356872558594 0.37285077571868896 0.9170138 0.1305982619524002 False -18 52003 30.541887044906616 7.830178499221802 387.1480712890625 0.06510081142187119 490.4608459472656 0.3705771565437317 0.917635 0.13105535507202148 True -19 54740 30.527836084365845 0.8721802234649658 443.6383056640625 0.09245945513248444 490.652099609375 0.3707171380519867 0.9177203 0.13140127062797546 True diff --git a/ENCSR729TYE/cherimoya.fold_0.performance.tsv b/ENCSR729TYE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b4b8c4bf742ec7bb1927b99c65f088e8f73b52bc..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -490.652099609375 0.40573158860206604 0.3707171380519867 0.13965199887752533 0.9177203178405762 0.9031565189361572 0.13140127062797546 \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_1.evaluate.json b/ENCSR729TYE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f308df23df5f91c34964ebcca6ff3e70377e6965..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF160ZNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_1.fit.json b/ENCSR729TYE/cherimoya.fold_1.fit.json deleted file mode 100644 index a40a374911976a74ae2c4a9ca68d7abdb50e232e..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF160ZNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_1.log b/ENCSR729TYE/cherimoya.fold_1.log deleted file mode 100644 index 62be4feabea36bc784cf7f53fec45804756475fc..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2711 35.26593899726868 3.7870516777038574 543.28955078125 0.366493821144104 669.4756469726562 0.27934420108795166 0.8041538 4.882681369781494 True -1 5422 30.166415214538574 0.6771857738494873 408.747802734375 0.3323710560798645 611.3793334960938 0.3475320339202881 0.85401076 1.1581043004989624 True -2 8133 30.158695220947266 0.6567931175231934 355.011962890625 0.1898544430732727 595.2899780273438 0.3642856180667877 0.87252015 0.3797529637813568 True -3 10844 30.17909073829651 2.455580472946167 430.3965148925781 0.20105412602424622 591.07568359375 0.3692091703414917 0.8762653 0.3343326151371002 True -4 13555 30.244491815567017 0.679084300994873 440.1739501953125 0.2800964117050171 588.2752075195312 0.37154749035835266 0.87724954 0.35591763257980347 True -5 16266 30.191082239151 0.9032847881317139 476.2062072753906 0.2789463400840759 585.38818359375 0.37391403317451477 0.88703275 0.2837447226047516 True -6 18977 30.20508337020874 0.6476380825042725 546.5169677734375 0.30985844135284424 582.057861328125 0.37957558035850525 0.8902754 0.2590824067592621 True -7 21688 30.214621543884277 1.603867530822754 431.1475830078125 0.3043692111968994 580.8484497070312 0.3801915943622589 0.8947247 0.23361150920391083 True -8 24399 30.33050298690796 0.6604406833648682 430.1737060546875 0.24702088534832 578.2713623046875 0.3840637803077698 0.8973879 0.2253955751657486 True -9 27110 30.166126489639282 1.9092357158660889 448.5157470703125 0.3044891953468323 577.529541015625 0.38320404291152954 0.9015435 0.20918066799640656 True -10 29821 30.188074350357056 14.518635511398315 504.8935546875 0.21135267615318298 575.0198364257812 0.3876832127571106 0.903351 0.20098549127578735 True -11 32532 30.456197261810303 0.6633334159851074 426.62628173828125 0.2069551646709442 573.9131469726562 0.3883129358291626 0.9064314 0.19207099080085754 True -12 35243 30.238540649414062 0.6652195453643799 420.4701232910156 0.16618382930755615 571.708251953125 0.3900621831417084 0.91181386 0.1775878667831421 True -13 37954 30.253384828567505 1.5117323398590088 460.5345153808594 0.1872023195028305 571.0430297851562 0.39128249883651733 0.91463906 0.16874244809150696 True -14 40665 30.271327018737793 0.6733434200286865 513.0904541015625 0.1434621810913086 570.1159057617188 0.39149436354637146 0.91734445 0.15928220748901367 True -15 43376 30.66752552986145 0.666057825088501 427.59515380859375 0.3183627724647522 569.1295166015625 0.3923681974411011 0.9211709 0.15014049410820007 True -16 46087 30.289068460464478 0.6637740135192871 374.096923828125 0.09564448893070221 568.8214111328125 0.3933117985725403 0.9228921 0.14656297862529755 True -17 48798 30.327636241912842 0.6694602966308594 471.8012390136719 0.17452500760555267 568.50146484375 0.3935540020465851 0.92334104 0.14457692205905914 True -18 51509 30.304176330566406 0.6775367259979248 397.59722900390625 0.16773787140846252 569.10888671875 0.3922966718673706 0.92210853 0.1439298391342163 False -19 54220 30.370198965072632 2.1371939182281494 406.9242858886719 0.11303086578845978 567.9010620117188 0.39458775520324707 0.9218908 0.14423058927059174 False diff --git a/ENCSR729TYE/cherimoya.fold_1.performance.tsv b/ENCSR729TYE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ef4d469ffe1c6f41aa2ef41a4694013ae53f4786..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -568.50146484375 0.38529953360557556 0.3935540020465851 0.16242042183876038 0.9233410358428955 0.9182940721511841 0.14457692205905914 \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_2.evaluate.json b/ENCSR729TYE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5a889256659ab454c74b865cb302d46a759db010..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF160ZNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_2.fit.json b/ENCSR729TYE/cherimoya.fold_2.fit.json deleted file mode 100644 index 8e214b7f42244ab4eff0546159a6b33218d63faf..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF160ZNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_2.log b/ENCSR729TYE/cherimoya.fold_2.log deleted file mode 100644 index ca323ba764db2f74313fff8ea4084d396c2dd4b2..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 36.79593777656555 4.260013580322266 447.57916259765625 0.22213220596313477 592.4549560546875 0.2807233929634094 0.802049 3.8776023387908936 True -1 5770 32.12253952026367 0.8543698787689209 444.8719177246094 0.2947652339935303 545.1052856445312 0.33891355991363525 0.85213023 0.7253646850585938 True -2 8655 32.112688064575195 0.5873425006866455 387.52166748046875 0.20316997170448303 536.6393432617188 0.34828421473503113 0.86023766 0.4398955702781677 True -3 11540 32.171244382858276 0.5427558422088623 429.865966796875 0.25488173961639404 533.3817749023438 0.35086655616760254 0.86742383 0.36106565594673157 True -4 14425 32.25081181526184 0.546795129776001 367.97216796875 0.25216856598854065 530.22314453125 0.35459041595458984 0.8711882 0.25781750679016113 True -5 17310 32.61897349357605 29.3603937625885 405.27386474609375 0.18922308087348938 527.6849365234375 0.3575182855129242 0.8782172 0.2254151999950409 True -6 20195 32.18543720245361 0.5478188991546631 458.9979248046875 0.24686011672019958 525.5079345703125 0.3608127236366272 0.8812627 0.2127859741449356 True -7 23080 32.167524099349976 0.5461325645446777 442.2099609375 0.1894560307264328 522.6288452148438 0.36572006344795227 0.885887 0.21113665401935577 True -8 25965 32.19968605041504 0.5512943267822266 517.4990234375 0.1692306399345398 521.4161376953125 0.36655697226524353 0.8872896 0.20154960453510284 True -9 28850 32.139264822006226 0.5393357276916504 404.71282958984375 0.2430650144815445 520.6077880859375 0.3664247393608093 0.8895936 0.19576901197433472 True -10 31735 32.13289713859558 4.343942642211914 441.1015319824219 0.16221246123313904 519.063720703125 0.3690555989742279 0.89562684 0.18582390248775482 True -11 34620 32.14284539222717 1.4738919734954834 401.4903869628906 0.17975547909736633 516.9877319335938 0.3720933496952057 0.8964222 0.173394575715065 True -12 37505 32.20803618431091 0.5538725852966309 427.4618225097656 0.16203145682811737 515.9412231445312 0.37325426936149597 0.9017273 0.16580723226070404 True -13 40390 32.316410064697266 2.026433229446411 436.87603759765625 0.1597156673669815 514.7423095703125 0.3748030364513397 0.90319383 0.16094933450222015 True -14 43275 32.380967140197754 0.5397822856903076 385.72186279296875 0.11518289148807526 513.6083374023438 0.3759631812572479 0.90479225 0.1546662300825119 True -15 46160 32.16849899291992 0.5402717590332031 411.1010437011719 0.17658840119838715 514.038330078125 0.37529683113098145 0.90755457 0.14987516403198242 True -16 49045 32.341712951660156 0.5668644905090332 408.0478515625 0.15358158946037292 512.1011352539062 0.3790171444416046 0.90996444 0.14548072218894958 True -17 51930 32.193848609924316 0.542189359664917 461.9443054199219 0.14211119711399078 513.080078125 0.37588703632354736 0.91016525 0.14486034214496613 True -18 54815 32.31476616859436 0.5392806529998779 430.764892578125 0.16116653382778168 513.6818237304688 0.37545308470726013 0.9108593 0.14553764462471008 True -19 57700 32.26590061187744 38.23853588104248 433.9579162597656 0.1587604284286499 513.7124633789062 0.37558504939079285 0.908175 0.14582855999469757 False diff --git a/ENCSR729TYE/cherimoya.fold_2.performance.tsv b/ENCSR729TYE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c7a674d56ee1ae5d4fd9413d85c31305289b4dc8..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -513.6818237304688 0.40029042959213257 0.37545308470726013 0.14541491866111755 0.9108592867851257 0.901134192943573 0.14553764462471008 \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_3.evaluate.json b/ENCSR729TYE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d8caa1d76e209a71a502f6eba3865a7235269181..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF160ZNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_3.fit.json b/ENCSR729TYE/cherimoya.fold_3.fit.json deleted file mode 100644 index 32aa69006ae79de20e5c5111dae0eef2a14775b8..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF160ZNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_3.log b/ENCSR729TYE/cherimoya.fold_3.log deleted file mode 100644 index b92715533a6966f2ba4106c2dc1124a2f90e9703..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.08271384239197 3.471433639526367 469.685546875 0.24789756536483765 543.136962890625 0.2900431454181671 0.7949329 3.9550957679748535 True -1 5492 30.252930641174316 0.5559771060943604 457.05511474609375 0.2837705612182617 502.1591491699219 0.34373950958251953 0.8591746 0.7887548804283142 True -2 8238 30.310806274414062 0.5603220462799072 553.5006103515625 0.2563147246837616 494.6307373046875 0.3503025770187378 0.87043226 0.36041828989982605 True -3 10984 30.350367307662964 0.5558204650878906 491.95379638671875 0.20813150703907013 491.2823791503906 0.3541335165500641 0.8792661 0.3090495467185974 True -4 13730 30.225515127182007 0.539069414138794 425.4700622558594 0.3289381265640259 489.9173889160156 0.3562992215156555 0.88123816 0.27781373262405396 True -5 16476 30.494656801223755 0.5448000431060791 424.31451416015625 0.1876692771911621 487.926513671875 0.3589203655719757 0.8845014 0.24044886231422424 True -6 19222 30.1987087726593 0.5484371185302734 405.8773193359375 0.1964416354894638 485.5137939453125 0.3630029559135437 0.8889539 0.22165468335151672 True -7 21968 30.255638360977173 0.5484485626220703 464.6866455078125 0.3381935954093933 485.15032958984375 0.3627137541770935 0.88991994 0.2135431319475174 True -8 24714 30.42679500579834 5.664393186569214 429.1946105957031 0.2251952737569809 484.30474853515625 0.3632371127605438 0.89453846 0.2083161324262619 True -9 27460 30.4123432636261 0.5487048625946045 458.3778991699219 0.373404324054718 482.41497802734375 0.366752952337265 0.8974904 0.20943932235240936 True -10 30206 30.269012689590454 0.5612154006958008 368.9957275390625 0.22832387685775757 481.68511962890625 0.36685648560523987 0.9020229 0.18132491409778595 True -11 32952 30.30494976043701 0.5571274757385254 446.0997314453125 0.15153449773788452 480.86859130859375 0.3680647611618042 0.9020333 0.1808347851037979 True -12 35698 30.25924825668335 0.552274227142334 449.98895263671875 0.18262869119644165 479.22149658203125 0.3711506724357605 0.90587467 0.16673488914966583 True -13 38444 30.230011701583862 0.5523650646209717 386.72821044921875 0.37220507860183716 478.88665771484375 0.37091660499572754 0.90841305 0.15967243909835815 True -14 41190 30.30745244026184 0.5672614574432373 435.5030517578125 0.1453818380832672 477.8101501464844 0.3722078502178192 0.91140723 0.15159322321414948 True -15 43936 30.3519868850708 0.5499262809753418 437.5547790527344 0.2253166288137436 476.70904541015625 0.37467092275619507 0.91264427 0.1457260102033615 True -16 46682 30.402057886123657 0.5469958782196045 505.82403564453125 0.1728774905204773 476.78607177734375 0.37336939573287964 0.91577387 0.14212363958358765 True -17 49428 30.30982756614685 0.5635726451873779 458.45635986328125 0.13528937101364136 475.63861083984375 0.3758510947227478 0.9160741 0.14023049175739288 True -18 52174 30.345388889312744 0.5586307048797607 420.56964111328125 0.13363175094127655 476.760986328125 0.3729458153247833 0.9160554 0.14087583124637604 False -19 54920 30.68667960166931 0.5600042343139648 466.6272277832031 0.13590051233768463 476.60955810546875 0.37378212809562683 0.91538656 0.1419883668422699 False diff --git a/ENCSR729TYE/cherimoya.fold_3.performance.tsv b/ENCSR729TYE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1bd289ddb14e29c226fd8f298aeefe52e4e909b3..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.63861083984375 0.4055572748184204 0.3758510649204254 0.14046619832515717 0.9160740971565247 0.8934327363967896 0.14023049175739288 \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_4.evaluate.json b/ENCSR729TYE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 974811226dfa998660ce12557e1dd4f1353dc4ee..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF160ZNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_4.fit.json b/ENCSR729TYE/cherimoya.fold_4.fit.json deleted file mode 100644 index fa440d4fd08bfffe16d6255def98798401e0aa1b..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF160ZNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR729TYE/cherimoya.fold_4.log b/ENCSR729TYE/cherimoya.fold_4.log deleted file mode 100644 index 74f40d3f1e1556c00be1eebe4770db5b42b7f3b4..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2831 35.01024866104126 2.8106350898742676 449.532470703125 0.2508951723575592 530.2151489257812 0.2777329087257385 0.79656774 3.6040151119232178 True -1 5662 31.21250629425049 0.573378324508667 402.5926208496094 0.3740800619125366 493.4815979003906 0.32798799872398376 0.8395091 0.7886093258857727 True -2 8493 31.186155080795288 0.5480952262878418 383.5707702636719 0.25025230646133423 483.78759765625 0.3394479751586914 0.858389 0.31897932291030884 True -3 11324 31.1232750415802 0.5493404865264893 388.0615234375 0.1747894287109375 479.3333740234375 0.3449489176273346 0.8676502 0.2239711433649063 True -4 14155 31.189857721328735 0.5483808517456055 458.4500732421875 0.3491135835647583 477.97528076171875 0.3462066352367401 0.8741362 0.19238342344760895 True -5 16986 31.177452087402344 0.5564205646514893 410.08648681640625 0.285555899143219 476.2484130859375 0.3492336571216583 0.8762949 0.1786716878414154 True -6 19817 31.20661997795105 0.5461351871490479 397.6838684082031 0.19547085464000702 475.3575439453125 0.3485434055328369 0.8845275 0.169163778424263 True -7 22648 31.215153217315674 0.5383298397064209 442.025146484375 0.10783999413251877 474.0450134277344 0.35116007924079895 0.8858165 0.16855226457118988 True -8 25479 31.147549390792847 0.5367813110351562 463.386474609375 0.15423119068145752 473.30413818359375 0.35143834352493286 0.8886937 0.16583098471164703 True -9 28310 31.145548105239868 0.5451076030731201 403.58587646484375 0.16740691661834717 472.3769226074219 0.3528285324573517 0.892622 0.1632503718137741 True -10 31141 31.226242303848267 5.451736927032471 385.29608154296875 0.1441155970096588 470.94158935546875 0.3552440404891968 0.89579123 0.16194836795330048 True -11 33972 31.275136470794678 0.5549054145812988 404.4222717285156 0.19474059343338013 469.44512939453125 0.35827872157096863 0.8983803 0.15280820429325104 True -12 36803 31.17255187034607 0.542686939239502 413.6549072265625 0.14813363552093506 469.1762390136719 0.35778093338012695 0.90199935 0.14813795685768127 True -13 39634 31.138110637664795 0.5485134124755859 355.14654541015625 0.19637620449066162 467.6577453613281 0.361098051071167 0.9039938 0.14346681535243988 True -14 42465 31.138455629348755 0.5406279563903809 397.9599609375 0.1618974208831787 466.86993408203125 0.36176902055740356 0.908954 0.13624067604541779 True -15 45296 31.12340474128723 0.5435850620269775 458.1242370605469 0.16676045954227448 465.9866027832031 0.3638092875480652 0.91005397 0.1300361156463623 True -16 48127 31.146958827972412 0.5457420349121094 476.4476318359375 0.11908052861690521 466.0844421386719 0.3637595772743225 0.9116227 0.12782710790634155 True -17 50958 31.19764494895935 0.5332763195037842 447.2154541015625 0.1343805342912674 465.8196105957031 0.3648734390735626 0.913632 0.12612587213516235 True -18 53789 31.192182779312134 0.5397942066192627 397.506103515625 0.1019703671336174 465.8375549316406 0.36414214968681335 0.9131629 0.12601596117019653 False -19 56620 31.382081985473633 19.039966821670532 397.5450134277344 0.07691165804862976 465.76690673828125 0.36428651213645935 0.9113347 0.12661494314670563 False diff --git a/ENCSR729TYE/cherimoya.fold_4.performance.tsv b/ENCSR729TYE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6dbb528870a0975bc41a3d3c8a87978f58918c69..0000000000000000000000000000000000000000 --- a/ENCSR729TYE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -465.8196105957031 0.4120107591152191 0.3648734390735626 0.13647739589214325 0.9136319756507874 0.8906092047691345 0.12612587213516235 \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_0.evaluate.json b/ENCSR730IHD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b3cdfd6192d9b5c0bbb7bfe0e592a13aeb86b821..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF361PAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_0.fit.json b/ENCSR730IHD/cherimoya.fold_0.fit.json deleted file mode 100644 index 8b69f4d107c80d320914173b3d83cccdce11cf69..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF361PAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_0.log b/ENCSR730IHD/cherimoya.fold_0.log deleted file mode 100644 index 7757c4f6e76feadbfbd0c31a7a581cd843d14ec8..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 35.461146116256714 3.8931710720062256 292.6173400878906 0.376117080450058 346.7427978515625 0.23825250566005707 0.821256 2.738189458847046 True -1 5496 30.624045848846436 0.6831321716308594 308.2285461425781 0.2348124384880066 328.149658203125 0.2837149202823639 0.841413 0.7092437148094177 True -2 8244 30.69557809829712 1.219278335571289 300.9322509765625 0.22685125470161438 324.6216735839844 0.2922120690345764 0.8572816 0.4178692400455475 True -3 10992 30.162997484207153 0.6316337585449219 287.0264892578125 0.23568928241729736 323.1021423339844 0.29480862617492676 0.8632407 0.2513940930366516 True -4 13740 30.68310022354126 12.652484893798828 306.1438293457031 0.2074311077594757 321.7652282714844 0.2986662685871124 0.8671433 0.21488706767559052 True -5 16488 30.013601064682007 1.1525654792785645 304.46826171875 0.13575133681297302 321.29400634765625 0.29905182123184204 0.8704155 0.20151326060295105 True -6 19236 29.99856925010681 0.713648796081543 339.60052490234375 0.391951322555542 321.0169677734375 0.29927390813827515 0.875423 0.17807289958000183 True -7 21984 29.965946435928345 0.6049478054046631 255.36920166015625 0.19563063979148865 320.61248779296875 0.2998805344104767 0.8773205 0.18390153348445892 True -8 24732 29.975271224975586 0.61916184425354 254.84027099609375 0.2325345277786255 319.9814758300781 0.3019544184207916 0.8814362 0.17640766501426697 True -9 27480 30.030437231063843 0.6165084838867188 326.8226318359375 0.23014861345291138 319.7716979980469 0.30222034454345703 0.8886742 0.1641807109117508 True -10 30228 30.042211771011353 0.6138927936553955 269.5690002441406 0.1541297733783722 318.8360900878906 0.30547401309013367 0.89044785 0.1440933793783188 True -11 32976 30.000439643859863 0.6091969013214111 268.4633483886719 0.1108594536781311 318.38189697265625 0.3063126802444458 0.8942134 0.1361849009990692 True -12 35724 30.040202617645264 0.6110453605651855 253.11248779296875 0.1814371943473816 317.8548889160156 0.30673491954803467 0.8971476 0.12481369823217392 True -13 38472 29.96783757209778 0.5894720554351807 293.9474182128906 0.15913614630699158 317.76385498046875 0.30712801218032837 0.9004567 0.12026101350784302 True -14 41220 29.999269247055054 0.609595537185669 295.63189697265625 0.11123467236757278 317.5480041503906 0.30759796500205994 0.9033491 0.11518846452236176 True -15 43968 29.98579454421997 0.6075644493103027 298.02398681640625 0.13034313917160034 317.1751403808594 0.3084564208984375 0.905667 0.11148975789546967 True -16 46716 29.977967739105225 0.6138801574707031 314.80535888671875 0.11533834785223007 316.9364318847656 0.309017151594162 0.905957 0.10968780517578125 True -17 49464 29.98763632774353 0.5982811450958252 301.2938232421875 0.10136577486991882 317.1533508300781 0.30883440375328064 0.9071125 0.10764484107494354 True -18 52212 29.98411798477173 1.3914790153503418 279.337646484375 0.15599378943443298 317.4121398925781 0.30798614025115967 0.9062926 0.1081119105219841 False -19 54960 30.019697904586792 0.6207914352416992 286.0353088378906 0.14047594368457794 317.3399658203125 0.30825644731521606 0.9052242 0.1090727299451828 False diff --git a/ENCSR730IHD/cherimoya.fold_0.performance.tsv b/ENCSR730IHD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index bffc1a8843c7f3e97184944d297853c7b3810cb5..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.1533508300781 0.4743225872516632 0.308834433555603 0.08802152425050735 0.9071124792098999 0.8828884959220886 0.10764484107494354 \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_1.evaluate.json b/ENCSR730IHD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 254de3d497df214f5b5e3f657d5e7bb48eee1277..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF361PAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_1.fit.json b/ENCSR730IHD/cherimoya.fold_1.fit.json deleted file mode 100644 index 02f3d180fe3283a28332bfcc555bef5aa722afa4..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF361PAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_1.log b/ENCSR730IHD/cherimoya.fold_1.log deleted file mode 100644 index fc7d9021febfdba0be09a0f38b15912aaee1370d..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.68135118484497 4.027806520462036 303.1400451660156 0.1481425166130066 403.7336120605469 0.2424221932888031 0.8123825 3.185007333755493 True -1 5454 30.514886617660522 0.8151841163635254 251.1486053466797 0.18788877129554749 383.3641662597656 0.2908129096031189 0.84169054 0.7331826686859131 True -2 8181 30.4690580368042 0.6846816539764404 326.4367370605469 0.26022791862487793 377.48028564453125 0.30161306262016296 0.8545505 0.46747303009033203 True -3 10908 30.44429588317871 0.6967365741729736 268.95831298828125 0.2419639527797699 374.3887939453125 0.3073284924030304 0.8642386 0.29275813698768616 True -4 13635 29.98818016052246 0.6742463111877441 306.8824462890625 0.14754408597946167 372.19610595703125 0.31205251812934875 0.87257594 0.25717398524284363 True -5 16362 30.488345623016357 10.326400518417358 239.64474487304688 0.20773157477378845 371.3204345703125 0.31313127279281616 0.8753883 0.247948557138443 True -6 19089 29.928446054458618 0.6794312000274658 288.5975341796875 0.2024841010570526 370.346923828125 0.31553664803504944 0.8792996 0.2264162003993988 True -7 21816 29.89098358154297 0.6642136573791504 315.02276611328125 0.247378408908844 369.3236999511719 0.3174293339252472 0.88664925 0.21076437830924988 True -8 24543 29.8154354095459 0.9938390254974365 281.79754638671875 0.1919221580028534 368.8509521484375 0.31864288449287415 0.8886893 0.19734841585159302 True -9 27270 29.757481575012207 0.7074849605560303 299.21466064453125 0.15115684270858765 368.1864929199219 0.31975042819976807 0.8958779 0.1755601018667221 True -10 29997 29.81685185432434 0.6860628128051758 281.2004089355469 0.13910406827926636 367.2929992675781 0.3220876157283783 0.8978531 0.16535991430282593 True -11 32724 29.799500226974487 1.8988444805145264 289.1917724609375 0.12941071391105652 366.7564697265625 0.32257145643234253 0.9003484 0.15457022190093994 True -12 35451 29.87661647796631 0.7137477397918701 242.793212890625 0.1203199252486229 366.484130859375 0.323104590177536 0.9039163 0.14498519897460938 True -13 38178 29.783565759658813 0.6919021606445312 297.36083984375 0.11661925911903381 365.4455871582031 0.3255079388618469 0.9060074 0.13873694837093353 True -14 40905 29.78403067588806 0.6790766716003418 304.4546813964844 0.08322405815124512 365.3985595703125 0.32506221532821655 0.9077551 0.13513074815273285 True -15 43632 29.737966060638428 0.6971044540405273 270.01226806640625 0.12616120278835297 364.8291931152344 0.3267520070075989 0.9114656 0.12781953811645508 True -16 46359 29.79337763786316 0.6992924213409424 255.18739318847656 0.12617753446102142 364.7264709472656 0.32646435499191284 0.91345483 0.12313608080148697 True -17 49086 29.77306318283081 0.6692578792572021 265.33709716796875 0.16558495163917542 364.9164123535156 0.32596462965011597 0.91191256 0.12230008840560913 False -18 51813 29.755271196365356 1.8621137142181396 342.82354736328125 0.09495612978935242 364.7462463378906 0.3267151117324829 0.9125719 0.12194838374853134 False -19 54540 29.7959942817688 0.6465513706207275 246.26611328125 0.16014505922794342 364.7128601074219 0.3269506096839905 0.9135304 0.12229609489440918 True diff --git a/ENCSR730IHD/cherimoya.fold_1.performance.tsv b/ENCSR730IHD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f69bb13a043058929e64b23fcc28c28b57df9c47..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -364.7128601074219 0.45863577723503113 0.3269505798816681 0.10070299357175827 0.9135304093360901 0.9055346250534058 0.12229609489440918 \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_2.evaluate.json b/ENCSR730IHD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2d7e8da62abb2ee8c816e3e0dccb50fc26ee5db2..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF361PAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_2.fit.json b/ENCSR730IHD/cherimoya.fold_2.fit.json deleted file mode 100644 index aec82ed15757dff1bd99abb46fcf63da4e23a8db..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF361PAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_2.log b/ENCSR730IHD/cherimoya.fold_2.log deleted file mode 100644 index 4787ef3cf0898de2b0c9e947cdfa154acc64d919..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.061392307281494 3.8110053539276123 297.65228271484375 0.26690346002578735 364.1016845703125 0.24334032833576202 0.80904406 2.5603513717651367 True -1 5754 32.12791323661804 0.675300121307373 325.1712341308594 0.19623371958732605 345.4596252441406 0.2886907756328583 0.8377594 0.5140894055366516 True -2 8631 32.11619234085083 0.5668609142303467 330.8177185058594 0.2631724774837494 342.42041015625 0.2941257953643799 0.8524948 0.3925880789756775 True -3 11508 31.98896312713623 0.5603716373443604 273.8752746582031 0.23517614603042603 340.37469482421875 0.2981867492198944 0.8610956 0.23448620736598969 True -4 14385 31.356874465942383 0.5621168613433838 233.34024047851562 0.17777572572231293 339.3207092285156 0.3011462986469269 0.8648257 0.22189830243587494 True -5 17262 31.391213417053223 0.5598087310791016 300.1402893066406 0.2969200015068054 338.4106140136719 0.3024229109287262 0.8705844 0.20029740035533905 True -6 20139 31.347191095352173 0.5725388526916504 328.5747375488281 0.20601314306259155 337.509521484375 0.30547136068344116 0.8734979 0.19485625624656677 True -7 23016 31.39896845817566 0.8496861457824707 322.41650390625 0.1352154016494751 337.3088684082031 0.30510905385017395 0.8763308 0.1884402632713318 True -8 25893 31.415812015533447 0.8245477676391602 294.5533447265625 0.17342227697372437 336.5472106933594 0.3074477016925812 0.8794464 0.17342430353164673 True -9 28770 31.362462759017944 1.0327811241149902 259.8249816894531 0.1293887197971344 335.71630859375 0.31055930256843567 0.88174397 0.16917279362678528 True -10 31647 31.53207755088806 0.8060507774353027 302.47650146484375 0.2481238692998886 334.9035339355469 0.3109016418457031 0.88536626 0.1631230115890503 True -11 34524 31.364476442337036 0.9057257175445557 274.541748046875 0.1328486204147339 335.50982666015625 0.30975332856178284 0.8882954 0.1547665297985077 True -12 37401 31.53363537788391 1.0131099224090576 289.05487060546875 0.16801343858242035 334.7352600097656 0.31221848726272583 0.89133984 0.14612430334091187 True -13 40278 31.434767484664917 0.9497549533843994 282.74798583984375 0.24004501104354858 334.0622863769531 0.313167542219162 0.8910193 0.13855326175689697 False -14 43155 31.431727409362793 0.9670932292938232 255.09744262695312 0.10184922814369202 333.748046875 0.3133256733417511 0.89428884 0.12985116243362427 True -15 46032 31.430325746536255 1.0611939430236816 290.41485595703125 0.12517860531806946 333.7625732421875 0.31338539719581604 0.8966534 0.12593847513198853 True -16 48909 31.381117343902588 10.409615755081177 268.54547119140625 0.25951820611953735 333.1629638671875 0.3151516616344452 0.8973247 0.12268205732107162 True -17 51786 31.40176510810852 17.24927592277527 215.568359375 0.10632002353668213 332.97222900390625 0.31605857610702515 0.89903796 0.12072689831256866 True -18 54663 31.428688049316406 14.633327722549438 271.4137268066406 0.12776601314544678 333.326416015625 0.31446483731269836 0.89846414 0.12117192149162292 False -19 57540 31.598900079727173 0.5740983486175537 253.28358459472656 0.10608455538749695 333.3243103027344 0.3138735294342041 0.8984262 0.12139175832271576 False diff --git a/ENCSR730IHD/cherimoya.fold_2.performance.tsv b/ENCSR730IHD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d2f1478d022229b9448622d6ef1628d0fee3ca34..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -332.97222900390625 0.46900343894958496 0.31605857610702515 0.08762417733669281 0.8990379571914673 0.880137026309967 0.12072689831256866 \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_3.evaluate.json b/ENCSR730IHD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ca88ed28194b14ea2e1f07cf5317671f7b0a88f9..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF361PAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_3.fit.json b/ENCSR730IHD/cherimoya.fold_3.fit.json deleted file mode 100644 index 46bfc4fd48d43be59355c0373fdea65ea23b6c78..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF361PAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_3.log b/ENCSR730IHD/cherimoya.fold_3.log deleted file mode 100644 index eb4111dd4e6d0cd63ed802dd0b214a229f5b569e..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.75560641288757 3.6529343128204346 389.1632995605469 0.2860042452812195 336.822265625 0.24552735686302185 0.79853624 2.6503591537475586 True -1 5516 30.684456825256348 0.6227247714996338 300.75897216796875 0.1475457400083542 319.82122802734375 0.2880953550338745 0.8423693 0.677086591720581 True -2 8274 30.788902282714844 0.5678939819335938 262.82586669921875 0.1866537183523178 315.85406494140625 0.2958008348941803 0.8571917 0.31712275743484497 True -3 11032 30.81755495071411 0.5675427913665771 261.3157958984375 0.18473222851753235 313.8517150878906 0.300862193107605 0.8682548 0.21412232518196106 True -4 13790 30.780990839004517 0.5888173580169678 298.19805908203125 0.23342405259609222 313.1272277832031 0.3035460412502289 0.8719731 0.19837601482868195 True -5 16548 30.78342604637146 0.5676305294036865 294.72442626953125 0.20125898718833923 313.0372009277344 0.3026306927204132 0.8721404 0.1802484393119812 True -6 19306 30.737250804901123 0.5717425346374512 318.41571044921875 0.1806146800518036 312.3227233886719 0.3041406571865082 0.87722313 0.18577241897583008 True -7 22064 30.749026775360107 0.5659682750701904 316.91912841796875 0.2043234407901764 312.16864013671875 0.30427247285842896 0.8810606 0.16865436732769012 True -8 24822 30.759003162384033 0.5681033134460449 269.19500732421875 0.15978620946407318 311.2655334472656 0.3076123297214508 0.8832371 0.16512298583984375 True -9 27580 30.757980585098267 0.5606899261474609 294.79278564453125 0.18480372428894043 311.04150390625 0.3076464831829071 0.886381 0.15758132934570312 True -10 30338 30.72083020210266 3.5346670150756836 298.158203125 0.1465444564819336 310.4884033203125 0.30930057168006897 0.8897382 0.148138165473938 True -11 33096 30.74210238456726 0.5720059871673584 337.66357421875 0.1276056170463562 309.8712463378906 0.31034210324287415 0.89236027 0.14116014540195465 True -12 35854 30.79390835762024 0.5685369968414307 240.5815887451172 0.0880880057811737 309.0560607910156 0.3134973645210266 0.8937447 0.137542262673378 True -13 38612 30.708883047103882 0.5759730339050293 289.8697509765625 0.10684344917535782 309.2455139160156 0.3116896450519562 0.8973971 0.13139960169792175 True -14 41370 31.38563060760498 0.5621256828308105 244.58425903320312 0.10196322947740555 308.902587890625 0.3129047155380249 0.900362 0.12669070065021515 True -15 44128 30.812407732009888 0.5746307373046875 249.00575256347656 0.205771803855896 308.326171875 0.31483861804008484 0.9040834 0.11968636512756348 True -16 46886 30.946443796157837 0.5653526782989502 253.4408721923828 0.0995776355266571 308.5002136230469 0.31406065821647644 0.904673 0.11695612967014313 True -17 49644 30.142720699310303 0.5561056137084961 285.45135498046875 0.11208412051200867 308.5787353515625 0.31360548734664917 0.9059403 0.1145862340927124 True -18 52402 30.221403121948242 0.5663502216339111 314.5589599609375 0.14899292588233948 308.2287292480469 0.3140523433685303 0.9055041 0.11402090638875961 False -19 55160 30.16788125038147 0.5680279731750488 285.9534912109375 0.15656137466430664 308.2207946777344 0.3147740364074707 0.9040791 0.1141372099518776 False diff --git a/ENCSR730IHD/cherimoya.fold_3.performance.tsv b/ENCSR730IHD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b3070a0d9263c3f414b52e3408358e575e36b0a9..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.5787353515625 0.4726812243461609 0.3136054575443268 0.08873782306909561 0.9059402942657471 0.8735264539718628 0.1145862340927124 \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_4.evaluate.json b/ENCSR730IHD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 59e45d644e7797658ec2bb556bd9b61a50df79a3..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF361PAG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_4.fit.json b/ENCSR730IHD/cherimoya.fold_4.fit.json deleted file mode 100644 index 32fe6f0c182699ba67055a8759213505096cbc0f..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF361PAG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR730IHD/cherimoya.fold_4.log b/ENCSR730IHD/cherimoya.fold_4.log deleted file mode 100644 index 4253e38d2fa621b8631524e663e4bf28584702a0..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2811 36.351988315582275 3.981387138366699 277.17083740234375 0.17874184250831604 332.96087646484375 0.24058480560779572 0.80534345 2.0463461875915527 True -1 5622 31.393568754196167 0.6182656288146973 274.94415283203125 0.1910618096590042 316.92291259765625 0.2818194329738617 0.83475405 0.5310021638870239 True -2 8433 31.343499660491943 0.6609723567962646 273.7301025390625 0.25014200806617737 313.3401184082031 0.2908138930797577 0.8525494 0.28579896688461304 True -3 11244 31.278751373291016 0.6028509140014648 280.27337646484375 0.23833055794239044 311.6361083984375 0.29483312368392944 0.86217797 0.2283979207277298 True -4 14055 31.300699710845947 0.6007397174835205 260.51153564453125 0.2071153223514557 312.1364440917969 0.2927176058292389 0.86249465 0.15403440594673157 True -5 16866 31.28266668319702 0.6043341159820557 323.76385498046875 0.14769169688224792 310.6899108886719 0.2964697778224945 0.8689233 0.14839611947536469 True -6 19677 31.59189462661743 10.033768653869629 292.0527038574219 0.20747865736484528 310.4302978515625 0.29624372720718384 0.8747768 0.1439080685377121 True -7 22488 31.22309970855713 0.614346981048584 291.59735107421875 0.1739225834608078 309.8811340332031 0.2982335686683655 0.87858105 0.1461121141910553 True -8 25299 30.69122552871704 0.6044974327087402 300.9872741699219 0.14932292699813843 309.018310546875 0.30009692907333374 0.8823249 0.13046035170555115 True -9 28110 30.667948484420776 0.5990297794342041 292.3687744140625 0.16235582530498505 308.61932373046875 0.3010236620903015 0.8827824 0.13409139215946198 True -10 30921 30.646851539611816 0.5916965007781982 282.07061767578125 0.11018683016300201 308.4151611328125 0.301959753036499 0.8867726 0.12575867772102356 True -11 33732 30.64875054359436 1.7589685916900635 270.81951904296875 0.17189565300941467 307.6122741699219 0.3035307228565216 0.8913047 0.1159394159913063 True -12 36543 30.68931245803833 0.6056845188140869 247.29763793945312 0.2162412852048874 307.6131591796875 0.3042176067829132 0.8938538 0.11558109521865845 True -13 39354 30.638821601867676 0.5927610397338867 276.3226013183594 0.08357327431440353 307.5976257324219 0.3040376603603363 0.897593 0.11041542887687683 True -14 42165 30.898125648498535 0.618666410446167 266.67523193359375 0.14790046215057373 306.98211669921875 0.3057425916194916 0.89946765 0.10908334702253342 True -15 44976 30.689146518707275 0.5911307334899902 265.21923828125 0.11746138334274292 307.03082275390625 0.30579832196235657 0.900979 0.10700760036706924 True -16 47787 30.713825225830078 0.5983633995056152 258.742431640625 0.21587225794792175 306.7217102050781 0.3061693608760834 0.9009363 0.1050521731376648 False -17 50598 30.717439889907837 0.6036083698272705 274.4981689453125 0.1252034306526184 306.78240966796875 0.3063626289367676 0.9029926 0.10275880247354507 True -18 53409 30.67459535598755 3.2017464637756348 269.2424621582031 0.15159061551094055 307.0265808105469 0.30595338344573975 0.9017257 0.10267550498247147 False -19 56220 30.649463415145874 0.6048450469970703 243.40142822265625 0.09216488152742386 306.84844970703125 0.3068327307701111 0.9015442 0.10319763422012329 False diff --git a/ENCSR730IHD/cherimoya.fold_4.performance.tsv b/ENCSR730IHD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index dfe9ba30810ab2a942ce5c44f5077c0349203bba..0000000000000000000000000000000000000000 --- a/ENCSR730IHD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -306.78240966796875 0.47710999846458435 0.3063626289367676 0.0853937566280365 0.9029926061630249 0.873458981513977 0.10275880247354507 \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_0.evaluate.json b/ENCSR731DJH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1fac6f8ebc8cbf454e1b812e3d850749e0dd2f55..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_0.fit.json b/ENCSR731DJH/cherimoya.fold_0.fit.json deleted file mode 100644 index 956e93c569ac9fda898de8b2495bdec0e2d69e12..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF367OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_0.log b/ENCSR731DJH/cherimoya.fold_0.log deleted file mode 100644 index ccd303d88b2f7b857cd0bb70b6702714b0398b89..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1819 24.602296829223633 3.9300622940063477 194.77731323242188 0.7029373049736023 286.3802185058594 0.1353921890258789 0.64105594 6.990392684936523 True -1 3638 20.027679920196533 13.188426971435547 215.16107177734375 0.6524391770362854 266.9847106933594 0.18922792375087738 0.7629973 2.9105348587036133 True -2 5457 21.030156135559082 0.4822835922241211 190.31829833984375 0.42092573642730713 253.41163635253906 0.21637916564941406 0.7964622 1.1503571271896362 True -3 7276 19.99246573448181 0.38556361198425293 272.8332214355469 0.5204428434371948 249.54440307617188 0.22234492003917694 0.8028035 0.7869168519973755 True -4 9095 20.028685808181763 0.3856971263885498 215.34912109375 0.4690149128437042 247.6507110595703 0.22745367884635925 0.80895495 0.6944587230682373 True -5 10914 20.013319969177246 0.41158270835876465 188.70111083984375 0.44889014959335327 246.47071838378906 0.2299167364835739 0.8168869 0.6016236543655396 True -6 12733 20.07186722755432 0.3890652656555176 230.72756958007812 0.5507361888885498 245.80137634277344 0.23244158923625946 0.82225496 0.5434869527816772 True -7 14552 20.00215768814087 0.4733586311340332 180.615234375 0.4573359787464142 245.37518310546875 0.23356862366199493 0.82952446 0.48295658826828003 True -8 16371 20.062371015548706 0.4105997085571289 188.87013244628906 0.3473700284957886 244.42137145996094 0.23629388213157654 0.8364406 0.4350252151489258 True -9 18190 20.03089213371277 10.162322759628296 241.13458251953125 0.48872509598731995 243.77333068847656 0.23776471614837646 0.8430163 0.4036378264427185 True -10 20009 20.05363368988037 0.7824878692626953 192.3212127685547 0.39206773042678833 243.2595672607422 0.23887529969215393 0.8462405 0.38521602749824524 True -11 21828 20.465498447418213 7.802356481552124 190.55157470703125 0.31942126154899597 242.54827880859375 0.2409161478281021 0.8512307 0.35612088441848755 True -12 23647 19.764871835708618 0.37700676918029785 233.9069366455078 0.342349648475647 242.3072967529297 0.2409035712480545 0.85630333 0.33459678292274475 True -13 25466 19.621607780456543 0.3701927661895752 216.0557403564453 0.5081621408462524 241.96151733398438 0.24210694432258606 0.8599495 0.32500845193862915 True -14 27285 19.638526916503906 0.7419173717498779 220.67210388183594 0.37400978803634644 241.47177124023438 0.24411937594413757 0.8632391 0.3188631534576416 True -15 29104 19.626783847808838 0.36409616470336914 189.81118774414062 0.3401021361351013 241.53895568847656 0.24332012236118317 0.8664499 0.3127841353416443 True -16 30923 19.580559492111206 0.37696337699890137 168.50633239746094 0.22483764588832855 241.5536346435547 0.24341793358325958 0.866736 0.3099152445793152 True -17 32742 19.583048105239868 3.00724458694458 210.74806213378906 0.2376766800880432 241.57032775878906 0.24336862564086914 0.8679468 0.3135265111923218 True -18 34561 19.581844091415405 0.3650045394897461 192.1560516357422 0.3325466513633728 241.80484008789062 0.2427826225757599 0.86619514 0.31791362166404724 False -19 36380 19.66133451461792 0.37930893898010254 214.1209716796875 0.24545344710350037 241.8828887939453 0.24264101684093475 0.8637087 0.3210979402065277 False diff --git a/ENCSR731DJH/cherimoya.fold_0.performance.tsv b/ENCSR731DJH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 20244720cdc4c6e23de040168396a383c0e5feb4..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -241.57032775878906 0.5239935517311096 0.24336865544319153 0.06731939315795898 0.8679468035697937 0.8008527159690857 0.3135265111923218 \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_1.evaluate.json b/ENCSR731DJH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index dac27f4c767f819964cfd207226613bdffc84690..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_1.fit.json b/ENCSR731DJH/cherimoya.fold_1.fit.json deleted file mode 100644 index bd278bdd301cde48c93eeed20107b4f1f35c095b..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF367OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_1.log b/ENCSR731DJH/cherimoya.fold_1.log deleted file mode 100644 index c3d2689d396f4fab287e9f1a6dd0e2786e5e255e..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1783 24.401522874832153 3.8753890991210938 221.34361267089844 0.7739164233207703 350.3504638671875 0.14666476845741272 0.6238598 8.585172653198242 True -1 3566 19.613807678222656 1.801243543624878 194.6114044189453 0.5962912440299988 326.98223876953125 0.2057059109210968 0.74969727 3.612062931060791 True -2 5349 19.611361980438232 0.5124733448028564 228.313232421875 0.4869644343852997 307.5719299316406 0.23958636820316315 0.79897165 1.6887967586517334 True -3 7132 19.63340663909912 0.6269290447235107 241.97998046875 0.5549187064170837 301.491455078125 0.2513134181499481 0.81033754 1.055477499961853 True -4 8915 19.606098890304565 0.5362668037414551 166.35720825195312 0.477039098739624 299.0440368652344 0.2558104395866394 0.8190863 0.8228203058242798 True -5 10698 19.586318731307983 0.49233198165893555 247.71446228027344 0.3927951157093048 298.4281005859375 0.25716468691825867 0.8236866 0.7352069020271301 True -6 12481 19.5712571144104 0.5003211498260498 224.59854125976562 0.641954779624939 296.4334716796875 0.2616773545742035 0.83666754 0.632038414478302 True -7 14264 19.578585386276245 0.5003747940063477 213.6537628173828 0.41488564014434814 295.5141906738281 0.26455241441726685 0.8412467 0.5664470791816711 True -8 16047 19.586845874786377 0.9575726985931396 225.88226318359375 0.5445688366889954 294.5946350097656 0.26636239886283875 0.85080415 0.49429699778556824 True -9 17830 19.236772298812866 0.5294785499572754 185.5284423828125 0.3970862030982971 293.4682922363281 0.2691824436187744 0.8575662 0.4764269292354584 True -10 19613 19.360138177871704 0.5303258895874023 188.8580322265625 0.6099586486816406 293.0766296386719 0.26947203278541565 0.8625578 0.4367039203643799 True -11 21396 19.31695294380188 0.5193960666656494 166.28109741210938 0.300098717212677 292.72216796875 0.270295649766922 0.8670824 0.40541934967041016 True -12 23179 19.299275159835815 0.5102674961090088 216.64239501953125 0.3729923963546753 292.0975341796875 0.2712148427963257 0.87118995 0.38912245631217957 True -13 24962 19.345008373260498 1.6095168590545654 229.7418975830078 0.2651161849498749 291.5446472167969 0.272767573595047 0.87417436 0.37613651156425476 True -14 26745 19.327213287353516 14.753492832183838 150.37269592285156 0.4326151907444 290.86328125 0.27457982301712036 0.8762355 0.3681499660015106 True -15 28528 20.053492069244385 0.796647310256958 229.6573944091797 0.28228116035461426 290.28570556640625 0.2753215432167053 0.87897146 0.3540945053100586 True -16 30311 19.305149793624878 0.5233523845672607 173.79388427734375 0.32221296429634094 290.5684509277344 0.27427083253860474 0.8787974 0.3527776896953583 False -17 32094 19.288766145706177 0.5195269584655762 207.6563262939453 0.2140275537967682 290.76470947265625 0.274409681558609 0.8786319 0.3570536971092224 False -18 33877 19.364427089691162 0.5119161605834961 212.6954345703125 0.31119248270988464 291.4302673339844 0.2716681957244873 0.87696105 0.36475470662117004 False -19 35660 19.29052734375 5.718394756317139 242.09542846679688 0.2666914463043213 291.57989501953125 0.27140429615974426 0.8753452 0.36871209740638733 False diff --git a/ENCSR731DJH/cherimoya.fold_1.performance.tsv b/ENCSR731DJH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3b0c702ae591d7f647af868d6d346aecd8b2affd..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -290.28570556640625 0.49790939688682556 0.2753215432167053 0.08270782977342606 0.8789714574813843 0.8405277729034424 0.3540945053100586 \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_2.evaluate.json b/ENCSR731DJH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 455f86bc73dac0ae129f28c7a05e3cb96d9d314c..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_2.fit.json b/ENCSR731DJH/cherimoya.fold_2.fit.json deleted file mode 100644 index 3c7212aea1fbe2d7ad9e6088cfe70dc6e7defb7f..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF367OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_2.log b/ENCSR731DJH/cherimoya.fold_2.log deleted file mode 100644 index ca4122acbc192a8aa1541ea5ccbfc57777f91189..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1916 25.449589252471924 3.2134060859680176 191.3072052001953 0.41362330317497253 299.0772399902344 0.13864269852638245 0.6126781 6.730035305023193 True -1 3832 21.036929845809937 2.2516660690307617 246.68475341796875 0.6542527079582214 276.9336242675781 0.1981092393398285 0.7434744 2.9829514026641846 True -2 5748 21.019596576690674 0.45064449310302734 227.5107421875 0.7515186667442322 261.3922119140625 0.22411315143108368 0.7911364 1.4331984519958496 True -3 7664 21.026945114135742 5.623767137527466 271.9964599609375 0.7944027781486511 257.7982177734375 0.2306632250547409 0.80308735 0.8189938068389893 True -4 9580 21.01360011100769 0.3897359371185303 254.05633544921875 0.6086976528167725 256.1790771484375 0.23326244950294495 0.8109556 0.6425475478172302 True -5 11496 21.058537006378174 0.38076043128967285 168.20465087890625 0.5092793703079224 255.69232177734375 0.2345060557126999 0.81774396 0.5759052038192749 True -6 13412 21.05151104927063 0.3831467628479004 193.91873168945312 0.33445942401885986 254.8560791015625 0.23674795031547546 0.82521045 0.5383989810943604 True -7 15328 20.834186792373657 0.3775153160095215 230.3365020751953 0.5352919101715088 253.965087890625 0.2398981899023056 0.83016944 0.5084574818611145 True -8 17244 21.12784171104431 0.36987924575805664 259.2906494140625 0.5550761222839355 253.21640014648438 0.24098242819309235 0.83713955 0.4609507620334625 True -9 19160 20.62328267097473 0.3778700828552246 202.25526428222656 0.5320473909378052 252.492919921875 0.24329206347465515 0.84349984 0.4204100966453552 True -10 21076 21.02426528930664 0.37690019607543945 225.03643798828125 0.5661284923553467 251.66297912597656 0.2455741912126541 0.84749866 0.39692625403404236 True -11 22992 20.608107805252075 0.3823206424713135 207.84869384765625 0.4089605510234833 251.1338348388672 0.24689903855323792 0.85174304 0.3819027543067932 True -12 24908 20.60625982284546 0.37334680557250977 212.44888305664062 0.41876542568206787 251.02210998535156 0.24657852947711945 0.8546618 0.36500298976898193 True -13 26824 20.60031819343567 0.3780038356781006 205.70962524414062 0.38481009006500244 250.43844604492188 0.24856281280517578 0.85799086 0.35396698117256165 True -14 28740 20.578552961349487 0.3716001510620117 173.93194580078125 0.2938900291919708 249.96258544921875 0.24990130960941315 0.86022043 0.34457507729530334 True -15 30656 20.687970638275146 0.373171329498291 185.42994689941406 0.36702123284339905 249.5786895751953 0.2508394122123718 0.86204576 0.3347519040107727 True -16 32572 20.654932022094727 0.37313055992126465 223.42848205566406 0.3027089238166809 249.85414123535156 0.2504514157772064 0.8633531 0.329683780670166 True -17 34488 20.59032917022705 0.40104031562805176 226.21969604492188 0.22509877383708954 250.17930603027344 0.24903693795204163 0.8641179 0.33012276887893677 True -18 36404 20.589274883270264 0.3703744411468506 152.22708129882812 0.3032435178756714 250.3422088623047 0.24915799498558044 0.8632824 0.3338237702846527 False -19 38320 20.60702610015869 0.3773179054260254 187.6131591796875 0.21663600206375122 250.49874877929688 0.2485606074333191 0.8615822 0.3381485044956207 False diff --git a/ENCSR731DJH/cherimoya.fold_2.performance.tsv b/ENCSR731DJH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0addc8c85549a065d09734a48949aeb92381ab98..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.17930603027344 0.5193681120872498 0.24903690814971924 0.07165757566690445 0.8641179203987122 0.804006814956665 0.33012276887893677 \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_3.evaluate.json b/ENCSR731DJH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 46dad02b96691a642c44db867b82d521e8a9f0dc..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_3.fit.json b/ENCSR731DJH/cherimoya.fold_3.fit.json deleted file mode 100644 index 3ac21199e58d1b59a236ea370e72af303674b040..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF367OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_3.log b/ENCSR731DJH/cherimoya.fold_3.log deleted file mode 100644 index 99b295ce232fb9e979d60e4bcd709a42e7db3498..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1835 24.71125841140747 3.8028359413146973 185.31065368652344 0.5421876907348633 303.71356201171875 0.14649564027786255 0.6050076 7.250184535980225 True -1 3670 20.166953086853027 2.4064278602600098 191.361572265625 0.741998016834259 284.39056396484375 0.19944700598716736 0.7284797 2.9592959880828857 True -2 5505 20.17814040184021 0.38828158378601074 253.23497009277344 0.7384178042411804 269.2840576171875 0.22746585309505463 0.7682371 1.7435163259506226 True -3 7340 20.165109157562256 0.4007735252380371 216.46546936035156 0.4327142834663391 265.8157043457031 0.23426562547683716 0.76582235 1.064799189567566 False -4 9175 20.127723217010498 0.3731811046600342 183.12335205078125 0.522155225276947 264.3783264160156 0.2377842515707016 0.77277976 0.875598669052124 True -5 11010 19.9892475605011 0.3697941303253174 234.16494750976562 0.4519345164299011 263.533447265625 0.23927520215511322 0.7837965 0.7970119714736938 True -6 12845 19.7424476146698 0.45384669303894043 260.97845458984375 0.6963952779769897 262.4565734863281 0.24320253729820251 0.79200053 0.723139226436615 True -7 14680 19.765610456466675 0.35689449310302734 267.87042236328125 0.9552828073501587 261.7159118652344 0.24466542899608612 0.8043838 0.6504293084144592 True -8 16515 19.72727680206299 0.379408597946167 186.57862854003906 0.5724870562553406 260.6730651855469 0.2476695477962494 0.8127292 0.5874307751655579 True -9 18350 19.7541766166687 0.36978578567504883 251.80072021484375 0.5305773019790649 259.8698425292969 0.2502332627773285 0.8210097 0.5704848170280457 True -10 20185 19.762216329574585 0.3720054626464844 243.34735107421875 0.3990670144557953 259.0250244140625 0.2523983418941498 0.83387583 0.5057814717292786 True -11 22020 19.748128414154053 0.3690488338470459 258.70782470703125 0.2994065284729004 258.6791076660156 0.25304660201072693 0.8378737 0.46771472692489624 True -12 23855 19.78073787689209 0.37270498275756836 218.3116455078125 0.5370866656303406 258.2729797363281 0.25339919328689575 0.8459265 0.4244520664215088 True -13 25690 19.749757766723633 0.3780069351196289 196.65545654296875 0.5749585628509521 257.5085144042969 0.2559571862220764 0.85060215 0.4074578583240509 True -14 27525 19.700162172317505 0.3770153522491455 229.8634033203125 0.4434836506843567 256.87200927734375 0.2571965157985687 0.85518533 0.39665693044662476 True -15 29360 19.76168131828308 0.36148834228515625 173.98211669921875 0.5807003974914551 256.5923156738281 0.2578483819961548 0.857877 0.37887638807296753 True -16 31195 19.72975492477417 0.36775708198547363 174.63137817382812 0.29409337043762207 256.69061279296875 0.25749671459198 0.85976 0.3698209822177887 True -17 33030 19.72253942489624 0.5331544876098633 195.66958618164062 0.2197110652923584 256.7854309082031 0.25721949338912964 0.8579114 0.37270036339759827 False -18 34865 19.71782612800598 0.3607518672943115 237.17315673828125 0.2080061435699463 256.7170715332031 0.25791099667549133 0.8566542 0.37547731399536133 False -19 36700 19.713335752487183 1.2236080169677734 221.0240020751953 0.15434084832668304 256.7756652832031 0.25753310322761536 0.8571816 0.37917765974998474 False diff --git a/ENCSR731DJH/cherimoya.fold_3.performance.tsv b/ENCSR731DJH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e882986f215bc9dbe303c1835a338a5c675bd70b..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -256.69061279296875 0.5130072236061096 0.25749671459198 0.076055608689785 0.8597599864006042 0.8048305511474609 0.3698209822177887 \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_4.evaluate.json b/ENCSR731DJH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6c1d33f60220219c8555a2988d23a293ec28a698..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF367OJK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_4.fit.json b/ENCSR731DJH/cherimoya.fold_4.fit.json deleted file mode 100644 index 9762d208114ac0fed1b60413daa325d03decf183..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF367OJK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731DJH/cherimoya.fold_4.log b/ENCSR731DJH/cherimoya.fold_4.log deleted file mode 100644 index 63d9ecb8a41b770f0b83131bafd0956e588685e3..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1855 24.94011926651001 3.3705058097839355 216.3483123779297 0.6490088701248169 269.13824462890625 0.13604183495044708 0.6205179 6.40653657913208 True -1 3710 20.350077867507935 1.038485050201416 178.64907836914062 0.4189414978027344 252.67527770996094 0.183037668466568 0.74264956 2.2812602519989014 True -2 5565 20.38218927383423 0.4381575584411621 233.00123596191406 0.42999202013015747 239.4892120361328 0.21174317598342896 0.7972306 1.1968649625778198 True -3 7420 20.36880326271057 0.37757277488708496 206.340576171875 0.40646326541900635 236.49008178710938 0.21560697257518768 0.8066575 0.5493553280830383 True -4 9275 20.009827613830566 0.3720390796661377 202.96890258789062 0.37664666771888733 235.2884063720703 0.21900954842567444 0.80953336 0.4819304943084717 True -5 11130 19.993700742721558 0.35547518730163574 179.6746826171875 0.33709782361984253 233.84304809570312 0.2229054570198059 0.82136863 0.43645694851875305 True -6 12985 19.942750930786133 0.3661477565765381 200.83470153808594 0.5163748860359192 233.16322326660156 0.22510457038879395 0.8276142 0.40177756547927856 True -7 14840 19.99667477607727 0.36531734466552734 213.39236450195312 0.5041413307189941 232.69712829589844 0.22614704072475433 0.8324128 0.3852696120738983 True -8 16695 20.023696660995483 0.36753344535827637 192.36373901367188 0.4464687705039978 232.30487060546875 0.22710764408111572 0.83815604 0.36439913511276245 True -9 18550 19.95893907546997 0.35716867446899414 218.2549591064453 0.5828273296356201 231.8641815185547 0.22818388044834137 0.8417582 0.35844886302948 True -10 20405 19.96248769760132 0.35596442222595215 195.48666381835938 0.2896917462348938 231.27706909179688 0.22961527109146118 0.84469676 0.3406970500946045 True -11 22260 19.965176105499268 0.35858631134033203 253.39178466796875 0.40383145213127136 230.5658721923828 0.23207876086235046 0.85048044 0.33221396803855896 True -12 24115 19.95969295501709 0.3608276844024658 245.66387939453125 0.3431781828403473 230.6229705810547 0.23159611225128174 0.8540188 0.3225696384906769 True -13 25970 19.92000389099121 0.3671867847442627 150.8248748779297 0.3712117671966553 230.31153869628906 0.2324267327785492 0.85710555 0.31315040588378906 True -14 27825 19.92039442062378 0.36113977432250977 198.00180053710938 0.2892625331878662 230.02732849121094 0.23364613950252533 0.8628192 0.302446573972702 True -15 29680 19.905240058898926 0.36251258850097656 169.40248107910156 0.154090017080307 229.82440185546875 0.23432384431362152 0.8642424 0.2961007356643677 True -16 31535 19.983781814575195 0.3603050708770752 166.79769897460938 0.18647253513336182 229.8976593017578 0.23447401821613312 0.86440104 0.29516589641571045 True -17 33390 19.951173543930054 0.3584260940551758 217.95156860351562 0.18962325155735016 230.13247680664062 0.23361726105213165 0.86720204 0.2960665822029114 True -18 35245 19.97676396369934 0.3668370246887207 164.27365112304688 0.16982479393482208 230.22586059570312 0.2333076298236847 0.865863 0.3014937937259674 False -19 37100 19.948450088500977 0.7126388549804688 216.84017944335938 0.17902986705303192 230.30117797851562 0.23364128172397614 0.86486584 0.30426064133644104 False diff --git a/ENCSR731DJH/cherimoya.fold_4.performance.tsv b/ENCSR731DJH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 72bdbad3cb895f576dd600feb196eaba8bd8f839..0000000000000000000000000000000000000000 --- a/ENCSR731DJH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -230.13247680664062 0.5304120779037476 0.23361726105213165 0.0661141648888588 0.8672020435333252 0.7947902679443359 0.2960665822029114 \ No newline at end of file diff --git a/ENCSR731KDL/cherimoya.fold_0.log b/ENCSR731KDL/cherimoya.fold_0.log deleted file mode 100644 index 83f50f9dcd94b3f1efda9a9a243bfc30a97d654c..0000000000000000000000000000000000000000 --- a/ENCSR731KDL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2732 35.346161127090454 3.52561354637146 718.6563720703125 0.5388879776000977 802.2508544921875 0.14729201793670654 0.7114607 5.785450458526611 True -1 5464 30.021080493927002 0.5753140449523926 855.6275634765625 0.578653872013092 727.368408203125 0.1915738433599472 0.7749635 1.5778776407241821 True -2 8196 29.97412419319153 0.5608265399932861 536.5765380859375 0.4000716209411621 724.4220581054688 0.19030801951885223 0.7815767 0.9359650611877441 True -3 10928 29.973268508911133 4.303564071655273 530.08154296875 0.22813166677951813 706.330078125 0.19825667142868042 0.8058234 0.6970260739326477 True -4 13660 29.98601460456848 0.5767807960510254 514.12451171875 0.2954859733581543 696.658935546875 0.20301580429077148 0.81864595 0.5864226222038269 True -5 16392 29.879257440567017 0.5529882907867432 611.7794189453125 0.3878477215766907 690.8460083007812 0.2060844600200653 0.82037354 0.4519386887550354 True -6 19124 29.8883159160614 0.5606625080108643 486.8297119140625 0.29051339626312256 686.9011840820312 0.2082068920135498 0.8230396 0.42039918899536133 True -7 21856 30.04790425300598 0.9859323501586914 637.8104248046875 0.3750486373901367 683.063232421875 0.21027269959449768 0.8322896 0.3991646468639374 True -8 24588 29.899511575698853 0.5574300289154053 458.37615966796875 0.2699302136898041 680.1524658203125 0.21167756617069244 0.83946764 0.37794849276542664 True -9 27320 30.682570695877075 24.274229049682617 662.4902954101562 0.5003964304924011 676.393310546875 0.21398286521434784 0.84572124 0.3667500615119934 True -10 30052 29.984319925308228 0.5795111656188965 621.3494873046875 0.37791550159454346 674.5991821289062 0.21553470194339752 0.84899145 0.35239502787590027 True -11 32784 29.979546546936035 0.5687351226806641 772.29443359375 0.1281891167163849 672.52587890625 0.21689273416996002 0.85279953 0.3557550013065338 True -12 35516 30.0263032913208 0.5613996982574463 678.392822265625 0.29644885659217834 669.7070922851562 0.21853820979595184 0.8625945 0.3195871412754059 True -13 38248 30.052892208099365 36.86416292190552 561.5712890625 0.2162196934223175 666.7507934570312 0.22073835134506226 0.8669034 0.3047362267971039 True -14 40980 30.513867139816284 0.5726213455200195 551.5834350585938 0.20566622912883759 664.0812377929688 0.22193759679794312 0.8731665 0.28271037340164185 True -15 43712 30.355106592178345 0.8101809024810791 517.36474609375 0.23145559430122375 663.9216918945312 0.22143936157226562 0.8773381 0.26728159189224243 True -16 46444 30.1199209690094 0.5677134990692139 585.9369506835938 0.3427458703517914 663.4172973632812 0.2222527116537094 0.88176364 0.25735488533973694 True -17 49176 30.024982452392578 34.89647841453552 564.130859375 0.2979484498500824 663.068115234375 0.22192546725273132 0.88179344 0.25240692496299744 True -18 51908 30.547409296035767 0.5616374015808105 745.17578125 0.182388037443161 663.7222290039062 0.22139041125774384 0.8812542 0.25321540236473083 False -19 54640 30.05864953994751 0.5725009441375732 538.7159423828125 0.25082916021347046 664.42578125 0.22049058973789215 0.8818582 0.253654807806015 True diff --git a/ENCSR731KDL/cherimoya.fold_2.evaluate.json b/ENCSR731KDL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 16207dd56090776671b482dfa0c39aa8c6bf05e6..0000000000000000000000000000000000000000 --- a/ENCSR731KDL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF807GIG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731KDL/cherimoya.fold_4.log b/ENCSR731KDL/cherimoya.fold_4.log deleted file mode 100644 index 02ffb4333d46924c1922d5d13279b9cd9e16f1b4..0000000000000000000000000000000000000000 --- a/ENCSR731KDL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2814 35.76241326332092 3.5807156562805176 742.570556640625 0.6974579095840454 730.717041015625 0.14759664237499237 0.6767585 4.9578399658203125 True -1 5628 30.951988697052002 0.588759183883667 478.56048583984375 0.4088195264339447 672.654052734375 0.18501640856266022 0.7225872 1.2365506887435913 True -2 8442 30.900578498840332 1.010129690170288 652.5882568359375 0.5596292018890381 665.0712890625 0.18625910580158234 0.74298155 0.6497867703437805 True -3 11256 30.894508123397827 35.54945182800293 628.255859375 0.5330135822296143 654.9459838867188 0.19013147056102753 0.77172244 0.5484498739242554 True -4 14070 31.179676055908203 1.435424566268921 531.763671875 0.22300073504447937 651.3237915039062 0.1916722059249878 0.77911687 0.5988470315933228 True -5 16884 38.045538663864136 19.923214197158813 557.079833984375 0.34963178634643555 641.4929809570312 0.19762346148490906 0.79041505 0.5128759741783142 True -6 19698 30.828630685806274 0.5834252834320068 633.8406982421875 0.5462961792945862 641.15869140625 0.1977015733718872 0.79739803 0.5412419438362122 True -7 22512 30.826889276504517 1.564366102218628 644.1007080078125 0.3562054932117462 633.0706176757812 0.20276793837547302 0.809978 0.47602126002311707 True -8 25326 30.89852285385132 0.5960001945495605 457.26361083984375 0.4662346839904785 629.6652221679688 0.20505504310131073 0.8178451 0.42830073833465576 True -9 28140 30.879038095474243 0.5706117153167725 613.287353515625 0.2688315510749817 629.185546875 0.2052503526210785 0.82394016 0.3974279761314392 True -10 30954 30.861424207687378 0.5683400630950928 460.49444580078125 0.20166993141174316 627.6849365234375 0.20647071301937103 0.83047247 0.3594866394996643 True -11 33768 30.889430284500122 0.5647308826446533 521.8343505859375 0.3779422640800476 627.055419921875 0.2067747414112091 0.8358205 0.33801543712615967 True -12 36582 30.924981832504272 0.5800583362579346 646.2841796875 0.405981183052063 623.639404296875 0.20944815874099731 0.8430559 0.3163984417915344 True -13 39396 31.965261459350586 38.67917060852051 514.7312622070312 0.31805849075317383 621.489013671875 0.2109542340040207 0.8509075 0.2931842505931854 True -14 42210 30.937694549560547 0.595280647277832 569.9415283203125 0.24953915178775787 620.0587158203125 0.21082526445388794 0.8569069 0.27485620975494385 True -15 45024 31.32385778427124 40.24355435371399 642.6002197265625 0.31924116611480713 619.2130126953125 0.2122892290353775 0.86221033 0.2612650394439697 True -16 47838 30.694881677627563 0.5776309967041016 508.9421081542969 0.29471510648727417 619.388916015625 0.21179039776325226 0.86580175 0.25215527415275574 True -17 50652 30.30386972427368 0.577385425567627 732.9581909179688 0.2991045117378235 618.9185791015625 0.21187548339366913 0.8679241 0.24986574053764343 True -18 53466 30.319912433624268 0.5688192844390869 496.02996826171875 0.3960861563682556 618.7285766601562 0.21221621334552765 0.867437 0.2493021935224533 False -19 56280 30.4031879901886 0.5739696025848389 593.90625 0.17850208282470703 619.7057495117188 0.21156245470046997 0.8685054 0.2508617043495178 True diff --git a/ENCSR731ODJ/cherimoya.fold_0.evaluate.json b/ENCSR731ODJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ec897fa2860b1b93025909c38b9010a1091542ae..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF629SON.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_0.fit.json b/ENCSR731ODJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 4be79db84f120bf90ab13b4b571388a20b553ed3..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF629SON.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_0.log b/ENCSR731ODJ/cherimoya.fold_0.log deleted file mode 100644 index b0bcfb98b4bf3ec239cfa04aafc29f51f33cacdd..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1603 21.49207329750061 21.44180965423584 265.87432861328125 0.6763482689857483 335.0034484863281 0.4096932113170624 0.7164905 10.768704414367676 True -1 3206 19.265519857406616 0.3352022171020508 219.32333374023438 0.7440938949584961 285.5425720214844 0.4920867085456848 0.7593915 2.9608376026153564 True -2 4809 17.67177414894104 0.3146636486053467 209.51934814453125 0.430941104888916 268.9465026855469 0.535214900970459 0.77647454 0.7554534673690796 True -3 6412 18.291507244110107 0.3131241798400879 200.17626953125 0.7806030511856079 263.3094482421875 0.5494065284729004 0.7845061 0.36767464876174927 True -4 8015 17.57635760307312 0.31157851219177246 206.46144104003906 0.5254772305488586 261.372314453125 0.5547994375228882 0.78859264 0.34763818979263306 True -5 9618 17.6154727935791 0.3134782314300537 214.91302490234375 0.5804731845855713 260.4634094238281 0.5576493740081787 0.7912067 0.34553882479667664 True -6 11221 17.626525163650513 0.31066465377807617 205.22467041015625 0.44719818234443665 259.7143249511719 0.5595206618309021 0.79360884 0.33791306614875793 True -7 12824 17.61472225189209 0.3068656921386719 211.83750915527344 0.5506880879402161 259.2395935058594 0.5612371563911438 0.79337615 0.32917213439941406 False -8 14427 17.615342617034912 0.31288766860961914 227.92343139648438 0.6082574129104614 258.6646423339844 0.5630881190299988 0.7970848 0.3272959291934967 True -9 16030 17.58926796913147 0.307300329208374 161.7406005859375 0.5769575834274292 258.1083984375 0.5647421479225159 0.8042738 0.3130034804344177 True -10 17633 17.60750722885132 0.3052804470062256 220.02362060546875 0.49437227845191956 257.5642395019531 0.5663208365440369 0.80519253 0.30861470103263855 True -11 19236 17.599777936935425 0.3140389919281006 231.72042846679688 0.5748865604400635 257.03106689453125 0.5678874254226685 0.8066605 0.30700141191482544 True -12 20839 17.653416395187378 0.31218552589416504 192.52047729492188 0.42651844024658203 256.63385009765625 0.5693463087081909 0.80865484 0.3052138388156891 True -13 22442 17.61588215827942 0.31275224685668945 185.26162719726562 0.5604313015937805 256.3913879394531 0.5703548192977905 0.81298673 0.3059769868850708 True -14 24045 17.676183462142944 0.7236378192901611 188.964111328125 0.3526737689971924 256.1520690917969 0.5709131956100464 0.81392163 0.304781436920166 True -15 25648 17.648709535598755 0.3086740970611572 202.98500061035156 0.2505187690258026 256.1341552734375 0.5710172653198242 0.81473386 0.3063369691371918 True -16 27251 17.655969858169556 0.30783653259277344 193.57061767578125 0.3155968189239502 256.3439025878906 0.5704959630966187 0.8133971 0.3153810501098633 False -17 28854 17.60834288597107 0.31392955780029297 229.87315368652344 0.19382096827030182 256.5728454589844 0.5696067214012146 0.8125439 0.32486048340797424 False -18 30457 17.65205979347229 0.30759525299072266 180.12188720703125 0.3668692111968994 256.8570556640625 0.5687658190727234 0.80814385 0.3386167883872986 False -19 32060 17.644378900527954 0.3047611713409424 220.92462158203125 0.17169292271137238 256.9977111816406 0.5681214928627014 0.80767596 0.34511420130729675 False diff --git a/ENCSR731ODJ/cherimoya.fold_0.performance.tsv b/ENCSR731ODJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index abd082ef931ec2900267f46dbc1ff2802621111f..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -256.1341552734375 0.34670501947402954 0.5710172653198242 0.1773761808872223 0.8147338628768921 0.7733440399169922 0.3063369691371918 \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_1.evaluate.json b/ENCSR731ODJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 305445c0c380dd756b4b81888cdf0c1a1b5e5ba1..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF629SON.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_1.fit.json b/ENCSR731ODJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 8dbdaa0f0fc1a755bdd86f0a9ea5e5e1414ec549..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF629SON.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_1.log b/ENCSR731ODJ/cherimoya.fold_1.log deleted file mode 100644 index 2875751cc40f29aef1ac8ea832d6f56aed26cee8..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1576 21.310008764266968 3.5935003757476807 225.53561401367188 0.8846123814582825 377.0798645019531 0.4261506199836731 0.66547334 11.737666130065918 True -1 3152 17.369215965270996 0.790834903717041 251.32334899902344 0.6270667314529419 319.4164733886719 0.5124075412750244 0.7371415 3.215688943862915 True -2 4728 17.461825847625732 0.5333507061004639 231.8741455078125 0.5107483863830566 300.7051086425781 0.5569024682044983 0.76296014 0.8075600862503052 True -3 6304 17.31225037574768 1.3453068733215332 200.87353515625 0.5408299565315247 294.4287414550781 0.5724868774414062 0.7805861 0.5212625861167908 True -4 7880 17.349117040634155 0.4418768882751465 208.03341674804688 0.5567679405212402 293.2162780761719 0.5761426687240601 0.786285 0.4109581708908081 True -5 9456 17.221429586410522 0.4392223358154297 167.70703125 0.5064637660980225 291.53240966796875 0.58049476146698 0.7941408 0.33794528245925903 True -6 11032 17.008267402648926 0.4399566650390625 207.89047241210938 0.4531661868095398 290.595947265625 0.5829150676727295 0.7938369 0.36321285367012024 False -7 12608 17.006733417510986 0.4308664798736572 206.38800048828125 0.4924342930316925 289.75823974609375 0.5851708650588989 0.7998287 0.3598828911781311 True -8 14184 16.987849473953247 0.4307734966278076 228.06602478027344 0.41021862626075745 288.7460632324219 0.5875976085662842 0.80427825 0.3452509939670563 True -9 15760 16.975030183792114 0.4317128658294678 198.75650024414062 0.6578073501586914 288.1600646972656 0.5893583297729492 0.8048757 0.3397798240184784 True -10 17336 16.96629285812378 0.4328324794769287 228.86062622070312 0.422321617603302 287.58807373046875 0.5910149812698364 0.80938554 0.33553868532180786 True -11 18912 16.982054948806763 0.43014025688171387 184.17254638671875 0.6583746671676636 287.0061340332031 0.5926021933555603 0.80926186 0.3327072858810425 False -12 20488 16.973408460617065 0.43102407455444336 188.1534423828125 0.5015631914138794 286.5863037109375 0.5939775705337524 0.81573236 0.3256669044494629 True -13 22064 16.96531629562378 0.4306514263153076 215.72828674316406 0.31558042764663696 286.1936340332031 0.5950282216072083 0.8196475 0.32555434107780457 True -14 23640 16.96713423728943 0.43567824363708496 240.0526580810547 0.6691074371337891 285.8590393066406 0.5957820415496826 0.8224679 0.31869572401046753 True -15 25216 16.95338535308838 0.4365389347076416 218.6199951171875 0.2853715419769287 285.7039794921875 0.5959272384643555 0.8234716 0.3206729590892792 True -16 26792 17.012622594833374 16.74229407310486 220.84222412109375 0.3544139862060547 285.88006591796875 0.5953763127326965 0.82442987 0.3266068398952484 True -17 28368 17.303547859191895 0.4343409538269043 205.01947021484375 0.2325815111398697 286.15020751953125 0.5944119095802307 0.82139224 0.3384195864200592 False -18 29944 16.942070245742798 0.4246494770050049 196.94287109375 0.1892399936914444 286.46893310546875 0.5933655500411987 0.8191841 0.34974566102027893 False -19 31520 16.93968629837036 0.42783117294311523 185.09857177734375 0.2476423680782318 286.6638488769531 0.5927101969718933 0.81728476 0.3607776463031769 False diff --git a/ENCSR731ODJ/cherimoya.fold_1.performance.tsv b/ENCSR731ODJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 769c95e5fad8e27bb8777f4041fd23d6ad79eff3..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -285.88006591796875 0.32827529311180115 0.5953763127326965 0.19779902696609497 0.8244298696517944 0.810274600982666 0.3266068398952484 \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_2.evaluate.json b/ENCSR731ODJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7f5b3f8a55b36a28487a6ddd4d1ff23650b2003a..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF629SON.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_2.fit.json b/ENCSR731ODJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 103c042c3425d270c6ef83815b2c1d8eb7494bb5..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF629SON.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_2.log b/ENCSR731ODJ/cherimoya.fold_2.log deleted file mode 100644 index 6070dcc87a8e527847dcbe032416f55c670e9bed..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1681 22.32279896736145 3.4304442405700684 197.80825805664062 0.6939105987548828 342.9200439453125 0.41822755336761475 0.68434966 9.746395111083984 True -1 3362 18.49920344352722 0.33248138427734375 222.76853942871094 0.8137122392654419 292.5423583984375 0.505459189414978 0.7498579 2.279862403869629 True -2 5043 18.480928897857666 1.5923874378204346 183.396484375 0.43086564540863037 277.6590270996094 0.5452492237091064 0.76206475 0.5879356861114502 True -3 6724 18.528199672698975 0.3265805244445801 197.38131713867188 0.5431022047996521 272.0881652832031 0.5592580437660217 0.77152216 0.4001798927783966 True -4 8405 18.45519518852234 0.3279600143432617 239.2022705078125 0.5726971626281738 270.6859130859375 0.56326824426651 0.7737355 0.4069255292415619 True -5 10086 18.450816869735718 0.8213143348693848 209.21707153320312 0.38086390495300293 269.53863525390625 0.5664310455322266 0.7750245 0.3757656514644623 True -6 11767 18.4699547290802 0.3260207176208496 212.92442321777344 0.5406696796417236 268.7054748535156 0.5684356689453125 0.77949125 0.3885380029678345 True -7 13448 18.447895526885986 0.3308601379394531 198.45672607421875 0.509386420249939 268.1173095703125 0.570464015007019 0.7828784 0.3709808588027954 True -8 15129 18.518896102905273 0.3283708095550537 213.7865753173828 0.3833424746990204 267.5313720703125 0.5723295211791992 0.7865115 0.3706004023551941 True -9 16810 18.582894563674927 0.3312523365020752 165.32559204101562 0.6144733428955078 266.8903503417969 0.574114203453064 0.79042035 0.36286428570747375 True -10 18491 18.46123743057251 0.3309056758880615 194.0482177734375 0.3470216691493988 266.2159423828125 0.5759268403053284 0.7920999 0.35654300451278687 True -11 20172 18.464906692504883 0.32744526863098145 204.13670349121094 0.3778875172138214 265.7547302246094 0.5771499276161194 0.79796165 0.3485270142555237 True -12 21853 18.456788539886475 0.33555102348327637 208.09963989257812 0.5827986001968384 265.4534912109375 0.5782548189163208 0.8005063 0.34784483909606934 True -13 23534 18.468294382095337 10.411150455474854 214.1032257080078 0.5493965744972229 265.0175476074219 0.5792639851570129 0.80530775 0.3368980586528778 True -14 25215 18.525189638137817 0.32836413383483887 226.89999389648438 0.3883291482925415 264.8388977050781 0.5797988176345825 0.80823785 0.33953574299812317 True -15 26896 18.461244344711304 0.5196247100830078 201.45623779296875 0.39948129653930664 264.6942138671875 0.579983651638031 0.81129545 0.3348774015903473 True -16 28577 18.47783088684082 0.32190465927124023 238.80154418945312 0.3228643834590912 264.8384704589844 0.5794187784194946 0.8078022 0.34914907813072205 False -17 30258 18.49402928352356 0.3262345790863037 219.006591796875 0.3302556872367859 265.09759521484375 0.5784802436828613 0.8039896 0.36308571696281433 False -18 31939 18.448485374450684 1.6333305835723877 195.426025390625 0.2836206555366516 265.356201171875 0.5773686170578003 0.8007401 0.3764829933643341 False -19 33620 18.593892574310303 0.33142852783203125 224.58084106445312 0.20793242752552032 265.5417175292969 0.5768314003944397 0.7990608 0.3819722533226013 False diff --git a/ENCSR731ODJ/cherimoya.fold_2.performance.tsv b/ENCSR731ODJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 81e46483adffc851cc443e35191494f3d92aa9db..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -264.6942138671875 0.3416152894496918 0.579983651638031 0.18126225471496582 0.8112954497337341 0.7761843800544739 0.3348774015903473 \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_3.evaluate.json b/ENCSR731ODJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1b3800b1546e970dc6811c6adc26d02dda265a12..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF629SON.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_3.fit.json b/ENCSR731ODJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 77346aaebefae8981faa2c3afab949794ccdf05e..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF629SON.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_3.log b/ENCSR731ODJ/cherimoya.fold_3.log deleted file mode 100644 index c38129356f2bb66d81bf9e3195b83d502c88803a..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1631 21.853471755981445 3.215794801712036 235.40451049804688 0.510987401008606 334.6072998046875 0.4123322665691376 0.68899566 10.879064559936523 True -1 3262 17.90230083465576 0.5800762176513672 232.21836853027344 0.5078889727592468 284.61785888671875 0.4956269860267639 0.7549803 2.750269889831543 True -2 4893 17.612883806228638 0.29634618759155273 232.35977172851562 0.5252788662910461 270.0582275390625 0.5351185202598572 0.777922 1.0552294254302979 True -3 6524 17.531697273254395 0.3017549514770508 193.1844940185547 0.5680066347122192 264.2225036621094 0.5495755076408386 0.79516023 0.5183374285697937 True -4 8155 17.53239917755127 0.29544663429260254 222.26356506347656 0.5117077827453613 262.2264099121094 0.5545286536216736 0.80058515 0.3617681860923767 True -5 9786 17.534295320510864 1.199169635772705 217.99664306640625 0.712787926197052 261.33612060546875 0.5572912096977234 0.80172473 0.35464411973953247 True -6 11417 17.60932159423828 0.30913615226745605 198.54859924316406 0.4605068862438202 260.7926330566406 0.5594837069511414 0.80371916 0.3510850965976715 True -7 13048 17.527638912200928 0.30347681045532227 189.17514038085938 0.5480820536613464 259.9744567871094 0.5619450807571411 0.80419046 0.34490546584129333 True -8 14679 17.515799522399902 0.3035926818847656 204.8922576904297 0.6204934120178223 259.4989013671875 0.5638386607170105 0.80387765 0.342831552028656 False -9 16310 17.523303985595703 0.29679250717163086 210.82325744628906 0.3942521810531616 259.02178955078125 0.5652454495429993 0.8025666 0.3563612997531891 False -10 17941 17.565868616104126 0.29999256134033203 216.7455596923828 0.3742709159851074 258.29437255859375 0.5673162341117859 0.80908245 0.3443739712238312 True -11 19572 17.581973552703857 0.30399441719055176 244.61717224121094 0.35328078269958496 258.0010070800781 0.5685028433799744 0.8083521 0.34054800868034363 False -12 21203 17.545854806900024 0.3036308288574219 236.8379364013672 0.3236072063446045 257.5969543457031 0.5694901347160339 0.81269443 0.3321273624897003 True -13 22834 17.53666114807129 0.2971079349517822 235.53018188476562 0.40216201543807983 257.17340087890625 0.5707546472549438 0.81587607 0.32373514771461487 True -14 24465 17.529788732528687 0.3011770248413086 173.97674560546875 0.3351988196372986 256.94573974609375 0.5715936422348022 0.8177375 0.32055795192718506 True -15 26096 17.555458068847656 0.3004307746887207 207.4232177734375 0.6440905332565308 256.9030456542969 0.5716478228569031 0.82003164 0.32000380754470825 True -16 27727 17.533718824386597 0.29634571075439453 181.635498046875 0.255453884601593 257.04193115234375 0.5713661313056946 0.8199613 0.3239949643611908 False -17 29358 17.979602575302124 0.30340051651000977 243.9964141845703 0.18634989857673645 257.27801513671875 0.5705745220184326 0.8189412 0.3337205946445465 False -18 30989 17.560776233673096 0.30383753776550293 176.7597198486328 0.2460610568523407 257.5162048339844 0.5695710778236389 0.81601715 0.3447137773036957 False -19 32620 17.533288955688477 0.2971222400665283 245.298828125 0.21368424594402313 257.6936950683594 0.5689902305603027 0.81466734 0.35188403725624084 False diff --git a/ENCSR731ODJ/cherimoya.fold_3.performance.tsv b/ENCSR731ODJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1535c2843457de4aa6a6b89a191ff1871ee8c3b7..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -256.9030456542969 0.34678971767425537 0.5716477632522583 0.17586413025856018 0.8200316429138184 0.7849466800689697 0.32000380754470825 \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_4.evaluate.json b/ENCSR731ODJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index be1076fb12ce22c6227ace021127895e1ba333d5..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF629SON.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_4.fit.json b/ENCSR731ODJ/cherimoya.fold_4.fit.json deleted file mode 100644 index b65ce1f423f16897c55b7e50c4898fe64a3df618..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF629SON.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731ODJ/cherimoya.fold_4.log b/ENCSR731ODJ/cherimoya.fold_4.log deleted file mode 100644 index d1d612e6c835c665f97e0f213130f48c72d36268..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1637 22.182803630828857 4.276559114456177 225.96719360351562 0.5470623970031738 320.12744140625 0.40879562497138977 0.69423574 10.539814949035645 True -1 3274 18.03573179244995 0.3417398929595947 206.37640380859375 0.5721694231033325 274.3148193359375 0.4905761480331421 0.7368858 2.900527000427246 True -2 4911 17.972846746444702 0.32205748558044434 222.5440673828125 0.3637829124927521 261.6720275878906 0.5276909470558167 0.75778866 0.9610942006111145 True -3 6548 17.96337080001831 0.3202338218688965 230.14959716796875 0.5837143659591675 256.1629943847656 0.5425857901573181 0.77026737 0.5137293338775635 True -4 8185 17.996519088745117 0.33773303031921387 204.73904418945312 0.7931235432624817 254.74493408203125 0.5466116070747375 0.76768017 0.46093320846557617 False -5 9822 17.979807376861572 0.33072566986083984 215.77090454101562 0.6178677678108215 253.62464904785156 0.5500566959381104 0.77499187 0.3764050602912903 True -6 11459 18.01876950263977 0.32097506523132324 231.06187438964844 0.36511749029159546 253.06405639648438 0.5520004630088806 0.7742222 0.3808210492134094 False -7 13096 18.00843596458435 5.2810258865356445 223.8599395751953 0.8459994792938232 252.4409942626953 0.5539929866790771 0.78008324 0.3730250597000122 True -8 14733 18.003599643707275 0.33400440216064453 214.18154907226562 0.48679110407829285 251.94650268554688 0.5559443831443787 0.7809956 0.3777482211589813 True -9 16370 18.05204677581787 0.3275775909423828 194.73883056640625 0.36590129137039185 251.4276123046875 0.5576189160346985 0.7869782 0.3540860712528229 True -10 18007 18.119493007659912 0.32990050315856934 215.2079620361328 0.3794242739677429 250.9064178466797 0.5593608617782593 0.79011285 0.34296876192092896 True -11 19644 18.00960683822632 0.3258175849914551 211.2398681640625 0.5104254484176636 250.39476013183594 0.5610613822937012 0.7955105 0.33843469619750977 True -12 21281 17.976690769195557 0.32136988639831543 199.84017944335938 0.4732115864753723 250.041015625 0.5625803470611572 0.79772824 0.3327640891075134 True -13 22918 17.981942892074585 0.32442665100097656 226.50198364257812 0.36808300018310547 249.64695739746094 0.5637651681900024 0.80185074 0.33593612909317017 True -14 24555 18.012601613998413 0.33336687088012695 223.27886962890625 0.3043506145477295 249.3820343017578 0.5645360946655273 0.80493546 0.3391706347465515 True -15 26192 17.995821952819824 0.32806944847106934 189.02989196777344 0.42766404151916504 249.3160858154297 0.564583420753479 0.8058927 0.3469880223274231 True -16 27829 17.88363289833069 0.3162522315979004 178.29531860351562 0.2741048336029053 249.48912048339844 0.5640351176261902 0.8091901 0.343189001083374 True -17 29466 17.660091876983643 0.3167872428894043 205.60537719726562 0.26924198865890503 249.73777770996094 0.5631997585296631 0.80544454 0.3545702397823334 False -18 31103 17.671897411346436 0.3243882656097412 192.78372192382812 0.31908321380615234 249.9083251953125 0.5624834895133972 0.8040829 0.3569241166114807 False -19 32740 17.70328998565674 0.32250380516052246 202.82846069335938 0.2798948585987091 250.04161071777344 0.5620005130767822 0.8018541 0.3616032004356384 False diff --git a/ENCSR731ODJ/cherimoya.fold_4.performance.tsv b/ENCSR731ODJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b01d28a103cd788369de86e006060a7ad59db5ea..0000000000000000000000000000000000000000 --- a/ENCSR731ODJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -249.48912048339844 0.3522073030471802 0.564035177230835 0.17131972312927246 0.8091900944709778 0.7471469640731812 0.343189001083374 \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_0.evaluate.json b/ENCSR731QLJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7c7d81a436f893a834e5442eec889b6cbb541bb8..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF255STG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_0.fit.json b/ENCSR731QLJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 492eb006614895083b86eebf90c0a81fec728140..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF255STG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_0.log b/ENCSR731QLJ/cherimoya.fold_0.log deleted file mode 100644 index 62a6d6224f6a76f201766ca4734c4a81936db4be..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.77381372451782 4.619738340377808 1339.6883544921875 2.384047746658325 1991.0841064453125 0.32474973797798157 0.4270602 10.26633071899414 True -1 5494 30.404666662216187 0.9376931190490723 1209.2880859375 1.8684592247009277 1603.3670654296875 0.4812625050544739 0.5149583 3.788084030151367 True -2 8241 30.302215814590454 2.2259373664855957 922.90673828125 1.2131450176239014 1574.3880615234375 0.4907384216785431 0.53310454 2.1321027278900146 True -3 10988 30.33779263496399 0.5928494930267334 1038.112548828125 1.2785165309906006 1540.3848876953125 0.5025790929794312 0.55733144 1.468379020690918 True -4 13735 30.24152898788452 0.6013591289520264 1033.8828125 1.1489996910095215 1522.497314453125 0.5104236006736755 0.5605675 1.5089884996414185 True -5 16482 30.22376775741577 0.566889762878418 1101.7225341796875 1.3448293209075928 1501.18212890625 0.5200141668319702 0.57665575 1.543904185295105 True -6 19229 29.637813806533813 0.5764524936676025 1196.761474609375 1.1789271831512451 1491.0496826171875 0.5256271362304688 0.578394 1.5258543491363525 True -7 21976 29.625948429107666 0.578270673751831 1079.435302734375 1.3028337955474854 1479.2352294921875 0.529029130935669 0.58748686 1.2620552778244019 True -8 24723 29.76377248764038 0.5705986022949219 1109.4442138671875 1.1310968399047852 1471.939697265625 0.532787561416626 0.5932755 1.2326847314834595 True -9 27470 29.71462082862854 0.5968389511108398 1104.6802978515625 1.2521941661834717 1462.3458251953125 0.5365045070648193 0.6060606 1.067007303237915 True -10 30217 29.738824129104614 0.5704553127288818 1336.8287353515625 0.9414324164390564 1452.01123046875 0.5400459170341492 0.6141249 1.0040006637573242 True -11 32964 29.62030029296875 0.5659892559051514 1204.253662109375 0.7356259822845459 1442.3516845703125 0.5435757040977478 0.62714875 0.9517877101898193 True -12 35711 29.66805410385132 0.5666341781616211 1110.896728515625 1.4889843463897705 1431.6102294921875 0.5476735234260559 0.63787824 0.879201352596283 True -13 38458 29.698341608047485 0.5725421905517578 1016.776123046875 0.9636510014533997 1419.4913330078125 0.5534730553627014 0.6493278 0.8642560243606567 True -14 41205 29.640216827392578 0.5664334297180176 1054.6884765625 0.7680217027664185 1413.733642578125 0.5545875430107117 0.6576271 0.8412642478942871 True -15 43952 29.67195701599121 1.516552209854126 981.5358276367188 0.6336713433265686 1403.3515625 0.5579160451889038 0.66821647 0.7717691659927368 True -16 46699 29.618343114852905 0.553335428237915 882.1785278320312 0.751889705657959 1399.6387939453125 0.5594322681427002 0.6764989 0.74589604139328 True -17 49446 29.661744117736816 0.5645952224731445 936.0050048828125 0.661825954914093 1403.6302490234375 0.5565817952156067 0.68061167 0.7345872521400452 True -18 52193 29.65752077102661 0.5488085746765137 1098.513427734375 0.42607468366622925 1403.85205078125 0.5573762655258179 0.68161047 0.7286968231201172 True -19 54940 29.60157060623169 0.9236557483673096 1013.9305419921875 0.5163427591323853 1404.217041015625 0.556527853012085 0.6829752 0.7257593870162964 True diff --git a/ENCSR731QLJ/cherimoya.fold_0.performance.tsv b/ENCSR731QLJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 473d9ac0128d0eaf3dce120444f95eca421442cf..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1404.217041015625 0.2414201945066452 0.556527853012085 0.33090877532958984 0.682975172996521 0.6440385580062866 0.7257593870162964 \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_1.evaluate.json b/ENCSR731QLJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 68739303db23de76c9bd4bca6bafb872a5d0fd96..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF255STG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_1.fit.json b/ENCSR731QLJ/cherimoya.fold_1.fit.json deleted file mode 100644 index a207408bc992952000e796831bc6c44cd26d17ec..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF255STG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_1.log b/ENCSR731QLJ/cherimoya.fold_1.log deleted file mode 100644 index aa99b0d07feab45e9fde08ca9fb2793dbab5fa8c..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 34.703879594802856 4.076625823974609 1196.66015625 1.2393138408660889 2295.868408203125 0.3133848011493683 0.4656552 10.977316856384277 True -1 5462 30.126810312271118 1.7675864696502686 1097.064453125 1.6015875339508057 1894.3748779296875 0.45974230766296387 0.56841266 6.347433090209961 True -2 8193 30.021671772003174 0.744635820388794 1233.312255859375 1.4610912799835205 1797.142822265625 0.49914002418518066 0.5698787 3.453249454498291 True -3 10924 30.089027404785156 0.7136218547821045 1068.471435546875 1.1131188869476318 1756.2265625 0.5103200078010559 0.57984376 2.6655147075653076 True -4 13655 30.160483837127686 0.7215249538421631 1177.569091796875 1.0321928262710571 1733.3201904296875 0.515076756477356 0.5847066 2.2417619228363037 True -5 16386 30.131969928741455 0.7450995445251465 1488.330322265625 1.0025379657745361 1721.3739013671875 0.5185141563415527 0.5821407 1.8936586380004883 False -6 19117 30.150697469711304 1.403778314590454 972.419189453125 0.9042142033576965 1705.4945068359375 0.5265364050865173 0.60888064 1.7077796459197998 True -7 21848 30.10631227493286 0.7085459232330322 1002.2295532226562 1.0712181329727173 1681.89697265625 0.5327350497245789 0.6180869 1.5011990070343018 True -8 24579 30.06398344039917 0.7119953632354736 994.9168701171875 1.2439601421356201 1672.4678955078125 0.5346300601959229 0.6311212 1.5060057640075684 True -9 27310 29.48693060874939 0.7129497528076172 1058.73681640625 1.2107094526290894 1668.7496337890625 0.5355758666992188 0.6383786 1.390982747077942 True -10 30041 29.470882892608643 0.67647385597229 1315.04248046875 0.9842069149017334 1643.840087890625 0.5452331900596619 0.6495077 1.268059492111206 True -11 32772 29.637592792510986 0.6994469165802002 936.4303588867188 0.9738215208053589 1631.576171875 0.5487259030342102 0.6670524 1.1207603216171265 True -12 35503 29.641489505767822 0.7298018932342529 805.6412353515625 1.1514180898666382 1609.3519287109375 0.5549477338790894 0.6824481 0.9894484877586365 True -13 38234 29.52822208404541 0.7226967811584473 1051.3997802734375 1.04029381275177 1604.0318603515625 0.5557693243026733 0.6949077 0.9332225918769836 True -14 40965 29.544238090515137 0.7142133712768555 917.9382934570312 0.960350513458252 1599.2225341796875 0.5573147535324097 0.7065468 0.8625656962394714 True -15 43696 29.48473572731018 0.7096230983734131 1049.0325927734375 0.8091358542442322 1589.4212646484375 0.5600687861442566 0.71419716 0.8218284249305725 True -16 46427 29.52714467048645 0.7878787517547607 1239.07470703125 0.9462763071060181 1591.6610107421875 0.5571471452713013 0.7177035 0.7914744019508362 True -17 49158 29.59020495414734 1.491515874862671 1001.3583374023438 0.5390036702156067 1576.8177490234375 0.565104067325592 0.72087514 0.763260543346405 True -18 51889 29.52365779876709 0.6826250553131104 1340.2158203125 0.6832213401794434 1589.739013671875 0.5582839250564575 0.72214836 0.7527561783790588 True -19 54620 29.531235218048096 0.6798591613769531 1097.857177734375 0.6913164258003235 1578.9351806640625 0.5657374262809753 0.7207204 0.7495036125183105 False diff --git a/ENCSR731QLJ/cherimoya.fold_1.performance.tsv b/ENCSR731QLJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1b550ada9f05660319edbf40e436c05ea5d86146..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1589.739013671875 0.23532985150814056 0.5582839846611023 0.3440539538860321 0.7221483588218689 0.692617654800415 0.7527561783790588 \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_2.evaluate.json b/ENCSR731QLJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 84bd86075b168c28c74203430e14e4f14913337b..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF255STG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_2.fit.json b/ENCSR731QLJ/cherimoya.fold_2.fit.json deleted file mode 100644 index bc6dd815f956c627788e1783702b42e6d3bde50b..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF255STG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_2.log b/ENCSR731QLJ/cherimoya.fold_2.log deleted file mode 100644 index 7940af909cf9837f8b5631a4907ed7592c70d6fa..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2898 36.57463836669922 3.559880495071411 1175.796142578125 1.242209792137146 1990.450927734375 0.32951620221138 0.43305475 7.7310285568237305 True -1 5796 31.823912382125854 0.7045373916625977 734.8172607421875 1.1078763008117676 1630.860107421875 0.46914392709732056 0.55444366 4.0172319412231445 True -2 8694 31.819321155548096 0.5390884876251221 1105.216552734375 1.2163183689117432 1603.001708984375 0.4817701280117035 0.55443203 2.183229684829712 False -3 11592 31.80832600593567 11.806651830673218 1144.9736328125 1.2144827842712402 1550.1942138671875 0.5045763850212097 0.57011575 1.395400047302246 True -4 14490 31.81692147254944 20.52745509147644 1193.2030029296875 1.2434203624725342 1530.34375 0.5119617581367493 0.58098835 1.0634838342666626 True -5 17388 31.201109647750854 0.5314164161682129 1180.545654296875 1.1545517444610596 1515.00146484375 0.5222801566123962 0.5837956 1.3072329759597778 True -6 20286 31.218833923339844 0.5261356830596924 993.7454833984375 1.1101045608520508 1508.956787109375 0.5217105150222778 0.599584 1.177072286605835 True -7 23184 31.21068048477173 0.521428108215332 1258.668701171875 1.4256587028503418 1496.8067626953125 0.5263833999633789 0.613247 1.0786923170089722 True -8 26082 31.228818893432617 0.519841194152832 988.4577026367188 1.127180814743042 1482.7977294921875 0.5339100360870361 0.62183017 1.0372488498687744 True -9 28980 31.251502752304077 0.5454058647155762 1004.91259765625 1.4231377840042114 1463.49658203125 0.543390154838562 0.62842166 1.0120539665222168 True -10 31878 31.247758865356445 0.5180270671844482 992.1447143554688 1.1101206541061401 1456.465087890625 0.5461946129798889 0.64023083 0.9376221299171448 True -11 34776 31.251086711883545 0.528496265411377 1130.5657958984375 0.9682188034057617 1447.973388671875 0.5478045344352722 0.6472475 0.9079101085662842 True -12 37674 31.255638360977173 0.5292913913726807 1154.9755859375 1.1380910873413086 1438.8302001953125 0.5506430864334106 0.66234404 0.8428565859794617 True -13 40572 31.303568601608276 0.5426669120788574 1094.27880859375 0.7662924528121948 1422.8709716796875 0.5573711395263672 0.67459214 0.8050193190574646 True -14 43470 31.32947087287903 0.5102541446685791 1802.7139892578125 0.83180171251297 1416.7276611328125 0.5583728551864624 0.68020296 0.7825984954833984 True -15 46368 31.27554678916931 16.29417324066162 1376.6324462890625 0.7757981419563293 1412.2996826171875 0.559709906578064 0.6870997 0.753453254699707 True -16 49266 31.372666120529175 0.8548445701599121 960.1195678710938 0.8083663582801819 1409.1683349609375 0.5598459839820862 0.6954537 0.7285948991775513 True -17 52164 31.339682817459106 0.5050625801086426 1072.54736328125 0.9622642993927002 1414.25537109375 0.555780827999115 0.6985601 0.7222433090209961 True -18 55062 31.40561318397522 0.5500826835632324 1117.38427734375 0.6661544442176819 1403.7745361328125 0.5629177689552307 0.7006316 0.7169780135154724 True -19 57960 31.408301830291748 1.2939059734344482 1012.650390625 0.6557873487472534 1410.60498046875 0.5584733486175537 0.699307 0.720820426940918 False diff --git a/ENCSR731QLJ/cherimoya.fold_2.performance.tsv b/ENCSR731QLJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d640cee2414c83a9f9b7eddb48b4ec9f85c030eb..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1403.7745361328125 0.24126484990119934 0.5629177689552307 0.3319646418094635 0.7006316184997559 0.655368983745575 0.7169780135154724 \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_3.evaluate.json b/ENCSR731QLJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7f674a8a5b67db151ba7c824d754bf54c1be4f0b..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF255STG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_3.fit.json b/ENCSR731QLJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 278d133ee670d26bebc002188640f782779e9b94..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF255STG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_3.log b/ENCSR731QLJ/cherimoya.fold_3.log deleted file mode 100644 index cd5220bb80010a18dd05615486d5604e65dff42a..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2810 35.57000803947449 3.9184703826904297 1144.9921875 1.4999535083770752 1992.7830810546875 0.3283679187297821 0.4871073 7.9830498695373535 True -1 5620 30.863367795944214 0.6028017997741699 1115.4862060546875 1.4794992208480835 1640.823486328125 0.47787654399871826 0.55655515 3.9492461681365967 True -2 8430 30.91246223449707 0.5794816017150879 1224.394287109375 1.2638851404190063 1608.9515380859375 0.4884938895702362 0.5660376 2.213106155395508 True -3 11240 30.89268660545349 0.5726592540740967 1100.316650390625 1.2128337621688843 1574.059814453125 0.5002506375312805 0.56054795 1.5122207403182983 False -4 14050 30.780951261520386 0.5660068988800049 1014.0469970703125 1.0629969835281372 1564.9892578125 0.5000075101852417 0.5808318 1.3293397426605225 True -5 16860 30.272515296936035 0.5603973865509033 1256.3623046875 1.1388287544250488 1549.305419921875 0.507746696472168 0.58479536 1.2701902389526367 True -6 19670 30.230066299438477 0.5664339065551758 998.0191040039062 0.834343433380127 1533.908935546875 0.5156329274177551 0.59112227 1.1312456130981445 True -7 22480 30.256965160369873 0.5589759349822998 1396.0657958984375 0.9550223350524902 1519.2269287109375 0.5234422087669373 0.5950722 1.1694616079330444 True -8 25290 30.22400689125061 0.5700671672821045 1000.641845703125 1.4361021518707275 1510.455322265625 0.5266557335853577 0.6028901 1.1543846130371094 True -9 28100 30.243024110794067 0.5657110214233398 1225.055419921875 1.4272266626358032 1496.998046875 0.5314891934394836 0.62045985 1.0334144830703735 True -10 30910 30.253572702407837 0.5588290691375732 1384.677001953125 1.1863579750061035 1477.10693359375 0.5415769815444946 0.63648725 1.0053430795669556 True -11 33720 30.268561840057373 0.5646178722381592 1059.2813720703125 0.9499778747558594 1473.963623046875 0.5404252409934998 0.641052 0.9601490497589111 True -12 36530 30.326882362365723 0.5657806396484375 870.3719482421875 0.8114532232284546 1466.0419921875 0.5434179902076721 0.65531534 0.9383158683776855 True -13 39340 30.333380699157715 0.5648837089538574 833.015869140625 0.6842141151428223 1463.2413330078125 0.5439774990081787 0.6660762 0.872266411781311 True -14 42150 30.358870029449463 0.5644190311431885 1005.7265625 0.7821661233901978 1449.4561767578125 0.549556314945221 0.676837 0.8079103231430054 True -15 44960 30.34732985496521 0.5683016777038574 1115.861083984375 0.8077259659767151 1445.1502685546875 0.5504062175750732 0.69182634 0.7706116437911987 True -16 47770 33.06843185424805 0.5675876140594482 1075.586669921875 0.836270809173584 1440.8819580078125 0.5519413948059082 0.6972855 0.7267791628837585 True -17 50580 31.70049738883972 8.641520023345947 1012.3155517578125 0.5997612476348877 1437.3094482421875 0.5527572631835938 0.70262945 0.7089245915412903 True -18 53390 30.33199119567871 0.9100840091705322 1108.57373046875 0.7546916007995605 1435.9224853515625 0.553861677646637 0.70449865 0.6994232535362244 True -19 56200 30.46447229385376 0.5917048454284668 1083.607177734375 0.739673376083374 1444.7744140625 0.5485952496528625 0.703949 0.7001294493675232 False diff --git a/ENCSR731QLJ/cherimoya.fold_3.performance.tsv b/ENCSR731QLJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 52860e3e124e92ae013d74f04bad3f3e9949406d..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1435.9224853515625 0.24283073842525482 0.553861677646637 0.32780134677886963 0.7044986486434937 0.6650111079216003 0.6994232535362244 \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_4.evaluate.json b/ENCSR731QLJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b55a123f9700bbdb4d73ec2ad1db1e73ca74d2eb..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF255STG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_4.fit.json b/ENCSR731QLJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 0e3b249ade5efa6794e179ea32538b0cc086bc47..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF255STG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR731QLJ/cherimoya.fold_4.log b/ENCSR731QLJ/cherimoya.fold_4.log deleted file mode 100644 index 5f44629c678d7098144da50c54ef8d0cc2f9faa8..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2887 36.10883617401123 3.4810333251953125 1576.4342041015625 1.5551486015319824 1918.616943359375 0.3204494118690491 0.45351967 11.309700965881348 True -1 5774 31.74238920211792 0.6304104328155518 1246.748046875 1.8981388807296753 1571.320068359375 0.4764966368675232 0.52102655 4.364430904388428 True -2 8661 31.571038722991943 1.0662767887115479 1174.7109375 1.372811198234558 1546.4425048828125 0.48346656560897827 0.5372435 3.1595582962036133 True -3 11548 31.1694073677063 0.9390964508056641 878.0468139648438 1.1614019870758057 1507.5360107421875 0.4995092749595642 0.54466677 2.047027587890625 True -4 14435 31.156750679016113 0.5481975078582764 1230.0445556640625 1.3316346406936646 1494.466064453125 0.5029784440994263 0.55275244 1.5804039239883423 True -5 17322 31.064948320388794 0.5483717918395996 1111.711181640625 0.919929027557373 1478.9825439453125 0.5115677714347839 0.5636311 1.5163129568099976 True -6 20209 31.139260292053223 0.5829422473907471 982.2880859375 0.9662654399871826 1457.235595703125 0.5230737924575806 0.5768644 1.390393614768982 True -7 23096 31.149810791015625 0.5608680248260498 943.85009765625 1.0379747152328491 1454.9481201171875 0.523292064666748 0.58753765 1.289459228515625 True -8 25983 31.173277854919434 0.5414731502532959 1036.7757568359375 1.262657642364502 1441.37109375 0.5284449458122253 0.5918471 1.0808241367340088 True -9 28870 31.17007541656494 0.5612225532531738 1033.76171875 0.8790708184242249 1434.9732666015625 0.5287898182868958 0.60739547 1.0593574047088623 True -10 31757 31.128085136413574 0.567007303237915 1220.8521728515625 0.939341127872467 1422.114013671875 0.5364046096801758 0.6153041 1.0080845355987549 True -11 34644 31.15963578224182 0.5591976642608643 1106.203857421875 1.1943168640136719 1410.24755859375 0.5406132340431213 0.62823355 0.9502942562103271 True -12 37531 31.166449785232544 0.5640397071838379 1067.90478515625 0.6770551800727844 1405.6707763671875 0.5429896116256714 0.64215004 0.8850713968276978 True -13 40418 31.134937286376953 0.5577833652496338 1268.975830078125 0.9995261430740356 1393.942626953125 0.5469073057174683 0.65217304 0.831765353679657 True -14 43305 31.13114643096924 0.5459432601928711 1006.558349609375 0.6445031762123108 1382.4033203125 0.552828311920166 0.66521794 0.780036211013794 True -15 46192 31.1417555809021 0.549480676651001 935.9376220703125 0.891864538192749 1385.3563232421875 0.5487192273139954 0.6746349 0.7399823069572449 True -16 49079 31.10965394973755 0.5572612285614014 813.6929321289062 0.9419794082641602 1385.4443359375 0.547997236251831 0.68070304 0.7248344421386719 True -17 51966 31.110317707061768 0.5494792461395264 988.566162109375 0.5000380277633667 1377.0784912109375 0.5546264052391052 0.6861849 0.7065790891647339 True -18 54853 31.105222940444946 11.106107234954834 1218.812255859375 0.7134116291999817 1376.8348388671875 0.5543373823165894 0.6862938 0.7019609808921814 True -19 57740 31.146388292312622 0.5585780143737793 1160.399169921875 0.6208560466766357 1378.730712890625 0.5524675846099854 0.68643355 0.7056897282600403 True diff --git a/ENCSR731QLJ/cherimoya.fold_4.performance.tsv b/ENCSR731QLJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1b795e0518cf33d2b96e68cc0316c5890c79d884..0000000000000000000000000000000000000000 --- a/ENCSR731QLJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1378.730712890625 0.24428251385688782 0.5524676442146301 0.3252028822898865 0.6864335536956787 0.6463464498519897 0.7056897282600403 \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_0.evaluate.json b/ENCSR734VFU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ce8c8620c9e4728268ca7249a9661918f4d17a42..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF432CCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_0.fit.json b/ENCSR734VFU/cherimoya.fold_0.fit.json deleted file mode 100644 index 5cb912776654cce23daf572da974bdbc91b3ba09..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF432CCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_0.log b/ENCSR734VFU/cherimoya.fold_0.log deleted file mode 100644 index da258ce034e089fe57c5916369a81c340dff7c85..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2654 33.76383662223816 3.3832027912139893 82.63018035888672 0.4732613265514374 144.14170837402344 0.0992254987359047 0.6950139 2.296360731124878 True -1 5308 29.121284246444702 0.687035322189331 131.76303100585938 0.4258984327316284 136.1551971435547 0.12296602874994278 0.7654736 1.1744798421859741 True -2 7962 28.63874840736389 0.5608546733856201 103.17399597167969 0.45652109384536743 134.42678833007812 0.12657082080841064 0.75132316 0.6997723579406738 False -3 10616 28.534446239471436 0.5615088939666748 96.42121887207031 0.24019695818424225 132.9018096923828 0.1290620118379593 0.7828765 0.4963615834712982 True -4 13270 28.511030673980713 2.32039213180542 145.5853271484375 0.36852288246154785 131.97357177734375 0.1319696456193924 0.7915782 0.4267878830432892 True -5 15924 28.50312852859497 0.5601174831390381 131.26364135742188 0.36839932203292847 131.4347686767578 0.13280639052391052 0.80266476 0.40764033794403076 True -6 18578 28.528244018554688 0.5685906410217285 117.59901428222656 0.23447683453559875 130.6770477294922 0.1352490782737732 0.81257397 0.3841768503189087 True -7 21232 28.46869158744812 18.09908890724182 116.70698547363281 0.33221638202667236 130.24806213378906 0.13643312454223633 0.815795 0.36235538125038147 True -8 23886 28.622480630874634 0.5715935230255127 111.2542724609375 0.35847216844558716 129.92970275878906 0.1370687037706375 0.82242227 0.33561429381370544 True -9 26540 28.538492918014526 0.5661542415618896 120.97796630859375 0.4465886354446411 129.4835205078125 0.13798920810222626 0.82865524 0.3258707523345947 True -10 29194 28.543784856796265 0.5651991367340088 79.6218032836914 0.45200103521347046 129.12399291992188 0.13991189002990723 0.8332408 0.3118237555027008 True -11 31848 28.51046895980835 0.5679397583007812 141.37103271484375 0.30272039771080017 128.89407348632812 0.14037100970745087 0.8374962 0.2936093211174011 True -12 34502 28.540335178375244 0.5692224502563477 95.89747619628906 0.386346697807312 128.28514099121094 0.14272579550743103 0.84187174 0.28108730912208557 True -13 37156 28.53181529045105 0.5697407722473145 84.33335876464844 0.3162226378917694 128.26473999023438 0.14239221811294556 0.848297 0.2635832726955414 True -14 39810 28.548819303512573 0.5641427040100098 127.23580932617188 0.35087019205093384 127.96322631835938 0.14349813759326935 0.85209674 0.25304844975471497 True -15 42464 28.592910528182983 0.5649409294128418 105.08351135253906 0.2336670309305191 127.95983123779297 0.143648162484169 0.8550489 0.24632737040519714 True -16 45118 28.59478783607483 0.5553023815155029 130.0386962890625 0.39262086153030396 127.86746215820312 0.14390142261981964 0.8575986 0.23761829733848572 True -17 47772 28.559139728546143 0.5656368732452393 118.21839904785156 0.19521962106227875 127.7308349609375 0.14388082921504974 0.85867167 0.23431317508220673 True -18 50426 28.553380727767944 1.1146156787872314 92.17366790771484 0.25742632150650024 127.75426483154297 0.1436871886253357 0.8595551 0.23463119566440582 True -19 53080 28.63166832923889 0.5593469142913818 104.96534729003906 0.3738309144973755 127.82200622558594 0.14334753155708313 0.8573725 0.2355876863002777 False diff --git a/ENCSR734VFU/cherimoya.fold_0.performance.tsv b/ENCSR734VFU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b2fecc62a084dd72563715463fba460c99fcc434..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -127.75426483154297 0.5996394157409668 0.1436871886253357 0.032106462866067886 0.8595551252365112 0.744451642036438 0.23463119566440582 \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_1.evaluate.json b/ENCSR734VFU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 81b37ff480f94854c59ced8f9633e093f16ab326..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF432CCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_1.fit.json b/ENCSR734VFU/cherimoya.fold_1.fit.json deleted file mode 100644 index 9c0acf81194ff8dbd5fbb6db631956e9f72a298e..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF432CCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_1.log b/ENCSR734VFU/cherimoya.fold_1.log deleted file mode 100644 index c99566d6ef8032c6cc756ea6b69330ec26ebac94..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2624 33.52261233329773 3.6584346294403076 103.07600402832031 0.37089329957962036 184.88221740722656 0.1133512482047081 0.67280287 3.1132559776306152 True -1 5248 28.85468578338623 7.287355899810791 114.18290710449219 0.5012824535369873 171.5107421875 0.15157440304756165 0.77062356 1.5767282247543335 True -2 7872 28.898765087127686 24.416523933410645 142.30776977539062 0.4502040147781372 169.0378875732422 0.15341158211231232 0.7748491 0.91617751121521 True -3 10496 28.85249376296997 0.6697239875793457 137.15347290039062 0.3479327857494354 166.8717803955078 0.1575092375278473 0.7854185 0.7755261063575745 True -4 13120 28.956446409225464 0.6726396083831787 104.41195678710938 0.3988170623779297 165.79518127441406 0.16007021069526672 0.7947526 0.7855774164199829 True -5 15744 28.80463409423828 0.7877118587493896 102.48985290527344 0.33316388726234436 164.8081512451172 0.16302278637886047 0.8035222 0.7198728322982788 True -6 18368 28.82381319999695 1.6179351806640625 107.3222885131836 0.5394856929779053 163.8175811767578 0.16482406854629517 0.8159311 0.6167237162590027 True -7 20992 28.773840188980103 0.6562719345092773 144.7882537841797 0.31061556935310364 162.68714904785156 0.16798272728919983 0.8213758 0.560287594795227 True -8 23616 28.643784999847412 0.6307146549224854 102.01322937011719 0.41943448781967163 162.24803161621094 0.1684381663799286 0.82655096 0.5350549221038818 True -9 26240 28.22442889213562 0.6370980739593506 76.26532745361328 0.3734901249408722 161.4633331298828 0.17133481800556183 0.83317316 0.5030307173728943 True -10 28864 28.288987159729004 0.6317923069000244 103.80012512207031 0.2624150514602661 160.99832153320312 0.1722598522901535 0.8390485 0.46225205063819885 True -11 31488 28.269817352294922 0.6491808891296387 101.74287414550781 0.20832566916942596 160.61607360839844 0.17372359335422516 0.8454026 0.4415881037712097 True -12 34112 28.264692783355713 0.6427912712097168 79.38137817382812 0.27461034059524536 160.11279296875 0.17517229914665222 0.8495133 0.419098824262619 True -13 36736 28.283073902130127 0.663550853729248 114.8616943359375 0.32022708654403687 159.5475616455078 0.17660675942897797 0.8574232 0.39014238119125366 True -14 39360 28.277777433395386 0.6546874046325684 110.29661560058594 0.4200679063796997 159.03741455078125 0.1779482662677765 0.86339736 0.35735973715782166 True -15 41984 28.244408130645752 0.6328248977661133 128.00428771972656 0.3325159549713135 158.7640838623047 0.1787647008895874 0.8680795 0.33112725615501404 True -16 44608 28.243791580200195 0.6509370803833008 106.08342742919922 0.3892098665237427 158.62709045410156 0.17835387587547302 0.8720882 0.31292054057121277 True -17 47232 28.28387951850891 0.6402499675750732 100.38948059082031 0.23760835826396942 158.61004638671875 0.17810189723968506 0.8739261 0.30543845891952515 True -18 49856 28.283838748931885 0.6395883560180664 108.86100769042969 0.447408527135849 158.88491821289062 0.17730890214443207 0.8734768 0.301699697971344 False -19 52480 28.273629665374756 0.6442368030548096 130.67893981933594 0.2609550356864929 159.01869201660156 0.17660124599933624 0.87373877 0.3003743886947632 False diff --git a/ENCSR734VFU/cherimoya.fold_1.performance.tsv b/ENCSR734VFU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4a1d22f730861c8783930d585a30ba4fd60b9ccd..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -158.61004638671875 0.5755870342254639 0.17810189723968506 0.0411408431828022 0.8739261031150818 0.8052224516868591 0.30543845891952515 \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_2.evaluate.json b/ENCSR734VFU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 12dd37d27d5cf3a4d35f1fcfea06e05d1efedf74..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF432CCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_2.fit.json b/ENCSR734VFU/cherimoya.fold_2.fit.json deleted file mode 100644 index 4eab71ffe700d57d9bbc9eabfc3d4a6bb6369288..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF432CCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_2.log b/ENCSR734VFU/cherimoya.fold_2.log deleted file mode 100644 index 11e08d6e56ee0c863d57281984cfba325d6ffc7a..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2788 35.276150703430176 3.962878942489624 90.91123962402344 0.4681248068809509 153.79400634765625 0.102163165807724 0.6739539 2.1839542388916016 True -1 5576 30.21902060508728 0.8621060848236084 97.10200500488281 0.30599117279052734 143.6308135986328 0.13303977251052856 0.7645662 1.0923750400543213 True -2 8364 30.681269884109497 0.5551326274871826 109.50688171386719 0.3241446018218994 142.59759521484375 0.1321130394935608 0.7525136 0.5758154988288879 False -3 11152 30.564234018325806 0.5524563789367676 101.47589111328125 0.46892213821411133 140.20298767089844 0.1350930780172348 0.7845303 0.5308375358581543 True -4 13940 30.58400535583496 0.6882650852203369 128.6946258544922 0.30393946170806885 138.83209228515625 0.13975219428539276 0.79427713 0.5008152723312378 True -5 16728 30.067349195480347 0.5533480644226074 97.61500549316406 0.3256133198738098 138.1033172607422 0.14133749902248383 0.8031846 0.4602046310901642 True -6 19516 29.91962504386902 0.557382345199585 148.67835998535156 0.3675735294818878 137.4483184814453 0.14276742935180664 0.810669 0.428242564201355 True -7 22304 29.958585739135742 0.6029336452484131 133.10134887695312 0.4157795011997223 137.0269012451172 0.14375247061252594 0.814203 0.3963680863380432 True -8 25092 29.960394620895386 0.5355575084686279 141.26629638671875 0.49714720249176025 136.69349670410156 0.14489375054836273 0.82163817 0.3744402527809143 True -9 27880 29.984212160110474 0.5446293354034424 141.7014617919922 0.4642089307308197 136.2865753173828 0.14613381028175354 0.82548976 0.35445618629455566 True -10 30668 29.997986316680908 0.546884298324585 111.10955810546875 0.2622196078300476 135.79054260253906 0.14821451902389526 0.83093816 0.3308161199092865 True -11 33456 30.081429719924927 0.5515868663787842 101.30615234375 0.4239323139190674 135.60614013671875 0.14843188226222992 0.83492464 0.3161110281944275 True -12 36244 30.395121097564697 0.5724008083343506 127.11470031738281 0.429331511259079 135.37860107421875 0.1488034725189209 0.84322935 0.29710614681243896 True -13 39032 30.276702165603638 0.5937044620513916 137.4514617919922 0.48350512981414795 134.9105987548828 0.1507880985736847 0.84620243 0.28170228004455566 True -14 41820 30.223636865615845 0.5513899326324463 97.06477355957031 0.2286750227212906 134.4728240966797 0.15249624848365784 0.85250634 0.26503410935401917 True -15 44608 30.303025722503662 0.5532853603363037 113.06336975097656 0.24291278421878815 134.59927368164062 0.15168023109436035 0.85570806 0.2572196424007416 True -16 47396 30.40325689315796 0.5630514621734619 119.47526550292969 0.3108821511268616 134.3000946044922 0.15265734493732452 0.86052245 0.24860753118991852 True -17 50184 30.382953882217407 0.5504112243652344 95.70917510986328 0.30247849225997925 134.35720825195312 0.15218493342399597 0.8622628 0.2464076429605484 True -18 52972 30.28454279899597 0.560248613357544 96.08187866210938 0.26117414236068726 134.27557373046875 0.15274620056152344 0.861916 0.2451988160610199 False -19 55760 30.335389375686646 0.5546319484710693 79.51467895507812 0.1964261829853058 134.3297119140625 0.15239061415195465 0.8618214 0.24692948162555695 False diff --git a/ENCSR734VFU/cherimoya.fold_2.performance.tsv b/ENCSR734VFU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7b499b11c8c8c55ee513e90bd42a692f1f37500e..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -134.35720825195312 0.5934787392616272 0.15218493342399597 0.03490205109119415 0.8622627854347229 0.7677477598190308 0.2464076429605484 \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_3.evaluate.json b/ENCSR734VFU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ac416154281ecc1ab9ba54d95de180056ce865af..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF432CCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_3.fit.json b/ENCSR734VFU/cherimoya.fold_3.fit.json deleted file mode 100644 index a6ef59fcce3d2d89a995ecf8b8e2ac9089f4363e..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF432CCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_3.log b/ENCSR734VFU/cherimoya.fold_3.log deleted file mode 100644 index d78c8012ec10db34c65236f215d0cc74937be3de..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2657 33.655715465545654 4.393585205078125 141.17184448242188 0.5357339382171631 150.8322296142578 0.10475458204746246 0.6406033 2.5674750804901123 True -1 5314 29.197035551071167 0.860119104385376 135.8179931640625 0.5469642877578735 141.7189178466797 0.13222846388816833 0.7359084 1.4493480920791626 True -2 7971 28.9132342338562 0.5381362438201904 130.4363250732422 0.5116680860519409 139.59349060058594 0.13698062300682068 0.7411354 0.7944537401199341 True -3 10628 28.581059217453003 0.52695631980896 143.87838745117188 0.48907849192619324 139.85244750976562 0.13659214973449707 0.7313056 0.7050173878669739 False -4 13285 28.584294319152832 0.53446364402771 87.12739562988281 0.343073308467865 138.5904083251953 0.13993792235851288 0.7511054 0.688125729560852 True -5 15942 28.584212064743042 0.521007776260376 97.94100952148438 0.6391794681549072 137.9687042236328 0.14137887954711914 0.75743544 0.5967573523521423 True -6 18599 28.638272762298584 0.5273606777191162 140.84774780273438 0.4347079396247864 137.23123168945312 0.14338773488998413 0.7676767 0.5693468451499939 True -7 21256 28.672733783721924 0.5269196033477783 101.89427185058594 0.3156995177268982 136.68980407714844 0.1446167677640915 0.7803824 0.5165857672691345 True -8 23913 28.553945541381836 1.426283836364746 104.05657958984375 0.2983851134777069 136.34706115722656 0.14622388780117035 0.78595644 0.48626118898391724 True -9 26570 28.60639786720276 0.5240688323974609 93.13600158691406 0.6361756920814514 135.96444702148438 0.14730492234230042 0.79877055 0.4592147469520569 True -10 29227 28.57825803756714 0.771355152130127 108.52299499511719 0.4214039146900177 135.32350158691406 0.1495605707168579 0.804555 0.4148927330970764 True -11 31884 28.572209119796753 11.258949518203735 152.80572509765625 0.2760846018791199 135.1698760986328 0.1498413234949112 0.81360704 0.3868655860424042 True -12 34541 28.650434970855713 0.5421013832092285 118.07231140136719 0.3850383162498474 134.6087188720703 0.15175695717334747 0.82214576 0.3666735887527466 True -13 37198 28.610333919525146 0.5377182960510254 119.64552307128906 0.36448583006858826 134.27099609375 0.15303444862365723 0.82840395 0.34238702058792114 True -14 39855 28.596724033355713 0.5377347469329834 138.49107360839844 0.26030123233795166 134.10580444335938 0.15299774706363678 0.83561915 0.3228289783000946 True -15 42512 28.60099768638611 0.5246500968933105 99.2811050415039 0.31731340289115906 133.8863067626953 0.15347690880298615 0.842978 0.30620306730270386 True -16 45169 28.66244673728943 0.5261094570159912 109.02721405029297 0.2241622805595398 133.6049346923828 0.1545267254114151 0.8469363 0.2907431125640869 True -17 47826 28.673694133758545 1.4471917152404785 115.88124084472656 0.4276990294456482 133.6101837158203 0.15439775586128235 0.8508186 0.28331202268600464 True -18 50483 28.59052348136902 0.5281021595001221 104.31602478027344 0.17490679025650024 133.86770629882812 0.15280325710773468 0.8522801 0.28044915199279785 True -19 53140 28.577962160110474 0.5233042240142822 142.99960327148438 0.22568181157112122 133.63137817382812 0.1546829342842102 0.85211205 0.2795739471912384 False diff --git a/ENCSR734VFU/cherimoya.fold_3.performance.tsv b/ENCSR734VFU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4d48762c21a6e1eec7b8635fbfa78f0ce45c1c8e..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -133.86770629882812 0.5938616991043091 0.15280325710773468 0.03528590500354767 0.8522800803184509 0.7571162581443787 0.28044915199279785 \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_4.evaluate.json b/ENCSR734VFU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 598138c75dac7938298506f6b87a7985e52e3c63..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF432CCB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_4.fit.json b/ENCSR734VFU/cherimoya.fold_4.fit.json deleted file mode 100644 index 977f8727f436b0387cea1cd3792b19de66191626..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF432CCB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR734VFU/cherimoya.fold_4.log b/ENCSR734VFU/cherimoya.fold_4.log deleted file mode 100644 index 78a6041fa511ddbded90d5d146f0c0348494d0e9..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.60045385360718 4.991583347320557 94.7914047241211 0.5336548686027527 133.5587921142578 0.10080462694168091 0.6430363 2.360435724258423 True -1 5478 30.223419427871704 0.5974586009979248 97.30196380615234 0.7059295773506165 126.86511993408203 0.12276237457990646 0.7299711 0.9273870587348938 True -2 8217 30.318135976791382 0.6678457260131836 132.1979217529297 0.5355969667434692 126.81112670898438 0.12031638622283936 0.7183986 0.4332450330257416 False -3 10956 30.141174793243408 1.3835504055023193 84.47331237792969 0.26040196418762207 125.29129028320312 0.1245187371969223 0.73531514 0.46696779131889343 True -4 13695 29.735124349594116 0.8256590366363525 135.5867156982422 0.4240516424179077 124.09976959228516 0.12827782332897186 0.75610703 0.4498339891433716 True -5 16434 29.506300687789917 0.5958154201507568 104.00830078125 0.4606854021549225 123.64479064941406 0.12910495698451996 0.76202005 0.43980860710144043 True -6 19173 30.177715301513672 0.5978589057922363 110.82976531982422 0.6049947142601013 123.0617446899414 0.13163504004478455 0.7719173 0.38933104276657104 True -7 21912 30.167246341705322 0.593879222869873 134.06124877929688 0.3773092031478882 122.84896087646484 0.13223960995674133 0.77884525 0.39387768507003784 True -8 24651 29.983054399490356 14.03998589515686 95.04962158203125 0.30299457907676697 122.48539733886719 0.13342174887657166 0.78870887 0.3564070165157318 True -9 27390 29.52605628967285 13.052245378494263 110.59422302246094 0.31543686985969543 122.19855499267578 0.13412345945835114 0.79522485 0.35077834129333496 True -10 30129 29.514556407928467 0.932586669921875 104.64323425292969 0.23735171556472778 122.03196716308594 0.13463811576366425 0.802904 0.31603744626045227 True -11 32868 29.535149335861206 0.5726191997528076 89.74273681640625 0.24996943771839142 121.71041870117188 0.1358938068151474 0.80881965 0.30270472168922424 True -12 35607 29.796689987182617 0.5774445533752441 102.30909729003906 0.47255760431289673 121.41913604736328 0.13679131865501404 0.8165052 0.28261297941207886 True -13 38346 29.52036738395691 0.5737996101379395 97.81623840332031 0.3315751552581787 121.34227752685547 0.13679195940494537 0.82282543 0.2638464868068695 True -14 41085 29.461843252182007 3.08394455909729 111.99114227294922 0.32475030422210693 121.06908416748047 0.13785839080810547 0.82713634 0.2511082589626312 True -15 43824 29.476611852645874 0.5775790214538574 116.85979461669922 0.2580198049545288 121.02579498291016 0.1379092037677765 0.83204263 0.24202033877372742 True -16 46563 29.572412967681885 0.5734868049621582 123.18830871582031 0.23457348346710205 120.91407012939453 0.1383773684501648 0.83670235 0.2351803481578827 True -17 49302 29.55875325202942 0.5635049343109131 78.3343276977539 0.18934749066829681 120.89568328857422 0.13856187462806702 0.83777374 0.23263992369174957 True -18 52041 29.6589674949646 0.579779863357544 108.2422866821289 0.30159419775009155 120.97920989990234 0.13795673847198486 0.8396597 0.23093877732753754 True -19 54780 29.608322381973267 0.5773839950561523 128.20455932617188 0.2225721776485443 120.95774841308594 0.13806818425655365 0.83781666 0.23240461945533752 False diff --git a/ENCSR734VFU/cherimoya.fold_4.performance.tsv b/ENCSR734VFU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1c3b5954ab24fb1d23795f8448583af17ea04645..0000000000000000000000000000000000000000 --- a/ENCSR734VFU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -120.97920989990234 0.6040322780609131 0.13795672357082367 0.024882424622774124 0.8396596908569336 0.7320257425308228 0.23093877732753754 \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_0.evaluate.json b/ENCSR735MJZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d30fb5d98fc977abce6237b52fbea06a3f23c3a4..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637UFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_0.fit.json b/ENCSR735MJZ/cherimoya.fold_0.fit.json deleted file mode 100644 index b7698d0352ffeed7495df22ed19f7e070fa06faf..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF637UFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_0.log b/ENCSR735MJZ/cherimoya.fold_0.log deleted file mode 100644 index 0e174af47787783bc963e7ae44b228fd7ee740eb..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 33.81144571304321 3.421175718307495 143.06271362304688 0.5684835910797119 189.45106506347656 0.11626637727022171 0.69441015 3.421020269393921 True -1 5474 30.249656438827515 0.581434965133667 164.4696044921875 0.5763123631477356 173.6502227783203 0.1490253508090973 0.7766698 1.5835813283920288 True -2 8211 30.179865837097168 0.5728151798248291 172.2060546875 0.5422126054763794 170.73231506347656 0.15493671596050262 0.7856998 0.9839378595352173 True -3 10948 30.164496183395386 0.570734977722168 164.18800354003906 0.5407895445823669 168.54466247558594 0.1571262925863266 0.798945 0.8414233922958374 True -4 13685 30.163031578063965 0.5670831203460693 95.02288818359375 0.3631478250026703 167.3873748779297 0.15938861668109894 0.8066183 0.7251874208450317 True -5 16422 30.202271699905396 0.571413516998291 131.04031372070312 0.4970283508300781 166.87890625 0.16051042079925537 0.8130876 0.7447147965431213 True -6 19159 30.196500062942505 0.5597798824310303 141.515869140625 0.4537851810455322 165.91815185546875 0.1618630290031433 0.82195085 0.6358146667480469 True -7 21896 30.161713361740112 0.5669748783111572 158.2151641845703 0.5267027616500854 165.33807373046875 0.16319753229618073 0.82735515 0.5984274744987488 True -8 24633 30.159884929656982 0.8118314743041992 110.82572937011719 0.4646562337875366 164.11410522460938 0.166083425283432 0.83469254 0.5662744641304016 True -9 27370 30.20885467529297 0.5738325119018555 139.51348876953125 0.47901737689971924 163.72915649414062 0.16684211790561676 0.8417051 0.5126430988311768 True -10 30107 30.201097011566162 0.5662181377410889 136.23171997070312 0.46092677116394043 163.4035186767578 0.1677260845899582 0.847072 0.48553231358528137 True -11 32844 30.169514894485474 0.5687036514282227 189.6607208251953 0.6095491051673889 162.7462615966797 0.16982340812683105 0.85252905 0.4436335861682892 True -12 35581 30.18877148628235 0.5658361911773682 135.97760009765625 0.39152899384498596 162.12611389160156 0.17102041840553284 0.85529894 0.41880303621292114 True -13 38318 30.23672580718994 0.5553479194641113 134.63546752929688 0.37405824661254883 161.66241455078125 0.17186322808265686 0.86036193 0.3854616582393646 True -14 41055 30.155996799468994 0.5655806064605713 128.27618408203125 0.3723486661911011 161.04893493652344 0.1737009882926941 0.864551 0.36696821451187134 True -15 43792 30.17659902572632 0.566638708114624 167.3148193359375 0.4370869994163513 160.91746520996094 0.17384734749794006 0.8674875 0.346377432346344 True -16 46529 29.846041202545166 0.5613274574279785 123.12933349609375 0.36413586139678955 160.8332061767578 0.17367234826087952 0.8679443 0.337053507566452 True -17 49266 29.582338094711304 0.5588560104370117 115.99726867675781 0.6485891342163086 160.77963256835938 0.17380423843860626 0.86828 0.33320191502571106 True -18 52003 29.637649536132812 0.5622618198394775 115.39518737792969 0.2564038038253784 161.0552520751953 0.17328880727291107 0.8675118 0.33085161447525024 False -19 54740 29.614457845687866 0.5617876052856445 115.74161529541016 0.2992810010910034 161.16360473632812 0.17297622561454773 0.86774105 0.33377087116241455 False diff --git a/ENCSR735MJZ/cherimoya.fold_0.performance.tsv b/ENCSR735MJZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ce76a1f94c604fd5d5f1a99da47b9b7d43a833e8..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -160.77963256835938 0.5788447260856628 0.17380423843860626 0.04663731902837753 0.8682799935340881 0.7810606360435486 0.33320191502571106 \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_1.evaluate.json b/ENCSR735MJZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 404a063e1db307fb6ef583f3f8428a6405d8fe7b..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637UFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_1.fit.json b/ENCSR735MJZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 2c7be0d4ae79035153c2d33b66f1e341a00e8e2c..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF637UFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_1.log b/ENCSR735MJZ/cherimoya.fold_1.log deleted file mode 100644 index 2a6c94f4001cec7b4a6a19e580ee6f3539c1829b..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2695 33.583372354507446 4.7490668296813965 120.71743774414062 0.597110390663147 250.9339141845703 0.13397791981697083 0.6837296 4.469289779663086 True -1 5390 29.777985334396362 0.7023308277130127 142.27145385742188 0.6252751350402832 227.3457489013672 0.1779891699552536 0.7784228 2.1062846183776855 True -2 8085 29.781686544418335 0.6861703395843506 106.06979370117188 0.5673505663871765 222.90402221679688 0.1831112951040268 0.788229 1.5085521936416626 True -3 10780 29.662901163101196 0.698418378829956 188.89315795898438 0.5070692300796509 220.60528564453125 0.18486833572387695 0.7918027 1.3418173789978027 True -4 13475 29.677887201309204 0.6860418319702148 141.82394409179688 0.6602109670639038 217.74501037597656 0.18993481993675232 0.80840755 1.0439090728759766 True -5 16170 29.615544319152832 0.6892199516296387 124.0316162109375 0.5524780750274658 216.49069213867188 0.19186754524707794 0.8168716 0.9472208023071289 True -6 18865 29.638267040252686 27.33034586906433 99.70878601074219 0.36322668194770813 215.4182586669922 0.1938704252243042 0.81913584 0.9448973536491394 True -7 21560 30.215455055236816 0.7019791603088379 162.9930419921875 0.5073950886726379 213.6712646484375 0.19741737842559814 0.82988274 0.8245558738708496 True -8 24255 29.920090675354004 0.7053539752960205 147.87496948242188 0.6554811596870422 212.68511962890625 0.19921532273292542 0.83561426 0.8417224884033203 True -9 26950 29.968202829360962 22.72928285598755 102.56394958496094 0.5314944982528687 211.7112274169922 0.20192278921604156 0.8395652 0.7707123160362244 True -10 29645 29.736175060272217 1.7536892890930176 164.7926025390625 0.48919498920440674 210.59825134277344 0.2032168209552765 0.85074604 0.6789457201957703 True -11 32340 29.724856853485107 0.707897424697876 97.16937255859375 0.4456629753112793 209.6257781982422 0.2053738385438919 0.85873634 0.6106587648391724 True -12 35035 29.680715084075928 0.6889028549194336 129.88015747070312 0.33108896017074585 208.6024627685547 0.2072901427745819 0.8631166 0.568706750869751 True -13 37730 29.74153995513916 1.294853687286377 140.67813110351562 0.39538949728012085 207.71925354003906 0.20861558616161346 0.8698867 0.5273118615150452 True -14 40425 29.69665551185608 0.690148115158081 107.29804992675781 0.37531042098999023 207.2880096435547 0.20900550484657288 0.8749619 0.48265695571899414 True -15 43120 29.714235305786133 0.6941454410552979 163.37261962890625 0.30744391679763794 206.83493041992188 0.2100263237953186 0.8779903 0.4462297558784485 True -16 45815 29.789766788482666 0.6874794960021973 154.46719360351562 0.42942917346954346 206.5204315185547 0.21015450358390808 0.8802677 0.425659716129303 True -17 48510 29.516226053237915 0.6702985763549805 102.31178283691406 0.21817293763160706 206.40318298339844 0.21034470200538635 0.88277286 0.4159417152404785 True -18 51205 29.1676664352417 0.6932706832885742 116.32614135742188 0.24179711937904358 206.5750274658203 0.20966771245002747 0.88265127 0.4119798541069031 False -19 53900 29.157548904418945 0.6877853870391846 114.06661987304688 0.26248136162757874 206.60928344726562 0.20983536541461945 0.88085324 0.41055017709732056 False diff --git a/ENCSR735MJZ/cherimoya.fold_1.performance.tsv b/ENCSR735MJZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 03bb7efef907b961a58aa0c07d57acf686f8d937..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -206.40318298339844 0.5513248443603516 0.21034470200538635 0.05500409007072449 0.8827728629112244 0.8236550092697144 0.4159417152404785 \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_2.evaluate.json b/ENCSR735MJZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ee110a8423ed0cbdbda5b7a2a80263259dec765d..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637UFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_2.fit.json b/ENCSR735MJZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 4d8fc6d2cf3575abcec109daf1d6a08103d2f1ef..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF637UFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_2.log b/ENCSR735MJZ/cherimoya.fold_2.log deleted file mode 100644 index 1c4fda5d400aa8b7a54f3dfc8034ab0da29083b5..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 35.532429218292236 3.4449973106384277 160.68898010253906 0.5682796239852905 200.22918701171875 0.1209917739033699 0.68218195 3.481846570968628 True -1 5762 31.879192113876343 0.5661840438842773 189.5419921875 0.8455092906951904 182.00753784179688 0.15793782472610474 0.78071296 1.9064241647720337 True -2 8643 31.763010025024414 0.5550167560577393 154.22531127929688 0.7764172554016113 180.11314392089844 0.15971976518630981 0.7880947 0.8116897344589233 True -3 11524 31.753053188323975 0.5545430183410645 154.0036163330078 0.4034031629562378 178.33572387695312 0.16157251596450806 0.7973739 0.6565992832183838 True -4 14405 31.749895572662354 0.5574202537536621 157.2764892578125 0.6322529911994934 176.99073791503906 0.16503861546516418 0.80413157 0.6661191582679749 True -5 17286 31.73971438407898 0.5586938858032227 126.91635131835938 0.47658437490463257 175.68946838378906 0.1665339320898056 0.811599 0.6613000631332397 True -6 20167 31.81022047996521 0.5579471588134766 141.41357421875 0.7830668687820435 174.6572265625 0.16856646537780762 0.81765157 0.6335024833679199 True -7 23048 31.722896337509155 0.5614888668060303 142.5819091796875 0.6860601305961609 173.485107421875 0.17086109519004822 0.82579637 0.5980696082115173 True -8 25929 31.80148220062256 2.758089065551758 129.05752563476562 0.44167715311050415 172.6493377685547 0.1724289506673813 0.8339393 0.5340679883956909 True -9 28810 31.714301109313965 0.5615887641906738 122.47113037109375 0.4559904932975769 172.33839416503906 0.1728523075580597 0.8414245 0.5168031454086304 True -10 31691 31.727619409561157 0.5619690418243408 118.04635620117188 0.4770905673503876 171.3592529296875 0.17541787028312683 0.8442902 0.48933738470077515 True -11 34572 31.703582525253296 2.1026601791381836 90.4087905883789 0.36458006501197815 170.63987731933594 0.17732776701450348 0.84791535 0.4724523723125458 True -12 37453 31.726895332336426 0.5589215755462646 114.71305847167969 0.37293827533721924 169.94012451171875 0.17971961200237274 0.8532477 0.44506368041038513 True -13 40334 31.81741690635681 0.5608301162719727 140.51695251464844 0.41641032695770264 169.5652313232422 0.18034499883651733 0.8581224 0.41137269139289856 True -14 43215 31.789872884750366 0.5668516159057617 129.7939453125 0.3998158574104309 169.00326538085938 0.18168486654758453 0.8617593 0.3876911699771881 True -15 46096 31.797567129135132 0.5681869983673096 169.37396240234375 0.42856860160827637 168.656005859375 0.18229731917381287 0.86378634 0.3700532615184784 True -16 48977 31.805455446243286 0.5626475811004639 164.79412841796875 0.612038791179657 168.6787567138672 0.18203440308570862 0.86761934 0.35428327322006226 True -17 51858 31.846563816070557 0.5751540660858154 129.4315185546875 0.3211356997489929 168.62184143066406 0.18227851390838623 0.8678427 0.34851017594337463 True -18 54739 31.442097187042236 0.568058967590332 145.65240478515625 0.5062669515609741 168.68431091308594 0.1822206974029541 0.868443 0.3461419939994812 True -19 57620 31.2509024143219 0.5627744197845459 114.82051086425781 0.26765236258506775 168.61436462402344 0.18262839317321777 0.86638284 0.3472208082675934 False diff --git a/ENCSR735MJZ/cherimoya.fold_2.performance.tsv b/ENCSR735MJZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 03679833d80251602f55e76439aab80d1b148656..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -168.68431091308594 0.5727636814117432 0.1822206974029541 0.050462737679481506 0.8684430122375488 0.7991051077842712 0.3461419939994812 \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_3.evaluate.json b/ENCSR735MJZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 249633608a321d191003ab3f7c491ec4a95e05ac..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637UFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_3.fit.json b/ENCSR735MJZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 9444d9d71d849fd4cb625902fc121955556976bc..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF637UFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_3.log b/ENCSR735MJZ/cherimoya.fold_3.log deleted file mode 100644 index 96876f51c2058e4ecdb16257996b322b79f46665..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 34.01505637168884 4.970946311950684 117.97972106933594 0.49513769149780273 203.84202575683594 0.12866535782814026 0.6639979 3.5453543663024902 True -1 5482 30.33788776397705 0.5437798500061035 144.48477172851562 0.5597022771835327 190.7849578857422 0.15633650124073029 0.7192987 2.0933024883270264 True -2 8223 30.351229190826416 0.534827470779419 168.33078002929688 0.5486494898796082 186.14634704589844 0.16480907797813416 0.7585557 1.244030237197876 True -3 10964 30.213781118392944 0.5277585983276367 110.00303649902344 0.7345259189605713 182.68093872070312 0.1706913262605667 0.7726468 0.9792149066925049 True -4 13705 30.16907787322998 0.5333590507507324 131.6746826171875 0.6411787271499634 181.2301788330078 0.17354509234428406 0.7894565 0.9512830972671509 True -5 16446 30.20746922492981 1.3775370121002197 146.40948486328125 0.43526822328567505 180.4120635986328 0.175552099943161 0.79959446 0.8996368646621704 True -6 19187 30.194181203842163 0.5300679206848145 113.90609741210938 0.5465899705886841 179.2716827392578 0.1776234209537506 0.80554205 0.8299854397773743 True -7 21928 30.2229585647583 0.5225400924682617 146.77127075195312 0.6085867285728455 178.38949584960938 0.17913055419921875 0.81181884 0.7883492708206177 True -8 24669 30.145034790039062 0.5284442901611328 181.64883422851562 0.47274571657180786 177.4400177001953 0.1816045045852661 0.812522 0.7741756439208984 True -9 27410 30.18420147895813 0.5269880294799805 117.9930419921875 0.4165690541267395 176.62539672851562 0.1837768852710724 0.82081074 0.7021089792251587 True -10 30151 30.21445393562317 0.5237765312194824 115.09603881835938 0.31679099798202515 175.9939422607422 0.1846727877855301 0.8279123 0.643013060092926 True -11 32892 30.186153173446655 0.5155467987060547 182.83370971679688 0.5876365900039673 175.5274658203125 0.18611086905002594 0.8357021 0.5748922228813171 True -12 35633 30.216447830200195 0.9211690425872803 104.63593292236328 0.4598276615142822 174.92604064941406 0.18753527104854584 0.84216744 0.5349656343460083 True -13 38374 30.26201295852661 0.5462958812713623 116.74732208251953 0.3177645206451416 174.5209197998047 0.18877293169498444 0.84952205 0.48218071460723877 True -14 41115 29.723888874053955 0.5247082710266113 146.16029357910156 0.49803513288497925 173.71852111816406 0.19012299180030823 0.8553441 0.4497508704662323 True -15 43856 29.730453968048096 0.5318899154663086 148.57763671875 0.36925753951072693 173.5814208984375 0.18969868123531342 0.85928303 0.42826247215270996 True -16 46597 29.662689924240112 0.5195474624633789 165.19900512695312 0.34442615509033203 173.03192138671875 0.19146478176116943 0.86371267 0.4075324535369873 True -17 49338 29.671573638916016 1.3129606246948242 136.32728576660156 0.37426888942718506 173.36276245117188 0.19028553366661072 0.8651197 0.39883625507354736 True -18 52079 29.63278865814209 0.5243327617645264 130.7103271484375 0.3313015103340149 173.77313232421875 0.18908950686454773 0.8644192 0.3956553339958191 False -19 54820 29.63863444328308 0.5236155986785889 185.02076721191406 0.36852914094924927 173.44140625 0.19058401882648468 0.8643481 0.397463321685791 False diff --git a/ENCSR735MJZ/cherimoya.fold_3.performance.tsv b/ENCSR735MJZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 14f9a1575cdc065b46a227d5529f2bff9de3db16..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -173.36276245117188 0.567674994468689 0.1902855634689331 0.049911756068468094 0.8651196956634521 0.7929943203926086 0.39883625507354736 \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_4.evaluate.json b/ENCSR735MJZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ae7c70acdedf238615e1cb0c9fcb240f4f7344d2..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637UFZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_4.fit.json b/ENCSR735MJZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 520955b92550fb1a5a794ef0f153948c4ae2d95b..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF637UFZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735MJZ/cherimoya.fold_4.log b/ENCSR735MJZ/cherimoya.fold_4.log deleted file mode 100644 index aab86052ddcd05b9f588da4dff0a75cc25a72fa9..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 34.057631492614746 4.213615417480469 121.68499755859375 1.0471265316009521 173.66908264160156 0.11288940161466599 0.6754852 3.029045581817627 True -1 5470 30.217262983322144 1.299804925918579 161.73001098632812 0.6535174250602722 160.64187622070312 0.14417259395122528 0.75563246 1.6675320863723755 True -2 8205 30.118741035461426 0.5561044216156006 138.70252990722656 0.691078245639801 158.69688415527344 0.14761634171009064 0.7663146 0.9098156094551086 True -3 10940 30.06993556022644 0.5773820877075195 169.54771423339844 0.8121560215950012 156.7869873046875 0.14949719607830048 0.7791327 0.7616556286811829 True -4 13675 30.084346771240234 1.0175871849060059 126.35357666015625 0.5019402503967285 155.20310974121094 0.15293580293655396 0.79132366 0.7010728120803833 True -5 16410 30.071574687957764 0.5630762577056885 113.49566650390625 0.4906468093395233 155.08346557617188 0.1530202329158783 0.7956856 0.646467924118042 True -6 19145 30.06631875038147 0.5731022357940674 129.78196716308594 0.3260573744773865 153.6443328857422 0.15533767640590668 0.80184484 0.580543577671051 True -7 21880 30.199304819107056 0.5737783908843994 123.00930786132812 0.35404062271118164 153.2344512939453 0.15597526729106903 0.8097508 0.5621911883354187 True -8 24615 30.172374486923218 0.5703356266021729 130.5129852294922 0.48276597261428833 152.61529541015625 0.15777137875556946 0.8146155 0.5387804508209229 True -9 27350 30.015793561935425 0.5671238899230957 139.03103637695312 0.4770762026309967 151.88682556152344 0.15936967730522156 0.8221071 0.5039105415344238 True -10 30085 29.543111562728882 0.568901777267456 130.14093017578125 0.4995676875114441 151.2957763671875 0.16079889237880707 0.8282394 0.4620961546897888 True -11 32820 29.57810688018799 0.5632686614990234 133.606689453125 0.566067099571228 150.5830535888672 0.16306278109550476 0.8328203 0.42876991629600525 True -12 35555 29.552866458892822 2.8487656116485596 143.91622924804688 0.406605988740921 150.5758056640625 0.16250166296958923 0.83951014 0.40112215280532837 True -13 38290 29.546983003616333 0.5681931972503662 200.07537841796875 0.4986265003681183 150.3573760986328 0.16306012868881226 0.8460923 0.37863612174987793 True -14 41025 29.534147262573242 0.5587241649627686 119.511474609375 0.35022586584091187 149.6786651611328 0.16491566598415375 0.8504693 0.35773420333862305 True -15 43760 29.559589624404907 0.5732066631317139 120.01630401611328 0.5114921927452087 149.5483856201172 0.16499747335910797 0.8542419 0.3431120812892914 True -16 46495 29.57634997367859 0.5703463554382324 107.82949829101562 0.30707305669784546 149.17225646972656 0.1661304533481598 0.85596204 0.32841530442237854 True -17 49230 29.57974338531494 0.570608377456665 155.61248779296875 0.36823511123657227 149.07913208007812 0.16637171804904938 0.8576079 0.3201597034931183 True -18 51965 29.56237483024597 0.5574920177459717 168.77719116210938 0.3397907614707947 149.36370849609375 0.165200874209404 0.85941404 0.31824278831481934 True -19 54700 29.544131994247437 0.5803477764129639 132.9346160888672 0.35425618290901184 149.26455688476562 0.165745347738266 0.85920733 0.3172110319137573 False diff --git a/ENCSR735MJZ/cherimoya.fold_4.performance.tsv b/ENCSR735MJZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4b2a79b188d06213e31c81b1134d7f3aa0de75c8..0000000000000000000000000000000000000000 --- a/ENCSR735MJZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -149.36370849609375 0.5854013562202454 0.16520088911056519 0.03773298114538193 0.8594140410423279 0.7596820592880249 0.31824278831481934 \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_0.evaluate.json b/ENCSR735NTV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6ebd0b75b52dc701b0c215b42993cafa2a674aab..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF037DQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_0.fit.json b/ENCSR735NTV/cherimoya.fold_0.fit.json deleted file mode 100644 index 96144d2216f26a4c41ab468b4ab7e14d00c59592..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF037DQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_0.log b/ENCSR735NTV/cherimoya.fold_0.log deleted file mode 100644 index ee132d72cd1dc6db1dde43760f3ba8b94e6851b2..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2717 35.458927631378174 4.019853353500366 614.2802124023438 0.3390926122665405 813.4498901367188 0.27086690068244934 0.7251468 4.875298023223877 True -1 5434 30.26636004447937 0.9432592391967773 572.90185546875 0.2526911199092865 749.76171875 0.3414642810821533 0.7757362 1.1871708631515503 True -2 8151 30.30713129043579 0.5923163890838623 660.85302734375 0.28246134519577026 738.5116577148438 0.3513233959674835 0.78254396 0.6837896108627319 True -3 10868 30.25830912590027 0.6039578914642334 678.8246459960938 0.3352317214012146 729.8583984375 0.3585037887096405 0.7937127 0.5394245386123657 True -4 13585 30.338062524795532 0.6276586055755615 587.856689453125 0.35667139291763306 727.0232543945312 0.36185815930366516 0.7967557 0.5112877488136292 True -5 16302 30.220602989196777 0.5972299575805664 680.2996826171875 0.31721585988998413 724.1459350585938 0.36504819989204407 0.8060187 0.3517502248287201 True -6 19019 30.227952480316162 0.5948066711425781 596.2720947265625 0.318857878446579 720.7373046875 0.36971598863601685 0.8101146 0.3528592586517334 True -7 21736 30.20377540588379 0.5968613624572754 620.0814208984375 0.47215932607650757 717.7245483398438 0.37375032901763916 0.81083673 0.3443499803543091 True -8 24453 30.20354127883911 0.5944840908050537 685.0040283203125 0.25392407178878784 717.4828491210938 0.3732932507991791 0.8186761 0.3473668694496155 True -9 27170 30.230106115341187 0.5989763736724854 561.1873779296875 0.27379751205444336 715.3557739257812 0.3755963146686554 0.8219193 0.33479127287864685 True -10 29887 30.218844890594482 0.5966808795928955 553.6131591796875 0.5060979127883911 715.1727294921875 0.3746207356452942 0.8263687 0.27939820289611816 True -11 32604 30.253886222839355 0.5984516143798828 603.0067749023438 0.2669161856174469 713.5089111328125 0.3767150044441223 0.83115095 0.2574172616004944 True -12 35321 30.227156162261963 0.5949056148529053 608.1146240234375 0.12227576971054077 710.735107421875 0.3800872266292572 0.8346597 0.25245964527130127 True -13 38038 30.201502323150635 0.6008682250976562 662.9066162109375 0.2571483850479126 707.5866088867188 0.38363873958587646 0.84023464 0.23692737519741058 True -14 40755 30.24848484992981 0.5954160690307617 621.523193359375 0.19649308919906616 706.6573486328125 0.38433143496513367 0.8465402 0.22694770991802216 True -15 43472 30.26837468147278 0.5986843109130859 615.7077026367188 0.2687322497367859 706.234375 0.3838881850242615 0.84744364 0.2188178151845932 True -16 46189 30.193021059036255 28.49373769760132 663.5401611328125 0.19887293875217438 706.216796875 0.38440296053886414 0.8515539 0.21546290814876556 True -17 48906 30.291178941726685 24.10110640525818 639.0359497070312 0.17980271577835083 705.7576904296875 0.3854631781578064 0.85181844 0.21242734789848328 True -18 51623 30.333534479141235 0.605238676071167 629.771484375 0.22188517451286316 706.7186889648438 0.38381657004356384 0.85165125 0.2120935171842575 False -19 54340 30.28846788406372 0.6050691604614258 580.266845703125 0.1514330804347992 705.5890502929688 0.38592663407325745 0.84971005 0.2128005027770996 False diff --git a/ENCSR735NTV/cherimoya.fold_0.performance.tsv b/ENCSR735NTV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b9dbeb1c6f8b1daf0d502fdbe7b8a8574af3b290..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -705.7576904296875 0.36704444885253906 0.385463148355484 0.16921301186084747 0.8518184423446655 0.8127690553665161 0.21242734789848328 \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_1.evaluate.json b/ENCSR735NTV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e0546635a999788e33af422e7c15ca11714a63f3..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF037DQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_1.fit.json b/ENCSR735NTV/cherimoya.fold_1.fit.json deleted file mode 100644 index 7b1ff9eac364a821e29e68107178ee382e539ad7..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF037DQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_1.log b/ENCSR735NTV/cherimoya.fold_1.log deleted file mode 100644 index 02710a07b664afe631bb6972702be8d1c2659595..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 35.00881242752075 4.333567380905151 623.4791259765625 0.43547922372817993 949.4335327148438 0.27864745259284973 0.7339588 6.2270402908325195 True -1 5418 30.190550327301025 0.7616868019104004 557.545166015625 0.36276763677597046 861.0545043945312 0.3659120500087738 0.7935799 1.406901478767395 True -2 8127 30.199727773666382 0.700930118560791 630.79443359375 0.41564762592315674 847.819091796875 0.3733368515968323 0.8053778 0.7025549411773682 True -3 10836 30.163398027420044 0.707294225692749 579.789794921875 0.18143603205680847 840.0638427734375 0.3778674602508545 0.81236315 0.5758980512619019 True -4 13545 30.2680823802948 0.7110888957977295 647.3569946289062 0.2705298662185669 834.727783203125 0.38322702050209045 0.814823 0.5758810043334961 True -5 16254 30.155524015426636 0.8370702266693115 626.2317504882812 0.3148645758628845 831.6030883789062 0.3866814076900482 0.817118 0.47326698899269104 True -6 18963 30.164151430130005 0.9144024848937988 716.2929077148438 0.36721503734588623 828.545166015625 0.38879910111427307 0.82364184 0.4531441926956177 True -7 21672 30.168153285980225 1.1024789810180664 701.3294677734375 0.5235083103179932 827.1312255859375 0.3910946547985077 0.8262429 0.4681849777698517 True -8 24381 30.21796154975891 0.7022383213043213 595.8214721679688 0.37859010696411133 824.4931640625 0.39336544275283813 0.83129233 0.44619324803352356 True -9 27090 30.216001987457275 0.9542140960693359 526.4877319335938 0.22118830680847168 822.43603515625 0.39474138617515564 0.8342858 0.401214599609375 True -10 29799 30.1775643825531 0.9837214946746826 671.6355590820312 0.29045024514198303 820.8883056640625 0.39599931240081787 0.8379225 0.3953823447227478 True -11 32508 30.171865701675415 0.9968116283416748 618.570556640625 0.2939584255218506 817.0556030273438 0.39937785267829895 0.84433943 0.36176612973213196 True -12 35217 30.160717248916626 0.889359712600708 600.0018310546875 0.2659924626350403 815.1184692382812 0.4009995460510254 0.84899485 0.3189808428287506 True -13 37926 30.196897983551025 1.5058953762054443 621.302001953125 0.29029709100723267 813.2080078125 0.40205278992652893 0.8548295 0.30237308144569397 True -14 40635 30.169670581817627 0.8059399127960205 574.6658935546875 0.23266667127609253 811.1885375976562 0.40340521931648254 0.8597304 0.2798825800418854 True -15 43344 30.22330117225647 0.7181050777435303 606.57275390625 0.23095335066318512 809.1796264648438 0.405689001083374 0.86468726 0.2537253201007843 True -16 46053 30.23607611656189 0.7104389667510986 505.52642822265625 0.2388557493686676 807.4336547851562 0.40768876671791077 0.8668644 0.24487662315368652 True -17 48762 30.164036750793457 0.7153027057647705 698.3998413085938 0.22199954092502594 808.2626953125 0.40632709860801697 0.8682937 0.2364971786737442 True -18 51471 30.180136919021606 14.565029621124268 647.3007202148438 0.17662018537521362 807.7186889648438 0.40713149309158325 0.8678834 0.2345914989709854 False -19 54180 30.24591898918152 1.5979595184326172 686.2053833007812 0.2143772840499878 807.6253662109375 0.4070607125759125 0.86723626 0.2349303811788559 False diff --git a/ENCSR735NTV/cherimoya.fold_1.performance.tsv b/ENCSR735NTV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b7ed5bda01e375a89d51d40b4047314223dec010..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -808.2626953125 0.34688159823417664 0.4063270390033722 0.19361667335033417 0.8682937026023865 0.8483262658119202 0.2364971786737442 \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_2.evaluate.json b/ENCSR735NTV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d6fae799d7eeb04e087d5d678b4a077de9407ecd..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF037DQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_2.fit.json b/ENCSR735NTV/cherimoya.fold_2.fit.json deleted file mode 100644 index 26907ffd4a6dba40f9bab894f2c78036805abdc4..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF037DQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_2.log b/ENCSR735NTV/cherimoya.fold_2.log deleted file mode 100644 index 412918d4caadadb4f05fc84d82cb178fdc8399b9..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 36.78837490081787 5.734586715698242 748.4560546875 0.7454272508621216 855.01611328125 0.27654021978378296 0.732755 3.927497148513794 True -1 5764 32.22648882865906 0.5819149017333984 596.9341430664062 0.2937988042831421 781.4651489257812 0.35039371252059937 0.78691024 1.0847322940826416 True -2 8646 32.06303405761719 0.5534436702728271 803.6901245117188 0.5870825052261353 770.191650390625 0.35866716504096985 0.7916502 0.6866430044174194 True -3 11528 32.11957263946533 0.562772274017334 574.0394287109375 0.32831645011901855 763.9979248046875 0.3661690056324005 0.7994627 0.6226063966751099 True -4 14410 32.134631872177124 0.5752029418945312 783.72412109375 0.3601207137107849 761.0123291015625 0.36866241693496704 0.8051943 0.495648592710495 True -5 17292 32.11602210998535 0.6292955875396729 646.8726806640625 0.27450141310691833 754.8680419921875 0.37602585554122925 0.81148255 0.4055364429950714 True -6 20174 32.11052894592285 0.5757482051849365 699.3641357421875 0.31138715147972107 754.4488525390625 0.37539955973625183 0.8136328 0.35316863656044006 True -7 23056 32.104416847229004 0.5544204711914062 695.0162353515625 0.36107462644577026 751.3009643554688 0.3789342939853668 0.81931925 0.34071585536003113 True -8 25938 32.110302209854126 0.5691084861755371 533.4962158203125 0.24010610580444336 749.2012939453125 0.3820192515850067 0.82425773 0.3372686207294464 True -9 28820 32.12655591964722 26.572055101394653 671.5267944335938 0.23245137929916382 746.9150390625 0.3836667239665985 0.82661194 0.32133105397224426 True -10 31702 32.36501359939575 0.5776932239532471 646.0394287109375 0.1977713704109192 745.27685546875 0.3861140310764313 0.8288255 0.30884024500846863 True -11 34584 32.14621829986572 0.5639450550079346 593.560791015625 0.22376292943954468 744.9317626953125 0.38504016399383545 0.83285844 0.2970614433288574 True -12 37466 32.1124324798584 0.5599484443664551 602.4967041015625 0.19501855969429016 742.6702880859375 0.38779520988464355 0.8387422 0.2804758846759796 True -13 40348 32.10876417160034 0.5707602500915527 486.9383544921875 0.29077935218811035 740.6476440429688 0.38982027769088745 0.8411862 0.2642575204372406 True -14 43230 32.10360145568848 1.5218687057495117 637.90087890625 0.2628004848957062 739.19677734375 0.39107075333595276 0.8465676 0.25408461689949036 True -15 46112 32.177738666534424 0.663069486618042 723.8947143554688 0.4419640004634857 737.712646484375 0.39323651790618896 0.8480568 0.24190859496593475 True -16 48994 32.10593771934509 0.5773477554321289 669.0191650390625 0.1639201045036316 737.7369995117188 0.3932074010372162 0.8507609 0.23295553028583527 True -17 51876 32.15297079086304 0.5840983390808105 599.48828125 0.1723552793264389 737.3151245117188 0.39333727955818176 0.8515687 0.22811336815357208 True -18 54758 32.133774757385254 0.5806136131286621 654.5759887695312 0.11834229528903961 738.0470581054688 0.39252156019210815 0.85241127 0.22648382186889648 True -19 57640 32.09996199607849 0.5621142387390137 512.8578491210938 0.16327165067195892 738.0925903320312 0.3929505944252014 0.8503517 0.22780954837799072 False diff --git a/ENCSR735NTV/cherimoya.fold_2.performance.tsv b/ENCSR735NTV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1c1fb081960eadbcef3b6eaef2e9ccce48c68536..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -738.0470581054688 0.3604530096054077 0.39252156019210815 0.17774556577205658 0.8524112701416016 0.8206622004508972 0.22648382186889648 \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_3.evaluate.json b/ENCSR735NTV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 178fd08871699561b52c201d57ee4bbc140ff000..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF037DQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_3.fit.json b/ENCSR735NTV/cherimoya.fold_3.fit.json deleted file mode 100644 index 76bde94382806562dd1299ac4910940c19ba0e17..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF037DQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_3.log b/ENCSR735NTV/cherimoya.fold_3.log deleted file mode 100644 index 4aa0b7642d7e932f073024d49c3550300aa975dc..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 35.2954216003418 17.472984075546265 631.97607421875 0.5225517153739929 797.4579467773438 0.27467942237854004 0.71996456 3.8690481185913086 True -1 5480 30.768188953399658 0.6456077098846436 606.8131713867188 0.27885860204696655 736.7063598632812 0.33683985471725464 0.76432693 1.0465656518936157 True -2 8220 30.604779720306396 0.6296021938323975 595.5684814453125 0.2968671917915344 722.1221313476562 0.3496987819671631 0.7856371 0.5938633680343628 True -3 10960 30.537142038345337 0.6034235954284668 628.1090087890625 0.2699417173862457 712.9657592773438 0.3585986793041229 0.79258376 0.6506164073944092 True -4 13700 30.552945852279663 0.5768370628356934 621.3251953125 0.4950094521045685 711.4776611328125 0.3610081672668457 0.7947628 0.5042398571968079 True -5 16440 30.550967931747437 0.6014108657836914 622.5525512695312 0.27411067485809326 707.512451171875 0.36460620164871216 0.79645663 0.43233156204223633 True -6 19180 30.520713806152344 1.1689295768737793 609.2460327148438 0.2709479331970215 704.05908203125 0.36762869358062744 0.80907696 0.4038184583187103 True -7 21920 30.528339624404907 0.5911777019500732 591.2476806640625 0.27479463815689087 702.2726440429688 0.36842647194862366 0.81353915 0.3784671127796173 True -8 24660 30.515039920806885 0.6135144233703613 664.0921630859375 0.326266884803772 700.5927734375 0.36998459696769714 0.8173341 0.3613191843032837 True -9 27400 30.5808527469635 0.6942176818847656 601.149658203125 0.2904773950576782 698.4119873046875 0.37292176485061646 0.8207563 0.3542095124721527 True -10 30140 30.5716872215271 0.5745677947998047 640.26318359375 0.27531683444976807 695.619873046875 0.376535564661026 0.8238798 0.32410672307014465 True -11 32880 30.606948852539062 0.5685346126556396 685.83984375 0.25749048590660095 693.390380859375 0.3792453706264496 0.8298966 0.3002958595752716 True -12 35620 30.526008367538452 0.587479829788208 631.8934936523438 0.3422144055366516 693.472412109375 0.3781016170978546 0.83342373 0.2841971814632416 True -13 38360 30.559839248657227 0.5848445892333984 643.9251708984375 0.1922103464603424 692.8082885742188 0.3781408369541168 0.83998024 0.2726821005344391 True -14 41100 30.51969075202942 0.583256721496582 690.5527954101562 0.20218369364738464 690.8626098632812 0.3802245855331421 0.8427878 0.2582140266895294 True -15 43840 30.574093103408813 0.5827476978302002 594.735107421875 0.2801451086997986 689.8873291015625 0.3814746141433716 0.8481321 0.24714314937591553 True -16 46580 30.534140586853027 1.1539499759674072 614.558349609375 0.09488438069820404 689.4041748046875 0.3814316391944885 0.8514262 0.23807179927825928 True -17 49320 30.552074432373047 0.5829033851623535 562.5755615234375 0.263812780380249 687.139404296875 0.38457998633384705 0.8534078 0.23193004727363586 True -18 52060 30.54334282875061 0.575812578201294 698.8448486328125 0.09697191417217255 687.9517822265625 0.38315173983573914 0.85219216 0.22964417934417725 False -19 54800 30.546026468276978 0.5842647552490234 598.4229125976562 0.19325534999370575 689.4252319335938 0.3805215060710907 0.85011923 0.22992463409900665 False diff --git a/ENCSR735NTV/cherimoya.fold_3.performance.tsv b/ENCSR735NTV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9731af7690d0a04345d510a78e15f922bda1cc0f..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -687.139404296875 0.3698861002922058 0.38457998633384705 0.16777706146240234 0.8534078001976013 0.807206392288208 0.23193004727363586 \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_4.evaluate.json b/ENCSR735NTV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6a9d0f7be1617e63ef24baf9dfc5f95debe7db4a..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF037DQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_4.fit.json b/ENCSR735NTV/cherimoya.fold_4.fit.json deleted file mode 100644 index 23e54c8455b125b77a13e1e5f7c3820dbccd14e3..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF037DQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR735NTV/cherimoya.fold_4.log b/ENCSR735NTV/cherimoya.fold_4.log deleted file mode 100644 index b9e5fc2cc68e785a6416a1994ddf84aaeacd6805..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2838 37.514167070388794 4.9105002880096436 651.3001098632812 0.2527458667755127 756.67919921875 0.272566020488739 0.7185149 4.09919548034668 True -1 5676 31.692907094955444 0.7129921913146973 612.09130859375 0.46721118688583374 704.961181640625 0.33439552783966064 0.7557526 0.9699594974517822 True -2 8514 31.665807723999023 0.6493237018585205 609.396728515625 0.19082021713256836 696.605224609375 0.34279048442840576 0.76988673 0.5397070050239563 True -3 11352 31.595420837402344 0.6393959522247314 616.3434448242188 0.3050691485404968 690.8402709960938 0.34904414415359497 0.7835177 0.4799652099609375 True -4 14190 31.651224374771118 22.505922317504883 571.9107055664062 0.24020430445671082 686.8536987304688 0.35293063521385193 0.7909305 0.4668320119380951 True -5 17028 32.39804768562317 0.633469820022583 663.992919921875 0.22326822578907013 684.20556640625 0.3566790819168091 0.7957664 0.36744070053100586 True -6 19866 31.591396808624268 0.6355240345001221 622.5338745117188 0.23214957118034363 681.4811401367188 0.35955479741096497 0.8012272 0.31595632433891296 True -7 22704 31.64122986793518 0.6230921745300293 614.9780883789062 0.29631587862968445 680.1204833984375 0.3606884181499481 0.8080473 0.3065282702445984 True -8 25542 31.606436491012573 22.95278835296631 672.576171875 0.5145150423049927 677.9388427734375 0.3642672002315521 0.8091142 0.31165412068367004 True -9 28380 31.733182191848755 1.3828718662261963 596.8411865234375 0.31015461683273315 676.3969116210938 0.3661099970340729 0.81511986 0.28424742817878723 True -10 31218 31.6323184967041 1.7053289413452148 664.64453125 0.2941121459007263 675.1951293945312 0.36684247851371765 0.82114726 0.2708992063999176 True -11 34056 31.726951599121094 16.83674144744873 467.1932678222656 0.23302659392356873 672.712890625 0.37065231800079346 0.823784 0.27426496148109436 True -12 36894 31.65319800376892 0.6513285636901855 576.1399536132812 0.17974773049354553 671.3366088867188 0.372381329536438 0.8272432 0.2642463743686676 True -13 39732 31.62121081352234 0.6356005668640137 651.1370849609375 0.18255577981472015 670.8932495117188 0.3726951777935028 0.8333177 0.24282711744308472 True -14 42570 31.600649118423462 0.639838457107544 567.133544921875 0.14245465397834778 669.240234375 0.3746318519115448 0.84104997 0.2278595268726349 True -15 45408 31.610679626464844 0.6645443439483643 552.386474609375 0.218939870595932 669.1114501953125 0.3745725154876709 0.8458488 0.2192355990409851 True -16 48246 31.631016969680786 0.6320555210113525 547.794189453125 0.1427019238471985 667.7508544921875 0.3763478696346283 0.8483694 0.2107781171798706 True -17 51084 31.713467836380005 0.637338399887085 598.3162231445312 0.13075877726078033 668.5518798828125 0.3747597336769104 0.84927887 0.20402765274047852 True -18 53922 31.689666032791138 0.6361367702484131 639.2244873046875 0.16531902551651 668.0899658203125 0.3765103816986084 0.85040534 0.20207664370536804 True -19 56760 31.632349014282227 0.8164691925048828 613.1551513671875 0.22963100671768188 668.9505615234375 0.37483471632003784 0.8518596 0.20272238552570343 True diff --git a/ENCSR735NTV/cherimoya.fold_4.performance.tsv b/ENCSR735NTV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8d4f0918a69252636ab5e20c3c5117ae89bf7628..0000000000000000000000000000000000000000 --- a/ENCSR735NTV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -668.9505615234375 0.3760867714881897 0.37483468651771545 0.1631142646074295 0.8518596291542053 0.8071057796478271 0.20272238552570343 \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_0.evaluate.json b/ENCSR736CIN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0d9bf4bcd63ae9903a04c1b6546fbc0a111c6de5..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF102OES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_0.fit.json b/ENCSR736CIN/cherimoya.fold_0.fit.json deleted file mode 100644 index 2ec8fded2c76ba0ba3d70943a00df0d94cbd2cf6..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF102OES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_0.log b/ENCSR736CIN/cherimoya.fold_0.log deleted file mode 100644 index 4df03b0c89d820f1fb395849c73650b722b6fa74..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1495 20.39107394218445 4.240674018859863 216.7103271484375 0.4155161380767822 354.95501708984375 0.4336070716381073 0.7136716 12.455903053283691 True -1 2990 16.55888557434082 0.5366406440734863 211.11135864257812 0.3583126962184906 294.0357971191406 0.5226397514343262 0.7678692 2.5307044982910156 True -2 4485 16.513479232788086 0.5439374446868896 248.69210815429688 0.377224862575531 278.2478942871094 0.5572202801704407 0.7931376 0.6130408644676208 True -3 5980 16.536942958831787 0.29245924949645996 218.07945251464844 0.3680439591407776 270.2581481933594 0.5758974552154541 0.80920273 0.4147946834564209 True -4 7475 16.544618606567383 0.2921793460845947 232.26699829101562 0.2695538401603699 267.3699645996094 0.5825474262237549 0.8160253 0.32582035660743713 True -5 8970 16.513986349105835 0.42807650566101074 265.49688720703125 0.40527182817459106 266.477294921875 0.5857346653938293 0.8208842 0.27028244733810425 True -6 10465 16.54494857788086 0.31875157356262207 251.11990356445312 0.4591638743877411 265.6556091308594 0.5882147550582886 0.824136 0.2470049262046814 True -7 11960 16.520931720733643 0.2859914302825928 229.65052795410156 0.2555234432220459 265.0603942871094 0.5901749134063721 0.8250618 0.24461910128593445 True -8 13455 16.531753063201904 0.2880127429962158 206.43601989746094 0.31439322233200073 264.4342346191406 0.5918297171592712 0.8281433 0.2391902059316635 True -9 14950 16.489518642425537 5.544064283370972 210.50051879882812 0.2874927520751953 263.78485107421875 0.5935412645339966 0.8315054 0.23552536964416504 True -10 16445 16.593666791915894 0.2901761531829834 212.2573699951172 0.43432822823524475 263.1614074707031 0.5951467156410217 0.8370357 0.22970180213451385 True -11 17940 16.530267238616943 0.29037928581237793 265.844482421875 0.2051682472229004 262.6760559082031 0.5966411232948303 0.83839923 0.22700829803943634 True -12 19435 16.491538286209106 0.29468441009521484 198.77078247070312 0.30674469470977783 262.27197265625 0.597892165184021 0.83773696 0.22481480240821838 False -13 20930 16.510767459869385 7.579779863357544 223.46826171875 0.31820395588874817 261.96014404296875 0.5986925959587097 0.84272134 0.22106391191482544 True -14 22425 16.54232096672058 0.29249000549316406 235.10882568359375 0.2178945541381836 261.69305419921875 0.5991758108139038 0.84572566 0.2194797694683075 True -15 23920 16.61741852760315 0.3045680522918701 227.36354064941406 0.23505227267742157 261.6043701171875 0.5993505120277405 0.84759754 0.22303147614002228 True -16 25415 16.551132917404175 0.30071353912353516 233.45730590820312 0.1596670001745224 261.72540283203125 0.5988205075263977 0.84798825 0.22454814612865448 True -17 26910 16.483436584472656 4.219177961349487 203.8772735595703 0.2387620210647583 261.95562744140625 0.5981714725494385 0.8480373 0.2289436012506485 True -18 28405 16.563106060028076 0.29863548278808594 199.99952697753906 0.12982848286628723 262.2425842285156 0.5972707271575928 0.84495485 0.23355363309383392 False -19 29900 16.55235743522644 0.2983708381652832 206.18621826171875 0.17498892545700073 262.4159240722656 0.5966783761978149 0.8438038 0.23773351311683655 False diff --git a/ENCSR736CIN/cherimoya.fold_0.performance.tsv b/ENCSR736CIN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 51771870794a0e4184a0de2201da31ea083febbb..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -261.95562744140625 0.32839229702949524 0.5981714129447937 0.18775297701358795 0.8480373024940491 0.7954829335212708 0.2289436012506485 \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_1.evaluate.json b/ENCSR736CIN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 92d466a23f7463ade6ee890d524bfc223b9c3e5e..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF102OES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_1.fit.json b/ENCSR736CIN/cherimoya.fold_1.fit.json deleted file mode 100644 index 1d40e819d6df30ee34ae556b47a06ca40a583a08..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF102OES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_1.log b/ENCSR736CIN/cherimoya.fold_1.log deleted file mode 100644 index 23000f13f33c577a296a84d8b8a02da662f3ff38..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1485 20.43074655532837 13.260637760162354 221.09786987304688 0.8831683397293091 417.82379150390625 0.4514908790588379 0.6525359 14.828327178955078 True -1 2970 16.449296712875366 0.42127156257629395 222.37461853027344 0.8935838937759399 339.0633239746094 0.5506556034088135 0.73291373 4.290685653686523 True -2 4455 16.425684213638306 0.3838939666748047 221.9172821044922 0.5773480534553528 320.1973876953125 0.5890517830848694 0.75928956 1.1622490882873535 True -3 5940 16.389067888259888 0.3767890930175781 229.61639404296875 0.5042633414268494 310.6328125 0.6080805063247681 0.7777753 0.5779989361763 True -4 7425 16.389450550079346 0.37972187995910645 237.09225463867188 0.31488919258117676 307.23797607421875 0.6140700578689575 0.7877131 0.4040701687335968 True -5 8910 16.397053003311157 0.3798258304595947 223.376708984375 0.6319183111190796 305.9170837402344 0.6170943379402161 0.79541856 0.32975074648857117 True -6 10395 16.410233974456787 0.6260979175567627 276.1248474121094 0.44018206000328064 304.93585205078125 0.6195270419120789 0.8000276 0.34041088819503784 True -7 11880 16.40235447883606 0.37764978408813477 201.7021484375 0.409618079662323 304.58966064453125 0.6208330392837524 0.8047155 0.3392593562602997 True -8 13365 16.404908180236816 1.164363145828247 219.65957641601562 0.8159115314483643 303.46490478515625 0.6231257319450378 0.8101738 0.33377569913864136 True -9 14850 16.40895962715149 0.39327359199523926 234.5152587890625 0.4580176770687103 302.50445556640625 0.6252469420433044 0.8168433 0.318254292011261 True -10 16335 16.423270225524902 0.3790397644042969 202.1854248046875 0.3480551838874817 301.60638427734375 0.6270487308502197 0.82347864 0.31493237614631653 True -11 17820 16.424331188201904 0.7443153858184814 248.43922424316406 0.3539506494998932 300.7080993652344 0.629011332988739 0.8296497 0.3009905219078064 True -12 19305 16.45783305168152 0.38449716567993164 220.58184814453125 0.3683973550796509 300.0264587402344 0.6305827498435974 0.83365893 0.29944396018981934 True -13 20790 16.46187448501587 0.38373756408691406 217.90481567382812 0.2373334765434265 299.3733825683594 0.6319897770881653 0.8411512 0.2856978476047516 True -14 22275 16.41640591621399 0.3773365020751953 226.47622680664062 0.6804954409599304 298.8105773925781 0.6330495476722717 0.8449402 0.2728239595890045 True -15 23760 16.41717290878296 0.38895201683044434 252.8467559814453 0.35993653535842896 298.66839599609375 0.6333657503128052 0.84620905 0.26731252670288086 True -16 25245 16.400125980377197 0.3773801326751709 237.29002380371094 0.19312526285648346 298.80377197265625 0.6327559351921082 0.8468726 0.2638649642467499 True -17 26730 16.416364431381226 0.38678407669067383 229.53123474121094 0.2366420328617096 299.0805969238281 0.6320208311080933 0.84598184 0.2664796710014343 False -18 28215 16.433418035507202 0.38794660568237305 217.39784240722656 0.16930952668190002 299.3995666503906 0.631179690361023 0.8410872 0.27102845907211304 False -19 29700 16.427443742752075 0.381817102432251 195.4364013671875 0.4160999059677124 299.57891845703125 0.6306003332138062 0.8373295 0.2770426571369171 False diff --git a/ENCSR736CIN/cherimoya.fold_1.performance.tsv b/ENCSR736CIN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a1dcf52df2bb40d9299c1d5f713e84eab161547f..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -298.80377197265625 0.30283960700035095 0.6327559351921082 0.21427570283412933 0.8468726277351379 0.8215327858924866 0.2638649642467499 \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_2.evaluate.json b/ENCSR736CIN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 070b4f3b162c264731b2eb6980e96579589d6716..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF102OES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_2.fit.json b/ENCSR736CIN/cherimoya.fold_2.fit.json deleted file mode 100644 index 1ce4a73e29cdb9d28785240f805424026cf55c40..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF102OES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_2.log b/ENCSR736CIN/cherimoya.fold_2.log deleted file mode 100644 index 45e5ac6841fa3ac81821da91726bccc73e679416..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1587 21.306599378585815 3.2977399826049805 214.3653564453125 0.7489414811134338 377.6545104980469 0.4443291425704956 0.66560084 11.645747184753418 True -1 3174 17.545929431915283 0.3205711841583252 280.685791015625 0.513700544834137 310.3673400878906 0.5385318398475647 0.7542529 2.7649903297424316 True -2 4761 17.614245414733887 0.31565356254577637 221.89990234375 0.4028972387313843 292.7106018066406 0.5745402574539185 0.7761219 0.8547365069389343 True -3 6348 17.565462350845337 3.593677282333374 264.0767822265625 0.6968451738357544 284.6210632324219 0.5912740230560303 0.79128927 0.3739258944988251 True -4 7935 17.899444103240967 0.3443000316619873 230.53280639648438 0.848709225654602 282.3617248535156 0.5960853099822998 0.7999749 0.3364228904247284 True -5 9522 17.55143451690674 0.3035604953765869 234.77572631835938 0.4226754605770111 281.5625305175781 0.5989465117454529 0.8017605 0.3068680167198181 True -6 11109 17.614190816879272 0.3054056167602539 216.3580322265625 0.634958028793335 280.71038818359375 0.600411593914032 0.80732995 0.30577167868614197 True -7 12696 17.514667510986328 0.3043246269226074 259.7945556640625 0.5710060596466064 280.3985900878906 0.6014888286590576 0.81087095 0.32884639501571655 True -8 14283 17.570859670639038 0.3034400939941406 228.19625854492188 0.5402621030807495 279.53839111328125 0.6036953330039978 0.8130136 0.3279397785663605 True -9 15870 17.5437490940094 1.1925387382507324 226.66708374023438 0.23142054677009583 278.8793640136719 0.6052376627922058 0.81639326 0.323684960603714 True -10 17457 17.51354432106018 0.30498576164245605 198.48919677734375 0.25706544518470764 277.92059326171875 0.6073147058486938 0.82317114 0.293689489364624 True -11 19044 17.514322996139526 0.309384822845459 232.57188415527344 0.371539443731308 277.2070617675781 0.6087149977684021 0.8242167 0.2869858145713806 True -12 20631 17.491063833236694 0.3066558837890625 258.4697265625 0.31539902091026306 276.7101745605469 0.6098728179931641 0.83189905 0.2696394920349121 True -13 22218 17.5394446849823 0.3069181442260742 206.5765380859375 0.26155197620391846 276.1944274902344 0.6111046075820923 0.83329594 0.26986899971961975 True -14 23805 17.565746784210205 0.30689477920532227 225.37342834472656 0.39380133152008057 275.9297180175781 0.6115671396255493 0.83819747 0.2633155584335327 True -15 25392 17.57813024520874 0.3058280944824219 229.56240844726562 0.43045976758003235 275.8160705566406 0.6119385957717896 0.8399142 0.2571103572845459 True -16 26979 17.57805347442627 0.30847787857055664 219.77908325195312 0.22223533689975739 275.8387451171875 0.6117091774940491 0.8400059 0.258846253156662 True -17 28566 17.58110475540161 0.3116767406463623 210.24398803710938 0.27599242329597473 276.0037536621094 0.6111986041069031 0.8378207 0.2634473443031311 False -18 30153 17.601852893829346 0.3086113929748535 191.56527709960938 0.2530316114425659 276.15667724609375 0.61049884557724 0.83700436 0.2649737596511841 False -19 31740 17.60049867630005 0.30853772163391113 216.78762817382812 0.2932671010494232 276.3605651855469 0.6099966764450073 0.83366656 0.26735734939575195 False diff --git a/ENCSR736CIN/cherimoya.fold_2.performance.tsv b/ENCSR736CIN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 94b08d538c4614cb616128dcce63d483c3a67fc3..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.8387451171875 0.3189408481121063 0.6117091774940491 0.19885660707950592 0.8400058746337891 0.7974454164505005 0.258846253156662 \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_3.evaluate.json b/ENCSR736CIN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9717c7f2b37f1f899d342dc46b522cfc4cf3af7d..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF102OES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_3.fit.json b/ENCSR736CIN/cherimoya.fold_3.fit.json deleted file mode 100644 index dc76df97743ade17cc294c3301aa7c54326babaa..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF102OES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_3.log b/ENCSR736CIN/cherimoya.fold_3.log deleted file mode 100644 index e51ef78b4f80ffa1a7c3edc48f198303c3fe5b53..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1537 20.920363426208496 3.20271372795105 249.79052734375 0.889348030090332 369.1789245605469 0.4387730062007904 0.68539083 11.863761901855469 True -1 3074 16.995485544204712 0.29227638244628906 243.47645568847656 0.7381201982498169 300.6507873535156 0.534019947052002 0.7581626 2.9381532669067383 True -2 4611 16.987144708633423 0.2851598262786865 221.98562622070312 0.6586617231369019 285.4838562011719 0.5672789812088013 0.76470673 0.9306936860084534 True -3 6148 16.985296964645386 0.2899768352508545 236.3289337158203 0.42995011806488037 278.43817138671875 0.5837391018867493 0.7929517 0.4680861234664917 True -4 7685 16.988948345184326 0.28639888763427734 219.80816650390625 0.6516970992088318 276.3515930175781 0.5890140533447266 0.7988386 0.4260934293270111 True -5 9222 16.992271661758423 0.2862427234649658 222.1393280029297 0.858285665512085 275.3341064453125 0.5921604037284851 0.8030555 0.34082484245300293 True -6 10759 17.001829385757446 0.28898048400878906 225.3711700439453 0.40473201870918274 274.6495666503906 0.5938925743103027 0.80401295 0.32204923033714294 True -7 12296 16.995701551437378 0.28907203674316406 211.6543731689453 0.7392761707305908 274.12127685546875 0.5957377552986145 0.8088102 0.3054982125759125 True -8 13833 16.995229482650757 0.6770861148834229 238.12359619140625 0.32043594121932983 273.31689453125 0.5977640748023987 0.80966115 0.3030719757080078 True -9 15370 17.73040223121643 11.216022491455078 210.5540313720703 0.4325816035270691 272.7090759277344 0.5996004939079285 0.81064785 0.30731940269470215 True -10 16907 17.008284091949463 0.2957632541656494 206.99761962890625 0.529126763343811 271.8393859863281 0.6017361283302307 0.8126782 0.30225592851638794 True -11 18444 16.99100971221924 0.2931694984436035 205.70889282226562 0.25090739130973816 271.3264465332031 0.6032713055610657 0.81403166 0.3023263216018677 True -12 19981 17.02937889099121 0.29337620735168457 237.84649658203125 0.29374903440475464 270.6518249511719 0.6051700115203857 0.8201126 0.2884334921836853 True -13 21518 17.0125253200531 0.2950570583343506 221.38243103027344 0.9021432399749756 270.1306457519531 0.6064231395721436 0.8266565 0.27764829993247986 True -14 23055 17.04589819908142 0.2949092388153076 221.04153442382812 0.24215395748615265 269.79718017578125 0.6072700619697571 0.8313899 0.2757759988307953 True -15 24592 16.98174023628235 0.2901766300201416 203.0164337158203 0.16415664553642273 269.66802978515625 0.6074637770652771 0.8277315 0.2865408957004547 False -16 26129 16.979897022247314 0.28983092308044434 205.46897888183594 0.5087021589279175 269.7466735839844 0.6071242094039917 0.82777166 0.2899472713470459 False -17 27666 16.991140365600586 0.29044485092163086 213.9880828857422 0.17387649416923523 269.91510009765625 0.6064673662185669 0.8219622 0.2974732220172882 False -18 29203 16.9959454536438 0.29825711250305176 197.63461303710938 0.39781442284584045 270.2005615234375 0.6057466864585876 0.8205513 0.300860732793808 False -19 30740 17.013046741485596 0.2932460308074951 245.88775634765625 0.14109346270561218 270.3225402832031 0.6053051352500916 0.8199803 0.30485427379608154 False diff --git a/ENCSR736CIN/cherimoya.fold_3.performance.tsv b/ENCSR736CIN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d9fe5a437e89b311a8a45563c08abaf85a5fa985..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -269.79718017578125 0.32237720489501953 0.6072701215744019 0.19107356667518616 0.8313899040222168 0.7925904393196106 0.2757759988307953 \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_4.evaluate.json b/ENCSR736CIN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 696250408c89b1955f32e614fa65d48ccae9f6e8..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF102OES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_4.fit.json b/ENCSR736CIN/cherimoya.fold_4.fit.json deleted file mode 100644 index 2d13a0f3498ba2b69b86a77a90709894e71de07b..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF102OES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736CIN/cherimoya.fold_4.log b/ENCSR736CIN/cherimoya.fold_4.log deleted file mode 100644 index b4861e78aa5c58f4c111b83a65a8c25a34bd3ced..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1535 21.7479145526886 3.2840402126312256 227.8015594482422 0.7219372987747192 351.7694091796875 0.43282896280288696 0.6868445 12.962646484375 True -1 3070 17.035289525985718 0.3186180591583252 248.65933227539062 0.6646848917007446 290.6737976074219 0.5248627662658691 0.7562813 2.7547080516815186 True -2 4605 16.961507558822632 0.3013341426849365 257.7691345214844 0.35057079792022705 273.524658203125 0.5623860359191895 0.78371525 0.7036646604537964 True -3 6140 17.001338720321655 0.3039717674255371 223.901611328125 0.4189319610595703 267.255615234375 0.5772985816001892 0.7958584 0.3232463002204895 True -4 7675 16.996227741241455 0.2988879680633545 248.14041137695312 0.34049192070961 266.15228271484375 0.5798344016075134 0.80128086 0.32970502972602844 True -5 9210 17.020743131637573 0.9317536354064941 217.60040283203125 0.5778745412826538 265.0932922363281 0.5834501385688782 0.804499 0.3019460439682007 True -6 10745 16.963254690170288 0.3065609931945801 239.962158203125 0.2850717008113861 264.29248046875 0.5860952734947205 0.80739295 0.31202012300491333 True -7 12280 17.00454807281494 0.3029794692993164 201.6011199951172 0.5946195125579834 263.5577392578125 0.5880257487297058 0.81035817 0.2904384732246399 True -8 13815 16.99906039237976 0.29995226860046387 239.8545684814453 0.7229390144348145 262.79949951171875 0.5895909070968628 0.8134233 0.26928460597991943 True -9 15350 17.474578142166138 3.9431052207946777 260.84454345703125 0.27766063809394836 262.4139099121094 0.5910791158676147 0.8180359 0.2584162950515747 True -10 16885 17.009135484695435 0.3806498050689697 224.91799926757812 0.38728755712509155 261.75067138671875 0.5925204753875732 0.82574207 0.2493802160024643 True -11 18420 17.038131952285767 0.3104262351989746 233.957275390625 0.2102651298046112 261.2667236328125 0.5937960147857666 0.82939076 0.23682694137096405 True -12 19955 17.030818462371826 0.3055741786956787 247.9796142578125 0.5893129110336304 260.9091491699219 0.5951931476593018 0.83197796 0.23601792752742767 True -13 21490 17.04582691192627 0.32448625564575195 217.23475646972656 0.6356242895126343 260.4322204589844 0.5963478088378906 0.8375958 0.23437505960464478 True -14 23025 16.98107409477234 0.30583882331848145 186.30413818359375 0.30617186427116394 260.095947265625 0.5973343849182129 0.838093 0.23562003672122955 True -15 24560 16.974937438964844 0.2965104579925537 238.548828125 0.27427342534065247 260.0166931152344 0.5976077914237976 0.8413739 0.23594079911708832 True -16 26095 16.94427990913391 1.418531894683838 207.49465942382812 0.34959647059440613 260.0294494628906 0.597368061542511 0.84025574 0.24085299670696259 False -17 27630 16.997638940811157 0.3011188507080078 204.90652465820312 0.19667699933052063 260.18072509765625 0.5967094898223877 0.8391921 0.24648278951644897 False -18 29165 16.987693309783936 0.3075435161590576 224.78079223632812 0.14721854031085968 260.3914794921875 0.5960883498191833 0.83694553 0.25432589650154114 False -19 30700 16.96829891204834 0.3058629035949707 214.34524536132812 0.1743357926607132 260.529052734375 0.595621645450592 0.83390343 0.25896432995796204 False diff --git a/ENCSR736CIN/cherimoya.fold_4.performance.tsv b/ENCSR736CIN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fbfd4984c51cfd1c1567a64c27848963441d7cd4..0000000000000000000000000000000000000000 --- a/ENCSR736CIN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -260.0166931152344 0.32931023836135864 0.5976077914237976 0.18452033400535583 0.8413739204406738 0.7724083662033081 0.23594079911708832 \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_0.evaluate.json b/ENCSR736VVP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 89556e9d0c7d916227b1ef0d88fedb9ef67f0450..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537PGL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_0.fit.json b/ENCSR736VVP/cherimoya.fold_0.fit.json deleted file mode 100644 index a00c2e95d360fd1270cb95ae8fd8a27de9133d1c..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF537PGL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_0.log b/ENCSR736VVP/cherimoya.fold_0.log deleted file mode 100644 index 557fe30b54a607cbc7450ffd7aabf65da8998c37..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.240700244903564 4.136237382888794 628.57080078125 0.21072626113891602 815.8253173828125 0.2096119076013565 0.7347816 5.052063465118408 True -1 5494 30.519425630569458 5.49216890335083 628.4476318359375 0.37077775597572327 769.4476318359375 0.26053300499916077 0.8049516 1.2956894636154175 True -2 8241 30.43970489501953 1.167827844619751 600.1575317382812 0.32302913069725037 759.380859375 0.2674314081668854 0.8233115 0.6175197958946228 True -3 10988 30.36120867729187 23.394110441207886 735.6824951171875 0.6774647235870361 756.1109008789062 0.27009347081184387 0.8278046 0.606490969657898 True -4 13735 30.403242588043213 0.5836491584777832 692.95458984375 0.44388559460639954 752.6514892578125 0.2735888957977295 0.8357417 0.4234490990638733 True -5 16482 30.321758031845093 26.819891691207886 563.806884765625 0.5282493829727173 751.8506469726562 0.27427130937576294 0.8397756 0.4079754650592804 True -6 19229 30.306669235229492 14.344870567321777 671.4500732421875 0.3251740336418152 750.562744140625 0.2748797535896301 0.84335744 0.37764909863471985 True -7 21976 30.332937240600586 16.215739965438843 666.8555297851562 0.3194994330406189 747.9212646484375 0.2783801853656769 0.8467275 0.36700111627578735 True -8 24723 30.420473337173462 0.578805685043335 590.6741333007812 0.3883879482746124 746.5013427734375 0.28014007210731506 0.85102934 0.36661383509635925 True -9 27470 33.503164291381836 0.527137041091919 561.5256958007812 0.40097713470458984 745.3966064453125 0.2813122868537903 0.85672814 0.33639824390411377 True -10 30217 30.324512243270874 0.5277459621429443 656.5372314453125 0.2885861396789551 743.0059204101562 0.28401172161102295 0.86282736 0.3303743898868561 True -11 32964 30.284377098083496 0.5222463607788086 603.27001953125 0.2600884437561035 744.8427124023438 0.2803179919719696 0.8668574 0.3083244264125824 True -12 35711 30.320743560791016 0.5274014472961426 553.9266357421875 0.2857874631881714 741.4262084960938 0.2859688699245453 0.8718963 0.2926660478115082 True -13 38458 30.276341915130615 0.6323189735412598 652.3626708984375 0.23039132356643677 740.4072875976562 0.2865910232067108 0.8756523 0.2853499948978424 True -14 41205 30.372677326202393 0.5230448246002197 598.6441040039062 0.18308526277542114 740.4369506835938 0.28643113374710083 0.877687 0.2724403440952301 True -15 43952 30.268800497055054 0.5240464210510254 598.1585693359375 0.14593447744846344 739.4462890625 0.2880638539791107 0.8793648 0.2665179371833801 True -16 46699 30.261892318725586 0.5252017974853516 609.3851318359375 0.28714069724082947 739.6354370117188 0.28667959570884705 0.87846535 0.2659227252006531 False -17 49446 30.61734175682068 19.35798716545105 625.8722534179688 0.1714068502187729 740.1533203125 0.28609585762023926 0.87753797 0.27107879519462585 False -18 52193 30.35402536392212 18.114461183547974 655.4013061523438 0.17455586791038513 741.0772705078125 0.284707248210907 0.87422556 0.2773992717266083 False -19 54940 30.53950548171997 0.6352627277374268 562.1776733398438 0.11770512908697128 740.466064453125 0.2859538495540619 0.8715954 0.2800811529159546 False diff --git a/ENCSR736VVP/cherimoya.fold_0.performance.tsv b/ENCSR736VVP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2cf8ee55b5d82eb20082423bf143568af1f8b944..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -739.4462890625 0.4226932227611542 0.2880638539791107 0.14298196136951447 0.8793647885322571 0.8523750901222229 0.2665179371833801 \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_1.evaluate.json b/ENCSR736VVP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bd056df863f24c89b7e208e15c1c87a3dd5143dc..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537PGL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_1.fit.json b/ENCSR736VVP/cherimoya.fold_1.fit.json deleted file mode 100644 index 473bf0c1009485f9387430f05820a34a0698c959..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF537PGL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_1.log b/ENCSR736VVP/cherimoya.fold_1.log deleted file mode 100644 index 95af08fe149cde16c165f6b04d9985a614b67810..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2690 33.701573848724365 4.383760690689087 642.04736328125 0.42958635091781616 908.953125 0.2145897001028061 0.7549478 5.909027099609375 True -1 5380 29.66396427154541 0.8183844089508057 609.19384765625 0.6275255680084229 854.2832641601562 0.2708747088909149 0.8267395 1.4037914276123047 True -2 8070 29.69567370414734 0.8078696727752686 590.3005981445312 0.2574199438095093 842.779541015625 0.2799379229545593 0.8493373 0.6648374199867249 True -3 10760 29.646485567092896 0.7805025577545166 538.9415893554688 0.42764753103256226 836.1556396484375 0.28756794333457947 0.8566933 0.6711334586143494 True -4 13450 29.63375210762024 1.0782427787780762 624.844482421875 0.5388104319572449 836.49072265625 0.28598034381866455 0.8557086 0.6178508996963501 False -5 16140 29.631856203079224 1.466890573501587 504.28082275390625 0.27440664172172546 834.0899658203125 0.2880658805370331 0.8643943 0.5556932091712952 True -6 18830 29.6513249874115 0.7799384593963623 830.6322021484375 0.3455004096031189 832.361083984375 0.29020944237709045 0.8654179 0.5160149931907654 True -7 21520 29.62442374229431 0.7762250900268555 596.890380859375 0.27594542503356934 830.0227661132812 0.29269275069236755 0.8704021 0.4746699333190918 True -8 24210 29.629231452941895 0.7733750343322754 586.7780151367188 0.2714692950248718 830.1948852539062 0.2926110625267029 0.8728817 0.448422372341156 True -9 26900 29.679080724716187 0.7739248275756836 604.9963989257812 0.27601584792137146 827.8245849609375 0.2947548031806946 0.87884337 0.41548463702201843 True -10 29590 29.59664750099182 0.7730753421783447 655.03125 0.3360826075077057 825.397705078125 0.297489732503891 0.8847504 0.36780786514282227 True -11 32280 29.676828145980835 1.1991498470306396 636.9677734375 0.3360435366630554 823.779541015625 0.29876020550727844 0.8870583 0.3346330523490906 True -12 34970 29.672449350357056 0.779271125793457 651.9088134765625 0.2511726915836334 823.0936279296875 0.29887428879737854 0.8908692 0.3136524558067322 True -13 37660 29.655457019805908 0.767967939376831 568.0993041992188 0.2317136526107788 822.0693359375 0.2999589443206787 0.89523077 0.29530370235443115 True -14 40350 29.634116888046265 0.7922763824462891 711.0881958007812 0.3361320495605469 821.9221801757812 0.3001280725002289 0.89769363 0.27529340982437134 True -15 43040 29.596489429473877 0.7922394275665283 574.99951171875 0.22734513878822327 822.4292602539062 0.2993156909942627 0.90060985 0.26431623101234436 True -16 45730 29.63968849182129 1.3802757263183594 568.505615234375 0.21179673075675964 820.1277465820312 0.301789253950119 0.89917964 0.258672297000885 False -17 48420 29.64377760887146 0.7763841152191162 701.2942504882812 0.18087294697761536 821.2597045898438 0.3009076714515686 0.89942205 0.26014429330825806 False -18 51110 29.60720920562744 0.7718038558959961 606.1395263671875 0.1162232905626297 823.096923828125 0.29880794882774353 0.89774823 0.26614415645599365 False -19 53800 29.645790576934814 1.1963169574737549 654.0940551757812 0.10167790949344635 822.6759643554688 0.2993311285972595 0.8972711 0.26734989881515503 False diff --git a/ENCSR736VVP/cherimoya.fold_1.performance.tsv b/ENCSR736VVP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c4d15815f8b6446fef11e82908e126243a670fb9..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -822.4292602539062 0.4055929481983185 0.2993156909942627 0.15832151472568512 0.9006098508834839 0.8885406255722046 0.26431623101234436 \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_2.evaluate.json b/ENCSR736VVP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6f05a6e6a1cba73af3027a72835ff1e206d4b211..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537PGL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_2.fit.json b/ENCSR736VVP/cherimoya.fold_2.fit.json deleted file mode 100644 index 17706077285199ba5a2f9c84a547c01bbf91cb1d..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF537PGL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_2.log b/ENCSR736VVP/cherimoya.fold_2.log deleted file mode 100644 index 061a5663d5caec7d62b85c04bdb2d4e90ed1c78a..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2918 36.147640228271484 3.805800199508667 614.677734375 0.45726338028907776 858.1201782226562 0.21562634408473969 0.729838 5.027417182922363 True -1 5836 32.484848499298096 0.5960507392883301 724.338134765625 0.3723282217979431 807.876708984375 0.2660778760910034 0.82207495 0.9810101389884949 True -2 8754 32.17983031272888 0.6795554161071777 576.419189453125 0.3490641117095947 799.3875732421875 0.2729918360710144 0.8271695 0.5429484844207764 True -3 11672 32.27250933647156 0.5814790725708008 755.8524169921875 0.30762380361557007 795.3486938476562 0.27676278352737427 0.8380532 0.5161925554275513 True -4 14590 32.19442796707153 0.5915586948394775 577.6776733398438 0.45565617084503174 795.629150390625 0.27516254782676697 0.83943546 0.4526771903038025 True -5 17508 32.276310443878174 0.5789754390716553 612.3809204101562 0.28469881415367126 792.834716796875 0.27937960624694824 0.8438929 0.4387999176979065 True -6 20426 32.22357511520386 7.82371187210083 553.118408203125 0.22743062674999237 790.1170043945312 0.28269022703170776 0.8458021 0.4266311824321747 True -7 23344 32.32199144363403 0.9249618053436279 702.348388671875 0.3380235433578491 789.6971435546875 0.2823875844478607 0.8525923 0.3980853855609894 True -8 26262 32.24449896812439 0.8131158351898193 565.1934204101562 0.37357640266418457 788.3563842773438 0.2837309241294861 0.85713 0.3629879653453827 True -9 29180 32.1728994846344 0.5727298259735107 598.0877685546875 0.3692491054534912 785.0458374023438 0.28812849521636963 0.8620214 0.341880738735199 True -10 32098 32.286685943603516 0.5728130340576172 600.6710815429688 0.2504028081893921 784.954345703125 0.28745877742767334 0.86476195 0.32359305024147034 True -11 35016 32.271867513656616 0.574810266494751 744.3975830078125 0.3782491683959961 783.1652221679688 0.2893260717391968 0.8714789 0.3054161071777344 True -12 37934 32.13618302345276 0.5928285121917725 558.8656005859375 0.28427112102508545 781.337890625 0.2913554012775421 0.87332386 0.2933805286884308 True -13 40852 32.17828321456909 0.5667543411254883 599.8405151367188 0.15511015057563782 781.0317993164062 0.29182636737823486 0.8779582 0.2763240933418274 True -14 43770 32.11958122253418 0.5810437202453613 582.4376220703125 0.16442051529884338 779.7950439453125 0.29297110438346863 0.8795146 0.2687496244907379 True -15 46688 32.13722085952759 0.5669753551483154 607.1177978515625 0.26178157329559326 779.0365600585938 0.2931785583496094 0.88015735 0.2644160985946655 True -16 49606 32.13943958282471 0.5652186870574951 734.0695190429688 0.1395074427127838 779.5162963867188 0.29252952337265015 0.88184285 0.2617204785346985 True -17 52524 32.17063546180725 0.5837001800537109 610.392333984375 0.1150791347026825 779.5927734375 0.29289010167121887 0.8789679 0.2648373544216156 False -18 55442 32.13292074203491 0.5507903099060059 581.13427734375 0.21814492344856262 779.7726440429688 0.2921660840511322 0.87763864 0.27076947689056396 False -19 58360 32.269094944000244 0.5763769149780273 603.946533203125 0.1825605034828186 779.9986572265625 0.29255735874176025 0.87550604 0.2749757766723633 False diff --git a/ENCSR736VVP/cherimoya.fold_2.performance.tsv b/ENCSR736VVP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 22dfc80333fd014cd8434bd850e4baec5f093834..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -779.5162963867188 0.4145953059196472 0.29252952337265015 0.15248516201972961 0.881842851638794 0.8607825040817261 0.2617204785346985 \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_3.evaluate.json b/ENCSR736VVP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 71480c7b3668f753d0f88523ba3c85305483a7dc..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537PGL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_3.fit.json b/ENCSR736VVP/cherimoya.fold_3.fit.json deleted file mode 100644 index 9bb122a940ae2acdb1ee03243c1b454a521ad9d0..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF537PGL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_3.log b/ENCSR736VVP/cherimoya.fold_3.log deleted file mode 100644 index 37e32f5971e5fc62a3e5a512564f73b70db1ba37..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2793 34.41301655769348 3.8224947452545166 636.7962646484375 0.33402666449546814 816.6303100585938 0.21498121321201324 0.69840205 4.901698589324951 True -1 5586 30.85757613182068 0.6056270599365234 729.233642578125 0.5611788034439087 774.4598388671875 0.26133233308792114 0.7806656 1.2369987964630127 True -2 8379 30.9216206073761 1.7753632068634033 678.7811279296875 0.3631781339645386 765.5200805664062 0.2698880732059479 0.80220026 0.6683700680732727 True -3 11172 30.92405867576599 0.6426701545715332 774.0675048828125 0.40000849962234497 762.8807373046875 0.27177664637565613 0.81209254 0.654400110244751 True -4 13965 30.79702615737915 0.540616512298584 659.1375732421875 0.43766775727272034 761.58544921875 0.2730403542518616 0.8133487 0.5701698064804077 True -5 16758 30.73918318748474 0.5343432426452637 652.0777587890625 0.4697321653366089 758.7034301757812 0.2772517800331116 0.81896836 0.5368990302085876 True -6 19551 31.002949953079224 0.5504460334777832 723.7400512695312 0.4097999334335327 757.3563842773438 0.2789374887943268 0.822186 0.520308256149292 True -7 22344 30.769868850708008 0.6256558895111084 615.035888671875 0.3276311755180359 756.04443359375 0.2805126905441284 0.8266156 0.5051296949386597 True -8 25137 30.784820556640625 0.528073787689209 565.4237060546875 0.26227205991744995 754.913818359375 0.28159016370773315 0.8321525 0.4626731276512146 True -9 27930 30.76889681816101 0.5394299030303955 691.0631713867188 0.2798713445663452 754.8731079101562 0.281227171421051 0.8363217 0.4279688596725464 True -10 30723 30.73797369003296 0.5317943096160889 678.34814453125 0.3128668963909149 753.2072143554688 0.28323090076446533 0.8434876 0.4106394052505493 True -11 33516 30.70179557800293 0.5272886753082275 592.420654296875 0.31198951601982117 750.8517456054688 0.2862042486667633 0.8460261 0.378481388092041 True -12 36309 30.76985788345337 0.5266540050506592 656.9798583984375 0.48603346943855286 750.7377319335938 0.2852659225463867 0.8531029 0.3642866909503937 True -13 39102 30.760069370269775 0.5257482528686523 631.2144165039062 0.19752901792526245 749.299560546875 0.2876884341239929 0.85756844 0.33975842595100403 True -14 41895 30.69240117073059 0.5501124858856201 644.9010620117188 0.2460484504699707 748.7625732421875 0.2878066301345825 0.8600833 0.33078110218048096 True -15 44688 30.74186611175537 0.5330297946929932 586.9447021484375 0.24501289427280426 747.2073974609375 0.28978511691093445 0.86276364 0.31716084480285645 True -16 47481 30.677004098892212 0.519312858581543 519.6302490234375 0.1910734474658966 748.3021850585938 0.288656622171402 0.86433667 0.3143790364265442 True -17 50274 30.71827793121338 0.5237593650817871 671.9461669921875 0.2139814794063568 748.0695190429688 0.28945863246917725 0.86346406 0.31494495272636414 False -18 53067 30.765215635299683 0.5492534637451172 642.7005615234375 0.14661066234111786 749.2461547851562 0.28703078627586365 0.8607135 0.31891143321990967 False -19 55860 30.78021264076233 0.5234627723693848 584.59912109375 0.13986676931381226 749.927001953125 0.2859838902950287 0.8591947 0.3206515610218048 False diff --git a/ENCSR736VVP/cherimoya.fold_3.performance.tsv b/ENCSR736VVP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c01eff2436d331f2ee39ef92c115e83c9995b5b8..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -748.3021850585938 0.41947734355926514 0.288656622171402 0.14490939676761627 0.8643366694450378 0.836434006690979 0.3143790364265442 \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_4.evaluate.json b/ENCSR736VVP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1b7df0f1b895394bc04657359e5f4dd10847465f..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF537PGL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_4.fit.json b/ENCSR736VVP/cherimoya.fold_4.fit.json deleted file mode 100644 index c80c26a097af07b03144a979fdd55481305c3905..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF537PGL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR736VVP/cherimoya.fold_4.log b/ENCSR736VVP/cherimoya.fold_4.log deleted file mode 100644 index 0c05545e21e79176d7c40bcfd9cc8cf618da82d0..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2775 34.98879623413086 3.651585102081299 537.298583984375 0.37001609802246094 722.2158203125 0.19975505769252777 0.7114239 4.668907165527344 True -1 5550 30.65139865875244 1.4059979915618896 571.80517578125 0.5730462074279785 687.6139526367188 0.24178962409496307 0.7775515 1.0517300367355347 True -2 8325 30.7133047580719 1.3777985572814941 649.5150146484375 0.29149332642555237 678.9910278320312 0.24821142852306366 0.80520844 0.5052394270896912 True -3 11100 30.776446104049683 0.8997418880462646 628.987060546875 0.5213279724121094 674.7958374023438 0.25333815813064575 0.81330585 0.4408845901489258 True -4 13875 30.787376642227173 0.5707197189331055 573.3450927734375 0.32501107454299927 673.8519897460938 0.25398004055023193 0.8202735 0.4291059970855713 True -5 16650 30.78521203994751 0.560338020324707 711.606201171875 0.3115280270576477 673.94384765625 0.25252658128738403 0.8232682 0.3566548228263855 True -6 19425 30.69693374633789 1.0495481491088867 682.555419921875 0.3260977268218994 670.4027099609375 0.25812068581581116 0.8301202 0.3351287245750427 True -7 22200 30.768372535705566 0.5448658466339111 661.3892211914062 0.3215196132659912 668.6185302734375 0.26027750968933105 0.83371025 0.3263184726238251 True -8 24975 30.618600845336914 0.5523698329925537 667.4556884765625 0.3103488087654114 669.4793701171875 0.258377343416214 0.839782 0.31740802526474 True -9 27750 30.584953784942627 0.5470476150512695 595.6728515625 0.3036249876022339 667.6306762695312 0.2604954242706299 0.8452602 0.30220919847488403 True -10 30525 30.619271516799927 0.549001932144165 562.0875244140625 0.3018416166305542 665.8893432617188 0.2626481354236603 0.85104764 0.2914295792579651 True -11 33300 30.625055074691772 0.5573506355285645 707.3314208984375 0.21411308646202087 666.1092529296875 0.26252052187919617 0.8559444 0.279613196849823 True -12 36075 30.7884418964386 0.5397391319274902 607.8265991210938 0.16843096911907196 663.7421875 0.2655615210533142 0.8587359 0.2762179374694824 True -13 38850 30.692768335342407 0.5555062294006348 679.8009033203125 0.23982404172420502 664.5319213867188 0.2638437747955322 0.8629443 0.269313246011734 True -14 41625 30.691224098205566 0.5385582447052002 535.0762329101562 0.15000838041305542 663.701904296875 0.26572185754776 0.8671756 0.2615334987640381 True -15 44400 30.6606662273407 0.5494205951690674 668.126708984375 0.1878613978624344 662.7672119140625 0.2664225697517395 0.8695138 0.2567739486694336 True -16 47175 30.74387550354004 2.2221198081970215 538.5807495117188 0.23461925983428955 662.51220703125 0.2679905295372009 0.87084347 0.25507408380508423 True -17 49950 30.724786281585693 0.5399868488311768 731.611083984375 0.12950937449932098 663.4777221679688 0.26496580243110657 0.8695965 0.2586744725704193 False -18 52725 30.810556173324585 0.5425190925598145 511.4452819824219 0.18547019362449646 663.7454223632812 0.26479247212409973 0.86769557 0.2637225389480591 False -19 55500 30.707720041275024 0.5455260276794434 634.6995849609375 0.16993138194084167 665.05810546875 0.26279282569885254 0.86556727 0.2672511637210846 False diff --git a/ENCSR736VVP/cherimoya.fold_4.performance.tsv b/ENCSR736VVP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d61357fe9a2cfbe477bdbf58ba4cfb587294263f..0000000000000000000000000000000000000000 --- a/ENCSR736VVP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -662.51220703125 0.44322749972343445 0.2679905295372009 0.12730897963047028 0.8708434700965881 0.8359374403953552 0.25507408380508423 \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_0.evaluate.json b/ENCSR739VKY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9c062dd4d41f7b1c656f0c32cb963b702cd82b2c..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184IUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_0.fit.json b/ENCSR739VKY/cherimoya.fold_0.fit.json deleted file mode 100644 index 5f446befb658395226bf76b8bd46ded51d24a180..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF184IUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_0.log b/ENCSR739VKY/cherimoya.fold_0.log deleted file mode 100644 index 7b8229c10a0aec3d3abd62e0df63878e35491d9c..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2437 31.992944717407227 3.376889705657959 468.6841735839844 0.516266405582428 651.998046875 0.16438880562782288 0.596573 6.82300329208374 True -1 4874 26.784903049468994 0.5567100048065186 549.4370727539062 0.894121527671814 594.1929321289062 0.221654012799263 0.7138569 2.2918877601623535 True -2 7311 26.78429365158081 0.5977911949157715 444.0276184082031 0.38556110858917236 586.3627319335938 0.22726385295391083 0.7184326 1.5708746910095215 True -3 9748 26.89116621017456 0.5177140235900879 470.17388916015625 0.41141730546951294 568.6345825195312 0.2404748946428299 0.73333263 1.167165994644165 True -4 12185 26.583978414535522 0.5257539749145508 567.3845825195312 0.5329872369766235 561.871826171875 0.24652865529060364 0.759599 0.8242607712745667 True -5 14622 26.329254388809204 0.5094997882843018 541.5789184570312 0.41736462712287903 557.4253540039062 0.24909661710262299 0.7684806 0.7695348262786865 True -6 17059 26.221302032470703 0.6915826797485352 435.9735412597656 0.3835600018501282 554.6455078125 0.25162461400032043 0.7799836 0.6965458393096924 True -7 19496 26.22460103034973 5.3682661056518555 510.637451171875 0.5737533569335938 551.9850463867188 0.2544845938682556 0.7862476 0.6566483378410339 True -8 21933 26.260226726531982 0.4907548427581787 497.7398681640625 0.4734064042568207 549.5315551757812 0.25683796405792236 0.7926587 0.611244797706604 True -9 24370 26.305615186691284 0.4977564811706543 504.47161865234375 0.2615569829940796 546.3955078125 0.2595090866088867 0.80017215 0.5676310062408447 True -10 26807 26.30417823791504 0.49332165718078613 513.8797607421875 0.25333523750305176 544.1795043945312 0.26135921478271484 0.8090166 0.5092498660087585 True -11 29244 26.296521425247192 0.48032569885253906 575.90283203125 0.5416545867919922 542.3413696289062 0.26365309953689575 0.817051 0.47367674112319946 True -12 31681 26.304895639419556 0.47923827171325684 348.407470703125 0.3883328139781952 538.49853515625 0.2674632668495178 0.8239003 0.4354591965675354 True -13 34118 26.312158346176147 1.132619857788086 499.7752990722656 0.35875123739242554 539.1737060546875 0.264805406332016 0.8314981 0.40317052602767944 True -14 36555 26.3003990650177 0.48770952224731445 560.0151977539062 0.27665287256240845 537.4368896484375 0.26677727699279785 0.837803 0.3841027021408081 True -15 38992 26.296998262405396 0.5037741661071777 533.6460571289062 0.18652142584323883 535.9635620117188 0.2675001621246338 0.8422136 0.3633597195148468 True -16 41429 26.246705770492554 0.5003199577331543 496.79736328125 0.30486321449279785 535.6513671875 0.26714852452278137 0.8463081 0.345999538898468 True -17 43866 26.269690990447998 0.5058825016021729 506.58673095703125 0.2398136407136917 535.5514526367188 0.26772525906562805 0.84477735 0.34354040026664734 False -18 46303 26.261598587036133 0.4856855869293213 460.9150695800781 0.16296795010566711 536.1837158203125 0.2671591639518738 0.8439206 0.3460879325866699 False -19 48740 26.29695749282837 0.5474107265472412 435.02801513671875 0.2673264145851135 537.640380859375 0.2647669315338135 0.84262115 0.3485119640827179 False diff --git a/ENCSR739VKY/cherimoya.fold_0.performance.tsv b/ENCSR739VKY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ed7248286381d16bc2fcd353b2ffdd6ff861e241..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -535.6513671875 0.4639776647090912 0.26714852452278137 0.111257404088974 0.8463081121444702 0.783746063709259 0.345999538898468 \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_1.evaluate.json b/ENCSR739VKY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a27306e35da2d6db33ceb7b4476ec00219ffbc02..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184IUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_1.fit.json b/ENCSR739VKY/cherimoya.fold_1.fit.json deleted file mode 100644 index 3965c886338adaf196b8fa9c2eafe68e83b4e794..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF184IUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_1.log b/ENCSR739VKY/cherimoya.fold_1.log deleted file mode 100644 index 2c1819b2945c6331b2567ea73b7811a9fb1cb5ff..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2384 31.113425493240356 3.7404983043670654 483.4947509765625 0.593860387802124 771.0919799804688 0.17698915302753448 0.5931406 8.103768348693848 True -1 4768 26.232306480407715 0.713226318359375 443.88427734375 0.2918283939361572 695.5498046875 0.24419823288917542 0.7268555 3.38311767578125 True -2 7152 26.487794876098633 0.6984124183654785 398.999267578125 0.2537820637226105 683.4937744140625 0.25316494703292847 0.73922384 1.8479357957839966 True -3 9536 26.179990530014038 0.6895115375518799 550.559814453125 0.5556201934814453 664.1658935546875 0.26696300506591797 0.7726932 1.3650612831115723 True -4 11920 25.728018283843994 0.6807219982147217 420.59454345703125 0.47073590755462646 655.349365234375 0.2704460322856903 0.78265685 0.8954821825027466 True -5 14304 25.805572509765625 0.6587262153625488 403.91412353515625 0.3123016953468323 649.38818359375 0.2740722894668579 0.7894878 0.7740545868873596 True -6 16688 25.70109510421753 0.655526876449585 561.302978515625 0.3833235204219818 646.7136840820312 0.2769615948200226 0.79867846 0.7003862857818604 True -7 19072 25.650668382644653 1.2950098514556885 540.2972412109375 0.37988799810409546 641.3702392578125 0.28230464458465576 0.80632883 0.6616351008415222 True -8 21456 25.63692307472229 0.6523559093475342 349.8009033203125 0.27409568428993225 640.76611328125 0.2821832001209259 0.81399685 0.5971886515617371 True -9 23840 25.6441969871521 0.6669449806213379 565.2589721679688 0.3110184073448181 634.8623046875 0.28836214542388916 0.8209075 0.5589489936828613 True -10 26224 25.664742708206177 0.6479244232177734 422.08355712890625 0.24840141832828522 632.98291015625 0.28958621621131897 0.82544994 0.5436826348304749 True -11 28608 26.17435121536255 0.6836225986480713 316.9645080566406 0.46611839532852173 630.7559814453125 0.29150083661079407 0.83090043 0.5236434936523438 True -12 30992 25.698848009109497 0.6482186317443848 478.1051025390625 0.44574281573295593 629.2635498046875 0.2921796441078186 0.8361665 0.4794697165489197 True -13 33376 25.669533491134644 15.562501668930054 476.0074462890625 0.26659587025642395 624.6301879882812 0.2959407567977905 0.8431789 0.4602280855178833 True -14 35760 25.735059022903442 0.6620149612426758 421.8069763183594 0.25067397952079773 624.681396484375 0.2948114573955536 0.8502537 0.43706580996513367 True -15 38144 25.764164686203003 0.660015344619751 371.0038757324219 0.22112347185611725 623.66455078125 0.2950451374053955 0.8541308 0.4082076847553253 True -16 40528 25.686790466308594 0.6642012596130371 458.79345703125 0.19966407120227814 620.9891967773438 0.29725077748298645 0.8584244 0.3950408101081848 True -17 42912 25.63424015045166 1.0718472003936768 428.4757385253906 0.16971126198768616 620.7754516601562 0.29692986607551575 0.8592833 0.3826291561126709 True -18 45296 25.626279830932617 1.0059304237365723 476.8889465332031 0.24822065234184265 622.6351318359375 0.2950732409954071 0.8593768 0.3794401288032532 True -19 47680 25.653409957885742 0.6681039333343506 383.8765869140625 0.22442185878753662 623.5014038085938 0.29420462250709534 0.8575097 0.38318416476249695 False diff --git a/ENCSR739VKY/cherimoya.fold_1.performance.tsv b/ENCSR739VKY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 97353865d0c73393f6d6624c02ce9f8aa8950eb7..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -622.6351318359375 0.44041693210601807 0.2950732707977295 0.1304491013288498 0.8593767881393433 0.8235106468200684 0.3794401288032532 \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_2.evaluate.json b/ENCSR739VKY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8eceb74f523b6a08dca8b84583f83e4f44ea9311..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184IUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_2.fit.json b/ENCSR739VKY/cherimoya.fold_2.fit.json deleted file mode 100644 index ad2f18458a0420507fcbf2d2478eca6a8cc962a3..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF184IUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_2.log b/ENCSR739VKY/cherimoya.fold_2.log deleted file mode 100644 index b21160baf3b6aa33c20f037757e2ea87705ecafd..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2561 32.51621699333191 4.488485097885132 521.563720703125 0.6409772634506226 671.67236328125 0.16557183861732483 0.57633555 7.033411502838135 True -1 5122 28.10950803756714 0.7080364227294922 432.7205810546875 0.7129620313644409 611.1271362304688 0.22851507365703583 0.7031088 1.988281488418579 True -2 7683 28.15487813949585 0.6088888645172119 446.50994873046875 0.4034450948238373 594.5736083984375 0.2356002926826477 0.73199475 1.1548731327056885 True -3 10244 28.072274684906006 0.5484070777893066 442.1680908203125 0.5091971755027771 583.6168823242188 0.2423562854528427 0.7501878 0.9341686367988586 True -4 12805 27.597967863082886 0.5346627235412598 445.0146789550781 0.4156608581542969 573.9705200195312 0.25153693556785583 0.7652058 0.6997344493865967 True -5 15366 27.65388536453247 1.2685818672180176 520.998779296875 0.7997772693634033 573.61865234375 0.24947620928287506 0.7670164 0.6642453670501709 True -6 17927 27.529500484466553 0.5321793556213379 443.72430419921875 0.5545709133148193 570.9602661132812 0.2526017129421234 0.77174735 0.6378443837165833 True -7 20488 27.52776336669922 0.5294044017791748 447.6865539550781 0.3019034266471863 567.9880981445312 0.2555128037929535 0.7758634 0.6156743764877319 True -8 23049 27.535079956054688 0.5302813053131104 376.2650146484375 0.28535526990890503 565.6237182617188 0.25692397356033325 0.7799923 0.5717479586601257 True -9 25610 27.547521591186523 0.5289063453674316 503.6536560058594 0.37360328435897827 563.1063232421875 0.2590298056602478 0.78876346 0.5252821445465088 True -10 28171 27.57232165336609 0.5243444442749023 416.0562438964844 0.33390945196151733 560.9723510742188 0.26251834630966187 0.7962763 0.513203501701355 True -11 30732 27.76658010482788 0.5419447422027588 434.0340576171875 0.4934048652648926 557.273193359375 0.26548731327056885 0.80541515 0.4781233072280884 True -12 33293 27.66162657737732 0.5554080009460449 468.5451965332031 0.37344229221343994 554.6456298828125 0.2671307325363159 0.8102239 0.451883465051651 True -13 35854 27.66844415664673 0.5368034839630127 450.39666748046875 0.45358195900917053 552.209228515625 0.2682972252368927 0.81967556 0.4219169616699219 True -14 38415 27.671292066574097 1.4021689891815186 460.9068298339844 0.30422526597976685 550.81201171875 0.2689903974533081 0.8299476 0.39220094680786133 True -15 40976 27.64054560661316 0.744877815246582 443.1937255859375 0.13033710420131683 548.6446533203125 0.2713383436203003 0.83504623 0.37190577387809753 True -16 43537 27.611902236938477 0.5391125679016113 451.0055847167969 0.31999439001083374 547.3311157226562 0.27191123366355896 0.8380056 0.3611738085746765 True -17 46098 27.61232876777649 0.5385963916778564 359.87762451171875 0.3693709969520569 547.8125610351562 0.271588534116745 0.83788574 0.3544849753379822 False -18 48659 27.682522296905518 0.5417780876159668 423.5426330566406 0.28592997789382935 547.1267700195312 0.27236446738243103 0.8371426 0.3559287190437317 False -19 51220 27.645405292510986 0.5418491363525391 512.381103515625 0.2168923318386078 547.9240112304688 0.2711322605609894 0.83526164 0.3593003451824188 False diff --git a/ENCSR739VKY/cherimoya.fold_2.performance.tsv b/ENCSR739VKY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 514db81ea916f189e47bb34f5459779a6c276777..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -547.3311157226562 0.45961910486221313 0.27191123366355896 0.11378328502178192 0.8380056023597717 0.7882795333862305 0.3611738085746765 \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_3.evaluate.json b/ENCSR739VKY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f5ba95694c5464479dbfee3740878e132e9e0bb5..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184IUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_3.fit.json b/ENCSR739VKY/cherimoya.fold_3.fit.json deleted file mode 100644 index fffefd9f0f6447388006cea411a21b583e7b9507..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF184IUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_3.log b/ENCSR739VKY/cherimoya.fold_3.log deleted file mode 100644 index b3f87945af614b6d84bd1a47280151857120f0ea..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2454 31.541325569152832 3.3618619441986084 444.1466979980469 0.5222883224487305 704.7194213867188 0.176273912191391 0.54333806 7.746291637420654 True -1 4908 27.638944625854492 0.6965241432189941 551.0712890625 0.4770689308643341 646.4453125 0.23684734106063843 0.6642687 2.1902098655700684 True -2 7362 26.994548320770264 0.5112807750701904 455.22076416015625 0.4893251061439514 638.5836181640625 0.23836465179920197 0.6777806 1.9038666486740112 True -3 9816 26.955248832702637 0.4609489440917969 460.026123046875 0.6609812378883362 624.346923828125 0.25011879205703735 0.6821842 1.445490837097168 True -4 12270 26.933168172836304 0.5142674446105957 457.5706787109375 0.7006646394729614 617.9498901367188 0.2554793357849121 0.7050232 1.2522956132888794 True -5 14724 26.880815982818604 0.4927561283111572 599.3038940429688 0.5290123224258423 609.3225708007812 0.26433610916137695 0.7222362 1.173582673072815 True -6 17178 26.502444744110107 0.44711995124816895 486.49688720703125 0.47164633870124817 605.8192138671875 0.26669684052467346 0.73394614 1.0492446422576904 True -7 19632 26.412322282791138 2.055540084838867 484.7665100097656 0.3624446392059326 601.5926513671875 0.2719199061393738 0.7438421 1.02189302444458 True -8 22086 26.494882106781006 0.47263574600219727 464.53570556640625 0.5930554866790771 600.3021240234375 0.2730724811553955 0.75333095 0.8892537951469421 True -9 24540 26.363118410110474 0.47246861457824707 441.96807861328125 0.3274957537651062 597.0556030273438 0.27684617042541504 0.7622799 0.8491433262825012 True -10 26994 26.423187017440796 0.4716470241546631 471.4527587890625 0.48663461208343506 594.4439086914062 0.2789078652858734 0.7688351 0.7482150197029114 True -11 29448 26.40275502204895 0.4721996784210205 578.0740966796875 0.571129560470581 591.47021484375 0.2821614146232605 0.7788291 0.6781521439552307 True -12 31902 26.397709846496582 0.4634225368499756 528.722900390625 0.38783901929855347 589.5223999023438 0.2838432490825653 0.78466296 0.634402871131897 True -13 34356 26.40837264060974 0.47173118591308594 439.60125732421875 0.33153843879699707 588.2680053710938 0.28348228335380554 0.79731476 0.5670668482780457 True -14 36810 26.772884130477905 0.4554867744445801 378.0602722167969 0.29236629605293274 583.9398803710938 0.2874298095703125 0.8080287 0.5176640748977661 True -15 39264 26.461016416549683 0.46051549911499023 420.1003723144531 0.4333359897136688 582.9392700195312 0.28790581226348877 0.81407195 0.48742467164993286 True -16 41718 26.454416751861572 0.46725940704345703 471.97821044921875 0.4079679548740387 582.202880859375 0.2884138822555542 0.8198306 0.4629081189632416 True -17 44172 26.43092107772827 0.462662935256958 438.4557189941406 0.2240346372127533 581.5682983398438 0.2880827486515045 0.823473 0.4473641812801361 True -18 46626 26.426010847091675 0.46831250190734863 501.9230651855469 0.1757798045873642 581.5988159179688 0.28823044896125793 0.821466 0.44713732600212097 False -19 49080 26.421492099761963 0.46816444396972656 387.3496398925781 0.28201887011528015 581.9230346679688 0.2876097559928894 0.81932646 0.44900283217430115 False diff --git a/ENCSR739VKY/cherimoya.fold_3.performance.tsv b/ENCSR739VKY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index df51dc6da8691152c4a02e2543c54972fa263880..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -581.5682983398438 0.4492966830730438 0.2880827486515045 0.12044812738895416 0.8234729766845703 0.775993287563324 0.4473641812801361 \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_4.evaluate.json b/ENCSR739VKY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 379df558566ed2ee92448ad0ff787ea11737c039..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184IUE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_4.fit.json b/ENCSR739VKY/cherimoya.fold_4.fit.json deleted file mode 100644 index 3bd40c6c7510860f18eebe87cb5b7e7ed097234a..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF184IUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR739VKY/cherimoya.fold_4.log b/ENCSR739VKY/cherimoya.fold_4.log deleted file mode 100644 index 4bd52238af53d2e825a35f6ccf98ac9b2025341f..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2431 31.322114944458008 3.798171281814575 458.650390625 0.6542477607727051 613.172607421875 0.1602017730474472 0.5502581 6.478008270263672 True -1 4862 26.69089102745056 0.5437772274017334 452.0215148925781 0.26707351207733154 566.7164306640625 0.2161874920129776 0.66148543 1.907891869544983 True -2 7293 26.713749647140503 0.5211317539215088 394.109130859375 0.3447217345237732 555.7908325195312 0.2250436693429947 0.66972756 1.4077101945877075 True -3 9724 26.78029155731201 0.5028948783874512 583.7427978515625 0.6886224746704102 546.10791015625 0.22848184406757355 0.70615995 0.8462411165237427 True -4 12155 26.697250604629517 0.47015881538391113 487.8760986328125 0.6455181241035461 539.7467041015625 0.23488521575927734 0.70900065 0.8025209307670593 True -5 14586 26.665432929992676 0.5407764911651611 551.4689331054688 0.6005953550338745 535.6129150390625 0.2391446828842163 0.71906835 0.7660618424415588 True -6 17017 26.65527081489563 0.4798316955566406 526.2611083984375 0.417439341545105 532.0794677734375 0.24145080149173737 0.73762596 0.6891527771949768 True -7 19448 26.674588918685913 0.48645877838134766 473.62860107421875 0.7135546207427979 528.7655639648438 0.2468017190694809 0.7451208 0.6309368014335632 True -8 21879 26.647439002990723 1.1827516555786133 531.1574096679688 0.3618721067905426 526.8853759765625 0.24807685613632202 0.75118124 0.5761864185333252 True -9 24310 26.657068490982056 0.47895050048828125 577.1194458007812 0.35941168665885925 523.7453002929688 0.2509814202785492 0.7590313 0.5476732850074768 True -10 26741 26.189467906951904 0.45839476585388184 430.44158935546875 0.39202749729156494 521.7277221679688 0.25349941849708557 0.7691906 0.5165026783943176 True -11 29172 26.176815509796143 0.46936941146850586 345.5418701171875 0.3119058907032013 519.2704467773438 0.2554408609867096 0.78180057 0.4688515365123749 True -12 31603 26.171295166015625 0.4585762023925781 485.39453125 0.48817357420921326 517.9342041015625 0.2567724883556366 0.78515446 0.45987173914909363 True -13 34034 26.15305256843567 0.4639115333557129 452.9862976074219 0.3599786162376404 515.5325317382812 0.25873205065727234 0.7986181 0.4219839572906494 True -14 36465 26.162955045700073 0.452770471572876 485.7242736816406 0.3007350564002991 514.4119873046875 0.2591257691383362 0.80607647 0.407122403383255 True -15 38896 26.159799098968506 0.4524214267730713 480.7828369140625 0.2949927747249603 513.477783203125 0.2603307366371155 0.81320435 0.3849295675754547 True -16 41327 26.16472887992859 0.46416568756103516 541.6297607421875 0.32711705565452576 515.4051513671875 0.25661513209342957 0.819416 0.37151673436164856 True -17 43758 26.14096474647522 0.45676159858703613 488.517822265625 0.29609501361846924 512.6765747070312 0.2601191997528076 0.8188675 0.36871108412742615 False -18 46189 26.160709857940674 0.48513174057006836 468.341552734375 0.2025260329246521 512.1533813476562 0.26121020317077637 0.81915677 0.36855801939964294 False -19 48620 26.194442987442017 0.4666929244995117 437.53369140625 0.18429604172706604 513.014892578125 0.2592753469944 0.81790864 0.3703243136405945 False diff --git a/ENCSR739VKY/cherimoya.fold_4.performance.tsv b/ENCSR739VKY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a962eddd61040c5341b7464b42b483b1fd2835a3..0000000000000000000000000000000000000000 --- a/ENCSR739VKY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -515.4051513671875 0.4708074927330017 0.25661516189575195 0.10307390242815018 0.8194159865379333 0.7686309814453125 0.37151673436164856 \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_0.evaluate.json b/ENCSR742HBK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 26b45aec2db7d44f6e82a41a4140cc0d9c20db5f..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416HCA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_0.fit.json b/ENCSR742HBK/cherimoya.fold_0.fit.json deleted file mode 100644 index a2f595f257d0128d3c760566982a5660bb0b7483..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF416HCA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_0.log b/ENCSR742HBK/cherimoya.fold_0.log deleted file mode 100644 index fe079b76bc7889e2025420d5bcc5f24f016f0ad1..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 34.17111396789551 3.712496519088745 1045.690185546875 0.6424422264099121 1291.0927734375 0.3266899883747101 0.7028148 7.973607063293457 True -1 5480 30.359475135803223 0.5926206111907959 1077.6593017578125 0.6098622679710388 1093.2366943359375 0.4167390465736389 0.76657295 2.3649368286132812 True -2 8220 30.338606119155884 0.5845448970794678 896.3764038085938 0.6002443432807922 1076.1181640625 0.42623457312583923 0.77156144 1.565040111541748 True -3 10960 30.32271695137024 0.5837364196777344 705.2987670898438 0.4314371347427368 1048.5333251953125 0.43857046961784363 0.78585213 1.0305554866790771 True -4 13700 30.129927158355713 0.5765557289123535 873.8626708984375 0.4947253465652466 1036.12451171875 0.447473406791687 0.78367686 0.9064722061157227 False -5 16440 29.566327571868896 0.570976734161377 984.3137817382812 0.6022777557373047 1032.4429931640625 0.4469352066516876 0.789502 0.7554143071174622 True -6 19180 29.616964101791382 2.4707939624786377 859.3287963867188 0.4417792856693268 1023.59619140625 0.4531805217266083 0.79043424 0.7224670052528381 True -7 21920 29.713306427001953 0.5760986804962158 928.619873046875 0.5333530902862549 1017.1878662109375 0.4556674063205719 0.79737836 0.5823518633842468 True -8 24660 29.588247537612915 0.57773756980896 838.790283203125 0.38519716262817383 1012.1798095703125 0.4595295488834381 0.80299014 0.5338611602783203 True -9 27400 29.651358127593994 0.5905797481536865 887.6015625 0.6386189460754395 1008.490966796875 0.4604853689670563 0.8074859 0.4998670220375061 True -10 30140 29.74623394012451 0.5704925060272217 862.7330932617188 0.5154765248298645 999.435546875 0.4665864408016205 0.8110859 0.47455257177352905 True -11 32880 29.72505283355713 17.833866119384766 873.5358276367188 0.29977643489837646 993.3871459960938 0.470106303691864 0.8138111 0.45416125655174255 True -12 35620 29.64947247505188 0.598285436630249 807.00537109375 0.3343883156776428 985.0037231445312 0.4759312570095062 0.8198037 0.42164722084999084 True -13 38360 29.773690223693848 0.5828847885131836 940.2705078125 0.4209896922111511 980.7313842773438 0.4765268564224243 0.82431185 0.3847808241844177 True -14 41100 29.613890647888184 0.5605387687683105 769.297607421875 0.341852068901062 977.2865600585938 0.4782565236091614 0.8281939 0.3665328025817871 True -15 43840 29.57461977005005 0.5656411647796631 810.5064697265625 0.273458868265152 971.919677734375 0.4821646809577942 0.83374727 0.3505266606807709 True -16 46580 29.601139307022095 0.5664839744567871 873.9696044921875 0.3556596636772156 969.891845703125 0.4835279583930969 0.83610934 0.33755162358283997 True -17 49320 29.674952745437622 0.5729525089263916 863.9688720703125 0.4095113277435303 973.3235473632812 0.4801720082759857 0.83669126 0.3296941816806793 True -18 52060 29.625863075256348 0.5704605579376221 829.4762573242188 0.4087578058242798 971.7060546875 0.48325803875923157 0.8368703 0.32792040705680847 True -19 54800 29.619397163391113 0.5741631984710693 778.9132690429688 0.2768213152885437 971.2140502929688 0.4833703935146332 0.8365224 0.3288557231426239 False diff --git a/ENCSR742HBK/cherimoya.fold_0.performance.tsv b/ENCSR742HBK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fde59b725838c1bc7b4007e30055ab4be8714bd3..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -971.7060546875 0.30848386883735657 0.4832580089569092 0.2389221042394638 0.8368703126907349 0.783991277217865 0.32792040705680847 \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_1.evaluate.json b/ENCSR742HBK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0bfbe45184c614cd4c1695f589fc8da88e29488e..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416HCA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_1.fit.json b/ENCSR742HBK/cherimoya.fold_1.fit.json deleted file mode 100644 index 72850f6346f73302f63af134c8d102d0b84e93d7..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF416HCA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_1.log b/ENCSR742HBK/cherimoya.fold_1.log deleted file mode 100644 index 4882b79f2b6f5c30699bac831cac49db7f7799c9..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2707 33.82613253593445 3.5729007720947266 1056.02197265625 0.579395055770874 1576.6329345703125 0.3197875916957855 0.68611836 9.01082992553711 True -1 5414 29.888683080673218 0.7004880905151367 954.4912109375 0.6545566320419312 1327.30126953125 0.4238656163215637 0.7568557 2.605966091156006 True -2 8121 29.90023422241211 0.6842663288116455 767.0827026367188 0.6541060209274292 1285.5220947265625 0.440717875957489 0.7645679 1.3921486139297485 True -3 10828 29.944329023361206 0.6879401206970215 1077.71923828125 0.5062311887741089 1254.7508544921875 0.4498051106929779 0.77088344 1.0375618934631348 True -4 13535 29.859870433807373 0.6741533279418945 844.3787841796875 0.5386178493499756 1225.0107421875 0.459264874458313 0.78422123 0.80229252576828 True -5 16242 29.81966805458069 0.6800327301025391 874.6739501953125 0.6268943548202515 1216.3514404296875 0.46056732535362244 0.7912808 0.7400643229484558 True -6 18949 29.791133403778076 0.6714541912078857 763.6419677734375 0.35905569791793823 1199.40380859375 0.4679074287414551 0.7993571 0.6306275725364685 True -7 21656 29.720701456069946 0.6646773815155029 679.5279541015625 0.655042827129364 1192.8056640625 0.4704161286354065 0.80349654 0.5909281373023987 True -8 24363 29.237526655197144 0.6731388568878174 796.5803833007812 0.3939972221851349 1179.49560546875 0.47650039196014404 0.80996054 0.5872198343276978 True -9 27070 29.18370485305786 0.6738345623016357 812.4520263671875 0.5640228986740112 1170.2796630859375 0.4818364381790161 0.8117546 0.5526720285415649 True -10 29777 29.230660915374756 0.6717753410339355 768.1099853515625 0.45431292057037354 1165.4432373046875 0.4835948944091797 0.8178823 0.516571581363678 True -11 32484 29.190157651901245 0.773850679397583 953.5208740234375 0.4575345516204834 1153.6129150390625 0.4904947876930237 0.8204627 0.4952739477157593 True -12 35191 29.248116493225098 0.6764135360717773 842.3018798828125 0.2941953241825104 1146.47998046875 0.4924607574939728 0.8285838 0.4720850884914398 True -13 37898 29.30589985847473 24.766245365142822 777.1927490234375 0.43646955490112305 1140.1798095703125 0.49474453926086426 0.83328426 0.43329155445098877 True -14 40605 29.342223405838013 0.676184892654419 692.1801147460938 0.37804341316223145 1132.3975830078125 0.4983077347278595 0.8367759 0.4125986099243164 True -15 43312 29.41081714630127 0.6794285774230957 1021.1244506835938 0.29577139019966125 1128.004638671875 0.4998699426651001 0.84203905 0.39091503620147705 True -16 46019 29.259305477142334 0.8275101184844971 811.7281494140625 0.377749502658844 1124.1673583984375 0.5011776089668274 0.84496313 0.3762822151184082 True -17 48726 29.327935934066772 0.6731553077697754 1048.67529296875 0.24448849260807037 1123.108642578125 0.5020194053649902 0.84788716 0.3697575628757477 True -18 51433 29.291937112808228 0.6794886589050293 963.9137573242188 0.24368000030517578 1123.888427734375 0.5009323954582214 0.8461823 0.36704254150390625 False -19 54140 29.28916645050049 0.6629056930541992 890.21484375 0.366704523563385 1126.9630126953125 0.49886956810951233 0.8455356 0.3677537441253662 False diff --git a/ENCSR742HBK/cherimoya.fold_1.performance.tsv b/ENCSR742HBK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3b0c5d90e344a5fdb80b6df024b5b3d84cf0d9f8..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1123.108642578125 0.2914131283760071 0.5020193457603455 0.26621711254119873 0.8478871583938599 0.8151562809944153 0.3697575628757477 \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_2.evaluate.json b/ENCSR742HBK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0d7638113a5621dc424a329e6788135f23ecf197..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416HCA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_2.fit.json b/ENCSR742HBK/cherimoya.fold_2.fit.json deleted file mode 100644 index b987abfb9eac946d0075a164411c814c00ad2a6f..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF416HCA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_2.log b/ENCSR742HBK/cherimoya.fold_2.log deleted file mode 100644 index e642e75d0805ad451b8e40370f361a0c74efd202..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 35.737640142440796 3.592592477798462 955.7492065429688 0.6463143825531006 1345.308349609375 0.32679158449172974 0.69893795 8.040590286254883 True -1 5740 31.837007999420166 10.341550588607788 930.3065795898438 0.34458860754966736 1131.526611328125 0.42219868302345276 0.764899 2.743574857711792 True -2 8610 31.67046046257019 0.5880722999572754 911.9061889648438 0.37592658400535583 1113.463134765625 0.43156200647354126 0.77029914 1.2761776447296143 True -3 11480 31.648891925811768 0.5739235877990723 804.21533203125 0.4341357350349426 1096.17041015625 0.4369916021823883 0.7741467 1.046043872833252 True -4 14350 31.699098348617554 0.573195219039917 924.18896484375 0.6933173537254333 1070.8134765625 0.4472827613353729 0.7859835 0.866776704788208 True -5 17220 31.647433042526245 0.5696594715118408 916.0570068359375 0.5288931131362915 1064.9586181640625 0.45063602924346924 0.7895508 0.7735575437545776 True -6 20090 31.63757848739624 0.5819568634033203 925.84033203125 0.45109879970550537 1050.0189208984375 0.45713016390800476 0.7981972 0.6806309819221497 True -7 22960 31.703726768493652 0.5781493186950684 854.7334594726562 0.6693830490112305 1044.00830078125 0.46027877926826477 0.8030932 0.5955829620361328 True -8 25830 31.69752025604248 0.5725114345550537 773.7769775390625 0.43444347381591797 1040.5635986328125 0.4622988700866699 0.8072061 0.5673819780349731 True -9 28700 31.67223310470581 0.5727269649505615 777.0969848632812 0.39883172512054443 1030.6025390625 0.4675835967063904 0.80993056 0.5403614640235901 True -10 31570 31.68760108947754 0.5631914138793945 723.7077026367188 0.2851922810077667 1027.849853515625 0.4694581925868988 0.81566775 0.514407753944397 True -11 34440 31.15970492362976 0.564079761505127 902.6876220703125 0.4540591835975647 1018.777099609375 0.4745771288871765 0.8173576 0.4693310260772705 True -12 37310 31.020021677017212 0.5593652725219727 794.3097534179688 0.24769194424152374 1013.5288696289062 0.47759753465652466 0.82227045 0.4184640645980835 True -13 40180 31.036674976348877 0.5574119091033936 794.749755859375 0.30413931608200073 1007.289306640625 0.4809449017047882 0.8248037 0.38772910833358765 True -14 43050 31.024983644485474 0.5667257308959961 851.95947265625 0.2691018581390381 1003.2472534179688 0.48224127292633057 0.82930356 0.36597228050231934 True -15 45920 31.084084510803223 0.5715487003326416 823.3282470703125 0.37818747758865356 1003.975341796875 0.48107588291168213 0.8335963 0.35355570912361145 True -16 48790 31.029762983322144 0.566795825958252 936.719970703125 0.18285273015499115 1000.6869506835938 0.48530086874961853 0.834625 0.3439653813838959 True -17 51660 31.113130569458008 0.5659546852111816 815.2377319335938 0.31359630823135376 997.5355834960938 0.48809555172920227 0.8375054 0.3397933840751648 True -18 54530 31.03700566291809 24.388129234313965 680.584228515625 0.24925820529460907 998.6469116210938 0.48702988028526306 0.8358893 0.340051531791687 False -19 57400 31.61655831336975 0.5673696994781494 801.6982421875 0.26905205845832825 997.4312744140625 0.4879935681819916 0.8367554 0.34114590287208557 False diff --git a/ENCSR742HBK/cherimoya.fold_2.performance.tsv b/ENCSR742HBK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 59b6b1a5ac15b51f77d2ea874b15f317709b1af9..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -997.5355834960938 0.3046865463256836 0.48809561133384705 0.2429393231868744 0.8375054001808167 0.7927830219268799 0.3397933840751648 \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_3.evaluate.json b/ENCSR742HBK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 31bb8e1b83474f278292e2b66c52ddacabf1a7b1..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416HCA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_3.fit.json b/ENCSR742HBK/cherimoya.fold_3.fit.json deleted file mode 100644 index 7628c79a482648308dc1a4b874b94de00c4e7535..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF416HCA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_3.log b/ENCSR742HBK/cherimoya.fold_3.log deleted file mode 100644 index b45bc48b34cf20befeaea582702edd01a9012276..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.23122954368591 2.739816904067993 1189.1448974609375 0.7250208854675293 1285.459228515625 0.33283451199531555 0.699718 8.06161117553711 True -1 5494 30.403968572616577 0.5002927780151367 1052.9189453125 0.6926443576812744 1081.244384765625 0.426129013299942 0.7799685 2.421548843383789 True -2 8241 30.278537273406982 0.4890766143798828 949.0387573242188 0.4435095191001892 1059.4268798828125 0.43779218196868896 0.78452015 1.613042950630188 True -3 10988 30.288525342941284 0.48917412757873535 980.987060546875 0.4841078519821167 1040.4190673828125 0.44776591658592224 0.7899672 1.2478281259536743 True -4 13735 30.278578519821167 0.4841153621673584 938.5650634765625 0.5378681421279907 1025.9007568359375 0.45672908425331116 0.79137903 1.141675591468811 True -5 16482 30.281359910964966 0.4908730983734131 859.109619140625 0.4066670835018158 1021.975341796875 0.4551889896392822 0.7943242 0.8938553333282471 True -6 19229 30.304425716400146 0.4846208095550537 954.1451416015625 0.521001935005188 1008.8759765625 0.46406152844429016 0.7969229 0.7603777050971985 True -7 21976 30.328662633895874 0.49329400062561035 876.5580444335938 0.328782320022583 1006.859619140625 0.464199036359787 0.79851794 0.6505919694900513 True -8 24723 30.276947021484375 0.488311767578125 894.71435546875 0.48948293924331665 998.4430541992188 0.46848955750465393 0.8035066 0.6650906205177307 True -9 27470 30.323589086532593 0.4938316345214844 770.7227783203125 0.3747440576553345 994.5455932617188 0.4701286554336548 0.80496246 0.5710609555244446 True -10 30217 30.283486127853394 0.4980459213256836 726.6862182617188 0.53118497133255 987.9102172851562 0.4733717441558838 0.81022274 0.538372814655304 True -11 32964 30.043537139892578 2.9429359436035156 925.884765625 0.37685516476631165 982.3292846679688 0.4762783944606781 0.8183998 0.5004604458808899 True -12 35711 29.688538312911987 0.49187493324279785 952.1029052734375 0.4823916256427765 974.972412109375 0.47988590598106384 0.82195586 0.46942806243896484 True -13 38458 29.724977016448975 0.490511417388916 846.1015014648438 0.26653870940208435 970.236572265625 0.48169761896133423 0.8285614 0.43172183632850647 True -14 41205 29.70053195953369 0.501046895980835 889.7625732421875 0.44252511858940125 961.3348999023438 0.4868329167366028 0.83436406 0.4025755524635315 True -15 43952 29.84033751487732 0.4930422306060791 977.9385986328125 0.2853545546531677 960.9864501953125 0.48642781376838684 0.83900833 0.3745266795158386 True -16 46699 29.714016675949097 0.5067696571350098 877.7908935546875 0.26203474402427673 955.5847778320312 0.48903605341911316 0.84234834 0.35638877749443054 True -17 49446 29.71769142150879 0.5450706481933594 830.65185546875 0.2212129533290863 954.6802978515625 0.4894229769706726 0.8450576 0.34767624735832214 True -18 52193 29.725875854492188 0.49634623527526855 836.3216552734375 0.2214016616344452 956.8136596679688 0.487216055393219 0.84470224 0.34532713890075684 False -19 54940 29.792463064193726 0.5030341148376465 947.907958984375 0.29186272621154785 958.2611694335938 0.4862035810947418 0.8444031 0.34666454792022705 False diff --git a/ENCSR742HBK/cherimoya.fold_3.performance.tsv b/ENCSR742HBK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3a0e250c09215c57f3822efc32921adeab092887..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -954.6802978515625 0.306841641664505 0.4894229471683502 0.24207566678524017 0.8450576066970825 0.7928272485733032 0.34767624735832214 \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_4.evaluate.json b/ENCSR742HBK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index aae25f372142a97cf0436f2535f90e6428a396d0..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416HCA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_4.fit.json b/ENCSR742HBK/cherimoya.fold_4.fit.json deleted file mode 100644 index 12dd31ed6f8bd6fdbf7bf206bdd33563c0979bbe..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF416HCA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR742HBK/cherimoya.fold_4.log b/ENCSR742HBK/cherimoya.fold_4.log deleted file mode 100644 index e3a7a64d5b36b32b363b9322e91aca576ae0aaaa..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2829 35.16411566734314 3.7082488536834717 738.853271484375 0.535637378692627 1228.443115234375 0.33205223083496094 0.69135725 7.098660469055176 True -1 5658 31.3295681476593 0.7096030712127686 680.1441040039062 0.411435604095459 1065.2598876953125 0.4124513566493988 0.7463464 2.103135108947754 True -2 8487 31.31159496307373 0.5773231983184814 780.5128784179688 0.41965222358703613 1040.0631103515625 0.4242974817752838 0.7521085 1.2138376235961914 True -3 11316 32.35849475860596 0.6951909065246582 966.2779541015625 0.40690597891807556 1019.067138671875 0.4332484304904938 0.7632579 0.9769358038902283 True -4 14145 31.29416060447693 22.632819890975952 745.9489135742188 0.5821247100830078 1006.2247314453125 0.438355416059494 0.77115405 1.0464767217636108 True -5 16974 31.280373334884644 10.351814270019531 744.693115234375 0.4042384922504425 994.4490356445312 0.44550880789756775 0.7768264 0.8628036975860596 True -6 19803 31.48243522644043 0.5953547954559326 810.3758544921875 0.4885513186454773 987.5835571289062 0.44830214977264404 0.7849521 0.7784857749938965 True -7 22632 31.19662308692932 0.5912222862243652 774.6341552734375 0.4153735637664795 978.2813720703125 0.4542193114757538 0.7910719 0.6736721992492676 True -8 25461 31.211856603622437 1.198854923248291 915.4485473632812 0.3685312271118164 971.3065795898438 0.4601656496524811 0.79572934 0.5760647654533386 True -9 28290 31.234371423721313 0.5795783996582031 888.6234741210938 0.36844515800476074 966.0562744140625 0.46219247579574585 0.79939073 0.5433090925216675 True -10 31119 31.17275834083557 0.5789921283721924 901.910400390625 0.5350484848022461 963.0167846679688 0.4634624719619751 0.8047354 0.5058432817459106 True -11 33948 31.057305097579956 0.5700421333312988 792.225830078125 0.3320629298686981 957.3004150390625 0.46798864006996155 0.8074867 0.489290326833725 True -12 36777 30.57318615913391 0.5633010864257812 764.28173828125 0.2960570454597473 951.76953125 0.47191497683525085 0.81065655 0.42592063546180725 True -13 39606 30.540505409240723 0.5695831775665283 729.0069580078125 0.39300069212913513 947.3195190429688 0.4739309251308441 0.8152942 0.40049654245376587 True -14 42435 30.591814041137695 0.5841152667999268 786.8751831054688 0.29896777868270874 942.8383178710938 0.4762069284915924 0.8201704 0.3707844614982605 True -15 45264 30.54869818687439 0.5787827968597412 989.0167846679688 0.43667924404144287 940.7703857421875 0.47814691066741943 0.82613903 0.35907483100891113 True -16 48093 30.64141297340393 0.5779728889465332 822.1214599609375 0.438322514295578 939.5060424804688 0.4795069694519043 0.82870495 0.3393484354019165 True -17 50922 30.574117183685303 0.5680563449859619 767.7125854492188 0.23188993334770203 939.0928955078125 0.48045963048934937 0.83117294 0.33140987157821655 True -18 53751 30.57338571548462 0.5768187046051025 812.3942260742188 0.32509467005729675 938.6053466796875 0.48012489080429077 0.83115864 0.3285420536994934 False -19 56580 30.617361545562744 0.5664253234863281 757.443115234375 0.2853902578353882 941.6481323242188 0.47798943519592285 0.8310601 0.32905760407447815 False diff --git a/ENCSR742HBK/cherimoya.fold_4.performance.tsv b/ENCSR742HBK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e5b9dfae64cc55c00c06b7d93d34224a249bef69..0000000000000000000000000000000000000000 --- a/ENCSR742HBK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -939.0928955078125 0.3100532293319702 0.48045963048934937 0.23850740492343903 0.8311729431152344 0.7787591814994812 0.33140987157821655 \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_0.evaluate.json b/ENCSR745CGG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d1d5e092a72e1e1d2c79ed4d9a01c32c39221444..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF031ANP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_0.fit.json b/ENCSR745CGG/cherimoya.fold_0.fit.json deleted file mode 100644 index 7a985e1b9c36235ab7383334b884d86d018a78d3..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF031ANP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_0.log b/ENCSR745CGG/cherimoya.fold_0.log deleted file mode 100644 index 30ae44e5f7a9d7dca7148595029610cdaef4c711..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2445 31.33204674720764 3.4537417888641357 314.0218505859375 0.37393999099731445 427.4642333984375 0.5646926760673523 0.63045526 4.574840068817139 True -1 4890 26.69994282722473 0.5330874919891357 328.91302490234375 0.32664525508880615 380.8478088378906 0.6331251859664917 0.703612 0.9611039757728577 True -2 7335 26.651769876480103 0.4957287311553955 365.9356994628906 0.29923316836357117 371.4139099121094 0.6492862701416016 0.72681946 0.4859343469142914 True -3 9780 26.787073135375977 19.47732377052307 324.1445617675781 0.2695130705833435 367.89727783203125 0.6550504565238953 0.740763 0.3774060308933258 True -4 12225 26.79852271080017 0.513216495513916 308.98114013671875 0.38420015573501587 366.95098876953125 0.6563105583190918 0.748294 0.31057968735694885 True -5 14670 26.69168496131897 0.5197107791900635 340.50604248046875 0.28232017159461975 364.9012451171875 0.6607011556625366 0.75382376 0.27673712372779846 True -6 17115 26.7834575176239 2.1902544498443604 339.6219482421875 0.20903471112251282 364.26800537109375 0.6622437834739685 0.7553575 0.27244141697883606 True -7 19560 26.675307035446167 0.5008933544158936 341.5589599609375 0.32705923914909363 363.5314636230469 0.663461446762085 0.75718015 0.26691797375679016 True -8 22005 27.658233880996704 21.486167430877686 278.1976318359375 0.30892640352249146 362.5779724121094 0.6653000712394714 0.7616666 0.2607876658439636 True -9 24450 26.72396230697632 0.5241496562957764 322.0496826171875 0.285849928855896 361.8495178222656 0.6667662262916565 0.7688596 0.24861396849155426 True -10 26895 27.850383043289185 30.243366479873657 325.9332275390625 0.28377610445022583 361.1962585449219 0.6680759191513062 0.7721275 0.24771252274513245 True -11 29340 26.942049503326416 0.5275354385375977 329.74542236328125 0.29243654012680054 360.37939453125 0.669445812702179 0.78030735 0.23398615419864655 True -12 31785 26.6857168674469 0.5094139575958252 293.26629638671875 0.270717978477478 359.6847839355469 0.6708911061286926 0.7853773 0.22730696201324463 True -13 34230 26.72867774963379 0.5028483867645264 308.9532470703125 0.2837946116924286 358.9147644042969 0.672010600566864 0.7888169 0.21987144649028778 True -14 36675 27.79149317741394 25.199482440948486 304.5219421386719 0.2904304563999176 358.63232421875 0.6731371879577637 0.7951973 0.22026225924491882 True -15 39120 26.9169921875 0.5027570724487305 300.3404541015625 0.2614169716835022 358.0183410644531 0.6738531589508057 0.79860634 0.2154257595539093 True -16 41565 26.774279356002808 0.5178184509277344 304.7591552734375 0.1829337477684021 357.9862976074219 0.6741925477981567 0.80129457 0.2128511220216751 True -17 44010 26.896601676940918 0.5038330554962158 319.78411865234375 0.1595282256603241 358.0678405761719 0.6740576028823853 0.79948926 0.21239009499549866 False -18 46455 26.52926993370056 0.497173547744751 332.2268981933594 0.14736688137054443 358.27032470703125 0.673701822757721 0.79777056 0.21373625099658966 False -19 48900 26.209640741348267 0.500324010848999 297.43572998046875 0.17931096255779266 358.4063720703125 0.6734418272972107 0.7956382 0.21616944670677185 False diff --git a/ENCSR745CGG/cherimoya.fold_0.performance.tsv b/ENCSR745CGG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e680c47d47e02ae38720fbb3131c85ed5cba8226..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -357.9862976074219 0.2663355767726898 0.6741925477981567 0.2609793245792389 0.8012945652008057 0.747222363948822 0.2128511220216751 \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_1.evaluate.json b/ENCSR745CGG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6712b4500592a10fb496198e684365563b88c823..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF031ANP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_1.fit.json b/ENCSR745CGG/cherimoya.fold_1.fit.json deleted file mode 100644 index 28475f1adbbe60d020ea8acc0f884c44090ed652..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF031ANP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_1.log b/ENCSR745CGG/cherimoya.fold_1.log deleted file mode 100644 index 8405dd7d43d5b21852a2362e1a6e1945cad9e32d..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2431 30.798388481140137 3.5600173473358154 343.1308898925781 0.4934307038784027 501.5055236816406 0.5823178291320801 0.6437364 6.164154052734375 True -1 4862 26.39997696876526 0.6600544452667236 333.3463439941406 0.5495873689651489 439.91510009765625 0.6544349193572998 0.7259036 1.3668897151947021 True -2 7293 26.42222309112549 0.6343765258789062 332.4075927734375 0.35603123903274536 427.6312255859375 0.6699167490005493 0.7304094 0.48192137479782104 True -3 9724 26.457454442977905 1.492110252380371 340.8970947265625 0.3220456838607788 422.6826171875 0.6772916316986084 0.7370958 0.4202026426792145 True -4 12155 26.400705099105835 0.6460652351379395 303.6082458496094 0.38849276304244995 420.8140563964844 0.6802842617034912 0.7403253 0.4089120030403137 True -5 14586 26.571219444274902 0.6534910202026367 347.82598876953125 0.8022118806838989 418.9390563964844 0.6823827028274536 0.75221175 0.3926328122615814 True -6 17017 26.443533182144165 0.64150071144104 318.5738525390625 0.3101680874824524 418.712158203125 0.6825869083404541 0.7572691 0.408397912979126 True -7 19448 26.441823482513428 0.6688170433044434 310.9923095703125 0.3819465637207031 416.7411804199219 0.6859845519065857 0.7632911 0.36460408568382263 True -8 21879 26.565945148468018 0.649101972579956 316.76275634765625 0.24646854400634766 415.3162536621094 0.6876442432403564 0.7733696 0.34609419107437134 True -9 24310 26.44522190093994 2.1733500957489014 301.94317626953125 0.39261847734451294 413.8386535644531 0.6896682977676392 0.78003985 0.3129020631313324 True -10 26741 26.52584409713745 34.96032929420471 338.52984619140625 0.2001054286956787 412.52545166015625 0.6914666295051575 0.7868675 0.29990074038505554 True -11 29172 26.656352519989014 2.832479238510132 322.2754821777344 0.3320046663284302 411.5535888671875 0.6930326819419861 0.7904134 0.29718685150146484 True -12 31603 26.476004600524902 1.6886248588562012 334.495849609375 0.6085987687110901 410.5989685058594 0.6943381428718567 0.8008133 0.2805456519126892 True -13 34034 26.460964918136597 0.648024320602417 332.43206787109375 0.25701647996902466 409.2588806152344 0.6961424946784973 0.8117 0.26348093152046204 True -14 36465 26.464285612106323 0.6506540775299072 334.50238037109375 0.25725695490837097 408.2696228027344 0.6976743936538696 0.8187779 0.2522295415401459 True -15 38896 26.438360452651978 0.6530230045318604 289.30108642578125 0.20030055940151215 407.5165100097656 0.6988540887832642 0.8214264 0.24286694824695587 True -16 41327 26.45427131652832 0.6493058204650879 256.37823486328125 0.5188896656036377 407.24871826171875 0.6993350982666016 0.8255331 0.2360725849866867 True -17 43758 26.472888946533203 0.652235746383667 300.5210266113281 0.2034028172492981 407.2073669433594 0.6993897557258606 0.8252698 0.236549511551857 False -18 46189 26.51493239402771 2.0908994674682617 287.574462890625 0.3244345784187317 407.3614807128906 0.6992493867874146 0.8235767 0.24290983378887177 False -19 48620 26.443700313568115 0.6551804542541504 293.8763732910156 0.13443146646022797 407.42919921875 0.6990867257118225 0.82220376 0.24489885568618774 False diff --git a/ENCSR745CGG/cherimoya.fold_1.performance.tsv b/ENCSR745CGG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b20dd0bb10beecf5dc2cede0abc2c1771acf3ae3..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -407.24871826171875 0.24640585482120514 0.6993350982666016 0.2937846779823303 0.8255330920219421 0.7876127362251282 0.2360725849866867 \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_2.evaluate.json b/ENCSR745CGG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2b25a4957b4909925227a4ec4ba75130c4a4f890..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF031ANP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_2.fit.json b/ENCSR745CGG/cherimoya.fold_2.fit.json deleted file mode 100644 index d2ba0d9a426dd74169256d774f116d634eae1d07..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF031ANP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_2.log b/ENCSR745CGG/cherimoya.fold_2.log deleted file mode 100644 index 3b819df99e3630df993cc081eae5e5772f115c48..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2591 32.80093812942505 3.4100844860076904 311.70452880859375 0.43993327021598816 449.565185546875 0.576185941696167 0.6311258 5.286695957183838 True -1 5182 27.936753273010254 0.524446964263916 367.4554443359375 0.5406659841537476 399.21331787109375 0.6421911716461182 0.7039834 1.0162639617919922 True -2 7773 28.244007110595703 0.5183405876159668 334.06396484375 0.5332595109939575 391.7151184082031 0.6527194976806641 0.71566606 0.5307408571243286 True -3 10364 28.2107195854187 0.5476517677307129 294.7557678222656 0.5218853950500488 387.054931640625 0.6591085195541382 0.729719 0.5004059076309204 True -4 12955 28.349294185638428 39.29209804534912 368.03607177734375 0.43646982312202454 385.25042724609375 0.6616427302360535 0.72866213 0.38872066140174866 False -5 15546 31.254413604736328 0.5677156448364258 313.11395263671875 0.3515949845314026 384.447265625 0.663436233997345 0.7398356 0.3850352168083191 True -6 18137 28.220210790634155 0.5163829326629639 286.9668884277344 0.32360437512397766 384.0260314941406 0.6645023822784424 0.7442058 0.37892186641693115 True -7 20728 28.286110401153564 0.5194802284240723 327.16156005859375 0.43258631229400635 382.9281311035156 0.6661399006843567 0.746777 0.40342918038368225 True -8 23319 28.271021842956543 0.5150585174560547 300.5075378417969 0.6576526165008545 382.734619140625 0.6673651337623596 0.7498292 0.48298659920692444 True -9 25910 28.633378505706787 40.18541979789734 300.8872375488281 0.3365219831466675 380.72540283203125 0.6697033643722534 0.75495446 0.3767351806163788 True -10 28501 29.098758459091187 0.5189528465270996 334.57196044921875 0.35726606845855713 379.57696533203125 0.6715415120124817 0.7628255 0.3240942060947418 True -11 31092 28.223435640335083 0.5188446044921875 333.43792724609375 0.3758172392845154 378.3854675292969 0.6731342077255249 0.7718948 0.3034112751483917 True -12 33683 28.234187841415405 23.433093070983887 295.83343505859375 0.26040270924568176 377.4920654296875 0.674787163734436 0.77923757 0.2922188937664032 True -13 36274 31.023022890090942 0.5279543399810791 324.4580078125 0.1918700486421585 376.2369079589844 0.6766296029090881 0.7879444 0.2698092758655548 True -14 38865 28.298585414886475 0.6001393795013428 327.07159423828125 0.2197926789522171 375.4370422363281 0.6778531670570374 0.79768115 0.24754376709461212 True -15 41456 28.283233880996704 0.5220999717712402 271.8896484375 0.3948146104812622 374.8612365722656 0.6788419485092163 0.80094296 0.24141937494277954 True -16 44047 28.240188121795654 0.5230166912078857 284.0376892089844 0.24777066707611084 374.54901123046875 0.6792300343513489 0.8060203 0.2324877828359604 True -17 46638 28.26541805267334 0.5151400566101074 313.84954833984375 0.25655272603034973 374.4888000488281 0.6792962551116943 0.8070575 0.23316597938537598 True -18 49229 28.189551830291748 2.4199931621551514 311.7756042480469 0.2568182349205017 374.580078125 0.6791930794715881 0.8035182 0.2363998293876648 False -19 51820 28.25045680999756 0.5194606781005859 307.10321044921875 0.16872859001159668 374.6185302734375 0.6789876818656921 0.8016737 0.23848280310630798 False diff --git a/ENCSR745CGG/cherimoya.fold_2.performance.tsv b/ENCSR745CGG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 42cc814bdfe17867498cec9dde716b0d026b4531..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -374.4888000488281 0.26125696301460266 0.6792961955070496 0.27094972133636475 0.8070574998855591 0.7503842115402222 0.23316597938537598 \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_3.evaluate.json b/ENCSR745CGG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0e78f59f6b629d2ab697b45beca58db6417e4d65..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF031ANP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_3.fit.json b/ENCSR745CGG/cherimoya.fold_3.fit.json deleted file mode 100644 index ab6c3892773c4f2898556573fb32f7480637fa10..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF031ANP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_3.log b/ENCSR745CGG/cherimoya.fold_3.log deleted file mode 100644 index 687323e23d6b4685a719844cbd1587d925f2626e..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2500 36.142006635665894 16.4137179851532 322.9075622558594 0.5640674829483032 438.24163818359375 0.5662329196929932 0.62807405 4.520549774169922 True -1 5000 27.010557413101196 0.5244879722595215 321.27874755859375 0.8512094616889954 385.1287536621094 0.6370669603347778 0.7115432 0.9026995897293091 True -2 7500 27.21989941596985 0.4827897548675537 328.1908874511719 0.5705883502960205 377.0371398925781 0.650637686252594 0.7282364 0.34742268919944763 True -3 10000 27.100354194641113 1.5801317691802979 363.91357421875 0.7163283824920654 373.0420227050781 0.6558846235275269 0.73453856 0.3119919002056122 True -4 12500 26.65471076965332 0.4745199680328369 340.9228210449219 0.3021170198917389 372.3680114746094 0.6573486924171448 0.73854107 0.32093340158462524 True -5 15000 26.687108039855957 0.47571444511413574 317.0348205566406 0.8541807532310486 372.1262512207031 0.6580626368522644 0.7324683 0.32613715529441833 False -6 17500 26.677148818969727 0.47226762771606445 297.5316162109375 0.5430631637573242 371.0024108886719 0.6603006720542908 0.7386256 0.30455994606018066 True -7 20000 26.717905521392822 0.4818425178527832 321.1251220703125 1.1528315544128418 370.2545471191406 0.662239134311676 0.74745315 0.31812724471092224 True -8 22500 26.67956829071045 0.4742615222930908 307.54913330078125 0.6968333721160889 369.24420166015625 0.663958728313446 0.7425698 0.33141565322875977 False -9 25000 26.71506404876709 1.2426512241363525 298.6444396972656 0.6937121152877808 368.51483154296875 0.6655891537666321 0.74228126 0.33107486367225647 False -10 27500 26.72051477432251 7.053746700286865 284.7464599609375 0.5710376501083374 367.33111572265625 0.6676481366157532 0.7484953 0.32756802439689636 True -11 30000 26.770679712295532 0.49533987045288086 285.2630615234375 0.4855024814605713 366.36187744140625 0.6695308089256287 0.7678836 0.306247740983963 True -12 32500 26.753684997558594 1.7075018882751465 316.95263671875 0.2864791452884674 365.5924987792969 0.67085200548172 0.7694735 0.29846736788749695 True -13 35000 26.71560573577881 0.47797346115112305 305.70806884765625 0.316602885723114 364.5882873535156 0.6724237203598022 0.7727414 0.2809062898159027 True -14 37500 26.75681233406067 0.47708606719970703 306.9560241699219 0.2350907176733017 363.923095703125 0.6737582087516785 0.7816466 0.2756669223308563 True -15 40000 26.717997074127197 0.4801173210144043 311.075927734375 0.3048679232597351 363.1507568359375 0.674723744392395 0.78597975 0.2622532248497009 True -16 42500 26.781420946121216 0.4768526554107666 321.4729309082031 0.2734285891056061 362.7823486328125 0.6752623915672302 0.79199827 0.2535717189311981 True -17 45000 26.734532594680786 0.48290252685546875 290.4730224609375 0.22005300223827362 362.7185974121094 0.6752819418907166 0.7920511 0.2546561658382416 True -18 47500 26.80265164375305 1.7910354137420654 311.59521484375 0.2667621374130249 362.8025817871094 0.6751401424407959 0.7859 0.2614177167415619 False -19 50000 26.713338136672974 0.6126866340637207 311.6574401855469 0.1704496145248413 362.90496826171875 0.674905002117157 0.7852117 0.2645115256309509 False diff --git a/ENCSR745CGG/cherimoya.fold_3.performance.tsv b/ENCSR745CGG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a3c3d15c24829a06a4f0fc6e51fc1cf2d871da53..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -362.7185974121094 0.266117125749588 0.6752819418907166 0.2599547803401947 0.7920510768890381 0.7283982038497925 0.2546561658382416 \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_4.evaluate.json b/ENCSR745CGG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5bd2135283757d1a2aabf84cd64e7a57abb013d2..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF031ANP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_4.fit.json b/ENCSR745CGG/cherimoya.fold_4.fit.json deleted file mode 100644 index f88a29020cf3f4d22bbfdef0ed6bf27d9e5ab620..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF031ANP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR745CGG/cherimoya.fold_4.log b/ENCSR745CGG/cherimoya.fold_4.log deleted file mode 100644 index 34307e3bd40722368f6c66f84d29a1f0c3154f53..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2553 33.06718468666077 3.433037042617798 315.2658996582031 0.5048946142196655 420.0576477050781 0.5715370774269104 0.62355304 4.033170700073242 True -1 5106 27.749671697616577 0.5245683193206787 339.45294189453125 0.433039128780365 378.7499084472656 0.6348705291748047 0.6928952 1.0591193437576294 True -2 7659 27.740026235580444 0.5060560703277588 320.82659912109375 0.37940317392349243 370.6886291503906 0.6469239592552185 0.7097717 0.4415220022201538 True -3 10212 27.76214361190796 0.5116705894470215 391.247314453125 0.5388465523719788 366.5104675292969 0.6524724960327148 0.7233162 0.4187328517436981 True -4 12765 27.809933185577393 1.2307944297790527 288.32659912109375 0.973193883895874 365.6451110839844 0.6550838947296143 0.7205889 0.516822099685669 False -5 15318 27.177398920059204 0.4946112632751465 313.0203857421875 0.18920354545116425 364.8603210449219 0.6568788290023804 0.71801037 0.4164011478424072 False -6 17871 27.1871075630188 0.50510573387146 333.4655456542969 0.24710309505462646 363.68231201171875 0.6586554646492004 0.7213934 0.3725222945213318 False -7 20424 27.25837230682373 0.4973466396331787 289.7204895019531 0.25341713428497314 363.1147766113281 0.6597446203231812 0.7335198 0.3723078668117523 True -8 22977 27.214171171188354 0.5055177211761475 336.49932861328125 0.7491044998168945 362.4594421386719 0.6612496972084045 0.73618907 0.3440152406692505 True -9 25530 27.182930946350098 0.5104303359985352 319.6358642578125 0.3277222216129303 361.2733154296875 0.6631906032562256 0.7449356 0.32926252484321594 True -10 28083 27.21297264099121 0.49297046661376953 325.6533203125 0.19748535752296448 360.3284912109375 0.664923369884491 0.7511573 0.31924277544021606 True -11 30636 27.18439793586731 24.75882339477539 302.1435546875 0.8435646295547485 359.30120849609375 0.6666406989097595 0.75808376 0.29057109355926514 True -12 33189 32.71544122695923 17.17616605758667 349.204345703125 0.2991402745246887 358.3822326660156 0.6681923270225525 0.7635513 0.28099456429481506 True -13 35742 31.239452838897705 26.35333013534546 322.00811767578125 0.34841203689575195 357.5630798339844 0.6699133515357971 0.7746892 0.25677913427352905 True -14 38295 27.27430009841919 0.5150761604309082 349.5992431640625 1.2973381280899048 356.8583068847656 0.6710201501846313 0.78228694 0.245829775929451 True -15 40848 27.238842248916626 1.1843247413635254 275.5784912109375 0.2151675522327423 356.44970703125 0.6717760562896729 0.78657746 0.24470779299736023 True -16 43401 27.313045263290405 0.4996311664581299 310.41790771484375 0.11954404413700104 356.01995849609375 0.6723055839538574 0.7893899 0.2377418428659439 True -17 45954 27.643349647521973 0.5029075145721436 314.7424621582031 0.15152785181999207 355.9656677246094 0.6725391745567322 0.7913215 0.2313581258058548 True -18 48507 27.248526573181152 0.49776339530944824 295.6639404296875 0.1609632968902588 355.9033508300781 0.672387421131134 0.789274 0.231904074549675 False -19 51060 27.282799243927002 0.4957563877105713 289.910400390625 0.18183624744415283 355.986083984375 0.6721956133842468 0.7879069 0.23524188995361328 False diff --git a/ENCSR745CGG/cherimoya.fold_4.performance.tsv b/ENCSR745CGG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 33bf377cf68067a22f4e8e607cc14cca21c018ea..0000000000000000000000000000000000000000 --- a/ENCSR745CGG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -355.9656677246094 0.2674260437488556 0.6725391745567322 0.2592187523841858 0.7913215160369873 0.7189233899116516 0.2313581258058548 \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_0.evaluate.json b/ENCSR746RDJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6613e39f36064446235ced7fcb9d4647b4310e40..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354TLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_0.fit.json b/ENCSR746RDJ/cherimoya.fold_0.fit.json deleted file mode 100644 index e4fff1824d9adaa853e4d9c3bc6cf3108d8bb456..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF354TLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_0.log b/ENCSR746RDJ/cherimoya.fold_0.log deleted file mode 100644 index 44adc33074873242bfb0e58d41e891eb19b514e1..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.6438090801239 3.3661370277404785 1038.037109375 1.0746500492095947 1652.3419189453125 0.276105135679245 0.5361793 7.529980182647705 True -1 5478 30.11779499053955 0.6773273944854736 1122.0404052734375 0.6130883693695068 1515.4556884765625 0.3889555037021637 0.5770088 1.2286564111709595 True -2 8217 30.118507862091064 0.5616109371185303 1196.26220703125 0.5815249681472778 1497.444580078125 0.39899033308029175 0.5589327 1.0712970495224 False -3 10956 29.962897539138794 0.9221012592315674 1045.491455078125 0.612880289554596 1485.3697509765625 0.40095841884613037 0.58070874 0.5880893468856812 True -4 13695 29.563104152679443 0.5860769748687744 1132.79248046875 0.5436656475067139 1478.9893798828125 0.4063754081726074 0.5848467 0.5320807099342346 True -5 16434 29.517447233200073 0.532827615737915 1191.6702880859375 0.7634537220001221 1467.898193359375 0.4114799201488495 0.6003934 0.4551381468772888 True -6 19173 29.513588428497314 0.6330795288085938 1064.8988037109375 0.5709506273269653 1462.542724609375 0.4157271683216095 0.6113304 0.40556666254997253 True -7 21912 29.50541591644287 0.5619850158691406 1121.798828125 0.7354260087013245 1447.11328125 0.4184810221195221 0.60372406 0.41771143674850464 False -8 24651 29.480947256088257 0.5344951152801514 1052.674072265625 0.430317759513855 1431.7960205078125 0.4229246973991394 0.6121147 0.3895873725414276 True -9 27390 29.474788665771484 1.3166394233703613 1106.44921875 1.039567232131958 1417.4300537109375 0.42785316705703735 0.6154473 0.40124380588531494 True -10 30129 29.51867938041687 0.5470647811889648 978.162353515625 0.6352174878120422 1405.0382080078125 0.4288501739501953 0.6201115 0.3787367343902588 True -11 32868 29.516204833984375 0.5610644817352295 1013.0839233398438 0.7585469484329224 1383.7841796875 0.43632736802101135 0.62975657 0.37289881706237793 True -12 35607 29.5757417678833 0.5496845245361328 1197.2822265625 0.38766011595726013 1372.0018310546875 0.44076892733573914 0.64607173 0.36763229966163635 True -13 38346 29.57204294204712 0.5533761978149414 971.693359375 0.4188011884689331 1358.3282470703125 0.4450992941856384 0.65860087 0.3618925213813782 True -14 41085 29.549151182174683 0.5496301651000977 1005.0609130859375 0.46740132570266724 1348.1832275390625 0.4478192627429962 0.6698213 0.3454643785953522 True -15 43824 29.554256200790405 0.5390989780426025 1222.915283203125 0.29212260246276855 1338.145263671875 0.4534111022949219 0.67688745 0.346050500869751 True -16 46563 29.552489042282104 0.5435919761657715 1175.0443115234375 0.4106820523738861 1335.243408203125 0.4541027843952179 0.6824017 0.33877813816070557 True -17 49302 29.544282913208008 0.527740478515625 1106.119873046875 0.27743372321128845 1333.807861328125 0.45540520548820496 0.6846573 0.3384488523006439 True -18 52041 29.970707178115845 0.5639433860778809 1078.974853515625 0.2921013832092285 1334.1385498046875 0.4553455114364624 0.68464565 0.34025636315345764 False -19 54780 29.644015312194824 0.5663530826568604 1074.131591796875 0.25655609369277954 1334.9500732421875 0.4552013874053955 0.68425286 0.3420739769935608 False diff --git a/ENCSR746RDJ/cherimoya.fold_0.performance.tsv b/ENCSR746RDJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7266fe2d2fa6fd0dc5d7ddbdb57d408cb5320131..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1333.807861328125 0.2753073573112488 0.45540520548820496 0.26475754380226135 0.6846572756767273 0.6475399732589722 0.3384488523006439 \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_1.evaluate.json b/ENCSR746RDJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 84c7af416a25d8bbcb2ae11d165972530f1091e6..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354TLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_1.fit.json b/ENCSR746RDJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 55d73f3ac753fc1476529425d0f8cd96bbb1d67e..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF354TLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_1.log b/ENCSR746RDJ/cherimoya.fold_1.log deleted file mode 100644 index 76ecd9db59a46be36931780f94117b29533bbf61..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 35.4154691696167 31.922061443328857 1210.3243408203125 0.966018557548523 1975.6168212890625 0.28865963220596313 0.5552792 7.150692939758301 True -1 5544 30.517595529556274 20.465558767318726 1168.47265625 0.7694765329360962 1808.1597900390625 0.40601009130477905 0.61880535 1.0787830352783203 True -2 8316 30.64859366416931 0.9165270328521729 1091.0498046875 0.6521683931350708 1793.7706298828125 0.4115809500217438 0.6160007 0.629074215888977 False -3 11088 29.827394485473633 0.687131404876709 1084.160888671875 0.7055162191390991 1760.8739013671875 0.4230369031429291 0.6394804 0.5000210404396057 True -4 13860 29.888119220733643 0.9390983581542969 1245.784912109375 0.5787461996078491 1733.7528076171875 0.4241010248661041 0.6300449 0.611947238445282 False -5 16632 29.858978033065796 1.1866302490234375 1050.3287353515625 0.31805193424224854 1713.884765625 0.4277693033218384 0.6335759 0.48595744371414185 False -6 19404 29.88563323020935 1.0453808307647705 1281.052978515625 0.524672269821167 1637.6221923828125 0.43214312195777893 0.6381888 0.47558319568634033 False -7 22176 29.875690698623657 0.6677744388580322 1180.7470703125 1.183283805847168 1627.263671875 0.43628165125846863 0.6451726 0.43361011147499084 True -8 24948 29.908781051635742 1.2379965782165527 1075.684326171875 0.4095720648765564 1609.2279052734375 0.43746209144592285 0.64990103 0.4333195388317108 True -9 27720 29.881600618362427 0.694706916809082 1064.656494140625 0.603426456451416 1569.6373291015625 0.44461479783058167 0.6593303 0.42571723461151123 True -10 30492 29.964921474456787 0.699089765548706 1076.29248046875 0.6039133071899414 1531.369140625 0.44877544045448303 0.6694192 0.4001730978488922 True -11 33264 30.036293506622314 0.7082910537719727 1318.405517578125 0.38280946016311646 1513.4898681640625 0.4549504518508911 0.6788721 0.3834318220615387 True -12 36036 29.9886257648468 0.6734280586242676 1014.0120239257812 1.0524405241012573 1502.6802978515625 0.4590008854866028 0.68873674 0.39024224877357483 True -13 38808 29.998204946517944 0.662153959274292 1169.2952880859375 0.5565454959869385 1482.4874267578125 0.46238091588020325 0.695575 0.3771746754646301 True -14 41580 29.99873995780945 0.7113332748413086 986.4568481445312 1.0908691883087158 1470.765869140625 0.4661095440387726 0.70757806 0.35761699080467224 True -15 44352 29.921945810317993 0.6445112228393555 835.83935546875 0.3901408314704895 1468.94677734375 0.4686221778392792 0.71973085 0.3537428677082062 True -16 47124 29.93608570098877 0.6544179916381836 1158.1192626953125 0.4854242205619812 1466.01025390625 0.47076886892318726 0.72619134 0.34276899695396423 True -17 49896 29.945695638656616 0.6924502849578857 1110.773193359375 0.33020031452178955 1466.5587158203125 0.47266480326652527 0.7316601 0.3427198529243469 True -18 52668 29.972933530807495 0.6648969650268555 1052.503173828125 0.2695695161819458 1468.935302734375 0.4729182720184326 0.73405725 0.33913183212280273 True -19 55440 29.964122772216797 0.6688530445098877 1049.5721435546875 0.33096450567245483 1471.32666015625 0.4721994996070862 0.7339957 0.339181125164032 False diff --git a/ENCSR746RDJ/cherimoya.fold_1.performance.tsv b/ENCSR746RDJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 29a954c73d385b69e03c5b088e061f7f67dd3184..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1468.935302734375 0.2616261839866638 0.4729182720184326 0.28847432136535645 0.7340572476387024 0.7102189660072327 0.33913183212280273 \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_2.evaluate.json b/ENCSR746RDJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b30b03ca62a04b80b8fdb3bb415b272a408bc4ad..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354TLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_2.fit.json b/ENCSR746RDJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 4f2a50848f3ef41aef94ae753a7dce7d8e14ac0b..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF354TLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_2.log b/ENCSR746RDJ/cherimoya.fold_2.log deleted file mode 100644 index 3931be5a951f4502a25c1bddc7013672497859a2..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 36.595415353775024 3.394779920578003 1664.365234375 0.7821899056434631 1925.552734375 0.29218676686286926 0.53740627 6.370640277862549 True -1 5782 31.81246304512024 0.6612327098846436 1234.844482421875 0.7027190923690796 1809.4833984375 0.38919582962989807 0.5738833 0.9635207056999207 True -2 8673 31.76880693435669 0.5443918704986572 1027.3515625 0.9478513598442078 1776.6715087890625 0.40254437923431396 0.59688145 0.6550305485725403 True -3 11564 32.146831035614014 0.5554172992706299 1155.8531494140625 0.6943801045417786 1739.976318359375 0.4115496873855591 0.5947794 0.6619064807891846 False -4 14455 31.706205129623413 0.5355873107910156 1073.794921875 0.637299656867981 1743.874755859375 0.41223350167274475 0.59438 0.607771098613739 False -5 17346 31.195812463760376 0.5508015155792236 1052.1044921875 0.6058819890022278 1686.8115234375 0.417321115732193 0.6088804 0.5220229625701904 True -6 20237 31.245482444763184 0.5353806018829346 1053.088623046875 0.6084724068641663 1629.2105712890625 0.4218631684780121 0.6124952 0.4812254309654236 True -7 23128 31.319275856018066 0.5229277610778809 1131.1055908203125 0.6112065315246582 1590.980712890625 0.424705445766449 0.61514443 0.46622827649116516 True -8 26019 31.197015047073364 0.535956621170044 1022.3167724609375 0.4884716868400574 1539.624755859375 0.43009868264198303 0.6160721 0.43821993470191956 True -9 28910 31.199515104293823 0.5327126979827881 1146.970458984375 0.6878354549407959 1524.6588134765625 0.4339195787906647 0.6186485 0.4466699957847595 True -10 31801 31.18654179573059 0.536736011505127 1204.4886474609375 0.3790634274482727 1497.34326171875 0.4375957250595093 0.6236332 0.4265275001525879 True -11 34692 31.15597629547119 0.5347332954406738 1277.5125732421875 0.31641972064971924 1492.172607421875 0.44360947608947754 0.6329637 0.4272228479385376 True -12 37583 31.238725423812866 0.5252439975738525 1117.931396484375 0.5455114841461182 1470.576416015625 0.4457634687423706 0.64396137 0.40863534808158875 True -13 40474 31.22882628440857 0.5121269226074219 995.211669921875 0.49996209144592285 1458.9613037109375 0.45052483677864075 0.65196157 0.40087786316871643 True -14 43365 31.263044595718384 0.5802171230316162 1121.8380126953125 0.38238030672073364 1439.9317626953125 0.45475995540618896 0.6645414 0.38590970635414124 True -15 46256 31.294054985046387 0.5368380546569824 1164.3359375 0.39078155159950256 1425.2965087890625 0.4572637677192688 0.67511404 0.3727741241455078 True -16 49147 31.42373251914978 0.5419466495513916 910.5614624023438 0.43264761567115784 1414.31201171875 0.4576357901096344 0.68352824 0.36234620213508606 True -17 52038 31.260661840438843 0.5373241901397705 1041.21435546875 0.39979398250579834 1404.704345703125 0.45966264605522156 0.688692 0.3587082624435425 True -18 54929 31.27393102645874 0.5948011875152588 1049.233642578125 0.5750101804733276 1412.499267578125 0.4601534307003021 0.6913478 0.35919317603111267 True -19 57820 31.22726321220398 0.5792083740234375 1044.3626708984375 0.2697182595729828 1418.360107421875 0.459934800863266 0.69063884 0.36120301485061646 False diff --git a/ENCSR746RDJ/cherimoya.fold_2.performance.tsv b/ENCSR746RDJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d6034677ea7f3cb84ec7528883c9dfc14e419e2a..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1412.499267578125 0.2719501852989197 0.46015337109565735 0.27233195304870605 0.6913477778434753 0.6547175645828247 0.35919317603111267 \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_3.evaluate.json b/ENCSR746RDJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9adb4f68e38589020f641918858d2edab7d4e671..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354TLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_3.fit.json b/ENCSR746RDJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 4a42a32968f1cd21b869060a9fc5cbba4a89b86a..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF354TLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_3.log b/ENCSR746RDJ/cherimoya.fold_3.log deleted file mode 100644 index 59682fbe8dd96b70e48e38715c25b7bcbd83a13c..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2810 35.73184657096863 3.891979455947876 1780.4664306640625 0.8927782773971558 1635.444580078125 0.28989043831825256 0.5587413 7.634716510772705 True -1 5620 30.918152809143066 1.67844557762146 1121.691650390625 0.9533049464225769 1515.593017578125 0.38554543256759644 0.5747404 1.2486132383346558 True -2 8430 30.853230953216553 0.6018123626708984 1233.218994140625 0.6486466526985168 1491.1898193359375 0.4001348316669464 0.5883036 0.7201138734817505 True -3 11240 30.8188579082489 0.5983259677886963 1177.986572265625 0.5140365958213806 1479.60693359375 0.4022267460823059 0.57336205 0.6304930448532104 False -4 14050 30.812446355819702 0.5733411312103271 1253.9288330078125 0.7711818218231201 1467.7108154296875 0.40846487879753113 0.5784109 0.6940807700157166 False -5 16860 30.65347695350647 0.9764950275421143 1036.459228515625 0.5884963274002075 1453.662109375 0.41279101371765137 0.5757818 0.574738085269928 False -6 19670 30.348018407821655 0.6991534233093262 1161.6754150390625 0.5337650179862976 1444.5087890625 0.4154564142227173 0.5842074 0.5564016699790955 False -7 22480 30.35276460647583 0.5649969577789307 1197.7144775390625 0.7767761945724487 1430.201171875 0.41994139552116394 0.60844445 0.4895366430282593 True -8 25290 30.44550323486328 0.5624127388000488 1213.82568359375 0.6999520063400269 1413.1407470703125 0.4270522892475128 0.61634386 0.4559611976146698 True -9 28100 30.324751377105713 0.560218334197998 1087.0401611328125 0.39104700088500977 1406.0748291015625 0.430144339799881 0.62192345 0.44650477170944214 True -10 30910 30.241851091384888 0.7438786029815674 1085.942138671875 0.5581567287445068 1393.83447265625 0.4353386461734772 0.6259464 0.45964953303337097 True -11 33720 30.35491132736206 17.283432722091675 1085.995849609375 0.4252082109451294 1387.736083984375 0.4384273886680603 0.63015527 0.44810184836387634 True -12 36530 30.3928964138031 0.564995288848877 999.5147705078125 0.8354944586753845 1378.5350341796875 0.4414215385913849 0.64709085 0.40323901176452637 True -13 39340 30.378347396850586 0.5673961639404297 1107.169921875 0.4174819886684418 1372.083740234375 0.44628462195396423 0.66293454 0.39353886246681213 True -14 42150 30.33415961265564 0.5672001838684082 1108.107177734375 0.38878151774406433 1368.0057373046875 0.4488096535205841 0.6797358 0.38066452741622925 True -15 44960 30.42922019958496 0.5605599880218506 1057.2017822265625 0.558678925037384 1363.4656982421875 0.4510411024093628 0.69329584 0.36031121015548706 True -16 47770 30.625417232513428 0.567859411239624 1051.346435546875 0.24572697281837463 1358.9427490234375 0.453986257314682 0.70312846 0.3415035307407379 True -17 50580 30.3527672290802 0.5703456401824951 1035.6888427734375 0.36219578981399536 1360.408447265625 0.45310890674591064 0.7073999 0.33267879486083984 True -18 53390 30.83310627937317 0.698716402053833 1081.267333984375 0.26187828183174133 1361.8668212890625 0.45225149393081665 0.7085618 0.333786278963089 True -19 56200 30.33530020713806 0.5668928623199463 991.063720703125 0.3460419178009033 1362.7830810546875 0.45153138041496277 0.70779085 0.3342888057231903 False diff --git a/ENCSR746RDJ/cherimoya.fold_3.performance.tsv b/ENCSR746RDJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c03d9c0838b01d03e902b1d529487ead957c3d46..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1361.8668212890625 0.2719561755657196 0.45225149393081665 0.2738056480884552 0.7085617780685425 0.6681116223335266 0.333786278963089 \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_4.evaluate.json b/ENCSR746RDJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0ce127d26e51e54f5896571f5efeeb5ca1a9f5a3..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF354TLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_4.fit.json b/ENCSR746RDJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 5053062f2d08c05cf9c8b02dda2da3233cd67918..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF354TLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746RDJ/cherimoya.fold_4.log b/ENCSR746RDJ/cherimoya.fold_4.log deleted file mode 100644 index 0928abd667e34b663b3d3b783ab37da5eb92e150..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 37.661378145217896 3.394556999206543 1244.7471923828125 0.7271252870559692 1616.69775390625 0.286991149187088 0.5262456 6.666743755340576 True -1 5782 31.79531502723694 0.8058652877807617 1181.929443359375 0.534439206123352 1481.9027099609375 0.3943360149860382 0.56207746 0.904212236404419 True -2 8673 31.75281023979187 0.592918872833252 1024.0059814453125 0.8088054656982422 1468.9664306640625 0.3979167342185974 0.5677543 0.5980772376060486 True -3 11564 31.719459533691406 0.5698533058166504 1145.8502197265625 0.7934161424636841 1450.7572021484375 0.40228384733200073 0.5771736 0.6166449189186096 True -4 14455 31.750624179840088 0.5945794582366943 1466.89501953125 1.0000348091125488 1440.7279052734375 0.4076095223426819 0.56417775 0.6202924251556396 False -5 17346 31.76047372817993 0.6035027503967285 1414.1834716796875 0.37879908084869385 1432.013916015625 0.4116508364677429 0.5779382 0.76169753074646 True -6 20237 31.41491985321045 0.5689265727996826 1318.52099609375 0.6976652145385742 1424.407470703125 0.4155377447605133 0.5840426 0.6692099571228027 True -7 23128 31.22708797454834 11.641204595565796 1154.02099609375 0.7082760334014893 1424.63916015625 0.41556060314178467 0.582299 0.6283435821533203 False -8 26019 31.21935772895813 0.6515603065490723 1322.9190673828125 0.5115733742713928 1401.157470703125 0.42058417201042175 0.57742506 0.7691384553909302 False -9 28910 31.200856685638428 0.6126222610473633 886.2650756835938 1.072826623916626 1384.389404296875 0.426198810338974 0.58817524 0.6046431660652161 True -10 31801 31.198007822036743 0.596238374710083 1010.2512817382812 0.6322191953659058 1371.0716552734375 0.42976903915405273 0.5952339 0.52693110704422 True -11 34692 31.36035990715027 0.6475162506103516 1030.7254638671875 1.029066801071167 1360.4215087890625 0.434871643781662 0.6093795 0.5162131786346436 True -12 37583 31.249247074127197 0.6260128021240234 1112.732666015625 0.4778454303741455 1355.320556640625 0.4366748034954071 0.62669694 0.49208518862724304 True -13 40474 31.34257984161377 0.6050028800964355 1023.662353515625 0.38158875703811646 1344.9931640625 0.4423770010471344 0.6446892 0.44344937801361084 True -14 43365 31.39739155769348 0.6228086948394775 1085.6536865234375 0.5538341999053955 1339.90380859375 0.44461074471473694 0.6592414 0.3989962339401245 True -15 46256 31.3693950176239 0.6144664287567139 1048.5916748046875 0.23632512986660004 1335.1717529296875 0.4484405219554901 0.67034 0.3819541335105896 True -16 49147 31.26864767074585 0.6855497360229492 1147.462646484375 0.27320438623428345 1331.363037109375 0.45093199610710144 0.678865 0.3611449897289276 True -17 52038 31.2980215549469 1.743837594985962 1057.9451904296875 0.3028070330619812 1330.8499755859375 0.45037978887557983 0.68561584 0.3523922562599182 True -18 54929 31.32979679107666 0.583730936050415 1018.351806640625 0.3677302598953247 1332.0189208984375 0.4496902525424957 0.68751246 0.3495670258998871 True -19 57820 31.350172519683838 0.6048645973205566 1031.81982421875 0.4038301706314087 1331.509521484375 0.4500657916069031 0.6868454 0.3485963046550751 False diff --git a/ENCSR746RDJ/cherimoya.fold_4.performance.tsv b/ENCSR746RDJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7a17a7a180692d7d67f67cf5bfa48a50626e023e..0000000000000000000000000000000000000000 --- a/ENCSR746RDJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1332.0189208984375 0.2751670777797699 0.4496902525424957 0.26641055941581726 0.6875124573707581 0.6442070603370667 0.3495670258998871 \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_0.evaluate.json b/ENCSR746ZPP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1e1ed0323ed82ded6653dc967decac91ce1f709e..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988XHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_0.fit.json b/ENCSR746ZPP/cherimoya.fold_0.fit.json deleted file mode 100644 index 20951d8e4cf5e69a93a548fa9a43db785955c5ca..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF988XHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_0.log b/ENCSR746ZPP/cherimoya.fold_0.log deleted file mode 100644 index c09a634ffb2123b7e819393d0acfbe3f8dd054f4..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 35.5289044380188 4.271170377731323 1546.6220703125 0.38280487060546875 1697.2843017578125 0.30085790157318115 0.5802119 7.92203426361084 True -1 5526 30.643341302871704 0.647024393081665 1253.04296875 0.32167404890060425 1474.6923828125 0.43031051754951477 0.6691604 2.7603373527526855 True -2 8289 30.65233302116394 0.5776960849761963 1232.130859375 0.4681812524795532 1440.4627685546875 0.4476141333580017 0.6851612 1.3180280923843384 True -3 11052 30.720556497573853 0.5918729305267334 1356.35009765625 0.5629257559776306 1411.0400390625 0.4630032479763031 0.7007796 0.9600173234939575 True -4 13815 30.678733110427856 0.56638503074646 1223.915771484375 0.7693701982498169 1398.935791015625 0.4654422700405121 0.71427375 0.7046207189559937 True -5 16578 30.70060634613037 0.5770776271820068 1210.1663818359375 0.4122755229473114 1394.09130859375 0.46745121479034424 0.7177737 0.6578924059867859 True -6 19341 30.685206174850464 1.245267629623413 1130.73779296875 0.4065462350845337 1377.4127197265625 0.4766981303691864 0.7234789 0.5510183572769165 True -7 22104 30.672423124313354 0.607560396194458 1187.501953125 0.5322269201278687 1376.7432861328125 0.47949889302253723 0.72999185 0.6041567921638489 True -8 24867 30.703613996505737 0.5764799118041992 1239.8582763671875 0.3930997848510742 1365.308349609375 0.4878101348876953 0.73872375 0.4948776364326477 True -9 27630 30.721579790115356 0.6758122444152832 1296.866455078125 0.3911585211753845 1359.4869384765625 0.4910118877887726 0.739269 0.4449352025985718 True -10 30393 30.6495840549469 0.5749180316925049 953.0519409179688 0.41413819789886475 1352.09912109375 0.4943852126598358 0.745529 0.4144369065761566 True -11 33156 30.650519847869873 0.5845000743865967 1228.4122314453125 0.31299346685409546 1345.6224365234375 0.4985946714878082 0.7538645 0.37306055426597595 True -12 35919 30.39636778831482 0.5678796768188477 1294.35888671875 0.2943313717842102 1337.755859375 0.5040529370307922 0.7633455 0.36157092452049255 True -13 38682 30.129576921463013 0.5826199054718018 1334.919921875 0.34166258573532104 1334.68896484375 0.5040426850318909 0.77091396 0.34746992588043213 True -14 41445 30.105881690979004 0.5781247615814209 1041.002197265625 0.2215263545513153 1327.43994140625 0.5095282793045044 0.78014284 0.317851722240448 True -15 44208 30.039988040924072 0.57521653175354 1110.9393310546875 0.20037615299224854 1323.747802734375 0.5109531283378601 0.7854212 0.29568159580230713 True -16 46971 30.25677800178528 0.5929949283599854 1013.031982421875 0.24916857481002808 1318.66845703125 0.5144852995872498 0.791064 0.2849074602127075 True -17 49734 30.226345777511597 0.5831265449523926 964.5142822265625 0.1600302904844284 1322.9664306640625 0.5115432739257812 0.7932993 0.28111571073532104 True -18 52497 30.295164585113525 0.6005654335021973 1067.88134765625 0.1514188051223755 1325.2943115234375 0.5088821053504944 0.79074645 0.27998027205467224 False -19 55260 30.2726891040802 0.5818202495574951 1313.77783203125 0.23262208700180054 1323.9139404296875 0.5108610987663269 0.79047626 0.2808741331100464 False diff --git a/ENCSR746ZPP/cherimoya.fold_0.performance.tsv b/ENCSR746ZPP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 331a9ee9637f8c6023355c871cb613265a28af4c..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1322.9664306640625 0.23880432546138763 0.5115432143211365 0.29084011912345886 0.7932993173599243 0.7273737192153931 0.28111571073532104 \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_1.evaluate.json b/ENCSR746ZPP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 70af5152e9cb2dbf17f1bccd61aa5de05ff3c05d..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988XHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_1.fit.json b/ENCSR746ZPP/cherimoya.fold_1.fit.json deleted file mode 100644 index 563132354dccf7a6a1d5ce669801a22e37ccf71f..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF988XHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_1.log b/ENCSR746ZPP/cherimoya.fold_1.log deleted file mode 100644 index 8c12df9d70b2be67d840cd0548243492f4d26a0c..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 35.26689314842224 4.3474366664886475 1384.0970458984375 0.4892902970314026 1993.97119140625 0.30502012372016907 0.5849283 7.749392986297607 True -1 5488 30.515610933303833 2.7356979846954346 1494.6226806640625 0.6434766054153442 1725.1065673828125 0.4445534944534302 0.69077003 2.9579315185546875 True -2 8232 30.467217445373535 0.6877303123474121 1340.9873046875 0.5426667928695679 1663.9072265625 0.46187469363212585 0.7117003 1.52937912940979 True -3 10976 30.456212282180786 0.6769616603851318 1382.563232421875 0.36168530583381653 1630.8135986328125 0.47257566452026367 0.72464114 1.159923791885376 True -4 13720 30.505987882614136 0.6890730857849121 1518.28662109375 0.4381038546562195 1609.3734130859375 0.4823414087295532 0.7278188 0.9996110796928406 True -5 16464 30.501217126846313 0.6782946586608887 1112.927734375 0.31334829330444336 1598.1624755859375 0.48618507385253906 0.7353763 0.8963959813117981 True -6 19208 30.46658444404602 0.6970829963684082 1030.507080078125 0.35539358854293823 1588.0396728515625 0.4896453022956848 0.7432489 0.7357165217399597 True -7 21952 30.50868010520935 2.67722225189209 1162.75732421875 0.36464056372642517 1573.8323974609375 0.495707631111145 0.7482283 0.7209969162940979 True -8 24696 30.548752784729004 24.673422813415527 1122.4859619140625 0.3527466058731079 1561.486572265625 0.5029393434524536 0.75694615 0.6368234753608704 True -9 27440 30.553451776504517 1.749833583831787 1276.0244140625 0.47548848390579224 1558.60205078125 0.5040188431739807 0.75782883 0.5744585990905762 True -10 30184 30.494892358779907 1.5577776432037354 978.6204833984375 0.3492002487182617 1549.2279052734375 0.5074090361595154 0.76343113 0.5405752062797546 True -11 32928 30.482832431793213 1.2830250263214111 1059.1842041015625 0.2348191738128662 1545.1163330078125 0.509070873260498 0.7694159 0.5080105066299438 True -12 35672 30.062967777252197 1.1908228397369385 1192.0028076171875 0.4817641079425812 1536.8089599609375 0.510658860206604 0.78251636 0.4627285897731781 True -13 38416 29.93078923225403 1.8861398696899414 1168.2840576171875 0.4226457178592682 1514.874755859375 0.5215914249420166 0.7927886 0.3976130485534668 True -14 41160 29.905774354934692 0.8549478054046631 1285.652587890625 0.2703046202659607 1506.689208984375 0.5237648487091064 0.8028965 0.3531785011291504 True -15 43904 29.988541841506958 0.8763561248779297 1280.9017333984375 0.3084787130355835 1500.6871337890625 0.5258612632751465 0.8137603 0.32379230856895447 True -16 46648 29.9707510471344 0.6904652118682861 989.439208984375 0.23376864194869995 1500.057373046875 0.5243148803710938 0.81889516 0.3083226680755615 True -17 49392 30.04649043083191 0.6798563003540039 1070.135009765625 0.2346501648426056 1493.3267822265625 0.5280300974845886 0.8215695 0.2958970367908478 True -18 52136 30.008193731307983 0.7133786678314209 1086.583251953125 0.18172584474086761 1495.7481689453125 0.525669515132904 0.82277733 0.2913912236690521 True -19 54880 30.077561378479004 1.1725714206695557 1099.103515625 0.19909179210662842 1492.921875 0.5278823375701904 0.82286453 0.29163429141044617 True diff --git a/ENCSR746ZPP/cherimoya.fold_1.performance.tsv b/ENCSR746ZPP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1e73b6f4bb588089e1984a5b65c3fc6181ef2c38..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1492.921875 0.22521206736564636 0.5278823971748352 0.32017338275909424 0.8228645324707031 0.771702229976654 0.29163429141044617 \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_2.evaluate.json b/ENCSR746ZPP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 56655bd4ab38a73add365f203357e5b0f3ce7d50..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988XHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_2.fit.json b/ENCSR746ZPP/cherimoya.fold_2.fit.json deleted file mode 100644 index 0f821f78811618e083a76db4276bee9162b86c62..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF988XHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_2.log b/ENCSR746ZPP/cherimoya.fold_2.log deleted file mode 100644 index dbfab7675757b38f269952281a54e5867eda8b91..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2894 36.6817421913147 4.254328966140747 1184.93603515625 0.5680817365646362 1767.6893310546875 0.3151191473007202 0.5853045 8.000983238220215 True -1 5788 32.178905963897705 0.9507479667663574 1545.932861328125 0.4995845854282379 1534.53076171875 0.4332064390182495 0.68524826 1.96409010887146 True -2 8682 32.20896077156067 0.565615177154541 1408.903564453125 0.5166724324226379 1496.7060546875 0.4514590799808502 0.6957982 1.2286694049835205 True -3 11576 32.14947485923767 0.5926592350006104 1171.5679931640625 0.4137957692146301 1472.506103515625 0.46216848492622375 0.71025676 0.9203864932060242 True -4 14470 32.260685205459595 0.561429500579834 1305.208251953125 0.5238507390022278 1457.1868896484375 0.4677812159061432 0.7220297 0.758206844329834 True -5 17364 32.23871183395386 0.5431914329528809 1210.967529296875 0.4212694764137268 1442.3380126953125 0.4769148826599121 0.72938824 0.6618530750274658 True -6 20258 32.3957405090332 0.5826585292816162 1281.39111328125 0.2343488335609436 1438.793701171875 0.47844669222831726 0.72992283 0.6183151602745056 True -7 23152 32.14830708503723 0.567767858505249 1249.82958984375 0.41141384840011597 1430.234375 0.48295414447784424 0.7351916 0.5530427694320679 True -8 26046 31.60047483444214 15.220813751220703 1144.899658203125 0.31252774596214294 1425.1087646484375 0.48625537753105164 0.73834693 0.6063446402549744 True -9 28940 31.724107027053833 1.7494990825653076 929.7808227539062 0.44776052236557007 1410.8565673828125 0.49494868516921997 0.74552816 0.485922247171402 True -10 31834 31.73311758041382 0.9333784580230713 1107.4102783203125 0.3494603633880615 1404.6943359375 0.4972984790802002 0.74671364 0.4515080153942108 True -11 34728 31.652913808822632 0.6055810451507568 1322.13720703125 0.35086530447006226 1396.4881591796875 0.5006936192512512 0.75661725 0.4152592718601227 True -12 37622 31.649843454360962 0.5708560943603516 1148.3016357421875 0.4199179410934448 1389.926513671875 0.5056459307670593 0.7650221 0.40383708477020264 True -13 40516 31.56753158569336 0.5342578887939453 1019.9465942382812 0.20803305506706238 1384.4971923828125 0.5063158869743347 0.77412236 0.3630939722061157 True -14 43410 31.59376859664917 0.5433399677276611 1236.9757080078125 0.22002843022346497 1377.5423583984375 0.510760486125946 0.7818535 0.3362729549407959 True -15 46304 31.58848547935486 1.7693250179290771 1262.516357421875 0.33841535449028015 1374.6201171875 0.5112731456756592 0.7893438 0.315523236989975 True -16 49198 31.563578367233276 0.5554702281951904 1116.74560546875 0.2829858660697937 1369.343994140625 0.5140075087547302 0.7938041 0.3022245466709137 True -17 52092 31.67926788330078 0.5648655891418457 1309.329833984375 0.2100883424282074 1367.528564453125 0.513843834400177 0.7969207 0.2949574887752533 True -18 54986 31.690547227859497 0.5327284336090088 1078.4805908203125 0.21634240448474884 1365.00341796875 0.5161065459251404 0.7953169 0.2935098111629486 False -19 57880 31.55968141555786 0.5464637279510498 1293.181884765625 0.249542236328125 1366.43896484375 0.5156688690185547 0.79531634 0.2941914498806 False diff --git a/ENCSR746ZPP/cherimoya.fold_2.performance.tsv b/ENCSR746ZPP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ed087e64af51cc945de4c55e5f4ac5cb7d51caad..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1367.528564453125 0.2351418137550354 0.513843834400177 0.3001270294189453 0.7969207167625427 0.734479546546936 0.2949574887752533 \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_3.evaluate.json b/ENCSR746ZPP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d5bdfd1be10923755c73f8bb3125fe760e5aa966..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988XHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_3.fit.json b/ENCSR746ZPP/cherimoya.fold_3.fit.json deleted file mode 100644 index 0fbbc857f2407baa2547e31a56d7e0f503c4bf40..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF988XHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_3.log b/ENCSR746ZPP/cherimoya.fold_3.log deleted file mode 100644 index 76808312535582f0ae7637e0a63dde616fb2c320..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 35.75485181808472 4.030543804168701 1261.600830078125 0.33643364906311035 1782.1197509765625 0.311799019575119 0.5747151 8.753131866455078 True -1 5612 31.164599895477295 0.5856022834777832 1288.939453125 0.5838600397109985 1573.3941650390625 0.4337137043476105 0.6599115 3.0029513835906982 True -2 8418 31.24300503730774 0.5498025417327881 1371.1099853515625 0.5795049071311951 1532.194091796875 0.4531029164791107 0.6746851 1.6627917289733887 True -3 11224 31.178603887557983 0.5485749244689941 1001.712890625 0.6454393863677979 1507.3896484375 0.4618549346923828 0.6910532 1.2111495733261108 True -4 14030 31.18603754043579 0.5436220169067383 1247.80078125 0.5751688480377197 1493.1041259765625 0.46682825684547424 0.6970142 1.0264098644256592 True -5 16836 31.232999324798584 0.5505955219268799 1144.2939453125 0.555598258972168 1479.9237060546875 0.47258639335632324 0.7009875 0.9218809008598328 True -6 19642 31.11504626274109 0.5529694557189941 1169.573974609375 0.4566456079483032 1467.192626953125 0.48007968068122864 0.7047508 0.8479250073432922 True -7 22448 31.067931175231934 0.5768094062805176 1183.0238037109375 0.3276565372943878 1463.820556640625 0.482148677110672 0.705371 0.7546150088310242 True -8 25254 30.654930114746094 0.5477170944213867 1268.19873046875 0.41460126638412476 1450.9166259765625 0.48775482177734375 0.7117659 0.601281464099884 True -9 28060 30.62203097343445 0.5409929752349854 1227.0927734375 0.4237632155418396 1445.7056884765625 0.4906632900238037 0.7209537 0.547621488571167 True -10 30866 30.599220514297485 0.5481417179107666 1133.8668212890625 0.212051659822464 1435.1104736328125 0.4960467517375946 0.71926486 0.485262393951416 False -11 33672 30.60055708885193 1.650517225265503 1237.611083984375 0.30272233486175537 1423.33056640625 0.5024162530899048 0.73165345 0.4479987919330597 True -12 36478 30.618757724761963 0.5481925010681152 1203.73974609375 0.3442026972770691 1419.785888671875 0.5026562213897705 0.74624777 0.4053422212600708 True -13 39284 30.55655550956726 0.5658438205718994 1091.4783935546875 0.28105103969573975 1413.0936279296875 0.5045340657234192 0.76025295 0.37554147839546204 True -14 42090 30.53758215904236 0.5572154521942139 995.861328125 0.24867793917655945 1405.078125 0.508228063583374 0.77226585 0.3499631881713867 True -15 44896 30.61176586151123 0.5373036861419678 1174.418212890625 0.39954590797424316 1399.8236083984375 0.5112125873565674 0.78495973 0.33277904987335205 True -16 47702 30.614386796951294 0.5538430213928223 1200.6966552734375 0.25869235396385193 1394.8543701171875 0.5117136836051941 0.79392123 0.31327131390571594 True -17 50508 30.583829879760742 0.5454628467559814 1238.537353515625 0.21219417452812195 1391.8104248046875 0.5128106474876404 0.7983594 0.3044617176055908 True -18 53314 30.53061270713806 0.5468502044677734 1019.9076538085938 0.1664576232433319 1390.63720703125 0.5137704014778137 0.80262196 0.2992035746574402 True -19 56120 30.52814817428589 0.5434298515319824 1152.9200439453125 0.13547958433628082 1393.5545654296875 0.5120307207107544 0.8018522 0.2979940176010132 False diff --git a/ENCSR746ZPP/cherimoya.fold_3.performance.tsv b/ENCSR746ZPP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index dfb4d6b5bafc6691f563412e105bdd7e09b52d7e..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1390.63720703125 0.23446984589099884 0.513770341873169 0.3010921776294708 0.8026219606399536 0.7462477684020996 0.2992035746574402 \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_4.evaluate.json b/ENCSR746ZPP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9568cfe2aeeba931a9bbe3018fad77d4f0aea308..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988XHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_4.fit.json b/ENCSR746ZPP/cherimoya.fold_4.fit.json deleted file mode 100644 index 3758bf1f2380a160b177b2ed51c03e66e8995112..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF988XHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR746ZPP/cherimoya.fold_4.log b/ENCSR746ZPP/cherimoya.fold_4.log deleted file mode 100644 index 90e516e706c91aafe41078a1ad3f4fd13a27afe8..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 36.53184509277344 4.242732286453247 1361.53466796875 0.5086296796798706 1678.70458984375 0.3070656955242157 0.5684758 6.375377655029297 True -1 5742 31.91261315345764 1.380509376525879 1274.39501953125 0.43055784702301025 1479.756591796875 0.42986586689949036 0.64669746 2.3472847938537598 True -2 8613 31.885659217834473 9.03650712966919 1240.11279296875 0.5013517141342163 1442.6019287109375 0.4501678943634033 0.6627694 1.141312837600708 True -3 11484 31.916868448257446 1.4554071426391602 1106.1573486328125 0.5988404154777527 1419.5821533203125 0.45535367727279663 0.68622935 0.9685002565383911 True -4 14355 31.892385959625244 0.5958695411682129 1248.057373046875 0.48200690746307373 1402.80615234375 0.46484604477882385 0.6970534 0.7995074391365051 True -5 17226 31.955101013183594 0.5861139297485352 1130.95361328125 0.32983821630477905 1384.7574462890625 0.4757626950740814 0.71085924 0.6701147556304932 True -6 20097 31.87247061729431 0.5551567077636719 1054.64599609375 0.38143736124038696 1380.7442626953125 0.4752807915210724 0.71893144 0.6624541282653809 True -7 22968 31.859355688095093 0.6319100856781006 1235.942138671875 0.43305808305740356 1375.1932373046875 0.4781257212162018 0.7216008 0.5427872538566589 True -8 25839 31.39396905899048 0.870835542678833 1185.946533203125 0.3867391347885132 1362.525390625 0.4870742857456207 0.72567934 0.45998597145080566 True -9 28710 31.255134105682373 0.5566205978393555 1219.115234375 0.33681362867355347 1359.744384765625 0.4890303313732147 0.7304713 0.43516024947166443 True -10 31581 31.355886697769165 0.5517699718475342 1104.348388671875 0.20849385857582092 1351.2974853515625 0.49327966570854187 0.7379633 0.4256570637226105 True -11 34452 31.369558334350586 0.5640296936035156 1107.6619873046875 0.20354387164115906 1343.107666015625 0.499390184879303 0.74191463 0.3967815637588501 True -12 37323 31.300341367721558 0.582817554473877 1103.452392578125 0.30286747217178345 1339.263427734375 0.49997055530548096 0.74956083 0.3759470582008362 True -13 40194 31.30686902999878 0.5559277534484863 1189.7315673828125 0.3721749186515808 1333.926513671875 0.5037320256233215 0.7589736 0.34474053978919983 True -14 43065 31.40819263458252 1.089094877243042 1348.454345703125 0.3984390199184418 1326.832763671875 0.5069468021392822 0.767428 0.3185473382472992 True -15 45936 31.383023500442505 0.5585100650787354 1108.017822265625 0.20138351619243622 1326.08349609375 0.5059379935264587 0.7782003 0.3032699227333069 True -16 48807 31.312927961349487 1.5897188186645508 1243.095947265625 0.25652891397476196 1323.8333740234375 0.5066846013069153 0.78239995 0.29124388098716736 True -17 51678 31.30688166618347 0.5540993213653564 1028.7667236328125 0.11568620055913925 1323.52734375 0.5067034363746643 0.7856182 0.2838872969150543 True -18 54549 31.308398485183716 0.9986026287078857 1170.572021484375 0.20349526405334473 1322.4859619140625 0.5081501007080078 0.7852397 0.28341150283813477 False -19 57420 31.270984888076782 0.5528864860534668 1161.349609375 0.14957711100578308 1320.731689453125 0.5091651678085327 0.7875842 0.2831138074398041 True diff --git a/ENCSR746ZPP/cherimoya.fold_4.performance.tsv b/ENCSR746ZPP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 629a5f171f882173abfc0fb971a49c8971f104cf..0000000000000000000000000000000000000000 --- a/ENCSR746ZPP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1320.731689453125 0.23884406685829163 0.5091651678085327 0.29062819480895996 0.7875841856002808 0.7175131440162659 0.2831138074398041 \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_0.evaluate.json b/ENCSR747RGR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index bc6c48bc587bc1484a9a6867479f09053d20ce26..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF991QRS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_0.fit.json b/ENCSR747RGR/cherimoya.fold_0.fit.json deleted file mode 100644 index 437054150b113f4229e116da35d45eb6977c5a75..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF991QRS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_0.log b/ENCSR747RGR/cherimoya.fold_0.log deleted file mode 100644 index 807ebd96de1193fce12db26ee125a2979c27256a..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2785 35.7606737613678 3.6647047996520996 275.0202331542969 0.32872259616851807 553.7999877929688 0.20762762427330017 0.75177175 6.303607940673828 True -1 5570 31.00231957435608 0.6092956066131592 358.6717529296875 0.3186717629432678 488.5341796875 0.24784913659095764 0.83234805 1.898361325263977 True -2 8355 31.036444187164307 0.5886094570159912 418.290283203125 0.6775326728820801 485.5611267089844 0.24878551065921783 0.8345104 1.0895105600357056 True -3 11140 31.05891489982605 0.589324951171875 468.6880187988281 0.33699414134025574 478.2029724121094 0.2521381378173828 0.8449204 0.5453449487686157 True -4 13925 31.001835346221924 1.2482197284698486 458.9547119140625 0.3134855628013611 472.8933410644531 0.25778380036354065 0.8508987 0.4524252116680145 True -5 16710 31.00218677520752 0.588416576385498 411.85003662109375 0.5255217552185059 469.7595520019531 0.2599925696849823 0.8578861 0.4344823658466339 True -6 19495 33.23296356201172 34.41064143180847 421.97247314453125 0.4507678747177124 465.11846923828125 0.2630537450313568 0.8662591 0.3766608238220215 True -7 22280 30.780813455581665 0.5946576595306396 437.277587890625 0.5839213132858276 462.6181335449219 0.2650405466556549 0.87215847 0.35700222849845886 True -8 25065 30.399832487106323 0.588670015335083 477.96575927734375 0.5978260040283203 460.074462890625 0.26677682995796204 0.8787048 0.33512115478515625 True -9 27850 30.344368934631348 0.600067138671875 328.4801330566406 0.5155313014984131 458.89361572265625 0.2677939534187317 0.88138956 0.309702068567276 True -10 30635 30.3455171585083 0.5820465087890625 470.29827880859375 0.3695582151412964 458.7214050292969 0.26682549715042114 0.8817962 0.309295117855072 True -11 33420 30.657448053359985 0.5825412273406982 355.56756591796875 0.22039803862571716 454.60955810546875 0.27051258087158203 0.88811916 0.3003207743167877 True -12 36205 30.461395502090454 0.7291727066040039 365.3546447753906 0.3353554904460907 454.9001159667969 0.269063264131546 0.8927531 0.2839437425136566 True -13 38990 30.542343378067017 0.592606782913208 430.94964599609375 0.3195265531539917 452.62908935546875 0.27136263251304626 0.8960478 0.27166274189949036 True -14 41775 30.471136331558228 0.5868873596191406 420.8578186035156 0.2598073482513428 450.8749694824219 0.2723919749259949 0.90021497 0.2559325695037842 True -15 44560 30.39961075782776 0.5767009258270264 308.56707763671875 0.3384160101413727 449.9742126464844 0.27307233214378357 0.9026337 0.24375934898853302 True -16 47345 30.365703105926514 0.5744707584381104 426.1707763671875 0.2770788073539734 448.9684143066406 0.273571252822876 0.90566504 0.2320147305727005 True -17 50130 30.398890256881714 0.5790984630584717 402.68646240234375 0.13146384060382843 447.9062194824219 0.2751150131225586 0.9079494 0.2295006513595581 True -18 52915 30.553468465805054 1.8619775772094727 496.95501708984375 0.1867789924144745 450.1082458496094 0.27242353558540344 0.9080142 0.23024041950702667 True -19 55700 30.56435227394104 0.583885669708252 342.6378173828125 0.2926885485649109 450.26019287109375 0.2727120518684387 0.90513116 0.23238976299762726 False diff --git a/ENCSR747RGR/cherimoya.fold_0.performance.tsv b/ENCSR747RGR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 022bba05ac3924aa014acbdd82436c3e7b3f1e2b..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -450.1082458496094 0.4854107201099396 0.27242350578308105 0.10033679753541946 0.908014178276062 0.8659454584121704 0.23024041950702667 \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_1.evaluate.json b/ENCSR747RGR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 88e6ca2e89579d2ae913694d9b31fe56827b7e82..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF991QRS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_1.fit.json b/ENCSR747RGR/cherimoya.fold_1.fit.json deleted file mode 100644 index 28a64f00115765b4bf80b1ffb0390eae706e8e96..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF991QRS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_1.log b/ENCSR747RGR/cherimoya.fold_1.log deleted file mode 100644 index 5ddaa2dc03e784b0e67f3b3782e54e11bfee026c..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2717 35.01084613800049 2.505786180496216 419.4571838378906 0.40885087847709656 722.4265747070312 0.22126278281211853 0.71710783 7.922393798828125 True -1 5434 30.372204780578613 0.6913650035858154 466.24664306640625 0.4650742709636688 632.4429931640625 0.27142876386642456 0.8022693 2.7370903491973877 True -2 8151 30.378371477127075 0.6691164970397949 344.1087646484375 0.689667820930481 614.4017333984375 0.2778962254524231 0.8183328 1.5737055540084839 True -3 10868 30.306914806365967 0.6875002384185791 378.5399169921875 0.42359572649002075 608.9174194335938 0.28042110800743103 0.8176176 1.4510204792022705 False -4 13585 30.258970975875854 0.6670739650726318 415.32049560546875 0.3767865002155304 598.0584106445312 0.2842933237552643 0.8331355 0.8917017579078674 True -5 16302 30.482768297195435 2.423630475997925 435.660400390625 0.3245187997817993 588.9469604492188 0.2901897430419922 0.8474813 0.7366788983345032 True -6 19019 30.23741888999939 0.6682116985321045 360.5040283203125 0.3704913854598999 584.4962158203125 0.29210200905799866 0.8603262 0.6412231922149658 True -7 21736 30.25845694541931 0.6491928100585938 380.02392578125 0.4327728748321533 580.0733032226562 0.29505327343940735 0.86433256 0.6319342851638794 True -8 24453 33.32713484764099 36.136298179626465 328.2033386230469 0.3567560315132141 573.7916870117188 0.30006536841392517 0.8732021 0.535147488117218 True -9 27170 30.339963912963867 2.219536304473877 362.7996826171875 0.38418424129486084 572.2178344726562 0.3004419505596161 0.87880343 0.49260619282722473 True -10 29887 29.856672286987305 4.955481052398682 430.2215270996094 0.46633195877075195 570.3599853515625 0.3016357123851776 0.88520527 0.4567202627658844 True -11 32604 29.691240549087524 0.6471376419067383 439.4021301269531 0.34621092677116394 566.6152954101562 0.30370664596557617 0.8923763 0.41483789682388306 True -12 35321 29.643900156021118 0.6568453311920166 496.4654541015625 0.3917735815048218 563.6183471679688 0.30614176392555237 0.8979153 0.3876400589942932 True -13 38038 29.691604614257812 0.6545703411102295 437.67340087890625 0.25145578384399414 558.7137451171875 0.3100331723690033 0.90233666 0.3595966696739197 True -14 40755 29.65066432952881 0.6427326202392578 445.76568603515625 0.4214608669281006 560.2906494140625 0.30736467242240906 0.90780264 0.32770997285842896 True -15 43472 29.575678825378418 0.6531548500061035 318.82781982421875 0.19068050384521484 557.725341796875 0.3088408410549164 0.9126118 0.30943354964256287 True -16 46189 29.62912917137146 36.64962577819824 354.87860107421875 0.40974098443984985 557.6572875976562 0.30907896161079407 0.91494143 0.290510892868042 True -17 48906 30.288862943649292 0.6624040603637695 323.8139343261719 0.21193665266036987 556.28369140625 0.310149222612381 0.9174825 0.2825038731098175 True -18 51623 29.668689250946045 0.6752843856811523 434.1844482421875 0.3687216639518738 557.5117797851562 0.30866238474845886 0.9158432 0.28270402550697327 False -19 54340 29.776742219924927 8.424753665924072 404.4429626464844 0.26146525144577026 558.0458984375 0.3089545965194702 0.9166014 0.28321292996406555 False diff --git a/ENCSR747RGR/cherimoya.fold_1.performance.tsv b/ENCSR747RGR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8e5d4ad2d0a8773ac384b7e6dc5a752ce778421b..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -556.28369140625 0.4557819962501526 0.310149222612381 0.1265573799610138 0.9174824953079224 0.8845897912979126 0.2825038731098175 \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_2.evaluate.json b/ENCSR747RGR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2d2252fc5f2a28293c7c5575e6ebacbe16a2f37d..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF991QRS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_2.fit.json b/ENCSR747RGR/cherimoya.fold_2.fit.json deleted file mode 100644 index aac5793cc8a127236e3ec1efd0e028a7e78e1b99..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF991QRS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_2.log b/ENCSR747RGR/cherimoya.fold_2.log deleted file mode 100644 index 4ad97a2776f22b0a124c64911e7d7c67756e0d0c..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2914 36.902666091918945 29.913925170898438 372.7911376953125 0.5563562512397766 606.8497924804688 0.21040226519107819 0.73257154 6.398648738861084 True -1 5828 34.397799253463745 1.6464028358459473 347.677490234375 0.6375752687454224 530.8663940429688 0.25375914573669434 0.827296 1.621997356414795 True -2 8742 32.52742052078247 0.5985875129699707 342.56103515625 0.4433993101119995 522.418701171875 0.2584320604801178 0.8419377 0.9020607471466064 True -3 11656 32.42627787590027 1.5466382503509521 451.23541259765625 0.444566011428833 513.4304809570312 0.2638571858406067 0.85426337 0.552598237991333 True -4 14570 32.391265869140625 0.6031475067138672 411.0931396484375 0.5426923632621765 507.3232727050781 0.26729676127433777 0.8632453 0.508451521396637 True -5 17484 33.22159504890442 0.591057538986206 431.29913330078125 0.33929187059402466 505.5657653808594 0.26821503043174744 0.86567324 0.559804379940033 True -6 20398 33.281885385513306 36.08516883850098 385.1211242675781 0.7202063798904419 502.92010498046875 0.269237756729126 0.8701822 0.48866501450538635 True -7 23312 32.690754652023315 0.630617618560791 404.17047119140625 0.39189833402633667 500.93389892578125 0.2711953818798065 0.87032 0.4450346529483795 True -8 26226 32.39528942108154 0.6033196449279785 402.16497802734375 0.4765029549598694 498.5419006347656 0.2730382978916168 0.87378407 0.44972649216651917 True -9 29140 32.3861870765686 0.6001591682434082 388.22314453125 0.30654314160346985 497.3571472167969 0.2737807631492615 0.87742066 0.4367195665836334 True -10 32054 31.948338747024536 0.6046972274780273 308.52783203125 0.21036988496780396 492.98883056640625 0.27756237983703613 0.8838182 0.3902877867221832 True -11 34968 31.755924701690674 0.5912954807281494 346.902587890625 0.4503472149372101 493.4490966796875 0.2766399085521698 0.8848202 0.3656157851219177 True -12 37882 31.751028537750244 0.5864074230194092 311.3746337890625 0.2850705683231354 491.31829833984375 0.2788662612438202 0.89189726 0.3370625674724579 True -13 40796 36.08138346672058 14.347753524780273 409.25604248046875 0.22796761989593506 488.64630126953125 0.28042978048324585 0.89481807 0.3073497712612152 True -14 43710 31.725638151168823 1.229654312133789 399.6512451171875 0.2553848922252655 486.3960876464844 0.2827425003051758 0.8990297 0.281354159116745 True -15 46624 31.76782488822937 0.5999305248260498 332.4817810058594 0.15482714772224426 486.25274658203125 0.282804936170578 0.90522575 0.2593342363834381 True -16 49538 31.75878620147705 0.59503173828125 336.33953857421875 0.24637320637702942 485.7068786621094 0.2820897400379181 0.9068594 0.2475213259458542 True -17 52452 31.71151041984558 0.9842522144317627 474.14532470703125 0.19213330745697021 485.51153564453125 0.2825588285923004 0.90639174 0.2440703809261322 False -18 55366 32.7446391582489 27.060269832611084 308.9328918457031 0.19776314496994019 488.037353515625 0.280009925365448 0.9067735 0.24469192326068878 False -19 58280 32.11153602600098 39.97512722015381 434.1981506347656 0.1639861911535263 488.62335205078125 0.2802659571170807 0.9056379 0.24558140337467194 False diff --git a/ENCSR747RGR/cherimoya.fold_2.performance.tsv b/ENCSR747RGR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 02c8b33599a9e75f504ad6b4dec69638139a4863..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -485.7068786621094 0.47503700852394104 0.2820897102355957 0.10816376656293869 0.9068593978881836 0.8712698817253113 0.2475213259458542 \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_3.evaluate.json b/ENCSR747RGR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3ddfaa0685752d1ba584f02fb8295d1ab590cfbb..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF991QRS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_3.fit.json b/ENCSR747RGR/cherimoya.fold_3.fit.json deleted file mode 100644 index 49c1d261bcebfc266484af855b775700c8d2ac8c..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF991QRS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_3.log b/ENCSR747RGR/cherimoya.fold_3.log deleted file mode 100644 index b63de7cf0def14c1b6716d50988cbba43fa8dd66..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.90602779388428 3.71980881690979 370.76531982421875 0.3652494251728058 572.5372924804688 0.2173074185848236 0.7090736 6.203017234802246 True -1 5500 30.699575901031494 0.5658185482025146 495.3551025390625 0.7353445887565613 508.9476623535156 0.2603077292442322 0.7792345 1.8121906518936157 True -2 8250 30.597516298294067 0.5487596988677979 411.7135925292969 0.32729095220565796 505.9019775390625 0.2624359130859375 0.78403836 1.327883243560791 True -3 11000 30.61841058731079 0.5484447479248047 286.76617431640625 0.26343774795532227 492.08172607421875 0.2689765393733978 0.8136424 0.8016905784606934 True -4 13750 30.6776282787323 0.5466318130493164 458.9044189453125 0.5532770156860352 488.49615478515625 0.2717914581298828 0.8130346 0.6717661619186401 False -5 16500 31.736002683639526 23.034214973449707 470.20159912109375 0.5830590128898621 486.4136657714844 0.272612601518631 0.81826043 0.6331704258918762 True -6 19250 34.4100284576416 32.6804735660553 399.86126708984375 0.25233757495880127 483.77191162109375 0.273541122674942 0.8294734 0.5980160236358643 True -7 22000 33.753541707992554 33.387415409088135 373.68011474609375 0.4774177670478821 480.3594665527344 0.27574214339256287 0.83548194 0.5503057241439819 True -8 24750 30.5803120136261 0.6068868637084961 501.4965515136719 0.4351781904697418 476.9214172363281 0.2785375416278839 0.8425864 0.5136808156967163 True -9 27500 30.674670934677124 0.5629804134368896 287.93603515625 0.3583854138851166 474.2890319824219 0.28076469898223877 0.85201836 0.49812930822372437 True -10 30250 30.643340826034546 1.0253658294677734 348.9111022949219 0.29045647382736206 472.5868225097656 0.2820092439651489 0.8559842 0.47453731298446655 True -11 33000 30.02264404296875 0.5530390739440918 380.3886413574219 0.3783518373966217 471.9373474121094 0.283066987991333 0.861775 0.43717193603515625 True -12 35750 30.06311559677124 0.5415129661560059 416.65435791015625 0.44130706787109375 471.69232177734375 0.28221407532691956 0.8667101 0.416683554649353 True -13 38500 38.047921657562256 3.0218734741210938 553.9841918945312 0.31492871046066284 466.96746826171875 0.28678953647613525 0.8743706 0.3751567602157593 True -14 41250 30.2520911693573 36.06294536590576 378.99871826171875 0.24384364485740662 466.0810241699219 0.285986065864563 0.87962496 0.34968698024749756 True -15 44000 30.003186464309692 0.547238826751709 390.4554443359375 0.5379924774169922 464.1533508300781 0.28807565569877625 0.88510674 0.3259756565093994 True -16 46750 30.030558347702026 0.5395677089691162 357.4080810546875 0.30662137269973755 463.3846130371094 0.28787916898727417 0.89072543 0.3074478209018707 True -17 49500 29.969784021377563 2.5731585025787354 381.4364013671875 0.1712217926979065 464.947021484375 0.2859756350517273 0.8944781 0.295993447303772 True -18 52250 29.976514101028442 0.5395205020904541 478.0967712402344 0.2780250310897827 463.8434753417969 0.28762316703796387 0.892153 0.29574939608573914 False -19 55000 30.0710186958313 0.5407364368438721 374.49468994140625 0.22478726506233215 464.5110168457031 0.2873304784297943 0.8938061 0.29608258605003357 False diff --git a/ENCSR747RGR/cherimoya.fold_3.performance.tsv b/ENCSR747RGR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9602bb3ab8458eb3553b2d2fbbef85e62bcf7801..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -464.947021484375 0.475587397813797 0.2859756350517273 0.10556997358798981 0.8944780826568604 0.852914571762085 0.295993447303772 \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_4.evaluate.json b/ENCSR747RGR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a12f5d26a89e22a9dc0ecbf63e2d647891ccc37d..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF991QRS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_4.fit.json b/ENCSR747RGR/cherimoya.fold_4.fit.json deleted file mode 100644 index 5cb0c4550cf9964337f712c7eee358e7d42e5763..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF991QRS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_4.log b/ENCSR747RGR/cherimoya.fold_4.log deleted file mode 100644 index 5864ef38a83a81a6154bfde0b698fb65675284c6..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2816 36.02520203590393 3.9510326385498047 429.0144348144531 0.4331618547439575 507.4842224121094 0.2062409520149231 0.71582365 5.82924222946167 True -1 5632 31.337936878204346 0.6387178897857666 327.05615234375 0.7357512712478638 457.50299072265625 0.24194775521755219 0.7871722 1.5150022506713867 True -2 8448 31.305371522903442 0.6282923221588135 353.72125244140625 0.37334635853767395 452.6225891113281 0.24511465430259705 0.79399633 1.2284828424453735 True -3 11264 30.94054365158081 3.9573299884796143 509.9273681640625 0.5531659722328186 444.32843017578125 0.24812717735767365 0.817944 0.6024667024612427 True -4 14080 30.717814445495605 0.6158847808837891 353.76995849609375 0.5405073761940002 439.47137451171875 0.2512400448322296 0.8243997 0.43357864022254944 True -5 16896 30.817349195480347 1.3079638481140137 365.74639892578125 0.3890128433704376 437.7562255859375 0.25245484709739685 0.8334412 0.44995149970054626 True -6 19712 30.773578882217407 0.6221907138824463 308.796875 0.46973347663879395 432.8579406738281 0.25556933879852295 0.8431259 0.38802486658096313 True -7 22528 30.736253261566162 0.6137826442718506 386.4859619140625 0.4181422293186188 430.7658996582031 0.25708675384521484 0.8509449 0.3516715466976166 True -8 25344 30.635976314544678 0.6145045757293701 418.1168212890625 0.5567663311958313 428.5710754394531 0.25848767161369324 0.8578541 0.33869391679763794 True -9 28160 30.773273468017578 0.6075599193572998 348.2579040527344 0.28057658672332764 425.33447265625 0.26145535707473755 0.861555 0.322631299495697 True -10 30976 30.585644483566284 0.609703779220581 331.80078125 0.2840108573436737 424.33587646484375 0.26226723194122314 0.8659348 0.3036518394947052 True -11 33792 30.82253885269165 0.6161677837371826 392.96405029296875 0.24702243506908417 423.435302734375 0.2621590495109558 0.8694304 0.2947912812232971 True -12 36608 30.726621627807617 0.6094386577606201 350.4825134277344 0.4092825651168823 421.0402526855469 0.26473209261894226 0.876594 0.27777722477912903 True -13 39424 30.697316646575928 0.6131820678710938 491.0291748046875 0.3164622485637665 420.8338623046875 0.26393765211105347 0.8847379 0.26040810346603394 True -14 42240 30.82286810874939 0.6370089054107666 431.367431640625 0.3201664388179779 419.4109191894531 0.26472094655036926 0.88721323 0.24947050213813782 True -15 45056 30.862350940704346 0.6193654537200928 308.992431640625 0.2351197451353073 419.25048828125 0.2649068236351013 0.8926471 0.23593761026859283 True -16 47872 31.038604736328125 2.4764163494110107 451.00140380859375 0.1391005963087082 418.116943359375 0.2650790810585022 0.89806336 0.22730033099651337 True -17 50688 30.924500703811646 31.911885499954224 472.8102722167969 0.344293475151062 418.85260009765625 0.26453813910484314 0.8982845 0.2219739407300949 True -18 53504 31.26623296737671 0.6573464870452881 449.59112548828125 0.17235678434371948 418.8022766113281 0.26503750681877136 0.89855725 0.2222907990217209 True -19 56320 31.47904634475708 0.6326889991760254 359.8194885253906 0.20071685314178467 419.30816650390625 0.26473841071128845 0.8998242 0.2229972630739212 True diff --git a/ENCSR747RGR/cherimoya.fold_4.performance.tsv b/ENCSR747RGR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c2e279e82a302811ef965742e4f14a81822e8ba9..0000000000000000000000000000000000000000 --- a/ENCSR747RGR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -419.30816650390625 0.49163463711738586 0.26473841071128845 0.09101825207471848 0.8998242020606995 0.8491501212120056 0.2229972630739212 \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_0.evaluate.json b/ENCSR747SEU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 92b870583f7d9538ecbb4890d2b5f6bdc5d0efb0..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387IUX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_0.fit.json b/ENCSR747SEU/cherimoya.fold_0.fit.json deleted file mode 100644 index cf9c942afbcb61fd6bf37f523fa70c7e3ee2aa5f..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF387IUX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_0.log b/ENCSR747SEU/cherimoya.fold_0.log deleted file mode 100644 index 0009f4ecabc94b86320a72e0dd811020661c0313..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.1096510887146 4.410450220108032 915.9168701171875 0.7217472791671753 1214.4267578125 0.2785796821117401 0.6754109 7.3810834884643555 True -1 5494 29.87271022796631 0.5934176445007324 1047.00634765625 0.8661757111549377 1040.2742919921875 0.365283727645874 0.7410221 2.118267297744751 True -2 8241 30.206889390945435 1.0860388278961182 711.3103637695312 0.7622064352035522 1022.7717895507812 0.3736260235309601 0.7554879 1.1760410070419312 True -3 10988 30.190069675445557 1.8774547576904297 1044.599853515625 1.1540639400482178 1005.297119140625 0.38265615701675415 0.7612224 0.9316361546516418 True -4 13735 30.250811338424683 2.713104486465454 944.4135131835938 0.5147057771682739 1001.33203125 0.3832760155200958 0.7644841 0.7992954850196838 True -5 16482 30.201969385147095 0.5734798908233643 756.9635009765625 0.46678394079208374 992.8065795898438 0.3890022039413452 0.7702478 0.6933202147483826 True -6 19229 30.197772979736328 0.571831464767456 803.096923828125 0.7623589038848877 984.591796875 0.39373093843460083 0.776838 0.6033759117126465 True -7 21976 30.19576072692871 0.5674409866333008 905.0978393554688 0.4156765937805176 981.50146484375 0.39449343085289 0.7835487 0.610539436340332 True -8 24723 30.209051847457886 0.5720570087432861 992.0471801757812 0.8218362331390381 977.2745971679688 0.3965098261833191 0.78620917 0.5616379380226135 True -9 27470 30.24903678894043 0.5695228576660156 721.984130859375 0.6337918043136597 970.7307739257812 0.4005909860134125 0.78923035 0.5150237679481506 True -10 30217 30.32763934135437 0.5696213245391846 946.1557006835938 0.6947209239006042 964.9100341796875 0.40450817346572876 0.7959039 0.4883687496185303 True -11 32964 30.369321584701538 0.5924098491668701 913.8560791015625 0.475230872631073 961.782470703125 0.4047521650791168 0.80251074 0.4773435592651367 True -12 35711 30.307294845581055 2.2414517402648926 924.3055419921875 0.5246322154998779 959.3267822265625 0.40602508187294006 0.80828106 0.4571307301521301 True -13 38458 30.282856941223145 0.5776324272155762 834.6683349609375 0.48824694752693176 954.3877563476562 0.4090363383293152 0.81444263 0.43956661224365234 True -14 41205 30.407203674316406 0.5774812698364258 692.3584594726562 0.36650580167770386 953.448974609375 0.4103212356567383 0.82031256 0.4211790859699249 True -15 43952 30.272248029708862 1.381941795349121 793.0888671875 0.4484716057777405 954.0233764648438 0.4096473157405853 0.82647276 0.41096290946006775 True -16 46699 30.345031023025513 0.595989465713501 760.8991088867188 0.46998828649520874 948.9266967773438 0.41213443875312805 0.8304333 0.39761579036712646 True -17 49446 30.36177921295166 0.5727605819702148 717.1713256835938 0.3485734462738037 950.1242065429688 0.41138893365859985 0.832571 0.389617919921875 True -18 52193 30.33947253227234 0.5738503932952881 845.08203125 0.40148431062698364 949.825927734375 0.41313987970352173 0.83342475 0.38869690895080566 True -19 54940 30.592182636260986 0.5764765739440918 897.4795532226562 0.377843976020813 949.8593139648438 0.4128504693508148 0.83321255 0.39022621512413025 False diff --git a/ENCSR747SEU/cherimoya.fold_0.performance.tsv b/ENCSR747SEU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 65bef5d80a0cebe9816119391cd6131ff4e46b7d..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -949.825927734375 0.3914037048816681 0.4131399095058441 0.1602213978767395 0.8334247469902039 0.7871685028076172 0.38869690895080566 \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_1.evaluate.json b/ENCSR747SEU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 34a0248771cecfa1964a3e25d4983be721b6620e..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387IUX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_1.fit.json b/ENCSR747SEU/cherimoya.fold_1.fit.json deleted file mode 100644 index e08f8aa04213160c7595d7f8ac6cd08ed991db2e..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF387IUX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_1.log b/ENCSR747SEU/cherimoya.fold_1.log deleted file mode 100644 index 82f76465cecc96d12597e84a39fc27cb2018dcfa..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2695 33.24697279930115 3.7868659496307373 875.33349609375 0.6915292739868164 1433.3026123046875 0.2783281207084656 0.6751244 9.083123207092285 True -1 5390 29.56811785697937 0.7409396171569824 950.2652587890625 0.7907798290252686 1220.9676513671875 0.3789064586162567 0.74710166 2.545604705810547 True -2 8085 29.61384391784668 0.7190952301025391 1007.08203125 0.6833465099334717 1194.3056640625 0.3871869146823883 0.7599851 1.6329596042633057 True -3 10780 29.643182516098022 0.711416482925415 823.2105102539062 0.5359748601913452 1175.858642578125 0.3929557204246521 0.7735296 1.099762201309204 True -4 13475 29.6499924659729 0.7213366031646729 1021.45068359375 0.7478077411651611 1160.8843994140625 0.4010545015335083 0.7814419 0.9208284020423889 True -5 16170 29.64586591720581 0.7123103141784668 848.2000732421875 0.4660567045211792 1155.9932861328125 0.40286487340927124 0.784406 0.7990028858184814 True -6 18865 29.942664861679077 8.968616008758545 694.2142333984375 0.6179338693618774 1151.53369140625 0.40443602204322815 0.78446114 0.751412034034729 True -7 21560 29.63023614883423 1.1294715404510498 679.23486328125 0.429881751537323 1143.24609375 0.40807652473449707 0.7899768 0.6820701956748962 True -8 24255 29.750587940216064 3.1906533241271973 712.58251953125 0.6311932802200317 1134.4576416015625 0.41318732500076294 0.7922988 0.6593030691146851 True -9 26950 29.636631727218628 26.043151140213013 793.72119140625 0.42500022053718567 1131.859619140625 0.414026141166687 0.7982121 0.6634018421173096 True -10 29645 29.680186986923218 0.7250642776489258 1052.347412109375 0.6226865649223328 1124.8387451171875 0.4173351228237152 0.8066797 0.579613447189331 True -11 32340 29.94286799430847 0.7215704917907715 1050.63427734375 0.4999454915523529 1120.2294921875 0.41927570104599 0.8119461 0.5827773809432983 True -12 35035 29.86853814125061 0.7204241752624512 836.7112426757812 0.4808826744556427 1115.646484375 0.4199400544166565 0.81820095 0.5320430994033813 True -13 37730 29.739985466003418 0.718064546585083 872.9483642578125 0.5866750478744507 1109.116455078125 0.4241587817668915 0.8278944 0.4899662435054779 True -14 40425 29.71587347984314 0.7191143035888672 855.100830078125 0.3933257460594177 1106.2181396484375 0.4254453480243683 0.8358615 0.47011128067970276 True -15 43120 29.698516368865967 0.7272219657897949 585.1500854492188 0.3805009126663208 1100.05322265625 0.42864200472831726 0.84028506 0.44179704785346985 True -16 45815 29.65227174758911 0.726757287979126 784.5104370117188 0.5269666910171509 1098.4278564453125 0.4293490946292877 0.8459913 0.42484250664711 True -17 48510 29.60724377632141 0.7238357067108154 786.7060546875 0.23310336470603943 1098.4259033203125 0.42813774943351746 0.8468864 0.41352978348731995 True -18 51205 29.61888837814331 0.7239987850189209 717.0308837890625 0.43855762481689453 1096.2464599609375 0.4308152496814728 0.84727615 0.41284701228141785 True -19 53900 29.623298406600952 0.7056734561920166 875.0848388671875 0.32197830080986023 1099.31494140625 0.4287295341491699 0.8471829 0.41223812103271484 False diff --git a/ENCSR747SEU/cherimoya.fold_1.performance.tsv b/ENCSR747SEU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 700d1337f3d7e35d7eda2a93d6907b85a62a2364..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1096.2464599609375 0.3753645122051239 0.4308152198791504 0.18142138421535492 0.8472761511802673 0.8242003917694092 0.41284701228141785 \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_2.evaluate.json b/ENCSR747SEU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 942280ef4fa8d6d63b7830ff7de5a7086ff22bb9..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387IUX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_2.fit.json b/ENCSR747SEU/cherimoya.fold_2.fit.json deleted file mode 100644 index 0b4527df2311ee2fb93a4355e90c1f3fb2339369..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF387IUX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_2.log b/ENCSR747SEU/cherimoya.fold_2.log deleted file mode 100644 index 635ca4b66fda301f9c2057fc775998c4942f55c9..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 34.891132831573486 3.6105129718780518 768.537353515625 0.713081419467926 1277.7684326171875 0.28073444962501526 0.6718628 6.8400373458862305 True -1 5776 31.513696908950806 0.5618491172790527 805.9105834960938 0.9455870389938354 1099.5194091796875 0.36698436737060547 0.7282707 1.954988718032837 True -2 8664 31.736119270324707 0.5497558116912842 791.968017578125 0.5783411860466003 1075.030517578125 0.3779955506324768 0.7432979 0.9929923415184021 True -3 11552 31.74277663230896 0.5561463832855225 867.130859375 0.4854061007499695 1062.774169921875 0.38380640745162964 0.7538877 0.8269903063774109 True -4 14440 31.73142647743225 0.5541212558746338 872.00927734375 0.8620157241821289 1054.234130859375 0.38822686672210693 0.7587397 0.8104634881019592 True -5 17328 31.77880096435547 0.5493736267089844 950.0118408203125 0.47238489985466003 1057.6563720703125 0.38644808530807495 0.76409936 1.0891972780227661 True -6 20216 31.738478899002075 1.6720936298370361 643.68798828125 1.2635245323181152 1047.3189697265625 0.3909924328327179 0.77110493 0.7245537638664246 True -7 23104 31.779598712921143 0.5500507354736328 858.7390747070312 0.5664806962013245 1038.568603515625 0.3964603543281555 0.77460885 0.6297377347946167 True -8 25992 31.748541355133057 0.5578382015228271 787.7890625 0.40541553497314453 1036.4241943359375 0.39626818895339966 0.78305995 0.6548956036567688 True -9 28880 31.77438473701477 5.080409526824951 778.1323852539062 0.7294242978096008 1030.2420654296875 0.39996418356895447 0.7851745 0.6101898550987244 True -10 31768 31.909224033355713 0.5973000526428223 793.9754638671875 0.5440199375152588 1025.731689453125 0.4017687439918518 0.7913306 0.6362536549568176 True -11 34656 31.764081478118896 0.5622930526733398 838.3565673828125 0.457681268453598 1020.609130859375 0.4044109582901001 0.7947295 0.5935238599777222 True -12 37544 31.807594537734985 3.3091025352478027 835.28955078125 0.41711053252220154 1016.8059692382812 0.4054819345474243 0.8029337 0.5601168274879456 True -13 40432 31.827125549316406 0.5683214664459229 840.0913696289062 0.3734230399131775 1012.418701171875 0.40849578380584717 0.8087877 0.5221932530403137 True -14 43320 31.84403371810913 0.5656051635742188 879.732666015625 0.38113510608673096 1007.554443359375 0.4100121855735779 0.81491905 0.4899522066116333 True -15 46208 31.849769592285156 0.576423168182373 701.77587890625 0.3411334753036499 1008.1915893554688 0.40912938117980957 0.8202909 0.44807669520378113 True -16 49096 31.896288871765137 0.5654709339141846 888.4017333984375 0.5107787847518921 1002.4837646484375 0.4130096733570099 0.8243919 0.42510804533958435 True -17 51984 31.888763427734375 0.5651328563690186 938.6764526367188 0.2894653081893921 1003.5443115234375 0.4118577241897583 0.8273262 0.41303756833076477 True -18 54872 31.827391147613525 0.565204381942749 655.79248046875 0.3423321545124054 1004.0225830078125 0.4116106927394867 0.82762897 0.4082516133785248 True -19 57760 31.835851907730103 0.5736610889434814 654.4183349609375 0.2734907269477844 1006.1888427734375 0.4097523093223572 0.8273968 0.4080558121204376 False diff --git a/ENCSR747SEU/cherimoya.fold_2.performance.tsv b/ENCSR747SEU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f88561a7bd76423e108519c6dcf548e10950b957..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1004.0225830078125 0.3894766569137573 0.4116106629371643 0.1612655520439148 0.8276289701461792 0.7933156490325928 0.4082516133785248 \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_3.evaluate.json b/ENCSR747SEU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 131a453e27ec7b3888453326e2813f6af6606d98..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387IUX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_3.fit.json b/ENCSR747SEU/cherimoya.fold_3.fit.json deleted file mode 100644 index 7f0511189473a35a5636cd11c50576948e81d814..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF387IUX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_3.log b/ENCSR747SEU/cherimoya.fold_3.log deleted file mode 100644 index 86b2861e6a30432e215bedc5497e2b171d78e2c0..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 34.051069021224976 3.6993370056152344 861.8731079101562 0.6062080264091492 1170.75634765625 0.2868708074092865 0.68771106 6.800388336181641 True -1 5522 30.29237127304077 0.5218250751495361 811.1956787109375 0.7093003988265991 1011.7171630859375 0.37005943059921265 0.75614494 2.0182573795318604 True -2 8283 30.386695384979248 0.5115816593170166 1012.243408203125 0.9172690510749817 987.4125366210938 0.3788392245769501 0.76868224 1.057119607925415 True -3 11044 30.453492879867554 0.5127441883087158 851.2481689453125 0.5784838199615479 972.0687255859375 0.38692522048950195 0.77819836 0.9571861028671265 True -4 13805 30.356128215789795 0.9669592380523682 804.5429077148438 0.7127218842506409 971.005615234375 0.3873743414878845 0.7830931 1.01742684841156 True -5 16566 30.393152713775635 0.5115599632263184 792.485107421875 0.901557981967926 962.8538208007812 0.39167582988739014 0.7820467 0.8687011003494263 False -6 19327 30.350194215774536 0.5175397396087646 868.59033203125 0.7266748547554016 956.8812866210938 0.3941900134086609 0.7870693 0.6816715598106384 True -7 22088 30.37815570831299 0.5145852565765381 864.2753295898438 0.6151978373527527 948.416015625 0.4006773829460144 0.7933098 0.6434175968170166 True -8 24849 30.341472625732422 0.5104503631591797 886.869384765625 0.5343981981277466 944.9816284179688 0.4019467532634735 0.7941673 0.6781550645828247 True -9 27610 30.39560341835022 0.5158774852752686 1109.297119140625 0.7881209850311279 941.8056640625 0.40281942486763 0.7976931 0.6354643702507019 True -10 30371 30.44321298599243 0.5167751312255859 779.2255249023438 0.49080297350883484 937.3998413085938 0.40518662333488464 0.8019174 0.5917180180549622 True -11 33132 30.43125820159912 0.5182054042816162 770.1859130859375 0.5765913724899292 937.74755859375 0.4041193723678589 0.80714387 0.5496281385421753 True -12 35893 30.419612169265747 0.5173959732055664 615.6712036132812 0.4529208540916443 927.4783935546875 0.41038310527801514 0.8158471 0.5293339490890503 True -13 38654 30.408429861068726 0.5132579803466797 791.0133056640625 0.40596678853034973 923.1531372070312 0.41268280148506165 0.8201211 0.48910728096961975 True -14 41415 30.4237322807312 0.5172121524810791 768.4266357421875 0.4915660619735718 925.6414184570312 0.4093349575996399 0.8259172 0.46749401092529297 True -15 44176 30.373804092407227 0.5112066268920898 711.9820556640625 0.38519832491874695 920.5038452148438 0.4134604334831238 0.83222425 0.4360864460468292 True -16 46937 30.373165607452393 0.5159566402435303 724.8720703125 0.7164135575294495 916.9338989257812 0.4153270125389099 0.8356406 0.4098644554615021 True -17 49698 30.363545417785645 0.519991397857666 779.969482421875 0.39463943243026733 918.1531372070312 0.41447243094444275 0.8388187 0.40035662055015564 True -18 52459 30.33521318435669 0.5147569179534912 812.168212890625 0.5253605246543884 916.2501831054688 0.41602587699890137 0.83888257 0.39737895131111145 True -19 55220 30.351513385772705 0.8753764629364014 807.6583251953125 0.19156385958194733 917.61328125 0.4149830639362335 0.83884865 0.39908620715141296 False diff --git a/ENCSR747SEU/cherimoya.fold_3.performance.tsv b/ENCSR747SEU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 68354c4c5830d8ac8552e734a982461e62acb585..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -916.2501831054688 0.39083096385002136 0.41602587699890137 0.15521888434886932 0.838882565498352 0.7913652062416077 0.39737895131111145 \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_4.evaluate.json b/ENCSR747SEU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c00987ad710cf00500a7fd5ef630536260804055..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF387IUX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_4.fit.json b/ENCSR747SEU/cherimoya.fold_4.fit.json deleted file mode 100644 index 4b5a42b009d4970e2d8c0723065d261d986e6503..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF387IUX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747SEU/cherimoya.fold_4.log b/ENCSR747SEU/cherimoya.fold_4.log deleted file mode 100644 index 46fa6a11bfd130bcd2c6871671082d3e82492d01..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2795 34.59208583831787 3.619769811630249 841.48291015625 0.9672176837921143 1108.1090087890625 0.27692532539367676 0.66361153 7.167598247528076 True -1 5590 30.421722412109375 0.603240966796875 785.9049072265625 0.7549573183059692 966.4415283203125 0.3599081039428711 0.7231266 2.2119052410125732 True -2 8385 30.731122732162476 0.6140477657318115 758.619140625 0.7745897769927979 947.8734741210938 0.36823639273643494 0.73373175 0.9910162091255188 True -3 11180 30.701369285583496 0.6050105094909668 750.8824462890625 0.7736676931381226 933.4807739257812 0.37570253014564514 0.743476 0.9371441006660461 True -4 13975 30.75669002532959 0.5855751037597656 1147.090087890625 0.5662445425987244 926.55126953125 0.37917429208755493 0.74772257 0.8667206764221191 True -5 16770 30.929691553115845 1.690129041671753 772.4481811523438 0.8632813692092896 921.1624755859375 0.3825540244579315 0.75753844 0.6817589998245239 True -6 19565 30.82716464996338 0.6123602390289307 853.070556640625 0.5546789169311523 912.9883422851562 0.38764286041259766 0.7587332 0.647765576839447 True -7 22360 30.900479316711426 0.5951845645904541 778.8175048828125 0.5507131814956665 912.587890625 0.38770052790641785 0.7634003 0.6542646288871765 True -8 25155 30.8133602142334 1.8361239433288574 690.9705810546875 0.5923600792884827 907.377685546875 0.3912111520767212 0.7674402 0.6409180164337158 True -9 27950 30.839332580566406 0.601017951965332 884.83544921875 0.7235617637634277 905.7105102539062 0.39114218950271606 0.7725656 0.625978946685791 True -10 30745 30.789879322052002 0.5889768600463867 934.4205322265625 0.5088337659835815 902.6871948242188 0.39200323820114136 0.7822637 0.5570800304412842 True -11 33540 30.727776050567627 0.5879740715026855 666.0529174804688 0.3177100419998169 898.1455078125 0.3966634273529053 0.7876974 0.5194724202156067 True -12 36335 30.823461055755615 0.5923547744750977 769.6132202148438 0.4996407628059387 896.2332153320312 0.39724603295326233 0.7948942 0.4979109764099121 True -13 39130 30.767358779907227 0.5976195335388184 713.641845703125 0.4618504047393799 890.4976806640625 0.4008758068084717 0.80335456 0.44505274295806885 True -14 41925 30.751323223114014 0.5824000835418701 798.3314208984375 0.5277848243713379 887.1470947265625 0.4026893377304077 0.8088753 0.42584991455078125 True -15 44720 30.76374840736389 0.5869741439819336 760.386962890625 0.4766950011253357 886.889404296875 0.40372228622436523 0.8162519 0.4087662696838379 True -16 47515 30.742627382278442 1.6730268001556396 765.7391357421875 0.44023045897483826 885.5866088867188 0.4037993848323822 0.8222721 0.3913561701774597 True -17 50310 30.78382110595703 0.5889575481414795 713.3109130859375 0.49739038944244385 884.974609375 0.40504395961761475 0.8236678 0.3853326737880707 True -18 53105 30.730682611465454 0.5837364196777344 796.5944213867188 0.4484427869319916 884.8206176757812 0.4060182571411133 0.8255936 0.38338395953178406 True -19 55900 30.75464177131653 0.5853257179260254 775.659423828125 0.3196653723716736 884.5555419921875 0.4061582088470459 0.8248181 0.38279464840888977 False diff --git a/ENCSR747SEU/cherimoya.fold_4.performance.tsv b/ENCSR747SEU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4fb8e9cf1fb31def4c6bf51754ba5fb6436c507c..0000000000000000000000000000000000000000 --- a/ENCSR747SEU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -884.8206176757812 0.3989814221858978 0.40601828694343567 0.14941638708114624 0.8255935907363892 0.7719823718070984 0.38338395953178406 \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_0.evaluate.json b/ENCSR749BWV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6ea69560b498b88eb502fab4243f77b8c77d942f..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF028OAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_0.fit.json b/ENCSR749BWV/cherimoya.fold_0.fit.json deleted file mode 100644 index fb5268f41299963e3b8ae170287b01505cf2b7d9..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF028OAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_0.log b/ENCSR749BWV/cherimoya.fold_0.log deleted file mode 100644 index 51673808fded3488e4571d576b4ecfb7eab44af4..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 33.697370290756226 3.9582791328430176 768.596923828125 0.8791283369064331 1342.140625 0.27534088492393494 0.57047427 6.464375972747803 True -1 5482 30.110865116119385 2.5473697185516357 944.1544189453125 0.7591885328292847 1206.8460693359375 0.3880123496055603 0.6209419 1.4253885746002197 True -2 8223 30.150395154953003 1.989412784576416 845.28759765625 1.0632574558258057 1191.881103515625 0.39807647466659546 0.63284844 0.6904018521308899 True -3 10964 30.063589334487915 1.5968637466430664 866.0939331054688 0.8077396750450134 1177.6475830078125 0.4047538936138153 0.6370153 0.5909039378166199 True -4 13705 30.099787950515747 1.9792087078094482 1048.381591796875 0.6793403625488281 1166.892578125 0.4089663028717041 0.6425013 0.5072827339172363 True -5 16446 29.87299346923828 1.3718030452728271 897.0767822265625 0.6326394081115723 1160.0330810546875 0.41219961643218994 0.6384341 0.5379690527915955 False -6 19187 29.61099863052368 0.550633430480957 1022.5042724609375 0.9066652655601501 1143.719482421875 0.417997270822525 0.6402891 0.5112903118133545 False -7 21928 29.46985125541687 0.5347945690155029 870.4359130859375 0.8782589435577393 1134.3509521484375 0.42031124234199524 0.6482296 0.5000026226043701 True -8 24669 29.442487001419067 0.5345101356506348 889.5708618164062 0.6568033695220947 1132.445556640625 0.4249473810195923 0.6475153 0.5626745223999023 False -9 27410 29.54020643234253 0.5365571975708008 742.7841796875 0.5127058029174805 1118.3148193359375 0.4319573938846588 0.65568244 0.5047832727432251 True -10 30151 29.5190691947937 0.5322279930114746 906.9005126953125 0.469828724861145 1114.81982421875 0.4312089681625366 0.6630736 0.5252854228019714 True -11 32892 29.56719398498535 0.5259857177734375 927.1117553710938 0.6979880928993225 1106.3858642578125 0.43782132863998413 0.6633024 0.538154661655426 True -12 35633 29.459484100341797 0.5223722457885742 865.6121215820312 0.7082798480987549 1104.0726318359375 0.4383296072483063 0.6739149 0.5357289910316467 True -13 38374 29.525909662246704 0.5278067588806152 866.26953125 0.5845991969108582 1095.723388671875 0.44414806365966797 0.67969334 0.5080334544181824 True -14 41115 29.46432614326477 0.5344128608703613 860.2874755859375 0.6983340978622437 1087.591796875 0.44911831617355347 0.6909857 0.4659494161605835 True -15 43856 29.46345090866089 0.5329580307006836 923.8439331054688 0.5325801372528076 1081.3187255859375 0.4521231949329376 0.70085233 0.4366200864315033 True -16 46597 29.476115465164185 0.5236778259277344 892.9515991210938 0.49513599276542664 1078.0667724609375 0.45541897416114807 0.7066907 0.41073527932167053 True -17 49338 29.471877574920654 0.5369834899902344 808.6422119140625 0.4002218246459961 1076.60791015625 0.45613884925842285 0.71073437 0.3994782567024231 True -18 52079 29.532867670059204 0.5263769626617432 849.5090942382812 0.30592864751815796 1077.93701171875 0.45441514253616333 0.7091679 0.40095990896224976 False -19 54820 29.485744953155518 0.5353095531463623 993.57275390625 0.2447918802499771 1076.8057861328125 0.45559942722320557 0.71033233 0.4005333185195923 False diff --git a/ENCSR749BWV/cherimoya.fold_0.performance.tsv b/ENCSR749BWV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index dabef884892d4d05cdc3890235b8e20777deeacc..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1076.60791015625 0.30822280049324036 0.45613884925842285 0.23160088062286377 0.7107343673706055 0.6477111577987671 0.3994782567024231 \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_1.evaluate.json b/ENCSR749BWV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1e68da234a28773ebad38b9c3dc477eb9b6384b2..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF028OAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_1.fit.json b/ENCSR749BWV/cherimoya.fold_1.fit.json deleted file mode 100644 index c9d629bacacc19fb1f9789717bfd1290ff3b3986..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF028OAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_1.log b/ENCSR749BWV/cherimoya.fold_1.log deleted file mode 100644 index 0a3f4d98d49389544eb5909eac0f16d6b75f748d..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 34.319019079208374 3.786518096923828 881.2080078125 0.7606794834136963 1615.5806884765625 0.2815838158130646 0.57857025 7.864569664001465 True -1 5540 30.570268630981445 0.6788103580474854 775.0791625976562 0.8004909157752991 1439.120849609375 0.408193975687027 0.612532 1.7623131275177002 True -2 8310 30.505937814712524 0.6701564788818359 801.9095458984375 0.7161877155303955 1419.618896484375 0.4116970896720886 0.62622344 1.0848454236984253 True -3 11080 30.452324867248535 0.6621131896972656 881.666259765625 0.6857101917266846 1403.05078125 0.42038196325302124 0.65602493 0.7083469033241272 True -4 13850 30.44294047355652 0.6652004718780518 1133.0032958984375 0.8211941123008728 1390.3992919921875 0.42503559589385986 0.6593674 0.628214955329895 True -5 16620 29.83488178253174 0.6607885360717773 949.625 0.5674422383308411 1360.337890625 0.42860105633735657 0.67107505 0.5753837823867798 True -6 19390 29.827736377716064 4.425720453262329 910.443603515625 0.569117546081543 1305.65380859375 0.4313930869102478 0.67413193 0.5868982076644897 True -7 22160 29.894291877746582 1.1178035736083984 1052.774169921875 0.7839999198913574 1282.19140625 0.4364244341850281 0.6743162 0.5806601643562317 True -8 24930 29.818488597869873 0.661240816116333 872.4927978515625 0.4061654806137085 1279.64794921875 0.4403715133666992 0.6819039 0.5324984192848206 True -9 27700 29.875348806381226 0.6725800037384033 895.8880004882812 0.6504933834075928 1258.5867919921875 0.4455919861793518 0.6874317 0.5351600646972656 True -10 30470 29.803189516067505 0.6618781089782715 1016.7996826171875 0.5516546964645386 1239.333251953125 0.449226975440979 0.69436145 0.528076708316803 True -11 33240 29.867641925811768 0.6709208488464355 923.161376953125 0.45320093631744385 1227.0626220703125 0.45173901319503784 0.70167226 0.5141906142234802 True -12 36010 29.933048486709595 23.307748317718506 865.4141235351562 0.4055476188659668 1221.1937255859375 0.4566247761249542 0.7063139 0.5219330191612244 True -13 38780 30.042659521102905 0.6757948398590088 832.3899536132812 0.4836007058620453 1212.73095703125 0.4593968391418457 0.71789986 0.48953866958618164 True -14 41550 29.974807024002075 0.677196741104126 893.291015625 0.4194393754005432 1204.1448974609375 0.4636576771736145 0.72690356 0.47116079926490784 True -15 44320 29.95232391357422 0.7007391452789307 891.3155517578125 0.5542288422584534 1197.53173828125 0.46769025921821594 0.7356191 0.46197110414505005 True -16 47090 29.89826798439026 0.6706478595733643 766.2832641601562 0.38390588760375977 1194.14794921875 0.4694303572177887 0.741222 0.4281083345413208 True -17 49860 29.928608655929565 0.6651408672332764 782.623291015625 0.3660852313041687 1194.0625 0.4704897999763489 0.7470269 0.4135177731513977 True -18 52630 29.931528091430664 0.6586723327636719 876.6324462890625 0.43013352155685425 1194.718017578125 0.47004351019859314 0.7475846 0.4109507203102112 True -19 55400 29.92405104637146 0.6563003063201904 976.5958862304688 0.36351847648620605 1194.2572021484375 0.47071292996406555 0.74675584 0.41254904866218567 False diff --git a/ENCSR749BWV/cherimoya.fold_1.performance.tsv b/ENCSR749BWV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2805189921fb7592783716aad728ef3ec7aef60d..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1194.718017578125 0.293495237827301 0.47004348039627075 0.2569904327392578 0.7475845813751221 0.7048406004905701 0.4109507203102112 \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_2.evaluate.json b/ENCSR749BWV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e4a08f016d61e30f449d02c6fe0d4de4b1521c2c..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF028OAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_2.fit.json b/ENCSR749BWV/cherimoya.fold_2.fit.json deleted file mode 100644 index 6c242482afd6848a97ed615bcafd42625d4f8243..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF028OAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_2.log b/ENCSR749BWV/cherimoya.fold_2.log deleted file mode 100644 index 64705f5aa22df46ea2e3acb6e3e08d17764eafc0..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2890 35.42611575126648 3.550340414047241 943.0452270507812 0.9629064798355103 1557.6019287109375 0.279121458530426 0.5563317 7.638575553894043 True -1 5780 31.858233213424683 24.651148080825806 1191.7557373046875 0.9413436055183411 1424.388427734375 0.39383506774902344 0.5914565 1.0529687404632568 True -2 8670 32.41421413421631 0.5341706275939941 888.3226318359375 0.6137491464614868 1400.942626953125 0.4068519175052643 0.609274 0.7049344182014465 True -3 11560 31.82489776611328 22.25676465034485 940.5908203125 0.58571457862854 1380.4547119140625 0.40845954418182373 0.6281111 0.507051408290863 True -4 14450 32.42070269584656 0.5416443347930908 935.0272216796875 0.5640995502471924 1331.214599609375 0.41906920075416565 0.63151115 0.5213300585746765 True -5 17340 31.379358530044556 0.5302305221557617 882.134765625 0.6949059367179871 1337.549072265625 0.4208134412765503 0.6355439 0.5248071551322937 True -6 20230 31.024718046188354 1.4783318042755127 966.1610107421875 0.5075293183326721 1290.9970703125 0.4237293601036072 0.63613886 0.5040058493614197 True -7 23120 31.06311535835266 1.3179593086242676 1011.8248291015625 0.5568631291389465 1262.2841796875 0.42587462067604065 0.64792883 0.491411030292511 True -8 26010 31.135488510131836 0.5291407108306885 923.4173583984375 0.5394630432128906 1251.407958984375 0.4317287504673004 0.6490324 0.49998313188552856 True -9 28900 31.082143545150757 0.5288641452789307 959.2756958007812 0.45214664936065674 1206.46337890625 0.43690523505210876 0.6610532 0.4980400502681732 True -10 31790 31.100170612335205 0.5314440727233887 872.9868774414062 0.598717451095581 1202.106689453125 0.441186785697937 0.6632686 0.510200023651123 True -11 34680 31.050689458847046 0.522742748260498 934.9988403320312 0.518141508102417 1201.5072021484375 0.44365036487579346 0.66968673 0.5395706295967102 True -12 37570 31.06077218055725 0.533134937286377 889.7061157226562 0.5351168513298035 1186.3564453125 0.44682231545448303 0.6728193 0.5415895581245422 True -13 40460 31.165058135986328 0.544334888458252 683.402587890625 0.5427600145339966 1179.0213623046875 0.44872361421585083 0.6826684 0.5223338007926941 True -14 43350 31.262022733688354 0.5377922058105469 936.779541015625 0.505721390247345 1174.782958984375 0.45295560359954834 0.6887266 0.49655330181121826 True -15 46240 31.26107120513916 0.5272562503814697 813.2464599609375 0.43828514218330383 1161.8486328125 0.45452600717544556 0.697188 0.46568331122398376 True -16 49130 31.256810903549194 0.5328848361968994 745.343017578125 0.6042723059654236 1158.6243896484375 0.4584054946899414 0.705093 0.4440837800502777 True -17 52020 31.138614416122437 0.5326159000396729 866.4510498046875 0.21001696586608887 1158.5328369140625 0.46036964654922485 0.7079923 0.42795658111572266 True -18 54910 31.12437629699707 0.5305817127227783 859.0645751953125 0.37049245834350586 1159.1387939453125 0.45971453189849854 0.7097608 0.42626386880874634 True -19 57800 31.134000778198242 0.5342240333557129 1001.306884765625 0.3289545774459839 1158.9281005859375 0.46164897084236145 0.7091439 0.4283856153488159 False diff --git a/ENCSR749BWV/cherimoya.fold_2.performance.tsv b/ENCSR749BWV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7b604e5dad5a1a8331c633eb67bb066203b4da08..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1159.1387939453125 0.3048887848854065 0.45971453189849854 0.239228293299675 0.7097607851028442 0.6571009159088135 0.42626386880874634 \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_3.evaluate.json b/ENCSR749BWV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 02e9fd9a2eb0f046f3480773404e6c28e3483c69..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF028OAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_3.fit.json b/ENCSR749BWV/cherimoya.fold_3.fit.json deleted file mode 100644 index aa10b26ce78bc95b4e721739b34dfd879af6bfd4..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF028OAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_3.log b/ENCSR749BWV/cherimoya.fold_3.log deleted file mode 100644 index 565a0da6d6ae1b772e5eb1563f1a46b08618de86..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2805 35.03906512260437 20.06207847595215 1255.692626953125 0.798888623714447 1345.23046875 0.2804237902164459 0.57787377 6.750492572784424 True -1 5610 31.20554232597351 23.614588022232056 901.4208984375 0.7637807726860046 1223.8355712890625 0.3862936198711395 0.6256194 1.166974663734436 True -2 8415 31.389693021774292 0.5617213249206543 910.0958251953125 0.933700442314148 1204.5201416015625 0.3973402678966522 0.62086797 0.8344455361366272 False -3 11220 31.008208513259888 0.5637674331665039 983.4805297851562 0.6266182661056519 1190.3870849609375 0.4029220938682556 0.6361764 0.6831601858139038 True -4 14025 30.80575442314148 1.0956346988677979 852.314208984375 0.7082347273826599 1190.99609375 0.40241554379463196 0.630006 0.6723681688308716 False -5 16830 30.443696975708008 1.0628533363342285 867.564697265625 0.9250123500823975 1177.08837890625 0.41139522194862366 0.63590735 0.5771984457969666 False -6 19635 30.447267055511475 0.561368465423584 698.4595947265625 0.7512933611869812 1170.4034423828125 0.41298389434814453 0.63651234 0.5575510263442993 True -7 22440 30.428165912628174 0.5649082660675049 924.7285766601562 0.4891815185546875 1159.8516845703125 0.41996997594833374 0.64522016 0.5846273303031921 True -8 25245 30.416225910186768 0.5695598125457764 865.8736572265625 1.0369179248809814 1151.3892822265625 0.42313700914382935 0.6510694 0.531050980091095 True -9 28050 30.47789239883423 0.5680170059204102 878.60986328125 0.6340281963348389 1137.9874267578125 0.428250253200531 0.6623174 0.5252781510353088 True -10 30855 30.62078547477722 1.3318336009979248 716.4085693359375 0.5771133899688721 1131.8648681640625 0.4312988221645355 0.67490065 0.5263397693634033 True -11 33660 30.664530038833618 0.5974581241607666 818.6016845703125 0.6518194675445557 1126.6468505859375 0.43423736095428467 0.67895097 0.5192317366600037 True -12 36465 30.646941661834717 0.5709657669067383 945.0010986328125 0.6065758466720581 1120.434326171875 0.43892666697502136 0.6851729 0.49129000306129456 True -13 39270 30.638710737228394 0.587233304977417 868.1762084960938 0.5891929268836975 1114.955078125 0.4414941072463989 0.7005901 0.49339941143989563 True -14 42075 30.68699288368225 0.5862710475921631 904.8889770507812 0.4963887631893158 1110.4486083984375 0.4433135986328125 0.70973915 0.46472427248954773 True -15 44880 30.61786437034607 0.5714480876922607 883.2031860351562 0.5729148387908936 1104.4105224609375 0.4480833113193512 0.71593815 0.4394333064556122 True -16 47685 30.699548959732056 0.5776927471160889 769.1497802734375 0.3972557485103607 1101.1851806640625 0.4495225250720978 0.7206876 0.4197782874107361 True -17 50490 30.664013147354126 0.5730128288269043 842.243896484375 0.4121215045452118 1098.5955810546875 0.45100805163383484 0.7246726 0.40836530923843384 True -18 53295 30.500848531723022 0.5689208507537842 788.0902099609375 0.4150770306587219 1097.9920654296875 0.4521786570549011 0.72633165 0.40164270997047424 True -19 56100 30.650434732437134 0.570777416229248 997.6778564453125 0.6970028877258301 1098.209228515625 0.4523058533668518 0.72696024 0.4036887288093567 True diff --git a/ENCSR749BWV/cherimoya.fold_3.performance.tsv b/ENCSR749BWV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fc51353dd43270aa2a654fe47089274f2b5ff791..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1098.209228515625 0.30548539757728577 0.4523058533668518 0.23775115609169006 0.7269602417945862 0.6649985313415527 0.4036887288093567 \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_4.evaluate.json b/ENCSR749BWV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ebee62003e7d62ba476d92c3c24d1cb958730309..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF028OAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_4.fit.json b/ENCSR749BWV/cherimoya.fold_4.fit.json deleted file mode 100644 index 381964831a273031a3b75666d1f09543929bbd9d..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF028OAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749BWV/cherimoya.fold_4.log b/ENCSR749BWV/cherimoya.fold_4.log deleted file mode 100644 index 34edfd025856e62160b176432f7d992a30ec67e0..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2889 35.892168045043945 4.8104798793792725 937.4364624023438 0.8051185011863708 1320.4990234375 0.2794547379016876 0.5585632 5.1682891845703125 True -1 5778 32.11346960067749 0.5937244892120361 904.17822265625 0.7601258754730225 1196.7275390625 0.3831263482570648 0.61029065 1.19744873046875 True -2 8667 32.02266883850098 0.5744097232818604 847.317626953125 1.1646873950958252 1186.5758056640625 0.38916411995887756 0.62013006 0.7127940058708191 True -3 11556 32.04192757606506 0.5760154724121094 1427.7593994140625 0.9585966467857361 1167.56884765625 0.3949410617351532 0.62499934 0.4946564733982086 True -4 14445 31.958524227142334 0.5753064155578613 849.24658203125 0.6637762188911438 1156.009521484375 0.40476635098457336 0.61958617 0.5114341378211975 False -5 17334 31.43022060394287 0.5722925662994385 981.453125 0.7512372732162476 1143.329345703125 0.4092984199523926 0.61753374 0.4651796519756317 False -6 20223 31.47725558280945 0.570490837097168 862.8090209960938 0.7254066467285156 1132.8167724609375 0.4143686294555664 0.62908864 0.4952549934387207 True -7 23112 31.506130933761597 0.5671238899230957 945.6334228515625 0.5329798460006714 1129.2628173828125 0.41699808835983276 0.62965876 0.5066665410995483 True -8 26001 31.418587923049927 0.5657777786254883 803.10791015625 0.48303741216659546 1123.38818359375 0.4193984568119049 0.6319632 0.4995732605457306 True -9 28890 31.45121431350708 1.6134521961212158 833.3489379882812 0.6175753474235535 1107.3577880859375 0.4244340658187866 0.6418159 0.5030346512794495 True -10 31779 31.48424243927002 0.5906927585601807 1067.310791015625 0.5994900465011597 1101.3336181640625 0.4263424873352051 0.64732116 0.5143431425094604 True -11 34668 31.50785183906555 0.5739529132843018 869.5881958007812 0.5140365362167358 1095.9674072265625 0.43059059977531433 0.656647 0.5109890699386597 True -12 37557 31.440521955490112 0.5669403076171875 821.865478515625 0.5143953561782837 1087.013671875 0.4360177218914032 0.66628015 0.4840770959854126 True -13 40446 31.552383422851562 0.9952216148376465 915.4520874023438 0.6090380549430847 1084.038330078125 0.4386012554168701 0.67585534 0.49056872725486755 True -14 43335 31.516788959503174 0.5744924545288086 749.8592529296875 0.44168972969055176 1078.211669921875 0.44266584515571594 0.6901377 0.4587653577327728 True -15 46224 31.498757123947144 0.5752630233764648 770.8681030273438 0.4540228247642517 1073.87744140625 0.44580140709877014 0.6988352 0.4376046657562256 True -16 49113 31.558401584625244 0.5754566192626953 943.48828125 0.4244072437286377 1072.43310546875 0.44568267464637756 0.70217484 0.42582908272743225 True -17 52002 31.535154819488525 0.5745024681091309 875.023681640625 0.5911135077476501 1070.95703125 0.44770535826683044 0.70647246 0.4124574065208435 True -18 54891 31.43317413330078 0.5661063194274902 970.745849609375 0.4842150807380676 1070.835693359375 0.4474292993545532 0.70997167 0.4067721664905548 True -19 57780 31.459151029586792 2.556086540222168 935.835205078125 0.3304840326309204 1070.71240234375 0.4479512870311737 0.7075825 0.41054779291152954 False diff --git a/ENCSR749BWV/cherimoya.fold_4.performance.tsv b/ENCSR749BWV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4d0cb27c45b6e5f11b852d9fd59e7cf2a82f35ce..0000000000000000000000000000000000000000 --- a/ENCSR749BWV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1070.835693359375 0.30977529287338257 0.4474292993545532 0.231076180934906 0.7099716663360596 0.6408976912498474 0.4067721664905548 \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_0.evaluate.json b/ENCSR749WVO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 18cda3c15611452c527d05990e3b28970e00a218..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_0.fit.json b/ENCSR749WVO/cherimoya.fold_0.fit.json deleted file mode 100644 index 45b35f302031e6c10723fecb4ef047cf3997529b..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF671MXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_0.log b/ENCSR749WVO/cherimoya.fold_0.log deleted file mode 100644 index 33b98f89d29d82e786ece6c2d2747013891b5499..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 34.322333097457886 4.3982086181640625 495.13800048828125 0.36129331588745117 594.9353637695312 0.26002785563468933 0.6890381 4.554357051849365 True -1 5516 30.46414542198181 0.5976934432983398 411.20794677734375 0.31995701789855957 540.3977661132812 0.31616848707199097 0.76928276 1.6931267976760864 True -2 8274 30.41993498802185 0.5714480876922607 466.1621398925781 0.4895367920398712 536.2638549804688 0.3204560875892639 0.7666018 0.7753341197967529 False -3 11032 30.36381459236145 2.34609317779541 523.2836303710938 0.6492011547088623 527.0361938476562 0.32810354232788086 0.7886145 0.7957898378372192 True -4 13790 30.3640296459198 0.5724341869354248 495.82049560546875 0.5432040691375732 523.0142822265625 0.3327951729297638 0.7965111 0.5862067937850952 True -5 16548 30.365455389022827 0.5794117450714111 465.72723388671875 0.4210667908191681 517.9999389648438 0.3395937383174896 0.8115715 0.48219579458236694 True -6 19306 30.923662900924683 22.58036708831787 458.0669860839844 0.3181799650192261 517.0226440429688 0.3393193185329437 0.81782985 0.4252750277519226 True -7 22064 30.487114429473877 1.1342430114746094 443.8927307128906 0.2615121901035309 515.6436767578125 0.3394399881362915 0.8272871 0.3813982903957367 True -8 24822 30.350212574005127 1.274169921875 471.0413818359375 0.3376896381378174 513.1558837890625 0.3428908884525299 0.831774 0.3560705780982971 True -9 27580 30.4399995803833 1.783548355102539 415.4920959472656 0.2882653474807739 512.1458740234375 0.3439144194126129 0.83537596 0.35292449593544006 True -10 30338 30.41867733001709 0.5595624446868896 485.189208984375 0.33369532227516174 510.3277893066406 0.3466687500476837 0.8401786 0.327341228723526 True -11 33096 30.397313594818115 0.562507152557373 457.6880798339844 0.3002396821975708 509.53216552734375 0.3467797636985779 0.8439328 0.30628594756126404 True -12 35854 30.273473978042603 3.2749698162078857 446.7016296386719 0.2403777837753296 507.9214172363281 0.34864485263824463 0.8488668 0.2875923216342926 True -13 38612 29.854007720947266 0.576134204864502 438.5829162597656 0.1411760002374649 505.1106262207031 0.3523857295513153 0.8523351 0.2702358067035675 True -14 41370 29.826021432876587 0.5625624656677246 496.1468505859375 0.24268656969070435 504.2232360839844 0.35296204686164856 0.8563757 0.2524566352367401 True -15 44128 29.83209776878357 1.3028888702392578 401.4255676269531 0.15937340259552002 504.1248474121094 0.3526768386363983 0.85955584 0.24196401238441467 True -16 46886 29.871098041534424 0.560845136642456 445.27777099609375 0.19657516479492188 503.9866638183594 0.3524077832698822 0.86280113 0.2304917573928833 True -17 49644 29.888312578201294 2.289607286453247 353.032958984375 0.17668119072914124 503.0570373535156 0.3545697331428528 0.86212575 0.2270362675189972 False -18 52402 29.83562135696411 0.5797145366668701 452.26995849609375 0.17238441109657288 503.31610107421875 0.3534829020500183 0.861637 0.22808347642421722 False -19 55160 29.867371320724487 0.572882890701294 527.0005493164062 0.13561934232711792 503.0804443359375 0.35431385040283203 0.8608218 0.228890523314476 False diff --git a/ENCSR749WVO/cherimoya.fold_0.performance.tsv b/ENCSR749WVO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 09ac3a220f259fb1ae06c213e89ad28774082272..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -503.9866638183594 0.4179786145687103 0.3524077832698822 0.1350487619638443 0.8628011345863342 0.8394774198532104 0.2304917573928833 \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_1.evaluate.json b/ENCSR749WVO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d0e4ed178d28c75e34043fad7174785959cfef7d..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_1.fit.json b/ENCSR749WVO/cherimoya.fold_1.fit.json deleted file mode 100644 index 7e383c37eb64236e29fe301c7fd9bf872730bbf4..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF671MXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_1.log b/ENCSR749WVO/cherimoya.fold_1.log deleted file mode 100644 index 9f62c94ba4d79ea827de0c912139e8f37984135e..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2724 34.14439415931702 3.7325809001922607 416.6357116699219 0.467048704624176 701.9806518554688 0.2671830654144287 0.7034081 5.098605632781982 True -1 5448 30.078693628311157 0.7167305946350098 492.58697509765625 0.52738356590271 630.5858764648438 0.3294200301170349 0.7690877 1.510199785232544 True -2 8172 30.009653568267822 0.6870741844177246 471.8914794921875 0.2992009222507477 619.323486328125 0.33843880891799927 0.7787835 0.8227133750915527 True -3 10896 30.02368688583374 1.4111318588256836 464.2109375 0.385004460811615 613.109130859375 0.3425518572330475 0.78350526 0.6770477890968323 True -4 13620 30.015609741210938 0.690030574798584 452.59735107421875 0.35477638244628906 603.6878051757812 0.3502512276172638 0.8040364 0.623055636882782 True -5 16344 29.999805688858032 0.7018930912017822 470.709716796875 0.4707101583480835 598.4000854492188 0.35556337237358093 0.81268376 0.5311272144317627 True -6 19068 30.01783561706543 0.6927416324615479 527.7302856445312 0.34273189306259155 595.7762451171875 0.35719525814056396 0.8190368 0.5091322660446167 True -7 21792 29.707975149154663 0.6859254837036133 445.62744140625 0.2314974069595337 593.458740234375 0.3586159348487854 0.82883024 0.4757215082645416 True -8 24516 29.44660758972168 0.6859407424926758 487.2315673828125 0.28358542919158936 590.9776611328125 0.36005881428718567 0.83567107 0.4350607395172119 True -9 27240 29.44388484954834 0.6847438812255859 396.30084228515625 0.292033314704895 587.364501953125 0.3646158277988434 0.8417147 0.4065167307853699 True -10 29964 29.51708197593689 0.6846418380737305 410.4722900390625 0.31021183729171753 585.6673583984375 0.3647349178791046 0.8500312 0.3814913034439087 True -11 32688 29.43234348297119 1.4585134983062744 389.14202880859375 0.17679540812969208 581.4541625976562 0.36984536051750183 0.8535394 0.3614247441291809 True -12 35412 29.389772415161133 0.6825258731842041 426.68841552734375 0.29799771308898926 580.0620727539062 0.37013205885887146 0.8598025 0.3305365741252899 True -13 38136 29.49919557571411 0.684476375579834 445.83721923828125 0.25913071632385254 578.1170654296875 0.371416836977005 0.8662458 0.30865293741226196 True -14 40860 29.432068347930908 0.673119068145752 433.82244873046875 0.217317134141922 576.1727294921875 0.3738327622413635 0.87041277 0.28461581468582153 True -15 43584 29.48936653137207 0.6744070053100586 392.80230712890625 0.27797508239746094 575.1278076171875 0.3739335536956787 0.87504315 0.26913750171661377 True -16 46308 29.464922428131104 20.62495493888855 396.7867431640625 0.1827555000782013 574.32177734375 0.37488287687301636 0.8778256 0.2615441679954529 True -17 49032 29.558117628097534 0.6964762210845947 321.3567199707031 0.21154740452766418 574.752197265625 0.37444114685058594 0.87928987 0.25554129481315613 True -18 51756 29.43935227394104 0.6882834434509277 419.09246826171875 0.18238094449043274 574.366455078125 0.3748416304588318 0.87899315 0.25667452812194824 False -19 54480 29.412229776382446 0.6829650402069092 411.6293640136719 0.2666242718696594 574.3726806640625 0.3752182722091675 0.8787563 0.2573968470096588 False diff --git a/ENCSR749WVO/cherimoya.fold_1.performance.tsv b/ENCSR749WVO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index dd3e1ec32ab36b87feea30350d3d32abedf27e45..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -574.752197265625 0.40186500549316406 0.3744411766529083 0.15160419046878815 0.8792898654937744 0.8705061674118042 0.25554129481315613 \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_2.evaluate.json b/ENCSR749WVO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 10a4ba58938625b04a271b865b2c32b88a17edb8..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_2.fit.json b/ENCSR749WVO/cherimoya.fold_2.fit.json deleted file mode 100644 index 920459d2713ef425513288a25dd2201499a51a54..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF671MXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_2.log b/ENCSR749WVO/cherimoya.fold_2.log deleted file mode 100644 index 50f79f3cd4ce0e5ea86d655245a8d88c9db6cf4d..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2859 35.50762987136841 3.5522491931915283 460.4448547363281 0.5159247517585754 637.7731323242188 0.2659587264060974 0.6865129 3.8638224601745605 True -1 5718 31.633530855178833 0.5552651882171631 424.2919921875 0.332938015460968 580.498046875 0.3242127001285553 0.7496371 1.338292121887207 True -2 8577 31.499239206314087 0.5439949035644531 455.7820129394531 0.40524667501449585 568.3023681640625 0.3323184549808502 0.7701141 0.6335076689720154 True -3 11436 30.86669421195984 0.5363357067108154 500.35113525390625 0.35749387741088867 564.0247802734375 0.33391645550727844 0.7801517 0.7165181636810303 True -4 14295 30.84728717803955 0.5476510524749756 375.221435546875 0.3111468553543091 558.4251708984375 0.3386547565460205 0.7929523 0.45199981331825256 True -5 17154 30.93853449821472 0.5364248752593994 502.0839538574219 0.36760857701301575 552.4744873046875 0.3454969525337219 0.8090011 0.40545278787612915 True -6 20013 30.908756256103516 0.96773362159729 426.6568908691406 0.4198685586452484 550.247314453125 0.34753820300102234 0.81600964 0.40927934646606445 True -7 22872 30.939747095108032 0.5316691398620605 445.5362854003906 0.22699186205863953 548.4000244140625 0.3489375710487366 0.82214093 0.3964579999446869 True -8 25731 30.86157727241516 0.5415816307067871 445.95343017578125 0.3279815912246704 546.5659790039062 0.3500496745109558 0.82810766 0.3772745728492737 True -9 28590 30.927908420562744 0.5465753078460693 509.95806884765625 0.2987555265426636 543.730712890625 0.35424599051475525 0.8337008 0.37218543887138367 True -10 31449 30.907979249954224 0.5355319976806641 507.5198974609375 0.284839391708374 543.082763671875 0.3548027575016022 0.83615345 0.35460031032562256 True -11 34308 30.94433331489563 0.538374662399292 504.2631530761719 0.2438061684370041 541.1303100585938 0.3570046126842499 0.8430977 0.3200395405292511 True -12 37167 30.939560413360596 0.5451762676239014 484.70123291015625 0.21933478116989136 539.134521484375 0.35899463295936584 0.84500235 0.303669273853302 True -13 40026 30.975958585739136 0.5392136573791504 465.2718505859375 0.340958833694458 537.0543823242188 0.36122065782546997 0.84906876 0.2881678342819214 True -14 42885 30.91989493370056 0.5467593669891357 471.6947021484375 0.29348060488700867 536.7840576171875 0.36121973395347595 0.85559577 0.2699832320213318 True -15 45744 30.97978687286377 0.5453066825866699 524.6624145507812 0.3380928933620453 535.6577758789062 0.3620905876159668 0.857621 0.2576011121273041 True -16 48603 30.927570819854736 0.5429272651672363 499.36102294921875 0.24782221019268036 535.6975708007812 0.36166736483573914 0.85972524 0.24911591410636902 True -17 51462 30.907674551010132 0.5394120216369629 428.285400390625 0.14339250326156616 535.858642578125 0.36114129424095154 0.85929537 0.2473313957452774 False -18 54321 30.88507390022278 0.5446515083312988 434.44659423828125 0.2306954264640808 535.0435180664062 0.3627364933490753 0.8590195 0.24698661267757416 False -19 57180 30.89868426322937 0.5450344085693359 428.70318603515625 0.29554906487464905 535.6771850585938 0.36192786693573 0.8598292 0.2484443038702011 True diff --git a/ENCSR749WVO/cherimoya.fold_2.performance.tsv b/ENCSR749WVO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 20fe580463e787363dc3d821c59307e5b70f0f05..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -535.6771850585938 0.41039833426475525 0.36192789673805237 0.14124317467212677 0.8598291873931885 0.8444943428039551 0.2484443038702011 \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_3.evaluate.json b/ENCSR749WVO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7b77d714574088177a88cf27b38ed9cb76bf2208..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_3.fit.json b/ENCSR749WVO/cherimoya.fold_3.fit.json deleted file mode 100644 index a67b5a5d0de3b4f2714aad8815d640e223db8928..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF671MXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_3.log b/ENCSR749WVO/cherimoya.fold_3.log deleted file mode 100644 index a3710b9806cb689b52a03942b6ffd89c62070c66..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 34.011258125305176 4.279356956481934 446.5646667480469 0.4894554913043976 593.109619140625 0.2732262909412384 0.6668382 4.347021102905273 True -1 5460 30.103559255599976 0.5518503189086914 571.9291381835938 0.4806177020072937 539.5709228515625 0.3263395428657532 0.75241405 1.6834572553634644 True -2 8190 30.15443181991577 0.5468528270721436 434.10748291015625 0.3659612536430359 530.662841796875 0.3359959125518799 0.7687754 0.7383133769035339 True -3 10920 30.080028533935547 2.6299121379852295 475.68084716796875 0.3553813099861145 524.5537719726562 0.33980318903923035 0.78581506 0.7755469679832458 True -4 13650 30.15271282196045 0.5444998741149902 416.61297607421875 0.37529128789901733 522.0514526367188 0.34206363558769226 0.7817582 0.5514896512031555 False -5 16380 30.061437368392944 0.5328285694122314 439.1051330566406 0.40032583475112915 519.9564819335938 0.3437744081020355 0.79577327 0.46178698539733887 True -6 19110 30.152055263519287 4.617430925369263 509.22808837890625 0.34732162952423096 518.2672729492188 0.3454218804836273 0.8029559 0.43827489018440247 True -7 21840 30.072762489318848 0.5402772426605225 483.33758544921875 0.3686895966529846 515.1199340820312 0.3494935929775238 0.80953014 0.42310258746147156 True -8 24570 30.05157494544983 0.536876916885376 445.9657287597656 0.24021419882774353 515.03271484375 0.34880927205085754 0.81540483 0.41761666536331177 True -9 27300 30.089366912841797 0.5380303859710693 435.17730712890625 0.3836439847946167 512.4231567382812 0.3517131507396698 0.8223327 0.3953031599521637 True -10 30030 30.122112035751343 0.5439717769622803 462.6302795410156 0.33591920137405396 510.12506103515625 0.353811115026474 0.83000416 0.3423531949520111 True -11 32760 30.13549256324768 0.5362787246704102 408.59515380859375 0.2839377522468567 508.1558532714844 0.3553195893764496 0.83543617 0.3258974850177765 True -12 35490 30.120221376419067 0.5330331325531006 401.5555114746094 0.21199476718902588 507.1659240722656 0.35656553506851196 0.83856386 0.31202536821365356 True -13 38220 30.095430374145508 0.5324220657348633 464.5596923828125 0.24571195244789124 505.81304931640625 0.35760927200317383 0.8432503 0.2977961301803589 True -14 40950 30.10370635986328 20.642667293548584 418.455322265625 0.22467324137687683 503.96429443359375 0.3602555990219116 0.84648025 0.28391364216804504 True -15 43680 30.278494358062744 0.5417490005493164 466.62188720703125 0.33653292059898376 502.1960144042969 0.3612446188926697 0.85140777 0.27024510502815247 True -16 46410 30.097520351409912 0.5339977741241455 440.8348083496094 0.2145508974790573 501.5426940917969 0.36255472898483276 0.85585105 0.25955650210380554 True -17 49140 29.538800477981567 0.5256834030151367 471.376953125 0.3004986047744751 501.33905029296875 0.3624974489212036 0.855149 0.2561807632446289 False -18 51870 29.60090136528015 0.5261085033416748 447.0826721191406 0.20172584056854248 502.7830810546875 0.3593188524246216 0.8565769 0.25360822677612305 True -19 54600 29.58461046218872 0.5500447750091553 514.107177734375 0.28143423795700073 502.6932678222656 0.35998788475990295 0.8570659 0.25513431429862976 True diff --git a/ENCSR749WVO/cherimoya.fold_3.performance.tsv b/ENCSR749WVO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a3f576ea89c4579641a0f6760fab94e7080600dc..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -502.6932678222656 0.41406717896461487 0.35998788475990295 0.13880929350852966 0.8570659160614014 0.8282341361045837 0.25513431429862976 \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_4.evaluate.json b/ENCSR749WVO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index df171fe4bdb6b0ae9be71c927ee203191dfe83b4..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_4.fit.json b/ENCSR749WVO/cherimoya.fold_4.fit.json deleted file mode 100644 index 1cec2da158254d973f1827acd3948da2412d80bc..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF671MXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749WVO/cherimoya.fold_4.log b/ENCSR749WVO/cherimoya.fold_4.log deleted file mode 100644 index d2fcf8e71376d641972e0acfe13a20aa6c48727c..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2816 37.066659927368164 20.389093160629272 468.7408752441406 0.538737416267395 541.6174926757812 0.258247435092926 0.68087465 3.8889787197113037 True -1 5632 31.234549045562744 17.180350065231323 497.09710693359375 0.44763973355293274 497.0293273925781 0.31065207719802856 0.75889164 1.059234857559204 True -2 8448 31.218653917312622 2.272533893585205 389.65234375 0.19561904668807983 492.3576354980469 0.3134887218475342 0.77388465 0.5768570899963379 True -3 11264 31.175947189331055 0.6521074771881104 464.6694641113281 0.43052878975868225 488.90338134765625 0.3158625066280365 0.7821415 0.6060768961906433 True -4 14080 31.011276721954346 0.633061408996582 413.10931396484375 0.34952211380004883 484.69744873046875 0.31947338581085205 0.7952258 0.454232782125473 True -5 16896 30.87219548225403 0.6284101009368896 445.98175048828125 0.39119330048561096 481.3150939941406 0.3230988383293152 0.8078244 0.42883577942848206 True -6 19712 30.57580327987671 5.391512155532837 498.28570556640625 0.21846377849578857 479.8170471191406 0.3242756426334381 0.8123255 0.4251019060611725 True -7 22528 30.43408441543579 21.192880630493164 513.8736572265625 0.3830341696739197 477.2165222167969 0.32729455828666687 0.82147014 0.3907093107700348 True -8 25344 30.60826849937439 0.6345021724700928 430.53509521484375 0.21228741109371185 475.649169921875 0.3293377757072449 0.8246263 0.3703605532646179 True -9 28160 31.564419507980347 0.638211727142334 368.5912170410156 0.2053525596857071 474.9730224609375 0.32951074838638306 0.8306544 0.35068315267562866 True -10 30976 30.471224784851074 1.680164098739624 430.66046142578125 0.2986345887184143 472.4528503417969 0.33296939730644226 0.8340751 0.32499852776527405 True -11 33792 32.10569787025452 16.808782815933228 452.85589599609375 0.2761954069137573 471.2449035644531 0.333700954914093 0.84175354 0.2950175106525421 True -12 36608 30.54384732246399 0.643413782119751 396.4854736328125 0.32520633935928345 470.26678466796875 0.3351789116859436 0.84458715 0.2735506296157837 True -13 39424 30.584482431411743 0.6562035083770752 492.97613525390625 0.363445520401001 467.9989013671875 0.33811455965042114 0.849153 0.2594992220401764 True -14 42240 30.6858651638031 0.6528675556182861 367.56231689453125 0.1729256957769394 467.543701171875 0.3379855155944824 0.8542138 0.24030573666095734 True -15 45056 30.644731521606445 0.6512949466705322 412.8056945800781 0.23628900945186615 466.46380615234375 0.34009331464767456 0.85861003 0.22703374922275543 True -16 47872 30.654373168945312 0.6600015163421631 521.2738037109375 0.22965556383132935 466.1505126953125 0.34037327766418457 0.8599466 0.2211657166481018 True -17 50688 30.60615634918213 0.648395299911499 440.10400390625 0.1848902702331543 465.9917907714844 0.3402225375175476 0.8618574 0.21514548361301422 True -18 53504 30.496920347213745 0.6443734169006348 504.9214782714844 0.2954939007759094 466.7156677246094 0.33792543411254883 0.86329836 0.21434944868087769 True -19 56320 30.495101928710938 1.1912121772766113 420.22607421875 0.17940495908260345 466.812744140625 0.33828842639923096 0.86142206 0.21503856778144836 False diff --git a/ENCSR749WVO/cherimoya.fold_4.performance.tsv b/ENCSR749WVO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index feae3a84cbb4d52c944009ea4db7447fd2fa52e3..0000000000000000000000000000000000000000 --- a/ENCSR749WVO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -466.7156677246094 0.429996520280838 0.33792540431022644 0.1262938529253006 0.8632983565330505 0.8389629125595093 0.21434944868087769 \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_0.evaluate.json b/ENCSR749YCR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6fd53ac30ae9e4c924cc0b35e6870ff11cd8824f..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF953WKL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_0.fit.json b/ENCSR749YCR/cherimoya.fold_0.fit.json deleted file mode 100644 index 18cc7f43782a31108bb2eda74efec4e9e3478bba..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF953WKL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_0.log b/ENCSR749YCR/cherimoya.fold_0.log deleted file mode 100644 index af0aa504ad69b3bb6ec510938a26b35d789c0c78..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2653 32.73316717147827 4.027395725250244 165.3165740966797 0.745986819267273 199.96778869628906 0.12549294531345367 0.7359179 3.4618680477142334 True -1 5306 29.27500867843628 0.5783514976501465 165.34751892089844 0.4740481376647949 180.2830352783203 0.1654411107301712 0.81454295 1.3572320938110352 True -2 7959 29.19205641746521 0.5641531944274902 140.7872314453125 0.29682186245918274 177.53944396972656 0.1687416285276413 0.8175477 0.816644012928009 True -3 10612 29.198145389556885 0.561007022857666 151.77352905273438 0.5819450616836548 175.3330841064453 0.17374640703201294 0.82671046 0.6812203526496887 True -4 13265 29.20421004295349 0.5617711544036865 90.02995300292969 0.4117395281791687 174.99261474609375 0.17299622297286987 0.83889055 0.6117581129074097 True -5 15918 29.20213770866394 0.5668594837188721 158.76544189453125 0.5836652517318726 174.17247009277344 0.17496366798877716 0.844065 0.6187679171562195 True -6 18571 29.14590096473694 3.928377628326416 163.47813415527344 0.36958837509155273 174.07803344726562 0.1752275824546814 0.847678 0.5574737191200256 True -7 21224 29.14735460281372 0.5668420791625977 142.6249237060547 0.5511304140090942 172.5668487548828 0.17986515164375305 0.85383004 0.49871793389320374 True -8 23877 29.243120193481445 0.5768029689788818 236.28981018066406 0.6214066743850708 171.94424438476562 0.1812913566827774 0.85808986 0.4773625135421753 True -9 26530 29.2042293548584 0.5597987174987793 147.92333984375 0.4585658311843872 171.7002716064453 0.18154376745224 0.86365277 0.42595934867858887 True -10 29183 29.177950620651245 0.5704269409179688 197.53732299804688 0.3731588125228882 171.26296997070312 0.1826295256614685 0.8679546 0.40259119868278503 True -11 31836 29.19319462776184 0.5650579929351807 201.376220703125 0.3616003394126892 170.5883331298828 0.1845761388540268 0.8718026 0.36961784958839417 True -12 34489 29.23182463645935 0.5692675113677979 125.7765884399414 0.29091233015060425 170.28619384765625 0.18496209383010864 0.877247 0.3304988145828247 True -13 37142 29.27659797668457 0.9926989078521729 141.41497802734375 0.4390057325363159 169.9206085205078 0.1865302175283432 0.88206077 0.3116820752620697 True -14 39795 29.2382173538208 0.5743682384490967 158.15255737304688 0.3129684627056122 169.27980041503906 0.1878518909215927 0.88472867 0.29775360226631165 True -15 42448 29.26167130470276 0.5699267387390137 133.88864135742188 0.25835737586021423 169.09278869628906 0.1880064606666565 0.88627934 0.28716152906417847 True -16 45101 29.24780583381653 0.5540122985839844 112.84178161621094 0.5384544730186462 169.10574340820312 0.18762263655662537 0.88737005 0.2803678810596466 True -17 47754 29.261330366134644 0.5639553070068359 151.17575073242188 0.32905876636505127 169.1353302001953 0.187547504901886 0.8872817 0.2784941792488098 False -18 50407 29.21323251724243 1.0324819087982178 128.0099334716797 0.19889682531356812 169.24400329589844 0.18701092898845673 0.8872871 0.2802697718143463 False -19 53060 29.274314880371094 0.5623588562011719 151.4505157470703 0.40675169229507446 169.131103515625 0.18756096065044403 0.886632 0.28039994835853577 False diff --git a/ENCSR749YCR/cherimoya.fold_0.performance.tsv b/ENCSR749YCR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 70951c5119f515c950cdfb14f88f150cd711cb78..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -169.10574340820312 0.5690857172012329 0.18762265145778656 0.0456317737698555 0.8873700499534607 0.7733817100524902 0.2803678810596466 \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_1.evaluate.json b/ENCSR749YCR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4ef0d74532f80bae5f2be7f1b4437a9d23605980..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF953WKL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_1.fit.json b/ENCSR749YCR/cherimoya.fold_1.fit.json deleted file mode 100644 index 4005c92fdf45ac459ec7bf573fb3b07a9cfc88ea..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF953WKL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_1.log b/ENCSR749YCR/cherimoya.fold_1.log deleted file mode 100644 index fbf805c88283062633a3e6e3807b54d172284e85..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2627 32.6695442199707 3.8480610847473145 132.0729522705078 0.5423204898834229 268.569091796875 0.14098700881004333 0.7323913 4.340267658233643 True -1 5254 28.984211683273315 0.7133769989013672 174.96817016601562 0.5655895471572876 240.7091827392578 0.1915099173784256 0.8009058 2.0302889347076416 True -2 7881 28.93344020843506 0.7607944011688232 185.84361267089844 0.6853007078170776 236.8811492919922 0.19640788435935974 0.81530505 1.1562756299972534 True -3 10508 28.941644191741943 0.68514084815979 117.90795135498047 0.4728033244609833 233.80020141601562 0.2001771330833435 0.8365349 0.8399983048439026 True -4 13135 28.861366271972656 0.6750931739807129 164.59146118164062 0.46713563799858093 232.25094604492188 0.2028813511133194 0.848217 0.8199588060379028 True -5 15762 28.889827251434326 0.6769065856933594 177.09385681152344 0.48787128925323486 230.4359130859375 0.20666956901550293 0.85554695 0.735397458076477 True -6 18389 28.901315689086914 0.6897275447845459 131.26882934570312 0.34519580006599426 228.48739624023438 0.21196496486663818 0.85662997 0.7393761277198792 True -7 21016 28.887656211853027 0.6959571838378906 160.156005859375 0.2641258239746094 228.1718292236328 0.2118917554616928 0.86220294 0.6785526275634766 True -8 23643 28.925157070159912 0.6903665065765381 142.77944946289062 0.3373976945877075 227.24755859375 0.21450716257095337 0.86325073 0.638956606388092 True -9 26270 28.949755430221558 0.6937863826751709 120.62581634521484 0.5012818574905396 226.60743713378906 0.21537260711193085 0.8732136 0.5870614051818848 True -10 28897 28.9332492351532 0.6877107620239258 158.637939453125 0.44274604320526123 225.47012329101562 0.21779167652130127 0.87723756 0.5224752426147461 True -11 31524 28.92226767539978 0.6874454021453857 135.75143432617188 0.3194832503795624 224.8472900390625 0.21912582218647003 0.88611245 0.4506441652774811 True -12 34151 28.913512706756592 0.687880277633667 149.5013885498047 0.3119499683380127 224.01939392089844 0.2210300862789154 0.88894045 0.43886813521385193 True -13 36778 28.908844232559204 0.6788899898529053 154.31808471679688 0.2940572202205658 223.37026977539062 0.22256359457969666 0.89613354 0.4002765119075775 True -14 39405 28.90941858291626 0.6809670925140381 179.77484130859375 0.4337975084781647 222.54150390625 0.22343477606773376 0.899383 0.36826232075691223 True -15 42032 28.9285147190094 0.7318944931030273 124.69747924804688 0.5965239405632019 222.08111572265625 0.22447608411312103 0.90269303 0.3529895544052124 True -16 44659 28.937453746795654 25.369940519332886 184.8801727294922 0.3381408751010895 221.3610382080078 0.22638629376888275 0.90546775 0.3410755395889282 True -17 47286 28.99055528640747 0.7386329174041748 153.53073120117188 0.4400002658367157 222.19000244140625 0.2232736349105835 0.90723306 0.3344535231590271 True -18 49913 28.91807794570923 0.6889379024505615 185.73605346679688 0.3445757031440735 222.10650634765625 0.22401079535484314 0.90624243 0.33470529317855835 False -19 52540 28.99885869026184 0.6886863708496094 156.20999145507812 0.34239739179611206 221.8917999267578 0.22453942894935608 0.9047088 0.333223432302475 False diff --git a/ENCSR749YCR/cherimoya.fold_1.performance.tsv b/ENCSR749YCR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 056f6e3426c2a26b406060b5c496591fdb43853c..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -222.19000244140625 0.5401076078414917 0.2232736349105835 0.06185067817568779 0.9072330594062805 0.8364508748054504 0.3344535231590271 \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_2.evaluate.json b/ENCSR749YCR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6e9141d2c2d12254b761de4e02aa3e1c613999bb..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF953WKL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_2.fit.json b/ENCSR749YCR/cherimoya.fold_2.fit.json deleted file mode 100644 index d0e77f93e2bfc911ad31131d806d56699a01ab1c..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF953WKL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_2.log b/ENCSR749YCR/cherimoya.fold_2.log deleted file mode 100644 index d30ee706702c2d191dfde1b88dd173b5fd17c4d5..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 34.76094317436218 3.972632646560669 142.81942749023438 0.30313318967819214 222.41583251953125 0.134462371468544 0.722752 3.153594732284546 True -1 5606 30.960577726364136 0.5518004894256592 126.02970886230469 0.5419293642044067 199.10435485839844 0.1767454594373703 0.8122555 1.6263675689697266 True -2 8409 30.84995722770691 0.5393502712249756 120.47119903564453 0.45600706338882446 197.2826385498047 0.1778590977191925 0.81337637 0.980520486831665 True -3 11212 30.78965973854065 0.5300757884979248 174.7435302734375 0.5967251658439636 194.50311279296875 0.1822126805782318 0.81928843 0.8478658199310303 True -4 14015 30.803972721099854 0.5374066829681396 158.95944213867188 0.43229395151138306 192.24037170410156 0.18671855330467224 0.8393464 0.7316135168075562 True -5 16818 30.756574392318726 0.5334820747375488 182.70333862304688 0.5098237991333008 191.26219177246094 0.18853606283664703 0.8417782 0.6939479112625122 True -6 19621 30.82428789138794 0.539297342300415 129.48672485351562 0.46992456912994385 190.66612243652344 0.18995097279548645 0.8467133 0.685003936290741 True -7 22424 30.858118772506714 0.5399818420410156 130.68484497070312 0.3961089849472046 190.18597412109375 0.1909501701593399 0.8545374 0.5975496768951416 True -8 25227 30.837854862213135 0.5195412635803223 183.60659790039062 0.32423996925354004 189.0794677734375 0.19383269548416138 0.86025184 0.5222877860069275 True -9 28030 30.906294107437134 0.5436501502990723 126.02051544189453 0.4483993649482727 189.13037109375 0.19349655508995056 0.86586064 0.47763457894325256 True -10 30833 30.860655307769775 0.5352017879486084 152.02725219726562 0.4734972417354584 188.4357452392578 0.19518664479255676 0.871173 0.4371549189090729 True -11 33636 30.822132349014282 1.2833304405212402 163.27639770507812 0.4286167621612549 187.70924377441406 0.1971748024225235 0.87770694 0.3882041275501251 True -12 36439 30.88160800933838 0.5408072471618652 125.5321044921875 0.33346468210220337 187.1876220703125 0.19819553196430206 0.88224155 0.35767418146133423 True -13 39242 30.87367343902588 0.5488641262054443 112.30735778808594 0.32851412892341614 187.07615661621094 0.19870580732822418 0.88698304 0.3366289436817169 True -14 42045 30.932878255844116 0.5433738231658936 139.6531982421875 0.38799670338630676 186.5091552734375 0.19986878335475922 0.8890715 0.318154513835907 True -15 44848 30.932386875152588 0.5421593189239502 152.57034301757812 0.3971635401248932 186.46578979492188 0.19907858967781067 0.89183223 0.3049130141735077 True -16 47651 30.880909204483032 0.5385856628417969 111.66654968261719 0.1850762814283371 186.12777709960938 0.20042404532432556 0.8944592 0.2943665087223053 True -17 50454 30.950190544128418 0.5501143932342529 170.57919311523438 0.2287762612104416 186.1126708984375 0.2002522349357605 0.8923956 0.29291069507598877 False -18 53257 30.97066569328308 0.5431869029998779 200.2953338623047 0.2640068233013153 186.28848266601562 0.19946986436843872 0.8913731 0.29534077644348145 False -19 56060 30.980150938034058 0.5423271656036377 152.99282836914062 0.18528887629508972 186.05213928222656 0.20060375332832336 0.8926456 0.2975656986236572 False diff --git a/ENCSR749YCR/cherimoya.fold_2.performance.tsv b/ENCSR749YCR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f3f20fba1d0f8d6616f6baf060e10211e69fdd15..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -186.12777709960938 0.5587655901908875 0.20042403042316437 0.05213935673236847 0.8944591879844666 0.8000411987304688 0.2943665087223053 \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_3.evaluate.json b/ENCSR749YCR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 55cd6e45b64a4b2710bce8db0ce37f9244955649..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF953WKL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_3.fit.json b/ENCSR749YCR/cherimoya.fold_3.fit.json deleted file mode 100644 index 78f25f34eb7779080a745e5146d8178c5fb5b82e..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF953WKL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_3.log b/ENCSR749YCR/cherimoya.fold_3.log deleted file mode 100644 index 68dc93c47d4ff624ad9396fc125f9e6c8ee223d8..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2668 33.044888973236084 3.8734872341156006 121.763427734375 0.8151713609695435 212.02413940429688 0.13753359019756317 0.71652365 3.432739496231079 True -1 5336 29.428022623062134 0.8248741626739502 121.39810180664062 0.31775951385498047 192.84487915039062 0.1745682656764984 0.7919473 1.7215900421142578 True -2 8004 29.362406015396118 0.5564579963684082 148.71705627441406 0.322405070066452 190.6626739501953 0.17661035060882568 0.7887556 1.1105022430419922 False -3 10672 29.400388479232788 1.6093549728393555 119.85389709472656 0.4539351463317871 188.86012268066406 0.18002967536449432 0.81306213 0.7479639053344727 True -4 13340 29.34850287437439 0.5369377136230469 118.46693420410156 0.4236459732055664 187.43539428710938 0.18383058905601501 0.81799245 0.6922025680541992 True -5 16008 29.305243730545044 0.5361723899841309 163.43191528320312 0.5454914569854736 186.4585418701172 0.18562333285808563 0.8268111 0.6380416750907898 True -6 18676 29.333759784698486 0.5385386943817139 119.57218933105469 0.34575986862182617 185.6750030517578 0.18739038705825806 0.8320361 0.5992954969406128 True -7 21344 29.41479754447937 0.5492663383483887 182.83096313476562 0.319918155670166 185.09695434570312 0.1889006495475769 0.83579296 0.5761295557022095 True -8 24012 29.3226318359375 1.2372503280639648 123.23529052734375 0.3272123336791992 184.49517822265625 0.19018182158470154 0.8416219 0.5473963022232056 True -9 26680 29.365264177322388 0.5550098419189453 131.65463256835938 0.3835316002368927 183.74349975585938 0.192148357629776 0.84840745 0.5035586357116699 True -10 29348 29.407663345336914 0.5349469184875488 150.2808074951172 0.44243231415748596 183.31483459472656 0.19298237562179565 0.8576978 0.4479694366455078 True -11 32016 29.411879539489746 1.1019577980041504 143.322998046875 0.2968827486038208 182.86703491210938 0.19412808120250702 0.8616228 0.4333416819572449 True -12 34684 29.35013175010681 0.7591269016265869 169.49850463867188 0.3969689905643463 182.51551818847656 0.1952550858259201 0.86807436 0.3990602493286133 True -13 37352 29.418230533599854 0.5461900234222412 207.7204132080078 0.44978320598602295 182.05807495117188 0.19608502089977264 0.8730813 0.3712158501148224 True -14 40020 29.41549062728882 0.5347468852996826 184.6681671142578 0.37001273036003113 181.42372131347656 0.19755467772483826 0.8797613 0.34611833095550537 True -15 42688 29.375500440597534 0.5342698097229004 168.9255828857422 0.24245353043079376 181.2091827392578 0.19811056554317474 0.8827485 0.33623600006103516 True -16 45356 29.3606014251709 0.539492130279541 140.33236694335938 0.46498340368270874 181.03704833984375 0.19826428592205048 0.8864497 0.3238011598587036 True -17 48024 29.478821277618408 20.947405099868774 180.61029052734375 0.290935218334198 180.8169403076172 0.19830971956253052 0.8888131 0.3146842122077942 True -18 50692 30.070639848709106 0.5374529361724854 125.95016479492188 0.319625586271286 180.7979736328125 0.1982158124446869 0.8877057 0.31886669993400574 False -19 53360 29.46326732635498 0.5393929481506348 141.01654052734375 0.3198350667953491 180.58807373046875 0.1992044299840927 0.88765657 0.3201369345188141 False diff --git a/ENCSR749YCR/cherimoya.fold_3.performance.tsv b/ENCSR749YCR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f0bfb8494d62edb03bda49119d72bd1d4f12fb82..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -180.8169403076172 0.5610891580581665 0.19830971956253052 0.05509620159864426 0.8888130784034729 0.7853131890296936 0.3146842122077942 \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_4.evaluate.json b/ENCSR749YCR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9697599133396358626790ec344d9a04b904ca0b..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF953WKL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_4.fit.json b/ENCSR749YCR/cherimoya.fold_4.fit.json deleted file mode 100644 index 703f30de44466fec2276df05edb43aceebf0d534..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF953WKL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR749YCR/cherimoya.fold_4.log b/ENCSR749YCR/cherimoya.fold_4.log deleted file mode 100644 index beb61d02ea95a2e5f35ae8aafb1143a612449cc9..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 33.86784648895264 4.262081623077393 148.87039184570312 0.457389235496521 185.54994201660156 0.1247503012418747 0.7133561 2.806455612182617 True -1 5516 30.397324800491333 0.6219933032989502 154.91729736328125 0.4203300178050995 170.6265869140625 0.15702877938747406 0.7784512 1.3441662788391113 True -2 8274 30.328089714050293 0.5607442855834961 223.1870880126953 0.6025874614715576 168.240966796875 0.15969064831733704 0.79138184 0.7402355074882507 True -3 11032 30.276360034942627 11.430449724197388 157.60174560546875 0.4848933219909668 165.944580078125 0.16391201317310333 0.81046814 0.5808990001678467 True -4 13790 30.517565727233887 0.591425895690918 150.4291229248047 0.48440369963645935 164.73585510253906 0.16693013906478882 0.8167902 0.5348529815673828 True -5 16548 30.3815336227417 0.5747826099395752 199.00502014160156 0.6200129389762878 164.26414489746094 0.16754288971424103 0.82271826 0.49108484387397766 True -6 19306 30.431082725524902 0.5658612251281738 175.5892791748047 0.22950010001659393 163.9502410888672 0.16826772689819336 0.8263939 0.49734190106391907 True -7 22064 30.271928310394287 0.5667853355407715 138.60595703125 0.3523973226547241 163.2507781982422 0.17007294297218323 0.82760066 0.46986326575279236 True -8 24822 30.346035957336426 0.5535736083984375 164.893310546875 0.5089523792266846 162.63906860351562 0.17173850536346436 0.837577 0.4180396497249603 True -9 27580 30.46530532836914 0.5753276348114014 114.50072479248047 0.33735692501068115 162.11688232421875 0.17267753183841705 0.84463537 0.38412103056907654 True -10 30338 30.31349468231201 0.5641133785247803 164.38372802734375 0.3951408565044403 161.8606719970703 0.17322978377342224 0.8541877 0.3497626781463623 True -11 33096 30.28093433380127 0.5768234729766846 112.30967712402344 0.3725569546222687 161.46713256835938 0.17362076044082642 0.85943836 0.3228120505809784 True -12 35854 30.334270477294922 0.5774943828582764 191.83990478515625 0.2094460427761078 160.86492919921875 0.17591729760169983 0.86623776 0.3090114891529083 True -13 38612 30.311835765838623 0.5774648189544678 130.24114990234375 0.6979362964630127 160.46365356445312 0.17647704482078552 0.8724893 0.28729110956192017 True -14 41370 30.288959503173828 0.7836041450500488 137.39515686035156 0.2832416594028473 160.2080535888672 0.17707453668117523 0.87571335 0.2793119549751282 True -15 44128 30.402477502822876 0.5735836029052734 126.0887451171875 0.2424335777759552 159.82473754882812 0.1781979650259018 0.8783929 0.26790177822113037 True -16 46886 30.306095838546753 0.6058857440948486 172.49978637695312 0.17480704188346863 159.77684020996094 0.17808446288108826 0.8805058 0.26350146532058716 True -17 49644 30.369569778442383 0.558483362197876 134.00148010253906 0.2241080403327942 160.0063018798828 0.17814947664737701 0.8821194 0.2602194845676422 True -18 52402 30.312676668167114 0.5672512054443359 138.74862670898438 0.2998284697532654 159.9971466064453 0.17831268906593323 0.8805313 0.2602458596229553 False -19 55160 30.346081018447876 0.5785412788391113 127.86749267578125 0.19883736968040466 159.97434997558594 0.17800678312778473 0.88143134 0.26134800910949707 False diff --git a/ENCSR749YCR/cherimoya.fold_4.performance.tsv b/ENCSR749YCR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2577150d4d9ff9dad1ae8b4d0fc4445ec1d34e52..0000000000000000000000000000000000000000 --- a/ENCSR749YCR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -160.0063018798828 0.5755791664123535 0.17814947664737701 0.04131767526268959 0.8821194171905518 0.7466554641723633 0.2602194845676422 \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_0.evaluate.json b/ENCSR752NTF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index dfc4db2ea98f70f09f08a69dfa6a61efbdac50a7..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF732CAB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_0.fit.json b/ENCSR752NTF/cherimoya.fold_0.fit.json deleted file mode 100644 index 914bc3dd446d0b5260fcce443b48720359bfae74..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF732CAB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_0.log b/ENCSR752NTF/cherimoya.fold_0.log deleted file mode 100644 index f072b251495d0213bbeafe962d3320ba933459b4..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 35.49712681770325 4.2434375286102295 223.546142578125 0.4780403673648834 299.0574645996094 0.1515953093767166 0.7219688 2.527825117111206 True -1 5560 30.763696908950806 1.1431529521942139 235.31341552734375 0.9925786256790161 288.3524475097656 0.20136019587516785 0.77733594 0.7336744666099548 True -2 8340 30.82346820831299 0.5731563568115234 230.21726989746094 0.4472787380218506 284.75677490234375 0.21359021961688995 0.7891587 0.4483610987663269 True -3 11120 30.662910223007202 0.5787773132324219 266.00860595703125 0.6875487565994263 283.5053405761719 0.21795602142810822 0.7910032 0.46181920170783997 True -4 13900 30.67566227912903 0.5630004405975342 259.84161376953125 0.5330637693405151 283.01043701171875 0.2202582061290741 0.7888935 0.5206845998764038 False -5 16680 31.334529399871826 0.5555844306945801 226.1623077392578 0.6107393503189087 282.7066955566406 0.2207886278629303 0.79219025 0.4987683892250061 True -6 19460 30.594581127166748 0.5664355754852295 236.0667724609375 0.5203116536140442 281.73944091796875 0.22591142356395721 0.7910748 0.4691607356071472 False -7 22240 30.61699652671814 0.5686261653900146 233.47711181640625 0.41337287425994873 281.3352966308594 0.2277456820011139 0.79256475 0.45703810453414917 True -8 25020 30.619677305221558 0.5733461380004883 215.69009399414062 0.4753352403640747 280.7419738769531 0.2293979376554489 0.7982587 0.4348243176937103 True -9 27800 30.545892238616943 0.5577647686004639 188.6605224609375 0.4272235631942749 280.20782470703125 0.232869952917099 0.802113 0.42340099811553955 True -10 30580 30.643787145614624 0.5770196914672852 250.55978393554688 0.3009940981864929 279.85626220703125 0.23444856703281403 0.80382824 0.40665167570114136 True -11 33360 30.685114860534668 1.2180805206298828 211.77850341796875 0.41818496584892273 279.7352294921875 0.2347417026758194 0.80586255 0.3752457797527313 True -12 36140 30.739487409591675 0.5686831474304199 204.70179748535156 0.31145960092544556 279.2476501464844 0.23647837340831757 0.80936056 0.3552922010421753 True -13 38920 30.728081464767456 0.5663983821868896 161.01229858398438 0.4598337709903717 278.74066162109375 0.23896868526935577 0.8123765 0.34567680954933167 True -14 41700 30.284093379974365 0.5600497722625732 243.23416137695312 0.3841244578361511 278.52239990234375 0.23950906097888947 0.8178545 0.3143271803855896 True -15 44480 29.962828874588013 0.5597655773162842 226.81085205078125 0.4998805522918701 278.2276916503906 0.2402377724647522 0.826234 0.28287172317504883 True -16 47260 29.981321811676025 0.5678431987762451 217.0297393798828 0.3487189710140228 278.3746643066406 0.23979470133781433 0.8286849 0.2699107527732849 True -17 50040 30.053946256637573 0.5644187927246094 184.50950622558594 0.341636598110199 278.3380126953125 0.2401217371225357 0.8308757 0.2645741105079651 True -18 52820 30.030229091644287 0.5659346580505371 197.62835693359375 0.2722703814506531 278.4942626953125 0.23890478909015656 0.8309955 0.25939545035362244 True -19 55600 29.998474836349487 1.1920359134674072 268.25213623046875 0.21435214579105377 278.5050964355469 0.23904144763946533 0.8300201 0.26075175404548645 False diff --git a/ENCSR752NTF/cherimoya.fold_0.performance.tsv b/ENCSR752NTF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b3bde632e5fef84ea5c54887d2e34014eb17d458..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -278.4942626953125 0.511757493019104 0.23890480399131775 0.06832963228225708 0.830995500087738 0.7863414287567139 0.25939545035362244 \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_1.evaluate.json b/ENCSR752NTF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 13fd710ca1cb1e6078d0cec370bbac79befbc771..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF732CAB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_1.fit.json b/ENCSR752NTF/cherimoya.fold_1.fit.json deleted file mode 100644 index d7ad647afb53f20c79b9dc4f6fc1c9c7c62467a1..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF732CAB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_1.log b/ENCSR752NTF/cherimoya.fold_1.log deleted file mode 100644 index 2b2d07988f6d57cc2f348631a01c6be2ad30e994..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 35.50719428062439 4.1247735023498535 270.98052978515625 0.5684950351715088 349.8299560546875 0.16365894675254822 0.70895565 3.261387586593628 True -1 5470 30.056973934173584 0.7749860286712646 163.79135131835938 0.6979839205741882 335.4839172363281 0.22253450751304626 0.79037875 0.891420304775238 True -2 8205 30.105307579040527 0.7203028202056885 223.82591247558594 0.5394802689552307 331.3631286621094 0.2342412918806076 0.80929476 0.4346528947353363 True -3 10940 30.09111475944519 0.7040102481842041 247.17355346679688 0.6345534324645996 329.86083984375 0.23732633888721466 0.81290793 0.36619681119918823 True -4 13675 30.04650902748108 0.7235682010650635 257.7012939453125 0.5383968353271484 328.854248046875 0.2403252124786377 0.81103295 0.3695245087146759 False -5 16410 29.626320838928223 0.7109692096710205 218.87791442871094 0.43920135498046875 328.4410095214844 0.24183078110218048 0.8119412 0.3840573728084564 False -6 19145 29.47565484046936 0.7041451930999756 304.05084228515625 0.47731173038482666 327.3896789550781 0.24562013149261475 0.81296533 0.3831336200237274 True -7 21880 29.46117901802063 1.3548715114593506 195.17349243164062 0.5352156758308411 326.513916015625 0.24897056818008423 0.81659 0.3705044984817505 True -8 24615 29.46953296661377 1.7922396659851074 203.62460327148438 0.48307985067367554 326.1777038574219 0.25003957748413086 0.81738025 0.3645998239517212 True -9 27350 29.501500129699707 0.7249588966369629 164.05711364746094 0.37954556941986084 325.14642333984375 0.254301518201828 0.8203759 0.3545273542404175 True -10 30085 29.509698629379272 0.7138369083404541 212.1007080078125 0.4710804522037506 325.11279296875 0.2541465163230896 0.82335407 0.3427097797393799 True -11 32820 29.489457607269287 0.7035231590270996 278.7918701171875 0.40321290493011475 324.7444763183594 0.25541552901268005 0.82688874 0.3208448588848114 True -12 35555 29.51909613609314 0.7265360355377197 212.09962463378906 0.44631466269493103 324.3333740234375 0.2562704086303711 0.8297366 0.32582539319992065 True -13 38290 29.590575695037842 0.7108888626098633 246.07980346679688 0.3967134356498718 324.27301025390625 0.2565477192401886 0.83456004 0.30629584193229675 True -14 41025 29.4903666973114 0.7347350120544434 239.8081817626953 0.29321184754371643 323.26611328125 0.2608761489391327 0.8404359 0.2937600910663605 True -15 43760 29.48823881149292 0.7253735065460205 222.18218994140625 0.34810978174209595 323.5257873535156 0.25947684049606323 0.84247345 0.2910541594028473 True -16 46495 29.504761457443237 0.7167057991027832 228.98052978515625 0.19434596598148346 323.6324157714844 0.25871995091438293 0.8470099 0.28143739700317383 True -17 49230 29.501831769943237 0.7073104381561279 247.4016876220703 0.1896732747554779 323.50250244140625 0.2589331865310669 0.84760046 0.28052806854248047 True -18 51965 29.520378589630127 0.7064385414123535 242.54754638671875 0.23960661888122559 323.2948303222656 0.2600861191749573 0.84690017 0.2809673547744751 False -19 54700 29.47290802001953 1.25709867477417 258.0792541503906 0.25076013803482056 323.4912414550781 0.25945308804512024 0.84577984 0.2821043133735657 False diff --git a/ENCSR752NTF/cherimoya.fold_1.performance.tsv b/ENCSR752NTF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ae5af255995c3acfded3fb2a5484565e3457541a..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -323.50250244140625 0.4915778934955597 0.2589331865310669 0.081825852394104 0.8476004600524902 0.8241825103759766 0.28052806854248047 \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_2.evaluate.json b/ENCSR752NTF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d412f16e1426b8e12cace687973313d2694ff8fb..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF732CAB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_2.fit.json b/ENCSR752NTF/cherimoya.fold_2.fit.json deleted file mode 100644 index b20fdc41a0909bf8cbbb2ba7c88d1a7265f0b019..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF732CAB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_2.log b/ENCSR752NTF/cherimoya.fold_2.log deleted file mode 100644 index 9321fa6425968036c3abcfd1cd36b9ecc03c1eb2..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2902 36.43943405151367 3.9292609691619873 204.36129760742188 0.7546963691711426 311.4191589355469 0.1584518700838089 0.7088699 2.689354658126831 True -1 5804 32.18756985664368 0.6098065376281738 239.05340576171875 0.555014967918396 299.0831604003906 0.2116616666316986 0.781003 0.6704012751579285 True -2 8706 32.05463719367981 0.544276237487793 228.7677764892578 0.8270678520202637 296.2839660644531 0.21900442242622375 0.79884 0.4007946848869324 True -3 11608 31.941417932510376 0.5596847534179688 260.56390380859375 0.45232468843460083 294.6834411621094 0.22328875958919525 0.80326426 0.35291731357574463 True -4 14510 32.05842185020447 0.5534212589263916 208.2780303955078 0.4220508337020874 293.7261962890625 0.22737599909305573 0.80852 0.35998719930648804 True -5 17412 32.044057846069336 0.5485761165618896 199.53085327148438 0.5509782433509827 293.19268798828125 0.2287374883890152 0.8112757 0.35014626383781433 True -6 20314 32.01784920692444 0.5461769104003906 205.04443359375 0.5372693538665771 292.43096923828125 0.2321864664554596 0.8111939 0.32691583037376404 False -7 23216 31.97904348373413 1.683305263519287 226.32199096679688 0.45770034193992615 291.6455078125 0.23548653721809387 0.81585926 0.30983132123947144 True -8 26118 32.05814242362976 2.6971793174743652 194.76693725585938 0.3569294214248657 291.7950134277344 0.23435059189796448 0.81789404 0.30878517031669617 True -9 29020 32.056631565093994 0.5662093162536621 237.9872589111328 0.3809407949447632 291.0999755859375 0.23717837035655975 0.81991786 0.29985249042510986 True -10 31922 32.03567171096802 0.5467109680175781 226.59231567382812 0.33468732237815857 290.760986328125 0.2388244867324829 0.8213292 0.29703742265701294 True -11 34824 32.037638902664185 0.5466811656951904 241.87939453125 0.4156125485897064 290.421875 0.24060097336769104 0.8226138 0.29361382126808167 True -12 37726 32.022745847702026 0.5497102737426758 218.22760009765625 0.27802813053131104 289.7997131347656 0.24345114827156067 0.82334775 0.29548534750938416 True -13 40628 32.08781695365906 25.534512042999268 207.53271484375 0.3537088632583618 289.7016906738281 0.24340586364269257 0.82597935 0.2904973328113556 True -14 43530 32.06749892234802 0.5856750011444092 211.33445739746094 0.32560238242149353 289.2626647949219 0.24476605653762817 0.82774067 0.283866822719574 True -15 46432 31.847825288772583 0.5410275459289551 227.83688354492188 0.329299658536911 289.2720947265625 0.24503037333488464 0.83343875 0.2745247483253479 True -16 49334 31.441835403442383 0.5394287109375 212.24960327148438 0.28256434202194214 289.0218200683594 0.2465585321187973 0.83544457 0.27209749817848206 True -17 52236 31.31524682044983 0.5434005260467529 239.12747192382812 0.23842063546180725 289.14288330078125 0.24598197638988495 0.83453745 0.2768537104129791 False -18 55138 31.375001668930054 0.536574125289917 213.82919311523438 0.2686014771461487 289.27874755859375 0.24503937363624573 0.8327481 0.2790735065937042 False -19 58040 31.31534218788147 0.6969363689422607 218.89837646484375 0.23738273978233337 289.52227783203125 0.24371077120304108 0.8331044 0.27928537130355835 False diff --git a/ENCSR752NTF/cherimoya.fold_2.performance.tsv b/ENCSR752NTF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 080016cdfc54368a1441164749ee5104988becac..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -289.0218200683594 0.5061585903167725 0.2465585321187973 0.07567894458770752 0.8354445695877075 0.7982878684997559 0.27209749817848206 \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_3.evaluate.json b/ENCSR752NTF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b1ab51ece459902e9495c8eedf23f65bdc962ecd..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF732CAB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_3.fit.json b/ENCSR752NTF/cherimoya.fold_3.fit.json deleted file mode 100644 index bdb730f3aa4722db7c2878b358f3b867854c27c6..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF732CAB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_3.log b/ENCSR752NTF/cherimoya.fold_3.log deleted file mode 100644 index fcf635bffecd0f356349632667df2580db37bb8b..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2789 35.45778274536133 3.9150490760803223 197.50633239746094 0.6962751746177673 319.83135986328125 0.1544133573770523 0.7125265 3.5089945793151855 True -1 5578 30.71153163909912 0.6323163509368896 242.8959503173828 0.600184440612793 308.1568908691406 0.2079930156469345 0.79341346 0.7973152995109558 True -2 8367 30.702635765075684 0.5936720371246338 207.9625701904297 0.8502770662307739 304.7354736328125 0.21856296062469482 0.80691457 0.489338755607605 True -3 11156 30.650855779647827 0.6107165813446045 182.3868408203125 0.6199353933334351 303.7872009277344 0.22063139081001282 0.80807424 0.4843839108943939 True -4 13945 30.590874433517456 0.5645160675048828 297.94122314453125 0.6984635591506958 303.07012939453125 0.22250811755657196 0.81260324 0.4669729471206665 True -5 16734 30.64366316795349 0.5705034732818604 244.17724609375 0.43843990564346313 302.1218566894531 0.22694364190101624 0.81303 0.4167284071445465 True -6 19523 30.711219310760498 0.5925407409667969 284.86102294921875 0.44007954001426697 301.5950927734375 0.2286694347858429 0.81512594 0.4029475152492523 True -7 22312 30.784483909606934 0.5706634521484375 214.56332397460938 0.3685804307460785 301.575439453125 0.22844475507736206 0.81578666 0.4033510088920593 True -8 25101 30.581982851028442 1.1090145111083984 259.001220703125 0.5368293523788452 300.762451171875 0.2322298139333725 0.8113635 0.4264080822467804 False -9 27890 30.196002960205078 0.5640618801116943 236.31842041015625 0.6795071363449097 300.50830078125 0.2338782399892807 0.81514204 0.37435367703437805 False -10 30679 30.228298902511597 0.5667591094970703 199.76254272460938 0.40705418586730957 299.9522705078125 0.23638826608657837 0.8177579 0.3747665286064148 True -11 33468 30.219482421875 0.565941572189331 207.67446899414062 0.43117284774780273 299.8310241699219 0.23713836073875427 0.82141465 0.3657478392124176 True -12 36257 30.26752519607544 0.5634689331054688 252.33261108398438 0.6300988793373108 299.5493469238281 0.2381233125925064 0.8245665 0.36806777119636536 True -13 39046 30.148295640945435 0.5700206756591797 236.48611450195312 0.3187945783138275 299.3277893066406 0.23870866000652313 0.82666487 0.35491159558296204 True -14 41835 30.104294300079346 19.573103189468384 250.42837524414062 0.4732552170753479 298.8838806152344 0.24032238125801086 0.83067644 0.33382076025009155 True -15 44624 30.111616373062134 0.5706658363342285 228.45486450195312 0.32409173250198364 299.0968017578125 0.23994825780391693 0.8334718 0.3211390972137451 True -16 47413 30.14445924758911 0.5803143978118896 256.2015075683594 0.37246260046958923 298.9997863769531 0.23998714983463287 0.8373663 0.3064492344856262 True -17 50202 30.109355688095093 0.5641481876373291 228.1312255859375 0.5427385568618774 299.2764892578125 0.23861810564994812 0.8388863 0.2923901677131653 True -18 52991 30.12523055076599 0.5633838176727295 229.09002685546875 0.18820813298225403 299.1471862792969 0.23934270441532135 0.8386642 0.2927900552749634 False -19 55780 30.11692476272583 0.5668017864227295 232.41510009765625 0.2261824607849121 299.074462890625 0.23965397477149963 0.8380827 0.2921682596206665 False diff --git a/ENCSR752NTF/cherimoya.fold_3.performance.tsv b/ENCSR752NTF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6fb1c66abc22d3270c987e22bdcb53014b2bc691..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -299.2764892578125 0.50629723072052 0.23861810564994812 0.07573424279689789 0.8388863205909729 0.7968077063560486 0.2923901677131653 \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_4.evaluate.json b/ENCSR752NTF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f57a9127a46d297c70d266e38cdb7e056166a1f5..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF732CAB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_4.fit.json b/ENCSR752NTF/cherimoya.fold_4.fit.json deleted file mode 100644 index 448b7bd108c6bf0283fc2701ebaf10758e627a8e..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF732CAB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR752NTF/cherimoya.fold_4.log b/ENCSR752NTF/cherimoya.fold_4.log deleted file mode 100644 index ee0826c181a6c929a8ccedc7ff4e069f164cb06d..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2853 36.08160710334778 4.3085455894470215 224.35256958007812 0.709604024887085 297.5965881347656 0.15360867977142334 0.71862 3.3049604892730713 True -1 5706 31.387216806411743 0.5748164653778076 190.10031127929688 0.7658493518829346 286.84661865234375 0.20362840592861176 0.77926433 0.7081993818283081 True -2 8559 30.858492374420166 0.5591177940368652 275.14373779296875 0.7761836051940918 284.7475280761719 0.20935818552970886 0.79489714 0.38702306151390076 True -3 11412 31.009872436523438 0.5438079833984375 219.7997589111328 0.4060453176498413 283.1663513183594 0.21521225571632385 0.80044377 0.3716052770614624 True -4 14265 30.817307949066162 0.5568454265594482 250.6732177734375 0.4840627908706665 282.3989562988281 0.21675191819667816 0.8037336 0.3965543508529663 True -5 17118 30.78201413154602 0.5482351779937744 229.15089416503906 0.44923222064971924 281.91009521484375 0.21951599419116974 0.8038651 0.3969261646270752 True -6 19971 30.726391315460205 0.523841142654419 201.26878356933594 0.39414483308792114 281.5697937011719 0.22051598131656647 0.80632734 0.43766480684280396 True -7 22824 30.74234437942505 0.5336358547210693 220.09213256835938 0.38741061091423035 281.0859069824219 0.22289110720157623 0.80669093 0.41578972339630127 True -8 25677 30.778234243392944 0.551577091217041 276.9163818359375 0.4967188537120819 280.71234130859375 0.22439664602279663 0.80992824 0.4005067050457001 True -9 28530 30.75407338142395 0.67421555519104 213.94662475585938 0.4267450273036957 279.9974670410156 0.22792445123195648 0.8129155 0.39609038829803467 True -10 31383 30.736055850982666 0.5454063415527344 195.28810119628906 0.3694605529308319 280.00445556640625 0.22757229208946228 0.8151571 0.3695424497127533 True -11 34236 30.790799379348755 0.5369141101837158 244.1569366455078 0.7958453297615051 279.5447692871094 0.23060594499111176 0.8186749 0.34772950410842896 True -12 37089 30.755861282348633 0.5380027294158936 164.08035278320312 0.6078260540962219 279.3480529785156 0.23134112358093262 0.82178944 0.3322405517101288 True -13 39942 30.751709938049316 1.2315673828125 220.58856201171875 0.34116455912590027 279.0577392578125 0.23211228847503662 0.8244253 0.3250316083431244 True -14 42795 30.775262355804443 0.5371294021606445 223.58946228027344 0.3161719739437103 278.9470520019531 0.23262476921081543 0.8292576 0.2937849462032318 True -15 45648 30.781872749328613 0.6788198947906494 225.40138244628906 0.2177658975124359 278.641845703125 0.2339027225971222 0.8334386 0.27245664596557617 True -16 48501 30.790804386138916 0.5398714542388916 226.7371368408203 0.36306363344192505 278.7200927734375 0.2340097278356552 0.8354241 0.2623346745967865 True -17 51354 30.729111194610596 0.5341260433197021 196.30029296875 0.30035653710365295 278.6023864746094 0.23402820527553558 0.8354641 0.2562592923641205 True -18 54207 30.765164136886597 0.5360269546508789 202.22369384765625 0.3733673691749573 278.71160888671875 0.2335623800754547 0.834911 0.25549501180648804 False -19 57060 30.773710250854492 0.5562880039215088 244.736328125 0.3073914051055908 278.8270568847656 0.23315207660198212 0.83472896 0.2558422386646271 False diff --git a/ENCSR752NTF/cherimoya.fold_4.performance.tsv b/ENCSR752NTF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d64814c8e413b20e029f4d42cd6d1f85fe5324a2..0000000000000000000000000000000000000000 --- a/ENCSR752NTF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -278.6023864746094 0.5135366320610046 0.23402820527553558 0.06970193237066269 0.8354641199111938 0.7853626608848572 0.2562592923641205 \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_0.evaluate.json b/ENCSR753QKD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0bef8f4ac935af963b822d0dc2889fd2ba726260..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF624UPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_0.fit.json b/ENCSR753QKD/cherimoya.fold_0.fit.json deleted file mode 100644 index c49d421f5313b9a593a1798e721dd80c698bbafb..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF624UPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_0.log b/ENCSR753QKD/cherimoya.fold_0.log deleted file mode 100644 index 4affddbe5e11f884b8b1326a9b436e38b7ae34b8..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 33.960081577301025 3.650242328643799 133.79823303222656 0.7767812609672546 249.10684204101562 0.16250909864902496 0.43910393 2.9370663166046143 True -1 5500 30.35905432701111 1.2428131103515625 168.73696899414062 0.4690617322921753 229.09323120117188 0.25193995237350464 0.58801544 1.8292945623397827 True -2 8250 30.373513221740723 0.6256706714630127 174.75308227539062 0.7869428396224976 225.78726196289062 0.2620702385902405 0.6075576 0.7781177163124084 True -3 11000 30.363975763320923 17.012709856033325 179.4221954345703 0.6783145666122437 224.33880615234375 0.26573774218559265 0.61848384 0.6664836406707764 True -4 13750 31.83127212524414 0.5989983081817627 168.28176879882812 0.6854960322380066 223.6604766845703 0.26873719692230225 0.6263892 0.6397418975830078 True -5 16500 30.38304901123047 0.6042194366455078 216.9721221923828 0.703679084777832 223.3450164794922 0.2695828676223755 0.62890416 0.5534244775772095 True -6 19250 30.334847927093506 0.588186502456665 148.59097290039062 0.6544142365455627 222.8273468017578 0.27199044823646545 0.636547 0.5355613231658936 True -7 22000 30.330738306045532 0.5800671577453613 176.96713256835938 0.5001381635665894 222.17218017578125 0.27533039450645447 0.6472035 0.5313877463340759 True -8 24750 30.428046703338623 0.6042826175689697 172.56591796875 0.5721385478973389 221.625244140625 0.27819666266441345 0.6525397 0.5025051832199097 True -9 27500 30.32061529159546 0.5863337516784668 196.38262939453125 0.5078023076057434 221.07015991210938 0.2803676426410675 0.66075647 0.48880842328071594 True -10 30250 30.35249662399292 0.5995995998382568 191.78736877441406 0.6995021104812622 220.457275390625 0.28299885988235474 0.6653477 0.4751918613910675 True -11 33000 30.409592866897583 0.5873851776123047 182.60606384277344 0.5176926255226135 220.0651397705078 0.2843035161495209 0.67636764 0.4546542167663574 True -12 35750 30.628211498260498 12.156737327575684 183.72842407226562 0.5483080148696899 219.3174285888672 0.2870655953884125 0.6842958 0.4407656788825989 True -13 38500 30.341651678085327 22.98910641670227 200.93499755859375 0.4431462585926056 219.0480499267578 0.28806939721107483 0.6972092 0.42886728048324585 True -14 41250 30.410947799682617 0.6011214256286621 169.46524047851562 0.4879131317138672 218.13575744628906 0.29275253415107727 0.704571 0.4209500253200531 True -15 44000 30.392371892929077 0.5907421112060547 145.28041076660156 0.3645286560058594 217.7171173095703 0.29505711793899536 0.7132935 0.4022843837738037 True -16 46750 30.3958899974823 0.5884571075439453 196.0257568359375 0.5321798324584961 217.8225860595703 0.2941642701625824 0.71744525 0.40393948554992676 True -17 49500 30.416069746017456 0.6085081100463867 186.3707275390625 0.3900146782398224 218.19740295410156 0.29124152660369873 0.7169844 0.4064360558986664 False -18 52250 30.323270559310913 0.5888903141021729 152.61288452148438 0.3185006380081177 218.00552368164062 0.29289472103118896 0.71739227 0.4119659662246704 False -19 55000 30.363013744354248 0.6054818630218506 178.97021484375 0.2794438600540161 217.97593688964844 0.2930361330509186 0.7166604 0.41688865423202515 False diff --git a/ENCSR753QKD/cherimoya.fold_0.performance.tsv b/ENCSR753QKD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b4eb97c727c704617426b1e64e2f8a1c2f4bf6b1..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -217.8225860595703 0.5066311955451965 0.2941642701625824 0.06882986426353455 0.7174452543258667 0.661392331123352 0.40393948554992676 \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_1.evaluate.json b/ENCSR753QKD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0821cd60754a6b1d9345dd55fa10b3922f37235d..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF624UPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_1.fit.json b/ENCSR753QKD/cherimoya.fold_1.fit.json deleted file mode 100644 index 191061544f181977a834eb71a6a3807239056f24..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF624UPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_1.log b/ENCSR753QKD/cherimoya.fold_1.log deleted file mode 100644 index 83a532a75399e84778186e40aa1b1eeded1bbf5b..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 33.807350873947144 6.069438219070435 182.92568969726562 0.6021131277084351 285.39935302734375 0.17111815512180328 0.4995916 2.765134811401367 True -1 5492 30.622363090515137 0.7078573703765869 205.63519287109375 0.7509627342224121 262.4541931152344 0.26234665513038635 0.6235179 1.6838399171829224 True -2 8238 30.295302867889404 0.7256135940551758 169.239013671875 0.45057737827301025 256.69378662109375 0.27560797333717346 0.65330005 0.7631730437278748 True -3 10984 30.261310815811157 0.683208703994751 180.6795196533203 0.7108055353164673 255.40499877929688 0.2788698673248291 0.6619825 0.7864596843719482 True -4 13730 30.300240993499756 1.5094974040985107 184.41099548339844 0.7050033807754517 253.41641235351562 0.2840055525302887 0.6793704 0.6616535186767578 True -5 16476 30.2745258808136 0.6663031578063965 204.18724060058594 0.7627602219581604 252.36761474609375 0.2863520085811615 0.68966764 0.5980329513549805 True -6 19222 30.28290605545044 0.6790063381195068 162.50341796875 0.5916586518287659 252.31532287597656 0.2864258289337158 0.6949078 0.5912766456604004 True -7 21968 30.28034257888794 0.6699016094207764 186.97792053222656 0.6698808670043945 251.12484741210938 0.291861355304718 0.7002926 0.5708101987838745 True -8 24714 30.35038113594055 0.6917073726654053 193.07798767089844 0.524361789226532 250.21572875976562 0.2952040731906891 0.70889217 0.5342844724655151 True -9 27460 30.437040328979492 0.6723744869232178 192.65924072265625 0.6231129765510559 250.1228790283203 0.29476726055145264 0.7124273 0.5081157684326172 True -10 30206 30.341294288635254 0.702509880065918 162.8625030517578 0.5839102268218994 249.2383270263672 0.2975623905658722 0.7219336 0.48342904448509216 True -11 32952 30.30765652656555 1.359259843826294 180.6716766357422 0.5287076234817505 248.42234802246094 0.30025702714920044 0.7276282 0.4728321135044098 True -12 35698 30.420294284820557 0.6705043315887451 171.853515625 0.41323786973953247 247.56838989257812 0.30310308933258057 0.7343872 0.4506136178970337 True -13 38444 30.3717143535614 0.6959507465362549 190.34591674804688 0.4456740617752075 246.7035369873047 0.3062446117401123 0.74613327 0.4281521141529083 True -14 41190 30.407232999801636 0.6941344738006592 165.55303955078125 0.4221116900444031 246.9838104248047 0.304794043302536 0.75050056 0.4271593987941742 True -15 43936 30.415510416030884 0.672560453414917 188.2467803955078 0.4796544015407562 246.90724182128906 0.3056466281414032 0.7574915 0.41992661356925964 True -16 46682 30.57158088684082 1.8756442070007324 152.54574584960938 0.5060018301010132 246.26589965820312 0.30869945883750916 0.76184374 0.41504815220832825 True -17 49428 30.4004385471344 0.6872949600219727 139.0867919921875 0.45863044261932373 246.47608947753906 0.306456059217453 0.76519346 0.41763994097709656 True -18 52174 30.348317861557007 5.3932530879974365 171.23171997070312 0.42338037490844727 246.19973754882812 0.30798500776290894 0.7643216 0.42167940735816956 False -19 54920 30.408507347106934 0.6763160228729248 172.0159912109375 0.42592155933380127 246.26861572265625 0.30757755041122437 0.7615946 0.4257943034172058 False diff --git a/ENCSR753QKD/cherimoya.fold_1.performance.tsv b/ENCSR753QKD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 164139b4f7426034237053544c99b5beafd5e111..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -246.47608947753906 0.4942733943462372 0.3064560890197754 0.07420117408037186 0.7651934623718262 0.7099667191505432 0.41763994097709656 \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_2.evaluate.json b/ENCSR753QKD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 96f5462a04f14eb0167ac1ef64b4d26dbe2959d3..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF624UPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_2.fit.json b/ENCSR753QKD/cherimoya.fold_2.fit.json deleted file mode 100644 index 4f3eb9af9b4587b014bb27a7b9a8409f05606830..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF624UPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_2.performance.tsv b/ENCSR753QKD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5f0c5b9a66683ed3080ed084b966c1c4b998e03c..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.68453979492188 0.5052595734596252 0.2965022325515747 0.06823195517063141 0.7185652852058411 0.654215931892395 0.42685890197753906 \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_3.fit.json b/ENCSR753QKD/cherimoya.fold_3.fit.json deleted file mode 100644 index 274e9e4e42f85be7ac8dbf8fa0a2fe5b07acb381..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF624UPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_3.log b/ENCSR753QKD/cherimoya.fold_3.log deleted file mode 100644 index 660c1c36502a84f41536a82344181b68cd3792a3..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 34.38065433502197 4.098113775253296 203.52581787109375 1.1584656238555908 262.3140563964844 0.16368834674358368 0.47989818 2.331934690475464 True -1 5534 30.609943866729736 0.621368408203125 210.91171264648438 0.8777931928634644 241.5653533935547 0.2529880404472351 0.5883144 1.9589215517044067 True -2 8301 30.60257649421692 0.597944974899292 176.54989624023438 0.8527653217315674 237.59954833984375 0.26732274889945984 0.60179853 0.9387615919113159 True -3 11068 30.583226680755615 0.5808498859405518 235.53860473632812 0.6364550590515137 235.81533813476562 0.2714605927467346 0.6255907 0.8042643070220947 True -4 13835 30.549206733703613 0.60408616065979 153.9512939453125 0.6083692312240601 234.99041748046875 0.2746061384677887 0.629674 0.7370305061340332 True -5 16602 30.57573652267456 0.5904324054718018 212.1208038330078 0.6134467124938965 234.2254638671875 0.2769125699996948 0.6434261 0.7895073294639587 True -6 19369 30.540773630142212 0.5913441181182861 153.12339782714844 0.7174341678619385 234.05068969726562 0.2773236632347107 0.64960074 0.720394492149353 True -7 22136 30.590399026870728 0.5910563468933105 214.0713348388672 0.6992147564888 233.37661743164062 0.2802186608314514 0.6571049 0.6769898533821106 True -8 24903 30.55094337463379 0.5908241271972656 174.6509246826172 0.5793595314025879 232.62689208984375 0.2844499349594116 0.66240793 0.6738396286964417 True -9 27670 30.49717903137207 0.638899564743042 194.76058959960938 0.5174381136894226 232.0178680419922 0.2864872217178345 0.6672521 0.6255043745040894 True -10 30437 30.601674556732178 0.5935657024383545 156.5589141845703 0.5929844975471497 231.78640747070312 0.28713279962539673 0.6717185 0.6051193475723267 True -11 33204 30.540703535079956 0.5906429290771484 156.92567443847656 0.5580942630767822 231.07131958007812 0.290179580450058 0.67883706 0.5838508009910583 True -12 35971 30.54192280769348 0.5908234119415283 177.4078826904297 0.4581751227378845 230.4266357421875 0.2922821640968323 0.6894216 0.5434238910675049 True -13 38738 30.56663227081299 0.595966100692749 199.7828369140625 0.6062859296798706 230.12869262695312 0.29360339045524597 0.70182806 0.5087000131607056 True -14 41505 30.5846951007843 0.5920796394348145 148.31512451171875 0.7526023983955383 229.26145935058594 0.2972128391265869 0.71013457 0.4705430567264557 True -15 44272 30.604719400405884 2.915113687515259 215.43325805664062 0.2967655658721924 229.06297302246094 0.2979154586791992 0.71741605 0.45334529876708984 True -16 47039 30.62001657485962 0.5999648571014404 156.1595916748047 0.33164775371551514 229.05519104003906 0.29739126563072205 0.7243997 0.4379163682460785 True -17 49806 30.638582944869995 0.632943868637085 171.4066162109375 0.4455232620239258 229.16189575195312 0.29729995131492615 0.7286615 0.43093135952949524 True -18 52573 30.62912893295288 0.6235787868499756 180.16204833984375 0.2601589560508728 228.90867614746094 0.29840728640556335 0.7272567 0.4333352744579315 False -19 55340 30.671968936920166 0.6137514114379883 172.79513549804688 0.471937358379364 229.0425262451172 0.2973655164241791 0.72804976 0.43694427609443665 False diff --git a/ENCSR753QKD/cherimoya.fold_3.performance.tsv b/ENCSR753QKD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b0dd3ed4b21b34a613efdea946441545048e98d2..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -229.16189575195312 0.5025182962417603 0.29729998111724854 0.06912359595298767 0.7286614775657654 0.6728489995002747 0.43093135952949524 \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_4.fit.json b/ENCSR753QKD/cherimoya.fold_4.fit.json deleted file mode 100644 index 6413c9753a22d87f5b25134303aa946eab251621..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF624UPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR753QKD/cherimoya.fold_4.log b/ENCSR753QKD/cherimoya.fold_4.log deleted file mode 100644 index 479a22f0c52a3928dcb8c9a80e8f27e337f5e27b..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2861 35.26151180267334 3.794574737548828 196.6276092529297 0.7300952672958374 254.59434509277344 0.16223709285259247 0.4440983 2.92588210105896 True -1 5722 31.554235219955444 1.934290885925293 166.71287536621094 0.9584627151489258 234.66629028320312 0.2511492371559143 0.57443124 1.491264820098877 True -2 8583 31.645503282546997 2.918699264526367 182.90228271484375 0.6871187686920166 231.92034912109375 0.2600168287754059 0.5848643 0.743423581123352 True -3 11444 31.60845708847046 0.610614538192749 172.0879364013672 0.7900500893592834 229.78587341308594 0.2683243453502655 0.60530466 0.6656761169433594 True -4 14305 31.65562677383423 0.6154236793518066 131.97364807128906 0.5657188892364502 228.9073944091797 0.2700618505477905 0.6125186 0.6169381141662598 True -5 17166 31.58063006401062 0.6153035163879395 163.58554077148438 0.656470000743866 228.55149841308594 0.2726304233074188 0.62090284 0.6426217555999756 True -6 20027 31.54095697402954 0.6050708293914795 202.4132537841797 0.6269518136978149 228.02366638183594 0.2746809124946594 0.6239874 0.631780743598938 True -7 22888 31.557687759399414 1.9503393173217773 186.57369995117188 0.6356252431869507 227.670166015625 0.27547118067741394 0.62913465 0.6149668097496033 True -8 25749 31.572834014892578 0.6384594440460205 177.2536163330078 0.6240488290786743 226.9854736328125 0.2789255380630493 0.63618016 0.5508633255958557 True -9 28610 31.563598155975342 0.593379020690918 172.02316284179688 0.7170381546020508 226.3988800048828 0.28096139430999756 0.64569724 0.5299943089485168 True -10 31471 31.636499166488647 0.6170492172241211 154.32550048828125 0.7837575078010559 225.68365478515625 0.28483846783638 0.6553846 0.5121787190437317 True -11 34332 31.66111445426941 0.6188356876373291 183.17172241210938 0.7843835949897766 225.51107788085938 0.2847216725349426 0.6639617 0.5025234818458557 True -12 37193 31.720987558364868 0.60335373878479 181.69822692871094 0.6008017063140869 224.8865509033203 0.28750160336494446 0.67408866 0.4716293215751648 True -13 40054 31.706639051437378 0.6367080211639404 169.97486877441406 0.43734070658683777 224.32290649414062 0.28956466913223267 0.6841263 0.45547112822532654 True -14 42915 31.751811027526855 0.6192574501037598 201.67620849609375 0.4078125059604645 223.9707489013672 0.29103338718414307 0.69476426 0.43766099214553833 True -15 45776 31.80029058456421 0.623488187789917 128.9707489013672 0.38550716638565063 223.5695037841797 0.29276520013809204 0.7061207 0.4232664406299591 True -16 48637 31.729180097579956 0.6210002899169922 164.91159057617188 0.42991840839385986 223.4481201171875 0.2939161956310272 0.7119003 0.41750475764274597 True -17 51498 31.812201976776123 0.6070530414581299 169.41763305664062 0.30098778009414673 223.19876098632812 0.2945978343486786 0.717683 0.41134849190711975 True -18 54359 31.78678584098816 3.04209566116333 188.24578857421875 0.3057273030281067 223.2801971435547 0.2946673631668091 0.71782875 0.4148164689540863 True -19 57220 31.766865015029907 0.6160650253295898 160.8424835205078 0.3296574354171753 223.33676147460938 0.29457610845565796 0.7169127 0.42062482237815857 False diff --git a/ENCSR753QKD/cherimoya.fold_4.performance.tsv b/ENCSR753QKD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 5b9e3b6e783cce18efe0f163e29322fc984fb7e5..0000000000000000000000000000000000000000 --- a/ENCSR753QKD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.2801971435547 0.5054148435592651 0.2946673631668091 0.06682046502828598 0.7178287506103516 0.6563116312026978 0.4148164689540863 \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_0.evaluate.json b/ENCSR754LIN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 48917832eeb0e2bebcf15d78927fd19af89eddac..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133VSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_0.fit.json b/ENCSR754LIN/cherimoya.fold_0.fit.json deleted file mode 100644 index 8e409f4f2db0323c6bafcb8ca57331c56fb16545..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF133VSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_0.log b/ENCSR754LIN/cherimoya.fold_0.log deleted file mode 100644 index 97685f77051b9ccfe3c791bf57baa004b6442304..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 35.249083042144775 4.15187406539917 1005.5955810546875 0.49998724460601807 1256.299560546875 0.2762976884841919 0.6272086 7.996551513671875 True -1 5468 30.375674724578857 0.5926229953765869 963.1486206054688 0.4253549575805664 1123.2156982421875 0.3933505713939667 0.7378673 0.745772659778595 True -2 8202 30.352931022644043 0.5683226585388184 930.467529296875 0.4163861870765686 1104.1612548828125 0.4063624441623688 0.7561095 0.3039611279964447 True -3 10936 30.333738803863525 0.5644910335540771 868.5674438476562 0.35754019021987915 1095.600830078125 0.4124499559402466 0.7699835 0.27326467633247375 True -4 13670 30.379215002059937 0.557159423828125 998.58349609375 0.20871679484844208 1090.325439453125 0.41687116026878357 0.7761661 0.26502498984336853 True -5 16404 30.379872798919678 0.5682666301727295 955.7880859375 0.33279961347579956 1085.6575927734375 0.4227220416069031 0.7792396 0.2540890872478485 True -6 19138 30.371659517288208 0.5668463706970215 888.122802734375 0.4660680294036865 1081.9630126953125 0.42587754130363464 0.77818906 0.25632914900779724 False -7 21872 30.360872745513916 0.5590243339538574 800.03271484375 0.24917618930339813 1081.460205078125 0.4260556697845459 0.7810127 0.24284090101718903 True -8 24606 30.33384943008423 0.5726497173309326 936.56689453125 0.27141842246055603 1078.2078857421875 0.42975202202796936 0.78412217 0.23346851766109467 True -9 27340 30.466003894805908 0.5764992237091064 853.5697021484375 0.23191002011299133 1075.8045654296875 0.4312867820262909 0.78603595 0.21974816918373108 True -10 30074 30.189069747924805 0.9221878051757812 845.7753295898438 0.29718899726867676 1071.5997314453125 0.43596774339675903 0.7927672 0.2102416604757309 True -11 32808 29.783203125 0.5944995880126953 906.5341796875 0.447413831949234 1072.3409423828125 0.4344550371170044 0.79718953 0.1963030993938446 True -12 35542 29.862409591674805 0.5691015720367432 936.638916015625 0.16156649589538574 1069.7222900390625 0.43688681721687317 0.80213976 0.18726618587970734 True -13 38276 29.857272386550903 0.5645904541015625 840.67529296875 0.2655588984489441 1066.7490234375 0.44047418236732483 0.80964583 0.180411234498024 True -14 41010 29.921340465545654 0.6055738925933838 902.2178955078125 0.15912136435508728 1063.8966064453125 0.4426884353160858 0.8163115 0.17127451300621033 True -15 43744 29.872934341430664 0.5859115123748779 900.9456787109375 0.15561039745807648 1063.4071044921875 0.4437764585018158 0.82072717 0.1686292439699173 True -16 46478 29.862143754959106 0.5806758403778076 887.5491943359375 0.16395728290081024 1064.4261474609375 0.4413478374481201 0.8241596 0.16418491303920746 True -17 49212 29.806315422058105 0.5598347187042236 816.952880859375 0.13136929273605347 1062.2156982421875 0.4444899260997772 0.82693285 0.16101227700710297 True -18 51946 29.749245405197144 0.5484580993652344 831.0799560546875 0.2349012941122055 1062.86376953125 0.4437447190284729 0.8262428 0.1608462780714035 False -19 54680 29.861482858657837 0.5891637802124023 964.472412109375 0.1611173301935196 1062.3585205078125 0.4445100724697113 0.8270852 0.16168051958084106 True diff --git a/ENCSR754LIN/cherimoya.fold_0.performance.tsv b/ENCSR754LIN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index df0689a651be118c5ead7dd4123f33e70edfe0d1..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1062.3585205078125 0.31170013546943665 0.4445100724697113 0.22014418244361877 0.8270851969718933 0.7995970845222473 0.16168051958084106 \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_1.evaluate.json b/ENCSR754LIN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0f3e1544bf2285bc304100e4a039b818b26abd2f..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133VSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_1.fit.json b/ENCSR754LIN/cherimoya.fold_1.fit.json deleted file mode 100644 index 159fceef048f714a801c8c64eb548440e08fa7ff..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF133VSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_1.log b/ENCSR754LIN/cherimoya.fold_1.log deleted file mode 100644 index 072c8489407dbd7027f5ccb1d499838d29010dcc..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 36.110254526138306 4.2168872356414795 931.7227172851562 0.5405250787734985 1392.24853515625 0.27733421325683594 0.64483595 7.3153157234191895 True -1 5466 30.376113653182983 1.2671029567718506 817.2575073242188 0.41901713609695435 1239.78515625 0.3982565402984619 0.75151867 0.7408335208892822 True -2 8199 30.360342741012573 0.6813178062438965 939.7294311523438 0.43965303897857666 1213.6546630859375 0.41659170389175415 0.7641134 0.408395379781723 True -3 10932 30.294211626052856 0.722306489944458 898.2596435546875 0.4175252318382263 1197.903564453125 0.427701473236084 0.77696466 0.35081472992897034 True -4 13665 30.424992322921753 26.944067239761353 933.3843994140625 0.277627170085907 1192.9326171875 0.431511253118515 0.7834486 0.31137335300445557 True -5 16398 30.40459394454956 0.7189946174621582 953.7467651367188 0.3001208007335663 1187.3514404296875 0.43654170632362366 0.7891717 0.26960650086402893 True -6 19131 30.42663812637329 0.7319960594177246 976.586669921875 0.39792218804359436 1185.31689453125 0.43766212463378906 0.7891694 0.2512921690940857 False -7 21864 30.414692163467407 0.7114572525024414 958.640625 0.23109811544418335 1180.581787109375 0.4418884217739105 0.791141 0.2359115034341812 True -8 24597 30.44460368156433 0.7215714454650879 924.653564453125 0.337958961725235 1177.21875 0.44497716426849365 0.79535764 0.23655195534229279 True -9 27330 30.027626752853394 0.7103781700134277 979.6483764648438 0.24035592377185822 1173.786865234375 0.4477967619895935 0.79864746 0.2238791137933731 True -10 30063 29.845540285110474 0.706284761428833 938.4269409179688 0.26980412006378174 1170.7900390625 0.4500208795070648 0.80106443 0.21278689801692963 True -11 32796 29.795875310897827 0.6787276268005371 817.269287109375 0.17822498083114624 1168.2427978515625 0.4530043601989746 0.805814 0.20372074842453003 True -12 35529 29.796154975891113 0.6701328754425049 877.311767578125 0.2506978511810303 1164.8431396484375 0.45442238450050354 0.81136024 0.2008359283208847 True -13 38262 29.784472227096558 0.6993265151977539 957.7333984375 0.20108899474143982 1164.42919921875 0.45433592796325684 0.8171902 0.1912335306406021 True -14 40995 29.7485613822937 0.6790032386779785 830.288818359375 0.1466381847858429 1160.5 0.4575999081134796 0.8257078 0.18296164274215698 True -15 43728 29.779523611068726 0.6848647594451904 876.0135498046875 0.17127937078475952 1158.7093505859375 0.4589557349681854 0.832061 0.17544043064117432 True -16 46461 29.764556646347046 0.7008249759674072 909.0587158203125 0.20245209336280823 1158.4112548828125 0.4590322971343994 0.8380699 0.16962464153766632 True -17 49194 29.845792770385742 0.6748878955841064 900.8115844726562 0.169944167137146 1159.5599365234375 0.457669734954834 0.8398049 0.16607972979545593 True -18 51927 29.795851945877075 0.6773228645324707 841.5877685546875 0.1473177969455719 1158.4423828125 0.45911043882369995 0.8409817 0.1648760735988617 True -19 54660 29.892767429351807 0.70123291015625 905.7755126953125 0.1259603500366211 1158.77783203125 0.45870575308799744 0.84196734 0.16587598621845245 True diff --git a/ENCSR754LIN/cherimoya.fold_1.performance.tsv b/ENCSR754LIN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5ee1ebdef6f8f4d5bda1d2ffc2ae0485271cef70..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1158.77783203125 0.29626989364624023 0.45870572328567505 0.24061600863933563 0.8419673442840576 0.8292253613471985 0.16587598621845245 \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_2.evaluate.json b/ENCSR754LIN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2e4799c0fdf9d2a71ce4ca85488c56eb7a1cadd5..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133VSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_2.fit.json b/ENCSR754LIN/cherimoya.fold_2.fit.json deleted file mode 100644 index 1998f7fbd0823aa379e58f721f59dc0c45291b5b..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF133VSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_2.log b/ENCSR754LIN/cherimoya.fold_2.log deleted file mode 100644 index 5b0e4ab5fb3e1626a793af5051aac0aa884610fd..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2865 36.32172513008118 4.422053337097168 1048.91455078125 0.37464427947998047 1276.45654296875 0.2865138053894043 0.62585783 6.061823844909668 True -1 5730 31.795483112335205 1.2196745872497559 889.8592529296875 0.2933494448661804 1146.5555419921875 0.3936966061592102 0.73101085 0.8615577816963196 True -2 8595 31.850798845291138 0.5638046264648438 960.755859375 0.38666635751724243 1125.9232177734375 0.4102189540863037 0.753378 0.32163169980049133 True -3 11460 31.820223093032837 1.908278226852417 900.0371704101562 0.4546229839324951 1117.0618896484375 0.41608306765556335 0.7608008 0.305544376373291 True -4 14325 31.808106660842896 0.5620930194854736 1009.6665649414062 0.29216450452804565 1111.489501953125 0.42147961258888245 0.76343834 0.2946479618549347 True -5 17190 31.756405353546143 0.5595905780792236 1030.142578125 0.4954591393470764 1106.537841796875 0.42626672983169556 0.7681045 0.29102784395217896 True -6 20055 31.782636165618896 0.5592894554138184 901.94482421875 0.30060991644859314 1105.7554931640625 0.42566990852355957 0.77238923 0.2770240306854248 True -7 22920 31.741971492767334 0.5572426319122314 949.502685546875 0.28441599011421204 1102.0260009765625 0.4294179379940033 0.77511317 0.26278412342071533 True -8 25785 31.759740591049194 0.5483601093292236 807.2423706054688 0.2623176872730255 1099.63916015625 0.4328930079936981 0.7743374 0.26251354813575745 False -9 28650 31.32434368133545 0.5730805397033691 895.17333984375 0.2019137144088745 1097.9747314453125 0.4336034953594208 0.78103876 0.23550766706466675 True -10 31515 31.544430017471313 0.559032678604126 921.81689453125 0.21969741582870483 1094.0103759765625 0.4372766613960266 0.78397256 0.22668729722499847 True -11 34380 31.284695386886597 0.5628817081451416 975.4168701171875 0.29151278734207153 1092.1241455078125 0.43900784850120544 0.78557324 0.22147898375988007 True -12 37245 31.53439974784851 0.5533678531646729 864.3245849609375 0.1559928059577942 1090.2579345703125 0.4398152232170105 0.7959052 0.20272614061832428 True -13 40110 31.561933994293213 0.777646541595459 1001.9254760742188 0.2030525505542755 1085.943359375 0.444731205701828 0.8003052 0.19603604078292847 True -14 42975 31.3733012676239 0.5469186305999756 882.196533203125 0.1479545533657074 1084.552734375 0.44585880637168884 0.807374 0.1908915936946869 True -15 45840 31.357930660247803 0.5480172634124756 890.84912109375 0.16697868704795837 1085.3663330078125 0.44488003849983215 0.8123269 0.18381233513355255 True -16 48705 31.415826320648193 0.5456490516662598 872.9315185546875 0.14154961705207825 1084.9088134765625 0.4444887042045593 0.8167265 0.17879581451416016 True -17 51570 31.461366176605225 0.5459945201873779 870.42578125 0.13899022340774536 1083.2947998046875 0.44593778252601624 0.8187692 0.1765221208333969 True -18 54435 31.455487966537476 0.5470349788665771 886.298583984375 0.12943485379219055 1083.4449462890625 0.4458906352519989 0.8202496 0.1752513349056244 True -19 57300 31.52535104751587 0.5428252220153809 787.5152587890625 0.09370285272598267 1083.5211181640625 0.445487380027771 0.8190803 0.17592981457710266 False diff --git a/ENCSR754LIN/cherimoya.fold_2.performance.tsv b/ENCSR754LIN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a55e4686d56ef997114beb48c7bc55137de345db..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1083.4449462890625 0.3084193170070648 0.4458905756473541 0.22450581192970276 0.820249617099762 0.7953304648399353 0.1752513349056244 \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_3.evaluate.json b/ENCSR754LIN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bd1fa9cffabbb7f20ac6327d80f76c100eb5f064..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133VSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_3.fit.json b/ENCSR754LIN/cherimoya.fold_3.fit.json deleted file mode 100644 index b0661043c43bd5f146c062bb22f94987d3db8147..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF133VSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_3.log b/ENCSR754LIN/cherimoya.fold_3.log deleted file mode 100644 index 8080c2e6d992be58096085623ebf72adc7d03d2e..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2809 35.848772287368774 5.429481029510498 978.3859252929688 0.3276810050010681 1286.1759033203125 0.283429890871048 0.6361072 7.276082992553711 True -1 5618 31.20591163635254 0.5920743942260742 862.0786743164062 0.47698473930358887 1161.93359375 0.3910052478313446 0.7269918 0.8557894825935364 True -2 8427 31.178081274032593 1.978393793106079 811.9053955078125 0.43140339851379395 1145.1790771484375 0.404155433177948 0.7451708 0.2827393114566803 True -3 11236 31.195820331573486 1.789654016494751 1004.781982421875 0.29173707962036133 1138.4407958984375 0.40986737608909607 0.75749415 0.2764466404914856 True -4 14045 31.189476251602173 1.0711486339569092 855.7019653320312 0.2731989324092865 1133.5001220703125 0.4134766757488251 0.75610834 0.29914599657058716 False -5 16854 31.13952350616455 0.5539910793304443 847.9391479492188 0.26301324367523193 1129.2440185546875 0.41747674345970154 0.76570827 0.24665801227092743 True -6 19663 31.125468015670776 0.5684719085693359 871.0647583007812 0.33539414405822754 1126.4283447265625 0.4205264151096344 0.7679648 0.2471788376569748 True -7 22472 31.185588836669922 0.5438776016235352 913.0264282226562 0.2983093857765198 1122.386962890625 0.4246017634868622 0.77324075 0.2361534833908081 True -8 25281 30.855996131896973 0.5437061786651611 817.7915649414062 0.41292479634284973 1121.0184326171875 0.4252598285675049 0.7747403 0.22284851968288422 True -9 28090 30.51933526992798 0.5362000465393066 937.5028686523438 0.28647392988204956 1118.5718994140625 0.42826738953590393 0.7755462 0.21542911231517792 True -10 30899 30.573099374771118 1.6695144176483154 859.27197265625 0.16449564695358276 1115.196044921875 0.4309651553630829 0.7827995 0.20409420132637024 True -11 33708 30.603708267211914 0.5385093688964844 946.2929077148438 0.17647600173950195 1113.7342529296875 0.43205517530441284 0.78616333 0.1998330056667328 True -12 36517 30.67207932472229 0.5381035804748535 997.8975830078125 0.19962868094444275 1109.6085205078125 0.4365001916885376 0.7935957 0.1951671540737152 True -13 39326 30.52055835723877 0.5435535907745361 930.1065673828125 0.20106951892375946 1110.419677734375 0.43502119183540344 0.7972471 0.19185426831245422 True -14 42135 30.56462836265564 0.5344870090484619 980.3665771484375 0.20995983481407166 1108.4296875 0.4363812506198883 0.808839 0.1843508630990982 True -15 44944 30.59048557281494 0.5348210334777832 836.4629516601562 0.18982268869876862 1106.4947509765625 0.4383394122123718 0.818507 0.17787133157253265 True -16 47753 30.593665599822998 0.5460870265960693 812.217529296875 0.1701720952987671 1105.604736328125 0.4388428032398224 0.82454824 0.17175264656543732 True -17 50562 30.545501232147217 0.5343422889709473 887.5482177734375 0.1321142315864563 1104.3416748046875 0.44042354822158813 0.8301075 0.16763414442539215 True -18 53371 30.57439160346985 0.5375595092773438 899.91552734375 0.12480005621910095 1105.592041015625 0.43870458006858826 0.83066124 0.1675443947315216 True -19 56180 30.552643537521362 0.5339043140411377 903.63720703125 0.2184131145477295 1105.4964599609375 0.43873411417007446 0.8312238 0.16599009931087494 True diff --git a/ENCSR754LIN/cherimoya.fold_3.performance.tsv b/ENCSR754LIN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b843e8ff198a5f2e8f1d0cf0f51c1b7bb4082525..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1105.4964599609375 0.30878397822380066 0.43873411417007446 0.2249656319618225 0.8312237858772278 0.8080945611000061 0.16599009931087494 \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_4.evaluate.json b/ENCSR754LIN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 213aad7dc8b1b534f3b3b5ff0beb167729bf691e..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF133VSI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_4.fit.json b/ENCSR754LIN/cherimoya.fold_4.fit.json deleted file mode 100644 index 348305765499500c9853b320d6be69566d1da607..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF133VSI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR754LIN/cherimoya.fold_4.log b/ENCSR754LIN/cherimoya.fold_4.log deleted file mode 100644 index 466b8368794fdc0cb79cc19c87f094b4b49a1a65..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2828 35.75891041755676 4.1663267612457275 899.236328125 0.42446887493133545 1212.6163330078125 0.27970290184020996 0.62251973 5.644298076629639 True -1 5656 31.34260654449463 0.5570168495178223 1025.01708984375 0.3036649823188782 1100.9149169921875 0.38311654329299927 0.7192531 0.6307081580162048 True -2 8484 31.38489580154419 0.509882926940918 1115.3262939453125 0.35669639706611633 1077.7080078125 0.4021873474121094 0.72849405 0.2767946124076843 True -3 11312 31.33502984046936 0.515451192855835 950.6257934570312 0.39366233348846436 1070.1275634765625 0.40741100907325745 0.7372991 0.2521004378795624 True -4 14140 31.36176347732544 0.5221278667449951 959.4254150390625 0.25647854804992676 1064.48876953125 0.4136006236076355 0.7453916 0.26279184222221375 True -5 16968 31.43516182899475 0.5221309661865234 852.7315673828125 0.2541074752807617 1060.722900390625 0.4172365069389343 0.7458295 0.24067598581314087 True -6 19796 31.3951358795166 0.5111782550811768 789.599365234375 0.32108163833618164 1058.6890869140625 0.4188288748264313 0.7500898 0.22738990187644958 True -7 22624 31.407778024673462 0.5196502208709717 958.5523071289062 0.20179790258407593 1056.2811279296875 0.42202621698379517 0.749279 0.23135562241077423 False -8 25452 31.304971933364868 0.5102226734161377 757.211669921875 1.9953186511993408 1053.885986328125 0.4243473708629608 0.7566112 0.2128414809703827 True -9 28280 30.82302498817444 0.5019702911376953 869.8980102539062 0.3017277717590332 1051.1898193359375 0.42747387290000916 0.75716585 0.2107892483472824 True -10 31108 30.79765820503235 0.49456024169921875 918.225830078125 0.2700362801551819 1050.088623046875 0.42819103598594666 0.76288736 0.20406289398670197 True -11 33936 30.83797574043274 0.5006048679351807 978.3546142578125 0.17162758111953735 1046.578125 0.43130114674568176 0.7694812 0.19931812584400177 True -12 36764 30.96229839324951 0.5168473720550537 879.6585693359375 0.20297417044639587 1045.7130126953125 0.43206092715263367 0.773507 0.19137969613075256 True -13 39592 31.40749502182007 0.5179433822631836 832.1373291015625 0.1934168040752411 1042.524169921875 0.4356958568096161 0.7795094 0.18964888155460358 True -14 42420 30.956358432769775 0.5099918842315674 810.9844970703125 0.16169150173664093 1042.6959228515625 0.43440595269203186 0.7881083 0.17999236285686493 True -15 45248 30.84684920310974 0.5179007053375244 773.6585693359375 0.16767817735671997 1041.3531494140625 0.43638089299201965 0.79610837 0.17501935362815857 True -16 48076 30.87999939918518 0.5185768604278564 892.28857421875 0.21127259731292725 1041.919677734375 0.4341653287410736 0.7990819 0.17187057435512543 True -17 50904 30.87935972213745 0.5169713497161865 827.9570922851562 0.1494966596364975 1039.1763916015625 0.43852514028549194 0.8022972 0.17082849144935608 True -18 53732 30.832112312316895 0.5184710025787354 1011.1968994140625 0.23348218202590942 1039.2955322265625 0.4385002851486206 0.8036827 0.17086167633533478 True -19 56560 30.824599981307983 0.5163314342498779 816.7391357421875 0.14358927309513092 1040.557373046875 0.436553418636322 0.8024746 0.1718275547027588 False diff --git a/ENCSR754LIN/cherimoya.fold_4.performance.tsv b/ENCSR754LIN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0bb99c51410f05f88abfe6d8dd1502a64181e370..0000000000000000000000000000000000000000 --- a/ENCSR754LIN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1039.2955322265625 0.3167894780635834 0.4385002553462982 0.2139945924282074 0.8036826848983765 0.7766103148460388 0.17086167633533478 \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_0.evaluate.json b/ENCSR757EPJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0eef86684a1d38c9fa6457a7b2908cfd69c572c6..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF601PTR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_0.fit.json b/ENCSR757EPJ/cherimoya.fold_0.fit.json deleted file mode 100644 index a21769c1213ee41f94451ef9b27d6b0dc6d60fb9..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF601PTR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_0.log b/ENCSR757EPJ/cherimoya.fold_0.log deleted file mode 100644 index 4db08ff39f88e2f09ba5f68a436782ff41e0eab1..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.11986017227173 4.009517669677734 288.2780456542969 0.7986695170402527 336.9573059082031 0.1890774518251419 0.6389269 2.7327539920806885 True -1 5508 30.650269508361816 0.905808687210083 331.7999267578125 0.9001744389533997 309.80145263671875 0.27643686532974243 0.6950237 1.8904695510864258 True -2 8262 30.656696557998657 0.6088161468505859 259.0655517578125 1.1747384071350098 303.04541015625 0.2971822917461395 0.69094497 1.1658915281295776 False -3 11016 30.643890142440796 0.5779764652252197 249.88357543945312 0.7422706484794617 299.0556640625 0.30902397632598877 0.70008755 0.871094822883606 True -4 13770 30.659637928009033 0.5967049598693848 232.07571411132812 0.8916090726852417 296.72100830078125 0.31540295481681824 0.7035639 0.8997432589530945 True -5 16524 30.699586153030396 0.5952675342559814 244.65826416015625 0.9060244560241699 294.9369201660156 0.3207279443740845 0.7100123 0.8128613829612732 True -6 19278 30.58867383003235 0.577061653137207 213.25762939453125 0.7397894859313965 293.9252624511719 0.3244992196559906 0.71437484 0.7207952737808228 True -7 22032 30.056975603103638 0.5762543678283691 218.8238983154297 0.8511620759963989 293.1026306152344 0.326464980840683 0.7104687 0.8162163496017456 False -8 24786 29.97622585296631 0.5997560024261475 236.08572387695312 0.46407073736190796 292.0919189453125 0.3296165466308594 0.7112712 0.7081896662712097 False -9 27540 29.997859716415405 0.6139767169952393 262.1016540527344 0.8728078603744507 291.8102722167969 0.3306296169757843 0.7173346 0.6972550749778748 True -10 30294 30.012866735458374 0.6205649375915527 263.419189453125 0.7690626382827759 290.4224548339844 0.33525145053863525 0.7183274 0.7141368389129639 True -11 33048 30.018848419189453 0.5935933589935303 226.08639526367188 0.6816909313201904 289.58526611328125 0.3386229872703552 0.72445613 0.6332017183303833 True -12 35802 29.977731466293335 1.1049604415893555 223.27716064453125 0.6036268472671509 289.2086486816406 0.3389650583267212 0.7287141 0.6111448407173157 True -13 38556 30.01351237297058 0.5808513164520264 228.45823669433594 0.6759361028671265 287.7875061035156 0.3439265191555023 0.7359744 0.5449061393737793 True -14 41310 30.034847259521484 0.5866029262542725 205.3560333251953 0.4400286376476288 287.2953796386719 0.3452012240886688 0.7419836 0.5075026750564575 True -15 44064 30.598100662231445 0.9047844409942627 216.57748413085938 0.8634347319602966 287.1238708496094 0.3446887135505676 0.75232446 0.4637216329574585 True -16 46818 29.97144079208374 0.5930516719818115 257.6124267578125 0.4844970107078552 286.3846435546875 0.34713566303253174 0.7548998 0.4429972469806671 True -17 49572 30.02620267868042 0.5921621322631836 226.12271118164062 0.5270429849624634 286.34130859375 0.34803488850593567 0.7589148 0.4263206720352173 True -18 52326 30.008199453353882 0.5997471809387207 193.56019592285156 0.3823759853839874 286.2844543457031 0.34794408082962036 0.76062703 0.41937029361724854 True -19 55080 30.04130482673645 1.0307111740112305 218.78237915039062 0.669169008731842 286.0870666503906 0.3492022156715393 0.7583486 0.4252752959728241 False diff --git a/ENCSR757EPJ/cherimoya.fold_0.performance.tsv b/ENCSR757EPJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f3b97c0dd35d92097a4b457af768f88bffd08f79..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -286.2844543457031 0.4624512791633606 0.34794408082962036 0.09102167189121246 0.760627031326294 0.709391713142395 0.41937029361724854 \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_1.evaluate.json b/ENCSR757EPJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 61df07c53cad55c3a0bf366c78cd9bf5be1b7ad2..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF601PTR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_1.fit.json b/ENCSR757EPJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 7958e669805aac3d67f4b28bf8f98e9c56571b9d..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF601PTR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_1.log b/ENCSR757EPJ/cherimoya.fold_1.log deleted file mode 100644 index 0bdb13d997dd3433893b5f694a123720c5807fe8..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2701 34.64374923706055 4.0914928913116455 274.80322265625 1.194000005722046 384.0596618652344 0.19501972198486328 0.6511304 3.9296226501464844 True -1 5402 30.049338817596436 0.7738034725189209 235.00047302246094 0.7580602169036865 346.5650634765625 0.2935909628868103 0.6940841 1.8149610757827759 True -2 8103 30.02986979484558 0.732851505279541 273.3817443847656 1.1646451950073242 338.8968811035156 0.3141348659992218 0.7063062 1.2654283046722412 True -3 10804 30.086207628250122 0.7333128452301025 281.6283874511719 0.8455890417098999 334.80908203125 0.32408541440963745 0.7098575 1.0974441766738892 True -4 13505 30.094029426574707 0.7184011936187744 246.84078979492188 0.9257742762565613 332.3248291015625 0.3310675621032715 0.71838206 0.8478527069091797 True -5 16206 29.998430967330933 23.604245901107788 276.2508239746094 0.7060363292694092 331.0314636230469 0.33524906635284424 0.7229183 0.9622690081596375 True -6 18907 30.361817598342896 0.7254033088684082 256.44891357421875 0.9132251143455505 329.36767578125 0.3389265835285187 0.7260424 0.8820652961730957 True -7 21608 29.490121364593506 0.7262108325958252 235.44287109375 0.6998553276062012 328.8194885253906 0.34066808223724365 0.7298039 0.8775772452354431 True -8 24309 29.427878618240356 0.7195789813995361 223.29522705078125 0.8049484491348267 327.53985595703125 0.344303160905838 0.7339892 0.8295327425003052 True -9 27010 29.396411418914795 0.7234995365142822 263.8778381347656 0.7823083996772766 326.5425720214844 0.3465275466442108 0.73615396 0.820122480392456 True -10 29711 29.435076475143433 0.7217724323272705 231.23468017578125 0.8380682468414307 325.53314208984375 0.34953492879867554 0.7363857 0.7040400505065918 True -11 32412 29.471827745437622 0.7315554618835449 241.913330078125 0.7098813056945801 324.3938903808594 0.35289761424064636 0.74004996 0.697891354560852 True -12 35113 29.454870462417603 0.7224287986755371 257.5317077636719 0.6242718696594238 323.2955627441406 0.3559052348136902 0.7470222 0.6942998170852661 True -13 37814 29.423998594284058 1.6060876846313477 212.43751525878906 0.71514493227005 322.24444580078125 0.3580515384674072 0.75195616 0.6316133737564087 True -14 40515 29.418638706207275 0.7443153858184814 224.8038330078125 0.5729349255561829 321.84686279296875 0.357639342546463 0.7609443 0.585457980632782 True -15 43216 29.439639806747437 0.7368459701538086 200.5389862060547 0.4724869728088379 320.7336730957031 0.36227303743362427 0.7682022 0.5381906628608704 True -16 45917 29.4325430393219 0.7415220737457275 199.35879516601562 0.597735583782196 320.310302734375 0.36321696639060974 0.7743485 0.504737138748169 True -17 48618 29.433209657669067 0.7199225425720215 195.975341796875 0.29418742656707764 320.4436950683594 0.3618592321872711 0.7765609 0.47942396998405457 True -18 51319 29.482365369796753 0.9457011222839355 264.61016845703125 0.402085542678833 320.4913635253906 0.36233723163604736 0.7777576 0.4638882577419281 True -19 54020 29.45064067840576 0.7409868240356445 261.86004638671875 0.49280455708503723 320.68475341796875 0.3610289990901947 0.77787346 0.4627242982387543 True diff --git a/ENCSR757EPJ/cherimoya.fold_1.performance.tsv b/ENCSR757EPJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4286fecbfd6382baf909c3c4213e85007d998544..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -320.68475341796875 0.44828155636787415 0.3610289990901947 0.10030613094568253 0.7778734564781189 0.753952145576477 0.4627242982387543 \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_2.evaluate.json b/ENCSR757EPJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index deeaf9566b39b7027040218349a80fb1c6a8f553..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF601PTR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_2.fit.json b/ENCSR757EPJ/cherimoya.fold_2.fit.json deleted file mode 100644 index f7b8bb974af6276b079b5d43911e957e2f989535..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF601PTR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_2.log b/ENCSR757EPJ/cherimoya.fold_2.log deleted file mode 100644 index f09a964a5c9c47c5aca87d8875e041c81589c6cb..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2865 36.47106575965881 4.528824806213379 237.4559326171875 0.7465528845787048 351.9349670410156 0.19539836049079895 0.6368881 3.6992123126983643 True -1 5730 31.97539234161377 0.8762309551239014 230.81314086914062 0.9416849613189697 320.1526184082031 0.28641265630722046 0.6948261 1.3705627918243408 True -2 8595 31.92238211631775 0.5830390453338623 222.6336212158203 0.8118583559989929 314.764404296875 0.30121561884880066 0.69982004 0.9438463449478149 True -3 11460 31.84659194946289 1.013385534286499 252.12664794921875 1.204837441444397 310.88580322265625 0.3123047649860382 0.70438963 0.9028798341751099 True -4 14325 31.925697803497314 0.5825810432434082 252.59896850585938 0.6343048214912415 308.6868591308594 0.3176671862602234 0.70942783 0.9413488507270813 True -5 17190 31.9807448387146 0.5591249465942383 252.80831909179688 0.9716305732727051 307.284423828125 0.32160717248916626 0.7157399 0.8767477869987488 True -6 20055 31.944677591323853 0.8897294998168945 223.37228393554688 0.8758863210678101 305.84033203125 0.32628610730171204 0.7167038 0.813429594039917 True -7 22920 31.913702964782715 0.5700490474700928 254.1387481689453 1.0242632627487183 305.1111755371094 0.3288170099258423 0.7173173 0.7961392998695374 True -8 25785 31.943973302841187 0.5593123435974121 291.5863342285156 0.49618715047836304 303.2359619140625 0.33473432064056396 0.7177398 0.7570223808288574 True -9 28650 31.875818252563477 0.5515537261962891 223.51947021484375 0.682307243347168 302.525634765625 0.33766523003578186 0.71980035 0.767261266708374 True -10 31515 31.916885137557983 0.5751047134399414 276.54052734375 0.7711219787597656 301.46966552734375 0.33966267108917236 0.71888787 0.752428412437439 False -11 34380 31.834998846054077 0.5526776313781738 238.220458984375 0.6746068000793457 300.3079528808594 0.3441997766494751 0.7193551 0.7195863723754883 False -12 37245 31.907081127166748 0.6924171447753906 225.21755981445312 0.5835817456245422 299.91741943359375 0.34530746936798096 0.7247619 0.7083176374435425 True -13 40110 31.910851001739502 0.5612759590148926 198.10952758789062 0.6468721628189087 299.1852722167969 0.3460949659347534 0.73276776 0.6542015671730042 True -14 42975 31.899291515350342 0.5735702514648438 235.92625427246094 0.563262939453125 298.17333984375 0.3508521616458893 0.73810875 0.5972567200660706 True -15 45840 31.897960662841797 0.5689992904663086 210.79037475585938 0.42536091804504395 297.28076171875 0.3529767096042633 0.7459505 0.5346265435218811 True -16 48705 31.43084454536438 0.5516550540924072 208.34860229492188 0.40813755989074707 297.3490295410156 0.35286879539489746 0.7534077 0.49729397892951965 True -17 51570 31.176355838775635 0.5484280586242676 274.5091552734375 0.5158233642578125 296.7835693359375 0.3539753556251526 0.7557451 0.4711773693561554 True -18 54435 31.177604913711548 0.5495755672454834 210.16482543945312 0.5964301228523254 296.6956481933594 0.3533754348754883 0.75922114 0.45935559272766113 True -19 57300 31.196553707122803 0.5366520881652832 218.36251831054688 0.5406108498573303 296.95562744140625 0.3527238965034485 0.7578011 0.4551002085208893 False diff --git a/ENCSR757EPJ/cherimoya.fold_2.performance.tsv b/ENCSR757EPJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 89777f8f368e4b9d790d21c48fecaaa6e86b2974..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -296.6956481933594 0.45703062415122986 0.3533754348754883 0.0917181670665741 0.7592211365699768 0.7232744693756104 0.45935559272766113 \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_3.evaluate.json b/ENCSR757EPJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b5a72b300fa272c2d0cad72aea179a9ba854db8c..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF601PTR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_3.fit.json b/ENCSR757EPJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 3635134fd5c0874813cc04f9909e1c9a12700087..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF601PTR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_3.log b/ENCSR757EPJ/cherimoya.fold_3.log deleted file mode 100644 index e06e695ece9aa1242e6f60bf2dd2821569c7c191..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.225801944732666 4.379491329193115 270.06048583984375 1.3694783449172974 353.4320068359375 0.1883355975151062 0.6543956 4.736643314361572 True -1 5508 31.071295976638794 21.496522188186646 205.69932556152344 0.835819661617279 324.1672058105469 0.2786904275417328 0.7034337 1.4034799337387085 True -2 8262 30.808918714523315 0.5944254398345947 215.66819763183594 0.9298791289329529 316.44195556640625 0.302729070186615 0.71666557 0.8891429901123047 True -3 11016 30.764989852905273 0.5801143646240234 280.1535339355469 0.7554948925971985 313.19598388671875 0.3093402683734894 0.7212316 0.869086742401123 True -4 13770 30.74784564971924 0.5829060077667236 184.8870086669922 0.6841787099838257 311.2918395996094 0.31650233268737793 0.71759754 0.8141376376152039 False -5 16524 30.794261693954468 23.0499427318573 224.60572814941406 0.717192530632019 309.8951721191406 0.3205832839012146 0.7160499 0.8348903059959412 False -6 19278 30.794095039367676 0.5653493404388428 246.29513549804688 0.7512618899345398 308.8402099609375 0.323690801858902 0.7148327 0.8353129029273987 False -7 22032 30.734549045562744 1.261441707611084 216.59109497070312 0.8464241623878479 307.7554626464844 0.32762911915779114 0.7222629 0.7512434124946594 True -8 24786 30.711609601974487 13.840054035186768 238.52906799316406 0.893317461013794 307.2422790527344 0.3291071951389313 0.7229516 0.7082948088645935 True -9 27540 30.971250534057617 0.5717654228210449 222.97378540039062 0.555235743522644 305.8380432128906 0.3325791358947754 0.72652024 0.6693875193595886 True -10 30294 30.784309148788452 0.55599045753479 230.0782470703125 0.6101837158203125 305.61334228515625 0.33396151661872864 0.72720397 0.6727275252342224 True -11 33048 30.726617574691772 0.5656309127807617 274.923828125 0.6661591529846191 304.87640380859375 0.33591750264167786 0.73701775 0.6081348061561584 True -12 35802 30.639208793640137 0.5766396522521973 246.62847900390625 0.42058807611465454 303.7830505371094 0.3388950526714325 0.74140716 0.5840793251991272 True -13 38556 30.634530067443848 0.5847201347351074 229.25985717773438 0.5598097443580627 303.0841979980469 0.3423740565776825 0.74860114 0.5550037622451782 True -14 41310 30.622694492340088 0.5560250282287598 231.1861572265625 0.4897753894329071 302.104736328125 0.3435180187225342 0.75891423 0.5235893130302429 True -15 44064 30.665490865707397 0.5616588592529297 269.6190185546875 0.5819282531738281 301.71978759765625 0.3464549481868744 0.7640341 0.4939044415950775 True -16 46818 30.64863109588623 0.5677061080932617 211.57891845703125 0.5732113122940063 300.7389831542969 0.3490026891231537 0.7730301 0.455268919467926 True -17 49572 30.64366912841797 0.5637552738189697 209.18389892578125 0.4982137084007263 300.9800109863281 0.34844374656677246 0.7755822 0.4393213391304016 True -18 52326 30.58838415145874 0.5577845573425293 216.16139221191406 0.5070194602012634 301.130859375 0.3479573726654053 0.7766316 0.4303635358810425 True -19 55080 30.67675757408142 0.5535187721252441 220.706787109375 0.5969172716140747 300.6031494140625 0.349725604057312 0.77593434 0.4302597641944885 False diff --git a/ENCSR757EPJ/cherimoya.fold_3.performance.tsv b/ENCSR757EPJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 66d5ac274665418f13feeac606292095a00843b9..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -301.130859375 0.4592626094818115 0.3479573726654053 0.09444192051887512 0.7766315937042236 0.727233350276947 0.4303635358810425 \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_4.evaluate.json b/ENCSR757EPJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index cc12c5f5cbff6e05981fbb362e3d8a0284be4aa0..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF601PTR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_4.fit.json b/ENCSR757EPJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 2efd2481769324a32ece628f28667166aefc43e0..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF601PTR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757EPJ/cherimoya.fold_4.log b/ENCSR757EPJ/cherimoya.fold_4.log deleted file mode 100644 index d5ebdd885b8ddeeeea00f823a814859bc837fe42..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2816 37.195786476135254 4.187489032745361 231.3036651611328 1.112820029258728 326.0615234375 0.1863158941268921 0.63229746 3.0804855823516846 True -1 5632 31.325281381607056 0.6829330921173096 192.72067260742188 1.1560156345367432 300.07623291015625 0.27176401019096375 0.68483967 1.3234789371490479 True -2 8448 31.136242389678955 0.6530513763427734 255.9748992919922 0.8986400365829468 295.626708984375 0.2843765318393707 0.6946538 0.7826163172721863 True -3 11264 30.69402241706848 0.644108772277832 255.36810302734375 0.9816468358039856 291.79229736328125 0.29691988229751587 0.700656 0.7403850555419922 True -4 14080 30.668288946151733 0.6516323089599609 240.06283569335938 0.5741252899169922 289.8045959472656 0.3035494387149811 0.7010526 0.7210195064544678 True -5 16896 31.12406086921692 0.6231594085693359 279.17236328125 0.6115436553955078 288.56494140625 0.3082067668437958 0.70218956 0.7725839018821716 True -6 19712 30.62991166114807 0.6222720146179199 222.23789978027344 0.5871791243553162 286.9161682128906 0.3135629892349243 0.70690745 0.7936369180679321 True -7 22528 30.685202598571777 0.6197381019592285 244.15963745117188 0.8871603012084961 286.5852355957031 0.31437328457832336 0.7049094 0.8105680346488953 False -8 25344 30.602304458618164 0.6200811862945557 212.64169311523438 0.6340374946594238 285.3143310546875 0.3198746144771576 0.7091419 0.7988203167915344 True -9 28160 30.61290454864502 0.6146924495697021 206.09320068359375 1.097980260848999 284.9073486328125 0.3204255700111389 0.70983094 0.7759655117988586 True -10 30976 30.712818145751953 2.325291872024536 236.12149047851562 0.7234119176864624 284.27008056640625 0.3226022720336914 0.7113136 0.7137383222579956 True -11 33792 30.655871868133545 1.3336389064788818 257.84912109375 0.7110888957977295 283.0566711425781 0.32715195417404175 0.71440864 0.7232533097267151 True -12 36608 30.665642499923706 1.0640709400177002 221.10247802734375 0.4719651937484741 282.2908935546875 0.33023107051849365 0.7212197 0.6456573009490967 True -13 39424 30.711644411087036 1.2346234321594238 199.1600799560547 0.4199845790863037 281.662353515625 0.3309002220630646 0.72814405 0.6187629103660583 True -14 42240 30.688088417053223 1.3693947792053223 240.92970275878906 0.4471496343612671 280.8719177246094 0.3342369794845581 0.7354439 0.5487782955169678 True -15 45056 30.72313165664673 1.4727756977081299 243.23046875 0.5283364057540894 280.2860412597656 0.33558154106140137 0.74559474 0.4839206337928772 True -16 47872 30.68254017829895 1.301774024963379 238.03744506835938 0.32762032747268677 280.1307678222656 0.3360503315925598 0.75202 0.45256975293159485 True -17 50688 30.670340299606323 0.6343498229980469 204.46270751953125 0.3598785400390625 279.9234924316406 0.3367478847503662 0.7575364 0.4258163869380951 True -18 53504 30.626840829849243 0.6315631866455078 210.9256591796875 0.5060082674026489 279.81640625 0.3373817503452301 0.75698024 0.4143032729625702 False -19 56320 30.724233865737915 0.6304855346679688 233.25836181640625 0.4020160436630249 279.91473388671875 0.337096631526947 0.7571947 0.4132721722126007 False diff --git a/ENCSR757EPJ/cherimoya.fold_4.performance.tsv b/ENCSR757EPJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e88f5e82876dc583754db2030f0aee28efcd1cd8..0000000000000000000000000000000000000000 --- a/ENCSR757EPJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -279.9234924316406 0.4687609076499939 0.3367478847503662 0.08869175612926483 0.7575364112854004 0.7100969552993774 0.4258163869380951 \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_0.evaluate.json b/ENCSR757NJT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8bbc9e320e36860e41eaa723fb5ae6c7cd3c5e4a..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF033KMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_0.fit.json b/ENCSR757NJT/cherimoya.fold_0.fit.json deleted file mode 100644 index 52a16da08659e226c1febacf72cf1958e388f172..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF033KMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_0.log b/ENCSR757NJT/cherimoya.fold_0.log deleted file mode 100644 index 078eb9483ca5a22698116f5555cd511b359141bb..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 35.393686056137085 3.9110920429229736 1157.3880615234375 0.45286399126052856 1258.1473388671875 0.31486934423446655 0.7728579 7.829717636108398 True -1 5490 30.597050666809082 0.9961724281311035 980.284423828125 0.2595198154449463 1118.5179443359375 0.3762773871421814 0.82009375 1.7116212844848633 True -2 8235 30.602785348892212 2.263611316680908 1257.761962890625 0.3976438641548157 1099.314208984375 0.38249099254608154 0.829073 0.840268611907959 True -3 10980 30.65061664581299 2.734950065612793 816.650390625 0.3079477548599243 1083.2685546875 0.38803231716156006 0.8412879 0.7398051619529724 True -4 13725 30.609325408935547 0.6482653617858887 825.376220703125 0.28092390298843384 1074.203369140625 0.3903104364871979 0.8449324 0.7139938473701477 True -5 16470 30.567715644836426 0.6353180408477783 921.702880859375 0.2609894275665283 1067.4310302734375 0.3925792872905731 0.8551555 0.6498937606811523 True -6 19215 30.56325125694275 2.8078858852386475 1060.6112060546875 0.3598055839538574 1061.650146484375 0.3964509665966034 0.85897815 0.5107220411300659 True -7 21960 30.14289903640747 0.620213508605957 870.4615478515625 0.2554117739200592 1055.846435546875 0.39978861808776855 0.86496764 0.48223069310188293 True -8 24705 30.035986185073853 0.6158468723297119 1160.141845703125 0.2647930681705475 1052.302001953125 0.4015487730503082 0.86845225 0.42549648880958557 True -9 27450 30.1710786819458 0.609980583190918 930.6336669921875 0.1609376221895218 1043.58056640625 0.40622714161872864 0.8743219 0.40944916009902954 True -10 30195 30.04069209098816 0.6028223037719727 1012.9859619140625 0.29494836926460266 1042.825439453125 0.40602216124534607 0.87882 0.38351351022720337 True -11 32940 30.10374689102173 0.5947589874267578 958.476806640625 0.3271743059158325 1036.7635498046875 0.4091314673423767 0.8812538 0.3416767418384552 True -12 35685 30.106566667556763 0.6396059989929199 883.1552124023438 0.320121169090271 1032.228271484375 0.4109736979007721 0.8883786 0.30910927057266235 True -13 38430 30.113627195358276 2.437340021133423 878.5419311523438 0.2437639832496643 1028.4581298828125 0.4121357202529907 0.8927472 0.28035804629325867 True -14 41175 30.049819231033325 0.6254305839538574 1066.70556640625 0.25451937317848206 1022.6375732421875 0.4159497022628784 0.89611 0.25453415513038635 True -15 43920 30.09384560585022 0.6279153823852539 1010.820556640625 0.1544668972492218 1021.2630615234375 0.41497665643692017 0.9011363 0.22659818828105927 True -16 46665 29.972216367721558 0.6180763244628906 996.5750732421875 0.21423928439617157 1021.206298828125 0.4156133830547333 0.9033908 0.21128074824810028 True -17 49410 29.97393822669983 0.6182427406311035 878.3787841796875 0.20786094665527344 1021.1801147460938 0.4149739146232605 0.90579784 0.2011766880750656 True -18 52155 29.930743932724 1.2851841449737549 826.446533203125 0.15704914927482605 1019.9866943359375 0.41660353541374207 0.9039466 0.1992928683757782 False -19 54900 30.100365161895752 0.6109776496887207 756.9112548828125 0.258284330368042 1022.9100952148438 0.41395413875579834 0.90413505 0.19899263978004456 False diff --git a/ENCSR757NJT/cherimoya.fold_0.performance.tsv b/ENCSR757NJT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 94f3f9f2d78ca1cd1efa6c16655824b5ec93f946..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1021.1801147460938 0.34680965542793274 0.4149739444255829 0.19937759637832642 0.9057978391647339 0.8746964931488037 0.2011766880750656 \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_1.evaluate.json b/ENCSR757NJT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5f97129f90c48381c3fb83825eb802bfb556fa98..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF033KMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_1.fit.json b/ENCSR757NJT/cherimoya.fold_1.fit.json deleted file mode 100644 index d8abe723425cd4bad034b0876cc12ad8a6b4b914..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF033KMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_1.log b/ENCSR757NJT/cherimoya.fold_1.log deleted file mode 100644 index bcfeee2a103fa2ee616d02d9986f06025ad1c53a..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2689 34.64880967140198 7.193007707595825 1041.581787109375 0.4950353801250458 1550.2069091796875 0.32079723477363586 0.76316446 7.879518032073975 True -1 5378 29.627756357192993 0.7929599285125732 1109.4989013671875 0.37897029519081116 1372.0125732421875 0.39100751280784607 0.81744134 2.0213210582733154 True -2 8067 30.0006103515625 0.7500579357147217 951.2709350585938 0.33665671944618225 1332.8739013671875 0.40622708201408386 0.8276729 1.0897026062011719 True -3 10756 30.03414559364319 0.7500519752502441 981.1488037109375 0.3488750755786896 1315.4197998046875 0.40960684418678284 0.83787155 0.9225953817367554 True -4 13445 29.9472815990448 0.7496640682220459 1102.730224609375 0.338072806596756 1293.6475830078125 0.41882383823394775 0.84390074 0.7888361811637878 True -5 16134 29.39687156677246 3.763352632522583 933.6282958984375 0.30290037393569946 1285.2320556640625 0.42235469818115234 0.8478336 0.7616659998893738 True -6 18823 29.331454515457153 0.7305471897125244 947.4837036132812 0.30502110719680786 1276.8819580078125 0.4246126413345337 0.85313785 0.6991147994995117 True -7 21512 29.33326268196106 0.7362077236175537 1016.2901000976562 0.2477281540632248 1268.1690673828125 0.42910170555114746 0.8575612 0.654148519039154 True -8 24201 29.330331802368164 0.7295637130737305 808.9674072265625 0.3201621174812317 1261.1405029296875 0.43216222524642944 0.8641435 0.5933963656425476 True -9 26890 29.321913242340088 0.7460815906524658 874.4776611328125 0.30810046195983887 1257.21826171875 0.43339914083480835 0.86804813 0.5800763964653015 True -10 29579 29.36627697944641 0.7870888710021973 942.5523681640625 0.320510596036911 1244.7835693359375 0.43822115659713745 0.87662655 0.4931586682796478 True -11 32268 29.348233222961426 0.7419471740722656 835.888916015625 0.24203786253929138 1238.2166748046875 0.4405646324157715 0.8800389 0.44816362857818604 True -12 34957 29.41394066810608 1.5269761085510254 849.6641845703125 0.2903250455856323 1232.47216796875 0.4421544373035431 0.8859696 0.3865453004837036 True -13 37646 29.35988759994507 0.7471165657043457 958.9750366210938 0.5473912954330444 1224.688720703125 0.44557979702949524 0.8939546 0.3339780569076538 True -14 40335 29.391754388809204 0.7442002296447754 924.2713623046875 0.17087224125862122 1219.12646484375 0.44742685556411743 0.89975244 0.3015054762363434 True -15 43024 29.383487701416016 0.7415006160736084 930.0821533203125 0.26700541377067566 1217.0087890625 0.44845134019851685 0.90176415 0.2730247974395752 True -16 45713 29.366283178329468 0.9596009254455566 898.5385131835938 0.17238543927669525 1212.4146728515625 0.44910290837287903 0.907649 0.248724564909935 True -17 48402 29.433936595916748 0.7531700134277344 888.4680786132812 0.2163960039615631 1215.1170654296875 0.4478236436843872 0.9093338 0.23551735281944275 True -18 51091 29.368451356887817 3.26243257522583 901.891357421875 0.23031356930732727 1216.41259765625 0.44778868556022644 0.9099658 0.22938567399978638 True -19 53780 29.41779327392578 0.7516040802001953 739.4888305664062 0.21380481123924255 1212.675048828125 0.4497949779033661 0.9095957 0.22832201421260834 False diff --git a/ENCSR757NJT/cherimoya.fold_1.performance.tsv b/ENCSR757NJT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ae4639f709f4a70e9bd9cb65870355c6d61a24ec..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1216.41259765625 0.3200799524784088 0.44778868556022644 0.2347525954246521 0.9099658131599426 0.8939719200134277 0.22938567399978638 \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_2.evaluate.json b/ENCSR757NJT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9153f0d352ca57e0e45c9437360772346e38abed..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF033KMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_2.fit.json b/ENCSR757NJT/cherimoya.fold_2.fit.json deleted file mode 100644 index c4f1cfe175cbac98ffa0526fa1c8ea8264b3ac73..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF033KMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_2.log b/ENCSR757NJT/cherimoya.fold_2.log deleted file mode 100644 index e32f52a40f87bee1d55ba3f4fb5e5a19039f2492..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2884 36.31894040107727 3.8614277839660645 867.596923828125 0.38468077778816223 1367.127685546875 0.31663742661476135 0.76072335 6.767962455749512 True -1 5768 32.12862730026245 0.6177246570587158 911.834228515625 0.4002789855003357 1207.1251220703125 0.3771912753582001 0.8274784 1.7646452188491821 True -2 8652 32.20072150230408 0.645427942276001 1024.7655029296875 0.41628414392471313 1183.7008056640625 0.3850559890270233 0.83988386 0.8702165484428406 True -3 11536 32.1572163105011 0.6341590881347656 945.9893188476562 0.37722674012184143 1167.3543701171875 0.3926650881767273 0.84658855 0.6129624843597412 True -4 14420 32.16775941848755 0.6922211647033691 974.54541015625 0.3996095657348633 1161.041015625 0.39497140049934387 0.85009867 0.6116254925727844 True -5 17304 32.11985802650452 0.5967814922332764 997.5823364257812 0.3379494547843933 1157.6912841796875 0.39673954248428345 0.8487827 0.6107014417648315 False -6 20188 32.105220317840576 0.6358909606933594 1087.828125 0.38001734018325806 1148.271240234375 0.4023553729057312 0.8511767 0.5602956414222717 True -7 23072 32.12928509712219 0.6152658462524414 860.3447265625 0.2356109917163849 1146.5958251953125 0.40090328454971313 0.8570561 0.5026831030845642 True -8 25956 32.213831424713135 0.5798614025115967 736.483642578125 0.2283046990633011 1137.955810546875 0.40518859028816223 0.86290056 0.42808660864830017 True -9 28840 32.12567901611328 12.310532569885254 863.7045288085938 0.3997914791107178 1135.1798095703125 0.4057692885398865 0.86734587 0.4198859632015228 True -10 31724 32.15129852294922 0.6078908443450928 978.430908203125 0.2593621015548706 1124.9837646484375 0.4111025035381317 0.8703223 0.37312760949134827 True -11 34608 32.19239282608032 0.615142822265625 942.62451171875 0.31390637159347534 1120.2681884765625 0.4122622013092041 0.87698853 0.3487193286418915 True -12 37492 32.17301630973816 0.6037940979003906 877.7637939453125 0.26866573095321655 1116.147216796875 0.41365930438041687 0.8814727 0.31475284695625305 True -13 40376 32.1863317489624 0.6231567859649658 869.4127197265625 0.20399264991283417 1113.348388671875 0.4148816168308258 0.8848924 0.2950705885887146 True -14 43260 31.84677481651306 0.5877044200897217 915.238037109375 0.1545233428478241 1107.218505859375 0.4176972806453705 0.8877743 0.2715494930744171 True -15 46144 31.460311889648438 0.609879732131958 902.2496337890625 0.1336301863193512 1104.2313232421875 0.42030206322669983 0.89250064 0.24801333248615265 True -16 49028 31.436786890029907 0.592026948928833 907.2881469726562 0.13756240904331207 1102.2607421875 0.42095866799354553 0.89675355 0.22986221313476562 True -17 51912 31.446110725402832 0.5825252532958984 779.0924072265625 0.15666118264198303 1102.351318359375 0.41938865184783936 0.89702094 0.22216349840164185 True -18 54796 31.442466735839844 0.59059739112854 867.5398559570312 0.12371384352445602 1101.8953857421875 0.4203029274940491 0.897598 0.2204253077507019 True -19 57680 31.492165565490723 0.5855746269226074 759.7730712890625 0.33478042483329773 1102.7177734375 0.4199870526790619 0.8971757 0.2208414375782013 False diff --git a/ENCSR757NJT/cherimoya.fold_2.performance.tsv b/ENCSR757NJT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index da56ec3c463dda94e5270aae9c920d5ae92c5de1..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1101.8953857421875 0.3379879295825958 0.4203029274940491 0.20962709188461304 0.8975980281829834 0.8704482316970825 0.2204253077507019 \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_3.evaluate.json b/ENCSR757NJT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9615ad8f61591f75e22cba0d629d44940025d5cc..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF033KMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_3.fit.json b/ENCSR757NJT/cherimoya.fold_3.fit.json deleted file mode 100644 index f1c487ed248fde17a131b1009d6530e31b8940cc..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF033KMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_3.log b/ENCSR757NJT/cherimoya.fold_3.log deleted file mode 100644 index dc3e1f39c1228c3aeb91aa85622e6abb5daec89f..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 34.85101103782654 3.8450865745544434 987.42236328125 0.5159999132156372 1239.308349609375 0.3198266625404358 0.74550223 7.920384883880615 True -1 5458 30.457627773284912 28.838815450668335 1063.5653076171875 0.3573493957519531 1103.0233154296875 0.37847068905830383 0.81363094 1.7196636199951172 True -2 8187 30.45807981491089 22.594686031341553 1194.91552734375 0.37732648849487305 1080.43017578125 0.38794705271720886 0.82124496 0.8949486017227173 True -3 10916 30.529817819595337 0.6270415782928467 859.931640625 0.43975120782852173 1063.1466064453125 0.39520463347435 0.8297074 0.734906017780304 True -4 13645 30.408344984054565 0.5875811576843262 924.1244506835938 0.24828630685806274 1053.9166259765625 0.40044641494750977 0.8352946 0.7039356231689453 True -5 16374 30.463956594467163 0.5888471603393555 1011.836669921875 0.593737006187439 1049.93408203125 0.4013387858867645 0.8389211 0.6574056148529053 True -6 19103 30.402769327163696 0.5924861431121826 939.1251220703125 0.3367723524570465 1045.552734375 0.40346506237983704 0.8432049 0.6356168389320374 True -7 21832 30.06277298927307 0.5753273963928223 761.4019775390625 0.2733733654022217 1042.060546875 0.4050982892513275 0.84842956 0.6098966598510742 True -8 24561 29.73285698890686 0.5828857421875 988.6613159179688 0.37628525495529175 1036.887939453125 0.4078843295574188 0.85101634 0.5722532868385315 True -9 27290 29.728858947753906 0.5844216346740723 1099.450927734375 0.25138550996780396 1032.2333984375 0.4100209176540375 0.8565482 0.5463513135910034 True -10 30019 29.806034803390503 0.5890562534332275 1116.8568115234375 0.288850873708725 1026.242919921875 0.41336241364479065 0.8633236 0.46511414647102356 True -11 32748 29.847290754318237 0.584402322769165 865.0113525390625 0.24864444136619568 1019.6456909179688 0.4169157147407532 0.86876696 0.4278047978878021 True -12 35477 29.791861057281494 0.5816600322723389 1063.367431640625 0.2697402238845825 1016.44921875 0.41723933815956116 0.8753179 0.3640366792678833 True -13 38206 29.79170870780945 1.2274243831634521 820.921875 0.28540387749671936 1011.7103881835938 0.41966646909713745 0.88017935 0.3258022964000702 True -14 40935 29.857218742370605 0.5969908237457275 879.0908203125 0.15974107384681702 1008.8570556640625 0.4205012321472168 0.88484156 0.2908993661403656 True -15 43664 29.7648708820343 0.5844640731811523 931.6137084960938 0.19089391827583313 1004.926513671875 0.42181265354156494 0.889635 0.2630542516708374 True -16 46393 29.86817455291748 0.6325948238372803 1088.9219970703125 0.2144961655139923 1005.7990112304688 0.42034319043159485 0.8933773 0.23986274003982544 True -17 49122 29.842961072921753 0.5909593105316162 835.5804443359375 0.1539006382226944 1005.2394409179688 0.4214167296886444 0.8965152 0.2258143573999405 True -18 51851 29.813872575759888 0.590442419052124 839.1175537109375 0.1621493697166443 1004.5693359375 0.4221764802932739 0.8960841 0.2220478355884552 False -19 54580 29.868813276290894 0.602400541305542 848.901611328125 0.1651005744934082 1004.8591918945312 0.42223888635635376 0.8953824 0.22151364386081696 False diff --git a/ENCSR757NJT/cherimoya.fold_3.performance.tsv b/ENCSR757NJT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 99546911029d76ebc52002c0499c10e86f125a0a..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1005.2394409179688 0.34380990266799927 0.421416699886322 0.20046143233776093 0.8965151906013489 0.8578334450721741 0.2258143573999405 \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_4.evaluate.json b/ENCSR757NJT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 35a57bca2dac027875748f5ce51776983df7e84e..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF033KMY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_4.fit.json b/ENCSR757NJT/cherimoya.fold_4.fit.json deleted file mode 100644 index 92983f7bf491ed2ec0062999bcab7158192f0ba6..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF033KMY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR757NJT/cherimoya.fold_4.log b/ENCSR757NJT/cherimoya.fold_4.log deleted file mode 100644 index d0ad089af91197780d71cc1601e526bc3d894d6f..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2805 36.115886926651 4.93572211265564 918.559814453125 0.3399858772754669 1173.8944091796875 0.30884626507759094 0.7594658 6.9010114669799805 True -1 5610 31.31527853012085 2.927225112915039 1082.9959716796875 0.3919009566307068 1046.5810546875 0.3694930076599121 0.8237592 1.3387056589126587 True -2 8415 31.24797010421753 0.6674103736877441 903.3470458984375 0.2873073220252991 1029.2802734375 0.37498870491981506 0.8278608 0.6542090773582458 True -3 11220 31.224918365478516 0.634028434753418 898.9097290039062 0.45131051540374756 1014.5352783203125 0.3811279237270355 0.8391153 0.5361982583999634 True -4 14025 31.806795358657837 0.6437845230102539 1019.5919799804688 0.37674760818481445 1010.4971923828125 0.3820655345916748 0.8401567 0.5268120169639587 True -5 16830 31.319390296936035 0.6381919384002686 936.0543823242188 0.3862137794494629 1007.83544921875 0.38405245542526245 0.8399117 0.557535707950592 False -6 19635 31.255221366882324 0.6375226974487305 919.754638671875 0.26684603095054626 1001.59228515625 0.38745060563087463 0.8454336 0.5417512059211731 True -7 22440 31.266075372695923 0.6349561214447021 1035.6796875 0.29538631439208984 996.8704833984375 0.3906473219394684 0.852352 0.48443126678466797 True -8 25245 31.28224539756775 0.6358804702758789 1068.9578857421875 0.4277478754520416 994.0515747070312 0.3919696509838104 0.8560655 0.442427396774292 True -9 28050 30.704254627227783 0.7560238838195801 960.5029296875 0.1830061823129654 988.5473022460938 0.39577022194862366 0.8620655 0.4171481728553772 True -10 30855 30.778756141662598 1.5309092998504639 817.5180053710938 0.21268486976623535 983.4793701171875 0.39767372608184814 0.8690979 0.3469974994659424 True -11 33660 30.671602725982666 1.8320107460021973 874.9464111328125 0.24985197186470032 981.4315185546875 0.3986365497112274 0.87230873 0.31551051139831543 True -12 36465 30.688408136367798 0.639061450958252 1084.689697265625 0.31392988562583923 976.9536743164062 0.4000891149044037 0.87810403 0.2788426876068115 True -13 39270 30.650623083114624 0.6298339366912842 845.780029296875 0.14903677999973297 972.796630859375 0.40308067202568054 0.8830367 0.2613758146762848 True -14 42075 30.705074071884155 0.6420083045959473 911.6808471679688 0.2513311505317688 970.7450561523438 0.4029200077056885 0.8886146 0.2366677075624466 True -15 44880 30.712003469467163 0.627722978591919 913.0889282226562 0.21982622146606445 966.678466796875 0.40666359663009644 0.89379543 0.21402263641357422 True -16 47685 30.692625045776367 0.659743070602417 884.1285400390625 0.12590420246124268 967.2830200195312 0.40491798520088196 0.89794904 0.19797684252262115 True -17 50490 30.73115372657776 1.256896734237671 785.9618530273438 0.13466480374336243 968.8464965820312 0.40377381443977356 0.900195 0.18968746066093445 True -18 53295 30.72329330444336 0.6284863948822021 935.1263427734375 0.15717381238937378 965.1280517578125 0.4065033793449402 0.90120035 0.1868847757577896 True -19 56100 30.746193170547485 0.6217341423034668 864.658447265625 0.08594569563865662 967.7495727539062 0.404323011636734 0.90029335 0.1870398223400116 False diff --git a/ENCSR757NJT/cherimoya.fold_4.performance.tsv b/ENCSR757NJT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index decd24d2207d89f001755484be5ef31dbd147dff..0000000000000000000000000000000000000000 --- a/ENCSR757NJT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -965.1280517578125 0.35305410623550415 0.4065033793449402 0.190303772687912 0.9012003540992737 0.8612387776374817 0.1868847757577896 \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_0.evaluate.json b/ENCSR759UNY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7d4e9ea3a2059d9a63cd3cebf325ebce28fd22fb..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF208MBC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_0.fit.json b/ENCSR759UNY/cherimoya.fold_0.fit.json deleted file mode 100644 index 70347cc444da58204733e692b65600b0801bad08..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF208MBC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_0.log b/ENCSR759UNY/cherimoya.fold_0.log deleted file mode 100644 index 3c99c60828483963ad03da20145456202fb8c124..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.165658950805664 3.6184651851654053 919.7530517578125 0.844390869140625 1418.969482421875 0.308039128780365 0.5466355 5.796005725860596 True -1 5478 30.524659156799316 0.6160285472869873 1023.4793701171875 0.6312606334686279 1230.5213623046875 0.4544198215007782 0.6505843 1.9730472564697266 True -2 8217 30.346887588500977 0.600527286529541 952.9168701171875 0.764304518699646 1208.8427734375 0.4681157171726227 0.64976317 1.0177278518676758 False -3 10956 30.323098182678223 0.5964031219482422 883.9619140625 0.2580759823322296 1201.684326171875 0.4722890257835388 0.6531206 0.7450093626976013 True -4 13695 30.378082036972046 0.6116816997528076 908.7208251953125 0.48767703771591187 1194.8817138671875 0.47778254747390747 0.66073334 0.6868888735771179 True -5 16434 30.385957956314087 10.140561819076538 901.5362548828125 0.7884702682495117 1188.21337890625 0.4841623902320862 0.6610698 0.6863790154457092 True -6 19173 30.27628493309021 1.2753095626831055 1037.2147216796875 0.41483274102211 1181.3426513671875 0.4888240098953247 0.66665006 0.5922553539276123 True -7 21912 30.464680194854736 0.6059460639953613 938.3572998046875 0.5414688587188721 1174.7935791015625 0.4958125650882721 0.6701722 0.5718727111816406 True -8 24651 30.31773567199707 0.6097917556762695 1071.986083984375 0.6406157612800598 1170.3375244140625 0.5001410245895386 0.67518675 0.5105248689651489 True -9 27390 30.336949348449707 0.5911593437194824 989.141357421875 0.6804596185684204 1161.85791015625 0.5062260031700134 0.68202174 0.5036185383796692 True -10 30129 30.27492880821228 0.638648271560669 889.8870849609375 0.28973501920700073 1158.1295166015625 0.508531928062439 0.68845564 0.4817650318145752 True -11 32868 30.33023953437805 0.5868782997131348 974.3009643554688 0.43720054626464844 1152.256591796875 0.5131367444992065 0.70061827 0.4528324604034424 True -12 35607 30.382224559783936 2.0081207752227783 912.0645141601562 0.28304553031921387 1148.0601806640625 0.5143648386001587 0.7049537 0.4206710159778595 True -13 38346 30.31046223640442 0.6071319580078125 986.5517578125 0.3497557044029236 1146.1796875 0.5164565443992615 0.71699864 0.39937832951545715 True -14 41085 30.319525003433228 0.5941493511199951 999.1578369140625 0.4773937165737152 1140.6798095703125 0.5203477740287781 0.7284499 0.3636472523212433 True -15 43824 30.341387033462524 11.734487533569336 1069.337158203125 0.30351853370666504 1138.11328125 0.5237064957618713 0.7366339 0.34630104899406433 True -16 46563 30.333545446395874 11.691858768463135 783.5901489257812 0.2513999342918396 1134.0543212890625 0.5263510942459106 0.74392444 0.3307039141654968 True -17 49302 30.36549711227417 23.836790800094604 805.923828125 0.3479943573474884 1134.679443359375 0.5257647633552551 0.747454 0.31961533427238464 True -18 52041 30.28068208694458 8.66969895362854 919.2176513671875 0.36670371890068054 1133.55224609375 0.527364194393158 0.74955016 0.31499797105789185 True -19 54780 30.400896072387695 0.6163854598999023 965.7567138671875 0.2670169770717621 1133.3687744140625 0.5268775820732117 0.74956596 0.3118215799331665 True diff --git a/ENCSR759UNY/cherimoya.fold_0.performance.tsv b/ENCSR759UNY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 51e987f28fb554ce5fa27fb650f198ea648ce505..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1133.3687744140625 0.25537222623825073 0.5268775820732117 0.2831437289714813 0.7495659589767456 0.6930535435676575 0.3118215799331665 \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_1.evaluate.json b/ENCSR759UNY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6c536419b9d26da8f48ac57abaf8935659aaa6ff..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF208MBC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_1.fit.json b/ENCSR759UNY/cherimoya.fold_1.fit.json deleted file mode 100644 index e20614d1201a11c72e442d6b1254daab03506a4f..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF208MBC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_1.log b/ENCSR759UNY/cherimoya.fold_1.log deleted file mode 100644 index 03ce09f7ff51ef3a1548164be3a12b6fd86aece8..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 33.77964401245117 3.725536346435547 1071.0361328125 0.5338373184204102 1585.3914794921875 0.3075411319732666 0.57151544 7.896903038024902 True -1 5406 29.896453380584717 0.7287144660949707 999.85791015625 0.5566384792327881 1357.456298828125 0.46281424164772034 0.6359869 2.3593950271606445 True -2 8109 29.87269401550293 18.961100101470947 949.692626953125 0.7739534378051758 1326.265625 0.4759029746055603 0.657496 0.8226247429847717 True -3 10812 29.915517330169678 0.7536189556121826 907.6741333007812 0.6208367347717285 1307.7608642578125 0.48709574341773987 0.66989225 0.6265199184417725 True -4 13515 29.89129877090454 0.7406604290008545 954.8106689453125 0.44306617975234985 1302.4979248046875 0.48885849118232727 0.6692132 0.6912628412246704 False -5 16218 29.89174509048462 0.7311081886291504 869.0018310546875 0.6754429936408997 1292.9326171875 0.4966210424900055 0.6690566 0.6388009190559387 False -6 18921 29.898802042007446 0.7368371486663818 856.9861450195312 0.5200681686401367 1286.27294921875 0.49986323714256287 0.67445993 0.5520507097244263 True -7 21624 29.92059302330017 0.7310094833374023 900.7980346679688 0.3207041025161743 1278.7706298828125 0.5055854320526123 0.67811817 0.5133712887763977 True -8 24327 30.210680723190308 0.7260603904724121 850.2431640625 0.5723235607147217 1272.140380859375 0.5096099376678467 0.69139516 0.4618160128593445 True -9 27030 29.943716049194336 2.4668586254119873 1026.3214111328125 0.4839593172073364 1265.0333251953125 0.5147855877876282 0.69790643 0.4545353353023529 True -10 29733 29.952099323272705 0.7445383071899414 922.473388671875 0.4492987394332886 1257.2930908203125 0.5196322202682495 0.7109688 0.43384167551994324 True -11 32436 29.906262397766113 2.1878650188446045 1040.779296875 0.3494468927383423 1251.7530517578125 0.5221306085586548 0.716255 0.43289706110954285 True -12 35139 29.90887212753296 1.0410871505737305 814.1400756835938 0.4712350368499756 1245.6649169921875 0.5268549919128418 0.72863394 0.4050552248954773 True -13 37842 29.99388837814331 4.0310022830963135 1017.6524047851562 0.46384096145629883 1237.804931640625 0.5312508344650269 0.7382569 0.3871658444404602 True -14 40545 29.919870615005493 1.955998420715332 915.8690185546875 0.3793235421180725 1236.22509765625 0.5336450934410095 0.7440946 0.3732452094554901 True -15 43248 29.96775984764099 0.7440264225006104 844.4649658203125 0.3353293240070343 1230.875 0.537135660648346 0.7550716 0.35482057929039 True -16 45951 29.963210821151733 0.7398111820220947 908.776123046875 0.4255565106868744 1227.7724609375 0.5378623008728027 0.7591102 0.3490392863750458 True -17 48654 29.96142840385437 0.7335569858551025 798.6906127929688 0.28711581230163574 1227.4788818359375 0.5385338664054871 0.7625267 0.34202444553375244 True -18 51357 29.92819309234619 0.7281293869018555 878.0252685546875 0.32014262676239014 1228.2142333984375 0.53763347864151 0.7647279 0.3404560983181 True -19 54060 29.938673496246338 0.7314472198486328 925.3748779296875 0.2490616738796234 1228.810302734375 0.5363947153091431 0.7638554 0.34253057837486267 False diff --git a/ENCSR759UNY/cherimoya.fold_1.performance.tsv b/ENCSR759UNY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c7e1b4b65ca0d2be52ea79f586a5ac67aa0f73f4..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1228.2142333984375 0.24429099261760712 0.53763347864151 0.3041824996471405 0.7647278904914856 0.7262383699417114 0.3404560983181 \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_2.evaluate.json b/ENCSR759UNY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ef13ab7c166fbb9bfb6a79a2a6bc9b953bf44eb5..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF208MBC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_2.fit.json b/ENCSR759UNY/cherimoya.fold_2.fit.json deleted file mode 100644 index 186f1b59387ff8949f6fdc5ccce2e783b7b32ddc..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF208MBC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_2.log b/ENCSR759UNY/cherimoya.fold_2.log deleted file mode 100644 index fe8e61dadc678c236c2bb2c81b1cca34a3c84e8b..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 35.77402091026306 3.5689074993133545 907.9073486328125 0.6868517398834229 1459.6099853515625 0.3111456632614136 0.5548217 8.36180305480957 True -1 5752 32.15363931655884 7.1827943325042725 1015.801513671875 0.7530626654624939 1256.568115234375 0.4653100371360779 0.6206136 1.6909911632537842 True -2 8628 32.11710000038147 0.5805304050445557 1071.59716796875 0.7398139238357544 1232.609619140625 0.4716377258300781 0.64092326 0.6604158878326416 True -3 11504 32.11767363548279 0.5711421966552734 923.5601806640625 0.9117052555084229 1221.137939453125 0.47921550273895264 0.65251374 0.5999047756195068 True -4 14380 32.12221145629883 0.5621898174285889 1135.250244140625 0.6201692819595337 1211.306640625 0.48568612337112427 0.6594278 0.5865833163261414 True -5 17256 32.151031732559204 0.5659067630767822 1107.07568359375 0.4473939538002014 1205.3077392578125 0.4897788166999817 0.6688698 0.5722129940986633 True -6 20132 32.1070761680603 0.5649917125701904 1156.9716796875 0.4651027023792267 1199.122802734375 0.4944576323032379 0.66683346 0.48747047781944275 False -7 23008 32.13052272796631 0.5652639865875244 877.0535278320312 0.748624324798584 1190.5887451171875 0.5006088614463806 0.6678723 0.4589118957519531 False -8 25884 32.19935083389282 10.235292434692383 898.92431640625 0.454785019159317 1182.8978271484375 0.5093269348144531 0.6715569 0.4344366490840912 True -9 28760 32.23758125305176 0.5711331367492676 914.9920043945312 0.3402841091156006 1180.22705078125 0.5107412934303284 0.67047566 0.44164788722991943 False -10 31636 32.173866271972656 0.570204496383667 860.4739990234375 0.42442286014556885 1172.1710205078125 0.5175788402557373 0.6794052 0.42398175597190857 True -11 34512 32.173750162124634 0.5662233829498291 995.1671142578125 0.47984743118286133 1169.3365478515625 0.5181096792221069 0.6870372 0.4233940839767456 True -12 37388 32.17333269119263 0.5675492286682129 990.5257568359375 0.5017305612564087 1163.3507080078125 0.523173451423645 0.6965242 0.42271044850349426 True -13 40264 32.18658494949341 0.5688278675079346 936.4996337890625 0.523124635219574 1158.017822265625 0.5281167030334473 0.7044722 0.4029330313205719 True -14 43140 32.2222044467926 0.5688266754150391 863.781982421875 0.3497859239578247 1157.27099609375 0.5277913808822632 0.71474785 0.37762829661369324 True -15 46016 32.23699474334717 0.5621356964111328 871.5805053710938 0.5744176506996155 1156.2498779296875 0.5272325873374939 0.7230113 0.36664488911628723 True -16 48892 32.16197919845581 0.5715768337249756 1025.062255859375 0.40080058574676514 1153.9129638671875 0.5294243097305298 0.7316309 0.35485324263572693 True -17 51768 32.204384565353394 0.5711603164672852 986.3935546875 0.371438592672348 1153.1363525390625 0.5294156670570374 0.7342731 0.3458062708377838 True -18 54644 32.21006631851196 0.5752298831939697 854.3775634765625 0.4155811369419098 1150.8167724609375 0.5324238538742065 0.7366495 0.34410086274147034 True -19 57520 32.13563680648804 0.5739567279815674 916.1026611328125 0.19740647077560425 1153.5552978515625 0.5291463732719421 0.7359344 0.34204015135765076 False diff --git a/ENCSR759UNY/cherimoya.fold_2.performance.tsv b/ENCSR759UNY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 94c1a4086924215969a88f364760f0d75ea66298..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1150.8167724609375 0.2518530786037445 0.5324238538742065 0.2910044491291046 0.7366495132446289 0.6851450800895691 0.34410086274147034 \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_3.evaluate.json b/ENCSR759UNY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 769d72bf4e795f6fd74ab6c9b775538f09322478..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF208MBC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_3.fit.json b/ENCSR759UNY/cherimoya.fold_3.fit.json deleted file mode 100644 index fe2cb42f74d07d356db4cf516adceb82d24a4d7f..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF208MBC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_3.log b/ENCSR759UNY/cherimoya.fold_3.log deleted file mode 100644 index 6e55efd1aa94088c6cc484fa0bda5439931dae51..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 34.234559535980225 2.9867773056030273 940.8320922851562 0.6293798685073853 1464.0938720703125 0.309213787317276 0.5865427 7.710418701171875 True -1 5520 30.534645318984985 0.5463409423828125 909.911865234375 0.5636262893676758 1271.88037109375 0.4559286832809448 0.65036565 2.019169807434082 True -2 8280 30.517812252044678 0.53914475440979 929.15087890625 0.6552706360816956 1252.7125244140625 0.4656180441379547 0.65041447 0.9686327576637268 True -3 11040 30.599773168563843 0.5382277965545654 1168.76904296875 0.7753269672393799 1238.9569091796875 0.4749147891998291 0.65067464 0.8663461208343506 True -4 13800 30.532557487487793 0.5452470779418945 1107.460205078125 0.5397739410400391 1233.7120361328125 0.4776207208633423 0.65724635 0.7635672092437744 True -5 16560 30.582037925720215 0.5363705158233643 1046.3565673828125 0.6207998991012573 1227.9891357421875 0.48178592324256897 0.66478246 0.6848529577255249 True -6 19320 30.583142518997192 0.5442359447479248 1040.070068359375 0.6004557013511658 1221.2012939453125 0.4878420829772949 0.6699465 0.5906509757041931 True -7 22080 30.55733323097229 0.5447080135345459 987.294189453125 0.5639581680297852 1215.579345703125 0.49149057269096375 0.6670221 0.5381183624267578 False -8 24840 30.53907346725464 5.176840543746948 862.80615234375 0.6540613770484924 1206.6031494140625 0.4990406930446625 0.67848665 0.4666691720485687 True -9 27600 30.55843496322632 1.2667663097381592 843.1534423828125 0.623481273651123 1204.69970703125 0.5004491209983826 0.68341297 0.45735037326812744 True -10 30360 30.581461191177368 0.5464150905609131 885.4130859375 0.434573233127594 1199.8292236328125 0.5042000412940979 0.6902526 0.44242334365844727 True -11 33120 30.550485134124756 0.546825647354126 1033.2001953125 0.46578800678253174 1194.630859375 0.5061302781105042 0.7026586 0.43126237392425537 True -12 35880 30.553319454193115 0.5371747016906738 945.038330078125 0.447595477104187 1192.0865478515625 0.508385956287384 0.7155937 0.4091264307498932 True -13 38640 30.609107732772827 0.544846773147583 1037.9703369140625 0.48009437322616577 1184.15625 0.5156922340393066 0.72665596 0.3881531059741974 True -14 41400 30.556504249572754 0.5401203632354736 972.1661987304688 0.29951852560043335 1182.5211181640625 0.5166022777557373 0.73626035 0.3706103265285492 True -15 44160 30.632956743240356 0.544090986251831 884.032470703125 0.4297385811805725 1177.9249267578125 0.5212522149085999 0.74824697 0.36091575026512146 True -16 46920 30.538790941238403 0.8618118762969971 862.0015258789062 0.4827283024787903 1177.949951171875 0.5196000933647156 0.7535351 0.3424668610095978 True -17 49680 30.607160568237305 0.5435657501220703 855.276123046875 0.278781533241272 1172.0206298828125 0.5256696939468384 0.7571798 0.3324088454246521 True -18 52440 30.597972631454468 0.5670361518859863 840.9928588867188 0.2109430730342865 1173.5804443359375 0.5232352614402771 0.75905776 0.3294026255607605 True -19 55200 30.611148357391357 0.5425386428833008 831.6988525390625 0.2995314598083496 1175.1197509765625 0.5216631889343262 0.7580957 0.3272011876106262 False diff --git a/ENCSR759UNY/cherimoya.fold_3.performance.tsv b/ENCSR759UNY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index cb6a05dc3076568acee3f18dc8a90b0ace9c1f38..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1173.5804443359375 0.25300291180610657 0.5232352614402771 0.28939247131347656 0.7590577602386475 0.7074668407440186 0.3294026255607605 \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_4.evaluate.json b/ENCSR759UNY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5c2689db1e2420426007497382769da798f3cb6f..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF208MBC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_4.fit.json b/ENCSR759UNY/cherimoya.fold_4.fit.json deleted file mode 100644 index 19669011b5d685b2368684d244ab701074b954c1..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF208MBC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR759UNY/cherimoya.fold_4.log b/ENCSR759UNY/cherimoya.fold_4.log deleted file mode 100644 index a5e1d3429c37112d10139239aeb54331653ceb91..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 35.41318202018738 3.537612199783325 982.2910766601562 0.5532342195510864 1407.250244140625 0.3104283809661865 0.5589379 7.705893516540527 True -1 5664 31.65605616569519 0.6201307773590088 949.05615234375 0.6556178331375122 1226.363037109375 0.45384886860847473 0.61479 1.917264699935913 True -2 8496 31.65349316596985 0.6112852096557617 904.9805908203125 0.5444945096969604 1210.6590576171875 0.45865073800086975 0.63214964 0.6785119771957397 True -3 11328 31.595149517059326 0.6170792579650879 953.4237060546875 0.6697310209274292 1198.8658447265625 0.46666961908340454 0.64588344 0.5876238942146301 True -4 14160 31.64059567451477 0.6138277053833008 1052.5797119140625 0.5388410091400146 1191.337646484375 0.473095178604126 0.65169674 0.7465689778327942 True -5 16992 31.621107816696167 2.2680625915527344 936.5728759765625 0.7427555918693542 1181.970458984375 0.482575923204422 0.65158784 0.6702576875686646 False -6 19824 31.615396738052368 0.6193265914916992 1045.045654296875 0.6176465749740601 1178.0509033203125 0.4850441813468933 0.6542163 0.566737174987793 True -7 22656 31.61576509475708 0.6184723377227783 911.56396484375 0.5363368988037109 1177.06005859375 0.48596400022506714 0.66205674 0.5352466702461243 True -8 25488 31.65152931213379 0.6196129322052002 1003.5818481445312 0.5573276281356812 1167.4259033203125 0.4944690465927124 0.6645548 0.47588807344436646 True -9 28320 31.637307167053223 0.7850708961486816 1032.4937744140625 0.5457162857055664 1162.4166259765625 0.49833354353904724 0.67152137 0.4881911873817444 True -10 31152 31.59188747406006 1.0675489902496338 927.3468017578125 0.5221878290176392 1159.5557861328125 0.5005331039428711 0.6801123 0.46729859709739685 True -11 33984 31.667800903320312 2.507289409637451 871.94091796875 0.415690541267395 1151.732177734375 0.5074572563171387 0.6886448 0.43153178691864014 True -12 36816 31.675382137298584 0.6158788204193115 1126.7574462890625 0.39658239483833313 1145.8575439453125 0.5118164420127869 0.7008072 0.4046338200569153 True -13 39648 31.69573187828064 0.622389554977417 1058.94091796875 0.5165414810180664 1143.0709228515625 0.5137218236923218 0.7095718 0.3844740688800812 True -14 42480 31.696147203445435 0.6163620948791504 874.7716064453125 0.30708980560302734 1136.79736328125 0.5196525454521179 0.71765614 0.3563753664493561 True -15 45312 31.640852689743042 0.6234598159790039 917.62646484375 0.3639487028121948 1134.4759521484375 0.5219653844833374 0.7295572 0.34287214279174805 True -16 48144 31.616966247558594 0.6123456954956055 984.0615234375 0.29624003171920776 1132.816162109375 0.5240946412086487 0.7346053 0.3316778540611267 True -17 50976 31.636459350585938 0.6321694850921631 952.7521362304688 0.2137027084827423 1135.912353515625 0.5194879770278931 0.7398036 0.31970083713531494 True -18 53808 31.64006471633911 2.168905258178711 1019.335693359375 0.36067235469818115 1131.906005859375 0.5237497091293335 0.7418638 0.31503522396087646 True -19 56640 31.61353826522827 0.6252398490905762 897.3533325195312 0.2531767785549164 1134.099365234375 0.5214409232139587 0.74170864 0.3155895173549652 False diff --git a/ENCSR759UNY/cherimoya.fold_4.performance.tsv b/ENCSR759UNY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ab5656fb1f10b38213cf2758ffc8153df351c6e6..0000000000000000000000000000000000000000 --- a/ENCSR759UNY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1131.906005859375 0.25460273027420044 0.5237497091293335 0.2849132716655731 0.7418637871742249 0.688263475894928 0.31503522396087646 \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_0.evaluate.json b/ENCSR761TKU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5d19941faa6419d4842c35007c7b445ba8ed10b1..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482VSL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_0.fit.json b/ENCSR761TKU/cherimoya.fold_0.fit.json deleted file mode 100644 index 0b657b00b18ce1020bfefe7cd51a37fe070f9ed1..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF482VSL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_0.log b/ENCSR761TKU/cherimoya.fold_0.log deleted file mode 100644 index 31e706f322b762ad0dcb62d79b127d5dcc0de77e..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1455 20.653321266174316 4.696643829345703 280.89825439453125 0.25681406259536743 397.341796875 0.458901584148407 0.72062683 13.997444152832031 True -1 2910 16.00952458381653 0.3002965450286865 233.2831573486328 0.21992427110671997 332.83038330078125 0.5484067797660828 0.7827653 2.787559747695923 True -2 4365 16.025120973587036 0.2917499542236328 243.72811889648438 0.28889769315719604 318.0401306152344 0.5777965188026428 0.8034668 0.6809611916542053 True -3 5820 16.00348472595215 0.28899502754211426 251.10665893554688 0.24370478093624115 310.6473693847656 0.5908066630363464 0.8196377 0.27482548356056213 True -4 7275 16.03717851638794 0.28562450408935547 262.79620361328125 0.19300949573516846 308.7679138183594 0.5944432020187378 0.8258225 0.2993682026863098 True -5 8730 16.022207021713257 0.2898228168487549 273.3970947265625 0.2626537084579468 307.6452331542969 0.5969324111938477 0.83189625 0.25519493222236633 True -6 10185 16.4635488986969 22.23820400238037 255.22645568847656 0.18358606100082397 307.02716064453125 0.5987389087677002 0.83747977 0.2080502212047577 True -7 11640 16.47002649307251 0.29195690155029297 286.61859130859375 0.28641799092292786 306.333740234375 0.6003198027610779 0.84028363 0.19274355471134186 True -8 13095 15.99062442779541 0.2898228168487549 276.4984130859375 0.19876684248447418 305.9703063964844 0.6013045310974121 0.8431738 0.19609150290489197 True -9 14550 16.0326988697052 0.2861659526824951 255.30343627929688 0.1916513890028 305.4181823730469 0.6028904318809509 0.84579086 0.18151767551898956 True -10 16005 16.034476041793823 0.28975725173950195 272.23211669921875 0.18668290972709656 304.91339111328125 0.6042089462280273 0.8481191 0.17646759748458862 True -11 17460 16.008594274520874 0.28510284423828125 283.86871337890625 0.17011496424674988 304.3934020996094 0.6056868433952332 0.85070586 0.16936737298965454 True -12 18915 16.020323753356934 2.470891237258911 269.27679443359375 0.18780416250228882 304.01971435546875 0.6066751480102539 0.8538511 0.16390477120876312 True -13 20370 16.01194977760315 0.2872626781463623 278.495361328125 0.18454967439174652 303.89501953125 0.6070964336395264 0.8568699 0.16334359347820282 True -14 21825 16.00750470161438 0.6264398097991943 240.51449584960938 0.14629459381103516 303.8977966308594 0.6070384383201599 0.8585455 0.162806436419487 True -15 23280 16.034717082977295 0.2931857109069824 242.8567657470703 0.12127576768398285 303.99420166015625 0.6068117618560791 0.85701644 0.16608934104442596 False -16 24735 16.075264930725098 0.2936704158782959 240.13421630859375 0.12995955348014832 304.2146301269531 0.6062727570533752 0.8555094 0.16854558885097504 False -17 26190 16.023232221603394 0.2942214012145996 261.939453125 0.08441602438688278 304.5710144042969 0.6052637100219727 0.8542625 0.1726837456226349 False -18 27645 16.30281162261963 18.806464195251465 239.5276336669922 0.08160296082496643 304.9385681152344 0.6041779518127441 0.8522674 0.1760343611240387 False -19 29100 16.433520317077637 0.30057644844055176 252.47442626953125 0.10618497431278229 305.12506103515625 0.603519082069397 0.8487675 0.1783178746700287 False diff --git a/ENCSR761TKU/cherimoya.fold_0.performance.tsv b/ENCSR761TKU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c2a519d0719aaf3a42eb5ceecf1a4c23c600ea8e..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -303.8977966308594 0.3135029673576355 0.6070383787155151 0.21754850447177887 0.8585454821586609 0.8227009177207947 0.162806436419487 \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_1.evaluate.json b/ENCSR761TKU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 45d2df74cca7f7b66a2eecaa2a5eaa23c871f52a..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482VSL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_1.fit.json b/ENCSR761TKU/cherimoya.fold_1.fit.json deleted file mode 100644 index df731130db668d3b24f0ec55aecba92a5f577e4f..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF482VSL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_1.log b/ENCSR761TKU/cherimoya.fold_1.log deleted file mode 100644 index ec6646e149f0d523a961bd6549682cf8558693c8..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1433 20.142572164535522 10.7628173828125 273.05059814453125 0.2808622121810913 443.81402587890625 0.4736543595790863 0.6412171 15.180680274963379 True -1 2866 15.781508684158325 0.6903786659240723 278.0657958984375 0.27152979373931885 368.8341979980469 0.566784143447876 0.73365444 3.061271905899048 True -2 4299 15.755494356155396 0.3899812698364258 274.22662353515625 0.2391529530286789 350.63995361328125 0.6018556952476501 0.7771593 0.6684597134590149 True -3 5732 15.72627067565918 0.38317227363586426 249.26162719726562 0.13929882645606995 341.3105773925781 0.6185746192932129 0.7993176 0.32624101638793945 True -4 7165 15.744763374328613 0.8528237342834473 241.7678680419922 0.22114868462085724 338.4654235839844 0.6241207122802734 0.80908483 0.3276108503341675 True -5 8598 15.754838705062866 0.38337278366088867 269.7444763183594 0.1469898521900177 337.24365234375 0.6265115141868591 0.812506 0.23384615778923035 True -6 10031 15.743953704833984 0.7070293426513672 265.91632080078125 0.2533424198627472 336.4849853515625 0.6287016868591309 0.82032466 0.20976373553276062 True -7 11464 15.466590404510498 0.3850243091583252 258.4668884277344 0.1620367020368576 336.9197082519531 0.6272363066673279 0.81500304 0.2496587634086609 False -8 12897 15.420563697814941 0.3857743740081787 319.85467529296875 0.2518751621246338 335.39178466796875 0.6310938596725464 0.8262235 0.2209230363368988 True -9 14330 15.408248901367188 0.3758573532104492 251.70745849609375 0.18791954219341278 334.5235595703125 0.6329888701438904 0.833482 0.20337992906570435 True -10 15763 15.470256805419922 0.3808724880218506 281.21527099609375 0.16252347826957703 333.9587097167969 0.6343550682067871 0.83973587 0.18819038569927216 True -11 17196 15.5611252784729 12.989829063415527 262.5106506347656 0.18174004554748535 333.5382995605469 0.6352245807647705 0.84295154 0.18107078969478607 True -12 18629 15.453484773635864 0.38120269775390625 265.6441955566406 0.17850738763809204 333.1705322265625 0.636134147644043 0.84915143 0.17183752357959747 True -13 20062 15.397518396377563 17.044443368911743 239.98422241210938 0.15355773270130157 332.95672607421875 0.6369150876998901 0.8509813 0.1717914342880249 True -14 21495 16.64486026763916 14.821118116378784 251.50852966308594 0.16730153560638428 332.88751220703125 0.6370036005973816 0.8519142 0.17144307494163513 True -15 22928 15.75072193145752 9.747686862945557 282.3456726074219 0.19838520884513855 333.1294860839844 0.6362994909286499 0.8491683 0.17522600293159485 False -16 24361 15.476609230041504 0.38655924797058105 274.42852783203125 0.10503888875246048 333.4967346191406 0.635337769985199 0.8501081 0.174651101231575 False -17 25794 15.488759517669678 0.37938642501831055 250.73031616210938 0.08470514416694641 333.9940185546875 0.6338673233985901 0.84703237 0.18038056790828705 False -18 27227 15.45584225654602 0.38546133041381836 244.981201171875 0.1106131374835968 334.47314453125 0.6325118541717529 0.84315354 0.18403103947639465 False -19 28660 15.424914598464966 0.3773527145385742 248.499755859375 0.09979330748319626 334.72564697265625 0.6317479014396667 0.8403861 0.18608585000038147 False diff --git a/ENCSR761TKU/cherimoya.fold_1.performance.tsv b/ENCSR761TKU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 48992d9b93b1a00d494453edfa5f0af5726524ed..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -332.88751220703125 0.2921096980571747 0.6370036005973816 0.2375723123550415 0.8519142270088196 0.8422116637229919 0.17144307494163513 \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_2.evaluate.json b/ENCSR761TKU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 50b12d15080fc165d4d692e3a1cdfc7134b4238d..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482VSL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_2.fit.json b/ENCSR761TKU/cherimoya.fold_2.fit.json deleted file mode 100644 index c3c606d601dc3e9f7b1cd955496151ca36bb69ad..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF482VSL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_2.log b/ENCSR761TKU/cherimoya.fold_2.log deleted file mode 100644 index 29c345b1057dc1bee4343ef28bf98476a3c701f5..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1525 21.392210960388184 3.291829824447632 241.46304321289062 0.25006458163261414 406.1897277832031 0.4695083498954773 0.66072243 13.001456260681152 True -1 3050 16.857654571533203 0.30539917945861816 285.0298156738281 0.31211936473846436 342.17901611328125 0.5586237907409668 0.7543145 2.624542474746704 True -2 4575 16.771019458770752 0.29547595977783203 315.04180908203125 0.19608519971370697 326.8586730957031 0.5879944562911987 0.7965598 0.4859674870967865 True -3 6100 16.73490619659424 0.3000805377960205 281.5885314941406 0.2540329098701477 320.6783142089844 0.5983748435974121 0.8153976 0.3546861410140991 True -4 7625 16.758496046066284 0.2925601005554199 229.24464416503906 0.2542199492454529 318.1663818359375 0.6038293838500977 0.8247333 0.2501813769340515 True -5 9150 16.809265613555908 0.2946305274963379 246.742431640625 0.19628949463367462 317.4794006347656 0.6053907871246338 0.8272218 0.20212240517139435 True -6 10675 16.764097929000854 0.2905609607696533 242.9049530029297 0.27412474155426025 318.0862731933594 0.6044417023658752 0.8257124 0.25098851323127747 False -7 12200 16.89031410217285 0.2916402816772461 265.2265625 0.18831351399421692 316.670166015625 0.6076645255088806 0.83077914 0.23389795422554016 True -8 13725 16.764960289001465 0.29438042640686035 247.91371154785156 0.17013490200042725 315.915283203125 0.6096546053886414 0.8358279 0.20807744562625885 True -9 15250 16.73528790473938 1.7597501277923584 227.06732177734375 0.1325272023677826 315.4619445800781 0.6107182502746582 0.83839965 0.19543743133544922 True -10 16775 16.779656887054443 0.29143285751342773 264.963134765625 0.1820213943719864 314.9468078613281 0.6120235323905945 0.8423296 0.19208157062530518 True -11 18300 16.78141975402832 0.29303717613220215 245.76376342773438 0.20629993081092834 314.3932800292969 0.6134904623031616 0.84417224 0.18860788643360138 True -12 19825 16.737767696380615 0.30303168296813965 290.323486328125 0.23774239420890808 314.0126953125 0.6145483255386353 0.8472252 0.18236039578914642 True -13 21350 16.728151321411133 0.2941746711730957 248.0236358642578 0.19042915105819702 313.71221923828125 0.6150974035263062 0.8472673 0.1784452348947525 True -14 22875 16.73610258102417 0.2962017059326172 265.15411376953125 0.15826764702796936 313.7090759277344 0.6152390241622925 0.8478174 0.17609703540802002 True -15 24400 16.739196062088013 0.2926619052886963 259.1506042480469 0.1799243539571762 313.8457336425781 0.6147869229316711 0.84837323 0.17836298048496246 True -16 25925 16.738398551940918 0.2971949577331543 266.06707763671875 0.15706878900527954 314.04571533203125 0.6140417456626892 0.8443305 0.1847873330116272 False -17 27450 16.720296382904053 1.7845852375030518 257.1176452636719 0.18389518558979034 314.5096130371094 0.6128466725349426 0.84166515 0.18965066969394684 False -18 28975 16.777587413787842 17.565142393112183 260.17828369140625 0.08496548235416412 314.8851013183594 0.6116576790809631 0.8388354 0.1929612159729004 False -19 30500 18.973236322402954 0.35699915885925293 266.70794677734375 0.08551390469074249 315.2228698730469 0.6110341548919678 0.83495563 0.19572944939136505 False diff --git a/ENCSR761TKU/cherimoya.fold_2.performance.tsv b/ENCSR761TKU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c4fa53ec1dc0d6cd305a1a842eed04085cbb0440..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -313.8457336425781 0.3072620928287506 0.6147869229316711 0.2221805304288864 0.8483732342720032 0.8206655979156494 0.17836298048496246 \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_3.evaluate.json b/ENCSR761TKU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 640f346ab1a33185ab7a47f05b11a4f6491583ed..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482VSL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_3.fit.json b/ENCSR761TKU/cherimoya.fold_3.fit.json deleted file mode 100644 index f1184e5c71d3ea45d4580a346227470550d2c7ac..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF482VSL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_3.log b/ENCSR761TKU/cherimoya.fold_3.log deleted file mode 100644 index 6bfcda86b26887375c7620924d626c6f7f3efbf7..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1496 21.157976865768433 3.2267282009124756 279.2008056640625 0.28219473361968994 403.16461181640625 0.4680476784706116 0.68263423 13.800795555114746 True -1 2992 16.4476101398468 0.3242518901824951 265.49383544921875 0.16789883375167847 338.74798583984375 0.5583163499832153 0.77057546 2.242363929748535 True -2 4488 16.442466974258423 0.2971360683441162 250.1173553466797 0.29794299602508545 323.243408203125 0.5858154892921448 0.8016726 0.5857433676719666 True -3 5984 16.497819423675537 0.29761815071105957 274.31646728515625 0.31525111198425293 316.7753601074219 0.5985702276229858 0.82689196 0.3739188313484192 True -4 7480 16.48501491546631 0.2974057197570801 255.83941650390625 0.20499955117702484 315.3347473144531 0.6018008589744568 0.8324243 0.25842252373695374 True -5 8976 16.473859786987305 0.2993500232696533 261.63189697265625 0.2317802459001541 314.69403076171875 0.6033997535705566 0.836068 0.21607615053653717 True -6 10472 16.447351932525635 0.30108213424682617 273.7745361328125 0.20263150334358215 314.1141052246094 0.6047430038452148 0.8380875 0.20880821347236633 True -7 11968 16.490959644317627 0.29660820960998535 265.73565673828125 0.27594828605651855 313.7518005371094 0.6057100892066956 0.8377389 0.21378302574157715 False -8 13464 16.460450887680054 1.4619200229644775 301.5960693359375 0.15942877531051636 313.0495910644531 0.6073008179664612 0.8414757 0.21364162862300873 True -9 14960 16.45080304145813 0.29531025886535645 267.9081726074219 0.15480437874794006 312.7274169921875 0.6082631349563599 0.841587 0.2189071774482727 True -10 16456 16.594831228256226 13.552252531051636 277.6658630371094 0.2326083779335022 312.11773681640625 0.6098456382751465 0.8410107 0.1998344361782074 False -11 17952 16.871260404586792 0.3059227466583252 259.718994140625 0.1754010021686554 311.73687744140625 0.6109144687652588 0.8451187 0.2043154090642929 True -12 19448 16.463261365890503 0.3058035373687744 270.97991943359375 0.12672558426856995 311.2955322265625 0.6119522452354431 0.8470168 0.2070995271205902 True -13 20944 16.508519887924194 1.0421490669250488 264.77374267578125 0.11751355975866318 311.002685546875 0.6125718355178833 0.848187 0.20074418187141418 True -14 22440 16.465199947357178 0.2991318702697754 257.10491943359375 0.13190121948719025 310.94842529296875 0.6126591563224792 0.8515483 0.19524165987968445 True -15 23936 16.447007417678833 0.29874610900878906 247.5775909423828 0.18111301958560944 311.0343933105469 0.6124234199523926 0.8500591 0.19267503917217255 False -16 25432 16.64523148536682 0.30252981185913086 255.14678955078125 0.11091628670692444 311.2745361328125 0.6117116808891296 0.85055596 0.19143402576446533 False -17 26928 16.155040979385376 0.3008277416229248 236.33290100097656 0.12110172212123871 311.66070556640625 0.6108273267745972 0.8478627 0.19336025416851044 False -18 28424 16.12804889678955 0.2935373783111572 289.2483825683594 0.09509360790252686 312.0323181152344 0.609746515750885 0.8453365 0.19480110704898834 False -19 29920 16.1312837600708 0.2960324287414551 279.97601318359375 0.08590757846832275 312.29150390625 0.6090251207351685 0.8429315 0.1956394463777542 False diff --git a/ENCSR761TKU/cherimoya.fold_3.performance.tsv b/ENCSR761TKU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 67eb1eafb4770969fd7e4b1155c9458e49aa4b23..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -310.94842529296875 0.30884748697280884 0.6126591563224792 0.22153371572494507 0.8515483140945435 0.8246981501579285 0.19524165987968445 \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_4.evaluate.json b/ENCSR761TKU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8b7ec214689f6425f755968633fa5196dde9f5ed..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482VSL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_4.fit.json b/ENCSR761TKU/cherimoya.fold_4.fit.json deleted file mode 100644 index 8a79a71be058383e6cde5afdc249133cbb80c0ab..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF482VSL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761TKU/cherimoya.fold_4.log b/ENCSR761TKU/cherimoya.fold_4.log deleted file mode 100644 index 251cc1c8839429732f5eaaf212dd973c1c4ff3bc..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1517 21.383004665374756 3.133340358734131 261.1148681640625 0.2428625226020813 393.714111328125 0.4646429419517517 0.698431 13.213628768920898 True -1 3034 16.799524068832397 0.2982966899871826 303.3908386230469 0.2640141546726227 334.1746520996094 0.5492125749588013 0.7655638 2.4376885890960693 True -2 4551 16.707106351852417 0.2837836742401123 262.1236572265625 0.1801528036594391 318.7974853515625 0.5774726271629333 0.7938843 0.45739439129829407 True -3 6068 16.72312307357788 0.2792496681213379 261.27642822265625 0.2316613644361496 314.0918884277344 0.5850629806518555 0.80408627 0.26750504970550537 True -4 7585 16.675920486450195 0.2840757369995117 249.6539306640625 0.25318536162376404 310.2657470703125 0.5935408473014832 0.8161668 0.22824673354625702 True -5 9102 16.679898500442505 1.4089300632476807 250.5346221923828 0.2994409501552582 309.8835754394531 0.5943595170974731 0.8212224 0.23410376906394958 True -6 10619 16.705111265182495 0.2860102653503418 251.90609741210938 0.23726850748062134 308.4343566894531 0.5981904864311218 0.82744414 0.21889963746070862 True -7 12136 16.69321322441101 0.2869119644165039 240.44287109375 0.21873335540294647 308.8675231933594 0.5968930721282959 0.8256425 0.26957598328590393 False -8 13653 16.698169231414795 0.28685855865478516 247.86407470703125 0.3295624554157257 307.72509765625 0.6000890135765076 0.83525366 0.22225216031074524 True -9 15170 16.671934127807617 0.28118085861206055 289.29296875 0.18326592445373535 306.9005432128906 0.602485716342926 0.8425259 0.18999427556991577 True -10 16687 16.714267015457153 0.27898359298706055 218.41265869140625 0.17241023480892181 306.40850830078125 0.6039707064628601 0.8459873 0.18814583122730255 True -11 18204 16.70070195198059 0.28106045722961426 272.41107177734375 0.20994806289672852 305.82830810546875 0.6052501797676086 0.8531134 0.1667560338973999 True -12 19721 16.697728872299194 0.28124237060546875 265.0069580078125 0.18999651074409485 305.3663330078125 0.6063055396080017 0.8557769 0.1578785926103592 True -13 21238 16.67713761329651 0.284898042678833 232.65211486816406 0.11804668605327606 305.0962219238281 0.6069469451904297 0.8583645 0.15570881962776184 True -14 22755 16.732619524002075 3.081784248352051 277.9068603515625 0.18322357535362244 305.0548400878906 0.6072835326194763 0.86135656 0.15330885350704193 True -15 24272 16.684258460998535 0.28740549087524414 247.44436645507812 0.11978993564844131 305.06939697265625 0.6070806384086609 0.8617303 0.15514619648456573 True -16 25789 16.681113243103027 0.4905846118927002 260.8409423828125 0.12703768908977509 305.3053283691406 0.6062610745429993 0.8605029 0.15804097056388855 False -17 27306 16.680681705474854 0.28226327896118164 280.0403137207031 0.09469693899154663 305.734619140625 0.605063796043396 0.86073583 0.1599234789609909 False -18 28823 16.679018259048462 1.0786361694335938 268.10858154296875 0.059487756341695786 306.091064453125 0.6040374040603638 0.8590519 0.16109751164913177 False -19 30340 16.79491138458252 0.28148484230041504 243.6905975341797 0.10132401436567307 306.3374938964844 0.6033742427825928 0.85553455 0.16285386681556702 False diff --git a/ENCSR761TKU/cherimoya.fold_4.performance.tsv b/ENCSR761TKU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f76e8c74c402ed66c2b5f83bc1c5421640a6655f..0000000000000000000000000000000000000000 --- a/ENCSR761TKU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -305.06939697265625 0.31193119287490845 0.6070806384086609 0.21732307970523834 0.8617302775382996 0.8228031396865845 0.15514619648456573 \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_0.evaluate.json b/ENCSR761ZFA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9fbd4246aa81a7708b67c0a4338af0a47c88a98f..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF121OUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_0.fit.json b/ENCSR761ZFA/cherimoya.fold_0.fit.json deleted file mode 100644 index be592db0dcec455ee214838edd411db90d4592f7..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF121OUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_0.log b/ENCSR761ZFA/cherimoya.fold_0.log deleted file mode 100644 index 275242f453002bd2c565b074eb94bd063cd373b2..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 35.0779767036438 4.543258190155029 200.72567749023438 0.49290549755096436 263.8816223144531 0.1546776294708252 0.6243488 3.202488660812378 True -1 5544 30.20966672897339 0.7412877082824707 214.246826171875 0.6287708282470703 252.18923950195312 0.21098624169826508 0.6844998 0.9247495532035828 True -2 8316 30.211174488067627 0.5622830390930176 190.34239196777344 0.6545473337173462 248.62142944335938 0.2262582927942276 0.69221747 0.464560329914093 True -3 11088 30.258052349090576 0.5487992763519287 171.745361328125 0.7473861575126648 246.90235900878906 0.23176032304763794 0.69902337 0.4507512152194977 True -4 13860 30.219204902648926 0.5580661296844482 176.56475830078125 0.8078069686889648 246.1683349609375 0.23383024334907532 0.70468354 0.5488304495811462 True -5 16632 30.22943091392517 0.5517268180847168 194.49081420898438 0.40306589007377625 245.53829956054688 0.2369696944952011 0.7109668 0.5568345189094543 True -6 19404 30.1472327709198 1.2658801078796387 189.03231811523438 0.981802225112915 244.84104919433594 0.2401801347732544 0.7141177 0.5824333429336548 True -7 22176 30.574413776397705 0.5752532482147217 179.95156860351562 0.7800800800323486 244.33035278320312 0.2423003762960434 0.7203967 0.5834484100341797 True -8 24948 30.181586265563965 12.70114803314209 192.48019409179688 0.4160194993019104 243.83538818359375 0.24528059363365173 0.7239481 0.547438383102417 True -9 27720 35.91799831390381 3.4890213012695312 234.88995361328125 0.5305888056755066 243.598876953125 0.24626588821411133 0.7267168 0.5413112640380859 True -10 30492 30.265112161636353 0.5626611709594727 201.58718872070312 0.49848636984825134 242.9236602783203 0.24994035065174103 0.7270591 0.5405969023704529 True -11 33264 30.23491883277893 0.5613205432891846 211.29830932617188 0.7343298196792603 242.3389892578125 0.2528420388698578 0.72918034 0.5156095027923584 True -12 36036 30.163132667541504 0.552422046661377 224.4483642578125 0.5148133635520935 241.63925170898438 0.2555142939090729 0.73357815 0.4766661822795868 True -13 38808 30.331334590911865 36.58067965507507 208.8044891357422 0.36170679330825806 241.68780517578125 0.25512954592704773 0.7393423 0.43886783719062805 True -14 41580 30.582890272140503 4.424805402755737 192.81640625 0.4370819926261902 241.2957305908203 0.25709038972854614 0.74499357 0.4102555215358734 True -15 44352 30.270463705062866 0.559807538986206 234.11810302734375 0.4349837899208069 241.11048889160156 0.25715991854667664 0.75201523 0.3818650245666504 True -16 47124 30.238579750061035 0.5566644668579102 187.9152069091797 0.44990867376327515 240.8946990966797 0.2586927115917206 0.7573567 0.3535224199295044 True -17 49896 30.331631898880005 38.23975110054016 170.2572479248047 0.45716074109077454 240.71749877929688 0.25984734296798706 0.7609037 0.33578988909721375 True -18 52668 30.567727088928223 3.3881938457489014 182.45193481445312 0.41525256633758545 240.77378845214844 0.2591342628002167 0.76108384 0.33035439252853394 True -19 55440 30.26489281654358 0.5755319595336914 208.4013214111328 0.37071698904037476 240.75558471679688 0.2596476078033447 0.76184595 0.3293386697769165 True diff --git a/ENCSR761ZFA/cherimoya.fold_0.performance.tsv b/ENCSR761ZFA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 13d610cd4222bcfd1d49046bbf7fb44531d1e5c0..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -240.75558471679688 0.5150511264801025 0.2596476376056671 0.06361398100852966 0.7618459463119507 0.7056993842124939 0.3293386697769165 \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_1.evaluate.json b/ENCSR761ZFA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 15fa1a6030ca7d3024e59edfb14b0fb3bc0ce9df..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF121OUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_1.fit.json b/ENCSR761ZFA/cherimoya.fold_1.fit.json deleted file mode 100644 index eefe1296d53ce0364538497f6c9da47b61c0d37f..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF121OUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_1.log b/ENCSR761ZFA/cherimoya.fold_1.log deleted file mode 100644 index c44cc3e38631bd87b1a0f624787545693a8175d6..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.47580814361572 4.372880458831787 250.1318359375 0.9126654863357544 298.1550598144531 0.16436615586280823 0.6315298 3.518439292907715 True -1 5484 30.02648162841797 0.7769248485565186 228.87010192871094 0.8533301949501038 281.67144775390625 0.23001566529273987 0.69230276 1.3892333507537842 True -2 8226 29.880195140838623 2.3388988971710205 201.07952880859375 1.0565786361694336 278.1327209472656 0.2399643063545227 0.71015835 0.700343668460846 True -3 10968 29.818805694580078 0.7095358371734619 221.91375732421875 0.6251334547996521 275.9589538574219 0.24548019468784332 0.7269957 0.6130548715591431 True -4 13710 29.924036741256714 0.7093117237091064 166.74034118652344 0.6321308612823486 275.7684631347656 0.24541383981704712 0.7301905 0.6213342547416687 True -5 16452 29.801957845687866 0.7054996490478516 185.0154571533203 0.5783922076225281 274.4644470214844 0.25123149156570435 0.73694867 0.6818352341651917 True -6 19194 29.83797860145569 0.7043247222900391 202.424560546875 0.5369030237197876 273.53857421875 0.2548566162586212 0.7405226 0.6560176610946655 True -7 21936 29.88851022720337 0.7144579887390137 187.61907958984375 0.7945386171340942 272.8851318359375 0.25743433833122253 0.7413628 0.6539960503578186 True -8 24678 30.41501021385193 18.519103527069092 234.94345092773438 0.4335576295852661 272.744384765625 0.25830191373825073 0.74568343 0.6289042830467224 True -9 27420 29.930150270462036 21.257081031799316 242.15106201171875 0.5030739307403564 271.9994201660156 0.2612239420413971 0.74805367 0.6164189577102661 True -10 30162 30.8667471408844 0.7115449905395508 178.9012451171875 0.8395304083824158 271.22930908203125 0.26443037390708923 0.7550842 0.5676440596580505 True -11 32904 29.815125703811646 0.7169008255004883 204.58770751953125 0.4192027747631073 270.43212890625 0.26807287335395813 0.7577578 0.5399655103683472 True -12 35646 29.833391666412354 0.7065219879150391 177.4209442138672 0.6354926228523254 270.0924377441406 0.26893603801727295 0.76505107 0.5232665538787842 True -13 38388 30.370988607406616 0.8365108966827393 167.8701171875 0.5194838643074036 269.6963806152344 0.27013054490089417 0.77043104 0.4896033704280853 True -14 41130 29.98636245727539 48.962167263031006 206.78341674804688 0.511709988117218 269.1650390625 0.272184818983078 0.7773491 0.43247002363204956 True -15 43872 32.277753829956055 42.429476737976074 177.47760009765625 0.3832213282585144 268.832763671875 0.27296847105026245 0.7841392 0.40292713046073914 True -16 46614 30.827446699142456 21.692501306533813 158.34349060058594 0.3742344379425049 268.61224365234375 0.27432629466056824 0.78906786 0.38016602396965027 True -17 49356 29.886395931243896 0.7065773010253906 185.69195556640625 0.3461054861545563 268.22149658203125 0.27594152092933655 0.7909921 0.3632239103317261 True -18 52098 29.877936601638794 0.722247838973999 186.87454223632812 0.3227473795413971 268.585205078125 0.27373138070106506 0.7910912 0.35965442657470703 True -19 54840 29.894139289855957 1.7515573501586914 179.64111328125 0.27692121267318726 268.9668273925781 0.272108793258667 0.79052585 0.3598420321941376 False diff --git a/ENCSR761ZFA/cherimoya.fold_1.performance.tsv b/ENCSR761ZFA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8a51809be65f9e0be8fbc3969b9cac06992cacae..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -268.585205078125 0.5016026496887207 0.27373138070106506 0.07557342946529388 0.7910912036895752 0.747195303440094 0.35965442657470703 \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_2.evaluate.json b/ENCSR761ZFA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6023298a585e7f4bd45e489e438ca46c141cb7cf..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF121OUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_2.fit.json b/ENCSR761ZFA/cherimoya.fold_2.fit.json deleted file mode 100644 index 22a188c6b90bcd91951b4fc18f58f4cf4fd34095..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF121OUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_2.log b/ENCSR761ZFA/cherimoya.fold_2.log deleted file mode 100644 index 87aaf291d457dd04e7cbfad362f6096202ee87fc..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.03237342834473 4.801652193069458 202.65792846679688 0.9406173825263977 275.1408996582031 0.15713341534137726 0.61145884 3.467270851135254 True -1 5772 31.627253532409668 0.557178258895874 223.44476318359375 0.8031795024871826 260.45355224609375 0.22133758664131165 0.6870952 1.0857375860214233 True -2 8658 31.639785528182983 0.5259499549865723 191.36117553710938 0.865705132484436 257.17584228515625 0.23073484003543854 0.7039585 0.553360641002655 True -3 11544 31.585804224014282 0.5340955257415771 214.35292053222656 0.4067728519439697 255.73031616210938 0.23590634763240814 0.7085163 0.5283622145652771 True -4 14430 32.15564703941345 0.5293979644775391 188.78555297851562 0.5258738994598389 255.2251739501953 0.23784109950065613 0.70842206 0.5876308679580688 False -5 17316 31.62821054458618 0.526357889175415 178.0968017578125 0.6585193276405334 254.83360290527344 0.24057307839393616 0.71085 0.6012750864028931 True -6 20202 31.50141215324402 28.54554295539856 178.90158081054688 0.6608895063400269 253.7627716064453 0.2456245720386505 0.7141909 0.6282556653022766 True -7 23088 32.36686944961548 0.5326066017150879 227.2542724609375 0.5112452507019043 253.1512908935547 0.24782243371009827 0.7134693 0.6143653988838196 False -8 25974 31.548457145690918 0.5349061489105225 216.39044189453125 0.4717399775981903 252.4536590576172 0.2514892816543579 0.719908 0.612489640712738 True -9 28860 31.583471059799194 0.5335211753845215 203.42208862304688 0.46988445520401 251.996337890625 0.25403788685798645 0.72329366 0.6094490885734558 True -10 31746 31.495033979415894 0.5248656272888184 202.13055419921875 0.6405701637268066 251.53480529785156 0.25618141889572144 0.7273077 0.5978847146034241 True -11 34632 31.389243841171265 0.5253829956054688 218.30844116210938 0.5652271509170532 251.0366668701172 0.25784969329833984 0.73412496 0.542231559753418 True -12 37518 31.406793355941772 0.5215229988098145 182.375732421875 0.37317803502082825 250.5004119873047 0.26038485765457153 0.7355109 0.5248453617095947 True -13 40404 31.515259265899658 0.5266861915588379 188.637939453125 0.31581634283065796 250.0379180908203 0.2621278464794159 0.74299544 0.48145654797554016 True -14 43290 31.3962504863739 0.5152249336242676 181.89060974121094 0.2915830910205841 249.5456085205078 0.26388296484947205 0.7507429 0.4357372224330902 True -15 46176 31.399018049240112 0.5264933109283447 191.76934814453125 0.40115785598754883 249.1457061767578 0.2664465010166168 0.7567129 0.4003129303455353 True -16 49062 31.52379083633423 30.066681385040283 183.79916381835938 0.4016888737678528 249.1420440673828 0.26612794399261475 0.7617789 0.3807185888290405 True -17 51948 32.246756076812744 0.5360136032104492 204.48101806640625 0.2439606785774231 249.30072021484375 0.265146940946579 0.7625098 0.361044704914093 True -18 54834 31.468626022338867 0.5335137844085693 192.55752563476562 0.3381766676902771 249.02638244628906 0.26661980152130127 0.7632355 0.35468265414237976 True -19 57720 31.512640714645386 0.6028201580047607 227.76168823242188 0.3007442355155945 249.1549835205078 0.26611635088920593 0.76124024 0.3583146035671234 False diff --git a/ENCSR761ZFA/cherimoya.fold_2.performance.tsv b/ENCSR761ZFA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5ebfee7feac5d27c2f0df94e3c9139687eb12986..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -249.02638244628906 0.5101696252822876 0.2666197717189789 0.06911955028772354 0.7632355093955994 0.7077217102050781 0.35468265414237976 \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_3.evaluate.json b/ENCSR761ZFA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index eebec5dccd400c02ecfcff715b41c003ddccdba2..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF121OUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_3.fit.json b/ENCSR761ZFA/cherimoya.fold_3.fit.json deleted file mode 100644 index 918b634c7f0e4c83ea760c2ae7dc5a4121724b3d..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF121OUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_3.log b/ENCSR761ZFA/cherimoya.fold_3.log deleted file mode 100644 index 6620992a96f64a07b2ee53c35e590769c15d4fbc..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2779 35.76805520057678 30.50304913520813 205.15628051757812 0.866195559501648 283.9056701660156 0.15916307270526886 0.6272899 3.4022583961486816 True -1 5558 30.399969816207886 0.6131820678710938 217.92083740234375 0.8179734945297241 270.9066467285156 0.21917390823364258 0.6903892 1.2488234043121338 True -2 8337 30.352421760559082 0.5749351978302002 184.19024658203125 0.9952863454818726 267.5125427246094 0.229221910238266 0.69466317 0.8576552271842957 True -3 11116 30.432376861572266 9.354727268218994 152.99099731445312 0.7602901458740234 266.5398254394531 0.23223212361335754 0.7075484 0.7403810620307922 True -4 13895 30.324339866638184 2.0988237857818604 188.26416015625 0.6658934354782104 265.8201904296875 0.23637066781520844 0.7117516 0.7224282026290894 True -5 16674 30.5318922996521 0.6019308567047119 175.980224609375 0.6899596452713013 265.1369934082031 0.23925898969173431 0.7189318 0.704502284526825 True -6 19453 30.33944272994995 0.5577454566955566 164.25173950195312 0.6099048852920532 264.3395690917969 0.24235263466835022 0.72568595 0.6784287691116333 True -7 22232 30.267224311828613 0.5620772838592529 206.72811889648438 0.6094619035720825 264.1630859375 0.24285684525966644 0.72816825 0.6525514721870422 True -8 25011 30.248196125030518 0.5571422576904297 182.42449951171875 0.5400071740150452 263.15704345703125 0.24806766211986542 0.73177737 0.6907068490982056 True -9 27790 30.21522283554077 0.5599524974822998 193.5319061279297 0.6521790623664856 262.85894775390625 0.2491150051355362 0.7347284 0.6327723264694214 True -10 30569 30.222870588302612 0.5602254867553711 174.8551483154297 0.9637002944946289 262.60968017578125 0.25112858414649963 0.7352011 0.6010404229164124 True -11 33348 30.26190209388733 0.5631616115570068 185.18505859375 0.4329183101654053 261.947265625 0.2533283829689026 0.7388499 0.5770269632339478 True -12 36127 31.772544384002686 0.8784170150756836 202.47561645507812 0.4622515141963959 261.60845947265625 0.25401175022125244 0.74563205 0.5310360789299011 True -13 38906 31.44977355003357 28.880168199539185 207.96347045898438 0.6166640520095825 261.2848205566406 0.25567010045051575 0.7529112 0.48736831545829773 True -14 41685 30.462767124176025 0.5741794109344482 195.71905517578125 0.3391192555427551 260.8300476074219 0.2580817937850952 0.758226 0.44666966795921326 True -15 44464 30.39646077156067 0.5628960132598877 185.51242065429688 0.40668660402297974 260.5916442871094 0.25882118940353394 0.7618057 0.4114548861980438 True -16 47243 30.28517436981201 0.5528585910797119 194.93096923828125 0.4307064712047577 260.5662536621094 0.2592192590236664 0.7656475 0.3832987844944 True -17 50022 30.603992700576782 27.26255702972412 226.62445068359375 0.36766350269317627 260.3236999511719 0.2599659264087677 0.7679702 0.368329793214798 True -18 52801 30.608535528182983 32.28298258781433 198.0995330810547 0.3167901933193207 260.4006652832031 0.25977960228919983 0.76845396 0.36166855692863464 True -19 55580 31.246297597885132 0.5728764533996582 201.02354431152344 0.42516106367111206 260.4486999511719 0.25979816913604736 0.76736 0.362268328666687 False diff --git a/ENCSR761ZFA/cherimoya.fold_3.performance.tsv b/ENCSR761ZFA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 67a567c72d4fd6cd8831a0ebd33440d5eaf31a95..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -260.4006652832031 0.5098261833190918 0.25977957248687744 0.06950794905424118 0.7684539556503296 0.7137256860733032 0.36166855692863464 \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_4.evaluate.json b/ENCSR761ZFA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4e899a33e7ec596dbbc537b7e42ec3fd67e34d9f..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF121OUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_4.fit.json b/ENCSR761ZFA/cherimoya.fold_4.fit.json deleted file mode 100644 index 180c31f9c482e0a0c879b9ba38702fb7c18335b5..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF121OUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR761ZFA/cherimoya.fold_4.log b/ENCSR761ZFA/cherimoya.fold_4.log deleted file mode 100644 index c39d62ba9497356c2c5e8c4befb2e64e53448d89..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2862 35.76909613609314 3.7953152656555176 189.1414031982422 0.7049610614776611 262.44647216796875 0.15199071168899536 0.61661047 2.355043411254883 True -1 5724 33.88043284416199 20.610783338546753 229.88919067382812 0.7688177824020386 249.93898010253906 0.21201373636722565 0.6734752 0.9996422529220581 True -2 8586 31.238911151885986 44.077088356018066 160.79995727539062 1.001276969909668 247.57839965820312 0.22008547186851501 0.6874008 0.6724192500114441 True -3 11448 31.639108419418335 0.6304399967193604 182.46337890625 0.8523688316345215 246.19007873535156 0.22398874163627625 0.70136267 0.5130814909934998 True -4 14310 31.21873450279236 0.6360795497894287 177.61244201660156 0.5126849412918091 245.49578857421875 0.22810067236423492 0.7024097 0.5518355369567871 True -5 17172 31.166834354400635 0.6344404220581055 180.05322265625 0.4824318289756775 244.9462432861328 0.23040790855884552 0.7085672 0.5998668074607849 True -6 20034 31.17851996421814 0.6310107707977295 191.56594848632812 0.7388863563537598 244.51507568359375 0.23168548941612244 0.711783 0.616597056388855 True -7 22896 31.1714186668396 0.6265609264373779 200.56634521484375 0.4842829704284668 244.2545928955078 0.2341591864824295 0.71720093 0.6191617250442505 True -8 25758 31.188443183898926 1.9590559005737305 216.67320251464844 0.5194225907325745 243.72921752929688 0.23672345280647278 0.72034395 0.6558401584625244 True -9 28620 31.18563151359558 1.240769624710083 201.36944580078125 0.44150084257125854 243.2346954345703 0.2389439046382904 0.72264284 0.6130293011665344 True -10 31482 31.48043417930603 43.55544924736023 197.03134155273438 0.6528825163841248 242.53347778320312 0.2421969473361969 0.7267318 0.5646243691444397 True -11 34344 31.345340490341187 1.4591453075408936 152.58590698242188 0.5412607192993164 242.23414611816406 0.24394865334033966 0.72971183 0.5664791464805603 True -12 37206 31.481063842773438 42.45561909675598 218.6901397705078 0.4850212633609772 242.24073791503906 0.24389132857322693 0.734325 0.5290714502334595 True -13 40068 31.313788652420044 0.6388797760009766 172.49050903320312 0.44850799441337585 241.61036682128906 0.24683350324630737 0.73938465 0.47770705819129944 True -14 42930 31.1930673122406 1.2633287906646729 196.5487060546875 0.3640066087245941 241.47784423828125 0.24779273569583893 0.7453073 0.4127311408519745 True -15 45792 31.235158681869507 1.6255881786346436 223.0380859375 0.3674278259277344 241.21412658691406 0.24830497801303864 0.75150007 0.38332176208496094 True -16 48654 31.25587797164917 1.5170164108276367 240.2017059326172 0.30003467202186584 240.8135223388672 0.25091516971588135 0.75683296 0.3578682243824005 True -17 51516 32.01910161972046 0.6180331707000732 201.03787231445312 0.38983261585235596 240.88368225097656 0.2501194477081299 0.7581692 0.3409990668296814 True -18 54378 31.360464572906494 0.6255402565002441 184.94952392578125 0.28915631771087646 240.7711181640625 0.25066855549812317 0.7597091 0.3347349166870117 True -19 57240 31.23977279663086 0.625201940536499 173.32803344726562 0.253978967666626 240.7833251953125 0.25065523386001587 0.75789326 0.33544448018074036 False diff --git a/ENCSR761ZFA/cherimoya.fold_4.performance.tsv b/ENCSR761ZFA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 22735a7a5867feb85d1d4497069dc78f3694feb3..0000000000000000000000000000000000000000 --- a/ENCSR761ZFA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -240.7711181640625 0.5186928510665894 0.25066855549812317 0.06267017126083374 0.7597091197967529 0.7009022235870361 0.3347349166870117 \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_0.evaluate.json b/ENCSR762FCX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1a1ef6db4325bc5a8d113e4e834fbc38974595e1..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF816LFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_0.fit.json b/ENCSR762FCX/cherimoya.fold_0.fit.json deleted file mode 100644 index 7699c21e499570a23f6139d220968ce161e5e1cf..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF816LFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_0.log b/ENCSR762FCX/cherimoya.fold_0.log deleted file mode 100644 index 11d01553ea766445f7617a7bc440d6a35a699323..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 34.79715418815613 14.941948175430298 152.52667236328125 0.6760088205337524 242.771484375 0.1348426789045334 0.66538936 3.082927703857422 True -1 5526 30.38507866859436 1.2419312000274658 175.65875244140625 0.481012761592865 234.47747802734375 0.17558026313781738 0.71707255 1.4053754806518555 True -2 8289 30.3914475440979 0.7031905651092529 198.06716918945312 0.6144708395004272 231.15347290039062 0.1889820396900177 0.73608124 0.8752548694610596 True -3 11052 30.585851669311523 0.8252298831939697 198.10044860839844 0.8481082916259766 229.9453582763672 0.19205230474472046 0.7459965 0.7946252226829529 True -4 13815 30.535707235336304 0.5389909744262695 176.97161865234375 0.7102251052856445 229.4487762451172 0.1935330033302307 0.75024086 0.7718563079833984 True -5 16578 30.307640075683594 0.5415811538696289 151.97279357910156 0.7693917751312256 228.99371337890625 0.19494383037090302 0.7599275 0.7769057750701904 True -6 19341 31.128114700317383 0.5376684665679932 153.54595947265625 0.6213513016700745 228.05255126953125 0.20026586949825287 0.76580685 0.7483125329017639 True -7 22104 30.408462047576904 0.5414505004882812 159.15155029296875 0.7571905851364136 227.8126220703125 0.2017129510641098 0.7688989 0.6680478453636169 True -8 24867 30.407207012176514 0.5427913665771484 141.0738525390625 0.6565946340560913 227.4045867919922 0.203689306974411 0.7748172 0.6234678626060486 True -9 27630 30.354855060577393 0.5358402729034424 159.9940185546875 0.8621416091918945 227.0049285888672 0.2053045630455017 0.77913344 0.5906708836555481 True -10 30393 30.62388825416565 32.518818855285645 221.87173461914062 0.4354732036590576 226.52264404296875 0.20804913341999054 0.7829376 0.5371652245521545 True -11 33156 31.002471685409546 0.5718128681182861 214.7168426513672 0.639829695224762 226.42205810546875 0.20781973004341125 0.7875349 0.5109997391700745 True -12 35919 29.76840853691101 0.5337724685668945 176.6745147705078 0.6775218844413757 225.9608917236328 0.20979253947734833 0.7916216 0.49264752864837646 True -13 38682 29.746066331863403 0.533045768737793 211.7445068359375 0.6606525778770447 225.55665588378906 0.21161065995693207 0.798156 0.47070541977882385 True -14 41445 29.886500597000122 9.053483247756958 171.6298828125 0.4873138666152954 225.39212036132812 0.21233779191970825 0.8057755 0.4521157443523407 True -15 44208 29.78946566581726 32.64986968040466 191.71270751953125 0.44969165325164795 225.2541961669922 0.21342594921588898 0.8091149 0.43764492869377136 True -16 46971 31.658937692642212 0.5392374992370605 207.638916015625 0.3671916127204895 225.14288330078125 0.2143983691930771 0.8117587 0.42481639981269836 True -17 49734 29.793824911117554 4.4707958698272705 158.81146240234375 0.3755064606666565 225.30538940429688 0.2134609818458557 0.81201345 0.42718377709388733 True -18 52497 29.792917013168335 0.5490498542785645 155.72341918945312 0.4124916195869446 225.37010192871094 0.2129308432340622 0.8094488 0.43368852138519287 False -19 55260 29.789471864700317 14.633744239807129 155.1309356689453 0.2991448640823364 225.33863830566406 0.2128315418958664 0.808812 0.43682995438575745 False diff --git a/ENCSR762FCX/cherimoya.fold_0.performance.tsv b/ENCSR762FCX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6caff7697175732fd3c354abfa678a721aa664f3..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -225.30538940429688 0.5400547385215759 0.2134609967470169 0.057270511984825134 0.8120134472846985 0.758945882320404 0.42718377709388733 \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_1.evaluate.json b/ENCSR762FCX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 60d9a366365c74a238e27103364352663fa951cd..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF816LFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_1.fit.json b/ENCSR762FCX/cherimoya.fold_1.fit.json deleted file mode 100644 index 15a62bebc1aa9edc8124f8674665629bea16106f..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF816LFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_1.log b/ENCSR762FCX/cherimoya.fold_1.log deleted file mode 100644 index 03349647f150aed1411099f95246339dd41ad47b..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 34.77483248710632 3.7645201683044434 217.465087890625 0.8199167251586914 277.2821960449219 0.13984332978725433 0.6705447 3.270150899887085 True -1 5504 30.717554330825806 20.926839113235474 246.04388427734375 0.8353146910667419 267.02545166015625 0.1875518411397934 0.724748 1.6554534435272217 True -2 8256 30.714792728424072 23.465802907943726 155.63681030273438 0.5963037014007568 262.6146545410156 0.20469997823238373 0.74880064 0.9618085026741028 True -3 11008 30.69141173362732 0.7298374176025391 190.22286987304688 0.786112904548645 261.2329406738281 0.20893742144107819 0.7603144 0.8753255605697632 True -4 13760 30.458365440368652 0.7273411750793457 165.1126708984375 0.7438905239105225 260.5354309082031 0.21136800944805145 0.7636411 0.852982223033905 True -5 16512 30.288484811782837 0.726107120513916 125.5406494140625 0.5728425979614258 259.7029113769531 0.21506430208683014 0.77233744 0.882954478263855 True -6 19264 30.37460470199585 0.7309703826904297 148.00531005859375 0.8521476984024048 258.677734375 0.21888259053230286 0.7787215 0.8420232534408569 True -7 22016 30.336868047714233 0.7299404144287109 155.23867797851562 0.7184229493141174 258.3014221191406 0.22043873369693756 0.78462005 0.7712110280990601 True -8 24768 30.31916856765747 0.7227494716644287 170.42970275878906 0.6567617654800415 257.8815612792969 0.2224491387605667 0.78796726 0.7130999565124512 True -9 27520 30.313344478607178 0.7317705154418945 183.74371337890625 0.47294801473617554 257.3489685058594 0.22346587479114532 0.7955786 0.6398326754570007 True -10 30272 30.347026109695435 19.552600860595703 160.8218994140625 0.56399005651474 256.95269775390625 0.22525683045387268 0.8041146 0.5946470499038696 True -11 33024 31.161554098129272 9.55724310874939 186.31838989257812 0.517623782157898 256.5785827636719 0.22640743851661682 0.8082322 0.5448941588401794 True -12 35776 29.844224214553833 38.806389570236206 184.3022003173828 0.4781566560268402 256.0564880371094 0.22872038185596466 0.81423575 0.5083839297294617 True -13 38528 29.868439197540283 2.9281537532806396 168.0179443359375 0.5791186094284058 255.529052734375 0.23070533573627472 0.81983465 0.4734818935394287 True -14 41280 29.680577278137207 1.426422357559204 161.277099609375 0.4580019414424896 255.5565643310547 0.23022475838661194 0.8271 0.4528535306453705 True -15 44032 29.711942434310913 1.1768085956573486 180.13095092773438 0.41783303022384644 255.2342529296875 0.2318050116300583 0.8288627 0.4342411160469055 True -16 46784 29.635822534561157 0.719214677810669 141.19728088378906 0.340192049741745 255.25123596191406 0.23130802810192108 0.83103424 0.4225052297115326 True -17 49536 29.608752489089966 0.7236225605010986 199.4013671875 0.32701051235198975 255.15423583984375 0.2328297197818756 0.8309351 0.42021527886390686 False -18 52288 29.656556367874146 0.7564816474914551 215.64523315429688 0.2683655023574829 255.6389617919922 0.23001965880393982 0.83093125 0.42489147186279297 False -19 55040 29.6596417427063 2.767054796218872 192.4031524658203 0.307411789894104 255.8229522705078 0.22916917502880096 0.82904184 0.4299437403678894 False diff --git a/ENCSR762FCX/cherimoya.fold_1.performance.tsv b/ENCSR762FCX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d22cb9038bda181a82aa529013b178d64d22e668..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -255.25123596191406 0.523811399936676 0.2313079982995987 0.06615789979696274 0.831034243106842 0.799263596534729 0.4225052297115326 \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_2.evaluate.json b/ENCSR762FCX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b953878b8fc1a5d245344e3fb1bbec79e78939b6..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF816LFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_2.fit.json b/ENCSR762FCX/cherimoya.fold_2.fit.json deleted file mode 100644 index c7eca5155e76416ca18b636a67520f1be8cce33d..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF816LFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_2.log b/ENCSR762FCX/cherimoya.fold_2.log deleted file mode 100644 index 45fe861914265b232c2345b0493e291e1f2c9386..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 36.49567174911499 3.559983968734741 202.0994873046875 0.834157407283783 251.96038818359375 0.1411239504814148 0.6622754 2.983065366744995 True -1 5800 31.9067120552063 1.1522791385650635 186.97390747070312 0.7898561954498291 242.18157958984375 0.1886615753173828 0.72948045 1.2454016208648682 True -2 8700 31.954046487808228 0.5474672317504883 237.0189208984375 0.6251879930496216 239.03868103027344 0.19957076013088226 0.7571371 0.7426676154136658 True -3 11600 32.012795209884644 29.624001502990723 175.03224182128906 0.7100979089736938 238.53704833984375 0.19859889149665833 0.76101637 0.6874464750289917 True -4 14500 32.557663917541504 0.5631229877471924 174.74618530273438 0.854459285736084 237.3728790283203 0.20424574613571167 0.7680924 0.8011908531188965 True -5 17400 31.863365650177002 0.5453324317932129 180.76397705078125 0.7435598373413086 236.7576904296875 0.2072107195854187 0.7714135 0.7844822406768799 True -6 20300 31.94809079170227 0.5490968227386475 181.5870361328125 0.7420142889022827 236.077392578125 0.21032239496707916 0.7746692 0.705924391746521 True -7 23200 31.94258689880371 0.542304515838623 213.97647094726562 0.9679577350616455 236.4051971435547 0.2084473967552185 0.7766318 0.7082379460334778 True -8 26100 31.856355905532837 0.5488128662109375 194.56271362304688 0.5023420453071594 235.58558654785156 0.21149396896362305 0.7822275 0.648760974407196 True -9 29000 31.478143453598022 0.5445287227630615 188.63558959960938 0.7361313104629517 235.24159240722656 0.2134544402360916 0.7861265 0.5759632587432861 True -10 31900 31.225532054901123 0.5366621017456055 183.67355346679688 0.7982950210571289 234.91854858398438 0.21466012299060822 0.7919217 0.5553755760192871 True -11 34800 31.25279402732849 0.5354456901550293 153.06658935546875 0.5168940424919128 234.4959716796875 0.21636639535427094 0.79371965 0.5179144144058228 True -12 37700 31.230034828186035 0.5373713970184326 195.5361785888672 0.3272949457168579 234.1286163330078 0.21785983443260193 0.8023595 0.5053898692131042 True -13 40600 31.29468297958374 3.561065673828125 216.0631103515625 0.5197189450263977 233.72225952148438 0.21929831802845 0.8052008 0.47692587971687317 True -14 43500 31.25822114944458 0.5418200492858887 160.92727661132812 0.44086164236068726 233.7272186279297 0.21955376863479614 0.8093868 0.4491296708583832 True -15 46400 31.700896978378296 0.5519015789031982 193.35374450683594 0.4935184121131897 233.4939422607422 0.22062738239765167 0.81457597 0.43292149901390076 True -16 49300 31.495595455169678 0.5352964401245117 178.23471069335938 0.5945342779159546 233.40164184570312 0.22111071646213531 0.81591755 0.424468070268631 True -17 52200 31.27023673057556 0.5291476249694824 175.4611053466797 0.4955180883407593 233.32437133789062 0.2222464382648468 0.81578976 0.4197728633880615 False -18 55100 31.207594633102417 4.012502431869507 203.5836944580078 0.3367213010787964 233.60247802734375 0.22049884498119354 0.8160769 0.4225429892539978 True -19 58000 31.23517084121704 0.5280194282531738 192.48855590820312 0.25347915291786194 233.7135467529297 0.21958540380001068 0.8138788 0.4293421506881714 False diff --git a/ENCSR762FCX/cherimoya.fold_2.performance.tsv b/ENCSR762FCX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5c7a5d90f3882fce74be8850fc799a2d70bf1ea2..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -233.60247802734375 0.5348635911941528 0.22049885988235474 0.06233462691307068 0.8160768747329712 0.7776287794113159 0.4225429892539978 \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_3.evaluate.json b/ENCSR762FCX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c62bdab0b2d68fa0c8346e4b0843073740a8f4ef..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF816LFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_3.fit.json b/ENCSR762FCX/cherimoya.fold_3.fit.json deleted file mode 100644 index aa89b4eb2642fa9fe0c64d59bbea8c5d2689090e..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF816LFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_3.log b/ENCSR762FCX/cherimoya.fold_3.log deleted file mode 100644 index 1cda790ae0f7a1bd0ae578b7d29904d96a6ca7fb..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2795 35.36925530433655 5.181300640106201 175.60678100585938 1.004954218864441 246.54331970214844 0.1363966017961502 0.67114913 3.324368476867676 True -1 5590 30.748148202896118 0.5862512588500977 223.09701538085938 0.7589731216430664 237.61160278320312 0.17943623661994934 0.7378239 1.3478199243545532 True -2 8385 30.738247871398926 0.5715935230255127 196.39468383789062 0.9547829627990723 235.29443359375 0.18837811052799225 0.76279956 0.7518605589866638 True -3 11180 30.75437045097351 0.5714194774627686 197.75942993164062 0.5922254920005798 233.85076904296875 0.19428333640098572 0.7680399 0.7365176677703857 True -4 13975 31.220674991607666 0.5629360675811768 171.06497192382812 0.7485095262527466 233.4551239013672 0.19566425681114197 0.7748623 0.7020598649978638 True -5 16770 30.762877702713013 2.3566360473632812 198.59779357910156 0.5004662871360779 233.04254150390625 0.19793538749217987 0.7775464 0.7472496628761292 True -6 19565 30.750126123428345 0.562786340713501 153.43592834472656 0.4315725266933441 232.728759765625 0.1996561735868454 0.7788094 0.8161250352859497 True -7 22360 30.73237156867981 0.5717580318450928 162.2168731689453 0.49815234541893005 232.09437561035156 0.20234498381614685 0.7808453 0.7499338388442993 True -8 25155 30.37589120864868 0.557903528213501 191.82241821289062 0.4830370843410492 231.69686889648438 0.20524826645851135 0.7861364 0.6577208638191223 True -9 27950 30.24876093864441 0.5771825313568115 162.51309204101562 0.4505253732204437 231.16677856445312 0.20729471743106842 0.78984576 0.5914221405982971 True -10 30745 30.33347201347351 0.5868418216705322 184.46755981445312 0.46123817563056946 231.0450439453125 0.20741355419158936 0.7966 0.5721361041069031 True -11 33540 30.22167134284973 2.2903499603271484 134.07443237304688 0.5390352010726929 231.0709991455078 0.20734205842018127 0.80049914 0.548324465751648 True -12 36335 30.19911241531372 0.5698308944702148 157.36334228515625 0.5174849033355713 230.48934936523438 0.2098371833562851 0.8019039 0.5093048214912415 True -13 39130 30.494037866592407 0.5915536880493164 169.75775146484375 0.44506147503852844 230.03257751464844 0.2125825732946396 0.80728966 0.48552095890045166 True -14 41925 30.604191303253174 31.104509115219116 198.57772827148438 0.7059279680252075 229.86416625976562 0.21327322721481323 0.81352127 0.47121474146842957 True -15 44720 33.40098714828491 0.6017541885375977 219.4403839111328 0.40855827927589417 229.9266357421875 0.21257679164409637 0.8186115 0.4412270188331604 True -16 47515 30.146567821502686 0.5785114765167236 149.4637451171875 0.40878528356552124 229.83265686035156 0.21309888362884521 0.82087916 0.42993101477622986 True -17 50310 30.165996074676514 0.5792462825775146 178.54931640625 0.3519153296947479 230.25343322753906 0.21099425852298737 0.82325697 0.4266716241836548 True -18 53105 30.15400791168213 0.5715668201446533 216.93984985351562 0.3509864807128906 230.19775390625 0.211441308259964 0.8205772 0.43212032318115234 False -19 55900 30.142781734466553 0.5760695934295654 167.04513549804688 0.3935438394546509 229.92807006835938 0.2130478471517563 0.81958514 0.43650686740875244 False diff --git a/ENCSR762FCX/cherimoya.fold_3.performance.tsv b/ENCSR762FCX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d859bfea1ff420d8a6293f6e5e801b639622bbd8..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -230.25343322753906 0.5394687652587891 0.21099428832530975 0.05099720507860184 0.8232569694519043 0.7741329073905945 0.4266716241836548 \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_4.evaluate.json b/ENCSR762FCX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2a7877ef7c01da5c7a7453e76b4483c19275bd24..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF816LFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_4.fit.json b/ENCSR762FCX/cherimoya.fold_4.fit.json deleted file mode 100644 index b35a772b4fedd1f9e09344562a5a539de2de6e1e..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF816LFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762FCX/cherimoya.fold_4.log b/ENCSR762FCX/cherimoya.fold_4.log deleted file mode 100644 index 94361c0ff5b2c36620dd09a3ba10cdcee20dbf2c..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2865 37.2266800403595 3.5852253437042236 182.36776733398438 0.650797963142395 233.41604614257812 0.13146968185901642 0.6643433 2.78995680809021 True -1 5730 31.47339940071106 0.5763287544250488 177.35479736328125 0.5499762296676636 225.3514862060547 0.17466489970684052 0.73352957 1.2963815927505493 True -2 8595 31.483433485031128 0.5649123191833496 178.63616943359375 0.9200098514556885 223.208251953125 0.18107561767101288 0.7509859 0.7382060289382935 True -3 11460 32.00117588043213 45.50649094581604 211.6151123046875 0.8177139759063721 221.926025390625 0.1853809654712677 0.75762415 0.7338994741439819 True -4 14325 32.05069136619568 0.5817515850067139 169.24444580078125 0.7096874117851257 221.2094268798828 0.19024641811847687 0.76378644 0.770713746547699 True -5 17190 31.53101944923401 0.5642597675323486 157.87442016601562 0.5168868899345398 220.60507202148438 0.1922108232975006 0.7692785 0.7671378254890442 True -6 20055 31.428616523742676 0.9026055335998535 163.2960205078125 0.44483762979507446 220.04713439941406 0.1950923055410385 0.7749 0.7481369972229004 True -7 22920 31.520209789276123 3.0056238174438477 200.72950744628906 0.41835737228393555 219.59170532226562 0.19698479771614075 0.7779926 0.6740623712539673 True -8 25785 30.91677951812744 0.5631685256958008 202.78567504882812 0.6218661069869995 219.06288146972656 0.19992373883724213 0.7829128 0.6274721026420593 True -9 28650 30.868942260742188 0.5781655311584473 186.328125 0.660913348197937 218.68865966796875 0.20123699307441711 0.7862735 0.5910155177116394 True -10 31515 30.836310863494873 0.5736098289489746 200.10015869140625 0.5673198699951172 218.61996459960938 0.20138412714004517 0.7919123 0.5516003966331482 True -11 34380 30.958455562591553 0.5638322830200195 180.14739990234375 0.6733120679855347 218.32884216308594 0.20265859365463257 0.7959004 0.5020440220832825 True -12 37245 30.838865280151367 0.6150228977203369 195.31256103515625 0.5172984004020691 217.99264526367188 0.20450140535831451 0.8035799 0.4769774377346039 True -13 40110 30.854372024536133 1.9932479858398438 164.11387634277344 0.5037035942077637 217.65419006347656 0.20608972012996674 0.80623364 0.44532665610313416 True -14 42975 30.911409616470337 0.5556867122650146 183.73068237304688 0.34759950637817383 217.8721923828125 0.20454201102256775 0.81109583 0.43076395988464355 True -15 45840 30.80833077430725 0.5623512268066406 204.71083068847656 0.5696637630462646 217.7787628173828 0.20526421070098877 0.81303734 0.42171695828437805 True -16 48705 33.036367893218994 30.789364337921143 191.95877075195312 0.4055778384208679 217.84422302246094 0.20460477471351624 0.8158952 0.41543281078338623 True -17 51570 30.84182620048523 30.93550968170166 195.7137451171875 0.29921430349349976 217.64463806152344 0.20567189157009125 0.8180634 0.41041111946105957 True -18 54435 32.76732659339905 0.5681207180023193 164.60797119140625 0.4222814440727234 218.02037048339844 0.2039712816476822 0.81712586 0.41311803460121155 False -19 57300 30.892125129699707 0.5582711696624756 193.1884002685547 0.26923835277557373 218.05361938476562 0.20377188920974731 0.81521356 0.41727420687675476 False diff --git a/ENCSR762FCX/cherimoya.fold_4.performance.tsv b/ENCSR762FCX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 47ef74c18e02bb91e4d67f5db3a80312748a4d0e..0000000000000000000000000000000000000000 --- a/ENCSR762FCX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -217.64463806152344 0.5455669164657593 0.20567189157009125 0.05532098561525345 0.8180633783340454 0.7626254558563232 0.41041111946105957 \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_0.evaluate.json b/ENCSR762YFD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6b416ede38a7464993876f2fba835a3fd1b8d3e0..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907GLK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_0.fit.json b/ENCSR762YFD/cherimoya.fold_0.fit.json deleted file mode 100644 index e7586ad23ad5f49f36d3dc4af3809446a83185ec..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF907GLK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_0.log b/ENCSR762YFD/cherimoya.fold_0.log deleted file mode 100644 index 341b17ac536fd832360f51b05a4a39f560a23b83..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1767 23.95536708831787 3.4360640048980713 295.5061340332031 1.1704130172729492 407.4812927246094 0.40007495880126953 0.47866148 11.708386421203613 True -1 3534 19.45589542388916 0.36974382400512695 262.4723815917969 0.632386326789856 346.3515625 0.5193774700164795 0.5578129 4.443264007568359 True -2 5301 19.477171659469604 0.367351770401001 259.32586669921875 1.0645062923431396 324.1471252441406 0.5774723291397095 0.5542291 1.7574728727340698 False -3 7068 19.387848138809204 0.35689640045166016 266.67059326171875 0.7804142236709595 316.3859558105469 0.5939233303070068 0.5980444 0.9238611459732056 True -4 8835 19.410226106643677 0.36599087715148926 235.55140686035156 0.6439170837402344 314.93603515625 0.5979241132736206 0.601996 0.710059404373169 True -5 10602 19.34937620162964 0.3631002902984619 194.18258666992188 0.7180998921394348 313.2905578613281 0.6017189025878906 0.6134886 0.6051271557807922 True -6 12369 19.052529335021973 1.0367143154144287 263.94171142578125 0.5716859102249146 312.5713806152344 0.6037923097610474 0.6104738 0.5856213569641113 False -7 14136 19.17658042907715 0.8008999824523926 200.21347045898438 0.5272088646888733 311.54022216796875 0.6066508889198303 0.621366 0.552849531173706 True -8 15903 19.016764879226685 0.3530881404876709 291.58209228515625 0.6413241028785706 310.3318176269531 0.6097674369812012 0.6310898 0.5208846926689148 True -9 17670 19.015016078948975 0.35899806022644043 230.2350616455078 0.6055787205696106 309.2352294921875 0.6123046875 0.6390478 0.5047999024391174 True -10 19437 19.028698444366455 0.4377310276031494 234.98843383789062 0.7765107154846191 308.2274169921875 0.614825427532196 0.64608306 0.4891357719898224 True -11 21204 19.056132555007935 0.35877227783203125 247.16708374023438 0.3644815683364868 307.3102111816406 0.6169542670249939 0.652913 0.46799755096435547 True -12 22971 19.007936477661133 2.2501988410949707 218.91262817382812 0.3907206654548645 306.6190185546875 0.6186749339103699 0.65996975 0.45320776104927063 True -13 24738 19.051219940185547 0.3598473072052002 229.8282928466797 0.4401789605617523 305.8715515136719 0.6202260851860046 0.6713066 0.43668052554130554 True -14 26505 19.0421142578125 0.36143064498901367 225.32260131835938 0.41834455728530884 305.37384033203125 0.6215217113494873 0.6759423 0.4302275776863098 True -15 28272 19.106127500534058 0.35843348503112793 240.00677490234375 0.3526940941810608 305.1083679199219 0.6218248605728149 0.6819594 0.4255249798297882 True -16 30039 19.093241691589355 0.37006044387817383 226.91799926757812 0.36622849106788635 304.9415588378906 0.6219096183776855 0.68846714 0.4237130284309387 True -17 31806 19.03086566925049 0.3732132911682129 213.73080444335938 0.4891747832298279 305.0753173828125 0.6213254928588867 0.6886365 0.4276173412799835 True -18 33573 19.04760193824768 0.37627410888671875 235.40853881835938 0.3422679901123047 305.2330322265625 0.6207045912742615 0.6868096 0.4324529469013214 False -19 35340 19.134127855300903 0.7684783935546875 226.1650390625 0.38397544622421265 305.342041015625 0.6203563213348389 0.6865688 0.43347370624542236 False diff --git a/ENCSR762YFD/cherimoya.fold_0.performance.tsv b/ENCSR762YFD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 09a90f1336272efb0c857ee0273cde00d5565b23..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -305.0753173828125 0.3146514594554901 0.6213254928588867 0.19470326602458954 0.6886364817619324 0.6323403120040894 0.4276173412799835 \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_1.evaluate.json b/ENCSR762YFD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b56404f127b3f6180ef93b7f9a27db27cdaab087..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907GLK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_1.fit.json b/ENCSR762YFD/cherimoya.fold_1.fit.json deleted file mode 100644 index 6f38e17d47d12e017197d46a87d4bb53e0e1fc57..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF907GLK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_1.log b/ENCSR762YFD/cherimoya.fold_1.log deleted file mode 100644 index 610b40b628b98c8de560eada8fe857891b623707..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1808 24.470015287399292 3.3730123043060303 252.51828002929688 1.1109102964401245 416.5082092285156 0.4148411452770233 0.47756785 10.480000495910645 True -1 3616 20.2196147441864 0.42945027351379395 224.6317138671875 0.8776355981826782 357.1974792480469 0.5313276648521423 0.6007979 4.29866886138916 True -2 5424 19.874658346176147 0.41918277740478516 267.277587890625 0.879091739654541 339.7674255371094 0.5769769549369812 0.6052952 1.2927181720733643 True -3 7232 19.88126540184021 0.40560388565063477 226.0169677734375 0.7813332080841064 333.8428955078125 0.5886151790618896 0.61568445 0.7932851314544678 True -4 9040 19.850173950195312 0.410555362701416 287.74615478515625 0.652616560459137 331.8008117675781 0.5937398076057434 0.636585 0.6272488832473755 True -5 10848 19.890483379364014 0.41227149963378906 225.84417724609375 0.5307183861732483 330.9588623046875 0.5965912938117981 0.6406511 0.5666773915290833 True -6 12656 19.8873770236969 0.40306878089904785 243.36593627929688 0.6068739891052246 330.4580993652344 0.5984389185905457 0.6480675 0.5635523200035095 True -7 14464 19.84931254386902 0.40816831588745117 261.8177795410156 0.6367014646530151 329.6762390136719 0.6006066799163818 0.6524153 0.5507524013519287 True -8 16272 19.92794179916382 0.41150569915771484 260.91326904296875 0.4278934597969055 328.6596984863281 0.6030907034873962 0.65512043 0.521136462688446 True -9 18080 19.946578979492188 0.4160490036010742 240.80313110351562 0.4783613383769989 328.0259704589844 0.6045740842819214 0.6653281 0.50596022605896 True -10 19888 19.90774893760681 0.41750526428222656 208.3612823486328 0.3380088210105896 326.97314453125 0.6070052981376648 0.6710587 0.4784905016422272 True -11 21696 19.899205684661865 0.4090423583984375 251.81166076660156 0.538954496383667 325.78106689453125 0.6099573373794556 0.6811493 0.44214990735054016 True -12 23504 19.929717779159546 0.42505478858947754 221.97915649414062 0.5703948736190796 325.2064514160156 0.6113839745521545 0.6844297 0.445751816034317 True -13 25312 19.931793689727783 0.4213724136352539 237.84033203125 0.4546240568161011 324.1618347167969 0.6132357120513916 0.6919983 0.42966678738594055 True -14 27120 19.920114517211914 0.41002440452575684 222.44479370117188 0.2535390853881836 323.4609375 0.6147739291191101 0.7008505 0.4078317880630493 True -15 28928 20.25653314590454 0.4154660701751709 250.9109649658203 0.46776989102363586 322.92718505859375 0.615806519985199 0.7037841 0.40468642115592957 True -16 30736 19.898283004760742 0.40255022048950195 201.3224334716797 0.4203703999519348 322.64697265625 0.6161350607872009 0.70875865 0.40263596177101135 True -17 32544 20.477306842803955 2.4355673789978027 227.2291717529297 0.4719284474849701 322.5539245605469 0.616043746471405 0.71023965 0.40629392862319946 True -18 34352 19.884690046310425 0.41541624069213867 258.9355163574219 0.2610591650009155 322.62384033203125 0.6156499981880188 0.7068969 0.4098004102706909 False -19 36160 19.812528610229492 0.4011516571044922 230.40988159179688 0.3245980143547058 322.6438903808594 0.6153466105461121 0.703917 0.41596585512161255 False diff --git a/ENCSR762YFD/cherimoya.fold_1.performance.tsv b/ENCSR762YFD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 52e79ac37ebf9a3e789b3f0f5836694134c75799..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -322.5539245605469 0.3110690116882324 0.616043746471405 0.2051309496164322 0.7102396488189697 0.6806146502494812 0.40629392862319946 \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_2.evaluate.json b/ENCSR762YFD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d75c83654658edb107262d0ae2b77aae8b2e622f..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907GLK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_2.fit.json b/ENCSR762YFD/cherimoya.fold_2.fit.json deleted file mode 100644 index 71db35512d1ceb77958bb68df877d942bfd4fab6..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF907GLK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_2.log b/ENCSR762YFD/cherimoya.fold_2.log deleted file mode 100644 index ff50729dd3044494d41eea267cf2637aa9b128fc..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1892 25.20154118537903 12.48880386352539 265.5584716796875 0.7658915519714355 406.9895324707031 0.4112842381000519 0.4987931 11.080567359924316 True -1 3784 21.148260354995728 0.9300370216369629 235.9654083251953 0.4753696918487549 347.39093017578125 0.5326820015907288 0.59397465 4.6132025718688965 True -2 5676 20.861745834350586 0.3164217472076416 228.09661865234375 0.6882452964782715 328.5116882324219 0.578041672706604 0.58773303 1.4578735828399658 False -3 7568 22.07706904411316 21.276485204696655 262.11383056640625 0.700864315032959 323.6238098144531 0.5890434384346008 0.6229456 0.7694336175918579 True -4 9460 22.57917857170105 0.3179190158843994 256.4990234375 0.5211305618286133 321.7481994628906 0.5942625403404236 0.63146764 0.6190808415412903 True -5 11352 20.89139485359192 0.31645750999450684 268.107177734375 0.5341742634773254 320.4230041503906 0.5976387858390808 0.63582253 0.5662401914596558 True -6 13244 20.848577976226807 0.31507349014282227 245.95567321777344 0.5193952322006226 319.195068359375 0.6004710793495178 0.64173424 0.5513788461685181 True -7 15136 20.861233472824097 0.3169386386871338 233.9786376953125 0.5253636837005615 318.13653564453125 0.602907657623291 0.65099376 0.5506165623664856 True -8 17028 20.831397771835327 0.31322669982910156 228.4727020263672 0.548247754573822 317.5916442871094 0.6049528121948242 0.6516821 0.5517014265060425 True -9 18920 20.786550998687744 0.30942416191101074 236.58450317382812 0.4897502064704895 316.3904724121094 0.607361912727356 0.6603237 0.5271994471549988 True -10 20812 20.850498914718628 0.32049107551574707 272.2178649902344 0.5342847108840942 315.2212829589844 0.6098712086677551 0.66339993 0.5063228607177734 True -11 22704 20.847203731536865 0.3181757926940918 201.3056640625 0.6154384016990662 314.15447998046875 0.6123764514923096 0.66902167 0.4827830195426941 True -12 24596 20.84838891029358 0.3192117214202881 198.08334350585938 0.3164806067943573 313.4863586425781 0.6140745878219604 0.6760852 0.4678591787815094 True -13 26488 20.84096097946167 2.653905153274536 251.3042449951172 0.4570399522781372 312.7560119628906 0.6155014634132385 0.6847582 0.45188766717910767 True -14 28380 20.84675168991089 0.34062623977661133 290.50848388671875 0.3841519355773926 312.0900573730469 0.6169498562812805 0.6922968 0.4397456645965576 True -15 30272 20.821244478225708 0.694737434387207 255.70724487304688 0.46570640802383423 311.6772766113281 0.6177988052368164 0.6954059 0.43320420384407043 True -16 32164 20.864557027816772 0.43381595611572266 227.86221313476562 0.3312680721282959 311.37066650390625 0.6181551218032837 0.69941616 0.42713621258735657 True -17 34056 20.857426643371582 0.31114983558654785 251.0819549560547 0.3506779074668884 311.4493713378906 0.6177085041999817 0.70302814 0.4282323718070984 True -18 35948 20.811344385147095 0.3138234615325928 241.49609375 0.3008555471897125 311.5428161621094 0.6171823143959045 0.70242804 0.4261432886123657 False -19 37840 20.828567504882812 0.3101828098297119 239.87252807617188 0.30055591464042664 311.6160888671875 0.6168324947357178 0.7013418 0.4345901310443878 False diff --git a/ENCSR762YFD/cherimoya.fold_2.performance.tsv b/ENCSR762YFD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4dd05c7a7c25d8857492e5db0229a3e0f129eef9..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -311.4493713378906 0.31452083587646484 0.6177085041999817 0.2020309865474701 0.70302814245224 0.6594286561012268 0.4282323718070984 \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_3.evaluate.json b/ENCSR762YFD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8e9839d856defa20b6cd8b28cef3a800a3f7e3e4..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907GLK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_3.fit.json b/ENCSR762YFD/cherimoya.fold_3.fit.json deleted file mode 100644 index b50d47b8e81d55e7dd21f254f16e5f9e827334d4..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF907GLK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_3.log b/ENCSR762YFD/cherimoya.fold_3.log deleted file mode 100644 index 04f366dd7334b6ba531e4f02435ed7e01a57a8a5..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1830 24.854363203048706 2.7838714122772217 238.80007934570312 0.9459378123283386 415.5751037597656 0.41016885638237 0.48298347 12.491438865661621 True -1 3660 20.153040885925293 0.3766334056854248 268.89495849609375 0.769356906414032 349.570556640625 0.5391070246696472 0.56295353 4.935826778411865 True -2 5490 20.155449151992798 0.3735322952270508 231.05758666992188 0.3673178553581238 331.7213134765625 0.5832578539848328 0.5407512 1.6895605325698853 False -3 7320 20.12497353553772 0.3728206157684326 267.5813293457031 0.6126440763473511 326.4109191894531 0.5935080647468567 0.5753129 0.9572359323501587 True -4 9150 20.27876853942871 0.36789608001708984 231.12136840820312 0.6513710021972656 324.380126953125 0.5978142619132996 0.5917052 0.8514705896377563 True -5 10980 20.123297691345215 1.5061452388763428 266.809814453125 0.4737081527709961 323.0391540527344 0.6008747816085815 0.60510975 0.8050283789634705 True -6 12810 20.177016258239746 0.3677647113800049 276.09307861328125 0.569098711013794 321.852294921875 0.6038308143615723 0.61929464 0.6808494925498962 True -7 14640 20.13420605659485 1.3213977813720703 243.29388427734375 0.6341962218284607 321.15728759765625 0.605605959892273 0.62101024 0.6294381618499756 True -8 16470 20.14867353439331 15.094439268112183 237.71829223632812 0.6553517580032349 320.3185729980469 0.6075063943862915 0.6235239 0.634144127368927 True -9 18300 20.82869291305542 0.4288153648376465 236.67347717285156 0.4683343470096588 319.3918151855469 0.609869122505188 0.62870234 0.5848996639251709 True -10 20130 19.758800268173218 0.8954102993011475 264.1287841796875 0.40123486518859863 318.2860412597656 0.6123754978179932 0.6411463 0.5517233610153198 True -11 21960 19.74713969230652 0.36722421646118164 305.13946533203125 0.4206310212612152 317.33038330078125 0.6143810153007507 0.6473379 0.5172704458236694 True -12 23790 19.715799570083618 0.3584926128387451 235.22705078125 0.34265702962875366 316.44879150390625 0.6166168451309204 0.6602398 0.49159568548202515 True -13 25620 19.710098266601562 0.370481014251709 224.58212280273438 0.5003105998039246 315.7598571777344 0.6180644631385803 0.66873306 0.47277793288230896 True -14 27450 19.805857181549072 0.3574256896972656 210.84315490722656 0.40888869762420654 315.3647155761719 0.6192399859428406 0.6778946 0.4597664177417755 True -15 29280 19.691558599472046 0.36101722717285156 205.41793823242188 0.3810335397720337 314.8369140625 0.6201252937316895 0.6815833 0.45508062839508057 True -16 31110 19.688538551330566 1.547959804534912 292.650390625 0.3496331572532654 314.4539489746094 0.6205510497093201 0.6863958 0.4487816095352173 True -17 32940 19.741358518600464 0.35839390754699707 213.17532348632812 0.3271946609020233 314.4394836425781 0.6203315258026123 0.68909055 0.44720232486724854 True -18 34770 19.74284815788269 0.3561086654663086 247.93133544921875 0.3840293884277344 314.55584716796875 0.6197769045829773 0.6875013 0.44934824109077454 False -19 36600 19.687397003173828 0.35633301734924316 230.05833435058594 0.20599204301834106 314.6247253417969 0.6194348931312561 0.6860175 0.4542687237262726 False diff --git a/ENCSR762YFD/cherimoya.fold_3.performance.tsv b/ENCSR762YFD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a6d5fe0fd5b5eb0ba17930cdfecf10c91def130b..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -314.4394836425781 0.3117045760154724 0.6203315258026123 0.20346324145793915 0.6890905499458313 0.6493769288063049 0.44720232486724854 \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_4.evaluate.json b/ENCSR762YFD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 98786d81a31c36db18d853f289f71b6afa50edce..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF907GLK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_4.fit.json b/ENCSR762YFD/cherimoya.fold_4.fit.json deleted file mode 100644 index 8525e740fd6116a212eba212320f4f6289bb4721..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF907GLK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR762YFD/cherimoya.fold_4.log b/ENCSR762YFD/cherimoya.fold_4.log deleted file mode 100644 index 522e6751d1c0463704507d301e029b186b060245..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1893 26.339495182037354 5.980492115020752 237.88925170898438 0.6990084648132324 399.3389587402344 0.4080912470817566 0.51087743 10.240413665771484 True -1 3786 20.820282220840454 0.3823821544647217 268.92596435546875 0.8654477596282959 341.0497131347656 0.531367838382721 0.5584929 3.582615375518799 True -2 5679 20.950453758239746 0.3606135845184326 248.90664672851562 0.7266498804092407 321.12030029296875 0.5808649659156799 0.59390014 1.2883682250976562 True -3 7572 20.881054639816284 0.3659787178039551 245.10202026367188 0.5574217438697815 315.5228576660156 0.592846691608429 0.60110587 0.7825538516044617 True -4 9465 20.83659863471985 0.3658597469329834 275.03350830078125 0.5525830388069153 313.72735595703125 0.5974087119102478 0.61522573 0.5864259004592896 True -5 11358 20.8326096534729 0.3588261604309082 255.10691833496094 0.5984557867050171 312.59039306640625 0.60057133436203 0.6259988 0.5286782383918762 True -6 13251 20.846541166305542 0.3648087978363037 249.82672119140625 0.48280656337738037 311.7618408203125 0.6030232310295105 0.6355675 0.5071089863777161 True -7 15144 20.809854745864868 0.3642449378967285 239.15567016601562 0.5142146944999695 311.02459716796875 0.6054392457008362 0.6394824 0.5228818655014038 True -8 17037 20.829308032989502 0.357196569442749 254.75949096679688 0.6383236050605774 310.0444030761719 0.6076093912124634 0.645357 0.4904804229736328 True -9 18930 21.078425407409668 0.3650362491607666 262.4222106933594 0.5760377645492554 309.34747314453125 0.609285295009613 0.6486742 0.4796658158302307 True -10 20823 20.81059169769287 0.358447790145874 259.66680908203125 0.7083818912506104 308.47705078125 0.6111900210380554 0.65893555 0.4542049169540405 True -11 22716 20.95470428466797 0.36322641372680664 232.42117309570312 0.7539604902267456 307.5663146972656 0.6134202480316162 0.66902435 0.4377431571483612 True -12 24609 20.795943021774292 0.36532139778137207 230.5864715576172 0.5250623226165771 306.6895446777344 0.6153220534324646 0.6718162 0.4302372932434082 True -13 26502 20.818158388137817 0.7561566829681396 292.0101318359375 0.4641173183917999 306.02020263671875 0.6169124245643616 0.6812744 0.4211738407611847 True -14 28395 20.857707738876343 0.37157702445983887 256.8037109375 0.43292081356048584 305.2546691894531 0.6183931231498718 0.68743193 0.41517987847328186 True -15 30288 20.839339017868042 0.3661949634552002 234.22328186035156 0.31116870045661926 304.79241943359375 0.6193117499351501 0.6903572 0.4154077470302582 True -16 32181 20.814382553100586 0.3610391616821289 261.3716735839844 0.32821422815322876 304.552978515625 0.6194900274276733 0.6952382 0.4139690101146698 True -17 34074 20.81909942626953 0.3575875759124756 201.15966796875 0.4119596779346466 304.62738037109375 0.6192862391471863 0.6941583 0.41913488507270813 False -18 35967 20.793863534927368 0.36010313034057617 226.40994262695312 0.37187498807907104 304.7359619140625 0.6188381314277649 0.6929417 0.4272729754447937 False -19 37860 20.923614501953125 14.420209884643555 196.70223999023438 0.2141120284795761 304.7956848144531 0.6185212731361389 0.6925218 0.431855171918869 False diff --git a/ENCSR762YFD/cherimoya.fold_4.performance.tsv b/ENCSR762YFD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 521b6511edd27547952a0b2bdde333d9656e5a55..0000000000000000000000000000000000000000 --- a/ENCSR762YFD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -304.552978515625 0.31464365124702454 0.6194900870323181 0.19935612380504608 0.6952381730079651 0.6435022354125977 0.4139690101146698 \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_0.evaluate.json b/ENCSR765BSU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c6f8f3a6845729829e07996aec70704c1617b81f..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF129GEA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_0.fit.json b/ENCSR765BSU/cherimoya.fold_0.fit.json deleted file mode 100644 index be86b188372c409a75ac29aeee4c9449ecf2349a..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF129GEA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_0.log b/ENCSR765BSU/cherimoya.fold_0.log deleted file mode 100644 index 4d89f8ca87d65734f0444376f1881f1d9d92f742..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 35.416738986968994 3.902971029281616 283.64422607421875 0.7116926908493042 283.9913024902344 0.15393860638141632 0.6158479 2.7153568267822266 True -1 5544 30.4668972492218 0.6175658702850342 236.30438232421875 0.5614050626754761 275.59918212890625 0.19511301815509796 0.6893063 0.8186454176902771 True -2 8316 30.464386701583862 0.6306676864624023 258.56121826171875 0.4453622102737427 272.5014343261719 0.2079990953207016 0.71142393 0.4354890286922455 True -3 11088 30.457218647003174 1.2188665866851807 188.8789520263672 0.48907744884490967 271.2030334472656 0.21326324343681335 0.71793234 0.3918740153312683 True -4 13860 30.49804377555847 0.5666179656982422 228.42098999023438 0.4262691140174866 270.8133239746094 0.21425671875476837 0.7243785 0.42849424481391907 True -5 16632 30.45907497406006 0.5521461963653564 186.96893310546875 0.5434412360191345 270.28302001953125 0.21686720848083496 0.7240453 0.4680984616279602 False -6 19404 30.454902172088623 0.5598452091217041 248.50816345214844 0.35468602180480957 269.7633972167969 0.2187844216823578 0.7233436 0.498796671628952 False -7 22176 30.476248264312744 0.5686399936676025 230.91796875 0.3346944749355316 269.7582702636719 0.21844138205051422 0.7271466 0.4773031175136566 True -8 24948 30.518301963806152 0.5679824352264404 193.08168029785156 0.6419317722320557 269.41082763671875 0.22002948820590973 0.7265512 0.4789867401123047 False -9 27720 30.65768575668335 0.5561354160308838 198.42919921875 0.630202054977417 268.783203125 0.22363276779651642 0.7326809 0.4266470968723297 True -10 30492 30.545519828796387 0.5573804378509521 254.67056274414062 0.3693196177482605 268.60797119140625 0.22473371028900146 0.7343414 0.41633179783821106 True -11 33264 30.45511531829834 0.5580410957336426 203.31356811523438 0.41449952125549316 268.23297119140625 0.22622813284397125 0.73636794 0.4009435176849365 True -12 36036 30.470361471176147 1.3016927242279053 242.38018798828125 0.44306305050849915 267.618408203125 0.2291395664215088 0.74578315 0.3615338206291199 True -13 38808 30.3894305229187 0.5515275001525879 197.35752868652344 0.34234100580215454 267.73297119140625 0.22834672033786774 0.7514219 0.32297512888908386 True -14 41580 29.908371686935425 0.5393178462982178 200.21206665039062 0.34878480434417725 267.14605712890625 0.2307511866092682 0.75679815 0.3078683316707611 True -15 44352 29.886378049850464 0.560800313949585 201.31398010253906 0.46471917629241943 267.0657958984375 0.23108240962028503 0.7620328 0.28921422362327576 True -16 47124 29.897095441818237 0.5392341613769531 229.85952758789062 0.3456484079360962 266.8854675292969 0.2324598878622055 0.76428795 0.2748323082923889 True -17 49896 29.970909357070923 0.5534219741821289 215.5115966796875 0.3424602150917053 267.0347900390625 0.23128116130828857 0.7690081 0.2670414447784424 True -18 52668 29.98710012435913 0.5633659362792969 200.04043579101562 0.2854839265346527 267.37042236328125 0.2292245626449585 0.7681462 0.2645074725151062 False -19 55440 29.931054830551147 0.5642886161804199 196.89572143554688 0.3175532817840576 267.2983093261719 0.2298029065132141 0.76661366 0.26654836535453796 False diff --git a/ENCSR765BSU/cherimoya.fold_0.performance.tsv b/ENCSR765BSU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 08b224727bd44888ab6ce401a4a9175002c6d4b3..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -267.0347900390625 0.5169903635978699 0.23128119111061096 0.06827527284622192 0.7690081000328064 0.7410851120948792 0.2670414447784424 \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_1.evaluate.json b/ENCSR765BSU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 13aea107164680b269d249fce8f6d7f3eaad9574..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF129GEA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_1.fit.json b/ENCSR765BSU/cherimoya.fold_1.fit.json deleted file mode 100644 index 12dd5c66b3c2ab7bf7592dfac79465dd0ea7c55c..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF129GEA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_1.log b/ENCSR765BSU/cherimoya.fold_1.log deleted file mode 100644 index 5988f377e8811c3baa23e52e7ef9b6899462e42b..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 34.71736764907837 4.010783433914185 241.7771759033203 0.4945927858352661 326.30963134765625 0.1622992753982544 0.6037789 3.3508899211883545 True -1 5480 30.1479651927948 2.548093795776367 236.6832733154297 1.0138647556304932 315.8136901855469 0.21033957600593567 0.71138257 0.9237310290336609 True -2 8220 30.249157428741455 0.7828037738800049 253.3179168701172 0.5048894286155701 312.7374572753906 0.2198788821697235 0.7212771 0.5262640118598938 True -3 10960 30.151649475097656 0.7338500022888184 249.39361572265625 0.522852897644043 310.51397705078125 0.2274920642375946 0.73499405 0.44862544536590576 True -4 13700 30.14672827720642 0.953195333480835 183.2144775390625 0.8838058114051819 309.4107666015625 0.23097161948680878 0.74872124 0.43300309777259827 True -5 16440 30.211806535720825 0.8662176132202148 203.32806396484375 0.5968208312988281 308.7978210449219 0.23266518115997314 0.75161195 0.4469512403011322 True -6 19180 30.17388892173767 0.7301959991455078 198.06309509277344 0.7374815940856934 307.893798828125 0.2362695038318634 0.7556972 0.45898231863975525 True -7 21920 30.19545888900757 0.7180061340332031 223.34706115722656 0.6806289553642273 307.5187072753906 0.23757703602313995 0.7568265 0.43130385875701904 True -8 24660 30.12395429611206 0.7062017917633057 252.72169494628906 0.2810554504394531 307.0454406738281 0.23885345458984375 0.7621284 0.42033565044403076 True -9 27400 30.138983249664307 0.7419843673706055 210.75572204589844 0.5254113674163818 306.4396057128906 0.24186599254608154 0.76829606 0.3883994221687317 True -10 30140 30.163739681243896 0.7224907875061035 223.28067016601562 0.41261014342308044 306.1288146972656 0.2423907220363617 0.7679766 0.38531073927879333 False -11 32880 30.115545749664307 0.7380425930023193 255.732177734375 0.4011366367340088 305.4819641113281 0.24543258547782898 0.77217305 0.35466381907463074 True -12 35620 30.28639006614685 1.5448849201202393 230.39146423339844 0.28461140394210815 305.0495300292969 0.24740450084209442 0.77381855 0.36666661500930786 True -13 38360 30.21298098564148 0.7442564964294434 203.51608276367188 0.39840179681777954 304.9624938964844 0.24741394817829132 0.7776697 0.35758906602859497 True -14 41100 30.150989055633545 0.7450995445251465 203.9581298828125 0.3753383159637451 304.7928771972656 0.24745547771453857 0.78565913 0.3326951563358307 True -15 43840 29.701801538467407 0.7255363464355469 246.82823181152344 0.373705118894577 303.8559875488281 0.2525117099285126 0.78861785 0.32174426317214966 True -16 46580 29.66681480407715 0.7308366298675537 224.05560302734375 0.24638353288173676 304.3819580078125 0.24992328882217407 0.79170924 0.30619949102401733 True -17 49320 29.67244577407837 0.7432386875152588 193.5342254638672 0.23936662077903748 304.42022705078125 0.2497774362564087 0.7918038 0.29571792483329773 True -18 52060 29.60059356689453 2.3038828372955322 184.55923461914062 0.3924349546432495 304.5450134277344 0.24900496006011963 0.79075116 0.2921663522720337 False -19 54800 29.660480976104736 0.7077515125274658 196.984130859375 0.20847545564174652 304.4973449707031 0.24934136867523193 0.79159963 0.2920570373535156 False diff --git a/ENCSR765BSU/cherimoya.fold_1.performance.tsv b/ENCSR765BSU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e44f1cbb9048bf60fccebecbaea6392d2e48ed88..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -304.42022705078125 0.4995948076248169 0.24977745115756989 0.07700631767511368 0.791803777217865 0.7748427391052246 0.29571792483329773 \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_2.evaluate.json b/ENCSR765BSU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0f145431cdc59f44d61363af2e2b63790b9f1a4b..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF129GEA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_2.fit.json b/ENCSR765BSU/cherimoya.fold_2.fit.json deleted file mode 100644 index 33acc15f7b78e2ca0ab4e23cdc18d41a3adb5075..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF129GEA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_2.log b/ENCSR765BSU/cherimoya.fold_2.log deleted file mode 100644 index b048a38f52de0631c40515b886fd701608f7b14d..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 36.807279109954834 3.91593599319458 208.14541625976562 0.47098851203918457 293.14129638671875 0.16080206632614136 0.61893487 2.6267645359039307 True -1 5800 32.04913353919983 0.6651127338409424 220.21783447265625 0.352355420589447 283.1227722167969 0.20535999536514282 0.7002379 0.8634820580482483 True -2 8700 32.439008712768555 2.9323055744171143 196.906494140625 0.5392569899559021 280.95672607421875 0.21248333156108856 0.71530515 0.505593478679657 True -3 11600 32.03972291946411 8.675104141235352 227.4241180419922 0.5698778629302979 279.68414306640625 0.21761970221996307 0.7253091 0.41978275775909424 True -4 14500 32.004820108413696 0.6316516399383545 244.32785034179688 0.4956778883934021 279.4295349121094 0.21760572493076324 0.72694725 0.46568024158477783 True -5 17400 31.994101762771606 0.5702428817749023 230.4383087158203 0.4252455234527588 278.9346923828125 0.21933434903621674 0.730271 0.39699745178222656 True -6 20300 32.17577362060547 21.78295087814331 201.68524169921875 0.3901020288467407 278.3235778808594 0.2225276678800583 0.73115695 0.4229050576686859 True -7 23200 32.065226316452026 1.1382904052734375 209.11520385742188 0.5337652564048767 277.8133850097656 0.22461870312690735 0.73636895 0.3983648419380188 True -8 26100 31.977509021759033 0.5630471706390381 244.54986572265625 0.38141465187072754 277.4107666015625 0.22634010016918182 0.73921293 0.3744201958179474 True -9 29000 32.17360877990723 0.5634462833404541 195.05377197265625 0.6079362630844116 276.9190368652344 0.22877658903598785 0.7442074 0.353488951921463 True -10 31900 32.14655375480652 10.76232647895813 208.1739501953125 0.4192134439945221 276.61273193359375 0.22936508059501648 0.7464505 0.3425968289375305 True -11 34800 32.02612233161926 0.5659453868865967 228.77061462402344 0.3504783809185028 276.333984375 0.23077844083309174 0.7472017 0.34784838557243347 True -12 37700 32.04464101791382 0.564849853515625 180.0718536376953 0.6825881004333496 275.9546203613281 0.2329811304807663 0.7510863 0.3415207862854004 True -13 40600 31.930699586868286 0.556464433670044 260.522216796875 0.2984430491924286 275.3975524902344 0.23534303903579712 0.75570536 0.3268480896949768 True -14 43500 32.00182056427002 0.581202507019043 244.07907104492188 0.3865165114402771 275.23211669921875 0.23594693839550018 0.7590745 0.3118545711040497 True -15 46400 32.04442119598389 0.676854133605957 239.48138427734375 0.2914333641529083 275.1563720703125 0.2361854761838913 0.76412594 0.3032231628894806 True -16 49300 32.01072096824646 0.5613255500793457 211.36293029785156 0.3651081323623657 275.1863098144531 0.23598499596118927 0.7679394 0.2919224798679352 True -17 52200 32.02648115158081 16.747009992599487 214.70535278320312 0.23394721746444702 274.9868469238281 0.23702113330364227 0.76761824 0.29078155755996704 False -18 55100 31.952242374420166 1.1660034656524658 192.35342407226562 0.24912236630916595 275.5130615234375 0.2337552160024643 0.7680942 0.292085736989975 True -19 58000 31.4586763381958 0.5574517250061035 201.78619384765625 0.3514695465564728 275.4056701660156 0.23493441939353943 0.7661752 0.2922631800174713 False diff --git a/ENCSR765BSU/cherimoya.fold_2.performance.tsv b/ENCSR765BSU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 62a7a3dff51b456c2ddfa7bba25c915e29d7ff2e..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.5130615234375 0.5133777260780334 0.2337552160024643 0.06529664248228073 0.7680941820144653 0.7478579878807068 0.292085736989975 \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_3.evaluate.json b/ENCSR765BSU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 77cc02dabea8e484bb0b2acf205d2394cc2faedd..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF129GEA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_3.fit.json b/ENCSR765BSU/cherimoya.fold_3.fit.json deleted file mode 100644 index 4b388cc54adb1b0af0c797da0060d003c2f0d261..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF129GEA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_3.log b/ENCSR765BSU/cherimoya.fold_3.log deleted file mode 100644 index 34b2201c087ce2d39d57364339dca09eb1009bc8..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2788 35.58872866630554 4.087815046310425 217.60592651367188 0.4962930381298065 309.8163757324219 0.16302542388439178 0.62650144 3.1111302375793457 True -1 5576 30.80801224708557 0.6854381561279297 221.36398315429688 0.48599034547805786 299.7322692871094 0.20804111659526825 0.70654875 1.0235075950622559 True -2 8364 30.836748600006104 0.6520686149597168 191.8882293701172 0.7109521627426147 297.38714599609375 0.2152225226163864 0.7367867 0.6265996098518372 True -3 11152 30.859923362731934 0.6604340076446533 201.40853881835938 0.5581964254379272 296.4088134765625 0.21800854802131653 0.7439141 0.5380135774612427 True -4 13940 30.766693830490112 0.5746972560882568 223.24256896972656 0.5241879224777222 296.02044677734375 0.2179926037788391 0.7467842 0.48577266931533813 True -5 16728 30.767014265060425 0.6751861572265625 201.60873413085938 0.47075092792510986 295.1285095214844 0.22230184078216553 0.7385606 0.5240542888641357 False -6 19516 30.821279048919678 0.5901391506195068 197.97637939453125 0.44148311018943787 294.7931823730469 0.2237018495798111 0.74394625 0.4769439399242401 False -7 22304 30.92253041267395 0.5988273620605469 213.3980712890625 0.5841422080993652 294.3851623535156 0.22538426518440247 0.7414923 0.47668391466140747 False -8 25092 30.73836588859558 0.59059739112854 243.06422424316406 0.4534393548965454 293.9942626953125 0.22695288062095642 0.74651587 0.4456082284450531 False -9 27880 30.717028617858887 0.5977368354797363 253.63803100585938 0.44952821731567383 293.69085693359375 0.22814281284809113 0.74805844 0.4178411364555359 True -10 30668 30.71601629257202 0.6345891952514648 234.8953094482422 0.5006030797958374 293.2505187988281 0.22998003661632538 0.7525216 0.4067845940589905 True -11 33456 30.674583673477173 0.6049749851226807 257.2981262207031 0.44450920820236206 293.2674255371094 0.2298930287361145 0.7571641 0.4026382267475128 True -12 36244 30.704294204711914 0.5880491733551025 208.35629272460938 0.5166723132133484 292.9896545410156 0.2308291345834732 0.7630426 0.3739626109600067 True -13 39032 30.692114114761353 0.6015918254852295 238.9912109375 0.2866080403327942 292.37677001953125 0.23408852517604828 0.7680322 0.3555185794830322 True -14 41820 30.68426752090454 0.6135625839233398 252.46763610839844 0.3691635727882385 291.9270324707031 0.23581121861934662 0.7719957 0.33945250511169434 True -15 44608 30.711519956588745 0.5783250331878662 219.60293579101562 0.26396656036376953 292.2952575683594 0.23393528163433075 0.7752722 0.3315010666847229 True -16 47396 30.739140272140503 1.1486780643463135 236.11233520507812 0.22613173723220825 292.3439636230469 0.23306523263454437 0.77877855 0.3094571530818939 True -17 50184 30.852994203567505 0.5825731754302979 202.34039306640625 0.28390538692474365 292.20989990234375 0.23482617735862732 0.78212965 0.3043930232524872 True -18 52972 30.77698278427124 6.827466249465942 190.5635986328125 0.29527080059051514 292.3359069824219 0.2337728589773178 0.782775 0.29887276887893677 True -19 55760 30.58265447616577 0.5993561744689941 222.96678161621094 0.2894552946090698 292.4685363769531 0.2330130785703659 0.7837924 0.29726138710975647 True diff --git a/ENCSR765BSU/cherimoya.fold_3.performance.tsv b/ENCSR765BSU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3d50743150db0e0722ea3f47d2b7af98bbcf358b..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -292.4685363769531 0.5090879797935486 0.2330130636692047 0.07089048624038696 0.7837923765182495 0.7562761306762695 0.29726138710975647 \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_4.evaluate.json b/ENCSR765BSU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 994e663dd3a8a7c9e73b2eaba39c033dc26e000c..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF129GEA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_4.fit.json b/ENCSR765BSU/cherimoya.fold_4.fit.json deleted file mode 100644 index 8a0f2bb01704f605e26a1c01a625d43f13e08d19..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF129GEA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR765BSU/cherimoya.fold_4.log b/ENCSR765BSU/cherimoya.fold_4.log deleted file mode 100644 index 25d370a609831314d537d4d2c23ebaa56eec944d..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2854 36.38553309440613 4.077490329742432 206.09686279296875 0.9354061484336853 286.4785461425781 0.15686765313148499 0.6246772 2.502525806427002 True -1 5708 31.60591721534729 0.6257376670837402 216.44976806640625 0.6281244158744812 278.1150207519531 0.19687747955322266 0.6982984 0.8526760935783386 True -2 8562 31.559765815734863 2.4365007877349854 225.0128173828125 0.5164667367935181 275.34771728515625 0.20787659287452698 0.72180253 0.5287806391716003 True -3 11416 31.471766233444214 22.35768961906433 243.48338317871094 0.5506538152694702 274.4843444824219 0.20953892171382904 0.7276742 0.4331241846084595 True -4 14270 31.847362995147705 10.501291990280151 220.97471618652344 0.6998788714408875 273.91436767578125 0.2123827487230301 0.72822934 0.4648256301879883 True -5 17124 32.00205087661743 0.6718974113464355 232.5514678955078 0.44479578733444214 273.7899475097656 0.2121436893939972 0.7314613 0.4524417817592621 True -6 19978 31.506279945373535 0.6172022819519043 239.8260040283203 0.3562169075012207 273.220947265625 0.21470686793327332 0.72456515 0.44491055607795715 False -7 22832 31.44786047935486 0.6055002212524414 208.78549194335938 0.6214370727539062 273.206298828125 0.21428169310092926 0.7314223 0.4654111862182617 False -8 25686 31.431585788726807 0.6177661418914795 210.7644500732422 0.6007692813873291 272.5847473144531 0.21798023581504822 0.73599005 0.455620676279068 True -9 28540 31.48645853996277 0.5989649295806885 183.25411987304688 0.6456548571586609 271.73785400390625 0.22269505262374878 0.7417351 0.4123026430606842 True -10 31394 31.460283041000366 0.6280887126922607 237.30943298339844 0.3645690083503723 271.7815856933594 0.22223496437072754 0.7459318 0.384391725063324 True -11 34248 31.47281312942505 2.5307505130767822 215.24661254882812 0.22706086933612823 271.173095703125 0.22504790127277374 0.7486837 0.35901033878326416 True -12 37102 31.533565998077393 0.6142051219940186 254.46849060058594 0.4300020635128021 270.8013000488281 0.22693254053592682 0.75509155 0.34599465131759644 True -13 39956 31.531141996383667 0.6200456619262695 206.04739379882812 0.3381863832473755 271.0393371582031 0.224971741437912 0.7590134 0.3273628354072571 True -14 42810 31.50481939315796 0.6131930351257324 221.59410095214844 0.3260515332221985 270.5714111328125 0.22697971761226654 0.7638819 0.3089236915111542 True -15 45664 31.49404764175415 0.6067042350769043 242.1245880126953 0.2998795509338379 270.4880065917969 0.2277086079120636 0.7667206 0.290875107049942 True -16 48518 31.494681358337402 0.6198222637176514 195.27113342285156 0.40304991602897644 270.5874328613281 0.22695645689964294 0.7740016 0.2779878079891205 True -17 51372 30.902100324630737 14.38145399093628 196.42144775390625 0.3928028345108032 270.4134826660156 0.2281278818845749 0.7736553 0.26821377873420715 False -18 54226 31.024149894714355 0.607292652130127 258.3906555175781 0.3861198127269745 270.71343994140625 0.22680266201496124 0.77534205 0.2652665972709656 True -19 57080 30.907042503356934 0.6093811988830566 201.65994262695312 0.3087088465690613 270.4493408203125 0.22828520834445953 0.7720137 0.26893308758735657 False diff --git a/ENCSR765BSU/cherimoya.fold_4.performance.tsv b/ENCSR765BSU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 42a4aeb74067e8800511db7c08fb55ef4a2da65b..0000000000000000000000000000000000000000 --- a/ENCSR765BSU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -270.71343994140625 0.5176052451133728 0.22680266201496124 0.06553827226161957 0.7753420472145081 0.7428086996078491 0.2652665972709656 \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_0.evaluate.json b/ENCSR768OLL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index df33947fdea294d5f28e96d1710165cae94a107b..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF418VOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_0.fit.json b/ENCSR768OLL/cherimoya.fold_0.fit.json deleted file mode 100644 index 52f9094b11a052abc79913af323a703f5b1e278d..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF418VOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_0.log b/ENCSR768OLL/cherimoya.fold_0.log deleted file mode 100644 index f1cfce41b6e1571a166adbcf15fb22dd851743d9..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2812 35.66994595527649 3.7209417819976807 1223.2442626953125 0.9846745133399963 1554.4244384765625 0.23807775974273682 0.79517704 8.123825073242188 True -1 5624 30.82430911064148 0.7536420822143555 1091.537353515625 0.7420141696929932 1465.5966796875 0.3104417026042938 0.823544 1.3429067134857178 True -2 8436 30.880281686782837 0.5665469169616699 986.6016845703125 0.8270748853683472 1443.030517578125 0.3223366141319275 0.8233379 0.7506052851676941 False -3 11248 30.81095814704895 0.5581953525543213 1188.388671875 0.49090737104415894 1432.0950927734375 0.32761701941490173 0.829593 0.5697191953659058 True -4 14060 30.88592505455017 1.8227078914642334 994.2669677734375 0.5976157188415527 1427.863525390625 0.3296143710613251 0.8305137 0.5206935405731201 True -5 16872 30.93980312347412 0.6263659000396729 1233.837890625 0.643212080001831 1424.7984619140625 0.33168578147888184 0.83035487 0.4941830039024353 False -6 19684 31.0807683467865 0.584136962890625 1121.3974609375 0.41509467363357544 1419.8868408203125 0.33542412519454956 0.83347243 0.5267589688301086 True -7 22496 30.983381986618042 0.6031138896942139 997.8853149414062 0.7041240334510803 1420.798583984375 0.33342671394348145 0.83598214 0.5104011297225952 True -8 25308 30.932363510131836 1.515697956085205 1223.59716796875 0.7029891014099121 1416.248291015625 0.3373325765132904 0.8389928 0.4962589740753174 True -9 28120 30.88434934616089 0.5698683261871338 1228.2047119140625 0.31758904457092285 1414.349365234375 0.3389492630958557 0.84119743 0.48203927278518677 True -10 30932 30.915112018585205 0.53395676612854 1035.639892578125 0.37330466508865356 1411.0328369140625 0.34094178676605225 0.84389436 0.4331352114677429 True -11 33744 31.008581399917603 9.753438234329224 1270.771484375 0.4224172830581665 1408.1407470703125 0.34302687644958496 0.84564376 0.4072266221046448 True -12 36556 31.0179123878479 0.570044994354248 1021.1857299804688 0.36701661348342896 1403.4119873046875 0.34657028317451477 0.85148406 0.3669797480106354 True -13 39368 31.011685609817505 0.5990526676177979 1214.862060546875 0.4775155484676361 1400.1190185546875 0.3486427366733551 0.85366976 0.3415113091468811 True -14 42180 30.94530439376831 0.5811560153961182 1070.839599609375 0.36894503235816956 1400.81982421875 0.34723013639450073 0.85810846 0.31086066365242004 True -15 44992 30.91576075553894 1.9238312244415283 1113.89208984375 0.39330607652664185 1399.5938720703125 0.34910640120506287 0.86100733 0.29108312726020813 True -16 47804 30.921432971954346 0.5794031620025635 1218.3104248046875 0.16357457637786865 1399.7738037109375 0.34851107001304626 0.860238 0.28940349817276 False -17 50616 31.016634225845337 0.5829825401306152 1105.703125 0.434853732585907 1401.1436767578125 0.34803760051727295 0.85902655 0.2870792746543884 False -18 53428 31.06259512901306 0.5744447708129883 1163.171630859375 0.30879145860671997 1404.878173828125 0.34493935108184814 0.85994285 0.2831996977329254 False -19 56240 31.04001498222351 0.5718173980712891 1078.984619140625 0.2402312159538269 1405.420166015625 0.34522414207458496 0.8597288 0.284792423248291 False diff --git a/ENCSR768OLL/cherimoya.fold_0.performance.tsv b/ENCSR768OLL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8403eb06e9f83e7ea626715f0b1fd731f15167ac..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1399.5938720703125 0.3298357129096985 0.34910643100738525 0.21797175705432892 0.8610073328018188 0.8535457253456116 0.29108312726020813 \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_1.evaluate.json b/ENCSR768OLL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 157cb329b6d06506cd4f1d05a50016c465892df1..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF418VOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_1.fit.json b/ENCSR768OLL/cherimoya.fold_1.fit.json deleted file mode 100644 index 81209706002f4fbcd446b195bb576f54f8c2d824..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF418VOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_1.log b/ENCSR768OLL/cherimoya.fold_1.log deleted file mode 100644 index 33f58fbbc5d84cb2418cf17de6f2847b4c48fbb2..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2708 35.8640718460083 4.462914228439331 1199.417236328125 0.5036652684211731 1775.805908203125 0.25056785345077515 0.77062744 12.032445907592773 True -1 5416 29.816405296325684 12.772485733032227 1105.5601806640625 1.1329562664031982 1675.223876953125 0.3252089321613312 0.8163447 1.586179494857788 True -2 8124 29.333511352539062 0.8587262630462646 1341.622802734375 0.598627507686615 1641.326171875 0.34258419275283813 0.83261925 0.7102947235107422 True -3 10832 29.312015771865845 0.8315999507904053 1251.798583984375 0.6205699443817139 1627.9122314453125 0.34931036829948425 0.8333454 0.5940606594085693 True -4 13540 29.176482677459717 0.781463623046875 1032.077880859375 0.5879193544387817 1618.76611328125 0.35434287786483765 0.8382853 0.5079727172851562 True -5 16248 29.193098545074463 0.7765316963195801 1143.4671630859375 0.45893678069114685 1618.8992919921875 0.3539319336414337 0.8348514 0.4680890738964081 False -6 18956 29.17460870742798 0.7776193618774414 1138.84375 0.3724900186061859 1611.6009521484375 0.35764139890670776 0.84034026 0.44925692677497864 True -7 21664 29.26705241203308 0.7685790061950684 1157.2744140625 0.6381253004074097 1607.85791015625 0.36075639724731445 0.8417362 0.4581284523010254 True -8 24372 29.232576847076416 0.7733442783355713 1196.9912109375 0.5282139778137207 1606.315673828125 0.36039912700653076 0.84249216 0.47179654240608215 True -9 27080 29.16705870628357 0.7773058414459229 1176.501708984375 0.4657690227031708 1598.577392578125 0.36622732877731323 0.84605926 0.4552313983440399 True -10 29788 29.184066772460938 0.7765762805938721 1198.751953125 0.4842435121536255 1592.366455078125 0.3706567585468292 0.8488196 0.4088945686817169 True -11 32496 29.1840181350708 2.2689480781555176 1308.428955078125 0.26654356718063354 1590.0723876953125 0.37135833501815796 0.85349965 0.3817950189113617 True -12 35204 29.174397468566895 0.7820079326629639 1068.763427734375 0.6107501983642578 1587.326171875 0.3725912272930145 0.85923564 0.36667653918266296 True -13 37912 29.161238193511963 0.7636256217956543 960.3614501953125 0.5672985315322876 1585.890869140625 0.3740561604499817 0.8637114 0.3318314552307129 True -14 40620 29.289106607437134 0.7590799331665039 1033.224365234375 0.40128615498542786 1584.8616943359375 0.3744022846221924 0.8682745 0.3076150119304657 True -15 43328 29.134841442108154 0.7768604755401611 948.8587646484375 0.3794823884963989 1585.6053466796875 0.3733653426170349 0.8682048 0.2995256185531616 False -16 46036 29.154998779296875 0.7711238861083984 1114.5479736328125 0.36932796239852905 1582.3743896484375 0.3756808936595917 0.86781174 0.29283052682876587 False -17 48744 29.158860683441162 0.761512279510498 988.7083740234375 0.5310837030410767 1589.400146484375 0.3700937032699585 0.86897224 0.28914424777030945 True -18 51452 29.14612650871277 0.7588715553283691 1050.8017578125 0.2500552237033844 1589.8006591796875 0.3709658980369568 0.8666561 0.29367464780807495 False -19 54160 29.1588613986969 0.7716281414031982 1346.837646484375 0.22144636511802673 1593.62158203125 0.367795467376709 0.8654208 0.29568174481391907 False diff --git a/ENCSR768OLL/cherimoya.fold_1.performance.tsv b/ENCSR768OLL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0c6a2c585408cfe0599720b88712c491d0b6476e..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1589.400146484375 0.3020225763320923 0.3700937330722809 0.24483749270439148 0.8689722418785095 0.8787133097648621 0.28914424777030945 \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_2.evaluate.json b/ENCSR768OLL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f4ea49bb0c2c359181622f03ded8f34cd4171354..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF418VOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_2.fit.json b/ENCSR768OLL/cherimoya.fold_2.fit.json deleted file mode 100644 index 6aa8fd19e4104e7542c635b9ced5a635d04a7d43..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF418VOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_2.log b/ENCSR768OLL/cherimoya.fold_2.log deleted file mode 100644 index 014e10abc52db8d751aa5a7d198fa8cc5722a113..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2912 36.8195219039917 3.624534845352173 1236.042236328125 0.6066900491714478 1627.529541015625 0.2476174235343933 0.78864783 7.7883758544921875 True -1 5824 32.01813983917236 0.5770673751831055 1197.3349609375 0.511908769607544 1530.0335693359375 0.322841614484787 0.81547475 1.0469640493392944 True -2 8736 31.53731369972229 0.5507409572601318 1191.9256591796875 0.5784685015678406 1509.216796875 0.3324752748012543 0.82724625 0.537236213684082 True -3 11648 31.321720123291016 0.5451905727386475 1045.1334228515625 0.5279040336608887 1498.501708984375 0.33694180846214294 0.82500106 0.5037873387336731 False -4 14560 31.34687304496765 0.5497195720672607 1256.9488525390625 0.4841684103012085 1497.7738037109375 0.3380609452724457 0.8281741 0.4552147686481476 True -5 17472 31.71754288673401 0.5494751930236816 1251.367431640625 0.430767297744751 1492.1328125 0.3416653871536255 0.8275063 0.48193809390068054 False -6 20384 31.360908031463623 0.549314022064209 1268.6534423828125 0.4376893639564514 1489.205078125 0.3431233763694763 0.8289142 0.48644089698791504 True -7 23296 31.382582426071167 0.5499145984649658 1273.444580078125 0.399711012840271 1482.6424560546875 0.34917235374450684 0.8323666 0.5105335712432861 True -8 26208 31.406104564666748 0.5503997802734375 1080.4345703125 0.576248288154602 1482.1170654296875 0.3489992022514343 0.83557934 0.4528266191482544 True -9 29120 31.49603533744812 0.5449080467224121 1319.0518798828125 0.34739917516708374 1477.2230224609375 0.35278546810150146 0.8357994 0.4357546269893646 True -10 32032 31.44705319404602 0.5515832901000977 1145.78759765625 0.6933531165122986 1474.625244140625 0.3543480932712555 0.83671165 0.42067867517471313 True -11 34944 31.3892924785614 0.5518176555633545 1306.4659423828125 0.33700430393218994 1473.4619140625 0.3543218970298767 0.83944917 0.3931817412376404 True -12 37856 31.43485999107361 0.5504655838012695 1203.90576171875 0.5491470694541931 1469.219970703125 0.3584819436073303 0.84614503 0.3906279504299164 True -13 40768 31.38823127746582 0.5452067852020264 1012.0033569335938 0.5512163043022156 1466.537109375 0.35973024368286133 0.84643054 0.3693772852420807 True -14 43680 31.3298921585083 0.5496871471405029 1056.97705078125 0.30513423681259155 1462.489013671875 0.36199912428855896 0.85056204 0.32139259576797485 True -15 46592 31.37716317176819 0.5463998317718506 1256.31298828125 0.3688501715660095 1463.3631591796875 0.361299604177475 0.85486853 0.3048599660396576 True -16 49504 31.41544508934021 0.551271915435791 1420.37451171875 0.45599839091300964 1464.517822265625 0.36011359095573425 0.8577155 0.2929324209690094 True -17 52416 31.400423765182495 0.5509040355682373 1040.7349853515625 0.24617213010787964 1467.8038330078125 0.3589046001434326 0.85772675 0.28606006503105164 True -18 55328 31.44240427017212 0.54508376121521 1029.1226806640625 0.4278624653816223 1470.35498046875 0.35718005895614624 0.85787356 0.2837238609790802 True -19 58240 31.400514841079712 0.5503721237182617 1130.9925537109375 0.2323414385318756 1470.582763671875 0.35689449310302734 0.8569033 0.2850951552391052 False diff --git a/ENCSR768OLL/cherimoya.fold_2.performance.tsv b/ENCSR768OLL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9f5683c95328e59b6ba3f3dc803b68394923e90d..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1470.35498046875 0.31769630312919617 0.35718005895614624 0.228891983628273 0.8578735589981079 0.8567764163017273 0.2837238609790802 \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_3.evaluate.json b/ENCSR768OLL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 48fb172aa39cac421513e11f0f57592540d66bfe..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF418VOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_3.fit.json b/ENCSR768OLL/cherimoya.fold_3.fit.json deleted file mode 100644 index 07cc0fde0625e30507ccfa95a9bcdd682699bab5..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF418VOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_3.log b/ENCSR768OLL/cherimoya.fold_3.log deleted file mode 100644 index ca4d1bdc3ee58ad227452a73ca8b9e3d901c3e83..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2818 35.82026934623718 3.3754990100860596 1220.73388671875 0.9387557506561279 1621.521728515625 0.25325441360473633 0.803484 9.612850189208984 True -1 5636 30.881415128707886 0.5461413860321045 1028.758544921875 0.9989612102508545 1540.7900390625 0.3135121464729309 0.8278296 1.2481361627578735 True -2 8454 30.860000610351562 0.5284123420715332 1082.25244140625 0.4580062925815582 1522.084228515625 0.32275155186653137 0.8292601 0.8020471930503845 True -3 11272 30.318805932998657 0.7793788909912109 1130.343994140625 1.1251431703567505 1509.970947265625 0.3307754397392273 0.8347503 0.6171656847000122 True -4 14090 30.354088306427002 0.5224847793579102 1256.3280029296875 0.6555641889572144 1508.67041015625 0.3298265337944031 0.8323712 0.6192185878753662 False -5 16908 30.40668487548828 0.7326948642730713 1016.04736328125 0.706557035446167 1506.1180419921875 0.33188682794570923 0.82865494 0.6256577372550964 False -6 19726 30.41982889175415 1.6035404205322266 1108.88232421875 0.37132877111434937 1499.605224609375 0.3365103006362915 0.8319238 0.6602012515068054 False -7 22544 30.390850067138672 0.5363154411315918 1080.3128662109375 0.723555326461792 1497.052001953125 0.3384700417518616 0.8327687 0.6980313062667847 False -8 25362 30.391329288482666 0.5362584590911865 1113.0460205078125 0.6683459281921387 1493.438232421875 0.3412812352180481 0.83855885 0.6312993764877319 True -9 28180 30.377516269683838 0.668220043182373 1036.294677734375 0.66853266954422 1490.441650390625 0.3433482050895691 0.83878416 0.5788561105728149 True -10 30998 30.360881567001343 2.1983702182769775 1126.29931640625 0.7846542596817017 1487.3992919921875 0.3455158472061157 0.8416962 0.5573468804359436 True -11 33816 30.541327238082886 0.5435400009155273 1086.166748046875 0.5547059178352356 1487.52099609375 0.34590110182762146 0.84925497 0.5034240484237671 True -12 36634 30.78496503829956 0.536797285079956 1024.145263671875 0.3064558207988739 1482.6895751953125 0.34817156195640564 0.85531646 0.4255886971950531 True -13 39452 30.383400201797485 0.534404993057251 1207.0357666015625 0.4058557450771332 1481.122314453125 0.3495776653289795 0.85595083 0.40089792013168335 True -14 42270 30.336870670318604 0.524395227432251 1025.570556640625 0.6604277491569519 1478.5570068359375 0.3516402542591095 0.86255217 0.37348857522010803 True -15 45088 30.37192940711975 0.8023736476898193 1288.687255859375 0.21587511897087097 1477.7646484375 0.3524181842803955 0.86487937 0.3409370481967926 True -16 47906 30.328256607055664 0.7828972339630127 1193.42236328125 0.3124277591705322 1481.816650390625 0.348676860332489 0.868207 0.32215267419815063 True -17 50724 30.401406288146973 0.5287933349609375 1027.19921875 0.2949540615081787 1480.13720703125 0.34997880458831787 0.86700064 0.3151870667934418 False -18 53542 30.36961054801941 0.5368778705596924 1232.0296630859375 0.2937857210636139 1481.6014404296875 0.34902217984199524 0.86569417 0.31295278668403625 False -19 56360 30.347962379455566 14.631932020187378 1251.94921875 0.2947233319282532 1483.0457763671875 0.3483547568321228 0.86400074 0.31628188490867615 False diff --git a/ENCSR768OLL/cherimoya.fold_3.performance.tsv b/ENCSR768OLL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 85f990d80a084777dac035bd809abcb65efad7bd..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1481.816650390625 0.3223467469215393 0.348676860332489 0.22386611998081207 0.8682069778442383 0.8561680912971497 0.32215267419815063 \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_4.evaluate.json b/ENCSR768OLL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 906daac1b6d7c2e972319505bb7e7de1436e9791..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF418VOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_4.fit.json b/ENCSR768OLL/cherimoya.fold_4.fit.json deleted file mode 100644 index 4499fdc4988b0c920c60fc51882f3489a759f56a..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF418VOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR768OLL/cherimoya.fold_4.log b/ENCSR768OLL/cherimoya.fold_4.log deleted file mode 100644 index fc586ce74badd3a2165da01d5e331452ea381f83..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2816 35.848952293395996 3.505340337753296 1234.9716796875 0.6975685954093933 1547.848876953125 0.24213629961013794 0.8151701 10.355148315429688 True -1 5632 31.01861262321472 0.6779923439025879 1167.117431640625 0.9823107719421387 1464.2706298828125 0.3090534508228302 0.8295673 1.5256952047348022 True -2 8448 31.13845205307007 0.6971597671508789 1328.6563720703125 0.5062488317489624 1445.202880859375 0.3197930157184601 0.8317409 0.8073558211326599 True -3 11264 30.624250173568726 0.5648384094238281 1069.81494140625 0.584518551826477 1437.2552490234375 0.3218611776828766 0.8321493 0.5983704924583435 True -4 14080 30.42491102218628 0.5684926509857178 1321.1234130859375 0.7840860486030579 1430.1705322265625 0.32598161697387695 0.8349787 0.523595929145813 True -5 16896 30.399730443954468 0.565762996673584 1040.938232421875 0.6473002433776855 1426.3236083984375 0.3288600742816925 0.8402216 0.4495483934879303 True -6 19712 30.36602783203125 0.5663633346557617 1111.2484130859375 0.5722743272781372 1424.9119873046875 0.32921746373176575 0.84101397 0.5223504900932312 True -7 22528 30.489740133285522 0.5704004764556885 1030.6121826171875 0.9623701572418213 1418.9517822265625 0.334280401468277 0.8436426 0.4629116356372833 True -8 25344 30.413186073303223 0.5701062679290771 1209.8836669921875 0.9153122901916504 1417.080322265625 0.334506094455719 0.8492158 0.44273412227630615 True -9 28160 30.42642641067505 0.56612229347229 1046.4044189453125 0.3904285430908203 1415.0093994140625 0.33607250452041626 0.84857154 0.4661928117275238 False -10 30976 30.399194478988647 0.5681025981903076 1210.29638671875 0.529448926448822 1412.178466796875 0.33863282203674316 0.8537346 0.4259367883205414 True -11 33792 30.40095281600952 1.2641172409057617 1112.47265625 0.4188886284828186 1410.4739990234375 0.33944639563560486 0.8578811 0.38859444856643677 True -12 36608 30.33324384689331 0.5612430572509766 1225.533935546875 0.24424168467521667 1408.26171875 0.34061557054519653 0.86063623 0.3749970495700836 True -13 39424 30.361978769302368 0.5698363780975342 1148.646728515625 0.4444531500339508 1404.7998046875 0.3443104326725006 0.8616956 0.3416561186313629 True -14 42240 30.319568634033203 0.5756528377532959 1072.809814453125 0.2122722864151001 1404.546875 0.34406813979148865 0.8662938 0.3170452117919922 True -15 45056 30.34121799468994 0.5589804649353027 1054.948974609375 0.4982113838195801 1404.225830078125 0.3444945812225342 0.86832494 0.2939293384552002 True -16 47872 30.2992103099823 0.5642144680023193 1165.56005859375 0.3234679102897644 1405.506103515625 0.34434184432029724 0.87075424 0.28273656964302063 True -17 50688 30.35566520690918 0.5541529655456543 1120.8232421875 0.3387877643108368 1410.5469970703125 0.33979034423828125 0.8702903 0.2792532742023468 False -18 53504 30.324203491210938 0.558814287185669 1126.74267578125 0.28844666481018066 1411.9013671875 0.33977583050727844 0.87040395 0.2743864059448242 False -19 56320 30.359323024749756 0.5708928108215332 1112.905029296875 0.31096091866493225 1411.4578857421875 0.3401878774166107 0.86799425 0.27861863374710083 False diff --git a/ENCSR768OLL/cherimoya.fold_4.performance.tsv b/ENCSR768OLL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7e3ac81384c69404e684d3f44aa260b19c00deaf..0000000000000000000000000000000000000000 --- a/ENCSR768OLL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1405.506103515625 0.33105072379112244 0.34434181451797485 0.21687115728855133 0.8707542419433594 0.8518952131271362 0.28273656964302063 \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_0.evaluate.json b/ENCSR769OIG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0f272bbde062beafa328d187990751c460caa720..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF452UII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_0.fit.json b/ENCSR769OIG/cherimoya.fold_0.fit.json deleted file mode 100644 index 6e2b11bac0eb9368213ca9d9a06fad13ef4f2656..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF452UII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_0.log b/ENCSR769OIG/cherimoya.fold_0.log deleted file mode 100644 index f6f94d1d7aefdbfa71874525b38f91478cb7dadf..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2610 33.284024477005005 3.7889575958251953 345.5870361328125 0.4831717610359192 679.3124389648438 0.16991199553012848 0.6113641 8.078428268432617 True -1 5220 28.57768487930298 0.5978653430938721 419.2962646484375 0.6719538569450378 585.9254760742188 0.22174246609210968 0.72575074 2.697183847427368 True -2 7830 28.796759605407715 0.5914256572723389 495.1307678222656 0.6798593401908875 575.9140625 0.22218935191631317 0.7150358 2.3698348999023438 False -3 10440 28.75843906402588 0.6329467296600342 396.1029052734375 0.944221556186676 553.8391723632812 0.22902311384677887 0.75636905 1.2491661310195923 True -4 13050 28.767019510269165 0.5676040649414062 431.2200927734375 0.9165207147598267 540.7078247070312 0.2365536391735077 0.77085716 1.0637987852096558 True -5 15660 28.652942895889282 0.7016005516052246 566.9384765625 0.6298034191131592 532.6846313476562 0.23817063868045807 0.7796682 0.9189310073852539 True -6 18270 28.27420687675476 0.5918459892272949 623.631103515625 0.3138987720012665 528.5489501953125 0.2402064949274063 0.78986317 0.841734766960144 True -7 20880 28.264188289642334 9.143535852432251 599.5616455078125 0.7616771459579468 523.912109375 0.2427617758512497 0.79375833 0.7883878350257874 True -8 23490 28.266549110412598 0.6045627593994141 368.197265625 0.6133034825325012 519.393310546875 0.2448543757200241 0.80340713 0.6902628540992737 True -9 26100 28.20028018951416 0.5945358276367188 463.05706787109375 0.3252198100090027 518.2859497070312 0.24531807005405426 0.8073615 0.642438530921936 True -10 28710 28.21607732772827 0.5952670574188232 403.60107421875 0.550298810005188 513.2930908203125 0.24901370704174042 0.8190727 0.5591767430305481 True -11 31320 28.286585330963135 0.5936088562011719 328.7020568847656 0.4462018311023712 510.9866943359375 0.25001171231269836 0.821731 0.551153302192688 True -12 33930 28.27485990524292 0.5836851596832275 480.8741760253906 0.6235003471374512 506.3769836425781 0.2534608542919159 0.83015084 0.49526992440223694 True -13 36540 28.335917472839355 0.5821986198425293 432.1690673828125 0.3886413872241974 503.1607666015625 0.255854994058609 0.8358865 0.46993517875671387 True -14 39150 28.30875563621521 0.5829672813415527 404.86981201171875 0.6062217950820923 500.2976379394531 0.2569781243801117 0.8432087 0.4453938901424408 True -15 41760 28.338745832443237 0.5729691982269287 326.9183654785156 0.2536807060241699 498.6161804199219 0.25858834385871887 0.84597737 0.4268890619277954 True -16 44370 28.376814365386963 0.5923795700073242 415.7255859375 0.21376235783100128 497.21124267578125 0.25902020931243896 0.8497324 0.41746705770492554 True -17 46980 28.33755850791931 0.5897676944732666 493.3196716308594 0.30590590834617615 500.53668212890625 0.2559191882610321 0.8496481 0.4123196005821228 False -18 49590 28.320502996444702 0.58567214012146 453.1256103515625 0.41181451082229614 498.5705261230469 0.2586142122745514 0.8497733 0.4130673110485077 True -19 52200 28.326236963272095 0.5793390274047852 504.60205078125 0.46275579929351807 498.3993225097656 0.25872260332107544 0.8487537 0.41456151008605957 False diff --git a/ENCSR769OIG/cherimoya.fold_0.performance.tsv b/ENCSR769OIG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 88b4ab97f6fe7eca6e3f2dc2b52cf1b825f705ef..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -498.5705261230469 0.4859323799610138 0.2586142122745514 0.10067170858383179 0.8497732877731323 0.7634785771369934 0.4130673110485077 \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_1.evaluate.json b/ENCSR769OIG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6312723fb4c2c9d9927b6288903b701f99f8f673..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF452UII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_1.fit.json b/ENCSR769OIG/cherimoya.fold_1.fit.json deleted file mode 100644 index 162a06e3205c7cb53512319bebea28ddebf54ce2..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF452UII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_1.log b/ENCSR769OIG/cherimoya.fold_1.log deleted file mode 100644 index 04f72b55674dd8d5f311816c2f677a15f58ffc64..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2546 32.668089151382446 4.597642660140991 323.3586120605469 0.5640838146209717 863.5485229492188 0.18314412236213684 0.58578956 9.468417167663574 True -1 5092 28.168540954589844 0.852470874786377 573.42578125 1.1285886764526367 734.7229614257812 0.2451057881116867 0.7094324 4.331638336181641 True -2 7638 28.121777296066284 0.732424259185791 523.6522827148438 0.6361266374588013 738.858642578125 0.24392466247081757 0.69168574 3.3897171020507812 False -3 10184 28.069679498672485 1.559709072113037 341.4639892578125 0.5637463927268982 711.0204467773438 0.25543221831321716 0.70831925 2.196049690246582 False -4 12730 28.05133581161499 0.7768585681915283 477.49981689453125 0.636892557144165 687.0047607421875 0.26368963718414307 0.74157333 1.8973429203033447 True -5 15276 27.597025632858276 0.739168643951416 551.8245849609375 0.6085758209228516 666.925048828125 0.27045246958732605 0.7623604 1.3892751932144165 True -6 17822 27.62790870666504 0.7226505279541016 353.5433349609375 0.2802138924598694 656.6488647460938 0.27503782510757446 0.77304906 1.3277215957641602 True -7 20368 27.54675006866455 0.7457058429718018 439.80908203125 0.43325722217559814 645.1024780273438 0.28045204281806946 0.7876229 1.1397488117218018 True -8 22914 27.550816535949707 0.7328388690948486 460.52606201171875 0.5797827243804932 639.4180908203125 0.28189417719841003 0.7979844 0.8946493864059448 True -9 25460 27.55482840538025 0.721954345703125 470.08282470703125 0.765336275100708 634.8500366210938 0.28317731618881226 0.80838025 0.8014014363288879 True -10 28006 27.49896216392517 0.7096750736236572 497.26702880859375 0.7294237613677979 626.78564453125 0.2873915731906891 0.820682 0.7070083618164062 True -11 30552 27.517470836639404 1.0950706005096436 551.360595703125 0.521410346031189 621.1791381835938 0.2898564040660858 0.82744706 0.6443799734115601 True -12 33098 27.56772541999817 2.5989911556243896 392.2797546386719 0.8446725606918335 616.194580078125 0.2927529215812683 0.83694 0.5883309841156006 True -13 35644 27.592719793319702 0.7349307537078857 294.73663330078125 0.5812255144119263 613.8313598632812 0.29324451088905334 0.84444267 0.5592077970504761 True -14 38190 27.608937740325928 0.7263438701629639 374.5014343261719 0.29027509689331055 608.8079833984375 0.2960488796234131 0.8511941 0.5317197442054749 True -15 40736 27.599623918533325 0.7269575595855713 356.53680419921875 0.3803110122680664 606.02783203125 0.2977873384952545 0.8562483 0.5155515670776367 True -16 43282 27.574347972869873 0.7313399314880371 349.73565673828125 0.42682212591171265 606.499267578125 0.29686394333839417 0.8600696 0.5062363147735596 True -17 45828 27.773456573486328 14.36651349067688 329.276123046875 0.32396334409713745 604.2730102539062 0.29858875274658203 0.8607487 0.4993695914745331 True -18 48374 28.04124116897583 0.7535858154296875 414.388916015625 0.44009101390838623 606.0924072265625 0.29798123240470886 0.8609582 0.4975041449069977 True -19 50920 27.719460248947144 0.7372894287109375 473.14410400390625 0.35663479566574097 607.087890625 0.2972771227359772 0.8593052 0.4995097219944 False diff --git a/ENCSR769OIG/cherimoya.fold_1.performance.tsv b/ENCSR769OIG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7cccf11941d771ea06b3d0d7f83565ca015afc08..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -606.0924072265625 0.4566062092781067 0.29798123240470886 0.12578921020030975 0.8609582185745239 0.811786413192749 0.4975041449069977 \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_2.evaluate.json b/ENCSR769OIG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7efb27f9280983ad4d0960e3bdf100b3e49f710d..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF452UII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_2.fit.json b/ENCSR769OIG/cherimoya.fold_2.fit.json deleted file mode 100644 index 0bc7f54fbd689d3967af1e9439941ac0aa576c3b..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF452UII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_2.log b/ENCSR769OIG/cherimoya.fold_2.log deleted file mode 100644 index 259563ed7a024b679e9cbc234ce652c4bcf51145..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 35.090333461761475 3.8706510066986084 496.7966613769531 0.8572129607200623 704.5733642578125 0.17208494246006012 0.57532716 6.757243633270264 True -1 5482 30.343756198883057 0.651371955871582 362.7571105957031 0.6653352379798889 602.9998779296875 0.22210517525672913 0.7302869 3.5135304927825928 True -2 8223 30.400270223617554 0.5742547512054443 456.5086669921875 0.8347048759460449 590.1113891601562 0.22247572243213654 0.7338208 2.237713098526001 True -3 10964 30.368253707885742 0.5817046165466309 451.97821044921875 0.5902711153030396 564.4144287109375 0.23251226544380188 0.7522721 1.2773230075836182 True -4 13705 30.356492042541504 0.5763473510742188 419.33673095703125 0.45720964670181274 552.990966796875 0.23651090264320374 0.76987755 1.1208842992782593 True -5 16446 30.27331018447876 0.5785512924194336 511.06475830078125 0.42261892557144165 546.9280395507812 0.24151407182216644 0.77371055 1.0661258697509766 True -6 19187 30.233069896697998 0.5759289264678955 538.612060546875 0.6021003127098083 540.4905395507812 0.24325577914714813 0.7819166 0.9812544584274292 True -7 21928 30.24213933944702 18.140124320983887 489.6339416503906 0.7142652273178101 535.9608764648438 0.2458132654428482 0.7902992 0.8830790519714355 True -8 24669 30.07200264930725 14.285386562347412 533.5479125976562 0.5409148335456848 531.2601318359375 0.24828359484672546 0.79382354 0.8453453183174133 True -9 27410 29.735063552856445 18.035372734069824 450.52685546875 0.5530786514282227 526.50048828125 0.25150251388549805 0.8034194 0.7119379639625549 True -10 30151 29.817468643188477 0.5930905342102051 378.1435241699219 0.5067793726921082 523.5240478515625 0.2531190812587738 0.80979514 0.615323543548584 True -11 32892 30.433057069778442 0.597266674041748 462.643798828125 0.3794986307621002 519.3389282226562 0.255506694316864 0.8178187 0.5602532625198364 True -12 35633 29.72913384437561 1.2349002361297607 586.3411865234375 0.5257576107978821 518.364990234375 0.255217969417572 0.8247364 0.5227659344673157 True -13 38374 29.842174291610718 0.5793633460998535 364.0577392578125 0.6714891195297241 514.3811645507812 0.25890403985977173 0.8311872 0.48957905173301697 True -14 41115 29.780322074890137 0.5831403732299805 441.86627197265625 0.4260424077510834 513.6666259765625 0.2594771385192871 0.8352738 0.4700702726840973 True -15 43856 29.809792041778564 0.6221458911895752 500.84814453125 0.4943838119506836 510.1206970214844 0.26295235753059387 0.83980405 0.4522504508495331 True -16 46597 29.821863412857056 0.5770843029022217 346.59991455078125 0.2456866353750229 510.62542724609375 0.26237013936042786 0.84364414 0.4392896890640259 True -17 49338 29.776375770568848 0.5787320137023926 367.8545837402344 0.38460445404052734 509.284423828125 0.2635440230369568 0.84497005 0.433621883392334 True -18 52079 29.799437284469604 0.5988123416900635 408.03472900390625 0.33022183179855347 509.83770751953125 0.263512521982193 0.8457587 0.4342443346977234 True -19 54820 29.76729917526245 2.11311936378479 356.96392822265625 0.17988325655460358 509.4127197265625 0.2639124095439911 0.8455763 0.43593940138816833 False diff --git a/ENCSR769OIG/cherimoya.fold_2.performance.tsv b/ENCSR769OIG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bff5f4a35978ef88a373751a2b4ee2edcf54c30a..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -509.83770751953125 0.4808812439441681 0.263512521982193 0.10896998643875122 0.8457586765289307 0.7694080471992493 0.4342443346977234 \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_3.evaluate.json b/ENCSR769OIG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 58477286ff8e7663c2dd027e1e8d48743ef1d950..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF452UII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_3.fit.json b/ENCSR769OIG/cherimoya.fold_3.fit.json deleted file mode 100644 index dd7b367d6bb237c00cb9cfc52169fe681216121a..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF452UII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_3.log b/ENCSR769OIG/cherimoya.fold_3.log deleted file mode 100644 index b779fb6e053d3b3d9ef02712d0a1aa899147b5f4..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2600 33.086841106414795 3.7447521686553955 315.7298278808594 0.4848772883415222 728.2428588867188 0.1835484802722931 0.5692475 7.7644429206848145 True -1 5200 28.909834623336792 0.7881569862365723 396.11053466796875 0.5230543613433838 630.0966796875 0.23667137324810028 0.6947311 3.689187526702881 True -2 7800 28.68056869506836 0.5407900810241699 459.97821044921875 0.5653497576713562 628.0486450195312 0.2348909229040146 0.68179846 3.1748650074005127 False -3 10400 28.688840627670288 0.5314583778381348 649.5098876953125 0.6243442296981812 607.8243408203125 0.2427358627319336 0.7019152 1.6847386360168457 True -4 13000 28.617235898971558 0.5275943279266357 534.8380737304688 0.6925825476646423 589.1210327148438 0.25169286131858826 0.7222991 1.4146517515182495 True -5 15600 28.686177968978882 1.6780011653900146 344.7140197753906 0.32068318128585815 579.10693359375 0.2580219507217407 0.7356032 1.4901536703109741 True -6 18200 28.726152896881104 0.5234248638153076 413.8199462890625 0.549188494682312 571.172119140625 0.26201125979423523 0.7408624 1.4875054359436035 True -7 20800 28.624393701553345 0.5256414413452148 358.153076171875 0.7622032761573792 566.1678466796875 0.2641509175300598 0.74973565 1.2731785774230957 True -8 23400 28.602707862854004 0.5601069927215576 430.1916198730469 0.441323459148407 563.6797485351562 0.26602914929389954 0.758093 1.1465606689453125 True -9 26000 28.564719438552856 0.5409033298492432 453.4854736328125 0.8206536173820496 559.3001708984375 0.2682921588420868 0.7688114 0.9948404431343079 True -10 28600 28.56235909461975 0.5363705158233643 724.8411865234375 0.5842707753181458 557.0673828125 0.2694739103317261 0.77689815 0.8992935419082642 True -11 31200 28.57238221168518 0.5558018684387207 501.69659423828125 0.7430119514465332 552.228515625 0.27222153544425964 0.78897023 0.7808981537818909 True -12 33800 28.38109064102173 0.5361378192901611 431.61590576171875 0.33281540870666504 548.7886352539062 0.2741406559944153 0.79899365 0.7055089473724365 True -13 36400 28.065490007400513 1.2385344505310059 403.85235595703125 0.45853686332702637 543.6903686523438 0.27848049998283386 0.8078575 0.6686338782310486 True -14 39000 28.153160095214844 0.5231804847717285 432.57171630859375 0.5154635906219482 541.7442626953125 0.278372198343277 0.8171101 0.610742449760437 True -15 41600 28.209990739822388 0.5239500999450684 466.96142578125 0.5858943462371826 539.32763671875 0.27826130390167236 0.8258588 0.5668754577636719 True -16 44200 28.127342462539673 0.5224330425262451 399.7187805175781 0.3919954299926758 536.4747314453125 0.28098729252815247 0.8320582 0.5322226285934448 True -17 46800 28.2391574382782 0.5113430023193359 324.851318359375 0.3404272198677063 533.7116088867188 0.28365013003349304 0.83541095 0.5125797390937805 True -18 49400 28.261253118515015 0.5134401321411133 382.10186767578125 0.3866747319698334 536.8273315429688 0.2798008620738983 0.8359001 0.5106377005577087 True -19 52000 28.143567323684692 0.519526481628418 344.987548828125 0.3694758415222168 536.1259155273438 0.28103765845298767 0.8350916 0.5121269226074219 False diff --git a/ENCSR769OIG/cherimoya.fold_3.performance.tsv b/ENCSR769OIG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 68264db08d846129c3a16ba2c7252522ebf95a79..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -536.8273315429688 0.47037553787231445 0.2798008620738983 0.11169777810573578 0.8359001278877258 0.77631014585495 0.5106377005577087 \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_4.evaluate.json b/ENCSR769OIG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 064c5d5e7b46a939a4b93a404668f6441a45c9cc..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF452UII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_4.fit.json b/ENCSR769OIG/cherimoya.fold_4.fit.json deleted file mode 100644 index 399b76a25b3ae5ddd335f12ee05e59124d9e51ab..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF452UII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR769OIG/cherimoya.fold_4.log b/ENCSR769OIG/cherimoya.fold_4.log deleted file mode 100644 index c0da7059da2d8b09a4f92a930c71dfe82142ffbc..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2649 33.74196648597717 3.9192934036254883 691.36328125 1.0517199039459229 601.2272338867188 0.1664130538702011 0.5831053 6.434420585632324 True -1 5298 29.2767231464386 0.7137086391448975 294.460693359375 0.5009819269180298 529.7262573242188 0.21247315406799316 0.7010236 2.8911056518554688 True -2 7947 29.341438055038452 0.5910704135894775 444.9739074707031 0.5762122273445129 529.572998046875 0.2073017954826355 0.6836041 2.0634207725524902 False -3 10596 28.837779998779297 0.579350471496582 543.5576171875 0.9691329598426819 506.9752197265625 0.22075225412845612 0.70675766 1.3011947870254517 True -4 13245 28.67931318283081 1.408207654953003 508.56640625 1.0041275024414062 496.6528015136719 0.2245461493730545 0.720256 1.2029656171798706 True -5 15894 28.648296117782593 0.6100058555603027 508.26019287109375 0.8400958180427551 489.2337951660156 0.22827893495559692 0.7279779 1.0458019971847534 True -6 18543 28.751720905303955 0.5876500606536865 486.5723571777344 0.4563073217868805 483.0132141113281 0.2312958836555481 0.74430096 0.9111398458480835 True -7 21192 28.702850341796875 2.3617146015167236 329.7957763671875 0.4353051781654358 478.14263916015625 0.23400628566741943 0.7660527 0.7411682605743408 True -8 23841 28.737722158432007 1.5257470607757568 427.03778076171875 0.36965686082839966 475.607666015625 0.2352508008480072 0.7718762 0.7012896537780762 True -9 26490 28.735445261001587 0.5857815742492676 483.17938232421875 0.577425479888916 469.8450012207031 0.23982156813144684 0.78037816 0.6161078810691833 True -10 29139 28.741167306900024 0.5816638469696045 406.8352355957031 0.6877272129058838 467.41754150390625 0.24180586636066437 0.790624 0.5539645552635193 True -11 31788 28.754828691482544 0.5742204189300537 341.7289733886719 0.4157160520553589 466.0897216796875 0.24258841574192047 0.79912055 0.5344411134719849 True -12 34437 28.672505617141724 1.2133088111877441 539.5367431640625 0.42116281390190125 463.881103515625 0.24403662979602814 0.80955523 0.4843864142894745 True -13 37086 28.727415084838867 0.5821466445922852 341.644287109375 0.4146033525466919 461.2265930175781 0.24614007771015167 0.8148066 0.4673091471195221 True -14 39735 28.73099112510681 0.5803647041320801 363.12957763671875 0.2585444748401642 460.1702575683594 0.24714432656764984 0.82205737 0.4430999457836151 True -15 42384 28.737171173095703 0.5821218490600586 473.439697265625 0.45127707719802856 458.1620178222656 0.2483355551958084 0.82935804 0.42208942770957947 True -16 45033 28.69501805305481 4.577760457992554 354.32379150390625 0.3542834520339966 457.98150634765625 0.24799910187721252 0.8340729 0.40645259618759155 True -17 47682 28.724981546401978 0.5786678791046143 522.535888671875 0.384890615940094 459.1851806640625 0.2470535784959793 0.83627677 0.3985123038291931 True -18 50331 28.74116539955139 0.5662353038787842 436.1681213378906 0.3313523828983307 458.3177490234375 0.24833057820796967 0.8359177 0.39888259768486023 False -19 52980 28.749804973602295 0.5666968822479248 315.9336242675781 0.3799871802330017 459.64874267578125 0.2469160258769989 0.83608496 0.40091001987457275 False diff --git a/ENCSR769OIG/cherimoya.fold_4.performance.tsv b/ENCSR769OIG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 20d3b331751d2b8fe9152c0ca50313ad3a099785..0000000000000000000000000000000000000000 --- a/ENCSR769OIG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.1851806640625 0.4943488538265228 0.2470535784959793 0.09577885270118713 0.8362767696380615 0.7501561641693115 0.3985123038291931 \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_0.evaluate.json b/ENCSR770JCP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1256076858e3509cf058e67eeb9d8dc51fa84fd9..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF227JYH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_0.fit.json b/ENCSR770JCP/cherimoya.fold_0.fit.json deleted file mode 100644 index 74833da438b91c9188ad69dc4cdc517b2b1567f3..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF227JYH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_0.log b/ENCSR770JCP/cherimoya.fold_0.log deleted file mode 100644 index 5647133cf6fe47a8d851d24a748f93a8227b5980..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 35.28383946418762 3.7361509799957275 403.545166015625 0.2949433922767639 460.1988830566406 0.24781262874603271 0.7851359 2.9104180335998535 True -1 5480 30.435534954071045 0.6777575016021729 368.0857849121094 0.3037579655647278 431.28167724609375 0.3024488389492035 0.8338359 0.8627139925956726 True -2 8220 30.430654525756836 0.5698583126068115 426.7487487792969 0.3492319881916046 425.5946350097656 0.3131997883319855 0.8447127 0.36396926641464233 True -3 10960 30.376105785369873 0.5670428276062012 354.12701416015625 0.18809650838375092 421.5062255859375 0.3214431405067444 0.85437006 0.2776334285736084 True -4 13700 30.413420915603638 0.5826330184936523 354.33319091796875 0.25207406282424927 419.97235107421875 0.32583364844322205 0.8570789 0.2032204270362854 True -5 16440 30.376526832580566 0.5481905937194824 314.64471435546875 0.2093421220779419 419.6007995605469 0.32476186752319336 0.8607587 0.1885795146226883 True -6 19180 30.404207944869995 0.565375566482544 357.9906005859375 0.18070702254772186 418.8211364746094 0.3262011408805847 0.86319506 0.1856812685728073 True -7 21920 30.43603253364563 0.5730764865875244 385.4793701171875 0.29543402791023254 417.5075378417969 0.32945606112480164 0.86724293 0.1762164682149887 True -8 24660 30.383082389831543 0.5620965957641602 345.6138916015625 0.23073799908161163 416.5667724609375 0.3321853280067444 0.8723424 0.1756262481212616 True -9 27400 30.38509964942932 0.5733885765075684 320.5552062988281 0.1854143738746643 415.82421875 0.33399394154548645 0.8741241 0.1708817183971405 True -10 30140 30.421183347702026 2.1571977138519287 324.87158203125 0.1412253975868225 415.1247863769531 0.33549320697784424 0.8763807 0.17133738100528717 True -11 32880 30.393003702163696 0.5706508159637451 396.3089599609375 0.22934512794017792 414.264404296875 0.33735841512680054 0.88070947 0.16181187331676483 True -12 35620 30.420008659362793 0.5868380069732666 356.76116943359375 0.20588502287864685 414.3266296386719 0.3361528217792511 0.88476723 0.15560969710350037 True -13 38360 30.40648651123047 0.5681002140045166 311.56298828125 0.14475375413894653 413.38922119140625 0.33784571290016174 0.8872774 0.14947359263896942 True -14 41100 30.380584001541138 0.5876555442810059 471.0580139160156 0.19313572347164154 413.0298767089844 0.33828553557395935 0.89028674 0.14687491953372955 True -15 43840 30.000668048858643 7.4170613288879395 347.84368896484375 0.09056743234395981 412.3756103515625 0.340291291475296 0.893177 0.14298994839191437 True -16 46580 30.34955406188965 0.5810470581054688 331.3274230957031 0.13370463252067566 412.0869445800781 0.3406618535518646 0.8932296 0.1400601714849472 True -17 49320 29.778543710708618 0.5635061264038086 362.5833740234375 0.17867310345172882 412.065185546875 0.34058085083961487 0.89541376 0.139078751206398 True -18 52060 29.79731059074402 0.5709538459777832 359.0224914550781 0.164899080991745 412.1584777832031 0.3399195075035095 0.8964358 0.1399838924407959 True -19 54800 29.780149459838867 0.5596742630004883 343.15814208984375 0.14789709448814392 412.2690124511719 0.3397476375102997 0.8945949 0.13977652788162231 False diff --git a/ENCSR770JCP/cherimoya.fold_0.performance.tsv b/ENCSR770JCP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 410b4259dda3a7cc8423240a625996cbfbe932cd..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -412.1584777832031 0.43337664008140564 0.33991947770118713 0.11717011779546738 0.8964357972145081 0.8768466711044312 0.1399838924407959 \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_1.evaluate.json b/ENCSR770JCP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ecb5d2eb38b6523332f66cbc6e4ca2d91b6d5cd2..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF227JYH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_1.fit.json b/ENCSR770JCP/cherimoya.fold_1.fit.json deleted file mode 100644 index bfda7049ace80f33d0c8381a58a9a566f9c06f6a..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF227JYH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_1.log b/ENCSR770JCP/cherimoya.fold_1.log deleted file mode 100644 index 7c84a9d12134ccf21b65a1a4377dbbdc5945a4ff..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2719 34.97833037376404 4.246304273605347 347.54144287109375 0.29897990822792053 512.1112060546875 0.25277554988861084 0.79036766 3.166278123855591 True -1 5438 30.160380601882935 0.710918664932251 353.9712829589844 0.3042905628681183 478.9732971191406 0.3143296539783478 0.8393438 0.8357968926429749 True -2 8157 30.123907804489136 0.7054619789123535 349.8255920410156 0.23386722803115845 470.4898376464844 0.325739324092865 0.85440344 0.36120036244392395 True -3 10876 30.183635473251343 0.6902327537536621 321.79107666015625 0.16401562094688416 466.54168701171875 0.33089679479599 0.8635058 0.2782021760940552 True -4 13595 30.183449506759644 0.6916368007659912 385.6574401855469 0.3345761299133301 465.0921630859375 0.33288997411727905 0.8656132 0.2686060965061188 True -5 16314 30.143616437911987 0.8869345188140869 429.23736572265625 0.1823330521583557 462.78546142578125 0.33711183071136475 0.871802 0.2437538057565689 True -6 19033 30.26444149017334 0.7083265781402588 378.634521484375 0.23037457466125488 462.0073547363281 0.33867859840393066 0.87241626 0.21163314580917358 True -7 21752 30.240052700042725 0.6979775428771973 360.3128356933594 0.17240551114082336 461.2415466308594 0.340618371963501 0.8767875 0.20215581357479095 True -8 24471 30.149938106536865 0.69657301902771 373.0481872558594 0.1981687992811203 459.911376953125 0.34274822473526 0.881393 0.1927987039089203 True -9 27190 30.47606062889099 0.6873140335083008 388.74407958984375 0.18165121972560883 459.5705261230469 0.3430580794811249 0.884948 0.19517390429973602 True -10 29909 30.161314249038696 18.322089433670044 323.2376708984375 0.15427394211292267 458.170166015625 0.3454427719116211 0.8883445 0.18169347941875458 True -11 32628 29.57514214515686 0.9375200271606445 317.64813232421875 0.2256687879562378 457.52191162109375 0.3464367389678955 0.89128435 0.17042334377765656 True -12 35347 29.5888032913208 0.6925501823425293 332.12506103515625 0.15635080635547638 456.784423828125 0.3474899232387543 0.89234847 0.17461587488651276 True -13 38066 29.58757734298706 0.6916899681091309 381.92095947265625 0.15083108842372894 455.6722717285156 0.34933191537857056 0.897409 0.17210085690021515 True -14 40785 29.58214831352234 0.6910600662231445 326.99908447265625 0.122693732380867 454.904296875 0.3503982722759247 0.8993826 0.1648254245519638 True -15 43504 29.545872449874878 0.6696827411651611 348.2100524902344 0.24765975773334503 453.87896728515625 0.3522968590259552 0.90263134 0.16005480289459229 True -16 46223 29.572099685668945 0.688495397567749 343.9048767089844 0.11786536872386932 453.610595703125 0.352726548910141 0.9036338 0.1553802639245987 True -17 48942 29.591475009918213 0.6866152286529541 315.17034912109375 0.16531464457511902 453.69281005859375 0.352607786655426 0.9039824 0.15312841534614563 True -18 51661 29.58183979988098 0.6866285800933838 277.96685791015625 0.1477125585079193 453.36834716796875 0.3533822298049927 0.9042323 0.15219950675964355 True -19 54380 29.543771028518677 0.6761906147003174 326.4012145996094 0.16519156098365784 453.6708679199219 0.35221022367477417 0.9041863 0.1525784134864807 False diff --git a/ENCSR770JCP/cherimoya.fold_1.performance.tsv b/ENCSR770JCP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5e6a0eba9e69b2a5055ab2fa303a5b6c79f782c7..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -453.36834716796875 0.42095503211021423 0.3533822298049927 0.12825042009353638 0.9042323231697083 0.8980918526649475 0.15219950675964355 \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_2.evaluate.json b/ENCSR770JCP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9ad3d904973be49d621425113d802d48f157556a..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF227JYH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_2.fit.json b/ENCSR770JCP/cherimoya.fold_2.fit.json deleted file mode 100644 index 89b086553481e7626dd86e50fa08e451813fc899..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF227JYH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_2.log b/ENCSR770JCP/cherimoya.fold_2.log deleted file mode 100644 index d75f79990fbc05e66598aeb77dcea3f7d99a97b8..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2880 36.19631552696228 3.929203510284424 349.62115478515625 0.2854037582874298 488.87811279296875 0.24945582449436188 0.78097814 3.399871587753296 True -1 5760 32.03300595283508 0.6101348400115967 349.129638671875 0.3189845085144043 456.8642272949219 0.31138280034065247 0.83489835 0.7515458464622498 True -2 8640 31.97482466697693 0.5544166564941406 348.66650390625 0.13803425431251526 449.2291564941406 0.32210054993629456 0.8437963 0.262655109167099 True -3 11520 31.94500708580017 0.8703007698059082 327.2644958496094 0.17061489820480347 446.73895263671875 0.32617053389549255 0.85053253 0.23890839517116547 True -4 14400 32.02511191368103 0.8546633720397949 323.90130615234375 0.26593905687332153 444.8851013183594 0.3298831284046173 0.85474837 0.20915862917900085 True -5 17280 31.96393394470215 0.5550932884216309 340.30517578125 0.21263352036476135 444.0460510253906 0.33096954226493835 0.8592966 0.1996043473482132 True -6 20160 31.70280885696411 0.5462961196899414 320.031005859375 0.14056998491287231 442.89788818359375 0.3334560692310333 0.86287713 0.1907009333372116 True -7 23040 31.257176637649536 0.5458157062530518 373.70355224609375 0.21449485421180725 442.0024719238281 0.3352000415325165 0.8680879 0.1961093693971634 True -8 25920 31.25891876220703 1.4574947357177734 403.26641845703125 0.2608756721019745 440.931640625 0.33737027645111084 0.86892766 0.1939896047115326 True -9 28800 31.3441641330719 0.5603249073028564 373.94305419921875 0.15416637063026428 439.73101806640625 0.33994075655937195 0.87259877 0.18554717302322388 True -10 31680 31.2932345867157 0.5232224464416504 417.62506103515625 0.17925435304641724 439.22589111328125 0.3409360945224762 0.8756701 0.18309982120990753 True -11 34560 32.06100010871887 0.5564930438995361 340.742919921875 0.24086233973503113 438.9502258300781 0.34067457914352417 0.87768275 0.1730969250202179 True -12 37440 31.332813501358032 0.5555787086486816 360.7817687988281 0.17410950362682343 437.9954833984375 0.3429384231567383 0.88130414 0.16835157573223114 True -13 40320 31.376530170440674 0.5488276481628418 403.9868469238281 0.1536475121974945 437.4867858886719 0.34429851174354553 0.881228 0.16536274552345276 False -14 43200 31.398674249649048 0.5544779300689697 367.86846923828125 0.15990808606147766 436.9586486816406 0.3454791307449341 0.88395375 0.1616055816411972 True -15 46080 31.306358337402344 0.5500872135162354 349.4669189453125 0.19852346181869507 436.23687744140625 0.3474261462688446 0.888012 0.15488842129707336 True -16 48960 31.336768627166748 0.5455384254455566 410.4947509765625 0.1192532628774643 435.9927978515625 0.34738659858703613 0.88894564 0.15369656682014465 True -17 51840 31.240938186645508 0.5330624580383301 373.043212890625 0.09230166673660278 435.85595703125 0.3472084105014801 0.8902905 0.1529979705810547 True -18 54720 31.30872941017151 0.5446817874908447 308.48651123046875 0.13676734268665314 436.18572998046875 0.3468605875968933 0.88899404 0.15193091332912445 False -19 57600 31.2920982837677 0.5391366481781006 349.0794372558594 0.06839776039123535 436.20367431640625 0.34699171781539917 0.8887996 0.15280616283416748 False diff --git a/ENCSR770JCP/cherimoya.fold_2.performance.tsv b/ENCSR770JCP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3e9446d0f4ea37268db0c7f443cfd9528a001c72..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -435.85595703125 0.4260810613632202 0.3472084105014801 0.12456060945987701 0.8902904987335205 0.8755204081535339 0.1529979705810547 \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_3.evaluate.json b/ENCSR770JCP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4a599f1e2de63cda66d0506d5d0fc2cfac23a6fd..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF227JYH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_3.fit.json b/ENCSR770JCP/cherimoya.fold_3.fit.json deleted file mode 100644 index 2f873a990637088cbf30554967166d19033b9483..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF227JYH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_3.log b/ENCSR770JCP/cherimoya.fold_3.log deleted file mode 100644 index 9869170a6ed148b29a542726fcfbd317fb9eb785..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 35.29342174530029 3.818026542663574 401.2712707519531 0.3185996413230896 435.6554260253906 0.25298261642456055 0.77599233 3.6497771739959717 True -1 5488 30.455042839050293 0.8514385223388672 336.62432861328125 0.35830044746398926 409.1487731933594 0.3026822507381439 0.83207893 0.5427705645561218 True -2 8232 30.44874906539917 0.5828609466552734 398.97332763671875 0.21938589215278625 403.77020263671875 0.31337928771972656 0.8468519 0.30124494433403015 True -3 10976 30.220627546310425 0.5829930305480957 400.87493896484375 0.25780603289604187 401.79815673828125 0.31566643714904785 0.85236907 0.24656905233860016 True -4 13720 29.854337692260742 0.5655097961425781 290.06439208984375 0.17514437437057495 399.708251953125 0.31950142979621887 0.8605912 0.20942358672618866 True -5 16464 29.78542685508728 0.570014238357544 350.4544677734375 0.19060561060905457 398.5477600097656 0.3216969668865204 0.86420137 0.20514211058616638 True -6 19208 29.784979820251465 0.5380795001983643 307.262451171875 0.22368352115154266 397.39984130859375 0.3248309791088104 0.86995304 0.20009541511535645 True -7 21952 29.81635093688965 0.5823915004730225 401.41497802734375 0.22627747058868408 397.2331848144531 0.3250550925731659 0.8702788 0.19908562302589417 True -8 24696 29.827523708343506 0.5500507354736328 344.9603271484375 0.2480085790157318 396.20166015625 0.3272375762462616 0.8720335 0.20010478794574738 True -9 27440 29.864060640335083 0.5900168418884277 328.51141357421875 0.17680414021015167 395.3062438964844 0.32949334383010864 0.87681407 0.1927224099636078 True -10 30184 29.804693698883057 0.7212913036346436 298.9853820800781 0.19798274338245392 394.75335693359375 0.33059948682785034 0.8784961 0.1828465610742569 True -11 32928 29.950475215911865 0.574784517288208 392.10467529296875 0.20254936814308167 393.65289306640625 0.3333927392959595 0.87958735 0.18585078418254852 True -12 35672 29.82477569580078 0.5533642768859863 412.06256103515625 0.19541621208190918 393.20697021484375 0.3340384066104889 0.88479936 0.17537745833396912 True -13 38416 29.83662724494934 0.58467698097229 372.0760498046875 0.2748691439628601 392.4114685058594 0.3353242874145508 0.88863504 0.1682034730911255 True -14 41160 29.858975410461426 0.5421276092529297 326.6204833984375 0.14935389161109924 391.6122131347656 0.3369803726673126 0.8923134 0.16204489767551422 True -15 43904 29.83654499053955 0.7464196681976318 335.5850524902344 0.1439981758594513 391.02679443359375 0.3382788896560669 0.8925824 0.15534420311450958 True -16 46648 29.90449047088623 0.5542125701904297 346.14447021484375 0.1890072524547577 391.4277038574219 0.3370296359062195 0.89685917 0.1506366729736328 True -17 49392 29.85115098953247 0.5777173042297363 355.06201171875 0.13065752387046814 390.4463806152344 0.3394739031791687 0.8968079 0.14752937853336334 False -18 52136 29.81325888633728 0.5518136024475098 374.9158020019531 0.17045575380325317 391.2419738769531 0.3367132842540741 0.8958063 0.14776663482189178 False -19 54880 30.06980562210083 0.5642061233520508 363.6092224121094 0.12656578421592712 391.1407165527344 0.3371882736682892 0.89585227 0.1478670984506607 False diff --git a/ENCSR770JCP/cherimoya.fold_3.performance.tsv b/ENCSR770JCP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4612187d6d4344e8129f44f6754601ad285e85c4..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -391.4277038574219 0.43802356719970703 0.33702966570854187 0.11413261294364929 0.8968591690063477 0.8720173835754395 0.1506366729736328 \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_4.evaluate.json b/ENCSR770JCP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b420cd12509c504ef1f0e723a6b771b3ed51f6d9..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF227JYH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_4.fit.json b/ENCSR770JCP/cherimoya.fold_4.fit.json deleted file mode 100644 index 227164ab63a1e75cfa981f0a1260b36dde3908a0..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF227JYH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770JCP/cherimoya.fold_4.log b/ENCSR770JCP/cherimoya.fold_4.log deleted file mode 100644 index c4eb64e5a886f05bd74533783387597cace3731d..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2843 36.14914131164551 4.1166815757751465 327.4054870605469 0.28681114315986633 420.55438232421875 0.24665774405002594 0.7851682 2.716500997543335 True -1 5686 31.617674589157104 0.6299335956573486 349.9632873535156 0.3056069612503052 396.4523010253906 0.2976856827735901 0.83356345 0.566734254360199 True -2 8529 31.600351333618164 0.5988409519195557 343.35693359375 0.22743892669677734 392.693603515625 0.3035883605480194 0.8378525 0.33196699619293213 True -3 11372 31.540709257125854 0.6508550643920898 327.95196533203125 0.21097765862941742 389.76275634765625 0.3088408410549164 0.8480565 0.2563353478908539 True -4 14215 31.539031505584717 0.6033968925476074 388.50537109375 0.1807103455066681 387.70123291015625 0.31298592686653137 0.8536451 0.20934729278087616 True -5 17058 31.596771955490112 0.5916707515716553 298.1275634765625 0.17616164684295654 386.6041259765625 0.31571853160858154 0.8566019 0.20563679933547974 True -6 19901 31.64219641685486 0.603797435760498 341.17755126953125 0.301331102848053 386.0725402832031 0.31587696075439453 0.86114377 0.21474233269691467 True -7 22744 31.525932788848877 0.6038517951965332 373.3902587890625 0.20609188079833984 385.4254150390625 0.3169761300086975 0.86294425 0.22995655238628387 True -8 25587 31.554850101470947 0.600499153137207 331.8656005859375 0.20743387937545776 384.5068664550781 0.31909042596817017 0.8696757 0.20862272381782532 True -9 28430 31.563075304031372 0.5922825336456299 339.0166931152344 0.18869413435459137 383.84844970703125 0.3200874626636505 0.87274677 0.18697406351566315 True -10 31273 31.54933476448059 0.5985751152038574 401.11846923828125 0.16951556503772736 383.0386962890625 0.32236000895500183 0.87842155 0.16742441058158875 True -11 34116 31.581409215927124 0.6005470752716064 311.8533630371094 0.1633310168981552 382.60052490234375 0.32293856143951416 0.8822083 0.16121789813041687 True -12 36959 31.55974292755127 0.600092887878418 353.0968017578125 0.1537923514842987 381.9548034667969 0.32475683093070984 0.8854341 0.15292082726955414 True -13 39802 31.578693628311157 0.5948221683502197 350.3612976074219 0.13720488548278809 381.1609802246094 0.32635602355003357 0.88715196 0.14553633332252502 True -14 42645 31.119754552841187 0.5925109386444092 369.23419189453125 0.1428644210100174 380.7411193847656 0.3270775377750397 0.8934886 0.13536034524440765 True -15 45488 30.912841081619263 0.5983302593231201 314.08880615234375 0.1406017690896988 380.4939270019531 0.32768508791923523 0.8936302 0.13282643258571625 True -16 48331 30.92277216911316 0.587261438369751 350.73236083984375 0.14883118867874146 380.1744384765625 0.3288680911064148 0.89705014 0.13010826706886292 True -17 51174 30.992220878601074 0.5949249267578125 376.97027587890625 0.20689578354358673 380.3839416503906 0.3278467357158661 0.89625084 0.12750761210918427 False -18 54017 30.902353048324585 16.05331802368164 379.63580322265625 0.1477762758731842 380.1631774902344 0.32891082763671875 0.89706516 0.12782509624958038 True -19 56860 30.96259832382202 0.916433572769165 357.55865478515625 0.12630103528499603 380.3721618652344 0.3281705677509308 0.89632356 0.1277446150779724 False diff --git a/ENCSR770JCP/cherimoya.fold_4.performance.tsv b/ENCSR770JCP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e58a6746a86cb555f27c92308d9b46bea4375f7f..0000000000000000000000000000000000000000 --- a/ENCSR770JCP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -380.1631774902344 0.44502490758895874 0.32891085743904114 0.10809154808521271 0.8970651626586914 0.8742639422416687 0.12782509624958038 \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_0.evaluate.json b/ENCSR770OTB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1f5f4780c95f6f524abcaea95ecd1949d1a86479..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF427AVE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_0.fit.json b/ENCSR770OTB/cherimoya.fold_0.fit.json deleted file mode 100644 index b9d447c4df51cc33fd3c284fcfc7651efceb8078..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF427AVE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_0.log b/ENCSR770OTB/cherimoya.fold_0.log deleted file mode 100644 index 977687b916502558a2d6a6c0dbb7233d08d18c9a..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 35.036579847335815 4.05480694770813 590.1866455078125 0.7661967277526855 801.5892944335938 0.286435067653656 0.70015115 5.2133378982543945 True -1 5488 30.218818426132202 0.7161288261413574 487.48614501953125 0.7526746988296509 701.0530395507812 0.36090531945228577 0.76422817 1.3842271566390991 True -2 8232 30.185301542282104 0.5853743553161621 497.079833984375 0.8281658887863159 680.4755249023438 0.3753465712070465 0.78012913 0.8067967295646667 True -3 10976 30.142112016677856 0.588961124420166 620.3839111328125 0.6441482305526733 674.9408569335938 0.3784027397632599 0.7880545 0.7458175420761108 True -4 13720 29.70260262489319 0.5738131999969482 613.207763671875 0.666485607624054 670.9468383789062 0.3824419677257538 0.79518837 0.7514984607696533 True -5 16464 29.51110005378723 0.5834295749664307 613.8663940429688 0.5079878568649292 667.1763916015625 0.38513147830963135 0.80225825 0.655163049697876 True -6 19208 29.511829376220703 0.573779821395874 542.71826171875 0.3666169047355652 663.8941040039062 0.38810083270072937 0.8057456 0.6436968445777893 True -7 21952 29.57633948326111 0.5789666175842285 563.2711181640625 0.38318076729774475 659.2218627929688 0.392809122800827 0.8145785 0.5541002750396729 True -8 24696 29.53259539604187 0.5736360549926758 673.3551635742188 0.3542610704898834 656.7503051757812 0.3947708010673523 0.8198825 0.5285710096359253 True -9 27440 29.562800645828247 0.5722413063049316 508.16387939453125 0.5261986255645752 652.969482421875 0.3984685242176056 0.8249359 0.5040551424026489 True -10 30184 29.52104377746582 0.5720820426940918 578.5687255859375 0.6092551946640015 650.4915161132812 0.39993998408317566 0.8316999 0.4395274519920349 True -11 32928 29.51405096054077 0.570030689239502 562.478515625 0.35527798533439636 649.2345581054688 0.40020227432250977 0.83637124 0.4176160991191864 True -12 35672 29.49431848526001 0.5627179145812988 540.415283203125 0.4393731653690338 645.9738159179688 0.4027637541294098 0.84063464 0.40712082386016846 True -13 38416 29.528568506240845 1.0161008834838867 646.6697998046875 0.5219955444335938 643.9320068359375 0.40410515666007996 0.8457982 0.39220932126045227 True -14 41160 30.151688814163208 0.5728387832641602 523.674072265625 0.4143436849117279 642.9984741210938 0.404969722032547 0.8487455 0.37981122732162476 True -15 43904 29.585750341415405 0.5740582942962646 594.12890625 0.20951171219348907 638.1507568359375 0.4085035026073456 0.85407084 0.359768271446228 True -16 46648 29.538684129714966 0.5838687419891357 539.388916015625 0.3953852653503418 638.839599609375 0.40856385231018066 0.85677946 0.3507516384124756 True -17 49392 29.588407516479492 0.579420804977417 496.39923095703125 0.45063018798828125 638.1016845703125 0.40764138102531433 0.85877985 0.34492799639701843 True -18 52136 29.559279918670654 0.9617083072662354 681.504150390625 0.27193683385849 638.1610717773438 0.40784868597984314 0.8577523 0.3463197350502014 False -19 54880 29.542558431625366 0.8009860515594482 515.6188354492188 0.4767007529735565 639.1243286132812 0.4067714214324951 0.856861 0.34649860858917236 False diff --git a/ENCSR770OTB/cherimoya.fold_0.performance.tsv b/ENCSR770OTB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3625ce38e1d0356a1c8f0f267f9b5aaca5c13adf..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -638.1016845703125 0.38884270191192627 0.40764138102531433 0.16048820316791534 0.8587798476219177 0.8139427900314331 0.34492799639701843 \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_1.evaluate.json b/ENCSR770OTB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a4c5901ced28de868f630279a52394565c52c396..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF427AVE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_1.fit.json b/ENCSR770OTB/cherimoya.fold_1.fit.json deleted file mode 100644 index d88852b6ccfa99de547777766a8fed0c605353fa..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF427AVE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_1.log b/ENCSR770OTB/cherimoya.fold_1.log deleted file mode 100644 index 2028d1e06554d656ad7284268714c3766af1a01b..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2688 33.941845417022705 4.137067794799805 638.7876586914062 0.6028808951377869 986.4618530273438 0.28876084089279175 0.71014714 7.075867652893066 True -1 5376 29.495078086853027 0.8660628795623779 579.6365966796875 0.7527437210083008 839.1248779296875 0.3843201696872711 0.7826797 2.045616865158081 True -2 8064 29.729838609695435 0.729306697845459 616.5181274414062 0.4950403571128845 821.0975341796875 0.39103344082832336 0.79320705 1.0412838459014893 True -3 10752 29.550212144851685 1.0278351306915283 495.2601318359375 0.7796504497528076 813.3583984375 0.3956652879714966 0.8007822 1.0514503717422485 True -4 13440 29.547935009002686 0.7216348648071289 493.0619201660156 0.616815447807312 807.9572143554688 0.4002496302127838 0.80663997 0.8466199040412903 True -5 16128 29.526135683059692 0.8033058643341064 604.0111083984375 0.7661604285240173 802.8802490234375 0.4039989113807678 0.8143823 0.7221062779426575 True -6 18816 29.527891159057617 1.150864601135254 660.6837158203125 0.30002573132514954 796.9564819335938 0.40765684843063354 0.8227422 0.6157068014144897 True -7 21504 29.50858736038208 0.7293298244476318 433.579833984375 0.46384698152542114 792.295654296875 0.410778284072876 0.8277216 0.5785908699035645 True -8 24192 29.562808990478516 0.7192575931549072 685.50830078125 0.5706506967544556 788.10791015625 0.41392794251441956 0.8317244 0.5373435616493225 True -9 26880 29.548331022262573 0.7368497848510742 580.86865234375 0.45817309617996216 781.8349609375 0.41827675700187683 0.8375441 0.5052207708358765 True -10 29568 29.528038263320923 0.9645519256591797 477.5880126953125 0.3501269221305847 780.951171875 0.4175797402858734 0.8420336 0.49889594316482544 True -11 32256 29.924195528030396 0.7287869453430176 669.505615234375 0.48092415928840637 777.9613647460938 0.41994357109069824 0.84767145 0.48023587465286255 True -12 34944 29.497217178344727 0.7222027778625488 614.5130615234375 0.3896641433238983 772.0470581054688 0.42448705434799194 0.8524478 0.4720675051212311 True -13 37632 29.547342538833618 0.7309942245483398 552.2982177734375 0.4089151620864868 769.3784790039062 0.42543843388557434 0.85681653 0.4442281126976013 True -14 40320 29.56559109687805 0.7235016822814941 503.6800537109375 0.4240911602973938 766.418212890625 0.42734453082084656 0.86109 0.41593030095100403 True -15 43008 29.548373699188232 0.7352471351623535 582.1951293945312 0.3710123300552368 764.4840698242188 0.4284541606903076 0.8672389 0.4022867679595947 True -16 45696 30.27948808670044 0.7309327125549316 547.5929565429688 0.33725374937057495 765.6846313476562 0.4268067181110382 0.8683378 0.38771557807922363 True -17 48384 29.576358318328857 0.733130693435669 536.4427490234375 0.3825039267539978 763.8594970703125 0.4288202226161957 0.8710096 0.3743835687637329 True -18 51072 29.55405879020691 0.7380125522613525 579.233642578125 0.27033933997154236 765.4092407226562 0.42740342020988464 0.8693789 0.3742907643318176 False -19 53760 29.21439838409424 0.7323684692382812 448.2264404296875 0.38791924715042114 764.1066284179688 0.42967504262924194 0.871006 0.3721540570259094 False diff --git a/ENCSR770OTB/cherimoya.fold_1.performance.tsv b/ENCSR770OTB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5d82ddaadd46c33bdc913df8f98b048ac390c335..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -763.8594970703125 0.3685784935951233 0.4288202226161957 0.18628911674022675 0.8710095882415771 0.8505116105079651 0.3743835687637329 \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_2.evaluate.json b/ENCSR770OTB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 41461b1940d7ae05dbcc4c368341404e6d2f39c1..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF427AVE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_2.fit.json b/ENCSR770OTB/cherimoya.fold_2.fit.json deleted file mode 100644 index 90a7224f1cdc8076f7c4b1c232ad2dc03b896dde..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF427AVE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_2.log b/ENCSR770OTB/cherimoya.fold_2.log deleted file mode 100644 index 725a255ca0ae8d318859aefb8f9f362d59288d34..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 36.16536211967468 3.8218419551849365 605.3721923828125 0.7391805648803711 853.6498413085938 0.28604212403297424 0.7018895 6.348210334777832 True -1 5762 31.64871644973755 1.2453832626342773 482.197021484375 0.8071048259735107 748.7525024414062 0.36406201124191284 0.76178217 1.7664111852645874 True -2 8643 31.7543523311615 1.460625410079956 542.7632446289062 0.5414049625396729 728.3948974609375 0.3749016225337982 0.7771469 1.1833940744400024 True -3 11524 31.678891897201538 0.9570844173431396 567.945556640625 0.4874194264411926 721.1531372070312 0.37876930832862854 0.7881149 0.8120134472846985 True -4 14405 31.77185297012329 0.5739421844482422 706.3717041015625 0.7453954219818115 714.298583984375 0.384662926197052 0.79278344 0.6671029925346375 True -5 17286 31.696635723114014 1.944045066833496 690.7305908203125 0.8143004775047302 710.6460571289062 0.386625200510025 0.80223805 0.5891407132148743 True -6 20167 31.72090721130371 0.5750021934509277 627.39404296875 0.5532904267311096 705.0135498046875 0.39120298624038696 0.80885106 0.5517261028289795 True -7 23048 31.704522132873535 0.5850262641906738 441.8909912109375 0.4177470803260803 701.3931274414062 0.3940403461456299 0.8132027 0.5035083889961243 True -8 25929 31.636448621749878 0.5777857303619385 574.1715087890625 0.46194636821746826 699.5848999023438 0.3943624496459961 0.81727356 0.4944535791873932 True -9 28810 31.590781688690186 2.49418044090271 630.8250732421875 0.4646106958389282 696.080810546875 0.3979681432247162 0.82060486 0.4894721210002899 True -10 31691 31.751935482025146 0.5763645172119141 610.7877197265625 0.47632473707199097 691.2943115234375 0.40101876854896545 0.82429206 0.45657551288604736 True -11 34572 31.700090169906616 0.5863027572631836 582.1407470703125 0.4901711344718933 688.02392578125 0.40365099906921387 0.8305299 0.44851285219192505 True -12 37453 31.519981384277344 0.5689456462860107 518.3108520507812 0.5354266166687012 686.9808959960938 0.4035378098487854 0.833967 0.4284726083278656 True -13 40334 31.175395250320435 0.5773708820343018 462.9439697265625 0.3086368441581726 684.649658203125 0.40650054812431335 0.8392272 0.41920727491378784 True -14 43215 31.11256694793701 0.5682966709136963 590.232421875 0.31031912565231323 681.4464721679688 0.40851521492004395 0.8439452 0.40015727281570435 True -15 46096 31.052135705947876 0.5686299800872803 556.7684326171875 0.46623456478118896 679.1936645507812 0.4093807637691498 0.84736705 0.38491424918174744 True -16 48977 31.02609372138977 0.5577774047851562 559.34326171875 0.21438226103782654 679.1412963867188 0.40898802876472473 0.85009384 0.37642979621887207 True -17 51858 31.072279453277588 2.3346738815307617 469.07464599609375 0.2935647964477539 677.9644165039062 0.41160836815834045 0.8518468 0.37026143074035645 True -18 54739 31.00459623336792 0.8486199378967285 460.9739074707031 0.25738614797592163 680.4317626953125 0.4088905155658722 0.85282075 0.3684866428375244 True -19 57620 31.077800989151 0.6208674907684326 564.13427734375 0.38400134444236755 678.9043579101562 0.41102173924446106 0.85099655 0.369276225566864 False diff --git a/ENCSR770OTB/cherimoya.fold_2.performance.tsv b/ENCSR770OTB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 15a266b4e419008f8abb140033e0bc25451bc679..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -680.4317626953125 0.38549476861953735 0.4088904857635498 0.1643710434436798 0.8528207540512085 0.8236814737319946 0.3684866428375244 \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_3.evaluate.json b/ENCSR770OTB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 67296ddb07595e9dbe599bca2b04765a2b98bc89..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF427AVE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_3.fit.json b/ENCSR770OTB/cherimoya.fold_3.fit.json deleted file mode 100644 index 3c3d020caeab24ad7eb9db134dbb612cf3288060..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF427AVE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_3.log b/ENCSR770OTB/cherimoya.fold_3.log deleted file mode 100644 index 6ad3283c897edc0d075fc13701f1e9f3f39e9714..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.70422577857971 3.748861789703369 555.22314453125 0.6138179302215576 779.0275268554688 0.29221054911613464 0.70572096 6.844095230102539 True -1 5488 30.117998600006104 0.6806232929229736 745.6697998046875 0.4953104555606842 687.2960815429688 0.3621625602245331 0.769918 1.6211086511611938 True -2 8232 30.21887445449829 16.780311584472656 662.7294311523438 0.6310003995895386 666.5608520507812 0.3763461709022522 0.78904474 0.9972693920135498 True -3 10976 30.576083660125732 0.6062760353088379 719.4341430664062 0.61661696434021 658.390625 0.38227608799934387 0.7951841 1.0394045114517212 True -4 13720 31.546623945236206 1.4982936382293701 564.7906494140625 0.5384855270385742 656.0877685546875 0.38188618421554565 0.80371016 0.9989710450172424 True -5 16464 30.250070571899414 1.0322985649108887 478.36029052734375 0.4036402702331543 652.31689453125 0.38500410318374634 0.8091212 0.7981660962104797 True -6 19208 30.252029418945312 0.575502872467041 596.2013549804688 0.599433422088623 648.243896484375 0.38891923427581787 0.8115907 0.7253270149230957 True -7 21952 30.093949794769287 0.6080753803253174 622.550537109375 0.5782135725021362 647.3846435546875 0.38906338810920715 0.81572896 0.6901015639305115 True -8 24696 30.138440132141113 0.5795614719390869 591.4586181640625 0.6940224170684814 642.29833984375 0.39361482858657837 0.81967515 0.6664954423904419 True -9 27440 30.19668197631836 0.5278735160827637 519.5001831054688 0.6272963881492615 637.5179443359375 0.3970010280609131 0.8262284 0.6318324208259583 True -10 30184 30.132411003112793 0.5578081607818604 646.4969482421875 0.5733921527862549 634.4712524414062 0.3996172249317169 0.8290084 0.559718668460846 True -11 32928 30.16071057319641 0.557380199432373 625.341064453125 0.30920591950416565 630.8094482421875 0.40259143710136414 0.834415 0.5131345987319946 True -12 35672 30.1676766872406 0.5345845222473145 569.9000244140625 0.38330987095832825 629.6987915039062 0.40246134996414185 0.84101635 0.4945340156555176 True -13 38416 29.545182466506958 0.5330905914306641 548.3466186523438 0.48708030581474304 626.6378173828125 0.40339821577072144 0.84699464 0.44499021768569946 True -14 41160 29.549341678619385 0.5611002445220947 639.9073486328125 0.4525502920150757 624.0244750976562 0.405876100063324 0.8523776 0.4174085855484009 True -15 43904 29.587022304534912 0.9238684177398682 604.864013671875 0.28101465106010437 621.3895263671875 0.4086093008518219 0.85825014 0.3891459107398987 True -16 46648 29.581673622131348 0.5194568634033203 580.8583984375 0.3848838210105896 620.7755737304688 0.4087221920490265 0.86023194 0.3697412610054016 True -17 49392 29.623650312423706 0.5591530799865723 494.61651611328125 0.2944994568824768 619.4927368164062 0.4095015823841095 0.86227816 0.357833594083786 True -18 52136 29.577892780303955 0.5307366847991943 617.78173828125 0.29654884338378906 620.518310546875 0.408791184425354 0.8613479 0.3562823534011841 False -19 54880 29.651658296585083 0.5646982192993164 496.96514892578125 0.2923946976661682 621.0232543945312 0.4079504907131195 0.8607785 0.35581332445144653 False diff --git a/ENCSR770OTB/cherimoya.fold_3.performance.tsv b/ENCSR770OTB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0ab190cd8d7809a087c73c99ebe5393be9336fef..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -619.4927368164062 0.38912490010261536 0.4095015823841095 0.15984734892845154 0.862278163433075 0.8185561299324036 0.357833594083786 \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_4.evaluate.json b/ENCSR770OTB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d08a939304b30323501c7f40bbb0444f734a2af6..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF427AVE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_4.fit.json b/ENCSR770OTB/cherimoya.fold_4.fit.json deleted file mode 100644 index 5c6c4856ccdb91a3e09734e170594180ba105977..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF427AVE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR770OTB/cherimoya.fold_4.log b/ENCSR770OTB/cherimoya.fold_4.log deleted file mode 100644 index 2bd9748bf0b20db92e35f6184ac691d1cbee65e0..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2807 35.62786293029785 4.318340301513672 654.5594482421875 0.9814411401748657 747.45654296875 0.2838522493839264 0.69989216 4.998470306396484 True -1 5614 30.845686435699463 1.0637500286102295 670.6426391601562 0.4920053482055664 658.5631103515625 0.3573320508003235 0.75609064 1.613501787185669 True -2 8421 30.832924842834473 0.6061346530914307 483.60284423828125 0.4500275254249573 644.1500244140625 0.3686305284500122 0.76605475 1.0194079875946045 True -3 11228 30.821667671203613 0.600609540939331 554.21044921875 0.4960693120956421 636.3284301757812 0.3723211884498596 0.77652365 0.8074179291725159 True -4 14035 30.856464624404907 0.6055247783660889 560.7987060546875 0.5627062916755676 632.0794067382812 0.3759795129299164 0.78197145 0.6129958629608154 True -5 16842 30.822572946548462 0.6116511821746826 504.3271484375 0.3996325135231018 627.323974609375 0.37988126277923584 0.7912142 0.5502980947494507 True -6 19649 30.869140148162842 0.5962367057800293 525.0017700195312 0.3615768849849701 623.7604370117188 0.38232049345970154 0.79359263 0.4992547333240509 True -7 22456 30.867854118347168 0.6053562164306641 511.505615234375 0.5237833261489868 621.5044555664062 0.3838811218738556 0.8028453 0.4785340130329132 True -8 25263 30.8742356300354 1.3292632102966309 564.1425170898438 0.6340749859809875 619.25146484375 0.3858833611011505 0.80897945 0.4505399167537689 True -9 28070 30.865962505340576 1.3194336891174316 566.8218994140625 0.37439924478530884 617.6790771484375 0.38672301173210144 0.81205606 0.4399126470088959 True -10 30877 30.850908279418945 0.5972456932067871 615.6303100585938 0.4290286898612976 613.6251831054688 0.39125943183898926 0.8184825 0.4280281662940979 True -11 33684 30.27397656440735 0.6033976078033447 462.06854248046875 0.43373677134513855 612.4580078125 0.39163100719451904 0.8226866 0.41784876585006714 True -12 36491 30.24156379699707 0.6569552421569824 485.7823486328125 0.4456847310066223 609.4754638671875 0.39503613114356995 0.8281277 0.40151411294937134 True -13 39298 30.236757516860962 0.5859172344207764 490.79046630859375 0.36647170782089233 607.0759887695312 0.3978762924671173 0.83117366 0.38414454460144043 True -14 42105 30.234163999557495 0.5970468521118164 509.6003723144531 0.3304520845413208 605.4672241210938 0.39833593368530273 0.83966297 0.3674241006374359 True -15 44912 30.208428621292114 0.5996363162994385 541.06982421875 0.3389761447906494 607.1653442382812 0.3968762159347534 0.8437317 0.3534860908985138 True -16 47719 30.22548484802246 0.5897819995880127 503.60015869140625 0.33414316177368164 604.8408203125 0.4002188742160797 0.8483234 0.3459876477718353 True -17 50526 30.213346242904663 0.586768388748169 537.606201171875 0.37973904609680176 604.845703125 0.40067771077156067 0.84881866 0.3395121991634369 True -18 53333 30.22972273826599 0.5854599475860596 550.3056030273438 0.3526245951652527 605.6552734375 0.3990853428840637 0.84929836 0.3371236026287079 True -19 56140 30.211419582366943 0.5961153507232666 445.41424560546875 0.25365352630615234 605.4139404296875 0.39967676997184753 0.8497596 0.33716362714767456 True diff --git a/ENCSR770OTB/cherimoya.fold_4.performance.tsv b/ENCSR770OTB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4cfcf3c12b861c1636ef15377433518648bebd83..0000000000000000000000000000000000000000 --- a/ENCSR770OTB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -605.4139404296875 0.39580848813056946 0.39967676997184753 0.1512562781572342 0.849759578704834 0.8013390898704529 0.33716362714767456 \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_0.evaluate.json b/ENCSR771JQH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 49efaae8daf42cd9e90e850c5833c3a4cd309d84..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959OIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_0.fit.json b/ENCSR771JQH/cherimoya.fold_0.fit.json deleted file mode 100644 index c756310d85be83285ec1ca9ffa2c0416b509d1bb..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF959OIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_0.log b/ENCSR771JQH/cherimoya.fold_0.log deleted file mode 100644 index c0168436f80dbc827d2e776ff55c263806d8ae58..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2769 34.599031925201416 2.1981780529022217 842.8338623046875 0.6478500962257385 1095.1817626953125 0.2913191616535187 0.69706476 8.747958183288574 True -1 5538 30.578514337539673 0.5571556091308594 628.552001953125 0.6345889568328857 947.5266723632812 0.3763411045074463 0.76215595 2.8094098567962646 True -2 8307 30.621167421340942 0.5130519866943359 582.3988037109375 0.740249752998352 930.2958374023438 0.386780709028244 0.7730349 1.444961428642273 True -3 11076 30.552661895751953 0.5128128528594971 751.9613037109375 0.7012863159179688 920.7265014648438 0.3951113820075989 0.7813808 1.1099801063537598 True -4 13845 30.531874179840088 21.200947761535645 771.5145874023438 0.6590521335601807 917.365234375 0.3987846076488495 0.7866442 1.080483317375183 True -5 16614 30.63865065574646 0.4869828224182129 630.6929931640625 0.9412527084350586 916.9310302734375 0.3972450792789459 0.78856367 0.984756588935852 True -6 19383 30.666280031204224 13.682721376419067 856.0567626953125 0.7038444876670837 910.594970703125 0.4031662940979004 0.78996724 0.924392819404602 True -7 22152 31.08223819732666 0.4869370460510254 647.8734130859375 0.43473684787750244 904.6702880859375 0.40709635615348816 0.79890347 0.7814770340919495 True -8 24921 31.29080367088318 0.48879098892211914 743.3472900390625 0.6061477065086365 903.8336181640625 0.40650662779808044 0.80286354 0.6991830468177795 True -9 27690 30.68402910232544 12.550275325775146 773.5772705078125 0.5831354856491089 900.333251953125 0.40937191247940063 0.80796796 0.6594242453575134 True -10 30459 30.60629677772522 21.80886936187744 745.9990234375 0.5456410646438599 896.403564453125 0.41175007820129395 0.81031036 0.6358629465103149 True -11 33228 30.69810461997986 0.4809434413909912 696.8035278320312 0.5007702112197876 893.9346313476562 0.41237175464630127 0.81608593 0.5959703922271729 True -12 35997 30.52030301094055 0.47698140144348145 662.4083862304688 0.4843403100967407 890.3053588867188 0.4159057140350342 0.82269824 0.5665327310562134 True -13 38766 30.50828456878662 0.48741936683654785 792.81689453125 0.38764387369155884 886.8809814453125 0.4163089692592621 0.82613975 0.535911500453949 True -14 41535 30.532617568969727 0.5015432834625244 857.653076171875 0.49199897050857544 885.6470947265625 0.41780638694763184 0.831459 0.5110657811164856 True -15 44304 30.555702924728394 0.49701929092407227 778.892822265625 0.4932610094547272 884.2381591796875 0.4183458387851715 0.83411264 0.48108890652656555 True -16 47073 30.58206534385681 0.49675583839416504 703.234619140625 0.35152772068977356 883.8327026367188 0.41865274310112 0.83618826 0.47207963466644287 True -17 49842 30.50680923461914 0.4926459789276123 688.499755859375 0.4678897261619568 882.6181640625 0.4201876223087311 0.83618313 0.47114595770835876 False -18 52611 30.54177761077881 23.20566439628601 633.7109985351562 0.35373616218566895 882.7431640625 0.41898733377456665 0.835484 0.469058096408844 False -19 55380 30.90352463722229 0.47765398025512695 601.4085693359375 0.3236742317676544 884.6029052734375 0.41778746247291565 0.83623534 0.4694949686527252 True diff --git a/ENCSR771JQH/cherimoya.fold_0.performance.tsv b/ENCSR771JQH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 44f926253f1a5b229f065413c3bcd8789c96bae7..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -884.6029052734375 0.35072141885757446 0.41778749227523804 0.21732565760612488 0.8362353444099426 0.7881268858909607 0.4694949686527252 \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_1.evaluate.json b/ENCSR771JQH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4590f0b597d383e0475a0610f52caf35acc07f45..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959OIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_1.fit.json b/ENCSR771JQH/cherimoya.fold_1.fit.json deleted file mode 100644 index 1fe6ddee6c5c4fef00dd9b79dfcc39d07e3261d5..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF959OIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_1.log b/ENCSR771JQH/cherimoya.fold_1.log deleted file mode 100644 index 0f56e2d32297bc1f08b2d9e5d4debf1fab7bc8bb..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 34.11085319519043 4.440926790237427 984.4588623046875 0.6382660269737244 1295.606201171875 0.2982473373413086 0.7214455 10.316675186157227 True -1 5458 30.23229455947876 0.8258030414581299 821.8338623046875 0.7717115879058838 1115.033203125 0.3891335129737854 0.7927761 2.924748182296753 True -2 8187 30.250656127929688 0.7984495162963867 773.158203125 0.3911263346672058 1086.6922607421875 0.40390345454216003 0.80330026 1.4703114032745361 True -3 10916 30.11629009246826 0.7710061073303223 715.362548828125 1.0188820362091064 1076.822021484375 0.40939268469810486 0.8120405 1.182505488395691 True -4 13645 30.080866813659668 0.7807133197784424 857.4295654296875 0.652637243270874 1067.9913330078125 0.4142548441886902 0.81731534 1.120495080947876 True -5 16374 30.141310930252075 0.7737421989440918 683.6046142578125 0.736865758895874 1066.4423828125 0.4139559864997864 0.82167244 0.947618842124939 True -6 19103 30.147992610931396 0.7620892524719238 727.65576171875 0.46746933460235596 1058.3548583984375 0.4179881811141968 0.82429 0.8530795574188232 True -7 21832 30.251065015792847 0.7992815971374512 754.2571411132812 0.48847538232803345 1055.8856201171875 0.42098748683929443 0.8288699 0.800251305103302 True -8 24561 30.20224094390869 0.7707812786102295 844.8310546875 0.6505246758460999 1048.4100341796875 0.424250990152359 0.8368266 0.7227301001548767 True -9 27290 30.183242321014404 0.7502293586730957 716.5413208007812 0.49375155568122864 1045.5272216796875 0.42596685886383057 0.8382116 0.6712161302566528 True -10 30019 30.176733255386353 0.7518312931060791 730.3970947265625 0.5626142024993896 1043.7901611328125 0.4261902868747711 0.84394664 0.6270408034324646 True -11 32748 30.178683280944824 0.7718601226806641 786.9729614257812 0.42628151178359985 1032.565673828125 0.4332258105278015 0.8484796 0.5929332375526428 True -12 35477 30.20585560798645 0.7687320709228516 672.8759765625 0.4302594065666199 1032.4844970703125 0.43207523226737976 0.8529032 0.5712194442749023 True -13 38206 30.129056453704834 0.7649378776550293 687.0823974609375 0.5496135354042053 1028.06005859375 0.43487221002578735 0.85740536 0.5455191731452942 True -14 40935 30.11288022994995 0.7649528980255127 583.8816528320312 0.46460819244384766 1028.00830078125 0.4331992566585541 0.8618044 0.5110382437705994 True -15 43664 30.16344451904297 0.7680065631866455 778.2192993164062 0.40450072288513184 1024.7745361328125 0.4346495568752289 0.8647828 0.48549363017082214 True -16 46393 30.113738775253296 0.76961350440979 686.1002197265625 0.40298500657081604 1023.787109375 0.43530529737472534 0.86765784 0.46920183300971985 True -17 49122 30.121183156967163 1.2260680198669434 793.8690185546875 0.30461299419403076 1023.422119140625 0.4370037913322449 0.8682197 0.4626661241054535 True -18 51851 30.08493733406067 0.7592768669128418 448.4123840332031 0.49931493401527405 1024.698974609375 0.4346480369567871 0.86742675 0.46334418654441833 False -19 54580 30.110047578811646 0.7585926055908203 853.4808349609375 0.2856486439704895 1028.364990234375 0.4314771294593811 0.8656871 0.46855416893959045 False diff --git a/ENCSR771JQH/cherimoya.fold_1.performance.tsv b/ENCSR771JQH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a680094ba4f6e89982e0f98bb5e77cc6387495b1..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1023.422119140625 0.3319728970527649 0.4370037913322449 0.24630053341388702 0.8682196736335754 0.8442224264144897 0.4626661241054535 \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_2.evaluate.json b/ENCSR771JQH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index aae181f0fa7cb573316ea678fbc454653d48d69f..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959OIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_2.fit.json b/ENCSR771JQH/cherimoya.fold_2.fit.json deleted file mode 100644 index 79e6479d0d5d3df9a89962a0337bfaf9c84e594e..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF959OIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_2.log b/ENCSR771JQH/cherimoya.fold_2.log deleted file mode 100644 index e7c0b6f24ee68ea3b71c054a53644b3bdf4af6ac..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2949 36.195149660110474 3.708268404006958 902.29736328125 0.9363071918487549 1161.5870361328125 0.29862841963768005 0.6869983 8.834278106689453 True -1 5898 32.47591042518616 1.0377602577209473 766.975830078125 0.7816666960716248 999.4097290039062 0.3836735188961029 0.7704788 2.4468348026275635 True -2 8847 32.4550998210907 0.5390005111694336 744.12841796875 0.8239916563034058 982.8641357421875 0.3932384252548218 0.7762249 1.4067360162734985 True -3 11796 32.439112424850464 0.5285384654998779 647.9000244140625 0.4690585732460022 973.726806640625 0.3991270363330841 0.7859016 1.1892651319503784 True -4 14745 32.456233501434326 0.538762092590332 645.513427734375 0.7220602631568909 968.2666015625 0.40248748660087585 0.7913706 0.9915559887886047 True -5 17694 32.46595120429993 0.5425698757171631 696.59814453125 0.7192187905311584 966.9188232421875 0.4020683169364929 0.79386914 0.9962640404701233 True -6 20643 32.44747996330261 0.5375232696533203 639.4002685546875 0.6902492046356201 965.0510864257812 0.4036448001861572 0.7977612 0.9013911485671997 True -7 23592 32.75818920135498 0.5404491424560547 793.1517944335938 0.6419696807861328 960.0621948242188 0.40702366828918457 0.80188316 0.8101559281349182 True -8 26541 32.51760959625244 0.5396933555603027 839.13037109375 0.6086522340774536 954.4834594726562 0.41033270955085754 0.8104346 0.7261428833007812 True -9 29490 32.47276997566223 0.5384485721588135 761.341552734375 0.46732956171035767 952.0367431640625 0.4117056429386139 0.81467456 0.6720074415206909 True -10 32439 32.5009708404541 1.1883444786071777 660.397705078125 0.39679282903671265 947.919677734375 0.4149615168571472 0.8182324 0.6373591423034668 True -11 35388 32.467140674591064 0.5304830074310303 642.9612426757812 0.47243380546569824 943.93994140625 0.41778984665870667 0.82114047 0.6068618297576904 True -12 38337 32.519731283187866 0.5316243171691895 706.45654296875 0.3714140057563782 937.4314575195312 0.42135095596313477 0.8271849 0.5638379454612732 True -13 41286 32.484845876693726 1.6828370094299316 811.6715698242188 0.4333549439907074 938.3974609375 0.4207935035228729 0.8312995 0.5405837893486023 True -14 44235 32.568135023117065 0.5440585613250732 764.4661865234375 0.34028178453445435 934.3431396484375 0.4225408732891083 0.83671784 0.5084157586097717 True -15 47184 32.51436901092529 2.351592540740967 706.6334228515625 0.3975590467453003 931.1438598632812 0.4250456690788269 0.8388893 0.49173498153686523 True -16 50133 32.46044039726257 0.5535604953765869 659.982177734375 0.5070805549621582 932.8903198242188 0.42486053705215454 0.8396713 0.47627297043800354 True -17 53082 32.51357698440552 0.5567605495452881 724.2970581054688 0.39955705404281616 932.947998046875 0.4244045615196228 0.8404208 0.47526517510414124 True -18 56031 32.51881432533264 0.552727460861206 728.0172119140625 0.31158962845802307 934.7656860351562 0.4226401150226593 0.8389399 0.4764818549156189 False -19 58980 32.52647399902344 0.5415749549865723 544.4549560546875 0.5009554028511047 934.2036743164062 0.42347753047943115 0.8373395 0.4786389172077179 False diff --git a/ENCSR771JQH/cherimoya.fold_2.performance.tsv b/ENCSR771JQH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6e0890be7fde9b4a6fa7e27c16697c0de52be7aa..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -932.947998046875 0.3444030284881592 0.4244045913219452 0.22870802879333496 0.8404207825660706 0.8012621402740479 0.47526517510414124 \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_3.evaluate.json b/ENCSR771JQH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7192cd0f5d3b57b732432aba27ac85bf0966dcfd..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959OIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_3.fit.json b/ENCSR771JQH/cherimoya.fold_3.fit.json deleted file mode 100644 index e31dd9e109587691c5f8a457789a7cdc30fb79b4..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF959OIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_3.log b/ENCSR771JQH/cherimoya.fold_3.log deleted file mode 100644 index 753028e0680425f151bf747994c8116d0b1d588b..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 34.542362213134766 4.500746726989746 776.2938842773438 0.7020272016525269 1067.50439453125 0.30331170558929443 0.68859375 9.361861228942871 True -1 5606 30.94731593132019 0.6828434467315674 960.6561889648438 0.9595683813095093 941.57470703125 0.3781982362270355 0.7481842 3.089722156524658 True -2 8409 31.033672094345093 1.8668427467346191 970.209228515625 0.7649198770523071 921.8558959960938 0.38880959153175354 0.7697898 1.715535283088684 True -3 11212 30.99003553390503 0.7177691459655762 694.249267578125 0.5937708616256714 914.8906860351562 0.3940241038799286 0.776778 1.441948652267456 True -4 14015 30.936770915985107 0.6042141914367676 644.6989135742188 0.6557019352912903 914.1183471679688 0.394741415977478 0.77886045 1.3040460348129272 True -5 16818 30.918153524398804 0.7039921283721924 605.44091796875 0.44340941309928894 907.7210083007812 0.39910590648651123 0.7853883 1.1723276376724243 True -6 19621 30.91063141822815 9.845847845077515 793.3434448242188 0.571857213973999 905.19775390625 0.40177178382873535 0.7810772 1.1125214099884033 False -7 22424 30.9628427028656 0.5880222320556641 750.9097900390625 0.6132806539535522 901.8682861328125 0.40413257479667664 0.7866167 1.0706950426101685 True -8 25227 31.020091772079468 0.620074987411499 900.7069091796875 0.747541069984436 896.704833984375 0.4078260660171509 0.7944895 0.9652068614959717 True -9 28030 30.965968132019043 0.588789701461792 710.0859375 0.43161970376968384 894.7949829101562 0.40907713770866394 0.7991231 0.9143701195716858 True -10 30833 30.96958875656128 0.5822174549102783 801.2606201171875 0.5702528953552246 892.2982177734375 0.4085942208766937 0.80541974 0.8501118421554565 True -11 33636 31.045887231826782 0.5802724361419678 676.0983276367188 0.6407017707824707 889.8284912109375 0.41086721420288086 0.81074154 0.8012620210647583 True -12 36439 30.9858558177948 0.5639727115631104 673.3799438476562 0.5752997398376465 883.1934204101562 0.4148966670036316 0.8165338 0.736183226108551 True -13 39242 30.99684762954712 0.5869996547698975 710.5633544921875 0.37467098236083984 881.1685791015625 0.41651833057403564 0.82287073 0.6672236323356628 True -14 42045 30.989630460739136 0.5934112071990967 669.4458618164062 0.4520528018474579 877.2935791015625 0.41836950182914734 0.83060557 0.5987981557846069 True -15 44848 30.88385510444641 0.5782263278961182 712.58544921875 0.36903488636016846 877.7439575195312 0.4160655736923218 0.83557904 0.5454087853431702 True -16 47651 30.854807138442993 0.585667610168457 784.5967407226562 0.3433051109313965 874.9085693359375 0.41889533400535583 0.83738774 0.5246996283531189 True -17 50454 30.815349340438843 0.5722830295562744 794.5115356445312 0.36371535062789917 877.3574829101562 0.41738075017929077 0.8379602 0.508709728717804 True -18 53257 30.937072277069092 0.5850951671600342 536.5164184570312 0.4416925013065338 875.8573608398438 0.41857442259788513 0.83709353 0.5071485638618469 False -19 56060 30.84856414794922 0.5827803611755371 690.2125244140625 0.3467261791229248 879.3900756835938 0.41454899311065674 0.83702075 0.50785893201828 False diff --git a/ENCSR771JQH/cherimoya.fold_3.performance.tsv b/ENCSR771JQH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0760e24ace9b1d55ae458cc59ba3ee2877ada1ac..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -877.3574829101562 0.3508716821670532 0.4173807203769684 0.21776577830314636 0.8379601836204529 0.7945954203605652 0.508709728717804 \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_4.evaluate.json b/ENCSR771JQH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 83550ad3fb632f86eea74c921b9d89ef43bb46e7..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF959OIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_4.fit.json b/ENCSR771JQH/cherimoya.fold_4.fit.json deleted file mode 100644 index 4e03cfb1aa79ac900701eacd46175597523897a8..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF959OIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR771JQH/cherimoya.fold_4.log b/ENCSR771JQH/cherimoya.fold_4.log deleted file mode 100644 index 0b75c25afb5800e6bc2e5fdd9a910e3a9fb318e2..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2823 35.577696323394775 3.818385601043701 925.843017578125 0.687943160533905 1004.8931884765625 0.2899623513221741 0.69593257 8.373285293579102 True -1 5646 31.13582134246826 1.3987023830413818 616.4613037109375 0.7601744532585144 880.2608032226562 0.367821604013443 0.7680544 2.111715316772461 True -2 8469 31.140379428863525 1.2346646785736084 590.3878173828125 0.7327708601951599 865.9166870117188 0.3745267391204834 0.77747256 1.0178875923156738 True -3 11292 31.13461184501648 0.8638393878936768 926.3302001953125 0.6283893585205078 857.7030029296875 0.38024476170539856 0.7862477 0.8450685739517212 True -4 14115 31.106947660446167 0.5524213314056396 855.7713012695312 0.5830285549163818 856.6322631835938 0.38096556067466736 0.79169375 0.8355356454849243 True -5 16938 31.114976167678833 0.5360288619995117 655.0838623046875 0.4609690308570862 851.3002319335938 0.3838253319263458 0.79531366 0.6667340397834778 True -6 19761 31.055421352386475 0.5305368900299072 725.741455078125 0.5615840554237366 845.8566284179688 0.3892148733139038 0.80053616 0.6205110549926758 True -7 22584 31.029525995254517 0.5566325187683105 761.0230712890625 0.5239583849906921 843.2222900390625 0.3905346393585205 0.80543864 0.55307537317276 True -8 25407 31.00099802017212 0.533287763595581 672.2617797851562 0.6654999256134033 840.5138549804688 0.3918835520744324 0.8100581 0.5447806119918823 True -9 28230 31.061134099960327 0.5575900077819824 741.89990234375 0.4995982050895691 835.7951049804688 0.3956015110015869 0.8113813 0.5465579032897949 True -10 31053 31.06934881210327 0.5463550090789795 734.35400390625 0.4991527795791626 835.0654907226562 0.39562416076660156 0.81840426 0.5145524144172668 True -11 33876 31.130001068115234 0.5464308261871338 582.87548828125 0.39970120787620544 829.981201171875 0.40029728412628174 0.82405263 0.49743762612342834 True -12 36699 31.0893337726593 0.5376689434051514 724.2636108398438 0.39108872413635254 827.8502197265625 0.40089550614356995 0.8280371 0.48131483793258667 True -13 39522 31.024583101272583 0.5549132823944092 694.16845703125 0.44210535287857056 826.6544799804688 0.4010430872440338 0.83282584 0.46438923478126526 True -14 42345 31.080901384353638 0.5431549549102783 749.9105834960938 0.5728176236152649 825.1764526367188 0.40324416756629944 0.8350336 0.45701485872268677 True -15 45168 31.1011745929718 0.5780477523803711 632.4063720703125 0.46498993039131165 824.2188720703125 0.40358707308769226 0.84188634 0.4440423250198364 True -16 47991 31.143109798431396 0.535334587097168 640.6463623046875 0.4518810510635376 823.8925170898438 0.40362730622291565 0.84392023 0.43436679244041443 True -17 50814 31.07951784133911 0.5338969230651855 696.8990478515625 0.3774142265319824 825.9041137695312 0.4016394317150116 0.84469026 0.4324246346950531 True -18 53637 31.107121229171753 0.5342893600463867 801.7958984375 0.3597866892814636 826.3939208984375 0.40064871311187744 0.8431556 0.43651309609413147 False -19 56460 31.060235023498535 0.5573141574859619 707.7750244140625 0.34037747979164124 826.3565063476562 0.401960551738739 0.84318995 0.436911016702652 False diff --git a/ENCSR771JQH/cherimoya.fold_4.performance.tsv b/ENCSR771JQH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fd870ad170f38129bfb6f570f462b2770e2752f8..0000000000000000000000000000000000000000 --- a/ENCSR771JQH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -825.9041137695312 0.36365342140197754 0.4016394317150116 0.20390240848064423 0.8446902632713318 0.8027686476707458 0.4324246346950531 \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_0.evaluate.json b/ENCSR773USD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2b66b62411cd110658305e4a098030688bda021f..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF860ZMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_0.fit.json b/ENCSR773USD/cherimoya.fold_0.fit.json deleted file mode 100644 index aabd88d289442a948427df5cc57174fd7a73f6a2..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF860ZMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_0.log b/ENCSR773USD/cherimoya.fold_0.log deleted file mode 100644 index 26d3a6f3b737b034b35963d2551f9adb0d62a22d..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1181 17.616748571395874 3.4754559993743896 192.66732788085938 0.26776307821273804 275.4182434082031 0.37593135237693787 0.7257044 13.420473098754883 True -1 2362 13.125836372375488 0.2639341354370117 188.35177612304688 0.1719638705253601 235.30911254882812 0.4469425082206726 0.7855983 3.1093013286590576 True -2 3543 13.118952512741089 0.2410273551940918 180.16600036621094 0.24663394689559937 226.9517364501953 0.4687845706939697 0.81043005 0.691192626953125 True -3 4724 13.121790885925293 0.23557615280151367 193.62734985351562 0.23812416195869446 221.36021423339844 0.4814077615737915 0.82331985 0.2686532735824585 True -4 5905 13.10143256187439 0.23525500297546387 174.73846435546875 0.2091088891029358 218.839111328125 0.488160640001297 0.832604 0.20570237934589386 True -5 7086 13.102332592010498 0.23507308959960938 217.77664184570312 0.12829867005348206 218.5776824951172 0.48929503560066223 0.83282495 0.23048369586467743 True -6 8267 13.111825704574585 0.23536205291748047 187.77972412109375 0.17647534608840942 217.8844451904297 0.49180731177330017 0.83952135 0.19614148139953613 True -7 9448 12.831911563873291 0.23839497566223145 188.85125732421875 0.20469744503498077 217.82481384277344 0.492196649312973 0.8436023 0.19673654437065125 True -8 10629 12.829084157943726 0.22855162620544434 176.28182983398438 0.2607154846191406 217.29396057128906 0.49439945816993713 0.84148437 0.18985018134117126 False -9 11810 12.848847389221191 0.23504972457885742 192.10348510742188 0.17411011457443237 216.7089385986328 0.4964587986469269 0.8494061 0.17403098940849304 True -10 12991 12.85430359840393 0.23348760604858398 194.00531005859375 0.22286251187324524 216.3314208984375 0.49794718623161316 0.854606 0.16360695660114288 True -11 14172 12.86215353012085 0.2384650707244873 187.600341796875 0.11772729456424713 216.1858367919922 0.4985380172729492 0.85871035 0.15985819697380066 True -12 15353 12.839869976043701 0.23744726181030273 214.5214080810547 0.20287099480628967 215.89566040039062 0.4996711015701294 0.8618095 0.15288111567497253 True -13 16534 12.876561403274536 0.2406017780303955 181.59780883789062 0.20496292412281036 215.76730346679688 0.5001480579376221 0.8658736 0.1473490297794342 True -14 17715 12.887454986572266 0.23429298400878906 188.14907836914062 0.15243381261825562 215.7068328857422 0.500255823135376 0.866243 0.14314770698547363 True -15 18896 12.912534952163696 0.23429203033447266 161.87313842773438 0.16464608907699585 215.7251434326172 0.49992117285728455 0.8683981 0.14218194782733917 True -16 20077 12.86270523071289 0.23384428024291992 188.63201904296875 0.08291283249855042 215.9229736328125 0.4990159571170807 0.86840504 0.14211662113666534 True -17 21258 12.829659461975098 0.2299487590789795 180.07373046875 0.08812566101551056 216.16482543945312 0.497711718082428 0.8664554 0.14493875205516815 False -18 22439 12.827474355697632 0.25228404998779297 184.94418334960938 0.11278842389583588 216.46307373046875 0.496439665555954 0.8637001 0.14533556997776031 False -19 23620 12.888471364974976 0.23740220069885254 160.84869384765625 0.15461911261081696 216.67169189453125 0.49542590975761414 0.8634206 0.14651808142662048 False diff --git a/ENCSR773USD/cherimoya.fold_0.performance.tsv b/ENCSR773USD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1e864ddf8aa4dde02a6f4a52e096f6274f9c8ba5..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -215.9229736328125 0.3885091543197632 0.4990159869194031 0.1466849446296692 0.8684050440788269 0.8354108929634094 0.14211662113666534 \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_1.evaluate.json b/ENCSR773USD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1ff37b7c9ce6195a0f3a953bcfa7717689687b6a..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF860ZMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_1.fit.json b/ENCSR773USD/cherimoya.fold_1.fit.json deleted file mode 100644 index f1a74a743e17495badf98c8aa53d07def6cfda28..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF860ZMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_1.log b/ENCSR773USD/cherimoya.fold_1.log deleted file mode 100644 index c58be871ff4c6c1ac2de6f1dded6601e31e1d887..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1167 17.487123727798462 3.924248695373535 212.43797302246094 0.2668280005455017 307.8389587402344 0.3921487331390381 0.6466947 14.756315231323242 True -1 2334 13.009110450744629 0.3198049068450928 188.03067016601562 0.23428308963775635 261.8222351074219 0.4653562307357788 0.7111287 4.010403633117676 True -2 3501 13.104767084121704 0.3006305694580078 188.83935546875 0.2589377462863922 254.2787322998047 0.4860849678516388 0.7305428 0.9359961748123169 True -3 4668 12.986466407775879 0.3028271198272705 175.83822631835938 0.2641097605228424 246.0146942138672 0.505253791809082 0.76382273 0.3142203986644745 True -4 5835 12.998926639556885 0.30835890769958496 193.89378356933594 0.25968098640441895 242.67800903320312 0.5126768946647644 0.77968526 0.27918189764022827 True -5 7002 12.949154138565063 0.2877020835876465 197.37417602539062 0.20188993215560913 241.68731689453125 0.5155910849571228 0.7873287 0.26601800322532654 True -6 8169 12.935365915298462 0.2947103977203369 212.39781188964844 0.2240724414587021 242.3978729248047 0.5135102868080139 0.78705496 0.2712024748325348 False -7 9336 12.973775148391724 0.28974342346191406 211.59901428222656 0.13001039624214172 240.9175262451172 0.5182508826255798 0.7960291 0.23013080656528473 True -8 10503 12.941062927246094 0.2973010540008545 195.57118225097656 0.13641738891601562 240.0485076904297 0.521264910697937 0.8042735 0.21801704168319702 True -9 11670 12.937547206878662 0.2918407917022705 182.03857421875 0.1467178910970688 239.62924194335938 0.5230092406272888 0.81055206 0.20527684688568115 True -10 12837 12.961353302001953 0.2900834083557129 186.7737579345703 0.14933931827545166 239.2053985595703 0.5245950222015381 0.8182731 0.1983223259449005 True -11 14004 12.953729629516602 0.29093122482299805 174.75157165527344 0.240141361951828 238.7136993408203 0.5261186361312866 0.8244484 0.18823948502540588 True -12 15171 13.078977823257446 0.2994675636291504 204.53953552246094 0.13036897778511047 238.30117797851562 0.5273721218109131 0.82944995 0.1852331906557083 True -13 16338 12.968318462371826 0.2921462059020996 190.46932983398438 0.13978461921215057 238.03822326660156 0.5281767249107361 0.83466846 0.17521700263023376 True -14 17505 12.987485885620117 0.28603553771972656 167.43917846679688 0.16545535624027252 237.95559692382812 0.5281901955604553 0.837403 0.17065295577049255 True -15 18672 12.986543655395508 0.28608274459838867 190.30824279785156 0.10616791248321533 238.0053253173828 0.5276327133178711 0.84048706 0.16699527204036713 True -16 19839 13.02879810333252 0.29515695571899414 175.57191467285156 0.09394928067922592 238.2506866455078 0.5264631509780884 0.8416102 0.16334256529808044 True -17 21006 13.003642082214355 0.29556870460510254 153.84014892578125 0.11651290208101273 238.5491943359375 0.5247158408164978 0.84221274 0.16382627189159393 True -18 22173 12.988588571548462 0.28595399856567383 217.76931762695312 0.09052735567092896 238.93711853027344 0.5230087041854858 0.84125197 0.16504859924316406 False -19 23340 13.004270553588867 0.29086828231811523 181.37457275390625 0.09506791830062866 239.16159057617188 0.5218924283981323 0.84047943 0.16581977903842926 False diff --git a/ENCSR773USD/cherimoya.fold_1.performance.tsv b/ENCSR773USD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 74f499ef6094e4d98048241cf52401fd2635f652..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -238.5491943359375 0.36898544430732727 0.5247158408164978 0.16126638650894165 0.8422127366065979 0.8401918411254883 0.16382627189159393 \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_2.evaluate.json b/ENCSR773USD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 526ab5fa75f7338c2b646c9f101399ba8ddbd932..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF860ZMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_2.fit.json b/ENCSR773USD/cherimoya.fold_2.fit.json deleted file mode 100644 index 64f88375b83a4f5b82004089aad8590e15beb4b8..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF860ZMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_2.log b/ENCSR773USD/cherimoya.fold_2.log deleted file mode 100644 index 4415d142088aa678e1c9d0c409105deccc3ae7fe..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1223 18.00974178314209 3.3772964477539062 186.40478515625 0.25671809911727905 287.3363037109375 0.3826824426651001 0.6803475 13.439577102661133 True -1 2446 13.601960182189941 3.8156168460845947 191.34085083007812 0.19741028547286987 245.35682678222656 0.4558892548084259 0.7474866 3.0801703929901123 True -2 3669 13.763663291931152 0.2600243091583252 184.46530151367188 0.10416756570339203 236.57943725585938 0.47837844491004944 0.7761547 0.6939297914505005 True -3 4892 13.5698983669281 0.25150132179260254 207.07046508789062 0.22476491332054138 230.08131408691406 0.49341893196105957 0.79401165 0.38595476746559143 True -4 6115 13.615711688995361 0.2603747844696045 196.82131958007812 0.23235571384429932 228.2022705078125 0.4975859522819519 0.7996414 0.25686198472976685 True -5 7338 13.62016487121582 0.25646257400512695 187.69168090820312 0.1653052121400833 227.48150634765625 0.4996200501918793 0.8058373 0.21812663972377777 True -6 8561 13.579014539718628 0.2558150291442871 191.25120544433594 0.22099673748016357 227.1327667236328 0.5009489059448242 0.8099851 0.21168360114097595 True -7 9784 13.58417820930481 0.8930923938751221 170.8824920654297 0.21223564445972443 226.56689453125 0.5031201243400574 0.8133164 0.20603357255458832 True -8 11007 13.577913284301758 0.26484131813049316 188.9507598876953 0.1125556081533432 226.13687133789062 0.5045360922813416 0.8163647 0.1986692100763321 True -9 12230 13.572592735290527 0.25959300994873047 202.41851806640625 0.15124323964118958 225.73858642578125 0.5059424042701721 0.82064885 0.2009456604719162 True -10 13453 13.603382349014282 0.25124406814575195 181.57052612304688 0.16784411668777466 225.53121948242188 0.5066252946853638 0.8226038 0.21103812754154205 True -11 14676 13.607589721679688 0.2503042221069336 184.93931579589844 0.22690005600452423 225.06118774414062 0.5084159970283508 0.82799137 0.1979251652956009 True -12 15899 13.60381031036377 0.29622817039489746 192.8251953125 0.2582152783870697 224.81727600097656 0.5094980597496033 0.8329281 0.18457794189453125 True -13 17122 13.611945629119873 0.2509431838989258 198.51437377929688 0.1396348774433136 224.57644653320312 0.5101726651191711 0.8367304 0.1780983954668045 True -14 18345 13.609503030776978 0.3127477169036865 192.78602600097656 0.16083687543869019 224.50079345703125 0.5102587342262268 0.837996 0.17493122816085815 True -15 19568 13.333556175231934 0.25232648849487305 189.042236328125 0.09254885464906693 224.61181640625 0.509757399559021 0.84034175 0.17125582695007324 True -16 20791 13.336730480194092 0.25438976287841797 176.79510498046875 0.10201796889305115 224.8476104736328 0.5086068511009216 0.840368 0.1707625538110733 True -17 22014 13.292193174362183 0.2519083023071289 206.29428100585938 0.09854231774806976 225.18194580078125 0.5069881081581116 0.84106755 0.17158757150173187 True -18 23237 13.29971981048584 0.2555861473083496 168.728759765625 0.11705540120601654 225.52577209472656 0.5054795145988464 0.8380447 0.17241346836090088 False -19 24460 13.32102084159851 0.24691987037658691 167.5415802001953 0.12444780021905899 225.72373962402344 0.5045627355575562 0.83821356 0.1748424619436264 False diff --git a/ENCSR773USD/cherimoya.fold_2.performance.tsv b/ENCSR773USD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cff3b5de420b929c7c6ad5e8bd2a22a04300d819..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -225.18194580078125 0.38163456320762634 0.5069881081581116 0.15208804607391357 0.8410675525665283 0.823094367980957 0.17158757150173187 \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_3.evaluate.json b/ENCSR773USD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4eb8a697722687bc0400da73af056ccc9b3aa009..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF860ZMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_3.fit.json b/ENCSR773USD/cherimoya.fold_3.fit.json deleted file mode 100644 index 381bfad0e76adba0897b47c5d9131cb067b048c3..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF860ZMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_3.log b/ENCSR773USD/cherimoya.fold_3.log deleted file mode 100644 index 9d81b022a645c41fe0605fc89d4d1d1736d6e59e..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1198 17.615920066833496 3.4545645713806152 188.04440307617188 0.2739187479019165 278.52020263671875 0.3751329779624939 0.69261086 13.265157699584961 True -1 2396 13.336185216903687 0.6102931499481201 197.38299560546875 0.27785176038742065 236.38140869140625 0.44903138279914856 0.75745213 3.222360372543335 True -2 3594 13.34151577949524 0.24120593070983887 187.66293334960938 0.1864856630563736 227.52928161621094 0.4728178083896637 0.7889887 0.5890021920204163 True -3 4792 13.333173751831055 0.24703121185302734 213.81103515625 0.2081913948059082 221.8927764892578 0.4860294461250305 0.817129 0.3566594421863556 True -4 5990 13.36054539680481 0.24454832077026367 174.91262817382812 0.14940068125724792 219.84841918945312 0.4909035265445709 0.8239779 0.2624528408050537 True -5 7188 13.310651302337646 0.2389514446258545 203.37620544433594 0.24870099127292633 219.4550018310547 0.49197372794151306 0.82594913 0.22879305481910706 True -6 8386 13.317910432815552 0.24157190322875977 179.3327178955078 0.1550460159778595 218.9828643798828 0.493724524974823 0.8321219 0.2049943506717682 True -7 9584 13.30785322189331 0.23922157287597656 208.84710693359375 0.1730128675699234 218.4945526123047 0.49593687057495117 0.83675724 0.19168023765087128 True -8 10782 13.305768728256226 0.24970269203186035 187.36639404296875 0.1657099425792694 218.2025146484375 0.4970577359199524 0.84072983 0.18578343093395233 True -9 11980 13.280542850494385 0.248152494430542 179.1932373046875 0.261834979057312 218.08578491210938 0.4978431463241577 0.8457475 0.18665163218975067 True -10 13178 13.3076651096344 0.7066552639007568 190.61891174316406 0.11586828529834747 217.62074279785156 0.49929794669151306 0.8495549 0.17684152722358704 True -11 14376 13.29812479019165 0.24469780921936035 178.99888610839844 0.181125670671463 217.5047149658203 0.4999758005142212 0.8512739 0.1759314388036728 True -12 15574 13.292624235153198 0.9477553367614746 167.295166015625 0.11924026906490326 217.2333984375 0.5009679794311523 0.8509239 0.1686268448829651 False -13 16772 13.298280000686646 0.24360370635986328 198.8575439453125 0.19157691299915314 217.0667266845703 0.5015864968299866 0.850954 0.1658681482076645 False -14 17970 13.316324949264526 0.24496746063232422 213.52395629882812 0.17444074153900146 216.93226623535156 0.5017763376235962 0.85149163 0.16458028554916382 True -15 19168 13.308141231536865 0.24779725074768066 189.0286102294922 0.11222676187753677 217.04063415527344 0.5014458298683167 0.84982365 0.16598741710186005 False -16 20366 13.299561977386475 0.2501058578491211 205.67831420898438 0.07859038561582565 217.20030212402344 0.5004808902740479 0.8503299 0.169828400015831 False -17 21564 13.30137848854065 0.29599714279174805 160.43153381347656 0.10319292545318604 217.5551300048828 0.4990290701389313 0.84659296 0.17182420194149017 False -18 22762 13.301158428192139 0.24580812454223633 185.44479370117188 0.06964211165904999 217.83619689941406 0.4977385103702545 0.8432578 0.17497003078460693 False -19 23960 13.311069250106812 0.2514011859893799 176.80801391601562 0.0987929180264473 218.09109497070312 0.49678534269332886 0.84171045 0.17591592669487 False diff --git a/ENCSR773USD/cherimoya.fold_3.performance.tsv b/ENCSR773USD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9c57cb488d56f56ddd6f894d26635adb5efc1c97..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -216.93226623535156 0.3868749737739563 0.5017762780189514 0.14515820145606995 0.8514916300773621 0.8194460272789001 0.16458028554916382 \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_4.evaluate.json b/ENCSR773USD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f024be0405e254c562106b1221c339e95a4bc553..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF860ZMO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_4.fit.json b/ENCSR773USD/cherimoya.fold_4.fit.json deleted file mode 100644 index 006565fa1c5262b234ced09bb488adf86512557a..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF860ZMO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR773USD/cherimoya.fold_4.log b/ENCSR773USD/cherimoya.fold_4.log deleted file mode 100644 index c2993ce7654ecf36ca071bbb2119087bececc724..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1184 17.807842254638672 3.3374719619750977 172.257568359375 0.19288945198059082 275.3896789550781 0.3757762908935547 0.7205939 13.596189498901367 True -1 2368 13.140346050262451 0.2557220458984375 197.57015991210938 0.24490778148174286 235.0464630126953 0.447081983089447 0.77082473 3.3269200325012207 True -2 3552 13.13889479637146 0.24260544776916504 224.27099609375 0.1612243354320526 227.3324737548828 0.46690893173217773 0.7925814 0.882084310054779 True -3 4736 13.1276273727417 0.23633480072021484 200.47616577148438 0.25179219245910645 222.19046020507812 0.478655606508255 0.8122851 0.4420291781425476 True -4 5920 13.132318019866943 1.5251295566558838 188.1530303955078 0.20221951603889465 218.95921325683594 0.4877382218837738 0.8288832 0.27938538789749146 True -5 7104 13.162402868270874 0.24663591384887695 184.07186889648438 0.20478954911231995 217.85992431640625 0.4909762740135193 0.83612335 0.19109652936458588 True -6 8288 13.137551069259644 0.24196386337280273 195.82640075683594 0.15313109755516052 217.55300903320312 0.4918888807296753 0.8421417 0.18550962209701538 True -7 9472 13.158581972122192 0.3590211868286133 170.30258178710938 0.15169760584831238 217.2421417236328 0.49309998750686646 0.84516186 0.18681266903877258 True -8 10656 13.127573013305664 0.5376513004302979 183.4150390625 0.1252618432044983 216.78213500976562 0.49463337659835815 0.8501642 0.17624162137508392 True -9 11840 13.15919542312622 0.25603461265563965 185.5579833984375 0.14214973151683807 216.4200439453125 0.49604108929634094 0.85464406 0.16423185169696808 True -10 13024 13.147718906402588 0.24468398094177246 208.41590881347656 0.1666419953107834 216.1831512451172 0.49697452783584595 0.8582556 0.16012682020664215 True -11 14208 13.176644325256348 0.24467158317565918 215.4396514892578 0.16620060801506042 215.9125518798828 0.49798664450645447 0.8628006 0.14989106357097626 True -12 15392 13.16411828994751 0.23731470108032227 170.38461303710938 0.11183281242847443 215.66043090820312 0.49882447719573975 0.8669189 0.1375102698802948 True -13 16576 13.176377058029175 0.2548043727874756 207.01490783691406 0.16744112968444824 215.4888916015625 0.49950966238975525 0.8699003 0.13462653756141663 True -14 17760 13.150232791900635 0.23995327949523926 162.7501220703125 0.09055930376052856 215.40850830078125 0.4997732937335968 0.8721078 0.13158056139945984 True -15 18944 13.145559549331665 0.24185729026794434 188.10183715820312 0.09640488028526306 215.51318359375 0.49923786520957947 0.8729024 0.13195157051086426 True -16 20128 13.139419555664062 0.24213480949401855 162.558349609375 0.1676172912120819 215.73829650878906 0.4980309307575226 0.8724004 0.13411004841327667 False -17 21312 13.145337104797363 0.24167728424072266 172.3776092529297 0.07994967699050903 216.06077575683594 0.4964504837989807 0.86811924 0.13788069784641266 False -18 22496 13.177812814712524 0.23827672004699707 182.89407348632812 0.08211851119995117 216.4189453125 0.4947279989719391 0.86530703 0.14181150496006012 False -19 23680 13.167184352874756 0.22996258735656738 195.42913818359375 0.11457329988479614 216.671630859375 0.49364572763442993 0.863302 0.1452532261610031 False diff --git a/ENCSR773USD/cherimoya.fold_4.performance.tsv b/ENCSR773USD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e5827024417633858798e2f04eefe1f63a1e558f..0000000000000000000000000000000000000000 --- a/ENCSR773USD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -215.51318359375 0.3891034424304962 0.49923786520957947 0.14305785298347473 0.8729023933410645 0.8356395363807678 0.13195157051086426 \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_0.evaluate.json b/ENCSR774NXA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e525ab978831b7a3fe5e7533f2db0f8a5c7846da..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495ANZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_0.fit.json b/ENCSR774NXA/cherimoya.fold_0.fit.json deleted file mode 100644 index f446541ca98f13f283d20343b74b0e21059f9c4f..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF495ANZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_0.log b/ENCSR774NXA/cherimoya.fold_0.log deleted file mode 100644 index 9b7dd228d394e40f08e54ebd43dfc30e5b139120..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3450 42.96952033042908 3.9195189476013184 737.4952392578125 1.1442185640335083 1019.7662963867188 0.6895791292190552 0.58696806 9.39871883392334 True -1 6900 38.32698607444763 0.7514128684997559 712.0936889648438 1.104557752609253 857.1143798828125 0.7711633443832397 0.6108563 2.195667266845703 True -2 10350 38.32350778579712 2.124764919281006 783.971435546875 2.138615131378174 832.4459838867188 0.7811921834945679 0.6032723 1.3009800910949707 False -3 13800 38.32441830635071 0.6747620105743408 700.726318359375 0.7896119356155396 820.1288452148438 0.7875043749809265 0.6151058 1.238263487815857 True -4 17250 38.291953325271606 0.6636910438537598 731.7651977539062 1.1289678812026978 815.9960327148438 0.7895119190216064 0.6066049 1.0982660055160522 False -5 20700 38.27554893493652 0.6753683090209961 731.8675537109375 1.235061526298523 810.9559326171875 0.7922520041465759 0.6148613 1.0709377527236938 False -6 24150 38.26509428024292 2.057194471359253 686.1710205078125 0.7451782822608948 805.8844604492188 0.7949413061141968 0.6237643 1.0549720525741577 True -7 27600 37.49198079109192 1.442899465560913 658.1504516601562 0.9443666934967041 801.7600708007812 0.7965512871742249 0.62919503 1.0015870332717896 True -8 31050 37.67634987831116 0.6514146327972412 574.955078125 0.8318156599998474 796.341552734375 0.7988406419754028 0.6264764 1.054466962814331 False -9 34500 37.73719930648804 0.6598525047302246 685.9168701171875 1.2679777145385742 789.0302734375 0.8022895455360413 0.64095813 0.9381059408187866 True -10 37950 37.70561480522156 0.6487107276916504 721.8275146484375 1.0292093753814697 782.5231323242188 0.805263876914978 0.6447095 0.9409214854240417 True -11 41400 37.67872667312622 0.6489784717559814 750.0587158203125 0.7178113460540771 778.96337890625 0.8072950839996338 0.6604913 0.8775562644004822 True -12 44850 37.67058825492859 0.6568763256072998 519.7863159179688 0.7694270014762878 774.019775390625 0.8098458647727966 0.66694677 0.8270664215087891 True -13 48300 37.678011894226074 0.6405847072601318 673.159423828125 1.175077199935913 768.3302001953125 0.8122046589851379 0.6794932 0.7768028378486633 True -14 51750 37.68300271034241 0.6484379768371582 616.745361328125 0.7102890014648438 765.612060546875 0.8140926361083984 0.6883754 0.7537466883659363 True -15 55200 37.77945017814636 0.6412491798400879 543.6387329101562 0.5984878540039062 762.1810913085938 0.8154681921005249 0.69411814 0.740888237953186 True -16 58650 37.631043434143066 0.654686689376831 594.5913696289062 0.5753481984138489 761.8384399414062 0.8158080577850342 0.69522685 0.7313619256019592 True -17 62100 37.68106150627136 0.6547026634216309 631.44287109375 0.5785813927650452 762.643310546875 0.8156439065933228 0.69318634 0.7450282573699951 False -18 65550 37.64209747314453 1.4489457607269287 555.930419921875 1.342120885848999 763.8694458007812 0.815191924571991 0.6896193 0.7651659846305847 False -19 69000 37.67419672012329 0.6441073417663574 601.861572265625 0.5343682765960693 764.7719116210938 0.8148121237754822 0.6843176 0.7811033725738525 False diff --git a/ENCSR774NXA/cherimoya.fold_0.performance.tsv b/ENCSR774NXA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b3c931bd5467f62adafb8b45033f0016e748f3c4..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -761.8384399414062 0.15032963454723358 0.8158079385757446 0.47280174493789673 0.6952268481254578 0.6391245126724243 0.7313619256019592 \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_1.evaluate.json b/ENCSR774NXA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 402bfc23e8074b30240e0c5d6b6ff4861a398d5b..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495ANZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_1.fit.json b/ENCSR774NXA/cherimoya.fold_1.fit.json deleted file mode 100644 index 50c3ac215c9a9ae6ed42f548577cda88d046f4ee..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF495ANZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_1.log b/ENCSR774NXA/cherimoya.fold_1.log deleted file mode 100644 index 15f18ddc92c838ac15b7b073d1f4c991eeb11794..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3419 44.32028651237488 4.280708312988281 712.28369140625 0.9013748168945312 1165.393798828125 0.6969984769821167 0.5942839 9.99909496307373 True -1 6838 37.93257761001587 1.0562126636505127 769.7073974609375 1.3911197185516357 960.5532836914062 0.7823578119277954 0.6429293 2.3953616619110107 True -2 10257 37.49512267112732 0.9272735118865967 747.4075927734375 1.058011770248413 929.9966430664062 0.7931625247001648 0.63929963 1.2898436784744263 False -3 13676 37.16059684753418 0.9042313098907471 657.5709228515625 1.0819655656814575 915.1420288085938 0.7987766861915588 0.6413547 1.0899683237075806 False -4 17095 37.12907528877258 0.9172775745391846 618.3609008789062 1.0220158100128174 905.048828125 0.8023324012756348 0.64423436 1.000463843345642 True -5 20514 37.19235920906067 0.9052712917327881 811.950927734375 1.1498522758483887 901.787109375 0.8035043478012085 0.64411896 0.9538489580154419 False -6 23933 37.17815613746643 1.559739351272583 718.7057495117188 0.7086843252182007 896.3880004882812 0.8068147897720337 0.6507336 0.9951954483985901 True -7 27352 37.13764786720276 0.9219870567321777 585.4081420898438 1.1696301698684692 890.8941650390625 0.8088282942771912 0.65794545 0.9329724311828613 True -8 30771 37.40324783325195 0.9202616214752197 650.5800170898438 1.2030271291732788 884.2853393554688 0.8111816644668579 0.67122364 0.9054200649261475 True -9 34190 37.15922689437866 1.4850332736968994 664.5136108398438 0.9337133169174194 880.311279296875 0.813435971736908 0.67069244 0.9089859127998352 False -10 37609 37.30031752586365 1.7280793190002441 615.7373046875 0.9049357175827026 873.2744750976562 0.8163361549377441 0.68226326 0.8783213496208191 True -11 41028 37.308263063430786 0.9321727752685547 599.3453979492188 1.4457671642303467 866.3594970703125 0.8188599944114685 0.6932162 0.8289860486984253 True -12 44447 37.36517357826233 1.0562362670898438 703.225341796875 1.0818922519683838 861.3804931640625 0.8207203149795532 0.7006602 0.776829719543457 True -13 47866 37.34936785697937 23.451109409332275 557.8775024414062 0.8803510069847107 856.3629760742188 0.823189377784729 0.70807624 0.7874094843864441 True -14 51285 37.30804467201233 0.9569082260131836 583.5634765625 0.7803384065628052 852.0081787109375 0.8248934745788574 0.7179568 0.749596118927002 True -15 54704 37.36054730415344 0.9544086456298828 584.3131103515625 0.7597448229789734 849.5435791015625 0.8260766267776489 0.72567517 0.7375020384788513 True -16 58123 37.369240283966064 0.9457230567932129 689.07373046875 0.5286737680435181 849.024169921875 0.8264175653457642 0.7285904 0.7288979887962341 True -17 61542 37.36320900917053 0.9397265911102295 686.9061279296875 0.5361765623092651 850.1112060546875 0.8259791731834412 0.7267702 0.7417269945144653 False -18 64961 37.424283266067505 16.477676153182983 568.87939453125 0.7801349759101868 851.98095703125 0.8252928853034973 0.7221496 0.7694545984268188 False -19 68380 37.348944902420044 0.9534332752227783 563.6660766601562 0.7718014717102051 852.7598876953125 0.8247631788253784 0.71853083 0.784221351146698 False diff --git a/ENCSR774NXA/cherimoya.fold_1.performance.tsv b/ENCSR774NXA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index de170d23e92414cba774dbfb123c8383158d2f0d..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -849.024169921875 0.13799749314785004 0.8264175653457642 0.5097604990005493 0.7285904288291931 0.6939082145690918 0.7288979887962341 \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_2.evaluate.json b/ENCSR774NXA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a2c48cd9d8ad9b62c4c5f9c04e7d738633920678..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495ANZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_2.fit.json b/ENCSR774NXA/cherimoya.fold_2.fit.json deleted file mode 100644 index 4df0f5e4498114f31ebd1726b20463af9b0cb23d..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF495ANZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_2.log b/ENCSR774NXA/cherimoya.fold_2.log deleted file mode 100644 index 62e601170f21402ce3d8002a0803bebcd1e2cfab..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3671 45.34721326828003 4.409353733062744 726.92431640625 1.4954419136047363 1035.2427978515625 0.7019311785697937 0.5822067 7.988208770751953 True -1 7342 40.61662220954895 0.9272050857543945 756.726806640625 1.5346479415893555 872.5921630859375 0.7806736826896667 0.6326869 2.42112135887146 True -2 11013 40.77776885032654 0.7524542808532715 564.8930053710938 1.2707061767578125 855.326904296875 0.7863180041313171 0.6280112 1.525503158569336 False -3 14684 40.73897910118103 0.7153899669647217 630.3118896484375 2.025550127029419 844.6790161132812 0.7918569445610046 0.63459754 1.3661367893218994 True -4 18355 40.70993399620056 0.7164397239685059 539.313720703125 1.642543911933899 838.967041015625 0.7947954535484314 0.63404906 1.1650006771087646 False -5 22026 40.74496150016785 1.94118332862854 675.9669189453125 0.9617660045623779 833.9810180664062 0.7967257499694824 0.63758314 1.0442681312561035 True -6 25697 40.74687147140503 0.7166099548339844 619.14208984375 1.1059744358062744 829.7784423828125 0.7986922860145569 0.6421746 1.0467417240142822 True -7 29368 40.733755588531494 0.7141017913818359 671.525634765625 1.315019965171814 823.7528076171875 0.8013461232185364 0.6471255 1.0089188814163208 True -8 33039 40.80416512489319 0.715336799621582 715.4140625 0.7657047510147095 819.7032470703125 0.8031625151634216 0.651288 0.9527613520622253 True -9 36710 40.71730065345764 0.7494513988494873 774.849853515625 0.8329994082450867 814.02783203125 0.80562824010849 0.65560234 0.939034640789032 True -10 40381 41.900023460388184 0.7411777973175049 746.7362060546875 0.7424953579902649 808.7865600585938 0.8075449466705322 0.66480595 0.8604781627655029 True -11 44052 40.861618518829346 1.9982757568359375 632.5772094726562 0.7644126415252686 803.3259887695312 0.8099048137664795 0.6725529 0.8228718638420105 True -12 47723 40.79006910324097 0.7220363616943359 506.950927734375 1.2747836112976074 798.622314453125 0.8123236894607544 0.68139637 0.8160770535469055 True -13 51394 40.76501965522766 0.7270429134368896 632.0333251953125 0.8175747394561768 793.2119140625 0.814298152923584 0.6879766 0.7789257764816284 True -14 55065 40.81295561790466 27.695804834365845 594.09765625 1.1264265775680542 789.4389038085938 0.816524863243103 0.6930526 0.7533385157585144 True -15 58736 41.43916058540344 4.693037271499634 634.7000122070312 0.8290964961051941 786.0617065429688 0.8180771470069885 0.7013273 0.7322600483894348 True -16 62407 40.91837430000305 0.7372307777404785 582.5568237304688 0.5272703170776367 785.4923095703125 0.8185811638832092 0.70154697 0.7343882322311401 True -17 66078 40.582900047302246 0.7233784198760986 521.6074829101562 0.6567612290382385 785.885498046875 0.8183146715164185 0.7009479 0.7537160515785217 False -18 69749 39.93648934364319 0.701000452041626 611.216796875 0.555927038192749 786.9625854492188 0.8179149031639099 0.7002621 0.7694571614265442 False -19 73420 39.932525873184204 0.7153134346008301 587.5125732421875 0.5804188251495361 787.6049194335938 0.8175380229949951 0.6975717 0.7771187424659729 False diff --git a/ENCSR774NXA/cherimoya.fold_2.performance.tsv b/ENCSR774NXA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4c949a83e43bfcf8c2a6ffd2032d085bcf3d1a9f..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -785.4923095703125 0.1460077315568924 0.8185811638832092 0.4866364896297455 0.7015469670295715 0.6535235643386841 0.7343882322311401 \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_3.evaluate.json b/ENCSR774NXA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fc3dbb2bcbe7f9f794eadb98605990c52475d957..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495ANZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_3.fit.json b/ENCSR774NXA/cherimoya.fold_3.fit.json deleted file mode 100644 index 1a73fcba6f45064a931ef6046ea037324b92f270..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF495ANZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_3.log b/ENCSR774NXA/cherimoya.fold_3.log deleted file mode 100644 index 69d44376a7e628b4cf2d7a6d8137a5dc5a96d9e4..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3515 44.220736265182495 16.579759120941162 640.2560424804688 1.3339629173278809 995.7935180664062 0.6965875625610352 0.5591337 7.855630397796631 True -1 7030 39.01267671585083 0.7614490985870361 751.2066040039062 1.314157247543335 835.6358032226562 0.7754039764404297 0.58975387 2.4356677532196045 True -2 10545 38.99807691574097 1.434513807296753 660.6399536132812 0.9561858177185059 819.9290771484375 0.7808783650398254 0.5926835 1.3729547262191772 True -3 14060 39.0192768573761 0.6967263221740723 813.772216796875 2.059021472930908 806.35595703125 0.7864538431167603 0.59114486 1.0611552000045776 False -4 17575 39.140376329422 0.7048561573028564 619.31689453125 1.0286509990692139 804.64111328125 0.7880985736846924 0.59877247 1.0781747102737427 True -5 21090 38.98882746696472 0.6883976459503174 628.7561645507812 0.9821847677230835 800.1930541992188 0.7899124026298523 0.59533215 1.0070980787277222 False -6 24605 39.020586252212524 0.6879770755767822 635.4755859375 0.863680899143219 795.7318115234375 0.7924627065658569 0.5994523 1.0075702667236328 True -7 28120 39.05028986930847 13.922582864761353 719.5206909179688 1.0576171875 789.1311645507812 0.7954010367393494 0.61390257 0.9666398167610168 True -8 31635 39.30536890029907 0.688838005065918 601.8801879882812 1.0307636260986328 784.3952026367188 0.7978682518005371 0.6245683 0.9222458004951477 True -9 35150 39.030823945999146 0.7509820461273193 554.970703125 0.8532195091247559 779.417236328125 0.8003147840499878 0.62878245 0.902845025062561 True -10 38665 39.12554121017456 0.6993939876556396 593.9119873046875 0.8752807378768921 775.63134765625 0.8024637699127197 0.64063734 0.8886228799819946 True -11 42180 39.06429171562195 1.4158756732940674 625.1927490234375 1.0388314723968506 770.5870971679688 0.804655134677887 0.65167785 0.8555246591567993 True -12 45695 38.98531150817871 1.937849521636963 591.8516845703125 1.1367132663726807 764.768798828125 0.80724036693573 0.6599127 0.8200811743736267 True -13 49210 38.72017979621887 0.7095096111297607 624.738037109375 1.0674723386764526 761.22314453125 0.8092561960220337 0.6649796 0.8018401265144348 True -14 52725 38.21325087547302 0.7725884914398193 675.826416015625 0.940954864025116 758.60498046875 0.810819149017334 0.6782379 0.7606400847434998 True -15 56240 38.181395053863525 0.697833776473999 589.94677734375 0.581086277961731 756.0400390625 0.812373161315918 0.68418264 0.7694765329360962 True -16 59755 38.16678309440613 0.6850113868713379 536.9933471679688 0.7936432361602783 755.8202514648438 0.8126694560050964 0.6863097 0.7830407023429871 True -17 63270 38.19129776954651 1.3337242603302002 627.5868530273438 0.5017228722572327 756.7240600585938 0.8123698830604553 0.6861158 0.7941820621490479 False -18 66785 38.24663233757019 0.6981279850006104 688.0013427734375 0.5512737035751343 757.982666015625 0.8118323683738708 0.6825076 0.824446439743042 False -19 70300 38.21127939224243 0.6816592216491699 652.2561645507812 0.6297008395195007 758.5473022460938 0.8115051984786987 0.6797009 0.838129460811615 False diff --git a/ENCSR774NXA/cherimoya.fold_3.performance.tsv b/ENCSR774NXA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 702cffbd677ed4ad3b6c195f880cfba5721cb269..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -755.8202514648438 0.15177246928215027 0.8126694560050964 0.4670169949531555 0.6863096952438354 0.63037109375 0.7830407023429871 \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_4.evaluate.json b/ENCSR774NXA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 60df9e68c462c9f16b12ebde7e365ff6b0fe2ced..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495ANZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_4.fit.json b/ENCSR774NXA/cherimoya.fold_4.fit.json deleted file mode 100644 index 62a90ab26f2003db501e8785f19fd094e101fa65..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF495ANZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774NXA/cherimoya.fold_4.log b/ENCSR774NXA/cherimoya.fold_4.log deleted file mode 100644 index dc44384b98adbdda3eae7ae6796e4016c6b22196..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3576 44.53649568557739 4.799795627593994 752.30224609375 1.371155023574829 968.5902099609375 0.6951303482055664 0.57560474 7.947691917419434 True -1 7152 39.69343042373657 0.7811036109924316 734.3268432617188 0.9192914962768555 820.936279296875 0.7756890058517456 0.58769363 2.5756242275238037 True -2 10728 39.627809047698975 0.7021400928497314 653.615966796875 1.3314236402511597 802.6465454101562 0.7829284071922302 0.59533685 1.6474218368530273 True -3 14304 39.701251745224 0.713031530380249 619.9366455078125 1.1568702459335327 790.328125 0.7880363464355469 0.5957021 1.2210571765899658 True -4 17880 39.66057324409485 0.7057123184204102 710.95751953125 1.1062097549438477 784.8529052734375 0.7911044359207153 0.6037506 1.1178432703018188 True -5 21456 39.687227725982666 1.2114078998565674 600.98095703125 1.4223339557647705 781.6627807617188 0.793135404586792 0.6072606 1.0526435375213623 True -6 25032 39.70115923881531 0.6980578899383545 641.1376953125 1.992781639099121 779.5975341796875 0.7943977117538452 0.609529 1.099892020225525 True -7 28608 39.65178298950195 1.8243849277496338 656.9000244140625 0.689664363861084 773.7447509765625 0.7973802089691162 0.6169609 0.9949871897697449 True -8 32184 39.75055718421936 0.7049918174743652 605.36474609375 0.9988328218460083 769.9465942382812 0.7992804646492004 0.6267636 0.9321277141571045 True -9 35760 39.648038148880005 1.0231685638427734 728.984130859375 1.1177335977554321 765.1934204101562 0.8017954230308533 0.6306492 0.9174343347549438 True -10 39336 38.88700842857361 0.6904845237731934 600.5116577148438 0.879391610622406 761.294189453125 0.8037642240524292 0.6353063 0.8587068319320679 True -11 42912 38.85831260681152 0.8877813816070557 688.7838134765625 0.8332099914550781 757.0838012695312 0.8061253428459167 0.65298474 0.8119546175003052 True -12 46488 38.94388937950134 0.6902518272399902 750.2276611328125 0.6814804673194885 752.3906860351562 0.8082186579704285 0.66010094 0.786923885345459 True -13 50064 38.85291528701782 0.689643144607544 584.5387573242188 0.7285867929458618 749.7176513671875 0.8101276755332947 0.66889405 0.7661202549934387 True -14 53640 38.96030569076538 3.694561243057251 556.7184448242188 0.6319389939308167 746.3038330078125 0.8118693828582764 0.6761346 0.7501972913742065 True -15 57216 39.058154582977295 0.7061960697174072 620.727783203125 0.8817461729049683 743.9406127929688 0.813110888004303 0.6856068 0.7387987971305847 True -16 60792 38.96815872192383 0.7242212295532227 505.74554443359375 0.6447619199752808 744.1279296875 0.8133783936500549 0.6877677 0.7396281957626343 True -17 64368 38.90588116645813 0.7065198421478271 615.7302856445312 0.9343299865722656 745.4177856445312 0.8128633499145508 0.68523115 0.7561439275741577 False -18 67944 38.91300415992737 0.6909608840942383 604.36669921875 0.8424696922302246 746.9204711914062 0.8120800256729126 0.68103015 0.7796416282653809 False -19 71520 38.8971745967865 0.7024142742156982 665.982666015625 0.5436811447143555 747.8275146484375 0.8116891384124756 0.6785447 0.8022884726524353 False diff --git a/ENCSR774NXA/cherimoya.fold_4.performance.tsv b/ENCSR774NXA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8ebd577e63301abd8ba28bb30c1de67d6fe82c8a..0000000000000000000000000000000000000000 --- a/ENCSR774NXA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -744.1279296875 0.15208743512630463 0.8133783936500549 0.4668375849723816 0.6877676844596863 0.6162157654762268 0.7396281957626343 \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_0.evaluate.json b/ENCSR774RCO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0b423f2a7d202dd2fb18284ca0c17c6ca93ff2c8..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957FHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_0.fit.json b/ENCSR774RCO/cherimoya.fold_0.fit.json deleted file mode 100644 index b3a268914aada10e8a10287248e6b1b399bcb022..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF957FHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_0.log b/ENCSR774RCO/cherimoya.fold_0.log deleted file mode 100644 index b69f2141436c185135bf82f559db6a1f4673f4ec..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2776 35.645896196365356 3.5369880199432373 927.9190673828125 1.090754747390747 1384.01806640625 0.2918861508369446 0.6619736 7.180527687072754 True -1 5552 30.589036226272583 0.7723393440246582 992.2125244140625 0.8907332420349121 1174.6644287109375 0.43600383400917053 0.71891904 2.7795987129211426 True -2 8328 30.525455474853516 0.5721840858459473 784.13623046875 0.6360353231430054 1152.5240478515625 0.44998058676719666 0.727005 1.134960651397705 True -3 11104 30.51047706604004 0.5626606941223145 1001.57421875 0.9585797786712646 1130.0242919921875 0.46390873193740845 0.72879755 1.019121766090393 True -4 13880 29.91280484199524 0.5623660087585449 884.8612060546875 0.9254012107849121 1114.4124755859375 0.4748358130455017 0.73389924 0.8161999583244324 True -5 16656 29.942312240600586 0.5562479496002197 805.1804809570312 1.2214441299438477 1101.8414306640625 0.48408937454223633 0.7317409 0.7790987491607666 False -6 19432 30.036664247512817 26.537378549575806 887.5704345703125 0.9494609832763672 1096.812744140625 0.4884495735168457 0.7320204 0.8037766814231873 False -7 22208 30.27873134613037 1.5728545188903809 899.34130859375 0.8754624128341675 1093.2921142578125 0.49023008346557617 0.7355274 0.6949758529663086 True -8 24984 30.039544582366943 0.5580763816833496 965.5541381835938 0.7799463272094727 1084.5467529296875 0.49927863478660583 0.7275681 0.6415154337882996 False -9 27760 29.999956846237183 0.5628061294555664 819.6343383789062 0.47421878576278687 1076.6400146484375 0.5048028230667114 0.7368232 0.5889329314231873 True -10 30536 29.913828372955322 0.5547208786010742 859.4544067382812 0.5150398015975952 1070.176025390625 0.5096926093101501 0.7396468 0.5993910431861877 True -11 33312 29.907469034194946 0.5554628372192383 844.565185546875 0.6963435411453247 1062.593017578125 0.5145637392997742 0.74789387 0.5377250909805298 True -12 36088 29.910705089569092 0.5543534755706787 883.1728515625 0.9717894792556763 1058.12109375 0.5165866613388062 0.75576454 0.5072184801101685 True -13 38864 29.970385551452637 0.5644631385803223 843.868408203125 0.49923837184906006 1052.545654296875 0.5215216875076294 0.7634875 0.4917745292186737 True -14 41640 29.964117288589478 0.5640041828155518 894.2980346679688 0.3942684233188629 1048.4293212890625 0.5233252644538879 0.7707387 0.43910518288612366 True -15 44416 30.007859230041504 0.5577709674835205 802.887939453125 0.9104358553886414 1043.328857421875 0.5273724794387817 0.77930415 0.41465282440185547 True -16 47192 29.912508726119995 0.5723237991333008 788.8735961914062 0.460655152797699 1045.7391357421875 0.5248425602912903 0.7853127 0.39082276821136475 True -17 49968 29.904743671417236 0.5702033042907715 944.2154541015625 0.4509129822254181 1041.0228271484375 0.529706597328186 0.79017663 0.37309837341308594 True -18 52744 29.996191263198853 0.579425573348999 870.2230834960938 0.3969515562057495 1044.1895751953125 0.5262137651443481 0.7905841 0.3663618862628937 True -19 55520 30.065117835998535 1.292137622833252 780.2852783203125 0.5050276517868042 1040.4156494140625 0.530611515045166 0.7893787 0.3651028275489807 False diff --git a/ENCSR774RCO/cherimoya.fold_0.performance.tsv b/ENCSR774RCO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index eab6025aa6f53a9ab8cf02670032eab976a6e5e7..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1044.1895751953125 0.2733227014541626 0.5262137651443481 0.26397889852523804 0.7905840873718262 0.7285234928131104 0.3663618862628937 \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_1.evaluate.json b/ENCSR774RCO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e709afd0126c143e621660e4c887306ff93f89a7..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957FHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_1.fit.json b/ENCSR774RCO/cherimoya.fold_1.fit.json deleted file mode 100644 index a82d011ac2267c04805a13bd9894324390f6ce20..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF957FHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_1.log b/ENCSR774RCO/cherimoya.fold_1.log deleted file mode 100644 index 80ce9c039c751ca15f3a68884d60b0e1b647656d..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2724 34.626739263534546 3.647643566131592 880.6141967773438 1.1154201030731201 1666.197021484375 0.30340227484703064 0.6710603 11.010330200195312 True -1 5448 30.014951705932617 0.7155165672302246 761.4359741210938 1.063947319984436 1411.3603515625 0.44780728220939636 0.73051786 4.149308681488037 True -2 8172 30.05319309234619 0.7057409286499023 1032.171630859375 1.0250695943832397 1362.6109619140625 0.4693472981452942 0.73921186 2.157740831375122 True -3 10896 29.851081132888794 0.7079553604125977 865.348388671875 0.8911621570587158 1336.16943359375 0.4796273708343506 0.7388347 1.602725863456726 False -4 13620 29.396997451782227 0.700477123260498 979.4462890625 0.831015944480896 1317.22412109375 0.4906217157840729 0.74192 1.4218404293060303 True -5 16344 29.610161542892456 0.9029152393341064 832.6197509765625 0.9516904354095459 1309.74853515625 0.4968005418777466 0.73707384 1.1493966579437256 False -6 19068 29.47993230819702 0.7757260799407959 726.8740844726562 0.7701364755630493 1291.9383544921875 0.5072967410087585 0.74308074 1.0822075605392456 True -7 21792 29.505775928497314 0.7204139232635498 757.2862548828125 1.0012143850326538 1285.620849609375 0.5084049701690674 0.75277656 0.9732934236526489 True -8 24516 29.688668251037598 0.7214798927307129 897.2693481445312 0.6951006650924683 1274.605712890625 0.515303909778595 0.75894916 0.9395780563354492 True -9 27240 29.429748058319092 0.7179625034332275 937.6979370117188 0.5863772034645081 1265.6912841796875 0.5178807377815247 0.76516664 0.8991844654083252 True -10 29964 29.348599910736084 2.145275115966797 782.2017822265625 1.1360743045806885 1250.633056640625 0.5263823866844177 0.7667665 0.8315937519073486 True -11 32688 29.50983214378357 22.243260383605957 1112.196044921875 0.48852506279945374 1245.192626953125 0.5284456014633179 0.7783845 0.6921690702438354 True -12 35412 30.23994517326355 0.7117352485656738 824.6407470703125 0.6106416583061218 1234.62744140625 0.5336917638778687 0.7850546 0.6271459460258484 True -13 38136 29.401272296905518 0.7085964679718018 796.146240234375 0.7716861963272095 1227.404296875 0.535205602645874 0.79371196 0.5746675133705139 True -14 40860 29.3978328704834 0.7060647010803223 794.9448852539062 0.6020470857620239 1222.49755859375 0.5386909246444702 0.80248964 0.5106589198112488 True -15 43584 29.897006511688232 21.461657524108887 1009.539306640625 0.5038341879844666 1213.693603515625 0.5447186231613159 0.80627877 0.4784512221813202 True -16 46308 29.415407180786133 8.724129676818848 903.7373046875 0.40093719959259033 1216.196533203125 0.5421668887138367 0.81412953 0.44055619835853577 True -17 49032 30.376739740371704 0.7046151161193848 846.7218017578125 0.48160016536712646 1210.90234375 0.5456276535987854 0.8150891 0.41550061106681824 True -18 51756 29.493800163269043 0.7003555297851562 634.1151733398438 0.6135736703872681 1211.716552734375 0.5443255305290222 0.81606865 0.4058849811553955 True -19 54480 29.45528221130371 16.46706223487854 706.4280395507812 0.6874637603759766 1209.7098388671875 0.5460408926010132 0.81597614 0.4006001651287079 False diff --git a/ENCSR774RCO/cherimoya.fold_1.performance.tsv b/ENCSR774RCO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cd8e9f0ff702431e39487ac55737b79a97fe8281..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1211.716552734375 0.2563318610191345 0.5443255305290222 0.29804664850234985 0.8160686492919922 0.7785154581069946 0.4058849811553955 \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_2.evaluate.json b/ENCSR774RCO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 18efa97bc250abb8796756a66a25288a5a89da29..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957FHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_2.fit.json b/ENCSR774RCO/cherimoya.fold_2.fit.json deleted file mode 100644 index 5e151bf8cfc8b9aa577875f25a2cfa77585325f3..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF957FHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_2.log b/ENCSR774RCO/cherimoya.fold_2.log deleted file mode 100644 index cabeda463d983704c10c79b3977475419d8667e9..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 37.07766318321228 19.782864809036255 1060.5958251953125 1.0726429224014282 1462.458251953125 0.30184468626976013 0.65781015 6.806028842926025 True -1 5794 31.901214838027954 26.61392092704773 864.4998779296875 1.1471037864685059 1236.10693359375 0.44012171030044556 0.72056973 2.0895471572875977 True -2 8691 32.0704984664917 0.5762293338775635 825.880859375 1.396654486656189 1209.7720947265625 0.4569281041622162 0.7214901 1.0846941471099854 True -3 11588 32.86745572090149 4.631319284439087 814.3292846679688 1.014324426651001 1179.3150634765625 0.4730696976184845 0.7297087 0.9332185983657837 True -4 14485 32.03563666343689 21.10910391807556 846.4656372070312 0.48113590478897095 1167.860595703125 0.4819575250148773 0.73220223 0.8501039147377014 True -5 17382 31.691593885421753 0.559729814529419 919.764892578125 0.8632000684738159 1157.835693359375 0.4886598587036133 0.7349427 0.9493058323860168 True -6 20279 31.197389841079712 0.5411901473999023 809.3828125 0.5454143285751343 1152.9173583984375 0.49201273918151855 0.7369285 0.8839620351791382 True -7 23176 31.236839771270752 0.5441465377807617 777.7404174804688 0.808501660823822 1141.68896484375 0.5007618069648743 0.7423276 0.8649327754974365 True -8 26073 31.234755277633667 0.5421528816223145 863.856201171875 0.8065577745437622 1133.8856201171875 0.5048660039901733 0.7439863 0.8814976215362549 True -9 28970 31.147339582443237 0.5407490730285645 876.0105590820312 0.6451923847198486 1131.15087890625 0.5075023174285889 0.7483532 0.844569742679596 True -10 31867 31.25816321372986 0.5519039630889893 790.9479370117188 0.6380364298820496 1120.9599609375 0.5141932964324951 0.7551054 0.777759850025177 True -11 34764 31.171164751052856 0.5426950454711914 867.0623168945312 0.6481736302375793 1113.1865234375 0.5190826654434204 0.7582537 0.6872462034225464 True -12 37661 31.526374101638794 0.5501630306243896 863.6303100585938 0.6345837116241455 1111.7542724609375 0.5194151401519775 0.76270074 0.6286066770553589 True -13 40558 31.489603757858276 0.549710750579834 799.941650390625 0.5680227279663086 1102.209716796875 0.5243356823921204 0.76712 0.5443140864372253 True -14 43455 31.451098680496216 0.9781217575073242 800.735107421875 0.535300612449646 1094.14501953125 0.5296900868415833 0.7776082 0.48680350184440613 True -15 46352 31.469836235046387 0.5559685230255127 840.0135498046875 0.4324481189250946 1089.5467529296875 0.5336733460426331 0.78268504 0.44758340716362 True -16 49249 31.44967269897461 0.5443382263183594 756.522216796875 0.5439378619194031 1089.595458984375 0.5315425395965576 0.78716695 0.4257729649543762 True -17 52146 31.33947491645813 0.5708930492401123 808.9315185546875 0.28968578577041626 1089.3221435546875 0.5304919481277466 0.7920343 0.4051145315170288 True -18 55043 31.418787002563477 2.863959312438965 812.272705078125 0.3472297191619873 1087.8204345703125 0.5334729552268982 0.79279566 0.3972885310649872 True -19 57940 31.30221438407898 0.54494309425354 878.626220703125 0.3950404226779938 1086.4866943359375 0.5339669585227966 0.79294145 0.39434680342674255 True diff --git a/ENCSR774RCO/cherimoya.fold_2.performance.tsv b/ENCSR774RCO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 10588a95ccfc4c632ce138e49efb887321eceba5..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1086.4866943359375 0.2683207392692566 0.5339670181274414 0.2779902219772339 0.7929414510726929 0.7387515902519226 0.39434680342674255 \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_3.evaluate.json b/ENCSR774RCO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ee4c4c1dc4adb30e7d49b60c699ae77ed10fbdb9..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957FHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_3.fit.json b/ENCSR774RCO/cherimoya.fold_3.fit.json deleted file mode 100644 index 953b9774459d3fa4594ab047666edd22e8ae99d0..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF957FHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_3.log b/ENCSR774RCO/cherimoya.fold_3.log deleted file mode 100644 index 685fcd5c33d577719bd8920a28357cc9beed012e..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2783 35.33635592460632 4.220064640045166 799.67626953125 1.27615225315094 1448.7869873046875 0.3002226948738098 0.6540636 9.406684875488281 True -1 5566 30.68884015083313 1.7871439456939697 879.3403930664062 0.7520711421966553 1244.703857421875 0.4372785687446594 0.7125643 2.460784912109375 True -2 8349 30.669753074645996 0.5847623348236084 943.200439453125 0.6680929660797119 1218.0997314453125 0.45370230078697205 0.7124924 1.0867887735366821 False -3 11132 30.750113248825073 0.5635271072387695 1036.8345947265625 0.7917591333389282 1194.968505859375 0.46509912610054016 0.7237013 0.8667994141578674 True -4 13915 33.603983640670776 9.293091773986816 936.4241943359375 1.0014491081237793 1182.478759765625 0.4720674753189087 0.7265922 0.8635520339012146 True -5 16698 30.00603175163269 0.5607030391693115 768.7550048828125 0.9958246946334839 1171.4976806640625 0.4801446795463562 0.7234485 0.9923027157783508 False -6 19481 30.1670880317688 0.5776393413543701 876.930419921875 0.936018705368042 1164.86376953125 0.4838947653770447 0.7297238 0.9844751954078674 True -7 22264 30.039372444152832 1.0973129272460938 780.9300537109375 0.8250128030776978 1155.2508544921875 0.4902268052101135 0.72922903 0.9800708293914795 False -8 25047 30.25568437576294 0.5603983402252197 1131.24853515625 0.5610412359237671 1151.30029296875 0.4964124262332916 0.73482937 0.9175114631652832 True -9 27830 30.11119556427002 0.5534546375274658 739.4793090820312 0.4469076693058014 1145.7623291015625 0.4996296465396881 0.7353292 0.774637758731842 True -10 30613 30.06751799583435 1.6994917392730713 726.0968017578125 0.5301094055175781 1137.858642578125 0.5041669607162476 0.7395973 0.7194221019744873 True -11 33396 29.965925931930542 0.5501620769500732 779.3743286132812 0.5480539798736572 1127.5821533203125 0.5111221671104431 0.74502075 0.6830126643180847 True -12 36179 29.964309453964233 0.5494885444641113 818.8748779296875 0.45922231674194336 1123.13916015625 0.5120462775230408 0.75560105 0.573533296585083 True -13 38962 30.233158588409424 0.5471696853637695 859.6044921875 0.8773182034492493 1117.1397705078125 0.5160190463066101 0.7631893 0.5506303906440735 True -14 41745 30.03557276725769 0.5499804019927979 840.0030517578125 0.5323992371559143 1110.1923828125 0.519172728061676 0.776207 0.5092068910598755 True -15 44528 30.232290744781494 0.5521576404571533 898.9202270507812 0.5483956336975098 1104.9608154296875 0.5225663781166077 0.7854658 0.4496234953403473 True -16 47311 30.02942943572998 0.5470552444458008 848.5107421875 0.45299261808395386 1102.4259033203125 0.522347092628479 0.7919179 0.42795059084892273 True -17 50094 30.042461395263672 0.5476722717285156 828.840087890625 0.4177970290184021 1099.6087646484375 0.5269184112548828 0.797551 0.4070636034011841 True -18 52877 30.022266149520874 0.5496103763580322 740.4991455078125 0.5041825771331787 1098.070556640625 0.5279820561408997 0.79710317 0.398261159658432 False -19 55660 30.093253135681152 0.5564846992492676 894.1173095703125 0.5705890655517578 1100.5247802734375 0.5254839062690735 0.79619294 0.3947222828865051 False diff --git a/ENCSR774RCO/cherimoya.fold_3.performance.tsv b/ENCSR774RCO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2618f6e8418a57997185f7a45459b62daed86494..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1099.6087646484375 0.270469069480896 0.5269184708595276 0.27222955226898193 0.7975509762763977 0.7377409338951111 0.4070636034011841 \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_4.evaluate.json b/ENCSR774RCO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f65d404d583e5cff95bafdbe34009066c53e8cff..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957FHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_4.fit.json b/ENCSR774RCO/cherimoya.fold_4.fit.json deleted file mode 100644 index b72ce0a791af197eceeca6e857f619bb13660949..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF957FHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR774RCO/cherimoya.fold_4.log b/ENCSR774RCO/cherimoya.fold_4.log deleted file mode 100644 index 32396831625f314be00e04a8416af2160f4cdd84..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2854 36.381767988204956 3.549595594406128 931.1239013671875 0.9515706300735474 1357.333984375 0.3019832372665405 0.6500442 7.648895263671875 True -1 5708 31.37833309173584 0.626920223236084 1059.175537109375 0.8466001749038696 1184.037841796875 0.426774263381958 0.7087718 2.3089253902435303 True -2 8562 31.465985536575317 0.6157927513122559 802.6162109375 0.6345081329345703 1147.1260986328125 0.44775500893592834 0.70578736 1.4655215740203857 False -3 11416 31.352054357528687 0.6070525646209717 911.3587646484375 1.0266947746276855 1126.1119384765625 0.4624548554420471 0.7134804 1.1488237380981445 True -4 14270 30.759607315063477 0.6095013618469238 809.6754150390625 0.861517608165741 1117.2294921875 0.4688359797000885 0.7075762 1.1319694519042969 False -5 17124 33.373642683029175 30.043187141418457 735.3802490234375 0.5897716283798218 1107.830810546875 0.4745699167251587 0.715559 0.9699811935424805 True -6 19978 31.865620851516724 0.6137371063232422 906.602294921875 1.0338807106018066 1104.878662109375 0.47741714119911194 0.71842283 0.8253849744796753 True -7 22832 30.756295680999756 0.6072027683258057 862.2699584960938 0.7580656409263611 1094.0833740234375 0.4865357577800751 0.71454895 0.8197100162506104 False -8 25686 30.769168853759766 0.6910073757171631 1021.4468994140625 0.4165169298648834 1089.278564453125 0.4895908832550049 0.72364557 0.7509171962738037 True -9 28540 30.787226676940918 0.613553524017334 837.9901123046875 0.8681938648223877 1080.8543701171875 0.4961174428462982 0.72972775 0.6793506741523743 True -10 31394 30.78343653678894 10.00130009651184 830.59228515625 0.7275828123092651 1074.8875732421875 0.5006031394004822 0.73543406 0.6247797012329102 True -11 34248 31.088818311691284 2.859708070755005 800.6390380859375 0.5146176218986511 1066.100341796875 0.5059235095977783 0.7485961 0.5794792175292969 True -12 37102 30.886500358581543 1.2327711582183838 816.7096557617188 0.6944129467010498 1061.74365234375 0.508335530757904 0.7546063 0.527975857257843 True -13 39956 31.412192583084106 0.6106042861938477 852.4647216796875 0.5593684315681458 1058.1748046875 0.5125400424003601 0.7606813 0.5336695909500122 True -14 42810 30.78737235069275 0.6134018898010254 892.0673217773438 0.517835795879364 1053.470458984375 0.5144027471542358 0.76940286 0.46483930945396423 True -15 45664 30.794309616088867 0.6084880828857422 818.6314697265625 0.42089593410491943 1050.052978515625 0.516188383102417 0.77618587 0.42776790261268616 True -16 48518 30.75625205039978 0.6073637008666992 882.837890625 0.31011784076690674 1046.3173828125 0.5198332071304321 0.7816562 0.4016202986240387 True -17 51372 30.808460474014282 0.6001906394958496 750.0078125 0.7268127202987671 1044.683837890625 0.5211097002029419 0.78468573 0.38209059834480286 True -18 54226 30.817229509353638 0.6012191772460938 852.557373046875 0.30169957876205444 1042.4571533203125 0.5234869122505188 0.78786296 0.37010034918785095 True -19 57080 30.806201219558716 0.6063473224639893 835.855224609375 0.24928128719329834 1046.155517578125 0.518623948097229 0.78658044 0.3722599148750305 False diff --git a/ENCSR774RCO/cherimoya.fold_4.performance.tsv b/ENCSR774RCO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 65bcc11b8d577f8e9987960973c728334a6935f9..0000000000000000000000000000000000000000 --- a/ENCSR774RCO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1042.4571533203125 0.2739624083042145 0.5234869122505188 0.26613909006118774 0.7878629565238953 0.7236688733100891 0.37010034918785095 \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_0.evaluate.json b/ENCSR775KLH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0da7ecaa2e5f3da346fc726ec8d387a6fe128b95..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF467SBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_0.fit.json b/ENCSR775KLH/cherimoya.fold_0.fit.json deleted file mode 100644 index b39784d5f07b0ff4795f1490aba41931c974ea4e..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF467SBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_0.log b/ENCSR775KLH/cherimoya.fold_0.log deleted file mode 100644 index 6d8a4839d5fa8a61ef4cd0c39af02b2b7b3ee868..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.35653066635132 15.56537914276123 593.357666015625 0.6358933448791504 798.5550537109375 0.300367146730423 0.77432674 6.9404706954956055 True -1 5510 30.65755867958069 1.5182042121887207 499.6551208496094 0.4666891098022461 704.822998046875 0.37821462750434875 0.83337593 1.589590072631836 True -2 8265 30.684022188186646 2.765742778778076 713.5559692382812 0.4023226201534271 685.7730712890625 0.39144057035446167 0.8433081 0.58661288022995 True -3 11020 30.60595703125 8.581573009490967 552.875 0.5435776114463806 678.1272583007812 0.39815980195999146 0.8501593 0.5500783920288086 True -4 13775 30.6016845703125 25.850550651550293 461.5341491699219 0.3067968487739563 673.5267333984375 0.40222886204719543 0.8537088 0.6588349342346191 True -5 16530 30.836824893951416 0.5630550384521484 619.3955688476562 0.6131238341331482 670.5767211914062 0.40467363595962524 0.85910296 0.4391653537750244 True -6 19285 31.131487607955933 0.5756978988647461 597.842529296875 0.24501743912696838 667.9039306640625 0.4072974622249603 0.86129993 0.3862791955471039 True -7 22040 30.5021014213562 0.5636322498321533 480.2848815917969 0.24745650589466095 664.0864868164062 0.4111514687538147 0.86744565 0.36595094203948975 True -8 24795 30.575986623764038 0.5793259143829346 532.399169921875 0.2930900454521179 661.7509765625 0.4133055806159973 0.8679607 0.36101463437080383 True -9 27550 30.57484197616577 16.771793127059937 649.9093627929688 0.27319303154945374 659.2948608398438 0.41540589928627014 0.8734832 0.34126871824264526 True -10 30305 30.598238468170166 2.254251718521118 675.06640625 0.3107565641403198 655.514404296875 0.41939404606819153 0.87573373 0.3150891065597534 True -11 33060 30.591517210006714 1.8827178478240967 546.5911865234375 0.25623852014541626 655.0510864257812 0.41862237453460693 0.87949634 0.2854045331478119 True -12 35815 30.67158794403076 0.8296585083007812 572.1047973632812 0.3885904848575592 650.63330078125 0.42295196652412415 0.8828159 0.2705218195915222 True -13 38570 30.62027406692505 0.585705041885376 538.9028930664062 0.2903009057044983 648.8516235351562 0.42448118329048157 0.88514096 0.25455841422080994 True -14 41325 30.548846006393433 0.5740342140197754 510.75885009765625 0.25237393379211426 648.1602783203125 0.42451921105384827 0.8881536 0.24344809353351593 True -15 44080 30.584768533706665 0.5760657787322998 517.3679809570312 0.3268947899341583 647.6876220703125 0.42494893074035645 0.8910632 0.23086893558502197 True -16 46835 30.70469570159912 0.5772895812988281 602.0164794921875 0.20187097787857056 646.6949462890625 0.4249615967273712 0.89161617 0.22490154206752777 True -17 49590 30.591394186019897 0.5699455738067627 559.7877197265625 0.22140154242515564 646.9353637695312 0.4255564212799072 0.8932688 0.22127676010131836 True -18 52345 30.568809747695923 0.5689067840576172 602.1981811523438 0.22368232905864716 647.2785034179688 0.4246637225151062 0.89221567 0.21964900195598602 False -19 55100 30.547500371932983 0.5608689785003662 555.3382568359375 0.20050135254859924 647.7033081054688 0.4247196614742279 0.8915663 0.22212792932987213 False diff --git a/ENCSR775KLH/cherimoya.fold_0.performance.tsv b/ENCSR775KLH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2ca1ac27aa733f35f605d689e9caf5fb03387003..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -646.9353637695312 0.3654557168483734 0.4255564212799072 0.18056190013885498 0.8932688236236572 0.8547976016998291 0.22127676010131836 \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_1.evaluate.json b/ENCSR775KLH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 21099e26eebc132f4420eff0d3c5d33bba93ce6d..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF467SBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_1.fit.json b/ENCSR775KLH/cherimoya.fold_1.fit.json deleted file mode 100644 index db22ad79239c9966dfad40e76637ff6fe10a192b..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF467SBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_1.log b/ENCSR775KLH/cherimoya.fold_1.log deleted file mode 100644 index d5300ae6ea3fed1844f4f5ce57654eda7caa01b4..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2701 33.20651388168335 4.602806806564331 469.3434143066406 0.5123218297958374 931.1802368164062 0.2976239323616028 0.76061493 8.3213472366333 True -1 5402 30.0472993850708 2.8969063758850098 646.860107421875 0.5149365663528442 807.830078125 0.39066892862319946 0.83125734 1.6971898078918457 True -2 8103 30.023820400238037 0.729736328125 627.3838500976562 0.5592399835586548 786.486328125 0.4025900959968567 0.84136266 0.730532705783844 True -3 10804 29.999025583267212 0.7143170833587646 569.6224975585938 0.3866207003593445 776.0636596679688 0.4098110795021057 0.8491099 0.5354089736938477 True -4 13505 30.079771280288696 0.7126827239990234 613.896484375 0.3424034118652344 766.6217041015625 0.4188498556613922 0.85418564 0.5237894654273987 True -5 16206 30.009961128234863 0.7041611671447754 568.199462890625 0.29645317792892456 765.6768188476562 0.4196363389492035 0.85623515 0.43018296360969543 True -6 18907 29.987493991851807 0.6998193264007568 642.887939453125 0.32484859228134155 760.7286376953125 0.42316538095474243 0.862685 0.3913842737674713 True -7 21608 30.28285789489746 0.7195074558258057 504.8360900878906 0.3308274745941162 758.0723266601562 0.42407509684562683 0.863902 0.35908693075180054 True -8 24309 30.227139472961426 1.6508841514587402 645.2996215820312 0.3615228235721588 753.6629028320312 0.4280732572078705 0.8699168 0.3523631691932678 True -9 27010 30.30369234085083 0.7135076522827148 503.31005859375 0.42047369480133057 751.05419921875 0.42976659536361694 0.87134445 0.3298415541648865 True -10 29711 30.191022634506226 0.6967296600341797 399.00067138671875 0.2620090842247009 748.9722290039062 0.4300912320613861 0.87838703 0.3124578297138214 True -11 32412 30.149718761444092 1.4155125617980957 546.3843994140625 0.2815917730331421 744.509521484375 0.434546560049057 0.8819274 0.3094516694545746 True -12 35113 30.24118709564209 0.7000226974487305 611.309326171875 0.2825687527656555 740.6375122070312 0.43713775277137756 0.8850081 0.29354435205459595 True -13 37814 30.153783082962036 0.7303118705749512 480.92877197265625 0.3013952374458313 738.7053833007812 0.4382050931453705 0.88929117 0.277386873960495 True -14 40515 30.081164121627808 0.704913854598999 497.20263671875 0.21225933730602264 737.357177734375 0.4393388032913208 0.89239264 0.2755481004714966 True -15 43216 30.132737636566162 0.7004835605621338 518.9302978515625 0.23343820869922638 734.2490234375 0.44180306792259216 0.89436865 0.26228195428848267 True -16 45917 30.25480818748474 0.6968843936920166 598.25 0.22799356281757355 732.9454345703125 0.44148585200309753 0.8958729 0.2541973888874054 True -17 48618 30.207778930664062 0.7078812122344971 578.6289672851562 0.23934882879257202 731.0757446289062 0.444595068693161 0.8958953 0.2482519894838333 True -18 51319 30.16826295852661 0.7079315185546875 616.610107421875 0.2564750909805298 734.0244140625 0.44068577885627747 0.89730865 0.24807672202587128 True -19 54020 30.271190643310547 0.7021403312683105 558.2601928710938 0.30078208446502686 734.0795288085938 0.4407021105289459 0.89616114 0.24911239743232727 False diff --git a/ENCSR775KLH/cherimoya.fold_1.performance.tsv b/ENCSR775KLH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c7e739c6925e7ad56e94e84cb212622e56169462..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -734.0244140625 0.3499726951122284 0.44068580865859985 0.20283092558383942 0.8973086476325989 0.8769748210906982 0.24807672202587128 \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_2.evaluate.json b/ENCSR775KLH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8a006130d89b23169f9b4a499ffa12138c94d980..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF467SBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_2.fit.json b/ENCSR775KLH/cherimoya.fold_2.fit.json deleted file mode 100644 index 4a967398ebf48049ff113edd25153cf904360505..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF467SBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_2.log b/ENCSR775KLH/cherimoya.fold_2.log deleted file mode 100644 index 0c55f030a652167e7d51f8277242b3d44a918909..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 35.57265496253967 4.5301454067230225 660.856201171875 0.38865387439727783 838.793701171875 0.30288800597190857 0.7643944 5.829405784606934 True -1 5758 31.9771568775177 0.601813793182373 625.379150390625 0.31697243452072144 732.6864624023438 0.38703376054763794 0.83182544 1.4119009971618652 True -2 8637 31.982863426208496 0.661956787109375 566.118896484375 0.4034665822982788 718.6474609375 0.3958456814289093 0.8358331 0.6137737035751343 True -3 11516 32.02104139328003 12.181704044342041 470.25634765625 0.35946688055992126 710.8919677734375 0.4009898006916046 0.8455246 0.5762501955032349 True -4 14395 31.950678825378418 0.547936201095581 564.9615478515625 0.5256533622741699 706.450439453125 0.40619954466819763 0.8459713 0.4324948191642761 True -5 17274 32.00875115394592 2.686413526535034 522.718994140625 0.3995018005371094 701.254638671875 0.4120763838291168 0.84967285 0.3797837197780609 True -6 20153 32.00947117805481 0.7070021629333496 603.9309692382812 0.5560904741287231 700.2378540039062 0.41189900040626526 0.85441655 0.35989367961883545 True -7 23032 32.115628480911255 1.8379933834075928 536.1494140625 0.3880987763404846 697.316650390625 0.41363030672073364 0.8590536 0.3464401066303253 True -8 25911 32.078147411346436 0.5669605731964111 494.53961181640625 0.30629077553749084 692.9402465820312 0.41756463050842285 0.8622415 0.3221381902694702 True -9 28790 31.99966335296631 0.5524625778198242 495.74188232421875 0.2930382788181305 689.4652099609375 0.41934388875961304 0.8659567 0.3016904294490814 True -10 31669 32.369133949279785 14.690073251724243 478.9910888671875 0.15339195728302002 684.7753295898438 0.42457902431488037 0.86933774 0.2973688244819641 True -11 34548 32.016732931137085 0.5554351806640625 648.904541015625 0.2704217731952667 682.8270263671875 0.4256689250469208 0.8735774 0.27825459837913513 True -12 37427 32.01987171173096 0.5559115409851074 679.2564697265625 0.25029534101486206 681.6677856445312 0.4258548319339752 0.8770997 0.269729346036911 True -13 40306 32.029842138290405 0.547351598739624 613.7802124023438 0.26347815990448 681.04931640625 0.426602303981781 0.877917 0.26001566648483276 True -14 43185 31.930119276046753 0.5407636165618896 558.0892333984375 0.25304195284843445 677.0994873046875 0.42952895164489746 0.8828339 0.25088950991630554 True -15 46064 31.92132258415222 0.5412046909332275 522.6490478515625 0.2228563278913498 677.5453491210938 0.4289277195930481 0.8835451 0.24521057307720184 True -16 48943 31.987914323806763 0.5447084903717041 655.75830078125 0.21723857522010803 676.2482299804688 0.430777907371521 0.8867597 0.24081377685070038 True -17 51822 31.753715991973877 0.5425851345062256 585.34228515625 0.18725493550300598 675.8104248046875 0.43111729621887207 0.885376 0.23882494866847992 False -18 54701 31.280632495880127 0.5788135528564453 508.7489013671875 0.188100665807724 676.2781982421875 0.4302346408367157 0.8851398 0.2393263727426529 False -19 57580 31.21311354637146 0.539299488067627 492.1121826171875 0.22314202785491943 675.6533203125 0.4315692186355591 0.88553995 0.24068261682987213 False diff --git a/ENCSR775KLH/cherimoya.fold_2.performance.tsv b/ENCSR775KLH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8c0fad49b7829111e1b1215657d80d5971d77fa2..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -676.2482299804688 0.3591489791870117 0.430777907371521 0.18907850980758667 0.8867596983909607 0.8528047204017639 0.24081377685070038 \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_3.evaluate.json b/ENCSR775KLH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cd2279f740409f5a21dc20ef1ddd4c8110171b9c..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF467SBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_3.fit.json b/ENCSR775KLH/cherimoya.fold_3.fit.json deleted file mode 100644 index 6182e032aae07a7ce0e3007a9564f1ff874211d2..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF467SBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_3.log b/ENCSR775KLH/cherimoya.fold_3.log deleted file mode 100644 index d51e62dc81af391f14d2c133358d70364da9cf88..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.23361372947693 3.6183643341064453 517.6129150390625 0.5503886938095093 800.2630615234375 0.3103492259979248 0.76043373 8.118261337280273 True -1 5492 30.51706075668335 0.5424008369445801 737.5849609375 0.5871773958206177 702.1802368164062 0.3909383714199066 0.83745545 1.311753749847412 True -2 8238 30.53048062324524 0.5286176204681396 613.6594848632812 0.35419338941574097 686.0846557617188 0.4011015295982361 0.84632015 0.6241015195846558 True -3 10984 30.450498342514038 0.5235660076141357 628.1917114257812 0.38053637742996216 679.1160278320312 0.4081183969974518 0.85082465 0.5670081973075867 True -4 13730 30.447953462600708 0.5250413417816162 599.69189453125 0.37385427951812744 672.582763671875 0.41274550557136536 0.8552926 0.5008646845817566 True -5 16476 30.468509435653687 0.5307738780975342 516.0750732421875 0.28763848543167114 670.1033325195312 0.4151700437068939 0.8561706 0.38625216484069824 True -6 19222 30.45769238471985 0.5240957736968994 525.6312866210938 0.3392972946166992 669.2198486328125 0.4154336452484131 0.85872626 0.3707680404186249 True -7 21968 30.43107509613037 0.5445530414581299 563.1126098632812 0.40617185831069946 664.4859008789062 0.4196537435054779 0.86344385 0.3504706621170044 True -8 24714 30.53091788291931 0.5376300811767578 590.6644287109375 0.3739107847213745 665.4302978515625 0.41835102438926697 0.8678615 0.34487807750701904 True -9 27460 30.47646713256836 17.244765758514404 647.5501098632812 0.421338826417923 661.569580078125 0.42260968685150146 0.871203 0.3330240845680237 True -10 30206 30.64797067642212 0.5597302913665771 541.4320678710938 0.26118770241737366 657.3768310546875 0.4274902045726776 0.8740737 0.32780921459198 True -11 32952 30.46375274658203 0.5516695976257324 686.5847778320312 0.3396736979484558 656.7254638671875 0.42742660641670227 0.87743664 0.3018200695514679 True -12 35698 30.51277494430542 0.5444860458374023 583.7666015625 0.3225312829017639 654.7860717773438 0.42889460921287537 0.8800813 0.28942787647247314 True -13 38444 30.421079635620117 0.5461733341217041 527.4953002929688 0.33744996786117554 652.9434814453125 0.42949220538139343 0.88338226 0.2781680226325989 True -14 41190 30.437273263931274 1.5688531398773193 576.4502563476562 0.3275788724422455 650.929931640625 0.4310041069984436 0.88621694 0.26333749294281006 True -15 43936 30.64548373222351 0.6416165828704834 471.15777587890625 0.31813299655914307 649.6495971679688 0.4318983554840088 0.8884474 0.25240108370780945 True -16 46682 30.578375577926636 0.5301947593688965 554.62939453125 0.2296077311038971 649.3917846679688 0.43268096446990967 0.8904706 0.2443070411682129 True -17 49428 30.09941530227661 0.519751787185669 443.1583251953125 0.1924237608909607 649.306884765625 0.4326876401901245 0.8914691 0.24351808428764343 True -18 52174 29.936355113983154 0.523066520690918 544.7017822265625 0.21729519963264465 648.2435913085938 0.43441736698150635 0.8909288 0.24383854866027832 False -19 54920 29.92493438720703 0.5221197605133057 566.87060546875 0.23031240701675415 649.4199829101562 0.4324973523616791 0.8909596 0.24480612576007843 False diff --git a/ENCSR775KLH/cherimoya.fold_3.performance.tsv b/ENCSR775KLH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 06c7d6e1d9e75014d7c4ee3ac9b330f8f968b6a7..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -649.306884765625 0.3609212636947632 0.43268758058547974 0.18501387536525726 0.8914691209793091 0.8521522879600525 0.24351808428764343 \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_4.evaluate.json b/ENCSR775KLH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 262ff0eeb85ef39966f6e9abbf72f1602bf4b69f..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF467SBV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_4.fit.json b/ENCSR775KLH/cherimoya.fold_4.fit.json deleted file mode 100644 index 4c6538a61a2bb222fd88d994f86574b8133f441a..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF467SBV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775KLH/cherimoya.fold_4.log b/ENCSR775KLH/cherimoya.fold_4.log deleted file mode 100644 index 8d6b5b5f207ab3a70a13782f3bb37b90f6aa7c17..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2823 35.38295865058899 21.700496196746826 635.8193969726562 0.6120350360870361 735.923095703125 0.2994643747806549 0.76895326 5.341174125671387 True -1 5646 31.41253638267517 0.6328094005584717 606.1756591796875 0.47506922483444214 656.8740234375 0.37109771370887756 0.8259115 1.3784528970718384 True -2 8469 31.302422523498535 0.6134424209594727 669.020751953125 0.49634861946105957 642.5169677734375 0.38301676511764526 0.83352625 0.632042407989502 True -3 11292 31.376060485839844 0.603959321975708 536.4888305664062 0.3575066328048706 634.9629516601562 0.38855788111686707 0.8415391 0.535947322845459 True -4 14115 31.340320110321045 7.975612163543701 443.34912109375 0.23592674732208252 631.2274780273438 0.3911903500556946 0.84771574 0.4886600077152252 True -5 16938 31.42467737197876 0.607755184173584 530.8154296875 0.40410280227661133 628.6220092773438 0.39370617270469666 0.8536113 0.36980679631233215 True -6 19761 31.385573625564575 0.6098361015319824 553.6724853515625 0.3081141710281372 624.3915405273438 0.3974113166332245 0.8585936 0.32978883385658264 True -7 22584 31.35255765914917 0.6055729389190674 507.62158203125 0.3708690404891968 622.410888671875 0.3995460271835327 0.8605287 0.3294922113418579 True -8 25407 31.298733949661255 0.5999424457550049 668.8439331054688 0.37388503551483154 620.0845336914062 0.4020161032676697 0.8639477 0.3062687814235687 True -9 28230 31.360922813415527 0.6049973964691162 633.02587890625 0.3178306519985199 618.2798461914062 0.40326565504074097 0.8665895 0.29620128870010376 True -10 31053 31.369768142700195 0.6057248115539551 575.31689453125 0.34424978494644165 616.0521850585938 0.406221479177475 0.86940616 0.27981269359588623 True -11 33876 31.36700987815857 0.6043956279754639 504.6282958984375 0.3049279451370239 614.7383422851562 0.40678074955940247 0.87285095 0.2666546702384949 True -12 36699 31.341463804244995 0.6036198139190674 498.45660400390625 0.18339261412620544 612.7315063476562 0.4092634916305542 0.87631077 0.2568719983100891 True -13 39522 31.37875986099243 0.6056733131408691 515.4878540039062 0.24053505063056946 610.601318359375 0.4116339385509491 0.8794441 0.24631337821483612 True -14 42345 31.348095893859863 0.5970423221588135 596.5313720703125 0.21231001615524292 608.138671875 0.41417697072029114 0.8808985 0.23598887026309967 True -15 45168 31.41104817390442 0.608443021774292 470.64886474609375 0.19282697141170502 608.3282470703125 0.4143330454826355 0.8853401 0.22753149271011353 True -16 47991 30.867345809936523 0.592822790145874 483.3143615722656 0.235741525888443 607.7185668945312 0.4148864150047302 0.8858307 0.22222130000591278 True -17 50814 30.750248908996582 0.5917186737060547 458.8590393066406 0.18206140398979187 607.6439208984375 0.41443371772766113 0.88691103 0.2203127145767212 True -18 53637 30.760876893997192 0.5979065895080566 539.189208984375 0.21258153021335602 608.149169921875 0.4143485426902771 0.8879396 0.22053484618663788 True -19 56460 30.74017882347107 0.6232085227966309 473.3333740234375 0.3042854964733124 607.2669677734375 0.41550368070602417 0.8869387 0.2214679718017578 False diff --git a/ENCSR775KLH/cherimoya.fold_4.performance.tsv b/ENCSR775KLH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e540e00870bfd1c0e6a9ecb92fb620c5b95273b1..0000000000000000000000000000000000000000 --- a/ENCSR775KLH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -608.149169921875 0.37448322772979736 0.4143485426902771 0.1746235191822052 0.8879395723342896 0.8432011604309082 0.22053484618663788 \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_0.evaluate.json b/ENCSR775SYU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b42bd64c6903fc598a7d9f5ad36b29f2c5bbc1de..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF533VLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_0.fit.json b/ENCSR775SYU/cherimoya.fold_0.fit.json deleted file mode 100644 index d01132abc26f0f1d9f7652497d99027aa28a2556..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF533VLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_0.log b/ENCSR775SYU/cherimoya.fold_0.log deleted file mode 100644 index 98923f13d049272fd50193bd80bc640cda638c3e..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3289 40.32675123214722 3.5186197757720947 688.979736328125 0.46542930603027344 875.8662719726562 0.6760492920875549 0.66690785 3.7339746952056885 True -1 6578 35.87200307846069 4.365505933761597 674.241455078125 0.5099287033081055 777.3683471679688 0.7414700388908386 0.69785225 0.8542307019233704 True -2 9867 35.88211941719055 0.6384599208831787 679.812744140625 0.6385310888290405 761.1190795898438 0.7501239776611328 0.7040894 0.4787459671497345 True -3 13156 35.76588439941406 0.6290593147277832 632.7227783203125 0.5266296863555908 755.4799194335938 0.7538967132568359 0.7071137 0.46089836955070496 True -4 16445 35.815595388412476 25.981577396392822 746.9314575195312 0.4624783992767334 751.4929809570312 0.7558881640434265 0.71374863 0.466148316860199 True -5 19734 36.110000133514404 0.6391324996948242 645.46826171875 0.3568271994590759 748.381103515625 0.7581213116645813 0.7132538 0.4066815972328186 False -6 23023 35.842243671417236 0.6359751224517822 620.4017333984375 0.4326566755771637 746.7166748046875 0.7598116397857666 0.7141551 0.40306225419044495 True -7 26312 35.9805121421814 1.8225512504577637 699.484130859375 0.4963874816894531 744.539794921875 0.7610371708869934 0.71920323 0.39346301555633545 True -8 29601 35.749680042266846 0.6390187740325928 683.744140625 0.2758551239967346 741.6981811523438 0.763429582118988 0.72740614 0.3843201994895935 True -9 32890 35.72801375389099 0.6329231262207031 630.06103515625 0.4178348779678345 739.7027587890625 0.7648026347160339 0.7287695 0.3914409875869751 True -10 36179 35.66814589500427 0.6239101886749268 563.9510498046875 0.5540815591812134 737.9320678710938 0.7664245963096619 0.7372168 0.38394322991371155 True -11 39468 35.73600196838379 1.3872394561767578 641.2813720703125 0.3848382234573364 736.0985717773438 0.7677102088928223 0.73727685 0.38801124691963196 True -12 42757 35.811086893081665 0.6409852504730225 619.8394165039062 0.21450626850128174 733.74169921875 0.7691323757171631 0.74271154 0.3827798366546631 True -13 46046 35.84167146682739 34.66314125061035 612.3990478515625 0.24025705456733704 732.1834106445312 0.7705382108688354 0.7512653 0.37305399775505066 True -14 49335 36.302414655685425 0.6327199935913086 551.2734375 0.22465084493160248 730.8543090820312 0.7715659141540527 0.7548222 0.36379843950271606 True -15 52624 37.29143309593201 0.6340892314910889 647.2405395507812 0.20379289984703064 730.2368774414062 0.7720906734466553 0.7600685 0.3505069315433502 True -16 55913 38.487701654434204 22.150854110717773 655.5661010742188 0.20605838298797607 730.0131225585938 0.7722223997116089 0.75587976 0.34453245997428894 False -17 59202 35.89413928985596 0.6446995735168457 601.8829956054688 0.13346530497074127 730.6434326171875 0.7717671990394592 0.75710595 0.34685906767845154 False -18 62491 36.56169939041138 32.278398275375366 640.6250610351562 0.23390747606754303 731.5999145507812 0.7711777687072754 0.75112766 0.34941136837005615 False -19 65780 35.760727405548096 0.6380949020385742 536.4400634765625 0.2054576873779297 731.81982421875 0.7708509564399719 0.7494005 0.3540409803390503 False diff --git a/ENCSR775SYU/cherimoya.fold_0.performance.tsv b/ENCSR775SYU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 00a0e3ca1ded49bdba5f95063e20d90ce7ef4c40..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -730.2368774414062 0.1692763715982437 0.7720906734466553 0.4771535396575928 0.7600684762001038 0.6840553283691406 0.3505069315433502 \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_1.evaluate.json b/ENCSR775SYU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 448cca92bd6d71a45f6f3abd877389096442bad4..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF533VLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_1.fit.json b/ENCSR775SYU/cherimoya.fold_1.fit.json deleted file mode 100644 index 3ac85b4715fe9febfd19cefd7a027680133c54e1..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF533VLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_1.log b/ENCSR775SYU/cherimoya.fold_1.log deleted file mode 100644 index 474ae466dfa0dc7562b8f973ac43e83abb4d4b88..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3220 40.3691987991333 26.831976413726807 702.38330078125 0.6986397504806519 982.4895629882812 0.6842724084854126 0.66422296 5.590188026428223 True -1 6440 35.01171803474426 1.5009658336639404 629.1632690429688 0.4710956811904907 863.517822265625 0.7553241848945618 0.7134164 1.2101173400878906 True -2 9660 35.16893458366394 1.3977279663085938 731.012939453125 0.4521789848804474 842.9906005859375 0.7643736004829407 0.72212225 0.6494373083114624 True -3 12880 35.09899830818176 0.9325788021087646 639.53466796875 0.45712074637413025 834.6431274414062 0.7677533626556396 0.72973484 0.5153693556785583 True -4 16100 35.072532176971436 0.9087722301483154 686.718994140625 0.40574342012405396 829.7255859375 0.7701995968818665 0.73868185 0.5125039219856262 True -5 19320 35.071823835372925 2.038638114929199 618.4100952148438 0.4458669424057007 825.7677612304688 0.7727979421615601 0.73793423 0.4452681839466095 False -6 22540 35.120545625686646 0.888786792755127 643.4161376953125 0.471068799495697 823.2501831054688 0.7742817997932434 0.73820513 0.47038736939430237 False -7 25760 35.066723346710205 0.8934483528137207 740.9532470703125 0.42340898513793945 819.8795776367188 0.7759487628936768 0.74334997 0.44031715393066406 True -8 28980 35.047874450683594 0.9039134979248047 617.4791259765625 0.2547224462032318 816.630615234375 0.7779359817504883 0.74913955 0.4311748147010803 True -9 32200 34.966882944107056 0.8946425914764404 651.792236328125 0.3248392343521118 813.5692749023438 0.7796446084976196 0.7492599 0.40598735213279724 True -10 35420 35.03430485725403 45.29938554763794 695.4913940429688 0.3307715058326721 810.271484375 0.7814644575119019 0.75414616 0.39735549688339233 True -11 38640 35.16092300415039 31.43158769607544 630.7203369140625 0.2543608248233795 806.7357788085938 0.7833666205406189 0.7647779 0.39111390709877014 True -12 41860 36.41589641571045 0.8979942798614502 635.8008422851562 0.33004483580589294 804.4718627929688 0.7852200269699097 0.771526 0.37853190302848816 True -13 45080 35.043131828308105 4.601633310317993 628.2198486328125 0.2994297444820404 801.6527709960938 0.7868695855140686 0.77719355 0.36085939407348633 True -14 48300 35.09749150276184 1.3566796779632568 664.1715698242188 0.24607020616531372 799.7171020507812 0.788144588470459 0.7829827 0.35737285017967224 True -15 51520 35.25612735748291 0.9196951389312744 653.17626953125 0.3076929450035095 798.8710327148438 0.7887542247772217 0.78775615 0.3472704291343689 True -16 54740 35.11252307891846 0.8870584964752197 561.4488525390625 0.22411802411079407 798.9716796875 0.7889691591262817 0.78832805 0.35266411304473877 True -17 57960 35.207995891571045 1.669194221496582 606.96728515625 0.2578698396682739 799.6389770507812 0.7884162664413452 0.7865936 0.35419732332229614 False -18 61180 35.25328803062439 0.9068617820739746 660.225341796875 0.22803449630737305 800.4092407226562 0.7877862453460693 0.782273 0.3579429090023041 False -19 64400 35.40282988548279 8.109387636184692 606.1809692382812 0.15282195806503296 800.934326171875 0.7873623371124268 0.7788717 0.36472049355506897 False diff --git a/ENCSR775SYU/cherimoya.fold_1.performance.tsv b/ENCSR775SYU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 70158b73a3e310588b6d11a048e5e2cda3a2c854..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -798.9716796875 0.15546764433383942 0.7889692187309265 0.5096854567527771 0.7883280515670776 0.7426499128341675 0.35266411304473877 \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_2.evaluate.json b/ENCSR775SYU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e2632f10df7c91dda402b06079a0de70900107f9..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF533VLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_2.fit.json b/ENCSR775SYU/cherimoya.fold_2.fit.json deleted file mode 100644 index 7e58632fcb153e502e775effdbe494c120c1c8a7..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF533VLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_2.log b/ENCSR775SYU/cherimoya.fold_2.log deleted file mode 100644 index df6432aea21a6e0c697286795a7a8b43e42b5664..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3428 42.02597188949585 4.132598161697388 654.9273681640625 0.5482234954833984 900.24755859375 0.6830587387084961 0.6687702 3.9398415088653564 True -1 6856 37.387290239334106 1.2381446361541748 661.2425537109375 0.40005433559417725 797.4091186523438 0.7461426854133606 0.71962345 0.8633570075035095 True -2 10284 37.53651309013367 37.029844522476196 659.3958740234375 0.4798620641231537 783.1392211914062 0.7534332275390625 0.72582805 0.5422964096069336 True -3 13712 37.31640863418579 0.6551320552825928 653.11767578125 0.38715478777885437 777.7518920898438 0.7561743259429932 0.73179156 0.47524476051330566 True -4 17140 37.25378155708313 0.6522059440612793 706.2244873046875 0.25459402799606323 774.4721069335938 0.7576084733009338 0.7359114 0.439650297164917 True -5 20568 37.27631378173828 0.6555032730102539 688.4854125976562 0.475492000579834 771.2362670898438 0.7601653933525085 0.7344919 0.42359185218811035 False -6 23996 37.26672649383545 42.44044208526611 645.9605102539062 0.45160597562789917 768.0796508789062 0.7623275518417358 0.7426349 0.4101874530315399 True -7 27424 37.73076581954956 0.6531004905700684 690.146240234375 0.49376600980758667 765.9239501953125 0.7641531229019165 0.7418356 0.39417195320129395 False -8 30852 37.362390756607056 0.658604621887207 701.7230224609375 0.3513423800468445 763.7901000976562 0.7653910517692566 0.74765074 0.38186660408973694 True -9 34280 37.35232973098755 0.8117406368255615 598.787109375 0.27336370944976807 761.19140625 0.767130434513092 0.74752396 0.39624935388565063 False -10 37708 37.31199622154236 0.6821370124816895 672.5096435546875 0.3097878694534302 758.4957275390625 0.7687987685203552 0.75286317 0.3820268213748932 True -11 41136 37.31420683860779 0.663590669631958 636.2095947265625 0.3432880640029907 756.3670654296875 0.7700265645980835 0.75950474 0.3750823140144348 True -12 44564 38.06444263458252 0.6623263359069824 587.8255615234375 0.2929709851741791 754.4412841796875 0.7714521884918213 0.7654032 0.37163597345352173 True -13 47992 37.350345849990845 0.6571259498596191 619.2108154296875 0.21083836257457733 752.1978759765625 0.7729292511940002 0.771038 0.3657257854938507 True -14 51420 37.33750319480896 32.636289834976196 627.2203979492188 0.32145100831985474 750.6718139648438 0.7739666104316711 0.77393675 0.35443058609962463 True -15 54848 37.73891758918762 0.6589946746826172 613.083984375 0.2699861526489258 750.0700073242188 0.7743261456489563 0.7763562 0.34747570753097534 True -16 58276 37.29989671707153 0.7489447593688965 574.2301025390625 0.2938016653060913 750.0184326171875 0.7744965553283691 0.77715987 0.3460104763507843 True -17 61704 37.33072519302368 0.653510570526123 630.75634765625 0.25661733746528625 750.8406982421875 0.7739777565002441 0.7726533 0.34875723719596863 False -18 65132 37.26939368247986 18.666767835617065 549.8150634765625 0.15111148357391357 751.7249755859375 0.7734688520431519 0.77022976 0.3558139503002167 False -19 68560 37.26389527320862 33.630871295928955 625.1638793945312 0.13385328650474548 751.7693481445312 0.7732035517692566 0.7663784 0.35852500796318054 False diff --git a/ENCSR775SYU/cherimoya.fold_2.performance.tsv b/ENCSR775SYU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6c23ad331fb2a6d611e4b950de01e7222452f745..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -750.0184326171875 0.1663028746843338 0.7744966149330139 0.48655492067337036 0.7771598696708679 0.7160807847976685 0.3460104763507843 \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_3.evaluate.json b/ENCSR775SYU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1a438df80f08550b44a11cd178484688b60b1788..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF533VLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_3.fit.json b/ENCSR775SYU/cherimoya.fold_3.fit.json deleted file mode 100644 index dfd9cc30de1225125694136e5b8199f652dfa8de..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF533VLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_3.log b/ENCSR775SYU/cherimoya.fold_3.log deleted file mode 100644 index 138a70df64ef5564626289d112e8694fa23fd7f8..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3329 40.979777336120605 5.195883274078369 620.9940795898438 0.52158522605896 889.4431762695312 0.679623544216156 0.6636086 3.947286367416382 True -1 6658 36.53449201583862 0.7026157379150391 704.234130859375 0.5468453764915466 796.8656616210938 0.7385203838348389 0.6965182 0.9633172154426575 True -2 9987 36.44617486000061 0.686272144317627 673.955078125 0.5235796570777893 781.8291015625 0.7460131645202637 0.70272046 0.5936810374259949 True -3 13316 36.596477031707764 0.6714181900024414 681.7929077148438 0.3919026851654053 773.6239013671875 0.7503558993339539 0.70792514 0.5378995537757874 True -4 16645 36.418609380722046 0.6733219623565674 686.6525268554688 0.39175283908843994 769.5811767578125 0.7526740431785583 0.7126241 0.5596564412117004 True -5 19974 36.510974168777466 31.558078050613403 660.2705078125 0.44112396240234375 766.328369140625 0.7549418210983276 0.7178573 0.4903002381324768 True -6 23303 38.7935733795166 0.6859767436981201 621.657958984375 0.4079543948173523 764.1316528320312 0.7561606764793396 0.7179409 0.4763360619544983 True -7 26632 36.362159729003906 0.6769263744354248 651.2103881835938 0.4080517888069153 761.6219482421875 0.757815420627594 0.7207229 0.4798278212547302 True -8 29961 36.23761200904846 0.6795237064361572 673.4903564453125 0.36304616928100586 757.9470825195312 0.7599166035652161 0.7304563 0.4622099995613098 True -9 33290 36.405481815338135 0.6902825832366943 605.5703125 0.43920236825942993 756.3133544921875 0.760980486869812 0.7315614 0.45559021830558777 True -10 36619 36.46163535118103 0.6776843070983887 616.4547729492188 0.36778759956359863 752.9111328125 0.7628661394119263 0.73931396 0.4359934628009796 True -11 39948 36.42990756034851 30.39935874938965 649.6697998046875 0.37921521067619324 750.8209838867188 0.764400064945221 0.74570864 0.4117904007434845 True -12 43277 39.53350782394409 0.668616533279419 693.3583984375 0.3627151548862457 748.3657836914062 0.766237735748291 0.7545941 0.39234840869903564 True -13 46606 36.4431848526001 25.974015474319458 657.7452392578125 0.26958298683166504 746.543212890625 0.7675178647041321 0.756652 0.3876160979270935 True -14 49935 42.27596950531006 28.612677574157715 656.0306396484375 0.16434022784233093 745.1925659179688 0.7685974836349487 0.7636682 0.37342649698257446 True -15 53264 41.62748312950134 19.39545226097107 571.79736328125 0.2962273061275482 744.66650390625 0.7692808508872986 0.76827216 0.3709981143474579 True -16 56593 36.48079037666321 0.6717772483825684 633.791259765625 0.3104516863822937 744.9525146484375 0.7692419290542603 0.76814324 0.37079405784606934 False -17 59922 36.30882406234741 1.462059736251831 692.3536376953125 0.2685227394104004 745.9328002929688 0.7686420679092407 0.7644203 0.373280793428421 False -18 63251 36.391820669174194 1.2788476943969727 658.25830078125 0.22840936481952667 746.8433837890625 0.768105149269104 0.7577911 0.3847167193889618 False -19 66580 36.3484570980072 0.662085771560669 620.3348999023438 0.17438574135303497 747.5403442382812 0.7677878737449646 0.75650215 0.3875310719013214 False diff --git a/ENCSR775SYU/cherimoya.fold_3.performance.tsv b/ENCSR775SYU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 13ebab99f823f19de2a812f4eea39949ce378ce6..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -744.66650390625 0.1697067767381668 0.7692808508872986 0.47742292284965515 0.7682721614837646 0.687042236328125 0.3709981143474579 \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_4.evaluate.json b/ENCSR775SYU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fcd2744aab0abe6d89d60fdca776a963af8ec898..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF533VLE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_4.fit.json b/ENCSR775SYU/cherimoya.fold_4.fit.json deleted file mode 100644 index c65211e0f7b316a03180aa78f5af5e5d6b0e15d3..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF533VLE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR775SYU/cherimoya.fold_4.log b/ENCSR775SYU/cherimoya.fold_4.log deleted file mode 100644 index 13d4cb4cfca10ef852d0d89213fe404f93078c27..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3358 41.05628538131714 3.965325117111206 618.189453125 0.5708470344543457 859.8318481445312 0.6779365539550781 0.6483755 3.9610612392425537 True -1 6716 36.56812286376953 0.7353360652923584 581.2742919921875 0.8189237117767334 765.8540649414062 0.7410630583763123 0.68538904 0.9475427269935608 True -2 10074 36.72726321220398 0.9907145500183105 611.5433959960938 0.4280015826225281 753.4522705078125 0.7486971020698547 0.69658965 0.49671775102615356 True -3 13432 36.803017377853394 0.664851188659668 689.878662109375 0.3324618339538574 746.5330200195312 0.7528731226921082 0.7051101 0.42587757110595703 True -4 16790 36.867323875427246 1.9885611534118652 662.8172607421875 0.4197530746459961 743.9317626953125 0.7540091276168823 0.7089964 0.4265837073326111 True -5 20148 36.79540467262268 0.6807286739349365 665.030029296875 0.5199955701828003 740.5164184570312 0.757059633731842 0.7129539 0.3761632442474365 True -6 23506 36.8231987953186 0.6588664054870605 659.4165649414062 0.30887067317962646 738.3848876953125 0.7585485577583313 0.7130374 0.3709647059440613 True -7 26864 36.717127323150635 2.998790740966797 646.4586181640625 0.3458135724067688 736.545166015625 0.7596237659454346 0.71450275 0.37885215878486633 True -8 30222 36.76806116104126 0.6635217666625977 625.4073486328125 0.4136804938316345 734.4168701171875 0.761313259601593 0.7205755 0.372409850358963 True -9 33580 36.78230261802673 0.6642048358917236 586.307861328125 0.2978897988796234 732.7699584960938 0.7627285122871399 0.72120446 0.36857348680496216 True -10 36938 36.91019797325134 23.140437841415405 661.0825805664062 0.33398932218551636 730.4548950195312 0.7645278573036194 0.7259129 0.3761734366416931 True -11 40296 36.767494201660156 0.6890442371368408 596.361572265625 0.3127192258834839 728.0845947265625 0.7659479379653931 0.7326723 0.3618358075618744 True -12 43654 38.428823709487915 40.283339738845825 683.3970336914062 0.28960931301116943 725.8341674804688 0.7675190567970276 0.73995066 0.35298267006874084 True -13 47012 39.30892205238342 25.528631687164307 657.5768432617188 0.42763906717300415 724.3202514648438 0.7687218189239502 0.7424768 0.3422371447086334 True -14 50370 39.75277876853943 0.6880290508270264 687.7561645507812 0.23866873979568481 723.2767333984375 0.7698256969451904 0.74814636 0.3439398407936096 True -15 53728 36.81446647644043 2.201523542404175 652.1378173828125 0.3371921479701996 722.451171875 0.770455002784729 0.7512223 0.33408328890800476 True -16 57086 36.91866421699524 0.6572225093841553 728.7198486328125 0.2010086178779602 722.3818969726562 0.7705413699150085 0.7523126 0.3358859717845917 True -17 60444 36.72029685974121 0.8162345886230469 545.4263916015625 0.2548530101776123 722.7904052734375 0.7701857686042786 0.74996996 0.33901485800743103 False -18 63802 36.794835805892944 0.6561288833618164 519.98681640625 0.19700634479522705 723.664306640625 0.7696758508682251 0.74490666 0.34500688314437866 False -19 67160 36.710002183914185 0.6629722118377686 643.015380859375 0.22302226722240448 724.2902221679688 0.7692895531654358 0.741418 0.3525422215461731 False diff --git a/ENCSR775SYU/cherimoya.fold_4.performance.tsv b/ENCSR775SYU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index eb044d34025b98074433c5fa556b523056b196ab..0000000000000000000000000000000000000000 --- a/ENCSR775SYU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -722.3818969726562 0.17005866765975952 0.7705413699150085 0.47476187348365784 0.7523126006126404 0.6683310270309448 0.3358859717845917 \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_0.evaluate.json b/ENCSR776BTO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 28c4047870774e6e1becee7ef865a669ac9b82ae..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811BHZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_0.fit.json b/ENCSR776BTO/cherimoya.fold_0.fit.json deleted file mode 100644 index 4e34b07476abb52fcdf000bd2d6174f3ac49a640..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF811BHZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_0.log b/ENCSR776BTO/cherimoya.fold_0.log deleted file mode 100644 index 267a66b6ab74f4bb326b0c2b130cc0814d8c1c7f..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 33.76443266868591 3.4514994621276855 885.219482421875 0.8601847887039185 1261.8109130859375 0.2354859858751297 0.60988426 9.07479476928711 True -1 5458 30.157177925109863 0.5560102462768555 1113.64453125 0.8186684846878052 1067.601318359375 0.3200809955596924 0.70084566 3.779348134994507 True -2 8187 30.150601387023926 0.5416107177734375 594.2552490234375 0.8006565570831299 1036.9775390625 0.33159685134887695 0.716837 3.0183072090148926 True -3 10916 30.150933980941772 1.1030075550079346 649.8165283203125 0.6227469444274902 1011.7988891601562 0.3377634882926941 0.73007804 2.5999906063079834 True -4 13645 30.176053762435913 1.0799198150634766 853.147705078125 0.7410777807235718 997.5873413085938 0.3414430320262909 0.74234825 1.4445112943649292 True -5 16374 30.183441162109375 2.5754332542419434 782.4981689453125 0.4635772109031677 987.7551879882812 0.34382569789886475 0.7559173 1.1468183994293213 True -6 19103 30.193784952163696 0.8365910053253174 641.98974609375 0.8155381679534912 974.85009765625 0.3506466746330261 0.7648336 0.913470447063446 True -7 21832 30.155816316604614 0.5448160171508789 748.55615234375 0.6684362888336182 966.03857421875 0.356241375207901 0.77411634 0.8355515599250793 True -8 24561 30.13858413696289 11.88155722618103 718.2686767578125 0.513434886932373 962.0504150390625 0.35734376311302185 0.782247 0.7930542826652527 True -9 27290 30.303035497665405 0.5617189407348633 746.37744140625 0.6664066910743713 959.350830078125 0.35729894042015076 0.790246 0.7409265637397766 True -10 30019 30.31368136405945 0.5606942176818848 907.1295776367188 0.7733474969863892 950.418212890625 0.3629886209964752 0.7974061 0.6814175844192505 True -11 32748 30.700129508972168 0.568279504776001 752.2010498046875 0.6907086968421936 944.522216796875 0.36491525173187256 0.8012259 0.6412363052368164 True -12 35477 30.37681007385254 0.5518102645874023 773.5778198242188 0.3748336732387543 937.017578125 0.36923307180404663 0.8101298 0.5849735140800476 True -13 38206 30.27020502090454 12.29897427558899 816.7890625 0.5644063949584961 933.1055297851562 0.3703288733959198 0.8145586 0.5642073154449463 True -14 40935 30.404633283615112 0.5692269802093506 855.417236328125 0.4480022192001343 922.7748413085938 0.37486615777015686 0.82119346 0.5181905627250671 True -15 43664 30.530100345611572 0.5766503810882568 826.0718994140625 0.5153295397758484 924.1368408203125 0.373960942029953 0.8263163 0.48061785101890564 True -16 46393 30.56965661048889 1.2252695560455322 702.48291015625 0.44047147035598755 919.0762939453125 0.3764493763446808 0.8298225 0.45700040459632874 True -17 49122 30.543906688690186 0.5550284385681152 752.4525146484375 0.4909317195415497 921.9468994140625 0.37476590275764465 0.83157665 0.44808635115623474 True -18 51851 30.430209159851074 0.5580976009368896 728.22412109375 0.3243233561515808 923.3062744140625 0.373343825340271 0.83011305 0.44368454813957214 False -19 54580 30.431058168411255 0.5442714691162109 731.3262939453125 0.2948458194732666 922.0390014648438 0.37436041235923767 0.8295709 0.4456312954425812 False diff --git a/ENCSR776BTO/cherimoya.fold_0.performance.tsv b/ENCSR776BTO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ae41e09a869a1a1a33ac6acbbc45fdf9fc98590c..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -921.9468994140625 0.3771984279155731 0.37476590275764465 0.17864586412906647 0.8315766453742981 0.7705929279327393 0.44808635115623474 \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_1.evaluate.json b/ENCSR776BTO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5db06278f59eaa9637331d0c613bc4128be9b8b7..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811BHZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_1.fit.json b/ENCSR776BTO/cherimoya.fold_1.fit.json deleted file mode 100644 index 0fba8b69ffebaa94751a7ae92226d7cb6b694a56..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF811BHZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_1.log b/ENCSR776BTO/cherimoya.fold_1.log deleted file mode 100644 index ccf06ecaac7660af81fd2923621f30d2767dbbd5..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2687 33.86540508270264 22.837150812149048 856.3475341796875 0.8068540096282959 1475.57080078125 0.24610236287117004 0.6050386 10.439557075500488 True -1 5374 29.869731664657593 27.961525917053223 617.359619140625 0.6820879578590393 1224.486328125 0.33716580271720886 0.7224231 4.286787509918213 True -2 8061 29.863722562789917 1.6955232620239258 642.8931884765625 0.5602092742919922 1211.215576171875 0.33778271079063416 0.7077293 3.3063974380493164 False -3 10748 29.847137928009033 2.1463770866394043 889.9371337890625 0.8289827108383179 1167.86962890625 0.35039955377578735 0.73149407 2.795820474624634 True -4 13435 29.788270235061646 2.3959269523620605 806.828125 0.8885140419006348 1146.77880859375 0.35933947563171387 0.7505435 1.8978264331817627 True -5 16122 29.79666018486023 2.7668380737304688 633.914794921875 0.4497707486152649 1130.482177734375 0.3636362850666046 0.76496047 1.3808863162994385 True -6 18809 29.768275260925293 2.458395481109619 789.9000244140625 1.1909141540527344 1118.3375244140625 0.3674144744873047 0.77923375 1.2687146663665771 True -7 21496 29.87042212486267 1.8704752922058105 760.9577026367188 0.6223756670951843 1112.683837890625 0.36794745922088623 0.7899267 1.2122596502304077 True -8 24183 29.816795349121094 2.0262985229492188 758.7208251953125 0.5450074672698975 1099.7860107421875 0.37428176403045654 0.795769 1.0888125896453857 True -9 26870 29.905238151550293 0.7742660045623779 825.3406982421875 0.5230301022529602 1094.590576171875 0.3766632676124573 0.8024014 0.9755852222442627 True -10 29557 29.730651378631592 0.7618224620819092 1032.305908203125 0.7860264182090759 1091.3349609375 0.37803909182548523 0.80858934 0.8714510202407837 True -11 32244 29.752123832702637 1.2284331321716309 758.2212524414062 0.6118872165679932 1078.9329833984375 0.38266924023628235 0.8179786 0.7787889242172241 True -12 34931 29.814822912216187 0.769676923751831 710.6813354492188 0.7214665412902832 1070.84326171875 0.3859896659851074 0.82289636 0.7402920722961426 True -13 37618 29.772765636444092 0.767101526260376 930.175537109375 0.6241738796234131 1061.38330078125 0.38793396949768066 0.8320387 0.6323098540306091 True -14 40305 29.78365707397461 0.7928845882415771 804.9024047851562 0.7732982039451599 1054.029052734375 0.3902229368686676 0.8397266 0.5709565281867981 True -15 42992 29.804760217666626 0.7702326774597168 688.3470458984375 0.42304691672325134 1049.8541259765625 0.39127564430236816 0.84361684 0.524699330329895 True -16 45679 29.760836839675903 0.7608721256256104 864.594482421875 0.35214963555336 1048.9630126953125 0.3912610709667206 0.847501 0.5019106864929199 True -17 48366 29.75366473197937 0.7594447135925293 656.6250610351562 0.2513536810874939 1048.5657958984375 0.39159098267555237 0.8486515 0.4871867895126343 True -18 51053 29.76637601852417 0.7828068733215332 615.3841552734375 0.5254195928573608 1049.0938720703125 0.3915228843688965 0.84918565 0.4798603057861328 True -19 53740 29.72807741165161 0.7718892097473145 814.0133056640625 0.43509215116500854 1049.4736328125 0.39163804054260254 0.8477971 0.48211362957954407 False diff --git a/ENCSR776BTO/cherimoya.fold_1.performance.tsv b/ENCSR776BTO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 012daa2c576412eb0c7b4944d9a2a8e42058e5db..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1049.0938720703125 0.36190831661224365 0.39152291417121887 0.20305249094963074 0.8491856455802917 0.8116574883460999 0.4798603057861328 \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_2.evaluate.json b/ENCSR776BTO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0769ac18e04e8eb1b97971236ac5479604e03d49..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811BHZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_2.fit.json b/ENCSR776BTO/cherimoya.fold_2.fit.json deleted file mode 100644 index 335ac86ec37e5506c78303390ba0700cd45f0185..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF811BHZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_2.log b/ENCSR776BTO/cherimoya.fold_2.log deleted file mode 100644 index 203b8fd51afcf3ef056a7bffe0c24ff278b90c25..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.05396270751953 3.4491615295410156 1066.00244140625 0.9585800170898438 1282.73828125 0.2505612075328827 0.5958439 8.816329002380371 True -1 5794 32.08123469352722 13.05364179611206 1046.3455810546875 1.17412531375885 1092.23095703125 0.3267354369163513 0.7040233 3.31410813331604 True -2 8691 32.11912441253662 1.8844397068023682 980.4522705078125 1.0321098566055298 1062.8558349609375 0.33353391289711 0.715339 1.9712660312652588 True -3 11588 32.086785078048706 0.5603609085083008 711.8209228515625 0.400431752204895 1031.667724609375 0.34196755290031433 0.74008346 1.4520291090011597 True -4 14485 32.060197830200195 0.5592615604400635 721.459716796875 0.7189264893531799 1019.7777099609375 0.34543517231941223 0.7455822 1.3292208909988403 True -5 17382 32.054309368133545 0.806220531463623 710.3748779296875 0.45057201385498047 1008.0353393554688 0.35005441308021545 0.7590424 1.031783938407898 True -6 20279 32.00077223777771 0.5552413463592529 813.8575439453125 0.7876392602920532 997.6827392578125 0.35400328040122986 0.7688584 0.9115229845046997 True -7 23176 32.10362887382507 0.5534474849700928 809.68896484375 0.6420338153839111 988.8235473632812 0.35765618085861206 0.7752392 0.9231417775154114 True -8 26073 32.03586983680725 1.0551400184631348 695.3407592773438 0.48265504837036133 982.0941162109375 0.36117762327194214 0.779421 0.9487077593803406 True -9 28970 32.06915354728699 0.5581710338592529 774.1432495117188 0.5588560104370117 977.6409301757812 0.3623800575733185 0.7874679 0.8645634651184082 True -10 31867 32.06295108795166 0.5523462295532227 851.4921264648438 0.49867314100265503 971.6619873046875 0.3643271327018738 0.79427814 0.7931524515151978 True -11 34764 32.09048533439636 0.5485496520996094 985.1377563476562 0.5834658741950989 965.4784545898438 0.3682882487773895 0.80212265 0.6914504170417786 True -12 37661 32.084715604782104 0.5457189083099365 627.0531005859375 0.4273480176925659 958.5347290039062 0.3709981441497803 0.80483073 0.6668309569358826 True -13 40558 31.990530014038086 0.5421652793884277 711.030029296875 0.5034187436103821 955.1425170898438 0.3722348213195801 0.81461906 0.600089967250824 True -14 43455 32.05917000770569 0.5595026016235352 863.15869140625 0.444399356842041 945.1858520507812 0.3765656352043152 0.8226825 0.5336143374443054 True -15 46352 32.022491693496704 0.54366135597229 984.2561645507812 0.45249757170677185 938.3680419921875 0.37999337911605835 0.82486945 0.49291765689849854 True -16 49249 32.06512260437012 0.5510995388031006 768.2166748046875 0.37353479862213135 940.27001953125 0.3791622817516327 0.82720876 0.47165563702583313 True -17 52146 32.079729080200195 0.5434525012969971 927.005126953125 0.44347870349884033 940.0050048828125 0.3789452910423279 0.82981884 0.45949068665504456 True -18 55043 32.725327253341675 0.5546963214874268 697.6871337890625 0.38733795285224915 939.997314453125 0.3786993622779846 0.82847387 0.4577304422855377 False -19 57940 32.041046142578125 16.792356967926025 722.8536987304688 0.22915127873420715 940.8867797851562 0.378595232963562 0.8290804 0.4589085876941681 False diff --git a/ENCSR776BTO/cherimoya.fold_2.performance.tsv b/ENCSR776BTO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c6c005c5558c7b07f75d51408ad985706579596d..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -940.0050048828125 0.373065322637558 0.3789452612400055 0.18590717017650604 0.829818844795227 0.7720199823379517 0.45949068665504456 \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_3.evaluate.json b/ENCSR776BTO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d925e23d8784b759db796ddc18e310e043cd7ce3..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811BHZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_3.fit.json b/ENCSR776BTO/cherimoya.fold_3.fit.json deleted file mode 100644 index 9d1fe8f2bdad4b163a86b35e9dc9f406a8cb5333..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF811BHZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_3.log b/ENCSR776BTO/cherimoya.fold_3.log deleted file mode 100644 index a7630baa9c3780b0ecdf8cbde7c3466fd15fdcfb..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 34.29686999320984 4.019800662994385 862.2906494140625 1.1407859325408936 1288.375 0.23974139988422394 0.58343506 10.271504402160645 True -1 5528 30.58873724937439 0.5822246074676514 1056.676025390625 0.8422592282295227 1090.5145263671875 0.32412171363830566 0.702212 4.072175979614258 True -2 8292 30.55050039291382 0.5529098510742188 663.630615234375 0.5191299915313721 1069.7686767578125 0.3287787139415741 0.7196242 2.96693754196167 True -3 11056 30.50431489944458 0.7227966785430908 886.2074584960938 0.792168378829956 1046.442138671875 0.34005725383758545 0.72678554 2.3194427490234375 True -4 13820 30.634294509887695 0.559638261795044 801.5106811523438 0.7017089128494263 1026.85400390625 0.34744828939437866 0.743471 1.8423491716384888 True -5 16584 30.594758987426758 0.5614664554595947 874.3441772460938 0.564676821231842 1014.7387084960938 0.35232675075531006 0.7441827 1.9721802473068237 True -6 19348 30.463683366775513 0.5601918697357178 754.69873046875 0.5860722064971924 1001.8455200195312 0.3578926622867584 0.7572446 1.3645378351211548 True -7 22112 30.511785745620728 1.688894510269165 873.7987060546875 0.5754730105400085 995.8185424804688 0.358778178691864 0.76845354 1.14699387550354 True -8 24876 30.580028772354126 8.528220415115356 870.338623046875 0.6066159009933472 987.05322265625 0.3638639748096466 0.7691992 1.0471562147140503 True -9 27640 30.65000581741333 0.5532257556915283 817.6847534179688 0.5634931325912476 980.7749633789062 0.36649322509765625 0.7795555 0.8833320736885071 True -10 30404 30.514353275299072 0.5553996562957764 961.06298828125 0.6064751148223877 976.0125732421875 0.3676397502422333 0.7852977 0.8392056226730347 True -11 33168 30.476282119750977 1.1807818412780762 1038.8515625 0.9152828454971313 969.88916015625 0.36963561177253723 0.7942718 0.7504764199256897 True -12 35932 30.597498655319214 0.5728905200958252 725.8500366210938 0.44160979986190796 964.5109252929688 0.3740982115268707 0.7966888 0.701114296913147 True -13 38696 30.501362085342407 0.555042028427124 806.8597412109375 0.47237756848335266 957.6744995117188 0.37594008445739746 0.80584294 0.6508350968360901 True -14 41460 30.648638248443604 14.596827745437622 805.728759765625 0.3016223609447479 953.4126586914062 0.3776565194129944 0.8156346 0.5804181098937988 True -15 44224 30.65908980369568 0.5853407382965088 661.5772705078125 0.5375002026557922 947.2037353515625 0.38101059198379517 0.8235647 0.54122394323349 True -16 46988 30.881147384643555 0.5744433403015137 846.778076171875 0.4831407070159912 946.7343139648438 0.3806909918785095 0.8270904 0.509428858757019 True -17 49752 30.55864143371582 0.5613882541656494 721.3751220703125 0.43220722675323486 948.0662841796875 0.37933337688446045 0.83092755 0.48655977845191956 True -18 52516 30.583176374435425 0.556739091873169 794.1689453125 0.41799089312553406 941.376953125 0.38345006108283997 0.83336365 0.47863826155662537 True -19 55280 31.19303274154663 0.5613884925842285 723.067138671875 0.3076620101928711 947.5477905273438 0.37830090522766113 0.83240384 0.47837918996810913 False diff --git a/ENCSR776BTO/cherimoya.fold_3.performance.tsv b/ENCSR776BTO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 54f17895fdee255a0d85ab44c35879375d665292..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -941.376953125 0.37111949920654297 0.38345009088516235 0.1877458393573761 0.8333636522293091 0.7764406204223633 0.47863826155662537 \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_4.evaluate.json b/ENCSR776BTO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0fa7407a34be6abe66c0f0f1d50c7794efb8c135..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811BHZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_4.fit.json b/ENCSR776BTO/cherimoya.fold_4.fit.json deleted file mode 100644 index ddec4721c18ad84feb2eb68985f753f8d69e4f1a..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF811BHZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR776BTO/cherimoya.fold_4.log b/ENCSR776BTO/cherimoya.fold_4.log deleted file mode 100644 index bc35ff862cad6679f2bc5f584828c257a631eef2..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2825 35.09477782249451 3.435271739959717 994.9880981445312 0.6708441376686096 1157.4600830078125 0.24262338876724243 0.594489 6.822945594787598 True -1 5650 31.282402753829956 0.533837080001831 821.65380859375 0.7680448889732361 993.6890258789062 0.3177804946899414 0.67338115 3.159050464630127 True -2 8475 31.353195190429688 0.5380821228027344 838.444580078125 0.48680931329727173 988.6626586914062 0.31713545322418213 0.6824741 2.117680549621582 True -3 11300 31.26313614845276 0.7796735763549805 797.5618896484375 0.9192959070205688 949.5137939453125 0.3311821520328522 0.7137186 1.8160232305526733 True -4 14125 31.25850820541382 0.5378439426422119 792.5046997070312 0.6860283613204956 940.162109375 0.33180171251296997 0.73139876 1.4045583009719849 True -5 16950 31.15626811981201 0.5248167514801025 1168.3243408203125 0.794428288936615 920.3084716796875 0.34275251626968384 0.7399218 1.264992117881775 True -6 19775 31.134387731552124 1.9309935569763184 708.8970947265625 0.7091147899627686 911.9122924804688 0.34683316946029663 0.751363 1.0625760555267334 True -7 22600 31.23786997795105 0.5638620853424072 770.1162109375 0.5812340378761292 906.3828735351562 0.3480874300003052 0.75818133 1.0341479778289795 True -8 25425 31.286979913711548 0.5285906791687012 784.0479125976562 0.578927755355835 901.0982055664062 0.35014283657073975 0.76523155 0.9262270331382751 True -9 28250 31.238348245620728 0.5343518257141113 768.498046875 0.48331937193870544 895.8516235351562 0.35236889123916626 0.77190936 0.8544631004333496 True -10 31075 31.215694665908813 0.5365104675292969 615.1572265625 0.45762917399406433 890.0538330078125 0.3567872941493988 0.7810429 0.7612155675888062 True -11 33900 31.21584677696228 2.131235361099243 703.4368896484375 0.639404296875 884.4058837890625 0.3590645492076874 0.7885053 0.6738602519035339 True -12 36725 31.218750715255737 0.8901216983795166 692.1731567382812 0.6571009159088135 880.1378784179688 0.36091604828834534 0.7936184 0.6110970973968506 True -13 39550 31.291874170303345 0.5757400989532471 755.1075439453125 0.4213877320289612 873.5930786132812 0.36390623450279236 0.8036492 0.5495544075965881 True -14 42375 31.18181562423706 0.5916299819946289 665.0009765625 0.4369538724422455 870.6306762695312 0.36557793617248535 0.8113358 0.49497509002685547 True -15 45200 31.161742210388184 0.530750036239624 774.5140380859375 0.45769572257995605 868.6624755859375 0.36574241518974304 0.81761354 0.4667789936065674 True -16 48025 31.191513776779175 0.5404746532440186 713.28076171875 0.28684741258621216 865.2666625976562 0.36898618936538696 0.8231668 0.4486914873123169 True -17 50850 31.15205430984497 0.5348424911499023 690.3888549804688 0.45097288489341736 864.7007446289062 0.3667546212673187 0.82488555 0.4361957907676697 True -18 53675 31.182386875152588 0.5424368381500244 768.6039428710938 0.41421443223953247 865.7835693359375 0.36687809228897095 0.82562685 0.43562203645706177 True -19 56500 31.17129421234131 0.5316677093505859 696.978271484375 0.2485053539276123 865.847900390625 0.36723577976226807 0.82387555 0.4376288950443268 False diff --git a/ENCSR776BTO/cherimoya.fold_4.performance.tsv b/ENCSR776BTO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a79b399419fe9904e2015ea0e33f62b17c685997..0000000000000000000000000000000000000000 --- a/ENCSR776BTO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -865.7835693359375 0.3841812312602997 0.36687812209129333 0.17135632038116455 0.8256268501281738 0.7547193169593811 0.43562203645706177 \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_0.evaluate.json b/ENCSR777USE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8b1bf5ea7c50c06242a9026c3cec09eda40cf63c..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF583TCS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_0.fit.json b/ENCSR777USE/cherimoya.fold_0.fit.json deleted file mode 100644 index 5179b462283a52244fe8ebd993adee3cd4029a07..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF583TCS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_0.log b/ENCSR777USE/cherimoya.fold_0.log deleted file mode 100644 index aa7321efdaca27414787c7ed30971ae07b5cd6c9..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.872071743011475 2.8798763751983643 216.9158935546875 0.7160658836364746 242.4866943359375 0.1359504908323288 0.5583504 2.3885233402252197 True -1 5478 30.171478986740112 0.5572006702423096 191.8455352783203 0.8121333718299866 232.29348754882812 0.18088512122631073 0.65205365 1.0890065431594849 True -2 8217 30.15513801574707 0.561098575592041 184.62353515625 0.5933268070220947 229.7687530517578 0.18783345818519592 0.6881975 0.6116835474967957 True -3 10956 30.09671401977539 0.4978330135345459 151.82785034179688 0.4532202482223511 228.2227020263672 0.19265133142471313 0.69738567 0.49954697489738464 True -4 13695 30.18336248397827 0.5067400932312012 172.57357788085938 0.6903778910636902 227.4236602783203 0.1957310438156128 0.70577586 0.4714077413082123 True -5 16434 30.14036464691162 2.080599546432495 174.47940063476562 0.640581488609314 226.724365234375 0.19931462407112122 0.71258825 0.47200530767440796 True -6 19173 30.22624635696411 0.820204496383667 176.03872680664062 0.5273627638816833 226.63839721679688 0.19895437359809875 0.7162275 0.4799550771713257 True -7 21912 30.123246669769287 0.5080342292785645 194.3158721923828 0.4757176637649536 225.9429473876953 0.2018599659204483 0.72510177 0.45301854610443115 True -8 24651 30.21597695350647 0.5255720615386963 164.73748779296875 0.7207950949668884 226.1016387939453 0.20047232508659363 0.7290084 0.44097328186035156 True -9 27390 30.234909772872925 0.5143754482269287 181.55313110351562 0.5267064571380615 225.2998809814453 0.20396240055561066 0.7339797 0.4329705834388733 True -10 30129 30.09452486038208 0.49816417694091797 193.65087890625 0.5942513942718506 224.939453125 0.20552900433540344 0.7426906 0.4278239905834198 True -11 32868 29.644811868667603 0.5075480937957764 222.1339111328125 0.44040948152542114 224.6412353515625 0.20716336369514465 0.7435474 0.42819803953170776 True -12 35607 29.67594575881958 0.4910769462585449 180.71160888671875 0.6808865070343018 224.32278442382812 0.2077753096818924 0.74761957 0.4208735227584839 True -13 38346 29.681366205215454 0.5563740730285645 176.30630493164062 0.4635971486568451 224.27476501464844 0.20817478001117706 0.7548177 0.41599830985069275 True -14 41085 29.68624973297119 0.514218807220459 160.6659393310547 0.4378604292869568 223.802734375 0.21070249378681183 0.7631439 0.4089347720146179 True -15 43824 29.598568439483643 0.5009477138519287 194.80364990234375 0.4851688742637634 223.7534637451172 0.21044182777404785 0.7645277 0.4081159830093384 True -16 46563 29.584912061691284 0.5007050037384033 175.10281372070312 0.2744417190551758 223.6688995361328 0.21056950092315674 0.76417774 0.4145970046520233 False -17 49302 29.533541440963745 0.4943406581878662 159.23361206054688 0.42013925313949585 223.92691040039062 0.20945239067077637 0.76332116 0.4266347587108612 False -18 52041 29.639715671539307 0.5170838832855225 174.59759521484375 0.29770171642303467 223.9481201171875 0.2091188132762909 0.7587219 0.4426659047603607 False -19 54780 29.590893745422363 0.4722635746002197 173.816650390625 0.3945011496543884 224.03927612304688 0.20899668335914612 0.7560866 0.4507473111152649 False diff --git a/ENCSR777USE/cherimoya.fold_0.performance.tsv b/ENCSR777USE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3d488f7cc06f49861bb137cad9914f6df786e358..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.7534637451172 0.5411269068717957 0.21044179797172546 0.058151427656412125 0.7645276784896851 0.7365028262138367 0.4081159830093384 \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_1.evaluate.json b/ENCSR777USE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0133c049086d30b57fbecae070f9c12809c5d3d7..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF583TCS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_1.fit.json b/ENCSR777USE/cherimoya.fold_1.fit.json deleted file mode 100644 index b1af4e072e4b1a12395142137cdaacfb56acd4a9..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF583TCS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_1.log b/ENCSR777USE/cherimoya.fold_1.log deleted file mode 100644 index db3a1cf1c6195f7c99afb1bceb0c011d53750660..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.76706051826477 3.526913642883301 199.24078369140625 1.114413857460022 293.2861022949219 0.1506628394126892 0.5508996 3.5108067989349365 True -1 5488 30.113126516342163 1.1349225044250488 203.67254638671875 0.7247238159179688 279.4051513671875 0.20374248921871185 0.6369998 1.6509565114974976 True -2 8232 30.116446018218994 10.632560729980469 168.531005859375 0.8148427605628967 274.79931640625 0.21566025912761688 0.68851984 0.7724984288215637 True -3 10976 30.164254903793335 0.7408783435821533 208.25326538085938 0.7635459899902344 273.3673095703125 0.21882431209087372 0.71568984 0.6731181740760803 True -4 13720 30.0855131149292 0.7405743598937988 176.03179931640625 0.7145056128501892 272.53265380859375 0.22121290862560272 0.7204568 0.6771642565727234 True -5 16464 30.08414578437805 0.7344143390655518 211.54714965820312 0.6270521879196167 271.899169921875 0.22322088479995728 0.72725254 0.632018506526947 True -6 19208 30.11150360107422 0.7378852367401123 144.7890167236328 0.6895004510879517 271.6612854003906 0.22348232567310333 0.73098546 0.6139125227928162 True -7 21952 30.172652006149292 0.7234752178192139 150.19869995117188 0.7860625982284546 271.03607177734375 0.22588692605495453 0.7389622 0.5574647188186646 True -8 24696 29.539738655090332 0.7329590320587158 241.5242919921875 0.5459800362586975 269.860595703125 0.23078125715255737 0.74654317 0.533848226070404 True -9 27440 29.53655171394348 0.7171573638916016 179.24969482421875 0.6719971895217896 269.5782775878906 0.2308524250984192 0.75074315 0.5205140113830566 True -10 30184 29.580031156539917 0.709559440612793 146.09213256835938 0.5568400621414185 269.515380859375 0.23119470477104187 0.756696 0.5036969184875488 True -11 32928 29.564287424087524 0.7173011302947998 196.5633544921875 0.5374982953071594 269.104248046875 0.23248665034770966 0.7614664 0.4877181351184845 True -12 35672 29.570727109909058 0.7182013988494873 168.7958221435547 0.46138298511505127 268.6499328613281 0.23344755172729492 0.76661044 0.48293933272361755 True -13 38416 29.524619817733765 0.7097954750061035 159.1759033203125 0.601933479309082 268.0268249511719 0.23611393570899963 0.7720173 0.47871410846710205 True -14 41160 29.566463232040405 1.1554651260375977 164.35205078125 0.443577378988266 267.9230041503906 0.23586343228816986 0.7769228 0.47202667593955994 True -15 43904 29.56034564971924 0.7264761924743652 194.79974365234375 0.40695321559906006 267.7655944824219 0.2362106442451477 0.7783442 0.47263219952583313 True -16 46648 29.62150549888611 0.7160131931304932 182.98199462890625 0.33629709482192993 267.4647521972656 0.23765280842781067 0.7783979 0.48636168241500854 True -17 49392 29.5772922039032 0.7008101940155029 157.27040100097656 0.4972382187843323 267.48040771484375 0.23742201924324036 0.7758161 0.5004633069038391 False -18 52136 29.616389274597168 0.7196054458618164 152.17396545410156 0.3236299753189087 267.8307189941406 0.23631715774536133 0.77253103 0.518008291721344 False -19 54880 29.6458842754364 0.7283549308776855 165.13876342773438 0.26217809319496155 268.0924377441406 0.23490941524505615 0.76937205 0.5286292433738708 False diff --git a/ENCSR777USE/cherimoya.fold_1.performance.tsv b/ENCSR777USE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5b232ecb9701d72662ac70a33e18637f828cc162..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -267.4647521972656 0.5180246233940125 0.23765280842781067 0.07001947611570358 0.7783979177474976 0.7467913031578064 0.48636168241500854 \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_2.evaluate.json b/ENCSR777USE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8e0b1d3f3312a242210e8566ba19d9bd867e159a..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF583TCS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_2.fit.json b/ENCSR777USE/cherimoya.fold_2.fit.json deleted file mode 100644 index 1e46b1f70d73f648425265a8461aab68766bff3d..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF583TCS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_2.log b/ENCSR777USE/cherimoya.fold_2.log deleted file mode 100644 index 75fd610eeab015f7443aee6420a24eb2d2a17f50..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2923 37.22058320045471 3.431652307510376 186.07571411132812 0.6907827854156494 255.9652099609375 0.14556729793548584 0.53953964 3.0740315914154053 True -1 5846 32.10414147377014 0.6964111328125 174.90872192382812 1.0234127044677734 244.9287109375 0.1903296858072281 0.5954246 1.0982811450958252 True -2 8769 31.99192214012146 0.8312497138977051 177.40179443359375 0.8199002742767334 242.12965393066406 0.1984267383813858 0.6614328 0.6751920580863953 True -3 11692 31.486645221710205 0.5320310592651367 227.18490600585938 0.5876833200454712 240.1947784423828 0.20558497309684753 0.68105376 0.6315950155258179 True -4 14615 31.55229139328003 2.5479061603546143 207.80615234375 0.6376997232437134 239.86178588867188 0.2057589441537857 0.6881294 0.638131320476532 True -5 17538 31.593097925186157 0.5479800701141357 178.74517822265625 0.7480067014694214 239.59371948242188 0.20644919574260712 0.7007881 0.615702211856842 True -6 20461 31.53871726989746 0.5318546295166016 199.9634246826172 0.6058445572853088 238.6839599609375 0.21025331318378448 0.7081772 0.614383339881897 True -7 23384 31.514394760131836 0.5184371471405029 196.20773315429688 0.619982123374939 238.25918579101562 0.21187594532966614 0.7168017 0.5561509132385254 True -8 26307 31.458061933517456 0.5151329040527344 191.34548950195312 0.4727572202682495 237.84613037109375 0.21301023662090302 0.7211626 0.5258119702339172 True -9 29230 31.475629091262817 0.521521806716919 182.47348022460938 0.7230547666549683 237.3950653076172 0.21518820524215698 0.72826993 0.5222179293632507 True -10 32153 31.460204601287842 1.2093636989593506 218.95301818847656 0.713521420955658 237.36990356445312 0.21436439454555511 0.7308268 0.5193790793418884 True -11 35076 31.527934074401855 0.5155115127563477 211.36471557617188 0.40869760513305664 236.9694061279297 0.21620255708694458 0.73504364 0.5102276802062988 True -12 37999 31.448806524276733 0.5053229331970215 169.42611694335938 0.3096141219139099 236.39077758789062 0.21875891089439392 0.7431918 0.48586785793304443 True -13 40922 31.495410442352295 0.529412031173706 225.65545654296875 0.5870201587677002 236.05471801757812 0.21940089762210846 0.74505854 0.478475421667099 True -14 43845 31.522136211395264 0.5163908004760742 173.9085693359375 0.4350782334804535 235.5946807861328 0.2218591421842575 0.75071836 0.47070205211639404 True -15 46768 31.526948928833008 0.5323710441589355 158.73916625976562 0.42570561170578003 235.4852294921875 0.22175787389278412 0.75275534 0.4656991958618164 True -16 49691 31.486833810806274 0.5115945339202881 154.14610290527344 0.7949732542037964 235.64892578125 0.22067783772945404 0.7523156 0.4739076495170593 False -17 52614 31.554939031600952 0.5152449607849121 194.3607177734375 0.39279526472091675 235.51478576660156 0.22192904353141785 0.7519781 0.4831100106239319 False -18 55537 31.569272994995117 0.5256316661834717 153.7249298095703 0.3346792757511139 235.94882202148438 0.21903079748153687 0.747457 0.4964076578617096 False -19 58460 31.568427562713623 14.440845966339111 164.0498046875 0.25460052490234375 235.89173889160156 0.22008872032165527 0.7453199 0.5029036998748779 False diff --git a/ENCSR777USE/cherimoya.fold_2.performance.tsv b/ENCSR777USE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8549df89b0ef324827e2345ef2270a57ea0b4bd2..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -235.4852294921875 0.5334473252296448 0.22175784409046173 0.05962224304676056 0.752755343914032 0.7229650020599365 0.4656991958618164 \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_3.evaluate.json b/ENCSR777USE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 03bad9fa9b069ffefd82bad1964c2ac7798d89d0..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF583TCS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_3.fit.json b/ENCSR777USE/cherimoya.fold_3.fit.json deleted file mode 100644 index f1973e8ef463d8a5a03547172afd351be8602638..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF583TCS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_3.log b/ENCSR777USE/cherimoya.fold_3.log deleted file mode 100644 index d3d8ea28d13f9745501061068eccfc0707339a1a..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2802 35.77718186378479 3.8936901092529297 200.7344512939453 0.9194068908691406 276.608642578125 0.14844731986522675 0.57381237 3.1980745792388916 True -1 5604 30.76676034927368 0.6680786609649658 256.7439880371094 0.7098348140716553 264.88372802734375 0.19378715753555298 0.6644804 1.0978622436523438 True -2 8406 30.778370141983032 0.6136853694915771 202.14407348632812 0.976497232913971 262.5022888183594 0.19960284233093262 0.6962791 0.7603783011436462 True -3 11208 30.820019006729126 0.6238992214202881 192.48574829101562 0.7853309512138367 261.07379150390625 0.20430468022823334 0.7109755 0.6907733678817749 True -4 14010 30.756936073303223 9.880555391311646 154.6614990234375 0.6867619752883911 259.9033203125 0.20852015912532806 0.71466345 0.6999930739402771 True -5 16812 30.161134958267212 0.6233193874359131 196.47207641601562 0.5344615578651428 259.9586486816406 0.2074320912361145 0.7221971 0.6650614738464355 True -6 19614 30.183746099472046 0.5876176357269287 152.6107940673828 0.622998833656311 259.0369567871094 0.21147312223911285 0.7296796 0.6508342623710632 True -7 22416 30.26510000228882 0.591585636138916 148.98512268066406 0.4427027404308319 259.1638488769531 0.21030418574810028 0.72988224 0.6097948551177979 True -8 25218 30.154686212539673 0.5959458351135254 164.44378662109375 0.9348200559616089 258.6573486328125 0.21255458891391754 0.7361076 0.5776126384735107 True -9 28020 30.216912984848022 0.5789766311645508 178.29937744140625 0.484359472990036 258.3900451660156 0.21306686103343964 0.7380296 0.5528207421302795 True -10 30822 30.14610195159912 0.6057665348052979 158.6958465576172 0.5547707080841064 257.9624328613281 0.21458734571933746 0.74184835 0.5476968884468079 True -11 33624 30.179415464401245 0.925513505935669 164.064208984375 0.7539668083190918 257.4855651855469 0.2153339982032776 0.74933684 0.5153225660324097 True -12 36426 30.13940167427063 1.9638431072235107 138.08798217773438 0.4289800524711609 257.2783203125 0.2163635790348053 0.75365406 0.5057633519172668 True -13 39228 30.365105390548706 13.343934535980225 162.74285888671875 0.588870108127594 256.62847900390625 0.21857976913452148 0.7619836 0.4947018623352051 True -14 42030 30.273325443267822 8.933202981948853 178.07400512695312 0.42485418915748596 255.95596313476562 0.22146974503993988 0.76909435 0.47889235615730286 True -15 44832 30.322240829467773 0.5870497226715088 163.69180297851562 0.56069415807724 256.2934875488281 0.2192240059375763 0.7739541 0.4718259871006012 True -16 47634 30.26151442527771 0.5866341590881348 204.16949462890625 0.2811242640018463 256.1846923828125 0.22005189955234528 0.7762557 0.47255370020866394 True -17 50436 30.228968858718872 0.8148057460784912 184.3392791748047 0.3739827871322632 256.6827697753906 0.21818409860134125 0.7721802 0.4861460328102112 False -18 53238 30.265719652175903 0.5855953693389893 178.31332397460938 0.3327927589416504 256.22894287109375 0.21976260840892792 0.76893586 0.5019464492797852 False -19 56040 30.14635443687439 0.5810961723327637 207.5081787109375 0.2814866304397583 256.3669128417969 0.21890118718147278 0.76837003 0.5085034966468811 False diff --git a/ENCSR777USE/cherimoya.fold_3.performance.tsv b/ENCSR777USE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 46ddd2e81d99eb773c203374db274f581007d99b..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -256.1846923828125 0.5294772386550903 0.22005189955234528 0.06480526179075241 0.77625572681427 0.748104453086853 0.47255370020866394 \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_4.evaluate.json b/ENCSR777USE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 36dcce11d84d70ba74b7aae68f62042e00c274dd..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF583TCS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_4.fit.json b/ENCSR777USE/cherimoya.fold_4.fit.json deleted file mode 100644 index b60b42e77fd81a22a8707120dc9fd59c7d282861..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF583TCS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR777USE/cherimoya.fold_4.log b/ENCSR777USE/cherimoya.fold_4.log deleted file mode 100644 index ae297ebf8614d49233659cbf37aff0931254c15a..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2862 36.01887106895447 4.137008905410767 233.24505615234375 0.8517863750457764 241.28184509277344 0.13949692249298096 0.57307637 2.1631150245666504 True -1 5724 30.921404361724854 0.7484779357910156 201.18736267089844 0.7804902791976929 230.90296936035156 0.18502554297447205 0.64565873 1.0252270698547363 True -2 8586 31.46518349647522 0.6650559902191162 174.06695556640625 0.8234515190124512 229.21408081054688 0.18868772685527802 0.6884586 0.5573627948760986 True -3 11448 31.444666147232056 0.5740938186645508 172.28665161132812 0.6712163090705872 228.0851287841797 0.19164404273033142 0.6961458 0.49348610639572144 True -4 14310 31.42075252532959 0.5588314533233643 185.19189453125 0.5481317639350891 227.55197143554688 0.19358444213867188 0.7083347 0.49320414662361145 True -5 17172 31.422290563583374 1.2053606510162354 198.2118682861328 0.8867383003234863 227.43409729003906 0.19373135268688202 0.7122514 0.4995897710323334 True -6 20034 31.354614734649658 0.5585417747497559 176.57699584960938 0.8684375882148743 226.7230682373047 0.19726057350635529 0.718856 0.5003390312194824 True -7 22896 30.861215829849243 0.5547394752502441 180.50726318359375 0.5677740573883057 226.36244201660156 0.1988084316253662 0.7202353 0.5000653862953186 True -8 25758 30.879212856292725 0.7374453544616699 167.13839721679688 0.46207642555236816 226.1585693359375 0.19925789535045624 0.7280277 0.4857965111732483 True -9 28620 30.919403076171875 0.5560777187347412 206.50225830078125 0.8555969595909119 225.7039337158203 0.20131097733974457 0.7313871 0.4745369553565979 True -10 31482 30.90941286087036 0.5688033103942871 146.1728057861328 0.46408915519714355 225.5154571533203 0.2019621729850769 0.73517185 0.4619351625442505 True -11 34344 30.867760181427002 1.4090735912322998 183.06857299804688 0.6686007976531982 225.16778564453125 0.20343883335590363 0.73846066 0.4484306275844574 True -12 37206 30.902055025100708 0.5544650554656982 215.97836303710938 0.8224442005157471 225.02890014648438 0.20363299548625946 0.7419783 0.44149479269981384 True -13 40068 30.888500928878784 0.5447096824645996 200.2156219482422 0.4768451154232025 224.8555450439453 0.2046271711587906 0.7490315 0.4343469440937042 True -14 42930 30.884686708450317 0.5551736354827881 181.84024047851562 0.36344295740127563 224.33750915527344 0.20718224346637726 0.75386596 0.4272870719432831 True -15 45792 30.86978268623352 0.9768886566162109 192.17437744140625 0.29617398977279663 224.55117797851562 0.2057250291109085 0.75916934 0.42779403924942017 True -16 48654 30.88030743598938 0.540874719619751 164.17669677734375 0.4367083013057709 224.08949279785156 0.2090061902999878 0.75948334 0.43120622634887695 True -17 51516 30.845495462417603 0.5538482666015625 192.97145080566406 0.41562435030937195 224.5056915283203 0.20600000023841858 0.75687534 0.44020387530326843 False -18 54378 30.98944354057312 0.566901445388794 207.5455322265625 0.37179985642433167 224.72634887695312 0.2048528790473938 0.75152093 0.45636287331581116 False -19 57240 30.97994589805603 0.5574951171875 211.00331115722656 0.35863709449768066 224.5755615234375 0.20593126118183136 0.74869174 0.4639464318752289 False diff --git a/ENCSR777USE/cherimoya.fold_4.performance.tsv b/ENCSR777USE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 537eb10a1c46ae52adf3e84b053eb3289ded9d97..0000000000000000000000000000000000000000 --- a/ENCSR777USE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -224.08949279785156 0.5423251986503601 0.2090061753988266 0.05690741166472435 0.7594833374023438 0.7276660203933716 0.43120622634887695 \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_0.evaluate.json b/ENCSR780ABS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1a9d7c469ed22029a043f8792ace11ac1a4cb821..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350GUO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_0.fit.json b/ENCSR780ABS/cherimoya.fold_0.fit.json deleted file mode 100644 index ca9d413a52e41861a9c69d85b06e2e4d845445e7..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF350GUO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_0.log b/ENCSR780ABS/cherimoya.fold_0.log deleted file mode 100644 index 0eebec96a12e93a3f89c5c1451a7a86ed8f2d997..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2722 34.80307936668396 3.897664785385132 494.5223083496094 0.3967892825603485 649.2542114257812 0.2029307335615158 0.6783942 6.157865047454834 True -1 5444 29.896562337875366 1.3536970615386963 514.8474731445312 0.4020770788192749 599.4608154296875 0.24593117833137512 0.75892 1.6449333429336548 True -2 8166 29.908098697662354 1.822016716003418 502.026123046875 0.24855925142765045 593.2843627929688 0.24778714776039124 0.7648565 0.9578644633293152 True -3 10888 29.90058970451355 3.834886312484741 399.5205078125 0.42500075697898865 584.139404296875 0.2540165185928345 0.7717023 1.2018585205078125 True -4 13610 29.707234621047974 0.5586533546447754 445.19024658203125 0.3502047061920166 580.15087890625 0.2565402686595917 0.78235966 0.7881550788879395 True -5 16332 29.289591550827026 0.5666871070861816 426.68267822265625 0.2865801751613617 573.6304321289062 0.2638554573059082 0.8008354 0.6885524392127991 True -6 19054 29.26173973083496 0.5557999610900879 581.224365234375 0.486702024936676 570.2477416992188 0.2671959698200226 0.8130604 0.6129640340805054 True -7 21776 29.251960515975952 0.5704569816589355 477.834716796875 0.24413006007671356 567.5174560546875 0.26883530616760254 0.82213145 0.5433369874954224 True -8 24498 29.304556369781494 0.5669200420379639 424.60443115234375 0.3825889825820923 565.6920776367188 0.27083417773246765 0.82963616 0.47558075189590454 True -9 27220 29.34533953666687 0.5615601539611816 482.6652526855469 0.24520625174045563 564.0647583007812 0.2728142738342285 0.8349686 0.4503648281097412 True -10 29942 29.348653078079224 0.5649979114532471 442.45892333984375 0.5223027467727661 562.1839599609375 0.27479061484336853 0.8426589 0.4168880879878998 True -11 32664 29.40894389152527 0.5488438606262207 492.29632568359375 0.40947407484054565 560.6522827148438 0.2760792374610901 0.8456646 0.3848605155944824 True -12 35386 29.292642831802368 0.559950590133667 354.066650390625 0.2707345187664032 559.5225830078125 0.2761767506599426 0.8531608 0.3524794578552246 True -13 38108 29.39066457748413 0.5495786666870117 562.3773193359375 0.4090907871723175 557.0953369140625 0.2796708047389984 0.85754764 0.32856008410453796 True -14 40830 29.392595529556274 0.5538415908813477 543.15771484375 0.2902824282646179 555.8787841796875 0.27992314100265503 0.8619792 0.3081480860710144 True -15 43552 29.362640619277954 0.5532705783843994 427.7467956542969 0.3345682621002197 554.279052734375 0.2810973525047302 0.8668038 0.2850176990032196 True -16 46274 29.306819915771484 0.5499801635742188 507.2657470703125 0.25493115186691284 554.854248046875 0.2800018787384033 0.87254184 0.26862484216690063 True -17 48996 29.32913064956665 0.5546050071716309 452.0239562988281 0.20000651478767395 554.6085815429688 0.28004735708236694 0.87177587 0.26432955265045166 False -18 51718 29.318773984909058 0.5497195720672607 586.424560546875 0.22555723786354065 555.96142578125 0.27774861454963684 0.8704794 0.2639480531215668 False -19 54440 29.353792190551758 0.5599241256713867 450.5233154296875 0.22189989686012268 553.833984375 0.28216853737831116 0.87060374 0.2642432153224945 False diff --git a/ENCSR780ABS/cherimoya.fold_0.performance.tsv b/ENCSR780ABS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 493145cd32f35d1e33f8c377d29e45dbc4418312..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -554.854248046875 0.44887009263038635 0.2800019085407257 0.11964169144630432 0.8725418448448181 0.7860005497932434 0.26862484216690063 \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_1.evaluate.json b/ENCSR780ABS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7e5d82468718c02ea68542ab4fc2e33760ba8398..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350GUO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_1.fit.json b/ENCSR780ABS/cherimoya.fold_1.fit.json deleted file mode 100644 index 693cc7ed4e7f8a3ff31fe34b312a94427ebb23de..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF350GUO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_1.log b/ENCSR780ABS/cherimoya.fold_1.log deleted file mode 100644 index 076ffde409b16f115b31ffa7455e2b5b7d8b20f8..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2682 34.40008759498596 4.023422718048096 536.55908203125 0.5793506503105164 777.407958984375 0.21266761422157288 0.68213886 6.478201866149902 True -1 5364 29.472322463989258 0.8715000152587891 532.3299560546875 0.4661865234375 707.6741333007812 0.26524144411087036 0.7498019 2.2572338581085205 True -2 8046 29.460408210754395 0.7051289081573486 404.720458984375 0.39026308059692383 690.7593994140625 0.2761547267436981 0.7770017 1.259145736694336 True -3 10728 29.200616121292114 0.7192308902740479 548.3538208007812 0.457690954208374 682.5596923828125 0.28085455298423767 0.7940622 1.3725188970565796 True -4 13410 28.9898202419281 0.7148032188415527 477.1636962890625 0.42216745018959045 677.4118041992188 0.2856103181838989 0.800752 0.9503524303436279 True -5 16092 28.968947649002075 2.1877098083496094 508.13934326171875 0.45774173736572266 672.8933715820312 0.288665771484375 0.8084598 0.8944503664970398 True -6 18774 29.026435136795044 0.7163519859313965 511.602294921875 0.5854412913322449 668.7921142578125 0.2931690216064453 0.81827486 0.8208107948303223 True -7 21456 29.001211643218994 0.7209587097167969 610.4946899414062 0.3942202925682068 664.1197509765625 0.29652413725852966 0.8229977 0.7150256633758545 True -8 24138 29.010651111602783 0.7168600559234619 479.7896423339844 0.3512967824935913 662.7227783203125 0.2979426085948944 0.8318556 0.6642797589302063 True -9 26820 29.012661695480347 0.8173844814300537 575.28076171875 0.40272921323776245 657.146728515625 0.30311211943626404 0.8438511 0.5855082869529724 True -10 29502 29.030690670013428 0.7101287841796875 391.23809814453125 0.3690035939216614 657.774658203125 0.3010295331478119 0.84595716 0.543938934803009 True -11 32184 29.117339849472046 28.63773274421692 444.25762939453125 0.3560130000114441 655.0538940429688 0.30254286527633667 0.85249 0.4886007010936737 True -12 34866 29.037960529327393 0.7213613986968994 499.63934326171875 0.2844880521297455 651.4468994140625 0.30603089928627014 0.8612002 0.4408804774284363 True -13 37548 29.051871061325073 1.703770399093628 395.18719482421875 0.22241273522377014 649.1182250976562 0.3078136444091797 0.8694136 0.39594101905822754 True -14 40230 29.08905601501465 0.7355577945709229 480.70098876953125 0.2599598467350006 648.2059936523438 0.3078990876674652 0.87278193 0.3691699206829071 True -15 42912 29.030502557754517 0.7315621376037598 496.5693054199219 0.2568085789680481 645.4666137695312 0.310615599155426 0.8767223 0.337338387966156 True -16 45594 29.03059673309326 2.1034419536590576 464.3924865722656 0.29641827940940857 645.451416015625 0.30967697501182556 0.8812157 0.32384535670280457 True -17 48276 29.04132056236267 0.7331571578979492 415.1717529296875 0.24884337186813354 645.1587524414062 0.30971071124076843 0.8805983 0.3166179060935974 False -18 50958 29.01578998565674 0.7338147163391113 521.3717041015625 0.21410946547985077 645.693359375 0.30946800112724304 0.8785802 0.31616950035095215 False -19 53640 29.042771577835083 0.7151608467102051 462.9783935546875 0.12694285809993744 645.6361694335938 0.3099367022514343 0.87874 0.3178716003894806 False diff --git a/ENCSR780ABS/cherimoya.fold_1.performance.tsv b/ENCSR780ABS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5735d4c8d2811238b47015ae6fca845c8053244f..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -645.451416015625 0.4254395365715027 0.30967700481414795 0.1405791938304901 0.8812156915664673 0.8332749605178833 0.32384535670280457 \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_2.evaluate.json b/ENCSR780ABS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 10533611265a833a4872e113cc8f454cdb171d9d..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350GUO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_2.fit.json b/ENCSR780ABS/cherimoya.fold_2.fit.json deleted file mode 100644 index e37484afe9a48a4560c7c8fc7222cb7a1c7da902..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF350GUO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_2.log b/ENCSR780ABS/cherimoya.fold_2.log deleted file mode 100644 index 7fea4832ea8995f7ef7dbec6af7c0ff503f4d9fa..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.23333144187927 3.7067220211029053 495.3917541503906 0.5019803047180176 674.0856323242188 0.20677173137664795 0.6544681 5.249978542327881 True -1 5772 31.743577480316162 0.6961784362792969 474.0560302734375 0.33526521921157837 617.628173828125 0.2530978322029114 0.7488432 1.539261817932129 True -2 8658 31.176527976989746 0.5837888717651367 563.18505859375 0.5444734692573547 610.8488159179688 0.2548167109489441 0.7561106 1.0127989053726196 True -3 11544 31.06965470314026 0.5708885192871094 536.7886962890625 0.4196747839450836 601.4193725585938 0.2611783742904663 0.776232 0.9333258271217346 True -4 14430 31.06364417076111 0.5585262775421143 505.1070556640625 0.27126920223236084 596.5377197265625 0.265991747379303 0.7933912 0.7669247984886169 True -5 17316 31.128100395202637 0.5747354030609131 461.09332275390625 0.3694949150085449 590.8557739257812 0.2702923119068146 0.8005918 0.6041281223297119 True -6 20202 31.07934069633484 0.5707035064697266 451.4566955566406 0.388136625289917 587.5819091796875 0.27233579754829407 0.8120955 0.4663727283477783 True -7 23088 31.055506467819214 0.5714774131774902 448.64215087890625 0.35744529962539673 585.6240844726562 0.2735481262207031 0.81891644 0.41930854320526123 True -8 25974 31.088642835617065 0.5710976123809814 406.2747497558594 0.27378368377685547 583.7542724609375 0.27529510855674744 0.82860285 0.40700095891952515 True -9 28860 31.07336187362671 0.5455210208892822 481.06951904296875 0.27268388867378235 582.5376586914062 0.2764620780944824 0.8321469 0.4028690457344055 True -10 31746 31.13054609298706 0.568753719329834 453.23358154296875 0.41062843799591064 579.5631103515625 0.2798163592815399 0.83840495 0.3719097077846527 True -11 34632 31.133517503738403 0.5559108257293701 497.73919677734375 0.3116723299026489 577.9169311523438 0.2812381386756897 0.8435817 0.35257700085639954 True -12 37518 31.166711568832397 0.5789196491241455 607.367919921875 0.23616096377372742 575.6226196289062 0.282187283039093 0.8479118 0.3335077166557312 True -13 40404 31.121631383895874 0.590843677520752 442.40545654296875 0.2829740047454834 574.9529418945312 0.28234943747520447 0.85171264 0.31932786107063293 True -14 43290 31.179152011871338 0.5824720859527588 427.1543273925781 0.2310214340686798 573.381103515625 0.2832206189632416 0.85588264 0.30512920022010803 True -15 46176 31.200640439987183 0.5796239376068115 523.2872314453125 0.3133723735809326 572.0993041992188 0.2848059833049774 0.85921663 0.2949645221233368 True -16 49062 31.117560386657715 0.589745283126831 547.687255859375 0.27612435817718506 571.3495483398438 0.2858220338821411 0.85976386 0.289776086807251 True -17 51948 31.197609186172485 1.0417993068695068 474.01043701171875 0.18271690607070923 572.3399047851562 0.2840285301208496 0.86029965 0.2873736619949341 True -18 54834 31.095603942871094 0.5871365070343018 425.9453125 0.16533908247947693 572.55615234375 0.28408458828926086 0.85952425 0.2903450131416321 False -19 57720 31.071059465408325 0.5693373680114746 438.76519775390625 0.4068394899368286 571.7941284179688 0.28579387068748474 0.858765 0.29405200481414795 False diff --git a/ENCSR780ABS/cherimoya.fold_2.performance.tsv b/ENCSR780ABS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 091b27d072bea225766b716fc853565364693288..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -572.3399047851562 0.4438263773918152 0.2840285301208496 0.12401466071605682 0.8602996468544006 0.79155033826828 0.2873736619949341 \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_3.evaluate.json b/ENCSR780ABS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1bbfb6ee1bd6436f00d4b042bc8821823636dec2..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350GUO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_3.fit.json b/ENCSR780ABS/cherimoya.fold_3.fit.json deleted file mode 100644 index cbd7f8e7c01b37e29e116fd250e8872c28c1c008..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF350GUO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_3.log b/ENCSR780ABS/cherimoya.fold_3.log deleted file mode 100644 index 9aaf16295f2cdf734e9c72cf57a28a96ad910db6..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 34.449622631073 3.52239990234375 692.640625 0.6711312532424927 654.5634765625 0.21125991642475128 0.64001864 5.58424186706543 True -1 5474 30.072977304458618 0.6543817520141602 505.94073486328125 0.5985071659088135 608.3095092773438 0.24931833148002625 0.7088295 2.0442395210266113 True -2 8211 29.70524525642395 1.1728627681732178 619.21923828125 0.4569738805294037 600.7279663085938 0.25639304518699646 0.7270182 1.3447140455245972 True -3 10948 29.570610761642456 14.80557632446289 617.4925537109375 0.6337434649467468 592.669921875 0.2625236213207245 0.7463119 1.1148251295089722 True -4 13685 29.459622144699097 0.703516960144043 422.1969299316406 0.6624335050582886 589.4829711914062 0.2641849219799042 0.7539334 0.8800522089004517 True -5 16422 29.47953963279724 0.5799689292907715 495.1547546386719 0.4295341372489929 583.4805908203125 0.27035900950431824 0.7654711 0.7850111722946167 True -6 19159 29.445918321609497 0.5761163234710693 399.0305480957031 0.30410268902778625 581.42529296875 0.2725629508495331 0.7741741 0.6995816826820374 True -7 21896 29.60101819038391 0.5762898921966553 575.1460571289062 0.41903215646743774 578.0618896484375 0.27631303668022156 0.7909603 0.6190721988677979 True -8 24633 29.455596685409546 0.579664945602417 441.04644775390625 0.4066993296146393 575.4913940429688 0.2786332070827484 0.8005016 0.5656204223632812 True -9 27370 29.467562437057495 0.5834286212921143 469.5957946777344 0.23965862393379211 574.8515625 0.2790185213088989 0.8055924 0.5272477865219116 True -10 30107 29.471843242645264 0.5708861351013184 482.91998291015625 0.25367599725723267 573.7628784179688 0.27901262044906616 0.8118502 0.4861988127231598 True -11 32844 29.47913360595703 0.5819330215454102 447.4524230957031 0.3252929449081421 570.6729125976562 0.28340691328048706 0.8202208 0.4383991062641144 True -12 35581 29.50951051712036 0.5753540992736816 433.98968505859375 0.29161715507507324 570.1529541015625 0.2828251123428345 0.8296098 0.40960782766342163 True -13 38318 29.504034757614136 0.5795226097106934 466.40380859375 0.36852413415908813 566.6422119140625 0.2866458594799042 0.8350126 0.37571078538894653 True -14 41055 29.522436141967773 0.5833828449249268 468.2789306640625 0.29747718572616577 566.5093383789062 0.28546142578125 0.8407434 0.3548891842365265 True -15 43792 29.52798295021057 1.5040678977966309 461.7911376953125 0.39339569211006165 566.099853515625 0.28634336590766907 0.8455285 0.33785003423690796 True -16 46529 29.531049489974976 0.5991723537445068 561.38525390625 0.2835046052932739 564.1686401367188 0.28867143392562866 0.8483738 0.3294775187969208 True -17 49266 29.613325834274292 0.5927650928497314 415.50250244140625 0.1462598443031311 564.3909301757812 0.28838008642196655 0.8521362 0.32567068934440613 True -18 52003 29.58568572998047 0.6085445880889893 354.83673095703125 0.1449863463640213 565.623779296875 0.2863256335258484 0.85033363 0.32389286160469055 False -19 54740 29.71466565132141 0.5837998390197754 520.2367553710938 0.17435956001281738 565.9879760742188 0.28581878542900085 0.8509229 0.3245694637298584 False diff --git a/ENCSR780ABS/cherimoya.fold_3.performance.tsv b/ENCSR780ABS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 73b1bb1b85b986f84ba7ad2b3bf104c3877ee6a7..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -564.3909301757812 0.44328317046165466 0.28838008642196655 0.12530946731567383 0.8521361947059631 0.7832311391830444 0.32567068934440613 \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_4.evaluate.json b/ENCSR780ABS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 14b5a9c92c263c8296c9ffe547878baf0e2f3141..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF350GUO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_4.fit.json b/ENCSR780ABS/cherimoya.fold_4.fit.json deleted file mode 100644 index b0c19f8340021a79ec07e06f5f1dda9eacb6ecb1..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF350GUO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR780ABS/cherimoya.fold_4.log b/ENCSR780ABS/cherimoya.fold_4.log deleted file mode 100644 index 8a02782654aa0f2e7e61a13084f9ee2afb4cb9d8..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2845 35.974785804748535 3.736064910888672 602.9361572265625 0.478569895029068 603.5473022460938 0.20295307040214539 0.6447968 4.187188148498535 True -1 5690 31.088303327560425 0.6404731273651123 444.85614013671875 0.6535314321517944 561.4678955078125 0.24118317663669586 0.7283292 1.3768970966339111 True -2 8535 31.323894023895264 1.0523812770843506 435.2673034667969 0.29030999541282654 555.9757690429688 0.2422332763671875 0.73890924 1.08125901222229 True -3 11380 31.251526594161987 0.5736815929412842 409.20648193359375 0.45476728677749634 545.6126098632812 0.24940063059329987 0.7587324 0.8832597732543945 True -4 14225 31.92194104194641 0.565312385559082 517.8654174804688 0.3881579041481018 541.34716796875 0.25531721115112305 0.7625314 0.7551831007003784 True -5 17070 31.239696264266968 3.4383931159973145 501.1041259765625 0.5177909731864929 536.939208984375 0.2596103549003601 0.7809894 0.5837457776069641 True -6 19915 31.227576732635498 0.5712416172027588 472.72784423828125 0.44706296920776367 536.0740966796875 0.25835415720939636 0.7933114 0.5311154723167419 True -7 22760 31.192825317382812 0.5791804790496826 590.3077392578125 0.5859249830245972 532.7066650390625 0.2621259391307831 0.80267835 0.4660640060901642 True -8 25605 31.63334822654724 0.5599765777587891 499.3288879394531 0.41058099269866943 529.332763671875 0.2656378746032715 0.8105403 0.4221717119216919 True -9 28450 31.365504026412964 16.774858236312866 409.04443359375 0.29182711243629456 528.2893676757812 0.267338365316391 0.8168904 0.3964286744594574 True -10 31295 31.307745456695557 0.592548131942749 530.9754638671875 0.48241594433784485 528.0975341796875 0.2664501667022705 0.822586 0.365445077419281 True -11 34140 31.216249227523804 0.5691094398498535 545.382080078125 0.41577038168907166 526.4823608398438 0.2676311433315277 0.8298158 0.3336021900177002 True -12 36985 31.196961402893066 0.6387875080108643 609.3038330078125 0.3876752257347107 524.06982421875 0.27072644233703613 0.8357825 0.3167632520198822 True -13 39830 31.213056802749634 1.0361263751983643 386.35748291015625 0.14552786946296692 522.4762573242188 0.2728791832923889 0.83923644 0.30710548162460327 True -14 42675 31.267921447753906 1.2560462951660156 557.6094360351562 0.23005756735801697 521.9200439453125 0.27266642451286316 0.84508324 0.2885284721851349 True -15 45520 31.267765522003174 1.3481378555297852 457.89727783203125 0.20653165876865387 523.1797485351562 0.27038437128067017 0.8499024 0.2740967869758606 True -16 48365 31.29663610458374 1.0645334720611572 383.8606872558594 0.5368983149528503 520.6862182617188 0.27459031343460083 0.85391223 0.26999038457870483 True -17 51210 31.24944519996643 0.6152288913726807 443.02532958984375 0.22433467209339142 520.9486083984375 0.2740795612335205 0.8550398 0.26713937520980835 True -18 54055 31.316555738449097 0.5833272933959961 479.1010437011719 0.2797231078147888 522.6513061523438 0.2715846300125122 0.85367125 0.2692927420139313 False -19 56900 31.437333345413208 0.586733341217041 377.2851867675781 0.13643865287303925 521.9363403320312 0.27352234721183777 0.8536637 0.2706117331981659 False diff --git a/ENCSR780ABS/cherimoya.fold_4.performance.tsv b/ENCSR780ABS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a785feeb3d1b623d0134f732252144d8fca8a331..0000000000000000000000000000000000000000 --- a/ENCSR780ABS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -520.9486083984375 0.45548319816589355 0.2740796208381653 0.11303289234638214 0.8550397753715515 0.7698527574539185 0.26713937520980835 \ No newline at end of file diff --git a/ENCSR784GVR/cherimoya.fold_0.log b/ENCSR784GVR/cherimoya.fold_0.log deleted file mode 100644 index e2c6dbf4ba28084a7dc907902c5f187bcd87922e..0000000000000000000000000000000000000000 --- a/ENCSR784GVR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.68637824058533 3.6523935794830322 380.42333984375 0.30073627829551697 451.6513366699219 0.2178993970155716 0.72750604 3.2543303966522217 True -1 5514 30.064512491226196 0.587982177734375 382.2271728515625 0.20736181735992432 422.50860595703125 0.27177804708480835 0.78518116 0.7986518740653992 True -2 8271 29.995399236679077 0.5655109882354736 395.08331298828125 0.38429099321365356 419.144287109375 0.2758640944957733 0.7888555 0.7919498085975647 True -3 11028 29.980273485183716 0.5657558441162109 320.6516418457031 0.2953258752822876 414.4428405761719 0.2823759615421295 0.80468726 0.37102004885673523 True -4 13785 31.157843112945557 23.432175874710083 322.26800537109375 0.26534584164619446 411.7047424316406 0.28771838545799255 0.8119926 0.37502437829971313 True -5 16542 29.937092065811157 0.5699882507324219 382.3941345214844 0.21074794232845306 410.27423095703125 0.2898353636264801 0.8206784 0.334869921207428 True -6 19299 30.03231906890869 19.258618354797363 337.4764709472656 0.32234734296798706 408.9166564941406 0.29243189096450806 0.82689583 0.34438610076904297 True -7 22056 29.92197847366333 32.14983415603638 373.26824951171875 0.3214392066001892 407.9709777832031 0.2941933274269104 0.8309129 0.35448285937309265 True -8 24813 31.37948203086853 0.6224524974822998 394.23492431640625 0.24546682834625244 407.34564208984375 0.2949621379375458 0.8367898 0.34285563230514526 True -9 27570 30.21268606185913 0.8920247554779053 323.9408264160156 0.26781949400901794 405.7957763671875 0.2994077801704407 0.83891094 0.31652072072029114 True -10 30327 30.012027502059937 0.5887682437896729 418.1280212402344 0.18729762732982635 405.6295166015625 0.2993403971195221 0.8429194 0.2848171591758728 True -11 33084 29.984060525894165 2.229379653930664 339.2402038574219 0.25375115871429443 404.681884765625 0.30083414912223816 0.8461264 0.26143720746040344 True -12 35841 30.063910245895386 22.175684928894043 358.27923583984375 0.3544684648513794 404.1192626953125 0.30105921626091003 0.8493681 0.24328279495239258 True -13 38598 30.243602514266968 0.5868237018585205 321.0536804199219 0.17070189118385315 403.3234558105469 0.30220797657966614 0.8543242 0.22099944949150085 True -14 41355 30.136773824691772 3.2570598125457764 375.10516357421875 0.17837822437286377 401.9454040527344 0.3054645359516144 0.8586728 0.2014205902814865 True -15 44112 30.016239166259766 2.2970499992370605 379.8455810546875 0.16410771012306213 401.39849853515625 0.3059219717979431 0.86113113 0.18295763432979584 True -16 46869 30.05253505706787 5.686189651489258 360.6387939453125 0.15685927867889404 401.07806396484375 0.3063901662826538 0.8636196 0.17516207695007324 True -17 49626 30.010600090026855 0.6294639110565186 335.60833740234375 0.13889795541763306 401.5036926269531 0.305449903011322 0.86240697 0.1713535636663437 False -18 52383 29.981748819351196 0.582780122756958 355.8526611328125 0.125876784324646 401.33795166015625 0.30589956045150757 0.86134857 0.17033985257148743 False -19 55140 29.934035062789917 0.5685250759124756 326.60772705078125 0.18234515190124512 401.4632568359375 0.30599817633628845 0.862109 0.17022323608398438 False diff --git a/ENCSR784GVR/cherimoya.fold_0.performance.tsv b/ENCSR784GVR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 919de235e2baa053718ac4334e6129f079daa5e5..0000000000000000000000000000000000000000 --- a/ENCSR784GVR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -401.07806396484375 0.4606645405292511 0.3063901662826538 0.10019171983003616 0.8636196255683899 0.8382306098937988 0.17516207695007324 \ No newline at end of file diff --git a/ENCSR784GVR/cherimoya.fold_1.performance.tsv b/ENCSR784GVR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b07e4fbf6d98369c114a168c3748d0ce8a06b127..0000000000000000000000000000000000000000 --- a/ENCSR784GVR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -436.2970275878906 0.4503229856491089 0.3184128701686859 0.10809676349163055 0.8793278932571411 0.8679641485214233 0.18430888652801514 \ No newline at end of file diff --git a/ENCSR784GVR/cherimoya.fold_2.performance.tsv b/ENCSR784GVR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 398aa96a4dd20b362bb405f5a8349ec99eefbbeb..0000000000000000000000000000000000000000 --- a/ENCSR784GVR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -416.4456787109375 0.45404118299484253 0.3157808780670166 0.10603336989879608 0.858051598072052 0.8369311094284058 0.18520532548427582 \ No newline at end of file diff --git a/ENCSR784GVR/cherimoya.fold_3.evaluate.json b/ENCSR784GVR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3105dc48ba845115eeae29f56b82a36743f3073e..0000000000000000000000000000000000000000 --- a/ENCSR784GVR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF905KXK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR784GVR/cherimoya.fold_3.fit.json b/ENCSR784GVR/cherimoya.fold_3.fit.json deleted file mode 100644 index 02ce48d3b582f293b96a02e6fcc57dda8244ec52..0000000000000000000000000000000000000000 --- a/ENCSR784GVR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF905KXK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_0.evaluate.json b/ENCSR785JXR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0b55138b176c69510df4f487a13a527705d934fc..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488SLH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_0.fit.json b/ENCSR785JXR/cherimoya.fold_0.fit.json deleted file mode 100644 index f89a9d280388afc06ffc02ba0fec0f1a3e808787..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF488SLH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_0.log b/ENCSR785JXR/cherimoya.fold_0.log deleted file mode 100644 index 0fe4f228942f73a129cf788c52119412ffb92177..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 35.298959493637085 4.318326234817505 735.4000854492188 0.5697400569915771 913.2806396484375 0.344839870929718 0.75558937 6.462919235229492 True -1 5496 30.51853036880493 0.6110401153564453 619.0340576171875 0.5289275646209717 794.2725219726562 0.41989386081695557 0.8087707 2.156604051589966 True -2 8244 30.45350670814514 0.571354866027832 654.6181640625 0.3954676687717438 781.2308349609375 0.4263770878314972 0.8190144 0.9819448590278625 True -3 10992 29.896323204040527 1.6969690322875977 536.857177734375 0.33830535411834717 770.4254150390625 0.43395164608955383 0.82763153 0.8107016682624817 True -4 13740 29.89253807067871 0.5783870220184326 523.27099609375 0.32051974534988403 763.0121459960938 0.43993306159973145 0.83394045 0.7214301824569702 True -5 16488 29.95001721382141 0.5786683559417725 714.6206665039062 0.4773765206336975 761.3788452148438 0.44215819239616394 0.83997834 0.6587802171707153 True -6 19236 29.9570255279541 0.5701954364776611 559.75439453125 0.31354525685310364 756.2993774414062 0.4439241886138916 0.8457886 0.5397285223007202 True -7 21984 29.915884733200073 0.569476842880249 710.94580078125 0.43277835845947266 752.0936889648438 0.44777992367744446 0.8517987 0.5398695468902588 True -8 24732 29.992158889770508 0.5664112567901611 770.1016845703125 0.557307243347168 748.2896118164062 0.4480349123477936 0.8563168 0.5124938488006592 True -9 27480 30.002724170684814 0.580531120300293 637.9249267578125 0.3413529396057129 741.1443481445312 0.45360806584358215 0.8624577 0.4888712167739868 True -10 30228 30.01854109764099 0.5783452987670898 606.6976318359375 0.31151193380355835 739.8544921875 0.4534420073032379 0.86807865 0.4378397762775421 True -11 32976 30.116294145584106 0.6128196716308594 699.0814819335938 0.2733558416366577 734.4427490234375 0.4575265347957611 0.8721477 0.4055975079536438 True -12 35724 30.140747547149658 1.0065667629241943 462.4084167480469 0.30696791410446167 730.2940673828125 0.4614027142524719 0.8758131 0.37328478693962097 True -13 38472 30.459672927856445 11.37968635559082 617.543701171875 0.22818401455879211 728.026611328125 0.4618610441684723 0.8824852 0.33081093430519104 True -14 41220 29.948559045791626 0.589235782623291 596.54345703125 0.20448723435401917 725.7257080078125 0.4634654223918915 0.8881135 0.2856377065181732 True -15 43968 30.026352882385254 1.1747760772705078 714.90771484375 0.2892795205116272 724.143798828125 0.4653646647930145 0.8919726 0.26508039236068726 True -16 46716 29.982368230819702 0.5801215171813965 670.1708984375 0.21737663447856903 725.4356689453125 0.46286118030548096 0.8937269 0.2499861866235733 True -17 49464 30.046414852142334 0.5977840423583984 722.52099609375 0.22398199141025543 722.4697875976562 0.46662437915802 0.8960905 0.23777686059474945 True -18 52212 30.167847394943237 0.5832555294036865 753.7190551757812 0.2875172793865204 721.8363647460938 0.4659079909324646 0.8963541 0.23390910029411316 True -19 54960 30.074333667755127 0.5715920925140381 578.9297485351562 0.14322564005851746 725.340087890625 0.4626697599887848 0.89647496 0.2344268411397934 True diff --git a/ENCSR785JXR/cherimoya.fold_0.performance.tsv b/ENCSR785JXR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2cb1c2bbaa7e0fa8e5f1a614f3f1d5be284414b6..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -725.340087890625 0.34185537695884705 0.4626697301864624 0.20058397948741913 0.8964749574661255 0.8629255294799805 0.2344268411397934 \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_1.evaluate.json b/ENCSR785JXR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b5a824c7fe28fb7ba677d1bbd52a283babf8128e..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488SLH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_1.fit.json b/ENCSR785JXR/cherimoya.fold_1.fit.json deleted file mode 100644 index e3f5c0ff17bd4b3927f3cdd9a0fb6b7f18f613ce..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF488SLH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_1.log b/ENCSR785JXR/cherimoya.fold_1.log deleted file mode 100644 index 3e13405b40434ba237714b4c31e5fa4722d06c0f..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2682 34.428216218948364 4.186473608016968 754.4605712890625 0.8109408617019653 1110.219970703125 0.35097917914390564 0.7474727 8.17101764678955 True -1 5364 29.811259031295776 2.1195778846740723 765.020263671875 0.4976229965686798 963.8023681640625 0.43011170625686646 0.8079673 2.660327196121216 True -2 8046 29.754995584487915 0.7402842044830322 571.628662109375 0.382144570350647 929.5235595703125 0.4451599717140198 0.820709 1.30195152759552 True -3 10728 29.737083196640015 0.7329416275024414 492.77655029296875 0.5706496238708496 919.4064331054688 0.4489477276802063 0.82909936 0.9787696003913879 True -4 13410 29.779202461242676 0.7284562587738037 624.3296508789062 0.3782764971256256 907.1312255859375 0.45778369903564453 0.8366662 1.0020498037338257 True -5 16092 29.762701988220215 20.24927854537964 735.7127685546875 0.4068753719329834 900.3134155273438 0.46081629395484924 0.8372878 0.8644806742668152 True -6 18774 29.982537031173706 0.7631347179412842 588.9949951171875 0.4622461497783661 893.8737182617188 0.46421778202056885 0.84790593 0.6925764083862305 True -7 21456 29.739657402038574 0.721198558807373 675.3497314453125 0.5016032457351685 889.6793212890625 0.46542128920555115 0.85448414 0.6286643147468567 True -8 24138 29.729268789291382 0.7331118583679199 712.9526977539062 0.4265180230140686 882.4395751953125 0.47102317214012146 0.8588851 0.6045692563056946 True -9 26820 29.754083156585693 0.7374582290649414 647.0770263671875 0.2698414623737335 879.8807373046875 0.4716189503669739 0.8608299 0.5945391654968262 True -10 29502 29.746028423309326 0.7346558570861816 630.0108032226562 0.39507412910461426 876.0933837890625 0.47364342212677 0.8666098 0.535112738609314 True -11 32184 29.744210481643677 0.7219963073730469 492.29498291015625 0.23828716576099396 868.1907348632812 0.47924864292144775 0.8698837 0.4956628978252411 True -12 34866 29.800492525100708 0.7366189956665039 478.4125061035156 0.3308607339859009 862.020751953125 0.4825151562690735 0.8783325 0.43298080563545227 True -13 37548 29.75551128387451 0.7741789817810059 608.7767944335938 0.24925456941127777 859.2951049804688 0.48236745595932007 0.88194835 0.3865116536617279 True -14 40230 29.5018572807312 0.7423598766326904 612.466064453125 0.4061843156814575 856.5631713867188 0.4848368763923645 0.88995993 0.34553104639053345 True -15 42912 29.34719228744507 0.740835428237915 603.6865234375 0.1749878227710724 854.5172119140625 0.48482635617256165 0.8947975 0.30706703662872314 True -16 45594 29.339564085006714 0.7412471771240234 540.7845458984375 0.20084621012210846 853.1939086914062 0.48575079441070557 0.9003265 0.28272634744644165 True -17 48276 29.3940110206604 0.7379932403564453 604.5059814453125 0.2263212651014328 855.159912109375 0.48375073075294495 0.9005341 0.267976850271225 True -18 50958 29.400198221206665 1.820091962814331 645.9148559570312 0.38293924927711487 856.0659790039062 0.48340535163879395 0.90051454 0.2613266110420227 False -19 53640 29.326526880264282 0.7397863864898682 596.3253173828125 0.1502685546875 851.8496704101562 0.48787668347358704 0.90227664 0.2611221671104431 True diff --git a/ENCSR785JXR/cherimoya.fold_1.performance.tsv b/ENCSR785JXR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index af4e0115fbd75b3751fe51a947addeafbbf37fb8..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -851.8496704101562 0.3210654556751251 0.48787668347358704 0.23199614882469177 0.9022766351699829 0.8846246004104614 0.2611221671104431 \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_2.evaluate.json b/ENCSR785JXR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2b42852069d3fff674f9a23b8fd49c8b488a854d..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488SLH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_2.fit.json b/ENCSR785JXR/cherimoya.fold_2.fit.json deleted file mode 100644 index 7c635a11fb91e074f820bf34104967597ddbce15..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF488SLH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_2.log b/ENCSR785JXR/cherimoya.fold_2.log deleted file mode 100644 index 902acbac3fd23fb3d17635f4fbd83f9089f8868b..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2890 36.611783504486084 3.9075257778167725 739.5604248046875 0.3167702555656433 970.0646362304688 0.3510851562023163 0.75496167 5.373443126678467 True -1 5780 32.10158038139343 0.6038427352905273 688.6094970703125 0.4281221926212311 854.623046875 0.4216312766075134 0.8049237 1.951914668083191 True -2 8670 32.10204458236694 0.5700757503509521 804.451171875 0.41004452109336853 835.778564453125 0.4283944368362427 0.8242357 1.0093213319778442 True -3 11560 32.09311819076538 0.5741074085235596 1083.8095703125 0.3516334295272827 825.6327514648438 0.4335273206233978 0.8298654 0.9097083806991577 True -4 14450 32.164206743240356 0.6029715538024902 700.2351684570312 0.5228554010391235 823.3900756835938 0.43567681312561035 0.83007973 0.7068313360214233 True -5 17340 32.11299014091492 0.5753188133239746 647.9241943359375 0.34243348240852356 813.4783325195312 0.444538414478302 0.8340841 0.7630054354667664 True -6 20230 32.123286485672 0.5722019672393799 685.8983154296875 0.3379874527454376 812.0580444335938 0.44320157170295715 0.8394133 0.6205833554267883 True -7 23120 32.128424406051636 0.5728378295898438 560.507568359375 0.4046952724456787 805.4603881835938 0.44827714562416077 0.8451904 0.5868340730667114 True -8 26010 32.10564112663269 0.5629746913909912 527.9014892578125 0.2997815012931824 801.6027221679688 0.44965511560440063 0.85212606 0.5568356513977051 True -9 28900 32.100759744644165 0.5608644485473633 629.0897827148438 0.17804038524627686 796.6370849609375 0.45308035612106323 0.85853374 0.49196603894233704 True -10 31790 32.09991931915283 0.5735049247741699 633.247314453125 0.28869956731796265 793.8997802734375 0.4542584717273712 0.8632097 0.45350000262260437 True -11 34680 32.1575562953949 0.5720877647399902 548.90087890625 0.24409876763820648 789.9039916992188 0.45739680528640747 0.86720896 0.3993869125843048 True -12 37570 32.11773180961609 0.5744950771331787 635.6087036132812 0.22102931141853333 785.837158203125 0.45922738313674927 0.87352985 0.3548348844051361 True -13 40460 32.229252576828 0.569821834564209 791.202392578125 0.3144613802433014 781.4517211914062 0.4630696475505829 0.87635833 0.3312152922153473 True -14 43350 32.17286968231201 0.571866512298584 566.128662109375 0.18842679262161255 780.4219970703125 0.4626789093017578 0.87996495 0.3031303584575653 True -15 46240 32.198771953582764 0.5753769874572754 583.1719970703125 0.2149139642715454 778.3950805664062 0.4636957049369812 0.8826532 0.2789922058582306 True -16 49130 32.167752504348755 8.204781770706177 689.768310546875 0.21275269985198975 778.658447265625 0.46398624777793884 0.8858142 0.2660149037837982 True -17 52020 32.17535901069641 0.5859408378601074 580.638671875 0.20413172245025635 777.7592163085938 0.46355047821998596 0.8861765 0.25908926129341125 True -18 54910 32.18391227722168 0.6096320152282715 821.4849243164062 0.1940024197101593 778.9793090820312 0.46239548921585083 0.8874673 0.25668108463287354 True -19 57800 31.698883533477783 0.5797550678253174 552.03564453125 0.2939043641090393 777.716064453125 0.4643406271934509 0.88712245 0.2565116286277771 False diff --git a/ENCSR785JXR/cherimoya.fold_2.performance.tsv b/ENCSR785JXR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3faeb4e72851194e0785c53001cbb16c09229cd5..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -778.9793090820312 0.3372812867164612 0.46239548921585083 0.20729146897792816 0.8874673247337341 0.863366425037384 0.25668108463287354 \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_3.evaluate.json b/ENCSR785JXR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a9e4317028456d5a8c644a756a2c9c657b52e187..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488SLH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_3.fit.json b/ENCSR785JXR/cherimoya.fold_3.fit.json deleted file mode 100644 index 1f0f98cad3aa063198def3e5a645e3e6d2405297..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF488SLH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_3.log b/ENCSR785JXR/cherimoya.fold_3.log deleted file mode 100644 index f1279f506db0cf225b5959ad362a6faa486b2d45..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 34.86814904212952 3.6853625774383545 606.6148681640625 0.27327030897140503 898.5120239257812 0.35577669739723206 0.7304249 6.7072248458862305 True -1 5470 30.29568076133728 0.5755932331085205 823.2244873046875 0.4297656714916229 781.7809448242188 0.4307078719139099 0.7960955 1.823723316192627 True -2 8205 30.376494646072388 0.560448169708252 777.8391723632812 0.3931136131286621 768.8763427734375 0.43627870082855225 0.81137383 1.0714261531829834 True -3 10940 30.354443550109863 0.585728645324707 626.0133056640625 0.26802366971969604 756.4937133789062 0.444749116897583 0.8203233 0.9892365336418152 True -4 13675 30.346286058425903 0.5663254261016846 632.1444091796875 0.34783935546875 750.1182250976562 0.447401762008667 0.8249556 0.892041802406311 True -5 16410 30.401414155960083 0.5629627704620361 600.3426513671875 0.5444356799125671 743.8660278320312 0.451546847820282 0.83257335 0.7348710298538208 True -6 19145 30.391324281692505 0.5648162364959717 563.064208984375 0.6180027723312378 739.7640380859375 0.4545457065105438 0.84042126 0.6901730298995972 True -7 21880 30.376702070236206 0.5571911334991455 547.5045776367188 0.38100242614746094 735.0680541992188 0.45690691471099854 0.84516364 0.5893785357475281 True -8 24615 30.357317209243774 0.5593080520629883 653.6370849609375 0.5092836618423462 732.5520629882812 0.4578404128551483 0.84987485 0.555149257183075 True -9 27350 30.36912703514099 0.5560307502746582 590.3431396484375 0.26827046275138855 729.1905517578125 0.461376428604126 0.854052 0.5256438255310059 True -10 30085 30.401254892349243 0.5598347187042236 646.884521484375 0.24977366626262665 725.4305419921875 0.46366944909095764 0.8581976 0.5158974528312683 True -11 32820 30.56719398498535 0.9302406311035156 499.3378601074219 0.25062620639801025 722.405517578125 0.4659424424171448 0.863413 0.4666391909122467 True -12 35555 30.31711459159851 0.5621237754821777 658.9291381835938 0.29846927523612976 719.52099609375 0.46685609221458435 0.8656525 0.42141392827033997 True -13 38290 30.393832206726074 0.5643630027770996 659.0010986328125 0.16228678822517395 717.873291015625 0.46811696887016296 0.8711992 0.36924540996551514 True -14 41025 30.366653203964233 0.5507833957672119 531.9989624023438 0.24353154003620148 714.2886352539062 0.4709879159927368 0.87608916 0.3388899564743042 True -15 43760 30.363653421401978 0.5607223510742188 638.665283203125 0.15357983112335205 712.3906860351562 0.4711308181285858 0.8810985 0.31072816252708435 True -16 46495 30.346764087677002 0.5574581623077393 641.2557983398438 0.3048168420791626 711.25244140625 0.4724084436893463 0.8839033 0.286565363407135 True -17 49230 30.32925009727478 0.5661201477050781 658.8605346679688 0.15169349312782288 712.3392333984375 0.4719044268131256 0.8873446 0.27370765805244446 True -18 51965 30.188237190246582 0.5605719089508057 565.9586791992188 0.20525754988193512 713.8111572265625 0.46893227100372314 0.8873333 0.2687922418117523 False -19 54700 29.796188831329346 1.2886767387390137 623.3550415039062 0.15630024671554565 711.12548828125 0.4728549122810364 0.886777 0.26883184909820557 False diff --git a/ENCSR785JXR/cherimoya.fold_3.performance.tsv b/ENCSR785JXR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bd7b32f1304695b4a5f195b47df31a1779d3e309..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -712.3392333984375 0.33700183033943176 0.4719044268131256 0.20208117365837097 0.8873445987701416 0.8499595522880554 0.27370765805244446 \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_4.evaluate.json b/ENCSR785JXR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 826201cdb8e808e9acf3f37133ee596c1b379607..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488SLH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_4.fit.json b/ENCSR785JXR/cherimoya.fold_4.fit.json deleted file mode 100644 index 041a0410ab5a5fe8bfce41a4464815c1cef79ab0..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF488SLH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785JXR/cherimoya.fold_4.log b/ENCSR785JXR/cherimoya.fold_4.log deleted file mode 100644 index 2d92bc51f3b76ff807a9e82a9fae07d07ba7a2bf..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2800 35.90317225456238 4.01935338973999 799.238525390625 0.5406782627105713 835.32861328125 0.3463253676891327 0.7427048 6.397088050842285 True -1 5600 31.105236768722534 0.6090240478515625 693.8714599609375 0.379397988319397 744.28564453125 0.41372761130332947 0.79392385 1.868533968925476 True -2 8400 31.142383337020874 0.9967160224914551 715.8154296875 0.4339359998703003 724.6967163085938 0.42487406730651855 0.8104216 0.9596933722496033 True -3 11200 31.0580313205719 0.6011955738067627 599.6632080078125 0.5682410001754761 714.5292358398438 0.4300011396408081 0.8187477 0.7486292123794556 True -4 14000 31.0537850856781 0.5897910594940186 525.5987548828125 0.21954892575740814 712.4432983398438 0.4325200617313385 0.8227051 0.7343719005584717 True -5 16800 31.089267253875732 0.5992288589477539 707.681396484375 0.4821118414402008 706.267578125 0.4354998469352722 0.82991683 0.6886751055717468 True -6 19600 31.06218385696411 0.6455707550048828 614.4500732421875 0.7676017880439758 700.86962890625 0.4398171901702881 0.82887167 0.5701218843460083 False -7 22400 31.051870346069336 0.600193977355957 616.5230712890625 0.3539116382598877 696.4501953125 0.4431673586368561 0.83699584 0.5451958775520325 True -8 25200 31.02108645439148 1.085247278213501 636.945068359375 0.4623512327671051 696.08935546875 0.4413335919380188 0.8438833 0.5241605639457703 True -9 28000 31.0745267868042 2.979221820831299 618.7174072265625 0.19976668059825897 693.4675903320312 0.44221556186676025 0.847529 0.4687475860118866 True -10 30800 31.083066701889038 0.6064178943634033 592.3160400390625 0.23852583765983582 687.4948120117188 0.4478335380554199 0.85681266 0.42163267731666565 True -11 33600 31.127907752990723 0.5962278842926025 648.4615478515625 0.31115591526031494 683.7365112304688 0.45103734731674194 0.86237216 0.3692167401313782 True -12 36400 31.165943145751953 0.5965840816497803 585.8118896484375 0.19272977113723755 681.6864624023438 0.45160648226737976 0.8685848 0.32890376448631287 True -13 39200 31.221107006072998 0.6055772304534912 722.4639892578125 0.28690487146377563 679.2150268554688 0.4524594843387604 0.87267774 0.293498694896698 True -14 42000 31.148175477981567 0.606215238571167 663.0296630859375 0.1665448695421219 677.0154418945312 0.45510390400886536 0.87663054 0.2690306305885315 True -15 44800 31.168036699295044 0.6033916473388672 479.85357666015625 0.16666288673877716 678.1698608398438 0.452923983335495 0.8812322 0.25157487392425537 True -16 47600 31.12857151031494 14.377185344696045 603.2149658203125 0.5229686498641968 674.4566040039062 0.45873355865478516 0.8848786 0.23729775846004486 True -17 50400 30.57515263557434 24.539634466171265 638.3084716796875 0.0956989973783493 675.015625 0.45677950978279114 0.88613987 0.23274879157543182 True -18 53200 30.61881923675537 30.077090740203857 656.9102172851562 0.22874465584754944 675.61328125 0.4563741087913513 0.88559306 0.23061630129814148 False -19 56000 30.56766104698181 0.7540125846862793 465.6506042480469 0.19397367537021637 675.2405395507812 0.45790186524391174 0.8860601 0.2305138111114502 False diff --git a/ENCSR785JXR/cherimoya.fold_4.performance.tsv b/ENCSR785JXR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f2450889ff83c71c3592c299ded6d51f15a25c09..0000000000000000000000000000000000000000 --- a/ENCSR785JXR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -675.015625 0.34871071577072144 0.45677950978279114 0.19136479496955872 0.8861398696899414 0.8455275297164917 0.23274879157543182 \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_0.evaluate.json b/ENCSR785MXI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ba1c6f14b8b920abd03c2910acc6c541bdd0b549..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF579CAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_0.fit.json b/ENCSR785MXI/cherimoya.fold_0.fit.json deleted file mode 100644 index 8bf00deea128795a3750e2971c075bb92baa7f2e..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF579CAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_0.log b/ENCSR785MXI/cherimoya.fold_0.log deleted file mode 100644 index f770d2124161a8e840c42026bef3d15ebd3a2fcd..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.96076822280884 4.440854072570801 480.69921875 0.7594369649887085 754.8311767578125 0.28944000601768494 0.6415401 7.068038463592529 True -1 5510 30.276472806930542 0.6195521354675293 717.5587158203125 0.9156204462051392 670.1845703125 0.3744949996471405 0.69586295 1.8416252136230469 True -2 8265 30.304807901382446 0.5763030052185059 528.0447998046875 0.664793074131012 656.5576171875 0.3894074559211731 0.7087082 0.8455610275268555 True -3 11020 30.30581259727478 0.6112990379333496 704.5045166015625 0.4702076017856598 651.8220825195312 0.3944529592990875 0.7122504 0.6966525912284851 True -4 13775 31.337831497192383 25.20636534690857 489.0321044921875 0.7936832904815674 650.7120361328125 0.3950999975204468 0.70939416 0.6439391374588013 False -5 16530 29.733179807662964 0.5862953662872314 546.376953125 0.6238940954208374 647.689453125 0.39793384075164795 0.7168904 0.6000605225563049 True -6 19285 29.718945741653442 1.1981613636016846 551.72021484375 0.6410840153694153 644.5482788085938 0.40064987540245056 0.7240691 0.5758819580078125 True -7 22040 29.7018780708313 0.5872185230255127 529.2420654296875 0.7815550565719604 644.3609008789062 0.39991384744644165 0.7320653 0.552495539188385 True -8 24795 29.981218576431274 0.6089508533477783 465.9410095214844 0.46180418133735657 642.800048828125 0.4008597135543823 0.7398578 0.5368369221687317 True -9 27550 30.229355573654175 35.51970601081848 587.1566772460938 0.4404895305633545 639.3321533203125 0.40459153056144714 0.7478251 0.5238639116287231 True -10 30305 30.00090742111206 0.5887649059295654 489.93865966796875 0.5709611177444458 636.4130249023438 0.406882107257843 0.7502724 0.5150114893913269 True -11 33060 30.08215308189392 0.600909948348999 489.3979797363281 0.4988303482532501 634.2267456054688 0.409464955329895 0.75921035 0.502103328704834 True -12 35815 29.981464385986328 0.5880627632141113 468.30963134765625 0.385502427816391 632.6962280273438 0.41101256012916565 0.7642409 0.49786967039108276 True -13 38570 30.337504386901855 0.5974256992340088 483.62054443359375 0.4338902235031128 630.8197631835938 0.413176566362381 0.77272224 0.4722732603549957 True -14 41325 30.03412938117981 0.6055631637573242 678.5062255859375 0.4700990617275238 627.3485717773438 0.41766443848609924 0.7780898 0.464389443397522 True -15 44080 29.871987342834473 0.6037063598632812 553.1348266601562 0.3850489854812622 626.79931640625 0.41658028960227966 0.7828424 0.45763280987739563 True -16 46835 30.097601413726807 2.3726117610931396 566.4056396484375 0.35511237382888794 626.8928833007812 0.41695424914360046 0.78459615 0.44940951466560364 True -17 49590 30.00656032562256 0.5902204513549805 554.7490234375 0.2966548502445221 626.0887451171875 0.41905677318573 0.78452307 0.45350533723831177 False -18 52345 30.521787643432617 0.587151288986206 584.1768798828125 0.2771211862564087 626.9307250976562 0.41746973991394043 0.78268796 0.45945680141448975 False -19 55100 29.987236738204956 0.5903961658477783 509.2018127441406 0.18467292189598083 627.1300659179688 0.41693174839019775 0.7813725 0.46263495087623596 False diff --git a/ENCSR785MXI/cherimoya.fold_0.performance.tsv b/ENCSR785MXI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index df9d5ed37e5465ebe55d67ab598fec624c93208e..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -626.8928833007812 0.3674834668636322 0.41695424914360046 0.18124954402446747 0.7845961451530457 0.7468368411064148 0.44940951466560364 \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_1.evaluate.json b/ENCSR785MXI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c01f3ae2333bfddd591591bbe10d193b66a91b78..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF579CAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_1.fit.json b/ENCSR785MXI/cherimoya.fold_1.fit.json deleted file mode 100644 index 3b1bc5938b7fb97ce973cc3916f1e257221cf0c5..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF579CAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_1.log b/ENCSR785MXI/cherimoya.fold_1.log deleted file mode 100644 index f56453028f0eb6a66434d41398b674ca0535e40c..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2697 34.33443212509155 3.0211353302001953 547.3052978515625 0.7332620620727539 877.785888671875 0.2887684404850006 0.6590833 6.938396453857422 True -1 5394 29.875607013702393 0.6890006065368652 607.55712890625 0.7727766036987305 779.72216796875 0.3820231556892395 0.71151584 3.06138014793396 True -2 8091 29.76742720603943 0.727271556854248 500.8587646484375 0.5202904343605042 759.21044921875 0.39381489157676697 0.7326583 0.9360637664794922 True -3 10788 29.813032627105713 0.683438777923584 501.74212646484375 0.8069537878036499 749.94580078125 0.40218448638916016 0.73731434 0.7519892454147339 True -4 13485 29.80918049812317 0.6932296752929688 581.71630859375 0.5105149149894714 744.2481079101562 0.40645796060562134 0.7471666 0.6722872257232666 True -5 16182 29.17786693572998 0.6578612327575684 534.4735717773438 0.66850745677948 740.7371215820312 0.4086335301399231 0.74835974 0.5931348204612732 True -6 18879 29.114601135253906 0.6590702533721924 577.6348876953125 0.6521360874176025 734.4891967773438 0.4163702726364136 0.75296265 0.5928860306739807 True -7 21576 29.085769414901733 0.6651797294616699 582.9584350585938 0.6816725730895996 731.4287109375 0.4173581600189209 0.76127046 0.5811099410057068 True -8 24273 29.120638608932495 0.6614401340484619 509.706787109375 0.46927157044410706 727.6907958984375 0.42045125365257263 0.77028424 0.5651768445968628 True -9 26970 29.015835285186768 11.196212768554688 590.5220336914062 0.5356117486953735 725.4453735351562 0.42177796363830566 0.77527875 0.5499535202980042 True -10 29667 29.132726430892944 0.6469898223876953 550.1312255859375 0.3336610794067383 721.5388793945312 0.42582547664642334 0.7825265 0.5133343935012817 True -11 32364 29.20090126991272 0.6755917072296143 541.370849609375 0.340705007314682 720.1979370117188 0.4265042245388031 0.7868975 0.5049835443496704 True -12 35061 29.352055549621582 0.6644542217254639 447.13427734375 0.42045092582702637 718.1353759765625 0.4276464879512787 0.79367006 0.4927009046077728 True -13 37758 29.13435387611389 0.669304609298706 473.1327209472656 0.46524229645729065 715.4740600585938 0.43060302734375 0.7988821 0.4813477098941803 True -14 40455 29.16363286972046 0.680020809173584 574.6126708984375 0.525023877620697 712.1548461914062 0.4344889521598816 0.8024864 0.4644832909107208 True -15 43152 29.10190176963806 0.6875302791595459 544.5315551757812 0.36481553316116333 713.0942993164062 0.4311554431915283 0.8101413 0.44747456908226013 True -16 45849 29.16912841796875 3.828002452850342 557.6585693359375 0.455763578414917 711.9398193359375 0.43262794613838196 0.8115855 0.4455145299434662 True -17 48546 29.23584532737732 1.3930246829986572 466.64398193359375 0.25883346796035767 711.8345947265625 0.43238428235054016 0.8135178 0.446747362613678 True -18 51243 29.194990873336792 0.6838836669921875 503.35040283203125 0.3681832551956177 712.918701171875 0.4317685663700104 0.8095072 0.4543226659297943 False -19 53940 29.444539308547974 0.6803452968597412 491.24761962890625 0.2684924900531769 712.36865234375 0.43254703283309937 0.8078545 0.4616650640964508 False diff --git a/ENCSR785MXI/cherimoya.fold_1.performance.tsv b/ENCSR785MXI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b1fa11144625a0edb76542cff01efe759cbb6aad..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -711.8345947265625 0.3512703478336334 0.43238434195518494 0.20032256841659546 0.8135178089141846 0.7937493920326233 0.446747362613678 \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_2.evaluate.json b/ENCSR785MXI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b443c3f803fde599555b130c5170004fc08067b7..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF579CAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_2.fit.json b/ENCSR785MXI/cherimoya.fold_2.fit.json deleted file mode 100644 index 642d98ef5bcde019593a789c03bab206edfcbb1a..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF579CAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_2.log b/ENCSR785MXI/cherimoya.fold_2.log deleted file mode 100644 index ae56ef30c17196e1a5d4d488c142f52b5c504956..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 36.201013803482056 5.6582865715026855 563.2173461914062 0.5652190446853638 779.8216552734375 0.2891407012939453 0.63517165 5.79865026473999 True -1 5736 31.528526544570923 0.6817724704742432 666.5280151367188 0.7796775698661804 695.8937377929688 0.37063321471214294 0.69041246 2.028871774673462 True -2 8604 31.584526538848877 1.4654929637908936 539.6046142578125 0.512681245803833 679.4239501953125 0.38590511679649353 0.71096796 0.9367985129356384 True -3 11472 31.528912782669067 2.3127222061157227 523.357666015625 0.6011362075805664 674.5801391601562 0.3904632329940796 0.71735597 0.7031862139701843 True -4 14340 33.790870666503906 9.324634075164795 503.15753173828125 0.4757670760154724 671.0779418945312 0.39253097772598267 0.7282598 0.6285884976387024 True -5 17208 31.641201496124268 0.6396262645721436 512.019775390625 0.5043511390686035 667.7913818359375 0.3957764804363251 0.73410326 0.5678408741950989 True -6 20076 30.9698326587677 0.6292064189910889 445.6370849609375 0.5758483409881592 663.353759765625 0.3993871212005615 0.73995596 0.51552414894104 True -7 22944 31.081494092941284 0.6113924980163574 613.1292114257812 0.533784031867981 662.0975341796875 0.39971938729286194 0.74299365 0.49695125222206116 True -8 25812 31.116594314575195 0.6175351142883301 597.6656494140625 0.6349438428878784 659.1233520507812 0.40263631939888 0.7435118 0.4914151728153229 True -9 28680 31.0757417678833 0.6122617721557617 566.0301513671875 0.48681026697158813 657.5592651367188 0.40397244691848755 0.7478652 0.48489025235176086 True -10 31548 31.03826093673706 0.6199698448181152 545.5242919921875 0.5600699186325073 655.8788452148438 0.40455231070518494 0.7576197 0.47216591238975525 True -11 34416 30.99771499633789 0.6025655269622803 486.0256042480469 0.43153756856918335 651.1038208007812 0.41122671961784363 0.7682401 0.45818963646888733 True -12 37284 30.959768056869507 0.6149318218231201 399.55859375 0.43457257747650146 649.2418212890625 0.41192319989204407 0.77627826 0.44456374645233154 True -13 40152 30.987085580825806 0.6096398830413818 505.1639404296875 0.42457255721092224 645.3417358398438 0.4173196852207184 0.78293717 0.43521419167518616 True -14 43020 30.940561771392822 0.6051692962646484 438.7472229003906 0.3634939193725586 644.9378662109375 0.4171953797340393 0.78860134 0.4257470667362213 True -15 45888 30.91140627861023 0.6044199466705322 430.0972900390625 0.24284198880195618 643.6690673828125 0.41874995827674866 0.7943395 0.42111489176750183 True -16 48756 30.911617040634155 0.5966076850891113 552.2451171875 0.34816086292266846 645.308349609375 0.415731281042099 0.7966992 0.42362555861473083 True -17 51624 30.945895671844482 0.6002295017242432 563.708740234375 0.22738006711006165 645.0073852539062 0.41696590185165405 0.7965652 0.4330254793167114 False -18 54492 31.180458784103394 0.6035404205322266 571.5506591796875 0.4332294464111328 645.5026245117188 0.4164723753929138 0.79495215 0.4422015845775604 False -19 57360 30.96478009223938 0.609581470489502 503.6559143066406 0.31602001190185547 644.3709716796875 0.41863957047462463 0.7929114 0.4499402940273285 False diff --git a/ENCSR785MXI/cherimoya.fold_2.performance.tsv b/ENCSR785MXI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cab680ac2ee4bbeffe7f161a2950b23abee5e0fc..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -645.308349609375 0.36517906188964844 0.415731281042099 0.18407699465751648 0.7966992259025574 0.7718578577041626 0.42362555861473083 \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_3.evaluate.json b/ENCSR785MXI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 516c851977601f6f6d4e1542678aa2c780426b22..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF579CAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_3.fit.json b/ENCSR785MXI/cherimoya.fold_3.fit.json deleted file mode 100644 index d121c36f576a1de38006eac5d757a5fdea9f1e21..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF579CAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_3.log b/ENCSR785MXI/cherimoya.fold_3.log deleted file mode 100644 index e4285ddab58e6040a13a86d5b39bd9984fc50a2a..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.11844849586487 4.073636770248413 679.8927612304688 0.7239211797714233 740.2498168945312 0.29166218638420105 0.64579886 6.478289604187012 True -1 5516 30.378520965576172 0.5839450359344482 510.7320251464844 0.6552340984344482 664.8721313476562 0.37100934982299805 0.70641524 2.052340030670166 True -2 8274 30.318585872650146 1.3754429817199707 442.67779541015625 0.5312554836273193 651.7979125976562 0.38333240151405334 0.7195992 0.969083845615387 True -3 11032 30.335427284240723 0.5185115337371826 637.2374267578125 0.48296886682510376 642.8967895507812 0.39057856798171997 0.7349355 0.9004001617431641 True -4 13790 29.890840530395508 0.4998657703399658 492.6821594238281 0.6055924892425537 636.4688720703125 0.39640459418296814 0.73542494 0.7079148292541504 True -5 16548 29.7437744140625 1.397334337234497 579.4932861328125 0.6699399948120117 636.24609375 0.39656952023506165 0.74044454 0.6085388660430908 True -6 19306 29.699126482009888 0.49511027336120605 614.51953125 0.8525354266166687 632.046630859375 0.40128543972969055 0.74385244 0.56764155626297 True -7 22064 29.762922763824463 0.5063164234161377 482.9007873535156 0.5423187613487244 630.0218505859375 0.40197277069091797 0.7490745 0.5726035237312317 True -8 24822 29.76935887336731 0.5018601417541504 572.4715576171875 0.6092218160629272 625.638427734375 0.40735340118408203 0.7547133 0.5539778470993042 True -9 27580 29.721786975860596 0.49537062644958496 604.7073974609375 0.4892534613609314 625.6168212890625 0.4059780240058899 0.7604991 0.540128231048584 True -10 30338 29.69171166419983 0.49822568893432617 513.8765869140625 0.372706800699234 622.6958618164062 0.40958932042121887 0.76826817 0.5141786336898804 True -11 33096 33.31865358352661 27.12780499458313 592.43701171875 0.4471955895423889 619.7513427734375 0.4123443365097046 0.77423435 0.5021054148674011 True -12 35854 29.774034023284912 1.4642009735107422 698.422607421875 0.42222923040390015 617.5413208007812 0.41434916853904724 0.780793 0.4850955903530121 True -13 38612 29.785460948944092 0.5226197242736816 490.6816711425781 0.45663005113601685 617.34814453125 0.41297322511672974 0.78811383 0.47139254212379456 True -14 41370 29.806277990341187 0.5002009868621826 640.0069580078125 0.3086988925933838 614.1561279296875 0.417398065328598 0.7961041 0.45044222474098206 True -15 44128 29.84156346321106 0.5078582763671875 530.9840087890625 0.4123988747596741 612.06591796875 0.4195651113986969 0.8002269 0.4377681612968445 True -16 46886 29.90629529953003 0.5063328742980957 522.6370849609375 0.476067453622818 612.2454223632812 0.4190930128097534 0.8066179 0.4284302592277527 True -17 49644 29.876529932022095 0.5052661895751953 482.6414489746094 0.2905293107032776 612.6834106445312 0.41763877868652344 0.8070322 0.42869654297828674 True -18 52402 29.73449444770813 0.5073492527008057 501.093994140625 0.23729398846626282 613.1947631835938 0.41678375005722046 0.8055757 0.43267253041267395 False -19 55160 29.911829710006714 0.5048165321350098 531.5570678710938 0.34620168805122375 613.630859375 0.41649043560028076 0.8042415 0.4371897876262665 False diff --git a/ENCSR785MXI/cherimoya.fold_3.performance.tsv b/ENCSR785MXI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a8922538bae2f7f922b153bc3bd754fad648e6e0..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -612.6834106445312 0.369928240776062 0.41763877868652344 0.18021203577518463 0.8070322275161743 0.7736387252807617 0.42869654297828674 \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_4.evaluate.json b/ENCSR785MXI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 636643948227603e50e9a7b0c317518b850ab024..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF579CAP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_4.fit.json b/ENCSR785MXI/cherimoya.fold_4.fit.json deleted file mode 100644 index 3704cde2947c73585aaf02594199094a3b71b61b..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF579CAP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785MXI/cherimoya.fold_4.log b/ENCSR785MXI/cherimoya.fold_4.log deleted file mode 100644 index c548e9ba92270f4d13ebacae926ed4e93242ee1e..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2799 35.55566072463989 3.4869301319122314 543.59814453125 0.6136125922203064 682.2581176757812 0.2808637022972107 0.6229945 5.157295227050781 True -1 5598 30.77315926551819 0.6064567565917969 731.3697509765625 0.7218277454376221 618.2923583984375 0.3528887629508972 0.6684532 1.9634701013565063 True -2 8397 30.937776803970337 41.26152753829956 513.9835205078125 0.6492643356323242 606.5584106445312 0.363858163356781 0.6922686 0.7568269371986389 True -3 11196 31.132923126220703 0.5921659469604492 472.14453125 0.6090062856674194 599.0715942382812 0.3717285990715027 0.7066742 0.6911046504974365 True -4 13995 30.145373106002808 0.5729148387908936 599.8001708984375 0.7045202851295471 594.7885131835938 0.37597784399986267 0.71491736 0.6222851276397705 True -5 16794 30.131319522857666 8.980266332626343 577.24169921875 0.6161104440689087 592.3815307617188 0.37752997875213623 0.7172743 0.5312945246696472 True -6 19593 33.55751085281372 0.5937273502349854 590.4205322265625 0.7160652279853821 589.3184814453125 0.38080331683158875 0.7246656 0.5139470100402832 True -7 22392 31.540611743927002 0.6335022449493408 588.8795166015625 0.4689735472202301 587.207763671875 0.3826037645339966 0.73129207 0.5064553618431091 True -8 25191 30.424299478530884 1.25667405128479 535.4819946289062 0.4721829295158386 585.6875 0.38400983810424805 0.7370893 0.49987921118736267 True -9 27990 30.38595151901245 0.5874466896057129 488.61920166015625 0.675990104675293 583.3373413085938 0.3863418698310852 0.74349385 0.4903258681297302 True -10 30789 30.35337471961975 0.5851316452026367 449.0892639160156 0.7070021629333496 582.7514038085938 0.38617071509361267 0.7482627 0.4856601357460022 True -11 33588 30.31760597229004 0.5880584716796875 517.5841064453125 0.4661562740802765 579.2001342773438 0.3919762969017029 0.7548733 0.4736018776893616 True -12 36387 30.332501888275146 0.583310604095459 529.1510009765625 0.38018208742141724 578.7620239257812 0.3916560113430023 0.7602479 0.464010089635849 True -13 39186 30.342373609542847 0.5868093967437744 533.0105590820312 0.5533295273780823 576.42431640625 0.3948952853679657 0.7664306 0.45358961820602417 True -14 41985 30.418699502944946 0.5867440700531006 578.7449951171875 0.260402649641037 576.6649169921875 0.39348849654197693 0.7718558 0.4449041485786438 True -15 44784 30.40123701095581 0.6090817451477051 468.23724365234375 0.46620362997055054 574.452392578125 0.3963581919670105 0.7775742 0.43646660447120667 True -16 47583 30.27979016304016 0.5823392868041992 499.8901062011719 0.2929307222366333 575.2044677734375 0.39543503522872925 0.7806924 0.43036922812461853 True -17 50382 30.23410201072693 0.585644006729126 506.9147033691406 0.19100189208984375 575.9038696289062 0.3941468596458435 0.7811616 0.43165990710258484 True -18 53181 30.29852271080017 0.5818021297454834 495.54351806640625 0.33180001378059387 575.3165893554688 0.3955458104610443 0.78086394 0.43803372979164124 False -19 55980 30.27795171737671 2.88346791267395 540.7418212890625 0.43054714798927307 576.001708984375 0.3944149315357208 0.7783142 0.4432319402694702 False diff --git a/ENCSR785MXI/cherimoya.fold_4.performance.tsv b/ENCSR785MXI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 32db8a8941db44ddaf42a83d6faf6947bf3f87f7..0000000000000000000000000000000000000000 --- a/ENCSR785MXI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -575.9038696289062 0.3850404620170593 0.3941468298435211 0.16473068296909332 0.7811616063117981 0.7332449555397034 0.43165990710258484 \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_0.evaluate.json b/ENCSR785RIM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 59a77a4cebf6fb835c3fb01b345c86380527af29..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178NIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_0.fit.json b/ENCSR785RIM/cherimoya.fold_0.fit.json deleted file mode 100644 index 861335e563873c064eaf94908d6a929d25030297..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF178NIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_0.log b/ENCSR785RIM/cherimoya.fold_0.log deleted file mode 100644 index e77c5dc726193a1880f06f9e7974772794255497..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1406 18.892083168029785 3.52774977684021 404.708740234375 2.1538119316101074 707.609375 0.1459856927394867 0.49769744 16.38326072692871 True -1 2812 15.63109016418457 0.3062901496887207 447.60150146484375 2.1298604011535645 612.1306762695312 0.2250206023454666 0.6517033 11.095224380493164 True -2 4218 15.593385934829712 0.2956862449645996 360.8340759277344 1.221137523651123 541.5423583984375 0.2798667550086975 0.6963659 6.54110860824585 True -3 5624 15.59709906578064 0.28020453453063965 391.1111755371094 1.106566309928894 499.1434326171875 0.3033731281757355 0.7286861 4.181118488311768 True -4 7030 15.584442377090454 0.2848827838897705 565.56396484375 1.7788984775543213 482.1191101074219 0.31403055787086487 0.74614966 2.9250264167785645 True -5 8436 15.57221794128418 0.2815682888031006 306.8154296875 1.6551172733306885 474.7677001953125 0.3195466697216034 0.75352085 2.128614902496338 True -6 9842 15.617280721664429 0.28151988983154297 364.7324523925781 1.0500929355621338 468.1276550292969 0.32518675923347473 0.7606402 1.8903130292892456 True -7 11248 15.600493431091309 0.5522778034210205 374.050048828125 0.9788464903831482 464.95574951171875 0.326999306678772 0.77091324 1.5643234252929688 True -8 12654 15.626455783843994 0.28115057945251465 393.7421569824219 1.3873661756515503 461.3922119140625 0.3287414312362671 0.77812976 1.3374896049499512 True -9 14060 15.577232122421265 0.28084897994995117 316.20379638671875 1.1204936504364014 454.7626953125 0.3355761468410492 0.78264564 1.21699857711792 True -10 15466 15.616130352020264 0.27948546409606934 470.1363525390625 1.3678075075149536 453.4857482910156 0.3359225392341614 0.79162747 1.1085703372955322 True -11 16872 15.594423294067383 0.2798905372619629 321.81134033203125 0.8348417282104492 448.6656188964844 0.33992835879325867 0.7962512 1.0420522689819336 True -12 18278 15.590257167816162 0.27608704566955566 380.8406677246094 0.817595362663269 443.5228576660156 0.3444812297821045 0.80049765 0.9923135042190552 True -13 19684 15.528352975845337 0.27581095695495605 362.97216796875 1.235490322113037 441.6808166503906 0.34578990936279297 0.8095134 0.9435855746269226 True -14 21090 15.5893394947052 0.2842752933502197 293.18487548828125 0.8416718244552612 439.11968994140625 0.34619951248168945 0.81367487 0.9099839925765991 True -15 22496 15.561043977737427 0.2837820053100586 307.73748779296875 0.7101274728775024 435.93072509765625 0.3498988747596741 0.8193859 0.8711308240890503 True -16 23902 15.57101559638977 0.28410816192626953 398.1988525390625 0.8950155377388 436.744384765625 0.348927766084671 0.82232046 0.8540135622024536 True -17 25308 15.572796821594238 1.0156869888305664 365.49273681640625 0.6086366772651672 436.1510009765625 0.3499213755130768 0.8251166 0.8445131778717041 True -18 26714 15.61128830909729 0.2787442207336426 324.50030517578125 0.5200546383857727 438.3364562988281 0.3471757471561432 0.82579964 0.8374997973442078 True -19 28120 15.559525728225708 0.2837226390838623 387.41314697265625 0.4130129814147949 437.091552734375 0.3493179976940155 0.8248531 0.8407285809516907 False diff --git a/ENCSR785RIM/cherimoya.fold_0.performance.tsv b/ENCSR785RIM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f6f1a068b0920244cb734e53fafd77ed8c98875a..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -438.3364562988281 0.44712474942207336 0.3471757173538208 0.12053296715021133 0.8257996439933777 0.790483832359314 0.8374997973442078 \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_1.evaluate.json b/ENCSR785RIM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8084d3358b43975829aeadcbbbc07cdab9b106c4..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178NIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_1.fit.json b/ENCSR785RIM/cherimoya.fold_1.fit.json deleted file mode 100644 index 80f48500495b0373f0943e3c5a34e2289cabc2b2..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF178NIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_1.log b/ENCSR785RIM/cherimoya.fold_1.log deleted file mode 100644 index f5a8417641c9c471d855b41d0bdd159f7e5f4168..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1360 18.342421293258667 25.935754537582397 563.037353515625 2.0992431640625 875.8427124023438 0.1559404879808426 0.4430162 19.059728622436523 True -1 2720 15.059607028961182 0.4564507007598877 355.3736877441406 1.3216421604156494 755.5968627929688 0.23727694153785706 0.6190949 13.921836853027344 True -2 4080 14.998650312423706 0.4227721691131592 475.69830322265625 1.4273015260696411 646.982666015625 0.30693888664245605 0.6988831 8.296517372131348 True -3 5440 15.032821893692017 0.41776490211486816 264.99334716796875 1.3529952764511108 603.8270874023438 0.3303043246269226 0.7387735 4.498875141143799 True -4 6800 15.015576839447021 0.4168524742126465 462.5854797363281 1.1369550228118896 587.1404418945312 0.33961182832717896 0.74566984 3.082430124282837 True -5 8160 14.990481615066528 0.4074280261993408 335.7801513671875 1.3847495317459106 574.203125 0.3468548655509949 0.754679 2.5497043132781982 True -6 9520 14.905524969100952 13.921390533447266 367.19281005859375 1.2573530673980713 566.8786010742188 0.35214340686798096 0.7632104 2.031208038330078 True -7 10880 15.140437126159668 0.4242527484893799 347.8555908203125 1.137660026550293 558.4474487304688 0.35751137137413025 0.77607876 1.7232356071472168 True -8 12240 14.952939748764038 0.40549468994140625 392.9124755859375 0.8948113918304443 553.5499267578125 0.36127233505249023 0.7831646 1.6810624599456787 True -9 13600 14.978549480438232 0.4000575542449951 425.9646911621094 1.1800442934036255 549.4005737304688 0.3647439479827881 0.791948 1.4771332740783691 True -10 14960 14.960538387298584 0.3989686965942383 456.080810546875 1.0209932327270508 547.3794555664062 0.36444202065467834 0.8000514 1.3387086391448975 True -11 16320 14.918152093887329 0.39851808547973633 323.7884826660156 0.7629798650741577 544.5127563476562 0.36599984765052795 0.80636275 1.2189090251922607 True -12 17680 14.919006109237671 0.4022676944732666 422.65203857421875 1.1505376100540161 539.3670043945312 0.3703063428401947 0.81361634 1.1358078718185425 True -13 19040 14.944376230239868 0.4070403575897217 267.3713684082031 0.8021633625030518 532.35498046875 0.3760799467563629 0.8178951 1.079951286315918 True -14 20400 14.921453714370728 0.39786291122436523 239.76144409179688 1.1983222961425781 527.5331420898438 0.37963441014289856 0.82512796 1.0154352188110352 True -15 21760 14.90982985496521 0.39832568168640137 296.33203125 0.541318953037262 524.5839233398438 0.3809944689273834 0.82983637 0.953374445438385 True -16 23120 14.891161680221558 0.3972938060760498 401.7618103027344 0.6845833659172058 524.6721801757812 0.3811703026294708 0.8322026 0.9175643920898438 True -17 24480 14.783188581466675 0.39380741119384766 444.7423095703125 0.7157686948776245 524.3682250976562 0.3803355395793915 0.83454275 0.9055935740470886 True -18 25840 14.639054775238037 0.39435338973999023 302.5653076171875 0.8047531843185425 525.5797729492188 0.37898361682891846 0.8342485 0.9063199758529663 False -19 27200 14.661220073699951 0.4044003486633301 276.5732727050781 0.4496370553970337 527.006103515625 0.37761837244033813 0.83400947 0.9156132340431213 False diff --git a/ENCSR785RIM/cherimoya.fold_1.performance.tsv b/ENCSR785RIM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7fe27b1656c571de82209229487db05b89ec7ee7..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -524.3682250976562 0.41968220472335815 0.3803355097770691 0.14600884914398193 0.8345427513122559 0.813091516494751 0.9055935740470886 \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_2.evaluate.json b/ENCSR785RIM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f08fda444a7d2c8b52c885be73f14c519d911cec..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178NIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_2.fit.json b/ENCSR785RIM/cherimoya.fold_2.fit.json deleted file mode 100644 index efce40f29af8001ccfdebcce991d2a2fc6fe192d..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF178NIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_2.log b/ENCSR785RIM/cherimoya.fold_2.log deleted file mode 100644 index 2f3c093dd81657ad282104a7c1a2050267cc9074..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1467 19.51256012916565 3.4786951541900635 457.3697814941406 1.3484275341033936 736.4254760742188 0.1465587466955185 0.4303358 15.7149658203125 True -1 2934 16.600799322128296 0.31653499603271484 362.00732421875 1.665832757949829 629.7247314453125 0.23033985495567322 0.62439096 11.683243751525879 True -2 4401 16.229276180267334 0.31179332733154297 466.1793212890625 1.317935585975647 544.0260009765625 0.2839706838130951 0.7013056 6.944754600524902 True -3 5868 16.197168827056885 9.205393075942993 331.9188537597656 0.984475314617157 503.11309814453125 0.3050992488861084 0.7358594 3.630995035171509 True -4 7335 16.180681228637695 0.31952333450317383 292.80078125 1.4507651329040527 492.024169921875 0.312052845954895 0.7480126 2.570038318634033 True -5 8802 16.22501516342163 0.30716705322265625 300.30548095703125 1.1699472665786743 485.0292663574219 0.3191607892513275 0.754127 2.2798051834106445 True -6 10269 16.216325998306274 0.3164355754852295 427.4055480957031 1.8069663047790527 478.5889587402344 0.32496213912963867 0.76544625 1.908357858657837 True -7 11736 16.273967504501343 2.4814798831939697 238.06634521484375 1.1069560050964355 474.8511657714844 0.3262834846973419 0.77467394 1.5704323053359985 True -8 13203 16.26613473892212 0.31912946701049805 408.28497314453125 0.9400831460952759 470.1324462890625 0.33015838265419006 0.7805488 1.3759520053863525 True -9 14670 16.239508390426636 1.5458979606628418 399.76953125 1.2875022888183594 465.61346435546875 0.3335545063018799 0.7878003 1.2138144969940186 True -10 16137 16.170528411865234 0.30231237411499023 342.7499084472656 1.6400048732757568 463.5813903808594 0.3350447118282318 0.79478306 1.1577503681182861 True -11 17604 16.122462034225464 0.30919814109802246 323.147216796875 0.8354977369308472 459.2961120605469 0.33910632133483887 0.800981 1.0599555969238281 True -12 19071 16.16415810585022 0.30200767517089844 276.2089538574219 1.657414197921753 455.37628173828125 0.3418908417224884 0.8063978 0.9993237257003784 True -13 20538 16.115514278411865 0.29858994483947754 361.1664733886719 1.1646606922149658 451.392578125 0.34427759051322937 0.8150316 0.9269976615905762 True -14 22005 16.14508605003357 0.2981123924255371 396.8915710449219 0.798098087310791 448.5133972167969 0.34700873494148254 0.8197094 0.8933910131454468 True -15 23472 16.11099123954773 0.8467609882354736 369.3586730957031 0.43315809965133667 445.9208068847656 0.34869053959846497 0.8236748 0.8641080260276794 True -16 24939 16.165999174118042 0.30287885665893555 385.8644104003906 0.7594573497772217 443.33404541015625 0.35093721747398376 0.8276072 0.844582736492157 True -17 26406 16.14633083343506 0.30219507217407227 246.23939514160156 0.5535537600517273 444.5696716308594 0.3490750193595886 0.8264085 0.8337734937667847 False -18 27873 16.11082673072815 0.30210351943969727 390.04345703125 0.6870224475860596 446.5475158691406 0.34668800234794617 0.82828623 0.8372766375541687 True -19 29340 16.10470986366272 0.3004739284515381 341.8102111816406 1.3105920553207397 446.98724365234375 0.3459356725215912 0.8275523 0.8410580158233643 False diff --git a/ENCSR785RIM/cherimoya.fold_2.performance.tsv b/ENCSR785RIM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f82a7de738a4abc2cf7dda337eaccfd9dc1fb32b..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -446.5475158691406 0.4463396668434143 0.34668800234794617 0.12607082724571228 0.8282862305641174 0.7931147813796997 0.8372766375541687 \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_3.evaluate.json b/ENCSR785RIM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7835f8979298afa59514713a714829eb78fc0af3..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178NIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_3.fit.json b/ENCSR785RIM/cherimoya.fold_3.fit.json deleted file mode 100644 index f8ffbe2df43c7c2737ed0672d0930dc0248bedbc..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF178NIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_3.log b/ENCSR785RIM/cherimoya.fold_3.log deleted file mode 100644 index 56c0d719e6fe6b3d0ddea41bcff0c7a2c6bc9c63..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1409 18.977846145629883 3.189242362976074 409.7248229980469 2.0826416015625 764.174560546875 0.16170884668827057 0.4394808 17.291820526123047 True -1 2818 15.486995697021484 0.29977846145629883 394.15118408203125 1.2593579292297363 657.2815551757812 0.24377937614917755 0.60911703 12.542380332946777 True -2 4227 15.759152173995972 0.2684342861175537 399.3384704589844 2.1375746726989746 563.6068115234375 0.3052966594696045 0.6889645 7.822520732879639 True -3 5636 15.492385387420654 2.181469440460205 644.6982421875 1.1204911470413208 534.8543090820312 0.3226276636123657 0.71476114 4.388924598693848 True -4 7045 15.475038051605225 0.26705002784729004 474.194580078125 1.7005290985107422 522.975341796875 0.33191680908203125 0.723218 3.241130828857422 True -5 8454 15.449896335601807 0.26671528816223145 309.7352294921875 1.5651639699935913 513.4594116210938 0.33738651871681213 0.7369406 2.328023910522461 True -6 9863 15.425103664398193 0.26770877838134766 376.4271240234375 1.113095998764038 504.70654296875 0.34463098645210266 0.74601775 1.9824514389038086 True -7 11272 15.425188541412354 0.6856131553649902 386.44921875 1.199150562286377 499.9176025390625 0.3476714491844177 0.75030404 1.7326494455337524 True -8 12681 15.454122304916382 0.27794933319091797 309.23577880859375 0.6848066449165344 494.5530700683594 0.3533008396625519 0.757706 1.4855432510375977 True -9 14090 15.432986497879028 0.271925687789917 342.400390625 1.1028803586959839 492.7105407714844 0.3537527024745941 0.76671934 1.2938233613967896 True -10 15499 15.429315328598022 0.2763798236846924 281.70855712890625 0.9402612447738647 487.6552429199219 0.35706448554992676 0.7743257 1.1856420040130615 True -11 16908 15.478651523590088 1.746140718460083 452.5058898925781 0.9126527309417725 484.2546081542969 0.359876811504364 0.78018725 1.1403635740280151 True -12 18317 15.471105813980103 0.27648091316223145 373.3498229980469 0.9729438424110413 478.9458312988281 0.3647817075252533 0.7873195 1.1037780046463013 True -13 19726 15.47140383720398 0.27434492111206055 334.065673828125 0.6502562761306763 475.630859375 0.36735352873802185 0.79648656 1.0390092134475708 True -14 21135 15.363600254058838 0.27845287322998047 313.9367980957031 0.9206772446632385 473.67205810546875 0.36921223998069763 0.80468255 0.9812362194061279 True -15 22544 15.148980140686035 0.26960301399230957 410.3981628417969 0.5885834097862244 470.9342346191406 0.3708980977535248 0.8108245 0.96058589220047 True -16 23953 15.132898330688477 0.26633715629577637 430.0689392089844 0.861177921295166 470.84381103515625 0.37053382396698 0.8110595 0.9409225583076477 True -17 25362 15.147765398025513 0.26958203315734863 341.93243408203125 0.6951100826263428 471.6665954589844 0.3697359263896942 0.8117691 0.9464828372001648 True -18 26771 15.14431118965149 0.26831746101379395 485.4956359863281 0.6108121871948242 472.005859375 0.36956456303596497 0.8112264 0.9530749320983887 False -19 28180 15.159995079040527 0.2720522880554199 468.02606201171875 0.5654305219650269 473.7080993652344 0.36765292286872864 0.81187016 0.9534972310066223 True diff --git a/ENCSR785RIM/cherimoya.fold_3.performance.tsv b/ENCSR785RIM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3de908ea55078d81c747d9164f73437a5d26d605..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -473.7080993652344 0.42990657687187195 0.36765292286872864 0.13982684910297394 0.8118701577186584 0.7808579206466675 0.9534972310066223 \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_4.evaluate.json b/ENCSR785RIM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0efa5c012085e8060cf1da979c48a085bf7b9252..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF178NIK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_4.fit.json b/ENCSR785RIM/cherimoya.fold_4.fit.json deleted file mode 100644 index deb2fe8c46048f567a22bfb90fb9fc55cc6906db..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF178NIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785RIM/cherimoya.fold_4.log b/ENCSR785RIM/cherimoya.fold_4.log deleted file mode 100644 index 4736522fa9c04074ab4ba95d2f18c00a08fc2a09..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1390 18.84563446044922 3.1985464096069336 363.3322448730469 1.9616258144378662 665.4777221679688 0.14799870550632477 0.46277586 15.69908618927002 True -1 2780 15.410660028457642 0.2680983543395996 384.9217834472656 1.0918307304382324 584.8292236328125 0.21869930624961853 0.60429144 11.468239784240723 True -2 4170 15.434845685958862 0.26497387886047363 483.6549072265625 1.6903539896011353 507.1131286621094 0.2764456272125244 0.682342 7.106864929199219 True -3 5560 15.390984296798706 0.259218692779541 441.52435302734375 1.4842106103897095 475.2332763671875 0.2961384654045105 0.70523393 4.183125019073486 True -4 6950 15.458629131317139 5.6094970703125 479.9747314453125 1.2859506607055664 459.4451904296875 0.30606964230537415 0.71147966 3.0639591217041016 True -5 8340 15.426170587539673 0.2709212303161621 390.5625915527344 1.101994276046753 451.5556335449219 0.3127391040325165 0.71609175 2.636650800704956 True -6 9730 15.922466278076172 0.2655925750732422 327.3299865722656 1.176508903503418 444.3875427246094 0.320117712020874 0.7272092 2.220818519592285 True -7 11120 15.352891683578491 0.2674431800842285 289.7026672363281 1.4470337629318237 442.7336730957031 0.320263534784317 0.73495 1.8615505695343018 True -8 12510 15.381286382675171 0.27019834518432617 332.34893798828125 1.0183038711547852 436.2386779785156 0.3265587389469147 0.74075997 1.560439944267273 True -9 13900 15.387794971466064 0.2663445472717285 376.81610107421875 1.3027966022491455 432.4945068359375 0.32952138781547546 0.7549437 1.3532540798187256 True -10 15290 15.4087815284729 0.26268553733825684 253.87936401367188 1.1328543424606323 431.3162841796875 0.3310980200767517 0.76323485 1.2127041816711426 True -11 16680 15.421874523162842 0.2662026882171631 401.68853759765625 1.0655028820037842 428.0523986816406 0.33333054184913635 0.7716149 1.1247373819351196 True -12 18070 15.384120464324951 0.26265954971313477 340.1539306640625 0.9206874966621399 425.0121154785156 0.3361594080924988 0.77938783 1.0749765634536743 True -13 19460 15.375241756439209 0.2681005001068115 370.4248046875 0.8718530535697937 422.21368408203125 0.33826979994773865 0.79010296 0.9984405040740967 True -14 20850 15.395081520080566 0.2682192325592041 284.4998474121094 0.7940143346786499 421.5456848144531 0.33746567368507385 0.7963823 0.9493960738182068 True -15 22240 15.39644193649292 0.26287055015563965 371.67510986328125 0.8977174758911133 418.5760803222656 0.34171968698501587 0.80307215 0.9169830083847046 True -16 23630 15.361467361450195 0.266221284866333 320.0107421875 0.715092658996582 418.24322509765625 0.34205392003059387 0.8048593 0.9074740409851074 True -17 25020 15.374740362167358 0.26523852348327637 245.72669982910156 0.5066146850585938 418.7837219238281 0.34155702590942383 0.8065516 0.8909615874290466 True -18 26410 15.436769962310791 0.26472020149230957 297.8932800292969 0.5242992639541626 419.06201171875 0.3417993485927582 0.80687785 0.892448365688324 True -19 27800 15.383866310119629 0.2653341293334961 286.0733337402344 0.5131531357765198 420.03802490234375 0.3406696021556854 0.80646807 0.8941068649291992 False diff --git a/ENCSR785RIM/cherimoya.fold_4.performance.tsv b/ENCSR785RIM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 142407a06400d73d3c9299c0627443d2c2d3badb..0000000000000000000000000000000000000000 --- a/ENCSR785RIM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -419.06201171875 0.45194587111473083 0.34179937839508057 0.12025783210992813 0.806877851486206 0.7713159322738647 0.892448365688324 \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_0.evaluate.json b/ENCSR785ZUI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1d52686a6ac274b8d6a31ff91a33336ca0e1cd06..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495XGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_0.fit.json b/ENCSR785ZUI/cherimoya.fold_0.fit.json deleted file mode 100644 index 40647f49550027317092642c2d397ec24325eff5..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF495XGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_0.log b/ENCSR785ZUI/cherimoya.fold_0.log deleted file mode 100644 index 8f036468790e12a24348f3734dae28958d992fa5..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.776472091674805 3.553417205810547 922.3486938476562 0.5333743095397949 1290.110107421875 0.34900906682014465 0.76658 8.896829605102539 True -1 5514 30.17853355407715 0.5127518177032471 905.1339111328125 0.5103707313537598 1077.4876708984375 0.46036842465400696 0.84369034 1.6413588523864746 True -2 8271 29.97737741470337 0.5017218589782715 833.4490356445312 0.3167913556098938 1054.5189208984375 0.47228729724884033 0.85526985 0.7442547678947449 True -3 11028 29.927329778671265 0.5034158229827881 874.399169921875 0.2856050133705139 1037.3863525390625 0.481059730052948 0.86097944 0.5910696387290955 True -4 13785 29.892574071884155 2.820446729660034 786.3930053710938 0.26682010293006897 1022.4573364257812 0.4911006987094879 0.8667609 0.4932635426521301 True -5 16542 29.930036067962646 0.6171417236328125 905.5419921875 0.37840455770492554 1013.194580078125 0.49720844626426697 0.8735404 0.5207440853118896 True -6 19299 29.942590951919556 0.5075511932373047 906.21240234375 0.44841268658638 1010.1234130859375 0.4999510645866394 0.8718778 0.4303451478481293 False -7 22056 29.921881198883057 0.4926424026489258 866.5946655273438 0.17553269863128662 1006.9922485351562 0.5016928911209106 0.8781848 0.3967742919921875 True -8 24813 30.00069832801819 2.2745749950408936 894.65576171875 0.23039287328720093 1001.0752563476562 0.5060051679611206 0.8804698 0.3792334496974945 True -9 27570 30.065338611602783 0.513744592666626 876.4935302734375 0.23310434818267822 997.41162109375 0.5087896585464478 0.88296795 0.3481462597846985 True -10 30327 30.075180053710938 0.5078492164611816 850.2186279296875 0.2925536632537842 993.82763671875 0.5102182030677795 0.8872207 0.3069234788417816 True -11 33084 29.977324724197388 0.508131742477417 852.30419921875 0.11786705255508423 988.6240234375 0.5131706595420837 0.8908855 0.26507723331451416 True -12 35841 30.07614803314209 0.5102779865264893 829.0737915039062 0.2908892035484314 981.7922973632812 0.518447756767273 0.8957964 0.2510796785354614 True -13 38598 30.00658130645752 0.8313689231872559 799.3575439453125 0.5449939966201782 979.4248657226562 0.5201662182807922 0.898899 0.22766447067260742 True -14 41355 29.960947275161743 0.49880456924438477 816.89697265625 0.17814502120018005 976.4217529296875 0.5229375958442688 0.9008149 0.21597224473953247 True -15 44112 30.060584783554077 0.5097064971923828 733.5924072265625 0.21717804670333862 976.8580322265625 0.5214554071426392 0.90547824 0.20085276663303375 True -16 46869 30.02504825592041 0.5094807147979736 622.503662109375 0.19286713004112244 972.20556640625 0.52410888671875 0.90763694 0.18966083228588104 True -17 49626 30.014458179473877 0.5061421394348145 830.1806640625 0.1393888294696808 973.71826171875 0.522889256477356 0.9077436 0.1859174519777298 True -18 52383 30.004993677139282 0.8680026531219482 754.6909790039062 0.13902436196804047 972.3908081054688 0.5244954824447632 0.90794975 0.18432770669460297 True -19 55140 29.923173904418945 8.13684368133545 850.9718017578125 0.18839523196220398 974.9277954101562 0.5217576622962952 0.9093197 0.18467216193675995 True diff --git a/ENCSR785ZUI/cherimoya.fold_0.performance.tsv b/ENCSR785ZUI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 78b95fe87f86adcc53e5949d3744309cae71c663..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -974.9277954101562 0.2760564684867859 0.5217577219009399 0.26314646005630493 0.9093196988105774 0.8814762830734253 0.18467216193675995 \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_1.evaluate.json b/ENCSR785ZUI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 584c295c47315479b98912902e9aa678040bed14..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495XGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_1.fit.json b/ENCSR785ZUI/cherimoya.fold_1.fit.json deleted file mode 100644 index 61e25309f8ff3556d1bc16b3dac66ee4bb51a7cd..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF495XGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_1.log b/ENCSR785ZUI/cherimoya.fold_1.log deleted file mode 100644 index bf56153e8e907f2c4eda9b83ed4af927cf16b445..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 34.17849040031433 3.709559440612793 836.2327880859375 0.30936169624328613 1530.2659912109375 0.3476729094982147 0.755783 8.648516654968262 True -1 5456 30.367775678634644 0.7084405422210693 865.9100952148438 0.334855318069458 1268.8712158203125 0.46636152267456055 0.8442748 2.027517795562744 True -2 8184 30.290676593780518 19.324471473693848 914.9827270507812 0.37752074003219604 1228.6903076171875 0.48575037717819214 0.85633266 0.8409627676010132 True -3 10912 30.35803771018982 0.9019250869750977 779.4849853515625 0.24704322218894958 1207.960693359375 0.4969881474971771 0.8650107 0.6564565300941467 True -4 13640 30.32606339454651 0.6852245330810547 745.6151733398438 0.3211880922317505 1200.7142333984375 0.4989077150821686 0.87240654 0.48424312472343445 True -5 16368 29.776092529296875 0.6788368225097656 849.6009521484375 0.33233970403671265 1189.6585693359375 0.5067060589790344 0.87797296 0.47482454776763916 True -6 19096 29.624863862991333 0.6785216331481934 817.07763671875 0.4752655029296875 1185.8941650390625 0.5073872804641724 0.8835724 0.4428693354129791 True -7 21824 29.62978744506836 0.6821789741516113 801.052734375 0.3481629192829132 1177.10546875 0.5125560760498047 0.8840092 0.41572222113609314 True -8 24552 29.674763441085815 0.6805388927459717 1023.0302734375 0.3331421911716461 1170.85595703125 0.5151882767677307 0.8864198 0.37029218673706055 True -9 27280 29.64196252822876 0.6790900230407715 985.5443725585938 0.2398117035627365 1164.19775390625 0.5197334885597229 0.89164376 0.3494608700275421 True -10 30008 29.702773571014404 0.6872856616973877 880.8425903320312 0.2042246162891388 1161.902099609375 0.519909679889679 0.8962261 0.3270426392555237 True -11 32736 29.724497079849243 0.7057163715362549 723.8751831054688 0.25942349433898926 1151.2266845703125 0.5264332294464111 0.8975133 0.30419301986694336 True -12 35464 29.758495807647705 0.6946377754211426 968.899169921875 0.215898334980011 1145.6112060546875 0.5285587906837463 0.9038778 0.27035388350486755 True -13 38192 29.642386198043823 0.6865677833557129 938.7212524414062 0.3118867576122284 1138.5902099609375 0.532437264919281 0.9095418 0.23711317777633667 True -14 40920 29.709195852279663 18.859118700027466 701.93994140625 0.2265165001153946 1134.16845703125 0.5345504283905029 0.9103217 0.22584104537963867 True -15 43648 29.644886016845703 28.31581401824951 869.5409545898438 0.1839110106229782 1133.8265380859375 0.5338066816329956 0.91342 0.2073453962802887 True -16 46376 29.711187839508057 0.6881322860717773 843.93115234375 0.14560487866401672 1131.2108154296875 0.5331041812896729 0.9161644 0.1944989114999771 True -17 49104 29.74541997909546 0.6989948749542236 775.9707641601562 0.17786593735218048 1127.815185546875 0.5358487963676453 0.91796577 0.1869196593761444 True -18 51832 29.74739646911621 0.6861846446990967 701.4811401367188 0.09958867728710175 1130.4527587890625 0.5341824293136597 0.9169775 0.18439935147762299 False -19 54560 29.690186500549316 0.6872270107269287 821.7626342773438 0.20254173874855042 1130.6470947265625 0.534444272518158 0.9179957 0.1837599277496338 True diff --git a/ENCSR785ZUI/cherimoya.fold_1.performance.tsv b/ENCSR785ZUI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9ab34e67c6ec39b65f89f9e7b3df1c563242f03e..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1130.6470947265625 0.2580001652240753 0.5344443321228027 0.2935134768486023 0.9179956912994385 0.9098027348518372 0.1837599277496338 \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_2.evaluate.json b/ENCSR785ZUI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 42fb7b9f43ced9bdfa5208cd3ac9e2b282f678f3..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495XGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_2.fit.json b/ENCSR785ZUI/cherimoya.fold_2.fit.json deleted file mode 100644 index 250852be8e8c633a6f463cca4f325790bc7d876c..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF495XGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_2.log b/ENCSR785ZUI/cherimoya.fold_2.log deleted file mode 100644 index b6b8c5e40526a9f28bac5a4a1ef1f5c89718e79c..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2859 35.548699378967285 3.75826096534729 1098.189453125 0.5486383438110352 1334.3223876953125 0.3482881784439087 0.7437995 8.47043514251709 True -1 5718 31.810681343078613 0.5338408946990967 939.018310546875 0.4077111482620239 1113.6390380859375 0.45766422152519226 0.83386457 1.6440784931182861 True -2 8577 31.717930555343628 0.5243642330169678 865.8897094726562 0.3410649597644806 1084.2449951171875 0.47423750162124634 0.8485869 0.6043253540992737 True -3 11436 31.72327709197998 1.2042558193206787 722.5601196289062 0.3072984516620636 1076.108154296875 0.4785461127758026 0.85611665 0.4947510361671448 True -4 14295 31.71299958229065 0.5305116176605225 917.621826171875 0.31095409393310547 1065.414306640625 0.48403388261795044 0.86193573 0.43924835324287415 True -5 17154 31.78991723060608 0.5317871570587158 794.47119140625 0.2826192378997803 1056.4573974609375 0.4899875223636627 0.8694589 0.386906236410141 True -6 20013 31.727752685546875 0.5251424312591553 831.4368896484375 0.29870766401290894 1048.9393310546875 0.49720844626426697 0.86904293 0.39320603013038635 False -7 22872 31.742996215820312 0.5322177410125732 778.3704833984375 0.4135584831237793 1046.406005859375 0.4978058934211731 0.87362015 0.3646833300590515 True -8 25731 31.753220081329346 0.5248386859893799 717.4509887695312 0.39979663491249084 1041.58349609375 0.5004308223724365 0.8786682 0.3479430675506592 True -9 28590 31.754222869873047 0.5335662364959717 862.5931396484375 0.44014284014701843 1037.336669921875 0.5024982690811157 0.88029605 0.30907729268074036 True -10 31449 31.140953063964844 0.5155627727508545 856.1728515625 0.3148916959762573 1030.3721923828125 0.5068301558494568 0.8856848 0.2898021638393402 True -11 34308 31.118823766708374 0.5289347171783447 856.5184936523438 0.18190816044807434 1027.667236328125 0.5074803829193115 0.8879021 0.28452372550964355 True -12 37167 31.113699913024902 0.5264267921447754 717.0955810546875 0.3312349319458008 1022.3238525390625 0.5113664269447327 0.8913565 0.2524249255657196 True -13 40026 31.165569305419922 0.521287202835083 912.60400390625 0.2210501730442047 1021.2669067382812 0.5111848711967468 0.8953129 0.23332375288009644 True -14 42885 31.20892834663391 14.999069690704346 812.5477905273438 0.2346678078174591 1014.51708984375 0.5158863663673401 0.8981 0.22495774924755096 True -15 45744 31.488364934921265 0.519996166229248 935.9974365234375 0.2031177580356598 1014.5828247070312 0.5156664848327637 0.90264595 0.20880813896656036 True -16 48603 31.096680641174316 0.5293514728546143 873.1718139648438 0.18834489583969116 1010.0679321289062 0.5189359784126282 0.9046755 0.2022067904472351 True -17 51462 31.11589813232422 0.5280399322509766 883.7976684570312 0.17410051822662354 1010.8532104492188 0.5172668099403381 0.9043592 0.19815514981746674 False -18 54321 31.114903688430786 0.5163860321044922 901.3404541015625 0.16625149548053741 1011.0783081054688 0.517580509185791 0.90470326 0.19676573574543 True -19 57180 31.104008436203003 0.5294942855834961 721.8922119140625 0.12895801663398743 1011.6881103515625 0.5171458721160889 0.9042184 0.19665880501270294 False diff --git a/ENCSR785ZUI/cherimoya.fold_2.performance.tsv b/ENCSR785ZUI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 158dc0032fb31d6a6869781278a527429d95546b..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1011.0783081054688 0.2736954092979431 0.5175805687904358 0.2665843963623047 0.9047032594680786 0.8868410587310791 0.19676573574543 \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_3.evaluate.json b/ENCSR785ZUI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ef1f2340df7369c703c256b57599c1e7eed0ebaa..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495XGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_3.fit.json b/ENCSR785ZUI/cherimoya.fold_3.fit.json deleted file mode 100644 index a5753da7228dc8d9d66cb259b486be5f0d4443fd..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF495XGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_3.log b/ENCSR785ZUI/cherimoya.fold_3.log deleted file mode 100644 index eeff4c2888aa51d1c48a30c190680322057c6318..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2769 35.2432119846344 3.654996156692505 980.2286376953125 0.42072561383247375 1250.630859375 0.3611438274383545 0.73918176 9.825919151306152 True -1 5538 30.858938932418823 0.6125843524932861 741.4290771484375 0.2600021958351135 1063.2357177734375 0.45580634474754333 0.82971174 1.5349429845809937 True -2 8307 30.813754558563232 0.5507605075836182 897.3610229492188 0.25266584753990173 1038.3760986328125 0.4723934531211853 0.84215444 0.8507541418075562 True -3 11076 30.703089237213135 9.738421201705933 827.8577880859375 0.3509446978569031 1024.79638671875 0.48135489225387573 0.8492485 0.609174370765686 True -4 13845 30.92626953125 1.8798773288726807 931.4248046875 0.3991994857788086 1017.8033447265625 0.4863193929195404 0.8518684 0.5075307488441467 True -5 16614 30.775925874710083 2.876523733139038 959.31396484375 0.3410162329673767 1008.2286987304688 0.49424174427986145 0.8555829 0.4633232355117798 True -6 19383 30.79385781288147 0.5406486988067627 892.6583251953125 0.2961995303630829 1008.2944946289062 0.49347004294395447 0.85735106 0.4600408375263214 True -7 22152 30.718817710876465 0.5455780029296875 796.0283203125 0.22788918018341064 1005.864501953125 0.4961465001106262 0.85619277 0.43830978870391846 False -8 24921 30.729748725891113 0.5352227687835693 808.1187133789062 0.3098713755607605 1000.0516357421875 0.49893224239349365 0.859107 0.39800238609313965 True -9 27690 30.706583976745605 0.5428111553192139 902.3081665039062 0.29137730598449707 994.1220703125 0.5032574534416199 0.8624273 0.39779460430145264 True -10 30459 30.69644522666931 0.5397264957427979 880.2554931640625 0.2692481279373169 987.9138793945312 0.5060710906982422 0.8696793 0.3492697775363922 True -11 33228 30.755383253097534 0.556607723236084 897.406494140625 0.23276525735855103 982.0573120117188 0.510408341884613 0.87321526 0.3213665187358856 True -12 35997 30.809503078460693 0.547631025314331 831.2227172851562 0.20670492947101593 978.784423828125 0.5113468170166016 0.88089937 0.2924983501434326 True -13 38766 30.785715579986572 0.550926685333252 890.1476440429688 0.25040674209594727 973.4349975585938 0.5140832662582397 0.88677174 0.2599976360797882 True -14 41535 30.650287628173828 0.5476202964782715 986.2386474609375 0.27290987968444824 969.282958984375 0.5162846446037292 0.8939269 0.2413734495639801 True -15 44304 30.26896858215332 0.5418527126312256 1039.5045166015625 0.22103796899318695 964.7700805664062 0.51950603723526 0.89693725 0.22339797019958496 True -16 47073 30.139453411102295 0.5438246726989746 747.4805908203125 0.10769661515951157 963.0357666015625 0.5194222331047058 0.90207154 0.21538807451725006 True -17 49842 30.125202655792236 0.5426766872406006 789.7898559570312 0.23683802783489227 963.4015502929688 0.5186539888381958 0.9025562 0.2078033983707428 True -18 52611 30.16701078414917 0.5440325736999512 850.220458984375 0.08916744589805603 964.5432739257812 0.5169022679328918 0.9050799 0.2032480686903 True -19 55380 30.077696561813354 0.5437369346618652 907.8226318359375 0.1365307867527008 962.5459594726562 0.5193087458610535 0.9052346 0.20270425081253052 True diff --git a/ENCSR785ZUI/cherimoya.fold_3.performance.tsv b/ENCSR785ZUI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 09e3542857d420bec294aba3f12f6b39f5bfe684..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -962.5459594726562 0.2775784134864807 0.5193087458610535 0.2602038085460663 0.9052345752716064 0.8770520091056824 0.20270425081253052 \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_4.evaluate.json b/ENCSR785ZUI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7b2aa98c0b278be1fdf276328961a274a0d8acc7..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495XGY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_4.fit.json b/ENCSR785ZUI/cherimoya.fold_4.fit.json deleted file mode 100644 index c05ca44b096d47cc52756d68dd863008d10b3a08..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF495XGY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR785ZUI/cherimoya.fold_4.log b/ENCSR785ZUI/cherimoya.fold_4.log deleted file mode 100644 index b3c5f9fe470828b2be66e4717cef697b95e46636..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.50261187553406 3.5691630840301514 926.4951782226562 0.3852219879627228 1197.820068359375 0.35327744483947754 0.74593854 8.121670722961426 True -1 5596 31.733771085739136 19.130715370178223 744.849365234375 0.2616645097732544 1012.8744506835938 0.4582759439945221 0.8346614 1.6577421426773071 True -2 8394 31.19472622871399 0.5604586601257324 844.80322265625 0.30130642652511597 993.7702026367188 0.46486780047416687 0.84299976 0.5102328062057495 True -3 11192 31.10870933532715 0.551868200302124 859.03662109375 0.5976464152336121 981.9884643554688 0.47148334980010986 0.85045326 0.49355101585388184 True -4 13990 31.061805725097656 0.5474159717559814 768.468505859375 0.39198625087738037 970.4329223632812 0.4822104573249817 0.8569767 0.46653932332992554 True -5 16788 31.09774875640869 0.5587821006774902 822.34423828125 0.45722252130508423 964.6852416992188 0.48678407073020935 0.86113834 0.5108845829963684 True -6 19586 31.081287145614624 0.5783774852752686 610.3045654296875 0.267146497964859 959.0496215820312 0.49033012986183167 0.8681439 0.4094303548336029 True -7 22384 31.089448928833008 0.5530877113342285 980.1840209960938 0.4353829324245453 954.4569091796875 0.4946444630622864 0.87048674 0.39170709252357483 True -8 25182 31.080703496932983 0.5627601146697998 977.0508422851562 0.22021839022636414 947.0308837890625 0.5004343390464783 0.8758188 0.3639432489871979 True -9 27980 31.033242225646973 0.5514347553253174 899.3345947265625 0.36636996269226074 946.6126708984375 0.4993966817855835 0.8792959 0.3237982988357544 True -10 30778 31.015579223632812 0.5526220798492432 1026.13427734375 0.23930217325687408 942.8290405273438 0.5021119713783264 0.88067347 0.2981857359409332 True -11 33576 31.022703170776367 0.5382204055786133 693.895263671875 0.2268197387456894 935.4266357421875 0.508439838886261 0.8852267 0.27713632583618164 True -12 36374 31.019630193710327 19.391587257385254 862.43310546875 0.22434957325458527 933.0800170898438 0.5087732076644897 0.8899934 0.24158786237239838 True -13 39172 31.097652673721313 0.5814957618713379 790.0104370117188 0.16025486588478088 929.2890014648438 0.5120787620544434 0.8932011 0.22381046414375305 True -14 41970 31.113057374954224 0.5577504634857178 848.3936767578125 0.2196984738111496 927.6693115234375 0.513322651386261 0.89783853 0.2046910971403122 True -15 44768 31.13938045501709 1.6049845218658447 818.1529541015625 0.16373716294765472 923.1177368164062 0.5159774422645569 0.90080667 0.19101211428642273 True -16 47566 31.122209072113037 0.5671200752258301 699.0491943359375 0.17086941003799438 923.7940063476562 0.514862060546875 0.902275 0.18649201095104218 True -17 50364 31.180249214172363 0.5598111152648926 712.9865112304688 0.1377687007188797 923.3948364257812 0.5155172944068909 0.90393865 0.18241994082927704 True -18 53162 31.186174154281616 0.567821741104126 734.9270629882812 0.1358904093503952 923.5394287109375 0.515477180480957 0.90423566 0.18063944578170776 True -19 55960 31.08414125442505 0.5605983734130859 889.9631958007812 0.08390378952026367 923.2069091796875 0.5157268643379211 0.9036962 0.18029813468456268 False diff --git a/ENCSR785ZUI/cherimoya.fold_4.performance.tsv b/ENCSR785ZUI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index efed9d720c99ecce81710cc86381fb7f82b440ba..0000000000000000000000000000000000000000 --- a/ENCSR785ZUI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -923.5394287109375 0.2821269631385803 0.515477180480957 0.25327715277671814 0.9042356610298157 0.8705860376358032 0.18063944578170776 \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_0.evaluate.json b/ENCSR786FWF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 292b704f6155199e3812a11ebc7e4d8e97369ee1..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644XIN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_0.fit.json b/ENCSR786FWF/cherimoya.fold_0.fit.json deleted file mode 100644 index 6d805dc4fe0ad2efa74ce5ad8eb7274f25e15e40..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF644XIN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_0.log b/ENCSR786FWF/cherimoya.fold_0.log deleted file mode 100644 index a5d25f46b9a261cc660d367b1a4cb0a3c9a8cf42..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 34.1315393447876 4.2613372802734375 261.88580322265625 0.7155010104179382 267.86029052734375 0.1448567658662796 0.50997317 3.4677202701568604 True -1 5496 30.166667461395264 1.1082875728607178 202.04412841796875 0.8720817565917969 258.6271057128906 0.19512677192687988 0.6233538 1.2868058681488037 True -2 8244 29.59973907470703 0.5845158100128174 228.8459930419922 0.8749458193778992 255.6005096435547 0.20389869809150696 0.6500167 0.6126492023468018 True -3 10992 29.62727928161621 0.5680637359619141 184.91897583007812 0.543501615524292 254.88009643554688 0.20646411180496216 0.6596478 0.544309675693512 True -4 13740 29.62977123260498 0.8280017375946045 158.82196044921875 0.4160689413547516 254.08547973632812 0.21030566096305847 0.65860736 0.5240374207496643 False -5 16488 29.734240770339966 0.5944373607635498 180.0977783203125 0.8112033605575562 253.9002685546875 0.210595041513443 0.66177994 0.5004189014434814 True -6 19236 29.74226951599121 0.5831382274627686 176.91580200195312 0.5276086330413818 253.70082092285156 0.21141782402992249 0.6686628 0.47590264678001404 True -7 21984 29.68928551673889 0.5780911445617676 170.99453735351562 0.506157398223877 253.1390380859375 0.21448898315429688 0.67633516 0.45185738801956177 True -8 24732 29.684207677841187 0.5861873626708984 198.06056213378906 0.6363778710365295 252.42396545410156 0.21843548119068146 0.68341565 0.4315817952156067 True -9 27480 29.640122413635254 0.5810534954071045 196.3372802734375 0.6659957766532898 252.0602569580078 0.22001692652702332 0.69105583 0.41178208589553833 True -10 30228 29.70228338241577 0.5966362953186035 185.80914306640625 0.35064005851745605 251.7799530029297 0.220823734998703 0.695866 0.4073958694934845 True -11 32976 29.796666383743286 0.594977855682373 209.35275268554688 0.4954591691493988 251.71029663085938 0.2210443913936615 0.7034395 0.39751529693603516 True -12 35724 29.786996841430664 15.789180040359497 232.8597869873047 0.518821656703949 251.23263549804688 0.22309358417987823 0.7081541 0.3920781910419464 True -13 38472 29.79768943786621 1.1204783916473389 215.15594482421875 0.4006187319755554 250.9202117919922 0.22452262043952942 0.71877843 0.38697612285614014 True -14 41220 29.66117525100708 13.940368890762329 174.38824462890625 0.4098251461982727 250.6945343017578 0.22618217766284943 0.72411406 0.37695080041885376 True -15 43968 29.759040355682373 0.593862771987915 196.78958129882812 0.3049050271511078 250.6153106689453 0.22611913084983826 0.73244685 0.36743420362472534 True -16 46716 29.76901388168335 0.9637842178344727 190.17108154296875 0.47735661268234253 250.75767517089844 0.22511346638202667 0.73698276 0.3664730489253998 True -17 49464 29.72408127784729 0.6158723831176758 138.46450805664062 0.43431976437568665 250.491455078125 0.22762040793895721 0.7359413 0.37558460235595703 False -18 52212 29.715900659561157 0.5839352607727051 183.14112854003906 0.30656588077545166 250.94003295898438 0.22438684105873108 0.7363199 0.38279208540916443 False -19 54960 30.128366470336914 0.5709521770477295 204.20123291015625 0.44940879940986633 250.7550506591797 0.2257883995771408 0.7329032 0.3892294764518738 False diff --git a/ENCSR786FWF/cherimoya.fold_0.performance.tsv b/ENCSR786FWF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6dc4c7c1a072ff39d005af39f30f8e8d059ab4a0..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.75767517089844 0.5251094698905945 0.22511346638202667 0.06605073809623718 0.7369827628135681 0.6957282423973083 0.3664730489253998 \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_1.evaluate.json b/ENCSR786FWF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0fd52f2be6cfd9c151783b4806f367d3de3f0d90..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644XIN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_1.fit.json b/ENCSR786FWF/cherimoya.fold_1.fit.json deleted file mode 100644 index da3a9c330cb90410dd57a417669b74bb365176e9..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF644XIN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_1.log b/ENCSR786FWF/cherimoya.fold_1.log deleted file mode 100644 index 12fa463abf2c0eb9643810876f6982765bf00d49..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.639952182769775 3.9755120277404785 216.43515014648438 0.8636470437049866 304.3260192871094 0.15098455548286438 0.56618875 3.2053520679473877 True -1 5494 30.60280203819275 1.685570478439331 201.9432830810547 0.7149412631988525 293.362060546875 0.2032708376646042 0.67568207 1.1032600402832031 True -2 8241 30.21561574935913 0.6880271434783936 203.70297241210938 0.7885444164276123 289.0654296875 0.21765536069869995 0.69282675 0.6184301376342773 True -3 10988 30.37352418899536 0.6838922500610352 199.1812744140625 0.5535104870796204 286.8099060058594 0.22510899603366852 0.7124533 0.4899974465370178 True -4 13735 30.19459104537964 0.6818726062774658 167.0571746826172 0.7413017153739929 286.5304870605469 0.22444067895412445 0.72049767 0.48838478326797485 True -5 16482 30.251487016677856 0.676414966583252 199.08506774902344 0.4865748882293701 285.57257080078125 0.2286832630634308 0.72521025 0.4627684950828552 True -6 19229 30.22341775894165 0.6828935146331787 199.16580200195312 0.48319995403289795 284.7471923828125 0.23234091699123383 0.72909886 0.46429288387298584 True -7 21976 30.35484528541565 0.6868774890899658 265.06536865234375 0.8959658741950989 284.5264892578125 0.23311278223991394 0.72846514 0.4562814235687256 False -8 24723 30.215638160705566 1.7924320697784424 212.03363037109375 0.4726814031600952 283.70513916015625 0.23618826270103455 0.73461264 0.44043800234794617 True -9 27470 30.11712908744812 0.6676614284515381 217.07577514648438 0.5575215816497803 283.61029052734375 0.2360994666814804 0.7382273 0.4367455840110779 True -10 30217 29.624695301055908 0.763049840927124 247.7696075439453 0.5744526386260986 283.28936767578125 0.23740048706531525 0.74733996 0.42017674446105957 True -11 32964 29.611108779907227 0.6798596382141113 214.33177185058594 0.6362897157669067 282.9471130371094 0.23889422416687012 0.75273585 0.41159412264823914 True -12 35711 29.590006113052368 0.9931573867797852 226.2952117919922 0.34471121430397034 282.8466491699219 0.23962604999542236 0.75715286 0.3897968828678131 True -13 38458 29.663907527923584 0.6681056022644043 207.4031524658203 0.39636993408203125 282.5096435546875 0.2403782606124878 0.7594932 0.3949775993824005 True -14 41205 29.609597206115723 0.6768245697021484 201.1629638671875 0.5194460153579712 282.308837890625 0.24112553894519806 0.76718193 0.38246434926986694 True -15 43952 29.616281270980835 0.6522092819213867 204.02833557128906 0.3639748990535736 282.069091796875 0.24206611514091492 0.77223206 0.38170915842056274 True -16 46699 30.002636671066284 2.3227553367614746 161.45437622070312 0.3428730368614197 281.8210754394531 0.2430192530155182 0.7740836 0.37968987226486206 True -17 49446 29.64273691177368 0.6672546863555908 214.57293701171875 0.32575714588165283 282.1495361328125 0.2417350858449936 0.7756426 0.3839030861854553 True -18 52193 29.641119241714478 0.6810884475708008 201.05923461914062 0.3408747911453247 282.167236328125 0.24121354520320892 0.77533764 0.3947635889053345 False -19 54940 29.64785885810852 0.6707990169525146 184.53408813476562 0.29896408319473267 282.066162109375 0.24223269522190094 0.7737803 0.402731716632843 False diff --git a/ENCSR786FWF/cherimoya.fold_1.performance.tsv b/ENCSR786FWF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ebe08f792ff2e9d65922d306cf79698971ccaf9b..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -282.1495361328125 0.5102269053459167 0.2417350858449936 0.07348387688398361 0.7756425738334656 0.7459193468093872 0.3839030861854553 \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_2.evaluate.json b/ENCSR786FWF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b4a22ebad14d979ecafd9095ac9d05820b8c1a6b..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644XIN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_2.fit.json b/ENCSR786FWF/cherimoya.fold_2.fit.json deleted file mode 100644 index 8c55974dc8054437437777685b571342295ca072..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF644XIN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_2.log b/ENCSR786FWF/cherimoya.fold_2.log deleted file mode 100644 index fea301e8b6006d9cd55c6d47f7442408f3be84e6..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2911 36.56421875953674 3.991586685180664 178.71463012695312 0.6047152876853943 270.8125915527344 0.1467660814523697 0.5358751 2.7701897621154785 True -1 5822 32.01825451850891 0.5652785301208496 221.7313232421875 0.6266317963600159 260.69573974609375 0.1990050971508026 0.6468497 1.0248943567276 True -2 8733 31.822458505630493 0.513845682144165 195.65866088867188 0.5080159902572632 257.8032531738281 0.20783619582653046 0.667711 0.6275639533996582 True -3 11644 31.407241582870483 0.5232081413269043 198.7491455078125 0.7332720160484314 257.0855712890625 0.20968934893608093 0.6772508 0.595370352268219 True -4 14555 31.3807475566864 0.5237226486206055 202.22494506835938 0.6296902894973755 256.44561767578125 0.2124805748462677 0.6817778 0.6648080945014954 True -5 17466 31.363508224487305 0.5228309631347656 187.33050537109375 0.8462314605712891 255.54493713378906 0.21698424220085144 0.68805563 0.6664727926254272 True -6 20377 31.368480443954468 0.5315546989440918 197.62109375 0.5072158575057983 255.3065643310547 0.21836644411087036 0.6912172 0.6402459740638733 True -7 23288 31.426978826522827 0.5473902225494385 223.47390747070312 0.6921757459640503 254.78744506835938 0.2212323397397995 0.695365 0.601004421710968 True -8 26199 31.377755880355835 0.5238299369812012 169.16273498535156 0.7912623286247253 254.63504028320312 0.220656156539917 0.70122397 0.5718421339988708 True -9 29110 31.39961075782776 0.5193490982055664 227.7086639404297 0.5065878629684448 254.1271514892578 0.22287501394748688 0.70503074 0.5159916281700134 True -10 32021 31.389253854751587 0.5180456638336182 171.17247009277344 0.480144739151001 253.73809814453125 0.22447729110717773 0.7127575 0.48410266637802124 True -11 34932 31.400060653686523 0.5165665149688721 165.27178955078125 0.4016324281692505 253.36856079101562 0.2263970524072647 0.7172263 0.4686497151851654 True -12 37843 31.407175540924072 0.7351551055908203 215.50942993164062 0.3111450672149658 252.9818572998047 0.2276114672422409 0.7264651 0.44025880098342896 True -13 40754 31.424397706985474 0.5243196487426758 183.26475524902344 0.421975314617157 252.8584442138672 0.22798307240009308 0.73276615 0.41464799642562866 True -14 43665 31.46075201034546 0.5235435962677002 199.0979766845703 0.511206328868866 252.45407104492188 0.22991523146629333 0.7388723 0.3982239067554474 True -15 46576 31.376896142959595 0.5455009937286377 193.2248077392578 0.34535878896713257 252.440673828125 0.22943031787872314 0.74493396 0.38681304454803467 True -16 49487 31.45725703239441 0.5243856906890869 167.42776489257812 0.32673996686935425 252.27320861816406 0.2303086668252945 0.7487742 0.3815459907054901 True -17 52398 31.46300721168518 0.5227601528167725 184.3487548828125 0.37091219425201416 252.62606811523438 0.2287209928035736 0.75159097 0.38101086020469666 True -18 55309 31.367884874343872 1.1759769916534424 203.60137939453125 0.36970779299736023 252.61058044433594 0.2289842814207077 0.7506952 0.38901790976524353 False -19 58220 31.468677759170532 0.5165834426879883 189.56288146972656 0.29756253957748413 252.80516052246094 0.2275315374135971 0.74862045 0.39231857657432556 False diff --git a/ENCSR786FWF/cherimoya.fold_2.performance.tsv b/ENCSR786FWF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 14d007f85ae4c2c438fbef7088cce7fba22a33cd..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -252.62606811523438 0.5237077474594116 0.22872097790241241 0.06803561002016068 0.7515909671783447 0.7096678614616394 0.38101086020469666 \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_3.evaluate.json b/ENCSR786FWF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 01dee19c0805f25bafb5c2a5ea31db31ddfaccef..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644XIN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_3.fit.json b/ENCSR786FWF/cherimoya.fold_3.fit.json deleted file mode 100644 index fb0f41d3078c7022ebbd00e625d196dff0c679e9..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF644XIN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_3.log b/ENCSR786FWF/cherimoya.fold_3.log deleted file mode 100644 index 27ff27b9f9cc4dfee04df36dd81bbdcd43693028..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2784 36.10769176483154 4.29900598526001 208.0970916748047 0.6307200193405151 283.6048889160156 0.1497560441493988 0.53833497 3.653982162475586 True -1 5568 30.39970326423645 0.6325039863586426 170.8408203125 0.776820182800293 273.9327392578125 0.19786402583122253 0.62489486 1.1574690341949463 True -2 8352 30.631047010421753 0.5962069034576416 203.4544677734375 0.6479050517082214 271.3605041503906 0.20798338949680328 0.6562627 0.5818011164665222 True -3 11136 30.531821727752686 0.5919013023376465 191.2215576171875 0.47223973274230957 270.4548645019531 0.21058470010757446 0.6659744 0.5518723726272583 True -4 13920 30.001112461090088 0.5896244049072266 201.80828857421875 0.6346415281295776 269.6571044921875 0.21374152600765228 0.6727336 0.5660295486450195 True -5 16704 30.025500059127808 1.28765869140625 187.74375915527344 0.7810555696487427 269.1327819824219 0.21563959121704102 0.6815713 0.5706615447998047 True -6 19488 29.99006676673889 0.6252861022949219 197.258056640625 0.49941301345825195 268.59490966796875 0.21836186945438385 0.68406945 0.5618728399276733 True -7 22272 29.978143215179443 0.6024777889251709 172.27011108398438 0.8911440968513489 268.4877014160156 0.21825623512268066 0.6908266 0.5494001507759094 True -8 25056 29.960427284240723 0.599301815032959 189.30642700195312 0.5903688073158264 268.1155090332031 0.21996232867240906 0.6939396 0.5873003602027893 True -9 27840 30.035980701446533 0.6000487804412842 176.90818786621094 0.5085079669952393 267.8583068847656 0.22119691967964172 0.69912773 0.5728362798690796 True -10 30624 30.03819179534912 0.5857052803039551 216.06512451171875 0.4731546640396118 267.1965637207031 0.22415810823440552 0.704833 0.5377010107040405 True -11 33408 30.022467374801636 0.5972905158996582 189.5586700439453 0.4808041751384735 266.934814453125 0.22536209225654602 0.71384776 0.5104312896728516 True -12 36192 30.086858987808228 0.6064741611480713 191.7696990966797 0.33207184076309204 266.5763244628906 0.22701631486415863 0.7197732 0.4659365117549896 True -13 38976 30.088465929031372 0.6155669689178467 196.632080078125 0.5285614728927612 266.3313293457031 0.22840937972068787 0.725567 0.4481915235519409 True -14 41760 30.172539472579956 0.5960636138916016 213.8388214111328 0.31757891178131104 266.044189453125 0.22946977615356445 0.73189455 0.4228343367576599 True -15 44544 30.14345645904541 0.5948965549468994 189.34486389160156 0.4126273989677429 266.2522277832031 0.2279915064573288 0.74101394 0.4061357080936432 True -16 47328 30.14937472343445 0.6172523498535156 218.50555419921875 0.3960864245891571 266.1038818359375 0.22912229597568512 0.7412012 0.4045628607273102 True -17 50112 30.168237447738647 0.5917465686798096 218.90199279785156 0.36848899722099304 266.003662109375 0.22904415428638458 0.7450088 0.40465477108955383 True -18 52896 31.57059597969055 20.691081762313843 203.4235382080078 0.3370164930820465 266.2381591796875 0.22794604301452637 0.73993796 0.4150662422180176 False -19 55680 30.166829109191895 0.5946874618530273 216.34121704101562 0.2112971842288971 266.0680236816406 0.22960685193538666 0.74076474 0.4232255816459656 False diff --git a/ENCSR786FWF/cherimoya.fold_3.performance.tsv b/ENCSR786FWF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bc44b6e7ea327ab993797d644c02fa984fa454d5..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -266.003662109375 0.5194312930107117 0.22904415428638458 0.06703833490610123 0.7450088262557983 0.7039909958839417 0.40465477108955383 \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_4.evaluate.json b/ENCSR786FWF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index df3bc1f3dddebb5a79acc8ed0408fa9ff836d24f..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF644XIN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_4.fit.json b/ENCSR786FWF/cherimoya.fold_4.fit.json deleted file mode 100644 index 419bf3f9af47462e302a114843a27de12a47d036..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF644XIN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR786FWF/cherimoya.fold_4.log b/ENCSR786FWF/cherimoya.fold_4.log deleted file mode 100644 index 43e3e1b5574f942cfa04fae76ad0dd603f403930..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 36.344850063323975 3.2232584953308105 212.1211395263672 0.7192659378051758 273.9408264160156 0.14810961484909058 0.5212337 3.237732410430908 True -1 5746 31.37828278541565 0.5532968044281006 188.83926391601562 0.7990205883979797 264.6486511230469 0.19668304920196533 0.6200424 1.1677278280258179 True -2 8619 31.05233359336853 0.5272595882415771 256.84735107421875 0.7095497846603394 262.30047607421875 0.20555254817008972 0.63480264 0.5945361256599426 True -3 11492 31.11681032180786 2.3754265308380127 227.05270385742188 0.5235766172409058 260.9613342285156 0.2103528082370758 0.6584038 0.5691965222358704 True -4 14365 31.12202477455139 0.5577359199523926 196.82217407226562 0.6281947493553162 260.68951416015625 0.21080458164215088 0.6637594 0.5933873057365417 True -5 17238 31.125682830810547 0.5425310134887695 232.4730224609375 0.7163866758346558 260.167724609375 0.2134910672903061 0.66650563 0.6475173830986023 True -6 20111 31.16611933708191 0.5551595687866211 234.606201171875 0.5493512153625488 259.67633056640625 0.2154923975467682 0.6723245 0.5851216316223145 True -7 22984 31.133962392807007 0.5522387027740479 198.06805419921875 0.6613023281097412 259.6772766113281 0.21518513560295105 0.67759675 0.559037446975708 True -8 25857 31.107996463775635 0.5660803318023682 206.5979766845703 0.6831424236297607 258.8427429199219 0.21948373317718506 0.68507415 0.5317720174789429 True -9 28730 31.205314874649048 0.5400335788726807 219.03082275390625 0.42937421798706055 258.5716247558594 0.22096864879131317 0.6881009 0.5282272100448608 True -10 31603 31.08908176422119 0.5403299331665039 230.290283203125 0.6070070266723633 258.523681640625 0.22101335227489471 0.6941059 0.5039599537849426 True -11 34476 31.22185969352722 0.5409533977508545 181.00527954101562 0.38370510935783386 257.7392578125 0.22505833208560944 0.70227796 0.48875269293785095 True -12 37349 31.099349975585938 0.5564122200012207 194.49835205078125 0.5485775470733643 257.5263671875 0.22583182156085968 0.7078697 0.4639163911342621 True -13 40222 31.047637701034546 0.535935640335083 161.66387939453125 0.3672115206718445 257.3821716308594 0.22554324567317963 0.7154758 0.42569297552108765 True -14 43095 31.089170694351196 0.544292688369751 205.463134765625 0.4700433909893036 257.2746276855469 0.2265387773513794 0.72304 0.4052664637565613 True -15 45968 31.12083125114441 0.5584979057312012 207.37893676757812 0.46750158071517944 257.1865234375 0.2265157550573349 0.73044425 0.39160868525505066 True -16 48841 31.096890211105347 0.5421774387359619 195.77276611328125 0.3784904479980469 256.8309326171875 0.22805136442184448 0.7330903 0.38972771167755127 True -17 51714 31.08560538291931 0.5267269611358643 159.16317749023438 0.4040711522102356 257.0129699707031 0.22761978209018707 0.73503846 0.38902992010116577 True -18 54587 31.155292987823486 0.5385849475860596 217.411376953125 0.2520865797996521 257.0508728027344 0.2270374596118927 0.7336082 0.3970473110675812 False -19 57460 31.03221821784973 0.5481536388397217 245.15411376953125 0.21377524733543396 257.12152099609375 0.22689850628376007 0.73372203 0.4034309685230255 False diff --git a/ENCSR786FWF/cherimoya.fold_4.performance.tsv b/ENCSR786FWF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6553a76dcd8f40dd7574eaad56ea7cd6f490690d..0000000000000000000000000000000000000000 --- a/ENCSR786FWF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -257.0129699707031 0.522157609462738 0.22761976718902588 0.06580040603876114 0.7350384593009949 0.6959848403930664 0.38902992010116577 \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_0.evaluate.json b/ENCSR788SKJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f1a9ca1c62e470d0802ec38f03af5b7b51296352..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF706XEC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_0.fit.json b/ENCSR788SKJ/cherimoya.fold_0.fit.json deleted file mode 100644 index f3e8f17df5766f943d4a4bb620f1a380e54f8d2a..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF706XEC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_0.log b/ENCSR788SKJ/cherimoya.fold_0.log deleted file mode 100644 index 812664be6c2d6e61a07516d5a939194d4fad3272..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1579 21.584004163742065 3.499392509460449 279.02227783203125 1.0255669355392456 572.28515625 0.15086375176906586 0.50911593 13.028569221496582 True -1 3158 17.58698081970215 0.33841419219970703 321.5693359375 1.1070153713226318 487.9692687988281 0.21367010474205017 0.6564272 8.521356582641602 True -2 4737 17.524133682250977 0.3132004737854004 220.42263793945312 1.051464557647705 436.3840637207031 0.2539055347442627 0.7300876 6.115843772888184 True -3 6316 17.564714908599854 0.31633830070495605 279.33050537109375 1.10423743724823 413.5689697265625 0.2686852216720581 0.7484947 3.2405083179473877 True -4 7895 17.561052799224854 0.3126375675201416 251.47836303710938 0.7310596704483032 405.32275390625 0.2753385007381439 0.761758 2.1635119915008545 True -5 9474 17.55782699584961 0.311798095703125 427.99639892578125 1.0019850730895996 398.84912109375 0.27976587414741516 0.76907814 1.6874072551727295 True -6 11053 17.539835214614868 0.30844759941101074 319.44012451171875 1.000273585319519 395.1391296386719 0.28332334756851196 0.7762339 1.526440978050232 True -7 12632 17.52784776687622 17.116609573364258 398.4942626953125 1.4703052043914795 392.78167724609375 0.28436964750289917 0.78288126 1.3205746412277222 True -8 14211 18.83728575706482 0.31763410568237305 325.9036865234375 0.7525937557220459 387.3219299316406 0.2899664044380188 0.7893161 1.174352765083313 True -9 15790 17.525643825531006 0.3161277770996094 413.0518798828125 0.8403021097183228 383.532958984375 0.2931571304798126 0.7981491 1.0671271085739136 True -10 17369 17.59858775138855 0.3147704601287842 355.1142578125 0.731191873550415 382.2254638671875 0.29380083084106445 0.8081956 0.9363465905189514 True -11 18948 17.54961323738098 0.3160827159881592 380.9525146484375 1.0334042310714722 378.2672119140625 0.296994149684906 0.8148714 0.846405565738678 True -12 20527 17.548814058303833 0.31043028831481934 294.728271484375 0.8596038818359375 374.395263671875 0.30045658349990845 0.8213067 0.7734171748161316 True -13 22106 17.620604515075684 0.31544065475463867 315.1864929199219 0.45998895168304443 373.3915710449219 0.30040889978408813 0.827849 0.7394892573356628 True -14 23685 17.54341197013855 0.32784247398376465 352.39031982421875 0.6033207178115845 370.52191162109375 0.3037738502025604 0.834699 0.6965594291687012 True -15 25264 17.57416605949402 0.320781946182251 226.14610290527344 0.6380194425582886 369.4336853027344 0.3036661148071289 0.83864546 0.6738356351852417 True -16 26843 17.566171646118164 0.592714786529541 332.6644287109375 0.44604355096817017 368.9167785644531 0.30440783500671387 0.84159786 0.6590591669082642 True -17 28422 17.55671739578247 0.31709718704223633 203.07415771484375 0.6246891021728516 369.3729553222656 0.30339881777763367 0.8419073 0.6545162200927734 True -18 30001 17.55614972114563 1.8910551071166992 334.48822021484375 0.5221940875053406 369.6996154785156 0.30304545164108276 0.84143597 0.6549239754676819 False -19 31580 17.618185997009277 0.31932759284973145 310.47076416015625 0.4341278374195099 369.7270202636719 0.30357852578163147 0.84085697 0.6581947803497314 False diff --git a/ENCSR788SKJ/cherimoya.fold_0.performance.tsv b/ENCSR788SKJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e74e9744d32269c6966f5a6b0d169ff5a7ba3b4b..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -369.3729553222656 0.4786983132362366 0.30339881777763367 0.10465783625841141 0.8419073224067688 0.7913230061531067 0.6545162200927734 \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_1.evaluate.json b/ENCSR788SKJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 91d07247c161093bb650639348e9771637d20903..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF706XEC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_1.fit.json b/ENCSR788SKJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 07fefa24fa6629e1bcf93eec493eb44908041108..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF706XEC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_1.log b/ENCSR788SKJ/cherimoya.fold_1.log deleted file mode 100644 index 18744951c493b9a04fce5398e587a4b1c6fd63a1..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1516 20.40389060974121 3.9557206630706787 284.59429931640625 1.077358603477478 718.5259399414062 0.16239146888256073 0.46234512 15.450685501098633 True -1 3032 16.693800926208496 0.4587540626525879 242.64251708984375 1.387831211090088 613.5487670898438 0.2334914207458496 0.6379123 11.159708023071289 True -2 4548 16.458975315093994 0.4392845630645752 267.8460693359375 1.3134276866912842 549.549560546875 0.27503252029418945 0.7122825 7.966084003448486 True -3 6064 16.370436191558838 0.43994760513305664 317.6787109375 0.9303230047225952 521.1554565429688 0.2891140282154083 0.73781216 4.867310523986816 True -4 7580 16.548014640808105 2.6640448570251465 439.69873046875 0.9386273622512817 502.335693359375 0.2979561686515808 0.7600868 2.884279489517212 True -5 9096 16.3820321559906 0.45508623123168945 368.19696044921875 1.0740292072296143 489.9012145996094 0.3046667277812958 0.7775487 2.24424409866333 True -6 10612 16.35054302215576 0.44504523277282715 486.22015380859375 0.8830349445343018 480.22406005859375 0.3113812804222107 0.7901022 1.8447281122207642 True -7 12128 16.341228246688843 0.4458029270172119 331.1293029785156 0.6748495101928711 476.5788879394531 0.31335142254829407 0.80099463 1.544528603553772 True -8 13644 16.326597452163696 0.44424915313720703 276.1001281738281 0.8666908740997314 471.0700988769531 0.317533016204834 0.808084 1.3814079761505127 True -9 15160 16.384319305419922 0.6060323715209961 274.03668212890625 1.1288648843765259 465.92645263671875 0.32357603311538696 0.8125318 1.3754847049713135 True -10 16676 16.403290510177612 0.6976034641265869 338.9622802734375 1.0403122901916504 460.8328857421875 0.32745781540870667 0.82398707 1.1607788801193237 True -11 18192 16.36589288711548 0.448667049407959 311.83721923828125 0.7370165586471558 456.0196838378906 0.3320070803165436 0.8300342 1.0693814754486084 True -12 19708 16.35964059829712 0.4489443302154541 344.31085205078125 0.8297896385192871 454.04345703125 0.33281001448631287 0.8356279 0.9601895809173584 True -13 21224 16.36782741546631 0.4522736072540283 242.35260009765625 0.5319973826408386 451.72052001953125 0.3339177966117859 0.84165996 0.8787023425102234 True -14 22740 16.369558572769165 0.45086097717285156 245.7724609375 0.730487585067749 450.03118896484375 0.3355572521686554 0.846336 0.8189562559127808 True -15 24256 16.355044841766357 1.5640454292297363 411.7626037597656 0.3822322189807892 448.06060791015625 0.33723968267440796 0.8516088 0.7850595116615295 True -16 25772 16.39085817337036 0.4455554485321045 205.6502685546875 0.5825297832489014 448.28424072265625 0.3362686038017273 0.8539621 0.7608000636100769 True -17 27288 16.352545499801636 0.45597004890441895 215.98289489746094 0.7162326574325562 448.70550537109375 0.33546704053878784 0.8536677 0.7385111451148987 False -18 28804 16.342294454574585 0.4521758556365967 381.6084289550781 0.4238688051700592 449.663818359375 0.33520644903182983 0.85456175 0.7341353297233582 True -19 30320 16.336693286895752 0.4471015930175781 309.0233459472656 0.4416347146034241 451.7231750488281 0.33290088176727295 0.8535661 0.7289354801177979 False diff --git a/ENCSR788SKJ/cherimoya.fold_1.performance.tsv b/ENCSR788SKJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 057779798bc59d187b466baada0459d13d2a96f9..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -449.663818359375 0.4527236819267273 0.33520644903182983 0.12319113314151764 0.8545617461204529 0.8199635148048401 0.7341353297233582 \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_2.evaluate.json b/ENCSR788SKJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0ff43c1375a4f48be66413befcb851193fb5d0fd..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF706XEC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_2.fit.json b/ENCSR788SKJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 8b06b19d15f4c4f3e9306bf8a6491e9dba8ac4ca..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF706XEC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_2.log b/ENCSR788SKJ/cherimoya.fold_2.log deleted file mode 100644 index d0674a901f6c4d9da929f01ed4db968a0fc859ef..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1629 21.710980653762817 3.2930166721343994 383.19744873046875 1.2531147003173828 574.016357421875 0.14995507895946503 0.46476474 12.564322471618652 True -1 3258 17.905182123184204 0.35853123664855957 301.4747619628906 1.6238224506378174 488.3432922363281 0.2155466228723526 0.6436445 8.821731567382812 True -2 4887 18.13338041305542 17.65152931213379 384.1195373535156 1.3619346618652344 436.1900939941406 0.2515549063682556 0.724935 4.9518208503723145 True -3 6516 17.95409655570984 0.3602423667907715 272.36785888671875 0.9983794093132019 413.64642333984375 0.26269495487213135 0.75024843 2.8769423961639404 True -4 8145 17.927536010742188 0.3540623188018799 431.8394775390625 1.0854768753051758 405.6535339355469 0.26793622970581055 0.75920904 2.0302369594573975 True -5 9774 17.94136619567871 0.3559093475341797 408.18316650390625 1.0371670722961426 396.8339538574219 0.2729879319667816 0.77528816 1.6799148321151733 True -6 11403 17.9242103099823 0.35204482078552246 247.4129638671875 1.0870846509933472 392.31341552734375 0.2745354175567627 0.7879544 1.3937748670578003 True -7 13032 17.954158782958984 1.2356398105621338 278.5003356933594 0.8010154962539673 387.8326110839844 0.27783122658729553 0.7956145 1.2679108381271362 True -8 14661 17.95679998397827 0.3606901168823242 502.21099853515625 1.106153964996338 382.6934509277344 0.2824074625968933 0.8039118 1.0959339141845703 True -9 16290 17.941335201263428 0.34941816329956055 426.98748779296875 0.652321457862854 378.8869323730469 0.28511932492256165 0.81033 0.9763849973678589 True -10 17919 17.967137813568115 0.3567769527435303 249.60809326171875 0.6567545533180237 376.8776550292969 0.286022424697876 0.81630766 0.87122642993927 True -11 19548 17.92732048034668 0.358814001083374 334.61639404296875 0.7751347422599792 373.5945739746094 0.28918617963790894 0.82241 0.8220514059066772 True -12 21177 17.889076232910156 0.35633111000061035 296.7034606933594 0.5522774457931519 371.91802978515625 0.29068419337272644 0.8280054 0.7643789052963257 True -13 22806 17.929869651794434 0.35381269454956055 309.1954345703125 0.4587206244468689 369.2445373535156 0.29267385601997375 0.833718 0.7082449793815613 True -14 24435 17.89452815055847 0.35504841804504395 365.3756408691406 0.8380663394927979 366.18194580078125 0.29481053352355957 0.8419947 0.6628538370132446 True -15 26064 17.528401374816895 0.3522772789001465 285.08599853515625 0.6539797782897949 365.83038330078125 0.2949332296848297 0.8445147 0.6412220001220703 True -16 27693 17.546518087387085 0.3487815856933594 198.3585205078125 0.4037788212299347 364.4088134765625 0.29719996452331543 0.8451558 0.6252920627593994 True -17 29322 17.55219292640686 0.3517873287200928 204.51968383789062 0.6470385789871216 366.00164794921875 0.294612318277359 0.84853506 0.6205904483795166 True -18 30951 17.55933117866516 0.3459622859954834 241.1483612060547 0.4624764323234558 366.12841796875 0.2935519516468048 0.8448452 0.6212913990020752 False -19 32580 17.537793159484863 0.35217952728271484 269.5193786621094 0.6789347529411316 366.9323425292969 0.29286453127861023 0.84651214 0.6235894560813904 False diff --git a/ENCSR788SKJ/cherimoya.fold_2.performance.tsv b/ENCSR788SKJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index db5d73fb6cd3dbfa8c28797f5f680660f182372b..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -366.00164794921875 0.4835047125816345 0.2946123480796814 0.10254880040884018 0.8485350608825684 0.7958145141601562 0.6205904483795166 \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_3.evaluate.json b/ENCSR788SKJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ea89335ed85d0952aea385b43734dd6879f4095c..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF706XEC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_3.fit.json b/ENCSR788SKJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 67d15ae0915cf61152ab3bd81524fe84e001d0d2..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF706XEC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_3.log b/ENCSR788SKJ/cherimoya.fold_3.log deleted file mode 100644 index 33abcdf3d0d337a2538aaf0cf154369cff0d3151..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1566 20.923519134521484 3.26403546333313 555.2001953125 1.9471213817596436 625.8745727539062 0.1662852168083191 0.4392907 13.772760391235352 True -1 3132 17.27327561378479 0.2979140281677246 306.138671875 1.3093671798706055 531.0143432617188 0.23787061870098114 0.60166985 10.411800384521484 True -2 4698 17.25058650970459 0.29399561882019043 366.67608642578125 1.06132173538208 472.1011657714844 0.27636653184890747 0.7009147 6.372778415679932 True -3 6264 17.267991304397583 0.3028836250305176 352.3926696777344 1.162672519683838 459.079833984375 0.28793397545814514 0.6878144 4.484740734100342 False -4 7830 17.20385503768921 0.29233407974243164 274.1591491699219 0.7659111022949219 448.5608825683594 0.29465746879577637 0.7001029 3.3478469848632812 False -5 9396 17.223193168640137 0.3169417381286621 404.4481506347656 1.4087963104248047 443.5822448730469 0.29819226264953613 0.72508705 2.5318942070007324 True -6 10962 17.234743356704712 0.28832173347473145 254.5779571533203 0.8879581689834595 436.441650390625 0.3051213026046753 0.74083936 2.1379306316375732 True -7 12528 17.194135427474976 0.2845487594604492 326.6170349121094 0.8565143942832947 432.054931640625 0.30885782837867737 0.7583841 1.782247543334961 True -8 14094 17.2086980342865 0.2877490520477295 322.160888671875 0.7327233552932739 426.0796203613281 0.3132196068763733 0.7658303 1.5022941827774048 True -9 15660 17.216289520263672 0.2870514392852783 381.5655212402344 1.1999621391296387 419.8304748535156 0.3191432058811188 0.7768632 1.3079735040664673 True -10 17226 17.227230310440063 0.28807926177978516 395.9058532714844 0.9177470207214355 419.1423034667969 0.32052409648895264 0.7830021 1.2009961605072021 True -11 18792 17.251033067703247 0.2856283187866211 314.02978515625 0.8816565275192261 416.2833557128906 0.3233514428138733 0.7906046 1.0737425088882446 True -12 20358 17.25709319114685 7.5889668464660645 335.25189208984375 0.660804271697998 414.0181884765625 0.32419633865356445 0.7978351 0.9711906909942627 True -13 21924 17.436370611190796 0.35816383361816406 333.2020263671875 0.900360107421875 409.00830078125 0.32951173186302185 0.8103838 0.8955240845680237 True -14 23490 17.238767862319946 0.29253506660461426 374.0283203125 1.0236603021621704 406.26531982421875 0.3302716612815857 0.81819564 0.8525277376174927 True -15 25056 17.277150869369507 0.2927401065826416 373.1193542480469 0.8187499046325684 404.7088623046875 0.3302548825740814 0.8256685 0.8031432032585144 True -16 26622 17.226102113723755 0.2900390625 238.20733642578125 0.6559363603591919 404.7825012207031 0.3292979598045349 0.8316409 0.7680178284645081 True -17 28188 17.28302502632141 0.2925229072570801 269.286865234375 0.940693736076355 404.2405090332031 0.3307526707649231 0.83404005 0.7505050301551819 True -18 29754 17.246761322021484 0.29068422317504883 227.34376525878906 0.31861376762390137 404.17962646484375 0.3312767446041107 0.83539903 0.7538047432899475 True -19 31320 17.26596713066101 0.2918095588684082 304.78271484375 0.6223116517066956 405.255615234375 0.3294028341770172 0.8358199 0.7523145079612732 True diff --git a/ENCSR788SKJ/cherimoya.fold_3.performance.tsv b/ENCSR788SKJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 268b15ce911a5d2bf9da243d775c1ca33ff22b76..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -405.255615234375 0.46001556515693665 0.3294028341770172 0.11691116541624069 0.8358199000358582 0.7976584434509277 0.7523145079612732 \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_4.evaluate.json b/ENCSR788SKJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1fdf98ad243d44112b882f68695082be86bebcd2..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF706XEC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_4.fit.json b/ENCSR788SKJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 84f449464eb0d05dc75d6b0465d01a8cd1534f11..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF706XEC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SKJ/cherimoya.fold_4.log b/ENCSR788SKJ/cherimoya.fold_4.log deleted file mode 100644 index 0ee9b5c715e45dd3c1561a117c8e6ae823893391..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1541 20.676459312438965 3.222522735595703 391.5865173339844 1.343386173248291 527.6627807617188 0.14927047491073608 0.4620626 12.555719375610352 True -1 3082 16.94908618927002 1.509902000427246 329.67193603515625 1.181559443473816 460.2232971191406 0.2072886973619461 0.58873796 8.239209175109863 True -2 4623 16.957075834274292 0.3026881217956543 428.3193359375 1.2621750831604004 411.91156005859375 0.24569566547870636 0.697987 4.977927207946777 True -3 6164 16.930288076400757 9.4880051612854 268.3575439453125 0.553343653678894 387.65533447265625 0.25918450951576233 0.7268969 2.6248457431793213 True -4 7705 17.57317280769348 5.345913887023926 349.8062744140625 1.5521271228790283 374.47576904296875 0.2667887508869171 0.75055504 1.7328602075576782 True -5 9246 16.97290277481079 0.3096609115600586 396.20208740234375 1.1394671201705933 368.8083190917969 0.27038973569869995 0.75817454 1.4923099279403687 True -6 10787 16.964484214782715 0.30415964126586914 332.71343994140625 0.8046923875808716 364.15631103515625 0.27364563941955566 0.7693207 1.317163348197937 True -7 12328 16.954198360443115 0.31061363220214844 296.7463684082031 0.8800709247589111 361.6754455566406 0.27550026774406433 0.77802587 1.1389790773391724 True -8 13869 16.965697765350342 0.30835437774658203 387.05694580078125 0.8432337045669556 358.2461853027344 0.27846091985702515 0.7833584 1.0380014181137085 True -9 15410 16.979885816574097 0.30950093269348145 339.347412109375 1.203331708908081 355.31341552734375 0.28265661001205444 0.7915709 0.9687886834144592 True -10 16951 16.91683530807495 2.478616952896118 228.0212860107422 0.7146242260932922 352.9971618652344 0.28585028648376465 0.7962017 0.8852330446243286 True -11 18492 17.022310495376587 0.3116011619567871 221.83811950683594 1.1753268241882324 350.8634338378906 0.2874392867088318 0.80427384 0.8096550703048706 True -12 20033 16.89871335029602 0.3045074939727783 349.85675048828125 0.8828513622283936 349.8540954589844 0.28761085867881775 0.8089727 0.7660999894142151 True -13 21574 16.701704502105713 0.30628085136413574 295.945068359375 0.6670032739639282 347.23272705078125 0.2902716100215912 0.81436193 0.7305142879486084 True -14 23115 16.63257145881653 1.3284308910369873 329.22161865234375 0.7131058573722839 345.851806640625 0.290711373090744 0.82044506 0.7029385566711426 True -15 24656 16.643861055374146 0.3051574230194092 154.31561279296875 0.545795202255249 344.6361389160156 0.2918831706047058 0.8273341 0.6791070103645325 True -16 26197 16.620790004730225 0.3178060054779053 419.8081970214844 0.4536108076572418 344.6519775390625 0.2921815514564514 0.8303593 0.6617205142974854 True -17 27738 16.654542207717896 0.3062300682067871 322.72711181640625 0.5106979012489319 343.950439453125 0.293668270111084 0.8327726 0.6549947261810303 True -18 29279 16.624670267105103 0.972557783126831 325.066650390625 0.6089613437652588 345.8993835449219 0.2915554642677307 0.83188534 0.656386137008667 False -19 30820 16.664721488952637 1.358555555343628 255.9038543701172 0.2391379475593567 346.74713134765625 0.290587842464447 0.832582 0.6596691012382507 False diff --git a/ENCSR788SKJ/cherimoya.fold_4.performance.tsv b/ENCSR788SKJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c37686f8e3d279e72ddc8510b76716230be24b06..0000000000000000000000000000000000000000 --- a/ENCSR788SKJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -343.950439453125 0.48661577701568604 0.29366829991340637 0.09541963040828705 0.8327726125717163 0.7728320360183716 0.6549947261810303 \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_0.evaluate.json b/ENCSR788SOI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3b5b0778ba15ff3c7be34ba6750b579d349206a1..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF056JEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_0.fit.json b/ENCSR788SOI/cherimoya.fold_0.fit.json deleted file mode 100644 index 5cee81be1ae0c7b5301d65e3a21eb4d8ea8e75a0..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF056JEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_0.log b/ENCSR788SOI/cherimoya.fold_0.log deleted file mode 100644 index b3125ba835604a1c43a0123163521f64b7863c86..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 34.35118889808655 4.328824281692505 181.0754852294922 0.49985307455062866 249.0189971923828 0.13562561571598053 0.6713529 2.9536755084991455 True -1 5496 30.376716136932373 0.5999617576599121 181.11056518554688 0.336063951253891 239.62904357910156 0.18867656588554382 0.70302624 0.7074207067489624 True -2 8244 30.381529569625854 0.5948352813720703 163.56773376464844 0.3623417615890503 236.85427856445312 0.19766882061958313 0.7389375 0.41727414727211 True -3 10992 30.413429260253906 1.320408821105957 211.5517578125 0.5234659910202026 235.7880096435547 0.20278075337409973 0.7478465 0.40012937784194946 True -4 13740 30.40334463119507 0.5814590454101562 182.44287109375 0.48626500368118286 235.30789184570312 0.204196959733963 0.7582858 0.3565545380115509 True -5 16488 30.394702196121216 0.590289831161499 175.85394287109375 0.5085738897323608 234.73886108398438 0.2069632112979889 0.76580083 0.340513676404953 True -6 19236 30.392035007476807 0.5922300815582275 186.394775390625 0.4517482817173004 234.56932067871094 0.20703241229057312 0.7702312 0.3404364287853241 True -7 21984 30.811156034469604 12.833769798278809 195.8534698486328 0.4456440210342407 234.19869995117188 0.2095671147108078 0.7755137 0.31973201036453247 True -8 24732 30.38437032699585 0.5960590839385986 190.7547607421875 0.24581870436668396 233.8684539794922 0.21066103875637054 0.7821471 0.3025979995727539 True -9 27480 30.35628914833069 0.5930507183074951 194.64366149902344 0.24132674932479858 233.5923309326172 0.21265101432800293 0.7843946 0.29726365208625793 True -10 30228 30.41764187812805 0.5903913974761963 176.78988647460938 0.6083437204360962 233.21202087402344 0.2143273502588272 0.785546 0.27460718154907227 True -11 32976 30.361270904541016 0.5861060619354248 221.6119384765625 0.3947937488555908 233.01380920410156 0.21477122604846954 0.789166 0.27909210324287415 True -12 35724 30.284514904022217 0.5910608768463135 177.2875213623047 0.3359106183052063 232.6534881591797 0.21674451231956482 0.7970863 0.25997745990753174 True -13 38472 30.290791749954224 3.16111421585083 223.39453125 0.29948943853378296 232.6156768798828 0.21648019552230835 0.8039546 0.24771837890148163 True -14 41220 30.348506450653076 0.5848665237426758 184.59866333007812 0.22569791972637177 232.2992401123047 0.21809373795986176 0.8100046 0.23797136545181274 True -15 43968 30.301113843917847 0.5909922122955322 198.96983337402344 0.2519700527191162 232.01882934570312 0.21950098872184753 0.8130155 0.22740143537521362 True -16 46716 30.383296251296997 1.6609125137329102 200.5129852294922 0.23959606885910034 232.0712890625 0.21924073994159698 0.81823623 0.2220163494348526 True -17 49464 30.402756452560425 0.5919983386993408 207.58303833007812 0.2561534643173218 232.11610412597656 0.21937835216522217 0.81847745 0.2204197645187378 True -18 52212 30.30504083633423 0.5921876430511475 196.26812744140625 0.2456057071685791 232.07752990722656 0.21988116204738617 0.81651926 0.2236795425415039 False -19 54960 30.32934808731079 0.6140563488006592 153.7608184814453 0.23824571073055267 232.23707580566406 0.2184891551733017 0.8176946 0.2263934463262558 False diff --git a/ENCSR788SOI/cherimoya.fold_0.performance.tsv b/ENCSR788SOI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 23b1c9e37b807ca98f1cccd09b58247a94be3cf9..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -232.11610412597656 0.5327509641647339 0.21937833726406097 0.057810597121715546 0.8184774518013 0.7646033763885498 0.2204197645187378 \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_1.evaluate.json b/ENCSR788SOI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4bcad52b46793fce1b1ecd977ae85657dbf99da4..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF056JEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_1.fit.json b/ENCSR788SOI/cherimoya.fold_1.fit.json deleted file mode 100644 index a11269e5c91a41d48ed3b6049e9292e89a56a8cf..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF056JEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_1.log b/ENCSR788SOI/cherimoya.fold_1.log deleted file mode 100644 index 6399d9e9aacd9bcf151f1dfeb544372d9c90729b..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 34.13172221183777 3.6411917209625244 229.57594299316406 0.6181806325912476 289.2641296386719 0.1484425812959671 0.6571327 3.5590996742248535 True -1 5474 30.26365065574646 0.7000584602355957 195.17062377929688 0.7002509832382202 277.4533386230469 0.20594778656959534 0.69967824 0.9605752825737 True -2 8211 30.284367322921753 0.6949536800384521 183.33172607421875 0.5276457667350769 272.4983215332031 0.22141247987747192 0.7434449 0.48773375153541565 True -3 10948 30.244080543518066 0.6832447052001953 166.1939697265625 0.5807039737701416 270.83001708984375 0.22695183753967285 0.764702 0.4106086492538452 True -4 13685 30.24829077720642 0.6847546100616455 202.00340270996094 0.5867795944213867 270.4584655761719 0.22859936952590942 0.7703835 0.40132400393486023 True -5 16422 30.295021057128906 0.8962686061859131 211.2093048095703 0.44390615820884705 269.888916015625 0.23174640536308289 0.7781581 0.36746326088905334 True -6 19159 30.31268286705017 0.6810660362243652 196.27670288085938 0.2488817423582077 269.76885986328125 0.2313641458749771 0.78677684 0.3408552408218384 True -7 21896 30.327871322631836 0.6841888427734375 191.3377227783203 0.3714867830276489 269.200439453125 0.23411227762699127 0.79069513 0.360789954662323 True -8 24633 30.272595643997192 0.6751837730407715 176.67837524414062 0.42164674401283264 268.7965393066406 0.235812246799469 0.7965538 0.3570478558540344 True -9 27370 30.43669819831848 0.6883642673492432 192.19105529785156 0.32274961471557617 268.6022644042969 0.23570211231708527 0.8018452 0.3247302174568176 True -10 30107 30.294004678726196 27.62417221069336 197.2303009033203 0.30996882915496826 268.3398742675781 0.2367837131023407 0.8071262 0.2984983026981354 True -11 32844 30.279557943344116 0.6930406093597412 210.87094116210938 0.3289315104484558 267.7827453613281 0.23881672322750092 0.8122167 0.2937667965888977 True -12 35581 30.263265371322632 0.6946225166320801 196.44024658203125 0.2913464307785034 267.22674560546875 0.2414340227842331 0.81503564 0.27741390466690063 True -13 38318 30.219125509262085 0.7026758193969727 195.10049438476562 0.33173614740371704 267.03265380859375 0.24240222573280334 0.8218949 0.2675631046295166 True -14 41055 30.22521162033081 0.6897237300872803 181.6857452392578 0.2541796565055847 266.4580993652344 0.24459479749202728 0.82629436 0.2572212815284729 True -15 43792 30.229846715927124 0.7916412353515625 195.15676879882812 0.36163759231567383 266.30853271484375 0.24546974897384644 0.83102304 0.24962039291858673 True -16 46529 30.24160408973694 0.6840064525604248 204.6744384765625 0.20169121026992798 266.3457336425781 0.24442559480667114 0.83305025 0.24560916423797607 True -17 49266 30.245323419570923 0.6769185066223145 191.13043212890625 0.2567631006240845 266.30804443359375 0.2446640580892563 0.8330175 0.2495729774236679 False -18 52003 30.24540901184082 0.67388916015625 179.09359741210938 0.1397281289100647 266.32794189453125 0.24455182254314423 0.83211744 0.25396814942359924 False -19 54740 30.579095125198364 0.681556224822998 197.997314453125 0.19540627300739288 266.4107360839844 0.2437671422958374 0.8312833 0.25642499327659607 False diff --git a/ENCSR788SOI/cherimoya.fold_1.performance.tsv b/ENCSR788SOI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7c5d6f32b20b1af0b59c066f85caf10a4a720f69..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -266.3457336425781 0.5126382112503052 0.24442562460899353 0.06322462111711502 0.8330502510070801 0.8013262748718262 0.24560916423797607 \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_2.evaluate.json b/ENCSR788SOI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 67b1eb325b93ca725bf860049b959b64a3a71979..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF056JEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_2.fit.json b/ENCSR788SOI/cherimoya.fold_2.fit.json deleted file mode 100644 index 0c98b8735ac07c02ec93fca34b6703820f3cbe2d..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF056JEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_2.log b/ENCSR788SOI/cherimoya.fold_2.log deleted file mode 100644 index bca3ff04850f1095ccf03c97b4368a0e4748e405..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2908 36.5985791683197 4.980233907699585 176.14437866210938 0.6359966993331909 262.6539306640625 0.1445348858833313 0.665129 2.813701868057251 True -1 5816 32.22664761543274 0.5443499088287354 244.51766967773438 0.4690721035003662 251.7364959716797 0.201427161693573 0.7205174 0.7193731069564819 True -2 8724 32.12290406227112 0.5305662155151367 194.286376953125 0.5521441102027893 248.43597412109375 0.21186918020248413 0.74565375 0.5430107116699219 True -3 11632 32.167505741119385 0.5357582569122314 198.17713928222656 0.5983881950378418 247.2212677001953 0.21605393290519714 0.7659489 0.4267922639846802 True -4 14540 32.19062328338623 0.5290923118591309 169.7462158203125 0.3170675039291382 246.83840942382812 0.21767540276050568 0.7709017 0.38615137338638306 True -5 17448 32.16206502914429 0.5266304016113281 180.27996826171875 0.4553912878036499 246.64698791503906 0.21831119060516357 0.7738927 0.3700043261051178 True -6 20356 32.20140838623047 0.8366312980651855 176.8331298828125 0.44183242321014404 246.07102966308594 0.22109009325504303 0.7800014 0.35283705592155457 True -7 23264 32.28782892227173 0.5344703197479248 189.01055908203125 0.34658801555633545 245.6515350341797 0.22284570336341858 0.78444725 0.3331035077571869 True -8 26172 32.144988775253296 2.1764461994171143 186.6178741455078 0.35215020179748535 245.5274658203125 0.2235693633556366 0.7867289 0.3160412609577179 True -9 29080 32.18611669540405 0.5514750480651855 220.45974731445312 0.31092262268066406 244.84329223632812 0.22660796344280243 0.7931134 0.30695289373397827 True -10 31988 32.16408634185791 1.0888793468475342 165.58152770996094 0.3352944850921631 244.96205139160156 0.22554707527160645 0.79491216 0.30220454931259155 True -11 34896 32.24123787879944 0.5404961109161377 180.7337646484375 0.4216839373111725 244.3196563720703 0.22873583436012268 0.7998483 0.2901478409767151 True -12 37804 32.206674337387085 2.05405592918396 263.1221923828125 0.22167834639549255 244.02627563476562 0.22948889434337616 0.8053868 0.27191275358200073 True -13 40712 32.17168617248535 0.5594232082366943 187.54544067382812 0.3841865360736847 243.71726989746094 0.23163248598575592 0.81121457 0.26319020986557007 True -14 43620 32.53773903846741 14.423898220062256 169.34918212890625 0.2109665423631668 243.6438446044922 0.23156042397022247 0.8165539 0.2534685730934143 True -15 46528 32.221343994140625 0.5319559574127197 195.75506591796875 0.29489484429359436 243.40390014648438 0.232538104057312 0.8201383 0.24025383591651917 True -16 49436 32.14955496788025 0.5358970165252686 171.25140380859375 0.228715717792511 243.31761169433594 0.23294536769390106 0.8227611 0.23624232411384583 True -17 52344 32.13388633728027 0.5755047798156738 186.65670776367188 0.359223335981369 243.2614288330078 0.233369842171669 0.82509714 0.23734596371650696 True -18 55252 32.14579463005066 0.5321626663208008 209.18557739257812 0.18853768706321716 243.2714080810547 0.23369042575359344 0.82559055 0.237251415848732 True -19 58160 32.20632076263428 0.5300800800323486 182.80853271484375 0.18802371621131897 243.58511352539062 0.2314709722995758 0.8220724 0.2411578744649887 False diff --git a/ENCSR788SOI/cherimoya.fold_2.performance.tsv b/ENCSR788SOI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bda2bc68830d20ed5de15c5ba5cc1a96f4b6dd28..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -243.2714080810547 0.5241181254386902 0.23369042575359344 0.0578276701271534 0.8255905508995056 0.7870448231697083 0.237251415848732 \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_3.evaluate.json b/ENCSR788SOI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 12806a9c469db463c70427d3271f6f88b2ca8eec..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF056JEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_3.fit.json b/ENCSR788SOI/cherimoya.fold_3.fit.json deleted file mode 100644 index 25c241f137884be447b480a99853cacb975e64be..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF056JEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_3.log b/ENCSR788SOI/cherimoya.fold_3.log deleted file mode 100644 index d7b52ee3bb4a829ab7b6344f6670c613ec5c3d55..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2775 34.5757040977478 3.4722070693969727 192.58981323242188 0.571552038192749 270.27557373046875 0.13901056349277496 0.6689086 3.5641987323760986 True -1 5550 30.674965620040894 0.5525100231170654 204.778564453125 0.3668118715286255 260.7818908691406 0.19067861139774323 0.73875266 0.6158288717269897 True -2 8325 30.906476736068726 0.5646326541900635 146.8808135986328 0.7437025904655457 257.46856689453125 0.20253916084766388 0.76456255 0.3484933376312256 True -3 11100 30.705012798309326 0.5450475215911865 175.42922973632812 0.511593759059906 255.76351928710938 0.20776242017745972 0.77241284 0.3351157009601593 True -4 13875 30.673863410949707 0.5445816516876221 227.03811645507812 0.4239259362220764 255.3957061767578 0.20911413431167603 0.7699793 0.32945042848587036 False -5 16650 30.630314111709595 0.5514123439788818 176.76422119140625 0.4128153324127197 254.8094482421875 0.21159005165100098 0.7710559 0.3397604525089264 False -6 19425 30.639421463012695 0.5522127151489258 193.1851806640625 0.3814431428909302 254.35948181152344 0.2133684605360031 0.7771092 0.335627019405365 True -7 22200 30.638777494430542 0.5446648597717285 204.67454528808594 0.3921145796775818 254.40077209472656 0.2128893882036209 0.7822458 0.31482914090156555 True -8 24975 30.70063829421997 1.093292474746704 215.57351684570312 0.3709263503551483 253.98712158203125 0.2148735523223877 0.78066677 0.33123189210891724 False -9 27750 30.729804515838623 0.5657637119293213 183.46861267089844 0.3749408423900604 253.64768981933594 0.21636004745960236 0.7866038 0.32679447531700134 True -10 30525 30.77615785598755 0.5464084148406982 163.7744140625 0.45543235540390015 253.2794189453125 0.2183675765991211 0.7898221 0.3117316663265228 True -11 33300 30.664270877838135 0.544189453125 178.15911865234375 0.4572824239730835 253.17869567871094 0.2192171961069107 0.7935874 0.3016373813152313 True -12 36075 30.699233770370483 0.5456600189208984 194.14991760253906 0.3393022119998932 252.72116088867188 0.22079278528690338 0.79800767 0.29481571912765503 True -13 38850 30.660730361938477 0.540917158126831 233.42214965820312 0.40199315547943115 252.5657958984375 0.2213672697544098 0.80499774 0.2829214632511139 True -14 41625 30.675400257110596 0.5541155338287354 176.7297821044922 0.29608577489852905 252.25393676757812 0.22255510091781616 0.80943364 0.2647298574447632 True -15 44400 30.70620846748352 0.5439651012420654 169.03480529785156 0.2560824751853943 251.92849731445312 0.22453619539737701 0.8151643 0.2566720247268677 True -16 47175 30.692423820495605 0.555959939956665 206.0059356689453 0.4881369471549988 252.1394500732422 0.2227068692445755 0.8165581 0.25041311979293823 True -17 49950 30.702863693237305 0.5451257228851318 184.79812622070312 0.23284666240215302 251.84335327148438 0.22435764968395233 0.8207756 0.24681420624256134 True -18 52725 30.75575065612793 0.5556261539459229 215.2279052734375 0.18442651629447937 252.1316375732422 0.22291967272758484 0.8198447 0.24826617538928986 False -19 55500 30.667875289916992 1.3444900512695312 219.5035400390625 0.2662501335144043 252.06915283203125 0.22345811128616333 0.8190114 0.24995923042297363 False diff --git a/ENCSR788SOI/cherimoya.fold_3.performance.tsv b/ENCSR788SOI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index dea92012db95b520605beac33a64a3cc8c780f48..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -251.84335327148438 0.5252388119697571 0.22435761988162994 0.06174148991703987 0.8207756280899048 0.7794582843780518 0.24681420624256134 \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_4.evaluate.json b/ENCSR788SOI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 66109c71d360d85a223c718b199e2ae2b7cb9b09..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF056JEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_4.fit.json b/ENCSR788SOI/cherimoya.fold_4.fit.json deleted file mode 100644 index b756067f99024fdf06f7f29b5b8bc0be1ad5f69e..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF056JEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788SOI/cherimoya.fold_4.log b/ENCSR788SOI/cherimoya.fold_4.log deleted file mode 100644 index 5c423cc5a8aaddad0cd966c47fb64887d77b878e..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 35.83502793312073 3.67282772064209 187.8201141357422 0.5801044702529907 250.9012451171875 0.13856619596481323 0.6822552 2.5278337001800537 True -1 5784 31.949113368988037 1.4554717540740967 207.7368927001953 0.40953919291496277 242.30538940429688 0.1867663413286209 0.7263695 0.6626998782157898 True -2 8676 32.0886914730072 0.6043839454650879 204.1773681640625 0.41521215438842773 238.9473876953125 0.19901174306869507 0.7555716 0.3515542447566986 True -3 11568 32.05652689933777 0.6041538715362549 180.348388671875 0.48816782236099243 237.79238891601562 0.2017204910516739 0.7650969 0.29770517349243164 True -4 14460 31.96139931678772 8.46060061454773 189.23162841796875 0.7142309546470642 237.3417510986328 0.20366182923316956 0.77211636 0.3005974590778351 True -5 17352 32.074190616607666 1.8280463218688965 171.156494140625 0.3376593291759491 237.4945526123047 0.2026660442352295 0.7738292 0.32229700684547424 True -6 20244 31.972364902496338 0.6143782138824463 197.85777282714844 0.28656595945358276 236.97198486328125 0.20491638779640198 0.7769675 0.296161025762558 True -7 23136 32.062782526016235 31.961215257644653 197.70950317382812 0.33747464418411255 236.90103149414062 0.20524784922599792 0.7785555 0.3133394122123718 True -8 26028 32.009862661361694 0.6107814311981201 200.9661102294922 0.35685455799102783 236.696533203125 0.2065434455871582 0.78392416 0.29266977310180664 True -9 28920 31.980518341064453 0.615196704864502 149.8107452392578 0.48051267862319946 236.1644744873047 0.20941650867462158 0.7901662 0.2719095051288605 True -10 31812 31.94653558731079 0.6021795272827148 172.86349487304688 0.27725449204444885 235.89315795898438 0.21069367229938507 0.7915838 0.2744801938533783 True -11 34704 31.947566032409668 0.6071701049804688 160.44744873046875 0.3427048325538635 235.6435089111328 0.21186870336532593 0.79725516 0.25807562470436096 True -12 37596 31.960847854614258 1.4883830547332764 189.0467987060547 0.19666963815689087 235.49755859375 0.21240901947021484 0.80160165 0.2585374116897583 True -13 40488 32.035664796829224 0.6061694622039795 197.33297729492188 0.3507155179977417 235.00033569335938 0.21518893539905548 0.80739796 0.24300259351730347 True -14 43380 31.92850351333618 0.5999865531921387 166.12286376953125 0.21757371723651886 234.73428344726562 0.21610045433044434 0.8123285 0.22888684272766113 True -15 46272 31.90768814086914 0.6022396087646484 209.56417846679688 0.20845334231853485 234.5686492919922 0.21705152094364166 0.8158989 0.2182590216398239 True -16 49164 31.99310278892517 0.6063785552978516 184.577392578125 0.24282720685005188 234.66676330566406 0.2166774570941925 0.81694865 0.21749281883239746 True -17 52056 31.92525887489319 2.632310628890991 194.55111694335938 0.23901262879371643 234.52334594726562 0.21736229956150055 0.81876236 0.21664217114448547 True -18 54948 32.00196623802185 0.6048758029937744 190.08407592773438 0.2700684070587158 234.6345672607422 0.21677610278129578 0.8190577 0.22140668332576752 True -19 57840 31.89099669456482 0.6049728393554688 188.16189575195312 0.20382943749427795 234.78289794921875 0.21602825820446014 0.81659937 0.22402501106262207 False diff --git a/ENCSR788SOI/cherimoya.fold_4.performance.tsv b/ENCSR788SOI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index dcf814ae87352c776813b60cd9f7b0ebae418d17..0000000000000000000000000000000000000000 --- a/ENCSR788SOI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -234.6345672607422 0.53316330909729 0.21677610278129578 0.0519595742225647 0.8190577030181885 0.764332115650177 0.22140668332576752 \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_0.evaluate.json b/ENCSR788TRR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0e547a8616990e5cfca9229c119c6d23daad9782..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF762VGW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_0.fit.json b/ENCSR788TRR/cherimoya.fold_0.fit.json deleted file mode 100644 index 1db4864d53eaa5aa260ec05e6980baaba5e07edd..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF762VGW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_0.log b/ENCSR788TRR/cherimoya.fold_0.log deleted file mode 100644 index ff2f1e42d6d80a00c186153ccc106d8660edfb1c..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2049 27.00418519973755 3.5797102451324463 336.69476318359375 0.34174644947052 417.5677490234375 0.5351208448410034 0.62451875 8.45527458190918 True -1 4098 22.7619526386261 0.5712466239929199 296.39886474609375 0.2895438075065613 360.47686767578125 0.6338452100753784 0.7136991 1.300819754600525 True -2 6147 22.73315405845642 0.4651761054992676 342.2625732421875 0.30616313219070435 348.0790100097656 0.6583639979362488 0.7360349 0.3928315043449402 True -3 8196 22.747162580490112 0.413405179977417 291.5555725097656 0.26901549100875854 344.5099792480469 0.6644168496131897 0.74046224 0.3211597204208374 True -4 10245 22.739224433898926 0.414945125579834 312.1426086425781 0.43533772230148315 343.5174560546875 0.6666168570518494 0.73976177 0.25904545187950134 False -5 12294 22.734100341796875 0.635629415512085 326.4507751464844 0.2542498707771301 342.82208251953125 0.6685372591018677 0.7446951 0.24981363117694855 True -6 14343 22.73707389831543 1.3210015296936035 329.7246398925781 0.3162975609302521 342.56683349609375 0.6694055199623108 0.75216573 0.25293028354644775 True -7 16392 22.80557346343994 0.4209742546081543 285.9624938964844 0.26055556535720825 341.6323547363281 0.671374499797821 0.7557769 0.23366405069828033 True -8 18441 22.740756034851074 0.41179633140563965 288.3331298828125 0.20697492361068726 341.0835876464844 0.6725380420684814 0.7620554 0.2258179783821106 True -9 20490 22.75931167602539 0.4148271083831787 288.87115478515625 0.2043633759021759 340.36865234375 0.6741775274276733 0.76602745 0.216792494058609 True -10 22539 22.77204155921936 0.40929388999938965 297.0989990234375 0.3094688951969147 339.8707580566406 0.6756913065910339 0.77462757 0.2123280018568039 True -11 24588 22.760598182678223 0.40541791915893555 300.16729736328125 0.34797632694244385 339.2935485839844 0.6767719388008118 0.7765006 0.2094520479440689 True -12 26637 22.737444400787354 0.42040395736694336 303.0611877441406 0.20427322387695312 338.8291320800781 0.6779177784919739 0.78236413 0.20398324728012085 True -13 28686 22.704368591308594 0.408184289932251 318.79730224609375 0.19330669939517975 338.47235107421875 0.6788471937179565 0.7883707 0.20090243220329285 True -14 30735 22.70548152923584 0.41483426094055176 302.46978759765625 0.19978277385234833 338.25592041015625 0.6795551180839539 0.79100806 0.20095862448215485 True -15 32784 22.73497986793518 0.4158444404602051 261.15472412109375 0.16811981797218323 338.0889587402344 0.6798982620239258 0.79329735 0.20185886323451996 True -16 34833 22.737499952316284 0.4187901020050049 267.95697021484375 0.16778598725795746 338.1864318847656 0.6796109676361084 0.7936709 0.2052702009677887 True -17 36882 22.745768785476685 0.4172346591949463 268.9595947265625 0.1655721217393875 338.3712158203125 0.6792193055152893 0.7878213 0.21004745364189148 False -18 38931 22.75789737701416 0.41571664810180664 281.07623291015625 0.13202664256095886 338.6499328613281 0.6786590218544006 0.7867439 0.2137332558631897 False -19 40980 22.31901478767395 0.40573811531066895 292.6224365234375 0.14207445085048676 338.6909484863281 0.6782620549201965 0.78288174 0.21863862872123718 False diff --git a/ENCSR788TRR/cherimoya.fold_0.performance.tsv b/ENCSR788TRR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4eefcfe1d0f1da03545e8fd91d4d465e4d95324b..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -338.1864318847656 0.2673806846141815 0.6796109080314636 0.2535955309867859 0.7936708927154541 0.7529255747795105 0.2052702009677887 \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_1.evaluate.json b/ENCSR788TRR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d15c8188ad7c225db67fb00db4040ad6da316a5a..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF762VGW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_1.fit.json b/ENCSR788TRR/cherimoya.fold_1.fit.json deleted file mode 100644 index 70e674e33031935ac712d17642d13672f4f45406..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF762VGW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_1.log b/ENCSR788TRR/cherimoya.fold_1.log deleted file mode 100644 index 0c76bbd5f078c7385b4696f2f0bc6114087b4e25..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2031 27.00968289375305 3.7427172660827637 288.4543762207031 0.25534331798553467 454.45458984375 0.5490309596061707 0.6295473 8.945261001586914 True -1 4062 22.55898356437683 0.5990216732025146 316.6644592285156 0.34808847308158875 387.7579345703125 0.6481661200523376 0.7185429 1.5104122161865234 True -2 6093 22.614355325698853 1.9772658348083496 311.9895935058594 0.45069560408592224 375.31878662109375 0.6711741089820862 0.73719466 0.44312819838523865 True -3 8124 22.5925030708313 0.5609374046325684 275.4122009277344 0.20969393849372864 371.1043395996094 0.6777269244194031 0.7452276 0.279100626707077 True -4 10155 22.58801770210266 0.5478286743164062 308.4544677734375 0.3051668405532837 369.41766357421875 0.6807882189750671 0.75669503 0.2501480281352997 True -5 12186 22.572457551956177 0.5597920417785645 293.4668273925781 0.34826481342315674 368.7106018066406 0.682135283946991 0.7582397 0.2344018965959549 True -6 14217 22.548025369644165 0.5606510639190674 271.20538330078125 0.2984849810600281 367.9822692871094 0.6836751699447632 0.7652125 0.22253096103668213 True -7 16248 22.541492462158203 1.276904582977295 260.1712646484375 0.23831677436828613 367.26763916015625 0.6853181719779968 0.77223176 0.21995043754577637 True -8 18279 22.54769492149353 0.5399377346038818 298.404541015625 0.22877871990203857 366.6072692871094 0.6868730783462524 0.7772319 0.2172437459230423 True -9 20310 22.534993171691895 2.0767271518707275 256.4814453125 0.2922458052635193 365.9884033203125 0.688376784324646 0.7833597 0.2101224809885025 True -10 22341 22.59391713142395 0.5510046482086182 275.97430419921875 0.2016311138868332 365.4796447753906 0.6895787119865417 0.79021 0.20156928896903992 True -11 24372 22.558433532714844 10.23106074333191 306.1437072753906 0.20402580499649048 364.89251708984375 0.6910116076469421 0.7952212 0.19700023531913757 True -12 26403 22.52599334716797 0.5554070472717285 271.9034423828125 0.18966084718704224 364.4588623046875 0.6921431422233582 0.8009437 0.19635187089443207 True -13 28434 22.638514757156372 0.571509599685669 291.1844482421875 0.2139458805322647 364.0274658203125 0.6930604577064514 0.8040381 0.1910090148448944 True -14 30465 22.619953870773315 0.5708212852478027 266.2726135253906 0.1525721251964569 363.7356262207031 0.6936982274055481 0.80769485 0.19084049761295319 True -15 32496 22.62934899330139 0.5483641624450684 301.95587158203125 0.1952228844165802 363.5776672363281 0.6939992308616638 0.81048477 0.19025717675685883 True -16 34527 22.580826997756958 0.5484457015991211 263.8190002441406 0.20296511054039001 363.6468505859375 0.693763017654419 0.8120017 0.1936904639005661 True -17 36558 22.62167191505432 0.5869498252868652 268.354736328125 0.14075186848640442 363.9519958496094 0.6931159496307373 0.8093296 0.19685561954975128 False -18 38589 22.630603790283203 0.5564281940460205 273.2363586425781 0.1367187798023224 364.16741943359375 0.6924430131912231 0.80671847 0.2030809372663498 False -19 40620 22.702625036239624 0.5544822216033936 277.15277099609375 0.15240931510925293 364.4425048828125 0.6919223666191101 0.8020408 0.20875611901283264 False diff --git a/ENCSR788TRR/cherimoya.fold_1.performance.tsv b/ENCSR788TRR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a0bd8afbfb93900277a06dab6a4cc71632b3fb4a..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -363.6468505859375 0.25520482659339905 0.6937629580497742 0.2718561589717865 0.8120017051696777 0.7979073524475098 0.1936904639005661 \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_2.evaluate.json b/ENCSR788TRR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d14127a25ddb19c9b2fff5ccb18a4df3dd41c205..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF762VGW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_2.fit.json b/ENCSR788TRR/cherimoya.fold_2.fit.json deleted file mode 100644 index e7b458e1213ebc581269e716bdc9932f60aac92d..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF762VGW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_2.log b/ENCSR788TRR/cherimoya.fold_2.log deleted file mode 100644 index 8d0dba7e9db71453fffc1a43fc8737b600781d27..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2163 28.53153657913208 3.5749948024749756 310.84857177734375 0.4121124744415283 424.44403076171875 0.5482149124145508 0.6153871 7.335192680358887 True -1 4326 24.00402045249939 0.48800063133239746 264.9991760253906 0.2983415722846985 369.2851257324219 0.6427574157714844 0.7162774 1.2493102550506592 True -2 6489 24.00602102279663 0.41368603706359863 286.4255676269531 0.3325379490852356 359.0137023925781 0.6609985828399658 0.72303873 0.41019177436828613 True -3 8652 24.00271487236023 0.4392218589782715 300.10772705078125 0.2604910731315613 356.1558532714844 0.6640944480895996 0.73832744 0.3036440312862396 True -4 10815 24.00736403465271 0.4137587547302246 279.8304443359375 0.2648058235645294 353.93927001953125 0.6687162518501282 0.7418205 0.2661740779876709 True -5 12978 23.664555311203003 0.40604686737060547 297.7968444824219 0.20830562710762024 353.2111511230469 0.6704761385917664 0.7398896 0.26600202918052673 False -6 15141 23.58858847618103 0.4144914150238037 284.5260009765625 0.33106279373168945 352.5465087890625 0.6718509197235107 0.7476304 0.26151639223098755 True -7 17304 23.517109632492065 0.413621187210083 294.88763427734375 0.41289088129997253 351.70220947265625 0.6736977100372314 0.75380033 0.2509963810443878 True -8 19467 23.924392223358154 0.4123718738555908 284.62420654296875 0.22767803072929382 351.0985107421875 0.675043523311615 0.75786364 0.25034672021865845 True -9 21630 23.597203731536865 0.40145015716552734 308.35479736328125 0.18370196223258972 350.6462097167969 0.6764600872993469 0.761881 0.25053808093070984 True -10 23793 23.571574926376343 0.4100830554962158 309.3979797363281 0.1631786823272705 350.26629638671875 0.6778299808502197 0.7695309 0.23492446541786194 True -11 25956 23.552979946136475 0.4185318946838379 289.11126708984375 0.2248658537864685 349.5938415527344 0.6789167523384094 0.7798703 0.22963958978652954 True -12 28119 23.57949209213257 0.4023561477661133 279.99029541015625 0.2722051441669464 348.7574157714844 0.6804301142692566 0.78374565 0.22196544706821442 True -13 30282 23.580443382263184 0.4041016101837158 255.0133056640625 0.21394138038158417 348.3729553222656 0.6813138127326965 0.7908567 0.21717147529125214 True -14 32445 23.579033613204956 0.40597105026245117 257.7798156738281 0.1889476478099823 347.744384765625 0.6820822358131409 0.7953719 0.21235516667366028 True -15 34608 23.542672634124756 0.40559816360473633 283.77569580078125 0.1871611773967743 347.66058349609375 0.6824908256530762 0.8008435 0.20769435167312622 True -16 36771 23.555495977401733 0.4028592109680176 305.22015380859375 0.19805139303207397 347.69879150390625 0.6823505163192749 0.8008106 0.2094893902540207 False -17 38934 23.55896759033203 0.4033198356628418 284.3768615722656 0.1607537418603897 348.514404296875 0.6815778017044067 0.7991934 0.21407842636108398 False -18 41097 23.534834623336792 0.6555197238922119 266.2375183105469 0.17317727208137512 348.2344665527344 0.6809306144714355 0.7975801 0.21601861715316772 False -19 43260 23.539098024368286 0.4095425605773926 281.173095703125 0.08752340078353882 348.8847961425781 0.6805862188339233 0.7948944 0.2191043347120285 False diff --git a/ENCSR788TRR/cherimoya.fold_2.performance.tsv b/ENCSR788TRR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ac73420030bd42ba61bf2d60abce7b2db09df4ce..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -347.66058349609375 0.2639481723308563 0.6824907064437866 0.2588488459587097 0.8008434772491455 0.7689827084541321 0.20769435167312622 \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_3.evaluate.json b/ENCSR788TRR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 51e9a4c028c273b7b542141f5031045c64e7dfd4..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF762VGW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_3.fit.json b/ENCSR788TRR/cherimoya.fold_3.fit.json deleted file mode 100644 index a697602313c7b2b45a083fea39dd2098e524d142..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF762VGW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_3.log b/ENCSR788TRR/cherimoya.fold_3.log deleted file mode 100644 index 280a0a1d57c2c15b7bcdeb508788de07104e07f4..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2102 27.87122893333435 3.550539970397949 297.4193115234375 0.4092823266983032 418.0683898925781 0.5413315296173096 0.62049145 8.4017972946167 True -1 4204 23.38045859336853 0.44910502433776855 301.259521484375 0.34976089000701904 361.5097351074219 0.6397601366043091 0.7100448 1.3182452917099 True -2 6306 23.33957052230835 0.41359853744506836 297.38067626953125 0.26105231046676636 350.9158935546875 0.6606975197792053 0.7271522 0.45629608631134033 True -3 8408 23.348023653030396 0.40812063217163086 279.7189636230469 0.3052898049354553 346.84478759765625 0.6666722297668457 0.73188186 0.35971343517303467 True -4 10510 23.29298496246338 0.41112589836120605 287.6917724609375 0.47376367449760437 345.4945983886719 0.6692488789558411 0.7314577 0.2557310461997986 False -5 12612 23.33302593231201 0.4140002727508545 286.15264892578125 0.37430691719055176 344.76300048828125 0.6710966229438782 0.7289828 0.2552453577518463 False -6 14714 23.3335018157959 0.41345906257629395 284.9120178222656 0.26697495579719543 343.9671325683594 0.6729251742362976 0.73871803 0.24491988122463226 True -7 16816 23.36199951171875 14.867554664611816 339.79278564453125 0.21712127327919006 343.1323547363281 0.6748725175857544 0.73911476 0.24593457579612732 True -8 18918 23.494542598724365 0.4159550666809082 320.8050231933594 0.28340303897857666 342.6011047363281 0.6763883233070374 0.7436568 0.24535948038101196 True -9 21020 23.39148259162903 0.41529202461242676 289.93060302734375 0.36108869314193726 342.0051574707031 0.6777628064155579 0.751198 0.24192498624324799 True -10 23122 23.3509418964386 0.4110081195831299 297.047119140625 0.23710966110229492 341.5650939941406 0.6791884303092957 0.7557635 0.23596946895122528 True -11 25224 23.339789867401123 2.1487772464752197 268.3598937988281 0.16263003647327423 340.8950500488281 0.6809003353118896 0.76493263 0.23446427285671234 True -12 27326 23.464659690856934 0.4231245517730713 293.61602783203125 0.20203453302383423 340.4451904296875 0.6819389462471008 0.7678202 0.2306855469942093 True -13 29428 23.10997438430786 0.42249059677124023 297.43212890625 0.20619821548461914 340.1226806640625 0.682939887046814 0.77267295 0.2272852212190628 True -14 31530 22.942349672317505 0.41681671142578125 279.0646667480469 0.19126185774803162 339.78582763671875 0.6834354400634766 0.77832735 0.22117972373962402 True -15 33632 23.344755172729492 0.4178314208984375 270.19073486328125 0.18605589866638184 339.69329833984375 0.6837210059165955 0.7797289 0.221440851688385 True -16 35734 22.896637439727783 0.41950249671936035 295.8930969238281 0.12541842460632324 339.9098205566406 0.68324214220047 0.7800858 0.22514726221561432 True -17 37836 22.90486192703247 0.42185544967651367 296.77764892578125 0.14549216628074646 340.1231689453125 0.6826830506324768 0.7789036 0.23200927674770355 False -18 39938 22.94213342666626 0.4249145984649658 258.0232849121094 0.10553388297557831 340.329345703125 0.6820316910743713 0.7748513 0.23779521882534027 False -19 42040 22.939871549606323 0.41666364669799805 262.952392578125 0.1423874944448471 340.5199890136719 0.6815747618675232 0.77310544 0.24251656234264374 False diff --git a/ENCSR788TRR/cherimoya.fold_3.performance.tsv b/ENCSR788TRR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index cf01462f7f711d243605e08591fa96827aaae1ea..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -339.9098205566406 0.26523271203041077 0.68324214220047 0.25309547781944275 0.7800858020782471 0.7488658428192139 0.22514726221561432 \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_4.evaluate.json b/ENCSR788TRR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4a6376ecda8a0358bafabe0607e054d80743fd4f..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF762VGW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_4.fit.json b/ENCSR788TRR/cherimoya.fold_4.fit.json deleted file mode 100644 index b7262c7a999905c57365e5fd3743e76fb579bc92..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF762VGW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR788TRR/cherimoya.fold_4.log b/ENCSR788TRR/cherimoya.fold_4.log deleted file mode 100644 index a2fb781f8ee7c1b6a36015ecf05a151fbe868372..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2126 28.1238911151886 3.4596774578094482 293.6547546386719 0.390792578458786 406.5988464355469 0.5418648719787598 0.6214081 7.007516860961914 True -1 4252 23.579782247543335 8.804146528244019 331.30279541015625 0.27847421169281006 355.1289978027344 0.6326339840888977 0.703399 1.2642953395843506 True -2 6378 23.650657415390015 0.39473938941955566 286.0318603515625 0.3623049855232239 343.7912292480469 0.6553874611854553 0.7198499 0.43596750497817993 True -3 8504 23.637165307998657 0.400770902633667 289.7764892578125 0.4564497768878937 340.67877197265625 0.6597207188606262 0.7310297 0.34575745463371277 True -4 10630 23.578572273254395 0.39065098762512207 304.364501953125 0.26845014095306396 339.7582092285156 0.6614136695861816 0.7328492 0.26372089982032776 True -5 12756 23.59852647781372 0.387897253036499 285.1463928222656 0.3426513075828552 338.6734924316406 0.664066731929779 0.73458916 0.2424733191728592 True -6 14882 23.566843509674072 0.3901841640472412 313.5086669921875 0.34299778938293457 338.0369873046875 0.6653549671173096 0.7395292 0.2461683303117752 True -7 17008 23.565288305282593 1.0488965511322021 277.2965087890625 0.2874281704425812 337.5146789550781 0.6666982173919678 0.747387 0.2570590078830719 True -8 19134 23.613707065582275 0.392409086227417 258.46429443359375 0.20469973981380463 336.8262939453125 0.6682166457176208 0.7515185 0.2402321994304657 True -9 21260 23.628677368164062 0.3820834159851074 304.53948974609375 0.24457211792469025 336.02001953125 0.6703013181686401 0.7596922 0.2351558357477188 True -10 23386 23.58505940437317 0.3972349166870117 289.8692626953125 0.14791788160800934 335.4516906738281 0.6720564961433411 0.76552 0.23645532131195068 True -11 25512 23.645081281661987 0.39498400688171387 271.1018371582031 0.2503613233566284 334.8423767089844 0.67350172996521 0.7722363 0.225846529006958 True -12 27638 23.617207288742065 0.3959496021270752 279.41204833984375 0.31861913204193115 334.19305419921875 0.6750828623771667 0.77785903 0.21935027837753296 True -13 29764 23.60060167312622 0.39054179191589355 327.3614501953125 0.19109180569648743 333.76873779296875 0.6761339902877808 0.78498244 0.21195219457149506 True -14 31890 23.580434799194336 0.3859386444091797 287.5675048828125 0.19366589188575745 333.2741394042969 0.6768612265586853 0.79187435 0.2039053589105606 True -15 34016 23.61580991744995 0.3964407444000244 291.0272216796875 0.15505638718605042 333.2298583984375 0.6772100925445557 0.79565424 0.20130731165409088 True -16 36142 23.61452078819275 0.3861827850341797 267.0622253417969 0.2286316454410553 333.167724609375 0.6770909428596497 0.7941873 0.20122936367988586 False -17 38268 23.59632682800293 0.3799417018890381 280.4581298828125 0.15261110663414001 333.3619079589844 0.6766417622566223 0.7924337 0.20274625718593597 False -18 40394 23.20406746864319 0.40140652656555176 268.20111083984375 0.1690942794084549 333.6159362792969 0.6761383414268494 0.7887129 0.2048744410276413 False -19 42520 23.16783833503723 0.4311678409576416 288.75897216796875 0.14057064056396484 333.7245788574219 0.6757704615592957 0.78659153 0.20945437252521515 False diff --git a/ENCSR788TRR/cherimoya.fold_4.performance.tsv b/ENCSR788TRR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0d6dd65fa815ddd9c44d72f66f6d6c1a339d0a7e..0000000000000000000000000000000000000000 --- a/ENCSR788TRR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -333.2298583984375 0.26936963200569153 0.6772100925445557 0.2482786476612091 0.7956542372703552 0.7492506504058838 0.20130731165409088 \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_0.evaluate.json b/ENCSR789FJF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d0e788524ba848089269ef043a30a7594639aa34..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272QHJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_0.fit.json b/ENCSR789FJF/cherimoya.fold_0.fit.json deleted file mode 100644 index 1961987c674839260a8842ca4cfbbb2bab908e15..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF272QHJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_0.log b/ENCSR789FJF/cherimoya.fold_0.log deleted file mode 100644 index bf8e5db443fdec57b7985186741a71e32672262e..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 34.00846600532532 3.913332223892212 507.17010498046875 0.275906503200531 588.0843505859375 0.26440566778182983 0.7585193 3.817901134490967 True -1 5490 30.28167223930359 0.6015889644622803 470.9197692871094 0.3070886731147766 546.3361206054688 0.3205310106277466 0.81774545 0.9230836033821106 True -2 8235 30.067935943603516 0.5864224433898926 394.9830322265625 0.26166781783103943 538.4227294921875 0.3307071030139923 0.8259981 0.3785378336906433 True -3 10980 29.657872438430786 0.586331844329834 435.35491943359375 0.26875677704811096 534.7778930664062 0.334491103887558 0.8376118 0.39197638630867004 True -4 13725 29.64630126953125 23.00971555709839 526.0089111328125 0.17762640118598938 532.4326171875 0.33756306767463684 0.84232646 0.25875788927078247 True -5 16470 29.934775829315186 0.6060903072357178 421.2083740234375 0.19929760694503784 530.4730224609375 0.3419507145881653 0.84679276 0.23416602611541748 True -6 19215 29.6178457736969 0.577899694442749 514.4163818359375 0.20322075486183167 528.613037109375 0.34477367997169495 0.850746 0.22525855898857117 True -7 21960 29.570099592208862 0.5899162292480469 403.0183410644531 0.29496490955352783 527.4342651367188 0.34587472677230835 0.8576784 0.2059778869152069 True -8 24705 29.576640129089355 0.5915920734405518 484.72613525390625 0.14165177941322327 526.7767333984375 0.34694886207580566 0.8604158 0.20269034802913666 True -9 27450 29.64233708381653 0.6000323295593262 503.66845703125 0.22387585043907166 525.6472778320312 0.34882280230522156 0.86487377 0.1944570690393448 True -10 30195 29.705249547958374 0.5982911586761475 429.0369873046875 0.20283928513526917 524.629638671875 0.3499218225479126 0.8675404 0.19365081191062927 True -11 32940 29.66763734817505 0.6104629039764404 436.2530212402344 0.2790321707725525 523.3489990234375 0.3524797260761261 0.8704934 0.18609395623207092 True -12 35685 29.66267204284668 0.603173017501831 472.1693115234375 0.2413029670715332 522.4216918945312 0.35255634784698486 0.87733 0.17998196184635162 True -13 38430 29.899481534957886 0.5990569591522217 457.72796630859375 0.23583801090717316 522.4522705078125 0.35212281346321106 0.8798544 0.17669206857681274 True -14 41175 29.67254948616028 3.4322588443756104 509.22216796875 0.36425158381462097 520.0956420898438 0.35662490129470825 0.884413 0.17139935493469238 True -15 43920 29.65994882583618 0.590827226638794 474.3304138183594 0.16430503129959106 520.2686767578125 0.3557637929916382 0.8861367 0.1681034415960312 True -16 46665 29.637073516845703 0.5900144577026367 442.3060302734375 0.22661978006362915 520.017578125 0.3559297025203705 0.8873767 0.16537714004516602 True -17 49410 29.610613584518433 0.5788614749908447 468.0087585449219 0.1494397222995758 519.580322265625 0.35745880007743835 0.8883549 0.16315479576587677 True -18 52155 29.861091375350952 0.5966405868530273 437.1385498046875 0.13729925453662872 520.384033203125 0.35612720251083374 0.8895145 0.16274666786193848 True -19 54900 29.647226333618164 0.578643798828125 484.53594970703125 0.1098833978176117 520.25244140625 0.35617879033088684 0.8886995 0.16304440796375275 False diff --git a/ENCSR789FJF/cherimoya.fold_0.performance.tsv b/ENCSR789FJF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 654e160035db07bdad02c52c08144bcc328561f1..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -520.384033203125 0.4118972718715668 0.35612720251083374 0.13704878091812134 0.8895145058631897 0.8688446283340454 0.16274666786193848 \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_1.evaluate.json b/ENCSR789FJF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0631ad38ab6253f666336c6aece63d40e0b9ee59..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272QHJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_1.fit.json b/ENCSR789FJF/cherimoya.fold_1.fit.json deleted file mode 100644 index bfbac7431928d2ea4b52680c0a0f76056b985881..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF272QHJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_1.log b/ENCSR789FJF/cherimoya.fold_1.log deleted file mode 100644 index 208436cb72c7004f026765daabaa0e136e9eee26..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2710 34.869295597076416 3.7619214057922363 493.0389404296875 0.3895217776298523 688.6121826171875 0.26786690950393677 0.7444212 4.090233325958252 True -1 5420 32.908118724823 12.604910135269165 414.79058837890625 0.2482084482908249 634.7827758789062 0.3379819989204407 0.816334 1.0255452394485474 True -2 8130 29.88232970237732 2.595107316970825 462.18048095703125 0.23115472495555878 626.0912475585938 0.347505122423172 0.82198375 0.47176000475883484 True -3 10840 29.825096607208252 40.9106662273407 552.9645385742188 0.38616251945495605 619.6082763671875 0.3541775047779083 0.83266395 0.4822303354740143 True -4 13550 29.815122365951538 0.6885757446289062 505.1736145019531 0.22450503706932068 617.6610107421875 0.3559657037258148 0.8353534 0.35768139362335205 True -5 16260 32.40978121757507 5.294096231460571 458.25238037109375 0.32427987456321716 615.3117065429688 0.3586139380931854 0.8419854 0.3222200572490692 True -6 18970 29.86312699317932 47.65657997131348 395.3951416015625 0.2530096173286438 612.7001342773438 0.3613062798976898 0.8472558 0.2991439700126648 True -7 21680 30.3268301486969 1.4528453350067139 468.03668212890625 0.27807432413101196 611.0584716796875 0.3634829819202423 0.85224867 0.27520644664764404 True -8 24390 29.88374948501587 1.8322429656982422 510.5166015625 0.2270592451095581 609.9810791015625 0.36356666684150696 0.8569519 0.25889816880226135 True -9 27100 29.795395135879517 2.8595755100250244 488.55712890625 0.23505635559558868 608.2139282226562 0.3666486144065857 0.86171293 0.25363191962242126 True -10 29810 29.814751386642456 17.724109411239624 417.482177734375 0.25862982869148254 606.4793701171875 0.36814001202583313 0.86693126 0.22932912409305573 True -11 32520 29.62928032875061 0.6950860023498535 393.08184814453125 0.19523541629314423 604.5872192382812 0.3706991672515869 0.87326396 0.22181977331638336 True -12 35230 29.243083715438843 0.6711094379425049 454.36065673828125 0.19325339794158936 602.4099731445312 0.37300071120262146 0.8761985 0.2110797017812729 True -13 37940 29.263598203659058 0.6692423820495605 413.2548828125 0.12979508936405182 600.0253295898438 0.37692251801490784 0.88011026 0.20518381893634796 True -14 40650 29.227339267730713 2.3532114028930664 499.95159912109375 0.20496191084384918 599.7560424804688 0.37674131989479065 0.8840729 0.19721727073192596 True -15 43360 29.241289854049683 0.6747217178344727 445.61297607421875 0.15759648382663727 599.676025390625 0.3764796555042267 0.888073 0.19080963730812073 True -16 46070 29.211641311645508 0.6757688522338867 429.16998291015625 0.3554297685623169 598.917724609375 0.3770766258239746 0.8921514 0.1867896020412445 True -17 48780 29.209662675857544 34.990676403045654 416.857177734375 0.13882815837860107 598.0390014648438 0.3791394531726837 0.8931419 0.18229395151138306 True -18 51490 29.19828724861145 1.022526502609253 420.50628662109375 0.12957336008548737 597.8505249023438 0.3792109787464142 0.89387417 0.18150648474693298 True -19 54200 29.224131107330322 1.5039136409759521 450.62445068359375 0.14232024550437927 598.292236328125 0.3782171905040741 0.89350414 0.18249572813510895 False diff --git a/ENCSR789FJF/cherimoya.fold_1.performance.tsv b/ENCSR789FJF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c4c0389c51a7c074988b21c50f28c1f32ab13226..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -597.8505249023438 0.39136797189712524 0.3792109787464142 0.15797001123428345 0.8938741683959961 0.8848400115966797 0.18150648474693298 \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_2.evaluate.json b/ENCSR789FJF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1f74d8019c6713a2bd0123ed15c064d612c51d4e..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272QHJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_2.fit.json b/ENCSR789FJF/cherimoya.fold_2.fit.json deleted file mode 100644 index c8ec2cce5da3337a1673f6637325e599fd3c3ec9..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF272QHJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_2.log b/ENCSR789FJF/cherimoya.fold_2.log deleted file mode 100644 index de74610d63ad0bab9d972f0486da2565afc6b0ed..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 36.08516550064087 26.65972924232483 444.0421142578125 0.3296302556991577 619.4495239257812 0.2635897099971771 0.74892056 3.120690107345581 True -1 5762 31.654797315597534 0.5751190185546875 575.906005859375 0.2891342341899872 573.728515625 0.3281019926071167 0.8095106 0.9374799728393555 True -2 8643 31.6065616607666 1.559342622756958 486.24249267578125 0.24733658134937286 564.0502319335938 0.3376942574977875 0.82258946 0.46238744258880615 True -3 11524 31.139211177825928 0.5521271228790283 435.35443115234375 0.23301467299461365 559.8165893554688 0.3433113098144531 0.831117 0.3268061578273773 True -4 14405 31.096994638442993 2.686121702194214 454.18914794921875 0.3387746214866638 558.9661865234375 0.34414029121398926 0.83660716 0.25716859102249146 True -5 17286 31.021070957183838 9.306607007980347 492.8667907714844 0.2855396568775177 558.7352294921875 0.3436393737792969 0.84023196 0.252858430147171 True -6 20167 31.315719604492188 0.5606894493103027 426.7042541503906 0.25731009244918823 557.0535278320312 0.3457726538181305 0.8468317 0.236991286277771 True -7 23048 31.03680443763733 0.5452995300292969 447.28900146484375 0.23099423944950104 555.5012817382812 0.34869956970214844 0.8507576 0.23789578676223755 True -8 25929 31.030874252319336 0.5526154041290283 484.7181396484375 0.2602212131023407 554.7936401367188 0.34893032908439636 0.85355866 0.2356085330247879 True -9 28810 30.973204851150513 2.233222246170044 481.2024841308594 0.1507866382598877 552.6738891601562 0.35248345136642456 0.85801613 0.2226666510105133 True -10 31691 31.208991289138794 0.5451564788818359 424.76116943359375 0.26774361729621887 552.1281127929688 0.3525797426700592 0.8628039 0.2143370807170868 True -11 34572 31.056154489517212 0.542344331741333 457.3567199707031 0.1637439876794815 549.9916381835938 0.355949342250824 0.8676668 0.21108929812908173 True -12 37453 31.73522424697876 2.190216064453125 542.91943359375 0.1909026801586151 548.8176879882812 0.3575259745121002 0.8707804 0.20284631848335266 True -13 40334 31.264039754867554 0.5636773109436035 441.1850280761719 0.17776036262512207 547.9735717773438 0.3579365313053131 0.8736826 0.19273827970027924 True -14 43215 31.094648122787476 0.5441217422485352 456.19696044921875 0.20488104224205017 547.2316284179688 0.3589867949485779 0.8801886 0.18353980779647827 True -15 46096 31.089937448501587 0.5490849018096924 480.9252014160156 0.1542755365371704 546.4895629882812 0.3597562909126282 0.88143945 0.17689530551433563 True -16 48977 31.42437195777893 0.5448551177978516 552.8108520507812 0.1482539027929306 545.7517700195312 0.3611326813697815 0.8836559 0.17526131868362427 True -17 51858 31.45357084274292 28.531702280044556 523.68798828125 0.135081946849823 546.5635375976562 0.3605029582977295 0.8847085 0.17447787523269653 True -18 54739 31.76684331893921 25.94244146347046 427.3482666015625 0.14111793041229248 546.2526245117188 0.36087319254875183 0.885575 0.17409950494766235 True -19 57620 31.04989218711853 0.5541646480560303 383.43798828125 0.16027116775512695 546.6695556640625 0.3600480258464813 0.8838779 0.17490191757678986 False diff --git a/ENCSR789FJF/cherimoya.fold_2.performance.tsv b/ENCSR789FJF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5333536726dfdcd1749ffd4aca7a3ddd202b3dbd..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -546.2526245117188 0.4062383770942688 0.36087316274642944 0.1430916041135788 0.885574996471405 0.8688780665397644 0.17409950494766235 \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_3.evaluate.json b/ENCSR789FJF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 37356ab82fa9a2fef6780fb4d1672eb149b982e0..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272QHJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_3.fit.json b/ENCSR789FJF/cherimoya.fold_3.fit.json deleted file mode 100644 index 4b0ab4e7b8fa647dc9e80c69f71269db9b6d8804..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF272QHJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_3.log b/ENCSR789FJF/cherimoya.fold_3.log deleted file mode 100644 index 3fd68f01c751f9fbd3b165427f2bb4fbc62fd811..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 34.76414656639099 3.8255600929260254 461.036376953125 0.3630215525627136 570.9671020507812 0.2684924304485321 0.730103 3.309077501296997 True -1 5522 30.328914642333984 0.559887170791626 515.233154296875 0.40242624282836914 529.3162231445312 0.3286300301551819 0.8029353 1.027838110923767 True -2 8283 31.070387363433838 0.5320024490356445 436.8430480957031 0.3652935326099396 522.2998046875 0.3358829915523529 0.8210064 0.4039769768714905 True -3 11044 30.473784923553467 31.881442070007324 584.7879028320312 0.20349660515785217 519.2545166015625 0.33939501643180847 0.82993954 0.3635546565055847 True -4 13805 30.52497363090515 0.5400116443634033 566.916015625 0.3375118374824524 517.1753540039062 0.34184136986732483 0.83327544 0.29792386293411255 True -5 16566 30.39451265335083 0.5320606231689453 486.40228271484375 0.304762065410614 515.1211547851562 0.3443034589290619 0.8359525 0.255880206823349 True -6 19327 30.415165185928345 0.5333836078643799 475.377685546875 0.23415601253509521 513.6998901367188 0.34681636095046997 0.8390868 0.2516437768936157 True -7 22088 30.346713304519653 0.5301315784454346 466.9263000488281 0.2553827166557312 512.5826416015625 0.34794682264328003 0.84748596 0.2628801465034485 True -8 24849 30.289174556732178 0.5248432159423828 407.2053527832031 0.2242514044046402 512.3727416992188 0.34790751338005066 0.85081553 0.2508799731731415 True -9 27610 30.30690908432007 0.5176329612731934 486.2652587890625 0.20704713463783264 510.7104187011719 0.35107025504112244 0.8547205 0.245403453707695 True -10 30371 30.369402408599854 0.5312004089355469 421.5505676269531 0.21033629775047302 510.0369873046875 0.3514512777328491 0.8547528 0.2271426022052765 True -11 33132 30.356730937957764 0.5219438076019287 483.50750732421875 0.29231131076812744 509.5827941894531 0.35130855441093445 0.8623416 0.215158611536026 True -12 35893 30.39982557296753 0.5303230285644531 425.4269714355469 0.1994936466217041 508.2020568847656 0.3539063632488251 0.8632638 0.21489226818084717 True -13 38654 30.35805916786194 0.5307149887084961 583.75439453125 0.14616289734840393 506.12823486328125 0.3569011092185974 0.87024087 0.20509342849254608 True -14 41415 30.448987007141113 0.5243403911590576 492.56939697265625 0.1846754550933838 505.8085021972656 0.3566214144229889 0.87280107 0.1966102421283722 True -15 44176 30.410728931427002 0.522897481918335 460.96624755859375 0.18309275805950165 504.5287780761719 0.35834550857543945 0.88029116 0.18732097744941711 True -16 46937 30.357136487960815 0.5311577320098877 448.202392578125 0.1661417931318283 504.42633056640625 0.3584514260292053 0.8813375 0.1812797486782074 True -17 49698 30.366520404815674 0.5350263118743896 432.5041809082031 0.16816513240337372 503.73553466796875 0.3604099452495575 0.88380015 0.17906616628170013 True -18 52459 30.41418981552124 0.5440781116485596 504.00555419921875 0.11572901904582977 504.97137451171875 0.3577151894569397 0.8842359 0.17766152322292328 True -19 55220 30.477754831314087 2.190910816192627 427.881591796875 0.20760858058929443 503.83697509765625 0.3603396415710449 0.88435924 0.1779906153678894 True diff --git a/ENCSR789FJF/cherimoya.fold_3.performance.tsv b/ENCSR789FJF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0ac5eb8fc02ff4d254211079ddfbbabc1359c481..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -503.83697509765625 0.41212472319602966 0.36033961176872253 0.13958048820495605 0.8843592405319214 0.8599306344985962 0.1779906153678894 \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_4.evaluate.json b/ENCSR789FJF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 048f141965ccc9045b5cabe2fb37dfb59cae892b..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272QHJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_4.fit.json b/ENCSR789FJF/cherimoya.fold_4.fit.json deleted file mode 100644 index 736e627f98156d5ed16ec887618379551f5c3784..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF272QHJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789FJF/cherimoya.fold_4.log b/ENCSR789FJF/cherimoya.fold_4.log deleted file mode 100644 index 260507c340b74140de05bd4d476b4eae496a59ab..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2813 36.8656120300293 3.659106731414795 522.4383544921875 0.41633856296539307 552.4114379882812 0.26119908690452576 0.73489684 3.2963321208953857 True -1 5626 30.979607105255127 0.6082980632781982 483.43890380859375 0.28546273708343506 518.4677734375 0.3157351016998291 0.7911044 0.8541746139526367 True -2 8439 31.091890335083008 0.5841007232666016 411.220947265625 0.38612282276153564 510.6568603515625 0.3247571587562561 0.81036574 0.4107345640659332 True -3 11252 31.09735655784607 3.396359443664551 466.7290954589844 0.22689297795295715 507.095458984375 0.33005785942077637 0.8189519 0.3028472065925598 True -4 14065 30.982551336288452 0.577500581741333 482.61431884765625 0.29175058007240295 504.69329833984375 0.33280569314956665 0.8296075 0.23854279518127441 True -5 16878 30.978670358657837 0.5900144577026367 362.4544982910156 0.3710673749446869 502.3316955566406 0.33629101514816284 0.8357987 0.22593876719474792 True -6 19691 30.945825338363647 0.5715305805206299 503.8811950683594 0.24100416898727417 501.50140380859375 0.3374914526939392 0.8401555 0.21906884014606476 True -7 22504 31.03747320175171 0.5798802375793457 466.30303955078125 0.2542968988418579 500.6685485839844 0.3384449779987335 0.84720564 0.20355236530303955 True -8 25317 30.965657472610474 0.575829029083252 425.74298095703125 0.22672171890735626 499.4556884765625 0.3409051299095154 0.84733224 0.2038804441690445 True -9 28130 30.905516624450684 0.5697059631347656 473.9441223144531 0.15554428100585938 498.69000244140625 0.34195929765701294 0.8502721 0.19308051466941833 True -10 30943 30.96762490272522 0.5825223922729492 476.8408508300781 0.2947064936161041 497.5260925292969 0.34364983439445496 0.85863006 0.18365393579006195 True -11 33756 30.942902088165283 0.5679826736450195 465.9093017578125 0.14820949733257294 497.61810302734375 0.34267982840538025 0.8621721 0.1761326938867569 True -12 36569 30.97801637649536 0.5676534175872803 406.93341064453125 0.28339093923568726 497.3089294433594 0.3431941568851471 0.8690953 0.17154009640216827 True -13 39382 30.932058572769165 0.5794105529785156 480.3098449707031 0.1449749767780304 495.5239562988281 0.3468816876411438 0.8733869 0.16735123097896576 True -14 42195 30.912946939468384 0.564316987991333 451.8240966796875 0.13952086865901947 495.04827880859375 0.34770628809928894 0.8768238 0.16226260364055634 True -15 45008 30.936814308166504 2.581144332885742 421.39581298828125 0.16897588968276978 494.13787841796875 0.3492231070995331 0.8787678 0.1579897254705429 True -16 47821 30.92312741279602 0.5733733177185059 447.26641845703125 0.32738977670669556 494.3984375 0.34830397367477417 0.8829735 0.15583336353302002 True -17 50634 30.952759742736816 0.5797667503356934 575.9766845703125 0.16471615433692932 494.1830749511719 0.34940090775489807 0.8840925 0.1546582281589508 True -18 53447 30.912559509277344 0.571253776550293 455.35888671875 0.19867286086082458 494.6928405761719 0.348382830619812 0.8852122 0.15468375384807587 True -19 56260 30.95079803466797 0.5797379016876221 428.414794921875 0.1210072785615921 494.29248046875 0.3495858609676361 0.8829725 0.15573404729366302 False diff --git a/ENCSR789FJF/cherimoya.fold_4.performance.tsv b/ENCSR789FJF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6124bf6572d975d064cf04cb9e5d955fc7d25857..0000000000000000000000000000000000000000 --- a/ENCSR789FJF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -494.6928405761719 0.41885313391685486 0.348382830619812 0.1300492137670517 0.8852121829986572 0.8585048913955688 0.15468375384807587 \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_0.evaluate.json b/ENCSR789VGQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8b0ed1d4d19472a90f8f454c2e4dcf224aa56d0d..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF014JPQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_0.fit.json b/ENCSR789VGQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 3a56d97241ae99cd7e924967d988252baa03ced3..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF014JPQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_0.log b/ENCSR789VGQ/cherimoya.fold_0.log deleted file mode 100644 index c3e79e30c3d7a1c338755dc4f2c87543ce8c2f6c..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2680 34.15476179122925 4.410798788070679 759.2417602539062 0.747604250907898 1255.795654296875 0.2816925048828125 0.437064 10.477054595947266 True -1 5360 29.89207887649536 0.6541118621826172 635.032958984375 0.7532845735549927 994.2749633789062 0.4951436519622803 0.47386762 4.8029584884643555 True -2 8040 29.907087087631226 2.1547908782958984 757.756591796875 0.9731562733650208 971.547607421875 0.5084486603736877 0.48767287 2.836308240890503 True -3 10720 29.910756587982178 0.5914726257324219 647.282470703125 0.9861257672309875 957.0811157226562 0.518133282661438 0.51713 2.2649126052856445 True -4 13400 29.92750835418701 0.5819857120513916 767.336181640625 0.7922406196594238 947.28955078125 0.5260284543037415 0.51997066 1.9860336780548096 True -5 16080 29.876484632492065 0.5789825916290283 725.1956787109375 0.8960645794868469 938.2546997070312 0.5348778963088989 0.53729564 1.6796398162841797 True -6 18760 30.25248122215271 32.678810834884644 674.19775390625 0.7165064811706543 934.0628662109375 0.5368861556053162 0.547682 1.4798061847686768 True -7 21440 29.84552812576294 0.5976467132568359 680.0006103515625 0.7215299606323242 926.7159423828125 0.540786862373352 0.56309515 1.3014920949935913 True -8 24120 30.37229609489441 1.2291035652160645 645.0236206054688 0.5834628343582153 922.5918579101562 0.543716311454773 0.5728379 1.1959242820739746 True -9 26800 29.421933889389038 32.42596960067749 781.9302978515625 0.8390573263168335 916.4576416015625 0.5487385392189026 0.5862071 1.1025161743164062 True -10 29480 29.633984565734863 0.5837559700012207 765.8626708984375 0.6696825623512268 910.3353881835938 0.5528993606567383 0.5955801 1.0262035131454468 True -11 32160 29.394006967544556 1.067755937576294 635.4468383789062 0.6128032207489014 904.43701171875 0.5569027662277222 0.6053864 0.9726834297180176 True -12 34840 29.3652286529541 0.5830669403076172 678.3072509765625 0.5424786806106567 901.025146484375 0.5580017566680908 0.62326026 0.8819115161895752 True -13 37520 29.27231478691101 0.5653214454650879 753.9134521484375 0.8433413505554199 894.4779663085938 0.5634027123451233 0.6401567 0.8178622722625732 True -14 40200 29.287920713424683 0.5725255012512207 627.0064086914062 0.5777177214622498 889.0794067382812 0.5669040083885193 0.6571699 0.7397912740707397 True -15 42880 29.252673149108887 0.5638368129730225 594.8897705078125 0.538237988948822 885.9265747070312 0.5699790716171265 0.6671855 0.6958881616592407 True -16 45560 29.342531204223633 0.5658643245697021 672.8453369140625 0.4638568162918091 885.53173828125 0.5692386627197266 0.67653316 0.6472412943840027 True -17 48240 29.346891164779663 17.826586723327637 679.2869873046875 0.6020565629005432 882.7891845703125 0.5712751746177673 0.6814787 0.6200291514396667 True -18 50920 29.473419904708862 3.263742208480835 628.07568359375 0.3205370604991913 886.0407104492188 0.567664384841919 0.6853861 0.5995545983314514 True -19 53600 29.524381637573242 0.5902144908905029 795.0449829101562 0.5386230945587158 887.6016845703125 0.5665518045425415 0.6841865 0.5990369319915771 False diff --git a/ENCSR789VGQ/cherimoya.fold_0.performance.tsv b/ENCSR789VGQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2b8cce5c15f22c057b6f492f5a2a6f78d3f2eea1..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -886.0407104492188 0.27306875586509705 0.5676644444465637 0.263263076543808 0.6853861212730408 0.6594923734664917 0.5995545983314514 \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_1.evaluate.json b/ENCSR789VGQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a3b2fcb98197464164a918cb6835b5f4f5462147..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF014JPQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_1.fit.json b/ENCSR789VGQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 8daba9a992241d411eb25e04a67d3a7d650f686a..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF014JPQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_1.log b/ENCSR789VGQ/cherimoya.fold_1.log deleted file mode 100644 index 2e81673a9c2b73b01df583c8665cff730151630d..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 35.101218700408936 3.7870774269104004 658.38818359375 1.5043718814849854 1335.4559326171875 0.28819164633750916 0.49357602 11.78978443145752 True -1 5466 30.462297916412354 0.6536118984222412 703.6307373046875 0.8904008865356445 1064.58349609375 0.5004658699035645 0.48864183 4.001867771148682 False -2 8199 30.41303062438965 0.6555600166320801 735.02783203125 1.2907581329345703 1042.168701171875 0.51313316822052 0.5002197 2.024519681930542 True -3 10932 30.407681703567505 11.29959750175476 772.4332885742188 0.8328132033348083 1024.3321533203125 0.5248932242393494 0.5309248 1.4688518047332764 True -4 13665 31.78041911125183 1.1446483135223389 661.1448974609375 0.6711172461509705 1017.7816772460938 0.5277276039123535 0.5529286 1.3130865097045898 True -5 16398 30.512029886245728 0.686349630355835 752.083984375 0.9503336548805237 1006.378662109375 0.5341810584068298 0.56558603 1.2007460594177246 True -6 19131 30.56098771095276 0.6984891891479492 661.6640625 0.7551177740097046 995.6105346679688 0.5446992516517639 0.57144237 1.1163054704666138 True -7 21864 30.567239999771118 0.6805202960968018 759.543701171875 0.8974115252494812 995.5189208984375 0.5419819951057434 0.58868665 1.053154468536377 True -8 24597 30.715501070022583 0.6742517948150635 780.5999755859375 0.5114556550979614 985.2102661132812 0.549648106098175 0.5948073 1.013441801071167 True -9 27330 30.51811170578003 1.8593859672546387 693.3451538085938 0.5952128767967224 977.0170288085938 0.5545560121536255 0.6169015 0.9380288124084473 True -10 30063 30.04816508293152 0.6638309955596924 616.3592529296875 0.9786906838417053 973.85302734375 0.5560872554779053 0.6209197 0.9117529392242432 True -11 32796 30.077884674072266 0.6651864051818848 656.0413208007812 0.6189179420471191 969.790771484375 0.5585299134254456 0.6356857 0.8648450374603271 True -12 35529 30.040615797042847 0.6672344207763672 643.158935546875 0.6278524994850159 961.5492553710938 0.5643540024757385 0.6570207 0.7899455428123474 True -13 38262 30.06285834312439 0.6620213985443115 683.897705078125 0.6628532409667969 957.1121215820312 0.5655580759048462 0.6759391 0.709979772567749 True -14 40995 30.011759519577026 0.6655311584472656 755.029541015625 0.48094475269317627 953.5716552734375 0.566760778427124 0.68845403 0.6746770143508911 True -15 43728 30.000938653945923 0.6623084545135498 632.87060546875 0.666350245475769 947.7766723632812 0.5709774494171143 0.70377 0.6381807327270508 True -16 46461 29.971594095230103 2.5408241748809814 787.8321533203125 0.5984435677528381 945.6655883789062 0.5732271075248718 0.7106552 0.5984192490577698 True -17 49194 30.025578022003174 33.14555859565735 540.8253173828125 0.3358752131462097 945.0081787109375 0.5737607479095459 0.7174356 0.5669678449630737 True -18 51927 30.66966438293457 1.9534237384796143 645.61083984375 0.3633807301521301 945.5259399414062 0.573167085647583 0.71810585 0.562274694442749 True -19 54660 30.0325665473938 2.027918577194214 615.250244140625 0.34639978408813477 943.1795043945312 0.5756734013557434 0.71928793 0.5592474341392517 True diff --git a/ENCSR789VGQ/cherimoya.fold_1.performance.tsv b/ENCSR789VGQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4007d52739b94b2611c5e51e97b7f7bb0b01a4e9..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -943.1795043945312 0.26528844237327576 0.5756734609603882 0.2795279622077942 0.7192879319190979 0.7006539106369019 0.5592474341392517 \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_2.evaluate.json b/ENCSR789VGQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 003f2777f11f9d787f6170d94db4fedda6f3482d..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF014JPQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_2.fit.json b/ENCSR789VGQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 09faa8d34c545ba447f7ce7731e92da626aacb2a..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF014JPQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_2.log b/ENCSR789VGQ/cherimoya.fold_2.log deleted file mode 100644 index b187cef4f05ad0772fdf9bcd1f67bb90ed3e6b68..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2898 36.83804965019226 16.61873483657837 777.4405517578125 0.8511868715286255 1217.5823974609375 0.29015347361564636 0.473908 8.62801456451416 True -1 5796 32.579063415527344 0.5093848705291748 892.31103515625 0.8073137402534485 970.92333984375 0.500430703163147 0.44138837 3.8106606006622314 False -2 8694 32.26670169830322 0.49184393882751465 633.797119140625 1.0218286514282227 953.8526000976562 0.5082283616065979 0.49587646 1.935604214668274 True -3 11592 32.429927825927734 1.1467750072479248 766.9759521484375 0.7100352048873901 941.7042236328125 0.5195128321647644 0.51378596 1.6105175018310547 True -4 14490 32.301865100860596 1.4142096042633057 736.10400390625 0.6197812557220459 929.6390991210938 0.5245980620384216 0.54650617 1.3844562768936157 True -5 17388 32.29500150680542 0.49554872512817383 590.5997314453125 0.7038668990135193 920.5365600585938 0.5328943729400635 0.57011455 1.0895174741744995 True -6 20286 32.33610153198242 29.973123788833618 919.8822631835938 1.4290294647216797 911.3033447265625 0.5404641032218933 0.5751447 0.9869725108146667 True -7 23184 32.518171310424805 0.502568244934082 851.0819702148438 0.8148408532142639 906.17138671875 0.5423542857170105 0.58977693 0.8866974115371704 True -8 26082 32.31339478492737 0.4913935661315918 806.2532958984375 0.6824090480804443 902.764892578125 0.544151246547699 0.60580754 0.828647255897522 True -9 28980 32.26593232154846 15.085670948028564 653.8949584960938 0.8117868900299072 896.21435546875 0.5499542355537415 0.6112499 0.8044971823692322 True -10 31878 32.51582956314087 0.492520809173584 632.1529541015625 0.6336761116981506 890.4376831054688 0.5539297461509705 0.62034124 0.7707942128181458 True -11 34776 32.25246548652649 0.49049925804138184 753.9984130859375 0.8318519592285156 887.145751953125 0.5555927157402039 0.63458997 0.731971800327301 True -12 37674 32.11490774154663 0.4883251190185547 617.9634399414062 0.8074138760566711 882.7710571289062 0.5585169196128845 0.64538807 0.6794928312301636 True -13 40572 31.61602234840393 0.48575568199157715 581.3155517578125 0.5259864926338196 878.8438110351562 0.560552179813385 0.6617997 0.6389541029930115 True -14 43470 31.605085849761963 1.8039929866790771 595.00048828125 0.4777759313583374 874.645263671875 0.563509464263916 0.67444175 0.6118695735931396 True -15 46368 31.707403659820557 0.485156774520874 683.8807373046875 0.45666712522506714 871.257568359375 0.5647394061088562 0.686572 0.5818541049957275 True -16 49266 31.646939516067505 0.4875152111053467 646.66162109375 0.6931000351905823 867.732421875 0.5687660574913025 0.7005933 0.5465649962425232 True -17 52164 31.615985870361328 0.4831526279449463 588.7993774414062 0.33441483974456787 867.4295654296875 0.5690573453903198 0.7066139 0.5334610939025879 True -18 55062 31.665587902069092 0.48546266555786133 596.6552734375 0.4066941440105438 868.3897705078125 0.5675513744354248 0.7096491 0.5275195837020874 True -19 57960 31.61488676071167 0.4907238483428955 546.126708984375 0.402948796749115 866.7119750976562 0.5698306560516357 0.70882344 0.5319083333015442 False diff --git a/ENCSR789VGQ/cherimoya.fold_2.performance.tsv b/ENCSR789VGQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7993cbcd81939fdf7f1437a1aa7390289dd141e7..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -868.3897705078125 0.27473416924476624 0.5675513744354248 0.2648318409919739 0.7096490859985352 0.681645929813385 0.5275195837020874 \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_3.evaluate.json b/ENCSR789VGQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2842b6ec53b30c93a6504b58181536f80262a6c1..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF014JPQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_3.fit.json b/ENCSR789VGQ/cherimoya.fold_3.fit.json deleted file mode 100644 index c9314859612f368e7b609af87c39fe21d2bdb792..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF014JPQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_3.log b/ENCSR789VGQ/cherimoya.fold_3.log deleted file mode 100644 index 446b40d73a15f5090425d66388e4e30fb62c233f..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 35.394126653671265 4.314990043640137 678.305908203125 0.7849165797233582 1229.35546875 0.2847878038883209 0.48690933 10.224684715270996 True -1 5564 31.032937049865723 0.5883622169494629 679.2194213867188 0.9046989679336548 984.4848022460938 0.4955853819847107 0.4763651 4.243526458740234 False -2 8346 30.996726274490356 2.068263292312622 740.6024169921875 0.7726367712020874 964.9807739257812 0.5094168782234192 0.44814223 2.4888551235198975 False -3 11128 31.03919553756714 0.5537207126617432 757.6429443359375 0.9369491338729858 956.693115234375 0.5151497721672058 0.4882313 2.1137442588806152 True -4 13910 31.116368293762207 0.5741746425628662 665.0206298828125 0.7810204029083252 949.3333129882812 0.5203188061714172 0.51200974 1.9034396409988403 True -5 16692 30.951035261154175 0.5531585216522217 844.2430419921875 1.196227788925171 940.20947265625 0.5281879901885986 0.5217463 1.6428077220916748 True -6 19474 31.2289981842041 33.52505803108215 783.120849609375 0.9735965728759766 935.49755859375 0.5301358699798584 0.55571294 1.3795884847640991 True -7 22256 32.631332874298096 0.5546622276306152 787.3753662109375 0.5862908959388733 925.5089721679688 0.5381412506103516 0.56752133 1.3176506757736206 True -8 25038 31.382931232452393 0.5654904842376709 756.47119140625 0.8752388954162598 919.2649536132812 0.5408487319946289 0.5939935 1.1136971712112427 True -9 27820 32.963242292404175 25.444989681243896 769.8770141601562 0.7800287008285522 912.97265625 0.5453270077705383 0.6112695 1.013428807258606 True -10 30602 31.205276250839233 3.3374807834625244 783.8674926757812 0.8754600286483765 908.5415649414062 0.5489614009857178 0.6173237 0.9384639859199524 True -11 33384 31.1536283493042 14.515893459320068 808.8988647460938 0.6631353497505188 901.6478271484375 0.5543655753135681 0.63817436 0.8752278089523315 True -12 36166 30.414064168930054 26.766427993774414 835.6201171875 0.6080568432807922 896.14501953125 0.5563309192657471 0.65867025 0.7789235711097717 True -13 38948 31.956555366516113 0.5623040199279785 812.4419555664062 0.7908586263656616 891.765869140625 0.558587908744812 0.6795972 0.7010323405265808 True -14 41730 32.111746311187744 19.885676622390747 607.3614501953125 0.7614955902099609 887.2431030273438 0.5613692402839661 0.6943818 0.6405325531959534 True -15 44512 30.48406147956848 1.5983951091766357 607.4676513671875 0.566430926322937 881.1953735351562 0.5676847696304321 0.7087698 0.584162712097168 True -16 47294 30.528529167175293 14.255049705505371 671.214111328125 0.4098685085773468 879.9869384765625 0.5676703453063965 0.720277 0.5380863547325134 True -17 50076 30.33392024040222 0.5580899715423584 666.4479370117188 0.527915358543396 880.2066650390625 0.5673041343688965 0.7281264 0.5178496837615967 True -18 52858 30.434393882751465 0.5441205501556396 725.1265869140625 0.4749525785446167 881.3400268554688 0.5652265548706055 0.7273935 0.5068987607955933 False -19 55640 30.392903327941895 0.5538671016693115 742.9251708984375 0.418374240398407 880.8214721679688 0.5662819743156433 0.7276049 0.5062304735183716 False diff --git a/ENCSR789VGQ/cherimoya.fold_3.performance.tsv b/ENCSR789VGQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d512df602167049956665506ef71e99ce455e206..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -880.2066650390625 0.27326440811157227 0.5673041343688965 0.26361382007598877 0.7281264066696167 0.7031807899475098 0.5178496837615967 \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_4.evaluate.json b/ENCSR789VGQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 15203645da613bafe2120d106fa9243cc78c2afd..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF014JPQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_4.fit.json b/ENCSR789VGQ/cherimoya.fold_4.fit.json deleted file mode 100644 index bbb5d48170a8d91d59b516eecf029c10a96d930a..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF014JPQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR789VGQ/cherimoya.fold_4.log b/ENCSR789VGQ/cherimoya.fold_4.log deleted file mode 100644 index 561e8385abee7ce7d6d4bef90aa267e0f00adf07..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2867 36.38438057899475 40.44568085670471 681.0792236328125 0.8923799991607666 1165.8309326171875 0.28865304589271545 0.46276817 8.136548042297363 True -1 5734 32.12593173980713 0.5919144153594971 775.1903076171875 0.8679147958755493 924.7193603515625 0.4970185160636902 0.4848006 4.11462926864624 True -2 8601 32.37884306907654 1.3330132961273193 652.0062866210938 1.598717212677002 906.046875 0.5099027752876282 0.50451493 1.9539413452148438 True -3 11468 32.52528619766235 28.20918321609497 849.1151733398438 1.1380112171173096 891.6226196289062 0.5226996541023254 0.52877015 1.54926598072052 True -4 14335 32.09854316711426 2.769641876220703 808.1097412109375 0.8966648578643799 888.0254516601562 0.5268294811248779 0.5202936 1.4155075550079346 False -5 17202 32.036784172058105 1.6404485702514648 613.044921875 0.8188798427581787 883.7116088867188 0.5300325155258179 0.53673524 1.3432894945144653 True -6 20069 32.36457180976868 0.5353105068206787 770.5016479492188 0.7051621079444885 872.7779541015625 0.5368807911872864 0.5493993 1.0470763444900513 True -7 22936 32.56135606765747 21.143065214157104 703.4652099609375 0.7577571868896484 869.1735229492188 0.5398677587509155 0.56052333 0.9872732162475586 True -8 25803 31.95334768295288 0.5378000736236572 694.534423828125 0.575294017791748 863.7012329101562 0.5435715317726135 0.5795116 0.8780966997146606 True -9 28670 31.323174715042114 2.9111568927764893 851.393798828125 0.7620959281921387 859.5650634765625 0.5467846989631653 0.59210384 0.8275555968284607 True -10 31537 31.370700359344482 0.5311648845672607 892.0521850585938 0.832036018371582 853.8060302734375 0.5507177114486694 0.6046981 0.7742825150489807 True -11 34404 31.33768630027771 0.5387122631072998 848.0309448242188 0.635424017906189 848.7092895507812 0.5557510852813721 0.62628657 0.7201231718063354 True -12 37271 31.368012189865112 0.5259702205657959 757.4898681640625 0.5152930617332458 846.296630859375 0.5567201972007751 0.64344114 0.6662665605545044 True -13 40138 31.328362464904785 0.54638671875 680.41845703125 0.5465052723884583 839.451904296875 0.5636781454086304 0.66094327 0.6157429814338684 True -14 43005 31.328943014144897 1.3675856590270996 740.8818969726562 0.4663701057434082 837.5499877929688 0.5635932087898254 0.6780132 0.5732364654541016 True -15 45872 31.323756456375122 0.5333583354949951 725.5595092773438 0.4919123947620392 834.5667724609375 0.5662609934806824 0.69129825 0.5416057705879211 True -16 48739 32.15538811683655 16.138545036315918 744.898681640625 0.41957539319992065 835.5447998046875 0.5627413392066956 0.7019768 0.5209987163543701 True -17 51606 31.328104496002197 0.5475916862487793 839.85009765625 0.24918563663959503 832.9065551757812 0.5669533610343933 0.7054791 0.5122633576393127 True -18 54473 31.42005228996277 0.9092452526092529 469.9015808105469 0.3582003116607666 835.4488525390625 0.5637177228927612 0.70831704 0.5083804726600647 True -19 57340 31.272441148757935 0.54034423828125 664.9346923828125 0.32139527797698975 833.4041748046875 0.5669103264808655 0.7079414 0.5111379623413086 False diff --git a/ENCSR789VGQ/cherimoya.fold_4.performance.tsv b/ENCSR789VGQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 052f35fb83b6a63645c599091cf206435ef48d45..0000000000000000000000000000000000000000 --- a/ENCSR789VGQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -835.4488525390625 0.2787596881389618 0.563717782497406 0.2548742890357971 0.7083170413970947 0.6768640279769897 0.5083804726600647 \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_0.evaluate.json b/ENCSR792QQE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a215884fa2c6a7fe7302db922311bb5a01f59e4a..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XQF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_0.fit.json b/ENCSR792QQE/cherimoya.fold_0.fit.json deleted file mode 100644 index ae6806eedb70bf1e384e0900f1c520add6dd7130..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF845XQF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_0.log b/ENCSR792QQE/cherimoya.fold_0.log deleted file mode 100644 index 334b0ec13543a02dc55aa5e67eefa3fe68cf180b..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2719 34.42365789413452 3.912822961807251 708.8160400390625 0.3627476394176483 819.5986938476562 0.28043216466903687 0.7149243 4.860452175140381 True -1 5438 29.945892333984375 1.573441743850708 653.6468505859375 0.47542518377304077 739.229248046875 0.36520159244537354 0.7755709 1.5166935920715332 True -2 8157 29.93447208404541 0.5730562210083008 794.817138671875 0.3444613218307495 726.1058959960938 0.3770442306995392 0.7883986 0.6298288702964783 True -3 10876 29.8557710647583 0.5727376937866211 740.924072265625 0.4314071536064148 719.1167602539062 0.3834846019744873 0.7942416 0.6452911496162415 True -4 13595 29.879260063171387 0.5680661201477051 664.3634643554688 0.5237674713134766 716.3499145507812 0.38822558522224426 0.7979691 0.5237627029418945 True -5 16314 29.858927011489868 14.821585416793823 664.240478515625 0.25941792130470276 712.8392944335938 0.3921380639076233 0.8005676 0.4635259807109833 True -6 19033 29.886518001556396 3.1044087409973145 638.0003051757812 0.33092495799064636 711.071044921875 0.3951040506362915 0.8016088 0.4289323389530182 True -7 21752 29.89510941505432 3.187668561935425 657.17626953125 0.3058420717716217 708.6131591796875 0.39721184968948364 0.80828816 0.39917317032814026 True -8 24471 29.884846448898315 9.891605138778687 630.5780639648438 0.3298816680908203 707.221923828125 0.399013876914978 0.808287 0.3661685585975647 False -9 27190 29.939205408096313 2.573439359664917 690.8361206054688 0.2883985638618469 704.6622924804688 0.4011414051055908 0.8173049 0.3354227542877197 True -10 29909 29.901345252990723 7.314697027206421 557.0233154296875 0.393877774477005 703.3048095703125 0.40188372135162354 0.82457733 0.32087740302085876 True -11 32628 29.858525276184082 22.64049792289734 568.2464599609375 0.313556045293808 701.963623046875 0.40315601229667664 0.826401 0.29342466592788696 True -12 35347 31.21247363090515 0.592693567276001 629.5020141601562 0.33372461795806885 698.3666381835938 0.4071504771709442 0.83265096 0.2854602038860321 True -13 38066 29.982807636260986 1.3324437141418457 627.8021850585938 0.32285237312316895 696.5973510742188 0.40872958302497864 0.83876354 0.2692493796348572 True -14 40785 29.90472650527954 0.5817000865936279 581.6256103515625 0.2358890324831009 695.561279296875 0.4099162518978119 0.84222156 0.2578606903553009 True -15 43504 29.843483448028564 0.5675435066223145 515.0745849609375 0.27623188495635986 693.6481323242188 0.4120335280895233 0.8481308 0.24378731846809387 True -16 46223 29.870217084884644 0.5766332149505615 763.9284057617188 0.24417266249656677 693.02001953125 0.4130946099758148 0.85176617 0.23492281138896942 True -17 48942 29.89246916770935 0.5738711357116699 605.1737060546875 0.29908159375190735 693.1193237304688 0.41216960549354553 0.8515423 0.23096200823783875 False -18 51661 29.891056299209595 0.575455904006958 573.451171875 0.13917580246925354 693.7125244140625 0.41130301356315613 0.8525888 0.23071978986263275 True -19 54380 29.887101411819458 0.5766201019287109 685.0504760742188 0.1756691187620163 694.169189453125 0.41036462783813477 0.85032266 0.2316245585680008 False diff --git a/ENCSR792QQE/cherimoya.fold_0.performance.tsv b/ENCSR792QQE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 223500c317447f36bcb618d10af51576aa070a15..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -693.7125244140625 0.3663221597671509 0.4113030433654785 0.17563258111476898 0.8525887727737427 0.8032981753349304 0.23071978986263275 \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_1.evaluate.json b/ENCSR792QQE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 062c25f06db5b548e98aab6768367afaa70626d9..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XQF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_1.fit.json b/ENCSR792QQE/cherimoya.fold_1.fit.json deleted file mode 100644 index e46f429ee7f17918f08b462b30d34643a2e5e4c0..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF845XQF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_1.log b/ENCSR792QQE/cherimoya.fold_1.log deleted file mode 100644 index 24b52f5641b31f89c13c508e3d9e569370aa78ba..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2701 34.39221954345703 3.7563507556915283 635.0235595703125 0.42865321040153503 980.8201904296875 0.2834450304508209 0.7139885 6.31559419631958 True -1 5402 29.78469204902649 0.7134420871734619 544.18408203125 0.4465067684650421 876.2680053710938 0.37929630279541016 0.780882 1.7629179954528809 True -2 8103 29.707626581192017 11.330647230148315 528.5577392578125 0.3010897636413574 852.570556640625 0.39706435799598694 0.7937329 0.7383751273155212 True -3 10804 29.659634828567505 0.705385684967041 704.7802124023438 0.3782275319099426 843.1255493164062 0.4053249657154083 0.80239606 0.6122851967811584 True -4 13505 31.44585633277893 0.7141814231872559 714.46435546875 0.3315240740776062 837.8251953125 0.4109475910663605 0.8079377 0.6789987683296204 True -5 16206 30.221230030059814 27.134807109832764 592.9672241210938 0.392459899187088 834.0028686523438 0.4136051833629608 0.812348 0.4938207268714905 True -6 18907 29.758755207061768 29.435211896896362 581.0125732421875 0.3543091416358948 831.5671997070312 0.41541585326194763 0.813717 0.4655572175979614 True -7 21608 30.05257487297058 0.7055513858795166 608.9432373046875 0.23570583760738373 829.4785766601562 0.416766881942749 0.8158851 0.5016844868659973 True -8 24309 29.74494957923889 0.7268040180206299 704.131591796875 0.29549089074134827 823.796875 0.421867311000824 0.8235878 0.39655712246894836 True -9 27010 29.78518295288086 0.6983404159545898 572.7138671875 0.34273555874824524 821.0134887695312 0.42545732855796814 0.8258777 0.38564085960388184 True -10 29711 29.73891544342041 0.7030577659606934 642.182861328125 0.36528247594833374 818.7266845703125 0.4267491400241852 0.8323136 0.3714004456996918 True -11 32412 29.719402313232422 0.710627555847168 572.307861328125 0.19900499284267426 815.802001953125 0.428631067276001 0.8394768 0.34189531207084656 True -12 35113 29.805200338363647 0.697882890701294 567.7200927734375 0.265977144241333 813.3312377929688 0.4305420219898224 0.84436506 0.33902233839035034 True -13 37814 29.735716104507446 0.7091724872589111 617.947265625 0.3216897249221802 810.0398559570312 0.4340837299823761 0.84811205 0.3122008442878723 True -14 40515 29.701151609420776 0.7014651298522949 596.234375 0.3467653691768646 808.2310791015625 0.4355510175228119 0.8531765 0.2941223978996277 True -15 43216 29.677801847457886 0.7100574970245361 602.383544921875 0.24752749502658844 805.8110961914062 0.43767255544662476 0.8588346 0.2749393582344055 True -16 45917 29.74623680114746 0.7322001457214355 645.1766357421875 0.15662360191345215 805.163818359375 0.4382724463939667 0.8607035 0.26377055048942566 True -17 48618 29.83970308303833 0.7313597202301025 538.2107543945312 0.21964989602565765 804.9490356445312 0.43800297379493713 0.8630625 0.25861838459968567 True -18 51319 29.895620584487915 18.0090172290802 516.9502563476562 0.17174993455410004 803.482666015625 0.4406658113002777 0.862712 0.25665634870529175 False -19 54020 29.697192192077637 39.57570028305054 593.7413330078125 0.3462536633014679 805.6744384765625 0.43745890259742737 0.8615411 0.2587825357913971 False diff --git a/ENCSR792QQE/cherimoya.fold_1.performance.tsv b/ENCSR792QQE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 014182c222e383ba92d1f18983ede81f5d09cca4..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -804.9490356445312 0.3426073491573334 0.4380030333995819 0.20264244079589844 0.8630625009536743 0.8361552953720093 0.25861838459968567 \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_2.evaluate.json b/ENCSR792QQE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 383c165dd3111adc5fd4d575a74c52d00d971c22..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XQF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_2.fit.json b/ENCSR792QQE/cherimoya.fold_2.fit.json deleted file mode 100644 index 800a10d75a7e539d2cbc8adc712be2f0afd7f175..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF845XQF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_2.log b/ENCSR792QQE/cherimoya.fold_2.log deleted file mode 100644 index 0cd9bca2bb227b260721d70e2ef730e1c257206e..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 45.34132647514343 47.947203636169434 648.1583251953125 0.4980286657810211 853.1860961914062 0.28521743416786194 0.7155709 4.218364715576172 True -1 5776 31.936219692230225 0.6032342910766602 570.251708984375 0.4870753884315491 770.7481689453125 0.3697319030761719 0.7788357 1.2440810203552246 True -2 8664 33.0936496257782 0.5810401439666748 563.1449584960938 0.3543574810028076 755.7807006835938 0.3817167282104492 0.7865328 0.5292279720306396 True -3 11552 32.188257932662964 0.5740740299224854 599.89599609375 0.37510353326797485 749.0584106445312 0.3869761824607849 0.7927052 0.5150051116943359 True -4 14440 32.29148864746094 0.5751135349273682 589.9495849609375 0.3787941336631775 746.8517456054688 0.3891655206680298 0.7987182 0.48878446221351624 True -5 17328 32.250914335250854 0.5762600898742676 584.9510498046875 0.4857291281223297 741.1849365234375 0.39598169922828674 0.8006979 0.4529894292354584 True -6 20216 33.76979422569275 0.5761888027191162 603.8385009765625 0.3977431058883667 740.616455078125 0.39547035098075867 0.80506027 0.45552003383636475 True -7 23104 32.09439778327942 0.9963688850402832 641.35546875 0.28445130586624146 738.0029907226562 0.39876630902290344 0.8078095 0.4313359260559082 True -8 25992 32.10037159919739 0.5940878391265869 514.2266845703125 0.29065683484077454 736.1395263671875 0.4004010558128357 0.8097207 0.4138258099555969 True -9 28880 32.06291222572327 0.5847935676574707 592.096923828125 0.3371516466140747 734.70703125 0.40196022391319275 0.8130044 0.39984312653541565 True -10 31768 32.0968062877655 0.5791902542114258 542.6395263671875 0.242030531167984 731.6019897460938 0.4045456647872925 0.8163776 0.37449800968170166 True -11 34656 32.13250160217285 0.5766427516937256 587.36962890625 0.35238826274871826 729.842529296875 0.40703901648521423 0.82229114 0.37329724431037903 True -12 37544 32.140114307403564 0.576239824295044 603.15234375 0.25612974166870117 726.6940307617188 0.41067662835121155 0.82536817 0.3419712483882904 True -13 40432 32.166181564331055 0.57608962059021 638.108154296875 0.3524729311466217 725.3330078125 0.410635381937027 0.83144987 0.30815884470939636 True -14 43320 32.79448103904724 0.57889723777771 613.3779907226562 0.34028369188308716 723.7244262695312 0.4125042259693146 0.83902484 0.28653544187545776 True -15 46208 32.90083336830139 0.578528881072998 685.1207275390625 0.2861671447753906 722.6646118164062 0.4134564697742462 0.8403263 0.27016159892082214 True -16 49096 32.23012328147888 0.5709240436553955 564.8235473632812 0.20302104949951172 722.7181396484375 0.4135390818119049 0.84395677 0.2571048438549042 True -17 51984 32.2558970451355 0.5701344013214111 534.4931640625 0.20643819868564606 720.7147216796875 0.4165305495262146 0.8458579 0.2500685751438141 True -18 54872 32.4802405834198 28.372394800186157 604.322998046875 0.21672013401985168 721.3895874023438 0.41519489884376526 0.84671926 0.24820652604103088 True -19 57760 31.932324171066284 0.9122631549835205 635.8057861328125 0.20268598198890686 724.0667114257812 0.4109659194946289 0.84530455 0.2491065263748169 False diff --git a/ENCSR792QQE/cherimoya.fold_2.performance.tsv b/ENCSR792QQE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4b2dab187ef4e4306e921d6806b902c9f1ca36c8..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -721.3895874023438 0.3618161380290985 0.41519489884376526 0.17757545411586761 0.8467192649841309 0.8077860474586487 0.24820652604103088 \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_3.evaluate.json b/ENCSR792QQE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f66234de11a4eec42e14860e33b80278c80700c1..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XQF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_3.fit.json b/ENCSR792QQE/cherimoya.fold_3.fit.json deleted file mode 100644 index 8f4ec6355b0e82e7deba15293f8a4214585527a4..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF845XQF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_3.log b/ENCSR792QQE/cherimoya.fold_3.log deleted file mode 100644 index 86a03e5eba2a9646933238d0fcad5de775acd2e8..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 35.03127980232239 3.8101966381073 733.0948486328125 0.4447965621948242 805.2024536132812 0.2851449251174927 0.7108709 5.81965970993042 True -1 5494 30.731804847717285 0.5914731025695801 736.6414794921875 0.6535626649856567 725.4580078125 0.3679094910621643 0.78220254 1.2246655225753784 True -2 8241 30.719475984573364 15.254812240600586 632.4087524414062 0.4263589382171631 711.7887573242188 0.3802793323993683 0.7868808 0.6890676617622375 True -3 10988 30.667372703552246 19.7955060005188 591.216796875 0.48167529702186584 705.9349975585938 0.3852629065513611 0.7945475 0.57554030418396 True -4 13735 31.688992023468018 0.6005470752716064 662.0665283203125 0.4960397481918335 702.8642578125 0.3888684809207916 0.7975682 0.5935205817222595 True -5 16482 30.805821180343628 0.586134672164917 681.8087768554688 0.4596799910068512 699.95263671875 0.3918040096759796 0.79801893 0.46930447220802307 True -6 19229 30.725296020507812 0.5909202098846436 585.0614624023438 0.3061442971229553 698.28076171875 0.3929798901081085 0.80115336 0.42578452825546265 True -7 21976 30.77901268005371 0.5913712978363037 598.21728515625 0.30509719252586365 696.4699096679688 0.3954852819442749 0.8004315 0.3781466782093048 False -8 24723 30.806695461273193 0.5858011245727539 556.237548828125 0.2539730370044708 693.3286743164062 0.3995194733142853 0.8088688 0.40539446473121643 True -9 27470 30.70409870147705 0.5882046222686768 615.80908203125 0.31522005796432495 690.086181640625 0.4024122953414917 0.8170464 0.3637765049934387 True -10 30217 30.67488408088684 0.5902156829833984 613.3052368164062 0.2520449757575989 688.2603149414062 0.4037257730960846 0.81765985 0.33716025948524475 True -11 32964 30.673641681671143 0.5909311771392822 482.2798767089844 0.40139204263687134 687.2499389648438 0.404803067445755 0.82027704 0.33025968074798584 True -12 35711 30.663747787475586 1.1319613456726074 563.4002685546875 0.21336014568805695 683.7176513671875 0.40886035561561584 0.82692766 0.30224350094795227 True -13 38458 30.738152265548706 0.591174840927124 670.6624755859375 0.2648969888687134 683.5433959960938 0.40783774852752686 0.83257335 0.2878659963607788 True -14 41205 30.741758823394775 0.5935091972351074 633.6767578125 0.25669628381729126 682.1141967773438 0.4083805978298187 0.83988744 0.271390438079834 True -15 43952 30.70261263847351 0.5886392593383789 616.5989990234375 0.22006571292877197 681.6875 0.409176230430603 0.8443061 0.2620115876197815 True -16 46699 30.744089365005493 1.5122082233428955 551.5343627929688 0.28043392300605774 681.214111328125 0.40982064604759216 0.8471828 0.25686225295066833 True -17 49446 30.753249883651733 1.3339636325836182 656.7591552734375 0.2099100649356842 678.885009765625 0.4121460020542145 0.8493136 0.25393667817115784 True -18 52193 30.73247003555298 0.7353630065917969 578.9296875 0.1395692229270935 678.903076171875 0.4128647744655609 0.84788173 0.25198787450790405 False -19 54940 30.75185489654541 0.5954489707946777 628.8892211914062 0.15134447813034058 679.5304565429688 0.41154181957244873 0.8492822 0.25367796421051025 False diff --git a/ENCSR792QQE/cherimoya.fold_3.performance.tsv b/ENCSR792QQE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2b44dd22bd5160c7b981d476df648361599fc058..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -678.885009765625 0.3674321472644806 0.4121460020542145 0.1778039187192917 0.8493136167526245 0.7968201637268066 0.25393667817115784 \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_4.evaluate.json b/ENCSR792QQE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bf5cf6ef281d5b70a1023f5f718e33d011979c5b..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XQF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_4.fit.json b/ENCSR792QQE/cherimoya.fold_4.fit.json deleted file mode 100644 index aacf4f418138dc95d8ea28040e00b789c01c132c..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF845XQF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792QQE/cherimoya.fold_4.log b/ENCSR792QQE/cherimoya.fold_4.log deleted file mode 100644 index b79e317e130512cba996405d20f033e58ccaca16..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2834 38.51558542251587 3.6702446937561035 485.569580078125 0.5788290500640869 786.3839721679688 0.2801527976989746 0.6983056 3.9777750968933105 True -1 5668 31.606806993484497 0.6521391868591309 706.13818359375 0.42759203910827637 716.2609252929688 0.3616616725921631 0.7558751 1.2823735475540161 True -2 8502 31.3901047706604 0.6282622814178467 567.3599853515625 0.44961798191070557 702.5781860351562 0.37626025080680847 0.7663406 0.5780699849128723 True -3 11336 31.406561136245728 0.6200265884399414 610.634033203125 0.42326173186302185 698.1526489257812 0.37992727756500244 0.77283645 0.6484482884407043 True -4 14170 31.40627670288086 0.6248738765716553 659.6494140625 0.3541812002658844 695.2255859375 0.38304510712623596 0.7801132 0.41136088967323303 True -5 17004 31.43023443222046 0.6248824596405029 580.1998291015625 0.39323899149894714 692.24365234375 0.3869185745716095 0.783316 0.3734627068042755 True -6 19838 31.367958307266235 0.6253163814544678 615.20703125 0.36369025707244873 689.3463745117188 0.39101189374923706 0.7896399 0.31177738308906555 True -7 22672 31.39125943183899 0.6287429332733154 604.3146362304688 0.31221675872802734 688.131103515625 0.3922896683216095 0.7934242 0.3044368624687195 True -8 25506 31.372709035873413 0.6249940395355225 627.8731079101562 0.3170987367630005 685.4556884765625 0.39540648460388184 0.79926926 0.3007405400276184 True -9 28340 31.384305953979492 0.6288425922393799 616.3692626953125 0.295545756816864 683.9094848632812 0.3974548280239105 0.80402374 0.304575651884079 True -10 31174 31.43352699279785 0.6188039779663086 546.3616333007812 0.30324071645736694 682.8485107421875 0.39838701486587524 0.8103879 0.2924135625362396 True -11 34008 31.469503164291382 0.6382191181182861 590.7970581054688 0.3761516213417053 679.8781127929688 0.402461439371109 0.81501675 0.27495893836021423 True -12 36842 31.428669691085815 0.6333236694335938 549.0411376953125 0.2419450283050537 677.3353881835938 0.40576910972595215 0.8215639 0.2648662030696869 True -13 39676 31.38753581047058 0.6288051605224609 532.540771484375 0.2508400082588196 677.8659057617188 0.4039352238178253 0.8235094 0.2613103985786438 True -14 42510 32.73686385154724 0.636216402053833 596.652099609375 0.17884604632854462 676.2337646484375 0.4064983129501343 0.8299274 0.2532738447189331 True -15 45344 31.424064874649048 0.6357970237731934 566.9905395507812 0.1862272322177887 674.9953002929688 0.40837377309799194 0.8352537 0.2445215880870819 True -16 48178 31.50660228729248 0.6389675140380859 645.137939453125 0.2230079472064972 674.5999755859375 0.40919286012649536 0.8378197 0.23713035881519318 True -17 51012 31.442171573638916 0.6291232109069824 473.21051025390625 0.19176170229911804 675.0282592773438 0.40831613540649414 0.84159344 0.2323484718799591 True -18 53846 31.500739336013794 0.6250631809234619 588.028076171875 0.20526109635829926 674.3408813476562 0.4092896282672882 0.84123886 0.22988763451576233 False -19 56680 31.499943494796753 0.6280744075775146 638.9180908203125 0.14432330429553986 675.5798950195312 0.40637683868408203 0.84035194 0.23141971230506897 False diff --git a/ENCSR792QQE/cherimoya.fold_4.performance.tsv b/ENCSR792QQE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3daa448f737cebcd3d4e796beacd64282b80ace7..0000000000000000000000000000000000000000 --- a/ENCSR792QQE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -675.0282592773438 0.3690415918827057 0.40831610560417175 0.17083901166915894 0.8415934443473816 0.786483645439148 0.2323484718799591 \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_0.evaluate.json b/ENCSR792ZXA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 17c452e494fda56ca6b0a2daa8a1adf909082625..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF189OUV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_0.fit.json b/ENCSR792ZXA/cherimoya.fold_0.fit.json deleted file mode 100644 index a5fa55035b6d79235578d7b0a3773109887f0d95..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF189OUV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_0.log b/ENCSR792ZXA/cherimoya.fold_0.log deleted file mode 100644 index 59e9f719183c3e6fd3478bfc6d3272c471b70fbe..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2775 35.14085268974304 4.710376262664795 1433.103759765625 0.4262596368789673 2085.59814453125 0.35057321190834045 0.7848958 9.909507751464844 True -1 5550 30.68594002723694 9.843488931655884 1520.6025390625 0.5677564144134521 1826.7275390625 0.4350008964538574 0.8329295 2.526493787765503 True -2 8325 30.285985708236694 0.5881175994873047 1507.00927734375 0.5161258578300476 1792.55126953125 0.4462658762931824 0.83769774 0.9312008023262024 True -3 11100 30.38817811012268 31.416878700256348 1500.426513671875 0.5540133118629456 1772.612060546875 0.4533099830150604 0.8407898 0.7764790654182434 True -4 13875 30.557685375213623 0.5771565437316895 1393.2288818359375 0.6999140977859497 1755.855224609375 0.45870983600616455 0.84607124 0.7054852247238159 True -5 16650 30.264349460601807 0.5765702724456787 1294.2083740234375 0.5252666473388672 1737.464111328125 0.46790555119514465 0.8497175 0.615233302116394 True -6 19425 30.31411075592041 0.5827915668487549 1551.7913818359375 0.5041962265968323 1727.6767578125 0.47271233797073364 0.8521141 0.5875259041786194 True -7 22200 30.275734663009644 0.5738718509674072 1652.062255859375 0.35236167907714844 1724.6595458984375 0.4720136523246765 0.8558209 0.5623989701271057 True -8 24975 31.106282949447632 0.5753066539764404 1403.8563232421875 0.5749466419219971 1720.2760009765625 0.47530409693717957 0.85653776 0.49125736951828003 True -9 27750 30.394922733306885 1.99635910987854 1341.1593017578125 0.4324294626712799 1710.40869140625 0.4794628918170929 0.8570538 0.43589603900909424 True -10 30525 30.550639867782593 0.5761079788208008 1199.12548828125 0.4071497321128845 1700.1119384765625 0.48392343521118164 0.86129403 0.42551878094673157 True -11 33300 30.43538212776184 0.5964081287384033 1391.193603515625 0.47243109345436096 1694.5399169921875 0.4861985743045807 0.86532694 0.39120373129844666 True -12 36075 31.230625867843628 3.4644384384155273 1235.2879638671875 0.39249250292778015 1692.17041015625 0.48466408252716064 0.8669305 0.35435014963150024 True -13 38850 30.650196075439453 21.645023584365845 1524.205322265625 0.17732644081115723 1688.5452880859375 0.48676231503486633 0.8731978 0.3258644938468933 True -14 41625 34.081992626190186 0.5979571342468262 1359.29931640625 0.2909819185733795 1680.6336669921875 0.4898969531059265 0.87362397 0.31254827976226807 True -15 44400 30.58383274078369 0.5705287456512451 1420.86328125 0.27227893471717834 1674.1134033203125 0.49173682928085327 0.8769163 0.29366534948349 True -16 47175 30.298359155654907 0.5681989192962646 1214.014892578125 0.2469954788684845 1672.2899169921875 0.4939274489879608 0.88000125 0.28328651189804077 True -17 49950 30.20393466949463 0.5645663738250732 1608.22607421875 0.20031830668449402 1672.2264404296875 0.49251264333724976 0.88028705 0.27623239159584045 True -18 52725 32.227442264556885 12.423787593841553 1700.5419921875 0.25157254934310913 1674.869140625 0.4923626184463501 0.8816091 0.2741548418998718 True -19 55500 30.470717191696167 0.6113412380218506 1358.591796875 0.22628122568130493 1670.784423828125 0.49444490671157837 0.88191324 0.27629661560058594 True diff --git a/ENCSR792ZXA/cherimoya.fold_0.performance.tsv b/ENCSR792ZXA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1ba3f48ac14047da5527ee0c499800d1e9bef7e0..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1670.784423828125 0.2579452693462372 0.49444490671157837 0.2967575788497925 0.8819132447242737 0.8474158048629761 0.27629661560058594 \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_1.evaluate.json b/ENCSR792ZXA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3277ed38c1252a8b12a4a71d6a526bff46c400df..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF189OUV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_1.fit.json b/ENCSR792ZXA/cherimoya.fold_1.fit.json deleted file mode 100644 index 8dae302d5bfe9b56821eac7d320b1a18d56b433e..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF189OUV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_1.log b/ENCSR792ZXA/cherimoya.fold_1.log deleted file mode 100644 index d2b474e67aee9232c1237ece644362e838820dc9..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2672 34.91399669647217 4.3168511390686035 1278.2579345703125 1.0307722091674805 2512.355224609375 0.35023272037506104 0.7646369 12.008719444274902 True -1 5344 29.128403425216675 0.742546558380127 1463.521240234375 0.516152560710907 2184.258544921875 0.4418952763080597 0.8257772 2.6569106578826904 True -2 8016 29.20864486694336 0.7281255722045898 1685.52880859375 0.31826239824295044 2115.71142578125 0.458708256483078 0.8353418 1.189992070198059 True -3 10688 29.152578830718994 0.7349095344543457 1465.5888671875 0.579862654209137 2088.13330078125 0.46841633319854736 0.8384471 1.1056597232818604 True -4 13360 29.059624671936035 0.7375755310058594 1254.3702392578125 0.48649847507476807 2065.69921875 0.4767870604991913 0.84383243 0.9828035235404968 True -5 16032 29.09487009048462 0.7337243556976318 1280.478515625 0.3017354905605316 2044.769287109375 0.48314106464385986 0.8466399 0.867695152759552 True -6 18704 29.08216643333435 0.7358977794647217 1528.3634033203125 0.46725380420684814 2040.240478515625 0.4850567877292633 0.8484145 0.7320483922958374 True -7 21376 29.067625284194946 1.7302801609039307 1246.205810546875 0.414170503616333 2021.298095703125 0.49134522676467896 0.8545457 0.5670115947723389 True -8 24048 29.057907342910767 0.7314093112945557 1139.5594482421875 0.6605951189994812 2015.4664306640625 0.4938592314720154 0.8501916 0.5588635802268982 False -9 26720 29.084758758544922 0.7312209606170654 1002.0764770507812 0.395389199256897 1999.95263671875 0.49822619557380676 0.85761845 0.46317243576049805 True -10 29392 29.102322578430176 0.7315313816070557 1577.501953125 0.4162691831588745 1989.3358154296875 0.5008000731468201 0.8629891 0.42833855748176575 True -11 32064 29.110081672668457 0.7341001033782959 1471.383544921875 0.3150801658630371 1981.4842529296875 0.5024852156639099 0.8659985 0.3905836045742035 True -12 34736 29.079766035079956 0.7371854782104492 1828.828369140625 0.3972946107387543 1974.9732666015625 0.5030175447463989 0.86850846 0.3704814910888672 True -13 37408 29.047597408294678 0.7292897701263428 1274.555419921875 0.2582104504108429 1964.6109619140625 0.5070021152496338 0.87370515 0.3434329628944397 True -14 40080 29.04826807975769 0.7331445217132568 1421.68310546875 0.2788793742656708 1960.9324951171875 0.5075834393501282 0.87746054 0.3275984823703766 True -15 42752 29.040648460388184 0.7409350872039795 1301.9024658203125 0.35255810618400574 1959.13330078125 0.5062336921691895 0.8824396 0.3136797547340393 True -16 45424 30.380246877670288 29.163569688796997 1194.3466796875 0.3247394263744354 1961.1409912109375 0.5044986009597778 0.8850048 0.3075115978717804 True -17 48096 29.265727519989014 0.7479772567749023 1461.726318359375 0.150860995054245 1954.51953125 0.5080010890960693 0.88418776 0.2973058521747589 False -18 50768 29.1725435256958 0.7465355396270752 1382.45654296875 0.22781944274902344 1956.4239501953125 0.5078393816947937 0.8841311 0.29781755805015564 False -19 53440 29.117571115493774 0.73529052734375 1502.508544921875 0.3594014644622803 1955.2999267578125 0.509527862071991 0.8834707 0.297798752784729 False diff --git a/ENCSR792ZXA/cherimoya.fold_1.performance.tsv b/ENCSR792ZXA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 34a5dadcf12e6dd26d61040425bed192471d4e68..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1961.1409912109375 0.2385379672050476 0.5044985413551331 0.32756561040878296 0.8850048184394836 0.8712192177772522 0.3075115978717804 \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_2.evaluate.json b/ENCSR792ZXA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 405f7f39ee3479c7df24f54da09a0777d2a75442..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF189OUV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_2.fit.json b/ENCSR792ZXA/cherimoya.fold_2.fit.json deleted file mode 100644 index 7a0b56bde8390fc1ef4c8f33dd598f72ffaef10f..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF189OUV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_2.log b/ENCSR792ZXA/cherimoya.fold_2.log deleted file mode 100644 index 687a5ae0525201791fdee0e025a88ec9c7264df8..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 35.897684812545776 3.6418445110321045 1592.560546875 0.5638786554336548 2223.871826171875 0.3558241128921509 0.76631516 9.338635444641113 True -1 5748 31.345450401306152 25.774967193603516 1384.07568359375 0.5469489693641663 1941.3016357421875 0.4385448098182678 0.82169276 1.6816463470458984 True -2 8622 32.83669686317444 0.5862534046173096 1845.898681640625 0.334099143743515 1906.680908203125 0.4467427134513855 0.8308898 0.848118007183075 True -3 11496 31.785706281661987 0.6027610301971436 1655.613525390625 0.6672173738479614 1877.2108154296875 0.45693010091781616 0.83576083 0.671328604221344 True -4 14370 31.54222798347473 0.5827593803405762 1707.7735595703125 0.8120813369750977 1871.60546875 0.45874568819999695 0.83752114 0.6750343441963196 True -5 17244 31.277388095855713 1.1357533931732178 1339.570068359375 0.5741480588912964 1855.0086669921875 0.4645226299762726 0.84378105 0.6051402688026428 True -6 20118 31.26578950881958 1.7505075931549072 1402.792236328125 0.4156157970428467 1841.714599609375 0.46993696689605713 0.8469579 0.5588546991348267 True -7 22992 31.25273323059082 0.5793247222900391 1501.875 0.6494901180267334 1829.8172607421875 0.47540757060050964 0.8492782 0.5039086937904358 True -8 25866 31.25165867805481 0.6077098846435547 1367.757568359375 0.4108861982822418 1819.8546142578125 0.4791317284107208 0.85094005 0.5012204647064209 True -9 28740 31.249685525894165 1.184157371520996 1451.8818359375 0.45850151777267456 1813.940673828125 0.48243415355682373 0.85388225 0.49469754099845886 True -10 31614 31.247579097747803 0.5736560821533203 1648.0836181640625 0.6339325308799744 1801.393798828125 0.4851694405078888 0.85241663 0.4471955895423889 False -11 34488 31.267762660980225 0.5811958312988281 1657.314208984375 0.4230184853076935 1802.8699951171875 0.48640546202659607 0.85410243 0.4352584481239319 True -12 37362 33.85376453399658 30.892230987548828 1551.39990234375 0.3332136273384094 1792.4764404296875 0.4888744354248047 0.858883 0.42871883511543274 True -13 40236 31.64614248275757 1.7972702980041504 1512.19189453125 0.32323533296585083 1794.470703125 0.4873201847076416 0.86100316 0.38133540749549866 True -14 43110 31.348291397094727 0.6006183624267578 1441.3629150390625 0.37299203872680664 1780.130859375 0.49278777837753296 0.8663408 0.3594415485858917 True -15 45984 31.371585369110107 0.5865542888641357 1206.3985595703125 0.3968077301979065 1777.552490234375 0.49344852566719055 0.86841416 0.3289480209350586 True -16 48858 31.537936210632324 30.214898824691772 1329.813720703125 0.2364981770515442 1773.4442138671875 0.49445047974586487 0.8711121 0.30857494473457336 True -17 51732 31.38044285774231 29.941439628601074 1470.3436279296875 0.25241395831108093 1774.2042236328125 0.4938691556453705 0.87536407 0.2971345782279968 True -18 54606 32.920389890670776 0.6052350997924805 1336.266357421875 0.19380967319011688 1784.3323974609375 0.4889509975910187 0.8756094 0.2922198474407196 True -19 57480 31.3265860080719 0.5879600048065186 1405.4154052734375 0.26203927397727966 1775.6617431640625 0.49413391947746277 0.87308544 0.2910548150539398 False diff --git a/ENCSR792ZXA/cherimoya.fold_2.performance.tsv b/ENCSR792ZXA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c63cd0693b1f4f90acb4e02e72b2997badf667b0..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1784.3323974609375 0.2515617311000824 0.48895108699798584 0.3062380850315094 0.8756093978881836 0.851676344871521 0.2922198474407196 \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_3.evaluate.json b/ENCSR792ZXA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 410ce4f613761adbc973ba246ebbe6bb8a25774e..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF189OUV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_3.fit.json b/ENCSR792ZXA/cherimoya.fold_3.fit.json deleted file mode 100644 index ce1f06d05c21e258d9360ca95b0ba3435d313368..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF189OUV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_3.log b/ENCSR792ZXA/cherimoya.fold_3.log deleted file mode 100644 index 40fe98fc00110558ca5fb5a705b9079c731173db..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 35.00753331184387 12.568862676620483 1497.600830078125 0.5273299813270569 2100.400146484375 0.3595693111419678 0.7673529 12.305962562561035 True -1 5506 30.198458671569824 7.025989770889282 1768.6121826171875 0.620658278465271 1869.716796875 0.43408438563346863 0.816971 2.697978973388672 True -2 8259 30.068203926086426 0.5711991786956787 1356.643798828125 0.36382514238357544 1839.682861328125 0.44206535816192627 0.82497734 1.3179432153701782 True -3 11012 29.94889807701111 0.9945170879364014 1025.763916015625 0.5200948119163513 1805.6373291015625 0.45602914690971375 0.82963717 0.9635030031204224 True -4 13765 29.924587726593018 0.5258896350860596 1484.710693359375 0.4356236755847931 1782.4930419921875 0.46409618854522705 0.8367463 0.7966443300247192 True -5 16518 30.052608728408813 0.5306096076965332 1508.0452880859375 0.5320242643356323 1774.4971923828125 0.4661678671836853 0.84162 0.8291019797325134 True -6 19271 30.195215225219727 33.63775610923767 1298.357666015625 0.456210196018219 1771.631103515625 0.46907299757003784 0.84186286 0.7250096201896667 True -7 22024 30.00779104232788 0.527245283126831 1468.8387451171875 0.4972350597381592 1759.28662109375 0.4750022292137146 0.8457157 0.6980385780334473 True -8 24777 29.987024068832397 0.5401864051818848 1425.678466796875 0.4260823428630829 1756.816650390625 0.47416752576828003 0.84725326 0.5946476459503174 True -9 27530 30.118515491485596 0.5332412719726562 1373.596435546875 0.31009209156036377 1749.5247802734375 0.47663381695747375 0.8493928 0.5383176207542419 True -10 30283 30.021996021270752 0.5353484153747559 1413.7059326171875 0.4514191746711731 1741.695556640625 0.4804108440876007 0.8549959 0.511504590511322 True -11 33036 29.971781015396118 1.5408568382263184 1430.78076171875 0.3127039968967438 1728.0748291015625 0.485490083694458 0.85644066 0.4850388765335083 True -12 35789 29.964502334594727 19.68950343132019 1516.0262451171875 0.3175918757915497 1719.9154052734375 0.4877125024795532 0.8649096 0.43406638503074646 True -13 38542 32.73541712760925 0.5895235538482666 1106.483154296875 0.4683951139450073 1711.1510009765625 0.491775244474411 0.8675272 0.4040674567222595 True -14 41295 29.94990634918213 0.5388805866241455 1751.4189453125 0.43867048621177673 1705.66259765625 0.4926627576351166 0.87144065 0.3749193847179413 True -15 44048 29.957367658615112 0.535590648651123 1280.7296142578125 0.31767699122428894 1704.4727783203125 0.4929460883140564 0.87647635 0.3469638228416443 True -16 46801 31.101312160491943 25.75939965248108 1391.1552734375 0.2547374963760376 1698.2760009765625 0.49538692831993103 0.8773499 0.32491636276245117 True -17 49554 30.075257062911987 0.5467245578765869 1327.18408203125 0.36498844623565674 1699.788330078125 0.49523159861564636 0.8793938 0.3112643361091614 True -18 52307 29.906240224838257 2.3722996711730957 1463.802734375 0.4302953779697418 1702.3763427734375 0.49254557490348816 0.8793277 0.306195467710495 False -19 55060 29.95905828475952 0.5310344696044922 1356.4818115234375 0.18104758858680725 1704.2728271484375 0.4912562668323517 0.8796743 0.30464622378349304 True diff --git a/ENCSR792ZXA/cherimoya.fold_3.performance.tsv b/ENCSR792ZXA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ea56ccfa7d99b3f81fa7a797852419ed203461b9..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1704.2728271484375 0.2569343149662018 0.4912562370300293 0.3013131022453308 0.8796743154525757 0.8456135392189026 0.30464622378349304 \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_4.evaluate.json b/ENCSR792ZXA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b2c13b9056aa302dd9309edc4048f9692472969d..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF189OUV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_4.fit.json b/ENCSR792ZXA/cherimoya.fold_4.fit.json deleted file mode 100644 index c595f6bb3558a9857eb297994cd1f0928a9b4a40..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF189OUV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR792ZXA/cherimoya.fold_4.log b/ENCSR792ZXA/cherimoya.fold_4.log deleted file mode 100644 index 47d78dce45bdd116c40681ccc061b16315b0788b..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2782 35.22612023353577 3.719890832901001 1449.57568359375 0.9991905689239502 1982.679931640625 0.3564099967479706 0.7734215 11.410056114196777 True -1 5564 30.292035341262817 1.1316490173339844 1191.838623046875 0.5608931183815002 1769.395263671875 0.4311189353466034 0.81697285 1.915308952331543 True -2 8346 30.32827138900757 0.590430498123169 1656.0478515625 0.41873085498809814 1727.2684326171875 0.4454386234283447 0.82261765 1.0813947916030884 True -3 11128 30.295220375061035 0.6056187152862549 1615.602294921875 0.5223598480224609 1713.022216796875 0.44866567850112915 0.8295773 0.8467395305633545 True -4 13910 30.246429681777954 0.5903637409210205 1512.809326171875 0.5119706392288208 1689.9566650390625 0.4597775936126709 0.8358632 0.7605379223823547 True -5 16692 30.24675703048706 0.5875363349914551 1354.9942626953125 0.47170841693878174 1684.8773193359375 0.46184900403022766 0.8389595 0.6589979529380798 True -6 19474 30.325495958328247 0.6018226146697998 1397.948486328125 0.48774009943008423 1667.9527587890625 0.47044211626052856 0.8432637 0.6365177631378174 True -7 22256 30.34032678604126 35.368712186813354 1480.128173828125 0.465096652507782 1667.58154296875 0.4693990647792816 0.8450401 0.49962618947029114 True -8 25038 30.504448413848877 36.80018734931946 1437.3115234375 0.5648206472396851 1661.609130859375 0.4724183976650238 0.8463556 0.458461731672287 True -9 27820 30.582281351089478 18.47839379310608 1207.404541015625 0.4725324511528015 1655.2305908203125 0.474086195230484 0.8503544 0.4046255946159363 True -10 30602 30.35857129096985 48.56649112701416 1145.6102294921875 0.2713908553123474 1646.5621337890625 0.47770997881889343 0.8525228 0.3974284529685974 True -11 33384 30.35678720474243 6.3883585929870605 1319.474609375 0.3286385238170624 1639.7225341796875 0.4800901412963867 0.8561574 0.3686342239379883 True -12 36166 30.379557847976685 2.505476236343384 1429.85107421875 0.4072268307209015 1640.689697265625 0.47984057664871216 0.86010224 0.3513915240764618 True -13 38948 30.35041308403015 10.587617874145508 1468.06787109375 0.2513453960418701 1629.0047607421875 0.4852237105369568 0.864478 0.3269883096218109 True -14 41730 30.420965433120728 27.153748750686646 1420.440673828125 0.4289988875389099 1625.9554443359375 0.48589494824409485 0.8658832 0.3191722333431244 True -15 44512 30.726797342300415 0.6242814064025879 1357.8115234375 0.3335147798061371 1625.06103515625 0.48671188950538635 0.870481 0.2996264398097992 True -16 47294 31.689010620117188 34.66250920295715 1426.7945556640625 0.29434508085250854 1619.8553466796875 0.4883788526058197 0.8733897 0.2858142852783203 True -17 50076 30.329410314559937 33.993237257003784 1344.892333984375 0.263950914144516 1625.069091796875 0.4852270185947418 0.8743205 0.2793777585029602 True -18 52858 30.337589502334595 0.6825287342071533 1690.9805908203125 0.2809668183326721 1622.6175537109375 0.4870436191558838 0.8739421 0.27735814452171326 False -19 55640 30.38892912864685 2.012922525405884 1298.12255859375 0.2065751552581787 1626.5450439453125 0.4848870038986206 0.8753089 0.2774542570114136 True diff --git a/ENCSR792ZXA/cherimoya.fold_4.performance.tsv b/ENCSR792ZXA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index bbedecae998dcd5d5b97bdf4871036d31aaeb309..0000000000000000000000000000000000000000 --- a/ENCSR792ZXA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1626.5450439453125 0.26045748591423035 0.48488694429397583 0.29180172085762024 0.8753088712692261 0.8347079753875732 0.2774542570114136 \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_0.evaluate.json b/ENCSR794TLA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 095f376c99833f89dc7cc22e6365390d6e73d3ba..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF928AWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_0.fit.json b/ENCSR794TLA/cherimoya.fold_0.fit.json deleted file mode 100644 index 3dc341ead04ca09656f3968f27e18e6d9f03f147..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF928AWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_0.log b/ENCSR794TLA/cherimoya.fold_0.log deleted file mode 100644 index 5fd99255d081b911bcb1d8d43601a9027fc587e7..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2766 35.60477352142334 3.770195245742798 675.4544677734375 0.3738945424556732 785.4410400390625 0.13618946075439453 0.73136604 4.393076419830322 True -1 5532 31.378589153289795 0.558485746383667 613.0036010742188 0.2767244279384613 745.740234375 0.1644652783870697 0.7862813 1.3926780223846436 True -2 8298 30.76467728614807 0.6238372325897217 616.7152709960938 0.3034297525882721 734.8599243164062 0.16992373764514923 0.80241764 0.8145307898521423 True -3 11064 30.72357726097107 0.5536129474639893 591.0499267578125 0.4159910976886749 727.999267578125 0.17377495765686035 0.8123135 0.5633981227874756 True -4 13830 30.703635215759277 0.5538120269775391 573.0489501953125 0.18106937408447266 725.4424438476562 0.1754440814256668 0.8214403 0.5164745450019836 True -5 16596 30.062126874923706 0.5536091327667236 537.4843139648438 0.25155144929885864 720.8386840820312 0.17907559871673584 0.83198714 0.4371078610420227 True -6 19362 30.057679414749146 0.7099127769470215 568.4483642578125 0.23146307468414307 719.8264770507812 0.1797323375940323 0.8349252 0.44732680916786194 True -7 22128 30.098322868347168 0.5593397617340088 631.0357666015625 0.2790156900882721 716.9392700195312 0.18242140114307404 0.8370733 0.41849973797798157 True -8 24894 30.074482679367065 0.5678455829620361 702.8619384765625 0.31215962767601013 714.93212890625 0.18374350666999817 0.8490062 0.35156551003456116 True -9 27660 30.03623867034912 0.5563623905181885 594.9859008789062 0.26987165212631226 712.6429443359375 0.18496879935264587 0.85445684 0.32018619775772095 True -10 30426 30.047911643981934 0.5547754764556885 656.9890747070312 0.21246744692325592 711.3878173828125 0.18627257645130157 0.8610496 0.27352315187454224 True -11 33192 30.07125186920166 0.5543789863586426 684.6727294921875 0.5715163350105286 708.7249755859375 0.18866252899169922 0.86350816 0.2641829550266266 True -12 35958 30.115058660507202 0.5566370487213135 625.9486694335938 0.32816898822784424 707.267822265625 0.1896357536315918 0.8707707 0.24544492363929749 True -13 38724 30.075433492660522 3.6995129585266113 704.9112548828125 0.3266880214214325 706.4899291992188 0.1898506134748459 0.8752958 0.23050402104854584 True -14 41490 30.17989754676819 0.5693700313568115 605.3375244140625 0.2133966088294983 704.8685913085938 0.19126905500888824 0.8783042 0.21974840760231018 True -15 44256 30.191298961639404 1.3222997188568115 580.040283203125 0.33814889192581177 705.1621704101562 0.19074760377407074 0.88007224 0.2055358588695526 True -16 47022 30.190418243408203 0.5507147312164307 552.1099853515625 0.25681570172309875 704.3701782226562 0.1911686509847641 0.88122135 0.19493813812732697 True -17 49788 30.263157606124878 0.5636770725250244 661.392822265625 0.19598019123077393 703.945068359375 0.1916321963071823 0.8828998 0.19029578566551208 True -18 52554 30.16235852241516 0.5656452178955078 643.57275390625 0.2033253163099289 704.4996948242188 0.19104711711406708 0.88110495 0.18925824761390686 False -19 55320 30.13413977622986 19.57226252555847 553.5911865234375 0.18474319577217102 704.8327026367188 0.19068649411201477 0.881025 0.19035358726978302 False diff --git a/ENCSR794TLA/cherimoya.fold_0.performance.tsv b/ENCSR794TLA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 33f8af88aaa6164d44c4065fc018be451372a4d0..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -703.945068359375 0.5401831269264221 0.1916321963071823 0.06511510908603668 0.882899820804596 0.8218404054641724 0.19029578566551208 \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_1.evaluate.json b/ENCSR794TLA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a08ce20b148ec6b9cb42b7cd62b9aed99381c222..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF928AWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_1.fit.json b/ENCSR794TLA/cherimoya.fold_1.fit.json deleted file mode 100644 index 87a6ce1bf6faa8568620f9b3b3b1772c828b8130..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF928AWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_1.log b/ENCSR794TLA/cherimoya.fold_1.log deleted file mode 100644 index ba33a32ac144957ce13d6d2f24e90bf312b69f6b..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 35.22985363006592 4.850070953369141 565.0263061523438 0.36233192682266235 908.5568237304688 0.14685533940792084 0.7183698 5.028810977935791 True -1 5470 30.515722036361694 1.2340600490570068 570.2232055664062 0.554253101348877 857.9537353515625 0.18335366249084473 0.7816145 1.5166155099868774 True -2 8205 30.493639707565308 0.8123760223388672 728.2534790039062 0.4348992705345154 846.88330078125 0.18688607215881348 0.7859447 0.9135294556617737 True -3 10940 30.41943907737732 0.720923900604248 592.119140625 0.4312567412853241 840.8348388671875 0.18957440555095673 0.79197776 0.8023626208305359 True -4 13675 30.46170735359192 0.7374248504638672 595.29541015625 0.436599463224411 830.4481811523438 0.19487173855304718 0.8073943 0.6470898985862732 True -5 16410 30.42512059211731 0.708601713180542 664.5341796875 0.27778223156929016 824.8831787109375 0.19928604364395142 0.81954944 0.5530818104743958 True -6 19145 30.347018241882324 0.7332324981689453 669.4068603515625 0.3805144727230072 821.216552734375 0.20191390812397003 0.83054024 0.5038281083106995 True -7 21880 30.174263954162598 0.7248082160949707 731.1142578125 0.2797696888446808 817.2888793945312 0.2043834775686264 0.8391975 0.4652213752269745 True -8 24615 29.86031150817871 0.733015775680542 523.0704345703125 0.3507632613182068 813.18408203125 0.20717257261276245 0.8473821 0.4156264364719391 True -9 27350 29.69293475151062 0.7242932319641113 562.9822387695312 0.27102208137512207 812.6119384765625 0.20719818770885468 0.8529241 0.4036334753036499 True -10 30085 29.719614505767822 0.713468074798584 619.587646484375 0.2794307470321655 809.6322631835938 0.2088325172662735 0.8601717 0.3852066993713379 True -11 32820 29.708271741867065 0.7204799652099609 508.6397399902344 0.24317345023155212 805.6089477539062 0.21199190616607666 0.8648276 0.34828850626945496 True -12 35555 29.71198320388794 0.7080717086791992 615.5179443359375 0.3219505548477173 804.3734130859375 0.2124638855457306 0.8721366 0.30872732400894165 True -13 38290 29.739874362945557 1.800086259841919 630.7059326171875 0.34003525972366333 801.5306396484375 0.21398651599884033 0.8773118 0.2874177396297455 True -14 41025 29.816983461380005 0.7295145988464355 625.6756591796875 0.1913658082485199 799.658447265625 0.21533353626728058 0.88230854 0.26693519949913025 True -15 43760 29.846014499664307 0.7023952007293701 562.9014892578125 0.2525128126144409 797.3261108398438 0.2170899212360382 0.88759184 0.2502143681049347 True -16 46495 29.794025659561157 0.7213492393493652 511.224365234375 0.1872285157442093 796.5157470703125 0.21739105880260468 0.890443 0.23410773277282715 True -17 49230 29.752758741378784 0.7138936519622803 658.650634765625 0.18469226360321045 798.3862915039062 0.21559731662273407 0.8926917 0.2243940830230713 True -18 51965 29.82149028778076 0.703944206237793 530.295166015625 0.13024643063545227 797.6549682617188 0.2163732796907425 0.8915896 0.2210271954536438 False -19 54700 29.809239149093628 0.7271766662597656 517.8560791015625 0.12711694836616516 797.7142333984375 0.2162085622549057 0.8906975 0.22186142206192017 False diff --git a/ENCSR794TLA/cherimoya.fold_1.performance.tsv b/ENCSR794TLA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 441291f961e7add82f99504888be74284e4c5c57..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -798.3862915039062 0.5200722217559814 0.21559733152389526 0.07953641563653946 0.8926916718482971 0.8605321049690247 0.2243940830230713 \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_2.evaluate.json b/ENCSR794TLA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index fcfc3137fca73cf4725859155658f46148ac6ca7..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF928AWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_2.fit.json b/ENCSR794TLA/cherimoya.fold_2.fit.json deleted file mode 100644 index 8f600425a4ad8f23c458dd5feffa47f915463fb4..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF928AWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_2.log b/ENCSR794TLA/cherimoya.fold_2.log deleted file mode 100644 index 0bdffbd60af19e4552eb9d6cd614bdce681ed1b9..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2895 36.70553922653198 4.391264200210571 623.840087890625 0.38369008898735046 826.5491333007812 0.14454148709774017 0.7147102 4.16375207901001 True -1 5790 32.19661736488342 0.8129305839538574 673.4930419921875 0.4038311839103699 782.0882568359375 0.1726759821176529 0.7851592 1.174983024597168 True -2 8685 32.23172879219055 0.5639638900756836 569.5186767578125 0.35199427604675293 773.0194702148438 0.17847223579883575 0.79257166 0.6831322312355042 True -3 11580 32.19352650642395 0.5546555519104004 665.044677734375 0.343339741230011 765.7072143554688 0.1824963390827179 0.80279094 0.653978168964386 True -4 14475 32.181339740753174 0.554668664932251 680.522705078125 0.3619791865348816 763.140380859375 0.1840762197971344 0.80760664 0.49792617559432983 True -5 17370 32.20568251609802 0.5538721084594727 597.5748291015625 0.44052180647850037 759.2095336914062 0.18741881847381592 0.81734186 0.42211177945137024 True -6 20265 32.22345995903015 0.5877563953399658 628.0401000976562 0.22225132584571838 756.3440551757812 0.18861792981624603 0.8299171 0.37910351157188416 True -7 23160 32.196667432785034 0.6539592742919922 522.061279296875 0.3231928050518036 754.5565795898438 0.19032908976078033 0.8333451 0.41500261425971985 True -8 26055 31.98453950881958 0.5458357334136963 617.2484741210938 0.26282161474227905 753.0684204101562 0.19111226499080658 0.8393571 0.37188684940338135 True -9 28950 31.532459497451782 0.5513925552368164 599.1185913085938 0.32222068309783936 750.2752685546875 0.19347600638866425 0.84695196 0.3433934152126312 True -10 31845 31.50276279449463 0.5767669677734375 576.816650390625 0.27622997760772705 749.1598510742188 0.19478268921375275 0.8492222 0.31782063841819763 True -11 34740 31.56337308883667 0.625403642654419 596.294921875 0.35847771167755127 747.1929931640625 0.19586831331253052 0.85596466 0.2840542793273926 True -12 37635 31.586561679840088 0.5358097553253174 580.682861328125 0.2981806695461273 745.8452758789062 0.1969538927078247 0.86081684 0.27150577306747437 True -13 40530 31.714372873306274 0.5659162998199463 552.18310546875 0.17327792942523956 743.680908203125 0.19847001135349274 0.8693717 0.24498535692691803 True -14 43425 31.673603296279907 0.6013302803039551 694.3572998046875 0.3267650604248047 742.057373046875 0.19937381148338318 0.8736877 0.23433257639408112 True -15 46320 31.619727849960327 1.0637304782867432 558.8880615234375 0.19366005063056946 741.0304565429688 0.2002919316291809 0.8763792 0.21385744214057922 True -16 49215 31.622286796569824 0.5581669807434082 593.90185546875 0.12600204348564148 740.5164794921875 0.20030322670936584 0.87828 0.20370963215827942 True -17 52110 31.689770698547363 0.5555005073547363 641.6793212890625 0.20660419762134552 740.6966552734375 0.19984742999076843 0.8810953 0.19939325749874115 True -18 55005 31.850757598876953 0.5478973388671875 551.6707153320312 0.2467907816171646 740.9446411132812 0.19964566826820374 0.8808234 0.19796155393123627 False -19 57900 31.61347246170044 0.5566205978393555 593.8089599609375 0.1529492437839508 741.2835693359375 0.19967594742774963 0.8812104 0.19809481501579285 True diff --git a/ENCSR794TLA/cherimoya.fold_2.performance.tsv b/ENCSR794TLA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 291c775bb53c3397fe0c625d726a873ca0af2fca..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -741.2835693359375 0.5320809483528137 0.19967594742774963 0.07100056111812592 0.8812103867530823 0.8369011282920837 0.19809481501579285 \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_3.evaluate.json b/ENCSR794TLA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e00a3ca51aeea5a441ff03144b49f915397ebc32..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF928AWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_3.fit.json b/ENCSR794TLA/cherimoya.fold_3.fit.json deleted file mode 100644 index 0e056e45332ac1027053c30f0fdc93905a6cb77b..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF928AWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_3.log b/ENCSR794TLA/cherimoya.fold_3.log deleted file mode 100644 index d227fa02137e3f623a2cc564a1ca2ea2ad4cced3..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2769 35.32569670677185 3.992828607559204 726.4600830078125 0.5877418518066406 804.3046875 0.14464962482452393 0.6926837 4.710881233215332 True -1 5538 30.800248622894287 0.5558891296386719 656.010986328125 0.6176113486289978 765.81396484375 0.1728670746088028 0.7511094 1.4337944984436035 True -2 8307 30.823229551315308 0.557990312576294 547.97119140625 0.27416473627090454 758.1381225585938 0.17714554071426392 0.75973904 1.1833553314208984 True -3 11076 30.781858682632446 0.56492018699646 520.6478881835938 0.2156977504491806 752.2918701171875 0.17998918890953064 0.7770032 0.6989494562149048 True -4 13845 30.775546073913574 0.5418291091918945 784.6331787109375 0.4669673442840576 746.2193603515625 0.18466317653656006 0.78991777 0.6032361388206482 True -5 16614 30.73188018798828 2.6819498538970947 642.9091796875 0.35911476612091064 741.17822265625 0.18733078241348267 0.80864143 0.5397650599479675 True -6 19383 30.806179761886597 0.5544958114624023 571.4730224609375 0.26505327224731445 739.2813720703125 0.18853029608726501 0.8150373 0.5821934342384338 True -7 22152 30.797446489334106 0.5481464862823486 602.5423583984375 0.33317840099334717 733.8844604492188 0.19264274835586548 0.8280121 0.4626138210296631 True -8 24921 30.76222825050354 0.536475658416748 650.835205078125 0.24233752489089966 732.6273803710938 0.19383864104747772 0.8318116 0.4405617415904999 True -9 27690 30.529611587524414 0.5393240451812744 535.8223876953125 0.32520151138305664 731.9078369140625 0.1947726458311081 0.8356942 0.41577214002609253 True -10 30459 30.17000102996826 0.5420424938201904 522.5968017578125 0.17929965257644653 728.6981811523438 0.19722388684749603 0.8426699 0.35798412561416626 True -11 33228 30.164247751235962 0.5327620506286621 550.3994140625 0.32844266295433044 728.9171142578125 0.19710911810398102 0.8448023 0.35035812854766846 True -12 35997 30.163334608078003 0.5291557312011719 620.0791625976562 0.29398614168167114 727.58642578125 0.19801269471645355 0.84934205 0.34076735377311707 True -13 38766 30.195791244506836 0.5305769443511963 536.8656005859375 0.2046094536781311 726.7838745117188 0.1984870731830597 0.853806 0.30555853247642517 True -14 41535 30.20540952682495 0.5451831817626953 574.1593017578125 0.1901567131280899 724.9424438476562 0.19968661665916443 0.85988903 0.2749488949775696 True -15 44304 30.2360782623291 0.5356845855712891 610.4380493164062 0.1789749711751938 723.2015380859375 0.20085400342941284 0.86619186 0.25407329201698303 True -16 47073 30.23298978805542 0.5356564521789551 597.7424926757812 0.1610540747642517 722.78076171875 0.2010831981897354 0.871729 0.23566928505897522 True -17 49842 30.2118399143219 0.5314576625823975 605.5123291015625 0.3051709532737732 721.3716430664062 0.20204922556877136 0.8718036 0.22835087776184082 True -18 52611 30.203271865844727 0.5327045917510986 588.1417236328125 0.1476065218448639 721.6607666015625 0.20160378515720367 0.873508 0.2252609133720398 True -19 55380 30.189245223999023 0.5251944065093994 542.7992553710938 0.18395015597343445 722.10302734375 0.20110520720481873 0.87312955 0.22570081055164337 False diff --git a/ENCSR794TLA/cherimoya.fold_3.performance.tsv b/ENCSR794TLA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4e6b4ed7f99a0551ab9108ac71c6d3991535c5d1..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -721.6607666015625 0.5333462953567505 0.20160377025604248 0.06932948529720306 0.8735079765319824 0.8218528628349304 0.2252609133720398 \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_4.evaluate.json b/ENCSR794TLA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ddb985a8e1f61f0609c3cab61eaea5eddcbbb966..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF928AWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_4.fit.json b/ENCSR794TLA/cherimoya.fold_4.fit.json deleted file mode 100644 index 5430e276d234fe5d6966d0fa4de4c3de33d801b2..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF928AWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR794TLA/cherimoya.fold_4.log b/ENCSR794TLA/cherimoya.fold_4.log deleted file mode 100644 index 60b6392bebcd26f8261d4b51cc1fc0b642e0e979..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 35.5329213142395 4.891925096511841 680.1006469726562 0.5523000955581665 719.110107421875 0.13266554474830627 0.709873 4.546489715576172 True -1 5536 30.85559868812561 0.8798673152923584 606.0460815429688 0.34904414415359497 688.2263793945312 0.1562557816505432 0.7622944 1.1873573064804077 True -2 8304 30.831555366516113 0.6057286262512207 642.6893310546875 0.417733371257782 681.4566040039062 0.16018682718276978 0.7818768 0.9617065191268921 True -3 11072 30.77185821533203 0.6435546875 620.4534912109375 0.32749128341674805 678.0421752929688 0.1625409871339798 0.7765774 0.4902186095714569 False -4 13840 30.78055238723755 0.626079797744751 695.085693359375 0.4582485258579254 672.3427734375 0.16586443781852722 0.80116117 0.4578813314437866 True -5 16608 30.81845259666443 0.624739408493042 596.5654296875 0.31788724660873413 668.938232421875 0.16829019784927368 0.80871284 0.4676351249217987 True -6 19376 30.390949010849 0.6138646602630615 701.04931640625 0.48403123021125793 667.5947875976562 0.16873577237129211 0.81905365 0.4046873152256012 True -7 22144 30.09061861038208 0.6125402450561523 557.0137329101562 0.28984200954437256 664.6892700195312 0.17097711563110352 0.8270564 0.38256996870040894 True -8 24912 30.140573263168335 0.6101899147033691 616.9957275390625 0.5584413409233093 663.6720581054688 0.17203311622142792 0.83071244 0.3757511079311371 True -9 27680 30.201707363128662 0.5968890190124512 488.0381774902344 0.36444270610809326 661.8343505859375 0.17366869747638702 0.8396712 0.3299823999404907 True -10 30448 30.181994915008545 0.6170575618743896 678.453125 0.16362632811069489 660.4442749023438 0.17488157749176025 0.84393793 0.2872599959373474 True -11 33216 30.223683834075928 0.6078166961669922 623.4578247070312 0.3000440001487732 659.1224365234375 0.17652517557144165 0.84876 0.2641736567020416 True -12 35984 30.319637775421143 0.6113505363464355 576.076171875 0.20946843922138214 658.076416015625 0.1768794059753418 0.8552468 0.240817591547966 True -13 38752 30.32562017440796 1.2262506484985352 584.4483642578125 0.18267899751663208 656.8004150390625 0.17810718715190887 0.8597818 0.2337595820426941 True -14 41520 30.28481101989746 21.748523235321045 525.6453247070312 0.19342288374900818 655.7010498046875 0.1788507103919983 0.8650901 0.21349330246448517 True -15 44288 30.67388677597046 0.9230308532714844 605.2216796875 0.11288245767354965 655.2535400390625 0.1791010946035385 0.86706644 0.1991971731185913 True -16 47056 30.343183040618896 2.0392398834228516 517.3805541992188 0.19003325700759888 654.1011352539062 0.18017572164535522 0.8709528 0.18689151108264923 True -17 49824 30.23169183731079 0.6608948707580566 589.2347412109375 0.17734965682029724 653.6898193359375 0.18036696314811707 0.87199324 0.1826217770576477 True -18 52592 30.290768146514893 0.6207666397094727 618.249755859375 0.11040537059307098 655.8328247070312 0.17810602486133575 0.87189144 0.1822357177734375 False -19 55360 30.22943949699402 0.6065406799316406 636.9639282226562 0.17826296389102936 655.0289306640625 0.17936448752880096 0.871218 0.1825573891401291 False diff --git a/ENCSR794TLA/cherimoya.fold_4.performance.tsv b/ENCSR794TLA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 055270a25580f0c4c780f2f8d3e7f548fc367e19..0000000000000000000000000000000000000000 --- a/ENCSR794TLA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -653.6898193359375 0.5498948693275452 0.18036696314811707 0.05732255429029465 0.8719932436943054 0.799778401851654 0.1826217770576477 \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_0.evaluate.json b/ENCSR798XLO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 547ac0c108a9fa6156d8e30e698d9b8adc18fabd..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF302WHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_0.fit.json b/ENCSR798XLO/cherimoya.fold_0.fit.json deleted file mode 100644 index f1f56cef7e601bee179b72fdb8a53d7b03703360..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF302WHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_0.log b/ENCSR798XLO/cherimoya.fold_0.log deleted file mode 100644 index c52d8646e58cfcde46f813310c33b7d3d2cf28d4..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 35.89378523826599 4.665123224258423 794.8870239257812 0.6788566708564758 1092.4595947265625 0.3070603013038635 0.7059449 7.370806694030762 True -1 5522 30.552894353866577 0.806781530380249 906.847412109375 0.5530865788459778 974.970947265625 0.3810553252696991 0.7606024 1.8243154287338257 True -2 8283 30.50674271583557 1.970346212387085 995.3900146484375 0.5039723515510559 952.4909057617188 0.39108791947364807 0.7772783 0.9618135690689087 True -3 11044 30.516388654708862 0.6009385585784912 913.2919311523438 0.6142368316650391 941.7191162109375 0.3972907066345215 0.78709286 0.9365537762641907 True -4 13805 30.461111545562744 0.5616796016693115 879.1696166992188 0.5232301354408264 935.3425903320312 0.39954113960266113 0.795814 0.8187047839164734 True -5 16566 30.443614959716797 0.5718770027160645 593.4723510742188 0.4193498492240906 930.9669189453125 0.4035223126411438 0.8028679 0.7621852159500122 True -6 19327 30.498839616775513 1.0169715881347656 648.6988525390625 0.44093814492225647 923.71728515625 0.4082239270210266 0.8101207 0.6576570272445679 True -7 22088 30.44895076751709 0.5632152557373047 680.913818359375 0.6136820316314697 920.0366821289062 0.4099498391151428 0.814795 0.5971376299858093 True -8 24849 30.47735285758972 0.6282329559326172 748.4447021484375 0.4716722369194031 916.040283203125 0.4135141670703888 0.8207355 0.5722234845161438 True -9 27610 30.447031021118164 0.5702159404754639 699.3189697265625 0.4808287024497986 913.9944458007812 0.414082795381546 0.8253573 0.5375645756721497 True -10 30371 30.493376970291138 0.5545368194580078 751.678955078125 0.41886985301971436 912.9745483398438 0.41470393538475037 0.8317034 0.5301011204719543 True -11 33132 30.49836254119873 0.559532880783081 610.677734375 0.3430309295654297 907.1180419921875 0.41938939690589905 0.83569205 0.4917246997356415 True -12 35893 30.46522355079651 0.6621034145355225 846.1956176757812 0.3800256848335266 905.4590454101562 0.4197310507297516 0.8399201 0.47032955288887024 True -13 38654 30.49221134185791 0.5705294609069824 682.4481811523438 0.5287033319473267 901.6402587890625 0.4232611060142517 0.84255344 0.449598103761673 True -14 41415 30.509271144866943 0.5518689155578613 869.544189453125 0.3501606583595276 898.6412353515625 0.4246286451816559 0.8458923 0.4252574145793915 True -15 44176 30.484744548797607 2.0944981575012207 968.9185180664062 0.29561299085617065 898.0513305664062 0.42619502544403076 0.85005826 0.4099978506565094 True -16 46937 30.483082056045532 0.5644099712371826 660.4248657226562 0.33149248361587524 897.5573120117188 0.4261135756969452 0.85144836 0.3966676890850067 True -17 49698 29.97640347480774 0.5547146797180176 608.8400268554688 0.34245479106903076 896.14404296875 0.42800968885421753 0.8513247 0.3909100890159607 False -18 52459 29.917897939682007 0.5691373348236084 884.5465087890625 0.37085819244384766 899.6787719726562 0.42423897981643677 0.8497942 0.3920828700065613 False -19 55220 29.89538288116455 0.5611701011657715 828.472412109375 0.4370112419128418 896.5543212890625 0.428244411945343 0.8477893 0.39483559131622314 False diff --git a/ENCSR798XLO/cherimoya.fold_0.performance.tsv b/ENCSR798XLO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 04ba0ae408bf72a5ff09626f25c88b24c67cb78f..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -897.5573120117188 0.3310096263885498 0.426113486289978 0.21848921477794647 0.8514483571052551 0.8010945320129395 0.3966676890850067 \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_1.evaluate.json b/ENCSR798XLO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index afd4bb764700ee37901b4c6e353bd336a3568afd..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF302WHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_1.fit.json b/ENCSR798XLO/cherimoya.fold_1.fit.json deleted file mode 100644 index 569fd814971e0a59e50e26b972647cb005699ae4..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF302WHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_1.log b/ENCSR798XLO/cherimoya.fold_1.log deleted file mode 100644 index 8218ed1d435ec72036e0df0ad611ec5a9d64630e..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2681 34.40944242477417 5.981354475021362 811.1071166992188 0.6762518882751465 1283.5841064453125 0.3102688491344452 0.7233657 8.324469566345215 True -1 5362 29.606361627578735 0.7929110527038574 956.322265625 0.6836466193199158 1130.7828369140625 0.3954326808452606 0.77821094 2.2714600563049316 True -2 8043 29.63622498512268 1.9687061309814453 882.435546875 1.0734323263168335 1101.98095703125 0.4071410596370697 0.7988405 1.0446974039077759 True -3 10724 29.584341049194336 1.0076253414154053 691.5513916015625 0.5137442350387573 1089.7159423828125 0.41353392601013184 0.8054359 0.9124301671981812 True -4 13405 29.638070583343506 0.7827792167663574 754.1858520507812 0.5922813415527344 1079.531982421875 0.4190250039100647 0.81455195 0.8144419193267822 True -5 16086 29.63289165496826 0.7883093357086182 836.73583984375 0.3911246359348297 1078.421630859375 0.41867607831954956 0.81833065 0.7134267091751099 True -6 18767 29.64015507698059 0.8026309013366699 865.5931396484375 0.6677760481834412 1070.6884765625 0.4236380457878113 0.82416266 0.660942018032074 True -7 21448 30.200652837753296 0.7722694873809814 665.627685546875 0.6391390562057495 1063.8095703125 0.4276939928531647 0.830215 0.6497650146484375 True -8 24129 29.608294010162354 1.082921028137207 651.7711181640625 0.4153643846511841 1060.8448486328125 0.4295464754104614 0.8358914 0.6295819282531738 True -9 26810 29.589827299118042 0.7877566814422607 836.31689453125 0.4194956123828888 1060.721435546875 0.42675212025642395 0.840079 0.5681447386741638 True -10 29491 29.644591808319092 0.7771708965301514 651.7294921875 0.3792128562927246 1054.3890380859375 0.4316293001174927 0.84466046 0.5296237468719482 True -11 32172 29.60280442237854 0.7836325168609619 631.898681640625 0.33193346858024597 1047.125 0.4362395703792572 0.84985936 0.5128334164619446 True -12 34853 29.615894556045532 0.8000462055206299 766.6290893554688 0.38060569763183594 1041.3756103515625 0.4400087296962738 0.8560308 0.4889509975910187 True -13 37534 29.618218660354614 0.7795231342315674 619.6673583984375 0.3854995369911194 1039.0836181640625 0.4404427111148834 0.8625407 0.46512123942375183 True -14 40215 29.596686363220215 0.7848160266876221 674.562255859375 0.312012255191803 1039.4515380859375 0.43866243958473206 0.8654771 0.4420376121997833 True -15 42896 29.671762228012085 0.7737362384796143 789.9360961914062 0.44812119007110596 1036.45556640625 0.44185107946395874 0.8692745 0.4149433672428131 True -16 45577 29.601322889328003 2.907928228378296 691.6375732421875 0.3372517228126526 1037.6578369140625 0.44035351276397705 0.8700039 0.40204980969429016 True -17 48258 29.662530422210693 0.7867379188537598 838.707763671875 0.2953556180000305 1033.5804443359375 0.44428160786628723 0.8718478 0.39470282196998596 True -18 50939 29.778927326202393 0.8083400726318359 741.9092407226562 0.22242429852485657 1035.755615234375 0.442139595746994 0.87023354 0.39577189087867737 False -19 53620 29.533768892288208 0.7865822315216064 808.1700439453125 0.24973216652870178 1039.3193359375 0.4392473101615906 0.86920416 0.39680996537208557 False diff --git a/ENCSR798XLO/cherimoya.fold_1.performance.tsv b/ENCSR798XLO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4e46b82b0dee5c74545c6c1ec0b25570267c636b..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1033.5804443359375 0.31098559498786926 0.44428154826164246 0.24497874081134796 0.8718478083610535 0.8484532833099365 0.39470282196998596 \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_2.evaluate.json b/ENCSR798XLO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5f1f1acac8954887b39b9de5880a1a46ba0966a3..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF302WHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_2.fit.json b/ENCSR798XLO/cherimoya.fold_2.fit.json deleted file mode 100644 index b6682b9e0fc0ad13cc00578e373f22392fb09929..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF302WHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_2.log b/ENCSR798XLO/cherimoya.fold_2.log deleted file mode 100644 index a7fdbad10677ae55ca9139eea18a377a41f2a47e..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2886 36.24595546722412 3.9189937114715576 811.9373779296875 0.6867959499359131 1141.9720458984375 0.307132750749588 0.70028234 7.84634256362915 True -1 5772 31.89478373527527 0.6241917610168457 688.870849609375 0.5581309199333191 1012.1866455078125 0.3794552683830261 0.77150166 1.9879459142684937 True -2 8658 31.849576234817505 0.634361743927002 859.605712890625 0.541211724281311 992.378173828125 0.39084604382514954 0.77855957 1.1005820035934448 True -3 11544 31.908665895462036 0.8173267841339111 671.1436767578125 0.6152445077896118 986.95263671875 0.3938697874546051 0.78827727 0.9274209141731262 True -4 14430 31.835920333862305 1.194718837738037 786.8154296875 0.5358877778053284 981.9646606445312 0.3960588872432709 0.7984695 0.8212569355964661 True -5 17316 31.8421893119812 0.6180384159088135 807.1689453125 0.4882946014404297 975.2715454101562 0.40001180768013 0.8050063 0.8160872459411621 True -6 20202 31.96058750152588 24.214850187301636 620.2374267578125 0.49807125329971313 970.6384887695312 0.4018092155456543 0.8103972 0.6008989810943604 True -7 23088 31.913135528564453 19.74716281890869 828.3775024414062 0.7146117687225342 964.4801635742188 0.4066984951496124 0.8182065 0.5906290411949158 True -8 25974 31.89795708656311 0.6171128749847412 886.896728515625 0.5493614673614502 962.13232421875 0.4074743688106537 0.82176137 0.5791091918945312 True -9 28860 31.854679107666016 0.6163454055786133 546.945068359375 0.41682687401771545 959.6090698242188 0.4090065658092499 0.82672256 0.5553379654884338 True -10 31746 31.861882209777832 0.6159837245941162 730.0272216796875 0.3478984832763672 954.8502197265625 0.41186001896858215 0.8327193 0.5247248411178589 True -11 34632 31.87506651878357 0.6071863174438477 719.5767211914062 0.29928499460220337 947.7760620117188 0.4173513352870941 0.8375256 0.49438896775245667 True -12 37518 31.825196266174316 1.7393038272857666 548.9580078125 0.45228326320648193 944.3201293945312 0.4190782308578491 0.8400307 0.46361595392227173 True -13 40404 31.89625334739685 0.6564199924468994 664.7659912109375 0.27839362621307373 942.5866088867188 0.4194582998752594 0.84682965 0.44572123885154724 True -14 43290 31.902526378631592 0.61069655418396 761.970947265625 0.5639572143554688 939.2548217773438 0.42193838953971863 0.8489561 0.41769593954086304 True -15 46176 31.969132900238037 0.6241664886474609 725.354248046875 0.37211111187934875 936.0394287109375 0.4234485626220703 0.8516842 0.39566344022750854 True -16 49062 31.904234886169434 0.6403725147247314 886.2777099609375 0.30835258960723877 935.96484375 0.42389535903930664 0.8520983 0.3862214982509613 True -17 51948 31.90448236465454 0.6093614101409912 843.781005859375 0.22989392280578613 936.514404296875 0.4228954315185547 0.85365474 0.3826991319656372 True -18 54834 31.834473848342896 0.5965936183929443 823.9625244140625 0.25029104948043823 939.1502685546875 0.42067950963974 0.8522901 0.3835022747516632 False -19 57720 32.05693459510803 0.6261217594146729 730.8655395507812 0.3170768618583679 939.1111450195312 0.42136403918266296 0.85156226 0.38494235277175903 False diff --git a/ENCSR798XLO/cherimoya.fold_2.performance.tsv b/ENCSR798XLO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cc70fbbccc00ad79bcb35179e76ac4ccccde40f1..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -936.514404296875 0.3262840211391449 0.4228953719139099 0.22372157871723175 0.8536547422409058 0.8139035701751709 0.3826991319656372 \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_3.evaluate.json b/ENCSR798XLO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bb044b32a40847427eb6a5be07aac05eb505fe1a..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF302WHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_3.fit.json b/ENCSR798XLO/cherimoya.fold_3.fit.json deleted file mode 100644 index 3681e8ec786344c64abd9d8bca1119796210d2bf..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF302WHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_3.log b/ENCSR798XLO/cherimoya.fold_3.log deleted file mode 100644 index 7e427fc9f4ed033f678e76034fed5910dfcb62fe..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 34.79873061180115 3.9023079872131348 830.462646484375 0.7140721082687378 1036.539794921875 0.3066704273223877 0.6887934 7.572253704071045 True -1 5506 30.29436731338501 0.6219100952148438 659.038330078125 0.7731571197509766 926.37255859375 0.37937867641448975 0.7672666 1.8258756399154663 True -2 8259 30.38459610939026 0.9211504459381104 794.8763427734375 0.6919979453086853 899.852783203125 0.39016714692115784 0.786724 1.017328143119812 True -3 11012 30.395203351974487 0.5836145877838135 833.031982421875 0.6080315709114075 893.8525390625 0.3922227919101715 0.7907135 1.07706618309021 True -4 13765 30.36353826522827 0.5712575912475586 708.5597534179688 0.3381631672382355 889.35791015625 0.39498642086982727 0.7963741 0.8904555439949036 True -5 16518 30.338117122650146 0.5544726848602295 918.266845703125 0.723709225654602 886.8712768554688 0.39564600586891174 0.80495554 0.7285537719726562 True -6 19271 30.356401205062866 0.5658121109008789 945.1334228515625 0.7538890838623047 880.1820068359375 0.401920884847641 0.81240934 0.6301252841949463 True -7 22024 30.358203411102295 0.5592014789581299 817.4951171875 0.5001646280288696 879.3571166992188 0.40159687399864197 0.8155807 0.5991248488426208 True -8 24777 30.34175729751587 0.5504429340362549 778.376953125 0.5553816556930542 876.652587890625 0.4040380120277405 0.82039315 0.5710174441337585 True -9 27530 30.419389963150024 0.5586752891540527 852.4366455078125 0.3820393681526184 873.213623046875 0.40661901235580444 0.8239717 0.5528162717819214 True -10 30283 30.42235279083252 2.0487823486328125 672.1570434570312 0.7030311226844788 868.4255981445312 0.40877315402030945 0.8282658 0.559073805809021 True -11 33036 30.392166137695312 0.5520117282867432 809.870361328125 0.4711986780166626 862.8279418945312 0.4131416380405426 0.8349292 0.5140028595924377 True -12 35789 30.35771679878235 0.5927114486694336 840.1497802734375 0.5105685591697693 862.8739624023438 0.4136626720428467 0.837813 0.4890097975730896 True -13 38542 30.336713790893555 0.5520024299621582 782.3489990234375 0.35062551498413086 860.249267578125 0.41516807675361633 0.84455043 0.4438685476779938 True -14 41295 30.364840269088745 0.5711932182312012 739.902099609375 0.30754539370536804 856.7030029296875 0.41888439655303955 0.84715575 0.43367061018943787 True -15 44048 30.414973497390747 0.5635409355163574 590.1168212890625 0.3836616277694702 855.228515625 0.41869619488716125 0.8489687 0.41234666109085083 True -16 46801 30.45254683494568 0.559556245803833 693.5528564453125 0.2630787491798401 854.44091796875 0.41962841153144836 0.85165846 0.3977351188659668 True -17 49554 30.370884656906128 0.5607814788818359 701.4043579101562 0.40410029888153076 858.6935424804688 0.41438812017440796 0.8497282 0.3944314122200012 False -18 52307 30.495317697525024 0.5765354633331299 673.3453979492188 0.44932377338409424 857.0942993164062 0.4169376790523529 0.8470062 0.3937709331512451 False -19 55060 30.433043241500854 0.5570335388183594 811.5546875 0.29030728340148926 858.4491577148438 0.4160599410533905 0.84795845 0.39779695868492126 False diff --git a/ENCSR798XLO/cherimoya.fold_3.performance.tsv b/ENCSR798XLO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3e4ba310ae25c31a8c7f66647a55d0f324dea515..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -854.44091796875 0.3376011252403259 0.41962841153144836 0.21212764084339142 0.8516584634780884 0.7935292720794678 0.3977351188659668 \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_4.evaluate.json b/ENCSR798XLO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7a75de3ea46b6da0b710e439b90855843eb42a0c..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF302WHH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_4.fit.json b/ENCSR798XLO/cherimoya.fold_4.fit.json deleted file mode 100644 index 959eae21098328e1dbab1d25afb8b000045551a9..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF302WHH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR798XLO/cherimoya.fold_4.log b/ENCSR798XLO/cherimoya.fold_4.log deleted file mode 100644 index efef4ba08defe66fb955c46aaeb0d4441ba42468..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2773 36.40821623802185 3.9434680938720703 759.5740966796875 0.5733456611633301 988.6553344726562 0.3107326030731201 0.7097901 7.073334693908691 True -1 5546 30.675002098083496 1.5500555038452148 829.7364501953125 0.600394606590271 900.22412109375 0.37519583106040955 0.7627736 1.7196975946426392 True -2 8319 30.316910982131958 0.6198563575744629 804.9483642578125 0.6742054224014282 881.3875732421875 0.38317713141441345 0.76826125 0.8515859246253967 True -3 11092 30.04495406150818 0.6058337688446045 694.0284423828125 0.6083378791809082 872.818359375 0.3866017162799835 0.779237 0.8063063025474548 True -4 13865 30.05325722694397 0.6100409030914307 782.5823974609375 1.008607029914856 866.65234375 0.3897534906864166 0.7870851 0.7412801384925842 True -5 16638 30.039914846420288 0.5999948978424072 817.6585083007812 0.469200074672699 861.6981201171875 0.3945607542991638 0.793274 0.6730973124504089 True -6 19411 30.0830295085907 0.6269888877868652 830.975341796875 0.9916252493858337 857.6400146484375 0.3970663547515869 0.8024462 0.641636848449707 True -7 22184 30.037532567977905 0.6047248840332031 742.8450927734375 0.6386721134185791 854.6370849609375 0.398717999458313 0.8094143 0.5410508513450623 True -8 24957 30.05786108970642 0.6132998466491699 714.0748291015625 0.4321926236152649 850.9666748046875 0.4011554718017578 0.8137175 0.51603102684021 True -9 27730 30.142388820648193 0.615997314453125 657.1104125976562 0.5333017706871033 845.6876220703125 0.4055245518684387 0.8205973 0.47889602184295654 True -10 30503 30.097797870635986 0.6268489360809326 644.3336181640625 0.3557407855987549 844.6578979492188 0.4069145619869232 0.82272357 0.4731670022010803 True -11 33276 30.09240484237671 0.6348586082458496 626.7154541015625 0.3497124910354614 842.3058471679688 0.4097397029399872 0.8282623 0.4609467685222626 True -12 36049 30.06920862197876 0.6155838966369629 775.163330078125 0.34923672676086426 838.7774658203125 0.4110080301761627 0.8335378 0.4242406487464905 True -13 38822 30.186657428741455 0.6209151744842529 632.8304443359375 0.4740670919418335 838.64599609375 0.4099799692630768 0.8360391 0.4167538285255432 True -14 41595 30.086491584777832 0.6041929721832275 822.29931640625 0.49149930477142334 834.8250732421875 0.41410550475120544 0.84032595 0.4053625762462616 True -15 44368 30.124651193618774 0.6118443012237549 798.759765625 0.41099515557289124 833.2531127929688 0.41642773151397705 0.843858 0.38806697726249695 True -16 47141 30.048748254776 0.6126492023468018 776.9508666992188 0.3859630227088928 831.9938354492188 0.4159514009952545 0.8470456 0.37609121203422546 True -17 49914 30.0085186958313 0.610663652420044 726.7404174804688 0.3077840209007263 833.507080078125 0.41518357396125793 0.8465198 0.3706863224506378 False -18 52687 30.00947642326355 1.2260169982910156 818.57568359375 0.1894901692867279 834.4385986328125 0.4144635498523712 0.84394616 0.37314486503601074 False -19 55460 30.11918354034424 1.0843513011932373 718.878173828125 0.2883451282978058 833.0932006835938 0.41601115465164185 0.8419702 0.37654635310173035 False diff --git a/ENCSR798XLO/cherimoya.fold_4.performance.tsv b/ENCSR798XLO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d8acb48cf4ad6bec10485dde0975a734b7b87ccf..0000000000000000000000000000000000000000 --- a/ENCSR798XLO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -831.9938354492188 0.33956068754196167 0.4159514605998993 0.20569373667240143 0.8470456004142761 0.7861407399177551 0.37609121203422546 \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_0.evaluate.json b/ENCSR799MAX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 56a7a2e231a77ceb698d5e131062e36b433b7301..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF487CTC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_0.fit.json b/ENCSR799MAX/cherimoya.fold_0.fit.json deleted file mode 100644 index e93bdc680137daf6eb186dba13f4c4bfa376f414..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF487CTC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_0.log b/ENCSR799MAX/cherimoya.fold_0.log deleted file mode 100644 index 3c1d083a1d5d89e24a6068ea76f905821cde1c6b..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2371 29.994778156280518 4.276463747024536 155.96221923828125 0.979663610458374 286.92218017578125 0.14412836730480194 0.6649175 5.416880130767822 True -1 4742 26.25041913986206 1.2433445453643799 232.36224365234375 0.8562440872192383 254.67608642578125 0.21349820494651794 0.77144194 2.449779987335205 True -2 7113 26.166619539260864 0.4877457618713379 195.0628204345703 0.7691594362258911 247.11009216308594 0.225986510515213 0.78712666 1.3961234092712402 True -3 9484 26.09667420387268 0.4856386184692383 196.69741821289062 0.6242102384567261 243.89244079589844 0.23257042467594147 0.7999071 1.0020774602890015 True -4 11855 26.09616446495056 0.48591184616088867 190.57669067382812 0.6155038475990295 242.8989715576172 0.23494672775268555 0.8087044 0.9178516268730164 True -5 14226 26.0934054851532 0.48839759826660156 203.475830078125 0.6190459132194519 241.05972290039062 0.23896899819374084 0.8181629 0.7984554171562195 True -6 16597 26.12194848060608 0.4855003356933594 147.84664916992188 0.7111647725105286 239.83273315429688 0.24198508262634277 0.8240446 0.7485821843147278 True -7 18968 26.11851477622986 9.135852098464966 187.12283325195312 0.7898902893066406 239.31565856933594 0.24271774291992188 0.8295492 0.6712923645973206 True -8 21339 25.769197463989258 0.47136616706848145 229.48834228515625 1.0550320148468018 237.95809936523438 0.24596364796161652 0.8350056 0.6313410997390747 True -9 23710 25.59909152984619 0.4782850742340088 175.8798828125 0.859915018081665 237.2362060546875 0.24788059294223785 0.84121794 0.6138846278190613 True -10 26081 25.593295097351074 0.47030043601989746 232.29527282714844 0.462607204914093 237.25775146484375 0.247481569647789 0.8434606 0.5905721783638 True -11 28452 25.580111742019653 1.0599851608276367 213.11146545410156 0.7127596139907837 235.8345184326172 0.25088372826576233 0.84908676 0.5421947836875916 True -12 30823 25.615540504455566 0.46773433685302734 258.235107421875 0.6309512853622437 235.4276580810547 0.2509339153766632 0.8532771 0.5158376693725586 True -13 33194 25.594021797180176 0.4790773391723633 219.63270568847656 0.5642791986465454 234.54258728027344 0.25403258204460144 0.8541389 0.5048335790634155 True -14 35565 25.576370239257812 0.4790215492248535 178.66122436523438 0.5600190162658691 234.08865356445312 0.2544838786125183 0.8585679 0.4886557459831238 True -15 37936 25.599004983901978 0.47291064262390137 189.83074951171875 0.4585127830505371 233.9792938232422 0.2543153166770935 0.8608812 0.4785575568675995 True -16 40307 25.61797547340393 0.4741642475128174 181.6680908203125 0.3263479471206665 233.84280395507812 0.2551654875278473 0.8621345 0.4733034372329712 True -17 42678 25.59026265144348 0.49191784858703613 167.57528686523438 0.38303902745246887 233.76553344726562 0.25515586137771606 0.8629607 0.4744354784488678 True -18 45049 25.603250741958618 0.46868276596069336 218.4860382080078 0.2875618636608124 233.88690185546875 0.25480741262435913 0.8638326 0.4782467782497406 True -19 47420 25.584164142608643 0.472942590713501 157.74862670898438 0.33177244663238525 234.08395385742188 0.2541823983192444 0.861138 0.4854430854320526 False diff --git a/ENCSR799MAX/cherimoya.fold_0.performance.tsv b/ENCSR799MAX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f779b77d9faf77e4caa2498ab7b30fff6a01c83b..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -233.88690185546875 0.5246460437774658 0.2548074424266815 0.06747591495513916 0.8638325929641724 0.8107736110687256 0.4782467782497406 \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_1.evaluate.json b/ENCSR799MAX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e64a52226985f08772733b9b1ba5d724bda5fce4..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF487CTC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_1.fit.json b/ENCSR799MAX/cherimoya.fold_1.fit.json deleted file mode 100644 index 6577a74e9273921e913211b58aedb746b36ed507..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF487CTC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_1.log b/ENCSR799MAX/cherimoya.fold_1.log deleted file mode 100644 index d2479c761baa6362e61a74dd53085e07adf2ee49..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2344 29.57827639579773 3.5461082458496094 175.37594604492188 0.6939600706100464 360.2103271484375 0.1605932116508484 0.6642034 6.817286968231201 True -1 4688 25.88371706008911 0.6600522994995117 181.9898223876953 0.7080708742141724 319.4430847167969 0.23211106657981873 0.7583647 3.5492401123046875 True -2 7032 25.799391269683838 0.6466822624206543 172.49075317382812 0.8213767409324646 306.6923828125 0.2544786036014557 0.7830325 1.7954151630401611 True -3 9376 25.783152103424072 0.6369750499725342 157.92135620117188 0.7798953056335449 303.4158020019531 0.25786930322647095 0.7984877 1.3727298974990845 True -4 11720 25.827802658081055 0.6452136039733887 207.22950744628906 1.1228041648864746 301.70184326171875 0.26152554154396057 0.80696714 1.3042858839035034 True -5 14064 25.812963008880615 0.6428139209747314 142.34735107421875 0.45052456855773926 299.3696594238281 0.26550495624542236 0.81635207 1.1567484140396118 True -6 16408 25.9077045917511 0.6463663578033447 185.65594482421875 0.5744200944900513 297.0907287597656 0.26992741227149963 0.82702255 1.0377384424209595 True -7 18752 25.864253044128418 1.6026184558868408 181.1348114013672 0.6431304216384888 296.37286376953125 0.27045848965644836 0.8339102 0.9774327874183655 True -8 21096 25.851670026779175 0.6505579948425293 225.47608947753906 0.8817432522773743 295.0278015136719 0.2736482620239258 0.84032893 0.8838295936584473 True -9 23440 25.878385305404663 0.6510574817657471 195.62973022460938 0.5509493947029114 293.92919921875 0.2755517363548279 0.84561175 0.8288394808769226 True -10 25784 25.902385711669922 0.6471593379974365 135.4760284423828 0.6984935998916626 293.1722106933594 0.27666163444519043 0.84938705 0.7825029492378235 True -11 28128 25.87886357307434 0.6480720043182373 160.34011840820312 0.6151323318481445 292.00323486328125 0.2791842520236969 0.857198 0.6842619776725769 True -12 30472 25.870253086090088 0.6457500457763672 128.12649536132812 0.6964003443717957 291.0788879394531 0.27995240688323975 0.8621598 0.6514909863471985 True -13 32816 25.29046106338501 2.366360664367676 254.92198181152344 0.701253354549408 289.61456298828125 0.2833595275878906 0.86590743 0.6218156814575195 True -14 35160 25.401984930038452 0.6445574760437012 153.4609832763672 0.4861752390861511 289.39599609375 0.28267011046409607 0.86924696 0.5827359557151794 True -15 37504 25.379667282104492 0.6525256633758545 202.77236938476562 0.612687885761261 288.9102478027344 0.28349995613098145 0.87072396 0.5616790652275085 True -16 39848 25.423208475112915 0.6435728073120117 176.63906860351562 0.5527653098106384 288.3101501464844 0.2848420739173889 0.87335134 0.5541124939918518 True -17 42192 25.410014390945435 0.6384375095367432 228.65090942382812 0.3743157684803009 289.08355712890625 0.28281229734420776 0.8726136 0.5499740839004517 False -18 44536 25.404513120651245 0.6408171653747559 188.17127990722656 0.5136651992797852 289.0527038574219 0.2832362651824951 0.8716966 0.5537368059158325 False -19 46880 25.344331741333008 2.3235912322998047 194.5880889892578 0.4934890866279602 289.0766296386719 0.28357553482055664 0.8704151 0.5558879375457764 False diff --git a/ENCSR799MAX/cherimoya.fold_1.performance.tsv b/ENCSR799MAX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 559ace3a2b3a7c5174c9a8a2a25354251d8399f9..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -288.3101501464844 0.49880948662757874 0.2848421037197113 0.08770443499088287 0.8733513355255127 0.8434464931488037 0.5541124939918518 \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_2.evaluate.json b/ENCSR799MAX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a6179c4f2c6d4f40fc0514caebc9496682221b1f..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF487CTC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_2.fit.json b/ENCSR799MAX/cherimoya.fold_2.fit.json deleted file mode 100644 index 562eff9eea510f24d37aa49b5647ac5ada213d30..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF487CTC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_2.log b/ENCSR799MAX/cherimoya.fold_2.log deleted file mode 100644 index c1d72c74be995b0123feb45338462533a3db4662..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2509 31.560874700546265 3.3846595287323 209.97103881835938 0.9208215475082397 303.48223876953125 0.145661398768425 0.6535288 5.878432273864746 True -1 5018 27.682301998138428 0.49376797676086426 182.3539276123047 1.0647752285003662 265.9076232910156 0.220006063580513 0.7640946 2.5297937393188477 True -2 7527 27.75810694694519 0.48138976097106934 159.47879028320312 0.6203805804252625 258.1069030761719 0.23275713622570038 0.7857758 1.2285839319229126 True -3 10036 27.809686183929443 0.4829683303833008 234.40310668945312 0.6638380289077759 255.58641052246094 0.23615171015262604 0.7987421 1.0057355165481567 True -4 12545 27.76529884338379 0.4833672046661377 167.82247924804688 1.0481922626495361 253.22842407226562 0.24125272035598755 0.8090315 0.9573277235031128 True -5 15054 27.650569200515747 0.4932868480682373 241.83529663085938 0.6353323459625244 251.65939331054688 0.24302427470684052 0.817712 0.8539409041404724 True -6 17563 27.711824655532837 0.48020482063293457 144.79739379882812 0.6160777807235718 250.2191619873047 0.24662195146083832 0.82327485 0.7682994604110718 True -7 20072 27.681007146835327 3.130464553833008 158.08599853515625 0.7438016533851624 249.82325744628906 0.24760867655277252 0.8266774 0.7771835923194885 True -8 22581 27.7338445186615 0.4921400547027588 250.34005737304688 0.5288952589035034 248.72116088867188 0.2490561306476593 0.8337878 0.7038869857788086 True -9 25090 27.675838470458984 0.49305152893066406 142.11837768554688 0.9197518825531006 248.21424865722656 0.25060880184173584 0.83538574 0.6550658941268921 True -10 27599 27.621291875839233 0.48372530937194824 192.9518585205078 0.7810200452804565 246.81724548339844 0.25339576601982117 0.84021103 0.6321996450424194 True -11 30108 27.704253911972046 0.4887542724609375 217.25753784179688 0.5039254426956177 245.96142578125 0.2553536295890808 0.84345394 0.6083315014839172 True -12 32617 27.744309425354004 0.4854905605316162 153.21890258789062 0.500584602355957 246.115234375 0.2544393837451935 0.84851694 0.5661429762840271 True -13 35126 27.710835456848145 0.4859175682067871 154.7427978515625 0.43269169330596924 244.81558227539062 0.25850987434387207 0.8535252 0.5464433431625366 True -14 37635 27.725512742996216 0.49199342727661133 210.98773193359375 0.5886468887329102 244.2617950439453 0.259986937046051 0.8569517 0.5237032771110535 True -15 40144 27.778727531433105 0.8816008567810059 206.987548828125 0.5315015912055969 243.7194061279297 0.2605922520160675 0.860786 0.5079562664031982 True -16 42653 27.14214515686035 0.48315930366516113 181.7213134765625 0.5374007225036621 243.4407196044922 0.2611426115036011 0.86204284 0.4956566095352173 True -17 45162 27.11331558227539 0.4818110466003418 166.01644897460938 0.5039932727813721 243.85975646972656 0.2609023153781891 0.8618533 0.4932679235935211 False -18 47671 27.14104986190796 0.48018646240234375 171.31622314453125 0.299737811088562 244.11557006835938 0.26033830642700195 0.86196375 0.4959838092327118 False -19 50180 27.238415718078613 0.4823167324066162 167.20059204101562 0.5522475838661194 244.7253875732422 0.2579754889011383 0.85902995 0.4982292950153351 False diff --git a/ENCSR799MAX/cherimoya.fold_2.performance.tsv b/ENCSR799MAX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a4fcb98c234e6d65b04c240bad17a044adc37e29..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -243.4407196044922 0.5193979144096375 0.2611426115036011 0.07505998760461807 0.8620428442955017 0.8193726539611816 0.4956566095352173 \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_3.evaluate.json b/ENCSR799MAX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e242a32cd5d5536b19e5cbaaef8701306519c84d..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF487CTC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_3.fit.json b/ENCSR799MAX/cherimoya.fold_3.fit.json deleted file mode 100644 index 186b072fe5b74ad861675428cb7f068e2b8f6847..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF487CTC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_3.log b/ENCSR799MAX/cherimoya.fold_3.log deleted file mode 100644 index 274199746183bc0a255bdb2572ee6e28caeb1c6f..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2398 30.249473094940186 3.3568434715270996 236.25942993164062 0.8423587083816528 299.640869140625 0.15459400415420532 0.62638533 6.068045616149902 True -1 4796 26.65159034729004 1.0414342880249023 183.09945678710938 0.6177891492843628 265.1897888183594 0.22486887872219086 0.7387069 2.702080488204956 True -2 7194 26.47174382209778 1.0082025527954102 183.33035278320312 0.8628617525100708 260.46453857421875 0.23302549123764038 0.7612823 1.5357258319854736 True -3 9592 26.411375284194946 0.48807716369628906 238.24551391601562 0.8558738827705383 256.9935302734375 0.2400289624929428 0.77735364 1.2130205631256104 True -4 11990 26.503507375717163 0.47951555252075195 243.73138427734375 0.7416415214538574 256.2248840332031 0.24111922085285187 0.7870379 1.1608821153640747 True -5 14388 26.460182666778564 0.4749927520751953 219.09033203125 0.6102566719055176 254.26638793945312 0.2465391904115677 0.7980683 1.0553127527236938 True -6 16786 26.41899347305298 2.4888062477111816 229.61846923828125 0.6649188995361328 253.81155395507812 0.2476431131362915 0.7999337 1.0737531185150146 True -7 19184 26.482406854629517 0.48697733879089355 243.96197509765625 0.9605001211166382 252.82472229003906 0.25005853176116943 0.8059603 0.9946920275688171 True -8 21582 26.41596817970276 0.4793834686279297 207.95579528808594 0.8457787036895752 251.4879150390625 0.25315767526626587 0.81135184 0.9006815552711487 True -9 23980 26.440773487091064 0.4797396659851074 211.00404357910156 0.7161937952041626 250.63967895507812 0.25439581274986267 0.82205194 0.8083893060684204 True -10 26378 26.58677339553833 0.49581241607666016 217.14251708984375 0.6684514284133911 249.70809936523438 0.2574215829372406 0.8279997 0.7286876440048218 True -11 28776 26.602226972579956 0.4860553741455078 280.6766357421875 1.0167161226272583 249.36419677734375 0.2576804757118225 0.8327996 0.688301682472229 True -12 31174 26.556072473526 0.4861419200897217 219.8704071044922 0.5505489706993103 248.5820770263672 0.2592867612838745 0.8367957 0.6658281087875366 True -13 33572 26.527421474456787 0.4988267421722412 182.64979553222656 0.3806731402873993 247.7447967529297 0.26109012961387634 0.8452413 0.6145616173744202 True -14 35970 26.54894208908081 0.49246859550476074 211.46636962890625 0.595747709274292 246.78074645996094 0.2635306119918823 0.8494713 0.5689327716827393 True -15 38368 26.532941341400146 2.4795210361480713 194.10952758789062 0.537652313709259 246.79823303222656 0.2634827792644501 0.8540304 0.5525528192520142 True -16 40766 26.599122762680054 0.5023880004882812 178.72552490234375 0.5074371099472046 246.3217315673828 0.26412901282310486 0.8566285 0.5382954478263855 True -17 43164 26.55612325668335 0.48941612243652344 191.05653381347656 0.4627307057380676 246.97093200683594 0.2611801028251648 0.85748506 0.5373242497444153 True -18 45562 26.133455991744995 0.4842805862426758 226.94607543945312 0.43808168172836304 246.5372772216797 0.26304295659065247 0.85601175 0.5375536680221558 False -19 47960 25.998751163482666 0.4857978820800781 267.45904541015625 0.3796716332435608 246.51388549804688 0.26295357942581177 0.85698146 0.5401677489280701 False diff --git a/ENCSR799MAX/cherimoya.fold_3.performance.tsv b/ENCSR799MAX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index def999abcc9a8c35e5c83710e69f62d7b8c97f3a..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -246.97093200683594 0.517332911491394 0.2611801028251648 0.075907863676548 0.8574850559234619 0.8154628872871399 0.5373242497444153 \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_4.evaluate.json b/ENCSR799MAX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 48110bf853f4ff165847fe831e80c65bde505115..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF487CTC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_4.fit.json b/ENCSR799MAX/cherimoya.fold_4.fit.json deleted file mode 100644 index 8c7e440c2a7e27b251fa50756c4a23d667676dea..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF487CTC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MAX/cherimoya.fold_4.log b/ENCSR799MAX/cherimoya.fold_4.log deleted file mode 100644 index beea7fc634941803ca91865cac0c842a904accd5..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2433 30.993284702301025 2.621558427810669 277.24658203125 0.8482741117477417 266.422607421875 0.13956713676452637 0.64836204 5.049000263214111 True -1 4866 26.882500648498535 0.4362349510192871 217.95095825195312 1.4149001836776733 238.74246215820312 0.20590266585350037 0.7548026 2.4102330207824707 True -2 7299 26.878396034240723 0.4355943202972412 167.96835327148438 0.8352041840553284 232.5732879638672 0.21429789066314697 0.7714207 1.3541412353515625 True -3 9732 26.856722354888916 0.428239107131958 160.17295837402344 0.7373470067977905 229.3887481689453 0.21978433430194855 0.786875 0.9775149822235107 True -4 12165 26.815281629562378 0.4371984004974365 207.91928100585938 0.7461626529693604 227.2540283203125 0.22347842156887054 0.7942492 0.9137927293777466 True -5 14598 26.8583767414093 0.4266529083251953 161.082275390625 0.550391435623169 226.37669372558594 0.22524355351924896 0.80117387 0.8193570375442505 True -6 17031 26.823363065719604 0.4297952651977539 269.1365966796875 0.7194837331771851 225.01895141601562 0.22875842452049255 0.81065917 0.741845965385437 True -7 19464 26.787060260772705 0.4356544017791748 201.28469848632812 0.5893403887748718 224.20236206054688 0.23044615983963013 0.814385 0.7076296210289001 True -8 21897 26.807377099990845 0.43030357360839844 191.32357788085938 0.6232889294624329 223.92605590820312 0.23101486265659332 0.82338905 0.6646528244018555 True -9 24330 26.800719261169434 0.4243752956390381 244.68942260742188 1.0359233617782593 223.31576538085938 0.2330499291419983 0.8298237 0.6542673707008362 True -10 26763 26.82626461982727 0.4280226230621338 176.74908447265625 0.750640869140625 222.7895050048828 0.23362265527248383 0.8329295 0.6002029180526733 True -11 29196 26.84456992149353 0.42713189125061035 176.57864379882812 0.723187267780304 222.38873291015625 0.2342943549156189 0.8393917 0.5736500024795532 True -12 31629 26.87237286567688 0.4328157901763916 211.60336303710938 0.4441862106323242 220.96900939941406 0.23853681981563568 0.8438776 0.5369653701782227 True -13 34062 26.799922704696655 0.4421122074127197 169.61944580078125 0.4703376293182373 220.503173828125 0.2393924742937088 0.8499556 0.5078009366989136 True -14 36495 26.800195455551147 0.43753981590270996 153.23223876953125 0.5382419228553772 220.21044921875 0.24014787375926971 0.854758 0.48672690987586975 True -15 38928 26.790107011795044 0.43866467475891113 193.193603515625 0.4771769046783447 219.81414794921875 0.24170419573783875 0.85640174 0.4696303606033325 True -16 41361 26.82290506362915 0.43551158905029297 212.77850341796875 0.30135154724121094 219.9083251953125 0.2410743534564972 0.8581375 0.4645153284072876 True -17 43794 26.871706247329712 0.4340333938598633 204.636962890625 0.4598374366760254 219.81443786621094 0.24176107347011566 0.8577909 0.46430128812789917 False -18 46227 26.89321494102478 0.43648433685302734 181.4005889892578 0.3722417950630188 220.1895294189453 0.24046318233013153 0.8580807 0.46811366081237793 False -19 48660 26.91565203666687 0.4309401512145996 199.92193603515625 0.30900609493255615 220.38499450683594 0.2395968735218048 0.85653377 0.47166112065315247 False diff --git a/ENCSR799MAX/cherimoya.fold_4.performance.tsv b/ENCSR799MAX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ec1beb57a10a85d1ca460d81f7d7297e06390cf1..0000000000000000000000000000000000000000 --- a/ENCSR799MAX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.9083251953125 0.533501386642456 0.241074338555336 0.0679967850446701 0.8581374883651733 0.805833101272583 0.4645153284072876 \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_0.evaluate.json b/ENCSR799MVH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1475d138a376dbeff868079de65e6c4c88ec9a70..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF410NGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_0.fit.json b/ENCSR799MVH/cherimoya.fold_0.fit.json deleted file mode 100644 index 5ae859cc6593b3d10f03014d862ba92879e1e445..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF410NGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_0.log b/ENCSR799MVH/cherimoya.fold_0.log deleted file mode 100644 index 3bc833a2428bcbc869cac04251956f0311cb3748..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 35.105610847473145 4.350811004638672 276.1998291015625 0.2713189721107483 462.3946533203125 0.18586108088493347 0.737401 4.277322292327881 True -1 5460 30.28787660598755 0.9561436176300049 371.10125732421875 0.6506986021995544 427.5398864746094 0.22350814938545227 0.7831606 1.4793953895568848 True -2 8190 30.257601022720337 0.7212753295898438 423.83868408203125 0.7438032031059265 420.76336669921875 0.22504939138889313 0.7857777 1.0445328950881958 True -3 10920 30.260212898254395 0.6056540012359619 294.4709777832031 0.32363104820251465 416.0023193359375 0.22666414082050323 0.7912954 1.0745362043380737 True -4 13650 30.246954202651978 0.5807218551635742 370.74859619140625 0.3919943869113922 411.85931396484375 0.23141233623027802 0.8052781 0.7573424577713013 True -5 16380 30.222333431243896 0.5919163227081299 292.58123779296875 0.44317716360092163 409.9944152832031 0.23271998763084412 0.814107 0.6949427127838135 True -6 19110 30.21323323249817 0.5678613185882568 320.18121337890625 0.4869428277015686 406.99407958984375 0.23659463226795197 0.8232455 0.633181631565094 True -7 21840 30.22055745124817 0.5772218704223633 352.87872314453125 0.2563336491584778 405.1596984863281 0.23708711564540863 0.83114123 0.5351607799530029 True -8 24570 29.79453992843628 0.5671586990356445 323.74493408203125 0.294290155172348 402.71441650390625 0.24001671373844147 0.8370002 0.4790663421154022 True -9 27300 29.532645225524902 0.5667688846588135 386.61480712890625 0.33082103729248047 402.58306884765625 0.23977236449718475 0.84505486 0.4264480471611023 True -10 30030 29.727809190750122 0.5784628391265869 416.7091064453125 0.377361536026001 401.3894958496094 0.24109093844890594 0.84894145 0.3895263671875 True -11 32760 29.774688959121704 0.6116611957550049 391.92669677734375 0.27900010347366333 399.712890625 0.24263332784175873 0.8591635 0.34608957171440125 True -12 35490 29.73969864845276 0.5782170295715332 305.35968017578125 0.4285431504249573 397.8358154296875 0.24456477165222168 0.8643062 0.3200182616710663 True -13 38220 29.67150354385376 0.5780425071716309 411.1025695800781 0.421641081571579 397.0597839355469 0.2452014982700348 0.8684619 0.2862318754196167 True -14 40950 29.805856227874756 0.5987591743469238 349.6776123046875 0.2189357429742813 395.7982177734375 0.2474532276391983 0.8764 0.2569483816623688 True -15 43680 29.803028106689453 0.5892257690429688 299.031494140625 0.3313162922859192 395.1758728027344 0.2476818859577179 0.88017136 0.24360118806362152 True -16 46410 29.773000478744507 0.582700252532959 319.32745361328125 0.18260270357131958 395.1796569824219 0.24740038812160492 0.88237727 0.23477545380592346 True -17 49140 29.72431755065918 0.5998079776763916 372.5084228515625 0.10082993656396866 394.21649169921875 0.24878668785095215 0.8823203 0.23046395182609558 False -18 51870 29.74463152885437 0.5922067165374756 313.10491943359375 0.19202983379364014 394.7518615722656 0.24817481637001038 0.88319397 0.23077963292598724 True -19 54600 29.684317111968994 0.6279995441436768 295.47564697265625 0.1678290069103241 395.16357421875 0.24747447669506073 0.88214016 0.23128998279571533 False diff --git a/ENCSR799MVH/cherimoya.fold_0.performance.tsv b/ENCSR799MVH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f0fe4b9161133fbad323d2ca1c58c81c9af5acd7..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -394.7518615722656 0.48814842104911804 0.24817484617233276 0.0863979235291481 0.8831939697265625 0.8278249502182007 0.23077963292598724 \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_1.evaluate.json b/ENCSR799MVH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bc9bc6dca4f30960b18eebb1f0f1bf0631f77ef2..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF410NGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_1.fit.json b/ENCSR799MVH/cherimoya.fold_1.fit.json deleted file mode 100644 index 1b8b6bca6b9dc2bc235a1cb19a96b9caef3669eb..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF410NGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_1.log b/ENCSR799MVH/cherimoya.fold_1.log deleted file mode 100644 index 71cdaf0327c7359b41a5ebf47c0f1f9460db9403..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 34.68829131126404 22.25406312942505 394.9057922363281 0.41085284948349 579.2636108398438 0.20207881927490234 0.726074 5.880375385284424 True -1 5406 29.98252773284912 14.867414474487305 374.990478515625 0.5002539157867432 529.2567138671875 0.24974128603935242 0.7929671 1.879117488861084 True -2 8109 29.95457935333252 1.7002153396606445 278.49822998046875 0.32678237557411194 521.3798828125 0.25303909182548523 0.80055225 1.2226040363311768 True -3 10812 29.910446405410767 1.2988476753234863 337.35009765625 0.38625508546829224 513.9461669921875 0.25605693459510803 0.8059417 1.0402255058288574 True -4 13515 29.61763834953308 0.8184247016906738 361.37884521484375 0.5029686689376831 505.36187744140625 0.2610040009021759 0.8209585 0.8721919059753418 True -5 16218 29.322535037994385 0.7076461315155029 346.430908203125 0.32050684094429016 503.4677734375 0.26221349835395813 0.82743967 0.6624549031257629 True -6 18921 29.282983779907227 0.6815197467803955 327.3706359863281 0.4682057797908783 498.54217529296875 0.2670432925224304 0.8382538 0.603641927242279 True -7 21624 29.259223222732544 0.6912703514099121 389.1634521484375 0.39361393451690674 495.05340576171875 0.2711693048477173 0.8428968 0.5565052032470703 True -8 24327 29.310282230377197 0.7096478939056396 346.9771728515625 0.3937312662601471 493.54412841796875 0.27193665504455566 0.849756 0.5508276224136353 True -9 27030 29.2481849193573 0.6799521446228027 503.3089294433594 0.4821189343929291 491.616455078125 0.27359482645988464 0.85285425 0.5160991549491882 True -10 29733 29.304431676864624 0.6919612884521484 413.57916259765625 0.4785464107990265 489.08355712890625 0.27680498361587524 0.8577111 0.49305492639541626 True -11 32436 29.25101065635681 0.7055485248565674 278.4024353027344 0.18727976083755493 487.53240966796875 0.27859053015708923 0.86393905 0.46046018600463867 True -12 35139 29.25844669342041 0.6837756633758545 459.5135192871094 0.5497263669967651 485.1416015625 0.2801720201969147 0.87095195 0.41598689556121826 True -13 37842 29.274592638015747 0.6732311248779297 314.64251708984375 0.22396615147590637 483.8111877441406 0.2818487882614136 0.8794049 0.3605852425098419 True -14 40545 29.40884017944336 0.7108213901519775 322.3214416503906 0.30804622173309326 482.18634033203125 0.28318649530410767 0.8857831 0.3325488865375519 True -15 43248 29.290770292282104 0.9446179866790771 390.95452880859375 0.28931301832199097 481.03228759765625 0.28403204679489136 0.88913214 0.31211698055267334 True -16 45951 29.348868131637573 0.6905393600463867 273.6806640625 0.19016748666763306 480.9403381347656 0.28420528769493103 0.89029306 0.30527985095977783 True -17 48654 29.34589457511902 0.6902616024017334 360.2806396484375 0.17518314719200134 480.05096435546875 0.28478530049324036 0.89086604 0.29527029395103455 True -18 51357 29.371885776519775 0.6934638023376465 358.06011962890625 0.15720507502555847 482.3099060058594 0.2816654145717621 0.8912114 0.29330068826675415 True -19 54060 29.34578537940979 0.6750564575195312 396.5001220703125 0.1682642698287964 483.0741882324219 0.2813195288181305 0.89018273 0.29544663429260254 False diff --git a/ENCSR799MVH/cherimoya.fold_1.performance.tsv b/ENCSR799MVH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b8f015656873423f2feb1ab9000ac38b23c4eb06..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -482.3099060058594 0.4598413407802582 0.2816654145717621 0.11353357136249542 0.8912113904953003 0.8720238208770752 0.29330068826675415 \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_2.evaluate.json b/ENCSR799MVH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3f4b73240d69f4c97a3d84f271fd5c2f9ee56696..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF410NGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_2.fit.json b/ENCSR799MVH/cherimoya.fold_2.fit.json deleted file mode 100644 index aa53857b728cde1fd8e39231f757b3ecdf98c641..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF410NGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_2.log b/ENCSR799MVH/cherimoya.fold_2.log deleted file mode 100644 index 99cdaf0fca55e088a9f0fe7246d7af669852633b..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 36.446138858795166 4.138463973999023 402.22406005859375 0.3749474883079529 487.3319396972656 0.19102893769741058 0.7109464 4.41226053237915 True -1 5758 31.959615468978882 2.3952231407165527 343.2840576171875 0.37499457597732544 447.4443664550781 0.22679178416728973 0.76130944 1.3058314323425293 True -2 8637 31.91873550415039 0.580669641494751 338.5664367675781 0.2956460118293762 441.79595947265625 0.23120157420635223 0.78817815 1.189466118812561 True -3 11516 31.916898012161255 0.5622298717498779 314.7060546875 0.24617651104927063 435.67681884765625 0.2329457700252533 0.8065271 0.6232513785362244 True -4 14395 31.881142139434814 0.5615558624267578 317.9398193359375 0.47446322441101074 431.18011474609375 0.23652735352516174 0.8190265 0.5632326602935791 True -5 17274 31.902134895324707 2.247816324234009 373.9075927734375 0.4201943278312683 429.11090087890625 0.23730722069740295 0.8233419 0.5190457701683044 True -6 20153 31.93730115890503 0.5666103363037109 387.5130920410156 0.33193546533584595 426.2232360839844 0.23998676240444183 0.82906646 0.47345760464668274 True -7 23032 31.692086935043335 0.5631983280181885 392.79339599609375 0.3350066542625427 426.03509521484375 0.24141058325767517 0.82963806 0.5207099914550781 True -8 25911 31.189193725585938 0.5559923648834229 398.2542724609375 0.2769821286201477 422.3575439453125 0.2442382425069809 0.8372963 0.44773373007774353 True -9 28790 31.24171257019043 0.5699057579040527 427.5960693359375 0.4485265612602234 420.5257873535156 0.2462291270494461 0.84148127 0.4256369471549988 True -10 31669 31.230342149734497 0.5572292804718018 423.2672119140625 0.3948885500431061 419.33502197265625 0.24811595678329468 0.8445997 0.40821969509124756 True -11 34548 31.381296157836914 0.5607633590698242 369.65814208984375 0.20706920325756073 418.11627197265625 0.24975109100341797 0.85230285 0.3819948732852936 True -12 37427 31.288403749465942 0.5597028732299805 317.9400939941406 0.26161685585975647 416.7027587890625 0.25144290924072266 0.8567436 0.3372083306312561 True -13 40306 31.32990002632141 0.5637249946594238 343.67254638671875 0.4279271960258484 415.79425048828125 0.2525606155395508 0.8621879 0.3114165663719177 True -14 43185 31.266189575195312 0.5549395084381104 356.87744140625 0.3913964033126831 413.9199523925781 0.25427332520484924 0.86876315 0.28222358226776123 True -15 46064 31.28123664855957 1.5111370086669922 384.7877197265625 0.361185759305954 413.94915771484375 0.25388652086257935 0.87306446 0.26729774475097656 True -16 48943 31.29534673690796 0.5576751232147217 342.66162109375 0.19313345849514008 413.2931213378906 0.25463423132896423 0.8768956 0.2555561363697052 True -17 51822 31.248661041259766 0.559535026550293 388.4507751464844 0.1384352147579193 413.0254211425781 0.2548515796661377 0.8778619 0.25149089097976685 True -18 54701 31.27520227432251 0.5668003559112549 386.753173828125 0.19305461645126343 412.9405517578125 0.2545529007911682 0.8774244 0.25159603357315063 False -19 57580 31.29453706741333 0.5620367527008057 337.329833984375 0.20580527186393738 413.6239929199219 0.25355345010757446 0.8776673 0.2527756690979004 False diff --git a/ENCSR799MVH/cherimoya.fold_2.performance.tsv b/ENCSR799MVH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8ba7143dc3d97b5c615b95c94addc6478e038850..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -413.0254211425781 0.48098325729370117 0.2548515796661377 0.09790340065956116 0.8778619170188904 0.8405317664146423 0.25149089097976685 \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_3.evaluate.json b/ENCSR799MVH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 37f0d4e599519c5d6220531fed184b0fcbef38b0..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF410NGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_3.fit.json b/ENCSR799MVH/cherimoya.fold_3.fit.json deleted file mode 100644 index 65325d86df2dca9f025bf403f808f35858a84557..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF410NGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_3.log b/ENCSR799MVH/cherimoya.fold_3.log deleted file mode 100644 index 53c95f8ab74ae7d54a65565d8e54df5f4d093db3..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2726 34.96405220031738 4.401885509490967 462.2384948730469 0.6372684836387634 470.3611755371094 0.19548416137695312 0.6761521 4.712283134460449 True -1 5452 30.188480854034424 0.6724941730499268 281.8326416015625 0.2958376109600067 435.0791931152344 0.22932365536689758 0.7240912 1.5179917812347412 True -2 8178 30.23259949684143 0.693148136138916 458.81585693359375 0.8651467561721802 434.48638916015625 0.22808130085468292 0.728561 1.3094412088394165 True -3 10904 30.140779733657837 0.6009173393249512 322.16943359375 0.4579908549785614 424.93634033203125 0.23528704047203064 0.75890595 0.8218616843223572 True -4 13630 30.19253969192505 0.5895218849182129 425.3359375 0.32152891159057617 421.9594421386719 0.2371446043252945 0.7754169 0.7311079502105713 True -5 16356 30.03849983215332 0.574110746383667 407.80511474609375 0.35497862100601196 419.17413330078125 0.24063348770141602 0.7865411 0.6981920003890991 True -6 19082 29.475882530212402 0.5869617462158203 311.60162353515625 0.2430947721004486 417.2774658203125 0.24361471831798553 0.7937582 0.6373270153999329 True -7 21808 29.479573965072632 0.5762355327606201 464.9829406738281 0.3359365463256836 415.897705078125 0.2445460855960846 0.80000794 0.564647376537323 True -8 24534 29.550269603729248 0.5932836532592773 299.74578857421875 0.3425205945968628 413.8807067871094 0.24646396934986115 0.8085834 0.5161212086677551 True -9 27260 29.537694215774536 0.5857980251312256 349.3988037109375 0.29695385694503784 411.64178466796875 0.24967318773269653 0.8139058 0.4926137626171112 True -10 29986 29.480170011520386 0.5945849418640137 339.75433349609375 0.27544671297073364 410.088134765625 0.2506271004676819 0.8211819 0.4355343282222748 True -11 32712 29.555540084838867 0.5969300270080566 336.11297607421875 0.39385467767715454 409.8076477050781 0.2506878077983856 0.8277774 0.41590696573257446 True -12 35438 29.526094913482666 0.5905008316040039 344.3420104980469 0.32753196358680725 408.2647705078125 0.25298863649368286 0.83636594 0.3917289972305298 True -13 38164 29.584553956985474 0.5774705410003662 366.2161865234375 0.2530115842819214 406.5887451171875 0.2546972632408142 0.84500015 0.3545997738838196 True -14 40890 29.53457522392273 0.5822718143463135 324.1062316894531 0.35232338309288025 404.9193115234375 0.2556355595588684 0.85229874 0.33181455731391907 True -15 43616 29.571737051010132 0.591275691986084 321.6780090332031 0.32062476873397827 404.97698974609375 0.25546184182167053 0.85865504 0.31366056203842163 True -16 46342 29.599072217941284 0.5821409225463867 270.0342712402344 0.1398387849330902 403.2391052246094 0.2568134367465973 0.8647699 0.29133298993110657 True -17 49068 29.534291982650757 1.8125557899475098 406.12939453125 0.26773303747177124 402.5475769042969 0.257259726524353 0.86881477 0.28185492753982544 True -18 51794 29.611212968826294 0.5882465839385986 322.072265625 0.1392030417919159 402.994384765625 0.2564464509487152 0.86839503 0.27934297919273376 False -19 54520 29.611206531524658 0.5847535133361816 360.3194885253906 0.29081347584724426 403.2093200683594 0.25552088022232056 0.8671873 0.2805294096469879 False diff --git a/ENCSR799MVH/cherimoya.fold_3.performance.tsv b/ENCSR799MVH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1767b902eb220a717af9969dd8773d3c87f512ff..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -402.5475769042969 0.482046514749527 0.257259726524353 0.09599921852350235 0.8688147664070129 0.816236674785614 0.28185492753982544 \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_4.evaluate.json b/ENCSR799MVH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fbb2f523dfae3e7d0b382e1180436cc45a1ec06f..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF410NGX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_4.fit.json b/ENCSR799MVH/cherimoya.fold_4.fit.json deleted file mode 100644 index 511e78a3f4f65e73b6995d62ebe511570096258b..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF410NGX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR799MVH/cherimoya.fold_4.log b/ENCSR799MVH/cherimoya.fold_4.log deleted file mode 100644 index 112ae78e5a7e8bde2e2071fbaa8da002449c5d35..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2831 36.31000471115112 4.336210489273071 357.0186767578125 0.39669495820999146 409.78997802734375 0.1836494654417038 0.7037276 4.352715492248535 True -1 5662 31.474594116210938 0.6586904525756836 317.04144287109375 0.3924519419670105 385.2355041503906 0.21129149198532104 0.73628724 1.3243088722229004 True -2 8493 31.426186561584473 0.6107726097106934 313.7192077636719 0.20657452940940857 382.77655029296875 0.2130584567785263 0.765105 0.6161409020423889 True -3 11324 31.389946937561035 18.126086711883545 320.30718994140625 0.4384605288505554 375.76165771484375 0.21775703132152557 0.79181194 0.6292470097541809 True -4 14155 31.430448055267334 1.784085988998413 476.8540954589844 0.4988086223602295 373.8132629394531 0.21839575469493866 0.80328816 0.47854912281036377 True -5 16986 31.214998722076416 1.422149658203125 414.66058349609375 0.440327525138855 373.48602294921875 0.21878957748413086 0.80825865 0.497244268655777 True -6 19817 30.7790207862854 0.7946193218231201 325.4218444824219 0.2963525652885437 370.0976867675781 0.2220015674829483 0.8148802 0.35055938363075256 True -7 22648 30.765161514282227 0.6408686637878418 411.1150817871094 0.293163925409317 366.7140197753906 0.2262430340051651 0.82087386 0.3216257095336914 True -8 25479 30.684147357940674 0.6111886501312256 347.5664367675781 0.32644540071487427 365.84283447265625 0.22707043588161469 0.82964945 0.3037201762199402 True -9 28310 30.675078868865967 0.615196943283081 335.4647521972656 0.276263028383255 365.1020202636719 0.2280014306306839 0.8310251 0.3035494089126587 True -10 31141 30.66722583770752 1.1752426624298096 308.116943359375 0.22822833061218262 363.48101806640625 0.23030796647071838 0.83745813 0.2931184470653534 True -11 33972 30.735166788101196 0.6025354862213135 336.2694091796875 0.25982150435447693 362.7507629394531 0.2310190051794052 0.8438993 0.2716372311115265 True -12 36803 30.682921886444092 0.6030354499816895 325.7106628417969 0.24318499863147736 361.9720764160156 0.23217496275901794 0.8495184 0.25664064288139343 True -13 39634 30.734400033950806 0.6020505428314209 342.1522521972656 0.3108551502227783 360.7536926269531 0.23379738628864288 0.8590291 0.24221815168857574 True -14 42465 30.724695920944214 0.6033787727355957 333.8234558105469 0.1938449740409851 359.94488525390625 0.2347194254398346 0.86353934 0.23139573633670807 True -15 45296 30.74971055984497 0.6023292541503906 296.82952880859375 0.1623804271221161 359.0932312011719 0.23561696708202362 0.86864614 0.21926331520080566 True -16 48127 30.707581996917725 0.6046109199523926 360.2605285644531 0.2531994581222534 359.16729736328125 0.2355550229549408 0.87003887 0.2144707888364792 True -17 50958 30.740111112594604 0.5958237648010254 339.49072265625 0.18880613148212433 359.92303466796875 0.23483149707317352 0.87164634 0.21177540719509125 True -18 53789 30.730583667755127 0.6004343032836914 445.99127197265625 0.23306524753570557 359.7645568847656 0.2353752702474594 0.8713458 0.21257439255714417 False -19 56620 30.70896077156067 0.6035149097442627 372.8143310546875 0.14325352013111115 359.95361328125 0.23543588817119598 0.8716524 0.21299584209918976 True diff --git a/ENCSR799MVH/cherimoya.fold_4.performance.tsv b/ENCSR799MVH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index cec7ad31453adac5b0bb94404fd0867317552fa9..0000000000000000000000000000000000000000 --- a/ENCSR799MVH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -359.95361328125 0.49837374687194824 0.2354358732700348 0.08050308376550674 0.8716524243354797 0.8177204132080078 0.21299584209918976 \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_0.evaluate.json b/ENCSR800ADR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e9689337b0e1fe2abf1177824a57b06f30bf2e2a..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130OAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_0.fit.json b/ENCSR800ADR/cherimoya.fold_0.fit.json deleted file mode 100644 index 18ff7260402d87edada6033448027f47ad3c2acc..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF130OAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_0.log b/ENCSR800ADR/cherimoya.fold_0.log deleted file mode 100644 index 9285bd3700f10966adde46b2201e208b21130dc1..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 34.25833582878113 3.4839608669281006 734.058837890625 0.33717480301856995 834.7955932617188 0.3111023008823395 0.75674874 5.2734503746032715 True -1 5508 30.36914086341858 0.5833797454833984 725.8154296875 0.37555602192878723 769.867919921875 0.36951130628585815 0.80593604 1.498824119567871 True -2 8262 30.326833248138428 0.5821535587310791 589.7825927734375 0.35975727438926697 755.769287109375 0.38016071915626526 0.81667924 0.7034822106361389 True -3 11016 30.31679606437683 0.5669796466827393 663.1885986328125 0.27488014101982117 746.4974975585938 0.3868418335914612 0.8288984 0.5165650844573975 True -4 13770 31.004034757614136 0.5720441341400146 732.6181030273438 0.4070848226547241 744.9231567382812 0.3877479135990143 0.8328185 0.5556045174598694 True -5 16524 30.386990785598755 0.5712518692016602 648.5786743164062 0.23887939751148224 744.2498168945312 0.38719919323921204 0.83570653 0.5437811613082886 True -6 19278 30.365649223327637 0.5687870979309082 689.11376953125 0.2799619138240814 740.395263671875 0.39170172810554504 0.84175444 0.4611179828643799 True -7 22032 30.34565567970276 2.4289186000823975 566.4421997070312 0.23833635449409485 736.8778076171875 0.39546918869018555 0.84470665 0.4691714644432068 True -8 24786 30.54008984565735 1.6385538578033447 723.78759765625 0.17559045553207397 734.73095703125 0.3977092504501343 0.85148907 0.44176262617111206 True -9 27540 30.438255310058594 0.6114151477813721 674.3952026367188 0.4313861131668091 731.3906860351562 0.40069127082824707 0.8585752 0.4046351909637451 True -10 30294 30.439799308776855 0.5798628330230713 625.5197143554688 0.21209284663200378 729.4432983398438 0.40056443214416504 0.863642 0.37332940101623535 True -11 33048 30.45077872276306 0.5858473777770996 686.25830078125 0.25686711072921753 727.398681640625 0.40318620204925537 0.8705085 0.3332560956478119 True -12 35802 30.338770866394043 0.5683293342590332 607.2938842773438 0.18398970365524292 725.2959594726562 0.4043292701244354 0.8728397 0.31583258509635925 True -13 38556 30.325619220733643 0.5732741355895996 734.8806762695312 0.1983550786972046 723.74365234375 0.40640944242477417 0.87943614 0.2778918147087097 True -14 41310 30.37279176712036 1.2204113006591797 524.6066284179688 0.14125797152519226 723.005615234375 0.4063809812068939 0.8828838 0.24631676077842712 True -15 44064 30.401025533676147 0.5737478733062744 583.5916748046875 0.16701146960258484 720.6427001953125 0.40899965167045593 0.88747394 0.22053401172161102 True -16 46818 30.3872172832489 0.5717437267303467 660.4581909179688 0.23094826936721802 720.60888671875 0.40804508328437805 0.8924212 0.20127566158771515 True -17 49572 30.31739068031311 0.5631725788116455 526.0270385742188 0.1371675580739975 719.7438354492188 0.40912190079689026 0.8921177 0.1908074915409088 False -18 52326 30.298888683319092 0.5617780685424805 805.8583984375 0.1945973038673401 719.9296264648438 0.4082161784172058 0.8932934 0.188066303730011 True -19 55080 30.325972318649292 0.565438985824585 545.50146484375 0.10002222657203674 720.4020385742188 0.40811702609062195 0.8929744 0.18764185905456543 False diff --git a/ENCSR800ADR/cherimoya.fold_0.performance.tsv b/ENCSR800ADR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ea4a39fb2f4334c39bfccb0120d1ee24b2a16d06..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -719.9296264648438 0.36033958196640015 0.4082162082195282 0.18426759541034698 0.8932933807373047 0.8592830300331116 0.188066303730011 \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_1.evaluate.json b/ENCSR800ADR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 18e61c2178e9631dd9e8becd87a40f5b7346b453..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130OAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_1.fit.json b/ENCSR800ADR/cherimoya.fold_1.fit.json deleted file mode 100644 index b3d55afa1e89e0b520c583c8460a7effea82c0ef..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF130OAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_1.log b/ENCSR800ADR/cherimoya.fold_1.log deleted file mode 100644 index f533447784df50427320c3d63f50252be077985d..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2716 33.86997365951538 3.7257914543151855 564.6821899414062 0.2961195707321167 992.9843139648438 0.322417676448822 0.7410475 5.3314714431762695 True -1 5432 29.95962357521057 0.7044110298156738 774.4625854492188 0.6211960315704346 915.471923828125 0.382544606924057 0.7962059 1.6126502752304077 True -2 8148 29.927546977996826 0.6914081573486328 606.4998779296875 0.4219314455986023 887.5064086914062 0.40076062083244324 0.8136722 0.7660211324691772 True -3 10864 29.947348594665527 0.6950540542602539 731.1546630859375 0.4065491855144501 878.1896362304688 0.4087323844432831 0.817853 0.7685333490371704 True -4 13580 29.95316219329834 0.6930844783782959 522.9605102539062 0.23948612809181213 875.0771484375 0.41106775403022766 0.8216773 0.6723397970199585 True -5 16296 29.885617971420288 1.3084087371826172 606.9920654296875 0.22567243874073029 869.7091674804688 0.41571134328842163 0.8256051 0.6457184553146362 True -6 19012 30.150627374649048 0.6977853775024414 683.507080078125 0.24998721480369568 864.6928100585938 0.418831467628479 0.83364755 0.5846340656280518 True -7 21728 29.89573645591736 0.6793813705444336 630.0382690429688 0.23181754350662231 862.1914672851562 0.4208483397960663 0.8388193 0.5549183487892151 True -8 24444 30.203999519348145 0.6903960704803467 676.1107177734375 0.26902735233306885 860.8462524414062 0.421387642621994 0.844837 0.5466228127479553 True -9 27160 29.88709306716919 0.6934144496917725 594.65283203125 0.18332239985466003 856.067626953125 0.42532527446746826 0.8483791 0.5046230554580688 True -10 29876 29.822675704956055 0.6920723915100098 526.8665161132812 0.227950781583786 850.840576171875 0.4289346933364868 0.8561835 0.45771321654319763 True -11 32592 29.84014129638672 0.6906883716583252 685.9205932617188 0.21397864818572998 846.656494140625 0.4328623116016388 0.86194897 0.4290473759174347 True -12 35308 30.045761108398438 28.277803897857666 597.272705078125 0.2047569453716278 845.6842651367188 0.432991623878479 0.86667824 0.40074700117111206 True -13 38024 29.965012311935425 1.9489328861236572 627.927978515625 0.2163345366716385 843.597412109375 0.4335078299045563 0.8710971 0.3583858013153076 True -14 40740 29.887887477874756 1.1791884899139404 634.3911743164062 0.09595999121665955 840.523193359375 0.43603628873825073 0.8785608 0.31504523754119873 True -15 43456 29.927048921585083 1.265909194946289 579.1323852539062 0.22730767726898193 838.142333984375 0.4384912848472595 0.88268554 0.2782367765903473 True -16 46172 29.97924566268921 0.874042272567749 675.71923828125 0.11986926198005676 840.323486328125 0.4353232979774475 0.8872779 0.2518039643764496 True -17 48888 29.930163145065308 0.6985578536987305 581.9305419921875 0.15632981061935425 838.9081420898438 0.43744519352912903 0.8881081 0.23709852993488312 True -18 51604 29.83860468864441 0.6974575519561768 527.3413696289062 0.14550051093101501 837.7708129882812 0.4383615553379059 0.88879585 0.22838817536830902 True -19 54320 29.92248296737671 10.582921028137207 588.7596435546875 0.10629218071699142 837.575439453125 0.438987672328949 0.88933223 0.22739475965499878 True diff --git a/ENCSR800ADR/cherimoya.fold_1.performance.tsv b/ENCSR800ADR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9b70fef0f869a290561dfec41df05cd42f210bc6..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -837.575439453125 0.33524879813194275 0.438987672328949 0.21672998368740082 0.8893322348594666 0.8730261325836182 0.22739475965499878 \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_2.evaluate.json b/ENCSR800ADR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 82e25bcdf4775d34ec75b0c054ba851d1963840c..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130OAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_2.fit.json b/ENCSR800ADR/cherimoya.fold_2.fit.json deleted file mode 100644 index 84d548e821c3d70ed0132a347225e4c87715733c..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF130OAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_2.log b/ENCSR800ADR/cherimoya.fold_2.log deleted file mode 100644 index 345ccfea99cbf972cc8a132d2666a92a8ef8302c..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2902 36.39024305343628 7.799747943878174 607.5650634765625 0.3944149613380432 881.13818359375 0.31575632095336914 0.741723 5.230478286743164 True -1 5804 32.29617881774902 0.5578892230987549 621.0650024414062 0.21803975105285645 810.4863891601562 0.37198179960250854 0.8022866 1.300959825515747 True -2 8706 32.28817963600159 0.5380568504333496 536.07373046875 0.16991332173347473 795.0791625976562 0.3832821249961853 0.81643206 0.6956944465637207 True -3 11608 32.34398365020752 0.5451865196228027 628.0400390625 0.2658287584781647 789.7552490234375 0.38729625940322876 0.82419974 0.6387901902198792 True -4 14510 32.31842756271362 0.5463523864746094 680.798095703125 0.36018335819244385 786.5706176757812 0.389537513256073 0.8243296 0.6952268481254578 True -5 17412 32.23156499862671 0.5391554832458496 687.6663818359375 0.3473777174949646 785.9239501953125 0.3895462453365326 0.83152175 0.5635107755661011 True -6 20314 32.267128467559814 1.1830437183380127 571.87744140625 0.3766767978668213 778.9075317382812 0.396239310503006 0.8388787 0.5207452774047852 True -7 23216 32.31737661361694 12.173835039138794 597.9798583984375 0.2121536284685135 777.9813232421875 0.39695560932159424 0.8445748 0.46711015701293945 True -8 26118 33.525126218795776 0.5694460868835449 636.706787109375 0.2753768265247345 776.1947631835938 0.39853280782699585 0.8455599 0.46745213866233826 True -9 29020 32.437528133392334 0.5436384677886963 720.3276977539062 0.37100717425346375 772.3807983398438 0.4018230438232422 0.8521499 0.43277037143707275 True -10 31922 32.311471462249756 0.5523412227630615 618.082275390625 0.22004318237304688 771.1832885742188 0.40131422877311707 0.85626715 0.3956139385700226 True -11 34824 32.274078130722046 0.5488376617431641 687.4622802734375 0.44018182158470154 767.7047119140625 0.4048134386539459 0.859306 0.35132843255996704 True -12 37726 32.32648491859436 0.561546802520752 627.5217895507812 0.23218011856079102 765.962646484375 0.4055473208427429 0.86359155 0.33237287402153015 True -13 40628 32.232085943222046 0.5495214462280273 650.200439453125 0.16875998675823212 763.0247802734375 0.40881362557411194 0.8683686 0.30561259388923645 True -14 43530 32.25333881378174 0.5531678199768066 542.4228515625 0.16497793793678284 762.6302490234375 0.4088716208934784 0.8737711 0.26529762148857117 True -15 46432 32.23419737815857 1.1019203662872314 607.3377685546875 0.1295316517353058 761.62353515625 0.4093743562698364 0.87876385 0.23617571592330933 True -16 49334 32.32997989654541 0.5456855297088623 564.1203002929688 0.18090029060840607 760.9218139648438 0.4091563820838928 0.8828855 0.21943560242652893 True -17 52236 32.201783418655396 0.5544676780700684 667.2142944335938 0.1128559410572052 760.5985717773438 0.41026341915130615 0.8848358 0.2097255289554596 True -18 55138 32.25301480293274 0.549309253692627 607.0137329101562 0.09932816028594971 759.3717651367188 0.41148799657821655 0.8836632 0.2077236920595169 False -19 58040 32.21659469604492 0.5491323471069336 656.8863525390625 0.10778501629829407 761.5245971679688 0.409071683883667 0.8840395 0.20874494314193726 False diff --git a/ENCSR800ADR/cherimoya.fold_2.performance.tsv b/ENCSR800ADR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 75735d0eb106a0fcd8a1bdf147958a5f0f370ef3..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -760.5985717773438 0.35456007719039917 0.41026341915130615 0.190133199095726 0.8848357796669006 0.8602670431137085 0.2097255289554596 \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_3.evaluate.json b/ENCSR800ADR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index bf34da3bf280873042fc9ff704fcf1fd254f6586..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130OAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_3.fit.json b/ENCSR800ADR/cherimoya.fold_3.fit.json deleted file mode 100644 index 45fbb45da9d1fca0fa7886025c5b78cbcc8e2ac9..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF130OAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_3.log b/ENCSR800ADR/cherimoya.fold_3.log deleted file mode 100644 index 24bc2c6417836cbc23eb0a52c01c8387d1c4fbe8..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 34.20479416847229 3.5880866050720215 660.3033447265625 0.47659680247306824 811.9664916992188 0.31951987743377686 0.725724 4.720422744750977 True -1 5496 30.310651779174805 0.5758340358734131 603.545166015625 0.3270041346549988 747.5759887695312 0.3720688223838806 0.7839246 1.2751338481903076 True -2 8244 30.319796800613403 0.5571184158325195 622.3517456054688 0.31343749165534973 732.9071655273438 0.3847925662994385 0.81051964 0.6698687672615051 True -3 10992 30.363930463790894 0.5541324615478516 690.292724609375 0.317639023065567 727.09423828125 0.3913709223270416 0.81569946 0.6310137510299683 True -4 13740 30.343353033065796 0.5578293800354004 618.7571411132812 0.39196065068244934 725.1212158203125 0.3941439092159271 0.8135654 0.5907223224639893 False -5 16488 30.337002754211426 0.5627772808074951 573.6478271484375 0.227177232503891 724.1377563476562 0.39372432231903076 0.8195218 0.5778207778930664 True -6 19236 31.027040719985962 0.5693531036376953 655.2727661132812 0.3053086996078491 721.6495971679688 0.39580005407333374 0.82261306 0.561037003993988 True -7 21984 30.67577576637268 28.121797800064087 740.2529296875 0.2958725094795227 718.48828125 0.3990150988101959 0.82741797 0.5070294141769409 True -8 24732 30.322174549102783 0.9083001613616943 627.826416015625 0.2513847351074219 716.2454833984375 0.40161368250846863 0.8364616 0.4624485969543457 True -9 27480 30.33834433555603 0.5612156391143799 633.6068115234375 0.2854805588722229 714.3367919921875 0.40232741832733154 0.8382583 0.45062512159347534 True -10 30228 30.347841501235962 0.5601198673248291 635.908203125 0.34765440225601196 711.86083984375 0.40404388308525085 0.8430877 0.4216994345188141 True -11 32976 30.391772508621216 0.5592713356018066 610.374267578125 0.27708083391189575 709.0569458007812 0.40697672963142395 0.85179263 0.38852986693382263 True -12 35724 30.342683792114258 0.5575447082519531 553.4859008789062 0.16830816864967346 706.8237915039062 0.40899354219436646 0.8558473 0.3543311059474945 True -13 38472 30.292121171951294 2.1218841075897217 567.2236328125 0.20099323987960815 706.7457885742188 0.4071364402770996 0.86213714 0.3161415755748749 True -14 41220 30.34668493270874 0.5662264823913574 698.8868408203125 0.23421356081962585 703.3143920898438 0.4116392135620117 0.86727023 0.286843866109848 True -15 43968 30.40114951133728 0.5607092380523682 563.3062744140625 0.23828676342964172 703.57373046875 0.41048088669776917 0.87206084 0.2521708309650421 True -16 46716 30.35141944885254 1.3782737255096436 649.0293579101562 0.17721879482269287 700.483154296875 0.41386592388153076 0.8770366 0.23205982148647308 True -17 49464 30.374074935913086 0.5545327663421631 581.8485107421875 0.22129610180854797 701.63623046875 0.41277092695236206 0.878627 0.2206532061100006 True -18 52212 30.350579261779785 0.5517325401306152 597.89892578125 0.16547852754592896 702.2366333007812 0.411801278591156 0.8782044 0.21645750105381012 False -19 54960 30.325831651687622 0.5557849407196045 687.3350830078125 0.13412126898765564 701.5706787109375 0.41373640298843384 0.8763786 0.21680696308612823 False diff --git a/ENCSR800ADR/cherimoya.fold_3.performance.tsv b/ENCSR800ADR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9c999091f6c9d96b6cbdddd6f68af65ccd682b61..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -701.63623046875 0.35958972573280334 0.4127708971500397 0.18523304164409637 0.8786270022392273 0.8376168608665466 0.2206532061100006 \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_4.evaluate.json b/ENCSR800ADR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 32f51ad5a2c6aa4c4e144cfb40dddcc9cab2801c..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130OAV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_4.fit.json b/ENCSR800ADR/cherimoya.fold_4.fit.json deleted file mode 100644 index 28d8eed94b396c258cc7ba8560ccb2b0b4020b4b..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF130OAV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800ADR/cherimoya.fold_4.log b/ENCSR800ADR/cherimoya.fold_4.log deleted file mode 100644 index ee7ec38c9bd019add303ed73cf3389261a363d11..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 34.50786781311035 3.7889151573181152 597.9026489257812 0.25453323125839233 777.32763671875 0.3065987527370453 0.73976344 5.053934574127197 True -1 5554 30.562774658203125 0.5999042987823486 617.9681396484375 0.24519510567188263 723.171630859375 0.3587302565574646 0.80165493 1.3278589248657227 True -2 8331 30.537991762161255 0.5768003463745117 632.033935546875 0.37580734491348267 706.8438110351562 0.3712831437587738 0.816533 0.5391457080841064 True -3 11108 30.629728078842163 0.5903172492980957 606.4623413085938 0.2490822821855545 697.6729736328125 0.38057741522789 0.8229526 0.4273568093776703 True -4 13885 30.613471508026123 2.0271098613739014 596.5865478515625 0.3750417232513428 695.4653930664062 0.38229894638061523 0.8275727 0.4700697362422943 True -5 16662 30.683273553848267 0.62164306640625 657.6403198242188 0.3294714093208313 694.9818115234375 0.3819118142127991 0.8349648 0.41777846217155457 True -6 19439 30.604316234588623 0.5987226963043213 570.191162109375 0.2775944173336029 692.2972412109375 0.3847624361515045 0.83847016 0.3945991098880768 True -7 22216 30.61740732192993 0.582303524017334 670.3956909179688 0.19321344792842865 691.7269897460938 0.38441917300224304 0.84177214 0.408321350812912 True -8 24993 30.56612801551819 0.5951342582702637 648.6405029296875 0.33374476432800293 688.47412109375 0.38869404792785645 0.8437585 0.402057409286499 True -9 27770 30.576873540878296 0.595984935760498 596.7998046875 0.17834068834781647 687.3867797851562 0.38785600662231445 0.8507913 0.36505088210105896 True -10 30547 30.682124614715576 26.44608759880066 624.8056030273438 0.16245119273662567 684.6184692382812 0.39192694425582886 0.85591394 0.3558111786842346 True -11 33324 30.590425729751587 11.769314765930176 767.9362182617188 0.23447099328041077 682.6747436523438 0.39389723539352417 0.8622084 0.3175182342529297 True -12 36101 30.77578353881836 0.5902173519134521 501.13232421875 0.21381917595863342 681.316162109375 0.39564716815948486 0.864165 0.3009791672229767 True -13 38878 30.628681898117065 0.6061880588531494 664.5211181640625 0.2988833487033844 679.6617431640625 0.3967798948287964 0.86985236 0.2691693902015686 True -14 41655 30.569483518600464 0.5919466018676758 596.1212158203125 0.167197585105896 678.1522216796875 0.39922428131103516 0.873509 0.243225559592247 True -15 44432 30.569798707962036 0.594057559967041 605.611083984375 0.18673738837242126 677.2855834960938 0.3997475504875183 0.8795944 0.21441838145256042 True -16 47209 30.56319785118103 0.5853962898254395 599.8427734375 0.17444728314876556 676.3511352539062 0.40013280510902405 0.88203335 0.19430120289325714 True -17 49986 31.018033742904663 0.5861432552337646 586.1367797851562 0.1715216040611267 677.281982421875 0.3994317948818207 0.8863641 0.18387867510318756 True -18 52763 30.624167680740356 1.509929895401001 536.23974609375 0.18293407559394836 677.3875122070312 0.3996121883392334 0.88557947 0.1811653971672058 False -19 55540 30.578776121139526 0.5870397090911865 548.523681640625 0.10459589958190918 678.8992919921875 0.3977019190788269 0.885502 0.1814507246017456 False diff --git a/ENCSR800ADR/cherimoya.fold_4.performance.tsv b/ENCSR800ADR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f8bebe73f5d1b15f872e2c4f65b05f1ef4eb3f5e..0000000000000000000000000000000000000000 --- a/ENCSR800ADR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -677.281982421875 0.3682034909725189 0.3994317948818207 0.175241157412529 0.8863641023635864 0.8445674180984497 0.18387867510318756 \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_0.evaluate.json b/ENCSR800KVI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 52d6eed2a1119b6771c6d402029b40d4518c5d2b..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF608ONY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_0.fit.json b/ENCSR800KVI/cherimoya.fold_0.fit.json deleted file mode 100644 index 00584ab83452a6cfbd3d8c0d5ab294131e637aa9..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF608ONY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_0.log b/ENCSR800KVI/cherimoya.fold_0.log deleted file mode 100644 index 57069ccc4c1c40368db16f6556135908d48429bb..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2797 36.10126781463623 14.28667688369751 443.6395263671875 0.20757360756397247 459.2662658691406 0.2812581956386566 0.8097806 2.7255351543426514 True -1 5594 30.83908700942993 23.36317753791809 438.0408020019531 0.4103633165359497 439.267333984375 0.32428988814353943 0.8337695 0.6187116503715515 True -2 8391 30.769835710525513 18.607977628707886 381.77435302734375 0.13448818027973175 432.51422119140625 0.33753347396850586 0.86336154 0.3566766083240509 True -3 11188 30.791651487350464 19.643068075180054 356.2075500488281 0.11511445790529251 431.5885009765625 0.33714690804481506 0.86747676 0.14483609795570374 True -4 13985 30.752628803253174 0.8674025535583496 389.441650390625 0.10980847477912903 430.0442199707031 0.34092235565185547 0.8700785 0.14672675728797913 True -5 16782 30.747171640396118 0.586575984954834 365.5862121582031 0.169071763753891 429.7439270019531 0.34015488624572754 0.8788563 0.14027303457260132 True -6 19579 30.340717554092407 0.5659887790679932 395.58758544921875 0.20479899644851685 427.72332763671875 0.3448386490345001 0.88448995 0.14768093824386597 True -7 22376 30.195727825164795 1.0360031127929688 381.25372314453125 0.13809414207935333 427.51483154296875 0.344703733921051 0.88863087 0.1436699628829956 True -8 25173 30.179956674575806 0.7025086879730225 376.11322021484375 0.10618916153907776 426.98333740234375 0.34538382291793823 0.89528763 0.1283765733242035 True -9 27970 30.197596073150635 0.5788943767547607 373.0079345703125 0.15865448117256165 425.9485778808594 0.3475669324398041 0.8976256 0.12004531174898148 True -10 30767 30.160271167755127 0.5752196311950684 351.60888671875 0.1616697907447815 425.11651611328125 0.34885966777801514 0.9049264 0.10800950229167938 True -11 33564 30.28270697593689 0.5705420970916748 370.0003662109375 0.08036215603351593 424.1273193359375 0.35173389315605164 0.9087045 0.09976101666688919 True -12 36361 30.18153405189514 0.5815598964691162 379.556640625 0.07232307642698288 423.6350402832031 0.3521236777305603 0.91454566 0.09245086461305618 True -13 39158 30.157177209854126 0.5816493034362793 343.57220458984375 0.4018588662147522 423.2131652832031 0.3523433804512024 0.9171466 0.0891956239938736 True -14 41955 30.182064294815063 0.578744649887085 347.64630126953125 0.07421663403511047 422.6234130859375 0.35387739539146423 0.91862476 0.08650089055299759 True -15 44752 30.23604464530945 0.5674171447753906 352.0032653808594 0.1505195051431656 422.68914794921875 0.35336655378341675 0.92033565 0.08341621607542038 True -16 47549 30.231601238250732 0.5790283679962158 371.1383972167969 0.08901533484458923 422.2978515625 0.3547362685203552 0.92266375 0.0819556787610054 True -17 50346 30.241233348846436 0.5657265186309814 374.827392578125 0.13603094220161438 422.3511657714844 0.3544261157512665 0.9218509 0.08059417456388474 False -18 53143 30.179065465927124 0.5679292678833008 383.8382568359375 0.09681542217731476 422.41357421875 0.3547336161136627 0.9221822 0.08013217896223068 False -19 55940 30.20373034477234 0.5700342655181885 322.90142822265625 0.2684459388256073 422.1105041503906 0.35562923550605774 0.9231339 0.08044764399528503 True diff --git a/ENCSR800KVI/cherimoya.fold_0.performance.tsv b/ENCSR800KVI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 03a7636ac1796bc806cd1ee86e154da533410fd4..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -422.1105041503906 0.4209045469760895 0.35562923550605774 0.12199230492115021 0.923133909702301 0.9173652529716492 0.08044764399528503 \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_1.evaluate.json b/ENCSR800KVI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5713cceef0c86b4ee592fce895a78b97647de1ff..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF608ONY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_1.fit.json b/ENCSR800KVI/cherimoya.fold_1.fit.json deleted file mode 100644 index b2d86e2a1ccd219d2d119e2942155de759e78003..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF608ONY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_1.log b/ENCSR800KVI/cherimoya.fold_1.log deleted file mode 100644 index 23bc7592fc1870a964f2253824ca66f9e1ce694a..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2778 35.62404203414917 3.578111171722412 375.77862548828125 0.3203500211238861 531.6181640625 0.28586700558662415 0.7865302 3.3206043243408203 True -1 5556 30.598208904266357 0.6498262882232666 421.7685241699219 0.2017679512500763 506.9801330566406 0.33372679352760315 0.824377 0.7586515545845032 True -2 8334 30.51359272003174 0.7530288696289062 399.48712158203125 0.21261277794837952 497.00738525390625 0.34650689363479614 0.8534109 0.5547296404838562 True -3 11112 30.56770086288452 0.6325182914733887 373.2866516113281 0.1922677904367447 493.1643981933594 0.3527829945087433 0.86368895 0.2210862636566162 True -4 13890 30.6063289642334 0.6598992347717285 362.18341064453125 0.10611384361982346 491.6594543457031 0.35325443744659424 0.8707284 0.1969453990459442 True -5 16668 30.565388917922974 0.6322264671325684 424.55535888671875 0.1950444132089615 489.6889953613281 0.35736680030822754 0.87676495 0.19337911903858185 True -6 19446 29.99697518348694 0.6329331398010254 394.0579528808594 0.12964719533920288 489.255859375 0.35756251215934753 0.88136387 0.18603917956352234 True -7 22224 29.948535442352295 0.6328799724578857 363.5823669433594 0.3239874243736267 488.0111389160156 0.35901468992233276 0.8881056 0.1620057076215744 True -8 25002 30.00256085395813 0.6584782600402832 450.52117919921875 0.29898983240127563 486.23583984375 0.36244818568229675 0.8947045 0.1509280800819397 True -9 27780 29.958924055099487 0.6285006999969482 377.8072814941406 0.09138591587543488 485.1016540527344 0.3632107079029083 0.9005514 0.13882915675640106 True -10 30558 29.998230934143066 1.3500492572784424 407.9464111328125 0.127211332321167 483.9651794433594 0.36551418900489807 0.90529895 0.12380354106426239 True -11 33336 29.959763526916504 0.6550693511962891 341.83099365234375 0.1496565043926239 482.96820068359375 0.3667503297328949 0.9086575 0.11818508058786392 True -12 36114 30.010629892349243 0.6285748481750488 397.08935546875 0.14964497089385986 481.27606201171875 0.36989837884902954 0.91095966 0.11068593710660934 True -13 38892 29.999194622039795 0.6384937763214111 341.10650634765625 0.08963321149349213 480.9654846191406 0.37003183364868164 0.9165146 0.10563720017671585 True -14 41670 29.962021112442017 0.6334333419799805 342.81610107421875 0.08541381359100342 480.0612487792969 0.3715536892414093 0.92100513 0.10028523951768875 True -15 44448 29.995709896087646 0.63871169090271 387.17059326171875 0.06920936703681946 479.31396484375 0.3720631003379822 0.9249766 0.09591390937566757 True -16 47226 29.951963663101196 0.6426000595092773 362.79534912109375 0.09341783076524734 478.7481994628906 0.37348437309265137 0.9265676 0.09284982830286026 True -17 50004 30.091089487075806 0.6339437961578369 338.43524169921875 0.1347501277923584 479.625732421875 0.3710545301437378 0.92860353 0.0915941596031189 True -18 52782 30.113062620162964 1.2037551403045654 394.1431884765625 0.07905689626932144 478.5053405761719 0.3741042912006378 0.9273264 0.09068550169467926 False -19 55560 30.140756845474243 0.6677699089050293 359.3475341796875 0.03838949650526047 478.8144226074219 0.37316611409187317 0.9278416 0.09054715931415558 False diff --git a/ENCSR800KVI/cherimoya.fold_1.performance.tsv b/ENCSR800KVI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 778913f6330136f4d351623d65d0a5497f6cb593..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -479.625732421875 0.4047417938709259 0.3710545003414154 0.1377306431531906 0.9286035299301147 0.9269753098487854 0.0915941596031189 \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_2.evaluate.json b/ENCSR800KVI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6c2a5529011d4f66a615a47cd7acd96ae07b09af..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF608ONY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_2.fit.json b/ENCSR800KVI/cherimoya.fold_2.fit.json deleted file mode 100644 index 1c20eaad3e16318a43ff00d43444a4253906553d..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF608ONY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_2.log b/ENCSR800KVI/cherimoya.fold_2.log deleted file mode 100644 index 369af89835a2c2ab66c98a55cf8874fe11eeb8f7..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2910 36.787588357925415 3.506211757659912 403.9847106933594 0.18072509765625 488.84844970703125 0.2782461941242218 0.7919107 2.6789894104003906 True -1 5820 31.990681409835815 0.6762526035308838 400.80712890625 0.2627319097518921 465.3684387207031 0.3252730965614319 0.8298194 0.6522759199142456 True -2 8730 32.02907419204712 0.6409592628479004 374.6181640625 0.11819316446781158 458.1216735839844 0.33549317717552185 0.8534711 0.4079281985759735 True -3 11640 32.05388164520264 0.572364091873169 386.972412109375 0.2541593313217163 455.3786926269531 0.34103864431381226 0.8548075 0.18963083624839783 True -4 14550 32.00030493736267 2.0840580463409424 373.2024841308594 0.11632558703422546 453.9056091308594 0.344004362821579 0.8627091 0.18734700977802277 True -5 17460 32.01818013191223 0.5734074115753174 339.31219482421875 0.15685756504535675 452.9474792480469 0.3445497155189514 0.86905056 0.17234069108963013 True -6 20370 31.400961875915527 1.3606789112091064 407.8035888671875 0.1969248503446579 452.2875061035156 0.3452809154987335 0.87456137 0.16120991110801697 True -7 23280 31.42803120613098 1.7138524055480957 413.107177734375 0.14945438504219055 450.8073425292969 0.34828925132751465 0.8797654 0.1613704264163971 True -8 26190 31.487926721572876 0.5623886585235596 437.12823486328125 0.1735508143901825 450.0308532714844 0.34988993406295776 0.88577884 0.15427570044994354 True -9 29100 31.837942600250244 0.5787770748138428 381.334228515625 0.11858977377414703 449.02423095703125 0.3507496416568756 0.8895378 0.13915987312793732 True -10 32010 31.562240600585938 0.566643238067627 380.83221435546875 0.2996988892555237 448.40606689453125 0.35189980268478394 0.8937391 0.13273562490940094 True -11 34920 31.558886528015137 0.5712718963623047 399.39630126953125 0.11603458970785141 447.24432373046875 0.35393407940864563 0.8976224 0.1218906044960022 True -12 37830 31.54102897644043 0.5686769485473633 366.66064453125 0.07077456265687943 447.2076110839844 0.3534524738788605 0.90185213 0.11552035063505173 True -13 40740 31.56935477256775 0.5614907741546631 380.3320617675781 0.08552873134613037 446.6055908203125 0.3539648652076721 0.90670276 0.10962119698524475 True -14 43650 31.556661367416382 0.5756916999816895 388.45941162109375 0.1936391443014145 445.5217590332031 0.35713765025138855 0.9089328 0.10412027686834335 True -15 46560 31.46255397796631 0.568324089050293 379.02593994140625 0.10417225956916809 444.68670654296875 0.3586987853050232 0.91222745 0.09878052026033401 True -16 49470 31.514649391174316 0.5603861808776855 408.8293762207031 0.10182694345712662 445.1734313964844 0.3570703864097595 0.9144826 0.09547743201255798 True -17 52380 31.530015468597412 0.5713496208190918 417.07537841796875 0.07316117733716965 444.751708984375 0.35849830508232117 0.91526157 0.09431161731481552 True -18 55290 31.512814044952393 0.5574758052825928 413.54132080078125 0.13019448518753052 445.119140625 0.35744866728782654 0.91539466 0.09436900913715363 True -19 58200 31.547878742218018 0.5691018104553223 408.12451171875 0.1030503511428833 444.9813232421875 0.3581022620201111 0.91492766 0.09434027224779129 False diff --git a/ENCSR800KVI/cherimoya.fold_2.performance.tsv b/ENCSR800KVI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index aab7f5aea7f5cad2b6f0d7981addc10a863f8fde..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -445.119140625 0.4164851903915405 0.35744860768318176 0.1295100897550583 0.91539466381073 0.9104325175285339 0.09436900913715363 \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_3.evaluate.json b/ENCSR800KVI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 668e09d9b684a32506e9dfe9d35440526a5df680..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF608ONY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_3.fit.json b/ENCSR800KVI/cherimoya.fold_3.fit.json deleted file mode 100644 index b27395ad9958bfa629520fc4ce7eb0ab444f7bb7..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF608ONY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_3.log b/ENCSR800KVI/cherimoya.fold_3.log deleted file mode 100644 index dcc65d6709ec84abf73b364e98e6f74146d53b48..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 35.42196869850159 4.258785009384155 393.28057861328125 0.2099589854478836 446.68621826171875 0.2862718999385834 0.779615 3.027350425720215 True -1 5554 30.54180884361267 0.5603611469268799 376.3319091796875 0.2821577787399292 425.36712646484375 0.33125928044319153 0.827282 0.575422465801239 True -2 8331 30.48960280418396 0.5627155303955078 412.4009094238281 0.2117634117603302 421.0148010253906 0.33898159861564636 0.8526617 0.23437972366809845 True -3 11108 30.60169792175293 4.930193662643433 395.1520080566406 0.12047532200813293 418.7399597167969 0.3425193727016449 0.85707504 0.18866178393363953 True -4 13885 30.53324866294861 14.145509481430054 343.0458068847656 0.13971972465515137 416.9448547363281 0.34602007269859314 0.8696339 0.15779978036880493 True -5 16662 30.21300768852234 7.29870343208313 423.12469482421875 0.11286627501249313 416.6379089355469 0.34549224376678467 0.8713487 0.1506856083869934 True -6 19439 30.412988662719727 0.5665841102600098 399.25885009765625 0.14502796530723572 415.49200439453125 0.3492143154144287 0.87884295 0.15716028213500977 True -7 22216 29.946723699569702 0.5621597766876221 372.7383117675781 0.06914757192134857 414.75030517578125 0.35041487216949463 0.88598144 0.1408412754535675 True -8 24993 29.961262941360474 0.5512838363647461 387.04522705078125 0.12003234773874283 414.300537109375 0.35085174441337585 0.89258236 0.13019153475761414 True -9 27770 29.86742067337036 0.547539472579956 376.2400207519531 0.1439504623413086 413.7801818847656 0.3519800007343292 0.8931451 0.1241542398929596 True -10 30547 29.882158279418945 0.5581815242767334 327.096923828125 0.10260137915611267 412.9571838378906 0.35286450386047363 0.89802665 0.11441611498594284 True -11 33324 29.857805967330933 0.5582280158996582 404.15087890625 0.09970429539680481 412.2393798828125 0.35507166385650635 0.9018345 0.1074681431055069 True -12 36101 29.93595576286316 0.547687292098999 341.447021484375 0.11103823781013489 411.6494445800781 0.3562120199203491 0.90435654 0.10326726734638214 True -13 38878 29.908879280090332 1.9172265529632568 371.163330078125 0.09710603207349777 411.5030822753906 0.3564895689487457 0.9070801 0.10014357417821884 True -14 41655 30.059804677963257 0.5455808639526367 340.4478454589844 0.08545967191457748 410.9272766113281 0.35744303464889526 0.90975285 0.09785597771406174 True -15 44432 29.940897941589355 0.5675187110900879 386.9849853515625 0.10442690551280975 410.5457458496094 0.3574294149875641 0.9119501 0.09484566003084183 True -16 47209 30.082059621810913 0.9289782047271729 401.81207275390625 0.11616059392690659 410.1504211425781 0.3590806722640991 0.9136111 0.09203913062810898 True -17 49986 30.049139976501465 0.5513999462127686 401.26947021484375 0.0835757851600647 410.6263122558594 0.35736149549484253 0.91242456 0.09133228659629822 False -18 52763 29.993317127227783 0.567734956741333 337.6857604980469 0.15904514491558075 410.2625427246094 0.3584599494934082 0.9133995 0.09135549515485764 False -19 55540 29.99342966079712 0.5651273727416992 356.0821228027344 0.13820743560791016 410.289794921875 0.3584151864051819 0.9128571 0.09181780368089676 False diff --git a/ENCSR800KVI/cherimoya.fold_3.performance.tsv b/ENCSR800KVI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 144be20f3a30cbb7c1b47f5fa3575cad201cb6a9..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -410.1504211425781 0.4204001724720001 0.35908064246177673 0.12108584493398666 0.913611114025116 0.9052043557167053 0.09203913062810898 \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_4.evaluate.json b/ENCSR800KVI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4e82d7f9d90bf8503347992d9cf060e5a7c12e94..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF608ONY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_4.fit.json b/ENCSR800KVI/cherimoya.fold_4.fit.json deleted file mode 100644 index 643922006608dd9db8279230e2dcc8e411f9f50e..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF608ONY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800KVI/cherimoya.fold_4.log b/ENCSR800KVI/cherimoya.fold_4.log deleted file mode 100644 index d16a2d1b85c0f97dd539922bfacd39c0cd2040a1..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2800 35.66728615760803 3.549427032470703 332.13018798828125 0.18526765704154968 442.92431640625 0.27965569496154785 0.80294603 2.61765456199646 True -1 5600 30.775049924850464 0.6035075187683105 392.87493896484375 0.15863803029060364 423.633056640625 0.3221724331378937 0.8288154 0.5646777749061584 True -2 8400 30.888901710510254 3.193678140640259 421.14569091796875 0.17036151885986328 417.74993896484375 0.3331146538257599 0.8576224 0.38684946298599243 True -3 11200 30.759273529052734 1.293351650238037 381.5081787109375 0.18879088759422302 415.9988708496094 0.3351522982120514 0.85643756 0.16810037195682526 False -4 14000 30.80077314376831 0.6179978847503662 365.84588623046875 0.12040141224861145 415.5462341308594 0.336618572473526 0.8560543 0.1633603721857071 False -5 16800 30.80080819129944 0.6030805110931396 397.1416320800781 0.12047021836042404 414.4713134765625 0.33938872814178467 0.8677048 0.15228967368602753 True -6 19600 30.803088665008545 0.6103670597076416 356.91265869140625 0.16357220709323883 413.53546142578125 0.3408399224281311 0.8751295 0.1392289251089096 True -7 22400 30.74739980697632 0.6065852642059326 330.6286315917969 0.1461499035358429 412.7589111328125 0.3416305184364319 0.8816817 0.12575574219226837 True -8 25200 30.14737296104431 0.6024539470672607 327.50299072265625 0.1993846744298935 411.5984802246094 0.3442094624042511 0.8879179 0.11978545039892197 True -9 28000 30.355350971221924 1.077744960784912 401.0614318847656 0.13174813985824585 411.33465576171875 0.3440376818180084 0.8949154 0.11379469931125641 True -10 30800 30.30147647857666 0.6056861877441406 355.8934326171875 0.09277698397636414 410.54876708984375 0.34624359011650085 0.89979696 0.10830016434192657 True -11 33600 30.193131685256958 0.9254107475280762 366.0777587890625 0.1522606462240219 409.4544982910156 0.3491092622280121 0.90218043 0.10031281411647797 True -12 36400 30.2056941986084 0.596616268157959 340.45794677734375 0.19036853313446045 409.246337890625 0.348543643951416 0.9066417 0.09605856984853745 True -13 39200 30.247689962387085 0.6007370948791504 378.28631591796875 0.13213719427585602 408.97479248046875 0.3490179181098938 0.9094706 0.09027592837810516 True -14 42000 30.37922191619873 0.6117889881134033 351.33074951171875 0.09744483232498169 408.7444152832031 0.34855812788009644 0.91313946 0.0853445753455162 True -15 44800 30.386184692382812 0.6016955375671387 356.54736328125 0.11649762094020844 408.00433349609375 0.3509077727794647 0.9164866 0.08249834924936295 True -16 47600 30.324452877044678 0.5912847518920898 392.0179748535156 0.1852874457836151 407.7822570800781 0.3509368300437927 0.9174355 0.07919298112392426 True -17 50400 30.353210926055908 0.5944902896881104 356.14031982421875 0.081997349858284 407.95050048828125 0.3505462110042572 0.91941124 0.07799148559570312 True -18 53200 30.305907726287842 0.6104393005371094 393.608642578125 0.1210729330778122 408.0943298339844 0.3502555191516876 0.91906714 0.07763469219207764 False -19 56000 30.399548292160034 0.5975327491760254 435.2931823730469 0.09416013956069946 407.8861999511719 0.35118111968040466 0.9187972 0.07754940539598465 False diff --git a/ENCSR800KVI/cherimoya.fold_4.performance.tsv b/ENCSR800KVI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index df433458af0a1fb8fed6a2a5504db6ef897e61f0..0000000000000000000000000000000000000000 --- a/ENCSR800KVI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -407.95050048828125 0.4250260889530182 0.3505462110042572 0.12092635780572891 0.9194112420082092 0.9131588339805603 0.07799148559570312 \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_0.evaluate.json b/ENCSR800QGE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3dbc9fb08105e2cb4d55ad2514d3c46165b086b1..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576JCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_0.fit.json b/ENCSR800QGE/cherimoya.fold_0.fit.json deleted file mode 100644 index 9bdef5f36e68e8f3d96c0a2c15073cfdd31d2e53..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF576JCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_0.log b/ENCSR800QGE/cherimoya.fold_0.log deleted file mode 100644 index 31f459d91b53e460eb7ff4beee0d50feb46814e8..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2553 32.90024447441101 4.439103841781616 132.8849334716797 0.5696892738342285 207.028076171875 0.1258411407470703 0.63832355 2.5700385570526123 True -1 5106 28.087119340896606 0.9218816757202148 140.90658569335938 0.4644474983215332 200.57447814941406 0.16393248736858368 0.7022966 0.9154296517372131 True -2 7659 28.34730362892151 0.5233018398284912 172.5216522216797 0.602237343788147 197.9573516845703 0.17621687054634094 0.72125417 0.6388773322105408 True -3 10212 28.37579321861267 0.532954216003418 135.9423370361328 0.4638047516345978 196.9707489013672 0.17889824509620667 0.73619777 0.5102981328964233 True -4 12765 28.326852321624756 0.5490541458129883 179.69326782226562 0.7169471979141235 196.40896606445312 0.1819894164800644 0.74358636 0.5206044912338257 True -5 15318 28.330806493759155 0.5142712593078613 163.89939880371094 0.40662524104118347 195.87403869628906 0.1848175972700119 0.7543141 0.49512824416160583 True -6 17871 28.369678258895874 0.5245003700256348 148.45558166503906 0.516404390335083 195.4930419921875 0.18756452202796936 0.754882 0.48519793152809143 True -7 20424 28.271233320236206 0.5172970294952393 156.33880615234375 0.669697642326355 195.16055297851562 0.1891126185655594 0.7617985 0.421230673789978 True -8 22977 28.284099340438843 0.5047774314880371 132.58822631835938 0.5129776000976562 194.95889282226562 0.19000034034252167 0.76677173 0.37716639041900635 True -9 25530 28.353541612625122 0.5374464988708496 139.31825256347656 0.33629587292671204 194.63587951660156 0.19238491356372833 0.7712895 0.37401342391967773 True -10 28083 28.362293004989624 0.5033440589904785 155.0386505126953 0.32601696252822876 194.488037109375 0.19212087988853455 0.7748958 0.3473435640335083 True -11 30636 28.25709843635559 0.5158858299255371 138.07565307617188 0.4406275153160095 194.13827514648438 0.19378270208835602 0.7807152 0.339962899684906 True -12 33189 28.372241735458374 0.521420955657959 164.5221710205078 0.395626962184906 193.77500915527344 0.19564548134803772 0.78433347 0.3211357295513153 True -13 35742 28.37536358833313 1.7678687572479248 151.72299194335938 0.4065324068069458 193.74111938476562 0.19567202031612396 0.7889069 0.3088649809360504 True -14 38295 28.3205726146698 0.5318896770477295 175.59140014648438 0.4285944700241089 193.47337341308594 0.19745057821273804 0.7952684 0.2897051274776459 True -15 40848 28.31951069831848 0.5092403888702393 150.04083251953125 0.5290981531143188 193.57102966308594 0.19688156247138977 0.80002016 0.28648287057876587 True -16 43401 28.367149114608765 0.5130574703216553 136.49378967285156 0.25239989161491394 193.24417114257812 0.1990085393190384 0.8021525 0.2785484194755554 True -17 45954 28.339973211288452 0.5221114158630371 145.3524169921875 0.29867252707481384 193.25537109375 0.19964319467544556 0.80321276 0.2776821553707123 True -18 48507 28.324070692062378 0.5117015838623047 135.47189331054688 0.28860199451446533 193.55020141601562 0.19705520570278168 0.80055326 0.27989351749420166 False -19 51060 28.35072374343872 0.5206851959228516 146.35397338867188 0.30754509568214417 193.5882568359375 0.19683916866779327 0.79948276 0.2805205285549164 False diff --git a/ENCSR800QGE/cherimoya.fold_0.performance.tsv b/ENCSR800QGE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 6edb8c19788011fd7b487589f5da889c78707deb..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -193.25537109375 0.5547786951065063 0.19964319467544556 0.05125938728451729 0.8032127618789673 0.7345564365386963 0.2776821553707123 \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_1.evaluate.json b/ENCSR800QGE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8cfb733f9224ce860cbdaeb84c06abeae739173e..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576JCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_1.fit.json b/ENCSR800QGE/cherimoya.fold_1.fit.json deleted file mode 100644 index dc7756502b60fa07fc6b042e7a64e35678d8b43a..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF576JCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_1.log b/ENCSR800QGE/cherimoya.fold_1.log deleted file mode 100644 index fbbdde926ab393b8deadba0dc63eaf59d1c0265a..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2533 32.47216725349426 4.3075196743011475 169.33084106445312 0.5202280879020691 240.82257080078125 0.13645227253437042 0.62883896 2.880699396133423 True -1 5066 28.180623054504395 0.6910934448242188 202.45147705078125 0.4751582741737366 232.17544555664062 0.17901292443275452 0.71993196 0.9942701458930969 True -2 7599 28.111024141311646 0.694969892501831 125.56767272949219 0.41671431064605713 228.41754150390625 0.1937934011220932 0.7365692 0.7313410043716431 True -3 10132 28.077354669570923 0.7160069942474365 137.1088409423828 0.5659694075584412 226.62338256835938 0.20111040771007538 0.74830437 0.642009437084198 True -4 12665 28.0654718875885 0.6918277740478516 158.81979370117188 0.45811399817466736 226.45880126953125 0.20133867859840393 0.7539212 0.6062291860580444 True -5 15198 27.83592939376831 0.6597537994384766 176.38221740722656 0.3369588255882263 225.94985961914062 0.20378102362155914 0.7621185 0.5983513593673706 True -6 17731 27.584561347961426 2.3859329223632812 154.66586303710938 0.7431662678718567 225.6026611328125 0.20581142604351044 0.7660732 0.5620758533477783 True -7 20264 27.620883226394653 1.3343994617462158 133.1422576904297 0.531062126159668 225.01031494140625 0.20820286870002747 0.77660966 0.49515393376350403 True -8 22797 27.547239303588867 0.6959819793701172 138.72958374023438 0.44530338048934937 224.69793701171875 0.2093609869480133 0.78390574 0.47393614053726196 True -9 25330 27.559574604034424 0.6660010814666748 136.037109375 0.26089227199554443 224.31484985351562 0.2107122391462326 0.78945154 0.45354968309402466 True -10 27863 27.561652660369873 0.7009530067443848 161.95599365234375 0.508110523223877 223.90260314941406 0.21302032470703125 0.79409003 0.43459653854370117 True -11 30396 27.645483255386353 0.6725597381591797 167.11163330078125 0.36232197284698486 223.46043395996094 0.21509785950183868 0.79877985 0.40984323620796204 True -12 32929 27.68937349319458 0.7153310775756836 144.90017700195312 0.34064316749572754 223.2616424560547 0.2153119295835495 0.8031847 0.38183295726776123 True -13 35462 27.705556869506836 0.671860933303833 175.91578674316406 0.3282729685306549 222.65989685058594 0.21773958206176758 0.8102016 0.3610095679759979 True -14 37995 27.692224502563477 0.6970467567443848 161.4883270263672 0.4745059013366699 222.65496826171875 0.21813994646072388 0.8153284 0.33965441584587097 True -15 40528 27.555811643600464 0.6831989288330078 159.162353515625 0.30053573846817017 222.33421325683594 0.2199578583240509 0.81890714 0.3188977837562561 True -16 43061 27.5092933177948 25.521260261535645 167.4879913330078 0.24850767850875854 222.39891052246094 0.21897044777870178 0.8217093 0.3076535165309906 True -17 45594 27.616580486297607 0.740955114364624 155.12579345703125 0.2946789562702179 222.5752716064453 0.21804426610469818 0.8224577 0.3002470135688782 True -18 48127 27.553574800491333 0.9851424694061279 159.3972625732422 0.25156426429748535 222.7283935546875 0.21761077642440796 0.8211517 0.30099040269851685 False -19 50660 27.591816663742065 0.6466267108917236 138.7899627685547 0.16680996119976044 222.7417449951172 0.21742448210716248 0.82051027 0.3021189868450165 False diff --git a/ENCSR800QGE/cherimoya.fold_1.performance.tsv b/ENCSR800QGE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 69a9a7bf1ef46818b15ad893d3df7c575cc5c697..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -222.5752716064453 0.5381451845169067 0.218044251203537 0.055518556386232376 0.8224576711654663 0.7748130559921265 0.3002470135688782 \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_2.evaluate.json b/ENCSR800QGE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f55d7e90928dc86be65956ec7b4d78ce7243960f..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576JCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_2.fit.json b/ENCSR800QGE/cherimoya.fold_2.fit.json deleted file mode 100644 index 538231510c807b70d779a378dd7c539c4d232972..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF576JCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_2.log b/ENCSR800QGE/cherimoya.fold_2.log deleted file mode 100644 index a832dc2245eaf28a422c2025f35ced34a87f6baa..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2700 34.36531662940979 4.106017589569092 176.1939697265625 0.8171356916427612 213.75999450683594 0.13057389855384827 0.6394552 1.968638300895691 True -1 5400 29.995070934295654 0.5570018291473389 136.63198852539062 0.36572206020355225 206.1134796142578 0.17212341725826263 0.7195762 0.9958153963088989 True -2 8100 29.949126958847046 0.49567174911499023 181.1619415283203 0.6461688280105591 203.64857482910156 0.18046937882900238 0.73557997 0.5484858751296997 True -3 10800 29.911725521087646 0.48769664764404297 166.8623504638672 0.517919659614563 202.78599548339844 0.18360376358032227 0.74746406 0.4993731379508972 True -4 13500 29.93558144569397 0.5057947635650635 173.6363983154297 0.3887617290019989 201.9335479736328 0.18867358565330505 0.75092113 0.5541163086891174 True -5 16200 29.910163164138794 0.4906470775604248 179.17123413085938 0.6768479347229004 201.4903106689453 0.1908978819847107 0.7521619 0.5086096525192261 True -6 18900 29.9040048122406 0.5058655738830566 183.84442138671875 0.4151104688644409 201.06341552734375 0.1934232860803604 0.76015353 0.4993579089641571 True -7 21600 29.933958292007446 0.49645018577575684 136.68020629882812 0.43724244832992554 200.7865447998047 0.19491484761238098 0.7628261 0.47298869490623474 True -8 24300 29.901009798049927 0.496474027633667 164.84805297851562 0.34361231327056885 200.59521484375 0.19598613679409027 0.7665527 0.4746696650981903 True -9 27000 29.910264253616333 0.5076406002044678 141.7880859375 0.43674150109291077 200.3232879638672 0.1975875049829483 0.76903313 0.4537607729434967 True -10 29700 29.966716527938843 0.5065627098083496 147.79837036132812 0.3681833744049072 199.95437622070312 0.1988140046596527 0.77625066 0.4127192199230194 True -11 32400 29.923224925994873 0.5071933269500732 192.3967742919922 0.38289788365364075 199.41525268554688 0.20218823850154877 0.77915937 0.38298675417900085 True -12 35100 29.93693447113037 0.49633145332336426 175.76144409179688 0.306810200214386 199.3502960205078 0.20241327583789825 0.7852834 0.3588283061981201 True -13 37800 29.940844774246216 0.49577975273132324 169.68475341796875 0.2995935082435608 199.02947998046875 0.2043459266424179 0.79485416 0.3337748050689697 True -14 40500 29.96011734008789 0.49652910232543945 145.01846313476562 0.2728577256202698 198.58641052246094 0.20620214939117432 0.8008945 0.31179237365722656 True -15 43200 29.980854988098145 0.5079882144927979 154.4203643798828 0.3791089951992035 198.7646026611328 0.20471425354480743 0.8045424 0.29176175594329834 True -16 45900 29.503142595291138 0.5031228065490723 181.61447143554688 0.2305094599723816 198.68312072753906 0.20515485107898712 0.8079319 0.2819238007068634 True -17 48600 29.378694772720337 0.49102306365966797 159.86581420898438 0.3319161832332611 198.6711883544922 0.20531076192855835 0.8103165 0.2788834571838379 True -18 51300 29.334891319274902 0.5033321380615234 169.1315155029297 0.21522170305252075 198.78048706054688 0.20433278381824493 0.8070825 0.279209166765213 False -19 54000 29.358567714691162 0.49221229553222656 141.02542114257812 0.25288325548171997 198.78526306152344 0.2046796679496765 0.8054858 0.2816516160964966 False diff --git a/ENCSR800QGE/cherimoya.fold_2.performance.tsv b/ENCSR800QGE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6aaed4d368bb24726ceb31d5483de330b59d6655..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -198.6711883544922 0.5507695078849792 0.20531077682971954 0.04640718176960945 0.8103165030479431 0.7543541789054871 0.2788834571838379 \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_3.evaluate.json b/ENCSR800QGE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 05adc935c1ed2cceb0f33b709934ed879cd4bb15..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576JCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_3.fit.json b/ENCSR800QGE/cherimoya.fold_3.fit.json deleted file mode 100644 index 25a5564ca195ab46b73b83b3fc19a1d22a1f42e3..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF576JCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_3.log b/ENCSR800QGE/cherimoya.fold_3.log deleted file mode 100644 index 51ff64e7217203584bd6e5304d10e6ad99154f56..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2593 33.68558979034424 4.0564961433410645 134.4666748046875 0.4880547523498535 217.60240173339844 0.12826478481292725 0.6445709 2.8818678855895996 True -1 5186 28.783498287200928 0.600074291229248 132.8992462158203 0.6159085035324097 210.41236877441406 0.16807501018047333 0.71765214 0.8253486156463623 True -2 7779 28.777918338775635 0.5315685272216797 146.93035888671875 0.38092657923698425 208.14627075195312 0.17762963473796844 0.7408521 0.6856865286827087 True -3 10372 28.791466236114502 0.5481657981872559 165.91879272460938 0.6129299402236938 207.02938842773438 0.1820686161518097 0.7531601 0.6121194362640381 True -4 12965 28.92907428741455 20.957369804382324 157.9025421142578 0.5684180855751038 206.164794921875 0.18685457110404968 0.75603586 0.6312329769134521 True -5 15558 29.505099296569824 0.5540809631347656 161.47265625 0.3858030438423157 206.1862030029297 0.1861475259065628 0.7557697 0.6584640145301819 False -6 18151 28.841234922409058 1.1824572086334229 156.89117431640625 0.6171934008598328 205.5806121826172 0.18916256725788116 0.7639326 0.5836581587791443 True -7 20744 28.864925861358643 14.936713933944702 181.7733612060547 0.3894329071044922 205.2456512451172 0.1907060444355011 0.77357996 0.5325941443443298 True -8 23337 29.67575764656067 1.270749568939209 185.3593292236328 0.48612162470817566 204.96607971191406 0.19228637218475342 0.7732229 0.5029594302177429 False -9 25930 28.88770818710327 0.5560622215270996 146.00289916992188 0.48808664083480835 204.7495880126953 0.19319626688957214 0.7757691 0.465378999710083 True -10 28523 28.93171501159668 0.5442228317260742 168.1538543701172 0.31390005350112915 204.22879028320312 0.19642089307308197 0.7808962 0.4402998983860016 True -11 31116 28.870064735412598 0.5356698036193848 153.92425537109375 0.33845728635787964 204.04026794433594 0.19734200835227966 0.78575766 0.40989696979522705 True -12 33709 28.867844820022583 0.8491370677947998 168.86520385742188 0.349161297082901 203.9337921142578 0.1974755972623825 0.79009765 0.3887414336204529 True -13 36302 28.783222198486328 0.5900182723999023 143.49761962890625 0.38425320386886597 203.4721221923828 0.2000884860754013 0.79365945 0.3595280647277832 True -14 38895 28.831353902816772 0.5317234992980957 194.41587829589844 0.2943671941757202 203.51129150390625 0.19982856512069702 0.80105174 0.33685803413391113 True -15 41488 28.76001477241516 0.6265201568603516 157.45916748046875 0.4010791778564453 203.4105987548828 0.2003227323293686 0.8076458 0.3188585042953491 True -16 44081 28.860745906829834 0.5493178367614746 140.26370239257812 0.288615345954895 203.29635620117188 0.20062223076820374 0.8095822 0.3004095256328583 True -17 46674 28.850368976593018 0.551408052444458 153.5010986328125 0.3433132767677307 203.1560516357422 0.20148992538452148 0.8127732 0.2922360599040985 True -18 49267 28.92490863800049 0.5468654632568359 159.87747192382812 0.2870855927467346 203.4477081298828 0.19977588951587677 0.8109255 0.2901686728000641 False -19 51860 28.912954330444336 0.5646219253540039 158.4058837890625 0.4198845624923706 203.40574645996094 0.20027470588684082 0.81235886 0.290851354598999 False diff --git a/ENCSR800QGE/cherimoya.fold_3.performance.tsv b/ENCSR800QGE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 24721603a121f656f7480161050758b075fba3b5..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -203.1560516357422 0.5512218475341797 0.20148992538452148 0.051628243178129196 0.8127732276916504 0.7497496604919434 0.2922360599040985 \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_4.evaluate.json b/ENCSR800QGE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c689e1dec8195956ed78d4cf4aadf14d1a2b6ad8..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF576JCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_4.fit.json b/ENCSR800QGE/cherimoya.fold_4.fit.json deleted file mode 100644 index e2287d85a9b2c8cc1a726b750f37b74e88bd1d3f..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF576JCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR800QGE/cherimoya.fold_4.log b/ENCSR800QGE/cherimoya.fold_4.log deleted file mode 100644 index 8b6453f67b10e8a3f86274ccb3003a637b5626bd..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2662 34.03465414047241 3.8195018768310547 153.8022918701172 0.537206768989563 201.74240112304688 0.1226053535938263 0.6426119 2.0878374576568604 True -1 5324 29.529868125915527 0.5891749858856201 160.3665771484375 0.6301742792129517 195.9998016357422 0.1583603471517563 0.7073676 1.1273088455200195 True -2 7986 29.30903434753418 0.5518312454223633 168.06851196289062 0.6686640381813049 193.28482055664062 0.17220136523246765 0.72013664 0.6020016074180603 True -3 10648 28.937917232513428 0.5431182384490967 191.04537963867188 0.6029767394065857 192.13514709472656 0.176105335354805 0.74089295 0.5122237205505371 True -4 13310 28.962308883666992 13.137787818908691 164.51828002929688 0.5263921022415161 191.804443359375 0.17787779867649078 0.7443329 0.4934321641921997 True -5 15972 28.98387336730957 0.5691008567810059 176.8886260986328 0.6679885983467102 191.3271026611328 0.18051347136497498 0.74724185 0.47878047823905945 True -6 18634 28.972652673721313 0.5354108810424805 175.503662109375 0.4228464961051941 190.90667724609375 0.1825971156358719 0.75184864 0.44703051447868347 True -7 21296 28.91966223716736 0.5520193576812744 173.02127075195312 0.5456035137176514 190.68162536621094 0.18434971570968628 0.7570859 0.45552676916122437 True -8 23958 28.914987802505493 0.530681848526001 172.59817504882812 0.3774123191833496 190.337158203125 0.1860443502664566 0.7590189 0.4142623841762543 True -9 26620 28.947143077850342 0.54447340965271 154.1607666015625 0.4230041205883026 190.08633422851562 0.18762756884098053 0.76537347 0.42108750343322754 True -10 29282 29.074588298797607 0.5343294143676758 153.0977783203125 0.35889244079589844 189.86590576171875 0.1890098750591278 0.76835054 0.4012446105480194 True -11 31944 28.963157176971436 0.541163444519043 172.2489471435547 0.4648679494857788 189.73822021484375 0.18960510194301605 0.7722744 0.3742111921310425 True -12 34606 28.997814893722534 1.2405452728271484 153.04400634765625 0.21758697926998138 189.50970458984375 0.1907629519701004 0.7771379 0.35311707854270935 True -13 37268 28.967501401901245 0.5304379463195801 160.60562133789062 0.2852630913257599 189.30787658691406 0.19235661625862122 0.78463864 0.3298455774784088 True -14 39930 28.982391357421875 0.5314362049102783 137.39588928222656 0.28104090690612793 189.14059448242188 0.193142369389534 0.7890954 0.3027692437171936 True -15 42592 28.941502571105957 0.5209832191467285 150.59542846679688 0.36117100715637207 189.1318359375 0.19283878803253174 0.7931144 0.28781595826148987 True -16 45254 28.98981809616089 0.5198614597320557 162.39288330078125 0.2824476361274719 188.99346923828125 0.19385673105716705 0.7947937 0.27636536955833435 True -17 47916 28.937734842300415 0.5467550754547119 181.6131591796875 0.27735912799835205 189.02685546875 0.19342291355133057 0.79734826 0.27286502718925476 True -18 50578 29.032265663146973 0.5306334495544434 139.58779907226562 0.2810852527618408 189.22714233398438 0.19220848381519318 0.7969682 0.2731240391731262 False -19 53240 29.318169355392456 1.427905797958374 190.2391357421875 0.1725020408630371 189.23728942871094 0.19268468022346497 0.7952675 0.2763092517852783 False diff --git a/ENCSR800QGE/cherimoya.fold_4.performance.tsv b/ENCSR800QGE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 93dd23a4b208bad9c1082d8274c81e7810e55a68..0000000000000000000000000000000000000000 --- a/ENCSR800QGE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -189.02685546875 0.5584219694137573 0.19342288374900818 0.043778885155916214 0.7973482608795166 0.7204256653785706 0.27286502718925476 \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_0.evaluate.json b/ENCSR801VSK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8000346372c665c369b93583ba69310bd0fc377e..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034ROW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_0.fit.json b/ENCSR801VSK/cherimoya.fold_0.fit.json deleted file mode 100644 index 569ead18bce4fb48029d84e174d1508897863439..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF034ROW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_0.log b/ENCSR801VSK/cherimoya.fold_0.log deleted file mode 100644 index c76b431b95ccb56337fef8cf9884b117218d5d44..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2163 28.31440567970276 6.165227174758911 406.8209228515625 0.6966233253479004 682.5894165039062 0.1902230829000473 0.46592548 8.18911361694336 True -1 4326 23.902212619781494 0.4743943214416504 389.2694091796875 1.1609814167022705 591.4706420898438 0.33565476536750793 0.593169 3.730855941772461 True -2 6489 23.840075731277466 0.4766111373901367 406.87921142578125 0.6643364429473877 555.4467163085938 0.3737245798110962 0.6076884 1.892140507698059 True -3 8652 23.880895614624023 0.4653329849243164 399.1942443847656 0.5936195850372314 547.2557373046875 0.38262781500816345 0.6204479 1.3248652219772339 True -4 10815 23.901089668273926 0.4719674587249756 446.0672912597656 0.89943528175354 542.3279418945312 0.3863535225391388 0.63774854 1.0128071308135986 True -5 12978 23.90599489212036 0.4648928642272949 440.544189453125 0.44675928354263306 540.7267456054688 0.38929545879364014 0.6423029 0.9283651113510132 True -6 15141 23.932213306427002 1.2610764503479004 439.4984436035156 0.6391414403915405 536.3984985351562 0.39520084857940674 0.654266 0.7728185057640076 True -7 17304 23.949033737182617 0.4563179016113281 411.0423583984375 0.4781227111816406 533.8884887695312 0.39828482270240784 0.66240484 0.6890897154808044 True -8 19467 23.951589822769165 0.479785680770874 430.34674072265625 0.5811545252799988 531.7366943359375 0.4019043743610382 0.6671194 0.6462897658348083 True -9 21630 23.943767309188843 0.44898295402526855 458.5126037597656 0.4879488945007324 530.6102905273438 0.40118691325187683 0.67725587 0.6166254281997681 True -10 23793 23.927608251571655 0.4964008331298828 363.8590087890625 0.6326916217803955 528.2295532226562 0.40485069155693054 0.6829191 0.5984580516815186 True -11 25956 23.912656784057617 0.4572577476501465 439.50054931640625 0.7300982475280762 525.9203491210938 0.4084572494029999 0.68979967 0.5768190622329712 True -12 28119 23.92865014076233 0.4795951843261719 450.25286865234375 0.6331789493560791 524.9202880859375 0.4089047908782959 0.6995593 0.5605933666229248 True -13 30282 23.934110403060913 0.46967434883117676 456.37005615234375 0.6569274067878723 523.9061889648438 0.4099644124507904 0.710148 0.5426980257034302 True -14 32445 23.99668550491333 0.45175862312316895 392.3228759765625 0.5515868067741394 522.130615234375 0.4124634861946106 0.7191707 0.5376918315887451 True -15 34608 23.933405876159668 0.4610259532928467 327.76220703125 0.3607698678970337 522.0700073242188 0.4112876355648041 0.7251399 0.5246139168739319 True -16 36771 23.857572078704834 0.8609166145324707 464.8666687011719 0.39151549339294434 520.9860229492188 0.4131927490234375 0.72888106 0.5270744562149048 True -17 38934 24.010271787643433 0.44802093505859375 488.4605712890625 0.4813467264175415 522.2687377929688 0.41039320826530457 0.730944 0.5307902097702026 True -18 41097 23.93749451637268 0.4656689167022705 408.617431640625 0.3676794767379761 521.175537109375 0.4133355915546417 0.7286775 0.5391026735305786 False -19 43260 23.842825889587402 0.45157408714294434 397.12103271484375 0.33215242624282837 520.7964477539062 0.41428878903388977 0.7258047 0.5486361980438232 False diff --git a/ENCSR801VSK/cherimoya.fold_0.performance.tsv b/ENCSR801VSK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8bce4abd74d8ca8a3a945096b067afa792f87021..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -522.2687377929688 0.385746031999588 0.41039320826530457 0.15422232449054718 0.7309439778327942 0.6697471141815186 0.5307902097702026 \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_1.evaluate.json b/ENCSR801VSK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 191cde24e14085863f9714411963ba77b2d71d58..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034ROW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_1.fit.json b/ENCSR801VSK/cherimoya.fold_1.fit.json deleted file mode 100644 index 314cd1f2e48ea8cde4a0ff1527cafcbb9007992b..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF034ROW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_1.log b/ENCSR801VSK/cherimoya.fold_1.log deleted file mode 100644 index 9321219d787ca0712c6a63402de72001ca9e8b4f..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2169 28.84831666946411 4.142227649688721 452.79168701171875 0.9116161465644836 769.2825927734375 0.20326486229896545 0.47773176 9.802334785461426 True -1 4338 23.84237051010132 0.6352372169494629 451.2763977050781 0.8099555969238281 665.1798095703125 0.34949353337287903 0.61633015 4.608064651489258 True -2 6507 23.98056936264038 0.6119191646575928 449.888916015625 0.9853972792625427 624.461181640625 0.38421109318733215 0.63080037 2.194282054901123 True -3 8676 23.92873525619507 0.6160726547241211 439.963134765625 0.5943940877914429 611.521240234375 0.39084547758102417 0.65297836 1.4639365673065186 True -4 10845 23.918867111206055 0.593707799911499 421.94525146484375 0.5762965083122253 605.985595703125 0.3970704674720764 0.663927 1.3326594829559326 True -5 13014 23.897956609725952 0.7067477703094482 450.0201416015625 0.630562961101532 602.1777954101562 0.4014573097229004 0.66564894 1.2696092128753662 True -6 15183 23.918328762054443 0.6045560836791992 424.7354431152344 0.5379253625869751 597.6456298828125 0.40700703859329224 0.6787529 1.0067579746246338 True -7 17352 23.93143105506897 0.6140463352203369 475.3653259277344 0.4885288178920746 596.1304931640625 0.40800169110298157 0.6889257 0.9370455741882324 True -8 19521 23.996893644332886 0.6075136661529541 494.6725769042969 0.7502366304397583 592.6038208007812 0.41223442554473877 0.69419295 0.8230732679367065 True -9 21690 23.933320999145508 0.6139562129974365 427.69677734375 0.7038865089416504 588.1102905273438 0.41767966747283936 0.7021766 0.7842972278594971 True -10 23859 23.911890029907227 0.6229753494262695 467.0887756347656 0.6270679235458374 586.47607421875 0.41825881600379944 0.71024746 0.7091952562332153 True -11 26028 23.966315984725952 0.5972864627838135 446.5023193359375 0.5170612335205078 583.7904663085938 0.42150676250457764 0.72033346 0.6930575966835022 True -12 28197 23.972497701644897 0.6181561946868896 473.77294921875 0.575513482093811 580.9710693359375 0.42571529746055603 0.73011 0.6292017102241516 True -13 30366 23.919211387634277 0.5948450565338135 440.91973876953125 0.5559671521186829 579.4617919921875 0.4256353974342346 0.7381088 0.6218558549880981 True -14 32535 23.914323806762695 0.5939369201660156 412.712646484375 0.5214511156082153 575.7348022460938 0.4300084412097931 0.74720734 0.5822637677192688 True -15 34704 23.90073251724243 2.4587488174438477 362.33233642578125 0.420582115650177 575.0913696289062 0.43126872181892395 0.75378746 0.5709294080734253 True -16 36873 23.935312509536743 0.6205582618713379 409.6778259277344 0.3798680305480957 575.600341796875 0.42970702052116394 0.7587822 0.5577659606933594 True -17 39042 23.93907880783081 0.74049973487854 387.84881591796875 0.2608676254749298 575.7905883789062 0.428897500038147 0.75886244 0.5526793003082275 True -18 41211 23.936480283737183 0.6127872467041016 410.2064208984375 0.28356432914733887 575.9843139648438 0.42985013127326965 0.75761944 0.5550863146781921 False -19 43380 23.966739892959595 0.6213538646697998 474.965087890625 0.3906143307685852 576.1287841796875 0.42978447675704956 0.7567169 0.5608914494514465 False diff --git a/ENCSR801VSK/cherimoya.fold_1.performance.tsv b/ENCSR801VSK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index aafa1429e64c32df63d12ff7a433d375d336db28..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -575.7905883789062 0.37130624055862427 0.42889752984046936 0.1703629344701767 0.7588624358177185 0.7141984105110168 0.5526793003082275 \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_2.evaluate.json b/ENCSR801VSK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index faa3a50bdc0b169fd8a12517b14235cc6f26cd73..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034ROW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_2.fit.json b/ENCSR801VSK/cherimoya.fold_2.fit.json deleted file mode 100644 index 4d8e7b807f23598ff514a153fb93fe833da6cc16..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF034ROW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_2.log b/ENCSR801VSK/cherimoya.fold_2.log deleted file mode 100644 index 384dd2f2179620f81ea895c254e3c18f165a8a03..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2326 31.75259494781494 3.710134983062744 491.7904052734375 0.8332990407943726 701.6686401367188 0.20490995049476624 0.477612 7.279366493225098 True -1 4652 25.627286434173584 12.515421152114868 461.31353759765625 0.868998646736145 594.6242065429688 0.35758811235427856 0.6095267 3.694732904434204 True -2 6978 25.4079532623291 0.4546318054199219 416.6883544921875 0.7314379811286926 568.9884643554688 0.3810093402862549 0.6216258 1.8107717037200928 True -3 9304 25.132251024246216 0.4386115074157715 487.97650146484375 0.7684566974639893 560.58837890625 0.38430681824684143 0.64262 1.273977518081665 True -4 11630 25.117006063461304 0.8064143657684326 475.1221923828125 0.61501145362854 555.07275390625 0.39082059264183044 0.65731543 0.9189174771308899 True -5 13956 25.25859498977661 0.9484548568725586 460.47039794921875 0.6057250499725342 553.2171020507812 0.3926565945148468 0.6632432 0.8831226229667664 True -6 16282 25.137131214141846 0.4290428161621094 433.85504150390625 0.6019509434700012 550.0493774414062 0.3974536955356598 0.67219144 0.8394996523857117 True -7 18608 25.125553369522095 0.4564850330352783 384.383544921875 0.5928186774253845 546.7244262695312 0.40151798725128174 0.67255926 0.8107864856719971 True -8 20934 25.115303993225098 0.45896244049072266 513.786376953125 0.511581540107727 544.1159057617188 0.40491563081741333 0.68322223 0.731077253818512 True -9 23260 25.25799798965454 0.4593617916107178 451.6328125 0.7610427737236023 543.3203735351562 0.4051399827003479 0.685824 0.7163881063461304 True -10 25586 25.211811780929565 0.4817802906036377 428.0358581542969 0.6109108328819275 540.3938598632812 0.40956130623817444 0.6921173 0.6805543899536133 True -11 27912 25.223135232925415 0.44586825370788574 403.25897216796875 0.3709106147289276 538.48193359375 0.41189050674438477 0.6994538 0.6488207578659058 True -12 30238 25.179821491241455 0.4280741214752197 476.06121826171875 0.560383677482605 536.3869018554688 0.4137750267982483 0.7085504 0.613471269607544 True -13 32564 25.214382648468018 0.4256925582885742 383.5975341796875 0.43262022733688354 534.7286376953125 0.41598019003868103 0.7163859 0.5885992050170898 True -14 34890 25.258206367492676 0.43408799171447754 387.04852294921875 0.5980890393257141 532.11328125 0.420163631439209 0.7246963 0.5732520222663879 True -15 37216 25.233492136001587 0.41939806938171387 467.3572082519531 0.4815870523452759 531.851806640625 0.4193820357322693 0.73275036 0.5552733540534973 True -16 39542 25.176042795181274 0.43140578269958496 319.1854248046875 0.4656829237937927 531.6753540039062 0.4202784597873688 0.7364006 0.5478712916374207 True -17 41868 25.269657611846924 0.43523621559143066 410.39288330078125 0.4168066382408142 532.030517578125 0.41892972588539124 0.740372 0.5443142652511597 True -18 44194 25.180120944976807 0.41765642166137695 368.63262939453125 0.4788755774497986 531.9138793945312 0.4195256233215332 0.7379764 0.548726499080658 False -19 46520 25.169767141342163 0.43624329566955566 430.1514587402344 0.23766788840293884 531.9840087890625 0.4195832908153534 0.73784906 0.5515865683555603 False diff --git a/ENCSR801VSK/cherimoya.fold_2.performance.tsv b/ENCSR801VSK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5d9a3377cc9180d5b4f12f4e7dec84b5b16f19d5..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -532.030517578125 0.38165101408958435 0.41892972588539124 0.1614031046628952 0.7403720021247864 0.6826849579811096 0.5443142652511597 \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_3.evaluate.json b/ENCSR801VSK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 30aa55fed581f7e4b34a235948bccd432471dd2e..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034ROW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_3.fit.json b/ENCSR801VSK/cherimoya.fold_3.fit.json deleted file mode 100644 index a58a9be225396bd5b4577538bf30f7523d4b7e77..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF034ROW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_3.log b/ENCSR801VSK/cherimoya.fold_3.log deleted file mode 100644 index 8f13edfa9f5a340f8c5d400112bcf99bbcd046e6..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2223 29.35236167907715 3.5731399059295654 481.1897888183594 1.1500434875488281 719.8978271484375 0.20320193469524384 0.472274 8.635321617126465 True -1 4446 24.516141653060913 0.6961736679077148 465.3967590332031 0.8864535093307495 619.386962890625 0.34918221831321716 0.5703202 4.423539638519287 True -2 6669 24.514962673187256 0.47153806686401367 439.09228515625 0.661239743232727 594.8052978515625 0.37672412395477295 0.5757134 2.3811440467834473 True -3 8892 24.50528073310852 0.47152042388916016 449.966796875 0.7931068539619446 584.7633056640625 0.38839131593704224 0.58162016 2.0717668533325195 True -4 11115 24.499184131622314 0.49039387702941895 452.2757263183594 0.7534226775169373 583.6864624023438 0.3888453543186188 0.5904867 1.6048513650894165 True -5 13338 24.540154933929443 2.756587266921997 395.0837097167969 0.6660052537918091 580.2555541992188 0.3929429054260254 0.595775 1.38672935962677 True -6 15561 24.539434909820557 0.49593305587768555 476.3842468261719 0.6362683773040771 578.63720703125 0.3952690064907074 0.60601 1.2481577396392822 True -7 17784 24.536312580108643 0.5054616928100586 463.9745178222656 0.7818348407745361 576.589599609375 0.39824333786964417 0.61561936 1.1209739446640015 True -8 20007 24.39906883239746 0.5026752948760986 360.77166748046875 0.6262905597686768 574.1284790039062 0.4009871780872345 0.6278873 0.9954739809036255 True -9 22230 24.05356478691101 0.48984432220458984 391.3673095703125 0.7459333539009094 571.885498046875 0.4040098786354065 0.636878 0.9619817733764648 True -10 24453 24.057326078414917 0.48737359046936035 439.30841064453125 0.59830641746521 569.8392944335938 0.4076034724712372 0.64345556 0.8929153084754944 True -11 26676 24.046302318572998 1.5439109802246094 455.94549560546875 0.5613890886306763 566.2586059570312 0.4103769361972809 0.6569076 0.8317810297012329 True -12 28899 24.003982305526733 0.47190332412719727 379.2198181152344 0.5214421153068542 563.5687866210938 0.41227462887763977 0.6735426 0.7724913954734802 True -13 31122 23.996224880218506 0.47002577781677246 442.10040283203125 0.3717716336250305 562.1243896484375 0.41197529435157776 0.68552667 0.7330904603004456 True -14 33345 23.995279550552368 0.47068333625793457 438.5572814941406 0.453956663608551 559.4424438476562 0.4156910479068756 0.6974587 0.6837905645370483 True -15 35568 23.982001304626465 0.46017885208129883 480.98992919921875 0.4724363386631012 558.1907958984375 0.41656577587127686 0.7101753 0.6477930545806885 True -16 37791 24.01533818244934 1.3422367572784424 458.02490234375 0.42984384298324585 557.4911499023438 0.41597259044647217 0.71827877 0.6272802948951721 True -17 40014 24.052860975265503 0.46952056884765625 486.7472839355469 0.44406116008758545 557.9754638671875 0.41497671604156494 0.7205279 0.6149908304214478 True -18 42237 24.012290954589844 0.4756152629852295 376.1988525390625 0.30453944206237793 557.079345703125 0.4167603850364685 0.72233564 0.6115733981132507 True -19 44460 24.010355234146118 0.4725327491760254 362.3421630859375 0.3647227883338928 557.6860961914062 0.4151160717010498 0.72058755 0.6147193908691406 False diff --git a/ENCSR801VSK/cherimoya.fold_3.performance.tsv b/ENCSR801VSK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9c5961f50d9ca5575cc05747caa82b177339c509..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -557.079345703125 0.37920448184013367 0.4167604148387909 0.1675763875246048 0.7223356366157532 0.6692011952400208 0.6115733981132507 \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_4.evaluate.json b/ENCSR801VSK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 31869fe65d2fa8cc9c44af1615517e2ce69fe164..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF034ROW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_4.fit.json b/ENCSR801VSK/cherimoya.fold_4.fit.json deleted file mode 100644 index e672fa7c567bc9e04885196cff891da806c935f2..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF034ROW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR801VSK/cherimoya.fold_4.log b/ENCSR801VSK/cherimoya.fold_4.log deleted file mode 100644 index bbfb574d795250a37444b9d1b6f8b9e5ca101ece..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2258 29.458690643310547 3.793767213821411 401.47149658203125 0.6230496168136597 660.1491088867188 0.19709397852420807 0.4584064 8.072694778442383 True -1 4516 24.910138368606567 0.523357629776001 436.31884765625 1.0426974296569824 569.8419799804688 0.3382652997970581 0.59664875 3.2351508140563965 True -2 6774 24.921608924865723 0.44297170639038086 493.6370849609375 0.9462507963180542 546.982666015625 0.36871257424354553 0.5990028 2.008890390396118 True -3 9032 24.86900234222412 0.43803906440734863 378.2171325683594 0.6780779361724854 535.2335205078125 0.3788069188594818 0.6071204 1.397392988204956 True -4 11290 24.88097095489502 0.43012118339538574 365.41876220703125 0.6352124214172363 529.1495971679688 0.3850887715816498 0.6180783 1.0972107648849487 True -5 13548 24.96910285949707 0.4405853748321533 420.9903564453125 0.49935537576675415 525.0107421875 0.3902469575405121 0.6303927 0.838820219039917 True -6 15806 24.88127565383911 2.582671880722046 405.4039306640625 0.4313528537750244 522.7622680664062 0.392479807138443 0.64500904 0.7498040795326233 True -7 18064 24.933772802352905 0.46874189376831055 401.5020446777344 0.6632325649261475 520.4136352539062 0.3953937590122223 0.6475875 0.705449640750885 True -8 20322 24.967037439346313 0.47033214569091797 420.43804931640625 0.8150041103363037 518.64404296875 0.39879488945007324 0.6513031 0.6888361573219299 True -9 22580 24.90870499610901 0.4463226795196533 416.13037109375 0.4600926637649536 517.235595703125 0.3994802236557007 0.6582128 0.6359744071960449 True -10 24838 24.95853328704834 0.4427368640899658 428.3519287109375 0.4006323218345642 514.762939453125 0.4035622179508209 0.6669752 0.6173087358474731 True -11 27096 24.888930082321167 0.4780540466308594 427.1261291503906 0.6545746326446533 513.230224609375 0.40607360005378723 0.6758571 0.6032773852348328 True -12 29354 24.861326694488525 0.45160984992980957 455.9634094238281 0.49341654777526855 511.89520263671875 0.40697839856147766 0.6858561 0.5743834376335144 True -13 31612 24.92935347557068 0.4455857276916504 371.1051025390625 0.5645633935928345 510.3568115234375 0.4086163341999054 0.69191587 0.5617714524269104 True -14 33870 24.927820444107056 0.4378044605255127 468.8197021484375 0.4214445948600769 509.3100280761719 0.4103166162967682 0.70351946 0.5461986064910889 True -15 36128 24.927315711975098 0.4431154727935791 419.3310546875 0.4956873655319214 508.3053894042969 0.41172319650650024 0.71279746 0.5324119329452515 True -16 38386 24.934296131134033 0.437300443649292 392.59197998046875 0.4792875051498413 508.106201171875 0.41188737750053406 0.7171719 0.5286887884140015 True -17 40644 24.917904138565063 0.4356701374053955 362.7442321777344 0.3466460704803467 506.7746276855469 0.4147479236125946 0.7206376 0.528261125087738 True -18 42902 24.93796706199646 0.4305083751678467 426.4266357421875 0.2636832594871521 508.0741271972656 0.41171273589134216 0.71801096 0.5330421924591064 False -19 45160 24.880890369415283 2.4137821197509766 380.9601745605469 0.2547091543674469 508.3056335449219 0.41119858622550964 0.71681917 0.5390645861625671 False diff --git a/ENCSR801VSK/cherimoya.fold_4.performance.tsv b/ENCSR801VSK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index de47e3b009504311e555d4356a0bb416a2459212..0000000000000000000000000000000000000000 --- a/ENCSR801VSK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -506.7746276855469 0.387444406747818 0.4147479236125946 0.15368972718715668 0.7206376194953918 0.6537225246429443 0.528261125087738 \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_0.evaluate.json b/ENCSR802NBC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 54ef7dbad0fc086334512e20d8904cf372958af0..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130DHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_0.fit.json b/ENCSR802NBC/cherimoya.fold_0.fit.json deleted file mode 100644 index 5587eb6dc4b6e186eb632e9076c769d33d72a0ac..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF130DHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_0.log b/ENCSR802NBC/cherimoya.fold_0.log deleted file mode 100644 index 6e0491fd6c354e4d7cfc90b9f688dc9b17f349a1..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 35.135348320007324 3.9656341075897217 814.011962890625 0.5997752547264099 1060.3876953125 0.3022601902484894 0.6988065 7.364095687866211 True -1 5510 30.309881687164307 0.647552490234375 812.2537231445312 0.5783278346061707 919.4384155273438 0.3992140293121338 0.7476051 2.692286729812622 True -2 8265 30.294018268585205 0.6245288848876953 891.1610107421875 0.7775071859359741 890.0802612304688 0.4198293685913086 0.76163834 1.4196958541870117 True -3 11020 30.304047346115112 0.5736565589904785 687.7149658203125 0.9158211946487427 879.679931640625 0.4275626540184021 0.7632965 1.1571829319000244 True -4 13775 30.279967069625854 0.5848727226257324 598.900390625 0.8773496747016907 870.7206420898438 0.4357651174068451 0.7710758 1.140467643737793 True -5 16530 30.265625953674316 0.5775339603424072 763.7340698242188 0.5877774953842163 864.8363037109375 0.4401664435863495 0.7728579 0.8605945706367493 True -6 19285 30.299286603927612 0.575141429901123 681.57763671875 0.6011710166931152 859.7655639648438 0.44572409987449646 0.77225375 0.8163473010063171 False -7 22040 30.27303981781006 0.5758063793182373 844.6884765625 0.9925013780593872 852.9176025390625 0.44952940940856934 0.7790048 0.6944077014923096 True -8 24795 30.24822974205017 0.5782835483551025 742.9378051757812 0.6258296966552734 848.620849609375 0.45298364758491516 0.78252125 0.6032795310020447 True -9 27550 30.229981184005737 0.5744032859802246 761.4694213867188 0.5303555727005005 842.3551635742188 0.4581924080848694 0.7876376 0.5599591135978699 True -10 30305 30.260170221328735 0.5748534202575684 743.7000732421875 0.5389461517333984 837.1630249023438 0.46345484256744385 0.7900949 0.519514799118042 True -11 33060 30.272282600402832 0.5760824680328369 780.870361328125 0.49794912338256836 833.8202514648438 0.4655705988407135 0.800579 0.4869626760482788 True -12 35815 30.24372148513794 0.5790421962738037 600.4091186523438 0.4287775456905365 831.3997192382812 0.46665453910827637 0.8038834 0.46333014965057373 True -13 38570 30.554699182510376 0.5808522701263428 813.4765625 0.5125445127487183 827.227294921875 0.4685792028903961 0.8121847 0.4299098551273346 True -14 41325 30.26190996170044 0.5787549018859863 597.533935546875 0.5147055983543396 823.2666015625 0.47196123003959656 0.8183481 0.41083022952079773 True -15 44080 30.3026385307312 0.5779159069061279 684.123291015625 0.33873042464256287 818.5822143554688 0.47607967257499695 0.82358354 0.39571914076805115 True -16 46835 30.24946117401123 0.5773847103118896 631.7818603515625 0.26734068989753723 819.8275756835938 0.47315672039985657 0.8260886 0.38023993372917175 True -17 49590 30.222621202468872 0.5774238109588623 687.126220703125 0.467343270778656 816.9556884765625 0.4770592749118805 0.82898176 0.3741615414619446 True -18 52345 30.27549433708191 0.5863943099975586 678.7098388671875 0.4056125283241272 820.0342407226562 0.47365519404411316 0.8285296 0.3736187517642975 False -19 55100 30.205880880355835 1.160832166671753 675.9063720703125 0.34142768383026123 818.2631225585938 0.4763646125793457 0.8291473 0.3751775324344635 True diff --git a/ENCSR802NBC/cherimoya.fold_0.performance.tsv b/ENCSR802NBC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 00811756446e6ea7604016dd7338e34d6e961041..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -818.2631225585938 0.32961246371269226 0.4763645827770233 0.21251855790615082 0.8291472792625427 0.7827429175376892 0.3751775324344635 \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_1.evaluate.json b/ENCSR802NBC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6532bbe3bd24011c6d135a4e0009a612cfa97911..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130DHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_1.fit.json b/ENCSR802NBC/cherimoya.fold_1.fit.json deleted file mode 100644 index 72dd59b58235a6f51958c52a4ba0775f39c7f145..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF130DHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_1.log b/ENCSR802NBC/cherimoya.fold_1.log deleted file mode 100644 index a4766090bae4d75e506e9564bdb1df11c29f9ce5..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2701 36.48454713821411 14.276697158813477 742.9365234375 0.8362207412719727 1219.688232421875 0.299622505903244 0.6825574 7.891422748565674 True -1 5402 29.665665864944458 1.6753466129302979 789.5804443359375 0.8257639408111572 1034.133056640625 0.4129951000213623 0.7518823 2.379242420196533 True -2 8103 29.668782949447632 2.041809558868408 604.1210327148438 0.7823513150215149 1010.3882446289062 0.42684391140937805 0.75581855 1.2294774055480957 True -3 10804 29.626168727874756 0.986541748046875 780.6021728515625 0.9166098833084106 992.1985473632812 0.4367482662200928 0.7670019 0.8890058398246765 True -4 13505 29.645405530929565 0.7031316757202148 553.208251953125 0.708920419216156 982.9263916015625 0.44179561734199524 0.7720405 0.8614100217819214 True -5 16206 29.583321809768677 0.7053499221801758 605.4473266601562 0.8170960545539856 972.9517211914062 0.44800451397895813 0.7815683 0.7691637277603149 True -6 18907 29.58202075958252 0.710798978805542 925.5686645507812 0.7603359222412109 964.2664794921875 0.4548836946487427 0.785407 0.7075461149215698 True -7 21608 29.61768651008606 29.758857250213623 635.039794921875 0.40053945779800415 959.9432373046875 0.4572683274745941 0.7889555 0.6036665439605713 True -8 24309 29.641382932662964 0.706512451171875 674.54248046875 0.5998858213424683 954.644287109375 0.46083101630210876 0.7908665 0.5810624361038208 True -9 27010 29.602585315704346 0.7254948616027832 624.5211181640625 0.4499419629573822 946.0697631835938 0.4658963084220886 0.7958173 0.5495828986167908 True -10 29711 29.650301933288574 31.036863803863525 714.314697265625 0.4931246042251587 938.6566772460938 0.4701079726219177 0.79949087 0.5143937468528748 True -11 32412 29.689754962921143 2.3798770904541016 771.0238037109375 0.6939036846160889 933.519287109375 0.4722389876842499 0.80904377 0.4827795624732971 True -12 35113 29.670934438705444 0.7607486248016357 671.53125 0.5009353160858154 926.8616333007812 0.4766829013824463 0.8175359 0.4706016480922699 True -13 37814 29.68224000930786 0.7137188911437988 747.470947265625 0.7023272514343262 922.9588012695312 0.47822117805480957 0.82484746 0.443044513463974 True -14 40515 29.681135654449463 0.7024307250976562 717.578369140625 0.374448299407959 918.3276977539062 0.4810427129268646 0.8318861 0.4204389750957489 True -15 43216 29.616891384124756 0.7088992595672607 687.0755615234375 0.42023271322250366 916.6851806640625 0.48125606775283813 0.83877236 0.40370815992355347 True -16 45917 29.618552923202515 1.3949081897735596 602.8324584960938 0.325417160987854 910.5751342773438 0.485124409198761 0.84121525 0.3903699815273285 True -17 48618 29.728229761123657 0.7019858360290527 553.1485595703125 0.44079750776290894 912.2111206054688 0.48391738533973694 0.84429157 0.3853735625743866 True -18 51319 29.745733976364136 0.7155389785766602 561.3222045898438 0.4675176739692688 911.1986083984375 0.4851689338684082 0.84535265 0.38558709621429443 True -19 54020 29.271146535873413 0.7121386528015137 722.8165893554688 0.27894675731658936 913.7139282226562 0.482946515083313 0.8450959 0.3854489028453827 False diff --git a/ENCSR802NBC/cherimoya.fold_1.performance.tsv b/ENCSR802NBC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 652f0ac11b6dc3fe527c59010a01d4f958745d6d..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -911.1986083984375 0.31912946701049805 0.485168993473053 0.22925902903079987 0.8453526496887207 0.8143876791000366 0.38558709621429443 \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_2.evaluate.json b/ENCSR802NBC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 211f5ffdab3a87fe8736883a440c9793e987357e..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130DHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_2.fit.json b/ENCSR802NBC/cherimoya.fold_2.fit.json deleted file mode 100644 index 8accaccbd8fa01d2b8f9f9b21b1fdadfadfa6347..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF130DHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_2.log b/ENCSR802NBC/cherimoya.fold_2.log deleted file mode 100644 index 1ecf1b189af0bd70642bb98cbb1b745358ab2d97..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 36.02138042449951 3.7921643257141113 603.7893676757812 0.589319109916687 1094.64453125 0.3059205114841461 0.6897085 6.969592094421387 True -1 5742 31.541231155395508 0.6706554889678955 711.921142578125 0.8565336465835571 932.3295288085938 0.4112239181995392 0.7481721 2.800330638885498 True -2 8613 31.580005645751953 0.602916955947876 653.4526977539062 0.6278074979782104 908.7643432617188 0.4264087975025177 0.75766945 1.175382375717163 True -3 11484 31.52535629272461 0.5940840244293213 886.9083251953125 0.619606614112854 894.5631103515625 0.4342907965183258 0.76601857 0.8557440042495728 True -4 14355 31.515363454818726 0.685856819152832 739.00439453125 0.6098434329032898 885.1907958984375 0.4422476589679718 0.76431996 0.718393087387085 False -5 17226 31.55984663963318 0.5666754245758057 636.578857421875 0.6149765849113464 878.87158203125 0.4452294111251831 0.77040434 0.6111533045768738 True -6 20097 31.524705171585083 0.6025164127349854 732.3714599609375 0.4254068434238434 872.09619140625 0.45204365253448486 0.77163255 0.6296400427818298 True -7 22968 31.538652658462524 0.6028909683227539 709.6243286132812 0.5516752004623413 868.1620483398438 0.453427255153656 0.7790539 0.5272735953330994 True -8 25839 31.52192997932434 0.5812695026397705 634.5404052734375 0.47733184695243835 860.681396484375 0.45959344506263733 0.7839681 0.4935028553009033 True -9 28710 31.556503534317017 0.6067812442779541 684.0386962890625 0.522566556930542 858.6991577148438 0.4588805139064789 0.79031676 0.48991432785987854 True -10 31581 31.551705598831177 0.6657774448394775 634.6849975585938 0.603590190410614 852.5900268554688 0.46485546231269836 0.79561096 0.4731299877166748 True -11 34452 31.608154773712158 0.6076095104217529 702.1666259765625 0.496095210313797 847.3746337890625 0.46776771545410156 0.80033565 0.4387035369873047 True -12 37323 31.50962257385254 0.5826783180236816 575.7884521484375 0.5054230093955994 844.69580078125 0.46944138407707214 0.80514836 0.4338374733924866 True -13 40194 31.63075566291809 0.5787913799285889 622.795166015625 0.49771440029144287 840.6231079101562 0.47239649295806885 0.81100243 0.4189983904361725 True -14 43065 31.683103799819946 0.6086282730102539 691.6659545898438 0.43511974811553955 837.81298828125 0.47407209873199463 0.81595045 0.4026324450969696 True -15 45936 31.61425018310547 1.5233640670776367 750.9735107421875 0.4274213910102844 834.9063110351562 0.4766256809234619 0.82036287 0.39273878931999207 True -16 48807 32.00676393508911 0.6172122955322266 712.5587158203125 0.550774335861206 837.8983764648438 0.473146915435791 0.8244706 0.3870038092136383 True -17 51678 31.34873080253601 0.5974977016448975 657.0757446289062 0.334781676530838 838.323486328125 0.47286203503608704 0.82735217 0.3830481469631195 True -18 54549 31.276004314422607 0.6201283931732178 542.2091064453125 0.30093905329704285 835.201904296875 0.47650429606437683 0.8269858 0.3852146863937378 False -19 57420 31.022553205490112 0.6109213829040527 702.25244140625 0.3147711157798767 835.6089477539062 0.47609132528305054 0.82611305 0.38796472549438477 False diff --git a/ENCSR802NBC/cherimoya.fold_2.performance.tsv b/ENCSR802NBC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 27050d4e27ed341f44b14be7779ce715f94da1ec..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -838.323486328125 0.3284341096878052 0.47286203503608704 0.21445880830287933 0.8273521661758423 0.7829561233520508 0.3830481469631195 \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_3.evaluate.json b/ENCSR802NBC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 38ec4f52fc605003423b7b44f335bc22c04a0054..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130DHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_3.fit.json b/ENCSR802NBC/cherimoya.fold_3.fit.json deleted file mode 100644 index 543688f4c1b319f885a5ea15b39979e2808fe758..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF130DHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_3.log b/ENCSR802NBC/cherimoya.fold_3.log deleted file mode 100644 index 6515cb3d19ff58af4fa0c9315c3529a8ac2bfa87..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 35.48990082740784 3.696641206741333 690.3924560546875 0.7192180752754211 1050.1551513671875 0.3125961720943451 0.7028473 9.086007118225098 True -1 5540 30.62296414375305 20.08919620513916 791.8906860351562 0.7030969858169556 906.601806640625 0.41205716133117676 0.7689809 2.417954683303833 True -2 8310 30.43592357635498 0.5460445880889893 627.6264038085938 0.5844679474830627 883.783935546875 0.42613017559051514 0.7723179 1.526140570640564 True -3 11080 30.393131971359253 0.524975061416626 511.0714111328125 0.5319267511367798 872.4537963867188 0.43554383516311646 0.77064896 1.1494821310043335 False -4 13850 30.400352478027344 0.5429222583770752 717.6366577148438 0.6553353667259216 861.8422241210938 0.44259849190711975 0.7759254 0.8020275235176086 True -5 16620 30.39332604408264 0.5247304439544678 773.3676147460938 0.5967617034912109 855.6930541992188 0.44713467359542847 0.7779391 0.6901466250419617 True -6 19390 30.432199954986572 0.5171658992767334 868.05859375 0.6316359043121338 848.1632690429688 0.4524504244327545 0.7865121 0.6036653518676758 True -7 22160 30.47135901451111 0.97074294090271 750.548095703125 0.5686389207839966 841.3992919921875 0.45689624547958374 0.7918725 0.5980938673019409 True -8 24930 30.45860767364502 0.5189194679260254 854.32470703125 0.8205852508544922 836.5073852539062 0.45999404788017273 0.79473114 0.5542921423912048 True -9 27700 30.446096658706665 0.5165667533874512 595.3489990234375 0.48141103982925415 833.1969604492188 0.462674081325531 0.7973166 0.5080573558807373 True -10 30470 30.414652109146118 0.5153350830078125 685.8849487304688 0.3974718451499939 828.4224243164062 0.46555188298225403 0.8051989 0.48628777265548706 True -11 33240 30.403967142105103 0.5613245964050293 779.5540161132812 0.5603998899459839 822.84814453125 0.4692158102989197 0.8099738 0.4734337031841278 True -12 36010 30.601778507232666 0.5325872898101807 744.826416015625 0.5105698108673096 817.9380493164062 0.4722157418727875 0.81585413 0.4667884409427643 True -13 38780 30.46115469932556 0.5339739322662354 528.3992919921875 0.365695595741272 815.3814697265625 0.47268834710121155 0.8218628 0.43738263845443726 True -14 41550 30.41733455657959 0.5336408615112305 604.4878540039062 0.46528518199920654 810.9264526367188 0.4754388928413391 0.8306258 0.41962340474128723 True -15 44320 30.456450939178467 0.520268440246582 798.4775390625 0.45941978693008423 806.551513671875 0.47963958978652954 0.83628684 0.40397709608078003 True -16 47090 30.45688796043396 0.5124082565307617 633.3194580078125 0.39750486612319946 803.7616577148438 0.4815075397491455 0.8393574 0.38865387439727783 True -17 49860 29.8513400554657 0.5113668441772461 747.1138916015625 0.4332260489463806 802.1812744140625 0.48226436972618103 0.8425899 0.38517996668815613 True -18 52630 29.882054328918457 0.5916509628295898 631.3040771484375 0.33064645528793335 804.2448120117188 0.47966820001602173 0.84408414 0.38337767124176025 True -19 55400 29.91047215461731 0.5114846229553223 688.1732177734375 0.2911831736564636 804.4556884765625 0.4798299968242645 0.8439102 0.385146826505661 False diff --git a/ENCSR802NBC/cherimoya.fold_3.performance.tsv b/ENCSR802NBC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b9ae7aade517a34336c83fca0bd4c28db6d9b31c..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -804.2448120117188 0.32830893993377686 0.47966817021369934 0.21533741056919098 0.8440841436386108 0.8007981777191162 0.38337767124176025 \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_4.evaluate.json b/ENCSR802NBC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e94fea27870ab84da67b8318a5179c6aad236a24..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130DHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_4.fit.json b/ENCSR802NBC/cherimoya.fold_4.fit.json deleted file mode 100644 index 7e1e4e6e93834cddbc91d7c533c2060e3b6112e4..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF130DHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802NBC/cherimoya.fold_4.log b/ENCSR802NBC/cherimoya.fold_4.log deleted file mode 100644 index 9fbf9c8fa14415d6bd20df9c8e22b35eeee9a6dd..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2812 35.82935547828674 4.348487854003906 667.00830078125 0.7780988216400146 981.5825805664062 0.3062455356121063 0.684909 7.63890266418457 True -1 5624 30.916550159454346 0.625617265701294 750.533447265625 0.7132734060287476 855.4771728515625 0.39923882484436035 0.73129535 3.09000563621521 True -2 8436 31.031487226486206 0.5964055061340332 859.1103515625 0.562440037727356 833.0755615234375 0.41710495948791504 0.7413595 1.077746868133545 True -3 11248 30.909271717071533 17.78649663925171 888.1343383789062 0.6167686581611633 825.3641357421875 0.4206797778606415 0.74468786 0.8007919192314148 True -4 14060 31.01335072517395 22.49644160270691 845.0845947265625 0.6749482750892639 816.7098999023438 0.4269128441810608 0.7460265 0.7647336721420288 True -5 16872 30.966567277908325 0.9680423736572266 608.1356201171875 0.6597877740859985 809.0987548828125 0.4339979588985443 0.7491887 0.6332150101661682 True -6 19684 30.97268557548523 21.65370750427246 791.2974853515625 0.5754218101501465 803.0135498046875 0.4375167787075043 0.76275206 0.5748308897018433 True -7 22496 31.028722286224365 1.4067537784576416 503.39404296875 0.5545721054077148 797.8156127929688 0.4419991374015808 0.76038694 0.5407522320747375 False -8 25308 30.900557279586792 1.7759063243865967 577.1593017578125 0.850605845451355 793.870849609375 0.44552847743034363 0.76434773 0.5331243872642517 True -9 28120 30.884334564208984 2.165140390396118 684.287353515625 0.7828584909439087 788.9588012695312 0.44859474897384644 0.77186996 0.48740461468696594 True -10 30932 30.910401105880737 1.6115295886993408 704.299072265625 0.5127655863761902 786.459228515625 0.4517064690589905 0.7779371 0.4786221385002136 True -11 33744 30.921100854873657 2.488210916519165 555.20068359375 0.41094231605529785 782.2168579101562 0.45425084233283997 0.7805931 0.4573715627193451 True -12 36556 30.946539640426636 1.5158648490905762 527.8685302734375 0.5512648820877075 777.8878173828125 0.45792460441589355 0.78945035 0.44239339232444763 True -13 39368 30.991008043289185 0.9845888614654541 820.978515625 0.6887734532356262 774.9036865234375 0.46048229932785034 0.794789 0.4339253902435303 True -14 42180 30.952617406845093 0.8847742080688477 720.7577514648438 0.464810311794281 771.6259155273438 0.46254584193229675 0.80488247 0.4052736163139343 True -15 44992 30.910356283187866 0.8045885562896729 516.94287109375 0.3894856572151184 769.6260375976562 0.4639970064163208 0.8125661 0.3912757933139801 True -16 47804 30.433154582977295 0.5577034950256348 510.35955810546875 0.5652918815612793 767.9443969726562 0.46484750509262085 0.81859404 0.3796365559101105 True -17 50616 30.30709934234619 0.5568222999572754 707.3670654296875 0.4485684931278229 767.4713134765625 0.4660561680793762 0.82058775 0.3731482923030853 True -18 53428 30.32919144630432 0.5585110187530518 639.2515869140625 0.3341413736343384 768.0831298828125 0.46515458822250366 0.82140833 0.3730148375034332 True -19 56240 30.357361793518066 0.5612192153930664 728.1478271484375 0.26602840423583984 767.1600952148438 0.4664536714553833 0.82278323 0.3732580244541168 True diff --git a/ENCSR802NBC/cherimoya.fold_4.performance.tsv b/ENCSR802NBC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 300094ea81974548b03ad1d8f1677c234468ac4c..0000000000000000000000000000000000000000 --- a/ENCSR802NBC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -767.1600952148438 0.33759310841560364 0.4664537310600281 0.20326223969459534 0.8227832317352295 0.7663289904594421 0.3732580244541168 \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_0.evaluate.json b/ENCSR802ZYE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a364d600e3d102f80ec8c9f0ff7658aea9d19087..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF477SNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_0.fit.json b/ENCSR802ZYE/cherimoya.fold_0.fit.json deleted file mode 100644 index 762721ea281fbdf8f07e99e6d9f997648e07cf55..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF477SNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_0.log b/ENCSR802ZYE/cherimoya.fold_0.log deleted file mode 100644 index 92f52af2b72f65f9bbe01755a27e47e0a3b7a50a..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 34.996402740478516 3.6705381870269775 663.241455078125 0.513434112071991 887.19580078125 0.29397666454315186 0.6450177 5.544455528259277 True -1 5462 29.85337996482849 0.8997607231140137 659.9305419921875 0.5133808851242065 800.7521362304688 0.3745001256465912 0.71970826 1.8647958040237427 True -2 8193 30.262168169021606 0.5593836307525635 630.3245849609375 0.2976066470146179 782.1923217773438 0.3863676190376282 0.75216794 0.9560730457305908 True -3 10924 30.284575700759888 0.568889856338501 681.3466796875 0.32817402482032776 776.947021484375 0.3896750211715698 0.761661 0.7242927551269531 True -4 13655 30.22545886039734 0.5712144374847412 568.0322875976562 0.3556177616119385 773.2467041015625 0.3934427797794342 0.76758707 0.7438277006149292 True -5 16386 30.210238695144653 2.9999351501464844 698.5206298828125 0.5171172022819519 767.8807373046875 0.3977474272251129 0.7767848 0.6872748136520386 True -6 19117 30.23566222190857 0.5897090435028076 708.982177734375 0.5576862692832947 765.6925048828125 0.4000323414802551 0.785737 0.6442819833755493 True -7 21848 30.243753910064697 1.7255148887634277 719.6165161132812 0.5736464858055115 763.3915405273438 0.4025493562221527 0.79281825 0.5424327850341797 True -8 24579 30.281967878341675 0.5778250694274902 639.1751708984375 0.4349905550479889 762.3568725585938 0.40346387028694153 0.79443896 0.5201035737991333 True -9 27310 30.279937505722046 0.5659465789794922 700.2806396484375 0.3472153842449188 760.330810546875 0.4052773416042328 0.80121696 0.46758565306663513 True -10 30041 30.264523029327393 0.5741605758666992 832.3782348632812 0.5283119678497314 756.2196044921875 0.4099304676055908 0.80876744 0.4406599700450897 True -11 32772 30.24577307701111 0.5735788345336914 583.4022216796875 0.3683915436267853 753.8732299804688 0.41112852096557617 0.81564045 0.40273770689964294 True -12 35503 30.2960422039032 0.5763516426086426 674.005615234375 0.2600555717945099 752.4154052734375 0.41239893436431885 0.8232418 0.3740595281124115 True -13 38234 30.301987886428833 0.5821847915649414 692.721923828125 0.4082801043987274 749.3380126953125 0.4149976968765259 0.8277473 0.3500467836856842 True -14 40965 30.25156331062317 0.5723237991333008 588.4166870117188 0.28071537613868713 747.0911865234375 0.41773372888565063 0.83424836 0.3255678713321686 True -15 43696 29.699692010879517 0.5706851482391357 727.6678466796875 0.33975473046302795 746.9520874023438 0.41780155897140503 0.8408404 0.30851924419403076 True -16 46427 29.70443820953369 0.5649614334106445 633.9200439453125 0.3613138794898987 747.6063232421875 0.41642776131629944 0.84239006 0.2979668080806732 True -17 49158 29.722394943237305 0.9152970314025879 624.7593994140625 0.21444636583328247 747.5983276367188 0.4162917733192444 0.84268785 0.29261836409568787 True -18 51889 29.786658763885498 0.5722718238830566 573.6213989257812 0.3049299716949463 748.3495483398438 0.4154006242752075 0.8438826 0.2917735278606415 True -19 54620 29.714147806167603 0.5838935375213623 780.779541015625 0.20487135648727417 748.2643432617188 0.41601142287254333 0.8421335 0.29500818252563477 False diff --git a/ENCSR802ZYE/cherimoya.fold_0.performance.tsv b/ENCSR802ZYE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3bbff0a71f14ef543e7185a479b6abf0fcd5debf..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -748.3495483398438 0.34307947754859924 0.4154006242752075 0.19397105276584625 0.8438826203346252 0.8027092814445496 0.2917735278606415 \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_1.evaluate.json b/ENCSR802ZYE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f3600ec5682f577e94059dce2363ad5f95f5cc68..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF477SNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_1.fit.json b/ENCSR802ZYE/cherimoya.fold_1.fit.json deleted file mode 100644 index dfc70f59c6fc353f9a3f206110c7307e5e053451..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF477SNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_1.log b/ENCSR802ZYE/cherimoya.fold_1.log deleted file mode 100644 index 25e066b54a7ccadec9b90deda816e039b0f12b0b..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2692 34.87135910987854 4.087476015090942 785.9908447265625 0.42884477972984314 1010.8529052734375 0.3019903600215912 0.6724114 5.716634750366211 True -1 5384 29.872652053833008 0.8665666580200195 642.7535400390625 0.594700276851654 912.8028564453125 0.3897228240966797 0.7431366 2.6490557193756104 True -2 8076 29.871195077896118 0.7208998203277588 605.8189697265625 0.5696038007736206 895.233642578125 0.39957013726234436 0.7617095 1.2747455835342407 True -3 10768 29.90572476387024 0.7156274318695068 694.9864501953125 0.5592700839042664 881.625732421875 0.4085281789302826 0.7746295 1.0011175870895386 True -4 13460 29.570838928222656 1.398888349533081 608.4375 0.5240465402603149 877.5606079101562 0.41075587272644043 0.7804912 0.9542345404624939 True -5 16152 29.23721933364868 24.513164281845093 712.534912109375 0.4985888600349426 879.4814453125 0.40928202867507935 0.7780223 0.9945996403694153 False -6 18844 29.297773122787476 0.7245392799377441 632.1114501953125 0.39951473474502563 872.7197265625 0.4131380617618561 0.788718 0.7983185052871704 True -7 21536 29.210357189178467 8.815228700637817 739.3821411132812 0.38814717531204224 867.3408203125 0.4164987802505493 0.7989265 0.6557543873786926 True -8 24228 29.67420721054077 0.754387617111206 622.89599609375 0.44731688499450684 864.0931396484375 0.4184814691543579 0.8063534 0.6020556092262268 True -9 26920 29.24240517616272 0.7093167304992676 637.2671508789062 0.3039294481277466 860.025390625 0.42197245359420776 0.8113582 0.584955096244812 True -10 29612 29.183545112609863 0.7104353904724121 691.928466796875 0.2947425842285156 858.748291015625 0.4224189519882202 0.81718606 0.5167475342750549 True -11 32304 29.19009304046631 0.7057361602783203 573.6474609375 0.3303626775741577 854.0247192382812 0.42516985535621643 0.8264848 0.461591899394989 True -12 34996 29.164308071136475 0.7024028301239014 615.420166015625 0.339596688747406 849.9524536132812 0.4290243685245514 0.8334537 0.4299885034561157 True -13 37688 29.195141553878784 0.7131226062774658 622.609375 0.29631972312927246 848.3770751953125 0.42949166893959045 0.8388974 0.3901708722114563 True -14 40380 29.1615469455719 0.7032008171081543 631.7655639648438 0.2808176875114441 845.8790283203125 0.4315800964832306 0.8465355 0.3545827865600586 True -15 43072 29.171283721923828 0.7068092823028564 595.6617431640625 0.16642440855503082 843.3130493164062 0.433931827545166 0.8502898 0.3379976153373718 True -16 45764 29.180046558380127 0.712653636932373 641.1248779296875 0.24161607027053833 843.7190551757812 0.4337291419506073 0.8527482 0.3210451006889343 True -17 48456 29.208292484283447 1.3741850852966309 727.4515380859375 0.18633154034614563 843.8164672851562 0.43258851766586304 0.85382915 0.3129825294017792 True -18 51148 29.165223360061646 0.7011644840240479 563.701416015625 0.24385444819927216 840.7063598632812 0.4369927942752838 0.85154444 0.3127651512622833 False -19 53840 29.24406147003174 1.69852876663208 621.26611328125 0.16785332560539246 843.3025512695312 0.4336263835430145 0.8503918 0.31319090723991394 False diff --git a/ENCSR802ZYE/cherimoya.fold_1.performance.tsv b/ENCSR802ZYE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 21f43fe32725afb5c0790d0622ce22390d0a1b32..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -843.8164672851562 0.32498764991760254 0.43258851766586304 0.218138188123703 0.8538291454315186 0.8368405103683472 0.3129825294017792 \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_2.evaluate.json b/ENCSR802ZYE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1e1ea3ec054e0e7792c6bfdaba8c251609c24750..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF477SNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_2.fit.json b/ENCSR802ZYE/cherimoya.fold_2.fit.json deleted file mode 100644 index 449dad2d7e93abc21d8b09ba32756682630355fc..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF477SNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_2.log b/ENCSR802ZYE/cherimoya.fold_2.log deleted file mode 100644 index 54befbafe29a004e59b9fd4dce014f43aec24e74..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 36.619187116622925 3.3684945106506348 704.2215576171875 0.5090363025665283 956.0733032226562 0.29735007882118225 0.65090436 5.7350358963012695 True -1 5752 31.91019320487976 0.5985705852508545 715.4906005859375 0.5414769649505615 862.5435791015625 0.3804945647716522 0.7261242 1.681652545928955 True -2 8628 31.857227563858032 0.601555585861206 625.5281372070312 0.42186394333839417 844.0899047851562 0.3938556909561157 0.7459931 1.0339370965957642 True -3 11504 31.81604814529419 0.589087724685669 658.011962890625 0.5281691551208496 838.5945434570312 0.3971598148345947 0.75537246 0.8593419790267944 True -4 14380 31.876057386398315 0.5648162364959717 694.6248168945312 0.49499788880348206 835.1990966796875 0.40025949478149414 0.75909555 0.8461669087409973 True -5 17256 31.938773155212402 0.5694441795349121 655.2918701171875 0.40569496154785156 831.0489501953125 0.4038102328777313 0.7661554 0.7810758352279663 True -6 20132 31.910691499710083 0.5573995113372803 708.096435546875 0.4624975621700287 827.9168701171875 0.407244473695755 0.77027965 0.7303403615951538 True -7 23008 31.90810775756836 0.5615761280059814 801.662841796875 0.4554823040962219 824.7724609375 0.40921133756637573 0.77790827 0.6315932273864746 True -8 25884 31.588316440582275 0.5575909614562988 675.6627197265625 0.32137447595596313 820.76025390625 0.4126632809638977 0.7869584 0.5519338846206665 True -9 28760 31.222357988357544 1.6064212322235107 632.7763671875 0.26914137601852417 818.8203125 0.4135172665119171 0.7933108 0.5360140204429626 True -10 31636 31.156720399856567 0.5560884475708008 769.80126953125 0.4822527766227722 815.200439453125 0.4159114956855774 0.80329794 0.4876243770122528 True -11 34512 31.165074825286865 0.5592770576477051 595.5386962890625 0.27907371520996094 812.7781372070312 0.41827625036239624 0.8064114 0.46483007073402405 True -12 37388 31.269339323043823 5.661133766174316 679.96484375 0.445830374956131 810.3304443359375 0.420463889837265 0.81364566 0.41777777671813965 True -13 40264 31.228588104248047 11.995793342590332 684.9600830078125 0.26646900177001953 807.1220092773438 0.42293447256088257 0.8195592 0.3829363286495209 True -14 43140 31.274146795272827 19.396169662475586 613.0948486328125 0.29881852865219116 805.447998046875 0.42516979575157166 0.82378036 0.3628233075141907 True -15 46016 31.212260484695435 0.5702931880950928 621.5352783203125 0.3854967951774597 806.2848510742188 0.42224442958831787 0.8298163 0.34327179193496704 True -16 48892 31.203444004058838 0.5672531127929688 645.654541015625 0.271018385887146 804.6178588867188 0.42390206456184387 0.8302738 0.3315294682979584 True -17 51768 31.182537078857422 0.5477519035339355 589.4249267578125 0.18587058782577515 803.4801635742188 0.4257415235042572 0.8330427 0.3235253393650055 True -18 54644 31.192321062088013 0.5613880157470703 767.3169555664062 0.2513340413570404 804.0250244140625 0.42494696378707886 0.8322649 0.3251267969608307 False -19 57520 31.176159620285034 0.5647635459899902 603.824951171875 0.2171185314655304 804.3323974609375 0.42487794160842896 0.8306024 0.32750609517097473 False diff --git a/ENCSR802ZYE/cherimoya.fold_2.performance.tsv b/ENCSR802ZYE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b9f628dca58b7b2424de78d89808b550d477408d..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -803.4801635742188 0.3329329192638397 0.4257415235042572 0.20789837837219238 0.8330426812171936 0.8103862404823303 0.3235253393650055 \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_3.evaluate.json b/ENCSR802ZYE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 281669d0207291c5bf0bd8bcc93c075e672d4e17..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF477SNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_3.fit.json b/ENCSR802ZYE/cherimoya.fold_3.fit.json deleted file mode 100644 index 12997ef906f1efa96ee1c75084c35d2f905c4b3f..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF477SNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_3.log b/ENCSR802ZYE/cherimoya.fold_3.log deleted file mode 100644 index 8d48d715e66f9b876af0c52dfa040538c7968376..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 34.7370970249176 4.291006565093994 750.2103881835938 0.6059579253196716 855.8756103515625 0.29671090841293335 0.6311166 5.964755058288574 True -1 5506 30.615882873535156 0.6242401599884033 707.7285766601562 0.4804832339286804 783.8447875976562 0.3696781098842621 0.698213 2.024561882019043 True -2 8259 30.627708435058594 0.5788149833679199 615.6785888671875 0.49033236503601074 762.2446899414062 0.38509002327919006 0.7284894 1.1977959871292114 True -3 11012 30.60704779624939 0.5646107196807861 791.0972900390625 0.438697874546051 754.544921875 0.3898317217826843 0.74630636 1.016226053237915 True -4 13765 30.651594638824463 0.5616614818572998 671.9348754882812 0.35610270500183105 751.4837646484375 0.3917640149593353 0.75561047 0.9149454832077026 True -5 16518 30.61624240875244 3.078176498413086 726.9481201171875 0.4655073285102844 749.959228515625 0.39282774925231934 0.75809044 0.7583622932434082 True -6 19271 30.676713228225708 0.5612866878509521 650.3604736328125 0.2672593891620636 744.080322265625 0.3981245756149292 0.76787436 0.7091189026832581 True -7 22024 30.57150959968567 0.564551830291748 660.3037719726562 0.5032663345336914 740.3583984375 0.40180322527885437 0.7769582 0.6570231318473816 True -8 24777 30.59667682647705 0.5618338584899902 796.2864990234375 0.4538452625274658 738.4739379882812 0.4036084711551666 0.78466433 0.5865671634674072 True -9 27530 30.593021631240845 0.5639376640319824 649.9583740234375 0.2502604126930237 736.9078369140625 0.40436774492263794 0.78967834 0.5251563191413879 True -10 30283 30.5367910861969 2.7367618083953857 629.262939453125 0.268232524394989 733.65771484375 0.4077742099761963 0.7960316 0.484531968832016 True -11 33036 30.504027605056763 1.418494462966919 816.9631958007812 0.4421589970588684 732.5956420898438 0.40713557600975037 0.80321914 0.4327429234981537 True -12 35789 30.189357042312622 0.5693905353546143 685.390625 0.3617944121360779 728.4260864257812 0.4117873013019562 0.8117017 0.401571124792099 True -13 38542 29.937947034835815 0.5585472583770752 672.455322265625 0.4417129158973694 728.705810546875 0.410656213760376 0.81940424 0.3812185823917389 True -14 41295 29.866153717041016 0.5542500019073486 719.1652221679688 0.3325200378894806 727.4042358398438 0.4113883674144745 0.8271212 0.34437328577041626 True -15 44048 29.84419822692871 0.5523920059204102 684.7540283203125 0.23825311660766602 725.6986083984375 0.4134434759616852 0.8315859 0.3268146514892578 True -16 46801 29.860445261001587 0.5448389053344727 700.4918212890625 0.35554587841033936 724.2975463867188 0.4155964255332947 0.83448094 0.3146265745162964 True -17 49554 29.95972442626953 0.55704665184021 694.746826171875 0.407518595457077 724.9630126953125 0.4144045412540436 0.8367277 0.3072417676448822 True -18 52307 29.89249849319458 2.5601184368133545 591.2655029296875 0.23111297190189362 725.8507690429688 0.41353943943977356 0.8357737 0.3094645142555237 False -19 55060 29.95801615715027 0.5479171276092529 575.8314208984375 0.2064480036497116 725.609130859375 0.41473644971847534 0.83471495 0.30992141366004944 False diff --git a/ENCSR802ZYE/cherimoya.fold_3.performance.tsv b/ENCSR802ZYE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4f1028c73be29ca4fc642bcab01e19a885b5a13a..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -724.9630126953125 0.34509220719337463 0.4144045412540436 0.19195321202278137 0.8367276787757874 0.794665515422821 0.3072417676448822 \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_4.evaluate.json b/ENCSR802ZYE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1b538b2bb3bb0e6271ece23ad40535768416f973..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF477SNS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_4.fit.json b/ENCSR802ZYE/cherimoya.fold_4.fit.json deleted file mode 100644 index 01d2fda9fedbba4ff68fd564a73eed23fefe8b7e..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF477SNS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR802ZYE/cherimoya.fold_4.log b/ENCSR802ZYE/cherimoya.fold_4.log deleted file mode 100644 index 3e033cba0b290eec0e32f5c47817487f9b992531..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2827 36.16051363945007 4.102183103561401 771.301513671875 0.5450118780136108 822.8923950195312 0.29482799768447876 0.62669384 5.5547637939453125 True -1 5654 31.293941736221313 1.4039502143859863 631.6489868164062 0.5576050281524658 753.6470947265625 0.36698463559150696 0.7036815 2.0624866485595703 True -2 8481 31.381944179534912 0.5844616889953613 608.0985107421875 0.5469239950180054 737.696533203125 0.379648357629776 0.7218111 0.9631357192993164 True -3 11308 31.27384376525879 0.5707082748413086 687.6690673828125 0.3881472647190094 739.80126953125 0.3810483515262604 0.7257625 0.8625893592834473 True -4 14135 31.2995388507843 0.5930020809173584 509.8246154785156 0.49727630615234375 728.0225219726562 0.3878624737262726 0.741279 0.7778347134590149 True -5 16962 31.308784246444702 0.6055476665496826 614.8388671875 0.35627979040145874 725.5167236328125 0.38941410183906555 0.74984 0.8152465224266052 True -6 19789 30.87937307357788 0.5682594776153564 697.2391967773438 0.3154759407043457 726.6722412109375 0.38847115635871887 0.7480987 0.7461657524108887 False -7 22616 30.63789963722229 0.5624592304229736 619.3968505859375 0.5949362516403198 720.4945068359375 0.3937080502510071 0.7618714 0.5720977187156677 True -8 25443 30.667857885360718 0.5833323001861572 558.3560791015625 0.4423421025276184 718.6553344726562 0.39466559886932373 0.77201325 0.4980265498161316 True -9 28270 30.711591005325317 0.6721422672271729 546.1190185546875 0.245828315615654 717.7197875976562 0.3955951929092407 0.7774508 0.48287805914878845 True -10 31097 30.687859535217285 0.583977460861206 544.0209350585938 0.4549512267112732 713.7537231445312 0.39963191747665405 0.7838453 0.4459926187992096 True -11 33924 30.725529670715332 0.5708773136138916 650.348876953125 0.34074610471725464 711.2280883789062 0.4014476537704468 0.79343027 0.3892155885696411 True -12 36751 30.716878414154053 0.593625545501709 575.9880981445312 0.2908642292022705 710.7822265625 0.40179258584976196 0.8005337 0.3724593222141266 True -13 39578 30.74540424346924 0.5754761695861816 813.05517578125 0.3498038649559021 708.6882934570312 0.40409794449806213 0.80604374 0.3482612371444702 True -14 42405 30.7235586643219 0.5748796463012695 667.5626220703125 0.30983150005340576 706.3504028320312 0.406145840883255 0.81268233 0.3323586881160736 True -15 45232 30.762815952301025 0.5877077579498291 535.429443359375 0.23659747838974 707.025146484375 0.40428999066352844 0.8197123 0.3135097920894623 True -16 48059 30.748886823654175 0.5776071548461914 556.1494140625 0.2371233105659485 706.60546875 0.4051348865032196 0.8223031 0.301398903131485 True -17 50886 30.71100163459778 0.601062536239624 641.3546142578125 0.25739192962646484 706.1377563476562 0.4062593877315521 0.82358515 0.2980997860431671 True -18 53713 30.933131217956543 0.5944621562957764 639.2425537109375 0.147889643907547 706.3429565429688 0.4063418507575989 0.82341844 0.2983801066875458 False -19 56540 30.81939959526062 0.5934779644012451 648.0318603515625 0.16213783621788025 706.00830078125 0.40738216042518616 0.8208247 0.3001912534236908 False diff --git a/ENCSR802ZYE/cherimoya.fold_4.performance.tsv b/ENCSR802ZYE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d696a7b5e1ce4769acd7db326645cf2ea2506cbf..0000000000000000000000000000000000000000 --- a/ENCSR802ZYE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -706.1377563476562 0.3511211574077606 0.4062593877315521 0.18502546846866608 0.8235851526260376 0.7741178274154663 0.2980997860431671 \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_0.evaluate.json b/ENCSR803JVQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4e065ccc5ad2b20c9d009c012c74e3b5477d3a91..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF518XJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_0.fit.json b/ENCSR803JVQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 696b552554d12dd7aa2798a70c15d69ec9f8f772..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF518XJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_0.log b/ENCSR803JVQ/cherimoya.fold_0.log deleted file mode 100644 index 4d62974ae2196422a3a7ab8aa963d62967664fdc..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2047 26.74376392364502 4.164023399353027 362.21112060546875 1.443476676940918 475.9798889160156 0.13232575356960297 0.55477405 8.549264907836914 True -1 4094 22.475836515426636 0.759188175201416 277.65545654296875 0.6669895648956299 422.1600341796875 0.18646344542503357 0.69892836 5.2622294425964355 True -2 6141 22.496742248535156 1.2817714214324951 279.59368896484375 0.6647064685821533 401.8276672363281 0.20188002288341522 0.73708963 2.8820295333862305 True -3 8188 22.312348127365112 0.41693639755249023 386.703857421875 0.8192152976989746 387.8944396972656 0.21100768446922302 0.7564951 1.737089991569519 True -4 10235 22.075077533721924 0.4308207035064697 269.912109375 0.7427588701248169 381.96612548828125 0.21431973576545715 0.76579064 1.184636116027832 True -5 12282 22.08000111579895 0.4125370979309082 405.9865417480469 0.8712431192398071 378.3149108886719 0.21806082129478455 0.7700448 1.0945091247558594 True -6 14329 22.046173095703125 0.40274906158447266 385.9737243652344 0.7196183204650879 374.7823486328125 0.22197063267230988 0.7783976 0.9642219543457031 True -7 16376 22.079485654830933 0.4063751697540283 293.9869384765625 0.6384457349777222 372.8673400878906 0.22259144484996796 0.78837156 0.9376999139785767 True -8 18423 22.150296688079834 0.411182165145874 293.9664001464844 0.5315917134284973 370.62884521484375 0.22620148956775665 0.79164606 0.9243582487106323 True -9 20470 22.036287307739258 0.42009663581848145 300.9866943359375 0.7005702257156372 368.1593017578125 0.2273528277873993 0.8002348 0.8128004670143127 True -10 22517 22.03774356842041 0.41367411613464355 245.6187744140625 0.6938583254814148 364.85858154296875 0.23287253081798553 0.8068121 0.7289925217628479 True -11 24564 22.070157051086426 2.441561222076416 308.34649658203125 0.5994851589202881 363.616455078125 0.23357747495174408 0.8128903 0.6719354391098022 True -12 26611 22.141367435455322 0.9977617263793945 275.75933837890625 0.455335408449173 363.4140625 0.23325814306735992 0.8201033 0.6148868203163147 True -13 28658 22.09561800956726 0.4238276481628418 288.4259033203125 0.5263580679893494 360.3580322265625 0.23625846207141876 0.8278914 0.5799997448921204 True -14 30705 22.16728711128235 0.43454575538635254 388.77911376953125 0.8891648650169373 359.3981018066406 0.23724134266376495 0.83148646 0.5698668956756592 True -15 32752 22.14451551437378 0.44756484031677246 254.30538940429688 0.4648371934890747 358.3570861816406 0.23779407143592834 0.8364675 0.5360646843910217 True -16 34799 22.209288597106934 0.4273829460144043 329.83673095703125 0.4862142503261566 358.6669921875 0.2374359369277954 0.8395859 0.5220072269439697 True -17 36846 22.184150218963623 0.4437229633331299 327.09906005859375 0.5328435897827148 357.6057434082031 0.2385926991701126 0.839469 0.5145513415336609 False -18 38893 22.181177377700806 0.44469141960144043 303.00244140625 0.3913379907608032 357.9974365234375 0.23880158364772797 0.83848083 0.5154005885124207 False -19 40940 22.2243812084198 1.4712872505187988 336.7326354980469 0.3547637164592743 357.587158203125 0.23946838080883026 0.8368766 0.5179048180580139 False diff --git a/ENCSR803JVQ/cherimoya.fold_0.performance.tsv b/ENCSR803JVQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 32f250e90c0ea91cce4683b25adbd6fac35c248b..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -358.6669921875 0.5141350626945496 0.2374359369277954 0.08822891861200333 0.8395859003067017 0.7858392596244812 0.5220072269439697 \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_1.evaluate.json b/ENCSR803JVQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 55dd831555294c469314b6e680ffa85c34d228d9..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF518XJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_1.fit.json b/ENCSR803JVQ/cherimoya.fold_1.fit.json deleted file mode 100644 index d6e03aa18f3e54acc3fd71f4e491469289eb12a8..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF518XJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_1.log b/ENCSR803JVQ/cherimoya.fold_1.log deleted file mode 100644 index 3f07a0e456d5cb2a6368506d3306e7b954766bbc..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2005 26.543925523757935 3.6640918254852295 360.39935302734375 1.2937202453613281 596.5139770507812 0.146370068192482 0.51882184 10.458113670349121 True -1 4010 22.014756202697754 0.6298551559448242 302.33319091796875 0.7257565855979919 528.7145385742188 0.2072608768939972 0.6989142 4.933536529541016 True -2 6015 22.03790259361267 0.6282768249511719 230.58303833007812 0.6647701859474182 500.5451965332031 0.2263081967830658 0.73440945 3.381528377532959 True -3 8020 22.044155597686768 0.627037763595581 287.1821594238281 0.9447091817855835 483.55322265625 0.2373742312192917 0.7487413 2.323915719985962 True -4 10025 22.054214000701904 0.568199634552002 263.1836853027344 0.6823718547821045 472.5958251953125 0.24173592031002045 0.76207715 1.856393814086914 True -5 12030 21.99948024749756 0.5745437145233154 311.06805419921875 0.5893922448158264 465.2398986816406 0.24794943630695343 0.7691129 1.527754306793213 True -6 14035 22.0009286403656 1.022627353668213 252.39324951171875 0.5421543121337891 460.589599609375 0.25081539154052734 0.78094965 1.3806591033935547 True -7 16040 22.011078119277954 0.5765831470489502 321.59857177734375 0.551744818687439 458.0448303222656 0.25293421745300293 0.79220355 1.216943383216858 True -8 18045 22.039701223373413 22.287009954452515 352.63470458984375 0.6354677677154541 451.296875 0.25896352529525757 0.8039358 1.0603588819503784 True -9 20050 22.036210775375366 0.5919215679168701 318.08746337890625 0.9761178493499756 450.6578674316406 0.260233610868454 0.8069229 1.0368283987045288 True -10 22055 22.563289642333984 2.1717166900634766 240.10455322265625 0.8281766176223755 446.6338195800781 0.263896107673645 0.8178264 0.8879923224449158 True -11 24060 22.03869318962097 0.5816261768341064 251.25025939941406 0.6907570362091064 446.5032043457031 0.26251715421676636 0.8254404 0.804172694683075 True -12 26065 22.703627586364746 0.5727720260620117 354.75567626953125 0.619391918182373 442.48358154296875 0.26652792096138 0.83223194 0.7331178784370422 True -13 28070 22.184348344802856 22.760973691940308 268.6985168457031 1.1631176471710205 441.1095275878906 0.26652276515960693 0.8405313 0.6676465272903442 True -14 30075 21.768503427505493 0.5694334506988525 307.6324768066406 0.5237753987312317 439.25018310546875 0.26879164576530457 0.8462678 0.647671639919281 True -15 32080 21.629037618637085 0.644953727722168 229.33120727539062 0.48906269669532776 435.8448486328125 0.2718140482902527 0.8492662 0.6220965385437012 True -16 34085 21.632532835006714 1.1809101104736328 416.2995910644531 0.3821938931941986 436.66510009765625 0.2696417570114136 0.8523241 0.5985321998596191 True -17 36090 21.63427209854126 0.5537421703338623 286.616943359375 0.44812268018722534 436.03826904296875 0.270219624042511 0.8516125 0.588300883769989 False -18 38095 21.64176368713379 0.556555986404419 330.9264221191406 0.3177952766418457 437.2508239746094 0.2693220376968384 0.8507047 0.5940812230110168 False -19 40100 21.705779790878296 0.5991256237030029 295.45440673828125 0.31681883335113525 436.1292724609375 0.27134737372398376 0.84984833 0.5942897796630859 False diff --git a/ENCSR803JVQ/cherimoya.fold_1.performance.tsv b/ENCSR803JVQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 41b755dc75eb1a18ed34ab7730a67fde08e16ad5..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -436.66510009765625 0.48811566829681396 0.2696417570114136 0.10138626396656036 0.8523241281509399 0.8211634755134583 0.5985321998596191 \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_2.evaluate.json b/ENCSR803JVQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b40a0fc334901a0b3ca8d289d6b8a9eb453f1358..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF518XJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_2.fit.json b/ENCSR803JVQ/cherimoya.fold_2.fit.json deleted file mode 100644 index fa2f56ee2bf10fbb31607d20021f288f8a516438..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF518XJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_2.log b/ENCSR803JVQ/cherimoya.fold_2.log deleted file mode 100644 index 3251ce5a0c365b85d080735b26d7c2552d2ebb1a..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2145 27.957924842834473 3.5760645866394043 380.282470703125 0.8160093426704407 485.9971923828125 0.13759474456310272 0.5296198 7.544097900390625 True -1 4290 23.607532024383545 0.7856733798980713 272.2760009765625 0.9025270342826843 420.9500732421875 0.1936345249414444 0.69865924 4.061366558074951 True -2 6435 23.652963638305664 0.48239588737487793 309.5087890625 1.058742642402649 404.3633117675781 0.20561543107032776 0.7251892 2.8992671966552734 True -3 8580 23.582007884979248 12.986912488937378 386.92462158203125 1.2450978755950928 390.5537109375 0.2125418484210968 0.7450004 1.5544309616088867 True -4 10725 23.73480772972107 0.4834275245666504 252.3973388671875 0.3765113055706024 385.1991882324219 0.21774379909038544 0.758176 1.1745457649230957 True -5 12870 23.573322057724 12.169461250305176 334.2574462890625 0.7045696377754211 381.756103515625 0.22033224999904633 0.7699508 1.0757728815078735 True -6 15015 23.624869346618652 0.4631068706512451 372.10809326171875 0.7850689888000488 376.7646484375 0.2248583883047104 0.7759755 0.9810746312141418 True -7 17160 23.56634521484375 0.4510834217071533 340.6421813964844 0.6299303770065308 375.4151611328125 0.22535187005996704 0.783524 0.9222618341445923 True -8 19305 23.529685497283936 1.2694532871246338 386.89892578125 0.7754288911819458 371.69091796875 0.2292814999818802 0.79381317 0.803199827671051 True -9 21450 23.630346298217773 1.1833138465881348 302.7280578613281 0.6703172922134399 369.14501953125 0.23080718517303467 0.80178916 0.7004154324531555 True -10 23595 23.61074471473694 0.45141077041625977 293.2828674316406 0.7959444522857666 367.7539978027344 0.232483372092247 0.8117026 0.6414598822593689 True -11 25740 23.606696128845215 0.44821739196777344 328.226806640625 0.7867809534072876 365.5733642578125 0.23491670191287994 0.81537503 0.6097870469093323 True -12 27885 23.60984444618225 0.4558596611022949 344.6603698730469 0.7214635014533997 364.02313232421875 0.23630967736244202 0.8211379 0.5817753672599792 True -13 30030 23.635443449020386 0.8132266998291016 305.91107177734375 0.5338253378868103 362.74169921875 0.236738383769989 0.82496923 0.568820059299469 True -14 32175 23.569799184799194 0.43816590309143066 303.09112548828125 0.45349258184432983 360.7436218261719 0.23882582783699036 0.832453 0.5416933298110962 True -15 34320 23.642218351364136 0.45347142219543457 348.0594787597656 0.7179723978042603 360.73065185546875 0.2391466498374939 0.83603525 0.5245964527130127 True -16 36465 23.680127143859863 1.5969774723052979 285.43560791015625 0.2912147641181946 359.61041259765625 0.2406182587146759 0.8366838 0.5184682607650757 True -17 38610 23.618757486343384 0.5904395580291748 303.337158203125 0.3101866841316223 359.99444580078125 0.2399943321943283 0.8385132 0.5168469548225403 True -18 40755 23.680745601654053 1.4649670124053955 290.5013732910156 0.31802594661712646 361.2902526855469 0.23797184228897095 0.8365346 0.5169486403465271 False -19 42900 23.57928729057312 0.4450974464416504 347.5484924316406 0.4875969886779785 360.62493896484375 0.23927682638168335 0.8377028 0.5181717872619629 False diff --git a/ENCSR803JVQ/cherimoya.fold_2.performance.tsv b/ENCSR803JVQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index be8a061a2e9b6dfe72093c513bd0a995ef6e5e58..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -359.99444580078125 0.5121092796325684 0.2399943321943283 0.08806616067886353 0.838513195514679 0.7853295207023621 0.5168469548225403 \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_3.evaluate.json b/ENCSR803JVQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8d3b22e867cea126c2de5527a942aa05d0a755f4..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF518XJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_3.fit.json b/ENCSR803JVQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 6f21aa752afbf0cd684f26808697b2d2b5019596..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF518XJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_3.log b/ENCSR803JVQ/cherimoya.fold_3.log deleted file mode 100644 index 14b28f8d12e858410b8a8ed29bdbb50ee49d4302..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2052 27.050644397735596 3.463926076889038 362.5667724609375 1.2941721677780151 513.9880981445312 0.1474675089120865 0.49276274 8.849820137023926 True -1 4104 22.578861951828003 1.9568257331848145 344.843505859375 0.959355890750885 449.7157287597656 0.2038373053073883 0.6559281 5.3886823654174805 True -2 6156 22.612362384796143 0.4700288772583008 348.1888427734375 0.6498059034347534 434.82476806640625 0.2135314643383026 0.6914597 3.386085271835327 True -3 8208 22.580771684646606 0.41881871223449707 225.9037628173828 0.825725793838501 422.47186279296875 0.22544491291046143 0.70755273 2.170389175415039 True -4 10260 22.25400400161743 1.5367083549499512 326.2911376953125 0.6521666646003723 413.68658447265625 0.22835756838321686 0.7316022 1.4887182712554932 True -5 12312 22.150946617126465 0.4386005401611328 231.04254150390625 0.7002377510070801 410.48095703125 0.23089219629764557 0.7409847 1.3539026975631714 True -6 14364 22.178876876831055 0.42132019996643066 367.31671142578125 0.8613426685333252 407.4129638671875 0.23311489820480347 0.7515408 1.2015799283981323 True -7 16416 22.166595220565796 0.7035269737243652 315.89581298828125 0.8962346911430359 403.2284851074219 0.2384834587574005 0.7531508 1.124224066734314 True -8 18468 22.14453935623169 0.40697646141052246 347.78192138671875 0.5362496376037598 400.6643981933594 0.2420814037322998 0.76477826 1.024130940437317 True -9 20520 22.465413331985474 0.4505472183227539 403.7835998535156 0.8073245882987976 399.1888122558594 0.2428687959909439 0.7739172 0.9498468637466431 True -10 22572 22.13684368133545 0.41732096672058105 249.89071655273438 0.7120113372802734 398.40411376953125 0.24433766305446625 0.7749952 0.9316792488098145 True -11 24624 22.142983436584473 0.42389917373657227 252.07318115234375 0.7366158962249756 395.4275817871094 0.24705716967582703 0.7878714 0.8405660390853882 True -12 26676 22.195894241333008 0.839707612991333 328.50982666015625 0.7957421541213989 393.46051025390625 0.24886208772659302 0.7963341 0.7729007601737976 True -13 28728 22.140097856521606 0.40329551696777344 227.15419006347656 0.4172056317329407 389.6767272949219 0.2531130015850067 0.80648 0.717509388923645 True -14 30780 22.143806219100952 0.4152350425720215 295.3880615234375 0.5995950698852539 388.9239807128906 0.25223708152770996 0.8122226 0.6853564977645874 True -15 32832 22.18789529800415 0.4367339611053467 309.13824462890625 0.5499267578125 388.0767822265625 0.2530349791049957 0.81905174 0.654764711856842 True -16 34884 22.167783975601196 12.133374214172363 320.09027099609375 0.5058737993240356 386.4608154296875 0.254346638917923 0.8235336 0.6313803791999817 True -17 36936 22.41001796722412 0.4184455871582031 318.6827697753906 0.47672346234321594 387.2940673828125 0.25286394357681274 0.82412285 0.623054563999176 True -18 38988 22.217179775238037 0.4093663692474365 300.8305969238281 0.4131154417991638 388.23431396484375 0.2520274817943573 0.8225347 0.624110221862793 False -19 41040 22.182021617889404 0.745563268661499 240.19781494140625 0.439059853553772 388.4730529785156 0.252271831035614 0.8222605 0.6266594529151917 False diff --git a/ENCSR803JVQ/cherimoya.fold_3.performance.tsv b/ENCSR803JVQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8e6d1391dc2bf198face4b6675e20d8ccc85cb6b..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -387.2940673828125 0.5020565986633301 0.25286394357681274 0.09443320333957672 0.8241228461265564 0.7801531553268433 0.623054563999176 \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_4.evaluate.json b/ENCSR803JVQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0598956622e03fc4a3eabeb6bc93da4d5ef35c70..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF518XJR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_4.fit.json b/ENCSR803JVQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 145076919a1f21115d780d2140964b3ec6baec7b..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF518XJR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR803JVQ/cherimoya.fold_4.log b/ENCSR803JVQ/cherimoya.fold_4.log deleted file mode 100644 index 08b5a7065cb37d5251778bc436f83deb3622428b..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2066 27.09029197692871 3.73456072807312 336.0701599121094 1.00065016746521 429.5735778808594 0.13275569677352905 0.51664615 7.384087562561035 True -1 4132 22.755568981170654 1.0206551551818848 343.26092529296875 0.8595055341720581 390.2472839355469 0.17455103993415833 0.64539784 4.544943332672119 True -2 6198 22.757757902145386 1.4503014087677002 345.71160888671875 0.7587379217147827 372.53753662109375 0.18852990865707397 0.6901293 2.2973618507385254 True -3 8264 22.708242416381836 0.43193745613098145 289.729736328125 0.7381212711334229 359.4395751953125 0.1964641511440277 0.723103 1.6969380378723145 True -4 10330 22.694390296936035 0.42592883110046387 322.5031433105469 0.5505784749984741 353.6780090332031 0.20163443684577942 0.7323961 1.2821083068847656 True -5 12396 22.690691471099854 0.4242684841156006 296.3858642578125 0.6964823007583618 347.8460693359375 0.20773759484291077 0.7427345 1.1230052709579468 True -6 14462 22.707154512405396 0.4258904457092285 242.01116943359375 0.5189522504806519 345.4029235839844 0.20752540230751038 0.7569569 0.9701395034790039 True -7 16528 22.692763566970825 0.41428184509277344 350.5102844238281 0.5476382970809937 342.06170654296875 0.21120429039001465 0.7676977 0.8860463500022888 True -8 18594 22.504692554473877 0.41486620903015137 260.04693603515625 0.7744184732437134 340.6246337890625 0.21179214119911194 0.78028303 0.8154993653297424 True -9 20660 22.330729484558105 0.41501355171203613 311.9957275390625 0.8873751759529114 338.6062927246094 0.21497482061386108 0.78135455 0.7917408347129822 True -10 22726 22.31492853164673 0.41704344749450684 294.85205078125 0.5543605089187622 336.9732360839844 0.21650388836860657 0.7951814 0.6971608996391296 True -11 24792 22.28065276145935 0.41681408882141113 305.92919921875 0.5427900552749634 335.3196105957031 0.21883215010166168 0.8009445 0.6495121717453003 True -12 26858 22.317532777786255 0.41388440132141113 289.68817138671875 0.6100770235061646 334.5093078613281 0.21924929320812225 0.81032234 0.5832309722900391 True -13 28924 22.306577444076538 0.4151439666748047 326.3367919921875 0.6861693859100342 333.0858459472656 0.22087320685386658 0.81627923 0.554098904132843 True -14 30990 22.280728578567505 0.40842199325561523 295.43878173828125 0.8308736085891724 332.862060546875 0.2199944406747818 0.82238054 0.5193126201629639 True -15 33056 22.329315185546875 0.4128384590148926 363.9932861328125 0.534796953201294 331.5498962402344 0.2219613790512085 0.8312872 0.4989534914493561 True -16 35122 22.318497896194458 0.7584238052368164 300.8297119140625 0.42389166355133057 330.2020263671875 0.22367161512374878 0.8329513 0.4888650178909302 True -17 37188 22.320111751556396 0.42372846603393555 340.35723876953125 0.30534476041793823 330.4024963378906 0.22358454763889313 0.8353814 0.4820675551891327 True -18 39254 22.289533138275146 2.4834976196289062 305.42694091796875 0.34484440088272095 331.1531982421875 0.2221616953611374 0.8348977 0.4824279844760895 False -19 41320 22.343446254730225 0.42864418029785156 258.8253479003906 0.31383442878723145 331.0693054199219 0.22278641164302826 0.8351412 0.48326802253723145 False diff --git a/ENCSR803JVQ/cherimoya.fold_4.performance.tsv b/ENCSR803JVQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 06dbd685f7931e356327c3710a5057347441ae44..0000000000000000000000000000000000000000 --- a/ENCSR803JVQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -330.4024963378906 0.5246286988258362 0.22358456254005432 0.07621020823717117 0.8353813886642456 0.7778169512748718 0.4820675551891327 \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_0.evaluate.json b/ENCSR804RSI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 426a2dd39bbe573bfc2afa8242dde58428fffaee..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF181SUB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_0.fit.json b/ENCSR804RSI/cherimoya.fold_0.fit.json deleted file mode 100644 index bcf107d68cf6bf2f1ca031eaba3f08bc5766b91c..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF181SUB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_0.log b/ENCSR804RSI/cherimoya.fold_0.log deleted file mode 100644 index 647e80da804ca67bd01f1e0ca30a4a342d7f1254..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 34.88771080970764 15.705095291137695 1293.269287109375 1.4489762783050537 1463.447998046875 0.23779188096523285 0.61998856 7.540207386016846 True -1 5486 30.397408485412598 0.5843617916107178 1025.4927978515625 0.6691906452178955 1295.2296142578125 0.3675396144390106 0.6627013 1.735945224761963 True -2 8229 30.343053579330444 0.5619735717773438 1054.431640625 1.1902151107788086 1270.205810546875 0.38138043880462646 0.67731196 0.9993197321891785 True -3 10972 30.417088985443115 0.608731746673584 961.4093017578125 1.3780267238616943 1251.0721435546875 0.3933776915073395 0.68541515 0.6649876832962036 True -4 13715 30.40436553955078 0.5691919326782227 1081.8026123046875 0.5840799808502197 1244.6021728515625 0.3973937928676605 0.6833597 0.6382797360420227 False -5 16458 30.157448768615723 0.5543291568756104 912.2005004882812 0.905608057975769 1243.2718505859375 0.3971458971500397 0.6850776 0.5989187955856323 False -6 19201 29.703783750534058 0.5507369041442871 886.4039306640625 0.5478041172027588 1239.2352294921875 0.4007267355918884 0.68825763 0.6025550961494446 True -7 21944 29.755523204803467 0.5577270984649658 957.632080078125 0.9894812107086182 1233.586669921875 0.40495479106903076 0.6890234 0.6240981817245483 True -8 24687 29.726938724517822 0.5522453784942627 998.731201171875 0.9560062885284424 1226.6243896484375 0.4103010594844818 0.6934879 0.612980306148529 True -9 27430 29.74339509010315 0.5570874214172363 1124.2880859375 0.5506298542022705 1226.7103271484375 0.40882447361946106 0.69696194 0.5648868680000305 True -10 30173 29.7910897731781 0.5520656108856201 834.1761474609375 0.8683195114135742 1222.7564697265625 0.41247299313545227 0.7018462 0.5524565577507019 True -11 32916 30.546860218048096 0.558568000793457 767.253662109375 0.6590426564216614 1218.0216064453125 0.4154431223869324 0.71164715 0.536178708076477 True -12 35659 29.73065948486328 0.5585708618164062 990.2034301757812 0.7503693103790283 1213.4947509765625 0.4195921719074249 0.7157509 0.5070769190788269 True -13 38402 29.71401333808899 0.5434963703155518 1019.8147583007812 0.4340018630027771 1210.0556640625 0.4214647710323334 0.72842795 0.48875588178634644 True -14 41145 29.737486124038696 0.5516350269317627 1116.1661376953125 0.491150438785553 1206.7625732421875 0.4240002930164337 0.7359409 0.4643252491950989 True -15 43888 29.700321435928345 0.530289888381958 1005.2296142578125 0.5368449091911316 1203.900146484375 0.4255300462245941 0.742448 0.43898844718933105 True -16 46631 29.73672366142273 0.55462646484375 906.348388671875 0.6188724040985107 1202.166748046875 0.42800354957580566 0.7489433 0.42521077394485474 True -17 49374 29.690673351287842 0.5516595840454102 947.4539184570312 0.34800946712493896 1204.4710693359375 0.4241374731063843 0.7517422 0.4202691614627838 True -18 52117 29.68987011909485 0.5473206043243408 898.5167236328125 0.396023690700531 1201.6298828125 0.4280411899089813 0.7521848 0.4215785264968872 True -19 54860 29.76841688156128 0.551245927810669 1028.0390625 0.43652811646461487 1204.0889892578125 0.42507126927375793 0.75071585 0.4227643311023712 False diff --git a/ENCSR804RSI/cherimoya.fold_0.performance.tsv b/ENCSR804RSI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e1a088850f2c176e5b26a712935ee8117cd06653..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1201.6298828125 0.32532060146331787 0.4280412197113037 0.21293984353542328 0.7521848082542419 0.6809772253036499 0.4215785264968872 \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_1.evaluate.json b/ENCSR804RSI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 76d7e5b15b4316fe821a09c723472417c4604606..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF181SUB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_1.fit.json b/ENCSR804RSI/cherimoya.fold_1.fit.json deleted file mode 100644 index f3ec3a4f360ad66a1b34610ff61d92d5ad6879f0..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF181SUB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_1.log b/ENCSR804RSI/cherimoya.fold_1.log deleted file mode 100644 index 9ad08d4aaa66a079ddeeab6cadc86c96e1e2c603..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 35.15805768966675 4.458839178085327 957.4771728515625 1.1308730840682983 1655.5689697265625 0.25160905718803406 0.6410809 6.5668044090271 True -1 5530 30.676303148269653 0.7210936546325684 1016.6197509765625 0.6505868434906006 1449.7052001953125 0.3895352780818939 0.66850084 1.551416277885437 True -2 8295 30.729331016540527 0.7124912738800049 1172.58349609375 0.8957645297050476 1417.927490234375 0.4026515483856201 0.6887682 0.8460013270378113 True -3 11060 30.63148522377014 0.6785101890563965 1115.511962890625 0.5785807967185974 1401.880126953125 0.4093806743621826 0.70429814 0.7068175673484802 True -4 13825 30.624335527420044 0.6831455230712891 910.703369140625 0.6727692484855652 1392.1324462890625 0.4137124717235565 0.71187764 0.6467292308807373 True -5 16590 30.65255331993103 0.6948451995849609 1012.4226684570312 0.9523589611053467 1386.20361328125 0.41703030467033386 0.71629995 0.6221339702606201 True -6 19355 30.174642324447632 0.7036628723144531 985.278564453125 0.8278311491012573 1379.9571533203125 0.42017844319343567 0.71976936 0.5975859761238098 True -7 22120 30.031648635864258 0.6766157150268555 1090.767578125 0.6598179340362549 1373.367919921875 0.4252276122570038 0.7234035 0.5778297185897827 True -8 24885 30.026528358459473 0.6827309131622314 954.6989135742188 1.28151273727417 1367.2119140625 0.4274258017539978 0.7309737 0.5717530846595764 True -9 27650 29.983178853988647 1.4388844966888428 1039.387451171875 0.8857538104057312 1364.6209716796875 0.4283728003501892 0.7385053 0.5254098773002625 True -10 30415 29.983265161514282 1.2360289096832275 952.0638427734375 0.9245291948318481 1359.2408447265625 0.43089744448661804 0.7450861 0.5122295022010803 True -11 33180 29.978282690048218 1.7476942539215088 879.0255126953125 0.6194666028022766 1350.0269775390625 0.4382856786251068 0.75140685 0.48821988701820374 True -12 35945 29.986066818237305 0.678818941116333 1032.971435546875 0.6025049686431885 1345.2098388671875 0.43964532017707825 0.76016 0.47054338455200195 True -13 38710 30.072062492370605 0.6985664367675781 936.422119140625 0.5127034187316895 1339.7335205078125 0.4425596296787262 0.7680411 0.4449976682662964 True -14 41475 30.04482889175415 0.6827261447906494 1102.8026123046875 0.4087657928466797 1334.3763427734375 0.4466099739074707 0.7763529 0.43039998412132263 True -15 44240 29.999991416931152 0.6719048023223877 971.71533203125 0.45382964611053467 1331.2479248046875 0.44818341732025146 0.7850904 0.4183913469314575 True -16 47005 29.99496364593506 0.6715035438537598 905.6669921875 0.6966025829315186 1336.7406005859375 0.44448122382164 0.7905536 0.408649742603302 True -17 49770 30.08238673210144 0.7301993370056152 1150.4296875 0.3953168988227844 1333.5018310546875 0.44716954231262207 0.79120106 0.41253677010536194 True -18 52535 30.04261589050293 1.0700926780700684 1070.6636962890625 0.4102746844291687 1333.5865478515625 0.44671428203582764 0.7917152 0.41778191924095154 True -19 55300 30.002224922180176 0.696892499923706 917.6849365234375 0.27711278200149536 1333.94921875 0.4470249116420746 0.79087156 0.41913703083992004 False diff --git a/ENCSR804RSI/cherimoya.fold_1.performance.tsv b/ENCSR804RSI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 89702573ba2a6a5a0830d026faef7ba216ab66e6..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1333.5865478515625 0.307691365480423 0.44671428203582764 0.23534804582595825 0.7917152047157288 0.7491583824157715 0.41778191924095154 \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_2.evaluate.json b/ENCSR804RSI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d05564b272b281c344374751f3ef8b961ee11e96..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF181SUB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_2.fit.json b/ENCSR804RSI/cherimoya.fold_2.fit.json deleted file mode 100644 index 37a2bf39fadea6c2a377ba07231ec8a2237a6531..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF181SUB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_2.log b/ENCSR804RSI/cherimoya.fold_2.log deleted file mode 100644 index 0525a03d260cd83bcba81fa180f7a5edf6bc0c99..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2898 36.27199172973633 3.6363961696624756 946.2235107421875 0.9422338604927063 1495.4647216796875 0.2538994252681732 0.6304083 7.82273006439209 True -1 5796 32.10579514503479 0.5833473205566406 977.822265625 0.867148220539093 1306.9805908203125 0.3792169392108917 0.6593816 1.925531268119812 True -2 8694 32.043636083602905 0.5412938594818115 1230.84521484375 0.7171756029129028 1280.942138671875 0.3950295150279999 0.6818356 0.7935952544212341 True -3 11592 31.790592908859253 0.5553467273712158 787.448486328125 1.0636075735092163 1272.003173828125 0.4016950726509094 0.6787496 0.7256655097007751 False -4 14490 31.918522119522095 0.5306899547576904 976.0100708007812 1.616487979888916 1268.2509765625 0.4025253355503082 0.6814745 0.6625694632530212 False -5 17388 31.46732258796692 0.5316038131713867 1048.7652587890625 0.648370087146759 1261.9395751953125 0.4069015681743622 0.6914587 0.6180418729782104 True -6 20286 31.452284574508667 0.5239033699035645 990.951416015625 0.8326935768127441 1260.527587890625 0.40759268403053284 0.6912815 0.6229528784751892 False -7 23184 31.408770322799683 0.5322949886322021 1169.16357421875 0.5699654817581177 1251.76513671875 0.41453883051872253 0.69706285 0.5835070013999939 True -8 26082 31.40455722808838 0.522637128829956 1186.7781982421875 0.7556154727935791 1248.395263671875 0.41617655754089355 0.70033497 0.577955961227417 True -9 28980 31.384543657302856 0.538435697555542 1230.21044921875 0.4807911515235901 1244.22705078125 0.4190828502178192 0.70398813 0.5801993012428284 True -10 31878 31.443572521209717 1.508646011352539 891.2552490234375 0.6719603538513184 1237.3331298828125 0.42340004444122314 0.7118913 0.5233485102653503 True -11 34776 31.435839891433716 0.5412538051605225 962.7595825195312 0.5706596970558167 1236.97412109375 0.4229898750782013 0.71049947 0.5429603457450867 False -12 37674 31.510663270950317 0.5295486450195312 804.9841918945312 1.219665765762329 1231.095458984375 0.4276389181613922 0.7175394 0.5154016613960266 True -13 40572 31.48566222190857 0.5393929481506348 944.8419799804688 0.36950933933258057 1228.7340087890625 0.42760732769966125 0.72380596 0.49996763467788696 True -14 43470 31.457430601119995 0.5276491641998291 1064.2904052734375 0.5178860425949097 1224.0263671875 0.4315425753593445 0.73722625 0.47244924306869507 True -15 46368 31.45771026611328 0.5312330722808838 867.8192138671875 0.6297764182090759 1221.69580078125 0.4324345290660858 0.74362725 0.4544213116168976 True -16 49266 31.46999216079712 0.5291464328765869 915.6922607421875 0.5558288097381592 1217.788330078125 0.43584316968917847 0.74723285 0.44715118408203125 True -17 52164 31.4542555809021 0.5364341735839844 929.19580078125 0.3936660587787628 1217.4195556640625 0.43591445684432983 0.7493995 0.4441652297973633 True -18 55062 31.462359189987183 0.5234363079071045 1000.2777099609375 0.47277599573135376 1220.0489501953125 0.4331716001033783 0.74997634 0.44522252678871155 True -19 57960 31.375240087509155 0.5266609191894531 1002.1687622070312 0.38809627294540405 1220.7899169921875 0.43326500058174133 0.7497329 0.4503844976425171 False diff --git a/ENCSR804RSI/cherimoya.fold_2.performance.tsv b/ENCSR804RSI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index dc2c7499f4acc975d0cb62bda8bcb10f49c85e9d..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1220.0489501953125 0.3213304877281189 0.43317165970802307 0.21885472536087036 0.7499763369560242 0.6883800029754639 0.44522252678871155 \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_3.evaluate.json b/ENCSR804RSI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5c3f73e113380c632c69a2bcac050a65e4d8f588..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF181SUB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_3.fit.json b/ENCSR804RSI/cherimoya.fold_3.fit.json deleted file mode 100644 index 05470128a8d09f5262ff8341d1a1f166caa57c7e..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF181SUB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_3.log b/ENCSR804RSI/cherimoya.fold_3.log deleted file mode 100644 index 84485880c01ce45ea43c77deb1670a618398c5dd..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2799 35.79570722579956 3.5855419635772705 963.7060546875 0.968002200126648 1486.7239990234375 0.24935464560985565 0.6465309 7.556527614593506 True -1 5598 30.950254440307617 0.8192276954650879 987.5809326171875 0.701366662979126 1324.808837890625 0.3660449683666229 0.67515355 1.7204375267028809 True -2 8397 30.97754693031311 0.6128973960876465 1006.051025390625 0.9336785078048706 1304.5458984375 0.3748907744884491 0.689639 0.8068551421165466 True -3 11196 30.951226949691772 0.596566915512085 972.5638427734375 0.6500768065452576 1289.276611328125 0.38595375418663025 0.69439405 0.6873579025268555 True -4 13995 31.63903284072876 0.5722601413726807 1059.2244873046875 0.8567835688591003 1285.3221435546875 0.3885137736797333 0.6924916 0.6655358672142029 False -5 16794 31.021907329559326 0.5669651031494141 1026.13525390625 0.8736880421638489 1283.3997802734375 0.3892064094543457 0.6962601 0.6582377552986145 True -6 19593 30.98364520072937 0.5691604614257812 940.9276123046875 0.7243012189865112 1275.7864990234375 0.3940463364124298 0.69343406 0.6104931235313416 False -7 22392 30.97808289527893 0.5730671882629395 1017.386474609375 0.8528832197189331 1272.7667236328125 0.396582692861557 0.7003728 0.5810909867286682 True -8 25191 31.021620750427246 0.5707137584686279 1011.4155883789062 0.7874617576599121 1273.016357421875 0.39590680599212646 0.70445114 0.5924666523933411 True -9 27990 31.08638310432434 0.5823702812194824 1042.52099609375 0.6581133604049683 1265.7305908203125 0.4012554883956909 0.71392363 0.5335842967033386 True -10 30789 31.022767305374146 0.5729367733001709 951.3720703125 0.7221016883850098 1259.900390625 0.4055470824241638 0.7195917 0.5148476958274841 True -11 33588 31.064666509628296 0.5699937343597412 1063.180908203125 0.6137624979019165 1259.7432861328125 0.4048523008823395 0.7265783 0.5275404453277588 True -12 36387 31.045027494430542 0.5708448886871338 1015.3474731445312 0.5924355387687683 1252.8187255859375 0.41121795773506165 0.73645675 0.4841580390930176 True -13 39186 31.056089878082275 1.4709811210632324 1063.9815673828125 0.6347786784172058 1249.8685302734375 0.41269540786743164 0.7484105 0.4560517370700836 True -14 41985 31.040629148483276 0.5809826850891113 771.6303100585938 0.7002978324890137 1246.5174560546875 0.41422131657600403 0.75829744 0.4322846531867981 True -15 44784 31.051766872406006 1.1158459186553955 928.4652709960938 0.39214110374450684 1245.5140380859375 0.4147495925426483 0.766856 0.414847195148468 True -16 47583 31.06218409538269 0.5840020179748535 1024.87890625 0.37153154611587524 1244.20068359375 0.41477349400520325 0.7680673 0.411941796541214 True -17 50382 30.482622146606445 0.5822947025299072 987.6981201171875 0.41094908118247986 1244.0914306640625 0.4157555401325226 0.77098393 0.40495818853378296 True -18 53181 30.36563467979431 0.583641767501831 908.0369873046875 0.5067771077156067 1246.14013671875 0.41400423645973206 0.7697444 0.4079970121383667 False -19 55980 30.40677523612976 0.5775890350341797 822.3175048828125 0.3629668354988098 1242.55126953125 0.41781148314476013 0.7698464 0.41138771176338196 False diff --git a/ENCSR804RSI/cherimoya.fold_3.performance.tsv b/ENCSR804RSI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 88309d802fa3ae594dff054a5030a590b5d3ddd6..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1244.0914306640625 0.32553088665008545 0.4157555103302002 0.21261316537857056 0.7709839344024658 0.7080619931221008 0.40495818853378296 \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_4.evaluate.json b/ENCSR804RSI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 156cc08314f8ba7e2fe886f07d0772860fe91ac1..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF181SUB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_4.fit.json b/ENCSR804RSI/cherimoya.fold_4.fit.json deleted file mode 100644 index 39516b5aa0716f67af4cf9d8f8925e8b4da006bf..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF181SUB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR804RSI/cherimoya.fold_4.log b/ENCSR804RSI/cherimoya.fold_4.log deleted file mode 100644 index 2bcbae01b0c92f8fb5d17b73bd87ceba11f8b4f6..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 36.77338767051697 3.9279677867889404 991.3623046875 0.9019180536270142 1451.9576416015625 0.2487594187259674 0.6318377 6.551177978515625 True -1 5764 32.06544089317322 0.6161868572235107 1179.421630859375 0.9446481466293335 1299.5885009765625 0.3629731237888336 0.6445574 1.4223941564559937 True -2 8646 31.964298009872437 0.5764205455780029 999.8477783203125 0.7065142393112183 1276.653076171875 0.3745732009410858 0.66577715 0.7140530347824097 True -3 11528 31.9811589717865 0.5925748348236084 960.0182495117188 0.8847188353538513 1263.3516845703125 0.38135260343551636 0.6763657 0.5862405300140381 True -4 14410 31.96445894241333 0.5815234184265137 811.6663208007812 0.7535746693611145 1256.3841552734375 0.3852144777774811 0.68813616 0.48710113763809204 True -5 17292 31.94055986404419 0.5697081089019775 1099.85107421875 0.6622702479362488 1249.885009765625 0.39033234119415283 0.6877781 0.48185214400291443 False -6 20174 31.98894166946411 0.5785467624664307 1042.27294921875 0.7018963098526001 1242.11376953125 0.39691829681396484 0.6938669 0.4982190728187561 True -7 23056 31.97461438179016 0.9166221618652344 1166.6488037109375 0.5890797972679138 1241.68505859375 0.3975464701652527 0.693725 0.4907422363758087 False -8 25938 31.815812587738037 0.5778634548187256 857.1947021484375 0.661342978477478 1239.42236328125 0.39838919043540955 0.69970757 0.4785540997982025 True -9 28820 31.341716527938843 0.5759460926055908 1059.361328125 0.386880487203598 1233.69775390625 0.40276074409484863 0.70263493 0.48997896909713745 True -10 31702 31.388811588287354 0.5756051540374756 1012.4207763671875 0.6577247381210327 1230.6846923828125 0.40587443113327026 0.71163595 0.47594600915908813 True -11 34584 31.373125314712524 19.101515769958496 940.2245483398438 0.4935266375541687 1227.4505615234375 0.408006489276886 0.7152379 0.47005343437194824 True -12 37466 31.509357929229736 1.0182056427001953 792.322998046875 0.4195566177368164 1222.0369873046875 0.41268908977508545 0.72507125 0.45422837138175964 True -13 40348 31.371297359466553 0.5945107936859131 860.9573974609375 0.44884055852890015 1221.1007080078125 0.41265878081321716 0.7345267 0.4313073754310608 True -14 43230 31.420621395111084 0.5834362506866455 951.59912109375 0.4435923993587494 1217.0250244140625 0.414816290140152 0.73947114 0.42416760325431824 True -15 46112 31.354429960250854 0.57958984375 978.3079833984375 0.4838711619377136 1216.7530517578125 0.41510117053985596 0.7483053 0.4167172908782959 True -16 48994 31.439316987991333 0.5919606685638428 1082.1412353515625 0.41758257150650024 1213.9949951171875 0.41669854521751404 0.7521179 0.417114794254303 True -17 51876 31.487720489501953 0.5977592468261719 930.9259643554688 0.5002589225769043 1212.5859375 0.41877835988998413 0.75660527 0.4125863313674927 True -18 54758 31.501875162124634 0.5830037593841553 1004.4581298828125 0.5485515594482422 1216.365234375 0.4154454171657562 0.7563517 0.4141761362552643 False -19 57640 31.459275484085083 0.5822434425354004 1016.6605834960938 0.3463698625564575 1214.750732421875 0.41681554913520813 0.75477594 0.41979309916496277 False diff --git a/ENCSR804RSI/cherimoya.fold_4.performance.tsv b/ENCSR804RSI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index abd7273a7d2b556e865878d84e0e9ce9b754f4b9..0000000000000000000000000000000000000000 --- a/ENCSR804RSI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1212.5859375 0.3258991241455078 0.41877835988998413 0.20957933366298676 0.7566052675247192 0.6863995790481567 0.4125863313674927 \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_0.evaluate.json b/ENCSR805EGZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 27d07262219dce8d6dd944d8a8a028076303a299..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF092BOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_0.fit.json b/ENCSR805EGZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 070497cb44cc500356bd9f55bfdd1ca3943ade20..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF092BOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_0.log b/ENCSR805EGZ/cherimoya.fold_0.log deleted file mode 100644 index ffd4fdcee33b6ad0b445c89a0c33002fd5b1da05..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 35.167112588882446 4.157177448272705 467.17852783203125 0.3178776204586029 519.896728515625 0.22796732187271118 0.682584 4.242866516113281 True -1 5466 30.227864980697632 0.6066412925720215 374.7911376953125 0.39907586574554443 480.692138671875 0.29634973406791687 0.7707932 1.1659209728240967 True -2 8199 30.24938678741455 0.5871856212615967 440.0042419433594 0.35768961906433105 471.2514343261719 0.31075847148895264 0.7845661 0.5661183595657349 True -3 10932 30.23305630683899 0.5811398029327393 383.42999267578125 0.44599345326423645 467.5940856933594 0.3167749345302582 0.7942668 0.5615463256835938 True -4 13665 30.240751028060913 0.842036247253418 371.2754821777344 0.2750580608844757 465.4475402832031 0.31977859139442444 0.8024718 0.40704864263534546 True -5 16398 30.187013626098633 11.868097305297852 355.60150146484375 0.2823209762573242 464.42730712890625 0.32276085019111633 0.8038517 0.40466827154159546 True -6 19131 30.199903964996338 0.5938804149627686 367.6065979003906 0.33137643337249756 462.3040466308594 0.32614755630493164 0.8128488 0.365600049495697 True -7 21864 30.218207120895386 0.5748395919799805 402.313720703125 0.23111248016357422 462.26837158203125 0.32571354508399963 0.8152503 0.37371325492858887 True -8 24597 30.21054172515869 0.5829124450683594 430.682373046875 0.33668747544288635 460.7501220703125 0.3288431465625763 0.82005596 0.3354697525501251 True -9 27330 30.212377309799194 0.5854089260101318 422.6568603515625 0.2516356408596039 459.2546081542969 0.3322811424732208 0.82622373 0.3227011263370514 True -10 30063 30.161438703536987 0.5844762325286865 444.9517822265625 0.31112226843833923 458.42852783203125 0.33256402611732483 0.83033204 0.30651286244392395 True -11 32796 30.247899055480957 0.585902214050293 422.248779296875 0.28494003415107727 458.2711181640625 0.3328450322151184 0.8344523 0.28687235713005066 True -12 35529 30.238781690597534 0.5848183631896973 364.58746337890625 0.2179085910320282 456.6446838378906 0.33631253242492676 0.8409175 0.27034035325050354 True -13 38262 30.20868420600891 0.5869157314300537 396.6010437011719 0.28042954206466675 456.06768798828125 0.3364553451538086 0.84611 0.24442915618419647 True -14 40995 30.23024845123291 0.5924544334411621 353.5732727050781 0.2751035988330841 455.4857177734375 0.33760973811149597 0.8521978 0.230327308177948 True -15 43728 30.268094778060913 0.5892436504364014 414.7558288574219 0.21803389489650726 454.67498779296875 0.33892622590065 0.85599893 0.21899950504302979 True -16 46461 30.301146745681763 0.5917749404907227 419.4521484375 0.20392686128616333 454.78228759765625 0.33834752440452576 0.8571362 0.20943713188171387 True -17 49194 30.208397150039673 0.618065595626831 327.4963684082031 0.24069471657276154 454.5406799316406 0.3386676609516144 0.85970557 0.2050761729478836 True -18 51927 29.621169805526733 0.588144063949585 407.6961669921875 0.22193016111850739 453.7405090332031 0.3414480984210968 0.8601156 0.20417246222496033 True -19 54660 29.597545385360718 0.5889537334442139 447.62554931640625 0.1651456505060196 454.6445617675781 0.3384641706943512 0.8592176 0.20467695593833923 False diff --git a/ENCSR805EGZ/cherimoya.fold_0.performance.tsv b/ENCSR805EGZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 942a67e0b6d5e7d1fc18729f5522553d59955fe1..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -453.7405090332031 0.42814764380455017 0.3414481282234192 0.12060152739286423 0.8601155877113342 0.8123040795326233 0.20417246222496033 \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_1.evaluate.json b/ENCSR805EGZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 092d98b249ceab5b1c9375c518da9efa32d801ff..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF092BOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_1.fit.json b/ENCSR805EGZ/cherimoya.fold_1.fit.json deleted file mode 100644 index c4a12fc7362ce04319a1a4c66c966c9ed390e4d7..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF092BOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_1.log b/ENCSR805EGZ/cherimoya.fold_1.log deleted file mode 100644 index 5962921f52fa604649e09fcf9609719f03dba5d1..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2700 34.4924054145813 4.176287651062012 364.60577392578125 0.3578992486000061 617.515380859375 0.23896916210651398 0.6834477 4.244299411773682 True -1 5400 29.83720636367798 0.8482232093811035 430.643310546875 0.3143382668495178 561.5989379882812 0.31934091448783875 0.77029896 1.3728909492492676 True -2 8100 29.812458515167236 0.7302157878875732 426.383056640625 1.099678874015808 549.4410400390625 0.33701378107070923 0.78982574 0.7688450217247009 True -3 10800 29.903828144073486 2.523557424545288 425.29461669921875 0.39002442359924316 543.41259765625 0.3461369276046753 0.8058663 0.585050642490387 True -4 13500 29.84161639213562 0.759244441986084 466.65777587890625 0.4804857671260834 541.5982666015625 0.34874722361564636 0.81292325 0.44525399804115295 True -5 16200 29.778046131134033 0.7563307285308838 422.7426452636719 0.3249634802341461 539.904296875 0.3504805862903595 0.8172438 0.43733713030815125 True -6 18900 29.807905912399292 32.69013261795044 385.9106140136719 0.3226546347141266 538.6290283203125 0.35329169034957886 0.82268107 0.4134065806865692 True -7 21600 29.869790077209473 1.8110175132751465 353.6783142089844 0.27176040410995483 537.482666015625 0.35458216071128845 0.8265573 0.4156685471534729 True -8 24300 30.067472457885742 1.6200170516967773 476.8091125488281 0.32960909605026245 535.5650634765625 0.3577617406845093 0.83304787 0.3845929503440857 True -9 27000 30.003249883651733 0.7864272594451904 356.0816650390625 0.24175015091896057 535.00146484375 0.35757240653038025 0.8376918 0.3651237487792969 True -10 29700 30.016072273254395 0.7528448104858398 373.87548828125 0.2143731415271759 532.8023681640625 0.36234813928604126 0.8418025 0.3407314717769623 True -11 32400 30.0057373046875 0.7587571144104004 374.6543884277344 0.2724931836128235 531.6259155273438 0.3638013005256653 0.8477848 0.3226243853569031 True -12 35100 29.887818098068237 0.7617406845092773 462.9559020996094 0.296997606754303 530.5740966796875 0.36505505442619324 0.8511979 0.3095453679561615 True -13 37800 30.47831082344055 28.34339141845703 420.0389099121094 0.21495898067951202 527.9713134765625 0.3695261776447296 0.8582268 0.2853834331035614 True -14 40500 29.959166765213013 0.7489418983459473 464.5135803222656 0.22103634476661682 527.5318603515625 0.3695966899394989 0.8629708 0.26615551114082336 True -15 43200 29.95707106590271 0.7833354473114014 415.01251220703125 0.2082878053188324 527.29052734375 0.36951249837875366 0.86760634 0.2505342662334442 True -16 45900 29.905240535736084 0.7691013813018799 356.6759948730469 0.16473178565502167 527.1632080078125 0.3694467544555664 0.86886305 0.23918095231056213 True -17 48600 29.90739345550537 0.7469265460968018 406.1660461425781 0.1832353174686432 527.324951171875 0.3693029284477234 0.87010986 0.23248329758644104 True -18 51300 29.81215000152588 1.6392204761505127 406.08392333984375 0.08596640825271606 527.4878540039062 0.3689696490764618 0.8709459 0.23099249601364136 True -19 54000 29.522165298461914 0.8362138271331787 423.4178466796875 0.14001989364624023 527.1199951171875 0.3702974021434784 0.8706033 0.23242710530757904 False diff --git a/ENCSR805EGZ/cherimoya.fold_1.performance.tsv b/ENCSR805EGZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index efd4fc3ecf2ca23fbb50c689b6bcb009dec9785a..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -527.4878540039062 0.40336352586746216 0.3689696490764618 0.14187850058078766 0.8709458708763123 0.8439491987228394 0.23099249601364136 \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_2.evaluate.json b/ENCSR805EGZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index c1e3c57f68c388dfe7dc169c53595ade83df9dc8..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF092BOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_2.fit.json b/ENCSR805EGZ/cherimoya.fold_2.fit.json deleted file mode 100644 index f8c9c1c28cd0a0f337e25144c95c98e9b267a035..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF092BOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_2.log b/ENCSR805EGZ/cherimoya.fold_2.log deleted file mode 100644 index c55cb7654f346093cd21ea6e0250e7e96e8b85f1..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2911 36.62242150306702 4.676112651824951 395.4188537597656 0.37099429965019226 548.82861328125 0.23411180078983307 0.6769944 3.765385389328003 True -1 5822 32.19318747520447 0.8853631019592285 338.19134521484375 0.3276365101337433 498.8773498535156 0.3077974319458008 0.77109826 1.0013513565063477 True -2 8733 32.20973587036133 0.5971343517303467 509.3193664550781 0.40986403822898865 493.5024108886719 0.3168686628341675 0.78484434 0.6160628199577332 True -3 11644 32.10835385322571 0.5523931980133057 383.2098388671875 0.2580775022506714 489.2535400390625 0.323015034198761 0.7941419 0.4596358835697174 True -4 14555 32.09178900718689 1.1334178447723389 372.0551452636719 0.2798261046409607 487.67169189453125 0.32550936937332153 0.80095226 0.40222030878067017 True -5 17466 32.16309881210327 0.5505552291870117 343.69097900390625 0.4082334637641907 486.34429931640625 0.32880648970603943 0.8085411 0.39967620372772217 True -6 20377 32.1610963344574 0.5594229698181152 392.33734130859375 0.19329605996608734 484.4528503417969 0.3312472701072693 0.8139425 0.3600659668445587 True -7 23288 32.13523483276367 0.6757783889770508 350.3126220703125 0.2147349715232849 483.64031982421875 0.3329103887081146 0.8210038 0.33447209000587463 True -8 26199 32.136878490448 1.4289822578430176 465.6253356933594 0.2318364381790161 482.49835205078125 0.33513981103897095 0.8224138 0.3291065990924835 True -9 29110 32.10028123855591 0.5667576789855957 417.19476318359375 0.33495184779167175 480.1518859863281 0.33965444564819336 0.8274819 0.29940512776374817 True -10 32021 32.419278383255005 0.5439155101776123 424.997802734375 0.3349292278289795 479.1574401855469 0.3409744203090668 0.8332851 0.29479557275772095 True -11 34932 32.152592420578 0.5516583919525146 383.9204406738281 0.256198912858963 478.68072509765625 0.342049241065979 0.8389177 0.2827939987182617 True -12 37843 32.16253185272217 0.5525586605072021 437.59539794921875 0.3699592351913452 477.8031921386719 0.342488169670105 0.84250706 0.26474860310554504 True -13 40754 32.1084988117218 0.5576865673065186 387.57586669921875 0.17005372047424316 477.20794677734375 0.3427569270133972 0.84690946 0.2524840533733368 True -14 43665 32.154622316360474 0.554603099822998 395.0637512207031 0.23902660608291626 475.7309875488281 0.3452327251434326 0.84902483 0.23891976475715637 True -15 46576 32.15184807777405 0.5470051765441895 369.98529052734375 0.20511117577552795 474.9091491699219 0.34780481457710266 0.85195655 0.23073670268058777 True -16 49487 32.0901300907135 1.722269058227539 383.8531494140625 0.1612452119588852 475.4975280761719 0.346328467130661 0.8535265 0.22521722316741943 True -17 52398 32.15863037109375 0.5575151443481445 379.8253479003906 0.1627615988254547 475.0106506347656 0.34720098972320557 0.8539021 0.22297942638397217 True -18 55309 32.11378216743469 0.5607123374938965 409.0181579589844 0.2029820680618286 475.38983154296875 0.34593886137008667 0.8547502 0.22391054034233093 True -19 58220 31.932040691375732 0.5358717441558838 379.25531005859375 0.1367933452129364 475.2852478027344 0.346998929977417 0.851775 0.2255193591117859 False diff --git a/ENCSR805EGZ/cherimoya.fold_2.performance.tsv b/ENCSR805EGZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f2e7971b87afbe82bb57d6443fc35551b0925001..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.38983154296875 0.42205408215522766 0.34593886137008667 0.1271180659532547 0.8547502160072327 0.8173348307609558 0.22391054034233093 \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_3.evaluate.json b/ENCSR805EGZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 59f3eb47487c5ef99913443bfd3e9c7cc005fa6a..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF092BOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_3.fit.json b/ENCSR805EGZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 72dc5cf560b5e354bc63a9295a0520f6298090b9..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF092BOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_3.log b/ENCSR805EGZ/cherimoya.fold_3.log deleted file mode 100644 index 2834db76535a752dc1007271cad6b79bcd39b52f..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 35.147125482559204 3.9741461277008057 445.62060546875 0.27988186478614807 526.3429565429688 0.23567825555801392 0.66393 4.588197231292725 True -1 5498 30.415027618408203 0.5925314426422119 396.13787841796875 0.28352493047714233 486.1618957519531 0.3010956346988678 0.7511118 1.2315796613693237 True -2 8247 30.414541721343994 0.5787732601165771 410.16265869140625 0.2673935294151306 476.81121826171875 0.313819944858551 0.77966017 0.5630965232849121 True -3 10996 30.348692655563354 0.580723762512207 430.60296630859375 0.25909295678138733 473.6033935546875 0.32201066613197327 0.78864974 0.5234813690185547 True -4 13745 30.34494400024414 0.5852921009063721 450.657958984375 0.43446195125579834 471.9241943359375 0.32456284761428833 0.7925297 0.4502314627170563 True -5 16494 30.459503412246704 1.5109789371490479 360.885498046875 0.33421462774276733 469.9311828613281 0.32730627059936523 0.7976871 0.4567667543888092 True -6 19243 30.327502012252808 0.5767455101013184 351.74273681640625 0.3269566595554352 468.9001770019531 0.3297230005264282 0.803074 0.43492990732192993 True -7 21992 30.886475086212158 0.5851054191589355 377.1383056640625 0.35515275597572327 467.38983154296875 0.33256569504737854 0.8046771 0.4358048439025879 True -8 24741 30.437194108963013 27.903156757354736 420.076416015625 0.22825519740581512 466.54656982421875 0.33329248428344727 0.80818754 0.41351374983787537 True -9 27490 30.374531745910645 0.9857113361358643 391.6772766113281 0.3438674509525299 465.27032470703125 0.3355556130409241 0.8121225 0.3772459328174591 True -10 30239 30.366788148880005 0.9794533252716064 423.5076904296875 0.27465957403182983 464.52166748046875 0.3363368511199951 0.8196975 0.3318530321121216 True -11 32988 30.348764896392822 0.5815219879150391 416.6541442871094 0.2606029212474823 463.6990966796875 0.33766835927963257 0.82582486 0.30944696068763733 True -12 35737 30.340646982192993 1.5911095142364502 432.0079345703125 0.21203860640525818 462.0074462890625 0.34006792306900024 0.8301717 0.29196473956108093 True -13 38486 30.335363388061523 0.5679066181182861 415.0384521484375 0.2148161679506302 460.59527587890625 0.34250321984291077 0.83743787 0.27485719323158264 True -14 41235 30.387197017669678 0.5919203758239746 409.1696472167969 0.16788603365421295 460.1903076171875 0.3431064486503601 0.8401119 0.2620735466480255 True -15 43984 30.400495290756226 0.5908944606781006 450.81964111328125 0.21081188321113586 459.1424865722656 0.3448672294616699 0.84569156 0.24825641512870789 True -16 46733 30.379575967788696 0.5887703895568848 389.3233642578125 0.3313993811607361 458.606201171875 0.34605297446250916 0.84696215 0.24117009341716766 True -17 49482 29.856629133224487 0.5816595554351807 386.6611328125 0.21721327304840088 458.7132873535156 0.3451404273509979 0.8481525 0.2393656224012375 True -18 52231 29.7680561542511 1.332310438156128 420.2647705078125 0.13955286145210266 459.62408447265625 0.3431489169597626 0.8468449 0.23967014253139496 False -19 54980 29.795111179351807 0.586920976638794 402.6289978027344 0.13943855464458466 459.46417236328125 0.34400156140327454 0.8483552 0.23939630389213562 True diff --git a/ENCSR805EGZ/cherimoya.fold_3.performance.tsv b/ENCSR805EGZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5a877b5ce86dbe7913a8664631d70585f3d69dff..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.46417236328125 0.4250379800796509 0.34400156140327454 0.12642456591129303 0.8483551740646362 0.7995353937149048 0.23939630389213562 \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_4.evaluate.json b/ENCSR805EGZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 84c5cd896c632589bba7319c78947c8ebd390134..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF092BOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_4.fit.json b/ENCSR805EGZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 8d8946145cfd1d94b567c29325a9620c164c7316..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF092BOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR805EGZ/cherimoya.fold_4.log b/ENCSR805EGZ/cherimoya.fold_4.log deleted file mode 100644 index adb0c05d48acf856fa893967ab87d0430a9a30e3..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.74156665802002 3.8897452354431152 491.0423583984375 0.4923178255558014 486.8381042480469 0.2238442748785019 0.65981513 3.3659331798553467 True -1 5596 30.907330751419067 1.8019051551818848 406.0146484375 0.4826398193836212 451.23248291015625 0.28769227862358093 0.75559103 0.9830296635627747 True -2 8394 30.838005542755127 0.677819013595581 430.7967224121094 0.5245422720909119 445.1058044433594 0.2968417704105377 0.77620065 0.5107437372207642 True -3 11192 30.842694997787476 0.6210570335388184 460.15447998046875 0.3012627065181732 442.7497863769531 0.30163735151290894 0.77826506 0.4490951895713806 True -4 13990 30.919437408447266 0.650670051574707 413.4803466796875 0.32702577114105225 439.1724548339844 0.30939972400665283 0.79193914 0.386431485414505 True -5 16788 30.84893798828125 0.6196255683898926 448.63262939453125 0.3810192346572876 437.9591369628906 0.31238681077957153 0.7943258 0.38828712701797485 True -6 19586 30.97264790534973 0.6404604911804199 417.5078125 0.28914251923561096 437.1984558105469 0.3135603964328766 0.7996275 0.40067628026008606 True -7 22384 30.909051656723022 0.6272151470184326 360.9684143066406 0.31438538432121277 436.4510803222656 0.31398484110832214 0.8090732 0.33574554324150085 True -8 25182 30.92080593109131 0.6285977363586426 381.17523193359375 0.1726122796535492 435.6416931152344 0.3157770037651062 0.8136079 0.3199811577796936 True -9 27980 30.9364972114563 0.6389858722686768 383.5957946777344 0.3114915192127228 434.6536560058594 0.3176460266113281 0.81660056 0.29005175828933716 True -10 30778 30.93813920021057 0.625828742980957 394.3138427734375 0.3040308952331543 433.6914367675781 0.3196640908718109 0.8245737 0.26567718386650085 True -11 33576 30.941105842590332 0.5996384620666504 373.4201965332031 0.3021904230117798 433.17822265625 0.32018929719924927 0.83040446 0.25779083371162415 True -12 36374 30.91583490371704 0.6307330131530762 481.60809326171875 0.23381701111793518 432.0150146484375 0.32293999195098877 0.83563644 0.24527715146541595 True -13 39172 30.914093017578125 0.6331212520599365 407.22314453125 0.18073947727680206 431.1473083496094 0.32472363114356995 0.8393802 0.23309950530529022 True -14 41970 30.860631465911865 0.6259160041809082 405.9637145996094 0.23333598673343658 430.8533935546875 0.32429051399230957 0.8442597 0.22075727581977844 True -15 44768 30.6693172454834 0.6188974380493164 378.71942138671875 0.1299283355474472 431.0036926269531 0.3235526382923126 0.84876543 0.20872735977172852 True -16 47566 30.29354953765869 0.6144587993621826 381.6977233886719 0.1672031730413437 431.25103759765625 0.3228691816329956 0.8516759 0.20373530685901642 True -17 50364 30.292808294296265 0.6071994304656982 358.47418212890625 0.19738826155662537 430.53619384765625 0.3253316283226013 0.85407364 0.2010156512260437 True -18 53162 30.33888530731201 0.6007893085479736 392.26708984375 0.10426754504442215 430.95849609375 0.3234711289405823 0.8532614 0.20027928054332733 False -19 55960 30.284636974334717 0.6299600601196289 426.3247375488281 0.206473708152771 430.7874755859375 0.32459837198257446 0.8548007 0.20105695724487305 True diff --git a/ENCSR805EGZ/cherimoya.fold_4.performance.tsv b/ENCSR805EGZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d8e8e2042c7dc06be1811fcd434cd453091b6634..0000000000000000000000000000000000000000 --- a/ENCSR805EGZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -430.7874755859375 0.4384683072566986 0.32459837198257446 0.11468251794576645 0.8548007011413574 0.8034926652908325 0.20105695724487305 \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_0.evaluate.json b/ENCSR809CEA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e2528ac117d19dd8b08332ae4aef6c3ac444bed4..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XYX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_0.fit.json b/ENCSR809CEA/cherimoya.fold_0.fit.json deleted file mode 100644 index 3edf1cf908e3829da36cc43b277e7206b63be7af..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF845XYX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_0.log b/ENCSR809CEA/cherimoya.fold_0.log deleted file mode 100644 index 0905e4f80e1e1367667ef7627a4660bb68322eef..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 35.53656244277954 3.9346086978912354 1117.321533203125 0.5555551648139954 1595.2982177734375 0.3195208013057709 0.4329387 8.1471529006958 True -1 5606 30.931962728500366 0.6497697830200195 1203.7076416015625 0.42985719442367554 1403.482421875 0.4532659649848938 0.5163261 3.301868200302124 True -2 8409 30.827848434448242 0.5795040130615234 924.5995483398438 0.3176257610321045 1362.3511962890625 0.46403566002845764 0.51558805 1.915839433670044 False -3 11212 30.805238246917725 0.5613682270050049 923.60205078125 0.4838021993637085 1321.3785400390625 0.47993168234825134 0.54621583 1.4419772624969482 True -4 14015 31.38536834716797 0.5747926235198975 1204.88427734375 0.40944427251815796 1299.7958984375 0.49215516448020935 0.553751 1.3692272901535034 True -5 16818 30.315032720565796 0.5621771812438965 1045.70361328125 0.4404361844062805 1299.71533203125 0.4898696839809418 0.5617528 1.1154273748397827 True -6 19621 30.28431463241577 0.5560750961303711 1259.6539306640625 0.5100051760673523 1284.4788818359375 0.499961256980896 0.57419705 0.987621009349823 True -7 22424 30.32007145881653 2.2578158378601074 1331.682373046875 0.6291353702545166 1281.677001953125 0.4975534677505493 0.5840073 0.8447940349578857 True -8 25227 30.27336072921753 0.5774188041687012 1057.260009765625 0.5650771856307983 1272.1488037109375 0.5036811232566833 0.5980575 0.7643166184425354 True -9 28030 30.268101692199707 0.5690107345581055 1082.062255859375 0.6370259523391724 1264.03759765625 0.5089040398597717 0.6141312 0.7324765920639038 True -10 30833 30.254318237304688 0.5525541305541992 1061.157470703125 0.583225667476654 1258.7989501953125 0.5119468569755554 0.6293083 0.6906346678733826 True -11 33636 30.194626569747925 0.548149824142456 1065.8284912109375 0.4200839698314667 1250.46484375 0.5161933302879333 0.6410294 0.6489289402961731 True -12 36439 30.247936964035034 0.5631864070892334 969.48486328125 0.3767538070678711 1240.32421875 0.5218334197998047 0.6548515 0.5918711423873901 True -13 39242 30.28154754638672 0.5655462741851807 1059.882568359375 0.47355735301971436 1235.581787109375 0.5219399333000183 0.6719074 0.5216175317764282 True -14 42045 30.223105907440186 0.5596675872802734 968.7510375976562 0.5134652256965637 1228.7784423828125 0.5258154273033142 0.68368757 0.47998276352882385 True -15 44848 30.197864055633545 0.5637354850769043 1044.492919921875 0.362277626991272 1221.395263671875 0.5299783945083618 0.6953207 0.42377081513404846 True -16 47651 30.24962878227234 0.55362868309021 985.42138671875 0.2572239637374878 1217.989013671875 0.5306819677352905 0.7033526 0.38723915815353394 True -17 50454 30.26158905029297 0.565565824508667 950.969970703125 0.25358766317367554 1216.24267578125 0.5311678051948547 0.7087268 0.3690294027328491 True -18 53257 30.277796030044556 0.5672438144683838 1124.55078125 0.41145971417427063 1220.585693359375 0.5265122056007385 0.7072696 0.3674379587173462 False -19 56060 30.303154706954956 0.5630545616149902 1175.319091796875 0.27969515323638916 1218.42236328125 0.5292694568634033 0.7067824 0.3691267967224121 False diff --git a/ENCSR809CEA/cherimoya.fold_0.performance.tsv b/ENCSR809CEA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ec29aac7bf59e9634adb104549152013dff9e9a0..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1216.24267578125 0.2548947334289551 0.5311678051948547 0.2936601936817169 0.7087268233299255 0.6612582802772522 0.3690294027328491 \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_1.evaluate.json b/ENCSR809CEA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 410ca054f91c65c336f80ff051674060b644c24e..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XYX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_1.fit.json b/ENCSR809CEA/cherimoya.fold_1.fit.json deleted file mode 100644 index 86f96ca8609bf174eee2f3d31884bca9952012ad..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF845XYX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_1.log b/ENCSR809CEA/cherimoya.fold_1.log deleted file mode 100644 index da9a874cb8a0c56c17568cb3a3d2df479282f6ef..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2796 35.91426086425781 4.828243970870972 1315.1787109375 0.939645528793335 1866.97802734375 0.3203634023666382 0.47935674 8.023531913757324 True -1 5592 30.75478959083557 0.7153058052062988 1102.4169921875 0.6146551966667175 1600.5423583984375 0.45777302980422974 0.5733241 3.111065626144409 True -2 8388 30.803273916244507 0.700209379196167 1156.9127197265625 0.6355794072151184 1555.69482421875 0.47189784049987793 0.5799201 1.8049312829971313 True -3 11184 30.730387687683105 0.6911604404449463 1094.41796875 0.5833710432052612 1524.461669921875 0.4850773215293884 0.58346784 1.8070029020309448 True -4 13980 30.68450355529785 0.6849396228790283 987.163818359375 0.42161548137664795 1497.1075439453125 0.49321210384368896 0.6073558 1.5213226079940796 True -5 16776 30.474491596221924 1.5177490711212158 1001.8214721679688 0.43039992451667786 1477.4765625 0.5014652609825134 0.6158968 1.1889393329620361 True -6 19572 30.157150268554688 0.6905660629272461 920.7188720703125 0.348732054233551 1468.757080078125 0.5018885135650635 0.62411743 1.0787272453308105 True -7 22368 30.107945442199707 0.6704113483428955 1197.1163330078125 0.7108744382858276 1455.015380859375 0.5085455775260925 0.6338667 0.8920453786849976 True -8 25164 30.122488260269165 0.6805338859558105 1177.443115234375 0.41503363847732544 1450.3082275390625 0.5094707012176514 0.6457677 0.951056718826294 True -9 27960 30.109383583068848 0.6642951965332031 999.517822265625 0.3864944875240326 1437.7906494140625 0.5142266154289246 0.6556486 0.8723981380462646 True -10 30756 31.10571026802063 6.3784074783325195 1065.876708984375 0.3624727129936218 1429.2978515625 0.5184248089790344 0.6700699 0.7844729423522949 True -11 33552 30.203930139541626 0.6820073127746582 955.8247680664062 0.30785343050956726 1418.1444091796875 0.5217366814613342 0.6844594 0.7158028483390808 True -12 36348 30.144796133041382 0.6941344738006592 925.117431640625 0.30215346813201904 1402.9002685546875 0.5273736715316772 0.6997687 0.6067195534706116 True -13 39144 30.214160919189453 0.6790871620178223 1037.7835693359375 0.37761059403419495 1394.791748046875 0.5280932188034058 0.71567506 0.5454831123352051 True -14 41940 30.14897847175598 0.6695237159729004 1029.397705078125 0.3381391763687134 1384.2923583984375 0.5337550640106201 0.7256257 0.49800899624824524 True -15 44736 30.123096466064453 0.6948540210723877 1152.25048828125 0.3137598931789398 1378.599365234375 0.5352778434753418 0.73335236 0.45920345187187195 True -16 47532 30.239409923553467 0.671475887298584 1117.9951171875 0.3075518012046814 1379.9193115234375 0.5329818725585938 0.74020797 0.426514208316803 True -17 50328 30.199131727218628 0.6764278411865234 1023.878173828125 0.31233471632003784 1373.0606689453125 0.5375535488128662 0.7423684 0.4069226086139679 True -18 53124 30.12151265144348 0.6764051914215088 977.033935546875 0.32755035161972046 1373.6112060546875 0.5364306569099426 0.7417977 0.4007691442966461 False -19 55920 30.139621019363403 0.6803669929504395 985.3344116210938 0.31331533193588257 1377.869140625 0.5328978896141052 0.7426458 0.39937540888786316 True diff --git a/ENCSR809CEA/cherimoya.fold_1.performance.tsv b/ENCSR809CEA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c095a43cd285700cef477b2b24b1f650ffa45e20..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1377.869140625 0.2446446567773819 0.53289794921875 0.3122357428073883 0.742645800113678 0.6985054016113281 0.39937540888786316 \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_2.evaluate.json b/ENCSR809CEA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 913d5604dbc4bf6b2b5831473849ad0ee636cc84..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XYX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_2.fit.json b/ENCSR809CEA/cherimoya.fold_2.fit.json deleted file mode 100644 index f5b94328bd379eb5b9b26c28e13852b398f4f003..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF845XYX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_2.log b/ENCSR809CEA/cherimoya.fold_2.log deleted file mode 100644 index cbb3f0644d1e2c955f9207b0d6f2c64eb2a58f42..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 35.21631741523743 4.501756906509399 1229.9595947265625 0.6654441356658936 1807.540283203125 0.3205944001674652 0.38584995 7.349050998687744 True -1 5584 30.654956817626953 0.7442190647125244 1062.094482421875 0.6051927804946899 1547.2996826171875 0.4402323067188263 0.5152046 2.8422765731811523 True -2 8376 30.71852469444275 0.7536354064941406 1002.9402465820312 0.694640576839447 1504.69580078125 0.4541342258453369 0.51583827 1.7813485860824585 True -3 11168 30.605870962142944 0.7647221088409424 1040.043701171875 0.4991675615310669 1478.24951171875 0.46058446168899536 0.53322184 1.9232592582702637 True -4 13960 30.138503789901733 0.7362043857574463 1087.729736328125 1.0218342542648315 1457.0123291015625 0.4661042094230652 0.55726826 1.3513414859771729 True -5 16752 30.071264266967773 1.427945852279663 1262.288818359375 0.5911376476287842 1447.0518798828125 0.4689209759235382 0.57515705 1.3270925283432007 True -6 19544 30.127338409423828 0.7307651042938232 987.48388671875 0.33814018964767456 1438.786376953125 0.47095853090286255 0.5827029 1.364125370979309 True -7 22336 30.1314799785614 0.719707727432251 1262.5123291015625 0.7396478652954102 1428.2440185546875 0.4756641089916229 0.59226435 1.318806767463684 True -8 25128 30.15178084373474 0.7169647216796875 953.81982421875 0.4682389795780182 1421.2520751953125 0.47825008630752563 0.6050802 1.2122020721435547 True -9 27920 30.090115785598755 0.7578661441802979 1145.6949462890625 0.49724018573760986 1412.235595703125 0.48422399163246155 0.6112243 1.197249174118042 True -10 30712 30.086911916732788 0.7898597717285156 961.560546875 0.45369914174079895 1403.440673828125 0.4875151813030243 0.62033546 1.120186448097229 True -11 33504 30.06002378463745 0.7568438053131104 1106.225830078125 0.4551163911819458 1392.2513427734375 0.49299436807632446 0.6313013 1.01577889919281 True -12 36296 30.070807933807373 1.718033790588379 1206.199951171875 0.5841052532196045 1386.295654296875 0.4948796331882477 0.6435747 0.956481397151947 True -13 39088 30.137110471725464 0.7445175647735596 1038.4134521484375 0.4194820523262024 1371.9014892578125 0.5021328330039978 0.6524703 0.8877226114273071 True -14 41880 30.256129026412964 0.7330811023712158 1000.67724609375 0.3995550572872162 1371.0059814453125 0.49823635816574097 0.66295654 0.7766700983047485 True -15 44672 30.162808656692505 0.7480528354644775 1204.21923828125 0.49219033122062683 1362.158935546875 0.503772497177124 0.67151284 0.7152153253555298 True -16 47464 30.106481313705444 0.746171236038208 1098.736572265625 0.34323763847351074 1364.0546875 0.4989157021045685 0.6783239 0.6539983749389648 True -17 50256 30.152090787887573 0.715073823928833 991.1025390625 0.2666197419166565 1359.6451416015625 0.5019099712371826 0.68224114 0.6076300740242004 True -18 53048 30.12789034843445 0.7815873622894287 1052.5821533203125 0.19607646763324738 1359.8623046875 0.5019501447677612 0.68408316 0.5794520974159241 True -19 55840 30.152657747268677 0.7538776397705078 1189.7344970703125 0.31320592761039734 1362.5953369140625 0.4997768998146057 0.6844994 0.573988676071167 True diff --git a/ENCSR809CEA/cherimoya.fold_2.performance.tsv b/ENCSR809CEA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b2bed03bcac700e97930a42b04d84fd89afddbf5..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1362.5953369140625 0.25037044286727905 0.4997768998146057 0.29690971970558167 0.6844993829727173 0.6200080513954163 0.573988676071167 \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_3.evaluate.json b/ENCSR809CEA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fcb226aafedb74c93cbb53c98055105678433ed9..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XYX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_3.fit.json b/ENCSR809CEA/cherimoya.fold_3.fit.json deleted file mode 100644 index 5673a076e9e190eacdb432c3f4e0162afec8e79d..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF845XYX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_3.log b/ENCSR809CEA/cherimoya.fold_3.log deleted file mode 100644 index e26fb41ad7ebb76140a8ce3f92439733b896525a..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2833 35.63709020614624 4.03223443031311 1179.8717041015625 0.7791301012039185 1621.51318359375 0.32603564858436584 0.4641494 7.118100643157959 True -1 5666 31.212890148162842 0.6088604927062988 1134.194091796875 0.6930935382843018 1397.6807861328125 0.4544609487056732 0.54251695 3.3372371196746826 True -2 8499 30.973439931869507 0.8410143852233887 1029.4320068359375 0.5857009887695312 1382.1134033203125 0.46294090151786804 0.52843857 1.8152046203613281 False -3 11332 30.526775360107422 1.0328147411346436 1055.3272705078125 0.4199097156524658 1338.25146484375 0.481268972158432 0.5669148 1.2296288013458252 True -4 14165 30.568032026290894 0.5347111225128174 1161.840087890625 0.5854933857917786 1316.2952880859375 0.49073997139930725 0.5897119 0.9982121586799622 True -5 16998 30.504990816116333 0.524519681930542 1016.8130493164062 0.5386110544204712 1310.841796875 0.49085479974746704 0.59451085 1.0385786294937134 True -6 19831 30.49975061416626 0.5296320915222168 1068.862060546875 0.5781779289245605 1302.599853515625 0.4981822669506073 0.5898507 1.12282133102417 False -7 22664 30.50783109664917 1.4755735397338867 1099.5943603515625 0.38900521397590637 1293.205322265625 0.50299072265625 0.5991166 0.9487723112106323 True -8 25497 30.527545928955078 0.5288033485412598 1113.420166015625 0.4813859462738037 1282.60595703125 0.5084033608436584 0.6060993 0.8285818696022034 True -9 28330 30.54442572593689 0.5159440040588379 988.61279296875 0.4248700737953186 1285.42333984375 0.506097674369812 0.60323817 0.8375747203826904 False -10 31163 30.593708038330078 0.5219807624816895 913.5957641601562 0.3847277760505676 1274.5423583984375 0.5128039717674255 0.61176884 0.8119412064552307 True -11 33996 30.54436182975769 0.5195438861846924 961.896484375 0.34443414211273193 1267.50390625 0.515536904335022 0.62978375 0.7110325694084167 True -12 36829 30.57869553565979 0.5314841270446777 984.3494873046875 0.4550076127052307 1256.4093017578125 0.522665798664093 0.6439025 0.6365122199058533 True -13 39662 30.554996252059937 0.5098044872283936 923.2921142578125 0.44274210929870605 1253.4486083984375 0.5214525461196899 0.65960675 0.5765441656112671 True -14 42495 30.543556690216064 0.531825065612793 1106.9862060546875 0.4346541166305542 1244.558349609375 0.5261259078979492 0.6724888 0.5286787748336792 True -15 45328 30.597936868667603 0.5333707332611084 1177.5887451171875 0.31090182065963745 1236.571044921875 0.5313413739204407 0.68482506 0.4641053378582001 True -16 48161 30.551358938217163 0.5223941802978516 1215.46484375 0.5327534079551697 1238.64306640625 0.5272179841995239 0.69325364 0.4300982356071472 True -17 50994 30.62815809249878 0.5332033634185791 972.39404296875 0.3856286406517029 1234.1253662109375 0.531217098236084 0.6968873 0.41439929604530334 True -18 53827 30.53894543647766 0.5151679515838623 1189.10400390625 0.27305206656455994 1236.120849609375 0.5287450551986694 0.6971176 0.41261744499206543 True -19 56660 30.59833788871765 1.1088922023773193 1013.1041259765625 0.23565825819969177 1233.5343017578125 0.5310890078544617 0.69518834 0.4144630432128906 False diff --git a/ENCSR809CEA/cherimoya.fold_3.performance.tsv b/ENCSR809CEA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 13755a26ff69763ecf4881c1277fe59ba5099fa5..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1236.120849609375 0.2554056644439697 0.5287451148033142 0.2942316234111786 0.6971176266670227 0.6439142227172852 0.41261744499206543 \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_4.evaluate.json b/ENCSR809CEA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0e879e4298d9c1ae29479f167b91c45dfb65d2e4..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF845XYX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_4.fit.json b/ENCSR809CEA/cherimoya.fold_4.fit.json deleted file mode 100644 index 3c06f747da448a44272ea2a0966087876200bccb..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF845XYX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809CEA/cherimoya.fold_4.log b/ENCSR809CEA/cherimoya.fold_4.log deleted file mode 100644 index e69f8b19303b7481bf10053ead4472f9b82898d3..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2790 35.496999740600586 7.481565237045288 1264.572998046875 0.7487777471542358 1557.9375 0.3217940330505371 0.42547858 7.716171741485596 True -1 5580 30.73679232597351 0.611004114151001 1270.056396484375 0.4650530517101288 1317.9644775390625 0.46284177899360657 0.5279378 2.7515056133270264 True -2 8370 30.62619376182556 0.521582841873169 1053.77294921875 0.5018874406814575 1296.66357421875 0.4777573347091675 0.52889144 1.6985670328140259 True -3 11160 30.22465181350708 0.5316987037658691 924.10791015625 0.5827014446258545 1270.1258544921875 0.48617497086524963 0.5359056 1.317368984222412 True -4 13950 30.03191876411438 0.5156328678131104 1118.9337158203125 0.5086739659309387 1262.6435546875 0.48964381217956543 0.5448446 1.0374263525009155 True -5 16740 30.056171655654907 0.5180206298828125 953.718017578125 0.4500522315502167 1249.5399169921875 0.4971555471420288 0.5611318 0.9495282173156738 True -6 19530 30.04075264930725 0.5255186557769775 1174.859130859375 0.546953558921814 1241.7803955078125 0.500313401222229 0.5737061 0.9742749929428101 True -7 22320 30.040906190872192 0.5012083053588867 1050.660400390625 0.4649451971054077 1230.4405517578125 0.5052699446678162 0.5869682 0.8048458695411682 True -8 25110 30.044943809509277 0.5266308784484863 1226.07958984375 0.5792069435119629 1222.92138671875 0.5100435018539429 0.5974093 0.6951408982276917 True -9 27900 30.365028381347656 1.404120683670044 1102.8125 0.5175950527191162 1218.930908203125 0.5113047957420349 0.6076431 0.6379213929176331 True -10 30690 30.072121381759644 0.5310475826263428 1256.4703369140625 0.45340877771377563 1211.5111083984375 0.515239953994751 0.6222409 0.6063418388366699 True -11 33480 30.148537635803223 0.9857585430145264 994.219970703125 0.27181437611579895 1200.922607421875 0.522103488445282 0.6375407 0.5702864527702332 True -12 36270 30.123703002929688 0.5218331813812256 975.732177734375 0.4138597249984741 1192.0679931640625 0.5268551111221313 0.6531357 0.5023208856582642 True -13 39060 30.171144008636475 0.5233991146087646 946.2391967773438 0.41058313846588135 1190.2708740234375 0.5266369581222534 0.66709197 0.4603719115257263 True -14 41850 30.22037363052368 0.5296087265014648 1098.46826171875 0.3437575697898865 1180.1412353515625 0.5328763127326965 0.67952263 0.428341805934906 True -15 44640 30.153562784194946 0.5316483974456787 923.40283203125 0.389869749546051 1179.35546875 0.5315804481506348 0.68819237 0.39839011430740356 True -16 47430 30.253417491912842 0.525017261505127 1016.9776611328125 0.33289021253585815 1176.9705810546875 0.5327655673027039 0.696685 0.3774242699146271 True -17 50220 30.24917507171631 8.920135974884033 1035.37744140625 0.42569631338119507 1175.303466796875 0.5344983339309692 0.6980019 0.3710133135318756 True -18 53010 30.174050092697144 0.5146253108978271 1023.7066040039062 0.26183897256851196 1177.8486328125 0.5312067270278931 0.6977836 0.37123245000839233 False -19 55800 30.161176204681396 0.5328009128570557 1070.5787353515625 0.3133998513221741 1178.467529296875 0.53084796667099 0.69647694 0.3736995756626129 False diff --git a/ENCSR809CEA/cherimoya.fold_4.performance.tsv b/ENCSR809CEA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 006324cd6ee46acb0484652ade7f73acf3a17275..0000000000000000000000000000000000000000 --- a/ENCSR809CEA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1175.303466796875 0.2561628222465515 0.5344983339309692 0.2890412211418152 0.6980019211769104 0.6487312912940979 0.3710133135318756 \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_0.evaluate.json b/ENCSR809LCE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b434ec5745977816a4fa35c7e34973e39269a13f..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692ZTH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_0.fit.json b/ENCSR809LCE/cherimoya.fold_0.fit.json deleted file mode 100644 index e8c1052b17b2bd025dc1b34ec7e14d99af090987..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF692ZTH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_0.log b/ENCSR809LCE/cherimoya.fold_0.log deleted file mode 100644 index ce6ef7d41e6835bf555e57525601ab2f60a84341..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2723 34.68049883842468 3.0358150005340576 702.265869140625 1.1759767532348633 1086.20166015625 0.22233766317367554 0.43004075 10.114686965942383 True -1 5446 30.075317859649658 0.5200216770172119 661.1500854492188 0.9452031254768372 933.3131713867188 0.3583686947822571 0.46722773 6.2160725593566895 True -2 8169 30.768304586410522 0.9994046688079834 779.5179443359375 1.4135398864746094 913.2724609375 0.3724859952926636 0.47436807 3.125936985015869 True -3 10892 30.069841861724854 0.8737332820892334 757.3919677734375 1.1125519275665283 903.1876220703125 0.3800569772720337 0.49617466 2.388152837753296 True -4 13615 29.958443641662598 2.5250558853149414 768.319580078125 0.7142527103424072 897.42236328125 0.3849564492702484 0.5170654 1.890762209892273 True -5 16338 30.671473026275635 0.5227854251861572 761.371826171875 1.218215823173523 895.3411865234375 0.3855760991573334 0.5313509 1.4977704286575317 True -6 19061 30.076984882354736 0.5039491653442383 765.26025390625 0.9196712970733643 892.2493286132812 0.38823577761650085 0.541357 1.4196492433547974 True -7 21784 30.199040412902832 0.5092487335205078 706.0877685546875 1.1355664730072021 886.9591674804688 0.3922828733921051 0.5517573 1.218968152999878 True -8 24507 30.272897243499756 0.9963212013244629 728.5165405273438 0.856682300567627 883.8292846679688 0.39498960971832275 0.55942076 1.0185712575912476 True -9 27230 30.24072575569153 1.3731718063354492 878.924072265625 0.7591474056243896 879.7777099609375 0.39843088388442993 0.57565814 0.9077748656272888 True -10 29953 29.579147338867188 1.530958652496338 743.2957153320312 0.6496517658233643 877.9002685546875 0.39896708726882935 0.5856083 0.835978090763092 True -11 32676 29.50107717514038 0.5035994052886963 704.156982421875 0.640965461730957 874.1453857421875 0.403020977973938 0.5961719 0.7869200706481934 True -12 35399 29.483892679214478 0.5014681816101074 713.9165649414062 0.8274437785148621 869.3492431640625 0.4072628617286682 0.607141 0.691455602645874 True -13 38122 29.71816635131836 0.4973421096801758 878.8363647460938 0.8653855919837952 867.4866333007812 0.40760165452957153 0.6235934 0.6392523646354675 True -14 40845 29.39831233024597 0.5022425651550293 615.5975341796875 0.4569932520389557 865.8922119140625 0.40843111276626587 0.6388025 0.6078155636787415 True -15 43568 29.448464393615723 18.211072206497192 569.8310546875 0.6354317665100098 862.9639892578125 0.41077762842178345 0.6504564 0.5674464106559753 True -16 46291 29.77254867553711 1.267632246017456 753.67578125 0.8460676670074463 861.7274169921875 0.41117116808891296 0.6604677 0.5321728587150574 True -17 49014 29.33686113357544 0.5022377967834473 502.7149658203125 0.531182587146759 861.1390991210938 0.4116895794868469 0.66441506 0.5142818689346313 True -18 51737 29.343058347702026 1.470334768295288 714.0899658203125 0.3599458634853363 861.3043212890625 0.41114580631256104 0.66776276 0.5019330382347107 True -19 54460 29.43423891067505 0.49546360969543457 639.9061279296875 0.3604012727737427 861.6185913085938 0.41102302074432373 0.6669513 0.5028277039527893 False diff --git a/ENCSR809LCE/cherimoya.fold_0.performance.tsv b/ENCSR809LCE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3a2af167dbad4bd17c274b0f0b94254c5d882dac..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -861.3043212890625 0.3918234705924988 0.41114580631256104 0.146031454205513 0.6677627563476562 0.6425925493240356 0.5019330382347107 \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_1.evaluate.json b/ENCSR809LCE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2f776fca3b9b20ed09c04a9501eca20ed82616fb..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692ZTH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_1.fit.json b/ENCSR809LCE/cherimoya.fold_1.fit.json deleted file mode 100644 index 9768b2aa4bed4f79e1898edb45adc2f31a9035cf..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF692ZTH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_1.log b/ENCSR809LCE/cherimoya.fold_1.log deleted file mode 100644 index b64cd64aa9f5eef254e75375d573c91a319562f9..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 34.799076795578 3.6328020095825195 658.6834106445312 0.8069961071014404 1175.989501953125 0.22005151212215424 0.45783094 10.681623458862305 True -1 5454 30.052943468093872 0.7196366786956787 641.807373046875 1.1027398109436035 1003.0230102539062 0.3650507926940918 0.48427296 5.4768385887146 True -2 8181 30.02109122276306 0.7058351039886475 808.223388671875 0.9357540607452393 981.6744995117188 0.37848174571990967 0.50319827 2.854715347290039 True -3 10908 30.019354104995728 0.7020978927612305 864.74072265625 1.2051138877868652 973.7232055664062 0.38370439410209656 0.5361871 2.0841455459594727 True -4 13635 30.646096229553223 32.132479667663574 820.6536865234375 0.9409313201904297 964.8439331054688 0.39157670736312866 0.5543532 1.5849545001983643 True -5 16362 29.979236602783203 1.8032174110412598 765.3115234375 0.7821713089942932 960.4682006835938 0.393806129693985 0.5681791 1.3363614082336426 True -6 19089 30.030628204345703 5.5758960247039795 779.3382568359375 0.6255483031272888 952.2306518554688 0.40014639496803284 0.5850332 1.117327094078064 True -7 21816 30.025243282318115 0.707533597946167 652.837890625 0.5273489952087402 949.818603515625 0.4007892608642578 0.59388536 1.0435309410095215 True -8 24543 30.0223069190979 0.7394130229949951 717.5204467773438 0.9986075162887573 945.8848266601562 0.4038015305995941 0.59908086 0.9393343329429626 True -9 27270 29.963759660720825 0.7058725357055664 683.2158813476562 0.7223331332206726 943.6024169921875 0.40389177203178406 0.614115 0.8389909863471985 True -10 29997 29.40974736213684 6.0791027545928955 613.6767578125 0.37286698818206787 938.3795166015625 0.4089290499687195 0.62380475 0.7900600433349609 True -11 32724 29.42473340034485 0.7013735771179199 847.7769165039062 0.954374372959137 934.4329223632812 0.41250017285346985 0.6337105 0.741814136505127 True -12 35451 29.430989980697632 0.7059164047241211 572.3457641601562 0.48673731088638306 931.0725708007812 0.4153641164302826 0.6407643 0.6884730458259583 True -13 38178 29.475573301315308 0.694265604019165 705.4630126953125 0.7776733636856079 927.1629028320312 0.4178275465965271 0.65431035 0.6427859663963318 True -14 40905 29.46344518661499 0.7434611320495605 706.1251220703125 0.8373207449913025 923.9762573242188 0.42043691873550415 0.66207474 0.6326207518577576 True -15 43632 29.459136486053467 0.696357250213623 604.808349609375 0.6310186386108398 922.2353515625 0.4207115173339844 0.6738948 0.5930416584014893 True -16 46359 29.58330464363098 0.7104189395904541 673.7626953125 0.46260908246040344 921.8949584960938 0.41994819045066833 0.6824519 0.5583215355873108 True -17 49086 29.465548992156982 1.2504401206970215 573.2371826171875 0.4969114065170288 921.9705810546875 0.41952240467071533 0.6880104 0.5376626253128052 True -18 51813 29.47177243232727 0.7050266265869141 668.81884765625 0.4453626275062561 919.4940185546875 0.42246657609939575 0.68911415 0.5269636511802673 True -19 54540 29.425901174545288 0.6947879791259766 560.8146362304688 0.5780532360076904 920.6043090820312 0.42134571075439453 0.6893627 0.5263179540634155 True diff --git a/ENCSR809LCE/cherimoya.fold_1.performance.tsv b/ENCSR809LCE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1272f3b7d985dce7cde344a27a1288f8d5736377..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -920.6043090820312 0.38212305307388306 0.42134568095207214 0.15635737776756287 0.6893627047538757 0.6746286749839783 0.5263179540634155 \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_2.evaluate.json b/ENCSR809LCE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8c79e4ac60916ad05a967c1b2d66de1872e5a096..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692ZTH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_2.fit.json b/ENCSR809LCE/cherimoya.fold_2.fit.json deleted file mode 100644 index 52124c6bd9f902bd1b4c3e94dbd599b43f11e953..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF692ZTH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_2.log b/ENCSR809LCE/cherimoya.fold_2.log deleted file mode 100644 index 1f9717b04f93c36d5e57067aaba3dad1eb88c8a1..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 36.30962562561035 3.393954038619995 810.4505004882812 0.9918863773345947 1134.380126953125 0.2348746508359909 0.43415338 9.668931007385254 True -1 5748 31.748419761657715 0.5693697929382324 630.7348022460938 1.1471730470657349 971.1332397460938 0.36653217673301697 0.4679628 4.276902198791504 True -2 8622 31.655430793762207 1.8029844760894775 742.7130126953125 0.9980367422103882 957.5751342773438 0.3764846622943878 0.5070792 2.9302494525909424 True -3 11496 31.65494966506958 8.408073425292969 738.8653564453125 0.8267370462417603 944.5358276367188 0.3882995843887329 0.5257297 2.0582306385040283 True -4 14370 32.56353950500488 30.522830486297607 602.556640625 0.9075523018836975 940.893798828125 0.39011150598526 0.54252934 1.691724419593811 True -5 17244 31.77045774459839 1.7398631572723389 871.5321044921875 0.5698195099830627 936.1801147460938 0.393730491399765 0.55106664 1.4174425601959229 True -6 20118 31.60771346092224 0.5573220252990723 713.474853515625 0.9940809011459351 931.068603515625 0.39787188172340393 0.5622651 1.3811216354370117 True -7 22992 31.671573400497437 1.0499978065490723 617.41748046875 1.043865442276001 926.9057006835938 0.4011499583721161 0.57423186 1.131356954574585 True -8 25866 31.014856338500977 0.5273332595825195 779.2900390625 0.8913558721542358 925.0423583984375 0.401388555765152 0.5749545 1.0858601331710815 True -9 28740 31.0296151638031 0.5611572265625 665.4017333984375 1.0150102376937866 921.8447265625 0.4040278196334839 0.5902418 0.9645602703094482 True -10 31614 31.11758065223694 0.5496985912322998 577.1076049804688 0.8021628856658936 916.7220458984375 0.40879738330841064 0.60036135 0.8819682598114014 True -11 34488 31.036686658859253 0.534935712814331 656.947509765625 0.7263736128807068 913.8176879882812 0.4109013080596924 0.6106987 0.7977665066719055 True -12 37362 31.057180643081665 0.5319802761077881 590.996826171875 0.7462314367294312 910.1006469726562 0.4140282869338989 0.620368 0.7438873648643494 True -13 40236 30.9451642036438 30.7031888961792 633.6199951171875 0.5129613876342773 907.6448974609375 0.4162851870059967 0.62985075 0.7334699630737305 True -14 43110 31.279804468154907 0.5390124320983887 684.9100341796875 0.6292696595191956 904.5819091796875 0.41767725348472595 0.6390066 0.6706240177154541 True -15 45984 31.04575490951538 0.5384607315063477 741.4044189453125 0.6786280870437622 902.672119140625 0.419173002243042 0.65326416 0.6126455068588257 True -16 48858 30.971302270889282 0.5347785949707031 654.1563720703125 0.51507568359375 902.051025390625 0.4188806116580963 0.66064245 0.5745427012443542 True -17 51732 30.97411346435547 0.5333454608917236 663.9076538085938 0.40369781851768494 900.5828857421875 0.4200820326805115 0.6653781 0.5500584244728088 True -18 54606 30.94518494606018 0.5353777408599854 751.49072265625 0.3987821936607361 900.3178100585938 0.41988858580589294 0.66851485 0.5342902541160583 True -19 57480 30.93294095993042 2.011021375656128 712.7743530273438 0.3469091057777405 899.9192504882812 0.4203697443008423 0.6675788 0.5334644913673401 False diff --git a/ENCSR809LCE/cherimoya.fold_2.performance.tsv b/ENCSR809LCE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bb572df97c85d9821ff194c347865328d1387253..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -900.3178100585938 0.38399043679237366 0.41988858580589294 0.15601174533367157 0.6685148477554321 0.6474694013595581 0.5342902541160583 \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_3.evaluate.json b/ENCSR809LCE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b73fd25105cf49ae7dcb223c37782e6916563f85..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692ZTH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_3.fit.json b/ENCSR809LCE/cherimoya.fold_3.fit.json deleted file mode 100644 index 56a24a9e86a1a20a52eccb2b41395015a53e370e..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF692ZTH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_3.log b/ENCSR809LCE/cherimoya.fold_3.log deleted file mode 100644 index 254e4a108c4b6d69ce91084ca11215fd8635fd0f..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.37562894821167 3.7304277420043945 817.0231323242188 0.8796055912971497 1083.5828857421875 0.23172783851623535 0.46450135 9.31350040435791 True -1 5596 30.861696004867554 3.481586456298828 832.21923828125 1.1244338750839233 940.6414794921875 0.35687607526779175 0.49859932 5.014804363250732 True -2 8394 30.91022562980652 0.5926506519317627 707.2974853515625 0.9922407269477844 921.8115844726562 0.3696170747280121 0.51695526 2.6088364124298096 True -3 11192 30.847219228744507 0.5562593936920166 773.0679931640625 1.0886573791503906 913.8046875 0.37561196088790894 0.54844874 2.3799209594726562 True -4 13990 30.875754833221436 0.5633070468902588 842.5045776367188 1.3675341606140137 908.0136108398438 0.38011541962623596 0.55960184 1.7355828285217285 True -5 16788 30.77182364463806 0.5512537956237793 726.65771484375 0.5759180784225464 902.5064086914062 0.385231077671051 0.5696247 1.4328033924102783 True -6 19586 31.398916959762573 20.6999990940094 748.7218017578125 0.7371373176574707 898.557373046875 0.38926661014556885 0.57500416 1.26129949092865 True -7 22384 30.279391050338745 0.562716007232666 677.057373046875 0.7585684061050415 896.7449951171875 0.39002394676208496 0.58234197 1.1411551237106323 True -8 25182 30.107514142990112 0.5569307804107666 760.2298583984375 0.6189762353897095 893.48779296875 0.3923647999763489 0.590019 0.9729575514793396 True -9 27980 30.405842304229736 19.41835045814514 706.74462890625 0.908437967300415 888.7076416015625 0.3968067467212677 0.60019815 0.8895463347434998 True -10 30778 30.141923427581787 0.557513952255249 706.344482421875 0.5881978273391724 884.9229736328125 0.3993777632713318 0.6119165 0.8201208114624023 True -11 33576 31.143910884857178 23.510056495666504 584.3656005859375 0.5853191018104553 880.826171875 0.4025118947029114 0.6267285 0.7230228781700134 True -12 36374 30.486706495285034 0.5624587535858154 675.53466796875 0.47909292578697205 878.2280883789062 0.4046892523765564 0.6360603 0.6901775598526001 True -13 39172 30.372462272644043 11.170564651489258 747.3425903320312 0.6452152729034424 875.16943359375 0.40624818205833435 0.64973056 0.6593798398971558 True -14 41970 30.234856367111206 0.5619935989379883 729.712158203125 0.8224062323570251 871.0775146484375 0.40948018431663513 0.662043 0.6004153490066528 True -15 44768 30.245503664016724 0.5403735637664795 620.938720703125 0.4672916531562805 869.3651123046875 0.41006696224212646 0.6746708 0.560903012752533 True -16 47566 30.170289993286133 0.5437920093536377 746.531494140625 0.35749849677085876 867.1311645507812 0.41212302446365356 0.6856248 0.5356181263923645 True -17 50364 30.173742294311523 0.5651733875274658 613.4202880859375 0.46797454357147217 867.4730834960938 0.41065514087677 0.6902165 0.5061620473861694 True -18 53162 30.13554811477661 0.5512802600860596 623.697998046875 0.5038201212882996 867.2763061523438 0.4112462103366852 0.69012564 0.49247118830680847 False -19 55960 30.24229645729065 0.5576038360595703 674.1610717773438 0.41479718685150146 866.363525390625 0.4122632145881653 0.6935839 0.49114370346069336 True diff --git a/ENCSR809LCE/cherimoya.fold_3.performance.tsv b/ENCSR809LCE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f003377bb7e4dc5e130b066f6fdd21ed8ec19adb..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -866.363525390625 0.3911120593547821 0.4122631847858429 0.14539815485477448 0.6935839056968689 0.6743442416191101 0.49114370346069336 \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_4.evaluate.json b/ENCSR809LCE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6c23e4aa883b75cfab4625e358acdc9148e39325..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692ZTH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_4.fit.json b/ENCSR809LCE/cherimoya.fold_4.fit.json deleted file mode 100644 index feb598435afd083476b58dca7eefea42305fdaab..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF692ZTH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR809LCE/cherimoya.fold_4.log b/ENCSR809LCE/cherimoya.fold_4.log deleted file mode 100644 index cda9c071976bf4e14193446d610ff5a86f2042d7..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2823 35.7242693901062 4.7487382888793945 775.5830078125 1.1295698881149292 1064.371337890625 0.22240760922431946 0.45252773 8.320484161376953 True -1 5646 31.264183044433594 31.13880228996277 788.3701171875 1.000045657157898 915.253173828125 0.3556942343711853 0.48564267 4.562241077423096 True -2 8469 33.40434813499451 21.348795890808105 672.4554443359375 0.7935700416564941 897.9055786132812 0.3693873882293701 0.5071457 1.9617053270339966 True -3 11292 30.98727774620056 0.5483078956604004 693.5960693359375 0.8803690075874329 888.2802124023438 0.37672707438468933 0.5427978 1.8756639957427979 True -4 14115 31.0392107963562 0.541102409362793 755.5780029296875 0.730401873588562 883.8010864257812 0.3796592950820923 0.5561919 1.3152744770050049 True -5 16938 31.02516746520996 0.5388333797454834 764.3912963867188 0.7591863870620728 879.5445556640625 0.38384881615638733 0.55307215 1.2704435586929321 False -6 19761 31.124431133270264 0.5341157913208008 635.2198486328125 0.9149917364120483 877.3742065429688 0.3861691951751709 0.5577969 1.1509673595428467 True -7 22584 30.823517084121704 0.5279405117034912 641.7095336914062 0.6082599759101868 872.7137451171875 0.39065903425216675 0.56802064 1.0205641984939575 True -8 25407 30.498449087142944 0.5317521095275879 623.442626953125 1.2372806072235107 870.3071899414062 0.39252614974975586 0.57294744 0.948630154132843 True -9 28230 30.44136095046997 0.5204625129699707 665.1156005859375 0.5016891956329346 867.7294921875 0.3939707577228546 0.5868144 0.8510682582855225 True -10 31053 30.499000072479248 0.5305769443511963 735.7673950195312 1.0391736030578613 861.6495361328125 0.3997833728790283 0.60273415 0.715160071849823 True -11 33876 30.41864275932312 0.5313630104064941 661.0841674804688 0.6978309154510498 860.7582397460938 0.399272620677948 0.613172 0.6724043488502502 True -12 36699 33.60090231895447 11.206615686416626 770.417724609375 0.7921407222747803 857.4157104492188 0.40207749605178833 0.6268734 0.6590386033058167 True -13 39522 30.45053219795227 0.5459914207458496 817.101318359375 0.5116856694221497 855.2411499023438 0.40348637104034424 0.63883865 0.6180409789085388 True -14 42345 30.55459976196289 0.5338807106018066 695.9498291015625 0.6089115142822266 852.8475341796875 0.40442749857902527 0.65394 0.5524197220802307 True -15 45168 30.442605018615723 0.5238156318664551 674.4344482421875 0.5218104124069214 850.8403930664062 0.4061047434806824 0.66475457 0.5411494374275208 True -16 47991 30.485679388046265 0.5247912406921387 599.7241821289062 0.504889726638794 849.0578002929688 0.4079231917858124 0.6746191 0.5135272741317749 True -17 50814 30.424358367919922 0.5282773971557617 703.3241577148438 0.3094140291213989 848.5232543945312 0.4084872305393219 0.6795982 0.4967149794101715 True -18 53637 30.439670085906982 0.5262110233306885 714.16162109375 0.5538058280944824 849.1900024414062 0.40665963292121887 0.68148446 0.4894665777683258 True -19 56460 30.37850856781006 0.5225462913513184 602.359619140625 0.596455991268158 847.89990234375 0.4086781442165375 0.68171734 0.4891130328178406 True diff --git a/ENCSR809LCE/cherimoya.fold_4.performance.tsv b/ENCSR809LCE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4e43d126526145e8e84b885782b689dd7af250fe..0000000000000000000000000000000000000000 --- a/ENCSR809LCE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -847.89990234375 0.39496925473213196 0.4086780548095703 0.14373567700386047 0.6817173361778259 0.6560326814651489 0.4891130328178406 \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_0.evaluate.json b/ENCSR810CTB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 13bd7e7c27ddf63b31f32c05a4583c3a9d37bf10..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF297BZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_0.fit.json b/ENCSR810CTB/cherimoya.fold_0.fit.json deleted file mode 100644 index e03466a4f2cfb9dfaeef7471a8e7354769fa16c4..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF297BZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_0.log b/ENCSR810CTB/cherimoya.fold_0.log deleted file mode 100644 index 02780a8f6534159b4aeb89b9cf235f8cf5afcb5e..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1785 23.503167629241943 2.2367312908172607 362.0658874511719 0.8221612572669983 444.063720703125 0.15440207719802856 0.59196335 10.3390531539917 True -1 3570 19.737005710601807 0.4177236557006836 249.0384979248047 0.5691848397254944 404.4531555175781 0.23216386139392853 0.72058016 4.548483848571777 True -2 5355 19.72158169746399 0.3330192565917969 376.4404296875 0.8116132020950317 375.86846923828125 0.2748400568962097 0.7547545 2.296102523803711 True -3 7140 19.754493713378906 0.33014416694641113 376.57122802734375 0.7462473511695862 368.93243408203125 0.28521332144737244 0.77123487 1.1498870849609375 True -4 8925 19.781581163406372 0.35254693031311035 318.735595703125 0.6384704113006592 366.5224609375 0.2901066839694977 0.7819971 0.8187146782875061 True -5 10710 19.73384952545166 0.35431742668151855 264.7218933105469 0.3427896499633789 365.1242370605469 0.2925924062728882 0.78758776 0.7511526942253113 True -6 12495 19.720155954360962 0.3339121341705322 291.8411865234375 0.47025254368782043 363.70269775390625 0.2950580418109894 0.8007489 0.6522752046585083 True -7 14280 19.675514936447144 12.397496938705444 330.4128723144531 0.6817790269851685 363.5675354003906 0.2954178750514984 0.80493814 0.6064815521240234 True -8 16065 19.706345319747925 0.3471980094909668 356.9111633300781 0.44127726554870605 361.5086669921875 0.2999526262283325 0.8090073 0.5539866089820862 True -9 17850 19.72805619239807 0.33361387252807617 265.38763427734375 0.5934892892837524 360.1636657714844 0.30211666226387024 0.8136525 0.5174934267997742 True -10 19635 19.711244344711304 0.3284602165222168 259.0678405761719 0.46761560440063477 359.21929931640625 0.3026740849018097 0.81575114 0.5018036365509033 True -11 21420 19.736350059509277 0.33146047592163086 390.577880859375 0.7676609754562378 358.9560241699219 0.302798867225647 0.82376033 0.46828025579452515 True -12 23205 19.733479499816895 0.336108922958374 280.3900146484375 0.4113127589225769 358.00177001953125 0.30485522747039795 0.82514673 0.45894885063171387 True -13 24990 19.743849992752075 0.32588768005371094 277.31201171875 0.5263928174972534 356.4268493652344 0.3075660169124603 0.83167756 0.4383283853530884 True -14 26775 19.728692054748535 0.3277852535247803 281.0574951171875 0.3681313693523407 356.0166320800781 0.3078877031803131 0.8351171 0.4256478250026703 True -15 28560 19.81003475189209 1.356438398361206 314.9498596191406 0.3587067723274231 355.3755187988281 0.3092077374458313 0.83918506 0.41801631450653076 True -16 30345 19.756765127182007 1.0905191898345947 349.82781982421875 0.37741535902023315 356.08905029296875 0.30712541937828064 0.83968735 0.41594794392585754 True -17 32130 19.745046138763428 0.3264124393463135 315.807373046875 0.2961229085922241 355.54779052734375 0.30767640471458435 0.839807 0.418630450963974 True -18 33915 19.732752799987793 0.33278346061706543 306.5632629394531 0.3393458127975464 356.4898681640625 0.30512821674346924 0.8396111 0.4235783815383911 False -19 35700 19.774611711502075 0.33266758918762207 240.14952087402344 0.306552529335022 356.76318359375 0.304851233959198 0.8381499 0.4289284348487854 False diff --git a/ENCSR810CTB/cherimoya.fold_0.performance.tsv b/ENCSR810CTB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b5fb2648ef6dec75c7b05738bdcfbbf50b4c6fa7..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -355.54779052734375 0.469896137714386 0.30767640471458435 0.10326772183179855 0.8398069739341736 0.7769731283187866 0.418630450963974 \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_1.evaluate.json b/ENCSR810CTB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5fff24cbf7a29ee3b91279de85222047ccc3d512..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF297BZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_1.fit.json b/ENCSR810CTB/cherimoya.fold_1.fit.json deleted file mode 100644 index 1b6c1bae399044e56cb4dd4650796e6b42822e89..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF297BZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_1.log b/ENCSR810CTB/cherimoya.fold_1.log deleted file mode 100644 index 36c2cfd982b9c6cad122f19b90ae955353ab6d17..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1761 23.120558977127075 3.983548164367676 352.5338439941406 0.6254956722259521 535.4147338867188 0.17218764126300812 0.5905161 11.557212829589844 True -1 3522 19.484909772872925 0.549196720123291 272.3736572265625 0.646493673324585 489.24420166015625 0.2537621259689331 0.7229683 4.995635986328125 True -2 5283 19.429201126098633 0.508460283279419 293.5233154296875 0.8815474510192871 451.1190185546875 0.30239006876945496 0.7682484 2.4934566020965576 True -3 7044 19.425262212753296 0.5079917907714844 331.95538330078125 0.4016200304031372 441.54388427734375 0.31315216422080994 0.7785552 1.695983648300171 True -4 8805 19.499720573425293 0.635338544845581 343.1580810546875 0.6155475378036499 437.9109191894531 0.31763580441474915 0.79184437 1.0121268033981323 True -5 10566 19.490817308425903 0.526430606842041 319.6534118652344 0.7744211554527283 436.1339416503906 0.3201430141925812 0.80074596 0.8309446573257446 True -6 12327 19.448628664016724 0.5089426040649414 326.4390869140625 0.6736437678337097 434.7144470214844 0.32357683777809143 0.8003294 0.789530873298645 False -7 14088 19.508851766586304 0.51584792137146 307.3257751464844 0.587047815322876 432.5818176269531 0.3265586495399475 0.8080495 0.6904602646827698 True -8 15849 19.496090173721313 0.5199508666992188 218.95620727539062 0.46261170506477356 430.16912841796875 0.3295454978942871 0.81470114 0.6246756911277771 True -9 17610 19.49628233909607 10.103307723999023 276.96661376953125 0.545930802822113 429.5264892578125 0.3303127586841583 0.8198436 0.5875536203384399 True -10 19371 19.498903036117554 0.5465986728668213 361.2149353027344 0.395327627658844 428.69189453125 0.33117279410362244 0.82740545 0.5476671457290649 True -11 21132 19.528239727020264 0.5250072479248047 352.22613525390625 0.5890644788742065 425.913818359375 0.3351185619831085 0.83564055 0.5122562646865845 True -12 22893 19.59172797203064 0.507631778717041 265.62359619140625 0.4416029453277588 425.0526428222656 0.33583882451057434 0.8389935 0.49791741371154785 True -13 24654 19.523683786392212 0.5051190853118896 286.29010009765625 0.4902753531932831 422.9591369628906 0.3392201364040375 0.8434141 0.4781186878681183 True -14 26415 19.52362084388733 0.5134530067443848 236.47708129882812 0.45278310775756836 422.35443115234375 0.34053000807762146 0.84812814 0.4746674597263336 True -15 28176 19.561510801315308 1.0284624099731445 231.0223388671875 0.2880471348762512 422.6717834472656 0.3392940163612366 0.8515001 0.4645114839076996 True -16 29937 19.52891230583191 0.5039248466491699 232.4786376953125 0.3784574270248413 422.03472900390625 0.34009331464767456 0.85233647 0.46743085980415344 True -17 31698 19.479496955871582 0.5222189426422119 316.3544921875 0.3085482120513916 422.8058776855469 0.3385043144226074 0.8495934 0.47501233220100403 False -18 33459 19.471463680267334 0.5158414840698242 278.81817626953125 0.31137433648109436 422.3773498535156 0.33977222442626953 0.84912467 0.48003947734832764 False -19 35220 19.478353023529053 24.809250831604004 307.80670166015625 0.3125920295715332 422.64422607421875 0.33895397186279297 0.8474882 0.487463116645813 False diff --git a/ENCSR810CTB/cherimoya.fold_1.performance.tsv b/ENCSR810CTB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c70c3c2eb3f042b907fdb9f0fa50d7ce8d9429af..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -422.03472900390625 0.4428062438964844 0.34009331464767456 0.12226485460996628 0.8523364663124084 0.8167804479598999 0.46743085980415344 \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_2.evaluate.json b/ENCSR810CTB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 503b00847c5de0d5c47befe1da6413666ff34c84..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF297BZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_2.fit.json b/ENCSR810CTB/cherimoya.fold_2.fit.json deleted file mode 100644 index 5dab76298d6de3bdb74c0120f2f5b65391bf6a70..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF297BZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_2.log b/ENCSR810CTB/cherimoya.fold_2.log deleted file mode 100644 index dfead916433e57f1dde35bd6cd591005afb6eec9..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1903 24.693155765533447 4.614793062210083 339.630615234375 0.6822550296783447 460.8101501464844 0.16379183530807495 0.5641762 9.459540367126465 True -1 3806 20.995333909988403 0.4594101905822754 307.73614501953125 0.4813114404678345 418.3551940917969 0.23893412947654724 0.69748557 4.016519069671631 True -2 5709 21.009337186813354 0.400005578994751 280.412353515625 0.654741644859314 386.72216796875 0.2803698480129242 0.74990696 2.251441240310669 True -3 7612 20.984654664993286 0.37829089164733887 329.7263488769531 0.5412504076957703 379.0489501953125 0.29140233993530273 0.774575 1.0188502073287964 True -4 9515 21.02492928504944 0.3620638847351074 318.4537353515625 0.6209075450897217 378.7170715332031 0.29121720790863037 0.77578926 0.9304950833320618 True -5 11418 21.009467601776123 0.3629112243652344 315.52197265625 0.7606908082962036 376.3570251464844 0.2949400246143341 0.7920866 0.7053539156913757 True -6 13321 21.013974905014038 0.47498607635498047 286.7214050292969 0.43499165773391724 375.3381042480469 0.2965506613254547 0.7977661 0.6151984930038452 True -7 15224 21.010634899139404 0.36879611015319824 297.1611328125 0.541640043258667 374.4553527832031 0.29903239011764526 0.804558 0.5856136679649353 True -8 17127 21.009800910949707 0.3684213161468506 314.7938232421875 0.4154283106327057 371.84832763671875 0.30320462584495544 0.80923736 0.5349303483963013 True -9 19030 21.046238899230957 0.41295433044433594 314.9764709472656 0.5925546288490295 370.815185546875 0.3050936460494995 0.81419927 0.5138576030731201 True -10 20933 21.030104637145996 0.36222290992736816 233.21322631835938 0.6599631309509277 369.6208190917969 0.3077879250049591 0.8174578 0.49152663350105286 True -11 22836 21.004977464675903 0.36662983894348145 416.09759521484375 0.5967466831207275 368.9690246582031 0.30793553590774536 0.8208717 0.4827839732170105 True -12 24739 21.00808334350586 0.36722445487976074 247.83387756347656 0.34966644644737244 367.95599365234375 0.3106364905834198 0.8247303 0.46843627095222473 True -13 26642 21.01163601875305 0.3662288188934326 290.0717468261719 0.39575761556625366 366.7021484375 0.3127215802669525 0.82781655 0.4589880108833313 True -14 28545 21.017133712768555 0.3700888156890869 339.90118408203125 0.39914342761039734 366.2997741699219 0.31253984570503235 0.83182156 0.4492756128311157 True -15 30448 21.06551456451416 0.37441134452819824 265.71142578125 0.36112484335899353 365.7792053222656 0.31454548239707947 0.8339495 0.4424068331718445 True -16 32351 21.050576210021973 0.37322998046875 296.1434631347656 0.3829464912414551 365.014404296875 0.31521791219711304 0.8355524 0.443073570728302 True -17 34254 21.045241832733154 0.3757591247558594 305.8382263183594 0.38553810119628906 365.2293395996094 0.31465786695480347 0.83532435 0.4458294212818146 False -18 36157 21.04303002357483 0.37097644805908203 314.2020263671875 0.29064446687698364 365.71484375 0.3135688602924347 0.8338698 0.45386016368865967 False -19 38060 21.024795532226562 0.36292505264282227 266.4638671875 0.24440397322177887 365.6505432128906 0.31417202949523926 0.83238465 0.4589627981185913 False diff --git a/ENCSR810CTB/cherimoya.fold_2.performance.tsv b/ENCSR810CTB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f19de7e6c1f2215f35bde00370c31d51c523108d..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -365.014404296875 0.46454569697380066 0.31521788239479065 0.10827608406543732 0.8355523943901062 0.7896203398704529 0.443073570728302 \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_3.evaluate.json b/ENCSR810CTB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3af37c4fee4eaa5a68ef7638d7e39ba3c0f22f70..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF297BZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_3.fit.json b/ENCSR810CTB/cherimoya.fold_3.fit.json deleted file mode 100644 index 53690fa2d458249c6ccd75745997fad84a0fdba4..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF297BZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_3.log b/ENCSR810CTB/cherimoya.fold_3.log deleted file mode 100644 index b2af6c0b1f92fce6e60c95a7e44be8eb0dc30320..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1812 23.689072132110596 5.738929986953735 319.5413818359375 0.5541194081306458 468.17822265625 0.17388832569122314 0.5674757 10.173787117004395 True -1 3624 20.006118059158325 0.4064161777496338 303.75579833984375 0.7934138178825378 429.13861083984375 0.24462847411632538 0.7086427 4.321371078491211 True -2 5436 20.01479434967041 0.3790159225463867 344.7420654296875 0.6863155364990234 402.31292724609375 0.2800477147102356 0.7418398 2.478482961654663 True -3 7248 20.02053451538086 0.3698453903198242 306.2484436035156 0.6502805948257446 395.631591796875 0.29070568084716797 0.7522131 1.6925476789474487 True -4 9060 20.025984287261963 0.3747997283935547 348.05767822265625 0.5056147575378418 392.5992736816406 0.29639914631843567 0.7592326 1.2129987478256226 True -5 10872 19.992594003677368 0.3746464252471924 292.41033935546875 0.8352999687194824 391.593017578125 0.2982040345668793 0.7671719 1.0282809734344482 True -6 12684 20.018866062164307 0.3697636127471924 306.8510437011719 0.7214873433113098 388.8938293457031 0.30284836888313293 0.77432954 0.9079782366752625 True -7 14496 20.02850079536438 0.372711181640625 271.825439453125 0.7076168656349182 387.43536376953125 0.30574244260787964 0.78137493 0.857574999332428 True -8 16308 19.997933387756348 7.216351747512817 267.4644470214844 0.494284987449646 386.4488525390625 0.30756181478500366 0.78910804 0.7874715924263 True -9 18120 20.389606952667236 0.3822166919708252 276.5403747558594 0.5684292316436768 385.2668151855469 0.30947908759117126 0.7944322 0.7316858768463135 True -10 19932 20.03898859024048 0.37905263900756836 267.4232482910156 0.37571805715560913 384.0914001464844 0.3118056058883667 0.79739624 0.6940383911132812 True -11 21744 20.015090227127075 0.6021389961242676 424.8096923828125 0.6266330480575562 382.52606201171875 0.313721239566803 0.8060196 0.6382044553756714 True -12 23556 19.997112274169922 0.8278019428253174 383.82098388671875 0.8315821886062622 381.16082763671875 0.316850870847702 0.81415373 0.5941413044929504 True -13 25368 20.05616044998169 0.3788163661956787 284.1407165527344 0.4895710051059723 379.57958984375 0.31913167238235474 0.8201291 0.5491157174110413 True -14 27180 20.047688961029053 0.38598179817199707 301.4123229980469 0.5216584205627441 378.8515930175781 0.3198947012424469 0.82570887 0.5246425867080688 True -15 28992 19.998270750045776 0.38265275955200195 289.8985900878906 0.46675339341163635 378.91668701171875 0.3194821774959564 0.8300106 0.49655386805534363 True -16 30804 20.03242039680481 0.37235307693481445 307.35858154296875 0.39972078800201416 378.669189453125 0.3190406858921051 0.8342988 0.48774993419647217 True -17 32616 20.018975257873535 0.38045763969421387 277.0913391113281 0.31876617670059204 379.19482421875 0.318128764629364 0.834132 0.48377084732055664 False -18 34428 20.0666925907135 0.3820812702178955 293.20306396484375 0.4318702816963196 379.7840576171875 0.31666746735572815 0.8319318 0.4892682731151581 False -19 36240 20.080849170684814 0.37392354011535645 281.1172790527344 0.2565433382987976 379.4876708984375 0.31752458214759827 0.83171743 0.49534520506858826 False diff --git a/ENCSR810CTB/cherimoya.fold_3.performance.tsv b/ENCSR810CTB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 297e048a804cce09957c4aad8f327962270f3f07..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -378.669189453125 0.4583114981651306 0.3190407156944275 0.11057224869728088 0.8342987895011902 0.786406934261322 0.48774993419647217 \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_4.evaluate.json b/ENCSR810CTB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7d7328eaba972f4b026416a290f55282a4f3d128..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF297BZU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_4.fit.json b/ENCSR810CTB/cherimoya.fold_4.fit.json deleted file mode 100644 index 0e2764ee1fbf2ac8050506de288cfd8e02192d29..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF297BZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR810CTB/cherimoya.fold_4.log b/ENCSR810CTB/cherimoya.fold_4.log deleted file mode 100644 index 0ef440facb4bf2f63ad46eae7da9ce4acdcc9853..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1833 23.887033939361572 3.574460029602051 264.6883239746094 0.6715301275253296 420.0242004394531 0.15572108328342438 0.56830573 9.369742393493652 True -1 3666 20.235774517059326 0.40172410011291504 253.1602020263672 0.5583840608596802 384.6378479003906 0.22744596004486084 0.7072161 3.749863386154175 True -2 5499 20.27494168281555 0.3709719181060791 341.6589050292969 0.6696019172668457 360.759521484375 0.26542243361473083 0.74855644 1.5656131505966187 True -3 7332 20.253387212753296 10.413639307022095 277.2042236328125 0.7146092653274536 353.9831848144531 0.2765381336212158 0.76142037 1.2140955924987793 True -4 9165 20.45377779006958 0.3565387725830078 337.9442443847656 0.9293056726455688 351.439697265625 0.27967217564582825 0.76592267 0.8399535417556763 True -5 10998 21.343806982040405 17.367048501968384 311.857177734375 0.5983483791351318 349.60833740234375 0.2843170762062073 0.7737989 0.7157340049743652 True -6 12831 20.320267915725708 0.3606534004211426 314.3576354980469 0.7055292129516602 348.1423645019531 0.2869320213794708 0.77738637 0.6537449955940247 True -7 14664 21.79896068572998 2.9722743034362793 374.86279296875 0.467686265707016 347.9266662597656 0.28803688287734985 0.7837687 0.606625497341156 True -8 16497 20.29751992225647 0.3542971611022949 280.3191833496094 0.4787077307701111 347.30859375 0.2891164720058441 0.78783876 0.5797429084777832 True -9 18330 20.284409523010254 0.527411699295044 261.99310302734375 0.6036244630813599 345.907470703125 0.2916871905326843 0.79388946 0.5352879166603088 True -10 20163 20.346420764923096 0.45401453971862793 243.60165405273438 0.4651426076889038 345.0831298828125 0.29240062832832336 0.8035683 0.5068987607955933 True -11 21996 20.27735710144043 0.3601870536804199 263.5820007324219 0.5719383358955383 343.93585205078125 0.2950803339481354 0.8115937 0.47640231251716614 True -12 23829 20.287638902664185 0.3504502773284912 267.4443664550781 0.34063416719436646 343.2748107910156 0.2963331937789917 0.8156371 0.463993638753891 True -13 25662 20.233287572860718 7.997157335281372 255.51060485839844 0.4597857594490051 342.56488037109375 0.29744964838027954 0.8200958 0.45245370268821716 True -14 27495 21.15770435333252 0.35547685623168945 280.57159423828125 0.4129495620727539 341.7498474121094 0.2992817759513855 0.82513916 0.4367285966873169 True -15 29328 20.239624977111816 0.3533444404602051 314.2906494140625 0.213988795876503 341.2223815917969 0.30015453696250916 0.8293599 0.424356073141098 True -16 31161 20.206170320510864 0.34763193130493164 310.6207275390625 0.3610471487045288 341.0319519042969 0.3005894720554352 0.8338749 0.4177684187889099 True -17 32994 20.199862480163574 0.3435661792755127 340.5935974121094 0.23382964730262756 342.1260070800781 0.29779306054115295 0.83391446 0.4181954860687256 True -18 34827 20.197278261184692 0.9293093681335449 312.42437744140625 0.3236556649208069 341.6561584472656 0.29964935779571533 0.833426 0.42312389612197876 False -19 36660 20.206724882125854 0.35152554512023926 255.06814575195312 0.22307734191417694 341.7326965332031 0.29943159222602844 0.8319361 0.42804384231567383 False diff --git a/ENCSR810CTB/cherimoya.fold_4.performance.tsv b/ENCSR810CTB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 842dd1c144c1a985528f141ab68f73cee1efe16a..0000000000000000000000000000000000000000 --- a/ENCSR810CTB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -342.1260070800781 0.4762120842933655 0.29779309034347534 0.09736282378435135 0.8339144587516785 0.7701495885848999 0.4181954860687256 \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_0.evaluate.json b/ENCSR812ZKP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b29c90021f4392dd86499cd0b01117b9bfb1c119..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF748VQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_0.fit.json b/ENCSR812ZKP/cherimoya.fold_0.fit.json deleted file mode 100644 index 3bafce7981bb896a5ccf1f23a28bbee2f220d8c9..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF748VQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_0.log b/ENCSR812ZKP/cherimoya.fold_0.log deleted file mode 100644 index f2b28a8fc8484ef9776bc6c29faaded02361693a..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3846 47.392284631729126 4.30384635925293 643.2550659179688 1.6548813581466675 1060.18896484375 0.6942659020423889 0.686087 9.744028091430664 True -1 7692 42.80580377578735 0.8857839107513428 576.291259765625 1.0721207857131958 884.1765747070312 0.7865658402442932 0.70385456 2.166172742843628 True -2 11538 42.836366176605225 0.8092703819274902 675.927490234375 1.2888554334640503 859.7958374023438 0.7978261113166809 0.70099914 1.4497814178466797 False -3 15384 42.69228196144104 0.794360876083374 797.3016967773438 1.2706882953643799 847.7565307617188 0.8043097853660583 0.7007295 1.1208713054656982 False -4 19230 42.731555461883545 19.63304376602173 706.33642578125 1.1892149448394775 839.230712890625 0.8084781169891357 0.6970529 1.0365495681762695 False -5 23076 42.71751666069031 0.8612957000732422 802.99560546875 1.6268653869628906 837.1290283203125 0.8098056316375732 0.69735014 1.0806264877319336 False -6 26922 42.64640688896179 0.7974774837493896 685.90234375 1.8326996564865112 830.9005737304688 0.8119158744812012 0.6999849 1.0739331245422363 False -7 30768 42.78369116783142 0.8303420543670654 804.84033203125 0.9843349456787109 824.2407836914062 0.8152103424072266 0.7067477 1.0003397464752197 True -8 34614 42.7214138507843 0.7955508232116699 875.1502685546875 0.966167688369751 816.59814453125 0.8182985782623291 0.71245354 0.8850257396697998 True -9 38460 42.75332474708557 2.096170425415039 622.4273681640625 0.6576249599456787 812.3915405273438 0.8204902410507202 0.71877563 0.8818835616111755 True -10 42306 42.8872766494751 0.8078269958496094 611.1983032226562 0.9018465876579285 806.5424194335938 0.8234650492668152 0.7235511 0.8244829773902893 True -11 46152 42.98280191421509 0.8382556438446045 646.9334716796875 1.1038084030151367 800.6456298828125 0.8261305689811707 0.72759014 0.7748690247535706 True -12 49998 42.98326921463013 27.450228929519653 639.624755859375 1.496094822883606 793.7345581054688 0.8290417194366455 0.7383095 0.7371625304222107 True -13 53844 42.390369176864624 1.1615078449249268 613.2501220703125 0.837158203125 789.1087036132812 0.831308901309967 0.7463551 0.6950426697731018 True -14 57690 41.87577748298645 1.6442341804504395 710.4602661132812 0.49977976083755493 783.154296875 0.8333367109298706 0.7552527 0.6679063439369202 True -15 61536 41.88646483421326 1.568314552307129 586.8417358398438 0.5429333448410034 779.9887084960938 0.8349732160568237 0.7621743 0.6607168316841125 True -16 65382 41.888206005096436 1.7970261573791504 471.2488708496094 0.7945355176925659 778.1591186523438 0.8359849452972412 0.7659202 0.6469593644142151 True -17 69228 41.86772394180298 1.9847939014434814 598.0840454101562 0.6842927932739258 777.177978515625 0.8362696170806885 0.7682265 0.648877739906311 True -18 73074 41.87679052352905 28.92895007133484 692.5812377929688 0.6625276803970337 778.033203125 0.8361223340034485 0.7666786 0.6423906683921814 False -19 76920 41.913137435913086 2.2049789428710938 573.2982788085938 0.6571888327598572 778.2057495117188 0.8359331488609314 0.7653831 0.6461015343666077 False diff --git a/ENCSR812ZKP/cherimoya.fold_0.performance.tsv b/ENCSR812ZKP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b94209d2c9b3c710daca285157e7e91a3bdf860d..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -777.177978515625 0.14076286554336548 0.8362696170806885 0.47295698523521423 0.7682265043258667 0.7062134742736816 0.648877739906311 \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_1.evaluate.json b/ENCSR812ZKP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index fc17224bc695e1a957568efec6052d6ae6a9f622..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF748VQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_1.fit.json b/ENCSR812ZKP/cherimoya.fold_1.fit.json deleted file mode 100644 index 24265ff92dde72c6f80e1bb28ba8274cc272cac1..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF748VQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_1.log b/ENCSR812ZKP/cherimoya.fold_1.log deleted file mode 100644 index dceb93fb95bdc5c42299a2655a6ebb34ea171a59..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3820 47.31005907058716 9.29014801979065 764.904052734375 1.2154054641723633 1240.0640869140625 0.703647255897522 0.70982736 10.78878402709961 True -1 7640 42.52169179916382 1.049006700515747 908.3702392578125 1.5500465631484985 1034.2691650390625 0.7954344153404236 0.72350836 2.55461049079895 True -2 11460 42.49475383758545 1.0995047092437744 584.9686279296875 1.0199261903762817 996.0470581054688 0.8054572939872742 0.73147154 1.390030860900879 True -3 15280 42.419594526290894 1.0205698013305664 658.9718017578125 1.7750279903411865 980.4789428710938 0.8116143941879272 0.7373419 1.1976611614227295 True -4 19100 42.44758605957031 1.0069406032562256 826.2566528320312 1.0296895503997803 969.771484375 0.8153229355812073 0.7365776 1.0895332098007202 False -5 22920 42.39645957946777 1.0002741813659668 674.2600708007812 1.107499361038208 959.0536499023438 0.8192406296730042 0.7403346 0.9760704636573792 True -6 26740 42.44120764732361 26.05294132232666 679.5789184570312 1.0502568483352661 952.1844482421875 0.8222549557685852 0.74347603 0.9373204708099365 True -7 30560 41.6461455821991 1.0486934185028076 681.4337158203125 0.9145184755325317 944.782958984375 0.8252003192901611 0.7475478 0.8773253560066223 True -8 34380 41.72872042655945 1.0351481437683105 617.5863647460938 1.2299673557281494 937.9625854492188 0.8274253010749817 0.7443437 0.9126995801925659 False -9 38200 41.57801842689514 1.0255539417266846 537.9361572265625 0.6676756143569946 928.2390747070312 0.8304336667060852 0.75568205 0.8141077160835266 True -10 42020 41.596287965774536 0.9976577758789062 792.1757202148438 0.9081701040267944 919.3726196289062 0.8335116505622864 0.7628419 0.7909630537033081 True -11 45840 41.65536689758301 0.9960086345672607 568.4537963867188 0.9702422618865967 913.0390625 0.8360080718994141 0.7710157 0.733776867389679 True -12 49660 41.53823256492615 0.9795548915863037 661.9840087890625 1.4042835235595703 905.8464965820312 0.8385565876960754 0.78007084 0.7148099541664124 True -13 53480 41.54026484489441 0.9955508708953857 630.7886962890625 0.7802066206932068 897.8220825195312 0.841248095035553 0.78545356 0.6668403744697571 True -14 57300 41.54959154129028 0.9836268424987793 604.5517578125 0.7005743384361267 891.9419555664062 0.8432704210281372 0.7936346 0.6494235396385193 True -15 61120 41.513370752334595 1.000375747680664 626.5115966796875 0.5171070694923401 889.2719116210938 0.8446807861328125 0.8000236 0.6288257241249084 True -16 64940 41.566773891448975 0.9905581474304199 583.435791015625 0.5516324043273926 886.3737182617188 0.8455820679664612 0.8023345 0.6328900456428528 True -17 68760 41.49395513534546 1.2127227783203125 455.8424072265625 0.7507255673408508 886.0140380859375 0.8456218242645264 0.8051934 0.6309927105903625 True -18 72580 41.698750495910645 1.006237268447876 565.6639404296875 0.5392618179321289 887.623291015625 0.84524005651474 0.80279267 0.6369568109512329 False -19 76400 41.57663297653198 1.318345546722412 560.7691650390625 0.8815498948097229 887.9966430664062 0.8449676632881165 0.80400807 0.6442030668258667 False diff --git a/ENCSR812ZKP/cherimoya.fold_1.performance.tsv b/ENCSR812ZKP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3863467eb82b253d1d330f590d512a5fa2c4924f..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -886.0140380859375 0.12991240620613098 0.8456219434738159 0.5097551941871643 0.8051934242248535 0.7694085836410522 0.6309927105903625 \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_2.evaluate.json b/ENCSR812ZKP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2cf78e93d23b06f4556e10b0bf71a0cba08cacde..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF748VQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_2.fit.json b/ENCSR812ZKP/cherimoya.fold_2.fit.json deleted file mode 100644 index 24ffd4f2326bb16300dddee3103a1d2d47d6cb50..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF748VQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_2.log b/ENCSR812ZKP/cherimoya.fold_2.log deleted file mode 100644 index f7cfc24911a3e7e472d6b638de85403430326d9f..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4048 49.919175148010254 4.158427953720093 671.5794677734375 1.3170400857925415 1108.3961181640625 0.7139243483543396 0.7199074 8.413400650024414 True -1 8096 44.89295744895935 1.0304079055786133 950.5555419921875 1.367364525794983 947.7835083007812 0.7925225496292114 0.7208577 2.0096700191497803 True -2 12144 44.949955463409424 0.8239178657531738 604.4503784179688 0.8528079390525818 917.7553100585938 0.800306499004364 0.7266267 1.297158122062683 True -3 16192 44.02091836929321 0.7780787944793701 753.7686157226562 0.8305726051330566 902.5106811523438 0.8065968155860901 0.72177064 1.1128877401351929 False -4 20240 44.061912059783936 0.7456719875335693 672.5757446289062 1.5193372964859009 897.5388793945312 0.8096610903739929 0.7212433 1.0619014501571655 False -5 24288 44.04637050628662 0.7569351196289062 741.1572265625 1.8298048973083496 890.006591796875 0.8125461935997009 0.7233001 0.9986803531646729 False -6 28336 43.981406450271606 0.7631337642669678 598.9132080078125 1.4496455192565918 883.0335693359375 0.8153529167175293 0.7229432 0.9119150042533875 False -7 32384 43.992865800857544 29.195249557495117 742.76904296875 0.8799247741699219 875.2189331054688 0.8182558417320251 0.7289524 0.8857833743095398 True -8 36432 44.057610750198364 0.7648677825927734 762.10791015625 0.5505244135856628 866.822509765625 0.8214164972305298 0.73557395 0.8199870586395264 True -9 40480 44.10140633583069 1.5337622165679932 772.6259765625 0.861809492111206 858.6285400390625 0.8243500590324402 0.74323916 0.7692248821258545 True -10 44528 44.04638051986694 0.7628092765808105 549.5401611328125 0.6960495114326477 852.2373046875 0.8269692659378052 0.7507724 0.7598251104354858 True -11 48576 44.03512382507324 0.7515685558319092 572.712890625 0.9515480399131775 844.7117309570312 0.8298517465591431 0.7601804 0.7125576734542847 True -12 52624 44.44994330406189 22.58929753303528 582.1279907226562 1.0616880655288696 839.09228515625 0.8320205211639404 0.76248896 0.70588618516922 True -13 56672 44.027710914611816 0.755774736404419 678.9266967773438 0.799447238445282 833.1450805664062 0.8345572352409363 0.7713375 0.6836597323417664 True -14 60720 43.97691297531128 31.278155088424683 665.498779296875 0.8155587911605835 828.0158081054688 0.8362395763397217 0.77547175 0.6716819405555725 True -15 64768 44.11570644378662 0.7788829803466797 614.10498046875 0.6858944296836853 824.1255493164062 0.8376498222351074 0.78249943 0.6605631709098816 True -16 68816 44.01836037635803 1.0341887474060059 686.6982421875 0.5361876487731934 821.9522094726562 0.8385916948318481 0.7877774 0.6418235301971436 True -17 72864 44.023542404174805 0.7518529891967773 593.6542358398438 0.9246071577072144 820.8466186523438 0.8389104008674622 0.789097 0.6396278142929077 True -18 76912 44.07698583602905 0.7576165199279785 576.7176513671875 0.740345299243927 821.78662109375 0.8387103080749512 0.7896707 0.6420676708221436 True -19 80960 44.07414889335632 0.755620002746582 618.0028076171875 0.5066372156143188 822.4515991210938 0.8384846448898315 0.7891715 0.6422919034957886 False diff --git a/ENCSR812ZKP/cherimoya.fold_2.performance.tsv b/ENCSR812ZKP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ef28ec27e8e271801130c82486d26003c4479379..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -821.78662109375 0.13749657571315765 0.8387102484703064 0.48632532358169556 0.7896707057952881 0.7354798316955566 0.6420676708221436 \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_3.evaluate.json b/ENCSR812ZKP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2b9665a7b512d167d8554061e355db7ee5f06faf..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF748VQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_3.fit.json b/ENCSR812ZKP/cherimoya.fold_3.fit.json deleted file mode 100644 index 408e565a21571c17e431cddcd328697bdc57eba7..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF748VQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_3.log b/ENCSR812ZKP/cherimoya.fold_3.log deleted file mode 100644 index 8d7d8bb89fa8c048e0911573f19b5b910bb51724..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3917 48.24338912963867 4.6916468143463135 724.268798828125 1.5293755531311035 1060.6326904296875 0.7126743197441101 0.7097334 9.134702682495117 True -1 7834 43.52863335609436 0.8605000972747803 759.8799438476562 1.3572213649749756 905.6229248046875 0.790583610534668 0.6828295 2.0926573276519775 False -2 11751 43.53463864326477 1.4546923637390137 844.432373046875 0.9569231867790222 884.1119384765625 0.7988324165344238 0.68705213 1.4725782871246338 False -3 15668 43.51781105995178 1.4063501358032227 733.530517578125 0.867838978767395 871.7333374023438 0.8047255277633667 0.6797847 1.3059948682785034 False -4 19585 43.52438735961914 0.814509391784668 752.667724609375 1.5676745176315308 862.2926635742188 0.8082458972930908 0.6969158 1.2467365264892578 False -5 23502 43.607178688049316 0.809640645980835 753.6502685546875 0.6709640026092529 860.173828125 0.8097229599952698 0.6943893 1.1509615182876587 False -6 27419 43.46734857559204 0.7962136268615723 569.6617431640625 1.6434528827667236 851.4288940429688 0.8133593201637268 0.69936275 1.0229015350341797 False -7 31336 43.41818070411682 0.8120603561401367 696.5670776367188 0.8380951285362244 844.3585815429688 0.8162825107574463 0.7060759 1.0246182680130005 False -8 35253 43.41183304786682 2.1514923572540283 673.98291015625 0.9761244058609009 837.8345336914062 0.8189185261726379 0.70741415 0.9298608899116516 False -9 39170 43.43726658821106 0.7997739315032959 627.2147216796875 0.799098014831543 834.9852905273438 0.8210921287536621 0.70779616 0.916100800037384 False -10 43087 43.45944857597351 1.5571794509887695 533.8268432617188 1.000913381576538 828.8324584960938 0.8239067792892456 0.7159077 0.8722918629646301 True -11 47004 43.678181171417236 0.7975034713745117 652.8589477539062 0.8781045079231262 823.0296020507812 0.8262478113174438 0.7216755 0.8733347058296204 True -12 50921 42.9790620803833 2.000190496444702 632.1448364257812 0.7591415643692017 816.7938232421875 0.829128623008728 0.73155516 0.7972538471221924 True -13 54838 42.56727337837219 0.7837350368499756 582.0670166015625 1.1180541515350342 812.1691284179688 0.8313957452774048 0.7441065 0.7761691212654114 True -14 58755 42.649800300598145 0.7690341472625732 694.937255859375 0.8999747037887573 805.26611328125 0.8339967727661133 0.753871 0.7209653258323669 True -15 62672 42.61158847808838 0.7983858585357666 658.0043334960938 0.9458034038543701 801.372314453125 0.8357329368591309 0.76134247 0.699884831905365 True -16 66589 42.54572892189026 0.7831084728240967 565.08544921875 0.8137675523757935 798.6228637695312 0.8367938995361328 0.7685535 0.6741458177566528 True -17 70506 42.73692345619202 0.7989029884338379 639.0821533203125 0.5438798666000366 799.2294921875 0.8368101119995117 0.77294934 0.6700359582901001 True -18 74423 43.572503328323364 0.7890720367431641 522.0640869140625 0.7359240055084229 800.3493041992188 0.8364240527153015 0.7707942 0.6698773503303528 False -19 78340 42.58019018173218 2.726578712463379 540.1046142578125 0.5672478675842285 801.241943359375 0.8362452387809753 0.77107507 0.6752673387527466 False diff --git a/ENCSR812ZKP/cherimoya.fold_3.performance.tsv b/ENCSR812ZKP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 33b21c15aee08a4db94eecf74d26589f86e004e9..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -799.2294921875 0.13885872066020966 0.8368101119995117 0.4776732921600342 0.7729493379592896 0.718855082988739 0.6700359582901001 \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_4.evaluate.json b/ENCSR812ZKP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 90274448f8ac1de103821d3d8dde134639d1e7dc..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF748VQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_4.fit.json b/ENCSR812ZKP/cherimoya.fold_4.fit.json deleted file mode 100644 index 976e512efd29566365100d5c88e7d7579850d598..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF748VQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR812ZKP/cherimoya.fold_4.log b/ENCSR812ZKP/cherimoya.fold_4.log deleted file mode 100644 index df156374b161657ee5eb8841270ecdd82838a949..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4018 49.52049732208252 4.7980592250823975 576.10498046875 1.2691752910614014 1017.9032592773438 0.7049582004547119 0.69932765 8.270977973937988 True -1 8036 44.673255443573 0.9247252941131592 762.5455322265625 1.2495067119598389 877.9210205078125 0.7854675054550171 0.70594215 2.3525338172912598 True -2 12054 44.60562467575073 0.7721130847930908 613.8319091796875 1.3654260635375977 845.9585571289062 0.800275444984436 0.7064958 1.2836378812789917 True -3 16072 44.61307406425476 0.7618470191955566 733.7116088867188 1.3714489936828613 835.9139404296875 0.8048697710037231 0.7111372 1.0479702949523926 True -4 20090 44.596962451934814 0.773688793182373 708.02490234375 1.18245267868042 829.8068237304688 0.8074052333831787 0.7058368 1.0043357610702515 False -5 24108 44.625893115997314 1.9614768028259277 529.421142578125 1.1822290420532227 821.767333984375 0.8103875517845154 0.7059436 0.9414018988609314 False -6 28126 44.51063013076782 0.8414466381072998 563.552978515625 1.5947226285934448 819.89404296875 0.8124762177467346 0.7033737 1.0706987380981445 False -7 32144 43.68984889984131 0.7772624492645264 544.1085205078125 0.7194411158561707 812.66943359375 0.8153994083404541 0.7085863 0.989622950553894 False -8 36162 43.68280029296875 0.8143479824066162 541.512939453125 1.1653683185577393 807.3679809570312 0.817756712436676 0.7167865 0.989867091178894 True -9 40180 43.71218705177307 0.7771825790405273 641.11572265625 1.3210794925689697 800.1947021484375 0.8210315108299255 0.7168193 0.925156831741333 True -10 44198 43.65454602241516 0.7695178985595703 685.0490112304688 0.7135464549064636 792.5816650390625 0.8241135478019714 0.72855324 0.8025071024894714 True -11 48216 43.67578864097595 0.7723391056060791 772.821533203125 1.1991207599639893 786.639404296875 0.8268362879753113 0.73746765 0.7276660799980164 True -12 52234 43.68982744216919 0.755702018737793 548.1616821289062 0.6547890901565552 780.4142456054688 0.8297739028930664 0.7484595 0.6669349670410156 True -13 56252 43.72648334503174 0.7715244293212891 765.5409545898438 0.7110623121261597 775.4335327148438 0.8319577574729919 0.7586297 0.6449881196022034 True -14 60270 43.762271881103516 0.7555618286132812 603.1303100585938 1.3981060981750488 770.4120483398438 0.8342161774635315 0.76921123 0.6230331063270569 True -15 64288 44.27445340156555 0.7508623600006104 566.1881103515625 0.7836738228797913 766.7085571289062 0.8353909254074097 0.77539545 0.5956524014472961 True -16 68306 44.9676239490509 0.770200252532959 654.8040161132812 0.7891820669174194 764.979736328125 0.8361753225326538 0.7822661 0.5797228217124939 True -17 72324 43.66662359237671 0.759493350982666 550.847412109375 0.444368839263916 764.98095703125 0.8361549377441406 0.78290623 0.5776948928833008 True -18 76342 45.88857913017273 0.7562806606292725 624.4425048828125 0.5584532618522644 766.2935791015625 0.8357089161872864 0.7839287 0.5755046010017395 True -19 80360 43.80021357536316 0.755530595779419 575.9218139648438 0.5906775593757629 766.2843627929688 0.8354678750038147 0.78191066 0.5810352563858032 False diff --git a/ENCSR812ZKP/cherimoya.fold_4.performance.tsv b/ENCSR812ZKP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8eb3bf24df1143bad83a7407b6ff7d21a4d9a824..0000000000000000000000000000000000000000 --- a/ENCSR812ZKP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -766.2935791015625 0.1418934166431427 0.8357090353965759 0.46832379698753357 0.7839286923408508 0.7139908075332642 0.5755046010017395 \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_0.evaluate.json b/ENCSR813CKU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7b9dfffd84a1f969af4c241769663dd0342f2cf0..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF546SNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_0.fit.json b/ENCSR813CKU/cherimoya.fold_0.fit.json deleted file mode 100644 index d115ec30ada16858e002632ce2e0c3987b65f418..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF546SNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_0.log b/ENCSR813CKU/cherimoya.fold_0.log deleted file mode 100644 index 00880c82c3ddc039f1ec12fc9c225571fe3b3a4a..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 33.880701541900635 3.609112024307251 285.590576171875 0.508056640625 351.0111999511719 0.1580038219690323 0.5265942 3.3881683349609375 True -1 5488 30.295817375183105 1.7382261753082275 262.9083557128906 0.6754624843597412 338.30181884765625 0.20454420149326324 0.6184414 0.9125973582267761 True -2 8232 30.307201147079468 0.9670238494873047 277.63623046875 0.584636926651001 334.2213439941406 0.2162380963563919 0.6407821 0.5594871640205383 True -3 10976 30.25389814376831 0.6928253173828125 244.07122802734375 0.4150885343551636 332.6518859863281 0.21930988132953644 0.64930576 0.44181159138679504 True -4 13720 30.20389986038208 0.5891296863555908 261.3867492675781 0.4493500292301178 331.8939514160156 0.22104574739933014 0.657373 0.41419917345046997 True -5 16464 30.171549797058105 0.5685091018676758 251.48873901367188 0.43267810344696045 330.9134216308594 0.225037083029747 0.66314054 0.38233885169029236 True -6 19208 30.149269580841064 0.576296329498291 256.8946533203125 0.476100891828537 330.29998779296875 0.22725924849510193 0.669838 0.37389853596687317 True -7 21952 30.185091018676758 0.6277403831481934 297.0741882324219 0.3595597743988037 329.8751220703125 0.22865578532218933 0.6738334 0.3539581596851349 True -8 24696 30.240699768066406 0.5789425373077393 300.1920166015625 0.318896621465683 329.3444519042969 0.2311594933271408 0.681703 0.3535366356372833 True -9 27440 30.335944652557373 0.5837447643280029 265.061279296875 0.5533901453018188 328.94342041015625 0.23201459646224976 0.6847934 0.36019283533096313 True -10 30184 30.31851577758789 0.6055810451507568 261.21368408203125 0.4082174599170685 328.4629211425781 0.23384076356887817 0.68963706 0.34482431411743164 True -11 32928 30.290685653686523 0.5903172492980957 287.0181884765625 0.30135825276374817 327.9247131347656 0.2359858602285385 0.69612294 0.3305911719799042 True -12 35672 30.71952772140503 0.5731794834136963 252.66329956054688 0.37761741876602173 327.2183532714844 0.23899003863334656 0.70498806 0.3197610378265381 True -13 38416 30.288715362548828 0.5684051513671875 261.3924560546875 0.3518747091293335 327.24407958984375 0.23919345438480377 0.71187156 0.301057904958725 True -14 41160 30.32567524909973 0.5844459533691406 242.99191284179688 0.35235774517059326 327.02301025390625 0.2401556521654129 0.71871585 0.27712252736091614 True -15 43904 30.330018520355225 0.5932254791259766 282.99371337890625 0.2747901976108551 326.6052551269531 0.24135512113571167 0.72495383 0.2705761790275574 True -16 46648 30.373754739761353 0.5835747718811035 227.4619598388672 0.25007665157318115 326.6283874511719 0.2410382479429245 0.72896546 0.2682664394378662 True -17 49392 30.32720971107483 0.5788185596466064 219.19830322265625 0.505642831325531 326.5411682128906 0.2409646064043045 0.7331999 0.2643730938434601 True -18 52136 30.397514820098877 0.5959603786468506 305.30889892578125 0.2701438069343567 326.67327880859375 0.24101334810256958 0.73285484 0.2638300955295563 False -19 54880 30.37275767326355 0.5760931968688965 248.5048370361328 0.28236937522888184 326.4955749511719 0.2407652735710144 0.732611 0.2657589018344879 False diff --git a/ENCSR813CKU/cherimoya.fold_0.performance.tsv b/ENCSR813CKU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 74a126ddf08c0085d1fc89eabcba4e472cdd08bb..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.5411682128906 0.5044664144515991 0.2409646064043045 0.0687355324625969 0.7331998944282532 0.676494836807251 0.2643730938434601 \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_1.evaluate.json b/ENCSR813CKU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c316a26e40d3cf91c9af63b4463073211e2df26f..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF546SNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_1.fit.json b/ENCSR813CKU/cherimoya.fold_1.fit.json deleted file mode 100644 index 989de5707e251d0e636fc67c28adf28f537dd17b..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF546SNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_1.log b/ENCSR813CKU/cherimoya.fold_1.log deleted file mode 100644 index cdbba66175f58663e329da8fd9a5e5dff2cc0bd4..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 34.185476541519165 4.033324718475342 235.1700897216797 0.46207717061042786 390.01806640625 0.1631886065006256 0.56260234 3.9986133575439453 True -1 5480 31.25800585746765 22.63984489440918 240.5120849609375 0.5317809581756592 373.8929443359375 0.21457797288894653 0.6601236 0.8218176960945129 True -2 8220 30.2909517288208 11.706433057785034 270.6029968261719 0.6249669790267944 367.42327880859375 0.23004071414470673 0.69395554 0.4991573393344879 True -3 10960 30.302855014801025 0.818866491317749 295.1983337402344 0.39833033084869385 365.24066162109375 0.23520241677761078 0.70652264 0.35558316111564636 True -4 13700 30.237857818603516 0.7422358989715576 235.14239501953125 0.25809451937675476 364.013671875 0.23760975897312164 0.708891 0.35276368260383606 True -5 16440 30.242235898971558 0.6892368793487549 286.57666015625 0.8001536130905151 362.6593933105469 0.24225355684757233 0.7167294 0.3407837748527527 True -6 19180 30.254150390625 0.6856420040130615 276.52783203125 0.5281636118888855 362.1070251464844 0.2430688738822937 0.7231189 0.3238813877105713 True -7 21920 30.192896604537964 0.6910357475280762 263.86419677734375 0.5303893685340881 361.7063903808594 0.24472063779830933 0.7256295 0.32577288150787354 True -8 24660 30.356210470199585 0.686276912689209 277.7990417480469 0.30260390043258667 361.2856140136719 0.24537186324596405 0.73190135 0.33232492208480835 True -9 27400 30.171794414520264 0.6993098258972168 287.23468017578125 0.6206266283988953 360.36102294921875 0.24825848639011383 0.7368209 0.3228914737701416 True -10 30140 30.147432327270508 1.675851821899414 261.2951965332031 0.3247321546077728 360.02825927734375 0.2489732801914215 0.7440568 0.30570676922798157 True -11 32880 30.20634651184082 0.6993880271911621 265.68585205078125 0.24886733293533325 359.451171875 0.2511945962905884 0.7467053 0.29971423745155334 True -12 35620 30.160738468170166 0.6821842193603516 260.22979736328125 0.3316369354724884 358.654296875 0.25423356890678406 0.75413555 0.30344074964523315 True -13 38360 30.43345594406128 0.6870212554931641 256.6947937011719 0.5362383723258972 358.0226745605469 0.25537171959877014 0.75774187 0.3016211986541748 True -14 41100 30.35009217262268 23.76585102081299 251.0994873046875 0.41336292028427124 357.744140625 0.256632924079895 0.76467276 0.2927185595035553 True -15 43840 30.25408411026001 23.681072473526 315.3520812988281 0.33110523223876953 357.09112548828125 0.2591511607170105 0.76877874 0.2846315801143646 True -16 46580 30.272143363952637 33.422033071517944 258.108154296875 0.34066087007522583 356.8293762207031 0.258921355009079 0.7727495 0.28257036209106445 True -17 49320 30.33348846435547 1.272608995437622 262.0434265136719 0.2403472512960434 356.7497863769531 0.2596440315246582 0.7750582 0.27963435649871826 True -18 52060 30.718294620513916 0.6912670135498047 275.613525390625 0.2282809466123581 357.1341247558594 0.2583124339580536 0.775106 0.2804412841796875 True -19 54800 30.32387089729309 0.7907028198242188 245.19955444335938 0.15495949983596802 357.3567199707031 0.25677528977394104 0.7734636 0.2828689217567444 False diff --git a/ENCSR813CKU/cherimoya.fold_1.performance.tsv b/ENCSR813CKU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5a5e256294850f4d30109a2f0bfe7d32777cb432..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -357.1341247558594 0.4909915328025818 0.2583124339580536 0.08028580248355865 0.7751060128211975 0.7213011980056763 0.2804412841796875 \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_2.evaluate.json b/ENCSR813CKU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e8ccbca38e823be3c6750ff3787fd597ed5aa9b2..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF546SNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_2.fit.json b/ENCSR813CKU/cherimoya.fold_2.fit.json deleted file mode 100644 index c0982e5953a22aef18e7705f2f4364f57919b8ff..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF546SNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_2.log b/ENCSR813CKU/cherimoya.fold_2.log deleted file mode 100644 index d871d72b6a86344368c95ea5ec3d0ac41fbd09c1..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2893 35.6659939289093 4.064669370651245 271.37158203125 0.6489654183387756 352.2815246582031 0.165078803896904 0.55736524 2.5702805519104004 True -1 5786 31.97356390953064 0.8182594776153564 234.31903076171875 0.49273326992988586 339.1141052246094 0.20906732976436615 0.6354944 0.7535583972930908 True -2 8679 31.932196855545044 0.5514538288116455 280.72552490234375 0.4545411467552185 335.7099914550781 0.21778543293476105 0.648941 0.42103031277656555 True -3 11572 31.878835201263428 0.5251340866088867 280.2210693359375 0.4078013300895691 334.2657775878906 0.22035250067710876 0.66433257 0.3984786868095398 True -4 14465 31.86341381072998 0.526057243347168 277.21533203125 0.26874637603759766 332.260986328125 0.22697840631008148 0.67536074 0.3859163522720337 True -5 17358 31.80784034729004 0.5143139362335205 276.673828125 0.6439100503921509 331.384033203125 0.22985300421714783 0.6815488 0.3981354534626007 True -6 20251 31.836137533187866 1.7153081893920898 268.1614685058594 0.6129258275032043 330.798828125 0.2315414845943451 0.6894431 0.40338191390037537 True -7 23144 31.807921409606934 1.0933239459991455 257.3426513671875 0.33963966369628906 330.31201171875 0.2340642362833023 0.695695 0.3902921676635742 True -8 26037 31.868328094482422 1.4312314987182617 288.003662109375 0.4468332827091217 329.8779602050781 0.23521478474140167 0.6986808 0.37366658449172974 True -9 28930 31.91130828857422 19.559242010116577 308.25531005859375 0.5110628604888916 329.5220947265625 0.23640474677085876 0.70205724 0.371777206659317 True -10 31823 31.97000479698181 0.6153583526611328 316.35064697265625 0.5031603574752808 328.6759948730469 0.23964370787143707 0.7083885 0.3633635640144348 True -11 34716 31.9000084400177 0.5253701210021973 230.61660766601562 0.39072680473327637 328.0602111816406 0.24238324165344238 0.71571296 0.3419228792190552 True -12 37609 31.904213190078735 0.5268890857696533 241.10067749023438 0.43572837114334106 328.0065612792969 0.2417668253183365 0.721191 0.3139346241950989 True -13 40502 31.902411937713623 0.5285265445709229 310.47198486328125 0.3461364209651947 327.2845764160156 0.24438787996768951 0.7281227 0.29780200123786926 True -14 43395 31.908830642700195 0.5212819576263428 265.2353515625 0.22347332537174225 326.8506164550781 0.24636442959308624 0.7349338 0.2881462872028351 True -15 46288 31.883196592330933 0.7605180740356445 208.1532745361328 0.41312670707702637 326.3033142089844 0.24826565384864807 0.74183136 0.27244633436203003 True -16 49181 31.877948760986328 0.5381827354431152 313.60284423828125 0.21839889883995056 326.562744140625 0.24654363095760345 0.74375886 0.27189183235168457 True -17 52074 31.859670639038086 0.5402519702911377 255.28717041015625 0.35842546820640564 326.4288330078125 0.24710489809513092 0.74556226 0.2682968080043793 True -18 54967 31.865503549575806 0.5197792053222656 293.6844482421875 0.19975140690803528 326.05902099609375 0.2489011287689209 0.7452549 0.2682487666606903 False -19 57860 31.86381983757019 0.5084528923034668 234.2803955078125 0.3503694236278534 326.4662780761719 0.24679258465766907 0.7447086 0.2732590138912201 False diff --git a/ENCSR813CKU/cherimoya.fold_2.performance.tsv b/ENCSR813CKU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 66134528776564710af3534aedda1c04bbbadc17..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.4288330078125 0.5024282336235046 0.24710489809513092 0.07141982764005661 0.7455622553825378 0.6854978799819946 0.2682968080043793 \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_3.evaluate.json b/ENCSR813CKU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0135a77bf4eaebe6be14f8c01887024176d9126b..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF546SNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_3.fit.json b/ENCSR813CKU/cherimoya.fold_3.fit.json deleted file mode 100644 index c1b0dd53914179c7b118d4105405019429f3f933..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF546SNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_3.log b/ENCSR813CKU/cherimoya.fold_3.log deleted file mode 100644 index ae79a2a1f596d986546c2c7d641e8ab32853415c..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2775 34.7337646484375 3.6912379264831543 288.58831787109375 0.5795080661773682 367.0733337402344 0.15594804286956787 0.5501978 3.4066100120544434 True -1 5550 30.67076086997986 0.5914325714111328 235.516845703125 0.5147979259490967 354.76531982421875 0.20085987448692322 0.6386023 0.7225417494773865 True -2 8325 30.679802417755127 0.5952801704406738 278.01080322265625 0.3448413610458374 350.2139587402344 0.21375629305839539 0.66383916 0.4445112943649292 True -3 11100 30.54036283493042 0.6012253761291504 287.91412353515625 0.5185620188713074 347.8162536621094 0.21960358321666718 0.6699617 0.3636319935321808 True -4 13875 30.546637773513794 0.5769670009613037 284.89886474609375 0.4121810495853424 346.6273498535156 0.22374215722084045 0.6744415 0.4126461148262024 True -5 16650 30.571072816848755 0.5775854587554932 275.62835693359375 0.4292229413986206 346.50762939453125 0.22337041795253754 0.6774296 0.4749526381492615 True -6 19425 30.512192249298096 0.5708274841308594 245.32188415527344 0.42569202184677124 345.28948974609375 0.22809840738773346 0.67768997 0.43384984135627747 True -7 22200 30.576204538345337 0.5784587860107422 299.4383544921875 0.40236711502075195 344.7428283691406 0.23041200637817383 0.68431985 0.4356144070625305 True -8 24975 30.55168604850769 0.5725104808807373 263.1341552734375 0.5429965853691101 344.8646545410156 0.2294178307056427 0.6901022 0.4378451704978943 True -9 27750 30.53224802017212 0.5780346393585205 304.2952575683594 0.44180935621261597 344.1988220214844 0.23154528439044952 0.69867355 0.41958096623420715 True -10 30525 30.55941414833069 1.0417454242706299 295.09771728515625 0.323936402797699 343.8027648925781 0.23417343199253082 0.7021492 0.42160943150520325 True -11 33300 30.645301580429077 1.250633716583252 287.55609130859375 0.3873579502105713 343.3274230957031 0.23508578538894653 0.7099815 0.40803155303001404 True -12 36075 30.63251495361328 1.8280932903289795 237.73582458496094 0.43025290966033936 342.61541748046875 0.23803801834583282 0.71293366 0.38598164916038513 True -13 38850 30.62547492980957 1.569648265838623 297.49102783203125 0.37308019399642944 342.3590087890625 0.23861101269721985 0.7237849 0.34842026233673096 True -14 41625 30.612940549850464 1.8498880863189697 279.60260009765625 0.5010743737220764 341.8929443359375 0.2399258017539978 0.73174816 0.3413347899913788 True -15 44400 30.555134534835815 1.142869472503662 268.19500732421875 0.3219691216945648 341.4004821777344 0.24116338789463043 0.7375918 0.3118998110294342 True -16 47175 30.52998113632202 1.2628843784332275 299.4967346191406 0.32492050528526306 340.92572021484375 0.24336594343185425 0.74513996 0.29762759804725647 True -17 49950 30.73964548110962 1.6586871147155762 249.5377197265625 0.2658425569534302 341.3212890625 0.24130962789058685 0.74822944 0.28967034816741943 True -18 52725 30.591214418411255 1.227815866470337 254.51669311523438 0.14753708243370056 340.94915771484375 0.24187685549259186 0.7490275 0.28620919585227966 True -19 55500 30.972126483917236 27.36977458000183 284.0492858886719 0.3107369542121887 341.3324279785156 0.24130307137966156 0.7471862 0.2830272316932678 False diff --git a/ENCSR813CKU/cherimoya.fold_3.performance.tsv b/ENCSR813CKU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 61becef7e0d3b4ae2e447f2f9f73b9a500ea9214..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -340.94915771484375 0.501370906829834 0.24187685549259186 0.07665155082941055 0.7490274906158447 0.6940208077430725 0.28620919585227966 \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_4.evaluate.json b/ENCSR813CKU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 830ab564eccab58d9499bcf575dd0e3c4124396c..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF546SNO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_4.fit.json b/ENCSR813CKU/cherimoya.fold_4.fit.json deleted file mode 100644 index 68ca7f22a74be87c3b6b331f06d62fdf9c34cd2d..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF546SNO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR813CKU/cherimoya.fold_4.log b/ENCSR813CKU/cherimoya.fold_4.log deleted file mode 100644 index d374e03894a7fd77c0310092091d0421111e9661..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2898 35.80929183959961 4.054818630218506 266.4215393066406 0.5597144961357117 346.03485107421875 0.15851469337940216 0.54912376 2.4889211654663086 True -1 5796 32.04284071922302 0.652961015701294 272.8269958496094 0.40903544425964355 335.3806457519531 0.19952821731567383 0.62891996 0.6452922224998474 True -2 8694 31.99268937110901 0.6250433921813965 266.5158996582031 0.4335189461708069 331.6400146484375 0.20925302803516388 0.6406143 0.3846074342727661 True -3 11592 31.93212628364563 0.6011078357696533 253.98362731933594 0.4980299174785614 329.6824645996094 0.21496351063251495 0.6509269 0.3692219853401184 True -4 14490 31.893845081329346 0.590142011642456 269.0879821777344 0.3440423011779785 328.8871154785156 0.21720275282859802 0.65949553 0.3774491846561432 True -5 17388 31.93519163131714 0.581587553024292 252.90338134765625 0.48979100584983826 328.3872985839844 0.21798162162303925 0.6687507 0.33764809370040894 True -6 20286 31.917523622512817 0.5964171886444092 268.8789978027344 0.3052266240119934 327.6444396972656 0.2212161123752594 0.67175514 0.35080021619796753 True -7 23184 31.926369428634644 0.5993928909301758 258.5934143066406 0.4107154905796051 327.4334411621094 0.22163692116737366 0.6763362 0.3483242690563202 True -8 26082 31.974910259246826 0.5969531536102295 307.7379455566406 0.5254343748092651 326.6139831542969 0.224763885140419 0.68358546 0.3539891839027405 True -9 28980 31.948376417160034 0.5995728969573975 256.67608642578125 0.3523211181163788 326.1617431640625 0.227057546377182 0.68709534 0.3384312689304352 True -10 31878 31.93047285079956 0.6009163856506348 253.1514434814453 0.34581756591796875 325.9462585449219 0.2280336618423462 0.69231766 0.32582682371139526 True -11 34776 31.953723907470703 0.5959577560424805 317.35821533203125 0.3809416592121124 325.67437744140625 0.22876910865306854 0.7005759 0.3294353783130646 True -12 37674 31.943279504776 0.5985932350158691 264.98809814453125 0.3830896019935608 324.8118896484375 0.23200826346874237 0.70573974 0.32678815722465515 True -13 40572 31.917399883270264 0.5975728034973145 271.7894287109375 0.41595524549484253 324.685791015625 0.2325267642736435 0.7147464 0.31215012073516846 True -14 43470 31.961602210998535 0.60050368309021 246.58175659179688 0.23797908425331116 324.32269287109375 0.2341989278793335 0.7213563 0.29551881551742554 True -15 46368 32.46003270149231 0.6007466316223145 252.94940185546875 0.4358524680137634 324.3357238769531 0.2336740791797638 0.72746265 0.28908663988113403 True -16 49266 31.954378366470337 0.5866029262542725 250.59524536132812 0.3409959673881531 324.0316162109375 0.23537752032279968 0.7317959 0.27317890524864197 True -17 52164 31.923759698867798 0.5847878456115723 299.906982421875 0.19087710976600647 323.7120056152344 0.23551508784294128 0.7346495 0.2641483545303345 True -18 55062 31.91177248954773 0.5968825817108154 270.06658935546875 0.2813417315483093 323.9106750488281 0.23571664094924927 0.734081 0.26232877373695374 False -19 57960 31.981101036071777 0.5982096195220947 251.1903076171875 0.2857635021209717 323.9802551269531 0.2345440685749054 0.73415875 0.26353296637535095 False diff --git a/ENCSR813CKU/cherimoya.fold_4.performance.tsv b/ENCSR813CKU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 974c4514ce5572ef561cec6fa8270b9c4f75c9b5..0000000000000000000000000000000000000000 --- a/ENCSR813CKU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -323.7120056152344 0.5076577067375183 0.23551508784294128 0.06767642498016357 0.7346494793891907 0.6744322776794434 0.2641483545303345 \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_0.evaluate.json b/ENCSR814DYF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d5e8183ff427926d4bc16bbbb9f9ccfa3f7c3168..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299IWW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_0.fit.json b/ENCSR814DYF/cherimoya.fold_0.fit.json deleted file mode 100644 index 0aced29bb43b7c14ba9e88653b4672c10ec919f7..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF299IWW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_0.log b/ENCSR814DYF/cherimoya.fold_0.log deleted file mode 100644 index 8690bae268c04472b64f8adaee847a11e91d6366..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 34.97180247306824 3.5621228218078613 486.818115234375 0.4508818984031677 721.6982421875 0.2705751061439514 0.71178156 5.133391857147217 True -1 5490 30.10956859588623 0.5980446338653564 546.1150512695312 0.3405587673187256 654.1753540039062 0.3574453294277191 0.76692563 1.5762338638305664 True -2 8235 30.104008436203003 2.8175668716430664 531.6546020507812 0.38652127981185913 642.8141479492188 0.3698253333568573 0.77351344 0.5610106587409973 True -3 10980 30.127211570739746 0.5806307792663574 589.251220703125 0.47159063816070557 637.4335327148438 0.3752790689468384 0.781681 0.6604567766189575 True -4 13725 32.74720907211304 6.823228120803833 481.57403564453125 0.3279581367969513 636.1768188476562 0.3767671287059784 0.784024 0.44011589884757996 True -5 16470 29.495164155960083 4.180705308914185 462.98260498046875 0.40246185660362244 633.4308471679688 0.38106250762939453 0.7855197 0.4114537239074707 True -6 19215 29.52596116065979 0.5846285820007324 487.955810546875 0.47961142659187317 631.4004516601562 0.38458600640296936 0.7860633 0.3736959993839264 True -7 21960 29.617400646209717 0.5758569240570068 647.283935546875 0.33448201417922974 627.4630737304688 0.3906795084476471 0.78952444 0.3567785322666168 True -8 24705 29.50049090385437 0.5719609260559082 518.5213012695312 0.3824212849140167 627.0719604492188 0.38903892040252686 0.7942553 0.3416858911514282 True -9 27450 29.616406440734863 0.604581356048584 479.3235168457031 0.3066949248313904 624.2359619140625 0.39358484745025635 0.79575855 0.3287985920906067 True -10 30195 29.827841997146606 0.592064619064331 516.5942993164062 0.3679924011230469 622.4737548828125 0.39547574520111084 0.8047085 0.2937081754207611 True -11 32940 29.46473264694214 2.859257698059082 495.7279052734375 0.34424519538879395 619.2525024414062 0.40007245540618896 0.8162666 0.2852175235748291 True -12 35685 29.532973289489746 0.571984052658081 514.8844604492188 0.32852235436439514 617.2421264648438 0.4020099639892578 0.82103366 0.272899329662323 True -13 38430 29.542179107666016 0.5720546245574951 543.8795166015625 0.19579917192459106 616.77783203125 0.40181830525398254 0.82978445 0.26598677039146423 True -14 41175 29.50115656852722 0.5721979141235352 535.2606201171875 0.30208778381347656 614.9110717773438 0.40439024567604065 0.8344628 0.2466639131307602 True -15 43920 29.480363607406616 0.5693278312683105 524.7257080078125 0.2024191915988922 614.337890625 0.40523794293403625 0.84180784 0.24456815421581268 True -16 46665 29.52050757408142 0.5628345012664795 515.7484741210938 0.32415124773979187 612.7613525390625 0.40755531191825867 0.844328 0.23917551338672638 True -17 49410 29.532771587371826 0.5700552463531494 470.97222900390625 0.21794383227825165 613.6940307617188 0.40547022223472595 0.8444507 0.2379605919122696 True -18 52155 29.456793308258057 0.5646500587463379 459.12884521484375 0.19057613611221313 613.6622924804688 0.405999094247818 0.84566337 0.2378925383090973 True -19 54900 32.00070095062256 0.566429615020752 449.8740539550781 0.2288881540298462 613.391845703125 0.4068138897418976 0.8433793 0.23939798772335052 False diff --git a/ENCSR814DYF/cherimoya.fold_0.performance.tsv b/ENCSR814DYF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9584f80e07f94107e1c2d09058d8a1150e630f25..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -613.6622924804688 0.3790759742259979 0.405999094247818 0.16427554190158844 0.8456633687019348 0.803413987159729 0.2378925383090973 \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_1.evaluate.json b/ENCSR814DYF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5f63811e5c37ef30be85d344d4f28d09eb4607fa..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299IWW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_1.fit.json b/ENCSR814DYF/cherimoya.fold_1.fit.json deleted file mode 100644 index 3a3fa0ba4d9fbff150bfc2d0a1abcf34f4e2e3ec..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF299IWW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_1.log b/ENCSR814DYF/cherimoya.fold_1.log deleted file mode 100644 index 78a2c24e167f7441c7bf7ac558b3c754f99a6808..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2707 35.63763189315796 26.890496492385864 529.92724609375 0.5248454213142395 814.9017944335938 0.26883506774902344 0.7125814 5.1081013679504395 True -1 5414 31.46967101097107 0.7484951019287109 480.2141418457031 0.5852528214454651 727.9141845703125 0.36241409182548523 0.77464026 1.3714946508407593 True -2 8121 30.91143488883972 40.397924184799194 595.995361328125 0.5837165713310242 712.6328735351562 0.3778780996799469 0.7871706 0.7735887765884399 True -3 10828 29.830699682235718 0.7073843479156494 533.2535400390625 0.41851237416267395 707.2354736328125 0.38273143768310547 0.7920317 0.6621310114860535 True -4 13535 29.759658575057983 0.7046358585357666 452.60540771484375 0.3941591680049896 701.3695678710938 0.38960397243499756 0.79594654 0.4316946268081665 True -5 16242 29.86040472984314 0.695725679397583 516.34423828125 0.537067711353302 698.9698486328125 0.3923148214817047 0.80023676 0.38945895433425903 True -6 18949 34.45791673660278 10.447652339935303 490.6256103515625 0.4288650453090668 696.5234375 0.39421579241752625 0.80642354 0.4082564115524292 True -7 21656 29.711637258529663 1.5413753986358643 715.572021484375 0.3049260377883911 691.8051147460938 0.3992045819759369 0.81305945 0.3710165023803711 True -8 24363 29.733349323272705 2.9238882064819336 496.9429626464844 0.3381860852241516 689.0892333984375 0.40280869603157043 0.8200882 0.321379154920578 True -9 27070 29.771855354309082 1.3576033115386963 477.7453308105469 0.2042677402496338 684.4843139648438 0.40866535902023315 0.8269705 0.3139333128929138 True -10 29777 29.758403062820435 0.9624323844909668 513.637939453125 0.2407514452934265 682.705078125 0.41081154346466064 0.8313054 0.29977765679359436 True -11 32484 29.927273988723755 1.32224702835083 454.7073974609375 0.2746405601501465 681.6396484375 0.4110252261161804 0.8351978 0.2924787104129791 True -12 35191 29.9128577709198 0.7110793590545654 584.3488159179688 0.4437427520751953 677.8130493164062 0.4156726896762848 0.84071416 0.29020851850509644 True -13 37898 30.094435453414917 0.7226958274841309 590.7703857421875 0.3660380244255066 675.6688842773438 0.4178204834461212 0.8451839 0.27392813563346863 True -14 40605 29.87369179725647 0.7258663177490234 467.8838195800781 0.38112565875053406 673.59423828125 0.41985806822776794 0.8508649 0.2615126371383667 True -15 43312 29.987818717956543 0.7055613994598389 465.33941650390625 0.18119150400161743 671.2605590820312 0.42242130637168884 0.8561119 0.2508147656917572 True -16 46019 29.98725962638855 0.7123837471008301 497.75323486328125 0.28854405879974365 671.8099975585938 0.4214465618133545 0.8608336 0.24879717826843262 True -17 48726 29.93395709991455 2.2533206939697266 460.77001953125 0.24239398539066315 671.4269409179688 0.42167147994041443 0.86125284 0.2481764554977417 True -18 51433 29.905785083770752 0.7027533054351807 516.9960327148438 0.16720934212207794 671.1419677734375 0.4226547181606293 0.8611363 0.2486819177865982 False -19 54140 29.874008655548096 0.7055234909057617 460.13641357421875 0.18144112825393677 672.487060546875 0.42027589678764343 0.8611431 0.24856935441493988 False diff --git a/ENCSR814DYF/cherimoya.fold_1.performance.tsv b/ENCSR814DYF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1f3a545abf6e792fcb159780ae41fa0e1b3da351..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -671.4269409179688 0.36628568172454834 0.4216715097427368 0.17723196744918823 0.8612528443336487 0.833254337310791 0.2481764554977417 \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_2.evaluate.json b/ENCSR814DYF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 55dce3e0dcf8aee9c7e3d852bf54166255c7f546..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299IWW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_2.fit.json b/ENCSR814DYF/cherimoya.fold_2.fit.json deleted file mode 100644 index 2464527a4883e8c9959b7a5349d7a11f4db1a192..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF299IWW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_2.log b/ENCSR814DYF/cherimoya.fold_2.log deleted file mode 100644 index 8afbfe70b34e48e07a797526d5ac9d568f6348d3..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2861 43.183327436447144 4.342326879501343 622.6835327148438 0.4700506925582886 741.0215454101562 0.27204570174217224 0.69770855 4.345139503479004 True -1 5722 31.47691583633423 2.8166584968566895 485.786376953125 0.5355287790298462 668.335693359375 0.359819233417511 0.7633626 1.623480200767517 True -2 8583 31.445197343826294 0.5616128444671631 620.78125 0.42491981387138367 655.46337890625 0.37144339084625244 0.77203584 0.6295418739318848 True -3 11444 31.155529022216797 0.5502398014068604 439.76422119140625 0.33397790789604187 648.7645263671875 0.379211962223053 0.7781229 0.5028364658355713 True -4 14305 30.82047963142395 0.5534729957580566 599.0435791015625 0.4020167589187622 648.1571655273438 0.3788507282733917 0.78070563 0.37630242109298706 True -5 17166 30.833457469940186 0.5425095558166504 519.9063720703125 0.3308406472206116 643.9388427734375 0.3852063715457916 0.7856263 0.3332788944244385 True -6 20027 30.811849355697632 0.5537877082824707 485.6820068359375 0.26489996910095215 642.4048461914062 0.38731929659843445 0.7872529 0.34677526354789734 True -7 22888 30.937848329544067 0.5554509162902832 458.53289794921875 0.4324624836444855 639.9747314453125 0.39085280895233154 0.79180026 0.3252449035644531 True -8 25749 31.78777050971985 35.77218747138977 518.0728759765625 0.4197421371936798 637.0827026367188 0.394848495721817 0.7984791 0.3225485682487488 True -9 28610 31.993385553359985 0.960421085357666 474.9254150390625 0.3586890697479248 634.3861083984375 0.39863717555999756 0.8011083 0.3038850426673889 True -10 31471 31.3265163898468 0.5478293895721436 429.1136474609375 0.3454227149486542 633.1160888671875 0.39987611770629883 0.8076479 0.30248796939849854 True -11 34332 30.867350101470947 0.5570864677429199 437.1802673339844 0.397606760263443 630.6957397460938 0.402614563703537 0.8129629 0.2912800908088684 True -12 37193 31.03743624687195 0.5618290901184082 525.4881591796875 0.38512206077575684 628.12451171875 0.4065493643283844 0.8168964 0.27732574939727783 True -13 40054 30.93569588661194 0.5551106929779053 508.06866455078125 0.33105653524398804 626.6439819335938 0.40737903118133545 0.8246542 0.260604590177536 True -14 42915 30.907620429992676 0.5566577911376953 520.3155517578125 0.25593405961990356 625.5226440429688 0.4082973599433899 0.8287119 0.25898540019989014 True -15 45776 32.267483949661255 40.92235708236694 472.6810607910156 0.22632306814193726 625.0594482421875 0.40868037939071655 0.8331701 0.2515408396720886 True -16 48637 31.35122060775757 0.6071805953979492 502.04815673828125 0.234541654586792 624.153564453125 0.40999430418014526 0.83570087 0.25032365322113037 True -17 51498 30.86946988105774 0.5582485198974609 540.193115234375 0.15383173525333405 624.4147338867188 0.4103904068470001 0.835758 0.25148043036460876 True -18 54359 30.812931537628174 1.6887693405151367 501.8946838378906 0.23919950425624847 623.798583984375 0.41128838062286377 0.83443046 0.2522790729999542 False -19 57220 30.84312605857849 0.5608766078948975 493.3482360839844 0.18228669464588165 624.5051879882812 0.40965965390205383 0.83408374 0.2537524700164795 False diff --git a/ENCSR814DYF/cherimoya.fold_2.performance.tsv b/ENCSR814DYF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2e98dbee0bf519f1d1f74087daacad6ef24cd73e..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -624.4147338867188 0.3757156431674957 0.4103904366493225 0.1652941107749939 0.8357579708099365 0.7976898550987244 0.25148043036460876 \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_3.evaluate.json b/ENCSR814DYF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f528e64e7c5d9e7da0ad337aeb0d11cdefca04a0..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299IWW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_3.fit.json b/ENCSR814DYF/cherimoya.fold_3.fit.json deleted file mode 100644 index b778de0dda8bed85a445e296c94aded2110a75ee..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF299IWW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_3.log b/ENCSR814DYF/cherimoya.fold_3.log deleted file mode 100644 index 52444c52f4193ded0623342319aa57f18aa9883b..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 36.31003165245056 6.021461009979248 515.4013671875 0.44112151861190796 713.5228271484375 0.2802634537220001 0.71681356 4.5858473777771 True -1 5524 30.31753897666931 0.5467488765716553 511.86474609375 0.45368659496307373 651.700439453125 0.3532455265522003 0.7828416 1.2087289094924927 True -2 8286 30.313461542129517 0.5268421173095703 518.1881103515625 0.49100199341773987 636.0390014648438 0.36908963322639465 0.79169726 0.6903692483901978 True -3 11048 30.306137800216675 0.5301294326782227 499.02081298828125 0.2975616455078125 629.072509765625 0.3769463002681732 0.7956817 0.7644166946411133 True -4 13810 30.398258209228516 0.5248677730560303 461.7803955078125 0.45741742849349976 624.1943359375 0.3830648362636566 0.7989205 0.43087202310562134 True -5 16572 30.351011276245117 0.5302908420562744 537.115966796875 0.39407265186309814 621.684814453125 0.3858841061592102 0.80247474 0.3984465003013611 True -6 19334 30.43838858604431 0.5181255340576172 552.6979370117188 0.391838401556015 618.8724975585938 0.3902883529663086 0.8081529 0.333428293466568 True -7 22096 30.304299354553223 0.5308828353881836 504.4990539550781 0.4276176691055298 616.8260498046875 0.393070250749588 0.81251174 0.34453773498535156 True -8 24858 30.47274661064148 27.642236948013306 613.2877197265625 0.35739266872406006 616.0614013671875 0.39277538657188416 0.8104442 0.321699321269989 False -9 27620 30.6696994304657 0.5404677391052246 517.7589111328125 0.3916621208190918 613.7123413085938 0.3968955874443054 0.81704766 0.3123592436313629 True -10 30382 30.315551042556763 0.5260920524597168 506.6488037109375 0.2905751168727875 611.146728515625 0.4000691771507263 0.82135487 0.31189513206481934 True -11 33144 30.32397985458374 0.5374674797058105 532.6889038085938 0.3382650911808014 609.415283203125 0.40189316868782043 0.8284674 0.2980960011482239 True -12 35906 29.937450408935547 0.5340332984924316 532.2567138671875 0.3404865562915802 608.5465087890625 0.40256157517433167 0.8313326 0.2824183702468872 True -13 38668 29.714123010635376 0.5235390663146973 494.83953857421875 0.29271578788757324 607.9995727539062 0.40219375491142273 0.8367006 0.276260644197464 True -14 41430 29.744300603866577 0.535651445388794 463.92230224609375 0.23578447103500366 605.2911987304688 0.40568840503692627 0.8419826 0.2632398307323456 True -15 44192 29.691362857818604 0.5186574459075928 453.077392578125 0.2582612931728363 603.5835571289062 0.40809640288352966 0.8482241 0.25765854120254517 True -16 46954 29.684858083724976 0.5250706672668457 451.3878173828125 0.19147330522537231 602.961181640625 0.4088400602340698 0.84945685 0.25232064723968506 True -17 49716 29.7789888381958 0.5186269283294678 494.71661376953125 0.2601255774497986 603.1591796875 0.40786099433898926 0.8534173 0.25175830721855164 True -18 52478 29.925710439682007 0.5972959995269775 466.484375 0.22583338618278503 604.046630859375 0.4067775011062622 0.85273546 0.25202035903930664 False -19 55240 29.805742740631104 1.7099711894989014 508.09149169921875 0.22275188565254211 603.5971069335938 0.4080926775932312 0.8534592 0.2524780035018921 True diff --git a/ENCSR814DYF/cherimoya.fold_3.performance.tsv b/ENCSR814DYF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4a490f779c744825c701b13eaeecc9782f956366..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -603.5971069335938 0.3797042667865753 0.4080926477909088 0.16522501409053802 0.8534591794013977 0.8088225722312927 0.2524780035018921 \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_4.evaluate.json b/ENCSR814DYF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 363a54b844bf7f11324be50233e049dbf64bb731..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF299IWW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_4.fit.json b/ENCSR814DYF/cherimoya.fold_4.fit.json deleted file mode 100644 index 6e10672fcc7cc5051fda560a116643c78efa29cb..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF299IWW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814DYF/cherimoya.fold_4.log b/ENCSR814DYF/cherimoya.fold_4.log deleted file mode 100644 index 28e357a16cc200cbc1f72787654fd693e091a360..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 36.938424587249756 5.132045030593872 568.657470703125 0.41200315952301025 670.2293701171875 0.2710220217704773 0.70530367 4.147481441497803 True -1 5664 31.212673902511597 0.6095418930053711 595.4216918945312 0.37774384021759033 610.99072265625 0.3498912453651428 0.76126224 1.3331109285354614 True -2 8496 31.168311834335327 0.6024594306945801 599.0272827148438 0.34847205877304077 602.5328369140625 0.35753345489501953 0.76991487 0.6099554300308228 True -3 11328 31.173365354537964 0.6032354831695557 406.64892578125 0.27141404151916504 595.3170776367188 0.3676135838031769 0.7759005 0.511711061000824 True -4 14160 31.148485898971558 0.5844829082489014 535.5841064453125 0.3966137170791626 592.060546875 0.37200257182121277 0.78306913 0.41594162583351135 True -5 16992 31.092760801315308 0.5894746780395508 553.274658203125 0.4722036123275757 589.4720458984375 0.3763290345668793 0.7882789 0.3373391628265381 True -6 19824 31.129029750823975 0.5810620784759521 592.80517578125 0.3660658001899719 587.616455078125 0.3774926960468292 0.7926533 0.3052249550819397 True -7 22656 31.152603149414062 1.063218116760254 485.86761474609375 0.3441401720046997 584.5355834960938 0.3818836212158203 0.8028408 0.3033539354801178 True -8 25488 31.109854221343994 0.5952308177947998 533.087646484375 0.30846619606018066 584.2055053710938 0.38113197684288025 0.8045393 0.2811083197593689 True -9 28320 31.21210527420044 0.5920596122741699 518.3380737304688 0.21991367638111115 582.4035034179688 0.3838629424571991 0.80682015 0.2831242084503174 True -10 31152 31.132656574249268 0.5886085033416748 532.418701171875 0.37154442071914673 580.8394165039062 0.38595864176750183 0.8149169 0.2640720009803772 True -11 33984 31.14357590675354 0.5923488140106201 488.2701416015625 0.24179355800151825 579.2089233398438 0.3875804841518402 0.818671 0.2604391276836395 True -12 36816 31.15690779685974 2.544863224029541 518.1705932617188 0.3897722363471985 577.7418212890625 0.38972243666648865 0.82629204 0.24967271089553833 True -13 39648 31.295385122299194 0.608361005783081 512.4482421875 0.210722878575325 575.67724609375 0.3921078145503998 0.830116 0.24341724812984467 True -14 42480 31.287203788757324 0.5857284069061279 507.6866455078125 0.2199416160583496 574.9317016601562 0.39400699734687805 0.8350909 0.236297145485878 True -15 45312 32.037490367889404 41.26206684112549 496.99761962890625 0.19387494027614594 575.2039184570312 0.39337968826293945 0.8414536 0.22824931144714355 True -16 48144 37.15583562850952 36.063863039016724 524.23828125 0.3447009027004242 574.5844116210938 0.3941787779331207 0.84373313 0.22640861570835114 True -17 50976 32.529454469680786 0.5995242595672607 498.40301513671875 0.16652905941009521 574.1316528320312 0.3953920602798462 0.84479153 0.22390200197696686 True -18 53808 31.2443950176239 1.2386000156402588 423.2200012207031 0.23490963876247406 574.7443237304688 0.39436835050582886 0.84585667 0.22555357217788696 True -19 56640 30.608842134475708 6.056981325149536 572.5345458984375 0.18075475096702576 574.350830078125 0.3956676423549652 0.84643626 0.22567979991436005 True diff --git a/ENCSR814DYF/cherimoya.fold_4.performance.tsv b/ENCSR814DYF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b8a0ff3fa924e06221b944601897abcc279abfbf..0000000000000000000000000000000000000000 --- a/ENCSR814DYF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -574.350830078125 0.38889750838279724 0.3956676423549652 0.1557070016860962 0.8464362621307373 0.7984988689422607 0.22567979991436005 \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_0.evaluate.json b/ENCSR814KRX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 321470a62540ac18d79e8e56ad851c598314f653..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF436KBP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_0.fit.json b/ENCSR814KRX/cherimoya.fold_0.fit.json deleted file mode 100644 index 86f24d2e5a1c9fb814e28b42deb278e2c8daedfc..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF436KBP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_0.log b/ENCSR814KRX/cherimoya.fold_0.log deleted file mode 100644 index 134e64c36bf33e7b390f7281afdbc686406b542f..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 34.87926530838013 2.952462673187256 1715.2783203125 0.8763731122016907 3211.794189453125 0.32114535570144653 0.48638523 15.352718353271484 True -1 5472 30.413772106170654 0.5699198246002197 1868.891845703125 0.9374774694442749 2566.661376953125 0.4909575879573822 0.51595 4.0305070877075195 True -2 8208 30.94434690475464 6.148518800735474 1879.837890625 1.2014667987823486 2506.4716796875 0.505623996257782 0.5113937 2.4146804809570312 False -3 10944 30.438159942626953 0.6010785102844238 2108.982666015625 0.9087052345275879 2472.865966796875 0.5116605758666992 0.533554 2.210334539413452 True -4 13680 30.579489707946777 0.5774009227752686 1892.38037109375 1.1478962898254395 2441.8466796875 0.5221503973007202 0.54096586 1.9289721250534058 True -5 16416 30.519846200942993 0.5662987232208252 2096.21142578125 0.894059419631958 2420.001220703125 0.5288681983947754 0.54082376 1.7852829694747925 False -6 19152 30.68401789665222 0.5747838020324707 2039.6668701171875 0.9915534257888794 2409.828369140625 0.5316834449768066 0.5480633 1.698127031326294 True -7 21888 30.456066370010376 0.5715389251708984 1643.322021484375 0.9046555757522583 2393.271484375 0.536805272102356 0.5505377 1.5931740999221802 True -8 24624 30.641369342803955 19.512333869934082 1776.12744140625 0.7038074731826782 2376.899169921875 0.5415388345718384 0.55373883 1.5092854499816895 True -9 27360 30.443443059921265 12.736263751983643 1879.00244140625 0.9240537881851196 2369.557373046875 0.5428311824798584 0.5507363 1.4241621494293213 False -10 30096 30.797218084335327 0.5747132301330566 3168.536865234375 0.8764360547065735 2347.478271484375 0.547671914100647 0.55601066 1.2600072622299194 True -11 32832 30.415842056274414 0.5681779384613037 1674.3560791015625 0.6581703424453735 2345.941650390625 0.54755699634552 0.55872995 1.2108917236328125 True -12 35568 30.464560508728027 0.5714566707611084 1579.9241943359375 0.7373185157775879 2325.199462890625 0.5518797039985657 0.5709279 1.1095210313796997 True -13 38304 30.468200206756592 0.5654442310333252 1640.362060546875 0.7174550890922546 2310.394775390625 0.5567507147789001 0.57945794 1.0373870134353638 True -14 41040 30.39110517501831 0.570711612701416 2953.0888671875 0.9993219375610352 2307.34423828125 0.5564640760421753 0.5939913 0.9611713290214539 True -15 43776 30.420470476150513 0.560516357421875 1834.7852783203125 0.7404308915138245 2298.35595703125 0.5576045513153076 0.60617614 0.9103990793228149 True -16 46512 30.484145164489746 0.5704448223114014 1744.470947265625 0.5994017720222473 2292.754638671875 0.5597752928733826 0.61807585 0.8426207304000854 True -17 49248 30.47010898590088 0.5616724491119385 1658.385986328125 0.4858057200908661 2285.0625 0.5613664984703064 0.62580115 0.810724675655365 True -18 51984 30.48141646385193 0.5720045566558838 1751.07373046875 0.7229163646697998 2291.391845703125 0.5588404536247253 0.6300991 0.7859140634536743 True -19 54720 30.44408941268921 0.569756031036377 1524.3021240234375 0.610914945602417 2291.283935546875 0.559104859828949 0.62945235 0.7814326882362366 False diff --git a/ENCSR814KRX/cherimoya.fold_0.performance.tsv b/ENCSR814KRX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c0547d8e2df9b6b5981247c712b060e0c0e8fbbf..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2291.391845703125 0.20772044360637665 0.5588403940200806 0.38485071063041687 0.6300991177558899 0.6087021231651306 0.7859140634536743 \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_1.evaluate.json b/ENCSR814KRX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3c1759d0360b46d781767551b67577cde1b18960..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF436KBP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_1.fit.json b/ENCSR814KRX/cherimoya.fold_1.fit.json deleted file mode 100644 index 04732b538ce294c326d46b1359a5d69574bcb63c..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF436KBP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_1.log b/ENCSR814KRX/cherimoya.fold_1.log deleted file mode 100644 index 60b31952f899114d58d1b187f6d743076b14329e..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 34.33685302734375 3.7157275676727295 1826.248291015625 1.052727222442627 3331.181396484375 0.33341196179389954 0.55869126 15.261322975158691 True -1 5466 30.418280124664307 0.7447071075439453 1890.24169921875 1.0260365009307861 2699.9638671875 0.5059616565704346 0.57171714 4.943542003631592 True -2 8199 30.484975337982178 2.057126045227051 1739.353271484375 1.278340458869934 2633.05712890625 0.519525945186615 0.6085834 2.6976699829101562 True -3 10932 30.492100715637207 1.3425211906433105 1821.5513916015625 1.119341254234314 2573.007568359375 0.5335378646850586 0.62114245 2.041508913040161 True -4 13665 30.422980546951294 0.7478103637695312 1599.9468994140625 0.899117112159729 2558.70556640625 0.5385993719100952 0.62284863 1.6795790195465088 True -5 16398 30.406924724578857 0.7354662418365479 1889.479248046875 1.1351473331451416 2531.1318359375 0.5462788343429565 0.6227989 1.6498240232467651 False -6 19131 30.375312089920044 0.7339189052581787 1577.05126953125 1.439164638519287 2526.852783203125 0.5471075177192688 0.62115127 1.4996849298477173 False -7 21864 30.470617055892944 0.7254719734191895 1694.34765625 0.7140759229660034 2508.961669921875 0.5508378148078918 0.6230281 1.299753189086914 True -8 24597 30.37895679473877 0.7243199348449707 1909.37939453125 0.6977202892303467 2494.548828125 0.5555098652839661 0.62740433 1.2355035543441772 True -9 27330 30.378265380859375 0.7252044677734375 1617.12353515625 0.7467511892318726 2469.109375 0.5607057809829712 0.63889736 1.0627294778823853 True -10 30063 30.364325761795044 0.7234673500061035 1935.083251953125 0.6159024834632874 2460.162353515625 0.5626038908958435 0.6463542 0.9483083486557007 True -11 32796 30.39302659034729 0.726215124130249 1850.2335205078125 0.6932637691497803 2441.094970703125 0.5661236643791199 0.6539038 0.8920144438743591 True -12 35529 30.366594314575195 0.7452681064605713 1734.520751953125 0.4759490489959717 2430.16259765625 0.5683773756027222 0.66746926 0.8099732995033264 True -13 38262 30.419755458831787 0.74745774269104 1675.87744140625 0.7508429288864136 2415.71875 0.571819543838501 0.6804793 0.7486366629600525 True -14 40995 30.390751600265503 0.7378823757171631 1652.1800537109375 0.490488201379776 2396.935791015625 0.5763571858406067 0.69218606 0.6836655139923096 True -15 43728 30.43236517906189 1.677659273147583 1806.735107421875 0.7785808444023132 2389.5048828125 0.5771933197975159 0.7078883 0.639177680015564 True -16 46461 30.451534748077393 1.7409017086029053 1714.342041015625 0.6273040175437927 2385.749755859375 0.577970027923584 0.7150841 0.6040740609169006 True -17 49194 30.473166704177856 0.8739058971405029 1835.051025390625 0.8315262794494629 2386.550048828125 0.5775539875030518 0.7234354 0.5740980505943298 True -18 51927 30.452478408813477 2.446352243423462 1706.476318359375 0.34761327505111694 2387.8984375 0.5773077607154846 0.72533464 0.562260091304779 True -19 54660 30.466498851776123 2.0795905590057373 1599.76318359375 0.4082295596599579 2390.2353515625 0.5766186118125916 0.7234893 0.5649616122245789 False diff --git a/ENCSR814KRX/cherimoya.fold_1.performance.tsv b/ENCSR814KRX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 40ee86cfcf2cc1f0cbbc8df67bdd0e298c62a576..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2387.8984375 0.19791683554649353 0.5773078203201294 0.4076923131942749 0.725334644317627 0.7196081280708313 0.562260091304779 \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_2.evaluate.json b/ENCSR814KRX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4abae4e866d13b140e6e6c28f228ab5842016777..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF436KBP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_2.fit.json b/ENCSR814KRX/cherimoya.fold_2.fit.json deleted file mode 100644 index 53fa921014c82502e8b1f20c13e99da5be0d38b6..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF436KBP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_2.log b/ENCSR814KRX/cherimoya.fold_2.log deleted file mode 100644 index ad23976c84f20091334636c777c89525eedefb82..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2831 35.11101675033569 3.5699145793914795 2129.990234375 1.0659810304641724 3106.106689453125 0.33499637246131897 0.5322672 13.294702529907227 True -1 5662 31.416234731674194 0.5913426876068115 2001.3856201171875 1.385225534439087 2528.00537109375 0.4920039772987366 0.5829455 3.983880043029785 True -2 8493 31.46416163444519 1.2359390258789062 1931.525634765625 0.8205139636993408 2481.11767578125 0.5029140710830688 0.5942388 2.0115246772766113 True -3 11324 31.52163052558899 0.6012547016143799 2035.23291015625 0.5956889390945435 2437.093994140625 0.5138329863548279 0.60250777 1.6459012031555176 True -4 14155 31.467517852783203 0.586496114730835 1945.1826171875 0.7896116375923157 2410.125732421875 0.5205920338630676 0.6157835 1.495796799659729 True -5 16986 31.54898953437805 0.5869596004486084 1636.80615234375 0.7119750380516052 2380.968505859375 0.5313699841499329 0.6161797 1.5885961055755615 True -6 19817 31.472362756729126 0.5844581127166748 1460.188720703125 0.6815786361694336 2373.62109375 0.5336067080497742 0.6060639 1.602346658706665 False -7 22648 31.513370752334595 0.5811572074890137 1584.510986328125 1.03920578956604 2363.131103515625 0.5363740921020508 0.61260015 1.4424246549606323 False -8 25479 31.625061988830566 0.5861859321594238 1882.080078125 1.2583539485931396 2350.24267578125 0.539880096912384 0.61519104 1.314292550086975 False -9 28310 31.630491733551025 0.5901455879211426 1724.30029296875 0.7130369544029236 2332.184814453125 0.544281542301178 0.61686444 1.2314543724060059 True -10 31141 31.599045991897583 0.5873513221740723 1640.02197265625 0.6089199781417847 2316.359130859375 0.5483329892158508 0.61902404 1.1675795316696167 True -11 33972 31.648388385772705 1.7533206939697266 1707.347900390625 0.9127275943756104 2301.381591796875 0.5516542792320251 0.62541705 1.0574733018875122 True -12 36803 31.719910144805908 0.6208651065826416 1703.822265625 0.6888300776481628 2288.555908203125 0.553266704082489 0.64012486 0.9126836061477661 True -13 39634 31.55015277862549 0.5852334499359131 1646.0322265625 0.8248944282531738 2277.540771484375 0.5561112761497498 0.65260834 0.8615309000015259 True -14 42465 31.493025302886963 0.5847117900848389 1406.282958984375 0.6615792512893677 2269.021484375 0.5573535561561584 0.6653105 0.7726827263832092 True -15 45296 31.517420291900635 0.583078145980835 2045.885986328125 0.9768822193145752 2255.009765625 0.5614960789680481 0.68158793 0.7091668844223022 True -16 48127 31.47154712677002 0.5862669944763184 1737.288818359375 0.5544500350952148 2250.74609375 0.5621444582939148 0.6930085 0.6597021818161011 True -17 50958 31.53481960296631 1.27586030960083 1986.1912841796875 0.7527107000350952 2254.942626953125 0.5611228942871094 0.70024693 0.6220656037330627 True -18 53789 31.55182671546936 0.5888352394104004 1645.4305419921875 0.5737978219985962 2250.239013671875 0.5626814961433411 0.70141596 0.6074331402778625 True -19 56620 31.511789798736572 0.5886929035186768 1714.8233642578125 0.4017805755138397 2253.832763671875 0.5609710812568665 0.70342284 0.5988348126411438 True diff --git a/ENCSR814KRX/cherimoya.fold_2.performance.tsv b/ENCSR814KRX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9f1d3165f548f493a8982f5e5d6d1fcdd2ba5afc..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2253.832763671875 0.21020740270614624 0.5609710812568665 0.38678687810897827 0.7034228444099426 0.6859450936317444 0.5988348126411438 \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_3.evaluate.json b/ENCSR814KRX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c2872474340001c33e22da2a5ec6e838140546ef..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF436KBP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_3.fit.json b/ENCSR814KRX/cherimoya.fold_3.fit.json deleted file mode 100644 index 21bd6aab75b9b40c2ef022f69ddb08897e1ce1b3..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF436KBP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_3.log b/ENCSR814KRX/cherimoya.fold_3.log deleted file mode 100644 index 19f36fc749050a5520500da4282e654deee1145c..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2844 35.398998737335205 3.83634090423584 1965.6427001953125 0.9164080619812012 2960.263671875 0.3320018947124481 0.56671834 12.845316886901855 True -1 5688 31.611879110336304 0.5659301280975342 2038.730224609375 0.8308379650115967 2460.845703125 0.4918256103992462 0.5861236 3.425363779067993 True -2 8532 31.763082265853882 0.5546350479125977 1498.197021484375 1.010306477546692 2417.08203125 0.5068163871765137 0.5752333 1.9924564361572266 False -3 11376 31.669037103652954 0.5464708805084229 1815.5655517578125 0.8349872827529907 2372.274169921875 0.5202866196632385 0.59254795 1.3844685554504395 True -4 14220 31.705750465393066 0.5508334636688232 2192.826416015625 0.8568695187568665 2356.708251953125 0.5237089991569519 0.5973333 1.2571910619735718 True -5 17064 31.684963703155518 0.5508782863616943 1911.2579345703125 0.7418774366378784 2341.60107421875 0.5294289588928223 0.60654193 1.198570728302002 True -6 19908 31.599461793899536 0.544933557510376 1989.02587890625 0.5985451936721802 2323.560302734375 0.533683180809021 0.6143327 1.092111587524414 True -7 22752 31.577144384384155 0.5517323017120361 1997.99169921875 0.9893903136253357 2322.0732421875 0.5344672799110413 0.6071661 1.0855281352996826 False -8 25596 31.581631183624268 0.5438508987426758 1810.6065673828125 0.7928230166435242 2309.051025390625 0.5381492972373962 0.6096639 1.0318185091018677 False -9 28440 31.96664810180664 0.5471444129943848 1739.5762939453125 0.8616805672645569 2298.416259765625 0.542398989200592 0.60889107 0.9530099630355835 False -10 31284 31.668185710906982 0.5522704124450684 2058.120849609375 0.8994711637496948 2281.0712890625 0.547697901725769 0.6220503 0.8538072109222412 True -11 34128 31.660632133483887 0.553370475769043 1688.4283447265625 0.6287293434143066 2278.093994140625 0.5479723811149597 0.6308638 0.7888239622116089 True -12 36972 31.950114965438843 19.363404989242554 1803.140625 0.9095613360404968 2267.564697265625 0.5509571433067322 0.6439269 0.7258948087692261 True -13 39816 31.694343328475952 1.1592402458190918 1552.75927734375 0.5279749035835266 2242.184326171875 0.5587283968925476 0.65841764 0.6679779291152954 True -14 42660 31.66583561897278 0.5669848918914795 1682.6597900390625 0.7512813806533813 2234.021240234375 0.5601639151573181 0.68080556 0.6091368198394775 True -15 45504 31.704559564590454 0.902313232421875 1671.054931640625 0.9350858926773071 2226.120849609375 0.5610198378562927 0.6999096 0.5627195239067078 True -16 48348 31.732494831085205 0.5733211040496826 1782.00341796875 0.8125369548797607 2215.423583984375 0.5647856593132019 0.71487916 0.527427613735199 True -17 51192 31.729936122894287 2.105726957321167 1682.15234375 0.4260854721069336 2223.644287109375 0.5602078437805176 0.72294605 0.5067344307899475 True -18 54036 31.683714866638184 0.5876610279083252 1619.168701171875 0.5529794692993164 2223.156005859375 0.5612004995346069 0.7225663 0.5030933022499084 False -19 56880 31.75498366355896 0.5642812252044678 1610.1966552734375 0.506721019744873 2225.582763671875 0.5597249269485474 0.72624475 0.4999115765094757 True diff --git a/ENCSR814KRX/cherimoya.fold_3.performance.tsv b/ENCSR814KRX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 194321d1d72c7b62cafe804a564ad1b81bc50f70..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2225.582763671875 0.2088775485754013 0.5597249865531921 0.38693690299987793 0.7262447476387024 0.710302472114563 0.4999115765094757 \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_4.evaluate.json b/ENCSR814KRX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b3f802172f93df22cf4ee5a1f0fa5bf370339e9d..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF436KBP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_4.fit.json b/ENCSR814KRX/cherimoya.fold_4.fit.json deleted file mode 100644 index 0c9202b7d857ced66a528ba84b240b1e612f7be6..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF436KBP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR814KRX/cherimoya.fold_4.log b/ENCSR814KRX/cherimoya.fold_4.log deleted file mode 100644 index 841ffe714094ee95b8a32189b0aae4094cb3ba51..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 35.212289333343506 3.4955363273620605 2212.42919921875 1.112388014793396 2835.12109375 0.32809072732925415 0.5447264 11.043355941772461 True -1 5612 31.16289782524109 0.5483016967773438 1781.717529296875 1.0601199865341187 2338.620361328125 0.4938342869281769 0.5425393 4.409984111785889 False -2 8418 31.18009305000305 0.5288326740264893 2014.364501953125 1.2965245246887207 2287.5419921875 0.5077786445617676 0.5783905 2.0831823348999023 True -3 11224 31.21447467803955 0.5118556022644043 1744.720458984375 1.2089922428131104 2245.53369140625 0.5198529362678528 0.5976017 1.5104154348373413 True -4 14030 31.254344701766968 0.5352809429168701 1987.142333984375 1.190622329711914 2231.5703125 0.5236388444900513 0.6019397 1.4532525539398193 True -5 16836 31.233264207839966 0.5242559909820557 1695.0006103515625 0.6782594919204712 2216.832763671875 0.5295794010162354 0.6053875 1.3050726652145386 True -6 19642 31.23202347755432 0.5313165187835693 1735.1654052734375 0.682731032371521 2201.76171875 0.5351366996765137 0.60319656 1.2541652917861938 False -7 22448 31.242605686187744 0.5158824920654297 1542.8798828125 0.7880260944366455 2190.612548828125 0.5383281707763672 0.601338 1.2150111198425293 False -8 25254 31.273355722427368 0.5319561958312988 1985.717041015625 0.7579395771026611 2182.920166015625 0.5410471558570862 0.5982878 1.1767879724502563 False -9 28060 31.209381818771362 0.527235746383667 1756.304443359375 0.6637436151504517 2167.09765625 0.5447567105293274 0.6110926 0.9831312894821167 True -10 30866 31.199551343917847 0.5198638439178467 1919.573974609375 0.8018960356712341 2145.69140625 0.5536225438117981 0.6162977 0.9197303056716919 True -11 33672 31.56438136100769 0.5243005752563477 1961.68212890625 0.5829566717147827 2145.704345703125 0.5510689616203308 0.6259875 0.8137344717979431 True -12 36478 31.295330047607422 0.5268621444702148 1620.1324462890625 0.6033356189727783 2132.896240234375 0.5555866956710815 0.640236 0.7549415230751038 True -13 39284 31.29173755645752 0.5764074325561523 1824.0496826171875 0.9780876636505127 2117.706787109375 0.5597347617149353 0.6487887 0.6935601830482483 True -14 42090 31.218360662460327 1.204500675201416 1696.330078125 0.7029542922973633 2115.525146484375 0.5589278340339661 0.6676074 0.6388309001922607 True -15 44896 31.242369174957275 0.5215768814086914 1801.7998046875 0.4242171049118042 2113.66455078125 0.558149516582489 0.6859926 0.5895951986312866 True -16 47702 31.216431140899658 0.5217254161834717 1748.6884765625 0.5545695424079895 2102.814453125 0.5624638795852661 0.70153576 0.5436212420463562 True -17 50508 31.23600697517395 0.5222713947296143 1574.8321533203125 0.6003307104110718 2099.973388671875 0.5630110502243042 0.71148413 0.5221635699272156 True -18 53314 31.245471239089966 0.524864673614502 1780.061767578125 0.4980333745479584 2098.850341796875 0.5631760954856873 0.71555644 0.5106460452079773 True -19 56120 31.198508501052856 0.514685869216919 1689.4189453125 0.38816308975219727 2100.46875 0.5626911520957947 0.71650416 0.511483907699585 True diff --git a/ENCSR814KRX/cherimoya.fold_4.performance.tsv b/ENCSR814KRX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b8baa998f149ef6fc1d8abfddf9953a9ade81181..0000000000000000000000000000000000000000 --- a/ENCSR814KRX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2100.46875 0.21427024900913239 0.5626912713050842 0.3774963915348053 0.7165041565895081 0.6943707466125488 0.511483907699585 \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_0.evaluate.json b/ENCSR815DWW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b0f1863d79fe2b179492decc48d5f60da454c4d1..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF314YZW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_0.fit.json b/ENCSR815DWW/cherimoya.fold_0.fit.json deleted file mode 100644 index 959e199988d1cb5b3da67c2ba39d89db32896da7..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF314YZW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_0.log b/ENCSR815DWW/cherimoya.fold_0.log deleted file mode 100644 index c1d4a88682c3b487a3694ecbe46bf48b1b229bbb..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2239 29.1939857006073 3.551893472671509 334.8620300292969 0.9937158226966858 501.5440673828125 0.14301110804080963 0.59947616 8.401347160339355 True -1 4478 24.685723543167114 0.46754908561706543 243.1736297607422 0.9597611427307129 425.3016052246094 0.19798871874809265 0.74390686 3.3977982997894287 True -2 6717 24.62794852256775 0.5086841583251953 313.1941223144531 0.6309478282928467 410.2997741699219 0.20346365869045258 0.7499427 2.7332193851470947 True -3 8956 24.6265869140625 12.095324277877808 388.752685546875 0.5611069202423096 397.9059753417969 0.21212543547153473 0.7668793 1.5592353343963623 True -4 11195 24.575027227401733 0.4617123603820801 224.20851135253906 0.6762146949768066 389.688720703125 0.2190367877483368 0.7825452 1.3062504529953003 True -5 13434 24.184346914291382 0.44864821434020996 400.3163146972656 0.5771811008453369 383.88616943359375 0.2238292098045349 0.79167384 1.1849174499511719 True -6 15673 24.061036109924316 0.4554572105407715 320.8226318359375 0.921533465385437 378.8490295410156 0.228653222322464 0.79772824 1.076826572418213 True -7 17912 24.115639209747314 0.4457578659057617 302.27227783203125 0.5841684341430664 375.51641845703125 0.2305867075920105 0.8063514 0.9469297528266907 True -8 20151 24.0904324054718 0.5122425556182861 423.8626708984375 1.0527325868606567 372.2237548828125 0.23373211920261383 0.81440836 0.8379883766174316 True -9 22390 24.37262535095215 0.4483072757720947 284.3585510253906 0.6704661250114441 370.1283264160156 0.23574964702129364 0.82096344 0.756829023361206 True -10 24629 24.109015703201294 15.152496814727783 481.9955139160156 0.9042662382125854 366.3270263671875 0.23988084495067596 0.8309428 0.665738582611084 True -11 26868 24.820435523986816 2.808610677719116 251.88592529296875 0.7483216524124146 364.27642822265625 0.24091723561286926 0.8341179 0.6284358501434326 True -12 29107 24.098180532455444 1.4502248764038086 340.9211120605469 0.7138506174087524 362.515380859375 0.24191848933696747 0.8404679 0.5748734474182129 True -13 31346 24.176881074905396 0.453244686126709 241.47190856933594 0.5197439193725586 361.2356262207031 0.2441001534461975 0.84568834 0.561403214931488 True -14 33585 24.09412407875061 0.4523482322692871 267.544921875 0.4046056270599365 357.9598388671875 0.2465582638978958 0.8523679 0.5199680328369141 True -15 35824 24.139324426651 0.4524991512298584 313.8201599121094 0.28371769189834595 356.9002380371094 0.24675340950489044 0.8548629 0.49983957409858704 True -16 38063 24.107399463653564 13.53860354423523 267.896728515625 0.3298015594482422 356.8210754394531 0.24673184752464294 0.85766107 0.4830476939678192 True -17 40302 24.65510320663452 0.45383429527282715 251.9840850830078 0.37158823013305664 357.2303771972656 0.24693110585212708 0.8600184 0.47799232602119446 True -18 42541 24.254071712493896 1.4020869731903076 295.0346984863281 0.6303156614303589 356.6019592285156 0.24794040620326996 0.8588581 0.47816091775894165 False -19 44780 24.119208574295044 0.45012998580932617 199.39157104492188 0.32424187660217285 356.3670654296875 0.2485426813364029 0.8572415 0.47870397567749023 False diff --git a/ENCSR815DWW/cherimoya.fold_0.performance.tsv b/ENCSR815DWW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7dfdf8b87e6905f33abb3ee2b13bca13df531af8..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -357.2303771972656 0.5140410661697388 0.24693110585212708 0.08220776170492172 0.8600183725357056 0.7958619594573975 0.47799232602119446 \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_1.evaluate.json b/ENCSR815DWW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f7f6f67bcd97df3ffb58c566ca435565b10ff98e..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF314YZW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_1.fit.json b/ENCSR815DWW/cherimoya.fold_1.fit.json deleted file mode 100644 index e07dd850e6b538f15b1b1315055090c1284bc392..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF314YZW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_1.log b/ENCSR815DWW/cherimoya.fold_1.log deleted file mode 100644 index b8e16145196761ef37f9990ef2dbccc8b0ac44d4..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2175 28.499566555023193 3.7871501445770264 313.72607421875 0.766861617565155 674.1133422851562 0.15776604413986206 0.5729689 9.579856872558594 True -1 4350 23.91385006904602 0.6591649055480957 303.91937255859375 0.6380186080932617 566.62939453125 0.22417515516281128 0.7395313 5.222386837005615 True -2 6525 23.916245698928833 2.053234815597534 354.1784362792969 1.0464167594909668 543.042724609375 0.23693740367889404 0.76695627 3.523681640625 True -3 8700 23.88957667350769 2.219860792160034 281.32000732421875 0.9861880540847778 520.2120361328125 0.2465813308954239 0.78785866 1.9511131048202515 True -4 10875 23.88018822669983 0.6274411678314209 297.43084716796875 0.7441697716712952 506.9493713378906 0.25491347908973694 0.8052299 1.4019038677215576 True -5 13050 23.845623016357422 0.623260498046875 396.2232971191406 1.0308051109313965 502.1789855957031 0.2566438913345337 0.8091086 1.3215283155441284 True -6 15225 23.883219718933105 0.6237781047821045 381.9874267578125 0.40480828285217285 491.4680480957031 0.2635461688041687 0.8190826 1.1885578632354736 True -7 17400 23.880431652069092 0.6162478923797607 413.3470458984375 1.067544937133789 486.361083984375 0.2674480676651001 0.82819694 1.0082788467407227 True -8 19575 23.858668088912964 0.6194555759429932 210.3069305419922 0.3656652271747589 484.1656188964844 0.26851552724838257 0.83498895 0.9198600053787231 True -9 21750 23.86499547958374 0.6174137592315674 337.1922607421875 0.41652175784111023 479.83056640625 0.2719227373600006 0.8394862 0.8790390491485596 True -10 23925 23.850625038146973 0.620063066482544 465.066650390625 0.5827445983886719 478.1383056640625 0.27412641048431396 0.84393495 0.8259968757629395 True -11 26100 23.653119802474976 0.609464168548584 242.41567993164062 0.5403187870979309 473.2220458984375 0.27714285254478455 0.8530203 0.7679258584976196 True -12 28275 23.41336488723755 0.6066606044769287 319.59039306640625 0.4843348562717438 471.95623779296875 0.2772820293903351 0.85901284 0.7113009691238403 True -13 30450 23.438835382461548 0.6090209484100342 311.2361755371094 0.4243724048137665 468.541748046875 0.28002166748046875 0.865424 0.6605607867240906 True -14 32625 23.400372982025146 0.6149351596832275 325.0760803222656 0.4565676152706146 465.1811218261719 0.28135624527931213 0.87118036 0.6216662526130676 True -15 34800 23.37695837020874 0.6134707927703857 334.4224853515625 0.47326239943504333 463.0820617675781 0.2823709547519684 0.87459236 0.5823609232902527 True -16 36975 23.40561842918396 0.6119101047515869 271.6348571777344 0.569077730178833 459.5809631347656 0.28370895981788635 0.87776965 0.5652807354927063 True -17 39150 23.40262770652771 0.6105034351348877 443.437255859375 0.4076438546180725 462.95587158203125 0.2798777222633362 0.8788874 0.5479545593261719 True -18 41325 23.37356424331665 0.6170675754547119 222.23309326171875 0.40781378746032715 462.52838134765625 0.2812248468399048 0.8792527 0.5409557223320007 True -19 43500 23.366779327392578 0.6192810535430908 285.37591552734375 0.4615957736968994 463.19903564453125 0.28044620156288147 0.8790214 0.5400694012641907 False diff --git a/ENCSR815DWW/cherimoya.fold_1.performance.tsv b/ENCSR815DWW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2716f30b2eaa39944621a825b42c98173f17b33c..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -462.52838134765625 0.4854058623313904 0.2812248468399048 0.10766062140464783 0.8792526721954346 0.8349028825759888 0.5409557223320007 \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_2.evaluate.json b/ENCSR815DWW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 01e1cb549401f7ab7bdeb8387abc8926e7529e11..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF314YZW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_2.fit.json b/ENCSR815DWW/cherimoya.fold_2.fit.json deleted file mode 100644 index 5641834d0cbfda20005f9edc8905372f5e0fb874..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF314YZW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_2.log b/ENCSR815DWW/cherimoya.fold_2.log deleted file mode 100644 index f3beaecd425d42c4629fa35f8f052edf4434778b..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2339 30.314533233642578 4.299604892730713 309.2249755859375 1.3352829217910767 537.843994140625 0.1477288007736206 0.57559544 8.000956535339355 True -1 4678 26.38517165184021 0.5030965805053711 337.9737243652344 0.8708516359329224 446.25506591796875 0.20867407321929932 0.7506503 4.118828773498535 True -2 7017 25.730623960494995 1.143183708190918 327.11688232421875 0.7639092206954956 432.02496337890625 0.21556128561496735 0.74748063 2.6221907138824463 False -3 9356 27.294015884399414 25.655487298965454 438.603271484375 0.7127963304519653 421.7243347167969 0.22177645564079285 0.76835394 1.5874370336532593 True -4 11695 25.820523262023926 0.5376660823822021 406.94635009765625 0.806419849395752 415.5224304199219 0.22503136098384857 0.7839691 1.3149604797363281 True -5 14034 25.721184730529785 0.48845481872558594 333.7165222167969 0.964299201965332 408.1405334472656 0.23119917511940002 0.79374343 1.2094380855560303 True -6 16373 25.719541549682617 23.03495216369629 255.43316650390625 0.6018187999725342 406.6009826660156 0.23150186240673065 0.79600424 1.1647288799285889 True -7 18712 26.6448872089386 0.4871814250946045 376.384521484375 0.6305965185165405 400.0879821777344 0.23653343319892883 0.8100154 0.9912397861480713 True -8 21051 25.905060291290283 0.48578882217407227 362.0793151855469 0.7543132305145264 396.54156494140625 0.23727187514305115 0.8174616 0.8054789304733276 True -9 23390 25.687270641326904 1.0329792499542236 450.1673889160156 0.9170096516609192 394.8945007324219 0.23934100568294525 0.82199365 0.8049274682998657 True -10 25729 25.737757205963135 1.275846242904663 206.5926971435547 0.38491636514663696 391.44122314453125 0.2424011379480362 0.8259952 0.7468071579933167 True -11 28068 25.767452239990234 1.0542032718658447 279.709228515625 0.7109229564666748 388.4753723144531 0.2442813366651535 0.8362719 0.6203465461730957 True -12 30407 25.713186979293823 0.4790976047515869 264.6648254394531 0.599084198474884 386.8556823730469 0.24641835689544678 0.8457776 0.5954493880271912 True -13 32746 25.745563745498657 0.4801464080810547 310.9720458984375 0.8153594732284546 385.82373046875 0.24666783213615417 0.8497149 0.5484685897827148 True -14 35085 25.72777557373047 0.47507452964782715 269.52447509765625 0.35540640354156494 383.7761535644531 0.24737948179244995 0.85494673 0.520375669002533 True -15 37424 25.180094480514526 0.4713587760925293 380.760498046875 0.5130677819252014 381.6257019042969 0.25061166286468506 0.8576992 0.5022234320640564 True -16 39763 25.188927173614502 0.4758181571960449 222.17904663085938 0.429027795791626 380.1826171875 0.2509459853172302 0.86217093 0.4835282862186432 True -17 42102 25.15007209777832 0.4730255603790283 260.4433288574219 0.47080183029174805 381.473388671875 0.24894122779369354 0.86292255 0.48253995180130005 True -18 44441 25.191807508468628 0.4779634475708008 249.74551391601562 0.3926617503166199 381.28717041015625 0.24993707239627838 0.86343664 0.4849662184715271 True -19 46780 25.21203875541687 27.690871000289917 348.9389343261719 0.38001227378845215 381.3767395019531 0.25009724497795105 0.8625573 0.4882446825504303 False diff --git a/ENCSR815DWW/cherimoya.fold_2.performance.tsv b/ENCSR815DWW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 234d8d01ca43cf583f79ed21b6a7c055dc506920..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -381.28717041015625 0.5097426772117615 0.249937042593956 0.08932261914014816 0.8634366393089294 0.7953377366065979 0.4849662184715271 \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_3.evaluate.json b/ENCSR815DWW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1c8215e5dfd759e98e0462e0baffa4dd200f28c1..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF314YZW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_3.fit.json b/ENCSR815DWW/cherimoya.fold_3.fit.json deleted file mode 100644 index 7643d0c1ab1e6100eb2e66c59841d406dfc02c6f..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF314YZW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_3.log b/ENCSR815DWW/cherimoya.fold_3.log deleted file mode 100644 index a60c21ae40bd085cc8084dd484bdacca10f7f097..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2231 29.148721933364868 3.3795361518859863 413.53472900390625 1.1729893684387207 550.8588256835938 0.1576935201883316 0.5588536 9.161797523498535 True -1 4462 24.52433753013611 14.264363050460815 287.9825134277344 0.9821279644966125 470.1654357910156 0.21564790606498718 0.70329905 4.367480754852295 True -2 6693 25.264814376831055 0.4451029300689697 354.9503479003906 0.5694513320922852 456.75518798828125 0.22074423730373383 0.7116819 3.288182020187378 True -3 8924 24.54871392250061 0.44675469398498535 278.44903564453125 0.7856640219688416 439.07891845703125 0.23215565085411072 0.7487627 1.9528083801269531 True -4 11155 25.343027591705322 18.287819385528564 293.3128356933594 0.7621954679489136 428.3063659667969 0.23841938376426697 0.76617223 1.6473522186279297 True -5 13386 24.623482942581177 1.065868616104126 504.61505126953125 1.0354663133621216 424.0674743652344 0.2411937564611435 0.77396286 1.4530892372131348 True -6 15617 24.51469135284424 0.4427182674407959 306.0223388671875 0.7596454620361328 419.9610290527344 0.24351270496845245 0.7818366 1.342807412147522 True -7 17848 24.664849519729614 0.4413580894470215 322.2561950683594 0.5807406902313232 416.89910888671875 0.24578331410884857 0.7850224 1.1987495422363281 True -8 20079 24.629631757736206 0.44234442710876465 321.23651123046875 0.7957512140274048 412.2699890136719 0.25037407875061035 0.7972129 1.123059630393982 True -9 22310 24.531685829162598 0.44307374954223633 326.1907958984375 0.5627424120903015 412.1565856933594 0.25163811445236206 0.79199284 1.1347728967666626 False -10 24541 24.503791332244873 0.43413758277893066 316.40087890625 0.6245946288108826 408.28692626953125 0.2555851340293884 0.80259985 1.0024816989898682 True -11 26772 25.101641178131104 1.3966550827026367 266.14801025390625 0.285028874874115 406.971923828125 0.25570711493492126 0.81340784 0.9261115789413452 True -12 29003 24.531668424606323 5.928942680358887 313.0643310546875 0.6693071722984314 403.2005615234375 0.25893500447273254 0.822457 0.8630372881889343 True -13 31234 24.143894910812378 0.4424781799316406 417.2635803222656 0.5351442098617554 399.50823974609375 0.26089268922805786 0.8314846 0.7498487234115601 True -14 33465 24.038885354995728 0.43558311462402344 292.2532043457031 0.8280444145202637 396.23553466796875 0.2628317177295685 0.83819395 0.6936770081520081 True -15 35696 24.06715703010559 0.434584379196167 413.03497314453125 0.6471037864685059 394.089599609375 0.26368585228919983 0.84593433 0.6390040516853333 True -16 37927 24.004143476486206 0.44617152214050293 306.7508544921875 0.6675942540168762 393.57550048828125 0.2636817395687103 0.85169464 0.5899866223335266 True -17 40158 24.016167163848877 0.4304521083831787 197.7896728515625 0.3313269019126892 393.1148681640625 0.26403185725212097 0.8581297 0.5591560006141663 True -18 42389 24.039367198944092 21.696315050125122 362.4361572265625 0.3988746404647827 394.8561706542969 0.26211628317832947 0.8601067 0.547118067741394 True -19 44620 24.823776245117188 0.43987298011779785 258.6498107910156 0.4748523235321045 394.1739501953125 0.26304230093955994 0.85853076 0.5398522019386292 False diff --git a/ENCSR815DWW/cherimoya.fold_3.performance.tsv b/ENCSR815DWW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 265a8fdf60fa6e4954ed927d9ea5bfef0db8673a..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -394.8561706542969 0.5012264251708984 0.26211628317832947 0.09243713319301605 0.8601067066192627 0.805830717086792 0.547118067741394 \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_4.evaluate.json b/ENCSR815DWW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d4cd3d4528a9ed0aa3656eae6881681cc93a574e..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF314YZW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_4.fit.json b/ENCSR815DWW/cherimoya.fold_4.fit.json deleted file mode 100644 index 1ebbb49eb27aa3f0e45643b226a511fe0c65b526..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF314YZW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR815DWW/cherimoya.fold_4.log b/ENCSR815DWW/cherimoya.fold_4.log deleted file mode 100644 index fbb5a567cf3f2fb41b4ca078bc8cfed749326427..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2255 29.604915142059326 5.229213237762451 396.8394775390625 0.9838159084320068 461.6158752441406 0.14327672123908997 0.57244074 7.865819931030273 True -1 4510 24.838858366012573 0.4983079433441162 310.5029296875 0.9909607768058777 398.04669189453125 0.19426023960113525 0.7018765 3.779195547103882 True -2 6765 24.820146083831787 0.466228723526001 368.8517150878906 0.6459251642227173 383.2181701660156 0.20664632320404053 0.7146082 2.2712574005126953 True -3 9020 24.79229760169983 0.47339415550231934 272.5545654296875 0.6466846466064453 373.82177734375 0.20832371711730957 0.73870564 1.4486730098724365 True -4 11275 25.14668607711792 24.542041778564453 268.9664306640625 0.9824138879776001 368.11474609375 0.21211986243724823 0.7512983 1.4203033447265625 True -5 13530 24.7530415058136 0.4810001850128174 190.72967529296875 0.6710371971130371 362.9012451171875 0.21744340658187866 0.76335835 1.2176414728164673 True -6 15785 24.8294575214386 0.470745325088501 359.19091796875 0.8205163478851318 359.0987548828125 0.2189210206270218 0.7710881 1.1672585010528564 True -7 18040 24.821793794631958 0.46624279022216797 426.16766357421875 0.815740704536438 357.5780029296875 0.21936775743961334 0.78185135 0.984387993812561 True -8 20295 24.961745262145996 25.03278923034668 281.9036865234375 1.2569289207458496 354.3922119140625 0.22190460562705994 0.7848691 0.9180794358253479 True -9 22550 24.91941738128662 0.4671638011932373 275.470458984375 0.8511136770248413 351.35369873046875 0.22395572066307068 0.7938232 0.804456889629364 True -10 24805 24.573877334594727 0.46496033668518066 296.1108703613281 0.6759120225906372 349.2714538574219 0.22541958093643188 0.80456376 0.7176753282546997 True -11 27060 24.315417051315308 0.4699127674102783 282.9813232421875 0.5651198625564575 346.2706298828125 0.22847245633602142 0.8119491 0.6526376008987427 True -12 29315 24.363487482070923 0.4660007953643799 232.3118896484375 0.870542585849762 343.6735534667969 0.23162348568439484 0.81889117 0.6169013977050781 True -13 31570 24.305952072143555 0.46769046783447266 334.19891357421875 0.6250982284545898 341.8238830566406 0.2326783984899521 0.82709277 0.5722433924674988 True -14 33825 24.30788493156433 0.4619326591491699 326.48138427734375 0.2813403606414795 341.357421875 0.23146231472492218 0.8343675 0.5392649173736572 True -15 36080 24.412944555282593 0.4675157070159912 344.266845703125 0.57527095079422 341.0033874511719 0.2329803854227066 0.84038293 0.5112690329551697 True -16 38335 24.3412766456604 0.46020030975341797 277.2452087402344 0.4964298605918884 338.8794250488281 0.23475471138954163 0.8452537 0.48987358808517456 True -17 40590 24.29365062713623 0.46002840995788574 331.2142639160156 0.47225087881088257 340.4380187988281 0.23197893798351288 0.847802 0.48003071546554565 True -18 42845 24.29550814628601 0.456026554107666 376.84619140625 0.5371803045272827 341.14581298828125 0.23080043494701385 0.84762084 0.4753477871417999 False -19 45100 24.32449507713318 0.4638972282409668 234.3190460205078 0.2800259292125702 340.5036315917969 0.23234206438064575 0.8493324 0.4760752320289612 True diff --git a/ENCSR815DWW/cherimoya.fold_4.performance.tsv b/ENCSR815DWW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7d903a7d6cde72dfcb1ab8c43ad1bec3e906690a..0000000000000000000000000000000000000000 --- a/ENCSR815DWW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -340.5036315917969 0.5233711004257202 0.23234209418296814 0.07724453508853912 0.8493323922157288 0.775795578956604 0.4760752320289612 \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_0.evaluate.json b/ENCSR818JGZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6106a27df465d4e3b37e8b020f2a81f5bac5efcc..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF819WUF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_0.fit.json b/ENCSR818JGZ/cherimoya.fold_0.fit.json deleted file mode 100644 index f6b44747822f2c718de4f39116324f1e802f383f..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF819WUF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_0.log b/ENCSR818JGZ/cherimoya.fold_0.log deleted file mode 100644 index 26f3649ac36d0e7c2d68f0d18a8d4354cc9e0c5d..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 35.09387922286987 3.503135919570923 1039.4501953125 0.41999876499176025 1423.86962890625 0.2874169647693634 0.7626308 9.685934066772461 True -1 5494 30.16747522354126 0.7908828258514404 1058.810302734375 0.37472158670425415 1292.5908203125 0.37308430671691895 0.832878 1.1736150979995728 True -2 8241 30.148884057998657 1.9158108234405518 1182.9931640625 0.3122183680534363 1274.6639404296875 0.38169926404953003 0.83696014 0.47244736552238464 True -3 10988 30.200167179107666 0.5751693248748779 1073.8896484375 0.5018909573554993 1257.2301025390625 0.39176949858665466 0.8407031 0.39858460426330566 True -4 13735 30.25078845024109 0.6367511749267578 1237.5048828125 0.29955390095710754 1251.3486328125 0.3964264988899231 0.84506226 0.38296428322792053 True -5 16482 29.58953022956848 0.5845203399658203 1032.418701171875 0.4896988272666931 1245.8565673828125 0.3999519646167755 0.8478869 0.44517630338668823 True -6 19229 29.619471788406372 0.5911529064178467 1051.696044921875 0.2226419746875763 1243.1221923828125 0.39949584007263184 0.8524567 0.3512403666973114 True -7 21976 29.58384680747986 0.5946886539459229 1033.7861328125 0.25306379795074463 1235.6773681640625 0.4056166708469391 0.85747993 0.2785909175872803 True -8 24723 29.594406843185425 0.5652861595153809 1087.24462890625 0.24131879210472107 1233.436767578125 0.40555253624916077 0.8601524 0.2649747133255005 True -9 27470 29.548938274383545 0.5744831562042236 870.16064453125 0.41237393021583557 1229.4005126953125 0.40702638030052185 0.8614207 0.2742295563220978 True -10 30217 29.59439730644226 0.5762441158294678 989.3417358398438 0.3645187020301819 1223.3062744140625 0.41233065724372864 0.8636409 0.2427923083305359 True -11 32964 29.64264678955078 0.5929145812988281 976.94482421875 0.24225419759750366 1221.26171875 0.41131988167762756 0.86720514 0.23617319762706757 True -12 35711 29.64314913749695 8.418326377868652 1016.65771484375 0.16804352402687073 1214.877685546875 0.41610288619995117 0.8709482 0.22794844210147858 True -13 38458 29.735198259353638 1.4565355777740479 1027.2930908203125 0.25145503878593445 1210.61962890625 0.4173958897590637 0.87742776 0.21283812820911407 True -14 41205 29.669080018997192 1.413804054260254 1057.5343017578125 0.21032941341400146 1208.90576171875 0.41883084177970886 0.8828036 0.20350871980190277 True -15 43952 29.699772357940674 1.5576307773590088 994.2740478515625 0.22822979092597961 1206.7447509765625 0.4198835790157318 0.88703877 0.19320103526115417 True -16 46699 29.76028347015381 1.0603773593902588 1053.9466552734375 0.20346969366073608 1207.9755859375 0.41833391785621643 0.88955694 0.1874007284641266 True -17 49446 29.75702476501465 0.9471807479858398 978.6256713867188 0.13426870107650757 1203.15380859375 0.42318660020828247 0.89303875 0.18397271633148193 True -18 52193 29.750450372695923 0.6000087261199951 1057.4072265625 0.16106420755386353 1202.6605224609375 0.42320361733436584 0.89226675 0.18314112722873688 False -19 54940 29.63115620613098 0.5873916149139404 864.8413696289062 0.22895090281963348 1206.88134765625 0.4190869629383087 0.89307 0.18276911973953247 True diff --git a/ENCSR818JGZ/cherimoya.fold_0.performance.tsv b/ENCSR818JGZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a771f9df87398ed7d8c0ba213345178863368506..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1206.88134765625 0.30780431628227234 0.4190869629383087 0.2285001128911972 0.8930699825286865 0.8453484177589417 0.18276911973953247 \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_1.evaluate.json b/ENCSR818JGZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3e53bd2f6069c9611dcb11befe8b1e8c94ac795a..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF819WUF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_1.fit.json b/ENCSR818JGZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 3510cc07d75a2881c7aab59950c423be2852d78b..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF819WUF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_1.log b/ENCSR818JGZ/cherimoya.fold_1.log deleted file mode 100644 index 5edcae4d69f4d119e4b3b917fdd8f354b8a3e34a..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2689 34.15560173988342 3.9440391063690186 1071.576416015625 0.47876715660095215 1678.060791015625 0.2913057208061218 0.7539949 10.741989135742188 True -1 5378 29.60716700553894 2.7693347930908203 1130.7496337890625 0.30944716930389404 1493.0797119140625 0.3971053957939148 0.8297068 1.387985348701477 True -2 8067 29.595436573028564 0.781442403793335 1119.9306640625 0.4136037826538086 1468.923828125 0.4053066074848175 0.84177333 0.53594571352005 True -3 10756 29.531777143478394 0.7330219745635986 1058.9803466796875 0.35837289690971375 1449.5660400390625 0.41510021686553955 0.84803474 0.4295439124107361 True -4 13445 29.55412721633911 0.6964433193206787 987.157958984375 0.4428897500038147 1441.946533203125 0.4194853901863098 0.8508779 0.4303092062473297 True -5 16134 29.60633635520935 0.8166186809539795 1019.2169799804688 0.2630102038383484 1435.340576171875 0.4230008125305176 0.8540373 0.4115404188632965 True -6 18823 29.22552514076233 0.6890194416046143 1069.6900634765625 0.36033353209495544 1433.589599609375 0.4223431348800659 0.8595873 0.36834412813186646 True -7 21512 29.047083854675293 0.7387959957122803 1135.986328125 0.24899473786354065 1426.8795166015625 0.42646726965904236 0.86421126 0.3433513641357422 True -8 24201 29.04473567008972 0.7087311744689941 791.9619140625 0.31959033012390137 1421.04736328125 0.42907989025115967 0.86863345 0.297141432762146 True -9 26890 29.015069246292114 0.7057771682739258 1181.1162109375 0.47732922434806824 1416.8184814453125 0.43141964077949524 0.8697363 0.28504782915115356 True -10 29579 28.98930549621582 1.527022123336792 881.4794921875 0.2528918981552124 1411.6475830078125 0.4343867301940918 0.87063175 0.2930416762828827 True -11 32268 28.968971490859985 0.6868424415588379 882.3291015625 0.24990184605121613 1403.5133056640625 0.43737879395484924 0.87589973 0.270298570394516 True -12 34957 29.058584690093994 0.6980319023132324 949.0914916992188 0.23788601160049438 1400.7005615234375 0.43888312578201294 0.8797554 0.25849416851997375 True -13 37646 29.028119325637817 0.6960036754608154 916.3670043945312 0.18113982677459717 1396.721435546875 0.4400913417339325 0.88473564 0.23656553030014038 True -14 40335 29.025615692138672 0.698284387588501 1156.1077880859375 0.20693445205688477 1393.6124267578125 0.4414406716823578 0.8904865 0.21871672570705414 True -15 43024 29.02634572982788 0.7045652866363525 1107.991943359375 0.16294509172439575 1386.052978515625 0.4455115795135498 0.8963104 0.20983949303627014 True -16 45713 29.038965463638306 0.7186641693115234 950.1693725585938 0.17596633732318878 1383.116455078125 0.44610750675201416 0.8989043 0.2019832730293274 True -17 48402 29.09118342399597 0.7208819389343262 933.1802978515625 0.13093003630638123 1385.7767333984375 0.44403076171875 0.90075326 0.20157751441001892 True -18 51091 29.05289125442505 3.888838768005371 1091.541259765625 0.2581431567668915 1385.2623291015625 0.4448997974395752 0.90051323 0.1994745433330536 False -19 53780 28.95217490196228 0.7006771564483643 999.9943237304688 0.17419233918190002 1381.59716796875 0.4479198455810547 0.90075475 0.19966982305049896 True diff --git a/ENCSR818JGZ/cherimoya.fold_1.performance.tsv b/ENCSR818JGZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 16866e6969a73660e7b02677b4c16d3848bce74a..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1381.59716796875 0.2842797338962555 0.44791990518569946 0.26442310214042664 0.9007547497749329 0.872904896736145 0.19966982305049896 \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_2.evaluate.json b/ENCSR818JGZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 70074c06ec0dd86f501f8659acecf6f4ecaa4598..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF819WUF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_2.fit.json b/ENCSR818JGZ/cherimoya.fold_2.fit.json deleted file mode 100644 index ec849b52e40c9bc22d0560a510e931501f3d90b6..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF819WUF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_2.log b/ENCSR818JGZ/cherimoya.fold_2.log deleted file mode 100644 index 86f161499afcf8d610e855e2d3339af512c2a63a..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 36.235475301742554 13.860056638717651 1174.8154296875 0.4364413022994995 1517.806884765625 0.294624000787735 0.76286024 6.684291839599609 True -1 5770 31.22810983657837 1.6879491806030273 1062.903076171875 0.29168206453323364 1364.90869140625 0.3820980489253998 0.82905024 1.1630430221557617 True -2 8655 31.723093032836914 12.115651607513428 1007.1396484375 0.3575178384780884 1350.64892578125 0.3875352442264557 0.8368901 0.4523833394050598 True -3 11540 31.709081649780273 4.486385345458984 1077.3353271484375 0.3643033802509308 1336.706298828125 0.39669883251190186 0.83846676 0.4351046085357666 True -4 14425 31.762178897857666 0.5500235557556152 1093.587890625 0.3286163806915283 1330.473388671875 0.4008024334907532 0.84284693 0.41162705421447754 True -5 17310 31.72788095474243 0.5521378517150879 994.1531982421875 0.31094110012054443 1326.5947265625 0.4020098149776459 0.8471156 0.34927186369895935 True -6 20195 31.20458459854126 0.5507268905639648 1078.0927734375 0.45120182633399963 1322.1954345703125 0.4046799838542938 0.84566283 0.3216197192668915 False -7 23080 31.117313861846924 0.5365104675292969 1229.071533203125 0.3444386124610901 1319.4080810546875 0.4056546092033386 0.8450437 0.3112325370311737 False -8 25965 31.120667457580566 0.5480618476867676 1042.355224609375 0.2569243609905243 1310.6129150390625 0.4112987816333771 0.8495047 0.30837762355804443 True -9 28850 31.124633312225342 0.5490026473999023 1094.247314453125 0.29047828912734985 1305.5008544921875 0.4129718542098999 0.8518672 0.27979567646980286 True -10 31735 31.15227961540222 0.5451374053955078 947.5423583984375 0.2889779210090637 1296.584716796875 0.4172282814979553 0.855797 0.2709559500217438 True -11 34620 31.175523281097412 0.5518038272857666 1075.7239990234375 0.2158946692943573 1291.48291015625 0.41999074816703796 0.8597176 0.2772972285747528 True -12 37505 31.123963594436646 0.5456926822662354 1024.22412109375 0.18136367201805115 1286.1241455078125 0.4214562773704529 0.8668219 0.25933006405830383 True -13 40390 31.184169054031372 0.5556097030639648 1028.441162109375 0.20463743805885315 1281.864013671875 0.4246784448623657 0.8702019 0.24276238679885864 True -14 43275 31.125723600387573 0.5525362491607666 1037.39990234375 0.2458132803440094 1276.4200439453125 0.4269707202911377 0.87519133 0.23284737765789032 True -15 46160 31.140730142593384 0.5549437999725342 1059.4119873046875 0.2547316551208496 1273.8837890625 0.4278055429458618 0.8824053 0.22101353108882904 True -16 49045 31.123424768447876 10.48235034942627 937.083251953125 0.1373145580291748 1274.01806640625 0.4276025891304016 0.8832051 0.21411773562431335 True -17 51930 31.169417142868042 0.5576541423797607 969.192626953125 0.17181015014648438 1272.001708984375 0.42893412709236145 0.8855932 0.20974135398864746 True -18 54815 31.1221182346344 0.5510032176971436 1002.6221313476562 0.22572416067123413 1273.455810546875 0.4275323450565338 0.8864065 0.20691022276878357 True -19 57700 31.144777059555054 0.5294761657714844 1109.48828125 0.1765536218881607 1271.05126953125 0.43035686016082764 0.8859843 0.20740607380867004 False diff --git a/ENCSR818JGZ/cherimoya.fold_2.performance.tsv b/ENCSR818JGZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d431a964504c0fbeea3971fc4889ea6f50ed729d..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1273.455810546875 0.29974886775016785 0.4275323450565338 0.2440410554409027 0.8864064812660217 0.8487638235092163 0.20691022276878357 \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_3.evaluate.json b/ENCSR818JGZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c75fb0ece80743ec858b1c423506abda79962f5d..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF819WUF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_3.fit.json b/ENCSR818JGZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 1bfe06caa6a319c2026e3d809f099a1e61dd5b9d..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF819WUF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_3.log b/ENCSR818JGZ/cherimoya.fold_3.log deleted file mode 100644 index b98bf983d308b36f421b5117fe42e893ef4cb8ce..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.724937438964844 3.505993604660034 1040.57080078125 0.519686758518219 1434.4334716796875 0.28877803683280945 0.7588312 9.408326148986816 True -1 5498 30.96444797515869 0.8322892189025879 1139.5850830078125 0.25265219807624817 1302.9495849609375 0.3734719455242157 0.8256835 1.2102820873260498 True -2 8247 30.584105968475342 0.5446329116821289 1105.5947265625 0.5070077180862427 1286.8035888671875 0.3806188106536865 0.83289915 0.6029359102249146 True -3 10996 29.64880132675171 0.5547919273376465 938.905029296875 0.29270339012145996 1278.3204345703125 0.38622891902923584 0.8397119 0.5527163743972778 True -4 13745 29.664947271347046 0.5424764156341553 1011.4727172851562 0.3468954265117645 1272.2120361328125 0.39116835594177246 0.84348494 0.4270843267440796 True -5 16494 29.671214818954468 0.5406830310821533 1040.125732421875 0.25093138217926025 1266.12646484375 0.3949486017227173 0.84125704 0.43775373697280884 False -6 19243 29.672799587249756 0.556145429611206 1035.85888671875 0.3617435097694397 1261.1622314453125 0.3986709713935852 0.8420338 0.388085275888443 False -7 21992 29.666958808898926 0.5719907283782959 1049.05615234375 0.22104254364967346 1256.3836669921875 0.40298548340797424 0.8460415 0.3598468005657196 True -8 24741 29.6051664352417 0.7240476608276367 1058.6163330078125 0.24593153595924377 1252.766357421875 0.4050437808036804 0.8504773 0.31247347593307495 True -9 27490 29.595143795013428 0.5421140193939209 1175.0654296875 0.32256051898002625 1248.923583984375 0.4066450893878937 0.8533678 0.300137460231781 True -10 30239 29.599247455596924 0.5517978668212891 1038.3861083984375 0.19121003150939941 1244.1143798828125 0.40982407331466675 0.8562583 0.2942192256450653 True -11 32988 29.601823091506958 0.5565464496612549 857.573974609375 0.32796263694763184 1238.439453125 0.41307780146598816 0.85962015 0.2903898060321808 True -12 35737 29.58748769760132 0.5541818141937256 936.3973388671875 0.2057802975177765 1235.08447265625 0.41492560505867004 0.866271 0.2686327397823334 True -13 38486 29.657856702804565 0.5852108001708984 1226.2086181640625 0.19730234146118164 1233.2047119140625 0.41589125990867615 0.87199706 0.2555367648601532 True -14 41235 29.583850383758545 0.5570666790008545 1007.6983032226562 0.20561863481998444 1228.550048828125 0.4195708930492401 0.87875485 0.24290409684181213 True -15 43984 29.636257648468018 0.5516202449798584 1127.7889404296875 0.18177834153175354 1223.4822998046875 0.4225778579711914 0.88403857 0.23011280596256256 True -16 46733 29.68870496749878 11.19618558883667 1021.4271850585938 0.20569977164268494 1220.004638671875 0.42450833320617676 0.8871736 0.21786276996135712 True -17 49482 29.632925510406494 0.5443601608276367 1031.6912841796875 0.276201993227005 1223.2647705078125 0.42243853211402893 0.8910974 0.20843294262886047 True -18 52231 29.64178967475891 0.5537238121032715 1176.30615234375 0.17926611006259918 1223.3780517578125 0.4220440983772278 0.89186215 0.20385245978832245 True -19 54980 29.6316978931427 0.5372104644775391 855.9068603515625 0.21533820033073425 1222.31884765625 0.4234905242919922 0.8907143 0.2029600441455841 False diff --git a/ENCSR818JGZ/cherimoya.fold_3.performance.tsv b/ENCSR818JGZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 06805fb00c546cf939730ef1589894fa70c340d0..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1223.3780517578125 0.30556797981262207 0.4220440685749054 0.23500250279903412 0.891862154006958 0.837976336479187 0.20385245978832245 \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_4.evaluate.json b/ENCSR818JGZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a5678b991af235019778251a783fdd96270ae836..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF819WUF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_4.fit.json b/ENCSR818JGZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 0c4f1b68299e0fabfb6bf6f2a9d01a19ba029702..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF819WUF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR818JGZ/cherimoya.fold_4.log b/ENCSR818JGZ/cherimoya.fold_4.log deleted file mode 100644 index 4fdbec6ce2b498f8392cf078cf338eddb12ff622..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2818 35.962960958480835 3.664559841156006 1012.1939697265625 0.3971833884716034 1371.0595703125 0.29148703813552856 0.76344085 6.795161724090576 True -1 5636 31.07772970199585 1.1036667823791504 1128.8212890625 0.38788557052612305 1258.831298828125 0.3710283935070038 0.81998426 1.1845602989196777 True -2 8454 31.11909532546997 0.6483330726623535 1055.97900390625 0.4803450107574463 1238.775634765625 0.3806622624397278 0.827383 0.48155099153518677 True -3 11272 31.112093448638916 0.6044459342956543 900.5467529296875 0.3459060788154602 1232.212158203125 0.38350263237953186 0.831093 0.38490110635757446 True -4 14090 30.553559064865112 1.8659331798553467 1032.976318359375 0.2064894437789917 1226.4964599609375 0.3878040015697479 0.83365995 0.3806329071521759 True -5 16908 30.604514598846436 0.5908913612365723 1055.3787841796875 0.27016735076904297 1224.517578125 0.38793134689331055 0.8377422 0.3215041160583496 True -6 19726 30.49393916130066 0.5883300304412842 1172.0181884765625 0.36964643001556396 1219.950439453125 0.3902852237224579 0.8394672 0.3138830065727234 True -7 22544 30.56390690803528 0.5707905292510986 1010.66455078125 0.3888058662414551 1211.8338623046875 0.39594313502311707 0.84258443 0.3230457305908203 True -8 25362 30.620018243789673 0.5969967842102051 1124.673095703125 0.3237731456756592 1210.847412109375 0.3953516483306885 0.84523433 0.2827368676662445 True -9 28180 30.438180446624756 0.5837092399597168 904.857421875 0.21280360221862793 1204.8258056640625 0.39970600605010986 0.8509949 0.26267194747924805 True -10 30998 30.439311265945435 0.5846247673034668 1001.5238037109375 0.23250290751457214 1198.5352783203125 0.404805988073349 0.85678744 0.2410891354084015 True -11 33816 30.505062103271484 32.97566294670105 1081.1236572265625 0.30998432636260986 1196.353515625 0.40481287240982056 0.86133975 0.2418854683637619 True -12 36634 30.642256259918213 22.290445804595947 1100.4193115234375 0.20804816484451294 1193.74169921875 0.40601325035095215 0.86594915 0.2209130823612213 True -13 39452 30.551520824432373 25.253459453582764 1039.9542236328125 0.19134390354156494 1190.1353759765625 0.4071744680404663 0.8699172 0.21453353762626648 True -14 42270 30.771016836166382 1.2435123920440674 1018.8062744140625 0.1810513734817505 1183.58349609375 0.4141346216201782 0.8743072 0.2077496498823166 True -15 45088 30.558626413345337 0.6103515625 978.9449462890625 0.2821285128593445 1183.522705078125 0.412484735250473 0.87955725 0.19526396691799164 True -16 47906 30.563367128372192 0.6215794086456299 905.3585205078125 0.27401015162467957 1181.6568603515625 0.4141295850276947 0.88224274 0.19122131168842316 True -17 50724 30.491873741149902 0.5919296741485596 907.7944946289062 0.14777028560638428 1182.3287353515625 0.41369616985321045 0.88560957 0.18631629645824432 True -18 53542 30.438507318496704 0.5846235752105713 964.2344360351562 0.15992014110088348 1181.9974365234375 0.4140794575214386 0.8857242 0.1854131668806076 True -19 56360 30.3770592212677 0.5815062522888184 951.9557495117188 0.2882903516292572 1182.8443603515625 0.4133877456188202 0.8857539 0.18526630103588104 True diff --git a/ENCSR818JGZ/cherimoya.fold_4.performance.tsv b/ENCSR818JGZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e6be5d9be580dc15ec40cc69cb4e58b5144d5345..0000000000000000000000000000000000000000 --- a/ENCSR818JGZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1182.8443603515625 0.30946677923202515 0.4133877456188202 0.22716966271400452 0.8857539296150208 0.8270809054374695 0.18526630103588104 \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_0.evaluate.json b/ENCSR819EPD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9cf001228398cb85c43cbb3c80f947d795793661..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF370BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_0.fit.json b/ENCSR819EPD/cherimoya.fold_0.fit.json deleted file mode 100644 index 153fe17cd9373e91179a91ef9c29bd5cd8faf34a..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF370BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_0.log b/ENCSR819EPD/cherimoya.fold_0.log deleted file mode 100644 index 3e0c1eb48d03c1d7b633ccec9fe70a06e5f65a86..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 35.00861144065857 3.5655405521392822 141.0985870361328 0.6183854937553406 184.9284210205078 0.12178193032741547 0.7408482 2.895982265472412 True -1 5502 30.773717164993286 0.5907468795776367 115.86328125 0.5688259601593018 169.7734375 0.15663772821426392 0.7972296 1.2330386638641357 True -2 8253 30.706512212753296 0.5804688930511475 137.54092407226562 0.3368161916732788 167.03013610839844 0.160047709941864 0.7997724 0.6398721933364868 True -3 11004 32.232011795043945 28.97749376296997 144.16110229492188 0.38147109746932983 165.69235229492188 0.16344451904296875 0.8146376 0.6223160624504089 True -4 13755 30.647177696228027 33.097086668014526 176.86752319335938 0.2937820553779602 164.6392364501953 0.16588981449604034 0.8251057 0.5841909646987915 True -5 16506 31.658840894699097 0.6671566963195801 151.8716583251953 0.5292648673057556 163.7627716064453 0.16771015524864197 0.83469856 0.5746989250183105 True -6 19257 33.39763331413269 0.5826671123504639 127.2825698852539 0.2719391882419586 163.279541015625 0.16841796040534973 0.8392719 0.5498011708259583 True -7 22008 30.67808246612549 2.316498041152954 145.8269500732422 0.43517008423805237 162.5060577392578 0.17070940136909485 0.8482968 0.49992477893829346 True -8 24759 30.698801517486572 0.5783936977386475 130.7609405517578 0.40997499227523804 162.16188049316406 0.17171703279018402 0.8469675 0.4905865490436554 False -9 27510 30.626631021499634 0.5813257694244385 122.81906127929688 0.324310302734375 161.82992553710938 0.17278806865215302 0.85372823 0.4354850649833679 True -10 30261 30.659080505371094 0.5783236026763916 149.6745147705078 0.24658752977848053 161.29611206054688 0.17430917918682098 0.8610335 0.3955279588699341 True -11 33012 30.65367102622986 4.599425792694092 110.35775756835938 0.25948649644851685 160.80044555664062 0.17586550116539001 0.8645691 0.3535154163837433 True -12 35763 30.768857717514038 0.6046082973480225 133.8309326171875 0.258977472782135 160.2873077392578 0.1774216592311859 0.87186384 0.3199883997440338 True -13 38514 30.428263425827026 0.5949678421020508 209.646728515625 0.2878856062889099 160.03225708007812 0.17807425558567047 0.8772331 0.29509398341178894 True -14 41265 30.124467611312866 0.5832045078277588 180.8790740966797 0.21836793422698975 159.79449462890625 0.17840194702148438 0.8814562 0.2778250277042389 True -15 44016 30.296695709228516 0.6596863269805908 151.5834197998047 0.3399685025215149 159.6011505126953 0.17910946905612946 0.883552 0.26627373695373535 True -16 46767 30.144372701644897 0.5888607501983643 154.99745178222656 0.3362613916397095 159.568359375 0.17906524240970612 0.8849165 0.25731194019317627 True -17 49518 30.047743558883667 0.5841708183288574 122.51460266113281 0.3128631114959717 159.36264038085938 0.17889688909053802 0.88612854 0.2499290108680725 True -18 52269 30.034024953842163 0.5809121131896973 131.32733154296875 0.2608256936073303 159.50827026367188 0.17858558893203735 0.886601 0.24960413575172424 True -19 55020 30.054148197174072 0.5716843605041504 125.73345947265625 0.29192328453063965 159.50668334960938 0.1786268800497055 0.88624126 0.2498067021369934 False diff --git a/ENCSR819EPD/cherimoya.fold_0.performance.tsv b/ENCSR819EPD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4f2d17f50ef67d60cb67d45f5f8e0f4eeb6b6f0f..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -159.50827026367188 0.5757086873054504 0.17858557403087616 0.04267517477273941 0.8866009712219238 0.7768223881721497 0.24960413575172424 \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_1.evaluate.json b/ENCSR819EPD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9092d3df3a0664506cb2ae4aea1f5f89ce628f97..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF370BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_1.fit.json b/ENCSR819EPD/cherimoya.fold_1.fit.json deleted file mode 100644 index 79c184e70574f4e617b2b2236d0bdbf610bab2a4..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF370BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_1.log b/ENCSR819EPD/cherimoya.fold_1.log deleted file mode 100644 index 56dfe481fc99221c2dd94c6e8a6bc7eb76dacac2..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 35.61395573616028 3.913884401321411 130.48904418945312 0.4600100815296173 253.01577758789062 0.13474909961223602 0.7289204 3.723785400390625 True -1 5476 30.57437014579773 2.1806905269622803 128.7469024658203 0.33820801973342896 227.2199249267578 0.18769389390945435 0.8003087 1.8975070714950562 True -2 8214 30.533846139907837 0.6908211708068848 172.31198120117188 0.5408094525337219 224.56781005859375 0.18978330492973328 0.80417585 1.083267092704773 True -3 10952 30.67981243133545 0.6895332336425781 115.03308868408203 0.30398863554000854 222.2115020751953 0.19252528250217438 0.8276269 0.8080633282661438 True -4 13690 30.42300009727478 0.6871345043182373 173.38104248046875 0.3714866042137146 219.35496520996094 0.19897601008415222 0.8369647 0.7786705493927002 True -5 16428 30.484816789627075 0.6808035373687744 177.30905151367188 0.3178051710128784 217.38107299804688 0.20374161005020142 0.8478312 0.7157812118530273 True -6 19166 30.9843168258667 0.6865553855895996 208.1704559326172 0.3367096483707428 216.8664093017578 0.2045845091342926 0.85146946 0.6675545573234558 True -7 21904 30.6802875995636 0.6781377792358398 98.48843383789062 0.30058035254478455 216.24392700195312 0.20544111728668213 0.8591773 0.601448118686676 True -8 24642 30.482954502105713 0.679675817489624 172.89390563964844 0.6610245704650879 215.11419677734375 0.20874916017055511 0.86416936 0.5510151386260986 True -9 27380 30.523995876312256 0.685187816619873 141.79888916015625 0.4928528070449829 214.65419006347656 0.20903797447681427 0.87077266 0.5062093138694763 True -10 30118 30.495076417922974 0.6764640808105469 136.08523559570312 0.26314252614974976 213.94708251953125 0.2113981693983078 0.87397426 0.4730391204357147 True -11 32856 30.46806836128235 0.6880369186401367 129.14285278320312 0.2970549464225769 213.24331665039062 0.21390162408351898 0.8836797 0.43212470412254333 True -12 35594 30.4617817401886 0.6834566593170166 128.2816619873047 0.28346139192581177 212.8224639892578 0.21430565416812897 0.88604975 0.4072861671447754 True -13 38332 30.427968978881836 0.6918578147888184 146.57086181640625 0.3703346848487854 211.69630432128906 0.21684382855892181 0.891379 0.37892720103263855 True -14 41070 30.2415452003479 0.6769142150878906 117.11323547363281 0.19877296686172485 211.46615600585938 0.2167425900697708 0.89480287 0.3555583953857422 True -15 43808 29.841230630874634 1.6179866790771484 112.80935668945312 0.3370276093482971 211.1607208251953 0.21700075268745422 0.89886105 0.332331120967865 True -16 46546 29.993828773498535 0.6917445659637451 106.35957336425781 0.2594740688800812 210.55018615722656 0.21868681907653809 0.90151983 0.317484050989151 True -17 49284 30.112629652023315 37.46632528305054 124.08721923828125 0.2371119111776352 210.82659912109375 0.21744319796562195 0.9015314 0.311722993850708 True -18 52022 29.916173934936523 2.317060708999634 152.43997192382812 0.20654428005218506 211.10440063476562 0.21650415658950806 0.9034765 0.3081662654876709 True -19 54760 30.16739559173584 1.2831244468688965 101.77972412109375 0.17967945337295532 211.2570343017578 0.216205433011055 0.9032357 0.30846700072288513 False diff --git a/ENCSR819EPD/cherimoya.fold_1.performance.tsv b/ENCSR819EPD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d474e180b6952568e200f1866e9f1cdbf1379d3c..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -211.10440063476562 0.5458682179450989 0.21650415658950806 0.05861051008105278 0.9034764766693115 0.8356426358222961 0.3081662654876709 \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_2.evaluate.json b/ENCSR819EPD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 23b18b345bee3fbdd22df492449a110bf09bbc3a..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF370BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_2.fit.json b/ENCSR819EPD/cherimoya.fold_2.fit.json deleted file mode 100644 index 94bb2cf28269bd23735c0dce269bcd35860816d6..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF370BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_2.log b/ENCSR819EPD/cherimoya.fold_2.log deleted file mode 100644 index 2a20e0c7b56a8b056ddff83eed47772ed1f768b1..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2906 37.01690340042114 3.6266746520996094 137.41903686523438 0.5081779360771179 202.04437255859375 0.1279919594526291 0.7200432 2.8610002994537354 True -1 5812 32.46190166473389 0.5739650726318359 152.43463134765625 0.6077824234962463 183.3693389892578 0.1654238998889923 0.7970384 1.2726765871047974 True -2 8718 33.19649147987366 5.561644792556763 139.47076416015625 0.39803576469421387 181.98590087890625 0.16658157110214233 0.80947274 0.6558403372764587 True -3 11624 32.38145184516907 0.5645928382873535 133.55850219726562 0.4709635078907013 179.6676788330078 0.1700182408094406 0.8223883 0.554324209690094 True -4 14530 32.631967544555664 28.45838212966919 157.93292236328125 0.4030716121196747 178.965087890625 0.17239147424697876 0.8286646 0.5978440046310425 True -5 17436 32.49933195114136 28.693397283554077 151.8772735595703 0.31627145409584045 177.683837890625 0.17531824111938477 0.8352878 0.5485861897468567 True -6 20342 32.60189509391785 0.5691721439361572 126.9790267944336 0.252515971660614 176.33750915527344 0.17855864763259888 0.84177905 0.5068448185920715 True -7 23248 32.3559787273407 0.5754032135009766 212.43435668945312 0.21611511707305908 175.92161560058594 0.1796509325504303 0.84425825 0.4893346428871155 True -8 26154 32.471442461013794 17.126906394958496 127.05465698242188 0.2621394991874695 175.4224395751953 0.1810040920972824 0.84864616 0.450573205947876 True -9 29060 32.40037274360657 0.5666646957397461 153.15914916992188 0.240273118019104 174.6064910888672 0.1829376220703125 0.8562024 0.4020425081253052 True -10 31966 32.40389800071716 0.5699653625488281 174.36746215820312 0.2999669909477234 173.9171905517578 0.18532904982566833 0.86296344 0.3805449604988098 True -11 34872 32.4255313873291 0.5554468631744385 144.7593231201172 0.2875522971153259 173.47366333007812 0.18590761721134186 0.8680593 0.3528059124946594 True -12 37778 32.41380310058594 0.5620994567871094 133.41236877441406 0.37276047468185425 173.2615966796875 0.18661020696163177 0.8735081 0.3320363759994507 True -13 40684 32.28947067260742 0.549619197845459 165.83860778808594 0.2889910340309143 172.93191528320312 0.18746577203273773 0.87721264 0.3182627260684967 True -14 43590 31.71259880065918 12.08319091796875 160.66600036621094 0.34155142307281494 172.4259490966797 0.18855859339237213 0.88100284 0.2964016795158386 True -15 46496 32.58178639411926 0.5639197826385498 136.13186645507812 0.2711126506328583 171.71176147460938 0.19085581600666046 0.8851303 0.28180962800979614 True -16 49402 31.78403115272522 0.5557386875152588 122.22693634033203 0.36758971214294434 171.7416534423828 0.18920421600341797 0.88666636 0.2729097902774811 True -17 52308 31.76637363433838 0.5498583316802979 123.96813201904297 0.25613823533058167 171.6639862060547 0.18992318212985992 0.8880724 0.2689726948738098 True -18 55214 31.865173816680908 0.5494768619537354 135.19451904296875 0.2045731097459793 171.64590454101562 0.18999317288398743 0.8870679 0.2688952088356018 False -19 58120 31.767146110534668 0.5504927635192871 120.18487548828125 0.21720415353775024 171.88352966308594 0.18893851339817047 0.8876587 0.2712830603122711 False diff --git a/ENCSR819EPD/cherimoya.fold_2.performance.tsv b/ENCSR819EPD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2ad99e993e4ea43a7e6f31f583be1989f5e6e0c6..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -171.6639862060547 0.5676848888397217 0.18992316722869873 0.05062595754861832 0.8880723714828491 0.7912828326225281 0.2689726948738098 \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_3.evaluate.json b/ENCSR819EPD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7e663cdb79424a28393681dd659c4d29518bce1a..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF370BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_3.fit.json b/ENCSR819EPD/cherimoya.fold_3.fit.json deleted file mode 100644 index 6cd0505d5cf7dd274fab9430378daf0219565cf8..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF370BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_3.log b/ENCSR819EPD/cherimoya.fold_3.log deleted file mode 100644 index ac7d741c79851e2d43d41e4adf380727051c4dc1..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 35.12904715538025 3.5047473907470703 119.55909729003906 0.49237096309661865 198.75015258789062 0.12957917153835297 0.7121539 2.781680107116699 True -1 5534 30.913978099822998 0.5827343463897705 100.73139953613281 0.5448448061943054 182.84695434570312 0.16517320275306702 0.78196 1.3772443532943726 True -2 8301 30.926853895187378 0.5732712745666504 193.35585021972656 0.3471240997314453 179.45614624023438 0.1699533611536026 0.7814595 0.891575813293457 False -3 11068 30.876386404037476 0.5701828002929688 113.04689025878906 0.34930193424224854 177.61712646484375 0.17344236373901367 0.8022948 0.7210956811904907 True -4 13835 30.80844807624817 0.5713269710540771 186.1324462890625 0.5273431539535522 177.11526489257812 0.17431782186031342 0.8113364 0.6408098340034485 True -5 16602 30.795937061309814 0.5668594837188721 166.9644012451172 0.3178657293319702 176.6853485107422 0.1752428412437439 0.816168 0.6093698740005493 True -6 19369 30.805810928344727 0.5735044479370117 137.6561279296875 0.4308079779148102 175.29010009765625 0.17903035879135132 0.8281463 0.5264362692832947 True -7 22136 30.86785316467285 0.5719625949859619 133.87750244140625 0.3085899353027344 174.76661682128906 0.18019001185894012 0.8322637 0.5182831287384033 True -8 24903 30.796022176742554 0.5632264614105225 143.9803466796875 0.3917044997215271 174.15061950683594 0.18199025094509125 0.8403401 0.504237949848175 True -9 27670 30.822365283966064 0.5736985206604004 103.24366760253906 0.30117374658584595 173.87478637695312 0.18305331468582153 0.84839517 0.4521527886390686 True -10 30437 31.40830159187317 26.5071804523468 183.2268829345703 0.2963991165161133 173.564208984375 0.18359336256980896 0.8533819 0.42955663800239563 True -11 33204 33.286452293395996 0.5956437587738037 112.13101196289062 0.2968311905860901 173.1128387451172 0.18488360941410065 0.8594899 0.39091822504997253 True -12 35971 30.83075737953186 0.5752742290496826 175.71878051757812 0.4180409610271454 172.5887908935547 0.18646791577339172 0.86441725 0.37777429819107056 True -13 38738 30.86774706840515 0.5808181762695312 122.54440307617188 0.3759368658065796 172.17445373535156 0.1876101940870285 0.8698737 0.3559398651123047 True -14 41505 30.48808264732361 1.0324006080627441 126.36676025390625 0.2556125819683075 171.87478637695312 0.18763311207294464 0.87589973 0.3265550136566162 True -15 44272 30.25585675239563 0.569239616394043 134.1204833984375 0.29295027256011963 171.2475128173828 0.1891379952430725 0.8801366 0.31194740533828735 True -16 47039 30.269393920898438 0.5815553665161133 167.24984741210938 0.32798802852630615 171.17071533203125 0.18911103904247284 0.88384545 0.29599785804748535 True -17 49806 30.251602172851562 0.5637485980987549 130.45956420898438 0.4208240509033203 171.1729736328125 0.18918178975582123 0.88513345 0.2910629212856293 True -18 52573 30.25049114227295 0.5710415840148926 121.66861724853516 0.2350388765335083 171.2344512939453 0.18904781341552734 0.8856804 0.28873443603515625 True -19 55340 30.237796306610107 0.5700452327728271 148.32908630371094 0.20674054324626923 171.36280822753906 0.18849481642246246 0.88473535 0.29015129804611206 False diff --git a/ENCSR819EPD/cherimoya.fold_3.performance.tsv b/ENCSR819EPD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 48701a53d20ad610ac06981e01b6259646d2847b..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -171.2344512939453 0.5683910846710205 0.18904781341552734 0.0492202527821064 0.8856803774833679 0.7776840329170227 0.28873443603515625 \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_4.evaluate.json b/ENCSR819EPD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2454d162e04e697fe646e80f7199807856b803a6..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF370BEY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_4.fit.json b/ENCSR819EPD/cherimoya.fold_4.fit.json deleted file mode 100644 index e84a6c9f76a2c6f718b7f445b4d1e936bed416db..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF370BEY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819EPD/cherimoya.fold_4.log b/ENCSR819EPD/cherimoya.fold_4.log deleted file mode 100644 index 0cd0b710e1efe664c091ca48416b00512b0fb4b6..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 36.42630743980408 3.6893999576568604 136.3431396484375 0.7019386291503906 171.6917724609375 0.12081889808177948 0.712434 2.4666595458984375 True -1 5748 32.1021409034729 0.6215710639953613 110.23584747314453 0.3924110531806946 158.9761962890625 0.15008951723575592 0.7782088 1.28639554977417 True -2 8622 32.689936876297 0.5974557399749756 134.59637451171875 0.29518479108810425 156.92161560058594 0.15371756255626678 0.79138386 0.6991133093833923 True -3 11496 32.03397274017334 0.595635175704956 131.01564025878906 0.3665796220302582 155.38583374023438 0.1562996804714203 0.8145079 0.5506889224052429 True -4 14370 31.991249084472656 0.5999894142150879 161.49114990234375 0.4878843426704407 155.01828002929688 0.15805314481258392 0.8185678 0.5403735637664795 True -5 17244 32.03685688972473 0.596113920211792 120.79332733154297 0.33747899532318115 154.1099853515625 0.16009333729743958 0.82759 0.5187655091285706 True -6 20118 32.3377320766449 38.81087017059326 149.52525329589844 0.3212493062019348 153.55325317382812 0.16134236752986908 0.8331689 0.4692347049713135 True -7 22992 32.10636496543884 0.6057875156402588 157.56185913085938 0.36360785365104675 152.96246337890625 0.1627982258796692 0.8367303 0.44217026233673096 True -8 25866 32.294273138046265 7.5940258502960205 140.34132385253906 0.4619531035423279 152.6210479736328 0.16424499452114105 0.842408 0.40043696761131287 True -9 28740 32.16933822631836 0.6119658946990967 149.6412353515625 0.35575616359710693 152.28204345703125 0.16481176018714905 0.84662306 0.36960774660110474 True -10 31614 32.1633083820343 0.6067564487457275 103.30435943603516 0.2529051899909973 151.75079345703125 0.1666659116744995 0.8534039 0.3501560688018799 True -11 34488 32.14348006248474 0.6189491748809814 150.23390197753906 0.32494571805000305 151.4757080078125 0.16744372248649597 0.86064184 0.3218019902706146 True -12 37362 32.17179083824158 0.6058294773101807 122.6185302734375 0.2259495109319687 150.95310974121094 0.16903479397296906 0.86670375 0.2939600944519043 True -13 40236 32.164403438568115 0.6106796264648438 145.96661376953125 0.36794304847717285 150.67758178710938 0.16955889761447906 0.87451226 0.2716315984725952 True -14 43110 31.816860675811768 0.6000995635986328 128.94264221191406 0.33657652139663696 150.3293914794922 0.17030613124370575 0.8776693 0.2586582601070404 True -15 45984 31.457316637039185 0.5939106941223145 102.37104797363281 0.2787390947341919 150.12579345703125 0.17094676196575165 0.8791459 0.2479134052991867 True -16 48858 31.440773010253906 0.6001126766204834 154.67840576171875 0.30686450004577637 149.94363403320312 0.1717832237482071 0.8818782 0.23785819113254547 True -17 51732 31.569714784622192 0.598459005355835 147.78884887695312 0.3112543523311615 150.34597778320312 0.17025768756866455 0.8842221 0.2326502799987793 True -18 54606 31.489484310150146 0.6041581630706787 146.44564819335938 0.22280147671699524 150.27264404296875 0.17050163447856903 0.8842542 0.2315881997346878 True -19 57480 33.01841068267822 11.041568756103516 133.83761596679688 0.14388063549995422 150.29794311523438 0.17037513852119446 0.8833571 0.23189276456832886 False diff --git a/ENCSR819EPD/cherimoya.fold_4.performance.tsv b/ENCSR819EPD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1ae4d9f67cb70a63cc3f809434d45dcbd4862110..0000000000000000000000000000000000000000 --- a/ENCSR819EPD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -150.27264404296875 0.5818372964859009 0.17050161957740784 0.040711574256420135 0.8842542171478271 0.7500454783439636 0.2315881997346878 \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_0.evaluate.json b/ENCSR819GAF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8e94a3ca403ebe27cf08ad9cd78cf674caf29658..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203WKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_0.fit.json b/ENCSR819GAF/cherimoya.fold_0.fit.json deleted file mode 100644 index 0c6824188b5b5c793cb14ce704c7ad94b4746749..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF203WKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_0.log b/ENCSR819GAF/cherimoya.fold_0.log deleted file mode 100644 index 61e83e62bcef49e459221783113ffec908806b6d..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 35.345906496047974 4.121315002441406 470.7969665527344 0.5110371112823486 681.8999633789062 0.29858556389808655 0.67074376 4.885701656341553 True -1 5474 30.563424110412598 0.6401216983795166 506.2794189453125 0.7038854360580444 602.565673828125 0.3928545415401459 0.7367115 1.368786096572876 True -2 8211 30.65992784500122 1.6552364826202393 574.9052734375 0.5270054340362549 591.4369506835938 0.4040362536907196 0.7446974 0.712541401386261 True -3 10948 29.942591905593872 0.6316330432891846 472.652587890625 0.37740933895111084 586.1529541015625 0.410624235868454 0.7499745 0.6226027011871338 True -4 13685 29.780876636505127 0.6379263401031494 574.5299682617188 0.4003757834434509 583.5359497070312 0.4138626754283905 0.7506179 0.45233944058418274 True -5 16422 29.770253658294678 0.6885194778442383 476.9449462890625 0.3394603133201599 581.2184448242188 0.4162941575050354 0.7611608 0.4568128287792206 True -6 19159 29.856439113616943 0.597245454788208 514.3504028320312 0.5950542092323303 579.5623779296875 0.4177596867084503 0.761112 0.4919997751712799 False -7 21896 29.812012434005737 0.6269500255584717 430.16009521484375 0.6053752899169922 577.2349243164062 0.4215327203273773 0.7633464 0.484331339597702 True -8 24633 29.82811164855957 0.6164278984069824 517.064208984375 0.5613199472427368 575.9764404296875 0.4229615032672882 0.7730129 0.4748062491416931 True -9 27370 29.853124141693115 0.6377158164978027 463.0588684082031 0.37876254320144653 573.086181640625 0.42642781138420105 0.7778784 0.4042588472366333 True -10 30107 29.78293228149414 0.617236852645874 585.522216796875 0.33872294425964355 570.1160278320312 0.43098974227905273 0.7831242 0.3710538446903229 True -11 32844 29.798662185668945 1.848191499710083 450.16851806640625 0.5321418642997742 569.2301025390625 0.430616557598114 0.7908539 0.3342474699020386 True -12 35581 29.8806893825531 0.6212725639343262 445.1754150390625 0.2887526750564575 567.2025146484375 0.4331345856189728 0.80060184 0.32099810242652893 True -13 38318 29.844003200531006 0.6078305244445801 466.5213928222656 0.2978513538837433 564.5013427734375 0.43650752305984497 0.804662 0.29721173644065857 True -14 41055 29.820574283599854 0.6134212017059326 468.9829406738281 0.3364279270172119 564.351318359375 0.4357912838459015 0.81009656 0.28960585594177246 True -15 43792 29.834676027297974 0.5940070152282715 394.25726318359375 0.31771907210350037 563.4723510742188 0.4372765123844147 0.8157186 0.27949258685112 True -16 46529 29.83892059326172 0.6097300052642822 537.1296997070312 0.291655033826828 561.8899536132812 0.4390174448490143 0.81873244 0.2784491777420044 True -17 49266 29.799586534500122 0.5965085029602051 461.9033508300781 0.19919368624687195 562.1007080078125 0.43857431411743164 0.8200935 0.27532050013542175 True -18 52003 29.772539138793945 0.60323166847229 491.03717041015625 0.3075472116470337 561.4117431640625 0.44014260172843933 0.8209303 0.2753992974758148 True -19 54740 29.860931158065796 0.6085166931152344 461.68951416015625 0.19244667887687683 561.890869140625 0.4389057755470276 0.81876725 0.27626097202301025 False diff --git a/ENCSR819GAF/cherimoya.fold_0.performance.tsv b/ENCSR819GAF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3a72b443e0a83c0a1d0e7459785d66c59c1db664..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -561.4117431640625 0.37051844596862793 0.44014257192611694 0.16769357025623322 0.8209303021430969 0.7866899967193604 0.2753992974758148 \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_1.evaluate.json b/ENCSR819GAF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b294790f8f200d54a7543af925893db910cd8c2c..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203WKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_1.fit.json b/ENCSR819GAF/cherimoya.fold_1.fit.json deleted file mode 100644 index 40cb5803a6224416666b16bd8057c64a207d7eaa..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF203WKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_1.log b/ENCSR819GAF/cherimoya.fold_1.log deleted file mode 100644 index e92051143e7dbf1a8cfb176bbe4b82bebbbc3eb6..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2698 35.91504621505737 4.757374286651611 495.03802490234375 0.3803313970565796 780.342529296875 0.2929840385913849 0.68406975 5.052320957183838 True -1 5396 30.56972646713257 21.93034291267395 555.64599609375 0.6374335885047913 679.223876953125 0.39822569489479065 0.74325156 1.7495455741882324 True -2 8094 30.08076524734497 0.7358822822570801 511.7577209472656 0.40235596895217896 663.3534545898438 0.4112364947795868 0.7522015 0.8010156154632568 True -3 10792 30.037383317947388 0.7359683513641357 562.3169555664062 0.6678209900856018 655.2827758789062 0.4179564118385315 0.7584491 0.8642076849937439 True -4 13490 30.016562700271606 0.7733819484710693 417.5286865234375 0.5029047727584839 649.232421875 0.4238196313381195 0.7686388 0.5406798124313354 True -5 16188 30.008448600769043 0.733900785446167 474.71588134765625 0.39567822217941284 646.4932861328125 0.4274422824382782 0.7739825 0.5216920375823975 True -6 18886 29.999174118041992 0.7326750755310059 375.32867431640625 0.5466328859329224 645.7496337890625 0.42670655250549316 0.779385 0.4894123673439026 True -7 21584 29.97280192375183 0.7348833084106445 472.45709228515625 0.47079548239707947 641.184326171875 0.4330601990222931 0.78702444 0.46730172634124756 True -8 24282 29.963685035705566 0.7334194183349609 450.424072265625 0.36881905794143677 639.1964111328125 0.4348711669445038 0.78985703 0.4563571512699127 True -9 26980 29.999065399169922 0.7623062133789062 397.5862731933594 0.28033989667892456 637.2462768554688 0.43693989515304565 0.79925674 0.42680707573890686 True -10 29678 29.98782515525818 0.7165515422821045 519.7948608398438 0.38783299922943115 635.3021850585938 0.4377964437007904 0.80287194 0.41526374220848083 True -11 32376 29.965991735458374 0.7345843315124512 501.66229248046875 0.27587559819221497 633.2080688476562 0.4399172365665436 0.81008077 0.3913050591945648 True -12 35074 29.976343870162964 0.7272090911865234 411.1548156738281 0.44256123900413513 629.8212890625 0.44420376420021057 0.8181567 0.3674783408641815 True -13 37772 30.07768416404724 0.7350351810455322 557.803466796875 0.37153249979019165 628.1240234375 0.44551360607147217 0.8223077 0.3576993942260742 True -14 40470 30.051135778427124 2.079619884490967 546.12353515625 0.30036991834640503 625.3138427734375 0.4485141634941101 0.8306743 0.3298080861568451 True -15 43168 30.032667636871338 0.7391984462738037 504.5239562988281 0.33717501163482666 625.2348022460938 0.44841262698173523 0.8356372 0.3079933822154999 True -16 45866 30.010326623916626 0.7312572002410889 457.4416198730469 0.24201703071594238 625.0779418945312 0.44816866517066956 0.8410967 0.2943388521671295 True -17 48564 29.439686059951782 0.7239820957183838 440.26104736328125 0.25741803646087646 623.2393798828125 0.45044615864753723 0.8421435 0.2865598499774933 True -18 51262 29.422037363052368 0.7242186069488525 443.5636901855469 0.3295576870441437 624.71435546875 0.4477464258670807 0.84361887 0.28347986936569214 True -19 53960 29.405691623687744 0.7209396362304688 591.432861328125 0.1515895128250122 623.603759765625 0.4506220519542694 0.8434158 0.2841501832008362 False diff --git a/ENCSR819GAF/cherimoya.fold_1.performance.tsv b/ENCSR819GAF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index eab04e9b34d0299d43c5da4bb56501b349dba12a..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -624.71435546875 0.3610033690929413 0.44774648547172546 0.17775152623653412 0.8436188697814941 0.8230772614479065 0.28347986936569214 \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_2.evaluate.json b/ENCSR819GAF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1265b3370a0060aec9dc32c7af36750e1d5664b7..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203WKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_2.fit.json b/ENCSR819GAF/cherimoya.fold_2.fit.json deleted file mode 100644 index 83b4ae5659ee828fa641cb4d325f8e238236e92e..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF203WKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_2.log b/ENCSR819GAF/cherimoya.fold_2.log deleted file mode 100644 index fb61c347475b9b8ee83da258ff26100d4259393b..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2869 36.37164616584778 4.225210428237915 440.37353515625 0.6366791129112244 707.7777709960938 0.3025151193141937 0.67835724 5.224304676055908 True -1 5738 31.912123680114746 1.946385145187378 557.7684936523438 0.629936933517456 624.628173828125 0.39320269227027893 0.7330769 1.5919673442840576 True -2 8607 31.974897146224976 0.5796821117401123 533.1270141601562 0.6156589984893799 612.9998168945312 0.4036628007888794 0.7492455 0.8234050273895264 True -3 11476 31.92840886116028 0.5679423809051514 550.709716796875 0.47925084829330444 606.3135986328125 0.41119909286499023 0.7582248 0.7370091080665588 True -4 14345 31.934699296951294 1.449608564376831 488.9452819824219 0.7353358268737793 601.3876342773438 0.41810232400894165 0.7619932 0.5717141032218933 True -5 17214 31.936935424804688 1.477653980255127 587.54248046875 0.3387848138809204 599.6083374023438 0.41996467113494873 0.76592755 0.5257524847984314 True -6 20083 31.872962713241577 0.5760524272918701 478.579833984375 0.47266340255737305 598.0451049804688 0.42160937190055847 0.765461 0.5090079307556152 False -7 22952 31.858225107192993 0.578502893447876 402.0968322753906 0.36916619539260864 597.5396118164062 0.42160719633102417 0.774251 0.5046107769012451 True -8 25821 31.851159811019897 0.5761797428131104 512.1571655273438 0.5877504348754883 593.5791015625 0.42589133977890015 0.7805421 0.47154584527015686 True -9 28690 31.83909320831299 0.568382740020752 417.396484375 0.6079461574554443 590.9244384765625 0.4301094114780426 0.7818491 0.3937365710735321 True -10 31559 31.90188765525818 1.983959674835205 470.148193359375 0.26363974809646606 588.8846435546875 0.4327738881111145 0.789157 0.3851751685142517 True -11 34428 31.41276788711548 0.5704343318939209 477.09185791015625 0.30763357877731323 586.791748046875 0.43412289023399353 0.7948838 0.36128053069114685 True -12 37297 31.24096941947937 0.6251320838928223 518.923583984375 0.33281847834587097 585.2494506835938 0.436712384223938 0.800066 0.3288554251194 True -13 40166 31.245753288269043 0.5686047077178955 454.1398010253906 0.42462700605392456 584.25439453125 0.4372526705265045 0.805594 0.3139302134513855 True -14 43035 31.28689742088318 1.0968573093414307 478.8253173828125 0.3139137625694275 582.9832763671875 0.43725714087486267 0.8136923 0.29852059483528137 True -15 45904 31.267170906066895 0.572284460067749 468.03326416015625 0.20481686294078827 580.4461059570312 0.44099509716033936 0.819187 0.287426620721817 True -16 48773 31.292200326919556 0.5634281635284424 450.5285339355469 0.2225010097026825 580.77587890625 0.43990376591682434 0.82333034 0.28005123138427734 True -17 51642 31.237022399902344 0.5614640712738037 458.57952880859375 0.2482149451971054 580.7435913085938 0.4405873119831085 0.8241628 0.2780875265598297 True -18 54511 31.239022493362427 0.5617315769195557 469.32464599609375 0.42444759607315063 580.8729858398438 0.4400465488433838 0.8244432 0.2775118350982666 True -19 57380 31.220484256744385 0.5802254676818848 509.9794006347656 0.22247424721717834 581.2721557617188 0.4391917586326599 0.82537675 0.278566837310791 True diff --git a/ENCSR819GAF/cherimoya.fold_2.performance.tsv b/ENCSR819GAF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 79dc765c8a21560e554576e9a951d46baa3280a3..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -581.2721557617188 0.36857470870018005 0.4391917288303375 0.17029651999473572 0.8253767490386963 0.7975141406059265 0.278566837310791 \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_3.evaluate.json b/ENCSR819GAF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3338b117fc3ea5ee1409c237c3b77441b0246677..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203WKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_3.fit.json b/ENCSR819GAF/cherimoya.fold_3.fit.json deleted file mode 100644 index 8d6a8efadafb44494ca4adc77bc9a05edc9744c4..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF203WKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_3.log b/ENCSR819GAF/cherimoya.fold_3.log deleted file mode 100644 index 964caf31e53cb74ee2cd376f00ca1d42896466c4..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 35.698214530944824 4.503244161605835 579.4609375 0.6235125064849854 685.6251220703125 0.3047313988208771 0.67552817 4.47516393661499 True -1 5540 30.88111138343811 0.5548229217529297 554.8018798828125 0.644787609577179 599.228515625 0.40223178267478943 0.75520426 1.4245426654815674 True -2 8310 30.857617139816284 1.9233007431030273 434.787353515625 0.39649415016174316 588.2321166992188 0.4104645848274231 0.76323086 0.8302759528160095 True -3 11080 30.832118034362793 0.5646414756774902 455.14569091796875 0.4496074914932251 582.3394775390625 0.4150508940219879 0.77065057 0.6789318919181824 True -4 13850 30.216241359710693 0.5495047569274902 414.0628662109375 0.520063042640686 578.4126586914062 0.42055758833885193 0.7723384 0.5603443384170532 True -5 16620 30.180684089660645 0.7900488376617432 506.6949462890625 0.6392829418182373 574.9718627929688 0.42391297221183777 0.7789202 0.487570196390152 True -6 19390 30.21827006340027 0.5722918510437012 488.0753173828125 0.44274139404296875 572.94482421875 0.4254198670387268 0.7847497 0.4695657193660736 True -7 22160 30.1487078666687 0.5272064208984375 429.86309814453125 0.3988422751426697 570.3336181640625 0.4295821785926819 0.7879811 0.46803903579711914 True -8 24930 30.143357276916504 0.5400209426879883 458.77935791015625 0.26309865713119507 569.1494140625 0.429977685213089 0.7912663 0.4493040144443512 True -9 27700 30.167402744293213 0.518103837966919 423.7210693359375 0.3444558084011078 566.6581420898438 0.43385574221611023 0.79629904 0.4157838821411133 True -10 30470 30.171931982040405 2.6864216327667236 540.2080078125 0.4654619097709656 565.939453125 0.43386590480804443 0.8031239 0.39427319169044495 True -11 33240 30.179653644561768 1.123650074005127 512.545654296875 0.3133314847946167 564.0274658203125 0.43630164861679077 0.80703616 0.3587620258331299 True -12 36010 30.16007900238037 1.5307495594024658 403.97509765625 0.301570326089859 561.8739013671875 0.4379250109195709 0.8116709 0.3461795747280121 True -13 38780 30.23041820526123 0.868889331817627 480.00537109375 0.3942505419254303 560.4348754882812 0.43993422389030457 0.8182688 0.3325749635696411 True -14 41550 30.208638906478882 0.9899654388427734 487.8544006347656 0.3732093572616577 558.3233032226562 0.44276371598243713 0.82396865 0.31158310174942017 True -15 44320 30.22404193878174 1.2604796886444092 489.9043884277344 0.26332539319992065 557.320556640625 0.44353190064430237 0.83093756 0.301563560962677 True -16 47090 30.31588077545166 1.0864360332489014 454.47320556640625 0.21594658493995667 557.4044799804688 0.44329550862312317 0.83456916 0.2899940013885498 True -17 49860 30.266517639160156 13.194632530212402 472.0722351074219 0.1874069720506668 555.9384155273438 0.44539716839790344 0.8369929 0.28614315390586853 True -18 52630 30.267635107040405 1.410940170288086 458.5453796386719 0.2232990562915802 555.92529296875 0.44547930359840393 0.8359379 0.2846541404724121 False -19 55400 30.224981784820557 0.5397794246673584 493.17730712890625 0.19151680171489716 555.6727905273438 0.44629979133605957 0.83530295 0.2855176329612732 False diff --git a/ENCSR819GAF/cherimoya.fold_3.performance.tsv b/ENCSR819GAF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bf02bf16111faa5ebf80eba41dc1d8eb2f934279..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -555.9384155273438 0.3679365813732147 0.44539716839790344 0.1707713007926941 0.8369929194450378 0.8045653104782104 0.28614315390586853 \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_4.evaluate.json b/ENCSR819GAF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a9051fc455c5ae91a24617301e156d062a82c741..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF203WKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_4.fit.json b/ENCSR819GAF/cherimoya.fold_4.fit.json deleted file mode 100644 index 0054c8b6d50567dfff5ff631e720f24ab8d8e852..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF203WKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR819GAF/cherimoya.fold_4.log b/ENCSR819GAF/cherimoya.fold_4.log deleted file mode 100644 index 22dce996e9962a328bdc3bc0edee63e93acfc5b0..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 36.54106426239014 4.573066234588623 491.31292724609375 0.7200601696968079 635.3788452148438 0.29724371433258057 0.6663924 3.6761491298675537 True -1 5664 31.62628436088562 0.795983076095581 491.8018798828125 0.5795587301254272 566.7655029296875 0.3862927258014679 0.7275396 1.6521227359771729 True -2 8496 31.622978448867798 17.226953744888306 408.675537109375 0.5762554407119751 557.185546875 0.3947550058364868 0.7359563 0.813380777835846 True -3 11328 31.713616609573364 0.6688928604125977 390.0938720703125 0.7569550275802612 549.7669067382812 0.4043012857437134 0.73971677 0.6850240230560303 True -4 14160 31.718045234680176 3.621640682220459 498.2696228027344 0.4144630432128906 546.806884765625 0.40645310282707214 0.7490785 0.5348771214485168 True -5 16992 31.082494497299194 0.622821569442749 490.30194091796875 0.5162261724472046 544.5401611328125 0.40835297107696533 0.75552845 0.45602017641067505 True -6 19824 31.01772141456604 0.6241922378540039 545.3372192382812 0.3257855176925659 542.0906982421875 0.4121328890323639 0.76155734 0.42721137404441833 True -7 22656 30.913955688476562 0.6367886066436768 522.6304321289062 0.31640559434890747 540.1315307617188 0.4147733747959137 0.7646999 0.4130360186100006 True -8 25488 30.94267463684082 0.6408395767211914 432.916259765625 0.555169939994812 539.6921997070312 0.41512298583984375 0.7711562 0.3853735327720642 True -9 28320 30.98549461364746 0.6005535125732422 417.8056335449219 0.4026302099227905 537.2140502929688 0.41818490624427795 0.7795289 0.37028709053993225 True -10 31152 30.966521501541138 0.5926928520202637 529.0425415039062 0.33944183588027954 536.2119140625 0.41947856545448303 0.7835938 0.34932106733322144 True -11 33984 30.887662887573242 0.6092579364776611 560.691650390625 0.414051353931427 535.0302124023438 0.4201744496822357 0.78965175 0.33601340651512146 True -12 36816 30.910032987594604 0.6050090789794922 448.194091796875 0.26211047172546387 533.75537109375 0.4212424159049988 0.7996534 0.3144631087779999 True -13 39648 31.15422558784485 2.9389853477478027 445.5982971191406 0.2965658903121948 532.2413940429688 0.4234781265258789 0.802751 0.2985357344150543 True -14 42480 30.885488510131836 29.439000129699707 472.2523498535156 0.3797123432159424 530.4673461914062 0.4262547492980957 0.8087427 0.29085400700569153 True -15 45312 30.974125385284424 0.9006378650665283 458.84869384765625 0.2279716283082962 529.3585205078125 0.4280627369880676 0.81507534 0.2770324945449829 True -16 48144 30.931133031845093 0.6536927223205566 400.42620849609375 0.2883957624435425 528.6581420898438 0.4295154809951782 0.81719244 0.26979827880859375 True -17 50976 30.891294956207275 0.6010479927062988 475.9437561035156 0.22850476205348969 528.7630615234375 0.42964741587638855 0.82090116 0.26443174481391907 True -18 53808 30.9531888961792 0.6571216583251953 391.13543701171875 0.25630688667297363 529.5371704101562 0.4280998408794403 0.82211953 0.26545873284339905 True -19 56640 31.00672197341919 0.6390337944030762 439.0591125488281 0.24240927398204803 529.33544921875 0.4294431209564209 0.82109636 0.26571932435035706 False diff --git a/ENCSR819GAF/cherimoya.fold_4.performance.tsv b/ENCSR819GAF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 716d3c5e337455aeee9a0e0142e19e59909c57b6..0000000000000000000000000000000000000000 --- a/ENCSR819GAF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -529.5371704101562 0.3794267177581787 0.4280999004840851 0.16169582307338715 0.8221195340156555 0.7859718799591064 0.26545873284339905 \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_0.evaluate.json b/ENCSR820WLP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 12dd1150980725b57db9fc4f841ccb0185243174..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809JEF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_0.fit.json b/ENCSR820WLP/cherimoya.fold_0.fit.json deleted file mode 100644 index 62e58e262e7fb211814daaa541704e6574c7910a..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF809JEF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_0.log b/ENCSR820WLP/cherimoya.fold_0.log deleted file mode 100644 index bbde20e5616077d2feb26858173ef23551eea62b..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2721 34.77115058898926 20.653325080871582 1239.71728515625 0.46175774931907654 1593.62353515625 0.22440434992313385 0.53641576 6.431257247924805 True -1 5442 30.526386499404907 13.233532428741455 1181.228759765625 0.4123288691043854 1424.3861083984375 0.35516858100891113 0.6293135 1.0641487836837769 True -2 8163 30.195244312286377 14.396265506744385 1148.02685546875 0.24648162722587585 1390.8873291015625 0.3666880428791046 0.6435342 0.5905511975288391 True -3 10884 30.50374150276184 2.239544630050659 1232.238525390625 0.4267232120037079 1372.97705078125 0.3748704493045807 0.6598368 0.41094791889190674 True -4 13605 30.43063259124756 0.5535306930541992 1227.672119140625 0.5233797430992126 1366.677001953125 0.37879258394241333 0.666376 0.4154784381389618 True -5 16326 30.230966091156006 0.5710597038269043 1109.55615234375 0.4623534083366394 1358.099365234375 0.3851456940174103 0.67262214 0.3319776654243469 True -6 19047 30.233718395233154 0.566138744354248 1038.0650634765625 0.3060123324394226 1354.590087890625 0.3865712285041809 0.68479276 0.33678287267684937 True -7 21768 30.261013746261597 0.5520424842834473 1205.040771484375 0.46593886613845825 1350.856201171875 0.3890642821788788 0.6948072 0.33345821499824524 True -8 24489 30.196340799331665 0.5623891353607178 1113.4285888671875 0.3045928478240967 1347.333740234375 0.39088374376296997 0.70013404 0.3219352662563324 True -9 27210 30.602081060409546 0.5516660213470459 1167.9222412109375 0.6553202271461487 1342.126708984375 0.3958125114440918 0.7062224 0.33136969804763794 True -10 29931 30.17443346977234 0.5504395961761475 1045.629638671875 0.49989038705825806 1336.8487548828125 0.39950644969940186 0.71897584 0.3065744638442993 True -11 32652 29.644920587539673 0.5603752136230469 1190.155029296875 0.320931077003479 1335.8536376953125 0.39898329973220825 0.7291508 0.28900182247161865 True -12 35373 29.641283750534058 0.5570197105407715 1111.185546875 0.1722438931465149 1328.1519775390625 0.405200719833374 0.7381156 0.27577272057533264 True -13 38094 29.63633632659912 0.6231200695037842 1087.27880859375 0.19100168347358704 1325.1800537109375 0.40700867772102356 0.7460277 0.25887247920036316 True -14 40815 29.60671329498291 1.0008516311645508 1034.71044921875 0.19613778591156006 1323.4290771484375 0.40638646483421326 0.75374025 0.24487046897411346 True -15 43536 29.655388116836548 0.5537521839141846 1098.881591796875 0.21041445434093475 1323.0689697265625 0.4066568911075592 0.7626233 0.23687657713890076 True -16 46257 29.64653182029724 0.5580713748931885 1210.1259765625 0.18789321184158325 1320.8365478515625 0.4080023765563965 0.7661793 0.23092614114284515 True -17 48978 29.687535047531128 0.5697393417358398 1082.6700439453125 0.16350777447223663 1318.586669921875 0.4098895192146301 0.7690529 0.2263861745595932 True -18 51699 29.715866327285767 0.5668530464172363 1109.6396484375 0.16404543817043304 1318.1773681640625 0.41012051701545715 0.76928985 0.22757253050804138 True -19 54420 29.734403133392334 0.555152177810669 1033.504638671875 0.1492682695388794 1318.457763671875 0.41016098856925964 0.76783556 0.22870799899101257 False diff --git a/ENCSR820WLP/cherimoya.fold_0.performance.tsv b/ENCSR820WLP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index eeefce072984176136fd118b4b586a7428fe4164..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1318.1773681640625 0.3124164342880249 0.41012051701545715 0.21820054948329926 0.7692898511886597 0.7187800407409668 0.22757253050804138 \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_1.evaluate.json b/ENCSR820WLP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 10d48ec637d88e335db969eb07600d09dd59095c..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809JEF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_1.fit.json b/ENCSR820WLP/cherimoya.fold_1.fit.json deleted file mode 100644 index 8d653a965db33cdb4a99bd6646a34caab648e462..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF809JEF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_1.log b/ENCSR820WLP/cherimoya.fold_1.log deleted file mode 100644 index 9547d73eb16d9be4accf35adf08a932661988c46..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.17460298538208 4.900365591049194 1146.397216796875 0.5544382333755493 1751.293212890625 0.23855645954608917 0.5578772 7.299857139587402 True -1 5508 30.577101469039917 0.6794040203094482 1140.3636474609375 0.715432345867157 1546.416748046875 0.37335366010665894 0.65823925 1.283989429473877 True -2 8262 30.62976574897766 0.6509454250335693 1191.482177734375 0.6348476409912109 1501.956787109375 0.3941825032234192 0.6528009 0.6880549192428589 False -3 11016 31.13344430923462 0.6384212970733643 1185.67333984375 0.8456575274467468 1481.7154541015625 0.3978825807571411 0.6826977 0.40530869364738464 True -4 13770 30.018673181533813 0.6529092788696289 1169.63525390625 0.41406840085983276 1469.551025390625 0.40574657917022705 0.6967489 0.38108310103416443 True -5 16524 30.005539894104004 0.6554374694824219 1038.58544921875 0.3540802299976349 1461.662353515625 0.40932729840278625 0.70823103 0.4059188961982727 True -6 19278 30.008130073547363 0.646111011505127 1136.42724609375 0.3523733615875244 1453.6776123046875 0.4147370159626007 0.7150184 0.3397218585014343 True -7 22032 29.973339796066284 0.6392159461975098 1073.19287109375 0.484344482421875 1455.3331298828125 0.41351985931396484 0.7166462 0.34917163848876953 True -8 24786 29.944979906082153 0.9996011257171631 1117.0181884765625 0.45667320489883423 1446.4918212890625 0.41862133145332336 0.7285694 0.3332946002483368 True -9 27540 30.004878759384155 0.6530735492706299 1197.891357421875 0.26137709617614746 1444.5406494140625 0.4189469814300537 0.7365452 0.32615330815315247 True -10 30294 29.927210330963135 0.6491625308990479 1018.0349731445312 0.2038756161928177 1437.684814453125 0.4234098494052887 0.7449549 0.30746859312057495 True -11 33048 29.95461368560791 0.790778398513794 1193.46484375 0.23742640018463135 1432.9560546875 0.4259950816631317 0.7561658 0.30604320764541626 True -12 35802 30.000531435012817 0.7296295166015625 1074.7724609375 0.25806835293769836 1428.7010498046875 0.42742565274238586 0.76309216 0.2823239266872406 True -13 38556 30.000693798065186 0.6498210430145264 1213.758056640625 0.20695362985134125 1424.298095703125 0.4291115403175354 0.77255076 0.2691366374492645 True -14 41310 30.026110410690308 0.6337437629699707 1109.16845703125 0.18674208223819733 1418.0379638671875 0.4334211051464081 0.7803668 0.26172441244125366 True -15 44064 30.04788851737976 0.649590253829956 1104.12158203125 0.3274232745170593 1416.791748046875 0.43308040499687195 0.78680336 0.25237393379211426 True -16 46818 30.063693284988403 0.667910099029541 942.683349609375 0.1871950626373291 1414.426025390625 0.43508246541023254 0.79122424 0.25160345435142517 True -17 49572 30.21340322494507 20.06882929801941 1013.3377685546875 0.2652130126953125 1415.703857421875 0.4333140254020691 0.7905492 0.24774795770645142 False -18 52326 30.017002820968628 1.3857593536376953 1114.829345703125 0.17362260818481445 1413.496337890625 0.4350821077823639 0.79131645 0.2466668337583542 True -19 55080 30.022597074508667 1.2867486476898193 1060.5965576171875 0.1375567615032196 1415.9725341796875 0.43311378359794617 0.7922042 0.24745699763298035 True diff --git a/ENCSR820WLP/cherimoya.fold_1.performance.tsv b/ENCSR820WLP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index daa8837449adf299dd114ff089de397f34ce8c36..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1415.9725341796875 0.29694730043411255 0.43311378359794617 0.2405170202255249 0.7922042012214661 0.7461604475975037 0.24745699763298035 \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_2.evaluate.json b/ENCSR820WLP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 428aee275abb56040a31b2164bde5e900181563b..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809JEF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_2.fit.json b/ENCSR820WLP/cherimoya.fold_2.fit.json deleted file mode 100644 index a60d07c6d4ba12c5341598495ee2ad78c1b3383e..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF809JEF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_2.log b/ENCSR820WLP/cherimoya.fold_2.log deleted file mode 100644 index 3be1eb29f7e7753906bd7c20099a4b03a723256e..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 38.10983681678772 3.861039161682129 1229.109130859375 0.6765218377113342 1629.48974609375 0.231993168592453 0.5459013 5.801793575286865 True -1 5782 32.048585653305054 0.8014025688171387 975.52294921875 0.8655341863632202 1439.08740234375 0.3614348769187927 0.65488243 1.0368781089782715 True -2 8673 32.142977237701416 0.5841188430786133 1186.057373046875 0.7654415369033813 1400.4810791015625 0.38098788261413574 0.6722032 0.3937007784843445 True -3 11564 32.18025207519531 0.5359935760498047 1067.202392578125 0.253470778465271 1386.3819580078125 0.387252539396286 0.68002206 0.3705267906188965 True -4 14455 32.11467409133911 0.534928560256958 1185.0306396484375 0.4172591269016266 1379.254638671875 0.3911069333553314 0.68696856 0.37776514887809753 True -5 17346 32.05407452583313 0.5380358695983887 1148.3865966796875 0.32879698276519775 1374.8602294921875 0.39400479197502136 0.6877648 0.34195277094841003 True -6 20237 32.11607480049133 0.5435528755187988 1109.5821533203125 0.2617095708847046 1367.6204833984375 0.3991850018501282 0.69481945 0.31618058681488037 True -7 23128 32.17120432853699 0.5698182582855225 1207.27490234375 0.3282001316547394 1367.8167724609375 0.397239625453949 0.70462584 0.30955082178115845 True -8 26019 32.04593825340271 0.5438318252563477 1181.347900390625 0.3944789469242096 1362.2669677734375 0.40258848667144775 0.7093085 0.32359153032302856 True -9 28910 32.451343059539795 0.5841243267059326 1065.228759765625 0.1876915693283081 1355.7071533203125 0.4069273769855499 0.71764565 0.31366604566574097 True -10 31801 32.31125569343567 0.5340559482574463 1247.7008056640625 0.31280532479286194 1349.412841796875 0.411070317029953 0.72451216 0.2913684546947479 True -11 34692 32.124772787094116 0.5669577121734619 1047.345947265625 0.3610804080963135 1347.8876953125 0.4109061062335968 0.73238266 0.2846957743167877 True -12 37583 32.20191431045532 0.5466601848602295 1163.781982421875 0.3016427755355835 1346.1796875 0.4115508496761322 0.7419005 0.2762892544269562 True -13 40474 32.2090961933136 0.5403692722320557 1069.4429931640625 0.2764861285686493 1341.3409423828125 0.4152088463306427 0.74752575 0.2688470184803009 True -14 43365 32.21256470680237 1.209205150604248 1262.844482421875 0.3114204704761505 1337.277099609375 0.4176770746707916 0.75696987 0.2576584815979004 True -15 46256 31.641558408737183 0.5334727764129639 1227.080322265625 0.5920116901397705 1338.5074462890625 0.41690436005592346 0.7615233 0.25021106004714966 True -16 49147 31.60302209854126 0.524662971496582 1116.47314453125 0.161379873752594 1338.235107421875 0.41529351472854614 0.76775 0.24605214595794678 True -17 52038 31.658447742462158 0.5250391960144043 1060.09912109375 0.25858187675476074 1331.6544189453125 0.42125165462493896 0.77064055 0.24133874475955963 True -18 54929 31.662818670272827 0.525341272354126 1111.01416015625 0.1618548333644867 1335.0908203125 0.41794222593307495 0.76971555 0.24227753281593323 False -19 57820 31.581880807876587 1.2508840560913086 1178.8291015625 0.2457127869129181 1335.78564453125 0.41729578375816345 0.76981896 0.24539542198181152 False diff --git a/ENCSR820WLP/cherimoya.fold_2.performance.tsv b/ENCSR820WLP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1d5103f36294141313c163b15470ad173cba39ae..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1331.6544189453125 0.3081812858581543 0.4212516248226166 0.2257661372423172 0.7706405520439148 0.7192107439041138 0.24133874475955963 \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_3.evaluate.json b/ENCSR820WLP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fb538faefbef610a449a004200302f40bfaabf96..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809JEF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_3.fit.json b/ENCSR820WLP/cherimoya.fold_3.fit.json deleted file mode 100644 index ad2348aaeacf4b157e9c4bb71e440ab3e3db2873..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF809JEF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_3.log b/ENCSR820WLP/cherimoya.fold_3.log deleted file mode 100644 index d1e935331fa4753f1a08038263d1e0e473d4835a..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2818 36.2256600856781 5.54568076133728 1299.44970703125 0.6101654767990112 1655.421142578125 0.2340688705444336 0.5568641 7.163476943969727 True -1 5636 31.2967586517334 0.7215487957000732 1293.319091796875 0.3463561534881592 1483.5703125 0.355503112077713 0.6209756 1.3587504625320435 True -2 8454 31.2941255569458 0.6759803295135498 1195.1043701171875 0.6557374000549316 1451.784912109375 0.36903703212738037 0.6446193 0.4858872592449188 True -3 11272 31.301632404327393 1.3867201805114746 1208.03662109375 0.3452815115451813 1435.252197265625 0.3763231337070465 0.6544681 0.44222068786621094 True -4 14090 31.30039644241333 0.5848960876464844 1247.447509765625 0.377450555562973 1426.4349365234375 0.3809604346752167 0.66838413 0.44130951166152954 True -5 16908 31.125906944274902 0.601503849029541 1085.26611328125 0.3207797408103943 1420.1070556640625 0.38451576232910156 0.6741156 0.3574693202972412 True -6 19726 30.693740844726562 0.5973029136657715 1067.339111328125 0.4176870584487915 1415.322265625 0.38814714550971985 0.68422794 0.3522854447364807 True -7 22544 30.6780686378479 0.5831410884857178 1154.630859375 0.3638419210910797 1414.9580078125 0.38775935769081116 0.6851036 0.35822227597236633 True -8 25362 30.649393558502197 0.6016302108764648 1116.51806640625 0.2672308385372162 1406.372802734375 0.3932570815086365 0.70116305 0.3313881456851959 True -9 28180 30.616262912750244 2.5584869384765625 1156.88671875 0.4399265646934509 1403.3800048828125 0.3955133557319641 0.7065215 0.3269335627555847 True -10 30998 30.680706024169922 0.5814523696899414 1075.9334716796875 0.30346059799194336 1398.854736328125 0.3977620601654053 0.71528757 0.3154437243938446 True -11 33816 30.750579118728638 0.5895242691040039 1260.05810546875 0.5137174129486084 1396.481201171875 0.39895322918891907 0.728529 0.2978363037109375 True -12 36634 30.909354209899902 0.6119215488433838 1192.9654541015625 0.28600531816482544 1391.998291015625 0.40169471502304077 0.7401803 0.2783866822719574 True -13 39452 30.999926567077637 0.6131923198699951 1116.2783203125 0.4368153214454651 1387.9686279296875 0.40532657504081726 0.74718356 0.273385226726532 True -14 42270 30.8599636554718 0.6159520149230957 1071.8919677734375 0.5067737102508545 1383.340576171875 0.40775078535079956 0.75601375 0.26222753524780273 True -15 45088 30.807151317596436 1.44386887550354 1193.64453125 0.20446911454200745 1383.7003173828125 0.40678897500038147 0.76262486 0.2531452775001526 True -16 47906 30.791834592819214 0.5880401134490967 1215.876708984375 0.322734534740448 1381.7830810546875 0.4083694815635681 0.76820445 0.2475481778383255 True -17 50724 30.722226858139038 0.5910625457763672 1031.1280517578125 0.23910097777843475 1381.2989501953125 0.40839502215385437 0.7726386 0.2430068403482437 True -18 53542 30.687225580215454 0.5921552181243896 1060.564697265625 0.2446318119764328 1384.3509521484375 0.40551722049713135 0.77254874 0.2426604926586151 False -19 56360 30.681238889694214 0.5888354778289795 1069.6953125 0.1426253318786621 1380.2742919921875 0.40982332825660706 0.7715848 0.24406389892101288 False diff --git a/ENCSR820WLP/cherimoya.fold_3.performance.tsv b/ENCSR820WLP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5e1d424632dc1ca3cec90893282cae1ba0eead68..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1381.2989501953125 0.3090997636318207 0.40839505195617676 0.224028542637825 0.7726386189460754 0.728187084197998 0.2430068403482437 \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_4.evaluate.json b/ENCSR820WLP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9e5594553213677a21b6305180b6c26da23369b1..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809JEF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_4.fit.json b/ENCSR820WLP/cherimoya.fold_4.fit.json deleted file mode 100644 index 232a8171cc9c07862672308064058a761ca3fe34..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF809JEF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR820WLP/cherimoya.fold_4.log b/ENCSR820WLP/cherimoya.fold_4.log deleted file mode 100644 index 70ef0e52fa6272adb65a74e006141b8ae13f4310..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2932 37.28626537322998 4.201032876968384 1115.141845703125 0.40040409564971924 1611.6119384765625 0.23191650211811066 0.53322667 6.59359884262085 True -1 5864 32.505953788757324 0.6051788330078125 1191.3360595703125 0.3312331438064575 1428.7620849609375 0.3611120283603668 0.6334922 0.8998233675956726 True -2 8796 32.554691553115845 0.5332162380218506 1133.146484375 0.6764615774154663 1404.5543212890625 0.37042713165283203 0.64251745 0.3289458751678467 True -3 11728 32.55988550186157 0.530186653137207 1068.8427734375 0.44175511598587036 1388.7994384765625 0.37717366218566895 0.6655407 0.32255566120147705 True -4 14660 32.3154501914978 0.5383772850036621 1189.186767578125 0.42541199922561646 1382.099609375 0.381387859582901 0.6696225 0.324832022190094 True -5 17592 31.936350107192993 0.5271849632263184 1205.945556640625 0.35785579681396484 1372.2337646484375 0.3886241614818573 0.68085825 0.3208096921443939 True -6 20524 31.91980504989624 0.5383062362670898 1253.946533203125 0.4262503981590271 1370.8326416015625 0.389192670583725 0.684394 0.3107011020183563 True -7 23456 31.99101948738098 0.5378425121307373 1004.7647705078125 0.2792870104312897 1367.07373046875 0.39139795303344727 0.6930349 0.29838332533836365 True -8 26388 31.982120037078857 0.542320728302002 1087.004150390625 0.3150121569633484 1359.728271484375 0.3956858813762665 0.7034149 0.2833268940448761 True -9 29320 31.94716477394104 0.9043962955474854 1013.9916381835938 0.7478334903717041 1358.609130859375 0.39586251974105835 0.7107866 0.27571508288383484 True -10 32252 31.946533679962158 0.9998247623443604 1098.4981689453125 0.25890976190567017 1351.3265380859375 0.4013410210609436 0.7204674 0.26368585228919983 True -11 35184 31.91979193687439 0.5461227893829346 1001.0255737304688 0.2628573775291443 1348.3963623046875 0.4032161831855774 0.72947896 0.2648025155067444 True -12 38116 31.906856775283813 0.5463266372680664 1089.30615234375 0.2738485038280487 1343.7830810546875 0.40634551644325256 0.7376383 0.2568312883377075 True -13 41048 31.905982494354248 0.5472776889801025 1275.955078125 0.35411977767944336 1341.39697265625 0.407553493976593 0.7475752 0.24355417490005493 True -14 43980 31.928058862686157 0.5397894382476807 1035.31884765625 0.16806557774543762 1338.156005859375 0.4096636176109314 0.75650346 0.238829106092453 True -15 46912 31.916156768798828 0.5474181175231934 1113.455322265625 0.4931454658508301 1338.8260498046875 0.40820908546447754 0.7600003 0.23381486535072327 True -16 49844 31.95241618156433 0.548088550567627 1082.801025390625 0.3281973600387573 1337.047119140625 0.4101329445838928 0.76608604 0.22962449491024017 True -17 52776 31.93454337120056 0.5465097427368164 1097.0059814453125 0.3260863721370697 1337.20751953125 0.411064475774765 0.7681741 0.2305595576763153 True -18 55708 31.93489408493042 0.5456664562225342 1153.063720703125 0.16677844524383545 1337.5286865234375 0.40982717275619507 0.7658618 0.2308422476053238 False -19 58640 31.848092079162598 0.5369687080383301 1048.4261474609375 0.2665252685546875 1337.811279296875 0.40967312455177307 0.7678995 0.2319326549768448 False diff --git a/ENCSR820WLP/cherimoya.fold_4.performance.tsv b/ENCSR820WLP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index de57041bcb190e345aa961ae9e07361221ab4868..0000000000000000000000000000000000000000 --- a/ENCSR820WLP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1337.20751953125 0.3107578456401825 0.4110645353794098 0.22211740911006927 0.7681741118431091 0.7145093679428101 0.2305595576763153 \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_0.evaluate.json b/ENCSR821JHD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 64376803db68c77a5f8092a151e79dac5b4b13a0..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF884GLN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_0.fit.json b/ENCSR821JHD/cherimoya.fold_0.fit.json deleted file mode 100644 index 373e5f0573264e2754ab7c54a8944b7c3362eb59..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF884GLN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_0.log b/ENCSR821JHD/cherimoya.fold_0.log deleted file mode 100644 index 56b7c159af32cb9e8d2412060f4c38e9a8e60937..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1994 26.644492149353027 5.899630784988403 244.35537719726562 0.6012274026870728 409.3749084472656 0.42617344856262207 0.5360481 10.037631034851074 True -1 3988 22.135071277618408 0.4417858123779297 238.6074676513672 0.7791674137115479 346.9851379394531 0.5442009568214417 0.6172121 4.2991132736206055 True -2 5982 22.15933632850647 7.695897102355957 226.638671875 0.7191125750541687 329.7086181640625 0.5855581164360046 0.6373488 1.0435059070587158 True -3 7976 22.16770362854004 0.41559815406799316 225.49484252929688 0.5311079025268555 325.03265380859375 0.5947684645652771 0.6540208 0.726109504699707 True -4 9970 22.147740125656128 14.578012466430664 281.93426513671875 0.6707306504249573 322.77056884765625 0.5997164249420166 0.659003 0.622574508190155 True -5 11964 22.119651794433594 0.42580747604370117 276.77484130859375 0.6501580476760864 321.1282043457031 0.6034579873085022 0.6652096 0.5972477793693542 True -6 13958 22.07827854156494 0.40523457527160645 226.57293701171875 0.7295970320701599 320.06854248046875 0.6061018109321594 0.67049605 0.5737478137016296 True -7 15952 22.08663582801819 0.3987722396850586 235.5714874267578 0.6927822232246399 319.177490234375 0.6082209348678589 0.6675132 0.5571179986000061 False -8 17946 22.07589888572693 1.047957420349121 269.4763488769531 0.5553117990493774 318.0879821777344 0.6104783415794373 0.6749369 0.5279332995414734 True -9 19940 22.158922910690308 1.5836024284362793 222.6954345703125 0.5409805178642273 317.2255554199219 0.6126306056976318 0.67970484 0.5176189541816711 True -10 21934 22.13217782974243 0.4072301387786865 219.12631225585938 0.5749225616455078 316.375244140625 0.6147942543029785 0.6864021 0.5143852829933167 True -11 23928 22.206721305847168 0.41658830642700195 271.96258544921875 0.47757795453071594 315.5452575683594 0.6165983080863953 0.68783885 0.505413830280304 True -12 25922 22.132273197174072 0.41553831100463867 262.55194091796875 0.4351578950881958 314.76861572265625 0.6184830069541931 0.6937332 0.4938821494579315 True -13 27916 22.059807062149048 0.42043495178222656 254.04388427734375 0.3710687756538391 314.3511962890625 0.6195670366287231 0.6999875 0.49583330750465393 True -14 29910 21.843839645385742 0.4248623847961426 225.2330322265625 0.557876706123352 313.664306640625 0.6208840012550354 0.70726794 0.48135703802108765 True -15 31904 21.84533452987671 0.7380361557006836 251.41793823242188 0.37695592641830444 313.5069885253906 0.6215620636940002 0.7108654 0.4839686453342438 True -16 33898 21.81738305091858 0.4086167812347412 264.91900634765625 0.31198984384536743 313.13336181640625 0.621633768081665 0.7134517 0.4867262542247772 True -17 35892 21.800498723983765 0.43703508377075195 222.55361938476562 0.32850581407546997 313.50054931640625 0.6210945248603821 0.70941556 0.5021937489509583 False -18 37886 21.81925630569458 0.4086790084838867 240.49688720703125 0.39443957805633545 313.834228515625 0.6206218004226685 0.7047744 0.5154134631156921 False -19 39880 21.76613211631775 0.4034407138824463 228.82554626464844 0.2388792783021927 313.7229919433594 0.6202104687690735 0.7022191 0.5242763161659241 False diff --git a/ENCSR821JHD/cherimoya.fold_0.performance.tsv b/ENCSR821JHD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 67db991b4b1c18ec393b5275bf2d065f7a21fb16..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -313.13336181640625 0.312574565410614 0.621633768081665 0.20558704435825348 0.7134516835212708 0.6672265529632568 0.4867262542247772 \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_1.evaluate.json b/ENCSR821JHD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c9a68740878bd4dfe8a216760862b4237127e70c..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF884GLN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_1.fit.json b/ENCSR821JHD/cherimoya.fold_1.fit.json deleted file mode 100644 index b57b0e32b2e1c7f00efc7b304f2bbd629400cc0b..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF884GLN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_1.log b/ENCSR821JHD/cherimoya.fold_1.log deleted file mode 100644 index 034164fcb60b33a7a349f440d420429dd723c69d..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2034 26.96057653427124 3.5533900260925293 272.0090026855469 1.2195930480957031 410.4678039550781 0.4355245530605316 0.523283 8.344813346862793 True -1 4068 22.59517240524292 0.5424010753631592 232.541748046875 0.8115771412849426 355.39178466796875 0.5444273948669434 0.6300869 3.2257392406463623 True -2 6102 22.585416078567505 23.025110960006714 250.22926330566406 0.7273328900337219 339.8680114746094 0.5814878344535828 0.6475108 1.1050500869750977 True -3 8136 22.638386011123657 0.46237874031066895 224.104248046875 0.8216375112533569 334.7939453125 0.5913326144218445 0.6651054 0.65312260389328 True -4 10170 22.560688734054565 0.4597952365875244 235.2946014404297 0.7614415287971497 333.3332824707031 0.5946407914161682 0.6796112 0.5891388058662415 True -5 12204 22.549389839172363 0.7540531158447266 243.09518432617188 0.706147313117981 332.8900451660156 0.5964982509613037 0.68502283 0.5687246918678284 True -6 14238 22.530417442321777 0.46973729133605957 247.99807739257812 0.472761869430542 331.8934631347656 0.5990798473358154 0.6886949 0.5705331563949585 True -7 16272 22.567250728607178 0.45398974418640137 248.17239379882812 0.7197359800338745 330.4400939941406 0.6022168397903442 0.6925676 0.5556380748748779 True -8 18306 22.598231077194214 0.4467458724975586 288.32806396484375 0.563096284866333 329.5048522949219 0.6040196418762207 0.6960564 0.5312232375144958 True -9 20340 22.593653678894043 0.46098923683166504 257.31500244140625 0.5830991268157959 328.3653869628906 0.6065922379493713 0.7033085 0.5139518976211548 True -10 22374 22.545056581497192 0.4588782787322998 252.01502990722656 0.47003433108329773 327.52667236328125 0.6087927222251892 0.7075057 0.48892298340797424 True -11 24408 22.607697248458862 0.4623525142669678 240.34140014648438 0.43315422534942627 326.5067443847656 0.6109229922294617 0.7138085 0.4733370244503021 True -12 26442 22.592377185821533 0.4624302387237549 242.42813110351562 0.5764771103858948 325.73406982421875 0.6128852963447571 0.72082347 0.466639906167984 True -13 28476 22.57143783569336 1.203348159790039 236.2943878173828 0.4438774287700653 325.0323791503906 0.6141552925109863 0.72501284 0.45462995767593384 True -14 30510 22.57503652572632 0.44665980339050293 206.52093505859375 0.48452436923980713 324.78192138671875 0.6151247024536133 0.7336971 0.4443102180957794 True -15 32544 22.638638496398926 0.5141017436981201 217.32412719726562 0.46361351013183594 324.2196960449219 0.6157985329627991 0.7338791 0.44075721502304077 True -16 34578 22.589414358139038 0.4607813358306885 224.92413330078125 0.34650707244873047 324.2699890136719 0.61586594581604 0.7361222 0.44179868698120117 True -17 36612 22.61388349533081 1.837705135345459 251.89796447753906 0.35007452964782715 324.2793273925781 0.6155174970626831 0.7345127 0.4471966326236725 False -18 38646 22.604008197784424 1.721170425415039 244.89756774902344 0.35657939314842224 324.5076599121094 0.615036129951477 0.73271626 0.4546070694923401 False -19 40680 22.78820562362671 0.45800065994262695 242.63375854492188 0.25167202949523926 324.3200378417969 0.6146712303161621 0.73043686 0.45931339263916016 False diff --git a/ENCSR821JHD/cherimoya.fold_1.performance.tsv b/ENCSR821JHD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 38811e685666fa142094c640fedda3146229e141..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.2699890136719 0.31119972467422485 0.61586594581604 0.2106482833623886 0.736122190952301 0.7204165458679199 0.44179868698120117 \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_2.evaluate.json b/ENCSR821JHD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 561341665dfcac7aa862f72fec9a1e2804e9c89b..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF884GLN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_2.fit.json b/ENCSR821JHD/cherimoya.fold_2.fit.json deleted file mode 100644 index d9983f001a593b3904512b59ed6b24630440aedb..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF884GLN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_2.log b/ENCSR821JHD/cherimoya.fold_2.log deleted file mode 100644 index c1ceeda4dba5957382a00abe31c2857cda667a78..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2115 28.25701355934143 4.849842071533203 269.9488525390625 0.7858608365058899 407.597900390625 0.43230804800987244 0.5352508 8.67229175567627 True -1 4230 23.254655122756958 0.4561007022857666 240.69989013671875 0.9088547229766846 348.7645263671875 0.5510179996490479 0.642746 3.8522372245788574 True -2 6345 23.511276245117188 0.39270830154418945 282.05975341796875 0.8134888410568237 334.11102294921875 0.5806580781936646 0.6593812 1.447947382926941 True -3 8460 23.571149587631226 0.3912177085876465 257.65130615234375 0.6535322070121765 329.298583984375 0.5906331539154053 0.6656764 0.8939449787139893 True -4 10575 23.527942180633545 0.3916497230529785 312.2656555175781 0.5965601801872253 327.49066162109375 0.5945776104927063 0.6668942 0.7655897736549377 True -5 12690 23.534189462661743 0.6885473728179932 286.816162109375 0.7164279818534851 326.2774658203125 0.5977421402931213 0.66879576 0.7286017537117004 True -6 14805 23.180631399154663 0.3903501033782959 230.18087768554688 0.5710210800170898 325.19488525390625 0.5999326109886169 0.674032 0.7065464854240417 True -7 16920 23.214651107788086 0.39316678047180176 292.1349182128906 0.5451048612594604 324.0422058105469 0.6024678349494934 0.6754144 0.6785598993301392 True -8 19035 23.132882833480835 0.39102745056152344 252.84689331054688 0.47256046533584595 322.9982604980469 0.6049867868423462 0.6771136 0.6593996286392212 True -9 21150 23.116498470306396 0.385007381439209 215.78768920898438 0.6145893335342407 321.8875732421875 0.6071847677230835 0.6842117 0.6166555285453796 True -10 23265 23.11210536956787 0.40363168716430664 242.26751708984375 0.5038629770278931 321.12176513671875 0.608986496925354 0.6921473 0.588965117931366 True -11 25380 23.092527627944946 0.3932681083679199 224.9322509765625 0.40633219480514526 319.9495544433594 0.6113767623901367 0.69661903 0.5604715943336487 True -12 27495 23.278862714767456 0.3958315849304199 254.54620361328125 0.5551958680152893 319.4031066894531 0.6129584312438965 0.70222867 0.5419096350669861 True -13 29610 23.03420639038086 0.38690781593322754 261.24432373046875 0.5077259540557861 318.4496154785156 0.6147889494895935 0.70838326 0.529188871383667 True -14 31725 23.015199661254883 0.391216516494751 211.91925048828125 0.5869594216346741 317.93890380859375 0.6159396767616272 0.71256006 0.5113767385482788 True -15 33840 22.997687101364136 0.3827989101409912 227.0132598876953 0.451069176197052 317.63543701171875 0.6164937615394592 0.7160032 0.5043414235115051 True -16 35955 23.086347341537476 12.88656997680664 256.77789306640625 0.25894051790237427 317.4806823730469 0.6165316700935364 0.7152693 0.5104755163192749 False -17 38070 23.371190547943115 0.3813447952270508 226.1956329345703 0.3323081433773041 317.65985107421875 0.6161864995956421 0.7151316 0.51276034116745 False -18 40185 23.144157648086548 0.3869168758392334 235.62025451660156 0.2774607539176941 317.7638244628906 0.615741491317749 0.7133701 0.516549289226532 False -19 42300 23.085436582565308 0.4494187831878662 267.9270935058594 0.4013863801956177 318.01263427734375 0.6152844429016113 0.7112995 0.5261228084564209 False diff --git a/ENCSR821JHD/cherimoya.fold_2.performance.tsv b/ENCSR821JHD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bff8db4f0c58d672c70cb940aad0574089421b32..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.63543701171875 0.3130960166454315 0.6164937615394592 0.2100827991962433 0.7160031795501709 0.6818215847015381 0.5043414235115051 \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_3.evaluate.json b/ENCSR821JHD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 28b31fb108eba29248c1c71c87d8d4b62b1e1b99..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF884GLN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_3.fit.json b/ENCSR821JHD/cherimoya.fold_3.fit.json deleted file mode 100644 index e7b9ac7bf848302f8d98c905b9299891a2c9e3bf..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF884GLN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_3.log b/ENCSR821JHD/cherimoya.fold_3.log deleted file mode 100644 index ece306758dcfe5a41432ade81c30f5ab47943092..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2062 27.43851637840271 3.5905165672302246 294.5326843261719 1.1396262645721436 411.55126953125 0.4347988963127136 0.5331586 10.058238983154297 True -1 4124 22.925974369049072 0.8727884292602539 259.13555908203125 0.735004186630249 349.0515441894531 0.554620087146759 0.61020017 3.9790711402893066 True -2 6186 22.891677618026733 0.4599795341491699 315.248779296875 0.6998345851898193 335.1123962402344 0.586394727230072 0.61537623 1.4075065851211548 True -3 8248 22.845343112945557 0.5057458877563477 234.95767211914062 0.6072158813476562 330.15362548828125 0.5953930020332336 0.6334086 0.9207842946052551 True -4 10310 22.870890617370605 0.4499022960662842 254.96966552734375 0.5738223791122437 328.5850830078125 0.5983588695526123 0.6403769 0.7979295253753662 True -5 12372 22.94905138015747 0.4560890197753906 237.3336181640625 1.0072402954101562 327.4342956542969 0.6009116768836975 0.6428706 0.7679750919342041 True -6 14434 22.872137308120728 0.4508037567138672 247.4246826171875 1.1250295639038086 326.44598388671875 0.6034788489341736 0.6575901 0.7505980730056763 True -7 16496 22.875826120376587 0.8850007057189941 230.17991638183594 0.6822852492332458 325.25537109375 0.6059879064559937 0.66701937 0.748846173286438 True -8 18558 22.930100917816162 0.46491456031799316 266.39154052734375 0.5290294885635376 324.3691101074219 0.6081700921058655 0.6668885 0.7447835206985474 False -9 20620 22.83412480354309 0.44572973251342773 232.3719024658203 0.7473695278167725 323.47796630859375 0.6101046204566956 0.6680829 0.6818466782569885 True -10 22682 22.456069231033325 1.7512333393096924 254.30950927734375 0.6202918291091919 322.4134826660156 0.6125549077987671 0.6756474 0.6583755612373352 True -11 24744 22.48197913169861 0.4516112804412842 248.5328369140625 0.4792896509170532 321.703369140625 0.6144865155220032 0.683605 0.6174747347831726 True -12 26806 22.41543459892273 0.4980306625366211 200.22970581054688 0.45304787158966064 320.9521179199219 0.6161800622940063 0.69266355 0.5785064101219177 True -13 28868 22.444392919540405 0.4529399871826172 226.91262817382812 0.4976979196071625 320.1443176269531 0.617798388004303 0.7037367 0.5525948405265808 True -14 30930 22.477985382080078 0.4487166404724121 234.87982177734375 0.4463050067424774 319.4898986816406 0.6191738247871399 0.70845306 0.5266776084899902 True -15 32992 22.499821186065674 0.4472169876098633 198.0404052734375 0.4487910270690918 319.12152099609375 0.6197695732116699 0.7118432 0.5251297950744629 True -16 35054 22.481091499328613 0.4620835781097412 261.8281555175781 0.4044777750968933 319.127197265625 0.6201605796813965 0.7152351 0.5185412764549255 True -17 37116 22.496751308441162 0.46648287773132324 235.13841247558594 0.4209713339805603 319.2032775878906 0.6198478937149048 0.7184361 0.5116910338401794 True -18 39178 22.531869888305664 0.44192934036254883 228.45001220703125 0.4293748736381531 319.07781982421875 0.6192294359207153 0.71541417 0.5184716582298279 False -19 41240 22.480076789855957 0.4404938220977783 221.65672302246094 0.2659199833869934 319.2627258300781 0.6188775300979614 0.7125284 0.5223804712295532 False diff --git a/ENCSR821JHD/cherimoya.fold_3.performance.tsv b/ENCSR821JHD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2c1c0b44a073db9e42ff6d7fa1feb0c033ae822b..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -319.2032775878906 0.31082582473754883 0.6198479533195496 0.21049043536186218 0.7184361219406128 0.6817277669906616 0.5116910338401794 \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_4.evaluate.json b/ENCSR821JHD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2c54177a5b3bd1226533bfde45f9aa2806e28b34..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF884GLN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_4.fit.json b/ENCSR821JHD/cherimoya.fold_4.fit.json deleted file mode 100644 index 74ffbd829b47bbf98fcd3010298b655d523584a0..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF884GLN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821JHD/cherimoya.fold_4.log b/ENCSR821JHD/cherimoya.fold_4.log deleted file mode 100644 index fa508ace03f4cdca0d9ec7ebf425cda938c73240..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2129 27.98481297492981 3.5901827812194824 270.6355895996094 0.8070829510688782 409.1693420410156 0.4344244599342346 0.57372665 9.527295112609863 True -1 4258 23.63798999786377 2.1449363231658936 266.271484375 0.8324127197265625 350.83270263671875 0.5540093779563904 0.6225453 3.127755641937256 True -2 6387 23.684210777282715 0.4190330505371094 270.9239501953125 0.662991464138031 336.1252746582031 0.5889896154403687 0.6434581 0.9856154322624207 True -3 8516 23.861459970474243 15.298579216003418 258.78466796875 0.4513794779777527 329.7451171875 0.5997675061225891 0.654788 0.700319766998291 True -4 10645 23.632533073425293 0.4269397258758545 262.93896484375 0.5953812003135681 327.9171142578125 0.6032883524894714 0.66179645 0.6537725925445557 True -5 12774 24.891401290893555 0.4702780246734619 260.7059326171875 0.4980858266353607 326.8146057128906 0.6057793498039246 0.6641118 0.62964928150177 True -6 14903 23.686568021774292 0.7192623615264893 288.3741455078125 0.7355257272720337 326.1631774902344 0.6072472333908081 0.66410524 0.6312893629074097 False -7 17032 23.630478382110596 0.42122459411621094 257.8236999511719 0.6652445197105408 325.27117919921875 0.6096648573875427 0.6721254 0.6107683777809143 True -8 19161 23.69720959663391 0.4266953468322754 241.72378540039062 0.6043703556060791 324.2296142578125 0.6118576526641846 0.674743 0.5988653898239136 True -9 21290 23.74885058403015 0.4256415367126465 251.46017456054688 0.4215536415576935 323.4803771972656 0.6133944988250732 0.68084705 0.5745683908462524 True -10 23419 23.6203351020813 0.7729752063751221 232.51513671875 0.6292041540145874 322.1725158691406 0.6163028478622437 0.6870031 0.5448251962661743 True -11 25548 23.67623281478882 0.4151186943054199 218.08193969726562 0.6305036544799805 321.3564758300781 0.6180986762046814 0.6965888 0.5170745253562927 True -12 27677 23.69139528274536 0.4219505786895752 209.79067993164062 0.4689708352088928 320.568359375 0.6199696660041809 0.7058283 0.49885454773902893 True -13 29806 23.619868278503418 0.4487893581390381 267.7919616699219 0.3501124382019043 319.86260986328125 0.6215569972991943 0.7087067 0.49090754985809326 True -14 31935 23.61461877822876 0.4293019771575928 271.9601135253906 0.4532393217086792 319.1930847167969 0.6231600046157837 0.71337914 0.4844729006290436 True -15 34064 23.61168646812439 0.41324615478515625 277.1264953613281 0.34535861015319824 318.81329345703125 0.6238817572593689 0.71948135 0.4798142910003662 True -16 36193 23.63689613342285 0.41475915908813477 254.4445343017578 0.46647727489471436 318.63812255859375 0.6239753365516663 0.7187955 0.4912854731082916 False -17 38322 23.721296787261963 0.4132051467895508 244.49078369140625 0.5968891978263855 318.76763916015625 0.6235969066619873 0.71769935 0.4984728693962097 False -18 40451 23.46640968322754 0.4072251319885254 229.85804748535156 0.31161290407180786 318.97393798828125 0.6229408383369446 0.7142413 0.510460615158081 False -19 42580 23.15854573249817 0.399369478225708 227.0367889404297 0.4110412001609802 319.1620788574219 0.6224814653396606 0.71291137 0.5152279138565063 False diff --git a/ENCSR821JHD/cherimoya.fold_4.performance.tsv b/ENCSR821JHD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3292fe862fefc970f23c706ad412a6edc44f06a6..0000000000000000000000000000000000000000 --- a/ENCSR821JHD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -318.81329345703125 0.3094032108783722 0.6238817572593689 0.21067661046981812 0.719481348991394 0.6679835319519043 0.4798142910003662 \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_0.evaluate.json b/ENCSR821QHC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index da9ad93b0959de4ed1ce6241ffa50cf999978735..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF493LUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_0.fit.json b/ENCSR821QHC/cherimoya.fold_0.fit.json deleted file mode 100644 index 3a92d922e806e1d0085a49aeb7b3c2baf516058c..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF493LUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_0.log b/ENCSR821QHC/cherimoya.fold_0.log deleted file mode 100644 index 854bd5588c694d131a012767842cc8b94dfc5c99..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2341 30.451773643493652 3.8208582401275635 325.26177978515625 0.6578224301338196 614.1982421875 0.5173395276069641 0.5620678 10.057798385620117 True -1 4682 25.834956407546997 0.8781347274780273 360.170654296875 0.7630492448806763 516.48779296875 0.637728750705719 0.65304506 3.1051700115203857 True -2 7023 25.801620960235596 0.483165979385376 426.9786682128906 0.7251836061477661 499.14990234375 0.6632974743843079 0.6554019 1.2488369941711426 True -3 9364 25.789555311203003 0.4809746742248535 396.203125 0.58122318983078 493.38787841796875 0.6701862812042236 0.67063135 0.9275065660476685 True -4 11705 25.28826904296875 0.47009706497192383 452.173095703125 0.6041279435157776 490.0440368652344 0.6738486886024475 0.6772351 0.8516033887863159 True -5 14046 25.316834926605225 0.47423720359802246 448.0830078125 0.6309268474578857 488.3271179199219 0.676357626914978 0.6819088 0.7636722922325134 True -6 16387 25.285764932632446 0.5089402198791504 390.2137451171875 0.5824247598648071 486.2644958496094 0.6791722774505615 0.68083054 0.7208782434463501 False -7 18728 25.284588098526 0.4801511764526367 372.1809997558594 0.4329030513763428 485.2371826171875 0.681119978427887 0.6850698 0.6829330921173096 True -8 21069 25.32999086380005 0.4762876033782959 414.48931884765625 0.705329418182373 484.2664489746094 0.6827822923660278 0.6927169 0.6149753332138062 True -9 23410 25.312610864639282 0.4757394790649414 438.7242431640625 0.6905604600906372 482.8908996582031 0.6844037771224976 0.7009685 0.5824720859527588 True -10 25751 25.305246829986572 0.4799375534057617 383.6051940917969 0.39025771617889404 481.58709716796875 0.6862234473228455 0.7059652 0.5633264780044556 True -11 28092 25.32683777809143 0.48131871223449707 413.9671630859375 0.4453467130661011 480.0569152832031 0.688052237033844 0.7130626 0.5398707389831543 True -12 30433 25.3132803440094 1.4267947673797607 412.4872131347656 0.41195884346961975 478.5203552246094 0.6899328231811523 0.720036 0.5261274576187134 True -13 32774 25.33232307434082 0.46955394744873047 413.35443115234375 0.3246024549007416 477.1502380371094 0.6916294097900391 0.7275176 0.4931764304637909 True -14 35115 25.3348228931427 0.48349690437316895 385.27630615234375 0.36882877349853516 476.5885925292969 0.6924299001693726 0.7322712 0.4847864806652069 True -15 37456 25.294027090072632 0.47490382194519043 357.41558837890625 0.28457126021385193 475.96307373046875 0.693012535572052 0.73234475 0.4803229570388794 True -16 39797 25.359628915786743 0.4786510467529297 336.49462890625 0.23152422904968262 475.9387512207031 0.6930590867996216 0.7350514 0.481584370136261 True -17 42138 25.368191957473755 0.48531222343444824 405.770263671875 0.20011422038078308 476.27764892578125 0.6926072835922241 0.7315891 0.4845549166202545 False -18 44479 25.359496593475342 0.48551106452941895 370.455322265625 0.22607392072677612 476.6912536621094 0.6920127868652344 0.72963357 0.4910627603530884 False -19 46820 25.30955171585083 0.4704279899597168 332.0557556152344 0.2626339793205261 476.7912292480469 0.6916695833206177 0.72603506 0.5003981590270996 False diff --git a/ENCSR821QHC/cherimoya.fold_0.performance.tsv b/ENCSR821QHC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c090973ecbcfcbf3191fa5968dd88df710ca4931..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.9387512207031 0.24928823113441467 0.6930590867996216 0.30900824069976807 0.7350513935089111 0.6663033962249756 0.481584370136261 \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_1.evaluate.json b/ENCSR821QHC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ed5e5cbe854033a1381c2dddc385ab57ae76be49..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF493LUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_1.fit.json b/ENCSR821QHC/cherimoya.fold_1.fit.json deleted file mode 100644 index 5c784101ce54445db183a064f73eaa977c6d04e2..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF493LUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_1.log b/ENCSR821QHC/cherimoya.fold_1.log deleted file mode 100644 index b87a71e512e6ef4107892de325c7bc8d05d120e6..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2368 30.85304546356201 5.859776973724365 369.21124267578125 0.6952129006385803 638.7845458984375 0.5334901213645935 0.5794881 10.5892333984375 True -1 4736 26.108505725860596 2.2802939414978027 378.7457275390625 1.08529531955719 551.2697143554688 0.6423236131668091 0.6926304 3.1500420570373535 True -2 7104 26.097301959991455 0.6282782554626465 409.2662353515625 0.7846170663833618 531.4752197265625 0.6670182347297668 0.69399965 0.9663870334625244 True -3 9472 26.121174335479736 0.5706326961517334 378.8167419433594 0.8463015556335449 524.8466186523438 0.6747754812240601 0.70513386 0.7319202423095703 True -4 11840 26.137009143829346 0.6189560890197754 343.95709228515625 0.6423424482345581 521.9663696289062 0.6786255836486816 0.71050537 0.6818827986717224 True -5 14208 26.145405292510986 0.5712707042694092 420.3072204589844 0.9380890727043152 520.5250854492188 0.6808587312698364 0.71423805 0.6074673533439636 True -6 16576 26.09382390975952 0.5761444568634033 377.95562744140625 0.5631849765777588 519.2045288085938 0.6830638647079468 0.7227904 0.5666348338127136 True -7 18944 26.15834379196167 0.5857131481170654 365.86785888671875 0.4608211815357208 517.3539428710938 0.685627818107605 0.726878 0.5637252926826477 True -8 21312 26.151041746139526 0.579582929611206 350.43841552734375 0.4879411458969116 515.6979370117188 0.6877138614654541 0.73285425 0.5202017426490784 True -9 23680 26.161139965057373 1.1436498165130615 371.2069091796875 0.5351299047470093 514.4442138671875 0.6895186901092529 0.7412452 0.48637598752975464 True -10 26048 25.83977198600769 0.5674562454223633 356.4190673828125 0.5334147214889526 513.408447265625 0.6912574768066406 0.7433128 0.4693857431411743 True -11 28416 25.61458730697632 0.5672135353088379 354.8575439453125 0.4615994989871979 512.3728637695312 0.6927187442779541 0.7474128 0.4671797752380371 True -12 30784 25.60262703895569 0.5833265781402588 421.8827209472656 0.5315030813217163 510.756591796875 0.694521963596344 0.7543243 0.448997437953949 True -13 33152 25.596757173538208 0.5693097114562988 361.8924865722656 0.24624121189117432 509.3214416503906 0.6962565183639526 0.7595993 0.43530145287513733 True -14 35520 25.584213256835938 0.5597422122955322 398.06561279296875 0.38826805353164673 508.3063659667969 0.6973893046379089 0.76792 0.4167011082172394 True -15 37888 25.580003023147583 0.5642170906066895 434.3206787109375 0.519736111164093 507.5898132324219 0.6979238986968994 0.77091056 0.4085603654384613 True -16 40256 25.553655862808228 0.5650253295898438 328.132568359375 0.3224688172340393 507.3669738769531 0.6981320977210999 0.77234006 0.41089704632759094 True -17 42624 25.625115394592285 0.5660619735717773 395.41668701171875 0.25143110752105713 507.5417175292969 0.6975265741348267 0.76989526 0.4159218370914459 False -18 44992 25.63019633293152 0.5625700950622559 307.3465881347656 0.2018764764070511 507.8876953125 0.6970411539077759 0.7672428 0.4271129369735718 False -19 47360 25.66502809524536 0.5675308704376221 341.2974853515625 0.16047316789627075 508.03350830078125 0.6967507600784302 0.76359 0.4330429136753082 False diff --git a/ENCSR821QHC/cherimoya.fold_1.performance.tsv b/ENCSR821QHC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2e051b9317021965af05dc9b4509573dd5ea931f..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -507.3669738769531 0.24090580642223358 0.6981321573257446 0.3261352479457855 0.7723400592803955 0.7365086078643799 0.41089704632759094 \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_2.evaluate.json b/ENCSR821QHC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 50afe7a0d7a9bc71e61cc3c5123a76c6ea5d9cee..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF493LUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_2.fit.json b/ENCSR821QHC/cherimoya.fold_2.fit.json deleted file mode 100644 index e41e3b3ddd9ce23a604452ccfcf751a97c77a17c..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF493LUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_2.log b/ENCSR821QHC/cherimoya.fold_2.log deleted file mode 100644 index 323df843a439f21088410086e41a82f5abf38203..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2467 31.93087649345398 3.857248544692993 401.14801025390625 0.46676337718963623 615.7340698242188 0.525732159614563 0.59282565 9.539807319641113 True -1 4934 27.22635579109192 1.0550525188446045 447.74420166015625 0.5812568068504333 525.4705200195312 0.6386951804161072 0.6717345 2.55614972114563 True -2 7401 27.26757311820984 0.5774295330047607 414.579833984375 0.6104270815849304 507.77276611328125 0.6585890650749207 0.69212544 1.0800997018814087 True -3 9868 27.189454793930054 0.4917731285095215 427.7060852050781 0.6265609264373779 502.7972106933594 0.6649188995361328 0.6876118 1.0118696689605713 False -4 12335 27.280245780944824 0.4905662536621094 435.9611511230469 0.7148905396461487 500.3939208984375 0.6682837009429932 0.6952612 0.8695347309112549 True -5 14802 27.22607398033142 0.4931957721710205 417.9324951171875 0.7005060911178589 498.4093322753906 0.6704690456390381 0.7025927 0.7246342301368713 True -6 17269 27.278860092163086 0.4801809787750244 379.51348876953125 0.6471312642097473 496.13763427734375 0.6735886335372925 0.70443916 0.6810640692710876 True -7 19736 27.281224489212036 0.48584437370300293 405.7352294921875 0.6682819724082947 495.43377685546875 0.6752169132232666 0.7093774 0.6527581214904785 True -8 22203 27.24634027481079 0.4885382652282715 369.61376953125 0.6215572357177734 493.518798828125 0.6772453784942627 0.71996087 0.5753025412559509 True -9 24670 27.234111785888672 0.8974380493164062 310.318115234375 0.44490277767181396 491.8834228515625 0.6793205142021179 0.7228584 0.5569113492965698 True -10 27137 27.315715074539185 0.48734426498413086 290.884765625 0.46979135274887085 490.5667419433594 0.6814572811126709 0.7252552 0.5463981032371521 True -11 29604 27.252723455429077 0.4903569221496582 355.94140625 0.3858339786529541 488.8865051269531 0.6833445429801941 0.7338818 0.5111158490180969 True -12 32071 27.201924324035645 0.4896364212036133 388.0752258300781 0.3380359709262848 487.5483093261719 0.6848510503768921 0.7389074 0.49963870644569397 True -13 34538 27.27933430671692 0.5410010814666748 353.8408508300781 0.3225240409374237 486.2557373046875 0.6867249608039856 0.74509126 0.48595941066741943 True -14 37005 27.358932971954346 0.5466926097869873 343.16583251953125 0.30961450934410095 485.21331787109375 0.6878477334976196 0.7491517 0.47517770528793335 True -15 39472 27.270772695541382 0.4927091598510742 451.797119140625 0.3074783682823181 484.79620361328125 0.6883454322814941 0.7525094 0.4654523432254791 True -16 41939 27.327683210372925 0.49643397331237793 336.66156005859375 0.30861443281173706 484.4869079589844 0.6883105635643005 0.75144005 0.4663700759410858 False -17 44406 26.80038857460022 0.48652195930480957 370.377197265625 0.27340203523635864 484.9062805175781 0.6881164312362671 0.74870884 0.47421932220458984 False -18 46873 26.819129467010498 0.5545694828033447 391.86419677734375 0.24788786470890045 485.37744140625 0.6876172423362732 0.7452926 0.48360487818717957 False -19 49340 26.779664993286133 0.4838840961456299 372.1699523925781 0.25623083114624023 485.3304443359375 0.6873564124107361 0.7415425 0.4917794167995453 False diff --git a/ENCSR821QHC/cherimoya.fold_2.performance.tsv b/ENCSR821QHC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b6bb0eca81ab924f0596204449523b45589f60cc..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -484.79620361328125 0.25002384185791016 0.6883453130722046 0.31230995059013367 0.7525094151496887 0.691440224647522 0.4654523432254791 \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_3.evaluate.json b/ENCSR821QHC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 664a8900978002f59fbc976d8f91797cab4b238f..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF493LUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_3.fit.json b/ENCSR821QHC/cherimoya.fold_3.fit.json deleted file mode 100644 index ae5f1152112b7c883075d9c2c6da91be90e63ce8..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF493LUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_3.log b/ENCSR821QHC/cherimoya.fold_3.log deleted file mode 100644 index 2dc136655373cd49667b9eebaeac55b450e5ddf9..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2407 31.132996559143066 4.7325029373168945 398.40771484375 0.5680118203163147 619.0491333007812 0.5290953516960144 0.5893344 10.31260871887207 True -1 4814 26.570484399795532 0.6305351257324219 440.8367004394531 0.7459038496017456 527.0669555664062 0.6426315903663635 0.6541977 2.9477298259735107 True -2 7221 26.663840770721436 0.5412180423736572 417.3568420410156 0.4398365616798401 506.8596496582031 0.6637129187583923 0.6600517 0.8499295115470886 True -3 9628 26.551498889923096 0.5587434768676758 443.5837097167969 0.6648392677307129 502.17803955078125 0.6694992184638977 0.6735674 0.7691810727119446 True -4 12035 26.846840858459473 0.5296967029571533 386.2752685546875 0.6536304354667664 498.7423400878906 0.6736127138137817 0.67634743 0.7019020915031433 True -5 14442 26.696359157562256 12.976160764694214 421.79412841796875 0.564539909362793 497.3794250488281 0.6757973432540894 0.68391186 0.687900960445404 True -6 16849 26.61856198310852 0.5370728969573975 352.63189697265625 0.6879490613937378 495.0531921386719 0.6784648895263672 0.6924071 0.6220076680183411 True -7 19256 26.686169147491455 0.5313575267791748 420.35797119140625 0.4435926079750061 493.6641540527344 0.6803434491157532 0.700059 0.5925755500793457 True -8 21663 26.610976457595825 0.5311360359191895 400.39776611328125 0.5768057703971863 492.4408874511719 0.6819908618927002 0.7038207 0.569786787033081 True -9 24070 26.58681035041809 0.5422930717468262 362.4366455078125 0.460054486989975 491.2047119140625 0.6839612126350403 0.71109676 0.547440230846405 True -10 26477 26.553695917129517 0.5423874855041504 446.99755859375 0.5576552152633667 489.44049072265625 0.6858008503913879 0.71851254 0.5267136096954346 True -11 28884 26.62870168685913 0.5252988338470459 409.54486083984375 0.5418078303337097 488.3432312011719 0.687380850315094 0.7235609 0.5109656453132629 True -12 31291 26.63780927658081 0.5268814563751221 385.3336486816406 0.4657559096813202 486.8257751464844 0.6894991397857666 0.7292124 0.49458274245262146 True -13 33698 26.62151312828064 0.5244994163513184 380.5299072265625 0.4673086404800415 485.8433837890625 0.6907365322113037 0.7354554 0.4780956208705902 True -14 36105 26.547149658203125 0.5373373031616211 339.6488037109375 0.29852402210235596 484.7054443359375 0.6919658780097961 0.74243724 0.4649887681007385 True -15 38512 27.301836252212524 0.5359389781951904 316.063720703125 0.41463199257850647 484.1388854980469 0.6925714612007141 0.74774224 0.4599796235561371 True -16 40919 26.808500289916992 12.721659660339355 356.80120849609375 0.3485216498374939 484.008056640625 0.6926406025886536 0.75162834 0.45714032649993896 True -17 43326 26.578986883163452 0.5290675163269043 342.97735595703125 0.39088451862335205 484.17059326171875 0.6922847628593445 0.7474188 0.46878576278686523 False -18 45733 26.646578788757324 0.5412211418151855 355.11572265625 0.38561105728149414 484.6387634277344 0.6916286945343018 0.74368787 0.4843912720680237 False -19 48140 26.621972799301147 0.5375001430511475 384.5975646972656 0.25829505920410156 484.760009765625 0.6912524700164795 0.7412409 0.4920009970664978 False diff --git a/ENCSR821QHC/cherimoya.fold_3.performance.tsv b/ENCSR821QHC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9aa30e92206fd2b8175268492669f17a9bf0c78a..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -484.008056640625 0.24701106548309326 0.6926406025886536 0.31209832429885864 0.7516283392906189 0.6934630274772644 0.45714032649993896 \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_4.evaluate.json b/ENCSR821QHC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7afaf91d484aea831bfa74fedaa612147ae40543..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF493LUD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_4.fit.json b/ENCSR821QHC/cherimoya.fold_4.fit.json deleted file mode 100644 index ff925d92dd7d059e68ed49fee40e4099e2b8ee88..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF493LUD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR821QHC/cherimoya.fold_4.log b/ENCSR821QHC/cherimoya.fold_4.log deleted file mode 100644 index e167e3acc18a79324166d58e24ed6994b9b231eb..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2472 31.955952644348145 3.715491533279419 485.5439453125 0.7671681046485901 612.1681518554688 0.5268054604530334 0.5987064 8.835893630981445 True -1 4944 27.272079944610596 0.5732946395874023 445.90496826171875 1.1314671039581299 520.3043212890625 0.6459710597991943 0.6656354 2.143505811691284 True -2 7416 27.167782306671143 0.5292739868164062 388.4991149902344 0.8411411046981812 504.7791442871094 0.6643186807632446 0.6700831 0.8681105375289917 True -3 9888 26.76611351966858 0.48612451553344727 383.27276611328125 0.7844665050506592 498.5877990722656 0.6707069873809814 0.6877483 0.7130653262138367 True -4 12360 26.74146056175232 1.0506134033203125 369.3785400390625 0.7669292688369751 495.2253112792969 0.6751940250396729 0.69038635 0.6788818836212158 True -5 14832 26.752702713012695 0.5169432163238525 400.34991455078125 0.7752707004547119 493.187255859375 0.6781067252159119 0.6955377 0.7034335136413574 True -6 17304 27.04084825515747 0.4895002841949463 416.9107971191406 0.6226083040237427 492.3222961425781 0.679814875125885 0.6982602 0.6147730350494385 True -7 19776 26.70796251296997 0.4836266040802002 369.7834777832031 0.3756958246231079 491.0602722167969 0.6820406317710876 0.70180553 0.5674979090690613 True -8 22248 26.73128867149353 0.49936699867248535 418.1826171875 0.48334893584251404 488.41455078125 0.6850549578666687 0.71232307 0.534249484539032 True -9 24720 26.730731964111328 0.4821600914001465 354.91943359375 0.681564450263977 487.2214050292969 0.6866748332977295 0.7142284 0.5155753493309021 True -10 27192 26.78783655166626 0.4985640048980713 379.3047180175781 0.42920076847076416 486.2053527832031 0.6883594393730164 0.719856 0.5088860392570496 True -11 29664 26.788925647735596 0.4921586513519287 358.0816650390625 0.43175020813941956 484.625732421875 0.6902408599853516 0.7277146 0.4937649071216583 True -12 32136 26.784607648849487 0.48303794860839844 377.9879150390625 0.5294054746627808 483.4897766113281 0.6918489933013916 0.72851324 0.49534156918525696 True -13 34608 26.72631812095642 0.48357605934143066 400.27215576171875 0.561930775642395 482.17950439453125 0.6937352418899536 0.7394859 0.4666096568107605 True -14 37080 26.757372856140137 0.5219225883483887 380.9602966308594 0.4590297043323517 481.0580749511719 0.6949276924133301 0.74562883 0.4608136713504791 True -15 39552 26.71367120742798 0.49027466773986816 358.74072265625 0.3380476236343384 480.75714111328125 0.6955788731575012 0.7488345 0.4593176245689392 True -16 42024 26.73184633255005 0.47833871841430664 304.76361083984375 0.3404533863067627 480.89727783203125 0.6953973174095154 0.74767894 0.4600841999053955 False -17 44496 26.725326776504517 0.48322272300720215 381.02386474609375 0.24350711703300476 481.1614685058594 0.6949324011802673 0.74620146 0.467953622341156 False -18 46968 26.77958869934082 0.4775536060333252 311.63525390625 0.30594897270202637 481.55316162109375 0.6941520571708679 0.7428057 0.47745978832244873 False -19 49440 26.77143883705139 1.4129674434661865 420.43804931640625 0.302606999874115 481.69403076171875 0.6938661932945251 0.73761535 0.4849868714809418 False diff --git a/ENCSR821QHC/cherimoya.fold_4.performance.tsv b/ENCSR821QHC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 59dca3a97a889c1bb3f86ef68fdf3b5d4e86cb42..0000000000000000000000000000000000000000 --- a/ENCSR821QHC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -480.75714111328125 0.2476503849029541 0.6955788731575012 0.3116094768047333 0.748834490776062 0.6720690131187439 0.4593176245689392 \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_0.evaluate.json b/ENCSR822BAD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b40e69a90af8fc47d16d5780cab9f77e0d1bfc0b..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF857XMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_0.fit.json b/ENCSR822BAD/cherimoya.fold_0.fit.json deleted file mode 100644 index 9b33b6fff5813af5ecf996253d00e5870e1cc6ed..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF857XMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_0.log b/ENCSR822BAD/cherimoya.fold_0.log deleted file mode 100644 index c2f9ce7618c4aad343831bdf35f435eecf26b0b5..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2153 27.600085496902466 3.45468807220459 371.36749267578125 0.4756903648376465 482.8511047363281 0.5440772771835327 0.6935533 7.85170316696167 True -1 4306 23.847059726715088 0.4519178867340088 308.77996826171875 0.475619375705719 412.0680847167969 0.6300265192985535 0.771346 1.4063897132873535 True -2 6459 23.37228512763977 0.4241940975189209 312.34228515625 0.36423182487487793 398.5190124511719 0.6493404507637024 0.78895795 0.4137153923511505 True -3 8612 23.2533757686615 0.41785311698913574 350.92120361328125 0.3331449627876282 396.5076904296875 0.6507068276405334 0.78978205 0.40743836760520935 True -4 10765 23.30379867553711 0.41757726669311523 383.6199951171875 0.3196091651916504 393.7964782714844 0.6563388705253601 0.7932039 0.40825697779655457 True -5 12918 23.36417245864868 0.41717052459716797 355.6405029296875 0.26814955472946167 392.09637451171875 0.6604319214820862 0.7996033 0.3391566276550293 True -6 15071 23.320721864700317 0.42044949531555176 349.29071044921875 0.31328898668289185 390.50439453125 0.6631510853767395 0.80314595 0.29884546995162964 True -7 17224 23.271910190582275 0.6461777687072754 350.414794921875 0.20974695682525635 389.2903137207031 0.6651176810264587 0.8057234 0.2776801884174347 True -8 19377 23.292943716049194 0.4215250015258789 344.74755859375 0.35067814588546753 388.4526062011719 0.6663783192634583 0.8105677 0.27107173204421997 True -9 21530 23.374544143676758 0.42716264724731445 346.8270263671875 0.23372842371463776 387.64935302734375 0.668043315410614 0.8116701 0.25898686051368713 True -10 23683 23.328308820724487 1.6607282161712646 351.711181640625 0.3477776050567627 386.7967224121094 0.6692473292350769 0.8204911 0.24688848853111267 True -11 25836 23.39603877067566 0.4235045909881592 361.6048889160156 0.2558233141899109 385.9014892578125 0.6706185936927795 0.8244685 0.23340794444084167 True -12 27989 23.38279390335083 0.43096423149108887 327.5941162109375 0.17131924629211426 385.2601623535156 0.6718466877937317 0.82864875 0.23483353853225708 True -13 30142 23.49103355407715 0.4367861747741699 317.8912353515625 0.15901638567447662 384.6805114746094 0.6728063225746155 0.83125275 0.22355173528194427 True -14 32295 23.367260217666626 0.42496490478515625 352.73809814453125 0.2170923352241516 384.3169250488281 0.6735196113586426 0.83357453 0.22174641489982605 True -15 34448 23.375148057937622 1.5140910148620605 327.41851806640625 0.19118505716323853 384.2004089355469 0.673906147480011 0.8361958 0.2203519642353058 True -16 36601 23.520419359207153 0.4247756004333496 340.5860290527344 0.15357373654842377 384.1189880371094 0.6739127039909363 0.83668786 0.2212337702512741 True -17 38754 23.330889463424683 5.098922491073608 322.3485107421875 0.14297103881835938 384.3624572753906 0.673443078994751 0.836153 0.2218526154756546 False -18 40907 23.37850594520569 0.41769933700561523 332.73870849609375 0.1543809473514557 384.5633239746094 0.6730771064758301 0.83276796 0.22395655512809753 False -19 43060 23.31688666343689 6.472214698791504 335.87353515625 0.13457949459552765 384.717529296875 0.6728017926216125 0.8333686 0.2266010046005249 False diff --git a/ENCSR822BAD/cherimoya.fold_0.performance.tsv b/ENCSR822BAD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7a5c9c802c365d55c396aee01dabc7ec5f839055..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -384.1189880371094 0.2645207345485687 0.6739127039909363 0.27599990367889404 0.8366878628730774 0.7690065503120422 0.2212337702512741 \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_1.evaluate.json b/ENCSR822BAD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9a74ea133743811f5d081bca0574c54f674ce1ad..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF857XMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_1.fit.json b/ENCSR822BAD/cherimoya.fold_1.fit.json deleted file mode 100644 index 7e2aad8ad93fb706e99ba7398ff0dd21da581b19..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF857XMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_1.log b/ENCSR822BAD/cherimoya.fold_1.log deleted file mode 100644 index 8a102b4378b46e8c51abc827b1787036dbcb4683..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2121 27.47388219833374 3.5494656562805176 340.4542236328125 0.5953429341316223 553.7285766601562 0.5587470531463623 0.67822534 8.575272560119629 True -1 4242 23.464850664138794 31.404284954071045 339.9579162597656 0.478365957736969 468.21051025390625 0.6474165916442871 0.7597197 1.9077117443084717 True -2 6363 23.42623472213745 0.5980370044708252 327.4231872558594 0.4007897675037384 449.0621032714844 0.6721822023391724 0.77710235 0.4765198230743408 True -3 8484 23.33670663833618 0.5952177047729492 330.67755126953125 0.49388667941093445 443.2503967285156 0.679433286190033 0.7865971 0.3708503544330597 True -4 10605 23.337973594665527 0.5795774459838867 352.89752197265625 0.5125089883804321 441.447998046875 0.6824424266815186 0.79290867 0.36720964312553406 True -5 12726 23.32298183441162 0.5806961059570312 367.8292236328125 0.3821234107017517 441.4704895019531 0.6832695603370667 0.7943465 0.36661094427108765 True -6 14847 22.933319807052612 0.5891523361206055 294.0688171386719 0.22773854434490204 439.7334289550781 0.6855138540267944 0.80041325 0.37339282035827637 True -7 16968 22.948484659194946 0.5870587825775146 383.1722412109375 0.34861212968826294 439.2013854980469 0.6864926218986511 0.80171084 0.38013461232185364 True -8 19089 22.944913148880005 0.5742297172546387 363.63677978515625 0.2219909429550171 438.2558898925781 0.6880894899368286 0.80795705 0.3649938404560089 True -9 21210 22.94280695915222 0.5893182754516602 353.0062255859375 0.2172352820634842 436.5780029296875 0.6899641156196594 0.8122594 0.3430136740207672 True -10 23331 22.944902896881104 0.5839300155639648 329.5194091796875 0.4155982732772827 434.8868713378906 0.6922997236251831 0.823689 0.31027331948280334 True -11 25452 22.935011386871338 0.577064037322998 359.25250244140625 0.34491318464279175 433.8970642089844 0.6938412189483643 0.8274897 0.28106674551963806 True -12 27573 22.992680311203003 0.5755729675292969 329.6051330566406 0.20860955119132996 432.4540100097656 0.6956182718276978 0.8383016 0.2673921287059784 True -13 29694 22.99683928489685 0.5827040672302246 316.97796630859375 0.6419071555137634 431.90057373046875 0.696934163570404 0.84034854 0.24722552299499512 True -14 31815 22.95116949081421 0.5821223258972168 336.0274963378906 0.3674244284629822 430.880859375 0.6981130242347717 0.84523565 0.2426442801952362 True -15 33936 23.01546001434326 0.583179235458374 327.4469909667969 0.49906760454177856 430.17315673828125 0.6988564729690552 0.85132176 0.23383867740631104 True -16 36057 22.983309507369995 0.5955989360809326 340.6007995605469 0.25333213806152344 430.1703796386719 0.6990292072296143 0.8513719 0.23002779483795166 True -17 38178 22.900665044784546 0.5916109085083008 351.0050354003906 0.274766743183136 430.6597900390625 0.6987854838371277 0.8520056 0.22973774373531342 True -18 40299 22.91716718673706 0.5824761390686035 323.8813781738281 0.15236902236938477 430.1778259277344 0.698410153388977 0.847802 0.2348172813653946 False -19 42420 22.942992448806763 0.6135659217834473 319.57476806640625 0.21723505854606628 431.1393127441406 0.698197066783905 0.8463754 0.23817618191242218 False diff --git a/ENCSR822BAD/cherimoya.fold_1.performance.tsv b/ENCSR822BAD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1ff1170b4c603e40f996ee0c92f553e2f4959c43..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -430.6597900390625 0.24446766078472137 0.6987854242324829 0.3089139461517334 0.8520056009292603 0.8140895366668701 0.22973774373531342 \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_2.evaluate.json b/ENCSR822BAD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 23d68a03d70cdd6cabd8b8e54d704a22388afadc..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF857XMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_2.fit.json b/ENCSR822BAD/cherimoya.fold_2.fit.json deleted file mode 100644 index d688f2d0443f6cf39505cc1c4c723f892d549954..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF857XMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_2.log b/ENCSR822BAD/cherimoya.fold_2.log deleted file mode 100644 index 0b41fa24b081abd0bf8b8e2193ef91cf8fc5c88c..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2274 29.12800931930542 4.072830677032471 392.6575622558594 0.7746262550354004 504.94720458984375 0.5560209155082703 0.68943626 6.64061975479126 True -1 4548 25.161635637283325 0.46483445167541504 309.1014709472656 0.861036479473114 430.9706726074219 0.6385026574134827 0.77928424 1.2091261148452759 True -2 6822 25.072439908981323 0.4424479007720947 368.9088134765625 0.39982518553733826 419.5511169433594 0.6561572551727295 0.7909759 0.4485495686531067 True -3 9096 25.031867742538452 0.4482567310333252 323.05303955078125 0.5427882671356201 413.95660400390625 0.6628034114837646 0.79887235 0.3155137002468109 True -4 11370 25.06466054916382 0.4479484558105469 377.31610107421875 0.33726227283477783 413.2083435058594 0.664221465587616 0.7999336 0.33819910883903503 True -5 13644 25.021381378173828 0.4477880001068115 364.8267822265625 0.6950188875198364 412.45367431640625 0.6655856370925903 0.804021 0.30263787508010864 True -6 15918 25.06637978553772 0.4410583972930908 320.76416015625 0.323467880487442 411.1607666015625 0.6676127910614014 0.80986494 0.2957926094532013 True -7 18192 25.05502986907959 0.4426889419555664 333.6707763671875 0.33484160900115967 410.2384948730469 0.6689676642417908 0.8112251 0.2840103805065155 True -8 20466 25.080007553100586 1.401454210281372 303.3480224609375 0.33844754099845886 408.9671936035156 0.6706495881080627 0.8212234 0.2621566653251648 True -9 22740 25.101508855819702 0.4426264762878418 306.014892578125 0.28514382243156433 408.1756286621094 0.6720579266548157 0.8224658 0.25940075516700745 True -10 25014 25.080382823944092 0.4494469165802002 302.9561767578125 0.329314649105072 406.9607238769531 0.6737775802612305 0.829729 0.23907573521137238 True -11 27288 25.092040300369263 2.067680835723877 330.8563232421875 0.41829612851142883 405.89129638671875 0.6752633452415466 0.83473325 0.24038814008235931 True -12 29562 25.212501764297485 11.122612237930298 333.6071472167969 0.2590081989765167 404.9537048339844 0.6765182614326477 0.835358 0.23481009900569916 True -13 31836 24.82617998123169 0.47266316413879395 354.77099609375 0.21290375292301178 404.358642578125 0.6776533722877502 0.84066355 0.23344707489013672 True -14 34110 24.80173134803772 0.4409170150756836 323.41046142578125 0.3256346881389618 403.7763366699219 0.6786830425262451 0.84342366 0.22566655278205872 True -15 36384 24.75127363204956 1.6219398975372314 310.01416015625 0.23076055943965912 403.3355407714844 0.6791994571685791 0.8465133 0.2220204919576645 True -16 38658 24.72987198829651 0.4392385482788086 337.93560791015625 0.15419720113277435 403.27984619140625 0.6795024871826172 0.8440244 0.22575852274894714 False -17 40932 24.651850938796997 0.4370911121368408 339.4263610839844 0.3948328495025635 403.3559265136719 0.6794081926345825 0.84378654 0.22861139476299286 False -18 43206 24.645217180252075 0.4459800720214844 339.95233154296875 0.4066591262817383 403.55694580078125 0.6789897084236145 0.84134644 0.23382054269313812 False -19 45480 24.623494386672974 0.4379119873046875 317.04827880859375 0.16951793432235718 403.5748596191406 0.6787322759628296 0.83978885 0.23849114775657654 False diff --git a/ENCSR822BAD/cherimoya.fold_2.performance.tsv b/ENCSR822BAD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cad38a090bd3906cbcceeb5db396d0171ce9555c..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -403.3355407714844 0.2584058940410614 0.6791993975639343 0.2875780761241913 0.8465132713317871 0.7917580008506775 0.2220204919576645 \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_3.evaluate.json b/ENCSR822BAD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2db25cfc4eb537aee698b96e481def93057762e6..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF857XMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_3.fit.json b/ENCSR822BAD/cherimoya.fold_3.fit.json deleted file mode 100644 index 5d8cc11581baddbe7c133c6953badad632c7a462..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF857XMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_3.log b/ENCSR822BAD/cherimoya.fold_3.log deleted file mode 100644 index 4e4b91a67c43827872cba4fe9b8e1d181a015696..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2205 28.22829031944275 3.5001959800720215 392.51446533203125 0.4405766725540161 488.6325378417969 0.5482897162437439 0.68750787 6.701710224151611 True -1 4410 24.350008010864258 0.42847180366516113 356.0731201171875 0.7607237696647644 421.0271301269531 0.6296856999397278 0.76668155 1.263249397277832 True -2 6615 24.368858575820923 0.41107845306396484 372.1412048339844 0.7861757278442383 407.1873779296875 0.6479045748710632 0.7850807 0.4400269091129303 True -3 8820 24.375206232070923 0.4087536334991455 325.3673095703125 0.35160234570503235 403.1266784667969 0.654369056224823 0.78673327 0.43113258481025696 True -4 11025 24.290221214294434 0.4081602096557617 338.4122009277344 0.5832182765007019 401.19439697265625 0.6580462455749512 0.78948665 0.4049113392829895 True -5 13230 23.99737286567688 0.4055004119873047 319.72235107421875 0.6870572566986084 400.12646484375 0.6600519418716431 0.7928591 0.36098816990852356 True -6 15435 23.782532453536987 0.3990771770477295 334.3197021484375 0.45185643434524536 399.5950622558594 0.6614289879798889 0.8016914 0.35768669843673706 True -7 17640 23.829179525375366 0.39684200286865234 321.5004577636719 0.4838484227657318 398.4717712402344 0.6625707745552063 0.7964684 0.34985336661338806 False -8 19845 23.86278986930847 0.4009571075439453 375.138671875 0.4480833411216736 397.88494873046875 0.6639247536659241 0.7986993 0.36522728204727173 False -9 22050 23.82069993019104 0.4011209011077881 329.91278076171875 0.26643702387809753 397.22210693359375 0.6657878160476685 0.7975278 0.35543206334114075 False -10 24255 23.839720487594604 0.40541672706604004 330.5770263671875 0.2607090473175049 395.71978759765625 0.6677298545837402 0.8078646 0.3266563415527344 True -11 26460 23.800047397613525 0.40309667587280273 345.9649658203125 0.5070308446884155 394.6595764160156 0.6692697405815125 0.808613 0.3183591663837433 True -12 28665 23.79347324371338 1.1682426929473877 324.9597473144531 0.9100056290626526 394.1198425292969 0.6702380180358887 0.81068414 0.2933233976364136 True -13 30870 23.84363102912903 1.2732632160186768 321.5141906738281 0.4646429419517517 393.0946350097656 0.671867847442627 0.8116133 0.2826710045337677 True -14 33075 23.824750661849976 0.3984251022338867 316.464111328125 0.6040465831756592 392.3657531738281 0.6731063723564148 0.8150344 0.283526211977005 True -15 35280 23.84124517440796 0.3979942798614502 371.2239990234375 0.2168034315109253 392.08966064453125 0.67353355884552 0.81729317 0.27346813678741455 True -16 37485 23.857749462127686 0.40210509300231934 319.8384094238281 0.2972007095813751 391.75750732421875 0.6738073229789734 0.81891906 0.26739248633384705 True -17 39690 23.842646598815918 15.345933198928833 296.806396484375 0.3826933801174164 391.63330078125 0.6736367344856262 0.8188748 0.26817116141319275 False -18 41895 23.94852876663208 0.41411495208740234 327.11712646484375 0.2382480800151825 391.8348388671875 0.6732194423675537 0.8161952 0.27344831824302673 False -19 44100 23.880130290985107 7.432023048400879 302.6876220703125 0.2407228946685791 391.8581848144531 0.6730916500091553 0.8140565 0.2767195403575897 False diff --git a/ENCSR822BAD/cherimoya.fold_3.performance.tsv b/ENCSR822BAD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ba66b4efd4ac5a232c6f93f09d47523b5483bb13..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -391.75750732421875 0.26309338212013245 0.6738073229789734 0.2777365446090698 0.8189190626144409 0.7627483606338501 0.26739248633384705 \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_4.evaluate.json b/ENCSR822BAD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 999c18d2ceb7a5435739d91c4ca8a96fe1da0434..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF857XMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_4.fit.json b/ENCSR822BAD/cherimoya.fold_4.fit.json deleted file mode 100644 index e14b339e0a51d154fc7167325076dc04ffe4d345..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF857XMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822BAD/cherimoya.fold_4.log b/ENCSR822BAD/cherimoya.fold_4.log deleted file mode 100644 index e9d30bd708119436282bef2a4c9704285d160af0..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2199 28.098307847976685 3.374040126800537 351.73785400390625 0.30895644426345825 472.8935852050781 0.5476841926574707 0.6882063 7.358002185821533 True -1 4398 24.370572805404663 0.44864940643310547 311.0626220703125 1.0794532299041748 409.6454772949219 0.6250401139259338 0.7584911 1.131056308746338 True -2 6597 24.36841654777527 0.4400503635406494 358.46563720703125 0.5135208368301392 396.6324462890625 0.645084798336029 0.7746562 0.375821053981781 True -3 8796 24.26023006439209 0.43650293350219727 348.1856689453125 0.429042249917984 391.70166015625 0.6513347625732422 0.78197515 0.31773263216018677 True -4 10995 24.58720302581787 0.821183443069458 301.762939453125 0.26282501220703125 390.05157470703125 0.6542132496833801 0.7868864 0.3397524058818817 True -5 13194 24.31727623939514 0.4357433319091797 301.2630615234375 0.6215626001358032 389.10186767578125 0.6561829447746277 0.7910256 0.2966831624507904 True -6 15393 24.223878622055054 0.4366879463195801 396.3060607910156 0.4756248891353607 388.1241760253906 0.6580232977867126 0.79922533 0.2811265289783478 True -7 17592 24.237516403198242 0.4334228038787842 330.6939697265625 0.8607999086380005 387.59259033203125 0.6592273712158203 0.8011079 0.28311431407928467 True -8 19791 24.218364238739014 0.4330136775970459 307.4526672363281 0.3400768041610718 386.6125793457031 0.6606703996658325 0.80476284 0.283504456281662 True -9 21990 24.266127824783325 0.43746066093444824 337.77630615234375 0.3772038221359253 385.43560791015625 0.6625091433525085 0.8129919 0.26541271805763245 True -10 24189 24.307128190994263 0.44172000885009766 292.9567565917969 0.7434661388397217 384.6955871582031 0.6640096306800842 0.8189304 0.2528127431869507 True -11 26388 24.30366086959839 0.4385032653808594 320.72705078125 0.3399471938610077 383.72607421875 0.6655279994010925 0.82499886 0.2445874959230423 True -12 28587 24.510262489318848 0.4314117431640625 343.0447082519531 0.22327613830566406 382.9057922363281 0.6667624711990356 0.8267059 0.2387731820344925 True -13 30786 24.282557725906372 0.43318939208984375 303.29913330078125 0.21543431282043457 382.0394592285156 0.6681025624275208 0.83019626 0.2306106835603714 True -14 32985 23.794273853302002 1.4819557666778564 321.0268249511719 0.3461667597293854 381.41485595703125 0.6689607501029968 0.83008814 0.233026921749115 False -15 35184 23.839444875717163 1.7310891151428223 296.0772705078125 0.23814770579338074 381.0744934082031 0.6692755222320557 0.8308757 0.2313190996646881 True -16 37383 23.820820569992065 0.4349195957183838 348.3789367675781 0.21654105186462402 381.0337829589844 0.6694118976593018 0.8324011 0.2306249588727951 True -17 39582 23.80465602874756 1.9200613498687744 301.0093994140625 0.2895842492580414 381.0946960449219 0.669094979763031 0.83017766 0.2336609661579132 False -18 41781 23.847045421600342 0.43015122413635254 298.1537780761719 0.200999915599823 381.2350769042969 0.6687268018722534 0.828323 0.23780184984207153 False -19 43980 23.82357907295227 0.4257395267486572 337.2344970703125 0.18254807591438293 381.32318115234375 0.668549120426178 0.82696307 0.24080903828144073 False diff --git a/ENCSR822BAD/cherimoya.fold_4.performance.tsv b/ENCSR822BAD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d2ce02e4207a8ec5a7bfdb0b1e82c180a036242f..0000000000000000000000000000000000000000 --- a/ENCSR822BAD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -381.0337829589844 0.26658815145492554 0.6694118976593018 0.2733912169933319 0.8324010968208313 0.7589778304100037 0.2306249588727951 \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_0.evaluate.json b/ENCSR822GDF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7482273868368432814fae6eea7d47ff47144842..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488ZAI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_0.fit.json b/ENCSR822GDF/cherimoya.fold_0.fit.json deleted file mode 100644 index 7b81ec29b5d92683dc50e2e2e267b6c4aaafffa8..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF488ZAI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_0.log b/ENCSR822GDF/cherimoya.fold_0.log deleted file mode 100644 index 812810d4824c5297dd159521e6c30ca7b4f5d870..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2725 34.635902404785156 16.471147775650024 509.33123779296875 0.67116379737854 685.6507568359375 0.22835958003997803 0.6556239 3.6644628047943115 True -1 5450 30.118715286254883 1.0166940689086914 526.3019409179688 0.3500494360923767 631.112060546875 0.30056482553482056 0.7236972 0.929598867893219 True -2 8175 30.407880067825317 0.6067180633544922 484.40399169921875 0.3767738938331604 621.72998046875 0.3096327483654022 0.7356768 0.4367268681526184 True -3 10900 30.04304528236389 0.6385908126831055 522.6846923828125 0.42307597398757935 617.0957641601562 0.31568214297294617 0.741875 0.36415237188339233 True -4 13625 30.101239681243896 0.6191468238830566 519.9066772460938 0.4668239951133728 613.6298217773438 0.3196760416030884 0.7527448 0.3165552020072937 True -5 16350 31.24875545501709 6.678385496139526 521.44580078125 0.3009965717792511 611.3505859375 0.32236093282699585 0.7600369 0.286819726228714 True -6 19075 30.07599925994873 0.6327052116394043 560.6931762695312 0.4552052915096283 608.7462768554688 0.32685792446136475 0.7594175 0.26993927359580994 False -7 21800 30.046606063842773 0.6340515613555908 574.0132446289062 0.4048681855201721 607.871826171875 0.32751891016960144 0.7641106 0.2987867593765259 True -8 24525 30.073439121246338 3.3291125297546387 524.4226684570312 0.4243144392967224 606.1751708984375 0.32971858978271484 0.76941705 0.25049108266830444 True -9 27250 30.065507411956787 16.35173797607422 533.4775390625 0.2503625750541687 604.4310913085938 0.3322637677192688 0.7741018 0.25385206937789917 True -10 29975 30.110025644302368 0.6386208534240723 511.49432373046875 0.3276347815990448 603.4691772460938 0.33317357301712036 0.779483 0.24344374239444733 True -11 32700 30.088823795318604 0.6248278617858887 517.7945556640625 0.23377910256385803 602.0032348632812 0.3353627920150757 0.7846615 0.23455800116062164 True -12 35425 30.13197135925293 0.6226742267608643 531.3875732421875 0.26632657647132874 601.0313720703125 0.33648890256881714 0.7902134 0.2309143841266632 True -13 38150 30.09170961380005 0.6077108383178711 525.84765625 0.3416784405708313 600.6593017578125 0.33639267086982727 0.79637825 0.22688491642475128 True -14 40875 30.14067029953003 0.6336193084716797 556.4220581054688 0.16433905065059662 599.2640991210938 0.33864626288414 0.802069 0.22375449538230896 True -15 43600 30.146159887313843 0.6294007301330566 548.6170654296875 0.18112064898014069 598.8350830078125 0.3391607701778412 0.8089006 0.2173605114221573 True -16 46325 30.12039875984192 0.6323792934417725 500.7271728515625 0.228848397731781 597.79833984375 0.34140217304229736 0.81189996 0.21241308748722076 True -17 49050 30.596773147583008 0.6337809562683105 466.1453552246094 0.22292572259902954 597.7084350585938 0.34059852361679077 0.8132323 0.21223688125610352 True -18 51775 29.69378638267517 1.1125686168670654 517.4591064453125 0.1995927393436432 598.1135864257812 0.3398747742176056 0.81280416 0.21159976720809937 False -19 54500 29.55170440673828 1.6583094596862793 518.2393798828125 0.1593792736530304 598.8488159179688 0.3385258615016937 0.8132281 0.21315446496009827 False diff --git a/ENCSR822GDF/cherimoya.fold_0.performance.tsv b/ENCSR822GDF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a0708d706bfc8ffc9118d8e8e3c1e477c04a2a12..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -597.7084350585938 0.4342086911201477 0.34059852361679077 0.11970225721597672 0.8132323026657104 0.7866201996803284 0.21223688125610352 \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_1.evaluate.json b/ENCSR822GDF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5d044fbd65605d3ab932be5e05c5c0f8f838c920..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488ZAI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_1.fit.json b/ENCSR822GDF/cherimoya.fold_1.fit.json deleted file mode 100644 index 3828b75691e09e4784b0d4cb50050c4c51bde585..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF488ZAI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_1.log b/ENCSR822GDF/cherimoya.fold_1.log deleted file mode 100644 index 4598102a0358ed3bb98589ebfa5118268c6568df..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2706 34.638421297073364 4.505338191986084 597.5125732421875 0.3773907423019409 769.3845825195312 0.2347455471754074 0.66053826 4.494295120239258 True -1 5412 29.972838401794434 0.7667768001556396 574.27978515625 0.44625532627105713 702.2340698242188 0.31595200300216675 0.72993064 1.0863622426986694 True -2 8118 29.93848705291748 0.7001335620880127 508.1010437011719 0.33149948716163635 687.8438110351562 0.3316750228404999 0.7441966 0.5325810313224792 True -3 10824 30.03701615333557 0.7368652820587158 622.7879638671875 0.4632151424884796 682.9837646484375 0.3346059024333954 0.7542592 0.3811551332473755 True -4 13530 29.996426105499268 0.7026557922363281 513.555419921875 0.4541085958480835 680.2572021484375 0.33719977736473083 0.759374 0.34593501687049866 True -5 16236 29.992948532104492 1.569847583770752 491.8617248535156 0.25063055753707886 677.5049438476562 0.3406361937522888 0.76243293 0.30840858817100525 True -6 18942 29.97259211540222 0.7110879421234131 454.61773681640625 0.32344499230384827 675.2854614257812 0.3431241810321808 0.7716104 0.30596083402633667 True -7 21648 29.9758083820343 0.7470417022705078 492.3446960449219 0.27813827991485596 673.8922119140625 0.34496113657951355 0.771949 0.3055315315723419 True -8 24354 29.924426317214966 0.7223412990570068 562.500244140625 0.40230685472488403 671.0958251953125 0.3482646942138672 0.7791943 0.31541940569877625 True -9 27060 29.905739545822144 0.7156693935394287 468.25836181640625 0.3876728415489197 669.8690795898438 0.34993091225624084 0.7811948 0.29804685711860657 True -10 29766 29.876832008361816 1.0342350006103516 488.83416748046875 0.22820113599300385 668.86865234375 0.35053423047065735 0.78580964 0.28291380405426025 True -11 32472 29.94206666946411 0.7381033897399902 425.6534423828125 0.29054582118988037 667.2332763671875 0.35139623284339905 0.79197145 0.2698272466659546 True -12 35178 30.028829097747803 0.7264642715454102 554.3436279296875 0.29761338233947754 665.1953735351562 0.35357680916786194 0.7994978 0.2527981996536255 True -13 37884 30.0515034198761 0.702315092086792 502.3074645996094 0.20501182973384857 663.1864013671875 0.3564755618572235 0.80644745 0.2458202838897705 True -14 40590 29.99110507965088 0.7091014385223389 455.0857238769531 0.25393837690353394 661.8936767578125 0.35782134532928467 0.8131745 0.24047870934009552 True -15 43296 29.981114149093628 2.312253713607788 497.60894775390625 0.33746179938316345 660.61328125 0.35989639163017273 0.8197036 0.23256148397922516 True -16 46002 29.894851684570312 0.6961395740509033 472.71246337890625 0.178275465965271 660.3212890625 0.35942256450653076 0.8226928 0.2280973643064499 True -17 48708 29.57991933822632 0.7082257270812988 502.05810546875 0.17037492990493774 660.3413696289062 0.35915467143058777 0.82582194 0.22324520349502563 True -18 51414 29.433257341384888 0.710120677947998 542.1427001953125 0.18152451515197754 660.2304077148438 0.3593345582485199 0.8273075 0.22503533959388733 True -19 54120 29.98241353034973 2.7545225620269775 489.87994384765625 0.22664840519428253 660.9498291015625 0.3581617474555969 0.8252842 0.22417126595973969 False diff --git a/ENCSR822GDF/cherimoya.fold_1.performance.tsv b/ENCSR822GDF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 709816fa4e8a45e66b2f974fe9801c01091d4e90..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -660.2304077148438 0.4183659255504608 0.3593345582485199 0.1334296613931656 0.8273075222969055 0.8075998425483704 0.22503533959388733 \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_2.evaluate.json b/ENCSR822GDF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 473b2adc9645087119777a0a5e8e1ca239432c76..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488ZAI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_2.fit.json b/ENCSR822GDF/cherimoya.fold_2.fit.json deleted file mode 100644 index ef5233cf091f7d3922390edf3c84d5d0231c39a2..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF488ZAI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_2.log b/ENCSR822GDF/cherimoya.fold_2.log deleted file mode 100644 index b33ec5dddfa24331a9c94b043fd9132de903cf53..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2875 36.50521206855774 4.991194725036621 553.407470703125 0.41607603430747986 704.8783569335938 0.2331232726573944 0.65349704 3.663254499435425 True -1 5750 31.82681155204773 0.5955603122711182 556.9678955078125 0.3636409342288971 645.3721923828125 0.30585500597953796 0.7208563 1.2405917644500732 True -2 8625 31.7786386013031 0.5725135803222656 479.6802978515625 0.7524465322494507 636.93798828125 0.31476080417633057 0.7230257 0.6385554075241089 True -3 11500 31.809492826461792 2.926617383956909 493.923583984375 0.3668142557144165 635.2081298828125 0.31517931818962097 0.7311192 0.6584540009498596 True -4 14375 31.831101655960083 20.271278142929077 539.9346923828125 0.2580510675907135 628.3883056640625 0.32388731837272644 0.7421256 0.46324992179870605 True -5 17250 32.366103172302246 0.6354799270629883 509.1328125 0.36958855390548706 626.1151123046875 0.32684606313705444 0.74813455 0.4041820466518402 True -6 20125 33.00327110290527 0.5730466842651367 496.6360168457031 0.19127750396728516 624.8954467773438 0.32833999395370483 0.75388664 0.3775905668735504 True -7 23000 31.77323031425476 1.449965000152588 541.9853515625 0.33761680126190186 622.8694458007812 0.3311883211135864 0.7585467 0.3636143207550049 True -8 25875 31.778249263763428 0.571021556854248 612.7392578125 0.353584349155426 621.447265625 0.33306849002838135 0.7614956 0.3137807250022888 True -9 28750 31.799291610717773 0.5662975311279297 607.4030151367188 0.26548200845718384 619.7596435546875 0.33507978916168213 0.7688063 0.2917644679546356 True -10 31625 31.822641611099243 0.5690016746520996 550.8319091796875 0.35791927576065063 617.7301025390625 0.3375469744205475 0.77427256 0.27598854899406433 True -11 34500 31.729061126708984 0.56058669090271 543.7274169921875 0.3883424401283264 615.9486694335938 0.3403005599975586 0.77972 0.26693645119667053 True -12 37375 31.723010301589966 0.5695648193359375 516.7325439453125 0.3077716827392578 615.9244995117188 0.33918124437332153 0.7862049 0.2598915994167328 True -13 40250 31.924498558044434 0.569566011428833 577.092041015625 0.20990058779716492 613.5719604492188 0.34264591336250305 0.7929494 0.2524353861808777 True -14 43125 31.62371301651001 0.5552332401275635 503.9462890625 0.39856964349746704 612.8028564453125 0.34320881962776184 0.7968102 0.2409900724887848 True -15 46000 31.143012523651123 0.552504301071167 495.2390441894531 0.16782209277153015 611.9470825195312 0.3444570302963257 0.80263376 0.23081350326538086 True -16 48875 31.178297996520996 0.7422113418579102 525.6759033203125 0.22050194442272186 611.3489379882812 0.34581178426742554 0.8093882 0.22149421274662018 True -17 51750 31.18336820602417 0.552222490310669 535.6776123046875 0.26376253366470337 611.8547973632812 0.34457147121429443 0.8101347 0.2190430760383606 True -18 54625 31.142246961593628 0.5732002258300781 500.53875732421875 0.2708079516887665 610.9296875 0.34652090072631836 0.8118579 0.21809406578540802 True -19 57500 31.84557342529297 0.5664429664611816 487.7886657714844 0.2096738964319229 611.0917358398438 0.34599044919013977 0.81123203 0.21824923157691956 False diff --git a/ENCSR822GDF/cherimoya.fold_2.performance.tsv b/ENCSR822GDF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 37d827b78c479c5649e00c52a51bb153cc00737a..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -610.9296875 0.4299582540988922 0.34652090072631836 0.12605930864810944 0.8118578791618347 0.7846164703369141 0.21809406578540802 \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_3.evaluate.json b/ENCSR822GDF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 74098dcd9e3709ff204263d71868b0f2bc55237e..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488ZAI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_3.fit.json b/ENCSR822GDF/cherimoya.fold_3.fit.json deleted file mode 100644 index a719a69df06bde920ca90e880be52208285bb0ec..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF488ZAI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_3.log b/ENCSR822GDF/cherimoya.fold_3.log deleted file mode 100644 index 5b0a4dcf7ccc90b6f4b801bcd47339dc6bcd0944..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 35.06913161277771 4.036224365234375 570.1467895507812 0.5318451523780823 674.6906127929688 0.24025078117847443 0.6570596 3.4624428749084473 True -1 5534 30.541569709777832 2.1429548263549805 571.8665771484375 0.47845685482025146 623.2527465820312 0.30883660912513733 0.72793156 1.1028661727905273 True -2 8301 30.60826539993286 0.5534572601318359 513.445068359375 0.34809792041778564 613.732177734375 0.31855589151382446 0.7375738 0.8497106432914734 True -3 11068 30.587502479553223 0.5373384952545166 606.8967895507812 0.38885557651519775 610.3395385742188 0.32104387879371643 0.75025237 0.36216863989830017 True -4 13835 30.569589376449585 0.5582530498504639 583.6532592773438 0.3773030638694763 606.8600463867188 0.32395148277282715 0.75834405 0.31536516547203064 True -5 16602 30.667978763580322 0.5502517223358154 588.8182373046875 0.4443696141242981 605.3123168945312 0.3259378671646118 0.76740783 0.32965853810310364 True -6 19369 30.559862852096558 0.5476267337799072 522.6326904296875 0.4727138578891754 603.8397827148438 0.32854554057121277 0.76688516 0.2916405498981476 False -7 22136 30.56545066833496 0.8220248222351074 541.3172607421875 0.31574422121047974 600.2808837890625 0.3336915373802185 0.7725648 0.2739311456680298 True -8 24903 30.50536322593689 0.8970038890838623 493.0158996582031 0.326408326625824 599.5078125 0.33425116539001465 0.7769486 0.2684630751609802 True -9 27670 30.507132291793823 2.4851715564727783 513.9428100585938 0.3755669891834259 597.6133422851562 0.3365980088710785 0.7823461 0.26570597290992737 True -10 30437 30.581796407699585 2.2902004718780518 450.37847900390625 0.31861138343811035 596.9935913085938 0.33665332198143005 0.7869808 0.25072112679481506 True -11 33204 30.575138092041016 0.5508017539978027 554.4559326171875 0.5450557470321655 595.9183959960938 0.33796223998069763 0.791811 0.24515852332115173 True -12 35971 30.220279693603516 0.5458848476409912 516.514404296875 0.3554290235042572 594.7850952148438 0.33851924538612366 0.7971673 0.2366095781326294 True -13 38738 29.960111618041992 0.543766975402832 524.1173095703125 0.3517211675643921 593.9703369140625 0.33925196528434753 0.8009384 0.2285165786743164 True -14 41505 29.963286876678467 2.4690561294555664 459.5185852050781 0.16589456796646118 590.3096923828125 0.34519830346107483 0.81017655 0.22199326753616333 True -15 44272 29.916816234588623 0.5502939224243164 515.71923828125 0.2384512722492218 590.7218627929688 0.3432937562465668 0.8163953 0.21599853038787842 True -16 47039 30.059473752975464 0.548698902130127 503.6791076660156 0.25575199723243713 589.7706298828125 0.34441012144088745 0.82289517 0.21289101243019104 True -17 49806 29.959211349487305 0.5361893177032471 576.73583984375 0.1896706074476242 590.027099609375 0.34360241889953613 0.82655084 0.21204057335853577 True -18 52573 29.953073740005493 1.2936367988586426 467.8272399902344 0.1796025037765503 588.7216796875 0.34644874930381775 0.8258418 0.21237587928771973 False -19 55340 29.93152689933777 0.5464043617248535 470.342041015625 0.17434915900230408 589.051513671875 0.34598544239997864 0.82580143 0.2136467844247818 False diff --git a/ENCSR822GDF/cherimoya.fold_3.performance.tsv b/ENCSR822GDF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2db939ffa5779af306a0ceab9a1de669f7ba2857..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -590.027099609375 0.4327870309352875 0.34360241889953613 0.12572406232357025 0.8265508413314819 0.8029653429985046 0.21204057335853577 \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_4.evaluate.json b/ENCSR822GDF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e5963a8b39de161e7486b140c4362c0440b4a0ec..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF488ZAI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_4.fit.json b/ENCSR822GDF/cherimoya.fold_4.fit.json deleted file mode 100644 index b73cf24ddf34a60e6b25c9286886b8543419d6ce..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF488ZAI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR822GDF/cherimoya.fold_4.log b/ENCSR822GDF/cherimoya.fold_4.log deleted file mode 100644 index bf5854ef91ad68c28b9a4f7216758b6ff94b061f..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2849 35.67872333526611 6.148033618927002 577.7318115234375 0.5121743679046631 664.8277587890625 0.23214706778526306 0.6417014 3.572340488433838 True -1 5698 31.549163103103638 0.6715295314788818 585.764404296875 0.38730472326278687 613.3259887695312 0.30244213342666626 0.7061262 1.0381817817687988 True -2 8547 31.583959102630615 1.6596720218658447 559.6552734375 0.4092285633087158 604.8373413085938 0.3114834725856781 0.71884805 0.49577710032463074 True -3 11396 31.5113468170166 0.5992445945739746 518.8244018554688 0.2947029173374176 601.3314208984375 0.31537556648254395 0.7304852 0.38478511571884155 True -4 14245 31.57343339920044 0.601830244064331 551.6331787109375 0.42448627948760986 598.6136474609375 0.31808018684387207 0.7347159 0.2973111569881439 True -5 17094 31.52282166481018 0.5998053550720215 462.7976989746094 0.35056886076927185 596.3295288085938 0.32100608944892883 0.74060184 0.29010990262031555 True -6 19943 31.49952530860901 0.5917174816131592 529.0098876953125 0.45894503593444824 594.5831298828125 0.32362526655197144 0.74744356 0.2758595645427704 True -7 22792 31.48461890220642 0.6488895416259766 517.9515991210938 0.18588462471961975 594.0938110351562 0.32355839014053345 0.7489036 0.2826307713985443 True -8 25641 31.448915481567383 0.6147308349609375 519.2100830078125 0.33778440952301025 592.5872192382812 0.3256496787071228 0.7581084 0.2683725357055664 True -9 28490 31.547302961349487 22.773339986801147 483.6356201171875 0.286932110786438 590.2613525390625 0.32891878485679626 0.7624361 0.24914531409740448 True -10 31339 31.69883632659912 0.6274478435516357 471.5087890625 0.31752243638038635 589.1410522460938 0.3305116295814514 0.76586735 0.23857304453849792 True -11 34188 31.488843202590942 0.6002891063690186 483.64166259765625 0.2873944342136383 587.7973022460938 0.33253371715545654 0.77336115 0.23104311525821686 True -12 37037 31.145533800125122 0.6122360229492188 534.8623046875 0.40023112297058105 586.9066772460938 0.3332529366016388 0.7806569 0.22942981123924255 True -13 39886 31.74406361579895 0.5912685394287109 497.3663330078125 0.22672244906425476 585.7774658203125 0.3344947397708893 0.7873736 0.22066369652748108 True -14 42735 30.953635931015015 0.5927364826202393 514.5732421875 0.249628946185112 585.1438598632812 0.3354480266571045 0.7938573 0.2152647227048874 True -15 45584 30.916767120361328 0.5838971138000488 536.9303588867188 0.23294927179813385 584.39794921875 0.3364078402519226 0.79916435 0.21293634176254272 True -16 48433 31.011857986450195 0.5908026695251465 556.635498046875 0.19929762184619904 583.4400024414062 0.3377523720264435 0.80481553 0.2092304527759552 True -17 51282 31.000715255737305 0.5871438980102539 509.6826477050781 0.17836859822273254 582.9107666015625 0.33861902356147766 0.8070745 0.20787683129310608 True -18 54131 30.93060612678528 0.5946440696716309 581.9284057617188 0.14226597547531128 584.2132568359375 0.33601444959640503 0.8069913 0.2081456184387207 False -19 56980 30.95703649520874 0.597059965133667 542.5355224609375 0.1648387610912323 583.8851928710938 0.3373942971229553 0.8074923 0.20844152569770813 True diff --git a/ENCSR822GDF/cherimoya.fold_4.performance.tsv b/ENCSR822GDF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d21917a8fae976899a8ff1dc3cb4b349b766db1c..0000000000000000000000000000000000000000 --- a/ENCSR822GDF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -583.8851928710938 0.4371168613433838 0.3373942971229553 0.11892054975032806 0.8074923157691956 0.7800636291503906 0.20844152569770813 \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_0.evaluate.json b/ENCSR823ZCR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6897bf00463aa6be57570f30d7630c9fa001d723..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF770FCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_0.fit.json b/ENCSR823ZCR/cherimoya.fold_0.fit.json deleted file mode 100644 index f8b670e1a15cba7e6ee7aed8acb40f6ea7cc0d7b..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF770FCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_0.log b/ENCSR823ZCR/cherimoya.fold_0.log deleted file mode 100644 index 169a4629fab336ff052e70acca0d3e42cbd904b4..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1224 18.048283100128174 3.3317339420318604 261.8714294433594 0.4701756238937378 402.873779296875 0.4300633370876312 0.60608715 16.695920944213867 True -1 2448 13.637129783630371 0.30128026008605957 279.2687072753906 0.4027644991874695 336.31939697265625 0.5160178542137146 0.65987945 4.45119571685791 True -2 3672 13.624228954315186 0.2483677864074707 265.263427734375 0.3414626121520996 319.9261169433594 0.5467777848243713 0.6798213 1.337666630744934 True -3 4896 13.618428945541382 0.24257159233093262 270.339111328125 0.3454432487487793 312.52294921875 0.5586943626403809 0.69993544 0.667279839515686 True -4 6120 13.623754739761353 0.23892521858215332 260.534423828125 0.3458191752433777 307.5955505371094 0.5690862536430359 0.7257889 0.41994717717170715 True -5 7344 13.619160175323486 0.2395458221435547 231.87991333007812 0.35024866461753845 307.0845947265625 0.5703078508377075 0.7326821 0.4317149817943573 True -6 8568 13.626515865325928 0.23981904983520508 259.68646240234375 0.30690905451774597 305.4818420410156 0.5737260580062866 0.74988043 0.37080344557762146 True -7 9792 13.623910427093506 0.24152827262878418 275.60284423828125 0.2556389570236206 304.73974609375 0.5758035778999329 0.75959945 0.3423895537853241 True -8 11016 13.623522758483887 0.2416231632232666 251.77125549316406 0.3417624235153198 304.1333312988281 0.5777901411056519 0.7638344 0.2941415011882782 True -9 12240 13.622359991073608 0.24152851104736328 321.113525390625 0.31373006105422974 303.5536193847656 0.5792317390441895 0.7726029 0.2713865041732788 True -10 13464 13.378716945648193 0.23746895790100098 234.8594512939453 0.3409639000892639 303.0420837402344 0.5805124640464783 0.77774215 0.2558867037296295 True -11 14688 13.404260635375977 0.237684965133667 279.034423828125 0.16396227478981018 302.7174072265625 0.5815008282661438 0.7805155 0.24861007928848267 True -12 15912 13.55734634399414 9.175127744674683 293.246337890625 0.2855759561061859 302.32183837890625 0.582332193851471 0.7819108 0.2476755827665329 True -13 17136 13.505767583847046 0.24799680709838867 248.35623168945312 0.17675694823265076 302.0943603515625 0.5829501748085022 0.78457206 0.24554960429668427 True -14 18360 13.415809154510498 0.24222421646118164 250.79736328125 0.1947331577539444 301.9641418457031 0.5832212567329407 0.788072 0.24594241380691528 True -15 19584 13.42123532295227 0.24047088623046875 264.829345703125 0.1828768253326416 302.02667236328125 0.5829384326934814 0.79010993 0.24840766191482544 True -16 20808 13.40438723564148 0.2359619140625 271.1812438964844 0.13393381237983704 302.3353576660156 0.582067608833313 0.7893807 0.25550487637519836 False -17 22032 13.405710697174072 0.7077560424804688 258.5325622558594 0.09815193712711334 302.75823974609375 0.5807386040687561 0.7867287 0.26469168066978455 False -18 23256 13.414063215255737 0.24023675918579102 270.1756286621094 0.09271077811717987 303.0965576171875 0.5796270370483398 0.78275436 0.273433655500412 False -19 24480 13.414669275283813 0.2383410930633545 241.61915588378906 0.0895104855298996 303.3721618652344 0.5788373947143555 0.7796566 0.2801724672317505 False diff --git a/ENCSR823ZCR/cherimoya.fold_0.performance.tsv b/ENCSR823ZCR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 03ed0adbdfccea8298698a9f7ec113d6d2f240b8..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.02667236328125 0.32856491208076477 0.5829384326934814 0.20847326517105103 0.7901099324226379 0.7734744548797607 0.24840766191482544 \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_1.evaluate.json b/ENCSR823ZCR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e98fdb34bb26270dad882f1741088fb0c62cbf69..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF770FCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_1.fit.json b/ENCSR823ZCR/cherimoya.fold_1.fit.json deleted file mode 100644 index 6a15ab9dbc492f6908204591c9c55e33dec0a971..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF770FCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_1.log b/ENCSR823ZCR/cherimoya.fold_1.log deleted file mode 100644 index 478b362710957ef7e6cf05e20f3942561b37a255..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1196 17.8348708152771 3.597634792327881 270.4476318359375 0.5065083503723145 430.11126708984375 0.43787094950675964 0.53483504 17.98854637145996 True -1 2392 13.970274686813354 0.37721705436706543 265.61309814453125 0.3879900872707367 357.2254638671875 0.5249059796333313 0.6078474 4.355486869812012 True -2 3588 13.315042734146118 1.0663714408874512 260.66827392578125 0.3210698068141937 337.30706787109375 0.5628973841667175 0.6475215 1.5259042978286743 True -3 4784 13.354012727737427 0.34546899795532227 268.07281494140625 0.2816413640975952 328.70208740234375 0.5793818831443787 0.6884823 0.6424914002418518 True -4 5980 13.343072175979614 0.33986902236938477 263.50372314453125 0.3289271295070648 325.1917724609375 0.58632892370224 0.7129218 0.4343675971031189 True -5 7176 13.349061012268066 0.33029747009277344 256.79742431640625 0.32456085085868835 324.285888671875 0.5883455872535706 0.7191041 0.4166191518306732 True -6 8372 13.320254802703857 0.3290276527404785 288.3233947753906 0.3634556531906128 323.48876953125 0.5901962518692017 0.731372 0.3249255120754242 True -7 9568 13.365254640579224 0.33932948112487793 247.21395874023438 0.2928306460380554 322.8150939941406 0.5918928980827332 0.74367523 0.27864599227905273 True -8 10764 13.329870462417603 0.33217644691467285 250.27249145507812 0.24170804023742676 322.30511474609375 0.5933818817138672 0.750504 0.2664634585380554 True -9 11960 13.310408115386963 0.34184908866882324 300.91461181640625 0.30825167894363403 321.87310791015625 0.594549298286438 0.760288 0.2519790530204773 True -10 13156 13.348193168640137 0.33952999114990234 220.0538330078125 0.24793711304664612 321.55621337890625 0.5952758193016052 0.7644637 0.2494141161441803 True -11 14352 13.357538938522339 0.34177327156066895 267.3719787597656 0.24261894822120667 321.07611083984375 0.5964595675468445 0.771936 0.2438136488199234 True -12 15548 13.317225933074951 0.3412325382232666 253.8148193359375 0.1652812659740448 320.8390808105469 0.5972633361816406 0.77814364 0.24106274545192719 True -13 16744 13.358443260192871 0.33463191986083984 260.43243408203125 0.14095336198806763 320.6239013671875 0.597709059715271 0.77927905 0.24046723544597626 True -14 17940 13.384494543075562 0.7347486019134521 242.24839782714844 0.1564491093158722 320.61639404296875 0.5975703597068787 0.78233296 0.23949512839317322 True -15 19136 13.342586755752563 0.3409135341644287 271.7085876464844 0.1253112554550171 320.7791442871094 0.597062349319458 0.78378737 0.24132788181304932 True -16 20332 13.326419353485107 0.3415191173553467 269.67669677734375 0.1565905660390854 321.0558166503906 0.5962169766426086 0.7788097 0.24781446158885956 False -17 21528 13.339429378509521 1.3666191101074219 271.17474365234375 0.08968416601419449 321.4319152832031 0.5947835445404053 0.7746704 0.2555636763572693 False -18 22724 13.342598915100098 0.335740327835083 241.71530151367188 0.0832068920135498 321.7997741699219 0.5935644507408142 0.7709006 0.26597222685813904 False -19 23920 13.336514711380005 0.33507728576660156 227.51901245117188 0.14029310643672943 322.05926513671875 0.5927616953849792 0.7661173 0.2723574936389923 False diff --git a/ENCSR823ZCR/cherimoya.fold_1.performance.tsv b/ENCSR823ZCR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ebd9836ee4f38334a0a9a85064b6d6f7ba393496..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -320.7791442871094 0.3153601586818695 0.597062349319458 0.22114744782447815 0.7837873697280884 0.7759802937507629 0.24132788181304932 \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_2.evaluate.json b/ENCSR823ZCR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 394d86ed808c9438e1847224fa3412a8e1ca9e2c..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF770FCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_2.fit.json b/ENCSR823ZCR/cherimoya.fold_2.fit.json deleted file mode 100644 index 93e77966fb80f3f22edd3859632eca9dc0d9bafd..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF770FCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_2.log b/ENCSR823ZCR/cherimoya.fold_2.log deleted file mode 100644 index 84d08797839f6ad61400cbbfa7edc8ded51decd0..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1284 18.645463705062866 3.44201922416687 249.21356201171875 0.47807860374450684 404.4458312988281 0.4357564449310303 0.5369175 16.383512496948242 True -1 2568 14.343716382980347 0.3657565116882324 269.1750183105469 0.4106251299381256 341.1968078613281 0.5187391638755798 0.6189944 3.5699820518493652 True -2 3852 14.280691146850586 0.2747476100921631 231.27059936523438 0.32473814487457275 324.822998046875 0.5496389269828796 0.6576381 0.8962202668190002 True -3 5136 14.032498121261597 0.7480590343475342 226.0821533203125 0.4176633954048157 317.150146484375 0.56388920545578 0.69347084 0.5657179951667786 True -4 6420 14.074175119400024 0.2566540241241455 242.03814697265625 0.3195417523384094 314.0950012207031 0.5698724389076233 0.7095728 0.5429472327232361 True -5 7704 14.067254304885864 0.2654707431793213 257.3853759765625 0.21223300695419312 312.2517395019531 0.5744270086288452 0.73042697 0.3800925314426422 True -6 8988 14.045108079910278 0.26105761528015137 275.061767578125 0.2819483280181885 312.15618896484375 0.5749325156211853 0.73024076 0.3523251712322235 False -7 10272 14.049886226654053 0.2592809200286865 272.0404052734375 0.2495405524969101 311.2728271484375 0.5772430896759033 0.7449336 0.31516456604003906 True -8 11556 14.043725728988647 0.26128149032592773 256.9788818359375 0.19830399751663208 310.34515380859375 0.579626202583313 0.75369686 0.2880183756351471 True -9 12840 14.044374942779541 0.2578389644622803 254.32958984375 0.2353253811597824 309.6911315917969 0.5812810659408569 0.7597999 0.27700331807136536 True -10 14124 14.037959814071655 1.4738900661468506 286.53778076171875 0.19920527935028076 309.1528625488281 0.5824576616287231 0.7656579 0.2580542266368866 True -11 15408 14.045805931091309 0.26013731956481934 254.29611206054688 0.37034523487091064 308.75189208984375 0.5836746096611023 0.7682896 0.2519010007381439 True -12 16692 14.034977436065674 0.25826191902160645 232.13681030273438 0.19205930829048157 308.3060607910156 0.5849354863166809 0.77086866 0.24818576872348785 True -13 17976 14.045867919921875 0.25832509994506836 265.9853515625 0.19829429686069489 308.0249328613281 0.5857147574424744 0.77189416 0.2493445873260498 True -14 19260 14.039177179336548 0.37940239906311035 235.1148223876953 0.137454554438591 307.97369384765625 0.5858214497566223 0.77139115 0.25274187326431274 False -15 20544 14.044703722000122 0.2633194923400879 244.1731414794922 0.24486008286476135 308.10980224609375 0.5853572487831116 0.7694167 0.2588239908218384 False -16 21828 14.045176029205322 0.253772497177124 258.3431091308594 0.09471110999584198 308.3294982910156 0.584575355052948 0.7656279 0.26712942123413086 False -17 23112 14.059624671936035 0.2621133327484131 251.3140411376953 0.14940065145492554 308.6877136230469 0.5832263231277466 0.7614674 0.27549445629119873 False -18 24396 14.048505306243896 0.2604999542236328 259.60357666015625 0.16633251309394836 309.1047058105469 0.5820190906524658 0.757531 0.2842942476272583 False -19 25680 14.054433822631836 7.16851019859314 204.40255737304688 0.1184815913438797 309.37017822265625 0.5812414884567261 0.7538412 0.2887944281101227 False diff --git a/ENCSR823ZCR/cherimoya.fold_2.performance.tsv b/ENCSR823ZCR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4f37784021d3cd3b4dbb066b63897504915b423d..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.0249328613281 0.32516080141067505 0.5857147574424744 0.21347901225090027 0.7718941569328308 0.7601925730705261 0.2493445873260498 \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_3.evaluate.json b/ENCSR823ZCR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 12b9bb2de0157a64c41bb41d43796f00a7cfeda9..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF770FCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_3.fit.json b/ENCSR823ZCR/cherimoya.fold_3.fit.json deleted file mode 100644 index 6972044fd1d22bd432f14453e1248e678f57eb0f..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF770FCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_3.log b/ENCSR823ZCR/cherimoya.fold_3.log deleted file mode 100644 index 9716aeb3ecb76912e1b0c712d7d9555e8cf290d9..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1252 18.33440113067627 4.412449598312378 281.5860595703125 0.5981319546699524 400.6510925292969 0.43153735995292664 0.54998785 16.698213577270508 True -1 2504 14.531262636184692 0.25363874435424805 276.5211181640625 0.4011054039001465 333.61578369140625 0.5201596021652222 0.6167496 3.632490873336792 True -2 3756 13.950514316558838 0.262683629989624 314.28875732421875 0.3510267734527588 317.9096984863281 0.5515894293785095 0.65755063 1.4394639730453491 True -3 5008 13.952844142913818 0.2569272518157959 258.20013427734375 0.3177259862422943 310.9881591796875 0.5629996657371521 0.685162 0.7189323902130127 True -4 6260 13.939558982849121 0.31861114501953125 242.33721923828125 0.21253132820129395 306.7897644042969 0.5724722743034363 0.70932525 0.4850948452949524 True -5 7512 13.934534788131714 0.2533457279205322 279.82086181640625 0.3598881661891937 306.2902526855469 0.5731330513954163 0.7129021 0.43338221311569214 True -6 8764 13.935565948486328 0.2501373291015625 234.5623321533203 0.2391710877418518 304.9373474121094 0.5770070552825928 0.73024786 0.39019206166267395 True -7 10016 13.94341778755188 0.25731492042541504 227.07676696777344 0.30622223019599915 304.3353576660156 0.5786159634590149 0.7432919 0.3207036256790161 True -8 11268 13.954895496368408 0.25249719619750977 288.7616882324219 0.31047874689102173 303.9338684082031 0.579814612865448 0.74811804 0.304476797580719 True -9 12520 13.966599941253662 0.2495431900024414 303.36700439453125 0.31201446056365967 303.6502685546875 0.5805652737617493 0.7554776 0.29033124446868896 True -10 13772 13.967598915100098 0.24464654922485352 257.76922607421875 0.24007484316825867 303.2688903808594 0.5815813541412354 0.76007265 0.2802243232727051 True -11 15024 13.946156740188599 0.24486756324768066 242.81459045410156 0.19291414320468903 302.8750915527344 0.5825806260108948 0.76158935 0.2710193693637848 True -12 16276 13.94600510597229 0.25652647018432617 234.97296142578125 0.23407094180583954 302.6689758300781 0.5831182599067688 0.7633673 0.27366429567337036 True -13 17528 13.939668655395508 0.24603557586669922 282.2096862792969 0.2296977937221527 302.40789794921875 0.583791196346283 0.7651729 0.2719751000404358 True -14 18780 13.939488410949707 0.245652437210083 260.9237060546875 0.20466572046279907 302.2546691894531 0.5840394496917725 0.76568466 0.27160316705703735 True -15 20032 13.946369409561157 0.2519493103027344 281.6340026855469 0.1493765264749527 302.27410888671875 0.5838236808776855 0.7675017 0.2724553346633911 True -16 21284 13.937121152877808 0.24945497512817383 262.4967346191406 0.1320822536945343 302.4969177246094 0.5830618143081665 0.7650251 0.2822459638118744 False -17 22536 13.974917888641357 0.2499678134918213 227.02601623535156 0.11435475945472717 302.8506164550781 0.5817797183990479 0.7610624 0.29400262236595154 False -18 23788 13.966071605682373 0.2530810832977295 260.6934509277344 0.1223190575838089 303.2630615234375 0.5805795788764954 0.756923 0.3035627007484436 False -19 25040 13.959964990615845 0.2509498596191406 244.8180694580078 0.07505179941654205 303.4614562988281 0.5798540115356445 0.75545233 0.3115113079547882 False diff --git a/ENCSR823ZCR/cherimoya.fold_3.performance.tsv b/ENCSR823ZCR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6d21df5eda9af5ec34ad3346a8cd79b6cb3b3657..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.27410888671875 0.326996386051178 0.5838236808776855 0.20905520021915436 0.767501711845398 0.7528331279754639 0.2724553346633911 \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_4.evaluate.json b/ENCSR823ZCR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 86b3f171b83b48b4f865f899cc6079af436900ba..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF770FCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_4.fit.json b/ENCSR823ZCR/cherimoya.fold_4.fit.json deleted file mode 100644 index 053388f734a97ae9ab0c082b11940e16f92507d7..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF770FCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR823ZCR/cherimoya.fold_4.log b/ENCSR823ZCR/cherimoya.fold_4.log deleted file mode 100644 index cf952ba061819081b315f816b264ca7aaab8d8bc..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1248 18.2696373462677 3.4113543033599854 244.6492919921875 0.42107611894607544 400.19403076171875 0.4292805790901184 0.5692494 16.407041549682617 True -1 2496 13.873546600341797 0.2552225589752197 241.88031005859375 0.3130665421485901 334.291259765625 0.5181086659431458 0.63397455 3.73643159866333 True -2 3744 13.889840364456177 0.2563788890838623 256.1434326171875 0.2695920467376709 317.0893249511719 0.55073481798172 0.67253935 1.2910810708999634 True -3 4992 13.892974138259888 0.9448511600494385 212.17120361328125 0.30432066321372986 312.20635986328125 0.5578150153160095 0.69572926 0.7033804655075073 True -4 6240 13.887897729873657 0.2422945499420166 243.52969360351562 0.31789839267730713 306.62774658203125 0.5700222253799438 0.7203692 0.5092335343360901 True -5 7488 13.907530546188354 0.24728941917419434 261.66827392578125 0.2754528522491455 305.2285461425781 0.5741477608680725 0.7362031 0.3838164806365967 True -6 8736 13.8879234790802 0.23845839500427246 238.8292236328125 0.2517337203025818 305.48919677734375 0.5741654634475708 0.7377436 0.39864954352378845 True -7 9984 13.908432960510254 0.23537826538085938 270.3990783691406 0.3017480969429016 304.6083679199219 0.5765306353569031 0.75214165 0.3199107348918915 True -8 11232 13.912741661071777 0.23824834823608398 224.38880920410156 0.3169363737106323 303.85845947265625 0.5782430768013 0.7601695 0.2875402569770813 True -9 12480 13.913365364074707 0.24460196495056152 227.8492431640625 0.22291013598442078 303.26446533203125 0.5795783996582031 0.76338655 0.2651069760322571 True -10 13728 13.893625497817993 0.24313688278198242 274.2081298828125 0.2593633532524109 302.7597351074219 0.5809250473976135 0.7672037 0.25494247674942017 True -11 14976 13.629226684570312 0.8883230686187744 230.99249267578125 0.389797568321228 302.5129089355469 0.5815861225128174 0.76896507 0.25795674324035645 True -12 16224 13.650694847106934 0.23856735229492188 253.38226318359375 0.19961300492286682 302.0768737792969 0.5826678276062012 0.77354485 0.24928177893161774 True -13 17472 13.640856266021729 0.23984098434448242 276.36846923828125 0.1451789289712906 301.7935791015625 0.5832565426826477 0.77770275 0.2435249537229538 True -14 18720 13.646504640579224 0.24084234237670898 223.30581665039062 0.24042049050331116 301.7947082519531 0.5833448767662048 0.7793408 0.24266332387924194 True -15 19968 13.658424139022827 0.8992247581481934 225.83316040039062 0.16390925645828247 301.74481201171875 0.5830490589141846 0.7779789 0.24562083184719086 False -16 21216 13.663349151611328 0.23606467247009277 275.91741943359375 0.18658769130706787 302.1051940917969 0.5820503830909729 0.77991897 0.2490270733833313 True -17 22464 13.669804811477661 0.232374906539917 254.7924041748047 0.11070653796195984 302.5251770019531 0.5807251930236816 0.77703893 0.2569082975387573 False -18 23712 13.677120685577393 0.2335672378540039 247.54684448242188 0.11580253392457962 302.89019775390625 0.5796063542366028 0.7737287 0.2637501060962677 False -19 24960 13.701191902160645 0.24055767059326172 262.4521484375 0.05887526273727417 303.1120300292969 0.5788440108299255 0.7736487 0.2716476023197174 False diff --git a/ENCSR823ZCR/cherimoya.fold_4.performance.tsv b/ENCSR823ZCR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 97aafd78dc2f3d34bd4b529b0316eb0b2dc2faba..0000000000000000000000000000000000000000 --- a/ENCSR823ZCR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.1051940917969 0.32822898030281067 0.5820502638816833 0.20722424983978271 0.7799189686775208 0.7532029747962952 0.2490270733833313 \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_0.evaluate.json b/ENCSR824DUE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c4b973ac48f0d1353826e268a53cae9bdfb3da43..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF290VYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_0.fit.json b/ENCSR824DUE/cherimoya.fold_0.fit.json deleted file mode 100644 index 0b283b179e6c682791144176c05f35190fa46cf1..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF290VYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_0.log b/ENCSR824DUE/cherimoya.fold_0.log deleted file mode 100644 index b96524d068a76b46bd8fa6384310d7f0afaf4be8..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2236 30.219180822372437 4.295178651809692 378.0338134765625 0.6446178555488586 497.0823059082031 0.47741591930389404 0.41218644 8.62391185760498 True -1 4472 24.701093673706055 0.6351885795593262 338.585693359375 0.5695998668670654 422.2408752441406 0.6011325120925903 0.5065103 2.6532998085021973 True -2 6708 24.751589059829712 0.5068192481994629 323.684814453125 0.5854074954986572 407.6405029296875 0.6286779642105103 0.5347488 0.977428138256073 True -3 8944 24.673330307006836 0.5145599842071533 292.45880126953125 0.5330349206924438 403.0712585449219 0.6364272832870483 0.55842847 0.7791998982429504 True -4 11180 24.69946575164795 0.4765465259552002 319.3154602050781 0.596139669418335 401.9601745605469 0.6392742395401001 0.5577665 0.6856993436813354 False -5 13416 24.169507026672363 0.49047350883483887 379.6230163574219 0.6243870258331299 400.4913330078125 0.6425487995147705 0.5584452 0.658016562461853 True -6 15652 24.178998947143555 0.4891524314880371 285.69500732421875 0.43383094668388367 399.1452331542969 0.6446518301963806 0.560289 0.6624930500984192 True -7 17888 24.180975675582886 0.475308895111084 339.780517578125 0.6234320998191833 398.4596862792969 0.6466459631919861 0.5629925 0.6537020802497864 True -8 20124 24.229812145233154 0.4774293899536133 354.0697937011719 0.46533113718032837 397.7138366699219 0.648619532585144 0.5709409 0.6073184609413147 True -9 22360 24.244317531585693 0.5323173999786377 354.8890380859375 0.5539074540138245 396.2540588378906 0.6511430740356445 0.57567656 0.5833054780960083 True -10 24596 24.24984836578369 0.47286033630371094 268.32757568359375 0.3694184720516205 394.9388427734375 0.6532765626907349 0.5835849 0.5524278879165649 True -11 26832 24.213902473449707 0.4793968200683594 299.349853515625 0.4163840115070343 393.57818603515625 0.655384361743927 0.5934371 0.5382498502731323 True -12 29068 24.187486171722412 0.47336673736572266 306.0595703125 0.3004140853881836 392.68634033203125 0.6571744084358215 0.601581 0.5252259969711304 True -13 31304 24.228296756744385 0.47220587730407715 348.742919921875 0.44366323947906494 391.8086853027344 0.6589462757110596 0.60793716 0.5088664293289185 True -14 33540 24.231232404708862 0.46654677391052246 308.38543701171875 0.31112533807754517 390.5380859375 0.6603310704231262 0.61551726 0.49275925755500793 True -15 35776 24.195841789245605 2.049103021621704 344.80194091796875 0.3108450770378113 390.2804870605469 0.6610096096992493 0.62225175 0.4831535518169403 True -16 38012 24.232023000717163 0.483123779296875 307.0665588378906 0.28014200925827026 390.01800537109375 0.6610453128814697 0.62376565 0.47124770283699036 True -17 40248 24.177140474319458 0.4795377254486084 269.6816711425781 0.45303916931152344 390.25811767578125 0.6606913208961487 0.62335306 0.47240662574768066 False -18 42484 24.238125562667847 0.479107141494751 313.529541015625 0.21332332491874695 391.132568359375 0.6601219177246094 0.6202105 0.47155043482780457 False -19 44720 24.19335174560547 0.472231388092041 363.0296936035156 0.27052849531173706 390.9170837402344 0.6598707437515259 0.6174429 0.4767950773239136 False diff --git a/ENCSR824DUE/cherimoya.fold_0.performance.tsv b/ENCSR824DUE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b2ce5d10e08f31af20ef65ead1ac276bd16df19f..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -390.01800537109375 0.2768597900867462 0.6610453128814697 0.2565942406654358 0.6237656474113464 0.5907011032104492 0.47124770283699036 \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_1.evaluate.json b/ENCSR824DUE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5168d418debdc53201ac772ba641e3a2bd511649..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF290VYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_1.fit.json b/ENCSR824DUE/cherimoya.fold_1.fit.json deleted file mode 100644 index 4526b8a4168c0a9be5c169c2eaeedc665b6da816..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF290VYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_1.log b/ENCSR824DUE/cherimoya.fold_1.log deleted file mode 100644 index 21dbe9538d9037b6a1fe9f058f81638b5a6ab016..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2272 29.764657974243164 3.557136058807373 289.809326171875 0.5402456521987915 488.65386962890625 0.4821815490722656 0.39372185 7.191227436065674 True -1 4544 25.107705116271973 0.6566166877746582 353.8834228515625 0.6946635246276855 423.4947204589844 0.5941887497901917 0.5238281 2.45196533203125 True -2 6816 25.085716247558594 0.6610989570617676 340.658203125 0.4745215177536011 412.58270263671875 0.6149924993515015 0.5312629 1.1130826473236084 True -3 9088 25.06392240524292 0.5179789066314697 304.5574951171875 0.46548205614089966 408.5011901855469 0.6226176619529724 0.55468684 0.7954214215278625 True -4 11360 25.0571026802063 0.5214314460754395 318.2686767578125 0.5496840476989746 407.00091552734375 0.6258399486541748 0.56283176 0.7052540183067322 True -5 13632 25.08441686630249 1.9304556846618652 355.99847412109375 0.6172012090682983 405.7945861816406 0.6285524964332581 0.5712765 0.6632207036018372 True -6 15904 25.10762596130371 0.5722088813781738 295.80352783203125 0.6233835220336914 404.8255615234375 0.6304494738578796 0.57749015 0.589678168296814 True -7 18176 25.145175218582153 0.5411438941955566 355.83135986328125 0.6278998851776123 403.8193054199219 0.6327733993530273 0.5860103 0.5619990825653076 True -8 20448 25.156648635864258 16.668757677078247 324.2960205078125 0.45114368200302124 402.0445251464844 0.635974645614624 0.593449 0.5139650106430054 True -9 22720 25.143122911453247 0.5275471210479736 325.1123962402344 0.3818511366844177 401.14764404296875 0.6380613446235657 0.5992603 0.4851193428039551 True -10 24992 25.47285485267639 19.411447763442993 293.9601135253906 0.4367276430130005 400.03662109375 0.6403229832649231 0.6108903 0.46940892934799194 True -11 27264 24.89267325401306 0.5362846851348877 359.9643859863281 0.6450337767601013 399.0657043457031 0.6421203017234802 0.6179217 0.44583776593208313 True -12 29536 24.628347635269165 0.5222220420837402 283.2503356933594 0.3080442547798157 398.119873046875 0.6440061330795288 0.62515265 0.43309032917022705 True -13 31808 24.618964910507202 0.520378828048706 284.87213134765625 0.3536529541015625 396.8158874511719 0.6458451151847839 0.63775617 0.419367253780365 True -14 34080 24.623355627059937 0.5082747936248779 320.4751281738281 0.40964698791503906 396.0741271972656 0.6473271250724792 0.64188826 0.41451725363731384 True -15 36352 24.60409426689148 0.5145285129547119 274.47711181640625 0.3466353416442871 395.5100402832031 0.6481722593307495 0.64993817 0.4062628448009491 True -16 38624 24.596389055252075 0.510129451751709 287.70556640625 0.300601601600647 395.4285888671875 0.6481512784957886 0.6531318 0.4033190608024597 True -17 40896 24.619245767593384 0.5160889625549316 291.3177490234375 0.2401885986328125 395.46240234375 0.6478398442268372 0.65386134 0.40544393658638 True -18 43168 24.62946105003357 0.5287983417510986 311.3968505859375 0.26321151852607727 395.6105041503906 0.6473878026008606 0.65310174 0.41222643852233887 False -19 45440 24.639556884765625 0.5263516902923584 275.281982421875 0.34016451239585876 395.67230224609375 0.6472353935241699 0.6503578 0.4174439311027527 False diff --git a/ENCSR824DUE/cherimoya.fold_1.performance.tsv b/ENCSR824DUE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 31673b60673334473e8c9878016c9a034d94c9a1..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -395.46240234375 0.28037020564079285 0.6478398442268372 0.2550838887691498 0.6538613438606262 0.6354653239250183 0.40544393658638 \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_2.evaluate.json b/ENCSR824DUE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 859c8765f53e8226613a489aba76916687899ad7..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF290VYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_2.fit.json b/ENCSR824DUE/cherimoya.fold_2.fit.json deleted file mode 100644 index 301d6a1d7bf943ac4f98163ad9d3b2c02e6cb405..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF290VYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_2.log b/ENCSR824DUE/cherimoya.fold_2.log deleted file mode 100644 index 5cc768a683b1f96c8f42b07279c9529f97dccb26..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2389 30.979312896728516 4.127469301223755 332.3480224609375 0.7973828911781311 485.9259033203125 0.4828135073184967 0.43636054 7.222506523132324 True -1 4778 26.472599029541016 0.48418092727661133 288.7145690917969 0.6375570893287659 421.9805603027344 0.5998541712760925 0.53628093 2.4570820331573486 True -2 7167 26.407076358795166 1.9498381614685059 372.9547119140625 0.6752269268035889 408.51007080078125 0.6232426762580872 0.5540681 0.8408332467079163 True -3 9556 26.392170429229736 0.44106006622314453 337.7790832519531 0.628520131111145 404.7237243652344 0.6290722489356995 0.56931514 0.7360697388648987 True -4 11945 26.404629230499268 0.43880534172058105 304.840087890625 0.638961911201477 403.0718078613281 0.6321307420730591 0.58004934 0.5954490303993225 True -5 14334 26.408704042434692 0.43447232246398926 275.9778137207031 0.640485405921936 400.9380798339844 0.6365452408790588 0.5849547 0.5596922636032104 True -6 16723 26.40890622138977 0.43537259101867676 298.11968994140625 0.3765416145324707 399.58941650390625 0.6388899683952332 0.5945226 0.5587274432182312 True -7 19112 26.40211534500122 0.4387795925140381 335.62615966796875 0.6454989910125732 398.6014099121094 0.640952467918396 0.5994131 0.5298374891281128 True -8 21501 26.32336735725403 0.6510105133056641 285.18756103515625 0.4579602777957916 397.5606384277344 0.6430697441101074 0.60475343 0.5099865198135376 True -9 23890 26.37271809577942 0.4382481575012207 306.54913330078125 0.4869229197502136 396.2635192871094 0.6453961730003357 0.6084604 0.4908987581729889 True -10 26279 26.36929225921631 0.44339442253112793 258.1763000488281 0.5088485479354858 395.1691589355469 0.6478299498558044 0.611401 0.4740980267524719 True -11 28668 26.35476279258728 0.44521141052246094 287.33892822265625 0.5129382610321045 394.2486877441406 0.6500943303108215 0.6165533 0.46126145124435425 True -12 31057 26.408244848251343 1.3875155448913574 347.52056884765625 0.3725084066390991 393.3385314941406 0.6519722938537598 0.6251673 0.4566226005554199 True -13 33446 26.384885549545288 0.44003891944885254 362.40435791015625 0.4356445372104645 392.5837097167969 0.653516411781311 0.62902933 0.4510222375392914 True -14 35835 26.25529170036316 0.4390900135040283 329.14239501953125 0.4078572988510132 391.84405517578125 0.6546341180801392 0.6400604 0.44221094250679016 True -15 38224 25.8754563331604 0.4287567138671875 320.2041931152344 0.4913293123245239 391.47711181640625 0.6553542017936707 0.64380306 0.4386674463748932 True -16 40613 25.925037622451782 0.42557430267333984 358.5665283203125 0.4247357249259949 391.33538818359375 0.6557937860488892 0.646919 0.4369284510612488 True -17 43002 25.924323320388794 0.4406888484954834 349.20831298828125 0.27611488103866577 391.4391784667969 0.6555466055870056 0.6498796 0.4372389316558838 True -18 45391 25.906609296798706 0.4335625171661377 310.4031677246094 0.3416900634765625 391.5901184082031 0.6550481915473938 0.6482245 0.4411202073097229 False -19 47780 25.909820795059204 0.5636782646179199 277.8437194824219 0.2697305679321289 391.8392639160156 0.6546536684036255 0.64496636 0.44806089997291565 False diff --git a/ENCSR824DUE/cherimoya.fold_2.performance.tsv b/ENCSR824DUE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b2e8de3c44aa0d91ba62d8bae5340267b4e5def6..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -391.4391784667969 0.27909064292907715 0.6555465459823608 0.2562193274497986 0.6498795747756958 0.6263574361801147 0.4372389316558838 \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_3.evaluate.json b/ENCSR824DUE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3ce0ac16534b4d29bcd8f6811b3789b8d6dd7070..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF290VYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_3.fit.json b/ENCSR824DUE/cherimoya.fold_3.fit.json deleted file mode 100644 index 8f41403e2af6e5b25e82f34d88f2a7ee60a22a07..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF290VYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_3.log b/ENCSR824DUE/cherimoya.fold_3.log deleted file mode 100644 index 8eb1caf0f8fb11d6593d6b0356e1908ac6838402..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2314 30.081071138381958 4.246746778488159 311.7950439453125 0.7122223377227783 505.2144470214844 0.48737141489982605 0.43021387 8.765698432922363 True -1 4628 25.580792903900146 0.8264164924621582 304.5060119628906 0.7953378558158875 431.6372985839844 0.6100009083747864 0.530711 2.531743049621582 True -2 6942 25.636034965515137 0.5819897651672363 346.3924865722656 0.6525331735610962 418.9479675292969 0.6293840408325195 0.5390536 0.9498260617256165 True -3 9256 25.541892528533936 0.5234553813934326 286.6278076171875 0.7455368638038635 414.7102966308594 0.6368197202682495 0.5429235 0.8408836126327515 True -4 11570 25.566030740737915 0.5201761722564697 352.473876953125 0.5122096538543701 412.7820739746094 0.6406959891319275 0.5571816 0.8626342415809631 True -5 13884 25.57733154296875 0.5266847610473633 273.42315673828125 0.5688725709915161 411.91912841796875 0.642294704914093 0.56866515 0.7172605991363525 True -6 16198 25.571158409118652 0.5425055027008057 306.03509521484375 0.6115125417709351 410.1986083984375 0.645235002040863 0.58510333 0.6933512687683105 True -7 18512 25.573494911193848 0.5712172985076904 261.40826416015625 0.8601462841033936 408.7811279296875 0.6478803753852844 0.5899908 0.6545735597610474 True -8 20826 25.57118797302246 1.1043219566345215 288.9004211425781 0.46057790517807007 407.5041809082031 0.6501954197883606 0.5950338 0.6385901570320129 True -9 23140 25.523605585098267 0.5256850719451904 294.9627685546875 0.48339027166366577 406.24017333984375 0.6523822546005249 0.6043918 0.5840587019920349 True -10 25454 25.526095390319824 0.5393116474151611 329.272705078125 0.5387939214706421 405.4154357910156 0.6544625759124756 0.612294 0.5725150108337402 True -11 27768 25.539860725402832 0.5283522605895996 266.2580261230469 0.4736446738243103 404.376220703125 0.6562306880950928 0.619668 0.5383305549621582 True -12 30082 25.614527463912964 0.5622196197509766 348.1662902832031 0.5851096510887146 403.1507263183594 0.6583849191665649 0.6269361 0.519366979598999 True -13 32396 25.695735931396484 0.5337786674499512 333.1533203125 0.39393144845962524 401.6366271972656 0.6605131030082703 0.63235426 0.5044366121292114 True -14 34710 25.71236300468445 0.5488111972808838 293.53265380859375 0.4125330448150635 400.5902099609375 0.6619365215301514 0.64309645 0.4737341105937958 True -15 37024 25.72672939300537 0.5289425849914551 317.37158203125 0.3278612494468689 400.3402099609375 0.6626320481300354 0.6517463 0.45977798104286194 True -16 39338 25.65014624595642 0.5390470027923584 307.26507568359375 0.36523622274398804 399.90081787109375 0.6630130410194397 0.6554694 0.4572339653968811 True -17 41652 25.765350580215454 0.5371885299682617 281.83709716796875 0.30961519479751587 400.0282287597656 0.662652850151062 0.6545934 0.46155211329460144 False -18 43966 25.667577266693115 0.5266819000244141 276.78228759765625 0.2960001230239868 400.6316223144531 0.662034273147583 0.64949507 0.4698089063167572 False -19 46280 25.270653009414673 0.5215563774108887 316.9259948730469 0.2742575705051422 400.2487487792969 0.6617783904075623 0.64707667 0.4745852053165436 False diff --git a/ENCSR824DUE/cherimoya.fold_3.performance.tsv b/ENCSR824DUE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b29375fc251f03f0f88403724797f9a889833295..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -399.90081787109375 0.2732340693473816 0.6630130410194397 0.2625420391559601 0.6554694175720215 0.6302915811538696 0.4572339653968811 \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_4.evaluate.json b/ENCSR824DUE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 32425903871cca28c788833916b80b8b6c284691..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF290VYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_4.fit.json b/ENCSR824DUE/cherimoya.fold_4.fit.json deleted file mode 100644 index 8ce06c5ebdf2fa9533eb977a0ec9a6c3e44b4805..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF290VYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824DUE/cherimoya.fold_4.log b/ENCSR824DUE/cherimoya.fold_4.log deleted file mode 100644 index ffce7b7bc8eddd5d7f987052874400ffc6cb0cb8..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2373 30.7372887134552 3.5976781845092773 343.0813903808594 0.8034312725067139 497.35247802734375 0.48844465613365173 0.45167378 6.401641845703125 True -1 4746 26.207271575927734 0.7508375644683838 313.48822021484375 0.48654454946517944 427.6553955078125 0.613139271736145 0.52899027 2.4531502723693848 True -2 7119 26.21013331413269 0.47585415840148926 300.2060546875 0.48513078689575195 414.8759460449219 0.6344617605209351 0.531483 1.0450057983398438 True -3 9492 26.23647117614746 0.47215795516967773 331.3203430175781 0.7728573083877563 410.49420166015625 0.6419311761856079 0.5495702 0.7687066197395325 True -4 11865 26.14876675605774 0.47304725646972656 304.20733642578125 0.6080405712127686 408.52880859375 0.6457836031913757 0.55940175 0.7231169939041138 True -5 14238 26.20386815071106 0.46607327461242676 323.6297912597656 0.3941500186920166 407.2010803222656 0.6484096050262451 0.56486803 0.6735922694206238 True -6 16611 26.155396223068237 0.46561121940612793 302.8565673828125 0.4859992265701294 405.8412780761719 0.6509829163551331 0.5717978 0.6540091037750244 True -7 18984 26.174911499023438 0.4673128128051758 300.576171875 0.583561897277832 404.3030700683594 0.6533897519111633 0.58111936 0.5685738325119019 True -8 21357 26.186763048171997 0.4788072109222412 300.30401611328125 0.43038588762283325 403.3220520019531 0.6551235914230347 0.5854791 0.574479877948761 True -9 23730 26.184995651245117 0.47533488273620605 334.0001220703125 0.6016936302185059 401.9561767578125 0.6579375863075256 0.5890698 0.5555766224861145 True -10 26103 26.18710160255432 0.46600818634033203 301.7377624511719 0.5589179396629333 400.50201416015625 0.6601448655128479 0.6000989 0.5293112993240356 True -11 28476 26.16254425048828 0.47118210792541504 302.32000732421875 0.3656141757965088 399.8621826171875 0.6616573929786682 0.60347164 0.5204389095306396 True -12 30849 26.230284929275513 0.47804927825927734 338.16033935546875 0.31507542729377747 398.59710693359375 0.6637351512908936 0.61404717 0.5070953965187073 True -13 33222 26.140825510025024 0.4676203727722168 291.3141174316406 0.4545304775238037 397.6131896972656 0.6653667092323303 0.6208515 0.4945884943008423 True -14 35595 26.146217346191406 0.4646871089935303 263.73016357421875 0.38715028762817383 396.8706359863281 0.6668718457221985 0.6309691 0.4754263460636139 True -15 37968 26.144553422927856 0.8110597133636475 298.9251708984375 0.3736698031425476 396.08892822265625 0.6678590178489685 0.63807195 0.46420323848724365 True -16 40341 26.204533576965332 0.4707298278808594 282.31353759765625 0.37282222509384155 395.93017578125 0.6682560443878174 0.6434423 0.4548541307449341 True -17 42714 26.18723702430725 0.4753892421722412 303.26446533203125 0.21089228987693787 396.0723571777344 0.6680727005004883 0.64357567 0.4596414268016815 True -18 45087 26.223033905029297 0.907289981842041 332.36334228515625 0.2669142782688141 395.9356994628906 0.6675594449043274 0.64346385 0.4573725759983063 False -19 47460 26.162928819656372 0.46529603004455566 332.1884765625 0.3144111633300781 396.3775329589844 0.6673904657363892 0.63997364 0.4602309465408325 False diff --git a/ENCSR824DUE/cherimoya.fold_4.performance.tsv b/ENCSR824DUE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 55ab731bea12300b69881d4e43f12876544ebbcd..0000000000000000000000000000000000000000 --- a/ENCSR824DUE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -396.0723571777344 0.272447407245636 0.6680726408958435 0.26298004388809204 0.6435756683349609 0.6072221398353577 0.4596414268016815 \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_0.evaluate.json b/ENCSR824YLD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e3a76322a8abedcd2e95ef249af2dc734907bf03..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415SVF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_0.fit.json b/ENCSR824YLD/cherimoya.fold_0.fit.json deleted file mode 100644 index ed144440bb627c09a2cbb3b0a263da5b9fa63785..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF415SVF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_0.log b/ENCSR824YLD/cherimoya.fold_0.log deleted file mode 100644 index 6084a015707563cbed3bebbabfaff635f8d0eaae..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2467 31.905940055847168 3.8203701972961426 214.5965576171875 0.46710237860679626 335.38043212890625 0.13883602619171143 0.6596916 4.785433769226074 True -1 4934 27.197026252746582 0.5013813972473145 231.8832244873047 0.5144285559654236 308.311279296875 0.18503519892692566 0.74926496 1.8285903930664062 True -2 7401 27.254005908966064 0.5341389179229736 232.05838012695312 0.6282567381858826 301.31634521484375 0.189222052693367 0.75289893 1.5110567808151245 True -3 9868 27.345444679260254 16.06972599029541 190.37274169921875 0.3697690963745117 295.7940368652344 0.1960214227437973 0.76672274 0.9340282082557678 True -4 12335 27.168343782424927 0.508155107498169 228.41236877441406 0.4955073595046997 293.29974365234375 0.19882644712924957 0.7785842 0.8183454871177673 True -5 14802 27.16755723953247 0.5062687397003174 226.3847198486328 0.3289859890937805 291.4530029296875 0.2019001990556717 0.7882259 0.7252251505851746 True -6 17269 27.198859691619873 1.0700404644012451 254.48641967773438 0.4850345551967621 289.7102355957031 0.20409639179706573 0.8037185 0.6095631718635559 True -7 19736 27.14924192428589 0.5038056373596191 242.46775817871094 0.481484055519104 288.2718811035156 0.20614269375801086 0.8069963 0.5820454359054565 True -8 22203 27.128260612487793 1.1104316711425781 273.27734375 0.5237767100334167 286.884521484375 0.20939604938030243 0.8160142 0.5401743054389954 True -9 24670 27.18088698387146 0.5055291652679443 241.5323486328125 0.5966503024101257 286.3674621582031 0.2098049819469452 0.8259255 0.47885918617248535 True -10 27137 27.159458875656128 0.4888627529144287 247.73228454589844 0.33678412437438965 285.0274658203125 0.2124718278646469 0.8298999 0.45121026039123535 True -11 29604 27.16659665107727 0.5034098625183105 218.7137451171875 0.2717462182044983 284.5701904296875 0.21289944648742676 0.83843106 0.39340662956237793 True -12 32071 27.165147304534912 0.5033535957336426 311.10748291015625 0.525757908821106 283.830078125 0.21331073343753815 0.84437925 0.3788033127784729 True -13 34538 27.128506660461426 0.49994587898254395 192.02108764648438 0.22053369879722595 282.6878967285156 0.21625062823295593 0.8497223 0.35493719577789307 True -14 37005 27.142946243286133 0.5003166198730469 216.4037628173828 0.3410024642944336 282.56549072265625 0.2164226919412613 0.8556562 0.3370214104652405 True -15 39472 27.1408634185791 0.4890017509460449 200.75262451171875 0.23392008244991302 282.0704650878906 0.21610583364963531 0.85838914 0.3264836072921753 True -16 41939 26.84910535812378 0.48367905616760254 228.36492919921875 0.22977453470230103 281.73797607421875 0.21720699965953827 0.8628127 0.3167780935764313 True -17 44406 26.668160676956177 0.4838542938232422 178.4572296142578 0.19979354739189148 281.6624450683594 0.2182500660419464 0.86208564 0.3133467733860016 False -18 46873 26.668359994888306 0.4905130863189697 247.53500366210938 0.2501499056816101 282.1869201660156 0.21641325950622559 0.86210066 0.3131353557109833 False -19 49340 26.67876362800598 0.49327921867370605 232.05392456054688 0.16830861568450928 281.8948059082031 0.21742554008960724 0.8622465 0.3142259120941162 False diff --git a/ENCSR824YLD/cherimoya.fold_0.performance.tsv b/ENCSR824YLD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 40082e326cf4d901925f802c5433a75e257f56b2..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -281.73797607421875 0.5319889187812805 0.21720699965953827 0.06926987320184708 0.8628126978874207 0.7943294048309326 0.3167780935764313 \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_1.evaluate.json b/ENCSR824YLD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1d9ddd713f9d3580fca558c6325e78ffe0a80541..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415SVF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_1.fit.json b/ENCSR824YLD/cherimoya.fold_1.fit.json deleted file mode 100644 index 66637abc65e01b3cca4a0171ec91fb3baffba3ea..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF415SVF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_1.log b/ENCSR824YLD/cherimoya.fold_1.log deleted file mode 100644 index 9194839ef165f0add465f19c13813b99ab5ed47c..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2432 31.42452883720398 4.028256893157959 277.47344970703125 0.48921939730644226 424.244140625 0.1557733714580536 0.64170325 6.176651954650879 True -1 4864 26.824310541152954 0.6893453598022461 262.2192077636719 0.5531339049339294 378.7565002441406 0.21613214910030365 0.7661125 2.4075851440429688 True -2 7296 26.83112335205078 0.6405632495880127 244.97830200195312 0.8752059936523438 373.05926513671875 0.2187962532043457 0.7739907 1.7121931314468384 True -3 9728 26.809319257736206 0.6378719806671143 304.7760314941406 0.45923441648483276 366.311767578125 0.22619259357452393 0.77712864 1.1041812896728516 True -4 12160 26.75221014022827 0.6480371952056885 252.83657836914062 0.6496201157569885 362.9233703613281 0.22909733653068542 0.79059845 0.946510910987854 True -5 14592 26.758800983428955 1.072312593460083 180.0423126220703 0.3385416269302368 359.7389831542969 0.2334240823984146 0.8054046 0.8149996995925903 True -6 17024 26.804487466812134 0.658501148223877 197.784423828125 0.475507915019989 357.46075439453125 0.23715372383594513 0.8109575 0.7634595036506653 True -7 19456 26.754793405532837 0.7761790752410889 247.70358276367188 0.5479515790939331 355.8043212890625 0.23873400688171387 0.81817687 0.6802934408187866 True -8 21888 26.751024961471558 0.6438159942626953 207.79873657226562 0.43839606642723083 354.26190185546875 0.24140292406082153 0.82758677 0.6248766183853149 True -9 24320 26.757753372192383 0.6292598247528076 253.85659790039062 0.4816923439502716 352.3432922363281 0.24471339583396912 0.8369077 0.5823761820793152 True -10 26752 27.10205626487732 7.569506406784058 223.91986083984375 0.4800875782966614 350.83099365234375 0.24745967984199524 0.8389647 0.5488302707672119 True -11 29184 26.910471200942993 0.6609523296356201 202.9693603515625 0.3938506841659546 349.410400390625 0.24945694208145142 0.8534497 0.47856324911117554 True -12 31616 26.87218165397644 0.6423377990722656 213.81541442871094 0.3048570454120636 348.4437255859375 0.2508172392845154 0.85847825 0.4559192359447479 True -13 34048 26.671265125274658 0.6510026454925537 252.03045654296875 0.2883683443069458 348.0908508300781 0.2506710886955261 0.86615 0.41514909267425537 True -14 36480 26.45071530342102 0.6525781154632568 322.23004150390625 0.3754972815513611 346.27484130859375 0.25387370586395264 0.8679469 0.3989890217781067 True -15 38912 26.429556369781494 0.651667594909668 252.66384887695312 0.4847790598869324 345.6407775878906 0.2539703845977783 0.8701167 0.3855850100517273 True -16 41344 26.281900644302368 0.6487545967102051 236.37933349609375 0.18968439102172852 346.4275817871094 0.2523382902145386 0.87328327 0.3808138370513916 True -17 43776 26.348907232284546 0.7146854400634766 189.97396850585938 0.21472260355949402 346.0472717285156 0.25315186381340027 0.8722962 0.38171324133872986 False -18 46208 26.380614042282104 0.658266544342041 234.24203491210938 0.23892703652381897 346.17626953125 0.25317448377609253 0.8714769 0.3833673894405365 False -19 48640 26.398863315582275 0.6586992740631104 251.52825927734375 0.21740320324897766 346.32159423828125 0.2530495226383209 0.8696934 0.3859821557998657 False diff --git a/ENCSR824YLD/cherimoya.fold_1.performance.tsv b/ENCSR824YLD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8ca05ca262ece951f4b87ac34997d467411739d5..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -346.4275817871094 0.5036930441856384 0.2523382902145386 0.0835312232375145 0.8732832670211792 0.838502824306488 0.3808138370513916 \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_2.evaluate.json b/ENCSR824YLD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9f585dddd75fe0cdea62325611da0a621bdaf548..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415SVF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_2.fit.json b/ENCSR824YLD/cherimoya.fold_2.fit.json deleted file mode 100644 index 6d2b61ea6add1fded67b9b7f6546789c00d1e982..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF415SVF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_2.log b/ENCSR824YLD/cherimoya.fold_2.log deleted file mode 100644 index f3b5893e0818b7259dccd826d59dbd584a7acc7d..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2613 33.27624988555908 3.6683297157287598 238.84225463867188 0.565272867679596 354.22210693359375 0.14771993458271027 0.6423666 4.4846954345703125 True -1 5226 28.754274129867554 0.5235998630523682 273.6465759277344 0.46057021617889404 321.5220947265625 0.19533295929431915 0.7532877 1.5717904567718506 True -2 7839 28.776970148086548 0.8511569499969482 272.934814453125 0.4008235037326813 317.5081481933594 0.19548653066158295 0.7607052 0.9951117634773254 True -3 10452 28.759365558624268 0.5006191730499268 304.192138671875 0.6117363572120667 310.5113525390625 0.20358815789222717 0.7768773 0.6419410109519958 True -4 13065 28.759405851364136 0.519158124923706 269.28570556640625 0.4913218319416046 307.06585693359375 0.20709030330181122 0.7840848 0.6336175203323364 True -5 15678 28.74307107925415 0.48373889923095703 261.4619140625 0.45002177357673645 304.7900085449219 0.2108907401561737 0.7943967 0.6088030934333801 True -6 18291 28.754318237304688 0.48415684700012207 292.7786865234375 0.28451696038246155 302.7823486328125 0.21316370368003845 0.8013763 0.5863417387008667 True -7 20904 28.71058988571167 1.1478233337402344 216.94583129882812 0.5382851362228394 301.2720947265625 0.2160004824399948 0.8078684 0.5689254403114319 True -8 23517 28.73933172225952 0.5376286506652832 225.63052368164062 0.4186933636665344 299.9237976074219 0.2177933305501938 0.8168317 0.5706002116203308 True -9 26130 28.42371964454651 0.5234260559082031 273.66400146484375 0.5376831889152527 298.64691162109375 0.2198937088251114 0.81872773 0.5277126431465149 True -10 28743 28.216400861740112 0.48538804054260254 206.96070861816406 0.24560561776161194 297.6871032714844 0.2224741280078888 0.8263145 0.48315516114234924 True -11 31356 28.203773975372314 0.5016474723815918 264.0471496582031 0.6258910894393921 297.02020263671875 0.22285455465316772 0.83254945 0.4385075271129608 True -12 33969 28.213496923446655 0.4985342025756836 248.1241455078125 0.447356641292572 296.6673583984375 0.22338196635246277 0.8363327 0.42367759346961975 True -13 36582 28.200655221939087 0.4901554584503174 208.51760864257812 0.41882872581481934 295.072265625 0.22612664103507996 0.8433184 0.39338576793670654 True -14 39195 28.266576766967773 0.49279141426086426 242.47988891601562 0.3323551118373871 294.7935485839844 0.22684593498706818 0.8459034 0.37854987382888794 True -15 41808 28.288966417312622 0.5091841220855713 231.523193359375 0.24535652995109558 294.49560546875 0.22714950144290924 0.8508592 0.35610923171043396 True -16 44421 28.36766481399536 0.510875940322876 186.79953002929688 0.26430273056030273 293.875732421875 0.22806894779205322 0.85325575 0.34696346521377563 True -17 47034 29.626296758651733 0.5351784229278564 228.00726318359375 0.3753650188446045 293.7779541015625 0.22811013460159302 0.85384876 0.34288156032562256 True -18 49647 29.2247953414917 12.605003595352173 303.5963134765625 0.21662992238998413 294.319091796875 0.2266532927751541 0.85255295 0.3446844518184662 False -19 52260 28.293171167373657 0.5488479137420654 218.01513671875 0.24291850626468658 294.8192138671875 0.22551050782203674 0.8534245 0.3470797538757324 False diff --git a/ENCSR824YLD/cherimoya.fold_2.performance.tsv b/ENCSR824YLD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2d14ed1077465cd99829e041359af9e19dc11e86..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -293.7779541015625 0.5245406627655029 0.22811008989810944 0.07102545350790024 0.8538487553596497 0.7973908185958862 0.34288156032562256 \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_3.evaluate.json b/ENCSR824YLD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d96f5a79846af24fb9fb081d6b4ea746f6b69d9a..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415SVF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_3.fit.json b/ENCSR824YLD/cherimoya.fold_3.fit.json deleted file mode 100644 index 5223ea1aec009e20d4c17803574958b7ee9a072b..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF415SVF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_3.log b/ENCSR824YLD/cherimoya.fold_3.log deleted file mode 100644 index 07fdf3b473e4e2797b69d662a4b634999945a470..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2488 32.28981423377991 4.808655023574829 266.94476318359375 0.5538734197616577 358.26983642578125 0.15155823528766632 0.62273014 5.8434953689575195 True -1 4976 27.48702120780945 0.47976112365722656 189.64437866210938 0.34359079599380493 325.6407775878906 0.19777384400367737 0.7242326 2.0476365089416504 True -2 7464 27.45708441734314 0.4936978816986084 276.7374267578125 0.7371950745582581 318.1550598144531 0.20658579468727112 0.7383109 1.330150842666626 True -3 9952 27.361170768737793 0.5064082145690918 252.36322021484375 0.31023770570755005 314.45538330078125 0.21021130681037903 0.75763535 0.9286953210830688 True -4 12440 27.409746885299683 12.169184923171997 268.66888427734375 0.46518242359161377 312.55322265625 0.21183514595031738 0.7679361 0.8472998738288879 True -5 14928 26.931625366210938 0.48583078384399414 305.87890625 0.47607356309890747 311.0870056152344 0.21525754034519196 0.7745566 0.8653439283370972 True -6 17416 26.85807466506958 0.4835841655731201 269.4435119628906 0.6727728843688965 309.54669189453125 0.21678124368190765 0.784254 0.7864680886268616 True -7 19904 26.856014490127563 0.5150079727172852 337.0518798828125 0.5667009353637695 308.12347412109375 0.22048833966255188 0.7965083 0.6746092438697815 True -8 22392 26.923888444900513 0.4898664951324463 188.400390625 0.32160425186157227 307.39581298828125 0.2209172397851944 0.8035598 0.6250782012939453 True -9 24880 26.864550352096558 2.6703689098358154 233.791748046875 0.4835026264190674 306.5469970703125 0.22311314940452576 0.8088146 0.571517288684845 True -10 27368 26.90561866760254 0.5040624141693115 181.74136352539062 0.2532855272293091 306.22650146484375 0.2236556112766266 0.8141729 0.5450350642204285 True -11 29856 26.895362377166748 0.5225951671600342 211.751708984375 0.23439040780067444 304.9166564941406 0.22605915367603302 0.82272464 0.512737512588501 True -12 32344 26.911930084228516 0.483673095703125 248.29965209960938 0.49862438440322876 303.4753723144531 0.22857551276683807 0.83687836 0.45725569128990173 True -13 34832 26.92548966407776 0.47834277153015137 225.3820037841797 0.4338931143283844 302.4756774902344 0.23016464710235596 0.8418292 0.43556708097457886 True -14 37320 26.955655813217163 0.49080348014831543 218.31622314453125 0.2483990341424942 302.0738220214844 0.23060649633407593 0.85092884 0.40182968974113464 True -15 39808 26.963382720947266 0.49190568923950195 221.33718872070312 0.26601001620292664 301.19061279296875 0.23122692108154297 0.85330385 0.3823918402194977 True -16 42296 26.90134620666504 2.5605735778808594 284.43798828125 0.3019176423549652 300.9789733886719 0.23159663379192352 0.8561123 0.37055784463882446 True -17 44784 26.919211387634277 0.48520660400390625 267.69091796875 0.29842227697372437 301.12457275390625 0.23086412250995636 0.8568823 0.3648075461387634 True -18 47272 27.00233244895935 0.4979724884033203 229.13812255859375 0.24950936436653137 301.0372619628906 0.2309444546699524 0.85547024 0.36856308579444885 False -19 49760 26.986603498458862 0.48137736320495605 237.31622314453125 0.19284890592098236 301.0448913574219 0.23110781610012054 0.8548673 0.3696255683898926 False diff --git a/ENCSR824YLD/cherimoya.fold_3.performance.tsv b/ENCSR824YLD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ab3b7889a316f86d60cf0fbb259bf384316715e8..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -301.12457275390625 0.5220658183097839 0.23086412250995636 0.0724250003695488 0.8568822741508484 0.8052381873130798 0.3648075461387634 \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_4.evaluate.json b/ENCSR824YLD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 13176d1e898f7f994dca89025168b7c91bc0bd01..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415SVF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_4.fit.json b/ENCSR824YLD/cherimoya.fold_4.fit.json deleted file mode 100644 index 03bc406184f5aa978a7b774617c13de857fbfd48..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF415SVF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR824YLD/cherimoya.fold_4.log b/ENCSR824YLD/cherimoya.fold_4.log deleted file mode 100644 index c4a0f865990642c91be10d89781f867119e85ef7..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2466 31.807038068771362 3.6863276958465576 235.06134033203125 0.6631141901016235 309.5721435546875 0.13755227625370026 0.6263106 4.551973819732666 True -1 4932 27.243586540222168 0.5364325046539307 272.52984619140625 0.43640947341918945 284.8851318359375 0.1797609031200409 0.73635644 1.6027610301971436 True -2 7398 27.226378917694092 0.5474498271942139 235.95852661132812 0.28617238998413086 280.8863525390625 0.1851823478937149 0.7381767 0.9872651696205139 True -3 9864 27.24571180343628 0.5229296684265137 233.45957946777344 0.5861740708351135 277.3317565917969 0.189641535282135 0.7466787 0.6614135503768921 True -4 12330 27.288851499557495 0.5124773979187012 218.1673583984375 0.5144374370574951 275.2893981933594 0.19204623997211456 0.7655391 0.6105142831802368 True -5 14796 27.185646533966064 0.5053191184997559 205.6658172607422 0.3146602213382721 273.4540100097656 0.1947626769542694 0.77905256 0.5740975737571716 True -6 17262 26.773963928222656 0.4998743534088135 219.50201416015625 0.37918633222579956 272.1233215332031 0.19661177694797516 0.78541774 0.5435464978218079 True -7 19728 26.648465394973755 0.4989738464355469 222.18014526367188 0.36096394062042236 271.1363830566406 0.19842609763145447 0.79077315 0.532049298286438 True -8 22194 26.666885375976562 0.5074472427368164 205.25389099121094 0.4616296589374542 270.2601623535156 0.20046335458755493 0.79722255 0.5089293122291565 True -9 24660 26.656047821044922 0.49644041061401367 202.81118774414062 0.3423336446285248 269.5531311035156 0.20171819627285004 0.8059316 0.4647271931171417 True -10 27126 26.655457258224487 0.48993515968322754 256.279541015625 0.6242785453796387 269.2066650390625 0.20222532749176025 0.80831563 0.4411866068840027 True -11 29592 26.64811682701111 0.49105191230773926 297.5206298828125 0.44904452562332153 267.95452880859375 0.20549124479293823 0.819073 0.40026384592056274 True -12 32058 26.727243185043335 0.4999260902404785 196.03515625 0.29538553953170776 267.7337341308594 0.20544223487377167 0.8265096 0.37745603919029236 True -13 34524 26.69675040245056 0.4975738525390625 214.4090118408203 0.4655521810054779 266.58050537109375 0.2074536383152008 0.83208466 0.35383227467536926 True -14 36990 26.721593618392944 0.4855537414550781 215.69949340820312 0.2929139733314514 266.8155212402344 0.20618849992752075 0.8387064 0.3382939398288727 True -15 39456 26.767557382583618 0.49782872200012207 262.583984375 0.2524365484714508 266.5128479003906 0.20719009637832642 0.8413876 0.3287598192691803 True -16 41922 26.69714665412903 0.49363088607788086 210.40330505371094 0.375894695520401 266.1395568847656 0.20780618488788605 0.84297323 0.3216134309768677 True -17 44388 26.655601739883423 0.5147831439971924 259.2685241699219 0.34398165345191956 266.3932800292969 0.20720873773097992 0.8443027 0.31837692856788635 True -18 46854 26.700377941131592 0.5151710510253906 216.59878540039062 0.28802749514579773 266.94158935546875 0.20598746836185455 0.8438643 0.3182869255542755 False -19 49320 26.649632930755615 0.5025122165679932 239.84152221679688 0.23158353567123413 266.985107421875 0.20640987157821655 0.8448455 0.31857022643089294 True diff --git a/ENCSR824YLD/cherimoya.fold_4.performance.tsv b/ENCSR824YLD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 54e7c86979c6e841d7ae77826bbb2ab88a3d9b29..0000000000000000000000000000000000000000 --- a/ENCSR824YLD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -266.985107421875 0.539616584777832 0.20640990138053894 0.0629911944270134 0.8448454737663269 0.761698305606842 0.31857022643089294 \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_0.evaluate.json b/ENCSR826ERZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b800a0d18ffc2617e28763321feb01bfe49b6d49..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF504IUK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_0.fit.json b/ENCSR826ERZ/cherimoya.fold_0.fit.json deleted file mode 100644 index b93630bee29d0606631e893340f9853bc669af71..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF504IUK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_0.log b/ENCSR826ERZ/cherimoya.fold_0.log deleted file mode 100644 index fc251bc92970cafcda8a96f4b644ce3e87a32a06..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 34.78794836997986 3.942152500152588 154.63427734375 1.2094144821166992 255.96925354003906 0.1594233214855194 0.44111618 4.273212909698486 True -1 5502 30.021657943725586 0.6225409507751465 209.95208740234375 0.7978431582450867 243.67813110351562 0.2200600951910019 0.58657753 1.3049896955490112 True -2 8253 30.40177583694458 0.7448451519012451 207.18035888671875 0.935532808303833 240.268310546875 0.23118102550506592 0.60394526 0.7598432898521423 True -3 11004 30.39230227470398 0.5676202774047852 197.9980010986328 0.7626650929450989 239.09954833984375 0.23558762669563293 0.6187581 0.780502438545227 True -4 13755 30.382699489593506 0.8596923351287842 203.1629638671875 1.2029904127120972 238.41285705566406 0.2382701337337494 0.630503 0.7719520330429077 True -5 16506 30.316934823989868 0.5753457546234131 217.4120330810547 0.5157746076583862 238.08773803710938 0.2402241826057434 0.63419706 0.8105447888374329 True -6 19257 30.234644174575806 0.558671236038208 222.52552795410156 0.5939422845840454 237.6689453125 0.2416791170835495 0.63624865 0.7887827157974243 True -7 22008 29.771664142608643 1.0258748531341553 175.5771026611328 0.7471767067909241 237.2474822998047 0.24374349415302277 0.6423683 0.6764710545539856 True -8 24759 29.74940299987793 0.5771350860595703 234.2672119140625 0.7705797553062439 236.54367065429688 0.24758441746234894 0.65102726 0.6599234938621521 True -9 27510 29.76046109199524 0.57448410987854 191.076171875 0.5433566570281982 236.0732879638672 0.25017213821411133 0.6588252 0.6349508166313171 True -10 30261 29.869452953338623 0.5958809852600098 194.12843322753906 0.7236829996109009 236.04222106933594 0.25018447637557983 0.6617184 0.6005005240440369 True -11 33012 29.867351531982422 0.9654641151428223 197.98745727539062 0.4927735924720764 235.57742309570312 0.2521406412124634 0.67071617 0.5530881285667419 True -12 35763 29.839090824127197 0.6126072406768799 191.2978973388672 0.6030802130699158 235.4523162841797 0.25257501006126404 0.6777039 0.5316405892372131 True -13 38514 29.834466695785522 1.8880786895751953 149.24276733398438 0.5151646137237549 234.7853240966797 0.25566479563713074 0.68382597 0.5159643888473511 True -14 41265 29.76539421081543 0.5945534706115723 175.635498046875 0.5629477500915527 234.4733428955078 0.2567462921142578 0.69585073 0.4888530373573303 True -15 44016 29.751709461212158 0.57012939453125 174.45516967773438 0.47885632514953613 234.52426147460938 0.2563869059085846 0.70213586 0.4670676290988922 True -16 46767 29.76311707496643 0.5706031322479248 140.7642822265625 0.5792851448059082 234.2154541015625 0.25799649953842163 0.7068762 0.45307281613349915 True -17 49518 29.778302431106567 0.5568783283233643 148.14559936523438 0.5391187071800232 234.5283203125 0.2562154233455658 0.7119211 0.44713327288627625 True -18 52269 29.752196073532104 0.5658228397369385 205.0799102783203 0.3670951724052429 234.67369079589844 0.2551381587982178 0.71080303 0.45003071427345276 False -19 55020 29.750062227249146 0.564467191696167 158.29244995117188 0.4305214285850525 234.35960388183594 0.25772619247436523 0.7082739 0.4559745490550995 False diff --git a/ENCSR826ERZ/cherimoya.fold_0.performance.tsv b/ENCSR826ERZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f74806731a8d3e054de83a300634cfc74f935903..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -234.5283203125 0.5198660492897034 0.2562154233455658 0.06795039772987366 0.7119210958480835 0.6724967360496521 0.44713327288627625 \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_1.evaluate.json b/ENCSR826ERZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 170ced026f27e0ed520cf8bebb511d7b9d8c0620..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF504IUK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_1.fit.json b/ENCSR826ERZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 36a2ee11926c8c1a854b2f758039ffe061caa53e..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF504IUK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_1.log b/ENCSR826ERZ/cherimoya.fold_1.log deleted file mode 100644 index be2308edc22194c1b5c3b91621b9ff00acbe5fca..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 34.87452745437622 4.528831243515015 244.3614501953125 0.9368494749069214 284.42926025390625 0.15712130069732666 0.50436527 3.783064365386963 True -1 5508 30.30609130859375 1.4373106956481934 207.83840942382812 0.7260947227478027 268.55645751953125 0.2285272628068924 0.6374133 1.3860938549041748 True -2 8262 30.364621877670288 0.6582667827606201 172.67544555664062 1.0717185735702515 264.5724182128906 0.2406260371208191 0.6614549 0.7204291224479675 True -3 11016 30.346355199813843 0.6668603420257568 232.06704711914062 0.6753334403038025 262.9316711425781 0.24683772027492523 0.68175465 0.6443024277687073 True -4 13770 30.42465329170227 0.6789922714233398 226.58297729492188 0.8491628170013428 262.0815124511719 0.24993081390857697 0.6900482 0.7224717736244202 True -5 16524 30.421234846115112 0.6528689861297607 171.9549560546875 0.8421562910079956 261.44488525390625 0.25248783826828003 0.6964186 0.7182984352111816 True -6 19278 30.152294158935547 0.663956880569458 212.9183349609375 0.8484938144683838 260.7555847167969 0.25569894909858704 0.7048039 0.674769937992096 True -7 22032 29.8322331905365 0.6639893054962158 194.07415771484375 0.5172086358070374 260.32794189453125 0.2571122646331787 0.7104502 0.6300622224807739 True -8 24786 29.788982152938843 0.6518924236297607 185.57925415039062 0.3761672377586365 259.9625549316406 0.2589079737663269 0.71402144 0.6037308573722839 True -9 27540 29.827744007110596 0.6481928825378418 212.7030792236328 0.5013659596443176 259.2746887207031 0.2618924379348755 0.71823245 0.5956477522850037 True -10 30294 29.80740761756897 0.6640775203704834 190.01902770996094 1.096707820892334 258.86846923828125 0.26301276683807373 0.7231779 0.5603553652763367 True -11 33048 29.807546615600586 0.6620194911956787 201.52194213867188 0.6840434074401855 258.39556884765625 0.265179306268692 0.7268695 0.5558449625968933 True -12 35802 29.795875072479248 1.3540468215942383 188.10743713378906 0.7846120595932007 258.2895812988281 0.26468801498413086 0.7384237 0.5115311145782471 True -13 38556 29.81268620491028 0.663222074508667 172.50660705566406 0.43360522389411926 258.03009033203125 0.2657296359539032 0.7422868 0.4888247549533844 True -14 41310 29.838050842285156 1.5768780708312988 221.62130737304688 0.5665594935417175 257.49420166015625 0.2679070234298706 0.7503353 0.4571518003940582 True -15 44064 30.038204193115234 0.6919867992401123 184.76815795898438 0.49628889560699463 257.1893615722656 0.26890018582344055 0.75914174 0.44990986585617065 True -16 46818 29.942519903182983 0.67380690574646 189.80532836914062 0.33090609312057495 257.34832763671875 0.2683411240577698 0.76239777 0.4386135935783386 True -17 49572 29.945138454437256 0.6603026390075684 178.04994201660156 0.37898558378219604 257.584228515625 0.26663148403167725 0.76385593 0.4360464811325073 True -18 52326 29.85396933555603 0.6630394458770752 196.65664672851562 0.36063021421432495 257.6563415527344 0.2665866017341614 0.76232195 0.43890076875686646 False -19 55080 29.941486835479736 0.6762330532073975 182.146728515625 0.361905038356781 257.53863525390625 0.26752418279647827 0.76170725 0.44673529267311096 False diff --git a/ENCSR826ERZ/cherimoya.fold_1.performance.tsv b/ENCSR826ERZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8aff5c8b8b27cbfd2fb77caf7e14b339d289f892..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -257.584228515625 0.5089847445487976 0.26663145422935486 0.07379510253667831 0.7638559341430664 0.7325318455696106 0.4360464811325073 \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_2.evaluate.json b/ENCSR826ERZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4563fd56a4f8c2522e5ffa0559ac64a3e72de921..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF504IUK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_2.fit.json b/ENCSR826ERZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 535b313b6860e75f4cc9ff3f8a6ad6f576887850..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF504IUK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_2.log b/ENCSR826ERZ/cherimoya.fold_2.log deleted file mode 100644 index fc740e5db0142f40a8f3ab38983849b61eaa9885..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2913 36.872923851013184 4.79856014251709 174.3125 0.9906227588653564 256.7045593261719 0.16164150834083557 0.475795 3.259141206741333 True -1 5826 31.53348994255066 0.7524223327636719 191.52047729492188 1.1386449337005615 243.97427368164062 0.22286728024482727 0.5947247 1.3234964609146118 True -2 8739 32.119263648986816 0.542595624923706 196.91783142089844 1.0262056589126587 240.42689514160156 0.2344580441713333 0.60929984 0.8454437255859375 True -3 11652 31.566187143325806 1.025742769241333 209.44821166992188 0.5690943002700806 238.9535675048828 0.24008220434188843 0.6281577 0.7093480825424194 True -4 14565 31.48890233039856 0.516493558883667 200.66879272460938 1.091907024383545 238.26856994628906 0.24306754767894745 0.6336791 0.6809086799621582 True -5 17478 31.53454303741455 0.5185706615447998 164.29901123046875 0.6345018148422241 238.05477905273438 0.24329817295074463 0.6417981 0.6817190647125244 True -6 20391 31.55693221092224 1.7080237865447998 185.8524169921875 0.6702107191085815 237.7519073486328 0.24478241801261902 0.64150596 0.6643037796020508 False -7 23304 31.576252937316895 0.5170979499816895 207.2906494140625 0.6502807140350342 237.10475158691406 0.2481113225221634 0.6436061 0.6754930019378662 True -8 26217 31.48641848564148 0.5094203948974609 158.54080200195312 0.7138170003890991 236.9141082763672 0.2492065280675888 0.65105224 0.6396924257278442 True -9 29130 31.511543035507202 0.5053362846374512 173.7681121826172 0.46638983488082886 236.5158233642578 0.25075921416282654 0.6538124 0.6461837291717529 True -10 32043 31.526236057281494 0.5075762271881104 198.04641723632812 0.5976816415786743 236.22531127929688 0.2520557641983032 0.65793395 0.59992915391922 True -11 34956 31.49497961997986 0.49720335006713867 207.06666564941406 0.794840931892395 235.62130737304688 0.25495344400405884 0.6641124 0.578821063041687 True -12 37869 31.486834287643433 0.5043294429779053 169.41390991210938 0.7361308336257935 235.403564453125 0.2553173303604126 0.6779374 0.5593428015708923 True -13 40782 31.532814979553223 0.8067018985748291 173.06964111328125 0.5446911454200745 235.15567016601562 0.25675076246261597 0.6859046 0.5126489996910095 True -14 43695 31.556232929229736 0.502631664276123 168.84750366210938 0.4270499646663666 234.84217834472656 0.25723814964294434 0.69282055 0.4914918541908264 True -15 46608 31.63353657722473 0.5110206604003906 149.40057373046875 0.477545827627182 234.64724731445312 0.2580692768096924 0.7020031 0.48133164644241333 True -16 49521 31.520389795303345 0.5089058876037598 199.7201690673828 0.4266642928123474 234.44525146484375 0.25975871086120605 0.7054563 0.46717482805252075 True -17 52434 31.559115409851074 2.4696648120880127 179.3266143798828 0.31873825192451477 234.32740783691406 0.2603702247142792 0.7099158 0.46432027220726013 True -18 55347 31.51283311843872 0.5090093612670898 191.46237182617188 0.4631083011627197 234.93374633789062 0.2566145360469818 0.7085302 0.4699642062187195 False -19 58260 31.576366662979126 0.5215041637420654 161.1000213623047 0.2945585548877716 234.56707763671875 0.25928688049316406 0.70881474 0.47357675433158875 False diff --git a/ENCSR826ERZ/cherimoya.fold_2.performance.tsv b/ENCSR826ERZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 38e06f72126977bfce5d160e94b97a0c52381906..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -234.32740783691406 0.5184072256088257 0.2603702247142792 0.06434205919504166 0.709915816783905 0.6697127819061279 0.46432027220726013 \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_3.evaluate.json b/ENCSR826ERZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 76b55b0f64f3d5b75efa76feca97bb122306f552..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF504IUK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_3.fit.json b/ENCSR826ERZ/cherimoya.fold_3.fit.json deleted file mode 100644 index f89598d484c5ec1c64cbe555f9a5d75c112a3bd7..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF504IUK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_3.log b/ENCSR826ERZ/cherimoya.fold_3.log deleted file mode 100644 index ff1b71fd17390509a8447c15d2b4975c088ee6c7..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2771 35.70351958274841 4.416179656982422 217.40281677246094 1.120182752609253 273.7452697753906 0.16057032346725464 0.4756822 3.870802402496338 True -1 5542 30.6068172454834 0.7378907203674316 149.95040893554688 1.1101136207580566 259.9699401855469 0.2250155508518219 0.5911786 1.9423563480377197 True -2 8313 30.631605625152588 0.5998489856719971 150.9815673828125 0.8154804706573486 256.42095947265625 0.23708947002887726 0.6222381 0.8179011940956116 True -3 11084 30.261455297470093 0.6741106510162354 184.92965698242188 0.5966100692749023 255.34512329101562 0.2414257824420929 0.63802373 0.729785144329071 True -4 13855 29.97654414176941 0.5854179859161377 184.2734375 0.5526514649391174 254.27162170410156 0.24633663892745972 0.6411817 0.7238817811012268 True -5 16626 30.115103483200073 3.2527334690093994 202.1811981201172 0.8807489275932312 254.72923278808594 0.24256840348243713 0.64222383 0.6725378632545471 True -6 19397 30.0613751411438 0.5858495235443115 165.85836791992188 0.8277077078819275 254.29251098632812 0.24511894583702087 0.65383124 0.689565896987915 True -7 22168 29.97679376602173 0.5808608531951904 172.60450744628906 0.563193142414093 253.49012756347656 0.24961557984352112 0.6609319 0.6851902604103088 True -8 24939 30.017335176467896 0.5779922008514404 200.06381225585938 0.7692922949790955 253.5570068359375 0.24883411824703217 0.6651618 0.6636222004890442 True -9 27710 29.99288010597229 0.5951237678527832 193.9608154296875 0.7143065929412842 252.96705627441406 0.25150924921035767 0.6695598 0.609554648399353 True -10 30481 30.316433668136597 20.515429496765137 161.02146911621094 0.9596624970436096 252.43325805664062 0.2537686228752136 0.67814827 0.6035261154174805 True -11 33252 29.98713707923889 0.5903334617614746 189.5692138671875 0.6522923707962036 252.21945190429688 0.2543327510356903 0.6838173 0.5723613500595093 True -12 36023 30.062328815460205 0.5991404056549072 198.76589965820312 0.37825390696525574 251.77699279785156 0.2569654583930969 0.69220006 0.5463337898254395 True -13 38794 29.966328382492065 0.5950708389282227 179.92913818359375 0.49962830543518066 251.7523193359375 0.25620949268341064 0.6974543 0.5108412504196167 True -14 41565 30.0327570438385 0.5866460800170898 161.9127197265625 0.5051013827323914 251.3186492919922 0.2580755650997162 0.7065561 0.4977990984916687 True -15 44336 30.021511793136597 0.6006510257720947 217.620849609375 0.3535575866699219 251.29830932617188 0.2578679919242859 0.7161621 0.4810248613357544 True -16 47107 29.97865319252014 0.6812527179718018 172.02572631835938 0.47299107909202576 250.8311309814453 0.2604069709777832 0.718933 0.4717760980129242 True -17 49878 29.96552610397339 0.5937910079956055 152.94131469726562 0.5580254197120667 251.09414672851562 0.25894472002983093 0.7228698 0.4706128239631653 True -18 52649 30.026852130889893 0.5910627841949463 168.45098876953125 0.3875090479850769 250.9677276611328 0.2599131464958191 0.7224154 0.47764143347740173 False -19 55420 29.938860654830933 0.5894975662231445 210.9019012451172 0.4443897604942322 251.1018829345703 0.2588737905025482 0.7209707 0.4804449677467346 False diff --git a/ENCSR826ERZ/cherimoya.fold_3.performance.tsv b/ENCSR826ERZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5c337d1fe8ceb37d62452bcfdf7123bf7b9413c5..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -251.09414672851562 0.5138291716575623 0.25894472002983093 0.06720540672540665 0.7228698134422302 0.6855895519256592 0.4706128239631653 \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_4.evaluate.json b/ENCSR826ERZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a30b101e1145fdd10c187e467fa916594079e4c6..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF504IUK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_4.fit.json b/ENCSR826ERZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 7016b8d491b9330e0731c5a15a4f9409288178be..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF504IUK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826ERZ/cherimoya.fold_4.log b/ENCSR826ERZ/cherimoya.fold_4.log deleted file mode 100644 index 47df2dc419dca2a6edd54381fa0b4e76f8a9ff8a..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.40602660179138 4.655912399291992 179.45616149902344 0.639639139175415 259.9697265625 0.15955913066864014 0.45178574 3.2219786643981934 True -1 5744 31.691722631454468 0.6431548595428467 178.57644653320312 0.9265842437744141 247.55975341796875 0.22057652473449707 0.5765818 1.4120322465896606 True -2 8616 31.71684694290161 0.6107006072998047 179.03631591796875 0.8824281692504883 244.6881866455078 0.2305775284767151 0.6043169 0.7046290040016174 True -3 11488 31.677022695541382 10.267102479934692 176.84005737304688 0.5307258367538452 243.60498046875 0.23443935811519623 0.62347823 0.6280075907707214 True -4 14360 31.71772837638855 0.6358413696289062 206.75140380859375 0.9769852757453918 242.54336547851562 0.24008809030056 0.6294246 0.6746065020561218 True -5 17232 31.69242763519287 0.6025240421295166 195.3107452392578 0.993780255317688 242.45437622070312 0.23969699442386627 0.6337074 0.6783613562583923 True -6 20104 31.642396450042725 0.6149849891662598 196.16714477539062 0.7844321727752686 242.11407470703125 0.24073882400989532 0.6432427 0.6757171750068665 True -7 22976 31.63043236732483 0.596895694732666 212.4837188720703 0.4963739514350891 241.6587677001953 0.24362345039844513 0.64516354 0.681176483631134 True -8 25848 31.186073541641235 0.603968620300293 167.51564025878906 0.47645145654678345 241.2446746826172 0.24611340463161469 0.6490317 0.6642153859138489 True -9 28720 31.082546710968018 0.6086454391479492 183.8135528564453 0.580596387386322 241.06982421875 0.24638798832893372 0.6566225 0.6217895150184631 True -10 31592 31.077263116836548 0.6085617542266846 161.87484741210938 0.598569393157959 240.79432678222656 0.2474333643913269 0.659133 0.6160802841186523 True -11 34464 31.035013675689697 1.6868221759796143 208.5113525390625 0.4528758227825165 240.25448608398438 0.2502824068069458 0.6692497 0.5760596394538879 True -12 37336 31.085537433624268 0.6147170066833496 190.96144104003906 0.41619494557380676 240.09303283691406 0.25015801191329956 0.6799766 0.5393664836883545 True -13 40208 31.16843867301941 1.141164779663086 159.45144653320312 0.5139161348342896 239.34628295898438 0.2543575167655945 0.69231224 0.5039481520652771 True -14 43080 31.14251208305359 0.6056311130523682 181.81373596191406 0.5117493867874146 239.22581481933594 0.25473159551620483 0.70094115 0.48761335015296936 True -15 45952 31.23789381980896 1.204498291015625 178.39483642578125 0.5659964680671692 238.8745574951172 0.2569356858730316 0.7069144 0.4712486267089844 True -16 48824 31.229625701904297 0.6914551258087158 158.11146545410156 0.3391120135784149 238.8950653076172 0.2568170130252838 0.7143638 0.45752257108688354 True -17 51696 31.22197961807251 0.6069564819335938 226.45269775390625 0.506362795829773 238.81419372558594 0.25655826926231384 0.7183558 0.4520513415336609 True -18 54568 31.12837028503418 0.629784107208252 186.36798095703125 0.35284334421157837 238.8594512939453 0.2566899359226227 0.71848446 0.4508883059024811 True -19 57440 31.102068424224854 0.6308784484863281 191.5798797607422 0.3242591619491577 239.0533447265625 0.2551245391368866 0.7196302 0.4559917151927948 True diff --git a/ENCSR826ERZ/cherimoya.fold_4.performance.tsv b/ENCSR826ERZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 55d1933061a2189655a6dc4eaac2af5f9c182250..0000000000000000000000000000000000000000 --- a/ENCSR826ERZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -239.0533447265625 0.5189462304115295 0.2551245391368866 0.06598930805921555 0.7196301817893982 0.6784324049949646 0.4559917151927948 \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_0.evaluate.json b/ENCSR826URD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4cad99ad984bab46b62d085b48ef976e2b2983df..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388RKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_0.fit.json b/ENCSR826URD/cherimoya.fold_0.fit.json deleted file mode 100644 index 65f20c2dbfcd4edb7a387972a3b6b977b770e907..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF388RKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_0.log b/ENCSR826URD/cherimoya.fold_0.log deleted file mode 100644 index d523e17f8d77dc098cf4b2a850e442ae3e2845d1..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2766 37.67419648170471 4.023393392562866 511.01715087890625 0.25784367322921753 644.0557861328125 0.2382456213235855 0.7640391 4.898571014404297 True -1 5532 31.216139554977417 0.5905451774597168 595.2239990234375 0.2934504449367523 584.7429809570312 0.3053925037384033 0.8451791 0.7120141983032227 True -2 8298 30.77769899368286 0.5984511375427246 530.8812866210938 0.5852522253990173 576.6403198242188 0.30976706743240356 0.8616906 0.37753793597221375 True -3 11064 30.64458441734314 0.5718209743499756 427.89990234375 0.311686635017395 571.4984741210938 0.31663912534713745 0.86609215 0.4279469847679138 True -4 13830 30.550299644470215 1.810929536819458 444.6028747558594 0.21574318408966064 569.1976928710938 0.3187480568885803 0.8720254 0.32569676637649536 True -5 16596 30.57234025001526 0.5721919536590576 415.29638671875 0.1616339385509491 566.6976318359375 0.32202309370040894 0.8771584 0.28627684712409973 True -6 19362 30.60481595993042 0.5739099979400635 599.1672973632812 0.3428756594657898 564.9075927734375 0.3239700496196747 0.8813181 0.26759156584739685 True -7 22128 30.567662239074707 0.5696160793304443 466.80126953125 0.2769036889076233 561.39599609375 0.3299197852611542 0.88622934 0.2521938383579254 True -8 24894 30.56391215324402 0.5721259117126465 455.9115905761719 0.21055136620998383 561.5863037109375 0.3280240297317505 0.89149225 0.24887365102767944 True -9 27660 30.546046257019043 0.579387903213501 488.1317138671875 0.19948595762252808 559.0800170898438 0.3324423134326935 0.89492404 0.23272952437400818 True -10 30426 30.611275672912598 0.5714535713195801 473.272216796875 0.1917770355939865 558.287353515625 0.33235642313957214 0.89833766 0.2198449671268463 True -11 33192 30.575989723205566 0.5684494972229004 501.69244384765625 0.29101645946502686 557.1412353515625 0.33349937200546265 0.9021402 0.21615011990070343 True -12 35958 32.0237455368042 39.36871099472046 509.2144775390625 0.13440848886966705 554.526611328125 0.3386757969856262 0.90570015 0.2028239220380783 True -13 38724 31.46957778930664 0.6022467613220215 423.0354309082031 0.08124765753746033 555.31103515625 0.336099773645401 0.9079836 0.19369126856327057 True -14 41490 30.654914617538452 12.98481273651123 502.24609375 0.15718793869018555 553.0881958007812 0.3394676446914673 0.9111511 0.18098339438438416 True -15 44256 30.72696018218994 1.3523824214935303 534.5738525390625 0.14015823602676392 551.9043579101562 0.34127458930015564 0.91389966 0.17237776517868042 True -16 47022 30.687939643859863 1.3206825256347656 460.960693359375 0.07612384110689163 551.3866577148438 0.3419317305088043 0.91679794 0.16748365759849548 True -17 49788 30.647833108901978 1.4196813106536865 402.41900634765625 0.1421087384223938 551.5956420898438 0.3409656882286072 0.9167908 0.16522523760795593 False -18 52554 30.59426522254944 1.101569652557373 525.8662719726562 0.07593555748462677 551.6620483398438 0.34114447236061096 0.9161303 0.1662297248840332 False -19 55320 30.606753826141357 3.145094871520996 414.4891052246094 0.1318242996931076 551.8759765625 0.34090563654899597 0.9149898 0.16741763055324554 False diff --git a/ENCSR826URD/cherimoya.fold_0.performance.tsv b/ENCSR826URD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 05326b539bf46ad60d79d081cfe69efa71e39717..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -551.3866577148438 0.41241297125816345 0.3419317305088043 0.14230291545391083 0.916797935962677 0.875393807888031 0.16748365759849548 \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_1.evaluate.json b/ENCSR826URD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6ccd1cf8c83cc4eca4d56de3f3b2acbbd8d08a63..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388RKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_1.fit.json b/ENCSR826URD/cherimoya.fold_1.fit.json deleted file mode 100644 index 16ab783a9165cb5133a9119299795da4d9a05b5c..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF388RKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_1.log b/ENCSR826URD/cherimoya.fold_1.log deleted file mode 100644 index 76122f421fe67437ece81cdc6bc4b13ad1daaf4a..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 34.593711853027344 3.983776092529297 518.526123046875 0.3558345437049866 761.2119140625 0.2471301108598709 0.7561332 5.5953240394592285 True -1 5406 29.891277313232422 0.7001430988311768 440.0972595214844 0.29072076082229614 687.58056640625 0.32202211022377014 0.8508833 0.872785210609436 True -2 8109 29.942697525024414 0.6948337554931641 472.8484802246094 0.26876169443130493 674.7452392578125 0.3318774104118347 0.8624916 0.46581482887268066 True -3 10812 29.90527033805847 2.066601276397705 513.748779296875 0.24182704091072083 667.245849609375 0.33945775032043457 0.86976117 0.4755711257457733 True -4 13515 29.823439121246338 0.691788911819458 430.979736328125 0.21524959802627563 662.13623046875 0.3459171652793884 0.87854755 0.3670099973678589 True -5 16218 29.88990044593811 0.692166805267334 536.606689453125 0.27710163593292236 660.9054565429688 0.3468690812587738 0.8846295 0.32172060012817383 True -6 18921 29.953048706054688 0.7004284858703613 530.94140625 0.23102055490016937 658.1165161132812 0.3491334021091461 0.8882378 0.29409268498420715 True -7 21624 29.9224796295166 0.6975734233856201 405.29638671875 0.18774624168872833 656.8400268554688 0.35086357593536377 0.89063686 0.30127599835395813 True -8 24327 29.799376964569092 1.6099915504455566 519.3695678710938 0.26475608348846436 653.2606811523438 0.35667335987091064 0.89807445 0.274628221988678 True -9 27030 29.907716035842896 0.7023098468780518 496.7010498046875 0.14467653632164001 652.667724609375 0.3556080162525177 0.90414935 0.2556123435497284 True -10 29733 29.79743504524231 0.7221519947052002 400.2548522949219 0.18170863389968872 649.574951171875 0.36022841930389404 0.90431446 0.24578455090522766 True -11 32436 29.839335680007935 0.7028124332427979 448.36212158203125 0.3302050828933716 648.2409057617188 0.3605458736419678 0.91072726 0.22703857719898224 True -12 35139 31.56343412399292 29.6676242351532 492.4164733886719 0.12521006166934967 646.7324829101562 0.36201056838035583 0.9141313 0.21057429909706116 True -13 37842 29.94578790664673 33.69319677352905 385.1623229980469 0.2506018280982971 644.7894287109375 0.36410218477249146 0.9177193 0.1957237720489502 True -14 40545 31.844595193862915 0.7704107761383057 443.44354248046875 0.19025519490242004 642.5681762695312 0.3667373061180115 0.9210804 0.1842944324016571 True -15 43248 29.7956440448761 0.7196624279022217 505.39459228515625 0.09461064636707306 642.3136596679688 0.3672162592411041 0.92207915 0.18032464385032654 True -16 45951 29.913643836975098 0.6971473693847656 491.19915771484375 0.12374082952737808 643.0698852539062 0.36543527245521545 0.92594665 0.17498572170734406 True -17 48654 29.948724508285522 0.7341628074645996 480.75018310546875 0.11232192069292068 642.2469482421875 0.36685773730278015 0.9271702 0.17227323353290558 True -18 51357 30.020609378814697 0.6947617530822754 468.598876953125 0.1673993468284607 643.1880493164062 0.36538389325141907 0.9239151 0.1742815375328064 False -19 54060 29.87932324409485 0.7052357196807861 483.31121826171875 0.13471193611621857 643.2984619140625 0.3652426600456238 0.9262148 0.17511846125125885 False diff --git a/ENCSR826URD/cherimoya.fold_1.performance.tsv b/ENCSR826URD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9f9df9c0a5face3028edcb0e24f95dd8d12f0d03..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -642.2469482421875 0.388200581073761 0.36685773730278015 0.16529986262321472 0.9271702170372009 0.9120298027992249 0.17227323353290558 \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_2.evaluate.json b/ENCSR826URD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bde72714358b10e102664ef8028477902d460ea8..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388RKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_2.fit.json b/ENCSR826URD/cherimoya.fold_2.fit.json deleted file mode 100644 index 0ec8160b1982a5e33cf4a5fd2eb9d722815dab6e..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF388RKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_2.log b/ENCSR826URD/cherimoya.fold_2.log deleted file mode 100644 index 1717595ea12bdd26ef5ecb6f3f0f7463584064a6..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 36.49545240402222 37.428631067276 496.14337158203125 0.2906757593154907 673.6009521484375 0.24064026772975922 0.7594705 4.421782493591309 True -1 5762 32.160067319869995 0.5933165550231934 499.5646057128906 0.3079029619693756 612.5375366210938 0.306310772895813 0.8469805 0.7208580374717712 True -2 8643 31.853200912475586 0.5569741725921631 476.5684814453125 0.34019559621810913 600.5491943359375 0.3168378472328186 0.86404073 0.3788920044898987 True -3 11524 31.85422158241272 0.5515398979187012 463.6686096191406 0.26277607679367065 596.2095336914062 0.3225923478603363 0.8716345 0.3193754255771637 True -4 14405 31.857204914093018 0.5642220973968506 473.0627136230469 0.16447563469409943 593.3948364257812 0.3277725279331207 0.8753158 0.3152512013912201 True -5 17286 31.814019680023193 0.5542528629302979 473.2987365722656 0.25422203540802 591.413818359375 0.3297436833381653 0.87903756 0.27563849091529846 True -6 20167 31.786062240600586 0.5426881313323975 545.329345703125 0.3530314564704895 591.9364624023438 0.3293389081954956 0.8828581 0.26139047741889954 True -7 23048 31.80680203437805 0.5455143451690674 523.0849609375 0.25664594769477844 589.5792846679688 0.3328396677970886 0.88689256 0.2510504126548767 True -8 25929 31.808918476104736 0.5476973056793213 499.6328430175781 0.22165055572986603 586.520751953125 0.3370916545391083 0.89092445 0.23899926245212555 True -9 28810 31.779025316238403 0.5508544445037842 418.32257080078125 0.15561258792877197 584.743408203125 0.3389149308204651 0.8943209 0.23217405378818512 True -10 31691 31.73202109336853 0.5449645519256592 447.0721435546875 0.2711312174797058 585.4022216796875 0.336783766746521 0.8980634 0.22476620972156525 True -11 34572 31.820521593093872 0.5502474308013916 384.76849365234375 0.1405966728925705 584.0198364257812 0.3383808135986328 0.9015842 0.21503636240959167 True -12 37453 31.786194562911987 0.5498189926147461 499.4325256347656 0.15841317176818848 580.9320678710938 0.3430882692337036 0.90593225 0.20163466036319733 True -13 40334 31.732773303985596 0.5496826171875 494.7965087890625 0.17366451025009155 579.6543579101562 0.34469589591026306 0.9073151 0.1963019222021103 True -14 43215 31.8039710521698 0.5496301651000977 498.9770202636719 0.21954545378684998 579.9823608398438 0.3429979085922241 0.91062117 0.1852867156267166 True -15 46096 31.754321575164795 0.5489599704742432 443.407958984375 0.22813990712165833 578.440185546875 0.34606674313545227 0.913106 0.179886594414711 True -16 48977 31.784336805343628 0.5504858493804932 457.5815734863281 0.22635461390018463 576.751953125 0.3485977053642273 0.91655815 0.1734522432088852 True -17 51858 31.8000066280365 0.5500075817108154 518.5257568359375 0.11700959503650665 578.0444946289062 0.34588339924812317 0.9162176 0.1705164611339569 False -18 54739 31.774163722991943 0.5502119064331055 416.6457214355469 0.1658322513103485 578.84326171875 0.3447675406932831 0.91612154 0.17151397466659546 False -19 57620 31.790101766586304 0.5412569046020508 587.202880859375 0.12693460285663605 579.0413818359375 0.3449115753173828 0.9155287 0.1723761409521103 False diff --git a/ENCSR826URD/cherimoya.fold_2.performance.tsv b/ENCSR826URD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cc7cd16a726ca71ba153260a882ef1c36cc4413d..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -576.751953125 0.40559688210487366 0.3485977053642273 0.14877033233642578 0.9165581464767456 0.888276994228363 0.1734522432088852 \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_3.evaluate.json b/ENCSR826URD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d07fbea9ae01e533809741e2d797ed92fec0b113..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388RKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_3.fit.json b/ENCSR826URD/cherimoya.fold_3.fit.json deleted file mode 100644 index 381fc596718f069cd4caa58f5a9307a0a702c290..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF388RKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_3.log b/ENCSR826URD/cherimoya.fold_3.log deleted file mode 100644 index 0c0aaa416ba492982fa6ec775a46e65badadf6de..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 34.783523082733154 4.544816493988037 532.0017700195312 0.3020486831665039 637.0474853515625 0.24299442768096924 0.7408666 5.07316780090332 True -1 5516 30.51670479774475 0.574246883392334 514.6639404296875 0.3514159023761749 587.79296875 0.2997378706932068 0.8332828 0.873593807220459 True -2 8274 30.49232268333435 0.5599269866943359 590.3968505859375 0.30758634209632874 577.3042602539062 0.30976927280426025 0.8526557 0.4582800269126892 True -3 11032 30.506362676620483 0.551612377166748 503.0984191894531 0.2520661950111389 571.3790893554688 0.3176458477973938 0.86487186 0.37586233019828796 True -4 13790 30.52815842628479 0.5547463893890381 537.2805786132812 0.3024134039878845 570.0805053710938 0.3195273280143738 0.86968756 0.3036182224750519 True -5 16548 30.540114164352417 0.5400762557983398 428.0626220703125 0.15355899930000305 568.9931640625 0.32003822922706604 0.87001294 0.299306720495224 True -6 19306 30.56215500831604 0.5528337955474854 408.3975830078125 0.2826020121574402 567.1531982421875 0.3236578106880188 0.8761413 0.28669169545173645 True -7 22064 30.479331254959106 2.179372787475586 480.3184509277344 0.2976222038269043 565.7864379882812 0.3252725303173065 0.8805974 0.2733842432498932 True -8 24822 30.51314616203308 14.739615678787231 532.93017578125 0.18443860113620758 564.6602172851562 0.3265310823917389 0.8848053 0.27049118280410767 True -9 27580 31.65890622138977 0.5487349033355713 608.58251953125 0.16288800537586212 563.2666625976562 0.3286260962486267 0.88592887 0.2703579366207123 True -10 30338 30.616406679153442 39.56863522529602 451.905029296875 0.1961367428302765 561.5772705078125 0.3308936059474945 0.88960826 0.2544001042842865 True -11 33096 30.619515895843506 0.5540950298309326 446.42889404296875 0.14423543214797974 560.5877685546875 0.33188799023628235 0.8955213 0.24305462837219238 True -12 35854 30.954126119613647 0.5541486740112305 546.1185302734375 0.22210735082626343 558.4561767578125 0.3341793119907379 0.8992946 0.23166194558143616 True -13 38612 30.79545521736145 33.972512006759644 545.194091796875 0.08365311473608017 556.6939697265625 0.33664119243621826 0.9042024 0.21432343125343323 True -14 41370 30.562533855438232 36.90007781982422 492.22943115234375 0.17843729257583618 556.1217651367188 0.337281733751297 0.9084754 0.20157121121883392 True -15 44128 30.743144035339355 0.5469183921813965 465.219970703125 0.17059901356697083 554.028564453125 0.3408663868904114 0.91201645 0.186921164393425 True -16 46886 30.461950302124023 0.5299468040466309 385.2850341796875 0.16035562753677368 555.0927734375 0.33773452043533325 0.91637284 0.1771850287914276 True -17 49644 30.42393159866333 0.5425734519958496 437.5142517089844 0.17227667570114136 554.8179321289062 0.3385818600654602 0.9179905 0.17457571625709534 True -18 52402 30.424753189086914 1.583871603012085 529.934814453125 0.16085804998874664 553.6829223632812 0.3409671485424042 0.9174321 0.17440804839134216 False -19 55160 30.515732765197754 1.7361862659454346 570.2120361328125 0.10614877939224243 554.5400390625 0.33881595730781555 0.91686755 0.17520815134048462 False diff --git a/ENCSR826URD/cherimoya.fold_3.performance.tsv b/ENCSR826URD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c294e48c998f2f137f0f2efdfa4a0852877732cc..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -554.8179321289062 0.4132458567619324 0.3385818898677826 0.1459132730960846 0.917990505695343 0.8803739547729492 0.17457571625709534 \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_4.evaluate.json b/ENCSR826URD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index abdc7346f13ac854408120129517b5920b1b1bab..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF388RKR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_4.fit.json b/ENCSR826URD/cherimoya.fold_4.fit.json deleted file mode 100644 index c49c033d39c3f05c68661dbac32f2a2ddeeb7829..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF388RKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR826URD/cherimoya.fold_4.log b/ENCSR826URD/cherimoya.fold_4.log deleted file mode 100644 index 8011a663f5590eb3ecc63e853af5ab63052ef8dc..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.73389148712158 3.653900623321533 511.79119873046875 0.28063029050827026 603.3380737304688 0.2352685034275055 0.7547274 4.221133708953857 True -1 5596 31.136884689331055 22.284674167633057 527.2047729492188 0.34440356492996216 553.2918090820312 0.2940726578235626 0.8529688 0.6364538073539734 True -2 8394 30.9587242603302 0.613961935043335 551.7514038085938 0.3832494616508484 545.0897216796875 0.30169180035591125 0.8600047 0.3612303137779236 True -3 11192 30.974748849868774 0.5964174270629883 460.9442138671875 0.21492134034633636 541.73046875 0.3047306537628174 0.86731195 0.33501675724983215 True -4 13990 30.966331243515015 0.5777838230133057 509.4734802246094 0.2955363988876343 538.4105834960938 0.3105399012565613 0.87445545 0.26569539308547974 True -5 16788 30.89517307281494 29.47108793258667 496.8711242675781 0.35508647561073303 536.7418212890625 0.3126544654369354 0.88198656 0.25898879766464233 True -6 19586 31.134188890457153 0.6317727565765381 466.8749694824219 0.22898760437965393 535.2157592773438 0.3142350912094116 0.88923717 0.2364453375339508 True -7 22384 30.994259357452393 0.6174530982971191 583.677490234375 0.27444663643836975 534.1843872070312 0.31515493988990784 0.89198416 0.23679594695568085 True -8 25182 30.850738525390625 0.5857040882110596 516.4373168945312 0.15876832604408264 531.88427734375 0.3197878897190094 0.8975705 0.22301186621189117 True -9 27980 30.97061038017273 0.5860629081726074 506.03759765625 0.24410101771354675 530.42626953125 0.3209606409072876 0.8999992 0.20281381905078888 True -10 30778 31.049789905548096 23.712430000305176 470.97857666015625 0.14960125088691711 529.6610107421875 0.3220043182373047 0.9028376 0.19127504527568817 True -11 33576 31.263351440429688 0.5773849487304688 482.44927978515625 0.09765505790710449 528.0687255859375 0.3233613967895508 0.9048592 0.18764059245586395 True -12 36374 31.131654024124146 9.08887791633606 598.2498779296875 0.16762816905975342 527.2166748046875 0.3240814805030823 0.9100371 0.17420488595962524 True -13 39172 30.974244594573975 2.812530040740967 462.89141845703125 0.3240157663822174 526.9735107421875 0.32428184151649475 0.91150814 0.16487514972686768 True -14 41970 31.430391311645508 2.393226146697998 491.0843200683594 0.11663095653057098 524.5057983398438 0.3290330171585083 0.9137775 0.1581968069076538 True -15 44768 31.122071266174316 0.5897514820098877 498.10931396484375 0.14795014262199402 524.500732421875 0.3282637894153595 0.9178367 0.15321001410484314 True -16 47566 31.017574787139893 0.5866885185241699 430.79669189453125 0.1251130998134613 524.1195068359375 0.328185111284256 0.9199221 0.1492723673582077 True -17 50364 30.999070167541504 0.5663115978240967 446.8714599609375 0.11594364792108536 523.735595703125 0.3299558758735657 0.9184097 0.14870195090770721 False -18 53162 30.90340542793274 44.305750608444214 474.6572570800781 0.13114826381206512 524.2864990234375 0.32761481404304504 0.91905487 0.1493162363767624 False -19 55960 31.425144910812378 0.6051201820373535 490.086181640625 0.1464918851852417 525.3986206054688 0.3254289925098419 0.9184416 0.1500144749879837 False diff --git a/ENCSR826URD/cherimoya.fold_4.performance.tsv b/ENCSR826URD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 34cf68293efdf3cf3abfbedc38454351d15abd4a..0000000000000000000000000000000000000000 --- a/ENCSR826URD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -524.1195068359375 0.42113447189331055 0.3281850814819336 0.13704334199428558 0.9199221134185791 0.8765296936035156 0.1492723673582077 \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_0.evaluate.json b/ENCSR828FVZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4a40accc811d6221e5af640933db747ccfece32a..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF515IWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_0.fit.json b/ENCSR828FVZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 43c86358791c7d7b3e1460d3e9a3f605764f0b02..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF515IWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_0.log b/ENCSR828FVZ/cherimoya.fold_0.log deleted file mode 100644 index e5327ef04220fac0b2348791763010f5bc50db2f..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.051623582839966 4.835503578186035 861.086669921875 1.2823388576507568 1302.2591552734375 0.3070017993450165 0.54891336 11.573014259338379 True -1 5518 30.38428783416748 0.6149065494537354 844.0170288085938 1.026914358139038 1059.422119140625 0.417038232088089 0.636055 4.077264785766602 True -2 8277 30.331472873687744 0.5741209983825684 931.095458984375 0.8003095388412476 1029.431396484375 0.4283662736415863 0.63748455 2.5628559589385986 True -3 11036 30.356149435043335 0.6434981822967529 922.8555908203125 1.0884060859680176 998.307861328125 0.43590593338012695 0.65059143 3.3424487113952637 True -4 13795 30.291807889938354 0.6408398151397705 839.558349609375 1.0733118057250977 979.6907958984375 0.44454503059387207 0.658168 1.9902915954589844 True -5 16554 30.346998929977417 0.6999168395996094 954.2030639648438 0.6046593189239502 966.3001098632812 0.4475061595439911 0.6702373 1.710362434387207 True -6 19313 30.30741286277771 0.5617799758911133 684.5012817382812 0.7727177143096924 957.2379760742188 0.449185311794281 0.6821963 1.622054100036621 True -7 22072 30.32765030860901 0.5784516334533691 580.7142333984375 0.598050594329834 946.8272094726562 0.4509723484516144 0.68714875 1.4757990837097168 True -8 24831 30.31374168395996 0.5707061290740967 735.2158813476562 0.5977015495300293 935.18896484375 0.4568215608596802 0.697614 1.4313850402832031 True -9 27590 30.323806762695312 0.5792832374572754 628.3818359375 0.6336901783943176 924.9049072265625 0.46206679940223694 0.7059419 1.2842274904251099 True -10 30349 30.29528021812439 0.5768060684204102 920.00048828125 0.6667316555976868 917.2892456054688 0.46599081158638 0.71691054 1.220595359802246 True -11 33108 30.342951774597168 0.566615104675293 860.7683715820312 0.8346682786941528 907.3126220703125 0.4693480134010315 0.72829294 1.0774074792861938 True -12 35867 30.330803394317627 2.29601788520813 678.2276611328125 0.6071631908416748 900.5604858398438 0.47247907519340515 0.7392594 0.9638780355453491 True -13 38626 30.361278295516968 0.5606236457824707 877.5472412109375 0.7303577661514282 890.4503173828125 0.4770483672618866 0.7490853 0.8684071898460388 True -14 41385 29.996685028076172 1.0811221599578857 721.8564453125 0.7201615571975708 883.8483276367188 0.4800749719142914 0.75791776 0.7605689167976379 True -15 44144 29.76299476623535 0.6052448749542236 685.830078125 0.5874481201171875 883.0294799804688 0.4783794581890106 0.7664282 0.6809090375900269 True -16 46903 29.744081258773804 0.5501046180725098 718.7408447265625 0.4166795611381531 878.3463134765625 0.48140594363212585 0.7720853 0.6302306652069092 True -17 49662 29.75078010559082 0.5590088367462158 679.698486328125 0.5048493146896362 877.3873901367188 0.48139041662216187 0.7743582 0.6037395596504211 True -18 52421 29.920260429382324 0.5752913951873779 781.76318359375 0.5486906170845032 876.3138427734375 0.4819600582122803 0.7737654 0.5967455506324768 False -19 55180 29.882492303848267 0.5825979709625244 795.280517578125 0.45801496505737305 879.6129150390625 0.47922417521476746 0.7722147 0.5961657166481018 False diff --git a/ENCSR828FVZ/cherimoya.fold_0.performance.tsv b/ENCSR828FVZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b4e48019307d3630e5c1122238f3be96e6cca814..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -877.3873901367188 0.3222220838069916 0.4813903868198395 0.223813995718956 0.7743582129478455 0.7158757448196411 0.6037395596504211 \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_1.evaluate.json b/ENCSR828FVZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ebcc8460fc3fc16170fdedcd4af61de6e7294861..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF515IWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_1.fit.json b/ENCSR828FVZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 33ce9a204d676c9be44d479965e6f00d0ae68a31..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF515IWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_1.log b/ENCSR828FVZ/cherimoya.fold_1.log deleted file mode 100644 index 565d11dfe349a6a6faea42720e8a40d470d14454..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2700 34.36345958709717 3.904729127883911 834.447998046875 1.256590723991394 1648.6932373046875 0.30757683515548706 0.5466054 8.73264217376709 True -1 5400 29.732726573944092 0.7324557304382324 946.6051635742188 0.9227966666221619 1354.20556640625 0.419695645570755 0.63678944 5.680165767669678 True -2 8100 29.7933931350708 24.84030771255493 850.8643188476562 0.7310240268707275 1294.5252685546875 0.4377913773059845 0.6506142 3.67136812210083 True -3 10800 29.712146043777466 1.1659138202667236 777.1209716796875 0.9444827437400818 1260.2777099609375 0.44452962279319763 0.66234654 2.642719030380249 True -4 13500 29.69179630279541 0.7091166973114014 859.397216796875 0.8358322381973267 1233.722900390625 0.45303863286972046 0.6663175 2.603255271911621 True -5 16200 29.704180479049683 1.6363134384155273 825.2058715820312 0.9020901918411255 1211.4478759765625 0.4604315161705017 0.6786207 2.371426582336426 True -6 18900 29.67691707611084 0.7090961933135986 988.5072631835938 0.7543783783912659 1187.0482177734375 0.467206746339798 0.691347 2.4056200981140137 True -7 21600 29.645938873291016 0.7240443229675293 841.3903198242188 0.7095205783843994 1172.2171630859375 0.47093260288238525 0.69785184 1.8500996828079224 True -8 24300 29.68563222885132 1.5375535488128662 967.9619140625 0.9249505996704102 1166.3099365234375 0.4750000536441803 0.70230913 1.734933614730835 True -9 27000 29.765329599380493 0.8126294612884521 1122.59033203125 0.9341349601745605 1139.6593017578125 0.4804488718509674 0.719166 1.435845971107483 True -10 29700 29.788194179534912 0.7271771430969238 731.2662963867188 0.717993438243866 1132.2535400390625 0.4810766577720642 0.72854275 1.296550989151001 True -11 32400 29.77759075164795 0.7235839366912842 772.884765625 0.6233595609664917 1114.998046875 0.4883503317832947 0.7412197 1.238324761390686 True -12 35100 29.707952976226807 1.4358854293823242 1115.1680908203125 0.8864210247993469 1099.390380859375 0.4951588809490204 0.75068486 1.2318874597549438 True -13 37800 29.968174695968628 0.6987416744232178 658.7752685546875 0.4364249110221863 1091.2333984375 0.49447619915008545 0.7642727 1.0247470140457153 True -14 40500 29.162462949752808 0.6987640857696533 802.134521484375 0.6596222519874573 1083.6900634765625 0.4952743351459503 0.7717742 0.909762978553772 True -15 43200 29.168272018432617 0.7132644653320312 881.7762451171875 0.6803615093231201 1075.9566650390625 0.49692779779434204 0.7799186 0.7966756224632263 True -16 45900 29.135887384414673 0.7284431457519531 652.423828125 0.5262922048568726 1067.9805908203125 0.5003523230552673 0.78598076 0.7097605466842651 True -17 48600 29.16027307510376 0.6981916427612305 806.1361083984375 0.33528268337249756 1068.4334716796875 0.49963533878326416 0.7903762 0.6631739735603333 True -18 51300 29.151859521865845 0.7075817584991455 684.8258666992188 0.5111584663391113 1063.524169921875 0.5027337074279785 0.7898847 0.6494633555412292 False -19 54000 29.10620951652527 0.6989836692810059 752.0513916015625 0.769087016582489 1061.9803466796875 0.5030916929244995 0.7886839 0.6481293439865112 False diff --git a/ENCSR828FVZ/cherimoya.fold_1.performance.tsv b/ENCSR828FVZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index db67619ca198bbbeb5427d7fa049aa05e9eee6ee..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1068.4334716796875 0.30383285880088806 0.49963533878326416 0.25343701243400574 0.7903761863708496 0.7549940943717957 0.6631739735603333 \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_2.evaluate.json b/ENCSR828FVZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 361a706b5ff186c0250569acbf6c69a6d999cdd8..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF515IWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_2.fit.json b/ENCSR828FVZ/cherimoya.fold_2.fit.json deleted file mode 100644 index ff2c86242d11808c55c1698c8f013ac35a4bfe5d..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF515IWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_2.log b/ENCSR828FVZ/cherimoya.fold_2.log deleted file mode 100644 index 5ff7e9c0f0066f98bcbb561a25e8d4deb53e7eca..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 36.22543382644653 3.2391793727874756 928.8305053710938 1.1245036125183105 1400.3155517578125 0.3084696829319 0.5323205 8.502009391784668 True -1 5776 31.737694263458252 0.5542912483215332 1335.152587890625 1.1596343517303467 1129.3179931640625 0.4216926097869873 0.6214802 5.3162689208984375 True -2 8664 31.70388412475586 1.0192153453826904 867.449462890625 0.9869565367698669 1124.9268798828125 0.4214727580547333 0.6286541 3.754666328430176 True -3 11552 31.166146278381348 0.6484940052032471 802.9413452148438 0.7176921963691711 1080.0172119140625 0.43343663215637207 0.6432807 2.8237764835357666 True -4 14440 31.181045055389404 2.3523316383361816 812.8893432617188 1.20951509475708 1062.9017333984375 0.43905240297317505 0.65184426 2.466599941253662 True -5 17328 31.13506269454956 0.5356683731079102 620.25146484375 1.0414307117462158 1044.979736328125 0.4461514949798584 0.66132677 2.5081229209899902 True -6 20216 31.17160725593567 0.5627415180206299 722.7632446289062 1.0331339836120605 1037.4212646484375 0.4487708508968353 0.66728914 1.8627119064331055 True -7 23104 31.08324384689331 0.5587506294250488 710.6865234375 1.0257786512374878 1020.6185302734375 0.45251989364624023 0.6810115 1.6713930368423462 True -8 25992 31.18605136871338 0.5504896640777588 799.9373779296875 0.8376559615135193 1012.3504028320312 0.4555371105670929 0.69212955 1.5690720081329346 True -9 28880 31.18329906463623 0.5650300979614258 614.7913208007812 0.7147849798202515 997.4852905273438 0.4637160301208496 0.70219344 1.465187430381775 True -10 31768 31.122507572174072 0.5570340156555176 694.5750732421875 0.7300159335136414 991.2337646484375 0.46702149510383606 0.7100045 1.548141598701477 True -11 34656 31.12555170059204 0.5283980369567871 866.6771240234375 0.9550037384033203 978.3201293945312 0.4689207077026367 0.7233069 1.1360756158828735 True -12 37544 31.12402892112732 0.5312237739562988 652.0545654296875 0.5737848877906799 966.0321655273438 0.4759056568145752 0.7334987 1.047621488571167 True -13 40432 31.240817546844482 0.8480329513549805 851.99755859375 0.5770836472511292 960.3814086914062 0.47524264454841614 0.7413633 0.917466938495636 True -14 43320 31.1750545501709 0.5638113021850586 695.93310546875 0.6062914729118347 954.8749389648438 0.4771578311920166 0.74856514 0.8134430050849915 True -15 46208 31.148334503173828 0.5657103061676025 681.9142456054688 0.6736271381378174 951.8998413085938 0.477586030960083 0.75397605 0.7482665777206421 True -16 49096 31.33552837371826 0.7751669883728027 806.369873046875 0.519194483757019 944.9945068359375 0.4814916253089905 0.758243 0.6880610585212708 True -17 51984 31.194124937057495 0.5479393005371094 862.2734985351562 0.6206551790237427 945.662353515625 0.47974225878715515 0.7606621 0.6551656126976013 True -18 54872 31.136381149291992 0.5528836250305176 510.62078857421875 0.3836796283721924 945.74658203125 0.4810347855091095 0.7619612 0.6472237706184387 True -19 57760 31.279428720474243 1.5275278091430664 619.746826171875 0.4670126140117645 946.91259765625 0.4802311360836029 0.76254725 0.6476056575775146 True diff --git a/ENCSR828FVZ/cherimoya.fold_2.performance.tsv b/ENCSR828FVZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0d5b2a44ecc0dce0ff009c6c169601b18d21602e..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -946.91259765625 0.31843143701553345 0.4802311360836029 0.230988547205925 0.7625472545623779 0.7144338488578796 0.6476056575775146 \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_3.evaluate.json b/ENCSR828FVZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c3c549409f0b90174f11fdd805da0b2464365b32..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF515IWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_3.fit.json b/ENCSR828FVZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 23805f613f5b12e05833f908f848b218830b32ca..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF515IWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_3.log b/ENCSR828FVZ/cherimoya.fold_3.log deleted file mode 100644 index 866e8a922e303127410ff1a19fbcdd642877ab4d..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 35.068830251693726 3.4167866706848145 771.8419189453125 1.0287582874298096 1308.3134765625 0.3181004822254181 0.54797465 9.625177383422852 True -1 5534 30.654349088668823 0.6385138034820557 818.9600830078125 0.7375168800354004 1062.5726318359375 0.4300282895565033 0.64999616 4.763030529022217 True -2 8301 30.49823021888733 0.5774340629577637 800.845703125 1.242393970489502 1062.7685546875 0.42544472217559814 0.6426558 4.041987419128418 False -3 11068 30.71182131767273 0.5364971160888672 794.6419677734375 0.7945142984390259 1023.51171875 0.43984079360961914 0.65684104 2.943760395050049 True -4 13835 30.43141484260559 0.5211665630340576 1249.32470703125 0.9539459943771362 993.0443725585938 0.4465849995613098 0.6715233 2.27340030670166 True -5 16602 30.447237730026245 0.5113077163696289 802.7964477539062 0.8130593299865723 977.1572875976562 0.45240187644958496 0.67418724 1.4119147062301636 True -6 19369 30.519245386123657 0.5219252109527588 720.976806640625 0.8057118654251099 963.5640258789062 0.45692306756973267 0.68568504 1.3243852853775024 True -7 22136 30.4993257522583 0.5222797393798828 668.8959350585938 0.6293421387672424 952.5217895507812 0.4614681005477905 0.69862056 1.3490816354751587 True -8 24903 31.00512433052063 3.42864990234375 660.788330078125 0.7587206959724426 946.171875 0.4631193280220032 0.70720094 1.2719366550445557 True -9 27670 30.302266359329224 0.6273238658905029 1025.4600830078125 0.6335946321487427 935.0232543945312 0.469085693359375 0.71563727 1.4054661989212036 True -10 30437 29.96927046775818 0.5087978839874268 668.8496704101562 0.8035020232200623 928.89990234375 0.4718957841396332 0.72429806 1.333400845527649 True -11 33204 29.881763458251953 0.5072989463806152 802.6842041015625 0.6599977016448975 920.057373046875 0.4771266281604767 0.7338481 1.2221883535385132 True -12 35971 29.92029595375061 0.5083444118499756 711.0174560546875 0.7892622351646423 910.4323120117188 0.481220543384552 0.74079645 1.0970698595046997 True -13 38738 29.939532041549683 0.5073268413543701 630.56103515625 0.6741268038749695 906.0488891601562 0.48378539085388184 0.74872816 1.0009300708770752 True -14 41505 29.835153102874756 0.5055654048919678 763.876953125 0.7231230735778809 898.7718505859375 0.485015332698822 0.7590361 0.8578859567642212 True -15 44272 29.81973433494568 0.519040584564209 812.465576171875 0.49307748675346375 888.893310546875 0.490029901266098 0.76704115 0.7648120522499084 True -16 47039 29.92563486099243 0.5083343982696533 653.197021484375 0.6443355679512024 891.0739135742188 0.4859352707862854 0.77335685 0.6773494482040405 True -17 49806 29.89627766609192 0.5058555603027344 517.8944091796875 0.4377412796020508 890.9931640625 0.4858737289905548 0.77611154 0.6369757056236267 True -18 52573 29.84410333633423 0.5168361663818359 638.1083984375 0.5471585392951965 885.7003784179688 0.49080735445022583 0.776067 0.6255905628204346 False -19 55340 29.902626991271973 0.5170838832855225 701.19921875 0.622837245464325 886.5009765625 0.4903048276901245 0.77654326 0.6228424310684204 True diff --git a/ENCSR828FVZ/cherimoya.fold_3.performance.tsv b/ENCSR828FVZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0643b3c117f96c1c60d929376ca0af5983b6620b..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -886.5009765625 0.3171723186969757 0.4903048276901245 0.22834518551826477 0.7765432596206665 0.7199835777282715 0.6228424310684204 \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_4.evaluate.json b/ENCSR828FVZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5dc71028991ae1b3b6425b150109a9ce7f9c7d60..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF515IWT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_4.fit.json b/ENCSR828FVZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 5118800834112735b21034f718b1a02a7ae122bf..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF515IWT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828FVZ/cherimoya.fold_4.log b/ENCSR828FVZ/cherimoya.fold_4.log deleted file mode 100644 index 1b09f9ce92096e01352244826d5a10835fb3112f..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2778 35.39550423622131 3.392794132232666 1093.347412109375 1.2550461292266846 1212.3411865234375 0.30568739771842957 0.5267433 8.273918151855469 True -1 5556 30.558737993240356 1.579911708831787 886.8635864257812 0.8393329977989197 996.4786376953125 0.4127119779586792 0.6166066 3.8928751945495605 True -2 8334 30.183855772018433 0.5679926872253418 1026.491455078125 0.8353080749511719 981.4523315429688 0.4182684123516083 0.6187608 3.206179618835449 True -3 11112 29.982516288757324 0.6033804416656494 921.3364868164062 1.2048027515411377 953.7999267578125 0.42568790912628174 0.63174987 2.045872211456299 True -4 13890 29.966410636901855 0.6786136627197266 839.7484130859375 0.9880353808403015 927.5706176757812 0.43643808364868164 0.63614327 1.7823002338409424 True -5 16668 29.958088159561157 0.5940003395080566 846.12353515625 0.9771420359611511 916.3135375976562 0.44053083658218384 0.65058285 1.3999806642532349 True -6 19446 29.861162662506104 0.5662076473236084 640.6029052734375 0.9180207252502441 904.9871826171875 0.44412651658058167 0.6580661 1.297629475593567 True -7 22224 29.870184421539307 0.5618565082550049 729.9921264648438 0.7419222593307495 895.0484619140625 0.44801557064056396 0.6724676 1.2817469835281372 True -8 25002 29.944438934326172 0.5747079849243164 667.7078857421875 1.0484510660171509 887.3208618164062 0.4513881802558899 0.682928 1.2155416011810303 True -9 27780 29.995707511901855 1.1120538711547852 904.75830078125 1.0976850986480713 880.49169921875 0.45322999358177185 0.69379115 1.1175315380096436 True -10 30558 29.924965143203735 0.5819592475891113 969.2133178710938 1.0709984302520752 870.8110961914062 0.45782119035720825 0.7062209 1.0190695524215698 True -11 33336 29.935660362243652 0.5829858779907227 772.3802490234375 0.7161599397659302 863.689208984375 0.4609662592411041 0.7145565 0.9628694653511047 True -12 36114 29.944326639175415 0.5763616561889648 870.7689208984375 0.6062366962432861 854.7504272460938 0.4655055105686188 0.7243492 0.894004762172699 True -13 38892 29.940531253814697 0.5719318389892578 551.770751953125 0.6346483826637268 844.146728515625 0.4720931649208069 0.73591113 0.8136865496635437 True -14 41670 29.95119881629944 0.5714254379272461 668.453857421875 0.6660681366920471 839.9336547851562 0.4727439880371094 0.74746495 0.7252034544944763 True -15 44448 29.956228733062744 0.5733678340911865 636.4852294921875 0.4365549683570862 840.2033081054688 0.4698579013347626 0.75149035 0.6611142158508301 True -16 47226 29.955434560775757 0.5503139495849609 742.5048828125 0.5008928775787354 836.4232177734375 0.471613347530365 0.7583927 0.6149206757545471 True -17 50004 29.962219715118408 0.5574188232421875 601.77587890625 0.3921505808830261 830.8416137695312 0.47681936621665955 0.7607113 0.59450364112854 True -18 52782 29.964013814926147 2.1001198291778564 695.763671875 0.4281427562236786 833.6243896484375 0.4749910235404968 0.75904125 0.5924733281135559 False -19 55560 29.967169284820557 0.5782864093780518 734.5020751953125 0.6249092221260071 834.5020141601562 0.47438645362854004 0.75918174 0.592534065246582 False diff --git a/ENCSR828FVZ/cherimoya.fold_4.performance.tsv b/ENCSR828FVZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 839c077bb98d19c06919b7ee00b20e9780095533..0000000000000000000000000000000000000000 --- a/ENCSR828FVZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -830.8416137695312 0.32645976543426514 0.47681936621665955 0.21960656344890594 0.7607113122940063 0.6966832280158997 0.59450364112854 \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_0.evaluate.json b/ENCSR828RNY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a1b1286b72181de8f999144fead27ba90b6f7acf..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF851WBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_0.fit.json b/ENCSR828RNY/cherimoya.fold_0.fit.json deleted file mode 100644 index 53e69637b8d8d62342850d2b5eb92fb6408793eb..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF851WBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_0.log b/ENCSR828RNY/cherimoya.fold_0.log deleted file mode 100644 index c613b3475a130a542a321b5c3c11a01a0da5adfd..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2774 35.425477266311646 3.7426958084106445 248.69932556152344 0.7160218954086304 293.857666015625 0.15049459040164948 0.6606841 2.5312280654907227 True -1 5548 30.55443286895752 0.5878317356109619 228.16873168945312 0.7590463161468506 283.08880615234375 0.20498892664909363 0.723731 0.9851506948471069 True -2 8322 30.47238254547119 0.5449721813201904 197.4789276123047 0.5714182257652283 279.8556213378906 0.214779794216156 0.73457247 0.4808507263660431 True -3 11096 30.585270166397095 0.5443453788757324 210.23207092285156 0.8383583426475525 278.1120910644531 0.2218288630247116 0.73565435 0.39194706082344055 True -4 13870 30.47645115852356 0.5488467216491699 221.9375457763672 0.6372649073600769 276.7547302246094 0.2275797426700592 0.74258506 0.39329081773757935 True -5 16644 30.468141317367554 0.5528042316436768 240.21484375 0.6546326875686646 276.3749084472656 0.2284298688173294 0.7436509 0.4319702684879303 True -6 19418 30.44861340522766 0.5434253215789795 205.69012451171875 0.3938679099082947 275.6979675292969 0.2322452813386917 0.7468839 0.41644003987312317 True -7 22192 30.460662126541138 0.5570144653320312 243.76467895507812 0.5794215202331543 275.11383056640625 0.23537933826446533 0.75074697 0.4318750500679016 True -8 24966 29.97188115119934 1.2577874660491943 206.4229736328125 0.7028965950012207 274.66326904296875 0.23720000684261322 0.75091434 0.42998698353767395 True -9 27740 29.840461492538452 0.5638644695281982 215.57876586914062 0.4633827209472656 274.15362548828125 0.23935727775096893 0.75676763 0.386726051568985 True -10 30514 29.833890676498413 1.3295893669128418 202.469970703125 0.4434318244457245 273.7566833496094 0.2414029985666275 0.75640726 0.38657304644584656 False -11 33288 29.924312829971313 0.7045283317565918 241.72579956054688 0.44156551361083984 273.5403747558594 0.2426038533449173 0.7586344 0.38751599192619324 True -12 36062 29.890723943710327 0.5499138832092285 209.43858337402344 0.40571969747543335 273.23016357421875 0.2442336231470108 0.7626551 0.37721049785614014 True -13 38836 29.866297006607056 0.5420234203338623 208.1707000732422 0.4080502986907959 272.8057861328125 0.24675998091697693 0.7666684 0.3611298203468323 True -14 41610 29.84802770614624 0.5443990230560303 187.73385620117188 0.3220190107822418 272.73175048828125 0.24686986207962036 0.7699369 0.34645935893058777 True -15 44384 29.89242172241211 0.5482282638549805 232.54409790039062 0.3520203232765198 272.4427490234375 0.24737486243247986 0.77704364 0.3274720013141632 True -16 47158 29.911282300949097 0.55118727684021 190.96514892578125 0.27960890531539917 272.4712219238281 0.24721182882785797 0.7849119 0.30683237314224243 True -17 49932 29.847949504852295 1.2088449001312256 227.0211944580078 0.21816977858543396 272.24847412109375 0.24830713868141174 0.7845698 0.2933363914489746 False -18 52706 29.940614223480225 0.5414202213287354 200.31869506835938 0.31631097197532654 272.39276123046875 0.24767976999282837 0.78567946 0.28777092695236206 True -19 55480 29.927265167236328 0.5480222702026367 225.25546264648438 0.4091018736362457 272.36590576171875 0.24790611863136292 0.78657407 0.2890927791595459 True diff --git a/ENCSR828RNY/cherimoya.fold_0.performance.tsv b/ENCSR828RNY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3842c9059eda6de92e493464971847c9e0164728..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -272.36590576171875 0.5086515545845032 0.2479061484336853 0.07036816328763962 0.7865740656852722 0.7647877931594849 0.2890927791595459 \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_1.evaluate.json b/ENCSR828RNY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a8ba749b65b648fe8968814e5bab5c16ba59ae9b..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF851WBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_1.fit.json b/ENCSR828RNY/cherimoya.fold_1.fit.json deleted file mode 100644 index 36e18a0c65cc7455c5cc23a7c3348758eb979787..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF851WBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_1.log b/ENCSR828RNY/cherimoya.fold_1.log deleted file mode 100644 index c02fce8fea3fe9f1ca375fcc4f8717947e49db54..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 34.74346470832825 4.437138557434082 199.64430236816406 0.48189476132392883 328.98162841796875 0.1568421721458435 0.6524452 3.1940393447875977 True -1 5490 30.702810287475586 0.7876343727111816 200.39959716796875 0.571281373500824 315.0735168457031 0.21710479259490967 0.73762715 1.189782977104187 True -2 8235 30.149683475494385 15.296469926834106 244.7111358642578 0.6355119347572327 311.42132568359375 0.22803601622581482 0.7581014 0.5577337145805359 True -3 10980 30.167379140853882 0.7457144260406494 240.32855224609375 0.499932199716568 309.4284973144531 0.2345430850982666 0.76685226 0.43751683831214905 True -4 13725 30.19343876838684 14.896274089813232 208.03955078125 1.4199116230010986 308.1770935058594 0.23944483697414398 0.7705419 0.4107779860496521 True -5 16470 30.521061420440674 0.7486734390258789 195.22804260253906 0.7508916258811951 306.8863830566406 0.24481569230556488 0.77209365 0.43027183413505554 True -6 19215 30.177699327468872 0.7523913383483887 210.4508514404297 0.43633535504341125 306.78643798828125 0.24494671821594238 0.7718594 0.4531875550746918 False -7 21960 30.146063566207886 0.7289316654205322 226.162109375 0.6292349100112915 305.8778991699219 0.24889786541461945 0.7755449 0.46474316716194153 True -8 24705 30.129843950271606 0.7337453365325928 216.2334442138672 0.47435855865478516 305.42718505859375 0.25094085931777954 0.7783171 0.4303435981273651 True -9 27450 30.12323307991028 1.0241494178771973 206.0294189453125 0.5325859785079956 305.1693115234375 0.2516096532344818 0.7816722 0.4383506178855896 True -10 30195 29.76668095588684 0.7236754894256592 188.1383819580078 0.49000728130340576 304.7321472167969 0.25351208448410034 0.78407174 0.45691537857055664 True -11 32940 29.65920853614807 0.742511510848999 222.250244140625 0.39510801434516907 303.9922180175781 0.2559957206249237 0.7852747 0.43691304326057434 True -12 35685 29.597418308258057 1.164245367050171 273.0811767578125 0.43084418773651123 303.6009216308594 0.2576008141040802 0.7927838 0.3987290561199188 True -13 38430 29.632147550582886 0.7335841655731201 187.73257446289062 0.4537160396575928 303.16943359375 0.2583266794681549 0.7984784 0.3871728479862213 True -14 41175 29.643535614013672 0.7278962135314941 192.14097595214844 0.32066282629966736 302.7352294921875 0.26008424162864685 0.8006731 0.37277770042419434 True -15 43920 29.587623834609985 1.1847572326660156 215.25987243652344 0.43835824728012085 302.63531494140625 0.2602742910385132 0.8044413 0.3536052703857422 True -16 46665 29.61420249938965 0.7270145416259766 211.55758666992188 0.47895070910453796 302.6010437011719 0.2603764235973358 0.80821353 0.3356645107269287 True -17 49410 29.613993406295776 0.7233560085296631 223.11697387695312 0.3439539968967438 302.79571533203125 0.2592706084251404 0.80896026 0.3237663507461548 True -18 52155 29.644660711288452 0.7225558757781982 189.4351806640625 0.5613502264022827 302.84881591796875 0.25881314277648926 0.8096889 0.3206774890422821 True -19 54900 29.576420307159424 0.7284805774688721 214.77659606933594 0.40774592757225037 302.5823974609375 0.26074549555778503 0.80884016 0.3203244209289551 False diff --git a/ENCSR828RNY/cherimoya.fold_1.performance.tsv b/ENCSR828RNY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2e231266c7f085de1c33724ab723d6dd455818f7..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.84881591796875 0.4956711530685425 0.25881314277648926 0.07785257697105408 0.809688925743103 0.7979968786239624 0.3206774890422821 \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_2.evaluate.json b/ENCSR828RNY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 69b837018364ddde9c2c6a5204eb44594d4c5909..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF851WBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_2.fit.json b/ENCSR828RNY/cherimoya.fold_2.fit.json deleted file mode 100644 index 0186a7818b802ef0cdc6978b2865fff723b94df0..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF851WBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_2.log b/ENCSR828RNY/cherimoya.fold_2.log deleted file mode 100644 index 613405cf1f0ce2ab2ac03ee6f41e75b4880cb800..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 36.51531434059143 3.8868632316589355 212.92547607421875 0.507239580154419 300.4141540527344 0.15635022521018982 0.65413266 2.2817821502685547 True -1 5776 31.76358151435852 0.9289796352386475 203.34120178222656 0.8549555540084839 288.43798828125 0.2121623456478119 0.70106643 1.095264196395874 True -2 8664 31.796465396881104 2.6076014041900635 253.7993927001953 0.600517749786377 285.7708435058594 0.21834741532802582 0.72631174 0.6119658350944519 True -3 11552 31.796634912490845 0.520498514175415 178.7798309326172 0.6284269094467163 284.3756408691406 0.22401593625545502 0.73738754 0.5573150515556335 True -4 14440 31.81205940246582 13.385390520095825 250.52166748046875 0.5686216354370117 283.3581848144531 0.2291053980588913 0.7436375 0.5823248028755188 True -5 17328 31.742509126663208 20.105899333953857 234.36996459960938 0.5209295749664307 282.2417907714844 0.23429878056049347 0.739013 0.535004734992981 False -6 20216 31.851351022720337 0.5619077682495117 253.7407989501953 0.5481798052787781 281.8583068847656 0.2353316694498062 0.74747187 0.5093119740486145 True -7 23104 31.776227235794067 19.856539726257324 188.091796875 0.7521713972091675 281.3243103027344 0.23823538422584534 0.74789 0.4626067280769348 True -8 25992 31.908272981643677 0.5617296695709229 204.62664794921875 0.8381863236427307 280.7832946777344 0.24074704945087433 0.74700195 0.4917766749858856 False -9 28880 31.74474787712097 0.531954288482666 261.7891540527344 0.49075111746788025 280.30426025390625 0.24230913817882538 0.7516874 0.44420546293258667 True -10 31768 31.546974182128906 0.530815839767456 244.68463134765625 0.38703954219818115 280.12957763671875 0.24352207779884338 0.7546797 0.44245678186416626 True -11 34656 31.230350255966187 0.5214385986328125 220.35496520996094 0.3009750247001648 279.4358825683594 0.2465386837720871 0.75399286 0.43990543484687805 False -12 37544 31.148600816726685 0.5232973098754883 199.25390625 0.4358593821525574 279.40899658203125 0.2456042766571045 0.75713205 0.4366684854030609 True -13 40432 31.229538440704346 1.1005537509918213 218.10316467285156 0.40697282552719116 278.9601745605469 0.2477722316980362 0.7637121 0.4048480689525604 True -14 43320 31.247934818267822 0.5203125476837158 219.1051025390625 0.38471609354019165 278.519775390625 0.24972732365131378 0.7665207 0.3861902952194214 True -15 46208 31.29733395576477 0.5249099731445312 210.34878540039062 0.26568159461021423 278.3965148925781 0.25062352418899536 0.7719988 0.3694406747817993 True -16 49096 31.220934867858887 0.5236766338348389 240.61788940429688 0.4080776572227478 278.0924377441406 0.25198104977607727 0.7764216 0.3493388891220093 True -17 51984 31.20126175880432 0.5215632915496826 179.6724853515625 0.41039910912513733 278.16436767578125 0.25093504786491394 0.7804746 0.33011162281036377 True -18 54872 31.145240545272827 0.5194277763366699 227.12600708007812 0.35243070125579834 278.19744873046875 0.2509486675262451 0.7809054 0.32284554839134216 True -19 57760 31.221471071243286 0.520627498626709 175.83462524414062 0.29833489656448364 278.0749816894531 0.2517614960670471 0.7821622 0.3211119472980499 True diff --git a/ENCSR828RNY/cherimoya.fold_2.performance.tsv b/ENCSR828RNY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c6dd2be0c15cc611e804449d41e61385e2686a43..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -278.0749816894531 0.5056516528129578 0.2517614960670471 0.06763239204883575 0.7821621894836426 0.7606832981109619 0.3211119472980499 \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_3.evaluate.json b/ENCSR828RNY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5e76c827045d55e20dfebbb52173f1c62611cb20..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF851WBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_3.fit.json b/ENCSR828RNY/cherimoya.fold_3.fit.json deleted file mode 100644 index 2e133d46e1d6f1ee1f439f423fba31591198077c..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF851WBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_3.log b/ENCSR828RNY/cherimoya.fold_3.log deleted file mode 100644 index f60572d0009a3db829b76f999aa4d1f5cc39709d..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2785 35.420001745224 4.741171836853027 204.91049194335938 0.7745947241783142 318.3976135253906 0.153673455119133 0.6546041 3.8155431747436523 True -1 5570 30.625871419906616 10.207770109176636 200.08973693847656 0.5947601795196533 307.47833251953125 0.20486798882484436 0.7303907 1.0235974788665771 True -2 8355 30.623119592666626 1.4637811183929443 195.36691284179688 0.8154088258743286 303.0917663574219 0.2213815450668335 0.74236655 0.6512958407402039 True -3 11140 30.604361534118652 1.3546509742736816 224.84722900390625 0.40366584062576294 301.71063232421875 0.22540223598480225 0.7526249 0.4542580842971802 True -4 13925 30.578051567077637 1.3579010963439941 216.08314514160156 0.6113057732582092 300.81060791015625 0.22951827943325043 0.75387937 0.44643744826316833 True -5 16710 30.603224992752075 1.0844366550445557 202.05020141601562 0.6899071931838989 300.09576416015625 0.2324870079755783 0.7515332 0.4437931478023529 False -6 19495 30.589378595352173 0.5639257431030273 228.78427124023438 0.47123488783836365 299.57281494140625 0.23460400104522705 0.75824153 0.42204606533050537 True -7 22280 30.58907389640808 1.416393756866455 159.27603149414062 0.711808979511261 299.1079406738281 0.23610523343086243 0.7579946 0.4456832706928253 False -8 25065 30.604548931121826 0.9673337936401367 208.61001586914062 0.4278947412967682 298.9784240722656 0.23648381233215332 0.7602625 0.43054986000061035 True -9 27850 30.312921285629272 0.5683598518371582 247.34947204589844 0.70789635181427 298.15704345703125 0.24036628007888794 0.7621776 0.43146026134490967 True -10 30635 30.06073522567749 0.5727536678314209 227.69273376464844 0.5803338289260864 297.6427001953125 0.2427089661359787 0.76627076 0.4235094487667084 True -11 33420 30.049588203430176 0.5499536991119385 216.9295654296875 0.392220139503479 298.07025146484375 0.24025017023086548 0.7670179 0.39817002415657043 True -12 36205 30.06158971786499 0.5554418563842773 236.93838500976562 0.5381456613540649 297.662109375 0.2421729862689972 0.7694521 0.3903194069862366 True -13 38990 30.028337240219116 0.5622825622558594 222.30130004882812 0.41241633892059326 297.21923828125 0.24423524737358093 0.77761096 0.3844161033630371 True -14 41775 30.05730438232422 0.5522727966308594 191.946044921875 0.3499850630760193 296.6914367675781 0.24676461517810822 0.7829374 0.3649376630783081 True -15 44560 30.083624362945557 0.5623631477355957 242.56045532226562 0.3521019518375397 296.8308410644531 0.2456623613834381 0.7858654 0.34729892015457153 True -16 47345 30.098817825317383 0.5665321350097656 186.58633422851562 0.33928382396698 296.5683898925781 0.2471216320991516 0.79285187 0.33509689569473267 True -17 50130 30.157283782958984 0.5661797523498535 234.23883056640625 0.2492120862007141 296.7680969238281 0.2460145503282547 0.7959338 0.3263859748840332 True -18 52915 30.106940984725952 0.5603852272033691 225.68609619140625 0.2406671941280365 296.64788818359375 0.24630846083164215 0.7960239 0.3226364850997925 True -19 55700 30.180917978286743 0.5546796321868896 201.2123565673828 0.3077511787414551 296.7452697753906 0.2461102157831192 0.79570085 0.32659032940864563 False diff --git a/ENCSR828RNY/cherimoya.fold_3.performance.tsv b/ENCSR828RNY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a11fda1fb6af628d8e0545156a8e053868ac7fa2..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -296.64788818359375 0.5020492076873779 0.24630849063396454 0.07599442452192307 0.7960239052772522 0.7725250124931335 0.3226364850997925 \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_4.evaluate.json b/ENCSR828RNY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4ec352d0783c2d3e8dcf4ba56bd532713f6fb095..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF851WBO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_4.fit.json b/ENCSR828RNY/cherimoya.fold_4.fit.json deleted file mode 100644 index f64abe13a87ef7ea0493acc028e1684ca046dc04..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF851WBO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR828RNY/cherimoya.fold_4.log b/ENCSR828RNY/cherimoya.fold_4.log deleted file mode 100644 index 50ea2f88640fef3570c1f3be60648d8d98731fe4..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2861 36.236124753952026 4.063483715057373 221.64303588867188 0.7485519647598267 286.9689025878906 0.1468508094549179 0.6529304 3.024306535720825 True -1 5722 31.502795219421387 0.7179601192474365 210.2569580078125 0.9364879131317139 276.1144104003906 0.20109941065311432 0.72218806 1.1743156909942627 True -2 8583 31.414441347122192 1.5142302513122559 228.073974609375 0.4873478412628174 273.3686828613281 0.21070891618728638 0.73013735 0.6259461641311646 True -3 11444 31.513573169708252 0.6286778450012207 222.3657684326172 0.5933400392532349 272.05767822265625 0.21453221142292023 0.73891556 0.6625417470932007 True -4 14305 31.492326974868774 0.6555576324462891 228.14715576171875 0.48201310634613037 271.20684814453125 0.2188117504119873 0.7458453 0.6206102967262268 True -5 17166 31.447115898132324 0.6272461414337158 249.5185546875 0.3251534700393677 270.9166564941406 0.22021996974945068 0.7475338 0.5999187231063843 True -6 20027 31.440197706222534 0.7276086807250977 228.97007751464844 0.7183780670166016 270.5504150390625 0.22239193320274353 0.750261 0.6302191019058228 True -7 22888 31.693638563156128 25.416995763778687 232.18576049804688 0.6819390058517456 270.3166198730469 0.22309386730194092 0.7505589 0.6029484272003174 True -8 25749 31.445897817611694 1.0608859062194824 218.06607055664062 0.5100594162940979 269.48345947265625 0.22745688259601593 0.7543428 0.5539901256561279 True -9 28610 31.444286108016968 0.9333207607269287 191.6911163330078 0.5010676383972168 269.2522888183594 0.2289251834154129 0.753978 0.5833536386489868 False -10 31471 30.95476269721985 1.5015628337860107 288.3428039550781 0.508854866027832 269.0762023925781 0.22962480783462524 0.75207156 0.5679996609687805 False -11 34332 30.87828230857849 1.1681180000305176 224.91720581054688 0.41706153750419617 268.6888427734375 0.23063881695270538 0.758413 0.5066818594932556 True -12 37193 30.888376474380493 0.8070840835571289 230.39161682128906 0.5724704265594482 268.55908203125 0.23115964233875275 0.76358527 0.47324028611183167 True -13 40054 30.822757482528687 0.633690595626831 191.90170288085938 0.415240615606308 268.0157775878906 0.2339775711297989 0.76934344 0.42081040143966675 True -14 42915 30.885959148406982 0.6046693325042725 244.099853515625 0.525392472743988 267.77685546875 0.2348691076040268 0.77545804 0.3808928430080414 True -15 45776 30.856895446777344 1.3225584030151367 220.9270477294922 0.46387988328933716 267.8009338378906 0.23491701483726501 0.7815873 0.3371559977531433 True -16 48637 30.826687574386597 7.12757682800293 235.71115112304688 0.48140543699264526 267.6533203125 0.23499242961406708 0.7874584 0.31514015793800354 True -17 51498 30.97069811820984 0.9071497917175293 212.66802978515625 0.3484344482421875 267.1124267578125 0.23801442980766296 0.78789425 0.3017931878566742 True -18 54359 30.92914867401123 0.6290059089660645 230.80874633789062 0.2947860360145569 267.55194091796875 0.2355324774980545 0.789739 0.2969314157962799 True -19 57220 31.00509762763977 0.6409130096435547 183.71739196777344 0.30999353528022766 267.5023498535156 0.23585616052150726 0.7886363 0.299603134393692 False diff --git a/ENCSR828RNY/cherimoya.fold_4.performance.tsv b/ENCSR828RNY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 10c00e8fe70f9290fbf6841c224703479d89edc9..0000000000000000000000000000000000000000 --- a/ENCSR828RNY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -267.55194091796875 0.5146546959877014 0.2355324923992157 0.06543398648500443 0.7897390127182007 0.7594112753868103 0.2969314157962799 \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_0.evaluate.json b/ENCSR829MXU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 26908f68037478d27b8a77930eb1796ffa6c3bae..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF824ATO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_0.fit.json b/ENCSR829MXU/cherimoya.fold_0.fit.json deleted file mode 100644 index 20d49b11253c062c3f1d648bda4ec53811210da1..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF824ATO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_0.log b/ENCSR829MXU/cherimoya.fold_0.log deleted file mode 100644 index 6e258e6a2e97b563cdf20d5741683658af712bf9..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 35.62869381904602 6.822494029998779 643.7315673828125 0.6738784909248352 989.3678588867188 0.28703486919403076 0.4166496 6.190530300140381 True -1 5476 30.11188578605652 0.6395158767700195 677.2066040039062 0.5760188698768616 891.087890625 0.39682066440582275 0.53487164 1.6073839664459229 True -2 8214 30.080408811569214 0.570880651473999 677.2349853515625 0.619954526424408 882.7915649414062 0.4032844305038452 0.53505963 0.575254499912262 True -3 10952 30.050661325454712 0.588435173034668 770.70166015625 0.5072109699249268 875.0972900390625 0.4104119539260864 0.5613059 0.5401059985160828 True -4 13690 30.119835376739502 0.5916328430175781 771.9283447265625 0.4757295250892639 874.4706420898438 0.4100545346736908 0.56437886 0.5173559188842773 True -5 16428 30.089751720428467 0.5729687213897705 657.6920166015625 0.47564440965652466 870.4197387695312 0.41668474674224854 0.5695434 0.5224833488464355 True -6 19166 30.11786723136902 1.2913119792938232 636.8944091796875 0.35677894949913025 868.2225341796875 0.4197668433189392 0.56904906 0.5171346068382263 False -7 21904 29.695308208465576 0.5501186847686768 656.8604736328125 0.4229544699192047 868.2848510742188 0.41896334290504456 0.57770896 0.5078930854797363 True -8 24642 29.56035017967224 0.5642292499542236 761.6156616210938 0.4879359304904938 865.1163330078125 0.42360812425613403 0.5873978 0.4741858243942261 True -9 27380 29.518418073654175 0.567387580871582 761.0372314453125 0.5115699768066406 862.2697143554688 0.4270942509174347 0.60011905 0.4448793828487396 True -10 30118 29.532500982284546 0.548905611038208 672.572509765625 0.5754215121269226 859.9880981445312 0.43014803528785706 0.60803896 0.4247860908508301 True -11 32856 29.694825649261475 0.5523476600646973 736.2775268554688 0.504332423210144 860.1622924804688 0.4296972453594208 0.62038684 0.3962087333202362 True -12 35594 29.600706338882446 0.5537192821502686 683.504150390625 0.6994072198867798 856.3220825195312 0.4346452057361603 0.63446695 0.3863533139228821 True -13 38332 29.553223133087158 1.51650071144104 682.3822021484375 0.47196057438850403 855.4606323242188 0.43598392605781555 0.64597124 0.3664547801017761 True -14 41070 29.561720609664917 0.5545005798339844 702.3475952148438 0.3517310917377472 854.1876220703125 0.4361891746520996 0.65565044 0.3493545651435852 True -15 43808 29.573229789733887 0.5583994388580322 600.18310546875 0.42910635471343994 851.6376953125 0.4406844973564148 0.66299045 0.34423506259918213 True -16 46546 29.563185691833496 0.5596134662628174 780.0606079101562 0.37757402658462524 851.647705078125 0.4402124583721161 0.66979057 0.33935821056365967 True -17 49284 29.528887033462524 3.3220131397247314 652.4306640625 0.36419641971588135 852.8196411132812 0.4373035728931427 0.66940063 0.339626282453537 False -18 52022 29.530158281326294 17.55191397666931 644.4535522460938 0.422014981508255 852.4563598632812 0.4390465319156647 0.66928905 0.3431777060031891 False -19 54760 29.543155670166016 0.544734001159668 727.5182495117188 0.30132344365119934 853.174072265625 0.43767833709716797 0.66673374 0.34795743227005005 False diff --git a/ENCSR829MXU/cherimoya.fold_0.performance.tsv b/ENCSR829MXU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e1d5ea42cc204d6bb9c0745ec751aa183d3d12b7..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -851.647705078125 0.323463499546051 0.4402124583721161 0.21422238647937775 0.6697905659675598 0.6120706796646118 0.33935821056365967 \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_1.evaluate.json b/ENCSR829MXU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 95cf91c4b6f2b97153cb0b5b044df366b6874d05..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF824ATO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_1.fit.json b/ENCSR829MXU/cherimoya.fold_1.fit.json deleted file mode 100644 index e93a21fa7c4c797ddeaec9a39473e5961bd78854..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF824ATO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_1.log b/ENCSR829MXU/cherimoya.fold_1.log deleted file mode 100644 index 7b428b38373278d98c79e2c1bd0bc3b71bf9c38e..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 34.42013216018677 4.133341550827026 703.35693359375 0.7632604837417603 1097.8201904296875 0.2965546250343323 0.4472512 6.349527835845947 True -1 5506 30.298697471618652 2.91357684135437 673.5698852539062 0.5317741632461548 985.665771484375 0.40964052081108093 0.52170694 1.9702608585357666 True -2 8259 30.355164527893066 0.6957798004150391 635.92724609375 0.5386768579483032 971.5482177734375 0.41750985383987427 0.5353938 0.8273895978927612 True -3 11012 30.329675436019897 0.6755721569061279 844.3468017578125 0.882238507270813 964.480224609375 0.42027217149734497 0.57128286 0.7249825596809387 True -4 13765 30.299538135528564 0.691206693649292 815.6854858398438 0.5039392709732056 956.7871704101562 0.4301821291446686 0.5925692 0.6932632923126221 True -5 16518 30.228365421295166 17.780384063720703 709.4080810546875 0.5252715349197388 953.8077392578125 0.4329828917980194 0.59945995 0.695341169834137 True -6 19271 30.288224697113037 0.6753818988800049 621.6099243164062 0.8888050317764282 951.4644775390625 0.4343877136707306 0.6035766 0.6536020636558533 True -7 22024 30.30019974708557 0.6773269176483154 726.240234375 0.4048290550708771 947.627685546875 0.43895718455314636 0.6151705 0.5838532447814941 True -8 24777 30.41034460067749 0.6818652153015137 700.02197265625 0.38397306203842163 943.8886108398438 0.4432263970375061 0.6235774 0.5314793586730957 True -9 27530 30.299163103103638 0.6765213012695312 725.6044311523438 0.39798828959465027 941.5169067382812 0.4464811682701111 0.6258827 0.5229315161705017 True -10 30283 30.27768039703369 0.6900589466094971 634.3261108398438 0.27702975273132324 938.4708862304688 0.44831886887550354 0.6440926 0.47656726837158203 True -11 33036 30.33671236038208 0.6751296520233154 758.5252685546875 0.3698766231536865 934.2901000976562 0.45277658104896545 0.6583221 0.45237404108047485 True -12 35789 30.31094479560852 0.6733195781707764 715.9649658203125 0.619135320186615 932.5039672851562 0.45442283153533936 0.6721789 0.42418786883354187 True -13 38542 30.285042762756348 0.6668312549591064 759.2445068359375 0.41781890392303467 927.86669921875 0.4587661623954773 0.6803665 0.4103044867515564 True -14 41295 30.266263484954834 0.6710331439971924 745.3958740234375 0.3969835042953491 927.9534301757812 0.45749929547309875 0.6947446 0.3891335129737854 True -15 44048 30.24970531463623 0.6894800662994385 770.6168823242188 0.5133959054946899 924.1265258789062 0.46232718229293823 0.7026997 0.3807388246059418 True -16 46801 30.141290187835693 1.5576534271240234 713.5228271484375 0.3648170232772827 922.5615844726562 0.46222370862960815 0.71064645 0.36250633001327515 True -17 49554 29.73088550567627 1.143585443496704 719.3536376953125 0.3124880790710449 923.5245361328125 0.46149304509162903 0.71608895 0.3590090572834015 True -18 52307 29.737593412399292 0.6735310554504395 796.832763671875 0.19401335716247559 923.0631713867188 0.4622920751571655 0.7165642 0.36099958419799805 True -19 55060 29.76280665397644 0.6818900108337402 686.3487548828125 0.23167684674263 922.8859252929688 0.4626365602016449 0.71394175 0.3629967272281647 False diff --git a/ENCSR829MXU/cherimoya.fold_1.performance.tsv b/ENCSR829MXU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 27d1c3fdcdee87652ff1759ba6c848e2dc43af12..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -923.0631713867188 0.3103252649307251 0.4622920751571655 0.23332715034484863 0.7165641784667969 0.65800940990448 0.36099958419799805 \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_2.evaluate.json b/ENCSR829MXU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3df1ca189b7d6de259a5f6f65018b202fdf1813d..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF824ATO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_2.fit.json b/ENCSR829MXU/cherimoya.fold_2.fit.json deleted file mode 100644 index d3aa3c1ccc362e5a970cdd79bcfd24269f445813..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF824ATO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_2.log b/ENCSR829MXU/cherimoya.fold_2.log deleted file mode 100644 index c6dd0993234639790ba2298cb15bb85d8068cc5a..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 36.65061354637146 3.9039478302001953 716.6138916015625 0.5774813890457153 1002.6815185546875 0.30122581124305725 0.4295982 4.725078105926514 True -1 5800 31.84552574157715 0.5754091739654541 623.2699584960938 0.5981225967407227 907.7982177734375 0.4054998755455017 0.53836113 1.264535903930664 True -2 8700 31.902696132659912 0.5366675853729248 722.1393432617188 0.4357451796531677 894.996337890625 0.41163942217826843 0.55140483 0.5931163430213928 True -3 11600 31.865782260894775 2.5170748233795166 723.4351806640625 0.5514634251594543 889.1310424804688 0.41589945554733276 0.5690448 0.5239112973213196 True -4 14500 31.896206378936768 1.1771214008331299 724.8272705078125 0.5664073824882507 885.6243896484375 0.418818861246109 0.5779346 0.5027707815170288 True -5 17400 31.904056787490845 0.5773546695709229 697.6585693359375 0.5285377502441406 884.5921630859375 0.4211012125015259 0.57221967 0.481474906206131 False -6 20300 31.850499153137207 0.5508713722229004 633.9190673828125 0.3668564558029175 882.9223022460938 0.42278674244880676 0.57860154 0.46882686018943787 True -7 23200 31.823582410812378 1.926384687423706 721.2471923828125 0.5847742557525635 877.4544067382812 0.4294699430465698 0.59486735 0.47244992852211 True -8 26100 31.722252368927002 0.5381970405578613 735.41455078125 0.40249350666999817 877.0037841796875 0.4288363754749298 0.5992223 0.4661101698875427 True -9 29000 31.253528356552124 0.5536885261535645 747.5330810546875 0.5328755974769592 874.0159912109375 0.43345025181770325 0.605326 0.452598512172699 True -10 31900 31.24816083908081 0.9850711822509766 728.049560546875 0.48235848546028137 872.1978149414062 0.4348861873149872 0.62025326 0.4246353209018707 True -11 34800 31.34150457382202 0.5437514781951904 687.6754760742188 0.2744542360305786 868.9718627929688 0.43773984909057617 0.6351239 0.4215398132801056 True -12 37700 31.322808265686035 0.5297830104827881 854.6737060546875 0.45942041277885437 866.7294311523438 0.4397311210632324 0.6459638 0.3983667492866516 True -13 40600 31.338452100753784 0.5428676605224609 659.6444702148438 1.0311598777770996 863.1558837890625 0.4443385601043701 0.65792197 0.3758659362792969 True -14 43500 31.33572244644165 0.526024341583252 687.9857788085938 0.39620664715766907 862.4253540039062 0.4447120428085327 0.6654763 0.36494821310043335 True -15 46400 31.306220531463623 0.5388555526733398 637.70166015625 0.3696041703224182 861.162109375 0.4461791217327118 0.6737811 0.3537150025367737 True -16 49300 31.292924404144287 0.5380215644836426 729.1280517578125 0.3390032649040222 859.5009155273438 0.4479106366634369 0.6795663 0.34945330023765564 True -17 52200 31.283787727355957 0.5271270275115967 658.3984375 0.4078041911125183 859.3883056640625 0.448872834444046 0.68360764 0.3470485806465149 True -18 55100 31.357155561447144 0.5399956703186035 679.3848876953125 0.2874513864517212 860.2879638671875 0.4472545087337494 0.6835886 0.3506612181663513 False -19 58000 31.32910704612732 0.5399138927459717 709.0654296875 0.3057211637496948 859.5769653320312 0.4490726590156555 0.68247205 0.3544694185256958 False diff --git a/ENCSR829MXU/cherimoya.fold_2.performance.tsv b/ENCSR829MXU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 391ba4ee8d4e0b11d4b8640dadab5a3e396d8559..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -859.3883056640625 0.3207571804523468 0.44887280464172363 0.22045068442821503 0.6836076378822327 0.616680920124054 0.3470485806465149 \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_3.evaluate.json b/ENCSR829MXU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 55a2669d51db3868bf60040f218844cd3756a009..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF824ATO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_3.fit.json b/ENCSR829MXU/cherimoya.fold_3.fit.json deleted file mode 100644 index 6b08dc65dcd7b738f7625fcb5d33d52f041a3db9..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF824ATO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_3.log b/ENCSR829MXU/cherimoya.fold_3.log deleted file mode 100644 index fed61bd1b72ec4ffe0a9a348d462a8df5564f1f4..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2795 35.81163740158081 3.941992998123169 701.7902221679688 0.6919823884963989 1050.8035888671875 0.30415359139442444 0.4532471 5.639142036437988 True -1 5590 30.697582244873047 0.923527717590332 836.1962280273438 1.1256638765335083 961.0269165039062 0.3964749872684479 0.5239809 1.2572695016860962 True -2 8385 30.18843913078308 0.5744171142578125 870.05712890625 0.8660205602645874 944.8634033203125 0.4106070101261139 0.5475409 0.5863145589828491 True -3 11180 30.146641969680786 0.5878994464874268 766.5067138671875 0.5930818319320679 937.3716430664062 0.4162946343421936 0.570437 0.5587990880012512 True -4 13975 30.151484489440918 0.5737781524658203 744.0590209960938 0.39521685242652893 933.2322387695312 0.42040780186653137 0.5641675 0.5572771430015564 False -5 16770 30.13036346435547 0.5775175094604492 748.40869140625 0.659123420715332 930.3695678710938 0.42463207244873047 0.566982 0.5775744915008545 False -6 19565 30.09366536140442 0.5755889415740967 711.3892211914062 0.44093117117881775 929.312744140625 0.42479023337364197 0.5731359 0.5644227862358093 True -7 22360 30.076354503631592 0.5625951290130615 724.3604125976562 0.4501546621322632 927.5359497070312 0.4276317059993744 0.58323133 0.5661020874977112 True -8 25155 30.164100646972656 0.5750386714935303 642.61962890625 0.41741910576820374 926.4202880859375 0.4285893738269806 0.58825684 0.5367095470428467 True -9 27950 30.125404834747314 0.5736362934112549 674.7017822265625 0.36306166648864746 923.42529296875 0.43094274401664734 0.5993525 0.4972734749317169 True -10 30745 30.119582653045654 0.607058048248291 780.8838500976562 0.34191203117370605 920.6853637695312 0.4342469871044159 0.6116987 0.4765463173389435 True -11 33540 30.07787299156189 0.563687801361084 660.9107666015625 0.5674604177474976 916.2991333007812 0.4395126402378082 0.61781484 0.455599308013916 True -12 36335 30.109015703201294 1.3423092365264893 655.8564453125 0.6967962384223938 914.2734375 0.4410393238067627 0.63196737 0.4457956552505493 True -13 39130 30.193658351898193 0.5835440158843994 653.3334350585938 0.44883474707603455 911.230224609375 0.4445107877254486 0.64240116 0.41148197650909424 True -14 41925 30.24068021774292 0.5955181121826172 715.5218505859375 0.37088122963905334 910.2857666015625 0.445488303899765 0.65222996 0.4004487693309784 True -15 44720 30.113889694213867 0.5869600772857666 754.42529296875 0.3697474002838135 910.055908203125 0.4446195065975189 0.66277695 0.38868916034698486 True -16 47515 30.161535501480103 1.7482311725616455 671.4544677734375 0.3874904215335846 910.4811401367188 0.4436326324939728 0.66690075 0.38000404834747314 True -17 50310 30.14824938774109 0.5772566795349121 655.61376953125 0.24871845543384552 906.2802124023438 0.45103397965431213 0.67125195 0.38113081455230713 True -18 53105 30.13199806213379 0.5730817317962646 677.6259765625 0.2468814253807068 910.2582397460938 0.44390588998794556 0.67051876 0.38380950689315796 False -19 55900 30.18810224533081 0.583078145980835 688.6605224609375 0.29506823420524597 907.2078247070312 0.4494403004646301 0.6704357 0.38715192675590515 False diff --git a/ENCSR829MXU/cherimoya.fold_3.performance.tsv b/ENCSR829MXU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d012c816dc16ce5b2b95cac1a2360c2dcfd3aac2..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -906.2802124023438 0.3142159879207611 0.4510340094566345 0.22892364859580994 0.6712519526481628 0.6188952326774597 0.38113081455230713 \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_4.evaluate.json b/ENCSR829MXU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f12d4019717dab9b87349ab3e1366823c8207c79..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF824ATO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_4.fit.json b/ENCSR829MXU/cherimoya.fold_4.fit.json deleted file mode 100644 index 6afda8398d10f4696faf2b7147656513c909aea6..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF824ATO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR829MXU/cherimoya.fold_4.log b/ENCSR829MXU/cherimoya.fold_4.log deleted file mode 100644 index 5070d486751534d5ee23c394c01bc4d47f796107..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2893 38.0202956199646 4.213756084442139 624.6982421875 0.5341485738754272 1006.144775390625 0.30313363671302795 0.43532395 6.041444301605225 True -1 5786 31.852697134017944 0.6773676872253418 707.855712890625 1.0104247331619263 917.7548828125 0.39850348234176636 0.4989455 1.398809552192688 True -2 8679 31.80860137939453 0.5849390029907227 710.741455078125 0.8601028323173523 905.9989013671875 0.4055859446525574 0.5286187 0.542345404624939 True -3 11572 31.78513526916504 2.6562647819519043 903.2557373046875 0.7119982838630676 900.8062133789062 0.4108889400959015 0.5396621 0.5230568647384644 True -4 14465 31.59711980819702 0.5745890140533447 718.1692504882812 0.6559168696403503 895.2465209960938 0.4144028425216675 0.5543906 0.5052403807640076 True -5 17358 31.214553594589233 0.6299798488616943 772.9586181640625 0.47345447540283203 893.2339477539062 0.4183014929294586 0.55225104 0.4949008524417877 False -6 20251 31.18441390991211 0.5840671062469482 719.0863037109375 0.5450153350830078 889.9371337890625 0.4219599664211273 0.5649184 0.4870489537715912 True -7 23144 31.23302459716797 0.5863204002380371 678.46826171875 0.6543796062469482 886.2664794921875 0.4268534779548645 0.5681676 0.452679842710495 True -8 26037 31.158060312271118 0.6053204536437988 764.9863891601562 0.8246774077415466 883.47412109375 0.43037569522857666 0.5788517 0.4425089955329895 True -9 28930 31.26692485809326 0.6916718482971191 768.85693359375 0.5305016040802002 884.057861328125 0.42795705795288086 0.5921021 0.4448651373386383 True -10 31823 31.184354305267334 0.6307196617126465 768.0697021484375 0.5105094909667969 882.0275268554688 0.4311465620994568 0.6010246 0.42659974098205566 True -11 34716 31.222731113433838 0.5836327075958252 732.52490234375 0.5186976790428162 877.5381469726562 0.4374242424964905 0.60800606 0.41925233602523804 True -12 37609 31.204641580581665 0.5667846202850342 744.7760009765625 0.3939799964427948 877.5180053710938 0.4361763894557953 0.6238775 0.4002663791179657 True -13 40502 31.23367929458618 0.5909266471862793 805.6268310546875 0.4362969994544983 876.0799560546875 0.43676674365997314 0.6338153 0.3871997594833374 True -14 43395 31.266868829727173 0.5820605754852295 650.8890380859375 0.3562431335449219 873.6903686523438 0.44080662727355957 0.6485866 0.37101492285728455 True -15 46288 31.319344997406006 0.847773551940918 666.93798828125 0.8203806281089783 872.3623657226562 0.4427805244922638 0.65628415 0.3692803382873535 True -16 49181 31.273504734039307 0.5685684680938721 684.657470703125 0.262640118598938 871.5068359375 0.44312039017677307 0.6630302 0.35748881101608276 True -17 52074 31.226665496826172 0.567960262298584 736.4625244140625 0.33654940128326416 869.4048461914062 0.4466143548488617 0.6669804 0.3560262620449066 True -18 54967 31.241611003875732 20.67263698577881 569.402587890625 0.19469040632247925 870.2945556640625 0.4454059302806854 0.66771233 0.358625590801239 True -19 57860 31.454182386398315 5.953311920166016 715.3428344726562 0.35653552412986755 870.8161010742188 0.4442403316497803 0.6657403 0.360944926738739 False diff --git a/ENCSR829MXU/cherimoya.fold_4.performance.tsv b/ENCSR829MXU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2c719510b578ba56478fd85910221b5960b5fc85..0000000000000000000000000000000000000000 --- a/ENCSR829MXU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -870.2945556640625 0.3195115625858307 0.4454059302806854 0.22320085763931274 0.6677123308181763 0.6079517602920532 0.358625590801239 \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_0.evaluate.json b/ENCSR830ALP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c13c4040390deb636029145ba1061c5990bf41ec..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF667FMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_0.fit.json b/ENCSR830ALP/cherimoya.fold_0.fit.json deleted file mode 100644 index faa432100a835b5cd8e5c549f26557537a3a4d1e..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF667FMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_0.log b/ENCSR830ALP/cherimoya.fold_0.log deleted file mode 100644 index e97d77a9a24b6efecbf5205bf2cf2bd06126ce90..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2622 33.8434317111969 3.46769118309021 552.3282470703125 1.8308753967285156 883.9852905273438 0.5987609028816223 0.5486471 12.896392822265625 True -1 5244 28.97228479385376 2.149259328842163 569.8380126953125 1.2155067920684814 667.0792846679688 0.7429702877998352 0.6191853 5.254141330718994 True -2 7866 28.972293615341187 0.520723819732666 493.532470703125 1.207360029220581 635.395751953125 0.7590737342834473 0.6177579 2.1669251918792725 False -3 10488 28.92315983772278 6.17700982093811 481.88861083984375 1.0644373893737793 622.5068359375 0.7660205960273743 0.6247369 1.3576375246047974 True -4 13110 28.9669029712677 0.5198779106140137 433.8973388671875 1.0885629653930664 617.2325439453125 0.7697277665138245 0.6292344 1.174975037574768 True -5 15732 28.964356660842896 0.5197927951812744 472.4350891113281 0.8761887550354004 613.7973022460938 0.7730339765548706 0.6290708 1.1191259622573853 False -6 18354 28.966257333755493 0.51810622215271 473.18560791015625 0.9502350091934204 608.560302734375 0.7759943604469299 0.6409113 1.0117992162704468 True -7 20976 29.525248289108276 1.0936305522918701 432.7691650390625 0.764828085899353 605.2230224609375 0.779008686542511 0.643738 0.9551321268081665 True -8 23598 28.916487216949463 0.5189409255981445 518.4388427734375 1.1150476932525635 600.71923828125 0.7819225192070007 0.6588164 0.9215269088745117 True -9 26220 28.90831446647644 1.0960559844970703 474.35552978515625 0.9330992698669434 597.4869995117188 0.7843433618545532 0.6650648 0.9013169407844543 True -10 28842 28.383590936660767 0.5001926422119141 474.5243225097656 1.0173313617706299 593.322998046875 0.7869600057601929 0.673822 0.8423108458518982 True -11 31464 28.325432300567627 0.5057258605957031 624.2542724609375 0.7440006732940674 589.3837280273438 0.7895542979240417 0.68618757 0.8184053897857666 True -12 34086 28.320973873138428 0.5138981342315674 358.08148193359375 0.9871623516082764 585.3255004882812 0.7921276092529297 0.69474965 0.7970656156539917 True -13 36708 28.35843777656555 1.167032241821289 502.796142578125 1.2077356576919556 582.978271484375 0.7939246296882629 0.70331436 0.7878394722938538 True -14 39330 28.407020807266235 0.5216720104217529 469.5397033691406 0.6583588123321533 579.4666748046875 0.7956880927085876 0.7153036 0.7583309412002563 True -15 41952 28.474152326583862 0.5128352642059326 413.2650146484375 1.1535024642944336 578.571533203125 0.7965273261070251 0.72219104 0.7460886836051941 True -16 44574 28.453524589538574 0.518972635269165 448.4265441894531 0.5700054168701172 578.31005859375 0.7968271374702454 0.72626895 0.7473869323730469 True -17 47196 28.435582399368286 0.5136218070983887 408.13006591796875 0.4023641347885132 579.06103515625 0.7962293028831482 0.7263488 0.7631109952926636 True -18 49818 28.367199182510376 0.5079362392425537 465.64801025390625 0.6631752252578735 579.5947875976562 0.7959152460098267 0.72597426 0.7739905714988708 False -19 52440 28.811842679977417 23.12438201904297 359.338623046875 0.6338133811950684 579.9119262695312 0.7955197095870972 0.7244361 0.7856120467185974 False diff --git a/ENCSR830ALP/cherimoya.fold_0.performance.tsv b/ENCSR830ALP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 133b925a329c56b543b1404631ff0c193b9afa7e..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -579.06103515625 0.1804615557193756 0.7962293028831482 0.3819812834262848 0.7263488173484802 0.6827640533447266 0.7631109952926636 \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_1.evaluate.json b/ENCSR830ALP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 78e38e3da647324390af9183d2e71ea09823213d..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF667FMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_1.fit.json b/ENCSR830ALP/cherimoya.fold_1.fit.json deleted file mode 100644 index aa5e942288cdf49d4272e64898f42fc3be9e943d..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF667FMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_1.log b/ENCSR830ALP/cherimoya.fold_1.log deleted file mode 100644 index 260bf381875981b139ecf6453de16b6679bba1fe..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2618 33.36274981498718 3.8008105754852295 480.00262451171875 1.3793723583221436 1006.6328735351562 0.6069937944412231 0.5694991 15.244966506958008 True -1 5236 28.90622568130493 0.9213230609893799 447.82623291015625 1.505516529083252 751.0188598632812 0.7503748536109924 0.64998454 5.76774263381958 True -2 7854 28.91489005088806 1.545374870300293 567.718505859375 1.5362398624420166 718.3754272460938 0.7655317783355713 0.6375333 2.161978006362915 False -3 10472 28.91353178024292 0.7185463905334473 548.994140625 1.0565447807312012 702.5758666992188 0.7744143605232239 0.64483523 1.6058409214019775 False -4 13090 28.967267990112305 1.4212632179260254 507.1578063964844 0.962110161781311 698.4489135742188 0.7773183584213257 0.6498543 1.5130904912948608 False -5 15708 29.735323429107666 4.75467848777771 422.19482421875 1.1199994087219238 690.146240234375 0.7822595238685608 0.6716327 1.2871490716934204 True -6 18326 28.90364909172058 0.8148019313812256 559.4185180664062 0.84742271900177 684.4056396484375 0.7862469553947449 0.6777207 1.1917082071304321 True -7 20944 28.68571972846985 36.29453110694885 384.1866760253906 0.6988680958747864 680.1621704101562 0.7881839275360107 0.6794549 1.1517647504806519 True -8 23562 28.328665256500244 32.10727500915527 609.1843872070312 0.9914029240608215 673.6070556640625 0.7919427156448364 0.69011515 1.0376098155975342 True -9 26180 28.53787922859192 0.7187871932983398 421.16973876953125 0.878148078918457 670.0841674804688 0.7945213317871094 0.6894703 0.9593489170074463 False -10 28798 28.293206930160522 0.7098469734191895 406.6107177734375 1.1186044216156006 663.3759155273438 0.7978684306144714 0.7035111 0.9101060032844543 True -11 31416 28.331239700317383 0.7151823043823242 402.66510009765625 0.7512894868850708 658.4502563476562 0.8005409240722656 0.7077991 0.8969767093658447 True -12 34034 28.762529373168945 0.691382646560669 393.02618408203125 0.6694798469543457 654.34521484375 0.8031314015388489 0.71883017 0.8527137637138367 True -13 36652 28.34847354888916 0.6980118751525879 453.51251220703125 1.1063880920410156 650.9509887695312 0.8051810264587402 0.72595346 0.824135959148407 True -14 39270 28.343244075775146 0.6975874900817871 384.12066650390625 0.7795122265815735 647.5514526367188 0.8070589900016785 0.73533076 0.8053492307662964 True -15 41888 28.330411195755005 0.7007052898406982 522.8775634765625 0.7710136771202087 645.6361694335938 0.8078051209449768 0.74535805 0.7838045358657837 True -16 44506 28.370899438858032 0.7025146484375 392.13641357421875 0.6252537965774536 645.1097412109375 0.8082427382469177 0.7498264 0.7746437191963196 True -17 47124 28.351025342941284 0.7157576084136963 408.20477294921875 0.5594529509544373 645.3435668945312 0.8079372644424438 0.74832314 0.7945736646652222 False -18 49742 28.394346475601196 0.6925103664398193 494.9751892089844 0.5699375867843628 646.0027465820312 0.8075258135795593 0.7467597 0.8011924028396606 False -19 52360 28.57268452644348 23.923234224319458 319.63531494140625 0.6035188436508179 646.6325073242188 0.8072224855422974 0.7454632 0.8135082125663757 False diff --git a/ENCSR830ALP/cherimoya.fold_1.performance.tsv b/ENCSR830ALP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7c13754cb4381082e39c9f37c59ff4dd8b1ba22f..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -645.1097412109375 0.16839465498924255 0.808242678642273 0.4111596643924713 0.7498263716697693 0.725409984588623 0.7746437191963196 \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_2.evaluate.json b/ENCSR830ALP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a66ed017960ddce58a0aa020be4f762daec0c39f..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF667FMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_2.fit.json b/ENCSR830ALP/cherimoya.fold_2.fit.json deleted file mode 100644 index b4ff1e978a8b13c6ceb2112f8dc0e6115a433f63..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF667FMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_2.log b/ENCSR830ALP/cherimoya.fold_2.log deleted file mode 100644 index 8e51204568becc828b58397603148228d00903dd..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2812 35.45408058166504 3.831977128982544 600.5181274414062 1.3238487243652344 908.5999145507812 0.6058835387229919 0.55966306 10.577681541442871 True -1 5624 31.09173846244812 0.5389904975891113 465.4989013671875 1.2357563972473145 692.6809692382812 0.7437145113945007 0.6504001 4.481112003326416 True -2 8436 30.543440341949463 0.5161492824554443 488.1033935546875 1.3031210899353027 663.9456787109375 0.7558685541152954 0.64418286 1.756519079208374 False -3 11248 30.438273668289185 0.5141439437866211 625.0653076171875 1.5671571493148804 648.25634765625 0.764508068561554 0.6548215 1.308163046836853 True -4 14060 30.458826065063477 0.5098567008972168 519.3375244140625 1.4268290996551514 641.5523681640625 0.7691090703010559 0.65808916 1.1320420503616333 True -5 16872 30.45556330680847 0.5124228000640869 481.77056884765625 1.639549732208252 636.0571899414062 0.7716588377952576 0.6704752 1.089424967765808 True -6 19684 30.55664849281311 0.5194122791290283 471.6441650390625 0.8875761032104492 633.8800659179688 0.774601936340332 0.67289263 1.053848147392273 True -7 22496 30.609198570251465 0.527707576751709 469.0823974609375 1.1105941534042358 629.2192993164062 0.7777783274650574 0.67879224 0.9646654725074768 True -8 25308 30.784103631973267 0.5304334163665771 491.17620849609375 0.7683948278427124 623.3929443359375 0.7812873721122742 0.6816577 0.9100888967514038 True -9 28120 30.533538341522217 0.5117323398590088 575.84228515625 0.7566515207290649 619.106201171875 0.7839317321777344 0.689482 0.884615957736969 True -10 30932 30.577892065048218 0.5217556953430176 435.3677978515625 0.8040887117385864 614.5374755859375 0.786956250667572 0.6977103 0.8434451222419739 True -11 33744 30.638201475143433 0.5114874839782715 493.2297058105469 0.9277928471565247 610.8515014648438 0.7894733548164368 0.7081859 0.8170109987258911 True -12 36556 30.726317167282104 0.5252377986907959 432.96478271484375 1.1381807327270508 607.5637817382812 0.7919560670852661 0.71543294 0.8008952736854553 True -13 39368 30.522554397583008 0.5241360664367676 415.7410888671875 0.9469848275184631 603.16015625 0.7940179109573364 0.7220561 0.7759552001953125 True -14 42180 30.498446941375732 0.5241446495056152 403.45196533203125 0.6306162476539612 600.6807861328125 0.7958870530128479 0.7310989 0.7580281496047974 True -15 44992 31.350857734680176 21.027889013290405 559.4732666015625 0.8104287385940552 598.9554443359375 0.7967500686645508 0.7392517 0.7486168146133423 True -16 47804 31.59573245048523 0.5219602584838867 448.5801086425781 0.7345356941223145 598.6087646484375 0.7971670627593994 0.7399989 0.7462908625602722 True -17 50616 30.440670251846313 0.5222711563110352 457.94781494140625 0.6478113532066345 599.1881103515625 0.7968699932098389 0.7415013 0.7554657459259033 True -18 53428 30.433777809143066 1.577561616897583 553.9614868164062 0.5666022300720215 599.9147338867188 0.7963557839393616 0.7408205 0.771312952041626 False -19 56240 30.565157413482666 0.5162603855133057 479.49981689453125 0.46453261375427246 600.5284423828125 0.7960110306739807 0.73920286 0.779454231262207 False diff --git a/ENCSR830ALP/cherimoya.fold_2.performance.tsv b/ENCSR830ALP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 81ce3ab7958d03d619b28367f4a8f0696ed71649..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -599.1881103515625 0.1787511110305786 0.7968699932098389 0.39026862382888794 0.7415012717247009 0.7046071887016296 0.7554657459259033 \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_3.evaluate.json b/ENCSR830ALP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9982549f3cbc0af3c3942ea1e8f4ac61661b0a5c..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF667FMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_3.fit.json b/ENCSR830ALP/cherimoya.fold_3.fit.json deleted file mode 100644 index 888f911f3dfefe27572d8d4136c87b4e25b3baeb..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF667FMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_3.log b/ENCSR830ALP/cherimoya.fold_3.log deleted file mode 100644 index 6ab2644625bdd8d247c93b61ffc4efb83631be3e..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2701 33.94845509529114 3.586982250213623 630.830322265625 1.4610862731933594 889.7061767578125 0.6043526530265808 0.5393844 10.949016571044922 True -1 5402 29.84076952934265 0.5826826095581055 563.8775634765625 0.8113330602645874 673.832275390625 0.7441935539245605 0.596819 4.773806571960449 True -2 8103 29.790336847305298 0.5506570339202881 420.8047180175781 0.9909107685089111 651.2756958007812 0.7547555565834045 0.59123605 1.9127240180969238 False -3 10804 29.819169282913208 0.5508308410644531 453.55450439453125 1.0283156633377075 639.4251098632812 0.761884331703186 0.6007022 1.4180809259414673 True -4 13505 29.78714418411255 0.562950849533081 401.1228942871094 1.3984284400939941 634.8106689453125 0.765898585319519 0.60388243 1.2941420078277588 True -5 16206 29.77240300178528 0.548579216003418 412.5070495605469 1.1567325592041016 630.576904296875 0.7699785232543945 0.6124039 1.2072889804840088 True -6 18907 29.80816102027893 0.576636791229248 459.75146484375 1.010977029800415 626.6463012695312 0.7723949551582336 0.6199406 1.121703028678894 True -7 21608 30.1655375957489 13.743537664413452 481.44744873046875 1.2948098182678223 622.2149658203125 0.7756127119064331 0.624082 1.0760538578033447 True -8 24309 29.84578275680542 1.8487918376922607 443.8327331542969 0.9659541845321655 618.5543212890625 0.7782849073410034 0.63468164 1.03217351436615 True -9 27010 29.945817232131958 1.6058063507080078 463.9557800292969 0.9875680804252625 614.9500732421875 0.7809436321258545 0.64680624 0.9796399474143982 True -10 29711 29.871052026748657 1.9912574291229248 515.3548583984375 0.9061744809150696 610.751953125 0.7839046716690063 0.6523531 0.9512815475463867 True -11 32412 29.805663585662842 9.734976768493652 460.9086608886719 0.7797979116439819 607.1672973632812 0.7864723205566406 0.6616745 0.9107961058616638 True -12 35113 30.8617205619812 18.255499362945557 545.26904296875 0.7487573623657227 604.01025390625 0.7889487743377686 0.6736638 0.8970708250999451 True -13 37814 29.914466857910156 0.571934700012207 399.4489440917969 0.8018372058868408 600.787109375 0.7909226417541504 0.6860542 0.8650810718536377 True -14 40515 29.827746868133545 7.093581438064575 430.6605224609375 0.7047058939933777 598.584228515625 0.7925006747245789 0.69664973 0.8526014685630798 True -15 43216 29.806941747665405 0.5599668025970459 392.11248779296875 0.5818147659301758 597.1927490234375 0.7934779524803162 0.7066387 0.842714786529541 True -16 45917 29.80241370201111 0.5576317310333252 461.12823486328125 0.7285655736923218 595.3115844726562 0.7939775586128235 0.7127069 0.8357790112495422 True -17 48618 29.851797342300415 0.5552551746368408 419.82318115234375 0.471586138010025 595.3137817382812 0.7938474416732788 0.71940345 0.8487198352813721 True -18 51319 29.811955213546753 1.7355139255523682 451.6158447265625 0.5992615222930908 596.1034545898438 0.793290913105011 0.71882164 0.8599103689193726 False -19 54020 29.250195026397705 0.5460715293884277 439.8848571777344 0.500431478023529 596.4404296875 0.7930098176002502 0.71603364 0.8689801096916199 False diff --git a/ENCSR830ALP/cherimoya.fold_3.performance.tsv b/ENCSR830ALP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 21be5d144f5397954195da347eea6ba19cbbdc50..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -595.3137817382812 0.1792674958705902 0.7938474416732788 0.385414183139801 0.7194034457206726 0.6838789582252502 0.8487198352813721 \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_4.evaluate.json b/ENCSR830ALP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 72f365b32fda3f3adcdd8b4a4f0ddb5fc0da44c2..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF667FMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_4.fit.json b/ENCSR830ALP/cherimoya.fold_4.fit.json deleted file mode 100644 index 01c9c7816f6b6f21dac906d3dabd6a88e1519124..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF667FMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR830ALP/cherimoya.fold_4.log b/ENCSR830ALP/cherimoya.fold_4.log deleted file mode 100644 index f96390eccb9d3cd6f6b80706eac785967c4f9c9a..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2710 34.358762979507446 3.4133799076080322 533.9970703125 1.3533660173416138 851.0397338867188 0.6020192503929138 0.5348311 10.888060569763184 True -1 5420 30.200953006744385 1.2373759746551514 577.7569580078125 1.5248234272003174 654.5630493164062 0.7377139329910278 0.608532 5.762406826019287 True -2 8130 29.87777853012085 0.48856306076049805 615.0557250976562 1.2203664779663086 625.2412109375 0.7519906163215637 0.5937061 2.2074012756347656 False -3 10840 30.012874364852905 28.251612424850464 510.9274597167969 1.1953421831130981 614.5474853515625 0.759585440158844 0.60390526 1.5477927923202515 False -4 13550 30.05551314353943 0.4916996955871582 452.511962890625 1.5105016231536865 607.264404296875 0.7638246417045593 0.60238105 1.2629508972167969 False -5 16260 29.960564613342285 0.4886958599090576 452.95465087890625 0.9368289113044739 601.689208984375 0.7673028707504272 0.6114377 1.1037037372589111 True -6 18970 29.993372678756714 0.48238539695739746 470.94049072265625 1.0229088068008423 597.4918212890625 0.7708751559257507 0.6176265 1.0647010803222656 True -7 21680 29.85269260406494 1.228269338607788 519.17333984375 1.3630077838897705 594.8078002929688 0.7733402848243713 0.6227553 1.0256389379501343 True -8 24390 29.912364721298218 0.5013120174407959 505.8388671875 1.2310404777526855 590.0358276367188 0.7769069671630859 0.6325335 0.974777340888977 True -9 27100 30.33489751815796 0.48974132537841797 486.12530517578125 0.9526853561401367 586.5946655273438 0.7794464826583862 0.64050967 0.9445130228996277 True -10 29810 29.88761806488037 0.49379420280456543 390.3939208984375 0.830437421798706 582.6362915039062 0.7823895215988159 0.6477581 0.9250246286392212 True -11 32520 29.912604808807373 0.48529529571533203 419.17236328125 0.9018280506134033 578.8563842773438 0.7852579355239868 0.6579481 0.8868111968040466 True -12 35230 29.94100856781006 0.49474120140075684 404.57843017578125 1.0242799520492554 575.8743896484375 0.7879632115364075 0.6689473 0.8679547905921936 True -13 37940 29.923386573791504 0.4967958927154541 455.7923278808594 0.9416807889938354 572.6364135742188 0.7900248765945435 0.67903405 0.8466299772262573 True -14 40650 30.297905683517456 24.7790846824646 396.5584716796875 0.6998412609100342 570.1700439453125 0.7917598485946655 0.6918639 0.8242882490158081 True -15 43360 30.020465850830078 0.4951591491699219 493.6497802734375 0.7070655822753906 568.935546875 0.7924247980117798 0.70130485 0.8059806227684021 True -16 46070 29.925076246261597 1.9485082626342773 477.5605773925781 0.5714328289031982 568.0756225585938 0.79278564453125 0.70613587 0.7973029017448425 True -17 48780 29.98344397544861 0.4906439781188965 427.54583740234375 0.5627981424331665 568.1356201171875 0.7927920818328857 0.7070795 0.805498480796814 True -18 51490 29.66875457763672 0.4862356185913086 370.5215148925781 0.6844373941421509 568.633544921875 0.7922834753990173 0.70319825 0.8251232504844666 False -19 54200 29.41450595855713 0.4969327449798584 396.1145324707031 0.7373816967010498 568.7057495117188 0.7920445203781128 0.70330316 0.8307873010635376 False diff --git a/ENCSR830ALP/cherimoya.fold_4.performance.tsv b/ENCSR830ALP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8832d860706c8ca8caf6f1f573a1cfcd1ef2a412..0000000000000000000000000000000000000000 --- a/ENCSR830ALP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -568.1356201171875 0.18408535420894623 0.7927921414375305 0.37366610765457153 0.7070795297622681 0.6588253378868103 0.805498480796814 \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_0.evaluate.json b/ENCSR831KAH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a4567acd87209a9045c87e0f7bd2a8966b3c838d..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925ZRY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_0.fit.json b/ENCSR831KAH/cherimoya.fold_0.fit.json deleted file mode 100644 index 22210ab1a72d1055bc02bf01739d68b5b92e8056..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF925ZRY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_0.log b/ENCSR831KAH/cherimoya.fold_0.log deleted file mode 100644 index b592c5f29819948fe663f70739b9574c826b8624..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1026 18.617226600646973 22.593286275863647 235.10809326171875 0.19653970003128052 326.1416320800781 0.3824422061443329 0.69266284 16.679174423217773 True -1 2052 11.707358360290527 0.22755813598632812 230.49270629882812 0.24390621483325958 273.358642578125 0.461189866065979 0.7427649 5.077082633972168 True -2 3078 11.293616533279419 0.21848559379577637 215.99755859375 0.14104227721691132 260.3778076171875 0.4934566020965576 0.77245784 1.2926099300384521 True -3 4104 11.28528380393982 0.21273350715637207 201.14413452148438 0.17768196761608124 252.0327911376953 0.5134267210960388 0.7917812 0.3192756474018097 True -4 5130 12.227577924728394 14.990953922271729 204.92098999023438 0.2873994708061218 248.39987182617188 0.5228599309921265 0.8047643 0.22308777272701263 True -5 6156 12.741061210632324 10.474518299102783 199.07333374023438 0.14329078793525696 247.12734985351562 0.5267927646636963 0.81529355 0.19092555344104767 True -6 7182 11.356810808181763 1.766190528869629 222.95291137695312 0.11036468297243118 246.1626739501953 0.5297186374664307 0.8234158 0.16850730776786804 True -7 8208 11.269116640090942 0.2159595489501953 193.97523498535156 0.14469650387763977 245.6642303466797 0.5314431190490723 0.8296617 0.16421526670455933 True -8 9234 11.290204763412476 0.21397662162780762 188.68482971191406 0.1912812888622284 245.25450134277344 0.5328472256660461 0.833474 0.15083397924900055 True -9 10260 11.286358118057251 0.2167043685913086 196.23486328125 0.18323077261447906 245.1078643798828 0.5331019759178162 0.83340716 0.16590198874473572 False -10 11286 11.187154293060303 0.21395134925842285 214.53211975097656 0.14791789650917053 244.6403045654297 0.5348492860794067 0.84220254 0.15109656751155853 True -11 12312 11.062430381774902 0.21001815795898438 211.71298217773438 0.11507716029882431 244.30734252929688 0.5361666679382324 0.8495918 0.13972295820713043 True -12 13338 11.072947263717651 0.20870566368103027 206.39498901367188 0.1068202406167984 244.1224822998047 0.5368530750274658 0.8535039 0.12907835841178894 True -13 14364 11.077948808670044 0.2162494659423828 197.59872436523438 0.2064512073993683 243.9061737060547 0.5372966527938843 0.85688436 0.1219693198800087 True -14 15390 11.080970048904419 0.21168994903564453 204.503662109375 0.0935516357421875 243.91928100585938 0.5372684597969055 0.85888755 0.11994421482086182 True -15 16416 11.04021692276001 0.21123981475830078 203.7745819091797 0.07160359621047974 244.03750610351562 0.5365551710128784 0.8608488 0.11953436583280563 True -16 17442 11.02952766418457 0.20915675163269043 208.4662628173828 0.07946432381868362 244.35177612304688 0.5350967645645142 0.8603445 0.1214856281876564 False -17 18468 11.058345317840576 0.6287956237792969 215.2954559326172 0.06625453382730484 244.7315673828125 0.5334500670433044 0.8564266 0.12499342858791351 False -18 19494 11.06049132347107 0.21288776397705078 203.45462036132812 0.08115553110837936 245.13525390625 0.5317370295524597 0.8557003 0.1281648427248001 False -19 20520 11.09033203125 0.21034526824951172 209.6212158203125 0.08451882004737854 245.40045166015625 0.5305783748626709 0.8551236 0.13073264062404633 False diff --git a/ENCSR831KAH/cherimoya.fold_0.performance.tsv b/ENCSR831KAH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1317f718ecd838ac1dc068508973d15f18407572..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -244.03750610351562 0.3622858226299286 0.5365551710128784 0.166327103972435 0.8608487844467163 0.8336536288261414 0.11953436583280563 \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_1.evaluate.json b/ENCSR831KAH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7ed95b774c60b4ceeb37e6beb4767605be2ffda1..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925ZRY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_1.fit.json b/ENCSR831KAH/cherimoya.fold_1.fit.json deleted file mode 100644 index 4a34b9c75dbbf24a4faa6c2aee546a4b5c55b21d..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF925ZRY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_1.log b/ENCSR831KAH/cherimoya.fold_1.log deleted file mode 100644 index 14bdbeb7f0f4819ca33cf8b765b3946dc7f0cd27..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1003 15.512071132659912 3.2091877460479736 211.38470458984375 0.22060389816761017 357.5091552734375 0.391143798828125 0.6173583 17.543424606323242 True -1 2006 11.041305303573608 0.27579689025878906 216.85626220703125 0.2562854290008545 301.3739013671875 0.47017571330070496 0.68104935 5.2275567054748535 True -2 3009 11.068249225616455 0.274463415145874 219.80947875976562 0.3696589469909668 284.2975769042969 0.5036998987197876 0.7172355 1.3368546962738037 True -3 4012 11.02493929862976 0.27502989768981934 210.17697143554688 0.16111880540847778 274.4899597167969 0.5270794630050659 0.74628013 0.43956124782562256 True -4 5015 11.101675271987915 0.2685842514038086 212.04733276367188 0.17576955258846283 269.6556701660156 0.5398378968238831 0.76358086 0.2356736958026886 True -5 6018 11.016422986984253 0.2747511863708496 242.71792602539062 0.19392022490501404 267.7572021484375 0.5449031591415405 0.7741833 0.2128671407699585 True -6 7021 11.032404661178589 8.533936738967896 196.35955810546875 0.14529427886009216 270.155517578125 0.5368344783782959 0.7482145 0.2511433959007263 False -7 8024 12.992860078811646 8.082812786102295 212.39889526367188 0.21966135501861572 267.9668273925781 0.5443232655525208 0.7691714 0.2128249704837799 False -8 9027 11.04922103881836 0.28016161918640137 174.50161743164062 0.1427885740995407 266.8046875 0.5483602285385132 0.78672934 0.19194446504116058 True -9 10030 11.072373390197754 0.26785755157470703 210.53585815429688 0.19436274468898773 266.0990295410156 0.5512338876724243 0.79742986 0.17926077544689178 True -10 11033 11.020788669586182 0.27228403091430664 201.82537841796875 0.15643320977687836 265.6875 0.5527470707893372 0.8064749 0.16870322823524475 True -11 12036 11.061702251434326 1.4244649410247803 216.8975830078125 0.1464802622795105 265.2148742675781 0.554397463798523 0.8148625 0.15929381549358368 True -12 13039 11.073458671569824 0.27019453048706055 219.6954345703125 0.11787992715835571 264.7244567871094 0.5559682846069336 0.8220621 0.1487458199262619 True -13 14042 11.081992387771606 0.5286638736724854 207.89297485351562 0.11276274174451828 264.4396057128906 0.5566585659980774 0.82589275 0.14356762170791626 True -14 15045 11.088176488876343 1.771423101425171 191.13290405273438 0.10271517932415009 264.3035888671875 0.5567178726196289 0.8328196 0.13938415050506592 True -15 16048 11.059678316116333 0.2783513069152832 218.08470153808594 0.09495961666107178 264.4105529785156 0.5559965372085571 0.83628535 0.13628411293029785 True -16 17051 11.07058835029602 0.2830193042755127 199.30636596679688 0.07678984105587006 264.6889343261719 0.5545571446418762 0.8374729 0.1359197348356247 True -17 18054 11.053353786468506 0.2711944580078125 198.04283142089844 0.06609553843736649 265.187255859375 0.5525342226028442 0.8358443 0.13669896125793457 False -18 19057 11.056760311126709 7.4050915241241455 209.70233154296875 0.07251517474651337 265.6189880371094 0.5506744384765625 0.83635104 0.13649186491966248 False -19 20060 11.482141017913818 0.27716994285583496 209.86383056640625 0.07019615173339844 265.9156188964844 0.5494447350502014 0.83590734 0.13804416358470917 False diff --git a/ENCSR831KAH/cherimoya.fold_1.performance.tsv b/ENCSR831KAH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 64a84dc1748c68564409fc2999913f539a3bd8fe..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -264.6889343261719 0.3468584418296814 0.5545571446418762 0.1774880588054657 0.8374729156494141 0.8307604789733887 0.1359197348356247 \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_2.evaluate.json b/ENCSR831KAH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 61faf5489eec6d1946f5ef6dbc834295c510972a..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925ZRY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_2.fit.json b/ENCSR831KAH/cherimoya.fold_2.fit.json deleted file mode 100644 index b2b6b7ee5ab27d97d9a5ac85083f0c7617ad7e71..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF925ZRY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_2.log b/ENCSR831KAH/cherimoya.fold_2.log deleted file mode 100644 index 3cbf6d0186df5d8a25ac7bcf64aa19397fa7b7e0..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1065 16.142945051193237 3.259326696395874 211.5147705078125 0.23827826976776123 333.0747985839844 0.38812851905822754 0.6475479 16.283449172973633 True -1 2130 11.728786706924438 1.0859606266021729 211.7715606689453 0.14701110124588013 280.6747131347656 0.4661754369735718 0.7202126 4.054886341094971 True -2 3195 11.713898181915283 0.21867895126342773 215.5870361328125 0.22289374470710754 266.09808349609375 0.5000985860824585 0.76664996 0.9804497957229614 True -3 4260 11.692800998687744 0.21983623504638672 207.732177734375 0.2357960045337677 258.15069580078125 0.5187720060348511 0.78911006 0.29801496863365173 True -4 5325 11.696883916854858 0.21991896629333496 201.80221557617188 0.3503521680831909 254.78408813476562 0.5268890261650085 0.80208176 0.25051775574684143 True -5 6390 11.680006980895996 7.005743980407715 224.0220184326172 0.2248624712228775 253.64410400390625 0.5300095677375793 0.8086358 0.1748199313879013 True -6 7455 12.008553981781006 7.641876459121704 218.13265991210938 0.2188936471939087 253.35519409179688 0.5311166048049927 0.81254035 0.15500980615615845 True -7 8520 11.686551809310913 0.21935510635375977 211.7135009765625 0.1402369737625122 252.86544799804688 0.5326216220855713 0.8177408 0.15200309455394745 True -8 9585 11.693567037582397 1.1820979118347168 222.92213439941406 0.20939205586910248 252.4824981689453 0.534449577331543 0.8211108 0.15030504763126373 True -9 10650 11.698671579360962 0.21881866455078125 218.1693878173828 0.18670612573623657 251.84642028808594 0.5364394783973694 0.82798487 0.1457979530096054 True -10 11715 11.690277338027954 0.21643352508544922 208.5752716064453 0.14648102223873138 251.43994140625 0.5379217863082886 0.8328633 0.13961565494537354 True -11 12780 11.758047342300415 0.7972016334533691 187.67568969726562 0.11372913420200348 250.98870849609375 0.539057731628418 0.83735585 0.1328396201133728 True -12 13845 11.746060848236084 0.21701931953430176 208.41354370117188 0.13221639394760132 250.68386840820312 0.5400922894477844 0.8410042 0.13087144494056702 True -13 14910 11.720852613449097 0.21868419647216797 199.30136108398438 0.10856515169143677 250.4866943359375 0.5405817627906799 0.84307694 0.1306448131799698 True -14 15975 11.703344821929932 0.21753573417663574 203.66189575195312 0.11610834300518036 250.48028564453125 0.5402616858482361 0.84646976 0.13013578951358795 True -15 17040 11.69747018814087 0.2153458595275879 223.3231201171875 0.12965820729732513 250.57249450683594 0.5396201014518738 0.84526354 0.13058538734912872 False -16 18105 11.715077638626099 10.003047704696655 209.88609313964844 0.09077610820531845 250.89939880371094 0.5381429195404053 0.8463444 0.13236530125141144 False -17 19170 12.336837530136108 16.412599563598633 199.9980010986328 0.10218298435211182 251.33311462402344 0.5362327694892883 0.8459279 0.1349819004535675 False -18 20235 11.944420337677002 0.21987342834472656 188.98406982421875 0.08468690514564514 251.7913360595703 0.5342822670936584 0.84379005 0.1371496319770813 False -19 21300 11.434964895248413 0.21754908561706543 201.81793212890625 0.10357288271188736 252.09310913085938 0.53294438123703 0.840847 0.13993924856185913 False diff --git a/ENCSR831KAH/cherimoya.fold_2.performance.tsv b/ENCSR831KAH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9df54f6c5d77cd6b7c44658a4c9f6cfdfd84d791..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.48028564453125 0.35864073038101196 0.5402616858482361 0.17004920542240143 0.8464697599411011 0.8305315971374512 0.13013578951358795 \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_3.evaluate.json b/ENCSR831KAH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a7e1c6ab5e865bfd6b6e2ca567d86dae1660402c..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925ZRY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_3.fit.json b/ENCSR831KAH/cherimoya.fold_3.fit.json deleted file mode 100644 index d00aabbb9e790bf5d95fbe90181190dbcae7ca1d..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF925ZRY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_3.log b/ENCSR831KAH/cherimoya.fold_3.log deleted file mode 100644 index f01b3ff0d3931a50eab704d74f96d4bc555dd2cb..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1046 17.410747528076172 3.1355161666870117 227.0100555419922 0.21921196579933167 328.6058044433594 0.3845861554145813 0.6668364 16.389728546142578 True -1 2092 11.546528577804565 0.20937395095825195 228.54251098632812 0.1349944770336151 276.04425048828125 0.46349412202835083 0.7224539 4.639372825622559 True -2 3138 11.51664137840271 0.3379032611846924 231.456787109375 0.2684263288974762 263.6438903808594 0.495600163936615 0.7590696 1.0878568887710571 True -3 4184 11.95716905593872 0.20879507064819336 202.5474395751953 0.21062704920768738 255.17181396484375 0.515837550163269 0.77554446 0.4809369742870331 True -4 5230 11.498643159866333 0.2027597427368164 223.73858642578125 0.18582330644130707 250.91139221191406 0.5258355736732483 0.78747267 0.2421250343322754 True -5 6276 11.535066604614258 0.20284080505371094 188.9512939453125 0.15220198035240173 249.80384826660156 0.5283741354942322 0.7966797 0.18470431864261627 True -6 7322 11.501577854156494 0.2024247646331787 192.17721557617188 0.1461436152458191 249.27413940429688 0.5305101871490479 0.80138576 0.17640891671180725 True -7 8368 11.58406949043274 0.2100675106048584 222.50830078125 0.13548198342323303 248.61749267578125 0.5330625772476196 0.80965495 0.16933463513851166 True -8 9414 11.487112045288086 0.2118523120880127 219.85153198242188 0.14207831025123596 248.19729614257812 0.5342479348182678 0.81588024 0.16746172308921814 True -9 10460 11.49250054359436 0.20740175247192383 203.83981323242188 0.10906563699245453 247.94898986816406 0.5353489518165588 0.82071453 0.16251380741596222 True -10 11506 11.490864038467407 0.21146726608276367 203.69131469726562 0.12717872858047485 247.53228759765625 0.5369510650634766 0.8245673 0.15364354848861694 True -11 12552 11.511841535568237 0.2025446891784668 217.81671142578125 0.13069556653499603 247.2860565185547 0.5378036499023438 0.8277074 0.14637593924999237 True -12 13598 11.520203590393066 0.24402832984924316 215.64401245117188 0.14236238598823547 247.12791442871094 0.538519024848938 0.8308049 0.14371135830879211 True -13 14644 11.520647048950195 0.2085731029510498 208.78411865234375 0.12269489467144012 246.9642791748047 0.5389761924743652 0.8317592 0.1418931484222412 True -14 15690 11.514206647872925 0.2035224437713623 193.19627380371094 0.11277174204587936 246.9512176513672 0.538955569267273 0.83324 0.1423409879207611 True -15 16736 11.497562170028687 0.20328927040100098 188.7318878173828 0.11937601119279861 247.16131591796875 0.5381054878234863 0.8316414 0.1449328362941742 False -16 17782 11.505735158920288 0.20388126373291016 191.2904052734375 0.08871640264987946 247.4423828125 0.536550760269165 0.83105004 0.1469161957502365 False -17 18828 11.53793478012085 1.7662055492401123 204.50877380371094 0.09787814319133759 247.81863403320312 0.5347236394882202 0.82975096 0.15010084211826324 False -18 19874 11.640810489654541 0.20677924156188965 195.44419860839844 0.0679045170545578 248.3297576904297 0.532820463180542 0.8276216 0.15302784740924835 False -19 20920 11.499994277954102 0.20405292510986328 188.93310546875 0.10871894657611847 248.63360595703125 0.5316122174263 0.8253445 0.15554291009902954 False diff --git a/ENCSR831KAH/cherimoya.fold_3.performance.tsv b/ENCSR831KAH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9eada1b360a06f41380969f534e76717ea7e5573..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -246.9512176513672 0.36022934317588806 0.538955569267273 0.16819995641708374 0.8332399725914001 0.8201005458831787 0.1423409879207611 \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_4.evaluate.json b/ENCSR831KAH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8668542a21a2627759787b6e9001f98d546da5ac..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925ZRY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_4.fit.json b/ENCSR831KAH/cherimoya.fold_4.fit.json deleted file mode 100644 index fbb48b289416052481eaeaf595a419ae3114bb12..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF925ZRY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831KAH/cherimoya.fold_4.log b/ENCSR831KAH/cherimoya.fold_4.log deleted file mode 100644 index eb6f67c96f01bc718c71df2db38a5040bf3a936e..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1031 15.778038501739502 3.065088987350464 213.945068359375 0.3342247009277344 317.5154113769531 0.38188380002975464 0.68972385 16.47684669494629 True -1 2062 11.33249020576477 0.7141499519348145 227.54803466796875 0.20152291655540466 266.7325134277344 0.4584108591079712 0.7353225 4.701655864715576 True -2 3093 11.334245681762695 0.20760226249694824 205.64572143554688 0.23038682341575623 255.18460083007812 0.4875006675720215 0.76672024 1.046062707901001 True -3 4124 11.318479061126709 0.20627522468566895 210.57705688476562 0.17177128791809082 247.0828399658203 0.5070874094963074 0.79757404 0.29789718985557556 True -4 5155 11.328782796859741 0.2022106647491455 238.65200805664062 0.23788326978683472 243.74301147460938 0.5154958367347717 0.8153739 0.22914010286331177 True -5 6186 11.303890228271484 0.40178561210632324 207.80995178222656 0.18109475076198578 242.6541290283203 0.517456591129303 0.8170667 0.1948249489068985 True -6 7217 11.30459451675415 0.2016136646270752 185.44761657714844 0.16635406017303467 241.45147705078125 0.5213488936424255 0.830839 0.14083218574523926 True -7 8248 11.315122365951538 0.2030324935913086 197.90145874023438 0.1953839659690857 241.0649871826172 0.5223108530044556 0.8392897 0.13545528054237366 True -8 9279 11.330599546432495 0.20255374908447266 218.2086181640625 0.10839630663394928 240.8377685546875 0.5232376456260681 0.84468055 0.13065558671951294 True -9 10310 11.314488410949707 0.20596098899841309 253.3414306640625 0.1523861289024353 240.6094207763672 0.5240758061408997 0.8489584 0.126543790102005 True -10 11341 11.333333015441895 0.20666885375976562 204.37742614746094 0.14128831028938293 240.3060760498047 0.5251695513725281 0.85346776 0.12207401543855667 True -11 12372 11.341349124908447 0.20985126495361328 214.6549530029297 0.13742636144161224 240.06478881835938 0.5260704159736633 0.86121684 0.11512027680873871 True -12 13403 11.378788232803345 0.21110868453979492 183.73776245117188 0.10397326946258545 239.87786865234375 0.5267925262451172 0.8611144 0.11477494984865189 False -13 14434 11.365813255310059 0.2037978172302246 211.96128845214844 0.12055771052837372 239.68214416503906 0.5274796485900879 0.86391884 0.11106687784194946 True -14 15465 11.417433977127075 0.20775485038757324 191.83340454101562 0.12778523564338684 239.72019958496094 0.5273743867874146 0.86516476 0.10829506814479828 True -15 16496 11.396390676498413 0.20665192604064941 222.11380004882812 0.1275882124900818 239.77879333496094 0.5270037055015564 0.868016 0.1070256158709526 True -16 17527 11.388391494750977 0.3919517993927002 229.41439819335938 0.08473842591047287 240.1344451904297 0.5258163809776306 0.8674838 0.1087120845913887 False -17 18558 11.504018545150757 0.21184539794921875 193.93826293945312 0.06031380593776703 240.52783203125 0.5241243839263916 0.8674325 0.1108676865696907 False -18 19589 11.408961296081543 0.20504021644592285 202.68955993652344 0.05974961072206497 240.9560089111328 0.5224692225456238 0.8654233 0.11260423809289932 False -19 20620 11.404796600341797 0.20811080932617188 199.3206787109375 0.06470314413309097 241.25064086914062 0.5212647318840027 0.8650799 0.11538251489400864 False diff --git a/ENCSR831KAH/cherimoya.fold_4.performance.tsv b/ENCSR831KAH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f5f53c71af5d0d386c2012c1f3c3315d9ef3f97e..0000000000000000000000000000000000000000 --- a/ENCSR831KAH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -239.77879333496094 0.36703720688819885 0.5270036458969116 0.16125260293483734 0.8680160045623779 0.8461505174636841 0.1070256158709526 \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_0.evaluate.json b/ENCSR831QMZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a9f7b9989fac59f0a1553c1ffd59adff11bfbcf3..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF228PLG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_0.fit.json b/ENCSR831QMZ/cherimoya.fold_0.fit.json deleted file mode 100644 index c6696b70f14bdd7c415805894920e07eed2c6ddc..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF228PLG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_0.log b/ENCSR831QMZ/cherimoya.fold_0.log deleted file mode 100644 index bf9ea6df761c067b81a31a7558ed0dd1301059b7..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 36.239856243133545 4.170270681381226 879.82275390625 0.6200340986251831 1302.3946533203125 0.2917557954788208 0.53961253 11.214649200439453 True -1 5498 30.403753757476807 1.5863549709320068 868.7832641601562 0.7682105302810669 1102.906982421875 0.3873160183429718 0.62087554 5.168484210968018 True -2 8247 30.393489599227905 0.5567123889923096 769.2520751953125 0.8581309914588928 1069.5621337890625 0.4025002717971802 0.64659196 2.8400237560272217 True -3 10996 30.342687368392944 0.5556848049163818 993.34619140625 0.8579909801483154 1045.4559326171875 0.41142427921295166 0.66086125 2.242300271987915 True -4 13745 30.342464208602905 0.555898904800415 830.1611328125 0.7044054865837097 1032.412841796875 0.41743189096450806 0.6713886 2.1787500381469727 True -5 16494 30.212536811828613 0.8302702903747559 933.7108764648438 0.5414401292800903 1022.8587646484375 0.42079174518585205 0.6809343 1.7294509410858154 True -6 19243 29.750261068344116 1.95988130569458 817.63525390625 0.5526822209358215 1015.1625366210938 0.4257346987724304 0.68707216 1.5921099185943604 True -7 21992 29.73155903816223 0.5358951091766357 924.0220947265625 0.6417545676231384 1006.5016479492188 0.42917847633361816 0.6966738 1.535788893699646 True -8 24741 29.68522548675537 0.5365409851074219 801.9091186523438 0.45615872740745544 997.4032592773438 0.43405476212501526 0.7096169 1.3975547552108765 True -9 27490 29.69825315475464 0.5469608306884766 908.8546752929688 0.5835609436035156 991.8428344726562 0.4367470145225525 0.71588016 1.166412591934204 True -10 30239 29.691604375839233 1.2970755100250244 928.6035766601562 0.6140286326408386 983.8478393554688 0.4405646324157715 0.72496724 1.0705763101577759 True -11 32988 29.728905200958252 0.5527951717376709 958.94775390625 0.39068108797073364 978.0584106445312 0.44288840889930725 0.7321902 0.9463566541671753 True -12 35737 29.734626054763794 0.5453705787658691 897.9413452148438 0.7820774912834167 974.3745727539062 0.44221919775009155 0.7431155 0.8057378530502319 True -13 38486 29.67755436897278 0.550856351852417 837.8125610351562 0.5424483418464661 964.1777954101562 0.44791388511657715 0.7526229 0.7144155502319336 True -14 41235 29.68752908706665 0.5479905605316162 812.59716796875 0.36084574460983276 958.46630859375 0.4514133930206299 0.7605442 0.6410427689552307 True -15 43984 29.67161226272583 0.5457017421722412 749.9019775390625 0.4812394380569458 955.2183837890625 0.4515501856803894 0.7693132 0.5842679142951965 True -16 46733 29.70437717437744 0.5383431911468506 773.7352294921875 0.4488409161567688 950.5423583984375 0.4546377658843994 0.7741093 0.5475167632102966 True -17 49482 29.663032054901123 0.548142671585083 969.921875 0.2277393788099289 950.9862060546875 0.45362919569015503 0.7768147 0.526076078414917 True -18 52231 29.713664770126343 0.5378966331481934 957.7681884765625 0.5152737498283386 953.645751953125 0.4515018165111542 0.7770153 0.517265260219574 True -19 54980 29.676000595092773 0.5505053997039795 863.9132080078125 0.37316277623176575 953.4559326171875 0.4524539113044739 0.7757593 0.5167503952980042 False diff --git a/ENCSR831QMZ/cherimoya.fold_0.performance.tsv b/ENCSR831QMZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e95216d50730a6f50573c310da136ad4f20150d7..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -953.645751953125 0.33861103653907776 0.4515018165111542 0.2109418511390686 0.7770153284072876 0.7350499033927917 0.517265260219574 \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_1.evaluate.json b/ENCSR831QMZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4f0d62dea8afc272d90143e1b6ed04bd1527df91..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF228PLG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_1.fit.json b/ENCSR831QMZ/cherimoya.fold_1.fit.json deleted file mode 100644 index c4a7c145ead2a2fe98f28b559ae040739fa0b27f..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF228PLG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_1.log b/ENCSR831QMZ/cherimoya.fold_1.log deleted file mode 100644 index e187188f1ea9acbf5f9d9f4bcb5af452ac63ecc0..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 34.86822271347046 4.638992547988892 936.1434326171875 0.8768395185470581 1489.5692138671875 0.29010578989982605 0.5865305 9.835826873779297 True -1 5468 30.423571825027466 0.8672304153442383 846.239990234375 0.7962260246276855 1237.5020751953125 0.3998671770095825 0.6752725 4.873569011688232 True -2 8202 30.249659538269043 27.303487539291382 898.5465087890625 0.762269139289856 1210.2735595703125 0.41304975748062134 0.69134086 3.326026678085327 True -3 10936 30.21855330467224 0.7483203411102295 856.379638671875 0.5796935558319092 1190.40380859375 0.4183582067489624 0.7011163 2.6607742309570312 True -4 13670 30.176292896270752 0.7391607761383057 831.3053588867188 0.745084285736084 1173.0428466796875 0.4251948297023773 0.7104191 2.436333656311035 True -5 16404 30.198976755142212 0.7376720905303955 903.1614379882812 0.5869079828262329 1158.8359375 0.4319394528865814 0.7209822 1.8541147708892822 True -6 19138 30.206648588180542 25.24573540687561 754.4990234375 0.47777438163757324 1144.2481689453125 0.4375818073749542 0.7312742 1.5436792373657227 True -7 21872 30.176319360733032 1.3972797393798828 767.4550170898438 0.5784590244293213 1137.1572265625 0.44077664613723755 0.73916036 1.5708822011947632 True -8 24606 30.201857566833496 0.7576751708984375 665.1967163085938 0.6132447123527527 1132.3052978515625 0.44502103328704834 0.73728484 1.549953579902649 False -9 27340 30.231635093688965 0.7504398822784424 710.676025390625 0.5614154934883118 1120.5347900390625 0.4505123794078827 0.7503454 1.4070895910263062 True -10 30074 31.23661160469055 0.739633321762085 871.0865478515625 0.549547553062439 1108.2628173828125 0.457286536693573 0.75518036 1.2065536975860596 True -11 32808 29.615177154541016 0.7221789360046387 846.9663696289062 0.33015334606170654 1107.786865234375 0.4538896083831787 0.7663995 0.9835415482521057 True -12 35542 29.57481551170349 0.7158041000366211 634.0577392578125 0.402126282453537 1096.0037841796875 0.4582093060016632 0.77532977 0.8566389679908752 True -13 38276 29.684197187423706 0.732079029083252 833.651123046875 0.6476074457168579 1086.4736328125 0.46132200956344604 0.78709537 0.7506893277168274 True -14 41010 29.70308494567871 0.7145664691925049 694.5421752929688 0.4181138873100281 1077.1412353515625 0.46546897292137146 0.7968105 0.6480783224105835 True -15 43744 29.67607545852661 0.7370586395263672 843.7159423828125 0.4890417456626892 1069.5633544921875 0.4682386815547943 0.8054132 0.5721136927604675 True -16 46478 29.626396656036377 0.7161619663238525 848.231689453125 0.3658561110496521 1069.350830078125 0.466131329536438 0.8084827 0.5232569575309753 True -17 49212 29.64164662361145 0.7310647964477539 774.3032836914062 0.3872694969177246 1069.0841064453125 0.46519002318382263 0.8101292 0.4989204704761505 True -18 51946 29.656925916671753 0.7282488346099854 765.36181640625 0.2647451162338257 1065.5167236328125 0.4682299792766571 0.81000334 0.4906253218650818 False -19 54680 29.684406518936157 0.7412095069885254 782.6947631835938 0.29705607891082764 1070.0643310546875 0.46474453806877136 0.81010115 0.4901217818260193 False diff --git a/ENCSR831QMZ/cherimoya.fold_1.performance.tsv b/ENCSR831QMZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f066f59f3d890817480d1be416c8459ad4e3bcae..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1069.0841064453125 0.3250608444213867 0.46519002318382263 0.231485977768898 0.8101292252540588 0.7826881408691406 0.4989204704761505 \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_2.evaluate.json b/ENCSR831QMZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e16a53dee17938f1f28e28f5bf871290a3ac6249..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF228PLG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_2.fit.json b/ENCSR831QMZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 4083a064a858da912cd5d0061e4ff6a2ee9a3b33..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF228PLG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_2.log b/ENCSR831QMZ/cherimoya.fold_2.log deleted file mode 100644 index 06f262003cd57c971fc11b7df5909185d06ed5b0..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 36.24213361740112 3.9928512573242188 1089.3470458984375 0.9848389625549316 1369.3984375 0.30028021335601807 0.5424337 11.637846946716309 True -1 5776 31.82649827003479 0.5745973587036133 828.3447265625 0.6935364007949829 1153.5120849609375 0.3944604694843292 0.63639796 4.037678241729736 True -2 8664 31.840563774108887 0.576263427734375 930.3411254882812 0.8560801148414612 1126.8306884765625 0.4056167006492615 0.6525741 2.6085307598114014 True -3 11552 31.816234588623047 0.5890843868255615 856.73828125 0.9911506772041321 1103.330322265625 0.41444486379623413 0.6644744 2.117860794067383 True -4 14440 31.864022970199585 13.567726850509644 669.5269165039062 0.4733637571334839 1091.0380859375 0.41777506470680237 0.6787102 2.0293397903442383 True -5 17328 31.898427486419678 0.6188428401947021 798.274169921875 0.6236056685447693 1079.3050537109375 0.42378056049346924 0.69009537 1.806466817855835 True -6 20216 31.88648295402527 0.606311559677124 863.398681640625 0.5379829406738281 1072.962646484375 0.42890629172325134 0.6934261 1.6792322397232056 True -7 23104 31.885333776474 0.6117408275604248 850.8980102539062 0.7070245146751404 1066.72265625 0.4318387806415558 0.7042168 1.57840895652771 True -8 25992 31.832067012786865 0.5978498458862305 846.0386962890625 0.4996820390224457 1061.150634765625 0.43473926186561584 0.70941025 1.5060458183288574 True -9 28880 31.820502758026123 0.5768928527832031 652.4185791015625 0.44100624322891235 1052.373046875 0.4394112229347229 0.7216268 1.3099310398101807 True -10 31768 31.89892315864563 0.5773937702178955 732.64990234375 0.49220511317253113 1042.8572998046875 0.4433840215206146 0.7299606 1.1550637483596802 True -11 34656 31.886680126190186 0.5940091609954834 779.4189453125 0.4511384069919586 1033.7467041015625 0.4479779601097107 0.7407482 1.0198134183883667 True -12 37544 31.88315486907959 0.5982792377471924 887.9891967773438 0.6365664005279541 1031.570068359375 0.4484378695487976 0.74645585 0.8902342915534973 True -13 40432 31.66736888885498 0.6235489845275879 898.791015625 0.45038557052612305 1023.076416015625 0.4509158134460449 0.7558683 0.7723112106323242 True -14 43320 31.437779903411865 0.6011395454406738 774.9918212890625 0.46008193492889404 1018.9617309570312 0.4526849687099457 0.7664807 0.6736488938331604 True -15 46208 31.55983257293701 0.5980024337768555 742.4420166015625 0.489935964345932 1010.1932983398438 0.45634305477142334 0.7746031 0.6106166243553162 True -16 49096 31.3666353225708 0.6033165454864502 815.2802734375 0.48615938425064087 1009.1422729492188 0.455742210149765 0.7793102 0.5621091723442078 True -17 51984 31.390965938568115 0.5863800048828125 708.61279296875 0.4339425265789032 1005.6748046875 0.4589361548423767 0.7828316 0.5320139527320862 True -18 54872 31.503032684326172 0.5869646072387695 930.9385986328125 0.37240707874298096 1003.3812255859375 0.46045538783073425 0.78427905 0.5210710167884827 True -19 57760 31.42152428627014 0.5954384803771973 832.0587768554688 0.3029117286205292 1006.77587890625 0.45721590518951416 0.7839864 0.5201279520988464 False diff --git a/ENCSR831QMZ/cherimoya.fold_2.performance.tsv b/ENCSR831QMZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 89cef99c544490e5119cadfa739c60a2fc412e16..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1003.3812255859375 0.33127835392951965 0.46045538783073425 0.2198585420846939 0.7842790484428406 0.7515398263931274 0.5210710167884827 \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_3.evaluate.json b/ENCSR831QMZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8223fe9a877740a6b4ed8fbb8b286bfda6aab366..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF228PLG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_3.fit.json b/ENCSR831QMZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 14a3096c8906fdc2a37db2408886a53cbf7b80b6..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF228PLG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_3.log b/ENCSR831QMZ/cherimoya.fold_3.log deleted file mode 100644 index 2ec588a9d2d64847fb09b5630a7ae71428ba2889..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 34.95021843910217 4.254476308822632 953.8457641601562 0.8179564476013184 1237.56591796875 0.29866787791252136 0.5342196 10.816461563110352 True -1 5540 30.593113899230957 1.5098848342895508 885.9171142578125 0.8314312696456909 1041.04833984375 0.39478325843811035 0.65036565 4.278172016143799 True -2 8310 30.79504656791687 0.613461971282959 830.67578125 0.7749254703521729 1023.5347900390625 0.4032142758369446 0.6603858 3.197381019592285 True -3 11080 30.657209396362305 0.5801587104797363 851.95166015625 0.9216156601905823 996.6500854492188 0.41576260328292847 0.68107146 2.485494375228882 True -4 13850 30.655420064926147 26.835481882095337 1076.771484375 0.9166526198387146 984.0098876953125 0.4202828109264374 0.69170976 2.0824203491210938 True -5 16620 31.713311195373535 0.5760023593902588 972.2376708984375 0.6856507062911987 974.1050415039062 0.42571529746055603 0.6985078 1.8226617574691772 True -6 19390 30.772008657455444 0.5652711391448975 872.7984619140625 0.45413756370544434 966.1830444335938 0.4288398027420044 0.7066622 1.7478574514389038 True -7 22160 30.747064113616943 0.5754668712615967 783.8798828125 0.7334495186805725 960.2281494140625 0.4328124523162842 0.71136945 1.4950768947601318 True -8 24930 30.641243934631348 0.5767157077789307 880.2496948242188 0.565055787563324 954.7860717773438 0.4349707365036011 0.7230839 1.2891285419464111 True -9 27700 30.663987398147583 0.5737729072570801 915.757568359375 0.60903400182724 946.2354125976562 0.44101080298423767 0.7303049 1.1929881572723389 True -10 30470 30.761449575424194 0.6164517402648926 823.6185302734375 0.6294698715209961 939.779296875 0.44398027658462524 0.7406229 1.059330701828003 True -11 33240 30.56936812400818 24.669121026992798 862.191162109375 0.48769980669021606 933.1690063476562 0.4474095404148102 0.7510687 0.9525222182273865 True -12 36010 31.423779249191284 0.5763099193572998 755.2733154296875 0.6241495013237 926.2584228515625 0.45052778720855713 0.7570196 0.8378440141677856 True -13 38780 30.579569816589355 0.5732114315032959 839.3593139648438 0.5373296141624451 922.3331909179688 0.4513227343559265 0.766368 0.7309743165969849 True -14 41550 30.484386444091797 0.57198166847229 712.9632568359375 0.3790351152420044 916.4345703125 0.45481061935424805 0.773905 0.6530765295028687 True -15 44320 30.50434398651123 0.6976017951965332 742.2681884765625 0.4137525260448456 914.1846923828125 0.45459383726119995 0.7802475 0.5877317190170288 True -16 47090 30.570858240127563 0.5621695518493652 809.8643798828125 0.4077787399291992 910.36474609375 0.45683208107948303 0.7854449 0.5362969636917114 True -17 49860 30.22577977180481 0.556612491607666 728.2542724609375 0.2954411208629608 909.6165771484375 0.45770102739334106 0.78624475 0.5088086128234863 True -18 52630 29.96077847480774 0.5585348606109619 755.8846435546875 0.2407209426164627 911.8536376953125 0.45554277300834656 0.7856376 0.4990662932395935 False -19 55400 29.93083953857422 0.5785932540893555 967.6563720703125 0.45311805605888367 911.6900634765625 0.4562295377254486 0.7841689 0.4957318603992462 False diff --git a/ENCSR831QMZ/cherimoya.fold_3.performance.tsv b/ENCSR831QMZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 17e1b674b9b8e191ff5c93576bc0ca3aa8ab6272..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -909.6165771484375 0.33679383993148804 0.45770105719566345 0.20846189558506012 0.7862447500228882 0.7465315461158752 0.5088086128234863 \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_4.evaluate.json b/ENCSR831QMZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index dbf4fa21f16ae642b68d04505aeb063d0f40eeee..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF228PLG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_4.fit.json b/ENCSR831QMZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 50a738212bfd19f5c1a4186b3710a6b814659bf8..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF228PLG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR831QMZ/cherimoya.fold_4.log b/ENCSR831QMZ/cherimoya.fold_4.log deleted file mode 100644 index fba2093e55b425b88cd3e4dfb1a1af56bc09927c..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 36.98445701599121 3.8543481826782227 895.3023681640625 0.9677146673202515 1177.5899658203125 0.28901776671409607 0.53228056 9.23335075378418 True -1 5560 30.699594736099243 0.6122026443481445 926.8299560546875 0.6615848541259766 1002.8536376953125 0.37611156702041626 0.6352882 4.5226922035217285 True -2 8340 30.66222310066223 0.5888137817382812 954.9044189453125 0.6836978197097778 980.1922607421875 0.3877960741519928 0.65235853 2.2799344062805176 True -3 11120 30.665661334991455 0.8722636699676514 801.2537841796875 0.7449028491973877 959.255859375 0.3966972529888153 0.6723155 1.8747119903564453 True -4 13900 30.673734188079834 0.5792253017425537 745.6302490234375 0.8003958463668823 943.1751708984375 0.4044179916381836 0.685021 1.7913997173309326 True -5 16680 30.677459716796875 0.5719799995422363 725.892578125 0.4803135097026825 934.6087036132812 0.407693088054657 0.6970281 1.7151100635528564 True -6 19460 30.61324167251587 1.055410623550415 766.866943359375 0.6657388210296631 929.4417114257812 0.41039592027664185 0.69882107 1.427620530128479 True -7 22240 30.604066371917725 0.5610671043395996 958.97509765625 0.8052797317504883 930.0401611328125 0.4098629057407379 0.71046764 1.4019027948379517 True -8 25020 30.615395545959473 0.5612516403198242 885.588134765625 0.5658158659934998 920.2947387695312 0.41418835520744324 0.7220855 1.0917783975601196 True -9 27800 30.5820050239563 0.5600438117980957 706.7724609375 0.46109557151794434 910.1361083984375 0.42082762718200684 0.72625154 0.9554895758628845 True -10 30580 30.576475858688354 0.5709524154663086 882.75439453125 0.555279016494751 906.5048217773438 0.42256486415863037 0.7375675 0.8557148575782776 True -11 33360 31.19436264038086 0.6187806129455566 651.7901611328125 0.6173511743545532 902.033935546875 0.4234001338481903 0.745472 0.777042031288147 True -12 36140 30.614295959472656 0.614936113357544 872.0595703125 0.5690172910690308 896.851318359375 0.4253172278404236 0.75430506 0.6803758144378662 True -13 38920 30.6112380027771 0.5882728099822998 936.22216796875 0.42972978949546814 891.3580932617188 0.4284464716911316 0.7624725 0.6101464629173279 True -14 41700 30.589659214019775 0.573930025100708 702.537353515625 0.35192781686782837 884.9740600585938 0.4330291152000427 0.7683538 0.5653761029243469 True -15 44480 30.669286727905273 1.211021900177002 793.3497314453125 0.5112813115119934 880.0865478515625 0.4348469078540802 0.7776999 0.511934220790863 True -16 47260 30.706342935562134 0.5847904682159424 899.101318359375 0.7319051027297974 879.9583129882812 0.43499404191970825 0.7800688 0.48693564534187317 True -17 50040 30.57741904258728 1.4591395854949951 717.738037109375 0.3464653193950653 877.0886840820312 0.436729371547699 0.7816174 0.47657448053359985 True -18 52820 30.066643953323364 0.5568892955780029 857.89404296875 0.38655585050582886 879.7940673828125 0.4348750114440918 0.7829073 0.4752241373062134 True -19 55600 30.011526346206665 0.5882143974304199 691.408935546875 0.4219358563423157 878.9255981445312 0.43590247631073 0.7822418 0.4764435291290283 False diff --git a/ENCSR831QMZ/cherimoya.fold_4.performance.tsv b/ENCSR831QMZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8343a4022cbc771cd61d5807eb5ef3e2d6b75cc2..0000000000000000000000000000000000000000 --- a/ENCSR831QMZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -879.7940673828125 0.3506489396095276 0.4348749816417694 0.19841143488883972 0.7829073071479797 0.7327757477760315 0.4752241373062134 \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_0.evaluate.json b/ENCSR833ACP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b6afbfac273bffdacc85765ff1b29b3c3537fa3a..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336IJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_0.fit.json b/ENCSR833ACP/cherimoya.fold_0.fit.json deleted file mode 100644 index 411855e42f3f6418ced9420ef823248ebeb4f40d..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF336IJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_0.log b/ENCSR833ACP/cherimoya.fold_0.log deleted file mode 100644 index 9e15a092eb19f64e047329ed34fee1727877cbd8..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1908 45.09941387176514 72.75045919418335 220.3300323486328 0.6451272368431091 393.6424255371094 0.41479796171188354 0.49535805 10.968758583068848 True -1 3816 21.235147714614868 0.4216911792755127 208.96527099609375 1.0639533996582031 334.40887451171875 0.5389825105667114 0.5953602 4.934459686279297 True -2 5724 21.357414484024048 0.42783164978027344 216.646484375 1.0463595390319824 318.3332214355469 0.580886721611023 0.59387213 1.1423321962356567 False -3 7632 21.194169282913208 0.47356128692626953 232.03176879882812 0.5575278997421265 313.2997741699219 0.591295599937439 0.60351473 0.7711138129234314 True -4 9540 21.239818811416626 0.4305534362792969 214.71951293945312 0.6175384521484375 311.0802917480469 0.5968666672706604 0.61299783 0.6825939416885376 True -5 11448 20.775737524032593 0.41675329208374023 231.28701782226562 0.6493798494338989 309.98193359375 0.5999248623847961 0.61864847 0.6559200882911682 True -6 13356 20.772339344024658 0.3952810764312744 215.80264282226562 0.7242252826690674 308.9012756347656 0.6027953028678894 0.6129327 0.6625375747680664 False -7 15264 20.74412727355957 0.4138011932373047 231.3055419921875 0.7834598422050476 308.0610046386719 0.6051738262176514 0.6238405 0.6393454670906067 True -8 17172 20.817545413970947 0.4308476448059082 227.02847290039062 0.6144225597381592 307.1956481933594 0.6075851917266846 0.6291563 0.600272536277771 True -9 19080 20.753774404525757 0.40036964416503906 277.92022705078125 0.6524401307106018 306.4895935058594 0.6093581914901733 0.6363555 0.5642411112785339 True -10 20988 20.80638027191162 1.1993505954742432 196.98089599609375 0.5066643357276917 305.6199035644531 0.6115784049034119 0.642095 0.5477900505065918 True -11 22896 20.78026843070984 0.39068078994750977 215.53309631347656 0.5445859432220459 304.97625732421875 0.6132479906082153 0.64543986 0.5511851906776428 True -12 24804 20.757311582565308 1.8746740818023682 236.96701049804688 0.402133584022522 304.2590026855469 0.6150147318840027 0.6520013 0.5393729209899902 True -13 26712 20.79698920249939 15.734157800674438 229.32559204101562 0.5822001695632935 303.6319580078125 0.616759717464447 0.65808576 0.531140148639679 True -14 28620 20.996422290802002 0.42248106002807617 250.6810760498047 0.38810062408447266 303.0712890625 0.6179889440536499 0.66510355 0.5263322591781616 True -15 30528 20.784476280212402 0.4565558433532715 238.30029296875 0.38665470480918884 302.81341552734375 0.6188085079193115 0.6672826 0.5216360092163086 True -16 32436 20.768989086151123 0.4004065990447998 216.6494140625 0.3479446768760681 302.8195495605469 0.6187277436256409 0.6704171 0.5272267460823059 True -17 34344 22.033954620361328 3.318331480026245 199.1170196533203 0.3468966484069824 302.91485595703125 0.6180865168571472 0.67207193 0.5210282206535339 True -18 36252 20.79699444770813 0.4114689826965332 202.1013946533203 0.27267879247665405 303.1425476074219 0.6174260377883911 0.6689032 0.5300005078315735 False -19 38160 21.44416046142578 12.235247373580933 225.6326904296875 0.3215634524822235 303.341552734375 0.616924524307251 0.6666295 0.5358366966247559 False diff --git a/ENCSR833ACP/cherimoya.fold_0.performance.tsv b/ENCSR833ACP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index bcf07456a9dcb09310355ec75b9652e833404c8d..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.91485595703125 0.3150959610939026 0.618086576461792 0.19927740097045898 0.6720719337463379 0.6463786363601685 0.5210282206535339 \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_1.evaluate.json b/ENCSR833ACP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 91acb917764bff0454d61da59ad99a89418cbea7..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336IJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_1.fit.json b/ENCSR833ACP/cherimoya.fold_1.fit.json deleted file mode 100644 index cd05f67183b80de6b7f6672df6f0aa47be570356..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF336IJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_1.log b/ENCSR833ACP/cherimoya.fold_1.log deleted file mode 100644 index 55eb833e6b9401e76c27c27bd3024296d0bf9941..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1943 26.147562503814697 3.6990673542022705 204.68234252929688 0.977959156036377 378.16058349609375 0.41719111800193787 0.4741277 11.216560363769531 True -1 3886 21.623322010040283 0.5522222518920898 253.5858612060547 0.7725619077682495 327.36370849609375 0.5322700142860413 0.5838038 4.269259929656982 True -2 5829 21.624723434448242 0.4821133613586426 223.8873291015625 1.0599068403244019 313.8160095214844 0.5659952163696289 0.6073851 0.7873478531837463 True -3 7772 21.61159920692444 0.4573404788970947 274.81292724609375 0.9552111625671387 308.4905700683594 0.5787795782089233 0.6337058 0.5472996234893799 True -4 9715 21.62527370452881 0.4374256134033203 279.56951904296875 0.9647811651229858 307.2057800292969 0.5822787880897522 0.64271146 0.48594826459884644 True -5 11658 21.674184322357178 0.43529701232910156 248.0967254638672 0.6185195446014404 306.2635192871094 0.5845711827278137 0.64616275 0.49735793471336365 True -6 13601 21.627350568771362 0.4269118309020996 268.61260986328125 0.583795428276062 305.2090759277344 0.5877596735954285 0.6476486 0.5095120668411255 True -7 15544 21.609836101531982 0.43508172035217285 226.57516479492188 0.9283531904220581 304.7763366699219 0.5896446704864502 0.651453 0.5056333541870117 True -8 17487 21.63826823234558 0.4351377487182617 237.47183227539062 0.7894724607467651 304.2501220703125 0.5914973020553589 0.6581372 0.4988225996494293 True -9 19430 21.687724351882935 0.43484044075012207 217.3983154296875 0.41093191504478455 303.49566650390625 0.593550980091095 0.6615625 0.4868101179599762 True -10 21373 21.65869665145874 0.4277827739715576 227.261962890625 0.7969397306442261 302.9414367675781 0.5952979326248169 0.65873104 0.4910862147808075 False -11 23316 21.61980438232422 0.4388437271118164 219.65045166015625 0.7664715647697449 302.1835632324219 0.597247838973999 0.6650488 0.48262861371040344 True -12 25259 21.62273406982422 1.1475746631622314 220.72299194335938 0.49239903688430786 301.5480041503906 0.599258303642273 0.6725719 0.45970991253852844 True -13 27202 21.24405574798584 0.4422733783721924 261.69659423828125 0.43013066053390503 300.9943542480469 0.6006608605384827 0.6781438 0.4481148421764374 True -14 29145 21.279293537139893 0.4592113494873047 221.29991149902344 0.5466932058334351 300.5360412597656 0.6016373038291931 0.68275785 0.44343116879463196 True -15 31088 21.157631397247314 0.43525171279907227 227.6031951904297 0.3659058213233948 300.2745361328125 0.6021510362625122 0.6843009 0.44855642318725586 True -16 33031 21.159952878952026 0.42981576919555664 201.42257690429688 0.4178515374660492 300.1761474609375 0.6023389101028442 0.6903979 0.4413588047027588 True -17 34974 21.162020921707153 0.43311452865600586 218.81744384765625 0.24112892150878906 300.2466735839844 0.6020218729972839 0.6916853 0.44109272956848145 True -18 36917 21.226871013641357 0.44041919708251953 186.0131072998047 0.3263964056968689 300.28472900390625 0.6014158725738525 0.68810976 0.44754865765571594 False -19 38860 21.217525720596313 0.42593955993652344 219.09390258789062 0.350885808467865 300.427978515625 0.6011433005332947 0.6857934 0.45395657420158386 False diff --git a/ENCSR833ACP/cherimoya.fold_1.performance.tsv b/ENCSR833ACP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7aec125d8453e945c2e13d1ed225577e8c68e9a2..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -300.2466735839844 0.32197850942611694 0.6020218729972839 0.19241583347320557 0.6916853189468384 0.6876681447029114 0.44109272956848145 \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_2.evaluate.json b/ENCSR833ACP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3c39780618e6ae3a0822dc0f40683a33ab4ac66f..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336IJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_2.fit.json b/ENCSR833ACP/cherimoya.fold_2.fit.json deleted file mode 100644 index 8c91cfec1585c9de60c742ab0cdb46e582d85be5..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF336IJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_2.log b/ENCSR833ACP/cherimoya.fold_2.log deleted file mode 100644 index fb6c0fb9e481cfabe718453712c7994a3d2af22d..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2040 26.960411071777344 3.6075122356414795 246.60275268554688 0.7024552822113037 386.701416015625 0.42156440019607544 0.4941842 10.540510177612305 True -1 4080 22.745230436325073 0.8215601444244385 244.77728271484375 0.7523573040962219 329.4104919433594 0.5465317964553833 0.59994125 4.260358810424805 True -2 6120 22.81347417831421 0.40779757499694824 209.81942749023438 0.6424819231033325 317.1802062988281 0.5760812163352966 0.6190182 0.9618654251098633 True -3 8160 22.691144227981567 1.341909646987915 290.3757019042969 0.8156058192253113 312.9773254394531 0.5852004289627075 0.6227049 0.6760565638542175 True -4 10200 22.748973846435547 0.3807492256164551 227.83462524414062 0.8392221927642822 311.3298034667969 0.5890818238258362 0.62764394 0.6459590792655945 True -5 12240 22.705357789993286 0.44837498664855957 239.58621215820312 0.7275003790855408 310.07879638671875 0.5931152701377869 0.62798315 0.640617847442627 True -6 14280 22.705873250961304 0.35979533195495605 270.9953308105469 0.6758013367652893 309.1546936035156 0.5958067774772644 0.6318238 0.6330642700195312 True -7 16320 22.682372570037842 0.35826921463012695 227.53622436523438 0.5477824807167053 308.5162048339844 0.5978077054023743 0.6344213 0.6144102215766907 True -8 18360 22.68502116203308 0.3596479892730713 251.7518768310547 0.8447310924530029 307.52191162109375 0.6005005836486816 0.64147156 0.584160566329956 True -9 20400 22.68064045906067 0.7426152229309082 255.94944763183594 0.36344581842422485 306.3075866699219 0.6034752726554871 0.64894336 0.5580140948295593 True -10 22440 22.68820285797119 0.3693869113922119 215.12083435058594 0.7071247100830078 305.6440124511719 0.605288028717041 0.64894193 0.5574498176574707 False -11 24480 22.716331958770752 0.3872101306915283 266.76947021484375 0.8911875486373901 304.8547668457031 0.6069670915603638 0.65220034 0.550957977771759 True -12 26520 22.726149082183838 0.909541130065918 243.63668823242188 0.6511870622634888 304.21209716796875 0.6085554957389832 0.6563035 0.5417312979698181 True -13 28560 22.681132078170776 0.3736584186553955 256.3189392089844 0.4006733000278473 303.5643310546875 0.6104567050933838 0.6632177 0.5326372981071472 True -14 30600 22.687437295913696 0.3759915828704834 181.47491455078125 0.6186414957046509 303.1092529296875 0.6114477515220642 0.66941524 0.5215290188789368 True -15 32640 22.739901304244995 0.3617410659790039 198.39227294921875 0.4287765622138977 302.7595520019531 0.6120644807815552 0.67527366 0.5172733068466187 True -16 34680 22.80579423904419 0.37585902214050293 217.88308715820312 0.6598163843154907 302.70245361328125 0.6123188138008118 0.6789137 0.5049578547477722 True -17 36720 22.717910051345825 0.3730294704437256 250.06524658203125 0.3775728940963745 302.74237060546875 0.6120219826698303 0.68077356 0.5020051598548889 True -18 38760 22.72433042526245 0.38350963592529297 252.857421875 0.21046054363250732 302.98931884765625 0.6113916039466858 0.67768425 0.5066254138946533 False -19 40800 22.75457000732422 0.3845231533050537 227.49118041992188 0.34595155715942383 303.0467834472656 0.6111068725585938 0.6760425 0.5101444721221924 False diff --git a/ENCSR833ACP/cherimoya.fold_2.performance.tsv b/ENCSR833ACP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 749042ff2adbc2e20db3ed7dd810a7ce3104738d..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.74237060546875 0.31804159283638 0.6120220422744751 0.200448140501976 0.6807735562324524 0.6639682054519653 0.5020051598548889 \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_3.evaluate.json b/ENCSR833ACP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b516f6ac1e89377d51fb7d8ccd38060c2415b8a3..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336IJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_3.fit.json b/ENCSR833ACP/cherimoya.fold_3.fit.json deleted file mode 100644 index c745205e478b668d14d694b5f568d41bb41ad196..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF336IJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_3.log b/ENCSR833ACP/cherimoya.fold_3.log deleted file mode 100644 index e7c7970447f39861250a4f9e9634f2ca039a32ed..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1981 26.679636001586914 3.6448113918304443 250.1114501953125 0.967767059803009 392.5162048339844 0.421949177980423 0.5022904 10.746299743652344 True -1 3962 22.084590673446655 0.8717982769012451 246.06634521484375 0.743964433670044 330.1192932128906 0.5530683398246765 0.5902423 3.774240016937256 True -2 5943 22.107076168060303 0.44335079193115234 247.3232421875 1.1708765029907227 317.881103515625 0.5829376578330994 0.59029126 0.901203989982605 True -3 7924 21.72958493232727 0.41274452209472656 323.2424011230469 0.6039667129516602 313.9840087890625 0.591300904750824 0.60677254 0.7763969898223877 True -4 9905 21.611310243606567 0.4206047058105469 240.80789184570312 0.706273078918457 312.7763671875 0.5940008759498596 0.6104815 0.6944493055343628 True -5 11886 21.592474699020386 0.4209482669830322 227.95681762695312 0.7291646003723145 311.5089416503906 0.5967599749565125 0.61523163 0.6746277809143066 True -6 13867 21.600597620010376 0.4157891273498535 242.16461181640625 0.578369677066803 310.5298767089844 0.5993230938911438 0.6195843 0.703711986541748 True -7 15848 21.60897421836853 0.4124622344970703 228.10714721679688 0.8359289765357971 309.7068786621094 0.6016569137573242 0.6259786 0.6780677437782288 True -8 17829 21.62564253807068 0.4231412410736084 239.3873748779297 0.7299844622612 308.6676940917969 0.604132354259491 0.6335781 0.6084119081497192 True -9 19810 21.581069946289062 0.41935157775878906 245.12814331054688 0.8559844493865967 307.8246154785156 0.6062949895858765 0.6390417 0.5901946425437927 True -10 21791 21.624293565750122 0.41245508193969727 245.83340454101562 0.7907981872558594 307.0086975097656 0.6084810495376587 0.64299804 0.5692142844200134 True -11 23772 21.539637088775635 0.4107358455657959 254.69508361816406 0.5179527997970581 306.1957092285156 0.6102743148803711 0.6546796 0.5364841222763062 True -12 25753 21.59920024871826 0.4178929328918457 219.85743713378906 0.5385282635688782 305.56298828125 0.6118271946907043 0.66363794 0.5235695838928223 True -13 27734 21.567833423614502 0.4267418384552002 246.7652130126953 0.4846823215484619 305.0056457519531 0.6130790710449219 0.67266566 0.5005670189857483 True -14 29715 21.563745260238647 0.4216632843017578 263.38311767578125 0.48713064193725586 304.5510559082031 0.6142894625663757 0.68092984 0.4896737039089203 True -15 31696 21.53474473953247 0.4185960292816162 235.52516174316406 0.5804536938667297 304.09112548828125 0.6151559352874756 0.68801373 0.48392149806022644 True -16 33677 21.55531907081604 0.4187190532684326 218.27249145507812 0.33017998933792114 304.22076416015625 0.6148866415023804 0.6915108 0.4795759618282318 True -17 35658 21.55957841873169 0.41880083084106445 250.3290252685547 0.3169997036457062 304.2098388671875 0.6145707964897156 0.69156253 0.4861524701118469 True -18 37639 21.55773687362671 0.42630577087402344 241.6668701171875 0.26604774594306946 304.4984436035156 0.6138585805892944 0.6921411 0.4937452971935272 True -19 39620 21.55957531929016 0.4177687168121338 177.08932495117188 0.313816636800766 304.642578125 0.6135002374649048 0.6906888 0.4962027966976166 False diff --git a/ENCSR833ACP/cherimoya.fold_3.performance.tsv b/ENCSR833ACP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 02c4c734a1129a2eb443a90d91277be42aed0750..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -304.4984436035156 0.3157818913459778 0.6138585805892944 0.20235486328601837 0.6921411156654358 0.6729181408882141 0.4937452971935272 \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_4.evaluate.json b/ENCSR833ACP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2f786ed054ebdf7d9a05445bdfe71309f250910a..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF336IJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_4.fit.json b/ENCSR833ACP/cherimoya.fold_4.fit.json deleted file mode 100644 index 742b491b1a85bac4117022bbfc8bcea91f79bada..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF336IJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR833ACP/cherimoya.fold_4.log b/ENCSR833ACP/cherimoya.fold_4.log deleted file mode 100644 index b9f8e50983559a593f0bd951c9c275a3efb06079..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2043 27.336185216903687 3.8921287059783936 275.8221130371094 0.9263710975646973 394.8383483886719 0.42801031470298767 0.5506857 9.083852767944336 True -1 4086 23.34550714492798 0.8173158168792725 223.09713745117188 0.8146001100540161 337.45538330078125 0.554736852645874 0.6021247 3.410879373550415 True -2 6129 22.792677640914917 0.9439339637756348 213.40626525878906 0.8620045185089111 324.81524658203125 0.5879305005073547 0.5975131 1.2077350616455078 False -3 8172 22.735661506652832 0.4171414375305176 222.95437622070312 0.7232412099838257 319.8983459472656 0.5972808003425598 0.62384003 0.799210250377655 True -4 10215 22.726868867874146 0.44771909713745117 266.2123107910156 0.744640588760376 318.2337646484375 0.6013222336769104 0.63185495 0.7171842455863953 True -5 12258 22.73121476173401 0.42301440238952637 224.54605102539062 0.4533350467681885 317.1304626464844 0.6042638421058655 0.6386453 0.6822611093521118 True -6 14301 22.793409824371338 0.4132816791534424 208.32232666015625 0.7076407670974731 315.91351318359375 0.6071400046348572 0.63903505 0.6582027077674866 True -7 16344 22.775901079177856 0.42646336555480957 233.35568237304688 0.8136231899261475 314.9743347167969 0.6093654036521912 0.64060766 0.6285509467124939 True -8 18387 22.824915647506714 1.0829200744628906 264.58526611328125 0.6593679785728455 314.10015869140625 0.6117938160896301 0.6424168 0.6215113997459412 True -9 20430 22.740795612335205 0.4052696228027344 207.67636108398438 0.8028151988983154 313.198974609375 0.6139777302742004 0.64239806 0.5945690274238586 False -10 22473 22.71299982070923 0.41452908515930176 225.86798095703125 0.463881254196167 312.55181884765625 0.6156556010246277 0.65220135 0.582594633102417 True -11 24516 22.720484256744385 1.2637062072753906 245.84194946289062 0.7234628200531006 311.8641357421875 0.6175279021263123 0.66204613 0.5603592395782471 True -12 26559 22.766582250595093 0.39687037467956543 232.4894256591797 0.5302643179893494 310.98388671875 0.6195544600486755 0.665043 0.5446953773498535 True -13 28602 22.621644735336304 0.38914942741394043 243.54287719726562 0.5384275317192078 310.1676025390625 0.6213071346282959 0.6744061 0.5287764072418213 True -14 30645 22.25211262702942 0.41950130462646484 228.40579223632812 0.5227270722389221 309.718505859375 0.6223345994949341 0.6780865 0.5199273824691772 True -15 32688 22.24598479270935 0.3904855251312256 260.8653259277344 0.6022493839263916 309.3321228027344 0.623147189617157 0.68535864 0.5070425271987915 True -16 34731 22.242546319961548 0.39791440963745117 227.980712890625 0.3056245446205139 309.2893981933594 0.6232000589370728 0.6877886 0.5060786604881287 True -17 36774 22.234394311904907 0.39031076431274414 244.46128845214844 0.35860687494277954 309.32037353515625 0.6226465702056885 0.68678194 0.5158052444458008 False -18 38817 22.291948318481445 0.39795351028442383 226.48577880859375 0.2957974374294281 309.5150451660156 0.6219868659973145 0.6849028 0.5190854668617249 False -19 40860 22.276695013046265 1.1491117477416992 245.1420135498047 0.27129364013671875 309.7015380859375 0.6215842366218567 0.6819639 0.5357086658477783 False diff --git a/ENCSR833ACP/cherimoya.fold_4.performance.tsv b/ENCSR833ACP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 692f5087afbe458357b834f563abe1bc4d8c1c90..0000000000000000000000000000000000000000 --- a/ENCSR833ACP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.2893981933594 0.3109641373157501 0.6232000589370728 0.2070256471633911 0.6877886056900024 0.6588349938392639 0.5060786604881287 \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_0.evaluate.json b/ENCSR835WBW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a197e0bce6b5ebf45ebea729bb6744297e5e1616..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF449YEO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_0.fit.json b/ENCSR835WBW/cherimoya.fold_0.fit.json deleted file mode 100644 index b37a033dcbe4425b560171e38affdcb19b0f628d..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF449YEO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_0.log b/ENCSR835WBW/cherimoya.fold_0.log deleted file mode 100644 index f9031dfab3e0d9507a33358836a8f627e3c8b641..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2064 27.38676381111145 4.544666767120361 293.5141296386719 0.8627418279647827 405.1382141113281 0.4222288727760315 0.4551666 9.998492240905762 True -1 4128 23.138882398605347 0.4674065113067627 240.80816650390625 0.5774048566818237 343.0868225097656 0.5514756441116333 0.5571257 3.9699292182922363 True -2 6192 22.663388967514038 0.43068909645080566 266.00537109375 0.7597402334213257 327.3641357421875 0.5902948975563049 0.5894757 1.1768379211425781 True -3 8256 22.684021472930908 0.5256896018981934 289.0609130859375 0.814859926700592 322.3591003417969 0.6008968353271484 0.60475236 0.6946302652359009 True -4 10320 22.715602159500122 0.4227015972137451 248.60235595703125 0.5924862027168274 320.7879943847656 0.6048564910888672 0.6081275 0.606518030166626 True -5 12384 22.72956347465515 0.44124412536621094 266.2606201171875 0.5866219997406006 319.7239685058594 0.6076528429985046 0.6072583 0.5635161399841309 False -6 14448 22.679505109786987 0.44777345657348633 229.32794189453125 0.5566385984420776 318.9334716796875 0.6101160049438477 0.6115797 0.5439857244491577 True -7 16512 22.716310262680054 0.43436241149902344 189.13316345214844 0.6764890551567078 318.03314208984375 0.612390398979187 0.61721677 0.5345137119293213 True -8 18576 22.66432547569275 0.4277365207672119 231.2781982421875 0.4159938097000122 316.8656311035156 0.6148477792739868 0.6203608 0.5244870185852051 True -9 20640 22.5931077003479 0.427901029586792 236.50057983398438 0.6323976516723633 316.0396728515625 0.617188572883606 0.62726516 0.5109421610832214 True -10 22704 22.256755590438843 0.43207311630249023 220.682861328125 0.6303372383117676 315.0555419921875 0.6193158626556396 0.63005567 0.48442313075065613 True -11 24768 22.301987409591675 0.4422945976257324 273.30255126953125 0.44434109330177307 314.0095520019531 0.6215821504592896 0.6429525 0.4618096351623535 True -12 26832 22.293830394744873 1.310877799987793 256.4161376953125 0.5839399099349976 313.1365966796875 0.6236517429351807 0.6503431 0.4489906430244446 True -13 28896 22.277003049850464 0.4327359199523926 211.967529296875 0.4047750234603882 312.48504638671875 0.6250979900360107 0.6568017 0.4442098140716553 True -14 30960 22.286070108413696 0.4183928966522217 222.80068969726562 0.5869288444519043 311.96636962890625 0.6260693073272705 0.6635695 0.4360942840576172 True -15 33024 22.27025079727173 0.4299743175506592 242.17904663085938 0.3711026906967163 311.4434509277344 0.6270428895950317 0.673063 0.4293864667415619 True -16 35088 22.285319566726685 0.4257240295410156 261.6607666015625 0.2866777777671814 311.34521484375 0.6271400451660156 0.6767952 0.429979532957077 True -17 37152 22.252075672149658 0.4273364543914795 297.766357421875 0.2664441466331482 311.32098388671875 0.6270941495895386 0.67700565 0.4351528286933899 True -18 39216 22.300318956375122 0.4088618755340576 266.2630615234375 0.27804985642433167 311.47125244140625 0.6266694664955139 0.6760497 0.44290316104888916 False -19 41280 22.285488843917847 0.4174168109893799 248.71139526367188 0.2929360270500183 311.6163330078125 0.6262872815132141 0.6739144 0.44954925775527954 False diff --git a/ENCSR835WBW/cherimoya.fold_0.performance.tsv b/ENCSR835WBW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 66394525fad9403acfbda3e0e26a804be75ea7a5..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -311.32098388671875 0.30931147933006287 0.6270940899848938 0.2007196545600891 0.6770056486129761 0.6376810073852539 0.4351528286933899 \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_1.evaluate.json b/ENCSR835WBW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f7ada0cb55ca6aaa409c03ceb5f2ba712f9ba422..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF449YEO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_1.fit.json b/ENCSR835WBW/cherimoya.fold_1.fit.json deleted file mode 100644 index bbc0363cbd5da9319fc14490aded6db6aae6e8eb..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF449YEO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_1.log b/ENCSR835WBW/cherimoya.fold_1.log deleted file mode 100644 index 06a537a6807cb1e9ad008766a4aa13b387d6ce5f..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2109 27.748725175857544 3.88631272315979 268.32562255859375 0.847520112991333 399.9677429199219 0.4325375258922577 0.47707963 10.154751777648926 True -1 4218 23.437029123306274 8.763459920883179 248.90972900390625 0.7752134203910828 345.3728942871094 0.556932270526886 0.5949352 3.3267688751220703 True -2 6327 23.25097346305847 0.6197638511657715 254.3955841064453 0.6847321391105652 335.7706298828125 0.5804042816162109 0.5657073 1.0239174365997314 False -3 8436 23.173319816589355 0.4695882797241211 271.8143615722656 0.8229141235351562 332.4209289550781 0.5869788527488708 0.60677695 0.7565588355064392 True -4 10545 23.234894037246704 0.7123806476593018 241.0287322998047 0.5365399122238159 331.414306640625 0.5901126265525818 0.62884796 0.6308923959732056 True -5 12654 23.222986698150635 0.4736137390136719 256.38616943359375 0.6374099254608154 330.5498962402344 0.5931127071380615 0.6343922 0.565356433391571 True -6 14763 23.348942756652832 0.4849815368652344 271.76220703125 0.5930960774421692 330.0347595214844 0.5950176119804382 0.63641995 0.5733664631843567 True -7 16872 23.241127490997314 0.4901542663574219 259.76239013671875 0.7940047383308411 328.6743469238281 0.5980936884880066 0.65421194 0.5351447463035583 True -8 18981 23.23330593109131 0.4940469264984131 268.3443603515625 0.4982754588127136 328.0292663574219 0.6000016331672668 0.6559612 0.4827632009983063 True -9 21090 23.246160984039307 0.47983884811401367 252.24948120117188 0.5591866970062256 326.8188781738281 0.6026638746261597 0.6625425 0.4639773964881897 True -10 23199 23.233955144882202 0.4701530933380127 234.54104614257812 0.7334483861923218 326.2463073730469 0.6046345829963684 0.6651416 0.46289217472076416 True -11 25308 23.259799242019653 0.46561288833618164 248.48329162597656 0.4087952673435211 325.0567932128906 0.6073729991912842 0.67527443 0.4275529086589813 True -12 27417 23.23593258857727 0.4666869640350342 291.6265869140625 0.6157734394073486 324.2434997558594 0.6094862222671509 0.68334466 0.4095410704612732 True -13 29526 23.28036642074585 0.4827287197113037 227.43292236328125 0.38546431064605713 323.2524719238281 0.6114471554756165 0.6922762 0.40130382776260376 True -14 31635 23.305176734924316 0.47216343879699707 233.9591064453125 0.3832126259803772 322.39373779296875 0.6133076548576355 0.7020626 0.38343170285224915 True -15 33744 23.298670053482056 2.3328588008880615 270.9416809082031 0.3650971055030823 321.77142333984375 0.6144554615020752 0.70883995 0.377450168132782 True -16 35853 23.357693910598755 0.48213768005371094 274.39666748046875 0.33918094635009766 321.4490051269531 0.6147531867027283 0.71421176 0.37340718507766724 True -17 37962 23.29947280883789 0.48152971267700195 248.06768798828125 0.25391897559165955 321.3113098144531 0.6148967146873474 0.71322745 0.37726226449012756 False -18 40071 23.251950979232788 0.5016186237335205 265.87188720703125 0.18510226905345917 321.36932373046875 0.6146222949028015 0.7123968 0.3771398961544037 False -19 42180 23.309038639068604 0.9683279991149902 253.39697265625 0.2414877861738205 321.3731994628906 0.6144245266914368 0.7102126 0.38303178548812866 False diff --git a/ENCSR835WBW/cherimoya.fold_1.performance.tsv b/ENCSR835WBW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f030f715703a0a42e3acb442fcb39db32ace7df4..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -321.4490051269531 0.31075984239578247 0.6147531867027283 0.20267876982688904 0.7142117619514465 0.6939128637313843 0.37340718507766724 \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_2.evaluate.json b/ENCSR835WBW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index daccaefe6300fe2586e03e3b3e09615bbd7b2d89..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF449YEO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_2.fit.json b/ENCSR835WBW/cherimoya.fold_2.fit.json deleted file mode 100644 index aa529c5fd20003b1924523c7369eff194c16b01d..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF449YEO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_2.log b/ENCSR835WBW/cherimoya.fold_2.log deleted file mode 100644 index d53f01e8af8cc2c9473a7c0351ba00de68f01663..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2196 28.216411590576172 3.504894971847534 247.03623962402344 0.7526565790176392 394.49090576171875 0.43289586901664734 0.4977083 9.260107040405273 True -1 4392 24.377323150634766 0.46171045303344727 241.23226928710938 0.6157872676849365 337.3614501953125 0.5578658580780029 0.59199584 3.151080846786499 True -2 6588 24.080853700637817 0.38611435890197754 261.43988037109375 0.573070764541626 326.3452453613281 0.5852112770080566 0.5971254 1.0599931478500366 True -3 8784 25.027902841567993 13.72201681137085 229.37796020507812 0.793563961982727 322.08148193359375 0.593614935874939 0.626067 0.7433203458786011 True -4 10980 24.223631858825684 0.3854715824127197 247.3294219970703 0.5674964189529419 320.9827880859375 0.5963934659957886 0.63441885 0.6665899157524109 True -5 13176 24.171830415725708 0.46100521087646484 248.26808166503906 0.7606350779533386 320.17926025390625 0.5986668467521667 0.63974714 0.6147418022155762 True -6 15372 24.13585090637207 0.3990824222564697 228.69570922851562 0.5252633094787598 319.3909912109375 0.601016640663147 0.643535 0.5961724519729614 True -7 17568 24.138728380203247 0.40034031867980957 245.7628631591797 0.7356683015823364 318.4256896972656 0.6033296585083008 0.64533854 0.5615686774253845 True -8 19764 24.16497254371643 0.39981627464294434 257.880859375 0.595220685005188 317.537353515625 0.6057468056678772 0.6471078 0.5486436486244202 True -9 21960 24.13837742805481 0.38565826416015625 230.0035858154297 0.43035393953323364 316.6689453125 0.6080977916717529 0.6492801 0.4981902241706848 True -10 24156 24.177883625030518 0.3995225429534912 220.70584106445312 0.5775269269943237 315.87530517578125 0.6098968982696533 0.6550201 0.4861988127231598 True -11 26352 24.144630193710327 0.3912985324859619 224.3212432861328 0.5058003067970276 314.9827880859375 0.6123121380805969 0.6622022 0.4617457389831543 True -12 28548 24.122978687286377 0.39461684226989746 257.267333984375 0.354800283908844 314.05157470703125 0.6146461367607117 0.6677712 0.44709697365760803 True -13 30744 24.182039499282837 0.3921647071838379 249.56521606445312 0.48374563455581665 313.4519958496094 0.6159029603004456 0.67317766 0.4454340636730194 True -14 32940 24.191344499588013 0.39913463592529297 242.03912353515625 0.31504297256469727 312.922119140625 0.6171727180480957 0.6815286 0.43476372957229614 True -15 35136 24.148845434188843 0.39540576934814453 218.404052734375 0.36590033769607544 312.287109375 0.6182041168212891 0.6893132 0.4223535656929016 True -16 37332 24.12416648864746 0.3949887752532959 295.42333984375 0.29527658224105835 312.21002197265625 0.6185818314552307 0.69227713 0.4210844933986664 True -17 39528 24.159663677215576 1.5299015045166016 236.4556884765625 0.2583390176296234 312.1067199707031 0.6185896396636963 0.6940904 0.42185118794441223 True -18 41724 24.16567897796631 1.9674181938171387 190.29061889648438 0.38936328887939453 312.439453125 0.6181793212890625 0.6929046 0.42461463809013367 False -19 43920 23.734875202178955 0.392500638961792 248.96047973632812 0.3625256419181824 312.4024353027344 0.6178621649742126 0.69051653 0.4292745590209961 False diff --git a/ENCSR835WBW/cherimoya.fold_2.performance.tsv b/ENCSR835WBW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 53dbdb7635357334c226f8a24bf796caae3d4ab8..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -312.1067199707031 0.3127158582210541 0.6185895800590515 0.20370498299598694 0.6940904259681702 0.6643872261047363 0.42185118794441223 \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_3.evaluate.json b/ENCSR835WBW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c5c8b688091f58209d6221fd69e7eb91d2241886..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF449YEO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_3.fit.json b/ENCSR835WBW/cherimoya.fold_3.fit.json deleted file mode 100644 index 6e6f83ab4218e1994f2ab35756cc4555a0df01d8..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF449YEO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_3.log b/ENCSR835WBW/cherimoya.fold_3.log deleted file mode 100644 index de2f8b91a31f7e35787ca8198ecbe5969b7faabc..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2140 28.14712142944336 3.7272298336029053 282.93292236328125 0.8302642107009888 405.7073669433594 0.433613121509552 0.45992398 10.283370018005371 True -1 4280 23.59782838821411 0.49933791160583496 228.2288818359375 0.7709115743637085 344.07196044921875 0.569769561290741 0.5689677 2.929893970489502 True -2 6420 23.55941939353943 0.7412488460540771 248.27435302734375 0.718865156173706 331.96588134765625 0.5950618386268616 0.5990702 0.8212890028953552 True -3 8560 23.52731943130493 0.742863655090332 261.81298828125 0.6092040538787842 328.3656921386719 0.6024279594421387 0.61105 0.5740767121315002 True -4 10700 23.557185649871826 0.4865598678588867 265.76239013671875 0.8893669843673706 326.78778076171875 0.6059665083885193 0.6128097 0.5097769498825073 True -5 12840 25.498993635177612 0.48689794540405273 247.2579345703125 0.7861014604568481 325.9358215332031 0.6079608201980591 0.6231951 0.49830362200737 True -6 14980 23.541907787322998 0.48699259757995605 238.91244506835938 0.5720100402832031 324.6612548828125 0.6112352609634399 0.62529635 0.5228447318077087 True -7 17120 23.54483675956726 0.47488903999328613 235.2140655517578 0.5816798210144043 323.752685546875 0.6135202050209045 0.63249683 0.47973641753196716 True -8 19260 23.525047063827515 0.46802783012390137 244.55880737304688 0.6052826642990112 322.946533203125 0.6156389117240906 0.6394154 0.4805562198162079 True -9 21400 23.5564227104187 0.45968079566955566 225.25897216796875 0.6272416114807129 322.05938720703125 0.617773175239563 0.6434873 0.46133607625961304 True -10 23540 23.60967254638672 1.2022032737731934 241.94784545898438 0.4702475368976593 321.1964416503906 0.619620144367218 0.6519266 0.44777509570121765 True -11 25680 23.644434928894043 0.47380995750427246 270.23260498046875 0.438597172498703 320.47369384765625 0.6214823722839355 0.6547328 0.45366278290748596 True -12 27820 23.61172914505005 0.4613802433013916 254.53762817382812 0.49405401945114136 319.5085144042969 0.6231074929237366 0.66030943 0.4511566460132599 True -13 29960 23.603286266326904 0.45982885360717773 245.74581909179688 0.3560120761394501 319.0890808105469 0.6242213845252991 0.66866463 0.4569929540157318 True -14 32100 23.589563369750977 0.45988893508911133 245.04159545898438 0.3259570598602295 318.3910827636719 0.625637412071228 0.6746664 0.4434427320957184 True -15 34240 23.701464653015137 0.47897934913635254 250.678466796875 0.423714280128479 317.8164367675781 0.6264781951904297 0.6848968 0.4278404414653778 True -16 36380 23.674413204193115 0.4822263717651367 237.5616455078125 0.29896780848503113 317.6430969238281 0.6267427802085876 0.68838733 0.4257062077522278 True -17 38520 23.634464025497437 0.467848539352417 252.16091918945312 0.38340264558792114 317.6579284667969 0.6265820860862732 0.68885404 0.428830623626709 True -18 40660 23.63174271583557 0.4558887481689453 243.93626403808594 0.5502157211303711 317.6853332519531 0.6262944340705872 0.687109 0.4301248788833618 False -19 42800 23.210044145584106 0.4534459114074707 232.62188720703125 0.28414463996887207 317.7713928222656 0.6260236501693726 0.68680656 0.4324478209018707 False diff --git a/ENCSR835WBW/cherimoya.fold_3.performance.tsv b/ENCSR835WBW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f89a4d49dedf7fed333d5266e2bebf7297377019..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.6579284667969 0.3072982728481293 0.6265820264816284 0.20711416006088257 0.6888540387153625 0.6635406613349915 0.428830623626709 \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_4.evaluate.json b/ENCSR835WBW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ec0dfee07d740926f0bf520b7b54bda547f10e1c..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF449YEO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_4.fit.json b/ENCSR835WBW/cherimoya.fold_4.fit.json deleted file mode 100644 index efe0b0d184f1eacb4f3d16f1b79584f6d1959b2e..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF449YEO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR835WBW/cherimoya.fold_4.log b/ENCSR835WBW/cherimoya.fold_4.log deleted file mode 100644 index a352a6c0462b3302f264754f1a673471b608cd9c..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2204 28.668346405029297 3.8698766231536865 261.4673767089844 0.9140846729278564 401.4647521972656 0.4307033121585846 0.48360673 7.506491661071777 True -1 4408 24.62039566040039 0.5366785526275635 248.5205078125 0.5725040435791016 341.0169372558594 0.5636940598487854 0.5496947 3.0012166500091553 True -2 6612 24.240456581115723 0.4469137191772461 269.843017578125 0.6243224143981934 329.2657775878906 0.5927255153656006 0.5696174 1.0881987810134888 True -3 8816 24.27610158920288 0.4427480697631836 265.13018798828125 0.6793122291564941 325.6758117675781 0.600484311580658 0.59634316 0.8615372776985168 True -4 11020 24.256348609924316 0.44083452224731445 239.049072265625 0.41446632146835327 323.87091064453125 0.605195939540863 0.59240645 0.7548316121101379 False -5 13224 24.247050285339355 0.443328857421875 259.50653076171875 0.7320515513420105 322.7925720214844 0.6084010004997253 0.5944606 0.6602175831794739 False -6 15428 24.220929384231567 0.436138391494751 285.64410400390625 0.9756625890731812 321.62994384765625 0.6112179160118103 0.59350616 0.663372814655304 False -7 17632 24.227649688720703 0.43489766120910645 259.41766357421875 0.5121110677719116 320.6202392578125 0.6140788197517395 0.6018015 0.6313880085945129 True -8 19836 24.239428997039795 0.42373013496398926 254.9962158203125 0.44721221923828125 319.7074279785156 0.6164785027503967 0.6021262 0.5925173163414001 True -9 22040 24.216301918029785 0.425579309463501 251.1016845703125 0.6024971008300781 318.408447265625 0.6191338300704956 0.61818683 0.5468919277191162 True -10 24244 24.253679037094116 0.439943790435791 271.7148132324219 0.46309664845466614 317.5458984375 0.6214318871498108 0.63124144 0.49991923570632935 True -11 26448 24.242844820022583 1.2050316333770752 265.02105712890625 0.6026813983917236 316.52197265625 0.6238670945167542 0.6369765 0.49261540174484253 True -12 28652 24.220176219940186 0.9416675567626953 268.18280029296875 0.4819622337818146 315.7978210449219 0.6257089376449585 0.64620495 0.481382817029953 True -13 30856 24.24212908744812 0.4394502639770508 246.18624877929688 0.4480464458465576 314.7882385253906 0.6276752948760986 0.65607834 0.471248984336853 True -14 33060 24.213613510131836 0.4364612102508545 251.43154907226562 0.4428999423980713 314.20172119140625 0.6289948225021362 0.66802937 0.4542638659477234 True -15 35264 24.21391797065735 0.4408729076385498 226.1940460205078 0.4056839048862457 313.84747314453125 0.6296454668045044 0.67298126 0.4488997459411621 True -16 37468 24.20669150352478 0.43056392669677734 243.54969787597656 0.3299470543861389 313.559326171875 0.6302385926246643 0.67966837 0.4430139660835266 True -17 39672 24.237149238586426 0.45325303077697754 267.3341979980469 0.36859992146492004 313.3970642089844 0.6302827000617981 0.6811055 0.4407767355442047 True -18 41876 24.23663020133972 0.43186473846435547 272.491455078125 0.2186804711818695 313.5665283203125 0.6298053860664368 0.68238443 0.4428231716156006 True -19 44080 23.77458906173706 0.43780970573425293 235.01551818847656 0.2950809597969055 313.6069641113281 0.6294813752174377 0.6804775 0.4456239342689514 False diff --git a/ENCSR835WBW/cherimoya.fold_4.performance.tsv b/ENCSR835WBW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0d078d25ee59750782ca2ec32ecd73ede306c062..0000000000000000000000000000000000000000 --- a/ENCSR835WBW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -313.5665283203125 0.308010458946228 0.629805326461792 0.20591428875923157 0.6823844313621521 0.6394166946411133 0.4428231716156006 \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_0.evaluate.json b/ENCSR836FIL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1fe2c8d85571c3e3328c165baeb9ef14259c8056..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF438ZUH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_0.fit.json b/ENCSR836FIL/cherimoya.fold_0.fit.json deleted file mode 100644 index 66494c1a286d82313f92b69f74a4653351e6cfe9..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF438ZUH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_0.log b/ENCSR836FIL/cherimoya.fold_0.log deleted file mode 100644 index fa88dc2145d8ea025e87f3e8184001cf9ff0e3ff..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3575 44.14597415924072 4.170715570449829 749.3024291992188 0.8579114675521851 1182.765869140625 0.6935878396034241 0.5964343 9.067534446716309 True -1 7150 39.549455642700195 0.7526113986968994 714.9847412109375 0.5916054248809814 967.3717651367188 0.7848067283630371 0.6837715 1.9988670349121094 True -2 10725 39.47042512893677 1.297226905822754 826.3208618164062 0.7955824136734009 946.8262939453125 0.792140781879425 0.6971016 1.038832426071167 True -3 14300 39.20689868927002 1.7539684772491455 818.3510131835938 0.6596437096595764 934.1219482421875 0.7968395352363586 0.7021511 0.888792872428894 True -4 17875 38.81694316864014 0.7066388130187988 829.8492431640625 0.6765758395195007 928.0447998046875 0.7993095517158508 0.7103835 0.9149027466773987 True -5 21450 38.8063280582428 1.7236716747283936 922.572021484375 0.801457405090332 922.00390625 0.8018260598182678 0.71350974 0.7581154704093933 True -6 25025 38.759281873703 0.7107686996459961 801.7792358398438 0.5615143179893494 916.6006469726562 0.8048551678657532 0.71506125 0.7110542058944702 True -7 28600 38.755589962005615 0.7147808074951172 802.1219482421875 0.6711211204528809 912.8145751953125 0.8068224191665649 0.7189957 0.6906946301460266 True -8 32175 38.726359605789185 1.4087378978729248 803.3080444335938 0.6587594747543335 906.0064086914062 0.8090981841087341 0.7229757 0.6248124241828918 True -9 35750 38.716954708099365 0.7102048397064209 939.8449096679688 0.41706520318984985 900.8146362304688 0.8111183643341064 0.7280181 0.5855327248573303 True -10 39325 38.78389835357666 0.7178895473480225 803.1513671875 0.4934238791465759 893.7056884765625 0.8137298822402954 0.73479575 0.5443158149719238 True -11 42900 38.70606088638306 0.6976697444915771 790.6300048828125 0.6810038089752197 888.6795654296875 0.8156868815422058 0.7383375 0.5368378162384033 True -12 46475 38.69969081878662 1.4488790035247803 712.0007934570312 0.6494319438934326 882.754638671875 0.8178400993347168 0.7456844 0.49968457221984863 True -13 50050 38.728792667388916 0.7130415439605713 783.7533569335938 0.3315933346748352 878.0234985351562 0.8197050094604492 0.7534274 0.4720762073993683 True -14 53625 38.744828939437866 0.7246818542480469 707.7420654296875 0.4613403081893921 874.0594482421875 0.8217988014221191 0.7587002 0.45798230171203613 True -15 57200 38.70743107795715 0.7216806411743164 699.4188232421875 0.5438047647476196 871.2970581054688 0.8233785629272461 0.7647086 0.45105835795402527 True -16 60775 38.68895769119263 0.7138290405273438 720.7376098632812 0.45291608572006226 870.2326049804688 0.8242881894111633 0.76696265 0.4462696611881256 True -17 64350 38.75442099571228 0.7336161136627197 757.084228515625 0.38490915298461914 870.0587158203125 0.8244892358779907 0.76831305 0.44760894775390625 True -18 67925 38.70082902908325 2.471994161605835 622.3464965820312 0.3493691682815552 871.0592651367188 0.8242875933647156 0.7670502 0.45122194290161133 False -19 71500 39.38935041427612 0.7166705131530762 678.2894287109375 0.4628884494304657 871.3370971679688 0.8241490721702576 0.7661761 0.4578971564769745 False diff --git a/ENCSR836FIL/cherimoya.fold_0.performance.tsv b/ENCSR836FIL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3d1f8e3e98754d94103ad9ad52e27eb862097063..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -870.0587158203125 0.13584434986114502 0.824489176273346 0.5214792490005493 0.7683130502700806 0.7045711278915405 0.44760894775390625 \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_1.evaluate.json b/ENCSR836FIL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 440e5ec77286b097950bac394d064f3684d44378..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF438ZUH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_1.fit.json b/ENCSR836FIL/cherimoya.fold_1.fit.json deleted file mode 100644 index 18596a8872134c2921318eba874c415d6e2a7418..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF438ZUH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_1.log b/ENCSR836FIL/cherimoya.fold_1.log deleted file mode 100644 index c698276dc1f6915c4c7cb31b8d5d5f86fc687bf5..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3520 43.721412658691406 4.295845985412598 826.490478515625 0.621350884437561 1271.8853759765625 0.6977363228797913 0.6124682 8.012868881225586 True -1 7040 38.89367723464966 1.1786880493164062 757.1246337890625 0.7020551562309265 1048.90771484375 0.7893179655075073 0.6864592 2.306673526763916 True -2 10560 38.95288801193237 0.9637298583984375 691.7999267578125 0.520897388458252 1011.6234130859375 0.7980143427848816 0.70506734 1.2162261009216309 True -3 14080 38.90998649597168 0.9462263584136963 858.058349609375 0.537580132484436 995.2293701171875 0.8024600148200989 0.71907717 0.912397563457489 True -4 17600 38.887181997299194 0.9677548408508301 879.5684204101562 0.7350566983222961 990.9857177734375 0.8037450909614563 0.71820503 0.9065656065940857 False -5 21120 38.92415452003479 2.7374651432037354 788.0279541015625 0.660131573677063 982.257080078125 0.8057633638381958 0.72332186 0.8002342581748962 True -6 24640 38.93346929550171 0.9649701118469238 662.7117919921875 0.6545172929763794 976.44091796875 0.808163583278656 0.7219551 0.7395193576812744 False -7 28160 38.85965657234192 0.9783823490142822 744.3038330078125 0.8251594305038452 969.7868041992188 0.8107228875160217 0.72997963 0.6793349981307983 True -8 31680 38.81572914123535 0.9775917530059814 714.9885864257812 0.7713240385055542 960.6017456054688 0.8139021396636963 0.7331675 0.6227821111679077 True -9 35200 38.844048261642456 2.9878671169281006 663.428466796875 0.442642480134964 956.1959228515625 0.8160423040390015 0.7411514 0.5769869089126587 True -10 38720 38.940733432769775 0.9572365283966064 727.768798828125 0.39044708013534546 948.0031127929688 0.8182912468910217 0.745755 0.5543972849845886 True -11 42240 38.845232248306274 0.9750161170959473 769.65185546875 0.43733900785446167 941.5077514648438 0.8214940428733826 0.7551878 0.5298458337783813 True -12 45760 38.789992809295654 0.9807226657867432 807.8007202148438 0.5746336579322815 934.9627075195312 0.8241651058197021 0.7620194 0.5063931941986084 True -13 49280 38.820165395736694 0.9740095138549805 755.2410278320312 0.6350052952766418 930.553466796875 0.8265710473060608 0.76983523 0.487504243850708 True -14 52800 38.80200552940369 1.7930240631103516 786.7911376953125 0.38942408561706543 925.7981567382812 0.8288573026657104 0.77691376 0.4721161127090454 True -15 56320 38.1716148853302 0.9643340110778809 811.159423828125 0.33702021837234497 922.333740234375 0.8306809067726135 0.78293157 0.45045414566993713 True -16 59840 38.08818507194519 0.9505317211151123 744.1446533203125 0.30411672592163086 921.1388549804688 0.8317168354988098 0.7873172 0.44800683856010437 True -17 63360 38.07957410812378 0.9424788951873779 680.9192504882812 0.5953027009963989 921.7821655273438 0.8320197463035583 0.7885949 0.44622668623924255 True -18 66880 38.06988191604614 0.9471786022186279 714.8323364257812 0.33660638332366943 923.072021484375 0.8318415284156799 0.7873635 0.4465767443180084 False -19 70400 38.050699949264526 0.9382147789001465 742.0453491210938 0.3629137873649597 923.16845703125 0.8316207528114319 0.78685653 0.45102018117904663 False diff --git a/ENCSR836FIL/cherimoya.fold_1.performance.tsv b/ENCSR836FIL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 953a26237417c847492c5aae800d20c989d0258b..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -921.7821655273438 0.12812447547912598 0.8320197463035583 0.5465770363807678 0.7885949015617371 0.7446310520172119 0.44622668623924255 \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_2.evaluate.json b/ENCSR836FIL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 076be3f0fe98e9345df77166c33631afbbbe88d0..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF438ZUH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_2.fit.json b/ENCSR836FIL/cherimoya.fold_2.fit.json deleted file mode 100644 index 4601254fea099bbd51a5096fe39242052a696127..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF438ZUH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_2.log b/ENCSR836FIL/cherimoya.fold_2.log deleted file mode 100644 index eaddcbc4ef72dde1560268769e05e9cf04421287..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3718 45.827658891677856 4.447505474090576 713.582275390625 0.6741359233856201 1212.4503173828125 0.700890302658081 0.5970902 7.773382663726807 True -1 7436 41.03668546676636 0.9921765327453613 736.141357421875 0.8183079957962036 1004.3353881835938 0.7878196239471436 0.69017214 1.8733233213424683 True -2 11154 41.03822350502014 0.796043872833252 809.0396728515625 0.8890743255615234 982.1798095703125 0.793507993221283 0.70318335 1.2161598205566406 True -3 14872 41.12427020072937 1.9566023349761963 688.67578125 0.4418722987174988 966.06982421875 0.7988907694816589 0.71581155 0.953622579574585 True -4 18590 41.06034255027771 0.7875735759735107 787.2357177734375 0.7059465646743774 960.1155395507812 0.8007370233535767 0.7186888 0.8341686129570007 True -5 22308 40.992647886276245 0.7717351913452148 841.3604736328125 0.8432703018188477 956.4913330078125 0.8013880848884583 0.7182348 0.8155067563056946 False -6 26026 40.985560178756714 2.3481478691101074 814.059814453125 0.968656599521637 949.3529052734375 0.8028777241706848 0.7211055 0.6556037068367004 True -7 29744 41.066142082214355 0.7865540981292725 799.1883544921875 0.6909445524215698 940.2138671875 0.8066993355751038 0.72631204 0.6051515936851501 True -8 33462 41.01449704170227 0.7802603244781494 798.5020751953125 0.5525231957435608 936.0444946289062 0.8082228899002075 0.7310596 0.597152054309845 True -9 37180 40.38458299636841 1.7638359069824219 738.140625 0.517815113067627 929.461181640625 0.8104372024536133 0.7367866 0.5621821880340576 True -10 40898 40.30682063102722 1.5130326747894287 642.8336181640625 0.41501784324645996 922.2236328125 0.8131945133209229 0.7417544 0.5386836528778076 True -11 44616 40.28894639015198 0.7734832763671875 704.1857299804688 0.4008136987686157 915.0870361328125 0.815991997718811 0.74973756 0.5208109617233276 True -12 48334 40.240116357803345 18.6063334941864 656.2656860351562 0.3834713101387024 910.4826049804688 0.8182365894317627 0.75570554 0.5071725249290466 True -13 52052 40.24911046028137 1.8035857677459717 810.2714233398438 0.49769747257232666 905.749267578125 0.8208747506141663 0.7647078 0.49736639857292175 True -14 55770 40.37568998336792 1.9392681121826172 681.0548095703125 0.41238290071487427 901.767333984375 0.8228663206100464 0.7686899 0.471717894077301 True -15 59488 40.28281021118164 0.7828068733215332 822.4024658203125 0.38703078031539917 897.415283203125 0.8249905705451965 0.77319497 0.4593510329723358 True -16 63206 40.309351205825806 0.7799193859100342 687.6083984375 0.3510110378265381 896.4231567382812 0.8260725736618042 0.7797089 0.4504520297050476 True -17 66924 40.343361139297485 0.7705657482147217 691.302734375 0.3112025856971741 896.3873901367188 0.8264741897583008 0.78051335 0.4500262439250946 True -18 70642 40.26392960548401 0.7760472297668457 817.1904907226562 0.22938838601112366 897.1160278320312 0.8264304399490356 0.77977353 0.45393162965774536 False -19 74360 40.25110983848572 0.7703275680541992 758.1594848632812 0.34833335876464844 897.608154296875 0.8262665867805481 0.7787256 0.45623767375946045 False diff --git a/ENCSR836FIL/cherimoya.fold_2.performance.tsv b/ENCSR836FIL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ffb56101fe95c3e14a897a2fe56e53df004a8ca0..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -896.3873901367188 0.13232725858688354 0.8264741897583008 0.535295307636261 0.780513346195221 0.7295493483543396 0.4500262439250946 \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_3.evaluate.json b/ENCSR836FIL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6811cebbf7c3a8a7be595f6db0988f83a91a64e9..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF438ZUH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_3.fit.json b/ENCSR836FIL/cherimoya.fold_3.fit.json deleted file mode 100644 index 9cb75e18a74a01502e204f81a8f010ab23ae04aa..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF438ZUH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_3.log b/ENCSR836FIL/cherimoya.fold_3.log deleted file mode 100644 index 1c968bdf44f4fc604af494209a1316667454afa7..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3620 44.86289572715759 5.7389750480651855 785.9650268554688 0.9100670218467712 1176.4564208984375 0.6941124200820923 0.60549396 9.442183494567871 True -1 7240 40.006591796875 0.8394980430603027 903.6116943359375 0.7376453280448914 982.9174194335938 0.7835735082626343 0.67951006 2.2002813816070557 True -2 10860 39.94726824760437 0.8959572315216064 794.4321899414062 0.5532196760177612 955.4568481445312 0.7908303141593933 0.69405264 1.2542564868927002 True -3 14480 40.016297817230225 2.292006015777588 884.1456298828125 0.4857555627822876 942.2822265625 0.7963669896125793 0.7059967 1.1752221584320068 True -4 18100 39.2520911693573 0.7322828769683838 820.42919921875 0.8970447182655334 936.521728515625 0.7994564175605774 0.71005005 1.109732747077942 True -5 21720 39.23100733757019 0.7196636199951172 771.405029296875 0.5467905402183533 929.4846801757812 0.801747739315033 0.7091334 0.9232226610183716 False -6 25340 39.178171157836914 0.7250745296478271 848.878173828125 0.7270652651786804 923.8680419921875 0.8035846948623657 0.7090038 0.8573322296142578 False -7 28960 39.19964933395386 0.7301678657531738 766.140869140625 0.5595300793647766 916.9911499023438 0.8059450387954712 0.7141049 0.78006511926651 True -8 32580 39.184595346450806 0.8627452850341797 673.3687133789062 0.41037100553512573 911.8876342773438 0.8078852295875549 0.7166958 0.7129967212677002 True -9 36200 39.29590845108032 0.7259178161621094 790.2598876953125 0.6088365316390991 905.510009765625 0.8100572228431702 0.72638345 0.6122308373451233 True -10 39820 39.24335598945618 0.7317678928375244 726.7440185546875 0.4246988892555237 901.0029907226562 0.812757670879364 0.7342966 0.6114470362663269 True -11 43440 39.2880744934082 0.751617431640625 787.279296875 0.4252890348434448 893.928955078125 0.8149563670158386 0.74075174 0.5583670139312744 True -12 47060 39.31150221824646 0.7396194934844971 610.2694091796875 0.5631575584411621 888.4032592773438 0.8178633451461792 0.74544334 0.5483569502830505 True -13 50680 39.23422884941101 0.7553961277008057 715.5035400390625 0.478366494178772 882.8778076171875 0.8203353881835938 0.7552619 0.5109521746635437 True -14 54300 39.32672381401062 0.7358624935150146 714.21826171875 0.6046883463859558 877.2257690429688 0.822807788848877 0.7651333 0.4939475953578949 True -15 57920 39.25353026390076 1.7794501781463623 633.921875 0.48954272270202637 872.9225463867188 0.8249379992485046 0.76863855 0.4702913761138916 True -16 61540 39.21724534034729 0.7463779449462891 793.739013671875 0.4048944115638733 870.7876586914062 0.825679361820221 0.77208704 0.45357072353363037 True -17 65160 39.2271294593811 0.7253117561340332 671.4063110351562 0.4099225401878357 871.096435546875 0.8257718086242676 0.77301306 0.4541778564453125 True -18 68780 39.29920244216919 0.7350847721099854 695.863037109375 0.4060367941856384 872.3870239257812 0.825385570526123 0.77218217 0.4542243480682373 False -19 72400 39.34207057952881 0.7369859218597412 805.03125 0.39200663566589355 872.70166015625 0.825213611125946 0.769857 0.4570778012275696 False diff --git a/ENCSR836FIL/cherimoya.fold_3.performance.tsv b/ENCSR836FIL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e41add776de58dd6de2ffa4394c9ddd01e782646..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -871.096435546875 0.13513390719890594 0.8257718086242676 0.5206359028816223 0.7730130553245544 0.7168211936950684 0.4541778564453125 \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_4.evaluate.json b/ENCSR836FIL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2384a2b4729672b6020c4d1fb31b990b8381e661..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF438ZUH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_4.fit.json b/ENCSR836FIL/cherimoya.fold_4.fit.json deleted file mode 100644 index 6100543e9b730412127543290199e2cb8cdff6bb..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF438ZUH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR836FIL/cherimoya.fold_4.log b/ENCSR836FIL/cherimoya.fold_4.log deleted file mode 100644 index b83fdc168219bc9ed8c8141bff28694f17bebaa7..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3663 44.4614577293396 4.415198564529419 744.2709350585938 0.6391335725784302 1157.4764404296875 0.6883536577224731 0.58033365 8.426647186279297 True -1 7326 40.39542818069458 0.8406434059143066 766.31396484375 0.41464465856552124 954.8267822265625 0.7812517881393433 0.66431546 2.4008748531341553 True -2 10989 40.19609832763672 0.7948033809661865 1033.637939453125 0.6116788387298584 933.18505859375 0.7868306636810303 0.68213737 1.140270471572876 True -3 14652 39.733845710754395 0.7472996711730957 796.301025390625 0.9241176843643188 915.656494140625 0.7942599058151245 0.6885166 0.9028188586235046 True -4 18315 39.61580514907837 0.7422387599945068 1001.19677734375 0.7710885405540466 909.1039428710938 0.7971018552780151 0.6930611 0.9167201519012451 True -5 21978 39.60789251327515 1.5237312316894531 855.7418212890625 0.8991426825523376 902.9840087890625 0.7989158034324646 0.6936929 0.9111625552177429 True -6 25641 39.702091455459595 0.7309579849243164 787.0671997070312 0.5339052677154541 897.0880126953125 0.8029651641845703 0.6971063 0.7865180969238281 True -7 29304 39.659886598587036 0.7356765270233154 806.35595703125 0.5464816093444824 891.0457763671875 0.8053622841835022 0.69931656 0.711469829082489 True -8 32967 39.66529607772827 0.7320168018341064 831.697509765625 0.5441106557846069 886.5333862304688 0.8071701526641846 0.70207 0.6803067326545715 True -9 36630 39.653562784194946 20.67793869972229 862.3818359375 0.7275975942611694 880.1300048828125 0.8097338676452637 0.70962095 0.627999484539032 True -10 40293 39.96447038650513 0.7606806755065918 825.3131713867188 0.5849138498306274 874.7015991210938 0.812094509601593 0.7152414 0.6014248728752136 True -11 43956 39.67146825790405 0.7403018474578857 687.1822509765625 0.3486005961894989 868.9690551757812 0.8142062425613403 0.72737706 0.5424132347106934 True -12 47619 39.61314082145691 0.7384552955627441 702.3401489257812 0.6927948594093323 864.38525390625 0.816618800163269 0.7314334 0.5375863909721375 True -13 51282 40.48142695426941 18.861582040786743 681.4762573242188 0.44296202063560486 859.8236083984375 0.8188701272010803 0.74092567 0.5016624331474304 True -14 54945 39.64590644836426 0.7362971305847168 786.8670043945312 0.4947407841682434 855.6951293945312 0.8208767175674438 0.7500139 0.47277024388313293 True -15 58608 39.59024739265442 0.7449407577514648 691.877197265625 0.4325112998485565 852.5972290039062 0.8224009275436401 0.755724 0.4597746729850769 True -16 62271 39.63428711891174 0.7312860488891602 642.6453857421875 0.3806949257850647 851.642822265625 0.8232090473175049 0.7584882 0.45068827271461487 True -17 65934 39.61282563209534 0.74526047706604 704.6158447265625 0.35117214918136597 850.50390625 0.823529064655304 0.7580966 0.4503534138202667 False -18 69597 39.619469165802 0.7551846504211426 678.1201782226562 0.2955405116081238 851.767333984375 0.8233492970466614 0.75595844 0.45447662472724915 False -19 73260 39.69845676422119 0.7438187599182129 705.4814453125 0.4233606457710266 852.4718017578125 0.8231145143508911 0.7547019 0.45707857608795166 False diff --git a/ENCSR836FIL/cherimoya.fold_4.performance.tsv b/ENCSR836FIL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index aea4497715e17cd8d8269d2bd0237f34c5c83e4c..0000000000000000000000000000000000000000 --- a/ENCSR836FIL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -851.642822265625 0.13718187808990479 0.8232090473175049 0.5173189043998718 0.7584881782531738 0.6946254372596741 0.45068827271461487 \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_0.evaluate.json b/ENCSR837ZSS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 61587eb2b76f7fbefd6c0585bacf93e965789edc..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF327HJI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_0.fit.json b/ENCSR837ZSS/cherimoya.fold_0.fit.json deleted file mode 100644 index 6e6008e7d8ff42d8191d423e162a3fd18cd3f14d..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF327HJI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_0.log b/ENCSR837ZSS/cherimoya.fold_0.log deleted file mode 100644 index 4276cdbe1d249b887a5de8d8ead877ce73080faa..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2091 28.904564142227173 6.889915704727173 169.57171630859375 0.4299296438694 265.7003479003906 0.12998513877391815 0.6798813 5.569102764129639 True -1 4182 23.355931997299194 0.4528052806854248 150.66619873046875 0.3041435480117798 242.06324768066406 0.17785002291202545 0.75424874 2.236131191253662 True -2 6273 23.23283815383911 9.822238206863403 218.5286865234375 0.399143248796463 234.17910766601562 0.18785157799720764 0.7848323 1.2968213558197021 True -3 8364 22.906532287597656 0.434826135635376 156.83538818359375 0.46623045206069946 228.8859405517578 0.19512763619422913 0.81337875 0.6968591213226318 True -4 10455 22.604952096939087 0.4111499786376953 184.29483032226562 0.4041416347026825 227.44227600097656 0.19762524962425232 0.8201071 0.647203803062439 True -5 12546 22.650683403015137 2.439748525619507 186.7718048095703 0.37739208340644836 226.66592407226562 0.19835545122623444 0.82545394 0.5913757681846619 True -6 14637 22.620753049850464 0.42491602897644043 186.889404296875 0.4126398265361786 225.9462432861328 0.1993970274925232 0.8340612 0.5648809671401978 True -7 16728 22.5966637134552 0.616727352142334 172.81927490234375 0.47468432784080505 224.8230438232422 0.20233045518398285 0.83635265 0.5400682091712952 True -8 18819 22.631483793258667 0.4096846580505371 207.11294555664062 0.5071730613708496 223.56996154785156 0.2052774280309677 0.83968353 0.5024550557136536 True -9 20910 22.593451023101807 0.44635629653930664 121.92143249511719 0.42235538363456726 222.88751220703125 0.20661911368370056 0.8436576 0.4641224443912506 True -10 23001 22.57587480545044 0.42632055282592773 229.74937438964844 0.47262370586395264 221.72146606445312 0.20893046259880066 0.85317147 0.40465080738067627 True -11 25092 22.596739768981934 0.4872925281524658 195.23724365234375 0.4988632798194885 221.2364501953125 0.21063101291656494 0.85597414 0.38681498169898987 True -12 27183 22.602694272994995 26.920682191848755 194.83709716796875 0.3095861077308655 220.8859405517578 0.21138696372509003 0.8619375 0.35259878635406494 True -13 29274 22.784212589263916 0.4700188636779785 143.45010375976562 0.34444761276245117 219.8549041748047 0.21312277019023895 0.868034 0.33295610547065735 True -14 31365 23.02503204345703 8.331941843032837 184.13897705078125 0.2050638347864151 219.3088836669922 0.21402136981487274 0.8726122 0.3154778778553009 True -15 33456 22.71478843688965 0.4220433235168457 176.21717834472656 0.3799632489681244 219.31423950195312 0.21314571797847748 0.87577903 0.301218718290329 True -16 35547 22.625600337982178 0.41830968856811523 179.27500915527344 0.1923840343952179 219.280029296875 0.2140885293483734 0.87776136 0.2935176193714142 True -17 37638 22.625231981277466 0.41701364517211914 154.3549041748047 0.15745878219604492 219.32675170898438 0.213208869099617 0.87927127 0.2890852689743042 True -18 39729 22.60948657989502 34.87713694572449 239.84242248535156 0.26081418991088867 219.13333129882812 0.21440401673316956 0.87771106 0.2907615303993225 False -19 41820 24.242743968963623 0.4442882537841797 216.6593017578125 0.41465461254119873 219.36386108398438 0.21370679140090942 0.87625235 0.29431208968162537 False diff --git a/ENCSR837ZSS/cherimoya.fold_0.performance.tsv b/ENCSR837ZSS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fd8e539aeed05b4b1a732694c79452ff4f6b170f..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -219.32675170898438 0.5476820468902588 0.213208869099617 0.059032946825027466 0.8792712688446045 0.7943102717399597 0.2890852689743042 \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_1.evaluate.json b/ENCSR837ZSS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 24cbd15777875184827db72c938fd9cd2a15f71e..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF327HJI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_1.fit.json b/ENCSR837ZSS/cherimoya.fold_1.fit.json deleted file mode 100644 index e81df30db65ca03f12d8f1bf2db09c55418a3446..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF327HJI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_1.log b/ENCSR837ZSS/cherimoya.fold_1.log deleted file mode 100644 index 5dab35f2bbfcc17b879b1a75aa0b46648ffbc7b2..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2036 28.42194128036499 4.045843124389648 284.7005615234375 0.5806639194488525 336.4962158203125 0.14040310680866241 0.6568281 6.814858436584473 True -1 4072 22.642614126205444 0.577735185623169 204.9126739501953 0.7117214798927307 306.3730163574219 0.19597390294075012 0.7571195 2.9978935718536377 True -2 6108 22.55545949935913 0.5655393600463867 195.45193481445312 0.5693057179450989 291.18182373046875 0.21463996171951294 0.8031447 1.5572803020477295 True -3 8144 22.529778480529785 1.0234575271606445 159.51644897460938 0.4531194269657135 286.1396179199219 0.2197464555501938 0.81541735 0.9312358498573303 True -4 10180 22.5107638835907 0.5662221908569336 228.81817626953125 0.5628141164779663 282.8898010253906 0.22476497292518616 0.82340395 0.8080384135246277 True -5 12216 22.51143741607666 0.5644323825836182 220.73773193359375 0.6194255352020264 281.2657165527344 0.22740335762500763 0.82702047 0.7294825315475464 True -6 14252 22.483195066452026 0.5626316070556641 178.8199920654297 0.4416763186454773 279.3856506347656 0.2310175746679306 0.83584785 0.6610056161880493 True -7 16288 22.52583932876587 0.6297333240509033 255.86703491210938 0.5537357330322266 279.8652648925781 0.22933919727802277 0.8406584 0.5929323434829712 True -8 18324 22.50698447227478 1.6351039409637451 121.77738952636719 0.2939702272415161 277.74676513671875 0.23343898355960846 0.85018045 0.5660044550895691 True -9 20360 22.578807830810547 0.5665187835693359 224.3474884033203 0.48213595151901245 275.8699035644531 0.2373923659324646 0.85955316 0.5257952213287354 True -10 22396 22.731581926345825 38.09790873527527 139.83270263671875 0.37503165006637573 275.448486328125 0.2382613569498062 0.8641934 0.505763053894043 True -11 24432 26.84652304649353 24.046048402786255 183.92950439453125 0.2748432159423828 273.40545654296875 0.2419869303703308 0.8731263 0.4526570439338684 True -12 26468 24.180383682250977 0.5663671493530273 211.0159454345703 0.29243409633636475 272.10418701171875 0.24477706849575043 0.87743205 0.41786909103393555 True -13 28504 22.12948775291443 0.5538020133972168 205.79000854492188 0.302665650844574 271.4833679199219 0.2446957528591156 0.88055915 0.39520880579948425 True -14 30540 22.156648635864258 0.5714728832244873 211.42945861816406 0.40095412731170654 270.629150390625 0.2456325739622116 0.88744617 0.36329174041748047 True -15 32576 22.12859869003296 0.5609080791473389 161.34442138671875 0.19477355480194092 269.7051696777344 0.24809367954730988 0.88963413 0.3526792526245117 True -16 34612 22.094452619552612 0.6329224109649658 180.47470092773438 0.2762129604816437 269.40411376953125 0.24778251349925995 0.89080757 0.3449113070964813 True -17 36648 22.128548622131348 0.5479443073272705 198.80987548828125 0.29669278860092163 269.54833984375 0.24788697063922882 0.88997227 0.34218165278434753 False -18 38684 22.110151290893555 38.59809589385986 206.7451629638672 0.30839642882347107 270.1308288574219 0.24624913930892944 0.8899194 0.345787912607193 False -19 40720 22.167391777038574 0.5590760707855225 166.1380157470703 0.21270452439785004 270.027587890625 0.24674777686595917 0.88778645 0.34678831696510315 False diff --git a/ENCSR837ZSS/cherimoya.fold_1.performance.tsv b/ENCSR837ZSS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ea00ddfe9c4aa53183a71a4a398ea3df3685d7ab..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -269.40411376953125 0.5209455490112305 0.24778252840042114 0.0742558166384697 0.890807569026947 0.8475273251533508 0.3449113070964813 \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_2.evaluate.json b/ENCSR837ZSS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a098e51dbfb6d8a0edfd8bda8c5f2ce377d7c202..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF327HJI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_2.fit.json b/ENCSR837ZSS/cherimoya.fold_2.fit.json deleted file mode 100644 index 6051f2fe568cae79562b7ad03495a6c206a28333..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF327HJI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_2.log b/ENCSR837ZSS/cherimoya.fold_2.log deleted file mode 100644 index 1e550e5bf7f5ae3b8f37fadb9b581c5e17a55091..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2184 28.12082028388977 3.488981246948242 181.2139129638672 0.6503134965896606 282.1095275878906 0.13266214728355408 0.6594379 4.905964374542236 True -1 4368 23.852009057998657 0.4500091075897217 173.80923461914062 0.5448176860809326 254.26547241210938 0.1867484450340271 0.7886021 1.9349795579910278 True -2 6552 23.85906481742859 0.4203007221221924 152.58200073242188 0.49329668283462524 246.04869079589844 0.19587454199790955 0.79719454 1.0470235347747803 True -3 8736 23.84508728981018 0.8991925716400146 191.00448608398438 0.46416816115379333 242.3260955810547 0.200021892786026 0.8070404 0.6781816482543945 True -4 10920 23.7942214012146 0.43607473373413086 237.25665283203125 0.5774521231651306 240.87696838378906 0.2011282742023468 0.8074915 0.6433942914009094 True -5 13104 23.778461694717407 0.7147936820983887 211.35498046875 0.49064871668815613 238.51406860351562 0.2054743617773056 0.82509506 0.5713971853256226 True -6 15288 23.764322996139526 21.759237051010132 236.94815063476562 0.37756577134132385 237.09979248046875 0.20876772701740265 0.83243275 0.5556938052177429 True -7 17472 23.86962580680847 0.43292713165283203 203.01881408691406 0.44641372561454773 236.1080780029297 0.2108353078365326 0.83303946 0.5269426703453064 True -8 19656 23.900627374649048 0.42613935470581055 193.42091369628906 0.31180906295776367 235.03248596191406 0.21226033568382263 0.84543157 0.4668259620666504 True -9 21840 23.864062786102295 0.42554402351379395 167.90304565429688 0.29235732555389404 234.29222106933594 0.21379354596138 0.85316753 0.41446998715400696 True -10 24024 24.7575786113739 22.511568069458008 223.71441650390625 0.35016950964927673 233.313232421875 0.21608711779117584 0.85834396 0.3959469199180603 True -11 26208 23.91045117378235 0.4357287883758545 206.85487365722656 0.37797290086746216 232.52401733398438 0.21752962470054626 0.86369944 0.3657430410385132 True -12 28392 23.856067419052124 0.4297478199005127 228.1808624267578 0.3229030966758728 231.59584045410156 0.2195274829864502 0.8704281 0.34145796298980713 True -13 30576 23.578904151916504 0.42337608337402344 210.43905639648438 0.37236925959587097 230.8701629638672 0.2209959328174591 0.87632024 0.3181670308113098 True -14 32760 23.345344305038452 0.4255404472351074 158.32765197753906 0.4534817337989807 230.22506713867188 0.22198571264743805 0.879843 0.3037327229976654 True -15 34944 23.351394653320312 0.4243474006652832 227.00961303710938 0.35621607303619385 229.94686889648438 0.22285374999046326 0.8824299 0.2948509156703949 True -16 37128 23.3629949092865 0.4200282096862793 210.7869110107422 0.13398492336273193 229.9696807861328 0.22210974991321564 0.88469744 0.28805217146873474 True -17 39312 23.385974645614624 9.994776964187622 174.59295654296875 0.15295228362083435 230.55014038085938 0.22050762176513672 0.8832961 0.2869093418121338 False -18 41496 23.789669036865234 0.4304080009460449 170.74725341796875 0.208469957113266 230.16464233398438 0.2223266065120697 0.88146776 0.291602224111557 False -19 43680 23.664677381515503 0.43627047538757324 189.69656372070312 0.28672608733177185 230.5121307373047 0.2212894707918167 0.8819095 0.2940952181816101 False diff --git a/ENCSR837ZSS/cherimoya.fold_2.performance.tsv b/ENCSR837ZSS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 23e6fe4b8bde357125bca0fd49885e887edd18e0..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -229.9696807861328 0.5404502749443054 0.22210974991321564 0.06411497294902802 0.884697437286377 0.8168773651123047 0.28805217146873474 \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_3.evaluate.json b/ENCSR837ZSS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c159502c759f23aaf86ad139f5b53964304061cf..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF327HJI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_3.fit.json b/ENCSR837ZSS/cherimoya.fold_3.fit.json deleted file mode 100644 index f280c862d18709a343bf1b792b928c350a961c3d..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF327HJI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_3.log b/ENCSR837ZSS/cherimoya.fold_3.log deleted file mode 100644 index 09ed67d2be75a30bcaa6c4e8131273923c1f4d1f..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2086 26.930424213409424 6.707637310028076 172.73153686523438 0.3457494378089905 290.6343078613281 0.14038287103176117 0.6330518 5.942139625549316 True -1 4172 22.790687084197998 0.4182150363922119 185.63101196289062 0.794348418712616 265.1537170410156 0.19015656411647797 0.745473 2.5101919174194336 True -2 6258 23.356788158416748 23.19361162185669 182.12057495117188 0.4740450978279114 254.37423706054688 0.20498833060264587 0.7732057 1.2901719808578491 True -3 8344 23.522106647491455 18.574458360671997 247.88836669921875 0.5376965999603271 250.20962524414062 0.2100805640220642 0.789444 0.8217989802360535 True -4 10430 23.580471992492676 26.19404101371765 151.3243408203125 0.2974022626876831 248.8335418701172 0.21215209364891052 0.7986491 0.7601925730705261 True -5 12516 23.628165245056152 16.38731074333191 209.978759765625 0.3406809866428375 247.53126525878906 0.21493221819400787 0.8031944 0.758455753326416 True -6 14602 23.024515390396118 0.412001371383667 170.16085815429688 0.3714684844017029 246.97494506835938 0.2156672179698944 0.80586374 0.7393857836723328 True -7 16688 22.930845737457275 0.41248106956481934 186.03045654296875 0.3953956067562103 245.44561767578125 0.21951833367347717 0.8163654 0.7397645115852356 True -8 18774 22.816917419433594 0.41161680221557617 212.93289184570312 0.49574339389801025 244.88656616210938 0.22011753916740417 0.8245376 0.6830522418022156 True -9 20860 22.707796335220337 1.0142648220062256 188.62313842773438 0.42773231863975525 243.28506469726562 0.2244996428489685 0.83153015 0.6230118274688721 True -10 22946 22.773566484451294 1.9938883781433105 223.89651489257812 0.3682459592819214 242.63247680664062 0.22577549517154694 0.83295894 0.5910182595252991 True -11 25032 22.988272190093994 0.41992616653442383 187.7533721923828 0.36539146304130554 241.69314575195312 0.22714358568191528 0.84261173 0.5129957795143127 True -12 27118 22.867557764053345 25.333292245864868 197.20159912109375 0.29872268438339233 241.43846130371094 0.22684887051582336 0.8500738 0.46735715866088867 True -13 29204 23.165329217910767 0.40619921684265137 181.18194580078125 0.38535165786743164 240.56491088867188 0.22883936762809753 0.8569283 0.43649551272392273 True -14 31290 22.965418815612793 20.11730694770813 229.61276245117188 0.4066084027290344 239.40011596679688 0.23097148537635803 0.86431646 0.393769770860672 True -15 33376 23.59770631790161 3.562346935272217 184.55242919921875 0.1776248812675476 238.79795837402344 0.23291702568531036 0.8680987 0.3687989115715027 True -16 35462 22.440014362335205 12.269411325454712 187.96011352539062 0.311484694480896 238.50828552246094 0.23301245272159576 0.87251276 0.3536030650138855 True -17 37548 22.355745315551758 0.4021263122558594 154.90264892578125 0.32358723878860474 238.61636352539062 0.23197385668754578 0.87388086 0.3444455564022064 True -18 39634 22.383312940597534 0.4006831645965576 164.51254272460938 0.19783824682235718 238.9569091796875 0.23167821764945984 0.87100893 0.34571292996406555 False -19 41720 22.36489748954773 0.39656972885131836 234.54046630859375 0.18515023589134216 238.9111785888672 0.23221297562122345 0.8723688 0.34884724020957947 False diff --git a/ENCSR837ZSS/cherimoya.fold_3.performance.tsv b/ENCSR837ZSS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 17f8c4b842704a78fad44590fa1e8ca3e391fc77..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -238.61636352539062 0.5338327288627625 0.23197387158870697 0.0663788691163063 0.8738808631896973 0.8097104430198669 0.3444455564022064 \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_4.evaluate.json b/ENCSR837ZSS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3d7f26d5530554dbe987715934ecf1dc93885165..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF327HJI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_4.fit.json b/ENCSR837ZSS/cherimoya.fold_4.fit.json deleted file mode 100644 index 8a00af044a8ff55c465cb41437041ea04974631b..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF327HJI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR837ZSS/cherimoya.fold_4.log b/ENCSR837ZSS/cherimoya.fold_4.log deleted file mode 100644 index acbc532d9c33d0b5eb9ecd5285a0c34f71bb4a66..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2064 28.637460231781006 15.564905166625977 200.01055908203125 0.6330580711364746 247.71661376953125 0.12890098989009857 0.65735364 5.04195499420166 True -1 4128 22.889450788497925 0.7294697761535645 177.84848022460938 0.6946110725402832 228.8917999267578 0.16957810521125793 0.75312245 2.0085408687591553 True -2 6192 22.575602293014526 0.4253053665161133 159.85089111328125 0.5971255898475647 220.29876708984375 0.18191134929656982 0.78288484 1.2386534214019775 True -3 8256 22.68796467781067 0.41774439811706543 185.45040893554688 0.46538376808166504 217.05943298339844 0.18470138311386108 0.7961316 0.6617730259895325 True -4 10320 22.574653148651123 0.4178614616394043 184.15994262695312 0.4641210734844208 215.4311981201172 0.18745246529579163 0.8045001 0.6387680172920227 True -5 12384 22.541836261749268 0.426222562789917 180.69024658203125 0.45880287885665894 214.19754028320312 0.1902991682291031 0.8160215 0.5894479155540466 True -6 14448 22.54670548439026 1.8567776679992676 186.94064331054688 0.36372947692871094 213.3815460205078 0.191414013504982 0.8237016 0.534650444984436 True -7 16512 22.62046480178833 0.44577622413635254 186.6880340576172 0.3137443959712982 211.92527770996094 0.1949501633644104 0.8331054 0.5077161192893982 True -8 18576 22.6411075592041 2.2904469966888428 245.24957275390625 0.32343801856040955 211.35284423828125 0.19653862714767456 0.8358731 0.4621492028236389 True -9 20640 22.64426898956299 1.5452594757080078 180.9810791015625 0.3308337330818176 210.5698699951172 0.19827258586883545 0.8420545 0.4349006414413452 True -10 22704 22.58659791946411 0.4313395023345947 180.84878540039062 0.30354663729667664 210.35610961914062 0.19842246174812317 0.8511801 0.37928488850593567 True -11 24768 22.564295053482056 0.4276247024536133 214.05841064453125 0.3337792754173279 209.76585388183594 0.20026621222496033 0.856983 0.35094255208969116 True -12 26832 22.7456476688385 24.308042287826538 174.78985595703125 0.25618183612823486 208.84967041015625 0.2020234316587448 0.86004025 0.3266373872756958 True -13 28896 23.140928268432617 0.42285752296447754 201.50454711914062 0.3737085461616516 208.40521240234375 0.2031739056110382 0.86721575 0.30340227484703064 True -14 30960 22.61575961112976 0.42212772369384766 237.49388122558594 0.31281495094299316 207.9723358154297 0.2044711709022522 0.86883885 0.29148390889167786 True -15 33024 22.60253620147705 0.42449188232421875 193.56649780273438 0.38305383920669556 207.1351318359375 0.2060936689376831 0.87061304 0.2851099669933319 True -16 35088 22.600544452667236 0.42488741874694824 179.55393981933594 0.34973299503326416 207.75216674804688 0.20426945388317108 0.8731832 0.27843067049980164 True -17 37152 22.578033447265625 0.4195408821105957 152.11123657226562 0.15824675559997559 208.062744140625 0.203584223985672 0.8750842 0.27723100781440735 True -18 39216 22.338395357131958 0.4166688919067383 154.9363250732422 0.29793643951416016 207.92149353027344 0.20441779494285583 0.8722569 0.2790376543998718 False -19 41280 22.10390329360962 0.41104865074157715 186.31028747558594 0.2771802842617035 208.5063934326172 0.20229926705360413 0.87293535 0.28078731894493103 False diff --git a/ENCSR837ZSS/cherimoya.fold_4.performance.tsv b/ENCSR837ZSS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8d33c1f2da5e4aa671a4ddaa314ba1efd7d4aa0c..0000000000000000000000000000000000000000 --- a/ENCSR837ZSS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -208.062744140625 0.5541043877601624 0.2035842090845108 0.05154126510024071 0.8750842213630676 0.7858584523200989 0.27723100781440735 \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_0.evaluate.json b/ENCSR838IPF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8be08af98a72eecc1d6a129cdbbbd4c4299a52e9..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809HYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_0.fit.json b/ENCSR838IPF/cherimoya.fold_0.fit.json deleted file mode 100644 index 7d0a998c3862200c5d8f51e19aebeb38e1e08cbc..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF809HYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_0.log b/ENCSR838IPF/cherimoya.fold_0.log deleted file mode 100644 index 7e3224cbd7fa4b00db96e342c09a016abf4b3298..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2052 27.342089891433716 10.185312747955322 178.1856231689453 0.6417831778526306 257.13031005859375 0.11847157776355743 0.65989894 5.296581745147705 True -1 4104 22.673221111297607 0.45079970359802246 227.40536499023438 0.7410920858383179 247.1839141845703 0.1635337769985199 0.74443376 1.3811984062194824 True -2 6156 22.633670330047607 0.42892003059387207 259.1483154296875 0.7453259825706482 240.30081176757812 0.18580947816371918 0.7765342 0.7075458765029907 True -3 8208 22.683462858200073 0.8047986030578613 217.9534454345703 0.7298429012298584 237.2616729736328 0.19336917996406555 0.78434485 0.5581792593002319 True -4 10260 22.656099557876587 0.4288666248321533 230.6993408203125 0.4106086492538452 236.35540771484375 0.19515952467918396 0.7887836 0.5707913041114807 True -5 12312 22.63131546974182 0.4225788116455078 172.0968475341797 0.44245490431785583 235.2881317138672 0.19885344803333282 0.79552275 0.523718535900116 True -6 14364 22.670866012573242 0.6914620399475098 216.32620239257812 0.41455504298210144 234.71963500976562 0.20067493617534637 0.80067754 0.4959189295768738 True -7 16416 22.7349534034729 0.4386320114135742 198.0068817138672 0.605783224105835 234.3309326171875 0.20150262117385864 0.803548 0.46451422572135925 True -8 18468 22.63793158531189 0.7711443901062012 192.65005493164062 0.6552785634994507 233.84898376464844 0.2036576122045517 0.810359 0.4408809542655945 True -9 20520 24.024911642074585 20.93220853805542 190.90740966796875 0.4063895046710968 233.03846740722656 0.2069389522075653 0.8150273 0.4164837598800659 True -10 22572 23.736387252807617 21.29207944869995 219.5324249267578 0.5219539403915405 232.77806091308594 0.20720739662647247 0.81949216 0.4021981358528137 True -11 24624 23.42119526863098 0.43515658378601074 205.64889526367188 0.41083383560180664 232.37030029296875 0.2089841514825821 0.82052755 0.3975909650325775 True -12 26676 22.83044981956482 0.4455718994140625 206.53045654296875 0.4123855531215668 232.13034057617188 0.20914703607559204 0.82565486 0.3781246840953827 True -13 28728 22.729258060455322 0.4311037063598633 226.69456481933594 0.41823315620422363 231.78814697265625 0.21087010204792023 0.8285555 0.36773934960365295 True -14 30780 23.188289642333984 0.4413785934448242 198.47543334960938 0.3550414443016052 231.6928253173828 0.21097713708877563 0.8335639 0.3568817973136902 True -15 32832 22.770507097244263 0.44096922874450684 210.990966796875 0.3133540749549866 231.67733764648438 0.21099501848220825 0.8346007 0.3560650646686554 True -16 34884 22.719919443130493 0.836658239364624 179.0628662109375 0.23457303643226624 231.70787048339844 0.2108248770236969 0.83455247 0.3568726181983948 False -17 36936 23.45416283607483 0.42838525772094727 173.2020263671875 0.2409779578447342 231.86448669433594 0.2102421522140503 0.8310538 0.36450710892677307 False -18 38988 22.697983980178833 0.429088830947876 152.10345458984375 0.20360690355300903 232.0807342529297 0.20956523716449738 0.8293352 0.37359514832496643 False -19 41040 22.674209117889404 17.296659469604492 191.1719512939453 0.20960822701454163 232.63006591796875 0.20679613947868347 0.8279089 0.379934698343277 False diff --git a/ENCSR838IPF/cherimoya.fold_0.performance.tsv b/ENCSR838IPF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5910f39e88c31fecdb7d95e089703bd0deeacb2c..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -231.67733764648438 0.5410813093185425 0.21099501848220825 0.0615808442234993 0.8346006870269775 0.772861123085022 0.3560650646686554 \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_1.evaluate.json b/ENCSR838IPF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4e88ec26207c71bff9766fae0e5218746dfb6b9d..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809HYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_1.fit.json b/ENCSR838IPF/cherimoya.fold_1.fit.json deleted file mode 100644 index 9f85142992f1fb8249062b7ca46d540f51dc0054..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF809HYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_1.log b/ENCSR838IPF/cherimoya.fold_1.log deleted file mode 100644 index bd418815dfb576baafb82c017850e95c2b1b2a77..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2028 27.15224027633667 3.4771013259887695 278.7535705566406 1.0831196308135986 312.6252746582031 0.13585734367370605 0.6200788 6.855615139007568 True -1 4056 22.412415742874146 0.8212423324584961 212.1994171142578 0.7350513339042664 297.10223388671875 0.19441089034080505 0.72946304 2.2707314491271973 True -2 6084 22.394774198532104 0.5494465827941895 161.16758728027344 0.5717036128044128 287.9875183105469 0.21731022000312805 0.77243537 1.021471619606018 True -3 8112 22.3987033367157 0.5534975528717041 176.0274658203125 0.5341141819953918 285.1265869140625 0.22420629858970642 0.78297424 0.6608301401138306 True -4 10140 22.386393070220947 1.085360050201416 200.25927734375 0.593530535697937 284.01373291015625 0.22703644633293152 0.7871091 0.6046315431594849 True -5 12168 22.54340410232544 2.20843505859375 243.011474609375 0.6009680032730103 283.22119140625 0.22885188460350037 0.7886534 0.6679580211639404 True -6 14196 22.492409467697144 0.5614416599273682 173.76522827148438 0.33190974593162537 282.3721923828125 0.23161976039409637 0.79384965 0.6366686820983887 True -7 16224 22.454580545425415 0.557305097579956 171.68173217773438 0.45841866731643677 281.89935302734375 0.2328873872756958 0.8005006 0.6077667474746704 True -8 18252 22.549856662750244 0.6547935009002686 217.0903778076172 0.44504743814468384 281.6385803222656 0.23312413692474365 0.8091744 0.5615459084510803 True -9 20280 22.421966791152954 0.5630335807800293 154.0303955078125 0.5349417924880981 280.2774963378906 0.23822221159934998 0.8166965 0.5185987949371338 True -10 22308 22.440407276153564 0.561870813369751 170.67202758789062 0.32133448123931885 280.1230163574219 0.23834876716136932 0.82100594 0.48186007142066956 True -11 24336 22.472082376480103 18.337633848190308 163.3740234375 0.4350564479827881 279.31939697265625 0.24085158109664917 0.8237523 0.4605618417263031 True -12 26364 23.33572483062744 0.5738906860351562 155.39422607421875 0.3499818742275238 279.0572814941406 0.24082201719284058 0.82857543 0.43853136897087097 True -13 28392 22.497257232666016 0.564690351486206 202.19619750976562 0.39988210797309875 278.47528076171875 0.24327152967453003 0.8335592 0.423423171043396 True -14 30420 22.45979619026184 0.755366325378418 172.96469116210938 0.40838944911956787 278.31134033203125 0.2430032193660736 0.8356146 0.4122034013271332 True -15 32448 22.4142427444458 0.8002719879150391 139.780029296875 0.35804975032806396 278.2168884277344 0.2438240498304367 0.83773035 0.4117012023925781 True -16 34476 22.458268642425537 0.5636031627655029 202.5679168701172 0.38507887721061707 278.6694641113281 0.241325244307518 0.83688027 0.41267576813697815 False -17 36504 22.41995644569397 0.5539834499359131 207.1612548828125 0.25161901116371155 278.9429626464844 0.24101528525352478 0.8353078 0.420573890209198 False -18 38532 22.434874534606934 0.5498921871185303 167.54119873046875 0.23077772557735443 279.2675476074219 0.24018096923828125 0.83286154 0.43448707461357117 False -19 40560 22.432358741760254 0.5487539768218994 188.58929443359375 0.24507126212120056 279.37066650390625 0.2396155297756195 0.83066446 0.4402522146701813 False diff --git a/ENCSR838IPF/cherimoya.fold_1.performance.tsv b/ENCSR838IPF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7413f27d98250ddedc05373156ac869399339a43..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -278.2168884277344 0.514578640460968 0.2438240498304367 0.07547032833099365 0.837730348110199 0.7986016869544983 0.4117012023925781 \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_2.evaluate.json b/ENCSR838IPF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4eb3fe70f588e6be8b40a2a1ddb8fde41a2d98cd..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809HYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_2.fit.json b/ENCSR838IPF/cherimoya.fold_2.fit.json deleted file mode 100644 index 4065650d46ffd0c0aafad609879d08da56c0d42b..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF809HYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_2.log b/ENCSR838IPF/cherimoya.fold_2.log deleted file mode 100644 index 156a063867d51377666641ab6c2656eceaac0844..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2188 28.772183656692505 3.8084001541137695 194.01788330078125 0.7027354836463928 267.16790771484375 0.12922590970993042 0.6309685 4.753931045532227 True -1 4376 24.168732166290283 1.389937400817871 183.7635955810547 0.48322734236717224 255.3397674560547 0.17822545766830444 0.7283088 1.666793704032898 True -2 6564 24.169128894805908 0.4773216247558594 185.04641723632812 0.8965449333190918 247.07369995117188 0.1969410926103592 0.7715407 0.7725560069084167 True -3 8752 24.19682788848877 0.41804957389831543 162.43472290039062 0.4715122878551483 245.18429565429688 0.20110023021697998 0.7871444 0.4488815367221832 True -4 10940 24.207278728485107 0.4192349910736084 192.68934631347656 0.47210341691970825 244.03927612304688 0.20511986315250397 0.789342 0.43762874603271484 True -5 13128 24.161523818969727 22.179699420928955 180.33544921875 0.6557687520980835 243.24644470214844 0.20781399309635162 0.792271 0.40706419944763184 True -6 15316 28.566439867019653 8.19143295288086 181.40634155273438 0.35880041122436523 242.7022705078125 0.20977699756622314 0.7940323 0.4103182554244995 True -7 17504 24.233052968978882 0.42583227157592773 166.31549072265625 0.49022984504699707 242.15304565429688 0.21163327991962433 0.7982472 0.41238152980804443 True -8 19692 24.394235372543335 20.725658178329468 202.32655334472656 0.8718769550323486 241.55186462402344 0.21387040615081787 0.80154026 0.3996034860610962 True -9 21880 24.672449111938477 1.3743181228637695 185.6721649169922 0.7459886074066162 241.16912841796875 0.21501560509204865 0.80428666 0.39784497022628784 True -10 24068 24.35119867324829 0.4196169376373291 191.33995056152344 0.39700520038604736 240.8576202392578 0.21625304222106934 0.80897826 0.39311346411705017 True -11 26256 24.296713829040527 0.5790340900421143 187.0106201171875 0.2861059904098511 240.79885864257812 0.21643783152103424 0.8134161 0.38469424843788147 True -12 28444 24.44100260734558 0.41410160064697266 179.53231811523438 0.5238603353500366 240.4757843017578 0.2180289626121521 0.8162771 0.3813647925853729 True -13 30632 24.283814907073975 0.4162132740020752 203.1557159423828 0.42489853501319885 240.05653381347656 0.21950021386146545 0.8197982 0.3772892653942108 True -14 32820 24.214078187942505 19.931146144866943 143.38816833496094 0.423305481672287 240.17364501953125 0.2189866155385971 0.8231756 0.37332379817962646 True -15 35008 26.44630217552185 19.774919748306274 204.82867431640625 0.3945622444152832 240.3197784423828 0.21821017563343048 0.8246915 0.37448179721832275 True -16 37196 29.094332456588745 12.757637977600098 217.4801025390625 0.2732257544994354 240.03738403320312 0.21918722987174988 0.82465434 0.381990909576416 False -17 39384 24.242944717407227 0.42002153396606445 160.00173950195312 0.30045634508132935 240.23147583007812 0.21895776689052582 0.82055056 0.39271336793899536 False -18 41572 24.248535633087158 0.41167354583740234 219.87918090820312 0.29381701350212097 240.5296630859375 0.21768218278884888 0.8183705 0.40404239296913147 False -19 43760 24.160359859466553 0.40856313705444336 212.48728942871094 0.29060155153274536 240.7816925048828 0.21723249554634094 0.8168165 0.410917729139328 False diff --git a/ENCSR838IPF/cherimoya.fold_2.performance.tsv b/ENCSR838IPF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d55a175097de3ed7c0fe5a42cf9432a2413bea6e..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -240.3197784423828 0.5346164107322693 0.21821017563343048 0.06427742540836334 0.8246914744377136 0.7777271270751953 0.37448179721832275 \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_3.evaluate.json b/ENCSR838IPF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 164b2ed322ee474c203163093ecbf825f911608b..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809HYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_3.fit.json b/ENCSR838IPF/cherimoya.fold_3.fit.json deleted file mode 100644 index 7bcb5d851fd06ba1a3740565745bb4cfe087aa2c..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF809HYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_3.log b/ENCSR838IPF/cherimoya.fold_3.log deleted file mode 100644 index ad7af0161076b09efd769f79c67f65ae136f383f..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2087 27.627267599105835 3.5770249366760254 186.37945556640625 0.6951769590377808 283.32623291015625 0.12581224739551544 0.6334262 5.345769882202148 True -1 4174 23.25192904472351 0.43192052841186523 168.78475952148438 0.6184006929397583 271.1062316894531 0.17713184654712677 0.7201112 1.9729114770889282 True -2 6261 23.06658363342285 0.4242539405822754 187.08981323242188 0.6442642211914062 263.3595886230469 0.20040445029735565 0.7588692 1.1528871059417725 True -3 8348 23.1048526763916 0.4238617420196533 235.15997314453125 0.6434241533279419 261.30828857421875 0.20380190014839172 0.77128386 0.7488342523574829 True -4 10435 23.222183227539062 0.4241600036621094 217.20501708984375 0.5840998888015747 259.7454833984375 0.20933771133422852 0.7813272 0.6576425433158875 True -5 12522 23.07764196395874 0.727349042892456 247.27537536621094 0.5146109461784363 258.8861999511719 0.21215373277664185 0.7826617 0.6067346930503845 True -6 14609 23.054103136062622 0.867260217666626 165.35011291503906 0.4546419382095337 258.1084899902344 0.21455472707748413 0.7928702 0.5662030577659607 True -7 16696 23.096895456314087 0.42405104637145996 159.85552978515625 0.6163408756256104 258.1094970703125 0.21419520676136017 0.7963858 0.5123209357261658 True -8 18783 23.05009150505066 0.4241759777069092 185.48818969726562 0.5403733253479004 257.509765625 0.21597930788993835 0.80660945 0.48828262090682983 True -9 20870 23.048882007598877 2.059028387069702 212.58045959472656 0.6246225833892822 256.6626892089844 0.2192545086145401 0.80810565 0.4651825428009033 True -10 22957 23.13909077644348 25.487247705459595 205.95138549804688 0.47996509075164795 256.5879821777344 0.21911947429180145 0.8153874 0.43605026602745056 True -11 25044 23.698185443878174 11.965531349182129 203.00778198242188 0.46442538499832153 256.0820617675781 0.22087208926677704 0.8207081 0.4200320541858673 True -12 27131 23.074097633361816 0.4285166263580322 208.35887145996094 0.3725146949291229 255.9483642578125 0.2208251655101776 0.8256987 0.40954580903053284 True -13 29218 23.038097381591797 0.42992520332336426 209.4034423828125 0.34696251153945923 255.58006286621094 0.22253106534481049 0.83001465 0.3959030508995056 True -14 31305 23.107959747314453 0.42539024353027344 225.9647216796875 0.34408921003341675 255.3677520751953 0.2230617105960846 0.83275974 0.3949233889579773 True -15 33392 23.16187071800232 0.4231579303741455 210.2406768798828 0.32054048776626587 255.27285766601562 0.22347690165042877 0.8372076 0.3929775059223175 True -16 35479 23.04565715789795 25.211515426635742 235.76788330078125 0.20334741473197937 255.0985870361328 0.22385990619659424 0.8345033 0.3977101445198059 False -17 37566 23.821390390396118 14.474076986312866 165.37835693359375 0.34024012088775635 255.55209350585938 0.22151510417461395 0.83300585 0.40509194135665894 False -18 39653 23.722037315368652 23.284085273742676 188.61354064941406 0.22213158011436462 255.97177124023438 0.2202920764684677 0.83072215 0.4190739393234253 False -19 41740 23.135910034179688 1.963430404663086 199.38330078125 0.25758832693099976 255.99673461914062 0.22039316594600677 0.82821757 0.4275244474411011 False diff --git a/ENCSR838IPF/cherimoya.fold_3.performance.tsv b/ENCSR838IPF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 53e2f7c0c581a16f6cd9090a396feb029a8dafc0..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -255.27285766601562 0.5296463966369629 0.22347690165042877 0.06699229776859283 0.8372076153755188 0.7949614524841309 0.3929775059223175 \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_4.evaluate.json b/ENCSR838IPF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ac3f4a9e2a1ca2fa44bd665c20b9909dae97b15f..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF809HYF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_4.fit.json b/ENCSR838IPF/cherimoya.fold_4.fit.json deleted file mode 100644 index 962e86e400dbfb37578473863596dc4399ada100..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF809HYF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR838IPF/cherimoya.fold_4.log b/ENCSR838IPF/cherimoya.fold_4.log deleted file mode 100644 index 655a1fe7a7336c162b41b9e9b38c9846b2ea8682..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2106 27.555131673812866 6.117677450180054 195.02987670898438 0.5337247848510742 253.17152404785156 0.12105648964643478 0.63798004 4.950699329376221 True -1 4212 23.316351175308228 0.4375877380371094 224.16082763671875 0.6036133766174316 243.0067596435547 0.16882212460041046 0.72668916 1.6248116493225098 True -2 6318 23.310927629470825 0.4110722541809082 209.23851013183594 0.5309706926345825 236.258056640625 0.1880538910627365 0.7604339 0.6566715836524963 True -3 8424 23.26763153076172 0.415985107421875 233.50088500976562 0.4967989921569824 233.9956817626953 0.1936068832874298 0.76889664 0.5163235664367676 True -4 10530 23.29525852203369 13.894489288330078 216.77911376953125 0.30608701705932617 232.8306121826172 0.19626134634017944 0.7783244 0.47292667627334595 True -5 12636 26.30173897743225 14.588869094848633 206.14065551757812 0.46995043754577637 232.26083374023438 0.19766102731227875 0.78325546 0.42191281914711 True -6 14742 26.29131841659546 21.827531814575195 229.35867309570312 0.5713282823562622 231.70260620117188 0.19975115358829498 0.78960586 0.4043811559677124 True -7 16848 26.467262744903564 25.243850708007812 177.392333984375 0.3699539303779602 231.384521484375 0.20029039680957794 0.79184276 0.40023529529571533 True -8 18954 26.66546630859375 6.816659927368164 202.61647033691406 0.3775242865085602 230.9853973388672 0.20241910219192505 0.79407257 0.394381582736969 True -9 21060 23.30168867111206 0.417738676071167 168.70970153808594 0.34738439321517944 230.46429443359375 0.20380085706710815 0.8006043 0.3865256905555725 True -10 23166 23.55015277862549 0.43645286560058594 177.4901580810547 0.34050655364990234 230.1311798095703 0.20511864125728607 0.80708426 0.37825852632522583 True -11 25272 23.429784059524536 0.4199371337890625 155.66131591796875 0.2780342102050781 230.04881286621094 0.20565016567707062 0.8073287 0.37613967061042786 True -12 27378 23.284196853637695 0.42351770401000977 154.93026733398438 0.28472861647605896 230.0702362060547 0.20519451797008514 0.812218 0.3699965178966522 True -13 29484 23.269208669662476 21.50035071372986 210.444580078125 0.38890695571899414 229.62205505371094 0.20714892446994781 0.81749034 0.36187979578971863 True -14 31590 27.881357431411743 0.47059082984924316 255.19911193847656 0.27448421716690063 229.46437072753906 0.20816731452941895 0.8214891 0.35770705342292786 True -15 33696 23.303544759750366 19.382878065109253 213.35377502441406 0.28749585151672363 229.4925079345703 0.2081284075975418 0.82372206 0.35588061809539795 True -16 35802 25.203622817993164 0.4174044132232666 187.6957550048828 0.2610170543193817 229.75234985351562 0.2071388065814972 0.82500285 0.36398476362228394 True -17 37908 23.255331993103027 0.8558695316314697 171.79815673828125 0.20290742814540863 230.0394744873047 0.20637276768684387 0.8245981 0.3699263632297516 False -18 40014 23.33033037185669 1.25276780128479 203.0400848388672 0.20521560311317444 230.2184295654297 0.20566807687282562 0.82172287 0.3788752257823944 False -19 42120 23.354098796844482 0.41713976860046387 214.5316162109375 0.21385939419269562 230.3842010498047 0.20548050105571747 0.82142836 0.38456711173057556 False diff --git a/ENCSR838IPF/cherimoya.fold_4.performance.tsv b/ENCSR838IPF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 26c1c33eb3b7a0325fe935d3537c5bd2c33e5b7e..0000000000000000000000000000000000000000 --- a/ENCSR838IPF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -229.75234985351562 0.5424747467041016 0.2071388065814972 0.060120079666376114 0.8250028491020203 0.7623975872993469 0.36398476362228394 \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_0.evaluate.json b/ENCSR839GHA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 71d2649456292cff46490686c6e60996b74e7af8..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF156GMU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_0.fit.json b/ENCSR839GHA/cherimoya.fold_0.fit.json deleted file mode 100644 index fb83776a5cfd5a67fc793d51badc84b6e929e777..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF156GMU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_0.log b/ENCSR839GHA/cherimoya.fold_0.log deleted file mode 100644 index 5c3f88f53f6271afbc3155c8ddafa55bc4283b94..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.49434804916382 3.5703928470611572 428.15106201171875 0.45215725898742676 572.7161865234375 0.2618063986301422 0.72805643 3.952178955078125 True -1 5484 30.531545639038086 0.6310641765594482 393.7353515625 0.3198773264884949 528.9434814453125 0.3230254650115967 0.78353935 1.025268793106079 True -2 8226 30.188344717025757 0.6241824626922607 397.61309814453125 0.3611754775047302 519.2504272460938 0.33814558386802673 0.7899934 0.5761734843254089 True -3 10968 29.81908392906189 0.5927107334136963 423.00848388671875 0.4251388907432556 514.78955078125 0.34305688738822937 0.7991072 0.49197354912757874 True -4 13710 29.850005865097046 0.5890769958496094 487.60284423828125 0.47435060143470764 512.130615234375 0.3465316593647003 0.80835354 0.4564611613750458 True -5 16452 29.855536699295044 0.5826554298400879 397.3950500488281 0.38577544689178467 509.6702880859375 0.35029730200767517 0.8123173 0.376386821269989 True -6 19194 29.797645330429077 0.5951411724090576 512.8369140625 0.31964004039764404 508.1816711425781 0.3524843752384186 0.8191033 0.3776508569717407 True -7 21936 29.847668886184692 0.594975471496582 544.15625 0.3926410675048828 506.5525817871094 0.3550592064857483 0.8238317 0.35239502787590027 True -8 24678 29.912814140319824 0.5889015197753906 458.5824279785156 0.3218028247356415 503.8586120605469 0.3606450855731964 0.8305599 0.34882399439811707 True -9 27420 29.820995330810547 0.6078734397888184 528.02587890625 0.23488131165504456 502.8758850097656 0.36124563217163086 0.835421 0.30438899993896484 True -10 30162 29.851320505142212 0.6060686111450195 427.35968017578125 0.3805183172225952 501.8746643066406 0.36306992173194885 0.8386337 0.2898910641670227 True -11 32904 30.014769554138184 0.6024322509765625 482.48382568359375 0.31834083795547485 499.65777587890625 0.3671831488609314 0.8452798 0.27094385027885437 True -12 35646 29.84982132911682 18.79146146774292 409.41912841796875 0.30275392532348633 498.493408203125 0.3679407238960266 0.8473997 0.24691900610923767 True -13 38388 30.079107761383057 0.6166749000549316 411.3924560546875 0.26841098070144653 498.1835021972656 0.3678476810455322 0.854126 0.23977357149124146 True -14 41130 30.151513814926147 0.6068270206451416 410.7867736816406 0.34549790620803833 496.063720703125 0.372162789106369 0.8568002 0.22781524062156677 True -15 43872 30.028074741363525 0.5876290798187256 426.244873046875 0.1884097456932068 495.43353271484375 0.37273478507995605 0.85961056 0.21902182698249817 True -16 46614 30.12917137145996 0.5873010158538818 345.28802490234375 0.17997556924819946 495.2909240722656 0.3722212314605713 0.8633298 0.2128477841615677 True -17 49356 29.959067344665527 1.5231349468231201 397.34210205078125 0.1874191015958786 495.6065979003906 0.3719567060470581 0.8641807 0.21038933098316193 True -18 52098 30.05381989479065 0.6988494396209717 441.0267333984375 0.16167095303535461 495.44989013671875 0.37263867259025574 0.8624166 0.2116037905216217 False -19 54840 30.013375759124756 0.6000251770019531 466.0141906738281 0.21538114547729492 495.1172180175781 0.3733856976032257 0.86294055 0.21271613240242004 False diff --git a/ENCSR839GHA/cherimoya.fold_0.performance.tsv b/ENCSR839GHA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7d0fb77b78be18831d449130f345c431f9cb6ffc..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -495.6065979003906 0.40699243545532227 0.3719567060470581 0.1386624574661255 0.8641806840896606 0.8355714678764343 0.21038933098316193 \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_1.evaluate.json b/ENCSR839GHA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5175e52ae11c0149969880ce2b40a09d50c529ae..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF156GMU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_1.fit.json b/ENCSR839GHA/cherimoya.fold_1.fit.json deleted file mode 100644 index 1544c339bc7cb9d5a84a600c2557cddfd1ba867a..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF156GMU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_1.log b/ENCSR839GHA/cherimoya.fold_1.log deleted file mode 100644 index 0671e4f760f86c0856f8e1973c5e566c62b9532c..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2710 33.233248233795166 4.443143844604492 538.8179321289062 0.5347008109092712 676.90478515625 0.2652667164802551 0.7218223 4.622128486633301 True -1 5420 30.148285388946533 1.058610439300537 508.18603515625 0.6781409978866577 619.8779296875 0.3415011465549469 0.7783046 1.2975701093673706 True -2 8130 30.002891063690186 2.20456600189209 467.4404296875 0.5072901844978333 604.5274047851562 0.3574492931365967 0.79552644 0.6406247019767761 True -3 10840 29.499034643173218 19.000353574752808 442.5606994628906 0.47601792216300964 598.5391845703125 0.36442476511001587 0.8016913 0.607569694519043 True -4 13550 29.506031036376953 0.6847822666168213 480.62762451171875 0.3868238925933838 595.451904296875 0.36761483550071716 0.8067726 0.49311429262161255 True -5 16260 29.521163940429688 0.6642985343933105 537.9437255859375 0.3592641353607178 592.4486694335938 0.3724517226219177 0.8118909 0.4471563398838043 True -6 18970 29.490051984786987 0.6586630344390869 425.8196716308594 0.31198108196258545 589.6956176757812 0.37633517384529114 0.81980073 0.4229348599910736 True -7 21680 29.445741891860962 0.6643469333648682 472.9968566894531 0.25677865743637085 586.9520263671875 0.38030368089675903 0.82450795 0.41042813658714294 True -8 24390 29.62192702293396 0.6561551094055176 453.9665832519531 0.374556303024292 585.0087890625 0.38347336649894714 0.8313895 0.3799251616001129 True -9 27100 29.47861123085022 0.6673271656036377 467.6186828613281 0.4027683138847351 583.9470825195312 0.38443949818611145 0.8311997 0.35605475306510925 False -10 29810 29.451388835906982 0.6612381935119629 418.5985412597656 0.29832667112350464 580.2066040039062 0.3896058201789856 0.84015346 0.3196168541908264 True -11 32520 29.5181782245636 0.9976198673248291 431.5002136230469 0.35317373275756836 578.769775390625 0.39113521575927734 0.8458369 0.29918476939201355 True -12 35230 29.491120100021362 0.6616830825805664 451.5433044433594 0.2638307213783264 577.3291015625 0.3925909101963043 0.849188 0.2878258526325226 True -13 37940 29.493369102478027 0.6614198684692383 420.29241943359375 0.317920446395874 575.4899291992188 0.39484530687332153 0.8528809 0.2706340551376343 True -14 40650 29.492237329483032 0.653071403503418 421.0979309082031 0.20246261358261108 574.027587890625 0.3967335522174835 0.8596024 0.26045310497283936 True -15 43360 29.500776290893555 0.6645865440368652 410.029052734375 0.30729591846466064 573.3519897460938 0.3965836465358734 0.8627817 0.2516856789588928 True -16 46070 29.49496817588806 0.6627733707427979 407.5963134765625 0.23473384976387024 572.380126953125 0.39800602197647095 0.86722064 0.24269168078899384 True -17 48780 29.48923659324646 0.6624376773834229 430.46923828125 0.17504772543907166 571.0221557617188 0.4001588225364685 0.8688237 0.23983943462371826 True -18 51490 29.480411529541016 0.6539533138275146 375.1885070800781 0.13976556062698364 571.8367919921875 0.3988407254219055 0.8683983 0.23799994587898254 False -19 54200 29.452449798583984 0.6468603610992432 355.34283447265625 0.2708909511566162 571.92626953125 0.39851200580596924 0.8678672 0.2390744388103485 False diff --git a/ENCSR839GHA/cherimoya.fold_1.performance.tsv b/ENCSR839GHA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 646f47eea9c5968c4c584c48db7892ce13a2b616..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -571.0221557617188 0.38450998067855835 0.4001588225364685 0.1618840992450714 0.8688237071037292 0.8528845310211182 0.23983943462371826 \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_2.evaluate.json b/ENCSR839GHA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 12c7f73ae3fdf4cc3554f37bb48f1d56cbf8cf12..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF156GMU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_2.fit.json b/ENCSR839GHA/cherimoya.fold_2.fit.json deleted file mode 100644 index 2481d6d0c465ca9ca234a009c53d55b6d1d3592c..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF156GMU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_2.log b/ENCSR839GHA/cherimoya.fold_2.log deleted file mode 100644 index 8f260f568eb0e3d66b3a8a152b94b78cf392f83d..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2884 35.788371086120605 4.7227983474731445 504.03363037109375 0.42181897163391113 599.5128784179688 0.2653694748878479 0.7233173 4.147848606109619 True -1 5768 31.426262855529785 0.596714973449707 496.19378662109375 0.25784313678741455 548.8749389648438 0.3365066349506378 0.78181285 1.08067786693573 True -2 8652 32.113179445266724 0.5670583248138428 445.93341064453125 0.33941006660461426 540.5255737304688 0.34637218713760376 0.7972769 0.49842575192451477 True -3 11536 31.647071361541748 0.5668706893920898 427.70587158203125 0.23176437616348267 536.9019775390625 0.3516830801963806 0.80368865 0.4873257279396057 True -4 14420 31.4461829662323 0.5476419925689697 443.21759033203125 0.29548680782318115 534.5328369140625 0.35464879870414734 0.81115735 0.4015955626964569 True -5 17304 31.47649049758911 0.5492632389068604 368.40826416015625 0.4643799066543579 531.1887817382812 0.3599384129047394 0.8169564 0.3476687967777252 True -6 20188 31.44592022895813 0.5450561046600342 379.64306640625 0.35827139019966125 530.6176147460938 0.3609476089477539 0.81884754 0.36479103565216064 True -7 23072 31.45384407043457 0.545018196105957 479.5987548828125 0.38972896337509155 528.96337890625 0.3627030551433563 0.82324314 0.3322370946407318 True -8 25956 31.425893545150757 0.5447185039520264 384.6417541503906 0.41950497031211853 527.200439453125 0.3654094934463501 0.82813823 0.3339473307132721 True -9 28840 31.40984582901001 0.5390579700469971 435.6236572265625 0.22540172934532166 525.84716796875 0.36876264214515686 0.83041877 0.3276929557323456 True -10 31724 31.42374014854431 0.5409173965454102 473.8551330566406 0.3147593140602112 523.259033203125 0.3734557628631592 0.8363165 0.32043978571891785 True -11 34608 31.370760917663574 0.5446443557739258 473.1177062988281 0.30343279242515564 522.2245483398438 0.3746952414512634 0.83842456 0.2917305529117584 True -12 37492 31.354711294174194 0.5354008674621582 438.7008056640625 0.23411419987678528 520.6766967773438 0.37754514813423157 0.8429205 0.26622235774993896 True -13 40376 31.49584650993347 0.5564768314361572 435.3733825683594 0.27830809354782104 519.9518432617188 0.3781892955303192 0.8453826 0.25715553760528564 True -14 43260 31.519460916519165 0.5624480247497559 432.1607666015625 0.1928245723247528 518.9453735351562 0.37888073921203613 0.84843725 0.24859188497066498 True -15 46144 31.54576349258423 0.5580916404724121 367.85980224609375 0.2814352512359619 517.9081420898438 0.38083216547966003 0.85474986 0.23480960726737976 True -16 49028 31.504979848861694 0.5543646812438965 394.53863525390625 0.17048251628875732 517.6046142578125 0.38141313195228577 0.85512406 0.22580939531326294 True -17 51912 31.50325059890747 4.69687557220459 442.84637451171875 0.16049794852733612 517.6417846679688 0.3815041482448578 0.85757375 0.2245282381772995 True -18 54796 31.5854389667511 0.5774509906768799 463.0689697265625 0.21089521050453186 517.848876953125 0.38105443120002747 0.85582006 0.22566667199134827 False -19 57680 31.693362951278687 0.5662670135498047 378.9517822265625 0.13793012499809265 518.2098999023438 0.38029399514198303 0.85430783 0.2267666608095169 False diff --git a/ENCSR839GHA/cherimoya.fold_2.performance.tsv b/ENCSR839GHA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 641930363e404a7ab28807541fa5369572ee79c7..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -517.6417846679688 0.3999219834804535 0.3815041482448578 0.1472485214471817 0.8575737476348877 0.8318259716033936 0.2245282381772995 \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_3.evaluate.json b/ENCSR839GHA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f1fd6cf6a436de379f205c33d1422075b0a5854f..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF156GMU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_3.fit.json b/ENCSR839GHA/cherimoya.fold_3.fit.json deleted file mode 100644 index 9e9976aaf84797e904d7881fa8879d6b39b12755..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF156GMU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_3.log b/ENCSR839GHA/cherimoya.fold_3.log deleted file mode 100644 index a8ba243a2959504bb8479013ad60fc262328256c..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.17187190055847 3.6015539169311523 415.6214904785156 0.496476948261261 565.4058837890625 0.2715286910533905 0.7079261 3.5588324069976807 True -1 5510 30.656739711761475 0.5475461483001709 501.3641357421875 0.3735731244087219 519.1807861328125 0.3373461365699768 0.78466094 1.4052236080169678 True -2 8265 30.37751030921936 0.5263972282409668 421.19586181640625 0.495211124420166 512.5778198242188 0.34386152029037476 0.7895192 0.7413858771324158 True -3 11020 30.02334475517273 0.5340652465820312 462.8988037109375 0.5725691318511963 507.65264892578125 0.3501167297363281 0.8025627 0.5601535439491272 True -4 13775 29.961441040039062 1.81001615524292 382.4486083984375 0.382608026266098 504.7564392089844 0.3536895215511322 0.8074213 0.506853461265564 True -5 16530 29.938355684280396 0.5321433544158936 501.5137023925781 0.38243579864501953 502.9863586425781 0.35587278008461 0.81283617 0.5116413235664368 True -6 19285 29.979785680770874 0.5257956981658936 464.98492431640625 0.27668213844299316 499.6221923828125 0.36166447401046753 0.8164593 0.4696713984012604 True -7 22040 29.991103410720825 0.5413036346435547 448.18353271484375 0.2676955759525299 498.136474609375 0.36416029930114746 0.82101107 0.4584506154060364 True -8 24795 30.004767656326294 2.4423251152038574 449.87347412109375 0.2179393768310547 496.7476806640625 0.3667689561843872 0.82576746 0.4263109564781189 True -9 27550 29.999278783798218 0.9593710899353027 460.08795166015625 0.23732255399227142 494.3365478515625 0.37091004848480225 0.8296778 0.40085211396217346 True -10 30305 30.011558055877686 0.5400240421295166 424.60455322265625 0.4117128551006317 492.9559020996094 0.3731249272823334 0.83682156 0.3825854957103729 True -11 33060 29.967441082000732 0.5287775993347168 468.4752197265625 0.26291972398757935 492.54473876953125 0.3721185326576233 0.84081745 0.33727264404296875 True -12 35815 30.00633430480957 0.536895751953125 515.51953125 0.23481905460357666 491.6593933105469 0.3733939230442047 0.8441158 0.3071382939815521 True -13 38570 29.954549074172974 0.7595086097717285 426.2816162109375 0.300229012966156 489.1375427246094 0.3772221803665161 0.84852666 0.2842250168323517 True -14 41325 29.994479656219482 0.5247862339019775 450.38104248046875 0.23164331912994385 488.1934509277344 0.37871167063713074 0.8535545 0.26185062527656555 True -15 44080 29.94734287261963 0.5382561683654785 388.9200439453125 0.22484557330608368 487.9441833496094 0.3782951831817627 0.85755527 0.24574044346809387 True -16 46835 29.957829475402832 0.5295310020446777 422.4771728515625 0.17498177289962769 487.1731872558594 0.379377156496048 0.8610536 0.2350834608078003 True -17 49590 30.025949001312256 0.5352706909179688 406.7677001953125 0.19904769957065582 486.8293151855469 0.379888117313385 0.861692 0.23089148104190826 True -18 52345 29.979243993759155 0.532874584197998 418.15557861328125 0.20964393019676208 487.2618408203125 0.37972792983055115 0.86173594 0.23058690130710602 True -19 55100 30.003031253814697 0.528892993927002 403.4952392578125 0.2004660815000534 487.4384460449219 0.37929797172546387 0.86151564 0.23124508559703827 False diff --git a/ENCSR839GHA/cherimoya.fold_3.performance.tsv b/ENCSR839GHA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 33f9f5c876cdefd7763a3cce15bc6b51a42fb988..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -487.2618408203125 0.40381649136543274 0.379727840423584 0.14292453229427338 0.8617359399795532 0.8273500800132751 0.23058690130710602 \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_4.evaluate.json b/ENCSR839GHA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index adfcc248ca2931eb9f2ed6568ef2f25cdf1cd00c..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF156GMU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_4.fit.json b/ENCSR839GHA/cherimoya.fold_4.fit.json deleted file mode 100644 index a3f6585c6282d4b74db0038ce16766cb6040e73c..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF156GMU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839GHA/cherimoya.fold_4.log b/ENCSR839GHA/cherimoya.fold_4.log deleted file mode 100644 index 8affdaacc3fc0009154d8efcc62a4795939fa118..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2816 35.219088315963745 3.620955467224121 454.2662353515625 0.2829848527908325 544.8475341796875 0.2636871337890625 0.70199776 3.3428492546081543 True -1 5632 30.886229515075684 0.5860912799835205 461.7737731933594 0.4980664849281311 504.69415283203125 0.32497408986091614 0.7564404 0.9087823033332825 True -2 8448 31.279900312423706 0.5734367370605469 455.8118896484375 0.4139849543571472 497.4612121582031 0.3348940312862396 0.7695171 0.4779907464981079 True -3 11264 31.16062331199646 0.5713751316070557 448.7442932128906 0.3614675998687744 492.8230285644531 0.34143489599227905 0.7788613 0.4394652545452118 True -4 14080 30.629907608032227 0.5711393356323242 441.68548583984375 0.29201775789260864 490.55322265625 0.34289228916168213 0.79137874 0.35348445177078247 True -5 16896 30.652207374572754 0.5776371955871582 485.4892578125 0.2411511093378067 487.31439208984375 0.3486997187137604 0.80005354 0.34150272607803345 True -6 19712 30.63712215423584 0.5680155754089355 395.7887878417969 0.30215683579444885 486.1639404296875 0.35072776675224304 0.80356336 0.32388821244239807 True -7 22528 30.596136569976807 0.5648226737976074 422.07073974609375 0.2532297372817993 485.21417236328125 0.35203543305397034 0.8118851 0.3055056035518646 True -8 25344 30.610361099243164 0.5679652690887451 446.867919921875 0.2962319552898407 483.5201721191406 0.3550405502319336 0.817881 0.2834392786026001 True -9 28160 30.645379066467285 0.5784556865692139 405.0528259277344 0.20323659479618073 482.63916015625 0.35610318183898926 0.82122445 0.2861499786376953 True -10 30976 30.66304922103882 0.5750613212585449 467.0758056640625 0.38694801926612854 480.6229248046875 0.3602254390716553 0.8290911 0.26948192715644836 True -11 33792 30.680898666381836 0.6007235050201416 429.724853515625 0.26067638397216797 480.0188293457031 0.36021333932876587 0.8318462 0.26097822189331055 True -12 36608 30.77919054031372 1.3075683116912842 398.27313232421875 0.24877849221229553 477.7942199707031 0.36435380578041077 0.8377775 0.24408139288425446 True -13 39424 30.670909643173218 0.5821866989135742 403.7914123535156 0.1953178346157074 477.01239013671875 0.3659493029117584 0.84166443 0.237578347325325 True -14 42240 30.629345893859863 0.5931200981140137 427.30877685546875 0.188900426030159 476.2379455566406 0.367599755525589 0.8459055 0.226022407412529 True -15 45056 30.78879189491272 0.5759656429290771 389.1541748046875 0.1996973305940628 475.8961486816406 0.367639422416687 0.85045177 0.21798521280288696 True -16 47872 30.653658866882324 0.5709025859832764 488.8301086425781 0.3319006562232971 475.27386474609375 0.36933284997940063 0.85394806 0.2135677933692932 True -17 50688 30.599907875061035 0.5691080093383789 364.93902587890625 0.17923441529273987 475.40069580078125 0.3689391613006592 0.8556666 0.21152888238430023 True -18 53504 30.6764817237854 0.5814180374145508 399.3909912109375 0.1428195834159851 475.32305908203125 0.36944833397865295 0.8536976 0.21125097572803497 False -19 56320 30.638970375061035 0.5703830718994141 376.782470703125 0.2002972960472107 475.5150451660156 0.36884477734565735 0.8536226 0.2121010571718216 False diff --git a/ENCSR839GHA/cherimoya.fold_4.performance.tsv b/ENCSR839GHA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f9bf01f1ead07573ac8f29413e45cf94f3f48652..0000000000000000000000000000000000000000 --- a/ENCSR839GHA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.40069580078125 0.4109446406364441 0.3689391613006592 0.13805535435676575 0.8556665778160095 0.8212835788726807 0.21152888238430023 \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_0.evaluate.json b/ENCSR839IAD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c7cec21d25902e4d990f842f0955059d7db32c9e..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF391FCK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_0.fit.json b/ENCSR839IAD/cherimoya.fold_0.fit.json deleted file mode 100644 index f1dc0204a907c5aaedb6a8ebfe6fe8f1a6df6029..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF391FCK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_0.log b/ENCSR839IAD/cherimoya.fold_0.log deleted file mode 100644 index 809facd0f515d8e22294d643ecae73a46fe51e61..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1979 27.418736934661865 28.324113607406616 304.7205810546875 0.7984914779663086 484.35345458984375 0.4562671482563019 0.562163 11.012896537780762 True -1 3958 22.71715021133423 0.4562366008758545 294.0950927734375 0.7458821535110474 413.1529846191406 0.5687764286994934 0.6430482 4.743173122406006 True -2 5937 22.019362926483154 0.48845553398132324 328.66632080078125 0.7948747873306274 391.7046813964844 0.6061280369758606 0.6553114 1.7652939558029175 True -3 7916 22.052857875823975 0.4046015739440918 297.4540710449219 0.5158113241195679 386.78216552734375 0.6136398911476135 0.66496843 1.1109248399734497 True -4 9895 22.025952339172363 0.40302157402038574 340.6683654785156 0.6682159900665283 384.21368408203125 0.6186302900314331 0.66842264 0.9734327793121338 True -5 11874 22.01363706588745 0.4072403907775879 327.0364074707031 0.663529634475708 382.56524658203125 0.6218116283416748 0.6796166 0.8871378302574158 True -6 13853 22.01780390739441 0.4024782180786133 311.7447509765625 0.38513457775115967 381.32635498046875 0.6241293549537659 0.6865657 0.7631704807281494 True -7 15832 22.016539335250854 0.40615057945251465 309.170166015625 0.3383684456348419 380.33831787109375 0.6261014342308044 0.69060284 0.7066841125488281 True -8 17811 21.757097959518433 0.39624643325805664 299.56414794921875 0.5853679180145264 379.174072265625 0.6283718347549438 0.6930152 0.648811399936676 True -9 19790 21.571406364440918 3.198298454284668 280.13006591796875 0.4825308322906494 378.2490539550781 0.6301718950271606 0.69716954 0.6350653767585754 True -10 21769 21.592211723327637 0.4018721580505371 344.59088134765625 0.6142182946205139 377.01531982421875 0.6321466565132141 0.7038246 0.5798776149749756 True -11 23748 21.65345001220703 0.3961174488067627 284.315185546875 0.3582246005535126 376.1289367675781 0.6338521838188171 0.70910275 0.5498459935188293 True -12 25727 21.592268466949463 3.231947660446167 278.83856201171875 0.5265723466873169 375.2481384277344 0.6353469491004944 0.71357137 0.5195316076278687 True -13 27706 21.568562269210815 0.3921976089477539 287.8533630371094 0.2702908515930176 374.8086853027344 0.6365540027618408 0.7185243 0.5176276564598083 True -14 29685 21.64178228378296 0.3975989818572998 274.29254150390625 0.3566277325153351 374.13006591796875 0.6375707983970642 0.7250716 0.49311569333076477 True -15 31664 21.594749689102173 0.3969101905822754 303.9111022949219 0.38752296566963196 373.69549560546875 0.6380075216293335 0.7267308 0.48773157596588135 True -16 33643 21.544199466705322 0.39757585525512695 257.1473388671875 0.2580377459526062 373.5978088378906 0.6377086639404297 0.7258495 0.49357616901397705 False -17 35622 21.587204933166504 0.39676594734191895 293.4589538574219 0.30589693784713745 374.0522766113281 0.6372600197792053 0.7247764 0.5007568597793579 False -18 37601 21.605788230895996 0.39220166206359863 274.07281494140625 0.27193406224250793 374.4574279785156 0.6365090608596802 0.7187341 0.5127212405204773 False -19 39580 21.66491985321045 25.573864936828613 280.4630126953125 0.11926206946372986 374.5479736328125 0.6360412240028381 0.71734947 0.5190812945365906 False diff --git a/ENCSR839IAD/cherimoya.fold_0.performance.tsv b/ENCSR839IAD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1695244403e315b6a2dff980126f3a351ca89280..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -373.69549560546875 0.2934597134590149 0.6380075216293335 0.24032160639762878 0.7267308235168457 0.6743649244308472 0.48773157596588135 \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_1.evaluate.json b/ENCSR839IAD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index fabe29788c7a475fe91784238f4c23f505c5a6c6..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF391FCK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_1.fit.json b/ENCSR839IAD/cherimoya.fold_1.fit.json deleted file mode 100644 index e4e8934e502f5538f9757a2fb89e56b1a1890a0f..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF391FCK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_1.log b/ENCSR839IAD/cherimoya.fold_1.log deleted file mode 100644 index f2605c68bc593001c96fcb2a53299f920e6b0017..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2003 26.696325063705444 3.3628923892974854 294.3041076660156 0.6503714323043823 495.44964599609375 0.46629345417022705 0.5689844 11.111680030822754 True -1 4006 22.38273811340332 1.4428434371948242 299.93682861328125 1.0732799768447876 427.5110778808594 0.5702685713768005 0.6770075 3.7923953533172607 True -2 6009 22.288357734680176 0.45852017402648926 304.4912109375 0.5497357845306396 410.3493957519531 0.6065031886100769 0.68342793 1.0988023281097412 True -3 8012 22.948847770690918 24.056798219680786 308.622314453125 0.8351789116859436 404.1829528808594 0.6157093048095703 0.69521856 0.656579315662384 True -4 10015 22.983569383621216 29.48370623588562 322.9946594238281 0.45071807503700256 401.4588317871094 0.6202673316001892 0.7047582 0.536968469619751 True -5 12018 22.835835933685303 0.48733997344970703 343.92681884765625 0.7003264427185059 400.3443908691406 0.6222824454307556 0.71002626 0.507326066493988 True -6 14021 22.405296802520752 0.4730985164642334 330.940673828125 0.5057811737060547 399.2880554199219 0.6242281794548035 0.7143363 0.4999428689479828 True -7 16024 22.337265968322754 0.4653651714324951 314.3538818359375 0.5627159476280212 398.15069580078125 0.6263062953948975 0.72011346 0.48475295305252075 True -8 18027 22.307070016860962 0.46083950996398926 362.97625732421875 0.4339406490325928 396.9814147949219 0.6284887790679932 0.7268176 0.4727466404438019 True -9 20030 22.2718608379364 0.4555704593658447 290.03662109375 0.9700188040733337 396.02142333984375 0.6303359270095825 0.7336702 0.4662618637084961 True -10 22033 22.439086437225342 0.46394872665405273 304.6801452636719 0.4773249328136444 395.1974182128906 0.6320080757141113 0.7371963 0.44947201013565063 True -11 24036 22.324630737304688 0.4576120376586914 345.59930419921875 0.6061975359916687 394.4223937988281 0.6336066722869873 0.74401516 0.4351838529109955 True -12 26039 22.28913187980652 0.4553670883178711 291.486328125 0.6869460344314575 393.7105407714844 0.6350831389427185 0.74936855 0.42567506432533264 True -13 28042 22.386260271072388 0.4527750015258789 257.28240966796875 0.4133198857307434 393.1000671386719 0.6364165544509888 0.7532566 0.4189319610595703 True -14 30045 22.571414947509766 23.558181762695312 297.18310546875 0.38877665996551514 392.6732482910156 0.6372500658035278 0.7572012 0.416338175535202 True -15 32048 22.912508249282837 19.027982473373413 285.25836181640625 0.38834962248802185 392.4179992675781 0.6376839280128479 0.7584364 0.4171028733253479 True -16 34051 23.018463611602783 22.680067777633667 311.61968994140625 0.2528623938560486 392.5534362792969 0.6373623013496399 0.757544 0.423250675201416 False -17 36054 23.025207996368408 29.3418607711792 259.49169921875 0.2728939652442932 392.7786865234375 0.6368697285652161 0.7521519 0.44134488701820374 False -18 38057 22.593809366226196 0.4617624282836914 278.418212890625 0.18392226099967957 392.99267578125 0.636196494102478 0.7481765 0.452740341424942 False -19 40060 21.89294147491455 0.4583323001861572 311.534912109375 0.322893887758255 393.29791259765625 0.635725200176239 0.7456416 0.4615589380264282 False diff --git a/ENCSR839IAD/cherimoya.fold_1.performance.tsv b/ENCSR839IAD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 51f6acdc5650c347f016e3b262e75a7ebadf1ae3..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -392.4179992675781 0.28891536593437195 0.6376839280128479 0.2535364031791687 0.758436381816864 0.7401087284088135 0.4171028733253479 \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_2.evaluate.json b/ENCSR839IAD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 76bd59f81d84d9d4435a20ba5c21605c3614a24c..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF391FCK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_2.fit.json b/ENCSR839IAD/cherimoya.fold_2.fit.json deleted file mode 100644 index d34c4f71c44e3b64fff3f624eba5f8e7ac817f6d..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF391FCK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_2.log b/ENCSR839IAD/cherimoya.fold_2.log deleted file mode 100644 index 6f36b25a05979abf51cd1dc03e6fee159b75eb58..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2092 27.35324501991272 3.2736237049102783 251.92434692382812 0.6710958480834961 485.811279296875 0.46212512254714966 0.5731611 9.137998580932617 True -1 4184 23.733397483825684 29.167046546936035 345.96307373046875 0.6657189726829529 418.7808532714844 0.5683816075325012 0.68207395 3.4014246463775635 True -2 6276 23.452929735183716 0.3810114860534668 268.5322265625 0.5888445973396301 400.0218505859375 0.6029273867607117 0.6893725 1.0805656909942627 True -3 8368 23.793840646743774 20.473700761795044 350.0848388671875 0.6549315452575684 394.1822509765625 0.6124000549316406 0.7016226 0.7670430541038513 True -4 10460 23.820831060409546 0.38739442825317383 334.26898193359375 0.7740174531936646 392.0570983886719 0.6160463690757751 0.706889 0.6842821836471558 True -5 12552 23.328622341156006 0.3867149353027344 298.1949462890625 0.5977827310562134 390.7059631347656 0.6187165379524231 0.7120971 0.6806549429893494 True -6 14644 23.355229377746582 0.3803703784942627 271.73272705078125 0.8341996073722839 389.7389221191406 0.6212148666381836 0.71055204 0.6143133044242859 False -7 16736 23.350311279296875 0.37773633003234863 300.6500244140625 0.6699458360671997 388.7238464355469 0.6231730580329895 0.7190648 0.6139580607414246 True -8 18828 23.31264615058899 13.532558679580688 289.5894775390625 0.5441231727600098 387.707763671875 0.6250080466270447 0.72172064 0.600622296333313 True -9 20920 23.503641843795776 0.3838968276977539 293.5716552734375 0.5075986981391907 386.7548522949219 0.6269087791442871 0.7271776 0.5483865141868591 True -10 23012 23.411222219467163 0.3816490173339844 267.5069580078125 0.5666295289993286 385.6138916015625 0.6293957829475403 0.72834283 0.545314610004425 True -11 25104 23.29221773147583 0.38208842277526855 302.10076904296875 0.4781665802001953 384.8833923339844 0.6310468912124634 0.7319892 0.5318419933319092 True -12 27196 23.532891035079956 0.388812780380249 253.3642578125 0.6257197856903076 384.08843994140625 0.6327757239341736 0.73937523 0.49849754571914673 True -13 29288 23.454469919204712 0.3968360424041748 310.635986328125 0.4837690591812134 383.3363342285156 0.634074330329895 0.74405366 0.49127519130706787 True -14 31380 23.4650616645813 0.3877451419830322 274.2821350097656 0.47382044792175293 382.886962890625 0.6349501609802246 0.74785966 0.4781486392021179 True -15 33472 23.451207637786865 0.3783845901489258 284.326171875 0.3630515933036804 382.38409423828125 0.635726809501648 0.75018 0.4627726972103119 True -16 35564 23.438294887542725 0.37559080123901367 283.3298034667969 0.3165179491043091 382.5914611816406 0.6355494260787964 0.7513679 0.46550253033638 True -17 37656 23.37788438796997 0.38050389289855957 369.5364074707031 0.2628045976161957 382.6688232421875 0.6350318193435669 0.74887043 0.47675371170043945 False -18 39748 23.38451099395752 0.3796060085296631 249.25662231445312 0.26335400342941284 382.98333740234375 0.6343135237693787 0.7449349 0.4853980839252472 False -19 41840 23.39768648147583 0.37566041946411133 302.3568115234375 0.23379862308502197 383.0984191894531 0.6339259147644043 0.7410275 0.4941718280315399 False diff --git a/ENCSR839IAD/cherimoya.fold_2.performance.tsv b/ENCSR839IAD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index be192b65f056e0d4167df10b2df6128012f792db..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -382.5914611816406 0.293069064617157 0.6355494856834412 0.24831067025661469 0.7513679265975952 0.7067126631736755 0.46550253033638 \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_3.evaluate.json b/ENCSR839IAD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 18a160d3173307fe993dc0324c0653239379b786..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF391FCK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_3.fit.json b/ENCSR839IAD/cherimoya.fold_3.fit.json deleted file mode 100644 index c0b4a6a23e8e4c9eb569a358da7b05388a0882d8..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF391FCK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_3.log b/ENCSR839IAD/cherimoya.fold_3.log deleted file mode 100644 index e07cfba7845117aa79cf216bcd91c75ff47254d2..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2034 26.95306134223938 3.4552974700927734 320.6488037109375 0.9345053434371948 485.56787109375 0.4640113115310669 0.57928056 10.117036819458008 True -1 4068 22.680492639541626 0.7227942943572998 259.49591064453125 0.9109338521957397 413.3481750488281 0.5733365416526794 0.6587145 3.972862482070923 True -2 6102 22.681795835494995 0.4279501438140869 270.9300842285156 0.9202840328216553 394.2032775878906 0.6096690893173218 0.634324 1.3941144943237305 False -3 8136 22.661171674728394 0.5059669017791748 311.061279296875 0.7168986201286316 390.4637145996094 0.6166050434112549 0.6557899 0.9703398942947388 False -4 10170 22.69502592086792 0.43372321128845215 335.94354248046875 0.87013840675354 388.46331787109375 0.6200475096702576 0.66279334 0.7842859625816345 True -5 12204 22.574021339416504 0.4230804443359375 302.126953125 0.6330088973045349 387.430419921875 0.6222509145736694 0.6718602 0.7416577935218811 True -6 14238 22.21623969078064 0.43034839630126953 291.2906799316406 0.45776820182800293 385.7962646484375 0.6252865791320801 0.67677754 0.6517641544342041 True -7 16272 22.237321615219116 1.0834696292877197 327.3391418457031 0.6489166617393494 385.1135559082031 0.6268279552459717 0.682847 0.657313346862793 True -8 18306 22.22724723815918 1.552262783050537 296.03009033203125 0.5353373289108276 384.5975341796875 0.6283251643180847 0.68843424 0.6132945418357849 True -9 20340 22.174023389816284 0.4282252788543701 276.922607421875 0.49526605010032654 383.4386901855469 0.6306711435317993 0.7002692 0.5486254692077637 True -10 22374 22.339149713516235 0.43404388427734375 299.1903076171875 0.5669643878936768 382.4309997558594 0.6323947310447693 0.70530057 0.5328124165534973 True -11 24408 22.163811683654785 1.3345892429351807 313.1607666015625 0.5982102155685425 381.24835205078125 0.6345438361167908 0.70972365 0.5203654170036316 True -12 26442 22.163706064224243 32.04544949531555 309.3507080078125 0.568711519241333 380.5576477050781 0.6358069181442261 0.7127683 0.5156806111335754 True -13 28476 24.942880630493164 0.439943790435791 317.20135498046875 0.45723390579223633 379.8973083496094 0.6371603012084961 0.7212013 0.5018242001533508 True -14 30510 22.799620866775513 28.37345242500305 333.7120361328125 0.30867859721183777 379.35430908203125 0.6380339860916138 0.7271816 0.4807695150375366 True -15 32544 22.237632274627686 0.43781185150146484 314.9261474609375 0.329165518283844 378.8235778808594 0.6385986804962158 0.7343999 0.46828600764274597 True -16 34578 22.18977999687195 0.4292421340942383 331.1080322265625 0.48128873109817505 378.7948913574219 0.6383938789367676 0.73470855 0.47338634729385376 True -17 36612 22.18331527709961 2.209172487258911 308.1382751464844 0.3511852025985718 378.9246520996094 0.6378306746482849 0.7302376 0.4817748963832855 False -18 38646 22.247907161712646 0.4304664134979248 301.69873046875 0.2215951383113861 379.1774597167969 0.6371905207633972 0.7306872 0.4909825325012207 False -19 40680 22.314287900924683 0.43151402473449707 244.62527465820312 0.1994297206401825 379.32794189453125 0.636829674243927 0.7290539 0.49916136264801025 False diff --git a/ENCSR839IAD/cherimoya.fold_3.performance.tsv b/ENCSR839IAD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 10308c2d3740aabd96b8e9f05502161594939f5b..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -378.7948913574219 0.2910841107368469 0.6383939385414124 0.24671624600887299 0.7347085475921631 0.6949284076690674 0.47338634729385376 \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_4.evaluate.json b/ENCSR839IAD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4f384fd530540db3ce53e682d5feb1b84445c62e..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF391FCK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_4.fit.json b/ENCSR839IAD/cherimoya.fold_4.fit.json deleted file mode 100644 index d44f577592577e50ab126407e27605f3ffb27f45..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF391FCK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839IAD/cherimoya.fold_4.log b/ENCSR839IAD/cherimoya.fold_4.log deleted file mode 100644 index 388bfb063f43d48e8fd09c0736298ba920ef166c..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2088 27.57481813430786 5.834248781204224 359.04986572265625 0.6654030084609985 484.95867919921875 0.4649806022644043 0.59280664 9.529446601867676 True -1 4176 23.325255870819092 0.4221303462982178 349.6787414550781 0.7110908627510071 414.287109375 0.5766785740852356 0.66666806 3.6334776878356934 True -2 6264 23.265116453170776 0.4011240005493164 328.53558349609375 0.4421626329421997 397.29644775390625 0.6089419722557068 0.66606134 1.083856225013733 False -3 8352 23.285426378250122 0.4067409038543701 295.4552001953125 0.3881530165672302 391.9065246582031 0.6174015402793884 0.67200994 0.8274086713790894 True -4 10440 23.27268671989441 0.40258240699768066 274.5512390136719 0.4574807286262512 390.6015319824219 0.6204826235771179 0.6815826 0.789910078048706 True -5 12528 23.237416982650757 0.4007906913757324 258.5567626953125 0.852704644203186 389.1038818359375 0.6231594681739807 0.6854418 0.7243332862854004 True -6 14616 23.268179893493652 0.4095265865325928 288.1040344238281 0.574056088924408 387.69818115234375 0.6255947947502136 0.68664783 0.6960422396659851 True -7 16704 23.253894805908203 0.9672262668609619 304.9457092285156 0.5565519332885742 386.3277282714844 0.6280306577682495 0.69374955 0.6123725771903992 True -8 18792 23.346806049346924 0.6329419612884521 300.461181640625 0.5407366752624512 385.4415283203125 0.6300593018531799 0.70090616 0.5761496424674988 True -9 20880 23.25637149810791 1.1327111721038818 303.358154296875 0.34993836283683777 384.3836669921875 0.6323812007904053 0.7078506 0.5472103357315063 True -10 22968 23.2357919216156 0.40416860580444336 284.187255859375 0.6736428737640381 383.5372009277344 0.6342520117759705 0.71106553 0.5313026905059814 True -11 25056 23.215917587280273 0.4094557762145996 293.2349853515625 0.45991599559783936 382.4267578125 0.6362631320953369 0.71624917 0.5138382911682129 True -12 27144 23.18118119239807 12.202588558197021 306.94085693359375 0.5462769269943237 381.361083984375 0.6380351185798645 0.7258479 0.4944671392440796 True -13 29232 25.29419994354248 9.962644338607788 292.2242431640625 0.681338906288147 380.4644470214844 0.6395280361175537 0.7293056 0.4812231659889221 True -14 31320 23.721693992614746 24.323570489883423 253.84829711914062 0.40800654888153076 379.958740234375 0.6405224800109863 0.73468906 0.4734320342540741 True -15 33408 24.93835711479187 0.4104886054992676 266.9322509765625 0.37464433908462524 379.7185974121094 0.6409565806388855 0.7402162 0.466593474149704 True -16 35496 22.74665856361389 1.1937897205352783 278.7729187011719 0.4021543860435486 379.6980285644531 0.6407643556594849 0.74056983 0.4685293734073639 True -17 37584 22.7601478099823 0.4005575180053711 219.94976806640625 0.2680284380912781 379.97698974609375 0.6401143670082092 0.73785913 0.48204779624938965 False -18 39672 22.79056215286255 0.403728723526001 255.3136749267578 0.26219862699508667 380.2854919433594 0.6394743919372559 0.73453456 0.49231234192848206 False -19 41760 22.807048797607422 0.9484539031982422 259.178466796875 0.28790518641471863 380.4523010253906 0.6390351057052612 0.7315267 0.4982312023639679 False diff --git a/ENCSR839IAD/cherimoya.fold_4.performance.tsv b/ENCSR839IAD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index da074ac82b8c7b894166337eb042e68aa67b78c6..0000000000000000000000000000000000000000 --- a/ENCSR839IAD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -379.6980285644531 0.2913641035556793 0.6407642960548401 0.24776382744312286 0.7405698299407959 0.6800636053085327 0.4685293734073639 \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_0.evaluate.json b/ENCSR839UOB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index fa74d5c940747ee71e3bb21a7ac4889c30993422..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539BHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_0.fit.json b/ENCSR839UOB/cherimoya.fold_0.fit.json deleted file mode 100644 index cdef82e2066d2f92c851f27f8268995b42ca354a..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF539BHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_0.log b/ENCSR839UOB/cherimoya.fold_0.log deleted file mode 100644 index dbf3ae6d54d499cf3b7987fcee795cc9897a1712..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3096 37.93951940536499 3.4764792919158936 408.25482177734375 0.9051631689071655 621.1307983398438 0.5601714849472046 0.57464653 7.272533893585205 True -1 6192 34.148932456970215 0.6385393142700195 378.4534912109375 1.0107460021972656 537.3613891601562 0.6643998026847839 0.63354564 1.5729706287384033 True -2 9288 33.870577812194824 0.655595064163208 408.3811950683594 0.5746350884437561 527.1278076171875 0.6748791337013245 0.6461346 1.069114327430725 True -3 12384 33.6350462436676 1.0134234428405762 533.9808349609375 0.9246832132339478 521.6237182617188 0.6805303692817688 0.6571727 0.9576180577278137 True -4 15480 33.55958867073059 0.6258816719055176 445.5841064453125 0.7335851192474365 518.9677124023438 0.683688223361969 0.6592986 0.8914461731910706 True -5 18576 33.542027711868286 0.6294832229614258 447.78179931640625 0.6428516507148743 517.4078979492188 0.6860237121582031 0.6624289 0.8136637210845947 True -6 21672 33.58898138999939 0.6381855010986328 460.87335205078125 0.7588573694229126 516.2808227539062 0.6876009106636047 0.66852945 0.7651528716087341 True -7 24768 33.48636269569397 1.918494701385498 386.31048583984375 0.5464187264442444 514.1846313476562 0.6901021003723145 0.6693585 0.7052768468856812 True -8 27864 33.4192898273468 15.792536497116089 429.16595458984375 0.6275572776794434 512.4466552734375 0.6922556757926941 0.6729761 0.6916937828063965 True -9 30960 33.547003984451294 0.6286306381225586 460.1073303222656 0.628283679485321 511.3121032714844 0.693981945514679 0.679377 0.649461567401886 True -10 34056 33.46727418899536 1.4204556941986084 427.03717041015625 0.5467321872711182 508.69378662109375 0.6964859962463379 0.6868226 0.6105394959449768 True -11 37152 33.472657203674316 1.5945780277252197 395.9437561035156 0.8191108703613281 506.6238708496094 0.698684573173523 0.69552255 0.5965154767036438 True -12 40248 33.48015379905701 0.6860082149505615 377.16741943359375 0.6166810989379883 504.424072265625 0.7012957334518433 0.70316887 0.5716146230697632 True -13 43344 33.457584857940674 0.6282424926757812 397.0130615234375 0.5289624929428101 503.08544921875 0.7030116319656372 0.7112615 0.5651090145111084 True -14 46440 33.61138606071472 13.026800394058228 366.9892578125 0.40699267387390137 501.8213806152344 0.7043280005455017 0.7194754 0.547361433506012 True -15 49536 33.55313324928284 0.6355793476104736 465.8797912597656 0.552587628364563 500.6754455566406 0.7055174708366394 0.72805595 0.5307969450950623 True -16 52632 33.56274175643921 0.6546463966369629 341.9036560058594 0.6142290234565735 500.55224609375 0.7059165239334106 0.73121864 0.5268266797065735 True -17 55728 33.57856488227844 0.6250708103179932 350.49639892578125 0.2550458312034607 500.7861633300781 0.7057629823684692 0.731017 0.5284501910209656 False -18 58824 33.50472831726074 0.6399967670440674 382.2503662109375 0.5008147954940796 501.0281677246094 0.7053264379501343 0.72786003 0.5376215577125549 False -19 61920 33.50335717201233 0.6265308856964111 417.58721923828125 0.33179450035095215 501.3929443359375 0.7050710320472717 0.72687477 0.5399880409240723 False diff --git a/ENCSR839UOB/cherimoya.fold_0.performance.tsv b/ENCSR839UOB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 04b83d150ecc8ccb43dd241442794af1fee4e751..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -500.55224609375 0.2403717190027237 0.7059165239334106 0.31963613629341125 0.7312186360359192 0.6662347316741943 0.5268266797065735 \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_1.evaluate.json b/ENCSR839UOB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 03a659b9b1aa5d1de8b86c2849ce0ef6afcac7fb..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539BHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_1.fit.json b/ENCSR839UOB/cherimoya.fold_1.fit.json deleted file mode 100644 index e06b2c7ac22edc3f36d116ce5497ee40ae00b70a..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF539BHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_1.log b/ENCSR839UOB/cherimoya.fold_1.log deleted file mode 100644 index 8e27f963b2ee0699dd3cc83050ec01d364913b3c..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3183 38.86033511161804 3.552051544189453 447.333251953125 0.8355081081390381 611.47705078125 0.5754498839378357 0.6032658 5.505409240722656 True -1 6366 35.11450481414795 0.6808934211730957 396.29473876953125 0.7039288878440857 545.8638305664062 0.6643733382225037 0.62312794 1.880491852760315 True -2 9549 35.130627155303955 0.6590232849121094 381.869140625 0.5822641849517822 535.6141357421875 0.6752890348434448 0.650939 0.9896695613861084 True -3 12732 35.11499261856079 0.7262547016143799 346.738037109375 0.8389332294464111 531.4895629882812 0.6799873113632202 0.6678252 0.859613299369812 True -4 15915 35.08523344993591 0.6585500240325928 387.656005859375 0.6063108444213867 529.6954345703125 0.6829774379730225 0.67245424 0.7404212951660156 True -5 19098 35.148041009902954 0.6567459106445312 411.7574462890625 0.45026832818984985 527.7850952148438 0.6854407787322998 0.67616385 0.7202582955360413 True -6 22281 35.15487194061279 0.6645059585571289 427.16192626953125 0.5494670867919922 526.001953125 0.6878820061683655 0.6839364 0.6806973814964294 True -7 25464 35.13677167892456 0.6482138633728027 347.2671813964844 0.715120792388916 524.5013427734375 0.6896607279777527 0.6846168 0.6433424353599548 True -8 28647 35.001442432403564 0.6706783771514893 366.5850524902344 0.5647250413894653 521.5240478515625 0.6930674314498901 0.69684684 0.6078411340713501 True -9 31830 34.57861948013306 0.659808874130249 379.2830810546875 0.39219528436660767 519.3772583007812 0.6952295899391174 0.69935805 0.5842653512954712 True -10 35013 34.517067432403564 1.6758432388305664 402.1051025390625 0.644593358039856 517.8209838867188 0.6970583200454712 0.7079589 0.5569441318511963 True -11 38196 34.56408143043518 0.6587848663330078 344.71795654296875 0.7798860669136047 516.2422485351562 0.6991710662841797 0.7152708 0.5297495722770691 True -12 41379 34.709399938583374 0.6606354713439941 470.69793701171875 0.6068349480628967 514.2821655273438 0.7012481689453125 0.72486454 0.503803551197052 True -13 44562 34.55578970909119 0.6635692119598389 406.3931579589844 0.4642852246761322 512.8190307617188 0.7029896974563599 0.7298734 0.4919390380382538 True -14 47745 34.59498929977417 0.655376672744751 393.12939453125 0.3029497265815735 511.5401306152344 0.7045210599899292 0.73821545 0.4762330949306488 True -15 50928 34.729902267456055 0.6713893413543701 390.2502136230469 0.5697566270828247 510.63165283203125 0.7053830623626709 0.7426708 0.46691298484802246 True -16 54111 34.622089862823486 0.6609752178192139 435.0295715332031 0.3206399083137512 510.21026611328125 0.7058638334274292 0.7459676 0.4625690281391144 True -17 57294 34.50547671318054 0.6479220390319824 394.733154296875 0.3717026114463806 510.2411804199219 0.7054830193519592 0.7477894 0.462152898311615 True -18 60477 34.56297969818115 2.9058313369750977 323.6253662109375 0.44142740964889526 510.5469665527344 0.7049896121025085 0.74553 0.47156161069869995 False -19 63660 34.55285692214966 0.6549944877624512 382.5705871582031 0.48517560958862305 510.761962890625 0.7046926617622375 0.7430752 0.4775422513484955 False diff --git a/ENCSR839UOB/cherimoya.fold_1.performance.tsv b/ENCSR839UOB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 58154341e49384db4f3c7df3dde1883f4dd2d61a..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -510.2411804199219 0.23718112707138062 0.7054830193519592 0.3280809223651886 0.7477893829345703 0.7234876155853271 0.462152898311615 \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_2.evaluate.json b/ENCSR839UOB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bb7f176381c29b18b62928866b5527c897b862a0..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539BHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_2.fit.json b/ENCSR839UOB/cherimoya.fold_2.fit.json deleted file mode 100644 index b705fbf4e9924b368040e23b0b5e7f64d6c89d62..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF539BHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_2.log b/ENCSR839UOB/cherimoya.fold_2.log deleted file mode 100644 index 959f9761ff6afb173f4838f2b30bea305d6f8655..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3282 40.30738401412964 3.5702223777770996 370.48309326171875 0.6393111944198608 614.6610107421875 0.5724063515663147 0.60174245 7.484897613525391 True -1 6564 36.39426040649414 0.6232781410217285 434.90423583984375 0.4285791516304016 541.0488891601562 0.6604647636413574 0.6478537 1.3008999824523926 True -2 9846 36.214702129364014 0.6043586730957031 379.9477844238281 0.9765465259552002 531.3590087890625 0.6704797744750977 0.65355235 0.9761006832122803 True -3 13128 36.2739691734314 0.6006863117218018 399.3804931640625 0.538993239402771 525.7603149414062 0.6765018701553345 0.6616089 0.8628801703453064 True -4 16410 36.152329206466675 0.5975608825683594 453.94659423828125 1.1393392086029053 523.3013916015625 0.6790866851806641 0.67339295 0.8066267967224121 True -5 19692 36.10345387458801 0.6064951419830322 377.9300842285156 0.6769457459449768 521.3587646484375 0.6814017295837402 0.67192596 0.786581814289093 False -6 22974 36.1212522983551 0.5945959091186523 496.90655517578125 0.6494029760360718 518.99853515625 0.6840226054191589 0.68060744 0.6982995271682739 True -7 26256 36.17653179168701 0.6086323261260986 380.2640380859375 0.669687032699585 517.4808349609375 0.6858887672424316 0.67974705 0.7073118090629578 False -8 29538 36.14670252799988 0.5997405052185059 324.0711669921875 0.8748207092285156 514.674560546875 0.6885985732078552 0.6922099 0.6527142524719238 True -9 32820 36.20075464248657 0.6343502998352051 355.4732666015625 0.7932621240615845 512.7313842773438 0.6904401779174805 0.6962293 0.6257052421569824 True -10 36102 36.16144347190857 0.6054611206054688 442.6436767578125 0.6178560256958008 510.9332580566406 0.6926127672195435 0.7079071 0.5963452458381653 True -11 39384 36.1376211643219 1.6810534000396729 420.0863037109375 0.5595381259918213 508.63800048828125 0.6948562860488892 0.71101356 0.5632245540618896 True -12 42666 36.29942750930786 0.6110188961029053 385.7525634765625 0.7945767641067505 507.0050048828125 0.6968501806259155 0.71688133 0.5580437779426575 True -13 45948 35.48493790626526 0.5955636501312256 408.86248779296875 0.5142302513122559 505.3390808105469 0.6987951993942261 0.726235 0.5362770557403564 True -14 49230 35.50534415245056 0.5950713157653809 377.8863830566406 0.487715482711792 504.0243835449219 0.7000347375869751 0.733089 0.526594340801239 True -15 52512 35.53843975067139 0.5947606563568115 386.9866943359375 0.5042159557342529 502.8689880371094 0.701091468334198 0.73878706 0.5206758379936218 True -16 55794 35.51458191871643 0.5879576206207275 399.8330078125 0.571785569190979 502.6044921875 0.7014724016189575 0.74176943 0.5137794613838196 True -17 59076 35.53071069717407 0.6036839485168457 403.13763427734375 0.3030281066894531 502.5499572753906 0.7013287544250488 0.7405509 0.5189758539199829 False -18 62358 35.47522044181824 1.8769216537475586 419.638671875 0.3627716302871704 502.95013427734375 0.7009212374687195 0.73859936 0.5257437229156494 False -19 65640 35.56550931930542 0.6052477359771729 458.87969970703125 0.33835551142692566 503.1671447753906 0.7006489038467407 0.73711795 0.5306112170219421 False diff --git a/ENCSR839UOB/cherimoya.fold_2.performance.tsv b/ENCSR839UOB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 035c59ad82c4c74f6d5ad086bcc988c7a925ab4c..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -502.6044921875 0.24151770770549774 0.7014724016189575 0.3236068785190582 0.7417694330215454 0.6876217126846313 0.5137794613838196 \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_3.evaluate.json b/ENCSR839UOB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1c41e4453593fa10bdd0f0a1f47f3d61dffb1529..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539BHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_3.fit.json b/ENCSR839UOB/cherimoya.fold_3.fit.json deleted file mode 100644 index ec69f9e768cc8e0625eb51c3b153b3635ebd92f5..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF539BHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_3.log b/ENCSR839UOB/cherimoya.fold_3.log deleted file mode 100644 index 65b008b29da63bb662b2a1541cd802e02e2ec9b3..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3215 39.55390667915344 3.5977721214294434 402.1161804199219 1.0691282749176025 608.48095703125 0.5730499625205994 0.5884134 7.103305339813232 True -1 6430 35.49382400512695 0.70566725730896 427.3009948730469 0.9503316879272461 531.0972900390625 0.6670534610748291 0.60348016 1.7297781705856323 True -2 9645 35.472360372543335 0.6953508853912354 343.6982421875 1.0697877407073975 523.4069213867188 0.6740418076515198 0.62549424 1.1235125064849854 True -3 12860 35.31626749038696 0.68589186668396 382.2393798828125 0.8030142784118652 518.361083984375 0.6793032288551331 0.64231735 0.9957869052886963 True -4 16075 34.866822242736816 2.402621030807495 364.996826171875 0.9998617172241211 516.1348266601562 0.6823690533638 0.63868237 0.9161637425422668 False -5 19290 34.84452819824219 0.6897053718566895 372.61572265625 0.6471320986747742 514.4410400390625 0.6837639808654785 0.63987386 0.819321870803833 False -6 22505 34.82231044769287 0.6894392967224121 464.18048095703125 0.7564486265182495 512.8258666992188 0.6858142018318176 0.6519418 0.7751613259315491 True -7 25720 34.75281000137329 0.6847667694091797 420.7433776855469 0.972152590751648 510.615478515625 0.6881217360496521 0.662632 0.724466860294342 True -8 28935 34.69332551956177 0.7053687572479248 375.0397644042969 0.8060171008110046 508.2895202636719 0.6903393268585205 0.67012495 0.6621173024177551 True -9 32150 34.768072843551636 0.6856577396392822 358.5624694824219 0.700019359588623 506.9205627441406 0.6919313669204712 0.67720413 0.6281770467758179 True -10 35365 34.84136343002319 0.6948840618133545 370.26763916015625 0.4480489492416382 505.28167724609375 0.6934992074966431 0.68493164 0.6268303990364075 True -11 38580 34.78164458274841 0.7003147602081299 390.13836669921875 0.6543952822685242 503.1488037109375 0.6958796977996826 0.6948942 0.5958104133605957 True -12 41795 34.8306348323822 0.697437047958374 371.04791259765625 0.8098368048667908 501.472900390625 0.6980260014533997 0.70324177 0.5878536105155945 True -13 45010 34.78397178649902 0.688187837600708 361.7287902832031 0.5639218091964722 499.8235168457031 0.699544370174408 0.71461004 0.5533696413040161 True -14 48225 34.8453688621521 0.7063286304473877 386.65960693359375 0.5118027925491333 498.4405517578125 0.7010881900787354 0.72320855 0.5397631525993347 True -15 51440 35.99309301376343 30.032306909561157 362.5208435058594 0.5236784219741821 497.169189453125 0.7022128105163574 0.7313818 0.524726152420044 True -16 54655 34.95232939720154 0.7107534408569336 359.20458984375 0.3459259271621704 496.8503112792969 0.7024477124214172 0.73484737 0.5200877785682678 True -17 57870 34.85085463523865 0.6957666873931885 376.0469970703125 0.3433126211166382 497.0844421386719 0.7023996114730835 0.7355169 0.521121621131897 True -18 61085 34.796972036361694 1.1689960956573486 363.1122131347656 0.3892006278038025 497.2121887207031 0.7019495368003845 0.7324477 0.5297914743423462 False -19 64300 34.774733781814575 0.6829180717468262 386.06707763671875 0.35400086641311646 497.4915466308594 0.7016305327415466 0.73126435 0.5329594612121582 False diff --git a/ENCSR839UOB/cherimoya.fold_3.performance.tsv b/ENCSR839UOB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9eb835650bc146853c80153df4defb595d67c747..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -497.0844421386719 0.24134914577007294 0.7023996710777283 0.3204619288444519 0.7355169057846069 0.6804676651954651 0.521121621131897 \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_4.evaluate.json b/ENCSR839UOB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 51e57a5853acaaaefb330e32e77fe9629f7073a2..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF539BHD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_4.fit.json b/ENCSR839UOB/cherimoya.fold_4.fit.json deleted file mode 100644 index e6f34e7aa00035671345141437dcf9a38afdb347..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF539BHD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR839UOB/cherimoya.fold_4.log b/ENCSR839UOB/cherimoya.fold_4.log deleted file mode 100644 index faa97b7190d900bf1b21887b30aaea035be68453..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3331 40.70312786102295 3.5890953540802 450.78936767578125 0.9252896904945374 611.7269897460938 0.5734277963638306 0.60354125 6.474081039428711 True -1 6662 36.79446244239807 0.6541087627410889 406.075439453125 1.2054972648620605 535.2747802734375 0.6685900092124939 0.61839414 1.0062870979309082 True -2 9993 37.076152324676514 0.6410129070281982 412.86859130859375 0.7719203233718872 526.156494140625 0.6779136657714844 0.6403894 0.8434780240058899 True -3 13324 36.740827322006226 0.631929874420166 412.9041748046875 0.621289849281311 521.7572631835938 0.6836066842079163 0.64960766 0.8458023071289062 True -4 16655 36.68226504325867 0.631140947341919 462.31134033203125 0.6449892520904541 519.4146118164062 0.6860060691833496 0.65488267 0.720045804977417 True -5 19986 36.72831320762634 0.6326193809509277 422.3805236816406 0.8531981110572815 517.1334228515625 0.6889019012451172 0.6604275 0.7018430829048157 True -6 23317 36.669320583343506 0.7962894439697266 491.80084228515625 0.637691080570221 514.884765625 0.6913837194442749 0.66925436 0.6675470471382141 True -7 26648 36.77401614189148 0.6335854530334473 419.2921142578125 0.7923139333724976 513.3019409179688 0.6933035254478455 0.6763818 0.6912834644317627 True -8 29979 36.65966200828552 0.6336493492126465 440.67205810546875 0.8228081464767456 511.8623046875 0.6952416300773621 0.6815521 0.6793190836906433 True -9 33310 36.708691120147705 0.6341683864593506 420.9624938964844 0.6502959132194519 510.36279296875 0.6971601843833923 0.68613195 0.6411780118942261 True -10 36641 36.74064254760742 0.6336042881011963 431.8460693359375 0.649114727973938 508.2908020019531 0.6992794871330261 0.6923068 0.6187037825584412 True -11 39972 36.72166705131531 0.6321513652801514 369.87420654296875 0.42109331488609314 506.46612548828125 0.7015730738639832 0.6994232 0.6052697896957397 True -12 43303 37.59539818763733 25.57092547416687 413.2352294921875 0.5763619542121887 504.7308044433594 0.7032729983329773 0.70605594 0.581008791923523 True -13 46634 36.090256452560425 0.6283190250396729 360.3529052734375 0.7322136163711548 503.166259765625 0.705260694026947 0.7129294 0.5591685771942139 True -14 49965 36.01344704627991 0.6319007873535156 370.81683349609375 0.41259098052978516 501.8841247558594 0.7067829370498657 0.7206075 0.5423682332038879 True -15 53296 35.91315007209778 31.168553113937378 411.4242248535156 0.34764331579208374 501.0486755371094 0.707801878452301 0.7268838 0.5351935029029846 True -16 56627 36.05807590484619 1.3719251155853271 382.24420166015625 0.42533665895462036 500.618408203125 0.7083948850631714 0.7304549 0.5244316458702087 True -17 59958 36.058082580566406 0.6280572414398193 320.7626037597656 0.37764179706573486 500.7159729003906 0.7080572843551636 0.728549 0.5280877947807312 False -18 63289 35.99375510215759 0.629683256149292 371.1883544921875 0.3375752866268158 501.1620178222656 0.7076891660690308 0.72540784 0.5355915427207947 False -19 66620 35.94787931442261 0.6225659847259521 408.24310302734375 0.3242385685443878 501.3522033691406 0.7074273228645325 0.72321874 0.5413231253623962 False diff --git a/ENCSR839UOB/cherimoya.fold_4.performance.tsv b/ENCSR839UOB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0762448168f084ec89002293e47d2eec0bb4c353..0000000000000000000000000000000000000000 --- a/ENCSR839UOB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -500.618408203125 0.23939932882785797 0.7083950042724609 0.3243040144443512 0.7304549217224121 0.659633994102478 0.5244316458702087 \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_0.evaluate.json b/ENCSR840QLA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 77110087423b923a05e54942c555ef3e14cc03ea..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF221UOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_0.fit.json b/ENCSR840QLA/cherimoya.fold_0.fit.json deleted file mode 100644 index d34ebac7b74fe8650a269dc26cee99d6ffcaa632..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF221UOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_0.log b/ENCSR840QLA/cherimoya.fold_0.log deleted file mode 100644 index c269b8071703f7086135fe047996cbe8c6ecebb9..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1843 24.1419677734375 3.401874542236328 222.0902862548828 1.052402377128601 281.2530822753906 0.1384560465812683 0.54297477 7.326906681060791 True -1 3686 20.457780599594116 0.39965391159057617 240.52120971679688 1.3462884426116943 252.44895935058594 0.21172334253787994 0.688789 4.851718425750732 True -2 5529 20.378293991088867 1.3148372173309326 137.20452880859375 0.7932111024856567 235.4254150390625 0.24524050951004028 0.7118144 2.838594913482666 True -3 7372 20.022644519805908 0.38814425468444824 169.74571228027344 0.8555952906608582 229.74684143066406 0.2555691599845886 0.7125834 1.8658192157745361 True -4 9215 20.007665872573853 0.37575721740722656 144.49374389648438 0.9304595589637756 227.32240295410156 0.26074114441871643 0.73572606 1.3653444051742554 True -5 11058 20.006811141967773 0.3714637756347656 220.7361602783203 0.7267323732376099 225.43406677246094 0.2646554112434387 0.74813193 1.2715110778808594 True -6 12901 20.01220178604126 0.37676548957824707 166.0673065185547 0.8852974772453308 223.9835205078125 0.2673003375530243 0.7611956 1.0409425497055054 True -7 14744 20.01820945739746 0.37900614738464355 167.96070861816406 0.8302496671676636 223.51051330566406 0.2692437171936035 0.767037 0.9512470364570618 True -8 16587 20.04572582244873 0.37733030319213867 169.47348022460938 0.8903899192810059 222.06906127929688 0.27301669120788574 0.7775753 0.8737099766731262 True -9 18430 20.06597089767456 0.3826150894165039 186.33970642089844 0.5620123744010925 221.2943878173828 0.2750900685787201 0.78660715 0.8139781951904297 True -10 20273 20.013482332229614 0.38057875633239746 162.47769165039062 0.6457074284553528 220.63853454589844 0.27574771642684937 0.79360616 0.7088651061058044 True -11 22116 20.469064235687256 8.717527866363525 195.1668701171875 0.6269565224647522 220.00462341308594 0.27750205993652344 0.8000211 0.6723451614379883 True -12 23959 20.195607900619507 0.38377952575683594 150.90863037109375 0.5285381078720093 219.70578002929688 0.27760568261146545 0.80556095 0.6344806551933289 True -13 25802 20.116930723190308 0.3911752700805664 264.38433837890625 0.89812171459198 218.74034118652344 0.2794986367225647 0.8118829 0.6088805198669434 True -14 27645 20.140323877334595 5.003647327423096 135.5381317138672 0.4728860855102539 218.28245544433594 0.28118181228637695 0.81739056 0.5921574234962463 True -15 29488 20.14957904815674 0.38521385192871094 143.95291137695312 0.5409295558929443 218.30723571777344 0.2801073491573334 0.82120943 0.5639535784721375 True -16 31331 20.12717318534851 0.3916358947753906 201.15658569335938 0.47120553255081177 218.35939025878906 0.28032952547073364 0.8235203 0.5552316904067993 True -17 33174 20.14282488822937 1.473853349685669 227.94468688964844 0.5105178356170654 218.12081909179688 0.28100115060806274 0.8245717 0.5511745810508728 True -18 35017 20.15945863723755 0.38854503631591797 152.92538452148438 0.3221646845340729 218.0841064453125 0.28097018599510193 0.8225002 0.5564450025558472 False -19 36860 20.123564958572388 0.3855247497558594 111.99057006835938 0.4789908528327942 218.13409423828125 0.28106191754341125 0.8226195 0.5607528686523438 False diff --git a/ENCSR840QLA/cherimoya.fold_0.performance.tsv b/ENCSR840QLA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f720e8b0e950964ec7e13ced88f8da241e2ba61e..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -218.12081909179688 0.5095155835151672 0.28100118041038513 0.07509955018758774 0.8245717287063599 0.7703514695167542 0.5511745810508728 \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_1.evaluate.json b/ENCSR840QLA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9f1348a6b87947bd6fda25f3621fcd476375a80a..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF221UOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_1.fit.json b/ENCSR840QLA/cherimoya.fold_1.fit.json deleted file mode 100644 index 10e6cc0d7c4426784e2cda74ef28453ca910f79d..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF221UOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_1.log b/ENCSR840QLA/cherimoya.fold_1.log deleted file mode 100644 index f90d99fbfdc38025694c92426fe3d7675d0f2320..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1812 23.81644558906555 3.4628121852874756 165.9921417236328 0.9578707218170166 346.0477294921875 0.14795000851154327 0.53487724 9.155632019042969 True -1 3624 20.108641624450684 0.7974278926849365 169.3079833984375 0.9491775035858154 308.71453857421875 0.22765979170799255 0.6814395 5.852298736572266 True -2 5436 20.15316653251648 0.5171568393707275 252.85581970214844 0.9033448696136475 287.8536376953125 0.26439961791038513 0.7277531 3.2482149600982666 True -3 7248 20.04387068748474 0.507411003112793 191.67361450195312 0.8598132133483887 280.81878662109375 0.2744221091270447 0.74323195 1.9837647676467896 True -4 9060 20.057212114334106 0.5102834701538086 149.35256958007812 0.6532607078552246 276.66070556640625 0.28206536173820496 0.7475965 1.5832613706588745 True -5 10872 20.07721781730652 0.5069506168365479 154.2452850341797 0.6797006130218506 274.6359558105469 0.2855987846851349 0.75746423 1.4370965957641602 True -6 12684 20.084600925445557 0.507671594619751 153.65512084960938 0.5225880146026611 272.83734130859375 0.28880786895751953 0.76874083 1.3047902584075928 True -7 14496 20.11631202697754 0.5102236270904541 218.8505859375 0.6809930205345154 270.92645263671875 0.29224103689193726 0.7815151 1.0956846475601196 True -8 16308 19.848116397857666 0.5025036334991455 180.11148071289062 0.5297861695289612 269.4768371582031 0.2951081395149231 0.79195285 0.9423077702522278 True -9 18120 19.66842770576477 0.5062270164489746 242.19827270507812 0.6416357755661011 268.5579528808594 0.2958619296550751 0.8003002 0.8448832035064697 True -10 19932 19.69778609275818 0.5026209354400635 201.86703491210938 0.8780897259712219 267.17626953125 0.29891133308410645 0.80637413 0.8209701180458069 True -11 21744 19.705193758010864 2.230750560760498 147.52479553222656 0.8916856646537781 265.3784484863281 0.30275553464889526 0.8149633 0.7736436724662781 True -12 23556 19.739373922348022 0.50502610206604 213.327392578125 0.5596280097961426 265.1264343261719 0.3032367527484894 0.82088226 0.7237433791160583 True -13 25368 19.683064937591553 0.5067918300628662 203.66537475585938 0.6287655234336853 264.5762939453125 0.3039180338382721 0.8258908 0.696993887424469 True -14 27180 19.739985466003418 0.9919841289520264 158.47862243652344 0.5666694045066833 263.1474304199219 0.3076282739639282 0.83240527 0.6727308034896851 True -15 28992 19.774534940719604 0.5115976333618164 173.75665283203125 0.5272600650787354 263.0496826171875 0.3073517084121704 0.83478093 0.642795979976654 True -16 30804 19.70591378211975 0.5094373226165771 169.9371337890625 0.5650852918624878 263.64794921875 0.30504506826400757 0.8376782 0.6334267854690552 True -17 32616 19.671415090560913 1.517941951751709 145.5067138671875 0.40118661522865295 263.5140686035156 0.3058232069015503 0.83761966 0.6300227046012878 False -18 34428 19.763121604919434 0.523831844329834 170.65419006347656 0.49601060152053833 263.0052185058594 0.30750158429145813 0.83601034 0.6262238025665283 False -19 36240 19.788461685180664 0.5086982250213623 138.87644958496094 0.330849826335907 263.4559020996094 0.3063560128211975 0.8353868 0.63018399477005 False diff --git a/ENCSR840QLA/cherimoya.fold_1.performance.tsv b/ENCSR840QLA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8752e33e14ac24458c62d3000f93fe4d92068cd2..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -263.64794921875 0.4886224567890167 0.30504506826400757 0.08717918395996094 0.8376781940460205 0.8022054433822632 0.6334267854690552 \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_2.evaluate.json b/ENCSR840QLA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4ecd3534627039523555aa9624431e03cc0c4da3..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF221UOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_2.fit.json b/ENCSR840QLA/cherimoya.fold_2.fit.json deleted file mode 100644 index b11eac037b76d33a5b7968bdf6fc97f2892635d8..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF221UOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_2.log b/ENCSR840QLA/cherimoya.fold_2.log deleted file mode 100644 index 213021f3c3f3f2f0d3574cf51d6bd57a48d8ecc3..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1959 25.12378239631653 3.3863699436187744 245.3903350830078 1.2752357721328735 294.1813049316406 0.1442842036485672 0.52506685 7.269378185272217 True -1 3918 21.707582473754883 0.3784453868865967 226.930419921875 1.2763426303863525 261.1980285644531 0.22303302586078644 0.68707 4.5294413566589355 True -2 5877 21.675779342651367 0.3696553707122803 216.596435546875 0.7405388355255127 243.8567657470703 0.25071150064468384 0.73501945 2.3357410430908203 True -3 7836 21.700109481811523 0.3703486919403076 206.52127075195312 0.8517006635665894 237.79244995117188 0.25935184955596924 0.7469191 1.6339008808135986 True -4 9795 21.646610260009766 0.36708879470825195 189.30679321289062 1.2586288452148438 234.44923400878906 0.2642306387424469 0.7615444 1.1721826791763306 True -5 11754 21.720500469207764 0.37174057960510254 140.037109375 0.931571364402771 232.62673950195312 0.26846152544021606 0.76382774 1.0700569152832031 True -6 13713 22.402217388153076 17.040143966674805 162.93707275390625 0.7019911408424377 231.53648376464844 0.26995253562927246 0.7710351 1.0059176683425903 True -7 15672 21.709346771240234 0.3726661205291748 185.55453491210938 0.48219725489616394 230.77317810058594 0.27164384722709656 0.7805713 0.8493223190307617 True -8 17631 21.638665914535522 0.3775944709777832 150.07632446289062 0.7771013975143433 229.5204620361328 0.2742067873477936 0.78676546 0.7564082741737366 True -9 19590 21.652745246887207 0.36975932121276855 152.66993713378906 0.8471857309341431 228.7221221923828 0.2764301300048828 0.7919951 0.6885406970977783 True -10 21549 21.720552444458008 0.371659517288208 155.2659912109375 0.5717179775238037 228.04771423339844 0.2773822546005249 0.7985426 0.6606655716896057 True -11 23508 21.276678562164307 0.3689875602722168 250.2987060546875 0.7726460695266724 227.21910095214844 0.2792094051837921 0.8078188 0.6218896508216858 True -12 25467 21.259953260421753 0.3660461902618408 134.0327911376953 0.8173049688339233 226.63487243652344 0.28147655725479126 0.81308913 0.6045054793357849 True -13 27426 21.250892162322998 0.4036078453063965 156.28103637695312 0.5724700093269348 225.9627227783203 0.2825593054294586 0.81722546 0.583672046661377 True -14 29385 21.28623056411743 0.3717198371887207 197.78366088867188 0.5176939964294434 225.00469970703125 0.28511756658554077 0.82360667 0.569639265537262 True -15 31344 21.267467737197876 0.3751218318939209 164.33096313476562 0.4501231014728546 224.41917419433594 0.2867361903190613 0.82591796 0.5564239025115967 True -16 33303 21.29385280609131 0.8900468349456787 212.17535400390625 0.4612388014793396 224.58132934570312 0.28602373600006104 0.82962173 0.5523545742034912 True -17 35262 21.246545553207397 0.36687564849853516 261.54364013671875 0.4155835211277008 224.7082061767578 0.28583016991615295 0.8306145 0.5510222911834717 True -18 37221 21.22320318222046 0.36971616744995117 195.61993408203125 0.30453211069107056 225.11805725097656 0.28489500284194946 0.82935166 0.5557612180709839 False -19 39180 21.263356685638428 0.37232208251953125 192.01388549804688 0.3327014148235321 224.99574279785156 0.28559818863868713 0.8291813 0.5580341815948486 False diff --git a/ENCSR840QLA/cherimoya.fold_2.performance.tsv b/ENCSR840QLA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 950484df9b9ccf668364816725288dcc141cd5c8..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -224.7082061767578 0.506508469581604 0.28583016991615295 0.0794176235795021 0.8306145071983337 0.7812168598175049 0.5510222911834717 \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_3.evaluate.json b/ENCSR840QLA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d84ff25d11ca54cb11d07e08a9033eee9be81cdc..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF221UOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_3.fit.json b/ENCSR840QLA/cherimoya.fold_3.fit.json deleted file mode 100644 index 430f4be4b956817b22bbebf9567819fe6ea3eb32..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF221UOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_3.log b/ENCSR840QLA/cherimoya.fold_3.log deleted file mode 100644 index b5a67c3334e25e4fd0cb4d8a9cd3fb89a5b6034a..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1866 24.46610403060913 3.4608304500579834 227.6619873046875 1.5374506711959839 306.8948669433594 0.15303628146648407 0.51571965 7.8582658767700195 True -1 3732 20.724956512451172 0.38564205169677734 195.59384155273438 1.0382977724075317 274.4053649902344 0.22668032348155975 0.67620736 4.98259973526001 True -2 5598 20.67794179916382 0.852365255355835 233.40016174316406 0.8279008865356445 259.43505859375 0.25906798243522644 0.70473844 3.3494482040405273 True -3 7464 20.638855695724487 0.37108898162841797 179.76385498046875 0.9869556427001953 252.2399139404297 0.2706165313720703 0.71961653 2.2760045528411865 True -4 9330 20.65878677368164 0.37785768508911133 251.37628173828125 0.764740526676178 249.4574432373047 0.27718091011047363 0.7184486 1.9292654991149902 False -5 11196 20.671910047531128 0.370621919631958 187.6092529296875 1.1225881576538086 248.31527709960938 0.2791118919849396 0.72998905 1.5911502838134766 True -6 13062 20.689883708953857 0.37133264541625977 196.39227294921875 0.7533701658248901 247.6128692626953 0.2807528078556061 0.73854434 1.366320013999939 True -7 14928 20.65888547897339 0.36957406997680664 135.3581085205078 0.8069643378257751 246.69613647460938 0.282486230134964 0.74272126 1.2463455200195312 True -8 16794 20.72698426246643 0.36913490295410156 267.90240478515625 1.0925862789154053 246.18014526367188 0.28471851348876953 0.74713564 1.1257964372634888 True -9 18660 20.750270128250122 0.37331676483154297 233.31405639648438 0.6509364247322083 245.18154907226562 0.28677889704704285 0.7571873 1.038214921951294 True -10 20526 20.708163261413574 0.3768575191497803 183.0091094970703 0.7016016244888306 244.2950439453125 0.2888890504837036 0.7673506 0.9574555158615112 True -11 22392 20.717854261398315 0.37462663650512695 155.6835479736328 0.7138104438781738 242.89950561523438 0.2918066680431366 0.7767365 0.8614134788513184 True -12 24258 20.695298194885254 0.37772345542907715 204.9803466796875 0.38381361961364746 241.97744750976562 0.29333072900772095 0.7884899 0.8153214454650879 True -13 26124 20.704426288604736 1.2943601608276367 189.83920288085938 0.4679240584373474 241.0338897705078 0.294483482837677 0.7961085 0.7528990507125854 True -14 27990 20.683159351348877 1.4435343742370605 238.31268310546875 0.6987737417221069 240.15135192871094 0.29655030369758606 0.8079512 0.678193211555481 True -15 29856 20.434630632400513 0.770571231842041 252.37469482421875 0.4390900731086731 239.95843505859375 0.29576656222343445 0.81499773 0.6545577049255371 True -16 31722 20.329768657684326 0.3811333179473877 174.6282958984375 0.5842000246047974 240.0863494873047 0.2957768142223358 0.81950146 0.6350708603858948 True -17 33588 20.359941959381104 0.37990570068359375 161.27488708496094 0.41991153359413147 239.2192840576172 0.2986523509025574 0.8204436 0.6285465359687805 True -18 35454 20.347240686416626 0.38149237632751465 191.19854736328125 0.42579418420791626 239.5550079345703 0.29752328991889954 0.8205103 0.6267029643058777 True -19 37320 20.432032585144043 0.3788285255432129 164.60662841796875 0.4368550181388855 239.73948669433594 0.29673999547958374 0.82090384 0.6291970610618591 True diff --git a/ENCSR840QLA/cherimoya.fold_3.performance.tsv b/ENCSR840QLA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a6485771a7ca49a356feed4beed4082be5dd2909..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -239.73948669433594 0.49641838669776917 0.29673999547958374 0.08160912990570068 0.8209038376808167 0.7787776589393616 0.6291970610618591 \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_4.evaluate.json b/ENCSR840QLA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6ab7e3a708f391d80ed42719492d758ce0c94d79..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF221UOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_4.fit.json b/ENCSR840QLA/cherimoya.fold_4.fit.json deleted file mode 100644 index 2a29fea64ce315f8d0b6b37aff5cda56a2ea2d89..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF221UOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840QLA/cherimoya.fold_4.log b/ENCSR840QLA/cherimoya.fold_4.log deleted file mode 100644 index 633893c4beb07d1a8b90af0e58c8bc1375398a18..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1879 24.319653511047363 15.7360360622406 227.89892578125 1.301894187927246 262.4525451660156 0.1362655758857727 0.52363485 7.121849060058594 True -1 3758 20.745976448059082 0.38262414932250977 194.88697814941406 1.2058863639831543 234.95913696289062 0.2077757567167282 0.6712923 4.597106456756592 True -2 5637 20.693528652191162 0.8771021366119385 184.81637573242188 0.8148897290229797 220.93313598632812 0.238005593419075 0.70822513 2.345393419265747 True -3 7516 20.64916205406189 0.37073612213134766 200.53604125976562 1.0334324836730957 215.94619750976562 0.246606707572937 0.7194801 1.6081308126449585 True -4 9395 20.608896255493164 0.3653371334075928 193.95120239257812 0.8555231094360352 213.91905212402344 0.24944189190864563 0.7322169 1.2891122102737427 True -5 11274 20.702975034713745 0.3671860694885254 149.06558227539062 0.684951663017273 212.43264770507812 0.25330790877342224 0.7420582 1.1240423917770386 True -6 13153 20.68678331375122 0.3710792064666748 208.1168212890625 0.8569967746734619 211.31991577148438 0.2557865381240845 0.7440396 1.0301036834716797 True -7 15032 20.67199969291687 0.36324381828308105 206.05596923828125 0.8837664127349854 209.87506103515625 0.2610795795917511 0.7538513 0.8615060448646545 True -8 16911 20.34629511833191 0.3621978759765625 213.33041381835938 0.7612500786781311 209.68116760253906 0.25932538509368896 0.7619531 0.8459593057632446 True -9 18790 20.247318506240845 0.36672329902648926 153.4748077392578 0.8061202764511108 208.61439514160156 0.26274868845939636 0.7718583 0.7573360800743103 True -10 20669 20.24283766746521 0.36215949058532715 155.8555908203125 0.6286447644233704 208.48492431640625 0.2623903751373291 0.7769645 0.7059410214424133 True -11 22548 20.22577667236328 0.3696434497833252 211.103271484375 0.9186887741088867 207.2046661376953 0.2663055658340454 0.78530264 0.6697558760643005 True -12 24427 20.28723406791687 0.9363551139831543 118.8341064453125 0.48342177271842957 206.34751892089844 0.2675824761390686 0.7954378 0.6266849637031555 True -13 26306 20.29108214378357 2.226954460144043 165.65663146972656 0.3917742073535919 206.06312561035156 0.2686834931373596 0.800555 0.6068118810653687 True -14 28185 20.333110094070435 0.369337797164917 159.4215087890625 0.6220998764038086 205.81031799316406 0.2698158919811249 0.80576324 0.5892482995986938 True -15 30064 20.238874673843384 1.097825527191162 145.5589141845703 0.5508192181587219 204.79653930664062 0.2727627754211426 0.8098544 0.5755941867828369 True -16 31943 20.383891582489014 0.3658163547515869 172.9146270751953 0.44725579023361206 205.1852569580078 0.27050697803497314 0.8122187 0.5608113408088684 True -17 33822 20.287776231765747 0.3675410747528076 164.70364379882812 0.37784427404403687 205.26942443847656 0.2705668807029724 0.8123771 0.5588250160217285 True -18 35701 20.227587938308716 0.36582088470458984 192.57647705078125 0.4688059091567993 205.08741760253906 0.27150335907936096 0.8122871 0.5607718229293823 False -19 37580 20.25041937828064 0.3888556957244873 155.58685302734375 0.4177337884902954 205.20166015625 0.27154698967933655 0.81142104 0.5634095072746277 False diff --git a/ENCSR840QLA/cherimoya.fold_4.performance.tsv b/ENCSR840QLA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e514fc8ee3422ace82bf0f4791ec937d4362f48d..0000000000000000000000000000000000000000 --- a/ENCSR840QLA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -205.26942443847656 0.5176426768302917 0.27056685090065 0.06849771738052368 0.8123770952224731 0.7635287642478943 0.5588250160217285 \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_0.evaluate.json b/ENCSR840USW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7f53424575c8207c20835f26034685b9a9ac715f..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF919CRX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_0.fit.json b/ENCSR840USW/cherimoya.fold_0.fit.json deleted file mode 100644 index 5378ea25ddbe329815e07f201741063cf5d8c315..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF919CRX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_0.log b/ENCSR840USW/cherimoya.fold_0.log deleted file mode 100644 index ea7861548a5c183a1ddaffddee4ac2a6f2ad95e8..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1498 21.576412200927734 3.2241833209991455 406.5180969238281 1.5511398315429688 573.6489868164062 0.17664732038974762 0.57152253 15.109915733337402 True -1 2996 16.515594005584717 0.3059539794921875 363.07391357421875 1.4015324115753174 501.8415832519531 0.27025356888771057 0.6780305 9.704341888427734 True -2 4494 16.44111680984497 0.3027033805847168 369.7942810058594 1.303818702697754 437.4946594238281 0.34391555190086365 0.73313797 4.633632659912109 True -3 5992 16.238072156906128 0.31247568130493164 366.504150390625 1.5647683143615723 420.7085266113281 0.3626613914966583 0.7453462 2.6353979110717773 True -4 7490 16.127968549728394 0.5457110404968262 356.7451171875 1.0955730676651 415.8958740234375 0.3700864613056183 0.75431275 1.7780829668045044 True -5 8988 16.187196493148804 0.3130338191986084 442.1949768066406 1.0050071477890015 413.1310119628906 0.3747727870941162 0.7580968 1.5857199430465698 True -6 10486 16.138151168823242 0.3437354564666748 302.664306640625 0.8305590152740479 408.5533447265625 0.3811112642288208 0.7680876 1.266871690750122 True -7 11984 16.166998147964478 0.3062143325805664 336.21612548828125 0.7331088781356812 406.9290771484375 0.3824491798877716 0.7779041 1.0215394496917725 True -8 13482 16.14399266242981 0.2953648567199707 270.291748046875 1.2614777088165283 404.7044372558594 0.3867483139038086 0.7808365 0.9334943890571594 True -9 14980 16.128897190093994 0.30179643630981445 356.86566162109375 1.0004609823226929 403.13079833984375 0.3899208903312683 0.78513515 0.9199678301811218 True -10 16478 16.173404455184937 0.3038191795349121 300.1949768066406 0.8783145546913147 399.7966003417969 0.3948978781700134 0.79195166 0.8665376305580139 True -11 17976 16.14520239830017 1.3725204467773438 285.28466796875 0.6602622270584106 398.4380798339844 0.3956489562988281 0.7966139 0.8028995394706726 True -12 19474 16.17949104309082 0.3001081943511963 320.02734375 0.5832316279411316 397.2165832519531 0.3968101143836975 0.8011369 0.7786831855773926 True -13 20972 16.167189836502075 0.29821276664733887 322.9551696777344 1.0984854698181152 395.6225891113281 0.39874112606048584 0.805859 0.7570736408233643 True -14 22470 16.171790599822998 0.29310107231140137 335.1681213378906 0.8714379668235779 394.1495666503906 0.40044206380844116 0.8096678 0.728577196598053 True -15 23968 16.179113388061523 0.299422025680542 320.16754150390625 0.5342103242874146 392.7350158691406 0.403154194355011 0.8140658 0.7079911828041077 True -16 25466 16.142866849899292 0.3037598133087158 327.8443298339844 0.31877565383911133 392.81854248046875 0.4029790461063385 0.8173563 0.6910181045532227 True -17 26964 16.351125478744507 3.161945343017578 216.935546875 0.6226664781570435 392.27984619140625 0.4037992060184479 0.81777114 0.6920867562294006 True -18 28462 16.1522114276886 0.3051304817199707 289.43804931640625 0.47510555386543274 393.1836242675781 0.4020654857158661 0.8165318 0.6974056959152222 False -19 29960 16.180785179138184 0.2957754135131836 270.92755126953125 0.49821895360946655 393.2462158203125 0.40208515524864197 0.8167798 0.7048178315162659 False diff --git a/ENCSR840USW/cherimoya.fold_0.performance.tsv b/ENCSR840USW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 81eb4132e956cd5d38d87a37f4733332586e18eb..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -392.27984619140625 0.41561180353164673 0.4037991762161255 0.13393981754779816 0.8177711367607117 0.773400068283081 0.6920867562294006 \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_1.evaluate.json b/ENCSR840USW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5d2394a6df332296012ede6434c939ccc9c51dcb..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF919CRX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_1.fit.json b/ENCSR840USW/cherimoya.fold_1.fit.json deleted file mode 100644 index 63e8da71451144d1fa6fc2a6c61636f5e03e91ef..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF919CRX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_1.log b/ENCSR840USW/cherimoya.fold_1.log deleted file mode 100644 index 88546495ad4918ae433674bf0e69505a84c97f28..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1460 20.776663303375244 2.6104660034179688 371.75506591796875 0.9757450819015503 691.9555053710938 0.18060259521007538 0.5404378 17.0242977142334 True -1 2920 16.069300651550293 1.060882806777954 314.7242736816406 1.4412579536437988 609.5557250976562 0.2745961844921112 0.6567626 11.628725051879883 True -2 4380 16.049397706985474 0.39849400520324707 240.8715362548828 1.5429909229278564 524.4693603515625 0.3580760061740875 0.7219209 6.387094974517822 True -3 5840 16.017297506332397 0.41284847259521484 285.96435546875 1.2514163255691528 503.82476806640625 0.37788504362106323 0.7446886 3.379194736480713 True -4 7300 16.074808597564697 0.39669251441955566 220.3975372314453 1.044111967086792 494.84930419921875 0.39024585485458374 0.7478591 2.3616840839385986 True -5 8760 16.049354553222656 0.40256834030151367 328.5389404296875 0.9150334000587463 490.333740234375 0.3954235017299652 0.75652933 1.7307311296463013 True -6 10220 16.043038606643677 0.4257545471191406 307.1582336425781 0.8260413408279419 487.5651550292969 0.39966094493865967 0.75912744 1.5258610248565674 True -7 11680 16.03783416748047 0.639592170715332 399.7283630371094 0.9996172189712524 484.5900573730469 0.40266910195350647 0.76733476 1.3945127725601196 True -8 13140 16.06887936592102 0.39994239807128906 362.686279296875 1.1855685710906982 482.3372802734375 0.40488696098327637 0.77566266 1.2581291198730469 True -9 14600 16.065407276153564 0.40185546875 285.46783447265625 0.7696937918663025 478.34320068359375 0.40923023223876953 0.7810696 1.1451970338821411 True -10 16060 16.04987144470215 0.39589929580688477 316.8968811035156 0.7878907918930054 474.97760009765625 0.4133586585521698 0.78951144 1.0194096565246582 True -11 17520 16.039602279663086 18.677239418029785 328.6092529296875 0.849707841873169 472.7517395019531 0.41537079215049744 0.7943857 0.9374902844429016 True -12 18980 16.156564235687256 0.42594289779663086 309.7972412109375 0.600824236869812 470.07049560546875 0.4177507758140564 0.80318904 0.9031097292900085 True -13 20440 16.047752618789673 18.256916522979736 292.32269287109375 1.1341111660003662 468.37127685546875 0.4202211797237396 0.8085703 0.8575430512428284 True -14 21900 17.135294675827026 1.3700199127197266 264.5704040527344 0.8088366389274597 466.4979553222656 0.42171016335487366 0.8159562 0.8040705919265747 True -15 23360 16.03187894821167 0.9246530532836914 298.4583740234375 0.53902268409729 464.7806091308594 0.4236692190170288 0.821879 0.7705394625663757 True -16 24820 16.083055019378662 0.397991418838501 298.25177001953125 0.5607085227966309 465.14117431640625 0.4220671057701111 0.82636774 0.7541399002075195 True -17 26280 16.040626525878906 0.3972201347351074 324.3593444824219 0.6281965970993042 465.2170104980469 0.4218690097332001 0.827024 0.7583457231521606 True -18 27740 16.010157585144043 0.409165620803833 230.87828063964844 0.38668325543403625 465.5689392089844 0.42098793387413025 0.82695705 0.7668852210044861 False -19 29200 16.00066328048706 0.3975837230682373 322.61102294921875 0.4458354711532593 465.72930908203125 0.4208224415779114 0.82597065 0.7743728756904602 False diff --git a/ENCSR840USW/cherimoya.fold_1.performance.tsv b/ENCSR840USW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 31de32c941af2f4b4184108bdf6a0dc3dafe0c49..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -465.2170104980469 0.39630240201950073 0.4218690097332001 0.15033932030200958 0.827023983001709 0.8030032515525818 0.7583457231521606 \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_2.evaluate.json b/ENCSR840USW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f8c19807a49fe8e40c6732fe645838365da2677b..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF919CRX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_2.fit.json b/ENCSR840USW/cherimoya.fold_2.fit.json deleted file mode 100644 index 909ff6e1fe8fc4b7df6ad03899c62ddfd40b4502..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF919CRX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_2.log b/ENCSR840USW/cherimoya.fold_2.log deleted file mode 100644 index fc188bd822537d0d721d5a35dfb12b4ca67b085a..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1586 22.0483341217041 3.1118130683898926 427.441162109375 1.6480307579040527 609.07421875 0.1753944605588913 0.5303467 14.076929092407227 True -1 3172 17.475250005722046 0.3693046569824219 394.9612731933594 1.2658206224441528 525.5590209960938 0.27919626235961914 0.6473303 8.933076858520508 True -2 4758 17.39143419265747 0.3246171474456787 401.37652587890625 1.1727815866470337 458.0486755371094 0.35061734914779663 0.72886103 4.801727294921875 True -3 6344 17.116893529891968 0.3026309013366699 385.52484130859375 0.9530174136161804 439.3474426269531 0.3683924376964569 0.7511764 2.4922876358032227 True -4 7930 17.144409656524658 0.3023970127105713 368.0611877441406 0.818523645401001 432.6170349121094 0.3776021897792816 0.75781673 1.793461799621582 True -5 9516 17.099134922027588 0.3071305751800537 317.44586181640625 1.5079069137573242 429.97509765625 0.3807815909385681 0.76577646 1.3791691064834595 True -6 11102 17.09395670890808 0.3022313117980957 370.98504638671875 1.0791168212890625 428.2710876464844 0.38275206089019775 0.7680634 1.217457890510559 True -7 12688 17.081377267837524 0.30121302604675293 352.69476318359375 1.0298511981964111 424.8223571777344 0.388406366109848 0.7727201 1.0942708253860474 True -8 14274 17.063429594039917 0.6520276069641113 276.0618591308594 1.325416088104248 424.1557922363281 0.38885194063186646 0.7800518 1.0116467475891113 True -9 15860 17.156988620758057 0.30313539505004883 394.44403076171875 0.6742737293243408 421.8607177734375 0.3926139771938324 0.7828159 0.9013025164604187 True -10 17446 17.11047387123108 0.3027176856994629 274.7518310546875 0.8335542678833008 419.6268310546875 0.394915908575058 0.78765947 0.8271409273147583 True -11 19032 17.064712047576904 0.29631972312927246 260.5721435546875 0.7838592529296875 416.7208557128906 0.3986116647720337 0.79473424 0.7906362414360046 True -12 20618 17.057286739349365 0.2989628314971924 255.80291748046875 0.9963659048080444 415.4514465332031 0.3994657099246979 0.7991271 0.7622348666191101 True -13 22204 17.07736301422119 0.3036224842071533 293.07177734375 0.7487590312957764 413.8275451660156 0.4012245535850525 0.8018666 0.7460843920707703 True -14 23790 17.089361906051636 0.2958378791809082 322.6525573730469 0.8238604664802551 411.7642517089844 0.40298429131507874 0.809307 0.7225009202957153 True -15 25376 17.1011643409729 0.2966952323913574 263.9485778808594 0.4529876112937927 410.1771545410156 0.4066447913646698 0.81382626 0.7082783579826355 True -16 26962 17.109620332717896 0.29599738121032715 328.9005126953125 0.48074567317962646 410.7903747558594 0.40545734763145447 0.81674325 0.7039567232131958 True -17 28548 17.097786903381348 0.30008816719055176 294.60308837890625 0.5766071677207947 411.2568054199219 0.40495428442955017 0.81832814 0.7074689269065857 True -18 30134 17.083470821380615 0.296938419342041 281.39239501953125 0.4163457155227661 411.7717590332031 0.4044898748397827 0.81732 0.7150185704231262 False -19 31720 17.052016258239746 0.29984593391418457 242.78701782226562 0.4561036229133606 411.9123840332031 0.40457800030708313 0.8168637 0.7242635488510132 False diff --git a/ENCSR840USW/cherimoya.fold_2.performance.tsv b/ENCSR840USW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 41873ac83abad56b30a1bb0d161b72c326d4a43e..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -411.2568054199219 0.4119834005832672 0.40495428442955017 0.14003264904022217 0.8183281421661377 0.7818529605865479 0.7074689269065857 \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_3.evaluate.json b/ENCSR840USW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 72713ecaf16ef06b68317cc6ea6e23369e655d18..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF919CRX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_3.fit.json b/ENCSR840USW/cherimoya.fold_3.fit.json deleted file mode 100644 index b295639fd5de849b562d4b04d2f67cc7bd7b7a04..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF919CRX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_3.log b/ENCSR840USW/cherimoya.fold_3.log deleted file mode 100644 index b4d9b96009bf1c33799c22f3de5a1dffe36f3d95..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1519 21.50249743461609 3.439340114593506 349.8654479980469 1.1075453758239746 599.4776000976562 0.19055205583572388 0.5451611 15.804978370666504 True -1 3038 16.747862100601196 0.3041059970855713 340.9394836425781 1.3154115676879883 524.2680053710938 0.2907329201698303 0.6475149 10.120102882385254 True -2 4557 16.718419790267944 0.3088855743408203 341.052734375 1.0798029899597168 463.32037353515625 0.356690376996994 0.72448283 4.813992023468018 True -3 6076 16.706734657287598 0.294008731842041 400.706787109375 1.3421462774276733 447.5965576171875 0.3697432279586792 0.73547804 2.78008770942688 True -4 7595 16.74879765510559 0.29463815689086914 387.2203369140625 0.8473654389381409 440.23516845703125 0.38093194365501404 0.7336801 1.8827526569366455 False -5 9114 16.794545650482178 0.2998046875 262.44268798828125 1.110130786895752 437.8905029296875 0.38406115770339966 0.73797905 1.5471394062042236 True -6 10633 16.699886798858643 0.30402374267578125 305.51910400390625 1.057910680770874 433.5941162109375 0.3919115960597992 0.74092954 1.332444190979004 True -7 12152 16.682036876678467 0.2921631336212158 375.0157775878906 1.012596845626831 430.8634948730469 0.3950059711933136 0.74878746 1.2077522277832031 True -8 13671 16.678290128707886 0.29242372512817383 331.22607421875 0.6913900971412659 429.3495788574219 0.39707550406455994 0.7541997 1.1073981523513794 True -9 15190 16.675230264663696 0.29186582565307617 291.3360595703125 0.7463629245758057 428.1062316894531 0.3980548679828644 0.7602277 1.0438390970230103 True -10 16709 16.680708646774292 0.2975480556488037 419.87322998046875 0.9022029042243958 425.6005859375 0.4019840657711029 0.7647375 0.9943380951881409 True -11 18228 16.680046796798706 0.2955021858215332 315.8540954589844 1.0701082944869995 423.97894287109375 0.40474459528923035 0.77332157 0.9566563963890076 True -12 19747 16.69183373451233 0.296309232711792 280.05999755859375 0.7674129605293274 421.7083740234375 0.4065341651439667 0.7833063 0.9114568829536438 True -13 21266 16.69699501991272 0.29764556884765625 364.21966552734375 0.7897210121154785 420.3048400878906 0.4085347056388855 0.7918981 0.8695338368415833 True -14 22785 16.70327925682068 0.29170680046081543 295.8406066894531 0.8668562173843384 417.2983093261719 0.41139113903045654 0.7992811 0.8118948936462402 True -15 24304 16.691916465759277 0.2916383743286133 392.8994445800781 0.517490029335022 415.52032470703125 0.4141339361667633 0.80708605 0.7870573997497559 True -16 25823 16.7005033493042 0.7879023551940918 326.0189208984375 0.5525493621826172 415.395263671875 0.4134388566017151 0.810786 0.7596003413200378 True -17 27342 16.729581832885742 0.30507659912109375 364.13568115234375 0.5557475090026855 415.68341064453125 0.4122777581214905 0.81215197 0.75384122133255 True -18 28861 16.737523794174194 0.3039689064025879 303.27178955078125 0.6045606136322021 415.6649475097656 0.41283124685287476 0.8130229 0.7623857259750366 True -19 30380 16.74518394470215 0.3002505302429199 247.67630004882812 0.6238868236541748 416.8323974609375 0.41054806113243103 0.81167054 0.7638273239135742 False diff --git a/ENCSR840USW/cherimoya.fold_3.performance.tsv b/ENCSR840USW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 71ee1dc63ab504f0ecf6511e0bb01d24a81e9f27..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -415.6649475097656 0.4052883982658386 0.41283118724823 0.14495383203029633 0.8130229115486145 0.7803938388824463 0.7623857259750366 \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_4.evaluate.json b/ENCSR840USW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ceb0c2cd50f51ccff6432549862298a3b3c27644..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF919CRX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_4.fit.json b/ENCSR840USW/cherimoya.fold_4.fit.json deleted file mode 100644 index beb0e09fea1edf9cd74855a390a8a58bf3cb8efe..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF919CRX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR840USW/cherimoya.fold_4.log b/ENCSR840USW/cherimoya.fold_4.log deleted file mode 100644 index 00551570da4435310c8dd286f2feac9ff6a08420..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1503 21.126800298690796 4.076899528503418 358.1609802246094 1.133757472038269 544.7628173828125 0.17590367794036865 0.55479306 14.399707794189453 True -1 3006 16.55829954147339 0.3323378562927246 355.3096923828125 1.2210676670074463 481.62152099609375 0.26629582047462463 0.652258 9.334107398986816 True -2 4509 16.298304080963135 0.30307435989379883 312.5408630371094 1.387557864189148 422.3936462402344 0.3418043255805969 0.7121306 4.557096481323242 True -3 6012 16.193514347076416 0.2975184917449951 348.37841796875 0.9914089441299438 406.6288146972656 0.3557053804397583 0.7360697 2.406954288482666 True -4 7515 16.191791534423828 0.2784104347229004 283.44287109375 1.1333106756210327 399.7100830078125 0.36437052488327026 0.75027555 1.6080050468444824 True -5 9018 16.2422091960907 0.2830383777618408 280.4190673828125 1.5375248193740845 395.29931640625 0.37180837988853455 0.75376916 1.2520617246627808 True -6 10521 16.238982439041138 0.30829954147338867 381.88250732421875 1.2528939247131348 393.78717041015625 0.37372735142707825 0.75817823 1.0544873476028442 True -7 12024 16.218623161315918 0.28818249702453613 431.00335693359375 1.288252830505371 391.21875 0.37766173481941223 0.7596184 0.9475241303443909 True -8 13527 16.203213453292847 0.2738158702850342 391.2054443359375 0.8299351334571838 388.4296875 0.3821083903312683 0.7651964 0.8527548909187317 True -9 15030 16.206291913986206 0.2741072177886963 321.1576843261719 0.9165605902671814 386.7170104980469 0.3849264979362488 0.7688761 0.8265987634658813 True -10 16533 16.20323944091797 0.27680444717407227 279.8256530761719 0.6998978853225708 386.1664733886719 0.38430550694465637 0.77866286 0.7950835227966309 True -11 18036 16.20498538017273 0.28061389923095703 356.20611572265625 1.089359998703003 383.5199279785156 0.3892921805381775 0.7818449 0.7619809508323669 True -12 19539 16.21599268913269 0.2737772464752197 306.88714599609375 0.8974220752716064 381.0044860839844 0.39399945735931396 0.7851261 0.741855800151825 True -13 21042 16.195796728134155 0.2804722785949707 281.31536865234375 0.9640803933143616 379.058837890625 0.3962867856025696 0.7944644 0.7174881100654602 True -14 22545 16.21057891845703 0.27620887756347656 321.5353698730469 0.5164863467216492 378.746826171875 0.39681077003479004 0.8026362 0.6914397478103638 True -15 24048 16.184070110321045 0.28523683547973633 293.07354736328125 0.7140655517578125 377.8912048339844 0.3983893394470215 0.8068311 0.681610107421875 True -16 25551 16.1747989654541 0.27550220489501953 206.55642700195312 0.7888233661651611 378.7664794921875 0.3976096212863922 0.81066746 0.67046719789505 True -17 27054 16.189656496047974 0.29537177085876465 353.54730224609375 0.6453112959861755 378.4995422363281 0.39861252903938293 0.8130887 0.6718177199363708 True -18 28557 16.1805477142334 0.2737545967102051 314.9585266113281 0.5273823738098145 379.23187255859375 0.3969350755214691 0.81147873 0.6795833706855774 False -19 30060 16.190805435180664 0.2741072177886963 300.922607421875 0.5638344883918762 379.27520751953125 0.3975910246372223 0.8111455 0.6856791973114014 False diff --git a/ENCSR840USW/cherimoya.fold_4.performance.tsv b/ENCSR840USW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 52ae3b8832fe0fc151a4924b0226e99c18b449ee..0000000000000000000000000000000000000000 --- a/ENCSR840USW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -378.4995422363281 0.42006587982177734 0.39861252903938293 0.12693648040294647 0.8130887150764465 0.766924262046814 0.6718177199363708 \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_0.evaluate.json b/ENCSR842KCP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7b96fd1b9173b82b55f66ccd689f741aac355545..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF621QWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_0.fit.json b/ENCSR842KCP/cherimoya.fold_0.fit.json deleted file mode 100644 index 417b63c027c6295ff34a0834c40b5f98f22e555e..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF621QWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_0.log b/ENCSR842KCP/cherimoya.fold_0.log deleted file mode 100644 index 070fe68f64e13963ee926905f498f74806b01c5e..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 35.884915351867676 4.173376083374023 1002.783447265625 0.5763066411018372 1290.23583984375 0.3072264790534973 0.710837 7.561090469360352 True -1 5456 30.393098831176758 1.6745069026947021 1090.8035888671875 0.5203382968902588 1106.2939453125 0.41344401240348816 0.76088566 1.6340500116348267 True -2 8184 30.266005039215088 7.30864143371582 780.2433471679688 0.5486419200897217 1062.663330078125 0.44094693660736084 0.7731256 0.9195554852485657 True -3 10912 30.284586906433105 0.5861301422119141 840.4782104492188 0.7232660055160522 1054.534423828125 0.44329720735549927 0.78346956 0.7759395241737366 True -4 13640 30.193207263946533 0.5429937839508057 792.6605224609375 0.4579245448112488 1041.95166015625 0.4515463411808014 0.79132766 0.678227424621582 True -5 16368 30.19308066368103 0.5744462013244629 874.220703125 0.48072904348373413 1031.918701171875 0.4584982097148895 0.79189485 0.587618350982666 True -6 19096 30.24661421775818 8.202415943145752 831.390869140625 0.541276216506958 1024.3050537109375 0.46538811922073364 0.79043955 0.549861490726471 False -7 21824 30.253472566604614 0.5846583843231201 766.7388916015625 0.3841697573661804 1017.625244140625 0.4692554473876953 0.7996303 0.4490359425544739 True -8 24552 30.191063404083252 0.5434608459472656 919.928466796875 0.39308440685272217 1016.478759765625 0.4695480167865753 0.807124 0.4098461866378784 True -9 27280 30.188323497772217 0.5506172180175781 837.160888671875 0.4449228048324585 1008.7452392578125 0.4760321080684662 0.8121439 0.39112579822540283 True -10 30008 30.18049192428589 0.5522351264953613 849.5045166015625 0.43571144342422485 1008.4417724609375 0.47430333495140076 0.81643826 0.36871641874313354 True -11 32736 30.180314540863037 0.5529139041900635 764.2133178710938 0.43449708819389343 1001.3932495117188 0.48040398955345154 0.8191221 0.35331621766090393 True -12 35464 30.242170572280884 0.5930385589599609 772.9649047851562 0.3643122613430023 997.8790283203125 0.4823375642299652 0.82349396 0.35005223751068115 True -13 38192 30.200217247009277 0.5350430011749268 770.7506103515625 0.552662193775177 991.734619140625 0.4857895076274872 0.83223253 0.32342106103897095 True -14 40920 30.195860862731934 0.5422940254211426 755.4150390625 0.4414668679237366 991.6901245117188 0.48570895195007324 0.83710414 0.3177949786186218 True -15 43648 30.199799299240112 0.546715497970581 713.6560668945312 0.28798598051071167 986.3338012695312 0.49021777510643005 0.8405142 0.3083237111568451 True -16 46376 30.173628330230713 0.5473611354827881 824.2923583984375 0.34272754192352295 988.061767578125 0.48748305439949036 0.84218097 0.30628716945648193 True -17 49104 30.219733238220215 0.5520193576812744 771.5431518554688 0.19995883107185364 989.6575317382812 0.48631495237350464 0.84292954 0.30415886640548706 True -18 51832 30.23814034461975 0.5519957542419434 781.8814697265625 0.2594468891620636 986.9116821289062 0.4889502227306366 0.843473 0.30832353234291077 True -19 54560 30.244177103042603 0.5646264553070068 745.2407836914062 0.27075156569480896 991.1382446289062 0.4840051829814911 0.84179753 0.30816659331321716 False diff --git a/ENCSR842KCP/cherimoya.fold_0.performance.tsv b/ENCSR842KCP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index aab80188ace32c4bcf2e2d5d2ae4d7b68ae2dbb1..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -986.9116821289062 0.30783170461654663 0.4889502227306366 0.23273809254169464 0.8434730172157288 0.7708923816680908 0.30832353234291077 \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_1.evaluate.json b/ENCSR842KCP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 954bb47ef09a73105b934d86fa14d37b23536072..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF621QWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_1.fit.json b/ENCSR842KCP/cherimoya.fold_1.fit.json deleted file mode 100644 index 153f10ba5d7411671fcad7cb56c3765f96029eaa..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF621QWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_1.log b/ENCSR842KCP/cherimoya.fold_1.log deleted file mode 100644 index 60f354be4abe22c3cc0d7aabbe0e68de67d37176..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 35.284902811050415 4.203553199768066 1042.3887939453125 1.023673176765442 1487.5174560546875 0.3107213079929352 0.7104506 8.942107200622559 True -1 5472 30.35022783279419 0.7415759563446045 948.9029541015625 0.6009031534194946 1276.1890869140625 0.42479458451271057 0.75617665 2.629796028137207 True -2 8208 30.19808340072632 0.70819091796875 782.77978515625 0.5282789468765259 1230.7911376953125 0.4476400911808014 0.76954746 1.0439585447311401 True -3 10944 29.673502922058105 0.7871706485748291 844.4542236328125 0.3367729187011719 1206.708251953125 0.4584399461746216 0.7866734 0.8155394792556763 True -4 13680 29.724289894104004 0.6791160106658936 983.7435302734375 0.4317997097969055 1188.3878173828125 0.46880221366882324 0.793591 0.6201660633087158 True -5 16416 29.96383833885193 0.7191133499145508 784.967041015625 0.546028733253479 1179.6502685546875 0.47189125418663025 0.79620725 0.6243374943733215 True -6 19152 29.768451690673828 0.7121198177337646 697.000244140625 0.6106235980987549 1171.286865234375 0.4769410490989685 0.79985476 0.5232636332511902 True -7 21888 29.673186779022217 0.7044732570648193 686.488525390625 0.4937344789505005 1164.5478515625 0.4806671440601349 0.8066094 0.4709705710411072 True -8 24624 29.73098349571228 0.728745698928833 775.51904296875 0.4510492980480194 1157.123046875 0.4845822751522064 0.8133475 0.43180158734321594 True -9 27360 29.753017902374268 0.6704385280609131 783.5558471679688 0.44289830327033997 1151.2008056640625 0.4872550368309021 0.8187267 0.4187608063220978 True -10 30096 29.705484628677368 1.1023097038269043 678.1422119140625 0.5355595350265503 1145.6851806640625 0.49013519287109375 0.8212379 0.4035826623439789 True -11 32832 29.78563666343689 0.714552640914917 978.7832641601562 0.3207712173461914 1138.9102783203125 0.4936056137084961 0.8285953 0.3802074193954468 True -12 35568 29.69508457183838 0.6860368251800537 837.4586181640625 0.46802181005477905 1135.3533935546875 0.4940607249736786 0.8351545 0.3700239062309265 True -13 38304 29.727593421936035 0.6978578567504883 784.8121337890625 0.38564810156822205 1128.35107421875 0.4985071122646332 0.8414771 0.34930387139320374 True -14 41040 29.73653292655945 0.6502082347869873 891.7921142578125 0.27902698516845703 1125.9117431640625 0.49947962164878845 0.84582824 0.3490273952484131 True -15 43776 29.689343452453613 0.6630513668060303 886.7938232421875 0.48030513525009155 1120.339599609375 0.5025702118873596 0.84999025 0.33974042534828186 True -16 46512 29.629132509231567 2.0098185539245605 847.4119262695312 0.2217313051223755 1122.9466552734375 0.5005348920822144 0.8529909 0.33251193165779114 True -17 49248 29.73447585105896 0.6820147037506104 855.84326171875 0.21896910667419434 1122.42919921875 0.5001599788665771 0.8538985 0.33259332180023193 True -18 51984 29.75681495666504 0.7314939498901367 809.183837890625 0.30066514015197754 1121.8502197265625 0.5006861090660095 0.8540523 0.3335496187210083 True -19 54720 29.759705305099487 0.6712303161621094 745.4732666015625 0.12873350083827972 1120.4453125 0.5022485256195068 0.8546889 0.3357783555984497 True diff --git a/ENCSR842KCP/cherimoya.fold_1.performance.tsv b/ENCSR842KCP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2e9198195bc50655dd147f1609cc1dcf17f8e1c3..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1120.4453125 0.29160845279693604 0.5022485256195068 0.25956785678863525 0.8546888828277588 0.8117905259132385 0.3357783555984497 \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_2.evaluate.json b/ENCSR842KCP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index dfa610f6b121f348ce6d71d6dcbe02769258c681..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF621QWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_2.fit.json b/ENCSR842KCP/cherimoya.fold_2.fit.json deleted file mode 100644 index 15ef775e34101a5733da0c847051c84081dbad0d..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF621QWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_2.log b/ENCSR842KCP/cherimoya.fold_2.log deleted file mode 100644 index 2e144f110437f11f1d71d02fe57d2d7c3f4b5aca..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2870 36.42562532424927 4.362426280975342 926.775634765625 0.4565576910972595 1310.4208984375 0.309136301279068 0.7058963 8.005850791931152 True -1 5740 31.376262426376343 0.7176446914672852 968.9539184570312 0.5919778943061829 1131.959716796875 0.4167312681674957 0.76153123 2.173281192779541 True -2 8610 31.727336645126343 0.5503225326538086 1059.38134765625 0.4516230821609497 1093.7896728515625 0.43591752648353577 0.78083605 0.8342329263687134 True -3 11480 31.72396969795227 0.5366075038909912 956.224365234375 0.49064958095550537 1076.8455810546875 0.4482605755329132 0.7885077 0.7313205599784851 True -4 14350 31.69243311882019 1.6714200973510742 827.049560546875 0.49324244260787964 1066.3841552734375 0.45470455288887024 0.79084826 0.6355190873146057 True -5 17220 31.742664098739624 0.5520150661468506 951.9656982421875 0.4689171314239502 1060.3634033203125 0.45863839983940125 0.79442215 0.6101873517036438 True -6 20090 31.794677734375 0.9982056617736816 802.6069946289062 0.41822946071624756 1049.5904541015625 0.4650071859359741 0.7994019 0.5350813865661621 True -7 22960 31.779579877853394 0.55690598487854 771.994384765625 0.47104790806770325 1044.463623046875 0.46838122606277466 0.80306125 0.4746786952018738 True -8 25830 31.707205295562744 0.5578882694244385 798.1151123046875 0.3708304166793823 1042.5809326171875 0.4675990045070648 0.80605173 0.451808363199234 True -9 28700 31.700746297836304 0.5456342697143555 847.1182250976562 0.21431739628314972 1038.350830078125 0.47137451171875 0.80810905 0.43042322993278503 True -10 31570 31.7146315574646 0.5287594795227051 1056.5841064453125 0.40733230113983154 1030.3948974609375 0.4758395552635193 0.80969733 0.3896240293979645 True -11 34440 31.731223821640015 0.523777961730957 840.0028076171875 0.3164663314819336 1027.6287841796875 0.4770089089870453 0.8176492 0.3661552667617798 True -12 37310 31.726146936416626 0.5294280052185059 785.7615966796875 0.43174004554748535 1019.3818969726562 0.4832650125026703 0.824465 0.35080862045288086 True -13 40180 31.745768070220947 0.5230228900909424 749.7982177734375 0.48104554414749146 1018.903564453125 0.48248639702796936 0.83059263 0.33897534012794495 True -14 43050 31.83526301383972 0.5406050682067871 964.11181640625 0.30641424655914307 1013.2008056640625 0.48698389530181885 0.83379126 0.32888907194137573 True -15 45920 31.751545667648315 0.5327718257904053 801.48779296875 0.36105331778526306 1011.6624145507812 0.4874117374420166 0.8379451 0.3235810101032257 True -16 48790 31.771509408950806 0.5422897338867188 693.9523315429688 0.2642922103404999 1010.0853881835938 0.48956918716430664 0.8396947 0.3211267292499542 True -17 51660 31.748321771621704 0.5327599048614502 877.8165893554688 0.291703462600708 1009.4536743164062 0.4893474578857422 0.8425743 0.3216167092323303 True -18 54530 31.764513969421387 0.5581908226013184 788.2457275390625 0.19541123509407043 1009.7156982421875 0.4901830554008484 0.8406966 0.3241240084171295 False -19 57400 31.767727613449097 0.5205228328704834 688.4306030273438 0.20008714497089386 1012.3947143554688 0.4866001307964325 0.8413898 0.3247264623641968 False diff --git a/ENCSR842KCP/cherimoya.fold_2.performance.tsv b/ENCSR842KCP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 63323f3806abf4a8c5c17b3075607cf39b3de0c1..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1009.4536743164062 0.3052583932876587 0.4893474876880646 0.23545730113983154 0.8425742983818054 0.77767014503479 0.3216167092323303 \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_3.evaluate.json b/ENCSR842KCP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 192a19145795b4cad987cb26319ef4314baa5084..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF621QWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_3.fit.json b/ENCSR842KCP/cherimoya.fold_3.fit.json deleted file mode 100644 index 90ef14c8c3616dcdae9472b8ecd7da37ca26575c..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF621QWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_3.log b/ENCSR842KCP/cherimoya.fold_3.log deleted file mode 100644 index f708d8695dbc10f6768c0e7f041b803b6c07af35..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2769 35.31125521659851 4.0058088302612305 851.889892578125 0.6323299407958984 1260.0064697265625 0.3100511133670807 0.71691155 6.607358455657959 True -1 5538 30.558911561965942 0.587780237197876 821.2325439453125 0.6305726766586304 1103.805419921875 0.4078141450881958 0.7640459 1.7969187498092651 True -2 8307 30.685086250305176 0.592637300491333 1097.439453125 0.7995986938476562 1068.9097900390625 0.42876312136650085 0.7801474 0.6916164755821228 True -3 11076 30.612139463424683 1.1605627536773682 755.3623046875 0.28929322957992554 1050.640869140625 0.439583957195282 0.7928065 0.5748340487480164 True -4 13845 30.6642587184906 0.542698860168457 747.0377807617188 0.48901912569999695 1036.9859619140625 0.449704110622406 0.79172343 0.5162109136581421 False -5 16614 30.673574447631836 0.555222749710083 842.73876953125 0.5562855005264282 1028.5238037109375 0.45433369278907776 0.7996096 0.4161880314350128 True -6 19383 30.680440187454224 0.5600812435150146 785.69580078125 0.4984040856361389 1023.001708984375 0.4581579267978668 0.8008432 0.4118393659591675 True -7 22152 30.602532625198364 1.0230021476745605 774.3683471679688 0.4715564250946045 1019.5660400390625 0.46058425307273865 0.80021214 0.42611226439476013 False -8 24921 30.619734048843384 17.237725019454956 832.4251098632812 0.6162903904914856 1014.3233642578125 0.46366822719573975 0.8030218 0.4046230614185333 True -9 27690 30.676154375076294 0.5510382652282715 860.893798828125 0.39328140020370483 1008.7236938476562 0.4679792523384094 0.8103499 0.3838089406490326 True -10 30459 30.627198457717896 0.5370769500732422 873.3538818359375 0.516839861869812 1004.2728881835938 0.4699273407459259 0.8134796 0.38287612795829773 True -11 33228 30.63046169281006 0.5467000007629395 747.80615234375 0.4030013680458069 997.1016235351562 0.4749322831630707 0.8178057 0.3581717908382416 True -12 35997 30.642094373703003 0.6310760974884033 784.136962890625 0.5120701789855957 998.1683959960938 0.47390279173851013 0.8240618 0.3478129506111145 True -13 38766 30.642335176467896 0.5523495674133301 931.4830322265625 0.3934856653213501 991.7991943359375 0.4778991937637329 0.8313298 0.33660757541656494 True -14 41535 30.592598915100098 1.3436720371246338 834.9395751953125 0.3811098337173462 988.4425659179688 0.4794280529022217 0.83734816 0.3213013708591461 True -15 44304 30.693588972091675 2.071193218231201 1041.610107421875 0.6072037220001221 988.3763427734375 0.47866788506507874 0.8432411 0.31510651111602783 True -16 47073 30.654711484909058 0.5545711517333984 647.378173828125 0.3198397159576416 985.6172485351562 0.48049241304397583 0.8442503 0.3131471574306488 True -17 49842 30.67423439025879 0.5509052276611328 723.0234375 0.27668994665145874 987.9483032226562 0.4787677824497223 0.8466739 0.31171512603759766 True -18 52611 30.66762137413025 0.5581648349761963 846.353271484375 0.25346457958221436 987.09765625 0.47948625683784485 0.8475186 0.3132602572441101 True -19 55380 30.719326734542847 0.5519764423370361 813.5650634765625 0.2149415910243988 988.3777465820312 0.47832730412483215 0.8467194 0.3140181005001068 False diff --git a/ENCSR842KCP/cherimoya.fold_3.performance.tsv b/ENCSR842KCP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f20ce108f5c376ae99c6ca1739a16b3e306cb513..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -987.09765625 0.3110966682434082 0.47948625683784485 0.2285201996564865 0.8475186228752136 0.7801476120948792 0.3132602572441101 \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_4.evaluate.json b/ENCSR842KCP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4c6055f34b22035033a93df5427d18ed9c3fc5c9..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF621QWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_4.fit.json b/ENCSR842KCP/cherimoya.fold_4.fit.json deleted file mode 100644 index 5685c9ccf6be272afce6c669df4469bd1d0f311e..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF621QWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842KCP/cherimoya.fold_4.log b/ENCSR842KCP/cherimoya.fold_4.log deleted file mode 100644 index 67f35f5dd2b5b5b655340bbf051c4cc0673eb174..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2836 35.998740911483765 4.084574222564697 1125.19921875 0.42733699083328247 1231.729736328125 0.3047979176044464 0.6958017 7.3997883796691895 True -1 5672 31.387524843215942 0.6169900894165039 792.98681640625 0.5677813291549683 1069.0413818359375 0.4067082107067108 0.7418354 1.530652642250061 True -2 8508 31.442455291748047 0.5867040157318115 925.6279907226562 0.3961818814277649 1036.9815673828125 0.4270803928375244 0.7645947 0.8147504329681396 True -3 11344 31.347840547561646 19.300450563430786 714.441650390625 0.5828289985656738 1026.5018310546875 0.4342562258243561 0.77074665 0.7065649628639221 True -4 14180 31.902324438095093 0.5925562381744385 649.419189453125 0.40131527185440063 1017.749755859375 0.44100821018218994 0.77480394 0.5699293613433838 True -5 17016 31.401243448257446 0.5886223316192627 695.3732299804688 0.49963638186454773 1008.3345336914062 0.4466213881969452 0.7804271 0.4612599313259125 True -6 19852 30.810418844223022 0.5815587043762207 875.7064819335938 0.45154955983161926 1002.6732177734375 0.44987353682518005 0.7812947 0.40708982944488525 True -7 22688 30.745651245117188 0.5780317783355713 861.6904907226562 0.4773634374141693 996.7281494140625 0.45425501465797424 0.7864992 0.40332499146461487 True -8 25524 30.820568561553955 0.580009937286377 757.594482421875 0.6901723146438599 989.4249877929688 0.45943665504455566 0.7898161 0.38768041133880615 True -9 28360 31.19398307800293 0.5821576118469238 959.5421752929688 0.5413777828216553 985.3815307617188 0.46190619468688965 0.7941186 0.3731207251548767 True -10 31196 30.984272241592407 0.5821082592010498 914.939453125 0.34705600142478943 982.1008911132812 0.46381059288978577 0.8001086 0.3654782176017761 True -11 34032 30.920305013656616 0.5710995197296143 1013.6585693359375 0.31639811396598816 978.588134765625 0.46567413210868835 0.80506384 0.35162609815597534 True -12 36868 30.78838086128235 0.5761353969573975 840.3262939453125 0.36164602637290955 972.9569702148438 0.46997034549713135 0.8131563 0.33414238691329956 True -13 39704 30.749181747436523 0.5824205875396729 845.6668090820312 0.40159866213798523 968.0830688476562 0.4738752543926239 0.8204596 0.3265506625175476 True -14 42540 30.725460529327393 0.5858445167541504 614.2020263671875 0.42567044496536255 966.9296264648438 0.47393080592155457 0.8245793 0.3202691972255707 True -15 45376 30.78347682952881 0.5786972045898438 701.2457885742188 0.32367345690727234 965.3203735351562 0.4745219349861145 0.82993937 0.31289517879486084 True -16 48212 30.76793336868286 0.5746595859527588 818.248046875 0.40949082374572754 966.7496948242188 0.4727726876735687 0.8338044 0.3113500773906708 True -17 51048 30.76416277885437 0.559199333190918 820.3330078125 0.3403325080871582 965.00927734375 0.4758366644382477 0.8371066 0.3106538951396942 True -18 53884 30.811339139938354 0.5731005668640137 654.4365234375 0.2545762360095978 963.5117797851562 0.477249413728714 0.8379279 0.3101648986339569 True -19 56720 30.75233483314514 0.5884344577789307 807.4740600585938 0.23045144975185394 965.5717163085938 0.47459089756011963 0.8374985 0.3098202347755432 False diff --git a/ENCSR842KCP/cherimoya.fold_4.performance.tsv b/ENCSR842KCP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c3cc5b89023a9dcbc8dcee6922f5c54dc2f6958c..0000000000000000000000000000000000000000 --- a/ENCSR842KCP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -963.5117797851562 0.31317275762557983 0.4772494435310364 0.2251867651939392 0.8379278779029846 0.7647222280502319 0.3101648986339569 \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_0.evaluate.json b/ENCSR842VTJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7bc57d190db90a04e091fee160a857ccc288b3b2..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF950YQD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_0.fit.json b/ENCSR842VTJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 9f7cdf33aada95e97c4bb9c9133be3ed87526d37..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF950YQD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_0.log b/ENCSR842VTJ/cherimoya.fold_0.log deleted file mode 100644 index 7e9b14727567d2ff32074556b30d9ae34f99e6dc..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1992 26.816927671432495 3.6939494609832764 222.94223022460938 0.8888128995895386 231.64479064941406 0.11669472604990005 0.6473803 4.939115047454834 True -1 3984 22.11084818840027 0.517979621887207 169.30276489257812 0.8382678031921387 221.71653747558594 0.1675562858581543 0.7249031 2.550774574279785 True -2 5976 22.08635425567627 12.511027097702026 183.46572875976562 0.7709676027297974 215.45294189453125 0.19036808609962463 0.757713 1.3075942993164062 True -3 7968 22.115684509277344 0.3979156017303467 220.03515625 0.5385484099388123 213.35659790039062 0.19727765023708344 0.77177036 0.8671735525131226 True -4 9960 22.11451029777527 0.3971548080444336 176.84120178222656 0.625015914440155 212.15170288085938 0.20172758400440216 0.78163564 0.7317896485328674 True -5 11952 22.09576153755188 0.4199364185333252 171.14419555664062 1.0212812423706055 211.36199951171875 0.2046651989221573 0.7883597 0.6537802219390869 True -6 13944 22.229273557662964 0.4046452045440674 221.3578338623047 1.0044875144958496 210.7915496826172 0.207710400223732 0.7906439 0.6049970984458923 True -7 15936 22.18842887878418 0.4142017364501953 181.27471923828125 0.6646860837936401 210.28492736816406 0.20974615216255188 0.7947923 0.5674852132797241 True -8 17928 22.172765254974365 0.4032444953918457 209.19113159179688 0.4637490510940552 209.9927215576172 0.2099057286977768 0.79904926 0.5211970806121826 True -9 19920 22.24792242050171 0.4024689197540283 152.02491760253906 0.639613151550293 208.94740295410156 0.21494591236114502 0.8013674 0.5130782723426819 True -10 21912 22.201655864715576 0.4053075313568115 139.63433837890625 0.6315264105796814 209.0933074951172 0.21398977935314178 0.80475867 0.49449771642684937 True -11 23904 22.193238496780396 0.936528205871582 145.72177124023438 0.6196439862251282 208.9005126953125 0.21533793210983276 0.8101321 0.4709016978740692 True -12 25896 22.232847929000854 0.4033064842224121 194.17056274414062 0.41790032386779785 208.3909454345703 0.21771296858787537 0.8183756 0.44926851987838745 True -13 27888 22.222792387008667 0.40615344047546387 147.12509155273438 0.533146858215332 208.18121337890625 0.21864597499370575 0.8195524 0.43551498651504517 True -14 29880 22.226973056793213 1.560662031173706 126.96743774414062 0.3606538474559784 207.82586669921875 0.21971498429775238 0.82510483 0.4251839220523834 True -15 31872 22.243040323257446 1.40256929397583 177.5044403076172 0.322759747505188 207.4937744140625 0.22157125174999237 0.82975274 0.41890040040016174 True -16 33864 22.218833923339844 0.40012526512145996 192.79147338867188 0.43155860900878906 207.60769653320312 0.22084815800189972 0.8306497 0.42289525270462036 True -17 35856 22.169134378433228 1.1026146411895752 173.39794921875 0.29162800312042236 207.7250213623047 0.2198607176542282 0.8297595 0.43056151270866394 False -18 37848 22.234871864318848 0.40782856941223145 184.66812133789062 0.30944114923477173 208.088623046875 0.21794618666172028 0.8262611 0.43990805745124817 False -19 39840 22.177016019821167 0.4042177200317383 183.93502807617188 0.25121474266052246 208.13009643554688 0.21747873723506927 0.8249013 0.446363627910614 False diff --git a/ENCSR842VTJ/cherimoya.fold_0.performance.tsv b/ENCSR842VTJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a3d669b2e9611895684ca699ba08ba1f98a94187..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -207.60769653320312 0.5454518795013428 0.2208481729030609 0.05623829364776611 0.8306496739387512 0.7743447422981262 0.42289525270462036 \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_1.evaluate.json b/ENCSR842VTJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6aa5ea6a22972a85d40b65ef18a7d942e238c2d5..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF950YQD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_1.fit.json b/ENCSR842VTJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 049ff5aeaceaff2ed376fa485b20088ea65d794e..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF950YQD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_1.log b/ENCSR842VTJ/cherimoya.fold_1.log deleted file mode 100644 index 42fd84c93b819e53cfbc0f6460c2febab8759d2a..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1997 27.115211963653564 3.4008092880249023 163.747314453125 0.7005157470703125 279.1505432128906 0.1264488697052002 0.6256659 5.899796009063721 True -1 3994 22.184821844100952 0.9100713729858398 118.1239013671875 1.1361790895462036 266.29962158203125 0.18473820388317108 0.7392966 2.5026023387908936 True -2 5991 22.249536752700806 0.558025598526001 194.31796264648438 0.5542863607406616 258.3945007324219 0.20924589037895203 0.77685213 1.1591023206710815 True -3 7988 22.172853231430054 0.5583298206329346 170.23056030273438 0.7183302640914917 255.06971740722656 0.21810370683670044 0.79176146 0.7607184052467346 True -4 9985 22.15561294555664 0.6035945415496826 145.59744262695312 0.6685864925384521 254.00904846191406 0.22190184891223907 0.79893255 0.7567543983459473 True -5 11982 22.179312705993652 0.5781090259552002 179.21331787109375 0.6412121057510376 253.53208923339844 0.22299066185951233 0.80695736 0.678666889667511 True -6 13979 22.167649269104004 0.5773830413818359 181.76597595214844 0.8540709018707275 252.41807556152344 0.22743774950504303 0.81134236 0.6428539156913757 True -7 15976 21.930613040924072 0.5789816379547119 161.24795532226562 0.5490461587905884 252.28773498535156 0.22785323858261108 0.8173025 0.6006342768669128 True -8 17973 21.770429134368896 0.5713810920715332 145.11019897460938 0.455089807510376 252.01905822753906 0.22827079892158508 0.8217268 0.5668954253196716 True -9 19970 21.749271392822266 0.5726449489593506 209.42611694335938 0.6887360215187073 251.0018310546875 0.2317306399345398 0.82751256 0.5212875604629517 True -10 21967 21.752407550811768 0.5607180595397949 172.8539276123047 0.5991679430007935 250.49374389648438 0.2331676185131073 0.83303773 0.49540069699287415 True -11 23964 21.732238054275513 0.6313860416412354 148.81124877929688 0.7409372329711914 250.09652709960938 0.2348606288433075 0.8324941 0.4760695695877075 False -12 25961 21.743513584136963 0.5656566619873047 140.31350708007812 0.5698515176773071 249.79449462890625 0.2345704436302185 0.8394766 0.466393381357193 True -13 27958 21.711739540100098 0.5516037940979004 147.75193786621094 0.40154898166656494 249.64952087402344 0.23643836379051208 0.84348184 0.4624703824520111 True -14 29955 21.720547914505005 0.5617296695709229 161.86679077148438 0.7403322458267212 249.72622680664062 0.2355983555316925 0.84649956 0.4482962191104889 True -15 31952 21.72383189201355 0.5754311084747314 149.83660888671875 0.3877890110015869 249.24331665039062 0.2385270744562149 0.8499652 0.4442063868045807 True -16 33949 21.769734621047974 0.558009147644043 144.18955993652344 0.5636278390884399 249.3628387451172 0.23753830790519714 0.8488135 0.44987958669662476 False -17 35946 21.72744393348694 0.5542774200439453 137.43556213378906 0.2591559588909149 248.98446655273438 0.2389288693666458 0.84715384 0.4653054475784302 False -18 37943 21.74152636528015 0.5519776344299316 196.0435333251953 0.3899516463279724 249.37689208984375 0.23710328340530396 0.8444043 0.477772057056427 False -19 39940 21.73378825187683 0.5530283451080322 133.69705200195312 0.4135010838508606 249.486572265625 0.2365889549255371 0.8417605 0.4904392659664154 False diff --git a/ENCSR842VTJ/cherimoya.fold_1.performance.tsv b/ENCSR842VTJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c1fe9f2fde39ea2e8294b98887b7fc0944bd53e3..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -249.24331665039062 0.5254309177398682 0.2385270893573761 0.06786076724529266 0.8499652147293091 0.8160331845283508 0.4442063868045807 \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_2.evaluate.json b/ENCSR842VTJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9d9450c48f02c51854ad2b9f67c489e9a6a638e5..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF950YQD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_2.fit.json b/ENCSR842VTJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 9bb255c226283a4f8d73820e7e38eb2641f23f7d..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF950YQD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_2.log b/ENCSR842VTJ/cherimoya.fold_2.log deleted file mode 100644 index 4124a6dcb865a71a616c0d5f65db6009139d411b..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2131 28.53369688987732 3.339362859725952 201.69192504882812 0.8679489493370056 234.90850830078125 0.1197315901517868 0.61529386 4.581733703613281 True -1 4262 23.69514513015747 0.5028796195983887 209.57949829101562 1.2531561851501465 223.66152954101562 0.17248429358005524 0.72760576 2.02555513381958 True -2 6393 23.689058542251587 0.44689249992370605 174.6410369873047 0.5685261487960815 217.67120361328125 0.19638106226921082 0.7675648 0.9173247814178467 True -3 8524 23.633013248443604 0.43712425231933594 198.52964782714844 0.6072933673858643 215.25743103027344 0.20198504626750946 0.77471197 0.699759840965271 True -4 10655 23.649751901626587 0.4206264019012451 207.70559692382812 0.5506051182746887 214.5989990234375 0.20245413482189178 0.78552157 0.6038811802864075 True -5 12786 23.644388914108276 0.423337459564209 167.00381469726562 0.522422194480896 213.51724243164062 0.20760028064250946 0.7915926 0.5709702372550964 True -6 14917 23.65981888771057 0.42470884323120117 194.16444396972656 0.8464387655258179 212.9864501953125 0.20926621556282043 0.79615766 0.583760678768158 True -7 17048 23.636414051055908 0.41837406158447266 155.21530151367188 0.5657078623771667 212.62734985351562 0.2104668915271759 0.79804677 0.5534215569496155 True -8 19179 23.69099450111389 0.42009687423706055 200.11407470703125 0.5804834365844727 212.0543212890625 0.21306617558002472 0.80255973 0.5335189700126648 True -9 21310 23.671796083450317 0.42751550674438477 174.23326110839844 0.5244830846786499 211.41567993164062 0.21586358547210693 0.8083246 0.5124158263206482 True -10 23441 23.384660482406616 0.4220893383026123 181.99951171875 0.6103320121765137 211.10142517089844 0.21663779020309448 0.8124418 0.48946264386177063 True -11 25572 23.164406538009644 0.4233379364013672 195.97366333007812 0.4786220192909241 210.48573303222656 0.21943818032741547 0.81639117 0.4719902575016022 True -12 27703 23.183599948883057 0.4122350215911865 180.09634399414062 0.34538596868515015 210.3587188720703 0.2192767858505249 0.8191658 0.461398184299469 True -13 29834 23.180914402008057 0.9193158149719238 199.77037048339844 0.48090070486068726 209.90878295898438 0.2221740335226059 0.8257287 0.4502573311328888 True -14 31965 23.272849082946777 1.9272353649139404 135.01010131835938 0.3554595112800598 209.6243896484375 0.22314320504665375 0.8300173 0.4331619143486023 True -15 34096 23.238232851028442 0.6407945156097412 186.46884155273438 0.3823191821575165 209.57542419433594 0.2235572785139084 0.8333941 0.42472609877586365 True -16 36227 23.190210103988647 0.42218494415283203 139.84646606445312 0.2824770212173462 209.34805297851562 0.2248423993587494 0.83477443 0.4262998700141907 True -17 38358 23.19991135597229 0.4134068489074707 147.20819091796875 0.4100673794746399 209.67529296875 0.2229779213666916 0.832128 0.4341469407081604 False -18 40489 23.208957195281982 0.4911067485809326 167.1865997314453 0.471148818731308 209.9627685546875 0.22174879908561707 0.8301537 0.4448237121105194 False -19 42620 23.219291925430298 0.7603607177734375 184.63861083984375 0.48916059732437134 209.8013153076172 0.223209947347641 0.82947516 0.4508723020553589 False diff --git a/ENCSR842VTJ/cherimoya.fold_2.performance.tsv b/ENCSR842VTJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2836503c0c0c569df29babcc4f7dc73c4b510711..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -209.34805297851562 0.5433430075645447 0.22484242916107178 0.057515211403369904 0.8347744345664978 0.7911767363548279 0.4262998700141907 \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_3.evaluate.json b/ENCSR842VTJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6fd3bea91118a625462159b2cac2ace0de1e10a4..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF950YQD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_3.fit.json b/ENCSR842VTJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 6ff6ed36c781d2ec34a565254f69a2b6126332e2..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF950YQD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_3.log b/ENCSR842VTJ/cherimoya.fold_3.log deleted file mode 100644 index 65fe47d98c69fb4fa999ee52dd0889661687a017..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2049 27.105000734329224 3.216017723083496 198.8227996826172 0.5551038980484009 249.39801025390625 0.11649887263774872 0.6182136 5.033746242523193 True -1 4098 22.7707462310791 0.4527721405029297 178.77723693847656 0.7366808652877808 237.96966552734375 0.1744135618209839 0.72131103 2.482360363006592 True -2 6147 22.746086597442627 0.466552734375 153.21905517578125 0.6486198306083679 231.5405731201172 0.1979953795671463 0.74064124 1.3628294467926025 True -3 8196 22.71793222427368 0.45572566986083984 201.14892578125 0.7231342196464539 229.85244750976562 0.20316025614738464 0.7595325 0.9382901191711426 True -4 10245 22.724061489105225 0.4115481376647949 139.156005859375 0.6640305519104004 228.63125610351562 0.2071831226348877 0.77193564 0.838441014289856 True -5 12294 22.764628171920776 0.4202280044555664 223.65774536132812 1.1159323453903198 228.51280212402344 0.206708163022995 0.7784499 0.7927542924880981 True -6 14343 22.720106601715088 0.41783595085144043 156.1761474609375 0.6693153977394104 228.17234802246094 0.20856228470802307 0.78346467 0.787532389163971 True -7 16392 22.714091777801514 0.4184441566467285 180.00453186035156 0.3523353338241577 227.85337829589844 0.21026913821697235 0.7819428 0.7620447278022766 False -8 18441 22.727253198623657 0.4205334186553955 189.52374267578125 0.5502100586891174 227.47872924804688 0.2113514244556427 0.7885602 0.6894012093544006 True -9 20490 22.748087406158447 0.41542625427246094 251.82382202148438 0.4371960759162903 226.9321746826172 0.21380774676799774 0.79419065 0.6751664280891418 True -10 22539 22.70691180229187 0.4160597324371338 148.8058319091797 0.5062915086746216 226.3304901123047 0.2158610075712204 0.7998856 0.6377410888671875 True -11 24588 22.71988606452942 1.0133159160614014 142.2422637939453 0.5251585245132446 226.32635498046875 0.2162369042634964 0.8010835 0.5986543297767639 True -12 26637 22.743281602859497 0.4258401393890381 201.51223754882812 0.4537769556045532 226.04537963867188 0.2170795053243637 0.80801094 0.5597760081291199 True -13 28686 22.70935082435608 0.4218454360961914 174.45797729492188 0.4684297740459442 225.367431640625 0.22075936198234558 0.8139797 0.5388811230659485 True -14 30735 22.804308891296387 15.600376605987549 146.89724731445312 0.33375638723373413 225.28677368164062 0.21982696652412415 0.81836164 0.510762095451355 True -15 32784 22.750751972198486 0.4243166446685791 183.12374877929688 0.4859590530395508 224.70965576171875 0.22253042459487915 0.8219634 0.49626269936561584 True -16 34833 22.65739941596985 0.41922903060913086 142.69534301757812 0.4829881191253662 225.25111389160156 0.21961577236652374 0.82623345 0.48176437616348267 True -17 36882 22.274564027786255 0.41847920417785645 182.31582641601562 0.35976651310920715 225.10687255859375 0.22031962871551514 0.8247352 0.48519980907440186 False -18 38931 22.26434898376465 0.41525983810424805 156.5751953125 0.21417436003684998 225.45103454589844 0.21866272389888763 0.8238798 0.4965651333332062 False -19 40980 22.32535743713379 0.4166724681854248 151.06666564941406 0.4630025625228882 225.76791381835938 0.21685606241226196 0.8203665 0.5045530200004578 False diff --git a/ENCSR842VTJ/cherimoya.fold_3.performance.tsv b/ENCSR842VTJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 379d51635e0bad06f76aaa032f900564e339c5c1..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -225.25111389160156 0.5400130748748779 0.21961578726768494 0.06094609573483467 0.826233446598053 0.7813127636909485 0.48176437616348267 \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_4.evaluate.json b/ENCSR842VTJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f47c25a7c8732ac1efd9bfe408b8396e7ea9fb7d..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF950YQD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_4.fit.json b/ENCSR842VTJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 75212a80dee804e8be7010e33bab2b42b8b418ed..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF950YQD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR842VTJ/cherimoya.fold_4.log b/ENCSR842VTJ/cherimoya.fold_4.log deleted file mode 100644 index 842de090d26aaad7e6c75ebfd4c1947ec09b9c49..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2073 27.695975065231323 3.6429388523101807 183.39218139648438 0.585553765296936 224.043701171875 0.11458371579647064 0.63320243 4.143888473510742 True -1 4146 23.08626937866211 0.684412956237793 187.31631469726562 1.2729318141937256 214.138671875 0.16937430202960968 0.7253634 1.9604920148849487 True -2 6219 23.015029191970825 0.39200425148010254 176.7158203125 0.8981369137763977 208.67733764648438 0.18747805058956146 0.74968165 1.0688402652740479 True -3 8292 22.977985858917236 0.38597917556762695 157.3093719482422 0.6173245906829834 206.79925537109375 0.19381533563137054 0.7660654 0.6487263441085815 True -4 10365 22.9706130027771 9.560587406158447 153.72203063964844 0.5287290811538696 205.8722381591797 0.19714321196079254 0.7731838 0.5952867269515991 True -5 12438 23.04498052597046 0.39428138732910156 191.2837371826172 0.814978837966919 205.24029541015625 0.20005172491073608 0.7768066 0.5810387134552002 True -6 14511 23.053791284561157 0.3974320888519287 159.5612030029297 0.7695604562759399 204.712158203125 0.202398419380188 0.7811311 0.582422137260437 True -7 16584 23.002016305923462 0.39382481575012207 157.50717163085938 0.5461549758911133 204.51736450195312 0.20357376337051392 0.7870849 0.5558364391326904 True -8 18657 23.000572443008423 0.39270544052124023 188.9993438720703 0.452147513628006 203.95989990234375 0.20548398792743683 0.792999 0.528287410736084 True -9 20730 23.026672840118408 0.3923606872558594 247.01126098632812 0.5698950290679932 203.46420288085938 0.2074824422597885 0.7975986 0.4981168210506439 True -10 22803 23.118682384490967 0.957148551940918 186.79042053222656 0.4569014608860016 203.3348388671875 0.20737023651599884 0.80036724 0.4838438630104065 True -11 24876 23.125519037246704 0.39972376823425293 162.53204345703125 0.6751805543899536 203.07749938964844 0.20880942046642303 0.8017323 0.476360559463501 True -12 26949 23.162482976913452 0.39049434661865234 153.39222717285156 0.6275835037231445 202.74761962890625 0.21106496453285217 0.8071981 0.4615533947944641 True -13 29022 23.1237576007843 0.3908722400665283 175.1592559814453 0.45432114601135254 202.01388549804688 0.21376916766166687 0.8138017 0.44185858964920044 True -14 31095 23.094024896621704 0.4039909839630127 127.16822814941406 0.3885538578033447 202.0731201171875 0.21293757855892181 0.81746197 0.4315851032733917 True -15 33168 23.114888906478882 0.40320682525634766 163.9566650390625 0.570392906665802 202.15513610839844 0.21316498517990112 0.8191222 0.43044495582580566 True -16 35241 23.12473964691162 0.9089462757110596 160.9287872314453 0.227339968085289 201.9576416015625 0.21389928460121155 0.8193983 0.4318743944168091 True -17 37314 23.11305594444275 18.20057249069214 189.78550720214844 0.3826533257961273 202.25718688964844 0.21248051524162292 0.81749946 0.44618597626686096 False -18 39387 23.31693458557129 0.39373278617858887 128.0516357421875 0.3615107834339142 202.45887756347656 0.21190455555915833 0.8134585 0.4565107524394989 False -19 41460 24.91230320930481 14.733730554580688 140.61524963378906 0.31507766246795654 202.41514587402344 0.21274608373641968 0.8114871 0.46344900131225586 False diff --git a/ENCSR842VTJ/cherimoya.fold_4.performance.tsv b/ENCSR842VTJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fe52d1592fee78c53eeb92879f1bcdfe71f68fbf..0000000000000000000000000000000000000000 --- a/ENCSR842VTJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.9576416015625 0.5497229695320129 0.21389928460121155 0.05382969230413437 0.8193982839584351 0.7633136510848999 0.4318743944168091 \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_0.evaluate.json b/ENCSR845CFB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 32ad14e7a8308d14d28fd942283565657fdec83a..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903ARJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_0.fit.json b/ENCSR845CFB/cherimoya.fold_0.fit.json deleted file mode 100644 index 980d2c82546fd8654d23f9e6d5c06bc69e3d0902..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF903ARJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_0.log b/ENCSR845CFB/cherimoya.fold_0.log deleted file mode 100644 index fb987bc4b280233064a91d63d6788613f0d4c5f7..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 33.848326444625854 3.527472972869873 2272.28857421875 0.9550204277038574 3255.90185546875 0.2691999077796936 0.47194663 17.789691925048828 True -1 5478 30.275859832763672 0.584080696105957 1685.340087890625 0.7716023921966553 2513.31884765625 0.43771040439605713 0.5197602 9.146838188171387 True -2 8217 30.278564453125 9.372254848480225 1963.1063232421875 1.0861269235610962 2446.79345703125 0.44168975949287415 0.5693929 4.408392429351807 True -3 10956 30.327540397644043 1.046910285949707 2204.443359375 0.866878867149353 2298.25634765625 0.4643605649471283 0.6025486 2.889679431915283 True -4 13695 30.440077304840088 1.438607931137085 1949.799560546875 1.571835994720459 2233.99462890625 0.47652098536491394 0.6144241 2.558053731918335 True -5 16434 30.47320055961609 0.5734171867370605 1561.5931396484375 1.347984790802002 2197.9072265625 0.48235753178596497 0.62562704 2.558320999145508 True -6 19173 30.386611461639404 0.5706984996795654 2144.408203125 0.9542266726493835 2178.443603515625 0.4863269627094269 0.63374126 2.16257905960083 True -7 21912 30.322856903076172 0.5686473846435547 1723.07763671875 0.7928896546363831 2150.62841796875 0.49539560079574585 0.6498718 1.8514388799667358 True -8 24651 30.307604551315308 0.5726327896118164 1437.464599609375 1.258545160293579 2116.5634765625 0.5044066309928894 0.6530581 1.629610538482666 True -9 27390 30.324810028076172 0.5652933120727539 1053.69091796875 0.6187808513641357 2107.412353515625 0.5058192014694214 0.656269 1.524378776550293 True -10 30129 30.344480991363525 0.5598552227020264 1753.17822265625 0.8107728362083435 2075.630615234375 0.5143095254898071 0.6586983 1.3721706867218018 True -11 32868 30.35580325126648 0.5613241195678711 1523.47412109375 1.3153879642486572 2056.899658203125 0.5183582305908203 0.66770834 1.2979331016540527 True -12 35607 30.343016386032104 0.5642263889312744 1833.210205078125 0.7889107465744019 2034.5340576171875 0.5239441394805908 0.67043555 1.1489096879959106 True -13 38346 30.352535009384155 0.5613338947296143 1669.7069091796875 0.775172233581543 2019.300537109375 0.5231910347938538 0.68332064 1.0392786264419556 True -14 41085 30.371061086654663 0.9960002899169922 1816.8221435546875 0.9871699810028076 1995.689208984375 0.5289632678031921 0.69224226 0.9387469291687012 True -15 43824 30.402501821517944 0.6144251823425293 1359.006591796875 0.8075392842292786 1978.762939453125 0.5319867730140686 0.7040875 0.8619160056114197 True -16 46563 30.43264603614807 0.5813355445861816 1398.947265625 0.6428754329681396 1965.6416015625 0.5332633852958679 0.71059144 0.7903956770896912 True -17 49302 30.365784645080566 0.5676136016845703 1784.5633544921875 0.44967877864837646 1953.3502197265625 0.5362598896026611 0.71662706 0.7520559430122375 True -18 52041 30.41754674911499 0.5799036026000977 1513.0487060546875 0.5501308441162109 1958.076904296875 0.5354832410812378 0.7182177 0.740759015083313 True -19 54780 30.479961395263672 0.5716497898101807 1415.568115234375 0.6958695650100708 1958.620849609375 0.5347621440887451 0.720074 0.7372598052024841 True diff --git a/ENCSR845CFB/cherimoya.fold_0.performance.tsv b/ENCSR845CFB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 01b01c720a236f50e386245be7eca6f5a8d374a5..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1958.620849609375 0.2516738474369049 0.5347621440887451 0.3102482259273529 0.7200739979743958 0.6394317150115967 0.7372598052024841 \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_1.evaluate.json b/ENCSR845CFB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2f6ae24dd974d7194ca6fafce3c0b3d65713c077..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903ARJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_1.fit.json b/ENCSR845CFB/cherimoya.fold_1.fit.json deleted file mode 100644 index 74d6146fa4461e16437f96b52472b816b86b9ba8..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF903ARJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_1.log b/ENCSR845CFB/cherimoya.fold_1.log deleted file mode 100644 index ae7fbb8d592484c2b46e6373c099ce2a283f06a2..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.25235724449158 3.8380815982818604 2220.736572265625 1.2451398372650146 3906.931884765625 0.28040817379951477 0.48454309 16.48306655883789 True -1 5484 30.418529748916626 0.7890875339508057 1730.287109375 1.4284793138504028 3148.73095703125 0.4333440065383911 0.49872768 11.933978080749512 True -2 8226 30.42502522468567 0.7721385955810547 2144.2548828125 1.522162675857544 3014.33349609375 0.44548624753952026 0.5754941 5.6715826988220215 True -3 10968 30.362383127212524 0.7883129119873047 1665.409912109375 0.583280086517334 2804.011962890625 0.46499988436698914 0.6128712 4.110505104064941 True -4 13710 30.325481176376343 12.396464109420776 2100.51708984375 1.2880271673202515 2706.08740234375 0.4797816276550293 0.6309345 3.007035255432129 True -5 16452 30.355168342590332 0.7749247550964355 1322.336181640625 1.2315168380737305 2650.302001953125 0.48746612668037415 0.6500685 2.9816055297851562 True -6 19194 30.333118438720703 0.7906701564788818 1635.7841796875 1.0218939781188965 2575.8916015625 0.4979695677757263 0.6663793 2.6745431423187256 True -7 21936 30.358193159103394 0.7936222553253174 1691.22412109375 0.9623091220855713 2527.705078125 0.5051445364952087 0.68055475 2.173938274383545 True -8 24678 30.37665581703186 0.7884483337402344 1481.0648193359375 0.716669499874115 2500.3994140625 0.5113773345947266 0.6920981 1.890285849571228 True -9 27420 30.344244718551636 2.0462846755981445 2161.89453125 1.035469889640808 2464.998046875 0.5191895365715027 0.696405 1.7005351781845093 True -10 30162 30.412996530532837 1.448718786239624 1489.844482421875 0.8017013669013977 2439.885498046875 0.5233873128890991 0.7029596 1.555617094039917 True -11 32904 30.41941523551941 0.8183739185333252 1764.233154296875 1.011951208114624 2427.12255859375 0.5244547724723816 0.70687455 1.401253581047058 True -12 35646 30.478626251220703 2.008699417114258 1686.5841064453125 0.9721015095710754 2391.8916015625 0.5326467156410217 0.71237624 1.3376710414886475 True -13 38388 30.411043643951416 0.8193249702453613 1880.7001953125 0.7927751541137695 2369.463623046875 0.5336118340492249 0.72347564 1.1304360628128052 True -14 41130 30.391273498535156 0.8028287887573242 1537.920654296875 0.9249259233474731 2335.574951171875 0.540367841720581 0.7310754 1.018673300743103 True -15 43872 30.41076397895813 0.808180570602417 1576.20068359375 0.6826503276824951 2323.3564453125 0.5393046140670776 0.74241686 0.9104330539703369 True -16 46614 30.402408361434937 0.7969770431518555 1449.21728515625 0.6732398271560669 2300.653076171875 0.5430928468704224 0.75152373 0.8134819865226746 True -17 49356 30.36602759361267 0.8006243705749512 1443.9222412109375 0.5143565535545349 2298.109619140625 0.5431050658226013 0.7564698 0.7681517601013184 True -18 52098 30.480714082717896 0.8112280368804932 2027.852294921875 0.9913842082023621 2291.50830078125 0.5449300408363342 0.7587869 0.7490857243537903 True -19 54840 30.561690092086792 1.2311820983886719 1508.6656494140625 0.40124988555908203 2300.772216796875 0.5427344441413879 0.7586089 0.7466891407966614 False diff --git a/ENCSR845CFB/cherimoya.fold_1.performance.tsv b/ENCSR845CFB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f382b06a604b5a2262db044eeb7fddc7e20825fe..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2291.50830078125 0.24119214713573456 0.544930100440979 0.333629310131073 0.7587869167327881 0.6938027739524841 0.7490857243537903 \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_2.evaluate.json b/ENCSR845CFB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ee68d35deabbebd7e247ef2a95c0ff5f55956b19..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903ARJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_2.fit.json b/ENCSR845CFB/cherimoya.fold_2.fit.json deleted file mode 100644 index 1b41b43cd944a32e6402ea62d88eb333b46d4c40..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF903ARJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_2.log b/ENCSR845CFB/cherimoya.fold_2.log deleted file mode 100644 index 51141e73980a126b9493a5c8d649ae9ba99b3230..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2905 36.2539279460907 3.5535812377929688 2528.069580078125 1.3882149457931519 3450.30126953125 0.2739514708518982 0.46465105 13.842925071716309 True -1 5810 32.43241763114929 0.6155567169189453 2455.19677734375 1.21251380443573 2688.39306640625 0.4320344626903534 0.49491465 8.317632675170898 True -2 8715 32.38658690452576 0.5988774299621582 1956.20947265625 1.152957558631897 2655.571533203125 0.43553897738456726 0.5312747 5.103763580322266 True -3 11620 32.41343069076538 0.5975494384765625 2175.044677734375 1.2391061782836914 2481.996337890625 0.4599425494670868 0.5902099 3.322871208190918 True -4 14525 32.41090989112854 0.5895843505859375 1737.8232421875 1.0356836318969727 2402.491943359375 0.47494855523109436 0.6052388 2.771562337875366 True -5 17430 32.4444899559021 0.5907337665557861 2095.18212890625 0.9855154156684875 2338.478759765625 0.4866650700569153 0.6182666 2.5874533653259277 True -6 20335 34.73288321495056 8.489249467849731 1962.839111328125 1.1375172138214111 2322.740234375 0.4899444282054901 0.63081026 2.120035409927368 True -7 23240 32.4507851600647 0.5884873867034912 1597.355224609375 0.9693937301635742 2287.28662109375 0.49946972727775574 0.6390024 1.9071470499038696 True -8 26145 32.46922039985657 0.5914993286132812 2037.8743896484375 1.300081491470337 2257.4833984375 0.5029692053794861 0.6519044 1.8222273588180542 True -9 29050 32.45222282409668 0.5873794555664062 2213.303466796875 0.9409369230270386 2242.98388671875 0.5082433819770813 0.657028 1.6981120109558105 True -10 31955 32.43664288520813 0.5925521850585938 1839.04736328125 0.8562142252922058 2222.910888671875 0.5099650025367737 0.6680717 1.6306774616241455 True -11 34860 32.45015549659729 0.5919883251190186 1549.015380859375 1.3618788719177246 2174.73681640625 0.5206677317619324 0.67320216 1.6179561614990234 True -12 37765 32.537792682647705 0.595099687576294 2006.0721435546875 1.1248935461044312 2156.837646484375 0.5234360098838806 0.6817577 1.4719963073730469 True -13 40670 32.46554374694824 0.5863304138183594 2072.627197265625 1.0939218997955322 2133.447265625 0.527732789516449 0.68951005 1.3052605390548706 True -14 43575 32.67882061004639 2.557049512863159 1664.400146484375 0.5524687767028809 2104.540283203125 0.5312777161598206 0.69786286 1.1228231191635132 True -15 46480 32.46208047866821 0.593742847442627 1555.4075927734375 0.8842525482177734 2085.550048828125 0.5328839421272278 0.7101271 0.9588286876678467 True -16 49385 32.513670682907104 0.7892904281616211 1774.279541015625 0.6811363101005554 2080.35986328125 0.533842146396637 0.7180919 0.8572472929954529 True -17 52290 32.46649622917175 0.860137939453125 1461.75244140625 0.6372411251068115 2063.441162109375 0.5383081436157227 0.72187483 0.8083347678184509 True -18 55195 32.42409014701843 0.5802619457244873 1745.035400390625 0.8150732517242432 2070.863525390625 0.5356495976448059 0.72186524 0.7850750684738159 False -19 58100 32.517624855041504 0.87152099609375 1611.0277099609375 0.8570144176483154 2073.107666015625 0.5347474217414856 0.7247279 0.77757328748703 True diff --git a/ENCSR845CFB/cherimoya.fold_2.performance.tsv b/ENCSR845CFB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bc3d310bc4c1d858929382a360524ad51a39f115..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2073.107666015625 0.24877841770648956 0.5347474217414856 0.3179636597633362 0.7247279286384583 0.647941529750824 0.77757328748703 \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_3.evaluate.json b/ENCSR845CFB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 85dfaeee9abd4c4986462790b4465f24bb348571..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903ARJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_3.fit.json b/ENCSR845CFB/cherimoya.fold_3.fit.json deleted file mode 100644 index a45b3c7d0ab7aa27b15f2cdbb3e4105c355231e5..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF903ARJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_3.log b/ENCSR845CFB/cherimoya.fold_3.log deleted file mode 100644 index 08a9d10b65349d731247c0d564cc20d6fa84c326..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2829 35.240660667419434 3.5802319049835205 2248.436279296875 1.0065386295318604 3537.409423828125 0.27433082461357117 0.4824933 17.016305923461914 True -1 5658 31.378658294677734 0.6129083633422852 2508.357421875 1.2360169887542725 2847.6474609375 0.42622455954551697 0.5051121 10.573991775512695 True -2 8487 31.37389612197876 1.3383972644805908 1953.6748046875 0.8362929224967957 2763.8486328125 0.43483588099479675 0.55841094 6.829073905944824 True -3 11316 31.51313352584839 0.6134753227233887 1894.86767578125 1.3561866283416748 2592.510009765625 0.4567939341068268 0.59088814 4.020694255828857 True -4 14145 31.34114694595337 0.5946118831634521 1947.9605712890625 0.7485641837120056 2542.06640625 0.4671984910964966 0.6039585 3.294508218765259 True -5 16974 31.301087141036987 0.5854530334472656 1843.962646484375 1.0165414810180664 2484.51953125 0.4779103994369507 0.6118753 2.829742431640625 True -6 19803 31.288899183273315 0.6067206859588623 1722.38134765625 0.9601637125015259 2453.140625 0.48374465107917786 0.62243587 2.609610080718994 True -7 22632 31.33047318458557 0.6108736991882324 1508.9234619140625 1.1418051719665527 2425.641357421875 0.4904019236564636 0.63352036 2.3527307510375977 True -8 25461 31.377314567565918 0.6017346382141113 1505.87744140625 0.9696133136749268 2398.75634765625 0.4959835410118103 0.6345553 2.1530284881591797 True -9 28290 31.31194281578064 0.5852305889129639 2088.60546875 1.4428786039352417 2368.755615234375 0.5027926564216614 0.6380269 1.7906206846237183 True -10 31119 31.33598303794861 8.342133045196533 2187.0810546875 0.8684113025665283 2349.0419921875 0.5088869333267212 0.6416177 1.5703315734863281 True -11 33948 31.386051177978516 0.6037096977233887 1959.5732421875 1.086124300956726 2330.4326171875 0.5126773118972778 0.6421585 1.4382972717285156 True -12 36777 31.3659770488739 0.5944535732269287 1454.9954833984375 0.8613841533660889 2300.854736328125 0.5173003077507019 0.6482055 1.360081434249878 True -13 39606 31.32727599143982 1.4917538166046143 1802.5250244140625 0.8873991966247559 2276.889892578125 0.5225739479064941 0.6588513 1.2436339855194092 True -14 42435 31.358808040618896 0.594735860824585 1859.2513427734375 0.8780266642570496 2255.20849609375 0.5268459320068359 0.673967 1.118488073348999 True -15 45264 31.393062114715576 0.5990893840789795 1425.8038330078125 0.8527635931968689 2249.227783203125 0.5254594683647156 0.69027036 1.0195326805114746 True -16 48093 31.457069396972656 0.9812695980072021 1233.394775390625 0.9247794151306152 2230.081787109375 0.5298271179199219 0.70488036 0.922474205493927 True -17 50922 31.383853673934937 0.598783016204834 1135.274658203125 0.506911039352417 2228.561767578125 0.527187705039978 0.7145535 0.8645305633544922 True -18 53751 31.38333535194397 0.5942733287811279 1602.35400390625 0.6019006371498108 2229.01416015625 0.5277289152145386 0.7192036 0.8442496657371521 True -19 56580 31.363832235336304 0.6273205280303955 1667.489990234375 0.6795210242271423 2231.583251953125 0.5275325775146484 0.7194952 0.8409894704818726 True diff --git a/ENCSR845CFB/cherimoya.fold_3.performance.tsv b/ENCSR845CFB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ab2a67c095fad5a57369f83325c0eff4ddbe3419..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2231.583251953125 0.25000178813934326 0.5275325775146484 0.31498807668685913 0.7194951772689819 0.6481601595878601 0.8409894704818726 \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_4.evaluate.json b/ENCSR845CFB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9fb571551e4f96348571e671b5d5d66602ec7d68..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF903ARJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_4.fit.json b/ENCSR845CFB/cherimoya.fold_4.fit.json deleted file mode 100644 index a88c9235f18c907d98d0c45e4b5859f5aa114e2e..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF903ARJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR845CFB/cherimoya.fold_4.log b/ENCSR845CFB/cherimoya.fold_4.log deleted file mode 100644 index 79625cd43a5c58c41bcbed8274f673a423ecb20f..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2860 35.50906157493591 3.4347825050354004 2410.91650390625 1.428410530090332 3193.351318359375 0.2702546715736389 0.47488856 13.543037414550781 True -1 5720 31.671473264694214 0.5473189353942871 1789.14111328125 0.7664830684661865 2468.69775390625 0.439461886882782 0.50970286 7.9481682777404785 True -2 8580 31.649515390396118 0.525390625 1901.110107421875 1.2688474655151367 2448.83203125 0.44619494676589966 0.5510501 5.400755405426025 True -3 11440 31.674596309661865 0.5316431522369385 1725.03076171875 0.7420708537101746 2305.475830078125 0.4638453722000122 0.5893602 3.7968733310699463 True -4 14300 31.600608825683594 0.5324211120605469 1771.6268310546875 1.186700701713562 2254.0439453125 0.4717820882797241 0.60336787 3.1234779357910156 True -5 17160 31.639972686767578 0.5278351306915283 1904.0155029296875 0.9695224761962891 2177.14501953125 0.4850994944572449 0.62095004 2.52896785736084 True -6 20020 31.616347789764404 0.5368719100952148 1682.226318359375 0.9241703152656555 2142.245361328125 0.49007993936538696 0.6311983 2.0523922443389893 True -7 22880 31.651451587677002 1.4239072799682617 1515.4356689453125 0.6541762351989746 2116.836181640625 0.49508869647979736 0.63743347 1.949084758758545 True -8 25740 31.64624571800232 0.5405254364013672 1415.7265625 1.1559737920761108 2093.074951171875 0.5025983452796936 0.6416348 1.7961583137512207 True -9 28600 31.670743227005005 0.5387051105499268 1815.620361328125 1.1168986558914185 2088.318115234375 0.5047013163566589 0.64299583 1.6735326051712036 True -10 31460 31.937920808792114 17.803913116455078 1410.8260498046875 0.7926757335662842 2062.069091796875 0.5095109343528748 0.64551574 1.425866723060608 True -11 34320 31.78429675102234 0.5926129817962646 1941.759521484375 0.9666058421134949 2033.930908203125 0.5151182413101196 0.65773976 1.2591818571090698 True -12 37180 31.714525938034058 0.5371003150939941 1738.53564453125 0.651564359664917 2016.80322265625 0.5188614130020142 0.6659251 1.166043758392334 True -13 40040 31.81214928627014 0.5466430187225342 1998.1177978515625 0.8153551816940308 1995.9896240234375 0.5228222608566284 0.67841834 1.0325324535369873 True -14 42900 31.817832946777344 0.537799596786499 1507.81494140625 0.8873683214187622 1970.3385009765625 0.5276917815208435 0.6906689 0.9301897883415222 True -15 45760 31.913485527038574 0.5376193523406982 1609.275390625 0.8394081592559814 1964.2117919921875 0.5275856852531433 0.70208895 0.8410307168960571 True -16 48620 31.808807373046875 0.539196252822876 1545.43994140625 0.5619614124298096 1947.1219482421875 0.5298773646354675 0.7112331 0.7790910601615906 True -17 51480 31.813670873641968 0.537757396697998 1425.764404296875 0.7202642560005188 1941.967529296875 0.5318623781204224 0.7185584 0.7520080208778381 True -18 54340 31.781352519989014 0.5345895290374756 1678.273193359375 0.793111264705658 1945.5225830078125 0.5302658081054688 0.7203974 0.7418150901794434 True -19 57200 31.813777446746826 0.5352592468261719 1631.750244140625 0.6831555962562561 1951.0986328125 0.5282336473464966 0.72030973 0.7365735769271851 False diff --git a/ENCSR845CFB/cherimoya.fold_4.performance.tsv b/ENCSR845CFB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2edf763adbbcf191f83b4648fbc369791767e4c3..0000000000000000000000000000000000000000 --- a/ENCSR845CFB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1945.5225830078125 0.25430622696876526 0.5302658677101135 0.30441123247146606 0.720397412776947 0.6395435333251953 0.7418150901794434 \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_0.evaluate.json b/ENCSR846VGZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 005a0e835a0dadaa362ff4d5bfe2bb92dacd6093..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF636ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_0.fit.json b/ENCSR846VGZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 6d471d79d2fdfb1ed384650d1408c030525afdf3..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF636ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_0.log b/ENCSR846VGZ/cherimoya.fold_0.log deleted file mode 100644 index 265a724d6efddf7592c182fc7c262f5da5ec68f9..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 35.48055982589722 3.632016897201538 474.00958251953125 0.23189467191696167 543.2520751953125 0.2869267463684082 0.8208618 3.414508104324341 True -1 5520 30.49438500404358 0.5774376392364502 420.580810546875 0.24385397136211395 517.93994140625 0.32935193181037903 0.85196364 0.502480685710907 True -2 8280 30.445003271102905 0.5743942260742188 438.38134765625 0.16648411750793457 511.34375 0.3384339213371277 0.87065816 0.23558788001537323 True -3 11040 30.49205446243286 0.5737166404724121 487.2854309082031 0.18493272364139557 507.8299560546875 0.343161404132843 0.8793525 0.22772443294525146 True -4 13800 30.401161432266235 0.5667135715484619 552.0843505859375 0.24305661022663116 507.6304016113281 0.3440410792827606 0.8755926 0.18333199620246887 False -5 16560 30.468300819396973 0.574913740158081 453.24932861328125 0.10538893938064575 505.0758056640625 0.34741947054862976 0.88718575 0.1711975634098053 True -6 19320 33.9360625743866 31.517201900482178 476.0275573730469 0.16961611807346344 504.1957702636719 0.3490579426288605 0.8925177 0.16471967101097107 True -7 22080 30.48101496696472 0.5793929100036621 501.069091796875 0.12267764657735825 502.74884033203125 0.3516925871372223 0.8966243 0.16081732511520386 True -8 24840 30.53977680206299 0.5732734203338623 451.1933898925781 0.09542854875326157 501.4407043457031 0.35410982370376587 0.9020394 0.13973575830459595 True -9 27600 30.50614023208618 0.57999587059021 461.234619140625 0.14667712152004242 500.9374694824219 0.3545842170715332 0.9051667 0.12955451011657715 True -10 30360 30.44716477394104 0.5731136798858643 441.3958740234375 0.12184923887252808 500.3537902832031 0.35535672307014465 0.90950036 0.11969932913780212 True -11 33120 30.467788696289062 0.5784001350402832 386.075927734375 0.143203467130661 499.6885986328125 0.3564261496067047 0.9117408 0.11735549569129944 True -12 35880 30.523107767105103 0.5705177783966064 397.17474365234375 0.11009436845779419 499.0202941894531 0.35683801770210266 0.9140433 0.11239594966173172 True -13 38640 30.554577350616455 1.023090124130249 404.393798828125 0.11251688748598099 498.13409423828125 0.35957393050193787 0.9180098 0.10487734526395798 True -14 41400 31.702303886413574 13.872679233551025 454.282958984375 0.15495052933692932 497.8608093261719 0.3596052825450897 0.9199881 0.10014338791370392 True -15 44160 30.523990154266357 0.579561710357666 461.42572021484375 0.10705244541168213 497.29583740234375 0.3602319061756134 0.9207065 0.09466324001550674 True -16 46920 30.564170837402344 0.5824582576751709 432.5596008300781 0.058900028467178345 496.93646240234375 0.36082226037979126 0.9220378 0.09189634025096893 True -17 49680 30.577213764190674 0.5721912384033203 423.61932373046875 0.11275564134120941 497.3940734863281 0.3596288859844208 0.92356026 0.09120546281337738 True -18 52440 30.521372079849243 11.717607736587524 468.0731201171875 0.08807576447725296 497.87109375 0.35902172327041626 0.92260164 0.09079483896493912 False -19 55200 30.496489763259888 0.5737495422363281 516.389404296875 0.10657714307308197 497.9812316894531 0.3586895167827606 0.92309725 0.09111630916595459 False diff --git a/ENCSR846VGZ/cherimoya.fold_0.performance.tsv b/ENCSR846VGZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 092e917b7d2509746bee7921208458af0260b078..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -497.3940734863281 0.4067223072052002 0.3596288859844208 0.13663995265960693 0.9235602617263794 0.9133948683738708 0.09120546281337738 \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_1.evaluate.json b/ENCSR846VGZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b33ac72624545f82ed4fb5ce7968f73dfda48a59..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF636ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_1.fit.json b/ENCSR846VGZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 949ef02a564e80274931a1b241c475655ba4b348..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF636ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_1.log b/ENCSR846VGZ/cherimoya.fold_1.log deleted file mode 100644 index a6601b45e9b40d56cc46d3131b51c35bbbb4e497..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2752 35.16253614425659 3.926624059677124 496.56097412109375 0.14867345988750458 624.6148681640625 0.2886938750743866 0.8108126 3.409872055053711 True -1 5504 30.465908527374268 7.190546035766602 412.2426452636719 0.1809861660003662 591.2528686523438 0.34017735719680786 0.846868 0.7495700120925903 True -2 8256 30.426453828811646 12.03387188911438 451.9068603515625 0.305162638425827 583.7546997070312 0.34972989559173584 0.8607867 0.31765085458755493 True -3 11008 30.56826615333557 0.6417150497436523 443.17449951171875 0.12281545996665955 578.3516235351562 0.3562534749507904 0.8738305 0.31494900584220886 True -4 13760 30.37447214126587 0.6385746002197266 401.3879699707031 0.2378648817539215 575.8540649414062 0.3597894608974457 0.8772527 0.21478994190692902 True -5 16512 30.400835275650024 0.6351022720336914 439.7320251464844 0.12062137573957443 574.6502075195312 0.36176663637161255 0.8816664 0.21288719773292542 True -6 19264 30.36107110977173 0.6238937377929688 486.7066345214844 0.10802783817052841 573.3408203125 0.3630058169364929 0.8843863 0.21028991043567657 True -7 22016 30.389917612075806 0.6313416957855225 416.62738037109375 0.14423131942749023 571.0081176757812 0.36683425307273865 0.8920099 0.18894648551940918 True -8 24768 30.33708095550537 0.6340830326080322 400.27667236328125 0.10816781967878342 569.2383422851562 0.36871588230133057 0.89859253 0.1687641441822052 True -9 27520 30.33541750907898 0.642632246017456 440.4322204589844 0.16143232583999634 567.326904296875 0.3721436858177185 0.90245754 0.15566378831863403 True -10 30272 30.34685492515564 0.6305036544799805 464.9930419921875 0.08759517967700958 567.0897216796875 0.37142181396484375 0.9062841 0.14436930418014526 True -11 33024 30.387923002243042 0.6446182727813721 454.1307373046875 0.08669985830783844 565.872802734375 0.37331727147102356 0.9103973 0.1350110024213791 True -12 35776 30.417600393295288 0.6296467781066895 414.93109130859375 0.16039595007896423 564.1163330078125 0.37648457288742065 0.9154054 0.12552256882190704 True -13 38528 30.362677812576294 0.6277596950531006 457.98651123046875 0.1957145631313324 563.406982421875 0.3772493004798889 0.9166211 0.11983233690261841 True -14 41280 30.32746720314026 0.6309130191802979 461.026611328125 0.09086553752422333 562.892333984375 0.37770357728004456 0.91914487 0.11359460651874542 True -15 44032 30.443206071853638 0.6293106079101562 459.8409423828125 0.15831035375595093 561.8017578125 0.37918901443481445 0.9221479 0.10902444273233414 True -16 46784 30.397709369659424 0.755408763885498 393.784912109375 0.11159105598926544 562.210693359375 0.37848493456840515 0.9238719 0.10491225123405457 True -17 49536 30.45108699798584 1.700430154800415 492.02471923828125 0.04626931995153427 561.7564697265625 0.3785950541496277 0.9254353 0.10305389761924744 True -18 52288 30.456233263015747 0.6306407451629639 426.81268310546875 0.0761377215385437 561.9310302734375 0.3786858916282654 0.9259595 0.1026730164885521 True -19 55040 30.429561138153076 1.144242763519287 449.94805908203125 0.06990088522434235 562.0664672851562 0.3787173926830292 0.92688537 0.10306195914745331 True diff --git a/ENCSR846VGZ/cherimoya.fold_1.performance.tsv b/ENCSR846VGZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cedbc03e820f5592546a4728fa02e8ef1dfab62c..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -562.0664672851562 0.3896048665046692 0.37871742248535156 0.15394867956638336 0.9268853664398193 0.9273581504821777 0.10306195914745331 \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_2.evaluate.json b/ENCSR846VGZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d891802e63db7ca991b6289580eb4e77b2f36b4c..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF636ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_2.fit.json b/ENCSR846VGZ/cherimoya.fold_2.fit.json deleted file mode 100644 index eeb124cae886da605b64e87e994e0178591accff..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF636ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_2.log b/ENCSR846VGZ/cherimoya.fold_2.log deleted file mode 100644 index 71e099caf2e0198f2215021f66d846ff354301c3..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 36.194263219833374 3.494335889816284 438.5826416015625 0.23134081065654755 564.7557983398438 0.2897351086139679 0.8136987 2.885648727416992 True -1 5756 32.119067907333374 0.5765891075134277 515.45654296875 0.1668703407049179 537.7054443359375 0.33242982625961304 0.85243505 0.5716356039047241 True -2 8634 31.787152528762817 3.0717413425445557 469.292236328125 0.11453143507242203 531.5232543945312 0.3404378592967987 0.86413306 0.23686093091964722 True -3 11512 31.843377351760864 0.5619795322418213 450.70269775390625 0.2331567108631134 527.2113037109375 0.3464195728302002 0.87430006 0.1719641238451004 True -4 14390 31.795308828353882 0.6727046966552734 386.4444885253906 0.11329860240221024 525.694580078125 0.34904950857162476 0.87717384 0.16754981875419617 True -5 17268 31.81492567062378 2.222928762435913 417.79791259765625 0.1748393028974533 525.5219116210938 0.3476516902446747 0.8787088 0.16322308778762817 True -6 20146 31.858038425445557 0.5851318836212158 440.7539978027344 0.1912916749715805 523.7568359375 0.35104477405548096 0.88624626 0.15660390257835388 True -7 23024 31.780197620391846 0.5614428520202637 523.394775390625 0.17058686912059784 523.8012084960938 0.35090211033821106 0.88185436 0.16815507411956787 False -8 25902 31.77914547920227 1.5490758419036865 419.4798889160156 0.1404438316822052 522.2968139648438 0.35264822840690613 0.8925039 0.14455954730510712 True -9 28780 35.516704082489014 25.922358512878418 418.9220275878906 0.18687979876995087 520.2540283203125 0.3566945195198059 0.897601 0.13730567693710327 True -10 31658 31.777777433395386 0.5673627853393555 518.2264404296875 0.09775280952453613 519.3750610351562 0.3581729233264923 0.90040714 0.13320668041706085 True -11 34536 31.825355291366577 1.686345100402832 489.7842102050781 0.14187870919704437 518.900634765625 0.35890111327171326 0.90195465 0.1255941092967987 True -12 37414 31.765761613845825 0.56007981300354 422.6824951171875 0.14389392733573914 518.1377563476562 0.3593992590904236 0.9072571 0.11792904138565063 True -13 40292 31.840631246566772 0.5638458728790283 440.1551208496094 0.09030874818563461 517.3408203125 0.36112168431282043 0.90889245 0.11560619622468948 True -14 43170 31.887683868408203 0.5614228248596191 460.31854248046875 0.11044982075691223 516.750244140625 0.36263471841812134 0.90841943 0.11323174834251404 False -15 46048 31.855679273605347 0.5667283535003662 413.21624755859375 0.09910795092582703 516.8887329101562 0.3611319065093994 0.9091914 0.11002697050571442 True -16 48926 31.832427263259888 0.5618691444396973 427.6083984375 0.03807920217514038 516.9055786132812 0.3611774742603302 0.9126539 0.10784487426280975 True -17 51804 31.90309715270996 0.5669472217559814 411.39154052734375 0.07454921305179596 516.5389404296875 0.3618639409542084 0.91338027 0.10676592588424683 True -18 54682 31.936229944229126 0.5665431022644043 383.99072265625 0.09524711221456528 516.8002319335938 0.36169129610061646 0.912805 0.10678417980670929 False -19 57560 31.788196086883545 28.204575777053833 451.1681823730469 0.0740581601858139 516.5632934570312 0.36263588070869446 0.9128443 0.10722720623016357 False diff --git a/ENCSR846VGZ/cherimoya.fold_2.performance.tsv b/ENCSR846VGZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a908d6436f33e3b760abd80014cb660be17ad0e4..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -516.5389404296875 0.4037732779979706 0.36186397075653076 0.14287778735160828 0.9133802652359009 0.9068763256072998 0.10676592588424683 \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_3.evaluate.json b/ENCSR846VGZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8d5e3efcba94096de97d028a636fca6988fcd0d3..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF636ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_3.fit.json b/ENCSR846VGZ/cherimoya.fold_3.fit.json deleted file mode 100644 index c9b1ddfd62d4d05504f0deaaa06e7c9bf2f7aa51..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF636ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_3.log b/ENCSR846VGZ/cherimoya.fold_3.log deleted file mode 100644 index c592ae2349cbd59275116eb02743aea807d83e1e..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 34.83430051803589 4.425090074539185 465.97027587890625 0.13401268422603607 523.2942504882812 0.2898959517478943 0.7989764 3.6008458137512207 True -1 5472 30.222986698150635 1.0400917530059814 460.5564270019531 0.18635250627994537 497.4205017089844 0.33319225907325745 0.8401448 0.5602861642837524 True -2 8208 30.28902816772461 12.663123369216919 424.22857666015625 0.11217694729566574 491.40325927734375 0.3416502773761749 0.8655648 0.2182823270559311 True -3 10944 30.194089651107788 2.149667263031006 455.59393310546875 0.14762096107006073 489.68414306640625 0.3449908494949341 0.87352914 0.24095100164413452 True -4 13680 30.171663284301758 0.681401252746582 397.77459716796875 0.11680034548044205 489.1036071777344 0.34707263112068176 0.86991775 0.18984141945838928 False -5 16416 30.175830602645874 0.562030553817749 444.05169677734375 0.15352290868759155 487.3804931640625 0.34926289319992065 0.8803676 0.16951945424079895 True -6 19152 30.288933753967285 0.5668866634368896 423.02069091796875 0.31792670488357544 486.5025939941406 0.3510660231113434 0.88403 0.16204962134361267 True -7 21888 30.235864400863647 0.5714490413665771 419.2633361816406 0.16878902912139893 485.6052551269531 0.35272350907325745 0.88688374 0.15902091562747955 True -8 24624 30.21900224685669 0.562157392501831 453.9398498535156 0.21202902495861053 484.6728820800781 0.3540904223918915 0.89186466 0.15823155641555786 True -9 27360 30.180585145950317 0.5708324909210205 429.7642822265625 0.09431523084640503 483.7921142578125 0.35600942373275757 0.89669555 0.1475898027420044 True -10 30096 30.145491361618042 0.5643877983093262 341.28228759765625 0.11788326501846313 483.5779113769531 0.3557635247707367 0.9009642 0.14319013059139252 True -11 32832 30.276586771011353 0.5720634460449219 436.0506591796875 0.20626571774482727 482.15826416015625 0.35866838693618774 0.90275246 0.13639868795871735 True -12 35568 30.20643639564514 0.573065996170044 496.83416748046875 0.11757199466228485 481.6915588378906 0.3584238886833191 0.9044979 0.1291305273771286 True -13 38304 30.3030264377594 0.5874552726745605 462.2407531738281 0.179688960313797 480.88037109375 0.3603943884372711 0.9103655 0.11707283556461334 True -14 41040 30.250632524490356 0.5769236087799072 523.9058837890625 0.13101595640182495 480.5627746582031 0.3603784441947937 0.91240066 0.11211717128753662 True -15 43776 30.335566520690918 0.5686843395233154 518.9077758789062 0.07743194699287415 479.8871765136719 0.36109688878059387 0.91502446 0.1065199002623558 True -16 46512 30.28600835800171 1.7257864475250244 448.5887451171875 0.11722434312105179 479.6930236816406 0.36139217019081116 0.91642195 0.10325309634208679 True -17 49248 31.818063497543335 18.251506567001343 484.3443603515625 0.11425840109586716 479.4997863769531 0.36232006549835205 0.916823 0.10219444334506989 True -18 51984 30.42389154434204 0.5733215808868408 448.974853515625 0.07156674563884735 479.7342529296875 0.36172717809677124 0.914911 0.10189896821975708 False -19 54720 30.345433473587036 0.5918624401092529 393.9554443359375 0.08453559875488281 479.5132141113281 0.3622742295265198 0.91710925 0.10235350579023361 True diff --git a/ENCSR846VGZ/cherimoya.fold_3.performance.tsv b/ENCSR846VGZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 22949fbe69f14f7b807238678fa64e148b6f690b..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -479.5132141113281 0.40827521681785583 0.3622742295265198 0.1360258162021637 0.9171092510223389 0.9040243029594421 0.10235350579023361 \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_4.evaluate.json b/ENCSR846VGZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3ccc8b14f878420679571334e87ce5f77d7c063d..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF636ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_4.fit.json b/ENCSR846VGZ/cherimoya.fold_4.fit.json deleted file mode 100644 index abf0e22175121bfbcaece61f15329b5347c8820c..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF636ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VGZ/cherimoya.fold_4.log b/ENCSR846VGZ/cherimoya.fold_4.log deleted file mode 100644 index e269ff953d0b6f40ec41e2a1f31afc0260056ac3..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2786 35.61931109428406 3.646087408065796 474.85430908203125 0.1502733677625656 516.5684814453125 0.2863674759864807 0.8201243 2.876833200454712 True -1 5572 30.8320095539093 0.6246926784515381 472.63800048828125 0.1490103006362915 492.77703857421875 0.3286473751068115 0.84828794 0.5002588629722595 True -2 8358 30.800758361816406 0.6164355278015137 449.6397705078125 0.23323743045330048 487.89227294921875 0.33597713708877563 0.8633613 0.22379170358181 True -3 11144 30.77026891708374 34.15252661705017 398.63720703125 0.14675423502922058 484.76702880859375 0.34026506543159485 0.8735239 0.1821397840976715 True -4 13930 31.05925989151001 0.6171801090240479 551.43408203125 0.1716010719537735 483.9165954589844 0.34084439277648926 0.88013273 0.15409982204437256 True -5 16716 30.746702909469604 0.6167757511138916 446.3067626953125 0.1040356457233429 483.6636962890625 0.34079548716545105 0.8811674 0.13929392397403717 True -6 19502 30.82794737815857 0.6060965061187744 424.728759765625 0.10811807215213776 482.06781005859375 0.34387925267219543 0.88948876 0.13351823389530182 True -7 22288 30.866572856903076 0.6469099521636963 465.65869140625 0.14393891394138336 480.4786071777344 0.34734535217285156 0.89537716 0.1276388168334961 True -8 25074 30.9257972240448 1.7254834175109863 453.4412841796875 0.17602825164794922 479.22686767578125 0.3494950532913208 0.8990782 0.11964356154203415 True -9 27860 30.962368965148926 0.6087205410003662 423.4842224121094 0.11105114221572876 479.0746765136719 0.34898102283477783 0.9048721 0.11331389844417572 True -10 30646 30.837489366531372 0.6206610202789307 447.85150146484375 0.11476962268352509 478.3050842285156 0.350149929523468 0.90847707 0.10344207286834717 True -11 33432 30.810500383377075 0.6092135906219482 446.81500244140625 0.10894957929849625 477.50732421875 0.3514960706233978 0.91286147 0.09819977730512619 True -12 36218 30.84351134300232 0.6092884540557861 460.52996826171875 0.11290767788887024 476.3584289550781 0.3545472323894501 0.9137716 0.09816046059131622 True -13 39004 30.851255416870117 0.6131927967071533 435.03460693359375 0.18108637630939484 476.10589599609375 0.35438522696495056 0.9169253 0.09361162036657333 True -14 41790 31.33225965499878 40.268301010131836 476.0389709472656 0.07394349575042725 475.7431335449219 0.354576051235199 0.9177868 0.09104558825492859 True -15 44576 30.77182102203369 41.84907531738281 435.13629150390625 0.1138094961643219 475.3291931152344 0.35502541065216064 0.9214677 0.08771690726280212 True -16 47362 31.38409185409546 0.6302335262298584 446.79345703125 0.13854536414146423 475.8465881347656 0.3543769121170044 0.9216001 0.0851370170712471 True -17 50148 30.867983102798462 0.6041824817657471 445.5703125 0.05212317407131195 475.1499328613281 0.3557201623916626 0.9240749 0.08393019437789917 True -18 52934 30.88437008857727 0.6400580406188965 452.90960693359375 0.08587902784347534 475.0347900390625 0.35592231154441833 0.9223538 0.0843234434723854 False -19 55720 30.86224865913391 0.6210696697235107 467.02301025390625 0.05389109626412392 475.2709655761719 0.3557797968387604 0.9220486 0.08455910533666611 False diff --git a/ENCSR846VGZ/cherimoya.fold_4.performance.tsv b/ENCSR846VGZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7110de62cf0e16a97a86af37c5541ea9c0434526..0000000000000000000000000000000000000000 --- a/ENCSR846VGZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -475.1499328613281 0.4118749499320984 0.3557201623916626 0.1347126066684723 0.9240748882293701 0.9129474759101868 0.08393019437789917 \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_0.evaluate.json b/ENCSR846VPV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6e1281bd33ccec60fe5aa5bca0065575cc91b22e..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723FWR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_0.fit.json b/ENCSR846VPV/cherimoya.fold_0.fit.json deleted file mode 100644 index 2f14a3018f5fb228ac4f960c1f2624a72570277f..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF723FWR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_0.log b/ENCSR846VPV/cherimoya.fold_0.log deleted file mode 100644 index 9536a6e31ae052f01eb8c98908c13351101dfd54..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2132 28.792027711868286 3.6369998455047607 292.12841796875 1.328834056854248 345.66656494140625 0.42419204115867615 0.7201166 6.933658123016357 True -1 4264 23.668671131134033 0.7489421367645264 232.32992553710938 0.7765182256698608 301.3714904785156 0.5093818306922913 0.75088197 2.0799427032470703 True -2 6396 23.65422511100769 0.43349623680114746 216.52020263671875 0.8816955089569092 289.6319885253906 0.5401802659034729 0.75784224 0.6894209980964661 True -3 8528 23.66553521156311 0.4698522090911865 239.69883728027344 0.9119863510131836 286.1502990722656 0.5482320785522461 0.76533014 0.5129755139350891 True -4 10660 23.67110824584961 10.097556591033936 241.54083251953125 1.0204107761383057 284.40081787109375 0.5533494353294373 0.76736575 0.4633157253265381 True -5 12792 23.685495376586914 0.43093109130859375 186.26809692382812 0.8196975588798523 283.716796875 0.5556641221046448 0.76993805 0.478214293718338 True -6 14924 23.748482704162598 0.4239969253540039 212.96743774414062 0.706924557685852 283.0110168457031 0.5577251315116882 0.7720136 0.47359809279441833 True -7 17056 23.68371081352234 0.4317021369934082 220.00711059570312 0.928328275680542 282.10125732421875 0.5604769587516785 0.7686113 0.4996333718299866 False -8 19188 23.66183376312256 0.43207740783691406 226.22491455078125 0.5155940651893616 281.45947265625 0.5623607039451599 0.77045053 0.4943070113658905 False -9 21320 23.662010669708252 0.43375229835510254 175.13363647460938 1.2401049137115479 280.90008544921875 0.5640844106674194 0.77305174 0.4990410804748535 True -10 23452 23.67554998397827 0.4323711395263672 221.65966796875 1.0862886905670166 280.1734924316406 0.566226601600647 0.7756492 0.48496612906455994 True -11 25584 23.393330812454224 0.4545023441314697 227.62582397460938 0.54525226354599 279.4792175292969 0.5680313110351562 0.7773637 0.4757946729660034 True -12 27716 23.153300046920776 0.4277369976043701 236.4134521484375 0.6634944081306458 278.7153015136719 0.5697860717773438 0.78147125 0.4626573920249939 True -13 29848 23.165172576904297 0.43607401847839355 209.17498779296875 0.5180567502975464 278.0751647949219 0.5713987350463867 0.7877096 0.4334101974964142 True -14 31980 23.206620931625366 0.4189462661743164 209.43917846679688 0.44424545764923096 277.7107849121094 0.572435200214386 0.79101294 0.44003230333328247 True -15 34112 23.202256679534912 0.42771172523498535 184.89476013183594 0.3877573609352112 277.4674987792969 0.573221743106842 0.79246527 0.4330877363681793 True -16 36244 23.478264331817627 6.4835662841796875 197.92941284179688 0.33071547746658325 277.5120544433594 0.5731370449066162 0.79630417 0.4253791570663452 True -17 38376 23.199976682662964 0.6063926219940186 195.15228271484375 0.4322230815887451 277.6956787109375 0.5726714134216309 0.7939856 0.43752166628837585 False -18 40508 23.4419002532959 0.4280674457550049 212.58279418945312 0.4661438465118408 277.8285827636719 0.5720263719558716 0.7930889 0.4465712308883667 False -19 42640 23.187055826187134 1.1194040775299072 232.37664794921875 0.4616550803184509 278.05731201171875 0.5716362595558167 0.7906399 0.4504457116127014 False diff --git a/ENCSR846VPV/cherimoya.fold_0.performance.tsv b/ENCSR846VPV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b583d8b558ae56f2989d3e50fc0c3297e31aee42..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -277.5120544433594 0.34426096081733704 0.573137104511261 0.18550488352775574 0.7963041663169861 0.7295768857002258 0.4253791570663452 \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_1.evaluate.json b/ENCSR846VPV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 57ebf6d429a859bf3e54286ef695043ade3fd78e..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723FWR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_1.fit.json b/ENCSR846VPV/cherimoya.fold_1.fit.json deleted file mode 100644 index 114485379855803e9febaec31705b6372c954e1e..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF723FWR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_1.log b/ENCSR846VPV/cherimoya.fold_1.log deleted file mode 100644 index 3f322a9075e58a5db4cdcac4aa90f3587979d538..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2121 28.115472316741943 2.9906227588653564 237.8101043701172 0.8071537017822266 393.0740661621094 0.4421343505382538 0.6980073 8.797770500183105 True -1 4242 23.535523176193237 0.7584514617919922 240.57513427734375 0.81048184633255 340.60186767578125 0.5323030352592468 0.7521395 2.2270774841308594 True -2 6363 23.595027208328247 0.7977185249328613 244.0531463623047 0.6957258582115173 327.227783203125 0.5640466809272766 0.76628333 0.7098785042762756 True -3 8484 23.56578540802002 0.5348453521728516 231.6948699951172 0.6965651512145996 321.8673095703125 0.5746995210647583 0.77468115 0.5375658869743347 True -4 10605 23.55106019973755 0.5121219158172607 204.55230712890625 0.4140268564224243 320.0715026855469 0.5780624151229858 0.78194624 0.5203742384910583 True -5 12726 23.639358043670654 0.5142431259155273 255.58200073242188 0.46625179052352905 318.9197692871094 0.5808957815170288 0.7841648 0.4647809863090515 True -6 14847 23.556899070739746 0.5168185234069824 228.68336486816406 0.4027937650680542 317.7604675292969 0.583491861820221 0.78839874 0.4391458034515381 True -7 16968 23.547887325286865 0.5072243213653564 211.09353637695312 0.7260168790817261 316.7328796386719 0.585444450378418 0.7897021 0.4454211890697479 True -8 19089 23.526655673980713 0.5170266628265381 235.99343872070312 0.7986017465591431 315.9697265625 0.587563157081604 0.79588157 0.4409157931804657 True -9 21210 23.599507093429565 0.5300414562225342 214.24993896484375 0.9442796111106873 314.91717529296875 0.5900672674179077 0.79973817 0.4187367856502533 True -10 23331 23.58581018447876 0.532426118850708 235.71197509765625 0.4736672639846802 314.01953125 0.5919902920722961 0.8024806 0.42063283920288086 True -11 25452 23.55215334892273 0.622471809387207 255.00355529785156 0.6217787265777588 313.3632507324219 0.5939320921897888 0.80285704 0.4262194335460663 True -12 27573 23.624452829360962 0.5145914554595947 227.40020751953125 0.5342129468917847 312.474853515625 0.5958818197250366 0.809933 0.4117455780506134 True -13 29694 23.561423540115356 0.5219614505767822 225.2301483154297 0.6364317536354065 311.7814636230469 0.5973197817802429 0.8142025 0.40764033794403076 True -14 31815 23.56696581840515 0.5090329647064209 209.04660034179688 0.46721094846725464 311.26068115234375 0.5984916090965271 0.8164721 0.40772661566734314 True -15 33936 23.53018069267273 1.2222425937652588 208.9893798828125 0.5073457956314087 310.9360046386719 0.599409818649292 0.81759346 0.4109753370285034 True -16 36057 23.153271913528442 0.5105288028717041 216.11871337890625 0.4598497748374939 310.90380859375 0.5994963645935059 0.81867796 0.40764060616493225 True -17 38178 23.082374572753906 0.513063907623291 197.32183837890625 0.36434444785118103 311.0953063964844 0.5990608930587769 0.81927353 0.41663116216659546 True -18 40299 23.041320085525513 0.5222005844116211 213.08084106445312 0.7483710050582886 311.2223815917969 0.5985522270202637 0.81611276 0.4289371967315674 False -19 42420 23.041419506072998 0.6740531921386719 238.6013946533203 0.25776606798171997 311.3712463378906 0.5982115268707275 0.8150475 0.4344143569469452 False diff --git a/ENCSR846VPV/cherimoya.fold_1.performance.tsv b/ENCSR846VPV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 947e36a42b5ff0c520bc545339b2c1348f002cca..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -311.0953063964844 0.32417866587638855 0.5990608930587769 0.20909248292446136 0.8192735314369202 0.7909284234046936 0.41663116216659546 \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_2.evaluate.json b/ENCSR846VPV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5d6820e15b0daa73dd1b6b94b67ffcd741cca160..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723FWR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_2.fit.json b/ENCSR846VPV/cherimoya.fold_2.fit.json deleted file mode 100644 index 646ac42992fab2785c7938ebf7441be3d2ad3a6b..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF723FWR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_2.log b/ENCSR846VPV/cherimoya.fold_2.log deleted file mode 100644 index ebe488a0365a975f8a3bb7dcac386731a06c5716..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2255 29.884514093399048 3.377185821533203 221.90341186523438 0.7976106405258179 357.8418884277344 0.43499958515167236 0.6983111 6.390110492706299 True -1 4510 24.96928119659424 0.45992136001586914 208.52511596679688 0.9367234706878662 310.794677734375 0.527775764465332 0.7533611 1.7808642387390137 True -2 6765 25.086766242980957 0.4755065441131592 204.2266845703125 0.9303659200668335 301.091064453125 0.5519934296607971 0.7580463 0.7705971002578735 True -3 9020 25.03884720802307 0.429607629776001 258.25274658203125 0.7096733450889587 297.11212158203125 0.5601781606674194 0.75916046 0.5389244556427002 True -4 11275 24.994548320770264 0.41512560844421387 233.31834411621094 0.6912415623664856 295.4588928222656 0.5638044476509094 0.7624443 0.49960654973983765 True -5 13530 24.944112539291382 0.8501455783843994 240.48890686035156 1.1445338726043701 294.44415283203125 0.5663288235664368 0.76333094 0.47479715943336487 True -6 15785 25.010027408599854 0.418074369430542 280.73974609375 0.824630856513977 293.6953430175781 0.5680630803108215 0.7647153 0.4754982888698578 True -7 18040 25.00221276283264 0.44537997245788574 205.66256713867188 0.6449341177940369 292.8355407714844 0.5705111026763916 0.7669896 0.4620654582977295 True -8 20295 24.977837562561035 2.4679510593414307 221.9608154296875 0.6021527051925659 291.769287109375 0.5730919241905212 0.7717709 0.452438622713089 True -9 22550 25.03337788581848 1.0531888008117676 203.8180694580078 0.5928874015808105 291.0643005371094 0.575016975402832 0.7768522 0.4410618543624878 True -10 24805 25.039271593093872 0.42275166511535645 191.5806121826172 0.4535548985004425 290.2572937011719 0.5772114396095276 0.7793267 0.43981075286865234 True -11 27060 25.419695615768433 0.42038917541503906 179.31663513183594 0.8308327198028564 289.6541442871094 0.5789119601249695 0.78032184 0.43995481729507446 True -12 29315 25.035012245178223 0.42453622817993164 228.51942443847656 0.8870935440063477 289.0224609375 0.580767810344696 0.782624 0.4338147044181824 True -13 31570 25.033336877822876 0.42876720428466797 208.5289764404297 1.028731107711792 288.4505920410156 0.581932008266449 0.78433496 0.44318127632141113 True -14 33825 25.11945128440857 0.4226644039154053 206.24342346191406 0.40328264236450195 288.0267333984375 0.5831806659698486 0.7901082 0.43041861057281494 True -15 36080 25.0958890914917 0.43336033821105957 207.91848754882812 0.4685785472393036 287.7078857421875 0.5840039253234863 0.79018277 0.435398668050766 True -16 38335 25.039081573486328 0.4234273433685303 221.20989990234375 0.459431529045105 287.64324951171875 0.5841574668884277 0.7906257 0.4519518315792084 True -17 40590 25.133833646774292 9.98673939704895 220.3292999267578 0.32281753420829773 287.8656005859375 0.58353590965271 0.78829193 0.4690503180027008 False -18 42845 25.144160509109497 0.4512448310852051 207.93128967285156 0.7490568161010742 288.0699157714844 0.5830402374267578 0.78779113 0.4790366590023041 False -19 45100 25.1189444065094 0.43300414085388184 166.07574462890625 0.4420388340950012 288.2069091796875 0.5825613141059875 0.7845238 0.4901917278766632 False diff --git a/ENCSR846VPV/cherimoya.fold_2.performance.tsv b/ENCSR846VPV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4dd5d0be65f39bed6419beae0939a4df026a60ed..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -287.64324951171875 0.33647239208221436 0.5841574668884277 0.19332875311374664 0.7906256914138794 0.7331520915031433 0.4519518315792084 \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_3.evaluate.json b/ENCSR846VPV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3d37f9b838b3bb8e20dbf97ef4e9b9b933bfc74d..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723FWR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_3.fit.json b/ENCSR846VPV/cherimoya.fold_3.fit.json deleted file mode 100644 index e626006464a36123345dcf305e0dd8ff2e660bb5..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF723FWR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_3.log b/ENCSR846VPV/cherimoya.fold_3.log deleted file mode 100644 index f5e37843713f5f94a6e45c31bb2a943e043ff446..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2181 28.766743421554565 3.5362794399261475 206.75830078125 1.1620575189590454 348.2427978515625 0.4298878014087677 0.7214016 8.259570121765137 True -1 4362 24.198643684387207 0.6208107471466064 242.14889526367188 0.8902626037597656 303.7085876464844 0.5158984065055847 0.7589304 2.0074470043182373 True -2 6543 24.065620183944702 0.5107839107513428 256.98834228515625 1.2483140230178833 292.6473388671875 0.5448399186134338 0.7730357 0.6534664034843445 True -3 8724 23.719619512557983 0.41863083839416504 230.85226440429688 0.9022704362869263 289.78692626953125 0.551701009273529 0.78259665 0.47150394320487976 True -4 10905 23.724323749542236 0.4235990047454834 212.1013641357422 0.8331652879714966 288.2921447753906 0.5556483268737793 0.78247553 0.4439142942428589 False -5 13086 23.664493560791016 0.4397411346435547 236.42970275878906 0.7303353548049927 287.17706298828125 0.5582600235939026 0.782235 0.451786071062088 False -6 15267 23.669776678085327 0.4217400550842285 194.46624755859375 0.6391259431838989 286.5952453613281 0.5599997639656067 0.78282523 0.4647686183452606 True -7 17448 23.670401334762573 0.5749931335449219 208.26803588867188 0.5942981243133545 285.6029968261719 0.562469482421875 0.7814558 0.4564516544342041 False -8 19629 23.649999380111694 0.4360847473144531 191.2155303955078 0.7538802623748779 284.7157897949219 0.5644898414611816 0.781862 0.46058282256126404 False -9 21810 23.69661021232605 9.326536893844604 219.03086853027344 0.5011724233627319 284.0928955078125 0.5665063261985779 0.78642505 0.45386001467704773 True -10 23991 23.725303173065186 0.4312300682067871 186.31358337402344 0.7329537272453308 283.3670349121094 0.5683096051216125 0.78776884 0.43714219331741333 True -11 26172 23.70108985900879 0.4199075698852539 226.36392211914062 0.4608363211154938 282.5511779785156 0.5705823302268982 0.792676 0.4249799847602844 True -12 28353 24.08725357055664 0.4283897876739502 223.9736785888672 0.47329825162887573 281.9546203613281 0.5721673965454102 0.7919037 0.43547001481056213 False -13 30534 23.647722721099854 0.41962599754333496 241.50521850585938 0.5021657943725586 281.2928466796875 0.5739142298698425 0.7966523 0.424344927072525 True -14 32715 23.65442943572998 0.4194815158843994 230.2324981689453 0.7070745825767517 280.8079528808594 0.5751416683197021 0.8006072 0.42741239070892334 True -15 34896 23.65837073326111 0.4245297908782959 269.0685119628906 0.42634519934654236 280.6415100097656 0.5757878422737122 0.8006928 0.4261682331562042 True -16 37077 23.76610827445984 0.43938279151916504 203.19497680664062 0.5308253169059753 280.65362548828125 0.5757654905319214 0.7980353 0.43631425499916077 False -17 39258 23.816694498062134 0.43469810485839844 222.71142578125 0.44157928228378296 280.78173828125 0.5753597617149353 0.79698986 0.4454532861709595 False -18 41439 23.78956627845764 0.4244213104248047 252.00570678710938 0.33146005868911743 280.9693603515625 0.5748941898345947 0.79806924 0.45034876465797424 False -19 43620 23.727320671081543 0.43076586723327637 207.85617065429688 0.4690284729003906 281.03118896484375 0.5745629668235779 0.79397416 0.4591434597969055 False diff --git a/ENCSR846VPV/cherimoya.fold_3.performance.tsv b/ENCSR846VPV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b2a2de2a781e0bdb844203859afa97941d086597..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -280.6415100097656 0.34221357107162476 0.5757877826690674 0.18466782569885254 0.8006927967071533 0.7371487617492676 0.4261682331562042 \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_4.evaluate.json b/ENCSR846VPV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6575e152d90d4abe272fe350abd6dc2bf5509ad5..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF723FWR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_4.fit.json b/ENCSR846VPV/cherimoya.fold_4.fit.json deleted file mode 100644 index 9dc82db4acaa058b99322126a84bcb20b3fb040d..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF723FWR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846VPV/cherimoya.fold_4.log b/ENCSR846VPV/cherimoya.fold_4.log deleted file mode 100644 index efbe84445039910c517dc5783e99542ca94db9bd..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2214 29.032582998275757 3.9052634239196777 206.30990600585938 0.5950284004211426 335.65008544921875 0.4297125041484833 0.7028671 6.870789527893066 True -1 4428 24.588967323303223 0.7407088279724121 190.12100219726562 1.1141763925552368 296.229736328125 0.5162620544433594 0.73159707 1.98409104347229 True -2 6642 24.61608862876892 0.4803285598754883 236.9150848388672 0.7455499172210693 286.2372131347656 0.5426552295684814 0.7367474 0.690443217754364 True -3 8856 24.32933473587036 0.4370460510253906 228.27703857421875 0.8831248879432678 282.95843505859375 0.5493829846382141 0.7480905 0.4933212697505951 True -4 11070 24.046870231628418 0.4340665340423584 203.31658935546875 0.7229968309402466 281.35064697265625 0.5534083247184753 0.75282925 0.47017326951026917 True -5 13284 23.98075532913208 0.42479634284973145 247.52923583984375 1.0542652606964111 280.9374084472656 0.5549677610397339 0.7537192 0.4656516909599304 True -6 15498 23.99969244003296 0.4327812194824219 196.41378784179688 0.9040771722793579 280.1124267578125 0.5574955344200134 0.75357157 0.4773769974708557 False -7 17712 24.030872106552124 0.43154120445251465 235.23812866210938 0.5946114659309387 279.3046569824219 0.559669554233551 0.75553375 0.47038891911506653 True -8 19926 24.030580282211304 0.42889904975891113 256.5924072265625 0.8568625450134277 278.79510498046875 0.5614250898361206 0.75671506 0.46823886036872864 True -9 22140 24.024142503738403 0.42557215690612793 210.23362731933594 0.7749597430229187 278.2813415527344 0.5631809234619141 0.76058793 0.46476420760154724 True -10 24354 24.02284049987793 0.4281785488128662 210.18630981445312 0.8046144247055054 277.62982177734375 0.5646272301673889 0.76391846 0.46626877784729004 True -11 26568 24.03381109237671 0.433135986328125 191.2578125 0.5678700804710388 277.07086181640625 0.566543459892273 0.76464313 0.44593051075935364 True -12 28782 24.07551121711731 0.4282350540161133 253.07870483398438 0.6295061111450195 276.2944641113281 0.5687234401702881 0.76956445 0.4469015598297119 True -13 30996 24.12021493911743 0.4276614189147949 244.58187866210938 0.7383665442466736 275.7955322265625 0.5698879957199097 0.77436 0.44554275274276733 True -14 33210 24.08744215965271 0.4437887668609619 239.01113891601562 0.5985925793647766 275.5329284667969 0.5709230899810791 0.7763401 0.4349899888038635 True -15 35424 24.154812335968018 0.4337880611419678 232.0858154296875 0.3745672106742859 275.1402282714844 0.5717214941978455 0.7782906 0.43182244896888733 True -16 37638 24.039425134658813 0.42636561393737793 194.0934295654297 0.5661240220069885 275.20361328125 0.5720041990280151 0.7808083 0.4356597363948822 True -17 39852 24.072479009628296 0.42562437057495117 203.2161102294922 0.5394446849822998 275.2813720703125 0.571567177772522 0.7767669 0.45148441195487976 False -18 42066 24.08051896095276 0.8762028217315674 223.8554229736328 0.3807108998298645 275.5246276855469 0.5710194706916809 0.7767537 0.46017342805862427 False -19 44280 24.064784288406372 0.4303722381591797 203.61990356445312 0.4102822542190552 275.5466003417969 0.5706395506858826 0.77385044 0.46895354986190796 False diff --git a/ENCSR846VPV/cherimoya.fold_4.performance.tsv b/ENCSR846VPV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 168202ff47d33bb501c262587cb89779d051b125..0000000000000000000000000000000000000000 --- a/ENCSR846VPV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.20361328125 0.34403955936431885 0.5720041990280151 0.18366475403308868 0.7808083295822144 0.7047191858291626 0.4356597363948822 \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_0.evaluate.json b/ENCSR846ZBX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b79be104e1d0957a1c175cb7b200e7754d8747b0..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695TXT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_0.fit.json b/ENCSR846ZBX/cherimoya.fold_0.fit.json deleted file mode 100644 index 17b15ac3f92c26509b40f7bae21c72e285f7ee9a..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF695TXT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_0.log b/ENCSR846ZBX/cherimoya.fold_0.log deleted file mode 100644 index cf01f8031551254969fa7daab94534c85249df79..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2005 26.802876472473145 11.304104089736938 325.90789794921875 0.5142466425895691 491.8837585449219 0.5196659564971924 0.59523743 8.235095977783203 True -1 4010 22.307246446609497 0.5997467041015625 361.9293212890625 0.4365469217300415 417.7442321777344 0.6080766916275024 0.69054556 1.7251530885696411 True -2 6015 22.332722187042236 0.44458937644958496 340.85394287109375 0.396986186504364 400.562744140625 0.6359688639640808 0.724729 0.6348994970321655 True -3 8020 22.315149545669556 0.42850637435913086 314.1452331542969 0.452764630317688 393.50616455078125 0.6446821093559265 0.74661344 0.4255673885345459 True -4 10025 22.233219623565674 0.43012571334838867 333.30181884765625 0.41813334822654724 391.272216796875 0.6482137441635132 0.7512698 0.3858760595321655 True -5 12030 22.25230073928833 0.4349093437194824 346.2708740234375 0.4678155779838562 389.91314697265625 0.650568962097168 0.75768113 0.329879492521286 True -6 14035 22.24090051651001 0.43013787269592285 333.4278259277344 0.40189751982688904 388.6666259765625 0.6527081727981567 0.7648602 0.3069147765636444 True -7 16040 22.33621597290039 0.8512284755706787 343.50701904296875 0.2599567770957947 387.57891845703125 0.6549381613731384 0.77197444 0.30627647042274475 True -8 18045 22.194270849227905 0.40749263763427734 326.62890625 0.27929654717445374 386.9468994140625 0.6563816666603088 0.77704567 0.29910317063331604 True -9 20050 22.291672229766846 0.4233360290527344 338.5755310058594 0.27697083353996277 386.0848083496094 0.6582534313201904 0.781947 0.2885066568851471 True -10 22055 22.227088451385498 0.4057910442352295 299.8955993652344 0.3448556065559387 385.36334228515625 0.6598498225212097 0.7855993 0.2890446186065674 True -11 24060 22.205618143081665 0.4209446907043457 327.8954772949219 0.34481388330459595 384.59014892578125 0.6610917448997498 0.79011166 0.28493213653564453 True -12 26065 22.175878047943115 0.44098949432373047 358.18487548828125 0.24793916940689087 383.9521789550781 0.6622182726860046 0.7944516 0.28162068128585815 True -13 28070 22.211257457733154 0.4148881435394287 318.708984375 0.2047145962715149 383.4339294433594 0.6633047461509705 0.7963738 0.2779187858104706 True -14 30075 22.130418300628662 1.745507001876831 321.67529296875 0.16074571013450623 383.0799865722656 0.664260983467102 0.79859847 0.27553823590278625 True -15 32080 22.16661047935486 0.4142897129058838 292.89398193359375 0.16126565635204315 383.0673828125 0.6645162105560303 0.8011271 0.2744939923286438 True -16 34085 22.245750665664673 0.4054524898529053 323.2563781738281 0.12352032214403152 383.0163269042969 0.6643245816230774 0.7977098 0.2740100920200348 False -17 36090 22.193225860595703 0.43759918212890625 347.82049560546875 0.18888726830482483 383.281494140625 0.6638564467430115 0.7963908 0.279100239276886 False -18 38095 22.17009949684143 0.4210383892059326 352.3292541503906 0.12439270317554474 383.7023620605469 0.6632487177848816 0.7931403 0.28117835521698 False -19 40100 22.174648761749268 0.41168975830078125 268.94378662109375 0.10227768123149872 383.91021728515625 0.6629120707511902 0.7894423 0.2845788896083832 False diff --git a/ENCSR846ZBX/cherimoya.fold_0.performance.tsv b/ENCSR846ZBX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4dda98b1852be6615842f09e19571e0685b5904b..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -383.0673828125 0.2697179913520813 0.6645162105560303 0.26967960596084595 0.8011270761489868 0.7529909014701843 0.2744939923286438 \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_1.evaluate.json b/ENCSR846ZBX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 488dde4f37160cb213c1d3f01f358cf51ccb71df..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695TXT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_1.fit.json b/ENCSR846ZBX/cherimoya.fold_1.fit.json deleted file mode 100644 index 86183e5bddf55b544ea9dfe2ab363fad2a3fb80e..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF695TXT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_1.log b/ENCSR846ZBX/cherimoya.fold_1.log deleted file mode 100644 index 2f055672779813c89d568faf0de583784e0d4a05..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1967 26.102338314056396 3.7355973720550537 362.3216247558594 0.40303176641464233 554.8727416992188 0.5356015563011169 0.5722909 9.106392860412598 True -1 3934 21.73079538345337 0.6718902587890625 279.63330078125 0.3257327377796173 469.42852783203125 0.6266257166862488 0.6777496 1.9445013999938965 True -2 5901 21.73623013496399 0.6422004699707031 352.2018737792969 0.6521538496017456 447.1995849609375 0.6572009921073914 0.71157134 0.7821336984634399 True -3 7868 21.744117259979248 3.425781011581421 300.95574951171875 0.3283144533634186 440.00567626953125 0.6665725708007812 0.73022413 0.6169641613960266 True -4 9835 21.375119924545288 0.5797595977783203 334.05517578125 0.36790502071380615 437.9534912109375 0.6702133417129517 0.740309 0.5801371932029724 True -5 11802 21.263816356658936 0.9860811233520508 328.0916748046875 0.37027740478515625 435.86865234375 0.6725060939788818 0.75052 0.5397313833236694 True -6 13769 21.39164972305298 0.6032509803771973 319.7767639160156 0.3647715151309967 434.87860107421875 0.6742274165153503 0.7555061 0.5354641079902649 True -7 15736 21.30651879310608 0.5721347332000732 356.0419921875 0.3248366117477417 433.1534423828125 0.6771922707557678 0.7637382 0.4886884391307831 True -8 17703 21.301992416381836 0.5580604076385498 279.7909851074219 0.3461940288543701 431.97552490234375 0.6795278191566467 0.76891845 0.4337332844734192 True -9 19670 21.28737211227417 0.5775492191314697 336.5252685546875 0.3935646414756775 430.7236633300781 0.6816233992576599 0.77316004 0.43857207894325256 True -10 21637 21.2564218044281 0.5613913536071777 350.8990173339844 0.39067143201828003 429.56573486328125 0.6834516525268555 0.7825773 0.4060550630092621 True -11 23604 21.28226327896118 0.7784731388092041 335.4755859375 0.3213235139846802 428.5677185058594 0.6850680112838745 0.78675103 0.3878052830696106 True -12 25571 21.31307601928711 1.3208651542663574 319.83880615234375 0.21074873208999634 427.300537109375 0.6865849494934082 0.7952068 0.35834527015686035 True -13 27538 21.313370943069458 0.579653263092041 288.4424743652344 0.22037248313426971 426.7154846191406 0.68790203332901 0.80083895 0.35107624530792236 True -14 29505 21.315181732177734 0.5596003532409668 322.55035400390625 0.16146732866764069 426.1033630371094 0.688409149646759 0.804595 0.33235111832618713 True -15 31472 21.37669849395752 0.5915915966033936 323.6978759765625 0.20531459152698517 426.1192932128906 0.6886587142944336 0.8101416 0.30988913774490356 True -16 33439 21.34745740890503 0.5732181072235107 364.2798156738281 0.10698328167200089 426.405029296875 0.6883840560913086 0.81024307 0.301628053188324 True -17 35406 21.28212809562683 0.5716147422790527 347.67901611328125 0.21942995488643646 426.8307800292969 0.6877503395080566 0.80804414 0.29470041394233704 False -18 37373 21.347830772399902 0.6097955703735352 310.25067138671875 0.1343597173690796 426.7317199707031 0.6870152950286865 0.8057651 0.29078879952430725 False -19 39340 21.38848352432251 1.148219108581543 334.6453857421875 0.13284781575202942 427.1325988769531 0.6866918802261353 0.8015853 0.2924402952194214 False diff --git a/ENCSR846ZBX/cherimoya.fold_1.performance.tsv b/ENCSR846ZBX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d2adbf834dee523a5ab1d4dad9e905da532f4b7d..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -426.405029296875 0.25046423077583313 0.6883840560913086 0.3004264831542969 0.8102430701255798 0.7918499708175659 0.301628053188324 \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_2.evaluate.json b/ENCSR846ZBX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 812db60660f88e052883ad3cefbaaed097ea8100..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695TXT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_2.fit.json b/ENCSR846ZBX/cherimoya.fold_2.fit.json deleted file mode 100644 index c14fe14f49c085a606a0c6d4e886f07ff7a44f16..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF695TXT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_2.log b/ENCSR846ZBX/cherimoya.fold_2.log deleted file mode 100644 index 41d4ab4b905058d0b38f350cf2c3322991089498..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2108 28.00906729698181 3.5288243293762207 318.13580322265625 0.5024046301841736 510.52777099609375 0.5323957204818726 0.5833329 7.833798408508301 True -1 4216 23.290462970733643 0.5097410678863525 363.46466064453125 0.444280743598938 434.3157653808594 0.6191191077232361 0.6895181 1.7014411687850952 True -2 6324 23.251707553863525 0.9550032615661621 377.211669921875 0.4927067458629608 415.61737060546875 0.6442275047302246 0.72994107 0.6125638484954834 True -3 8432 23.255783081054688 0.4281442165374756 328.7031555175781 0.3740314543247223 410.44140625 0.6508916020393372 0.7525452 0.43131229281425476 True -4 10540 23.234694719314575 0.4248170852661133 332.307861328125 0.38340866565704346 408.1749267578125 0.6542819738388062 0.76394933 0.4313615560531616 True -5 12648 23.24826216697693 0.4225447177886963 344.7218017578125 0.3897517919540405 407.0014343261719 0.656819760799408 0.76587135 0.4267490804195404 True -6 14756 23.228460550308228 0.4220418930053711 305.91851806640625 0.3633797764778137 405.87420654296875 0.6589305996894836 0.7719793 0.38313332200050354 True -7 16864 23.26827621459961 0.4284803867340088 300.20330810546875 0.20347079634666443 404.600341796875 0.6606269478797913 0.7787945 0.3555201292037964 True -8 18972 23.776460647583008 13.416026830673218 324.90496826171875 0.44130903482437134 403.7959289550781 0.6621959209442139 0.78217983 0.35271620750427246 True -9 21080 22.959152698516846 0.7834060192108154 350.99139404296875 0.30877357721328735 402.61590576171875 0.664021909236908 0.7862376 0.3318248689174652 True -10 23188 22.847189903259277 0.41829657554626465 326.3802185058594 0.2491464465856552 401.8570251464844 0.6653323769569397 0.79133195 0.32360151410102844 True -11 25296 22.84335207939148 0.41832637786865234 345.6360778808594 0.37347719073295593 401.0437316894531 0.6669272780418396 0.79632 0.31588587164878845 True -12 27404 22.880033493041992 0.7159204483032227 309.5758056640625 0.3097940683364868 400.3526611328125 0.6680958271026611 0.80017877 0.3083881139755249 True -13 29512 22.873145818710327 0.4281423091888428 344.3578796386719 0.18712970614433289 399.8109436035156 0.6688832640647888 0.8042364 0.3003907799720764 True -14 31620 22.98338747024536 0.41989636421203613 317.5184326171875 0.20263493061065674 399.43402099609375 0.669816255569458 0.8073329 0.29002514481544495 True -15 33728 22.80155372619629 0.41727542877197266 272.8194580078125 0.18260815739631653 399.2497253417969 0.6701469421386719 0.8070617 0.28409937024116516 False -16 35836 22.773378133773804 0.4216420650482178 304.5353088378906 0.20821639895439148 399.45556640625 0.6698608994483948 0.8076796 0.27797335386276245 True -17 37944 22.77217125892639 0.4206669330596924 316.9280090332031 0.13409797847270966 399.8670959472656 0.6692171096801758 0.8057108 0.27852264046669006 False -18 40052 22.779369831085205 0.4156482219696045 284.033935546875 0.12356545776128769 400.1837158203125 0.66846764087677 0.8026611 0.2793809175491333 False -19 42160 22.772709846496582 0.41589903831481934 276.52789306640625 0.11260682344436646 400.42181396484375 0.6680189371109009 0.8002311 0.2824946641921997 False diff --git a/ENCSR846ZBX/cherimoya.fold_2.performance.tsv b/ENCSR846ZBX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 071f88ee7168b555ff148835358bc29002576209..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -399.45556640625 0.26429271697998047 0.6698609590530396 0.28301334381103516 0.8076795935630798 0.7757856845855713 0.27797335386276245 \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_3.evaluate.json b/ENCSR846ZBX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f3b7345fd61dd3220a352e4575a69683d954411a..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695TXT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_3.fit.json b/ENCSR846ZBX/cherimoya.fold_3.fit.json deleted file mode 100644 index 14fe3a0c019e3e9381f7748f4b9d2f40e68d42a2..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF695TXT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_3.log b/ENCSR846ZBX/cherimoya.fold_3.log deleted file mode 100644 index f68b95118328517709397cc5bbbffc048a4753e8..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2035 26.831552982330322 3.788019895553589 316.23077392578125 0.3345750868320465 496.1719055175781 0.5236427783966064 0.58600605 8.095974922180176 True -1 4070 22.50779438018799 0.5133371353149414 327.07513427734375 0.43030571937561035 423.071044921875 0.6133083701133728 0.68996847 1.8453936576843262 True -2 6105 22.528724431991577 0.4327878952026367 331.1119384765625 0.4939710199832916 404.2691650390625 0.6394770741462708 0.72462785 0.7107522487640381 True -3 8140 22.487316846847534 0.43232202529907227 333.48211669921875 0.30109280347824097 398.7473449707031 0.646052896976471 0.74244857 0.5268375277519226 True -4 10175 22.487676858901978 0.4125795364379883 310.33221435546875 0.3370676636695862 396.6195373535156 0.6502050161361694 0.7501046 0.3895489573478699 True -5 12210 22.43371319770813 0.4075288772583008 341.0157470703125 0.37352514266967773 394.6023864746094 0.653875470161438 0.75829077 0.35728344321250916 True -6 14245 22.519192695617676 0.4103717803955078 339.68646240234375 0.3179137110710144 393.8024597167969 0.6552072167396545 0.76098704 0.37048110365867615 True -7 16280 22.478968858718872 0.6934123039245605 301.1287841796875 0.31490907073020935 392.7922058105469 0.6570361852645874 0.7638424 0.3783577084541321 True -8 18315 22.503614902496338 0.4086456298828125 342.74859619140625 0.24926510453224182 391.73541259765625 0.6592193245887756 0.7650719 0.3676436245441437 True -9 20350 22.468481063842773 0.4046642780303955 343.81109619140625 0.41866135597229004 390.6262512207031 0.6610461473464966 0.76956433 0.37260696291923523 True -10 22385 22.461751222610474 0.9561362266540527 305.2581481933594 0.25057297945022583 389.6512145996094 0.6628810167312622 0.77441794 0.3506573438644409 True -11 24420 22.48561143875122 0.42167234420776367 341.6387634277344 0.18820306658744812 389.31329345703125 0.6638084650039673 0.778717 0.34526902437210083 True -12 26455 23.256885051727295 0.4194674491882324 329.8809509277344 0.29552823305130005 388.47833251953125 0.6654338240623474 0.78111124 0.3337095379829407 True -13 28490 22.45618772506714 0.4190948009490967 380.60821533203125 0.32387644052505493 387.9087219238281 0.6665962934494019 0.7879309 0.3148174285888672 True -14 30525 22.45292854309082 0.41266751289367676 341.6667175292969 0.2977710962295532 387.48162841796875 0.6674798727035522 0.79329866 0.31310921907424927 True -15 32560 22.439351320266724 1.1122477054595947 312.07720947265625 0.17688703536987305 387.4183044433594 0.6677827835083008 0.7907261 0.3112383484840393 False -16 34595 22.442708730697632 0.41358327865600586 337.99615478515625 0.23715566098690033 387.6857604980469 0.6674032807350159 0.7934906 0.30193546414375305 True -17 36630 22.456795692443848 0.41057538986206055 348.43017578125 0.1221601665019989 388.039306640625 0.6668422222137451 0.7919432 0.3017420172691345 False -18 38665 22.46870493888855 0.40473318099975586 310.9713134765625 0.11522410809993744 388.2969665527344 0.6663041114807129 0.78937984 0.303020179271698 False -19 40700 22.35922908782959 0.40070223808288574 325.3644104003906 0.09689836204051971 388.5537109375 0.6658430695533752 0.7867815 0.30916351079940796 False diff --git a/ENCSR846ZBX/cherimoya.fold_3.performance.tsv b/ENCSR846ZBX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b3842af6b9538da5db4a8c99bd33778bd4659805..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -387.6857604980469 0.2673649787902832 0.6674032807350159 0.2730419337749481 0.7934905886650085 0.7559676766395569 0.30193546414375305 \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_4.evaluate.json b/ENCSR846ZBX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 329be8159c82e9bb245d942a2bb53dba932c5547..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF695TXT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_4.fit.json b/ENCSR846ZBX/cherimoya.fold_4.fit.json deleted file mode 100644 index 359564ad5ba560e0dbbc86371185df50878cd8b7..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF695TXT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR846ZBX/cherimoya.fold_4.log b/ENCSR846ZBX/cherimoya.fold_4.log deleted file mode 100644 index c96a879609f57a4fcdf0ae021ea806b2554ab9d2..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2029 26.660980463027954 3.7069854736328125 351.6368103027344 0.36806520819664 469.1304626464844 0.5182095170021057 0.5874405 7.380474090576172 True -1 4058 22.393383264541626 0.4524095058441162 336.1391906738281 0.4138332009315491 403.41375732421875 0.602256715297699 0.6905194 1.5703105926513672 True -2 6087 22.37254524230957 0.4540293216705322 316.1902770996094 0.2916713058948517 387.7272033691406 0.6287205815315247 0.7303585 0.5414431095123291 True -3 8116 22.418256044387817 0.4136471748352051 409.2772521972656 0.6415916681289673 380.9083557128906 0.6372557878494263 0.74878216 0.38774558901786804 True -4 10145 22.389121532440186 0.4076864719390869 329.1725158691406 0.37266087532043457 379.1856384277344 0.6397037506103516 0.7545464 0.3818202614784241 True -5 12174 22.370108604431152 0.3968231678009033 337.7943420410156 0.3691192865371704 378.81256103515625 0.6405041813850403 0.7599641 0.3716071546077728 True -6 14203 22.354841709136963 0.3959658145904541 322.8148193359375 0.47381290793418884 377.18902587890625 0.6438001394271851 0.76774144 0.3062189817428589 True -7 16232 22.378061771392822 0.4020214080810547 314.1654052734375 0.37890303134918213 375.9031677246094 0.6458175182342529 0.77247083 0.2953997850418091 True -8 18261 22.3895263671875 0.40181803703308105 325.146728515625 0.38227519392967224 374.5433044433594 0.6487427949905396 0.7786387 0.2844524085521698 True -9 20290 22.383543014526367 0.4092862606048584 357.1327819824219 0.32601892948150635 373.75701904296875 0.6500966548919678 0.7837359 0.2740040719509125 True -10 22319 22.39536690711975 0.4040415287017822 361.236083984375 0.38418644666671753 372.9382629394531 0.6519857048988342 0.790687 0.2800545394420624 True -11 24348 22.39127492904663 0.4129307270050049 316.11651611328125 0.2259460687637329 372.1328430175781 0.65352463722229 0.7941692 0.2633063793182373 True -12 26377 22.371423721313477 0.39728736877441406 322.7183532714844 0.21245026588439941 371.41583251953125 0.6549327373504639 0.7993642 0.2560420036315918 True -13 28406 22.361427545547485 0.4027698040008545 342.8966979980469 0.2998916208744049 371.00860595703125 0.6559284925460815 0.8023896 0.25198304653167725 True -14 30435 22.353355884552002 0.39705777168273926 332.00311279296875 0.28098928928375244 370.52703857421875 0.65691739320755 0.8083946 0.24841205775737762 True -15 32464 22.89039897918701 12.092021465301514 325.3091735839844 0.1862044334411621 370.4576110839844 0.6572728753089905 0.81161094 0.2478562444448471 True -16 34493 22.427613973617554 0.4107029438018799 312.2471618652344 0.17876511812210083 370.6534118652344 0.6569392085075378 0.8103026 0.24773389101028442 False -17 36522 22.437297582626343 0.40142083168029785 323.8071594238281 0.13361981511116028 371.1110534667969 0.6562033891677856 0.807048 0.249827578663826 False -18 38551 22.3831946849823 0.4281001091003418 341.54638671875 0.16417932510375977 371.2502136230469 0.6553135514259338 0.80293024 0.2548257112503052 False -19 40580 22.377812385559082 10.544942617416382 306.05096435546875 0.1480615735054016 371.41888427734375 0.6547977924346924 0.8018585 0.256084680557251 False diff --git a/ENCSR846ZBX/cherimoya.fold_4.performance.tsv b/ENCSR846ZBX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 881dcfd35c0225e3ce510e70c2956e0dbacbc094..0000000000000000000000000000000000000000 --- a/ENCSR846ZBX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -370.4576110839844 0.27555903792381287 0.6572728753089905 0.2623991370201111 0.8116109371185303 0.7583125829696655 0.2478562444448471 \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_0.evaluate.json b/ENCSR848TMJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c747fb4f395d5bf24fcec1adb0248e1b8b038a0d..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396FBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_0.fit.json b/ENCSR848TMJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 43cf344851909b8e0277a900d99340adf331683a..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF396FBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_0.log b/ENCSR848TMJ/cherimoya.fold_0.log deleted file mode 100644 index 3dbceab85152a145b1a4e660c5a66592f0f8285d..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2243 29.869813919067383 4.010908603668213 357.08563232421875 0.5229753851890564 469.25927734375 0.5232305526733398 0.67180973 7.457801342010498 True -1 4486 24.99056124687195 0.5096385478973389 368.79248046875 0.6231843829154968 397.17962646484375 0.6179400086402893 0.7247412 1.8302643299102783 True -2 6729 24.983245849609375 0.4558873176574707 266.25750732421875 0.41771960258483887 380.9839782714844 0.6417906880378723 0.73721933 0.6336075067520142 True -3 8972 24.95975089073181 0.45941925048828125 328.8536376953125 0.7686331272125244 374.4603576660156 0.6516914367675781 0.7448659 0.4635191261768341 True -4 11215 24.952048778533936 0.4525759220123291 295.7884826660156 0.4370514154434204 372.5570068359375 0.6545484662055969 0.74397314 0.39819860458374023 False -5 13458 24.971604347229004 0.4570186138153076 335.8740234375 0.3661905527114868 370.85601806640625 0.6580045223236084 0.747416 0.3885532021522522 True -6 15701 24.99456477165222 11.83478569984436 300.6055908203125 0.2783889174461365 370.2049560546875 0.6596665382385254 0.751279 0.3838964104652405 True -7 17944 25.359726190567017 0.46886634826660156 267.7215881347656 0.4220588207244873 368.991943359375 0.6619154214859009 0.753669 0.3841135799884796 True -8 20187 25.057358503341675 0.4613022804260254 320.6513977050781 0.4406275451183319 367.5656433105469 0.6638102531433105 0.75542456 0.3766164183616638 True -9 22430 24.56719660758972 0.45926475524902344 307.972412109375 0.4006229043006897 366.58197021484375 0.6656806468963623 0.757646 0.36992838978767395 True -10 24673 24.42823839187622 0.454326868057251 323.6661376953125 0.6156905889511108 365.7658386230469 0.6678368449211121 0.7616285 0.36150768399238586 True -11 26916 25.090214729309082 0.4541749954223633 280.78131103515625 0.6127880215644836 364.2350158691406 0.6698247194290161 0.76414657 0.35784322023391724 True -12 29159 24.585826635360718 0.4572291374206543 297.9782409667969 0.46585580706596375 363.3360595703125 0.6716870665550232 0.7686129 0.3591409921646118 True -13 31402 24.582736015319824 10.090025186538696 306.64373779296875 0.44559815526008606 362.2268981933594 0.6734472513198853 0.7761891 0.34719932079315186 True -14 33645 24.55168604850769 0.4551210403442383 293.9141845703125 0.3443857431411743 361.91656494140625 0.6752063632011414 0.7800747 0.34809526801109314 True -15 35888 25.13539481163025 0.45645928382873535 294.598876953125 0.3598553538322449 361.2174377441406 0.6761099100112915 0.7808436 0.3501422703266144 True -16 38131 24.49409294128418 0.4556889533996582 361.3519287109375 0.46446511149406433 361.5279235839844 0.6761310696601868 0.7820473 0.3548696041107178 True -17 40374 24.483022689819336 0.9861001968383789 268.4066162109375 0.2951228618621826 361.7254638671875 0.6754847168922424 0.77897966 0.36570069193840027 False -18 42617 24.61706829071045 0.4839293956756592 324.763427734375 0.35015684366226196 362.5533142089844 0.6748683452606201 0.7744516 0.3725796639919281 False -19 44860 25.143280267715454 0.45996689796447754 302.68719482421875 0.3520725667476654 362.3431091308594 0.6744903326034546 0.7731879 0.3788674771785736 False diff --git a/ENCSR848TMJ/cherimoya.fold_0.performance.tsv b/ENCSR848TMJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 58b5f177c4e453fc4c7d935c408f6cd318687c5e..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.5279235839844 0.2688279449939728 0.6761310696601868 0.2561243176460266 0.7820472717285156 0.718601405620575 0.3548696041107178 \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_1.evaluate.json b/ENCSR848TMJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9849c0b420587563ca4bbb42bb3ab65ba9aabaaa..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396FBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_1.fit.json b/ENCSR848TMJ/cherimoya.fold_1.fit.json deleted file mode 100644 index f4239cf24e40a12ad8783219592df94d9701f287..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF396FBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_1.log b/ENCSR848TMJ/cherimoya.fold_1.log deleted file mode 100644 index bb4d1f1630be344af5674b713b73cb9b4c02b047..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2246 29.72011160850525 5.170193433761597 344.9176940917969 1.878728985786438 549.4651489257812 0.541713535785675 0.6558635 8.72726821899414 True -1 4492 25.09237551689148 1.34214186668396 305.3287353515625 1.2443618774414062 458.84649658203125 0.6384708881378174 0.72381604 2.3885297775268555 True -2 6738 25.029326677322388 0.6632661819458008 304.75506591796875 0.7570871710777283 439.7908020019531 0.6648174524307251 0.72143716 0.7918176651000977 False -3 8984 25.051227807998657 0.6309125423431396 316.431884765625 0.5131628513336182 433.11529541015625 0.6718997955322266 0.7329418 0.5485131144523621 True -4 11230 24.97565484046936 0.6203827857971191 303.7029724121094 0.570815920829773 431.12957763671875 0.6748490333557129 0.72791165 0.5166794657707214 False -5 13476 24.978333711624146 0.6352276802062988 347.74688720703125 0.5330709218978882 429.7665710449219 0.6760380268096924 0.73355585 0.4997909367084503 True -6 15722 25.03803038597107 0.6356158256530762 318.37725830078125 0.5707706212997437 427.3467102050781 0.6790741682052612 0.7454866 0.4457872807979584 True -7 17968 25.084354877471924 0.6286664009094238 337.7389831542969 0.4324877858161926 426.69390869140625 0.6803542375564575 0.7493549 0.43739986419677734 True -8 20214 25.05201268196106 0.6308531761169434 320.2474365234375 0.7835140228271484 424.8260192871094 0.6830399632453918 0.752152 0.4395812749862671 True -9 22460 25.01499104499817 0.632251501083374 315.7018737792969 0.7676801681518555 422.3342590332031 0.6860448718070984 0.76325744 0.41666293144226074 True -10 24706 25.022191762924194 0.6162528991699219 314.67333984375 1.008044719696045 421.2350158691406 0.6877504587173462 0.7735891 0.38848721981048584 True -11 26952 25.023140907287598 0.6209335327148438 316.7347106933594 0.53507399559021 419.3019104003906 0.6907199025154114 0.78334033 0.37390387058258057 True -12 29198 25.04456853866577 0.6243014335632324 318.8980712890625 0.44538846611976624 417.993896484375 0.6928982138633728 0.7920121 0.36664918065071106 True -13 31444 25.04271626472473 0.6130142211914062 314.15802001953125 0.4837428331375122 416.8549499511719 0.6950731873512268 0.80052394 0.35891425609588623 True -14 33690 25.04359531402588 0.6238768100738525 300.78826904296875 0.5103651285171509 415.80303955078125 0.6965588927268982 0.8053543 0.3502752482891083 True -15 35936 24.99570345878601 0.6238229274749756 273.5473937988281 0.34845930337905884 414.8223876953125 0.6979674696922302 0.8098149 0.3480149209499359 True -16 38182 24.98718810081482 0.6166207790374756 305.5029602050781 0.5099514126777649 414.6298828125 0.6982693076133728 0.8135051 0.350800096988678 True -17 40428 24.792030572891235 0.6071977615356445 263.7474365234375 0.27190524339675903 415.4604797363281 0.6977841854095459 0.8122378 0.35899773240089417 False -18 42674 24.47433066368103 0.6152195930480957 313.6728515625 0.4485628008842468 414.5302734375 0.6972619891166687 0.80771875 0.3736732304096222 False -19 44920 24.470937967300415 0.6136102676391602 278.95806884765625 0.20148207247257233 415.8185119628906 0.6968507766723633 0.8051976 0.380582332611084 False diff --git a/ENCSR848TMJ/cherimoya.fold_1.performance.tsv b/ENCSR848TMJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 499c44395b48f2738689ffa0c91b9449017b25ca..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -414.6298828125 0.24926966428756714 0.698269248008728 0.28783711791038513 0.8135051131248474 0.7774494290351868 0.350800096988678 \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_2.evaluate.json b/ENCSR848TMJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ccdcd79b55fab56bd8c9720c9e8392701f6d68e4..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396FBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_2.fit.json b/ENCSR848TMJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 8e4d82345c320c108c45da01a8805869c19513eb..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF396FBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_2.log b/ENCSR848TMJ/cherimoya.fold_2.log deleted file mode 100644 index cd8370268a991154fdd5aa854ecef1a0c9065a01..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2384 31.09407138824463 15.24226427078247 339.1539611816406 0.7952577471733093 493.74713134765625 0.5396277904510498 0.65095484 7.172133922576904 True -1 4768 26.578567504882812 0.559880256652832 286.46795654296875 0.8629939556121826 414.9402770996094 0.6353417634963989 0.7168996 2.1309080123901367 True -2 7152 29.3511061668396 17.868791103363037 287.9808349609375 0.8427708148956299 403.18292236328125 0.6546989679336548 0.7139062 0.5640152096748352 False -3 9536 26.81863522529602 0.509951114654541 314.9852294921875 0.6781203150749207 397.8701477050781 0.6616179943084717 0.7191932 0.5195174217224121 True -4 11920 26.76027488708496 0.48351144790649414 314.3276672363281 0.945752739906311 395.91961669921875 0.6644399762153625 0.7286764 0.4839020371437073 True -5 14304 26.75917387008667 0.4880359172821045 337.47894287109375 0.43891584873199463 393.93145751953125 0.6675536036491394 0.7304255 0.4915335178375244 True -6 16688 26.738491535186768 0.5153157711029053 271.50909423828125 0.514884352684021 392.70928955078125 0.669525146484375 0.7378828 0.4775164723396301 True -7 19072 26.70367169380188 0.4808497428894043 283.0698547363281 0.5144285559654236 392.1813049316406 0.670680046081543 0.7394848 0.4707928001880646 True -8 21456 26.706236124038696 0.49672865867614746 357.654296875 0.4485284686088562 390.2707824707031 0.6733825206756592 0.7430767 0.4462251365184784 True -9 23840 26.627613067626953 0.48534417152404785 327.2404479980469 0.8487883806228638 388.7625427246094 0.6758683919906616 0.75069517 0.4314629137516022 True -10 26224 26.631083488464355 0.49060606956481934 300.9040222167969 0.5170915126800537 387.45794677734375 0.6781249046325684 0.75318253 0.42815878987312317 True -11 28608 26.668962240219116 0.47601747512817383 324.21441650390625 1.159557580947876 386.0041198730469 0.6800182461738586 0.75918174 0.4080749750137329 True -12 30992 26.622812032699585 0.4876432418823242 305.7811279296875 0.8394458293914795 385.07843017578125 0.6819049715995789 0.7668419 0.4035877287387848 True -13 33376 26.61298179626465 0.4861750602722168 274.537841796875 0.41010618209838867 383.9783020019531 0.6837261915206909 0.7713548 0.39322158694267273 True -14 35760 26.599909782409668 0.48729801177978516 318.94049072265625 0.35963720083236694 383.32647705078125 0.6851512789726257 0.7774948 0.3783532679080963 True -15 38144 26.5994975566864 0.4852278232574463 256.80230712890625 0.44329506158828735 382.92169189453125 0.6860208511352539 0.77967024 0.3760364353656769 True -16 40528 26.59797954559326 0.5021119117736816 348.90216064453125 0.24242547154426575 382.8399353027344 0.6862683296203613 0.78315204 0.3770759105682373 True -17 42912 26.69016146659851 0.4857823848724365 289.6634216308594 0.3863847851753235 382.97332763671875 0.6859983205795288 0.78144383 0.3878757357597351 False -18 45296 26.69798994064331 0.4931681156158447 292.93670654296875 0.3421432077884674 383.29925537109375 0.6855173707008362 0.776561 0.40463927388191223 False -19 47680 26.65370464324951 0.4767131805419922 264.1457214355469 0.27518266439437866 383.34210205078125 0.6851188540458679 0.77237785 0.4161677956581116 False diff --git a/ENCSR848TMJ/cherimoya.fold_2.performance.tsv b/ENCSR848TMJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7f2a7bba49e47553460448f1854e4fc5e83a78a4..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -382.8399353027344 0.2608194947242737 0.6862683296203613 0.26805758476257324 0.7831520438194275 0.7244256138801575 0.3770759105682373 \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_3.evaluate.json b/ENCSR848TMJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1778f08d8ff9d1f45ef70279656dd1e74d9607ce..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396FBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_3.fit.json b/ENCSR848TMJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 6d20fc469199aaa04f2a8576e18db0dc30a29089..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF396FBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_3.log b/ENCSR848TMJ/cherimoya.fold_3.log deleted file mode 100644 index cc3d641c96fdb56654985222681bc7a7d2ccdda6..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2319 30.416645288467407 4.016830205917358 316.90106201171875 0.5579083561897278 472.145263671875 0.5291813611984253 0.66133696 8.144800186157227 True -1 4638 25.49050498008728 0.5222692489624023 354.6077880859375 0.7671953439712524 400.1460266113281 0.6199729442596436 0.7167616 2.064375638961792 True -2 6957 25.87326431274414 0.49642086029052734 294.8161926269531 0.5815455913543701 382.8056945800781 0.6466674208641052 0.73385274 0.48992225527763367 True -3 9276 25.854219913482666 0.4584972858428955 277.75872802734375 0.8244335651397705 378.8374328613281 0.65272057056427 0.7388523 0.4262202978134155 True -4 11595 25.841552019119263 1.269803524017334 348.96826171875 0.5747069120407104 376.2772216796875 0.6568997502326965 0.7366956 0.468127578496933 False -5 13914 25.678478479385376 0.4419877529144287 289.7778625488281 0.4332221746444702 375.3220520019531 0.658933699131012 0.74290687 0.4387568533420563 True -6 16233 25.272275924682617 0.43465304374694824 289.36517333984375 0.5255280137062073 374.379638671875 0.6607715487480164 0.7428893 0.42531412839889526 False -7 18552 25.284172534942627 0.4331779479980469 296.1850280761719 0.5689921379089355 373.5367126464844 0.66230309009552 0.7435949 0.42352405190467834 True -8 20871 25.38062357902527 0.4369237422943115 275.89813232421875 0.8833840489387512 372.4962463378906 0.6642369627952576 0.7447599 0.42163804173469543 True -9 23190 25.279833793640137 0.4463632106781006 294.799560546875 0.7783148288726807 371.28057861328125 0.6662295460700989 0.7534267 0.3997974395751953 True -10 25509 25.27059817314148 0.44082045555114746 300.2798767089844 0.5212604999542236 370.1443786621094 0.6681680679321289 0.7551898 0.393640398979187 True -11 27828 25.238584518432617 0.4340066909790039 302.8578186035156 0.5783615112304688 368.70989990234375 0.6704421043395996 0.77021474 0.3723767101764679 True -12 30147 25.36665439605713 0.43517398834228516 349.5797119140625 0.5490928292274475 367.53924560546875 0.672026515007019 0.77505636 0.3684324622154236 True -13 32466 25.39992666244507 0.4424772262573242 268.5069274902344 0.47570478916168213 366.89300537109375 0.6737407445907593 0.7769252 0.37295666337013245 True -14 34785 25.32396125793457 0.44525909423828125 297.755615234375 0.6049148440361023 366.2292785644531 0.6753260493278503 0.78406245 0.36197522282600403 True -15 37104 25.261937856674194 0.44476962089538574 337.848388671875 0.576606810092926 365.8360595703125 0.6763812303543091 0.7865052 0.3649999797344208 True -16 39423 25.32970905303955 0.44630002975463867 286.18994140625 0.4299362599849701 365.0868225097656 0.6768050193786621 0.7881756 0.37165090441703796 True -17 41742 25.26420831680298 0.42939090728759766 240.21371459960938 0.44912850856781006 365.5864562988281 0.6765491962432861 0.7866305 0.38064247369766235 False -18 44061 25.277633905410767 0.4317154884338379 272.1999206542969 0.4016956686973572 365.82781982421875 0.676138162612915 0.7830256 0.39307624101638794 False -19 46380 25.246116876602173 1.686349630355835 330.2441101074219 0.31435489654541016 366.1791076660156 0.6757321953773499 0.7789359 0.4000130295753479 False diff --git a/ENCSR848TMJ/cherimoya.fold_3.performance.tsv b/ENCSR848TMJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1f0a191a2cf1f40f7660012df0f81bf5767250a4..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -365.0868225097656 0.2687471807003021 0.6768050193786621 0.25330084562301636 0.7881755828857422 0.7275422215461731 0.37165090441703796 \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_4.evaluate.json b/ENCSR848TMJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ca60b5bab723e8ecd3f9b78e5e82679d75012e3e..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF396FBH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_4.fit.json b/ENCSR848TMJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 9e855aecdc0b44af6a913b3957286dfc50b4aee2..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF396FBH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR848TMJ/cherimoya.fold_4.log b/ENCSR848TMJ/cherimoya.fold_4.log deleted file mode 100644 index b48a817e93f486fa59dabb73a163d021b37df4a6..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2337 30.588939428329468 3.9842424392700195 277.77752685546875 1.0323758125305176 452.4068603515625 0.5302661061286926 0.65172386 7.051645755767822 True -1 4674 26.026532649993896 0.5238909721374512 369.1852722167969 0.9369350671768188 385.62420654296875 0.6212351322174072 0.6901244 1.3253694772720337 True -2 7011 26.074082612991333 0.4933192729949951 326.464599609375 0.587205171585083 375.07281494140625 0.6414176225662231 0.69365174 0.5429275035858154 True -3 9348 26.09021520614624 0.5061016082763672 355.13519287109375 0.4952070116996765 369.4130859375 0.6477978229522705 0.70164704 0.41663381457328796 True -4 11685 25.99947953224182 0.4744715690612793 305.53985595703125 1.1203311681747437 367.341552734375 0.6504337787628174 0.71560854 0.4015330970287323 True -5 14022 26.04111099243164 0.4772918224334717 325.1038818359375 0.7691351175308228 365.93572998046875 0.6525892019271851 0.7133455 0.40296125411987305 False -6 16359 25.98970055580139 1.747239589691162 301.62713623046875 0.5614596009254456 364.5734558105469 0.6548977494239807 0.7159508 0.4009382724761963 True -7 18696 26.046618938446045 0.47638392448425293 344.27691650390625 0.4184630513191223 363.3279113769531 0.6571534276008606 0.72691375 0.39911314845085144 True -8 21033 25.639601230621338 0.48061156272888184 289.73834228515625 0.3557305634021759 362.6291198730469 0.6588919162750244 0.7283566 0.3864784836769104 True -9 23370 25.475909948349 0.47199535369873047 296.03045654296875 1.1065068244934082 361.66314697265625 0.6606661081314087 0.7317778 0.38382744789123535 True -10 25707 25.494949340820312 0.4757192134857178 323.30029296875 0.372276246547699 360.6390075683594 0.6623201370239258 0.739682 0.3870124816894531 True -11 28044 25.49212121963501 0.47115182876586914 296.74700927734375 0.7141256332397461 359.6266174316406 0.6644032597541809 0.74691653 0.3724835515022278 True -12 30381 25.47738027572632 0.4675478935241699 281.12225341796875 0.34790951013565063 358.603271484375 0.6662210822105408 0.753109 0.369594544172287 True -13 32718 25.47631049156189 0.4671649932861328 294.8817443847656 0.8136447668075562 357.7494201660156 0.6682615280151367 0.76013327 0.37191158533096313 True -14 35055 25.43557071685791 0.47150564193725586 311.21197509765625 0.4055391848087311 357.1382141113281 0.6697174310684204 0.7655631 0.36832520365715027 True -15 37392 25.433271646499634 0.5632681846618652 264.2237243652344 0.363264799118042 356.564453125 0.6707855463027954 0.769523 0.3682165741920471 True -16 39729 25.53002381324768 0.6434347629547119 344.54071044921875 0.37605908513069153 356.3583984375 0.6713002920150757 0.77177805 0.3711601197719574 True -17 42066 25.542702198028564 0.4743053913116455 327.3397216796875 0.5239765644073486 356.6382141113281 0.6709153652191162 0.76928896 0.3798018991947174 False -18 44403 25.595242500305176 0.47220420837402344 260.4455261230469 0.4378783106803894 356.987060546875 0.6703863739967346 0.76714396 0.38853394985198975 False -19 46740 25.56215214729309 0.477825403213501 281.1851806640625 0.2730143070220947 357.1891784667969 0.6700332164764404 0.7616719 0.3960111141204834 False diff --git a/ENCSR848TMJ/cherimoya.fold_4.performance.tsv b/ENCSR848TMJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 71cd9b69343cbb8d617427607840c7f21302c1f6..0000000000000000000000000000000000000000 --- a/ENCSR848TMJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -356.3583984375 0.2721761167049408 0.6713002920150757 0.2500515878200531 0.7717780470848083 0.6799489855766296 0.3711601197719574 \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_0.evaluate.json b/ENCSR849CYU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d32288491b8123c4b7ed01cb6bb5cc6e204e074d..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325GWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_0.fit.json b/ENCSR849CYU/cherimoya.fold_0.fit.json deleted file mode 100644 index 15d355ea8f75ab7c4d58725dd66abda4cb0fd91a..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF325GWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_0.log b/ENCSR849CYU/cherimoya.fold_0.log deleted file mode 100644 index f736f2711b6d52e7143480d4c0db680ad1944d7a..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 35.2741641998291 3.9697413444519043 662.635009765625 0.43508169054985046 852.1956787109375 0.29229530692100525 0.77337277 5.175480365753174 True -1 5494 30.25829005241394 0.6569230556488037 721.105224609375 0.25068196654319763 773.8078002929688 0.36899930238723755 0.83059424 0.8732762336730957 True -2 8241 30.237332582473755 0.6000833511352539 708.1804809570312 0.2876773178577423 764.7332763671875 0.3785112202167511 0.8371804 0.4051647186279297 True -3 10988 30.236549854278564 0.6007153987884521 711.7470703125 0.3224436044692993 759.3936767578125 0.38234588503837585 0.84135073 0.3717256486415863 True -4 13735 30.172475814819336 0.8882155418395996 622.6649169921875 0.3589545488357544 755.6768798828125 0.38693729043006897 0.84783196 0.38330844044685364 True -5 16482 30.35578989982605 0.5968167781829834 666.0770263671875 0.229598730802536 751.8364868164062 0.391260027885437 0.8533497 0.29186132550239563 True -6 19229 30.32184362411499 0.5909984111785889 595.9054565429688 0.30997103452682495 750.4865112304688 0.3929678797721863 0.85596544 0.2983528971672058 True -7 21976 30.038718700408936 0.5869848728179932 686.1849975585938 0.3109908699989319 747.646240234375 0.39673539996147156 0.8593758 0.31537923216819763 True -8 24723 29.69341278076172 0.5793230533599854 618.8218994140625 0.2930455207824707 746.4505004882812 0.39786916971206665 0.8619388 0.305965781211853 True -9 27470 29.767426013946533 0.6029946804046631 654.91943359375 0.2788889408111572 742.1327514648438 0.40238186717033386 0.8678004 0.28004223108291626 True -10 30217 29.78069806098938 0.5865113735198975 678.0099487304688 0.21877968311309814 742.2316284179688 0.40203091502189636 0.8713453 0.248857781291008 True -11 32964 29.78642773628235 0.6018304824829102 677.6275024414062 0.30081629753112793 740.5377807617188 0.40334653854370117 0.87295187 0.2386699616909027 True -12 35711 29.706928253173828 0.5991780757904053 608.952392578125 0.16739703714847565 738.4680786132812 0.4055771231651306 0.8775511 0.21562378108501434 True -13 38458 29.67281675338745 0.5877377986907959 570.5103759765625 0.1739465296268463 735.5759887695312 0.4090677499771118 0.88333654 0.19881480932235718 True -14 41205 29.661309719085693 0.586967945098877 517.84326171875 0.15509644150733948 734.5498046875 0.409923255443573 0.8867528 0.18653537333011627 True -15 43952 29.68274450302124 0.5778660774230957 633.03466796875 0.22802725434303284 733.106689453125 0.4106493592262268 0.8893376 0.17932036519050598 True -16 46699 29.692636966705322 0.5798234939575195 623.9852294921875 0.1567767858505249 733.7157592773438 0.41000697016716003 0.8908828 0.1724323332309723 True -17 49446 29.63767409324646 0.5855011940002441 604.17236328125 0.1617969423532486 731.4572143554688 0.41370171308517456 0.8919266 0.17003180086612701 True -18 52193 29.58352565765381 0.5738065242767334 574.4905395507812 0.19587929546833038 733.3399658203125 0.4107273817062378 0.8925019 0.16967244446277618 True -19 54940 29.630502223968506 0.5801737308502197 619.87255859375 0.122845359146595 732.5383911132812 0.41258928179740906 0.89121234 0.16943593323230743 False diff --git a/ENCSR849CYU/cherimoya.fold_0.performance.tsv b/ENCSR849CYU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7e1ffdcf2a8617db1cfa0c1aa15bc24a44666a29..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -733.3399658203125 0.36618274450302124 0.4107273817062378 0.1794554889202118 0.8925018906593323 0.866684079170227 0.16967244446277618 \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_1.evaluate.json b/ENCSR849CYU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3b866245a6bf9c79ba8870e7323dc9be38a806a7..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325GWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_1.fit.json b/ENCSR849CYU/cherimoya.fold_1.fit.json deleted file mode 100644 index 6be76e647ae799c423c60656ce48763997b941dc..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF325GWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_1.log b/ENCSR849CYU/cherimoya.fold_1.log deleted file mode 100644 index 39bfaeb03f3aa8c75d71ef17cde68d2f4f3bd5c3..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2711 34.871395111083984 3.903498888015747 684.1751708984375 0.3640412986278534 1002.7802124023438 0.29428067803382874 0.75938636 6.559111595153809 True -1 5422 29.83503222465515 0.7154605388641357 739.4799194335938 0.2861746549606323 901.65869140625 0.37991392612457275 0.821782 1.5837668180465698 True -2 8133 29.843762636184692 0.964207649230957 754.463134765625 0.20588579773902893 885.009765625 0.39414089918136597 0.83519346 0.5329993367195129 True -3 10844 29.800522565841675 0.7202532291412354 634.2439575195312 0.348629355430603 875.9400634765625 0.4004005789756775 0.84097916 0.35321101546287537 True -4 13555 29.82871413230896 0.6713182926177979 682.7763671875 0.297514945268631 872.183837890625 0.40379878878593445 0.84364694 0.34437283873558044 True -5 16266 29.807300567626953 0.7178943157196045 647.9163208007812 0.2708801031112671 868.2409057617188 0.40743565559387207 0.84752345 0.3662903904914856 True -6 18977 29.82905149459839 0.6871871948242188 572.1021728515625 0.1611228883266449 864.2871704101562 0.41075214743614197 0.84858245 0.314762681722641 True -7 21688 29.689191579818726 0.7045769691467285 668.4953002929688 0.2710404098033905 859.2644653320312 0.4158293306827545 0.855885 0.3004051446914673 True -8 24399 29.29950976371765 0.6908960342407227 650.6016845703125 0.3184693455696106 856.8535766601562 0.41715118288993835 0.8619043 0.27757129073143005 True -9 27110 29.34015917778015 5.535750389099121 680.4440307617188 0.26025277376174927 853.4995727539062 0.419555127620697 0.86434454 0.25909897685050964 True -10 29821 29.29966115951538 0.7048308849334717 588.6302490234375 0.466198205947876 849.4155883789062 0.4238074719905853 0.8693843 0.24506862461566925 True -11 32532 29.222563982009888 0.7122242450714111 607.2042846679688 0.22168737649917603 845.7402954101562 0.42619407176971436 0.8740624 0.23715561628341675 True -12 35243 29.295987606048584 0.6959071159362793 775.6810302734375 0.34950536489486694 842.5949096679688 0.42867547273635864 0.88061774 0.22081074118614197 True -13 37954 29.37152671813965 0.6947832107543945 571.5745849609375 0.23826684057712555 841.4512329101562 0.4291974604129791 0.88549066 0.20883513987064362 True -14 40665 29.215551376342773 0.6710922718048096 575.7288818359375 0.11437541991472244 839.0004272460938 0.43164995312690735 0.88962656 0.20003953576087952 True -15 43376 29.26896619796753 1.3331339359283447 574.1563110351562 0.19364267587661743 837.3872680664062 0.4330204725265503 0.89213115 0.19507484138011932 True -16 46087 29.3578839302063 0.6959266662597656 658.4376220703125 0.2583348751068115 836.646484375 0.4329606592655182 0.89668244 0.1868450939655304 True -17 48798 29.279890537261963 0.6773216724395752 643.166748046875 0.12118717283010483 836.3755493164062 0.43365418910980225 0.8987946 0.18396484851837158 True -18 51509 29.364277601242065 0.6741714477539062 559.0460205078125 0.14572089910507202 836.5233764648438 0.43299388885498047 0.8970059 0.18374581634998322 False -19 54220 29.43386697769165 0.6750650405883789 516.7416381835938 0.08615049719810486 836.9115600585938 0.43271324038505554 0.89709926 0.18354927003383636 False diff --git a/ENCSR849CYU/cherimoya.fold_1.performance.tsv b/ENCSR849CYU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ac51b313a688731b24579998b5e7cf1226414265..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -836.3755493164062 0.3458195626735687 0.43365418910980225 0.20473206043243408 0.8987945914268494 0.8841590881347656 0.18396484851837158 \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_2.evaluate.json b/ENCSR849CYU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 85d2960529d34e29efb79cd8c60a0f0c8039c194..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325GWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_2.fit.json b/ENCSR849CYU/cherimoya.fold_2.fit.json deleted file mode 100644 index eedb26fba9c807b563f5c5e1c82262b4a66459d7..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF325GWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_2.log b/ENCSR849CYU/cherimoya.fold_2.log deleted file mode 100644 index 68cdd9b9064b9795d8a799b1a2d04c2162fafe93..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 36.261077642440796 3.5406017303466797 684.6460571289062 0.261324942111969 888.5779418945312 0.29516783356666565 0.7676356 3.856344223022461 True -1 5756 31.803539752960205 0.6771104335784912 732.008544921875 0.3533829152584076 817.7222900390625 0.3645113706588745 0.81765443 1.1008834838867188 True -2 8634 31.69420313835144 0.6289887428283691 640.0419311523438 0.30183178186416626 798.5596313476562 0.3793414533138275 0.83122164 0.4638769328594208 True -3 11512 31.705058097839355 0.5649287700653076 562.201416015625 0.3224628269672394 791.1076049804688 0.38713338971138 0.83453417 0.33926084637641907 True -4 14390 31.671669244766235 0.5728287696838379 749.78955078125 0.267175555229187 787.103759765625 0.39059722423553467 0.84223306 0.31356263160705566 True -5 17268 31.671475648880005 0.5597126483917236 670.124267578125 0.36215680837631226 785.1884765625 0.3928234577178955 0.8450198 0.2849045693874359 True -6 20146 31.605770349502563 0.557544469833374 652.4217529296875 0.2996861934661865 782.26318359375 0.39571863412857056 0.84949124 0.28293031454086304 True -7 23024 31.63565731048584 0.6000304222106934 679.1450805664062 0.34999656677246094 779.14404296875 0.39994102716445923 0.8537764 0.27633771300315857 True -8 25902 31.60213613510132 1.16568922996521 567.691650390625 0.35095542669296265 777.3461303710938 0.401070237159729 0.85432494 0.2756638824939728 True -9 28780 31.477593421936035 0.62691330909729 682.8578491210938 0.2190203219652176 774.0339965820312 0.40463486313819885 0.85891116 0.2576458752155304 True -10 31658 31.102999687194824 0.5528874397277832 543.9713745117188 0.24757423996925354 772.0506591796875 0.4058254659175873 0.86605066 0.23330160975456238 True -11 34536 31.11582326889038 0.5521981716156006 555.6884765625 0.1880909949541092 768.7693481445312 0.40929511189460754 0.8721358 0.22646674513816833 True -12 37414 31.105807065963745 1.0751965045928955 627.4091186523438 0.2193913608789444 766.2490844726562 0.41201052069664 0.8742272 0.21151597797870636 True -13 40292 31.055814266204834 0.5518486499786377 544.4203491210938 0.2017229199409485 764.5558471679688 0.4138372838497162 0.8811114 0.1999821662902832 True -14 43170 31.10145878791809 0.5714750289916992 767.85498046875 0.16365179419517517 762.4490356445312 0.41531068086624146 0.8840881 0.19013264775276184 True -15 46048 31.034894704818726 0.560924768447876 640.0750122070312 0.19175544381141663 762.3411865234375 0.41456934809684753 0.8880147 0.18264001607894897 True -16 48926 31.17217183113098 0.5571169853210449 663.047119140625 0.18672600388526917 762.9134521484375 0.4139760136604309 0.8885914 0.17693039774894714 True -17 51804 31.095707893371582 0.5562970638275146 737.4928588867188 0.11604498326778412 763.2055053710938 0.414523184299469 0.8904075 0.17525972425937653 True -18 54682 31.065897464752197 0.547893762588501 678.161376953125 0.14185477793216705 762.0299682617188 0.41617318987846375 0.89015895 0.17671382427215576 False -19 57560 31.034894227981567 0.5507590770721436 632.2439575195312 0.15618249773979187 763.0337524414062 0.4149814546108246 0.8890344 0.1766427904367447 False diff --git a/ENCSR849CYU/cherimoya.fold_2.performance.tsv b/ENCSR849CYU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index be0cc84641c5161dca6709f09970591d6064b8fd..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -763.2055053710938 0.36075466871261597 0.4145231544971466 0.18731535971164703 0.8904075026512146 0.8674238920211792 0.17525972425937653 \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_3.evaluate.json b/ENCSR849CYU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ab39dcc671c7f825eadd9ea6b5876a227d131da3..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325GWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_3.fit.json b/ENCSR849CYU/cherimoya.fold_3.fit.json deleted file mode 100644 index 465f96117b789ccca68f0905bcdc407d7daf18fd..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF325GWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_3.log b/ENCSR849CYU/cherimoya.fold_3.log deleted file mode 100644 index ff9f3b62f2ad1b2b6ade4a9175676c9c7c85e2e6..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 34.99279189109802 3.730989456176758 727.468017578125 0.3396141231060028 843.7633056640625 0.29814961552619934 0.75874424 5.453060626983643 True -1 5518 30.312854766845703 0.5641231536865234 666.4805297851562 0.29311567544937134 766.1348876953125 0.37133851647377014 0.82580006 1.1940048933029175 True -2 8277 30.392383337020874 0.5477547645568848 578.1605834960938 0.5291184782981873 752.1807861328125 0.38370150327682495 0.83818424 0.46602877974510193 True -3 11036 30.374743700027466 0.5379087924957275 608.2354125976562 0.31513211131095886 746.9996948242188 0.38723593950271606 0.84440875 0.3626551330089569 True -4 13795 30.312042236328125 0.5447306632995605 634.67724609375 0.26040253043174744 742.8756103515625 0.39290887117385864 0.84932476 0.32145896553993225 True -5 16554 30.301254272460938 0.5438916683197021 678.1884765625 0.24674072861671448 740.3871459960938 0.39574894309043884 0.8492971 0.3318970203399658 False -6 19313 30.368716955184937 0.5420002937316895 638.365234375 0.226487934589386 738.1738891601562 0.3980754613876343 0.8540562 0.2828844487667084 True -7 22072 30.318679332733154 0.544947624206543 754.4901123046875 0.3175634443759918 739.2546997070312 0.3960322141647339 0.8576676 0.30713602900505066 True -8 24831 30.357975959777832 2.2075977325439453 680.3983154296875 0.2884010076522827 734.5684814453125 0.40218332409858704 0.8587976 0.2650080621242523 True -9 27590 30.32732129096985 0.545311450958252 714.6788330078125 0.4173389971256256 731.8660888671875 0.40495142340660095 0.8627832 0.2495788335800171 True -10 30349 29.810946464538574 3.092048406600952 571.412109375 0.1644737869501114 729.3272705078125 0.40683791041374207 0.8657571 0.23968832194805145 True -11 33108 29.90712022781372 0.5594234466552734 793.9844970703125 0.20454980432987213 727.1719360351562 0.40883299708366394 0.87153 0.23112057149410248 True -12 35867 29.88139271736145 0.5342764854431152 636.4195556640625 0.2985423803329468 725.1853637695312 0.4103103578090668 0.8795783 0.21712596714496613 True -13 38626 29.813945293426514 0.551215648651123 626.4318237304688 0.21151436865329742 724.1553955078125 0.4114741384983063 0.88154286 0.21012642979621887 True -14 41385 29.75766110420227 0.5428566932678223 583.5573120117188 0.193169504404068 721.2532958984375 0.4136351943016052 0.8875466 0.19395260512828827 True -15 44144 29.868834018707275 0.5560157299041748 691.985107421875 0.22558724880218506 720.7739868164062 0.4139972925186157 0.88950837 0.18579256534576416 True -16 46903 29.893016815185547 0.5385298728942871 688.67041015625 0.14372676610946655 720.29833984375 0.41424164175987244 0.892006 0.18050770461559296 True -17 49662 29.867647171020508 0.5539782047271729 665.2435302734375 0.13312508165836334 719.51806640625 0.4162430167198181 0.8954308 0.17936915159225464 True -18 52421 29.835811853408813 1.58897066116333 620.379150390625 0.14421972632408142 719.15869140625 0.41599565744400024 0.894985 0.17900808155536652 False -19 55180 29.845736265182495 0.5273220539093018 733.34765625 0.2611997425556183 720.3679809570312 0.4144046902656555 0.8940101 0.1790095418691635 False diff --git a/ENCSR849CYU/cherimoya.fold_3.performance.tsv b/ENCSR849CYU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6d34ba5e7c5cc250d57cef0ce8970977dd9d2d89..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -719.51806640625 0.36494383215904236 0.4162429869174957 0.18366703391075134 0.8954308032989502 0.8625583052635193 0.17936915159225464 \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_4.evaluate.json b/ENCSR849CYU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f4b668b75f4ad551ffb9e0ae0aeac29d10238ec9..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325GWC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_4.fit.json b/ENCSR849CYU/cherimoya.fold_4.fit.json deleted file mode 100644 index 7ed4ac665bb03da556520325fe8cefbfd27cc590..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF325GWC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR849CYU/cherimoya.fold_4.log b/ENCSR849CYU/cherimoya.fold_4.log deleted file mode 100644 index 6ca1e37f45b09bfa65a5af53da8eb13dcf644569..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2807 35.695213079452515 4.955110788345337 673.3789672851562 0.2931598424911499 808.4816284179688 0.2913665175437927 0.75272804 4.200687408447266 True -1 5614 30.864585638046265 0.7474522590637207 696.2352294921875 0.36833953857421875 746.9306030273438 0.3607029914855957 0.80424464 1.1347156763076782 True -2 8421 30.91111660003662 0.8236083984375 608.572021484375 0.29736700654029846 733.314453125 0.3713422417640686 0.8188269 0.4786461293697357 True -3 11228 30.926652431488037 0.6002240180969238 734.575439453125 0.304858922958374 728.955322265625 0.3754784166812897 0.8240124 0.39132368564605713 True -4 14035 30.941873788833618 0.5806887149810791 592.96923828125 0.3391265273094177 723.2472534179688 0.3820471167564392 0.83228225 0.40505489706993103 True -5 16842 30.892228364944458 0.6686291694641113 737.83349609375 0.32774317264556885 720.9718627929688 0.38466736674308777 0.8380184 0.29911530017852783 True -6 19649 30.90154790878296 0.6080491542816162 601.49072265625 0.21001607179641724 717.5824584960938 0.3892088830471039 0.84280246 0.2716153562068939 True -7 22456 30.888789892196655 0.5991380214691162 632.4329223632812 0.21701407432556152 715.4667358398438 0.39015114307403564 0.85024214 0.2521205544471741 True -8 25263 30.907551527023315 0.6093723773956299 534.6017456054688 0.21499963104724884 714.4424438476562 0.3903559744358063 0.8551201 0.245133638381958 True -9 28070 30.874711751937866 1.2495744228363037 535.821044921875 0.2738363742828369 711.1338500976562 0.39509934186935425 0.85795105 0.23301741480827332 True -10 30877 30.918042182922363 1.721924066543579 685.8214111328125 0.3235737383365631 709.0799560546875 0.3971557021141052 0.8655061 0.21704916656017303 True -11 33684 30.384721279144287 0.6028883457183838 579.252685546875 0.23714646697044373 709.2198486328125 0.39559847116470337 0.86790305 0.20489995181560516 True -12 36491 30.30436134338379 0.6713929176330566 651.838623046875 0.20963944494724274 705.77001953125 0.4005572199821472 0.8725602 0.19198058545589447 True -13 39298 30.2592031955719 0.5704455375671387 671.1680908203125 0.18427005410194397 704.3406372070312 0.4018861651420593 0.8764535 0.1859874129295349 True -14 42105 30.306442737579346 0.6151895523071289 649.1868896484375 0.15520553290843964 702.2257080078125 0.4048398435115814 0.8801957 0.1781928837299347 True -15 44912 30.25795006752014 1.0280132293701172 650.0611572265625 0.1663147658109665 700.4194946289062 0.4068126678466797 0.8826778 0.17058712244033813 True -16 47719 30.315415620803833 1.6960291862487793 745.7449951171875 0.14128737151622772 701.11572265625 0.4054315388202667 0.8871048 0.16649582982063293 True -17 50526 30.280877113342285 3.4400269985198975 544.3734130859375 0.13904884457588196 701.6324462890625 0.40518656373023987 0.8879784 0.16453395783901215 True -18 53333 30.34969997406006 0.5916099548339844 625.7261962890625 0.09277728199958801 702.2325439453125 0.40396741032600403 0.8870806 0.16380462050437927 False -19 56140 30.334132194519043 0.623314619064331 598.16259765625 0.09477467834949493 702.662109375 0.4034023582935333 0.88725954 0.16368690133094788 False diff --git a/ENCSR849CYU/cherimoya.fold_4.performance.tsv b/ENCSR849CYU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b74cb075b5b5dc8c8dd8c2183485ff26144b8265..0000000000000000000000000000000000000000 --- a/ENCSR849CYU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -701.6324462890625 0.37067338824272156 0.40518656373023987 0.1754510998725891 0.8879783749580383 0.8490177392959595 0.16453395783901215 \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_0.evaluate.json b/ENCSR851EBF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b410ee62e234d50729b3629470604f63c392a5f4..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF335YBU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_0.fit.json b/ENCSR851EBF/cherimoya.fold_0.fit.json deleted file mode 100644 index 89b15a4fa2ed08138b119afc08f2aabb56211eb8..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF335YBU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_0.log b/ENCSR851EBF/cherimoya.fold_0.log deleted file mode 100644 index b74201ed40cdf6758815f94b12bf5f60ee932c37..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1245 18.264575242996216 3.4480483531951904 178.60671997070312 0.36231929063796997 263.7937927246094 0.37019413709640503 0.7207297 12.615274429321289 True -1 2490 13.796738386154175 0.2853267192840576 189.07447814941406 0.24325832724571228 226.1645050048828 0.4447898864746094 0.7646682 3.074744462966919 True -2 3735 13.775381326675415 0.2421584129333496 169.90249633789062 0.2752152681350708 217.1328582763672 0.47185036540031433 0.77309585 0.9736318588256836 True -3 4980 13.7599515914917 0.2566370964050293 154.10848999023438 0.42577844858169556 211.344970703125 0.4900820553302765 0.7967061 0.40080487728118896 True -4 6225 13.650507688522339 0.2530174255371094 178.4632568359375 0.31324195861816406 209.4576416015625 0.4969692826271057 0.80948937 0.3297562003135681 True -5 7470 13.486469030380249 0.24619674682617188 177.16259765625 0.4328768253326416 208.5707244873047 0.5003513097763062 0.815603 0.29509299993515015 True -6 8715 13.522875785827637 0.24793100357055664 162.75357055664062 0.3042692244052887 208.05068969726562 0.5025017857551575 0.8187025 0.26277610659599304 True -7 9960 13.510151624679565 0.24834203720092773 167.23077392578125 0.2738398611545563 207.564453125 0.5045022964477539 0.8230817 0.2628585696220398 True -8 11205 13.475934267044067 0.25299787521362305 169.4349365234375 0.2653360366821289 207.27871704101562 0.5058785080909729 0.82517594 0.24639010429382324 True -9 12450 13.496764659881592 1.304095983505249 179.56863403320312 0.2465129941701889 206.89015197753906 0.5073671936988831 0.82916516 0.23726320266723633 True -10 13695 13.496309757232666 0.24730825424194336 176.72064208984375 0.24163055419921875 206.56942749023438 0.5086726546287537 0.832039 0.2206215113401413 True -11 14940 13.491756916046143 0.25058937072753906 171.0615692138672 0.23673191666603088 206.29132080078125 0.509941041469574 0.83463496 0.2091296762228012 True -12 16185 13.508061408996582 0.2527492046356201 180.8172607421875 0.1633799970149994 206.04888916015625 0.5107914805412292 0.8375625 0.20025195181369781 True -13 17430 13.523056983947754 0.25410985946655273 179.67520141601562 0.22572627663612366 205.81951904296875 0.5115481019020081 0.8402761 0.19695362448692322 True -14 18675 13.487244129180908 0.2557978630065918 172.3369598388672 0.20489749312400818 205.75453186035156 0.5115881562232971 0.84429884 0.19022181630134583 True -15 19920 13.489643812179565 0.2563958168029785 157.06002807617188 0.20723295211791992 205.77407836914062 0.5112830996513367 0.8479707 0.18667475879192352 True -16 21165 13.521612167358398 0.252979040145874 160.07571411132812 0.16299967467784882 206.00732421875 0.5100494027137756 0.84720355 0.1859021782875061 False -17 22410 13.502466917037964 0.25269055366516113 152.00054931640625 0.20578047633171082 206.2955780029297 0.5084356665611267 0.84645665 0.185251384973526 False -18 23655 13.485144138336182 0.24980378150939941 163.43124389648438 0.15039576590061188 206.63162231445312 0.5067282319068909 0.8437111 0.1892588585615158 False -19 24900 13.490938425064087 0.8535716533660889 157.8284149169922 0.10081354528665543 206.87210083007812 0.505634069442749 0.841304 0.19012418389320374 False diff --git a/ENCSR851EBF/cherimoya.fold_0.performance.tsv b/ENCSR851EBF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4840bfe1ce5ce943efa1afdbad4ba35ba6d1ab4d..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -205.77407836914062 0.38634616136550903 0.5112830996513367 0.13555596768856049 0.847970724105835 0.8259491324424744 0.18667475879192352 \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_1.evaluate.json b/ENCSR851EBF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a33c547e9d51a489b814a60db84ec30d3560a8c3..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF335YBU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_1.fit.json b/ENCSR851EBF/cherimoya.fold_1.fit.json deleted file mode 100644 index 1e76e610d27391d27e16605a681b9d7db80e5a05..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF335YBU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_1.log b/ENCSR851EBF/cherimoya.fold_1.log deleted file mode 100644 index cd403219dbfbee2e0951f3b2ca7a70efe0ba58ec..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1224 18.05380630493164 3.359133720397949 198.04971313476562 0.2877105474472046 290.5001220703125 0.3826199173927307 0.6674521 13.509293556213379 True -1 2448 13.544535398483276 0.37160468101501465 164.78610229492188 0.3424815237522125 249.4698486328125 0.4553152024745941 0.71696484 3.5797946453094482 True -2 3672 13.577870845794678 0.3560004234313965 175.08584594726562 0.31412485241889954 237.8186492919922 0.48943617939949036 0.7351216 1.0606344938278198 True -3 4896 13.540824174880981 0.3503284454345703 183.83555603027344 0.3570415675640106 230.6414794921875 0.5116857886314392 0.7606195 0.4617399573326111 True -4 6120 13.53006386756897 0.3505985736846924 185.8577117919922 0.2568311095237732 227.6143341064453 0.5212332606315613 0.7771769 0.31718024611473083 True -5 7344 13.56493854522705 0.35584545135498047 162.2461395263672 0.29584717750549316 226.54147338867188 0.5255959630012512 0.7851782 0.2785562574863434 True -6 8568 13.560664892196655 0.35474133491516113 164.91030883789062 0.34723585844039917 226.22671508789062 0.5269603133201599 0.7931089 0.26666831970214844 True -7 9792 13.567123413085938 0.3573300838470459 182.50437927246094 0.21080519258975983 225.84854125976562 0.5285875201225281 0.79851836 0.24356535077095032 True -8 11016 13.544983863830566 0.3571033477783203 193.78182983398438 0.2667485475540161 225.47445678710938 0.5302529335021973 0.8055045 0.23420311510562897 True -9 12240 13.53349232673645 0.5706577301025391 173.7572021484375 0.1747351735830307 225.14169311523438 0.5316308736801147 0.8108371 0.22141629457473755 True -10 13464 13.564754247665405 0.34072327613830566 170.04437255859375 0.22649046778678894 224.74497985839844 0.5331505537033081 0.8119543 0.21659013628959656 True -11 14688 13.53302526473999 0.3528261184692383 184.49127197265625 0.2111208736896515 224.38482666015625 0.534518301486969 0.8169043 0.20848478376865387 True -12 15912 13.539910316467285 0.35349225997924805 173.854736328125 0.17373788356781006 224.03009033203125 0.535703718662262 0.8234489 0.20333102345466614 True -13 17136 13.52293610572815 0.35636448860168457 143.66287231445312 0.16354352235794067 223.82167053222656 0.5365145802497864 0.828078 0.19880864024162292 True -14 18360 13.552568435668945 0.3564262390136719 175.34376525878906 0.1665455400943756 223.76046752929688 0.5366120338439941 0.8306095 0.19344234466552734 True -15 19584 13.528982639312744 0.35757970809936523 176.1605682373047 0.11760769039392471 223.8604736328125 0.5359598398208618 0.83460605 0.18865618109703064 True -16 20808 13.54528021812439 0.3536713123321533 149.05029296875 0.18401864171028137 224.1255340576172 0.5345200896263123 0.8345827 0.19092273712158203 False -17 22032 13.542667150497437 0.3515350818634033 179.33865356445312 0.13668537139892578 224.50433349609375 0.5326834321022034 0.83430314 0.19339928030967712 False -18 23256 13.525314807891846 0.34331560134887695 178.79745483398438 0.10309308022260666 224.8905029296875 0.5307806730270386 0.8322749 0.1945243626832962 False -19 24480 13.566625833511353 0.3421461582183838 170.68682861328125 0.10647948086261749 225.1491241455078 0.529518187046051 0.8314974 0.1970938742160797 False diff --git a/ENCSR851EBF/cherimoya.fold_1.performance.tsv b/ENCSR851EBF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c7906b662ebd4a52301fe64751136ae29a08d5b0..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.8604736328125 0.368534654378891 0.535959780216217 0.1513197422027588 0.8346060514450073 0.8280068635940552 0.18865618109703064 \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_2.evaluate.json b/ENCSR851EBF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 945f821ca8255e76d5951af2d0d3f52df5b04678..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF335YBU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_2.fit.json b/ENCSR851EBF/cherimoya.fold_2.fit.json deleted file mode 100644 index 6144ff72501e5740d2288480ba033411f1c3de8c..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF335YBU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_2.log b/ENCSR851EBF/cherimoya.fold_2.log deleted file mode 100644 index 1a3ea6b3bdb11eab4d48f0461419d3bf4fe4e5d9..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1301 18.907105445861816 3.4766857624053955 174.16787719726562 0.3854561150074005 267.4823913574219 0.3764052987098694 0.6822737 12.269134521484375 True -1 2602 14.502111434936523 13.396667003631592 170.84152221679688 0.32119572162628174 230.28968811035156 0.45113879442214966 0.73900676 2.8223049640655518 True -2 3903 15.22877812385559 5.079444169998169 158.15647888183594 0.41009050607681274 220.9484100341797 0.4831618666648865 0.7605006 0.7094768285751343 True -3 5204 14.429597854614258 0.2667555809020996 161.9492645263672 0.2665928900241852 214.8826446533203 0.4995582103729248 0.7775452 0.43962129950523376 True -4 6505 14.413551568984985 0.26863861083984375 148.2523193359375 0.2816537618637085 212.8095703125 0.5064271092414856 0.78625464 0.318908154964447 True -5 7806 14.406988620758057 0.26616597175598145 164.93276977539062 0.30014798045158386 212.90428161621094 0.505358099937439 0.7837522 0.4233784079551697 False -6 9107 14.413977861404419 0.25905871391296387 176.0995330810547 0.24854892492294312 211.8678436279297 0.5099124908447266 0.7895496 0.297340452671051 True -7 10408 14.39374327659607 0.2624647617340088 181.1590576171875 0.24390622973442078 211.48130798339844 0.5114331245422363 0.79507124 0.2581210434436798 True -8 11709 14.422998905181885 0.25911712646484375 181.85260009765625 0.3790106177330017 211.0564422607422 0.513120174407959 0.7970654 0.254129022359848 True -9 13010 14.383276462554932 0.26529979705810547 177.7134246826172 0.1952441930770874 210.693359375 0.5145984292030334 0.80067086 0.23785869777202606 True -10 14311 14.406862020492554 0.25850462913513184 175.107177734375 0.3557872772216797 210.4544219970703 0.5157753229141235 0.8028789 0.26854339241981506 True -11 15612 14.37219762802124 0.2522099018096924 152.48922729492188 0.3286135792732239 210.0689697265625 0.5172372460365295 0.80898386 0.2371213287115097 True -12 16913 14.382853507995605 0.26459479331970215 155.66903686523438 0.23144608736038208 209.8067169189453 0.5183160305023193 0.81214255 0.21811577677726746 True -13 18214 14.42364764213562 0.2838282585144043 177.6641082763672 0.18131428956985474 209.5749053955078 0.5192476511001587 0.8177355 0.21140079200267792 True -14 19515 14.412402153015137 0.9785208702087402 145.94444274902344 0.2130778282880783 209.55860900878906 0.5192776322364807 0.82140315 0.2085776925086975 True -15 20816 14.379611730575562 0.2596879005432129 172.584228515625 0.20871959626674652 209.64102172851562 0.518695056438446 0.8227175 0.21033795177936554 True -16 22117 14.231858015060425 0.29355621337890625 166.83749389648438 0.16530688107013702 209.89309692382812 0.5172925591468811 0.82299143 0.21341662108898163 True -17 23418 14.134443521499634 0.25648021697998047 148.30020141601562 0.21977657079696655 210.20635986328125 0.515598475933075 0.82177377 0.21750092506408691 False -18 24719 14.128682374954224 0.27042198181152344 173.36065673828125 0.13773474097251892 210.555419921875 0.513902485370636 0.819786 0.2207442969083786 False -19 26020 14.124459981918335 0.25374937057495117 163.22943115234375 0.15738718211650848 210.72543334960938 0.5128603577613831 0.8183475 0.22336101531982422 False diff --git a/ENCSR851EBF/cherimoya.fold_2.performance.tsv b/ENCSR851EBF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c814271eabcd89357faee232ff63cb65f1c810b3..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -209.89309692382812 0.3820001780986786 0.5172925591468811 0.14237014949321747 0.8229914307594299 0.8071768283843994 0.21341662108898163 \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_3.evaluate.json b/ENCSR851EBF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c9939875fcec33efde287b48f49bd27f2ac83684..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF335YBU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_3.fit.json b/ENCSR851EBF/cherimoya.fold_3.fit.json deleted file mode 100644 index 07ffe575983550787c343ba63646bd67cdc4d999..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF335YBU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_3.log b/ENCSR851EBF/cherimoya.fold_3.log deleted file mode 100644 index e8f62d53f85b23a8933130c54cb92d8f88f52054..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1269 18.477970361709595 3.553882122039795 206.2268524169922 0.27935004234313965 258.3747253417969 0.36793121695518494 0.6947386 12.067124366760254 True -1 2538 14.056259393692017 0.25904083251953125 193.81040954589844 0.4142005443572998 221.0358428955078 0.44440484046936035 0.7536163 2.8354990482330322 True -2 3807 14.035718441009521 0.2548830509185791 171.61788940429688 0.45781567692756653 212.86276245117188 0.4701998233795166 0.77677256 0.9281044602394104 True -3 5076 14.023820161819458 0.24082446098327637 187.8111572265625 0.32254937291145325 207.5101776123047 0.48829540610313416 0.79833865 0.4293995797634125 True -4 6345 14.021628618240356 0.23803925514221191 186.60536193847656 0.29118698835372925 205.32772827148438 0.49661439657211304 0.8080687 0.3440811336040497 True -5 7614 14.027174949645996 0.24947047233581543 155.19366455078125 0.2976643443107605 204.9042205810547 0.4985792934894562 0.8102821 0.4520804286003113 True -6 8883 14.038995742797852 0.2502868175506592 160.3909454345703 0.288663387298584 204.3148956298828 0.5014441013336182 0.8122718 0.31373172998428345 True -7 10152 14.036348819732666 1.0414233207702637 173.11077880859375 0.24445712566375732 203.89752197265625 0.5036466121673584 0.8145306 0.26653367280960083 True -8 11421 14.039368629455566 0.24061822891235352 171.30845642089844 0.4412228763103485 203.53172302246094 0.5052048563957214 0.8186648 0.24194224178791046 True -9 12690 14.055615425109863 0.2432396411895752 178.10092163085938 0.2607143223285675 203.17478942871094 0.5065897703170776 0.821351 0.22875969111919403 True -10 13959 14.059170484542847 0.24236059188842773 181.9772491455078 0.22716329991817474 202.8936309814453 0.5077381730079651 0.82239836 0.2239522635936737 True -11 15228 14.06376600265503 0.24474167823791504 166.16049194335938 0.2290828824043274 202.5273895263672 0.5091829895973206 0.82617027 0.2177911102771759 True -12 16497 14.072888612747192 0.23918747901916504 152.38902282714844 0.17124098539352417 202.27484130859375 0.5102476477622986 0.8271858 0.2123514711856842 True -13 17766 14.048655271530151 0.24047350883483887 168.6972198486328 0.20780430734157562 202.07589721679688 0.5110804438591003 0.82917094 0.20331867039203644 True -14 19035 14.084326267242432 0.2507052421569824 158.77371215820312 0.2551015615463257 201.9523468017578 0.5114195346832275 0.8307741 0.19991274178028107 True -15 20304 14.066518068313599 0.24569416046142578 164.38436889648438 0.13276682794094086 201.97091674804688 0.511069118976593 0.8335683 0.19940900802612305 True -16 21573 14.095499753952026 1.0876109600067139 174.56875610351562 0.14240917563438416 202.18804931640625 0.5097622871398926 0.8320671 0.19922903180122375 False -17 22842 14.08303713798523 0.25664782524108887 155.718994140625 0.17966116964817047 202.48594665527344 0.5082292556762695 0.831553 0.2011454850435257 False -18 24111 14.086588621139526 0.24810314178466797 196.00042724609375 0.13353483378887177 202.7617950439453 0.5067294239997864 0.8292748 0.20262311398983002 False -19 25380 14.089280843734741 0.24681949615478516 160.25491333007812 0.18629969656467438 202.9572296142578 0.5057215690612793 0.82775116 0.20431271195411682 False diff --git a/ENCSR851EBF/cherimoya.fold_3.performance.tsv b/ENCSR851EBF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fd955bda7cdcc087d308834421872734ba01267f..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.97091674804688 0.3871619999408722 0.511069118976593 0.13575826585292816 0.833568274974823 0.8134320378303528 0.19940900802612305 \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_4.evaluate.json b/ENCSR851EBF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b8c01dc4b05d4ebf7f5c91964f6683e76208d26c..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF335YBU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_4.fit.json b/ENCSR851EBF/cherimoya.fold_4.fit.json deleted file mode 100644 index 7bcd93a4cee3bf518221b99094f5c19fa78891c6..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF335YBU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851EBF/cherimoya.fold_4.log b/ENCSR851EBF/cherimoya.fold_4.log deleted file mode 100644 index 497377b59433df3cf9d7241cc869ee3fe6a49c7f..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1261 18.240659475326538 3.293780565261841 171.7857666015625 0.3986867070198059 254.79705810546875 0.36760544776916504 0.7019463 12.115729331970215 True -1 2522 14.00706148147583 0.8716058731079102 178.035400390625 0.36175984144210815 219.45838928222656 0.4397299587726593 0.7403723 2.684464931488037 True -2 3783 14.002372026443481 0.2986295223236084 168.91021728515625 0.3381579518318176 210.23678588867188 0.46856188774108887 0.75965375 0.647727370262146 True -3 5044 13.987802028656006 0.25899505615234375 156.36878967285156 0.3435016870498657 204.46401977539062 0.4888254404067993 0.7888588 0.3480404317378998 True -4 6305 13.958243370056152 0.26169705390930176 173.55703735351562 0.1888531744480133 203.24549865722656 0.4925694763660431 0.7937412 0.34198516607284546 True -5 7566 13.99040675163269 0.25236034393310547 159.10623168945312 0.34925293922424316 202.21908569335938 0.49648240208625793 0.7995569 0.2906376123428345 True -6 8827 13.989130020141602 0.24405980110168457 154.38421630859375 0.20207437872886658 201.65219116210938 0.49907538294792175 0.8047804 0.26300859451293945 True -7 10088 13.992689371109009 0.9408013820648193 160.08041381835938 0.2346351146697998 201.25601196289062 0.5006769895553589 0.810094 0.23763689398765564 True -8 11349 13.97485065460205 0.25421142578125 177.16961669921875 0.16728416085243225 201.0390167236328 0.5017116665840149 0.8129788 0.2246636301279068 True -9 12610 14.207395076751709 9.281959056854248 167.80047607421875 0.2641838788986206 200.69522094726562 0.5032901167869568 0.8172324 0.21023494005203247 True -10 13871 14.048217058181763 0.25818824768066406 182.7500762939453 0.14967969059944153 200.3883056640625 0.5042644739151001 0.8210536 0.19971926510334015 True -11 15132 13.969836235046387 0.2627999782562256 171.96212768554688 0.20812390744686127 200.19859313964844 0.5050073862075806 0.82607925 0.19726911187171936 True -12 16393 14.011426448822021 0.24839329719543457 173.17800903320312 0.182417631149292 199.91830444335938 0.5061225295066833 0.83047575 0.18840721249580383 True -13 17654 13.961124420166016 0.2658348083496094 170.90823364257812 0.24732641875743866 199.76065063476562 0.5067822933197021 0.83280915 0.186269149184227 True -14 18915 13.96575140953064 0.25255608558654785 162.54098510742188 0.14846119284629822 199.71975708007812 0.5068573951721191 0.83493817 0.18240763247013092 True -15 20176 14.009025573730469 0.24565839767456055 157.1771240234375 0.18509113788604736 199.81358337402344 0.5066311359405518 0.8377518 0.18130382895469666 True -16 21437 14.00989842414856 0.25197291374206543 172.0424041748047 0.22495761513710022 200.02792358398438 0.5053736567497253 0.83971196 0.18501479923725128 True -17 22698 14.00739073753357 0.2470409870147705 159.16961669921875 0.12876641750335693 200.3135986328125 0.5036985278129578 0.8396524 0.1885320544242859 False -18 23959 14.007968664169312 0.2495288848876953 179.82855224609375 0.12648898363113403 200.62265014648438 0.5020579695701599 0.83762425 0.19193170964717865 False -19 25220 13.993880987167358 0.24683904647827148 164.953369140625 0.19527634978294373 200.82337951660156 0.5010402202606201 0.8357679 0.19600674510002136 False diff --git a/ENCSR851EBF/cherimoya.fold_4.performance.tsv b/ENCSR851EBF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0516dbce301478b69ee392d28801cb257965ee20..0000000000000000000000000000000000000000 --- a/ENCSR851EBF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -200.02792358398438 0.38978996872901917 0.5053736567497253 0.13274362683296204 0.8397119641304016 0.8068262338638306 0.18501479923725128 \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_0.evaluate.json b/ENCSR851SBY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 89cafa6108a1762891d52841993baa628c988602..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF668OMF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_0.fit.json b/ENCSR851SBY/cherimoya.fold_0.fit.json deleted file mode 100644 index 7f057322cc9b55edb6ee78bb3462e5b9ca502097..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF668OMF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_0.log b/ENCSR851SBY/cherimoya.fold_0.log deleted file mode 100644 index 739709d30121579f9c2ec3a848e09ba3e2a4913a..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1434 19.5981707572937 16.73851728439331 252.12416076660156 0.26969611644744873 439.75555419921875 0.46976208686828613 0.6943787 15.098002433776855 True -1 2868 15.824405908584595 0.30609703063964844 311.4769287109375 0.4440935254096985 361.7183532714844 0.5667984485626221 0.77089036 3.432199716567993 True -2 4302 16.0892391204834 0.7426893711090088 318.05706787109375 0.324574738740921 340.7906188964844 0.6033233404159546 0.79603547 0.889340341091156 True -3 5736 15.76006555557251 0.2821364402770996 276.57598876953125 0.2491716742515564 330.2623291015625 0.622036337852478 0.81575793 0.4086098074913025 True -4 7170 15.77531123161316 0.28241491317749023 275.041748046875 0.24468104541301727 328.77386474609375 0.6223946809768677 0.8164336 0.33420607447624207 True -5 8604 15.759719133377075 0.281888484954834 273.4337158203125 0.2212591916322708 326.8628234863281 0.6284894943237305 0.8235556 0.30258819460868835 True -6 10038 15.775124311447144 0.28231263160705566 275.23699951171875 0.12138162553310394 325.4722900390625 0.631868839263916 0.83206624 0.25105518102645874 True -7 11472 15.770043849945068 0.28528761863708496 291.0628356933594 0.1717624068260193 324.54547119140625 0.6342292428016663 0.8343685 0.21947409212589264 True -8 12906 15.753100156784058 0.2814059257507324 261.0579833984375 0.22518132627010345 324.1177062988281 0.635516881942749 0.8355797 0.2241288423538208 True -9 14340 15.728802919387817 0.2849409580230713 263.6310119628906 0.2198891043663025 323.4656982421875 0.6369152069091797 0.83910406 0.22245100140571594 True -10 15774 15.73410964012146 0.28028011322021484 299.3720397949219 0.15087993443012238 322.5340881347656 0.6389004588127136 0.84281045 0.1942508965730667 True -11 17208 15.735153436660767 0.28006601333618164 274.9248046875 0.17315801978111267 321.80523681640625 0.6405344605445862 0.84559005 0.1857895851135254 True -12 18642 15.733705520629883 0.27967333793640137 274.114990234375 0.11707709729671478 321.42901611328125 0.6414450407028198 0.8508944 0.18223069608211517 True -13 20076 15.740675926208496 0.2803938388824463 269.22381591796875 0.13385018706321716 321.06927490234375 0.6421793103218079 0.8545531 0.17950928211212158 True -14 21510 15.743147850036621 0.28367161750793457 262.5107421875 0.15545716881752014 320.9588928222656 0.6423718929290771 0.85863745 0.17285595834255219 True -15 22944 15.74197793006897 1.0200715065002441 246.28839111328125 0.14407342672348022 320.9728088378906 0.642365038394928 0.8609572 0.1687280535697937 True -16 24378 15.794080972671509 0.2859952449798584 288.5579833984375 0.18451088666915894 321.1295471191406 0.6419845819473267 0.8611017 0.1644624024629593 True -17 25812 15.774893522262573 0.2808387279510498 269.9337158203125 0.11268357187509537 321.4353332519531 0.6412421464920044 0.8594223 0.1652373969554901 False -18 27246 15.73711371421814 0.2806260585784912 257.8861999511719 0.1391656994819641 321.74920654296875 0.6404039859771729 0.85818166 0.1644936501979828 False -19 28680 15.75252652168274 0.28075480461120605 274.16339111328125 0.13211007416248322 321.8963928222656 0.6399032473564148 0.8565968 0.16433148086071014 False diff --git a/ENCSR851SBY/cherimoya.fold_0.performance.tsv b/ENCSR851SBY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 23f85fd1ee132386fb518d97a7c80f2f87af2b19..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -321.1295471191406 0.292455792427063 0.6419846415519714 0.2291116565465927 0.8611016869544983 0.8130316138267517 0.1644624024629593 \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_1.evaluate.json b/ENCSR851SBY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 73ed4e5ec8b598bacd6c1bdc9b3534531e94bf35..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF668OMF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_1.fit.json b/ENCSR851SBY/cherimoya.fold_1.fit.json deleted file mode 100644 index fd53d5266fa0da3c14f0c251c5f1476493ffc5f4..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF668OMF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_1.log b/ENCSR851SBY/cherimoya.fold_1.log deleted file mode 100644 index 3fc511e7eefecf329caae7c5e20bf6ee07e65f8d..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1393 18.914232969284058 3.6678121089935303 278.34429931640625 0.3473445177078247 473.68853759765625 0.47689288854599 0.63492906 16.584659576416016 True -1 2786 15.36308479309082 0.4054231643676758 256.5116882324219 0.38478636741638184 385.0940856933594 0.5818824172019958 0.7229212 3.3175346851348877 True -2 4179 15.363561391830444 0.39178919792175293 289.12548828125 0.2515357732772827 364.5286865234375 0.6175922751426697 0.7514699 1.018301248550415 True -3 5572 15.400373220443726 0.3982870578765869 272.3597412109375 0.18900631368160248 352.5091247558594 0.6390763521194458 0.7770914 0.40135276317596436 True -4 6965 15.356413841247559 0.39345288276672363 296.6084289550781 0.2931843400001526 349.3276062011719 0.6453040242195129 0.79038274 0.3095540702342987 True -5 8358 15.395033836364746 0.3892219066619873 266.9735412597656 0.21469751000404358 350.4109802246094 0.6414848566055298 0.787431 0.3182017505168915 False -6 9751 15.348750114440918 0.39621520042419434 266.95831298828125 0.17144013941287994 348.613525390625 0.6467840671539307 0.7975611 0.278969407081604 True -7 11144 15.37168264389038 0.3828153610229492 274.1389465332031 0.21018445491790771 346.8778991699219 0.6508885622024536 0.8047875 0.25009819865226746 True -8 12537 15.373208284378052 0.6265957355499268 277.9609375 0.24615955352783203 345.8896484375 0.6532986760139465 0.8103956 0.22411960363388062 True -9 13930 15.461827993392944 7.479564666748047 271.56134033203125 0.1781993806362152 345.3548583984375 0.6544460654258728 0.81336355 0.21760383248329163 True -10 15323 15.388670206069946 0.3828887939453125 261.70977783203125 0.15540990233421326 344.8858947753906 0.6552476286888123 0.81484437 0.2382802963256836 True -11 16716 15.37636423110962 0.39815306663513184 273.64227294921875 0.17958730459213257 343.6811828613281 0.6577490568161011 0.8224558 0.217227503657341 True -12 18109 15.390290260314941 0.38616085052490234 259.4053649902344 0.12840023636817932 342.9619445800781 0.6593798398971558 0.8285817 0.19953104853630066 True -13 19502 15.39067029953003 0.3839285373687744 266.91510009765625 0.1956603229045868 342.5332336425781 0.6604587435722351 0.832652 0.19532649219036102 True -14 20895 15.365657091140747 0.3905308246612549 260.4346923828125 0.168885737657547 342.3082275390625 0.6609556674957275 0.83512694 0.18806086480617523 True -15 22288 15.3749418258667 0.38739609718322754 250.9383087158203 0.15532879531383514 342.268310546875 0.6608838438987732 0.8386101 0.18241441249847412 True -16 23681 15.33462929725647 0.3842742443084717 268.9534912109375 0.12235298752784729 342.4297180175781 0.6606578230857849 0.8410867 0.17849768698215485 True -17 25074 15.326480865478516 0.3869643211364746 239.37637329101562 0.08489940315485 342.71636962890625 0.6597331762313843 0.84082305 0.1765165477991104 False -18 26467 15.310925722122192 0.38254833221435547 249.60928344726562 0.14574740827083588 343.0631408691406 0.6588103771209717 0.83946717 0.17410193383693695 False -19 27860 15.306506156921387 0.3752920627593994 263.02679443359375 0.08284623920917511 343.2841796875 0.6581466794013977 0.8379868 0.1741471141576767 False diff --git a/ENCSR851SBY/cherimoya.fold_1.performance.tsv b/ENCSR851SBY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4e80a5015691647b9306e9adfc38fe171df2cd32..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -342.4297180175781 0.27840644121170044 0.6606578230857849 0.24671688675880432 0.8410866856575012 0.8193284869194031 0.17849768698215485 \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_2.evaluate.json b/ENCSR851SBY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9b9a7e0e97d2bb6b474bd508fccc328630b6e24b..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF668OMF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_2.fit.json b/ENCSR851SBY/cherimoya.fold_2.fit.json deleted file mode 100644 index c086e9a6f4158bddff218313600bda37971bfcfe..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF668OMF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_2.log b/ENCSR851SBY/cherimoya.fold_2.log deleted file mode 100644 index 79080405725b1d53ab8f87345763633a9780afc9..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1488 20.35895013809204 3.216115951538086 315.66851806640625 0.31777727603912354 445.112548828125 0.4741094708442688 0.6479681 15.591919898986816 True -1 2976 16.56664752960205 0.3194880485534668 299.77410888671875 0.2394595444202423 368.7245788574219 0.5710574984550476 0.73594034 2.850916624069214 True -2 4464 16.37770938873291 0.320512056350708 279.4189758300781 0.2525350749492645 347.4625549316406 0.6109016537666321 0.7774368 0.7734211087226868 True -3 5952 16.380692958831787 0.2977254390716553 271.1824645996094 0.29670119285583496 337.4693603515625 0.6278926134109497 0.79630625 0.45808038115501404 True -4 7440 16.360366821289062 1.5399987697601318 238.52871704101562 0.24028518795967102 334.5436096191406 0.6338784098625183 0.8031385 0.3273647129535675 True -5 8928 16.38948702812195 0.29469895362854004 280.5875244140625 0.1717303991317749 332.9284973144531 0.6374101042747498 0.8104227 0.24141453206539154 True -6 10416 16.35988140106201 0.29737305641174316 262.5062255859375 0.17780381441116333 332.4163818359375 0.6388031244277954 0.8153406 0.2309035062789917 True -7 11904 16.372394323349 0.29401469230651855 261.6426696777344 0.18907400965690613 331.83892822265625 0.6399773359298706 0.81897634 0.2398536056280136 True -8 13392 16.394351482391357 0.7772383689880371 266.2965393066406 0.16136972606182098 330.9562683105469 0.6418788433074951 0.82439846 0.20709481835365295 True -9 14880 16.394495964050293 0.29520344734191895 273.52215576171875 0.22552329301834106 330.3169250488281 0.643860936164856 0.82766724 0.20241332054138184 True -10 16368 16.351107597351074 0.29144906997680664 276.66180419921875 0.15413731336593628 329.7956848144531 0.6452597975730896 0.8305807 0.19957679510116577 True -11 17856 16.34179186820984 0.29410362243652344 261.4042663574219 0.22867122292518616 328.993896484375 0.6471264958381653 0.83335197 0.196172297000885 True -12 19344 16.342936515808105 0.29090213775634766 275.3471984863281 0.12948726117610931 328.531982421875 0.6482335329055786 0.83676136 0.19377203285694122 True -13 20832 16.346538066864014 0.2924180030822754 283.9627685546875 0.16542492806911469 328.125 0.6491039991378784 0.8390918 0.19163425266742706 True -14 22320 16.37367868423462 0.2909824848175049 291.59954833984375 0.12689751386642456 327.9626159667969 0.6493380665779114 0.8419599 0.18506178259849548 True -15 23808 16.375075578689575 0.293393611907959 268.74322509765625 0.1492486596107483 327.99505615234375 0.6493673324584961 0.84305894 0.18011727929115295 True -16 25296 16.385894298553467 0.29621195793151855 267.92431640625 0.11821427196264267 328.0729675292969 0.6490021347999573 0.8450291 0.17652291059494019 True -17 26784 16.389784574508667 0.29381227493286133 267.96539306640625 0.09304440021514893 328.3617248535156 0.6482546925544739 0.8425642 0.17610035836696625 False -18 28272 16.36277198791504 0.29492783546447754 278.7162170410156 0.06271148473024368 328.7156982421875 0.6474153399467468 0.84117424 0.17785240709781647 False -19 29760 16.35254693031311 0.2923591136932373 276.18359375 0.11490361392498016 328.9280090332031 0.6468138098716736 0.84020656 0.1767975091934204 False diff --git a/ENCSR851SBY/cherimoya.fold_2.performance.tsv b/ENCSR851SBY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b548bf6b38ecbcd6de2d8c815a914d4f6fedc225..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -328.0729675292969 0.28743162751197815 0.6490021347999573 0.23657482862472534 0.8450291156768799 0.8099714517593384 0.17652291059494019 \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_3.evaluate.json b/ENCSR851SBY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9b0f577d039e8b639b3798bc5c464d1221de68a6..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF668OMF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_3.fit.json b/ENCSR851SBY/cherimoya.fold_3.fit.json deleted file mode 100644 index 8e810cd5a5320563a4887c2beb8783abd7c2d668..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF668OMF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_3.log b/ENCSR851SBY/cherimoya.fold_3.log deleted file mode 100644 index 302bd6e8de08ffee581d80ca4568574858e62b0a..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1450 20.120521783828735 3.2533349990844727 275.2769470214844 0.3388286530971527 431.2321472167969 0.4690372049808502 0.6683506 15.524840354919434 True -1 2900 16.00490951538086 0.3029904365539551 254.50704956054688 0.37015968561172485 356.3857421875 0.5665192604064941 0.74924475 3.173203706741333 True -2 4350 16.289341688156128 0.29373621940612793 269.408447265625 0.24779294431209564 338.5085144042969 0.6010359525680542 0.77401525 0.638507604598999 True -3 5800 15.997355699539185 0.2987043857574463 279.3086853027344 0.2419261336326599 328.5057678222656 0.6200755834579468 0.80011195 0.3212588131427765 True -4 7250 16.007518768310547 0.2905604839324951 269.4228210449219 0.2446238100528717 325.56878662109375 0.6258167028427124 0.80644643 0.3146275281906128 True -5 8700 15.990491390228271 0.2935824394226074 319.4508972167969 0.21452035009860992 324.3081359863281 0.6285059452056885 0.8112019 0.28158360719680786 True -6 10150 16.00252938270569 0.29395461082458496 262.905517578125 0.2702069878578186 323.39697265625 0.6310144066810608 0.8143795 0.23831762373447418 True -7 11600 15.961645603179932 0.29103565216064453 293.64544677734375 0.2044622004032135 322.47113037109375 0.6327521800994873 0.8195114 0.22389085590839386 True -8 13050 15.959580898284912 0.29497408866882324 255.2123565673828 0.1636747419834137 321.78369140625 0.6342371702194214 0.81730086 0.21421962976455688 False -9 14500 15.957382202148438 1.2529575824737549 256.49407958984375 0.22795212268829346 321.3193664550781 0.6355510950088501 0.8219651 0.21432411670684814 True -10 15950 16.00820541381836 0.2958993911743164 290.6949462890625 0.17110471427440643 320.59173583984375 0.6372677087783813 0.82374066 0.2141280323266983 True -11 17400 15.964903831481934 0.2953026294708252 281.874267578125 0.1305975615978241 320.1485595703125 0.6384326219558716 0.8262827 0.1986386775970459 True -12 18850 15.967384099960327 0.2912476062774658 263.677490234375 0.1266382336616516 319.7866516113281 0.6396386027336121 0.8274943 0.19250521063804626 True -13 20300 16.01273202896118 0.29773545265197754 270.949462890625 0.17060548067092896 319.5506286621094 0.64022296667099 0.8296111 0.1921912431716919 True -14 21750 15.991538763046265 0.2944517135620117 266.69708251953125 0.1547161042690277 319.32745361328125 0.6406910419464111 0.833376 0.18769124150276184 True -15 23200 15.989578008651733 0.29495906829833984 298.36181640625 0.09119504690170288 319.3189697265625 0.6406075954437256 0.8351347 0.1844223439693451 True -16 24650 15.961035966873169 0.2940175533294678 273.1948547363281 0.10485690087080002 319.48846435546875 0.6400436758995056 0.8378176 0.18298432230949402 True -17 26100 15.93239712715149 0.2936229705810547 277.88836669921875 0.10673591494560242 319.76031494140625 0.6391034722328186 0.8356948 0.18290963768959045 False -18 27550 15.947296857833862 0.46680116653442383 284.75543212890625 0.06383736431598663 320.2178039550781 0.6381841897964478 0.835319 0.18548181653022766 False -19 29000 15.9847571849823 0.29737353324890137 292.72283935546875 0.11093603819608688 320.3297424316406 0.6376048922538757 0.83187807 0.18808947503566742 False diff --git a/ENCSR851SBY/cherimoya.fold_3.performance.tsv b/ENCSR851SBY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2001a81bc4fcadeaa87c398a718ff650c8e55f71..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -319.48846435546875 0.29289546608924866 0.6400436758995056 0.22890371084213257 0.8378176093101501 0.7945153117179871 0.18298432230949402 \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_4.evaluate.json b/ENCSR851SBY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 302375b47ea515090a964f19598686ceab35ce9e..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF668OMF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_4.fit.json b/ENCSR851SBY/cherimoya.fold_4.fit.json deleted file mode 100644 index 49696c21e0b1ca39eb23c12c68532fea3df300a9..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF668OMF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851SBY/cherimoya.fold_4.log b/ENCSR851SBY/cherimoya.fold_4.log deleted file mode 100644 index 3ab8e7c93eb86aa604a4205f0d56a3a582a4b260..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1464 19.787054300308228 3.183248519897461 275.8486633300781 0.314889132976532 419.8168640136719 0.46528342366218567 0.68048555 14.996933937072754 True -1 2928 16.126206159591675 0.29644083976745605 285.8353271484375 0.26303088665008545 346.93157958984375 0.5637568831443787 0.7470826 2.7134199142456055 True -2 4392 16.129617929458618 0.27518153190612793 294.951416015625 0.1988338828086853 327.6289978027344 0.602596640586853 0.7831076 0.6625618934631348 True -3 5856 16.110570192337036 0.27384233474731445 266.702392578125 0.3809822201728821 320.86077880859375 0.6152772307395935 0.80471236 0.35040977597236633 True -4 7320 16.133881092071533 0.2708711624145508 270.38861083984375 0.25394564867019653 317.51312255859375 0.6227198839187622 0.8164431 0.2992927134037018 True -5 8784 16.11211848258972 0.27402162551879883 253.4716796875 0.31458011269569397 317.0266418457031 0.6229868531227112 0.8176613 0.2801007032394409 True -6 10248 16.139936208724976 0.27284932136535645 299.43511962890625 0.14118720591068268 315.7610168457031 0.6264075040817261 0.8274162 0.23938658833503723 True -7 11712 16.136420726776123 0.2716853618621826 279.0013427734375 0.28537431359291077 316.3348388671875 0.6245189905166626 0.81958544 0.30476823449134827 False -8 13176 16.147486209869385 0.27588343620300293 265.76104736328125 0.15660731494426727 314.4971923828125 0.6291520595550537 0.82973963 0.24372901022434235 True -9 14640 16.17662477493286 0.3096945285797119 265.7118835449219 0.216831237077713 313.56207275390625 0.6314369440078735 0.8380957 0.20901493728160858 True -10 16104 16.108847856521606 0.27597594261169434 260.27850341796875 0.1952187716960907 313.0050964355469 0.6329105496406555 0.8424985 0.1895321160554886 True -11 17568 16.120999336242676 0.27245497703552246 286.8869934082031 0.13854511082172394 312.4600830078125 0.6344001889228821 0.84423494 0.1717173159122467 True -12 19032 16.150954723358154 1.630936861038208 264.3675537109375 0.22826871275901794 312.1567077636719 0.6349741816520691 0.84687346 0.16598771512508392 True -13 20496 16.162299394607544 0.5371315479278564 248.265869140625 0.14591266214847565 311.7391357421875 0.6358542442321777 0.85143685 0.15777552127838135 True -14 21960 16.178110599517822 0.27546000480651855 231.91912841796875 0.1972775012254715 311.6176452636719 0.6362707614898682 0.8555748 0.15232320129871368 True -15 23424 16.130351066589355 0.27480316162109375 282.56072998046875 0.204187273979187 311.572998046875 0.6364076733589172 0.85806227 0.14728869497776031 True -16 24888 16.17179036140442 0.27649736404418945 266.80096435546875 0.09994151443243027 311.739501953125 0.6358201503753662 0.86023194 0.1453307569026947 True -17 26352 16.125288009643555 0.2709968090057373 267.905029296875 0.09616963565349579 312.0062255859375 0.6350319981575012 0.85985494 0.1427851915359497 False -18 27816 16.15176010131836 0.271364688873291 253.6235809326172 0.05968696251511574 312.3077087402344 0.6341214776039124 0.85903835 0.14392566680908203 False -19 29280 16.121344089508057 0.2783994674682617 261.250244140625 0.10932125896215439 312.564453125 0.6334061622619629 0.8575423 0.1444506198167801 False diff --git a/ENCSR851SBY/cherimoya.fold_4.performance.tsv b/ENCSR851SBY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 703f0dffd8bb0d0383b288b0197e095a71cebf5e..0000000000000000000000000000000000000000 --- a/ENCSR851SBY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -311.739501953125 0.29727956652641296 0.6358200311660767 0.22427162528038025 0.8602319359779358 0.8040673732757568 0.1453307569026947 \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_0.evaluate.json b/ENCSR851ZFT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 37644acd12824e99e2253972cd1e0025c9582c1d..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495DPV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_0.fit.json b/ENCSR851ZFT/cherimoya.fold_0.fit.json deleted file mode 100644 index 21acce4cab8929f413746f9ed6b6404d3035071d..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF495DPV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_0.log b/ENCSR851ZFT/cherimoya.fold_0.log deleted file mode 100644 index 2eb1c89d08c3f27b2ea10abcd2f20dee191a13cc..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.59070920944214 4.524574041366577 238.4573974609375 0.8174364566802979 303.72991943359375 0.1677425652742386 0.6525904 3.7431912422180176 True -1 5478 30.206904649734497 0.8795242309570312 198.34300231933594 0.5000380277633667 287.173095703125 0.23754055798053741 0.6929973 1.2761372327804565 True -2 8217 30.25113320350647 0.5717456340789795 197.267822265625 0.5405114889144897 282.19720458984375 0.2540808916091919 0.7058195 0.7205948233604431 True -3 10956 30.20908832550049 0.5701396465301514 263.44281005859375 1.0205527544021606 280.1775817871094 0.2590184807777405 0.71133107 0.6066973805427551 True -4 13695 30.255249977111816 0.5720970630645752 242.3145294189453 0.7804689407348633 279.3578796386719 0.2615925967693329 0.71492743 0.6557166576385498 True -5 16434 30.232858419418335 0.57157301902771 239.24371337890625 0.8029173016548157 278.2613830566406 0.26603370904922485 0.71231866 0.6315107941627502 False -6 19173 30.241695404052734 0.564633846282959 249.82440185546875 0.4896681308746338 276.9822082519531 0.2721109390258789 0.71445036 0.6310219168663025 False -7 21912 30.357219457626343 0.5708763599395752 241.725830078125 0.5636645555496216 276.235595703125 0.2754100561141968 0.7195328 0.6044306755065918 True -8 24651 30.261130809783936 0.5710241794586182 191.03587341308594 0.7316814661026001 275.8337097167969 0.2764647901058197 0.71764123 0.6127116680145264 False -9 27390 29.97754693031311 14.82154107093811 214.28067016601562 0.5022457838058472 275.07904052734375 0.27976855635643005 0.724466 0.5631648302078247 True -10 30129 29.648002862930298 0.5776007175445557 245.9381103515625 0.8805398941040039 274.6764221191406 0.2810554504394531 0.72979814 0.5227288007736206 True -11 32868 29.764227151870728 1.8161396980285645 218.58775329589844 0.5098615288734436 273.909423828125 0.2845434546470642 0.73498684 0.5073281526565552 True -12 35607 29.78242540359497 0.5660934448242188 208.5703125 0.6575162410736084 273.4478759765625 0.28573593497276306 0.73972744 0.4688783884048462 True -13 38346 29.671327114105225 0.5640990734100342 220.70321655273438 0.38632383942604065 272.5964660644531 0.2895694375038147 0.74558014 0.44168299436569214 True -14 41085 29.657048225402832 0.5647115707397461 228.1014862060547 0.5439033508300781 272.4195861816406 0.29017555713653564 0.75266224 0.4226301908493042 True -15 43824 29.642560482025146 0.5637166500091553 201.26211547851562 0.39001715183258057 272.08026123046875 0.29153138399124146 0.7582218 0.401460736989975 True -16 46563 29.923304319381714 3.343233585357666 225.62405395507812 0.40471699833869934 271.8076477050781 0.29293888807296753 0.76393753 0.3782685101032257 True -17 49302 29.735161066055298 1.158337116241455 226.58270263671875 0.35476741194725037 271.94610595703125 0.29143622517585754 0.7647766 0.370652973651886 True -18 52041 29.682324409484863 0.5982873439788818 210.900390625 0.3694947361946106 271.5408935546875 0.2941131591796875 0.76537645 0.3655244708061218 True -19 54780 29.702380895614624 0.5692470073699951 207.9694061279297 0.4944778084754944 271.4550476074219 0.2946447730064392 0.7631404 0.368351012468338 False diff --git a/ENCSR851ZFT/cherimoya.fold_0.performance.tsv b/ENCSR851ZFT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index de67f0a97882a87f377833957e027e5aa355f9d5..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.5408935546875 0.4914934039115906 0.2941131889820099 0.07700362056493759 0.7653764486312866 0.713714599609375 0.3655244708061218 \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_1.evaluate.json b/ENCSR851ZFT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8db88a70d59a9275d8f50334bb90745f0efa4ab5..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495DPV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_1.fit.json b/ENCSR851ZFT/cherimoya.fold_1.fit.json deleted file mode 100644 index 45d3c42d4c8361223fa409d9bab379ef46891b60..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF495DPV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_1.log b/ENCSR851ZFT/cherimoya.fold_1.log deleted file mode 100644 index 918d826bd999b2de1888e157f23a28a0656e9647..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 34.559727907180786 3.875901222229004 206.39186096191406 0.7590221762657166 344.8016357421875 0.17968763411045074 0.65205246 3.928163766860962 True -1 5418 29.905617475509644 0.7221207618713379 231.795654296875 0.9470008611679077 322.6558837890625 0.2583315670490265 0.70226544 1.8936914205551147 True -2 8127 29.939165353775024 0.693871021270752 176.10015869140625 0.6180168390274048 317.2643737792969 0.27240800857543945 0.70624423 1.14690363407135 True -3 10836 29.9071786403656 0.6948380470275879 247.58078002929688 0.55998295545578 314.1597595214844 0.281756728887558 0.7147097 1.0465928316116333 True -4 13545 30.56699299812317 20.01271414756775 195.85113525390625 0.9353212118148804 312.93951416015625 0.28519317507743835 0.7203278 0.9721248745918274 True -5 16254 30.13343596458435 1.684650182723999 224.32049560546875 0.6707947254180908 312.183349609375 0.2876870930194855 0.72393054 0.9987794756889343 True -6 18963 30.174678325653076 0.9105629920959473 200.52557373046875 0.5906559228897095 311.1331787109375 0.29149946570396423 0.7296618 0.9137783050537109 True -7 21672 29.663915395736694 0.6990532875061035 211.60736083984375 0.6868401169776917 310.0610656738281 0.2949703335762024 0.7314335 0.9469103813171387 True -8 24381 29.771939277648926 0.6911485195159912 203.2858428955078 0.5238290429115295 310.0252380371094 0.2952854633331299 0.730623 0.9510034918785095 False -9 27090 29.715580940246582 0.6892397403717041 189.03298950195312 0.6793437004089355 308.63433837890625 0.3010995090007782 0.73390615 0.8523231148719788 True -10 29799 29.590734004974365 1.1873252391815186 218.43405151367188 0.45106855034828186 307.8909606933594 0.3035597503185272 0.73789203 0.8291864395141602 True -11 32508 29.4510235786438 0.6802346706390381 237.23292541503906 0.45307618379592896 306.936279296875 0.307110995054245 0.74174356 0.764218807220459 True -12 35217 29.602458953857422 0.6918075084686279 236.20738220214844 0.46228885650634766 306.023681640625 0.31011703610420227 0.75067747 0.6735942959785461 True -13 37926 30.049727201461792 39.36082935333252 238.81362915039062 0.4912952780723572 305.6473388671875 0.3105803430080414 0.75430024 0.6265767812728882 True -14 40635 29.42067575454712 1.5281987190246582 189.70018005371094 0.40272754430770874 305.2949523925781 0.31135255098342896 0.76349664 0.5578657984733582 True -15 43344 29.506523847579956 0.693242073059082 212.0816192626953 0.5905895233154297 304.67962646484375 0.3138507902622223 0.7720305 0.4866577088832855 True -16 46053 30.058438301086426 34.25675940513611 182.604248046875 0.342426061630249 304.47607421875 0.31378358602523804 0.77774006 0.4504336416721344 True -17 48762 29.327303171157837 0.6818585395812988 241.79803466796875 0.3129454553127289 304.40618896484375 0.3144398629665375 0.782061 0.41846564412117004 True -18 51471 29.432541847229004 0.6823651790618896 179.00173950195312 0.37722474336624146 304.3648681640625 0.3144262433052063 0.78187674 0.4098767638206482 False -19 54180 29.323415517807007 0.6820275783538818 179.11492919921875 0.44504374265670776 304.44952392578125 0.3145401179790497 0.7805383 0.40500307083129883 False diff --git a/ENCSR851ZFT/cherimoya.fold_1.performance.tsv b/ENCSR851ZFT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6cabf79dbef5b3d7147a1f0f1df839b9916abc5b..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -304.40618896484375 0.4740698039531708 0.3144398629665375 0.08779384940862656 0.782060980796814 0.7501663565635681 0.41846564412117004 \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_2.evaluate.json b/ENCSR851ZFT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1af83ec6114354c8cf29ce5203454de7f05aca6e..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495DPV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_2.fit.json b/ENCSR851ZFT/cherimoya.fold_2.fit.json deleted file mode 100644 index fb02f3fa05a02ccf47b6286c8cecc5f93595299b..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF495DPV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_2.log b/ENCSR851ZFT/cherimoya.fold_2.log deleted file mode 100644 index 3876a9944579772c98415a0dda96e87cc54d79eb..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2869 36.756699323654175 4.44598126411438 227.23541259765625 0.70154869556427 310.6426696777344 0.17566415667533875 0.636738 3.471341371536255 True -1 5738 31.70214557647705 0.5617160797119141 206.0075225830078 0.8859656453132629 292.4446105957031 0.24336519837379456 0.6968144 1.0713272094726562 True -2 8607 31.719400882720947 0.5341043472290039 225.7994384765625 0.6547515392303467 287.85748291015625 0.2563890814781189 0.7097507 0.8022640347480774 True -3 11476 31.69916272163391 0.5352978706359863 216.7806396484375 0.5917366743087769 285.4022216796875 0.26547321677207947 0.7130508 0.7306536436080933 True -4 14345 31.72129774093628 6.907348871231079 221.10198974609375 0.7425398826599121 284.4086608886719 0.2692887783050537 0.7112681 0.7728549838066101 False -5 17214 31.358840465545654 1.1051137447357178 256.96575927734375 0.49936747550964355 283.7961120605469 0.2718826234340668 0.71518844 0.7813501954078674 True -6 20083 31.08928894996643 0.5304121971130371 221.42068481445312 0.7367432117462158 282.7276306152344 0.2768101990222931 0.71229607 0.8420462608337402 False -7 22952 31.020957708358765 2.4270710945129395 244.2763214111328 0.6116772890090942 282.022705078125 0.27969083189964294 0.71423566 0.8077384233474731 False -8 25821 31.133885145187378 0.8877701759338379 187.493896484375 0.6155394911766052 281.3876037597656 0.28238674998283386 0.72042245 0.7804732918739319 True -9 28690 31.003044843673706 0.5378875732421875 193.88519287109375 0.5260927677154541 280.4307861328125 0.2856498956680298 0.724749 0.7332658171653748 True -10 31559 31.059263706207275 0.5327188968658447 234.57215881347656 0.6290837526321411 280.11383056640625 0.28684762120246887 0.7281583 0.7047927975654602 True -11 34428 31.04945707321167 0.5340831279754639 231.15676879882812 0.5177046656608582 279.2503356933594 0.28948357701301575 0.7370153 0.6117157340049744 True -12 37297 31.081923723220825 0.5280740261077881 226.1130828857422 0.5760400295257568 278.3412780761719 0.29344823956489563 0.74032104 0.5824989676475525 True -13 40166 31.04575824737549 0.528653621673584 197.12911987304688 0.6685218214988708 278.1891784667969 0.29363590478897095 0.74947757 0.5353171825408936 True -14 43035 31.056846380233765 0.5327863693237305 215.3466339111328 0.6400868892669678 277.53924560546875 0.2957970201969147 0.7517031 0.4898528456687927 True -15 45904 31.033159971237183 0.5348267555236816 219.07998657226562 0.5042506456375122 277.19091796875 0.2973998486995697 0.7595336 0.4531440734863281 True -16 48773 31.11901545524597 1.5353550910949707 195.97613525390625 0.3983363211154938 277.05523681640625 0.29771268367767334 0.7638377 0.4158777594566345 True -17 51642 31.202410459518433 24.377641916275024 250.83314514160156 0.3043120801448822 276.8484191894531 0.2976332902908325 0.7661858 0.3939184844493866 True -18 54511 31.081957817077637 27.216028690338135 245.061767578125 0.2801167964935303 277.1099548339844 0.2964071035385132 0.7664204 0.3904244303703308 True -19 57380 31.258737564086914 0.5420942306518555 238.51910400390625 0.35148704051971436 276.9113464355469 0.29788273572921753 0.7677422 0.38904163241386414 True diff --git a/ENCSR851ZFT/cherimoya.fold_2.performance.tsv b/ENCSR851ZFT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 645ed1757075aa68c3c68b355fc8a849a9cccb3a..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -276.9113464355469 0.4880900979042053 0.29788273572921753 0.0796305313706398 0.7677422165870667 0.7244591116905212 0.38904163241386414 \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_3.evaluate.json b/ENCSR851ZFT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ca040486f0d7dca8d4b5ea25a3bd713efb53c38d..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495DPV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_3.fit.json b/ENCSR851ZFT/cherimoya.fold_3.fit.json deleted file mode 100644 index 47082e17e4241dac347fabc86c11007d0aec2a71..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF495DPV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_3.log b/ENCSR851ZFT/cherimoya.fold_3.log deleted file mode 100644 index ff0fef6bbf572340a9361b6a7d29eb3b1ac98efa..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 35.02626299858093 4.3348963260650635 248.2187042236328 0.915066659450531 317.4410095214844 0.16911587119102478 0.6636555 4.209629058837891 True -1 5500 30.451419830322266 2.0039541721343994 216.70330810546875 1.0582808256149292 300.436279296875 0.24206389486789703 0.7023119 1.3845051527023315 True -2 8250 30.41672706604004 0.5678224563598633 237.73837280273438 0.8380981683731079 296.85589599609375 0.25019916892051697 0.71348864 0.7377897500991821 True -3 11000 30.29699730873108 0.5573689937591553 293.2237854003906 0.9870140552520752 294.32684326171875 0.2578701674938202 0.7204501 0.6616408824920654 True -4 13750 30.156523942947388 30.765791177749634 165.60977172851562 0.9585673809051514 292.7729797363281 0.26366448402404785 0.72065604 0.7487362623214722 True -5 16500 30.00234079360962 0.5599756240844727 227.97047424316406 0.7052385210990906 291.33966064453125 0.2700711190700531 0.7176552 0.7453204989433289 False -6 19250 29.841165781021118 0.553708553314209 205.61708068847656 0.9014819264411926 290.3074951171875 0.27379536628723145 0.72076875 0.7332719564437866 True -7 22000 29.8423752784729 0.6642954349517822 207.4179229736328 0.8344854712486267 290.00244140625 0.2738983929157257 0.71653193 0.6946525573730469 False -8 24750 29.801451683044434 0.5528371334075928 207.8846435546875 0.7146139144897461 289.37225341796875 0.27729693055152893 0.7173626 0.6587854027748108 False -9 27500 29.922511100769043 5.5905420780181885 267.21124267578125 0.7120921015739441 288.79949951171875 0.27943292260169983 0.72440606 0.6473199725151062 True -10 30250 29.82504963874817 39.63419222831726 197.80006408691406 0.4646168351173401 287.800048828125 0.2843967378139496 0.7253718 0.6682853102684021 True -11 33000 29.948678493499756 0.557816743850708 234.53025817871094 0.490471214056015 287.3285217285156 0.2860822379589081 0.73310643 0.5938252210617065 True -12 35750 30.646031141281128 14.548889875411987 203.308349609375 0.4567730128765106 286.6871032714844 0.28852126002311707 0.7364597 0.5821276903152466 True -13 38500 29.749463319778442 1.739762306213379 164.19073486328125 0.5282944440841675 286.3619689941406 0.2888738214969635 0.74221027 0.5369948148727417 True -14 41250 29.835979461669922 0.5433564186096191 198.23577880859375 0.4570288062095642 285.6574401855469 0.29166707396507263 0.7500639 0.5166782140731812 True -15 44000 29.884857654571533 2.070862054824829 246.68435668945312 0.25851812958717346 285.4232177734375 0.2924858033657074 0.7618694 0.4591655135154724 True -16 46750 29.833213806152344 0.5444610118865967 224.82049560546875 0.47163867950439453 284.9598388671875 0.2948683500289917 0.7684972 0.4209466576576233 True -17 49500 29.83372926712036 0.5512776374816895 218.72271728515625 0.42113471031188965 284.8121032714844 0.29500532150268555 0.7724747 0.39537444710731506 True -18 52250 29.830644607543945 0.5556602478027344 227.93594360351562 0.4521539807319641 284.7315979003906 0.2944762408733368 0.77405566 0.3876727819442749 True -19 55000 30.232057332992554 0.5413191318511963 210.62120056152344 0.29821842908859253 284.5342102050781 0.29548266530036926 0.7716382 0.3850596249103546 False diff --git a/ENCSR851ZFT/cherimoya.fold_3.performance.tsv b/ENCSR851ZFT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1fb57e7ce1c52e3c5ada9b11ceb9e6c4f50e047f..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -284.7315979003906 0.4883139431476593 0.2944762408733368 0.07893054932355881 0.7740556597709656 0.7239831686019897 0.3876727819442749 \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_4.evaluate.json b/ENCSR851ZFT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 879bca8482951ece597886140b3e1b075d6d2b8e..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF495DPV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_4.fit.json b/ENCSR851ZFT/cherimoya.fold_4.fit.json deleted file mode 100644 index 2b27612c461e1e240318c1369ba12e98eec0fe19..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF495DPV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR851ZFT/cherimoya.fold_4.log b/ENCSR851ZFT/cherimoya.fold_4.log deleted file mode 100644 index 3a54f882fdfc3c193d7b17a64e7fb214f30c5f72..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2825 35.612658977508545 3.578195333480835 236.09463500976562 1.0091962814331055 302.56256103515625 0.169648215174675 0.6412315 2.987579345703125 True -1 5650 31.122374057769775 0.6273820400238037 267.682373046875 0.8773675560951233 287.88653564453125 0.23280930519104004 0.68001324 1.1641526222229004 True -2 8475 30.870344161987305 0.6212875843048096 202.94097900390625 0.5368425846099854 283.9495849609375 0.24639660120010376 0.68893045 0.9716877937316895 True -3 11300 30.60393786430359 0.6011786460876465 224.1850128173828 0.6447898149490356 281.2374572753906 0.25480759143829346 0.70093906 0.8525392413139343 True -4 14125 30.573269605636597 0.8708803653717041 221.20993041992188 0.5438922047615051 279.50848388671875 0.26127108931541443 0.7064416 0.7442302703857422 True -5 16950 30.56327724456787 0.5977420806884766 256.1669616699219 0.6956164240837097 278.6377868652344 0.26479804515838623 0.70657337 0.7301533222198486 True -6 19775 30.87882089614868 0.6084825992584229 229.8017120361328 0.5919064283370972 277.74981689453125 0.2680143713951111 0.70942867 0.7181830406188965 True -7 22600 30.685242414474487 0.5877807140350342 224.7202606201172 0.6782281398773193 276.897705078125 0.27156057953834534 0.7097118 0.7342076897621155 True -8 25425 30.63477373123169 0.5967929363250732 167.235107421875 0.6587029099464417 276.1769104003906 0.27445656061172485 0.714938 0.6967394351959229 True -9 28250 30.548750638961792 0.5902156829833984 221.40283203125 0.46674323081970215 275.531982421875 0.2775668501853943 0.7127487 0.7586146593093872 False -10 31075 30.57055354118347 3.5015745162963867 223.36167907714844 0.6495445966720581 275.3819274902344 0.277999609708786 0.71652436 0.7240207195281982 True -11 33900 30.611604690551758 0.6004867553710938 199.5617218017578 0.6211790442466736 274.8251037597656 0.2801395356655121 0.722478 0.6426552534103394 True -12 36725 30.725977659225464 0.6230676174163818 228.54342651367188 0.45027193427085876 274.1762390136719 0.28272154927253723 0.726228 0.5990626215934753 True -13 39550 30.79487681388855 0.6029403209686279 210.09300231933594 0.46381455659866333 273.5058288574219 0.28526341915130615 0.7329621 0.5232617855072021 True -14 42375 30.875896215438843 1.5081608295440674 224.78048706054688 0.44765886664390564 273.2553405761719 0.285500168800354 0.7407533 0.47776156663894653 True -15 45200 31.280272245407104 22.178277254104614 171.97201538085938 0.4757365584373474 272.5439453125 0.2889561355113983 0.75082356 0.42151835560798645 True -16 48025 34.170098066329956 0.6098253726959229 186.91726684570312 0.583741307258606 272.4045715332031 0.28903722763061523 0.7579151 0.38815945386886597 True -17 50850 30.791541576385498 0.6076929569244385 233.35182189941406 0.28566038608551025 272.5108642578125 0.2890981137752533 0.76028854 0.37395691871643066 True -18 53675 30.692619800567627 1.2331442832946777 202.57473754882812 0.380281537771225 272.444580078125 0.2890966534614563 0.76105535 0.359589546918869 True -19 56500 30.618767023086548 0.6474075317382812 202.4783172607422 0.4261191189289093 272.5174560546875 0.28906455636024475 0.7610169 0.35951054096221924 False diff --git a/ENCSR851ZFT/cherimoya.fold_4.performance.tsv b/ENCSR851ZFT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 66a1ea35bedc3b02b7e311d77a874c3b99048622..0000000000000000000000000000000000000000 --- a/ENCSR851ZFT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -272.444580078125 0.49316874146461487 0.2890966236591339 0.07564893364906311 0.7610553503036499 0.7096095085144043 0.359589546918869 \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_0.evaluate.json b/ENCSR854TTM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2416214f61730da0b7390c4b6f4b2486cc7d23fd..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF589FLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_0.fit.json b/ENCSR854TTM/cherimoya.fold_0.fit.json deleted file mode 100644 index 91bbcf1b11c8787513de8c212e507db0340ef21d..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF589FLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_0.log b/ENCSR854TTM/cherimoya.fold_0.log deleted file mode 100644 index e0bac6f5863d1d3c3342b9591ea4eeac160d4012..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2243 29.710899829864502 4.37446141242981 379.7742004394531 0.7790400981903076 657.0570678710938 0.5514758229255676 0.5752492 10.083860397338867 True -1 4486 25.01727604866028 0.46990418434143066 441.3531799316406 0.9282935261726379 515.2774658203125 0.6591564416885376 0.73468053 3.3551104068756104 True -2 6729 25.02105140686035 0.4596390724182129 435.6646728515625 0.5977915525436401 487.8374328613281 0.6799550652503967 0.76535195 1.2451099157333374 True -3 8972 24.987770557403564 0.4612851142883301 357.6358337402344 0.46463751792907715 478.71923828125 0.686433732509613 0.7701909 0.810114860534668 True -4 11215 24.987634658813477 0.4547858238220215 443.7469482421875 0.5647643804550171 474.4476623535156 0.6885313987731934 0.7778226 0.7225126028060913 True -5 13458 24.999515056610107 0.4597890377044678 337.7635498046875 0.5162384510040283 471.63037109375 0.6911671161651611 0.78512233 0.6387080550193787 True -6 15701 24.980082750320435 2.683995008468628 428.60858154296875 0.4157271385192871 469.32000732421875 0.6934329867362976 0.78595906 0.6126839518547058 True -7 17944 25.06800651550293 0.4545247554779053 369.6409606933594 0.5409523248672485 467.594482421875 0.6952144503593445 0.78996557 0.5719884037971497 True -8 20187 25.024779319763184 1.0178165435791016 369.0383605957031 0.35513561964035034 465.8998107910156 0.6972211599349976 0.79746485 0.5208945870399475 True -9 22430 25.0424382686615 0.4620707035064697 446.5109558105469 0.5883944034576416 464.02410888671875 0.6988393068313599 0.8033589 0.5018967986106873 True -10 24673 25.035743236541748 0.45446014404296875 364.0680847167969 0.23168647289276123 462.0082702636719 0.7007624506950378 0.81021243 0.46442756056785583 True -11 26916 25.241782188415527 0.4554460048675537 378.7373046875 0.41237249970436096 459.9127197265625 0.7026680707931519 0.8156479 0.446504682302475 True -12 29159 24.500784873962402 0.45732951164245605 324.795166015625 0.3301389217376709 457.8171691894531 0.7045280933380127 0.82389003 0.4126238524913788 True -13 31402 24.48469376564026 0.45439863204956055 369.64080810546875 0.2400413453578949 456.46453857421875 0.7059479355812073 0.8283778 0.3947112560272217 True -14 33645 24.53601598739624 0.4551661014556885 410.24560546875 0.21340711414813995 455.458984375 0.7075093388557434 0.83509856 0.37625157833099365 True -15 35888 24.51615619659424 0.4563748836517334 347.01837158203125 0.21015670895576477 454.8416748046875 0.7082697749137878 0.8387883 0.3670632839202881 True -16 38131 24.479915142059326 0.456209659576416 371.35955810546875 0.42667168378829956 454.6524353027344 0.7085848450660706 0.83898693 0.3636734187602997 True -17 40374 24.49874210357666 0.4508957862854004 417.8190002441406 0.24326574802398682 454.93072509765625 0.7085352540016174 0.83751655 0.3677290976047516 False -18 42617 24.51669192314148 0.4797689914703369 421.957275390625 0.15511348843574524 455.1159362792969 0.7082678079605103 0.8370469 0.3721659481525421 False -19 44860 24.552845001220703 0.7471923828125 343.68609619140625 0.3382929563522339 455.47607421875 0.70805823802948 0.83438104 0.37485620379447937 False diff --git a/ENCSR854TTM/cherimoya.fold_0.performance.tsv b/ENCSR854TTM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 075ec6db9ae98e2796701cebc86b59f7d9b1bdb4..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -454.6524353027344 0.23937539756298065 0.7085848450660706 0.3068951666355133 0.8389869332313538 0.7684764266014099 0.3636734187602997 \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_1.evaluate.json b/ENCSR854TTM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c6bf349e8d22953d431e90110234d13a93cf62af..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF589FLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_1.fit.json b/ENCSR854TTM/cherimoya.fold_1.fit.json deleted file mode 100644 index 27b62e869b9cd95651281a1453fda327cb1f781b..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF589FLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_1.log b/ENCSR854TTM/cherimoya.fold_1.log deleted file mode 100644 index 0f33cb869584dd38d79f5e3c2f746199b6827f85..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2203 29.157378673553467 4.043218612670898 370.80328369140625 0.574212908744812 788.2220458984375 0.5596745610237122 0.56439257 10.63413143157959 True -1 4406 24.619138479232788 0.6417098045349121 496.9002990722656 0.6958857774734497 606.53369140625 0.6731640696525574 0.7191483 3.8151581287384033 True -2 6609 24.637380599975586 0.6187410354614258 429.0409240722656 0.4475492835044861 565.3735961914062 0.705737292766571 0.7672563 1.4444990158081055 True -3 8812 25.533196210861206 13.707059383392334 368.7337646484375 0.4489699602127075 551.039306640625 0.7141108512878418 0.78287375 0.9600362181663513 True -4 11015 24.58565330505371 14.12330174446106 426.9719543457031 0.549364447593689 545.70849609375 0.7190442681312561 0.7900368 0.8258943557739258 True -5 13218 25.006396055221558 0.6322052478790283 350.41778564453125 0.4541066884994507 542.2966918945312 0.7214493751525879 0.7954071 0.7779550552368164 True -6 15421 24.61716079711914 1.4706907272338867 374.0791931152344 0.49369001388549805 540.1719970703125 0.7235161066055298 0.7970991 0.7347242832183838 True -7 17624 24.591570615768433 0.6251935958862305 407.0624694824219 0.402332067489624 536.2084350585938 0.725916862487793 0.80113214 0.6568080186843872 True -8 19827 24.577264070510864 0.6170060634613037 404.78521728515625 0.37800532579421997 533.943359375 0.7279356122016907 0.8066013 0.5829925537109375 True -9 22030 24.632251024246216 0.6149139404296875 363.7708435058594 0.4295094609260559 531.4227294921875 0.7299176454544067 0.81065285 0.5332997441291809 True -10 24233 24.570432424545288 0.6238491535186768 367.391357421875 0.3798612058162689 529.1347045898438 0.7319512367248535 0.8170818 0.5024465322494507 True -11 26436 24.597402572631836 0.618025541305542 459.92767333984375 0.3929811716079712 526.0072631835938 0.7340583801269531 0.8215029 0.47848445177078247 True -12 28639 24.559574365615845 0.6264095306396484 363.70733642578125 0.4761008620262146 524.1088256835938 0.7358267903327942 0.82583004 0.4613240957260132 True -13 30842 24.587859869003296 0.6242227554321289 425.5066223144531 0.24137568473815918 522.3074340820312 0.7375906109809875 0.83204675 0.4510655999183655 True -14 33045 24.54940676689148 1.1061069965362549 396.9934997558594 0.19560012221336365 520.80322265625 0.7388636469841003 0.83707684 0.4323556125164032 True -15 35248 24.520215272903442 0.6209049224853516 413.6647644042969 0.322049081325531 520.01220703125 0.7396156191825867 0.8420319 0.4146559536457062 True -16 37451 24.481812715530396 0.599968433380127 371.6435852050781 0.24177232384681702 519.6597290039062 0.7398352026939392 0.8415619 0.41339293122291565 False -17 39654 24.493705987930298 0.605003833770752 363.70452880859375 0.1942923665046692 520.033935546875 0.7396043539047241 0.8419452 0.4163048565387726 False -18 41857 24.585479259490967 0.624173641204834 340.57208251953125 0.18868982791900635 520.6144409179688 0.7391487956047058 0.84048605 0.42088302969932556 False -19 44060 24.566837787628174 0.6228232383728027 374.38446044921875 0.22023510932922363 521.0134887695312 0.7388531565666199 0.83682144 0.4284968376159668 False diff --git a/ENCSR854TTM/cherimoya.fold_1.performance.tsv b/ENCSR854TTM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 127bc06609692efbaf630d2c34f76a0894f75ad9..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -520.01220703125 0.21594680845737457 0.7396156191825867 0.3454892635345459 0.8420318961143494 0.7969973683357239 0.4146559536457062 \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_2.evaluate.json b/ENCSR854TTM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0e024b0311ab9658c78b8156477cccdeb002b943..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF589FLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_2.fit.json b/ENCSR854TTM/cherimoya.fold_2.fit.json deleted file mode 100644 index b30c96015600a2a9d9d6737cc606eccabc5ee5b6..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF589FLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_2.log b/ENCSR854TTM/cherimoya.fold_2.log deleted file mode 100644 index ce9c3bc0c8786d12e9db89354b457b9e91c2fd38..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2372 31.12110924720764 3.7046656608581543 491.1951904296875 0.726921796798706 671.3549194335938 0.5616169571876526 0.5739233 10.260299682617188 True -1 4744 26.474268198013306 0.5121006965637207 426.1456298828125 0.4168429672718048 533.9519653320312 0.6595072746276855 0.7398888 3.071063995361328 True -2 7116 26.485496282577515 0.5457735061645508 519.3115234375 0.6309588551521301 503.4287109375 0.6822871565818787 0.7794238 1.0337252616882324 True -3 9488 26.44649386405945 0.48659229278564453 368.711181640625 0.48742440342903137 492.1279296875 0.6884313225746155 0.7932403 0.6804395318031311 True -4 11860 26.4392032623291 0.4730048179626465 412.181640625 0.44848281145095825 488.2636413574219 0.6918041110038757 0.7990473 0.6980417370796204 True -5 14232 25.851845264434814 2.6431238651275635 402.1524658203125 0.6655744314193726 485.2738342285156 0.6938270330429077 0.80016094 0.6536155343055725 True -6 16604 25.954617977142334 0.5257668495178223 414.488525390625 0.5232730507850647 483.3985290527344 0.6960076093673706 0.8013771 0.5943599343299866 True -7 18976 25.813265800476074 0.4947535991668701 371.20501708984375 0.4417199492454529 480.3780517578125 0.6982622742652893 0.8087808 0.5222315788269043 True -8 21348 25.85969066619873 0.4882388114929199 414.36279296875 0.56379634141922 478.4973449707031 0.6995081305503845 0.8114531 0.4824047386646271 True -9 23720 25.85832715034485 0.4798915386199951 427.8310852050781 0.38185280561447144 476.2712097167969 0.7017370462417603 0.8172073 0.46135208010673523 True -10 26092 25.866127490997314 0.4723622798919678 366.39447021484375 0.63242506980896 473.8949279785156 0.703446090221405 0.8191016 0.4463347792625427 True -11 28464 25.837486743927002 0.4773581027984619 364.1966552734375 0.32605016231536865 471.5560607910156 0.7054835557937622 0.82545835 0.42227885127067566 True -12 30836 25.832257986068726 0.4833359718322754 394.8803405761719 0.42083969712257385 470.0404968261719 0.7068690657615662 0.833229 0.39866527915000916 True -13 33208 25.82668423652649 0.47856736183166504 394.2567138671875 0.3467150032520294 468.6238708496094 0.7083943486213684 0.83903897 0.38389861583709717 True -14 35580 25.82996940612793 0.4725525379180908 468.6959533691406 0.4780828654766083 467.2344665527344 0.7099458575248718 0.84199464 0.37597984075546265 True -15 37952 25.83525037765503 0.47902798652648926 398.3189697265625 0.4399290680885315 466.57220458984375 0.7105706334114075 0.84446406 0.3652787506580353 True -16 40324 25.84352469444275 0.48917651176452637 382.2325439453125 0.2724733352661133 466.3128356933594 0.710748016834259 0.8464006 0.36139681935310364 True -17 42696 25.818941354751587 0.48731160163879395 376.59954833984375 0.2803189158439636 466.4282531738281 0.7105439901351929 0.84710056 0.36180755496025085 True -18 45068 25.88948655128479 0.4814455509185791 437.0583801269531 0.18557065725326538 466.837646484375 0.7100691199302673 0.84467703 0.36901357769966125 False -19 47440 25.87824320793152 0.48071765899658203 414.56256103515625 0.13767607510089874 467.0564270019531 0.7098336219787598 0.84506494 0.37290456891059875 False diff --git a/ENCSR854TTM/cherimoya.fold_2.performance.tsv b/ENCSR854TTM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3dfb209891246ba2bd7caa6f94f7d6072b6591d2..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -466.4282531738281 0.23687338829040527 0.7105439901351929 0.315309077501297 0.847100555896759 0.7750436067581177 0.36180755496025085 \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_3.evaluate.json b/ENCSR854TTM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 378603a720997e553bf1c7b749452b2969813161..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF589FLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_3.fit.json b/ENCSR854TTM/cherimoya.fold_3.fit.json deleted file mode 100644 index 3dc4bb08aaec6e9010c43584575ae1f5ad5ca7c6..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF589FLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_3.log b/ENCSR854TTM/cherimoya.fold_3.log deleted file mode 100644 index 18a65ce5aa19139471d7a047fd3516f10d709cbd..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2258 29.88345241546631 3.837932586669922 467.52960205078125 0.7683459520339966 681.3778076171875 0.557559072971344 0.5434238 10.027585983276367 True -1 4516 25.286149263381958 0.4958958625793457 375.3390808105469 0.5915676355361938 536.3343505859375 0.6688802242279053 0.7033311 3.5022926330566406 True -2 6774 25.203437089920044 1.1772069931030273 401.596435546875 0.6319422125816345 505.83612060546875 0.6904487609863281 0.7181582 1.403550148010254 True -3 9032 25.21701455116272 0.47397637367248535 507.008544921875 0.714491605758667 497.77764892578125 0.6971221566200256 0.72444105 1.0627803802490234 True -4 11290 25.118004322052002 0.4747648239135742 476.67919921875 0.5176212191581726 493.37164306640625 0.7007185816764832 0.7351757 0.868564784526825 True -5 13548 25.117488861083984 0.46445345878601074 387.963623046875 0.44669631123542786 491.0068054199219 0.7035467028617859 0.74351525 0.8194316029548645 True -6 15806 24.840572834014893 0.46454930305480957 448.29241943359375 0.4620663523674011 488.75885009765625 0.7053613066673279 0.7467629 0.7135313749313354 True -7 18064 24.598466157913208 0.46491003036499023 441.3221435546875 0.5654094219207764 486.7646179199219 0.7076555490493774 0.7493612 0.7087039351463318 True -8 20322 24.62069344520569 0.4628756046295166 356.39764404296875 0.5254210829734802 483.8590087890625 0.7102360129356384 0.75772923 0.6592379212379456 True -9 22580 24.571653604507446 0.4653208255767822 377.233642578125 0.3513405919075012 481.99005126953125 0.7118204236030579 0.7618071 0.603051483631134 True -10 24838 24.65298056602478 0.5304131507873535 425.7713623046875 0.4773995876312256 480.4642639160156 0.7138479948043823 0.7720912 0.5803170204162598 True -11 27096 24.614486932754517 0.46259164810180664 367.0819091796875 0.37607717514038086 478.17218017578125 0.7154135704040527 0.77762115 0.5589017271995544 True -12 29354 24.66331458091736 0.9837126731872559 428.1761169433594 0.3703746497631073 476.2301330566406 0.717211902141571 0.78252 0.5234946608543396 True -13 31612 24.692721128463745 2.6408557891845703 344.19476318359375 0.2566366493701935 474.97637939453125 0.7187010645866394 0.79191726 0.4958536922931671 True -14 33870 24.802797317504883 0.46431565284729004 402.36077880859375 0.23172464966773987 473.37664794921875 0.7202038764953613 0.7955334 0.4777335524559021 True -15 36128 24.670554876327515 0.47214365005493164 376.34454345703125 0.2516355812549591 472.7029724121094 0.7208439111709595 0.8018693 0.459815114736557 True -16 38386 24.742114305496216 0.4754955768585205 401.19696044921875 0.28019869327545166 472.2999267578125 0.7212543487548828 0.8053795 0.45181870460510254 True -17 40644 24.697441577911377 0.4626920223236084 350.8575134277344 0.284591943025589 472.8089599609375 0.7208477854728699 0.8056408 0.4565572142601013 True -18 42902 24.639804363250732 0.46286606788635254 404.29998779296875 0.24332080781459808 473.1502685546875 0.7205283045768738 0.8039935 0.4572243094444275 False -19 45160 24.621387720108032 0.45763564109802246 369.5232849121094 0.1897423267364502 473.4320068359375 0.7202346324920654 0.803534 0.4616731107234955 False diff --git a/ENCSR854TTM/cherimoya.fold_3.performance.tsv b/ENCSR854TTM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3d50e9787ba397483a9960c1cdd957a04188b6fc..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -472.8089599609375 0.22985248267650604 0.7208477854728699 0.3173108696937561 0.8056408166885376 0.7365854382514954 0.4565572142601013 \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_4.evaluate.json b/ENCSR854TTM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d6389d3a41d162e351c78f6973e1ec91c818580d..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF589FLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_4.fit.json b/ENCSR854TTM/cherimoya.fold_4.fit.json deleted file mode 100644 index 232021b85f80b7b9e54a8d4fcca5c8e118a7f0ec..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF589FLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854TTM/cherimoya.fold_4.log b/ENCSR854TTM/cherimoya.fold_4.log deleted file mode 100644 index 476ba5c7dd9f3cd1318fb2485c95c5e916f2969a..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2282 30.288158893585205 4.6255714893341064 395.066162109375 0.7473171949386597 618.5634155273438 0.547223687171936 0.5328908 9.034093856811523 True -1 4564 25.495972394943237 21.00335717201233 454.2582702636719 0.7028099298477173 498.06768798828125 0.6434981822967529 0.69432634 3.140303611755371 True -2 6846 25.512962818145752 0.512641429901123 348.81884765625 0.3414619565010071 466.65460205078125 0.6661532521247864 0.7438186 0.9558731317520142 True -3 9128 25.445953130722046 0.49013710021972656 380.90179443359375 0.3607803285121918 457.8722839355469 0.6719354391098022 0.7637398 0.6505107283592224 True -4 11410 25.482019424438477 0.47190260887145996 392.9889221191406 0.5502108335494995 454.47406005859375 0.6747891902923584 0.76913214 0.5887791514396667 True -5 13692 25.50127339363098 12.34957218170166 363.7552490234375 0.44735080003738403 451.77117919921875 0.6768097281455994 0.7789826 0.5330364108085632 True -6 15974 25.441420316696167 0.48396921157836914 401.151123046875 0.25445282459259033 449.6976623535156 0.679288923740387 0.7821162 0.5010095834732056 True -7 18256 25.491459608078003 0.46904730796813965 364.09637451171875 0.36661648750305176 449.06207275390625 0.6800863146781921 0.78481174 0.4920376241207123 True -8 20538 25.506778478622437 0.4678776264190674 387.4980773925781 0.38560038805007935 446.33099365234375 0.6826939582824707 0.78979737 0.4598703682422638 True -9 22820 25.407867193222046 0.47791099548339844 429.38055419921875 0.9098002314567566 443.9278259277344 0.6849356293678284 0.79477966 0.43823423981666565 True -10 25102 25.41926383972168 0.47451329231262207 430.5621032714844 0.6190109848976135 442.3822021484375 0.6871981620788574 0.8010825 0.42958971858024597 True -11 27384 25.46548295021057 0.47411489486694336 414.2830810546875 0.41352027654647827 440.7379150390625 0.6887467503547668 0.8071954 0.41300439834594727 True -12 29666 25.52326512336731 0.47637224197387695 374.01312255859375 0.5174676179885864 439.1995849609375 0.6908314824104309 0.80909824 0.3996465802192688 True -13 31948 25.57971477508545 15.041324377059937 432.65484619140625 0.54929518699646 437.99273681640625 0.6925356388092041 0.8166519 0.38889890909194946 True -14 34230 25.090033292770386 0.4728279113769531 405.1628723144531 0.31950467824935913 436.87750244140625 0.6942126750946045 0.8216047 0.3780369162559509 True -15 36512 24.935392141342163 0.47533559799194336 343.3001403808594 0.2206704467535019 436.1698913574219 0.6949825882911682 0.82423145 0.3684086799621582 True -16 38794 24.945867776870728 0.4716312885284424 358.1004638671875 0.2709471583366394 436.13177490234375 0.6953552961349487 0.8281833 0.36278536915779114 True -17 41076 24.913238048553467 0.4629487991333008 389.3788146972656 0.2338579148054123 436.20263671875 0.6953368186950684 0.8267945 0.3638949692249298 False -18 43358 24.90450406074524 0.4570276737213135 349.3875732421875 0.1686110496520996 436.6118469238281 0.695139467716217 0.82516545 0.36945050954818726 False -19 45640 24.90563941001892 0.4901909828186035 403.5985412597656 0.21201567351818085 436.6929931640625 0.6950441002845764 0.8260729 0.3718952238559723 False diff --git a/ENCSR854TTM/cherimoya.fold_4.performance.tsv b/ENCSR854TTM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6082895a81d5468a3ec8183e559244f012ceb3fc..0000000000000000000000000000000000000000 --- a/ENCSR854TTM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -436.13177490234375 0.24702546000480652 0.6953552961349487 0.2958618104457855 0.8281832933425903 0.7449880242347717 0.36278536915779114 \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_0.evaluate.json b/ENCSR854ZBA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0746512b1e5479c27c1920eb87f8de33fc9327ca..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF657WIZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_0.fit.json b/ENCSR854ZBA/cherimoya.fold_0.fit.json deleted file mode 100644 index e7de6a35574750b55c3c21e55360363bec12af85..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF657WIZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_0.log b/ENCSR854ZBA/cherimoya.fold_0.log deleted file mode 100644 index d41500db65f7949acd197184dca4b21c96b071d9..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1622 23.5638644695282 3.3248493671417236 277.47296142578125 0.7954620122909546 467.2260437011719 0.42257818579673767 0.5568682 14.310956001281738 True -1 3244 18.07081389427185 0.3292262554168701 323.03619384765625 0.5419706702232361 400.6678771972656 0.5204929709434509 0.6401166 5.453333854675293 True -2 4866 18.014015674591064 0.3234288692474365 288.208740234375 0.5406513214111328 377.05169677734375 0.5739687085151672 0.6650402 1.7789208889007568 True -3 6488 18.043561935424805 0.3184387683868408 312.69964599609375 0.401204377412796 369.57830810546875 0.5895189642906189 0.66992617 0.9572494029998779 True -4 8110 17.994921922683716 0.3208599090576172 310.13299560546875 0.5280425548553467 367.3830261230469 0.5943574905395508 0.67635536 0.7246809005737305 True -5 9732 18.039985179901123 0.31841206550598145 355.14892578125 0.4415501058101654 365.8827209472656 0.5978001952171326 0.68096304 0.6334210634231567 True -6 11354 18.100440502166748 0.32275891304016113 281.63177490234375 0.5220086574554443 364.707275390625 0.6005918979644775 0.68912655 0.5882256627082825 True -7 12976 18.00691056251526 6.095131874084473 287.42706298828125 0.5678079724311829 363.7192077636719 0.602698564529419 0.6913173 0.5667480826377869 True -8 14598 18.074273586273193 0.32317113876342773 247.47947692871094 0.6739504337310791 363.1766357421875 0.6041999459266663 0.69686013 0.5081074237823486 True -9 16220 18.023930072784424 1.826517105102539 282.531005859375 0.3622913360595703 362.3623962402344 0.6060090065002441 0.70588225 0.47123661637306213 True -10 17842 18.08160638809204 0.3252904415130615 260.4806823730469 0.44171059131622314 361.6586608886719 0.6075446605682373 0.7071891 0.46098440885543823 True -11 19464 18.100630283355713 0.3255641460418701 301.77606201171875 0.47119247913360596 361.02471923828125 0.6092132329940796 0.71184593 0.44309133291244507 True -12 21086 18.01170778274536 0.3268406391143799 324.08306884765625 0.3780072331428528 360.2889404296875 0.61077481508255 0.7184325 0.4240961968898773 True -13 22708 18.278422355651855 11.375066757202148 284.98309326171875 0.5202115774154663 359.9035339355469 0.6117958426475525 0.72408515 0.4103541076183319 True -14 24330 18.033337831497192 0.3263587951660156 290.8442077636719 0.3706377148628235 359.7840881347656 0.6121737957000732 0.7251643 0.40909796953201294 True -15 25952 18.130833625793457 0.35332751274108887 325.016357421875 0.28102242946624756 359.6748352050781 0.6122872233390808 0.7260496 0.41278958320617676 True -16 27574 18.05511784553528 0.3256685733795166 257.17413330078125 0.31708651781082153 359.7483215332031 0.6116687059402466 0.72372323 0.41772863268852234 False -17 29196 18.027518272399902 13.922857999801636 274.984619140625 0.25403666496276855 360.0904846191406 0.6106429100036621 0.7213837 0.42352986335754395 False -18 30818 18.57392406463623 0.32147812843322754 257.40234375 0.23251774907112122 360.3757629394531 0.609734833240509 0.71919835 0.4353702962398529 False -19 32440 18.04926085472107 0.911076545715332 281.23333740234375 0.26717376708984375 360.6219787597656 0.6090559363365173 0.7162278 0.4414399564266205 False diff --git a/ENCSR854ZBA/cherimoya.fold_0.performance.tsv b/ENCSR854ZBA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 841eeee31171f3913067f72730c875ea68e7b844..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -359.6748352050781 0.30787229537963867 0.6122871041297913 0.23059213161468506 0.7260496020317078 0.6892755627632141 0.41278958320617676 \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_1.evaluate.json b/ENCSR854ZBA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bc29a2330a6b3cebd7482e02c7d89e169f8c77c9..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF657WIZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_1.fit.json b/ENCSR854ZBA/cherimoya.fold_1.fit.json deleted file mode 100644 index fc0c526dd66b900d90f9a90cbc3032ce0027eb8a..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF657WIZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_1.log b/ENCSR854ZBA/cherimoya.fold_1.log deleted file mode 100644 index e4948b644aa16f1af3d0ad9462a24b3f1fd0221c..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1636 22.721112966537476 4.199847459793091 282.91497802734375 0.5889970064163208 482.5710144042969 0.43337270617485046 0.5298067 14.485142707824707 True -1 3272 18.751295804977417 1.2062251567840576 307.3273620605469 0.5923765897750854 418.5931091308594 0.5236121416091919 0.63851845 5.289702892303467 True -2 4908 18.204972982406616 0.4314143657684326 313.1124572753906 0.6539627313613892 397.6971435546875 0.5709665417671204 0.6605247 1.731802225112915 True -3 6544 18.182746410369873 0.3944060802459717 302.8987731933594 0.4437488317489624 391.11285400390625 0.5849518775939941 0.68163437 0.8037801384925842 True -4 8180 17.8123300075531 0.3939943313598633 310.6066589355469 0.69558185338974 389.1123046875 0.590110719203949 0.6877667 0.6638746857643127 True -5 9816 17.83601665496826 0.39252686500549316 270.76593017578125 0.5636348724365234 387.7650451660156 0.5936652421951294 0.6925097 0.5873392224311829 True -6 11452 17.785548448562622 0.8725883960723877 238.42562866210938 0.5381038784980774 386.9224853515625 0.5955408215522766 0.69646305 0.5540744066238403 True -7 13088 17.78844404220581 0.3928210735321045 287.85235595703125 0.5640883445739746 385.7446594238281 0.5978375673294067 0.70505065 0.4981922507286072 True -8 14724 17.77719521522522 0.3965420722961426 348.830322265625 0.5292720794677734 384.9535827636719 0.5997315645217896 0.7146651 0.4358797073364258 True -9 16360 17.78750514984131 0.7419178485870361 261.94329833984375 0.4073883891105652 384.3277893066406 0.6015569567680359 0.7180229 0.42681998014450073 True -10 17996 17.79365062713623 0.3898935317993164 302.533203125 0.596824049949646 383.56890869140625 0.6032158732414246 0.7235501 0.4036187529563904 True -11 19632 17.777626752853394 0.39850926399230957 300.81146240234375 0.5202363133430481 383.050048828125 0.6046103835105896 0.730371 0.3820239007472992 True -12 21268 17.82205820083618 0.3927936553955078 283.1017150878906 0.42903923988342285 382.50244140625 0.605876624584198 0.7352228 0.3732651472091675 True -13 22904 17.828696250915527 16.688213109970093 284.9287414550781 0.43155762553215027 382.0045166015625 0.6071674823760986 0.74206746 0.3576197624206543 True -14 24540 17.923832178115845 0.3983583450317383 282.42620849609375 0.2562955617904663 381.7194519042969 0.6078587174415588 0.74685216 0.356548547744751 True -15 26176 17.785839796066284 0.39313197135925293 303.07611083984375 0.4012261629104614 381.58343505859375 0.608092188835144 0.7482178 0.36077356338500977 True -16 27812 18.06618356704712 2.882700204849243 306.71661376953125 0.27044621109962463 381.47930908203125 0.607657253742218 0.7517539 0.3596183657646179 True -17 29448 17.831590175628662 0.40355348587036133 251.92144775390625 0.2360852062702179 381.77337646484375 0.6068346500396729 0.7493546 0.37104466557502747 False -18 31084 17.992156505584717 10.832747459411621 295.36932373046875 0.2169196456670761 382.0550842285156 0.6058552265167236 0.74595785 0.38087838888168335 False -19 32720 17.816898345947266 0.39035725593566895 284.1505126953125 0.1663976013660431 382.31988525390625 0.605317234992981 0.74414057 0.3874693512916565 False diff --git a/ENCSR854ZBA/cherimoya.fold_1.performance.tsv b/ENCSR854ZBA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 04183d6ba61b719f1f5a2a6995bfff0c6e6ab138..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -381.47930908203125 0.3036048412322998 0.6076571941375732 0.2414780557155609 0.7517539262771606 0.7431201934814453 0.3596183657646179 \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_2.evaluate.json b/ENCSR854ZBA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9250fd627c5245762c92e2678d19a883065c9b03..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF657WIZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_2.fit.json b/ENCSR854ZBA/cherimoya.fold_2.fit.json deleted file mode 100644 index c62bc6d5b6aba93e85600eb82b1328020f030080..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF657WIZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_2.log b/ENCSR854ZBA/cherimoya.fold_2.log deleted file mode 100644 index 18ed038e716f0f92af24faa7e3a26c050b2f1cd9..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1722 25.282559871673584 3.3493382930755615 286.7186279296875 0.7433360815048218 466.179931640625 0.4300019145011902 0.5718837 12.007868766784668 True -1 3444 19.222099781036377 0.3460814952850342 307.22686767578125 0.6772392988204956 403.0071105957031 0.5265023112297058 0.66338 4.617832660675049 True -2 5166 19.151663780212402 0.3214137554168701 301.9700927734375 0.5140032768249512 382.16375732421875 0.5741497278213501 0.677286 1.1802945137023926 True -3 6888 18.964532613754272 0.31238436698913574 279.56561279296875 0.7119311094284058 375.6412658691406 0.5876205563545227 0.69181144 0.6216010451316833 True -4 8610 18.708824396133423 0.3164510726928711 275.180908203125 0.510012686252594 373.48394775390625 0.5924130082130432 0.7033615 0.4991928040981293 True -5 10332 18.71283745765686 0.3997828960418701 296.1817932128906 0.5484446883201599 372.1864929199219 0.5953060388565063 0.7052557 0.46835604310035706 True -6 12054 18.780171394348145 0.3169441223144531 290.8978271484375 0.6672446727752686 371.1280822753906 0.5979093909263611 0.7109673 0.43592169880867004 True -7 13776 18.745816230773926 0.3138461112976074 324.2431945800781 0.3560423254966736 370.3161926269531 0.5994951725006104 0.7112647 0.4237436354160309 True -8 15498 18.71528148651123 0.31182312965393066 266.35015869140625 0.5229257345199585 369.37860107421875 0.6015108227729797 0.71639276 0.4105520248413086 True -9 17220 18.72648048400879 1.4998607635498047 299.3861083984375 0.5212063193321228 368.5801696777344 0.6032892465591431 0.7187438 0.39739862084388733 True -10 18942 18.738251209259033 1.820483684539795 310.90631103515625 0.2740309238433838 368.0753479003906 0.6044408679008484 0.7230357 0.3843051791191101 True -11 20664 18.753947257995605 0.31320905685424805 257.515380859375 0.3732392191886902 367.484619140625 0.6056308746337891 0.72442216 0.3927985429763794 True -12 22386 18.757636308670044 0.31773805618286133 287.4117431640625 0.37039750814437866 366.9662170410156 0.6068712472915649 0.73193485 0.37961050868034363 True -13 24108 18.897311687469482 21.21256160736084 257.1915283203125 0.31792622804641724 366.6470642089844 0.6077998280525208 0.7326536 0.38395756483078003 True -14 25830 19.43517756462097 10.37187647819519 261.62744140625 0.4728858470916748 366.378173828125 0.6084444522857666 0.73502517 0.38182333111763 True -15 27552 18.77763032913208 0.3203091621398926 264.4449462890625 0.32972633838653564 366.3314208984375 0.6084508299827576 0.73781604 0.386966347694397 True -16 29274 18.739486932754517 0.3182837963104248 258.7799987792969 0.3508247137069702 366.3495788574219 0.6082291007041931 0.7342041 0.3960722088813782 False -17 30996 18.763212203979492 1.3954098224639893 312.1357116699219 0.2639092803001404 366.66485595703125 0.6074185371398926 0.7349352 0.40489694476127625 False -18 32718 18.738490343093872 0.6242473125457764 276.86517333984375 0.2789236605167389 367.0657958984375 0.6065886616706848 0.73052704 0.4169621169567108 False -19 34440 18.755157232284546 0.31357836723327637 262.066650390625 0.2667466700077057 367.2946472167969 0.6060603260993958 0.7284487 0.4256218671798706 False diff --git a/ENCSR854ZBA/cherimoya.fold_2.performance.tsv b/ENCSR854ZBA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 778a17bf214e11321f19de8428ca1fa1692cea00..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -366.3314208984375 0.30771881341934204 0.6084507703781128 0.23576369881629944 0.7378160357475281 0.712974488735199 0.386966347694397 \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_3.evaluate.json b/ENCSR854ZBA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1c60ff51e6c4c09a9bdff319eb543f902f0831c7..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF657WIZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_3.fit.json b/ENCSR854ZBA/cherimoya.fold_3.fit.json deleted file mode 100644 index 5e34cc4b7e035d52a10cf06142deb3186d23355b..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF657WIZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_3.log b/ENCSR854ZBA/cherimoya.fold_3.log deleted file mode 100644 index 435d002cdcda2a4ec3a23ea668010a064cb5a49b..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1673 23.18318200111389 3.318242073059082 280.7520751953125 0.5763955116271973 473.77294921875 0.4305611848831177 0.5519795 14.160271644592285 True -1 3346 18.617628812789917 0.36417126655578613 331.6195068359375 0.4495144486427307 409.4897155761719 0.5254916548728943 0.6231334 5.305189609527588 True -2 5019 18.615532398223877 0.35399436950683594 308.6499328613281 0.4474199116230011 384.1444396972656 0.581424355506897 0.63532966 1.817380428314209 True -3 6692 18.740518808364868 0.411484956741333 299.2043762207031 0.4594762325286865 378.1268615722656 0.5931936502456665 0.64882326 0.9555355906486511 True -4 8365 18.476711750030518 1.1547975540161133 281.10430908203125 0.4621603190898895 376.0986022949219 0.5974878668785095 0.6606308 0.6391425728797913 True -5 10038 18.321569442749023 0.36363744735717773 319.54083251953125 0.6327521800994873 374.5435791015625 0.6007488965988159 0.669339 0.5316979885101318 True -6 11711 18.261743545532227 0.3865358829498291 275.8717956542969 0.49289315938949585 373.781494140625 0.6024361848831177 0.6775388 0.5184269547462463 True -7 13384 18.241084337234497 0.36357545852661133 244.66262817382812 0.6850561499595642 372.6603698730469 0.604909360408783 0.68470466 0.48444223403930664 True -8 15057 18.21753191947937 0.36060261726379395 285.60064697265625 0.7102308869361877 371.90350341796875 0.6066603660583496 0.6885387 0.46114227175712585 True -9 16730 18.49051594734192 14.302323818206787 295.99609375 0.4023004174232483 370.914306640625 0.6089155077934265 0.69891745 0.43936043977737427 True -10 18403 18.265270471572876 0.3853611946105957 292.5210266113281 0.5162593126296997 370.1905212402344 0.6103306412696838 0.7038122 0.4224950671195984 True -11 20076 18.24306082725525 0.35819530487060547 292.4709167480469 0.3961069881916046 369.45599365234375 0.6119799613952637 0.7075795 0.41927099227905273 True -12 21749 18.285547494888306 0.3582618236541748 277.4080505371094 0.3981093466281891 368.87725830078125 0.6131585836410522 0.7120617 0.41891351342201233 True -13 23422 18.22917628288269 1.243307113647461 268.1517639160156 0.42212867736816406 368.4424743652344 0.6139737963676453 0.71411884 0.4126111567020416 True -14 25095 18.218971967697144 0.35088539123535156 288.587646484375 0.26709169149398804 368.1543273925781 0.6145772337913513 0.71951187 0.41107532382011414 True -15 26768 18.301885843276978 0.5923361778259277 284.9928894042969 0.3918435573577881 367.7778625488281 0.6149641275405884 0.72430503 0.40920788049697876 True -16 28441 18.28270649909973 0.3641953468322754 257.971923828125 0.38093215227127075 367.9599304199219 0.6144086122512817 0.723786 0.419559121131897 False -17 30114 18.19701600074768 1.4531395435333252 248.12344360351562 0.24300967156887054 368.2108154296875 0.6135294437408447 0.71879834 0.4390311539173126 False -18 31787 18.22573685646057 2.234158754348755 304.39202880859375 0.24888652563095093 368.50341796875 0.6126888394355774 0.7171882 0.45094034075737 False -19 33460 18.235700130462646 1.0495679378509521 297.8016357421875 0.17531125247478485 368.6433410644531 0.6121652722358704 0.7139696 0.461372435092926 False diff --git a/ENCSR854ZBA/cherimoya.fold_3.performance.tsv b/ENCSR854ZBA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 35a7c027c667c6c8be7870725a35e658934fe295..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -367.7778625488281 0.3039321005344391 0.6149641871452332 0.2353508025407791 0.7243050336837769 0.6997414827346802 0.40920788049697876 \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_4.evaluate.json b/ENCSR854ZBA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d607a6041ce6dc2339932345ea3efb017b7637df..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF657WIZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_4.fit.json b/ENCSR854ZBA/cherimoya.fold_4.fit.json deleted file mode 100644 index 37cd814d58ef891801aef43bdece27e3bcf58e67..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF657WIZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR854ZBA/cherimoya.fold_4.log b/ENCSR854ZBA/cherimoya.fold_4.log deleted file mode 100644 index bc535f52fcc9842f87275aab81ae8972ea44d671..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1704 23.45687961578369 3.324927568435669 287.9344787597656 0.7465205788612366 469.23663330078125 0.42975935339927673 0.5852429 13.40327262878418 True -1 3408 18.881048917770386 0.34882450103759766 287.7763671875 0.7661226391792297 406.07647705078125 0.5234807133674622 0.64242035 4.577929496765137 True -2 5112 18.89652442932129 0.7696163654327393 293.63348388671875 0.5380518436431885 382.34393310546875 0.5792484283447266 0.6653265 1.6349260807037354 True -3 6816 19.099857330322266 0.3152484893798828 319.0074462890625 0.5049518346786499 375.4842834472656 0.5932016968727112 0.67761016 0.8409429788589478 True -4 8520 18.916051864624023 0.31229591369628906 263.06317138671875 0.7267358303070068 373.3825378417969 0.598154604434967 0.68416274 0.6998456120491028 True -5 10224 19.419124364852905 14.45795226097107 291.63861083984375 0.5864354372024536 371.6177673339844 0.6015578508377075 0.6909186 0.5715165734291077 True -6 11928 20.508121490478516 15.791210174560547 281.08251953125 0.41297781467437744 370.7883605957031 0.6037233471870422 0.7003079 0.5264601707458496 True -7 13632 18.934147357940674 0.31616663932800293 285.16448974609375 0.4573284089565277 369.7215270996094 0.6060165762901306 0.7034488 0.4754678010940552 True -8 15336 18.575929641723633 0.3215219974517822 298.04583740234375 0.39795005321502686 368.85003662109375 0.6079632043838501 0.70719093 0.4602203965187073 True -9 17040 18.54133653640747 0.3191993236541748 279.96307373046875 0.5885205268859863 368.08709716796875 0.6097050905227661 0.7140512 0.4543112516403198 True -10 18744 18.570584297180176 2.073970079421997 257.3701171875 0.41166993975639343 367.2559814453125 0.6113234758377075 0.7196285 0.42304542660713196 True -11 20448 18.52959156036377 0.31710076332092285 283.6619873046875 0.448513388633728 366.56732177734375 0.6130312085151672 0.72503114 0.4091855585575104 True -12 22152 18.522778511047363 0.3097236156463623 274.1583251953125 0.4403490722179413 365.9219665527344 0.614632248878479 0.7317215 0.3949440121650696 True -13 23856 18.567400217056274 0.898906946182251 311.24822998046875 0.3238741457462311 365.4724426269531 0.6158088445663452 0.736689 0.3848097622394562 True -14 25560 18.57427716255188 0.46966075897216797 265.4323425292969 0.5033540725708008 365.2522888183594 0.6162571907043457 0.7409762 0.381337434053421 True -15 27264 18.499409675598145 0.31421971321105957 320.8017883300781 0.3556152880191803 365.0954895019531 0.616395890712738 0.73972774 0.38719478249549866 False -16 28968 18.529637336730957 0.31385302543640137 267.102783203125 0.19387005269527435 365.339111328125 0.6159528493881226 0.73852646 0.3998224139213562 False -17 30672 18.520742893218994 1.0738883018493652 228.69140625 0.2942928075790405 365.6631164550781 0.614835798740387 0.7329732 0.41721850633621216 False -18 32376 18.53439426422119 0.3175356388092041 254.46707153320312 0.24401095509529114 365.98760986328125 0.6138809323310852 0.7292206 0.4310036599636078 False -19 34080 18.525888681411743 0.3110694885253906 244.74191284179688 0.18971487879753113 366.1764221191406 0.6135551333427429 0.7246028 0.43917304277420044 False diff --git a/ENCSR854ZBA/cherimoya.fold_4.performance.tsv b/ENCSR854ZBA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index bfbbfe6a6c98303854b5761100c01d0cb5360041..0000000000000000000000000000000000000000 --- a/ENCSR854ZBA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -365.2522888183594 0.3046121597290039 0.6162572503089905 0.23604856431484222 0.7409762144088745 0.6995896697044373 0.381337434053421 \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_0.evaluate.json b/ENCSR855FOP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e966fb6c3ca30c6bdb5c3ba50a44f9056f8cf781..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF279KTY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_0.fit.json b/ENCSR855FOP/cherimoya.fold_0.fit.json deleted file mode 100644 index e165fc100845b64555101c526f55a498336a39ac..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF279KTY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_0.log b/ENCSR855FOP/cherimoya.fold_0.log deleted file mode 100644 index 7acfa5d708b2fe168550098ba7a95ea394e91138..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 36.017929792404175 3.500328779220581 1043.4813232421875 0.531499445438385 1315.9000244140625 0.20060434937477112 0.6409385 8.228150367736816 True -1 5418 30.14508581161499 0.5363607406616211 774.4451904296875 0.44711217284202576 1207.7178955078125 0.27409565448760986 0.57602346 1.6249324083328247 False -2 8127 30.145296812057495 0.5232181549072266 897.530029296875 0.4625239968299866 1184.27490234375 0.285130113363266 0.61960864 0.8215449452400208 False -3 10836 30.037834644317627 0.5113680362701416 954.781005859375 0.21770110726356506 1147.143310546875 0.2970910966396332 0.67405117 0.6667437553405762 True -4 13545 30.059282779693604 0.5128092765808105 927.5096435546875 0.33415287733078003 1138.7259521484375 0.30263403058052063 0.68968433 0.5991799235343933 True -5 16254 30.080499410629272 0.5187051296234131 894.5582885742188 0.22425563633441925 1122.7958984375 0.3115255832672119 0.71036726 0.5674105286598206 True -6 18963 30.050246477127075 0.5074355602264404 913.3125 0.4652923345565796 1116.534912109375 0.31461554765701294 0.732014 0.5900386571884155 True -7 21672 29.406705617904663 0.5141010284423828 1027.553466796875 0.3225715160369873 1106.4937744140625 0.31930214166641235 0.7487626 0.46901917457580566 True -8 24381 29.478793382644653 0.5657241344451904 1070.4095458984375 0.34087854623794556 1099.936279296875 0.32140564918518066 0.76486135 0.39220646023750305 True -9 27090 29.470057725906372 0.5388987064361572 1081.6094970703125 0.4321213960647583 1097.6478271484375 0.3235313594341278 0.7678111 0.38458186388015747 True -10 29799 29.437514543533325 3.2447509765625 1101.2216796875 0.23834842443466187 1091.7576904296875 0.32846033573150635 0.77333754 0.3544462025165558 True -11 32508 29.43505573272705 0.5074598789215088 876.9381103515625 0.28388938307762146 1088.044189453125 0.3303421437740326 0.7800414 0.317033052444458 True -12 35217 29.472727298736572 0.5142922401428223 872.309814453125 0.2741553485393524 1086.31396484375 0.33129769563674927 0.7827761 0.3073548972606659 True -13 37926 29.443707942962646 0.5041112899780273 1050.0672607421875 0.35939881205558777 1081.0699462890625 0.3339756429195404 0.79019177 0.28716811537742615 True -14 40635 29.466477870941162 0.5363562107086182 966.7613525390625 0.33051344752311707 1078.1943359375 0.33497485518455505 0.7967097 0.2732289135456085 True -15 43344 29.440509557724 1.1081452369689941 923.1251220703125 0.28741365671157837 1076.09423828125 0.33567142486572266 0.80574244 0.2532414495944977 True -16 46053 29.519947052001953 0.5076508522033691 897.252197265625 0.16568174958229065 1075.4742431640625 0.336853951215744 0.8075788 0.24884724617004395 True -17 48762 29.454113960266113 0.5115756988525391 943.8631591796875 0.15706439316272736 1075.182373046875 0.33620569109916687 0.8088389 0.24510237574577332 True -18 51471 29.49018955230713 0.5083158016204834 903.52880859375 0.20546294748783112 1076.8372802734375 0.334762841463089 0.8094863 0.24486574530601501 True -19 54180 29.476197242736816 0.510019063949585 823.1167602539062 0.19010689854621887 1074.5216064453125 0.33700844645500183 0.80949676 0.2451457679271698 True diff --git a/ENCSR855FOP/cherimoya.fold_0.performance.tsv b/ENCSR855FOP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cc1421c440229eefaa6136e7099ce35eef30a680..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1074.5216064453125 0.3157886564731598 0.33700844645500183 0.17484131455421448 0.8094967603683472 0.7020283341407776 0.2451457679271698 \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_1.evaluate.json b/ENCSR855FOP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6a56215427da56c491908d8bb991f7925901e436..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF279KTY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_1.fit.json b/ENCSR855FOP/cherimoya.fold_1.fit.json deleted file mode 100644 index c2ef068776d1debd206180f748aa195f1fecaae2..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF279KTY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_1.log b/ENCSR855FOP/cherimoya.fold_1.log deleted file mode 100644 index 4d60555e6a64f14f5b247ae649f83fff20a483ab..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2714 35.2070255279541 3.941042900085449 1041.262939453125 0.4702715277671814 1484.652587890625 0.21232381463050842 0.6379629 8.363415718078613 True -1 5428 30.20451807975769 1.6913161277770996 938.861083984375 0.39516305923461914 1356.035888671875 0.2863902747631073 0.5569315 1.9562361240386963 False -2 8142 30.088338136672974 0.7872498035430908 1119.30810546875 0.37263354659080505 1320.5130615234375 0.3000984191894531 0.64986163 1.0885813236236572 True -3 10856 30.11616039276123 0.7824382781982422 1073.388916015625 0.3710840940475464 1287.427490234375 0.3108009994029999 0.67592305 0.9195614457130432 True -4 13570 30.06782627105713 0.7735965251922607 1112.4127197265625 0.5423035621643066 1260.71240234375 0.3200412094593048 0.7128529 0.7698149085044861 True -5 16284 30.02457094192505 0.7670910358428955 1098.171630859375 0.4775039255619049 1242.836181640625 0.32676032185554504 0.73701364 0.7320965528488159 True -6 18998 30.113343477249146 0.7677433490753174 954.356201171875 0.3645671606063843 1233.4791259765625 0.3314695656299591 0.74333525 0.6377502083778381 True -7 21712 29.89038348197937 0.763096809387207 973.79443359375 0.32402461767196655 1220.235595703125 0.3374478816986084 0.7618105 0.6016688346862793 True -8 24426 29.508430004119873 0.7545111179351807 826.7424926757812 0.32288792729377747 1210.9683837890625 0.34023964405059814 0.7766364 0.5437137484550476 True -9 27140 29.475846529006958 0.7657687664031982 947.5914916992188 0.4732532501220703 1201.5379638671875 0.34403157234191895 0.78692865 0.4914894104003906 True -10 29854 29.414050340652466 0.7558557987213135 977.9715576171875 0.3200485110282898 1197.2777099609375 0.3455813527107239 0.79573303 0.4464561939239502 True -11 32568 29.487971544265747 1.515812635421753 867.4624633789062 0.2031824141740799 1191.9244384765625 0.34842121601104736 0.7986475 0.42444396018981934 True -12 35282 29.556988954544067 0.7544684410095215 1050.5115966796875 0.22862699627876282 1187.4105224609375 0.35064008831977844 0.80455554 0.39066076278686523 True -13 37996 29.486109495162964 5.21172571182251 871.5599365234375 0.2709197998046875 1182.05029296875 0.352034330368042 0.8112967 0.3613569736480713 True -14 40710 29.67026424407959 32.78821682929993 954.5245971679688 0.2912619113922119 1174.328369140625 0.3561941683292389 0.8191086 0.32117316126823425 True -15 43424 30.140644788742065 1.6278259754180908 939.4553833007812 0.306379497051239 1173.4093017578125 0.354769766330719 0.8267638 0.29564669728279114 True -16 46138 29.48002552986145 5.913545608520508 930.1871948242188 0.23398250341415405 1171.789306640625 0.3555205166339874 0.8318152 0.28200361132621765 True -17 48852 29.60347580909729 9.069014310836792 910.3265991210938 0.19992151856422424 1172.298095703125 0.35481753945350647 0.833131 0.270990788936615 True -18 51566 29.502714157104492 2.126408576965332 941.1238403320312 0.1527789980173111 1170.962890625 0.3555126190185547 0.8339405 0.2692042887210846 True -19 54280 29.5648832321167 0.7596607208251953 762.3904418945312 0.20620521903038025 1169.5035400390625 0.3566738963127136 0.83400285 0.2673359811306 True diff --git a/ENCSR855FOP/cherimoya.fold_1.performance.tsv b/ENCSR855FOP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8c5191d2ae6c63a141ed1760edb48c41f3b35994..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1169.5035400390625 0.3043769896030426 0.356673926115036 0.19457140564918518 0.8340028524398804 0.7449472546577454 0.2673359811306 \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_2.evaluate.json b/ENCSR855FOP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3a80ab90d23c29cdcd0b3526c90800497f0cb368..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF279KTY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_2.fit.json b/ENCSR855FOP/cherimoya.fold_2.fit.json deleted file mode 100644 index 1493a0e8d958eeded48bfa89fc349eb6e44648d5..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF279KTY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_2.log b/ENCSR855FOP/cherimoya.fold_2.log deleted file mode 100644 index 053520fc11f6a3c0c2d86bd4e6dc88b81d7a0a73..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 36.69710087776184 3.6385059356689453 954.7638549804688 0.34144091606140137 1389.8699951171875 0.2162180244922638 0.63963914 7.71415901184082 True -1 5776 32.086366176605225 0.5558333396911621 1027.991455078125 0.38215702772140503 1261.410400390625 0.28877198696136475 0.5897866 1.8246984481811523 False -2 8664 32.010859966278076 0.5462017059326172 1208.58251953125 0.4284963011741638 1231.5430908203125 0.29642027616500854 0.65658087 0.9025210738182068 True -3 11552 32.0719428062439 1.4702157974243164 1077.220947265625 0.6011922359466553 1207.9268798828125 0.3059810400009155 0.6774675 0.802086591720581 True -4 14440 32.065890073776245 0.5391824245452881 943.890869140625 0.5157430171966553 1188.6033935546875 0.3160368800163269 0.6955335 0.8048166036605835 True -5 17328 32.005125522613525 0.5374970436096191 935.5748901367188 0.5177614688873291 1178.7066650390625 0.320795476436615 0.7023606 0.8267250657081604 True -6 20216 31.94731640815735 0.5276732444763184 956.4341430664062 0.26936349272727966 1173.43603515625 0.32404255867004395 0.71095484 0.7355389595031738 True -7 23104 31.993733406066895 0.5383105278015137 935.1488037109375 0.3242075443267822 1163.513916015625 0.3296317458152771 0.72852886 0.6714714169502258 True -8 25992 31.996279001235962 0.5286974906921387 939.81982421875 0.26433753967285156 1158.371337890625 0.33271685242652893 0.7373743 0.617631196975708 True -9 28880 31.941452026367188 0.528761625289917 1056.9434814453125 0.21348837018013 1153.2869873046875 0.3351593017578125 0.75172067 0.5387152433395386 True -10 31768 34.709557056427 7.925141334533691 879.0533447265625 0.23836137354373932 1145.69775390625 0.3385230600833893 0.7609877 0.4728098213672638 True -11 34656 32.129175662994385 29.881080627441406 943.0481567382812 0.4084906280040741 1139.09814453125 0.34109780192375183 0.7737224 0.4115300178527832 True -12 37544 33.82127094268799 0.5503809452056885 870.2123413085938 0.27170950174331665 1133.017333984375 0.34389829635620117 0.7819341 0.3746562898159027 True -13 40432 31.45889139175415 0.5473031997680664 1006.1922607421875 0.3174225687980652 1125.91650390625 0.3465383052825928 0.7880807 0.34909912943840027 True -14 43320 31.551878452301025 1.4960553646087646 1046.616943359375 0.24725505709648132 1121.447265625 0.3502882719039917 0.7961684 0.3173055648803711 True -15 46208 31.418505907058716 0.5348806381225586 862.8419189453125 0.2889176607131958 1119.02490234375 0.35056692361831665 0.8006256 0.30082952976226807 True -16 49096 31.426527738571167 0.5283026695251465 947.37109375 0.16774383187294006 1119.008544921875 0.3489571213722229 0.80822027 0.2789643108844757 True -17 51984 31.39203429222107 0.5337445735931396 998.41162109375 0.25205421447753906 1114.9559326171875 0.3516763746738434 0.8098995 0.2739393413066864 True -18 54872 31.44248938560486 0.5402612686157227 837.151123046875 0.14053623378276825 1114.5928955078125 0.35147207975387573 0.80991024 0.2720397710800171 True -19 57760 31.41480851173401 0.5404458045959473 925.1326904296875 0.1440945714712143 1117.0963134765625 0.3490913212299347 0.8090982 0.2734951972961426 False diff --git a/ENCSR855FOP/cherimoya.fold_2.performance.tsv b/ENCSR855FOP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index fc24dac033f4604d459f5aa141476d6a07882e3f..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1114.5928955078125 0.308688759803772 0.3514721095561981 0.1870993673801422 0.809910237789154 0.7127023935317993 0.2720397710800171 \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_3.evaluate.json b/ENCSR855FOP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5ecf1ebc86a97ea6c6483c8b381fe5b7cae88103..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF279KTY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_3.fit.json b/ENCSR855FOP/cherimoya.fold_3.fit.json deleted file mode 100644 index 1ecd4fdb355c42c49161bc18c7fabc8efe200bbb..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF279KTY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_3.log b/ENCSR855FOP/cherimoya.fold_3.log deleted file mode 100644 index d899e0451b1208f39ec96a6f209040a109eb0b40..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 35.595847845077515 41.01070284843445 1095.17138671875 0.5293136239051819 1369.340087890625 0.204527348279953 0.63246346 8.402986526489258 True -1 5606 31.313720226287842 39.889469146728516 951.4243774414062 0.460964560508728 1282.4031982421875 0.2682296633720398 0.5449888 1.9034403562545776 False -2 8409 31.22388243675232 0.5833966732025146 1025.7978515625 0.42197656631469727 1253.0615234375 0.27793943881988525 0.6171522 1.2061556577682495 False -3 11212 31.783083200454712 2.5297563076019287 1054.88427734375 0.40804144740104675 1221.270751953125 0.28951114416122437 0.6519223 1.036090612411499 True -4 14015 31.425803899765015 0.5704917907714844 808.0589599609375 0.2793274521827698 1201.8221435546875 0.30060043931007385 0.6665209 0.9104949235916138 True -5 16818 31.31368327140808 0.5682098865509033 944.4666137695312 0.33166688680648804 1189.908935546875 0.30730172991752625 0.6722387 0.8752843141555786 True -6 19621 31.30639672279358 1.4068591594696045 946.3819580078125 0.31167536973953247 1182.7720947265625 0.3121040165424347 0.68857855 1.0359476804733276 True -7 22424 31.665712356567383 0.5677580833435059 1058.087890625 0.2607211768627167 1175.487060546875 0.31249603629112244 0.705202 0.7192091345787048 True -8 25227 31.176392078399658 0.565361499786377 901.0292358398438 0.4426978826522827 1168.8250732421875 0.31668248772621155 0.7163722 0.642874538898468 True -9 28030 31.191834211349487 0.5661954879760742 958.9036865234375 0.18818530440330505 1161.50048828125 0.32142916321754456 0.72542024 0.58590167760849 True -10 30833 31.331881284713745 0.6325602531433105 933.0974731445312 0.33488571643829346 1159.291259765625 0.32142582535743713 0.7376275 0.5112632513046265 True -11 33636 31.33598828315735 0.5637044906616211 937.3634643554688 0.4758339822292328 1150.2288818359375 0.3274846076965332 0.7474422 0.4775654077529907 True -12 36439 30.873106002807617 0.5627286434173584 1106.479248046875 0.42138999700546265 1146.906982421875 0.3283790051937103 0.75878924 0.42380595207214355 True -13 39242 30.463061809539795 0.5615584850311279 1058.033935546875 0.3715952932834625 1144.991455078125 0.32929834723472595 0.7681648 0.400738388299942 True -14 42045 30.47661328315735 0.5622522830963135 950.1715087890625 0.2597234845161438 1138.0997314453125 0.3332422375679016 0.7816892 0.36168327927589417 True -15 44848 30.494497299194336 0.551180362701416 952.0244140625 0.27508899569511414 1136.529296875 0.33306053280830383 0.78833145 0.3322092890739441 True -16 47651 30.482563972473145 0.5614795684814453 874.1126708984375 0.23788395524024963 1135.109375 0.33405494689941406 0.7908607 0.3170747458934784 True -17 50454 30.452972650527954 0.8523051738739014 1047.627197265625 0.22907257080078125 1134.9183349609375 0.33293724060058594 0.79382294 0.30250269174575806 True -18 53257 30.449252367019653 0.5540070533752441 897.9213256835938 0.2507680654525757 1134.8883056640625 0.33429384231567383 0.7927982 0.30018967390060425 False -19 56060 30.452404975891113 0.5542511940002441 977.4532470703125 0.2443358600139618 1135.98779296875 0.3330423831939697 0.79303 0.2998847961425781 False diff --git a/ENCSR855FOP/cherimoya.fold_3.performance.tsv b/ENCSR855FOP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0100d1600fec3e4da36f0481e14fc08281cbdd62..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1134.9183349609375 0.31104981899261475 0.33293724060058594 0.17996464669704437 0.7938229441642761 0.7150865197181702 0.30250269174575806 \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_4.evaluate.json b/ENCSR855FOP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 977c0aee4709ef086536fe9663dc6f33a883e4d4..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF279KTY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_4.fit.json b/ENCSR855FOP/cherimoya.fold_4.fit.json deleted file mode 100644 index 77d51c93a4b38a904de1b9dd9366c71d9c9a7ee6..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF279KTY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR855FOP/cherimoya.fold_4.log b/ENCSR855FOP/cherimoya.fold_4.log deleted file mode 100644 index 82a022f6fb991d15dec7d9d34adca1620ed7a880..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2951 37.260281801223755 3.6528825759887695 1060.7408447265625 0.4799098074436188 1271.3553466796875 0.2029050886631012 0.63042796 7.55012321472168 True -1 5902 32.77807283401489 0.5771567821502686 840.30126953125 0.37932905554771423 1180.437255859375 0.26597151160240173 0.5031635 1.708010196685791 False -2 8853 32.814783811569214 0.5359053611755371 994.5559692382812 0.3210675120353699 1156.982421875 0.27283498644828796 0.618078 0.9157490134239197 False -3 11804 32.7539336681366 0.5465552806854248 912.5589599609375 0.3073696494102478 1131.3759765625 0.2835995852947235 0.68025 0.7355421781539917 True -4 14755 32.749427318573 0.5363163948059082 1056.0894775390625 0.46580246090888977 1113.864990234375 0.2955663502216339 0.6985093 0.8200034499168396 True -5 17706 32.73931097984314 0.5358145236968994 944.0056762695312 0.23047135770320892 1107.115478515625 0.29683342576026917 0.710394 0.6087718605995178 True -6 20657 32.73830842971802 0.5390770435333252 862.67578125 0.2679117023944855 1096.8978271484375 0.3021717965602875 0.7245533 0.5288153290748596 True -7 23608 32.80071210861206 0.5355472564697266 931.48681640625 0.324662446975708 1091.020751953125 0.3066622018814087 0.7390174 0.47885793447494507 True -8 26559 32.98458933830261 0.5426406860351562 892.5079956054688 0.19360150396823883 1085.23779296875 0.30865177512168884 0.76021206 0.4251149892807007 True -9 29510 32.73620653152466 0.5356101989746094 1044.1163330078125 0.331170916557312 1079.0399169921875 0.3120923638343811 0.76547706 0.38130608201026917 True -10 32461 32.72982859611511 0.5359032154083252 905.3273315429688 0.2581517696380615 1079.020751953125 0.3122522830963135 0.77014196 0.3645302951335907 True -11 35412 32.316731452941895 0.5329780578613281 900.4028930664062 0.2909489870071411 1073.8486328125 0.3165968656539917 0.778142 0.3285292685031891 True -12 38363 32.09392285346985 0.5319547653198242 988.4783325195312 0.2911376357078552 1067.4412841796875 0.3187818229198456 0.78645885 0.3068796992301941 True -13 41314 32.0769681930542 0.538719892501831 835.4169921875 0.25621235370635986 1064.7037353515625 0.3210684061050415 0.7920868 0.2869035005569458 True -14 44265 32.06037211418152 0.5329751968383789 1096.5662841796875 0.2625870108604431 1059.4317626953125 0.32413581013679504 0.7978653 0.26857829093933105 True -15 47216 32.133660554885864 0.5351259708404541 872.3731689453125 0.2276688814163208 1059.867431640625 0.3243951201438904 0.80288076 0.2555467486381531 True -16 50167 32.07847213745117 0.5234401226043701 935.8681640625 0.2975179851055145 1056.669921875 0.32559719681739807 0.8080089 0.24223129451274872 True -17 53118 32.207868576049805 0.9165668487548828 857.9334716796875 0.24181032180786133 1056.4212646484375 0.3259527385234833 0.8118049 0.23532825708389282 True -18 56069 32.1715772151947 0.5331358909606934 1028.94091796875 0.1510637104511261 1056.8138427734375 0.3259252905845642 0.8110278 0.23530098795890808 False -19 59020 32.09609532356262 0.5343968868255615 870.2688598632812 0.1368638277053833 1057.84228515625 0.3253798186779022 0.80972534 0.23680908977985382 False diff --git a/ENCSR855FOP/cherimoya.fold_4.performance.tsv b/ENCSR855FOP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index aab083914deb4d21fe0ba352c93c421bddd90ac0..0000000000000000000000000000000000000000 --- a/ENCSR855FOP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1056.4212646484375 0.32024455070495605 0.3259527385234833 0.16889183223247528 0.8118048906326294 0.7122414112091064 0.23532825708389282 \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_0.evaluate.json b/ENCSR856NXV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7b4aa6be59cd10906663eb528cf3c8aded769e83..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF613LWD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_0.fit.json b/ENCSR856NXV/cherimoya.fold_0.fit.json deleted file mode 100644 index d7f0199281d332e97d2342463d9e4e2ccb9c3d8a..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF613LWD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_0.log b/ENCSR856NXV/cherimoya.fold_0.log deleted file mode 100644 index 1c789d4fd9b2448bb89cdaa1087a4fbd7fd28e92..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.506941080093384 3.7800121307373047 1158.6400146484375 1.145106315612793 1531.00048828125 0.2887832820415497 0.403491 6.8279337882995605 True -1 5478 30.54502296447754 19.046029090881348 1195.85009765625 1.2680096626281738 1320.2396240234375 0.4466005861759186 0.46057382 2.5242748260498047 True -2 8217 30.197625160217285 0.5610561370849609 882.3172607421875 0.8572674989700317 1292.178955078125 0.45944005250930786 0.48236138 0.91733717918396 True -3 10956 30.02085781097412 0.5596485137939453 1070.7515869140625 0.8830984830856323 1266.5802001953125 0.4714021384716034 0.5388525 0.5199437141418457 True -4 13695 29.48406958580017 0.5600731372833252 856.0689086914062 0.815769612789154 1252.8856201171875 0.47789567708969116 0.56114435 0.5004644393920898 True -5 16434 29.547417640686035 0.549483060836792 948.9889526367188 0.606132984161377 1247.1927490234375 0.48061874508857727 0.5618289 0.4896177053451538 True -6 19173 29.438077688217163 0.5477714538574219 876.8355712890625 0.668274462223053 1242.4178466796875 0.4834084212779999 0.57195956 0.48714229464530945 True -7 21912 29.456249237060547 2.197361469268799 1138.6474609375 0.4914851784706116 1236.143310546875 0.4887007176876068 0.5789127 0.5005009770393372 True -8 24651 29.523441314697266 0.5489645004272461 915.4182739257812 0.7571191787719727 1232.7073974609375 0.49093106389045715 0.58783793 0.5095970630645752 True -9 27390 29.637153387069702 24.042202472686768 1073.68212890625 0.3601626753807068 1228.3992919921875 0.4935533404350281 0.60251296 0.5076231360435486 True -10 30129 34.16923809051514 0.5634386539459229 937.6640625 0.7424899339675903 1223.0673828125 0.4968332052230835 0.608966 0.5197415351867676 True -11 32868 29.582380771636963 0.5531835556030273 1016.8234252929688 0.5316073894500732 1221.3599853515625 0.4976322650909424 0.62186325 0.4750905930995941 True -12 35607 29.56651282310486 0.5462710857391357 1025.2364501953125 0.643239438533783 1216.4443359375 0.500686764717102 0.63003725 0.4757402837276459 True -13 38346 29.69405961036682 0.5782589912414551 1008.80615234375 0.4421379566192627 1206.971435546875 0.5031209588050842 0.6423777 0.43643078207969666 True -14 41085 29.650787115097046 0.5471045970916748 986.8286743164062 0.4116330146789551 1196.2794189453125 0.5049461126327515 0.65214884 0.4084259569644928 True -15 43824 29.55662202835083 0.54091477394104 910.3936767578125 0.28913891315460205 1186.9095458984375 0.5094337463378906 0.6632781 0.39016780257225037 True -16 46563 37.28245568275452 14.421083211898804 973.722412109375 0.3841749429702759 1188.1746826171875 0.5070879459381104 0.6717089 0.37752634286880493 True -17 49302 29.548331022262573 25.598356008529663 996.3656616210938 0.28005075454711914 1187.0875244140625 0.5077582001686096 0.677807 0.3724929392337799 True -18 52041 32.51687002182007 0.5665388107299805 792.376708984375 0.362247109413147 1183.7396240234375 0.5099801421165466 0.67936677 0.3708668351173401 True -19 54780 29.875052213668823 30.098872184753418 924.1763916015625 0.2965456545352936 1183.9010009765625 0.5098186731338501 0.6781688 0.37206894159317017 False diff --git a/ENCSR856NXV/cherimoya.fold_0.performance.tsv b/ENCSR856NXV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 42f88acae5bfd98b80d54deeeb0aee76db932b12..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1183.7396240234375 0.28105947375297546 0.5099801421165466 0.2630767226219177 0.6793667674064636 0.6447767019271851 0.3708668351173401 \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_1.evaluate.json b/ENCSR856NXV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 650d068f83f689946d59c4e7ea1ee714d363b0c2..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF613LWD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_1.fit.json b/ENCSR856NXV/cherimoya.fold_1.fit.json deleted file mode 100644 index c7778e3307886de6fd9e50ebcecd8bdef37b6834..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF613LWD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_1.log b/ENCSR856NXV/cherimoya.fold_1.log deleted file mode 100644 index 724026828a038996a0576edf486baff4689c112d..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.01670718193054 3.7270941734313965 1004.9946899414062 1.0690701007843018 1725.7579345703125 0.295852929353714 0.43853754 7.2975850105285645 True -1 5510 30.318593978881836 0.9425523281097412 1065.06982421875 0.8934049606323242 1488.659912109375 0.45703983306884766 0.4884059 1.889693260192871 True -2 8265 30.307257890701294 0.6793360710144043 934.9503173828125 0.53546142578125 1470.8167724609375 0.46480023860931396 0.5151111 0.7620574235916138 True -3 11020 30.31602907180786 0.6752171516418457 1062.74609375 0.7016998529434204 1430.3590087890625 0.4777798056602478 0.5670961 0.5500314831733704 True -4 13775 30.308871507644653 0.6674022674560547 1107.4169921875 0.7497090101242065 1415.9432373046875 0.4841443598270416 0.57045114 0.48243263363838196 True -5 16530 30.314553022384644 0.6740140914916992 986.9840087890625 0.8796600699424744 1407.2623291015625 0.4881891906261444 0.58635104 0.4712933897972107 True -6 19285 30.295648097991943 0.6786057949066162 871.599609375 0.7249913215637207 1399.7984619140625 0.4934315085411072 0.595139 0.4649101197719574 True -7 22040 30.25123357772827 0.6736290454864502 964.6671752929688 0.4403572082519531 1395.1485595703125 0.49466487765312195 0.6062478 0.4665748178958893 True -8 24795 29.763435125350952 0.6702437400817871 1040.0880126953125 0.4637683033943176 1387.4140625 0.49962806701660156 0.6255504 0.44632166624069214 True -9 27550 29.651347637176514 0.662086009979248 861.2938232421875 0.47801733016967773 1383.7904052734375 0.5004444122314453 0.63166875 0.451888769865036 True -10 30305 29.725724697113037 0.6679825782775879 990.0747680664062 0.4137856960296631 1377.5374755859375 0.5052417516708374 0.6388865 0.44687536358833313 True -11 33060 29.741291522979736 0.6539390087127686 1031.15185546875 0.7097830772399902 1373.89697265625 0.5065262317657471 0.650973 0.4302182197570801 True -12 35815 29.729630947113037 0.6571056842803955 1034.0311279296875 0.6184585094451904 1366.644775390625 0.5090029835700989 0.6642494 0.4221719801425934 True -13 38570 29.646993160247803 0.8642313480377197 1002.37646484375 0.5703307390213013 1347.5830078125 0.5128713250160217 0.67742705 0.41279342770576477 True -14 41325 29.72364068031311 0.6773078441619873 970.9801635742188 0.38184550404548645 1320.524658203125 0.5162049531936646 0.6868326 0.4066644310951233 True -15 44080 29.65123438835144 0.6596164703369141 975.5013427734375 0.505673885345459 1323.131103515625 0.5188906192779541 0.6955167 0.3938761353492737 True -16 46835 29.63831615447998 0.6821553707122803 921.5055541992188 0.21431727707386017 1303.151123046875 0.519432008266449 0.7050486 0.3911919593811035 True -17 49590 29.68622660636902 4.425548791885376 1068.2666015625 0.3892251253128052 1297.5294189453125 0.5207157731056213 0.7108773 0.3882334530353546 True -18 52345 29.792131423950195 0.6721169948577881 887.7391967773438 0.3651019334793091 1292.2720947265625 0.5214903354644775 0.7111136 0.38822075724601746 True -19 55100 29.711631536483765 0.6640729904174805 861.416748046875 0.5206254124641418 1293.627197265625 0.5213181972503662 0.71193904 0.3895159661769867 True diff --git a/ENCSR856NXV/cherimoya.fold_1.performance.tsv b/ENCSR856NXV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 524d325f7b6b2bc1217591f104aa9c042b802ce2..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1293.627197265625 0.27115920186042786 0.5213181972503662 0.2805106043815613 0.7119390368461609 0.6774255037307739 0.3895159661769867 \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_2.evaluate.json b/ENCSR856NXV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0f5cb019bf2ae129cea24f03d71dc4441bdd4ba1..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF613LWD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_2.fit.json b/ENCSR856NXV/cherimoya.fold_2.fit.json deleted file mode 100644 index c2adf6f00ed534009f832d919ffd05ee1a54ad04..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF613LWD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_2.log b/ENCSR856NXV/cherimoya.fold_2.log deleted file mode 100644 index 90bad426edaa71704e011b20541ed6894d68c5a4..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_2.log +++ /dev/null @@ -1,7 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2890 35.584372997283936 3.5474932193756104 1043.023193359375 0.9954788684844971 1588.3873291015625 0.2933860719203949 0.40160137 6.609004020690918 True -1 5780 31.797316789627075 0.5523991584777832 1039.663818359375 1.1916134357452393 1377.88623046875 0.45041754841804504 0.5010249 1.8846098184585571 True -2 8670 31.804357051849365 0.5981311798095703 908.8541259765625 0.7153520584106445 1347.7320556640625 0.4622456431388855 0.50836676 0.9890345335006714 True -3 11560 31.79841637611389 0.5137715339660645 1088.34716796875 0.558774471282959 1325.498291015625 0.47336915135383606 0.5342512 0.6548399329185486 True -4 14450 31.53298020362854 0.5091636180877686 951.2601318359375 0.7482950687408447 1309.843017578125 0.48112350702285767 0.55741894 0.620701253414154 True -5 17340 31.143747329711914 0.5096421241760254 938.398681640625 0.560397744178772 1305.7218017578125 0.48526531457901 0.55988973 0.7021439671516418 True diff --git a/ENCSR856NXV/cherimoya.fold_2.performance.tsv b/ENCSR856NXV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c3aaedfaaa799f7ef2e9750f2d2ee51e1e118256..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1309.862060546875 0.29464036226272583 0.48112356662750244 0.2562299966812134 0.5574262738227844 0.5210304260253906 0.6206891536712646 \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_3.evaluate.json b/ENCSR856NXV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9a15dbfd9d138b5c9cc5448c7d18452dbbbef216..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF613LWD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_3.fit.json b/ENCSR856NXV/cherimoya.fold_3.fit.json deleted file mode 100644 index 3012d5391b9bf3d7622096c337c22465269248e1..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF613LWD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_3.log b/ENCSR856NXV/cherimoya.fold_3.log deleted file mode 100644 index eed2349b8e9c6324ed6d0733a58e1ed404ce1eb5..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2814 35.720855951309204 22.128814697265625 1272.809814453125 0.8005210161209106 1562.5435791015625 0.2983977496623993 0.44008908 6.808633327484131 True -1 5628 31.336060285568237 0.5875556468963623 1029.392578125 0.7990626096725464 1350.5390625 0.4520314633846283 0.5133148 1.9798232316970825 True -2 8442 38.38913083076477 4.768640518188477 929.99169921875 0.6512503623962402 1319.1318359375 0.46527576446533203 0.52535945 0.8831883072853088 True -3 11256 31.041548490524292 0.5632898807525635 1177.360595703125 0.67070472240448 1299.0418701171875 0.4715481102466583 0.5466883 0.6101597547531128 True -4 14070 31.00331139564514 0.5822653770446777 934.8076171875 0.672464907169342 1289.759765625 0.47553327679634094 0.5520169 0.5083744525909424 True -5 16884 31.141258239746094 0.5769267082214355 1111.559326171875 0.4767398238182068 1284.221923828125 0.4790864884853363 0.54614156 0.5063786506652832 False -6 19698 31.15898633003235 0.8397784233093262 1001.8603515625 0.3991907238960266 1277.2291259765625 0.483757346868515 0.55926293 0.48818960785865784 True -7 22512 31.115114450454712 0.5670077800750732 808.7936401367188 0.49265822768211365 1273.52880859375 0.48587387800216675 0.5694765 0.48455512523651123 True -8 25326 31.15808916091919 0.5815489292144775 1004.3365478515625 0.4850565791130066 1271.872314453125 0.48738306760787964 0.5662859 0.49942508339881897 False -9 28140 31.05199098587036 0.5706281661987305 955.1412353515625 0.47934579849243164 1265.356201171875 0.49169012904167175 0.5791722 0.4840165674686432 True -10 30954 30.909567832946777 1.5015754699707031 1002.294921875 0.5895387530326843 1259.8748779296875 0.4952022135257721 0.5864365 0.47890791296958923 True -11 33768 30.777679443359375 1.4501008987426758 1090.054443359375 0.5865395069122314 1254.9678955078125 0.4983586370944977 0.6013419 0.469765841960907 True -12 36582 30.732290267944336 1.6504030227661133 974.091552734375 0.6672720909118652 1249.4991455078125 0.5013565421104431 0.62421185 0.454539030790329 True -13 39396 30.698246240615845 0.5649375915527344 876.77392578125 0.3568452298641205 1247.445556640625 0.502006471157074 0.636109 0.4439203441143036 True -14 42210 30.598847150802612 0.5682418346405029 1031.900634765625 0.3332084119319916 1239.0399169921875 0.5056725144386292 0.65017325 0.4229733943939209 True -15 45024 30.514108180999756 0.568152666091919 993.024169921875 0.3678347170352936 1233.981689453125 0.5075204372406006 0.6658321 0.41253235936164856 True -16 47838 30.53161883354187 0.5576589107513428 892.937744140625 0.30178266763687134 1230.6871337890625 0.5090847611427307 0.67908823 0.39673835039138794 True -17 50652 30.52164125442505 0.5652954578399658 1009.5462646484375 0.39570364356040955 1227.5189208984375 0.510571300983429 0.6864995 0.38923779129981995 True -18 53466 30.63206934928894 0.5570113658905029 894.6798095703125 0.41870033740997314 1228.8223876953125 0.509096622467041 0.68841726 0.38546666502952576 True -19 56280 30.536148071289062 0.5995237827301025 915.1884155273438 0.24799829721450806 1228.0601806640625 0.509885847568512 0.6885053 0.3873603343963623 True diff --git a/ENCSR856NXV/cherimoya.fold_3.performance.tsv b/ENCSR856NXV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 72e7a02a29fb924e758a089444a1bbca10f8dc6b..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1228.0601806640625 0.27778899669647217 0.5098857879638672 0.2720315456390381 0.6885052919387817 0.653475821018219 0.3873603343963623 \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_4.evaluate.json b/ENCSR856NXV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index cfb1bb8fe21ca653f862f022e3cad95f3e2fd61f..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF613LWD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_4.fit.json b/ENCSR856NXV/cherimoya.fold_4.fit.json deleted file mode 100644 index c875051085b3ac848192f2bdcb252bd869753313..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF613LWD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856NXV/cherimoya.fold_4.log b/ENCSR856NXV/cherimoya.fold_4.log deleted file mode 100644 index d800629126c00a9cac58528b82fc738bae29d353..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2904 36.626999616622925 4.433922052383423 981.2078247070312 0.9489105343818665 1502.2991943359375 0.3023735284805298 0.41973755 5.575805187225342 True -1 5808 31.96547770500183 0.6130714416503906 1027.795654296875 0.6589157581329346 1281.403564453125 0.45675548911094666 0.50522983 1.875954508781433 True -2 8712 31.924337148666382 0.5928664207458496 1247.454833984375 0.6917393803596497 1277.4642333984375 0.45961248874664307 0.5016778 1.0903280973434448 False -3 11616 31.918049097061157 0.5817601680755615 1021.0220336914062 0.7667063474655151 1260.4248046875 0.4665418565273285 0.53749603 0.6757275462150574 True -4 14520 31.87930941581726 0.5851621627807617 978.4551391601562 0.8041543960571289 1246.5064697265625 0.4740559756755829 0.5441472 0.5556041598320007 True -5 17424 31.994850158691406 0.5812017917633057 938.7184448242188 0.5798366069793701 1238.786865234375 0.4784724712371826 0.56456554 0.5323530435562134 True -6 20328 31.896100521087646 0.5761034488677979 1150.021484375 0.5786842703819275 1235.879150390625 0.47952914237976074 0.57330203 0.508179247379303 True -7 23232 31.925591945648193 0.5784091949462891 1080.9429931640625 0.38521820306777954 1229.8817138671875 0.4844418466091156 0.57463795 0.505083441734314 True -8 26136 31.97764015197754 0.5647704601287842 948.7550659179688 0.7045385837554932 1224.2452392578125 0.48780640959739685 0.58977276 0.4723895788192749 True -9 29040 31.97139573097229 0.5754232406616211 996.3927612304688 0.6568706631660461 1220.3143310546875 0.48989415168762207 0.5965415 0.4672641456127167 True -10 31944 31.93976640701294 0.5774216651916504 921.056884765625 0.9475905299186707 1217.4251708984375 0.491310179233551 0.60315406 0.459693968296051 True -11 34848 31.925170421600342 0.5725412368774414 917.533447265625 0.5294713973999023 1210.5223388671875 0.49631401896476746 0.6159772 0.4532839357852936 True -12 37752 31.94756054878235 0.8219320774078369 1022.2943725585938 0.524063766002655 1207.8443603515625 0.49659761786460876 0.6272981 0.42557448148727417 True -13 40656 31.966341733932495 0.5857126712799072 942.8463745117188 0.46244683861732483 1200.0555419921875 0.5012220740318298 0.64199764 0.40398159623146057 True -14 43560 31.867836475372314 0.5671298503875732 1005.60107421875 0.5165691375732422 1194.645263671875 0.5047650337219238 0.65370905 0.39875200390815735 True -15 46464 31.36716341972351 0.5783853530883789 934.02392578125 0.6981200575828552 1191.50341796875 0.5059363842010498 0.6642111 0.3948799669742584 True -16 49368 31.35342240333557 0.5648396015167236 988.1375122070312 0.4456534683704376 1189.1890869140625 0.5067998766899109 0.6736031 0.3785412013530731 True -17 52272 31.52219557762146 0.5654184818267822 962.5888061523438 0.36534005403518677 1190.3673095703125 0.504992663860321 0.67908335 0.3729724586009979 True -18 55176 31.276029348373413 4.744171380996704 880.7647705078125 0.18870976567268372 1187.322998046875 0.5082477331161499 0.6804046 0.3740217089653015 True -19 58080 31.26140069961548 1.1701745986938477 1005.6348876953125 0.44894295930862427 1187.8829345703125 0.507453978061676 0.68066907 0.37471917271614075 True diff --git a/ENCSR856NXV/cherimoya.fold_4.performance.tsv b/ENCSR856NXV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8fd775da06bbd7dcd40c886a7ebf8f195d6db8ad..0000000000000000000000000000000000000000 --- a/ENCSR856NXV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1187.8829345703125 0.28178656101226807 0.507453978061676 0.26732563972473145 0.6806690692901611 0.6426728963851929 0.37471917271614075 \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_0.evaluate.json b/ENCSR856XGY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 791f171f99fb72c377d063b1b2c230c70a259319..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130VBA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_0.fit.json b/ENCSR856XGY/cherimoya.fold_0.fit.json deleted file mode 100644 index 7fcea55ebd531e41cb53a5434872d698794ee29f..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF130VBA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_0.log b/ENCSR856XGY/cherimoya.fold_0.log deleted file mode 100644 index 14b407d049f347b2dd369263cf07c507b0809379..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 35.36744523048401 3.9770443439483643 670.2510375976562 0.31103843450546265 789.6682739257812 0.2872881591320038 0.79942095 5.192607879638672 True -1 5514 30.648783922195435 1.0695865154266357 648.3167724609375 0.5008811354637146 705.5679321289062 0.3634101450443268 0.8417133 1.1897796392440796 True -2 8271 30.581634044647217 0.6004910469055176 652.2825927734375 0.36651769280433655 688.1503295898438 0.37929093837738037 0.850544 0.5445590615272522 True -3 11028 30.556687831878662 0.6379737854003906 483.8602600097656 0.38576075434684753 682.6762084960938 0.38486555218696594 0.85595715 0.41749241948127747 True -4 13785 30.574007272720337 0.6040205955505371 644.157958984375 0.22197723388671875 679.7713012695312 0.38806015253067017 0.8595889 0.3672516942024231 True -5 16542 30.540611505508423 0.5662879943847656 652.6104736328125 0.30425769090652466 677.2404174804688 0.3898070752620697 0.86485034 0.36055800318717957 True -6 19299 30.54417610168457 0.6968982219696045 598.1651000976562 0.23117870092391968 675.4881591796875 0.3915649950504303 0.86992496 0.30685850977897644 True -7 22056 30.58474636077881 0.6353724002838135 512.7359619140625 0.2171604335308075 671.9752807617188 0.3951193690299988 0.8692757 0.27962300181388855 False -8 24813 30.55807614326477 0.5763106346130371 607.5675048828125 0.3871691823005676 671.5728759765625 0.3961794376373291 0.8721801 0.2989487051963806 True -9 27570 30.55643391609192 1.094468355178833 643.3529052734375 0.34172630310058594 667.8671875 0.4002397954463959 0.87639797 0.27996018528938293 True -10 30327 30.56429147720337 0.5991659164428711 623.5415649414062 0.22363489866256714 666.1763916015625 0.4013720750808716 0.87894 0.27274927496910095 True -11 33084 30.111194610595703 0.568406343460083 601.5391235351562 0.2166713923215866 663.473388671875 0.4047582149505615 0.88240236 0.24875546991825104 True -12 35841 29.9222731590271 0.5791053771972656 499.99676513671875 0.28635847568511963 660.3372802734375 0.40924978256225586 0.8864647 0.22757293283939362 True -13 38598 29.931843519210815 0.5868923664093018 472.0791320800781 0.3522992730140686 658.685302734375 0.4103904664516449 0.8906898 0.2204315960407257 True -14 41355 30.006654262542725 0.557182788848877 520.4082641601562 0.18065345287322998 655.2509765625 0.41327840089797974 0.8945371 0.20159883797168732 True -15 44112 30.01513648033142 0.5555362701416016 613.5980224609375 0.2011040449142456 656.8085327148438 0.4116078019142151 0.8976037 0.19332505762577057 True -16 46869 29.961915254592896 0.589440107345581 514.1351928710938 0.17933085560798645 655.1343383789062 0.4138692319393158 0.89950407 0.18689966201782227 True -17 49626 29.98514699935913 0.5804193019866943 468.3934020996094 0.11239941418170929 657.0931396484375 0.41058048605918884 0.8997032 0.1850111186504364 True -18 52383 29.927496194839478 0.5690219402313232 500.3389892578125 0.1308862864971161 655.8494262695312 0.4131976068019867 0.8982612 0.1860240250825882 False -19 55140 29.98956036567688 0.5778615474700928 470.25299072265625 0.1222648173570633 656.1806640625 0.41296806931495667 0.8984377 0.18655838072299957 False diff --git a/ENCSR856XGY/cherimoya.fold_0.performance.tsv b/ENCSR856XGY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 403189fa58c7ce88649eacc08a3c500cee83f192..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -657.0931396484375 0.3750845193862915 0.4105805456638336 0.16987377405166626 0.8997032046318054 0.8617536425590515 0.1850111186504364 \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_1.evaluate.json b/ENCSR856XGY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8c79262c943a22777b19db97e8e7e48e7ef69a15..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130VBA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_1.fit.json b/ENCSR856XGY/cherimoya.fold_1.fit.json deleted file mode 100644 index c2768816f9a214891e1f8b138f44d63779027d3a..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF130VBA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_1.log b/ENCSR856XGY/cherimoya.fold_1.log deleted file mode 100644 index 1c321e5be085dba23bdd83f5d08c95f3b06f8e84..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 34.89233684539795 4.106532096862793 532.9849243164062 0.3683846890926361 912.2901611328125 0.2856914699077606 0.7866189 6.2060346603393555 True -1 5406 30.019021034240723 0.7187743186950684 637.874267578125 0.3883896470069885 805.6163940429688 0.3731020390987396 0.84210134 1.578749179840088 True -2 8109 29.9716579914093 0.7495269775390625 562.341064453125 0.48114776611328125 781.2630004882812 0.391106516122818 0.8521727 0.5858359932899475 True -3 10812 29.981914043426514 0.7596940994262695 556.7957763671875 0.3428841233253479 772.8411865234375 0.3974626660346985 0.8577713 0.5135654807090759 True -4 13515 29.992462396621704 0.7214088439941406 610.425048828125 0.2767678499221802 767.5282592773438 0.40183424949645996 0.86151123 0.47694331407546997 True -5 16218 29.97616982460022 28.801135540008545 723.9853515625 0.314397394657135 763.7385864257812 0.4053652584552765 0.8674028 0.4149025082588196 True -6 18921 30.189640760421753 0.7729089260101318 572.89794921875 0.30376893281936646 761.514404296875 0.40808728337287903 0.86866874 0.40197089314460754 True -7 21624 29.928351163864136 0.7281582355499268 618.7220458984375 0.314397394657135 756.90185546875 0.4129980504512787 0.8707984 0.36470460891723633 True -8 24327 29.967959880828857 0.7148630619049072 595.568115234375 0.35584694147109985 753.2303466796875 0.41564682126045227 0.87347615 0.35594379901885986 True -9 27030 29.924323797225952 0.7229087352752686 532.3456420898438 0.21080099046230316 752.3290405273438 0.41575926542282104 0.8763308 0.3355211615562439 True -10 29733 29.914451360702515 0.7273786067962646 486.25054931640625 0.23218795657157898 747.5010986328125 0.4208660423755646 0.8821618 0.320968896150589 True -11 32436 29.927979707717896 0.718052864074707 632.180419921875 0.1395317167043686 744.5 0.42293885350227356 0.88643855 0.30011186003685 True -12 35139 29.89347529411316 0.7184493541717529 473.5879211425781 0.3501119911670685 740.9915771484375 0.4261840283870697 0.8899305 0.27901536226272583 True -13 37842 29.920162200927734 0.7085797786712646 530.1243896484375 0.21824908256530762 738.3997192382812 0.4278082847595215 0.895512 0.2618230879306793 True -14 40545 29.88839840888977 0.7067427635192871 572.784912109375 0.1912396252155304 736.0271606445312 0.4296720027923584 0.89937806 0.23424388468265533 True -15 43248 29.862823724746704 0.7089560031890869 575.8502197265625 0.2117987424135208 734.6244506835938 0.43045833706855774 0.9032975 0.21478475630283356 True -16 45951 29.329128980636597 0.7031111717224121 538.6249389648438 0.20051699876785278 734.0781860351562 0.43056613206863403 0.90792274 0.20380036532878876 True -17 48654 29.363292932510376 2.0174031257629395 622.386962890625 0.14904755353927612 734.5450439453125 0.4292198717594147 0.908581 0.20061206817626953 True -18 51357 29.333482027053833 0.715688943862915 606.913330078125 0.17318496108055115 733.947509765625 0.43000155687332153 0.9091559 0.19828712940216064 True -19 54060 29.318955183029175 0.7237608432769775 455.3984069824219 0.129594624042511 733.9833374023438 0.4300186336040497 0.90693396 0.19841620326042175 False diff --git a/ENCSR856XGY/cherimoya.fold_1.performance.tsv b/ENCSR856XGY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c963f4309223e9a133f97a8a2967acd84bf01a6a..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -733.947509765625 0.35947656631469727 0.43000152707099915 0.1906907558441162 0.9091559052467346 0.8879115581512451 0.19828712940216064 \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_2.evaluate.json b/ENCSR856XGY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2d94cdb103c9b6d92d639388049f760cdc8300fc..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130VBA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_2.fit.json b/ENCSR856XGY/cherimoya.fold_2.fit.json deleted file mode 100644 index 0e7f70b18f5f4352cda1c6455df769995ec37acd..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF130VBA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_2.log b/ENCSR856XGY/cherimoya.fold_2.log deleted file mode 100644 index 065a4db32c8fbb5d1ea12afcac000c87a41a634d..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 36.29957890510559 3.606032133102417 440.767333984375 0.3975878953933716 837.7064819335938 0.2840402126312256 0.78395045 6.2026591300964355 True -1 5748 31.833829641342163 0.7291085720062256 605.3124389648438 0.4071509540081024 743.0368041992188 0.3669186532497406 0.84188527 1.178220510482788 True -2 8622 31.84420394897461 0.542067289352417 559.52587890625 0.3114803433418274 724.69189453125 0.37864845991134644 0.85122806 0.4910150170326233 True -3 11496 31.824817657470703 0.5743076801300049 504.0023193359375 0.2479780614376068 717.52880859375 0.38411471247673035 0.85562724 0.4167788624763489 True -4 14370 31.849201917648315 0.5665736198425293 480.3292541503906 0.257490336894989 712.2213745117188 0.38871821761131287 0.8594709 0.3659340739250183 True -5 17244 31.79214859008789 0.5630137920379639 603.7264404296875 0.23151469230651855 708.5681762695312 0.3934171497821808 0.8602341 0.3832316994667053 True -6 20118 31.815097093582153 0.5728402137756348 579.9885864257812 0.23494073748588562 704.3575439453125 0.39735862612724304 0.86459374 0.3415491282939911 True -7 22992 31.78042984008789 0.5544052124023438 541.1978759765625 0.21356280148029327 702.7189331054688 0.39913856983184814 0.86768466 0.3397411108016968 True -8 25866 31.858444213867188 0.5758821964263916 555.787109375 0.21969597041606903 699.9537353515625 0.40242260694503784 0.8699906 0.3245121240615845 True -9 28740 31.802484273910522 0.5666859149932861 561.4720458984375 0.26991161704063416 698.0817260742188 0.403939425945282 0.87358165 0.3043498694896698 True -10 31614 31.903146505355835 0.5675458908081055 548.469970703125 0.1789112091064453 695.0357055664062 0.40629711747169495 0.8759111 0.3023766875267029 True -11 34488 31.7924861907959 15.61919379234314 507.62530517578125 0.2111589014530182 691.1011352539062 0.4111584722995758 0.8789717 0.281223326921463 True -12 37362 32.213093280792236 0.7170383930206299 575.24755859375 0.16164547204971313 689.3104858398438 0.41334599256515503 0.8814284 0.2645896375179291 True -13 40236 31.950708150863647 0.5693752765655518 579.3155517578125 0.17886051535606384 687.6344604492188 0.4144327938556671 0.8866862 0.2487901747226715 True -14 43110 31.989468336105347 0.5765631198883057 504.93231201171875 0.17992816865444183 685.8422241210938 0.4163571000099182 0.8886781 0.22697460651397705 True -15 45984 31.929441690444946 0.5815136432647705 502.17840576171875 0.14330190420150757 683.4208374023438 0.417269229888916 0.89383495 0.2114359438419342 True -16 48858 31.85200262069702 0.6017928123474121 571.258544921875 0.2949911653995514 684.359130859375 0.4162994623184204 0.89511794 0.20257818698883057 True -17 51732 31.92642378807068 0.5703108310699463 556.8062744140625 0.17230555415153503 683.8038940429688 0.41727930307388306 0.89592963 0.1992620974779129 True -18 54606 31.89951229095459 0.5704855918884277 587.4901733398438 0.3333744704723358 684.2554931640625 0.41676220297813416 0.8964257 0.19808711111545563 True -19 57480 31.876073122024536 0.5795483589172363 585.7630615234375 0.13199007511138916 683.8275146484375 0.41765981912612915 0.8961092 0.19775615632534027 False diff --git a/ENCSR856XGY/cherimoya.fold_2.performance.tsv b/ENCSR856XGY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f410f56ec7a5a9fb9eba9ded42efff1e0161bd86..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -684.2554931640625 0.3693277835845947 0.41676220297813416 0.17769399285316467 0.896425724029541 0.8637669682502747 0.19808711111545563 \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_3.evaluate.json b/ENCSR856XGY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2f81935f642ca9484861ad57a1715df78aef90dd..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130VBA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_3.fit.json b/ENCSR856XGY/cherimoya.fold_3.fit.json deleted file mode 100644 index f382caef8bb6ee3afb85525312e314c296be55c4..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF130VBA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_3.log b/ENCSR856XGY/cherimoya.fold_3.log deleted file mode 100644 index 4edc98f500207a12772dae97b4640c3cef1debac..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.09113049507141 3.9656035900115967 659.7429809570312 0.44350725412368774 788.6136474609375 0.2999691665172577 0.78524405 6.329095363616943 True -1 5516 30.567709922790527 0.7911262512207031 562.1318359375 0.4307480454444885 705.1364135742188 0.37294802069664 0.84766835 1.0969336032867432 True -2 8274 30.611740112304688 3.864887237548828 647.000244140625 0.3492964804172516 688.14990234375 0.38578012585639954 0.8540211 0.49051082134246826 True -3 11032 30.65254497528076 0.5436596870422363 579.6553955078125 0.3784623146057129 682.0310668945312 0.3906487226486206 0.8635951 0.4904135465621948 True -4 13790 30.574289798736572 0.8762667179107666 576.8533325195312 0.29701417684555054 680.9793701171875 0.39283326268196106 0.8619044 0.47633257508277893 False -5 16548 30.571715593338013 0.5505802631378174 630.5399780273438 0.503883957862854 676.7216186523438 0.398207426071167 0.8657306 0.4348527491092682 True -6 19306 30.563559532165527 1.9403014183044434 490.1508483886719 0.40682318806648254 677.4478759765625 0.39622801542282104 0.866946 0.44994083046913147 True -7 22064 30.582720518112183 0.5471999645233154 691.3092041015625 0.40382152795791626 671.8397216796875 0.4016810953617096 0.86891377 0.3958640992641449 True -8 24822 30.592950582504272 0.550400972366333 641.8170166015625 0.3212614059448242 669.7677612304688 0.40385326743125916 0.8712508 0.3937528431415558 True -9 27580 30.556600332260132 0.5363097190856934 560.4005126953125 0.2066502869129181 668.0438232421875 0.4055269658565521 0.8726187 0.4131758511066437 True -10 30338 30.534104347229004 0.5523715019226074 509.8763427734375 0.1994902491569519 665.3600463867188 0.4082363247871399 0.8750019 0.3830104470252991 True -11 33096 30.60866928100586 0.548084020614624 524.96875 0.15455521643161774 663.1265258789062 0.4111652970314026 0.877262 0.35381612181663513 True -12 35854 30.57425856590271 0.5623509883880615 556.8165283203125 0.27546048164367676 661.4415893554688 0.410983145236969 0.8823475 0.3270018696784973 True -13 38612 30.587384939193726 0.5439572334289551 548.4708251953125 0.2285056859254837 657.93603515625 0.41525110602378845 0.8896631 0.2918604910373688 True -14 41370 30.595178604125977 0.5215244293212891 524.7535400390625 0.26135048270225525 656.21435546875 0.41631999611854553 0.8932287 0.2507724165916443 True -15 44128 30.546226024627686 0.5294129848480225 637.4876708984375 0.1564791202545166 655.4917602539062 0.41715025901794434 0.8985942 0.229500412940979 True -16 46886 30.553683042526245 0.5407552719116211 503.8170166015625 0.20666946470737457 653.9080810546875 0.4173908531665802 0.90088767 0.2119518667459488 True -17 49644 30.60136342048645 0.5449461936950684 569.5111083984375 0.13457517325878143 654.091552734375 0.4174402356147766 0.901272 0.20372046530246735 True -18 52402 30.569293975830078 0.5589900016784668 522.8511962890625 0.2173384577035904 653.6398315429688 0.4188969135284424 0.9026862 0.20217154920101166 True -19 55160 30.65355086326599 0.7550926208496094 493.6551818847656 0.17069080471992493 652.697021484375 0.42052507400512695 0.9006538 0.20045006275177002 False diff --git a/ENCSR856XGY/cherimoya.fold_3.performance.tsv b/ENCSR856XGY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ceb3c80b2f70074ffb610b2c25b2c80446139271..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -653.6398315429688 0.3719523847103119 0.41889694333076477 0.17530913650989532 0.9026861786842346 0.8601033687591553 0.20217154920101166 \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_4.evaluate.json b/ENCSR856XGY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5597f47beb1f138d2af95de45071f4126d51defe..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF130VBA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_4.fit.json b/ENCSR856XGY/cherimoya.fold_4.fit.json deleted file mode 100644 index 47f82ac2cd9010f482bec5e697cfcd95f2af2fb2..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF130VBA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR856XGY/cherimoya.fold_4.log b/ENCSR856XGY/cherimoya.fold_4.log deleted file mode 100644 index 00cf17ef33beee9dd0a356f87e75be68ec32cfc5..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2800 36.91689085960388 4.128120422363281 636.5074462890625 0.351790189743042 735.2938842773438 0.2877865135669708 0.7945655 6.217514991760254 True -1 5600 31.14209747314453 0.6294944286346436 563.1151123046875 0.342607319355011 663.9080810546875 0.35668623447418213 0.8392669 1.1028085947036743 True -2 8400 31.083354949951172 0.613034725189209 543.9933471679688 0.3425372242927551 652.877685546875 0.36682620644569397 0.845719 0.5055912137031555 True -3 11200 31.079006910324097 0.6023714542388916 706.0825805664062 0.2706852853298187 644.952392578125 0.3729093670845032 0.8521306 0.4607539176940918 True -4 14000 31.022051095962524 2.842684030532837 474.2181396484375 0.4337308704853058 641.6848754882812 0.3775390088558197 0.8562509 0.35810989141464233 True -5 16800 31.03622555732727 6.61175799369812 623.4268798828125 0.279232382774353 638.1309204101562 0.3816756010055542 0.8583007 0.32629790902137756 True -6 19600 31.03104329109192 0.6086921691894531 600.3294067382812 0.28994476795196533 636.0491943359375 0.38375699520111084 0.86187184 0.29475080966949463 True -7 22400 31.01988410949707 0.6121957302093506 519.1688232421875 0.19111913442611694 632.8245239257812 0.38778892159461975 0.86590767 0.2936899960041046 True -8 25200 30.997678756713867 0.5943934917449951 626.3729858398438 0.2730872631072998 630.4476318359375 0.3898088335990906 0.87013453 0.2861039638519287 True -9 28000 31.019972562789917 0.5994856357574463 587.1506958007812 0.4205855131149292 627.9683227539062 0.39315903186798096 0.8714783 0.2741395831108093 True -10 30800 31.02347230911255 0.5930259227752686 535.5059814453125 0.3141882121562958 628.0224609375 0.3913492262363434 0.8740892 0.2626760005950928 True -11 33600 31.046759128570557 0.589221715927124 588.07666015625 0.289777934551239 626.4717407226562 0.3936166763305664 0.8790204 0.24998806416988373 True -12 36400 31.076868534088135 0.6069316864013672 555.5046997070312 0.2762010395526886 624.10791015625 0.39594125747680664 0.88462865 0.2272511124610901 True -13 39200 31.064531087875366 0.6039597988128662 515.1062622070312 0.21112501621246338 621.1640625 0.39907723665237427 0.8862835 0.21369816362857819 True -14 42000 31.066729307174683 0.5962510108947754 514.910400390625 0.2193140983581543 619.9803466796875 0.40154147148132324 0.89127415 0.20261052250862122 True -15 44800 31.055717706680298 1.5124731063842773 574.4929809570312 0.2786586284637451 619.445068359375 0.4019147455692291 0.89489883 0.18919943273067474 True -16 47600 31.036936044692993 0.6116766929626465 521.4287719726562 0.2016409933567047 618.7059936523438 0.40287357568740845 0.8974236 0.18338777124881744 True -17 50400 31.11191987991333 0.6061177253723145 571.6192626953125 0.21147911250591278 617.6175537109375 0.4041343033313751 0.8972296 0.1806454360485077 False -18 53200 31.149263858795166 0.612708330154419 623.9215698242188 0.13162003457546234 618.5233764648438 0.4031505882740021 0.8974091 0.17914868891239166 False -19 56000 31.109033346176147 0.6066584587097168 502.3604736328125 0.18253572285175323 617.54736328125 0.40459173917770386 0.8991779 0.17972858250141144 True diff --git a/ENCSR856XGY/cherimoya.fold_4.performance.tsv b/ENCSR856XGY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e13d7c19d4764a34debd5cc2c368274a83824a2a..0000000000000000000000000000000000000000 --- a/ENCSR856XGY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -617.54736328125 0.3830583691596985 0.40459176898002625 0.16604691743850708 0.8991779088973999 0.8499875664710999 0.17972858250141144 \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_0.evaluate.json b/ENCSR857AEB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f511da4dd950a8bb58f57406cd442f46ca3dad0a..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF073KWU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_0.fit.json b/ENCSR857AEB/cherimoya.fold_0.fit.json deleted file mode 100644 index 0b7b6b778465ba1b03007c76ebc66d7b8f3ff441..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF073KWU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_0.log b/ENCSR857AEB/cherimoya.fold_0.log deleted file mode 100644 index da45b92f995fdd67a8546a735e68392628525d0a..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 36.63872766494751 4.262413740158081 1294.138427734375 1.1965569257736206 1960.6324462890625 0.27452948689460754 0.5512244 9.700211524963379 True -1 5506 30.267664194107056 0.8335320949554443 1290.5634765625 0.9337337017059326 1711.8271484375 0.39295676350593567 0.64086866 3.6487131118774414 True -2 8259 30.65179944038391 0.5613586902618408 1381.295654296875 1.1768168210983276 1665.0252685546875 0.4126341938972473 0.643642 1.511250615119934 True -3 11012 30.670910358428955 0.5652105808258057 1387.41259765625 0.9044870734214783 1649.4517822265625 0.4163506329059601 0.6438167 1.1002254486083984 True -4 13765 30.594009160995483 0.5250411033630371 1184.706787109375 0.9964582920074463 1638.7398681640625 0.4229274392127991 0.65513027 1.2693161964416504 True -5 16518 30.606233835220337 0.5613775253295898 1333.8160400390625 1.019851803779602 1627.222412109375 0.4269177317619324 0.66629183 1.0906751155853271 True -6 19271 30.5892493724823 0.550642728805542 1405.6695556640625 0.5452919602394104 1619.3343505859375 0.4305189549922943 0.67054546 1.0191336870193481 True -7 22024 30.58463406562805 0.7936272621154785 1254.9423828125 0.6827564239501953 1612.2864990234375 0.4342876970767975 0.67839295 1.013654112815857 True -8 24777 30.645588397979736 0.570380449295044 1545.6796875 0.7403741478919983 1606.4661865234375 0.43756726384162903 0.68495256 0.9345489144325256 True -9 27530 30.57939839363098 0.5512087345123291 1276.1109619140625 1.1187764406204224 1605.51513671875 0.43647512793540955 0.6949193 0.893552839756012 True -10 30283 30.630097150802612 1.972470998764038 1162.9232177734375 0.5492919683456421 1591.28662109375 0.44476044178009033 0.7017091 0.7983971238136292 True -11 33036 30.787935733795166 13.447298765182495 1397.29541015625 0.7761400938034058 1589.4686279296875 0.4449010491371155 0.7081763 0.7430707812309265 True -12 35789 30.787472248077393 0.5627906322479248 1038.32958984375 0.830649197101593 1582.9605712890625 0.44706153869628906 0.7183849 0.7005788683891296 True -13 38542 30.79839539527893 0.5625653266906738 1145.315673828125 0.6804804801940918 1576.67919921875 0.4504188895225525 0.7247432 0.623369038105011 True -14 41295 31.005881309509277 17.398502826690674 1239.5975341796875 0.769271194934845 1570.0640869140625 0.45287948846817017 0.7328004 0.5740801095962524 True -15 44048 30.831554412841797 0.5423672199249268 1137.8060302734375 0.49029746651649475 1568.9583740234375 0.4519694149494171 0.73951364 0.5441961884498596 True -16 46801 30.833789825439453 0.6850183010101318 1171.668701171875 0.4883793890476227 1565.08056640625 0.4544355571269989 0.7451774 0.51922607421875 True -17 49554 30.836750745773315 1.4179472923278809 1271.4903564453125 0.43732085824012756 1568.3056640625 0.4519762396812439 0.7473766 0.502476155757904 True -18 52307 30.678237915039062 1.695288896560669 1178.217529296875 0.5083091259002686 1570.571044921875 0.4511781930923462 0.7487014 0.50138920545578 True -19 55060 30.758066177368164 1.1227717399597168 1264.426513671875 0.41823339462280273 1567.05517578125 0.4541340470314026 0.7477763 0.5067077279090881 False diff --git a/ENCSR857AEB/cherimoya.fold_0.performance.tsv b/ENCSR857AEB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 80df533db77c307f17467d8d23722a97515f429e..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1570.571044921875 0.2648938000202179 0.4511781930923462 0.29942408204078674 0.7487013936042786 0.7115085124969482 0.50138920545578 \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_1.evaluate.json b/ENCSR857AEB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f4de22d3567daf172d406d1eeee72547efefd5c5..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF073KWU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_1.fit.json b/ENCSR857AEB/cherimoya.fold_1.fit.json deleted file mode 100644 index f8bf454389eeed876bb138f73e67181f045441ec..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF073KWU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_1.log b/ENCSR857AEB/cherimoya.fold_1.log deleted file mode 100644 index 97c1a8c0a8d6ec67ab5cb575f83bbcd051bf00f3..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 34.669355630874634 4.744689702987671 1292.1488037109375 0.9410570859909058 2197.03564453125 0.27968016266822815 0.5711485 11.239916801452637 True -1 5502 30.850470066070557 0.7844667434692383 1275.91650390625 1.5218842029571533 1898.138916015625 0.40915828943252563 0.6571626 3.521780014038086 True -2 8253 30.644810438156128 0.7447047233581543 1579.067138671875 1.119679570198059 1861.1502685546875 0.4189710319042206 0.6640807 1.3410303592681885 True -3 11004 30.63031816482544 0.727053165435791 1320.104248046875 0.7103005051612854 1835.5120849609375 0.42826661467552185 0.67384166 1.1190179586410522 True -4 13755 30.58902621269226 0.7276768684387207 989.920654296875 0.7652223110198975 1811.778564453125 0.436006098985672 0.6831487 1.017820119857788 True -5 16506 30.56870150566101 0.7123522758483887 1169.79833984375 0.5665001273155212 1800.0877685546875 0.4426266849040985 0.6962223 1.0502169132232666 True -6 19257 30.557866096496582 0.721304178237915 1376.70849609375 0.8172925710678101 1792.6043701171875 0.4443046748638153 0.70414937 0.9616940021514893 True -7 22008 30.520569562911987 0.7260491847991943 1189.61572265625 0.9456780552864075 1781.371826171875 0.44967713952064514 0.7087028 0.8754900097846985 True -8 24759 30.568349599838257 0.7176690101623535 1407.5545654296875 0.7132948637008667 1770.3599853515625 0.453143835067749 0.7194337 0.894406259059906 True -9 27510 30.59694004058838 0.7494792938232422 1145.1573486328125 0.43586498498916626 1764.675048828125 0.4547205865383148 0.7230674 0.8034420013427734 True -10 30261 30.654757738113403 0.7372386455535889 1140.312255859375 0.6517325639724731 1751.105712890625 0.46037712693214417 0.7349749 0.719023585319519 True -11 33012 30.692758083343506 0.7304184436798096 1439.2117919921875 0.7253458499908447 1741.6934814453125 0.4630599021911621 0.74395984 0.6561377644538879 True -12 35763 30.606122255325317 0.7316169738769531 1415.5196533203125 0.8205119371414185 1733.8834228515625 0.4664008915424347 0.7513746 0.6174811124801636 True -13 38514 30.621630430221558 0.7263069152832031 1286.223876953125 0.9054290652275085 1733.6085205078125 0.4652266204357147 0.76069564 0.5808830857276917 True -14 41265 30.600502967834473 0.7217409610748291 1372.699951171875 0.7902461290359497 1720.920166015625 0.4710003733634949 0.76856506 0.5395205616950989 True -15 44016 30.65548038482666 0.732659101486206 1056.069580078125 0.6741726398468018 1726.0296630859375 0.46814122796058655 0.7747315 0.5160950422286987 True -16 46767 30.641250371932983 0.7315912246704102 1166.935791015625 0.5604561567306519 1716.935791015625 0.4718678295612335 0.78072643 0.4994339346885681 True -17 49518 30.579511404037476 0.7199952602386475 1298.932373046875 0.6139551401138306 1721.7474365234375 0.4686836004257202 0.7806642 0.49008867144584656 False -18 52269 32.91102147102356 1.381821870803833 1088.5704345703125 0.5139787793159485 1725.672119140625 0.4681416451931 0.78168476 0.4847056269645691 True -19 55020 30.638275146484375 0.7145016193389893 1012.0150146484375 0.26111018657684326 1725.739990234375 0.4681164026260376 0.78068966 0.4875369966030121 False diff --git a/ENCSR857AEB/cherimoya.fold_1.performance.tsv b/ENCSR857AEB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f1450f5894d8ef73860fce2fc2a7757999204872..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1725.672119140625 0.25240981578826904 0.4681416451931 0.32289180159568787 0.7816847562789917 0.7564366459846497 0.4847056269645691 \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_2.evaluate.json b/ENCSR857AEB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6d4600aa3dcaea8c881a480fc0bcc5b0d2ecd86c..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF073KWU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_2.fit.json b/ENCSR857AEB/cherimoya.fold_2.fit.json deleted file mode 100644 index 46243e061dc2bb38226e8e79bbe3e2765dd10723..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF073KWU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_2.log b/ENCSR857AEB/cherimoya.fold_2.log deleted file mode 100644 index a2f73a99ed4b23edb7a1b6eef2d7c5f134d1ddbb..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 36.89547944068909 4.635316610336304 1836.56640625 1.0989329814910889 2008.614013671875 0.2858999967575073 0.55605525 9.226302146911621 True -1 5784 32.21324896812439 0.6385130882263184 1604.2998046875 1.737754225730896 1748.7454833984375 0.39997732639312744 0.64520967 3.3425848484039307 True -2 8676 32.192829847335815 0.6087045669555664 1235.3031005859375 0.8615853190422058 1718.58740234375 0.41214534640312195 0.6504246 1.7821143865585327 True -3 11568 32.2251238822937 0.5590684413909912 1475.28125 0.8695040941238403 1693.3759765625 0.4231919050216675 0.6526847 1.3846439123153687 True -4 14460 32.30392503738403 21.723124742507935 1407.302001953125 1.0289160013198853 1678.454345703125 0.4290514886379242 0.6648681 1.09946608543396 True -5 17352 32.27422618865967 0.550633430480957 1340.394775390625 0.6428439021110535 1675.4971923828125 0.4308833181858063 0.67315996 1.1397993564605713 True -6 20244 32.27534341812134 0.5432648658752441 1381.454833984375 0.7178991436958313 1668.11474609375 0.4348609149456024 0.6773066 1.1348133087158203 True -7 23136 32.180195569992065 0.5485501289367676 1436.130859375 0.7451776266098022 1659.398681640625 0.436723530292511 0.6875271 0.9702505469322205 True -8 26028 32.19182300567627 0.5549271106719971 1069.556884765625 0.6684926152229309 1649.6424560546875 0.4411355257034302 0.6925844 0.9077585935592651 True -9 28920 32.24125385284424 0.5392210483551025 1372.485107421875 0.865626335144043 1643.4273681640625 0.4427705705165863 0.7008948 0.7951058149337769 True -10 31812 32.25822877883911 0.5442335605621338 1079.51123046875 0.6505369544029236 1636.85595703125 0.4458421468734741 0.7086505 0.7579596638679504 True -11 34704 32.18224740028381 0.5430054664611816 1276.6409912109375 0.5454058647155762 1627.907958984375 0.45007964968681335 0.7188578 0.6919546127319336 True -12 37596 32.15348482131958 0.5477862358093262 1259.0645751953125 0.7011888027191162 1618.806640625 0.45403873920440674 0.72882307 0.6385818123817444 True -13 40488 32.23085641860962 0.5442190170288086 1722.630126953125 0.5392024517059326 1616.2347412109375 0.453927606344223 0.73679173 0.5805941224098206 True -14 43380 32.15058970451355 0.5281836986541748 1242.68994140625 0.6018083691596985 1607.76806640625 0.45875829458236694 0.74470615 0.5541328191757202 True -15 46272 32.46871829032898 0.5448827743530273 1315.267333984375 0.4108985364437103 1599.7789306640625 0.46162891387939453 0.7519357 0.5249349474906921 True -16 49164 32.16621255874634 1.0139074325561523 1014.7691040039062 0.5208216905593872 1601.821044921875 0.46021682024002075 0.7575696 0.5008375644683838 True -17 52056 32.18564987182617 0.5381691455841064 1185.28955078125 0.5380218029022217 1599.7276611328125 0.4618358314037323 0.76113075 0.4903748333454132 True -18 54948 31.520564317703247 0.5291635990142822 1170.115234375 0.316858172416687 1604.274169921875 0.4599396586418152 0.75950426 0.4928310811519623 False -19 57840 31.53646445274353 0.5956497192382812 1065.1004638671875 0.7497797608375549 1607.23583984375 0.45816293358802795 0.76076907 0.49407967925071716 False diff --git a/ENCSR857AEB/cherimoya.fold_2.performance.tsv b/ENCSR857AEB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6ce2a9a0590b231a1650d0a0a59a25f3a8e2a6ff..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1599.7276611328125 0.26149114966392517 0.4618358016014099 0.30838337540626526 0.7611307501792908 0.7307131886482239 0.4903748333454132 \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_3.evaluate.json b/ENCSR857AEB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f9d534a19405b8cf3423fb4656da17344b23a8e9..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF073KWU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_3.fit.json b/ENCSR857AEB/cherimoya.fold_3.fit.json deleted file mode 100644 index 6828bac9d509b16f6eab0c869cf2884f4c0c9eab..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF073KWU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_3.log b/ENCSR857AEB/cherimoya.fold_3.log deleted file mode 100644 index 6fe14ae2f2e020a8346510343e15a9e5e7640eb3..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2813 36.067575454711914 4.617370843887329 1300.5911865234375 0.9461543560028076 2021.3780517578125 0.2868606150150299 0.5786614 11.530374526977539 True -1 5626 31.397926092147827 0.6054069995880127 1456.357421875 0.9393323063850403 1763.30029296875 0.4045930504798889 0.65514296 3.3047397136688232 True -2 8439 31.92052912712097 0.5881917476654053 1411.73779296875 1.198848009109497 1732.4014892578125 0.416841983795166 0.6613314 1.4567298889160156 True -3 11252 31.439118146896362 0.5950007438659668 1333.546875 0.8638882040977478 1720.5234375 0.42043060064315796 0.67049974 1.2008649110794067 True -4 14065 31.39868450164795 0.5663497447967529 1184.82568359375 1.1162986755371094 1703.9677734375 0.42927488684654236 0.67780215 1.149025797843933 True -5 16878 31.37303137779236 0.5711276531219482 1316.100341796875 0.6197942495346069 1692.689208984375 0.43306297063827515 0.6885314 0.9426494240760803 True -6 19691 31.172682762145996 0.5778899192810059 1109.646728515625 0.9450774192810059 1676.927001953125 0.4417211711406708 0.6907395 0.8729989528656006 True -7 22504 30.625654220581055 0.5650997161865234 1187.325927734375 0.8611254692077637 1678.4105224609375 0.4385276734828949 0.6992542 0.7948841452598572 True -8 25317 30.719319105148315 0.5629067420959473 1131.51611328125 1.3692262172698975 1667.089599609375 0.4451589286327362 0.70427454 0.8630701303482056 True -9 28130 30.682383060455322 0.5651359558105469 1431.36865234375 0.9575772881507874 1662.177978515625 0.4473195970058441 0.71114296 0.8099921941757202 True -10 30943 30.687255859375 0.5618619918823242 1150.2978515625 0.36181989312171936 1653.9169921875 0.4516147971153259 0.71909934 0.7706307172775269 True -11 33756 30.730653762817383 0.5577666759490967 1195.025146484375 0.8546743392944336 1651.3839111328125 0.4520578682422638 0.7262693 0.6896836757659912 True -12 36569 30.69886827468872 0.9930219650268555 1581.869384765625 0.7910411357879639 1642.4002685546875 0.45646199584007263 0.7334872 0.6316170692443848 True -13 39382 30.74305772781372 0.5605061054229736 1089.9757080078125 0.5173105597496033 1641.554443359375 0.45562565326690674 0.7428867 0.6024472713470459 True -14 42195 30.71389889717102 0.5599310398101807 1400.9962158203125 0.9676904678344727 1628.5860595703125 0.4633610248565674 0.7507355 0.5585669875144958 True -15 45008 30.724117279052734 1.3877146244049072 1378.5394287109375 0.4999420940876007 1630.2620849609375 0.4609951674938202 0.75940925 0.5205740928649902 True -16 47821 30.811225414276123 0.5700085163116455 1249.5760498046875 0.2838069200515747 1625.703369140625 0.46480444073677063 0.7609385 0.5172132253646851 True -17 50634 30.632097721099854 0.5839622020721436 1142.166748046875 0.45610788464546204 1632.511474609375 0.4587710499763489 0.76542574 0.5011179447174072 True -18 53447 30.746842622756958 0.9396510124206543 1390.9864501953125 0.6134219169616699 1626.19775390625 0.4625723958015442 0.7655885 0.4919292628765106 True -19 56260 30.7319815158844 2.035285234451294 1236.935546875 0.2755172848701477 1631.5889892578125 0.45879220962524414 0.76445425 0.49677860736846924 False diff --git a/ENCSR857AEB/cherimoya.fold_3.performance.tsv b/ENCSR857AEB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9f2999546aef79a467e0fd879378628ec30c78c4..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1626.19775390625 0.258694589138031 0.4625723958015442 0.3082995116710663 0.7655885219573975 0.735545814037323 0.4919292628765106 \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_4.evaluate.json b/ENCSR857AEB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 366b64b09b9aa8388d3d68c22f3772ba7663a881..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF073KWU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_4.fit.json b/ENCSR857AEB/cherimoya.fold_4.fit.json deleted file mode 100644 index 1d42edde31288bf4e6ba421656f42deb6c923dfc..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF073KWU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857AEB/cherimoya.fold_4.log b/ENCSR857AEB/cherimoya.fold_4.log deleted file mode 100644 index df1b01e775a02760f487b8c5f77ee4cd72d7c389..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.706331968307495 4.611979961395264 1259.1475830078125 1.1829025745391846 1917.6470947265625 0.28549259901046753 0.5576515 9.550329208374023 True -1 5744 32.0639386177063 0.5843906402587891 1752.8885498046875 1.2362185716629028 1676.791259765625 0.40063029527664185 0.64490277 3.1074347496032715 True -2 8616 32.046332597732544 0.6277263164520264 1873.89697265625 1.2534637451171875 1652.844482421875 0.41057145595550537 0.6523881 2.00746488571167 True -3 11488 31.99330186843872 0.5459990501403809 1482.3348388671875 1.4543224573135376 1637.476318359375 0.41695380210876465 0.6537594 1.573594331741333 True -4 14360 32.05800795555115 0.5451757907867432 1385.028076171875 0.7284415364265442 1623.992919921875 0.42227259278297424 0.6624741 1.228108286857605 True -5 17232 32.00249981880188 0.5619397163391113 1376.642333984375 0.9314211010932922 1612.3492431640625 0.4283306896686554 0.6719904 1.1968696117401123 True -6 20104 32.073034048080444 0.561145544052124 1411.03271484375 0.9173291325569153 1604.95458984375 0.4301709532737732 0.6815646 0.9979801774024963 True -7 22976 31.957297563552856 1.6417438983917236 1161.066162109375 0.7635773420333862 1592.782470703125 0.43719080090522766 0.69181406 0.9069724082946777 True -8 25848 31.56571674346924 0.540386438369751 1230.708984375 0.71465665102005 1591.8778076171875 0.43581604957580566 0.6988549 0.8296594023704529 True -9 28720 31.356280088424683 0.5472683906555176 1098.39697265625 0.4392450451850891 1582.17529296875 0.44089871644973755 0.7074908 0.726989209651947 True -10 31592 31.2960946559906 0.538341760635376 1358.128662109375 0.9147657155990601 1574.2806396484375 0.4451518654823303 0.713424 0.7137558460235596 True -11 34464 31.298635959625244 0.5343103408813477 1238.29052734375 0.5568175315856934 1572.78564453125 0.44461730122566223 0.72173315 0.6622698307037354 True -12 37336 31.315414905548096 0.5408649444580078 1034.776123046875 0.9997262358665466 1569.2342529296875 0.44585585594177246 0.72744554 0.6340147852897644 True -13 40208 31.349419593811035 0.5481455326080322 1305.000244140625 0.3774273991584778 1561.7274169921875 0.44950273633003235 0.73588765 0.5777573585510254 True -14 43080 31.334542751312256 0.5483524799346924 1276.478515625 0.5540096759796143 1557.3619384765625 0.45117852091789246 0.7425143 0.5430039763450623 True -15 45952 32.015392541885376 0.5467581748962402 1421.43017578125 0.48106369376182556 1550.59423828125 0.45424574613571167 0.7494813 0.5096922516822815 True -16 48824 31.34697961807251 0.5448119640350342 1218.025146484375 0.43727725744247437 1555.019287109375 0.4519791603088379 0.7535503 0.4961053133010864 True -17 51696 31.398491382598877 0.5477242469787598 1308.4739990234375 0.4030040502548218 1553.212890625 0.45369598269462585 0.755751 0.4810205399990082 True -18 54568 31.348665475845337 0.5454039573669434 1283.008544921875 0.40069109201431274 1555.730224609375 0.45314711332321167 0.75562996 0.48260653018951416 False -19 57440 31.366764307022095 0.5484311580657959 1282.9052734375 0.34031885862350464 1557.7186279296875 0.4520167410373688 0.755085 0.4845086634159088 False diff --git a/ENCSR857AEB/cherimoya.fold_4.performance.tsv b/ENCSR857AEB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a7cdb0c623f660592f5efd8db93241d131e1e673..0000000000000000000000000000000000000000 --- a/ENCSR857AEB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1553.212890625 0.26423579454421997 0.45369598269462585 0.29918545484542847 0.7557510137557983 0.7175980806350708 0.4810205399990082 \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_0.evaluate.json b/ENCSR857MCZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 32502c1e06b9663e3fa2a1ac4733d853b01a01a1..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF865BDK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_0.fit.json b/ENCSR857MCZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 0af37410f8f47f79cae63a82cccd90f7566f69b1..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF865BDK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_0.log b/ENCSR857MCZ/cherimoya.fold_0.log deleted file mode 100644 index 442972a3c07226324f7587987eb1b6dc885664a1..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1492 21.206793308258057 4.7670652866363525 282.9105529785156 0.5081546306610107 420.3342590332031 0.40595492720603943 0.59161806 14.682380676269531 True -1 2984 16.560439586639404 0.39978718757629395 223.1804962158203 0.47254809737205505 363.409912109375 0.4905877709388733 0.6769243 4.786588668823242 True -2 4476 16.518741607666016 0.3378417491912842 258.1905822753906 0.6762704849243164 343.294677734375 0.5445960760116577 0.6992042 1.66679048538208 True -3 5968 16.61802339553833 0.31585192680358887 315.55828857421875 0.5528421401977539 335.9804382324219 0.560912013053894 0.714511 0.6030241250991821 True -4 7460 16.57009482383728 0.3080463409423828 265.42279052734375 0.42977359890937805 333.431884765625 0.5662867426872253 0.72397 0.46568983793258667 True -5 8952 16.559889554977417 0.3119935989379883 257.54461669921875 0.6102244853973389 332.2371520996094 0.5695272088050842 0.72776103 0.41487452387809753 True -6 10444 16.52579140663147 0.3065361976623535 230.2866668701172 0.3699776530265808 331.37774658203125 0.5715972185134888 0.73353946 0.39079350233078003 True -7 11936 16.566265106201172 0.30992746353149414 252.80593872070312 0.32979387044906616 330.7608947753906 0.5731293559074402 0.7337116 0.3968367576599121 True -8 13428 17.324782848358154 0.3165600299835205 276.6208190917969 0.45935213565826416 330.260009765625 0.5746439099311829 0.7340539 0.3859204649925232 True -9 14920 16.602652549743652 0.31624364852905273 301.17474365234375 0.3113071322441101 329.65374755859375 0.5763137340545654 0.73716253 0.3610530197620392 True -10 16412 16.60361361503601 0.31473755836486816 256.821044921875 0.3380083441734314 329.05780029296875 0.5778002142906189 0.7437367 0.34683817625045776 True -11 17904 16.621873140335083 0.3147850036621094 294.44488525390625 0.26432204246520996 328.5264587402344 0.5791513323783875 0.7488465 0.34024888277053833 True -12 19396 16.580387592315674 0.3045778274536133 253.63645935058594 0.3674634099006653 328.0984191894531 0.5803674459457397 0.75389755 0.334605872631073 True -13 20888 16.26947259902954 0.30260777473449707 287.0301818847656 0.2262335568666458 327.57379150390625 0.5816132426261902 0.7605588 0.32514142990112305 True -14 22380 16.24813437461853 0.29624247550964355 264.71307373046875 0.27037984132766724 327.4832763671875 0.5820301175117493 0.7646807 0.3187922537326813 True -15 23872 16.227553606033325 0.30309057235717773 268.1455993652344 0.17749974131584167 327.5849609375 0.5815792679786682 0.7644519 0.32239288091659546 False -16 25364 16.244226217269897 0.5865335464477539 292.3456115722656 0.1632949411869049 327.7704162597656 0.5809637308120728 0.76199096 0.3261620104312897 False -17 26856 16.255568265914917 0.3037302494049072 253.01708984375 0.20949316024780273 328.06658935546875 0.5797967910766602 0.7588836 0.3361875116825104 False -18 28348 16.24982237815857 0.3004112243652344 225.87692260742188 0.14764615893363953 328.3532409667969 0.5790504813194275 0.75495166 0.3429122269153595 False -19 29840 16.24609351158142 0.3073995113372803 267.5169372558594 0.16416004300117493 328.57330322265625 0.5783522129058838 0.75354683 0.34856441617012024 False diff --git a/ENCSR857MCZ/cherimoya.fold_0.performance.tsv b/ENCSR857MCZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1f823f59780c8d79dd089b2af738e7fa3e68735a..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -327.4832763671875 0.3279072046279907 0.5820301175117493 0.21136590838432312 0.7646806836128235 0.7138631343841553 0.3187922537326813 \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_1.evaluate.json b/ENCSR857MCZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bc44cb10e6b88d57d668c604a6625c5edb70e05a..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF865BDK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_1.fit.json b/ENCSR857MCZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 090ceef1f28e9aabd4da012066bc2338488cf92f..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF865BDK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_1.log b/ENCSR857MCZ/cherimoya.fold_1.log deleted file mode 100644 index ff982d4af8544191a52074e2d106dad008f2edfe..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1508 21.382890939712524 4.015592575073242 321.8916015625 0.5257432460784912 449.0426940917969 0.4225136637687683 0.5476255 15.315113067626953 True -1 3016 16.74928307533264 0.4364302158355713 243.07794189453125 0.5325788259506226 390.1642761230469 0.5042203664779663 0.6687021 4.4017205238342285 True -2 4524 16.755051374435425 0.372694730758667 304.609375 0.5269016027450562 370.18804931640625 0.5516744256019592 0.6970789 1.4272239208221436 True -3 6032 16.732958555221558 0.36237382888793945 247.08441162109375 0.41634005308151245 363.3483581542969 0.5685912370681763 0.7145184 0.5690474510192871 True -4 7540 16.721817016601562 9.648066997528076 250.51478576660156 0.5775784254074097 361.5062255859375 0.5732636451721191 0.7266211 0.40177592635154724 True -5 9048 16.701205730438232 0.37093663215637207 246.75267028808594 0.376614511013031 360.4555358886719 0.5758864283561707 0.73695296 0.3871481120586395 True -6 10556 16.716254472732544 1.1065287590026855 254.47097778320312 0.5310462713241577 359.740966796875 0.57765793800354 0.74025714 0.38575637340545654 True -7 12064 16.72045135498047 0.3649146556854248 242.41468811035156 0.5836499333381653 359.025634765625 0.5794048309326172 0.7439103 0.3646673858165741 True -8 13572 16.728609561920166 0.37021613121032715 279.99017333984375 0.5042623281478882 358.2903747558594 0.5814763903617859 0.7485171 0.3371376693248749 True -9 15080 16.69319796562195 0.35935330390930176 219.62564086914062 0.34162646532058716 357.7713928222656 0.5827797651290894 0.754254 0.32736796140670776 True -10 16588 16.720946311950684 0.36557888984680176 275.6791076660156 0.315113365650177 357.4358215332031 0.5839437246322632 0.7602565 0.3088829815387726 True -11 18096 16.716334581375122 0.3651115894317627 255.31837463378906 0.2843095660209656 356.86614990234375 0.585444986820221 0.7675956 0.30160877108573914 True -12 19604 16.688534259796143 0.364093542098999 270.3023681640625 0.23916520178318024 356.29852294921875 0.5867206454277039 0.76850885 0.30176210403442383 True -13 21112 16.713144540786743 0.7450249195098877 292.9289855957031 0.24294614791870117 355.9800109863281 0.5874553918838501 0.77247065 0.29416030645370483 True -14 22620 16.749739170074463 0.3641641139984131 226.67950439453125 0.26338571310043335 355.781005859375 0.5878793597221375 0.77325135 0.2948663532733917 True -15 24128 16.71584939956665 0.36235475540161133 239.06689453125 0.2552897036075592 355.5787048339844 0.5880029201507568 0.77725947 0.2965278625488281 True -16 25636 16.717459440231323 0.3713498115539551 307.53143310546875 0.23032860457897186 355.7059631347656 0.5872893929481506 0.7741154 0.30555492639541626 False -17 27144 16.69612741470337 0.36914992332458496 244.67108154296875 0.1246972382068634 356.0401306152344 0.5862592458724976 0.7722281 0.31345850229263306 False -18 28652 16.688573360443115 0.3630094528198242 229.6778564453125 0.15849874913692474 356.4149475097656 0.5852771401405334 0.768388 0.32257041335105896 False -19 30160 16.71594786643982 0.362384557723999 229.12408447265625 0.11101047694683075 356.5305480957031 0.5847364664077759 0.7677063 0.3255441188812256 False diff --git a/ENCSR857MCZ/cherimoya.fold_1.performance.tsv b/ENCSR857MCZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 68c8a2dc866d0425ad268ff1ea3f4fb0db64205b..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -355.5787048339844 0.3166385591030121 0.5880029201507568 0.2255610227584839 0.7772594690322876 0.7560768127441406 0.2965278625488281 \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_2.evaluate.json b/ENCSR857MCZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 772aa08e3ba50d05b5a4999036c1ceb9447a612a..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF865BDK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_2.fit.json b/ENCSR857MCZ/cherimoya.fold_2.fit.json deleted file mode 100644 index aaa2d062d6c28a238ea515e25a79c9ef7724c527..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF865BDK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_2.log b/ENCSR857MCZ/cherimoya.fold_2.log deleted file mode 100644 index a7b2ea32a5c5b14ee70910b298e33e19ba15c1dd..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1592 22.15825343132019 3.590826988220215 269.62347412109375 0.5199637413024902 424.2259521484375 0.4149153530597687 0.58177626 13.703837394714355 True -1 3184 17.684369325637817 0.33399224281311035 318.6165771484375 0.439639151096344 367.7745056152344 0.5004004240036011 0.683202 4.72882080078125 True -2 4776 17.62834620475769 0.30324792861938477 245.37020874023438 0.5641471147537231 350.12713623046875 0.548184871673584 0.71169126 1.3061001300811768 True -3 6368 17.65639638900757 0.30551648139953613 273.376220703125 0.5472171306610107 344.50994873046875 0.5604773163795471 0.7366228 0.573368489742279 True -4 7960 17.60994243621826 0.29735732078552246 285.10198974609375 0.3080452084541321 342.3721923828125 0.5656870007514954 0.74656165 0.4218335747718811 True -5 9552 17.614652633666992 0.3067905902862549 293.010498046875 0.34046947956085205 341.04937744140625 0.5682830214500427 0.7527198 0.3776041567325592 True -6 11144 17.624380588531494 0.292893648147583 243.69442749023438 0.32924550771713257 340.211669921875 0.5703402757644653 0.756771 0.3461001515388489 True -7 12736 17.616843223571777 0.2960786819458008 299.67010498046875 0.41286396980285645 339.5257568359375 0.5721526741981506 0.7622547 0.33537977933883667 True -8 14328 17.60382080078125 0.29285693168640137 255.33355712890625 0.35715365409851074 338.6910095214844 0.5740105509757996 0.7682052 0.3231918215751648 True -9 15920 17.64913320541382 0.49468517303466797 270.2606201171875 0.36500346660614014 337.8576965332031 0.5759432315826416 0.7741983 0.3028687536716461 True -10 17512 17.54790163040161 0.2977175712585449 249.89930725097656 0.2990933656692505 337.3170166015625 0.5772575736045837 0.778363 0.29822593927383423 True -11 19104 17.29660439491272 0.28696489334106445 270.88983154296875 0.4112357497215271 336.7331237792969 0.5786733031272888 0.7817625 0.2931624948978424 True -12 20696 17.25949239730835 0.29775166511535645 228.99703979492188 0.25072115659713745 336.27655029296875 0.5798759460449219 0.78562295 0.2891516387462616 True -13 22288 17.28635263442993 0.2896585464477539 309.15380859375 0.28462329506874084 336.0852966308594 0.5804323554039001 0.78975046 0.28761789202690125 True -14 23880 17.276221990585327 0.29392409324645996 216.6434783935547 0.2814216911792755 335.8309631347656 0.5807105302810669 0.79019237 0.28748318552970886 True -15 25472 17.29654097557068 0.2879157066345215 257.6860046386719 0.20700988173484802 335.6846008300781 0.5808798670768738 0.79032636 0.28756752610206604 True -16 27064 17.248857736587524 0.2946782112121582 218.9120635986328 0.17601361870765686 335.84771728515625 0.5803635120391846 0.79164934 0.29394644498825073 True -17 28656 17.264631032943726 0.28380370140075684 320.5751953125 0.12624764442443848 336.0400695800781 0.5794961452484131 0.78812075 0.3005400002002716 False -18 30248 17.247849941253662 0.288130521774292 266.3536071777344 0.13138338923454285 336.3395080566406 0.5785064101219177 0.78397834 0.3084026575088501 False -19 31840 17.225908994674683 0.28638696670532227 305.8221130371094 0.12872835993766785 336.51568603515625 0.5779614448547363 0.7828628 0.3118685781955719 False diff --git a/ENCSR857MCZ/cherimoya.fold_2.performance.tsv b/ENCSR857MCZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index eda7f872a9328856207cd3817f48c72e0980ab41..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -335.84771728515625 0.32671141624450684 0.5803635120391846 0.21513742208480835 0.791649341583252 0.7549192309379578 0.29394644498825073 \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_3.evaluate.json b/ENCSR857MCZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cf9f81b069024c4bc388382619e4ba68d559cfc3..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF865BDK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_3.fit.json b/ENCSR857MCZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 08697509f73fb7c97cab6c123ddadff2d02527f5..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF865BDK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_3.log b/ENCSR857MCZ/cherimoya.fold_3.log deleted file mode 100644 index 45c1a72dfc9e953cc7d4c2d5c73e760048725fbd..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1549 23.233763456344604 15.051138401031494 288.86346435546875 0.9457120299339294 425.7455749511719 0.41675177216529846 0.56260526 14.533153533935547 True -1 3098 17.168565034866333 0.4403374195098877 286.4477844238281 0.5486171841621399 370.7506103515625 0.49715110659599304 0.63206595 4.8811726570129395 True -2 4647 17.156835556030273 0.3560457229614258 263.2991638183594 0.488523006439209 352.8797912597656 0.5456370711326599 0.6528262 1.7633075714111328 True -3 6196 17.154268741607666 0.3312709331512451 241.41082763671875 0.5117312669754028 346.1336975097656 0.5603861808776855 0.67554146 0.7296517491340637 True -4 7745 17.228276014328003 0.3273756504058838 282.61663818359375 0.3466310501098633 343.5141296386719 0.5659404397010803 0.68895364 0.5101613402366638 True -5 9294 17.18231201171875 0.3432297706604004 240.3098907470703 0.39244064688682556 342.5348205566406 0.5684852600097656 0.702267 0.4431755542755127 True -6 10843 17.17914366722107 0.48032188415527344 270.26080322265625 0.41024690866470337 341.54827880859375 0.5704081058502197 0.70942813 0.3921479880809784 True -7 12392 17.178478717803955 0.3451535701751709 275.11395263671875 0.24806351959705353 341.16839599609375 0.5718613266944885 0.7164231 0.38298389315605164 True -8 13941 17.221277713775635 0.3378279209136963 260.0836181640625 0.4263944625854492 340.8158874511719 0.5730644464492798 0.7233261 0.366957426071167 True -9 15490 17.159661769866943 0.33793067932128906 256.40887451171875 0.4186127781867981 340.0535888671875 0.5748827457427979 0.7261317 0.35894328355789185 True -10 17039 17.162598848342896 0.34517979621887207 239.15126037597656 0.3383982181549072 339.617919921875 0.5760844945907593 0.73577994 0.3447365164756775 True -11 18588 17.16883134841919 8.793728351593018 253.3947296142578 0.3386719822883606 338.86199951171875 0.5777236819267273 0.7393071 0.3453814685344696 True -12 20137 17.153950691223145 0.37697362899780273 283.5802917480469 0.31660139560699463 338.3819580078125 0.5789390802383423 0.74505776 0.3359517753124237 True -13 21686 17.13133454322815 0.3407402038574219 260.1998291015625 0.32666289806365967 337.9578857421875 0.5799267888069153 0.7522447 0.32729899883270264 True -14 23235 17.165783643722534 0.3498966693878174 261.2835693359375 0.26938483119010925 337.5112609863281 0.5806623697280884 0.7541416 0.3240569531917572 True -15 24784 17.201977014541626 0.40289902687072754 241.29904174804688 0.21814866364002228 337.30303955078125 0.5810791850090027 0.7558112 0.3319438099861145 True -16 26333 17.132892370224 0.33844733238220215 243.01370239257812 0.23722730576992035 337.3841857910156 0.5806928873062134 0.7563131 0.338186115026474 True -17 27882 17.141115427017212 0.35088133811950684 237.52947998046875 0.1586335152387619 337.76031494140625 0.5798435807228088 0.7538607 0.35028448700904846 False -18 29431 17.14264750480652 7.521227121353149 205.88766479492188 0.14295756816864014 337.97882080078125 0.5791184902191162 0.7512718 0.3551746904850006 False -19 30980 17.283470392227173 0.3375818729400635 251.7158660888672 0.1499585211277008 338.1708984375 0.5786338448524475 0.749909 0.35897591710090637 False diff --git a/ENCSR857MCZ/cherimoya.fold_3.performance.tsv b/ENCSR857MCZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 38261af0de69659cb6e861e53c9a12b0c9814e27..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -337.3841857910156 0.3247537910938263 0.5806928277015686 0.21821251511573792 0.7563130855560303 0.7142382860183716 0.338186115026474 \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_4.evaluate.json b/ENCSR857MCZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f796ed89bb71d6fd9d58807aef66e695ca04d023..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF865BDK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_4.fit.json b/ENCSR857MCZ/cherimoya.fold_4.fit.json deleted file mode 100644 index a45b87c5d7cd403b672fafb73aced4fee2ca55d1..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF865BDK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR857MCZ/cherimoya.fold_4.log b/ENCSR857MCZ/cherimoya.fold_4.log deleted file mode 100644 index f1d601bc38a0d68a78d784399ae2a50509e24c7d..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1577 22.112276315689087 3.54709792137146 316.23321533203125 0.5703017711639404 412.46148681640625 0.4093911647796631 0.58233607 12.639419555664062 True -1 3154 17.49104595184326 0.32331347465515137 265.3885498046875 0.6191064119338989 360.0762939453125 0.49055424332618713 0.64333564 4.161390781402588 True -2 4731 17.520439386367798 0.38358521461486816 277.90985107421875 0.4473191499710083 343.3927001953125 0.5407619476318359 0.67779833 1.1732099056243896 True -3 6308 17.446216344833374 0.2944321632385254 267.4095458984375 0.5677307844161987 335.63531494140625 0.5577647686004639 0.6907653 0.5612438321113586 True -4 7885 17.440456867218018 0.2990865707397461 270.052734375 0.43812498450279236 333.32244873046875 0.5623772144317627 0.70581156 0.4163743257522583 True -5 9462 17.44940686225891 0.3084590435028076 251.67491149902344 0.2640581727027893 332.18499755859375 0.5653437376022339 0.70962095 0.37566816806793213 True -6 11039 17.1164710521698 0.3038017749786377 247.23919677734375 0.24631251394748688 331.41131591796875 0.5672677159309387 0.7135161 0.3657732307910919 True -7 12616 17.084928512573242 0.45070910453796387 226.81649780273438 0.4331701993942261 330.7652587890625 0.5688800811767578 0.72411096 0.34912174940109253 True -8 14193 17.112764596939087 1.2159690856933594 274.3410949707031 0.44282013177871704 329.8500061035156 0.5711514949798584 0.73368657 0.33086836338043213 True -9 15770 17.11365556716919 0.3056671619415283 234.10098266601562 0.28148093819618225 329.2391662597656 0.5726796388626099 0.73851275 0.3215212821960449 True -10 17347 17.08334469795227 0.29544591903686523 242.8258056640625 0.22828620672225952 328.52606201171875 0.5745410919189453 0.7431643 0.311280220746994 True -11 18924 17.13588285446167 0.9731857776641846 306.04058837890625 0.3574030101299286 327.7740478515625 0.5763567686080933 0.7484613 0.3070273995399475 True -12 20501 17.138202667236328 0.30510449409484863 287.1181335449219 0.44149476289749146 327.3614196777344 0.5774423480033875 0.75028485 0.3044538199901581 True -13 22078 17.140872716903687 0.31368541717529297 261.0533447265625 0.27522313594818115 326.8804626464844 0.5785470008850098 0.7585351 0.29796332120895386 True -14 23655 17.100873231887817 0.2878224849700928 238.81661987304688 0.29318666458129883 326.7744445800781 0.5791029334068298 0.7624913 0.299151211977005 True -15 25232 17.133711099624634 0.29564571380615234 221.15025329589844 0.2780649662017822 326.6570129394531 0.5789983868598938 0.7630549 0.30175861716270447 True -16 26809 17.118358373641968 0.2984597682952881 258.1297912597656 0.1909911185503006 326.7256774902344 0.5783844590187073 0.76443774 0.3032706081867218 True -17 28386 17.125410079956055 0.30461859703063965 243.03228759765625 0.21249490976333618 327.065185546875 0.57716304063797 0.7614661 0.3152620792388916 False -18 29963 17.107205629348755 0.29598069190979004 225.54518127441406 0.15874263644218445 327.3349914550781 0.5762102603912354 0.7576684 0.3260815441608429 False -19 31540 17.097022533416748 0.2972698211669922 238.97232055664062 0.12725336849689484 327.591552734375 0.5755977034568787 0.7540276 0.33445465564727783 False diff --git a/ENCSR857MCZ/cherimoya.fold_4.performance.tsv b/ENCSR857MCZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8e17328bf5b99e2910bab68236a79bceb99071da..0000000000000000000000000000000000000000 --- a/ENCSR857MCZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.7256774902344 0.32938385009765625 0.578384518623352 0.21225933730602264 0.764437735080719 0.7131294012069702 0.3032706081867218 \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_0.evaluate.json b/ENCSR859KGQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0dc9ab322c48ec7ca452aa4051e498f0a84d6611..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836TQP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_0.fit.json b/ENCSR859KGQ/cherimoya.fold_0.fit.json deleted file mode 100644 index c61750bbc0aca540de1ccb0fcf1b9b64e58cb365..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF836TQP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_0.log b/ENCSR859KGQ/cherimoya.fold_0.log deleted file mode 100644 index 5ad843f17bdd1c2b8e1f0ec153139fc050e8f274..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.7888970375061 4.444772243499756 210.510009765625 1.2781741619110107 338.9031066894531 0.15371401607990265 0.5852901 3.9044902324676514 True -1 5494 30.412184238433838 0.608684778213501 314.8554382324219 0.9462108612060547 318.2874755859375 0.234641432762146 0.6658136 1.9751871824264526 True -2 8241 30.30717635154724 1.1209611892700195 236.79196166992188 1.0281894207000732 313.267822265625 0.24661099910736084 0.6773841 0.7907913327217102 True -3 10988 30.304301738739014 0.562222957611084 229.43896484375 0.6903596520423889 311.4431457519531 0.25236910581588745 0.68719584 0.7487043738365173 True -4 13735 30.23159384727478 0.5590944290161133 245.3246307373047 0.7121100425720215 310.33819580078125 0.2568298876285553 0.69102603 0.7604236602783203 True -5 16482 30.266533374786377 0.5705001354217529 250.39837646484375 0.7427124977111816 310.1117858886719 0.256979376077652 0.69659585 0.7558907270431519 True -6 19229 30.335694074630737 0.5696258544921875 243.4718475341797 0.7384241819381714 309.1563415527344 0.2604226768016815 0.702393 0.7211097478866577 True -7 21976 30.16698908805847 0.5623188018798828 258.83050537109375 0.5328176021575928 308.8236083984375 0.26118120551109314 0.7060201 0.69102543592453 True -8 24723 29.7389874458313 3.0831456184387207 207.92242431640625 0.771872878074646 307.6175842285156 0.2656244933605194 0.7085801 0.692704439163208 True -9 27470 29.819729804992676 16.68657159805298 265.514892578125 0.869337260723114 306.8922119140625 0.26882749795913696 0.7115436 0.6886141300201416 True -10 30217 29.76349639892578 1.7682580947875977 207.34249877929688 0.572848379611969 306.1170654296875 0.2721467912197113 0.71936864 0.6542918682098389 True -11 32964 29.727411031723022 1.7865486145019531 249.9835205078125 0.610893726348877 305.20831298828125 0.27527865767478943 0.7237385 0.6246566772460938 True -12 35711 29.73168444633484 1.1162781715393066 258.90826416015625 0.5870595574378967 304.7477111816406 0.27638503909111023 0.72892845 0.602838397026062 True -13 38458 29.785770654678345 7.317994594573975 280.39453125 0.7243431806564331 304.4386901855469 0.2774825692176819 0.7370384 0.570254921913147 True -14 41205 29.766966104507446 23.64029097557068 243.27743530273438 0.46735280752182007 303.69561767578125 0.278974324464798 0.74429375 0.5345860123634338 True -15 43952 29.87338638305664 0.573737621307373 209.75759887695312 0.3824648857116699 303.6167297363281 0.27938905358314514 0.75248367 0.5239776372909546 True -16 46699 29.712090253829956 0.5678730010986328 212.78250122070312 0.6483216285705566 303.1487731933594 0.2811092138290405 0.75729895 0.4985910952091217 True -17 49446 29.771225214004517 0.5653650760650635 209.2647705078125 0.3269079327583313 303.3410339355469 0.2809375822544098 0.75910896 0.4957892596721649 True -18 52193 29.688976526260376 0.563075065612793 273.16522216796875 0.5015824437141418 303.5099182128906 0.2801651060581207 0.75855064 0.4988466203212738 False -19 54940 29.66628861427307 0.5761244297027588 211.368896484375 0.30318915843963623 303.6169738769531 0.27967241406440735 0.75755954 0.5005462765693665 False diff --git a/ENCSR859KGQ/cherimoya.fold_0.performance.tsv b/ENCSR859KGQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 89a0cb9a8ef02dcdb7a9385c2f5b0801e2edf559..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -303.3410339355469 0.4921794533729553 0.2809376120567322 0.08390922099351883 0.7591089606285095 0.7098080515861511 0.4957892596721649 \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_1.evaluate.json b/ENCSR859KGQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 742c9b304abee2a55ef0ff442e233df3e9b3e7bc..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836TQP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_1.fit.json b/ENCSR859KGQ/cherimoya.fold_1.fit.json deleted file mode 100644 index e8074de10592b4adc288cb1823289495cb7d188b..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF836TQP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_1.log b/ENCSR859KGQ/cherimoya.fold_1.log deleted file mode 100644 index da360d69b94388860d68220754b6612d1b999020..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.85166788101196 4.33665657043457 225.29031372070312 0.9431768655776978 393.3063659667969 0.16603140532970428 0.6117061 4.853076934814453 True -1 5498 30.334845066070557 0.7497255802154541 239.78106689453125 1.3415532112121582 367.7215270996094 0.2498573511838913 0.70680314 1.9374895095825195 True -2 8247 30.367018222808838 0.6708269119262695 193.584228515625 1.4115869998931885 360.8986511230469 0.2645530104637146 0.7203444 0.9944359660148621 True -3 10996 30.359930276870728 0.9701676368713379 194.32717895507812 0.9428688287734985 358.7881774902344 0.2694818377494812 0.72816974 0.757600724697113 True -4 13745 30.329867124557495 1.7490711212158203 199.45175170898438 1.0057616233825684 357.3235778808594 0.27260953187942505 0.73134226 0.8172050714492798 True -5 16494 30.356961250305176 8.891997337341309 204.15843200683594 0.6203217506408691 355.3400573730469 0.27927398681640625 0.7339859 0.7311179637908936 True -6 19243 30.142200708389282 0.6753215789794922 219.30453491210938 0.8294763565063477 354.76373291015625 0.28086066246032715 0.73748165 0.7359195947647095 True -7 21992 29.773880004882812 0.671647310256958 212.3399658203125 0.7926979064941406 353.9984130859375 0.2830078601837158 0.7396087 0.7269102334976196 True -8 24741 29.846893072128296 0.6798393726348877 258.54949951171875 0.9577454328536987 353.63330078125 0.28455865383148193 0.74373883 0.7185168862342834 True -9 27490 29.727309226989746 0.6753861904144287 239.88775634765625 0.7590989470481873 352.610107421875 0.2871449887752533 0.74736226 0.6781795620918274 True -10 30239 29.70215678215027 0.6746413707733154 241.260986328125 0.6438295841217041 351.87158203125 0.28951549530029297 0.75147414 0.6615809202194214 True -11 32988 29.702942609786987 0.6642727851867676 222.71180725097656 0.6976584196090698 350.3799743652344 0.29412657022476196 0.7567159 0.6296043395996094 True -12 35737 29.659608840942383 0.6619815826416016 296.39703369140625 0.6279975175857544 350.2265930175781 0.29360049962997437 0.7626618 0.5982362627983093 True -13 38486 29.727619647979736 0.6782057285308838 173.82203674316406 0.4515151083469391 349.78472900390625 0.294417142868042 0.76951236 0.5734318494796753 True -14 41235 29.70830011367798 0.6669924259185791 225.73924255371094 0.49995720386505127 349.0103454589844 0.29730314016342163 0.77387 0.5594345331192017 True -15 43984 29.705004453659058 0.9805490970611572 202.4233856201172 0.6155663728713989 348.02423095703125 0.29936811327934265 0.7807299 0.534927487373352 True -16 46733 29.785766124725342 0.6875021457672119 241.15248107910156 0.5286679863929749 347.9250793457031 0.30020755529403687 0.78453314 0.5261238813400269 True -17 49482 29.715903520584106 0.6909933090209961 228.3936004638672 0.46893641352653503 347.5934143066406 0.3005502223968506 0.78619653 0.5193504691123962 True -18 52231 29.751914739608765 0.6840312480926514 227.85650634765625 0.41836971044540405 348.0539245605469 0.2988949418067932 0.78692544 0.5253254771232605 True -19 54980 29.67493963241577 0.6711821556091309 224.9345703125 0.3540404438972473 348.0179138183594 0.2988708019256592 0.7857727 0.5280507206916809 False diff --git a/ENCSR859KGQ/cherimoya.fold_1.performance.tsv b/ENCSR859KGQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b813899403f31761f1a884fb1d920d7fa4bb407c..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -348.0539245605469 0.4738038182258606 0.2988949418067932 0.0957317128777504 0.7869254350662231 0.7519840598106384 0.5253254771232605 \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_2.evaluate.json b/ENCSR859KGQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 27a1fc689f60830becb812362f71c1e08fd4f445..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836TQP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_2.fit.json b/ENCSR859KGQ/cherimoya.fold_2.fit.json deleted file mode 100644 index bae227d4076f9cf944d28c4b836f55181c61f2d6..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF836TQP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_2.log b/ENCSR859KGQ/cherimoya.fold_2.log deleted file mode 100644 index 55de3c86b98b08fdf22dcd69ce843c5eac10458a..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2921 36.89322304725647 20.39488458633423 256.957275390625 1.087675929069519 349.42669677734375 0.16540788114070892 0.5931676 4.3083062171936035 True -1 5842 32.51234245300293 0.6627035140991211 237.99642944335938 0.8658308982849121 327.5174255371094 0.24139127135276794 0.6817207 1.5885365009307861 True -2 8763 32.25926852226257 0.5467736721038818 255.43209838867188 1.4266021251678467 322.4077453613281 0.2519051134586334 0.69242066 0.8406282663345337 True -3 11684 32.072953939437866 0.5129358768463135 229.9404754638672 0.6309524774551392 320.5736389160156 0.2571480870246887 0.7031408 0.7200356125831604 True -4 14605 31.59380340576172 0.5139114856719971 260.92138671875 0.6834222078323364 319.6697998046875 0.26040783524513245 0.70930696 0.6784012317657471 True -5 17526 31.521310091018677 0.5196175575256348 231.69400024414062 0.6478939056396484 319.0975341796875 0.2625606954097748 0.7098309 0.6962054967880249 True -6 20447 31.55954098701477 0.5724446773529053 205.20089721679688 0.6550120115280151 318.6589660644531 0.2644687592983246 0.71186626 0.702099084854126 True -7 23368 31.5500009059906 0.5238213539123535 254.06588745117188 0.7362237572669983 317.2297668457031 0.2690698504447937 0.7160205 0.7126535177230835 True -8 26289 31.531980752944946 0.5231482982635498 300.42388916015625 0.9937845468521118 316.7704162597656 0.2711692750453949 0.71903163 0.6915373802185059 True -9 29210 31.580842971801758 0.5221812725067139 250.66001892089844 0.7363048195838928 316.427978515625 0.2712288796901703 0.7241141 0.665786623954773 True -10 32131 31.564278602600098 0.5251326560974121 234.05374145507812 0.5928434133529663 315.650146484375 0.2728930711746216 0.7283907 0.660778284072876 True -11 35052 31.604601860046387 0.5179147720336914 263.1845703125 0.9390891790390015 314.5520324707031 0.27736860513687134 0.73098165 0.6422029137611389 True -12 37973 31.61575174331665 0.5269598960876465 242.70494079589844 0.5608189105987549 313.6644592285156 0.279806524515152 0.73713523 0.6274656653404236 True -13 40894 31.596837520599365 0.5197052955627441 262.1839904785156 0.5838391780853271 313.3916015625 0.280227392911911 0.74367803 0.5921972393989563 True -14 43815 31.5455322265625 0.545548677444458 196.36309814453125 0.7773479223251343 312.1548767089844 0.28425106406211853 0.7491808 0.5747938752174377 True -15 46736 31.58045196533203 0.5148065090179443 219.26824951171875 0.516693115234375 311.45123291015625 0.2860548794269562 0.7557558 0.5511950254440308 True -16 49657 31.537678003311157 0.5226345062255859 270.5450439453125 0.737933337688446 311.30181884765625 0.28587305545806885 0.7601748 0.5450558066368103 True -17 52578 31.55405879020691 0.5258193016052246 227.3634490966797 0.3618212938308716 311.9735107421875 0.28373050689697266 0.76242363 0.5320158004760742 True -18 55499 31.552327632904053 0.5196084976196289 243.35618591308594 0.42963361740112305 311.9973449707031 0.28343117237091064 0.7637508 0.5313159823417664 True -19 58420 31.651216745376587 0.5254912376403809 228.19952392578125 0.2905951738357544 311.5039367675781 0.28568848967552185 0.76272017 0.5370731353759766 False diff --git a/ENCSR859KGQ/cherimoya.fold_2.performance.tsv b/ENCSR859KGQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6bfa252912005c7140772b5d48f525ac47e679c2..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -311.9973449707031 0.4888164699077606 0.28343117237091064 0.08325336873531342 0.7637507915496826 0.7187587022781372 0.5313159823417664 \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_3.evaluate.json b/ENCSR859KGQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f707d552499ef539ad686d6056c5d7fc41eabe97..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836TQP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_3.fit.json b/ENCSR859KGQ/cherimoya.fold_3.fit.json deleted file mode 100644 index c21018bc250d5a1e4519b98d2e3a22590c6e7236..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF836TQP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_3.log b/ENCSR859KGQ/cherimoya.fold_3.log deleted file mode 100644 index 2e71f36f22fc6ce670a65afd38e37ec3c2f18d62..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2783 35.56724309921265 4.171264171600342 223.04803466796875 1.352480173110962 353.7386474609375 0.1580546647310257 0.6059939 5.2456278800964355 True -1 5566 30.533337116241455 0.6018152236938477 213.81185913085938 1.0517469644546509 332.8747863769531 0.23471412062644958 0.6837974 1.5101649761199951 True -2 8349 30.693092107772827 0.5974688529968262 295.391357421875 1.1225244998931885 328.2867736816406 0.24491199851036072 0.69034815 0.9113194346427917 True -3 11132 30.656647205352783 0.5695939064025879 244.558349609375 0.7670016884803772 327.48187255859375 0.24841991066932678 0.6922331 0.8499373197555542 True -4 13915 30.727165937423706 0.5731875896453857 272.7532043457031 0.5678184628486633 326.107666015625 0.2517841160297394 0.7043763 0.8055887222290039 True -5 16698 30.5763578414917 0.5724058151245117 293.21466064453125 1.006380319595337 324.4317932128906 0.2579081952571869 0.7129441 0.8001072406768799 True -6 19481 30.02809429168701 0.5678412914276123 271.3919677734375 0.4825512766838074 323.74822998046875 0.25986433029174805 0.7186837 0.7992504835128784 True -7 22264 30.066683292388916 0.5680298805236816 201.6330108642578 0.735309362411499 323.1689758300781 0.2616492807865143 0.71997094 0.7984997034072876 True -8 25047 30.0566246509552 0.5722062587738037 239.92601013183594 1.180377721786499 322.8985900878906 0.2623272240161896 0.72170407 0.7855324149131775 True -9 27830 30.029026746749878 0.5679211616516113 246.71563720703125 0.887292206287384 321.5335388183594 0.26704907417297363 0.7288445 0.7309008836746216 True -10 30613 30.088591814041138 0.5643167495727539 278.4472961425781 0.6571092009544373 321.126953125 0.26833587884902954 0.73313785 0.6683126091957092 True -11 33396 30.081681966781616 2.101651430130005 241.99215698242188 0.5052959322929382 320.8929748535156 0.2686043083667755 0.7381014 0.6500363349914551 True -12 36179 30.158068656921387 1.389099359512329 237.11935424804688 0.6820554733276367 319.95782470703125 0.27213817834854126 0.74664116 0.5968813300132751 True -13 38962 30.146108865737915 1.135664939880371 246.27548217773438 0.5592328310012817 319.4725646972656 0.27354326844215393 0.754903 0.5651252269744873 True -14 41745 30.20940136909485 1.936535120010376 214.1208953857422 0.49401578307151794 319.1100769042969 0.2745814621448517 0.75943494 0.542125403881073 True -15 44528 30.08356785774231 2.9275853633880615 205.72286987304688 0.4958260655403137 318.5475158691406 0.2764644920825958 0.76656085 0.5325310826301575 True -16 47311 30.1889328956604 0.5659751892089844 188.5623321533203 0.764342188835144 318.6477355957031 0.27564817667007446 0.77028704 0.5075143575668335 True -17 50094 30.2153217792511 0.563896656036377 278.2489929199219 0.48101797699928284 318.49432373046875 0.27639269828796387 0.7700726 0.5101041793823242 False -18 52877 30.118499755859375 0.566946268081665 187.9085235595703 0.6299792528152466 318.3125915527344 0.2764608561992645 0.7699873 0.5083737373352051 False -19 55660 30.609336614608765 0.5975916385650635 236.2267608642578 0.4905228018760681 318.11785888671875 0.27762794494628906 0.7690201 0.5142019987106323 False diff --git a/ENCSR859KGQ/cherimoya.fold_3.performance.tsv b/ENCSR859KGQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6368b2f8f6a7582c7945f1a146b56caaa196fd56..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -318.6477355957031 0.4895564019680023 0.2756481468677521 0.08405093848705292 0.770287036895752 0.7227078676223755 0.5075143575668335 \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_4.evaluate.json b/ENCSR859KGQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3496eea8a53ffefe9d071e712f76e7930688105c..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF836TQP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_4.fit.json b/ENCSR859KGQ/cherimoya.fold_4.fit.json deleted file mode 100644 index f9c14233a95d3eb4828eec51b3752c83e06ed71c..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF836TQP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_4.log b/ENCSR859KGQ/cherimoya.fold_4.log deleted file mode 100644 index 3a0ae0de763a1b7d7811244f60220f37f2441095..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2866 36.41678190231323 3.9033520221710205 312.10736083984375 1.7068326473236084 338.8717956542969 0.1594129353761673 0.5804243 3.851992130279541 True -1 5732 31.607226848602295 1.3409423828125 222.60462951660156 0.9534720778465271 319.9460754394531 0.23343713581562042 0.650222 1.8503625392913818 True -2 8598 31.172186374664307 0.6595878601074219 220.6105194091797 0.8243741393089294 316.004638671875 0.2421182543039322 0.6637934 0.9554376006126404 True -3 11464 31.005390167236328 1.1637420654296875 254.31192016601562 0.8238002061843872 313.7659606933594 0.24917452037334442 0.6720069 0.980254054069519 True -4 14330 31.212419509887695 0.6129188537597656 191.7132568359375 0.7396342754364014 312.90765380859375 0.25137677788734436 0.6784162 0.9328338503837585 True -5 17196 31.120842456817627 0.600020170211792 252.7136993408203 1.1583218574523926 311.89337158203125 0.25619223713874817 0.6806984 0.9683232307434082 True -6 20062 31.11400580406189 0.5949490070343018 278.29571533203125 1.0577961206436157 310.9280090332031 0.2598758339881897 0.6870348 0.8525477647781372 True -7 22928 31.107923984527588 0.6051557064056396 236.386474609375 0.512514591217041 310.5849609375 0.26075926423072815 0.69109905 0.8139963746070862 True -8 25794 31.034615993499756 0.5935044288635254 247.38426208496094 0.7185953855514526 309.98419189453125 0.2624756395816803 0.69778436 0.7460598945617676 True -9 28660 31.041290760040283 1.0197758674621582 222.97862243652344 0.8093240261077881 309.2698974609375 0.2648928761482239 0.7008399 0.7327752113342285 True -10 31526 30.997187852859497 0.6035807132720947 273.5623474121094 0.7019133567810059 309.16217041015625 0.26581230759620667 0.7068918 0.730083167552948 True -11 34392 30.993010997772217 0.6420071125030518 178.95249938964844 0.8371572494506836 308.05401611328125 0.2691185772418976 0.71214336 0.6877884268760681 True -12 37258 31.21248459815979 0.637047290802002 228.26437377929688 0.4427546262741089 307.5218811035156 0.2706414759159088 0.71724826 0.6440470814704895 True -13 40124 31.26048731803894 17.023589611053467 266.1468505859375 0.2727544903755188 306.40631103515625 0.2752333879470825 0.72275156 0.5990733504295349 True -14 42990 32.06291747093201 0.6018640995025635 210.8252410888672 0.6911957859992981 306.0486755371094 0.2767307460308075 0.72973377 0.5808225274085999 True -15 45856 31.244614601135254 0.6094439029693604 243.19241333007812 0.5029165744781494 306.1020812988281 0.27538901567459106 0.73837346 0.5428208708763123 True -16 48722 31.132152318954468 1.0944569110870361 236.5909423828125 0.5483322143554688 305.36456298828125 0.27826809883117676 0.7417049 0.5356250405311584 True -17 51588 31.14192223548889 0.6083040237426758 228.14849853515625 0.33619868755340576 305.6537780761719 0.27718067169189453 0.74432373 0.5218853950500488 True -18 54454 31.155362606048584 0.6127173900604248 243.57803344726562 0.3841862976551056 306.0947265625 0.2757675349712372 0.74216026 0.5311049818992615 False -19 57320 31.18927502632141 0.608262300491333 196.87738037109375 0.46754276752471924 305.85174560546875 0.276488721370697 0.73979694 0.5376033186912537 False diff --git a/ENCSR859KGQ/cherimoya.fold_4.performance.tsv b/ENCSR859KGQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8dabcb2c34e8b17af4465fb05980d732f5f0a551..0000000000000000000000000000000000000000 --- a/ENCSR859KGQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -305.6537780761719 0.49243125319480896 0.27718064188957214 0.07964059710502625 0.74432373046875 0.693183422088623 0.5218853950500488 \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_0.evaluate.json b/ENCSR859LTL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index bc09c9ea6c15718ed9586a4a5db8404be155c81b..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF429XFC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_0.fit.json b/ENCSR859LTL/cherimoya.fold_0.fit.json deleted file mode 100644 index 8ec4f107a191e7c98789d38beabeebb6e6769e69..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF429XFC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_0.log b/ENCSR859LTL/cherimoya.fold_0.log deleted file mode 100644 index c39bb1fb35aadb9a6280c5fa983c77ce958e737e..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2732 35.030603647232056 3.6880972385406494 582.7376708984375 0.6610091924667358 689.8829956054688 0.2553960382938385 0.6598031 5.004834175109863 True -1 5464 30.33087921142578 1.9434552192687988 482.87017822265625 0.5131034255027771 628.851318359375 0.325187087059021 0.7170966 2.221234083175659 True -2 8196 30.172314643859863 0.5808916091918945 605.1500244140625 0.5903259515762329 617.42822265625 0.33800145983695984 0.73188555 1.2485935688018799 True -3 10928 30.138712882995605 0.5784335136413574 479.6711730957031 0.33841627836227417 612.5975341796875 0.34184035658836365 0.74219215 1.1097688674926758 True -4 13660 30.182711839675903 0.621112585067749 515.18603515625 0.454241007566452 609.3778686523438 0.34472110867500305 0.747906 1.0001559257507324 True -5 16392 30.179224252700806 0.5683410167694092 542.92578125 0.5401664972305298 605.428955078125 0.3488127589225769 0.76177645 0.7952099442481995 True -6 19124 30.107869625091553 0.5772368907928467 536.1971435546875 0.4101693630218506 603.9869384765625 0.3499029576778412 0.76904416 0.7295042872428894 True -7 21856 30.2594096660614 14.006991147994995 590.7913818359375 0.4893808364868164 600.3695068359375 0.35476282238960266 0.7771322 0.7123305797576904 True -8 24588 30.163819789886475 25.283483505249023 471.24725341796875 0.3497786521911621 599.5390625 0.3558153808116913 0.77966815 0.7229056358337402 True -9 27320 30.377020359039307 0.5755577087402344 505.10040283203125 0.36500948667526245 597.1528930664062 0.35750868916511536 0.78993356 0.6160523295402527 True -10 30052 30.300171852111816 0.57098388671875 528.1925048828125 0.32378071546554565 595.13916015625 0.360035240650177 0.7962083 0.577207088470459 True -11 32784 29.614691972732544 1.2961411476135254 453.2137756347656 0.2876896262168884 593.210205078125 0.3625398278236389 0.7999086 0.5142859816551208 True -12 35516 29.620813369750977 0.5681939125061035 475.847412109375 0.33741551637649536 591.4725341796875 0.36411720514297485 0.80783767 0.4546293318271637 True -13 38248 29.552173137664795 0.5629029273986816 493.95733642578125 0.3853151202201843 589.7107543945312 0.36539480090141296 0.81090325 0.40952643752098083 True -14 40980 29.780913829803467 46.45308327674866 607.6927490234375 0.24461892247200012 588.9572143554688 0.3665328323841095 0.81481934 0.38530784845352173 True -15 43712 29.956541299819946 31.718461990356445 552.884765625 0.38710522651672363 589.8565673828125 0.3648834824562073 0.819966 0.3562650978565216 True -16 46444 29.756179571151733 0.5711662769317627 510.0277404785156 0.2774140536785126 587.7100219726562 0.3682634234428406 0.8222894 0.33333563804626465 True -17 49176 29.739003896713257 0.5696382522583008 565.4625244140625 0.21345362067222595 587.8668212890625 0.3690487742424011 0.82312 0.3166666328907013 True -18 51908 29.532814264297485 0.5586817264556885 423.0137023925781 0.16772739589214325 587.7069702148438 0.369264155626297 0.8202848 0.31445807218551636 False -19 54640 29.571759939193726 0.5528774261474609 531.0303955078125 0.3770573139190674 587.9341430664062 0.36873629689216614 0.8209642 0.31461143493652344 False diff --git a/ENCSR859LTL/cherimoya.fold_0.performance.tsv b/ENCSR859LTL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b977cc800f30790e923bbdbde215e2094ff298e3..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -587.8668212890625 0.4119698703289032 0.3690487742424011 0.14394748210906982 0.8231199979782104 0.8025594353675842 0.3166666328907013 \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_1.evaluate.json b/ENCSR859LTL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index bb26c916cc967a3c20041721c79ba9c04a19cbcb..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF429XFC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_1.fit.json b/ENCSR859LTL/cherimoya.fold_1.fit.json deleted file mode 100644 index f52e309bd385433a6bcc575177d882357ed63363..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF429XFC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_1.log b/ENCSR859LTL/cherimoya.fold_1.log deleted file mode 100644 index d9836b7887d74bf8ba8eb429a89befe130517e55..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2704 34.58777141571045 4.067896604537964 573.0873413085938 0.5429848432540894 819.6390380859375 0.26479658484458923 0.68369645 6.433288097381592 True -1 5408 29.85890293121338 13.944796085357666 524.8778686523438 0.412773072719574 742.429931640625 0.33793511986732483 0.7429494 2.58536696434021 True -2 8112 29.844433784484863 2.294243812561035 545.3382568359375 0.47779664397239685 726.5462036132812 0.35177361965179443 0.76099926 1.3662511110305786 True -3 10816 30.084744215011597 2.093568801879883 491.9705810546875 0.4386354982852936 717.7496948242188 0.3609360158443451 0.7727877 1.0650500059127808 True -4 13520 29.805959701538086 0.7318520545959473 587.1931762695312 0.4770699739456177 714.6222534179688 0.36338189244270325 0.779646 1.2430318593978882 True -5 16224 29.817818641662598 0.7522342205047607 587.8953247070312 0.460979163646698 711.3181762695312 0.36608433723449707 0.78605604 0.9746694564819336 True -6 18928 30.393076419830322 32.06326746940613 487.1856994628906 0.5331560373306274 708.390625 0.37020769715309143 0.78771645 0.9855268001556396 True -7 21632 29.962764263153076 0.9966974258422852 491.874267578125 0.509437084197998 704.777587890625 0.3717385530471802 0.7961755 0.8877192735671997 True -8 24336 29.50606632232666 33.65688157081604 511.90545654296875 0.5064924955368042 700.0538940429688 0.37708836793899536 0.8016526 0.7627246379852295 True -9 27040 29.697306871414185 0.7350413799285889 444.55242919921875 0.4128756523132324 697.8404541015625 0.37971973419189453 0.8068133 0.7574630975723267 True -10 29744 29.353618383407593 0.7343840599060059 559.7550048828125 0.4036943018436432 696.039306640625 0.38032248616218567 0.81050426 0.6668304800987244 True -11 32448 29.327492713928223 0.7201523780822754 556.3424072265625 0.3166005611419678 693.9332275390625 0.3819977641105652 0.8189522 0.571458637714386 True -12 35152 29.220430850982666 1.0449135303497314 469.3248291015625 0.33161771297454834 691.5950927734375 0.38411983847618103 0.8220366 0.5140231251716614 True -13 37856 29.24430251121521 0.7213790416717529 515.209228515625 0.3037930130958557 689.5512084960938 0.3867509663105011 0.8272011 0.47199636697769165 True -14 40560 29.24910879135132 0.7160437107086182 457.5932312011719 0.2695876359939575 687.6210327148438 0.38817867636680603 0.8332368 0.4289144277572632 True -15 43264 29.2314293384552 0.7175357341766357 591.050537109375 0.3125603199005127 686.6116333007812 0.3894636034965515 0.84063125 0.38707995414733887 True -16 45968 29.249114274978638 0.7028899192810059 510.65045166015625 0.3018015921115875 686.6849365234375 0.38917794823646545 0.8443822 0.34989437460899353 True -17 48672 29.237600088119507 22.65513253211975 493.93341064453125 0.26048919558525085 685.8925170898438 0.38969671726226807 0.84490514 0.3347398638725281 True -18 51376 29.88221836090088 0.7226829528808594 540.498046875 0.21507307887077332 688.5661010742188 0.38614481687545776 0.84377825 0.3270323574542999 False -19 54080 29.275101900100708 0.7256276607513428 557.8359375 0.24127507209777832 688.1376953125 0.38713157176971436 0.8434943 0.3263835310935974 False diff --git a/ENCSR859LTL/cherimoya.fold_1.performance.tsv b/ENCSR859LTL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 97f0f7e8885ab40b88aee57aeb57b9ce8596da5b..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -685.8925170898438 0.3918231129646301 0.3896966874599457 0.16694758832454681 0.8449051380157471 0.8373280167579651 0.3347398638725281 \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_2.evaluate.json b/ENCSR859LTL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ed9665a1205a28efe6b4cc6b65c525e3cee738cc..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF429XFC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_2.fit.json b/ENCSR859LTL/cherimoya.fold_2.fit.json deleted file mode 100644 index a8187cb3a5bf397a94e8ef7ba3f88803e89e0749..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF429XFC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_2.log b/ENCSR859LTL/cherimoya.fold_2.log deleted file mode 100644 index 2a4960cb7d28bfd4d22e6b5306dea7f2eefb4ef9..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 37.410802602767944 28.689322233200073 466.15374755859375 0.3289341926574707 732.3155517578125 0.2625678777694702 0.669597 4.038578033447266 True -1 5784 32.653186082839966 35.945091009140015 495.6859436035156 0.4669888913631439 665.7328491210938 0.3314249813556671 0.7303809 1.7096866369247437 True -2 8676 32.9775767326355 35.47561287879944 504.30389404296875 0.5464861392974854 654.9512939453125 0.34085968136787415 0.7418288 1.180506706237793 True -3 11568 33.042213916778564 0.5392405986785889 488.7580261230469 0.5350594520568848 647.8401489257812 0.3464008569717407 0.75181943 1.048427700996399 True -4 14460 31.990853309631348 0.9323432445526123 650.7147216796875 0.5715011358261108 645.1914672851562 0.34839555621147156 0.7589945 0.8933360576629639 True -5 17352 32.024675607681274 0.5364737510681152 509.1902770996094 0.45029351115226746 644.6912841796875 0.34747380018234253 0.7593159 0.8749457597732544 True -6 20244 31.415197134017944 0.5305178165435791 593.7947998046875 0.5410604476928711 638.8235473632812 0.3549247086048126 0.7740465 0.7395204305648804 True -7 23136 31.291661024093628 0.5323784351348877 436.1542053222656 0.36852842569351196 636.144775390625 0.35833677649497986 0.78034776 0.6608874201774597 True -8 26028 31.255281925201416 0.5331435203552246 575.9036865234375 0.4264158606529236 634.0064697265625 0.36089280247688293 0.7866939 0.6179953217506409 True -9 28920 31.264421463012695 30.25457763671875 530.8275146484375 0.4076422452926636 631.4208374023438 0.3631237745285034 0.7922248 0.5260087847709656 True -10 31812 32.55682587623596 0.5328929424285889 546.1876220703125 0.38177287578582764 630.13720703125 0.3644002079963684 0.7979585 0.496046245098114 True -11 34704 31.832679510116577 1.7902638912200928 515.3431396484375 0.5723121166229248 628.4073486328125 0.3653726577758789 0.8020338 0.47014448046684265 True -12 37596 31.2791645526886 16.27114748954773 443.2428894042969 0.28164738416671753 626.6543579101562 0.36664995551109314 0.8078534 0.43060538172721863 True -13 40488 31.357717514038086 0.5401272773742676 551.1367797851562 0.2852581739425659 624.687255859375 0.3697412610054016 0.81432056 0.39333808422088623 True -14 43380 32.0167601108551 0.533390998840332 584.9133911132812 0.3283716142177582 623.115478515625 0.37151315808296204 0.81801796 0.3646671175956726 True -15 46272 31.25927186012268 0.5300090312957764 545.084716796875 0.24694785475730896 622.6959228515625 0.37060704827308655 0.82148415 0.34428873658180237 True -16 49164 31.241766691207886 1.7888460159301758 499.43988037109375 0.2740183174610138 622.5872802734375 0.37100720405578613 0.8251373 0.327028751373291 True -17 52056 31.54766035079956 10.014899015426636 458.7228698730469 0.26817989349365234 623.0723266601562 0.369994580745697 0.824952 0.320224404335022 False -18 54948 31.259557962417603 0.5519287586212158 487.72369384765625 0.22247980535030365 622.4768676757812 0.37058621644973755 0.8234218 0.31864890456199646 False -19 57840 31.243438959121704 0.5402657985687256 537.0203857421875 0.23972518742084503 621.7385864257812 0.3723165690898895 0.82271624 0.3200620710849762 False diff --git a/ENCSR859LTL/cherimoya.fold_2.performance.tsv b/ENCSR859LTL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 72fc7b52118f125d8bad154d827745dd12d817eb..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -622.5872802734375 0.4065546691417694 0.37100720405578613 0.15304787456989288 0.8251373171806335 0.8097930550575256 0.327028751373291 \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_3.evaluate.json b/ENCSR859LTL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1a5a6e25551f7c818860b4277d5e847a3c86b2f0..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF429XFC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_3.fit.json b/ENCSR859LTL/cherimoya.fold_3.fit.json deleted file mode 100644 index 6b9486b0ea3dff72b2764883f81ab59d0a78ce9c..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF429XFC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_3.log b/ENCSR859LTL/cherimoya.fold_3.log deleted file mode 100644 index 6266c0fc5e5f85ce86fc127320f38c4d982e91a2..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.99547863006592 3.812877893447876 466.7174072265625 0.7367120385169983 687.2998046875 0.264719694852829 0.65777373 4.923251628875732 True -1 5478 30.289691925048828 0.5790822505950928 521.4573364257812 0.6214287281036377 625.1622314453125 0.33537521958351135 0.7212901 1.9845565557479858 True -2 8217 30.35773229598999 0.5507540702819824 570.3555297851562 0.42728084325790405 616.2213745117188 0.3437524437904358 0.7376473 1.189061164855957 True -3 10956 30.015937089920044 0.5631084442138672 581.5758666992188 0.2891213893890381 611.7623901367188 0.3469233214855194 0.7479618 1.3265478610992432 True -4 13695 29.996726274490356 0.5567348003387451 483.64697265625 0.4749675393104553 608.1071166992188 0.3495275676250458 0.7565118 0.8727930784225464 True -5 16434 29.703039169311523 0.5555758476257324 539.1884765625 0.4776974320411682 606.7515258789062 0.3517049551010132 0.75963676 0.9501621723175049 True -6 19173 29.79812741279602 0.551537275314331 519.5360107421875 0.49533724784851074 605.3101196289062 0.3524401783943176 0.7628243 1.0036742687225342 True -7 21912 29.65788245201111 0.5505876541137695 558.93505859375 0.5632347464561462 601.0687866210938 0.35771140456199646 0.77417433 0.8259758949279785 True -8 24651 29.69823122024536 0.5468823909759521 543.9283447265625 0.4888942837715149 598.2525634765625 0.36099621653556824 0.7838139 0.7170068025588989 True -9 27390 29.663845777511597 0.554950475692749 513.8055419921875 0.4524747431278229 596.2032470703125 0.3639349341392517 0.78909934 0.6868672966957092 True -10 30129 29.57552933692932 0.6090445518493652 553.4302978515625 0.5151922702789307 593.3173828125 0.3678129315376282 0.7960366 0.6272827386856079 True -11 32868 29.711309671401978 0.5508913993835449 504.4817199707031 0.30279919505119324 591.7638549804688 0.36915141344070435 0.8027646 0.5654203295707703 True -12 35607 29.79056477546692 0.5497837066650391 558.5831298828125 0.48893460631370544 591.0415649414062 0.36864325404167175 0.8080148 0.48093509674072266 True -13 38346 29.887147903442383 17.282928466796875 477.00970458984375 0.37195807695388794 589.4512329101562 0.37057799100875854 0.8148108 0.43136799335479736 True -14 41085 34.087018966674805 0.5735931396484375 537.9830932617188 0.264875203371048 587.7791137695312 0.37242671847343445 0.82272387 0.3878568112850189 True -15 43824 30.24899697303772 0.8724968433380127 482.72314453125 0.4136420786380768 586.8689575195312 0.3731342554092407 0.8264266 0.3556338846683502 True -16 46563 29.90674901008606 0.5492918491363525 492.6923828125 0.18918181955814362 586.6261596679688 0.37308046221733093 0.8255433 0.3311103880405426 False -17 49302 29.884461402893066 0.559422492980957 512.4617309570312 0.32372134923934937 587.4256591796875 0.37130364775657654 0.82700634 0.32219746708869934 True -18 52041 29.91991424560547 0.5451176166534424 521.036376953125 0.23664826154708862 586.3551635742188 0.3738865554332733 0.8275766 0.31717294454574585 True -19 54780 29.766256093978882 0.544823408126831 487.54864501953125 0.197572261095047 587.38037109375 0.3718374967575073 0.8256194 0.31962859630584717 False diff --git a/ENCSR859LTL/cherimoya.fold_3.performance.tsv b/ENCSR859LTL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0be7fdfa0e81940e3989623278de3c0978abd015..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -586.3551635742188 0.40921327471733093 0.3738865554332733 0.14853617548942566 0.8275765776634216 0.8010068535804749 0.31717294454574585 \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_4.evaluate.json b/ENCSR859LTL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e036ef73562bbb9cad112fc49af0d7ce2a4fa2b5..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF429XFC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_4.fit.json b/ENCSR859LTL/cherimoya.fold_4.fit.json deleted file mode 100644 index d4c6719709e583f865361d32709d87b3e0538b4b..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF429XFC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859LTL/cherimoya.fold_4.log b/ENCSR859LTL/cherimoya.fold_4.log deleted file mode 100644 index b84afb1febc113f013f56003ffc472159ef85a5d..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 35.48100304603577 3.8124539852142334 446.98553466796875 0.5480507612228394 623.4586791992188 0.2526196539402008 0.6590932 3.4946045875549316 True -1 5612 31.252583026885986 0.6114444732666016 566.6197509765625 0.5464602708816528 573.3546142578125 0.31893420219421387 0.72090054 1.6226006746292114 True -2 8418 30.96627187728882 0.5971963405609131 592.8524780273438 0.4448925852775574 564.6732177734375 0.3246627449989319 0.7378916 0.9960207939147949 True -3 11224 31.01352548599243 0.6091327667236328 512.8212890625 0.4151870906352997 561.9697875976562 0.32792723178863525 0.7333972 0.8674211502075195 False -4 14030 30.976212978363037 0.6050424575805664 544.6277465820312 0.4873688519001007 556.910400390625 0.33358854055404663 0.74939704 0.7605466246604919 True -5 16836 30.971717834472656 2.718522787094116 445.39508056640625 0.3810109496116638 556.9547119140625 0.3323533535003662 0.7511141 0.8020978569984436 True -6 19642 30.980629682540894 0.6238296031951904 584.4890747070312 0.5623563528060913 554.50146484375 0.3361295461654663 0.7634304 0.706902801990509 True -7 22448 31.034472465515137 0.6235454082489014 459.83587646484375 0.43738240003585815 552.2047119140625 0.339237242937088 0.7676037 0.7098838686943054 True -8 25254 30.971170663833618 4.807667016983032 594.6798095703125 0.3920665681362152 550.1126708984375 0.34153884649276733 0.778046 0.5989270210266113 True -9 28060 30.99193239212036 0.6068623065948486 512.7014770507812 0.3564474582672119 548.3834838867188 0.34326988458633423 0.7839613 0.5482348799705505 True -10 30866 30.97551918029785 0.6125974655151367 547.8897094726562 0.2718818187713623 548.1785278320312 0.34277433156967163 0.79055387 0.5129442811012268 True -11 33672 30.9676296710968 0.6266932487487793 387.1102600097656 0.348222017288208 545.113525390625 0.347856730222702 0.8001398 0.4442060887813568 True -12 36478 30.99348473548889 2.0824880599975586 461.39202880859375 0.26784661412239075 543.513671875 0.34923771023750305 0.8073294 0.3891552984714508 True -13 39284 31.172135591506958 0.66983962059021 434.82940673828125 0.26247894763946533 541.799560546875 0.3518403470516205 0.8151492 0.35179564356803894 True -14 42090 31.148033380508423 0.6360225677490234 412.7974548339844 0.25237002968788147 540.9326782226562 0.3531840145587921 0.8203188 0.3189392387866974 True -15 44896 30.63525629043579 0.6342146396636963 525.4719848632812 0.3004169464111328 540.6943969726562 0.3527238070964813 0.8232248 0.2929978668689728 True -16 47702 30.418647050857544 21.15275001525879 474.3481750488281 0.3782682418823242 540.2656860351562 0.35362744331359863 0.82767797 0.2776908874511719 True -17 50508 30.929293155670166 0.6020114421844482 567.6099853515625 0.23468618094921112 540.6616821289062 0.35275208950042725 0.8278425 0.2727507948875427 True -18 53314 30.54583740234375 0.6012139320373535 490.9093017578125 0.14762865006923676 540.4262084960938 0.35284215211868286 0.82459587 0.27298080921173096 False -19 56120 30.5088210105896 0.6090826988220215 573.375732421875 0.16394661366939545 541.2081909179688 0.3514149487018585 0.8244457 0.27470576763153076 False diff --git a/ENCSR859LTL/cherimoya.fold_4.performance.tsv b/ENCSR859LTL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d7ed685af74d5a0b4ac64f45a8126479ad393826..0000000000000000000000000000000000000000 --- a/ENCSR859LTL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -540.6616821289062 0.4242115020751953 0.35275208950042725 0.13230285048484802 0.8278424739837646 0.8061330318450928 0.2727507948875427 \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_0.evaluate.json b/ENCSR860IDO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 20494b9c35484109660c8798038fe50c9ad59250..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917IFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_0.fit.json b/ENCSR860IDO/cherimoya.fold_0.fit.json deleted file mode 100644 index 060f2293ae36b3c801b742309e4f474d9ad06f00..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF917IFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_0.log b/ENCSR860IDO/cherimoya.fold_0.log deleted file mode 100644 index e23504bdb9728bfa6ff9a851dd3f6b78204a3904..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 35.409990072250366 3.513105630874634 176.48446655273438 0.6828199625015259 189.00509643554688 0.11800181865692139 0.72355205 2.9923133850097656 True -1 5520 30.622222185134888 0.6367237567901611 196.37869262695312 0.3712700605392456 174.68600463867188 0.15085440874099731 0.7913618 1.4096651077270508 True -2 8280 30.12063765525818 0.5252199172973633 164.74057006835938 0.6497255563735962 172.77098083496094 0.15257605910301208 0.79668313 0.8278653621673584 True -3 11040 29.92650055885315 0.5449559688568115 127.08087921142578 0.4034794867038727 170.78695678710938 0.15882538259029388 0.80746233 0.6547390222549438 True -4 13800 29.937822341918945 0.5500137805938721 137.33865356445312 0.44569677114486694 170.08984375 0.1599833369255066 0.8150005 0.6567745208740234 True -5 16560 29.935688972473145 0.5417296886444092 142.4108428955078 0.5652948617935181 168.94400024414062 0.1637645661830902 0.81884503 0.6077531576156616 True -6 19320 29.872640132904053 0.5413377285003662 150.86024475097656 0.46381762623786926 168.95217895507812 0.1628023386001587 0.8254661 0.5562497973442078 True -7 22080 29.89477849006653 0.5278244018554688 111.14521026611328 0.5879985094070435 168.3985595703125 0.1648624688386917 0.82601553 0.5622420310974121 True -8 24840 29.887548208236694 0.5305800437927246 167.07554626464844 0.3627278208732605 167.52584838867188 0.1676485240459442 0.83106273 0.5173969864845276 True -9 27600 29.887809991836548 0.5397887229919434 112.42800903320312 0.2969610095024109 167.1540069580078 0.16850244998931885 0.8379144 0.4826987683773041 True -10 30360 29.856571435928345 0.537186861038208 109.49913024902344 0.2730884552001953 166.50648498535156 0.1701003462076187 0.8464401 0.4459555447101593 True -11 33120 29.883674144744873 0.5427682399749756 132.6971893310547 0.4029347002506256 166.15203857421875 0.17095524072647095 0.85534966 0.3949122726917267 True -12 35880 29.931713104248047 0.5326313972473145 99.6293716430664 0.32211410999298096 165.7843475341797 0.17202621698379517 0.86048025 0.3642567992210388 True -13 38640 29.9392147064209 0.5279784202575684 165.15145874023438 0.3017902076244354 165.39845275878906 0.17301028966903687 0.8666234 0.33616864681243896 True -14 41400 29.932994604110718 0.7801849842071533 107.249267578125 0.26688724756240845 165.1280517578125 0.17367295920848846 0.87096375 0.3198516070842743 True -15 44160 29.906877756118774 0.5363664627075195 140.32289123535156 0.44363856315612793 164.74502563476562 0.1741306036710739 0.87250704 0.30172064900398254 True -16 46920 29.943434476852417 0.5466403961181641 132.48341369628906 0.2390306293964386 164.5851593017578 0.17473605275154114 0.8767425 0.2849962115287781 True -17 49680 29.89411163330078 0.5430412292480469 160.52536010742188 0.3365289866924286 164.7118682861328 0.1739911139011383 0.8764342 0.277790367603302 False -18 52440 29.985702514648438 0.5429873466491699 129.62765502929688 0.36114007234573364 164.71131896972656 0.17387278378009796 0.8757647 0.2781272232532501 False -19 55200 29.960580348968506 0.5426318645477295 140.76370239257812 0.24769824743270874 164.78021240234375 0.17389081418514252 0.87621033 0.2791120707988739 False diff --git a/ENCSR860IDO/cherimoya.fold_0.performance.tsv b/ENCSR860IDO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 821c8559204d7791f097db1f03e5b3de454f06a9..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -164.5851593017578 0.5775155425071716 0.17473605275154114 0.04092637076973915 0.8767424821853638 0.7727161049842834 0.2849962115287781 \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_1.evaluate.json b/ENCSR860IDO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4940afdb13abc67d0f920be3a228d848a0547a2c..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917IFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_1.fit.json b/ENCSR860IDO/cherimoya.fold_1.fit.json deleted file mode 100644 index fca9de74a637c6f77be0a8cdd84038e60e5862ac..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF917IFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_1.log b/ENCSR860IDO/cherimoya.fold_1.log deleted file mode 100644 index 964a97d9bfd73e8fbf97515f6524e051bcb916ff..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 35.44773268699646 5.484956979751587 166.00042724609375 0.5260437726974487 243.85462951660156 0.13291095197200775 0.7227243 3.2159628868103027 True -1 5514 30.487473726272583 0.823401689529419 123.25703430175781 0.2789800763130188 224.58090209960938 0.17576324939727783 0.7840546 1.932255744934082 True -2 8271 30.518181324005127 0.7120237350463867 132.3094482421875 0.33328670263290405 221.28836059570312 0.18219219148159027 0.7848517 1.1731046438217163 True -3 11028 29.91314435005188 0.6778380870819092 171.22232055664062 0.7551442384719849 219.26913452148438 0.1841561496257782 0.8012813 1.0662157535552979 True -4 13785 29.835902452468872 0.6667163372039795 163.87100219726562 0.41420966386795044 217.81146240234375 0.18596309423446655 0.8117361 0.9830955266952515 True -5 16542 29.791329383850098 0.6775681972503662 134.13623046875 0.2630417048931122 216.5447540283203 0.1901686042547226 0.81346965 0.9672613143920898 True -6 19299 29.83196258544922 0.6755108833312988 114.72709655761719 0.41918930411338806 214.73489379882812 0.19466371834278107 0.8208539 0.826484203338623 True -7 22056 29.8964741230011 0.6566781997680664 160.50778198242188 0.5244115591049194 213.701171875 0.19649016857147217 0.8295968 0.7609812021255493 True -8 24813 29.84178638458252 0.6771693229675293 153.59423828125 0.4173169732093811 212.75465393066406 0.1988707333803177 0.8362909 0.6950357556343079 True -9 27570 29.83242154121399 0.6730282306671143 184.48822021484375 0.4147762358188629 212.08030700683594 0.2003001570701599 0.84637946 0.6411053538322449 True -10 30327 29.8552143573761 0.6701557636260986 140.05636596679688 0.43623948097229004 210.98281860351562 0.2030348926782608 0.8568449 0.5781213045120239 True -11 33084 29.82998251914978 0.6725540161132812 114.57914733886719 0.34430480003356934 211.03799438476562 0.20262804627418518 0.85988575 0.5263539552688599 True -12 35841 29.820011138916016 0.6643505096435547 150.29275512695312 0.21756333112716675 210.25042724609375 0.20483314990997314 0.8669268 0.48162174224853516 True -13 38598 29.838005304336548 0.8375608921051025 103.33920288085938 0.43489211797714233 209.33424377441406 0.2069055736064911 0.87696934 0.4320620596408844 True -14 41355 29.813356637954712 0.6623187065124512 136.21131896972656 0.5595962405204773 208.69052124023438 0.20794975757598877 0.8810226 0.40582218766212463 True -15 44112 29.88736343383789 0.6532192230224609 136.95367431640625 0.4290262460708618 208.62725830078125 0.20804719626903534 0.8850994 0.3771771788597107 True -16 46869 29.86749577522278 0.6495299339294434 131.88265991210938 0.22005873918533325 208.18714904785156 0.2087058126926422 0.8886134 0.35241198539733887 True -17 49626 29.906596422195435 7.084819555282593 135.04339599609375 0.24442236125469208 208.0257568359375 0.20921297371387482 0.8915541 0.34191790223121643 True -18 52383 29.906758785247803 0.6900990009307861 127.1163330078125 0.2796255052089691 208.04608154296875 0.20900605618953705 0.89144313 0.3376587927341461 False -19 55140 29.889626502990723 0.6667745113372803 133.37118530273438 0.2695845365524292 208.16615295410156 0.20839935541152954 0.8910844 0.3378962278366089 False diff --git a/ENCSR860IDO/cherimoya.fold_1.performance.tsv b/ENCSR860IDO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 45200517f554aa33f895bb5cd7f12f293f1d12c8..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -208.0257568359375 0.5513066649436951 0.209212988615036 0.05262627452611923 0.8915541172027588 0.8319199085235596 0.34191790223121643 \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_2.evaluate.json b/ENCSR860IDO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 88b44686a86011a4463879d104a6ce58e995929d..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917IFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_2.fit.json b/ENCSR860IDO/cherimoya.fold_2.fit.json deleted file mode 100644 index 8c1de545fdc9912a749a0e27cdddb6212ea59cb8..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF917IFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_2.log b/ENCSR860IDO/cherimoya.fold_2.log deleted file mode 100644 index e84b286e75f2e07f0cfb76f0b6111d9ede34484a..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2890 37.58267664909363 3.542487621307373 143.99142456054688 0.5192743539810181 199.72097778320312 0.12160851806402206 0.68311477 2.9132156372070312 True -1 5780 32.01067876815796 7.151365280151367 167.2547607421875 1.0112799406051636 183.1074676513672 0.15890802443027496 0.7884811 1.449313759803772 True -2 8670 31.440873861312866 0.5638208389282227 121.97280883789062 0.6341044902801514 182.07765197753906 0.15901099145412445 0.78627086 0.9481757879257202 False -3 11560 31.31167221069336 0.5269544124603271 127.96964263916016 0.4008575975894928 179.84423828125 0.16375094652175903 0.79545 0.6628822088241577 True -4 14450 31.28947949409485 0.5325126647949219 105.06330871582031 0.45868736505508423 178.48104858398438 0.16636435687541962 0.80585176 0.6159565448760986 True -5 17340 31.28026533126831 0.5211708545684814 120.65068054199219 0.36090850830078125 177.6939697265625 0.16811636090278625 0.8117867 0.5554260611534119 True -6 20230 31.619778394699097 21.681277751922607 148.78562927246094 0.49537408351898193 176.5432891845703 0.17135044932365417 0.8210417 0.5694617033004761 True -7 23120 31.298089265823364 1.7324473857879639 173.84518432617188 0.6133719682693481 175.8935546875 0.17330698668956757 0.8247194 0.5273427367210388 True -8 26010 31.346147775650024 0.541001558303833 134.6638946533203 0.3619180917739868 175.51605224609375 0.17401671409606934 0.8313747 0.5097067952156067 True -9 28900 31.34731960296631 0.5263612270355225 127.56878662109375 0.3396787643432617 174.5847625732422 0.17711597681045532 0.8396328 0.4641737639904022 True -10 31790 31.68648052215576 19.296300649642944 188.65786743164062 0.4198184013366699 174.34938049316406 0.17718805372714996 0.846791 0.41285040974617004 True -11 34680 31.368535041809082 17.955774307250977 190.71051025390625 0.3083598017692566 173.75711059570312 0.1795656681060791 0.85325736 0.3935478925704956 True -12 37570 31.368881702423096 19.426286935806274 139.70132446289062 0.391394704580307 173.45526123046875 0.18026623129844666 0.8586344 0.3656647503376007 True -13 40460 31.321395874023438 0.5472426414489746 132.81979370117188 0.42538613080978394 173.10321044921875 0.18042516708374023 0.86560977 0.3337786793708801 True -14 43350 31.320090293884277 0.5321619510650635 161.73426818847656 0.2766002118587494 172.9458770751953 0.1808108240365982 0.86986035 0.31614238023757935 True -15 46240 31.318633794784546 0.5323162078857422 139.48602294921875 0.3485015034675598 172.4098663330078 0.18246188759803772 0.87399626 0.3013109862804413 True -16 49130 31.38154172897339 0.5301952362060547 118.33740234375 0.3365275263786316 171.9539794921875 0.18432193994522095 0.8749846 0.29477405548095703 True -17 52020 31.347304821014404 0.9464676380157471 156.83529663085938 0.30031511187553406 172.29441833496094 0.1828785538673401 0.8744963 0.2911042869091034 False -18 54910 31.37765884399414 0.5323328971862793 119.97866821289062 0.3630940318107605 172.41004943847656 0.1827387511730194 0.8735753 0.2925068438053131 False -19 57800 31.403820037841797 0.5295591354370117 144.98899841308594 0.404621422290802 172.46908569335938 0.1823965162038803 0.8722516 0.29435911774635315 False diff --git a/ENCSR860IDO/cherimoya.fold_2.performance.tsv b/ENCSR860IDO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c6e71233b29f4d54be423a426cb5158fe534405e..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -171.9539794921875 0.5710499286651611 0.18432192504405975 0.04312059283256531 0.874984622001648 0.7937236428260803 0.29477405548095703 \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_3.evaluate.json b/ENCSR860IDO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index db5deda93f2c269bb62d69a430f9c78bf756698d..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917IFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_3.fit.json b/ENCSR860IDO/cherimoya.fold_3.fit.json deleted file mode 100644 index 953b40d7084441db474c8e5578d77670332db8cb..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF917IFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_3.log b/ENCSR860IDO/cherimoya.fold_3.log deleted file mode 100644 index 85e2d60ca773d3e0fa00b71e13a452f32fc49ed8..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2753 35.36834239959717 3.491004228591919 156.69615173339844 0.38174569606781006 201.1048583984375 0.13024519383907318 0.6852688 3.224924325942993 True -1 5506 30.06870985031128 0.6516029834747314 186.01705932617188 0.7666780948638916 187.0476531982422 0.1639595329761505 0.77271634 1.5489686727523804 True -2 8259 30.51929545402527 0.5404481887817383 137.43765258789062 0.3216126561164856 185.13543701171875 0.16637423634529114 0.77492476 0.9270767569541931 True -3 11012 30.290069818496704 0.5278050899505615 161.3118896484375 0.6597273349761963 183.6822509765625 0.1692531257867813 0.78902376 0.7688407897949219 True -4 13765 29.780760526657104 0.5233297348022461 142.15936279296875 0.5033657550811768 182.35816955566406 0.1722724437713623 0.794757 0.7396273016929626 True -5 16518 29.78161096572876 0.5282270908355713 138.68191528320312 0.5023501515388489 181.52076721191406 0.17457500100135803 0.7993489 0.70915287733078 True -6 19271 29.815316677093506 0.5999741554260254 127.62846374511719 0.3601069748401642 181.3153839111328 0.1743955761194229 0.8038729 0.6888558268547058 True -7 22024 29.82806396484375 0.8992886543273926 99.17184448242188 0.31336474418640137 180.51107788085938 0.17654795944690704 0.81399673 0.6625087261199951 True -8 24777 29.861363172531128 0.5228514671325684 158.03900146484375 0.40854257345199585 179.56585693359375 0.17967697978019714 0.8157979 0.6349619030952454 True -9 27530 29.82812738418579 0.53212571144104 142.2626953125 0.35564589500427246 179.28927612304688 0.1805335283279419 0.8207242 0.6066926717758179 True -10 30283 30.14244794845581 0.9257557392120361 139.02685546875 0.46462830901145935 178.80667114257812 0.18245893716812134 0.8299841 0.5721484422683716 True -11 33036 29.805137157440186 0.5229659080505371 121.80030822753906 0.5161149501800537 178.39572143554688 0.18288804590702057 0.8360737 0.5128602981567383 True -12 35789 29.893937826156616 0.522709846496582 170.5821990966797 0.47011798620224 177.57273864746094 0.18519842624664307 0.8485905 0.4517170190811157 True -13 38542 29.861210107803345 0.5360715389251709 142.2449493408203 0.2514761686325073 177.31024169921875 0.18573851883411407 0.85408205 0.4195820093154907 True -14 41295 29.862592458724976 0.5243716239929199 162.99732971191406 0.43241870403289795 176.7598419189453 0.18676264584064484 0.8597367 0.38466572761535645 True -15 44048 29.907721757888794 0.5216770172119141 113.14241790771484 0.31183433532714844 176.57412719726562 0.18716908991336823 0.86651254 0.3623666763305664 True -16 46801 29.88396978378296 0.5241413116455078 175.96078491210938 0.3131657838821411 176.0410919189453 0.18892192840576172 0.8702673 0.34330347180366516 True -17 49554 29.86372447013855 2.5721778869628906 141.14793395996094 0.3534435033798218 176.13656616210938 0.18802256882190704 0.87159413 0.33696824312210083 True -18 52307 29.931373596191406 0.546097993850708 128.13296508789062 0.24704520404338837 176.3853759765625 0.18703961372375488 0.8726719 0.3305608928203583 True -19 55060 29.98193335533142 0.5759215354919434 110.49736022949219 0.1415901482105255 176.31324768066406 0.18751510977745056 0.8721394 0.330161988735199 False diff --git a/ENCSR860IDO/cherimoya.fold_3.performance.tsv b/ENCSR860IDO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 083133cbbec59ebf0b278b06bb0a50354d566334..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -176.3853759765625 0.5687917470932007 0.18703961372375488 0.046406153589487076 0.872671902179718 0.779835045337677 0.3305608928203583 \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_4.evaluate.json b/ENCSR860IDO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f139e6a910e475771763b017e1749bc4f1ed9fcd..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF917IFD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_4.fit.json b/ENCSR860IDO/cherimoya.fold_4.fit.json deleted file mode 100644 index 42930fdcb74feb088c5220d6a8326dc116c8c2e6..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF917IFD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR860IDO/cherimoya.fold_4.log b/ENCSR860IDO/cherimoya.fold_4.log deleted file mode 100644 index 2007705927490149bd2e6022cb016e5407d11fe2..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 35.17601561546326 4.08804726600647 139.451904296875 0.3687949776649475 159.3397216796875 0.10921832919120789 0.70127875 2.3492631912231445 True -1 5502 30.565048217773438 0.7664163112640381 125.3975830078125 0.505570650100708 149.95321655273438 0.13631686568260193 0.76151353 1.2603689432144165 True -2 8253 30.508373022079468 0.6785399913787842 137.32254028320312 0.48903965950012207 148.18450927734375 0.1384725272655487 0.7687237 0.7549563646316528 True -3 11004 30.41551375389099 0.6398673057556152 133.7833251953125 0.4718599319458008 146.9626007080078 0.14065775275230408 0.78730017 0.5413367748260498 True -4 13755 30.43646478652954 1.423079013824463 118.37149047851562 0.47085344791412354 146.53968811035156 0.14211738109588623 0.7911819 0.5035334825515747 True -5 16506 30.48075246810913 0.6402342319488525 148.1673583984375 0.38872429728507996 145.8038330078125 0.14353221654891968 0.7978845 0.49650248885154724 True -6 19257 30.482529401779175 1.450200080871582 107.57894134521484 0.33636540174484253 145.22686767578125 0.14566262066364288 0.8060367 0.4450702369213104 True -7 22008 30.48443579673767 0.6489262580871582 142.59182739257812 0.5012363195419312 145.0010223388672 0.14648091793060303 0.80473477 0.4481618106365204 False -8 24759 30.516889810562134 0.6495592594146729 161.7130889892578 0.4123779833316803 144.2882537841797 0.14846378564834595 0.8167283 0.40778544545173645 True -9 27510 30.306897401809692 1.8303894996643066 142.23275756835938 0.4528384804725647 144.11805725097656 0.14866109192371368 0.81826663 0.3989035189151764 True -10 30261 29.806026220321655 2.9058780670166016 114.38615417480469 0.4093655049800873 143.69972229003906 0.15050609409809113 0.82728976 0.36176708340644836 True -11 33012 29.876782655715942 2.1488661766052246 137.372314453125 0.443990021944046 143.2863006591797 0.15179555118083954 0.83358365 0.3344920575618744 True -12 35763 29.919184684753418 12.917365074157715 105.26890563964844 0.3707340657711029 142.91079711914062 0.1530621200799942 0.84147286 0.31718704104423523 True -13 38514 30.09309482574463 24.35925054550171 90.5065689086914 0.26452118158340454 143.00686645507812 0.15224166214466095 0.8479816 0.2902619242668152 True -14 41265 29.987582683563232 19.89397120475769 172.28343200683594 0.4456550180912018 142.54409790039062 0.15385590493679047 0.85309523 0.2752313017845154 True -15 44016 30.025670766830444 21.578855514526367 149.62503051757812 0.30266448855400085 142.40618896484375 0.1541554033756256 0.8594375 0.26349297165870667 True -16 46767 30.03665828704834 2.0508761405944824 160.91786193847656 0.3791147470474243 142.39492797851562 0.15375247597694397 0.8611547 0.2563072443008423 True -17 49518 29.97764015197754 1.0100963115692139 142.15115356445312 0.3874259889125824 142.25645446777344 0.15463367104530334 0.8610258 0.25474581122398376 False -18 52269 29.99971866607666 0.6582088470458984 129.34982299804688 0.29187849164009094 142.31382751464844 0.1544157713651657 0.8628283 0.25380030274391174 True -19 55020 30.08930540084839 0.633807897567749 149.14892578125 0.2931017279624939 142.25872802734375 0.1544504165649414 0.86102 0.2559015154838562 False diff --git a/ENCSR860IDO/cherimoya.fold_4.performance.tsv b/ENCSR860IDO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a77e646011494cd3c184472cbd30ddb832cd1237..0000000000000000000000000000000000000000 --- a/ENCSR860IDO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -142.31382751464844 0.5924669504165649 0.1544157862663269 0.032893236726522446 0.8628283143043518 0.7440327405929565 0.25380030274391174 \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_0.evaluate.json b/ENCSR861NUH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f282162d225e548f1aff545e080564e909035303..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF981UJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_0.fit.json b/ENCSR861NUH/cherimoya.fold_0.fit.json deleted file mode 100644 index 8481d7b7f2c1b5921eb7c7dec86aa9b6ce69f17d..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF981UJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_0.log b/ENCSR861NUH/cherimoya.fold_0.log deleted file mode 100644 index cc7298614d4668449af0ed6aeb223a9e5f5df236..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.98816657066345 3.5865821838378906 195.22091674804688 0.7399237751960754 255.92320251464844 0.15340854227542877 0.41647676 3.4581034183502197 True -1 5498 30.69746708869934 0.6925430297851562 167.84356689453125 0.92347252368927 237.2390899658203 0.24054890871047974 0.57906365 1.801660418510437 True -2 8247 30.654320240020752 0.6525535583496094 180.240478515625 0.6256997585296631 233.0094451904297 0.25466668605804443 0.5856914 0.8091700673103333 True -3 10996 30.699724912643433 0.6097748279571533 180.286376953125 0.6202970743179321 230.90951538085938 0.26298102736473083 0.60325855 0.6309868693351746 True -4 13745 30.70218276977539 0.6293306350708008 163.85658264160156 0.985995888710022 230.4146270751953 0.26425108313560486 0.61256725 0.6109817028045654 True -5 16494 30.701921939849854 0.6175665855407715 185.04884338378906 0.8050676584243774 229.8590545654297 0.26632145047187805 0.6149224 0.6460548043251038 True -6 19243 30.653291702270508 0.6184065341949463 163.33209228515625 0.4832914173603058 229.2472686767578 0.2706172466278076 0.6196701 0.6476001143455505 True -7 21992 30.69413733482361 0.6248898506164551 124.42587280273438 0.6372021436691284 228.81005859375 0.2727605402469635 0.6220014 0.6424493789672852 True -8 24741 30.69783902168274 0.6126377582550049 162.93978881835938 0.915412425994873 228.5990753173828 0.2729184627532959 0.62802136 0.6021996140480042 True -9 27490 30.783823013305664 0.6174860000610352 178.8893585205078 0.6342145204544067 227.73736572265625 0.2772931754589081 0.6345459 0.5711296200752258 True -10 30239 30.72373914718628 0.621868371963501 185.8471221923828 0.5259621143341064 227.01771545410156 0.2803732752799988 0.64116466 0.5423232913017273 True -11 32988 30.715435028076172 0.6155064105987549 169.8631591796875 0.47137054800987244 226.75009155273438 0.2815901041030884 0.6499428 0.5490501523017883 True -12 35737 30.688031435012817 0.6193089485168457 168.73573303222656 0.5879495739936829 226.35488891601562 0.28269413113594055 0.66001356 0.5047650933265686 True -13 38486 30.79328989982605 17.546191453933716 166.4097900390625 0.5298141241073608 225.78945922851562 0.2855812609195709 0.66762906 0.48887255787849426 True -14 41235 31.37462091445923 0.6345393657684326 173.46725463867188 0.47427862882614136 225.42514038085938 0.28745025396347046 0.67472357 0.47885820269584656 True -15 43984 30.89536690711975 0.6388535499572754 162.3510284423828 0.38946783542633057 225.0665740966797 0.28820085525512695 0.68367696 0.45893847942352295 True -16 46733 30.755050659179688 1.0105056762695312 203.03326416015625 0.5262489914894104 224.685302734375 0.29023757576942444 0.69157326 0.4438038766384125 True -17 49482 30.761148691177368 0.6206185817718506 161.76266479492188 0.3951355814933777 224.7382049560547 0.2899650037288666 0.6970409 0.4389825165271759 True -18 52231 30.676603317260742 1.5303776264190674 136.54112243652344 0.42939725518226624 224.884765625 0.2892145812511444 0.69540924 0.4401313066482544 False -19 54980 30.93565320968628 0.6352643966674805 180.99072265625 0.35615336894989014 224.78477478027344 0.28959921002388 0.694887 0.4441142678260803 False diff --git a/ENCSR861NUH/cherimoya.fold_0.performance.tsv b/ENCSR861NUH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a2924ddb682c62f8f37b7898692257740cb05632..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -224.7382049560547 0.5073296427726746 0.2899650037288666 0.06846381723880768 0.6970409154891968 0.6523264050483704 0.4389825165271759 \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_1.evaluate.json b/ENCSR861NUH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 78838f6902ef17e507f80378322f58b66e6cd505..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF981UJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_1.fit.json b/ENCSR861NUH/cherimoya.fold_1.fit.json deleted file mode 100644 index 2673237125e5b08d8aa72c0b025e3e770d3ac655..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF981UJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_1.log b/ENCSR861NUH/cherimoya.fold_1.log deleted file mode 100644 index 02a4c6f6c62fae7619787dbf96fbef04bab78210..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 34.57061457633972 3.645704507827759 184.52328491210938 0.7752488851547241 288.8724060058594 0.16153357923030853 0.48153955 3.7331383228302 True -1 5488 30.94810390472412 0.7344932556152344 196.83560180664062 1.0106654167175293 265.8217468261719 0.25744596123695374 0.6088895 1.4219121932983398 True -2 8232 30.661319732666016 0.6992475986480713 185.27108764648438 0.9719946980476379 261.0578308105469 0.2678695619106293 0.6343191 0.7687860131263733 True -3 10976 30.75272560119629 0.7163786888122559 166.20274353027344 0.5514442920684814 258.487060546875 0.27519911527633667 0.6528301 0.6501204967498779 True -4 13720 30.717305183410645 0.7094569206237793 188.95904541015625 0.7302511930465698 257.60894775390625 0.2778710126876831 0.6617378 0.6067776083946228 True -5 16464 30.68130898475647 0.7082366943359375 166.17869567871094 0.8496924638748169 256.94482421875 0.2798703610897064 0.6709842 0.6271068453788757 True -6 19208 30.717130661010742 0.709052562713623 171.0211181640625 0.6256669163703918 256.1981201171875 0.2821945250034332 0.6812136 0.6089627742767334 True -7 21952 30.714301586151123 1.2373323440551758 206.81558227539062 0.6419944763183594 255.48797607421875 0.2845930755138397 0.6833089 0.6219323873519897 True -8 24696 30.724608182907104 0.7349188327789307 125.03881072998047 0.6889975070953369 254.77789306640625 0.2875809073448181 0.6888582 0.5996761322021484 True -9 27440 30.705768823623657 0.7156362533569336 140.16160583496094 0.798556923866272 254.5478057861328 0.2883019745349884 0.69292927 0.5871351957321167 True -10 30184 30.736894607543945 0.7115178108215332 159.72775268554688 0.6792989373207092 253.6260223388672 0.29231658577919006 0.6975888 0.5682687759399414 True -11 32928 30.700823307037354 0.7096264362335205 152.83021545410156 0.5337189435958862 253.3140411376953 0.29241135716438293 0.7067597 0.5385206937789917 True -12 35672 30.65095067024231 0.7084856033325195 191.43936157226562 0.6930572986602783 252.518310546875 0.2948281466960907 0.70991826 0.5294806957244873 True -13 38416 30.75752353668213 0.7090632915496826 184.4242401123047 0.49675673246383667 251.65167236328125 0.2986326515674591 0.7220155 0.48567822575569153 True -14 41160 30.708404302597046 0.7072453498840332 158.46205139160156 0.5848277807235718 251.24742126464844 0.2988494336605072 0.7304535 0.47328704595565796 True -15 43904 30.73684000968933 2.7494921684265137 198.3391876220703 0.5807515382766724 250.90333557128906 0.3016660213470459 0.73682183 0.4571267366409302 True -16 46648 30.72265100479126 0.7139372825622559 196.28851318359375 0.7003949880599976 250.8046112060547 0.30086076259613037 0.744021 0.4482780992984772 True -17 49392 30.65795588493347 0.71527099609375 166.7666473388672 0.3703616261482239 250.3083953857422 0.30287620425224304 0.7464396 0.45061442255973816 True -18 52136 30.657697677612305 0.7027084827423096 156.89524841308594 0.4479285478591919 250.44276428222656 0.3023239076137543 0.7460957 0.4497552514076233 False -19 54880 30.699684381484985 0.70304274559021 173.776611328125 0.26426759362220764 250.7338104248047 0.3009604811668396 0.7453926 0.45686566829681396 False diff --git a/ENCSR861NUH/cherimoya.fold_1.performance.tsv b/ENCSR861NUH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 79d7d03be5f3e0d35b2301ca7e7c19e6dc5335ed..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.3083953857422 0.49484166502952576 0.30287623405456543 0.07390422374010086 0.7464395761489868 0.7005389332771301 0.45061442255973816 \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_2.evaluate.json b/ENCSR861NUH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8059e5bf8e37567db74e764252cda84b804086fd..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF981UJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_2.fit.json b/ENCSR861NUH/cherimoya.fold_2.fit.json deleted file mode 100644 index 083bfb5cacb261e8cfdf0d5eca523ef4dee507ef..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF981UJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_2.log b/ENCSR861NUH/cherimoya.fold_2.log deleted file mode 100644 index cc8ac9b6f59b0afa42aca4c0b225a21ff14c1656..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2906 36.11459469795227 3.5543124675750732 196.4710693359375 1.0800150632858276 257.42852783203125 0.15997931361198425 0.4484864 2.118858575820923 True -1 5812 32.17175340652466 0.5806028842926025 198.39881896972656 0.9125581383705139 237.3659210205078 0.25140395760536194 0.56349623 1.0970810651779175 True -2 8718 32.21357846260071 0.5844788551330566 143.35739135742188 0.8612676858901978 233.2972412109375 0.26227685809135437 0.5954858 0.6624139547348022 True -3 11624 32.24898433685303 0.5541384220123291 180.44088745117188 0.5635837316513062 232.03689575195312 0.2660718858242035 0.6100413 0.5897263884544373 True -4 14530 32.2552592754364 0.555161714553833 156.99676513671875 0.9946877956390381 231.2657928466797 0.2700191140174866 0.6160594 0.6553851962089539 True -5 17436 32.219244956970215 0.5575728416442871 164.19888305664062 1.082414984703064 230.56019592285156 0.27213749289512634 0.6226858 0.7420856356620789 True -6 20342 32.27270579338074 0.5673027038574219 215.34454345703125 0.9433907270431519 230.32809448242188 0.27394646406173706 0.62521183 0.7539255619049072 True -7 23248 32.24076843261719 0.5569913387298584 163.138427734375 0.9591264724731445 229.9227294921875 0.27639198303222656 0.6267908 0.7349172830581665 True -8 26154 32.26745271682739 4.621299982070923 160.11590576171875 0.5795885324478149 229.33131408691406 0.2786431610584259 0.63281643 0.7102259397506714 True -9 29060 32.28497791290283 0.5714247226715088 168.29200744628906 0.8642534613609314 228.70657348632812 0.28116077184677124 0.6419238 0.6366787552833557 True -10 31966 32.27119827270508 0.5637416839599609 199.80316162109375 0.5522926449775696 228.15701293945312 0.28269162774086 0.64712054 0.631847083568573 True -11 34872 32.22758674621582 0.559088945388794 179.94686889648438 0.736011266708374 227.67274475097656 0.284280925989151 0.6560456 0.5871904492378235 True -12 37778 32.271371841430664 0.5568602085113525 182.01585388183594 0.5057395696640015 226.99005126953125 0.28763505816459656 0.66446257 0.573731541633606 True -13 40684 32.26373624801636 0.5520236492156982 194.69265747070312 0.5053369998931885 226.60142517089844 0.2888258695602417 0.6729822 0.5192897915840149 True -14 43590 32.32367300987244 0.5690298080444336 177.03543090820312 0.4644174575805664 226.0697021484375 0.29087215662002563 0.6798024 0.49670177698135376 True -15 46496 32.25471377372742 1.337913990020752 191.39437866210938 0.49855881929397583 225.63742065429688 0.2929370105266571 0.68850327 0.47717082500457764 True -16 49402 32.24375772476196 0.5620772838592529 209.34234619140625 0.480774462223053 225.2230987548828 0.29507890343666077 0.6943565 0.4621039032936096 True -17 52308 32.246147871017456 0.5520627498626709 147.27975463867188 0.6301187872886658 225.31353759765625 0.29444774985313416 0.6947178 0.4626878798007965 True -18 55214 32.17278051376343 0.547652006149292 203.15150451660156 0.3179626762866974 225.40328979492188 0.2934972941875458 0.69573116 0.4644996225833893 True -19 58120 32.18328356742859 0.5541846752166748 152.86944580078125 0.583398163318634 225.6316375732422 0.2919083535671234 0.6936004 0.4661792814731598 False diff --git a/ENCSR861NUH/cherimoya.fold_2.performance.tsv b/ENCSR861NUH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8b08b24179c466296249b71b1cfa1646b5a8dd8b..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -225.40328979492188 0.5054987668991089 0.2934972941875458 0.0665254071354866 0.6957311630249023 0.6403284072875977 0.4644996225833893 \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_3.evaluate.json b/ENCSR861NUH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1b00c55260093d46e3bf8dd471cb5fa4bd0dfb3e..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF981UJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_3.fit.json b/ENCSR861NUH/cherimoya.fold_3.fit.json deleted file mode 100644 index 7d491a3cc66483378b42e3217ccaae16ba326c68..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF981UJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_3.log b/ENCSR861NUH/cherimoya.fold_3.log deleted file mode 100644 index 426f467ea19032292625eb118389079b2407b3d2..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 34.97423505783081 3.4258975982666016 170.92503356933594 0.6500383615493774 268.62603759765625 0.15815356373786926 0.4589139 3.9711873531341553 True -1 5536 30.923271417617798 0.6385984420776367 196.7650604248047 0.8088136911392212 249.2805938720703 0.24643480777740479 0.56205404 1.622161865234375 True -2 8304 30.91159987449646 0.6188714504241943 181.8997802734375 0.7163720726966858 245.5590057373047 0.25684359669685364 0.5893507 0.8438406586647034 True -3 11072 30.9222469329834 0.6171581745147705 175.185546875 0.4764072895050049 243.36647033691406 0.26452821493148804 0.6050887 0.8081254363059998 True -4 13840 30.933895587921143 0.6307811737060547 169.01658630371094 1.022895097732544 242.7058868408203 0.26656776666641235 0.61626357 0.714621365070343 True -5 16608 31.165281057357788 0.655756950378418 168.54888916015625 0.6031478643417358 242.0605926513672 0.26888394355773926 0.6227161 0.7481234669685364 True -6 19376 31.01936650276184 0.6355171203613281 155.79986572265625 0.6346426606178284 241.75694274902344 0.2701720595359802 0.630324 0.7417404055595398 True -7 22144 30.935394048690796 0.6342911720275879 155.11700439453125 0.6699419617652893 241.27029418945312 0.27191051840782166 0.639131 0.6849052906036377 True -8 24912 30.981420040130615 0.6421592235565186 217.46075439453125 0.497383713722229 240.355712890625 0.2758270800113678 0.6438287 0.6771512031555176 True -9 27680 30.9338161945343 1.9030554294586182 182.27703857421875 0.6970009803771973 240.08102416992188 0.2765827775001526 0.64926124 0.6380838751792908 True -10 30448 30.998339891433716 0.6347944736480713 160.87864685058594 0.6403870582580566 239.10546875 0.2811596989631653 0.65199983 0.6058441400527954 True -11 33216 30.942776441574097 0.6261203289031982 194.40573120117188 0.5354306101799011 238.78785705566406 0.28199502825737 0.6654411 0.5670245289802551 True -12 35984 30.949668169021606 0.6412851810455322 221.034423828125 0.6482048630714417 238.4729766845703 0.2831488251686096 0.67556864 0.549588680267334 True -13 38752 31.06006956100464 0.6417818069458008 190.70452880859375 0.6817895770072937 237.73390197753906 0.2866171896457672 0.68376833 0.509908139705658 True -14 41520 31.06265354156494 0.6412196159362793 173.29736328125 0.6404757499694824 237.34722900390625 0.2880178391933441 0.69223076 0.4824100732803345 True -15 44288 31.056261777877808 0.8656139373779297 189.00189208984375 0.5819193124771118 236.98838806152344 0.2892574071884155 0.7016767 0.47052422165870667 True -16 47056 31.02813482284546 1.185405969619751 182.44236755371094 0.4730101525783539 236.85365295410156 0.2897927761077881 0.7069842 0.4568314254283905 True -17 49824 30.999852180480957 0.6260771751403809 217.65386962890625 0.33081942796707153 236.842529296875 0.2901454269886017 0.7106442 0.45470282435417175 True -18 52592 30.987905979156494 0.6375260353088379 180.48011779785156 0.5070697665214539 236.9293975830078 0.28979021310806274 0.7102283 0.45980775356292725 False -19 55360 31.074209213256836 0.6369974613189697 183.16647338867188 0.3223896622657776 236.9871368408203 0.2894144356250763 0.7117216 0.462528258562088 True diff --git a/ENCSR861NUH/cherimoya.fold_3.performance.tsv b/ENCSR861NUH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b8eb45cc4a6401d1ad5b3609e3f123af9464dd10..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -236.9871368408203 0.5039365291595459 0.2894144654273987 0.07038135081529617 0.7117215991020203 0.6675031781196594 0.462528258562088 \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_4.evaluate.json b/ENCSR861NUH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d1a60ed8c9f310cb5551949b19e46e71b6126cb1..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF981UJU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_4.fit.json b/ENCSR861NUH/cherimoya.fold_4.fit.json deleted file mode 100644 index c257a7f84bff5f577d47b349d366a617d1a3fba6..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF981UJU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR861NUH/cherimoya.fold_4.log b/ENCSR861NUH/cherimoya.fold_4.log deleted file mode 100644 index 31491a337e5b27370360c09c47a9bda741cdc3bf..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 36.3952112197876 3.845689535140991 172.96273803710938 0.8576252460479736 260.54095458984375 0.16189181804656982 0.4334755 2.6034767627716064 True -1 5742 32.12644672393799 2.346576452255249 174.0107879638672 0.6386811137199402 241.26747131347656 0.251578688621521 0.5361556 1.7809573411941528 True -2 8613 32.17788338661194 0.6319701671600342 161.13665771484375 0.5315548777580261 238.5832061767578 0.2578542232513428 0.5559827 0.7935087084770203 True -3 11484 32.12521696090698 0.627784252166748 223.8614501953125 1.1998703479766846 236.8085174560547 0.2635708749294281 0.5732147 0.745172917842865 True -4 14355 32.137247800827026 1.3356258869171143 222.0174560546875 0.6727635264396667 236.04298400878906 0.2667399048805237 0.5874074 0.6975497007369995 True -5 17226 32.10591220855713 0.6298024654388428 196.995361328125 0.836100161075592 235.82347106933594 0.2673089802265167 0.60002273 0.700095534324646 True -6 20097 32.08436369895935 1.878645420074463 178.2554168701172 0.9084765911102295 235.30857849121094 0.2697712779045105 0.60479236 0.7194569110870361 True -7 22968 32.1289758682251 0.6281759738922119 193.47976684570312 0.5822430849075317 234.95538330078125 0.27159589529037476 0.6117771 0.6751226186752319 True -8 25839 32.130247592926025 1.1672110557556152 176.9229736328125 0.5566943287849426 234.35791015625 0.27434241771698 0.6207719 0.6768665909767151 True -9 28710 32.20117950439453 0.6315746307373047 159.9940185546875 0.5887317061424255 233.90200805664062 0.27660802006721497 0.6241082 0.6400772929191589 True -10 31581 32.10262107849121 0.6327505111694336 177.93771362304688 0.6116823554039001 233.4967041015625 0.27832385897636414 0.63162416 0.5937883853912354 True -11 34452 32.11356043815613 0.6294248104095459 195.0618896484375 0.6151281595230103 232.88070678710938 0.2802857458591461 0.64134276 0.5602284669876099 True -12 37323 32.103338956832886 1.414567470550537 209.62203979492188 0.5386217832565308 232.65838623046875 0.28072109818458557 0.6484734 0.5605211853981018 True -13 40194 32.139886140823364 0.6263453960418701 189.74383544921875 0.46694400906562805 232.00958251953125 0.2835792303085327 0.6623291 0.5229408144950867 True -14 43065 32.10821318626404 0.6293354034423828 183.70941162109375 0.6073885560035706 231.6876220703125 0.2849750816822052 0.6731632 0.48880621790885925 True -15 45936 32.127809047698975 0.6211075782775879 167.2041778564453 0.6646595001220703 231.01763916015625 0.28838929533958435 0.6797855 0.47116079926490784 True -16 48807 32.12033033370972 0.6293683052062988 179.52679443359375 0.30668219923973083 230.89096069335938 0.2886762320995331 0.6868591 0.463378369808197 True -17 51678 32.09239220619202 0.6311960220336914 183.54531860351562 0.32202041149139404 230.7051544189453 0.289465069770813 0.69059324 0.46010416746139526 True -18 54549 32.09581184387207 0.6271705627441406 154.511474609375 0.41381916403770447 230.8651885986328 0.28828534483909607 0.6935407 0.4617225229740143 True -19 57420 32.08398771286011 1.6614830493927002 124.73914337158203 0.4108229875564575 231.0862579345703 0.28704026341438293 0.6898613 0.468850702047348 False diff --git a/ENCSR861NUH/cherimoya.fold_4.performance.tsv b/ENCSR861NUH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0a5524b9f4343be2690fb49f6e3ee8b27a5d81b1..0000000000000000000000000000000000000000 --- a/ENCSR861NUH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -230.8651885986328 0.5060330629348755 0.28828534483909607 0.06650174409151077 0.6935406923294067 0.6461060047149658 0.4617225229740143 \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_0.evaluate.json b/ENCSR862SQC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e5a9050aac77429e6a54eb506f50b99e216c8976..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF722GJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_0.fit.json b/ENCSR862SQC/cherimoya.fold_0.fit.json deleted file mode 100644 index 4c7f46999461f84b61c69690d0dae5d86b901b06..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF722GJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_0.log b/ENCSR862SQC/cherimoya.fold_0.log deleted file mode 100644 index f793a2c0b61d76f0612e9afc985670a5d5af6e1f..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 34.641618967056274 3.6178812980651855 468.2276611328125 0.7252777814865112 633.455322265625 0.23785459995269775 0.6157278 4.873493671417236 True -1 5474 30.20578646659851 0.9252016544342041 453.85443115234375 0.6537401080131531 588.0961303710938 0.31538674235343933 0.68115515 1.7167928218841553 True -2 8211 30.23182702064514 0.5614643096923828 500.819091796875 0.4885618984699249 575.3944091796875 0.335761696100235 0.6816285 0.7773928642272949 True -3 10948 30.167147636413574 1.8195452690124512 518.0777587890625 0.687055766582489 569.4039916992188 0.34579554200172424 0.68824166 0.6442999839782715 True -4 13685 30.203881978988647 0.5742354393005371 491.1080322265625 0.6479892730712891 567.552734375 0.34858983755111694 0.6781371 0.5202129483222961 False -5 16422 30.177469968795776 0.5733301639556885 428.49237060546875 0.40719103813171387 564.3963623046875 0.35428526997566223 0.68955153 0.41861796379089355 True -6 19159 30.501989126205444 0.5718648433685303 454.56982421875 0.4567200839519501 562.73095703125 0.35699978470802307 0.69016373 0.4227222204208374 True -7 21896 32.778311014175415 29.309732913970947 430.74652099609375 0.35423022508621216 561.2929077148438 0.3595847189426422 0.7008968 0.3790813684463501 True -8 24633 31.988900661468506 0.5649075508117676 464.0733642578125 0.44833409786224365 559.4037475585938 0.3631576597690582 0.70549995 0.3798750638961792 True -9 27370 30.4546377658844 0.5769717693328857 476.7787170410156 0.40477555990219116 557.4939575195312 0.3675346076488495 0.7028057 0.3690330386161804 False -10 30107 30.30522346496582 0.5712594985961914 426.63531494140625 0.4488579034805298 556.022705078125 0.3692927062511444 0.71292126 0.3613404333591461 True -11 32844 30.20694851875305 0.8566441535949707 457.3077087402344 0.4798460304737091 554.8761596679688 0.37049993872642517 0.7208219 0.34339508414268494 True -12 35581 30.245760202407837 13.364144325256348 430.8081359863281 0.46368882060050964 552.0494384765625 0.37579619884490967 0.7353258 0.32319796085357666 True -13 38318 31.17037081718445 0.5812435150146484 476.4183654785156 0.4478166699409485 551.6724243164062 0.3756544888019562 0.7461276 0.31438151001930237 True -14 41055 34.601272106170654 15.98117208480835 440.24169921875 0.2653881311416626 550.2890014648438 0.3783724009990692 0.7526298 0.30873700976371765 True -15 43792 30.452741861343384 2.11147403717041 426.4127197265625 0.30617502331733704 548.8682250976562 0.3810092508792877 0.76182085 0.3002232015132904 True -16 46529 30.30990719795227 6.037740230560303 403.0948486328125 0.3318268656730652 549.043701171875 0.38009658455848694 0.76469284 0.29900699853897095 True -17 49266 30.322824954986572 0.5900156497955322 435.960693359375 0.21682195365428925 548.5804443359375 0.38128310441970825 0.76712555 0.2962493300437927 True -18 52003 30.311726808547974 0.569847822189331 512.0963745117188 0.24146762490272522 548.431396484375 0.381977915763855 0.7659394 0.2996962070465088 False -19 54740 30.3655948638916 0.5810854434967041 379.18414306640625 0.23190462589263916 548.8692626953125 0.38087233901023865 0.7663877 0.30086550116539 False diff --git a/ENCSR862SQC/cherimoya.fold_0.performance.tsv b/ENCSR862SQC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c59a77fc212666a4a663d09d072bf7481cba863a..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -548.5804443359375 0.3909449875354767 0.38128310441970825 0.14958696067333221 0.7671255469322205 0.68171626329422 0.2962493300437927 \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_1.evaluate.json b/ENCSR862SQC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b0370518816e9dfd48fe1edcd9ca757578b7a5d3..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF722GJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_1.fit.json b/ENCSR862SQC/cherimoya.fold_1.fit.json deleted file mode 100644 index a1df066254051e0ec8365645d99c6d829d5bdfcf..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF722GJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_1.log b/ENCSR862SQC/cherimoya.fold_1.log deleted file mode 100644 index ec627fad4eed02c8577df2f498c6d099cf973af1..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2722 40.42500567436218 5.164434194564819 429.64532470703125 0.7798373103141785 698.0216064453125 0.24115216732025146 0.62358916 5.668730735778809 True -1 5444 30.100741863250732 0.7530415058135986 492.35809326171875 0.6779631972312927 640.3082275390625 0.33149176836013794 0.67707586 1.5290727615356445 True -2 8166 30.113360166549683 0.6768624782562256 445.5778503417969 0.6784500479698181 628.2429809570312 0.3438264727592468 0.6939288 0.7760055661201477 True -3 10888 30.019729375839233 0.8214576244354248 455.79412841796875 0.4637572765350342 620.1577758789062 0.3522811233997345 0.7084948 0.578151524066925 True -4 13610 30.021135330200195 0.674354076385498 461.1368103027344 0.5421938896179199 615.5068359375 0.36059439182281494 0.6998552 0.5578638315200806 False -5 16332 30.049317836761475 0.6758871078491211 468.6300048828125 0.6611201763153076 612.6600952148438 0.3643679916858673 0.7033702 0.5041054487228394 False -6 19054 30.061488389968872 2.6020867824554443 444.13433837890625 0.5287883281707764 608.8291015625 0.37061697244644165 0.70827806 0.4887027442455292 False -7 21776 30.11522912979126 0.6801214218139648 395.6604919433594 0.4429837465286255 606.2908935546875 0.3740846514701843 0.71270144 0.4649756848812103 True -8 24498 30.991502285003662 35.00296711921692 393.58831787109375 0.49306386709213257 604.0929565429688 0.377341628074646 0.70981157 0.4535905122756958 False -9 27220 30.345710515975952 0.7061419486999512 444.477783203125 0.47838538885116577 602.175537109375 0.37926408648490906 0.72250974 0.4406422972679138 True -10 29942 30.087875843048096 0.6785430908203125 492.11297607421875 0.29565712809562683 601.135009765625 0.380920946598053 0.7266122 0.4307504892349243 True -11 32664 30.06803870201111 0.7001774311065674 374.5223388671875 0.3104747533798218 598.0599975585938 0.3851635456085205 0.74128014 0.3944455683231354 True -12 35386 30.058817625045776 0.6776387691497803 456.4227600097656 0.44028329849243164 595.3143310546875 0.38910213112831116 0.7512098 0.3891623318195343 True -13 38108 30.05438470840454 0.6777622699737549 434.89764404296875 0.2855343222618103 594.1144409179688 0.3899422585964203 0.7635386 0.37140125036239624 True -14 40830 30.094330072402954 0.6771740913391113 453.04620361328125 0.42129477858543396 592.7451171875 0.3922610282897949 0.7735444 0.3520148992538452 True -15 43552 30.10697913169861 0.669003963470459 460.4537353515625 0.3988959789276123 590.865966796875 0.3947352170944214 0.7811172 0.3355174958705902 True -16 46274 30.085434675216675 34.41962933540344 404.8640441894531 0.264521062374115 590.9202880859375 0.3946165144443512 0.791156 0.32271140813827515 True -17 48996 30.340466260910034 0.6669907569885254 400.7254333496094 0.2889420688152313 590.6945190429688 0.3950921893119812 0.7943145 0.31515657901763916 True -18 51718 30.012120008468628 42.26112174987793 466.76458740234375 0.19491687417030334 590.1011352539062 0.39589229226112366 0.7946892 0.3159901797771454 True -19 54440 30.550769090652466 0.6804413795471191 393.1465148925781 0.2431831806898117 590.2487182617188 0.3956943452358246 0.7941771 0.3188462555408478 False diff --git a/ENCSR862SQC/cherimoya.fold_1.performance.tsv b/ENCSR862SQC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cb68d7201c288e65c35c2be2fa3976fa6c2ce776..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -590.1011352539062 0.38018473982810974 0.39589229226112366 0.16082024574279785 0.7946891784667969 0.7301053404808044 0.3159901797771454 \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_2.evaluate.json b/ENCSR862SQC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9a19c62e4f5467a5a57d490c8fa8539c8f95ec2c..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF722GJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_2.fit.json b/ENCSR862SQC/cherimoya.fold_2.fit.json deleted file mode 100644 index 9522b78272eaf6debbaf542dbba0e81bdea32e5e..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF722GJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_2.log b/ENCSR862SQC/cherimoya.fold_2.log deleted file mode 100644 index 370dad5c0f91cfb40be84561d1823590913827b1..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2863 36.17162346839905 3.5602240562438965 437.8599853515625 0.6472591161727905 641.6339111328125 0.24146252870559692 0.62001055 4.404956340789795 True -1 5726 31.621270418167114 0.5543930530548096 462.2139892578125 0.6682065725326538 590.0825805664062 0.32823339104652405 0.6748646 1.2775636911392212 True -2 8589 31.644310474395752 0.5328383445739746 478.4884033203125 0.48470252752304077 579.4288330078125 0.3406689465045929 0.6769859 0.7755059599876404 True -3 11452 34.48305559158325 3.7094759941101074 491.618408203125 0.7783259749412537 572.7137451171875 0.35097551345825195 0.66812414 0.505184531211853 False -4 14315 31.79776906967163 0.5458416938781738 404.7147216796875 0.4693562984466553 570.9884643554688 0.35335052013397217 0.665326 0.4814196228981018 False -5 17178 32.71393084526062 0.5547647476196289 445.57330322265625 0.34014514088630676 568.173828125 0.3576466739177704 0.6839837 0.43855205178260803 True -6 20041 31.710638284683228 0.5356605052947998 405.8973388671875 0.5319046974182129 563.6878662109375 0.36771705746650696 0.688576 0.4301641285419464 True -7 22904 31.655308961868286 0.5328609943389893 474.479248046875 0.3767876625061035 563.9102172851562 0.3658941090106964 0.69139314 0.43405091762542725 True -8 25767 32.94830942153931 36.43358898162842 382.8370361328125 0.4168328046798706 562.3989868164062 0.36801767349243164 0.69637287 0.41405752301216125 True -9 28630 31.82288694381714 0.5352268218994141 503.7317810058594 0.48718249797821045 560.99560546875 0.37016308307647705 0.6997502 0.4163255989551544 True -10 31493 31.646539211273193 1.4185874462127686 481.03955078125 0.3799653649330139 557.552978515625 0.37607094645500183 0.7135755 0.3793458640575409 True -11 34356 31.574387550354004 1.178262710571289 468.56744384765625 0.47584569454193115 557.7119140625 0.3756241202354431 0.72457063 0.37781694531440735 True -12 37219 31.555004358291626 0.520310640335083 434.15191650390625 0.3698076605796814 555.3264770507812 0.37999650835990906 0.73264587 0.358432412147522 True -13 40082 31.571996688842773 0.5365359783172607 440.8121337890625 0.34104281663894653 554.5999755859375 0.38083311915397644 0.74541706 0.34071967005729675 True -14 42945 31.788485050201416 41.91799712181091 423.9546203613281 0.2567758560180664 552.818603515625 0.3844234347343445 0.7546402 0.32153427600860596 True -15 45808 31.818835020065308 30.568331241607666 429.72979736328125 0.289287269115448 552.2613525390625 0.38448724150657654 0.7602735 0.31274479627609253 True -16 48671 31.73587656021118 0.5559005737304688 502.8233642578125 0.463304728269577 551.2512817382812 0.38684213161468506 0.76602817 0.3098496198654175 True -17 51534 33.27309250831604 1.6466264724731445 424.23297119140625 0.274442195892334 551.2999877929688 0.3861367404460907 0.7687036 0.30408596992492676 True -18 54397 31.641175746917725 0.5334453582763672 410.51373291015625 0.2899738550186157 551.0540771484375 0.38656651973724365 0.77002984 0.3054819405078888 True -19 57260 31.63257360458374 0.5336992740631104 478.43658447265625 0.30629634857177734 551.290283203125 0.38621583580970764 0.76757413 0.3088007867336273 False diff --git a/ENCSR862SQC/cherimoya.fold_2.performance.tsv b/ENCSR862SQC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7c244dfddb5088dab5df7c0a18c0eb5a995668d4..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -551.0540771484375 0.3888821601867676 0.38656651973724365 0.1508558690547943 0.7700298428535461 0.6856791377067566 0.3054819405078888 \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_3.evaluate.json b/ENCSR862SQC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e52be4bfb71d6053bd133f1970e8700da3e5cad9..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF722GJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_3.fit.json b/ENCSR862SQC/cherimoya.fold_3.fit.json deleted file mode 100644 index 4390651ab64b6d2902ddd5560b4e5ff1c731a1ea..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF722GJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_3.log b/ENCSR862SQC/cherimoya.fold_3.log deleted file mode 100644 index 5b377340b9bb2d51b99fc64d27e4356691a4629b..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 35.56660175323486 23.022336721420288 426.04742431640625 0.6284972429275513 637.33203125 0.24303214251995087 0.6332243 4.187509536743164 True -1 5530 30.98669719696045 0.5716087818145752 534.87744140625 0.7039029598236084 591.4843139648438 0.32016608119010925 0.6963794 1.2746511697769165 True -2 8295 30.624709606170654 0.5390479564666748 453.99853515625 0.5038564205169678 580.8323974609375 0.33498114347457886 0.6916381 1.0050965547561646 False -3 11060 30.64073944091797 0.5328857898712158 519.6807861328125 0.6220273971557617 574.3536376953125 0.34412992000579834 0.70056343 0.7485646605491638 True -4 13825 30.49097514152527 0.5364315509796143 529.2090454101562 0.5505163669586182 570.7261352539062 0.3505944013595581 0.693638 0.6139004230499268 False -5 16590 30.629228353500366 0.5482549667358398 456.2535095214844 0.42188429832458496 570.0519409179688 0.3525581359863281 0.68552274 0.5631169676780701 False -6 19355 30.65485429763794 0.546032190322876 387.16510009765625 0.5642421841621399 567.3767700195312 0.3565368950366974 0.69493335 0.561776340007782 False -7 22120 30.61906385421753 0.537766695022583 518.9815673828125 0.37807026505470276 566.217041015625 0.3593412935733795 0.68742114 0.5403321981430054 False -8 24885 30.59216070175171 0.5283920764923096 373.931884765625 0.3790969252586365 563.9859008789062 0.36244118213653564 0.7029455 0.4948199987411499 True -9 27650 30.555349111557007 0.5303194522857666 439.09503173828125 0.4240204691886902 562.7128295898438 0.36448800563812256 0.7098348 0.45837074518203735 True -10 30415 30.60196876525879 0.7128074169158936 416.0020446777344 0.36249682307243347 560.9686279296875 0.3667387366294861 0.7204669 0.4366541802883148 True -11 33180 30.650038957595825 0.5575897693634033 435.04443359375 0.33503401279449463 559.033935546875 0.37053433060646057 0.7308511 0.41301974654197693 True -12 35945 30.606555223464966 0.5392248630523682 522.9815673828125 0.27403494715690613 557.8648071289062 0.37120521068573 0.7415964 0.38516804575920105 True -13 38710 30.551645755767822 0.5367650985717773 429.9453125 0.26961714029312134 555.4285278320312 0.3752549886703491 0.75555104 0.34827351570129395 True -14 41475 31.1105375289917 25.5184485912323 480.71038818359375 0.288124144077301 554.1019897460938 0.3775618076324463 0.765679 0.32996866106987 True -15 44240 31.17264223098755 0.5699596405029297 418.1385803222656 0.3233174681663513 553.6704711914062 0.3780197203159332 0.77493703 0.3184552490711212 True -16 47005 30.980814933776855 0.550774097442627 425.395751953125 0.48359215259552 553.6436767578125 0.37792283296585083 0.77939004 0.3058430850505829 True -17 49770 30.91207242012024 0.5594494342803955 452.2232666015625 0.2541237771511078 553.0667114257812 0.3788268566131592 0.78201777 0.30137184262275696 True -18 52535 30.853917837142944 0.5458564758300781 390.21441650390625 0.25282660126686096 552.2640991210938 0.3812238574028015 0.78286797 0.299817830324173 True -19 55300 30.813971281051636 0.535607099533081 418.62432861328125 0.3154166042804718 552.4674072265625 0.38029107451438904 0.7822305 0.3001559376716614 False diff --git a/ENCSR862SQC/cherimoya.fold_3.performance.tsv b/ENCSR862SQC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 958e3236ae49bec63d44b79a9615b06d56ae8c3e..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -552.2640991210938 0.39079609513282776 0.3812239170074463 0.15270835161209106 0.782867968082428 0.7028493285179138 0.299817830324173 \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_4.evaluate.json b/ENCSR862SQC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 283e0b487a88a2e6a9570c1d5a4ec7a90c9b5b6f..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF722GJD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_4.fit.json b/ENCSR862SQC/cherimoya.fold_4.fit.json deleted file mode 100644 index ace6bf935b8244820d98aef3c226b12361b8f76b..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF722GJD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR862SQC/cherimoya.fold_4.log b/ENCSR862SQC/cherimoya.fold_4.log deleted file mode 100644 index 5d5a49f905164cfb405dea648d93c2773f41cdd5..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2851 36.031190156936646 3.626636505126953 527.15234375 0.5081326365470886 605.3716430664062 0.24024666845798492 0.6115501 4.108322620391846 True -1 5702 31.53956174850464 0.5972170829772949 426.1407470703125 0.637231707572937 564.8761596679688 0.31513750553131104 0.65311664 1.1185200214385986 True -2 8553 31.474271297454834 0.5640547275543213 494.29095458984375 0.5395369529724121 555.5478515625 0.3279283344745636 0.66587526 0.604614794254303 True -3 11404 31.43666982650757 0.5561363697052002 458.5203857421875 0.5563845634460449 549.7928466796875 0.33717143535614014 0.6824742 0.5557157397270203 True -4 14255 31.52905011177063 16.941417455673218 487.5890808105469 0.6660169363021851 548.5350952148438 0.3385239839553833 0.6741053 0.5160102248191833 False -5 17106 31.447110891342163 1.529862403869629 451.1822509765625 0.4622132182121277 545.3601684570312 0.34462374448776245 0.6814841 0.45232048630714417 False -6 19957 31.427913427352905 26.565165519714355 442.67401123046875 0.38016730546951294 543.2792358398438 0.3491225242614746 0.686343 0.42597851157188416 True -7 22808 31.515321493148804 1.0690200328826904 426.8465576171875 0.44315773248672485 541.1180419921875 0.3533238172531128 0.69119775 0.43034493923187256 True -8 25659 31.517439603805542 0.5647978782653809 402.7598876953125 0.4868112802505493 540.227783203125 0.35465601086616516 0.69907224 0.41058942675590515 True -9 28510 31.470507383346558 23.907361268997192 420.8871765136719 0.26489245891571045 539.2175903320312 0.3560481667518616 0.7005796 0.39420241117477417 True -10 31361 32.317888498306274 0.5736005306243896 464.70697021484375 0.3713526129722595 537.1035766601562 0.3600832521915436 0.70296645 0.3670424818992615 True -11 34212 31.433967351913452 2.4677324295043945 409.4011535644531 0.5663380026817322 536.2409057617188 0.3614526391029358 0.71128595 0.3612126410007477 True -12 37063 31.529555320739746 0.5676321983337402 493.13665771484375 0.49935925006866455 534.9545288085938 0.3631809651851654 0.72060144 0.33637598156929016 True -13 39914 31.675636768341064 0.9832804203033447 446.65313720703125 0.2399274855852127 533.3421630859375 0.36594438552856445 0.73177856 0.3232651650905609 True -14 42765 31.451414823532104 1.922917127609253 398.82708740234375 0.2916131019592285 531.6935424804688 0.36922958493232727 0.74087405 0.31013059616088867 True -15 45616 31.47149419784546 0.6732039451599121 484.8882751464844 0.44008928537368774 531.1963500976562 0.37053364515304565 0.74925727 0.3019591271877289 True -16 48467 31.51220464706421 0.5602295398712158 450.1495666503906 0.43355292081832886 531.0599975585938 0.371066689491272 0.75707823 0.29517778754234314 True -17 51318 31.533010721206665 0.5681729316711426 401.36181640625 0.2600981593132019 530.513427734375 0.3722209930419922 0.75883687 0.29456183314323425 True -18 54169 31.44426202774048 0.5597825050354004 472.689208984375 0.23776252567768097 530.131591796875 0.3731369972229004 0.7580541 0.2930062711238861 False -19 57020 32.068556785583496 22.61755919456482 434.84869384765625 0.2134140580892563 530.4555053710938 0.3722696006298065 0.7579847 0.295512855052948 False diff --git a/ENCSR862SQC/cherimoya.fold_4.performance.tsv b/ENCSR862SQC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d6beeae12c351f37006b88d196cfd75675edd5f3..0000000000000000000000000000000000000000 --- a/ENCSR862SQC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -530.513427734375 0.3972488045692444 0.3722209930419922 0.14524708688259125 0.7588368654251099 0.6665995121002197 0.29456183314323425 \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_0.evaluate.json b/ENCSR866ODX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 888ead759715cffa2387ee8cbd7acc3f17e424bd..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF399RQJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_0.fit.json b/ENCSR866ODX/cherimoya.fold_0.fit.json deleted file mode 100644 index 07fc258303956cecdd75367545136736c6f3c490..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF399RQJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_0.log b/ENCSR866ODX/cherimoya.fold_0.log deleted file mode 100644 index 7e86dfc573ea087c5bf3af5177e4a6b14f55d056..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.13441300392151 3.562478542327881 767.5614013671875 0.6516077518463135 995.6243286132812 0.32370349764823914 0.676515 7.809492588043213 True -1 5476 30.182540893554688 1.1061818599700928 631.9071044921875 0.7904177904129028 839.234619140625 0.44615086913108826 0.73489594 2.4394748210906982 True -2 8214 29.84637689590454 0.5608460903167725 686.205322265625 0.49704641103744507 805.8590087890625 0.46944963932037354 0.74490255 1.2123723030090332 True -3 10952 29.5761399269104 0.5576727390289307 602.8673095703125 0.7153201699256897 797.7686767578125 0.4737909138202667 0.7519503 0.9688764214515686 True -4 13690 29.569605112075806 0.5572137832641602 618.19775390625 0.4665752053260803 791.29150390625 0.47987788915634155 0.76048106 0.7468827962875366 True -5 16428 29.558438777923584 0.5508880615234375 610.782470703125 0.7147647142410278 790.710693359375 0.47923344373703003 0.7616841 0.6733912229537964 True -6 19166 29.602400541305542 0.5685381889343262 731.9097900390625 0.5904847979545593 786.7728271484375 0.48289069533348083 0.75853944 0.5953194499015808 False -7 21904 29.638769149780273 0.5753593444824219 738.380859375 0.44851982593536377 782.0470581054688 0.4874036908149719 0.7682531 0.5693373084068298 True -8 24642 29.67244005203247 0.5642602443695068 675.51318359375 0.5161498785018921 776.6365966796875 0.4931820333003998 0.77333456 0.5517887473106384 True -9 27380 29.59256649017334 0.5836398601531982 658.274658203125 0.6592381000518799 774.7899169921875 0.493503212928772 0.7788426 0.5405429005622864 True -10 30118 29.633086919784546 0.5693967342376709 680.6807861328125 0.37497496604919434 769.3433227539062 0.4989149272441864 0.78465766 0.5362692475318909 True -11 32856 29.58782124519348 0.5660803318023682 784.50634765625 0.25485533475875854 764.5010375976562 0.5029446482658386 0.7928863 0.5042851567268372 True -12 35594 29.592729330062866 0.5685975551605225 531.8846435546875 0.316714882850647 761.772705078125 0.5046519041061401 0.7998414 0.47747164964675903 True -13 38332 29.585691928863525 0.5700194835662842 625.205078125 0.4575885832309723 759.361572265625 0.5050420165061951 0.8064124 0.43935906887054443 True -14 41070 29.639257669448853 2.741840362548828 552.01025390625 0.33274662494659424 754.6798095703125 0.5102940201759338 0.8100042 0.39805981516838074 True -15 43808 29.763970136642456 10.980865955352783 669.0787963867188 0.3770627975463867 753.6166381835938 0.5111208558082581 0.8172191 0.3636637330055237 True -16 46546 29.761130332946777 0.5751750469207764 621.48974609375 0.2856384515762329 750.3328857421875 0.5141401886940002 0.82089204 0.34593895077705383 True -17 49284 29.677255153656006 0.5857357978820801 674.767822265625 0.34919556975364685 752.666259765625 0.5106212496757507 0.82286483 0.3352759778499603 True -18 52022 29.622374534606934 0.5676498413085938 815.2569580078125 0.37347307801246643 752.5546875 0.5106722712516785 0.8220647 0.3328438997268677 False -19 54760 29.588577270507812 0.5656037330627441 676.19580078125 0.3335222601890564 752.3732299804688 0.5115172266960144 0.82240564 0.3308377265930176 False diff --git a/ENCSR866ODX/cherimoya.fold_0.performance.tsv b/ENCSR866ODX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 0966f431a37f87108a7702c35b8c1da53452959f..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -752.666259765625 0.31336185336112976 0.5106212496757507 0.22643092274665833 0.822864830493927 0.7805171608924866 0.3352759778499603 \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_1.evaluate.json b/ENCSR866ODX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a8a825b4722c463a2aa913d22e80c5bcb02c8bf1..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF399RQJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_1.fit.json b/ENCSR866ODX/cherimoya.fold_1.fit.json deleted file mode 100644 index 3d37340428686ea3bd2d5ffa00330771cd33ad72..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF399RQJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_1.log b/ENCSR866ODX/cherimoya.fold_1.log deleted file mode 100644 index 33502cba730564a9ab05abfa65c38680610d63bd..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 33.36079216003418 3.698866605758667 769.5503540039062 0.6906591653823853 1167.0450439453125 0.3236251175403595 0.6724161 7.784251689910889 True -1 5418 29.943500518798828 0.7066802978515625 671.7667236328125 0.630806028842926 965.1122436523438 0.4530371129512787 0.743155 2.6878998279571533 True -2 8127 29.448030710220337 0.6834132671356201 715.052978515625 0.6420432925224304 939.747314453125 0.472055047750473 0.75356954 1.4581959247589111 True -3 10836 29.23118782043457 0.677377462387085 715.4031982421875 0.4534696936607361 923.9080810546875 0.48242706060409546 0.7641984 1.1999069452285767 True -4 13545 29.21846914291382 0.68328857421875 724.223388671875 0.4990094304084778 918.5492553710938 0.4859209954738617 0.7726549 1.0022727251052856 True -5 16254 29.240926504135132 0.6872119903564453 702.1299438476562 0.4749775528907776 913.7785034179688 0.4898792505264282 0.7715181 0.9222497344017029 False -6 18963 29.222938537597656 1.8169405460357666 658.095703125 0.5025925636291504 906.15478515625 0.49526962637901306 0.78355944 0.7888456583023071 True -7 21672 29.32162618637085 0.6886637210845947 599.4481201171875 0.4914274513721466 899.780029296875 0.49951204657554626 0.79211855 0.8487127423286438 True -8 24381 29.32566547393799 0.6854538917541504 612.1649169921875 0.602622926235199 894.8591918945312 0.5028102993965149 0.7952453 0.7009347081184387 True -9 27090 29.321858167648315 0.6959021091461182 617.620849609375 0.45971667766571045 888.7026977539062 0.5052484273910522 0.805026 0.6331505179405212 True -10 29799 29.28971815109253 11.824017524719238 696.0125732421875 0.3625040650367737 883.3092651367188 0.5083723664283752 0.80979663 0.5865646004676819 True -11 32508 29.262009859085083 1.7012062072753906 689.1019287109375 0.3963090181350708 877.0554809570312 0.5123252272605896 0.8145393 0.5851188898086548 True -12 35217 29.24819779396057 0.6836509704589844 691.2747192382812 0.31952905654907227 874.6964111328125 0.5130661725997925 0.82250124 0.5213542580604553 True -13 37926 29.259742736816406 0.6907439231872559 589.31640625 0.3479325473308563 867.8248901367188 0.5175617337226868 0.8295631 0.44886118173599243 True -14 40635 29.244577884674072 0.6911458969116211 552.2279052734375 0.26980724930763245 866.14501953125 0.5174865126609802 0.83635545 0.4029536545276642 True -15 43344 29.24258780479431 0.6843616962432861 518.4329223632812 0.261308878660202 863.6083374023438 0.5188296437263489 0.84078777 0.3776908814907074 True -16 46053 29.278181791305542 0.6932783126831055 586.486328125 0.32398155331611633 860.2163696289062 0.5222234725952148 0.8454246 0.34301626682281494 True -17 48762 29.26239514350891 0.6900544166564941 577.710205078125 0.26164698600769043 859.1212768554688 0.5221925377845764 0.8475413 0.3297816812992096 True -18 51471 29.296497583389282 0.6717343330383301 685.8126220703125 0.3930702209472656 858.5270385742188 0.5224068760871887 0.84932214 0.3221956491470337 True -19 54180 29.28368377685547 0.6822521686553955 594.6144409179688 0.1823561191558838 859.2628173828125 0.5215491652488708 0.8469548 0.3207988739013672 False diff --git a/ENCSR866ODX/cherimoya.fold_1.performance.tsv b/ENCSR866ODX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e6b93ea560217fa24d6f6dcb162eac17970e6f80..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -858.5270385742188 0.3000679016113281 0.5224068760871887 0.24283839762210846 0.8493221402168274 0.822841465473175 0.3221956491470337 \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_2.evaluate.json b/ENCSR866ODX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a11211b32b3d35ee5e56c3d657f461a34543da2e..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF399RQJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_2.fit.json b/ENCSR866ODX/cherimoya.fold_2.fit.json deleted file mode 100644 index 09134d6860315747a22166be3d7a4a034a5a01ad..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF399RQJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_2.log b/ENCSR866ODX/cherimoya.fold_2.log deleted file mode 100644 index 0e9bc75aa696e77fefc02aae9580652a0e995156..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 35.01409029960632 3.4799985885620117 724.090576171875 0.6729395389556885 1035.2587890625 0.3280697464942932 0.6662541 6.2859015464782715 True -1 5776 31.82522678375244 1.3946526050567627 752.2152099609375 0.5127049684524536 855.7726440429688 0.4553088843822479 0.7439243 2.034275531768799 True -2 8664 31.766952991485596 0.5762598514556885 687.507568359375 0.39195942878723145 844.0172119140625 0.46355894207954407 0.75669986 1.0375003814697266 True -3 11552 31.247199773788452 0.5553929805755615 616.245361328125 0.660061776638031 830.2919921875 0.4772966206073761 0.7619108 0.804065465927124 True -4 14440 32.341023683547974 0.560692548751831 693.84375 0.41064441204071045 829.9525756835938 0.4753979742527008 0.76773345 0.6273313760757446 True -5 17328 31.39607000350952 0.5561845302581787 654.0595703125 0.4997478723526001 823.1776733398438 0.481507807970047 0.7710079 0.5905604362487793 True -6 20216 31.23340606689453 0.5468688011169434 624.298583984375 0.47760963439941406 818.6787109375 0.4854581654071808 0.77262473 0.5597135424613953 True -7 23104 31.267194747924805 2.072732448577881 682.1197509765625 0.4116732180118561 815.5784301757812 0.48768770694732666 0.7774478 0.5066124200820923 True -8 25992 31.36853790283203 0.552924394607544 740.9735107421875 0.5945142507553101 810.799560546875 0.49147313833236694 0.78244066 0.5004773139953613 True -9 28880 31.47569704055786 0.9129610061645508 660.5288696289062 0.4491548538208008 803.825927734375 0.49808743596076965 0.7872907 0.5075163245201111 True -10 31768 31.470210790634155 0.5484428405761719 724.1351928710938 0.4091514050960541 802.2687377929688 0.49845197796821594 0.7956646 0.47199153900146484 True -11 34656 31.29997444152832 0.5562479496002197 639.359375 0.46613049507141113 799.7285766601562 0.49895429611206055 0.7998299 0.44984886050224304 True -12 37544 31.533681392669678 0.5693478584289551 625.09521484375 0.5725377798080444 793.0678100585938 0.5049840211868286 0.8043273 0.43259862065315247 True -13 40432 31.4301335811615 0.5554533004760742 569.188720703125 0.4627828001976013 789.748779296875 0.5068415403366089 0.81054354 0.4006699025630951 True -14 43320 31.343501091003418 0.5600109100341797 665.5360717773438 0.5221267342567444 788.9862060546875 0.5075947642326355 0.8158265 0.37671634554862976 True -15 46208 31.248812198638916 0.5448174476623535 551.756103515625 0.38825079798698425 783.9700317382812 0.5126745700836182 0.81989604 0.3612402379512787 True -16 49096 31.20379328727722 0.5447282791137695 488.51141357421875 0.2230326533317566 784.493408203125 0.5098843574523926 0.82440484 0.3375388979911804 True -17 51984 31.215303897857666 0.5423791408538818 650.3668212890625 0.31829872727394104 784.8855590820312 0.5099809765815735 0.82526976 0.33047693967819214 True -18 54872 31.212793588638306 0.539085865020752 661.801025390625 0.37423497438430786 784.1293334960938 0.5114869475364685 0.8260054 0.3283686935901642 True -19 57760 31.155102014541626 0.5433504581451416 623.3424072265625 0.35303330421447754 784.6416015625 0.5105493664741516 0.8264819 0.32778453826904297 True diff --git a/ENCSR866ODX/cherimoya.fold_2.performance.tsv b/ENCSR866ODX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ee20a62dbfe55c996e7a67c6e3ac8b71d02469e3..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -784.6416015625 0.31096625328063965 0.5105493068695068 0.2297603189945221 0.8264818787574768 0.7907227873802185 0.32778453826904297 \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_3.evaluate.json b/ENCSR866ODX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index deaf90e38164a8e74826046c340a2943a5f363af..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF399RQJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_3.fit.json b/ENCSR866ODX/cherimoya.fold_3.fit.json deleted file mode 100644 index 130e31ecd1120329a411078df1560022f936cfc7..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF399RQJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_3.log b/ENCSR866ODX/cherimoya.fold_3.log deleted file mode 100644 index 2cdab039110e2e88390e05bc4846d7bdd2bb784a..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 34.54421067237854 3.4612207412719727 755.0140380859375 0.7083547115325928 994.6260375976562 0.3354148268699646 0.6853848 7.921971321105957 True -1 5530 30.48287796974182 0.5640454292297363 657.619873046875 0.6614089012145996 838.2864990234375 0.4509786069393158 0.7468551 2.4479501247406006 True -2 8295 30.37889528274536 0.5348105430603027 765.4591064453125 0.6526026725769043 817.5975341796875 0.4644410312175751 0.763252 1.1894159317016602 True -3 11060 30.313864707946777 0.5513701438903809 725.5035400390625 0.5954389572143555 805.0765991210938 0.4742349088191986 0.76148736 0.9233974814414978 False -4 13825 29.87809991836548 0.5501120090484619 576.9969482421875 0.6694605350494385 802.3077392578125 0.4761064052581787 0.76300395 0.7488264441490173 False -5 16590 29.871246337890625 0.5484619140625 640.3707275390625 0.4844944179058075 798.59814453125 0.4801470637321472 0.75937307 0.6846477389335632 False -6 19355 29.86339569091797 22.084264993667603 593.485595703125 0.7348383665084839 796.4495849609375 0.48148879408836365 0.7634969 0.6403930187225342 True -7 22120 30.015398740768433 0.5952730178833008 566.1599731445312 0.5157907009124756 792.07568359375 0.4858191907405853 0.7729312 0.6364344358444214 True -8 24885 29.955305814743042 0.5369613170623779 572.3357543945312 0.6323444843292236 787.7389526367188 0.4878937304019928 0.7788916 0.660304844379425 True -9 27650 29.917559146881104 0.5511274337768555 625.5570678710938 0.5333936214447021 782.2827758789062 0.49285727739334106 0.78619474 0.5936943292617798 True -10 30415 29.959132194519043 0.5444791316986084 528.3084716796875 0.452573299407959 776.9451904296875 0.4968557357788086 0.790588 0.5492634773254395 True -11 33180 29.903701305389404 0.5456829071044922 560.4307861328125 0.3313823342323303 773.2349243164062 0.4992274045944214 0.80200857 0.513024091720581 True -12 35945 29.871270895004272 0.5438525676727295 615.09765625 0.3960789740085602 768.3873291015625 0.50303053855896 0.81005496 0.48328036069869995 True -13 38710 29.973973989486694 0.5456798076629639 580.9217529296875 0.2838277220726013 763.724365234375 0.5053918957710266 0.82109565 0.4474279582500458 True -14 41475 30.01390051841736 0.5462794303894043 607.3514404296875 0.4051637649536133 762.3845825195312 0.5066003203392029 0.82875913 0.40163806080818176 True -15 44240 29.97156262397766 0.5478603839874268 675.1619873046875 0.4026847183704376 757.5064086914062 0.5092743635177612 0.8361222 0.36896178126335144 True -16 47005 30.115350246429443 1.236321210861206 649.8120727539062 0.3734450340270996 759.0226440429688 0.5077981352806091 0.8429992 0.3408084809780121 True -17 49770 30.00256633758545 1.1731345653533936 629.8706665039062 0.2663615942001343 755.3322143554688 0.5114630460739136 0.8437007 0.3230205178260803 True -18 52535 29.994888305664062 19.822922706604004 661.7349853515625 0.19352656602859497 757.7157592773438 0.5084326863288879 0.844314 0.3155274987220764 True -19 55300 31.25984001159668 0.5502486228942871 666.228515625 0.2770797610282898 758.7833251953125 0.5072205066680908 0.8458757 0.3139762282371521 True diff --git a/ENCSR866ODX/cherimoya.fold_3.performance.tsv b/ENCSR866ODX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f696f779e2dd11250589510c3c6e312a53fbf3ef..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -758.7833251953125 0.3121573030948639 0.507220447063446 0.2272811383008957 0.8458756804466248 0.8070024251937866 0.3139762282371521 \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_4.evaluate.json b/ENCSR866ODX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fc86b2fbc2663214ec7e92c40a9e12f1c868327d..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF399RQJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_4.fit.json b/ENCSR866ODX/cherimoya.fold_4.fit.json deleted file mode 100644 index e87d6e96dc7b7b4047ca59b617e28cce905ceacd..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF399RQJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR866ODX/cherimoya.fold_4.log b/ENCSR866ODX/cherimoya.fold_4.log deleted file mode 100644 index 0c81a2d1a2e1132d60570c5cc3217ce4076b17cd..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2813 34.61861300468445 3.497403860092163 521.9970092773438 0.7040327787399292 933.4088745117188 0.3245193064212799 0.67256045 5.924471855163574 True -1 5626 30.960591793060303 0.5842118263244629 668.6282958984375 0.7243252396583557 791.3301391601562 0.44218310713768005 0.7284585 1.8082911968231201 True -2 8439 30.95941972732544 0.5541524887084961 731.2099609375 0.44207441806793213 768.8875732421875 0.4604092538356781 0.7283876 0.7480023503303528 False -3 11252 30.360485076904297 0.5643253326416016 696.2779541015625 0.6525385975837708 758.6033325195312 0.4692952334880829 0.74468404 0.6165580153465271 True -4 14065 30.31680130958557 0.5550761222839355 648.551025390625 0.6189177632331848 755.7960205078125 0.47092172503471375 0.75042194 0.6031203866004944 True -5 16878 30.42545771598816 0.5544168949127197 520.1253051757812 0.3653016686439514 752.5894165039062 0.47411951422691345 0.747222 0.5184200406074524 False -6 19691 30.443413972854614 0.5536651611328125 596.816162109375 0.3843730688095093 746.7041625976562 0.47981691360473633 0.74694365 0.5025725364685059 False -7 22504 30.379817724227905 0.5559115409851074 668.2274169921875 0.4240916967391968 742.7376098632812 0.48378902673721313 0.75388724 0.44124647974967957 True -8 25317 30.353355884552002 0.5527706146240234 744.3295288085938 0.35162708163261414 740.1427001953125 0.48564717173576355 0.7672229 0.45202091336250305 True -9 28130 30.408467292785645 0.5551705360412598 596.698974609375 0.38368332386016846 736.9496459960938 0.48655104637145996 0.7757212 0.43861469626426697 True -10 30943 30.396143913269043 0.553424596786499 564.1034545898438 0.2833216190338135 731.6818237304688 0.4928671717643738 0.7836554 0.4322124421596527 True -11 33756 30.381665229797363 0.6936957836151123 642.4130249023438 0.4112395644187927 729.3535766601562 0.49397146701812744 0.7898539 0.42386990785598755 True -12 36569 30.354112148284912 1.5538945198059082 607.9598999023438 0.4213595390319824 725.977294921875 0.4970966577529907 0.79580593 0.38735705614089966 True -13 39382 30.356515884399414 0.5557761192321777 600.0831298828125 0.4346199929714203 722.218505859375 0.4993569552898407 0.80237097 0.3808862864971161 True -14 42195 30.32763671875 0.5601413249969482 660.8455200195312 0.2733422815799713 720.1825561523438 0.5024684071540833 0.80978996 0.3492527902126312 True -15 45008 30.350652933120728 0.5585577487945557 607.1756591796875 0.2693657875061035 718.51806640625 0.5026993155479431 0.81572396 0.3368379771709442 True -16 47821 30.37645673751831 0.5604777336120605 524.2694091796875 0.3101673722267151 716.0217895507812 0.5052132606506348 0.82075363 0.32338082790374756 True -17 50634 30.32753562927246 0.5539412498474121 698.0791625976562 0.38557302951812744 715.7821044921875 0.5045626759529114 0.8243904 0.3126407563686371 True -18 53447 30.422382831573486 0.5628125667572021 641.7852172851562 0.27510565519332886 715.6174926757812 0.5058498978614807 0.8239789 0.3070501983165741 False -19 56260 30.357133150100708 0.5525557994842529 567.1890869140625 0.25424063205718994 717.0145263671875 0.5038509368896484 0.8246751 0.306746244430542 True diff --git a/ENCSR866ODX/cherimoya.fold_4.performance.tsv b/ENCSR866ODX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f287b883db22302ccaaa061ac49ddb166ab30960..0000000000000000000000000000000000000000 --- a/ENCSR866ODX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -717.0145263671875 0.319219172000885 0.5038509964942932 0.22009938955307007 0.8246750831604004 0.7772960662841797 0.306746244430542 \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_0.evaluate.json b/ENCSR867XFA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f88b30417f0dc258c7b67af2237336785ab0982d..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF486ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_0.fit.json b/ENCSR867XFA/cherimoya.fold_0.fit.json deleted file mode 100644 index 4e819aaa0ad449706914fefb0d11e07d9908c14d..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF486ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_0.log b/ENCSR867XFA/cherimoya.fold_0.log deleted file mode 100644 index 8e5bde0d09003b7f62e89cd96f310ffad10edfa6..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.81953001022339 4.072896480560303 725.3554077148438 0.7462900876998901 907.0784301757812 0.25925397872924805 0.6626723 5.791481018066406 True -1 5492 30.2571542263031 1.0387449264526367 676.7677001953125 0.7178980112075806 818.4817504882812 0.33005350828170776 0.7247753 2.0012853145599365 True -2 8238 30.49004030227661 2.2642879486083984 604.9686279296875 0.3966881334781647 804.232666015625 0.3383517861366272 0.7368134 1.0757611989974976 True -3 10984 31.426172733306885 1.4709136486053467 647.248779296875 0.9674066305160522 792.7616577148438 0.34788721799850464 0.74639505 1.0367374420166016 True -4 13730 30.203819751739502 1.052293062210083 712.0977783203125 0.5454927682876587 784.99853515625 0.3552669286727905 0.75830793 1.1570022106170654 True -5 16476 30.183059692382812 0.5766348838806152 638.66748046875 0.5464470386505127 782.9937133789062 0.3563111424446106 0.763586 0.9572974443435669 True -6 19222 30.353477716445923 0.5907895565032959 724.6104736328125 0.8107506036758423 778.7229614257812 0.3605208992958069 0.7675142 0.8703923225402832 True -7 21968 30.144532442092896 0.5925588607788086 714.1876220703125 0.4644167423248291 774.9142456054688 0.3620409369468689 0.7751381 0.8035308122634888 True -8 24714 30.165759086608887 0.5931005477905273 772.33642578125 0.43673184514045715 769.9260864257812 0.3675268590450287 0.7807627 0.7162330746650696 True -9 27460 30.554619550704956 23.05758500099182 703.5469360351562 0.4821106195449829 766.7031860351562 0.3697856068611145 0.7869955 0.6752251982688904 True -10 30206 31.045110940933228 11.226763010025024 706.1209106445312 0.5214157700538635 766.2333984375 0.3689005374908447 0.7920739 0.6453298330307007 True -11 32952 30.17978262901306 0.6077461242675781 679.46923828125 0.3577806055545807 762.5018310546875 0.3721926808357239 0.796951 0.6089552044868469 True -12 35698 30.178086757659912 0.5838606357574463 659.4141845703125 0.3640887141227722 760.5963745117188 0.3724249601364136 0.8044211 0.5275749564170837 True -13 38444 30.161246299743652 0.5727310180664062 667.2279052734375 0.35025763511657715 757.9359741210938 0.3750218451023102 0.81265503 0.4751034677028656 True -14 41190 29.56037425994873 0.5784721374511719 699.719970703125 0.4097897410392761 754.5640869140625 0.37765300273895264 0.8181062 0.4460165202617645 True -15 43936 29.82524561882019 0.5878057479858398 626.2020263671875 0.2055206000804901 752.752685546875 0.37995198369026184 0.82600355 0.3924764096736908 True -16 46682 29.635753631591797 0.578263521194458 651.9967041015625 0.34730494022369385 753.0698852539062 0.37933284044265747 0.8284952 0.35817208886146545 True -17 49428 29.62338423728943 8.377990007400513 561.3341064453125 0.3561956584453583 752.5206298828125 0.3800213634967804 0.83170706 0.33879533410072327 True -18 52174 29.92689800262451 0.5734186172485352 582.9652709960938 0.24593102931976318 752.7042846679688 0.3792138397693634 0.8322108 0.33240148425102234 True -19 54920 29.656821727752686 0.6111264228820801 626.5238647460938 0.3162444829940796 752.7362060546875 0.3794395327568054 0.8307976 0.3325796127319336 False diff --git a/ENCSR867XFA/cherimoya.fold_0.performance.tsv b/ENCSR867XFA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d49a8b30b2463dcc4bc825b4812f5c84390ac0f1..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -752.7042846679688 0.3910605013370514 0.3792138993740082 0.16150391101837158 0.8322107791900635 0.7839017510414124 0.33240148425102234 \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_1.evaluate.json b/ENCSR867XFA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7823df0d3e1b8816a438260810db140db05a3b3f..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF486ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_1.fit.json b/ENCSR867XFA/cherimoya.fold_1.fit.json deleted file mode 100644 index 032e3545f8bed8ab7e272cdd29f6f550076e5078..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF486ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_1.log b/ENCSR867XFA/cherimoya.fold_1.log deleted file mode 100644 index 6242313e8d59e653a1d4bee8bad24d87ffb69675..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2694 34.451619386672974 3.7353763580322266 723.0794677734375 0.6479192972183228 1087.1856689453125 0.261684775352478 0.65726167 7.421522617340088 True -1 5388 29.619845867156982 0.7440869808197021 805.9521484375 0.497611939907074 962.9036254882812 0.3458658456802368 0.7318194 2.5200984477996826 True -2 8082 29.648433685302734 0.7470736503601074 757.6265869140625 0.5745424032211304 945.3160400390625 0.3602813482284546 0.7354601 1.6219366788864136 True -3 10776 29.60932493209839 0.7255992889404297 677.52587890625 0.4322975277900696 933.8792724609375 0.3690197467803955 0.74664193 1.2562822103500366 True -4 13470 29.563774347305298 0.7101695537567139 583.5836181640625 0.5724546909332275 921.0838012695312 0.3783501088619232 0.7567339 1.189369559288025 True -5 16164 29.696732759475708 0.722193717956543 694.7763061523438 0.6641423106193542 917.8168334960938 0.38054701685905457 0.7637616 1.2292253971099854 True -6 18858 30.936201572418213 31.93245553970337 688.414306640625 0.8266986012458801 913.0751953125 0.38284894824028015 0.7711067 1.0672417879104614 True -7 21552 29.62930989265442 45.71875333786011 631.742919921875 0.43187591433525085 907.3482666015625 0.3871842622756958 0.7815409 0.9610947966575623 True -8 24246 29.874839544296265 1.4585773944854736 664.1162719726562 0.4959847331047058 904.7911376953125 0.38819584250450134 0.78732115 0.9011803865432739 True -9 26940 29.624816417694092 1.4316740036010742 653.9427490234375 0.48984283208847046 897.5761108398438 0.39450302720069885 0.79381645 0.8144785761833191 True -10 29634 29.555460214614868 37.88060450553894 652.5917358398438 0.7075774073600769 894.7766723632812 0.39639216661453247 0.7992001 0.7777283787727356 True -11 32328 29.700905084609985 46.00427269935608 751.041259765625 0.4476672410964966 889.6810302734375 0.3993135094642639 0.8065944 0.6800400018692017 True -12 35022 29.655020236968994 34.273436307907104 732.645751953125 0.5704189538955688 888.0997924804688 0.3988287150859833 0.8143335 0.6056832671165466 True -13 37716 31.26652765274048 0.7309768199920654 761.0712280273438 0.3518645167350769 881.0018310546875 0.40572553873062134 0.821755 0.5336818099021912 True -14 40410 28.95878314971924 0.7052969932556152 546.2966918945312 0.3166161775588989 877.4282836914062 0.4080161154270172 0.827387 0.4843781590461731 True -15 43104 29.004040956497192 0.7174203395843506 634.6610107421875 0.37037038803100586 878.2179565429688 0.40678444504737854 0.8296496 0.4357064962387085 True -16 45798 28.98467755317688 0.7130343914031982 660.51416015625 0.3310607075691223 875.564697265625 0.4084874987602234 0.8343699 0.40174880623817444 True -17 48492 28.99491238594055 3.5254547595977783 548.3121337890625 0.4769562780857086 875.1651611328125 0.40888622403144836 0.83651316 0.37849923968315125 True -18 51186 29.04320454597473 0.7063488960266113 660.8944091796875 0.42617326974868774 877.0322265625 0.40705934166908264 0.834904 0.3702618479728699 False -19 53880 29.04408836364746 0.718336820602417 673.7357788085938 0.15993919968605042 876.291015625 0.40836527943611145 0.83746177 0.3682215213775635 True diff --git a/ENCSR867XFA/cherimoya.fold_1.performance.tsv b/ENCSR867XFA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d7436342873e4a7bb39385edaa882847a0a17ee1..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -876.291015625 0.36663737893104553 0.40836527943611145 0.18886539340019226 0.8374617695808411 0.8116572499275208 0.3682215213775635 \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_2.evaluate.json b/ENCSR867XFA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b4823812d0cd5234e1068509895571597804b71d..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF486ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_2.fit.json b/ENCSR867XFA/cherimoya.fold_2.fit.json deleted file mode 100644 index d4315bc15b41b6437636ce4783c35b593cef6875..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF486ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_2.log b/ENCSR867XFA/cherimoya.fold_2.log deleted file mode 100644 index 3f4195f334c21c7a730710e156daf7ca6f994e73..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2901 38.90460824966431 3.4893574714660645 645.0479736328125 0.6353520154953003 972.71728515625 0.2603380084037781 0.6530495 5.472278118133545 True -1 5802 33.467580795288086 6.939102411270142 765.883056640625 0.5782684087753296 872.890625 0.32984623312950134 0.7219689 1.9171520471572876 True -2 8703 31.981021404266357 0.5777888298034668 648.3146362304688 0.4903026223182678 858.6213989257812 0.34168127179145813 0.7308655 1.2559328079223633 True -3 11604 31.826136589050293 0.5411128997802734 590.4405517578125 0.5142170190811157 846.2757568359375 0.3521598279476166 0.742271 1.1577553749084473 True -4 14505 31.832764863967896 0.5420849323272705 699.7175903320312 0.6160619854927063 843.1343383789062 0.3540535867214203 0.74852777 1.1612550020217896 True -5 17406 31.847851753234863 0.5407781600952148 830.9954223632812 0.6407380104064941 837.5247802734375 0.358125239610672 0.7577478 1.0641957521438599 True -6 20307 31.913893699645996 0.5403435230255127 680.4451904296875 0.4944707155227661 833.5809936523438 0.36171290278434753 0.763366 1.0739580392837524 True -7 23208 31.86142086982727 0.5411574840545654 617.08984375 0.5100512504577637 831.207763671875 0.3627423644065857 0.7683424 0.9686756730079651 True -8 26109 31.87170696258545 0.5546495914459229 696.7066650390625 0.5618764162063599 824.73291015625 0.3679952025413513 0.7765219 0.8673470616340637 True -9 29010 31.973456144332886 0.5528936386108398 672.791015625 0.5456048250198364 819.7528076171875 0.37167418003082275 0.7836553 0.7633339166641235 True -10 31911 31.933466911315918 0.5471374988555908 648.530517578125 0.3829911947250366 815.9000244140625 0.37503838539123535 0.79142183 0.6919039487838745 True -11 34812 31.868114233016968 0.5469281673431396 646.2393798828125 0.24931207299232483 812.5823974609375 0.3769983649253845 0.7955211 0.6493210196495056 True -12 37713 32.153549909591675 36.86673927307129 623.9306030273438 0.5080525875091553 808.5904541015625 0.379428505897522 0.8026205 0.5766181945800781 True -13 40614 31.489956378936768 0.560523509979248 602.9422607421875 0.4591624438762665 806.93408203125 0.3804813027381897 0.80923015 0.502194881439209 True -14 43515 31.182098150253296 0.5433626174926758 695.9322509765625 0.415298730134964 805.0047607421875 0.3821510374546051 0.8168941 0.4457237720489502 True -15 46416 31.568649768829346 0.5474083423614502 576.53759765625 0.3314213156700134 802.0272827148438 0.3840039074420929 0.820898 0.4053944945335388 True -16 49317 31.239276885986328 0.5413029193878174 613.5782470703125 0.3863702714443207 801.3720092773438 0.38440048694610596 0.82600427 0.36970949172973633 True -17 52218 31.158008813858032 0.5425634384155273 574.6571044921875 0.2476753145456314 801.8485717773438 0.3842109441757202 0.8266128 0.3568389117717743 True -18 55119 31.312185049057007 0.5412437915802002 697.2029418945312 0.32033681869506836 800.8703002929688 0.38558200001716614 0.82625836 0.3520350456237793 False -19 58020 31.211846113204956 0.5413699150085449 652.200439453125 0.3732708692550659 801.795654296875 0.3844743072986603 0.8260568 0.3523772656917572 False diff --git a/ENCSR867XFA/cherimoya.fold_2.performance.tsv b/ENCSR867XFA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c4bbe55d2265112444532b3109c146cd5d1f8b76..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -801.8485717773438 0.3837372958660126 0.3842109441757202 0.1689167022705078 0.8266127705574036 0.7955552935600281 0.3568389117717743 \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_3.evaluate.json b/ENCSR867XFA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 57f9f4d57d62aa655eabc9e4db7e1be9d3b3cded..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF486ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_3.fit.json b/ENCSR867XFA/cherimoya.fold_3.fit.json deleted file mode 100644 index 004dbb050e1216ba1ddffa29950a0f2bdb35e2e4..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF486ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_3.log b/ENCSR867XFA/cherimoya.fold_3.log deleted file mode 100644 index a34fbc61e4598433106467ed40ce7b0c59397195..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.04272675514221 4.410117149353027 760.709228515625 0.785609245300293 899.3772583007812 0.2673647701740265 0.653267 5.682103633880615 True -1 5518 30.33700704574585 32.76959180831909 857.8720092773438 0.9577627182006836 806.5304565429688 0.3372717797756195 0.7217911 2.4821746349334717 True -2 8277 30.637325286865234 0.5670583248138428 671.7813110351562 0.49755263328552246 787.6373901367188 0.34924086928367615 0.7365641 1.4416379928588867 True -3 11036 30.30539846420288 0.547877311706543 768.243896484375 0.5701351165771484 778.1396484375 0.35637614130973816 0.7453727 1.2654691934585571 True -4 13795 30.30615210533142 0.5422096252441406 820.57958984375 0.8265525102615356 774.3080444335938 0.3595835864543915 0.74711484 1.0856382846832275 True -5 16554 30.508049488067627 0.5430972576141357 691.6788330078125 0.4456714987754822 768.951171875 0.36360418796539307 0.75518006 1.0863564014434814 True -6 19313 30.357601404190063 0.5430734157562256 697.0598754882812 0.6438485383987427 766.038330078125 0.36617642641067505 0.7638833 1.074259638786316 True -7 22072 30.319836854934692 0.5453081130981445 681.748291015625 0.5102210640907288 760.817626953125 0.3698596954345703 0.7715739 0.9848302006721497 True -8 24831 30.350069761276245 0.5450730323791504 718.5546264648438 0.513911247253418 757.8192138671875 0.37167662382125854 0.77746385 0.934362530708313 True -9 27590 30.47162699699402 0.5421640872955322 529.5596313476562 0.5704423785209656 754.0426025390625 0.37614473700523376 0.7836451 0.8690885305404663 True -10 30349 30.631558895111084 0.5498013496398926 598.2675170898438 0.44720736145973206 751.0704956054688 0.3785301446914673 0.7894073 0.7953552007675171 True -11 33108 30.494956254959106 0.5418446063995361 619.494384765625 0.3749401867389679 748.0635986328125 0.3806435465812683 0.7969113 0.676667332649231 True -12 35867 29.993030786514282 0.5363729000091553 667.967529296875 0.32321465015411377 745.2528686523438 0.382167249917984 0.8036259 0.6255311965942383 True -13 38626 29.75276470184326 1.3022956848144531 638.08447265625 0.31017348170280457 741.8682250976562 0.3854225277900696 0.81018585 0.5555754899978638 True -14 41385 29.69305109977722 0.534700870513916 745.583251953125 0.322269082069397 741.105224609375 0.3859374523162842 0.8161731 0.4965161383152008 True -15 44144 29.63849425315857 0.5405066013336182 606.14208984375 0.39977791905403137 738.00732421875 0.3890194892883301 0.8218185 0.4396522045135498 True -16 46903 29.789824724197388 0.5356237888336182 616.028564453125 0.2706369459629059 737.8655395507812 0.3879406750202179 0.8252526 0.3978107273578644 True -17 49662 29.701446294784546 1.1645615100860596 566.587646484375 0.24793890118598938 738.239990234375 0.38795796036720276 0.82602787 0.3729521930217743 True -18 52421 29.6393883228302 0.5433416366577148 628.383544921875 0.27747440338134766 736.6438598632812 0.38992151618003845 0.82617855 0.3641560673713684 True -19 55180 29.67526865005493 0.5437922477722168 638.8931884765625 0.2844041585922241 737.498291015625 0.38912373781204224 0.8263168 0.3623742163181305 True diff --git a/ENCSR867XFA/cherimoya.fold_3.performance.tsv b/ENCSR867XFA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e19bd737531a0a3fc83498b7b609a60b13b55231..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -737.498291015625 0.3874673843383789 0.38912373781204224 0.16749919950962067 0.826316773891449 0.7790625691413879 0.3623742163181305 \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_4.evaluate.json b/ENCSR867XFA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 263318f6fd702dfa9f9b8f09d9e613462d0b63dd..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF486ADR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_4.fit.json b/ENCSR867XFA/cherimoya.fold_4.fit.json deleted file mode 100644 index 7f288195a652b052e3998022fc01e987ba4c5a38..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF486ADR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR867XFA/cherimoya.fold_4.log b/ENCSR867XFA/cherimoya.fold_4.log deleted file mode 100644 index 7dc0fd66661f59b10c9196caee4fd1b802cea9ca..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2796 35.5454523563385 3.510089635848999 618.5628662109375 0.8321272730827332 848.853759765625 0.25964444875717163 0.6161536 4.825646877288818 True -1 5592 30.711259126663208 10.168912887573242 584.679931640625 0.8537770509719849 767.5104370117188 0.32543620467185974 0.69775033 2.065276861190796 True -2 8388 30.782760620117188 0.5900404453277588 687.4369506835938 0.5498175621032715 753.8517456054688 0.33467525243759155 0.7022729 1.17935311794281 True -3 11184 30.688874006271362 2.9823994636535645 715.3909912109375 0.5548335313796997 743.3787231445312 0.3437962234020233 0.7134097 1.0997129678726196 True -4 13980 30.65312933921814 0.564042329788208 636.4906005859375 0.6326004266738892 740.4730224609375 0.34542378783226013 0.72051954 1.1791874170303345 True -5 16776 30.68917226791382 0.5708861351013184 625.8809814453125 0.41595035791397095 735.6634521484375 0.3508346974849701 0.7318442 1.0085127353668213 True -6 19572 30.714680194854736 0.5749228000640869 654.0955810546875 0.3975374698638916 731.5784912109375 0.35427600145339966 0.7421248 0.9047554135322571 True -7 22368 30.720038175582886 0.5679090023040771 619.8278198242188 0.37483876943588257 729.1702270507812 0.35637158155441284 0.74817 0.8741518259048462 True -8 25164 30.83815860748291 0.5897486209869385 529.48876953125 0.6663992404937744 727.0331420898438 0.3578236401081085 0.7542449 0.8324257731437683 True -9 27960 30.85735821723938 0.5861191749572754 670.5093994140625 0.5135199427604675 724.3095703125 0.35960376262664795 0.76162887 0.7342421412467957 True -10 30756 30.731059789657593 0.5786070823669434 644.4193115234375 0.46488818526268005 721.6478271484375 0.36169978976249695 0.7707296 0.663032591342926 True -11 33552 30.709245443344116 1.241079568862915 750.9876708984375 0.5138711333274841 719.1019287109375 0.36395031213760376 0.7791991 0.5909290909767151 True -12 36348 30.07480502128601 1.6736783981323242 607.186279296875 0.40713632106781006 716.6636962890625 0.3662509024143219 0.7870578 0.522892415523529 True -13 39144 30.06092071533203 0.5845930576324463 659.50439453125 0.4022848308086395 715.8290405273438 0.36657214164733887 0.7928936 0.4811811149120331 True -14 41940 30.18460512161255 0.5766589641571045 628.0587768554688 0.2610728442668915 714.1340942382812 0.36800700426101685 0.8011599 0.42928802967071533 True -15 44736 30.32974600791931 0.5662572383880615 604.1338500976562 0.5363712906837463 711.4615478515625 0.3712784945964813 0.8071151 0.38837194442749023 True -16 47532 30.074104070663452 0.5741443634033203 723.0592651367188 0.414408415555954 711.2085571289062 0.3713986873626709 0.81332636 0.3519703447818756 True -17 50328 30.149255990982056 0.5748579502105713 522.9124755859375 0.24634096026420593 709.2606811523438 0.37418118119239807 0.81596303 0.3374134600162506 True -18 53124 30.37520670890808 25.735147714614868 589.23486328125 0.34131312370300293 711.0916137695312 0.37192344665527344 0.8153627 0.32991692423820496 False -19 55920 30.38161611557007 0.5731971263885498 736.69091796875 0.3059532344341278 711.5061645507812 0.3715057373046875 0.81614196 0.33103063702583313 True diff --git a/ENCSR867XFA/cherimoya.fold_4.performance.tsv b/ENCSR867XFA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8c4ba9bb458f02175d6d7ef27eb5649f6f4336a0..0000000000000000000000000000000000000000 --- a/ENCSR867XFA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -711.5061645507812 0.3975185751914978 0.3715057373046875 0.155497208237648 0.8161419630050659 0.7600588798522949 0.33103063702583313 \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_0.evaluate.json b/ENCSR868FGK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d83bcd146e843d078a5f2127e7293ef3a8ba840b..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF874FUM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_0.fit.json b/ENCSR868FGK/cherimoya.fold_0.fit.json deleted file mode 100644 index d8c96721b4f85b5f5abfbe606b07534ebe8fa673..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF874FUM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_0.log b/ENCSR868FGK/cherimoya.fold_0.log deleted file mode 100644 index 04810df471a877dbca6f0bbf163d85bb5fe77068..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3570 44.73310446739197 30.97646403312683 976.194091796875 0.9757479429244995 1275.794677734375 0.7239728569984436 0.6700812 7.132092475891113 True -1 7140 39.454070806503296 27.566304683685303 785.59912109375 1.0285626649856567 1066.1265869140625 0.8095555901527405 0.6780534 1.6054773330688477 True -2 10710 40.21074628829956 0.691309928894043 985.482666015625 0.5106613039970398 1033.6326904296875 0.8208787441253662 0.6932376 0.8119747638702393 True -3 14280 39.24301886558533 0.6820628643035889 910.8671875 0.7291480898857117 1014.3914794921875 0.8266501426696777 0.7045903 0.6557799577713013 True -4 17850 39.351892948150635 32.4603328704834 839.9075927734375 1.0393736362457275 1005.4071044921875 0.830665111541748 0.704967 0.6697697043418884 True -5 21420 39.5821373462677 0.7220568656921387 917.8545532226562 0.8782833814620972 1002.4589233398438 0.8325942158699036 0.70297486 0.7092370390892029 False -6 24990 39.54371690750122 0.6880707740783691 904.1904296875 0.8620011210441589 994.1898193359375 0.8351789116859436 0.7051946 0.6945804953575134 True -7 28560 39.303730964660645 0.6842060089111328 810.21533203125 1.1322389841079712 985.8978881835938 0.8381550312042236 0.71242 0.5830763578414917 True -8 32130 39.41595458984375 0.6818737983703613 762.9476318359375 0.6698184013366699 979.5205078125 0.8408459424972534 0.71581644 0.5857782959938049 True -9 35700 39.3026864528656 0.6874902248382568 928.4984741210938 0.9597032070159912 972.9359130859375 0.8434368968009949 0.7118435 0.5937578082084656 False -10 39270 39.28911352157593 0.6785633563995361 762.5069580078125 0.9054709076881409 965.1236572265625 0.84613037109375 0.7188123 0.5650413632392883 True -11 42840 39.387216567993164 0.6864259243011475 609.5612182617188 1.0057939291000366 957.7062377929688 0.849030613899231 0.7187045 0.5599861145019531 False -12 46410 39.38307476043701 0.6803267002105713 790.4822998046875 0.3595382571220398 951.19140625 0.8512296080589294 0.7250683 0.5514237880706787 True -13 49980 39.324487924575806 0.680687427520752 743.52587890625 0.4684288501739502 944.869384765625 0.8531713485717773 0.7292573 0.5300378203392029 True -14 53550 39.31527638435364 0.6762280464172363 762.5709228515625 0.6181478500366211 940.6066284179688 0.8547260165214539 0.7361395 0.5191051959991455 True -15 57120 38.92505168914795 0.6712794303894043 825.7169799804688 0.7286279201507568 937.7178344726562 0.8558295965194702 0.7399401 0.5175923109054565 True -16 60690 38.477911949157715 0.6704003810882568 740.6778564453125 0.4608805179595947 936.5556640625 0.8560830950737 0.7429619 0.5117695927619934 True -17 64260 39.549710750579834 16.1299467086792 859.554443359375 0.6774179935455322 937.4087524414062 0.8558980226516724 0.7436128 0.5187197327613831 True -18 67830 38.547067642211914 0.6762452125549316 670.9085083007812 0.342802494764328 938.515380859375 0.85543292760849 0.7421418 0.5273359417915344 False -19 71400 38.45542788505554 0.6784536838531494 673.6139526367188 0.5788949131965637 940.1367797851562 0.855043351650238 0.74168926 0.5318285822868347 False diff --git a/ENCSR868FGK/cherimoya.fold_0.performance.tsv b/ENCSR868FGK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 996b5f84d9dc74505e0d47c41d68f34d6127764e..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -937.4087524414062 0.11787400394678116 0.8558979630470276 0.5432602763175964 0.7436128258705139 0.6668516397476196 0.5187197327613831 \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_1.evaluate.json b/ENCSR868FGK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3ca32948d6e5ae67a15a4b0e388972526aac3654..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF874FUM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_1.fit.json b/ENCSR868FGK/cherimoya.fold_1.fit.json deleted file mode 100644 index dc951fc3a1931d8d97cdfcf8d01895188ae405ff..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF874FUM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_1.log b/ENCSR868FGK/cherimoya.fold_1.log deleted file mode 100644 index 27f8bc750e81247455520eba054f0a6134a54f54..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3738 45.67391276359558 3.8767635822296143 973.5806274414062 0.7235097885131836 1374.0545654296875 0.7337015867233276 0.698646 8.371865272521973 True -1 7476 41.28831672668457 50.3453528881073 1129.597412109375 0.7690834999084473 1164.1141357421875 0.81461101770401 0.704845 2.0619351863861084 True -2 11214 42.08774662017822 1.005810260772705 739.73486328125 0.9173197746276855 1129.1314697265625 0.8243177533149719 0.7168687 1.0203453302383423 True -3 14952 41.19428896903992 0.9379243850708008 737.516845703125 0.6194007992744446 1112.1773681640625 0.8295937776565552 0.72336197 0.9339924454689026 True -4 18690 41.19660544395447 0.9243841171264648 894.4688720703125 0.5960423946380615 1100.8157958984375 0.8339182734489441 0.7306253 0.8350305557250977 True -5 22428 41.0716757774353 0.9431798458099365 950.811767578125 0.7353008985519409 1090.6944580078125 0.8370374441146851 0.73295593 0.8338515758514404 True -6 26166 41.35912799835205 53.17686486244202 934.516357421875 0.7320457696914673 1086.2220458984375 0.838844358921051 0.7344019 0.781649649143219 True -7 29904 41.29687976837158 0.9734554290771484 889.4734497070312 0.8550775051116943 1071.4124755859375 0.8427578806877136 0.7391205 0.6641489267349243 True -8 33642 41.240060567855835 0.9119260311126709 865.5260620117188 0.7199268341064453 1060.9090576171875 0.8457548022270203 0.744068 0.6065295934677124 True -9 37380 41.354830265045166 52.77466559410095 815.5673828125 0.4969027042388916 1054.4818115234375 0.848098635673523 0.74602354 0.60772705078125 True -10 41118 40.533634662628174 0.9036805629730225 765.64697265625 0.7111718654632568 1047.3922119140625 0.8503694534301758 0.7487739 0.5692362785339355 True -11 44856 40.750192403793335 38.008756160736084 952.4193115234375 0.5363429188728333 1036.0377197265625 0.8532386422157288 0.75747305 0.5295554995536804 True -12 48594 40.44141960144043 0.9404234886169434 770.695556640625 0.5393401384353638 1030.0531005859375 0.8553999066352844 0.7613926 0.5009087324142456 True -13 52332 40.495145320892334 0.9068353176116943 835.0853271484375 0.6387065649032593 1021.6964721679688 0.857864260673523 0.7626845 0.4870235323905945 True -14 56070 40.678616523742676 0.9113643169403076 595.4895629882812 0.8379231095314026 1015.9142456054688 0.8599315285682678 0.7697289 0.4706805646419525 True -15 59808 40.56357955932617 0.9049975872039795 728.87548828125 0.5863451957702637 1011.1056518554688 0.8613201975822449 0.77445513 0.4563194811344147 True -16 63546 40.46274137496948 1.4110939502716064 783.903076171875 0.4936407804489136 1009.2737426757812 0.8618896007537842 0.7771635 0.4503873288631439 True -17 67284 41.080368757247925 38.41339039802551 711.068359375 0.45520803332328796 1009.3251953125 0.8616010546684265 0.77704746 0.4541124701499939 False -18 71022 40.413657665252686 0.9243745803833008 752.1339721679688 0.4866129159927368 1011.190673828125 0.8612075448036194 0.7758892 0.45753923058509827 False -19 74760 40.406110763549805 2.1874988079071045 805.7996826171875 0.7057802677154541 1012.9772338867188 0.8608930110931396 0.7755829 0.4586462676525116 False diff --git a/ENCSR868FGK/cherimoya.fold_1.performance.tsv b/ENCSR868FGK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3dfcca21b396c0ae18ac6ad0dee78c264fb657f2..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1009.2737426757812 0.11058947443962097 0.8618895411491394 0.5701344013214111 0.7771635055541992 0.7401825785636902 0.4503873288631439 \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_2.evaluate.json b/ENCSR868FGK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7b359cc7f1a2cea666533bb7a7d7889ffa6e34a2..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF874FUM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_2.fit.json b/ENCSR868FGK/cherimoya.fold_2.fit.json deleted file mode 100644 index 16907fb811be3383b196bcded2d0e7595506df40..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF874FUM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_2.log b/ENCSR868FGK/cherimoya.fold_2.log deleted file mode 100644 index 8b5aad7e6bd20be537605aa6ff900cba842ffd37..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3832 46.88885498046875 3.842956066131592 834.6535034179688 0.9345927238464355 1311.0689697265625 0.7498753070831299 0.6007015 6.587422847747803 True -1 7664 42.23914980888367 0.9560365676879883 993.4638061523438 1.0344107151031494 1102.0401611328125 0.8195422291755676 0.6278155 2.1813840866088867 True -2 11496 42.62282633781433 0.9518816471099854 982.49609375 0.8851110339164734 1083.1552734375 0.8262251615524292 0.6382625 1.2324645519256592 True -3 15328 42.180076599121094 1.9235353469848633 961.2257080078125 0.7692861557006836 1063.7769775390625 0.8320268988609314 0.644539 0.9704492688179016 True -4 19160 41.35515594482422 0.8959691524505615 735.72802734375 1.183562994003296 1058.9361572265625 0.8331243991851807 0.64240277 0.951744019985199 False -5 22992 41.331592082977295 0.8980796337127686 946.383056640625 0.5803347826004028 1048.375732421875 0.836828351020813 0.64826864 0.9614974856376648 True -6 26824 41.38937544822693 1.5258047580718994 879.0529174804688 0.9453397989273071 1040.2265625 0.8392654061317444 0.65160096 0.9277234673500061 True -7 30656 41.54568791389465 0.8965742588043213 904.5648193359375 0.6422098875045776 1037.1898193359375 0.8410508632659912 0.6518174 0.9015152454376221 True -8 34488 41.36643862724304 0.9025146961212158 834.636474609375 0.7959121465682983 1027.767333984375 0.8437896370887756 0.65223557 0.8677310347557068 True -9 38320 41.25065207481384 0.8947832584381104 899.0938110351562 0.7771972417831421 1018.498779296875 0.8468288779258728 0.6552768 0.8295268416404724 True -10 42152 41.30324101448059 0.8974478244781494 803.7218627929688 0.6027718782424927 1011.83740234375 0.8487807512283325 0.6520234 0.8454345464706421 False -11 45984 41.23783040046692 0.9058306217193604 739.46533203125 0.6279078722000122 1004.2410278320312 0.8509448766708374 0.65878713 0.8238211274147034 True -12 49816 41.3328115940094 3.2480199337005615 918.88427734375 0.6524966359138489 998.5009765625 0.8528724908828735 0.6614253 0.8028619289398193 True -13 53648 41.415040016174316 0.9121229648590088 793.5116577148438 0.7298639416694641 991.1409301757812 0.8550864458084106 0.66561884 0.7671710252761841 True -14 57480 41.259307622909546 0.946204423904419 753.172119140625 0.5333440899848938 985.38671875 0.8566678166389465 0.6688891 0.7490851879119873 True -15 61312 41.36663317680359 0.9105806350708008 703.938232421875 0.6841772794723511 980.7380981445312 0.8578140735626221 0.6736831 0.7374063730239868 True -16 65144 41.29823637008667 0.8952057361602783 906.2366943359375 0.5343531370162964 980.1689453125 0.8583458065986633 0.6774242 0.7250320911407471 True -17 68976 41.81334400177002 53.30930852890015 679.7521362304688 0.5791822075843811 979.92626953125 0.8582201600074768 0.6791912 0.7225646376609802 True -18 72808 48.959285736083984 22.95640206336975 784.2432861328125 0.4278864562511444 981.2205810546875 0.8578097820281982 0.6790434 0.7264822721481323 False -19 76640 41.298161029815674 0.9184291362762451 781.218994140625 0.3966858386993408 981.8265380859375 0.8575983047485352 0.67762846 0.7303922772407532 False diff --git a/ENCSR868FGK/cherimoya.fold_2.performance.tsv b/ENCSR868FGK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1997e7cdb795ba380a8948674fee28964715095b..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -979.92626953125 0.11178907006978989 0.858220100402832 0.5659275054931641 0.6791911721229553 0.6055245399475098 0.7225646376609802 \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_3.evaluate.json b/ENCSR868FGK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ff3645afbccc018d089c7d9083432ca84040068e..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF874FUM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_3.fit.json b/ENCSR868FGK/cherimoya.fold_3.fit.json deleted file mode 100644 index a25c2f30b16eb185f57703ecd404523a139928b5..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF874FUM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_3.log b/ENCSR868FGK/cherimoya.fold_3.log deleted file mode 100644 index 50666725fa65738c1b5e87547a651750eec16225..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3796 47.00292491912842 4.766171216964722 860.890625 1.140259027481079 1274.2852783203125 0.7555951476097107 0.593363 7.977657794952393 True -1 7592 41.73634696006775 0.887221097946167 838.8088989257812 0.8651721477508545 1083.713623046875 0.8214316964149475 0.61682516 1.9528409242630005 True -2 11388 41.766690492630005 0.8737814426422119 818.124267578125 1.3760595321655273 1060.67041015625 0.8285354375839233 0.63085085 1.2421354055404663 True -3 15184 41.82482409477234 2.751518964767456 951.3572998046875 0.7213554382324219 1049.4764404296875 0.832133412361145 0.6450731 1.0485831499099731 True -4 18980 41.82732033729553 3.6177494525909424 932.6367797851562 0.9722372889518738 1038.52099609375 0.8357258439064026 0.6459856 1.0826386213302612 True -5 22776 41.893009662628174 12.378331661224365 889.490478515625 0.9572153687477112 1033.108154296875 0.8367552161216736 0.6537268 0.9995034337043762 True -6 26572 42.00884652137756 0.8786993026733398 695.255859375 0.7735812664031982 1027.500244140625 0.8389760851860046 0.656741 0.9019384384155273 True -7 30368 42.0894660949707 0.8755185604095459 821.2567138671875 0.7529697418212891 1023.1917114257812 0.8413090705871582 0.6578193 0.9279853701591492 True -8 34164 42.01806139945984 0.8735475540161133 763.0887451171875 0.9321689009666443 1015.65673828125 0.8433153033256531 0.65855634 0.9016762971878052 True -9 37960 41.9431836605072 0.8699846267700195 777.978271484375 0.8618701696395874 1009.8704833984375 0.8454999923706055 0.6628643 0.8653283715248108 True -10 41756 41.98493528366089 21.93627405166626 766.5155029296875 0.5012173056602478 1003.2511596679688 0.8479882478713989 0.6687556 0.8776583075523376 True -11 45552 43.43851113319397 0.8819022178649902 859.964111328125 0.7318966388702393 996.80029296875 0.8501923084259033 0.66935974 0.8514522910118103 True -12 49348 41.8818302154541 21.277300596237183 770.7252807617188 0.7017989158630371 991.5269775390625 0.8519030213356018 0.67186993 0.8373265266418457 True -13 53144 45.2868595123291 0.8871116638183594 939.6992797851562 0.7658743858337402 985.785400390625 0.8538526296615601 0.67561275 0.8000643849372864 True -14 56940 42.17516326904297 0.8800346851348877 774.5003051757812 0.6190023422241211 979.2064208984375 0.8554880619049072 0.68087786 0.7672909498214722 True -15 60736 41.26132655143738 0.8599183559417725 815.861328125 0.45864129066467285 975.396484375 0.8567171096801758 0.690376 0.742569625377655 True -16 64532 41.01279640197754 0.8573117256164551 755.2418212890625 0.5223638415336609 972.6947631835938 0.8575809597969055 0.69782066 0.713944137096405 True -17 68328 41.00409388542175 1.7677714824676514 781.56640625 0.5440095663070679 972.3555908203125 0.8576676249504089 0.6980202 0.7069305181503296 True -18 72124 41.21445274353027 0.8805060386657715 742.20263671875 0.7280805706977844 973.558349609375 0.8573248386383057 0.6971026 0.7078343033790588 False -19 75920 41.07254076004028 0.8547656536102295 878.353515625 0.4987979531288147 974.7710571289062 0.8570055365562439 0.69668597 0.7162854671478271 False diff --git a/ENCSR868FGK/cherimoya.fold_3.performance.tsv b/ENCSR868FGK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 53d4ad43acaca8387a77baea8743ec6e2f6229d1..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -972.3555908203125 0.11320386081933975 0.8576676249504089 0.5580214262008667 0.6980202198028564 0.6130295395851135 0.7069305181503296 \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_4.evaluate.json b/ENCSR868FGK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ff90b2676238216741fdb2ac08014e9f3d618044..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF874FUM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_4.fit.json b/ENCSR868FGK/cherimoya.fold_4.fit.json deleted file mode 100644 index 7cd29bc33a8ee2d0f63cef03ca9d1fb2d68f9150..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF874FUM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR868FGK/cherimoya.fold_4.log b/ENCSR868FGK/cherimoya.fold_4.log deleted file mode 100644 index fc6e2112745ce8c02d3ce09c2615252a184e10ae..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3800 51.29239344596863 4.700885772705078 1023.3583984375 0.8378620147705078 1186.693115234375 0.7402637600898743 0.6495985 6.129153251647949 True -1 7600 42.12012314796448 0.692284107208252 889.5924072265625 0.9768885374069214 1017.63037109375 0.8150831460952759 0.6586428 1.5900696516036987 True -2 11400 42.22119760513306 0.6568644046783447 915.0463256835938 0.885456919670105 995.1011962890625 0.8235558867454529 0.6665502 0.8507515788078308 True -3 15200 41.83222413063049 0.6585328578948975 888.2764282226562 0.8287597894668579 982.3507080078125 0.8276391625404358 0.67692953 0.7904817461967468 True -4 19000 41.76969933509827 0.6549127101898193 867.4876708984375 0.9001699686050415 972.527099609375 0.8302154541015625 0.6861948 0.7944859862327576 True -5 22800 41.88201332092285 0.6542279720306396 960.434814453125 0.7243513464927673 966.8974609375 0.8329734802246094 0.685594 0.7623883485794067 False -6 26600 41.937732458114624 0.6553876399993896 938.8612670898438 0.6578146815299988 958.4852905273438 0.8358540534973145 0.6876498 0.6589954495429993 True -7 30400 41.736165285110474 0.6538918018341064 842.6707763671875 0.918594241142273 950.7684326171875 0.8386311531066895 0.68862 0.6427248120307922 True -8 34200 41.7820463180542 0.6607904434204102 879.1278076171875 0.8528332710266113 946.5452880859375 0.8412212133407593 0.690265 0.6416198015213013 True -9 38000 41.25887942314148 0.6512768268585205 891.8822021484375 0.8424286842346191 938.6713256835938 0.8435197472572327 0.6931473 0.6061214208602905 True -10 41800 40.97392463684082 0.6492640972137451 808.678955078125 1.0413925647735596 934.2692260742188 0.8455560803413391 0.69521713 0.5952003598213196 True -11 45600 40.952205181121826 0.647956371307373 929.7606201171875 0.6046094298362732 929.0101928710938 0.8476124405860901 0.7018132 0.5783355236053467 True -12 49400 41.05588388442993 0.6493594646453857 801.980224609375 0.5871936678886414 922.1669311523438 0.8504148721694946 0.69854313 0.5874346494674683 False -13 53200 41.13146495819092 0.651148796081543 683.8488159179688 0.7800172567367554 915.4296875 0.8523111939430237 0.7074303 0.5610119700431824 True -14 57000 41.0078558921814 0.6468560695648193 887.1193237304688 0.7398853302001953 909.9716796875 0.8542299270629883 0.71240497 0.5490089058876038 True -15 60800 41.094141721725464 2.3518009185791016 727.3388671875 0.6047718524932861 907.3500366210938 0.8550752401351929 0.71634465 0.5406812429428101 True -16 64600 40.993173360824585 0.6457018852233887 832.029296875 0.7559239268302917 906.0111694335938 0.8554906845092773 0.7217758 0.5338600277900696 True -17 68400 41.02188563346863 0.6591653823852539 829.43310546875 0.6413835287094116 906.97705078125 0.8551490306854248 0.72235656 0.5309018492698669 True -18 72200 40.95954442024231 0.6493675708770752 831.226806640625 0.4636639952659607 907.9052734375 0.8546844720840454 0.72292465 0.5357879400253296 True -19 76000 40.96573042869568 0.6532325744628906 851.2027587890625 0.4794613718986511 908.89697265625 0.8544270396232605 0.72145647 0.5434882044792175 False diff --git a/ENCSR868FGK/cherimoya.fold_4.performance.tsv b/ENCSR868FGK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7b0214eec3e7b5d62bc48fc725e1197d400a475a..0000000000000000000000000000000000000000 --- a/ENCSR868FGK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -907.9052734375 0.11892944574356079 0.8546845316886902 0.5381367802619934 0.7229246497154236 0.6377781629562378 0.5357879400253296 \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_0.evaluate.json b/ENCSR869JYO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5395788f635e66c5f7c330faa21205cb811fb523..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586JTE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_0.fit.json b/ENCSR869JYO/cherimoya.fold_0.fit.json deleted file mode 100644 index 23dfdc2e3c821db74aee7a611cc42b51859715dc..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF586JTE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_0.log b/ENCSR869JYO/cherimoya.fold_0.log deleted file mode 100644 index a75a9944cdb89a0e96dd3cfc0beb6f80f7eda702..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.37079644203186 3.3105833530426025 319.2027282714844 0.6704767942428589 366.7123718261719 0.1717556118965149 0.7091942 4.423672199249268 True -1 5508 30.58697485923767 0.8105919361114502 243.88888549804688 0.426641583442688 334.70404052734375 0.21043647825717926 0.77466494 1.3488614559173584 True -2 8262 30.587251901626587 1.1325712203979492 252.50389099121094 0.2943348288536072 330.17864990234375 0.2131006419658661 0.79215354 0.9187721014022827 True -3 11016 30.608596324920654 0.5849971771240234 280.6520690917969 0.44304853677749634 324.46600341796875 0.219038724899292 0.80350214 0.7539045214653015 True -4 13770 30.568277597427368 0.5932760238647461 268.5802001953125 0.5308101773262024 322.55975341796875 0.21959316730499268 0.81024945 0.6395126581192017 True -5 16524 30.564090967178345 0.6334068775177002 248.15516662597656 0.29579973220825195 319.39691162109375 0.22497788071632385 0.81928146 0.6033293604850769 True -6 19278 30.568082332611084 1.3930213451385498 329.5968017578125 0.39303988218307495 318.2498779296875 0.22571726143360138 0.8263073 0.5347930788993835 True -7 22032 30.5260648727417 0.685462474822998 199.48770141601562 0.23147781193256378 317.1487121582031 0.22704361379146576 0.8372419 0.4801918566226959 True -8 24786 30.53923487663269 0.5843997001647949 226.21310424804688 0.4498516023159027 315.9911804199219 0.22923007607460022 0.84107834 0.44374027848243713 True -9 27540 30.552311897277832 0.5803208351135254 348.022705078125 0.4434831142425537 314.8525085449219 0.23138955235481262 0.8440913 0.4289027452468872 True -10 30294 30.574254035949707 0.5785243511199951 281.6219787597656 0.4155537486076355 313.67535400390625 0.23283739387989044 0.85242254 0.38509228825569153 True -11 33048 30.62353801727295 0.5800786018371582 259.09320068359375 0.2833574414253235 312.28070068359375 0.2354097217321396 0.85684633 0.3499396741390228 True -12 35802 30.64123773574829 4.413616418838501 239.0078125 0.229373037815094 312.4320373535156 0.23488666117191315 0.8600636 0.33872541785240173 True -13 38556 30.37683939933777 0.5787403583526611 256.2731628417969 0.33621305227279663 310.9613037109375 0.23655197024345398 0.864916 0.31635674834251404 True -14 41310 29.942779779434204 0.5915215015411377 240.32229614257812 0.20303526520729065 309.5669860839844 0.2387264370918274 0.8705154 0.3000538945198059 True -15 44064 29.962678909301758 0.5661134719848633 270.58636474609375 0.2198718935251236 308.9408874511719 0.2391093373298645 0.87562627 0.2827160954475403 True -16 46818 29.975619316101074 0.577406644821167 270.4252014160156 0.30735689401626587 308.1036682128906 0.2400551587343216 0.87968093 0.27008458971977234 True -17 49572 29.964503049850464 0.5568649768829346 220.94337463378906 0.23431681096553802 308.10943603515625 0.24009665846824646 0.8809687 0.26006612181663513 True -18 52326 30.034050464630127 0.5705890655517578 340.16619873046875 0.23834359645843506 309.0695495605469 0.23857755959033966 0.8811427 0.25846004486083984 True -19 55080 29.959880352020264 0.5620605945587158 222.00140380859375 0.20928344130516052 308.99261474609375 0.23898838460445404 0.88055646 0.26073721051216125 False diff --git a/ENCSR869JYO/cherimoya.fold_0.performance.tsv b/ENCSR869JYO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2bc639010a23cfb02f00d5a72bc99c3ef64010ad..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.0695495605469 0.515291154384613 0.23857754468917847 0.07276105135679245 0.8811426758766174 0.8226205110549927 0.25846004486083984 \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_1.evaluate.json b/ENCSR869JYO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9d84c9859205e0d34373b1e39fe6d61be11279a0..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586JTE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_1.fit.json b/ENCSR869JYO/cherimoya.fold_1.fit.json deleted file mode 100644 index 322904d13638aca33b99b55693e074a12973879f..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF586JTE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_1.log b/ENCSR869JYO/cherimoya.fold_1.log deleted file mode 100644 index 62230c4d6119eeee44c04503f0c3fd0462cd883e..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2732 35.059091567993164 4.031893730163574 229.39657592773438 0.31141579151153564 473.75848388671875 0.18482059240341187 0.69031674 5.3656206130981445 True -1 5464 30.481414556503296 0.7635796070098877 243.07852172851562 0.3911641240119934 421.3645324707031 0.24110108613967896 0.7846121 1.9888205528259277 True -2 8196 30.385045528411865 0.8018081188201904 265.98370361328125 0.48163336515426636 414.3209533691406 0.24536143243312836 0.7939782 1.4592297077178955 True -3 10928 30.326881408691406 0.6815571784973145 230.55267333984375 0.32354822754859924 411.8415222167969 0.24800771474838257 0.80017537 0.9351233243942261 True -4 13660 30.306187391281128 0.6776344776153564 282.082275390625 0.5161305069923401 406.63018798828125 0.2540851831436157 0.8146955 0.9136987328529358 True -5 16392 30.23538637161255 0.6816964149475098 257.7267150878906 0.43170905113220215 403.0920104980469 0.25839996337890625 0.8247166 0.8408832550048828 True -6 19124 30.23044443130493 0.6861622333526611 255.78817749023438 0.33032870292663574 400.48040771484375 0.26124170422554016 0.8312201 0.7584003210067749 True -7 21856 30.234094381332397 0.6681082248687744 314.4827880859375 0.36942291259765625 398.9477233886719 0.262063205242157 0.83261037 0.6995606422424316 True -8 24588 30.25528120994568 0.6660315990447998 257.07794189453125 0.6234185695648193 395.9128723144531 0.2663761079311371 0.8421407 0.6509050130844116 True -9 27320 30.237468004226685 0.6699347496032715 281.53387451171875 0.23891322314739227 394.3039245605469 0.2680172026157379 0.8443548 0.6025791764259338 True -10 30052 30.24053168296814 0.6738672256469727 274.7853088378906 0.4294719696044922 392.1332092285156 0.27066200971603394 0.8538273 0.5217582583427429 True -11 32784 30.253999948501587 0.6619415283203125 272.88653564453125 0.331943541765213 391.4756164550781 0.270321249961853 0.8603957 0.47634387016296387 True -12 35516 30.233901262283325 0.6693103313446045 223.81036376953125 0.31134048104286194 388.6640930175781 0.27431344985961914 0.8713525 0.41746655106544495 True -13 38248 30.250325202941895 0.6684229373931885 263.6842041015625 0.3744203448295593 387.8984069824219 0.2743130028247833 0.8792936 0.37808936834335327 True -14 40980 30.30168080329895 1.2847881317138672 327.88043212890625 0.3253282308578491 387.0604553222656 0.2753373086452484 0.8832885 0.35794365406036377 True -15 43712 30.145556211471558 1.117490291595459 231.03131103515625 0.31049203872680664 385.5447998046875 0.27619558572769165 0.88944083 0.3326031267642975 True -16 46444 29.70027256011963 0.6609876155853271 315.16204833984375 0.2619870901107788 384.4608459472656 0.2787128984928131 0.89123696 0.3206983208656311 True -17 49176 29.70301389694214 0.6573226451873779 211.95501708984375 0.26856058835983276 384.7315673828125 0.2775791585445404 0.89297456 0.31507986783981323 True -18 51908 29.736629724502563 0.6631975173950195 236.371826171875 0.3197488784790039 385.3233947753906 0.276933878660202 0.8912914 0.3148622214794159 False -19 54640 29.805166244506836 2.410106658935547 304.834228515625 0.1774052083492279 384.94757080078125 0.2780799865722656 0.8910377 0.3162095248699188 False diff --git a/ENCSR869JYO/cherimoya.fold_1.performance.tsv b/ENCSR869JYO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 290dcdd390fe70a6f085ff58b15f01bf7d8380f6..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -384.7315673828125 0.48497968912124634 0.277579128742218 0.09365639835596085 0.8929745554924011 0.8623026013374329 0.31507986783981323 \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_2.evaluate.json b/ENCSR869JYO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 30a976f54a51d0445d22751c0d8e506438920235..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586JTE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_2.fit.json b/ENCSR869JYO/cherimoya.fold_2.fit.json deleted file mode 100644 index 247e27e437055b2a1f9cf1a8f7770683b9aa8313..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF586JTE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_2.log b/ENCSR869JYO/cherimoya.fold_2.log deleted file mode 100644 index 990fe1b4f9bb681db2c122f705b0c7831bc361ca..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.4211745262146 3.5400278568267822 257.848388671875 0.43221908807754517 389.7258605957031 0.1714278608560562 0.6887244 4.1245198249816895 True -1 5754 35.02193522453308 1.1647822856903076 261.6009521484375 0.5536243319511414 350.142822265625 0.21489349007606506 0.77167106 1.4379240274429321 True -2 8631 32.06581377983093 0.6672120094299316 327.80810546875 0.3920544981956482 346.06689453125 0.21625228226184845 0.79639524 1.0977869033813477 True -3 11508 32.20872974395752 0.5929074287414551 284.4649353027344 0.3755166530609131 341.00738525390625 0.22236758470535278 0.7947553 0.6856728196144104 False -4 14385 31.96824550628662 0.5740616321563721 287.4520263671875 0.6185665130615234 336.3736267089844 0.22708219289779663 0.811762 0.5261054635047913 True -5 17262 31.893693923950195 0.5657224655151367 268.819580078125 0.44272953271865845 334.45391845703125 0.22955438494682312 0.8210656 0.48298388719558716 True -6 20139 31.886117696762085 0.5622730255126953 277.1772766113281 0.37700432538986206 333.1329040527344 0.23068584501743317 0.8266439 0.4502231180667877 True -7 23016 31.845845937728882 0.5678548812866211 247.75921630859375 0.4469546377658844 331.53814697265625 0.2329712212085724 0.8317249 0.4280359745025635 True -8 25893 31.859540462493896 0.565218448638916 303.8963317871094 0.3409522771835327 329.0757751464844 0.23681128025054932 0.8389965 0.4071827232837677 True -9 28770 31.920373916625977 0.5540094375610352 305.7432861328125 0.3351672887802124 328.1296081542969 0.23717743158340454 0.84431416 0.3724764585494995 True -10 31647 31.92563009262085 0.6377828121185303 235.237060546875 0.4205887019634247 326.88116455078125 0.23912595212459564 0.8511918 0.3586578965187073 True -11 34524 31.90821671485901 0.5672128200531006 293.4496154785156 0.46357643604278564 325.6993713378906 0.24043825268745422 0.85541147 0.33378082513809204 True -12 37401 31.93530249595642 0.5702886581420898 191.43026733398438 0.270292729139328 325.00494384765625 0.24114951491355896 0.86214703 0.31727442145347595 True -13 40278 31.871675491333008 0.5664348602294922 258.10504150390625 0.26323822140693665 324.2538146972656 0.24267800152301788 0.86585015 0.3052213191986084 True -14 43155 31.958411931991577 0.5595912933349609 238.32029724121094 0.3914363384246826 323.23974609375 0.24483850598335266 0.8708419 0.290625661611557 True -15 46032 32.08667969703674 0.6103827953338623 310.033935546875 0.22737658023834229 322.9412841796875 0.24463245272636414 0.8741557 0.2845192551612854 True -16 48909 32.173768520355225 0.5672702789306641 223.90875244140625 0.22364330291748047 322.64190673828125 0.24483786523342133 0.8758276 0.278239905834198 True -17 51786 31.85712742805481 0.9999425411224365 294.9605712890625 0.26735785603523254 323.1347961425781 0.24433265626430511 0.87501216 0.27828043699264526 False -18 54663 31.41439938545227 1.9681551456451416 263.9510498046875 0.1613278090953827 323.5204772949219 0.24338220059871674 0.87425566 0.2814088761806488 False -19 57540 31.54527449607849 0.5837254524230957 273.5699768066406 0.1757219433784485 323.4342956542969 0.24437293410301208 0.8735464 0.2836625277996063 False diff --git a/ENCSR869JYO/cherimoya.fold_2.performance.tsv b/ENCSR869JYO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0cf65a41956479c33e4a9d7a3bf3ceb58eda0fc7..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -322.64190673828125 0.5094902515411377 0.24483786523342133 0.08087894320487976 0.8758276104927063 0.8310615420341492 0.278239905834198 \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_3.evaluate.json b/ENCSR869JYO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3c30264d619cb4579c0feb8613b41b157d1bf1d4..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586JTE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_3.fit.json b/ENCSR869JYO/cherimoya.fold_3.fit.json deleted file mode 100644 index 948f5b8b1af9ceb98b0fd7c800e15c8fe2a0725d..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF586JTE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_3.log b/ENCSR869JYO/cherimoya.fold_3.log deleted file mode 100644 index 655d2e7cf35fa8a1b71f1a01e90d7cf1e35a07ba..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2714 35.050262451171875 2.6270804405212402 256.96478271484375 0.4864405393600464 383.93609619140625 0.18170036375522614 0.6532172 4.8794989585876465 True -1 5428 30.243163585662842 1.7114801406860352 279.4075012207031 0.5644223093986511 353.1396179199219 0.2198592573404312 0.7295774 1.7350530624389648 True -2 8142 30.22238326072693 0.543846845626831 291.19818115234375 0.3374406695365906 346.1141662597656 0.22351178526878357 0.75458086 1.307387113571167 True -3 10856 30.18023371696472 0.5192980766296387 273.89208984375 0.4304765462875366 340.99932861328125 0.22895018756389618 0.7686132 0.8336088061332703 True -4 13570 30.150513172149658 0.5352809429168701 288.45196533203125 0.4995620846748352 337.9568786621094 0.23380866646766663 0.7788715 0.8062852621078491 True -5 16284 30.257686138153076 0.5964598655700684 289.67254638671875 0.6122125387191772 336.4580078125 0.23547741770744324 0.7798208 0.8375208973884583 True -6 18998 30.166908740997314 0.59287428855896 275.420654296875 0.2529781460762024 334.63983154296875 0.23761974275112152 0.78980756 0.7915781140327454 True -7 21712 30.086212635040283 0.5013368129730225 282.6246337890625 0.3110678791999817 333.0716857910156 0.24004307389259338 0.79171693 0.7793641090393066 True -8 24426 30.12740445137024 0.520465612411499 257.96832275390625 0.37856772541999817 332.00634765625 0.24068330228328705 0.80389506 0.6821386218070984 True -9 27140 30.097566843032837 0.5170955657958984 246.63595581054688 0.6279684901237488 330.873779296875 0.24256707727909088 0.81453836 0.6497899293899536 True -10 29854 30.099870443344116 0.5195784568786621 338.74884033203125 0.6173696517944336 329.48480224609375 0.24525852501392365 0.82275236 0.5754576325416565 True -11 32568 30.092569589614868 1.8507280349731445 260.9776306152344 0.3549300730228424 328.3821716308594 0.24660712480545044 0.8279789 0.5256843566894531 True -12 35282 30.118598699569702 0.49378347396850586 289.9193115234375 0.23754747211933136 327.0806579589844 0.24873624742031097 0.8363542 0.47290411591529846 True -13 37996 30.098830223083496 0.5070254802703857 293.98284912109375 0.38968271017074585 325.39013671875 0.25119733810424805 0.84581965 0.4228834807872772 True -14 40710 30.13682270050049 0.5260744094848633 283.4819641113281 0.4968729019165039 324.2413330078125 0.25207075476646423 0.85249645 0.39297038316726685 True -15 43424 30.14099407196045 0.48505425453186035 325.79840087890625 0.268138587474823 323.7311706542969 0.2522518038749695 0.85739124 0.3673514425754547 True -16 46138 30.147956371307373 0.5107479095458984 210.36553955078125 0.21172268688678741 322.5570373535156 0.25419315695762634 0.8633498 0.34406593441963196 True -17 48852 30.175503730773926 0.5033767223358154 280.66741943359375 0.267639696598053 323.38775634765625 0.2524496614933014 0.86457497 0.33145397901535034 True -18 51566 30.06244468688965 0.5064723491668701 263.03216552734375 0.14132271707057953 323.13330078125 0.2523224353790283 0.8649848 0.3288848102092743 True -19 54280 29.570497751235962 0.50850510597229 261.247314453125 0.16344597935676575 322.8672180175781 0.2531784474849701 0.86416346 0.32815420627593994 False diff --git a/ENCSR869JYO/cherimoya.fold_3.performance.tsv b/ENCSR869JYO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3abff6e4c23e491f9fb236d09a5ff67d86f05bee..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -323.13330078125 0.5054565072059631 0.25232240557670593 0.0820859968662262 0.8649848103523254 0.8126051425933838 0.3288848102092743 \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_4.evaluate.json b/ENCSR869JYO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 97bfc5c3e1797f3f9a6adbb2e01d921d6f8f8f01..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF586JTE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_4.fit.json b/ENCSR869JYO/cherimoya.fold_4.fit.json deleted file mode 100644 index 3c462a7951fec2e16d626bbe7f5638b46e6d840c..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF586JTE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR869JYO/cherimoya.fold_4.log b/ENCSR869JYO/cherimoya.fold_4.log deleted file mode 100644 index 7406f8f34452242463a0665fd5439b8a7ffccedd..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 35.74074697494507 3.847278356552124 219.09124755859375 0.4627060294151306 313.1630554199219 0.15974606573581696 0.6893196 3.6702041625976562 True -1 5584 31.019188404083252 0.767611026763916 244.37515258789062 0.30476391315460205 288.94915771484375 0.19353850185871124 0.75766534 1.2022573947906494 True -2 8376 30.991600275039673 16.231308937072754 228.5970001220703 0.32337313890457153 285.4198913574219 0.19750593602657318 0.7666911 0.7568528652191162 True -3 11168 30.964333534240723 2.058406352996826 211.57168579101562 0.48151281476020813 281.9635925292969 0.20021727681159973 0.7942097 0.5500722527503967 True -4 13960 30.95848774909973 15.019460916519165 298.9817810058594 0.5245635509490967 280.88397216796875 0.20078206062316895 0.79790235 0.5548816323280334 True -5 16752 30.93375015258789 18.96615242958069 243.78919982910156 0.46327492594718933 279.493408203125 0.2042076736688614 0.7964329 0.5596621632575989 False -6 19544 31.238025665283203 0.6883525848388672 231.34375 0.3354445695877075 277.2317199707031 0.2066807895898819 0.81074184 0.505241334438324 True -7 22336 31.06082010269165 0.6994190216064453 298.05889892578125 0.37092190980911255 276.8915100097656 0.2065703570842743 0.8132141 0.4608709216117859 True -8 25128 30.916364669799805 0.6751759052276611 246.66233825683594 0.40069788694381714 275.77398681640625 0.20825815200805664 0.81931 0.41138333082199097 True -9 27920 31.096168518066406 0.6783733367919922 232.61102294921875 0.4951024353504181 274.9367980957031 0.20979811251163483 0.82717955 0.3889608681201935 True -10 30712 31.066232204437256 24.324731588363647 265.5369567871094 0.27903038263320923 273.6389465332031 0.21217341721057892 0.8327488 0.3615374267101288 True -11 33504 31.932955980300903 0.6907718181610107 273.87835693359375 0.26236218214035034 273.5640869140625 0.21061459183692932 0.84534866 0.3231782019138336 True -12 36296 32.25114345550537 0.6970508098602295 207.35470581054688 0.45922932028770447 272.39727783203125 0.21358837187290192 0.84897786 0.30077609419822693 True -13 39088 30.961762189865112 0.6896905899047852 292.68963623046875 0.42500314116477966 271.4522399902344 0.2153172641992569 0.8551282 0.27562424540519714 True -14 41880 31.05569314956665 0.6861531734466553 314.8231201171875 0.34568434953689575 270.87554931640625 0.21561051905155182 0.8603728 0.26667892932891846 True -15 44672 31.01841378211975 0.6839814186096191 289.4529724121094 0.3341074287891388 271.2774658203125 0.2146630585193634 0.8635541 0.2510187029838562 True -16 47464 30.979142904281616 0.7078719139099121 311.8403625488281 0.18927577137947083 270.3382263183594 0.2163269817829132 0.8678415 0.2396654486656189 True -17 50256 31.020835638046265 0.6784529685974121 279.7517395019531 0.3073172867298126 270.2788391113281 0.21647882461547852 0.8709467 0.2337133139371872 True -18 53048 31.047778606414795 0.6647694110870361 232.21864318847656 0.4433239698410034 270.2245178222656 0.2167799174785614 0.8710703 0.23388271033763885 True -19 55840 30.99518918991089 0.6624581813812256 285.1690979003906 0.10802506655454636 270.4278564453125 0.21623188257217407 0.87118506 0.23448511958122253 True diff --git a/ENCSR869JYO/cherimoya.fold_4.performance.tsv b/ENCSR869JYO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 35fe943f7cd1bd9fc60a9b115327b8a26c3e0cb5..0000000000000000000000000000000000000000 --- a/ENCSR869JYO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -270.4278564453125 0.5328648090362549 0.21623189747333527 0.06410191208124161 0.8711850643157959 0.8070340752601624 0.23448511958122253 \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_0.evaluate.json b/ENCSR871APX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 378dcce4a371d6ef3b1897a7ddfc60751ee94816..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF548WMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_0.fit.json b/ENCSR871APX/cherimoya.fold_0.fit.json deleted file mode 100644 index f935a737ac2f0974a6262749aad00cfc5584fe17..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF548WMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_0.log b/ENCSR871APX/cherimoya.fold_0.log deleted file mode 100644 index 168a1668bc579e3bbdae7f2c80b1d881e719dc9d..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2766 35.3316388130188 3.400156021118164 208.57431030273438 0.5657020807266235 268.97344970703125 0.15429699420928955 0.5961893 2.1651196479797363 True -1 5532 30.78642964363098 1.3420171737670898 201.6228790283203 0.7054176330566406 257.32379150390625 0.20795807242393494 0.67406213 1.0159673690795898 True -2 8298 30.775961875915527 2.3853230476379395 174.89425659179688 0.797789454460144 254.05075073242188 0.21976521611213684 0.6918534 0.5259789228439331 True -3 11064 30.8664972782135 0.6348092555999756 231.84327697753906 0.6177061796188354 252.9410400390625 0.22250035405158997 0.7010375 0.43106240034103394 True -4 13830 30.864964723587036 0.5832197666168213 208.5932159423828 0.42836645245552063 252.23085021972656 0.22496409714221954 0.70195544 0.47215402126312256 True -5 16596 30.77545428276062 0.566795825958252 234.55218505859375 0.519018292427063 251.93679809570312 0.22642110288143158 0.7054985 0.4795627295970917 True -6 19362 30.71657085418701 0.5612437725067139 174.21054077148438 0.4231981635093689 251.3282012939453 0.22925834357738495 0.70840496 0.4719139337539673 True -7 22128 30.67184019088745 0.5682528018951416 223.93106079101562 0.5439028739929199 250.99583435058594 0.23084813356399536 0.71374273 0.452006995677948 True -8 24894 30.734869956970215 0.5821065902709961 185.348388671875 0.48115092515945435 250.56683349609375 0.23264218866825104 0.7190852 0.4490325450897217 True -9 27660 30.636093378067017 0.5762147903442383 201.45196533203125 0.41014280915260315 250.28189086914062 0.2343873232603073 0.72245884 0.4283696413040161 True -10 30426 30.161164045333862 0.5560786724090576 210.0385284423828 0.24039395153522491 249.66790771484375 0.23727582395076752 0.7275217 0.4126989245414734 True -11 33192 30.191917896270752 0.5623197555541992 189.5736083984375 0.5388602018356323 249.15142822265625 0.23940669000148773 0.73732835 0.40489912033081055 True -12 35958 30.218088626861572 0.5719168186187744 173.68441772460938 0.36784130334854126 248.46658325195312 0.2425880879163742 0.74119765 0.3715934753417969 True -13 38724 30.189913511276245 0.5722792148590088 192.3693389892578 0.3787449598312378 248.32562255859375 0.24276046454906464 0.7480685 0.35820919275283813 True -14 41490 30.132664680480957 1.0220952033996582 185.8896484375 0.4417386054992676 248.03660583496094 0.24408216774463654 0.75540984 0.3348999619483948 True -15 44256 30.146171808242798 1.4786005020141602 216.29608154296875 0.2968851923942566 247.6873779296875 0.24579395353794098 0.7631536 0.3116401433944702 True -16 47022 30.13976216316223 0.5807254314422607 156.10330200195312 0.40957939624786377 247.62449645996094 0.2456963211297989 0.7684406 0.29486578702926636 True -17 49788 30.167697429656982 0.5709619522094727 183.39068603515625 0.34112247824668884 247.5006866455078 0.24579793214797974 0.77042156 0.28660449385643005 True -18 52554 30.19282293319702 0.5539586544036865 199.4848175048828 0.25774312019348145 247.7681427001953 0.24453966319561005 0.76938194 0.28348082304000854 False -19 55320 30.301908493041992 0.5603766441345215 166.5216064453125 0.2089015543460846 247.72715759277344 0.24497881531715393 0.7688983 0.28316530585289 False diff --git a/ENCSR871APX/cherimoya.fold_0.performance.tsv b/ENCSR871APX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 85867c818df563a0beb4b72950b56fe4763e210b..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -247.5006866455078 0.5194107294082642 0.24579796195030212 0.06283252686262131 0.77042156457901 0.7068183422088623 0.28660449385643005 \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_1.evaluate.json b/ENCSR871APX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d2c5418b9605b4124bd2246acb0295d6d54f522c..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF548WMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_1.fit.json b/ENCSR871APX/cherimoya.fold_1.fit.json deleted file mode 100644 index 516f3e1e0eed3027191083ad37e7d84410bcc1a7..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF548WMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_1.log b/ENCSR871APX/cherimoya.fold_1.log deleted file mode 100644 index 157aa6997cf417dc455d9663fada039c9a296e0c..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 35.20000123977661 2.1724839210510254 232.6000518798828 0.5936397314071655 312.8984375 0.16383738815784454 0.6010947 3.5214176177978516 True -1 5486 30.502065658569336 0.9312539100646973 229.09861755371094 0.7758128643035889 298.3994445800781 0.22080032527446747 0.6909336 1.0328009128570557 True -2 8229 30.470677137374878 0.6314828395843506 224.140380859375 0.38594430685043335 293.6532897949219 0.23435571789741516 0.7178544 0.6084033250808716 True -3 10972 30.416438817977905 0.6155471801757812 205.18724060058594 0.4925108850002289 291.1626892089844 0.24046790599822998 0.726546 0.4585435390472412 True -4 13715 30.411128520965576 0.6438877582550049 214.20867919921875 0.722371518611908 290.48687744140625 0.2419280707836151 0.7291769 0.5373992919921875 True -5 16458 30.445421934127808 0.6407580375671387 168.25161743164062 0.572271466255188 290.26470947265625 0.24262121319770813 0.73169553 0.6372877359390259 True -6 19201 30.458721160888672 0.6304793357849121 197.32333374023438 0.3615482747554779 289.6464538574219 0.24468709528446198 0.7387955 0.6107046604156494 True -7 21944 30.396572589874268 0.6479332447052002 207.8501434326172 0.32322245836257935 288.4231262207031 0.25013384222984314 0.7429183 0.5767821073532104 True -8 24687 30.4590106010437 0.6235172748565674 176.66207885742188 0.5169082880020142 287.8594970703125 0.2517460882663727 0.7474371 0.5481236577033997 True -9 27430 30.393505096435547 14.371250867843628 186.66336059570312 0.5547047853469849 287.4881591796875 0.25314608216285706 0.7490413 0.5377151370048523 True -10 30173 30.43960666656494 0.6617422103881836 169.46231079101562 0.4631689190864563 286.9497985839844 0.25464507937431335 0.7573562 0.5209184288978577 True -11 32916 30.555082321166992 0.6398663520812988 155.67910766601562 0.637965202331543 286.2652893066406 0.25721052289009094 0.7669132 0.48627522587776184 True -12 35659 30.89335823059082 0.6451506614685059 194.5391082763672 0.4444607198238373 285.93768310546875 0.2578980326652527 0.7739048 0.4643484652042389 True -13 38402 31.000057697296143 9.360951900482178 189.50103759765625 0.44887426495552063 285.06243896484375 0.2613358795642853 0.7807247 0.4282917380332947 True -14 41145 30.463355541229248 1.0386428833007812 189.92996215820312 0.4124745726585388 284.75030517578125 0.26231008768081665 0.78778225 0.3898187279701233 True -15 43888 30.524218797683716 0.6348409652709961 209.27691650390625 0.34374040365219116 284.15814208984375 0.26476380228996277 0.7976665 0.3552590012550354 True -16 46631 30.425828456878662 0.6105809211730957 205.5674591064453 0.31741952896118164 284.2115783691406 0.2640892565250397 0.8002839 0.33356913924217224 True -17 49374 30.29768705368042 0.6285631656646729 187.35910034179688 0.35611987113952637 284.25909423828125 0.2637513279914856 0.8033893 0.3169645667076111 True -18 52117 29.911911964416504 28.348070859909058 158.07472229003906 0.22131726145744324 284.2005615234375 0.26403623819351196 0.8021974 0.31120023131370544 False -19 54860 30.014188289642334 0.728710412979126 209.37680053710938 0.3092118501663208 284.5002746582031 0.2627517879009247 0.80254513 0.31260597705841064 False diff --git a/ENCSR871APX/cherimoya.fold_1.performance.tsv b/ENCSR871APX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 623b3e187deabb25d362757ece18c1ba26da470e..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -284.25909423828125 0.5023725628852844 0.2637513279914856 0.07335720211267471 0.803389310836792 0.7529497742652893 0.3169645667076111 \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_2.evaluate.json b/ENCSR871APX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 56ee687583ce54658615f3254322352c30f188cd..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF548WMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_2.fit.json b/ENCSR871APX/cherimoya.fold_2.fit.json deleted file mode 100644 index cec49755c1f0c40179ad2bc9d85bac3c57f7c70d..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF548WMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_2.log b/ENCSR871APX/cherimoya.fold_2.log deleted file mode 100644 index 46ab618a7670e05e718e181b7dc15bdf7622961e..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.948874950408936 3.4334630966186523 234.64747619628906 0.6349383592605591 276.9402160644531 0.16087035834789276 0.59520763 2.551589012145996 True -1 5794 32.236286640167236 0.6657445430755615 198.77804565429688 0.7923535108566284 264.2516784667969 0.2153470814228058 0.6874272 0.9955249428749084 True -2 8691 32.18082308769226 0.5332891941070557 193.23544311523438 0.8068717122077942 261.8202209472656 0.22139734029769897 0.69809777 0.7457468509674072 True -3 11588 32.1837944984436 0.5180602073669434 198.69158935546875 0.5277762413024902 260.312744140625 0.22414754331111908 0.7085268 0.5765976309776306 True -4 14485 32.20412063598633 0.5079789161682129 194.76654052734375 0.4773346483707428 259.1089782714844 0.2294565886259079 0.7138892 0.5461146235466003 True -5 17382 32.12358212471008 0.5240561962127686 215.32427978515625 0.47720929980278015 258.0862121582031 0.2343454360961914 0.7189247 0.5659230351448059 True -6 20279 32.10640740394592 0.5263543128967285 206.010009765625 0.599647581577301 257.8844909667969 0.23541663587093353 0.720687 0.5298513174057007 True -7 23176 32.08200025558472 0.5354268550872803 170.91590881347656 0.4417685270309448 257.4683837890625 0.23697946965694427 0.725361 0.5176675915718079 True -8 26073 32.11803364753723 0.5280711650848389 223.57154846191406 0.42518049478530884 257.1112976074219 0.23859594762325287 0.729712 0.49988460540771484 True -9 28970 32.152015924453735 0.529923677444458 209.07603454589844 0.3845682144165039 256.8311462402344 0.23955073952674866 0.734232 0.4718760848045349 True -10 31867 32.11143398284912 0.5271966457366943 205.56040954589844 0.47734448313713074 256.6437683105469 0.24021553993225098 0.7397999 0.4562841057777405 True -11 34764 32.17952013015747 0.5221066474914551 207.44805908203125 0.3152734935283661 256.1473083496094 0.24210458993911743 0.7423108 0.4173068106174469 True -12 37661 32.1660532951355 0.5272719860076904 214.00535583496094 0.3717957139015198 255.33155822753906 0.2458207756280899 0.7495218 0.4129239320755005 True -13 40558 32.17089343070984 0.5267593860626221 193.86529541015625 0.434805303812027 254.7708282470703 0.24735614657402039 0.7538161 0.38861367106437683 True -14 43455 32.139973878860474 0.5276734828948975 201.47988891601562 0.33327433466911316 254.49786376953125 0.2485257089138031 0.75819194 0.3684994876384735 True -15 46352 31.89189314842224 0.5249958038330078 218.78952026367188 0.320521742105484 254.24395751953125 0.2488221675157547 0.76593393 0.3320033550262451 True -16 49249 31.57995843887329 0.5222113132476807 189.59510803222656 0.27161705493927 254.03919982910156 0.25047415494918823 0.769804 0.3146122395992279 True -17 52146 31.521559715270996 0.5156543254852295 214.04078674316406 0.19429554045200348 253.9320068359375 0.25064659118652344 0.7729328 0.3055253028869629 True -18 55043 31.60269522666931 0.5278182029724121 202.7939910888672 0.2967374622821808 253.84153747558594 0.2508685290813446 0.7734116 0.30439966917037964 True -19 57940 31.751653909683228 1.3310184478759766 171.70330810546875 0.28934210538864136 254.11566162109375 0.2493419051170349 0.7727917 0.3046404719352722 False diff --git a/ENCSR871APX/cherimoya.fold_2.performance.tsv b/ENCSR871APX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index af1ed4c2d661273ca37d9512d63df822b1f212f6..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -253.84153747558594 0.5156173706054688 0.2508684992790222 0.06475107371807098 0.7734115719795227 0.7158347964286804 0.30439966917037964 \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_3.evaluate.json b/ENCSR871APX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5aec86cb2582367ba009512021c738b1d6f727fe..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF548WMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_3.fit.json b/ENCSR871APX/cherimoya.fold_3.fit.json deleted file mode 100644 index fa2319e34c1c557ca87a67d27d30ca18c9b61512..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF548WMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_3.log b/ENCSR871APX/cherimoya.fold_3.log deleted file mode 100644 index 5b257018b4f8de295acc50fa8659b43ccc6e473b..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2774 35.503689765930176 4.285162687301636 193.97042846679688 0.6566646099090576 286.55450439453125 0.1593935340642929 0.60593295 2.729318857192993 True -1 5548 30.838023900985718 0.599785327911377 225.49844360351562 0.5134692192077637 275.4917297363281 0.2061116248369217 0.68185556 0.8758241534233093 True -2 8322 30.783473253250122 0.590341329574585 219.49322509765625 0.4810454845428467 271.4542541503906 0.2224772423505783 0.6931912 0.6503790616989136 True -3 11096 30.823947429656982 0.557758092880249 207.74472045898438 0.6205098628997803 270.2957458496094 0.22445864975452423 0.6964242 0.4603777527809143 True -4 13870 30.799135208129883 1.9890480041503906 205.7926025390625 0.5979276299476624 269.6201171875 0.22641150653362274 0.70092636 0.4679267704486847 True -5 16644 30.870134353637695 0.5570166110992432 223.96261596679688 0.5261996388435364 268.6473693847656 0.22995570302009583 0.7051906 0.5037013292312622 True -6 19418 30.86715316772461 0.5699868202209473 213.5955810546875 0.6298120617866516 268.2702941894531 0.23180070519447327 0.710198 0.4944859743118286 True -7 22192 30.83901572227478 0.5766010284423828 198.354248046875 0.6231034398078918 267.67926025390625 0.23416686058044434 0.71699303 0.49478650093078613 True -8 24966 30.828611612319946 0.5818197727203369 195.61776733398438 0.5140504837036133 267.55413818359375 0.2351231575012207 0.72034204 0.518196165561676 True -9 27740 30.82427215576172 1.7154364585876465 226.3817596435547 0.3896216154098511 267.0317687988281 0.2373238354921341 0.72542405 0.5005918741226196 True -10 30514 30.944233894348145 0.585350513458252 186.50376892089844 0.44999122619628906 266.6453552246094 0.23887105286121368 0.72864014 0.5090665221214294 True -11 33288 30.841465950012207 0.5826199054718018 225.17652893066406 0.6044017672538757 266.0881042480469 0.24140994250774384 0.73833525 0.4973786473274231 True -12 36062 30.841026067733765 0.5844199657440186 195.64239501953125 0.48750412464141846 265.9746398925781 0.24131813645362854 0.74715316 0.4550371766090393 True -13 38836 30.825714588165283 1.0036756992340088 189.8568572998047 0.3439803123474121 265.3467712402344 0.24383544921875 0.7566958 0.42663806676864624 True -14 41610 30.324825286865234 1.4114816188812256 203.66506958007812 0.28312984108924866 264.8387145996094 0.24606551229953766 0.7619024 0.39909952878952026 True -15 44384 30.225260734558105 0.5862374305725098 228.4898223876953 0.39390289783477783 264.733642578125 0.24661996960639954 0.7703217 0.36561912298202515 True -16 47158 30.276521682739258 0.5715999603271484 196.48745727539062 0.35398292541503906 264.69415283203125 0.24630050361156464 0.77389205 0.3344920873641968 True -17 49932 30.240773677825928 0.573925256729126 200.61978149414062 0.4144758880138397 264.710205078125 0.24584843218326569 0.7787979 0.3189137279987335 True -18 52706 30.2428617477417 0.5632081031799316 182.62936401367188 0.3739813268184662 264.69464111328125 0.24636521935462952 0.77988225 0.30889657139778137 True -19 55480 30.36099100112915 0.5959804058074951 183.21743774414062 0.28837910294532776 264.91436767578125 0.24536095559597015 0.7781282 0.31024837493896484 False diff --git a/ENCSR871APX/cherimoya.fold_3.performance.tsv b/ENCSR871APX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 45a50a080769b1e8eae77f03c59401d745e161b7..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -264.69464111328125 0.5146684050559998 0.24636520445346832 0.06827547401189804 0.7798822522163391 0.716695249080658 0.30889657139778137 \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_4.evaluate.json b/ENCSR871APX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 308506cabe8a8fcc0f515bc82491572d3c61a3cf..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF548WMA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_4.fit.json b/ENCSR871APX/cherimoya.fold_4.fit.json deleted file mode 100644 index 24661ff99313b74d65c9f2cf3db0f841767aab05..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF548WMA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR871APX/cherimoya.fold_4.log b/ENCSR871APX/cherimoya.fold_4.log deleted file mode 100644 index a37311b4ca23950060a77036b28aaf29b8d570a8..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2861 36.42823672294617 4.211076736450195 207.5909881591797 0.5826196670532227 270.4707336425781 0.15708263218402863 0.5913439 2.035288095474243 True -1 5722 31.896636724472046 13.703626155853271 218.27212524414062 0.4899367690086365 260.37188720703125 0.20390833914279938 0.6817284 0.8247748613357544 True -2 8583 31.831170320510864 0.6975157260894775 207.63478088378906 0.7282750606536865 256.92059326171875 0.21580307185649872 0.69832927 0.5000945329666138 True -3 11444 31.81514620780945 0.6134035587310791 217.85400390625 0.531467854976654 256.05926513671875 0.2177669107913971 0.70368135 0.45673248171806335 True -4 14305 31.75986075401306 0.9038035869598389 223.5926971435547 0.3778614401817322 255.1369171142578 0.2227858453989029 0.7087823 0.47132304310798645 True -5 17166 31.737595319747925 10.40899133682251 166.9488067626953 0.7214767932891846 255.2076873779297 0.22147393226623535 0.7108857 0.5009760856628418 True -6 20027 31.794556856155396 1.3874809741973877 219.4863739013672 0.43392565846443176 254.68988037109375 0.22417351603507996 0.7162484 0.5061066746711731 True -7 22888 31.8008394241333 11.727531671524048 223.21652221679688 0.5758968591690063 254.47645568847656 0.22506313025951385 0.7171358 0.5002632141113281 True -8 25749 31.834439516067505 5.894861459732056 192.13775634765625 0.4155998229980469 253.8440399169922 0.22772417962551117 0.7210533 0.48772090673446655 True -9 28610 31.762598037719727 0.6306724548339844 224.14556884765625 0.5163530111312866 253.76998901367188 0.22814281284809113 0.723308 0.48501989245414734 True -10 31471 31.77526617050171 0.6399054527282715 182.90997314453125 0.4214903712272644 252.87460327148438 0.23285715281963348 0.7304507 0.46824225783348083 True -11 34332 31.810843467712402 0.6181254386901855 200.33816528320312 0.3832181692123413 252.52101135253906 0.23472151160240173 0.7342156 0.42053255438804626 True -12 37193 31.85406184196472 0.6161036491394043 186.97581481933594 0.32376909255981445 252.2845458984375 0.23533807694911957 0.7387486 0.404018759727478 True -13 40054 31.350553512573242 0.6028788089752197 206.375732421875 0.6756709814071655 251.572998046875 0.2386387586593628 0.7452283 0.3660317361354828 True -14 42915 31.122291564941406 0.5995738506317139 228.38644409179688 0.2085535228252411 251.3812255859375 0.23885494470596313 0.7532542 0.3453071713447571 True -15 45776 31.19169569015503 0.5998134613037109 205.6962890625 0.27239686250686646 251.39691162109375 0.23875336349010468 0.75927895 0.32112061977386475 True -16 48637 31.174471378326416 0.5999374389648438 207.88055419921875 0.24922579526901245 251.35687255859375 0.23916536569595337 0.7628598 0.3087477385997772 True -17 51498 31.19737672805786 0.7353420257568359 215.37063598632812 0.26072144508361816 251.0663604736328 0.24071089923381805 0.76452315 0.29699623584747314 True -18 54359 31.171815633773804 0.6028547286987305 207.16940307617188 0.24982097744941711 251.25054931640625 0.2398327738046646 0.7656593 0.2911642789840698 True -19 57220 31.13032627105713 0.6132161617279053 163.54440307617188 0.20387665927410126 250.98439025878906 0.24175262451171875 0.7616323 0.29497623443603516 False diff --git a/ENCSR871APX/cherimoya.fold_4.performance.tsv b/ENCSR871APX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9ac3fc1ef76075414c126fa239481d10e4e4bc96..0000000000000000000000000000000000000000 --- a/ENCSR871APX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -251.25054931640625 0.520332932472229 0.2398327887058258 0.06600802391767502 0.7656592726707458 0.7017262578010559 0.2911642789840698 \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_0.evaluate.json b/ENCSR872MAO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1d76c5e2c7e8e2e7662cdda73d3d845ef10d234d..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029JFA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_0.fit.json b/ENCSR872MAO/cherimoya.fold_0.fit.json deleted file mode 100644 index 49329f0110b6e7a31c5456d8fc1369ce525a46b8..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF029JFA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_0.log b/ENCSR872MAO/cherimoya.fold_0.log deleted file mode 100644 index cad5860919d32d8d70afa98bc4fac1ef8233682d..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1294 17.784839630126953 3.2243783473968506 281.21124267578125 0.4774489998817444 412.2013244628906 0.39986559748649597 0.71606135 16.18634605407715 True -1 2588 14.398598432540894 0.2540261745452881 294.93701171875 0.3877512812614441 353.1989440917969 0.47281983494758606 0.78410727 4.609587669372559 True -2 3882 14.392709255218506 0.24198484420776367 271.6070556640625 0.38996827602386475 331.9650573730469 0.5170878171920776 0.80753696 1.222409725189209 True -3 5176 14.405209064483643 0.2416698932647705 266.8538513183594 0.3986436128616333 320.9511413574219 0.539333701133728 0.82378477 0.4337431490421295 True -4 6470 14.387753009796143 0.24117016792297363 265.34716796875 0.3955708146095276 317.5847473144531 0.5475612878799438 0.82970446 0.29449620842933655 True -5 7764 14.392359018325806 0.24726653099060059 258.7318115234375 0.39247381687164307 316.1239013671875 0.5511838793754578 0.8345282 0.25721314549446106 True -6 9058 14.39518141746521 10.87445616722107 266.2099914550781 0.2540269196033478 315.1822509765625 0.5533968806266785 0.83514017 0.2394990622997284 True -7 10352 14.531879901885986 0.24758362770080566 264.271484375 0.23705750703811646 314.6097412109375 0.5550000071525574 0.8361355 0.2381572425365448 True -8 11646 14.39572787284851 0.2418196201324463 304.1860046386719 0.28102821111679077 314.0366516113281 0.5566906929016113 0.83923143 0.23540735244750977 True -9 12940 14.39201831817627 0.24233388900756836 266.40093994140625 0.23228026926517487 313.4832458496094 0.5581998825073242 0.84114033 0.23384828865528107 True -10 14234 14.382760286331177 0.25913381576538086 289.2955017089844 0.18608194589614868 313.1280517578125 0.5593830943107605 0.84363204 0.22496362030506134 True -11 15528 14.131577491760254 0.24321269989013672 243.59225463867188 0.17782136797904968 312.61883544921875 0.5606672763824463 0.84682935 0.22340665757656097 True -12 16822 14.08902359008789 0.24068999290466309 255.38511657714844 0.16887083649635315 312.4293518066406 0.5612550973892212 0.85105515 0.21715843677520752 True -13 18116 14.084092855453491 0.24036121368408203 265.177978515625 0.21397076547145844 312.3035583496094 0.5615670680999756 0.857311 0.21228234469890594 True -14 19410 14.094567775726318 0.25599026679992676 304.557861328125 0.16540470719337463 312.2951354980469 0.5615075826644897 0.8552948 0.21470825374126434 False -15 20704 14.121146440505981 1.0812268257141113 241.83349609375 0.1588362604379654 312.6593017578125 0.5606075525283813 0.85619736 0.2163865566253662 False -16 21998 14.09425687789917 0.2471606731414795 252.04385375976562 0.20124559104442596 313.1656799316406 0.5590922832489014 0.8551029 0.22367098927497864 False -17 23292 14.117894649505615 10.245526552200317 275.263427734375 0.11666975170373917 313.761474609375 0.5573444962501526 0.8544793 0.23250709474086761 False -18 24586 15.061742305755615 0.2492692470550537 237.6332244873047 0.1264670193195343 314.3012390136719 0.555666446685791 0.8512128 0.2394513189792633 False -19 25880 14.087403059005737 0.24675416946411133 253.96875 0.11415529996156693 314.6782531738281 0.5544978380203247 0.848378 0.24410955607891083 False diff --git a/ENCSR872MAO/cherimoya.fold_0.performance.tsv b/ENCSR872MAO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 94cf3745ce37b8340af7e1bc27ad963dc1feb0bb..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -312.3035583496094 0.34114137291908264 0.5615670680999756 0.20748865604400635 0.8573110103607178 0.8288712501525879 0.21228234469890594 \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_1.evaluate.json b/ENCSR872MAO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 75a2cadc695c39d25858c8ca47b88e78ea071619..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029JFA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_1.fit.json b/ENCSR872MAO/cherimoya.fold_1.fit.json deleted file mode 100644 index c8ecf3d8df0ca037af6704022a2e5120dfd80514..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF029JFA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_1.log b/ENCSR872MAO/cherimoya.fold_1.log deleted file mode 100644 index 62c0dcc54242212f133e53ce1dc1e9ddf9f643ec..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1270 17.511760234832764 3.2884442806243896 298.5714111328125 0.524081826210022 464.2154541015625 0.42036524415016174 0.6368069 17.494638442993164 True -1 2540 14.153050422668457 0.37866878509521484 258.8721618652344 0.37704387307167053 391.5176696777344 0.5007163286209106 0.73949116 5.313427448272705 True -2 3810 14.125161409378052 0.36835670471191406 267.34381103515625 0.45597782731056213 370.6343994140625 0.5411867499351501 0.7707128 1.456379771232605 True -3 5080 14.117044925689697 0.3722085952758789 263.2646179199219 0.314270943403244 358.34228515625 0.5681161284446716 0.7949263 0.5508683919906616 True -4 6350 14.071813821792603 14.573527812957764 247.96395874023438 0.282414972782135 353.3443603515625 0.5789868831634521 0.8081084 0.35127443075180054 True -5 7620 14.268522262573242 0.3691749572753906 246.21484375 0.20744949579238892 351.0606994628906 0.5839194655418396 0.8169415 0.26647263765335083 True -6 8890 14.09184741973877 0.363950252532959 261.2401428222656 0.44741135835647583 350.1224670410156 0.5863465666770935 0.8204129 0.25719329714775085 True -7 10160 14.081207036972046 0.3613770008087158 281.98583984375 0.35393738746643066 349.1384582519531 0.588660717010498 0.8264724 0.24852097034454346 True -8 11430 14.093441486358643 1.6665902137756348 217.12545776367188 0.33246999979019165 348.5744323730469 0.5902637839317322 0.8281146 0.24509280920028687 True -9 12700 14.207465648651123 0.3709867000579834 273.6109619140625 0.34172746539115906 347.85498046875 0.5917910933494568 0.8323242 0.23917017877101898 True -10 13970 14.074557304382324 0.36929988861083984 270.37078857421875 0.23812025785446167 347.5291748046875 0.5928524732589722 0.83905524 0.22833426296710968 True -11 15240 14.08515477180481 0.3686401844024658 246.51394653320312 0.2587451934814453 346.9681396484375 0.5941806435585022 0.84341973 0.2223159372806549 True -12 16510 14.072947978973389 0.3577086925506592 287.213134765625 0.32271596789360046 346.6491394042969 0.594954788684845 0.84904706 0.21755675971508026 True -13 17780 14.055084466934204 0.3642895221710205 265.4853820800781 0.19598883390426636 346.42236328125 0.5954101085662842 0.85146195 0.22134298086166382 True -14 19050 14.080689907073975 0.363375186920166 255.24850463867188 0.21102318167686462 346.5201110839844 0.5949892401695251 0.85424376 0.22022143006324768 True -15 20320 14.070289611816406 0.7902421951293945 250.54476928710938 0.16726425290107727 346.94683837890625 0.5939343571662903 0.85431504 0.2217404693365097 True -16 21590 13.867480516433716 0.3567843437194824 233.21469116210938 0.17234277725219727 347.4570617675781 0.5921546816825867 0.85362077 0.22679543495178223 False -17 22860 13.79089069366455 0.36081790924072266 295.97320556640625 0.09696220606565475 348.05291748046875 0.590258777141571 0.8529689 0.23584796488285065 False -18 24130 13.828706741333008 0.35405588150024414 272.2279357910156 0.13648498058319092 348.781494140625 0.5883549451828003 0.8499106 0.24287115037441254 False -19 25400 13.795798540115356 0.36089134216308594 275.368896484375 0.09282074123620987 349.17535400390625 0.5871659517288208 0.84850305 0.2474670559167862 False diff --git a/ENCSR872MAO/cherimoya.fold_1.performance.tsv b/ENCSR872MAO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ee5b802a06943b12d500ec8920a4592da7730860..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -346.94683837890625 0.3163708448410034 0.5939343571662903 0.23319193720817566 0.8543150424957275 0.8542786836624146 0.2217404693365097 \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_2.evaluate.json b/ENCSR872MAO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9e2ee60d4297c21786cd48ac657b8c3d85a4f831..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029JFA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_2.fit.json b/ENCSR872MAO/cherimoya.fold_2.fit.json deleted file mode 100644 index b368ff521c933a66804a50834aadd4cdfca92c62..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF029JFA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_2.log b/ENCSR872MAO/cherimoya.fold_2.log deleted file mode 100644 index c8b5cbafe85d1ff152c1c30054521b35a6029aed..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1358 18.575279474258423 3.194348096847534 282.69287109375 0.38392502069473267 431.9610290527344 0.41297611594200134 0.66664165 15.77481460571289 True -1 2716 14.958201169967651 0.2798628807067871 274.3910217285156 0.5426911115646362 369.7724609375 0.489300012588501 0.76486284 4.407660007476807 True -2 4074 15.0576753616333 0.26490211486816406 239.27037048339844 0.3792189955711365 348.6255798339844 0.5317413806915283 0.79904145 1.083034873008728 True -3 5432 14.961583375930786 1.7430462837219238 256.7716064453125 0.48909902572631836 338.1130065917969 0.5559038519859314 0.81280965 0.4521264433860779 True -4 6790 14.94644284248352 0.2640402317047119 254.20843505859375 0.2591627836227417 334.2594909667969 0.5637531876564026 0.8230721 0.33321064710617065 True -5 8148 14.965174674987793 7.30600380897522 254.30519104003906 0.350279301404953 332.6977844238281 0.567345380783081 0.8281223 0.2766195237636566 True -6 9506 15.030736923217773 0.2597615718841553 262.87493896484375 0.23150724172592163 331.72747802734375 0.569907546043396 0.83214235 0.2557748258113861 True -7 10864 14.928470611572266 0.2595963478088379 268.50921630859375 0.35499101877212524 331.1522521972656 0.571470320224762 0.8345825 0.24820667505264282 True -8 12222 14.950713872909546 0.30887913703918457 270.8580322265625 0.2574707269668579 330.72027587890625 0.5725507736206055 0.8378612 0.2352747768163681 True -9 13580 14.969932079315186 0.260392427444458 278.7991943359375 0.30384573340415955 330.0014343261719 0.5737744569778442 0.84222907 0.2293807864189148 True -10 14938 14.993747234344482 0.26263928413391113 296.05902099609375 0.19343264400959015 329.7037658691406 0.5749238729476929 0.84397584 0.22548820078372955 True -11 16296 14.922451257705688 0.2606523036956787 233.79660034179688 0.19443155825138092 329.2708435058594 0.5761538147926331 0.8494628 0.220910906791687 True -12 17654 14.943864107131958 0.2625761032104492 270.2347106933594 0.25172239542007446 328.8052062988281 0.5770812630653381 0.8508279 0.2153540551662445 True -13 19012 14.932007312774658 0.2607717514038086 243.93165588378906 0.17580746114253998 328.5458679199219 0.5774880051612854 0.8547327 0.216071218252182 True -14 20370 15.021400213241577 0.2675025463104248 258.18695068359375 0.13667570054531097 328.6736145019531 0.5772650241851807 0.8558119 0.21621821820735931 True -15 21728 14.978810787200928 1.8761579990386963 266.30963134765625 0.1713387668132782 328.67645263671875 0.5763580203056335 0.8568836 0.21910808980464935 True -16 23086 14.982972383499146 0.26255035400390625 263.10906982421875 0.11469781398773193 329.2047119140625 0.5750399231910706 0.85493755 0.2272253930568695 False -17 24444 14.971447467803955 0.26816725730895996 270.0482177734375 0.18662568926811218 329.8143615722656 0.5731945037841797 0.85343605 0.23829035460948944 False -18 25802 14.971736431121826 0.2619156837463379 275.2838134765625 0.13800491392612457 330.3363952636719 0.5716413259506226 0.85083824 0.24551257491111755 False -19 27160 14.980690717697144 0.2597815990447998 240.08859252929688 0.20478078722953796 330.7038269042969 0.5705936551094055 0.848381 0.2519204914569855 False diff --git a/ENCSR872MAO/cherimoya.fold_2.performance.tsv b/ENCSR872MAO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a399fda05b3d0078025f00f742d440463d9d6646..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -328.67645263671875 0.3289763629436493 0.5763580799102783 0.21931692957878113 0.8568835854530334 0.8450981378555298 0.21910808980464935 \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_3.evaluate.json b/ENCSR872MAO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ac818a552f6f1570bb06ff0432eaf21dd766ce2a..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029JFA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_3.fit.json b/ENCSR872MAO/cherimoya.fold_3.fit.json deleted file mode 100644 index 2ae3e79271ef7944603f4e62b833100e0e0e5db9..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF029JFA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_3.log b/ENCSR872MAO/cherimoya.fold_3.log deleted file mode 100644 index d265b36a2cd51a32799d8ff6597aa5b27cdb9a29..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1330 18.162827253341675 2.749119520187378 289.228515625 0.4260473847389221 426.2249755859375 0.40761104226112366 0.69027877 16.172306060791016 True -1 2660 14.605127811431885 0.24770593643188477 237.07223510742188 0.3149978816509247 361.236328125 0.48665446043014526 0.77728313 4.7404093742370605 True -2 3990 14.658718824386597 0.2454826831817627 267.0574645996094 0.3958687484264374 343.36932373046875 0.5255656838417053 0.807823 1.191017508506775 True -3 5320 14.612435579299927 0.2455763816833496 257.08685302734375 0.30549007654190063 333.590576171875 0.5477871894836426 0.8189716 0.4399664103984833 True -4 6650 14.601428270339966 1.2320737838745117 277.8328552246094 0.212914377450943 329.7568054199219 0.555929958820343 0.8328935 0.34494102001190186 True -5 7980 14.642627000808716 0.2523655891418457 267.9736328125 0.24368877708911896 328.2572937011719 0.5592993497848511 0.83543134 0.2840547263622284 True -6 9310 14.635137557983398 0.24926233291625977 257.5545959472656 0.2937644124031067 327.42376708984375 0.5610655546188354 0.8384048 0.2585996985435486 True -7 10640 14.633738279342651 0.2510802745819092 238.2836456298828 0.27879369258880615 326.78680419921875 0.5627409815788269 0.8375391 0.25260451436042786 False -8 11970 14.63321304321289 0.23882389068603516 271.6561584472656 0.3819340467453003 326.22442626953125 0.5644689202308655 0.8369276 0.24888138473033905 False -9 13300 14.63086724281311 1.160118579864502 212.60296630859375 0.26829829812049866 325.7276306152344 0.5659497976303101 0.8398771 0.24266400933265686 True -10 14630 14.638281345367432 0.2477436065673828 267.810302734375 0.2471867948770523 325.0621643066406 0.567423403263092 0.8380763 0.24459891021251678 False -11 15960 14.621143341064453 0.23944687843322754 275.50665283203125 0.23567646741867065 324.6742248535156 0.5686030387878418 0.84291255 0.24094268679618835 True -12 17290 14.615433931350708 0.23882007598876953 280.53704833984375 0.12721741199493408 324.64166259765625 0.5689589381217957 0.84621036 0.24164816737174988 True -13 18620 14.626102924346924 0.2429819107055664 264.8544921875 0.20875674486160278 324.412109375 0.5696617364883423 0.8499218 0.2418643832206726 True -14 19950 14.612154722213745 9.764263153076172 262.4277648925781 0.18389679491519928 324.5412292480469 0.5696150064468384 0.84994423 0.24280908703804016 True -15 21280 14.657451391220093 7.642455816268921 308.462646484375 0.16259333491325378 324.8821105957031 0.568594753742218 0.8511612 0.24431441724300385 True -16 22610 14.637056827545166 0.23712420463562012 217.21261596679688 0.22781528532505035 325.37384033203125 0.5672542452812195 0.8485017 0.25119608640670776 False -17 23940 14.34864091873169 0.23869109153747559 244.57269287109375 0.0996149554848671 325.9773254394531 0.565510094165802 0.84799725 0.25962457060813904 False -18 25270 14.342446565628052 0.9136579036712646 263.4173583984375 0.10539360344409943 326.5315856933594 0.5637902617454529 0.8439737 0.2691786587238312 False -19 26600 14.352535009384155 0.24203205108642578 256.1718444824219 0.22524261474609375 326.8349914550781 0.5627149343490601 0.84298164 0.2729202210903168 False diff --git a/ENCSR872MAO/cherimoya.fold_3.performance.tsv b/ENCSR872MAO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b2490b0488ac799a338e3e777f798b4ed21ed087..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.8821105957031 0.3342245817184448 0.5685946941375732 0.21334877610206604 0.8511611819267273 0.8430340886116028 0.24431441724300385 \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_4.evaluate.json b/ENCSR872MAO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 36a67d958b62fca61a225fa8466aa001c0f6378e..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF029JFA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_4.fit.json b/ENCSR872MAO/cherimoya.fold_4.fit.json deleted file mode 100644 index aa3e2f653405ed9a94c47afb7ed8315b6b2fb65f..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF029JFA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872MAO/cherimoya.fold_4.log b/ENCSR872MAO/cherimoya.fold_4.log deleted file mode 100644 index d3e01caa6947e01931801add6a73b3099a64760c..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1313 17.92759108543396 3.1556172370910645 270.68121337890625 0.3788634240627289 412.7586975097656 0.4051375091075897 0.7011139 16.129379272460938 True -1 2626 14.445382595062256 0.2857818603515625 280.631591796875 0.5599143505096436 353.6071472167969 0.47864484786987305 0.7868837 4.17093563079834 True -2 3939 14.433256387710571 0.24117207527160645 261.2998352050781 0.5075953006744385 334.61627197265625 0.5174888372421265 0.8089181 1.178112506866455 True -3 5252 14.449746131896973 0.2441720962524414 260.844970703125 0.3008970022201538 323.96142578125 0.5415470600128174 0.82957846 0.48015856742858887 True -4 6565 14.410888195037842 0.2404320240020752 235.74647521972656 0.366985559463501 320.8345642089844 0.5491707921028137 0.83388346 0.30358147621154785 True -5 7878 14.46069860458374 0.24884796142578125 233.772216796875 0.3524027168750763 319.07379150390625 0.5533509254455566 0.8351445 0.2524368464946747 True -6 9191 14.443176031112671 0.8470768928527832 307.3837585449219 0.30367618799209595 318.0260925292969 0.5561180710792542 0.8375734 0.24683009088039398 True -7 10504 14.434306144714355 0.24315786361694336 262.2921447753906 0.23709793388843536 317.2925109863281 0.557915449142456 0.8433667 0.2315807342529297 True -8 11817 14.427140474319458 0.2467207908630371 261.0289306640625 0.2819117307662964 316.7145690917969 0.5594569444656372 0.84127426 0.2361014038324356 False -9 13130 14.446388721466064 0.24336671829223633 225.00103759765625 0.28226161003112793 316.1534729003906 0.5608421564102173 0.84452647 0.2334001213312149 True -10 14443 14.445667028427124 0.2427511215209961 282.12908935546875 0.22852358222007751 315.7098083496094 0.5619864463806152 0.84855646 0.2261076122522354 True -11 15756 14.451930284500122 0.24295616149902344 240.83450317382812 0.379895955324173 315.4551696777344 0.5628361701965332 0.85204506 0.22543516755104065 True -12 17069 14.417503595352173 0.24675965309143066 249.93182373046875 0.18793489038944244 315.2572021484375 0.5634120106697083 0.85273737 0.2300797700881958 True -13 18382 14.409858703613281 0.24518227577209473 250.2367706298828 0.15797191858291626 315.113525390625 0.5637111663818359 0.857711 0.22381025552749634 True -14 19695 14.439579010009766 0.24413394927978516 229.42718505859375 0.23099049925804138 315.1341247558594 0.5634881258010864 0.86044586 0.22104328870773315 True -15 21008 14.441625595092773 7.53371524810791 245.93417358398438 0.12368637323379517 315.37359619140625 0.5627762675285339 0.86139417 0.22403079271316528 True -16 22321 14.456522703170776 0.24209308624267578 242.23158264160156 0.1618615686893463 315.82220458984375 0.5611684918403625 0.8630201 0.22310850024223328 True -17 23634 14.439407587051392 0.2395002841949463 243.53567504882812 0.2004319131374359 316.4604187011719 0.5593530535697937 0.86222905 0.2239019125699997 False -18 24947 14.451873540878296 0.2438521385192871 216.48373413085938 0.13266421854496002 316.9429931640625 0.5577898621559143 0.86084944 0.22886979579925537 False -19 26260 14.43988847732544 0.24264764785766602 218.292236328125 0.11738824844360352 317.3567810058594 0.556700587272644 0.8600481 0.2326786071062088 False diff --git a/ENCSR872MAO/cherimoya.fold_4.performance.tsv b/ENCSR872MAO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 53dfa5a73eaec3e79ff556c7cd3f572399dbdf63..0000000000000000000000000000000000000000 --- a/ENCSR872MAO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -315.82220458984375 0.33954402804374695 0.5611684918403625 0.20719340443611145 0.863020122051239 0.8371809720993042 0.22310850024223328 \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_0.evaluate.json b/ENCSR872WGW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c878c7629d684f90772f078168591571beeb9f0a..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF977JQR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_0.fit.json b/ENCSR872WGW/cherimoya.fold_0.fit.json deleted file mode 100644 index e0f3bcb74c9d0081498ca8f456485a7e22cebdff..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF977JQR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_0.log b/ENCSR872WGW/cherimoya.fold_0.log deleted file mode 100644 index 19e2e307d4ec06391918d597da6ce7010125b9dc..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2985 36.85639214515686 3.4989044666290283 522.3424682617188 1.1159710884094238 764.3359375 0.5894612073898315 0.65752894 10.301891326904297 True -1 5970 32.96758270263672 0.6299271583557129 462.80645751953125 1.0071017742156982 615.8405151367188 0.7234197854995728 0.66755766 2.4182369709014893 True -2 8955 32.94467234611511 0.6123669147491455 471.4507141113281 0.8738670349121094 595.84619140625 0.7365675568580627 0.6769041 1.4402315616607666 True -3 11940 32.995575189590454 0.6161665916442871 519.6488037109375 0.8469151258468628 589.3697509765625 0.7436370253562927 0.68256474 1.254677414894104 True -4 14925 32.91504263877869 0.6504347324371338 468.39801025390625 1.1771392822265625 585.4837646484375 0.7476850748062134 0.68034804 1.2924481630325317 False -5 17910 32.958491563797 0.609581708908081 488.2193298339844 0.5186505913734436 582.07861328125 0.7510151863098145 0.6783064 1.2233831882476807 False -6 20895 32.934274196624756 0.6137068271636963 473.35223388671875 0.7002093195915222 580.32470703125 0.753206729888916 0.6796998 1.1261262893676758 False -7 23880 32.89436721801758 1.0212082862854004 443.1516418457031 0.5500679016113281 576.6179809570312 0.7563863396644592 0.68756026 1.016717553138733 True -8 26865 32.998618602752686 0.8611581325531006 465.988525390625 1.128900170326233 573.9771728515625 0.7588004469871521 0.6860618 0.9486539959907532 False -9 29850 32.89609408378601 0.6130456924438477 380.639404296875 0.6329909563064575 570.7421264648438 0.7616154551506042 0.69520694 0.9521598815917969 True -10 32835 32.9052460193634 0.6097733974456787 388.83697509765625 0.7824844121932983 566.8847045898438 0.7642039060592651 0.7045707 0.8698460459709167 True -11 35820 32.8987250328064 0.6121761798858643 462.02386474609375 0.4858015477657318 563.9962768554688 0.7666097283363342 0.7099912 0.8213983774185181 True -12 38805 32.573824882507324 1.6412239074707031 489.1729736328125 0.41396617889404297 560.2001953125 0.7690575122833252 0.72282463 0.7818198204040527 True -13 41790 32.39366292953491 0.6149427890777588 470.3136901855469 0.6065378189086914 558.0263671875 0.7705462574958801 0.73126835 0.7670431733131409 True -14 44775 32.39905524253845 0.6093876361846924 491.70745849609375 0.7044912576675415 556.0485229492188 0.7719138860702515 0.7443942 0.7250691652297974 True -15 47760 32.29905843734741 0.6096236705780029 423.92108154296875 0.43647506833076477 554.7437744140625 0.7725368142127991 0.74838424 0.7287547588348389 True -16 50745 32.2367217540741 0.6075034141540527 487.4791259765625 0.40868645906448364 554.1610107421875 0.7725926041603088 0.7487672 0.7338827252388 True -17 53730 32.28661751747131 0.6110610961914062 454.2235107421875 0.4187982678413391 554.2341918945312 0.7722524404525757 0.7490904 0.7382579445838928 True -18 56715 32.30059361457825 0.6030070781707764 448.47357177734375 0.473488450050354 554.7001953125 0.7716661095619202 0.7433151 0.7659074068069458 False -19 59700 32.60374474525452 0.6150212287902832 427.0501403808594 0.34796667098999023 555.0722045898438 0.7713022232055664 0.7422403 0.7817505598068237 False diff --git a/ENCSR872WGW/cherimoya.fold_0.performance.tsv b/ENCSR872WGW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index adcbdc1b592d39459dc4d6a80a75d2060db9d35d..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -554.2341918945312 0.1969015896320343 0.7722524404525757 0.36648643016815186 0.7490903735160828 0.726166307926178 0.7382579445838928 \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_1.evaluate.json b/ENCSR872WGW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b88e63bf7351a7acac7d733fdffa1858aeac0b8d..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF977JQR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_1.fit.json b/ENCSR872WGW/cherimoya.fold_1.fit.json deleted file mode 100644 index 1727b144c10a0924e7cf5232a8db8ded6a880ca4..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF977JQR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_1.log b/ENCSR872WGW/cherimoya.fold_1.log deleted file mode 100644 index aa734139899b8187cf65d59943ba576e9e48c560..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2907 36.481592893600464 3.692171096801758 500.50213623046875 0.9128856658935547 872.4862060546875 0.5995795726776123 0.6677067 11.667959213256836 True -1 5814 32.026907205581665 0.8700532913208008 488.1736145019531 0.950977623462677 698.9698486328125 0.7386841773986816 0.6759814 2.9475743770599365 True -2 8721 32.09058094024658 0.8628628253936768 422.3580017089844 0.733548641204834 672.9921264648438 0.7515943050384521 0.68779296 1.5761122703552246 True -3 11628 32.0734224319458 0.854994535446167 464.70245361328125 1.2794386148452759 665.7141723632812 0.7579343914985657 0.6787036 1.3533239364624023 False -4 14535 32.013373613357544 0.8595068454742432 388.2742919921875 0.8044921159744263 659.8548583984375 0.7634285688400269 0.67197335 1.2281339168548584 False -5 17442 32.02765440940857 34.662155866622925 458.83966064453125 0.5465316772460938 655.9903564453125 0.7664965391159058 0.6871939 1.19962477684021 False -6 20349 32.105961322784424 7.786501169204712 496.0084533691406 0.8103011846542358 651.4738159179688 0.769369900226593 0.6958695 1.0919817686080933 True -7 23256 32.08036470413208 34.1490638256073 458.08880615234375 0.7190820574760437 648.3171997070312 0.7716749906539917 0.7047044 1.0035779476165771 True -8 26163 32.132084131240845 1.143477201461792 407.0426025390625 0.7471346855163574 645.49755859375 0.774200439453125 0.70865273 0.9855026602745056 True -9 29070 32.09816527366638 0.8700728416442871 482.23529052734375 0.4678024649620056 640.1326904296875 0.777179479598999 0.71920645 0.8979611992835999 True -10 31977 32.112797021865845 0.8707790374755859 459.4227294921875 1.0272276401519775 636.0524291992188 0.7794007658958435 0.71948725 0.8964788913726807 True -11 34884 32.100385904312134 0.8616921901702881 468.85980224609375 0.7644892930984497 632.1222534179688 0.7817202210426331 0.7277484 0.8411332368850708 True -12 37791 31.482842683792114 0.846672534942627 486.7125244140625 0.5635166168212891 627.9529418945312 0.7841832041740417 0.73376775 0.8413984179496765 True -13 40698 31.451783895492554 1.130380630493164 427.7314147949219 0.6037090420722961 625.4288330078125 0.7857077717781067 0.74460125 0.8001700639724731 True -14 43605 31.45973539352417 0.8576252460479736 503.77471923828125 0.6768234372138977 621.6834106445312 0.7874786257743835 0.7518703 0.7730714082717896 True -15 46512 31.48982810974121 0.8659396171569824 477.1717529296875 0.6686891913414001 620.380615234375 0.788097620010376 0.7580432 0.769773542881012 True -16 49419 31.438217401504517 1.1571409702301025 487.4703369140625 0.4430101811885834 619.3270874023438 0.7882590889930725 0.76088125 0.7664780020713806 True -17 52326 31.48777747154236 0.8727376461029053 453.31103515625 0.38514211773872375 619.5413818359375 0.7878870368003845 0.7577158 0.7924677133560181 False -18 55233 31.50169849395752 2.089594841003418 401.43621826171875 0.2654309868812561 620.2254028320312 0.7873716950416565 0.75189996 0.8161966800689697 False -19 58140 31.506624937057495 0.8634583950042725 413.2578125 0.28939110040664673 620.7811279296875 0.7870065569877625 0.74946177 0.8368405103683472 False diff --git a/ENCSR872WGW/cherimoya.fold_1.performance.tsv b/ENCSR872WGW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5035153ffddf01bcd20b7b05d529a219325df90e..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -619.3270874023438 0.1805097758769989 0.788258969783783 0.4007415473461151 0.760881245136261 0.76252281665802 0.7664780020713806 \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_2.evaluate.json b/ENCSR872WGW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 753001f147a8d55e3d7e6028eca769d889547738..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF977JQR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_2.fit.json b/ENCSR872WGW/cherimoya.fold_2.fit.json deleted file mode 100644 index 1b20e7dac802739ec6a1e17fe4f8cfb9b61af465..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF977JQR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_2.log b/ENCSR872WGW/cherimoya.fold_2.log deleted file mode 100644 index 2084396691eacd311bead68201b53e8e0920b193..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3131 38.422441482543945 3.649217128753662 461.72454833984375 1.3010098934173584 774.0562744140625 0.6050568222999573 0.69903654 8.743511199951172 True -1 6262 34.60579013824463 0.6369991302490234 502.7069091796875 0.9546310901641846 636.941162109375 0.7329028844833374 0.6982481 2.0415096282958984 False -2 9393 34.61282014846802 0.6193816661834717 412.37347412109375 0.9882314205169678 618.6635131835938 0.7465654015541077 0.6958077 1.1721986532211304 False -3 12524 34.52114176750183 0.6235804557800293 397.3055419921875 0.6567287445068359 610.3114624023438 0.7538278102874756 0.69210607 1.0172911882400513 False -4 15655 34.553473472595215 0.6194989681243896 410.84478759765625 1.2281138896942139 608.117431640625 0.7563750147819519 0.7014946 0.9195743203163147 True -5 18786 34.685099840164185 2.49416446685791 464.44073486328125 1.396979808807373 605.1989135742188 0.7597731351852417 0.6985279 0.8739493489265442 False -6 21917 34.57701253890991 0.9653129577636719 400.9136657714844 0.77899569272995 601.3480224609375 0.7623916268348694 0.7089863 0.8234509825706482 True -7 25048 34.5658118724823 0.6225714683532715 478.52880859375 1.0209418535232544 599.4496459960938 0.7641580700874329 0.6969821 0.855844259262085 False -8 28179 34.622636795043945 0.6243102550506592 408.5049743652344 0.7347756624221802 596.2421264648438 0.7669631242752075 0.7086701 0.7894724011421204 False -9 31310 34.558143854141235 1.4235997200012207 376.3980712890625 0.7237255573272705 592.6788940429688 0.7692773938179016 0.71325856 0.7782944440841675 True -10 34441 34.39093565940857 0.618908166885376 452.21356201171875 0.6333012580871582 588.4222412109375 0.7717761397361755 0.7278068 0.7374239563941956 True -11 37572 33.91297149658203 0.6217348575592041 506.15093994140625 0.6749805808067322 585.0203247070312 0.7740967273712158 0.734527 0.7150735855102539 True -12 40703 33.951611280441284 0.6178405284881592 414.22601318359375 0.49640411138534546 581.4452514648438 0.7764276266098022 0.75131863 0.6573012471199036 True -13 43834 33.893776178359985 0.6127767562866211 443.683837890625 0.6411674618721008 579.11962890625 0.7782372236251831 0.7565277 0.6597217917442322 True -14 46965 33.83923697471619 0.6185524463653564 366.1717529296875 0.6548428535461426 576.365966796875 0.7798840999603271 0.76474243 0.6371046304702759 True -15 50096 33.89009642601013 0.619957447052002 478.1605529785156 0.49231672286987305 574.9639892578125 0.7805537581443787 0.7724981 0.6243239641189575 True -16 53227 33.944639444351196 0.609691858291626 345.975341796875 0.5207929015159607 574.2725830078125 0.7806640267372131 0.77596986 0.6223737597465515 True -17 56358 33.946755170822144 0.6114296913146973 452.95526123046875 0.3296216130256653 574.5762329101562 0.7801356911659241 0.7718364 0.6372118592262268 False -18 59489 33.89439058303833 1.5094168186187744 463.463623046875 0.2801320552825928 575.2603149414062 0.7794368863105774 0.7697127 0.6523663997650146 False -19 62620 33.91746234893799 1.333742380142212 433.8423156738281 0.21390670537948608 575.7704467773438 0.7791347503662109 0.7662737 0.6614457964897156 False diff --git a/ENCSR872WGW/cherimoya.fold_2.performance.tsv b/ENCSR872WGW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 10142be7afff5f4474033a7f8f48976209fa687c..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -574.2725830078125 0.18973806500434875 0.7806640863418579 0.3805667757987976 0.7759698629379272 0.7641609907150269 0.6223737597465515 \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_3.evaluate.json b/ENCSR872WGW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f0a801c677c46d293f2468bed22cb9162e7a839d..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF977JQR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_3.fit.json b/ENCSR872WGW/cherimoya.fold_3.fit.json deleted file mode 100644 index 09b43bcb77ff13776278ca4acda02dfabb18b505..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF977JQR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_3.log b/ENCSR872WGW/cherimoya.fold_3.log deleted file mode 100644 index ba58e08db8951491e9d3f9f041107a26ef878877..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3091 37.95216512680054 3.5601720809936523 544.6378173828125 1.0770673751831055 739.0208129882812 0.6048872470855713 0.6694101 11.12549877166748 True -1 6182 34.185394525527954 0.5924761295318604 521.6156005859375 0.9064858555793762 611.3677368164062 0.7343101501464844 0.6340779 2.54079532623291 False -2 9273 34.18356156349182 0.5765326023101807 481.29949951171875 1.3666043281555176 596.8262939453125 0.7437103986740112 0.6287209 1.3363720178604126 False -3 12364 34.16416263580322 0.5649487972259521 569.746826171875 1.5711719989776611 589.6072387695312 0.7508756518363953 0.63049734 1.3241220712661743 False -4 15455 34.15006875991821 0.5611064434051514 441.4903564453125 1.094799280166626 585.940185546875 0.7550339102745056 0.629666 1.201149344444275 False -5 18546 34.128174781799316 0.5682938098907471 407.6729736328125 0.8988298177719116 584.4150390625 0.7570862174034119 0.61826664 1.2438597679138184 False -6 21637 34.15309381484985 0.5675430297851562 479.91748046875 0.8243757486343384 584.0313720703125 0.7581090927124023 0.6252685 1.1406100988388062 False -7 24728 34.12537121772766 0.9499015808105469 415.52392578125 0.759838879108429 579.9099731445312 0.7613756656646729 0.6363354 1.0778539180755615 False -8 27819 34.133471965789795 0.573955774307251 404.4211730957031 1.1002476215362549 577.9661254882812 0.7632415890693665 0.6426322 1.0485669374465942 False -9 30910 33.845993518829346 0.5599682331085205 459.68505859375 1.188615083694458 575.280029296875 0.7655376195907593 0.65223795 1.0101101398468018 False -10 34001 33.48595142364502 0.5530712604522705 494.5503234863281 0.660244345664978 573.4746704101562 0.7673859596252441 0.65355986 0.9903925061225891 False -11 37092 33.430628061294556 0.7103979587554932 452.2210693359375 0.690592885017395 569.8732299804688 0.7699765563011169 0.6716809 0.9430294036865234 True -12 40183 33.40895986557007 0.5485024452209473 391.84381103515625 0.8118241429328918 566.6301879882812 0.7719958424568176 0.6876343 0.8843535780906677 True -13 43274 33.53177833557129 0.5647668838500977 509.02044677734375 0.7393364310264587 563.9264526367188 0.7738813757896423 0.706526 0.8292068839073181 True -14 46365 33.467570543289185 0.5594744682312012 453.4647216796875 0.8470014333724976 560.8613891601562 0.7755836248397827 0.7292146 0.7594444751739502 True -15 49456 33.500403881073 2.1131904125213623 433.23358154296875 0.4373370409011841 559.146484375 0.7767413854598999 0.73719853 0.7245762348175049 True -16 52547 33.53298354148865 1.1221728324890137 335.661376953125 0.47308480739593506 558.3860473632812 0.7769178152084351 0.74292743 0.7198428511619568 True -17 55638 33.45687484741211 0.5685088634490967 422.47479248046875 0.3980221748352051 558.3447875976562 0.7765552401542664 0.74363893 0.720087468624115 True -18 58729 33.45391273498535 0.5507106781005859 404.4645690917969 0.26404136419296265 558.4346923828125 0.7760599851608276 0.7407051 0.7315182685852051 False -19 61820 33.467994928359985 0.554922342300415 440.0750732421875 0.4316038191318512 558.7452392578125 0.7757779359817505 0.74013144 0.7442700266838074 False diff --git a/ENCSR872WGW/cherimoya.fold_3.performance.tsv b/ENCSR872WGW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ede22bfa0e1b8893f78fffb097d9533bb3331069..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -558.3447875976562 0.19295410811901093 0.7765552997589111 0.3686120808124542 0.7436389327049255 0.7326467633247375 0.720087468624115 \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_4.evaluate.json b/ENCSR872WGW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e8436222e75f38d773b905482ede111885e1376c..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF977JQR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_4.fit.json b/ENCSR872WGW/cherimoya.fold_4.fit.json deleted file mode 100644 index fedf90e08ff4dc9f85341a5dbd00581e564e15ae..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF977JQR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR872WGW/cherimoya.fold_4.log b/ENCSR872WGW/cherimoya.fold_4.log deleted file mode 100644 index b36289eccd65eb494810d960aa652ad7d9f4f8ff..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3065 37.692063331604004 4.577380180358887 528.46630859375 1.049269199371338 734.3694458007812 0.5981839895248413 0.6648392 8.936867713928223 True -1 6130 33.77261710166931 0.5230684280395508 465.7317199707031 0.9175602197647095 598.1947021484375 0.7314686179161072 0.67249507 2.145087242126465 True -2 9195 33.784759283065796 1.2967870235443115 438.021484375 0.8635467886924744 582.8699340820312 0.7409070134162903 0.6688469 1.191420078277588 False -3 12260 33.87976598739624 0.5159454345703125 516.1669311523438 0.9121016263961792 577.244140625 0.746242105960846 0.68135726 1.0773030519485474 True -4 15325 33.7440345287323 0.5180821418762207 454.42742919921875 0.8772444725036621 573.5824584960938 0.7513188123703003 0.6690733 1.1096261739730835 False -5 18390 33.77741479873657 0.5144510269165039 461.7687683105469 1.1308257579803467 570.1181030273438 0.753420889377594 0.6739284 1.0873806476593018 False -6 21455 33.79821228981018 0.5169088840484619 391.7331848144531 0.9109224677085876 567.8540649414062 0.7565578818321228 0.67092305 1.0135221481323242 False -7 24520 33.77989673614502 0.5175273418426514 399.5784606933594 0.5689328908920288 564.7428588867188 0.7595371007919312 0.68418264 0.9076660871505737 True -8 27585 33.599228620529175 0.5124099254608154 398.3056335449219 0.5431740283966064 560.5615234375 0.7622977495193481 0.6898443 0.8609751462936401 True -9 30650 33.110339641571045 0.5009486675262451 457.9656066894531 0.736117959022522 557.1843872070312 0.7652060985565186 0.69857436 0.798992931842804 True -10 33715 33.11148548126221 0.5061347484588623 536.5696411132812 1.090114712715149 553.7835693359375 0.7678284645080566 0.70252293 0.7799308896064758 True -11 36780 33.08672904968262 0.510612964630127 432.9672546386719 0.7310433387756348 551.1024169921875 0.7696467638015747 0.71466833 0.7392052412033081 True -12 39845 33.21828532218933 0.511430025100708 391.24554443359375 0.5525891780853271 548.0056762695312 0.7716949582099915 0.72152996 0.7293185591697693 True -13 42910 33.11142826080322 0.5128927230834961 338.41796875 0.9376160502433777 545.4970092773438 0.7735364437103271 0.732104 0.7045832276344299 True -14 45975 33.078598499298096 17.37808585166931 360.81622314453125 0.5334943532943726 543.8298950195312 0.7748920917510986 0.7414807 0.6955989599227905 True -15 49040 33.15609431266785 0.5132222175598145 484.123046875 0.3881646990776062 542.5227661132812 0.7755419015884399 0.7484722 0.6766478419303894 True -16 52105 33.12196111679077 0.5087964534759521 462.24090576171875 0.3600715696811676 541.8253173828125 0.7758020758628845 0.7484917 0.6868568062782288 True -17 55170 33.16346454620361 0.5056052207946777 432.6414794921875 0.4580807089805603 542.3250732421875 0.7754281163215637 0.74565417 0.7021845579147339 False -18 58235 33.1641845703125 0.5025074481964111 417.84393310546875 0.3099660277366638 542.4268798828125 0.7748326063156128 0.74186206 0.7220562696456909 False -19 61300 33.17595839500427 10.736457824707031 462.2643127441406 0.2789475917816162 542.9930419921875 0.774461030960083 0.7390722 0.7394856214523315 False diff --git a/ENCSR872WGW/cherimoya.fold_4.performance.tsv b/ENCSR872WGW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3e8b749624297137f398f5b305540f3ffd4d1844..0000000000000000000000000000000000000000 --- a/ENCSR872WGW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -541.8253173828125 0.19571976363658905 0.7758020162582397 0.36308753490448 0.7484917044639587 0.7262188196182251 0.6868568062782288 \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_0.evaluate.json b/ENCSR873ANE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index bba432e3bb20a141100fd83ebeaec92e3b6dbdfc..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020LSG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_0.fit.json b/ENCSR873ANE/cherimoya.fold_0.fit.json deleted file mode 100644 index b815290c24d1e353e0b54423caaa1f53f12a95a3..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF020LSG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_0.log b/ENCSR873ANE/cherimoya.fold_0.log deleted file mode 100644 index c36319bd6380b4953fb3321647d894db9699eabd..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 35.30650329589844 3.9923603534698486 1284.060791015625 0.6519664525985718 1978.2210693359375 0.3469509482383728 0.75858676 9.705297470092773 True -1 5536 30.57492446899414 0.611215353012085 1433.1029052734375 0.9014424085617065 1712.616943359375 0.4357863664627075 0.80146086 3.136698007583618 True -2 8304 30.629844665527344 0.6011028289794922 1219.3837890625 0.6683676242828369 1666.5244140625 0.4515891671180725 0.8115481 1.353948712348938 True -3 11072 30.639552354812622 0.6471872329711914 1438.1533203125 0.5708034038543701 1632.076171875 0.46498817205429077 0.8182681 1.1258352994918823 True -4 13840 30.55147886276245 0.6400213241577148 1075.630126953125 0.48393678665161133 1611.267333984375 0.47444337606430054 0.82214606 1.1088143587112427 True -5 16608 30.025858402252197 0.5840461254119873 1286.412353515625 0.704466700553894 1594.7806396484375 0.4808250069618225 0.82114637 0.8791430592536926 False -6 19376 29.9880313873291 0.5833797454833984 1186.06103515625 0.4607413411140442 1584.202880859375 0.4860391914844513 0.82446265 0.7349793314933777 True -7 22144 29.95681118965149 0.5820953845977783 1383.888916015625 0.5428197979927063 1580.463134765625 0.4864393174648285 0.82924175 0.5997844338417053 True -8 24912 29.951019763946533 0.566270112991333 1413.189697265625 0.5966770648956299 1567.7327880859375 0.4930948317050934 0.83018 0.5530818104743958 True -9 27680 29.975297451019287 0.5794498920440674 1331.24609375 0.4799211323261261 1559.2547607421875 0.4967691898345947 0.83398515 0.5245082378387451 True -10 30448 29.93181276321411 0.5718569755554199 1298.4808349609375 0.37084248661994934 1554.0489501953125 0.49820199608802795 0.8379434 0.48041296005249023 True -11 33216 29.9430410861969 0.5849463939666748 1415.631103515625 0.7544982433319092 1540.350830078125 0.5047323703765869 0.84255403 0.4491393566131592 True -12 35984 29.964922189712524 0.596203088760376 1344.079345703125 0.4678688645362854 1536.2091064453125 0.5056573152542114 0.8470054 0.4001316428184509 True -13 38752 30.03799843788147 0.5976390838623047 1446.314453125 0.3515458106994629 1529.1365966796875 0.5089240074157715 0.8496535 0.37403491139411926 True -14 41520 29.98723077774048 0.5901861190795898 1494.524169921875 0.6015491485595703 1526.060791015625 0.5073641538619995 0.8540069 0.3519039750099182 True -15 44288 30.05682110786438 0.5884244441986084 962.601318359375 0.5101866722106934 1511.5501708984375 0.5154932737350464 0.8569912 0.3419434130191803 True -16 47056 30.00068712234497 0.6005890369415283 993.6097412109375 0.39987611770629883 1514.71240234375 0.5141143202781677 0.8600112 0.3254503905773163 True -17 49824 30.144713878631592 0.5885472297668457 1327.05615234375 0.2690957188606262 1513.8240966796875 0.5131267309188843 0.86153185 0.3207283914089203 True -18 52592 30.08486843109131 0.597663164138794 1249.39111328125 0.2828584611415863 1509.661376953125 0.5145066976547241 0.8613395 0.3165387511253357 False -19 55360 30.03924036026001 0.6162858009338379 996.5606079101562 0.48367878794670105 1514.1192626953125 0.5125782489776611 0.862199 0.31764012575149536 True diff --git a/ENCSR873ANE/cherimoya.fold_0.performance.tsv b/ENCSR873ANE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 710421249a809a8365a4f229b846d2fe3b9987a1..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1514.1192626953125 0.2582375705242157 0.5125782489776611 0.2940237820148468 0.8621990084648132 0.820666491985321 0.31764012575149536 \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_1.evaluate.json b/ENCSR873ANE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 066db828ee638e550a166c8531fa98f6a1102a3b..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020LSG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_1.fit.json b/ENCSR873ANE/cherimoya.fold_1.fit.json deleted file mode 100644 index 4fe45b3c8a259d8f12e5576d98db7b0ef86fd945..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF020LSG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_1.log b/ENCSR873ANE/cherimoya.fold_1.log deleted file mode 100644 index 0d1f4b41f5d91a145caf005f55670f4a0834808c..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2684 35.55018496513367 4.642558813095093 1575.85693359375 0.7187375426292419 2375.43212890625 0.34022441506385803 0.7443654 12.514841079711914 True -1 5368 29.637165546417236 0.7742581367492676 1223.99658203125 0.7956647872924805 2034.8359375 0.4403344392776489 0.79785997 2.577700138092041 True -2 8052 29.961365222930908 6.855627775192261 1107.158447265625 0.7803076505661011 1962.7940673828125 0.46094998717308044 0.80804324 1.8073288202285767 True -3 10736 29.638882875442505 0.7808070182800293 1084.7535400390625 0.9532839059829712 1922.2420654296875 0.47547122836112976 0.81552756 1.222393274307251 True -4 13420 29.58808135986328 0.7632205486297607 1210.7330322265625 0.5919811129570007 1891.974365234375 0.485931932926178 0.8212419 1.0396672487258911 True -5 16104 29.626479864120483 0.7729527950286865 1376.01904296875 0.43447744846343994 1882.2813720703125 0.48986515402793884 0.82533437 0.9112183451652527 True -6 18788 29.622653245925903 0.7670290470123291 1179.96240234375 0.44863852858543396 1864.9130859375 0.494782418012619 0.8269271 0.7369717359542847 True -7 21472 29.652256727218628 0.7770671844482422 1190.3499755859375 0.5433688163757324 1844.639892578125 0.50217604637146 0.8285801 0.626023530960083 True -8 24156 29.714004516601562 0.7593934535980225 1512.1495361328125 0.8095424771308899 1841.567626953125 0.5017443895339966 0.8303895 0.5971025824546814 True -9 26840 29.67837691307068 0.7973384857177734 1032.2906494140625 0.6047070622444153 1825.8309326171875 0.5074599385261536 0.832799 0.5734463334083557 True -10 29524 29.64457130432129 1.6506531238555908 1616.87646484375 0.41241157054901123 1807.2281494140625 0.5138174295425415 0.8349426 0.518832266330719 True -11 32208 29.659430980682373 0.7858591079711914 1465.117431640625 0.43885940313339233 1801.880859375 0.5147134065628052 0.8359499 0.48647627234458923 True -12 34892 29.758655309677124 0.7686803340911865 1141.5931396484375 0.3946216106414795 1792.4267578125 0.5166099667549133 0.84294254 0.4682173430919647 True -13 37576 29.852354049682617 2.215909004211426 1334.893310546875 0.3328602910041809 1778.0782470703125 0.5211907625198364 0.84891653 0.46084898710250854 True -14 40260 29.48850178718567 0.7665555477142334 1437.186767578125 0.3561069369316101 1766.134033203125 0.524813711643219 0.8543712 0.41922619938850403 True -15 42944 29.324123859405518 1.6446177959442139 1247.404296875 0.5412853956222534 1764.4451904296875 0.5242679715156555 0.8603591 0.3964971601963043 True -16 45628 29.26119327545166 0.7469897270202637 1187.65869140625 0.34961244463920593 1763.587890625 0.524662971496582 0.86410487 0.37079671025276184 True -17 48312 29.205600023269653 0.8478684425354004 1181.34326171875 0.35519424080848694 1754.6190185546875 0.5280224084854126 0.864822 0.36016207933425903 True -18 50996 29.32826805114746 0.7660195827484131 1125.124267578125 0.4525749981403351 1766.98388671875 0.5222273468971252 0.86616033 0.35497525334358215 True -19 53680 29.28202533721924 0.7476739883422852 1039.177978515625 0.29936206340789795 1764.3515625 0.5235471129417419 0.86625063 0.34937846660614014 True diff --git a/ENCSR873ANE/cherimoya.fold_1.performance.tsv b/ENCSR873ANE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 819f57bad7cd2ad6fb55933be096b319908aa294..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1764.3515625 0.24141882359981537 0.5235471129417419 0.3261128067970276 0.8662506341934204 0.8450546860694885 0.34937846660614014 \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_2.evaluate.json b/ENCSR873ANE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b65337e589bd38afde9e3e3f9b8efd6aa2c2ee20..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020LSG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_2.fit.json b/ENCSR873ANE/cherimoya.fold_2.fit.json deleted file mode 100644 index 6844aee1b778807cfbd973e1af95b3b09e690df3..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF020LSG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_2.log b/ENCSR873ANE/cherimoya.fold_2.log deleted file mode 100644 index 719005b3aeeb83759f7d85e52dd1a4364ddce44a..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2880 36.37122130393982 3.994440793991089 1624.684326171875 0.8090701103210449 2124.01708984375 0.345519483089447 0.74887055 8.946749687194824 True -1 5760 31.869292736053467 0.6018383502960205 1367.041748046875 0.8938469886779785 1820.7471923828125 0.43733009696006775 0.7886805 2.729814052581787 True -2 8640 31.895097255706787 0.6295428276062012 1296.498046875 0.37147071957588196 1782.5172119140625 0.452019602060318 0.7952674 1.5471018552780151 True -3 11520 31.819934606552124 0.5827517509460449 1195.7381591796875 0.6619669198989868 1742.8082275390625 0.46810925006866455 0.8053875 1.113129734992981 True -4 14400 31.787702322006226 0.5767943859100342 1470.4749755859375 0.7685861587524414 1729.169677734375 0.474660724401474 0.8078231 1.0349750518798828 True -5 17280 31.834569454193115 0.5802874565124512 1163.4886474609375 0.6734117269515991 1715.491943359375 0.4785246253013611 0.81292075 0.9428131580352783 True -6 20160 31.730714797973633 0.5731780529022217 1320.3016357421875 0.4851311147212982 1698.6337890625 0.4843549430370331 0.81956464 0.7159959077835083 True -7 23040 31.777790546417236 0.582505464553833 1220.1820068359375 0.6036472320556641 1688.7364501953125 0.4875928461551666 0.8222231 0.6352728605270386 True -8 25920 31.7981595993042 2.8976423740386963 1193.08349609375 0.4357052445411682 1676.7557373046875 0.4936433434486389 0.8228584 0.5766257643699646 True -9 28800 31.870840311050415 0.5897650718688965 1252.767822265625 0.5556612014770508 1656.2415771484375 0.5021589398384094 0.8263052 0.5211693048477173 True -10 31680 31.764421701431274 0.5740749835968018 1381.641845703125 0.46973031759262085 1653.0018310546875 0.5027357339859009 0.8289398 0.4840104877948761 True -11 34560 31.998561143875122 0.5770056247711182 1090.622802734375 0.27267301082611084 1649.2684326171875 0.5037881731987 0.8313963 0.46170881390571594 True -12 37440 31.783453702926636 0.6299891471862793 970.5592041015625 0.3554672598838806 1638.2366943359375 0.5058683753013611 0.8368313 0.42148199677467346 True -13 40320 31.80766487121582 0.5861155986785889 1310.864501953125 0.6014091968536377 1628.623779296875 0.5087718367576599 0.84439296 0.39686518907546997 True -14 43200 31.17392873764038 0.5701634883880615 1383.3165283203125 0.40169253945350647 1623.4150390625 0.5112020373344421 0.8473314 0.3873313069343567 True -15 46080 31.145256996154785 3.2228784561157227 962.354736328125 0.3372958302497864 1614.4686279296875 0.5138755440711975 0.8518276 0.3656240403652191 True -16 48960 31.187626600265503 0.5795466899871826 1297.2657470703125 0.2423795759677887 1610.3857421875 0.5161796808242798 0.8539533 0.35229966044425964 True -17 51840 31.158079862594604 0.5620677471160889 1245.6234130859375 0.29852086305618286 1612.799072265625 0.5153214335441589 0.8561644 0.3439346253871918 True -18 54720 31.173253536224365 0.5692801475524902 1493.5093994140625 0.2969977855682373 1611.295654296875 0.5162991881370544 0.8554937 0.3409345746040344 False -19 57600 31.194379568099976 0.5758087635040283 1314.40966796875 0.3339812755584717 1615.909912109375 0.51344895362854 0.8547672 0.3427673578262329 False diff --git a/ENCSR873ANE/cherimoya.fold_2.performance.tsv b/ENCSR873ANE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index eda55bcf036a242f5151ba98d9ad7324845c19bc..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1612.799072265625 0.25067514181137085 0.5153213739395142 0.30901437997817993 0.8561643958091736 0.8264189958572388 0.3439346253871918 \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_3.evaluate.json b/ENCSR873ANE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 34dd8ae9d4da6786445ea11f3b171c98205abdaa..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020LSG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_3.fit.json b/ENCSR873ANE/cherimoya.fold_3.fit.json deleted file mode 100644 index 5f6a0fd63290c28827cfae220cc316251ea9d9e8..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF020LSG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_3.log b/ENCSR873ANE/cherimoya.fold_3.log deleted file mode 100644 index 8058fb9a5743d3c7a04eac3e69a5941001c070b8..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 34.78658127784729 3.789484739303589 1229.9052734375 1.0346202850341797 2009.6357421875 0.3504229784011841 0.7587483 10.391958236694336 True -1 5508 30.412059545516968 1.0160975456237793 1325.23779296875 0.7475227117538452 1747.568115234375 0.4420570135116577 0.8063057 3.067932367324829 True -2 8262 30.45248031616211 0.5935256481170654 1416.4835205078125 0.6018993854522705 1695.27490234375 0.4602743089199066 0.8133812 1.3459428548812866 True -3 11016 30.42168378829956 3.2820661067962646 2018.3685302734375 0.6565642356872559 1676.1334228515625 0.466137170791626 0.81979614 1.0513733625411987 True -4 13770 30.4084792137146 0.5653283596038818 1385.37744140625 0.7144877910614014 1667.218017578125 0.4695855379104614 0.82023954 0.9384595155715942 True -5 16524 30.45533299446106 0.5764980316162109 1586.1622314453125 0.7258459329605103 1651.5283203125 0.4775351881980896 0.8246894 0.8166667819023132 True -6 19278 30.39943265914917 0.5682551860809326 1344.66552734375 0.6480573415756226 1639.5296630859375 0.482774943113327 0.824051 0.7348030209541321 False -7 22032 30.359519958496094 0.5397334098815918 1374.962158203125 0.46247634291648865 1634.083740234375 0.4860604703426361 0.8286318 0.690750777721405 True -8 24786 30.433032751083374 0.5728611946105957 1063.9061279296875 0.5408278107643127 1622.590087890625 0.49104824662208557 0.82831067 0.6464852094650269 False -9 27540 30.367415189743042 0.5718173980712891 1208.5546875 0.41966524720191956 1621.156982421875 0.4905855059623718 0.8284687 0.615664541721344 False -10 30294 30.3886821269989 0.555901288986206 1427.7320556640625 0.7377357482910156 1610.7003173828125 0.494464635848999 0.83181727 0.5456650853157043 True -11 33048 30.363667726516724 0.5885753631591797 1611.5167236328125 0.472998708486557 1599.27978515625 0.4997037947177887 0.83529705 0.5294070243835449 True -12 35802 30.397891998291016 0.5729691982269287 1586.398681640625 0.5053700804710388 1593.6591796875 0.5011628866195679 0.842744 0.4687716066837311 True -13 38556 30.392653465270996 0.5570073127746582 1279.378173828125 0.559325098991394 1577.051025390625 0.5084922313690186 0.84742147 0.41432029008865356 True -14 41310 29.821749210357666 0.5518360137939453 1319.4503173828125 0.3852841258049011 1566.1273193359375 0.5114414095878601 0.8523065 0.39472296833992004 True -15 44064 29.872217416763306 0.5647189617156982 1293.6448974609375 0.34688279032707214 1561.7913818359375 0.5124205350875854 0.85787153 0.3766668438911438 True -16 46818 29.951421976089478 0.5679655075073242 1385.55419921875 0.2591648995876312 1564.564697265625 0.5101571083068848 0.8602374 0.3615237772464752 True -17 49572 29.915628910064697 0.5815832614898682 1196.138671875 0.45944610238075256 1563.80078125 0.5112406611442566 0.861918 0.35439422726631165 True -18 52326 29.909541606903076 0.5629904270172119 1254.223388671875 0.4649312198162079 1562.232666015625 0.5112424492835999 0.8629619 0.3499094843864441 True -19 55080 29.95826554298401 12.6734778881073 1290.998779296875 0.3073681592941284 1561.947265625 0.5121710300445557 0.8630318 0.3505524694919586 True diff --git a/ENCSR873ANE/cherimoya.fold_3.performance.tsv b/ENCSR873ANE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7a87bee653890ad27c09b7e93d877d31581412ab..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1561.947265625 0.255553662776947 0.5121710300445557 0.3015763461589813 0.863031804561615 0.8262505531311035 0.3505524694919586 \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_4.evaluate.json b/ENCSR873ANE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index d38ee8ce3222ccf7b06ec00cfa1ece8a48cbabb0..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF020LSG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_4.fit.json b/ENCSR873ANE/cherimoya.fold_4.fit.json deleted file mode 100644 index 6dad90ef486bb5fcbc29cbf7e832e01d7e451574..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF020LSG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR873ANE/cherimoya.fold_4.log b/ENCSR873ANE/cherimoya.fold_4.log deleted file mode 100644 index 69cd72c197df43fed93529306791bed65a95ecdf..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2792 35.601969718933105 4.097350835800171 1403.1986083984375 0.7658313512802124 1903.489990234375 0.34692975878715515 0.7512757 10.450787544250488 True -1 5584 30.849427700042725 0.6313512325286865 1494.772216796875 0.6237056255340576 1640.7957763671875 0.4409046173095703 0.7930244 2.6731271743774414 True -2 8376 30.87110662460327 0.6224446296691895 1425.228271484375 0.8068128228187561 1598.09375 0.45480409264564514 0.8038853 1.1934808492660522 True -3 11168 30.808598518371582 0.6354331970214844 1471.552490234375 0.4331696927547455 1580.259521484375 0.46199703216552734 0.80787337 0.8415423631668091 True -4 13960 30.782934188842773 0.613654375076294 1143.5242919921875 0.7871464490890503 1565.3294677734375 0.46982336044311523 0.8122597 0.6538635492324829 True -5 16752 30.831696271896362 0.6270179748535156 1274.3770751953125 0.47768890857696533 1551.2099609375 0.4756358563899994 0.8172656 0.6012739539146423 True -6 19544 30.77483105659485 0.6118113994598389 1367.441162109375 0.5710999965667725 1538.3426513671875 0.4839426875114441 0.81962234 0.5216767191886902 True -7 22336 30.757332801818848 0.6334249973297119 1149.671630859375 0.5679341554641724 1533.2764892578125 0.48382702469825745 0.8238894 0.46145036816596985 True -8 25128 30.750191926956177 0.6279299259185791 1406.3458251953125 0.4472164511680603 1527.7486572265625 0.48539578914642334 0.82671547 0.4108762741088867 True -9 27920 30.757487058639526 0.6320705413818359 1159.082763671875 0.46218186616897583 1518.0291748046875 0.491231769323349 0.82779014 0.4148763418197632 True -10 30712 31.60399842262268 8.627413749694824 1111.922119140625 0.415300577878952 1513.1422119140625 0.4937363862991333 0.83087254 0.39168089628219604 True -11 33504 30.868797063827515 24.750293254852295 1254.54443359375 0.4075568914413452 1506.7449951171875 0.4953686594963074 0.83413976 0.3784221410751343 True -12 36296 30.947214365005493 0.6423025131225586 1083.443115234375 0.510706901550293 1498.624267578125 0.49791157245635986 0.83687305 0.3732926547527313 True -13 39088 30.833738565444946 0.64263916015625 1264.27001953125 0.4816613793373108 1497.8775634765625 0.49924078583717346 0.84150624 0.3496043384075165 True -14 41880 30.691213607788086 0.6284117698669434 1242.4019775390625 0.4286280572414398 1482.48876953125 0.5068570971488953 0.84459907 0.3407451808452606 True -15 44672 30.27036142349243 0.6360456943511963 1283.7200927734375 0.3361611068248749 1488.15966796875 0.5031050443649292 0.8501618 0.33767232298851013 True -16 47464 30.261236667633057 0.6328830718994141 1106.76953125 0.26238012313842773 1481.74609375 0.5059457421302795 0.85151726 0.3324625492095947 True -17 50256 30.228222131729126 0.616567850112915 1147.8857421875 0.2800375819206238 1476.9835205078125 0.5083735585212708 0.8543961 0.3265749216079712 True -18 53048 30.26203203201294 0.6082127094268799 1386.489013671875 0.20844878256320953 1478.620361328125 0.5063702464103699 0.85478073 0.3253609240055084 True -19 55840 30.288395881652832 0.5963573455810547 1098.939453125 0.28162771463394165 1482.9268798828125 0.5036836862564087 0.8531774 0.3230564594268799 False diff --git a/ENCSR873ANE/cherimoya.fold_4.performance.tsv b/ENCSR873ANE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a7f24020b6affe286d3b9733f89f9c7399d9054a..0000000000000000000000000000000000000000 --- a/ENCSR873ANE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1478.620361328125 0.26034852862358093 0.5063703060150146 0.2942816913127899 0.8547807335853577 0.8075831532478333 0.3253609240055084 \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_0.evaluate.json b/ENCSR874CAK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ee072342b4d4a106c9ba8f57e8c16444b8446830..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF379JGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_0.fit.json b/ENCSR874CAK/cherimoya.fold_0.fit.json deleted file mode 100644 index 38f737361390cc2707eed26be72d31273be90e78..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF379JGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_0.log b/ENCSR874CAK/cherimoya.fold_0.log deleted file mode 100644 index da77707655c75c4f47392f2a2bbf8ee1c3b85c36..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 34.95030236244202 3.975734233856201 347.84759521484375 0.6345013380050659 419.6315612792969 0.19276191294193268 0.5983903 3.382972240447998 True -1 5522 30.482332706451416 0.5831530094146729 303.38525390625 0.6526041626930237 397.6754150390625 0.2542070746421814 0.67034 1.0077788829803467 True -2 8283 30.5230131149292 0.7117102146148682 315.33001708984375 0.5006288290023804 393.1413879394531 0.26496177911758423 0.6729721 0.7093364000320435 True -3 11044 30.494662046432495 0.5522193908691406 366.2761535644531 0.5075216889381409 390.0852355957031 0.2706422507762909 0.6915689 0.6479746699333191 True -4 13805 30.437426567077637 0.5880885124206543 300.2679748535156 0.6219785213470459 388.2012634277344 0.27598151564598083 0.705013 0.6216669082641602 True -5 16566 30.475476503372192 0.5499393939971924 314.771728515625 0.4772503077983856 387.37457275390625 0.2792789041996002 0.71063936 0.617577314376831 True -6 19327 30.48421573638916 0.5623860359191895 270.5484619140625 0.7744593024253845 386.77081298828125 0.28005653619766235 0.7104843 0.6211518049240112 False -7 22088 30.411284923553467 12.232381820678711 276.1448669433594 0.506726861000061 385.9853210449219 0.28316089510917664 0.7168449 0.6540502905845642 True -8 24849 30.445918083190918 19.964709520339966 314.51324462890625 0.548743486404419 385.3414306640625 0.2843770682811737 0.7197442 0.6163790225982666 True -9 27610 31.31290102005005 0.5855724811553955 282.3526611328125 0.4347720146179199 384.2524719238281 0.2870996296405792 0.7271802 0.5786328315734863 True -10 30371 30.481907844543457 0.5725674629211426 285.71136474609375 0.41187894344329834 383.7159423828125 0.2887052297592163 0.7323924 0.5502199530601501 True -11 33132 30.62444519996643 0.5656814575195312 334.4405517578125 0.7160683274269104 382.4645080566406 0.29234400391578674 0.7400276 0.5187538862228394 True -12 35893 30.524346113204956 0.5970008373260498 269.09661865234375 0.4111143946647644 382.3134460449219 0.2927934527397156 0.7469871 0.46332690119743347 True -13 38654 30.502360820770264 0.6801061630249023 298.02276611328125 0.48999375104904175 381.5097351074219 0.29466426372528076 0.7548189 0.42234092950820923 True -14 41415 30.49435806274414 1.2807588577270508 271.567138671875 0.3800559341907501 381.1037292480469 0.2951730191707611 0.75984246 0.398163765668869 True -15 44176 30.264777183532715 0.5651330947875977 286.2716369628906 0.24982641637325287 380.4721374511719 0.297399640083313 0.76735926 0.37979963421821594 True -16 46937 29.923710107803345 0.5443136692047119 280.74005126953125 0.24532903730869293 380.6733703613281 0.29717206954956055 0.7694155 0.36213451623916626 True -17 49698 29.90126061439514 0.5598616600036621 335.4334716796875 0.41284552216529846 380.0471496582031 0.29943832755088806 0.77036107 0.35479283332824707 True -18 52459 29.891956567764282 0.5422494411468506 332.81036376953125 0.3356863260269165 380.68280029296875 0.297439843416214 0.76964635 0.3545510470867157 False -19 55220 29.974626779556274 0.5857899188995361 329.9559326171875 0.19135639071464539 380.8034973144531 0.29555031657218933 0.7671181 0.35608983039855957 False diff --git a/ENCSR874CAK/cherimoya.fold_0.performance.tsv b/ENCSR874CAK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 33d6d86d0cdd2514b510aeef2b0b4e9bebdaa9b4..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -380.0471496582031 0.463441401720047 0.29943832755088806 0.0983499065041542 0.770361065864563 0.7019848823547363 0.35479283332824707 \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_1.evaluate.json b/ENCSR874CAK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6659987a94b4fa0a66bfe3ad7910a6f7d24f7844..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF379JGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_1.fit.json b/ENCSR874CAK/cherimoya.fold_1.fit.json deleted file mode 100644 index f65666009bce0f99e9bf0bce6ddc9ddfe30e9420..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF379JGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_1.log b/ENCSR874CAK/cherimoya.fold_1.log deleted file mode 100644 index 02c9dac390653a475ec0de0dd1dd6c3780469438..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 34.91921353340149 4.137439250946045 306.5991516113281 0.5864770412445068 467.8977355957031 0.19717158377170563 0.60294765 4.299188137054443 True -1 5508 30.369296550750732 1.1172096729278564 322.5731201171875 0.7718894481658936 440.0628662109375 0.27001044154167175 0.69124687 1.1484707593917847 True -2 8262 30.384609699249268 0.7750442028045654 319.0387878417969 0.6222660541534424 433.35797119140625 0.28330084681510925 0.7021979 0.7995752096176147 True -3 11016 30.424713373184204 1.003664255142212 283.75341796875 0.5723986625671387 430.0172424316406 0.29067617654800415 0.7140441 0.7765859365463257 True -4 13770 30.427993535995483 0.917377233505249 288.5428466796875 0.5811009407043457 428.96142578125 0.29228878021240234 0.72371536 0.7417353987693787 True -5 16524 30.437886238098145 0.7633669376373291 271.15057373046875 0.5523398518562317 427.9095153808594 0.2954292595386505 0.7264851 0.666948139667511 True -6 19278 30.386800527572632 0.761969804763794 354.7918701171875 0.5456541180610657 426.00750732421875 0.2993370294570923 0.7376248 0.5699964165687561 True -7 22032 30.361114263534546 0.7711927890777588 277.73175048828125 0.3395981788635254 425.59320068359375 0.2994667589664459 0.74126834 0.5469488501548767 True -8 24786 30.299010515213013 0.7473020553588867 292.5699462890625 0.5049948692321777 424.46551513671875 0.30190616846084595 0.7486186 0.5292169451713562 True -9 27540 30.292410373687744 0.805109977722168 408.87054443359375 0.3247002363204956 422.853271484375 0.3067631423473358 0.7539348 0.5110223293304443 True -10 30294 30.384706020355225 0.8020293712615967 373.69927978515625 0.39792656898498535 421.9061584472656 0.30827441811561584 0.75977063 0.47292661666870117 True -11 33048 30.324915647506714 0.7432270050048828 292.4035949707031 0.6692429184913635 421.9830017089844 0.3063671588897705 0.7665911 0.4629759192466736 True -12 35802 30.35204577445984 0.7542362213134766 337.42657470703125 0.42440518736839294 420.76007080078125 0.310530424118042 0.7722877 0.4375831186771393 True -13 38556 30.39595603942871 0.7612292766571045 337.8732604980469 0.4814307689666748 420.0997009277344 0.31150639057159424 0.77894956 0.41958680748939514 True -14 41310 30.400058031082153 0.7876133918762207 337.16546630859375 0.2230345606803894 419.52996826171875 0.31343716382980347 0.78693277 0.40014681220054626 True -15 44064 30.575907707214355 0.7882330417633057 276.70404052734375 0.40036243200302124 418.8133850097656 0.3147662281990051 0.7908721 0.37979856133461 True -16 46818 29.80409836769104 0.7559046745300293 370.9735107421875 0.3725942075252533 418.9769287109375 0.31456074118614197 0.7954954 0.36439070105552673 True -17 49572 29.824921369552612 0.7881221771240234 303.3548583984375 0.34494155645370483 419.0552673339844 0.31369155645370483 0.7967265 0.35827726125717163 True -18 52326 29.731598138809204 0.7488784790039062 281.671142578125 0.23884551227092743 419.6585998535156 0.3112742304801941 0.79531544 0.36210522055625916 False -19 55080 29.738926649093628 0.7630314826965332 333.0351867675781 0.5270830988883972 419.0557861328125 0.3142385482788086 0.79375684 0.364147812128067 False diff --git a/ENCSR874CAK/cherimoya.fold_1.performance.tsv b/ENCSR874CAK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4f4e66a9ae33498255910baae9f84f76e6b5bc4b..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -419.0552673339844 0.4487564265727997 0.31369152665138245 0.1137133464217186 0.7967265248298645 0.7477525472640991 0.35827726125717163 \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_2.evaluate.json b/ENCSR874CAK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8506bbffc99f0217a5200bd980b01448ce651c09..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF379JGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_2.fit.json b/ENCSR874CAK/cherimoya.fold_2.fit.json deleted file mode 100644 index d4df8cc12f4842b7737590eb18a15a1b7a513f48..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF379JGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_2.log b/ENCSR874CAK/cherimoya.fold_2.log deleted file mode 100644 index e16d4024cbad090cf851f9b9ebd02b6dfa5ce246..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 36.590601444244385 4.011391639709473 283.7100830078125 0.7206177711486816 431.5297546386719 0.19069795310497284 0.58775073 3.1775763034820557 True -1 5782 31.95710062980652 0.5898144245147705 386.2001037597656 0.6126065850257874 405.6009216308594 0.26649466156959534 0.6796517 1.070566177368164 True -2 8673 32.0356171131134 0.7106335163116455 328.7662353515625 0.6716030240058899 400.5321350097656 0.276187926530838 0.69836664 0.5345779657363892 True -3 11564 32.05202317237854 0.5524439811706543 315.652099609375 0.5267717242240906 397.2041931152344 0.2840471863746643 0.70697033 0.5239065885543823 True -4 14455 31.97584104537964 0.5593531131744385 327.6731872558594 0.4377252161502838 396.694091796875 0.28490838408470154 0.71364146 0.5273786783218384 True -5 17346 31.980210781097412 0.5701487064361572 265.094482421875 0.6739011406898499 396.119140625 0.2854829728603363 0.71559274 0.5563495755195618 True -6 20237 31.92723822593689 0.5610640048980713 324.9573059082031 0.47777843475341797 395.39263916015625 0.28750842809677124 0.71704257 0.5893995761871338 True -7 23128 31.907286643981934 0.5587739944458008 279.22552490234375 0.8955454230308533 395.1720886230469 0.28817328810691833 0.72244114 0.5460441708564758 True -8 26019 31.983638286590576 0.5641899108886719 335.24273681640625 0.4029647707939148 393.7784423828125 0.29218563437461853 0.72540534 0.5458544492721558 True -9 28910 31.874616622924805 0.5639557838439941 321.69720458984375 0.38668292760849 393.0247497558594 0.2938790023326874 0.7353839 0.4884280860424042 True -10 31801 31.933420419692993 0.5501809120178223 272.8094787597656 0.3064495325088501 392.27789306640625 0.29614201188087463 0.7409205 0.4856770932674408 True -11 34692 31.911412000656128 0.5652022361755371 294.3267822265625 0.5462301969528198 391.1203918457031 0.2994479537010193 0.74400216 0.46186670660972595 True -12 37583 32.002527475357056 0.5600502490997314 317.7593078613281 0.34731525182724 390.3212890625 0.30141621828079224 0.75488126 0.42624640464782715 True -13 40474 31.98141074180603 0.5598030090332031 236.85818481445312 0.2748473286628723 389.9317626953125 0.3021482527256012 0.7618137 0.40989527106285095 True -14 43365 31.99129819869995 0.5628080368041992 310.83013916015625 0.4896599352359772 389.5511169433594 0.3027012348175049 0.7679863 0.3911290466785431 True -15 46256 31.804417848587036 0.5588157176971436 274.49102783203125 0.31991517543792725 388.9447326660156 0.3041309416294098 0.7720511 0.36930322647094727 True -16 49147 31.3223397731781 0.5538499355316162 347.93994140625 0.23758713901042938 388.66204833984375 0.3053268790245056 0.77689785 0.35337692499160767 True -17 52038 31.253731966018677 0.5588452816009521 277.6957702636719 0.26388347148895264 388.9569091796875 0.3035753667354584 0.77563155 0.35237470269203186 False -18 54929 31.352514266967773 1.3771185874938965 248.44927978515625 0.3569435477256775 388.9981384277344 0.30407029390335083 0.7751252 0.3540154993534088 False -19 57820 31.34485626220703 0.5478301048278809 303.3187561035156 0.19689059257507324 388.80291748046875 0.3047431707382202 0.772608 0.3592354953289032 False diff --git a/ENCSR874CAK/cherimoya.fold_2.performance.tsv b/ENCSR874CAK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6d56b21db1639252ef4ef4f0853bf79176aa5887..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -388.66204833984375 0.4588235020637512 0.3053268790245056 0.10567162185907364 0.7768978476524353 0.7192878723144531 0.35337692499160767 \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_3.evaluate.json b/ENCSR874CAK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f775ce28fc8ae285d7b82c5a56003e5220684c37..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF379JGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_3.fit.json b/ENCSR874CAK/cherimoya.fold_3.fit.json deleted file mode 100644 index b6a8062c359869f4d22d130bff4019913afa6df8..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF379JGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_3.log b/ENCSR874CAK/cherimoya.fold_3.log deleted file mode 100644 index 4dbd2d6c9e33ac5c4b0d04960396d8a12c58563f..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 35.731181383132935 3.6725809574127197 336.557861328125 0.7684651017189026 436.3463439941406 0.192313551902771 0.60242194 3.680659055709839 True -1 5606 30.980717182159424 0.6080741882324219 305.1564025878906 0.7479959726333618 413.3863220214844 0.25587204098701477 0.69137704 1.1590214967727661 True -2 8409 31.038909435272217 2.998805522918701 284.6075134277344 0.5601186752319336 407.4388427734375 0.27133047580718994 0.70325947 0.7861478328704834 True -3 11212 30.98992395401001 0.6202905178070068 362.2449951171875 0.8951679468154907 404.6753234863281 0.27755701541900635 0.71436733 0.5765116214752197 True -4 14015 30.89727020263672 0.6036553382873535 278.7268371582031 0.6037323474884033 404.07757568359375 0.2778584063053131 0.7149492 0.6059346199035645 True -5 16818 30.839035749435425 0.5731320381164551 301.55865478515625 0.4445107877254486 404.3712463378906 0.27814608812332153 0.7087068 0.7909731268882751 False -6 19621 30.87338399887085 0.602031946182251 281.70001220703125 0.5780725479125977 401.8908386230469 0.2851652503013611 0.71913254 0.6472165584564209 True -7 22424 30.84463667869568 0.5654439926147461 379.1854553222656 0.6252875328063965 400.8192138671875 0.28907740116119385 0.72069466 0.6021985411643982 True -8 25227 30.8176531791687 0.5593938827514648 336.30010986328125 0.33451682329177856 399.8545837402344 0.2903749942779541 0.73354185 0.519727349281311 True -9 28030 30.84246015548706 0.5837907791137695 328.671875 0.376039981842041 399.2249755859375 0.2929617166519165 0.73430866 0.5270693302154541 True -10 30833 30.824467182159424 0.5964822769165039 306.8436279296875 0.5462567210197449 399.25360107421875 0.29254764318466187 0.7441518 0.49994713068008423 True -11 33636 30.89748978614807 0.572455883026123 305.2763977050781 0.39085081219673157 398.7434997558594 0.29336562752723694 0.75381196 0.4547051191329956 True -12 36439 30.867658853530884 1.5010275840759277 287.17181396484375 0.4557662606239319 397.9501953125 0.29478394985198975 0.76402676 0.4287222623825073 True -13 39242 30.932660818099976 0.5751712322235107 306.6531066894531 0.26994800567626953 396.69635009765625 0.2986835241317749 0.76834214 0.41157934069633484 True -14 42045 30.8804988861084 0.5767500400543213 302.33306884765625 0.27706360816955566 396.67474365234375 0.29895755648612976 0.7757282 0.38583478331565857 True -15 44848 30.748251914978027 0.5839698314666748 355.67254638671875 0.31722575426101685 396.4207763671875 0.29931214451789856 0.78324646 0.3654067814350128 True -16 47651 30.27045226097107 0.5536997318267822 340.48291015625 0.42865607142448425 396.27813720703125 0.2995794117450714 0.78620726 0.3524737060070038 True -17 50454 30.21487522125244 0.5777809619903564 328.33673095703125 0.29558879137039185 396.1070861816406 0.2998068034648895 0.78742766 0.3535122871398926 True -18 53257 30.27738857269287 0.5660266876220703 313.7339172363281 0.2545151710510254 395.99371337890625 0.3008390963077545 0.78473806 0.3534272611141205 False -19 56060 30.21444821357727 0.5777938365936279 334.1566162109375 0.3102441728115082 396.1310119628906 0.3005308210849762 0.78493935 0.35429123044013977 False diff --git a/ENCSR874CAK/cherimoya.fold_3.performance.tsv b/ENCSR874CAK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f1d61478b1893daa64ca36cc5f009de6d49d43cb..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -396.1070861816406 0.45921850204467773 0.29980677366256714 0.10364862531423569 0.7874276638031006 0.7315359711647034 0.3535122871398926 \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_4.evaluate.json b/ENCSR874CAK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2d127de2071f76b715c439670ca3f4ab553486df..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF379JGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_4.fit.json b/ENCSR874CAK/cherimoya.fold_4.fit.json deleted file mode 100644 index e4bd86b752af8305c8deeecf03a115dec37dc159..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF379JGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874CAK/cherimoya.fold_4.log b/ENCSR874CAK/cherimoya.fold_4.log deleted file mode 100644 index ada85502bbbeb8f7e44532b019cc5ba54c015d28..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2860 36.17431902885437 3.8637168407440186 303.593994140625 0.5656044483184814 406.3282775878906 0.19011534750461578 0.5942724 3.0851798057556152 True -1 5720 31.570024490356445 0.6046586036682129 270.9896240234375 0.6400855779647827 386.24407958984375 0.25088024139404297 0.6695721 1.009265661239624 True -2 8580 31.584888219833374 0.5765702724456787 321.9778747558594 0.7969455122947693 380.6198425292969 0.26564791798591614 0.69161934 0.6470655202865601 True -3 11440 31.522382020950317 0.934117317199707 286.3872985839844 0.5582427382469177 378.7190856933594 0.2672179043292999 0.7091869 0.5553085803985596 True -4 14300 31.541689157485962 17.97775888442993 323.99462890625 0.7827174663543701 377.8164978027344 0.2698543071746826 0.7145189 0.5828256011009216 True -5 17160 31.51382327079773 0.5898768901824951 294.4310607910156 0.6736233830451965 376.7278747558594 0.2718208134174347 0.717201 0.5483875274658203 True -6 20020 31.632652759552002 10.97992730140686 294.6649475097656 0.8388010263442993 375.4942321777344 0.27602627873420715 0.7230988 0.5218896865844727 True -7 22880 31.516965627670288 0.7774093151092529 325.2670593261719 0.3578840494155884 373.8233947753906 0.28089889883995056 0.73260283 0.48434677720069885 True -8 25740 31.579728841781616 0.5694539546966553 316.090576171875 0.34294188022613525 374.3371887207031 0.27940642833709717 0.7384362 0.49044305086135864 True -9 28600 31.5131733417511 0.5762615203857422 273.8455810546875 0.5923246145248413 373.5175476074219 0.2820618450641632 0.7422578 0.4495856463909149 True -10 31460 31.522273778915405 1.2971153259277344 303.17333984375 0.6807186603546143 372.68975830078125 0.28371596336364746 0.7467705 0.4347102642059326 True -11 34320 31.516521692276 25.075268507003784 258.2659606933594 0.2896233797073364 372.56890869140625 0.2844775319099426 0.7536442 0.4247984290122986 True -12 37180 31.057685613632202 1.1564111709594727 294.92333984375 0.31937292218208313 371.9488830566406 0.28566786646842957 0.7598994 0.3948460519313812 True -13 40040 30.950202226638794 0.5909206867218018 332.1568603515625 0.40234071016311646 371.1983947753906 0.2883293032646179 0.7664239 0.37584933638572693 True -14 42900 30.930971145629883 0.5728027820587158 281.69384765625 0.689192533493042 370.8299560546875 0.28934168815612793 0.7727299 0.3622210919857025 True -15 45760 30.959948301315308 0.5754835605621338 240.37994384765625 0.2358497530221939 370.68389892578125 0.28900420665740967 0.7755367 0.3499416410923004 True -16 48620 31.01270604133606 1.3588547706604004 285.50701904296875 0.3522129952907562 370.4595947265625 0.29055365920066833 0.7803736 0.33455872535705566 True -17 51480 31.0421724319458 0.5917093753814697 307.272705078125 0.317188560962677 370.6612854003906 0.2896210551261902 0.7793535 0.3339221477508545 False -18 54340 30.952630519866943 0.5781781673431396 302.82513427734375 0.17092588543891907 370.7399597167969 0.2889462113380432 0.7786656 0.337104856967926 False -19 57200 30.937187433242798 0.5681142807006836 334.5672607421875 0.15071266889572144 371.1672668457031 0.2881414592266083 0.7784665 0.3397684097290039 False diff --git a/ENCSR874CAK/cherimoya.fold_4.performance.tsv b/ENCSR874CAK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6b71660f6d1941eb240765c7303693dc8b63135d..0000000000000000000000000000000000000000 --- a/ENCSR874CAK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -370.4595947265625 0.4690117835998535 0.29055365920066833 0.09871465712785721 0.7803735733032227 0.7180843353271484 0.33455872535705566 \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_0.evaluate.json b/ENCSR874DUP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e4472fdf4632394869ca139312cab2feb86eeab0..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF822PRE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_0.fit.json b/ENCSR874DUP/cherimoya.fold_0.fit.json deleted file mode 100644 index 1979412821347bb120b0d8fa97c718cfbdb01eb4..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF822PRE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_0.log b/ENCSR874DUP/cherimoya.fold_0.log deleted file mode 100644 index 1bea9c5af22dc9685aaa6ce1cde7a61f0681001d..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2176 27.562777042388916 8.626502990722656 459.115966796875 0.8733335733413696 488.8399963378906 0.15562626719474792 0.61130565 8.080039024353027 True -1 4352 24.00668740272522 0.7481696605682373 369.90478515625 0.8313191533088684 414.2734069824219 0.2236320972442627 0.74082536 3.12890887260437 True -2 6528 24.06883692741394 0.4509456157684326 415.0567321777344 0.9601801633834839 401.6725158691406 0.23321987688541412 0.7554488 2.0725128650665283 True -3 8704 24.010782480239868 0.44880008697509766 344.0843811035156 0.6277412176132202 392.5518798828125 0.2391585260629654 0.7663408 1.3491263389587402 True -4 10880 23.987140417099 0.4439995288848877 425.13824462890625 0.8830717206001282 386.86297607421875 0.24445953965187073 0.7741797 1.1427793502807617 True -5 13056 23.912429809570312 0.43590283393859863 357.3897705078125 0.8834782838821411 382.416259765625 0.24969272315502167 0.7844288 1.0662659406661987 True -6 15232 23.91353416442871 0.43724679946899414 239.854736328125 0.6594421863555908 379.6611633300781 0.25204625725746155 0.798566 0.9298801422119141 True -7 17408 23.948267221450806 0.4411506652832031 334.98236083984375 0.8001735806465149 377.0523681640625 0.2541932761669159 0.80979395 0.7945055961608887 True -8 19584 23.956419467926025 0.4358234405517578 262.5413513183594 0.6392967104911804 374.4443054199219 0.2579207122325897 0.8166082 0.7182324528694153 True -9 21760 23.95318627357483 0.43793559074401855 366.6350402832031 0.9458802938461304 372.57843017578125 0.25959035754203796 0.8218049 0.6862796545028687 True -10 23936 23.9706871509552 0.453263521194458 233.70596313476562 0.6020060777664185 371.31103515625 0.26098939776420593 0.8270455 0.6281885504722595 True -11 26112 23.98591637611389 8.581041812896729 345.5594482421875 0.6369420289993286 368.9927062988281 0.26374176144599915 0.8347173 0.5857592821121216 True -12 28288 24.06905174255371 0.6344649791717529 289.33673095703125 0.5625423789024353 367.10430908203125 0.26658937335014343 0.8387473 0.5561825037002563 True -13 30464 24.019832611083984 0.9400627613067627 348.91552734375 0.6214384436607361 366.9432373046875 0.2659410238265991 0.84363973 0.5345585942268372 True -14 32640 24.04945731163025 0.45963406562805176 315.98211669921875 0.6065189838409424 365.0248718261719 0.2678411900997162 0.84842575 0.5055106282234192 True -15 34816 23.989490509033203 0.4551386833190918 288.40252685546875 0.4214681088924408 363.56414794921875 0.2694358825683594 0.8514446 0.4966377317905426 True -16 36992 24.03421115875244 0.4522206783294678 300.160400390625 0.3362099826335907 363.38568115234375 0.26948684453964233 0.8530437 0.49100035429000854 True -17 39168 24.010817527770996 0.4528379440307617 258.56719970703125 0.5511022806167603 362.9310607910156 0.270392507314682 0.85284436 0.4938051402568817 False -18 41344 23.943225860595703 0.4359416961669922 308.18585205078125 0.4079626798629761 363.9408264160156 0.2693538963794708 0.85333836 0.4997725188732147 True -19 43520 24.052621603012085 0.4564788341522217 249.36874389648438 0.38627469539642334 364.3239440917969 0.2686839997768402 0.852408 0.5015971660614014 False diff --git a/ENCSR874DUP/cherimoya.fold_0.performance.tsv b/ENCSR874DUP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7cca9eb0f54ec0eb3a8127074e324f551e630de0..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -363.9408264160156 0.49790287017822266 0.26935386657714844 0.09606412798166275 0.853338360786438 0.7912354469299316 0.4997725188732147 \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_1.evaluate.json b/ENCSR874DUP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4da07853ef7be9352c2c66d85c37d62dc9607f97..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF822PRE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_1.fit.json b/ENCSR874DUP/cherimoya.fold_1.fit.json deleted file mode 100644 index 577d84e34e6e402324a65c083e595f0730247b3a..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF822PRE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_1.log b/ENCSR874DUP/cherimoya.fold_1.log deleted file mode 100644 index f3b0a6b34db1fd593d50b21ab755928ebed8ccbd..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2124 27.134084463119507 5.223470449447632 293.3907165527344 0.8923661708831787 629.0277709960938 0.1669107973575592 0.5935477 9.69783878326416 True -1 4248 23.409817218780518 1.1830251216888428 336.71624755859375 0.648002564907074 537.4584350585938 0.24983114004135132 0.74876463 4.5314507484436035 True -2 6372 23.508863925933838 0.6122884750366211 259.05670166015625 0.8163979649543762 503.189453125 0.2659246325492859 0.7791577 2.207554578781128 True -3 8496 23.44559621810913 0.598090410232544 347.52874755859375 0.8242546319961548 489.3224182128906 0.27656352519989014 0.7905325 1.5035995244979858 True -4 10620 23.35179877281189 0.6180615425109863 297.8841552734375 0.6072153449058533 483.33978271484375 0.28133413195610046 0.79913634 1.1364296674728394 True -5 12744 23.429052591323853 0.6042325496673584 387.93780517578125 0.9813870191574097 480.0325012207031 0.2847231924533844 0.80108213 1.0896539688110352 True -6 14868 23.400063514709473 0.5980103015899658 269.2421875 0.6517108082771301 476.3739929199219 0.28790390491485596 0.81145555 1.0072782039642334 True -7 16992 23.49514603614807 1.7075531482696533 502.2413330078125 0.8606925010681152 473.0748596191406 0.29234832525253296 0.8166584 1.0171899795532227 True -8 19116 23.540661334991455 0.6121306419372559 376.696044921875 0.5375422835350037 470.7494812011719 0.2942335307598114 0.8257572 0.9518611431121826 True -9 21240 23.467844009399414 1.2036993503570557 306.0377197265625 0.5372771620750427 469.4427490234375 0.29606708884239197 0.8313462 0.875409722328186 True -10 23364 23.515621185302734 0.6300091743469238 307.59381103515625 0.5820127129554749 466.5306091308594 0.29819029569625854 0.84253913 0.783428966999054 True -11 25488 23.511926651000977 0.6381769180297852 286.5862731933594 0.5310176610946655 463.23773193359375 0.30152010917663574 0.85061157 0.7226889133453369 True -12 27612 23.444124937057495 0.6162421703338623 224.52850341796875 0.5453332662582397 461.6603698730469 0.302857905626297 0.8580224 0.6732684373855591 True -13 29736 23.417601346969604 0.6058673858642578 324.6164245605469 0.6734998822212219 458.1622619628906 0.3059784770011902 0.8614591 0.6338456273078918 True -14 31860 23.433924674987793 0.599388599395752 256.28106689453125 0.5529780387878418 455.7402648925781 0.30808860063552856 0.8674613 0.5968299508094788 True -15 33984 23.417574644088745 1.3959102630615234 401.13714599609375 0.5424553751945496 455.04571533203125 0.308190256357193 0.8701351 0.5641382336616516 True -16 36108 23.454490423202515 0.5998961925506592 307.3963317871094 0.4517732262611389 454.8352355957031 0.3073820173740387 0.871857 0.5520926117897034 True -17 38232 23.40662693977356 0.5945549011230469 324.9169006347656 0.5582420825958252 454.870361328125 0.3070254325866699 0.87144303 0.5442796349525452 False -18 40356 23.407367706298828 0.595954418182373 209.3280029296875 0.3877599239349365 454.7584533691406 0.3074445426464081 0.8720123 0.5423265099525452 True -19 42480 23.392401695251465 0.60788893699646 338.4251708984375 0.3877999782562256 454.3619384765625 0.30843353271484375 0.87105423 0.5470123291015625 False diff --git a/ENCSR874DUP/cherimoya.fold_1.performance.tsv b/ENCSR874DUP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0ce291f205e913a9d4cc9057ff2622b2fcadf5f9..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -454.7584533691406 0.4664521813392639 0.3074445426464081 0.11715763062238693 0.8720123171806335 0.8413534760475159 0.5423265099525452 \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_2.evaluate.json b/ENCSR874DUP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 44824ad8b08440aaea6fe650f071194062acd8a2..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF822PRE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_2.fit.json b/ENCSR874DUP/cherimoya.fold_2.fit.json deleted file mode 100644 index 3022ace41babde304ad9d94c496f558280f3df80..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF822PRE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_2.log b/ENCSR874DUP/cherimoya.fold_2.log deleted file mode 100644 index b884ade2dba2e1165174402084530e9b3aea5e6a..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2292 29.287137746810913 3.6428184509277344 317.071044921875 1.278312087059021 510.7548522949219 0.15649735927581787 0.5890318 7.49179220199585 True -1 4584 25.353596448898315 1.019104242324829 367.21563720703125 0.7991528511047363 432.5008544921875 0.22940076887607574 0.72474635 3.518785238265991 True -2 6876 25.294217824935913 0.6707603931427002 299.56005859375 0.804367184638977 412.36651611328125 0.2402510643005371 0.7577624 2.1640841960906982 True -3 9168 25.31787657737732 0.45473647117614746 323.37762451171875 0.6261501312255859 402.52325439453125 0.24558347463607788 0.7753182 1.2269392013549805 True -4 11460 25.317867040634155 0.5137333869934082 337.72979736328125 0.6759149432182312 397.6353454589844 0.25018176436424255 0.7820693 0.9871861338615417 True -5 13752 25.186416625976562 0.46659088134765625 355.7001953125 1.0407516956329346 395.74749755859375 0.25078409910202026 0.79305273 0.9466414451599121 True -6 16044 25.215074062347412 0.4571561813354492 267.1969909667969 0.5190536975860596 392.8956298828125 0.25444433093070984 0.7982903 0.8678044080734253 True -7 18336 25.17714214324951 0.5299417972564697 373.3238220214844 0.8411481976509094 390.5807800292969 0.25670549273490906 0.80786115 0.8078939914703369 True -8 20628 25.187416791915894 0.45571374893188477 327.83477783203125 0.3993037939071655 387.57684326171875 0.2613607943058014 0.8130799 0.7563389539718628 True -9 22920 25.204320192337036 0.4602699279785156 327.2998046875 1.0274968147277832 385.49365234375 0.2632453441619873 0.817515 0.7248788475990295 True -10 25212 25.194375038146973 0.4610164165496826 358.1335144042969 0.5600508451461792 384.0212707519531 0.26521778106689453 0.8220736 0.6686148047447205 True -11 27504 25.218688011169434 0.46703243255615234 359.65447998046875 0.6548351049423218 380.54156494140625 0.2692922353744507 0.833247 0.6144785284996033 True -12 29796 25.18536615371704 0.45082736015319824 325.26171875 0.5377925634384155 379.5613708496094 0.2694477140903473 0.8364617 0.5772364735603333 True -13 32088 25.190606832504272 0.456453800201416 285.73895263671875 0.8016977310180664 377.9362487792969 0.27079999446868896 0.84393173 0.547230064868927 True -14 34380 25.234837532043457 9.937687635421753 296.51104736328125 0.4631459712982178 376.25628662109375 0.27263569831848145 0.8461608 0.5301610827445984 True -15 36672 25.360546827316284 0.47014880180358887 326.92572021484375 0.510910153388977 374.6971740722656 0.27347439527511597 0.85069305 0.5125529170036316 True -16 38964 25.297617435455322 0.7067735195159912 279.2296447753906 0.2880774736404419 375.15484619140625 0.27266165614128113 0.8513682 0.5076424479484558 True -17 41256 25.349143505096436 0.4623451232910156 312.55743408203125 0.3662105202674866 375.50030517578125 0.2725190818309784 0.8530667 0.5060497522354126 True -18 43548 25.281360387802124 0.4578378200531006 227.44113159179688 0.5126289129257202 375.6112060546875 0.2733031213283539 0.8518299 0.5114831924438477 False -19 45840 25.276381969451904 0.45674920082092285 349.5187072753906 0.17946848273277283 376.25091552734375 0.27291280031204224 0.8525028 0.5141571760177612 False diff --git a/ENCSR874DUP/cherimoya.fold_2.performance.tsv b/ENCSR874DUP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f612a67811239eb3581752618e251d15c4c83184..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -375.50030517578125 0.49397310614585876 0.2725190818309784 0.09492496401071548 0.8530666828155518 0.7954179048538208 0.5060497522354126 \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_3.evaluate.json b/ENCSR874DUP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 63bc733306abd8bc2e96e8361590338d1b4cb96f..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF822PRE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_3.fit.json b/ENCSR874DUP/cherimoya.fold_3.fit.json deleted file mode 100644 index 980174c7708ef4b6bc4f42959b5a8cdc8dd5909b..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF822PRE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_3.log b/ENCSR874DUP/cherimoya.fold_3.log deleted file mode 100644 index 1e3aca9aacd2c54a310928e4763596d3faa894b3..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2171 27.469812393188477 3.545476198196411 328.32763671875 0.7972393035888672 539.8924560546875 0.16934552788734436 0.56989014 9.583465576171875 True -1 4342 23.942028045654297 0.5964663028717041 417.5640869140625 1.1955143213272095 461.104736328125 0.24361196160316467 0.71423435 4.47190523147583 True -2 6513 23.99989080429077 0.530297040939331 390.86920166015625 0.6505844593048096 443.6390075683594 0.25241366028785706 0.73444915 2.65952467918396 True -3 8684 23.95715618133545 1.5404272079467773 349.14306640625 0.8063890337944031 434.9180603027344 0.25964370369911194 0.7484252 1.8147331476211548 True -4 10855 23.999301195144653 0.4479391574859619 291.8900146484375 0.5573629140853882 427.6996765136719 0.2648734450340271 0.7644718 1.2890909910202026 True -5 13026 23.992650270462036 0.4560403823852539 350.5656433105469 0.8185688257217407 425.1664123535156 0.2675848603248596 0.7686393 1.208377718925476 True -6 15197 24.062981128692627 1.8116645812988281 306.926025390625 0.5002063512802124 421.5973205566406 0.27084940671920776 0.7732612 1.1868144273757935 True -7 17368 23.965408086776733 0.5909316539764404 283.52178955078125 0.7607842683792114 419.07421875 0.27402034401893616 0.7835583 1.1202435493469238 True -8 19539 23.92370867729187 0.4258437156677246 345.8558349609375 0.5713323354721069 416.2437438964844 0.2765576243400574 0.79564345 0.9688534736633301 True -9 21710 23.842324256896973 0.425020694732666 337.561767578125 0.3705264925956726 414.8479919433594 0.2785404622554779 0.8025489 0.9357788562774658 True -10 23881 23.91827082633972 0.4350454807281494 311.27093505859375 0.5369440317153931 412.2477111816406 0.28056272864341736 0.81232005 0.8507140278816223 True -11 26052 23.883754014968872 0.4490320682525635 389.49566650390625 0.8588764071464539 410.1273498535156 0.2830614745616913 0.8187346 0.8032369017601013 True -12 28223 23.874449491500854 0.43554210662841797 369.5264587402344 0.8198434114456177 407.7806091308594 0.28526434302330017 0.8272507 0.7330611348152161 True -13 30394 23.894084930419922 0.8962600231170654 395.6442565917969 0.6644928455352783 405.17364501953125 0.2868814468383789 0.8364074 0.6668893098831177 True -14 32565 23.998413801193237 0.4412062168121338 363.71649169921875 0.39349180459976196 403.27398681640625 0.28791946172714233 0.8407727 0.6343743801116943 True -15 34736 23.887327432632446 0.4554257392883301 338.3387451171875 0.46027249097824097 401.4222412109375 0.2897154688835144 0.84493 0.6003828644752502 True -16 36907 23.88294506072998 0.42771172523498535 275.63983154296875 0.4016485810279846 401.0168151855469 0.29039016366004944 0.84988564 0.5849965810775757 True -17 39078 23.881975650787354 0.4275202751159668 260.82177734375 0.4510567784309387 400.5152282714844 0.29143646359443665 0.85038304 0.5755229592323303 True -18 41249 23.878357887268066 0.43022704124450684 400.81170654296875 0.25277870893478394 401.86968994140625 0.28909313678741455 0.8490418 0.5749632120132446 False -19 43420 23.929858446121216 0.43776583671569824 345.9073486328125 0.4151241183280945 401.1063537597656 0.2907741367816925 0.8480369 0.5780347585678101 False diff --git a/ENCSR874DUP/cherimoya.fold_3.performance.tsv b/ENCSR874DUP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0f1346385f70dba5a310d994db4f77e998c27443..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -400.5152282714844 0.4804207980632782 0.29143643379211426 0.10508882999420166 0.8503830432891846 0.8002263903617859 0.5755229592323303 \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_4.evaluate.json b/ENCSR874DUP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0febc87b7d3ee4e2f98963bfae59b72c03da6740..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF822PRE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_4.fit.json b/ENCSR874DUP/cherimoya.fold_4.fit.json deleted file mode 100644 index 0d6ca12480c0520ba39dcdbf01d4db8a5fa5fdb4..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF822PRE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR874DUP/cherimoya.fold_4.log b/ENCSR874DUP/cherimoya.fold_4.log deleted file mode 100644 index eefe4b661ab43df4a92d404b2e226859b3d38ce8..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2195 27.70963954925537 3.6127097606658936 367.07769775390625 0.8811625242233276 448.2073059082031 0.15141437947750092 0.5772834 7.622847557067871 True -1 4390 24.34090518951416 18.634962558746338 318.9867858886719 1.210585355758667 384.8022155761719 0.21736356616020203 0.729948 3.1528379917144775 True -2 6585 25.31291890144348 0.5184116363525391 325.75970458984375 0.7961246371269226 372.2179260253906 0.22922608256340027 0.7492773 1.9218450784683228 True -3 8780 24.43562602996826 0.49735450744628906 263.6814880371094 0.765487790107727 363.594970703125 0.2350538969039917 0.7602641 1.1447007656097412 True -4 10975 24.2808358669281 0.4779195785522461 305.21746826171875 0.7016961574554443 358.6694641113281 0.23881419003009796 0.77439636 0.9624831676483154 True -5 13170 24.355709075927734 0.47064805030822754 351.64947509765625 0.8854897022247314 356.30633544921875 0.24121667444705963 0.77997947 0.9292150139808655 True -6 15365 24.18549919128418 0.9120826721191406 367.1397705078125 0.6757570505142212 353.5121765136719 0.24500958621501923 0.7859494 0.8757373094558716 True -7 17560 24.179229497909546 0.4554321765899658 387.109619140625 0.7284890413284302 352.4470520019531 0.2459883987903595 0.7905197 0.8316182494163513 True -8 19755 24.17524290084839 0.4443953037261963 414.5145263671875 0.587870717048645 351.1462707519531 0.24687159061431885 0.79515773 0.7691536545753479 True -9 21950 24.189292192459106 0.44487452507019043 435.78271484375 0.9370065927505493 348.0599365234375 0.2520063817501068 0.80539614 0.6942607760429382 True -10 24145 24.18561887741089 0.4400174617767334 292.0031433105469 0.482736200094223 347.2135314941406 0.25222015380859375 0.81416947 0.6418981552124023 True -11 26340 24.146978855133057 0.4435579776763916 270.9510498046875 0.5503576993942261 345.239501953125 0.25587156414985657 0.82168055 0.593084454536438 True -12 28535 24.163278341293335 0.43998098373413086 251.3873291015625 0.39160099625587463 344.2294921875 0.25579363107681274 0.8280133 0.5616235136985779 True -13 30730 24.185539484024048 0.44711995124816895 304.5434875488281 0.7259901762008667 342.35357666015625 0.25864025950431824 0.832511 0.5305604338645935 True -14 32925 24.207459449768066 1.0777256488800049 281.29974365234375 0.5502793788909912 342.01812744140625 0.25804147124290466 0.8397746 0.510314404964447 True -15 35120 24.15832281112671 2.59289813041687 399.404296875 0.38063114881515503 342.54052734375 0.25670185685157776 0.8435433 0.4886327385902405 True -16 37315 24.27414894104004 0.4406921863555908 214.35662841796875 0.3510240316390991 342.3770446777344 0.2563077211380005 0.84775466 0.4792357385158539 True -17 39510 24.140131950378418 0.4397010803222656 304.71600341796875 0.36693814396858215 341.3601379394531 0.258979469537735 0.8466672 0.4801015853881836 False -18 41705 24.133535385131836 0.43758058547973633 257.40716552734375 0.5595995783805847 340.6994323730469 0.26040759682655334 0.8471883 0.48229295015335083 False -19 43900 24.120346069335938 0.45293474197387695 259.5987548828125 0.3777150511741638 340.9831848144531 0.2599668800830841 0.8449799 0.4860385060310364 False diff --git a/ENCSR874DUP/cherimoya.fold_4.performance.tsv b/ENCSR874DUP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fe7cdcb0806a993dee23ea4cfe08cd796b8df2cb..0000000000000000000000000000000000000000 --- a/ENCSR874DUP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -342.3770446777344 0.5060078501701355 0.2563077211380005 0.08930548280477524 0.8477546572685242 0.785869300365448 0.4792357385158539 \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_0.evaluate.json b/ENCSR878ITC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e7d169bcfd838e01941a812cdd7eeb8511882ae8..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187HBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_0.fit.json b/ENCSR878ITC/cherimoya.fold_0.fit.json deleted file mode 100644 index 7879c61713f9ccc5f89165fbf33bc8e326cf0d27..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF187HBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_0.log b/ENCSR878ITC/cherimoya.fold_0.log deleted file mode 100644 index 0301d7b42a9be758f8b006611d64cc19c856876f..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2500 32.90362787246704 3.651949405670166 329.69952392578125 0.8922291994094849 442.3097839355469 0.16417661309242249 0.63975286 6.676033020019531 True -1 5000 27.783461093902588 0.5377793312072754 263.7444152832031 0.6751146912574768 378.6532897949219 0.22063390910625458 0.76088816 3.046090602874756 True -2 7500 27.811243295669556 0.5190703868865967 269.7362365722656 0.7008865475654602 368.8367614746094 0.22758817672729492 0.7704772 2.0834269523620605 True -3 10000 27.205297470092773 0.5433642864227295 269.2154235839844 0.5572718381881714 365.1940612792969 0.22954052686691284 0.7755091 1.34672212600708 True -4 12500 27.154300928115845 0.5365216732025146 278.03265380859375 0.901671826839447 361.7457275390625 0.23253293335437775 0.782212 1.2189438343048096 True -5 15000 27.205602169036865 2.5744788646698 361.08172607421875 0.822684645652771 357.6650085449219 0.23551203310489655 0.7928711 1.076616883277893 True -6 17500 27.20638418197632 1.8835022449493408 253.484130859375 0.5406911373138428 354.0949401855469 0.23878073692321777 0.80171734 0.9508959650993347 True -7 20000 27.313565492630005 0.5328958034515381 316.9181823730469 0.6015007495880127 352.5644226074219 0.2400183081626892 0.8082388 0.8996477723121643 True -8 22500 27.251118421554565 0.5254805088043213 367.44293212890625 1.42511785030365 348.5218505859375 0.24377192556858063 0.8158676 0.7883849740028381 True -9 25000 27.227169275283813 0.7143452167510986 236.08932495117188 0.5812615156173706 346.283203125 0.24623647332191467 0.8237116 0.7148619294166565 True -10 27500 27.276643753051758 0.5245177745819092 291.72479248046875 0.4663029909133911 345.4756774902344 0.24687114357948303 0.8299981 0.6243492364883423 True -11 30000 27.221230268478394 0.5248918533325195 241.7230224609375 0.49263983964920044 343.3825378417969 0.24906136095523834 0.8380807 0.5654823184013367 True -12 32500 27.17161798477173 0.5128514766693115 263.0527648925781 0.5840623378753662 341.58154296875 0.25081866979599 0.8435865 0.5321640968322754 True -13 35000 27.22145366668701 0.5219571590423584 339.2263488769531 0.4118120074272156 340.3280944824219 0.2510535418987274 0.84995437 0.48541250824928284 True -14 37500 27.25146722793579 0.5103967189788818 316.26812744140625 0.5334935188293457 339.0005798339844 0.2521180212497711 0.8556337 0.45247551798820496 True -15 40000 27.3002986907959 0.52459716796875 320.75897216796875 0.45316261053085327 337.5517272949219 0.25410017371177673 0.8615239 0.42973002791404724 True -16 42500 27.234274864196777 0.5236759185791016 313.93206787109375 0.7206815481185913 337.2018737792969 0.25458261370658875 0.863955 0.4227530062198639 True -17 45000 27.281144380569458 0.5207581520080566 287.3500671386719 0.28482818603515625 338.03985595703125 0.253212034702301 0.86477107 0.41869857907295227 True -18 47500 27.247224807739258 0.5368571281433105 307.6407165527344 0.2753249406814575 338.3258361816406 0.2532879412174225 0.8630058 0.4234287142753601 False -19 50000 27.246788024902344 0.5194201469421387 232.71327209472656 0.23736044764518738 337.83917236328125 0.25456300377845764 0.8628635 0.42676958441734314 False diff --git a/ENCSR878ITC/cherimoya.fold_0.performance.tsv b/ENCSR878ITC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ea0b21186a6bdcdec4a405c1d2eb82a594c86bae..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -338.03985595703125 0.5121685862541199 0.253212034702301 0.08313564956188202 0.8647710680961609 0.8092525005340576 0.41869857907295227 \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_1.evaluate.json b/ENCSR878ITC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 43c57bde16a47baf39aa2e7eb57505140305b20a..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187HBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_1.fit.json b/ENCSR878ITC/cherimoya.fold_1.fit.json deleted file mode 100644 index d4babd77f275e0e5c95d6795a18bb555c6c702e8..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF187HBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_1.log b/ENCSR878ITC/cherimoya.fold_1.log deleted file mode 100644 index 4a992185f6d94b4bb9ade1b33aa8c31afde80db2..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2434 31.71025586128235 4.226119518280029 288.4007873535156 0.6202184557914734 558.3707885742188 0.17832279205322266 0.607461 8.37801456451416 True -1 4868 27.034465074539185 0.8602170944213867 265.6012878417969 0.7672805190086365 479.7560119628906 0.24451762437820435 0.7309273 3.90525484085083 True -2 7302 27.06839942932129 0.7618916034698486 236.27850341796875 0.8288492560386658 469.6354675292969 0.25003960728645325 0.74267775 2.7245419025421143 True -3 9736 27.238566160202026 0.6970486640930176 346.436767578125 0.9691731929779053 458.0130920410156 0.2567310035228729 0.7539224 1.7615644931793213 True -4 12170 27.03518795967102 0.6919550895690918 243.83900451660156 0.9014310836791992 450.12542724609375 0.25922322273254395 0.77164423 1.5647379159927368 True -5 14604 27.022497415542603 0.6761074066162109 296.634765625 0.5573500990867615 444.45562744140625 0.2645849287509918 0.78206265 1.3955289125442505 True -6 17038 27.01878023147583 0.6717183589935303 368.8868713378906 0.9830161333084106 438.8653564453125 0.26813074946403503 0.79508936 1.2360337972640991 True -7 19472 26.955525875091553 0.6758620738983154 253.738525390625 0.4202868938446045 435.48187255859375 0.2695288062095642 0.80442816 1.1036180257797241 True -8 21906 26.41625714302063 2.686072826385498 386.31103515625 1.1494156122207642 429.79156494140625 0.27475351095199585 0.8135531 0.9814002513885498 True -9 24340 26.509186506271362 0.711169958114624 242.76565551757812 0.6887951493263245 427.5290832519531 0.2750120162963867 0.82290256 0.8923016786575317 True -10 26774 26.45895218849182 0.7000138759613037 349.050537109375 0.6844414472579956 424.52508544921875 0.2773621082305908 0.83377874 0.790949285030365 True -11 29208 26.464835166931152 0.6709702014923096 286.3860778808594 0.3490612506866455 421.5599670410156 0.2794707417488098 0.84428495 0.6943593621253967 True -12 31642 26.478278875350952 0.6817941665649414 333.7139892578125 0.5625580549240112 417.798828125 0.28426381945610046 0.8513693 0.6265087127685547 True -13 34076 26.494988203048706 0.698632001876831 259.15692138671875 0.529434084892273 414.10882568359375 0.2870160639286041 0.8600917 0.5740734934806824 True -14 36510 26.505616903305054 0.691847562789917 286.77471923828125 0.4442429542541504 412.6703186035156 0.2878628373146057 0.8659386 0.5323589444160461 True -15 38944 26.52673649787903 0.701068639755249 312.6990966796875 0.383695125579834 410.4789733886719 0.2901268005371094 0.8698164 0.5122101902961731 True -16 41378 26.48255157470703 0.6810693740844727 308.9334716796875 0.5469794273376465 411.13018798828125 0.288727730512619 0.8712446 0.4972841441631317 True -17 43812 26.464746475219727 0.6741406917572021 268.50146484375 0.40882977843284607 412.4219665527344 0.2865750789642334 0.8711972 0.4970080256462097 False -18 46246 26.50321364402771 0.6776714324951172 270.181640625 0.3382740914821625 412.04840087890625 0.28847062587738037 0.8704906 0.5001791715621948 False -19 48680 26.47121810913086 1.8039054870605469 228.07269287109375 0.3059627413749695 413.0221252441406 0.2871147692203522 0.8691185 0.5047847032546997 False diff --git a/ENCSR878ITC/cherimoya.fold_1.performance.tsv b/ENCSR878ITC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c00e5224e7d711807a5e1607dfe40e416a5f0cc1..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -411.13018798828125 0.484505295753479 0.2887277603149414 0.10484901070594788 0.8712446093559265 0.8404397964477539 0.4972841441631317 \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_2.evaluate.json b/ENCSR878ITC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b9b1ec326883eb99a061cc91efd79428996ffdf6..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187HBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_2.fit.json b/ENCSR878ITC/cherimoya.fold_2.fit.json deleted file mode 100644 index a3c4d005b92c11bbd73dac00882bb357c6dec8b0..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF187HBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_2.log b/ENCSR878ITC/cherimoya.fold_2.log deleted file mode 100644 index 0c211ad6cc7fac1192e339dcef7e4b0af4a56742..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2602 33.30098009109497 4.438178539276123 336.0167236328125 0.7387695908546448 460.17510986328125 0.17085622251033783 0.6186147 5.9383225440979 True -1 5204 28.985677242279053 0.8798048496246338 337.73565673828125 0.5805093050003052 393.08673095703125 0.22472108900547028 0.7635738 2.5259337425231934 True -2 7806 28.96800208091736 0.9170966148376465 275.3063659667969 0.6409355401992798 383.6686096191406 0.2304220050573349 0.7673412 1.7022968530654907 True -3 10408 28.902717113494873 0.5351274013519287 243.8255615234375 0.9023052453994751 376.1810302734375 0.23568738996982574 0.7812229 1.0479142665863037 True -4 13010 28.894132137298584 0.534268856048584 293.77520751953125 0.7947387099266052 372.7894592285156 0.23741653561592102 0.7848658 1.0178757905960083 True -5 15612 28.898110389709473 0.575791597366333 311.3439636230469 0.6926978230476379 370.5733337402344 0.23885942995548248 0.7955571 0.9599590301513672 True -6 18214 28.902479648590088 0.5587983131408691 277.5479736328125 0.5614407062530518 366.08343505859375 0.24311725795269012 0.8077042 0.8875215649604797 True -7 20816 28.904699563980103 0.5481677055358887 438.2826232910156 0.6047123074531555 363.4809875488281 0.24483633041381836 0.8158947 0.8063465356826782 True -8 23418 28.908000230789185 0.9736983776092529 383.1885986328125 0.709709644317627 361.8075866699219 0.24634753167629242 0.8207294 0.7538385987281799 True -9 26020 28.927642583847046 0.5595109462738037 243.8685302734375 0.5550988912582397 357.9589538574219 0.25127655267715454 0.8312712 0.673129677772522 True -10 28622 28.920140743255615 0.5978477001190186 248.03985595703125 0.4672049582004547 357.1336669921875 0.25277766585350037 0.8283017 0.6977492570877075 False -11 31224 28.98867964744568 0.5863118171691895 437.7716369628906 0.7051570415496826 354.6704406738281 0.2551354765892029 0.8438138 0.5834817290306091 True -12 33826 28.427701711654663 0.5831813812255859 238.6142578125 0.38108599185943604 351.8199462890625 0.258330374956131 0.851354 0.5318664908409119 True -13 36428 28.318626642227173 0.5532271862030029 251.4666748046875 0.4578248858451843 351.4163818359375 0.257377564907074 0.856959 0.47515660524368286 True -14 39030 28.365691900253296 0.5826303958892822 212.31781005859375 0.4469759464263916 350.5963134765625 0.25708529353141785 0.86055964 0.45015454292297363 True -15 41632 28.415515899658203 0.5576250553131104 239.92982482910156 0.38221943378448486 349.2753601074219 0.2585054337978363 0.863711 0.43533095717430115 True -16 44234 28.368655920028687 0.5625364780426025 302.9114990234375 0.35679835081100464 348.68170166015625 0.25949302315711975 0.8645744 0.4244961142539978 True -17 46836 28.348612070083618 0.5498819351196289 339.1387939453125 0.45085734128952026 349.16094970703125 0.2599211037158966 0.86636996 0.4219931960105896 True -18 49438 28.355615377426147 0.5307106971740723 382.5848693847656 0.7614651918411255 349.8313903808594 0.2587151527404785 0.86579555 0.42494893074035645 False -19 52040 28.36376953125 0.5608515739440918 314.2900390625 0.2709994316101074 350.6993103027344 0.25740405917167664 0.86343527 0.42778998613357544 False diff --git a/ENCSR878ITC/cherimoya.fold_2.performance.tsv b/ENCSR878ITC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 15feb118e1d447f78a22dbb220896fadf898168a..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -349.16094970703125 0.5069485902786255 0.2599211037158966 0.08572381734848022 0.8663699626922607 0.8191629648208618 0.4219931960105896 \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_3.evaluate.json b/ENCSR878ITC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 044a96be8a735e06d690698cd70cf75bbcf112e6..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187HBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_3.fit.json b/ENCSR878ITC/cherimoya.fold_3.fit.json deleted file mode 100644 index 6a159475b56ba06d5704214e13ccb3a85fc96821..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF187HBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_3.log b/ENCSR878ITC/cherimoya.fold_3.log deleted file mode 100644 index a6e34bc6525cfae505d89904064a7490f36aacaf..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2487 32.58388638496399 3.642751932144165 306.3046875 0.6013966798782349 485.0472717285156 0.18032370507717133 0.5908883 6.931756973266602 True -1 4974 27.711562633514404 1.6834032535552979 376.2430419921875 0.6769607067108154 413.5827941894531 0.2397041916847229 0.73469347 3.1261229515075684 True -2 7461 27.75982642173767 0.5376982688903809 317.99517822265625 0.706474781036377 410.54736328125 0.24208520352840424 0.71467924 2.2463130950927734 False -3 9948 27.676945686340332 1.20729660987854 268.894287109375 0.7375681400299072 398.7822570800781 0.24953199923038483 0.75176877 1.3800302743911743 True -4 12435 27.683584690093994 18.573983669281006 338.03411865234375 0.5531110763549805 393.718994140625 0.2517983019351959 0.77066433 1.0855531692504883 True -5 14922 27.874674558639526 0.5183193683624268 290.90447998046875 0.6054854393005371 388.172119140625 0.25746485590934753 0.7828004 1.0145611763000488 True -6 17409 28.107066869735718 0.930870532989502 275.447509765625 0.6160005331039429 384.97442626953125 0.25954484939575195 0.7952918 0.9629569053649902 True -7 19896 28.00790500640869 19.88047170639038 381.8311462402344 0.5902515649795532 382.6058349609375 0.26223164796829224 0.8006175 0.8873592019081116 True -8 22383 27.68638777732849 0.48534369468688965 277.32489013671875 0.5647780895233154 380.00762939453125 0.26511961221694946 0.80743426 0.8255336880683899 True -9 24870 27.717370986938477 1.6642177104949951 354.6446533203125 0.6955461502075195 378.1993713378906 0.26638689637184143 0.81193817 0.8167932033538818 True -10 27357 27.72991394996643 0.4939689636230469 315.9642028808594 0.7929860949516296 375.946533203125 0.2700653672218323 0.8168186 0.785637617111206 True -11 29844 27.657211780548096 0.4772815704345703 263.46307373046875 0.45877736806869507 375.68316650390625 0.2692105174064636 0.8236963 0.748085081577301 True -12 32331 27.73257851600647 0.4888191223144531 211.00534057617188 0.7457202672958374 371.7684326171875 0.27394428849220276 0.82853425 0.70439612865448 True -13 34818 27.672040700912476 0.4738142490386963 231.9324188232422 0.40219539403915405 371.11712646484375 0.2742086946964264 0.8342677 0.6493094563484192 True -14 37305 27.66846799850464 0.4895141124725342 332.9515380859375 0.5764732360839844 368.3658447265625 0.2766258716583252 0.84165394 0.6004512310028076 True -15 39792 27.65441370010376 0.47130560874938965 364.1640625 0.5024486780166626 366.8308410644531 0.278076708316803 0.84710085 0.5591422319412231 True -16 42279 27.721301555633545 0.4683694839477539 349.61077880859375 0.2934896647930145 365.7938232421875 0.27860739827156067 0.8521398 0.5278525948524475 True -17 44766 27.070481300354004 0.8975718021392822 237.62307739257812 0.27810171246528625 366.83612060546875 0.2777310311794281 0.85508555 0.5112072825431824 True -18 47253 27.13397789001465 0.4771597385406494 250.656982421875 0.3087314963340759 366.8583679199219 0.27763843536376953 0.8569138 0.5090355277061462 True -19 49740 27.099408864974976 0.47859621047973633 273.36572265625 0.32964324951171875 367.0660095214844 0.27771690487861633 0.85687625 0.5116138458251953 False diff --git a/ENCSR878ITC/cherimoya.fold_3.performance.tsv b/ENCSR878ITC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 441091f745fad94592184efeeafccd10332f9e6b..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -366.8583679199219 0.49553173780441284 0.27763843536376953 0.09488870203495026 0.8569138050079346 0.8042242527008057 0.5090355277061462 \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_4.evaluate.json b/ENCSR878ITC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 415d16b6d623d4bdef006da16d1f6715a5a4ba63..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF187HBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_4.fit.json b/ENCSR878ITC/cherimoya.fold_4.fit.json deleted file mode 100644 index 3662a00633388c972ac6b08632ae078117a1ba51..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF187HBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR878ITC/cherimoya.fold_4.log b/ENCSR878ITC/cherimoya.fold_4.log deleted file mode 100644 index 784d818626e46e8860d347c064fdeabff6c7573d..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2508 33.49323391914368 4.033404588699341 280.914306640625 0.5527744293212891 390.6832275390625 0.1625487059354782 0.598086 6.042891979217529 True -1 5016 27.952630281448364 0.5953021049499512 305.2198486328125 0.7196617722511292 342.8587646484375 0.21052157878875732 0.7167955 2.144026041030884 True -2 7524 27.900519132614136 0.588965654373169 303.17803955078125 0.6650933027267456 337.0130615234375 0.21618282794952393 0.72495717 1.4897730350494385 True -3 10032 27.944987297058105 0.5371780395507812 317.81353759765625 0.6547725200653076 328.4437561035156 0.22211690247058868 0.74963224 0.9252413511276245 True -4 12540 27.95689845085144 0.5418908596038818 242.44532775878906 0.749889075756073 324.2033386230469 0.22334066033363342 0.76604134 0.7557056546211243 True -5 15048 27.91683077812195 0.6444652080535889 203.02108764648438 0.5808936953544617 321.7214050292969 0.22599661350250244 0.77439547 0.7322767972946167 True -6 17556 27.936166524887085 0.5368373394012451 408.0462951660156 0.813865065574646 318.9694519042969 0.2282356172800064 0.78207433 0.7172664403915405 True -7 20064 27.98007297515869 10.488178491592407 206.0463409423828 0.6439829468727112 316.8641357421875 0.22970758378505707 0.7921044 0.6964003443717957 True -8 22572 27.950499534606934 0.5321362018585205 295.3852233886719 0.5603065490722656 315.8663024902344 0.23046836256980896 0.8000819 0.6429775953292847 True -9 25080 27.939859867095947 0.5267982482910156 416.1041564941406 0.6291290521621704 313.7866516113281 0.23307622969150543 0.8080788 0.6243616938591003 True -10 27588 27.978864431381226 0.5368397235870361 197.57577514648438 0.7607104778289795 312.0015563964844 0.2360418289899826 0.81285745 0.5856172442436218 True -11 30096 27.957287073135376 0.5396807193756104 267.5701599121094 0.4609963297843933 311.1241149902344 0.2363302856683731 0.8169072 0.5466533899307251 True -12 32604 27.951959371566772 0.5303993225097656 249.85093688964844 0.46627694368362427 310.2510986328125 0.23708447813987732 0.8250357 0.5119685530662537 True -13 35112 28.006171941757202 0.5609405040740967 262.6280517578125 0.4660664498806 308.4392395019531 0.23985223472118378 0.8289661 0.496568500995636 True -14 37620 27.99307942390442 12.377918720245361 250.35606384277344 0.6188218593597412 307.12628173828125 0.24043697118759155 0.8366767 0.467673122882843 True -15 40128 28.42280149459839 0.557929515838623 276.8920593261719 0.3568996787071228 306.0560607910156 0.24205176532268524 0.8427448 0.434815913438797 True -16 42636 28.024362325668335 0.545555591583252 314.66485595703125 0.28083908557891846 305.375732421875 0.2418326884508133 0.84663033 0.4210115671157837 True -17 45144 28.08307933807373 0.5487282276153564 321.684814453125 0.27799028158187866 306.1100158691406 0.24122567474842072 0.8484927 0.4139588475227356 True -18 47652 28.00091290473938 0.5486330986022949 220.72488403320312 0.5743845105171204 306.0489807128906 0.24102291464805603 0.8485191 0.4138524830341339 True -19 50160 27.94459366798401 1.5008087158203125 250.1660614013672 0.46102118492126465 306.9420471191406 0.23933374881744385 0.8486725 0.4151802659034729 True diff --git a/ENCSR878ITC/cherimoya.fold_4.performance.tsv b/ENCSR878ITC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0bdbf2e8175fd1307e0575d5df0d5826f935c90f..0000000000000000000000000000000000000000 --- a/ENCSR878ITC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -306.9420471191406 0.5223615169525146 0.23933377861976624 0.07530316710472107 0.8486725091934204 0.782018780708313 0.4151802659034729 \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_0.evaluate.json b/ENCSR879EVD/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ada7a61361bf5eeea8de574ab2ba51d7b8fad596..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF529OII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_0.fit.json b/ENCSR879EVD/cherimoya.fold_0.fit.json deleted file mode 100644 index 68859e0bc3d4d67d002b6902ab1f546326c95a29..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF529OII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_0.log b/ENCSR879EVD/cherimoya.fold_0.log deleted file mode 100644 index e6d73af45c1b9c93a4471a0690e4444ddef39575..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 34.215166330337524 3.660569667816162 613.5157470703125 0.5415008664131165 870.693603515625 0.29157742857933044 0.6989296 7.346479415893555 True -1 5482 30.896748304367065 0.6345829963684082 735.8789672851562 1.0377240180969238 763.334228515625 0.3759530782699585 0.7605315 1.8299015760421753 True -2 8223 30.675023078918457 0.6096181869506836 632.9935913085938 0.7183693051338196 742.8433837890625 0.39080703258514404 0.77340025 0.9570671916007996 True -3 10964 30.740238428115845 0.6219279766082764 594.8638916015625 0.694501519203186 734.0455322265625 0.39632904529571533 0.7796545 0.8498448729515076 True -4 13705 30.77663016319275 0.6171875 573.656494140625 0.6384634971618652 725.7272338867188 0.4018257260322571 0.78187823 0.8434574604034424 True -5 16446 30.694803953170776 0.6208310127258301 542.264404296875 0.6022331714630127 718.7733764648438 0.4076444208621979 0.7872697 0.6425763964653015 True -6 19187 30.73116183280945 0.6157073974609375 620.7809448242188 0.5773147940635681 716.4833374023438 0.40812432765960693 0.78953046 0.65764981508255 True -7 21928 30.67816948890686 0.6199848651885986 546.5049438476562 0.5355933904647827 711.53662109375 0.4132634699344635 0.7985596 0.5950501561164856 True -8 24669 30.663572788238525 0.6130671501159668 598.8445434570312 0.7253023386001587 707.6461791992188 0.4164300560951233 0.8026784 0.5495655536651611 True -9 27410 31.144400119781494 5.06493353843689 539.472900390625 0.5964629650115967 703.2521362304688 0.4218120872974396 0.8088986 0.5224394202232361 True -10 30151 30.649399042129517 0.6246047019958496 621.8330078125 0.5198267698287964 701.0362548828125 0.42288529872894287 0.81405646 0.4844760596752167 True -11 32892 30.71041464805603 0.6307904720306396 482.14166259765625 0.5251383781433105 697.41162109375 0.4269247055053711 0.820078 0.4637240469455719 True -12 35633 30.67662501335144 0.9101152420043945 555.1798095703125 0.4732667803764343 693.3234252929688 0.4295336902141571 0.8279123 0.4230741262435913 True -13 38374 30.734461069107056 0.656449556350708 515.7484741210938 0.5717877149581909 689.9909057617188 0.4319703280925751 0.8326289 0.4033125042915344 True -14 41115 30.7162823677063 0.6188647747039795 548.8779907226562 0.44220268726348877 687.7474975585938 0.43409934639930725 0.8362156 0.3848446309566498 True -15 43856 30.663024425506592 0.6278998851776123 430.0269775390625 0.3869592249393463 687.451416015625 0.43414944410324097 0.8423958 0.3659272789955139 True -16 46597 30.72465443611145 0.6205050945281982 496.7922058105469 0.4080708920955658 685.63232421875 0.43582022190093994 0.8454054 0.35217878222465515 True -17 49338 30.756128549575806 0.6197168827056885 531.874755859375 0.3965698480606079 685.8682861328125 0.4354061186313629 0.8459524 0.3493342995643616 True -18 52079 30.70964217185974 0.6176824569702148 711.0909423828125 0.19169119000434875 685.838134765625 0.4357754588127136 0.84815735 0.34726786613464355 True -19 54820 30.650038242340088 0.619159460067749 535.4439086914062 0.4504935145378113 686.6170654296875 0.43479031324386597 0.8474079 0.3481113910675049 False diff --git a/ENCSR879EVD/cherimoya.fold_0.performance.tsv b/ENCSR879EVD/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 72c54da2ec7e5a915a945da566bf2a7f0180de97..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -685.838134765625 0.3542829751968384 0.43577542901039124 0.1937226951122284 0.8481573462486267 0.8023404479026794 0.34726786613464355 \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_1.evaluate.json b/ENCSR879EVD/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3645b102e3e858e7e1726e4dd4ed0bc55bacc985..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF529OII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_1.fit.json b/ENCSR879EVD/cherimoya.fold_1.fit.json deleted file mode 100644 index 35ecaa14b78c98e699bebebd95ff846c9c9dd69a..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF529OII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_1.log b/ENCSR879EVD/cherimoya.fold_1.log deleted file mode 100644 index ada5898ad132dda2d1c221989fea520015134af3..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 34.11402225494385 3.759631872177124 600.817626953125 0.7659818530082703 1055.24658203125 0.29910725355148315 0.6981737 7.5536065101623535 True -1 5404 30.69014835357666 0.7365803718566895 601.50439453125 0.8061907291412354 905.48876953125 0.3927030861377716 0.76480496 2.290195941925049 True -2 8106 30.245943784713745 0.7249555587768555 553.3350830078125 0.7158254384994507 882.9662475585938 0.4052582085132599 0.77684957 1.3244140148162842 True -3 10808 30.19570302963257 0.726973295211792 604.9872436523438 0.6729571223258972 867.2177734375 0.4164101779460907 0.7842257 1.214050054550171 True -4 13510 30.213399171829224 0.726773738861084 579.71435546875 0.47690221667289734 857.740966796875 0.42122992873191833 0.7866706 1.0301482677459717 True -5 16212 30.223533391952515 6.536746501922607 651.190673828125 0.7617884874343872 848.8519287109375 0.42642807960510254 0.79713386 0.847618043422699 True -6 18914 30.28231430053711 0.759364128112793 583.4189453125 0.5865713357925415 844.52734375 0.42883676290512085 0.80130786 0.7771847248077393 True -7 21616 30.31942057609558 0.7235031127929688 636.6455078125 0.4920465648174286 838.8363037109375 0.4327470660209656 0.8086831 0.6790828704833984 True -8 24318 30.270470142364502 0.8050222396850586 601.90283203125 0.6783962845802307 832.4267578125 0.43765097856521606 0.8128332 0.6054300665855408 True -9 27020 30.48240089416504 0.7573602199554443 518.8479614257812 0.5471303462982178 831.2899169921875 0.43708303570747375 0.81712097 0.6047353744506836 True -10 29722 30.295392274856567 0.753455638885498 524.2891235351562 0.3190963864326477 825.8081665039062 0.4413948059082031 0.8246027 0.5530440807342529 True -11 32424 30.23669195175171 0.7375223636627197 662.1385498046875 0.5753891468048096 820.8499145507812 0.4448159337043762 0.82940435 0.5284709334373474 True -12 35126 30.22531008720398 0.7368354797363281 569.1143798828125 0.42547607421875 816.3902587890625 0.44841545820236206 0.8349763 0.4930507242679596 True -13 37828 30.249050617218018 0.7324376106262207 654.2260131835938 0.43422192335128784 810.6690673828125 0.45197609066963196 0.84133786 0.45970460772514343 True -14 40530 30.29158663749695 0.7282683849334717 484.8175354003906 0.41657739877700806 808.6047973632812 0.4514501690864563 0.8469686 0.4377526044845581 True -15 43232 30.220451831817627 0.7376394271850586 678.8480224609375 0.5104141235351562 803.918701171875 0.45625582337379456 0.85066175 0.4124707877635956 True -16 45934 30.210351943969727 0.7342085838317871 657.91357421875 0.4006742537021637 804.392822265625 0.45558494329452515 0.85509264 0.39572909474372864 True -17 48636 30.20782494544983 0.7259194850921631 551.3795776367188 0.31725379824638367 803.62646484375 0.45614010095596313 0.8556458 0.3868427574634552 True -18 51338 30.23920750617981 0.7362229824066162 546.7808837890625 0.3152962625026703 801.4697265625 0.45773884654045105 0.8569161 0.3852262794971466 True -19 54040 30.281642198562622 0.7347018718719482 601.4803466796875 0.3496793508529663 803.801513671875 0.4551217257976532 0.8577426 0.3845062255859375 True diff --git a/ENCSR879EVD/cherimoya.fold_1.performance.tsv b/ENCSR879EVD/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cad2a11f1dcf9d33a5daee4ebc66f7bc32fa3ddb..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -803.801513671875 0.33493831753730774 0.455121785402298 0.2168220579624176 0.8577426075935364 0.8282480835914612 0.3845062255859375 \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_2.evaluate.json b/ENCSR879EVD/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 76fb77fdfa3df04cfb970e0769c3ee34b531efb3..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF529OII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_2.fit.json b/ENCSR879EVD/cherimoya.fold_2.fit.json deleted file mode 100644 index e62ecdd28c4f9bc14721ff510ed37baf1b97f54c..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF529OII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_2.log b/ENCSR879EVD/cherimoya.fold_2.log deleted file mode 100644 index 580ad6d92a3e144c35e4d508bab25c3d66625773..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 36.086687326431274 3.6924986839294434 680.4090576171875 0.793342113494873 911.9597778320312 0.29902058839797974 0.7068551 5.466585636138916 True -1 5748 32.22273516654968 0.6233789920806885 624.0170288085938 0.646936297416687 795.1326904296875 0.3817741274833679 0.76528126 2.025099277496338 True -2 8622 32.22456431388855 0.6268706321716309 608.6751708984375 0.4130326509475708 776.0679321289062 0.3909364640712738 0.77207965 1.1030067205429077 True -3 11496 32.184333086013794 0.6108379364013672 658.1370849609375 0.5088204145431519 766.0778198242188 0.3984679877758026 0.7788797 0.8674092292785645 True -4 14370 32.19110941886902 0.6082198619842529 490.82061767578125 0.6331931352615356 756.0790405273438 0.4051019549369812 0.7857569 0.7845180034637451 True -5 17244 32.24779176712036 0.6046285629272461 423.8577880859375 0.5841208696365356 748.8724365234375 0.4109835624694824 0.79032815 0.6864945888519287 True -6 20118 32.17622184753418 1.0692462921142578 569.76708984375 0.4560537338256836 744.7437133789062 0.41337865591049194 0.7964634 0.6415310502052307 True -7 22992 32.112542390823364 0.6051890850067139 483.32037353515625 0.6657730340957642 740.1087036132812 0.4166601002216339 0.79909223 0.633650541305542 True -8 25866 32.1151978969574 0.6109602451324463 518.3803100585938 0.5683591365814209 734.3264770507812 0.4220411479473114 0.8040253 0.6254527568817139 True -9 28740 32.122318506240845 0.6182498931884766 622.52880859375 0.5388689041137695 730.69482421875 0.4247468411922455 0.81232804 0.5957944393157959 True -10 31614 32.17817997932434 0.6172506809234619 626.1944580078125 0.4512787163257599 727.5233764648438 0.4273883104324341 0.8153201 0.5371140837669373 True -11 34488 32.190085649490356 0.6319587230682373 634.5160522460938 0.38110992312431335 723.0947875976562 0.4309692680835724 0.8207418 0.49952030181884766 True -12 37362 32.18107318878174 0.6074962615966797 534.3544921875 0.3695937991142273 721.1882934570312 0.4323532283306122 0.82756406 0.44596004486083984 True -13 40236 32.2126841545105 0.6218421459197998 540.5714111328125 0.5410007238388062 716.6552734375 0.43648022413253784 0.83139193 0.4274749159812927 True -14 43110 32.18505549430847 0.626807689666748 587.6898193359375 0.2649751305580139 713.2029418945312 0.44032615423202515 0.83516794 0.4037308692932129 True -15 45984 32.321364641189575 0.6259090900421143 508.19146728515625 0.3137049376964569 713.7684936523438 0.43889084458351135 0.83867586 0.3875316381454468 True -16 48858 32.212053060531616 0.6288003921508789 655.8682861328125 0.3676729202270508 713.3809204101562 0.4390299618244171 0.8412815 0.3746454119682312 True -17 51732 32.47347021102905 5.5351245403289795 524.92431640625 0.24852962791919708 710.1131591796875 0.4431728720664978 0.8419192 0.37093159556388855 True -18 54606 32.39996314048767 0.6239628791809082 553.163818359375 0.3614766001701355 714.4999389648438 0.43720677495002747 0.8420005 0.36960482597351074 True -19 57480 32.33651399612427 0.7234947681427002 503.0628662109375 0.4298984706401825 714.8507080078125 0.43699896335601807 0.8411685 0.37398412823677063 False diff --git a/ENCSR879EVD/cherimoya.fold_2.performance.tsv b/ENCSR879EVD/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6440c0df6087a1e106227791ffa6161282095957..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -714.4999389648438 0.3507375419139862 0.43720680475234985 0.19493331015110016 0.8420004844665527 0.80189049243927 0.36960482597351074 \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_3.evaluate.json b/ENCSR879EVD/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4d4900a14df7c448b7fd524b3515e40a568ee739..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF529OII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_3.fit.json b/ENCSR879EVD/cherimoya.fold_3.fit.json deleted file mode 100644 index 05eff72bb74237af3f7c33044f49399c5376c118..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF529OII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_3.log b/ENCSR879EVD/cherimoya.fold_3.log deleted file mode 100644 index a674a9c11de8c4197413985e114f9c710e1b3ce7..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 34.64651799201965 3.541134834289551 755.2957153320312 0.9235049486160278 866.4118041992188 0.306213915348053 0.6939481 5.968529224395752 True -1 5502 30.94337558746338 0.5874617099761963 739.495849609375 0.5045254230499268 752.324951171875 0.3898838460445404 0.77109146 2.1354928016662598 True -2 8253 30.91384983062744 0.5595624446868896 522.1549072265625 0.58318030834198 736.4913330078125 0.39936843514442444 0.7775072 1.5257458686828613 True -3 11004 30.773550748825073 0.5616528987884521 579.875732421875 0.5578064918518066 727.3035888671875 0.4057422876358032 0.78570664 1.0859249830245972 True -4 13755 30.79471254348755 0.5663444995880127 659.23291015625 0.615605890750885 720.5997924804688 0.4094238579273224 0.78875095 1.0453300476074219 True -5 16506 30.87257409095764 1.223633050918579 756.5478515625 0.6391599178314209 715.6590576171875 0.4144284427165985 0.7913374 0.8747624158859253 True -6 19257 30.78190779685974 0.5656435489654541 490.32177734375 0.6223544478416443 713.890625 0.4133644998073578 0.7967759 0.7986251711845398 True -7 22008 30.79537010192871 0.567633867263794 625.1246948242188 0.4699987471103668 708.3209228515625 0.4178585410118103 0.80249065 0.7747917175292969 True -8 24759 30.732805252075195 0.5611636638641357 570.6067504882812 0.5095974802970886 702.8897094726562 0.42311230301856995 0.80678076 0.7479420900344849 True -9 27510 30.735386610031128 0.5685896873474121 606.8333740234375 0.5514045357704163 701.3062744140625 0.42395511269569397 0.80857587 0.7242454290390015 True -10 30261 30.731927633285522 0.5668153762817383 545.8258666992188 0.6054056286811829 695.441650390625 0.42955848574638367 0.81332725 0.6642863154411316 True -11 33012 30.775520086288452 0.5616304874420166 476.87677001953125 0.6540574431419373 691.63525390625 0.43172550201416016 0.81864595 0.5876522064208984 True -12 35763 30.881248712539673 0.5672969818115234 630.3489990234375 0.4224529266357422 686.7675170898438 0.4358508586883545 0.82367396 0.5351070761680603 True -13 38514 30.829582452774048 0.560316801071167 532.0438232421875 0.5299245119094849 683.7853393554688 0.43828222155570984 0.833738 0.4855087101459503 True -14 41265 30.794137239456177 0.5616738796234131 529.2185668945312 0.5180172324180603 680.8404541015625 0.44070714712142944 0.8393503 0.4365842938423157 True -15 44016 30.82572603225708 0.5642096996307373 551.00537109375 0.45452702045440674 678.5908203125 0.4413956105709076 0.8447194 0.40531280636787415 True -16 46767 30.80340051651001 0.5554709434509277 599.6521606445312 0.35344040393829346 679.054931640625 0.4395793080329895 0.8483323 0.3903875946998596 True -17 49518 30.81176233291626 0.5611495971679688 532.7599487304688 0.3424624800682068 678.074951171875 0.4412708282470703 0.849196 0.3810793161392212 True -18 52269 31.286747694015503 1.7060127258300781 485.86102294921875 0.27178674936294556 678.1911010742188 0.44076207280158997 0.84846747 0.37847843766212463 False -19 55020 30.80373525619507 0.5829520225524902 554.154052734375 0.2793043851852417 677.4161376953125 0.44156956672668457 0.8479929 0.3775758743286133 False diff --git a/ENCSR879EVD/cherimoya.fold_3.performance.tsv b/ENCSR879EVD/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1be18e309d0c3179534eaea99d992fc7f1c5663b..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -678.074951171875 0.3518235683441162 0.4412708878517151 0.19561661779880524 0.8491960167884827 0.8012198805809021 0.3810793161392212 \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_4.evaluate.json b/ENCSR879EVD/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 22439e63c7557ca58962ccda0871b7343a3d895c..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF529OII.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_4.fit.json b/ENCSR879EVD/cherimoya.fold_4.fit.json deleted file mode 100644 index 24e38790c78f460242a73edfe0de420b8b9d754a..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF529OII.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879EVD/cherimoya.fold_4.log b/ENCSR879EVD/cherimoya.fold_4.log deleted file mode 100644 index 662242215960bdc335fc5d57c7c118301d70bab5..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2818 35.413984060287476 3.658266067504883 600.0218505859375 0.8348844051361084 812.7700805664062 0.304426372051239 0.69562536 5.577076435089111 True -1 5636 31.582424640655518 0.6364791393280029 563.0846557617188 0.5649656057357788 719.31494140625 0.3763515055179596 0.7486768 2.0734009742736816 True -2 8454 31.54280161857605 0.615490198135376 529.06787109375 0.6463461518287659 704.3016967773438 0.386415958404541 0.76230264 1.0839823484420776 True -3 11272 31.561655044555664 0.6274635791778564 562.1007080078125 0.45819365978240967 695.2962646484375 0.3934323489665985 0.768178 1.0076968669891357 True -4 14090 31.52834963798523 0.639301061630249 559.6878662109375 0.5437126159667969 686.1873168945312 0.4017348885536194 0.7767775 0.9092133045196533 True -5 16908 31.522738218307495 0.6210422515869141 512.808837890625 0.3991575837135315 684.2557373046875 0.40184929966926575 0.7797982 0.7383341193199158 True -6 19726 31.483391523361206 0.6213116645812988 661.3759765625 0.5619686841964722 679.34375 0.40613824129104614 0.7872893 0.7129775285720825 True -7 22544 31.48836064338684 1.7519383430480957 534.9500732421875 0.33024606108665466 676.9322509765625 0.4081912338733673 0.7917776 0.6289933323860168 True -8 25362 31.479724645614624 0.6244411468505859 551.9189453125 0.5812224745750427 675.1201171875 0.40892672538757324 0.7972062 0.5829488635063171 True -9 28180 31.479458332061768 1.5167691707611084 605.79052734375 0.4266625642776489 670.0526123046875 0.4142514169216156 0.8041503 0.5429767370223999 True -10 30998 31.625796794891357 0.6306891441345215 612.3831787109375 0.4114287495613098 666.3428344726562 0.417557954788208 0.8078577 0.5094395875930786 True -11 33816 31.522337913513184 0.6406421661376953 687.440185546875 0.2641723155975342 664.0322265625 0.419828325510025 0.81310827 0.48439985513687134 True -12 36634 31.558438539505005 0.6282210350036621 625.034423828125 0.2623288333415985 660.1512451171875 0.4233076870441437 0.817586 0.4561167061328888 True -13 39452 31.5395667552948 0.6127190589904785 553.7255859375 0.3637241721153259 657.8091430664062 0.4267504811286926 0.8225158 0.42903634905815125 True -14 42270 31.520403146743774 0.6241157054901123 528.798828125 0.468498170375824 654.1416625976562 0.4293711483478546 0.8277987 0.40050676465034485 True -15 45088 31.49904441833496 0.6248660087585449 554.9276123046875 0.3592228591442108 653.7464599609375 0.42942014336586 0.8330553 0.37416693568229675 True -16 47906 31.510426998138428 0.6266510486602783 554.5914306640625 0.48690712451934814 653.0712890625 0.4297940731048584 0.8356792 0.3611176311969757 True -17 50724 31.503514766693115 0.619807243347168 547.6951904296875 0.3260851502418518 653.182373046875 0.42927175760269165 0.8371392 0.3544679284095764 True -18 53542 31.582743644714355 0.6306159496307373 603.6777954101562 0.22739355266094208 654.5662231445312 0.4280494153499603 0.8376548 0.35465100407600403 True -19 56360 31.570281267166138 0.6224033832550049 516.382568359375 0.32483556866645813 653.2027587890625 0.43027785420417786 0.8373927 0.3557027280330658 False diff --git a/ENCSR879EVD/cherimoya.fold_4.performance.tsv b/ENCSR879EVD/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fc8e028da03a643ddf858f98ab10453a8d530f4d..0000000000000000000000000000000000000000 --- a/ENCSR879EVD/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -654.5662231445312 0.35949093103408813 0.4280494451522827 0.19094571471214294 0.8376548290252686 0.7844452857971191 0.35465100407600403 \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_0.evaluate.json b/ENCSR879XUH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index def9f38bb24a35dd9f427701fb8b87f843a96437..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325MUR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_0.fit.json b/ENCSR879XUH/cherimoya.fold_0.fit.json deleted file mode 100644 index 587c5375ed7f88c87164be90f39275607e49a5f9..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF325MUR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_0.log b/ENCSR879XUH/cherimoya.fold_0.log deleted file mode 100644 index a99e02c8fabbe0022017e34aec88ce85f594b0a5..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 35.1435010433197 3.939927816390991 379.2542724609375 0.3084152638912201 551.40234375 0.26525089144706726 0.7586886 3.647653341293335 True -1 5482 30.345075130462646 0.6316921710968018 428.3104248046875 0.26410815119743347 507.2109069824219 0.335290789604187 0.8133668 1.2076994180679321 True -2 8223 30.418726682662964 0.5896003246307373 424.5716552734375 0.23396828770637512 497.0966491699219 0.35116592049598694 0.82939726 0.44257020950317383 True -3 10964 30.35438299179077 0.5914795398712158 435.6505126953125 0.3011400103569031 494.2069396972656 0.3559948205947876 0.83344966 0.38093987107276917 True -4 13705 30.35512924194336 1.1286890506744385 415.7792053222656 0.4368840157985687 492.6807556152344 0.35811710357666016 0.8370341 0.3522713780403137 True -5 16446 30.3830509185791 0.6227965354919434 437.01409912109375 0.26217809319496155 491.5001525878906 0.3610377013683319 0.8437328 0.35094475746154785 True -6 19187 30.359262943267822 0.6187260150909424 418.08929443359375 0.42692244052886963 488.9422302246094 0.36579975485801697 0.85022867 0.2656915783882141 True -7 21928 30.42103338241577 1.2918386459350586 401.8573913574219 0.3205086588859558 487.6774597167969 0.36786022782325745 0.8524966 0.2505013942718506 True -8 24669 30.384297132492065 0.5797348022460938 445.07867431640625 0.29752400517463684 486.4714050292969 0.3696175515651703 0.8576921 0.23402704298496246 True -9 27410 30.35633611679077 0.5902831554412842 458.62109375 0.2398337572813034 485.8339538574219 0.3699730932712555 0.8571727 0.2490188628435135 False -10 30151 30.37332510948181 0.5864825248718262 498.8276062011719 0.22362640500068665 484.7441711425781 0.3722555339336395 0.8622609 0.22190134227275848 True -11 32892 30.346399068832397 0.6342020034790039 427.47576904296875 0.2197532206773758 482.3367004394531 0.3767741918563843 0.8656776 0.20261090993881226 True -12 35633 30.400866270065308 0.5961284637451172 442.7554931640625 0.28445398807525635 482.48828125 0.37572306394577026 0.8687023 0.19896739721298218 True -13 38374 30.420592069625854 0.5840141773223877 380.1431884765625 0.18851767480373383 481.3296203613281 0.377083957195282 0.87320113 0.1893845498561859 True -14 41115 30.446568727493286 0.5866649150848389 378.428466796875 0.1979435384273529 479.8154296875 0.38002893328666687 0.8768282 0.18222583830356598 True -15 43856 30.396162271499634 0.5917062759399414 363.63714599609375 0.1607322096824646 479.4043273925781 0.38003408908843994 0.8805022 0.17426098883152008 True -16 46597 30.346763134002686 0.5830199718475342 435.54132080078125 0.1824863851070404 478.7410583496094 0.3809846043586731 0.88299614 0.17116312682628632 True -17 49338 30.349406957626343 0.5876362323760986 418.6439514160156 0.17218981683254242 479.2640686035156 0.3797500431537628 0.8840714 0.16894908249378204 True -18 52079 30.44055700302124 1.6176903247833252 436.88336181640625 0.12240791320800781 478.2901306152344 0.38280048966407776 0.88624746 0.1700953245162964 True -19 54820 30.21204113960266 0.5850744247436523 407.3724670410156 0.23853141069412231 478.9112854003906 0.3811399042606354 0.88370657 0.17068159580230713 False diff --git a/ENCSR879XUH/cherimoya.fold_0.performance.tsv b/ENCSR879XUH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8a1a0edc97a4960c0dbfbaf36034acebb93ce301..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -478.2901306152344 0.40736520290374756 0.38280048966407776 0.13636910915374756 0.886247456073761 0.8598275780677795 0.1700953245162964 \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_1.evaluate.json b/ENCSR879XUH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index fe6770f1789d889fed0702637fb6f04421be0111..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325MUR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_1.fit.json b/ENCSR879XUH/cherimoya.fold_1.fit.json deleted file mode 100644 index ecbf55ec364448e6080d5cd4e691069ed58b6198..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF325MUR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_1.log b/ENCSR879XUH/cherimoya.fold_1.log deleted file mode 100644 index cb86a9b89cf1b3a525073bf0a3e7bcbe4c378cf2..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 35.04944634437561 5.026365280151367 466.1341247558594 0.3660314083099365 642.4249267578125 0.268051415681839 0.7616399 4.353548049926758 True -1 5410 30.01019263267517 0.7186546325683594 438.080078125 0.33205926418304443 583.939697265625 0.35230252146720886 0.8152662 1.0761992931365967 True -2 8115 29.97909927368164 0.6806988716125488 402.4949645996094 0.30247414112091064 571.3983154296875 0.36904528737068176 0.8311781 0.4118850827217102 True -3 10820 29.94693613052368 0.6765823364257812 396.0834655761719 0.2630908787250519 566.1263427734375 0.3744925260543823 0.831322 0.3993692994117737 True -4 13525 29.92657494544983 0.8105738162994385 448.3411560058594 0.2685004472732544 562.8566284179688 0.37935078144073486 0.8361789 0.31423893570899963 True -5 16230 29.922232151031494 0.6888747215270996 467.3824768066406 0.24814473092556 560.6642456054688 0.38139083981513977 0.8411396 0.29504188895225525 True -6 18935 29.97375798225403 0.7000746726989746 397.20550537109375 0.20779144763946533 558.7346801757812 0.38341769576072693 0.849609 0.2653064727783203 True -7 21640 29.937761545181274 30.127197265625 434.36627197265625 0.3221036195755005 556.7044067382812 0.38651612401008606 0.8533452 0.26540058851242065 True -8 24345 30.06379985809326 0.6843070983886719 436.6206970214844 0.37996694445610046 554.875244140625 0.3891673982143402 0.8563553 0.26513800024986267 True -9 27050 29.996051788330078 0.7022433280944824 414.2865905761719 0.21454867720603943 552.1099853515625 0.39347466826438904 0.8606577 0.2518191933631897 True -10 29755 29.97922110557556 0.6842622756958008 416.0006103515625 0.21467188000679016 551.3101806640625 0.39395731687545776 0.86527693 0.23624247312545776 True -11 32460 29.98283576965332 1.1309678554534912 462.1648864746094 0.24342337250709534 549.1878051757812 0.3972228467464447 0.8682176 0.23403117060661316 True -12 35165 29.997398614883423 0.9877622127532959 432.695556640625 0.1361159384250641 548.75146484375 0.3968777060508728 0.87392104 0.22542627155780792 True -13 37870 29.991756200790405 0.6782939434051514 370.9814147949219 0.23144519329071045 547.7675170898438 0.39822205901145935 0.8788258 0.2180992066860199 True -14 40575 29.962830305099487 0.6840159893035889 452.4062805175781 0.24248379468917847 546.6005859375 0.3990556299686432 0.88232046 0.20242013037204742 True -15 43280 29.96629571914673 0.7069196701049805 372.28826904296875 0.18553468585014343 545.8694458007812 0.39974552392959595 0.8862485 0.19629348814487457 True -16 45985 29.962109804153442 0.7128415107727051 454.5308837890625 0.13953734934329987 544.6905517578125 0.4018295109272003 0.8895194 0.18787778913974762 True -17 48690 29.940279722213745 0.7264657020568848 375.9981384277344 0.13984854519367218 544.3414306640625 0.4020076394081116 0.89003336 0.18496321141719818 True -18 51395 29.943009853363037 0.703380823135376 370.5643005371094 0.2183387577533722 545.0736083984375 0.4008723497390747 0.89127874 0.18514353036880493 True -19 54100 29.454509258270264 0.6961677074432373 431.72845458984375 0.11012497544288635 545.2786865234375 0.4003276824951172 0.8905996 0.18511585891246796 False diff --git a/ENCSR879XUH/cherimoya.fold_1.performance.tsv b/ENCSR879XUH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ece39629a6ce09dbc2999317890c91656a60a855..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -545.0736083984375 0.3893285393714905 0.4008723497390747 0.1550336629152298 0.8912787437438965 0.8801797032356262 0.18514353036880493 \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_2.evaluate.json b/ENCSR879XUH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6a31f456944ac963796dbeb03d929009271bcf62..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325MUR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_2.fit.json b/ENCSR879XUH/cherimoya.fold_2.fit.json deleted file mode 100644 index 6d889a77debee157bc5ea987d9a7e814e6edb7bf..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF325MUR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_2.log b/ENCSR879XUH/cherimoya.fold_2.log deleted file mode 100644 index 3438d83f505d8d6e830175cf3beabed5aa8c20fb..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.450397968292236 4.134557723999023 476.0924987792969 0.3197897970676422 573.6375732421875 0.27138751745224 0.7488658 3.3185553550720215 True -1 5754 31.87131977081299 0.5595827102661133 375.1669921875 0.3459821343421936 524.5586547851562 0.34728890657424927 0.8085449 0.8868560194969177 True -2 8631 31.84460425376892 0.6183090209960938 371.0985107421875 0.22822734713554382 517.6520385742188 0.3539870083332062 0.81630594 0.39952316880226135 True -3 11508 31.8664231300354 0.5842483043670654 364.56951904296875 0.21247035264968872 514.4290161132812 0.3567808270454407 0.8245561 0.34802746772766113 True -4 14385 31.81940507888794 0.6659810543060303 435.934814453125 0.31253546476364136 509.8091735839844 0.36478447914123535 0.8285873 0.28732436895370483 True -5 17262 31.915293216705322 0.5583193302154541 367.740966796875 0.2413027584552765 508.3172607421875 0.3671588897705078 0.8329868 0.27090713381767273 True -6 20139 31.902841806411743 0.5425169467926025 385.4427185058594 0.38720738887786865 507.14483642578125 0.36942794919013977 0.8357762 0.2728406488895416 True -7 23016 31.864909410476685 0.5638761520385742 482.80499267578125 0.3089316487312317 505.5432434082031 0.37122687697410583 0.8418536 0.24211585521697998 True -8 25893 31.92603874206543 0.5644714832305908 380.9818115234375 0.2306908816099167 503.773193359375 0.3736450970172882 0.8477253 0.23484504222869873 True -9 28770 31.88323736190796 0.5455000400543213 410.7790832519531 0.2892402708530426 503.097900390625 0.3741755485534668 0.8491062 0.22421520948410034 True -10 31647 31.877543210983276 0.5671393871307373 454.2357177734375 0.2695583701133728 501.5467834472656 0.37643879652023315 0.8531985 0.2182973474264145 True -11 34524 31.895387411117554 0.5665004253387451 407.71185302734375 0.21945536136627197 500.0049743652344 0.379479318857193 0.8595391 0.210993692278862 True -12 37401 32.608794927597046 1.3453619480133057 408.32476806640625 0.17903196811676025 499.2283630371094 0.38065510988235474 0.86319464 0.2096155285835266 True -13 40278 31.936152696609497 0.976585865020752 397.8388671875 0.13876543939113617 498.4875793457031 0.38139015436172485 0.8658585 0.20205701887607574 True -14 43155 31.929842472076416 0.5775060653686523 433.681884765625 0.26978564262390137 498.34991455078125 0.381012886762619 0.87200004 0.19431985914707184 True -15 46032 31.92419147491455 0.5750670433044434 395.19464111328125 0.1412602961063385 497.273681640625 0.38355693221092224 0.8724152 0.18838059902191162 True -16 48909 31.87416362762451 0.5935173034667969 398.1397705078125 0.17966102063655853 496.17889404296875 0.3857361674308777 0.8763637 0.1835814267396927 True -17 51786 31.85258936882019 0.5629029273986816 418.81768798828125 0.21875566244125366 496.8701171875 0.3842192590236664 0.8765683 0.18337883055210114 True -18 54663 31.882645845413208 0.6022205352783203 423.92462158203125 0.1014731377363205 496.57366943359375 0.3852396309375763 0.8752095 0.18407617509365082 False -19 57540 31.192344665527344 0.5701828002929688 401.274658203125 0.09749390929937363 497.0321350097656 0.3839944005012512 0.87481123 0.18568556010723114 False diff --git a/ENCSR879XUH/cherimoya.fold_2.performance.tsv b/ENCSR879XUH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5dea209ffa848c22b89e9f9c2782f6eb51b68868..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -496.8701171875 0.4034305810928345 0.3842192590236664 0.1435985267162323 0.8765683174133301 0.8581412434577942 0.18337883055210114 \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_3.evaluate.json b/ENCSR879XUH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e6f254b06755b47d896ffb172dd35b0e4e7d0f75..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325MUR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_3.fit.json b/ENCSR879XUH/cherimoya.fold_3.fit.json deleted file mode 100644 index 8e2c63d42b48f03fbcd021b62e6ddb15901f8ff7..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF325MUR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_3.log b/ENCSR879XUH/cherimoya.fold_3.log deleted file mode 100644 index 982e1c35fa970ff761af34f128bb76ea28f47191..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 35.0897331237793 4.612671613693237 443.4068603515625 0.2675918638706207 539.5567626953125 0.2738136649131775 0.7499966 3.943162441253662 True -1 5524 30.623063802719116 0.5792458057403564 467.99371337890625 0.2806234359741211 496.4017639160156 0.34481093287467957 0.8134036 0.8564582467079163 True -2 8286 30.628029823303223 0.9354643821716309 416.3902587890625 0.37382772564888 486.06195068359375 0.35883966088294983 0.8264158 0.4384195804595947 True -3 11048 30.602283239364624 0.5477912425994873 413.06976318359375 0.2686256766319275 483.75933837890625 0.3606864809989929 0.8313616 0.3697413206100464 True -4 13810 30.62092161178589 0.5272457599639893 502.7347412109375 0.5152332186698914 482.33306884765625 0.3627340793609619 0.8393654 0.3383883833885193 True -5 16572 30.60136914253235 1.4964103698730469 398.5243225097656 0.24481500685214996 479.4679870605469 0.3681683838367462 0.84328985 0.3108885586261749 True -6 19334 30.633745908737183 0.5401124954223633 425.677978515625 0.2179807722568512 479.03729248046875 0.3684244155883789 0.8452999 0.29221776127815247 True -7 22096 30.575226545333862 0.5508103370666504 409.5195617675781 0.19870251417160034 477.0108642578125 0.3717147409915924 0.8518555 0.26956212520599365 True -8 24858 30.638134002685547 0.5354657173156738 430.53204345703125 0.24161294102668762 474.6334228515625 0.3752042353153229 0.8554667 0.24445846676826477 True -9 27620 30.65412735939026 0.5267643928527832 423.2589111328125 0.1960563361644745 474.0905456542969 0.37564143538475037 0.8589994 0.23010501265525818 True -10 30382 30.587573051452637 1.001828908920288 390.83575439453125 0.26273828744888306 472.6260986328125 0.3773403763771057 0.862571 0.22113430500030518 True -11 33144 30.676201820373535 0.5558404922485352 424.23138427734375 0.23101593554019928 471.44085693359375 0.3796933591365814 0.86745363 0.21456259489059448 True -12 35906 30.664672374725342 0.5423939228057861 366.93115234375 0.3009212911128998 470.0511474609375 0.3818152844905853 0.8697849 0.2069750875234604 True -13 38668 30.740291118621826 1.660980224609375 384.1787109375 0.20368072390556335 469.59490966796875 0.3818826973438263 0.87502706 0.19858144223690033 True -14 41430 30.758689165115356 0.5579030513763428 466.04449462890625 0.14103323221206665 468.9542236328125 0.38256657123565674 0.8795738 0.1894114762544632 True -15 44192 30.710322618484497 0.5585083961486816 422.4415588378906 0.10821224749088287 467.9625244140625 0.3842288553714752 0.88169014 0.18550695478916168 True -16 46954 30.765151262283325 0.5456936359405518 378.4164123535156 0.13222579658031464 467.5389709472656 0.38512885570526123 0.88556725 0.18002565205097198 True -17 49716 30.711272478103638 0.5421843528747559 394.9107666015625 0.13029572367668152 467.6103515625 0.3843620717525482 0.88730574 0.1771075576543808 True -18 52478 30.790881872177124 0.5578837394714355 407.549560546875 0.10213600099086761 467.41290283203125 0.3850336968898773 0.88828933 0.17664241790771484 True -19 55240 30.958271503448486 0.5420784950256348 384.47613525390625 0.18225151300430298 467.9053649902344 0.38406720757484436 0.8881747 0.17766910791397095 False diff --git a/ENCSR879XUH/cherimoya.fold_3.performance.tsv b/ENCSR879XUH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1962c72a5e33b092038629da216f2d85e741c370..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -467.41290283203125 0.40708282589912415 0.3850336968898773 0.1408119797706604 0.8882893323898315 0.8599126935005188 0.17664241790771484 \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_4.evaluate.json b/ENCSR879XUH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 54fe39a352257a56b04ad1d0a26323be654ca521..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF325MUR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_4.fit.json b/ENCSR879XUH/cherimoya.fold_4.fit.json deleted file mode 100644 index ad13b6f7965621c7795c813723f71a2e24b93005..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF325MUR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR879XUH/cherimoya.fold_4.log b/ENCSR879XUH/cherimoya.fold_4.log deleted file mode 100644 index 0569986319f894dc75691532efdd68b4092ea6b7..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2823 36.1079375743866 4.761593341827393 516.7506103515625 0.38776546716690063 525.9971313476562 0.2656438946723938 0.7467012 3.486100196838379 True -1 5646 31.301658153533936 3.1330080032348633 448.3475036621094 0.39077359437942505 484.00286865234375 0.3364983797073364 0.80301714 0.9223476052284241 True -2 8469 31.24572443962097 0.5705533027648926 403.44818115234375 0.25770145654678345 475.4086608886719 0.34983038902282715 0.8155537 0.3814507722854614 True -3 11292 31.206371784210205 2.100332021713257 405.1992492675781 0.3087817132472992 472.98828125 0.3534991443157196 0.8219089 0.3344912528991699 True -4 14115 31.29050087928772 0.5739974975585938 429.20513916015625 0.3192770481109619 469.5794372558594 0.3600333333015442 0.828927 0.2484419047832489 True -5 16938 31.311611652374268 0.606421947479248 533.57373046875 0.1737593114376068 469.34857177734375 0.36066991090774536 0.83424973 0.2247837632894516 True -6 19761 31.37049913406372 1.2833614349365234 477.5721740722656 0.31698623299598694 468.9419250488281 0.36018699407577515 0.8401366 0.21684932708740234 True -7 22584 31.23143172264099 0.557157039642334 436.91424560546875 0.27620503306388855 466.9010314941406 0.36387553811073303 0.8468163 0.2059486210346222 True -8 25407 31.246376514434814 0.5766549110412598 406.2864074707031 0.2075434923171997 466.07073974609375 0.36530834436416626 0.8517654 0.19824868440628052 True -9 28230 31.25036883354187 0.5750296115875244 350.75164794921875 0.2700267434120178 464.8153076171875 0.36773163080215454 0.85200423 0.1933360993862152 True -10 31053 31.228654384613037 0.5708966255187988 391.291259765625 0.13091349601745605 463.739013671875 0.3692157566547394 0.8573789 0.18784622848033905 True -11 33876 31.29813027381897 0.5751848220825195 375.61602783203125 0.3614961504936218 463.4142761230469 0.368858277797699 0.8635898 0.18208284676074982 True -12 36699 31.28719162940979 0.568894624710083 424.8184814453125 0.1526523232460022 462.78839111328125 0.37094172835350037 0.86602515 0.18088670074939728 True -13 39522 31.34326148033142 0.5746033191680908 352.061767578125 0.21078436076641083 461.47955322265625 0.37299609184265137 0.86946416 0.17684172093868256 True -14 42345 31.33109712600708 0.5677156448364258 402.690673828125 0.1367843598127365 460.57269287109375 0.37464243173599243 0.8748745 0.17025035619735718 True -15 45168 31.30208468437195 0.5563452243804932 421.6691589355469 0.13836036622524261 460.4726867675781 0.3751848042011261 0.8772275 0.16630858182907104 True -16 47991 31.294212341308594 0.577195405960083 423.3783264160156 0.2769770622253418 460.0710144042969 0.37585511803627014 0.8808645 0.16397057473659515 True -17 50814 31.335404634475708 0.5770523548126221 388.6539611816406 0.13171285390853882 459.9849853515625 0.3758036494255066 0.8797439 0.163669615983963 False -18 53637 31.204503536224365 0.5652725696563721 382.7271728515625 0.14925530552864075 460.391845703125 0.37462079524993896 0.88031656 0.16362562775611877 False -19 56460 31.27392816543579 0.5767555236816406 455.06549072265625 0.1457827091217041 460.31756591796875 0.3750387728214264 0.8804983 0.16480083763599396 False diff --git a/ENCSR879XUH/cherimoya.fold_4.performance.tsv b/ENCSR879XUH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3036ffccd4c0543582d952393264c6fe1acb7dae..0000000000000000000000000000000000000000 --- a/ENCSR879XUH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -460.0710144042969 0.41183939576148987 0.37585511803627014 0.13532015681266785 0.8808645009994507 0.8504582047462463 0.16397057473659515 \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_0.evaluate.json b/ENCSR881CRY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 1e6b7cf0530e3bf5222d93afc2b5f17ae8270686..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF806ZLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_0.fit.json b/ENCSR881CRY/cherimoya.fold_0.fit.json deleted file mode 100644 index 51ad250dfe093b123628e6e7d065017b243bc6dd..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF806ZLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_0.log b/ENCSR881CRY/cherimoya.fold_0.log deleted file mode 100644 index 2b6f481b1692667a5a605350125dbfeb5b5c4ff3..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1880 25.30575394630432 4.776461601257324 316.45050048828125 0.8616350889205933 382.71905517578125 0.1534193754196167 0.58595747 9.233662605285645 True -1 3760 21.27753210067749 0.4027738571166992 350.82421875 0.9731374979019165 341.8023681640625 0.24346855282783508 0.70364743 4.832815647125244 True -2 5640 20.99237847328186 0.3881034851074219 270.1702575683594 0.9465952515602112 315.3700866699219 0.28222161531448364 0.7338448 2.648468255996704 True -3 7520 20.93445134162903 0.37621092796325684 230.39111328125 0.850548505783081 309.2222595214844 0.2926669418811798 0.7465137 1.2499579191207886 True -4 9400 21.007309675216675 1.3675851821899414 251.82130432128906 0.5714926719665527 306.2588195800781 0.29924866557121277 0.7587567 0.954092264175415 True -5 11280 21.016401052474976 0.3833928108215332 250.8089599609375 0.7665261030197144 305.1547546386719 0.3016780614852905 0.7693934 0.920314610004425 True -6 13160 21.064173460006714 0.385986328125 385.1720275878906 0.9298298954963684 303.3756408691406 0.3062211871147156 0.77702963 0.8784634470939636 True -7 15040 21.677098274230957 23.825933694839478 212.890380859375 0.8619531393051147 301.8333740234375 0.309384286403656 0.7838605 0.7997575998306274 True -8 16920 21.423546314239502 0.387160062789917 229.2330780029297 0.5798987746238708 300.6454772949219 0.3103962540626526 0.79320824 0.7335572242736816 True -9 18800 20.878764390945435 0.3846161365509033 247.60687255859375 0.7092418670654297 299.2490539550781 0.31356242299079895 0.79815847 0.6963776350021362 True -10 20680 20.644366979599 0.3765542507171631 279.2589111328125 0.4739551544189453 298.2344665527344 0.3156124949455261 0.8062319 0.6447507739067078 True -11 22560 20.605931282043457 0.3804595470428467 257.41461181640625 0.7569199800491333 297.1868591308594 0.3183290660381317 0.8091713 0.6001889705657959 True -12 24440 20.60256576538086 0.38483524322509766 267.8931884765625 0.6484107971191406 296.2668151855469 0.32005852460861206 0.81492794 0.5794413089752197 True -13 26320 20.506158351898193 0.4760589599609375 235.24014282226562 0.8159728646278381 295.2373352050781 0.321636438369751 0.81760365 0.5557709336280823 True -14 28200 20.50975227355957 0.38039278984069824 340.15606689453125 0.6152132153511047 294.78436279296875 0.3225368857383728 0.8226289 0.5404856204986572 True -15 30080 20.541256427764893 2.886688709259033 243.18270874023438 0.4235859513282776 294.8426513671875 0.32192036509513855 0.8252803 0.5320961475372314 True -16 31960 20.56091547012329 0.3799166679382324 267.8265075683594 0.5967391729354858 294.9476318359375 0.32126468420028687 0.8272641 0.5195353031158447 True -17 33840 20.58719253540039 0.37728404998779297 270.115966796875 0.33291852474212646 295.12451171875 0.3199167251586914 0.8291099 0.520321249961853 True -18 35720 20.560935735702515 0.3802320957183838 171.28981018066406 0.33523350954055786 295.8467712402344 0.31818029284477234 0.82830364 0.521974503993988 False -19 37600 20.480751991271973 0.3848738670349121 225.5623321533203 0.4341660439968109 295.0196228027344 0.32142359018325806 0.8275425 0.5249732732772827 False diff --git a/ENCSR881CRY/cherimoya.fold_0.performance.tsv b/ENCSR881CRY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8f3ffb07ec8b4bc9fa477dea2b338ac18f5ed89c..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -295.12451171875 0.47617053985595703 0.3199167549610138 0.0936364084482193 0.8291099071502686 0.78472900390625 0.520321249961853 \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_1.evaluate.json b/ENCSR881CRY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6cd141101b8528d49a63ce04cda08accd22c8f29..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF806ZLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_1.fit.json b/ENCSR881CRY/cherimoya.fold_1.fit.json deleted file mode 100644 index 3931126858772347064d8f5a8d2df180c0627db6..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF806ZLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_1.log b/ENCSR881CRY/cherimoya.fold_1.log deleted file mode 100644 index ec4a493fe00a4ccd4f6c13fcbdf42e895afc1f72..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1853 25.083470821380615 3.51472806930542 317.1452941894531 1.288191318511963 463.8145751953125 0.16342321038246155 0.57254136 10.085783958435059 True -1 3706 20.709704160690308 0.5287604331970215 252.72161865234375 0.5929011106491089 410.9002685546875 0.2618819773197174 0.71289337 4.7048234939575195 True -2 5559 20.66454768180847 0.5094575881958008 249.19900512695312 1.0921757221221924 377.21746826171875 0.31158459186553955 0.74630415 3.0828356742858887 True -3 7412 20.718512058258057 1.291839599609375 228.58392333984375 0.6034939885139465 369.4737548828125 0.321996808052063 0.76499957 1.5994549989700317 True -4 9265 20.68420672416687 0.5326793193817139 290.83880615234375 0.834443211555481 366.95953369140625 0.32466480135917664 0.7698254 1.1203081607818604 True -5 11118 20.629380226135254 0.5212078094482422 258.7586364746094 0.9087600708007812 366.40167236328125 0.32545390725135803 0.77570564 1.0317633152008057 True -6 12971 20.64258575439453 34.86762976646423 220.43630981445312 0.7128562927246094 363.9283447265625 0.33086222410202026 0.7810667 0.9583487510681152 True -7 14824 20.797868490219116 0.5246093273162842 221.20550537109375 0.7830633521080017 362.3723449707031 0.33332762122154236 0.79194754 0.8517017960548401 True -8 16677 20.655569791793823 2.7887063026428223 281.53094482421875 0.8803053498268127 360.87738037109375 0.33501818776130676 0.7986226 0.7935629487037659 True -9 18530 20.661537885665894 10.619096755981445 305.8162841796875 0.787495493888855 359.8258056640625 0.3363017439842224 0.8052817 0.7110576033592224 True -10 20383 20.666735887527466 0.5198197364807129 284.74749755859375 0.6802823543548584 358.49053955078125 0.33743083477020264 0.81177825 0.6876177191734314 True -11 22236 20.695321321487427 0.5244786739349365 227.90087890625 0.7863537669181824 355.8827209472656 0.3427742123603821 0.8184453 0.653247058391571 True -12 24089 20.709131240844727 0.5225458145141602 254.27389526367188 0.4029213786125183 354.38421630859375 0.3447836935520172 0.8268988 0.6422526240348816 True -13 25942 20.715983152389526 0.5433080196380615 217.7735595703125 0.766743540763855 354.3108215332031 0.3452201187610626 0.8316662 0.6143997311592102 True -14 27795 20.71207880973816 0.5219085216522217 247.15711975097656 0.507697343826294 352.6302795410156 0.3490513265132904 0.83670807 0.5912766456604004 True -15 29648 20.69796347618103 0.5251641273498535 210.90985107421875 0.428225576877594 352.5203552246094 0.3480096161365509 0.84172195 0.5692306756973267 True -16 31501 20.67745089530945 0.51800537109375 199.86875915527344 0.40257835388183594 352.0270690917969 0.34917572140693665 0.84350646 0.5651293992996216 True -17 33354 20.678127765655518 1.1817867755889893 215.08731079101562 0.31215012073516846 351.9225158691406 0.3493092358112335 0.8454777 0.5601174235343933 True -18 35207 20.714231729507446 29.06409454345703 200.20843505859375 0.3005676865577698 352.710205078125 0.34774693846702576 0.84476775 0.5594508647918701 False -19 37060 21.973721981048584 9.138214111328125 270.3130187988281 0.34131911396980286 353.03973388671875 0.3468669056892395 0.8458363 0.5625690221786499 True diff --git a/ENCSR881CRY/cherimoya.fold_1.performance.tsv b/ENCSR881CRY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8373bf19e0b1bfac16a868ab36000e33dc5c909e..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -353.03973388671875 0.4533933103084564 0.3468669056892395 0.11009254306554794 0.8458362817764282 0.8207651376724243 0.5625690221786499 \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_2.evaluate.json b/ENCSR881CRY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 49b3fb47af827d40e75e1ff433032fc1955cc174..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF806ZLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_2.fit.json b/ENCSR881CRY/cherimoya.fold_2.fit.json deleted file mode 100644 index 195b3a933fbc058a96abf663a577d7d37e8c4453..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF806ZLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_2.log b/ENCSR881CRY/cherimoya.fold_2.log deleted file mode 100644 index 2ff34217387e85b4d8d388377ce73724191efb18..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2004 27.497553825378418 3.5075290203094482 226.76954650878906 1.2677215337753296 406.8844909667969 0.15859860181808472 0.5624081 8.089228630065918 True -1 4008 22.3215274810791 0.3876039981842041 321.3536682128906 0.7094728350639343 355.7099914550781 0.2594507336616516 0.7114208 4.785006046295166 True -2 6012 22.386342525482178 0.37421679496765137 241.73373413085938 0.7125589847564697 332.2713317871094 0.29048293828964233 0.7530916 2.192263126373291 True -3 8016 22.465004920959473 0.3839402198791504 252.10800170898438 1.073671579360962 325.11151123046875 0.3014104962348938 0.75907445 1.211172342300415 True -4 10020 22.402251720428467 0.3742654323577881 256.467529296875 0.6031923294067383 322.6313171386719 0.3038061261177063 0.7721076 0.9910358786582947 True -5 12024 22.437049388885498 0.37834835052490234 248.20455932617188 0.7510511875152588 320.57208251953125 0.30790212750434875 0.78100014 0.8337159156799316 True -6 14028 22.479506731033325 6.356741905212402 229.92843627929688 0.5944859981536865 318.99774169921875 0.3108484745025635 0.78925365 0.7617617249488831 True -7 16032 22.616315841674805 3.1188695430755615 276.90679931640625 0.8269208669662476 316.77581787109375 0.315249502658844 0.797176 0.7052736878395081 True -8 18036 22.447829246520996 0.3781850337982178 219.70396423339844 0.6092183589935303 316.10101318359375 0.31625470519065857 0.8015481 0.6735279560089111 True -9 20040 22.466108083724976 0.3755989074707031 267.8827209472656 0.746406614780426 314.4320983886719 0.31981486082077026 0.8074349 0.6391806602478027 True -10 22044 22.489948272705078 0.3698873519897461 202.36441040039062 0.4907780587673187 313.4417724609375 0.3223978877067566 0.8126256 0.6088347434997559 True -11 24048 22.423537492752075 0.37497377395629883 237.16455078125 0.46708226203918457 311.9419860839844 0.32497933506965637 0.81669253 0.5936208367347717 True -12 26052 22.52353858947754 0.8932433128356934 208.1900634765625 0.6318817734718323 311.3161315917969 0.3262670636177063 0.8196228 0.5782227516174316 True -13 28056 22.50121235847473 25.836440324783325 243.32215881347656 0.5307832956314087 310.6446838378906 0.3279481828212738 0.82508045 0.5547292232513428 True -14 30060 24.335569858551025 0.3816385269165039 256.8977355957031 0.3900695741176605 309.5108337402344 0.3302758038043976 0.8284957 0.5470178723335266 True -15 32064 22.414191484451294 0.3888249397277832 261.2274475097656 0.518141508102417 308.9005126953125 0.3309791088104248 0.8319105 0.5361880660057068 True -16 34068 22.43706226348877 0.37965846061706543 287.89892578125 0.443539559841156 309.1990051269531 0.33037617802619934 0.83314973 0.528703510761261 True -17 36072 22.446016788482666 10.391255617141724 226.98028564453125 0.34654611349105835 309.4803466796875 0.32997822761535645 0.8334708 0.5328638553619385 True -18 38076 22.46410298347473 0.38875389099121094 243.6951446533203 0.3685010075569153 309.6216125488281 0.33016809821128845 0.8323084 0.5357339382171631 False -19 40080 22.53381657600403 0.3876056671142578 287.75732421875 0.3638051450252533 309.7760925292969 0.3302866518497467 0.830929 0.5389546751976013 False diff --git a/ENCSR881CRY/cherimoya.fold_2.performance.tsv b/ENCSR881CRY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cc78a3c2f6af334812256fdb6ba6b1afa574ab7d..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -309.4803466796875 0.46947816014289856 0.32997819781303406 0.09976324439048767 0.8334708213806152 0.7947814464569092 0.5328638553619385 \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_3.evaluate.json b/ENCSR881CRY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1e819368e8920a28bf27fa034a445f82663743e5..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF806ZLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_3.fit.json b/ENCSR881CRY/cherimoya.fold_3.fit.json deleted file mode 100644 index 6c8f7f147d13ac9c4f43ab566db58a6a15c0a42c..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF806ZLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_3.log b/ENCSR881CRY/cherimoya.fold_3.log deleted file mode 100644 index 65d3c534d661bea5e26ce58fc72b819d80bd1e35..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1908 25.514683485031128 4.423676490783691 207.79405212402344 0.6917378902435303 400.2372741699219 0.17044858634471893 0.56668645 10.652985572814941 True -1 3816 21.2552330493927 0.37873268127441406 339.740234375 0.6216457486152649 351.78643798828125 0.26507431268692017 0.71513855 5.456682205200195 True -2 5724 21.284571170806885 0.8334774971008301 187.98605346679688 0.6718755960464478 333.8403625488281 0.28971943259239197 0.74026 2.278111457824707 True -3 7632 21.2867534160614 16.069843292236328 279.6842041015625 0.7686038017272949 329.6197509765625 0.29618802666664124 0.74466753 1.5440177917480469 True -4 9540 21.831145763397217 26.824035167694092 318.4928283691406 0.7953952550888062 325.73602294921875 0.30319473147392273 0.75199425 1.205559253692627 True -5 11448 21.882243871688843 24.876417875289917 317.18988037109375 0.8274331092834473 323.2772521972656 0.3093205392360687 0.7565364 1.0642306804656982 True -6 13356 22.42014765739441 28.268160104751587 283.58990478515625 0.863785982131958 321.8229675292969 0.31259992718696594 0.7664769 1.0111570358276367 True -7 15264 21.517593383789062 0.37939906120300293 231.35906982421875 0.7248029708862305 320.6802062988281 0.31412747502326965 0.7764783 0.9102070927619934 True -8 17172 20.856473684310913 0.37756824493408203 227.60797119140625 0.7186503410339355 319.227294921875 0.31817933917045593 0.7801474 0.8633869290351868 True -9 19080 20.821585178375244 0.37436366081237793 238.49285888671875 0.6555985808372498 318.3572082519531 0.31878504157066345 0.7889496 0.7637962102890015 True -10 20988 20.84972357749939 0.3779611587524414 300.60833740234375 0.8621090054512024 317.80523681640625 0.3212210237979889 0.7928053 0.7356778979301453 True -11 22896 20.857511520385742 0.37896180152893066 222.96800231933594 0.6486223340034485 316.2357482910156 0.32428884506225586 0.7988207 0.7001173496246338 True -12 24804 20.885801792144775 0.3787577152252197 252.06146240234375 0.482235312461853 314.4747619628906 0.32792580127716064 0.8072404 0.6706289649009705 True -13 26712 20.8752281665802 0.38031482696533203 241.23187255859375 0.6820954084396362 314.1116943359375 0.32842445373535156 0.81375164 0.6319535970687866 True -14 28620 20.833244800567627 0.37996530532836914 210.31619262695312 0.6567161083221436 313.61798095703125 0.32916688919067383 0.82105714 0.6060473322868347 True -15 30528 20.870662212371826 0.37898731231689453 259.9435729980469 0.43550699949264526 312.4718933105469 0.3321755528450012 0.8245338 0.584976851940155 True -16 32436 20.900252103805542 1.5092167854309082 220.39749145507812 0.39597445726394653 312.7371520996094 0.329937219619751 0.8264159 0.5799031853675842 True -17 34344 20.892428874969482 0.37618231773376465 214.96485900878906 0.3702024221420288 312.58758544921875 0.33126240968704224 0.827699 0.5718737244606018 True -18 36252 20.96698236465454 0.3877546787261963 247.24542236328125 0.29297101497650146 312.7331237792969 0.330122172832489 0.8259809 0.5795803070068359 False -19 38160 20.918941497802734 0.8219804763793945 273.2049560546875 0.33022403717041016 312.6510009765625 0.33048567175865173 0.82561606 0.5817972421646118 False diff --git a/ENCSR881CRY/cherimoya.fold_3.performance.tsv b/ENCSR881CRY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9e46060a8d0f57ab472027da76c5da5d8aa8dc3e..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -312.58758544921875 0.46660420298576355 0.33126240968704224 0.09785831719636917 0.8276990056037903 0.7883643507957458 0.5718737244606018 \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_4.evaluate.json b/ENCSR881CRY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 150cad212d4e455e2ecf5a6de7bef69d846a6bc2..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF806ZLO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_4.fit.json b/ENCSR881CRY/cherimoya.fold_4.fit.json deleted file mode 100644 index 20032da2ac211f81f71ed5e0537ae3c9f28e0dd4..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF806ZLO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881CRY/cherimoya.fold_4.log b/ENCSR881CRY/cherimoya.fold_4.log deleted file mode 100644 index 19a6486a04592216ce663796858191ea707b9050..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1900 25.68787384033203 3.4749763011932373 278.657470703125 0.8990997076034546 367.26751708984375 0.15005438029766083 0.5653711 8.360376358032227 True -1 3800 21.202918767929077 0.36664485931396484 229.7200927734375 0.546099841594696 326.500732421875 0.24289995431900024 0.7008444 4.603000640869141 True -2 5700 21.181623935699463 0.3488178253173828 279.23004150390625 1.024870753288269 305.2102355957031 0.27873343229293823 0.7391225 1.719758152961731 True -3 7600 21.217125177383423 0.35565972328186035 193.3277587890625 0.7383382320404053 299.13446044921875 0.289150595664978 0.7527266 1.0261476039886475 True -4 9500 21.146029710769653 16.980926990509033 261.53070068359375 0.6414710879325867 297.1360778808594 0.2912793457508087 0.765609 0.8837732076644897 True -5 11400 21.85635280609131 7.977062702178955 220.55979919433594 1.1414077281951904 296.01422119140625 0.2942642569541931 0.76559955 0.8191776275634766 False -6 13300 21.139151573181152 1.8889071941375732 222.34420776367188 0.6282156705856323 294.51141357421875 0.2974064350128174 0.77041453 0.7262879610061646 True -7 15200 21.195253133773804 0.35533642768859863 220.85906982421875 0.6374266147613525 293.1820373535156 0.300405889749527 0.77629036 0.6848655343055725 True -8 17100 21.194794178009033 0.7734255790710449 317.99334716796875 0.8001325130462646 292.3553161621094 0.30265089869499207 0.77899045 0.6840400695800781 True -9 19000 21.221027612686157 18.013208866119385 242.98077392578125 0.6662124991416931 290.84259033203125 0.305156946182251 0.78603756 0.6248204112052917 True -10 20900 21.711928844451904 0.36008739471435547 227.29632568359375 0.7023071050643921 290.0487976074219 0.3081205487251282 0.79036057 0.6057308316230774 True -11 22800 21.201393127441406 0.3580458164215088 240.75143432617188 0.6294357776641846 289.0029602050781 0.3110787272453308 0.7979181 0.5790546536445618 True -12 24700 21.23191475868225 0.3564481735229492 239.25009155273438 0.765849232673645 287.82440185546875 0.31265994906425476 0.80482316 0.5603300333023071 True -13 26600 21.168092250823975 0.3567085266113281 218.71450805664062 0.6104518175125122 286.98809814453125 0.31435564160346985 0.8092099 0.5483769178390503 True -14 28500 21.192631721496582 7.237084865570068 192.14276123046875 0.5413144826889038 286.35009765625 0.31514477729797363 0.81568193 0.5315210223197937 True -15 30400 21.20445203781128 0.3620731830596924 228.78228759765625 0.7576603293418884 285.9987487792969 0.31626051664352417 0.8197471 0.5186874866485596 True -16 32300 21.301358938217163 0.36106014251708984 236.0288848876953 0.7011133432388306 286.0122375488281 0.31618791818618774 0.82122946 0.5144290924072266 True -17 34200 21.330599308013916 1.9814343452453613 206.3336944580078 0.5203828811645508 285.71234130859375 0.31782007217407227 0.8224759 0.5155733227729797 True -18 36100 20.879044771194458 0.35631895065307617 292.421142578125 0.3064672350883484 286.0871276855469 0.3172430396080017 0.8213195 0.5206074714660645 False -19 38000 20.750530242919922 1.7545342445373535 233.40768432617188 0.35688745975494385 286.8974304199219 0.3149683475494385 0.8208493 0.5260753631591797 False diff --git a/ENCSR881CRY/cherimoya.fold_4.performance.tsv b/ENCSR881CRY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a12362df6424610a8c1559fe9de7fb3c264c26d0..0000000000000000000000000000000000000000 --- a/ENCSR881CRY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -285.71234130859375 0.47917306423187256 0.31782010197639465 0.0895778238773346 0.8224759101867676 0.7782893180847168 0.5155733227729797 \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_0.evaluate.json b/ENCSR881FBS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 00adf16b94f4ba064920bab737067d5d950408bd..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF741LCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_0.fit.json b/ENCSR881FBS/cherimoya.fold_0.fit.json deleted file mode 100644 index a8aa357a6190449c6ad42688e5225bcc3efb82c8..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF741LCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_0.log b/ENCSR881FBS/cherimoya.fold_0.log deleted file mode 100644 index 9f2231f4226d2bb07c945ff00ab49efee993a33b..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 34.349812030792236 3.679863452911377 508.48388671875 0.5145679116249084 668.5189208984375 0.297299861907959 0.68655974 5.649894714355469 True -1 5502 30.453243494033813 0.6046848297119141 555.9348754882812 0.6945003271102905 599.617919921875 0.3731760084629059 0.736086 1.9142932891845703 True -2 8253 32.70596218109131 24.29542589187622 523.595947265625 0.6452034711837769 587.8734130859375 0.383880078792572 0.7509734 1.0452677011489868 True -3 11004 30.493628978729248 0.5968456268310547 530.1029663085938 0.6627895832061768 579.9760131835938 0.3902508318424225 0.7607616 1.2190660238265991 True -4 13755 30.45884108543396 0.5868129730224609 452.06573486328125 0.5256071090698242 576.6348876953125 0.39462119340896606 0.7691757 0.7791808843612671 True -5 16506 30.445674657821655 0.5925111770629883 583.0715942382812 0.7164982557296753 572.9780883789062 0.39829200506210327 0.7760632 0.7256203293800354 True -6 19257 30.48609447479248 0.5975666046142578 549.4344482421875 0.5343747735023499 567.2742309570312 0.40489861369132996 0.7874096 0.6504331231117249 True -7 22008 30.39689564704895 0.5810389518737793 561.6788330078125 0.3884428143501282 564.2703857421875 0.40832164883613586 0.7932416 0.5751796960830688 True -8 24759 30.392769813537598 0.5907871723175049 405.28704833984375 0.48484671115875244 561.2989501953125 0.4119047522544861 0.79848486 0.5696169137954712 True -9 27510 30.402464866638184 0.5783431529998779 491.44036865234375 0.4690362811088562 559.3797607421875 0.41386884450912476 0.8029488 0.5087110996246338 True -10 30261 30.38339591026306 0.5875277519226074 544.3883056640625 0.4379230737686157 557.1873168945312 0.416343629360199 0.8065892 0.45097795128822327 True -11 33012 30.42403817176819 0.5896403789520264 492.3504638671875 0.3306519389152527 555.0280151367188 0.4186243414878845 0.80833876 0.41165128350257874 True -12 35763 30.464057683944702 0.5976846218109131 501.52984619140625 0.5777617692947388 552.7435913085938 0.421345055103302 0.81286484 0.3732912540435791 True -13 38514 30.4227237701416 0.5955476760864258 530.940673828125 0.3447856605052948 551.0617065429688 0.42313334345817566 0.8214418 0.3475274443626404 True -14 41265 30.886849880218506 0.5968430042266846 456.91680908203125 0.22187970578670502 550.5234375 0.42405563592910767 0.82681155 0.3257704973220825 True -15 44016 30.419496536254883 1.2554564476013184 407.879150390625 0.2670283913612366 548.068603515625 0.4261470139026642 0.8315558 0.31202638149261475 True -16 46767 30.474783420562744 0.5960967540740967 482.5441589355469 0.34737128019332886 547.1128540039062 0.42743566632270813 0.83654654 0.3009431064128876 True -17 49518 30.457031726837158 0.5875835418701172 439.22222900390625 0.24850228428840637 546.9628295898438 0.42799779772758484 0.8377127 0.29314953088760376 True -18 52269 30.352193593978882 0.5864884853363037 510.2551574707031 0.2537020742893219 546.7755126953125 0.4280633330345154 0.8375452 0.29345598816871643 False -19 55020 30.418428659439087 0.5951004028320312 500.2693176269531 0.3027067184448242 548.5579833984375 0.4241512417793274 0.83638895 0.2944641411304474 False diff --git a/ENCSR881FBS/cherimoya.fold_0.performance.tsv b/ENCSR881FBS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2bd1497eaeb8061aeffc08d0890664769446785f..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -546.9628295898438 0.3770785331726074 0.42799779772758484 0.16181406378746033 0.8377127051353455 0.8115471005439758 0.29314953088760376 \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_1.evaluate.json b/ENCSR881FBS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ec05ac710f443fb6d9acb13bf50a3fb7996df681..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF741LCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_1.fit.json b/ENCSR881FBS/cherimoya.fold_1.fit.json deleted file mode 100644 index e425c37423fe992cf87d5e25c1c53dbed617ddb6..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF741LCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_1.log b/ENCSR881FBS/cherimoya.fold_1.log deleted file mode 100644 index 633aa8fadeeb8ba9460e492179eea6eba833cc1d..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 33.88827133178711 3.924171209335327 612.5779418945312 0.7287745475769043 802.2269287109375 0.29326000809669495 0.6788999 6.857023239135742 True -1 5406 29.925676584243774 0.7147316932678223 577.6829223632812 0.6485366821289062 716.1073608398438 0.37929707765579224 0.7392779 2.5231707096099854 True -2 8109 29.9182550907135 0.6769273281097412 510.17401123046875 0.5119929313659668 692.4215698242188 0.3975732922554016 0.74860615 1.2575901746749878 True -3 10812 29.90539264678955 0.6788718700408936 566.7431030273438 0.7406014204025269 684.7217407226562 0.4012207090854645 0.7577568 1.2246084213256836 True -4 13515 29.91401982307434 0.687471866607666 483.91583251953125 0.48167917132377625 678.9717407226562 0.40512996912002563 0.7612083 0.987723171710968 True -5 16218 29.90295672416687 28.143983602523804 515.827880859375 0.7732493877410889 672.5157470703125 0.4102948307991028 0.77137595 0.8448809385299683 True -6 18921 29.956952810287476 0.6943542957305908 474.9394836425781 0.6025340557098389 663.2885131835938 0.4195380210876465 0.78319985 0.6554442644119263 True -7 21624 29.952056169509888 3.0934371948242188 454.408935546875 0.5049430131912231 657.9215698242188 0.4252239465713501 0.79425293 0.650451123714447 True -8 24327 29.91171956062317 0.681394100189209 465.7804260253906 0.529197633266449 653.4927368164062 0.4295910596847534 0.8015935 0.5566967725753784 True -9 27030 29.93769884109497 2.057760715484619 473.4871826171875 0.394306480884552 651.420166015625 0.4314543604850769 0.8067444 0.5206740498542786 True -10 29733 29.9587562084198 0.6791625022888184 500.4721374511719 0.34249207377433777 647.1017456054688 0.43559953570365906 0.81132996 0.4549633264541626 True -11 32436 29.885451555252075 0.689424991607666 457.18865966796875 0.26668089628219604 644.5859985351562 0.437399685382843 0.8175874 0.4436182975769043 True -12 35139 33.08482122421265 12.638046979904175 485.7305603027344 0.3316898047924042 642.9776000976562 0.43801969289779663 0.8251498 0.4072225093841553 True -13 37842 29.940025568008423 0.6911323070526123 452.3607482910156 0.34656548500061035 638.7744750976562 0.44341111183166504 0.82960516 0.3934883177280426 True -14 40545 29.91793704032898 0.6948733329772949 536.8045654296875 0.3746274709701538 636.3690795898438 0.44529014825820923 0.83476025 0.37241214513778687 True -15 43248 29.885854482650757 0.6884253025054932 462.39215087890625 0.37612542510032654 635.3374633789062 0.4453124701976776 0.8403687 0.3435860276222229 True -16 45951 29.858612775802612 0.6875789165496826 412.1900939941406 0.2855483293533325 634.0233764648438 0.44696271419525146 0.84456795 0.3298550248146057 True -17 48654 29.86192560195923 0.6961405277252197 445.0808410644531 0.2488107979297638 630.5369262695312 0.4522143602371216 0.84689814 0.31745806336402893 True -18 51357 29.876758575439453 0.7677023410797119 448.92486572265625 0.21544183790683746 631.5712280273438 0.4503157436847687 0.8482761 0.31410229206085205 True -19 54060 29.877378940582275 1.294114112854004 386.0897521972656 0.26361897587776184 632.7542114257812 0.44807136058807373 0.84758973 0.31312093138694763 False diff --git a/ENCSR881FBS/cherimoya.fold_1.performance.tsv b/ENCSR881FBS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7a27d1cc51147d0fb97cde2436d683a41bd6c3b3..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -631.5712280273438 0.3591518998146057 0.4503157436847687 0.18254999816417694 0.8482760787010193 0.8304544687271118 0.31410229206085205 \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_2.evaluate.json b/ENCSR881FBS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e1a7d6605953684573696c9f977069a9c48b68ee..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF741LCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_2.fit.json b/ENCSR881FBS/cherimoya.fold_2.fit.json deleted file mode 100644 index c15ba9a2b7b360f73c16a88165cdc91efb7a290a..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF741LCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_2.log b/ENCSR881FBS/cherimoya.fold_2.log deleted file mode 100644 index 3b5d1717ca17aa746610c357592aa77b046149ae..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 35.623841285705566 3.5849742889404297 479.73748779296875 0.46381253004074097 698.7759399414062 0.2934621572494507 0.6809687 5.3800554275512695 True -1 5758 31.89541530609131 0.585416316986084 675.2550048828125 0.813675045967102 626.1201782226562 0.37006595730781555 0.72810197 2.052074432373047 True -2 8637 31.920506238937378 0.5713703632354736 468.97674560546875 0.4317093789577484 614.7597045898438 0.383939653635025 0.74048805 0.9331873059272766 True -3 11516 31.95214819908142 0.5714764595031738 526.4774169921875 0.48767709732055664 603.0734252929688 0.39207014441490173 0.75305074 0.7441572546958923 True -4 14395 31.868518829345703 0.5951364040374756 575.2490844726562 0.4941120445728302 597.447265625 0.3967835009098053 0.76358557 0.5890074968338013 True -5 17274 31.86549186706543 2.95633602142334 380.5790710449219 0.4937989115715027 592.0751342773438 0.4020218849182129 0.77213424 0.5406904816627502 True -6 20153 31.878721714019775 0.7359473705291748 416.6220703125 0.5329902768135071 587.3604736328125 0.40625813603401184 0.7811185 0.5213111042976379 True -7 23032 31.81029462814331 0.5601153373718262 557.30517578125 0.6174759864807129 583.9677734375 0.41126853227615356 0.78413105 0.5262489914894104 True -8 25911 31.810831308364868 0.5639228820800781 440.1053466796875 0.5350964665412903 581.206298828125 0.4149307906627655 0.78979814 0.5272803902626038 True -9 28790 31.832594871520996 0.5621137619018555 377.62481689453125 0.4091339707374573 577.7088012695312 0.4192800223827362 0.79583484 0.4653450548648834 True -10 31669 32.39995884895325 13.493690252304077 552.1243286132812 0.35145771503448486 577.8482055664062 0.41681021451950073 0.80366075 0.43226560950279236 True -11 34548 31.85175609588623 1.2606596946716309 408.9711608886719 0.4661228656768799 574.833251953125 0.4220125079154968 0.8075171 0.40205010771751404 True -12 37427 31.901102304458618 0.6186079978942871 441.6113586425781 0.24615927040576935 572.6268920898438 0.42409059405326843 0.81201726 0.37301865220069885 True -13 40306 31.86821436882019 0.5685946941375732 426.04443359375 0.44741591811180115 571.3255004882812 0.42561042308807373 0.8188413 0.3504484295845032 True -14 43185 31.81966519355774 0.5562539100646973 404.29132080078125 0.24361500144004822 569.2322998046875 0.4276895225048065 0.82264864 0.33492401242256165 True -15 46064 31.80691647529602 0.5648255348205566 474.3416748046875 0.30262356996536255 566.6671142578125 0.4309929609298706 0.82819986 0.32080936431884766 True -16 48943 31.87249183654785 0.5740706920623779 443.7989196777344 0.26663804054260254 567.3443603515625 0.4289551079273224 0.8291254 0.30895766615867615 True -17 51822 31.861767768859863 0.566164493560791 492.236328125 0.2475510835647583 566.0562133789062 0.43206319212913513 0.8303452 0.30730774998664856 True -18 54701 31.818528413772583 0.5793817043304443 428.0824890136719 0.25367653369903564 566.833984375 0.4306575059890747 0.83114916 0.3041705787181854 True -19 57580 31.803863286972046 0.5636448860168457 577.3644409179688 0.28144586086273193 567.5372924804688 0.4294286370277405 0.8291147 0.3057918846607208 False diff --git a/ENCSR881FBS/cherimoya.fold_2.performance.tsv b/ENCSR881FBS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4782b9b647613bc457e3bd8ef3e7af5ae1f14494..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -566.833984375 0.3739508092403412 0.4306574761867523 0.1660478711128235 0.831149160861969 0.8036907911300659 0.3041705787181854 \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_3.evaluate.json b/ENCSR881FBS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f30385cbabef9756877b45b59cc7eff2fe438e22..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF741LCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_3.fit.json b/ENCSR881FBS/cherimoya.fold_3.fit.json deleted file mode 100644 index 51ce0c536d87c5549efb8f5f5c6059f2005bddef..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF741LCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_3.log b/ENCSR881FBS/cherimoya.fold_3.log deleted file mode 100644 index c94f8b9b7baf01c27450713691fa9433eb10a1dc..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 34.34562945365906 3.4901835918426514 504.64495849609375 0.6239680051803589 656.1480102539062 0.30466607213020325 0.67669505 5.996753692626953 True -1 5524 30.5062255859375 0.5389063358306885 530.1531982421875 0.6009499430656433 587.7713012695312 0.37669554352760315 0.74597394 2.116809129714966 True -2 8286 30.570961952209473 0.521397590637207 451.3726806640625 0.6479386687278748 575.7210083007812 0.3895418643951416 0.7615232 1.202715277671814 True -3 11048 30.52185606956482 0.5311801433563232 469.09881591796875 0.32282671332359314 563.1571655273438 0.40348055958747864 0.7706862 0.9055895805358887 True -4 13810 30.525574684143066 3.3101048469543457 490.5715026855469 0.433082640171051 562.4500732421875 0.4014118015766144 0.77559686 0.8890779614448547 True -5 16572 30.542776346206665 0.5249190330505371 512.3974609375 0.5068767666816711 558.046875 0.40645384788513184 0.78427213 0.6808003187179565 True -6 19334 30.54959487915039 0.5295224189758301 494.43572998046875 0.37257516384124756 554.9077758789062 0.40919944643974304 0.7908407 0.596469521522522 True -7 22096 30.56262516975403 2.4048469066619873 511.1085205078125 0.4993789494037628 552.00927734375 0.4128621220588684 0.79525656 0.5270124077796936 True -8 24858 30.58233118057251 0.5165159702301025 551.693115234375 0.5277430415153503 550.7896728515625 0.4141746461391449 0.7983401 0.5430244207382202 True -9 27620 30.614267349243164 0.5335144996643066 418.87799072265625 0.4982989430427551 547.9293212890625 0.41850781440734863 0.801413 0.49533724784851074 True -10 30382 30.501803636550903 0.533153772354126 536.4144897460938 0.48736172914505005 546.7985229492188 0.41943445801734924 0.80713785 0.45627090334892273 True -11 33144 30.50128674507141 0.5341012477874756 519.1517333984375 0.3722275197505951 544.7720336914062 0.4211081564426422 0.81204283 0.4382128417491913 True -12 35906 30.505785703659058 0.9622344970703125 501.7427978515625 0.33080312609672546 541.52880859375 0.4247749149799347 0.82134664 0.39942848682403564 True -13 38668 30.640037536621094 0.5355932712554932 483.5449523925781 0.28721344470977783 538.8209228515625 0.4273357093334198 0.82615757 0.36468830704689026 True -14 41430 31.018759727478027 0.5299122333526611 470.6637878417969 0.3843764662742615 537.2338256835938 0.4299668073654175 0.83387196 0.3477943241596222 True -15 44192 30.513904333114624 0.5248777866363525 597.2411499023438 0.281865656375885 536.0764770507812 0.4302641451358795 0.83888406 0.32700446248054504 True -16 46954 30.555422067642212 0.5332839488983154 441.0091552734375 0.29643720388412476 535.3417358398438 0.4317217171192169 0.84231466 0.3138148784637451 True -17 49716 30.54473090171814 0.526442289352417 411.8304138183594 0.24938265979290009 534.5427856445312 0.4320526123046875 0.84423107 0.3075689375400543 True -18 52478 30.596370220184326 0.9543933868408203 524.0111694335938 0.2817627191543579 534.5580444335938 0.43200626969337463 0.84367734 0.30555734038352966 False -19 55240 30.55163860321045 0.5252687931060791 427.0735168457031 0.2413824200630188 534.9352416992188 0.4317680597305298 0.843327 0.3066348135471344 False diff --git a/ENCSR881FBS/cherimoya.fold_3.performance.tsv b/ENCSR881FBS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 241a5e927bdd7ae06405f1b3366eab86b6ea75ff..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -534.5427856445312 0.37593942880630493 0.4320525825023651 0.16308411955833435 0.8442310690879822 0.8114460706710815 0.3075689375400543 \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_4.evaluate.json b/ENCSR881FBS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 926b1874b1b3e39d6ecaeb64323a953e686bd3dd..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF741LCM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_4.fit.json b/ENCSR881FBS/cherimoya.fold_4.fit.json deleted file mode 100644 index 1056d5f3b3dcd950c6f2d1ef3a2a304d18b16cce..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF741LCM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR881FBS/cherimoya.fold_4.log b/ENCSR881FBS/cherimoya.fold_4.log deleted file mode 100644 index 16c5a5afa0e8aad10e51ff557b69c479370e993c..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2804 35.27906513214111 3.545494318008423 437.6106872558594 0.595466673374176 624.00341796875 0.29900288581848145 0.66563284 4.902773380279541 True -1 5608 31.006527185440063 2.507082462310791 538.08203125 0.5495213270187378 563.6655883789062 0.36942258477211 0.7274331 1.7371459007263184 True -2 8412 31.053779125213623 0.5951797962188721 489.81488037109375 0.5328043699264526 553.8125610351562 0.37931737303733826 0.7331712 1.0810614824295044 True -3 11216 31.016757249832153 0.5866036415100098 523.3128662109375 0.4424218535423279 546.1874389648438 0.3879762291908264 0.7437019 1.0008795261383057 True -4 14020 31.02572989463806 0.5804638862609863 434.28485107421875 0.5363682508468628 542.2638549804688 0.3929981291294098 0.75122994 0.8050642609596252 True -5 16824 31.013877630233765 0.5869045257568359 462.304443359375 0.49471786618232727 538.8897705078125 0.39527231454849243 0.76235855 0.6211984157562256 True -6 19628 31.057696104049683 2.3920648097991943 504.3743896484375 0.5163465738296509 536.3373413085938 0.3979348838329315 0.76817924 0.6081798076629639 True -7 22432 31.08323907852173 0.5979619026184082 502.4993896484375 0.34413015842437744 534.47021484375 0.3991316258907318 0.77954245 0.580122709274292 True -8 25236 31.053789615631104 0.5963554382324219 431.3700866699219 0.523332953453064 530.9945068359375 0.4044877886772156 0.7843318 0.5327453017234802 True -9 28040 31.042300939559937 1.734133243560791 464.0471496582031 0.46430760622024536 528.1957397460938 0.4072341024875641 0.79074514 0.4197578728199005 True -10 30844 31.072402715682983 0.5905413627624512 572.1251220703125 0.3379335403442383 527.6128540039062 0.4074694812297821 0.79249465 0.4154210686683655 True -11 33648 31.069807291030884 0.5981636047363281 414.08099365234375 0.26229026913642883 525.9398193359375 0.4094332754611969 0.79950917 0.39021337032318115 True -12 36452 31.09282088279724 0.5924804210662842 497.453857421875 0.5788658857345581 523.2952880859375 0.41276970505714417 0.8054655 0.36071905493736267 True -13 39256 31.031208276748657 1.870631217956543 414.3543701171875 0.38735872507095337 521.7354736328125 0.4147734045982361 0.8113949 0.3368028998374939 True -14 42060 31.04204535484314 0.7775070667266846 489.349609375 0.312921404838562 520.630615234375 0.41663655638694763 0.8183952 0.3173760771751404 True -15 44864 31.02543330192566 0.5882489681243896 408.2782287597656 0.3245035409927368 518.7227783203125 0.41976526379585266 0.8264404 0.30193892121315 True -16 47668 31.017569541931152 0.5855507850646973 484.3078308105469 0.2546837329864502 518.2000122070312 0.42006996273994446 0.8280541 0.29015281796455383 True -17 50472 30.989153385162354 0.5849292278289795 377.1330261230469 0.4570813775062561 518.2316284179688 0.41985759139060974 0.8314832 0.28469642996788025 True -18 53276 31.15574073791504 1.1660027503967285 446.24615478515625 0.3126416504383087 518.4358520507812 0.41910821199417114 0.8315581 0.28408652544021606 True -19 56080 31.005032062530518 0.5937750339508057 451.3704528808594 0.23707111179828644 519.6007690429688 0.41677770018577576 0.8311493 0.284186452627182 False diff --git a/ENCSR881FBS/cherimoya.fold_4.performance.tsv b/ENCSR881FBS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6d1f73c0c192776dd14c0242541a7a870769f6a3..0000000000000000000000000000000000000000 --- a/ENCSR881FBS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -518.4358520507812 0.3836826980113983 0.41910824179649353 0.15498386323451996 0.831558108329773 0.795559823513031 0.28408652544021606 \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_0.evaluate.json b/ENCSR884MCZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d9555c959cb21c6cfeec54ef8c3e65d30f00d912..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF417TEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_0.fit.json b/ENCSR884MCZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 620649010d754764dcace278046be098ded3da19..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF417TEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_0.log b/ENCSR884MCZ/cherimoya.fold_0.log deleted file mode 100644 index 46eb3fdd4ed4f1ba4e8570f48115f15df42af0c6..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2773 35.734089612960815 4.877866744995117 217.12823486328125 0.5783478617668152 309.7484130859375 0.16435039043426514 0.65695727 3.6432507038116455 True -1 5546 30.902361631393433 0.60005784034729 264.1370849609375 0.5409716963768005 289.797607421875 0.24279561638832092 0.71909475 1.0143811702728271 True -2 8319 30.914578199386597 0.5494611263275146 263.04931640625 0.7932429313659668 285.5870056152344 0.2549634575843811 0.73171115 0.5534258484840393 True -3 11092 30.991079568862915 0.5650084018707275 279.7095031738281 1.0560142993927002 282.70672607421875 0.2626357972621918 0.7334277 0.5144179463386536 True -4 13865 30.90292763710022 0.5651073455810547 203.14707946777344 0.6180278658866882 281.5314636230469 0.2656477093696594 0.7368689 0.5330233573913574 True -5 16638 30.445342302322388 0.5703568458557129 265.72943115234375 0.5854765772819519 280.3682556152344 0.27080920338630676 0.7409597 0.5079392790794373 True -6 19411 30.317582607269287 0.5701062679290771 214.451904296875 0.7154598236083984 279.85430908203125 0.2726173996925354 0.74365485 0.4776178002357483 True -7 22184 30.31717848777771 0.5718092918395996 234.76380920410156 0.48377424478530884 278.61004638671875 0.27784463763237 0.74754536 0.48412489891052246 True -8 24957 30.206798791885376 0.5648818016052246 257.63543701171875 0.5838754177093506 277.8502502441406 0.28050345182418823 0.750433 0.46761080622673035 True -9 27730 30.25232195854187 0.5588281154632568 257.6596374511719 0.5284597873687744 277.26959228515625 0.28378191590309143 0.7497659 0.4748782813549042 False -10 30503 30.223509311676025 0.5708198547363281 245.65699768066406 0.816258430480957 276.0597229003906 0.2882542908191681 0.75601554 0.4314582645893097 True -11 33276 30.24509620666504 0.5723817348480225 221.7408447265625 0.33033275604248047 275.87957763671875 0.288997083902359 0.76089376 0.41157689690589905 True -12 36049 30.28239345550537 0.5708816051483154 241.43321228027344 0.29120051860809326 275.40032958984375 0.2905125021934509 0.76743793 0.3815884292125702 True -13 38822 30.270452737808228 0.5576348304748535 191.42694091796875 0.4834180474281311 274.7484130859375 0.29307740926742554 0.77172214 0.37855204939842224 True -14 41595 30.241219758987427 0.5679080486297607 253.97686767578125 0.4081543982028961 274.24737548828125 0.2952865958213806 0.7780655 0.35189348459243774 True -15 44368 30.221970796585083 0.5564708709716797 207.7613983154297 0.37026721239089966 274.10504150390625 0.29524895548820496 0.7840968 0.33622750639915466 True -16 47141 30.23171067237854 0.5704495906829834 197.06336975097656 0.31305229663848877 273.4169006347656 0.2976768910884857 0.7895523 0.31682121753692627 True -17 49914 30.20415163040161 0.5616915225982666 231.32626342773438 0.3373434543609619 273.1242980957031 0.2985335886478424 0.7906433 0.31269803643226624 True -18 52687 30.311683654785156 0.5744595527648926 233.13827514648438 0.3119969666004181 273.2732849121094 0.2975538671016693 0.79244375 0.30754950642585754 True -19 55460 30.27145290374756 0.5653855800628662 254.5234375 0.31959331035614014 273.4011535644531 0.29688018560409546 0.79071254 0.30894050002098083 False diff --git a/ENCSR884MCZ/cherimoya.fold_0.performance.tsv b/ENCSR884MCZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8985b7732ad0e21dda0f9e4df2eabfa286ae28eb..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -273.2732849121094 0.489769846200943 0.2975539267063141 0.07746634632349014 0.7924437522888184 0.73265141248703 0.30754950642585754 \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_1.evaluate.json b/ENCSR884MCZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c438fbb39e654127dccd74f75a9ed88b96067df0..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF417TEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_1.fit.json b/ENCSR884MCZ/cherimoya.fold_1.fit.json deleted file mode 100644 index cc9aa141efe3b64c2d90d596c3adf2d02cdda813..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF417TEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_1.log b/ENCSR884MCZ/cherimoya.fold_1.log deleted file mode 100644 index 8e7cd3252cb15691fb9183f9a9dd140173ce01c8..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 34.936110973358154 4.027810335159302 210.48385620117188 0.607587456703186 362.683837890625 0.18020913004875183 0.65395945 4.195413112640381 True -1 5476 31.055060863494873 0.7779252529144287 264.6975402832031 0.7385357022285461 338.0374450683594 0.2598724961280823 0.7112897 1.767483115196228 True -2 8214 30.546281814575195 0.6916472911834717 259.73577880859375 0.6882773041725159 329.8956298828125 0.2797863781452179 0.7359798 0.8442772030830383 True -3 10952 30.450615882873535 0.7117657661437988 225.53228759765625 0.7024430632591248 326.6650085449219 0.28785136342048645 0.7460712 0.8108548521995544 True -4 13690 30.469136953353882 0.7058022022247314 209.17462158203125 0.7947713732719421 325.3134460449219 0.2909935712814331 0.75802505 0.7383285760879517 True -5 16428 30.46483063697815 0.704524040222168 238.30914306640625 0.6403181552886963 324.55975341796875 0.2927425801753998 0.7590681 0.6948241591453552 True -6 19166 30.3115336894989 0.718517541885376 219.28689575195312 0.6713135242462158 323.4896240234375 0.2965258061885834 0.7622358 0.7132647037506104 True -7 21904 29.93688178062439 0.701362133026123 201.90695190429688 0.4682183861732483 322.1280822753906 0.3015081286430359 0.76355743 0.6635910868644714 True -8 24642 29.851406574249268 1.5426335334777832 196.0137939453125 0.5432049036026001 321.5226135253906 0.30368369817733765 0.764824 0.722937285900116 True -9 27380 29.921278715133667 0.6987850666046143 241.21746826171875 0.6393570303916931 321.11322021484375 0.3039444088935852 0.7658819 0.6757830381393433 True -10 30118 29.917980194091797 0.6916804313659668 223.0070343017578 0.5113657712936401 319.810791015625 0.3086721897125244 0.7716413 0.6162078976631165 True -11 32856 29.90186071395874 0.6901285648345947 234.58050537109375 0.46571677923202515 318.4759826660156 0.31317898631095886 0.77734214 0.564175546169281 True -12 35594 29.861883878707886 0.6886301040649414 251.94998168945312 0.5662216544151306 317.7469482421875 0.3147813081741333 0.78775096 0.5096218585968018 True -13 38332 29.889981031417847 0.6885826587677002 210.463623046875 0.42257171869277954 317.35699462890625 0.3153601884841919 0.7949222 0.4687100052833557 True -14 41070 29.815898895263672 23.657132148742676 244.6761932373047 0.3624492883682251 316.6750183105469 0.31602075695991516 0.80088216 0.42424651980400085 True -15 43808 29.922415256500244 0.6995584964752197 266.4123229980469 0.26871442794799805 316.49151611328125 0.31652015447616577 0.80751276 0.3875362277030945 True -16 46546 30.001014232635498 0.7008397579193115 206.635009765625 0.45975521206855774 315.8963317871094 0.31919652223587036 0.8120154 0.36974194645881653 True -17 49284 29.920079469680786 0.700157880783081 249.32501220703125 0.24189190566539764 315.8814697265625 0.3192462921142578 0.8147625 0.35586732625961304 True -18 52022 29.965496301651 0.735419511795044 231.00491333007812 0.5031278133392334 315.6870422363281 0.3201940357685089 0.814732 0.3491363227367401 False -19 54760 29.94003129005432 0.69974684715271 237.20974731445312 0.26557400822639465 315.822021484375 0.3193475902080536 0.81511927 0.3479706943035126 True diff --git a/ENCSR884MCZ/cherimoya.fold_1.performance.tsv b/ENCSR884MCZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 08e7407f5bfe7cb110c91976aa24070eedb19acd..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -315.822021484375 0.4699510931968689 0.3193475306034088 0.09227108955383301 0.8151192665100098 0.7747902870178223 0.3479706943035126 \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_2.evaluate.json b/ENCSR884MCZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5d7c886dc96e0e97e0c3e0934953fa93b5f576f4..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF417TEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_2.fit.json b/ENCSR884MCZ/cherimoya.fold_2.fit.json deleted file mode 100644 index fe97d5e727e157cbeee31762d52b431adee43d6d..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF417TEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_2.log b/ENCSR884MCZ/cherimoya.fold_2.log deleted file mode 100644 index 1e9cfd1ee6a93f948e206552a0a01b326f0519ec..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2895 36.91211438179016 6.751746416091919 253.1255645751953 0.5167703628540039 318.25579833984375 0.17472493648529053 0.6551097 2.532454490661621 True -1 5790 32.30091643333435 0.9310569763183594 263.54595947265625 0.6444981694221497 297.37872314453125 0.24651221930980682 0.7239258 0.9942069053649902 True -2 8685 32.3495352268219 0.5932650566101074 247.86524963378906 0.9213485717773438 292.9427795410156 0.25981178879737854 0.73572844 0.5492343306541443 True -3 11580 32.29467964172363 1.0129115581512451 179.5748291015625 0.7415640950202942 290.4198303222656 0.2668383717536926 0.7403332 0.5463786721229553 True -4 14475 31.64182186126709 0.554863452911377 199.21273803710938 0.6580938696861267 289.0536193847656 0.27197107672691345 0.7450078 0.5053534507751465 True -5 17370 31.628418922424316 2.6511120796203613 215.68397521972656 0.491397500038147 288.3994445800781 0.2735307812690735 0.7472933 0.514923095703125 True -6 20265 31.57095432281494 0.5418412685394287 239.9920654296875 0.631203830242157 287.5262451171875 0.2769850492477417 0.7500432 0.5098002552986145 True -7 23160 31.54147219657898 0.544501543045044 216.20892333984375 0.4726773202419281 286.5242614746094 0.2811633348464966 0.7523142 0.534281849861145 True -8 26055 31.55480980873108 0.5591027736663818 215.9830322265625 0.5372314453125 285.8912353515625 0.2824837267398834 0.7521984 0.5300740599632263 False -9 28950 31.52222752571106 0.5454006195068359 220.58078002929688 0.493810772895813 284.8586730957031 0.28690463304519653 0.76141757 0.4954710006713867 True -10 31845 31.551921844482422 0.5964596271514893 209.34031677246094 0.48440051078796387 284.4945983886719 0.2877373993396759 0.761023 0.4812738299369812 False -11 34740 31.513312101364136 11.179301738739014 180.01260375976562 0.6174601912498474 283.5137939453125 0.29199647903442383 0.76333034 0.44862183928489685 True -12 37635 31.674790859222412 0.5410447120666504 222.05337524414062 0.4062955975532532 283.2836608886719 0.2920662760734558 0.76935625 0.438175231218338 True -13 40530 32.01273036003113 0.5520291328430176 194.87832641601562 0.6184650659561157 282.38226318359375 0.29515179991722107 0.77422214 0.4070259928703308 True -14 43425 31.620962142944336 0.5484881401062012 212.94041442871094 0.45589637756347656 281.63409423828125 0.2979414761066437 0.77787787 0.38346046209335327 True -15 46320 31.57781195640564 0.5428240299224854 215.29165649414062 0.43310290575027466 281.58917236328125 0.2976272404193878 0.78406626 0.36637192964553833 True -16 49215 31.572291612625122 0.5410716533660889 239.35308837890625 0.32783472537994385 281.2700500488281 0.2986200153827667 0.7884435 0.3501128554344177 True -17 52110 31.600667476654053 0.5404312610626221 210.5402374267578 0.3756144046783447 281.034423828125 0.30035728216171265 0.7886187 0.34223490953445435 True -18 55005 31.55532217025757 0.5360066890716553 241.35122680664062 0.2274358570575714 281.138671875 0.29900670051574707 0.7891574 0.3376331925392151 True -19 57900 31.57858657836914 0.5397288799285889 215.612060546875 0.4199351370334625 280.8367919921875 0.3005264699459076 0.79021996 0.3384122848510742 True diff --git a/ENCSR884MCZ/cherimoya.fold_2.performance.tsv b/ENCSR884MCZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bb8e03e1a73e18e929483581709701604d98b209..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -280.8367919921875 0.48663589358329773 0.3005264699459076 0.08082962781190872 0.7902199625968933 0.735361635684967 0.3384122848510742 \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_3.evaluate.json b/ENCSR884MCZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6b16557a47a3592c62784197bdfc7ec34c5da761..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF417TEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_3.fit.json b/ENCSR884MCZ/cherimoya.fold_3.fit.json deleted file mode 100644 index a86182aa10c6daad80c3531ba1a02db306ab75b2..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF417TEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_3.log b/ENCSR884MCZ/cherimoya.fold_3.log deleted file mode 100644 index 5bb2c054957a0b34b838db11f17e42f11a189a1e..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 35.57743763923645 4.244562149047852 272.39776611328125 0.8225550651550293 329.2171325683594 0.16898618638515472 0.6650901 3.050403594970703 True -1 5554 30.69719672203064 1.8058221340179443 204.7606201171875 0.821690559387207 308.9505920410156 0.24532324075698853 0.7318148 0.9013937711715698 True -2 8331 30.99643087387085 0.6080930233001709 269.1761474609375 0.7980868816375732 304.44781494140625 0.25767382979393005 0.7426825 0.5489588975906372 True -3 11108 30.914035320281982 0.5930297374725342 224.531982421875 0.5870578289031982 301.78265380859375 0.26242488622665405 0.7512043 0.5068657398223877 True -4 13885 30.92208242416382 0.7195899486541748 180.29946899414062 0.5673970580101013 300.12451171875 0.26858362555503845 0.7549835 0.5221519470214844 True -5 16662 30.478654146194458 0.5668303966522217 237.52796936035156 0.9317307472229004 298.9437255859375 0.2721654772758484 0.75579625 0.5408341884613037 True -6 19439 30.29978346824646 0.582960844039917 215.945556640625 0.702518880367279 298.3081359863281 0.2750726342201233 0.7603277 0.5421010255813599 True -7 22216 30.261906385421753 0.5831387042999268 199.07394409179688 0.513501763343811 297.4337463378906 0.2790910005569458 0.75931835 0.5776160955429077 False -8 24993 30.24622416496277 0.5837376117706299 208.80807495117188 0.6144704818725586 297.18060302734375 0.2796872854232788 0.7562438 0.6050624251365662 False -9 27770 30.277842044830322 1.8294506072998047 223.02127075195312 0.41751301288604736 296.361572265625 0.28341102600097656 0.7544528 0.5652502179145813 False -10 30547 30.382646560668945 0.5725681781768799 230.55422973632812 0.42972323298454285 295.8923034667969 0.28556767106056213 0.7594808 0.5606718063354492 False -11 33324 30.516756057739258 11.700014114379883 250.477294921875 0.5853874683380127 295.15948486328125 0.2881919741630554 0.7626351 0.5561995506286621 True -12 36101 31.061739683151245 0.5862760543823242 215.93177795410156 0.4423358142375946 294.9276428222656 0.2889377772808075 0.76893806 0.5054488778114319 True -13 38878 30.523550033569336 0.5873205661773682 207.13681030273438 0.40539246797561646 293.84912109375 0.29265061020851135 0.7787109 0.4509688913822174 True -14 41655 30.429617166519165 0.574256181716919 237.79794311523438 0.4564037024974823 293.3062744140625 0.294866681098938 0.7848352 0.42144671082496643 True -15 44432 30.35964012145996 0.592890739440918 253.53982543945312 0.2679605782032013 292.6779479980469 0.296720415353775 0.79213375 0.38228458166122437 True -16 47209 30.389351844787598 1.025853157043457 225.6470947265625 0.23123736679553986 292.51312255859375 0.29636070132255554 0.7993658 0.3577100932598114 True -17 49986 30.393657684326172 0.5752441883087158 217.45651245117188 0.6784060597419739 292.4860534667969 0.2958689033985138 0.8017002 0.3412713408470154 True -18 52763 30.350075483322144 0.5967223644256592 233.67822265625 0.38202574849128723 292.75384521484375 0.29506438970565796 0.8041487 0.33502447605133057 True -19 55540 30.30425477027893 0.577195405960083 227.69979858398438 0.40846800804138184 292.5738525390625 0.29617229104042053 0.8018003 0.33439451456069946 False diff --git a/ENCSR884MCZ/cherimoya.fold_3.performance.tsv b/ENCSR884MCZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ff07c475164f506a9e47dbc8638c75e18712428e..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -292.75384521484375 0.4862508177757263 0.29506438970565796 0.08261529356241226 0.8041486740112305 0.7452670931816101 0.33502447605133057 \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_4.evaluate.json b/ENCSR884MCZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a1f376f214de1c8e782e2cea20f188cbd0efbf27..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF417TEE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_4.fit.json b/ENCSR884MCZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 85b3f2a3087c60c237af42971c7982e41f02c37e..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF417TEE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884MCZ/cherimoya.fold_4.log b/ENCSR884MCZ/cherimoya.fold_4.log deleted file mode 100644 index 989d21c8cf6208f42249122a9f6fb95ea18ce56e..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2855 36.74715328216553 4.394172191619873 287.09844970703125 0.4829058051109314 307.80694580078125 0.16976332664489746 0.66115445 2.831350088119507 True -1 5710 31.83584976196289 0.6206722259521484 276.75555419921875 0.7239779829978943 290.700439453125 0.23634810745716095 0.7174895 0.9013512134552002 True -2 8565 31.834630966186523 2.0709128379821777 249.997314453125 0.7534865140914917 285.25140380859375 0.25095462799072266 0.7241501 0.5829458236694336 True -3 11420 31.85273575782776 0.6706404685974121 206.13690185546875 0.7072999477386475 282.6432189941406 0.2595147490501404 0.73093194 0.5525801777839661 True -4 14275 31.60655164718628 0.615023136138916 186.816650390625 0.532306432723999 282.010498046875 0.2614368498325348 0.73357165 0.554248034954071 True -5 17130 31.256829261779785 0.5988585948944092 240.45391845703125 0.5754784941673279 280.8526916503906 0.26683950424194336 0.73614764 0.4811743497848511 True -6 19985 31.185144662857056 0.5972127914428711 281.977294921875 0.6628954410552979 280.36676025390625 0.2691181004047394 0.73860985 0.4607294797897339 True -7 22840 31.084968090057373 0.6219441890716553 187.59812927246094 0.7984387278556824 279.9178161621094 0.2708587646484375 0.7438459 0.47825121879577637 True -8 25695 31.145159006118774 0.6172926425933838 209.614501953125 0.46514591574668884 278.7857971191406 0.27592483162879944 0.7502849 0.4540577232837677 True -9 28550 31.223633527755737 22.057568311691284 237.879638671875 0.47358790040016174 278.2084655761719 0.2780325710773468 0.75309616 0.439151793718338 True -10 31405 31.122125387191772 5.57214879989624 237.5924072265625 0.4575282335281372 277.9761657714844 0.27856290340423584 0.75887203 0.4396195113658905 True -11 34260 31.20588207244873 0.6003451347351074 215.6351776123047 0.3431696593761444 277.3446960449219 0.2812347114086151 0.7583342 0.44569697976112366 False -12 37115 31.18065309524536 7.899188995361328 264.9197998046875 0.48420852422714233 276.66473388671875 0.28350991010665894 0.7645364 0.4226253032684326 True -13 39970 31.208181142807007 0.598334550857544 246.78868103027344 0.3943556547164917 276.4415283203125 0.28464168310165405 0.7711139 0.37811967730522156 True -14 42825 31.17365026473999 0.617053747177124 234.33779907226562 0.5837446451187134 275.6470642089844 0.28802254796028137 0.7790396 0.3606186509132385 True -15 45680 31.15567111968994 0.6022355556488037 215.747802734375 0.5954955816268921 275.3287353515625 0.2883700430393219 0.7838969 0.3431952893733978 True -16 48535 31.163716316223145 0.5871758460998535 230.3672332763672 0.281735897064209 275.4292297363281 0.2879936397075653 0.791198 0.31896549463272095 True -17 51390 31.122844457626343 0.5878448486328125 228.84622192382812 0.23988012969493866 275.6092529296875 0.2868908941745758 0.793098 0.3083055913448334 True -18 54245 31.15449857711792 0.6079585552215576 230.20809936523438 0.24747514724731445 275.1479187011719 0.28964659571647644 0.79507315 0.3013007640838623 True -19 57100 31.123250722885132 0.6057262420654297 183.86648559570312 0.3883632719516754 275.1788635253906 0.2892513871192932 0.793886 0.30393534898757935 False diff --git a/ENCSR884MCZ/cherimoya.fold_4.performance.tsv b/ENCSR884MCZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4cdb9f97c4f4ad58506dd5e087a0d7926495ae9a..0000000000000000000000000000000000000000 --- a/ENCSR884MCZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.1479187011719 0.49232009053230286 0.28964659571647644 0.07588936388492584 0.7950731515884399 0.7316874265670776 0.3013007640838623 \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_0.evaluate.json b/ENCSR884ODJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 30b452da2fc1b07626ba28542c4802388c1512ce..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF728IYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_0.fit.json b/ENCSR884ODJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 5a4ab34c5621a4eaaa77b6e1a288bfde8b159ffb..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF728IYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_0.log b/ENCSR884ODJ/cherimoya.fold_0.log deleted file mode 100644 index e5562ad5b414cac39254f70c23ed5e51528271e9..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2490 32.28970003128052 3.947067975997925 178.97775268554688 0.941525936126709 236.8834991455078 0.142562136054039 0.60379183 4.116786479949951 True -1 4980 27.623652458190918 0.5611367225646973 245.64854431152344 0.9216117262840271 213.5174560546875 0.19525595009326935 0.718645 2.4159908294677734 True -2 7470 27.653342247009277 0.5918619632720947 187.1729736328125 0.9484261870384216 207.9048309326172 0.20649045705795288 0.7396104 1.2908380031585693 True -3 9960 27.6018226146698 0.5389401912689209 128.05780029296875 0.7134852409362793 205.47872924804688 0.21046213805675507 0.74739444 1.0783711671829224 True -4 12450 27.627827167510986 0.52349853515625 141.00210571289062 0.7360453009605408 203.65956115722656 0.2138507217168808 0.76305 0.9649629592895508 True -5 14940 27.64519166946411 0.5172488689422607 206.2781219482422 0.5689449310302734 202.80181884765625 0.21619440615177155 0.77124166 0.9157981276512146 True -6 17430 27.614476919174194 0.5268194675445557 198.41256713867188 0.5975936651229858 201.96876525878906 0.21817317605018616 0.78118175 0.8296475410461426 True -7 19920 27.612507820129395 0.5156435966491699 163.27182006835938 0.6951394081115723 200.9813232421875 0.22078891098499298 0.7870885 0.8099856972694397 True -8 22410 27.607365608215332 0.5240335464477539 184.80514526367188 0.9773715734481812 200.05906677246094 0.22334936261177063 0.79643345 0.747973620891571 True -9 24900 27.652686595916748 0.5340991020202637 210.10218811035156 0.9755949378013611 199.40512084960938 0.2253716140985489 0.80278933 0.6900051236152649 True -10 27390 27.645539045333862 0.5478003025054932 150.86138916015625 0.41416507959365845 198.39212036132812 0.22785863280296326 0.8103347 0.622455358505249 True -11 29880 27.77306342124939 0.5322487354278564 159.83555603027344 0.4786273241043091 198.1876983642578 0.22816728055477142 0.81699795 0.5833759903907776 True -12 32370 27.721039295196533 1.4333856105804443 189.94496154785156 0.4563528299331665 197.54981994628906 0.22937333583831787 0.8262657 0.5391628742218018 True -13 34860 27.6977801322937 0.5296287536621094 184.26235961914062 0.52902752161026 197.01499938964844 0.23112882673740387 0.8292137 0.5289303064346313 True -14 37350 27.223406314849854 0.5227761268615723 207.41226196289062 0.6809709072113037 196.39157104492188 0.23275096714496613 0.83483243 0.5073942542076111 True -15 39840 27.217909336090088 0.5243399143218994 214.2854461669922 0.5790952444076538 196.1872100830078 0.2331257462501526 0.8387285 0.48235753178596497 True -16 42330 27.249316453933716 0.5324623584747314 160.0897216796875 0.39682620763778687 196.07659912109375 0.23299717903137207 0.84004843 0.47407644987106323 True -17 44820 27.238794565200806 0.5135159492492676 159.8229217529297 0.37953999638557434 196.2542266845703 0.2320399284362793 0.8415589 0.4672146439552307 True -18 47310 27.257376432418823 0.5249221324920654 139.3671875 0.4558650553226471 196.45559692382812 0.23121871054172516 0.84088117 0.46902284026145935 False -19 49800 27.226136207580566 0.5320184230804443 147.15457153320312 0.36068612337112427 196.0671844482422 0.23300707340240479 0.8406542 0.4701908528804779 False diff --git a/ENCSR884ODJ/cherimoya.fold_0.performance.tsv b/ENCSR884ODJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 98c8a49ab1d056d2790bdb33349ed32574de7367..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -196.2542266845703 0.5416179299354553 0.2320399284362793 0.06078881397843361 0.8415588736534119 0.7856174111366272 0.4672146439552307 \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_1.evaluate.json b/ENCSR884ODJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3c65494c67ae5e8812e65336fc29ad85c5fffeae..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF728IYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_1.fit.json b/ENCSR884ODJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 2d8233f74e06b178328905237d449852ad7c48b1..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF728IYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_1.log b/ENCSR884ODJ/cherimoya.fold_1.log deleted file mode 100644 index 968faa59c45b982b0ad3caeba4e73cc6ef1ab81e..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2458 31.973695039749146 4.210763931274414 183.6191864013672 0.8413892388343811 299.11273193359375 0.1518595814704895 0.6174376 4.91642951965332 True -1 4916 27.302695512771606 0.6557309627532959 195.0612030029297 1.0321180820465088 266.0505676269531 0.21850213408470154 0.7401283 3.0769400596618652 True -2 7374 27.29797887802124 0.676856517791748 187.00070190429688 0.646073043346405 260.194091796875 0.22676759958267212 0.7476571 2.0354156494140625 True -3 9832 27.3267662525177 0.6693053245544434 151.12600708007812 0.7608757019042969 256.4369812011719 0.23239505290985107 0.76468027 1.75653076171875 True -4 12290 27.272854328155518 17.145069122314453 161.09596252441406 0.8741738796234131 253.87210083007812 0.236917644739151 0.77947885 1.3109248876571655 True -5 14748 27.32658076286316 0.7153449058532715 122.98057556152344 0.703886866569519 253.13328552246094 0.2371852546930313 0.78680545 1.1045267581939697 True -6 17206 27.31694531440735 0.659172773361206 174.64820861816406 0.6424418687820435 250.96380615234375 0.2420555055141449 0.79773504 1.0232479572296143 True -7 19664 27.36011815071106 0.6605613231658936 157.03961181640625 1.0228240489959717 249.7213134765625 0.24441596865653992 0.8093165 0.8603782653808594 True -8 22122 30.336025714874268 15.76106595993042 175.97891235351562 0.6289324760437012 249.30735778808594 0.2451724112033844 0.8150017 0.8079447746276855 True -9 24580 27.304836988449097 0.6952147483825684 142.72833251953125 0.6956978440284729 247.79876708984375 0.2489219605922699 0.8200124 0.7497708797454834 True -10 27038 27.372756004333496 0.6718299388885498 176.90733337402344 0.5227118730545044 246.79220581054688 0.25084826350212097 0.83007586 0.6476045250892639 True -11 29496 27.33344268798828 1.0157480239868164 205.41775512695312 0.4957219064235687 246.75592041015625 0.2501731812953949 0.8351794 0.6274768710136414 True -12 31954 27.41903281211853 0.6715559959411621 147.80104064941406 0.5919662714004517 245.17369079589844 0.25342026352882385 0.8420635 0.6039000153541565 True -13 34412 27.290462255477905 0.667931318283081 153.43983459472656 0.4107498824596405 244.6011505126953 0.2542332410812378 0.8463111 0.5600114464759827 True -14 36870 27.309781074523926 0.6514627933502197 138.550537109375 0.7955998778343201 244.1096954345703 0.25498947501182556 0.85232365 0.5412764549255371 True -15 39328 27.334848165512085 0.6581780910491943 197.08741760253906 0.3908161520957947 243.0908660888672 0.25732186436653137 0.8570097 0.5289304256439209 True -16 41786 27.29136323928833 0.6433882713317871 135.7113494873047 0.41148263216018677 243.3473358154297 0.2568313777446747 0.8585169 0.5179792046546936 True -17 44244 27.257099628448486 0.6432962417602539 157.32359313964844 0.3319581151008606 242.83261108398438 0.25806280970573425 0.858996 0.5199482440948486 True -18 46702 27.33174157142639 1.567795991897583 209.75387573242188 0.23589196801185608 243.13746643066406 0.25730952620506287 0.85679245 0.5255597829818726 False -19 49160 26.81147265434265 0.6661345958709717 147.2335968017578 0.4978805482387543 242.8761749267578 0.2584870755672455 0.854828 0.5319932103157043 False diff --git a/ENCSR884ODJ/cherimoya.fold_1.performance.tsv b/ENCSR884ODJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c159c5f3b6c34b5a940294f820dfe78401ba2c34..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -242.83261108398438 0.5193049311637878 0.25806280970573425 0.07212729752063751 0.8589959740638733 0.8226135969161987 0.5199482440948486 \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_2.evaluate.json b/ENCSR884ODJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e0d6ea48a5dea9a723eaa4456f28b309c3b06c02..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF728IYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_2.fit.json b/ENCSR884ODJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 228cb49f3053b90c20abaea5b6296a6347161749..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF728IYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_2.log b/ENCSR884ODJ/cherimoya.fold_2.log deleted file mode 100644 index 204440b304a16b9eeb8d495c680f359c2739cfd1..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2641 33.76486921310425 3.8859455585479736 184.33050537109375 0.7575583457946777 244.6849365234375 0.14236928522586823 0.58864015 4.768275260925293 True -1 5282 29.298570156097412 0.6283564567565918 140.385986328125 0.7634487152099609 219.17970275878906 0.20043523609638214 0.7220082 2.5637264251708984 True -2 7923 29.313522577285767 0.5210797786712646 177.18264770507812 1.0996019840240479 213.7689208984375 0.20809614658355713 0.7415557 1.4728859663009644 True -3 10564 29.288681745529175 0.5034041404724121 149.47454833984375 0.7671084403991699 210.9664306640625 0.21211326122283936 0.7525841 1.1827473640441895 True -4 13205 29.29052734375 0.5078587532043457 150.71255493164062 0.7582719922065735 209.5840606689453 0.21436801552772522 0.7639614 1.0579179525375366 True -5 15846 29.27678918838501 0.5074679851531982 195.38467407226562 0.7002410292625427 207.85189819335938 0.21687863767147064 0.7755506 0.905108630657196 True -6 18487 29.33451247215271 0.5024969577789307 174.4419403076172 0.5950650572776794 207.13006591796875 0.21867534518241882 0.78194535 0.9672644138336182 True -7 21128 29.279200315475464 0.5099830627441406 183.75933837890625 0.9812393188476562 206.33535766601562 0.22019116580486298 0.7907145 0.8711977005004883 True -8 23769 29.293288469314575 0.5069727897644043 140.9672088623047 0.6173443794250488 205.2169189453125 0.22227077186107635 0.7996775 0.7332895398139954 True -9 26410 29.276785850524902 0.50390625 132.7018280029297 0.7105499505996704 204.84976196289062 0.22342762351036072 0.80658716 0.6701391339302063 True -10 29051 29.300813913345337 0.50899338722229 212.54518127441406 0.5337111949920654 203.78448486328125 0.22631140053272247 0.81044286 0.6247323751449585 True -11 31692 29.290802001953125 0.5076110363006592 139.23414611816406 0.938710629940033 203.2021942138672 0.227682426571846 0.81612116 0.589562714099884 True -12 34333 29.329294443130493 0.5021688938140869 162.25497436523438 0.39611345529556274 202.77294921875 0.2286049872636795 0.81986815 0.5665104985237122 True -13 36974 29.34316873550415 1.2425081729888916 132.09051513671875 0.7289931178092957 202.27236938476562 0.22967563569545746 0.8236726 0.541684627532959 True -14 39615 29.343550205230713 0.5340855121612549 189.83087158203125 0.4727804362773895 202.1519775390625 0.22976616024971008 0.8302639 0.518746554851532 True -15 42256 29.30394148826599 4.139157772064209 182.47386169433594 0.5611882209777832 201.48855590820312 0.23181253671646118 0.8352848 0.4992690980434418 True -16 44897 29.457963228225708 0.5189921855926514 189.4342041015625 0.34260839223861694 201.8019561767578 0.23121562600135803 0.8361056 0.4843851923942566 True -17 47538 29.314286708831787 0.5183596611022949 169.97389221191406 0.454639196395874 201.7993927001953 0.231424018740654 0.83668983 0.48122164607048035 True -18 50179 29.297252893447876 0.507366418838501 200.7764129638672 0.353256493806839 201.61618041992188 0.23250238597393036 0.83635014 0.4826774597167969 False -19 52820 29.381391048431396 0.5123805999755859 120.1742172241211 0.28277888894081116 201.56146240234375 0.23271557688713074 0.83580977 0.4867335855960846 False diff --git a/ENCSR884ODJ/cherimoya.fold_2.performance.tsv b/ENCSR884ODJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 89d1cd1ade923f684ea877f366de1e3619914a8c..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.7993927001953 0.5403957962989807 0.231424018740654 0.06412137299776077 0.836689829826355 0.7830213904380798 0.48122164607048035 \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_3.evaluate.json b/ENCSR884ODJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0ea766d8b31a536cd7a50c3a2954b2032a5279bc..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF728IYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_3.fit.json b/ENCSR884ODJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 2c65e15a446a1a92508e8f0a9b977bf3b2378888..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF728IYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_3.log b/ENCSR884ODJ/cherimoya.fold_3.log deleted file mode 100644 index 39b1b557d39eb5c4322e1bcb3194710a6393d06b..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2516 32.55351758003235 56.65572905540466 217.6212158203125 0.7975530624389648 252.31967163085938 0.1526971161365509 0.5808795 5.32002592086792 True -1 5032 27.906030893325806 3.0384013652801514 109.05653381347656 0.9992015361785889 227.7937469482422 0.20817458629608154 0.7096931 2.4570820331573486 True -2 7548 27.98281455039978 0.5807056427001953 164.0052032470703 0.8508507013320923 222.21009826660156 0.218543142080307 0.723971 1.703201413154602 True -3 10064 28.03588843345642 0.5323162078857422 136.97354125976562 0.632172703742981 220.3590850830078 0.22149571776390076 0.7386553 1.3243745565414429 True -4 12580 27.97537660598755 0.5117640495300293 225.46742248535156 0.688750147819519 218.31716918945312 0.2267116755247116 0.7462268 1.301474690437317 True -5 15096 27.898593187332153 0.5396294593811035 258.67535400390625 0.7249388694763184 217.25697326660156 0.22877374291419983 0.75326544 1.232374906539917 True -6 17612 28.048311948776245 0.5314915180206299 197.46337890625 0.6448739171028137 216.6072998046875 0.22993943095207214 0.75948846 1.1500812768936157 True -7 20128 28.023009777069092 0.5234293937683105 161.15072631835938 0.8639147281646729 216.0101318359375 0.2317526936531067 0.7685053 1.0301533937454224 True -8 22644 27.99391746520996 0.5407006740570068 151.00567626953125 0.5749846696853638 215.01425170898438 0.23491723835468292 0.7729446 0.9695602059364319 True -9 25160 27.986835479736328 0.5187139511108398 203.31317138671875 0.7511006593704224 213.94105529785156 0.23753856122493744 0.7859755 0.8599175810813904 True -10 27676 27.915210485458374 0.5163223743438721 161.93028259277344 0.6351818442344666 213.6359405517578 0.2383362203836441 0.7947303 0.7881876826286316 True -11 30192 27.893701791763306 0.5172843933105469 128.9584503173828 0.6763930320739746 212.7591552734375 0.24002118408679962 0.79718995 0.7693138122558594 True -12 32708 27.891425132751465 2.819892406463623 187.3566131591797 0.6819403171539307 212.31527709960938 0.2409553825855255 0.80921686 0.6949663162231445 True -13 35224 27.939939975738525 0.5167341232299805 151.793212890625 0.5812493562698364 211.18161010742188 0.24384525418281555 0.81554484 0.6575239300727844 True -14 37740 27.967308282852173 0.5260708332061768 156.8270263671875 0.47215506434440613 211.04583740234375 0.24318692088127136 0.82302064 0.6099021434783936 True -15 40256 27.941874742507935 0.5095417499542236 184.82626342773438 0.5615909695625305 210.27145385742188 0.2457689344882965 0.82915574 0.5799528956413269 True -16 42772 27.982309103012085 0.4991569519042969 156.7397003173828 0.6799778938293457 210.6591339111328 0.24370026588439941 0.8319945 0.5572741031646729 True -17 45288 27.96552348136902 0.5137045383453369 166.86317443847656 0.4378899335861206 210.3924102783203 0.24454687535762787 0.8332703 0.5469011068344116 True -18 47804 28.569106101989746 15.650925636291504 147.48907470703125 0.5973861217498779 209.86924743652344 0.24599318206310272 0.8333407 0.5467542409896851 True -19 50320 28.058730363845825 0.5616016387939453 175.60610961914062 0.3838462829589844 210.5365447998047 0.24375483393669128 0.8320766 0.5477269887924194 False diff --git a/ENCSR884ODJ/cherimoya.fold_3.performance.tsv b/ENCSR884ODJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ac2882b9f26e5bf4854b101149f86279fa314290..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -209.86924743652344 0.5313482880592346 0.24599316716194153 0.06801243871450424 0.8333407044410706 0.7856540083885193 0.5467542409896851 \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_4.evaluate.json b/ENCSR884ODJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c0c4ddd32596134e0226c048d934d69645f8aade..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF728IYG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_4.fit.json b/ENCSR884ODJ/cherimoya.fold_4.fit.json deleted file mode 100644 index db2808801d3ab1590ab0d1d30305dcff34e97a38..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF728IYG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR884ODJ/cherimoya.fold_4.log b/ENCSR884ODJ/cherimoya.fold_4.log deleted file mode 100644 index de435adb0147934745eafbf6614a430148e5cfdc..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2570 33.123252868652344 3.6859853267669678 169.39215087890625 0.8586792945861816 213.76463317871094 0.13532084226608276 0.58264655 3.6974430084228516 True -1 5140 28.435014009475708 1.613229751586914 174.20413208007812 0.9193227291107178 195.41262817382812 0.18320941925048828 0.7022847 2.0427627563476562 True -2 7710 28.498093128204346 0.5366005897521973 149.52969360351562 0.6607420444488525 190.1226348876953 0.1934402734041214 0.7221461 1.172836184501648 True -3 10280 28.52501130104065 0.5188708305358887 232.31332397460938 0.9138232469558716 188.15695190429688 0.19687660038471222 0.72956264 0.9263641834259033 True -4 12850 28.486789226531982 0.5510597229003906 165.82870483398438 0.8660858273506165 187.0123748779297 0.1985878199338913 0.7427598 0.9450328350067139 True -5 15420 28.44990038871765 0.5304741859436035 155.95297241210938 1.038101315498352 186.03524780273438 0.20081524550914764 0.75129825 0.9622141122817993 True -6 17990 28.437023878097534 0.5183990001678467 130.90533447265625 0.8530466556549072 184.57444763183594 0.20533233880996704 0.7625044 0.836100161075592 True -7 20560 28.47999382019043 0.5238394737243652 160.1763916015625 0.7185075283050537 184.0771026611328 0.20584702491760254 0.77147156 0.751549482345581 True -8 23130 27.873233318328857 0.5414252281188965 166.67535400390625 0.8922096490859985 183.55435180664062 0.2071629911661148 0.7786824 0.7108333110809326 True -9 25700 28.027347326278687 0.5327563285827637 124.09837341308594 0.6231216192245483 182.5595703125 0.2102336436510086 0.78476083 0.6586557626724243 True -10 28270 27.938481092453003 0.5088398456573486 187.0212860107422 0.7294772863388062 182.29147338867188 0.2102108597755432 0.794045 0.6007752418518066 True -11 30840 27.879005193710327 0.5221326351165771 110.46958923339844 0.5969838500022888 181.96849060058594 0.21137972176074982 0.79930633 0.5690209865570068 True -12 33410 27.959739923477173 0.516310453414917 179.8484344482422 0.732758641242981 181.14453125 0.213278666138649 0.8058301 0.5485706925392151 True -13 35980 27.964658975601196 0.511005163192749 196.45297241210938 0.4811108112335205 180.5443878173828 0.21549811959266663 0.8128274 0.5139767527580261 True -14 38550 27.957504272460938 0.507077693939209 124.14661407470703 0.38083916902542114 180.22061157226562 0.21602995693683624 0.81789035 0.49330440163612366 True -15 41120 28.014623641967773 0.5253632068634033 152.6943359375 0.5723122358322144 179.9483642578125 0.21651360392570496 0.8224575 0.47400930523872375 True -16 43690 27.932465076446533 0.5311048030853271 123.82720947265625 0.3007078766822815 179.83985900878906 0.2176060676574707 0.8265342 0.46050000190734863 True -17 46260 27.96723437309265 0.5231895446777344 120.55148315429688 0.3229038715362549 179.90728759765625 0.2170799970626831 0.82642275 0.4579481780529022 False -18 48830 28.008488655090332 0.5361320972442627 150.1998291015625 0.4159266948699951 180.0928497314453 0.2164260596036911 0.82737064 0.4550849497318268 True -19 51400 28.053702354431152 0.5203652381896973 197.175537109375 0.49926894903182983 180.05677795410156 0.21670763194561005 0.82680917 0.4575517177581787 False diff --git a/ENCSR884ODJ/cherimoya.fold_4.performance.tsv b/ENCSR884ODJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d680adc5d7c7d497b546a4985c015936c01659ea..0000000000000000000000000000000000000000 --- a/ENCSR884ODJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -180.0928497314453 0.5522079467773438 0.2164260596036911 0.0572708398103714 0.8273706436157227 0.7613328099250793 0.4550849497318268 \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_0.evaluate.json b/ENCSR885AWF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b0856b552b76c1a85f88fda679136ae0c3d067b2..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF779AQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_0.fit.json b/ENCSR885AWF/cherimoya.fold_0.fit.json deleted file mode 100644 index 50b013cf7da7d53b8530e1cb36479841d872327a..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF779AQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_0.log b/ENCSR885AWF/cherimoya.fold_0.log deleted file mode 100644 index 5c137b1e8f315ceb2c76bbb88f8ca5b031ca5a16..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 33.9870126247406 3.538597345352173 237.65237426757812 0.7036162614822388 336.7242736816406 0.15248948335647583 0.70021844 4.652324199676514 True -1 5496 30.369531393051147 0.5897986888885498 254.39987182617188 0.6851677894592285 308.3169860839844 0.21806131303310394 0.771772 1.6698390245437622 True -2 8244 30.33820605278015 1.2684755325317383 252.39892578125 0.7197083234786987 303.1729431152344 0.22744566202163696 0.78996545 0.8849475979804993 True -3 10992 30.31924319267273 20.29410147666931 203.56163024902344 0.38764724135398865 300.6169128417969 0.23201823234558105 0.80051446 0.6930162906646729 True -4 13740 30.403435468673706 0.5308349132537842 268.7898254394531 0.48436662554740906 299.9397888183594 0.23268510401248932 0.8050614 0.6904516816139221 True -5 16488 30.333539247512817 0.5161325931549072 302.3512268066406 0.5573009252548218 299.0245056152344 0.2344888299703598 0.80943626 0.677859365940094 True -6 19236 30.345252752304077 0.5238909721374512 219.9458465576172 0.5291040539741516 297.8634033203125 0.23819656670093536 0.814601 0.6267014145851135 True -7 21984 30.333019495010376 0.5236711502075195 265.695556640625 0.47614529728889465 297.43548583984375 0.2387574315071106 0.8212923 0.5798841118812561 True -8 24732 30.371071577072144 19.73559856414795 232.2754364013672 0.39326080679893494 296.0649719238281 0.24247388541698456 0.8286561 0.5618366003036499 True -9 27480 30.400477647781372 1.9631059169769287 287.0548400878906 0.5692274570465088 295.2828369140625 0.24407587945461273 0.833663 0.5322881937026978 True -10 30228 30.406643867492676 1.2059290409088135 249.48724365234375 0.34951335191726685 294.9265441894531 0.2449808269739151 0.84072614 0.4746648967266083 True -11 32976 30.375072479248047 1.1087570190429688 215.1202392578125 0.37751084566116333 293.7681884765625 0.2476043403148651 0.84414244 0.4671372175216675 True -12 35724 30.635860443115234 0.5405189990997314 272.908447265625 0.45906633138656616 293.67926025390625 0.2476620227098465 0.8465686 0.4459081292152405 True -13 38472 30.358529090881348 0.5569779872894287 244.30764770507812 0.53943932056427 293.4228515625 0.24831530451774597 0.8516664 0.4294021725654602 True -14 41220 30.339627027511597 0.5294499397277832 243.66189575195312 0.35633906722068787 292.4634094238281 0.25128763914108276 0.8518145 0.4149536192417145 True -15 43968 30.35515809059143 0.5222630500793457 232.569091796875 0.3449288606643677 292.57696533203125 0.2506479024887085 0.8549025 0.4020427167415619 True -16 46716 30.310471534729004 0.5314719676971436 219.3251495361328 0.5370569825172424 292.4662170410156 0.2507748603820801 0.85657084 0.3980032801628113 True -17 49464 30.383647680282593 0.5329430103302002 238.4597930908203 0.34246182441711426 291.82073974609375 0.25272637605667114 0.8575586 0.3973158895969391 True -18 52212 30.37147045135498 0.5168013572692871 186.0863037109375 0.38913673162460327 292.4228210449219 0.2505883574485779 0.8547832 0.40066424012184143 False -19 54960 30.35864520072937 0.5281007289886475 274.9642028808594 0.2507144808769226 292.64141845703125 0.2500954568386078 0.8537473 0.4032684564590454 False diff --git a/ENCSR885AWF/cherimoya.fold_0.performance.tsv b/ENCSR885AWF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f1f285ade2604a445f58c76d784fb472c062b890..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -291.82073974609375 0.5148090720176697 0.25272637605667114 0.0758209377527237 0.8575586080551147 0.8198056817054749 0.3973158895969391 \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_1.evaluate.json b/ENCSR885AWF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 31bd9b9cd415b746e0b0c50e486555c45fcaffad..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF779AQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_1.fit.json b/ENCSR885AWF/cherimoya.fold_1.fit.json deleted file mode 100644 index 4f9d90040dd8468456f2cac8e60e5d3fb6aa9728..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF779AQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_1.log b/ENCSR885AWF/cherimoya.fold_1.log deleted file mode 100644 index 02fecb5c5d3517cfb6bce9ab683e66d7bb939c89..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2721 33.60165739059448 4.007798194885254 219.78382873535156 0.6516473293304443 381.49407958984375 0.159539595246315 0.7128578 4.875380039215088 True -1 5442 30.120698928833008 0.9120607376098633 175.64837646484375 0.49921464920043945 344.8580017089844 0.2340172678232193 0.79652476 1.5789862871170044 True -2 8163 30.098283290863037 0.7888970375061035 313.9991455078125 0.528128445148468 340.449951171875 0.23906904458999634 0.8145205 0.8507381081581116 True -3 10884 30.232751846313477 1.188814640045166 249.6713104248047 0.8241236805915833 337.15509033203125 0.24465632438659668 0.8265823 0.7256295084953308 True -4 13605 30.160385847091675 0.7527704238891602 205.84091186523438 0.540336549282074 336.26116943359375 0.24677132070064545 0.8298725 0.6850689053535461 True -5 16326 30.011101961135864 0.753777027130127 261.7060241699219 0.37427186965942383 333.9773254394531 0.2511143386363983 0.8397199 0.6059749126434326 True -6 19047 30.00638222694397 0.7505569458007812 295.3827209472656 0.568143367767334 333.3447265625 0.2522996962070465 0.84190345 0.5981690883636475 True -7 21768 30.003989458084106 0.7431986331939697 186.85845947265625 0.4834555387496948 332.78497314453125 0.25313785672187805 0.8467538 0.5757400989532471 True -8 24489 29.985904693603516 0.7526872158050537 216.32537841796875 0.4913461208343506 331.7454528808594 0.25597190856933594 0.8545637 0.5218965411186218 True -9 27210 30.019357442855835 0.749849796295166 201.69259643554688 0.5886536240577698 331.05499267578125 0.2571013867855072 0.8591165 0.5051826238632202 True -10 29931 30.011332750320435 0.7385363578796387 318.0829162597656 0.584787130355835 329.6692199707031 0.260282427072525 0.8628333 0.4668126702308655 True -11 32652 30.009419679641724 0.7490639686584473 208.50262451171875 0.3758240342140198 328.7152404785156 0.2623102068901062 0.867341 0.4606603980064392 True -12 35373 30.00475788116455 0.7517709732055664 211.80880737304688 0.4622969925403595 328.5610656738281 0.26178601384162903 0.87058574 0.432854026556015 True -13 38094 29.99685502052307 0.7763228416442871 201.42330932617188 0.38826996088027954 327.8213806152344 0.26407480239868164 0.87383986 0.43921035528182983 True -14 40815 29.96515393257141 0.7505738735198975 216.42178344726562 0.3149130344390869 326.9488830566406 0.26555854082107544 0.87724787 0.4206198751926422 True -15 43536 30.06050395965576 0.7402191162109375 223.1924591064453 0.5829591751098633 326.57391357421875 0.2668341398239136 0.8815064 0.4000624716281891 True -16 46257 30.06830620765686 0.7656700611114502 240.669189453125 0.2885573208332062 326.4783935546875 0.2674204111099243 0.88136905 0.39721909165382385 False -17 48978 30.02395987510681 0.762566328048706 240.89901733398438 0.38590487837791443 326.786865234375 0.2660200595855713 0.8814508 0.39915814995765686 False -18 51699 30.04001545906067 0.7606563568115234 222.46157836914062 0.31765615940093994 326.5726318359375 0.26650649309158325 0.88109046 0.3983366787433624 False -19 54420 30.061728954315186 0.747225284576416 204.11154174804688 0.29456251859664917 326.5953674316406 0.2666209936141968 0.87920403 0.4007636308670044 False diff --git a/ENCSR885AWF/cherimoya.fold_1.performance.tsv b/ENCSR885AWF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index fcf4ad4c2c27ee661bca2a00b04598d4cb38dff3..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.57391357421875 0.5005559325218201 0.2668341100215912 0.08586252480745316 0.8815063834190369 0.8594300150871277 0.4000624716281891 \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_2.evaluate.json b/ENCSR885AWF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0dc1e0373998b8544ac8d2f0a1566f5dca955e55..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF779AQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_2.fit.json b/ENCSR885AWF/cherimoya.fold_2.fit.json deleted file mode 100644 index cc4f2a7bd8ae5815b772b3485ffa85d971c2f42a..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF779AQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_2.log b/ENCSR885AWF/cherimoya.fold_2.log deleted file mode 100644 index fede037aa74e5360b283292698f8d6fd388a4935..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 35.603600025177 3.5513999462127686 196.62548828125 0.7271499037742615 356.6189880371094 0.1599053591489792 0.6912452 4.386979579925537 True -1 5800 32.06631112098694 0.6735880374908447 290.171142578125 0.6169085502624512 321.8517761230469 0.22941243648529053 0.7854204 1.2161933183670044 True -2 8700 32.013946533203125 0.5124778747558594 249.18017578125 0.547074556350708 319.02679443359375 0.23426994681358337 0.7923735 0.826809287071228 True -3 11600 32.47784638404846 0.5133013725280762 215.63442993164062 0.41366422176361084 316.8684997558594 0.2376389354467392 0.8023062 0.6662349104881287 True -4 14500 32.02482342720032 0.5086712837219238 251.22854614257812 0.5131044387817383 315.4986877441406 0.23958173394203186 0.8147387 0.6352422833442688 True -5 17400 32.03584384918213 0.513253927230835 258.60614013671875 0.5884590744972229 313.5468444824219 0.24418038129806519 0.8220506 0.6004834771156311 True -6 20300 31.922380924224854 0.5102081298828125 211.60028076171875 0.29374778270721436 312.7479553222656 0.24602927267551422 0.82706475 0.5996375679969788 True -7 23200 32.00093674659729 0.5140905380249023 299.8516845703125 0.7654776573181152 311.3747863769531 0.2499765008687973 0.83538395 0.5382112860679626 True -8 26100 31.99239182472229 0.5147006511688232 225.700927734375 0.53581303358078 310.83746337890625 0.2512191832065582 0.8381062 0.5404179096221924 True -9 29000 32.00893807411194 0.5126185417175293 246.8066864013672 0.6294643878936768 309.630859375 0.2539922595024109 0.84340435 0.5178521871566772 True -10 31900 32.00892353057861 0.5175538063049316 217.86044311523438 0.3926095962524414 308.931396484375 0.25567176938056946 0.84488875 0.4882730543613434 True -11 34800 31.964264154434204 0.5452752113342285 218.032470703125 0.4457379877567291 308.160400390625 0.25706228613853455 0.84923726 0.4748995304107666 True -12 37700 31.954954147338867 0.5110504627227783 237.3969268798828 0.3178776204586029 307.9876708984375 0.25733494758605957 0.85381174 0.45652124285697937 True -13 40600 31.95525097846985 0.5128517150878906 248.6344757080078 0.4686393439769745 307.5534362792969 0.2584131062030792 0.8570055 0.43836262822151184 True -14 43500 31.986549615859985 0.5064435005187988 321.33709716796875 0.3782377243041992 307.02056884765625 0.26001617312431335 0.85969746 0.4206869900226593 True -15 46400 32.038737535476685 0.5080544948577881 207.47314453125 0.33577948808670044 306.28704833984375 0.2609958350658417 0.8618471 0.4064526855945587 True -16 49300 32.0247278213501 0.5128169059753418 184.32455444335938 0.39765268564224243 305.7783508300781 0.26375484466552734 0.861087 0.3994675278663635 False -17 52200 32.00777316093445 0.5113339424133301 264.30780029296875 0.3517148494720459 305.98944091796875 0.26229625940322876 0.8597518 0.3996185064315796 False -18 55100 31.98587465286255 1.6827785968780518 263.8021545410156 0.26350265741348267 306.28863525390625 0.26191726326942444 0.8599144 0.40621018409729004 False -19 58000 32.07284164428711 19.393104553222656 233.58518981933594 0.3769438862800598 306.13031005859375 0.2625056803226471 0.8576979 0.4104093611240387 False diff --git a/ENCSR885AWF/cherimoya.fold_2.performance.tsv b/ENCSR885AWF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d5823c702b21cde762ee241870bbde562ee9c18c..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -306.28704833984375 0.507267951965332 0.2609958052635193 0.08106823265552521 0.8618471026420593 0.832503080368042 0.4064526855945587 \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_3.evaluate.json b/ENCSR885AWF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3ef76a22821d0f1343a6d254615079986a790ca6..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF779AQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_3.fit.json b/ENCSR885AWF/cherimoya.fold_3.fit.json deleted file mode 100644 index 4229e9423068300324ef330d8d0634cb16fdfdb3..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF779AQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_3.log b/ENCSR885AWF/cherimoya.fold_3.log deleted file mode 100644 index 8d318750c2f757a79ec4bf77aa6fc3bd296c0920..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 34.32901883125305 4.816520690917969 291.32611083984375 0.7923338413238525 344.52081298828125 0.15939940512180328 0.6805784 4.822450637817383 True -1 5560 30.795758962631226 1.2525150775909424 195.56790161132812 0.6436682939529419 316.7269287109375 0.22008611261844635 0.7619241 1.5766828060150146 True -2 8340 30.676814794540405 0.5248405933380127 233.37005615234375 0.47905030846595764 311.880859375 0.22838447988033295 0.77654755 1.1243884563446045 True -3 11120 30.67353630065918 0.5280261039733887 219.05319213867188 0.5214381217956543 309.3929443359375 0.23292042315006256 0.787508 0.8314369916915894 True -4 13900 30.62100386619568 0.7005302906036377 222.13658142089844 0.6283210515975952 308.4181213378906 0.23529589176177979 0.79246384 0.8144046068191528 True -5 16680 30.709391117095947 0.5250608921051025 232.7553253173828 0.8213729858398438 307.9178771972656 0.23674342036247253 0.7985188 0.7544969320297241 True -6 19460 30.637662649154663 0.5289478302001953 211.64703369140625 0.5537185668945312 307.2001647949219 0.2386305332183838 0.8013767 0.7642478942871094 True -7 22240 30.645026683807373 0.5441226959228516 196.74176025390625 0.397829532623291 306.05120849609375 0.24201981723308563 0.80882835 0.6768150329589844 True -8 25020 30.68389892578125 1.0795187950134277 297.2236633300781 0.3815675377845764 304.93280029296875 0.24556775391101837 0.81603634 0.6421865224838257 True -9 27800 30.660361528396606 0.532250165939331 199.13128662109375 0.6641066074371338 304.8879699707031 0.2448587417602539 0.82238775 0.620975136756897 True -10 30580 30.67253851890564 0.5390164852142334 195.0791015625 0.5171157121658325 304.7587585449219 0.24581830203533173 0.825193 0.6311823725700378 True -11 33360 30.67383885383606 0.5414228439331055 231.62200927734375 0.6460307240486145 303.9775085449219 0.2478935718536377 0.8315682 0.5734535455703735 True -12 36140 30.707075595855713 0.555699348449707 256.98486328125 0.4851348102092743 302.7719421386719 0.25134900212287903 0.8373868 0.5551878213882446 True -13 38920 30.684919357299805 1.1432101726531982 203.57843017578125 0.5242583155632019 302.1065979003906 0.25233063101768494 0.8414665 0.5137028694152832 True -14 41700 30.964330673217773 20.78366780281067 205.6328125 0.46471744775772095 301.3140869140625 0.2541111707687378 0.84765315 0.4838726222515106 True -15 44480 31.08686399459839 0.5343570709228516 220.98764038085938 0.3443584144115448 301.0566101074219 0.2542862594127655 0.8536302 0.4503012001514435 True -16 47260 30.74039602279663 0.5369021892547607 289.0624694824219 0.5285080075263977 300.87127685546875 0.25513750314712524 0.85579044 0.4380086660385132 True -17 50040 30.74074697494507 0.5385780334472656 223.945556640625 0.5797032117843628 301.18804931640625 0.2542366683483124 0.8551717 0.43465906381607056 False -18 52820 30.699469804763794 0.5395646095275879 201.0260772705078 0.27809938788414 301.2567138671875 0.25374382734298706 0.8531083 0.43552106618881226 False -19 55600 30.65525197982788 0.5338711738586426 175.27392578125 0.26234495639801025 301.17364501953125 0.2539752423763275 0.85113156 0.4368811547756195 False diff --git a/ENCSR885AWF/cherimoya.fold_3.performance.tsv b/ENCSR885AWF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 13f642a1d63adf44fee07c622e5117b1c2e897d4..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -300.87127685546875 0.510369598865509 0.25513750314712524 0.07808893918991089 0.8557904362678528 0.8221299052238464 0.4380086660385132 \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_4.evaluate.json b/ENCSR885AWF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9379ac4c796732291ad494f46e2eb888ae26d677..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF779AQZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_4.fit.json b/ENCSR885AWF/cherimoya.fold_4.fit.json deleted file mode 100644 index 1060e362e0c771879114f54bfd3b049ea976c670..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF779AQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885AWF/cherimoya.fold_4.log b/ENCSR885AWF/cherimoya.fold_4.log deleted file mode 100644 index 6acae8fc8c5aa3f2c498711d1e7a0de91539fea3..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2809 34.776968002319336 3.5556986331939697 205.66339111328125 0.5418748259544373 298.66033935546875 0.14092864096164703 0.69791555 3.8422932624816895 True -1 5618 31.058736085891724 0.6010005474090576 254.19601440429688 0.37889569997787476 274.5745544433594 0.19860410690307617 0.7810241 1.3202290534973145 True -2 8427 31.01914143562317 0.576005220413208 214.48834228515625 0.8548210859298706 270.9720153808594 0.20490506291389465 0.79723626 0.6635666489601135 True -3 11236 30.991719961166382 0.5513763427734375 240.9392547607422 0.6302824020385742 269.1363220214844 0.20814913511276245 0.80514747 0.5845538377761841 True -4 14045 30.944042205810547 0.9737308025360107 238.83563232421875 0.5183607935905457 268.3215637207031 0.2103210985660553 0.81244427 0.5548397898674011 True -5 16854 30.986490964889526 0.5635190010070801 262.071533203125 0.7112239599227905 267.4076232910156 0.21319155395030975 0.818642 0.5290873646736145 True -6 19663 30.972168684005737 0.5568225383758545 248.52426147460938 0.5984123945236206 267.1158142089844 0.21390177309513092 0.81928146 0.5407384634017944 True -7 22472 30.98979902267456 0.5543370246887207 204.04591369628906 0.7044559121131897 266.232421875 0.21631452441215515 0.8265946 0.507455587387085 True -8 25281 30.952279806137085 0.5576663017272949 249.56256103515625 0.4591186046600342 265.45220947265625 0.21778574585914612 0.83605283 0.48726895451545715 True -9 28090 30.961333513259888 0.5587711334228516 223.87564086914062 0.45224326848983765 264.9781494140625 0.2190757840871811 0.8397854 0.44780433177948 True -10 30899 30.992860794067383 0.5573065280914307 196.77490234375 0.5656348466873169 264.9337158203125 0.21865789592266083 0.8452867 0.4157983958721161 True -11 33708 30.96480369567871 0.5589420795440674 268.2225341796875 0.5998325943946838 264.0433349609375 0.2219480574131012 0.84861994 0.4102807939052582 True -12 36517 31.009231090545654 1.2469966411590576 241.792236328125 0.39707523584365845 263.5437927246094 0.22286570072174072 0.852919 0.3914043605327606 True -13 39326 31.030568838119507 0.5601403713226318 252.96548461914062 0.39798980951309204 262.6268615722656 0.22537708282470703 0.85639167 0.3834434747695923 True -14 42135 30.978375911712646 0.5585172176361084 228.464111328125 0.5421638488769531 262.4923095703125 0.22557243704795837 0.8598759 0.36818215250968933 True -15 44944 31.004483938217163 0.5565612316131592 276.6041564941406 0.25927573442459106 262.4276428222656 0.22571615874767303 0.8654615 0.356926828622818 True -16 47753 31.006449460983276 0.5822758674621582 208.2469482421875 0.4480048716068268 262.1130065917969 0.22734712064266205 0.86399025 0.35229864716529846 False -17 50562 31.040157794952393 0.5583286285400391 200.57449340820312 0.43970754742622375 262.079833984375 0.2280275523662567 0.8643769 0.35288041830062866 False -18 53371 31.039108514785767 0.5584301948547363 255.59487915039062 0.3487980365753174 262.2530517578125 0.22759199142456055 0.86534435 0.3548405170440674 False -19 56180 30.995986223220825 0.555518388748169 225.43719482421875 0.39039015769958496 262.6188659667969 0.2264118492603302 0.8653971 0.3565528988838196 False diff --git a/ENCSR885AWF/cherimoya.fold_4.performance.tsv b/ENCSR885AWF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e27d6f00bc43b922c7aee0780b10ff4c596da072..0000000000000000000000000000000000000000 --- a/ENCSR885AWF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -262.4276428222656 0.5324077010154724 0.22571614384651184 0.06715679913759232 0.865461528301239 0.8271855115890503 0.356926828622818 \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_0.evaluate.json b/ENCSR885ZBV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c8acd079153672acb9a690da32158f62fbba1130..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743UBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_0.fit.json b/ENCSR885ZBV/cherimoya.fold_0.fit.json deleted file mode 100644 index 2821bedd30c6280ced16e8c2e103fb1c82dbd8d2..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF743UBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_0.log b/ENCSR885ZBV/cherimoya.fold_0.log deleted file mode 100644 index 130e7a98505eb9db8bf68042d1cd76fd61f6df10..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 34.5426459312439 3.668147087097168 390.86328125 0.23236194252967834 529.028076171875 0.27808570861816406 0.8042951 3.662005662918091 True -1 5520 30.568227529525757 0.6295769214630127 505.3349304199219 0.19127127528190613 497.8077392578125 0.33581775426864624 0.843453 0.63630610704422 True -2 8280 30.584635496139526 0.6012115478515625 499.0793151855469 0.21792466938495636 490.62554931640625 0.34551653265953064 0.86034644 0.26292309165000916 True -3 11040 30.59213924407959 0.6120014190673828 429.032470703125 0.1885622888803482 486.2192077636719 0.3534083366394043 0.86888415 0.21564224362373352 True -4 13800 30.634806871414185 0.6196215152740479 401.0469970703125 0.252909392118454 484.7695007324219 0.35590046644210815 0.8723167 0.16977709531784058 True -5 16560 30.59047293663025 1.314422845840454 445.70562744140625 0.18395595252513885 482.7081604003906 0.3597451448440552 0.8776908 0.17228029668331146 True -6 19320 30.637428045272827 0.6213717460632324 505.5468444824219 0.19042953848838806 482.2958679199219 0.3598250448703766 0.88125044 0.17347657680511475 True -7 22080 30.55561113357544 0.6275327205657959 420.5927429199219 0.11999537795782089 480.7072448730469 0.36309486627578735 0.8851251 0.16786809265613556 True -8 24840 30.62332320213318 0.6136000156402588 409.9761962890625 0.14016923308372498 479.84527587890625 0.365433931350708 0.888061 0.16605645418167114 True -9 27600 30.587022304534912 0.6056029796600342 437.3331298828125 0.1803218126296997 479.2141418457031 0.3659152388572693 0.8908978 0.15612360835075378 True -10 30360 30.624420404434204 0.6178719997406006 405.7349853515625 0.18494956195354462 478.0432434082031 0.3683207929134369 0.89466405 0.16180257499217987 True -11 33120 30.546536207199097 0.876291036605835 422.43927001953125 0.19731901586055756 477.5119934082031 0.36850985884666443 0.8965724 0.14057917892932892 True -12 35880 30.612478733062744 0.6179013252258301 420.57684326171875 0.26997748017311096 476.7984619140625 0.36979085206985474 0.8984486 0.13398075103759766 True -13 38640 30.609798908233643 0.6198694705963135 441.26904296875 0.15467388927936554 476.0334167480469 0.37111517786979675 0.90009046 0.12727299332618713 True -14 41400 30.583706855773926 0.6248266696929932 436.204345703125 0.08300552517175674 476.1971740722656 0.3705161511898041 0.9045504 0.12339325249195099 True -15 44160 30.6506130695343 0.6177990436553955 415.32745361328125 0.1593928039073944 474.5269470214844 0.37467026710510254 0.90597486 0.1202746033668518 True -16 46920 30.58728861808777 0.6278119087219238 451.46051025390625 0.15596239268779755 474.783447265625 0.3731153905391693 0.90792423 0.11778786778450012 True -17 49680 30.57063055038452 0.6306109428405762 406.5196228027344 0.10018733143806458 474.5367736816406 0.3741624653339386 0.9106378 0.11726176738739014 True -18 52440 30.583828449249268 0.6188054084777832 426.9644775390625 0.08061768859624863 474.688232421875 0.37371787428855896 0.91033536 0.1167430430650711 False -19 55200 30.91677474975586 0.6250956058502197 446.79302978515625 0.08136969804763794 475.0722961425781 0.3725023567676544 0.9098155 0.11718714982271194 False diff --git a/ENCSR885ZBV/cherimoya.fold_0.performance.tsv b/ENCSR885ZBV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e73aa929f7ebedeb486c82ef6bb0bf4f059ba358..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -474.5367736816406 0.40777647495269775 0.3741624355316162 0.138681098818779 0.9106377959251404 0.8872451782226562 0.11726176738739014 \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_1.evaluate.json b/ENCSR885ZBV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9fcb39cab6ffbd7cfc8116a3ad65b0512ec4e20c..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743UBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_1.fit.json b/ENCSR885ZBV/cherimoya.fold_1.fit.json deleted file mode 100644 index 086c2f9d53db68637a176fbb8fde43ad364227a4..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF743UBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_1.log b/ENCSR885ZBV/cherimoya.fold_1.log deleted file mode 100644 index 83302955064760286d0b2b2a7f3b221d3677f6bc..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2720 34.39660453796387 3.903831720352173 489.34600830078125 0.26732057332992554 592.6829223632812 0.27703583240509033 0.7962299 3.6366617679595947 True -1 5440 30.14596462249756 0.7288718223571777 401.20965576171875 0.2588754892349243 551.9224243164062 0.346686989068985 0.8459735 0.7436960935592651 True -2 8160 30.213310718536377 0.7379779815673828 408.8837585449219 2.491009473800659 542.9994506835938 0.35789167881011963 0.85779476 0.2486550509929657 True -3 10880 30.11806035041809 0.7354063987731934 419.00579833984375 0.24003386497497559 541.2913818359375 0.35957223176956177 0.8632365 0.22117704153060913 True -4 13600 30.110289573669434 0.7372472286224365 425.71319580078125 0.2304919958114624 537.1968383789062 0.3660055696964264 0.87205464 0.190761998295784 True -5 16320 30.163735151290894 0.7314941883087158 404.3922119140625 0.1928846538066864 535.661865234375 0.3676544725894928 0.8740528 0.18213489651679993 True -6 19040 30.126287698745728 0.7268064022064209 433.012939453125 0.2168487310409546 532.7892456054688 0.37248140573501587 0.88058966 0.17521238327026367 True -7 21760 30.096957445144653 0.7311937808990479 462.5257263183594 0.17280088365077972 531.4485473632812 0.3748013973236084 0.8818851 0.17930011451244354 True -8 24480 30.12341547012329 0.7228395938873291 471.9659729003906 0.1611434817314148 529.9701538085938 0.37708204984664917 0.8880374 0.17763757705688477 True -9 27200 30.139044284820557 0.7175681591033936 439.25299072265625 0.16094070672988892 529.5806274414062 0.37660685181617737 0.89120376 0.1702924221754074 True -10 29920 30.133557319641113 0.7219913005828857 446.53192138671875 0.09535027295351028 527.1524047851562 0.38122135400772095 0.8953145 0.16032591462135315 True -11 32640 30.119691610336304 0.7196476459503174 441.6796875 0.1542474925518036 525.383056640625 0.38437169790267944 0.897775 0.15435490012168884 True -12 35360 30.11650252342224 0.7331509590148926 428.37091064453125 0.14761891961097717 525.0089111328125 0.3841107487678528 0.9018924 0.14438684284687042 True -13 38080 30.13019061088562 0.7259232997894287 390.76739501953125 0.07517912983894348 524.4993286132812 0.3844507336616516 0.9053884 0.1450626701116562 True -14 40800 30.197710752487183 0.736515998840332 417.10919189453125 0.1774584800004959 522.0933837890625 0.3892170190811157 0.9088988 0.13835157454013824 True -15 43520 30.208640575408936 0.7416436672210693 376.14117431640625 0.14390528202056885 522.1538696289062 0.38842350244522095 0.91065955 0.13429929316043854 True -16 46240 30.190964221954346 0.7408847808837891 447.2398986816406 0.1414628028869629 522.16357421875 0.38824594020843506 0.9133538 0.1306191235780716 True -17 48960 30.186681032180786 0.732215404510498 409.3102111816406 0.1379297971725464 522.5133056640625 0.38747984170913696 0.91409 0.12773264944553375 True -18 51680 30.171196460723877 0.7414610385894775 386.78704833984375 0.07609659433364868 521.7743530273438 0.3894941806793213 0.9142954 0.12741875648498535 True -19 54400 30.183007955551147 0.749478816986084 390.00396728515625 0.09911493211984634 522.385009765625 0.38779178261756897 0.91363734 0.1282835602760315 False diff --git a/ENCSR885ZBV/cherimoya.fold_1.performance.tsv b/ENCSR885ZBV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f2c29b9cc4a8cd87925ac5eda3efbddeed967921..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -521.7743530273438 0.3949143886566162 0.3894942104816437 0.15112513303756714 0.9142953753471375 0.9069212675094604 0.12741875648498535 \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_2.evaluate.json b/ENCSR885ZBV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 24e47fa83b89b02e857334dc8829d8089cf5dc7f..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743UBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_2.fit.json b/ENCSR885ZBV/cherimoya.fold_2.fit.json deleted file mode 100644 index 8d4d25043a0b7b8c27de65c06b0329a440b7b82a..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF743UBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_2.log b/ENCSR885ZBV/cherimoya.fold_2.log deleted file mode 100644 index 7b5147138c1c0514b4fe32c11660ef7c413ff875..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 36.42242360115051 3.65325665473938 405.5089416503906 0.28158384561538696 558.9492797851562 0.2807837128639221 0.7957775 3.265324115753174 True -1 5758 31.95768690109253 7.417476415634155 419.08599853515625 0.20708014070987701 524.2791748046875 0.340991735458374 0.8386449 0.6543395519256592 True -2 8637 31.951281785964966 0.605172872543335 455.9869384765625 0.239376500248909 515.0205688476562 0.3551768958568573 0.8528658 0.249515101313591 True -3 11516 31.953801155090332 0.581965446472168 445.9708557128906 0.28127366304397583 513.1234130859375 0.3574846386909485 0.85769945 0.2061835527420044 True -4 14395 31.99505043029785 0.5825822353363037 370.8050537109375 0.12890875339508057 510.52801513671875 0.3615323305130005 0.8631538 0.18775859475135803 True -5 17274 31.95503330230713 0.5766072273254395 419.7796630859375 0.10791703313589096 509.13873291015625 0.3640211224555969 0.8676082 0.17352160811424255 True -6 20153 31.934042930603027 0.5770905017852783 420.28436279296875 0.164973646402359 508.0556335449219 0.3654046654701233 0.8712826 0.17305399477481842 True -7 23032 31.94599175453186 0.5778460502624512 418.7005615234375 0.14490331709384918 506.6459655761719 0.3680642545223236 0.87513614 0.1624860167503357 True -8 25911 31.92855477333069 0.5705678462982178 437.114013671875 0.20096662640571594 504.9150390625 0.37150949239730835 0.87814045 0.1557605117559433 True -9 28790 31.941193103790283 0.5710928440093994 416.1307678222656 0.17838767170906067 504.7239990234375 0.37117743492126465 0.8803442 0.1537390500307083 True -10 31669 31.923330545425415 0.579679012298584 456.750732421875 0.1397564709186554 503.7861022949219 0.37273144721984863 0.88495183 0.14635033905506134 True -11 34548 31.98934555053711 0.5780258178710938 352.3023986816406 0.23962751030921936 502.97430419921875 0.37387821078300476 0.887671 0.1466694176197052 True -12 37427 31.979186534881592 0.578899621963501 420.1492919921875 0.1536216139793396 502.41973876953125 0.3747231960296631 0.8899537 0.13930538296699524 True -13 40306 32.04270696640015 7.461229562759399 424.22296142578125 0.1844712495803833 501.2524719238281 0.3773004710674286 0.8917373 0.1372404396533966 True -14 43185 31.948803901672363 0.5894134044647217 470.30816650390625 0.19075244665145874 500.9296875 0.3773956000804901 0.89480764 0.1344105303287506 True -15 46064 32.002500772476196 0.6013896465301514 436.7994384765625 0.10906464606523514 500.3877868652344 0.37884756922721863 0.89798564 0.1303619146347046 True -16 48943 32.015838861465454 0.588693380355835 352.68798828125 0.14966227114200592 500.06451416015625 0.3791438639163971 0.90111464 0.128350168466568 True -17 51822 32.05658936500549 1.5636839866638184 400.6497802734375 0.08078387379646301 499.8137512207031 0.37973037362098694 0.899582 0.1277366280555725 False -18 54701 32.009358167648315 0.5731077194213867 496.6581726074219 0.16954325139522552 500.6047668457031 0.3778335750102997 0.89856094 0.12877945601940155 False -19 57580 32.01167011260986 0.5808076858520508 363.5168762207031 0.08286002278327942 500.28448486328125 0.37885552644729614 0.9005255 0.129665806889534 False diff --git a/ENCSR885ZBV/cherimoya.fold_2.performance.tsv b/ENCSR885ZBV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 93f7991aa0c2fa642e30c6bd14451c35e90ed702..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -500.06451416015625 0.40088504552841187 0.3791438639163971 0.14274123311042786 0.9011146426200867 0.8849062323570251 0.128350168466568 \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_3.evaluate.json b/ENCSR885ZBV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3d344a95bcc321b56c84bb3f9b4e0473e08c6956..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743UBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_3.fit.json b/ENCSR885ZBV/cherimoya.fold_3.fit.json deleted file mode 100644 index 960dde31939ed49570e3a0ba87389526d1ab0501..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF743UBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_3.log b/ENCSR885ZBV/cherimoya.fold_3.log deleted file mode 100644 index a855599fa62fc89f1c9ef0a08e06bf283b138c99..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.82433795928955 3.549177885055542 395.17401123046875 0.3194682002067566 527.3176879882812 0.28428781032562256 0.784043 3.619899272918701 True -1 5514 30.556102514266968 0.5504744052886963 399.299072265625 0.23384734988212585 494.7679443359375 0.34261560440063477 0.8333413 0.6475526690483093 True -2 8271 30.579313039779663 1.4073166847229004 512.8023681640625 0.23339325189590454 488.7342529296875 0.34955480694770813 0.8508399 0.325809508562088 True -3 11028 30.596913814544678 0.5320594310760498 425.4417419433594 0.1923515498638153 484.21038818359375 0.35762694478034973 0.86006266 0.23764123022556305 True -4 13785 30.602619409561157 0.6927692890167236 461.6668395996094 0.09903024882078171 482.111572265625 0.3610627353191376 0.86777973 0.19904345273971558 True -5 16542 30.549198389053345 1.702641248703003 387.0923767089844 0.22479520738124847 481.1888122558594 0.36282050609588623 0.87059206 0.20173093676567078 True -6 19299 30.629537343978882 0.5861625671386719 411.25897216796875 0.28126755356788635 480.29461669921875 0.364551842212677 0.87362957 0.187411829829216 True -7 22056 30.578428983688354 0.545921802520752 404.50665283203125 0.15260538458824158 479.5522766113281 0.36582309007644653 0.87799037 0.17730407416820526 True -8 24813 30.612651824951172 0.5510439872741699 422.9696350097656 0.17050057649612427 478.27069091796875 0.36816564202308655 0.88176084 0.1807498037815094 True -9 27570 30.60621213912964 0.5434584617614746 437.5953063964844 0.1287384182214737 477.1756896972656 0.3700244724750519 0.88410586 0.18290048837661743 True -10 30327 30.593220472335815 0.5780866146087646 398.6330871582031 0.18337640166282654 476.5193176269531 0.371396005153656 0.88850266 0.1635674089193344 True -11 33084 31.184782028198242 0.5586838722229004 421.5775146484375 0.1031835749745369 475.20111083984375 0.37358108162879944 0.8902076 0.1552390158176422 True -12 35841 30.611915826797485 0.5535502433776855 499.54925537109375 0.11640363931655884 474.8415222167969 0.37398409843444824 0.89382756 0.1483769714832306 True -13 38598 30.567056894302368 0.7090804576873779 365.8909912109375 0.11199373006820679 473.64501953125 0.3763234615325928 0.8974935 0.14432662725448608 True -14 41355 30.61908268928528 15.889046430587769 407.4169921875 0.14336076378822327 473.11865234375 0.37655869126319885 0.89979625 0.1377907693386078 True -15 44112 30.61291241645813 0.7892217636108398 473.80975341796875 0.09584084153175354 472.3247985839844 0.37793615460395813 0.90371513 0.13352163136005402 True -16 46869 30.58654475212097 0.5396904945373535 405.3828125 0.1109599769115448 472.2310791015625 0.37708935141563416 0.90403116 0.13030298054218292 True -17 49626 30.642740488052368 0.575545072555542 395.5765075683594 0.09047366678714752 471.89056396484375 0.37835466861724854 0.9068096 0.1282745748758316 True -18 52383 30.551000118255615 0.5385215282440186 375.6197509765625 0.11367280781269073 472.1246032714844 0.3777235448360443 0.9074033 0.12828369438648224 True -19 55140 30.53184700012207 0.552764892578125 418.96234130859375 0.12529578804969788 472.3255920410156 0.37759557366371155 0.9060027 0.1286737322807312 False diff --git a/ENCSR885ZBV/cherimoya.fold_3.performance.tsv b/ENCSR885ZBV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d403c5f33176ea8cd0e5c1965cf1c913e6ac4f0a..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -472.1246032714844 0.40610620379447937 0.3777235150337219 0.14141079783439636 0.907403290271759 0.8798809051513672 0.12828369438648224 \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_4.evaluate.json b/ENCSR885ZBV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1bcce1497f25ce4b1df3609006e0e1c83801b5e7..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF743UBB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_4.fit.json b/ENCSR885ZBV/cherimoya.fold_4.fit.json deleted file mode 100644 index e048bda4fb4afe3eb2d380aca72b88fa0c27146b..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF743UBB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR885ZBV/cherimoya.fold_4.log b/ENCSR885ZBV/cherimoya.fold_4.log deleted file mode 100644 index 3c050f282c5da9f4c4dd0e8f084f6bf23f0cd2cf..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2791 35.369550466537476 3.644019842147827 383.5614013671875 0.2090526521205902 491.46661376953125 0.2709141969680786 0.79784423 3.3804092407226562 True -1 5582 30.958442449569702 0.664287805557251 378.31085205078125 0.1945730745792389 460.6138000488281 0.33147913217544556 0.84194565 0.49884411692619324 True -2 8373 31.821186542510986 4.1200783252716064 377.8165283203125 0.40774452686309814 456.4093322753906 0.33771970868110657 0.8498608 0.21192511916160583 True -3 11164 31.125895977020264 1.042708158493042 455.2603759765625 0.21050377190113068 451.7933349609375 0.34389206767082214 0.8687459 0.16697776317596436 True -4 13955 31.033984422683716 0.6561572551727295 467.2103271484375 0.2283589392900467 451.01763916015625 0.3447970449924469 0.8722668 0.16187039017677307 True -5 16746 31.05121088027954 0.6716651916503906 413.0993347167969 0.23941846191883087 449.8536071777344 0.3471835255622864 0.87549496 0.1485701948404312 True -6 19537 31.070838451385498 0.6629278659820557 352.29864501953125 0.11074020713567734 449.71905517578125 0.3460247218608856 0.8796771 0.14229123294353485 True -7 22328 31.07469367980957 0.6718189716339111 400.3160095214844 0.14184433221817017 448.1595458984375 0.3503611981868744 0.8849888 0.1412794440984726 True -8 25119 31.057815551757812 0.6570253372192383 387.2228698730469 0.14262637495994568 447.3899841308594 0.35177165269851685 0.88677865 0.1384948045015335 True -9 27910 31.081814527511597 0.6835663318634033 398.5931396484375 0.13791385293006897 446.6224060058594 0.35334882140159607 0.8901462 0.12990586459636688 True -10 30701 31.104455947875977 0.6764230728149414 416.5267333984375 0.10350380837917328 445.8777160644531 0.35472920536994934 0.8949812 0.1266697645187378 True -11 33492 31.069828271865845 0.6774899959564209 375.280029296875 0.1470153033733368 444.9456481933594 0.3565800189971924 0.89559495 0.12449727952480316 True -12 36283 31.032015323638916 0.680377721786499 374.27435302734375 0.1834077537059784 445.1531066894531 0.3556539714336395 0.8974842 0.12103217095136642 True -13 39074 30.9626784324646 0.6753787994384766 463.923583984375 0.1350773721933365 443.56414794921875 0.35978782176971436 0.9013614 0.11777521669864655 True -14 41865 31.031324863433838 0.6666786670684814 410.8706359863281 0.12896986305713654 442.99591064453125 0.3610420525074005 0.90321267 0.11444032937288284 True -15 44656 31.11305069923401 0.6645188331604004 425.65020751953125 0.11217513680458069 443.0356140136719 0.36075037717819214 0.9075196 0.11283435672521591 True -16 47447 31.33817982673645 0.6715717315673828 385.2001953125 0.10727426409721375 442.2602844238281 0.36251047253608704 0.9078916 0.10865528881549835 True -17 50238 31.127806425094604 0.6788480281829834 375.39178466796875 0.1144496351480484 442.6387023925781 0.3602775037288666 0.9109881 0.10777650028467178 True -18 53029 31.225117683410645 0.6614487171173096 404.740966796875 0.18110397458076477 442.35455322265625 0.3617658019065857 0.9084575 0.10789123922586441 False -19 55820 31.12691354751587 0.6574509143829346 421.9913330078125 0.12985871732234955 442.9886474609375 0.3602384924888611 0.9096489 0.1082317903637886 False diff --git a/ENCSR885ZBV/cherimoya.fold_4.performance.tsv b/ENCSR885ZBV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7cd0ee882d7ab175d83e4c8242a49ec55363d849..0000000000000000000000000000000000000000 --- a/ENCSR885ZBV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -442.6387023925781 0.41958087682724 0.3602775037288666 0.12905342876911163 0.9109880924224854 0.8836561441421509 0.10777650028467178 \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_0.evaluate.json b/ENCSR886VCC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 415497bcc18caa997bd5fb7b1afd534ae41a8f17..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF835APK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_0.fit.json b/ENCSR886VCC/cherimoya.fold_0.fit.json deleted file mode 100644 index 1a27a73a1843eb57320ab461049d6585e07d73b6..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF835APK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_0.log b/ENCSR886VCC/cherimoya.fold_0.log deleted file mode 100644 index 27e4fde834c3f96a970e5e68b77ee7d439c1c811..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2913 36.9079430103302 4.272339105606079 696.8440551757812 0.8539028167724609 989.8101806640625 0.6715061664581299 0.5599128 10.911468505859375 True -1 5826 32.49130845069885 1.567960500717163 653.8895263671875 1.0517666339874268 790.107666015625 0.7695394158363342 0.5930207 3.5939013957977295 True -2 8739 32.50501537322998 0.5487501621246338 604.6153564453125 0.9974039793014526 761.3910522460938 0.7830953598022461 0.59465575 1.6663388013839722 True -3 11652 32.44098138809204 0.552391529083252 630.6207275390625 1.4804034233093262 750.442138671875 0.7889876961708069 0.6039645 1.5426290035247803 True -4 14565 32.45881962776184 0.5429823398590088 557.2998046875 1.0550966262817383 742.4130249023438 0.7934049963951111 0.6101817 1.353600263595581 True -5 17478 32.499839782714844 0.5411429405212402 581.8568115234375 0.9903541803359985 737.3915405273438 0.7957844138145447 0.6134659 1.2043862342834473 True -6 20391 32.49636220932007 0.5415933132171631 647.353759765625 0.8041790723800659 735.779052734375 0.7963109016418457 0.60679084 1.1736876964569092 False -7 23304 32.45931959152222 0.5468549728393555 567.3006591796875 0.7180910110473633 727.5401000976562 0.8001291751861572 0.6191196 1.0817416906356812 True -8 26217 32.62357783317566 0.5610954761505127 554.6717529296875 0.6376920938491821 723.207275390625 0.8027116656303406 0.62829494 0.977901041507721 True -9 29130 32.51197409629822 11.2058846950531 595.947021484375 0.6574271321296692 718.1495361328125 0.8053542375564575 0.632651 0.9140233397483826 True -10 32043 32.93595027923584 0.545501708984375 553.1094970703125 0.5753152370452881 712.5552978515625 0.8074304461479187 0.6385367 0.8615952730178833 True -11 34956 32.470564126968384 0.5457420349121094 521.083984375 0.7951860427856445 708.8098754882812 0.8097583055496216 0.6468421 0.8294473886489868 True -12 37869 32.51052689552307 1.7057514190673828 636.4134521484375 0.6224730014801025 704.27197265625 0.8118064999580383 0.6574454 0.8132681846618652 True -13 40782 32.68127942085266 0.5398271083831787 574.0423583984375 0.7169183492660522 700.718017578125 0.8138197660446167 0.6675927 0.7609813213348389 True -14 43695 32.62809205055237 0.5487899780273438 631.9909057617188 0.8253150582313538 697.1134643554688 0.8157913088798523 0.67278206 0.739055871963501 True -15 46608 32.64546060562134 0.5423200130462646 558.3165893554688 0.7313801050186157 694.0239868164062 0.8173255920410156 0.67658395 0.7230706214904785 True -16 49521 32.9695999622345 0.5520083904266357 517.9095458984375 0.6926343441009521 693.3953247070312 0.8177745342254639 0.67621815 0.7191517353057861 False -17 52434 32.007959604263306 0.5456209182739258 581.124267578125 0.7251178026199341 694.1326904296875 0.8176798820495605 0.67409843 0.7245270609855652 False -18 55347 31.93125033378601 0.5377590656280518 512.915283203125 0.48520055413246155 694.8601684570312 0.8172998428344727 0.6679261 0.7399064898490906 False -19 58260 31.844024181365967 0.7121806144714355 530.307373046875 0.42594996094703674 695.6817626953125 0.8168850541114807 0.6638843 0.752302885055542 False diff --git a/ENCSR886VCC/cherimoya.fold_0.performance.tsv b/ENCSR886VCC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7f2977d8a0302ae5dcda6b7395df5eb952819b1e..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -694.0239868164062 0.1536046713590622 0.8173255920410156 0.44907569885253906 0.6765839457511902 0.6191903948783875 0.7230706214904785 \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_1.evaluate.json b/ENCSR886VCC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7a58253d4020404c2514accdb835d7a44cb2d2ad..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF835APK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_1.fit.json b/ENCSR886VCC/cherimoya.fold_1.fit.json deleted file mode 100644 index 63c5256fe1fc45f048296b4a7e9b1242536adc4e..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF835APK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_1.log b/ENCSR886VCC/cherimoya.fold_1.log deleted file mode 100644 index 0c67eaac87462608e80468de93807f789c9375d6..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2883 36.951189041137695 4.136930704116821 519.9073486328125 1.1245399713516235 1096.9910888671875 0.6737352609634399 0.5512759 11.211465835571289 True -1 5766 32.11589503288269 1.3826231956481934 537.1116943359375 1.1125532388687134 874.4780883789062 0.7698962688446045 0.5992097 4.208966255187988 True -2 8649 32.16223168373108 2.0721263885498047 526.26025390625 1.269056797027588 831.7727661132812 0.7871713638305664 0.6007132 1.7317264080047607 True -3 11532 32.153167963027954 0.7635436058044434 615.8837890625 0.9938712120056152 815.93505859375 0.7943528890609741 0.6018507 1.3603618144989014 True -4 14415 32.679060220718384 24.453227281570435 561.5250854492188 0.8684775233268738 810.053466796875 0.7984300255775452 0.6073785 1.2795989513397217 True -5 17298 32.203829765319824 1.931993007659912 661.621337890625 1.068200707435608 804.3846435546875 0.8018512725830078 0.61573005 1.1356037855148315 True -6 20181 32.23826003074646 0.7961344718933105 636.6751708984375 1.0029808282852173 797.685791015625 0.8048385381698608 0.62054896 1.0257682800292969 True -7 23064 32.38149547576904 0.8084781169891357 501.240966796875 0.8299952745437622 792.69677734375 0.8074498772621155 0.625818 0.9746952056884766 True -8 25947 32.322367906570435 1.552816390991211 606.09814453125 0.9128653407096863 787.8062133789062 0.8095628619194031 0.6317249 0.9603250622749329 True -9 28830 32.288021087646484 0.7770583629608154 513.3575439453125 0.8206521272659302 780.3863525390625 0.8125511407852173 0.6394156 0.9053414463996887 True -10 31713 32.26355028152466 0.774378776550293 485.0123291015625 0.5552042722702026 776.3860473632812 0.8144035935401917 0.64619476 0.8633986115455627 True -11 34596 32.26905131340027 0.7849535942077637 565.3258666992188 0.7945927381515503 770.9112548828125 0.816641628742218 0.6533481 0.8250727653503418 True -12 37479 32.4337043762207 29.51385474205017 576.00048828125 0.5688185691833496 765.57861328125 0.8193948864936829 0.6620553 0.8190697431564331 True -13 40362 34.66999793052673 0.7705004215240479 548.4796142578125 0.7731953859329224 760.5664672851562 0.8217308521270752 0.6752614 0.800099790096283 True -14 43245 32.85610055923462 0.7753438949584961 562.2569580078125 0.7412804365158081 756.4562377929688 0.8234419226646423 0.6849829 0.7741711735725403 True -15 46128 33.99410843849182 40.690327405929565 490.0345764160156 0.815689206123352 753.7750854492188 0.8246756792068481 0.6911465 0.7414328455924988 True -16 49011 31.802654027938843 2.0945444107055664 547.3702392578125 0.47616928815841675 752.469482421875 0.8251795172691345 0.69379073 0.7367297410964966 True -17 51894 31.71107769012451 0.7666776180267334 590.650634765625 0.5248280167579651 752.7216186523438 0.824992835521698 0.6958062 0.7261096239089966 True -18 54777 31.662588596343994 0.7545630931854248 497.6872863769531 0.4406062364578247 753.9885864257812 0.8244666457176208 0.6913178 0.7340025305747986 False -19 57660 31.674663066864014 0.7612128257751465 472.3675231933594 0.7306286096572876 754.8366088867188 0.8240886926651001 0.69032276 0.738739550113678 False diff --git a/ENCSR886VCC/cherimoya.fold_1.performance.tsv b/ENCSR886VCC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 429ad5538d2e0df15a3d41cecd5b5f58837010ed..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -752.7216186523438 0.14496564865112305 0.8249929547309875 0.47713035345077515 0.6958062052726746 0.653516948223114 0.7261096239089966 \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_2.evaluate.json b/ENCSR886VCC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d53e1c2ff42169daf30ad0ca484f3743bb071f0a..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF835APK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_2.fit.json b/ENCSR886VCC/cherimoya.fold_2.fit.json deleted file mode 100644 index 9fdc3db1d5fd8ff96e69b82fbc228ccca700e424..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF835APK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_2.log b/ENCSR886VCC/cherimoya.fold_2.log deleted file mode 100644 index 0f877ff921652a996be39c6e953d2396732c9a81..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3091 40.83935570716858 3.603127956390381 525.0608520507812 1.1541130542755127 968.4688720703125 0.6831273436546326 0.5346982 8.867016792297363 True -1 6182 34.47271800041199 0.6252689361572266 705.1360473632812 1.1157413721084595 785.6005859375 0.7725721597671509 0.6051099 3.2158586978912354 True -2 9273 34.48738980293274 0.6105549335479736 626.2879638671875 0.9091119766235352 762.4353637695312 0.7831729650497437 0.61068356 1.6277709007263184 True -3 12364 34.50464987754822 2.1158223152160645 576.7221069335938 0.7796969413757324 753.3515625 0.7885102033615112 0.6102429 1.2701873779296875 False -4 15455 34.6983277797699 0.6188492774963379 715.86083984375 0.7816927433013916 745.9043579101562 0.7905118465423584 0.6113917 1.1677335500717163 True -5 18546 34.76029944419861 0.6338579654693604 663.9378662109375 1.1041264533996582 740.5677490234375 0.7946445345878601 0.60775477 1.1140012741088867 False -6 21637 34.64834213256836 2.403519868850708 551.6296997070312 0.9313784837722778 735.01953125 0.7975906729698181 0.61678946 0.9962988495826721 True -7 24728 34.74525165557861 0.6199758052825928 525.891845703125 0.8831902742385864 732.294189453125 0.8001291751861572 0.6261629 1.0264772176742554 True -8 27819 34.57708168029785 0.6268818378448486 626.3978271484375 0.9267964959144592 728.0100708007812 0.8023380637168884 0.6296944 0.9787006974220276 True -9 30910 34.6198673248291 0.6272871494293213 644.7723388671875 0.9400486350059509 722.8109130859375 0.8043703436851501 0.6341251 0.9233687520027161 True -10 34001 34.48300766944885 0.61183762550354 590.1430053710938 0.8721834421157837 717.7928466796875 0.8069009184837341 0.64364207 0.8573430180549622 True -11 37092 34.453601360321045 0.6091098785400391 571.2734375 0.6838489174842834 713.7599487304688 0.8084396123886108 0.6510161 0.7963371872901917 True -12 40183 34.46713972091675 0.597675085067749 529.7921142578125 0.6337695717811584 709.212890625 0.8110901713371277 0.6571185 0.7869402170181274 True -13 43274 34.51111841201782 0.6111958026885986 583.5238037109375 0.8255022764205933 705.7615356445312 0.8130369782447815 0.66619796 0.774196207523346 True -14 46365 34.4696900844574 0.6083545684814453 529.256103515625 0.9079979658126831 702.7520141601562 0.8144171237945557 0.67524046 0.7292141318321228 True -15 49456 33.864442110061646 24.2990779876709 576.0440063476562 0.7881855964660645 700.3953247070312 0.8159705996513367 0.68018556 0.7142747640609741 True -16 52547 33.88612151145935 29.685917615890503 564.0697631835938 0.44038689136505127 700.298828125 0.8163192272186279 0.6817889 0.7045261263847351 True -17 55638 33.745508909225464 0.6075811386108398 465.0587158203125 0.5672889947891235 700.3124389648438 0.8160976767539978 0.6806796 0.7046141624450684 False -18 58729 33.79181742668152 0.6053688526153564 545.0199584960938 0.7181746959686279 701.567626953125 0.8155643939971924 0.67859304 0.7170124053955078 False -19 61820 33.69551086425781 0.6019468307495117 532.9247436523438 0.6028666496276855 702.4874267578125 0.815234899520874 0.67640597 0.7270394563674927 False diff --git a/ENCSR886VCC/cherimoya.fold_2.performance.tsv b/ENCSR886VCC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4183fc390be74ca60bea58c240d79ce0cef7e20a..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -700.298828125 0.1531151682138443 0.8163192272186279 0.453782856464386 0.6817889213562012 0.6286342740058899 0.7045261263847351 \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_3.evaluate.json b/ENCSR886VCC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c1dd6260a71e89fb7b361145fd7a551676dedcc5..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF835APK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_3.fit.json b/ENCSR886VCC/cherimoya.fold_3.fit.json deleted file mode 100644 index 2d755f3d779f88b0f553bde1fdf525a8863897f2..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF835APK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_3.log b/ENCSR886VCC/cherimoya.fold_3.log deleted file mode 100644 index 43a2202953619251a2725f88ba3b9c2f5dc680ea..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2968 38.04407286643982 3.486034393310547 706.4000854492188 1.0763208866119385 933.4542236328125 0.6768248081207275 0.5218891 7.550706386566162 True -1 5936 33.13868474960327 0.599531888961792 579.7959594726562 0.8233972787857056 753.3252563476562 0.7639937400817871 0.56689346 2.485051393508911 True -2 8904 33.095905780792236 28.301254272460938 686.9874267578125 0.8801258206367493 733.1005249023438 0.7762826085090637 0.5790439 1.5039031505584717 True -3 11872 33.46635317802429 0.5966587066650391 624.3885498046875 0.8824707269668579 722.9549560546875 0.7817169427871704 0.5754682 1.4036636352539062 False -4 14840 33.11107516288757 0.6026706695556641 559.475830078125 1.1945444345474243 718.3201293945312 0.7847816348075867 0.58216405 1.267245888710022 True -5 17808 33.132834672927856 0.5791306495666504 662.5823364257812 0.9772277474403381 711.6376953125 0.7879980802536011 0.5918455 1.1972668170928955 True -6 20776 33.07797932624817 0.5916728973388672 671.4982299804688 0.7753459215164185 707.4065551757812 0.7905210256576538 0.5894618 1.04848313331604 False -7 23744 33.353822469711304 0.5898754596710205 724.4061889648438 0.9599125385284424 703.4440307617188 0.7923674583435059 0.60053205 0.9891872406005859 True -8 26712 33.30470681190491 37.98367214202881 554.0845947265625 0.6297346353530884 698.9910278320312 0.7945607900619507 0.6036067 0.9694185256958008 True -9 29680 33.63144540786743 26.46732258796692 650.800048828125 0.9626801013946533 693.5140380859375 0.7977333664894104 0.6145977 0.9597770571708679 True -10 32648 34.65009593963623 0.5925853252410889 518.2913818359375 0.7035751342773438 690.0477294921875 0.7992731332778931 0.6173582 0.9306172132492065 True -11 35616 33.23232126235962 0.5896284580230713 560.3299560546875 0.8981726765632629 685.2335815429688 0.8023465871810913 0.6263649 0.9090854525566101 True -12 38584 33.00778365135193 1.6676900386810303 640.585693359375 0.8301166296005249 680.4000244140625 0.8049840331077576 0.63986367 0.859411895275116 True -13 41552 32.51147437095642 0.578383207321167 559.9005126953125 0.8707656860351562 677.161865234375 0.8069713711738586 0.6482873 0.8206369876861572 True -14 44520 32.33077645301819 1.5399231910705566 585.781494140625 0.7498369216918945 674.4791259765625 0.808558464050293 0.6574108 0.7979230880737305 True -15 47488 32.44013333320618 18.80491852760315 540.5390625 0.4328807294368744 671.5975341796875 0.810245931148529 0.6638865 0.7684966921806335 True -16 50456 32.47379922866821 1.0382099151611328 545.4862060546875 0.6558612585067749 670.8756103515625 0.8107759952545166 0.669069 0.7463756203651428 True -17 53424 32.53642821311951 0.5999133586883545 626.0194091796875 0.5344283580780029 671.3451538085938 0.8107624053955078 0.66891927 0.7391891479492188 False -18 56392 32.41641712188721 0.5843682289123535 583.3875732421875 0.5403933525085449 672.333740234375 0.8102419376373291 0.66674304 0.7515400052070618 False -19 59360 32.48613357543945 0.5835027694702148 557.7760009765625 0.4371452331542969 672.9603881835938 0.8098050951957703 0.66569006 0.757630467414856 False diff --git a/ENCSR886VCC/cherimoya.fold_3.performance.tsv b/ENCSR886VCC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 06dd234a1f1b330f517faf699201e81fd275b37a..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -670.8756103515625 0.1581866443157196 0.8107759952545166 0.4343617856502533 0.6690689921379089 0.6035302877426147 0.7463756203651428 \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_4.evaluate.json b/ENCSR886VCC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f15eb38ba40f5b683774b7f37c59ad5ca5a1a1e0..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF835APK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_4.fit.json b/ENCSR886VCC/cherimoya.fold_4.fit.json deleted file mode 100644 index 93f2e20e7fe70cacff5fa76b6adc6d79eaf1cccb..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF835APK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR886VCC/cherimoya.fold_4.log b/ENCSR886VCC/cherimoya.fold_4.log deleted file mode 100644 index 62f8e5dd6d5604967487a224985e730f06424fcd..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3010 38.515374183654785 3.78857421875 672.2294921875 1.06304132938385 935.7715454101562 0.6765602231025696 0.5368694 10.029974937438965 True -1 6020 33.494789361953735 0.5922791957855225 638.3673095703125 1.0478999614715576 756.9334106445312 0.7700152397155762 0.5803925 3.117116689682007 True -2 9030 33.692360401153564 2.025481700897217 631.0557861328125 0.7015604376792908 730.9706420898438 0.7829844355583191 0.5773697 1.4133607149124146 False -3 12040 33.555007457733154 0.5812578201293945 706.1482543945312 1.0058820247650146 721.3792114257812 0.7890121936798096 0.5853814 1.3483190536499023 True -4 15050 33.566744327545166 0.5709340572357178 568.0184326171875 0.741830587387085 713.3237915039062 0.7935943007469177 0.59563327 1.1828925609588623 True -5 18060 33.654818058013916 0.5788755416870117 628.7581176757812 0.6802407503128052 707.9365844726562 0.7961284518241882 0.59794533 0.9700030088424683 True -6 21070 33.51535940170288 0.5791416168212891 529.965576171875 0.7019521594047546 704.9111328125 0.7987308502197266 0.5996249 1.0240708589553833 True -7 24080 33.52965068817139 1.4941575527191162 702.8446044921875 1.018857717514038 701.5552368164062 0.8006231784820557 0.6058667 0.9980904459953308 True -8 27090 33.579060316085815 0.5795300006866455 521.4063110351562 1.373633861541748 697.5426025390625 0.8026657700538635 0.6045892 0.9830164313316345 False -9 30100 33.546520709991455 1.9937446117401123 501.1285400390625 0.9868333339691162 693.8981323242188 0.8043674230575562 0.6123744 0.9526376128196716 True -10 33110 33.59412860870361 0.5828871726989746 583.9617919921875 0.7787653207778931 689.5634155273438 0.8062576651573181 0.62144834 0.8906724452972412 True -11 36120 34.36119890213013 23.65013837814331 594.447998046875 0.8298195600509644 685.402587890625 0.8082942366600037 0.62692225 0.8274389505386353 True -12 39130 33.12184524536133 1.6658966541290283 506.2779846191406 0.8316700458526611 681.587890625 0.8105227947235107 0.63959664 0.8242986798286438 True -13 42140 32.87389826774597 1.409482479095459 638.501708984375 0.8379485607147217 678.0206298828125 0.8123476505279541 0.6519302 0.7662027478218079 True -14 45150 32.85700607299805 0.5619652271270752 670.399169921875 0.8494419455528259 675.3883666992188 0.8138347268104553 0.65615946 0.7311582565307617 True -15 48160 32.94475436210632 0.5670034885406494 577.9595947265625 0.6622896194458008 673.626220703125 0.8150039911270142 0.66300035 0.7159411311149597 True -16 51170 33.92120361328125 3.6764750480651855 532.120849609375 0.6950095891952515 672.6436157226562 0.8153238892555237 0.6697504 0.6974466443061829 True -17 54180 33.02568817138672 33.02720832824707 531.1793823242188 0.5270317196846008 673.65771484375 0.8146929144859314 0.6683894 0.7041499614715576 False -18 57190 33.05341362953186 1.4480559825897217 480.5946044921875 0.5589686632156372 674.6072387695312 0.8141442537307739 0.66381955 0.71966552734375 False -19 60200 32.898439168930054 6.078867673873901 521.9317626953125 0.5484901070594788 675.4454345703125 0.8137077689170837 0.66129875 0.7270182371139526 False diff --git a/ENCSR886VCC/cherimoya.fold_4.performance.tsv b/ENCSR886VCC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c7c8f5f9306913097817c3ebe4942d4a36f0dab3..0000000000000000000000000000000000000000 --- a/ENCSR886VCC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -672.6436157226562 0.15663370490074158 0.8153238892555237 0.43792179226875305 0.6697503924369812 0.6047545075416565 0.6974466443061829 \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_0.log b/ENCSR887BNC/cherimoya.fold_0.log deleted file mode 100644 index 140f779c3d9bf8ad46c5c9843c86d32ed8adfe17..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 34.424540281295776 4.895450592041016 191.1333770751953 0.7187877893447876 239.72650146484375 0.14108896255493164 0.6636556 2.398432493209839 True -1 5540 30.533371448516846 1.3149583339691162 231.2262420654297 0.442862868309021 231.02687072753906 0.18843340873718262 0.7183693 0.8512080907821655 True -2 8310 30.548214197158813 1.9719164371490479 142.30050659179688 0.6518019437789917 227.63522338867188 0.20294936001300812 0.73266244 0.43473997712135315 True -3 11080 30.551271200180054 1.6301770210266113 184.7274169921875 0.5454010963439941 226.0663299560547 0.2089422643184662 0.7411909 0.4417174756526947 True -4 13850 30.60841941833496 1.9655814170837402 186.66757202148438 0.605326771736145 225.53834533691406 0.21124202013015747 0.7446595 0.4657049775123596 True -5 16620 30.59273910522461 0.9608657360076904 160.72256469726562 0.3986854553222656 225.0732421875 0.21374176442623138 0.7476747 0.48648184537887573 True -6 19390 30.532166242599487 1.4138922691345215 179.85086059570312 0.5734755992889404 224.69142150878906 0.21587058901786804 0.74820596 0.4611455798149109 True -7 22160 30.723581552505493 1.5606977939605713 190.1980743408203 0.7268548011779785 224.60694885253906 0.21586324274539948 0.74808073 0.4403636157512665 False -8 24930 30.581310987472534 1.1644682884216309 171.1006622314453 0.3361261487007141 223.90985107421875 0.22000323235988617 0.75297564 0.4212782084941864 True -9 27700 30.88182783126831 27.267341375350952 155.50685119628906 0.34028303623199463 223.43182373046875 0.22279688715934753 0.7555966 0.42056193947792053 True -10 30470 30.687785625457764 0.5777719020843506 173.59127807617188 0.5168312788009644 223.09381103515625 0.22395926713943481 0.75428027 0.3995519280433655 False -11 33240 30.597808837890625 0.5818221569061279 195.44447326660156 0.3643583059310913 222.59751892089844 0.22714339196681976 0.7610156 0.3841186761856079 True -12 36010 30.668826818466187 0.5669803619384766 188.260498046875 0.3801628351211548 222.4037628173828 0.22766751050949097 0.76885414 0.3684089183807373 True -13 38780 30.60085105895996 0.5880577564239502 162.23382568359375 0.5388219356536865 221.83816528320312 0.2315903753042221 0.77526796 0.34922468662261963 True -14 41550 30.60173010826111 0.7319426536560059 193.2488250732422 0.3375905156135559 221.63482666015625 0.23152035474777222 0.7803698 0.3309555649757385 True -15 44320 30.60753846168518 0.5804779529571533 147.00425720214844 0.3820807933807373 221.60679626464844 0.23206457495689392 0.787319 0.310458242893219 True -16 47090 30.583223819732666 0.5866265296936035 184.68630981445312 0.3551425337791443 221.51907348632812 0.23250146210193634 0.7895421 0.30152344703674316 True -17 49860 30.606566667556763 0.574455738067627 156.09950256347656 0.22651061415672302 221.7566375732422 0.230805441737175 0.79330486 0.28877267241477966 True -18 52630 30.60471796989441 0.5680725574493408 222.53826904296875 0.23132511973381042 221.58505249023438 0.23208041489124298 0.7941015 0.2847920060157776 True -19 55400 30.593653678894043 0.5715835094451904 167.89051818847656 0.2776385545730591 221.75094604492188 0.230804905295372 0.7946577 0.2841920256614685 True diff --git a/ENCSR887BNC/cherimoya.fold_0.performance.tsv b/ENCSR887BNC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index eb2c221df75e07ec3a665f98f0273bd422cf9c20..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -221.75094604492188 0.5321434140205383 0.230804905295372 0.05980209633708 0.7946577072143555 0.7431676983833313 0.2841920256614685 \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_1.evaluate.json b/ENCSR887BNC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index dce946987ac0994633e70ff894405f0ddfe9046d..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF287SWO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_1.fit.json b/ENCSR887BNC/cherimoya.fold_1.fit.json deleted file mode 100644 index 88646c0ba6a9af0b48654f4040efab85071e220e..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF287SWO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_1.performance.tsv b/ENCSR887BNC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 641d1804b9ff513b341e6f2ce37859375854858b..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -256.0343933105469 0.5144400000572205 0.250643253326416 0.07159730792045593 0.8148171305656433 0.7767974734306335 0.32317012548446655 \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_2.evaluate.json b/ENCSR887BNC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d41df1fdd4571866a61fbd590cbadbc2bd6b869a..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF287SWO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_2.fit.json b/ENCSR887BNC/cherimoya.fold_2.fit.json deleted file mode 100644 index f1a161fac7a85e8ac1c694fd22c6db2184ea2d13..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF287SWO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_2.log b/ENCSR887BNC/cherimoya.fold_2.log deleted file mode 100644 index 05a2254e5278ae081913d6efcb79e7b7e81142be..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2895 36.39610457420349 3.8760018348693848 205.88156127929688 0.7805893421173096 248.68601989746094 0.14569959044456482 0.6642236 2.2782137393951416 True -1 5790 31.88094687461853 0.5393569469451904 197.9889678955078 0.8643526434898376 238.3348388671875 0.19931678473949432 0.73614836 0.8472715616226196 True -2 8685 31.893226861953735 0.5374393463134766 229.5520782470703 0.47968801856040955 235.0649871826172 0.21087144315242767 0.7477424 0.4480259418487549 True -3 11580 31.810482263565063 0.5453078746795654 197.26046752929688 0.6008806824684143 233.53750610351562 0.21694475412368774 0.7569507 0.4361708164215088 True -4 14475 31.843122005462646 0.5305509567260742 180.25732421875 0.531351625919342 233.42543029785156 0.21679124236106873 0.7553531 0.4422048032283783 False -5 17370 31.812566995620728 0.5284912586212158 215.04776000976562 0.521575927734375 232.93572998046875 0.2194409817457199 0.75862604 0.4444502294063568 True -6 20265 31.92329740524292 0.5349502563476562 170.26275634765625 0.41829535365104675 232.47769165039062 0.22140951454639435 0.7616099 0.42853689193725586 True -7 23160 31.87248945236206 0.5378985404968262 154.79965209960938 0.5425270795822144 231.79957580566406 0.22570042312145233 0.76678365 0.42856451869010925 True -8 26055 31.86300253868103 0.5451703071594238 188.03411865234375 0.3551916480064392 231.62423706054688 0.22538107633590698 0.77136415 0.4213823974132538 True -9 28950 31.84128212928772 0.5389425754547119 201.31240844726562 0.4579785466194153 231.18934631347656 0.2274412363767624 0.7686022 0.436344712972641 False -10 31845 31.881845474243164 0.5396409034729004 226.39443969726562 0.33639347553253174 230.74949645996094 0.2299138754606247 0.77494586 0.4043098986148834 True -11 34740 31.90813970565796 0.5403087139129639 154.69863891601562 0.41738206148147583 230.61953735351562 0.2304188460111618 0.7760218 0.3862786889076233 True -12 37635 31.92763376235962 0.5420000553131104 161.9678955078125 0.412006676197052 230.2338104248047 0.23269303143024445 0.7810968 0.3863566815853119 True -13 40530 31.917659044265747 0.5387849807739258 171.37545776367188 0.30755022168159485 229.81011962890625 0.2346799671649933 0.7856059 0.3686584532260895 True -14 43425 31.982244968414307 0.5405199527740479 193.93450927734375 0.38209009170532227 229.78500366210938 0.2341495156288147 0.79188085 0.3559362590312958 True -15 46320 31.873294830322266 0.5388758182525635 165.03750610351562 0.4745251536369324 229.56741333007812 0.23550933599472046 0.79598445 0.3342965543270111 True -16 49215 31.881791353225708 0.5404174327850342 174.76559448242188 0.33202260732650757 229.30917358398438 0.23683227598667145 0.7997588 0.31732746958732605 True -17 52110 31.704187154769897 0.518958330154419 171.02780151367188 0.27610543370246887 229.28179931640625 0.23660960793495178 0.80219847 0.30745023488998413 True -18 55005 31.240209579467773 0.5242197513580322 159.6522674560547 0.606460690498352 229.57025146484375 0.23530174791812897 0.8013086 0.30760401487350464 False -19 57900 31.229727268218994 0.5181849002838135 190.39157104492188 0.25151124596595764 229.53814697265625 0.2356690913438797 0.80106086 0.3073554039001465 False diff --git a/ENCSR887BNC/cherimoya.fold_2.performance.tsv b/ENCSR887BNC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 57ca8b366c5a17630fa06705757c69c41343db3d..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -229.28179931640625 0.5277186632156372 0.2366095930337906 0.05677841603755951 0.8021984696388245 0.7553183436393738 0.30745023488998413 \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_4.fit.json b/ENCSR887BNC/cherimoya.fold_4.fit.json deleted file mode 100644 index be3c7c0b14bbcd82e93963451a0b6e83f2376f4f..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF287SWO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887BNC/cherimoya.fold_4.log b/ENCSR887BNC/cherimoya.fold_4.log deleted file mode 100644 index d28d40a4193e8b654c0c96d84cd01731b2b8d570..0000000000000000000000000000000000000000 --- a/ENCSR887BNC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2862 36.593778133392334 3.622607946395874 175.7544708251953 0.9754879474639893 240.75318908691406 0.14296293258666992 0.65923125 2.633247137069702 True -1 5724 31.48536777496338 0.6246154308319092 199.18600463867188 0.44682592153549194 232.25436401367188 0.19038259983062744 0.7217848 0.7861723899841309 True -2 8586 31.46005344390869 0.6070106029510498 150.1531524658203 0.6856544017791748 229.48074340820312 0.20091696083545685 0.7342832 0.49918967485427856 True -3 11448 31.456994771957397 0.6036739349365234 164.0784149169922 0.5987708568572998 228.6323699951172 0.20391830801963806 0.7466833 0.4013623893260956 True -4 14310 31.459145545959473 0.6031622886657715 165.87088012695312 0.6352800130844116 227.9000701904297 0.20679785311222076 0.747198 0.4318675994873047 True -5 17172 31.390111207962036 0.6056363582611084 156.44683837890625 0.5108168721199036 227.5020751953125 0.209061399102211 0.75485665 0.40587860345840454 True -6 20034 31.371564865112305 0.593515157699585 180.38534545898438 0.37329602241516113 226.888916015625 0.21243126690387726 0.75838125 0.4025607109069824 True -7 22896 31.380303621292114 0.6030488014221191 164.64511108398438 0.3833461403846741 226.44061279296875 0.2146473228931427 0.75932354 0.398413747549057 True -8 25758 31.46026039123535 0.6039042472839355 185.83261108398438 0.6249507665634155 226.24996948242188 0.21574601531028748 0.7623238 0.40036648511886597 True -9 28620 31.388749361038208 0.6040170192718506 191.82791137695312 0.364357054233551 225.9071502685547 0.21794119477272034 0.7661162 0.3851640522480011 True -10 31482 31.393062114715576 1.9041006565093994 174.2275390625 0.43516892194747925 225.4468231201172 0.22038839757442474 0.7672394 0.3804311156272888 True -11 34344 31.51684069633484 2.5848166942596436 173.92596435546875 0.4161607027053833 224.97994995117188 0.22294451296329498 0.7731863 0.34227368235588074 True -12 37206 31.454277992248535 1.5768728256225586 181.45518493652344 0.49136584997177124 224.6579132080078 0.22430554032325745 0.7780263 0.33632710576057434 True -13 40068 31.443302869796753 23.372236251831055 181.1954345703125 0.4177917540073395 224.45884704589844 0.22506234049797058 0.7821436 0.32915762066841125 True -14 42930 31.454781532287598 0.6178135871887207 167.84228515625 0.3790580630302429 224.3866729736328 0.22515662014484406 0.78828764 0.31813836097717285 True -15 45792 31.49821639060974 0.6092250347137451 147.5835418701172 0.5099329948425293 224.18943786621094 0.22635959088802338 0.7915562 0.299034059047699 True -16 48654 31.421197175979614 0.6332659721374512 206.5050048828125 0.4017699360847473 223.9413604736328 0.22775624692440033 0.7952543 0.2886985242366791 True -17 51516 31.003180742263794 0.5813746452331543 168.10232543945312 0.20793983340263367 224.43234252929688 0.22485798597335815 0.7973362 0.28337153792381287 True -18 54378 30.91369867324829 0.5892438888549805 171.33624267578125 0.15827897191047668 224.17120361328125 0.22648437321186066 0.79721695 0.2880915701389313 False -19 57240 30.903849124908447 0.5985276699066162 190.44712829589844 0.2833564877510071 224.22531127929688 0.22620093822479248 0.7935195 0.29071635007858276 False diff --git a/ENCSR887VUC/cherimoya.fold_0.evaluate.json b/ENCSR887VUC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8a55b6ac261e35a71643c9092d949d44905317d5..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF665YXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_0.fit.json b/ENCSR887VUC/cherimoya.fold_0.fit.json deleted file mode 100644 index dc018dcacfd0ceca3a30397258261757b1268035..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF665YXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_0.log b/ENCSR887VUC/cherimoya.fold_0.log deleted file mode 100644 index 0fcb786bb899fb3a99cf0b1fb7ad56292fcbf6ef..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.25300049781799 3.534440279006958 522.4456787109375 0.6285606622695923 590.9525146484375 0.26065772771835327 0.7329681 4.340841770172119 True -1 5510 30.325581789016724 0.5853338241577148 380.8088684082031 0.5312809944152832 536.1873779296875 0.3327712118625641 0.8025619 1.0393389463424683 True -2 8265 30.306002616882324 0.9491267204284668 421.7311096191406 0.4442044794559479 524.7761840820312 0.34265002608299255 0.817406 0.5001527667045593 True -3 11020 30.278039693832397 0.5884366035461426 418.35052490234375 0.34019219875335693 522.1819458007812 0.3459637761116028 0.81473017 0.4719533920288086 False -4 13775 30.279871463775635 0.59110426902771 412.34735107421875 0.29040780663490295 520.3417358398438 0.3478347957134247 0.82341355 0.42765316367149353 True -5 16530 30.29441213607788 0.5758202075958252 393.04119873046875 0.3006707727909088 518.7692260742188 0.3485170602798462 0.8286159 0.4147789478302002 True -6 19285 30.30526304244995 0.5681750774383545 453.14111328125 0.3152264356613159 515.9830322265625 0.35335007309913635 0.83187044 0.39006561040878296 True -7 22040 30.248088598251343 0.5727493762969971 359.1982421875 0.4135702848434448 513.2742919921875 0.3568668067455292 0.8384419 0.34683653712272644 True -8 24795 30.28805160522461 0.6115710735321045 429.89874267578125 0.33214905858039856 511.8378601074219 0.35878512263298035 0.8408188 0.3492400646209717 True -9 27550 30.356387853622437 1.2694165706634521 455.54736328125 0.3514300286769867 510.5381774902344 0.3605450987815857 0.8483596 0.3449344038963318 True -10 30305 30.36783766746521 0.5900835990905762 404.75445556640625 0.32344934344291687 508.6385803222656 0.36286282539367676 0.85241437 0.3150888979434967 True -11 33060 30.25749897956848 0.5978977680206299 444.2677001953125 0.2789318859577179 507.0368957519531 0.365178644657135 0.8558587 0.2921651303768158 True -12 35815 30.301753044128418 0.5911576747894287 373.9570007324219 0.32672765851020813 505.3703918457031 0.36722269654273987 0.8624715 0.28888747096061707 True -13 38570 30.35241675376892 0.5909340381622314 417.91650390625 0.31179118156433105 503.8404235839844 0.36856961250305176 0.8657698 0.2647238075733185 True -14 41325 30.286587715148926 0.5764827728271484 425.73712158203125 0.21381792426109314 503.3219909667969 0.3695550858974457 0.87146837 0.24735930562019348 True -15 44080 30.327131748199463 0.6100735664367676 404.2884521484375 0.2984054982662201 502.4342956542969 0.36985623836517334 0.8737407 0.24217092990875244 True -16 46835 30.28695821762085 0.5873897075653076 391.50140380859375 0.3104473948478699 503.28656005859375 0.3682980239391327 0.87648356 0.23202961683273315 True -17 49590 30.323543787002563 0.5781869888305664 452.5126953125 0.2551692724227905 502.3135681152344 0.37128788232803345 0.87728184 0.22726504504680634 True -18 52345 30.36053204536438 0.5838854312896729 451.0749206542969 0.27390530705451965 502.4635925292969 0.3717392086982727 0.8769414 0.22671683132648468 False -19 55100 29.731523752212524 0.5767335891723633 385.3903503417969 0.1527818888425827 501.9444580078125 0.372331440448761 0.87641424 0.22709541022777557 False diff --git a/ENCSR887VUC/cherimoya.fold_0.performance.tsv b/ENCSR887VUC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b102cc42ad7ae2ffbba89188b969d3cc6333db78..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -502.3135681152344 0.4112718105316162 0.37128785252571106 0.13953298330307007 0.8772818446159363 0.8474984765052795 0.22726504504680634 \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_1.evaluate.json b/ENCSR887VUC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b8d30af8b9140fc9888e2d36b6a9ed39f5d38806..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF665YXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_1.fit.json b/ENCSR887VUC/cherimoya.fold_1.fit.json deleted file mode 100644 index 49cfea081b8fbcad1830328d8994b36094eb70b0..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF665YXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_1.log b/ENCSR887VUC/cherimoya.fold_1.log deleted file mode 100644 index a9d9c8a1aba70c96143d2710881f63dec901cd9b..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2697 34.79511260986328 3.6887998580932617 416.3681640625 0.38104134798049927 668.4523315429688 0.25975075364112854 0.7329852 4.528629302978516 True -1 5394 30.630157470703125 0.7742834091186523 503.4687805175781 0.42365577816963196 600.4984741210938 0.3352135121822357 0.80917466 1.3883358240127563 True -2 8091 29.885141611099243 0.7385556697845459 378.7806701660156 0.30694955587387085 590.0450439453125 0.34454071521759033 0.81609315 0.7419735789299011 True -3 10788 29.98565173149109 0.7448878288269043 400.33880615234375 0.41828495264053345 582.7882080078125 0.35201945900917053 0.82671785 0.5714882016181946 True -4 13485 30.046056032180786 0.7430684566497803 376.7200622558594 0.22488124668598175 577.30810546875 0.3563072085380554 0.83297914 0.43847429752349854 True -5 16182 29.9804425239563 0.7377431392669678 371.4193115234375 0.5171395540237427 573.5715942382812 0.3608112335205078 0.8394946 0.42950332164764404 True -6 18879 29.968106269836426 0.7529911994934082 513.812744140625 0.5345984697341919 571.0983276367188 0.3641268312931061 0.8423932 0.4044530391693115 True -7 21576 29.971088647842407 0.7620542049407959 426.18402099609375 0.32912230491638184 568.7318725585938 0.36734551191329956 0.8488496 0.3944193422794342 True -8 24273 32.95883536338806 27.933440923690796 449.0140686035156 0.24607370793819427 566.3325805664062 0.3699835240840912 0.852865 0.3808801472187042 True -9 26970 29.386897563934326 0.773587703704834 396.99749755859375 0.31957918405532837 565.103271484375 0.37166687846183777 0.8573141 0.35083258152008057 True -10 29667 30.152751684188843 28.507801055908203 361.24200439453125 0.37052831053733826 562.1516723632812 0.3744158148765564 0.8644732 0.330524206161499 True -11 32364 29.35491180419922 5.089852809906006 522.534423828125 0.2896302342414856 560.6262817382812 0.375786155462265 0.86650485 0.33139386773109436 True -12 35061 30.227399349212646 2.0496156215667725 402.1470947265625 0.24571017920970917 558.6528930664062 0.37720349431037903 0.87359333 0.30486828088760376 True -13 37758 29.319249629974365 1.2236857414245605 436.8983154296875 0.3431461751461029 557.4232788085938 0.37855374813079834 0.8793695 0.28538432717323303 True -14 40455 29.30561852455139 1.6037936210632324 489.764404296875 0.330160528421402 556.6416625976562 0.3790520131587982 0.8830558 0.2644960582256317 True -15 43152 29.356128215789795 2.5496156215667725 444.9773864746094 0.2042970359325409 555.0360107421875 0.38076022267341614 0.88696426 0.2525750696659088 True -16 45849 29.316351175308228 51.659082889556885 397.22418212890625 0.2605004906654358 553.3107299804688 0.38328051567077637 0.8890504 0.24259307980537415 True -17 48546 29.33183217048645 1.495410680770874 442.2388000488281 0.22454656660556793 554.232666015625 0.3817593455314636 0.8903412 0.2366989701986313 True -18 51243 29.318928241729736 0.7199952602386475 387.0194091796875 0.1459166407585144 554.0918579101562 0.38204824924468994 0.8920995 0.23671194911003113 True -19 53940 29.364189624786377 0.7068507671356201 353.0020751953125 0.13307680189609528 554.3366088867188 0.3821239769458771 0.89029276 0.23722173273563385 False diff --git a/ENCSR887VUC/cherimoya.fold_1.performance.tsv b/ENCSR887VUC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6ab4e33eaa13c5eb575cf46b44b4b5bbdb638ea0..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -554.0918579101562 0.4006882905960083 0.38204827904701233 0.14953115582466125 0.8920994997024536 0.8783641457557678 0.23671194911003113 \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_2.evaluate.json b/ENCSR887VUC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f33e5d7e953b4406d0d6c1b33139e547f2b5fac4..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF665YXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_2.fit.json b/ENCSR887VUC/cherimoya.fold_2.fit.json deleted file mode 100644 index 67c9a7eb9c13a9e8b2e0367968fb24e42689a91a..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF665YXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_2.log b/ENCSR887VUC/cherimoya.fold_2.log deleted file mode 100644 index 4df6d83b7a737380bfb31b6b52c9c2f7c3eb5053..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2860 36.10802435874939 4.139964580535889 415.68341064453125 0.361613005399704 617.6820678710938 0.2648956775665283 0.7224246 4.619168758392334 True -1 5720 31.707437992095947 0.5936009883880615 578.2837524414062 0.4904027283191681 557.5599365234375 0.3371642827987671 0.79618937 1.0803232192993164 True -2 8580 31.820302963256836 0.5598611831665039 454.7564697265625 0.4312520921230316 551.3621215820312 0.3416951596736908 0.7994401 0.5037291646003723 True -3 11440 31.66961431503296 1.1912317276000977 435.42767333984375 0.25761646032333374 545.563232421875 0.3479869067668915 0.8064898 0.43443360924720764 True -4 14300 31.963122606277466 1.8594820499420166 424.89642333984375 0.316327840089798 543.1298828125 0.350641667842865 0.81244224 0.37484627962112427 True -5 17160 32.141597747802734 23.42763638496399 383.9434814453125 0.3847181797027588 539.8550415039062 0.3552563786506653 0.81419694 0.34739354252815247 True -6 20020 31.34138536453247 0.5701496601104736 398.8780517578125 0.6025881171226501 537.9517822265625 0.35626035928726196 0.8210106 0.3349038064479828 True -7 22880 31.093513250350952 0.5525174140930176 433.01171875 0.3396254777908325 535.63232421875 0.35886630415916443 0.82645714 0.31703636050224304 True -8 25740 31.086061239242554 8.659302949905396 469.99896240234375 0.2597382068634033 533.0020141601562 0.3635364770889282 0.831958 0.30870842933654785 True -9 28600 31.388713836669922 0.6513562202453613 417.1903076171875 0.3267408311367035 531.4751586914062 0.36439305543899536 0.83545285 0.3005930483341217 True -10 31460 31.080424785614014 0.5555217266082764 425.8969421386719 0.4304918646812439 529.5062866210938 0.3673640787601471 0.84233934 0.28981664776802063 True -11 34320 31.13616681098938 0.5560274124145508 400.3652038574219 0.2577820420265198 530.0087890625 0.3651356101036072 0.8459869 0.29005351662635803 True -12 37180 31.22085952758789 0.547032356262207 388.2730407714844 0.3067633807659149 527.9536743164062 0.36784136295318604 0.8518944 0.2733669877052307 True -13 40040 31.201067209243774 0.5463485717773438 368.7249755859375 0.1708371341228485 526.3038330078125 0.3701052963733673 0.8583685 0.26133617758750916 True -14 42900 31.187095642089844 0.5474097728729248 488.0660400390625 0.16812415421009064 524.833251953125 0.37224438786506653 0.8616182 0.25300484895706177 True -15 45760 31.15757393836975 0.5462124347686768 414.50128173828125 0.24761885404586792 524.7413330078125 0.3716975152492523 0.8652409 0.24790401756763458 True -16 48620 31.185826063156128 0.5443086624145508 465.6055908203125 0.2748824954032898 523.5682373046875 0.3737115263938904 0.86697763 0.23978304862976074 True -17 51480 31.12931537628174 0.5454535484313965 443.9376220703125 0.2395748347043991 524.4811401367188 0.37148943543434143 0.8687138 0.23664037883281708 True -18 54340 31.193792819976807 0.6138720512390137 355.4778137207031 0.19880928099155426 523.2428588867188 0.3745359480381012 0.8694537 0.23804880678653717 True -19 57200 31.20270800590515 0.5542972087860107 368.80621337890625 0.19534093141555786 524.5123291015625 0.3716479241847992 0.86757857 0.2393282800912857 False diff --git a/ENCSR887VUC/cherimoya.fold_2.performance.tsv b/ENCSR887VUC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1babe382dbc2ac8f40a5e588013fd1db00c1734c..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -523.2428588867188 0.4066137373447418 0.3745359778404236 0.1431591957807541 0.8694537281990051 0.8462328314781189 0.23804880678653717 \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_3.evaluate.json b/ENCSR887VUC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5479e5ad575ba80bd8858a63ac56713739b7b9ce..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF665YXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_3.fit.json b/ENCSR887VUC/cherimoya.fold_3.fit.json deleted file mode 100644 index 52883e7e084108adbc90aa4e77e1423a5c969e06..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF665YXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_3.log b/ENCSR887VUC/cherimoya.fold_3.log deleted file mode 100644 index 46676e4d1e081e1d88e1c3839bb68b9274c0bfcf..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.43790006637573 3.490607738494873 429.77447509765625 0.4391856789588928 580.498779296875 0.26686787605285645 0.7096243 4.593043804168701 True -1 5516 30.61568307876587 0.517667293548584 417.31195068359375 0.5660487413406372 526.1636962890625 0.33572009205818176 0.7969807 1.1729614734649658 True -2 8274 30.59563708305359 0.49950551986694336 468.76116943359375 0.32469338178634644 517.1273193359375 0.3458917438983917 0.8076059 0.4946969747543335 True -3 11032 30.550169229507446 0.48723745346069336 441.80316162109375 0.4646461308002472 511.2391662597656 0.35184594988822937 0.8191828 0.4234151840209961 True -4 13790 30.41530156135559 0.5005536079406738 465.45904541015625 0.42432719469070435 509.4198913574219 0.35373157262802124 0.81898934 0.39701950550079346 False -5 16548 29.986526250839233 0.49908018112182617 424.39324951171875 0.3085087239742279 507.9292297363281 0.35475072264671326 0.82375365 0.38465210795402527 True -6 19306 29.956809759140015 0.4925801753997803 439.20159912109375 0.33612847328186035 506.39227294921875 0.3570539951324463 0.83078635 0.39492303133010864 True -7 22064 29.939226388931274 0.4958641529083252 537.1795654296875 0.23154792189598083 505.0751647949219 0.35773006081581116 0.83509916 0.3499089777469635 True -8 24822 29.999472618103027 0.49993443489074707 492.66766357421875 0.30078399181365967 503.13323974609375 0.3612014949321747 0.8408997 0.37898799777030945 True -9 27580 30.09517478942871 0.4936642646789551 460.6639709472656 0.3609301745891571 500.86773681640625 0.3650738298892975 0.84289 0.3322352170944214 True -10 30338 29.996886253356934 0.4976320266723633 396.33953857421875 0.45297592878341675 499.4718933105469 0.3665313720703125 0.8475005 0.3180255889892578 True -11 33096 29.99547529220581 0.5002400875091553 441.0851745605469 0.24040862917900085 497.4980773925781 0.3685450851917267 0.85282135 0.2993372976779938 True -12 35854 30.008326053619385 0.49935126304626465 422.776123046875 0.2804461717605591 496.6863708496094 0.3694336414337158 0.8564073 0.2896568477153778 True -13 38612 30.188026189804077 0.8694286346435547 398.1641540527344 0.22693726420402527 496.3807678222656 0.36914563179016113 0.861515 0.27895036339759827 True -14 41370 29.976245164871216 0.5033466815948486 454.0018310546875 0.475796103477478 495.0075988769531 0.3711668848991394 0.8668141 0.2699514627456665 True -15 44128 29.995379209518433 0.4983398914337158 440.3435363769531 0.24277544021606445 492.5679626464844 0.3747590482234955 0.86974937 0.2532958388328552 True -16 46886 29.932809352874756 0.49794840812683105 427.6187744140625 0.20923452079296112 492.37921142578125 0.37446096539497375 0.8735774 0.24642148613929749 True -17 49644 29.981922388076782 0.502849817276001 388.58746337890625 0.21977490186691284 493.4895324707031 0.3719235062599182 0.87661904 0.2414666712284088 True -18 52402 31.302446126937866 15.809096813201904 401.8216247558594 0.16498810052871704 492.5690002441406 0.3744661211967468 0.8773753 0.24227730929851532 True -19 55160 29.940992832183838 0.4938781261444092 453.9410095214844 0.2207777202129364 492.8410949707031 0.37357404828071594 0.876247 0.24303710460662842 False diff --git a/ENCSR887VUC/cherimoya.fold_3.performance.tsv b/ENCSR887VUC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2ef0e963b1dc162505fc23843b492fbb5be6dc2e..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -492.5690002441406 0.41031375527381897 0.3744661211967468 0.14089693129062653 0.8773753046989441 0.8428100347518921 0.24227730929851532 \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_4.evaluate.json b/ENCSR887VUC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 41d8762e924feedfd2b578510f16c61326794ba9..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF665YXM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_4.fit.json b/ENCSR887VUC/cherimoya.fold_4.fit.json deleted file mode 100644 index 26e700eb8bcc8e545e4125ba557bbe3d7f161352..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF665YXM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR887VUC/cherimoya.fold_4.log b/ENCSR887VUC/cherimoya.fold_4.log deleted file mode 100644 index 64bb8c6fc18677e41bdbd1a6544de432d73e724b..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2819 35.99764013290405 3.6163241863250732 366.6063232421875 0.4342496395111084 535.6707763671875 0.25328966975212097 0.71664447 3.8607568740844727 True -1 5638 31.275336503982544 0.6048200130462646 465.87298583984375 0.5087814331054688 489.3658142089844 0.3179807960987091 0.7925703 0.944529116153717 True -2 8457 31.2522189617157 0.5845859050750732 445.93719482421875 0.4168446660041809 482.2178649902344 0.32655781507492065 0.79884243 0.4355891942977905 True -3 11276 30.63009762763977 0.5923018455505371 497.44378662109375 0.4631749391555786 476.3428039550781 0.3333874046802521 0.8091732 0.3690284788608551 True -4 14095 30.63186287879944 0.5810925960540771 404.4976806640625 0.3058870732784271 474.4159851074219 0.33425235748291016 0.81563824 0.33802881836891174 True -5 16914 30.622676610946655 0.5947926044464111 351.3218078613281 0.34350135922431946 472.5865478515625 0.3366619050502777 0.82109207 0.309449166059494 True -6 19733 30.683517932891846 0.5915396213531494 391.24530029296875 0.3506316840648651 470.14862060546875 0.34055525064468384 0.8248423 0.2812851667404175 True -7 22552 30.632021188735962 0.5919971466064453 438.38922119140625 0.35839778184890747 468.809814453125 0.3425162434577942 0.82971203 0.26954349875450134 True -8 25371 30.89245915412903 24.17745876312256 428.986328125 0.2901798188686371 467.0944519042969 0.3453858196735382 0.8352931 0.26220133900642395 True -9 28190 33.538779735565186 0.5989186763763428 405.5361633300781 0.5110270977020264 467.0869445800781 0.3435384929180145 0.8411121 0.2558087110519409 True -10 31009 30.60301637649536 0.600888729095459 413.28125 0.36051127314567566 465.193115234375 0.34659257531166077 0.84911954 0.24753032624721527 True -11 33828 30.641082048416138 1.5610785484313965 388.2259521484375 0.2174113690853119 464.52392578125 0.3481922447681427 0.85095745 0.24469847977161407 True -12 36647 30.726173877716064 0.6005642414093018 402.9266357421875 0.357699453830719 463.4167175292969 0.34908178448677063 0.8552796 0.23885801434516907 True -13 39466 30.731707096099854 0.6440341472625732 385.934814453125 0.2183958739042282 462.4726867675781 0.3503824770450592 0.8608239 0.23122452199459076 True -14 42285 30.687483549118042 0.5946033000946045 477.5546875 0.18490439653396606 461.90692138671875 0.3510354161262512 0.86696076 0.22234855592250824 True -15 45104 30.607136011123657 1.3078432083129883 397.43743896484375 0.18610462546348572 460.3825378417969 0.3541569113731384 0.87212557 0.21475112438201904 True -16 47923 30.650810718536377 2.1454811096191406 509.7001647949219 0.20323818922042847 460.8950500488281 0.35261836647987366 0.8738553 0.21168845891952515 True -17 50742 30.624141693115234 1.4831480979919434 398.5462341308594 0.2222691774368286 459.872314453125 0.354960560798645 0.87614244 0.20976608991622925 True -18 53561 30.59923243522644 26.618242502212524 439.19757080078125 0.17795932292938232 460.4262390136719 0.3540631830692291 0.8761323 0.2104634940624237 False -19 56380 32.77525281906128 0.6047990322113037 435.1708068847656 0.21890269219875336 460.7416076660156 0.35312506556510925 0.875901 0.21196585893630981 False diff --git a/ENCSR887VUC/cherimoya.fold_4.performance.tsv b/ENCSR887VUC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index aed6882c648a3b8f6d938a1441baf6858ced24a2..0000000000000000000000000000000000000000 --- a/ENCSR887VUC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -459.872314453125 0.4255073070526123 0.354960560798645 0.12487960606813431 0.8761424422264099 0.8408850431442261 0.20976608991622925 \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_0.evaluate.json b/ENCSR888GBS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a53e11433b5d84ad340afe2ee0f30715c1587fdd..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074QDR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_0.fit.json b/ENCSR888GBS/cherimoya.fold_0.fit.json deleted file mode 100644 index 261a7b6c5e173069c587921a469cf91ec78b643d..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF074QDR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_0.log b/ENCSR888GBS/cherimoya.fold_0.log deleted file mode 100644 index 91a90eb4a4aac38e0310a6cace047caaf40d4233..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 35.18659996986389 4.016158819198608 251.4740753173828 0.8029080033302307 298.16143798828125 0.150738924741745 0.5512181 3.359680652618408 True -1 5508 30.643911361694336 0.5924615859985352 238.08157348632812 0.6970183253288269 288.7427062988281 0.19737201929092407 0.65116525 0.9579127430915833 True -2 8262 30.605520725250244 0.5595715045928955 219.58871459960938 0.6114064455032349 286.4472351074219 0.20531868934631348 0.6692218 0.560907244682312 True -3 11016 30.571744918823242 0.5756223201751709 249.41615295410156 0.6206095218658447 285.044677734375 0.21145090460777283 0.6726176 0.4603482186794281 True -4 13770 30.566802740097046 0.5743553638458252 224.34506225585938 0.2931246757507324 284.7645263671875 0.2117990255355835 0.67615354 0.42259442806243896 True -5 16524 30.57924747467041 0.576953649520874 211.84866333007812 0.424410879611969 284.00640869140625 0.21538512408733368 0.6814419 0.42388805747032166 True -6 19278 30.5609769821167 0.5718574523925781 161.43972778320312 0.5134387612342834 283.6700744628906 0.21656665205955505 0.6862841 0.41790464520454407 True -7 22032 30.547757625579834 0.5729696750640869 240.45504760742188 0.5542107820510864 283.1027526855469 0.21936309337615967 0.691701 0.42675164341926575 True -8 24786 30.52066445350647 0.5765962600708008 228.12820434570312 0.47666528820991516 282.6009521484375 0.22175061702728271 0.6987527 0.4229893386363983 True -9 27540 30.55396795272827 0.5782685279846191 235.8180694580078 0.6338963508605957 282.29833984375 0.22323361039161682 0.7000688 0.39131584763526917 True -10 30294 30.61645269393921 0.5767970085144043 194.47842407226562 0.44286826252937317 281.8925476074219 0.22536510229110718 0.7074 0.3748818635940552 True -11 33048 30.581485271453857 0.5714068412780762 228.28463745117188 0.5112869143486023 281.69873046875 0.22571925818920135 0.7122167 0.36332425475120544 True -12 35802 30.607393503189087 0.5749692916870117 230.0625 0.3399314880371094 281.58074951171875 0.22594159841537476 0.7205954 0.3338887691497803 True -13 38556 30.545793771743774 0.5778441429138184 189.68460083007812 0.3649370074272156 281.1683349609375 0.22835732996463776 0.72533876 0.3299369215965271 True -14 41310 30.626540184020996 10.996982336044312 214.775634765625 0.38264602422714233 281.2265319824219 0.2274850457906723 0.7340749 0.3180353343486786 True -15 44064 30.662321090698242 0.5852153301239014 211.59124755859375 0.422657310962677 280.9870300292969 0.2284540832042694 0.7402725 0.3057795464992523 True -16 46818 30.581648111343384 0.6004588603973389 261.1985778808594 0.28766852617263794 280.3515625 0.23186059296131134 0.7461246 0.29833680391311646 True -17 49572 30.63861393928528 0.5742688179016113 233.13406372070312 0.20140555500984192 280.80255126953125 0.22880953550338745 0.74712044 0.29874229431152344 True -18 52326 30.282215118408203 0.5743064880371094 239.1808624267578 0.2605162262916565 280.7514953613281 0.2293998748064041 0.74440384 0.3064407408237457 False -19 55080 30.115660905838013 0.5774321556091309 201.47299194335938 0.2801668345928192 280.807861328125 0.2294035404920578 0.74338645 0.310189813375473 False diff --git a/ENCSR888GBS/cherimoya.fold_0.performance.tsv b/ENCSR888GBS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3627303a1ad12be43df9c4e36c85a69903cef19e..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -280.80255126953125 0.5127710103988647 0.22880956530570984 0.0708390399813652 0.7471204400062561 0.7066574692726135 0.29874229431152344 \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_1.evaluate.json b/ENCSR888GBS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 28f0827416a8d05fc1b73a42e5839d64919824d5..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074QDR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_1.fit.json b/ENCSR888GBS/cherimoya.fold_1.fit.json deleted file mode 100644 index 79c6a19167c458b7b9e7f88797e8dcbaa68046a7..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF074QDR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_1.log b/ENCSR888GBS/cherimoya.fold_1.log deleted file mode 100644 index b179f10237c80f7707f115611d1bcf465c30a603..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 35.230313301086426 5.030848741531372 225.1892852783203 0.8130480051040649 337.2790832519531 0.15792280435562134 0.5829441 3.470917224884033 True -1 5512 30.624562740325928 0.8409404754638672 253.1727294921875 0.7853089570999146 325.853271484375 0.21095626056194305 0.677718 1.2039382457733154 True -2 8268 30.641005277633667 2.465646743774414 238.73236083984375 0.5612397789955139 322.2816467285156 0.2222672700881958 0.71167713 0.4672955870628357 True -3 11024 31.063963174819946 0.9737727642059326 242.0864715576172 0.420210063457489 321.2424011230469 0.22360195219516754 0.7187808 0.42626670002937317 True -4 13780 30.982406854629517 22.2328941822052 246.52906799316406 0.44122135639190674 319.8169860839844 0.2295519858598709 0.7275125 0.38094180822372437 True -5 16536 30.643844604492188 0.6771619319915771 221.62315368652344 0.6960292458534241 319.21112060546875 0.23122751712799072 0.72883135 0.39270779490470886 True -6 19292 30.62041711807251 0.6762335300445557 235.23342895507812 0.6326184868812561 318.58740234375 0.2338079810142517 0.7356881 0.3990218937397003 True -7 22048 30.584795475006104 0.6765456199645996 231.07249450683594 0.3542746305465698 318.3626708984375 0.23483341932296753 0.73631173 0.39100006222724915 True -8 24804 30.565186977386475 0.680788516998291 259.6024169921875 0.45137232542037964 317.7417297363281 0.23686282336711884 0.7427653 0.3859768807888031 True -9 27560 30.57519555091858 0.6762900352478027 228.04440307617188 0.3884371519088745 317.53900146484375 0.2377539724111557 0.74786925 0.37611818313598633 True -10 30316 30.565449714660645 0.6785502433776855 234.9641876220703 0.5910630226135254 316.982666015625 0.240183487534523 0.7493374 0.3721449077129364 True -11 33072 30.641053199768066 0.6992039680480957 241.7726287841797 0.4105225205421448 316.6213684082031 0.24144887924194336 0.75842863 0.3557552099227905 True -12 35828 30.615957021713257 0.6892099380493164 249.83261108398438 0.3537279963493347 316.30841064453125 0.2426958531141281 0.7639058 0.35185539722442627 True -13 38584 30.55202293395996 0.6639618873596191 245.85964965820312 0.26144900918006897 315.9297180175781 0.24441544711589813 0.7710561 0.3345695734024048 True -14 41340 30.039339303970337 0.8242835998535156 219.66871643066406 0.390220046043396 315.9271240234375 0.24399225413799286 0.77678734 0.31814730167388916 True -15 44096 29.985652208328247 0.6694536209106445 255.54527282714844 0.37572893500328064 315.468505859375 0.24639320373535156 0.7810146 0.313395619392395 True -16 46852 30.013049602508545 0.6732773780822754 193.39781188964844 0.3101162016391754 315.63629150390625 0.24498248100280762 0.7857882 0.31327787041664124 True -17 49608 30.04216504096985 0.6787097454071045 227.22312927246094 0.23139746487140656 315.6672058105469 0.24522560834884644 0.784772 0.3133922815322876 False -18 52364 30.043243646621704 1.146885633468628 159.53924560546875 0.4129714071750641 315.7859191894531 0.2448279857635498 0.78464127 0.3173113465309143 False -19 55120 30.021848440170288 0.669201135635376 220.67819213867188 0.2999124526977539 315.8806457519531 0.2441021054983139 0.78366363 0.32098880410194397 False diff --git a/ENCSR888GBS/cherimoya.fold_1.performance.tsv b/ENCSR888GBS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f2bbc768e6c6a2d3d278121ad6a0f37b497bfb4e..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -315.63629150390625 0.4967139661312103 0.24498248100280762 0.0800720602273941 0.7857881784439087 0.7616248726844788 0.31327787041664124 \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_2.evaluate.json b/ENCSR888GBS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 96b2d9a0c0a7e163d390ac2fa5f28ed1a7f22f68..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074QDR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_2.fit.json b/ENCSR888GBS/cherimoya.fold_2.fit.json deleted file mode 100644 index 8a661c49e6a5d61563a6ea897f8990a4aea62f2e..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF074QDR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_2.log b/ENCSR888GBS/cherimoya.fold_2.log deleted file mode 100644 index 94720276b59b58d91c8a7915897b05fc414bd525..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2908 38.121646881103516 3.766261100769043 247.19711303710938 0.6277940273284912 303.784423828125 0.1541006714105606 0.554663 2.960319995880127 True -1 5816 32.434037923812866 0.5850489139556885 209.74977111816406 0.5524858832359314 293.8750915527344 0.20251134037971497 0.651451 0.9574664831161499 True -2 8724 32.41787886619568 0.5254158973693848 220.0771484375 0.42570069432258606 290.94964599609375 0.2111929953098297 0.6642397 0.48282480239868164 True -3 11632 32.396432638168335 0.5553505420684814 246.0219268798828 0.4905112683773041 289.63116455078125 0.2167152762413025 0.6762749 0.4845680892467499 True -4 14540 32.39658999443054 1.231529712677002 198.25315856933594 0.7334672212600708 289.1610412597656 0.2184108942747116 0.6784858 0.5255348086357117 True -5 17448 32.41591143608093 0.5947532653808594 226.24298095703125 0.49690982699394226 288.8131408691406 0.2196636199951172 0.68498397 0.6096851825714111 True -6 20356 32.39858317375183 1.1635568141937256 238.62156677246094 0.4774598181247711 288.2532043457031 0.22207291424274445 0.6899714 0.5572550296783447 True -7 23264 32.40415835380554 0.5289196968078613 222.39862060546875 0.42637670040130615 287.9840393066406 0.22283075749874115 0.6934031 0.5327044129371643 True -8 26172 32.40939211845398 0.5236930847167969 224.61181640625 0.47295188903808594 287.8959655761719 0.22319263219833374 0.69865155 0.48352065682411194 True -9 29080 32.423847913742065 0.5628020763397217 218.88671875 0.5224833488464355 287.5096130371094 0.22489185631275177 0.70187956 0.46454474329948425 True -10 31988 32.39990186691284 3.187206506729126 231.36328125 0.450203537940979 286.81341552734375 0.2280813455581665 0.7054202 0.43067100644111633 True -11 34896 31.827404975891113 0.5891239643096924 242.06297302246094 0.45177799463272095 286.2589111328125 0.2305292934179306 0.71084327 0.398529589176178 True -12 37804 31.825209617614746 0.5322356224060059 240.12423706054688 0.39898908138275146 286.2330322265625 0.2304246574640274 0.7182571 0.3788197636604309 True -13 40712 31.841201305389404 0.5239229202270508 221.4244384765625 0.36291056871414185 285.87701416015625 0.23171532154083252 0.7228577 0.35614535212516785 True -14 43620 31.841793060302734 0.530419111251831 228.75160217285156 0.33576369285583496 285.7345886230469 0.2329869270324707 0.7302954 0.34270933270454407 True -15 46528 31.795639038085938 0.5196902751922607 239.54998779296875 0.3489478826522827 285.5899353027344 0.2327912151813507 0.73342955 0.33791494369506836 True -16 49436 31.80319333076477 0.5358827114105225 244.7882537841797 0.2443746030330658 285.47467041015625 0.2328970730304718 0.73805994 0.33024728298187256 True -17 52344 31.93008017539978 20.937828063964844 193.77037048339844 0.31399041414260864 285.8238220214844 0.2314244657754898 0.7391472 0.3332992494106293 True -18 55252 31.864500999450684 0.5695765018463135 245.00808715820312 0.30111682415008545 285.722900390625 0.23240594565868378 0.738722 0.34170377254486084 False -19 58160 31.781401872634888 0.5078201293945312 240.27877807617188 0.25409042835235596 285.7774963378906 0.23181109130382538 0.7360686 0.3461366295814514 False diff --git a/ENCSR888GBS/cherimoya.fold_2.performance.tsv b/ENCSR888GBS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 35c2275b0a87699b87642f934b86a01a65436de1..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -285.8238220214844 0.5101739764213562 0.2314244508743286 0.06794770061969757 0.7391471862792969 0.7007498741149902 0.3332992494106293 \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_3.evaluate.json b/ENCSR888GBS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8036329b73c24d99b23ba733d51d21d72424b627..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074QDR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_3.fit.json b/ENCSR888GBS/cherimoya.fold_3.fit.json deleted file mode 100644 index 7acf0ad752eff32975b14da30055dec3dfef1775..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF074QDR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_3.log b/ENCSR888GBS/cherimoya.fold_3.log deleted file mode 100644 index d8ac2cee4030c77c2c91450d1d7be7387d78783d..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2771 35.572795391082764 3.7676384449005127 234.52383422851562 0.6499552726745605 314.13348388671875 0.15037734806537628 0.55930185 3.7228407859802246 True -1 5542 30.734275579452515 0.6145529747009277 248.35494995117188 0.8711365461349487 303.84368896484375 0.20065632462501526 0.6506491 1.2526663541793823 True -2 8313 30.830893993377686 0.6478724479675293 252.39175415039062 0.9009232521057129 301.6390075683594 0.20854072272777557 0.6761896 0.49208974838256836 True -3 11084 30.742765188217163 0.5770111083984375 224.171142578125 0.49178192019462585 300.6357116699219 0.21184033155441284 0.6834437 0.4539400637149811 True -4 13855 30.731106519699097 0.5821876525878906 194.64273071289062 0.45877736806869507 300.31048583984375 0.21281996369361877 0.6811381 0.4700213074684143 False -5 16626 30.563913106918335 0.579542875289917 238.73931884765625 0.406493604183197 299.4359436035156 0.21729572117328644 0.6882399 0.44614556431770325 True -6 19397 30.17211937904358 0.5727646350860596 239.6387939453125 0.8009443283081055 298.9621276855469 0.21832215785980225 0.69216096 0.4275512993335724 True -7 22168 30.119943141937256 0.5755419731140137 244.7618865966797 0.8142374753952026 298.69317626953125 0.21999044716358185 0.69009686 0.44557297229766846 False -8 24939 30.163103103637695 0.5896143913269043 209.3329315185547 0.43435874581336975 298.7506408691406 0.21912194788455963 0.6899943 0.4302475154399872 False -9 27710 30.173566818237305 0.5665457248687744 235.67388916015625 0.41115960478782654 298.0919189453125 0.22248192131519318 0.70162994 0.4140872359275818 True -10 30481 30.215905904769897 0.6066758632659912 235.70252990722656 0.48711931705474854 297.6297607421875 0.22464239597320557 0.7040937 0.3927370607852936 True -11 33252 30.146155834197998 1.2746708393096924 225.85940551757812 0.5656648874282837 297.1385192871094 0.22736503183841705 0.707972 0.4040015637874603 True -12 36023 30.236959218978882 0.6740658283233643 194.7909698486328 0.6920672655105591 297.2033996582031 0.22656527161598206 0.7174203 0.3768545985221863 True -13 38794 30.238422632217407 0.6086149215698242 232.59405517578125 0.3531419038772583 296.9239196777344 0.22811156511306763 0.72618765 0.3625844120979309 True -14 41565 30.18127202987671 0.630730390548706 225.31716918945312 0.5177531242370605 296.9259033203125 0.22776903212070465 0.73641217 0.3466297388076782 True -15 44336 30.234551668167114 0.5899050235748291 238.51478576660156 0.29000020027160645 296.3672790527344 0.23042474687099457 0.74167746 0.3379601240158081 True -16 47107 30.227843046188354 0.598412275314331 235.64511108398438 0.2998684048652649 296.1620788574219 0.2314016968011856 0.7501733 0.3287295401096344 True -17 49878 30.22510814666748 0.5983049869537354 244.37942504882812 0.393544465303421 296.14111328125 0.23159052431583405 0.75501597 0.32998546957969666 True -18 52649 30.15298819541931 0.6057741641998291 261.471435546875 0.20290948450565338 296.4316101074219 0.22961579263210297 0.75244033 0.33738839626312256 False -19 55420 30.15943169593811 0.6031537055969238 194.19094848632812 0.19781222939491272 296.62786865234375 0.22850655019283295 0.75285274 0.3378637433052063 False diff --git a/ENCSR888GBS/cherimoya.fold_3.performance.tsv b/ENCSR888GBS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index aa3901fb12e35927af0f2a098887077c30596be8..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -296.14111328125 0.5070551037788391 0.23159052431583405 0.07262970507144928 0.7550159692764282 0.717428982257843 0.32998546957969666 \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_4.evaluate.json b/ENCSR888GBS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 25bf663c27425a91f2bfce20d50da6a3801e4621..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF074QDR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_4.fit.json b/ENCSR888GBS/cherimoya.fold_4.fit.json deleted file mode 100644 index 9f382a7e15ec2586bd6defc860c59d11eb1da811..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF074QDR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888GBS/cherimoya.fold_4.log b/ENCSR888GBS/cherimoya.fold_4.log deleted file mode 100644 index ddc3d5bdd5df007cf9a4a21305978a5df7890511..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2866 36.601773500442505 4.0044777393341064 213.56863403320312 0.6164873838424683 298.2592468261719 0.15194055438041687 0.54088694 3.260338544845581 True -1 5732 31.83880352973938 0.6645417213439941 219.01918029785156 0.5231308937072754 289.3995056152344 0.19692206382751465 0.62748986 1.0849778652191162 True -2 8598 31.890685319900513 0.6199121475219727 212.03611755371094 0.6221579313278198 287.3089599609375 0.20325493812561035 0.65090245 0.4475843906402588 True -3 11464 31.89659333229065 2.1218338012695312 233.6585235595703 0.3255344033241272 286.2105407714844 0.20715537667274475 0.6629394 0.3941873610019684 True -4 14330 31.27520513534546 1.9201643466949463 212.7161865234375 0.5223175287246704 285.6982116699219 0.20874722301959991 0.6706212 0.37693798542022705 True -5 17196 31.279335498809814 0.6144623756408691 205.2841339111328 0.4363228380680084 285.1309814453125 0.21151919662952423 0.6736471 0.40466585755348206 True -6 20062 31.274155378341675 0.6317446231842041 200.07614135742188 0.4426320195198059 285.04364013671875 0.2121296226978302 0.6804759 0.4305015802383423 True -7 22928 31.214492082595825 0.6319117546081543 205.0770721435547 0.338262140750885 284.7520751953125 0.21331995725631714 0.6870556 0.4182364344596863 True -8 25794 31.213364124298096 0.6238241195678711 222.16502380371094 0.5339801907539368 284.2785949707031 0.2157747447490692 0.6908553 0.40314915776252747 True -9 28660 31.283855676651 1.344911813735962 219.8209228515625 0.4069090783596039 283.8622131347656 0.21777118742465973 0.6973827 0.39687108993530273 True -10 31526 31.231388807296753 2.848083972930908 208.29837036132812 0.37313634157180786 283.52410888671875 0.2191123068332672 0.70501137 0.37338483333587646 True -11 34392 31.30899977684021 18.2177414894104 212.37095642089844 0.45131611824035645 283.29620361328125 0.21989625692367554 0.7114712 0.35791879892349243 True -12 37258 31.265174388885498 0.631788969039917 214.617431640625 0.35399842262268066 283.18402099609375 0.2202957421541214 0.71765167 0.33828917145729065 True -13 40124 31.303263425827026 0.6159501075744629 227.74269104003906 0.5077216029167175 282.6718444824219 0.22335052490234375 0.7254316 0.32882559299468994 True -14 42990 31.344116687774658 2.9222114086151123 237.23568725585938 0.40623223781585693 282.4944152832031 0.22426636517047882 0.73143506 0.3173083961009979 True -15 45856 31.344624042510986 11.186843872070312 216.87380981445312 0.3866529166698456 282.2385559082031 0.22602815926074982 0.7375487 0.313631534576416 True -16 48722 31.282353401184082 13.368827819824219 222.33023071289062 0.21510739624500275 282.2801818847656 0.2251586616039276 0.7434472 0.311989963054657 True -17 51588 31.237892150878906 0.9959075450897217 224.6168212890625 0.21504411101341248 282.3851013183594 0.22435790300369263 0.74481076 0.31440573930740356 True -18 54454 31.24368643760681 1.324983835220337 224.92916870117188 0.2956267297267914 282.4976501464844 0.22371748089790344 0.74245054 0.32261428236961365 False -19 57320 31.210973501205444 15.470498323440552 213.1636962890625 0.3356824815273285 282.52093505859375 0.223528653383255 0.74041307 0.32702314853668213 False diff --git a/ENCSR888GBS/cherimoya.fold_4.performance.tsv b/ENCSR888GBS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 936287ca695fb33c32de4a1d77e3a3fff31d1130..0000000000000000000000000000000000000000 --- a/ENCSR888GBS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -282.3851013183594 0.5137139558792114 0.22435791790485382 0.06807631999254227 0.7448107600212097 0.7071377635002136 0.31440573930740356 \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_0.evaluate.json b/ENCSR888UPQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 367b06876fe4c8bad0735205a7ebafe9d00d60e8..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF584KWN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_0.fit.json b/ENCSR888UPQ/cherimoya.fold_0.fit.json deleted file mode 100644 index e7c9e08716d67b6a48451887051d3af8b65bbe22..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF584KWN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_0.log b/ENCSR888UPQ/cherimoya.fold_0.log deleted file mode 100644 index f4a84cf3353ae6f9cde9baf43e40f9c41826131b..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1858 24.60281753540039 3.221529960632324 175.73716735839844 0.6036696434020996 226.0522918701172 0.10546974837779999 0.5162704 5.908261299133301 True -1 3716 19.933810234069824 0.378619909286499 167.4275360107422 0.5485411882400513 218.13314819335938 0.15628406405448914 0.58751696 2.111132860183716 True -2 5574 20.186589241027832 0.37013745307922363 160.27719116210938 0.5445330142974854 209.9677276611328 0.19298146665096283 0.6656241 0.7687427997589111 True -3 7432 20.17813229560852 0.3699831962585449 146.30072021484375 0.731122612953186 206.74533081054688 0.20270541310310364 0.68793404 0.5176267027854919 True -4 9290 20.137261390686035 0.36174464225769043 145.5089111328125 0.4688774347305298 205.6173553466797 0.2073957473039627 0.69106865 0.4906891882419586 True -5 11148 19.8188214302063 0.3613772392272949 190.57388305664062 0.4959704279899597 204.65965270996094 0.21138174831867218 0.7056965 0.4441578984260559 True -6 13006 19.84619903564453 0.3610532283782959 178.22203063964844 0.575753927230835 204.51593017578125 0.21104696393013 0.71606123 0.4030148684978485 True -7 14864 20.144922256469727 24.411257028579712 152.98138427734375 0.7236705422401428 203.8910675048828 0.21455395221710205 0.7213592 0.40271076560020447 True -8 16722 20.34326934814453 0.3687252998352051 143.15194702148438 0.6170250773429871 203.69854736328125 0.21526260673999786 0.72420233 0.39544323086738586 True -9 18580 19.92745018005371 0.36896491050720215 190.45973205566406 0.5432993173599243 203.20118713378906 0.2183685600757599 0.73469776 0.38368457555770874 True -10 20438 19.899009943008423 0.3643460273742676 166.11724853515625 0.4432690143585205 202.90689086914062 0.21962115168571472 0.7368453 0.3743145763874054 True -11 22296 19.843690633773804 3.558788299560547 169.4425048828125 0.3751792907714844 202.65272521972656 0.22089847922325134 0.74214053 0.3683292269706726 True -12 24154 19.83496332168579 0.37142300605773926 168.60797119140625 0.4129698872566223 202.20819091796875 0.2228652983903885 0.7475018 0.36460596323013306 True -13 26012 19.819822549819946 0.37098026275634766 164.32803344726562 0.5632757544517517 201.93568420410156 0.2242775708436966 0.7523484 0.36159324645996094 True -14 27870 19.789032459259033 0.36330246925354004 174.60531616210938 0.4149874150753021 201.85879516601562 0.22456908226013184 0.7548381 0.360665500164032 True -15 29728 19.804797649383545 0.37062954902648926 161.8085174560547 0.34640294313430786 201.80369567871094 0.22513727843761444 0.75864273 0.3603900969028473 True -16 31586 19.80444097518921 0.3617057800292969 155.6951904296875 0.3333914279937744 201.8235626220703 0.22461993992328644 0.76072615 0.36462298035621643 True -17 33444 19.795955657958984 6.2940075397491455 147.97930908203125 0.3484131097793579 201.89364624023438 0.22409828007221222 0.76027554 0.37308254837989807 False -18 35302 19.87171745300293 0.3706090450286865 156.23516845703125 0.34850552678108215 202.14283752441406 0.22264836728572845 0.7578869 0.3834904134273529 False -19 37160 19.827089309692383 0.3604590892791748 166.57562255859375 0.25462013483047485 202.23480224609375 0.22213438153266907 0.75535643 0.3926297128200531 False diff --git a/ENCSR888UPQ/cherimoya.fold_0.performance.tsv b/ENCSR888UPQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3a5ee1cbc50ac15f58b4301652839fa90ec23bac..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.8235626220703 0.5402193665504456 0.22461996972560883 0.05110952630639076 0.7607261538505554 0.7191829681396484 0.36462298035621643 \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_1.evaluate.json b/ENCSR888UPQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c817917bdcbafb45c27d20f3ff8a095694173b75..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF584KWN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_1.fit.json b/ENCSR888UPQ/cherimoya.fold_1.fit.json deleted file mode 100644 index ca1b001d47e80a65432f6a82f74ed6be6044c028..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF584KWN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_1.log b/ENCSR888UPQ/cherimoya.fold_1.log deleted file mode 100644 index 06d4d84447b7356a018dc61256f0746834ecfcc7..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1859 24.582780122756958 4.214863538742065 141.5589141845703 0.8707081079483032 270.4526062011719 0.11566688865423203 0.4836093 6.5094733238220215 True -1 3718 20.23066759109497 2.3959193229675293 134.37075805664062 0.6854872703552246 260.49346923828125 0.17261454463005066 0.61295533 2.1925718784332275 True -2 5577 20.220776557922363 0.5037150382995605 212.6527099609375 0.894676148891449 248.7537384033203 0.21961846947669983 0.6604832 1.2140849828720093 True -3 7436 20.217076063156128 0.5068521499633789 137.8687286376953 0.7861987352371216 244.42984008789062 0.23094220459461212 0.686898 0.6857009530067444 True -4 9295 20.223228931427002 0.5055053234100342 124.58483123779297 0.6666111946105957 243.237548828125 0.2337263524532318 0.70179486 0.5897412896156311 True -5 11154 20.207220554351807 0.508965253829956 232.02651977539062 0.5739517211914062 242.37893676757812 0.23665407299995422 0.71178144 0.5382447838783264 True -6 13013 20.188783407211304 0.5045907497406006 168.62582397460938 0.5991055965423584 241.72311401367188 0.23899205029010773 0.7202389 0.5288336277008057 True -7 14872 20.282768726348877 25.619293212890625 185.19406127929688 0.4917725920677185 241.29978942871094 0.24077492952346802 0.72590965 0.4811529219150543 True -8 16731 21.87909173965454 17.052291870117188 181.57986450195312 0.525253176689148 240.99612426757812 0.2415950894355774 0.73256767 0.4526956379413605 True -9 18590 20.258247137069702 3.136091947555542 136.49639892578125 0.5740381479263306 240.44869995117188 0.2439083456993103 0.73786914 0.42126989364624023 True -10 20449 20.24162530899048 0.49796342849731445 155.94461059570312 0.5231485366821289 240.05548095703125 0.24600709974765778 0.74405956 0.4148690402507782 True -11 22308 20.211490869522095 1.405055284500122 160.9903564453125 0.6387441158294678 239.21798706054688 0.2501307427883148 0.7483749 0.3970491886138916 True -12 24167 20.2805757522583 0.49869608879089355 184.67123413085938 0.45332783460617065 238.90321350097656 0.25144675374031067 0.7540714 0.39392197132110596 True -13 26026 20.23232865333557 0.5056729316711426 163.61227416992188 0.3991160988807678 239.0975799560547 0.24999642372131348 0.7546386 0.39757537841796875 True -14 27885 20.256516456604004 3.0419788360595703 173.44715881347656 0.380743145942688 238.27085876464844 0.2537834644317627 0.758874 0.3943643271923065 True -15 29744 19.908589601516724 0.4978933334350586 132.26425170898438 0.3225335478782654 238.42662048339844 0.2521914839744568 0.76419884 0.395542711019516 True -16 31603 19.814443349838257 0.8838984966278076 152.68032836914062 0.43536436557769775 238.5796661376953 0.2517079710960388 0.76430786 0.41241946816444397 True -17 33462 19.884907960891724 1.2015180587768555 152.1198272705078 0.2333235889673233 238.5420684814453 0.2525935471057892 0.7649105 0.4258350133895874 True -18 35321 19.854814052581787 0.5205614566802979 191.40316772460938 0.3144945800304413 238.69151306152344 0.251564085483551 0.7626143 0.4422411024570465 False -19 37180 20.301962852478027 18.14262819290161 178.85198974609375 0.345503568649292 238.70333862304688 0.2516442537307739 0.7618504 0.4512667655944824 False diff --git a/ENCSR888UPQ/cherimoya.fold_1.performance.tsv b/ENCSR888UPQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d008d21bb4cdc9415bba1967bc1deb33509e08dd..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -238.5420684814453 0.5175673961639404 0.2525935769081116 0.05782549828290939 0.7649105191230774 0.725956916809082 0.4258350133895874 \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_2.evaluate.json b/ENCSR888UPQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 285a52e568cb4565e0792f91e6b1e460e4fb7778..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF584KWN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_2.fit.json b/ENCSR888UPQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 4d66b3b8d53ebf3c5568f4d5bf0ac3411ff348a2..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF584KWN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_2.log b/ENCSR888UPQ/cherimoya.fold_2.log deleted file mode 100644 index b3cd9b542110c2eec8acd531c9f9872ab3b67b94..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1994 26.213820934295654 3.4117250442504883 192.28167724609375 0.7807983160018921 238.71652221679688 0.1104503870010376 0.48993626 5.755151748657227 True -1 3988 21.698928594589233 0.3690505027770996 205.24334716796875 0.6933295726776123 228.01321411132812 0.17505773901939392 0.5877753 1.7569010257720947 True -2 5982 21.688414096832275 1.022937536239624 184.89898681640625 0.7193373441696167 219.66796875 0.20519334077835083 0.6609733 0.7267169952392578 True -3 7976 21.732202291488647 0.352571964263916 184.751953125 0.7429718375205994 217.00341796875 0.21310457587242126 0.676382 0.48008039593696594 True -4 9970 21.706488847732544 0.36229681968688965 161.9345703125 0.49936938285827637 215.74209594726562 0.216788649559021 0.68904835 0.435159832239151 True -5 11964 21.679965257644653 0.3589794635772705 200.99533081054688 0.7441819906234741 214.63848876953125 0.2216629534959793 0.6956725 0.44535934925079346 True -6 13958 21.70291042327881 0.3534564971923828 203.01136779785156 0.609265923500061 214.0839080810547 0.22393791377544403 0.7019466 0.4288013279438019 True -7 15952 21.698205947875977 0.4439876079559326 210.09805297851562 0.5501256585121155 213.53004455566406 0.22638839483261108 0.70492095 0.4214581251144409 True -8 17946 21.67235517501831 0.35416388511657715 169.01510620117188 0.5390316247940063 213.0238494873047 0.22810807824134827 0.71182597 0.41571158170700073 True -9 19940 21.86843514442444 22.30326747894287 175.66363525390625 0.44608843326568604 212.43490600585938 0.23089490830898285 0.7244668 0.4025214612483978 True -10 21934 21.925220012664795 0.36027050018310547 219.83995056152344 0.42524221539497375 212.28868103027344 0.23191869258880615 0.7277744 0.40125927329063416 True -11 23928 21.766295909881592 0.36066532135009766 199.37118530273438 0.6506527662277222 211.80255126953125 0.23436996340751648 0.73242646 0.3946443200111389 True -12 25922 21.702604055404663 0.3597230911254883 144.5003662109375 0.49945342540740967 211.35159301757812 0.23672246932983398 0.73634547 0.3893597722053528 True -13 27916 21.733216285705566 0.36089491844177246 167.36749267578125 0.44315406680107117 211.09030151367188 0.23800769448280334 0.74312276 0.38324394822120667 True -14 29910 21.75022792816162 0.3641788959503174 158.17947387695312 0.5160312652587891 210.99749755859375 0.23780786991119385 0.7476145 0.3841770589351654 True -15 31904 21.6838219165802 0.37059569358825684 165.97500610351562 0.45661264657974243 210.6176300048828 0.24050982296466827 0.75024194 0.38738757371902466 True -16 33898 21.758439302444458 0.36121034622192383 150.95945739746094 0.45346570014953613 210.6084442138672 0.23972666263580322 0.7550962 0.3937227725982666 True -17 35892 21.752020120620728 0.365311861038208 150.43521118164062 0.3088657855987549 210.89981079101562 0.23814398050308228 0.75315845 0.40555864572525024 False -18 37886 21.771646738052368 0.3581082820892334 159.40228271484375 0.36908918619155884 211.0966033935547 0.23728451132774353 0.7507862 0.4197373688220978 False -19 39880 21.72788643836975 0.3612062931060791 198.75360107421875 0.3836742639541626 211.31210327148438 0.23582684993743896 0.75062376 0.4253028631210327 False diff --git a/ENCSR888UPQ/cherimoya.fold_2.performance.tsv b/ENCSR888UPQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b16aedbeb8ba2bbf74cacfbc4f17af657b8b7dbe..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -210.6084442138672 0.5318712592124939 0.23972666263580322 0.05490751937031746 0.7550961971282959 0.717659592628479 0.3937227725982666 \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_3.evaluate.json b/ENCSR888UPQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f9e06182f01661c39036d859139b62a41844a117..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF584KWN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_3.fit.json b/ENCSR888UPQ/cherimoya.fold_3.fit.json deleted file mode 100644 index cb02c9e59246475c5d87dfe92f8ad0bfe0a04418..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF584KWN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_3.log b/ENCSR888UPQ/cherimoya.fold_3.log deleted file mode 100644 index c6690e69bdc6b4333f9b4d9347bccec8eac99e64..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1905 25.03482985496521 4.025083780288696 171.17849731445312 0.7496188282966614 252.8613739013672 0.11086192727088928 0.5132676 6.470523357391357 True -1 3810 20.738120555877686 0.4258913993835449 180.25747680664062 0.6305139064788818 243.7683868408203 0.1659143716096878 0.57175833 2.5789990425109863 True -2 5715 20.788991451263428 0.415111780166626 190.19749450683594 0.703072190284729 234.51380920410156 0.19987840950489044 0.65221715 0.9217017292976379 True -3 7620 20.754707098007202 0.405689001083374 177.835205078125 0.9317846298217773 232.16616821289062 0.20721304416656494 0.68354595 0.6716338992118835 True -4 9525 20.754859685897827 0.4074234962463379 167.88916015625 0.5049558877944946 231.24229431152344 0.21066030859947205 0.68977547 0.612592875957489 True -5 11430 20.748210668563843 0.4120333194732666 213.4349365234375 0.5118148326873779 230.44671630859375 0.2143143117427826 0.7058996 0.5285845398902893 True -6 13335 20.723766565322876 0.4079244136810303 171.76007080078125 0.42118269205093384 230.08010864257812 0.21560728549957275 0.7167414 0.5005075335502625 True -7 15240 20.699583053588867 0.40868520736694336 152.06643676757812 0.4581754207611084 229.77249145507812 0.2166466861963272 0.7146411 0.5002120733261108 False -8 17145 20.8032009601593 4.389448404312134 177.3600616455078 0.30407220125198364 229.18409729003906 0.21908457577228546 0.7234075 0.4664173126220703 True -9 19050 21.370214462280273 17.61711096763611 151.16259765625 0.5933160781860352 228.792236328125 0.2199912965297699 0.72665423 0.45556166768074036 True -10 20955 20.757176160812378 0.41521167755126953 192.52264404296875 0.4547865390777588 228.7120361328125 0.22048625349998474 0.736108 0.43545886874198914 True -11 22860 20.702425479888916 0.4091935157775879 157.439208984375 0.3969043791294098 228.1024627685547 0.22363513708114624 0.74153346 0.4288991391658783 True -12 24765 20.72169280052185 0.4110758304595947 178.82139587402344 0.45258307456970215 228.0576171875 0.22307057678699493 0.74893874 0.41629457473754883 True -13 26670 20.697125911712646 16.65716862678528 143.83355712890625 0.5665388703346252 227.615478515625 0.22536157071590424 0.7560728 0.40661007165908813 True -14 28575 21.008421182632446 0.415435791015625 146.2010040283203 0.3768428862094879 227.44239807128906 0.22550302743911743 0.76396096 0.395368754863739 True -15 30480 20.733712911605835 11.113665342330933 167.722900390625 0.34087255597114563 227.26199340820312 0.22637362778186798 0.7725672 0.3942737281322479 True -16 32385 21.33046793937683 19.33156991004944 172.033203125 0.4053453207015991 227.2602081298828 0.22704729437828064 0.7754999 0.3974841833114624 True -17 34290 21.228743314743042 0.4084029197692871 156.42694091796875 0.351453572511673 227.5814208984375 0.2247406244277954 0.7756224 0.40761372447013855 True -18 36195 20.731308221817017 0.40345120429992676 174.85556030273438 0.28804072737693787 227.59280395507812 0.22512491047382355 0.7755205 0.41898998618125916 False -19 38100 20.986696481704712 10.5300133228302 182.98583984375 0.320803165435791 227.55459594726562 0.2251329869031906 0.77465147 0.4244219958782196 False diff --git a/ENCSR888UPQ/cherimoya.fold_3.performance.tsv b/ENCSR888UPQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 89b85782e06dbeef1cc32abc5d83c7403e36c050..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -227.5814208984375 0.5327557325363159 0.22474059462547302 0.05730593949556351 0.7756224274635315 0.7459638714790344 0.40761372447013855 \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_4.evaluate.json b/ENCSR888UPQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 319d0d4b6f70ac46e1a4dfbc867e3c52a34c0d77..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF584KWN.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_4.fit.json b/ENCSR888UPQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 4eb2d2f8a553f7813ce81adac8385e3f51218415..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF584KWN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR888UPQ/cherimoya.fold_4.log b/ENCSR888UPQ/cherimoya.fold_4.log deleted file mode 100644 index 732a2ea46df573b32bf2a6e22c209bba8d053188..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1955 25.900227308273315 3.328819990158081 185.521484375 0.8694137334823608 226.17286682128906 0.10574126243591309 0.5099014 5.241888523101807 True -1 3910 21.326136112213135 0.6338038444519043 173.125244140625 0.9205811023712158 217.815185546875 0.1614288091659546 0.5943737 1.712613582611084 True -2 5865 21.367681741714478 0.37201428413391113 156.34913635253906 0.7783265709877014 209.94183349609375 0.1937880963087082 0.6746845 0.6465780138969421 True -3 7820 21.38476300239563 0.37991881370544434 151.26148986816406 0.5675370097160339 207.97132873535156 0.19968640804290771 0.69002175 0.44397374987602234 True -4 9775 21.55482029914856 0.37479066848754883 175.6690216064453 0.8159918785095215 206.8765106201172 0.20431575179100037 0.7004378 0.39849287271499634 True -5 11730 21.347615718841553 0.3753318786621094 175.69204711914062 0.5484710931777954 206.41136169433594 0.20598316192626953 0.7072171 0.38661888241767883 True -6 13685 21.330216646194458 1.3117685317993164 158.08773803710938 0.658755898475647 205.90902709960938 0.207569420337677 0.7167453 0.3815663158893585 True -7 15640 21.40731406211853 0.37566041946411133 155.9665069580078 0.5085951089859009 205.40283203125 0.21012301743030548 0.7208085 0.37996843457221985 True -8 17595 21.410715341567993 0.3696913719177246 159.39654541015625 0.462529718875885 205.13870239257812 0.21139666438102722 0.72535616 0.37390434741973877 True -9 19550 21.3546040058136 0.3720428943634033 186.64871215820312 0.4969095289707184 204.95225524902344 0.21248632669448853 0.7258689 0.37949660420417786 True -10 21505 21.37901520729065 0.37894678115844727 162.9354248046875 0.6035946607589722 204.64471435546875 0.21355664730072021 0.7331806 0.3749302625656128 True -11 23460 22.366371154785156 22.852720975875854 162.56719970703125 0.493949294090271 204.20062255859375 0.215809166431427 0.73384714 0.37072721123695374 True -12 25415 21.98771047592163 20.095356225967407 160.7882080078125 0.6390203237533569 203.7788543701172 0.21900099515914917 0.73762995 0.3693782687187195 True -13 27370 21.49981999397278 0.37189316749572754 154.02993774414062 0.33170294761657715 203.75592041015625 0.2182183861732483 0.74190456 0.3657757341861725 True -14 29325 20.85632348060608 0.3730173110961914 145.55718994140625 0.36396074295043945 203.53160095214844 0.21929721534252167 0.7487374 0.3569467067718506 True -15 31280 20.880131721496582 0.3671684265136719 168.59434509277344 0.32114776968955994 203.65560913085938 0.21836456656455994 0.75395024 0.35368114709854126 True -16 33235 20.923085689544678 0.3659381866455078 157.15414428710938 0.30690711736679077 203.5291748046875 0.21940942108631134 0.75574255 0.36344873905181885 True -17 35190 20.860118865966797 2.318005084991455 132.84922790527344 0.280788779258728 203.71336364746094 0.21828265488147736 0.75506276 0.3746311664581299 False -18 37145 20.87877106666565 0.3712489604949951 161.16064453125 0.3138508200645447 203.8638153076172 0.2177734673023224 0.75328195 0.389201283454895 False -19 39100 21.187740802764893 0.36795973777770996 194.06460571289062 0.38156864047050476 204.02731323242188 0.21638606488704681 0.74990606 0.3980836570262909 False diff --git a/ENCSR888UPQ/cherimoya.fold_4.performance.tsv b/ENCSR888UPQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ff68bfac3a69ba73e3e796db7f40f14de335db45..0000000000000000000000000000000000000000 --- a/ENCSR888UPQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -203.5291748046875 0.5416085720062256 0.21940946578979492 0.051699526607990265 0.7557425498962402 0.7195048332214355 0.36344873905181885 \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_0.evaluate.json b/ENCSR889ONK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 01a47bf1d810625378afd41f6e815bae82531735..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506VHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_0.fit.json b/ENCSR889ONK/cherimoya.fold_0.fit.json deleted file mode 100644 index 5de896f8ae57a1c28b50fd2c9398984a75b917cc..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF506VHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_0.log b/ENCSR889ONK/cherimoya.fold_0.log deleted file mode 100644 index 39b84c0cd409c28bd255978269260afe712c4efe..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2732 34.49622130393982 3.6510424613952637 313.05126953125 0.3673819303512573 490.08233642578125 0.16634035110473633 0.7036345 4.6301493644714355 True -1 5464 30.262438774108887 0.5790863037109375 392.1404113769531 0.5292410254478455 438.2945251464844 0.21764808893203735 0.7940096 1.5099307298660278 True -2 8196 30.228530883789062 0.5621225833892822 484.2411804199219 0.5787508487701416 433.299560546875 0.22083112597465515 0.79578453 1.5496312379837036 True -3 10928 30.16915011405945 0.560431957244873 355.6040344238281 0.4350694715976715 426.44488525390625 0.22684045135974884 0.7954353 0.9305118322372437 False -4 13660 30.252028465270996 1.2388901710510254 401.1031799316406 0.46850210428237915 422.7573547363281 0.22878137230873108 0.8154901 0.7323215007781982 True -5 16392 30.15144920349121 0.5669288635253906 395.1068115234375 0.48449432849884033 419.6014099121094 0.23346756398677826 0.82114893 0.7262681126594543 True -6 19124 30.12703800201416 0.5611047744750977 346.4471130371094 0.4622059762477875 417.865966796875 0.23472177982330322 0.8279793 0.6799877882003784 True -7 21856 30.086087465286255 0.5552990436553955 421.4676818847656 0.518263578414917 416.1184997558594 0.23724029958248138 0.8367513 0.6014503836631775 True -8 24588 30.543332815170288 31.681952953338623 412.89764404296875 0.2737116515636444 414.71490478515625 0.23864494264125824 0.8422915 0.5417895913124084 True -9 27320 30.19998526573181 9.530933856964111 372.3634948730469 0.6185686588287354 413.4811096191406 0.24070009589195251 0.8472581 0.4967707693576813 True -10 30052 30.123668432235718 30.152931690216064 331.70654296875 0.33046260476112366 411.1188049316406 0.24388723075389862 0.855261 0.43157902359962463 True -11 32784 30.458024263381958 0.5673518180847168 378.3831787109375 0.4206436574459076 409.3534851074219 0.24517370760440826 0.85946494 0.37089255452156067 True -12 35516 30.31730818748474 1.1360809803009033 297.5068359375 0.38396626710891724 408.4456481933594 0.2470385730266571 0.8627271 0.34296366572380066 True -13 38248 30.567740440368652 0.5676672458648682 420.810302734375 0.35326310992240906 407.3797302246094 0.24819396436214447 0.86696696 0.3181303143501282 True -14 40980 30.29094672203064 28.603699684143066 323.1351623535156 0.3096980154514313 406.64324951171875 0.24915970861911774 0.87103975 0.29483482241630554 True -15 43712 30.52448582649231 0.5743312835693359 363.66766357421875 0.42178499698638916 406.1719055175781 0.24959643185138702 0.8716301 0.27979397773742676 True -16 46444 30.86904263496399 17.278928518295288 374.6419677734375 0.3630967140197754 405.3178405761719 0.25075504183769226 0.8737228 0.2739524841308594 True -17 49176 30.327463626861572 1.8368890285491943 283.45159912109375 0.19868555665016174 405.9473571777344 0.25035393238067627 0.87470406 0.26916056871414185 True -18 51908 30.2313334941864 12.86839509010315 414.9100036621094 0.20150607824325562 405.31573486328125 0.2510887682437897 0.8741803 0.2712356448173523 False -19 54640 30.15847635269165 0.56768798828125 384.302734375 0.235719695687294 405.779052734375 0.2506527304649353 0.8724249 0.2738029658794403 False diff --git a/ENCSR889ONK/cherimoya.fold_0.performance.tsv b/ENCSR889ONK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2dd2ffeb38cc7c4f7b2e624d25c2e12b55fce909..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -405.9473571777344 0.49507877230644226 0.25035393238067627 0.08691028505563736 0.8747040629386902 0.8007024526596069 0.26916056871414185 \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_1.evaluate.json b/ENCSR889ONK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a6f4f8b33007445bee9f2897cfbe6dc727d5de7d..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506VHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_1.fit.json b/ENCSR889ONK/cherimoya.fold_1.fit.json deleted file mode 100644 index 27f799ea30e048db10371d9bef91158b9ef6d48b..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF506VHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_1.log b/ENCSR889ONK/cherimoya.fold_1.log deleted file mode 100644 index a98a268a98d09a4aa5521e04d766f4db9ad1e7ca..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2697 40.78289532661438 7.618497610092163 406.64453125 0.700644850730896 600.1504516601562 0.18363018333911896 0.6950451 5.367339134216309 True -1 5394 29.86649751663208 0.6816129684448242 433.38433837890625 0.6059610843658447 535.602783203125 0.24288861453533173 0.79218245 2.043344497680664 True -2 8091 29.766640424728394 0.6704518795013428 346.4046630859375 0.5427266359329224 530.746337890625 0.24470850825309753 0.786265 1.5991462469100952 False -3 10788 29.748773097991943 0.6654376983642578 314.53729248046875 0.37321335077285767 518.078125 0.2532118856906891 0.8066909 0.9151650071144104 True -4 13485 29.757400274276733 33.01078772544861 321.38690185546875 0.3297526240348816 511.6363220214844 0.25906452536582947 0.81447554 0.8430611491203308 True -5 16182 32.20376706123352 1.950798749923706 369.89080810546875 0.3136481046676636 509.52642822265625 0.26116472482681274 0.81802773 0.7655757069587708 True -6 18879 30.68142867088318 0.6747665405273438 401.3074035644531 0.4799766540527344 505.98663330078125 0.26464343070983887 0.8263349 0.7136511206626892 True -7 21576 30.053097248077393 38.92111158370972 420.7736511230469 0.40167534351348877 503.9182434082031 0.26657041907310486 0.832174 0.6994262337684631 True -8 24273 29.816165924072266 0.6644752025604248 333.5798034667969 0.4055129289627075 500.2058410644531 0.26993072032928467 0.84410006 0.6313185691833496 True -9 26970 29.787257194519043 2.1273560523986816 422.4766540527344 0.37803196907043457 498.2788391113281 0.272104948759079 0.8463658 0.601559579372406 True -10 29667 30.245783805847168 0.6653759479522705 454.3754577636719 0.3703469932079315 495.60760498046875 0.27535560727119446 0.85217905 0.5406578183174133 True -11 32364 31.167853832244873 30.12540555000305 368.0359802246094 0.5534818768501282 493.57666015625 0.2780570089817047 0.86014825 0.49205708503723145 True -12 35061 29.834219932556152 1.2139647006988525 429.0444641113281 0.459808349609375 490.8944091796875 0.2802650034427643 0.86563355 0.4448162317276001 True -13 37758 29.78532600402832 0.6702985763549805 290.35272216796875 0.38541072607040405 489.7970275878906 0.281721830368042 0.8706166 0.42242318391799927 True -14 40455 29.88437008857727 0.6957731246948242 371.10870361328125 0.3379533886909485 487.47991943359375 0.28380024433135986 0.87433374 0.38481494784355164 True -15 43152 29.85512375831604 0.7531194686889648 268.3817443847656 0.22591036558151245 486.5529479980469 0.2846677005290985 0.8789329 0.3505421280860901 True -16 45849 29.94827175140381 0.6860010623931885 303.550537109375 0.2596302032470703 485.7962951660156 0.2851036489009857 0.8819197 0.33451253175735474 True -17 48546 30.006030321121216 0.6678786277770996 279.310302734375 0.24391227960586548 484.9324645996094 0.2859339118003845 0.88298243 0.326661080121994 True -18 51243 29.892810106277466 0.656965970993042 340.304931640625 0.20507366955280304 485.738525390625 0.28482934832572937 0.8834731 0.3272874653339386 True -19 53940 29.968525409698486 0.667996883392334 346.4124755859375 0.34151822328567505 486.63287353515625 0.2836008667945862 0.88321257 0.3281886577606201 False diff --git a/ENCSR889ONK/cherimoya.fold_1.performance.tsv b/ENCSR889ONK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 98ea22eef61b62c77cf9f203644a61f79f8ea44c..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -485.738525390625 0.4672330915927887 0.28482934832572937 0.10726945102214813 0.8834730982780457 0.8379807472229004 0.3272874653339386 \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_2.evaluate.json b/ENCSR889ONK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 04b3fe98cfb5a05487904b39a2a710a881d4a642..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506VHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_2.fit.json b/ENCSR889ONK/cherimoya.fold_2.fit.json deleted file mode 100644 index 77450bb288e2d828d54f0a090d8c87420aeaeef6..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF506VHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_2.log b/ENCSR889ONK/cherimoya.fold_2.log deleted file mode 100644 index 9619926261c002d2e533ce59aa51aae16376e855..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 36.64416265487671 4.004096269607544 308.592529296875 0.5353449583053589 524.4901733398438 0.1745612770318985 0.6814881 4.869625091552734 True -1 5756 31.82118558883667 0.5922901630401611 335.0837707519531 0.28873395919799805 467.8282165527344 0.22853057086467743 0.7876299 1.5204836130142212 True -2 8634 31.821412563323975 0.5592646598815918 392.87445068359375 0.5920732617378235 462.22845458984375 0.22941328585147858 0.78891253 1.2639129161834717 True -3 11512 31.734771013259888 0.5527424812316895 328.6408386230469 0.4254956841468811 453.951904296875 0.23629546165466309 0.799379 0.8651783466339111 True -4 14390 31.801627159118652 0.5628657341003418 377.7112121582031 0.5474916696548462 451.4630432128906 0.23977608978748322 0.80717045 0.6792750954627991 True -5 17268 32.78079414367676 32.6739284992218 369.66900634765625 0.27699384093284607 447.3211669921875 0.2440342903137207 0.81959045 0.6547470688819885 True -6 20146 32.41881084442139 0.5589601993560791 405.826171875 0.41644078493118286 444.0198059082031 0.2477506399154663 0.8271081 0.5798243880271912 True -7 23024 31.837899208068848 0.5650753974914551 332.89166259765625 0.39275655150413513 443.38775634765625 0.24774062633514404 0.8334106 0.5335649847984314 True -8 25902 31.727343320846558 0.5607852935791016 404.31719970703125 0.466494619846344 440.6976623535156 0.2519018054008484 0.83761615 0.5357270240783691 True -9 28780 31.842483043670654 0.5609490871429443 319.1272277832031 0.40363621711730957 438.99359130859375 0.25357306003570557 0.843911 0.47248443961143494 True -10 31658 31.73884129524231 0.5646224021911621 284.6682434082031 0.5736761093139648 437.578857421875 0.2549331784248352 0.8501572 0.4431772828102112 True -11 34536 31.80330467224121 2.3650739192962646 412.729736328125 0.23566341400146484 436.6005859375 0.2554769515991211 0.85484064 0.4079395532608032 True -12 37414 31.913986682891846 40.55124855041504 353.8457946777344 0.3972289562225342 434.8464050292969 0.2582409083843231 0.8585931 0.37023434042930603 True -13 40292 33.50825881958008 0.6032969951629639 374.137939453125 0.3531155288219452 433.4933776855469 0.25954458117485046 0.8618541 0.34232085943222046 True -14 43170 31.949424266815186 0.5676558017730713 361.5765380859375 0.38441944122314453 431.509033203125 0.26242774724960327 0.86740804 0.32078370451927185 True -15 46048 31.801218032836914 0.5594606399536133 401.4319763183594 0.3311203122138977 430.84234619140625 0.262743204832077 0.8691617 0.3035988509654999 True -16 48926 31.792129516601562 0.5625245571136475 399.7586975097656 0.22960036993026733 430.5414123535156 0.262888103723526 0.87088317 0.2941141128540039 True -17 51804 31.801417350769043 0.5654997825622559 318.12109375 0.23245787620544434 431.17352294921875 0.26196983456611633 0.8716407 0.28898200392723083 True -18 54682 31.849007844924927 0.5554823875427246 354.9111328125 0.20040135085582733 431.50982666015625 0.26135173439979553 0.87224567 0.2898125946521759 True -19 57560 31.945134162902832 0.5587294101715088 288.0940856933594 0.24500486254692078 430.65740966796875 0.262847900390625 0.8718105 0.28926756978034973 False diff --git a/ENCSR889ONK/cherimoya.fold_2.performance.tsv b/ENCSR889ONK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index fa8a607f1dc9f7396303b96a1dbd65f99f658461..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -431.50982666015625 0.4853076636791229 0.26135173439979553 0.09238652884960175 0.8722456693649292 0.8158031702041626 0.2898125946521759 \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_3.evaluate.json b/ENCSR889ONK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 74404ec7d7eb291c5ebd034914320ce491b6a49e..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506VHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_3.fit.json b/ENCSR889ONK/cherimoya.fold_3.fit.json deleted file mode 100644 index 536946a4926801944cdfcab3e1e73dfed664d288..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF506VHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_3.log b/ENCSR889ONK/cherimoya.fold_3.log deleted file mode 100644 index 2219a32c538ce9bddd91f52ebeafdf2a49bf091f..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 34.69502520561218 14.61601448059082 449.8608703613281 0.5741626620292664 507.299072265625 0.1805162876844406 0.671408 5.8868536949157715 True -1 5482 30.314067125320435 0.5738718509674072 342.74212646484375 0.7252056002616882 460.1400146484375 0.22868581116199493 0.75563 1.7163281440734863 True -2 8223 30.316744804382324 0.7527868747711182 326.8492736816406 0.2317827045917511 453.6153564453125 0.23121176660060883 0.7754148 1.2143970727920532 True -3 10964 30.40016460418701 0.5665633678436279 328.4666442871094 0.44937583804130554 447.9410095214844 0.23435764014720917 0.77428275 1.1460944414138794 False -4 13705 30.523324012756348 0.5653870105743408 441.50360107421875 0.361361026763916 443.72064208984375 0.2390955239534378 0.78418255 0.8340467810630798 True -5 16446 30.428586959838867 0.5721902847290039 308.24322509765625 0.37465429306030273 439.1134338378906 0.24414435029029846 0.7993254 0.7572579979896545 True -6 19187 30.425464868545532 0.5655732154846191 339.1127624511719 0.3722568452358246 437.4713439941406 0.24602773785591125 0.8099246 0.6540417075157166 True -7 21928 30.493868350982666 0.5771355628967285 464.87701416015625 0.6667845845222473 434.39501953125 0.24977508187294006 0.8152235 0.6720296740531921 True -8 24669 31.498236656188965 9.060779809951782 357.0643310546875 0.37326037883758545 432.885498046875 0.2506153881549835 0.82578474 0.5876997709274292 True -9 27410 30.349522829055786 32.87490129470825 418.438232421875 0.2937825918197632 431.0351257324219 0.2532985210418701 0.82994986 0.5519008040428162 True -10 30151 34.451178789138794 0.5574007034301758 404.42742919921875 0.5635616183280945 430.29046630859375 0.2545185387134552 0.83671665 0.4973437786102295 True -11 32892 30.428380012512207 0.5550715923309326 345.90374755859375 0.49686580896377563 428.2594299316406 0.25640302896499634 0.8425684 0.4578871726989746 True -12 35633 30.478124141693115 0.5524303913116455 426.12432861328125 0.26300644874572754 427.2781066894531 0.2581765949726105 0.8467864 0.41859742999076843 True -13 38374 30.42870283126831 0.5554153919219971 348.84234619140625 0.33329010009765625 426.62445068359375 0.2587818503379822 0.85239977 0.4030441641807556 True -14 41115 30.480603218078613 0.5596580505371094 333.08544921875 0.4118703305721283 424.523193359375 0.26138219237327576 0.8600056 0.3687542676925659 True -15 43856 30.637361526489258 0.5824196338653564 365.13031005859375 0.40551668405532837 423.4692077636719 0.26280295848846436 0.8620221 0.35073181986808777 True -16 46597 30.44757342338562 0.5656957626342773 405.0494384765625 0.2925114333629608 422.45660400390625 0.26368993520736694 0.86833507 0.32840123772621155 True -17 49338 30.497753620147705 0.7792425155639648 324.76739501953125 0.23621594905853271 423.0036315917969 0.2623654901981354 0.86795413 0.31581979990005493 False -18 52079 30.49906039237976 0.5652170181274414 307.5503234863281 0.2449282854795456 423.10418701171875 0.2621691823005676 0.86792 0.3133334517478943 False -19 54820 30.593621015548706 24.126797437667847 313.77459716796875 0.21947601437568665 422.5308532714844 0.2632914185523987 0.8676058 0.314698189496994 False diff --git a/ENCSR889ONK/cherimoya.fold_3.performance.tsv b/ENCSR889ONK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b82cf142bb224e4cb0612f1298dfc702aba2210f..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -422.45660400390625 0.4860690236091614 0.26368993520736694 0.096951924264431 0.8683350682258606 0.8042436242103577 0.32840123772621155 \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_4.evaluate.json b/ENCSR889ONK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4ad383ebec782dec7b6fe757a96d5cead896b1ad..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF506VHT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_4.fit.json b/ENCSR889ONK/cherimoya.fold_4.fit.json deleted file mode 100644 index 15a0ead312f605eff93297a30329c62cd4737e89..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF506VHT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889ONK/cherimoya.fold_4.log b/ENCSR889ONK/cherimoya.fold_4.log deleted file mode 100644 index 5973b153e0ea526d2fbdea06cd161be6f3fb17c4..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2813 35.74374556541443 3.601076602935791 404.37298583984375 0.5486286878585815 429.0296936035156 0.1653575748205185 0.6860976 3.18782377243042 True -1 5626 31.109766244888306 3.6077191829681396 331.72705078125 0.46578532457351685 396.3647155761719 0.20284302532672882 0.76838076 1.3342926502227783 True -2 8439 31.08791494369507 0.5905590057373047 352.64788818359375 0.3316846191883087 389.5572509765625 0.2068893313407898 0.7773123 0.9784941673278809 True -3 11252 30.965920448303223 0.6092369556427002 365.3866271972656 0.4485933482646942 384.69647216796875 0.21108418703079224 0.7762823 0.6102361083030701 False -4 14065 31.02924394607544 0.6055388450622559 355.5101013183594 0.41459038853645325 382.3214111328125 0.21401700377464294 0.7896752 0.6064488291740417 True -5 16878 30.99300456047058 0.6466555595397949 294.628173828125 0.5481118559837341 379.785400390625 0.21718740463256836 0.8007045 0.5832444429397583 True -6 19691 31.15004849433899 0.612105131149292 328.193115234375 0.5887413024902344 377.9591979980469 0.21929867565631866 0.8055916 0.5454273819923401 True -7 22504 30.967752695083618 0.6116847991943359 320.40692138671875 0.21316871047019958 375.6247863769531 0.2222404181957245 0.8121026 0.48450854420661926 True -8 25317 31.135078191757202 0.6067214012145996 340.3006591796875 0.4760251045227051 374.81207275390625 0.2237308770418167 0.8200084 0.4762515127658844 True -9 28130 31.32694911956787 0.6063077449798584 400.0555725097656 0.47819066047668457 373.9534606933594 0.22452127933502197 0.827172 0.42465731501579285 True -10 30943 31.273643493652344 0.6115171909332275 303.73345947265625 0.4000876843929291 372.8834228515625 0.22623978555202484 0.837852 0.3825181722640991 True -11 33756 32.669920921325684 35.88502860069275 407.62158203125 0.5306861400604248 371.4604187011719 0.22864897549152374 0.84197295 0.3606356084346771 True -12 36569 32.10629677772522 0.6015317440032959 380.30804443359375 0.25370800495147705 369.9710998535156 0.23054923117160797 0.8481835 0.31822362542152405 True -13 39382 31.379181385040283 0.6093316078186035 380.29730224609375 0.3704177737236023 369.2226257324219 0.23187203705310822 0.8521287 0.3029840588569641 True -14 42195 31.91043758392334 2.6430118083953857 328.2893981933594 0.20770151913166046 368.09100341796875 0.23320002853870392 0.85526955 0.27479100227355957 True -15 45008 31.43690037727356 0.6006450653076172 367.52008056640625 0.23023894429206848 367.47576904296875 0.23355120420455933 0.85860807 0.2620011568069458 True -16 47821 31.34831666946411 12.970163345336914 324.27777099609375 0.2187156081199646 367.60235595703125 0.23341165482997894 0.8621619 0.2542349398136139 True -17 50634 31.402293920516968 0.6021270751953125 367.66180419921875 0.19460263848304749 367.2051086425781 0.2347671538591385 0.8623106 0.25172242522239685 True -18 53447 31.374473094940186 0.6180939674377441 297.0721130371094 0.19112595915794373 367.8857727050781 0.23323939740657806 0.86472625 0.25043487548828125 True -19 56260 31.335396766662598 0.5976026058197021 292.538818359375 0.1871919482946396 368.1673583984375 0.23302878439426422 0.86299056 0.2522169053554535 False diff --git a/ENCSR889ONK/cherimoya.fold_4.performance.tsv b/ENCSR889ONK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b10537dfb3a2d5686d92fd83c86f888b06a1257e..0000000000000000000000000000000000000000 --- a/ENCSR889ONK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -367.8857727050781 0.5087041258811951 0.23323939740657806 0.07255091518163681 0.8647262454032898 0.7855342030525208 0.25043487548828125 \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_0.evaluate.json b/ENCSR889YWJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9822578741af9d7493c51dec16f3ffeec86f4ff8..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF139FFL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_0.fit.json b/ENCSR889YWJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 7313101470a65d1c794e7b43e6650ff02b5c6fdc..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF139FFL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_0.log b/ENCSR889YWJ/cherimoya.fold_0.log deleted file mode 100644 index f2ebefb378f22120b94827be98022e93421d5349..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2723 35.24541711807251 4.279268026351929 166.83030700683594 0.6730531454086304 243.9405059814453 0.14099612832069397 0.6606262 3.9707367420196533 True -1 5446 29.73174524307251 0.5948491096496582 219.49720764160156 1.058329701423645 218.34097290039062 0.19256579875946045 0.74516696 2.430915117263794 True -2 8169 29.729386568069458 30.53151226043701 164.96014404296875 0.8979845643043518 215.0166015625 0.19757887721061707 0.7596205 1.437117099761963 True -3 10892 33.95169973373413 0.590146541595459 159.55386352539062 0.5017106533050537 211.47921752929688 0.20321865379810333 0.77138376 1.1143238544464111 True -4 13615 32.20597052574158 4.345561742782593 151.0690460205078 0.9926930665969849 209.7224884033203 0.20787419378757477 0.7859244 0.9931577444076538 True -5 16338 30.24963116645813 35.233452558517456 193.57492065429688 0.7470853328704834 208.40692138671875 0.2095845490694046 0.79619837 0.8635734915733337 True -6 19061 29.628496646881104 4.732349395751953 146.2239990234375 0.6908242106437683 207.58154296875 0.21064510941505432 0.80679446 0.80950927734375 True -7 21784 29.65044665336609 1.2911901473999023 162.61123657226562 0.6502302885055542 207.10479736328125 0.21164831519126892 0.8102065 0.7680832147598267 True -8 24507 29.664888620376587 1.282654047012329 131.70236206054688 0.44924595952033997 205.80230712890625 0.21434125304222107 0.8199508 0.6573607921600342 True -9 27230 29.725000619888306 2.0579750537872314 191.2041473388672 0.6128418445587158 205.23846435546875 0.21542778611183167 0.8241768 0.6340522766113281 True -10 29953 29.676729440689087 1.6037590503692627 154.19712829589844 0.9869239330291748 204.5682830810547 0.21719931066036224 0.82973135 0.5818947553634644 True -11 32676 29.646625518798828 8.069289684295654 197.49880981445312 0.9518948793411255 203.92083740234375 0.21907158195972443 0.8341208 0.5673147439956665 True -12 35399 29.750114917755127 1.5944979190826416 152.93455505371094 0.5592305660247803 203.12550354003906 0.22099608182907104 0.83812207 0.533942461013794 True -13 38122 30.050944089889526 0.5782825946807861 172.47589111328125 0.32478243112564087 202.87156677246094 0.22078324854373932 0.8413072 0.5075165033340454 True -14 40845 29.748137950897217 0.5780553817749023 181.1553955078125 0.6002449989318848 201.97935485839844 0.22312311828136444 0.8473001 0.4885905385017395 True -15 43568 29.8775634765625 9.014683485031128 133.8943634033203 0.6244529485702515 201.6836395263672 0.2236887365579605 0.8484674 0.47593605518341064 True -16 46291 29.68209195137024 0.5736148357391357 195.34423828125 0.3482745885848999 201.49716186523438 0.22415873408317566 0.8511251 0.466354101896286 True -17 49014 30.20224142074585 0.5805556774139404 184.8905792236328 0.3178686797618866 201.51121520996094 0.22425545752048492 0.85381025 0.4592023193836212 True -18 51737 29.702619791030884 0.5760848522186279 226.39523315429688 0.3627350628376007 201.95994567871094 0.2227824479341507 0.8530318 0.45855388045310974 False -19 54460 29.71482276916504 24.72896385192871 149.24765014648438 0.31841641664505005 202.01792907714844 0.22312943637371063 0.8518484 0.46336448192596436 False diff --git a/ENCSR889YWJ/cherimoya.fold_0.performance.tsv b/ENCSR889YWJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 752aca6cdab237845e64b2037e840a9187ff35c9..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.51121520996094 0.5446556806564331 0.2242554873228073 0.05915491282939911 0.8538102507591248 0.7881264090538025 0.4592023193836212 \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_1.evaluate.json b/ENCSR889YWJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e120adb7c022c0eeedb13c5c3c1bd455134a5581..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF139FFL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_1.fit.json b/ENCSR889YWJ/cherimoya.fold_1.fit.json deleted file mode 100644 index 2264ef56e543b4d3b2200153282beabbe53653b2..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF139FFL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_1.log b/ENCSR889YWJ/cherimoya.fold_1.log deleted file mode 100644 index 9b697892c22dc5bcb2e2a266791d14de6b116f81..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2685 33.94122505187988 3.836047649383545 154.55215454101562 0.7793247699737549 306.84735107421875 0.1555366963148117 0.65890574 5.035743713378906 True -1 5370 29.323485136032104 0.7436349391937256 117.27822875976562 0.6399913430213928 273.3003845214844 0.21375703811645508 0.74478513 3.22182559967041 True -2 8055 29.3157057762146 3.9798943996429443 171.85189819335938 0.6676095724105835 268.1601257324219 0.22293032705783844 0.7549319 2.1751809120178223 True -3 10740 29.385867595672607 0.7375571727752686 150.3861083984375 0.7784570455551147 265.2856750488281 0.2282995581626892 0.7674887 1.7846643924713135 True -4 13425 29.403565406799316 0.720834493637085 171.0065155029297 0.8342448472976685 262.8827209472656 0.231035515666008 0.7834641 1.4175965785980225 True -5 16110 29.28546714782715 0.7175805568695068 179.46209716796875 0.6253657341003418 259.3440856933594 0.23667116463184357 0.7986032 1.2135111093521118 True -6 18795 29.26341462135315 0.7180113792419434 192.43045043945312 1.101776361465454 258.17791748046875 0.23800958693027496 0.80945235 1.072933554649353 True -7 21480 29.268697500228882 0.7134473323822021 198.96600341796875 0.8108788728713989 256.79583740234375 0.24026717245578766 0.8186238 0.9430124163627625 True -8 24165 29.43196392059326 27.841768741607666 159.4591064453125 0.722227931022644 255.62977600097656 0.24256817996501923 0.8273311 0.8713244795799255 True -9 26850 29.652074813842773 0.7481048107147217 161.620361328125 0.49841439723968506 254.45411682128906 0.24464665353298187 0.83351934 0.7672904133796692 True -10 29535 29.25903010368347 38.564886808395386 112.92654418945312 0.6014961004257202 253.22080993652344 0.2472568303346634 0.8399852 0.7308430075645447 True -11 32220 30.743126392364502 0.7584881782531738 186.1502685546875 0.677271842956543 252.82891845703125 0.24715664982795715 0.84733236 0.6659518480300903 True -12 34905 29.457574605941772 0.734093427658081 213.90863037109375 0.6019585132598877 251.53854370117188 0.24983586370944977 0.85224086 0.6239531636238098 True -13 37590 29.45952272415161 0.7272071838378906 149.25791931152344 0.713202953338623 250.16799926757812 0.25300323963165283 0.85846275 0.5739618539810181 True -14 40275 29.344604969024658 0.7232227325439453 138.76414489746094 0.7324352264404297 249.0475616455078 0.2550411820411682 0.8629235 0.5476827621459961 True -15 42960 29.888157844543457 33.522653579711914 205.5233154296875 0.39095139503479004 248.97711181640625 0.2540504038333893 0.86625904 0.5248100757598877 True -16 45645 30.22002601623535 0.7279634475708008 206.89895629882812 0.38712137937545776 248.43263244628906 0.2551570236682892 0.8678371 0.5138093829154968 True -17 48330 29.430476427078247 1.4642906188964844 140.03988647460938 0.5255641341209412 248.8379669189453 0.2547242045402527 0.8671222 0.5114055275917053 False -18 51015 29.37402367591858 0.7113251686096191 194.78140258789062 0.3567572832107544 248.8071746826172 0.2549704909324646 0.86730444 0.5149669051170349 False -19 53700 29.38653326034546 0.714543342590332 204.12794494628906 0.461961567401886 249.05230712890625 0.254337340593338 0.8650995 0.5216847658157349 False diff --git a/ENCSR889YWJ/cherimoya.fold_1.performance.tsv b/ENCSR889YWJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f1ce381579a8eefa52283556f8fec8502d54c9c9..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -248.43263244628906 0.519844114780426 0.2551569938659668 0.07666780799627304 0.8678370714187622 0.8251013159751892 0.5138093829154968 \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_2.evaluate.json b/ENCSR889YWJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2baa033ac259205c2078d06bd78103359895b3d7..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF139FFL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_2.fit.json b/ENCSR889YWJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 62f91954f7388fff9ee0271547b7df51acba3747..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF139FFL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_2.log b/ENCSR889YWJ/cherimoya.fold_2.log deleted file mode 100644 index 4a55cc402b6a6975ee2e19c4de326a424e9107c8..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 35.93714904785156 4.304805517196655 200.58737182617188 0.845228910446167 252.32228088378906 0.14407488703727722 0.6564978 3.6153793334960938 True -1 5752 31.284026384353638 0.5830192565917969 218.9012908935547 0.9919865131378174 224.80284118652344 0.19731755554676056 0.7515886 2.7449584007263184 True -2 8628 31.820991039276123 0.5611279010772705 146.62905883789062 0.7530955076217651 221.988037109375 0.20164579153060913 0.7613934 1.5088099241256714 True -3 11504 31.34621548652649 0.5617978572845459 185.42498779296875 0.7390509843826294 218.88893127441406 0.20834529399871826 0.7775339 1.1948440074920654 True -4 14380 31.424888849258423 0.5592451095581055 227.95782470703125 1.0822641849517822 217.48440551757812 0.20866899192333221 0.7890903 1.0522217750549316 True -5 17256 31.559187412261963 0.5628173351287842 178.3648681640625 0.7793408632278442 216.14645385742188 0.2112753838300705 0.80535686 0.879631757736206 True -6 20132 31.335142612457275 0.5598311424255371 151.63394165039062 0.5510504245758057 213.96762084960938 0.21592730283737183 0.8124092 0.7967656254768372 True -7 23008 31.59588098526001 0.5622870922088623 151.36758422851562 0.79598069190979 213.17031860351562 0.2172848880290985 0.81795275 0.7606320977210999 True -8 25884 31.333557605743408 1.258852481842041 197.41018676757812 0.8797630071640015 212.26336669921875 0.21934567391872406 0.8249615 0.6524314880371094 True -9 28760 31.360981464385986 0.5691230297088623 190.39205932617188 0.6648101806640625 211.40357971191406 0.22097264230251312 0.8296509 0.6280516386032104 True -10 31636 31.29928421974182 0.5642094612121582 169.31100463867188 0.3654964566230774 210.8859100341797 0.2215738296508789 0.83650565 0.5690758228302002 True -11 34512 31.279509782791138 20.1704421043396 145.44900512695312 0.5884795784950256 210.53738403320312 0.22284555435180664 0.8411044 0.5330929160118103 True -12 37388 32.429465770721436 0.5889606475830078 161.4256591796875 0.3497953414916992 209.7605438232422 0.2238224744796753 0.8438169 0.5111286640167236 True -13 40264 31.42896795272827 0.5777649879455566 181.45138549804688 0.5640869140625 209.60617065429688 0.22376616299152374 0.848517 0.4963585436344147 True -14 43140 31.319219827651978 0.5676000118255615 132.79595947265625 0.5237875580787659 208.4137420654297 0.22764891386032104 0.8516173 0.4792267084121704 True -15 46016 31.304848194122314 0.5597193241119385 150.1193389892578 0.5314164161682129 207.7734375 0.22920095920562744 0.8560896 0.4633108973503113 True -16 48892 31.687607526779175 0.5687346458435059 149.9802703857422 0.5849947929382324 207.58888244628906 0.2290661334991455 0.8571107 0.452549010515213 True -17 51768 31.68826389312744 34.73091244697571 196.46600341796875 0.4128771424293518 207.85719299316406 0.2285756915807724 0.85919404 0.44788673520088196 True -18 54644 31.307154417037964 0.5751702785491943 181.67669677734375 0.4340496063232422 207.81817626953125 0.22871939837932587 0.85799146 0.45088618993759155 False -19 57520 31.47870135307312 0.5829734802246094 170.58358764648438 0.34347712993621826 208.2266082763672 0.2272159457206726 0.8574296 0.4527182877063751 False diff --git a/ENCSR889YWJ/cherimoya.fold_2.performance.tsv b/ENCSR889YWJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index db3ea6d77b54c93060aeb67a6816cfbba7ac1107..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -207.85719299316406 0.5414946675300598 0.2285756915807724 0.062228329479694366 0.8591940402984619 0.798118531703949 0.44788673520088196 \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_3.evaluate.json b/ENCSR889YWJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fd8a663fd611642fbd5c5369ee18b263740c6ca3..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF139FFL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_3.fit.json b/ENCSR889YWJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 0ea0ea03c6a6cbffc47e39cbd78b0cba7b5ba8ca..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF139FFL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_3.log b/ENCSR889YWJ/cherimoya.fold_3.log deleted file mode 100644 index a288d72c0e8038ec4b699567a42f161e71408bf8..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.63457655906677 3.5223519802093506 240.39108276367188 0.979584813117981 253.9947052001953 0.15476363897323608 0.63233757 4.697175979614258 True -1 5492 29.922751665115356 2.5132038593292236 191.47470092773438 0.4749586582183838 228.4351348876953 0.2048627734184265 0.7381221 2.6252899169921875 True -2 8238 29.914268016815186 2.1386828422546387 167.51568603515625 0.6237620115280151 224.83209228515625 0.21180956065654755 0.7535761 1.5162571668624878 True -3 10984 29.96126127243042 29.571772575378418 184.2913360595703 0.45214080810546875 222.3966522216797 0.21549372375011444 0.77055943 1.2809805870056152 True -4 13730 30.286897897720337 23.887187480926514 133.1735076904297 0.8934822082519531 220.9257049560547 0.2179432064294815 0.7804182 1.1473485231399536 True -5 16476 30.560109853744507 0.5579628944396973 175.15914916992188 0.7092607617378235 219.46278381347656 0.2211160659790039 0.7874836 1.10405433177948 True -6 19222 30.097972869873047 0.5485541820526123 154.58717346191406 0.43374359607696533 219.11080932617188 0.22137562930583954 0.7921671 0.9950727224349976 True -7 21968 29.93986439704895 0.5441062450408936 209.66616821289062 0.6056578755378723 218.2960968017578 0.2237383872270584 0.796747 0.9136419296264648 True -8 24714 30.000864267349243 2.179023504257202 172.24615478515625 0.6930787563323975 217.77940368652344 0.22475656867027283 0.8033757 0.863702118396759 True -9 27460 30.066057682037354 1.2048943042755127 164.35269165039062 0.6081782579421997 216.4049072265625 0.22811685502529144 0.8052227 0.8636272549629211 True -10 30206 30.067051649093628 1.861034870147705 206.2030792236328 0.5717028975486755 216.17103576660156 0.22842402756214142 0.812604 0.7665421962738037 True -11 32952 30.087691068649292 1.5819530487060547 130.9295654296875 0.5364534258842468 215.02743530273438 0.23085391521453857 0.8196485 0.7130373120307922 True -12 35698 29.964818954467773 1.8678925037384033 173.25851440429688 0.5280098915100098 214.5252227783203 0.2326771318912506 0.8248095 0.6712723970413208 True -13 38444 31.013405561447144 32.22761273384094 202.771728515625 0.709437906742096 213.48333740234375 0.23491345345973969 0.83265686 0.6245174407958984 True -14 41190 29.970013856887817 32.84275436401367 159.69268798828125 0.658699631690979 213.3105926513672 0.2352123111486435 0.8401065 0.5724215507507324 True -15 43936 30.15919542312622 2.7966196537017822 169.94677734375 0.39240193367004395 212.7408905029297 0.23632501065731049 0.84427255 0.5477970242500305 True -16 46682 29.971367359161377 0.537790060043335 177.03897094726562 0.5214503407478333 212.02638244628906 0.23717714846134186 0.84950215 0.5245065689086914 True -17 49428 30.0463604927063 0.5473606586456299 206.12179565429688 0.48260498046875 212.4993438720703 0.2358192354440689 0.850311 0.5150110125541687 True -18 52174 29.9489426612854 0.5353310108184814 158.68043518066406 0.5200366973876953 212.28968811035156 0.23707029223442078 0.8495915 0.514042317867279 False -19 54920 29.890105962753296 0.538752555847168 164.59722900390625 0.30300426483154297 212.55584716796875 0.23611655831336975 0.84953123 0.5122365355491638 False diff --git a/ENCSR889YWJ/cherimoya.fold_3.performance.tsv b/ENCSR889YWJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0fcc8e387c5d1ddc99b1f000b849ad4e6a59ebf6..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -212.4993438720703 0.5357562303543091 0.2358192354440689 0.06451494991779327 0.8503109812736511 0.788958728313446 0.5150110125541687 \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_4.evaluate.json b/ENCSR889YWJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f976981440ace0e15d1373db503cea4f52f4533f..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF139FFL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_4.fit.json b/ENCSR889YWJ/cherimoya.fold_4.fit.json deleted file mode 100644 index deb4f19893dbd7fe95fa56729334a17884cac2bf..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF139FFL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR889YWJ/cherimoya.fold_4.log b/ENCSR889YWJ/cherimoya.fold_4.log deleted file mode 100644 index 87951c9f3dc71d2d7d85833ee046f3a8285e0cd1..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2802 35.66202259063721 3.5228111743927 244.85691833496094 1.1213631629943848 222.05026245117188 0.13680730760097504 0.62899077 3.9914426803588867 True -1 5604 30.594700813293457 0.5682055950164795 173.2126922607422 0.7949990034103394 202.41598510742188 0.18125270307064056 0.7272666 2.2213451862335205 True -2 8406 30.513885736465454 0.7550499439239502 191.044677734375 0.5805193185806274 198.22682189941406 0.18852750957012177 0.74540293 1.3048639297485352 True -3 11208 30.458691835403442 0.5641705989837646 158.85092163085938 0.833247721195221 195.4185791015625 0.1942005604505539 0.75385594 1.1236977577209473 True -4 14010 30.532552003860474 0.5560624599456787 158.47312927246094 0.7933511734008789 193.9473114013672 0.19655992090702057 0.7637773 0.9903505444526672 True -5 16812 30.496575832366943 0.5591228008270264 110.42015075683594 0.6480872631072998 193.00665283203125 0.1969934105873108 0.77042353 0.8810444474220276 True -6 19614 30.53286576271057 1.4535236358642578 141.879150390625 0.6758095026016235 191.7401123046875 0.19974038004875183 0.7825617 0.7625272870063782 True -7 22416 30.900899648666382 33.14655613899231 158.9465789794922 0.6904033422470093 190.6431427001953 0.2017785757780075 0.7948369 0.6974396705627441 True -8 25218 30.705799102783203 0.6299943923950195 171.69166564941406 0.6458566188812256 190.4497833251953 0.20202413201332092 0.80125785 0.6591070294380188 True -9 28020 30.548258781433105 2.4491944313049316 149.8583984375 0.5196536183357239 189.49545288085938 0.20488347113132477 0.8106112 0.5951102375984192 True -10 30822 30.52307367324829 0.5689182281494141 152.23480224609375 0.6120953559875488 188.7482147216797 0.20671190321445465 0.8177222 0.5787246227264404 True -11 33624 30.474345445632935 0.5667843818664551 144.52838134765625 0.8163371086120605 188.5937957763672 0.20657384395599365 0.8226447 0.5555539131164551 True -12 36426 30.48143720626831 0.5646622180938721 192.54995727539062 0.7167561054229736 188.21231079101562 0.2079702466726303 0.8290226 0.5270652174949646 True -13 39228 30.477830410003662 0.5609152317047119 201.81057739257812 0.6240293979644775 187.34751892089844 0.21025902032852173 0.8331164 0.4937296211719513 True -14 42030 30.48810601234436 0.5671436786651611 132.75241088867188 0.46011102199554443 186.97113037109375 0.2112259417772293 0.83934504 0.47390949726104736 True -15 44832 30.558844804763794 0.5632591247558594 180.9407958984375 0.522038459777832 186.6833038330078 0.212001234292984 0.8426985 0.45509448647499084 True -16 47634 30.556217193603516 0.5674383640289307 122.2327651977539 0.38317930698394775 186.47987365722656 0.2116222232580185 0.84681857 0.4418178200721741 True -17 50436 30.737592458724976 0.5631265640258789 175.8775634765625 0.46936896443367004 186.27720642089844 0.21259236335754395 0.8459374 0.43428149819374084 False -18 53238 30.509238243103027 0.5770590305328369 157.20460510253906 0.3437681794166565 186.55177307128906 0.2119612842798233 0.84535336 0.4335085451602936 False -19 56040 30.83975052833557 0.5685896873474121 149.3845977783203 0.3648640513420105 186.74853515625 0.21135397255420685 0.8456758 0.4353601038455963 False diff --git a/ENCSR889YWJ/cherimoya.fold_4.performance.tsv b/ENCSR889YWJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6541470a5101140dfbe7e0d7f78cc2bdd2035f4f..0000000000000000000000000000000000000000 --- a/ENCSR889YWJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -186.47987365722656 0.5535358190536499 0.2116222232580185 0.05555569380521774 0.8468185663223267 0.7704563736915588 0.4418178200721741 \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_0.evaluate.json b/ENCSR890DWH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 105168ebb59a5c4200181929ca14e9c4b34c8635..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF344NXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_0.fit.json b/ENCSR890DWH/cherimoya.fold_0.fit.json deleted file mode 100644 index 70cae692276f201559de5ddd836032f8f7d81e92..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF344NXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_0.log b/ENCSR890DWH/cherimoya.fold_0.log deleted file mode 100644 index 81479f938a97ffdeb24650fd33e1a584d4e28cf7..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2263 29.659233331680298 3.5820260047912598 496.2113342285156 0.8653208017349243 786.7908325195312 0.606246829032898 0.5720545 9.978877067565918 True -1 4526 24.92683458328247 2.8804619312286377 494.8083801269531 0.6211557984352112 628.1192626953125 0.7154024243354797 0.61451703 3.2158613204956055 True -2 6789 24.932011127471924 0.4510338306427002 487.08575439453125 0.7399369478225708 588.4386596679688 0.7481837272644043 0.6197992 1.1493020057678223 True -3 9052 24.889375686645508 0.4164774417877197 487.4580078125 0.8142634630203247 579.5068359375 0.7555511593818665 0.6188938 0.8389185070991516 False -4 11315 24.780433177947998 0.42718076705932617 465.60498046875 0.7219701409339905 575.9264526367188 0.7585810422897339 0.6231148 0.7657015919685364 True -5 13578 24.464622497558594 0.43785715103149414 548.0767822265625 0.5493243932723999 572.9528198242188 0.7613828182220459 0.626838 0.7421731948852539 True -6 15841 24.472626209259033 0.4284391403198242 483.150146484375 0.786795973777771 569.8458862304688 0.7633832693099976 0.6340212 0.7425434589385986 True -7 18104 24.41518998146057 0.42897820472717285 503.2320556640625 0.6458268165588379 567.6022338867188 0.7663594484329224 0.6430646 0.7153312563896179 True -8 20367 24.434698820114136 0.4402017593383789 453.023681640625 0.7265325784683228 565.9559936523438 0.767957866191864 0.6404697 0.6852540969848633 False -9 22630 24.4250385761261 0.4414095878601074 418.8615417480469 0.7523726224899292 562.8257446289062 0.7704544067382812 0.65146476 0.6472223401069641 True -10 24893 24.485159397125244 0.4390594959259033 423.10040283203125 0.591620683670044 560.175537109375 0.7726573944091797 0.65930945 0.6310977935791016 True -11 27156 24.45172643661499 0.43177342414855957 510.4522399902344 0.7288857102394104 558.2260131835938 0.7745134234428406 0.66407716 0.610562264919281 True -12 29419 24.463032484054565 0.42113232612609863 453.9211120605469 0.4220052659511566 555.878173828125 0.7762057781219482 0.67546225 0.5904061794281006 True -13 31682 24.445930004119873 0.4402034282684326 487.3712158203125 0.4701455235481262 554.34423828125 0.7779380679130554 0.68522304 0.5686100721359253 True -14 33945 24.46249008178711 1.1254405975341797 471.45355224609375 0.45396918058395386 553.111083984375 0.7787653803825378 0.6928378 0.5561972856521606 True -15 36208 24.49825382232666 0.43679380416870117 465.7425537109375 0.4448982775211334 552.445068359375 0.7794615030288696 0.69586736 0.555774986743927 True -16 38471 24.461868286132812 0.4422800540924072 430.128173828125 0.40804392099380493 552.359130859375 0.7792894244194031 0.697564 0.5507288575172424 True -17 40734 24.396798610687256 0.4320223331451416 416.64892578125 0.4242963194847107 552.7094116210938 0.7787388563156128 0.6936395 0.5651101469993591 False -18 42997 24.394322633743286 0.42923521995544434 415.84381103515625 0.3968883156776428 553.2432250976562 0.7780053615570068 0.6883242 0.5772351026535034 False -19 45260 24.39906096458435 0.4351189136505127 415.13702392578125 0.30205345153808594 553.749755859375 0.7776314616203308 0.68372214 0.5891175866127014 False diff --git a/ENCSR890DWH/cherimoya.fold_0.performance.tsv b/ENCSR890DWH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 044c37e5e563ce95b242e6572a725c67c841991c..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -552.359130859375 0.18746943771839142 0.7792894244194031 0.3808782398700714 0.6975640058517456 0.6381426453590393 0.5507288575172424 \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_1.evaluate.json b/ENCSR890DWH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ef9d9199c9e7152b8c02a2964ece8f5ff48b4595..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF344NXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_1.fit.json b/ENCSR890DWH/cherimoya.fold_1.fit.json deleted file mode 100644 index 2a1b7f847142061b9d5af2e313036003bdb1fb10..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF344NXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_1.log b/ENCSR890DWH/cherimoya.fold_1.log deleted file mode 100644 index 056623f2747f97339cfe1b32952db645a88a8493..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2235 29.197715044021606 4.017116546630859 435.7803955078125 0.7604962587356567 881.243408203125 0.6094304919242859 0.5425131 11.632452964782715 True -1 4470 27.512432098388672 15.615119218826294 467.34808349609375 0.8352346420288086 693.4281616210938 0.7219784259796143 0.6041153 4.243338108062744 True -2 6705 24.822619915008545 0.6290590763092041 481.2913818359375 0.6864606142044067 643.6764526367188 0.7575164437294006 0.621451 1.4158223867416382 True -3 8940 24.752514600753784 0.6167941093444824 381.3681640625 0.6636489629745483 633.2632446289062 0.7638207674026489 0.61922824 0.9511265158653259 False -4 11175 24.62482786178589 19.427668809890747 457.81280517578125 0.7982164621353149 627.771484375 0.7679265141487122 0.62323534 0.8732927441596985 True -5 13410 24.719047784805298 1.4811537265777588 445.2280578613281 0.6532905101776123 625.1439208984375 0.7702693343162537 0.63016754 0.8336631655693054 True -6 15645 24.6567223072052 0.6116800308227539 497.7388916015625 0.8623195290565491 621.3102416992188 0.7738100290298462 0.6422642 0.8056542873382568 True -7 17880 24.67702054977417 0.6117477416992188 510.1719970703125 0.7736793160438538 618.3895263671875 0.7760216593742371 0.64891666 0.7492714524269104 True -8 20115 24.20518922805786 0.6113362312316895 407.7575988769531 0.5826244354248047 615.6080932617188 0.7789043188095093 0.65325904 0.7577666640281677 True -9 22350 24.12343740463257 0.5963232517242432 441.48699951171875 0.5907338857650757 611.4940185546875 0.7816583514213562 0.6612804 0.6872273087501526 True -10 24585 24.14949607849121 0.5887188911437988 484.62774658203125 0.48057669401168823 608.462890625 0.7839242815971375 0.6710991 0.6737936735153198 True -11 26820 24.2139892578125 1.1480412483215332 464.3540954589844 0.4521551728248596 605.8844604492188 0.7860745787620544 0.6853442 0.6378286480903625 True -12 29055 24.23299789428711 0.6002681255340576 579.4549560546875 0.5998949408531189 603.6911010742188 0.7879543900489807 0.6955217 0.6142756342887878 True -13 31290 24.212767362594604 0.6096019744873047 438.99200439453125 0.5156640410423279 601.6633911132812 0.7897122502326965 0.70472574 0.5912755727767944 True -14 33525 24.2542827129364 0.6118333339691162 531.8304443359375 0.3588150441646576 600.2785034179688 0.7906408905982971 0.7130466 0.565375030040741 True -15 35760 24.187586307525635 0.5951666831970215 366.6544189453125 0.3552449941635132 599.8516235351562 0.7909373641014099 0.7195957 0.5579872131347656 True -16 37995 24.20497751235962 1.3218379020690918 464.83892822265625 0.38786616921424866 600.1312866210938 0.7906981110572815 0.7185254 0.5644989013671875 False -17 40230 24.19428777694702 0.5972280502319336 442.9769592285156 0.3340997099876404 600.8839111328125 0.7899386882781982 0.7153402 0.5704022645950317 False -18 42465 24.219042778015137 0.5972557067871094 432.89227294921875 0.2541152536869049 601.8932495117188 0.7889857888221741 0.70897293 0.587353527545929 False -19 44700 24.13287091255188 0.60701584815979 391.63714599609375 0.31857916712760925 602.5704956054688 0.7884594202041626 0.70528483 0.5977463722229004 False diff --git a/ENCSR890DWH/cherimoya.fold_1.performance.tsv b/ENCSR890DWH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7d48f31f31a906a67bee3b5f6652f0ceee77a3bf..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -599.8516235351562 0.17574039101600647 0.7909374237060547 0.408975750207901 0.7195956707000732 0.6859034299850464 0.5579872131347656 \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_2.evaluate.json b/ENCSR890DWH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e581fc6445dd50a2bfe82313762da3570a2b4b5e..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF344NXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_2.fit.json b/ENCSR890DWH/cherimoya.fold_2.fit.json deleted file mode 100644 index cbbadfb244de6b7c0a70a1f6e3a617fcf74dacbf..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF344NXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_2.log b/ENCSR890DWH/cherimoya.fold_2.log deleted file mode 100644 index baa2147e05a35b89640e7ecb7dcb93f3fb692eff..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2410 31.248439073562622 4.800354242324829 562.1007690429688 0.7312621474266052 791.0069580078125 0.6134253740310669 0.5478617 10.333541870117188 True -1 4820 26.50567865371704 0.5333094596862793 471.0118103027344 0.6992424726486206 625.9368286132812 0.7247608304023743 0.62413573 3.7215633392333984 True -2 7230 26.512584924697876 0.47986340522766113 509.2818908691406 0.7394119501113892 598.61962890625 0.7462982535362244 0.64658636 1.1420332193374634 True -3 9640 26.471227169036865 0.47269272804260254 481.40594482421875 0.7281907796859741 587.8077392578125 0.7535949945449829 0.6454411 0.7580428719520569 False -4 12050 26.48739981651306 0.4665966033935547 469.113037109375 0.609477162361145 582.8941650390625 0.758275032043457 0.64612675 0.7117070555686951 False -5 14460 26.459425687789917 0.4700901508331299 455.41046142578125 0.8070425987243652 580.822265625 0.7600657939910889 0.6548819 0.7000225186347961 True -6 16870 26.397043228149414 0.46277570724487305 408.84808349609375 0.6062304377555847 578.75732421875 0.7622136473655701 0.65953267 0.6583501100540161 True -7 19280 26.442376852035522 0.4924793243408203 500.6308898925781 0.7054346799850464 575.57470703125 0.7649674415588379 0.66506845 0.6170288324356079 True -8 21690 27.061028718948364 2.4347450733184814 469.463623046875 0.6066973805427551 573.6097412109375 0.7666360139846802 0.6700721 0.5993118286132812 True -9 24100 26.49496030807495 0.468242883682251 521.85546875 0.6270251274108887 571.5360107421875 0.7683438658714294 0.6701816 0.5907015204429626 True -10 26510 26.435649394989014 0.4636869430541992 440.1172790527344 0.6890736222267151 568.9967651367188 0.7705099582672119 0.6799136 0.5850101709365845 True -11 28920 26.481959581375122 0.47835206985473633 447.5804443359375 0.5317452549934387 566.9505004882812 0.7725510597229004 0.6821832 0.5774032473564148 True -12 31330 26.51102924346924 0.4763908386230469 443.742919921875 0.47014522552490234 564.7451171875 0.7744123935699463 0.69271106 0.5805959701538086 True -13 33740 26.47930121421814 0.47754335403442383 468.0440368652344 0.42200666666030884 562.6990966796875 0.7764436602592468 0.7037058 0.5580819249153137 True -14 36150 26.458221197128296 3.674412965774536 434.43255615234375 0.631200909614563 560.7177124023438 0.7781399488449097 0.71215117 0.5335971713066101 True -15 38560 26.090787649154663 0.46808648109436035 449.81817626953125 0.4969702661037445 559.892822265625 0.7787482142448425 0.71918184 0.5241867303848267 True -16 40970 25.986753702163696 0.47267651557922363 465.0328369140625 0.3489845395088196 559.9876098632812 0.778680145740509 0.7182994 0.5291540622711182 False -17 43380 25.993754386901855 0.4649379253387451 491.5474853515625 0.3115132451057434 560.74072265625 0.7780687212944031 0.7169424 0.5365637540817261 False -18 45790 25.946022987365723 0.45810556411743164 455.6230773925781 0.2910706400871277 561.3598022460938 0.7773543000221252 0.7140078 0.5489082932472229 False -19 48200 26.006234884262085 0.46480846405029297 439.5732421875 0.2023809850215912 561.5762329101562 0.7768747806549072 0.7100425 0.5563859343528748 False diff --git a/ENCSR890DWH/cherimoya.fold_2.performance.tsv b/ENCSR890DWH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9327c5eb3967ded62c0e0a13a1e7062ec1d2506f..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -559.892822265625 0.18542855978012085 0.7787482142448425 0.3873489201068878 0.7191818356513977 0.6673073768615723 0.5241867303848267 \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_3.evaluate.json b/ENCSR890DWH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fc510f568db0397849078681fdd713c6218227c4..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF344NXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_3.fit.json b/ENCSR890DWH/cherimoya.fold_3.fit.json deleted file mode 100644 index fbec9115275fd8cb95e9f0d9884020dbfd8d0a80..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF344NXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_3.log b/ENCSR890DWH/cherimoya.fold_3.log deleted file mode 100644 index 7d8f2c1c55d271aebe05af1c1ae8ef695d159ca2..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2317 30.07639217376709 2.1113440990448 516.5855712890625 0.9493094086647034 763.4795532226562 0.6143752932548523 0.5286381 10.737163543701172 True -1 4634 25.570752382278442 7.730006456375122 544.721923828125 0.9489722847938538 607.2576904296875 0.7193657755851746 0.5989869 3.385631561279297 True -2 6951 25.502119302749634 0.4282660484313965 499.86688232421875 0.6410813331604004 580.8170776367188 0.7434656023979187 0.6216299 1.1298264265060425 True -3 9268 25.48736047744751 0.4188053607940674 608.3509521484375 0.806734561920166 571.0364379882812 0.750464677810669 0.62710154 0.778312087059021 True -4 11585 25.471973657608032 1.0399830341339111 500.21826171875 0.9211457967758179 567.1463623046875 0.7541056871414185 0.63402236 0.7036799788475037 True -5 13902 25.45793867111206 0.42267704010009766 483.5895690917969 0.7110588550567627 565.1553344726562 0.7560426592826843 0.6303843 0.7325307726860046 False -6 16219 25.48099684715271 0.42342352867126465 416.5986328125 0.3973597586154938 562.2542114257812 0.7585094571113586 0.6385311 0.6615588068962097 True -7 18536 25.433927536010742 2.485488176345825 488.5210266113281 0.6880422830581665 560.598876953125 0.7601333260536194 0.64119124 0.6258790493011475 True -8 20853 25.486913919448853 0.4254300594329834 499.3058776855469 0.5646340847015381 558.5847778320312 0.762398362159729 0.6484998 0.6151068806648254 True -9 23170 25.555209159851074 0.43786144256591797 446.0096130371094 0.582743763923645 555.43896484375 0.7651322484016418 0.65536517 0.6048291921615601 True -10 25487 25.480576038360596 0.49759936332702637 519.0721435546875 0.6369709968566895 553.9336547851562 0.766747236251831 0.66128397 0.6074405908584595 True -11 27804 25.53972339630127 9.613380670547485 488.4256896972656 0.5948513150215149 551.5460815429688 0.7691050171852112 0.6705706 0.5930484533309937 True -12 30121 25.58422303199768 0.43169569969177246 503.7396240234375 0.35793131589889526 550.0023803710938 0.7709220051765442 0.6786731 0.5810928344726562 True -13 32438 25.511664867401123 0.4401063919067383 485.55645751953125 0.8092246055603027 548.0512084960938 0.7727381587028503 0.68893754 0.564486026763916 True -14 34755 25.468528509140015 0.4158618450164795 445.28582763671875 0.501351535320282 546.892333984375 0.7737742066383362 0.69279814 0.5569838881492615 True -15 37072 25.526334762573242 2.0721375942230225 410.39007568359375 0.33733054995536804 546.5991821289062 0.7740203738212585 0.69747025 0.5631446838378906 True -16 39389 25.589937448501587 16.637890338897705 467.5937194824219 0.412067174911499 546.2794799804688 0.7742812633514404 0.69366556 0.5746766924858093 False -17 41706 25.851779460906982 0.43105030059814453 395.59326171875 0.41345542669296265 546.4876098632812 0.7737482786178589 0.6917975 0.5867123007774353 False -18 44023 25.679794311523438 0.42560553550720215 412.0649719238281 0.22651740908622742 547.1099243164062 0.7730627059936523 0.68592376 0.6069007515907288 False -19 46340 25.647703170776367 0.44312167167663574 458.9237976074219 0.20661213994026184 547.5400390625 0.7727221250534058 0.68075734 0.6154615879058838 False diff --git a/ENCSR890DWH/cherimoya.fold_3.performance.tsv b/ENCSR890DWH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3118cf9781cfba5e9d70cb5c4bd3aeb937e63ec1..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -546.5991821289062 0.1889568269252777 0.7740203738212585 0.37543150782585144 0.6974702477455139 0.6445602178573608 0.5631446838378906 \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_4.evaluate.json b/ENCSR890DWH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ee0bb7176f0e99dbf6325343e9f495d263eae3b6..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF344NXX.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_4.fit.json b/ENCSR890DWH/cherimoya.fold_4.fit.json deleted file mode 100644 index fd9134cc946727a09441e5049b69ee507ad60572..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF344NXX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR890DWH/cherimoya.fold_4.log b/ENCSR890DWH/cherimoya.fold_4.log deleted file mode 100644 index 8992ab4dd264bb006ab098dc31fe15af51bba7a5..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2340 30.477712869644165 3.651467800140381 500.3935852050781 0.8484093546867371 748.4723510742188 0.611092209815979 0.5640303 11.143138885498047 True -1 4680 25.71696376800537 0.6803081035614014 600.4893798828125 0.8541609048843384 593.4949340820312 0.7254239320755005 0.6161125 2.829195737838745 True -2 7020 25.74198341369629 0.8822484016418457 545.2320556640625 0.869394838809967 567.564453125 0.7478197813034058 0.63208675 0.9833990335464478 True -3 9360 25.7741641998291 0.4676051139831543 491.28411865234375 0.8159719109535217 559.7880249023438 0.7549793124198914 0.6295453 0.7139469385147095 False -4 11700 25.282474040985107 0.4539923667907715 535.0526733398438 0.6273683309555054 557.376220703125 0.7568467259407043 0.62316227 0.6429320573806763 False -5 14040 25.277755975723267 0.43861889839172363 482.1092529296875 0.7134439945220947 554.2432250976562 0.7597272992134094 0.6179708 0.7045305967330933 False -6 16380 25.215939044952393 1.2274806499481201 424.448486328125 0.8413145542144775 552.9580078125 0.7605701684951782 0.6306744 0.7649385333061218 False -7 18720 25.27483892440796 0.45606064796447754 478.3921203613281 0.6295148730278015 549.8134155273438 0.7635747790336609 0.6338323 0.664135754108429 True -8 21060 25.31813955307007 0.45673036575317383 496.3471984863281 0.580464243888855 547.225341796875 0.7657483816146851 0.64293474 0.6159811019897461 True -9 23400 25.313307762145996 0.4575467109680176 473.49395751953125 0.6791591644287109 545.3651123046875 0.7675865888595581 0.6487944 0.6106513738632202 True -10 25740 25.32705307006836 0.44851016998291016 489.4701843261719 0.6743714213371277 543.0451049804688 0.7696279883384705 0.6584287 0.5963561534881592 True -11 28080 25.27437949180603 2.1920645236968994 502.56622314453125 0.6670443415641785 541.795654296875 0.7710427045822144 0.66222465 0.5883983373641968 True -12 30420 25.332502603530884 0.455425500869751 482.26910400390625 0.5205945372581482 540.2119140625 0.7724440693855286 0.66918474 0.5804241895675659 True -13 32760 25.355651378631592 0.46259450912475586 423.7723693847656 0.7745496034622192 538.4307250976562 0.7738571166992188 0.68119603 0.5580319166183472 True -14 35100 25.388936758041382 0.4511892795562744 415.4423828125 0.3974865972995758 537.4373779296875 0.7753919959068298 0.6893879 0.5472257137298584 True -15 37440 25.353557109832764 0.4533100128173828 452.1507568359375 0.30956536531448364 536.7492065429688 0.7761567831039429 0.70007604 0.538855791091919 True -16 39780 25.357486963272095 2.2706735134124756 440.5260009765625 0.2541978061199188 536.6549072265625 0.7759228348731995 0.70214456 0.5371792912483215 True -17 42120 25.30978751182556 0.44344139099121094 445.75714111328125 0.28074294328689575 537.6124267578125 0.7750357985496521 0.7000543 0.551184892654419 False -18 44460 25.285309553146362 1.258819341659546 458.47247314453125 0.23543190956115723 538.1765747070312 0.7743384838104248 0.69239175 0.5644212365150452 False -19 46800 25.290315866470337 0.44764280319213867 383.211669921875 0.2667710483074188 538.58984375 0.773817241191864 0.6899267 0.5715358257293701 False diff --git a/ENCSR890DWH/cherimoya.fold_4.performance.tsv b/ENCSR890DWH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c3b71340bd3da97ae8393f89b2ea2a4b90ce5522..0000000000000000000000000000000000000000 --- a/ENCSR890DWH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -536.6549072265625 0.19011171162128448 0.7759227156639099 0.3736009895801544 0.7021445631980896 0.6416933536529541 0.5371792912483215 \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_0.evaluate.json b/ENCSR891VOV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7e4f8347faec5c88897678838f29d1ddc3b84e9c..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF580LPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_0.fit.json b/ENCSR891VOV/cherimoya.fold_0.fit.json deleted file mode 100644 index f5f49371af19bd9672b4f3aef3b5c82bbd7ea836..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF580LPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_0.log b/ENCSR891VOV/cherimoya.fold_0.log deleted file mode 100644 index 160441f36476b77f74baef38239d4395b1bdb9a6..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1808 23.629708290100098 3.283689260482788 187.36575317382812 0.9446429014205933 286.6003112792969 0.11031897366046906 0.5806525 7.09807014465332 True -1 3616 19.85792875289917 0.3711977005004883 210.44805908203125 1.1441774368286133 273.3723449707031 0.16413971781730652 0.6612821 3.8983895778656006 True -2 5424 19.895273447036743 0.35535621643066406 189.85780334472656 0.9274691343307495 261.6678161621094 0.19830138981342316 0.71905327 1.789596676826477 True -3 7232 19.846489191055298 1.3203649520874023 275.9122009277344 0.8884379267692566 258.1092529296875 0.20754918456077576 0.7590203 1.022046446800232 True -4 9040 19.814608335494995 0.38117408752441406 210.571533203125 0.6308567523956299 256.2165832519531 0.21153971552848816 0.7742927 0.8366180062294006 True -5 10848 19.832775592803955 0.35685038566589355 264.93194580078125 1.0942130088806152 255.44566345214844 0.21386712789535522 0.78050417 0.7486782073974609 True -6 12656 19.78808093070984 0.3577265739440918 236.2401885986328 0.5986745953559875 254.64157104492188 0.21557661890983582 0.7885434 0.6835168600082397 True -7 14464 19.838315725326538 1.3883681297302246 238.07559204101562 0.7068589925765991 254.2213134765625 0.21673764288425446 0.79151267 0.6594927906990051 True -8 16272 19.84094262123108 0.3587613105773926 197.05105590820312 0.6371968984603882 253.14605712890625 0.22058482468128204 0.7964707 0.6566072702407837 True -9 18080 19.82860255241394 0.36223411560058594 234.85748291015625 0.8270231485366821 253.00271606445312 0.2204216718673706 0.79744714 0.6322323083877563 True -10 19888 19.819846630096436 0.46862363815307617 177.11697387695312 0.5894695520401001 252.4949951171875 0.22202791273593903 0.8029242 0.6109321117401123 True -11 21696 19.828481912612915 0.3544127941131592 189.27545166015625 0.6634745001792908 251.86087036132812 0.2237672656774521 0.8081997 0.5911263227462769 True -12 23504 19.4452702999115 8.318328619003296 218.35394287109375 0.5756725072860718 251.25730895996094 0.22528931498527527 0.8126387 0.5683277249336243 True -13 25312 19.484824419021606 0.3650064468383789 184.59884643554688 0.4457557797431946 251.0315704345703 0.22609540820121765 0.8144613 0.5742679238319397 True -14 27120 19.498199462890625 0.3615388870239258 236.6627960205078 0.38069725036621094 250.47747802734375 0.22822313010692596 0.81609464 0.5681672692298889 True -15 28928 19.468065977096558 0.355832576751709 183.96710205078125 0.3749489188194275 250.80218505859375 0.22675079107284546 0.8176618 0.5633978247642517 True -16 30736 19.465572834014893 0.3605163097381592 160.59658813476562 0.4890061020851135 250.62643432617188 0.22720669209957123 0.8183074 0.5699336528778076 True -17 32544 19.45725107192993 0.3544905185699463 168.0045928955078 0.4572201669216156 251.0183868408203 0.2259221225976944 0.8167042 0.5798622965812683 False -18 34352 19.436692476272583 0.3490793704986572 135.77606201171875 0.40288227796554565 251.35540771484375 0.22524544596672058 0.8141216 0.5971891283988953 False -19 36160 19.399855852127075 0.35349106788635254 163.2158966064453 0.36143290996551514 251.61671447753906 0.22395102679729462 0.8126364 0.6093547344207764 False diff --git a/ENCSR891VOV/cherimoya.fold_0.performance.tsv b/ENCSR891VOV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 427ae92910a8b3e52457b3b12890639083290806..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.62643432617188 0.5299636721611023 0.22720669209957123 0.06441766768693924 0.8183073997497559 0.7936651110649109 0.5699336528778076 \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_1.evaluate.json b/ENCSR891VOV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5c068d298c6e2137e5c8030043973eb858fbac21..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF580LPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_1.fit.json b/ENCSR891VOV/cherimoya.fold_1.fit.json deleted file mode 100644 index 8d1d5ba899b44d3941b658cf119f66ac34fc1463..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF580LPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_1.log b/ENCSR891VOV/cherimoya.fold_1.log deleted file mode 100644 index 2af7dcada7b92b42f53cb85762e6e7ca170a4993..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1796 23.355781078338623 27.453835487365723 204.39759826660156 0.8969461917877197 343.76361083984375 0.12110253423452377 0.55734336 7.858838081359863 True -1 3592 20.040234565734863 0.5534896850585938 184.9276123046875 1.6639223098754883 326.6759033203125 0.18272744119167328 0.6837745 4.581047534942627 True -2 5388 19.78385829925537 11.437118768692017 160.0738983154297 0.7513474822044373 309.5794677734375 0.22592394053936005 0.75216347 2.053988456726074 True -3 7184 19.77529740333557 0.5306215286254883 172.64364624023438 0.66041499376297 306.21142578125 0.231757253408432 0.7755057 1.1462197303771973 True -4 8980 19.744462728500366 1.3009254932403564 139.52981567382812 0.7756563425064087 304.2456970214844 0.2367774099111557 0.78191686 1.0527561902999878 True -5 10776 19.772255420684814 0.5253243446350098 203.7044219970703 0.7420015931129456 303.8280944824219 0.23715965449810028 0.7890361 0.9719300270080566 True -6 12572 19.787116050720215 0.5290930271148682 224.9401092529297 0.7465610504150391 302.4453125 0.24133819341659546 0.7948615 0.8776566386222839 True -7 14368 19.72414517402649 0.5238416194915771 205.5587921142578 0.7073913216590881 302.09735107421875 0.24137845635414124 0.8001961 0.8151088356971741 True -8 16164 19.70390558242798 0.5244357585906982 249.5303955078125 0.5401706695556641 301.35687255859375 0.242784321308136 0.80276126 0.7838711738586426 True -9 17960 19.72837781906128 0.5276608467102051 253.22068786621094 0.9995933771133423 300.3733825683594 0.24586156010627747 0.80935806 0.7485091686248779 True -10 19756 19.70766568183899 0.5310978889465332 175.3807830810547 0.5896347761154175 299.0079345703125 0.24955877661705017 0.8135948 0.7042008638381958 True -11 21552 19.704846143722534 0.5210363864898682 190.96343994140625 0.8940026760101318 298.7536315917969 0.24940431118011475 0.8224537 0.6505542993545532 True -12 23348 19.99134349822998 0.5590462684631348 167.6096649169922 0.5807013511657715 297.98736572265625 0.25151440501213074 0.82551855 0.6295799016952515 True -13 25144 19.85639238357544 0.5444064140319824 250.6236572265625 0.8742737770080566 297.94488525390625 0.25115442276000977 0.83328444 0.6080601811408997 True -14 26940 19.834991455078125 0.5365068912506104 206.50198364257812 0.4117864668369293 297.43316650390625 0.25238093733787537 0.83936745 0.5748758912086487 True -15 28736 19.845714807510376 0.5237472057342529 253.39173889160156 0.47220271825790405 297.3704528808594 0.25221630930900574 0.8414244 0.571049153804779 True -16 30532 19.748980283737183 18.517170906066895 237.7920684814453 0.5812075138092041 298.2730712890625 0.24868199229240417 0.84424865 0.5683305263519287 True -17 32328 19.797757387161255 0.5275347232818604 212.07614135742188 0.30295151472091675 297.79400634765625 0.25125792622566223 0.8402169 0.5823008418083191 False -18 34124 19.810004472732544 0.5263454914093018 201.54583740234375 0.3960944712162018 298.2625732421875 0.24931427836418152 0.83604145 0.6009557247161865 False -19 35920 19.841537714004517 0.5220658779144287 206.05201721191406 0.3206706643104553 298.86474609375 0.24722309410572052 0.83437306 0.6108527779579163 False diff --git a/ENCSR891VOV/cherimoya.fold_1.performance.tsv b/ENCSR891VOV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4a4017a9e9ec10d1cf7de0dfd48da75403c754f5..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -298.2730712890625 0.5081212520599365 0.24868200719356537 0.08311819285154343 0.8442486524581909 0.825508177280426 0.5683305263519287 \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_2.evaluate.json b/ENCSR891VOV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f4bf4e9e09187b838e4c45768e7dea28f41c40ac..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF580LPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_2.fit.json b/ENCSR891VOV/cherimoya.fold_2.fit.json deleted file mode 100644 index bb52a453a81cd315a163b61b76e4058698ed867a..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF580LPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_2.log b/ENCSR891VOV/cherimoya.fold_2.log deleted file mode 100644 index 44c647226e2ad4a8c390996d727b53b2bfec8a30..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1927 24.989068031311035 3.485539674758911 244.28021240234375 0.8398208022117615 292.94647216796875 0.11420474201440811 0.5593689 6.234755039215088 True -1 3854 21.660679578781128 0.3874809741973877 225.52603149414062 1.023558259010315 276.5322570800781 0.17621488869190216 0.6784084 3.809049606323242 True -2 5781 21.451900720596313 0.3684353828430176 217.2116241455078 0.7687835693359375 264.1691589355469 0.20860499143600464 0.74826807 1.4195579290390015 True -3 7708 21.31791853904724 0.3637704849243164 252.8590087890625 0.793128490447998 260.97064208984375 0.21561577916145325 0.7591577 0.9592233896255493 True -4 9635 21.035001516342163 0.3660547733306885 208.82192993164062 0.9011520147323608 259.1974792480469 0.22051271796226501 0.76667637 0.8631834983825684 True -5 11562 21.01796817779541 0.359433650970459 238.6672821044922 0.7928451895713806 258.8099060058594 0.22117039561271667 0.7745742 0.8002959489822388 True -6 13489 21.065460681915283 0.3888568878173828 194.50982666015625 0.7730021476745605 258.3475646972656 0.22216801345348358 0.7758867 0.7719584703445435 True -7 15416 21.016835927963257 0.3735368251800537 252.72412109375 0.7716641426086426 257.4215393066406 0.22537468373775482 0.7824853 0.7293975949287415 True -8 17343 21.051525354385376 0.36983203887939453 213.42071533203125 0.6676800847053528 257.1263732910156 0.22595283389091492 0.7879852 0.7009234428405762 True -9 19270 21.042959690093994 0.8191878795623779 266.0185852050781 0.7285929918289185 255.8187713623047 0.23076891899108887 0.78820676 0.6779519319534302 True -10 21197 21.031545877456665 0.37865567207336426 213.02101135253906 0.6363644599914551 255.66770935058594 0.22986291348934174 0.7958151 0.6439419388771057 True -11 23124 21.043230533599854 0.37636733055114746 176.6126251220703 0.500556468963623 255.02484130859375 0.23223835229873657 0.7990197 0.6319979429244995 True -12 25051 21.035948276519775 0.5150771141052246 146.91342163085938 0.6101008653640747 254.60655212402344 0.23317337036132812 0.80486846 0.6081355810165405 True -13 26978 21.070274829864502 0.3715834617614746 210.06460571289062 0.8926237225532532 254.30343627929688 0.23244966566562653 0.81057703 0.5898349285125732 True -14 28905 21.07859492301941 0.3707590103149414 199.52374267578125 0.3700788915157318 253.85098266601562 0.23393183946609497 0.8150967 0.5760016441345215 True -15 30832 21.063889265060425 0.3736240863800049 154.29742431640625 0.48358994722366333 253.90663146972656 0.23386242985725403 0.8167608 0.5714479684829712 True -16 32759 21.05654740333557 0.37125587463378906 167.4697265625 0.3170170187950134 254.08213806152344 0.23258092999458313 0.81784403 0.5705285668373108 True -17 34686 21.087382316589355 0.37034130096435547 290.30810546875 0.5014207363128662 254.0599822998047 0.2332664281129837 0.815335 0.5811537504196167 False -18 36613 21.029216527938843 11.806535720825195 171.96771240234375 0.2726914584636688 254.51564025878906 0.2311617136001587 0.8135156 0.5933301448822021 False -19 38540 21.117345809936523 0.371657133102417 199.828369140625 0.29002025723457336 254.83749389648438 0.23058462142944336 0.8114439 0.6064530611038208 False diff --git a/ENCSR891VOV/cherimoya.fold_2.performance.tsv b/ENCSR891VOV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bb7905f06a0d09698f3c26c0cc282d98b2bb77f7..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -254.08213806152344 0.5265499949455261 0.23258090019226074 0.07243835926055908 0.817844033241272 0.8007388114929199 0.5705285668373108 \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_3.evaluate.json b/ENCSR891VOV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b311b5a007acd2acd1a67a21aea128957df99d14..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF580LPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_3.fit.json b/ENCSR891VOV/cherimoya.fold_3.fit.json deleted file mode 100644 index 463af9d580a31fe36e830583e7d51a67033277aa..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF580LPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_3.log b/ENCSR891VOV/cherimoya.fold_3.log deleted file mode 100644 index ab27a9408db1a0684923083a2ddf334427b56dd0..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1866 24.351388454437256 3.3609986305236816 227.60182189941406 1.1756527423858643 316.5609436035156 0.11679772287607193 0.55933034 7.629655361175537 True -1 3732 20.78208899497986 0.4046914577484131 169.96592712402344 0.8112874031066895 301.1257629394531 0.17801342904567719 0.64157635 5.023339748382568 True -2 5598 20.805419206619263 0.3822133541107178 243.2440185546875 0.8737874031066895 288.6722412109375 0.21070830523967743 0.71914554 2.41992449760437 True -3 7464 20.81717824935913 0.38157224655151367 225.58702087402344 0.9466536045074463 286.0284118652344 0.2162940949201584 0.73307276 1.5350345373153687 True -4 9330 20.756351709365845 0.3817322254180908 170.43984985351562 0.5918917655944824 285.1436462402344 0.21830801665782928 0.73695487 1.278239130973816 True -5 11196 20.745988368988037 0.3911168575286865 191.14308166503906 0.9182556867599487 284.4169006347656 0.22044406831264496 0.74447244 1.128129482269287 True -6 13062 20.711504697799683 0.3821225166320801 222.42498779296875 0.7413038015365601 282.8319091796875 0.2254880964756012 0.74917614 1.0742367506027222 True -7 14928 20.72816777229309 0.38543176651000977 208.2401123046875 1.0566697120666504 282.60797119140625 0.22608742117881775 0.76161087 1.0087637901306152 True -8 16794 20.717238664627075 0.3847823143005371 201.31423950195312 0.6034293174743652 282.4302062988281 0.22644223272800446 0.7618859 0.9812623262405396 True -9 18660 20.744660139083862 0.3880734443664551 213.20001220703125 0.8738483786582947 281.6331481933594 0.22867389023303986 0.7724756 0.9097502827644348 True -10 20526 20.71676254272461 0.37759828567504883 179.24392700195312 0.9209837913513184 281.04022216796875 0.23059314489364624 0.7824765 0.8411838412284851 True -11 22392 20.26984453201294 0.3789651393890381 174.11355590820312 0.6800470352172852 280.2931823730469 0.23207604885101318 0.7887718 0.8056531548500061 True -12 24258 20.306215047836304 0.379929780960083 181.4142608642578 0.696109414100647 279.84661865234375 0.23279516398906708 0.79453593 0.7396178245544434 True -13 26124 20.26717472076416 0.910538911819458 250.83624267578125 0.45875948667526245 279.4999084472656 0.23310963809490204 0.8021235 0.69403076171875 True -14 27990 20.302911520004272 0.3753345012664795 210.26116943359375 1.0107181072235107 278.91595458984375 0.23457194864749908 0.8104923 0.6684492826461792 True -15 29856 20.25785732269287 0.37865543365478516 184.20423889160156 0.6260123252868652 278.28326416015625 0.23662270605564117 0.8135631 0.6458908915519714 True -16 31722 20.28220772743225 0.3762946128845215 175.6428985595703 0.6010780334472656 278.6925048828125 0.23424047231674194 0.81589675 0.6485857963562012 True -17 33588 20.276047229766846 0.3777632713317871 195.4864501953125 0.3861175775527954 278.5628356933594 0.23501765727996826 0.8140719 0.6531050205230713 False -18 35454 20.25495982170105 0.3759174346923828 165.74766540527344 0.33367106318473816 278.6536865234375 0.2346048206090927 0.8106389 0.6679530143737793 False -19 37320 20.253644943237305 0.37941408157348633 186.5902099609375 0.2445695996284485 279.0737609863281 0.23339955508708954 0.8094359 0.6787939667701721 False diff --git a/ENCSR891VOV/cherimoya.fold_3.performance.tsv b/ENCSR891VOV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3ba63ec9a9e8e3fe92766d24cf1a41be56faefc2..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -278.6925048828125 0.5198731422424316 0.23424047231674194 0.07085412740707397 0.81589674949646 0.7953565716743469 0.6485857963562012 \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_4.evaluate.json b/ENCSR891VOV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b75faf18420a4d5272ee9c5c85603c0aab31e6b2..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF580LPC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_4.fit.json b/ENCSR891VOV/cherimoya.fold_4.fit.json deleted file mode 100644 index 1daa2b1fc61289ce64bf5a4bee22ebfb28a795ba..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF580LPC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR891VOV/cherimoya.fold_4.log b/ENCSR891VOV/cherimoya.fold_4.log deleted file mode 100644 index f8919aeaa1a1cc48c2d93227ea37124185f90217..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1863 24.003914833068848 3.312894821166992 175.56292724609375 0.9517924785614014 282.980712890625 0.10948891192674637 0.56768346 6.595977783203125 True -1 3726 20.518497943878174 0.346956729888916 220.74063110351562 0.8156064748764038 269.1657409667969 0.16789419949054718 0.67237663 4.188765048980713 True -2 5589 20.502673864364624 1.0710864067077637 221.02853393554688 0.7646013498306274 258.574462890625 0.19988557696342468 0.7162728 2.264836549758911 True -3 7452 20.490679025650024 0.3379690647125244 181.03231811523438 0.671688437461853 255.55760192871094 0.20604801177978516 0.7264331 1.440748691558838 True -4 9315 20.49748969078064 0.33817434310913086 180.73733520507812 0.7970468997955322 253.68310546875 0.209477037191391 0.73862225 1.1492602825164795 True -5 11178 20.51503896713257 0.3342933654785156 195.78958129882812 0.9641518592834473 253.3706512451172 0.209132581949234 0.7502504 1.0672358274459839 True -6 13041 20.522350311279297 0.33673572540283203 196.06640625 0.729123592376709 251.7729949951172 0.21503832936286926 0.7573884 0.9792317748069763 True -7 14904 20.496506929397583 0.3372926712036133 184.3442840576172 0.8481281995773315 251.43731689453125 0.21483048796653748 0.76103467 0.9074320793151855 True -8 16767 20.501041889190674 0.3384873867034912 233.99972534179688 0.6444963216781616 250.24093627929688 0.21876195073127747 0.7717307 0.8416171669960022 True -9 18630 20.439536333084106 0.3346133232116699 250.2308807373047 0.7261725664138794 250.06307983398438 0.21925963461399078 0.777775 0.8050025701522827 True -10 20493 20.44406008720398 0.3385603427886963 191.85958862304688 0.6180115938186646 249.65037536621094 0.21970750391483307 0.78272134 0.7688208818435669 True -11 22356 20.45744562149048 0.3355720043182373 157.7621612548828 0.8317857980728149 249.32794189453125 0.22036689519882202 0.7880907 0.7288215160369873 True -12 24219 20.446760654449463 0.3340635299682617 224.3187713623047 0.857822597026825 248.3765411376953 0.22372455894947052 0.7935035 0.6935901641845703 True -13 26082 20.472224473953247 0.3378322124481201 217.32542419433594 0.5874959230422974 248.17820739746094 0.2235935479402542 0.8017303 0.6533344388008118 True -14 27945 20.463709831237793 0.339155912399292 200.8614044189453 0.45711416006088257 248.15951538085938 0.222970649600029 0.80612 0.6299149394035339 True -15 29808 20.469987869262695 0.347027063369751 192.48733520507812 0.4957892894744873 248.15432739257812 0.22301720082759857 0.8060528 0.6191156506538391 False -16 31671 20.44737434387207 0.33928537368774414 208.74139404296875 0.3683663010597229 247.68980407714844 0.22429761290550232 0.8074594 0.612831175327301 True -17 33534 20.484564304351807 0.3450298309326172 261.41552734375 0.28997132182121277 248.5689697265625 0.22127798199653625 0.80638754 0.6150478720664978 False -18 35397 20.492586374282837 0.34256958961486816 245.52403259277344 0.40894728899002075 248.7018280029297 0.22152939438819885 0.80379987 0.6259152889251709 False -19 37260 20.488272190093994 0.34097743034362793 178.26341247558594 0.3045176863670349 248.78407287597656 0.22136010229587555 0.8037219 0.6313802599906921 False diff --git a/ENCSR891VOV/cherimoya.fold_4.performance.tsv b/ENCSR891VOV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 467aaf60a3f83713e3901a82ba02777464ccc66f..0000000000000000000000000000000000000000 --- a/ENCSR891VOV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -247.68980407714844 0.5321311354637146 0.2242976427078247 0.07151318341493607 0.8074594140052795 0.7858145833015442 0.612831175327301 \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_0.evaluate.json b/ENCSR895GSY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index bba662cc5ebe2c26c0cf5b4aa1bb5d419aacd189..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871ELO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_0.fit.json b/ENCSR895GSY/cherimoya.fold_0.fit.json deleted file mode 100644 index 66a95d3ce2817e97fb7d53a5ca459d6def7dcfcb..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF871ELO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_0.log b/ENCSR895GSY/cherimoya.fold_0.log deleted file mode 100644 index cf365460cb64be553eac7b592c753f30401424d4..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 34.287718057632446 4.099164009094238 694.21875 0.4301024079322815 1124.94482421875 0.30496057868003845 0.71913785 6.714602470397949 True -1 5508 30.344683170318604 0.5870912075042725 842.1400146484375 0.6521110534667969 956.523193359375 0.3826298117637634 0.7847101 1.9819062948226929 True -2 8262 30.435344219207764 0.5691604614257812 712.5975341796875 0.6003215312957764 936.6376953125 0.3909124732017517 0.79149365 1.147418737411499 True -3 11016 30.330626487731934 0.5600183010101318 782.892822265625 0.5366249084472656 924.5691528320312 0.3958456516265869 0.80268747 0.950175940990448 True -4 13770 30.384103775024414 6.335217237472534 939.02294921875 0.4146813750267029 916.9447631835938 0.3995729982852936 0.81161135 0.892068088054657 True -5 16524 30.536783933639526 0.56884765625 870.2171020507812 0.4802810549736023 910.2673950195312 0.403216153383255 0.8174741 0.7352781891822815 True -6 19278 30.49029016494751 0.5851130485534668 908.2702026367188 0.32745426893234253 907.491943359375 0.404572069644928 0.8235476 0.7113865613937378 True -7 22032 30.456902980804443 0.5834059715270996 988.9334716796875 0.7004067897796631 902.3504638671875 0.4072294235229492 0.8275324 0.7392345070838928 True -8 24786 30.44550895690918 1.4400370121002197 775.1171875 0.7269593477249146 895.4071044921875 0.4114161431789398 0.83199674 0.5924597382545471 True -9 27540 30.434348106384277 0.5801692008972168 769.5826416015625 0.39880186319351196 892.10009765625 0.41379398107528687 0.8357784 0.5667596459388733 True -10 30294 30.13769841194153 0.5606677532196045 874.244140625 0.4070713520050049 888.510009765625 0.41463759541511536 0.8388542 0.5855305790901184 True -11 33048 29.76580238342285 0.5588419437408447 716.7696533203125 0.3142193853855133 882.03662109375 0.41885828971862793 0.8464896 0.48246362805366516 True -12 35802 29.958842992782593 0.5706350803375244 736.0936889648438 0.3960449695587158 877.7103881835938 0.4204479455947876 0.85278666 0.4250444769859314 True -13 38556 29.956097841262817 0.5752394199371338 817.8011474609375 0.3623352348804474 871.55029296875 0.4234175682067871 0.85903466 0.38956740498542786 True -14 41310 29.91398000717163 0.5689513683319092 654.0816650390625 0.35449090600013733 870.3926391601562 0.42350026965141296 0.8631588 0.3558482825756073 True -15 44064 29.90682888031006 0.559436559677124 608.3702392578125 0.7748413681983948 868.0825805664062 0.4245201051235199 0.8684458 0.3306664228439331 True -16 46818 29.911202907562256 0.5664365291595459 906.7603149414062 0.21247804164886475 866.4481811523438 0.42496204376220703 0.87150574 0.3170354664325714 True -17 49572 29.887765645980835 0.565598726272583 689.216064453125 0.30592525005340576 867.1109008789062 0.424173504114151 0.87368083 0.3066082298755646 True -18 52326 29.909385204315186 0.5593516826629639 659.7315673828125 0.26573050022125244 867.6770629882812 0.4247654676437378 0.87451875 0.3040114641189575 True -19 55080 29.89282202720642 1.3248391151428223 727.0997314453125 0.24586813151836395 867.00537109375 0.42576804757118225 0.8750152 0.30396682024002075 True diff --git a/ENCSR895GSY/cherimoya.fold_0.performance.tsv b/ENCSR895GSY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 0492eeb6b06f74117bc38d67873fbcb43823c48d..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -867.00537109375 0.3798452615737915 0.42576804757118225 0.16948045790195465 0.8750151991844177 0.8358769416809082 0.30396682024002075 \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_1.evaluate.json b/ENCSR895GSY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5db9218e1b64c84bc1d4347e76aa85f669aa8559..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871ELO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_1.fit.json b/ENCSR895GSY/cherimoya.fold_1.fit.json deleted file mode 100644 index 6d98bba26697d1dc4aa09785039e4b66a1354974..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF871ELO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_1.log b/ENCSR895GSY/cherimoya.fold_1.log deleted file mode 100644 index e94eb098746748f03e12a07e8e4dd4408f5bd5f4..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2686 37.552950859069824 3.8677525520324707 683.247314453125 0.6255677938461304 1338.8489990234375 0.30481308698654175 0.7324511 7.438717842102051 True -1 5372 29.646086931228638 0.7530245780944824 840.25 0.40091148018836975 1144.8924560546875 0.38748809695243835 0.79464436 2.5489816665649414 True -2 8058 29.652514934539795 0.7276923656463623 832.0606689453125 0.563819408416748 1103.768798828125 0.3994462788105011 0.8104997 1.4800372123718262 True -3 10744 29.58069682121277 1.0494167804718018 858.3281860351562 0.6257326602935791 1083.0926513671875 0.4088563024997711 0.81388366 1.2163934707641602 True -4 13430 29.62574315071106 2.585196018218994 911.587646484375 0.6652684211730957 1072.480712890625 0.41181516647338867 0.8236757 0.9635710716247559 True -5 16116 29.62710666656494 0.7185952663421631 866.3185424804688 0.6879721283912659 1064.296875 0.414261132478714 0.8273573 0.706364631652832 True -6 18802 29.581268548965454 0.7198560237884521 738.1837158203125 0.48253732919692993 1056.7960205078125 0.4187917709350586 0.8342421 0.6397772431373596 True -7 21488 29.578165769577026 0.7189257144927979 668.10498046875 0.4063369631767273 1051.454833984375 0.42070886492729187 0.8413557 0.6377174854278564 True -8 24174 29.585903644561768 0.7261292934417725 657.9144287109375 0.4035065174102783 1039.6123046875 0.4260548949241638 0.84856194 0.5517972111701965 True -9 26860 29.61229133605957 0.7238836288452148 698.7081298828125 0.4459671974182129 1038.91943359375 0.4255070984363556 0.8540534 0.5516771674156189 True -10 29546 29.604971408843994 21.648513793945312 767.1947021484375 0.5133353471755981 1032.12255859375 0.42873266339302063 0.85772294 0.5186952948570251 True -11 32232 30.187973260879517 0.7244551181793213 852.2530517578125 0.3438743054866791 1029.6807861328125 0.42942681908607483 0.86213833 0.477670282125473 True -12 34918 29.160009622573853 0.7243986129760742 726.1534423828125 0.4628974497318268 1019.2698364257812 0.43441686034202576 0.8683389 0.42760103940963745 True -13 37604 29.19403862953186 0.7209169864654541 749.1389770507812 0.4517694115638733 1008.0101928710938 0.44159188866615295 0.8742548 0.4044550359249115 True -14 40290 29.04556369781494 0.7185194492340088 702.133056640625 0.47378289699554443 1010.5687866210938 0.4380367696285248 0.8778009 0.37934696674346924 True -15 42976 29.070138692855835 0.714881420135498 680.7418212890625 0.30749011039733887 1009.2219848632812 0.43806588649749756 0.88463664 0.3467399775981903 True -16 45662 29.089219570159912 0.7253627777099609 651.0169067382812 0.30412769317626953 1002.6405029296875 0.44271525740623474 0.88735163 0.32890573143959045 True -17 48348 29.08208918571472 0.7537815570831299 804.9534912109375 0.2635851502418518 1004.2589111328125 0.4407956898212433 0.8881147 0.3204588294029236 True -18 51034 29.333771228790283 0.7330021858215332 609.9139404296875 0.22695669531822205 1003.1741943359375 0.4418443441390991 0.8902428 0.315225750207901 True -19 53720 29.11237931251526 0.7137892246246338 633.2682495117188 0.27708718180656433 1002.4164428710938 0.4425766170024872 0.88780534 0.3169637620449066 False diff --git a/ENCSR895GSY/cherimoya.fold_1.performance.tsv b/ENCSR895GSY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7cdf8726b29c2358cab1b9f6eb9b597d38ffd46e..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1003.1741943359375 0.36518311500549316 0.4418443441390991 0.19182436168193817 0.8902428150177002 0.8712813854217529 0.315225750207901 \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_2.evaluate.json b/ENCSR895GSY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9068b647f36c1da183b4583dd9931db3c54aee84..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871ELO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_2.fit.json b/ENCSR895GSY/cherimoya.fold_2.fit.json deleted file mode 100644 index 9fb510f6b08fca5d69c54baec865cb937935f86b..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF871ELO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_2.log b/ENCSR895GSY/cherimoya.fold_2.log deleted file mode 100644 index c7d4e0bab9e3e6266109cd9f0434354be434d944..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 35.64091467857361 5.068939447402954 870.9852905273438 0.7118625044822693 1193.4696044921875 0.3064034879207611 0.7175738 5.802734375 True -1 5770 31.87056255340576 0.5918581485748291 719.553466796875 0.5480397939682007 1015.3135375976562 0.38186943531036377 0.7859741 1.591201663017273 True -2 8655 31.854907989501953 0.5626659393310547 842.61474609375 0.5260896682739258 992.38671875 0.39049702882766724 0.79610306 0.8911566734313965 True -3 11540 31.833972454071045 0.5613815784454346 785.39892578125 0.6102005839347839 983.7835083007812 0.39516112208366394 0.80144274 0.8108552694320679 True -4 14425 31.828340530395508 0.5488920211791992 780.88037109375 0.7159225940704346 977.7891845703125 0.3986349403858185 0.80838144 0.8743711709976196 True -5 17310 31.814152240753174 0.55403733253479 707.6787719726562 0.5197954177856445 968.3213500976562 0.4034286141395569 0.817582 0.6742585897445679 True -6 20195 31.768451929092407 0.5594465732574463 916.1605224609375 0.472111314535141 960.6507568359375 0.40717068314552307 0.82133436 0.6268725991249084 True -7 23080 31.773247480392456 0.558295726776123 638.9279174804688 0.42481017112731934 958.56884765625 0.40716353058815 0.8268493 0.5668848752975464 True -8 25965 31.761724710464478 1.3814795017242432 760.5305786132812 0.6215789318084717 951.1455688476562 0.41199544072151184 0.8300261 0.5440851449966431 True -9 28850 31.81606912612915 1.0025033950805664 828.642578125 0.6192572712898254 946.497314453125 0.4133787453174591 0.8362318 0.5422040224075317 True -10 31735 31.891265869140625 0.825127363204956 775.659423828125 0.5131728649139404 943.6294555664062 0.41445210576057434 0.8417116 0.5200355648994446 True -11 34620 31.84889817237854 2.9626305103302 661.2280883789062 0.4547964930534363 937.1416015625 0.41753584146499634 0.846695 0.46471449732780457 True -12 37505 31.617777347564697 0.5549745559692383 666.524169921875 0.31286147236824036 934.409912109375 0.41900700330734253 0.85139203 0.43148767948150635 True -13 40390 31.263896226882935 0.5537641048431396 765.3465576171875 0.3981366753578186 928.0545654296875 0.4228643774986267 0.85618806 0.40164923667907715 True -14 43275 31.239157915115356 0.5537853240966797 657.134765625 0.42025864124298096 926.6986694335938 0.4214124083518982 0.8606831 0.3678622841835022 True -15 46160 31.27899479866028 0.5518825054168701 667.2185668945312 0.34132346510887146 924.1943359375 0.42287012934684753 0.8659546 0.3465549051761627 True -16 49045 31.20472526550293 0.5581955909729004 664.1485595703125 0.256194144487381 919.34033203125 0.4271354377269745 0.868421 0.33209314942359924 True -17 51930 31.19855499267578 0.5526041984558105 684.236328125 0.33200547099113464 923.1553344726562 0.4232432544231415 0.8704474 0.324065238237381 True -18 54815 31.399796724319458 0.5662550926208496 718.44677734375 0.2699287235736847 924.02783203125 0.42304977774620056 0.8708583 0.32116684317588806 True -19 57700 31.187740564346313 0.5507149696350098 640.9631958007812 0.3685598075389862 922.6666259765625 0.42413967847824097 0.8686523 0.321509450674057 False diff --git a/ENCSR895GSY/cherimoya.fold_2.performance.tsv b/ENCSR895GSY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ce3c5e0667a2656ce0562dfcfadf439c188ae791..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -924.02783203125 0.3781130313873291 0.4230497181415558 0.17376869916915894 0.8708583116531372 0.84278404712677 0.32116684317588806 \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_3.evaluate.json b/ENCSR895GSY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 01b5438e3b652907da51ea05fa780288ef716ff7..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871ELO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_3.fit.json b/ENCSR895GSY/cherimoya.fold_3.fit.json deleted file mode 100644 index a34d91d27cd7ef71a6b0f8c85305d81f3cc63671..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF871ELO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_3.log b/ENCSR895GSY/cherimoya.fold_3.log deleted file mode 100644 index 55a56862708708cdfebd52df0309ec6c83a6e4c9..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 34.41539931297302 3.7545347213745117 832.3901977539062 0.6596603393554688 1085.7596435546875 0.3103175163269043 0.7153349 8.94003963470459 True -1 5490 30.38241410255432 0.5624969005584717 982.0465087890625 0.7640864849090576 921.8993530273438 0.3882324695587158 0.79246503 2.1657516956329346 True -2 8235 30.38100266456604 0.5380785465240479 808.656494140625 0.8637104034423828 907.4784545898438 0.3934022784233093 0.79413503 1.325046420097351 True -3 10980 30.366064310073853 0.5332934856414795 844.3327026367188 0.444658100605011 893.7565307617188 0.39992332458496094 0.8108441 1.131980299949646 True -4 13725 30.342308044433594 0.5368180274963379 652.912841796875 0.4588488042354584 888.8761596679688 0.40215206146240234 0.8186286 0.9679018259048462 True -5 16470 31.30560612678528 0.545767068862915 827.984619140625 0.542181134223938 884.2615356445312 0.40313902497291565 0.82105005 0.6734927296638489 True -6 19215 30.34888243675232 0.5444750785827637 623.7330322265625 0.5025661587715149 878.8323364257812 0.4060114920139313 0.82622695 0.6007769107818604 True -7 21960 30.361262559890747 0.5458049774169922 856.5568237304688 0.4543282091617584 874.1378173828125 0.40909749269485474 0.83054805 0.6250624656677246 True -8 24705 30.250613689422607 0.5274500846862793 790.8717651367188 0.4783177971839905 869.411376953125 0.41157543659210205 0.8338665 0.5517778396606445 True -9 27450 29.85424494743347 0.5376071929931641 855.68310546875 0.38804006576538086 865.0177612304688 0.4139387011528015 0.83772975 0.5072004199028015 True -10 30195 29.76002073287964 0.5358366966247559 675.10009765625 0.3833276927471161 859.7852783203125 0.4178332984447479 0.8429589 0.48309293389320374 True -11 32940 29.73022150993347 0.5324602127075195 829.1619262695312 0.4168073832988739 856.0488891601562 0.418802410364151 0.8504594 0.43119168281555176 True -12 35685 29.77944827079773 0.5413737297058105 810.7196655273438 0.2555413544178009 853.2039184570312 0.419729083776474 0.8549892 0.41327252984046936 True -13 38430 29.77679181098938 2.154226779937744 900.069580078125 0.6617310643196106 852.80615234375 0.41920098662376404 0.859327 0.3936235010623932 True -14 41175 29.776177644729614 0.5413975715637207 694.3409423828125 0.31035906076431274 845.6725463867188 0.42409366369247437 0.86453444 0.37092289328575134 True -15 43920 29.770946979522705 0.5252084732055664 693.5560913085938 0.31001168489456177 843.4430541992188 0.4247150123119354 0.87006086 0.3432632088661194 True -16 46665 29.801223278045654 0.5236554145812988 751.1803588867188 0.30927571654319763 842.2608642578125 0.42556488513946533 0.8730517 0.3287271559238434 True -17 49410 29.769885063171387 0.5221073627471924 756.8474731445312 0.21413013339042664 841.2526245117188 0.4262295961380005 0.8757142 0.3176288902759552 True -18 52155 30.011587858200073 0.520313024520874 690.7783203125 0.2225022315979004 842.9071655273438 0.4248010516166687 0.8749611 0.31527939438819885 False -19 54900 30.214905738830566 19.363613605499268 700.8301391601562 0.3399856686592102 843.5302734375 0.42453646659851074 0.8751354 0.31632745265960693 False diff --git a/ENCSR895GSY/cherimoya.fold_3.performance.tsv b/ENCSR895GSY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1af484aab26601ea924923cdc1676918d7045d04..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -841.2526245117188 0.3798636794090271 0.4262295961380005 0.1661883294582367 0.8757141828536987 0.8386306166648865 0.3176288902759552 \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_4.evaluate.json b/ENCSR895GSY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4adeb53c40891d5426114de510788e12d7cd4d7b..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF871ELO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_4.fit.json b/ENCSR895GSY/cherimoya.fold_4.fit.json deleted file mode 100644 index c82ef2d7539c9179ceeafd0b54978311b850c7e9..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF871ELO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895GSY/cherimoya.fold_4.log b/ENCSR895GSY/cherimoya.fold_4.log deleted file mode 100644 index 77246fe348e5451207a004e2c23b35f1b6a7df97..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2808 34.869633436203 2.778775930404663 818.0835571289062 0.566706657409668 1003.33544921875 0.2952723801136017 0.7106203 7.317447185516357 True -1 5616 31.031906366348267 0.563744306564331 599.1327514648438 0.7125940918922424 872.6294555664062 0.3692229688167572 0.7728278 1.8189677000045776 True -2 8424 30.979069232940674 0.5532131195068359 576.9755859375 0.49924910068511963 850.6585083007812 0.3777766227722168 0.7831464 0.8228261470794678 True -3 11232 30.90271806716919 0.5494041442871094 649.7296142578125 0.3749644160270691 836.794921875 0.38292741775512695 0.79470634 0.5748322010040283 True -4 14040 30.909074783325195 2.560450553894043 659.6717529296875 0.5486993789672852 831.6605224609375 0.386140376329422 0.80282414 0.5675336718559265 True -5 16848 30.5007381439209 0.5506598949432373 671.910400390625 0.5010766983032227 824.8134155273438 0.3899630308151245 0.8070213 0.5425814986228943 True -6 19656 30.349554538726807 0.5459811687469482 811.7835693359375 0.3525207042694092 822.132080078125 0.39128220081329346 0.81381077 0.5190026164054871 True -7 22464 30.370275735855103 0.5417838096618652 765.229736328125 0.5077056288719177 818.2545776367188 0.39322417974472046 0.8185929 0.5228171944618225 True -8 25272 30.361866235733032 0.5580763816833496 755.4912109375 0.4427137076854706 815.118408203125 0.39543911814689636 0.8196777 0.48979055881500244 True -9 28080 30.64333462715149 12.148890733718872 616.604736328125 0.319648802280426 810.1156005859375 0.3992132842540741 0.82776254 0.4803198277950287 True -10 30888 30.368084192276 0.558652400970459 661.026611328125 0.28285014629364014 806.5511474609375 0.4008543789386749 0.83440596 0.479915589094162 True -11 33696 30.39623737335205 0.5500922203063965 563.2603759765625 0.37415093183517456 804.6741943359375 0.4010494649410248 0.83827883 0.4440624713897705 True -12 36504 30.360677003860474 0.5471396446228027 706.8599243164062 0.3617878258228302 799.68994140625 0.40529271960258484 0.8452982 0.40803852677345276 True -13 39312 30.401123523712158 0.5509090423583984 761.6775512695312 0.4191588759422302 795.4765014648438 0.4080868065357208 0.85027874 0.3722464144229889 True -14 42120 30.359774827957153 1.729990005493164 544.951416015625 0.3356844186782837 792.807373046875 0.40941035747528076 0.85599655 0.3453366756439209 True -15 44928 30.41766619682312 1.4915530681610107 694.8065185546875 0.2779199481010437 790.9823608398438 0.4108482599258423 0.86067164 0.3198099136352539 True -16 47736 30.463729858398438 0.9703705310821533 686.6908569335938 0.2859354317188263 792.7612915039062 0.40893110632896423 0.8650483 0.30413469672203064 True -17 50544 30.36574673652649 0.5728826522827148 703.7059326171875 0.3130301237106323 792.2567138671875 0.4091980457305908 0.8687311 0.29261863231658936 True -18 53352 30.36347270011902 0.5535845756530762 695.8934326171875 0.38210421800613403 791.166015625 0.41073229908943176 0.86838216 0.28888586163520813 False -19 56160 30.351253271102905 0.5538482666015625 765.693359375 0.24725711345672607 792.2081298828125 0.4090562164783478 0.8677874 0.28860408067703247 False diff --git a/ENCSR895GSY/cherimoya.fold_4.performance.tsv b/ENCSR895GSY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index cd468d2ed8a0ec7d2fc4016f8f1530d4624ae42d..0000000000000000000000000000000000000000 --- a/ENCSR895GSY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -792.2567138671875 0.3930787444114685 0.4091980457305908 0.1548333317041397 0.8687310814857483 0.826266348361969 0.29261863231658936 \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_0.evaluate.json b/ENCSR895KTN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ba88d60b624b6c8e2cbf7c60c745fef3f9007db2..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373QLZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_0.fit.json b/ENCSR895KTN/cherimoya.fold_0.fit.json deleted file mode 100644 index 2ecee0e2a04bb6f5b8a33f4a36d404298d2f6ff4..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF373QLZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_0.log b/ENCSR895KTN/cherimoya.fold_0.log deleted file mode 100644 index d055e384591a6b1bb7515ce3c69256f106c86c6b..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 34.95282244682312 3.9449610710144043 1254.64990234375 0.5847376585006714 1966.051513671875 0.33162233233451843 0.6608446 12.171045303344727 True -1 5560 30.231614589691162 0.5421464443206787 1206.406982421875 0.9538078904151917 1574.6292724609375 0.4523315727710724 0.7306515 3.600696086883545 True -2 8340 30.19738507270813 0.5165507793426514 1344.1363525390625 0.6281346678733826 1530.1107177734375 0.46372729539871216 0.74502116 1.874467134475708 True -3 11120 30.07947564125061 2.7803444862365723 950.2870483398438 0.8423823118209839 1495.2197265625 0.47423264384269714 0.75987905 1.7119357585906982 True -4 13900 29.619133710861206 0.5144705772399902 906.4923095703125 0.7471935749053955 1462.6141357421875 0.48366180062294006 0.7756703 1.5365272760391235 True -5 16680 29.754838466644287 0.5231881141662598 1008.3082275390625 0.57530677318573 1433.64794921875 0.4933423399925232 0.7852391 1.2284280061721802 True -6 19460 29.586626768112183 0.5036177635192871 985.6991577148438 0.7168283462524414 1415.7677001953125 0.5007752776145935 0.79130405 1.2034755945205688 True -7 22240 29.813936471939087 0.526853084564209 1084.2080078125 0.6920454502105713 1405.2874755859375 0.5041019320487976 0.7967469 1.1093182563781738 True -8 25020 29.636435508728027 0.5028555393218994 1081.20654296875 0.8814219832420349 1391.3076171875 0.508440375328064 0.8001929 0.9140945672988892 True -9 27800 29.588371753692627 17.62663960456848 1383.66455078125 0.6833117008209229 1384.724609375 0.5109893083572388 0.8031796 0.7658447623252869 True -10 30580 29.91276454925537 0.5060663223266602 1039.1484375 0.5364784002304077 1372.2100830078125 0.5163607001304626 0.80656785 0.7163800001144409 True -11 33360 30.183404445648193 2.025256872177124 1137.29541015625 0.5471420884132385 1363.6502685546875 0.5195247530937195 0.8128711 0.6455513834953308 True -12 36140 29.665810108184814 0.503352165222168 1153.900634765625 0.5687373876571655 1356.777587890625 0.5199236273765564 0.817179 0.5734895467758179 True -13 38920 30.425007343292236 0.5180861949920654 935.5584106445312 0.34103646874427795 1344.9808349609375 0.5233892202377319 0.82287747 0.5087466835975647 True -14 41700 29.786227703094482 0.5095100402832031 1074.178466796875 0.33415237069129944 1335.621826171875 0.5271008014678955 0.82786644 0.4795982837677002 True -15 44480 29.682442903518677 0.5134665966033936 1100.68994140625 0.4876737594604492 1330.15869140625 0.5290331840515137 0.8340791 0.4463512897491455 True -16 47260 29.645326852798462 0.4987304210662842 1065.08984375 0.3075783848762512 1318.4178466796875 0.5326412320137024 0.8395322 0.42146825790405273 True -17 50040 29.637864589691162 0.510673999786377 802.1051635742188 0.3267488479614258 1320.06201171875 0.5309925079345703 0.8403776 0.4122273325920105 True -18 52820 29.6476047039032 0.534867525100708 936.2742919921875 0.53537917137146 1320.1300048828125 0.530838131904602 0.84183353 0.4099256694316864 True -19 55600 29.63529896736145 0.51615309715271 959.2728881835938 0.46122485399246216 1320.0531005859375 0.5318061709403992 0.8411849 0.4098722040653229 False diff --git a/ENCSR895KTN/cherimoya.fold_0.performance.tsv b/ENCSR895KTN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ab2583cbc844c43934e593319c06a81fb3f3ad44..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1320.1300048828125 0.2666369676589966 0.5308381915092468 0.28740474581718445 0.8418335318565369 0.7708900570869446 0.4099256694316864 \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_1.evaluate.json b/ENCSR895KTN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6d2f3a297e38065772769f9ed10de298b31fbefc..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373QLZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_1.fit.json b/ENCSR895KTN/cherimoya.fold_1.fit.json deleted file mode 100644 index 8c097373b4637bd6dba37e79e168eb49d0ba213d..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF373QLZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_1.log b/ENCSR895KTN/cherimoya.fold_1.log deleted file mode 100644 index 7fe232c952a4e43e313587ed4bfd51dcede5c2bc..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 34.276965618133545 5.594419002532959 1198.39794921875 0.6012088060379028 2319.24951171875 0.3404967188835144 0.6755756 11.759390830993652 True -1 5518 29.684927701950073 36.80234622955322 1400.4742431640625 0.8963340520858765 1867.9063720703125 0.4496235251426697 0.7425222 3.8119678497314453 True -2 8277 31.404847145080566 0.7383043766021729 1117.6146240234375 0.7930986881256104 1827.6727294921875 0.4657154977321625 0.7522282 2.770195960998535 True -3 11036 30.02431559562683 0.699495792388916 1223.346435546875 0.5976887941360474 1758.8836669921875 0.4759988784790039 0.7804548 1.6356067657470703 True -4 13795 29.980440139770508 0.6968145370483398 1189.037109375 0.6361234188079834 1715.1927490234375 0.48622214794158936 0.78622633 1.5255671739578247 True -5 16554 29.996864318847656 0.7272658348083496 1121.66943359375 0.5505456924438477 1689.3817138671875 0.49394455552101135 0.7920049 1.4548356533050537 True -6 19313 29.993705987930298 0.6902127265930176 1183.1966552734375 0.8381139636039734 1660.144287109375 0.5014032125473022 0.7978286 1.353919267654419 True -7 22072 30.074769735336304 2.1260299682617188 1480.4715576171875 0.5150200724601746 1648.30419921875 0.5042608976364136 0.8051512 1.1714926958084106 True -8 24831 30.257427215576172 0.7182528972625732 1425.220458984375 0.36581656336784363 1625.5938720703125 0.5109001398086548 0.81263566 1.0960875749588013 True -9 27590 30.230817794799805 0.719083309173584 1131.0712890625 0.4780704379081726 1609.782470703125 0.5148967504501343 0.81989187 0.9418900609016418 True -10 30349 32.111815214157104 39.665870666503906 1390.859130859375 0.6157844066619873 1593.99462890625 0.5175676345825195 0.8252568 0.8433606624603271 True -11 33108 32.02430295944214 0.7254626750946045 1017.3839721679688 0.8097407817840576 1585.3172607421875 0.5205430388450623 0.83431697 0.7148988246917725 True -12 35867 33.05365443229675 0.7137150764465332 1289.5604248046875 0.5421536564826965 1568.6121826171875 0.5237091183662415 0.83871305 0.6433281898498535 True -13 38626 30.15677809715271 0.7038757801055908 1419.2381591796875 0.680921733379364 1549.7479248046875 0.5264574885368347 0.84569997 0.5783525705337524 True -14 41385 30.159340143203735 0.7069778442382812 914.5816650390625 0.5551213026046753 1531.4581298828125 0.5319913029670715 0.8515919 0.5046722888946533 True -15 44144 31.44792079925537 18.438445329666138 975.1976928710938 0.5648403763771057 1524.7860107421875 0.5318610072135925 0.85525465 0.4611349105834961 True -16 46903 30.243795156478882 0.7157728672027588 973.4962158203125 0.4655606746673584 1522.5440673828125 0.5332698225975037 0.85929817 0.4301303029060364 True -17 49662 30.190354585647583 0.7118232250213623 1132.0721435546875 0.35383540391921997 1513.5487060546875 0.5366731286048889 0.86246777 0.41745665669441223 True -18 52421 30.008506774902344 0.708296537399292 1085.2938232421875 0.33573389053344727 1518.5921630859375 0.5330200791358948 0.8627009 0.41125303506851196 True -19 55180 29.775518894195557 0.695852518081665 1125.0537109375 0.37634700536727905 1523.6915283203125 0.5314013957977295 0.8641605 0.4095587134361267 True diff --git a/ENCSR895KTN/cherimoya.fold_1.performance.tsv b/ENCSR895KTN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e0a3312c566302b53a651ece5c9441d3fb55abba..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1523.6915283203125 0.2572014331817627 0.5314014554023743 0.30867162346839905 0.8641604781150818 0.8192799687385559 0.4095587134361267 \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_2.evaluate.json b/ENCSR895KTN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3c304e0d8397f174d6957127b34298a1eb711f3d..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373QLZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_2.fit.json b/ENCSR895KTN/cherimoya.fold_2.fit.json deleted file mode 100644 index 576dd193fc8862d5cff364b246f27ef9eda27c16..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF373QLZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_2.log b/ENCSR895KTN/cherimoya.fold_2.log deleted file mode 100644 index cb1d0d4f62d7135e927178f9035d054e2338b78d..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2811 35.375996112823486 3.5052502155303955 1229.0439453125 0.7485955953598022 2046.2862548828125 0.3342514932155609 0.6597658 10.936400413513184 True -1 5622 30.578829526901245 1.6723763942718506 1623.62744140625 1.181351661682129 1653.4483642578125 0.4461790919303894 0.72962934 4.358658313751221 True -2 8433 30.546982526779175 2.0724146366119385 1542.75048828125 0.8888612985610962 1611.0963134765625 0.4597724378108978 0.74833834 2.1048150062561035 True -3 11244 31.106719970703125 14.94940996170044 1023.6566772460938 0.5069395899772644 1557.2667236328125 0.4723319709300995 0.7672825 1.550042748451233 True -4 14055 31.591886520385742 34.01169276237488 952.8583374023438 0.5844125747680664 1522.6549072265625 0.4814298450946808 0.78127265 1.255799651145935 True -5 16866 31.481406927108765 13.3245108127594 1204.094482421875 0.6178179383277893 1507.8819580078125 0.4863649904727936 0.7848029 1.2922251224517822 True -6 19677 30.768277645111084 0.5669801235198975 1104.658203125 0.5328866839408875 1486.48291015625 0.4936443567276001 0.789509 1.2644511461257935 True -7 22488 30.599692821502686 0.5696947574615479 1191.1953125 0.7420750856399536 1470.0028076171875 0.4992562532424927 0.7923752 1.1727629899978638 True -8 25299 30.649782180786133 0.5603704452514648 1522.3548583984375 1.047835111618042 1456.9403076171875 0.5034216046333313 0.7990894 1.0949656963348389 True -9 28110 30.630203008651733 0.5538158416748047 903.39501953125 0.46054598689079285 1449.52587890625 0.5054876804351807 0.80349576 1.0246098041534424 True -10 30921 30.688228368759155 0.5531871318817139 1135.4814453125 0.5318601131439209 1439.469970703125 0.5078738927841187 0.8072672 0.9127296209335327 True -11 33732 30.69429349899292 1.3467612266540527 1729.8785400390625 0.4724257290363312 1422.1966552734375 0.5133825540542603 0.8131938 0.7861517667770386 True -12 36543 31.061065196990967 0.5594203472137451 1214.945556640625 0.5609099864959717 1408.7001953125 0.5155600309371948 0.81956565 0.6518388390541077 True -13 39354 30.58935856819153 3.210408926010132 1015.90087890625 0.39732062816619873 1397.0396728515625 0.5198963284492493 0.82258654 0.582071840763092 True -14 42165 30.878285884857178 28.23639178276062 923.99609375 0.5645724534988403 1388.516357421875 0.5212107300758362 0.82917875 0.5227787494659424 True -15 44976 30.097700834274292 0.5526373386383057 1160.681396484375 0.3973366618156433 1370.9913330078125 0.5265675783157349 0.8351738 0.47697338461875916 True -16 47787 30.060140132904053 0.5494177341461182 941.808837890625 0.3628575801849365 1369.3359375 0.5258229970932007 0.83920354 0.44580966234207153 True -17 50598 29.980108499526978 0.5475673675537109 954.02294921875 0.1824047714471817 1373.7518310546875 0.5242648720741272 0.84145427 0.43148165941238403 True -18 53409 30.08476734161377 0.5350015163421631 988.2764892578125 0.2343558520078659 1372.6058349609375 0.5246281623840332 0.8397131 0.4264376759529114 False -19 56220 30.577377796173096 0.5487079620361328 1494.2445068359375 0.39865338802337646 1376.52197265625 0.5236690044403076 0.84027123 0.42636334896087646 False diff --git a/ENCSR895KTN/cherimoya.fold_2.performance.tsv b/ENCSR895KTN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2fa6d12d381061906f2785d62a851b8483494acc..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1373.7518310546875 0.2645343244075775 0.5242648720741272 0.28988465666770935 0.841454267501831 0.781781792640686 0.43148165941238403 \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_3.evaluate.json b/ENCSR895KTN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1a8eefc8aba65a1f4a354fdcdb421c28d5c7d6a4..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373QLZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_3.fit.json b/ENCSR895KTN/cherimoya.fold_3.fit.json deleted file mode 100644 index 6d2668dfe6563488df55baadab83d20ed0bce8f9..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF373QLZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_3.log b/ENCSR895KTN/cherimoya.fold_3.log deleted file mode 100644 index 5e32402fd7c6bf95b5bd2bc94e3477b35765c3a8..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 35.19940447807312 3.961313486099243 1471.026611328125 0.5167762041091919 1939.761474609375 0.35240304470062256 0.6566322 11.346332550048828 True -1 5664 31.75804591178894 0.545250415802002 1163.38916015625 0.5851956605911255 1607.5396728515625 0.4554155766963959 0.7168969 3.8286550045013428 True -2 8496 31.9920916557312 24.47516965866089 1037.16162109375 0.7312289476394653 1566.1724853515625 0.46595215797424316 0.72750694 2.1083178520202637 True -3 11328 30.95784306526184 0.5440535545349121 1533.280517578125 0.8153152465820312 1518.53369140625 0.47909000515937805 0.7449675 1.771060824394226 True -4 14160 30.91136860847473 0.5188474655151367 1257.4422607421875 0.565448522567749 1497.5814208984375 0.4863618314266205 0.7554164 1.838868260383606 True -5 16992 30.78366184234619 0.521214485168457 1413.915771484375 0.9673589468002319 1476.331298828125 0.49570947885513306 0.7493659 2.1120193004608154 False -6 19824 30.80841875076294 21.985325813293457 1243.631103515625 0.6763354539871216 1445.7830810546875 0.5062545537948608 0.7649518 1.5385624170303345 True -7 22656 31.050604820251465 2.9631552696228027 1282.423828125 0.6210867166519165 1444.356201171875 0.5059546232223511 0.7675282 1.4467724561691284 True -8 25488 30.83016037940979 0.539024829864502 1169.696533203125 0.7165030837059021 1430.0228271484375 0.5114019513130188 0.7800535 1.1256827116012573 True -9 28320 30.389793634414673 0.5235683917999268 1023.1719970703125 0.644771158695221 1413.5831298828125 0.5186156034469604 0.78439474 1.0046449899673462 True -10 31152 30.328428983688354 0.5128662586212158 1044.669677734375 0.9641479849815369 1404.4024658203125 0.520950198173523 0.7896757 0.9186384081840515 True -11 33984 30.363165616989136 0.5296776294708252 1207.44580078125 0.7425833940505981 1385.790771484375 0.5276256799697876 0.79941064 0.8186092972755432 True -12 36816 30.225627183914185 0.5082459449768066 1021.0304565429688 0.569638729095459 1372.7645263671875 0.5297718644142151 0.8058721 0.710471510887146 True -13 39648 30.286161422729492 0.5103845596313477 1230.303955078125 0.5411934852600098 1367.1593017578125 0.5305008292198181 0.8125255 0.6296989917755127 True -14 42480 30.420194625854492 0.5376894474029541 985.8508911132812 0.49477851390838623 1354.2091064453125 0.5340100526809692 0.82017565 0.5581589341163635 True -15 45312 30.322717666625977 0.524409294128418 1135.7930908203125 0.4622071385383606 1345.45654296875 0.5358219742774963 0.82568985 0.5162021517753601 True -16 48144 30.309894561767578 2.5766563415527344 1323.2137451171875 0.3664722442626953 1346.43017578125 0.5352574586868286 0.8293244 0.48512789607048035 True -17 50976 30.267833948135376 0.5110416412353516 1113.46240234375 0.40970879793167114 1342.695556640625 0.5373446345329285 0.8338251 0.4647921919822693 True -18 53808 30.32483410835266 0.5357365608215332 949.2493896484375 0.4188098609447479 1338.8023681640625 0.5383467078208923 0.83439094 0.458537220954895 True -19 56640 30.419302940368652 0.5350496768951416 1032.183349609375 0.29938554763793945 1343.583740234375 0.5357877016067505 0.8339908 0.4591776430606842 False diff --git a/ENCSR895KTN/cherimoya.fold_3.performance.tsv b/ENCSR895KTN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5188a637dd866ee2ec30b1a378e9f5f5e8ee76d8..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1338.8023681640625 0.26258718967437744 0.5383467078208923 0.29609397053718567 0.8343909382820129 0.7652791142463684 0.458537220954895 \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_4.evaluate.json b/ENCSR895KTN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 92087e27f6e55af66bb639dca99a9e8ec3716ab9..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373QLZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_4.fit.json b/ENCSR895KTN/cherimoya.fold_4.fit.json deleted file mode 100644 index 66547c99f5fce33a5606d314e6d373eab4c5eac0..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF373QLZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895KTN/cherimoya.fold_4.log b/ENCSR895KTN/cherimoya.fold_4.log deleted file mode 100644 index 2cf9726ee1aebf33ba5cda7a0e2e9ce0c5a78d0d..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2797 35.09530591964722 3.8456366062164307 1170.746337890625 0.6426080465316772 1810.6173095703125 0.33682742714881897 0.6430362 10.247474670410156 True -1 5594 30.46780252456665 0.5350742340087891 1247.706298828125 0.7001233100891113 1501.557373046875 0.442105233669281 0.7142767 3.8598175048828125 True -2 8391 30.431512355804443 0.5154209136962891 1305.0166015625 0.7150365710258484 1460.5150146484375 0.45612385869026184 0.7267692 2.005206823348999 True -3 11188 30.41462469100952 0.5139718055725098 918.8989868164062 0.7514307498931885 1409.477294921875 0.4676239788532257 0.7502018 1.2894822359085083 True -4 13985 33.458855867385864 20.36660861968994 1113.1220703125 0.8892799615859985 1380.1177978515625 0.4745190441608429 0.76243323 1.2861405611038208 True -5 16782 29.888087034225464 0.5101957321166992 1351.260498046875 0.645736038684845 1347.7933349609375 0.4866030216217041 0.77282315 1.2763543128967285 True -6 19579 29.834739446640015 0.5187218189239502 1238.4114990234375 0.7357401847839355 1331.282470703125 0.49187198281288147 0.77271813 1.0404133796691895 False -7 22376 29.952428579330444 0.5127694606781006 1018.0722045898438 0.6355926394462585 1315.4737548828125 0.4990605115890503 0.7792444 0.9015312790870667 True -8 25173 30.46378993988037 1.5774266719818115 1081.14404296875 0.4398738741874695 1303.4632568359375 0.5035279989242554 0.78217477 0.7709681391716003 True -9 27970 30.11972403526306 22.27493667602539 899.1595458984375 0.5008663535118103 1293.101806640625 0.5092249512672424 0.78887564 0.6860883831977844 True -10 30767 32.75014019012451 0.5147931575775146 1123.655517578125 0.529456377029419 1283.699951171875 0.5096054077148438 0.79627746 0.6503603458404541 True -11 33564 30.021707773208618 0.5188145637512207 1016.8778076171875 0.5190082788467407 1277.3331298828125 0.5108312368392944 0.802801 0.5790290832519531 True -12 36361 30.054845094680786 13.06212592124939 1187.9620361328125 0.5437467098236084 1270.19921875 0.5158519744873047 0.8060978 0.5425814390182495 True -13 39158 31.847211837768555 0.9682831764221191 1104.33935546875 0.580500602722168 1254.7987060546875 0.5194540619850159 0.81358105 0.4916647672653198 True -14 41955 30.441540479660034 0.516939640045166 973.1672973632812 0.42400050163269043 1245.3662109375 0.5213947296142578 0.82153255 0.45613759756088257 True -15 44752 30.215025186538696 0.5174434185028076 1177.150634765625 0.27813029289245605 1243.7872314453125 0.521845281124115 0.82570994 0.4315345585346222 True -16 47549 30.0786714553833 0.5213673114776611 1149.8057861328125 0.3492264747619629 1233.739501953125 0.5253826379776001 0.8313114 0.41787970066070557 True -17 50346 30.1107177734375 0.5141973495483398 1094.1356201171875 0.44056886434555054 1232.8770751953125 0.5260953903198242 0.8331705 0.41153663396835327 True -18 53143 30.084378004074097 0.5205433368682861 1040.4990234375 0.4049244523048401 1236.008544921875 0.5246797800064087 0.8348585 0.4105643332004547 True -19 55940 30.07020378112793 0.5200107097625732 1259.456298828125 0.31709906458854675 1237.63720703125 0.5235944390296936 0.8347419 0.41142264008522034 False diff --git a/ENCSR895KTN/cherimoya.fold_4.performance.tsv b/ENCSR895KTN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 11ac9a5e54bfe660249cb4bb59374b960b725e35..0000000000000000000000000000000000000000 --- a/ENCSR895KTN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1236.008544921875 0.27186039090156555 0.5246797800064087 0.2808062732219696 0.8348584771156311 0.7699103355407715 0.4105643332004547 \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_0.evaluate.json b/ENCSR895SEG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8dcc53b6d37e0aa542c3f5d4f071b5fc52b53c37..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF284ICA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_0.fit.json b/ENCSR895SEG/cherimoya.fold_0.fit.json deleted file mode 100644 index 99b51b8b88374c679dff90a7f7f35d63ede1790b..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF284ICA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_0.log b/ENCSR895SEG/cherimoya.fold_0.log deleted file mode 100644 index bcc5df02c7a354626fef0406983f55a9b860f648..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3077 38.76801681518555 4.116107225418091 596.0936279296875 0.24045318365097046 839.0800170898438 0.7038162350654602 0.7371354 4.541680335998535 True -1 6154 34.0361008644104 0.7495012283325195 604.663818359375 0.31198927760124207 717.8111572265625 0.7753465175628662 0.80203885 0.6163874864578247 True -2 9231 34.094656467437744 0.6770176887512207 633.2774047851562 0.2999527156352997 699.1671142578125 0.7857059836387634 0.8091585 0.2988821268081665 True -3 12308 33.36974287033081 0.6574513912200928 604.5628662109375 0.20420634746551514 692.04638671875 0.7893558740615845 0.81830066 0.24813811480998993 True -4 15385 33.359614849090576 0.6417224407196045 587.1770629882812 0.15362295508384705 688.9555053710938 0.7907494902610779 0.82135093 0.2558424174785614 True -5 18462 33.309378147125244 0.6510052680969238 642.0723876953125 0.20039451122283936 686.8146362304688 0.7925902009010315 0.8236143 0.2245911955833435 True -6 21539 33.36162066459656 1.797374963760376 659.6473388671875 0.2352612465620041 684.2832641601562 0.7944323420524597 0.82477665 0.22101570665836334 True -7 24616 33.40905165672302 0.63808274269104 604.2696533203125 0.19902265071868896 681.2424926757812 0.796970546245575 0.82806414 0.22213385999202728 True -8 27693 33.2706344127655 0.631964921951294 586.49951171875 0.25542256236076355 679.9285278320312 0.7977400422096252 0.83044803 0.21894851326942444 True -9 30770 33.26983380317688 0.635155200958252 630.31884765625 0.24096699059009552 677.3278198242188 0.7995392084121704 0.83212095 0.22170159220695496 True -10 33847 33.26112675666809 0.6396620273590088 562.6962890625 0.16296562552452087 674.6229248046875 0.8013564944267273 0.8359884 0.21734628081321716 True -11 36924 33.26045346260071 0.636411190032959 664.1971435546875 0.19899195432662964 672.3372802734375 0.8029779195785522 0.8436475 0.21512196958065033 True -12 40001 33.318525314331055 0.6327412128448486 622.8282470703125 0.13333237171173096 670.262939453125 0.8046338558197021 0.84741026 0.20260344445705414 True -13 43078 33.286521911621094 0.6499311923980713 540.7508544921875 0.08692187815904617 668.4938354492188 0.8061185479164124 0.85187364 0.20375795662403107 True -14 46155 33.25663208961487 0.634619951248169 533.5402221679688 0.17936107516288757 666.9755859375 0.8074060082435608 0.85703015 0.19143374264240265 True -15 49232 33.334470987319946 0.649528980255127 557.4926147460938 0.1532014012336731 666.01025390625 0.808477520942688 0.86024153 0.18603098392486572 True -16 52309 33.2592294216156 0.6446771621704102 561.701904296875 0.12195643782615662 665.8344116210938 0.8087813854217529 0.8633287 0.18063731491565704 True -17 55386 33.23727488517761 25.758163690567017 531.51611328125 0.14176911115646362 666.148193359375 0.8086438775062561 0.86441374 0.17802849411964417 True -18 58463 34.02499055862427 25.319886207580566 601.5060424804688 0.09969675540924072 666.5565185546875 0.8083709478378296 0.8624887 0.17797507345676422 False -19 61540 33.39231991767883 0.6589422225952148 605.1803588867188 0.1278422772884369 667.1192016601562 0.8081907033920288 0.8639189 0.17829611897468567 False diff --git a/ENCSR895SEG/cherimoya.fold_0.performance.tsv b/ENCSR895SEG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ecb6c8bede8167e8d6f7b64de54e22e0fe55433f..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -666.148193359375 0.15558846294879913 0.8086438775062561 0.4638703465461731 0.8644137382507324 0.782374918460846 0.17802849411964417 \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_1.evaluate.json b/ENCSR895SEG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b3483138f7dd4893f97e5c168ac77542c21e46ed..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF284ICA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_1.fit.json b/ENCSR895SEG/cherimoya.fold_1.fit.json deleted file mode 100644 index dd44fc2d715060d0c6ce9d89a569a2b4ccf31e8e..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF284ICA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_1.log b/ENCSR895SEG/cherimoya.fold_1.log deleted file mode 100644 index 1c9d9c08406d0d0b8a07375d004bb68e32947912..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3040 38.340660095214844 4.303586721420288 652.0680541992188 0.2829931974411011 919.2151489257812 0.7089810967445374 0.7476752 4.62252950668335 True -1 6080 33.441678285598755 1.3712353706359863 588.0455322265625 0.37038764357566833 780.7056884765625 0.7870554327964783 0.8138163 0.9035650491714478 True -2 9120 33.62182068824768 0.8182163238525391 661.4552001953125 0.2192663997411728 759.93798828125 0.7972701787948608 0.82120866 0.39614957571029663 True -3 12160 33.61584424972534 0.824669361114502 639.98583984375 0.26654472947120667 750.920166015625 0.801153838634491 0.8236554 0.3026309609413147 True -4 15200 33.57374620437622 0.8334052562713623 564.8358154296875 0.17600151896476746 747.8897094726562 0.803007960319519 0.8328733 0.30848002433776855 True -5 18240 33.55820894241333 1.6058416366577148 596.718017578125 0.19845324754714966 742.3812255859375 0.8050079345703125 0.83934057 0.2362041175365448 True -6 21280 33.64325451850891 0.8243269920349121 653.7027587890625 0.17486998438835144 740.2825927734375 0.8068685531616211 0.8413088 0.23096226155757904 True -7 24320 33.53270864486694 0.8213319778442383 628.4530639648438 0.25203830003738403 737.561279296875 0.8085014820098877 0.8463734 0.2235843390226364 True -8 27360 33.55842709541321 0.834296703338623 556.2041625976562 0.29959815740585327 734.9229125976562 0.8099282383918762 0.8503631 0.22339919209480286 True -9 30400 33.52572011947632 0.824272632598877 633.74462890625 0.19602066278457642 732.0760498046875 0.8115521669387817 0.8538107 0.21930857002735138 True -10 33440 33.597909450531006 0.8209714889526367 553.3795166015625 0.14061929285526276 729.4055786132812 0.8130313158035278 0.8567057 0.2069218009710312 True -11 36480 33.53282403945923 1.374661922454834 574.1488037109375 0.13167288899421692 726.3678588867188 0.8147045373916626 0.86238676 0.19917815923690796 True -12 39520 33.636423110961914 0.8232154846191406 580.228271484375 0.11248083412647247 724.6880493164062 0.8163973093032837 0.86860913 0.19323913753032684 True -13 42560 33.52802872657776 0.8099410533905029 567.1032104492188 0.2165767252445221 722.7879028320312 0.8179945945739746 0.8711696 0.18683697283267975 True -14 45600 33.59989404678345 0.8208930492401123 632.06591796875 0.20063403248786926 720.9034423828125 0.8193573355674744 0.87633616 0.1825263798236847 True -15 48640 33.534443855285645 1.250368356704712 655.4456787109375 0.16881966590881348 719.7762451171875 0.8204980492591858 0.8795805 0.1759379804134369 True -16 51680 33.54226279258728 2.3139896392822266 567.4902954101562 0.20072095096111298 719.3316040039062 0.8209923505783081 0.8826817 0.17362971603870392 True -17 54720 33.684670209884644 0.8203444480895996 529.1075439453125 0.13753841817378998 719.5534057617188 0.8209814429283142 0.88384396 0.17280317842960358 True -18 57760 33.58153176307678 15.373542547225952 608.1011962890625 0.12577247619628906 720.066162109375 0.8206183314323425 0.8817791 0.17445008456707 False -19 60800 33.639450788497925 0.8446962833404541 589.5317993164062 0.17966870963573456 720.3322143554688 0.8204099535942078 0.88038975 0.17576149106025696 False diff --git a/ENCSR895SEG/cherimoya.fold_1.performance.tsv b/ENCSR895SEG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 425dee8f3918c73724a86be33af2d684b4c05346..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -719.5534057617188 0.14531275629997253 0.8209814429283142 0.4899643361568451 0.8838439583778381 0.8323290348052979 0.17280317842960358 \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_2.evaluate.json b/ENCSR895SEG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index ca4d00fc3d1cb1c23b3d93d2233556332ee3da3f..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF284ICA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_2.fit.json b/ENCSR895SEG/cherimoya.fold_2.fit.json deleted file mode 100644 index 866719d421dde73c01b1edbac1d048bbc002f0cf..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF284ICA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_2.log b/ENCSR895SEG/cherimoya.fold_2.log deleted file mode 100644 index bc168f8bb830fa1f0cbfa76e4a275b49bfd68a21..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3244 40.31717395782471 4.808495283126831 554.8255615234375 0.27652329206466675 840.3744506835938 0.7136844396591187 0.7417798 3.5960235595703125 True -1 6488 35.85022568702698 2.806011915206909 611.8370971679688 0.34525686502456665 728.7714233398438 0.7812632322311401 0.81171066 0.6081651449203491 True -2 9732 35.89161038398743 0.9265267848968506 596.1920776367188 0.24746736884117126 713.3240356445312 0.7888069152832031 0.8204992 0.30564701557159424 True -3 12976 35.816800355911255 0.6719105243682861 622.1033325195312 0.2599296569824219 708.0857543945312 0.7914477586746216 0.8250575 0.2827621400356293 True -4 16220 35.82665514945984 0.6719410419464111 581.6990966796875 0.31850501894950867 704.2535400390625 0.7940846681594849 0.8274521 0.22917212545871735 True -5 19464 35.90238642692566 0.8626317977905273 623.9012451171875 0.22711534798145294 701.6986694335938 0.7949269413948059 0.8258014 0.22561374306678772 False -6 22708 35.87815475463867 0.664738655090332 601.9420166015625 0.3178505301475525 699.4036865234375 0.7968348860740662 0.8297701 0.2219005972146988 True -7 25952 35.845789670944214 1.044646978378296 553.16259765625 0.27204933762550354 696.7274780273438 0.7987332940101624 0.83305514 0.21860846877098083 True -8 29196 35.877235412597656 0.6564929485321045 606.0103759765625 0.2516463100910187 694.616455078125 0.8004128336906433 0.8325434 0.22517003118991852 False -9 32440 35.804524421691895 28.0188250541687 588.486083984375 0.21890604496002197 692.4295043945312 0.801923930644989 0.8376216 0.23288694024085999 True -10 35684 36.12894034385681 1.898404598236084 621.7545166015625 0.22442527115345 690.7739868164062 0.803234338760376 0.84218943 0.22768665850162506 True -11 38928 35.87777900695801 0.6577513217926025 575.1223754882812 0.2036852240562439 687.9385375976562 0.8049461841583252 0.847159 0.21950876712799072 True -12 42172 35.85785889625549 0.6419219970703125 597.6001586914062 0.12868043780326843 686.0411987304688 0.8065863251686096 0.8494781 0.2154759019613266 True -13 45416 35.82172608375549 0.6568818092346191 560.8914794921875 0.23585668206214905 683.8237915039062 0.8084273934364319 0.85681266 0.20348329842090607 True -14 48660 35.944559812545776 0.6515662670135498 657.3726806640625 0.14273226261138916 681.7794799804688 0.8099029660224915 0.8573843 0.20053359866142273 True -15 51904 35.900224685668945 0.6535234451293945 573.601806640625 0.21694546937942505 680.8335571289062 0.8108903169631958 0.8628105 0.19216389954090118 True -16 55148 35.91361212730408 0.6452846527099609 568.130615234375 0.11233112961053848 680.5418090820312 0.8111910820007324 0.8643147 0.18668416142463684 True -17 58392 35.807509660720825 0.631148099899292 606.2696533203125 0.12174826860427856 681.0270385742188 0.8112056255340576 0.8649952 0.18678335845470428 True -18 61636 35.85689854621887 0.6351110935211182 589.1763916015625 0.12115871906280518 681.406005859375 0.8109961152076721 0.8627235 0.1870018094778061 False -19 64880 35.25374746322632 0.6352949142456055 652.9148559570312 0.14708822965621948 681.8379516601562 0.8107331395149231 0.86058307 0.18756592273712158 False diff --git a/ENCSR895SEG/cherimoya.fold_2.performance.tsv b/ENCSR895SEG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ab27bca8c63988bdc4b553e88e753b92848d5d46..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -681.0270385742188 0.15302878618240356 0.8112056851387024 0.4705905020236969 0.8649951815605164 0.7873330116271973 0.18678335845470428 \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_3.evaluate.json b/ENCSR895SEG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c228251b58a5d794ee9886708ba0b43237e382ce..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF284ICA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_3.fit.json b/ENCSR895SEG/cherimoya.fold_3.fit.json deleted file mode 100644 index 23defd0f35d88a700ec29308f7eb892f78ce4fe4..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF284ICA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_3.log b/ENCSR895SEG/cherimoya.fold_3.log deleted file mode 100644 index 6ff0c7042a4d9b7db7f5ec9cf8ba133805b8ac73..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3125 39.2483696937561 20.452998399734497 609.4224853515625 0.29643023014068604 823.3101806640625 0.7104386687278748 0.73401135 3.8685522079467773 True -1 6250 34.607985973358154 0.7197198867797852 688.0717163085938 0.24488964676856995 717.4096069335938 0.7770528793334961 0.79031193 0.6925498247146606 True -2 9375 34.620938539505005 0.7891204357147217 604.974609375 0.2316848784685135 700.6370239257812 0.7866357564926147 0.7971581 0.3453678488731384 True -3 12500 34.664435148239136 0.6815152168273926 649.41845703125 0.3172774910926819 693.5155029296875 0.7903098464012146 0.80517226 0.29903626441955566 True -4 15625 34.63571214675903 0.6773338317871094 575.4222412109375 0.2036585807800293 691.2227783203125 0.7918163537979126 0.8055236 0.29960471391677856 True -5 18750 34.624064207077026 0.6636526584625244 573.1405029296875 0.21511049568653107 688.9496459960938 0.7935266494750977 0.80477065 0.2695465385913849 False -6 21875 34.6292827129364 0.6766390800476074 626.181396484375 0.31424713134765625 686.1615600585938 0.7957577705383301 0.80583894 0.25872939825057983 True -7 25000 34.6247456073761 0.7459943294525146 585.443359375 0.24001875519752502 684.4033203125 0.7967836856842041 0.8151091 0.2456539273262024 True -8 28125 34.6623420715332 1.07086181640625 658.5018310546875 0.18307125568389893 682.57373046875 0.798328161239624 0.81877947 0.24434779584407806 True -9 31250 34.63272976875305 0.661705732345581 646.1920166015625 0.26123151183128357 679.5795288085938 0.7996751070022583 0.82531184 0.23785407841205597 True -10 34375 34.56174063682556 0.7163400650024414 595.10693359375 0.1973666548728943 677.8572998046875 0.8012734651565552 0.8271808 0.2338489443063736 True -11 37500 34.547199964523315 1.4303641319274902 581.639404296875 0.1810649037361145 676.2485961914062 0.8027678728103638 0.83077455 0.23543906211853027 True -12 40625 34.66992712020874 0.6714065074920654 578.7470703125 0.21622192859649658 674.0042724609375 0.8045130968093872 0.8335224 0.22899135947227478 True -13 43750 34.58069634437561 0.6502327919006348 581.4767456054688 0.0833343118429184 671.9615478515625 0.8063217997550964 0.8409683 0.22025100886821747 True -14 46875 34.61664414405823 1.5505313873291016 584.1063232421875 0.17332801222801208 670.0265502929688 0.8077974915504456 0.8493149 0.21329522132873535 True -15 50000 34.61563158035278 0.670771598815918 599.234375 0.1551286280155182 668.7784423828125 0.8086706399917603 0.85184354 0.20312856137752533 True -16 53125 34.61045742034912 0.6575024127960205 547.4243774414062 0.12417114526033401 668.4104614257812 0.8092087507247925 0.85458636 0.20024850964546204 True -17 56250 34.584585666656494 0.6564216613769531 599.31103515625 0.10840008407831192 668.7305297851562 0.809114396572113 0.85298944 0.19896169006824493 False -18 59375 34.01071739196777 0.6504507064819336 589.8087158203125 0.08922319859266281 668.9473266601562 0.8088424801826477 0.8518736 0.2008194923400879 False -19 62500 34.07177519798279 0.651881217956543 605.7224731445312 0.14127378165721893 669.5261840820312 0.8087054491043091 0.8509059 0.20161139965057373 False diff --git a/ENCSR895SEG/cherimoya.fold_3.performance.tsv b/ENCSR895SEG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1b274837d36d307786fc23f8672b5741db60e90a..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -668.4104614257812 0.1548280268907547 0.8092087507247925 0.4631939232349396 0.8545863628387451 0.7678479552268982 0.20024850964546204 \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_4.evaluate.json b/ENCSR895SEG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 4093ea4070a9c9a131b1d154a0bb9b0119688f57..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF284ICA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_4.fit.json b/ENCSR895SEG/cherimoya.fold_4.fit.json deleted file mode 100644 index dfa0d2213be9141375b3397f8775d692780cf50e..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF284ICA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR895SEG/cherimoya.fold_4.log b/ENCSR895SEG/cherimoya.fold_4.log deleted file mode 100644 index 6bf980761fd8261666eaf182a16e182a9649160b..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3184 40.05132985115051 4.180495500564575 603.57373046875 0.3204474449157715 796.279541015625 0.7078775763511658 0.73638785 3.3184115886688232 True -1 6368 35.16600513458252 0.6922378540039062 600.5487060546875 0.2539510428905487 694.8875732421875 0.7768312096595764 0.8060685 0.4814450442790985 True -2 9552 35.19214487075806 0.657325029373169 675.942138671875 0.27202698588371277 680.7088623046875 0.7846208214759827 0.81451136 0.26822397112846375 True -3 12736 36.97917413711548 9.925137281417847 657.658935546875 0.20784540474414825 675.2322998046875 0.7876540422439575 0.8196875 0.23078595101833344 True -4 15920 35.173884868621826 0.6653873920440674 561.9154663085938 0.19193753600120544 673.3472900390625 0.7882130146026611 0.81943005 0.22176577150821686 False -5 19104 35.291075706481934 0.6791377067565918 657.17919921875 0.19296894967556 671.8262939453125 0.7895018458366394 0.8221006 0.20547708868980408 True -6 22288 35.282994985580444 0.653904914855957 569.2366333007812 0.21335627138614655 669.8832397460938 0.7913926839828491 0.82634205 0.20181463658809662 True -7 25472 36.369887351989746 3.5984137058258057 591.9837036132812 0.23789656162261963 667.42626953125 0.7930214405059814 0.82968557 0.19917570054531097 True -8 28656 35.266473054885864 0.669581413269043 629.347900390625 0.15565301477909088 665.1907958984375 0.7946195602416992 0.8339485 0.1942843794822693 True -9 31840 35.22364401817322 0.6651611328125 596.0841064453125 0.1485326588153839 663.5812377929688 0.796024739742279 0.83521 0.19237302243709564 True -10 35024 36.01819038391113 4.132320404052734 631.9806518554688 0.20273327827453613 661.902587890625 0.7973644733428955 0.8377326 0.1914028525352478 True -11 38208 35.302998781204224 0.6787643432617188 546.56787109375 0.20375430583953857 659.6387939453125 0.7989955544471741 0.8434443 0.1851096898317337 True -12 41392 35.21521472930908 0.6593499183654785 613.2283935546875 0.11439868062734604 657.741943359375 0.800775408744812 0.85119563 0.17721867561340332 True -13 44576 35.37111020088196 0.6699385643005371 639.6854248046875 0.16219863295555115 656.02099609375 0.8023144602775574 0.85494775 0.1745348423719406 True -14 47760 35.288347244262695 0.668407678604126 572.8155517578125 0.128508523106575 654.7523803710938 0.803631603717804 0.86152935 0.17326296865940094 True -15 50944 35.16640019416809 1.2596700191497803 635.7310791015625 0.11353617906570435 653.541748046875 0.8048385381698608 0.8653524 0.16588038206100464 True -16 54128 35.26333737373352 0.6704587936401367 570.4276123046875 0.1614457070827484 653.2987670898438 0.8053218126296997 0.8671909 0.16407571732997894 True -17 57312 35.23310923576355 0.6688485145568848 657.9376831054688 0.10549496114253998 653.4288940429688 0.8052988648414612 0.8665673 0.16343562304973602 False -18 60496 34.86770820617676 0.6739449501037598 578.4981079101562 0.17356254160404205 653.7656860351562 0.805128812789917 0.86569476 0.16536329686641693 False -19 63680 34.525102853775024 0.6548945903778076 592.9401245117188 0.08059026300907135 654.164794921875 0.8049155473709106 0.86540246 0.16627830266952515 False diff --git a/ENCSR895SEG/cherimoya.fold_4.performance.tsv b/ENCSR895SEG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 171258fff3e7177a5559f2c9e5c4ccd873fbebf9..0000000000000000000000000000000000000000 --- a/ENCSR895SEG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -653.2987670898438 0.15797603130340576 0.8053217530250549 0.45634496212005615 0.8671908974647522 0.7712898254394531 0.16407571732997894 \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_0.evaluate.json b/ENCSR899YEP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 65d473fa8cc95a90977a6dc79219c7dd3dc483dc..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF700BHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_0.fit.json b/ENCSR899YEP/cherimoya.fold_0.fit.json deleted file mode 100644 index 9e34af7f4a92f99880524d161b47a2c1a5f8c97b..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF700BHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_0.log b/ENCSR899YEP/cherimoya.fold_0.log deleted file mode 100644 index b19e41ba9bbaeea2428ed59c683ad0959c0b1c3e..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1721 23.511010885238647 4.1416916847229 252.48394775390625 0.842138946056366 342.02825927734375 0.4520067274570465 0.5398316 10.942252159118652 True -1 3442 18.947145462036133 0.4553558826446533 204.72210693359375 0.7910246849060059 290.90533447265625 0.5439546704292297 0.6081226 2.981868267059326 True -2 5163 18.92892813682556 0.4026458263397217 237.41525268554688 0.5848950743675232 274.4946594238281 0.5825070142745972 0.62664014 0.9692159295082092 True -3 6884 18.91021752357483 0.345257043838501 230.07501220703125 0.45339563488960266 270.1709899902344 0.593369722366333 0.64232445 0.58539217710495 True -4 8605 18.954951763153076 0.34352684020996094 231.50018310546875 1.21977698802948 268.26287841796875 0.5988792181015015 0.65032154 0.4433485269546509 True -5 10326 19.02714514732361 0.3808631896972656 232.696044921875 0.7695997953414917 267.93902587890625 0.5999706387519836 0.65764654 0.4596298635005951 True -6 12047 18.910857915878296 0.35040879249572754 217.75045776367188 0.4439171850681305 266.88336181640625 0.6029366850852966 0.65924865 0.4103761315345764 True -7 13768 18.93771481513977 0.383770227432251 229.10714721679688 0.5289737582206726 266.3729553222656 0.6045401096343994 0.6540932 0.3907986581325531 False -8 15489 18.908597946166992 0.34088134765625 211.5191650390625 0.7848113775253296 265.6552734375 0.6066468358039856 0.66571134 0.3654438853263855 True -9 17210 18.96060061454773 0.348879337310791 191.31259155273438 0.41156020760536194 264.96270751953125 0.6084834933280945 0.67646724 0.34970778226852417 True -10 18931 19.004456281661987 0.3596017360687256 213.34378051757812 0.3475116491317749 264.4401550292969 0.6101776361465454 0.680774 0.34556859731674194 True -11 20652 18.926482915878296 0.35434770584106445 222.83456420898438 0.6994203925132751 263.8705749511719 0.6119080185890198 0.6876792 0.34396228194236755 True -12 22373 18.950682878494263 0.3430795669555664 176.53564453125 0.6094750165939331 263.42742919921875 0.6131190657615662 0.69082963 0.3403777480125427 True -13 24094 18.889631271362305 0.3418407440185547 238.4167938232422 0.3964715003967285 263.0346984863281 0.6143971681594849 0.6971553 0.3360383212566376 True -14 25815 18.910518646240234 0.33971118927001953 232.70936584472656 0.37290310859680176 262.66156005859375 0.6155070662498474 0.7052314 0.33527877926826477 True -15 27536 19.05200433731079 2.3101320266723633 220.72314453125 0.31251227855682373 262.60174560546875 0.6158090233802795 0.7110143 0.3380850553512573 True -16 29257 19.046125173568726 0.5610165596008301 205.01083374023438 0.37829989194869995 262.6814270019531 0.6156787276268005 0.7131166 0.3432380259037018 True -17 30978 18.944695711135864 0.3415646553039551 224.59918212890625 0.3470533490180969 262.80059814453125 0.6151571273803711 0.7130726 0.3525071442127228 False -18 32699 18.931411266326904 0.3510615825653076 204.28085327148438 0.5361737012863159 262.9985656738281 0.6144363284111023 0.7119063 0.36314085125923157 False -19 34420 18.986507415771484 0.3476598262786865 221.2607421875 0.4479514956474304 263.0694580078125 0.6140217185020447 0.708194 0.372563898563385 False diff --git a/ENCSR899YEP/cherimoya.fold_0.performance.tsv b/ENCSR899YEP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8db20c43409568a330c3a65a7ca458eec12703db..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -262.6814270019531 0.31885668635368347 0.6156787276268005 0.18878835439682007 0.7131165862083435 0.6642192602157593 0.3432380259037018 \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_1.evaluate.json b/ENCSR899YEP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3142a35b305763ba50d74679e424ab26cdd8c217..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF700BHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_1.fit.json b/ENCSR899YEP/cherimoya.fold_1.fit.json deleted file mode 100644 index 8cee2eb8d10674174d0b8ed2c3650479c3aa0f11..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF700BHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_1.log b/ENCSR899YEP/cherimoya.fold_1.log deleted file mode 100644 index 009db56fdad77d4ba9fdccee473a2138ef3e02b5..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1718 23.951424837112427 3.9125378131866455 209.34657287597656 0.9551382064819336 392.17840576171875 0.4627572298049927 0.51726854 11.82201099395752 True -1 3436 18.921356201171875 0.6068246364593506 214.0265350341797 0.9647518396377563 327.6630554199219 0.5600375533103943 0.63027817 3.116032600402832 True -2 5154 18.926269054412842 0.4710366725921631 214.84152221679688 0.7550370693206787 310.3081359863281 0.5982475280761719 0.65263915 0.8570156097412109 True -3 6872 18.901915788650513 0.5274486541748047 242.44561767578125 0.8480727672576904 302.8511047363281 0.6127606630325317 0.6698378 0.5173909068107605 True -4 8590 18.6796612739563 0.4509129524230957 246.9834442138672 0.6009640693664551 300.7781982421875 0.6174101233482361 0.6837038 0.4410514235496521 True -5 10308 18.468149662017822 0.7688736915588379 220.19049072265625 0.5578179359436035 299.99835205078125 0.6196339726448059 0.69057506 0.4165828227996826 True -6 12026 18.49089550971985 0.5212926864624023 230.01593017578125 0.5394871234893799 299.2421875 0.6218345761299133 0.698954 0.42864805459976196 True -7 13744 18.47349977493286 0.47535157203674316 242.5874786376953 0.7439365386962891 298.40325927734375 0.6241121292114258 0.7056548 0.40709686279296875 True -8 15462 18.49070429801941 0.46320533752441406 220.10365295410156 0.5202363133430481 297.4984436035156 0.6263249516487122 0.7083512 0.40772637724876404 True -9 17180 18.523719787597656 0.45805811882019043 245.374267578125 0.5987753868103027 296.8183288574219 0.6277602314949036 0.7157452 0.40356069803237915 True -10 18898 18.52555513381958 0.46544647216796875 201.20579528808594 0.5048677325248718 296.10943603515625 0.6293761134147644 0.7204687 0.39906713366508484 True -11 20616 18.48494243621826 0.45310378074645996 236.82998657226562 0.5351911783218384 295.6331481933594 0.6306610107421875 0.7228682 0.3969135582447052 True -12 22334 18.47259020805359 0.45340418815612793 236.34097290039062 0.3565961718559265 294.7919006347656 0.6325239539146423 0.72780657 0.39782556891441345 True -13 24052 18.482483863830566 0.4752824306488037 199.75015258789062 0.3927028179168701 294.2112731933594 0.6339224576950073 0.73432773 0.3863156735897064 True -14 25770 18.508488416671753 0.46242737770080566 229.1865692138672 0.4027059078216553 293.6271057128906 0.6353303790092468 0.7449504 0.3667775094509125 True -15 27488 18.486724615097046 0.45846056938171387 229.31393432617188 0.5059019923210144 293.3510437011719 0.6358121037483215 0.74720925 0.36368033289909363 True -16 29206 18.49517297744751 0.9146180152893066 221.31060791015625 0.3484154939651489 293.4228820800781 0.6357317566871643 0.74863046 0.37165090441703796 True -17 30924 18.507627725601196 0.45194268226623535 242.2718048095703 0.2826026678085327 293.5594177246094 0.6353551745414734 0.7473063 0.3708743155002594 False -18 32642 18.479079723358154 0.45709824562072754 205.17556762695312 0.2836627960205078 293.75518798828125 0.6347057819366455 0.74383944 0.37790635228157043 False -19 34360 18.480165481567383 0.4633467197418213 228.26528930664062 0.2526131272315979 293.86260986328125 0.6342679262161255 0.741312 0.3847707509994507 False diff --git a/ENCSR899YEP/cherimoya.fold_1.performance.tsv b/ENCSR899YEP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5ae50095859cd19189179e4a097d9d49a602397a..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -293.4228820800781 0.30262407660484314 0.6357317566871643 0.20956885814666748 0.7486304640769958 0.7134005427360535 0.37165090441703796 \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_2.evaluate.json b/ENCSR899YEP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 98a0d56666f39825913471378013bc99954330fd..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF700BHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_2.fit.json b/ENCSR899YEP/cherimoya.fold_2.fit.json deleted file mode 100644 index 85b2586d5becd49c86c3f11084cce9031153593e..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF700BHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_2.log b/ENCSR899YEP/cherimoya.fold_2.log deleted file mode 100644 index d58fed1674262e89f57dac6416ae667c0d9bc255..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1823 24.65527057647705 3.6600852012634277 215.19248962402344 0.8723338842391968 352.4112243652344 0.46172529458999634 0.51183987 9.540630340576172 True -1 3646 20.0722553730011 0.5252859592437744 237.61412048339844 0.7502245903015137 298.2279357910156 0.5555523633956909 0.5980904 3.2038426399230957 True -2 5469 20.071810007095337 0.35700464248657227 231.3018035888672 0.6318355202674866 285.56878662109375 0.5895757079124451 0.61457837 0.8805511593818665 True -3 7292 20.091333627700806 0.4025297164916992 222.85536193847656 0.5441876649856567 279.67767333984375 0.6015543341636658 0.63596076 0.6007252335548401 True -4 9115 20.092684507369995 0.35956668853759766 248.99583435058594 0.47129788994789124 277.68695068359375 0.6059211492538452 0.6406941 0.46451231837272644 True -5 10938 20.07380986213684 0.36582517623901367 208.63723754882812 0.5297714471817017 277.0679931640625 0.6077755093574524 0.64613557 0.4695813059806824 True -6 12761 20.11030125617981 0.3568277359008789 221.47177124023438 0.6566548347473145 276.26824951171875 0.6101354956626892 0.65259373 0.43767252564430237 True -7 14584 20.0876522064209 0.3643674850463867 206.85797119140625 0.8050621747970581 275.7564392089844 0.6114288568496704 0.65881866 0.4145561456680298 True -8 16407 20.070528745651245 1.8061442375183105 220.92959594726562 0.4683743417263031 274.8892517089844 0.6134979724884033 0.67467546 0.4028524160385132 True -9 18230 20.067750930786133 0.38054919242858887 241.8078155517578 0.4737749397754669 274.4279479980469 0.6151427626609802 0.6801061 0.411504328250885 True -10 20053 20.0809166431427 0.4239976406097412 205.36544799804688 0.46577173471450806 273.8628845214844 0.6165434122085571 0.68476385 0.40204858779907227 True -11 21876 20.104593753814697 1.6725702285766602 221.05294799804688 0.547092080116272 273.2904052734375 0.6179124712944031 0.6866406 0.40376511216163635 True -12 23699 20.095444917678833 0.34398937225341797 176.31341552734375 0.5092541575431824 272.7192687988281 0.6194780468940735 0.6931557 0.3963033854961395 True -13 25522 19.732463598251343 0.37020444869995117 214.4375 0.4230417311191559 272.1820983886719 0.6206192374229431 0.6956398 0.3960478603839874 True -14 27345 19.714494705200195 0.36422181129455566 239.25242614746094 0.60829758644104 271.79290771484375 0.6217449903488159 0.7006328 0.3874998688697815 True -15 29168 19.6955668926239 0.7468011379241943 258.21099853515625 0.2989513874053955 271.5133972167969 0.6224915981292725 0.706971 0.38409504294395447 True -16 30991 19.624507427215576 0.3714570999145508 193.88851928710938 0.42866837978363037 271.4112854003906 0.6225844025611877 0.7109913 0.3798643946647644 True -17 32814 19.627286672592163 0.35099053382873535 200.63320922851562 0.292977511882782 271.5529479980469 0.6222012042999268 0.7097801 0.38720735907554626 False -18 34637 19.668591260910034 0.38011908531188965 227.43048095703125 0.28664320707321167 271.7725524902344 0.6214680671691895 0.70535034 0.3982141315937042 False -19 36460 19.653687715530396 0.5052366256713867 206.74020385742188 0.38569700717926025 271.83453369140625 0.6211386919021606 0.70353156 0.404077410697937 False diff --git a/ENCSR899YEP/cherimoya.fold_2.performance.tsv b/ENCSR899YEP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7ff2adce719bfc48c5171ffa541434f23245b17b..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.4112854003906 0.31384947896003723 0.6225844025611877 0.1952683925628662 0.7109913229942322 0.6557542085647583 0.3798643946647644 \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_3.evaluate.json b/ENCSR899YEP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 8a6f671ad225d9d5e5dfd4d6270f5fac16929c55..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF700BHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_3.fit.json b/ENCSR899YEP/cherimoya.fold_3.fit.json deleted file mode 100644 index a9070d29f86b457405cf02e81623c8d64d055d31..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF700BHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_3.log b/ENCSR899YEP/cherimoya.fold_3.log deleted file mode 100644 index 379cc25244ce49bac5fbb0abcf3b42716845ca20..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1771 23.860941410064697 3.4396347999572754 212.61227416992188 0.6979193091392517 343.6225280761719 0.45609238743782043 0.53541166 10.060297966003418 True -1 3542 19.4870707988739 0.5256423950195312 212.49295043945312 0.6689011454582214 288.9389343261719 0.5491907596588135 0.6218766 2.8336143493652344 True -2 5313 19.460921049118042 0.3383748531341553 219.05555725097656 0.8147692680358887 274.9622802734375 0.5845992565155029 0.643052 0.8110218644142151 True -3 7084 19.507150411605835 0.3820669651031494 229.94781494140625 0.6130803823471069 270.6241149902344 0.5959520936012268 0.65836596 0.47890937328338623 True -4 8855 19.48073387145996 0.34363555908203125 237.01173400878906 0.7198686599731445 269.2833557128906 0.5996639132499695 0.66817075 0.4003756642341614 True -5 10626 19.455445766448975 0.34345269203186035 233.32618713378906 0.6385507583618164 268.410888671875 0.601943850517273 0.6702364 0.3872750699520111 True -6 12397 19.444868803024292 7.157407283782959 242.31787109375 0.4247395992279053 268.1370849609375 0.6033154726028442 0.655677 0.40622204542160034 False -7 14168 19.154136657714844 0.3455965518951416 237.0912628173828 0.46095705032348633 267.4530029296875 0.6048774719238281 0.6660094 0.40269434452056885 False -8 15939 19.11563205718994 0.34057164192199707 223.1056365966797 0.6396437883377075 266.8359375 0.6064566969871521 0.66352993 0.4001769423484802 False -9 17710 19.093321561813354 0.33449792861938477 259.4616394042969 0.5333160758018494 266.2868957519531 0.608404278755188 0.6666481 0.420060932636261 False -10 19481 19.073959350585938 0.3332195281982422 272.7657775878906 0.5314759016036987 265.7230224609375 0.6099920868873596 0.67614627 0.3964167535305023 True -11 21252 19.078911066055298 0.3442509174346924 185.35791015625 0.45461827516555786 264.9232177734375 0.6120787262916565 0.6885865 0.3871241509914398 True -12 23023 19.102238655090332 0.3361966609954834 262.18182373046875 0.3887636363506317 264.29412841796875 0.6136289834976196 0.6940322 0.38767778873443604 True -13 24794 19.0749351978302 0.33087968826293945 220.46328735351562 0.664482831954956 263.903076171875 0.6148987412452698 0.69510293 0.3855464458465576 True -14 26565 19.109373331069946 0.3268153667449951 228.40089416503906 0.38278162479400635 263.55517578125 0.6158834099769592 0.703904 0.3861899971961975 True -15 28336 19.06720209121704 0.33329224586486816 207.78421020507812 0.41622230410575867 263.3634948730469 0.6162878274917603 0.70912004 0.38626182079315186 True -16 30107 19.09104633331299 1.1774163246154785 215.70387268066406 0.3225436210632324 263.2908935546875 0.6163690686225891 0.71243036 0.3886302411556244 True -17 31878 19.151183366775513 0.3411440849304199 207.44720458984375 0.37264084815979004 263.47955322265625 0.6160292625427246 0.71152985 0.3941195011138916 False -18 33649 19.10324788093567 0.34006357192993164 205.13253784179688 0.39000043272972107 263.6536865234375 0.6153831481933594 0.7065052 0.4032832682132721 False -19 35420 19.11529231071472 0.33933520317077637 234.548828125 0.1531832218170166 263.806396484375 0.6149237155914307 0.7047162 0.40925464034080505 False diff --git a/ENCSR899YEP/cherimoya.fold_3.performance.tsv b/ENCSR899YEP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f865e2fbf657adcca01bd743b6ec7e1527259657..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -263.2908935546875 0.31840917468070984 0.6163691282272339 0.18696698546409607 0.7124303579330444 0.6684139966964722 0.3886302411556244 \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_4.evaluate.json b/ENCSR899YEP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8e51c64746b8dbc179052d73878be6c13ed5ffa6..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF700BHG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_4.fit.json b/ENCSR899YEP/cherimoya.fold_4.fit.json deleted file mode 100644 index 8d6078e0448e8abc2670b393a748404cac8ed86b..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF700BHG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR899YEP/cherimoya.fold_4.log b/ENCSR899YEP/cherimoya.fold_4.log deleted file mode 100644 index 87dbfaf983490e69a9198b64543011539c8ca115..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1800 24.213260650634766 3.423499584197998 226.09063720703125 0.597291111946106 339.4726257324219 0.456472784280777 0.5202558 9.987969398498535 True -1 3600 19.759921550750732 1.373922348022461 259.47564697265625 0.762274444103241 288.88232421875 0.549485981464386 0.5787018 2.9136712551116943 True -2 5400 19.42242169380188 0.36627864837646484 245.678466796875 0.5612502098083496 274.3305358886719 0.5855560302734375 0.58397746 0.7751297354698181 True -3 7200 19.362836599349976 0.34709596633911133 237.85678100585938 0.8388110399246216 270.00677490234375 0.5970338582992554 0.61009943 0.6323164701461792 True -4 9000 19.352978229522705 0.3432648181915283 224.62619018554688 0.7320628762245178 268.406005859375 0.6014754176139832 0.63298583 0.4285788834095001 True -5 10800 19.355650663375854 1.055652141571045 229.88735961914062 0.7114483118057251 267.6979675292969 0.6039331555366516 0.64512956 0.41495221853256226 True -6 12600 19.359182834625244 0.35261964797973633 254.77731323242188 0.5160284638404846 266.9119873046875 0.6060567498207092 0.6484161 0.40447965264320374 True -7 14400 19.34776473045349 0.376448392868042 220.86917114257812 0.4491352438926697 266.291748046875 0.6077791452407837 0.65239966 0.39025384187698364 True -8 16200 19.330589532852173 0.3637394905090332 220.11007690429688 0.5972096920013428 265.85626220703125 0.6090342402458191 0.657907 0.38552549481391907 True -9 18000 19.331204414367676 0.3493485450744629 204.4531707763672 0.6920584440231323 265.26739501953125 0.6110238432884216 0.6625131 0.37927573919296265 True -10 19800 19.334487676620483 0.3446183204650879 248.5910186767578 0.6268290877342224 264.965087890625 0.6122683882713318 0.66826504 0.37872910499572754 True -11 21600 19.338013172149658 0.34794044494628906 245.8870391845703 0.46122145652770996 264.460693359375 0.613535463809967 0.67282534 0.36836308240890503 True -12 23400 19.3387291431427 0.34824323654174805 210.90304565429688 0.3720073103904724 263.9745178222656 0.6148301959037781 0.6785208 0.3657498359680176 True -13 25200 19.343294382095337 0.3610203266143799 219.9173126220703 0.31986838579177856 263.5705871582031 0.6160231232643127 0.6853801 0.3567458987236023 True -14 27000 19.398030281066895 0.3637840747833252 238.9990234375 0.29972952604293823 263.2055358886719 0.6171417236328125 0.69198936 0.3538857102394104 True -15 28800 19.358906507492065 0.36266040802001953 206.0061798095703 0.32700371742248535 263.059326171875 0.6177773475646973 0.6930185 0.3563034236431122 True -16 30600 19.776670694351196 0.3527710437774658 221.94366455078125 0.3039976954460144 263.00970458984375 0.617884635925293 0.69121116 0.36324381828308105 False -17 32400 19.36485981941223 0.35614514350891113 212.4825439453125 0.2910197377204895 263.1744079589844 0.61716228723526 0.6903716 0.3733730614185333 False -18 34200 19.4089834690094 0.3507707118988037 202.09500122070312 0.274429589509964 263.4272155761719 0.6163321137428284 0.6861724 0.3908804655075073 False -19 36000 19.492230653762817 0.3762507438659668 218.25726318359375 0.21946871280670166 263.59552001953125 0.6158645749092102 0.68212277 0.4031384289264679 False diff --git a/ENCSR899YEP/cherimoya.fold_4.performance.tsv b/ENCSR899YEP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 266ea5fe12ca4d07f51406d31191f75522ad6949..0000000000000000000000000000000000000000 --- a/ENCSR899YEP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -263.059326171875 0.3174881935119629 0.617777407169342 0.1875983327627182 0.6930184960365295 0.628649890422821 0.3563034236431122 \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_0.evaluate.json b/ENCSR903SKE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 22aab683de7a5395f14c9c1f00f1aed3ee15f544..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF492IQG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_0.fit.json b/ENCSR903SKE/cherimoya.fold_0.fit.json deleted file mode 100644 index 485e31ceda8552662cfd5519daa5f24479e4ee40..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF492IQG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_0.log b/ENCSR903SKE/cherimoya.fold_0.log deleted file mode 100644 index 8f8f3892db1159259291d84a200394246172d2dc..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2122 27.11498260498047 3.5700249671936035 2306.331298828125 1.5536417961120605 2846.63916015625 0.27733272314071655 0.5052727 22.50937271118164 True -1 4244 23.366214752197266 0.5140440464019775 1603.09228515625 1.6009279489517212 2219.730712890625 0.37740808725357056 0.653334 9.644652366638184 True -2 6366 23.357510805130005 0.5048189163208008 1470.848388671875 1.9593764543533325 2127.85205078125 0.3911440670490265 0.65722233 5.198185443878174 True -3 8488 23.34248995780945 0.5384140014648438 1478.3834228515625 1.3432064056396484 2038.6326904296875 0.4037492573261261 0.67377657 3.414238214492798 True -4 10610 23.36276626586914 2.3676884174346924 1261.90625 1.3498241901397705 1951.832763671875 0.4199311137199402 0.6828992 3.2114408016204834 True -5 12732 23.403054237365723 0.5143954753875732 1495.16162109375 1.2794480323791504 1895.124755859375 0.4245832860469818 0.693725 2.5227725505828857 True -6 14854 23.423231840133667 0.5232129096984863 1332.87060546875 1.0788815021514893 1854.7237548828125 0.4320761561393738 0.70361537 2.198887825012207 True -7 16976 23.099215745925903 0.504680871963501 1648.804443359375 1.2711803913116455 1824.6099853515625 0.43569111824035645 0.7090367 1.7670724391937256 True -8 19098 22.85226559638977 1.7210991382598877 1384.081298828125 0.898766040802002 1811.141845703125 0.43841153383255005 0.7182919 1.5341989994049072 True -9 21220 22.8651340007782 0.5027880668640137 1665.6400146484375 1.1328346729278564 1787.2799072265625 0.4436926543712616 0.7233339 1.3349448442459106 True -10 23342 22.975988149642944 0.49775004386901855 1913.207275390625 1.2441654205322266 1759.4261474609375 0.447698712348938 0.7286575 1.1961888074874878 True -11 25464 22.99882674217224 16.73970866203308 1626.750732421875 1.012394666671753 1735.3519287109375 0.45281827449798584 0.7380025 1.120644450187683 True -12 27586 23.069868564605713 0.50616455078125 1808.4720458984375 0.6233090162277222 1704.4151611328125 0.4606173038482666 0.74708223 1.0452430248260498 True -13 29708 23.921128273010254 21.806349754333496 1268.2919921875 1.7358444929122925 1685.9598388671875 0.46567270159721375 0.7528573 0.9948425889015198 True -14 31830 22.949055910110474 0.9145469665527344 1458.2593994140625 1.069895625114441 1657.3326416015625 0.4734981656074524 0.75834256 0.9286024570465088 True -15 33952 22.894203901290894 0.4929013252258301 1346.92578125 0.8166728615760803 1660.2183837890625 0.4714730978012085 0.7642257 0.8918148279190063 True -16 36074 23.001288175582886 0.508530855178833 1167.977783203125 0.5724411606788635 1653.2772216796875 0.47369900345802307 0.7694537 0.8601434826850891 True -17 38196 22.950549125671387 0.695948600769043 1121.737060546875 0.6560980081558228 1657.23388671875 0.47296497225761414 0.77167 0.8501494526863098 True -18 40318 22.98934268951416 0.4969010353088379 1083.009765625 0.9282884001731873 1667.763916015625 0.47125244140625 0.77472925 0.8441018462181091 True -19 42440 22.933350086212158 0.5055148601531982 1294.5008544921875 0.7467761039733887 1653.891845703125 0.47617408633232117 0.77415466 0.8404870629310608 False diff --git a/ENCSR903SKE/cherimoya.fold_0.performance.tsv b/ENCSR903SKE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 63a6b65ecab3c98d44cdb0a1d9e1ad5d516e0a58..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1667.763916015625 0.29015350341796875 0.4712525010108948 0.26446446776390076 0.7747292518615723 0.6553278565406799 0.8441018462181091 \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_1.evaluate.json b/ENCSR903SKE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7928e5951492e4abf54fc67402e37c882f41a75a..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF492IQG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_1.fit.json b/ENCSR903SKE/cherimoya.fold_1.fit.json deleted file mode 100644 index e3d961b9a6e6fc305deee67f8d50fcdf9f9a28c4..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF492IQG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_1.log b/ENCSR903SKE/cherimoya.fold_1.log deleted file mode 100644 index a774d3c47edc37a0dd4544434a91afd2af1620fc..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2138 27.117106914520264 3.572835922241211 2239.69482421875 1.9485007524490356 3884.85107421875 0.2801610827445984 0.5371181 22.168502807617188 True -1 4276 23.608705282211304 0.6035349369049072 1587.031982421875 1.1860833168029785 2944.942626953125 0.3938791751861572 0.678616 8.508267402648926 True -2 6414 23.472776651382446 11.510346174240112 1481.8067626953125 1.5610058307647705 2830.663330078125 0.4095606207847595 0.6898358 5.544577598571777 True -3 8552 23.485455989837646 0.6012334823608398 1493.8311767578125 1.7790336608886719 2656.34228515625 0.4302217364311218 0.7135302 3.9791882038116455 True -4 10690 23.57820773124695 0.8599207401275635 1010.3614501953125 1.4735418558120728 2539.704833984375 0.4458678066730499 0.72817254 3.15718936920166 True -5 12828 23.48283576965332 0.5846352577209473 2136.533203125 1.476604700088501 2503.313720703125 0.44934895634651184 0.7360139 2.5756936073303223 True -6 14966 23.43037700653076 0.579770565032959 1928.291259765625 1.9690322875976562 2414.1826171875 0.46249639987945557 0.7461074 2.297666072845459 True -7 17104 23.47638511657715 0.5796473026275635 910.1387939453125 0.9155592918395996 2400.36328125 0.4616549611091614 0.7535619 1.8508802652359009 True -8 19242 23.521464586257935 0.5826416015625 938.9389038085938 0.8985524773597717 2361.790283203125 0.4647713303565979 0.7585042 1.521504282951355 True -9 21380 23.476288318634033 0.5836706161499023 1528.845458984375 1.1858124732971191 2329.99755859375 0.4733681380748749 0.76161885 1.3982188701629639 True -10 23518 23.493746995925903 0.5784235000610352 1225.99462890625 1.7263209819793701 2302.2646484375 0.4754796028137207 0.7700772 1.226928472518921 True -11 25656 23.484923362731934 0.5837156772613525 1725.2330322265625 1.263519048690796 2264.99951171875 0.48259976506233215 0.7784455 1.1286532878875732 True -12 27794 23.520673513412476 0.5879487991333008 1225.07958984375 0.8914566040039062 2247.494140625 0.4849857687950134 0.78282076 1.0911439657211304 True -13 29932 23.5009548664093 0.5848488807678223 1497.721435546875 1.1100085973739624 2208.300048828125 0.4918244183063507 0.7891453 1.0282204151153564 True -14 32070 23.533556938171387 0.5805816650390625 1111.998779296875 0.8882795572280884 2194.580078125 0.49319422245025635 0.79510576 0.9823572039604187 True -15 34208 23.099109888076782 0.5743634700775146 1149.07275390625 0.6547009944915771 2154.40576171875 0.49910640716552734 0.80062574 0.9567945003509521 True -16 36346 23.019020080566406 0.5798873901367188 1767.1832275390625 1.0602338314056396 2152.9873046875 0.5001153349876404 0.8055982 0.9180176854133606 True -17 38484 23.04179549217224 0.5735414028167725 1180.17333984375 0.6293187141418457 2159.1044921875 0.4976506531238556 0.8071391 0.9048870801925659 True -18 40622 23.029011487960815 0.5749301910400391 1266.101318359375 0.5924656391143799 2151.98291015625 0.50006103515625 0.8084906 0.8924329876899719 True -19 42760 23.056880235671997 0.5743353366851807 1824.3299560546875 0.6267420053482056 2147.80322265625 0.5020601153373718 0.8086736 0.8938407301902771 True diff --git a/ENCSR903SKE/cherimoya.fold_1.performance.tsv b/ENCSR903SKE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c44f90cb2407b9a071a35630b04c8246d8149039..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2147.80322265625 0.267072856426239 0.5020601153373718 0.31272804737091064 0.808673620223999 0.7388531565666199 0.8938407301902771 \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_2.evaluate.json b/ENCSR903SKE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 146a2a05466add33b518854642739c65b845f5ce..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF492IQG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_2.fit.json b/ENCSR903SKE/cherimoya.fold_2.fit.json deleted file mode 100644 index 729d8cfae7ced8952cc0eb64fd3a8b0883d7e5a0..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF492IQG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_2.log b/ENCSR903SKE/cherimoya.fold_2.log deleted file mode 100644 index 3514ff35493b7e9f8ef056b44649cb9c14869f29..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2285 28.952682495117188 3.368346691131592 1726.1566162109375 1.2899471521377563 3078.9677734375 0.27831071615219116 0.48436067 19.700359344482422 True -1 4570 25.157397270202637 0.46254587173461914 1538.37548828125 1.5906075239181519 2356.50390625 0.38102108240127563 0.6554351 8.909375190734863 True -2 6855 25.118943214416504 2.0166966915130615 1569.401123046875 1.506890058517456 2253.5869140625 0.40250322222709656 0.6683795 4.987585067749023 True -3 9140 25.163992881774902 24.821940183639526 1367.67236328125 0.8389909267425537 2141.6103515625 0.41499632596969604 0.6841299 3.7826735973358154 True -4 11425 25.398827075958252 0.4689209461212158 1696.3919677734375 1.497471570968628 2059.67041015625 0.43204736709594727 0.6932112 3.215151071548462 True -5 13710 25.096072673797607 0.47524499893188477 1982.79443359375 1.5318938493728638 2027.8790283203125 0.4352548122406006 0.7001918 2.888556957244873 True -6 15995 25.23245406150818 0.466381311416626 2221.6123046875 1.5912437438964844 1991.14208984375 0.4409354627132416 0.7079972 2.3366763591766357 True -7 18280 25.105084896087646 0.4823641777038574 1322.71826171875 0.7989168167114258 1968.797119140625 0.44279778003692627 0.71674955 1.6733946800231934 True -8 20565 25.097721576690674 0.45282673835754395 1704.029296875 1.5051801204681396 1936.55419921875 0.4473482370376587 0.7216228 1.5908375978469849 True -9 22850 25.19049382209778 0.46916866302490234 1321.88134765625 1.172744870185852 1904.282958984375 0.45352450013160706 0.73100746 1.4504667520523071 True -10 25135 25.16180157661438 0.45256686210632324 1033.124267578125 0.8162097334861755 1903.87451171875 0.45675554871559143 0.7337113 1.4636011123657227 True -11 27420 24.687199592590332 0.46253037452697754 1390.7109375 0.7110324501991272 1863.4404296875 0.4648745656013489 0.74166393 1.2519946098327637 True -12 29705 24.69695472717285 0.46328043937683105 1432.2464599609375 1.0335724353790283 1838.051025390625 0.470752090215683 0.74674374 1.0967100858688354 True -13 31990 24.687614917755127 0.45426440238952637 1507.212890625 1.154214859008789 1830.52783203125 0.4730810523033142 0.7547755 1.0412825345993042 True -14 34275 24.692639350891113 0.8818521499633789 991.95263671875 1.0634715557098389 1812.1595458984375 0.4772942364215851 0.75841844 0.9948480725288391 True -15 36560 24.733550786972046 0.45770764350891113 1020.5797119140625 0.8879975080490112 1806.7154541015625 0.4787501394748688 0.76406825 0.965309739112854 True -16 38845 24.661293268203735 0.4479343891143799 1545.968505859375 0.8853748440742493 1799.4166259765625 0.47735345363616943 0.7696375 0.9279573559761047 True -17 41130 24.64499068260193 0.4561502933502197 1255.72021484375 1.1311438083648682 1795.213623046875 0.4799731373786926 0.77079386 0.9066248536109924 True -18 43415 24.63960909843445 0.4633145332336426 1266.29345703125 0.7452908754348755 1797.9061279296875 0.4786301553249359 0.7708297 0.8961968421936035 True -19 45700 24.63649868965149 0.46528100967407227 1378.33544921875 0.9405900239944458 1791.89794921875 0.4809340834617615 0.77049345 0.8961766958236694 False diff --git a/ENCSR903SKE/cherimoya.fold_2.performance.tsv b/ENCSR903SKE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 92a1a73cc4c9d553dc1dda1c771c1a8d886f0a73..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1797.9061279296875 0.2827635109424591 0.4786301553249359 0.28558415174484253 0.7708296775817871 0.6640859842300415 0.8961968421936035 \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_3.evaluate.json b/ENCSR903SKE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e98d03cea07618dc4749adfde3e973a877f5cd12..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF492IQG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_3.fit.json b/ENCSR903SKE/cherimoya.fold_3.fit.json deleted file mode 100644 index 0341a05517e597c57a3f525504f6b92a827e26ba..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF492IQG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_3.log b/ENCSR903SKE/cherimoya.fold_3.log deleted file mode 100644 index 051de352a1d61a3476b305b361d93a3fea3ab7c6..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2119 26.817748546600342 3.3395659923553467 1295.73046875 1.5520020723342896 3339.0703125 0.2940252423286438 0.5160823 23.58733367919922 True -1 4238 23.317952394485474 0.42568349838256836 1679.255859375 1.536806344985962 2596.289306640625 0.3971130847930908 0.65180504 9.31517505645752 True -2 6357 23.293408632278442 0.9877297878265381 2114.88818359375 1.5981814861297607 2474.533203125 0.422985315322876 0.6483382 6.278715133666992 False -3 8476 23.30348777770996 0.4245765209197998 2039.92919921875 1.5570075511932373 2360.616943359375 0.4384266138076782 0.6753399 4.501228332519531 True -4 10595 23.251492977142334 0.4136471748352051 1509.419189453125 1.2407710552215576 2269.45166015625 0.4518497884273529 0.690798 3.7191972732543945 True -5 12714 23.25964617729187 0.4202442169189453 1269.558837890625 1.09675931930542 2212.78662109375 0.4621354639530182 0.6986549 2.807767629623413 True -6 14833 23.28071928024292 0.4158759117126465 2026.7607421875 1.6610095500946045 2195.698974609375 0.4637441039085388 0.7076618 2.369478464126587 True -7 16952 23.116912603378296 0.4092426300048828 1331.936767578125 0.8581879138946533 2159.80419921875 0.4702393710613251 0.7091965 2.190852642059326 True -8 19071 22.826186180114746 0.41106343269348145 1352.2978515625 1.2824375629425049 2110.08349609375 0.479954332113266 0.7149428 1.892948865890503 True -9 21190 22.845722913742065 0.4141554832458496 1491.964599609375 1.2468702793121338 2099.76318359375 0.4803382456302643 0.72143877 1.655978798866272 True -10 23309 22.872087955474854 0.4156606197357178 2064.39990234375 1.4633409976959229 2080.031982421875 0.4832521975040436 0.72644657 1.417968511581421 True -11 25428 22.85451078414917 0.41049981117248535 1265.848876953125 1.2601182460784912 2043.111572265625 0.49316293001174927 0.7317059 1.362721562385559 True -12 27547 22.85355281829834 0.4099740982055664 1654.3096923828125 1.1570523977279663 2025.8984375 0.4941989481449127 0.7341586 1.2400026321411133 True -13 29666 22.832399368286133 0.4145164489746094 992.7982177734375 1.1298636198043823 1998.2364501953125 0.4983014762401581 0.74448746 1.1517306566238403 True -14 31785 22.836520433425903 1.4061708450317383 901.3720703125 0.9556689262390137 1973.9940185546875 0.5025441646575928 0.7530238 1.0840420722961426 True -15 33904 22.839384078979492 13.964122772216797 1559.13720703125 0.6673609018325806 1964.9427490234375 0.5033105611801147 0.7599632 1.0475780963897705 True -16 36023 24.819059371948242 0.4221622943878174 1469.0045166015625 0.9125363230705261 1972.1556396484375 0.5013088583946228 0.7647741 1.025740146636963 True -17 38142 22.855939388275146 0.4167482852935791 1349.1220703125 1.080857276916504 1945.089111328125 0.5086305737495422 0.769692 1.0078810453414917 True -18 40261 22.839805603027344 0.41170787811279297 1466.6268310546875 1.2504644393920898 1949.4605712890625 0.5089348554611206 0.7699784 1.0041033029556274 True -19 42380 22.874249935150146 0.41770434379577637 1169.658447265625 0.7980543971061707 1950.494384765625 0.5084570646286011 0.7700806 1.0014690160751343 True diff --git a/ENCSR903SKE/cherimoya.fold_3.performance.tsv b/ENCSR903SKE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2d2f998ddf1303c9d1b332cd1fc736ddb2ae2ef4..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1950.494384765625 0.2687877416610718 0.5084571242332458 0.3020656108856201 0.7700806260108948 0.6778963804244995 1.0014690160751343 \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_4.evaluate.json b/ENCSR903SKE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index f1578327045aece8cc8754e1aa98604a84e3834b..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF492IQG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_4.fit.json b/ENCSR903SKE/cherimoya.fold_4.fit.json deleted file mode 100644 index 2802608a73ef7f1307fa971bc5d73a1c62a00cc3..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF492IQG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903SKE/cherimoya.fold_4.log b/ENCSR903SKE/cherimoya.fold_4.log deleted file mode 100644 index b72c087452c007106ac9cc8c9ae18cda5a3eaea6..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2167 27.381742000579834 3.3607375621795654 1738.5750732421875 1.6738600730895996 2899.3984375 0.28996220231056213 0.5261241 20.12999725341797 True -1 4334 23.863500833511353 1.3294594287872314 1508.789306640625 0.7825616598129272 2262.2001953125 0.3977745771408081 0.635888 8.974509239196777 True -2 6501 23.808005571365356 0.4098818302154541 1697.2967529296875 1.2749450206756592 2163.7763671875 0.4192553758621216 0.634831 6.0252299308776855 False -3 8668 23.8254656791687 0.4136817455291748 1763.6566162109375 1.3572003841400146 2088.5986328125 0.4311327338218689 0.65842676 4.704689025878906 True -4 10835 23.74510407447815 0.4058501720428467 1781.5030517578125 1.6087032556533813 2017.115478515625 0.4405970573425293 0.67523104 2.881495714187622 True -5 13002 23.42515730857849 0.4161257743835449 1327.31640625 0.9410114288330078 1952.5208740234375 0.4506126642227173 0.69119567 2.0393247604370117 True -6 15169 23.392134428024292 0.41077446937561035 1694.071044921875 1.5281860828399658 1904.5057373046875 0.4571864604949951 0.69700664 1.7292771339416504 True -7 17336 23.37636637687683 0.41016483306884766 2034.690185546875 1.1529929637908936 1867.5081787109375 0.465116411447525 0.6993878 1.5862282514572144 True -8 19503 23.4246928691864 0.4109480381011963 1447.1875 1.0580768585205078 1836.89453125 0.4713066816329956 0.7097392 1.3961516618728638 True -9 21670 23.494059801101685 0.4139444828033447 1773.138427734375 0.913170337677002 1828.1383056640625 0.4719218611717224 0.7147227 1.1967167854309082 True -10 23837 23.441807985305786 0.4141852855682373 1275.013427734375 1.380438208580017 1797.6116943359375 0.481806218624115 0.71874636 1.1429338455200195 True -11 26004 23.394429445266724 2.5476431846618652 1224.5006103515625 0.8634162545204163 1783.392822265625 0.4853520095348358 0.72063214 1.0700156688690186 True -12 28171 23.471008777618408 0.4106786251068115 1871.807861328125 1.2739179134368896 1755.13232421875 0.49130141735076904 0.73034775 1.0387521982192993 True -13 30338 23.45792055130005 1.371462345123291 1591.2274169921875 1.1705796718597412 1726.0260009765625 0.4994479715824127 0.73803055 1.0044147968292236 True -14 32505 23.471761226654053 0.4134221076965332 1402.716796875 1.0821404457092285 1721.73486328125 0.49915722012519836 0.74096054 0.9729026556015015 True -15 34672 23.52379536628723 0.4117147922515869 1427.785888671875 0.5179508924484253 1706.4539794921875 0.5033837556838989 0.7472649 0.950199544429779 True -16 36839 23.456523895263672 0.7571725845336914 1177.808837890625 0.8386154770851135 1705.247802734375 0.5029574036598206 0.7525123 0.9316125512123108 True -17 39006 23.337871313095093 0.43445801734924316 977.614501953125 0.7879133224487305 1708.9378662109375 0.5017311573028564 0.7562612 0.923977255821228 True -18 41173 23.356333017349243 0.4163370132446289 1633.796142578125 1.0217480659484863 1715.6219482421875 0.5014087557792664 0.75685835 0.9264475703239441 True -19 43340 23.40642285346985 1.155893087387085 1327.793701171875 0.6309823393821716 1711.392822265625 0.5026342272758484 0.757567 0.9269734025001526 True diff --git a/ENCSR903SKE/cherimoya.fold_4.performance.tsv b/ENCSR903SKE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index caa1d2adab786aa688da92da3433253eb93ca4dd..0000000000000000000000000000000000000000 --- a/ENCSR903SKE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1711.392822265625 0.2762328088283539 0.5026342272758484 0.28684571385383606 0.7575669884681702 0.6577633619308472 0.9269734025001526 \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_0.evaluate.json b/ENCSR903WVU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 985c211fefe3d98024fb9fe02e0785c7ec376362..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126FUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_0.fit.json b/ENCSR903WVU/cherimoya.fold_0.fit.json deleted file mode 100644 index 24e0a76e474bc258e2b0b34659eca26586ca8155..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF126FUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_0.log b/ENCSR903WVU/cherimoya.fold_0.log deleted file mode 100644 index 9f19154548da8c0426ce75afe68d7b8b4ea021e8..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1764 23.420323848724365 3.2785980701446533 474.92578125 2.4844675064086914 1324.1519775390625 0.4644722044467926 0.5540109 25.786422729492188 True -1 3528 19.561853408813477 0.3768324851989746 738.3568115234375 1.3248193264007568 875.378662109375 0.6545785665512085 0.6350538 15.4183931350708 True -2 5292 19.527182817459106 0.35146117210388184 531.3327026367188 1.7793264389038086 750.92041015625 0.7288926243782043 0.6348521 5.799767017364502 False -3 7056 19.527471780776978 0.35134172439575195 530.201171875 1.7863752841949463 718.615478515625 0.7433642148971558 0.6325084 3.664752244949341 False -4 8820 19.583537817001343 0.5867791175842285 477.68316650390625 1.7293932437896729 702.8953857421875 0.7519370317459106 0.63523877 3.0375900268554688 True -5 10584 19.558717489242554 0.35298895835876465 547.677734375 1.4903228282928467 694.798095703125 0.7566571235656738 0.64679736 2.67832612991333 True -6 12348 19.566302061080933 0.3473076820373535 568.7291259765625 1.2270700931549072 687.5679321289062 0.7611068487167358 0.6434184 2.5740721225738525 False -7 14112 19.546607494354248 0.3477363586425781 411.69970703125 1.1452125310897827 677.8895263671875 0.7670331597328186 0.65130424 2.3427088260650635 True -8 15876 19.545693159103394 0.35471439361572266 481.63665771484375 1.5850188732147217 667.608642578125 0.7721110582351685 0.6608178 1.95844566822052 True -9 17640 19.535133838653564 0.3497152328491211 387.99346923828125 1.337387204170227 661.0623779296875 0.7760477066040039 0.67623144 1.6605530977249146 True -10 19404 19.526544332504272 0.34864115715026855 492.744384765625 1.1112544536590576 655.6522216796875 0.7797655463218689 0.6798375 1.5955665111541748 True -11 21168 19.596007585525513 0.35086584091186523 468.6178894042969 1.489909052848816 646.1179809570312 0.7835460305213928 0.69659144 1.4015675783157349 True -12 22932 19.563246965408325 0.3479917049407959 443.033447265625 1.1354341506958008 640.0564575195312 0.7864664793014526 0.7089647 1.2374762296676636 True -13 24696 19.540476083755493 0.34725427627563477 410.500732421875 1.122772216796875 634.6046142578125 0.7884607911109924 0.72153914 1.1456300020217896 True -14 26460 19.543006896972656 0.35153961181640625 450.968505859375 0.7628977298736572 630.7319946289062 0.7902507185935974 0.7272989 1.1110318899154663 True -15 28224 19.543158292770386 0.35080981254577637 503.72845458984375 0.7803245782852173 627.8790893554688 0.7917764782905579 0.7322953 1.077246069908142 True -16 29988 19.5446195602417 0.35204648971557617 465.4233093261719 0.9110588431358337 627.3482055664062 0.7915112376213074 0.7351059 1.0701977014541626 True -17 31752 19.54410696029663 0.3484225273132324 549.4008178710938 0.43738359212875366 629.2412109375 0.7904007434844971 0.7356129 1.0671416521072388 True -18 33516 19.53826069831848 0.34804868698120117 497.66937255859375 0.6669207215309143 630.9522094726562 0.7891780734062195 0.7338334 1.0853670835494995 False -19 35280 19.544427633285522 0.3507847785949707 408.54522705078125 0.5362597107887268 632.10205078125 0.7884935736656189 0.7328585 1.1016829013824463 False diff --git a/ENCSR903WVU/cherimoya.fold_0.performance.tsv b/ENCSR903WVU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index be72be011bf1fe7c78b956d6028719da8b364af0..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -629.2412109375 0.18468135595321655 0.7904006838798523 0.35967203974723816 0.7356129288673401 0.7098321318626404 1.0671416521072388 \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_1.evaluate.json b/ENCSR903WVU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 622e7b753768bf636a31c3813481e511bc3f68d0..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126FUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_1.fit.json b/ENCSR903WVU/cherimoya.fold_1.fit.json deleted file mode 100644 index 1da2f9dfe05938a6da2b64a0b5de1c02675e32e4..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF126FUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_1.log b/ENCSR903WVU/cherimoya.fold_1.log deleted file mode 100644 index da4e9f3c9ffe1f937dbac12e1a14cad04b5f9a67..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1738 23.094006776809692 3.5131819248199463 747.8013916015625 2.111185073852539 1514.0225830078125 0.4712778925895691 0.53221995 26.55674934387207 True -1 3476 19.233771324157715 1.1596040725708008 582.9346313476562 2.1614956855773926 997.3800048828125 0.6560050845146179 0.62692803 18.895254135131836 True -2 5214 19.288289308547974 0.540900468826294 565.1245727539062 1.6945111751556396 850.7568359375 0.7387908101081848 0.64456856 5.973522663116455 True -3 6952 19.23771381378174 0.5389578342437744 536.9384765625 2.109804391860962 801.044921875 0.7554963231086731 0.64540064 3.0716028213500977 True -4 8690 19.248949766159058 1.8528203964233398 562.4251708984375 1.4472334384918213 782.8012084960938 0.7640770673751831 0.6507215 2.571611166000366 True -5 10428 19.20897078514099 0.5428740978240967 558.16357421875 2.053555727005005 770.69970703125 0.7707542181015015 0.6604168 2.1607022285461426 True -6 12166 19.231076955795288 0.5400359630584717 601.3051147460938 1.8433524370193481 757.2639770507812 0.7770002484321594 0.6709065 1.9040673971176147 True -7 13904 19.209141731262207 0.5352368354797363 519.322998046875 1.0931944847106934 745.3525390625 0.7818047404289246 0.6765289 1.75338613986969 True -8 15642 19.210086822509766 0.536113977432251 517.195556640625 1.2016429901123047 740.0477294921875 0.7857442498207092 0.68231595 1.5995824337005615 True -9 17380 19.24148654937744 0.5622050762176514 577.682861328125 1.580958366394043 729.3832397460938 0.790362536907196 0.6892637 1.419801115989685 True -10 19118 19.22675848007202 0.5351800918579102 473.31561279296875 1.9755702018737793 722.2706909179688 0.794266402721405 0.6929561 1.4432517290115356 True -11 20856 19.207393646240234 0.534907341003418 434.93310546875 1.2751280069351196 713.7556762695312 0.7979510426521301 0.71234363 1.2951606512069702 True -12 22594 19.245851755142212 0.5420839786529541 566.696533203125 0.8518354296684265 705.9891967773438 0.8015337586402893 0.7172418 1.2282549142837524 True -13 24332 19.227065324783325 0.5422492027282715 523.820068359375 1.121353030204773 700.262451171875 0.8039891719818115 0.724936 1.1876020431518555 True -14 26070 19.259310007095337 0.5426328182220459 501.5569763183594 1.1898581981658936 693.8075561523438 0.8065506815910339 0.7375935 1.0927635431289673 True -15 27808 19.26960277557373 12.508718252182007 423.7803955078125 0.9038840532302856 690.7632446289062 0.807590663433075 0.74271494 1.0667810440063477 True -16 29546 19.3989679813385 0.5371079444885254 453.46429443359375 0.9206379055976868 690.2793579101562 0.8074125647544861 0.74951494 1.040717363357544 True -17 31284 19.346065044403076 0.5376555919647217 463.21563720703125 0.632535457611084 690.719970703125 0.8068752884864807 0.75226814 1.0376731157302856 True -18 33022 19.2799334526062 0.5397372245788574 540.899658203125 0.7679862380027771 692.1434326171875 0.8060759902000427 0.750618 1.0396214723587036 False -19 34760 19.28538465499878 0.5360846519470215 420.0212097167969 0.7746552228927612 692.955322265625 0.8054143786430359 0.7509542 1.0475916862487793 False diff --git a/ENCSR903WVU/cherimoya.fold_1.performance.tsv b/ENCSR903WVU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f6fb51fc3fabaf1093fa308bb09c3db55c6564c0..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -690.719970703125 0.16966168582439423 0.8068752884864807 0.39051616191864014 0.7522681355476379 0.7517859935760498 1.0376731157302856 \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_2.evaluate.json b/ENCSR903WVU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4b8156c149214bb4374843af722a311cc2d4f7b1..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126FUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_2.fit.json b/ENCSR903WVU/cherimoya.fold_2.fit.json deleted file mode 100644 index 1d17562dd2f30d647c5fd2bdc55307fce0d2d5b2..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF126FUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_2.log b/ENCSR903WVU/cherimoya.fold_2.log deleted file mode 100644 index 4cf4ef6085dd99042d15892428da855e0bc557d9..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1861 24.408806562423706 3.3376879692077637 533.4468994140625 2.502115249633789 1376.1907958984375 0.4748647212982178 0.5427708 23.410987854003906 True -1 3722 20.561776638031006 0.4078660011291504 577.4832153320312 1.536446213722229 892.7791137695312 0.678596556186676 0.62126726 15.331475257873535 True -2 5583 20.594071626663208 0.39290332794189453 442.32568359375 1.680541753768921 793.0883178710938 0.7370973825454712 0.6373646 6.046139717102051 True -3 7444 20.554476022720337 0.38744592666625977 568.75341796875 1.917830467224121 752.9448852539062 0.7525308728218079 0.64653563 3.383930206298828 True -4 9305 20.581136226654053 0.38775134086608887 590.511962890625 1.553383231163025 735.9763793945312 0.7612596154212952 0.6572998 2.80832839012146 True -5 11166 20.55370330810547 0.38539862632751465 596.0541381835938 1.3010693788528442 727.4036865234375 0.766528844833374 0.66509634 2.633657932281494 True -6 13027 20.574275732040405 0.46314120292663574 548.0515747070312 1.3591067790985107 713.5269775390625 0.7722300887107849 0.6726905 2.351235866546631 True -7 14888 20.578307390213013 0.38578224182128906 630.6858520507812 1.2401856184005737 707.6597900390625 0.7757775187492371 0.67145276 2.070269823074341 False -8 16749 20.585734367370605 0.3961334228515625 635.983154296875 1.1305383443832397 699.2806396484375 0.7797123789787292 0.6776807 1.8393293619155884 True -9 18610 20.6656391620636 0.3900320529937744 545.84521484375 1.4379591941833496 690.070068359375 0.7843098044395447 0.6833402 1.6260371208190918 True -10 20471 20.630557775497437 0.3903815746307373 536.2388916015625 1.1799249649047852 679.30419921875 0.7888758182525635 0.69609296 1.4149600267410278 True -11 22332 20.57333469390869 0.3906736373901367 579.614501953125 1.4323440790176392 672.3124389648438 0.7924262881278992 0.704709 1.316676378250122 True -12 24193 20.584407091140747 1.3866991996765137 569.2452392578125 1.4374346733093262 665.2781982421875 0.7960003018379211 0.71636564 1.2265058755874634 True -13 26054 20.611023664474487 0.3902716636657715 477.43902587890625 0.842140257358551 657.8187255859375 0.7985230684280396 0.7273151 1.1558747291564941 True -14 27915 20.59597158432007 0.38558197021484375 432.877685546875 1.2009204626083374 652.1265258789062 0.8003354072570801 0.736275 1.0830378532409668 True -15 29776 20.61870837211609 0.7167832851409912 500.396240234375 1.2373747825622559 649.00927734375 0.8018051981925964 0.745631 1.0470319986343384 True -16 31637 20.618363618850708 0.39097166061401367 358.94482421875 0.6448597311973572 648.472900390625 0.8018330335617065 0.7489704 1.0259039402008057 True -17 33498 20.603893995285034 0.38390541076660156 524.323486328125 0.8816036581993103 649.6808471679688 0.801358699798584 0.7517141 1.0207093954086304 True -18 35359 20.587096452713013 0.38147830963134766 635.001708984375 0.586885392665863 650.6401977539062 0.8003109097480774 0.754546 1.0189743041992188 True -19 37220 20.641520500183105 0.386521577835083 452.4419250488281 0.5082963109016418 652.1835327148438 0.7996258735656738 0.7527801 1.0212613344192505 False diff --git a/ENCSR903WVU/cherimoya.fold_2.performance.tsv b/ENCSR903WVU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 07efb0fdda2a93b7baff233a324ad7de8d4e3c37..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -650.6401977539062 0.17756164073944092 0.8003110289573669 0.37335580587387085 0.7545459866523743 0.7387719750404358 1.0189743041992188 \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_3.evaluate.json b/ENCSR903WVU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 680065a0c0c32bb035e08f83fda22dfa760bc2c5..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126FUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_3.fit.json b/ENCSR903WVU/cherimoya.fold_3.fit.json deleted file mode 100644 index 3f43790697606cde96b26d2a5c27214be7cf9c5a..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF126FUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_3.log b/ENCSR903WVU/cherimoya.fold_3.log deleted file mode 100644 index db2bc1536431ef1531b4c7f25f7ef863ccbd839d..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1808 24.116379022598267 3.3255300521850586 491.3128967285156 2.8706936836242676 1341.8167724609375 0.4722830355167389 0.55068344 26.008665084838867 True -1 3616 20.23832106590271 0.4107227325439453 557.2445068359375 1.7885680198669434 875.9521484375 0.6681821942329407 0.6214673 15.586642265319824 True -2 5424 20.23266363143921 0.3953835964202881 491.88775634765625 1.8760466575622559 773.5404663085938 0.730414092540741 0.60506976 5.817634582519531 False -3 7232 20.231790781021118 0.39746975898742676 542.1509399414062 1.8370774984359741 733.8131713867188 0.7482950687408447 0.605517 3.2321488857269287 False -4 9040 20.19914221763611 0.39067792892456055 539.67041015625 1.8622510433197021 722.0813598632812 0.7551524043083191 0.6076493 2.898193359375 False -5 10848 20.226964712142944 0.6276004314422607 562.394287109375 2.0469579696655273 717.4601440429688 0.7588887810707092 0.6107408 2.626093626022339 False -6 12656 20.219210863113403 0.40145349502563477 571.7294921875 1.4629111289978027 709.9629516601562 0.7633234858512878 0.61504143 2.3671956062316895 False -7 14464 20.192912578582764 0.39672279357910156 689.3515625 2.252955436706543 703.4082641601562 0.7664432525634766 0.63135594 2.2542524337768555 True -8 16272 20.199432134628296 0.39141345024108887 435.6922607421875 1.2879483699798584 694.41455078125 0.7711020708084106 0.64948374 1.9658491611480713 True -9 18080 20.211013317108154 0.6442074775695801 621.8126220703125 1.1344842910766602 686.829345703125 0.774817943572998 0.65582776 1.8381421566009521 True -10 19888 20.20815873146057 0.3896970748901367 442.85491943359375 1.2423765659332275 680.5227661132812 0.7787027359008789 0.6664014 1.7110517024993896 True -11 21696 20.208902835845947 0.39583849906921387 451.2557373046875 1.4850234985351562 671.3461303710938 0.7836706638336182 0.68089885 1.5586243867874146 True -12 23504 20.214269161224365 0.39531731605529785 391.67938232421875 0.9862232208251953 662.5638427734375 0.787326455116272 0.6902889 1.4625799655914307 True -13 25312 20.2187283039093 0.39699625968933105 470.01312255859375 1.0787843465805054 655.6280517578125 0.7900336980819702 0.6993494 1.3385432958602905 True -14 27120 20.19860816001892 0.3926095962524414 441.5429382324219 1.0107917785644531 651.21435546875 0.792044997215271 0.71300745 1.248307228088379 True -15 28928 20.216644763946533 0.3907182216644287 405.805419921875 1.5702264308929443 648.6148681640625 0.7929275035858154 0.723764 1.1849902868270874 True -16 30736 20.18102717399597 0.39511656761169434 461.935302734375 0.5951166749000549 648.5628662109375 0.7928493618965149 0.72986084 1.1681156158447266 True -17 32544 20.198511362075806 0.39211440086364746 397.8659362792969 0.7848794460296631 649.4362182617188 0.7921133041381836 0.7333016 1.1555793285369873 True -18 34352 20.215104341506958 0.4015979766845703 416.2662353515625 0.5642963647842407 650.54541015625 0.791363537311554 0.7330117 1.1606500148773193 False -19 36160 20.19704508781433 0.3942289352416992 424.391845703125 0.5514581799507141 651.3914794921875 0.7909651398658752 0.73180395 1.1718571186065674 False diff --git a/ENCSR903WVU/cherimoya.fold_3.performance.tsv b/ENCSR903WVU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d7eb6acc7cb0b6b24de449adebf33a1ae6afdca6..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -649.4362182617188 0.1810992956161499 0.7921133041381836 0.36408695578575134 0.73330157995224 0.7183524966239929 1.1555793285369873 \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_4.evaluate.json b/ENCSR903WVU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ac89cdd4d23d8d300ba35d7fc3366b9d740afb7d..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF126FUJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_4.fit.json b/ENCSR903WVU/cherimoya.fold_4.fit.json deleted file mode 100644 index b4aa954158cca7ae9ff232890e27e3289bc98b94..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF126FUJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR903WVU/cherimoya.fold_4.log b/ENCSR903WVU/cherimoya.fold_4.log deleted file mode 100644 index d772f29e11611fba1b84a0bebe00a6e69b29994f..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1778 23.74151349067688 3.2556917667388916 646.2528686523438 2.378554582595825 1290.601318359375 0.4635077118873596 0.5471707 21.13709259033203 True -1 3556 19.90347146987915 0.364013671875 523.7020263671875 1.5232439041137695 862.5277099609375 0.650537371635437 0.62279683 14.166279792785645 True -2 5334 19.912821292877197 0.3393678665161133 712.9175415039062 1.665196418762207 733.21533203125 0.727235734462738 0.5971426 5.3436431884765625 False -3 7112 19.864452362060547 0.3358490467071533 509.8898620605469 1.4544525146484375 700.9509887695312 0.7410969138145447 0.6047982 2.838087558746338 False -4 8890 19.861180305480957 0.33575940132141113 512.1049194335938 1.821819543838501 684.9143676757812 0.7499817609786987 0.6085988 2.3936617374420166 False -5 10668 19.861689567565918 0.33062219619750977 471.6620178222656 2.2629594802856445 675.0001220703125 0.7561286687850952 0.6194563 2.2566676139831543 False -6 12446 19.867281913757324 0.3347511291503906 555.7703857421875 2.1595914363861084 667.287841796875 0.7610734701156616 0.63125294 2.1563315391540527 True -7 14224 19.875786542892456 0.3315579891204834 611.0494995117188 1.5841364860534668 656.6806640625 0.7663354277610779 0.6422787 1.7809498310089111 True -8 16002 19.872183799743652 0.33110833168029785 430.77032470703125 1.7474336624145508 651.4456176757812 0.7704836130142212 0.64585084 1.7968512773513794 True -9 17780 19.86925506591797 0.33594322204589844 564.8013916015625 1.176855206489563 644.1492919921875 0.7743704319000244 0.6495453 1.6924704313278198 True -10 19558 19.874570846557617 0.3395872116088867 396.31103515625 1.380892038345337 637.5048828125 0.7780311107635498 0.66193706 1.5497441291809082 True -11 21336 19.88577127456665 0.3348538875579834 403.4604797363281 0.824232816696167 630.082275390625 0.781064510345459 0.6678719 1.4158097505569458 True -12 23114 19.909615516662598 0.3447995185852051 369.04644775390625 1.1341707706451416 624.2031860351562 0.7839965224266052 0.68372256 1.302871823310852 True -13 24892 19.916438579559326 0.3358330726623535 339.5079650878906 1.1345839500427246 619.9129028320312 0.7863094806671143 0.6974134 1.2017970085144043 True -14 26670 19.885738372802734 3.061065912246704 513.57861328125 1.2088642120361328 617.0821533203125 0.7877611517906189 0.7064139 1.1643264293670654 True -15 28448 19.926931142807007 0.3337996006011963 451.9075927734375 1.1258543729782104 613.685302734375 0.788507342338562 0.7151033 1.1187211275100708 True -16 30226 19.877747058868408 0.33461761474609375 445.84765625 0.8135351538658142 613.0 0.7884414792060852 0.71739 1.0993032455444336 True -17 32004 19.873941659927368 0.3317604064941406 498.8182678222656 0.41168397665023804 612.6728515625 0.7880154252052307 0.7190618 1.1054145097732544 True -18 33782 19.882328748703003 0.33497071266174316 464.83697509765625 0.8054057955741882 613.95068359375 0.7870975732803345 0.71991974 1.1119909286499023 True -19 35560 19.87874126434326 0.33307766914367676 374.17236328125 0.47701239585876465 614.9480590820312 0.7866038680076599 0.7174563 1.117063283920288 False diff --git a/ENCSR903WVU/cherimoya.fold_4.performance.tsv b/ENCSR903WVU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e3f8b46e393a51ac3721b4d208d81b66287c968c..0000000000000000000000000000000000000000 --- a/ENCSR903WVU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -613.95068359375 0.1869664043188095 0.7870975136756897 0.3541293144226074 0.719919741153717 0.6889775991439819 1.1119909286499023 \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_0.evaluate.json b/ENCSR904GDU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 54f4c1ce170a8cfe861fd0fa0ba8ad6c89967574..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF565TTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_0.fit.json b/ENCSR904GDU/cherimoya.fold_0.fit.json deleted file mode 100644 index 6051c26ec54a3033de5a98bd36483bd4f199429f..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF565TTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_0.log b/ENCSR904GDU/cherimoya.fold_0.log deleted file mode 100644 index e2049b1f7839c35b28fbb5d57519d4aad217a74a..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1820 24.195356369018555 2.7312023639678955 225.98739624023438 1.0532602071762085 325.3045959472656 0.11869388073682785 0.64319354 8.140169143676758 True -1 3640 20.117655992507935 0.4642817974090576 232.27940368652344 1.0618870258331299 296.0164794921875 0.1727333515882492 0.7605897 4.040107727050781 True -2 5460 20.138532400131226 2.333162307739258 218.26878356933594 0.632404088973999 276.6652526855469 0.19334836304187775 0.77618223 2.248425006866455 True -3 7280 20.13173198699951 0.3486666679382324 263.619384765625 0.6208494901657104 269.2183532714844 0.19945868849754333 0.7919887 1.1106170415878296 True -4 9100 20.134766817092896 0.34825658798217773 226.68211364746094 0.8904381990432739 265.5567321777344 0.2044171541929245 0.7999989 0.8823164701461792 True -5 10920 20.110650300979614 0.7135579586029053 279.63677978515625 0.8220535516738892 263.1719665527344 0.20761121809482574 0.8098158 0.7852498292922974 True -6 12740 20.11417293548584 0.3523848056793213 185.80078125 0.3064820468425751 262.0291442871094 0.20879428088665009 0.8229233 0.7391888499259949 True -7 14560 20.052831649780273 0.34086179733276367 252.6566925048828 0.6402124166488647 261.1831970214844 0.21083424985408783 0.83138895 0.6830636262893677 True -8 16380 20.059223413467407 0.521338701248169 172.1394805908203 0.4739910066127777 259.2195739746094 0.21476025879383087 0.84387344 0.5854806900024414 True -9 18200 20.10201382637024 0.3941216468811035 232.464599609375 0.5489292740821838 258.38818359375 0.21612131595611572 0.8485815 0.5527589321136475 True -10 20020 20.06788682937622 0.41901230812072754 226.61074829101562 0.580965518951416 257.4261169433594 0.21757638454437256 0.8543413 0.509931206703186 True -11 21840 20.07225489616394 0.3456916809082031 258.856201171875 0.4936080873012543 256.4283142089844 0.21858325600624084 0.8587299 0.4897083044052124 True -12 23660 20.093844175338745 0.3506770133972168 294.18011474609375 0.49719011783599854 255.8809814453125 0.21988458931446075 0.8611058 0.4551427364349365 True -13 25480 20.03898787498474 0.3347301483154297 235.04103088378906 0.5418356657028198 255.20440673828125 0.2211342304944992 0.86586255 0.44077610969543457 True -14 27300 20.040018320083618 0.334120512008667 187.50958251953125 0.3393985629081726 254.51412963867188 0.22195588052272797 0.86778617 0.4286056458950043 True -15 29120 20.058380126953125 0.3395261764526367 213.9801025390625 0.2410603165626526 253.99147033691406 0.22259627282619476 0.87094724 0.41163504123687744 True -16 30940 20.07294249534607 0.600116491317749 209.3618927001953 0.30344316363334656 253.47348022460938 0.22294922173023224 0.87235284 0.4056605398654938 True -17 32760 20.161924123764038 0.34638500213623047 229.2269287109375 0.42800092697143555 253.81336975097656 0.2223440408706665 0.8743669 0.40197595953941345 True -18 34580 20.11405324935913 0.41625499725341797 193.54774475097656 0.30846232175827026 254.24745178222656 0.2217477709054947 0.87285197 0.4057399332523346 False -19 36400 20.075202465057373 0.35227155685424805 190.74459838867188 0.34224212169647217 253.84927368164062 0.22319845855236053 0.8714276 0.4096187949180603 False diff --git a/ENCSR904GDU/cherimoya.fold_0.performance.tsv b/ENCSR904GDU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d878d6c81a5e5338e5e41f58a46e207f4c7ea8ec..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -253.81336975097656 0.5343835353851318 0.2223440706729889 0.06566150486469269 0.8743668794631958 0.8130836486816406 0.40197595953941345 \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_1.evaluate.json b/ENCSR904GDU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b710a0eafb5a43fd9e21829b962985aa48031074..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF565TTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_1.fit.json b/ENCSR904GDU/cherimoya.fold_1.fit.json deleted file mode 100644 index b216c7cd6997d6dd4405edf13d065aa3c84891c8..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF565TTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_1.log b/ENCSR904GDU/cherimoya.fold_1.log deleted file mode 100644 index b24de3961edcd0f0875c8c803e38f0819831cd8d..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1781 23.408038854599 3.8910577297210693 299.0224304199219 1.160404920578003 416.5398254394531 0.12908481061458588 0.60529566 10.39001750946045 True -1 3562 19.6695499420166 0.5222568511962891 173.491943359375 0.7707464694976807 374.33355712890625 0.20070397853851318 0.7386793 4.561309337615967 True -2 5343 19.7084481716156 7.875472068786621 209.4501190185547 0.7029389142990112 349.5317687988281 0.22580234706401825 0.7686563 2.9337451457977295 True -3 7124 19.677982568740845 0.49926042556762695 198.9761962890625 1.0464611053466797 337.5116271972656 0.23552203178405762 0.79214406 1.59281587600708 True -4 8905 19.657835721969604 1.0652599334716797 228.64532470703125 0.9107532501220703 332.0089111328125 0.24052953720092773 0.806188 1.3509559631347656 True -5 10686 19.67810559272766 0.5145542621612549 203.21055603027344 0.9059550166130066 328.5982666015625 0.244983971118927 0.8197467 1.1599723100662231 True -6 12467 19.67060089111328 0.5048720836639404 213.1291961669922 0.7308316230773926 326.1472473144531 0.2479163259267807 0.8304022 0.9425304532051086 True -7 14248 19.648080348968506 0.48763108253479004 196.1498260498047 0.5196422338485718 323.6430358886719 0.252742201089859 0.8365707 0.8385078310966492 True -8 16029 19.65325140953064 0.4943842887878418 240.8685302734375 0.66064453125 322.4541015625 0.25417181849479675 0.8455959 0.7787889242172241 True -9 17810 19.638807773590088 0.4875986576080322 172.84886169433594 0.4880240857601166 320.5164489746094 0.25627726316452026 0.85642797 0.6752853989601135 True -10 19591 19.633814096450806 0.4989945888519287 244.36788940429688 0.4360949695110321 319.1907043457031 0.2575890123844147 0.864112 0.5977350473403931 True -11 21372 19.654565572738647 0.49616408348083496 238.22406005859375 0.6087234020233154 317.3412170410156 0.26141834259033203 0.8656216 0.5589215755462646 True -12 23153 19.67090940475464 0.502601146697998 186.2715301513672 0.5847950577735901 316.761474609375 0.2617751955986023 0.8685792 0.544517993927002 True -13 24934 19.63469171524048 0.5150659084320068 194.95895385742188 0.4175899028778076 316.432373046875 0.262148380279541 0.8720719 0.5242860913276672 True -14 26715 19.656036853790283 0.5005984306335449 199.63427734375 0.3873004913330078 316.43170166015625 0.2616853713989258 0.8742315 0.5090900659561157 True -15 28496 19.66246199607849 0.5050435066223145 240.80055236816406 0.5061405897140503 314.9020080566406 0.2638426721096039 0.87846607 0.49054041504859924 True -16 30277 19.65511655807495 0.5004725456237793 187.6121368408203 0.4844900369644165 314.5043640136719 0.2647308111190796 0.8791667 0.4781176447868347 True -17 32058 19.662779569625854 0.4898037910461426 233.32095336914062 0.2757600247859955 313.95379638671875 0.2655068337917328 0.8787915 0.475241482257843 False -18 33839 19.640150785446167 0.49785614013671875 248.6533203125 0.34203028678894043 314.5024719238281 0.2647014260292053 0.8761324 0.4813154339790344 False -19 35620 19.666009187698364 0.5011227130889893 165.77926635742188 0.19418056309223175 315.1072082519531 0.26362326741218567 0.877045 0.48626232147216797 False diff --git a/ENCSR904GDU/cherimoya.fold_1.performance.tsv b/ENCSR904GDU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 01bdeb7c7b59446515c422424db2b8a4a177e554..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -314.5043640136719 0.5024710893630981 0.2647308111190796 0.0834745317697525 0.8791667222976685 0.8481079339981079 0.4781176447868347 \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_2.evaluate.json b/ENCSR904GDU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 042a96892dc8830467fd62ca094c2979122e59f3..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF565TTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_2.fit.json b/ENCSR904GDU/cherimoya.fold_2.fit.json deleted file mode 100644 index 66d7b9bb0a4c93f22e818f8c9afc83345df2f425..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF565TTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_2.log b/ENCSR904GDU/cherimoya.fold_2.log deleted file mode 100644 index 6722f6b2852e620b8c524589578ba975d676db2e..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1919 25.07138967514038 4.356678009033203 239.14846801757812 0.6966410875320435 348.89019775390625 0.12128212302923203 0.6138301 8.128413200378418 True -1 3838 21.261903285980225 0.6049854755401611 270.8862609863281 0.8902382850646973 308.633056640625 0.18663080036640167 0.75221497 3.6869876384735107 True -2 5757 21.193597078323364 0.39070558547973633 221.88421630859375 0.5765888094902039 286.68438720703125 0.20591451227664948 0.7884393 1.870976448059082 True -3 7676 21.120545864105225 0.374279260635376 239.24234008789062 0.7424774765968323 281.78216552734375 0.21008536219596863 0.797704 1.221085548400879 True -4 9595 21.15256953239441 0.37116146087646484 220.56057739257812 0.5694136619567871 278.57659912109375 0.2147413194179535 0.8070366 0.9268733263015747 True -5 11514 21.161041259765625 0.4464418888092041 239.96334838867188 0.4560638666152954 277.16229248046875 0.21668396890163422 0.81820077 0.7679577469825745 True -6 13433 21.162700176239014 0.38809943199157715 157.65792846679688 0.43154847621917725 275.4668884277344 0.22005106508731842 0.82494175 0.6889305114746094 True -7 15352 21.140867710113525 0.4123053550720215 179.11019897460938 0.5139189958572388 273.7854919433594 0.2221059948205948 0.83455366 0.621719479560852 True -8 17271 21.16647171974182 0.37153196334838867 238.12405395507812 0.6150933504104614 272.35498046875 0.22415827214717865 0.8393126 0.5985668301582336 True -9 19190 21.1490261554718 0.40639162063598633 275.18426513671875 0.3094075918197632 271.2688293457031 0.2258150726556778 0.84422 0.5537261962890625 True -10 21109 21.145572662353516 0.3936176300048828 239.73655700683594 0.4980224668979645 270.10552978515625 0.22738754749298096 0.850313 0.49896103143692017 True -11 23028 21.18011975288391 0.38630199432373047 168.7493896484375 0.5452039837837219 269.6103820800781 0.2281789928674698 0.8554827 0.4777146875858307 True -12 24947 21.18352198600769 0.3888871669769287 197.21734619140625 0.6549698710441589 268.4305725097656 0.22989203035831451 0.85870856 0.4515793025493622 True -13 26866 21.194318771362305 1.104585886001587 237.2109375 0.32459086179733276 267.2984619140625 0.23203442990779877 0.86093324 0.44931986927986145 True -14 28785 21.188875675201416 0.3912239074707031 171.85604858398438 0.565849781036377 265.9223327636719 0.2341739386320114 0.86467093 0.4277360737323761 True -15 30704 21.19580364227295 0.8192603588104248 202.56640625 0.533446192741394 265.849853515625 0.23413486778736115 0.8668785 0.4236287772655487 True -16 32623 21.194815397262573 0.3950181007385254 171.1549530029297 0.31876081228256226 265.80657958984375 0.23365212976932526 0.8669637 0.4224592447280884 True -17 34542 21.20701289176941 0.3760499954223633 214.36895751953125 0.22935467958450317 265.9105529785156 0.2334015667438507 0.8674489 0.42665502429008484 True -18 36461 21.20884609222412 0.37693262100219727 231.98977661132812 0.36613932251930237 266.5403137207031 0.23222346603870392 0.8657476 0.4305470585823059 False -19 38380 21.25194525718689 1.0968971252441406 233.73182678222656 0.31229734420776367 266.7528076171875 0.23179346323013306 0.86637855 0.4344964623451233 False diff --git a/ENCSR904GDU/cherimoya.fold_2.performance.tsv b/ENCSR904GDU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 37a7f6584514f3dc01dc25a4822ad687f5af0be0..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -265.9105529785156 0.5259382724761963 0.2334015667438507 0.07762286812067032 0.8674489259719849 0.816007137298584 0.42665502429008484 \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_3.evaluate.json b/ENCSR904GDU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index acd22a138aae6a72631995f5610be3c0b71f5073..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF565TTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_3.fit.json b/ENCSR904GDU/cherimoya.fold_3.fit.json deleted file mode 100644 index d35bc76463c965665faf5af85cf986e7f468bbf0..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF565TTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_3.log b/ENCSR904GDU/cherimoya.fold_3.log deleted file mode 100644 index 1543a92bdb20eb4df6337795e2299b75b682661b..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1827 23.775604486465454 3.599367141723633 272.9032897949219 0.6860384941101074 351.31573486328125 0.12761683762073517 0.6131356 8.583344459533691 True -1 3654 20.242318391799927 0.3652787208557129 244.51284790039062 0.9627721905708313 315.5091247558594 0.18758301436901093 0.73944783 3.69356632232666 True -2 5481 20.213378190994263 0.362562894821167 296.7821960449219 0.9342672824859619 295.7778625488281 0.20930838584899902 0.76434696 2.239410400390625 True -3 7308 20.173401355743408 0.363358736038208 211.05810546875 0.7988187074661255 290.1288757324219 0.21464969217777252 0.7838919 1.3241782188415527 True -4 9135 20.17596435546875 0.35734081268310547 227.11753845214844 0.597413182258606 287.5115051269531 0.21846970915794373 0.7956984 1.0639371871948242 True -5 10962 20.191206216812134 0.35894131660461426 173.8537139892578 0.592364490032196 285.9448547363281 0.22045572102069855 0.805293 0.975696861743927 True -6 12789 20.202364683151245 0.36168742179870605 244.80364990234375 0.5810686349868774 284.11297607421875 0.22383776307106018 0.8177239 0.8748049736022949 True -7 14616 20.321351528167725 0.3593144416809082 215.92120361328125 0.44257086515426636 282.5243835449219 0.22614139318466187 0.8254399 0.7445806264877319 True -8 16443 20.161627769470215 0.36065220832824707 176.2947540283203 0.7344634532928467 281.3340148925781 0.22845712304115295 0.8333726 0.6850923299789429 True -9 18270 20.16556215286255 0.3760688304901123 245.4476776123047 0.6620991826057434 279.63702392578125 0.23150350153446198 0.837496 0.614623486995697 True -10 20097 20.160906076431274 0.3588082790374756 218.31402587890625 0.6691340804100037 279.39666748046875 0.23143118619918823 0.8403097 0.5646842122077942 True -11 21924 20.20240068435669 0.3601996898651123 218.09230041503906 0.3728039860725403 278.9422912597656 0.23333784937858582 0.8458371 0.559367835521698 True -12 23751 20.164741277694702 0.3585624694824219 198.00254821777344 0.33889713883399963 277.5101318359375 0.2347777634859085 0.8511998 0.5351791381835938 True -13 25578 20.1893150806427 0.36308884620666504 215.55111694335938 0.39410164952278137 276.571044921875 0.23588398098945618 0.8557606 0.5064048171043396 True -14 27405 20.13699436187744 0.36130642890930176 212.27130126953125 0.7179796099662781 275.7044372558594 0.23668690025806427 0.86149865 0.49190831184387207 True -15 29232 20.21508002281189 0.7608048915863037 301.53997802734375 0.41659536957740784 275.084716796875 0.23791195452213287 0.86538666 0.47355374693870544 True -16 31059 20.214731693267822 0.360642671585083 199.53829956054688 0.5108023881912231 274.5373229980469 0.23883818089962006 0.870296 0.45891180634498596 True -17 32886 20.15849733352661 0.3618154525756836 180.17356872558594 0.2174229621887207 275.1081237792969 0.23749606311321259 0.8689553 0.4554997384548187 False -18 34713 20.17423725128174 0.36193108558654785 224.4699249267578 0.2398899346590042 275.09539794921875 0.23689886927604675 0.86977017 0.45326030254364014 False -19 36540 20.1651291847229 0.35692501068115234 187.69406127929688 0.2940911054611206 274.7341003417969 0.23806817829608917 0.8711581 0.45473673939704895 True diff --git a/ENCSR904GDU/cherimoya.fold_3.performance.tsv b/ENCSR904GDU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b5c1ccc1a604b96f4cbe923e9986c8f39a5f1fae..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -274.7341003417969 0.5224458575248718 0.23806814849376678 0.07588551193475723 0.8711581230163574 0.8237354755401611 0.45473673939704895 \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_4.evaluate.json b/ENCSR904GDU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c4f874677ba2b92ea3f0ca3df08751c9df4b492a..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF565TTO.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_4.fit.json b/ENCSR904GDU/cherimoya.fold_4.fit.json deleted file mode 100644 index b5700d633ecbe41fe35c619e965438921389f6ea..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF565TTO.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR904GDU/cherimoya.fold_4.log b/ENCSR904GDU/cherimoya.fold_4.log deleted file mode 100644 index 365a29b86a76181628e9fc38e765276acbe853e9..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1850 24.123286724090576 3.3771185874938965 227.09149169921875 0.6670436859130859 301.4117431640625 0.11366575211286545 0.6222457 7.156510829925537 True -1 3700 20.444416522979736 0.4010758399963379 200.53622436523438 0.9398161172866821 274.71038818359375 0.16708147525787354 0.7520138 3.111220359802246 True -2 5550 20.488388061523438 2.240570068359375 234.22080993652344 0.7606983780860901 256.0605163574219 0.1882217824459076 0.76836675 1.6510087251663208 True -3 7400 20.497381448745728 0.3736894130706787 198.23654174804688 0.6331954002380371 251.50013732910156 0.19216297566890717 0.78946316 0.920050323009491 True -4 9250 20.42456865310669 0.3851780891418457 292.19720458984375 0.4070449769496918 248.47488403320312 0.1956208497285843 0.7973475 0.8849942088127136 True -5 11100 20.423022270202637 0.38440585136413574 162.95233154296875 0.786380410194397 246.58775329589844 0.19654913246631622 0.80693007 0.7571826577186584 True -6 12950 20.38665223121643 0.3779590129852295 214.115478515625 0.9106926918029785 244.57351684570312 0.19996172189712524 0.822148 0.6512961387634277 True -7 14800 20.358633041381836 0.3971707820892334 260.96856689453125 0.5251627564430237 243.25318908691406 0.20206233859062195 0.82875085 0.5628947615623474 True -8 16650 20.375292778015137 0.37476611137390137 211.68087768554688 0.5548655390739441 242.20199584960938 0.20395150780677795 0.8351362 0.517554759979248 True -9 18500 20.36169743537903 0.3812255859375 223.1388397216797 0.458601176738739 241.07992553710938 0.20631203055381775 0.8375592 0.4985741376876831 True -10 20350 20.372217655181885 0.40634918212890625 243.07089233398438 0.6608466506004333 240.341796875 0.20707036554813385 0.84427863 0.47324466705322266 True -11 22200 20.428276777267456 0.9779424667358398 177.2272491455078 0.5998216867446899 239.7060546875 0.20748063921928406 0.8490262 0.4518675208091736 True -12 24050 20.480939149856567 0.36443400382995605 183.31320190429688 0.5145136117935181 238.5746612548828 0.20991045236587524 0.85125744 0.440413236618042 True -13 25900 20.436900854110718 0.3613772392272949 218.3292236328125 0.5255551338195801 238.0679931640625 0.21041269600391388 0.85406035 0.42647314071655273 True -14 27750 20.486563682556152 0.3601524829864502 238.10244750976562 0.7932313084602356 238.1581268310547 0.21027271449565887 0.85956407 0.40851864218711853 True -15 29600 20.43223738670349 0.37048912048339844 171.37335205078125 0.31711214780807495 237.58279418945312 0.21152253448963165 0.8621383 0.40285781025886536 True -16 31450 20.407745599746704 0.3668212890625 277.50140380859375 0.3721937835216522 237.46005249023438 0.21175238490104675 0.8676131 0.3901810944080353 True -17 33300 20.391513109207153 0.3653223514556885 210.03819274902344 0.4171873927116394 237.4029083251953 0.21180014312267303 0.8675094 0.387971431016922 False -18 35150 20.395427703857422 0.3743605613708496 178.0816650390625 0.33703431487083435 237.95314025878906 0.21081723272800446 0.86724335 0.3909161686897278 False -19 37000 20.460395574569702 0.37392449378967285 167.45947265625 0.38077396154403687 237.9835662841797 0.21120499074459076 0.8669615 0.3913070261478424 False diff --git a/ENCSR904GDU/cherimoya.fold_4.performance.tsv b/ENCSR904GDU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 08cf3560ec364ac39b8382c8df54727605d96896..0000000000000000000000000000000000000000 --- a/ENCSR904GDU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -237.46005249023438 0.5423282980918884 0.21175238490104675 0.0625080093741417 0.8676130771636963 0.791515588760376 0.3901810944080353 \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_0.evaluate.json b/ENCSR908MUU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5a5c7280cb796dccde49d9efebdc4699ffa55663..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF153LXY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_0.fit.json b/ENCSR908MUU/cherimoya.fold_0.fit.json deleted file mode 100644 index 593d5551c9ba5dc222fa28bd600b081e27ebae88..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF153LXY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_0.log b/ENCSR908MUU/cherimoya.fold_0.log deleted file mode 100644 index 5c3853c0452dce0d493d15371a22c9930820c0fd..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 34.8129198551178 3.644963026046753 448.8127746582031 0.7603369951248169 608.7138061523438 0.22045588493347168 0.7231143 5.163824558258057 True -1 5478 30.240370273590088 0.592625617980957 432.20318603515625 0.48680561780929565 557.7352294921875 0.2699681520462036 0.78847754 1.314319133758545 True -2 8217 30.24942398071289 0.5818436145782471 676.5989990234375 0.3340415954589844 551.5099487304688 0.276176780462265 0.7968577 0.775705099105835 True -3 10956 30.22174906730652 1.4869298934936523 482.21820068359375 0.36848828196525574 542.9231567382812 0.2815447747707367 0.8100342 0.7152850031852722 True -4 13695 30.231316804885864 0.5699291229248047 457.5628967285156 0.4577355980873108 537.7479858398438 0.2876882255077362 0.8208843 0.5369041562080383 True -5 16434 29.91872477531433 0.5701475143432617 491.7697448730469 0.3388989269733429 535.4288940429688 0.2901839017868042 0.82606345 0.44039905071258545 True -6 19173 29.542686939239502 0.5629303455352783 437.0399169921875 0.38646399974823 533.5116577148438 0.2922230660915375 0.831842 0.44112667441368103 True -7 21912 29.545854330062866 2.5040042400360107 546.0497436523438 0.3943023979663849 531.54443359375 0.2947463095188141 0.83727354 0.4430173933506012 True -8 24651 29.59106421470642 0.5727748870849609 511.843017578125 0.40930595993995667 529.5146484375 0.2967674136161804 0.83834183 0.4188469648361206 True -9 27390 29.708534955978394 0.5729923248291016 425.02227783203125 0.4722300171852112 528.359130859375 0.29771333932876587 0.8444329 0.37418851256370544 True -10 30129 29.657699823379517 1.7625579833984375 511.93701171875 0.3516872227191925 527.8862915039062 0.2983333170413971 0.8470612 0.3569197654724121 True -11 32868 29.584568738937378 0.5724027156829834 429.6407470703125 0.343453049659729 525.4661254882812 0.30080538988113403 0.8507607 0.3388993740081787 True -12 35607 29.663841009140015 0.5769407749176025 428.72216796875 0.2118627279996872 523.4794311523438 0.30380943417549133 0.8533816 0.3215974271297455 True -13 38346 29.718897104263306 0.5765743255615234 465.8155212402344 0.30221235752105713 521.6748657226562 0.3057047724723816 0.85865283 0.29421037435531616 True -14 41085 29.75763177871704 30.735867738723755 388.5548095703125 0.3185473680496216 520.15869140625 0.30693092942237854 0.8634248 0.2732497751712799 True -15 43824 32.273879528045654 0.6093389987945557 363.0931091308594 0.225001722574234 518.9940185546875 0.30763310194015503 0.86762047 0.25826409459114075 True -16 46563 30.124517679214478 1.3524847030639648 523.1219482421875 0.1700979322195053 518.9102172851562 0.30706632137298584 0.8679522 0.2506386935710907 True -17 49302 29.79745841026306 34.830299854278564 436.1587219238281 0.2014901041984558 519.4590454101562 0.3065318167209625 0.8687307 0.25024864077568054 True -18 52041 29.74367380142212 0.7326674461364746 456.0363464355469 0.2153746783733368 519.617431640625 0.3065974712371826 0.86833006 0.25099968910217285 False -19 54780 29.73780369758606 0.5732557773590088 411.49847412109375 0.22757668793201447 519.823974609375 0.30615484714508057 0.86834157 0.2529769241809845 False diff --git a/ENCSR908MUU/cherimoya.fold_0.performance.tsv b/ENCSR908MUU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 26648132ea27f16f5daa0585c0e5a3a3a4fcca13..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -519.4590454101562 0.45374202728271484 0.3065318167209625 0.11386169493198395 0.8687307238578796 0.8444401621818542 0.25024864077568054 \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_1.evaluate.json b/ENCSR908MUU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 7ce65e1973c06036c7b55e9cfe7352c9c270b4c6..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF153LXY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_1.fit.json b/ENCSR908MUU/cherimoya.fold_1.fit.json deleted file mode 100644 index dadb7dd770a7ab604a1cb9f21fa7d819f2a19921..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF153LXY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_1.log b/ENCSR908MUU/cherimoya.fold_1.log deleted file mode 100644 index 15f7e319506ca5730d360c2fd3eebc8977b6cdf2..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2715 36.638208627700806 26.049092292785645 391.1157531738281 0.42071354389190674 744.4954223632812 0.22575809061527252 0.7255121 4.636109352111816 True -1 5430 32.279760122299194 0.6659767627716064 400.637451171875 0.3852320611476898 672.6732177734375 0.29057398438453674 0.79462826 1.4651979207992554 True -2 8145 30.11280393600464 0.913834810256958 446.5614013671875 0.45457834005355835 660.4985961914062 0.2979714274406433 0.80929774 0.7540913820266724 True -3 10860 30.584731101989746 0.6662836074829102 501.98406982421875 0.5928157567977905 648.1451416015625 0.30891433358192444 0.81670946 0.5672656893730164 True -4 13575 29.915791273117065 0.6634173393249512 571.5718994140625 0.5175018310546875 642.4983520507812 0.3138540983200073 0.8256961 0.4964771866798401 True -5 16290 29.922750234603882 0.6603517532348633 483.98419189453125 0.303907573223114 639.7691040039062 0.314704567193985 0.8333107 0.5037519335746765 True -6 19005 29.9568932056427 0.6611614227294922 421.45477294921875 0.31208091974258423 637.211181640625 0.316716730594635 0.8390881 0.4845750033855438 True -7 21720 32.079471826553345 22.309197902679443 527.192626953125 0.4117788076400757 634.833984375 0.3188152313232422 0.8425164 0.4587915241718292 True -8 24435 29.46763563156128 0.6602175235748291 504.30364990234375 0.36879289150238037 630.7981567382812 0.32266420125961304 0.8502347 0.4340372681617737 True -9 27150 29.288378477096558 0.651848316192627 479.95697021484375 0.47681909799575806 629.328857421875 0.32450369000434875 0.8533639 0.40381428599357605 True -10 29865 29.343208074569702 0.6619532108306885 533.0299682617188 0.39468467235565186 625.9012451171875 0.32745054364204407 0.8579222 0.40144816040992737 True -11 32580 29.339261054992676 0.6485588550567627 402.47882080078125 0.22133468091487885 624.4725952148438 0.32755377888679504 0.8601117 0.3764852285385132 True -12 35295 36.148428440093994 13.46169900894165 458.66265869140625 0.2614074945449829 621.5421752929688 0.33024027943611145 0.8652437 0.34724345803260803 True -13 38010 29.435714721679688 17.30101704597473 508.17620849609375 0.32288843393325806 619.7374267578125 0.3319871127605438 0.87083846 0.32723820209503174 True -14 40725 29.386595249176025 37.973212003707886 491.49151611328125 0.27601587772369385 617.1492919921875 0.33410829305648804 0.87513244 0.31173816323280334 True -15 43440 29.640486478805542 0.6595687866210938 424.36285400390625 0.232625812292099 617.1895751953125 0.3334782123565674 0.8771596 0.2961980998516083 True -16 46155 29.42213201522827 0.6643939018249512 401.9980163574219 0.16235017776489258 615.141357421875 0.33599692583084106 0.88029295 0.28526929020881653 True -17 48870 29.71720814704895 0.6468853950500488 464.06768798828125 0.25812894105911255 615.6295166015625 0.334942102432251 0.8799084 0.28030839562416077 False -18 51585 29.343510150909424 33.66186547279358 388.507080078125 0.2087496966123581 615.822021484375 0.3348086178302765 0.87965757 0.2833867371082306 False -19 54300 29.952033281326294 0.6550765037536621 403.14361572265625 0.24754109978675842 616.6644897460938 0.33340659737586975 0.88072234 0.2830868661403656 True diff --git a/ENCSR908MUU/cherimoya.fold_1.performance.tsv b/ENCSR908MUU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4081715f67d5ae79d081b3a1646c0bb60d288495..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -616.6644897460938 0.4301050007343292 0.33340662717819214 0.13368915021419525 0.8807223439216614 0.8693236708641052 0.2830868661403656 \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_2.evaluate.json b/ENCSR908MUU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 58ee5383af3cb077365ba26f029a944e26ccacae..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF153LXY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_2.fit.json b/ENCSR908MUU/cherimoya.fold_2.fit.json deleted file mode 100644 index dedd9da335e545340d62b8697eea12ba00ec42e7..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF153LXY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_2.log b/ENCSR908MUU/cherimoya.fold_2.log deleted file mode 100644 index 61e11e7e73147bf2080ebb610e010cc2eba5cb15..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.46744966506958 3.7185230255126953 432.4831237792969 0.39586496353149414 650.7432250976562 0.22294752299785614 0.7266938 3.714383840560913 True -1 5754 31.804012775421143 0.56587815284729 482.1658020019531 0.47185999155044556 590.5725708007812 0.2789040803909302 0.7907869 1.1436004638671875 True -2 8631 31.75678777694702 0.5512797832489014 364.944091796875 0.34827762842178345 578.9764404296875 0.28678181767463684 0.8057888 0.8284060955047607 True -3 11508 31.768256664276123 1.035336971282959 477.8309326171875 0.37328362464904785 570.9795532226562 0.2923431992530823 0.814418 0.5235434770584106 True -4 14385 31.80281710624695 31.25684094429016 445.0538330078125 0.37647736072540283 566.809814453125 0.29580724239349365 0.8252939 0.4967776834964752 True -5 17262 32.45338034629822 0.5728347301483154 499.9003601074219 0.4608115553855896 564.4949340820312 0.2973844110965729 0.83205044 0.4829704463481903 True -6 20139 31.673651695251465 0.8873131275177002 471.8681335449219 0.39192235469818115 562.1363525390625 0.30015692114830017 0.8332981 0.4913952350616455 True -7 23016 31.77969717979431 0.5548632144927979 496.0921325683594 0.34266674518585205 560.1991577148438 0.30205437541007996 0.84352773 0.4498337209224701 True -8 25893 31.331672191619873 0.729236364364624 493.4773864746094 0.3549425005912781 557.5716552734375 0.3051285147666931 0.8478293 0.4181068241596222 True -9 28770 31.121691942214966 0.5920169353485107 481.72540283203125 0.2763529419898987 555.9265747070312 0.3069281578063965 0.85312384 0.3746298551559448 True -10 31647 31.178996801376343 2.308014392852783 447.00146484375 0.2974432706832886 555.208251953125 0.307577520608902 0.8546204 0.38388878107070923 True -11 34524 31.146384477615356 20.880988597869873 565.2328491210938 0.26063272356987 552.5404663085938 0.3108009397983551 0.8596307 0.35901498794555664 True -12 37401 35.48848342895508 0.6333897113800049 496.9373779296875 0.15771378576755524 551.3296508789062 0.31112396717071533 0.8616285 0.32549524307250977 True -13 40278 31.231537103652954 2.119859457015991 492.9931640625 0.3172021508216858 549.6681518554688 0.313346803188324 0.86289334 0.30502742528915405 True -14 43155 31.1511812210083 0.5482313632965088 435.58392333984375 0.2558603882789612 548.1954956054688 0.3143415153026581 0.8672438 0.28923580050468445 True -15 46032 31.161151885986328 0.5707297325134277 403.853515625 0.3632509112358093 547.6311645507812 0.3148076832294464 0.8705389 0.27580198645591736 True -16 48909 31.29887366294861 0.5560038089752197 536.237060546875 0.323308527469635 547.1521606445312 0.3153693974018097 0.87407744 0.26475653052330017 True -17 51786 31.110139846801758 0.543865442276001 405.59283447265625 0.21034033596515656 548.1726684570312 0.3139588534832001 0.87503874 0.2591642737388611 True -18 54663 31.23521399497986 0.54624342918396 494.27337646484375 0.20809341967105865 546.7574462890625 0.3166694939136505 0.87391895 0.25890636444091797 False -19 57540 31.4692485332489 42.54972267150879 332.1222839355469 0.33813849091529846 546.5159912109375 0.31696075201034546 0.87295884 0.2596563696861267 False diff --git a/ENCSR908MUU/cherimoya.fold_2.performance.tsv b/ENCSR908MUU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bdc742069301ecb66b7b663e6de8584913204e7d..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -548.1726684570312 0.44636550545692444 0.3139588534832001 0.12192481756210327 0.875038743019104 0.8556712865829468 0.2591642737388611 \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_3.evaluate.json b/ENCSR908MUU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ff16e0b8d5dad0a93ee729493d86d3bececa0311..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF153LXY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_3.fit.json b/ENCSR908MUU/cherimoya.fold_3.fit.json deleted file mode 100644 index c9deb231cf5238a8231c30b4da74d835fe6fe618..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF153LXY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_3.log b/ENCSR908MUU/cherimoya.fold_3.log deleted file mode 100644 index dbd0a0402fef9222fd4308ec507fb3614c918121..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 35.09629487991333 3.616776704788208 452.60626220703125 0.6717016696929932 603.1349487304688 0.22858339548110962 0.70677274 4.940282821655273 True -1 5492 30.307679891586304 0.5568413734436035 519.9683837890625 0.43871521949768066 553.5665893554688 0.27775609493255615 0.78374684 1.4330705404281616 True -2 8238 30.26906132698059 0.5580244064331055 453.62127685546875 0.4175646901130676 543.9915161132812 0.28704774379730225 0.79471886 0.7251863479614258 True -3 10984 30.293581247329712 0.5496981143951416 471.8626708984375 0.5026142597198486 537.6996459960938 0.29267698526382446 0.8080242 0.5250691771507263 True -4 13730 30.352233409881592 0.5561959743499756 474.63336181640625 0.2866772413253784 534.9478149414062 0.29405203461647034 0.8181386 0.44130799174308777 True -5 16476 30.317903518676758 1.9223430156707764 419.93707275390625 0.442684531211853 531.5092163085938 0.29779064655303955 0.82732224 0.4218291938304901 True -6 19222 30.30055022239685 0.5561647415161133 395.38189697265625 0.3254775404930115 530.3345947265625 0.29869934916496277 0.8305482 0.43227455019950867 True -7 21968 30.253830671310425 0.9591946601867676 473.1544189453125 0.30025821924209595 528.0827026367188 0.30128392577171326 0.8344927 0.4608536958694458 True -8 24714 30.54888129234314 0.5536158084869385 436.3714294433594 0.5207920074462891 526.771484375 0.3029070198535919 0.8353442 0.4196946322917938 True -9 27460 29.75124716758728 0.5502619743347168 493.4688720703125 0.25574541091918945 526.19091796875 0.30250152945518494 0.841275 0.3914530873298645 True -10 30206 29.6637020111084 0.5426132678985596 386.34832763671875 0.28415507078170776 523.7055053710938 0.305449515581131 0.84355265 0.3703242838382721 True -11 32952 29.713502168655396 0.5471041202545166 425.11712646484375 0.45928478240966797 521.3425903320312 0.308584600687027 0.848723 0.34543853998184204 True -12 35698 29.74276089668274 0.5450520515441895 500.9453125 0.345574289560318 520.2744140625 0.31000903248786926 0.85335237 0.3300711512565613 True -13 38444 29.673405647277832 1.3708813190460205 432.4107666015625 0.4207068681716919 518.4315185546875 0.3116872012615204 0.8564641 0.30784887075424194 True -14 41190 29.645964860916138 0.5463125705718994 471.28106689453125 0.22017842531204224 517.93017578125 0.3111007511615753 0.860359 0.29419493675231934 True -15 43936 29.76180934906006 0.5493419170379639 489.6639099121094 0.24500565230846405 516.4446411132812 0.313245564699173 0.86558425 0.2829176187515259 True -16 46682 30.550532579421997 0.5480170249938965 476.94793701171875 0.4669443368911743 516.4668579101562 0.31316637992858887 0.8688066 0.2750486135482788 True -17 49428 29.889540433883667 37.869911909103394 407.2889404296875 0.23567020893096924 515.8369750976562 0.31321054697036743 0.86862326 0.27155786752700806 False -18 52174 30.69898819923401 0.5542502403259277 446.27520751953125 0.3347623646259308 516.2930297851562 0.31287166476249695 0.868539 0.2727098762989044 False -19 54920 29.714865684509277 0.5480468273162842 453.08197021484375 0.21204251050949097 515.7506103515625 0.3140972852706909 0.8684922 0.2730984687805176 False diff --git a/ENCSR908MUU/cherimoya.fold_3.performance.tsv b/ENCSR908MUU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d8420c1e336f87fb3cd58e8e984c0b20650a1bb5..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -516.4668579101562 0.4499138593673706 0.31316637992858887 0.11252319067716599 0.8688066005706787 0.8352462649345398 0.2750486135482788 \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_4.evaluate.json b/ENCSR908MUU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 678df77ffffe872c6a3eeb785ec1a3b47e075756..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF153LXY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_4.fit.json b/ENCSR908MUU/cherimoya.fold_4.fit.json deleted file mode 100644 index 8922f0010876cf71ac0f06a42b99582bf9441ccc..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF153LXY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR908MUU/cherimoya.fold_4.log b/ENCSR908MUU/cherimoya.fold_4.log deleted file mode 100644 index 5dc15a98b6f13c6dd33c87f4a8f997f0f01a57e6..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2826 35.93505525588989 3.5723347663879395 418.79278564453125 0.40845704078674316 581.281005859375 0.22028307616710663 0.70553976 4.302145004272461 True -1 5652 31.3232684135437 0.6056737899780273 504.84185791015625 0.5820193886756897 531.4180297851562 0.2744784951210022 0.7783964 1.3880269527435303 True -2 8478 31.23873996734619 0.6098136901855469 408.8872375488281 0.343211829662323 525.48291015625 0.27890992164611816 0.78682435 0.7360128164291382 True -3 11304 31.22697162628174 0.5868484973907471 549.6373901367188 0.41478613018989563 518.4923095703125 0.2856202721595764 0.8024946 0.570949375629425 True -4 14130 31.143092393875122 1.7104039192199707 418.6720886230469 0.7612726092338562 516.8814086914062 0.28635305166244507 0.8073442 0.47222787141799927 True -5 16956 33.17314291000366 33.965879678726196 507.834228515625 0.5154424905776978 515.6630859375 0.2877436578273773 0.8144551 0.4247063398361206 True -6 19782 33.190057039260864 0.59716796875 453.6895751953125 0.3152613043785095 513.6148071289062 0.289601594209671 0.82498413 0.38027095794677734 True -7 22608 31.20317316055298 26.028053760528564 471.53277587890625 0.38949328660964966 511.3921813964844 0.2928769886493683 0.8285762 0.38122764229774475 True -8 25434 31.660424947738647 0.6385316848754883 413.708251953125 0.435680091381073 509.5710754394531 0.2939563989639282 0.83416045 0.35576578974723816 True -9 28260 30.824288368225098 0.5873503684997559 441.2234802246094 0.3063943386077881 508.9335632324219 0.2941921055316925 0.83918846 0.3344528377056122 True -10 31086 30.607579946517944 0.5763232707977295 329.8110656738281 0.4571447968482971 507.1235656738281 0.2963750958442688 0.8453293 0.301807165145874 True -11 33912 30.61791968345642 0.5850489139556885 388.222412109375 0.3193817138671875 505.8980407714844 0.2980375289916992 0.8483497 0.2952152192592621 True -12 36738 30.59531807899475 0.5736827850341797 440.7410888671875 0.4997481405735016 504.3124694824219 0.30010050535202026 0.8521894 0.2840319275856018 True -13 39564 30.528300046920776 0.5856177806854248 406.8898620605469 0.4215756952762604 502.81414794921875 0.3020781874656677 0.8576442 0.2738078534603119 True -14 42390 30.56215786933899 0.5798938274383545 519.2495727539062 0.236406147480011 502.0669250488281 0.30251410603523254 0.862114 0.26126793026924133 True -15 45216 30.61934208869934 0.5782997608184814 484.2811279296875 0.27972137928009033 502.0306396484375 0.30169785022735596 0.86379266 0.25116172432899475 True -16 48042 30.669586181640625 0.5838978290557861 470.71807861328125 0.2230013608932495 500.7623291015625 0.3038148880004883 0.8679037 0.2455100119113922 True -17 50868 30.603992700576782 0.580413818359375 526.1898803710938 0.17852309346199036 500.6490783691406 0.3039843738079071 0.8676526 0.24277633428573608 False -18 53694 30.58230996131897 0.5779597759246826 421.3479919433594 0.20917218923568726 500.86920166015625 0.3036901652812958 0.86684984 0.2435620278120041 False -19 56520 30.620544910430908 0.579667329788208 462.9404602050781 0.26593562960624695 500.4719543457031 0.3045912981033325 0.8674904 0.24458615481853485 False diff --git a/ENCSR908MUU/cherimoya.fold_4.performance.tsv b/ENCSR908MUU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0c6af4df6d09caa1c280268e71bede46c8365638..0000000000000000000000000000000000000000 --- a/ENCSR908MUU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -500.7623291015625 0.4566769301891327 0.3038148880004883 0.11193065345287323 0.8679037094116211 0.8364700675010681 0.2455100119113922 \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_0.evaluate.json b/ENCSR909HFI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 38584f352eb011e98d1a3a194d30672a6ad48db3..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF993LPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_0.fit.json b/ENCSR909HFI/cherimoya.fold_0.fit.json deleted file mode 100644 index 1ad0b56d608dc37f4b166eced939f3bb38de83c7..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF993LPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_0.log b/ENCSR909HFI/cherimoya.fold_0.log deleted file mode 100644 index aeedfd40dcab2ae7f36e67f124cbb1d4acc3c3db..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2740 33.96966028213501 3.76029372215271 653.7985229492188 0.6588326096534729 969.2999877929688 0.3288174271583557 0.6255614 7.1311354637146 True -1 5480 30.208425521850586 0.6251909732818604 776.142578125 0.4922213554382324 861.4960327148438 0.41758936643600464 0.68069685 2.385366916656494 True -2 8220 30.177767038345337 2.513338565826416 653.7672119140625 0.4189349114894867 836.2704467773438 0.43521663546562195 0.7072068 1.1081544160842896 True -3 10960 30.227441549301147 0.8299331665039062 732.4321899414062 0.4252697229385376 827.58447265625 0.43895965814590454 0.7183864 0.9068290591239929 True -4 13700 30.203184366226196 0.5690934658050537 688.2110595703125 0.38223928213119507 822.2130737304688 0.44317445158958435 0.7298543 1.1855548620224 True -5 16440 30.162840604782104 0.5730440616607666 723.7184448242188 0.35238680243492126 818.7308959960938 0.4466089904308319 0.73761433 0.7501721382141113 True -6 19180 30.20548439025879 0.5752224922180176 611.5925903320312 0.31269535422325134 814.3050537109375 0.45022234320640564 0.7425347 0.6728311777114868 True -7 21920 30.191017150878906 0.5723752975463867 573.8374633789062 0.3536354899406433 811.701171875 0.45270583033561707 0.7509422 0.6137498617172241 True -8 24660 30.189507961273193 0.572376012802124 744.247314453125 0.3887832760810852 808.7879638671875 0.45451629161834717 0.75787777 0.5530145764350891 True -9 27400 30.171149969100952 0.5731680393218994 711.0921630859375 0.4581427276134491 806.704345703125 0.45677614212036133 0.75963664 0.5200746655464172 True -10 30140 30.168519973754883 0.561164140701294 642.1478271484375 0.3806133270263672 807.423828125 0.4561444818973541 0.7586245 0.565936267375946 False -11 32880 30.21564531326294 1.8478031158447266 659.8671875 0.3886041045188904 800.6068115234375 0.4619844853878021 0.7740763 0.4393584132194519 True -12 35620 30.20459008216858 0.5751748085021973 687.1318969726562 0.3285309076309204 798.9303588867188 0.46234676241874695 0.78140014 0.40948963165283203 True -13 38360 30.505021810531616 11.424588203430176 736.2766723632812 0.30639195442199707 796.62109375 0.4633788764476776 0.7879403 0.3706241548061371 True -14 41100 30.23708462715149 9.655434370040894 689.8596801757812 0.3178088068962097 793.0592651367188 0.46690285205841064 0.79772794 0.34161141514778137 True -15 43840 30.25748109817505 5.879183053970337 656.7623291015625 0.27553680539131165 791.0367431640625 0.4695873260498047 0.8038011 0.3253113031387329 True -16 46580 30.25173258781433 1.3388352394104004 670.35302734375 0.25247395038604736 789.7911987304688 0.470314621925354 0.8070429 0.31136181950569153 True -17 49320 30.25378131866455 1.1006953716278076 614.6142578125 0.3189794719219208 788.757080078125 0.47105324268341064 0.8101844 0.3016293942928314 True -18 52060 30.16081738471985 1.1254966259002686 699.4549560546875 0.190617173910141 789.7018432617188 0.4693908989429474 0.8078297 0.30004703998565674 False -19 54800 30.143389463424683 1.5146825313568115 710.90576171875 0.16231565177440643 791.7774658203125 0.4672067165374756 0.80932915 0.29902100563049316 False diff --git a/ENCSR909HFI/cherimoya.fold_0.performance.tsv b/ENCSR909HFI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 04a48a524dc2145949a1eefa29105803c5d4a0fc..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -788.757080078125 0.32263967394828796 0.47105318307876587 0.22227367758750916 0.8101844191551208 0.7797444462776184 0.3016293942928314 \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_1.evaluate.json b/ENCSR909HFI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2acd0bc869e00f98904b932463a1a39b6e27e4cf..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF993LPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_1.fit.json b/ENCSR909HFI/cherimoya.fold_1.fit.json deleted file mode 100644 index 5ca0662b14cda993834540091b771f7229f5f7bf..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF993LPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_1.log b/ENCSR909HFI/cherimoya.fold_1.log deleted file mode 100644 index 5aa503a39420c0ae904084afbe45393a915ad59a..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2694 33.48180603981018 4.692287921905518 719.8770751953125 0.4990658462047577 1081.7041015625 0.32440078258514404 0.64841956 6.966213703155518 True -1 5388 29.720317363739014 0.7635247707366943 732.0169677734375 0.4794974625110626 951.182373046875 0.42200833559036255 0.7125129 2.796369791030884 True -2 8082 29.724952697753906 0.7177727222442627 837.7035522460938 0.6852824687957764 923.8073120117188 0.4394395053386688 0.7330566 1.2717516422271729 True -3 10776 29.670934677124023 0.7009551525115967 745.2904052734375 0.5986549854278564 912.7861938476562 0.44542554020881653 0.74535096 1.0307902097702026 True -4 13470 29.617342472076416 0.6880450248718262 715.478515625 0.41030722856521606 908.1235961914062 0.4482247531414032 0.7558404 0.9090439081192017 True -5 16164 29.619130611419678 1.8665452003479004 666.1998901367188 0.3291322588920593 902.6611328125 0.4516289234161377 0.76425296 0.6261460781097412 True -6 18858 29.64162015914917 0.6906538009643555 565.6822509765625 0.5592060089111328 897.5038452148438 0.4539042115211487 0.769241 0.5736779570579529 True -7 21552 29.66091752052307 0.691983699798584 716.4720458984375 0.5737345814704895 892.9264526367188 0.45737898349761963 0.7715025 0.5903473496437073 True -8 24246 29.701399087905884 0.7144119739532471 630.4891967773438 0.3769804835319519 888.8899536132812 0.46009141206741333 0.7763118 0.5046982765197754 True -9 26940 30.141955137252808 0.7067563533782959 809.1483764648438 0.4743051826953888 884.7568359375 0.4632321298122406 0.7847855 0.46344298124313354 True -10 29634 29.665539264678955 0.7093000411987305 780.200439453125 0.36016911268234253 880.9828491210938 0.4656093120574951 0.79030824 0.43167904019355774 True -11 32328 29.629974126815796 0.7025396823883057 720.0123901367188 0.3353666663169861 877.3133544921875 0.46840816736221313 0.7957915 0.40856844186782837 True -12 35022 29.64376473426819 0.7175209522247314 741.2010498046875 0.2256658673286438 874.2225952148438 0.470703661441803 0.8011668 0.39239633083343506 True -13 37716 29.652523279190063 0.7077956199645996 666.2947998046875 0.33402734994888306 870.2135620117188 0.47432941198349 0.8080599 0.37076249718666077 True -14 40410 29.712494134902954 0.7129359245300293 649.2189331054688 0.31839269399642944 868.7115478515625 0.4752602279186249 0.8152184 0.34527578949928284 True -15 43104 29.675658464431763 0.7003676891326904 810.3450927734375 0.2681954503059387 867.5692138671875 0.47590458393096924 0.81939477 0.3261295258998871 True -16 45798 29.72698664665222 34.29115653038025 587.6187744140625 0.27911654114723206 864.6119995117188 0.4787258803844452 0.8232216 0.3096332550048828 True -17 48492 29.741767644882202 15.369688987731934 673.5630493164062 0.22204053401947021 863.906005859375 0.47987350821495056 0.82510924 0.3035825192928314 True -18 51186 29.701377630233765 14.303863763809204 600.434814453125 0.1991000920534134 866.224365234375 0.4767208993434906 0.8258811 0.3005039691925049 True -19 53880 29.780720472335815 25.363730669021606 626.82470703125 0.35368630290031433 864.3533325195312 0.4791947603225708 0.8247491 0.3014090657234192 False diff --git a/ENCSR909HFI/cherimoya.fold_1.performance.tsv b/ENCSR909HFI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d072ce2cf09ea2ac742ae8f0f442ae525156f32e..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -866.224365234375 0.31382355093955994 0.4767208993434906 0.23673275113105774 0.8258811235427856 0.807434618473053 0.3005039691925049 \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_2.evaluate.json b/ENCSR909HFI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index eb5e63baefbe72f293e9b6e4fcac3c57bf426038..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF993LPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_2.fit.json b/ENCSR909HFI/cherimoya.fold_2.fit.json deleted file mode 100644 index 26bb36208b93f3e1072e32ae3f2bbee98ec92c4d..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF993LPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_2.log b/ENCSR909HFI/cherimoya.fold_2.log deleted file mode 100644 index 488814ad032b914a0031633f90224a1415c06450..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2892 35.45628809928894 3.8325822353363037 809.9427490234375 0.6874936819076538 1037.2144775390625 0.33073559403419495 0.63226914 6.370535373687744 True -1 5784 32.192071199417114 0.5837433338165283 853.975341796875 0.6452540159225464 910.09765625 0.4285239577293396 0.7036659 2.121279001235962 True -2 8676 31.994799852371216 0.5506751537322998 662.470458984375 0.5767589807510376 896.90673828125 0.43484896421432495 0.71642023 1.1990635395050049 True -3 11568 31.863137245178223 0.5441858768463135 757.521484375 0.38270002603530884 885.2732543945312 0.4422427713871002 0.7304541 1.2504243850708008 True -4 14460 31.836743354797363 1.094449758529663 771.9569091796875 0.386655330657959 877.5269165039062 0.44679465889930725 0.7415009 0.7441343665122986 True -5 17352 31.903629064559937 0.5471296310424805 676.3948364257812 0.3314625024795532 872.85205078125 0.4506089389324188 0.74633396 0.6355683207511902 True -6 20244 31.902775049209595 0.551234245300293 848.8704833984375 0.31374263763427734 868.882568359375 0.45340681076049805 0.75230706 0.5594267845153809 True -7 23136 31.854722499847412 0.5455741882324219 669.5665283203125 0.4137149453163147 866.8114624023438 0.4548064172267914 0.7572749 0.6009133458137512 True -8 26028 31.809082508087158 0.5406811237335205 629.4471435546875 0.4309757351875305 862.9961547851562 0.45790040493011475 0.7622089 0.5380709171295166 True -9 28920 31.822100162506104 1.279599905014038 643.1387939453125 0.38374191522598267 859.4815063476562 0.4608778953552246 0.7649468 0.49279624223709106 True -10 31812 31.844231367111206 0.5426654815673828 617.900390625 0.2741120755672455 856.0008544921875 0.4633799195289612 0.7713038 0.4765007495880127 True -11 34704 31.850069761276245 0.5415565967559814 644.1964111328125 0.30988144874572754 853.3443603515625 0.46515893936157227 0.7757714 0.4507245123386383 True -12 37596 31.834147453308105 0.5408110618591309 719.2875366210938 0.2977379560470581 850.0758666992188 0.46800723671913147 0.7794476 0.4085198938846588 True -13 40488 31.87488102912903 0.5401651859283447 638.4859619140625 0.4102499485015869 850.1439819335938 0.46701425313949585 0.7871756 0.38713347911834717 True -14 43380 31.840014457702637 0.5393028259277344 656.2545776367188 0.2604670524597168 845.7750854492188 0.47091570496559143 0.7955679 0.3625982105731964 True -15 46272 31.85424017906189 0.5376613140106201 698.9254150390625 0.28998082876205444 842.8431396484375 0.47335439920425415 0.7996307 0.339375376701355 True -16 49164 31.832653522491455 0.5488977432250977 677.9237060546875 0.25745952129364014 843.035400390625 0.47269049286842346 0.80268264 0.32183974981307983 True -17 52056 31.8255033493042 0.5402483940124512 769.5078125 0.3005577325820923 843.1199951171875 0.4728313684463501 0.8051448 0.3129725158214569 True -18 54948 31.889873027801514 0.539358377456665 642.0563354492188 0.19247838854789734 844.7603149414062 0.4706799387931824 0.80376315 0.3129339814186096 False -19 57840 31.921701192855835 0.5307173728942871 672.584228515625 0.17606689035892487 842.3970336914062 0.47402215003967285 0.80286884 0.3129485845565796 False diff --git a/ENCSR909HFI/cherimoya.fold_2.performance.tsv b/ENCSR909HFI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a0fd060ec1d407f494c1e8bec863d3b5a7ad7011..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -843.1199951171875 0.3168197274208069 0.47283127903938293 0.2292596399784088 0.8051447868347168 0.7833398580551147 0.3129725158214569 \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_3.evaluate.json b/ENCSR909HFI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 67168deae1ef0af544e17de1aa8df8ff2d2c9dcd..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF993LPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_3.fit.json b/ENCSR909HFI/cherimoya.fold_3.fit.json deleted file mode 100644 index b22a7ed9f1e85cf18f053915912cbe500bfb887c..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF993LPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_3.log b/ENCSR909HFI/cherimoya.fold_3.log deleted file mode 100644 index 8dee6895dc9641790fa7c552eae98ce55e808d10..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 34.25260376930237 4.155450105667114 752.492431640625 0.46804559230804443 949.2695922851562 0.3335511088371277 0.6188489 5.867443084716797 True -1 5536 30.579760551452637 0.7506322860717773 653.63525390625 0.5428372621536255 833.613037109375 0.42230984568595886 0.69670606 2.5332179069519043 True -2 8304 30.5712149143219 0.5416207313537598 668.6632080078125 0.576645016670227 811.7752075195312 0.4377804398536682 0.719568 1.138552188873291 True -3 11072 30.499106407165527 0.5447137355804443 791.37890625 0.39756160974502563 804.5513916015625 0.43994367122650146 0.7247907 0.9162883758544922 True -4 13840 30.479790210723877 0.5413603782653809 783.587646484375 0.4256311357021332 800.4691162109375 0.4440649747848511 0.7342736 1.1637012958526611 True -5 16608 30.436288595199585 1.089172601699829 718.0914306640625 0.34044432640075684 795.771728515625 0.4488965570926666 0.73812836 0.8847827911376953 True -6 19376 30.519978046417236 0.5662863254547119 729.2750854492188 0.3301926553249359 791.0106811523438 0.45140188932418823 0.7423013 0.6997767686843872 True -7 22144 30.47498345375061 0.5372397899627686 641.772705078125 0.272700697183609 787.6075439453125 0.45450276136398315 0.7491544 0.7200421690940857 True -8 24912 30.482971668243408 0.5419704914093018 648.498779296875 0.24199765920639038 784.3906860351562 0.45546889305114746 0.75521064 0.5930835008621216 True -9 27680 30.501139402389526 0.7478041648864746 701.3134155273438 0.25226032733917236 784.315673828125 0.4560217559337616 0.76016784 0.6710215210914612 True -10 30448 30.497191905975342 0.5579733848571777 717.873291015625 0.4331474304199219 778.995849609375 0.45903319120407104 0.76723945 0.529304027557373 True -11 33216 30.49062204360962 0.5397186279296875 715.6435546875 0.3467962443828583 776.10693359375 0.4612663686275482 0.7749713 0.47122636437416077 True -12 35984 30.540161848068237 0.5398769378662109 727.97265625 0.31512266397476196 772.6055297851562 0.4639233350753784 0.78152496 0.4336734414100647 True -13 38752 30.478199243545532 0.5664262771606445 696.406982421875 0.2842661142349243 769.8312377929688 0.46637964248657227 0.7896684 0.3882220387458801 True -14 41520 30.52079463005066 0.5517079830169678 617.2164306640625 0.30419832468032837 768.9259643554688 0.46642014384269714 0.7951243 0.36520785093307495 True -15 44288 30.53137707710266 0.5460278987884521 650.0064697265625 0.291845440864563 766.913818359375 0.4690670073032379 0.8014253 0.3400696814060211 True -16 47056 31.79775333404541 4.942622661590576 719.5292358398438 0.29279130697250366 765.237548828125 0.47008705139160156 0.806338 0.3229348957538605 True -17 49824 30.651737451553345 0.5520703792572021 592.4286499023438 0.14099255204200745 764.7918090820312 0.47108590602874756 0.80740386 0.31526505947113037 True -18 52592 30.58106255531311 0.5467610359191895 706.5739135742188 0.20109030604362488 765.23828125 0.4703715741634369 0.8057006 0.31351688504219055 False -19 55360 30.730780124664307 0.5441365242004395 708.9685668945312 0.20380482077598572 765.9585571289062 0.46967628598213196 0.8061902 0.3139282763004303 False diff --git a/ENCSR909HFI/cherimoya.fold_3.performance.tsv b/ENCSR909HFI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 751f72ec0b132f1abb05c09e8ad7385233e8a07e..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -764.7918090820312 0.32437804341316223 0.47108593583106995 0.21856427192687988 0.8074038624763489 0.7705599069595337 0.31526505947113037 \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_4.evaluate.json b/ENCSR909HFI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 226dc8780ed665a0950fa112222ea4a3d370c727..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF993LPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_4.fit.json b/ENCSR909HFI/cherimoya.fold_4.fit.json deleted file mode 100644 index 19c6abfe1f8986771d30309a5d44faa9109e6df7..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF993LPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR909HFI/cherimoya.fold_4.log b/ENCSR909HFI/cherimoya.fold_4.log deleted file mode 100644 index 2ddd9753ff85d1b710986e6549c50d22e1d6eb1e..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2812 34.827552795410156 4.106290578842163 807.83837890625 0.7800771594047546 891.5630493164062 0.3252868056297302 0.60050344 5.479989051818848 True -1 5624 32.280083894729614 0.6205708980560303 818.5775146484375 0.41217106580734253 795.6513671875 0.4110059142112732 0.67165303 2.0459630489349365 True -2 8436 31.064884185791016 0.5889155864715576 635.1995849609375 0.4268673062324524 777.6085205078125 0.42418405413627625 0.6930479 1.0676031112670898 True -3 11248 30.911285638809204 0.5985603332519531 623.4085693359375 0.6751471757888794 766.6150512695312 0.43063580989837646 0.70833087 0.8441364765167236 True -4 14060 30.942765951156616 0.5800061225891113 713.3138427734375 0.401091992855072 762.7263793945312 0.43374407291412354 0.7167007 0.8030182123184204 True -5 16872 30.92654061317444 0.5814211368560791 643.1656494140625 0.3549824059009552 760.5530395507812 0.4350426197052002 0.72317165 0.5980938673019409 True -6 19684 31.014389276504517 0.6706516742706299 737.2530517578125 0.3704873323440552 756.3788452148438 0.43869030475616455 0.72655255 0.5296903848648071 True -7 22496 30.97056818008423 0.6116626262664795 678.4153442382812 0.3800269663333893 754.3019409179688 0.43977320194244385 0.73474056 0.49762311577796936 True -8 25308 31.07073140144348 0.5922608375549316 709.0469970703125 0.4268445372581482 751.872314453125 0.4421136975288391 0.7418764 0.4789544343948364 True -9 28120 30.990397453308105 0.5938763618469238 671.0320434570312 0.35456544160842896 748.2510986328125 0.44526207447052 0.74891436 0.4437333047389984 True -10 30932 31.109868049621582 1.8930423259735107 730.0145263671875 0.43900519609451294 745.9141845703125 0.4473516345024109 0.7585745 0.442139595746994 True -11 33744 31.060459852218628 0.5952885150909424 660.4130859375 0.20631590485572815 742.6085205078125 0.45022615790367126 0.76508397 0.4117814004421234 True -12 36556 31.15035104751587 0.58573317527771 603.34326171875 0.46242091059684753 739.9442749023438 0.4527667760848999 0.77114046 0.37295064330101013 True -13 39368 31.114384651184082 0.5903592109680176 651.851318359375 0.3350667655467987 739.0319213867188 0.4528977870941162 0.77623045 0.34928053617477417 True -14 42180 31.096909761428833 0.7918405532836914 634.11376953125 0.3079584538936615 736.5284423828125 0.455647349357605 0.7869609 0.32909634709358215 True -15 44992 31.049719095230103 1.575721263885498 590.765869140625 0.25846415758132935 735.8688354492188 0.4562259316444397 0.79088783 0.31178200244903564 True -16 47804 30.988953351974487 0.5906813144683838 644.313720703125 0.35060644149780273 734.0037841796875 0.4586597681045532 0.79588705 0.29600295424461365 True -17 50616 31.000662088394165 0.5802903175354004 710.8536376953125 0.23012350499629974 733.6104125976562 0.4587123692035675 0.79772544 0.28947335481643677 True -18 53428 31.045207262039185 0.5907375812530518 703.8876953125 0.2638475000858307 735.624755859375 0.45563945174217224 0.7974151 0.2880692780017853 False -19 56240 30.978696584701538 0.5833494663238525 678.003173828125 0.20719312131404877 735.3092041015625 0.4566536545753479 0.79591537 0.28897589445114136 False diff --git a/ENCSR909HFI/cherimoya.fold_4.performance.tsv b/ENCSR909HFI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3ba6bdee6dff0a9a6ce273e44b91425034423661..0000000000000000000000000000000000000000 --- a/ENCSR909HFI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -733.6104125976562 0.3329293727874756 0.4587123394012451 0.20935450494289398 0.7977254390716553 0.763904333114624 0.28947335481643677 \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_0.evaluate.json b/ENCSR910OQF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a1b14e65ae7bb63d48a51c582477b7a6764dc2e1..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF936GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_0.fit.json b/ENCSR910OQF/cherimoya.fold_0.fit.json deleted file mode 100644 index 4de7678e71ebe126c658f5663cebaa62f8baac9b..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF936GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_0.log b/ENCSR910OQF/cherimoya.fold_0.log deleted file mode 100644 index ca4b321af76ecd1091789585a9a989e12d1cf216..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.09836554527283 3.538292646408081 1873.322265625 0.8111993074417114 2208.892333984375 0.31470972299575806 0.59138286 11.230602264404297 True -1 5514 30.40308427810669 0.6292328834533691 1449.076904296875 1.3452723026275635 1885.0753173828125 0.4486445188522339 0.69382334 2.974181652069092 True -2 8271 30.41321873664856 0.5981643199920654 1379.3497314453125 0.6315759420394897 1833.56494140625 0.46485447883605957 0.69636977 0.7645931839942932 True -3 11028 30.574403762817383 0.5917532444000244 1276.1080322265625 0.4336060881614685 1803.098876953125 0.4755486249923706 0.7031415 0.5499168038368225 True -4 13785 30.562875509262085 29.840161323547363 1242.8768310546875 0.9508872032165527 1786.8587646484375 0.4833161234855652 0.7049341 0.4909643828868866 True -5 16542 30.807507038116455 0.5911345481872559 1262.7786865234375 0.5657060146331787 1780.3546142578125 0.4836839437484741 0.71159893 0.4008399248123169 True -6 19299 29.9199378490448 0.5964882373809814 1097.822265625 0.6688637733459473 1754.8851318359375 0.4953669011592865 0.7170985 0.37827661633491516 True -7 22056 29.954020023345947 0.5907418727874756 1481.0423583984375 0.6483051180839539 1754.5301513671875 0.49367696046829224 0.71466774 0.4292242228984833 False -8 24813 29.8995099067688 0.5891320705413818 1395.88427734375 0.6472432613372803 1740.2757568359375 0.5012754201889038 0.72570306 0.3813529312610626 True -9 27570 29.876846313476562 0.5975346565246582 1309.833984375 0.5475763082504272 1726.8958740234375 0.5069000720977783 0.7270897 0.36298611760139465 True -10 30327 29.92020893096924 0.5966706275939941 1520.7587890625 0.7389299869537354 1721.1383056640625 0.5089296102523804 0.730281 0.3471890091896057 True -11 33084 29.9081711769104 0.5815081596374512 1373.86865234375 0.38442012667655945 1712.8040771484375 0.5110861659049988 0.7396422 0.34010228514671326 True -12 35841 29.857173681259155 0.584266185760498 1397.990234375 0.6803063154220581 1705.741455078125 0.5140062570571899 0.75181884 0.3145965337753296 True -13 38598 29.870616674423218 0.5864040851593018 1226.34814453125 0.5915687084197998 1692.324462890625 0.5205978751182556 0.7642923 0.299981027841568 True -14 41355 29.893392086029053 0.591820478439331 1498.599609375 0.39480656385421753 1689.436279296875 0.5210581421852112 0.7757292 0.28896015882492065 True -15 44112 29.8692729473114 0.589486837387085 1470.4228515625 0.34426432847976685 1685.4718017578125 0.5213815569877625 0.7856221 0.2792889475822449 True -16 46869 29.937941789627075 0.5990755558013916 1354.861083984375 0.42890113592147827 1676.6309814453125 0.5265811085700989 0.7941065 0.27349212765693665 True -17 49626 29.910151481628418 0.5899062156677246 1246.22509765625 0.32499706745147705 1677.9765625 0.5240887403488159 0.8011684 0.2711467444896698 True -18 52383 29.933246612548828 0.5911784172058105 1279.93994140625 0.41855040192604065 1678.2362060546875 0.524011492729187 0.80531204 0.2710695266723633 True -19 55140 29.964197158813477 0.5914938449859619 1114.232666015625 0.2387295961380005 1673.2315673828125 0.5274175405502319 0.8041625 0.2730444669723511 False diff --git a/ENCSR910OQF/cherimoya.fold_0.performance.tsv b/ENCSR910OQF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e7154a965d60cc105f62edaa27fbf4f5c6da4110..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1678.2362060546875 0.22457289695739746 0.524011492729187 0.32971683144569397 0.8053120374679565 0.7484010457992554 0.2710695266723633 \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_1.evaluate.json b/ENCSR910OQF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5b0a7351ebd2e374b9b64b9d5a32f1fa57e33ec4..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF936GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_1.fit.json b/ENCSR910OQF/cherimoya.fold_1.fit.json deleted file mode 100644 index ef28167786f9850a6439d90d9d79a5de73a8b93a..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF936GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_1.log b/ENCSR910OQF/cherimoya.fold_1.log deleted file mode 100644 index fe3d2b66f0864eacaa8945f6b508755bfbc12092..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 33.7620735168457 5.626577854156494 1678.28076171875 0.9090792536735535 2666.706298828125 0.3155249059200287 0.59746134 12.363165855407715 True -1 5456 30.106043577194214 1.0799052715301514 1486.9283447265625 1.1900720596313477 2224.03076171875 0.45721757411956787 0.70244515 2.5125904083251953 True -2 8184 30.128089904785156 0.6894052028656006 1356.028076171875 0.6406870484352112 2147.68212890625 0.4791390299797058 0.7095555 1.2692527770996094 True -3 10912 30.114795923233032 0.6806178092956543 1769.1708984375 0.6469590067863464 2109.036376953125 0.48787441849708557 0.71989423 0.8324825763702393 True -4 13640 30.061751127243042 0.6764912605285645 1487.4027099609375 0.5158033967018127 2068.730712890625 0.5007522702217102 0.72785956 0.6290141940116882 True -5 16368 29.939879179000854 0.6578369140625 1375.3592529296875 0.35087600350379944 2045.597412109375 0.5074238777160645 0.7365791 0.5549535155296326 True -6 19096 29.47198510169983 0.647413969039917 1945.267333984375 0.5542267560958862 2028.8463134765625 0.511199414730072 0.74128973 0.4956512749195099 True -7 21824 29.496988534927368 0.6600594520568848 1470.736083984375 0.5612918734550476 2000.2366943359375 0.5212316513061523 0.74028426 0.48175403475761414 False -8 24552 29.494925260543823 0.6610250473022461 1341.758544921875 0.9184349775314331 1996.0113525390625 0.5199177265167236 0.75117475 0.4270800054073334 True -9 27280 29.56833004951477 0.6653399467468262 1142.318359375 0.3253105878829956 1993.22900390625 0.5192165374755859 0.7546408 0.4163781404495239 True -10 30008 29.56733751296997 0.6686410903930664 1421.673095703125 0.540102481842041 1977.3658447265625 0.5247713923454285 0.76622564 0.39426958560943604 True -11 32736 31.24648690223694 18.8358633518219 1534.393798828125 1.0315582752227783 1960.6663818359375 0.5291375517845154 0.77482307 0.38404902815818787 True -12 35464 29.645082712173462 24.91320776939392 1273.12939453125 0.43176883459091187 1947.8123779296875 0.5330770015716553 0.78713506 0.3562818765640259 True -13 38192 29.67224431037903 0.6583664417266846 1309.7255859375 0.4019908308982849 1940.7982177734375 0.5325120687484741 0.8003958 0.3409821689128876 True -14 40920 30.962462663650513 0.6585068702697754 1343.04345703125 0.22868090867996216 1920.8172607421875 0.5383912324905396 0.81012034 0.3281801640987396 True -15 43648 29.630505800247192 0.6591415405273438 1272.63330078125 0.5638951063156128 1914.708740234375 0.5396679639816284 0.8187532 0.31539249420166016 True -16 46376 29.563936233520508 0.6579875946044922 1401.4705810546875 0.42291027307510376 1906.752197265625 0.5406811237335205 0.8268992 0.3052685260772705 True -17 49104 29.553483247756958 0.6586992740631104 1160.6085205078125 0.24569739401340485 1904.2069091796875 0.5423755049705505 0.8300925 0.30395784974098206 True -18 51832 29.53770661354065 0.6555519104003906 1077.272705078125 0.48444879055023193 1900.499755859375 0.5432158708572388 0.83346134 0.30713367462158203 True -19 54560 29.58624815940857 0.6628906726837158 1381.54638671875 0.290696382522583 1905.2498779296875 0.5423963665962219 0.8339075 0.30787545442581177 True diff --git a/ENCSR910OQF/cherimoya.fold_1.performance.tsv b/ENCSR910OQF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e25c020821690c1d30b5261dae33add1dfd5e68b..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1905.2498779296875 0.21469520032405853 0.5423963665962219 0.35265129804611206 0.8339074850082397 0.7845691442489624 0.30787545442581177 \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_2.evaluate.json b/ENCSR910OQF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 174f9b1cee84935a62dbec39e0855bf4c64e1575..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF936GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_2.fit.json b/ENCSR910OQF/cherimoya.fold_2.fit.json deleted file mode 100644 index d92cb48e6c985041d08ef1c1a75cc27682e3c47b..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF936GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_2.log b/ENCSR910OQF/cherimoya.fold_2.log deleted file mode 100644 index 2c07868c45547417a0702d082dd7226f8a930cf7..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 36.13688039779663 4.836720943450928 1533.615966796875 0.8287355303764343 2305.65185546875 0.3243468105792999 0.6010772 10.530336380004883 True -1 5800 32.00207757949829 0.5586891174316406 1460.893798828125 0.9638909697532654 1945.738037109375 0.4600639343261719 0.6976808 2.9662270545959473 True -2 8700 32.06159162521362 0.539766788482666 1213.634033203125 0.687235951423645 1890.343017578125 0.4748505651950836 0.70974076 1.210730791091919 True -3 11600 31.987769603729248 0.5506021976470947 1185.986572265625 0.38875001668930054 1860.168701171875 0.4832991659641266 0.71927094 0.6240943074226379 True -4 14500 31.854667901992798 2.326854944229126 1114.55224609375 0.47891515493392944 1847.6807861328125 0.4876062273979187 0.71763426 0.5143958926200867 False -5 17400 31.387656927108765 17.961206436157227 1616.314697265625 0.8178441524505615 1827.7430419921875 0.49482402205467224 0.72490644 0.4771678149700165 True -6 20300 31.53983783721924 1.261805772781372 1465.7921142578125 0.7575557231903076 1817.2554931640625 0.4982606768608093 0.73094463 0.48282766342163086 True -7 23200 31.447975635528564 0.5470433235168457 1533.7554931640625 0.48028576374053955 1797.130615234375 0.5060522556304932 0.73771495 0.42099061608314514 True -8 26100 31.31551766395569 0.5544390678405762 1341.7236328125 0.5062907338142395 1784.5892333984375 0.5120476484298706 0.74516374 0.3794984817504883 True -9 29000 31.44219422340393 0.5478386878967285 1437.315185546875 0.600450873374939 1776.6507568359375 0.5134676098823547 0.75182706 0.34751638770103455 True -10 31900 31.334943771362305 0.8135416507720947 1482.4146728515625 0.5303893089294434 1760.3819580078125 0.5189291834831238 0.75471026 0.33878546953201294 True -11 34800 31.544798612594604 0.5438814163208008 1267.3353271484375 0.4675392210483551 1754.0093994140625 0.5208963751792908 0.7647949 0.32717975974082947 True -12 37700 31.500528812408447 0.5354244709014893 1491.7437744140625 0.6144959330558777 1745.862060546875 0.5230672359466553 0.7743642 0.31639254093170166 True -13 40600 31.41990375518799 0.5415570735931396 1385.9052734375 1.0473829507827759 1740.9447021484375 0.5261234641075134 0.7848588 0.3048805296421051 True -14 43500 31.450620651245117 0.5502495765686035 1591.99267578125 0.36585456132888794 1723.70751953125 0.5318224430084229 0.79137397 0.29982486367225647 True -15 46400 31.376705408096313 0.5417351722717285 1352.90478515625 0.42516815662384033 1717.3465576171875 0.533081591129303 0.8007292 0.2867819368839264 True -16 49300 31.493603944778442 0.5417625904083252 1174.286376953125 0.1820627897977829 1717.140380859375 0.5325629711151123 0.8107171 0.2793423533439636 True -17 52200 31.51692509651184 0.5394775867462158 1326.097900390625 0.23753622174263 1706.5347900390625 0.5385176539421082 0.81361896 0.2779960632324219 True -18 55100 31.420351266860962 0.5400424003601074 1620.6575927734375 0.21079689264297485 1711.72265625 0.5338414311408997 0.8160562 0.27807295322418213 True -19 58000 31.42756986618042 0.5424330234527588 1290.8426513671875 0.5284444093704224 1714.709716796875 0.5317126512527466 0.81569374 0.2774695158004761 False diff --git a/ENCSR910OQF/cherimoya.fold_2.performance.tsv b/ENCSR910OQF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6767e0ef319d2c91e947cdffd03b7da384200c2f..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1711.72265625 0.22267654538154602 0.5338414907455444 0.3350185453891754 0.8160561919212341 0.7600206732749939 0.27807295322418213 \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_3.evaluate.json b/ENCSR910OQF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9bb8e6fe995868d58442c21df30b62dfec6c165f..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF936GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_3.fit.json b/ENCSR910OQF/cherimoya.fold_3.fit.json deleted file mode 100644 index 469a952bfd3061a69cf4e15eb2be043c876c6d79..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF936GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_3.log b/ENCSR910OQF/cherimoya.fold_3.log deleted file mode 100644 index 7c56272eda6734e1651227813d0ff042baf24f02..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2779 34.51340436935425 3.965702533721924 1577.9853515625 0.671470046043396 2371.19287109375 0.32137393951416016 0.61786157 13.403343200683594 True -1 5558 30.67001700401306 1.029529333114624 2117.037109375 0.9824320077896118 2023.0948486328125 0.4519341289997101 0.69968355 3.1770007610321045 True -2 8337 30.711544036865234 0.9400131702423096 1958.59130859375 0.9822800159454346 1977.427490234375 0.4696158170700073 0.70216566 1.2558116912841797 True -3 11116 30.303531646728516 1.0819931030273438 1357.064453125 0.9034072756767273 1933.52294921875 0.4822459816932678 0.7093996 0.6475939154624939 True -4 13895 30.12832260131836 0.5338084697723389 1353.705322265625 0.9382854104042053 1924.3978271484375 0.4808467924594879 0.71840936 0.5373955368995667 True -5 16674 30.098999500274658 0.5320777893066406 1439.47705078125 0.9624443650245667 1899.6036376953125 0.49206361174583435 0.72125477 0.46584853529930115 True -6 19453 29.985795497894287 0.5309343338012695 1363.3740234375 0.6205774545669556 1890.8387451171875 0.49286991357803345 0.7276222 0.4431018829345703 True -7 22232 30.117258071899414 0.5271735191345215 1392.160888671875 0.7201167345046997 1880.0933837890625 0.4977252185344696 0.7248042 0.4597720205783844 False -8 25011 30.06748104095459 0.5263440608978271 1359.867431640625 0.38418418169021606 1869.0096435546875 0.501622200012207 0.728616 0.4150323271751404 True -9 27790 30.081621646881104 0.5242300033569336 1480.175537109375 0.46749573945999146 1861.85498046875 0.5036993622779846 0.7377552 0.38760054111480713 True -10 30569 30.027716398239136 0.5340821743011475 1458.1826171875 0.3537934124469757 1844.018310546875 0.5104699730873108 0.744875 0.36997145414352417 True -11 33348 30.10342311859131 0.540123462677002 1157.0211181640625 0.4130396246910095 1840.7330322265625 0.5114697813987732 0.748435 0.3753427267074585 True -12 36127 30.10396385192871 0.5536110401153564 1307.445556640625 0.4392532706260681 1829.63818359375 0.5131624937057495 0.76326054 0.35671910643577576 True -13 38906 30.103379487991333 0.539597749710083 1335.8438720703125 0.5372950434684753 1805.977783203125 0.5231138467788696 0.7753025 0.34244248270988464 True -14 41685 30.052262783050537 0.534191370010376 1140.0772705078125 0.3774440586566925 1800.0712890625 0.5216959118843079 0.78795433 0.3183819651603699 True -15 44464 30.06938862800598 0.5290689468383789 1453.135009765625 0.25846147537231445 1791.490234375 0.5237897038459778 0.79947597 0.3043241798877716 True -16 47243 30.167541027069092 0.5234873294830322 1246.649169921875 0.39456844329833984 1793.4127197265625 0.522432804107666 0.8078483 0.2951253652572632 True -17 50022 30.191096782684326 0.5304951667785645 1248.6636962890625 0.2157059609889984 1789.6263427734375 0.5241298675537109 0.8114116 0.288484662771225 True -18 52801 30.17078948020935 0.5321063995361328 1245.1064453125 0.24426597356796265 1784.0235595703125 0.5277359485626221 0.81526184 0.28826355934143066 True -19 55580 30.084559202194214 0.5297951698303223 1218.8031005859375 0.19013559818267822 1790.65380859375 0.5235442519187927 0.81784296 0.289280503988266 True diff --git a/ENCSR910OQF/cherimoya.fold_3.performance.tsv b/ENCSR910OQF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3c3c1917b01dd3759967008f05ea71a3506bf049..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1790.65380859375 0.22294758260250092 0.5235442519187927 0.33521831035614014 0.817842960357666 0.7610644698143005 0.289280503988266 \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_4.evaluate.json b/ENCSR910OQF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c5b10f59162161c438cd034de53f9a377b25d0e0..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF936GWY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_4.fit.json b/ENCSR910OQF/cherimoya.fold_4.fit.json deleted file mode 100644 index 212054afe3b57d0d18055f18524de475442573f4..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF936GWY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR910OQF/cherimoya.fold_4.log b/ENCSR910OQF/cherimoya.fold_4.log deleted file mode 100644 index e8ac53c60237ee6cb9548a8ed4761a7c9a854551..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 35.64298367500305 5.199408769607544 1457.1844482421875 0.7999489307403564 2125.60400390625 0.32370373606681824 0.60877013 10.300447463989258 True -1 5776 31.915913581848145 0.6504316329956055 1441.1705322265625 0.8729218244552612 1847.4305419921875 0.443713515996933 0.6779621 2.6095874309539795 True -2 8664 31.77953290939331 0.6204874515533447 1530.2431640625 0.6436713933944702 1806.53662109375 0.45864060521125793 0.69376504 1.0757420063018799 True -3 11552 31.251901865005493 0.5989291667938232 1409.10546875 0.5427170991897583 1771.9984130859375 0.47038695216178894 0.7101114 0.6554822325706482 True -4 14440 31.19570779800415 0.6222689151763916 1695.3360595703125 0.6968941688537598 1752.8287353515625 0.4773898720741272 0.7186894 0.5651604533195496 True -5 17328 31.184672594070435 0.6159095764160156 1363.876708984375 0.41472935676574707 1747.36328125 0.4763962924480438 0.72074497 0.48461341857910156 True -6 20216 31.159407377243042 2.7055792808532715 1350.52978515625 0.5706074237823486 1726.535888671875 0.4870019257068634 0.726805 0.3671661615371704 True -7 23104 31.224769115447998 0.6041765213012695 1477.8525390625 0.7611836194992065 1721.758056640625 0.4871431291103363 0.73633105 0.33065107464790344 True -8 25992 31.215673446655273 0.6075880527496338 1395.402099609375 0.5234965085983276 1706.19580078125 0.4956640601158142 0.7424074 0.34129148721694946 True -9 28880 31.19923734664917 0.6055428981781006 1260.0399169921875 0.42697620391845703 1703.61181640625 0.49447762966156006 0.7511799 0.3177614212036133 True -10 31768 31.20804786682129 0.6030781269073486 1581.284423828125 0.5834997296333313 1693.609130859375 0.4992494285106659 0.7562383 0.30535751581192017 True -11 34656 31.213680267333984 0.6036555767059326 1413.201904296875 0.607502818107605 1679.3565673828125 0.5070684552192688 0.76393616 0.2916763424873352 True -12 37544 31.199225425720215 0.6133663654327393 1280.1353759765625 0.532995879650116 1675.3612060546875 0.5070759654045105 0.77345884 0.27891281247138977 True -13 40432 31.24959659576416 0.6131701469421387 1397.5963134765625 0.35235750675201416 1664.961181640625 0.5116413235664368 0.78532726 0.2674923241138458 True -14 43320 31.266795873641968 0.608612060546875 1509.2086181640625 0.2793653905391693 1658.3824462890625 0.5145432353019714 0.7937004 0.2593022286891937 True -15 46208 31.285253047943115 6.390620708465576 1286.8955078125 0.3936268091201782 1653.9609375 0.5152633190155029 0.80122274 0.25021716952323914 True -16 49096 31.32245373725891 0.6043598651885986 1269.9891357421875 0.3743124008178711 1651.47509765625 0.515092134475708 0.8084381 0.2430756837129593 True -17 51984 31.261791706085205 0.5973458290100098 1284.3104248046875 0.15888509154319763 1650.2509765625 0.5165411233901978 0.8138299 0.2420385330915451 True -18 54872 31.273442029953003 0.6109218597412109 1511.0230712890625 0.40826621651649475 1648.4537353515625 0.5172752141952515 0.8146805 0.24127130210399628 True -19 57760 31.249998331069946 0.6047844886779785 1229.993896484375 0.20877951383590698 1651.8104248046875 0.5153834223747253 0.8156788 0.2430928647518158 True diff --git a/ENCSR910OQF/cherimoya.fold_4.performance.tsv b/ENCSR910OQF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c7f3fa3734763d4232b086f81e70d2cc7bb55225..0000000000000000000000000000000000000000 --- a/ENCSR910OQF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1651.8104248046875 0.22680360078811646 0.5153834819793701 0.32755324244499207 0.8156787753105164 0.7562126517295837 0.2430928647518158 \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_0.evaluate.json b/ENCSR911YVV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5063fff1f502f2019f548411dcffa10d3559302b..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF864EIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_0.fit.json b/ENCSR911YVV/cherimoya.fold_0.fit.json deleted file mode 100644 index a1ef51e99d85cb0c37cf31ec6e9dcda20b566075..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF864EIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_0.log b/ENCSR911YVV/cherimoya.fold_0.log deleted file mode 100644 index 830b1ab5215945a7b5cc8dba57b41e166dc5062c..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 35.24121451377869 2.2423489093780518 268.39239501953125 0.5545377731323242 338.46148681640625 0.17949934303760529 0.6862026 3.268871545791626 True -1 5494 30.730504989624023 0.5171334743499756 213.69131469726562 0.7996166348457336 317.12286376953125 0.25523310899734497 0.7277566 1.0108633041381836 True -2 8241 30.675720930099487 4.347163677215576 223.08297729492188 0.7853379249572754 312.514404296875 0.2662658393383026 0.7418735 0.8328150510787964 True -3 10988 30.672139883041382 0.5136370658874512 274.83648681640625 0.7161307334899902 309.07958984375 0.27727916836738586 0.75158006 0.6513484716415405 True -4 13735 30.82046103477478 0.5155141353607178 227.87615966796875 1.2409113645553589 307.8507385253906 0.2812808156013489 0.7573888 0.5868127346038818 True -5 16482 30.739842653274536 0.5055131912231445 202.48870849609375 0.9727987051010132 306.97601318359375 0.2843306362628937 0.75421447 0.561051607131958 False -6 19229 30.668413162231445 0.5055789947509766 209.8494873046875 0.5567618012428284 306.52081298828125 0.28604093194007874 0.7541516 0.616216778755188 False -7 21976 30.763598680496216 25.031081438064575 217.7680206298828 0.4589879810810089 305.11639404296875 0.29272764921188354 0.75232506 0.6361674070358276 False -8 24723 31.25696849822998 0.5152411460876465 218.01116943359375 0.6060128211975098 304.46185302734375 0.2950591444969177 0.75649714 0.5890210866928101 False -9 27470 30.60310459136963 0.509117603302002 294.2391357421875 0.417751669883728 303.7630310058594 0.2968156337738037 0.76058525 0.512947678565979 True -10 30217 30.57073211669922 0.5071687698364258 247.78265380859375 0.4957001209259033 303.43463134765625 0.2982611358165741 0.7589152 0.48618289828300476 False -11 32964 30.38463282585144 0.5027496814727783 242.44351196289062 0.5357842445373535 302.6590270996094 0.3021828234195709 0.76269275 0.47597500681877136 True -12 35711 30.025784969329834 0.5048913955688477 212.9619903564453 0.5839661359786987 301.84307861328125 0.3042592704296112 0.7666929 0.43568721413612366 True -13 38458 30.010146617889404 0.5005879402160645 188.6767578125 0.37049052119255066 301.2754211425781 0.305785208940506 0.77159905 0.4192951023578644 True -14 41205 30.173795223236084 0.5058913230895996 232.8953399658203 0.43959540128707886 301.1488037109375 0.30630379915237427 0.7788512 0.3843070864677429 True -15 43952 30.012453079223633 0.5057568550109863 243.1504669189453 0.3613887131214142 300.7178039550781 0.3076629638671875 0.7864564 0.3650836944580078 True -16 46699 30.054369926452637 1.736774206161499 174.89590454101562 0.555282473564148 300.3262023925781 0.30855217576026917 0.7925011 0.34183940291404724 True -17 49446 30.046254873275757 0.5001492500305176 234.37847900390625 0.31803154945373535 300.3937683105469 0.30917567014694214 0.795505 0.3296663463115692 True -18 52193 29.966740608215332 0.49432802200317383 237.29202270507812 0.2424440234899521 300.237060546875 0.3095773160457611 0.79487854 0.3224957585334778 False -19 54940 29.970476865768433 0.49941468238830566 231.74246215820312 0.3028351962566376 300.1258850097656 0.30986249446868896 0.7951086 0.32350537180900574 False diff --git a/ENCSR911YVV/cherimoya.fold_0.performance.tsv b/ENCSR911YVV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 004dae466928aac0bb708191664d019d963cc7f0..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -300.3937683105469 0.47783780097961426 0.30917567014694214 0.08369866758584976 0.7955049872398376 0.7387456893920898 0.3296663463115692 \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_1.evaluate.json b/ENCSR911YVV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 72bb57096cb732269d92eb844c7b728a9e1dac69..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF864EIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_1.fit.json b/ENCSR911YVV/cherimoya.fold_1.fit.json deleted file mode 100644 index 627142e6cc44f331c605741cb56779ae9ffdaad3..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF864EIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_1.log b/ENCSR911YVV/cherimoya.fold_1.log deleted file mode 100644 index e6c5724fcd7ba71b9a545f49f689fed819f136fa..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2707 34.6557297706604 4.719541788101196 257.08685302734375 0.47264617681503296 388.20526123046875 0.184007927775383 0.6733152 4.311438083648682 True -1 5414 30.137562036514282 0.71988844871521 259.8959045410156 0.7155972719192505 358.87646484375 0.27396342158317566 0.734556 1.218151569366455 True -2 8121 30.33173131942749 0.7026267051696777 213.5941619873047 0.6635363101959229 353.36322021484375 0.2861073315143585 0.7533474 0.7043179273605347 True -3 10828 30.273759841918945 1.003645896911621 205.6702880859375 0.7524924278259277 350.7724609375 0.2935211956501007 0.7501628 0.7396247386932373 False -4 13535 30.20932412147522 0.7105932235717773 236.672119140625 0.610187292098999 348.738525390625 0.2988277077674866 0.7545443 0.6310915946960449 True -5 16242 32.05428743362427 22.690426349639893 222.41995239257812 0.5462031364440918 347.45660400390625 0.3021831512451172 0.7565994 0.6168103218078613 True -6 18949 30.342873096466064 1.4774141311645508 232.6362762451172 0.6777437329292297 346.2688293457031 0.3060469329357147 0.7569521 0.6495091319084167 True -7 21656 30.168410301208496 15.98094916343689 244.04627990722656 0.5678451061248779 344.87823486328125 0.31101441383361816 0.7583152 0.6350735425949097 True -8 24363 30.291872262954712 1.6129450798034668 182.6561737060547 0.7111896276473999 344.7530517578125 0.3113459348678589 0.76024586 0.6409288048744202 True -9 27070 30.267249584197998 1.8174195289611816 278.9334716796875 0.6683446168899536 343.35614013671875 0.3164355158805847 0.7630264 0.5958129167556763 True -10 29777 30.295743703842163 3.8163156509399414 266.4683532714844 0.7360814809799194 342.9010009765625 0.31718510389328003 0.7688005 0.5892590284347534 True -11 32484 30.309624910354614 40.78283953666687 177.06497192382812 0.5809522867202759 341.5760803222656 0.32256197929382324 0.77309 0.5498142838478088 True -12 35191 29.91944408416748 0.6936829090118408 210.65838623046875 0.47629106044769287 341.0106201171875 0.3234533965587616 0.77561116 0.5167020559310913 True -13 37898 29.539271354675293 0.69136643409729 270.6963195800781 0.8668403029441833 340.2099609375 0.32483622431755066 0.7820244 0.4834020733833313 True -14 40605 29.5435574054718 0.6872279644012451 276.7879638671875 0.5219654440879822 339.50238037109375 0.3262244760990143 0.7902784 0.4321991503238678 True -15 43312 29.649291038513184 0.6861770153045654 224.67950439453125 0.457498699426651 339.0557861328125 0.3287604749202728 0.7944665 0.42126643657684326 True -16 46019 29.695720434188843 0.6816897392272949 275.3692932128906 0.4114229381084442 338.516357421875 0.3295544683933258 0.79924035 0.39809751510620117 True -17 48726 29.631410121917725 1.3617243766784668 252.729248046875 0.33388516306877136 338.50921630859375 0.32904052734375 0.8033099 0.3811197578907013 True -18 51433 30.890681743621826 0.687244176864624 213.13177490234375 0.27070558071136475 338.72332763671875 0.32877877354621887 0.80517113 0.37548553943634033 True -19 54140 29.618571043014526 37.24435377120972 229.6703643798828 0.4815821647644043 338.8226623535156 0.32769444584846497 0.8048113 0.3734281361103058 False diff --git a/ENCSR911YVV/cherimoya.fold_1.performance.tsv b/ENCSR911YVV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 57661e8e94af7c3ec525399a2b5e06d712c20e38..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -338.72332763671875 0.46038156747817993 0.32877883315086365 0.10019363462924957 0.8051711320877075 0.7734524011611938 0.37548553943634033 \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_2.evaluate.json b/ENCSR911YVV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f873ce0f5ff04cdcc385d639cb93d7ba88d42d44..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF864EIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_2.fit.json b/ENCSR911YVV/cherimoya.fold_2.fit.json deleted file mode 100644 index 160ba03c8b392b9c4720aa16966056b309ba067e..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF864EIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_2.log b/ENCSR911YVV/cherimoya.fold_2.log deleted file mode 100644 index cee2eb5d37bf5a462a0ad1eff182694142491bb9..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 36.558738708496094 3.552000045776367 233.771240234375 0.5514609217643738 349.425537109375 0.18500250577926636 0.67247975 3.2350575923919678 True -1 5742 32.03434681892395 0.5473582744598389 247.87864685058594 0.7513538002967834 327.2574157714844 0.26000961661338806 0.7254056 0.7581149935722351 True -2 8613 32.09407639503479 2.444721221923828 275.5340270996094 0.6619195938110352 321.42010498046875 0.27277836203575134 0.7367826 0.6279165148735046 True -3 11484 32.46799278259277 26.79790496826172 209.6545867919922 0.5845868587493896 319.45263671875 0.27696219086647034 0.74527967 0.5751160979270935 True -4 14355 32.26720833778381 0.5539541244506836 263.65533447265625 0.6777918338775635 316.7408447265625 0.2848435342311859 0.7515291 0.5428680777549744 True -5 17226 32.23150396347046 0.5482954978942871 195.46392822265625 0.5583528876304626 315.5946350097656 0.28843364119529724 0.75365144 0.571553111076355 True -6 20097 32.24448275566101 27.93982243537903 245.7397918701172 0.591893196105957 314.35870361328125 0.2931821346282959 0.75291836 0.5768535137176514 False -7 22968 32.227997064590454 0.5804967880249023 223.06948852539062 0.553597092628479 313.1831359863281 0.2967544496059418 0.7565254 0.5493342280387878 True -8 25839 32.059022188186646 0.9283745288848877 238.9026336669922 0.6484687328338623 313.1399230957031 0.2967761754989624 0.7566606 0.5370082855224609 True -9 28710 32.1502788066864 40.8049955368042 196.19989013671875 0.4994313716888428 311.899658203125 0.3020527958869934 0.7569234 0.5378652811050415 True -10 31581 34.264206409454346 38.8098087310791 266.2442626953125 0.7386069297790527 311.5575256347656 0.3037435710430145 0.75861615 0.5440798401832581 True -11 34452 36.73027467727661 0.5561151504516602 217.6280517578125 0.5553311109542847 310.98907470703125 0.30478474497795105 0.7624559 0.5136203169822693 True -12 37323 32.19212031364441 0.5433042049407959 243.1272430419922 0.7710701823234558 310.2920837402344 0.3076852858066559 0.7665368 0.4820469319820404 True -13 40194 31.624431610107422 0.5407297611236572 229.318603515625 0.7900426387786865 309.26763916015625 0.310385525226593 0.77630824 0.4330809712409973 True -14 43065 31.573775053024292 0.5664405822753906 281.306396484375 0.36474236845970154 308.87689208984375 0.31167489290237427 0.7808472 0.42961591482162476 True -15 45936 31.500751495361328 0.5490930080413818 281.7016296386719 0.46974626183509827 308.593994140625 0.3124132454395294 0.78521794 0.40813586115837097 True -16 48807 31.44779658317566 0.5540919303894043 257.6201171875 0.42026737332344055 308.6018371582031 0.31233397126197815 0.7896842 0.37779372930526733 True -17 51678 31.491812229156494 0.5444850921630859 236.13369750976562 0.3603425920009613 308.20159912109375 0.3139338493347168 0.79103094 0.3644767701625824 True -18 54549 31.653571128845215 0.5390901565551758 226.27340698242188 0.2908029854297638 308.1810302734375 0.3142228126525879 0.79338485 0.35754141211509705 True -19 57420 31.65537166595459 37.66616415977478 239.8057098388672 0.39299988746643066 308.3390197753906 0.31364545226097107 0.791676 0.36162158846855164 False diff --git a/ENCSR911YVV/cherimoya.fold_2.performance.tsv b/ENCSR911YVV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5d3b1732fd3fd91f0977a5432941bbdec7032e12..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.1810302734375 0.4738941788673401 0.3142228126525879 0.08699280023574829 0.793384850025177 0.7512108087539673 0.35754141211509705 \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_3.evaluate.json b/ENCSR911YVV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index dc479231a21abf369f68c942158d94cc38377e59..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF864EIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_3.fit.json b/ENCSR911YVV/cherimoya.fold_3.fit.json deleted file mode 100644 index 0c2a3812e90558da12f2020626e3190759a3f0d7..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF864EIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_3.log b/ENCSR911YVV/cherimoya.fold_3.log deleted file mode 100644 index dfe1c9a5cfe4c22383d8c42640895699d77a8ff3..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 35.25815963745117 3.506026029586792 291.69500732421875 0.6325451135635376 356.0975036621094 0.17607887089252472 0.6798607 4.649312973022461 True -1 5514 30.745933294296265 0.908268928527832 301.47283935546875 1.1223881244659424 332.5594787597656 0.2583131194114685 0.73854584 1.1382005214691162 True -2 8271 30.78548264503479 0.5438258647918701 261.2132263183594 0.5233181715011597 328.30670166015625 0.2696627080440521 0.74414605 0.7809982299804688 True -3 11028 30.742271900177002 0.5437610149383545 248.09298706054688 0.5815850496292114 326.0985107421875 0.2738600969314575 0.7480613 0.699606716632843 True -4 13785 30.69800043106079 0.5447640419006348 267.81005859375 0.5167220830917358 324.3309631347656 0.2800453007221222 0.7525303 0.6403056979179382 True -5 16542 30.698761701583862 0.5481994152069092 242.8817901611328 0.8900060653686523 323.465087890625 0.2835855484008789 0.7500186 0.70799320936203 False -6 19299 30.71714162826538 0.5317263603210449 279.5083312988281 0.6012060642242432 322.451904296875 0.2871329188346863 0.7506888 0.712039589881897 False -7 22056 30.722634077072144 0.5601584911346436 267.7511901855469 0.5607345700263977 321.64349365234375 0.29068130254745483 0.75202537 0.6951191425323486 False -8 24813 30.706062078475952 0.535818338394165 285.58544921875 0.7137670516967773 321.00335693359375 0.29256418347358704 0.7503971 0.6704421043395996 False -9 27570 30.701262950897217 0.5347070693969727 203.66236877441406 0.6278061270713806 320.6728515625 0.29353222250938416 0.75462115 0.6391249299049377 True -10 30327 30.73213267326355 0.5466084480285645 241.62741088867188 0.5402404069900513 320.0773620605469 0.29631322622299194 0.75626826 0.6405385136604309 True -11 33084 30.79029154777527 0.5437319278717041 242.79913330078125 0.3834214210510254 319.4739074707031 0.29833394289016724 0.76103354 0.6029711365699768 True -12 35841 30.757264852523804 0.5432300567626953 243.27154541015625 0.5226936936378479 318.9319763183594 0.30049872398376465 0.7660604 0.5265421271324158 True -13 38598 30.179985523223877 0.5428159236907959 239.60589599609375 0.3719741702079773 317.9039306640625 0.3044114410877228 0.769908 0.5248289704322815 True -14 41355 30.07628083229065 0.5509788990020752 283.2999572753906 0.6127496361732483 317.6291809082031 0.30491578578948975 0.77775073 0.48286667466163635 True -15 44112 30.199009895324707 0.5454721450805664 254.61830139160156 0.34477031230926514 317.48406982421875 0.3036024570465088 0.78531396 0.43759453296661377 True -16 46869 30.2369487285614 0.5441522598266602 220.7874755859375 0.38119471073150635 316.71343994140625 0.30687186121940613 0.7949755 0.39488494396209717 True -17 49626 30.28412890434265 0.5518798828125 199.65267944335938 0.39181503653526306 316.6772766113281 0.3075958788394928 0.79795665 0.3699144124984741 True -18 52383 30.376217365264893 1.1611740589141846 243.34188842773438 0.28197136521339417 316.7021484375 0.3072323501110077 0.7996612 0.35817408561706543 True -19 55140 30.34711980819702 0.5646815299987793 201.2265625 0.24482929706573486 316.7326354980469 0.306770384311676 0.79819 0.3554885983467102 False diff --git a/ENCSR911YVV/cherimoya.fold_3.performance.tsv b/ENCSR911YVV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7b273b36a34f89acaf55cf8c3b0c64bec10e6ad9..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -316.7021484375 0.47577956318855286 0.3072323799133301 0.09084033966064453 0.7996612191200256 0.7452502250671387 0.35817408561706543 \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_4.evaluate.json b/ENCSR911YVV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ac00f0c97d8212b632a27d3e356b69fd78f1f64c..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF864EIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_4.fit.json b/ENCSR911YVV/cherimoya.fold_4.fit.json deleted file mode 100644 index 97e34e091053147e2e4e6e4b5f3ae28fdbe78da1..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF864EIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR911YVV/cherimoya.fold_4.log b/ENCSR911YVV/cherimoya.fold_4.log deleted file mode 100644 index 423267c033afbef46be9c0ebdc14948af260ba2c..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2817 36.2548041343689 4.122982740402222 215.20953369140625 0.7811620235443115 332.44720458984375 0.17634925246238708 0.67126125 2.915358304977417 True -1 5634 31.431832313537598 0.6460685729980469 276.9078369140625 0.7103796601295471 313.4914855957031 0.2490597665309906 0.7246393 1.0906554460525513 True -2 8451 31.48617911338806 12.887638330459595 234.80926513671875 0.7604773640632629 309.14892578125 0.2601071298122406 0.7292226 0.5786089897155762 True -3 11268 31.88921093940735 30.907781839370728 225.7381134033203 0.7246588468551636 307.1698303222656 0.26435840129852295 0.73855835 0.5753734111785889 True -4 14085 31.536262273788452 1.9645307064056396 244.05142211914062 0.6022366285324097 305.5517272949219 0.27052730321884155 0.7414707 0.5910859107971191 True -5 16902 31.45949387550354 0.6050469875335693 252.70938110351562 0.5057277679443359 304.0995788574219 0.27686819434165955 0.7375694 0.5288224220275879 False -6 19719 31.40818738937378 0.7795243263244629 246.0231170654297 0.619086742401123 303.0850830078125 0.2811993360519409 0.7407752 0.5073421001434326 False -7 22536 32.309847593307495 0.5973482131958008 313.77099609375 0.3881162703037262 302.4468078613281 0.28317025303840637 0.7467172 0.483267605304718 True -8 25353 31.491297006607056 1.7278976440429688 256.50433349609375 0.8048262000083923 301.8406066894531 0.2854933738708496 0.74908245 0.45201078057289124 True -9 28170 31.38957190513611 0.5956192016601562 238.7318878173828 0.36867353320121765 301.36572265625 0.28705596923828125 0.7512929 0.42777732014656067 True -10 30987 31.89533519744873 0.594902515411377 224.00457763671875 0.5651828050613403 300.7772216796875 0.2891966998577118 0.75468963 0.40136846899986267 True -11 33804 31.449790477752686 0.9146339893341064 236.93252563476562 0.7294049263000488 299.9003601074219 0.2925992012023926 0.75638974 0.3893066346645355 True -12 36621 31.468095779418945 0.5885088443756104 287.4896240234375 0.4237891435623169 299.4373474121094 0.29508206248283386 0.7592819 0.3967151641845703 True -13 39438 31.49897027015686 0.5995848178863525 214.6990966796875 0.4257306456565857 298.8282165527344 0.29714933037757874 0.76411915 0.38880959153175354 True -14 42255 30.884032487869263 0.5855498313903809 226.08328247070312 0.5000234246253967 298.3905334472656 0.29847821593284607 0.77000904 0.3764399588108063 True -15 45072 30.941284656524658 8.633412837982178 253.28610229492188 0.3743152618408203 298.70233154296875 0.29698920249938965 0.77500844 0.3602202236652374 True -16 47889 30.799100875854492 0.5853016376495361 219.70977783203125 0.30562371015548706 297.9867248535156 0.3009898364543915 0.7805553 0.34275466203689575 True -17 50706 31.990538120269775 0.5896010398864746 205.4900665283203 0.3307727575302124 298.4185791015625 0.2981010675430298 0.78461534 0.33067184686660767 True -18 53523 31.06577754020691 0.6042699813842773 231.4105987548828 0.2499697357416153 297.81005859375 0.30164751410484314 0.7860112 0.33007413148880005 True -19 56340 30.922457695007324 1.9519524574279785 238.88873291015625 0.23656271398067474 298.06671142578125 0.30031028389930725 0.7857533 0.32796481251716614 False diff --git a/ENCSR911YVV/cherimoya.fold_4.performance.tsv b/ENCSR911YVV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 85aaebf1f0d540faaa81d2e790e11c79c64bd6a4..0000000000000000000000000000000000000000 --- a/ENCSR911YVV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -297.81005859375 0.4818592071533203 0.30164745450019836 0.08557974547147751 0.7860112190246582 0.7311407923698425 0.33007413148880005 \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_0.evaluate.json b/ENCSR913FZQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 70789bb89b123a90c5f6fa588f236623ea4061aa..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925WJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_0.fit.json b/ENCSR913FZQ/cherimoya.fold_0.fit.json deleted file mode 100644 index d50b9d8af20e2625ccb1216c33d682d2e17a717f..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF925WJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_0.log b/ENCSR913FZQ/cherimoya.fold_0.log deleted file mode 100644 index 956b862eca551442e248983a010b8a3f8e2fc001..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1741 23.594845294952393 49.827228307724 320.89398193359375 0.21154536306858063 438.5639343261719 0.5218073129653931 0.6547013 10.651901245117188 True -1 3482 21.367980241775513 0.4019782543182373 325.6328125 0.20618295669555664 374.22698974609375 0.6046125292778015 0.74851936 1.2026071548461914 True -2 5223 19.03917169570923 14.05484414100647 350.1041259765625 0.32342037558555603 360.4191589355469 0.6287769675254822 0.77671283 0.367951363325119 True -3 6964 22.090197563171387 4.071317434310913 292.3184814453125 0.1943589150905609 353.77691650390625 0.6381500363349915 0.7832743 0.2258838415145874 True -4 8705 18.96214509010315 0.36451220512390137 329.764404296875 0.19628658890724182 352.05810546875 0.6411730647087097 0.7931673 0.19791585206985474 True -5 10446 19.010635137557983 1.2160451412200928 321.6408386230469 0.19045257568359375 351.0453186035156 0.6430800557136536 0.80263793 0.1786075234413147 True -6 12187 19.42471957206726 0.3706929683685303 289.8387451171875 0.17172294855117798 350.4070129394531 0.6445807814598083 0.8082063 0.15732821822166443 True -7 13928 18.94389247894287 0.36238908767700195 320.1595458984375 0.16837187111377716 350.24237060546875 0.64543616771698 0.8103984 0.15715917944908142 True -8 15669 18.95378541946411 0.3554377555847168 316.33154296875 0.18471096456050873 350.40472412109375 0.6449120044708252 0.8131473 0.16225427389144897 True -9 17410 19.029099941253662 0.36527180671691895 324.3785705566406 0.17785555124282837 349.5113525390625 0.6468426585197449 0.82127494 0.14709854125976562 True -10 19151 19.00685405731201 0.36269164085388184 296.51702880859375 0.12108449637889862 348.70599365234375 0.6484934687614441 0.8261986 0.1376822590827942 True -11 20892 19.01068639755249 0.3660619258880615 323.4541931152344 0.160334050655365 348.56451416015625 0.6489609479904175 0.82946277 0.14712642133235931 True -12 22633 18.954532623291016 2.6044867038726807 298.27752685546875 0.11024213582277298 348.0948181152344 0.6502266526222229 0.83395344 0.13566523790359497 True -13 24374 19.032318353652954 0.3597903251647949 327.102783203125 0.1361149102449417 347.68414306640625 0.6509422063827515 0.8363692 0.12887904047966003 True -14 26115 19.37494993209839 17.763972282409668 344.50030517578125 0.08304688334465027 347.47235107421875 0.6516412496566772 0.8398382 0.1277034431695938 True -15 27856 19.519063711166382 0.3621530532836914 333.46331787109375 0.08119689673185349 347.1803894042969 0.6519922614097595 0.8431059 0.1281585991382599 True -16 29597 18.99396514892578 0.35885071754455566 320.0064697265625 0.09761638939380646 347.2682189941406 0.6516916751861572 0.84367627 0.1265287697315216 True -17 31338 18.939188480377197 7.212207555770874 328.42681884765625 0.10258222371339798 347.4007873535156 0.6512154340744019 0.844928 0.12778973579406738 True -18 33079 19.87175679206848 20.41562509536743 300.77880859375 0.06607382744550705 347.70330810546875 0.6507232785224915 0.8425406 0.1291353851556778 False -19 34820 19.049276113510132 0.36751556396484375 311.9915771484375 0.06479667127132416 347.7648620605469 0.6504945158958435 0.8416454 0.129846453666687 False diff --git a/ENCSR913FZQ/cherimoya.fold_0.performance.tsv b/ENCSR913FZQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 03729f2940f21f26cf94b3ddc725542ae2cd7398..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -347.4007873535156 0.2771003842353821 0.6512154340744019 0.25800561904907227 0.8449280261993408 0.7969598174095154 0.12778973579406738 \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_1.evaluate.json b/ENCSR913FZQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 818f451c57b67c621b4dd9d3213e31dda28650d8..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925WJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_1.fit.json b/ENCSR913FZQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 2ba4211f552728d776d91a1ea61b4ca1f1c704f7..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF925WJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_1.log b/ENCSR913FZQ/cherimoya.fold_1.log deleted file mode 100644 index 3b2028c0f48c9d3199552f652e5ebbc510fc6144..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1715 22.870065212249756 27.942790031433105 315.96929931640625 0.31761252880096436 508.96173095703125 0.5380487442016602 0.6030958 12.87839126586914 True -1 3430 19.187292098999023 0.4899172782897949 329.811767578125 0.7000540494918823 424.24700927734375 0.627949595451355 0.73079693 1.6443828344345093 True -2 5145 18.665703773498535 0.47299718856811523 316.9996337890625 0.5603941679000854 406.4566955566406 0.6548376083374023 0.75320005 0.3992176055908203 True -3 6860 18.735606908798218 0.786921501159668 297.04522705078125 0.30571791529655457 398.82781982421875 0.6648975610733032 0.7567981 0.2689898610115051 True -4 8575 18.705114603042603 0.48299670219421387 303.17547607421875 0.5282161235809326 396.4389953613281 0.6686117649078369 0.7691644 0.23205536603927612 True -5 10290 18.62576413154602 0.4679374694824219 314.7156982421875 0.540449321269989 397.3129577636719 0.6676191091537476 0.7603704 0.2675737738609314 False -6 12005 18.69668459892273 20.3167884349823 318.3829345703125 0.3474288880825043 394.9776611328125 0.6718363165855408 0.78417206 0.20552964508533478 True -7 13720 19.225974321365356 27.101535320281982 289.269287109375 0.1734084039926529 394.4319152832031 0.672909140586853 0.7920354 0.19245471060276031 True -8 15435 18.91477060317993 0.4735679626464844 318.7600402832031 0.21186156570911407 393.1987609863281 0.6747294664382935 0.80109906 0.1827031522989273 True -9 17150 18.314806938171387 0.47027087211608887 321.1822509765625 0.31465357542037964 392.3841552734375 0.6763238310813904 0.8088831 0.17609097063541412 True -10 18865 18.72514796257019 27.642424821853638 280.23529052734375 0.8808369636535645 391.9430236816406 0.6771470308303833 0.81363 0.17310957610607147 True -11 20580 18.399460077285767 0.47510433197021484 327.78326416015625 0.1677548885345459 391.03033447265625 0.6789944767951965 0.82167506 0.16380895674228668 True -12 22295 18.344865322113037 0.46782445907592773 318.5924987792969 0.36450624465942383 390.3513488769531 0.6802493333816528 0.8273266 0.161699578166008 True -13 24010 18.424700260162354 0.4636971950531006 305.1150817871094 0.24963641166687012 389.7574768066406 0.6813247799873352 0.8337829 0.15370869636535645 True -14 25725 18.405329942703247 0.46362900733947754 312.67486572265625 0.15648317337036133 389.34344482421875 0.6822197437286377 0.8362286 0.1521734595298767 True -15 27440 18.366711854934692 23.907111406326294 321.693115234375 0.16978882253170013 389.1325988769531 0.6825471520423889 0.8378531 0.14958378672599792 True -16 29155 18.465569496154785 0.47090983390808105 311.87249755859375 0.2166794240474701 389.2181396484375 0.6825125813484192 0.83977056 0.149612694978714 True -17 30870 18.396332263946533 0.47024035453796387 285.7035217285156 0.15758392214775085 389.2803649902344 0.6822136044502258 0.83839643 0.1516575664281845 False -18 32585 18.332630395889282 0.4648611545562744 309.7685852050781 0.10785764455795288 389.48260498046875 0.6818147897720337 0.8340715 0.15556828677654266 False -19 34300 18.307409286499023 0.47103166580200195 307.80889892578125 0.06679070740938187 389.6576843261719 0.6813997030258179 0.8333735 0.16105695068836212 False diff --git a/ENCSR913FZQ/cherimoya.fold_1.performance.tsv b/ENCSR913FZQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 375f4d850fed76bea35d1cecd91c41f265d2009d..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -389.2181396484375 0.25502002239227295 0.6825125813484192 0.2883511185646057 0.8397705554962158 0.8141456842422485 0.149612694978714 \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_2.evaluate.json b/ENCSR913FZQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 781adb8863c4193b59cf3d35fbc0980fbfe30d28..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925WJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_2.fit.json b/ENCSR913FZQ/cherimoya.fold_2.fit.json deleted file mode 100644 index aaf41bb39c4e30c5d1e9d193f421f9b9be55bd65..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF925WJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_2.log b/ENCSR913FZQ/cherimoya.fold_2.log deleted file mode 100644 index f6185f769292fbb30ea893cf0f8518282697b6b2..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1843 24.490996599197388 25.944808959960938 306.4833984375 0.32781630754470825 457.0152587890625 0.5356354117393494 0.6310397 9.886472702026367 True -1 3686 20.78134298324585 5.549887418746948 311.74310302734375 0.2691217064857483 391.4019470214844 0.6163867712020874 0.74496883 1.3489996194839478 True -2 5529 20.0604190826416 0.3760242462158203 326.2744140625 0.23576635122299194 375.08184814453125 0.640009343624115 0.77884436 0.3711971342563629 True -3 7372 20.431230545043945 14.608818769454956 292.2261047363281 0.230072021484375 371.6311950683594 0.6448703408241272 0.78764635 0.24268731474876404 True -4 9215 20.206359148025513 0.3692772388458252 321.57568359375 0.18854328989982605 368.8861389160156 0.6497557163238525 0.7978263 0.18591438233852386 True -5 11058 20.08681344985962 0.3623695373535156 291.33197021484375 0.2740945816040039 367.92840576171875 0.651375949382782 0.80417454 0.18254990875720978 True -6 12901 20.08013153076172 1.1818015575408936 290.11676025390625 0.3328051269054413 367.4869079589844 0.6522611379623413 0.81047183 0.17321670055389404 True -7 14744 20.019451141357422 0.3572545051574707 294.17041015625 0.418407678604126 366.7717590332031 0.653656542301178 0.81385463 0.17113789916038513 True -8 16587 19.694230318069458 0.356306791305542 310.0383605957031 0.7361222505569458 366.19610595703125 0.654751181602478 0.81835353 0.16499286890029907 True -9 18430 19.71949338912964 0.3572683334350586 300.5094299316406 0.18845614790916443 365.6476135253906 0.6557631492614746 0.82197315 0.15551438927650452 True -10 20273 19.702613830566406 0.35866570472717285 331.8061218261719 0.2947213053703308 365.1020202636719 0.6566474437713623 0.8254841 0.1503712236881256 True -11 22116 19.659658193588257 0.3564729690551758 288.1934814453125 0.2143147587776184 364.48333740234375 0.6578823328018188 0.8335795 0.14515823125839233 True -12 23959 19.659117937088013 0.3548760414123535 323.1978759765625 0.18104109168052673 363.9180908203125 0.6588448286056519 0.8351787 0.14322422444820404 True -13 25802 19.666966915130615 0.3632924556732178 301.28668212890625 0.10580860078334808 363.3402404785156 0.6600013375282288 0.8381994 0.14051294326782227 True -14 27645 19.709413051605225 0.7915403842926025 304.84967041015625 0.21479421854019165 362.9154357910156 0.6607850193977356 0.835492 0.1447424441576004 False -15 29488 19.69116973876953 13.973756074905396 339.01123046875 0.08485409617424011 362.7109680175781 0.6611583828926086 0.8342529 0.14718413352966309 False -16 31331 21.250351905822754 20.127192735671997 293.2694091796875 0.2949325442314148 362.8270263671875 0.6610473394393921 0.82393163 0.15985745191574097 False -17 33174 19.67793560028076 0.361907958984375 287.58306884765625 0.20588837563991547 362.9886779785156 0.6606230735778809 0.8225385 0.16430887579917908 False -18 35017 19.77449631690979 0.3933892250061035 299.8712463378906 0.14338773488998413 363.20623779296875 0.6603601574897766 0.8178367 0.17096857726573944 False -19 36860 19.69329810142517 2.7809605598449707 318.17156982421875 0.10049626231193542 363.376220703125 0.6599900126457214 0.81440896 0.1760847270488739 False diff --git a/ENCSR913FZQ/cherimoya.fold_2.performance.tsv b/ENCSR913FZQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 2e36a0f82d52222d4013ed7e140d0fe2cbac5517..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -363.3402404785156 0.26968204975128174 0.6600013375282288 0.2688543200492859 0.8381993770599365 0.8003589510917664 0.14051294326782227 \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_3.evaluate.json b/ENCSR913FZQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c7429f7564d6de68160124f180c8982eae05a53a..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925WJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_3.fit.json b/ENCSR913FZQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 0e41fb7932c181eca32a3d0d6a8e061cd504b560..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF925WJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_3.log b/ENCSR913FZQ/cherimoya.fold_3.log deleted file mode 100644 index 04709b76d38c13233c29e822f95077283ce26d87..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1784 23.6311457157135 24.812296390533447 317.306640625 0.2340918779373169 457.7269287109375 0.5304994583129883 0.5995627 11.308889389038086 True -1 3568 20.139527320861816 13.739161014556885 331.7721862792969 0.4162099063396454 387.2270202636719 0.6171069145202637 0.72611916 1.3512736558914185 True -2 5352 19.414066076278687 0.35213279724121094 334.991455078125 0.3230753540992737 375.1592712402344 0.6367112398147583 0.73986644 0.45168358087539673 True -3 7136 19.417786359786987 0.3544187545776367 335.039794921875 0.23343026638031006 368.4752502441406 0.6459190845489502 0.74221134 0.28936684131622314 True -4 8920 19.477740049362183 1.0354034900665283 345.547607421875 0.1896335631608963 366.8309020996094 0.6483860015869141 0.7504808 0.27174243330955505 True -5 10704 19.171090602874756 1.3603456020355225 347.41162109375 0.21796062588691711 365.7712707519531 0.6503459215164185 0.7552931 0.24875915050506592 True -6 12488 19.086498260498047 9.485707998275757 334.0796813964844 0.3845764398574829 365.1153259277344 0.6519266366958618 0.763777 0.23056863248348236 True -7 14272 19.05250382423401 0.34183764457702637 311.97100830078125 0.17647874355316162 364.49908447265625 0.6529662013053894 0.76851255 0.22676324844360352 True -8 16056 19.593945741653442 18.129006385803223 295.08807373046875 0.43005114793777466 364.31829833984375 0.6539604663848877 0.7713665 0.2266973853111267 True -9 17840 19.192106246948242 0.34890294075012207 300.4404602050781 0.6305957436561584 363.7249450683594 0.6554981470108032 0.76900935 0.23121340572834015 False -10 19624 19.093528985977173 0.339982271194458 296.2251281738281 0.2867848575115204 363.18743896484375 0.656440794467926 0.7597028 0.24709592759609222 False -11 21408 19.10570001602173 0.3341805934906006 296.08245849609375 0.18411065638065338 362.621826171875 0.6575368642807007 0.76300144 0.23823486268520355 False -12 23192 19.063148021697998 0.34423279762268066 320.6306457519531 0.3696262538433075 362.5085144042969 0.6581364870071411 0.77441514 0.222027987241745 True -13 24976 19.076305627822876 0.33541321754455566 314.68927001953125 0.5746093988418579 361.9328308105469 0.6591857075691223 0.76887184 0.22201241552829742 False -14 26760 19.232889413833618 12.864176273345947 326.025634765625 0.48095613718032837 361.4237976074219 0.6600773334503174 0.76797646 0.2234019935131073 False -15 28544 19.24865961074829 0.34064435958862305 307.73992919921875 0.16792550683021545 361.06988525390625 0.6604902148246765 0.7759249 0.2127770036458969 True -16 30328 19.05908989906311 0.3469538688659668 297.9095764160156 0.06086599826812744 361.0032043457031 0.6604639291763306 0.78283006 0.2049778550863266 True -17 32112 19.196202039718628 0.3367345333099365 311.0927734375 0.13197894394397736 361.1944274902344 0.6602766513824463 0.7800237 0.2097964584827423 False -18 33896 19.079906463623047 0.3381309509277344 309.2395935058594 0.10123910009860992 361.30511474609375 0.6598080396652222 0.77839094 0.21318091452121735 False -19 35680 19.179754972457886 14.790478229522705 302.2650146484375 0.1026172935962677 361.31365966796875 0.6596446633338928 0.77700573 0.21657152473926544 False diff --git a/ENCSR913FZQ/cherimoya.fold_3.performance.tsv b/ENCSR913FZQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 2ce0df3b1b6ad13d40d0a549d79828a0bbd2f77e..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.0032043457031 0.27047598361968994 0.6604639291763306 0.2654866576194763 0.7828300595283508 0.7700321078300476 0.2049778550863266 \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_4.evaluate.json b/ENCSR913FZQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 51346a4dc0f41027df5bfe48c73dd4882c088a26..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF925WJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_4.fit.json b/ENCSR913FZQ/cherimoya.fold_4.fit.json deleted file mode 100644 index a59bac990b58d15cd0211f2225f7f5dfbc829fdf..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF925WJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913FZQ/cherimoya.fold_4.log b/ENCSR913FZQ/cherimoya.fold_4.log deleted file mode 100644 index 515ed5f91fc6340c3e0e3bc6093b594f2cf8fdcc..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1770 23.862613439559937 3.568307638168335 301.6611022949219 0.2358633279800415 439.75537109375 0.528207004070282 0.6315783 10.240059852600098 True -1 3540 19.305488348007202 0.3563241958618164 357.7298583984375 0.20825675129890442 374.6741943359375 0.6099086403846741 0.7304116 1.3026421070098877 True -2 5310 19.326348304748535 0.3428022861480713 343.40087890625 0.3583301901817322 363.8768005371094 0.6279298067092896 0.7675157 0.4383593201637268 True -3 7080 19.14136791229248 0.33833861351013184 327.82659912109375 0.15707531571388245 356.31976318359375 0.6397249102592468 0.78261065 0.21168486773967743 True -4 8850 18.90330195426941 0.33505988121032715 309.9432373046875 0.26942503452301025 354.96142578125 0.6425458192825317 0.78718066 0.2113116979598999 True -5 10620 18.878846645355225 0.34003233909606934 288.7425537109375 0.2153116762638092 354.1979064941406 0.6443221569061279 0.7920139 0.19733594357967377 True -6 12390 18.858198404312134 0.3357064723968506 297.10693359375 0.2135246992111206 353.5076599121094 0.6459900736808777 0.8001384 0.17258374392986298 True -7 14160 18.90597677230835 0.33394384384155273 312.4581298828125 0.1365152895450592 353.5737609863281 0.6459594964981079 0.80303574 0.18168112635612488 True -8 15930 18.866339445114136 0.33484721183776855 322.81103515625 0.18717244267463684 352.6642150878906 0.6476167440414429 0.81104434 0.16385236382484436 True -9 17700 18.941372871398926 0.33320140838623047 341.9984130859375 0.5100985169410706 352.18817138671875 0.6487898230552673 0.81609654 0.16386015713214874 True -10 19470 18.900909423828125 0.4587383270263672 297.4516906738281 0.4811062514781952 351.4621276855469 0.6499642133712769 0.82250154 0.14543087780475616 True -11 21240 18.914381980895996 0.3365910053253174 302.79620361328125 0.2522844970226288 350.9969177246094 0.6511195302009583 0.82677794 0.14374178647994995 True -12 23010 18.967121601104736 0.34021568298339844 322.6611022949219 0.14119361340999603 350.4734191894531 0.6522693037986755 0.8308453 0.1404772698879242 True -13 24780 18.909653902053833 0.3740561008453369 308.6810607910156 0.15854507684707642 349.946044921875 0.6532761454582214 0.83465374 0.1377955973148346 True -14 26550 18.89036512374878 1.4456462860107422 328.69805908203125 0.1496245115995407 349.5692138671875 0.6538334488868713 0.8346208 0.13652171194553375 False -15 28320 18.947675228118896 0.33409595489501953 295.15740966796875 0.11597881466150284 349.48486328125 0.6542962193489075 0.83379203 0.1388721764087677 False -16 30090 18.886162281036377 0.337770938873291 312.394287109375 0.11523759365081787 349.4653625488281 0.6542932987213135 0.8355367 0.1365274339914322 True -17 31860 18.89887809753418 0.3357083797454834 314.15582275390625 0.13098421692848206 349.53564453125 0.654036283493042 0.8352952 0.13829830288887024 False -18 33630 18.904316663742065 0.33536243438720703 310.4186706542969 0.07056715339422226 349.6463317871094 0.6536723375320435 0.8316261 0.14283248782157898 False -19 35400 18.887782335281372 0.34903788566589355 282.29266357421875 0.4110465943813324 349.7708740234375 0.6533477306365967 0.83044595 0.14524444937705994 False diff --git a/ENCSR913FZQ/cherimoya.fold_4.performance.tsv b/ENCSR913FZQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3ebea5d576a4b6222db612aa3b30b1aafaa941cf..0000000000000000000000000000000000000000 --- a/ENCSR913FZQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -349.4653625488281 0.2751627266407013 0.6542932987213135 0.25787094235420227 0.8355367183685303 0.7865435481071472 0.1365274339914322 \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_0.evaluate.json b/ENCSR913NYL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ede67d3457f6ab8784098ff213b7bad531b917fa..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF550RXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_0.fit.json b/ENCSR913NYL/cherimoya.fold_0.fit.json deleted file mode 100644 index da9adbc67a0256db0eeca9cdf30cc2916072f516..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF550RXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_0.log b/ENCSR913NYL/cherimoya.fold_0.log deleted file mode 100644 index 0fa82dd98d4f7c6ee1e0de474da7992477864b7b..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2768 34.24485731124878 3.8410277366638184 190.64669799804688 0.686853289604187 255.0828399658203 0.16507655382156372 0.61348724 2.2777764797210693 True -1 5536 30.558659553527832 0.5658786296844482 190.05332946777344 1.0664292573928833 237.90570068359375 0.2392929047346115 0.67963517 1.0589262247085571 True -2 8304 30.5811870098114 0.560344934463501 185.05584716796875 0.45731180906295776 234.31793212890625 0.2510587275028229 0.69201964 0.7180135846138 True -3 11072 30.578454732894897 0.550800085067749 143.91473388671875 0.5439667701721191 232.38504028320312 0.25880783796310425 0.69904983 0.6422365307807922 True -4 13840 30.6056969165802 5.469822883605957 170.02999877929688 0.716886579990387 231.75607299804688 0.26246407628059387 0.70157075 0.676019012928009 True -5 16608 30.629911422729492 0.5615546703338623 187.6502227783203 0.5796986222267151 231.1146697998047 0.2642728388309479 0.7039667 0.608468770980835 True -6 19376 30.624369621276855 0.7285809516906738 223.27804565429688 0.6198363304138184 230.58123779296875 0.2672443091869354 0.70502126 0.6353179812431335 True -7 22144 30.585769176483154 0.5551514625549316 201.3374786376953 0.5907900929450989 229.7460174560547 0.2713039219379425 0.7124178 0.6282479166984558 True -8 24912 30.589705228805542 0.5564115047454834 174.258056640625 0.6534258723258972 229.45909118652344 0.2721285820007324 0.7148756 0.589495837688446 True -9 27680 30.636650323867798 0.5543918609619141 232.1650390625 0.6146857738494873 228.86288452148438 0.27606555819511414 0.715778 0.6213094592094421 True -10 30448 30.616257667541504 0.5601911544799805 170.91128540039062 0.7073189616203308 228.13616943359375 0.2786577343940735 0.72427326 0.5486946105957031 True -11 33216 30.563257932662964 0.5428228378295898 177.76544189453125 0.37402933835983276 227.44638061523438 0.28240278363227844 0.7252053 0.5144553184509277 True -12 35984 30.618470191955566 0.5528457164764404 169.21536254882812 0.3902207314968109 226.77456665039062 0.2849141061306 0.7324094 0.45927679538726807 True -13 38752 30.727093935012817 0.5909709930419922 152.83013916015625 0.41836017370224 226.2477264404297 0.2854595184326172 0.74064225 0.4302169680595398 True -14 41520 30.910075187683105 0.5641694068908691 177.3280487060547 0.3857277035713196 225.6728515625 0.28892743587493896 0.74674875 0.4132242500782013 True -15 44288 30.602458000183105 0.565540075302124 160.87359619140625 0.6083948612213135 225.39149475097656 0.2892768681049347 0.7541244 0.38501638174057007 True -16 47056 30.602660655975342 0.5501611232757568 180.9788055419922 0.361052006483078 225.16246032714844 0.2901698350906372 0.7618236 0.3622228503227234 True -17 49824 30.647751569747925 0.554023265838623 164.89117431640625 0.2849298417568207 225.27490234375 0.28918275237083435 0.76324344 0.35380128026008606 True -18 52592 30.7458655834198 14.98989725112915 167.64520263671875 0.37069955468177795 225.21409606933594 0.2900012731552124 0.7618421 0.3517533838748932 False -19 55360 30.69119930267334 0.5737600326538086 146.24864196777344 0.31054967641830444 225.35385131835938 0.2887878715991974 0.7629001 0.3541858196258545 False diff --git a/ENCSR913NYL/cherimoya.fold_0.performance.tsv b/ENCSR913NYL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8daa132ff529c41f4ac39ec18b6808b2c2a1a3e1..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -225.27490234375 0.5060184001922607 0.28918278217315674 0.06328359246253967 0.7632434368133545 0.6931193470954895 0.35380128026008606 \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_1.evaluate.json b/ENCSR913NYL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ad4852df71ef1817f3b04cfc692b5ff30c122de1..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF550RXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_1.fit.json b/ENCSR913NYL/cherimoya.fold_1.fit.json deleted file mode 100644 index 2ceab3d07eddcf890fd662663b56c0d89703650d..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF550RXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_1.log b/ENCSR913NYL/cherimoya.fold_1.log deleted file mode 100644 index bf444467c08821e841b3939ea18dadd873550c9b..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 33.93276286125183 3.6645760536193848 191.29391479492188 0.9104992151260376 294.0475769042969 0.17217034101486206 0.6421247 2.9428865909576416 True -1 5470 30.238120794296265 0.7283563613891602 181.66075134277344 0.9439306259155273 273.6097717285156 0.24817506968975067 0.71229273 1.2716904878616333 True -2 8205 30.356390476226807 3.4605965614318848 198.11578369140625 0.6049647331237793 267.4104919433594 0.263559490442276 0.7273327 0.8274878263473511 True -3 10940 30.258933544158936 0.7275257110595703 184.80197143554688 0.8112303018569946 264.3594970703125 0.2728971242904663 0.73447424 0.8685377240180969 True -4 13675 30.28923988342285 2.505329132080078 171.53466796875 0.5728561282157898 263.7099914550781 0.27447274327278137 0.73547816 0.8767025470733643 True -5 16410 30.250430583953857 0.7122206687927246 177.8896484375 0.6186889410018921 262.6380310058594 0.27858269214630127 0.7409014 0.8259682059288025 True -6 19145 30.22736096382141 0.7123916149139404 178.07955932617188 0.524670422077179 261.7693786621094 0.2826388478279114 0.74407923 0.8268413543701172 True -7 21880 30.23616313934326 0.7230944633483887 176.10317993164062 0.5048755407333374 261.6672668457031 0.28332409262657166 0.7472478 0.7695096135139465 True -8 24615 30.265108346939087 1.8787841796875 173.03480529785156 0.41455909609794617 260.40252685546875 0.2874361574649811 0.75587815 0.7092534899711609 True -9 27350 30.29550552368164 0.7214293479919434 155.2381134033203 0.44421133399009705 259.7462463378906 0.2891862690448761 0.75869006 0.6436281800270081 True -10 30085 30.210832357406616 0.7215230464935303 188.45819091796875 0.4242316484451294 258.6813659667969 0.29369136691093445 0.7651761 0.5881884098052979 True -11 32820 30.234694719314575 0.7137980461120605 179.9845733642578 0.4499168395996094 257.98193359375 0.29544195532798767 0.77077067 0.5185672640800476 True -12 35555 30.23342490196228 0.7223553657531738 175.60940551757812 0.306082546710968 257.0327453613281 0.29895779490470886 0.775878 0.481425940990448 True -13 38290 30.347809076309204 0.7183799743652344 193.66595458984375 0.3710377812385559 256.7973327636719 0.2999483346939087 0.7833252 0.4552892744541168 True -14 41025 30.30345582962036 0.7238039970397949 189.65512084960938 0.32875388860702515 256.0527038574219 0.30084338784217834 0.78732073 0.4255029857158661 True -15 43760 30.310819625854492 2.3047094345092773 207.67523193359375 0.5140661001205444 255.5734100341797 0.30228179693222046 0.7940737 0.4019695222377777 True -16 46495 30.27019214630127 0.7174279689788818 163.09959411621094 0.42348819971084595 255.0507354736328 0.30535897612571716 0.79947746 0.38654381036758423 True -17 49230 30.322969913482666 0.7155311107635498 161.92062377929688 0.3752588629722595 254.68580627441406 0.3062705397605896 0.8006748 0.3767109215259552 True -18 51965 30.3067307472229 15.767763376235962 180.77291870117188 0.32339489459991455 254.69149780273438 0.30566394329071045 0.7997983 0.3729742467403412 False -19 54700 30.26165270805359 1.2020378112792969 152.75868225097656 0.3260580897331238 254.9977264404297 0.30392760038375854 0.798984 0.3734484910964966 False diff --git a/ENCSR913NYL/cherimoya.fold_1.performance.tsv b/ENCSR913NYL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index dfb02f03f2e0478151b14e261da76b6b70e511a0..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -254.68580627441406 0.4917154610157013 0.306270569562912 0.07622078061103821 0.8006747961044312 0.7498299479484558 0.3767109215259552 \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_2.evaluate.json b/ENCSR913NYL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 302e9e3ca0bad7e722f17f9b7573ba618c3cff46..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF550RXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_2.fit.json b/ENCSR913NYL/cherimoya.fold_2.fit.json deleted file mode 100644 index aaadd124ef5c92305cd83c5247e71108e5e9a83a..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF550RXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_2.log b/ENCSR913NYL/cherimoya.fold_2.log deleted file mode 100644 index c799be69f08f6f5333b680be930a80fcbd7ec942..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2898 35.987196922302246 4.798043727874756 216.71092224121094 0.7400813102722168 265.20159912109375 0.17224319279193878 0.6268943 2.360827922821045 True -1 5796 32.09295129776001 0.5421617031097412 218.08230590820312 0.8092696070671082 247.49456787109375 0.24529989063739777 0.7042171 1.0125207901000977 True -2 8694 32.02917146682739 0.5293774604797363 173.61502075195312 0.5413451194763184 243.48529052734375 0.2571578621864319 0.7160339 0.6858553886413574 True -3 11592 32.053221702575684 0.5228650569915771 181.1544952392578 0.6375116109848022 242.13949584960938 0.26043885946273804 0.71948284 0.7704607844352722 True -4 14490 32.04731369018555 0.5236802101135254 146.32803344726562 0.5695154666900635 241.07208251953125 0.2651650905609131 0.7202144 0.7758840322494507 True -5 17388 32.106440782547 2.7955682277679443 239.44436645507812 0.7269420027732849 240.21803283691406 0.26820775866508484 0.72429967 0.7013865113258362 True -6 20286 32.072569847106934 0.5253691673278809 220.77313232421875 0.41478121280670166 239.37461853027344 0.27269667387008667 0.7259439 0.7355097532272339 True -7 23184 32.03973054885864 0.5227019786834717 207.02401733398438 0.5098135471343994 238.4737091064453 0.27642977237701416 0.7263026 0.7518764734268188 True -8 26082 32.02168035507202 0.5245137214660645 163.02618408203125 0.5511035323143005 238.20884704589844 0.2771835923194885 0.732714 0.6965920925140381 True -9 28980 32.076725244522095 0.5142433643341064 224.19110107421875 0.6501010656356812 237.3192138671875 0.28083062171936035 0.73437464 0.6821746230125427 True -10 31878 32.06728434562683 0.5292279720306396 173.89730834960938 0.3737912178039551 236.3143768310547 0.28488394618034363 0.74013495 0.6331430077552795 True -11 34776 32.02351498603821 0.790579080581665 140.0745391845703 0.31909245252609253 235.694580078125 0.28808334469795227 0.7449525 0.5948889255523682 True -12 37674 32.08836388587952 0.5286245346069336 155.75050354003906 0.5191735029220581 234.9810028076172 0.290483295917511 0.7486022 0.5456389784812927 True -13 40572 32.081071853637695 0.5242891311645508 208.48587036132812 0.41489964723587036 234.07203674316406 0.29417088627815247 0.7550984 0.4931069612503052 True -14 43470 32.07272410392761 0.525139570236206 166.4251251220703 0.41098636388778687 233.84573364257812 0.2938821017742157 0.7608547 0.44146597385406494 True -15 46368 32.232375144958496 12.420660972595215 214.65481567382812 0.6219480633735657 233.4550018310547 0.2959286868572235 0.76732415 0.42133545875549316 True -16 49266 32.09178900718689 0.522819995880127 185.69769287109375 0.42912203073501587 233.21603393554688 0.29554903507232666 0.77177095 0.39359280467033386 True -17 52164 32.13182997703552 0.5320076942443848 164.798583984375 0.4072689414024353 233.18394470214844 0.2957448363304138 0.7763081 0.3738532066345215 True -18 55062 32.07758021354675 0.5171959400177002 198.3482208251953 0.3242487609386444 233.13026428222656 0.2956794500350952 0.77665335 0.36691582202911377 True -19 57960 32.030821084976196 0.5224578380584717 230.80181884765625 0.2972427010536194 233.0696258544922 0.2964865267276764 0.7776132 0.36953654885292053 True diff --git a/ENCSR913NYL/cherimoya.fold_2.performance.tsv b/ENCSR913NYL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 023b8e0c49a0c32c251dfb6544f50b106298fd80..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -233.0696258544922 0.5013835430145264 0.2964865267276764 0.06910593807697296 0.7776132225990295 0.7148634791374207 0.36953654885292053 \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_3.evaluate.json b/ENCSR913NYL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c1d826b0e80c8a137a8a43cf9ca1aae51861d45e..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF550RXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_3.fit.json b/ENCSR913NYL/cherimoya.fold_3.fit.json deleted file mode 100644 index b9d07d2cee388aa4efc4d26ab38e89a08c26a192..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF550RXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_3.log b/ENCSR913NYL/cherimoya.fold_3.log deleted file mode 100644 index 68c1a0aeac6bbb1a721b2e31d54fe57eca1974ab..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2780 34.367429971694946 3.407163619995117 168.6035919189453 0.7722171545028687 268.07843017578125 0.17035187780857086 0.62765473 2.8901824951171875 True -1 5560 30.707329034805298 0.5679817199707031 201.19741821289062 0.7372738122940063 251.0845947265625 0.23823750019073486 0.68629354 1.3147368431091309 True -2 8340 30.762860774993896 0.5507774353027344 185.95098876953125 0.7953413724899292 246.31629943847656 0.2539463937282562 0.69690025 0.9020904898643494 True -3 11120 30.7044415473938 0.5439565181732178 157.31588745117188 0.7593200206756592 244.51019287109375 0.25978416204452515 0.7057972 0.8633964657783508 True -4 13900 30.6536865234375 0.5554080009460449 193.70941162109375 0.7919368147850037 243.77488708496094 0.2631416320800781 0.7090276 0.8726312518119812 True -5 16680 30.67732071876526 0.5467405319213867 185.7884063720703 0.5368866920471191 242.46868896484375 0.2693576216697693 0.7118149 0.9073143005371094 True -6 19460 30.72725510597229 7.36816930770874 229.34521484375 0.6281911134719849 242.35830688476562 0.2694796919822693 0.7150226 0.8834021687507629 True -7 22240 31.25861954689026 0.5540680885314941 170.25057983398438 0.39662331342697144 241.47222900390625 0.27368855476379395 0.7186446 0.8588689565658569 True -8 25020 30.938952445983887 13.322106122970581 173.65460205078125 0.9813979864120483 240.85865783691406 0.2770775854587555 0.7203944 0.8123319745063782 True -9 27800 30.788949012756348 5.434142112731934 171.09121704101562 0.5793169736862183 240.1533966064453 0.27920785546302795 0.730402 0.7469180822372437 True -10 30580 30.7631778717041 1.6615502834320068 170.12814331054688 0.7643399238586426 239.22259521484375 0.2835398316383362 0.73222923 0.6760901808738708 True -11 33360 30.707805395126343 0.5773792266845703 176.72293090820312 0.5045103430747986 238.59059143066406 0.2864071726799011 0.7385902 0.583571195602417 True -12 36140 30.750340700149536 2.0051393508911133 195.34033203125 0.42944490909576416 238.4873504638672 0.28459039330482483 0.7456824 0.5563546419143677 True -13 38920 30.74846863746643 0.5508098602294922 149.51101684570312 0.6377738118171692 237.69793701171875 0.287546306848526 0.75429887 0.4896927773952484 True -14 41700 30.731314659118652 0.5623400211334229 169.60354614257812 0.3980797529220581 237.00343322753906 0.29165104031562805 0.7620358 0.4477202594280243 True -15 44480 30.79437232017517 0.5603659152984619 178.57382202148438 0.5286847352981567 236.99203491210938 0.29084327816963196 0.76783824 0.41233325004577637 True -16 47260 30.735448837280273 0.5603795051574707 139.71170043945312 0.41023582220077515 236.47866821289062 0.2943283021450043 0.77396214 0.3935282528400421 True -17 50040 30.70393943786621 0.5523471832275391 192.6971435546875 0.2410443276166916 236.47811889648438 0.293457955121994 0.77522635 0.3827650845050812 True -18 52820 30.718750476837158 0.55228590965271 179.9320068359375 0.3843020796775818 236.64474487304688 0.2927626371383667 0.77392775 0.37909629940986633 False -19 55600 30.747130393981934 0.5609025955200195 210.6031036376953 0.28852951526641846 237.0436553955078 0.29013198614120483 0.77465504 0.3778251111507416 False diff --git a/ENCSR913NYL/cherimoya.fold_3.performance.tsv b/ENCSR913NYL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6e2839b206096c25c9ae5cdc708587d2d00668f7..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -236.47811889648438 0.5019177794456482 0.293457955121994 0.07139486819505692 0.775226354598999 0.7080221772193909 0.3827650845050812 \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_4.evaluate.json b/ENCSR913NYL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 24551308ce77e74e567e813d6cbcd7bfc2f3ffe5..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF550RXC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_4.fit.json b/ENCSR913NYL/cherimoya.fold_4.fit.json deleted file mode 100644 index 0a34a2fa37369c108aa42c7fe6f34793c1b92150..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF550RXC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913NYL/cherimoya.fold_4.log b/ENCSR913NYL/cherimoya.fold_4.log deleted file mode 100644 index 0911faec1b277a371ad93472c07538a1d18a0608..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2864 35.580267667770386 5.967217922210693 176.52362060546875 0.8027987480163574 245.8391876220703 0.1630041003227234 0.61372 2.0340209007263184 True -1 5728 31.67635989189148 0.6371698379516602 198.72824096679688 0.828324556350708 230.74571228027344 0.23062269389629364 0.6817881 0.9856610894203186 True -2 8592 31.72285485267639 0.6159367561340332 166.1256103515625 0.6433923244476318 227.5734100341797 0.24105572700500488 0.6919574 0.6606912016868591 True -3 11456 31.58545422554016 0.6086971759796143 192.9319610595703 0.6673944592475891 225.70831298828125 0.2479431927204132 0.694527 0.6711692214012146 True -4 14320 31.57957100868225 0.6130125522613525 197.09042358398438 0.555526614189148 225.0684356689453 0.24920806288719177 0.702935 0.6340309977531433 True -5 17184 31.562729835510254 0.6012506484985352 199.50393676757812 0.5376818180084229 224.294189453125 0.2537084221839905 0.7063949 0.6320594549179077 True -6 20048 31.548274278640747 0.5997860431671143 166.19406127929688 0.7000659704208374 223.339111328125 0.2585957944393158 0.7077591 0.6289098858833313 True -7 22912 31.56295871734619 0.6059949398040771 201.18812561035156 0.8371529579162598 223.25497436523438 0.2586708068847656 0.7120898 0.6172922849655151 True -8 25776 31.623934984207153 0.6136689186096191 170.33078002929688 0.5907117128372192 222.4671173095703 0.26281678676605225 0.71277356 0.6521045565605164 True -9 28640 31.603312969207764 0.6126744747161865 184.11663818359375 0.5402330160140991 221.79965209960938 0.266162633895874 0.72038656 0.5990310907363892 True -10 31504 31.615329265594482 1.0183079242706299 188.26251220703125 0.6679455041885376 221.30516052246094 0.2686067521572113 0.71986663 0.5676906108856201 False -11 34368 31.671432495117188 0.6174571514129639 188.98995971679688 0.4598172903060913 220.66751098632812 0.27132532000541687 0.72515225 0.5332993865013123 True -12 37232 31.70535159111023 0.6158792972564697 134.41244506835938 0.6564295887947083 219.87171936035156 0.27405619621276855 0.73214096 0.5007369518280029 True -13 40096 31.617387294769287 0.6154935359954834 190.6001739501953 0.35420721769332886 219.60690307617188 0.2753189504146576 0.7410113 0.4670264720916748 True -14 42960 31.594117164611816 0.6129722595214844 218.12161254882812 0.5069564580917358 219.54615783691406 0.27507442235946655 0.74848455 0.4219399690628052 True -15 45824 31.579838275909424 0.6142048835754395 187.95895385742188 0.4975630044937134 218.97242736816406 0.27770018577575684 0.7558739 0.3871650993824005 True -16 48688 31.58061146736145 0.6078259944915771 181.56887817382812 0.31413203477859497 218.58782958984375 0.2789762616157532 0.7629972 0.3591478168964386 True -17 51552 31.63769006729126 0.6046693325042725 168.06130981445312 0.39639127254486084 218.6446990966797 0.27844035625457764 0.76749825 0.3458990454673767 True -18 54416 31.613525390625 0.6080155372619629 180.7754669189453 0.35955286026000977 218.5218048095703 0.27979692816734314 0.76840776 0.34180620312690735 True -19 57280 31.810633182525635 0.6001765727996826 189.13055419921875 0.2285807579755783 218.58514404296875 0.2789576053619385 0.7657176 0.34050166606903076 False diff --git a/ENCSR913NYL/cherimoya.fold_4.performance.tsv b/ENCSR913NYL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b847be1f96fb3aa078699d3a9a6a02628aebaba9..0000000000000000000000000000000000000000 --- a/ENCSR913NYL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -218.5218048095703 0.5127961039543152 0.27979692816734314 0.06258408725261688 0.7684077620506287 0.6985953450202942 0.34180620312690735 \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_0.evaluate.json b/ENCSR913OWV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 58c854bcab910d3103ea40b0f6fc1c48bc82e3bb..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802YBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_0.fit.json b/ENCSR913OWV/cherimoya.fold_0.fit.json deleted file mode 100644 index 5b38d093b538d10e10972bc56de2a86ca4cb8eec..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF802YBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_0.log b/ENCSR913OWV/cherimoya.fold_0.log deleted file mode 100644 index a23143d7b56fa65adbcfe9c5efa3a081731b2d2c..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3857 48.27371788024902 25.332732677459717 642.9715576171875 0.976784348487854 1046.8143310546875 0.7178229689598083 0.7283504 5.7462239265441895 True -1 7714 42.947065353393555 22.28817319869995 738.220703125 1.2501766681671143 899.545654296875 0.7802289724349976 0.732834 1.1030043363571167 True -2 11571 42.84211349487305 0.8006620407104492 610.834228515625 0.8517371416091919 875.5018920898438 0.7928917407989502 0.7530927 0.898946225643158 True -3 15428 42.91641664505005 0.7880828380584717 633.7347412109375 1.5211472511291504 861.7913208007812 0.7981588244438171 0.7548422 0.7697438597679138 True -4 19285 42.24378991127014 0.8275587558746338 690.9839477539062 1.0687191486358643 850.8745727539062 0.8021253943443298 0.7592906 0.6856652498245239 True -5 23142 41.85101580619812 0.7788810729980469 762.2674560546875 1.1073172092437744 847.4810791015625 0.8039829134941101 0.76025957 0.6422845125198364 True -6 26999 41.89035964012146 0.7823667526245117 740.0457763671875 0.861603319644928 839.863037109375 0.8072009086608887 0.7652944 0.6007023453712463 True -7 30856 41.92407751083374 2.568632125854492 561.03369140625 1.161422848701477 831.8720092773438 0.8100273609161377 0.77077967 0.5841788649559021 True -8 34713 42.15395760536194 0.8059937953948975 668.5684204101562 0.6913033723831177 826.4974365234375 0.8124926686286926 0.7721029 0.5933636426925659 True -9 38570 42.060314655303955 0.7925093173980713 774.298828125 0.8566212058067322 819.9644165039062 0.8155996799468994 0.77889526 0.5740957856178284 True -10 42427 41.88207817077637 1.46236252784729 590.8724365234375 0.8900109529495239 812.9422607421875 0.8188828229904175 0.78426695 0.5642744302749634 True -11 46284 41.81955623626709 26.794039964675903 557.759765625 0.5745192766189575 806.3938598632812 0.8217883706092834 0.7932214 0.5417851209640503 True -12 50141 42.65527820587158 0.7801992893218994 591.3484497070312 0.721883237361908 801.1414184570312 0.8241424560546875 0.7994841 0.5261073112487793 True -13 53998 42.36118674278259 0.7767889499664307 522.8607177734375 0.8281745910644531 795.9038696289062 0.826748251914978 0.8039631 0.516619086265564 True -14 57855 43.58161115646362 10.511130094528198 652.5552978515625 0.9728800654411316 791.3267822265625 0.8286145925521851 0.8124748 0.50150066614151 True -15 61712 42.010602712631226 0.7959280014038086 658.3438110351562 0.6519335508346558 788.1299438476562 0.8302819132804871 0.815888 0.4998369812965393 True -16 65569 41.952006816864014 2.449479103088379 587.9501953125 0.5601017475128174 786.755615234375 0.8311135172843933 0.82095146 0.4986427128314972 True -17 69426 41.93488931655884 0.7764039039611816 576.5260009765625 0.5160754323005676 786.634765625 0.8312439322471619 0.8214156 0.5113850831985474 True -18 73283 41.89458131790161 32.66559553146362 471.5682067871094 0.605145275592804 786.5508422851562 0.8314840793609619 0.82137275 0.5200093388557434 False -19 77140 41.74313735961914 0.7848358154296875 638.1543579101562 0.5150257349014282 786.535888671875 0.8312966227531433 0.8207125 0.526129961013794 False diff --git a/ENCSR913OWV/cherimoya.fold_0.performance.tsv b/ENCSR913OWV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index addbe713fd5fe93dc8825dd9bbac2f33c77b8bc7..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -786.634765625 0.143769308924675 0.8312439322471619 0.46802133321762085 0.8214156031608582 0.7643151879310608 0.5113850831985474 \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_1.evaluate.json b/ENCSR913OWV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4cadc258b2e796dcdfcd16ec41b059b17dc68eaa..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802YBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_1.fit.json b/ENCSR913OWV/cherimoya.fold_1.fit.json deleted file mode 100644 index 7d1f5561c9d22e3ee841021320d92e6e63bbb3c1..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF802YBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_1.log b/ENCSR913OWV/cherimoya.fold_1.log deleted file mode 100644 index 0fa8aa65799aac823040615ca3c4147dba0e91df..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3805 47.618852376937866 5.445389270782471 638.1260986328125 1.3677070140838623 1265.7576904296875 0.7266086339950562 0.7370136 6.075265884399414 True -1 7610 41.971004009246826 0.9683783054351807 711.2506713867188 1.6932014226913452 1068.855712890625 0.7954009175300598 0.7575793 1.593273401260376 True -2 11415 41.95101284980774 0.9328339099884033 689.8451538085938 1.8501229286193848 1041.033935546875 0.8051407337188721 0.75804466 0.9953093528747559 True -3 15220 41.97615385055542 1.5478949546813965 669.7703857421875 1.2933416366577148 1025.9107666015625 0.8100985884666443 0.76154274 0.8695615530014038 True -4 19025 42.008793354034424 0.9330224990844727 627.1320190429688 0.9492403268814087 1013.3255004882812 0.8137847781181335 0.76648355 0.7857887148857117 True -5 22830 42.01687502861023 0.9267401695251465 705.0328369140625 0.9701777696609497 1007.6082153320312 0.8160986304283142 0.76589143 0.7169145941734314 False -6 26635 42.02899932861328 4.8542704582214355 709.959228515625 0.8014376163482666 995.2112426757812 0.8199987411499023 0.77561086 0.6559578776359558 True -7 30440 42.469555616378784 0.9342546463012695 683.4462890625 0.8236698508262634 984.8333129882812 0.8225597739219666 0.7808915 0.6332079768180847 True -8 34245 42.11522889137268 0.9288902282714844 557.3770751953125 1.2502522468566895 973.6393432617188 0.8259106278419495 0.78646183 0.618626594543457 True -9 38050 42.035462379455566 0.9316809177398682 588.760009765625 0.9291903972625732 965.711181640625 0.8286840915679932 0.7910576 0.6093569993972778 True -10 41855 41.57204723358154 0.9278583526611328 591.448974609375 1.375584602355957 954.9688110351562 0.8319758772850037 0.7984214 0.5853704810142517 True -11 45660 41.25199866294861 1.8623359203338623 632.877197265625 0.9955167770385742 946.3113403320312 0.8349120020866394 0.80500007 0.5728243589401245 True -12 49465 41.20015025138855 0.931143045425415 526.17333984375 0.8780614137649536 938.6224365234375 0.8375422954559326 0.81409895 0.5611814260482788 True -13 53270 41.20622539520264 0.9382472038269043 550.2875366210938 0.9259164333343506 931.2313842773438 0.8399307727813721 0.8212278 0.543411910533905 True -14 57075 41.59431838989258 0.9136497974395752 621.6187744140625 1.2538087368011475 925.2857055664062 0.8419685959815979 0.8263427 0.5351933240890503 True -15 60880 41.22956585884094 26.686670780181885 577.7396240234375 0.7119110822677612 919.5138549804688 0.8434755802154541 0.8300383 0.5418635606765747 True -16 64685 41.86691975593567 26.40907907485962 675.9510498046875 0.7704544067382812 917.6139526367188 0.844441831111908 0.83562434 0.5405921936035156 True -17 68490 41.45566439628601 0.9479691982269287 608.4263916015625 0.5211191177368164 917.7854614257812 0.8444148898124695 0.8362226 0.5516760349273682 True -18 72295 41.22265601158142 1.334442377090454 557.947021484375 0.6725834608078003 917.8446044921875 0.8442757725715637 0.8369484 0.5600653290748596 True -19 76100 41.208701848983765 0.9240908622741699 558.516357421875 0.5304682850837708 918.6195068359375 0.8440671563148499 0.8352039 0.5650959610939026 False diff --git a/ENCSR913OWV/cherimoya.fold_1.performance.tsv b/ENCSR913OWV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 6e1eed17fe2b73441b4526f1f608ede67bfcd785..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -917.8446044921875 0.12919467687606812 0.8442758321762085 0.516280472278595 0.8369483947753906 0.8082420825958252 0.5600653290748596 \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_2.evaluate.json b/ENCSR913OWV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 272e50b4cb49707e14ecb0e62a795afbd6b9bf0f..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802YBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_2.fit.json b/ENCSR913OWV/cherimoya.fold_2.fit.json deleted file mode 100644 index 1172ac59c1264a2a374b059a00c125def527eea2..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF802YBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_2.log b/ENCSR913OWV/cherimoya.fold_2.log deleted file mode 100644 index 0ac758c3a67b9eaf53e1453a39b7f709f4b73028..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4040 48.930787324905396 3.7334625720977783 609.0975341796875 1.2192715406417847 1121.5093994140625 0.7342694997787476 0.74579746 8.065768241882324 True -1 8080 44.28595733642578 0.7749323844909668 644.0260620117188 1.3711904287338257 979.0634155273438 0.7910156846046448 0.76554775 1.8060731887817383 True -2 12120 44.415505170822144 0.756014347076416 618.6702880859375 0.9181258678436279 956.5552368164062 0.7992880344390869 0.7691528 0.9496976733207703 True -3 16160 44.46592831611633 0.7546663284301758 689.9852294921875 1.1680986881256104 944.1380615234375 0.8048210740089417 0.76461333 0.8404871821403503 False -4 20200 44.51660180091858 0.7988491058349609 737.4183959960938 1.2587988376617432 931.8953247070312 0.8084354996681213 0.77332693 0.807586133480072 True -5 24240 44.43158769607544 24.018961906433105 818.39404296875 1.0653693675994873 923.823974609375 0.8108859658241272 0.7785643 0.7166107892990112 True -6 28280 45.40307688713074 0.7588441371917725 900.573486328125 0.6795312762260437 914.69091796875 0.8134325742721558 0.7753605 0.6646193265914917 False -7 32320 44.58543014526367 34.16183614730835 618.179443359375 1.0794779062271118 904.9345092773438 0.8165589570999146 0.7796167 0.6392287611961365 True -8 36360 45.051722049713135 6.769252777099609 586.9459838867188 1.0451642274856567 898.1390380859375 0.8192049860954285 0.78591996 0.5991553664207458 True -9 40400 44.64258027076721 1.2032489776611328 714.90087890625 0.7038511633872986 888.4336547851562 0.8224842548370361 0.79240906 0.5723350048065186 True -10 44440 44.88787603378296 0.7719120979309082 622.4631958007812 0.8508888483047485 880.38330078125 0.8251293897628784 0.79727495 0.5602039694786072 True -11 48480 44.783483028411865 43.40320563316345 623.5542602539062 1.178619146347046 871.3399658203125 0.8284987211227417 0.8053035 0.5417136549949646 True -12 52520 47.28160643577576 0.7778284549713135 722.3192138671875 0.721396803855896 864.0546264648438 0.8310709595680237 0.81246996 0.5233323574066162 True -13 56560 43.65958094596863 1.765681505203247 694.1990966796875 0.9793208837509155 854.9407348632812 0.8337435126304626 0.82185507 0.5024040341377258 True -14 60600 43.796536684036255 0.7581615447998047 618.9400634765625 0.7938060164451599 850.5835571289062 0.8357849717140198 0.82624215 0.5008969306945801 True -15 64640 43.70888423919678 0.74542236328125 649.3641967773438 0.48100826144218445 845.7321166992188 0.8374064564704895 0.83153206 0.49965474009513855 True -16 68680 43.62769436836243 0.755112886428833 614.4141845703125 0.5131124258041382 843.9452514648438 0.8380682468414307 0.83597976 0.49631747603416443 True -17 72720 43.76269221305847 0.7429463863372803 540.7774658203125 0.63764488697052 842.8746948242188 0.8383336663246155 0.8368033 0.5077096819877625 True -18 76760 43.716004610061646 0.7594850063323975 561.2828369140625 1.0179812908172607 843.8305053710938 0.8382042050361633 0.8388026 0.5118736624717712 True -19 80800 43.89460563659668 0.7522275447845459 477.64349365234375 0.536997377872467 844.5633544921875 0.8380948305130005 0.83755624 0.5214049220085144 False diff --git a/ENCSR913OWV/cherimoya.fold_2.performance.tsv b/ENCSR913OWV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e40ab9885c44714938cee10abb1b8ed8a957c30c..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -843.8305053710938 0.13643009960651398 0.8382042050361633 0.49196311831474304 0.8388025760650635 0.7956919074058533 0.5118736624717712 \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_3.evaluate.json b/ENCSR913OWV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a5926b38a9e54d620ab20c9c9765a4c8e8c7eeb6..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802YBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_3.fit.json b/ENCSR913OWV/cherimoya.fold_3.fit.json deleted file mode 100644 index da3b4038b16af5597823847e1559eda377363724..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF802YBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_3.log b/ENCSR913OWV/cherimoya.fold_3.log deleted file mode 100644 index be5040955a31f98961f1f1f72a93f938fe8a22c8..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3874 47.38252353668213 14.292211055755615 789.5830688476562 1.1614599227905273 1030.94580078125 0.7238008379936218 0.73178834 7.560280799865723 True -1 7748 42.73384928703308 0.787327766418457 664.9273681640625 1.999187707901001 887.997802734375 0.7842297554016113 0.7444745 1.3573644161224365 True -2 11622 42.57204246520996 0.7519254684448242 622.6788940429688 0.9784953594207764 868.1110229492188 0.7931053638458252 0.75118977 1.0346015691757202 True -3 15496 42.265411376953125 0.7411048412322998 672.69873046875 0.9005661010742188 860.4689331054688 0.7964867353439331 0.7498644 0.890001118183136 False -4 19370 41.7151780128479 0.7353253364562988 707.96875 1.1314586400985718 849.7130737304688 0.803598940372467 0.7428605 0.755335807800293 False -5 23244 41.71612286567688 0.7453174591064453 816.976318359375 1.1474063396453857 843.68408203125 0.8065735101699829 0.74647105 0.7153274416923523 False -6 27118 41.70238256454468 0.7399296760559082 589.6304931640625 0.9824106693267822 837.4761352539062 0.8088111877441406 0.74548775 0.677322268486023 False -7 30992 41.67753577232361 0.7414693832397461 723.8951416015625 0.8313534259796143 830.6265869140625 0.8116918802261353 0.75080895 0.6655203700065613 False -8 34866 41.67271113395691 2.2183101177215576 816.510498046875 1.4443310499191284 824.2627563476562 0.8142433762550354 0.7548962 0.6712462306022644 True -9 38740 42.46682357788086 1.4686932563781738 634.3045654296875 1.168825626373291 816.7431640625 0.8172761797904968 0.7659506 0.6415959596633911 True -10 42614 41.7904999256134 1.5695717334747314 662.2022705078125 1.0360512733459473 811.4766845703125 0.8197110891342163 0.7736893 0.6105254292488098 True -11 46488 41.74581027030945 0.7444782257080078 607.0970458984375 0.8746424913406372 803.3275146484375 0.8225261569023132 0.7743812 0.6194419860839844 True -12 50362 41.769538164138794 0.7541587352752686 651.723388671875 0.7411748766899109 798.8221435546875 0.8250883221626282 0.78113 0.6042168140411377 True -13 54236 41.7624671459198 0.7329301834106445 788.8424072265625 0.860755443572998 794.167236328125 0.8270992040634155 0.79308504 0.5778803825378418 True -14 58110 41.91379737854004 0.734105110168457 625.3367919921875 0.6235465407371521 788.5130004882812 0.8295892477035522 0.8029464 0.5561448335647583 True -15 61984 41.800323247909546 0.7455809116363525 631.4427490234375 0.6223740577697754 784.7691040039062 0.8311063647270203 0.8072393 0.5529719591140747 True -16 65858 42.010465145111084 0.7606689929962158 582.2860107421875 1.1385293006896973 782.4517211914062 0.8319360613822937 0.8103643 0.5523281693458557 True -17 69732 41.89454936981201 1.6003077030181885 571.61474609375 0.5904752016067505 781.3906860351562 0.8324262499809265 0.81338793 0.5578029155731201 True -18 73606 41.96414256095886 2.3296194076538086 449.1500244140625 0.7352051734924316 781.6068725585938 0.8324275016784668 0.81355536 0.5615385174751282 True -19 77480 41.830475091934204 0.7678413391113281 568.7840576171875 0.46788281202316284 781.8067016601562 0.8322367072105408 0.8133128 0.5721947550773621 False diff --git a/ENCSR913OWV/cherimoya.fold_3.performance.tsv b/ENCSR913OWV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c326106880a7af5e038549bed2f1a0ce3e8f9530..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -781.6068725585938 0.14375649392604828 0.8324275016784668 0.4648098349571228 0.8135553598403931 0.7500460147857666 0.5615385174751282 \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_4.evaluate.json b/ENCSR913OWV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6ed6feb0c7503b5d4da5d70e32e4cb00c6deb42a..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF802YBZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_4.fit.json b/ENCSR913OWV/cherimoya.fold_4.fit.json deleted file mode 100644 index e645e2860396b0e0cfda57c2443907d972eb73b8..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF802YBZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR913OWV/cherimoya.fold_4.log b/ENCSR913OWV/cherimoya.fold_4.log deleted file mode 100644 index 88069d2d9f1fa947d0c81986d5788ded8fb4f7c4..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3980 48.67452645301819 3.830458164215088 755.7147216796875 1.779625654220581 974.986328125 0.7210590839385986 0.7258429 7.886408805847168 True -1 7960 43.79399657249451 29.434112310409546 667.9769287109375 2.253939390182495 859.330322265625 0.7811480760574341 0.72779995 1.1026601791381836 True -2 11940 43.8786838054657 0.8465399742126465 626.5176391601562 1.498937964439392 843.6741943359375 0.7876183390617371 0.72551864 0.8660879135131836 False -3 15920 43.8222861289978 0.8441264629364014 512.7198486328125 0.9598286151885986 827.4722900390625 0.7952698469161987 0.7377715 0.68526291847229 True -4 19900 43.77959489822388 0.8157615661621094 624.2698974609375 1.092792272567749 820.08203125 0.7987278699874878 0.7401476 0.6618598699569702 True -5 23880 43.742077589035034 0.8171164989471436 685.8475952148438 1.6698033809661865 812.5038452148438 0.8008829951286316 0.7473766 0.6103090643882751 True -6 27860 43.748733043670654 0.8212916851043701 688.773193359375 1.2152104377746582 806.6653442382812 0.8040538430213928 0.7552548 0.5855884552001953 True -7 31840 43.72018313407898 0.8205747604370117 624.1521606445312 0.996337890625 800.666748046875 0.807302713394165 0.75675267 0.5827786922454834 True -8 35820 43.832881927490234 0.8153688907623291 622.01953125 0.9786908626556396 793.1554565429688 0.8104188442230225 0.76079595 0.5715433359146118 True -9 39800 43.73141026496887 0.8128376007080078 602.4764404296875 0.5961570739746094 786.042724609375 0.8139435052871704 0.7645415 0.5647446513175964 True -10 43780 44.288296937942505 41.22632598876953 590.6515502929688 0.9290574789047241 780.4390869140625 0.8172982931137085 0.7719798 0.5523979663848877 True -11 47760 42.9868803024292 0.8176822662353516 529.6043701171875 1.0279269218444824 773.6045532226562 0.8203126788139343 0.78124815 0.5307810306549072 True -12 51740 43.00639057159424 0.8094480037689209 644.7445678710938 0.8857395648956299 767.5645141601562 0.8227242827415466 0.788785 0.5175837278366089 True -13 55720 42.95401334762573 0.8733267784118652 645.19775390625 0.7474045753479004 762.6231079101562 0.8252317309379578 0.7987971 0.49598702788352966 True -14 59700 42.96278119087219 0.8070180416107178 538.3076171875 1.2937430143356323 758.2783813476562 0.8269982933998108 0.8037391 0.49131685495376587 True -15 63680 43.05424952507019 0.8157296180725098 475.5209655761719 1.683648705482483 755.5335083007812 0.8286473155021667 0.80845046 0.4918985962867737 True -16 67660 42.97934126853943 0.8076801300048828 633.619873046875 0.8413416147232056 753.5494384765625 0.829606294631958 0.8122169 0.4909169673919678 True -17 71640 43.41474723815918 32.670300245285034 647.1983032226562 0.8778067231178284 753.4083251953125 0.8295482993125916 0.8110703 0.5020900368690491 False -18 75620 42.92044639587402 0.8259909152984619 434.0215148925781 0.4913784861564636 754.1431274414062 0.8294657468795776 0.8121576 0.5091548562049866 False -19 79600 42.91483235359192 0.8234641551971436 575.9547119140625 0.48482227325439453 754.8681030273438 0.8292940258979797 0.8102103 0.5126008987426758 False diff --git a/ENCSR913OWV/cherimoya.fold_4.performance.tsv b/ENCSR913OWV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ec62a8429de553f0e532151ba0875b679844152e..0000000000000000000000000000000000000000 --- a/ENCSR913OWV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -753.5494384765625 0.1469450742006302 0.8296064138412476 0.4573134481906891 0.8122168779373169 0.7450644373893738 0.4909169673919678 \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_0.evaluate.json b/ENCSR914DOH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3d42cbb7c99062f0bdc77069b7a1e98413f96ae6..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625DHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_0.fit.json b/ENCSR914DOH/cherimoya.fold_0.fit.json deleted file mode 100644 index 8f9242b2d583728076fa46815cb1429475a91192..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF625DHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_0.log b/ENCSR914DOH/cherimoya.fold_0.log deleted file mode 100644 index 19085174f6c0979884842c771dfe3a9c87dd1d67..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2729 34.49788999557495 4.0336713790893555 259.570556640625 0.9203504920005798 276.9288330078125 0.1358502209186554 0.46662685 3.0331902503967285 True -1 5458 29.942582845687866 2.3650102615356445 180.44711303710938 1.671995759010315 268.3675231933594 0.1757650375366211 0.553482 1.213707685470581 True -2 8187 29.969783544540405 0.539398193359375 235.3751220703125 1.3347645998001099 265.6317138671875 0.18412229418754578 0.5813393 0.8987337350845337 True -3 10916 29.951265811920166 0.5333583354949951 229.72703552246094 0.8289151787757874 264.40673828125 0.18726645410060883 0.5862614 0.7787289023399353 True -4 13645 29.687459230422974 0.5210938453674316 185.54534912109375 1.185634970664978 263.51580810546875 0.19103610515594482 0.5913555 0.8522849678993225 True -5 16374 29.378998041152954 0.5243003368377686 214.93038940429688 1.220132827758789 262.9532165527344 0.19365128874778748 0.5896443 0.9080318212509155 False -6 19103 29.396209239959717 0.5325887203216553 214.97499084472656 0.8929157853126526 262.1496276855469 0.19679681956768036 0.60082704 0.824390709400177 True -7 21832 29.491272926330566 0.5306503772735596 213.26629638671875 0.7066881656646729 261.8987121582031 0.19729647040367126 0.6094882 0.783610463142395 True -8 24561 29.353909492492676 0.5250685214996338 213.155029296875 0.8426289558410645 261.5013732910156 0.1991606056690216 0.62009794 0.7453129887580872 True -9 27290 29.397562742233276 0.5231599807739258 206.2854461669922 0.8811321258544922 261.4562683105469 0.1986800730228424 0.62608504 0.7244853377342224 True -10 30019 29.420262336730957 0.5321812629699707 209.79510498046875 0.8867775201797485 260.8587341308594 0.20124714076519012 0.6316056 0.6705780625343323 True -11 32748 29.4203462600708 0.5290453433990479 173.93531799316406 0.8097826242446899 260.2203369140625 0.20438289642333984 0.6361444 0.6478469371795654 True -12 35477 29.396095991134644 0.5312466621398926 198.39979553222656 0.9993477463722229 260.095703125 0.20473185181617737 0.64466894 0.6238715052604675 True -13 38206 29.33738684654236 0.5331728458404541 188.46902465820312 0.591852605342865 259.8517761230469 0.2055245190858841 0.6515288 0.5991308093070984 True -14 40935 29.371267080307007 0.5383021831512451 217.86947631835938 0.8067853450775146 259.5494384765625 0.20669634640216827 0.6566932 0.5848693251609802 True -15 43664 29.374492168426514 0.5249752998352051 199.42213439941406 0.4392092823982239 259.5352783203125 0.20649246871471405 0.6619687 0.5751131176948547 True -16 46393 29.420292615890503 0.5197594165802002 202.6540069580078 0.8541668653488159 259.6495361328125 0.20580223202705383 0.66367567 0.5800594091415405 True -17 49122 29.356280088424683 0.5343492031097412 214.15582275390625 0.9145899415016174 259.6673278808594 0.20622023940086365 0.6624022 0.5898793935775757 False -18 51851 29.369072675704956 0.5339384078979492 175.77023315429688 0.39544275403022766 259.63201904296875 0.20613953471183777 0.65960264 0.602131724357605 False -19 54580 29.34048342704773 0.5348210334777832 167.02340698242188 0.7100761532783508 259.7108459472656 0.20561785995960236 0.65703636 0.614393949508667 False diff --git a/ENCSR914DOH/cherimoya.fold_0.performance.tsv b/ENCSR914DOH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4bec076b3bc5a67a2a87179e76c2b83ec51b288d..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -259.6495361328125 0.5324263572692871 0.20580224692821503 0.057652831077575684 0.6636756658554077 0.6538073420524597 0.5800594091415405 \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_1.evaluate.json b/ENCSR914DOH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a99546098056e577d94c3b32545893e27c2df87b..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625DHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_1.fit.json b/ENCSR914DOH/cherimoya.fold_1.fit.json deleted file mode 100644 index 724ecd7c9027d25d51952e241a0122aaa91fa22d..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF625DHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_1.log b/ENCSR914DOH/cherimoya.fold_1.log deleted file mode 100644 index 33a1fa031b8eb674452636d1701ef16fc5d15632..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2783 35.453476667404175 2.7127132415771484 213.60475158691406 1.2556018829345703 308.9189453125 0.14640037715435028 0.49962947 2.7208001613616943 True -1 5566 30.538906812667847 1.5681087970733643 208.5413818359375 0.8450077772140503 299.5208435058594 0.18555115163326263 0.54843044 1.5116016864776611 True -2 8349 30.546048641204834 0.617922306060791 190.3995819091797 0.7937633991241455 296.00732421875 0.1969364732503891 0.571493 0.9522007703781128 True -3 11132 30.583864212036133 0.7147824764251709 230.15277099609375 0.9735499024391174 293.85345458984375 0.20434656739234924 0.5992068 0.7960008382797241 True -4 13915 30.295106410980225 3.086611747741699 169.25698852539062 0.7780708074569702 292.98626708984375 0.20684416592121124 0.6168929 0.7718011736869812 True -5 16698 29.956782341003418 0.5911910533905029 233.92527770996094 1.1219152212142944 292.2952575683594 0.2095823734998703 0.626318 0.7030091285705566 True -6 19481 29.91843557357788 0.5880584716796875 229.0755615234375 1.0974502563476562 291.6949462890625 0.21130089461803436 0.63780797 0.6641318798065186 True -7 22264 29.959598541259766 0.6044237613677979 204.18966674804688 0.8230921030044556 291.0503234863281 0.21376295387744904 0.64362377 0.6576440334320068 True -8 25047 29.92146062850952 0.6188039779663086 219.4860076904297 0.912557065486908 290.54522705078125 0.21590319275856018 0.6456593 0.6486127376556396 True -9 27830 29.920410633087158 0.6625347137451172 179.8969268798828 1.0114083290100098 290.5230407714844 0.21518155932426453 0.6543659 0.6353711485862732 True -10 30613 29.987715482711792 0.6386270523071289 216.81396484375 0.6763511300086975 289.91387939453125 0.21743322908878326 0.66186756 0.6221276521682739 True -11 33396 29.960944890975952 0.6269979476928711 239.64089965820312 0.6189929246902466 289.3604431152344 0.21992193162441254 0.6685245 0.6045554876327515 True -12 36179 29.950237274169922 0.6295793056488037 211.91375732421875 0.8122107982635498 288.95758056640625 0.22126740217208862 0.67375135 0.5991177558898926 True -13 38962 29.916494846343994 0.6203176975250244 197.82763671875 0.6467616558074951 288.67425537109375 0.22174622118473053 0.6793617 0.5811830163002014 True -14 41745 29.915711879730225 1.6289737224578857 215.84176635742188 0.7187613248825073 288.48138427734375 0.22245216369628906 0.6874143 0.569202184677124 True -15 44528 30.003698587417603 0.6206352710723877 202.77435302734375 0.877522885799408 288.3528747558594 0.2227916419506073 0.69223386 0.5618513822555542 True -16 47311 29.903906106948853 0.6001086235046387 192.15093994140625 0.5932161211967468 288.0244445800781 0.2242102026939392 0.69598466 0.5551542043685913 True -17 50094 29.895732402801514 0.637092113494873 215.89813232421875 0.5804283618927002 288.04736328125 0.22420445084571838 0.6955858 0.5681519508361816 False -18 52877 30.00365400314331 0.6125848293304443 189.6110382080078 0.5536346435546875 288.2776184082031 0.222906693816185 0.6953815 0.5814979076385498 False -19 55660 29.90311098098755 1.6352131366729736 206.78851318359375 0.4912268817424774 288.32476806640625 0.223202645778656 0.69386256 0.591552734375 False diff --git a/ENCSR914DOH/cherimoya.fold_1.performance.tsv b/ENCSR914DOH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 642957b9b5bf5d7a29753e4df536c76b3ef5f1ed..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -288.0244445800781 0.5175333619117737 0.22421018779277802 0.07089255005121231 0.6959846615791321 0.6902737021446228 0.5551542043685913 \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_2.evaluate.json b/ENCSR914DOH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b11387f62d07311670949a1ea0aa2a751025a39e..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625DHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_2.fit.json b/ENCSR914DOH/cherimoya.fold_2.fit.json deleted file mode 100644 index 432c5537bb80cb7c0857c0c082fc132b2fc03f46..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF625DHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_2.log b/ENCSR914DOH/cherimoya.fold_2.log deleted file mode 100644 index 42289239d650697e90ebe1c26098482fc0be2e8f..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2889 36.41445732116699 3.82053542137146 256.24920654296875 1.1941814422607422 280.42877197265625 0.14651194214820862 0.45815963 2.855761766433716 True -1 5778 31.746870279312134 0.6826398372650146 206.73492431640625 1.4330449104309082 272.3701477050781 0.1803344041109085 0.5128303 1.5052289962768555 True -2 8667 31.735944509506226 0.6324105262756348 164.14498901367188 1.031188726425171 268.9189758300781 0.19318155944347382 0.5329946 1.0905866622924805 True -3 11556 31.744268655776978 0.7658178806304932 197.90135192871094 0.8645834922790527 268.1390686035156 0.19395674765110016 0.5561278 0.8286494016647339 True -4 14445 31.483776807785034 0.5275571346282959 208.82708740234375 0.7725024819374084 267.352294921875 0.19680136442184448 0.577091 0.7545602321624756 True -5 17334 31.129215955734253 0.6195828914642334 199.7090301513672 0.9074064493179321 266.9922790527344 0.19791173934936523 0.58551383 0.797723114490509 True -6 20223 31.059746026992798 0.5246365070343018 232.85430908203125 1.0709068775177002 266.2217102050781 0.2012227475643158 0.5884501 0.7690116167068481 True -7 23112 31.064486026763916 0.6288771629333496 235.42776489257812 1.007894515991211 265.9130859375 0.20233465731143951 0.60083956 0.7372137904167175 True -8 26001 31.077691316604614 0.5680665969848633 217.6825714111328 0.9140164852142334 265.3514404296875 0.20498675107955933 0.6059545 0.7521728277206421 True -9 28890 31.086934566497803 0.5188145637512207 183.52053833007812 0.8283843994140625 264.92132568359375 0.2063600718975067 0.6116282 0.7134711742401123 True -10 31779 31.11788773536682 1.8403329849243164 203.70806884765625 0.8011735677719116 264.6640930175781 0.20752456784248352 0.6192885 0.7212352752685547 True -11 34668 31.150973796844482 0.542017936706543 196.9974365234375 0.9220924377441406 264.5482177734375 0.20778381824493408 0.6268228 0.6905710697174072 True -12 37557 31.132441759109497 1.1895956993103027 203.9932861328125 0.5995575189590454 263.8887023925781 0.21057608723640442 0.6335508 0.6573834419250488 True -13 40446 31.12335467338562 0.5527615547180176 245.90237426757812 0.7349159717559814 263.9933776855469 0.2097112238407135 0.6429088 0.6170817017555237 True -14 43335 31.126248121261597 0.5423972606658936 232.56265258789062 0.6360414028167725 263.712646484375 0.21069197356700897 0.64841944 0.6198017597198486 True -15 46224 31.076151371002197 0.538203239440918 171.55194091796875 0.8675768971443176 263.19329833984375 0.21336135268211365 0.6537886 0.6054209470748901 True -16 49113 31.22343420982361 0.5473542213439941 223.01686096191406 0.649250328540802 263.37725830078125 0.2122538983821869 0.6560494 0.6071958541870117 True -17 52002 31.178903818130493 0.5167367458343506 205.73805236816406 0.4325631260871887 263.3952941894531 0.21252763271331787 0.6550294 0.6071803569793701 False -18 54891 31.121196746826172 0.5309901237487793 200.65797424316406 0.5107529759407043 263.6248474121094 0.2113506942987442 0.65396 0.6211333870887756 False -19 57780 31.129584074020386 0.5387914180755615 147.51785278320312 0.4567398726940155 263.4241027832031 0.2124340981245041 0.6521556 0.6300895810127258 False diff --git a/ENCSR914DOH/cherimoya.fold_2.performance.tsv b/ENCSR914DOH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1c53b91978114b93a88d075d65782292cce75d12..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -263.37725830078125 0.5286437273025513 0.21225392818450928 0.06734205782413483 0.656049370765686 0.6488040685653687 0.6071958541870117 \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_3.evaluate.json b/ENCSR914DOH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c6724464b893737f008411709f7014a45aec13b8..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625DHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_3.fit.json b/ENCSR914DOH/cherimoya.fold_3.fit.json deleted file mode 100644 index 3cd4901ff3a607747cbb4553eec45bd03e315445..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF625DHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_3.log b/ENCSR914DOH/cherimoya.fold_3.log deleted file mode 100644 index 860fcda9d42ef13ade1f0314d637bcd5ddcb1b02..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2808 35.87678408622742 4.956601858139038 237.32086181640625 1.0024889707565308 292.2127990722656 0.14697036147117615 0.49115056 2.9230425357818604 True -1 5616 30.87873148918152 1.6148207187652588 223.3880615234375 1.171422004699707 284.1171569824219 0.18145619332790375 0.5652993 1.595327615737915 True -2 8424 31.028156518936157 0.6134331226348877 190.24461364746094 0.632186770439148 281.2668151855469 0.1912725269794464 0.58795875 0.8763969540596008 True -3 11232 30.500454664230347 0.6026928424835205 206.75865173339844 0.9142933487892151 280.1717529296875 0.19291602075099945 0.6045878 0.7822356820106506 True -4 14040 30.286523580551147 0.5897157192230225 220.1751251220703 0.962203860282898 279.36407470703125 0.19619931280612946 0.61286443 0.8226552605628967 True -5 16848 30.277939558029175 0.5821523666381836 202.05859375 0.8609644174575806 278.89727783203125 0.19766055047512054 0.6140373 0.8022071719169617 True -6 19656 30.273757934570312 1.6476895809173584 226.82711791992188 0.9967768788337708 278.27813720703125 0.20075836777687073 0.6181474 0.7942643761634827 True -7 22464 30.35355544090271 0.5849707126617432 185.80816650390625 1.1113111972808838 278.0260314941406 0.20091338455677032 0.6253379 0.7687849998474121 True -8 25272 30.330000162124634 0.5775113105773926 215.25286865234375 0.6842377185821533 277.6140441894531 0.20287169516086578 0.632567 0.721345841884613 True -9 28080 30.435009479522705 0.5831003189086914 234.2100830078125 0.5683456659317017 277.58502197265625 0.20215319097042084 0.6381791 0.7219600677490234 True -10 30888 30.311744451522827 0.5854189395904541 199.18548583984375 0.8453179597854614 276.7878723144531 0.20524927973747253 0.64447534 0.6751039624214172 True -11 33696 30.302874088287354 0.5832252502441406 198.7156219482422 0.6224541068077087 276.5152893066406 0.20662793517112732 0.65414995 0.6340964436531067 True -12 36504 30.209434032440186 0.5646092891693115 176.40184020996094 0.7779576778411865 276.262451171875 0.20752833783626556 0.6611198 0.6179597973823547 True -13 39312 30.31609606742859 0.5845119953155518 202.36253356933594 0.6345229744911194 276.2403869628906 0.2070520520210266 0.6663149 0.614531397819519 True -14 42120 30.267616748809814 0.5692365169525146 192.08016967773438 0.7450278401374817 276.0877990722656 0.20728912949562073 0.67160213 0.596096932888031 True -15 44928 30.29750156402588 0.5843806266784668 202.59275817871094 0.7841296792030334 275.8856506347656 0.20830444991588593 0.6770174 0.5850862860679626 True -16 47736 30.27552318572998 0.5822749137878418 194.15670776367188 0.8354265093803406 275.67608642578125 0.20888112485408783 0.6773837 0.5758939385414124 True -17 50544 30.364299535751343 0.8298509120941162 200.34951782226562 0.5775316953659058 275.98187255859375 0.20770876109600067 0.6792134 0.582217276096344 True -18 53352 30.440903902053833 0.5843234062194824 207.45094299316406 0.5789674520492554 275.54888916015625 0.21021533012390137 0.6786337 0.5921005010604858 False -19 56160 30.310113430023193 0.5826766490936279 179.6143035888672 0.5801259279251099 276.1238708496094 0.20673783123493195 0.67806786 0.5980067253112793 False diff --git a/ENCSR914DOH/cherimoya.fold_3.performance.tsv b/ENCSR914DOH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 48efe47c8abe66c3a2045e48a68cc9559bffc8fd..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.98187255859375 0.5271705985069275 0.20770879089832306 0.05857335403561592 0.6792134046554565 0.66890949010849 0.582217276096344 \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_4.evaluate.json b/ENCSR914DOH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 99ca5eab76ee44239895a9b7b1c273a26963b912..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF625DHQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_4.fit.json b/ENCSR914DOH/cherimoya.fold_4.fit.json deleted file mode 100644 index b3b8004ca5eb9d9976adcd4b8bf44da4afabf0c5..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF625DHQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DOH/cherimoya.fold_4.log b/ENCSR914DOH/cherimoya.fold_4.log deleted file mode 100644 index d4b066959230acf947f9a997ebfeec0518ce4372..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2904 36.747560262680054 4.533309459686279 214.18612670898438 1.134588360786438 283.768798828125 0.13868233561515808 0.4627417 2.4501490592956543 True -1 5808 31.928977966308594 0.7168412208557129 198.7738037109375 0.9078283905982971 275.2388916015625 0.1782982349395752 0.5286056 1.7171062231063843 True -2 8712 31.488145351409912 0.6851115226745605 230.54534912109375 1.1412060260772705 272.30682373046875 0.1887172907590866 0.5539489 0.9469287991523743 True -3 11616 31.349290132522583 0.5831291675567627 178.81008911132812 0.8421761989593506 271.22442626953125 0.19267669320106506 0.5718618 0.9193037748336792 True -4 14520 31.27349281311035 0.5634987354278564 201.13482666015625 1.0519335269927979 270.5404052734375 0.19492122530937195 0.5804033 0.9930732250213623 True -5 17424 31.273818969726562 0.6141111850738525 201.9001007080078 1.0709267854690552 270.3504638671875 0.19510163366794586 0.58254415 1.035813570022583 True -6 20328 31.29387593269348 0.5641894340515137 193.57376098632812 0.8361178040504456 269.6664733886719 0.19791179895401 0.5878738 1.0292202234268188 True -7 23232 31.3052339553833 1.2747068405151367 231.03567504882812 0.7502175569534302 269.3770751953125 0.19895052909851074 0.5944925 1.0106244087219238 True -8 26136 31.29555583000183 0.602595329284668 193.2442169189453 0.7798610329627991 269.21649169921875 0.19878222048282623 0.6014094 0.9525254368782043 True -9 29040 31.280471801757812 0.5915782451629639 161.91802978515625 0.8193752765655518 268.75567626953125 0.20090441405773163 0.606102 0.8473146557807922 True -10 31944 31.34049963951111 0.6757948398590088 173.28358459472656 0.6568533182144165 268.3330993652344 0.20241045951843262 0.6117427 0.7918781042098999 True -11 34848 31.333417892456055 8.309297800064087 199.17495727539062 0.7345666885375977 267.9764404296875 0.20367194712162018 0.6187877 0.7432166934013367 True -12 37752 31.37070059776306 0.5691771507263184 234.27552795410156 0.7942125797271729 267.544677734375 0.2058553248643875 0.6302392 0.683722198009491 True -13 40656 31.25671076774597 0.5818171501159668 198.74183654785156 0.8446604013442993 267.6734619140625 0.20429237186908722 0.63543636 0.6698371171951294 True -14 43560 31.296067476272583 0.5629100799560547 192.9246826171875 0.8612198829650879 267.15069580078125 0.20656165480613708 0.6429492 0.6287198066711426 True -15 46464 31.367290019989014 0.5834345817565918 211.00843811035156 0.5841832160949707 267.1819763183594 0.207132488489151 0.64868695 0.614589273929596 True -16 49368 31.35798668861389 0.574695348739624 253.86044311523438 0.46564140915870667 266.780029296875 0.2089112550020218 0.65239996 0.6112576127052307 True -17 52272 31.294203281402588 1.3326401710510254 172.90933227539062 0.404416024684906 267.2115173339844 0.20645016431808472 0.6543137 0.6102179884910583 True -18 55176 31.33733582496643 0.5717053413391113 202.68356323242188 0.5977044105529785 267.1549072265625 0.20708338916301727 0.65330744 0.6263580918312073 False -19 58080 31.36339259147644 0.5788600444793701 220.7765350341797 0.4782159924507141 267.14691162109375 0.20684926211833954 0.6534516 0.6349817514419556 False diff --git a/ENCSR914DOH/cherimoya.fold_4.performance.tsv b/ENCSR914DOH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4fac5f7f15f3e6bf8a4076e26815aaf28e02f8c0..0000000000000000000000000000000000000000 --- a/ENCSR914DOH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -267.2115173339844 0.5302129983901978 0.2064501792192459 0.05951867997646332 0.6543136835098267 0.643872082233429 0.6102179884910583 \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_0.evaluate.json b/ENCSR914DTI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8290e4e4178f4576dadad5d6fc2ac29bc6388933..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF162QEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_0.fit.json b/ENCSR914DTI/cherimoya.fold_0.fit.json deleted file mode 100644 index a92bbd343538b3ef04d1c34c780cf03711f2cf02..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF162QEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_0.log b/ENCSR914DTI/cherimoya.fold_0.log deleted file mode 100644 index 0be6f549575dfc90d786953c3781a06ae4eda94e..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1591 21.297037839889526 3.347097158432007 218.38954162597656 0.4428706169128418 370.046630859375 0.44335439801216125 0.6133131 11.90998363494873 True -1 3182 17.514593362808228 0.33528637886047363 239.60372924804688 0.7015913128852844 312.85003662109375 0.5309791564941406 0.66874903 3.241122245788574 True -2 4773 17.498754024505615 0.31409716606140137 249.88153076171875 0.6138651371002197 298.9591979980469 0.5570783019065857 0.6963535 1.1565093994140625 True -3 6364 17.472266912460327 0.3196110725402832 194.39657592773438 0.5110863447189331 292.8580627441406 0.5685225129127502 0.7148078 0.7811874151229858 True -4 7955 17.46977186203003 0.315565824508667 222.4066162109375 0.40674906969070435 291.04345703125 0.572545051574707 0.7181307 0.6630149483680725 True -5 9546 17.445979118347168 0.31516551971435547 226.910400390625 0.2635706067085266 289.7619323730469 0.575644850730896 0.7230954 0.6393546462059021 True -6 11137 17.504704475402832 0.3220634460449219 272.05926513671875 0.46858036518096924 290.5557556152344 0.572935163974762 0.7161503 0.7140970230102539 False -7 12728 17.500566005706787 0.3788290023803711 222.01876831054688 0.2518916726112366 288.30975341796875 0.5798744559288025 0.73474556 0.5796091556549072 True -8 14319 17.49117422103882 0.3190317153930664 225.30914306640625 0.4157143235206604 286.9349060058594 0.5832678079605103 0.7500192 0.4980167746543884 True -9 15910 17.523093461990356 0.3181881904602051 222.02206420898438 0.38952741026878357 286.3682861328125 0.5851894617080688 0.7556672 0.4696754217147827 True -10 17501 17.50075602531433 1.0362474918365479 262.6680908203125 0.24823227524757385 285.7149658203125 0.5868485569953918 0.7638533 0.43561670184135437 True -11 19092 17.5003764629364 0.3141634464263916 248.784423828125 0.3292591869831085 285.12847900390625 0.5883389115333557 0.76676565 0.41374847292900085 True -12 20683 17.513110399246216 0.3144714832305908 244.26048278808594 0.2574794888496399 284.6029968261719 0.5897893309593201 0.7700105 0.39962542057037354 True -13 22274 17.520915269851685 0.3157351016998291 244.65689086914062 0.2239159643650055 284.29779052734375 0.5905552506446838 0.7736459 0.3918401002883911 True -14 23865 17.513100147247314 0.31564927101135254 225.09573364257812 0.31313857436180115 284.0138854980469 0.5912875533103943 0.7752906 0.38286662101745605 True -15 25456 17.518836736679077 0.3220958709716797 217.15322875976562 0.21142363548278809 283.9123840332031 0.591438889503479 0.77473944 0.3743695914745331 False -16 27047 17.51033639907837 1.4433269500732422 201.40406799316406 0.1680641770362854 283.9520568847656 0.5913788676261902 0.7743121 0.3642621636390686 False -17 28638 17.538036823272705 0.321260929107666 260.5284118652344 0.17506827414035797 284.1233215332031 0.5905641913414001 0.77105784 0.36642545461654663 False -18 30229 17.550750970840454 8.992443323135376 244.4423828125 0.17428290843963623 284.3363342285156 0.5899433493614197 0.76713884 0.3680419325828552 False -19 31820 17.49355697631836 0.32268476486206055 223.14956665039062 0.1445033848285675 284.43389892578125 0.5894308686256409 0.7646147 0.37107938528060913 False diff --git a/ENCSR914DTI/cherimoya.fold_0.performance.tsv b/ENCSR914DTI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3318853a297ed33175b2c59c5930286b4c849181..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -284.0138854980469 0.32859331369400024 0.5912874937057495 0.1977205127477646 0.7752906084060669 0.7382621169090271 0.38286662101745605 \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_1.evaluate.json b/ENCSR914DTI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 193435c202abb0713c55a52f0331f0d225066f56..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF162QEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_1.fit.json b/ENCSR914DTI/cherimoya.fold_1.fit.json deleted file mode 100644 index 6f3368a88754f74b1b2cbb54417ec4b488187f54..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF162QEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_1.log b/ENCSR914DTI/cherimoya.fold_1.log deleted file mode 100644 index 1f780fffb93ae9a1a7c1932b4561bf8e06cbce64..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1566 21.16608214378357 3.4096152782440186 242.1612548828125 0.5386103391647339 398.8871765136719 0.454610675573349 0.5938379 12.835572242736816 True -1 3132 17.29940915107727 0.4294416904449463 217.73663330078125 0.5863898992538452 334.87298583984375 0.5471013784408569 0.6636571 3.330383539199829 True -2 4698 16.967365741729736 0.40456366539001465 217.64376831054688 0.4424501061439514 322.61859130859375 0.5686356425285339 0.68914837 1.2164195775985718 True -3 6264 16.838029384613037 0.4051647186279297 253.777587890625 0.4043462872505188 313.6780090332031 0.5846136212348938 0.7159598 0.854225218296051 True -4 7830 16.8351993560791 0.39951205253601074 221.59815979003906 0.43299180269241333 310.69708251953125 0.5914155840873718 0.72999537 0.5767871141433716 True -5 9396 16.830892086029053 0.39543581008911133 224.50489807128906 0.5442912578582764 309.0009765625 0.595646321773529 0.7418038 0.5022485852241516 True -6 10962 16.849443435668945 0.40363597869873047 242.2299346923828 0.47704750299453735 308.121826171875 0.5980278849601746 0.7506644 0.4725877344608307 True -7 12528 16.851097583770752 0.40500760078430176 253.24671936035156 0.35881394147872925 307.87353515625 0.5988459587097168 0.75199056 0.5002960562705994 True -8 14094 16.90858554840088 0.4003746509552002 234.26068115234375 0.4265725016593933 306.7946472167969 0.6010907292366028 0.7619297 0.45621389150619507 True -9 15660 16.864596605300903 0.40361785888671875 232.8465576171875 0.3773719072341919 305.87030029296875 0.6032925844192505 0.76889426 0.42782899737358093 True -10 17226 16.86011242866516 0.40340518951416016 215.51953125 0.368476539850235 305.1972351074219 0.605074942111969 0.775092 0.40184369683265686 True -11 18792 16.862696409225464 0.39789652824401855 194.77069091796875 0.30225127935409546 304.4920654296875 0.6066339612007141 0.7823798 0.38246381282806396 True -12 20358 16.867764234542847 0.40207552909851074 209.7932586669922 0.3002985119819641 303.81121826171875 0.6083460450172424 0.78884554 0.3515928387641907 True -13 21924 16.890828609466553 0.39799976348876953 241.49668884277344 0.2533922493457794 303.26104736328125 0.6095041632652283 0.79220396 0.3433900773525238 True -14 23490 16.886554956436157 0.40224647521972656 243.81109619140625 0.2532978057861328 303.0109558105469 0.6101855039596558 0.79364526 0.3304669260978699 True -15 25056 16.878782987594604 0.39884328842163086 213.97982788085938 0.22942331433296204 302.9677734375 0.6102486252784729 0.7962302 0.3185110092163086 True -16 26622 16.876671314239502 0.3982117176055908 253.25527954101562 0.17771629989147186 303.0252685546875 0.6099008917808533 0.79555 0.31581637263298035 False -17 28188 16.877725839614868 0.4073941707611084 223.35755920410156 0.18548601865768433 303.32293701171875 0.6092292070388794 0.7957977 0.3159865736961365 False -18 29754 16.87736177444458 0.39838123321533203 220.39706420898438 0.18206103146076202 303.5599365234375 0.6084482669830322 0.7944257 0.31435924768447876 False -19 31320 16.87754774093628 0.39771175384521484 237.30496215820312 0.20611274242401123 303.7322692871094 0.6079366207122803 0.79262793 0.31651046872138977 False diff --git a/ENCSR914DTI/cherimoya.fold_1.performance.tsv b/ENCSR914DTI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bd465056ac3cd0b204711a219b24c627f76f0cca..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -302.9677734375 0.31473445892333984 0.6102486252784729 0.21081672608852386 0.7962301969528198 0.7820447683334351 0.3185110092163086 \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_2.evaluate.json b/ENCSR914DTI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 9202f14566b97e1e845cfbae5d0736a9759c4fb1..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF162QEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_2.fit.json b/ENCSR914DTI/cherimoya.fold_2.fit.json deleted file mode 100644 index 1134a4368cd5a31e70efa7db889921b20fea5f05..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF162QEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_2.log b/ENCSR914DTI/cherimoya.fold_2.log deleted file mode 100644 index 8738db62d7df54c06bf253af439b227af8659fa0..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1668 22.355344533920288 3.3680036067962646 227.6177520751953 0.42016685009002686 369.0393371582031 0.4448353350162506 0.5961385 11.27505874633789 True -1 3336 18.39068341255188 0.3332221508026123 252.5602569580078 0.3817503750324249 312.6038513183594 0.5314221978187561 0.67032903 2.4262936115264893 True -2 5004 18.367623567581177 0.3221001625061035 234.1389617919922 0.3875064253807068 298.64312744140625 0.5564172267913818 0.7061293 0.772273063659668 True -3 6672 18.3216073513031 0.3121020793914795 231.64352416992188 0.29501163959503174 292.5809020996094 0.5688790082931519 0.7297131 0.6219993829727173 True -4 8340 18.311530590057373 0.3206441402435303 229.09234619140625 0.47023841738700867 291.6479797363281 0.5718284249305725 0.73642987 0.495457261800766 True -5 10008 18.323282957077026 0.3154785633087158 223.63772583007812 0.39727652072906494 289.84716796875 0.5755542516708374 0.7477348 0.425801545381546 True -6 11676 18.38545560836792 0.3132352828979492 223.6053466796875 0.5065619349479675 288.54669189453125 0.5784202218055725 0.7595541 0.3867713510990143 True -7 13344 18.347549200057983 0.33119893074035645 230.042236328125 0.3272077143192291 287.9436340332031 0.5806395411491394 0.7657725 0.35607051849365234 True -8 15012 18.36174988746643 0.3151826858520508 205.47604370117188 0.3103717863559723 287.234130859375 0.5824248194694519 0.7715007 0.3474516272544861 True -9 16680 18.35291028022766 0.3210484981536865 218.64535522460938 0.23952513933181763 286.71514892578125 0.5839098691940308 0.77469057 0.3440109193325043 True -10 18348 18.308339595794678 0.31586408615112305 205.7047576904297 0.4535455107688904 286.1143493652344 0.5856579542160034 0.78125924 0.33223119378089905 True -11 20016 18.716373205184937 0.31996750831604004 222.59796142578125 0.31546297669410706 285.6258239746094 0.5870380997657776 0.7850794 0.32101619243621826 True -12 21684 18.34413456916809 0.3227345943450928 215.40585327148438 0.32851430773735046 285.2165222167969 0.5880694389343262 0.7910118 0.31246739625930786 True -13 23352 18.432613372802734 0.3178098201751709 248.44105529785156 0.264803409576416 284.841552734375 0.5888157486915588 0.7940551 0.3051592707633972 True -14 25020 18.312804222106934 0.3200681209564209 236.069091796875 0.2974812388420105 284.6260986328125 0.5895898342132568 0.7968515 0.3007395267486572 True -15 26688 18.353553295135498 0.3161139488220215 227.40878295898438 0.23511704802513123 284.55792236328125 0.5897099375724792 0.7970487 0.3028944134712219 True -16 28356 18.351032257080078 0.31485819816589355 220.03042602539062 0.20621943473815918 284.6499328613281 0.5894970297813416 0.79729587 0.30242982506752014 True -17 30024 18.31228542327881 11.135183334350586 238.4188232421875 0.23508471250534058 284.8306579589844 0.5888261198997498 0.79376036 0.3078998625278473 False -18 31692 18.456109046936035 0.3167457580566406 227.19869995117188 0.1031278669834137 285.09765625 0.5880287885665894 0.79151154 0.3136489689350128 False -19 33360 17.965503931045532 0.3165156841278076 215.46058654785156 0.1334560513496399 285.3194580078125 0.5875440835952759 0.7873557 0.31930065155029297 False diff --git a/ENCSR914DTI/cherimoya.fold_2.performance.tsv b/ENCSR914DTI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4d8c0d99e40a6f326aa91ac65a03f5728588851d..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -284.6499328613281 0.3288743793964386 0.5894969701766968 0.19823360443115234 0.797295868396759 0.7708969116210938 0.30242982506752014 \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_3.evaluate.json b/ENCSR914DTI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6e7fa19c5a8f5b93f67dd3c8b5d94ace340aed1c..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF162QEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_3.fit.json b/ENCSR914DTI/cherimoya.fold_3.fit.json deleted file mode 100644 index f63e573b42463d52d4107a0b5848c1a24d76dc9e..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF162QEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_3.log b/ENCSR914DTI/cherimoya.fold_3.log deleted file mode 100644 index eef86745c9301046d89514d4655c70960758f830..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1614 21.755568027496338 3.289854049682617 245.69180297851562 0.5041245222091675 366.8865051269531 0.44390884041786194 0.6105472 11.988977432250977 True -1 3228 17.755999326705933 0.33853673934936523 260.6260070800781 0.4946819543838501 309.2939453125 0.533903956413269 0.68419427 2.6956470012664795 True -2 4842 17.70821189880371 0.9781155586242676 206.34371948242188 0.36021071672439575 299.1044006347656 0.5515996217727661 0.7069281 0.9569140076637268 True -3 6456 17.737828493118286 0.3238823413848877 232.45513916015625 0.5018755197525024 290.68359375 0.5683727264404297 0.732632 0.6548317074775696 True -4 8070 17.722816705703735 0.31044816970825195 260.39031982421875 0.37407857179641724 288.5978698730469 0.5737291574478149 0.74024814 0.5784110426902771 True -5 9684 17.77682065963745 0.3154430389404297 240.28672790527344 0.5251153707504272 287.562744140625 0.5769641995429993 0.7460166 0.5289361476898193 True -6 11298 17.756162881851196 0.32111120223999023 242.56005859375 0.2793853282928467 287.8062744140625 0.5753956437110901 0.74567264 0.5850683450698853 False -7 12912 17.75363826751709 0.31897497177124023 249.9638214111328 0.4726253151893616 286.373779296875 0.5805129408836365 0.75518686 0.5467349886894226 True -8 14526 17.74973702430725 0.319507360458374 257.5719299316406 0.388605535030365 285.73028564453125 0.583019495010376 0.7628769 0.4933378994464874 True -9 16140 17.75838875770569 0.3211801052093506 239.33035278320312 0.3720166087150574 284.899658203125 0.5852261185646057 0.76871294 0.4309728145599365 True -10 17754 17.753833055496216 0.3166325092315674 221.4705352783203 0.2522503137588501 284.3764343261719 0.5866155624389648 0.7746974 0.4240827262401581 True -11 19368 17.754207611083984 0.3179502487182617 229.43788146972656 0.25978732109069824 283.80859375 0.5882689356803894 0.77660847 0.3935558795928955 True -12 20982 17.74814486503601 0.31258344650268555 245.8612518310547 0.3940039873123169 283.34368896484375 0.589353621006012 0.7807194 0.3849722146987915 True -13 22596 17.71679949760437 0.3141791820526123 248.73672485351562 0.3471129536628723 283.0111083984375 0.5903692245483398 0.7839069 0.3805702328681946 True -14 24210 17.752047777175903 0.3164646625518799 257.1396179199219 0.28984534740448 282.7189636230469 0.5909848213195801 0.7877208 0.36302343010902405 True -15 25824 17.71106219291687 0.3163735866546631 223.14935302734375 0.18893373012542725 282.5906677246094 0.5914382338523865 0.79061085 0.35236451029777527 True -16 27438 17.758896112442017 0.31177282333374023 234.05441284179688 0.2346375584602356 282.5845031738281 0.5913566946983337 0.7888849 0.3441968560218811 False -17 29052 17.74612832069397 0.3170809745788574 233.8060302734375 0.19187074899673462 282.74395751953125 0.5910032391548157 0.7894163 0.33477407693862915 False -18 30666 17.77081274986267 0.32035160064697266 268.9897155761719 0.20851267874240875 282.987060546875 0.5901452302932739 0.784309 0.33578500151634216 False -19 32280 17.772180795669556 0.32060933113098145 239.7711944580078 0.16566020250320435 283.1322326660156 0.5897080302238464 0.78217596 0.33696648478507996 False diff --git a/ENCSR914DTI/cherimoya.fold_3.performance.tsv b/ENCSR914DTI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0d46fd37a2e73805a26e0363f050c9db473a9d16..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -282.5906677246094 0.32847753167152405 0.5914382934570312 0.1962674856185913 0.7906108498573303 0.7565624713897705 0.35236451029777527 \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_4.evaluate.json b/ENCSR914DTI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 488c6520d913db7a8bd9917df2ed09fd9ad34f29..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF162QEB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_4.fit.json b/ENCSR914DTI/cherimoya.fold_4.fit.json deleted file mode 100644 index 7f2528152a9d9ce035ae872120145a66ebfa40dc..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF162QEB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR914DTI/cherimoya.fold_4.log b/ENCSR914DTI/cherimoya.fold_4.log deleted file mode 100644 index 7ebdca72d67f7847fbd33fcbcc8d997dd053e368..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1626 21.829999208450317 3.508207082748413 244.3056640625 0.6334912776947021 362.81103515625 0.44572123885154724 0.60264844 11.446918487548828 True -1 3252 17.92128849029541 0.33886027336120605 285.2867431640625 0.5769307613372803 308.2584533691406 0.5313869118690491 0.66415364 2.5963938236236572 True -2 4878 17.90217876434326 0.3159332275390625 234.3231964111328 0.41551053524017334 295.7161560058594 0.5563288331031799 0.6976059 0.955683708190918 True -3 6504 17.905226707458496 0.33069610595703125 284.3233642578125 0.46795493364334106 290.323486328125 0.5641729235649109 0.7081057 0.6266568303108215 True -4 8130 17.88398814201355 7.277936220169067 279.74041748046875 0.3093874156475067 287.5567626953125 0.5713797211647034 0.7210693 0.6277020573616028 True -5 9756 17.87504482269287 0.3160741329193115 243.36289978027344 0.4050171375274658 286.7633361816406 0.5738793611526489 0.72698873 0.5917649269104004 True -6 11382 17.827343225479126 0.32293176651000977 243.81552124023438 0.4112052619457245 285.3571472167969 0.5781186819076538 0.7421611 0.5033132433891296 True -7 13008 17.84222722053528 0.3163025379180908 240.2454376220703 0.528264045715332 284.5716857910156 0.5808805823326111 0.75358945 0.4377833604812622 True -8 14634 17.85949158668518 0.3160219192504883 235.37918090820312 0.3454669713973999 283.8210754394531 0.583235502243042 0.76057947 0.4054512083530426 True -9 16260 17.853123664855957 0.33015871047973633 272.05609130859375 0.24323678016662598 283.216552734375 0.5845065116882324 0.76846284 0.3776269853115082 True -10 17886 17.848264694213867 0.33408355712890625 213.99591064453125 0.45286935567855835 282.7017822265625 0.5862435698509216 0.7748957 0.3598138093948364 True -11 19512 17.873430967330933 0.32125043869018555 220.9936981201172 0.3851373493671417 282.12646484375 0.5878386497497559 0.7799875 0.33691370487213135 True -12 21138 17.6014301776886 0.3133881092071533 274.2717590332031 0.2781662940979004 281.7358703613281 0.5892165899276733 0.78677434 0.3320486545562744 True -13 22764 17.49048137664795 13.51668643951416 234.73252868652344 0.31649044156074524 281.3538818359375 0.5900362730026245 0.7924277 0.32423919439315796 True -14 24390 18.22358202934265 0.33252596855163574 243.74696350097656 0.28023022413253784 281.17449951171875 0.5905755162239075 0.7951007 0.3106325566768646 True -15 26016 17.572657585144043 0.3130378723144531 246.574951171875 0.22501933574676514 281.036376953125 0.5909953117370605 0.79810774 0.30900999903678894 True -16 27642 17.571518182754517 0.3215823173522949 223.10679626464844 0.21444618701934814 281.1198425292969 0.5906851887702942 0.799711 0.30757346749305725 True -17 29268 17.624857425689697 0.33446240425109863 209.2571563720703 0.17169344425201416 281.3087158203125 0.5899413228034973 0.7975461 0.30863529443740845 False -18 30894 17.6518611907959 0.32279133796691895 214.5059814453125 0.1743227243423462 281.4919128417969 0.5892285704612732 0.79415196 0.3128545582294464 False -19 32520 17.528544425964355 0.3229255676269531 241.59197998046875 0.156126469373703 281.69647216796875 0.5886725783348083 0.7909834 0.317279577255249 False diff --git a/ENCSR914DTI/cherimoya.fold_4.performance.tsv b/ENCSR914DTI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index cc66b8467fb9fccaca8d7b4e04a7f019fcaf01e5..0000000000000000000000000000000000000000 --- a/ENCSR914DTI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -281.1198425292969 0.32924044132232666 0.5906851887702942 0.1975145787000656 0.7997109889984131 0.7639723420143127 0.30757346749305725 \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_0.evaluate.json b/ENCSR915MTG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8552cd173b222ee5219b82917e1565cc0dc3ba2c..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038DPP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_0.fit.json b/ENCSR915MTG/cherimoya.fold_0.fit.json deleted file mode 100644 index 662d7dc179fff328683d3dd436f88df7e3bbdb8d..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF038DPP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_0.log b/ENCSR915MTG/cherimoya.fold_0.log deleted file mode 100644 index 6510dc20235a8c089f03212cf7f7788baf796b10..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1869 70.61964440345764 71.60960793495178 396.90081787109375 1.3873875141143799 747.4641723632812 0.5014657974243164 0.5962587 15.1046142578125 True -1 3738 20.76711416244507 0.368776798248291 406.7412414550781 1.4448163509368896 558.6220703125 0.638417661190033 0.66328 10.089125633239746 True -2 5607 20.810594081878662 0.3566410541534424 483.59893798828125 1.7414724826812744 513.0665283203125 0.6859676241874695 0.672972 2.57456374168396 True -3 7476 20.717923402786255 0.3547954559326172 432.3851013183594 1.2095980644226074 498.2343444824219 0.6973341703414917 0.6898652 1.3932961225509644 True -4 9345 20.708158493041992 0.34633660316467285 391.629150390625 1.042657494544983 492.37322998046875 0.7033147811889648 0.7021306 1.0571180582046509 True -5 11214 20.705907106399536 0.3489072322845459 429.4010009765625 0.8575732111930847 489.759521484375 0.706687867641449 0.6999065 1.041902780532837 False -6 13083 20.7286958694458 0.3493077754974365 438.747314453125 1.2976518869400024 488.2638854980469 0.7090065479278564 0.7074748 1.0045936107635498 True -7 14952 20.724021911621094 0.3504295349121094 333.70556640625 1.6899387836456299 485.6068420410156 0.7119612097740173 0.7129724 0.9711616635322571 True -8 16821 20.695607900619507 0.3487694263458252 394.411865234375 1.1590757369995117 483.1683349609375 0.7147118449211121 0.7202143 0.9118415713310242 True -9 18690 20.679891109466553 0.34833836555480957 381.2109375 1.0777559280395508 480.965087890625 0.7171644568443298 0.7246651 0.8544809222221375 True -10 20559 20.729280710220337 0.3517732620239258 355.7901611328125 1.1285436153411865 478.9536437988281 0.719482958316803 0.7316614 0.828432023525238 True -11 22428 20.71865963935852 0.34899306297302246 339.14190673828125 1.0309340953826904 477.5406188964844 0.7208166718482971 0.7344619 0.8307225704193115 True -12 24297 20.740410327911377 0.3498103618621826 349.611328125 1.22294020652771 475.51788330078125 0.7224957346916199 0.7422399 0.8075342774391174 True -13 26166 20.683136463165283 0.3530089855194092 345.3458557128906 0.7600967884063721 474.379150390625 0.7238198518753052 0.7434487 0.7906560301780701 True -14 28035 20.69168972969055 0.3517882823944092 380.927978515625 0.6617186069488525 473.6477966308594 0.7247656583786011 0.7485363 0.7779651880264282 True -15 29904 20.781525135040283 0.34860706329345703 359.2644958496094 0.6649731397628784 473.34552001953125 0.7248996496200562 0.7480725 0.7908796668052673 False -16 31773 20.703623056411743 0.3530275821685791 338.487548828125 0.9619717597961426 473.2930603027344 0.724826455116272 0.74723977 0.8020973801612854 False -17 33642 20.730984926223755 0.7738721370697021 325.8851623535156 0.38217440247535706 474.1507263183594 0.7239460945129395 0.7442158 0.8353343605995178 False -18 35511 20.82914638519287 0.3478848934173584 348.81298828125 0.5001101493835449 474.48394775390625 0.7234452366828918 0.7413317 0.8617411851882935 False -19 37380 20.72047519683838 0.3517796993255615 392.1936340332031 0.2830885648727417 474.64276123046875 0.7230036854743958 0.73757374 0.8858951330184937 False diff --git a/ENCSR915MTG/cherimoya.fold_0.performance.tsv b/ENCSR915MTG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 04359f26572ce12f560d217e9818074f648fdeef..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -473.6477966308594 0.23327450454235077 0.7247656583786011 0.3203476071357727 0.7485362887382507 0.7144024968147278 0.7779651880264282 \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_1.evaluate.json b/ENCSR915MTG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a5ff6de47e0093354789d1527772bfc10841c8cd..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038DPP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_1.fit.json b/ENCSR915MTG/cherimoya.fold_1.fit.json deleted file mode 100644 index 3167a25c87fc84eb41cf9eeef14bcdd8c0e2c989..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF038DPP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_1.log b/ENCSR915MTG/cherimoya.fold_1.log deleted file mode 100644 index 64f6a4dc378f911efc52d68b9d2c5c5720ae0206..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1845 23.96349000930786 3.5429766178131104 363.0609130859375 1.7710583209991455 872.0755615234375 0.5147644281387329 0.5735272 18.200424194335938 True -1 3690 20.501018047332764 0.5715813636779785 386.36273193359375 2.020291566848755 645.584228515625 0.6492680311203003 0.6720722 9.948522567749023 True -2 5535 20.52576446533203 0.5360538959503174 407.44598388671875 1.6128989458084106 585.8772583007812 0.705676794052124 0.68718064 3.288357973098755 True -3 7380 20.511051893234253 0.5405244827270508 404.22857666015625 1.4383957386016846 567.34130859375 0.719422459602356 0.70236194 1.854421615600586 True -4 9225 20.523473262786865 0.5380327701568604 392.7909851074219 1.536589503288269 560.1642456054688 0.7255170941352844 0.71631455 1.380711555480957 True -5 11070 20.511150360107422 0.5367112159729004 379.71234130859375 1.0750606060028076 555.4537353515625 0.729112982749939 0.72100043 1.163967251777649 True -6 12915 20.516311645507812 0.5376992225646973 384.4420166015625 1.1122419834136963 550.8037109375 0.7327157258987427 0.7327186 0.9821789860725403 True -7 14760 20.387813091278076 0.5275523662567139 392.70599365234375 1.2230818271636963 547.7532348632812 0.7355815768241882 0.73647946 0.9223535656929016 True -8 16605 20.078051805496216 0.5303151607513428 366.4068908691406 1.4951300621032715 545.16015625 0.7382794618606567 0.74108887 0.8521929383277893 True -9 18450 20.039204597473145 0.525094747543335 367.3471984863281 1.6114979982376099 542.472900390625 0.7408733367919922 0.7462557 0.8392416834831238 True -10 20295 20.101096153259277 0.5300812721252441 358.89892578125 0.6636503338813782 539.7637939453125 0.7436155080795288 0.7529249 0.8003982305526733 True -11 22140 20.1017324924469 0.5444648265838623 307.5596618652344 0.7428687810897827 537.2599487304688 0.7456098198890686 0.7587067 0.7992465496063232 True -12 23985 20.129488229751587 0.5316886901855469 416.64422607421875 0.7120993733406067 535.0721435546875 0.7476337552070618 0.7632813 0.7598740458488464 True -13 25830 20.087477207183838 0.5300366878509521 382.40234375 0.8030830025672913 533.0836181640625 0.7491984963417053 0.76938313 0.7408232688903809 True -14 27675 20.169105291366577 2.158634901046753 423.4487609863281 0.5613280534744263 531.8216552734375 0.7503454685211182 0.7744969 0.7459926605224609 True -15 29520 20.200459003448486 0.5330548286437988 371.5778503417969 0.6704599261283875 530.9469604492188 0.7509363293647766 0.77459943 0.7582273483276367 True -16 31365 20.176578998565674 0.530566930770874 377.9105224609375 0.49998778104782104 530.8084106445312 0.7508687376976013 0.7746742 0.7846254706382751 True -17 33210 20.107051849365234 0.5285162925720215 416.54473876953125 0.3171045184135437 531.6915283203125 0.7501718401908875 0.7736132 0.8259256482124329 False -18 35055 20.10188388824463 0.5286929607391357 366.9151611328125 0.3325272798538208 532.0574951171875 0.7495148181915283 0.768525 0.8630034923553467 False -19 36900 20.158475875854492 0.5257339477539062 376.2013244628906 0.5158792734146118 532.5485229492188 0.7490295767784119 0.7665646 0.8869003057479858 False diff --git a/ENCSR915MTG/cherimoya.fold_1.performance.tsv b/ENCSR915MTG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7009ebcbce77145f5199828711ba56dd61fd5961..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -530.8084106445312 0.21236540377140045 0.7508686780929565 0.35448095202445984 0.7746741771697998 0.7643890976905823 0.7846254706382751 \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_2.evaluate.json b/ENCSR915MTG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a8a53f3a0a8ddd3ccc45d49a768aa2512f2d55b8..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038DPP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_2.fit.json b/ENCSR915MTG/cherimoya.fold_2.fit.json deleted file mode 100644 index 497c4b0da98338506a188fee09f24e26ac515976..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF038DPP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_2.log b/ENCSR915MTG/cherimoya.fold_2.log deleted file mode 100644 index 17283ab991cb3930d60ea89e2ce09e904ff95819..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1984 25.578755617141724 3.3444106578826904 446.115478515625 1.9404971599578857 778.7486572265625 0.5130374431610107 0.5857519 13.948965072631836 True -1 3968 22.020076990127563 0.40865325927734375 396.73406982421875 1.3211733102798462 583.8062133789062 0.6494714617729187 0.6865773 7.625426769256592 True -2 5952 22.04539203643799 0.37156200408935547 403.9329833984375 1.5896437168121338 533.9967651367188 0.6978594660758972 0.6943939 2.638293504714966 True -3 7936 22.05187463760376 0.3709697723388672 445.1448974609375 1.196904182434082 522.9899291992188 0.7064576745033264 0.69660985 1.73247492313385 True -4 9920 22.035010814666748 0.37030649185180664 430.53509521484375 0.8430883884429932 518.2090454101562 0.7105037569999695 0.70361066 1.3350169658660889 True -5 11904 22.049647569656372 0.38177919387817383 416.866943359375 1.0097291469573975 515.917236328125 0.7129141688346863 0.7121224 1.140427589416504 True -6 13888 21.993804693222046 0.3717324733734131 425.42633056640625 1.1201927661895752 511.60205078125 0.716403603553772 0.7218416 0.9706064462661743 True -7 15872 22.037977933883667 0.3736128807067871 401.0777587890625 1.3024241924285889 508.6415710449219 0.7193186283111572 0.72120184 0.9336230158805847 False -8 17856 21.974040746688843 0.37201523780822754 336.29498291015625 1.0034116506576538 505.9683532714844 0.7219433188438416 0.7308993 0.8767814040184021 True -9 19840 22.017184257507324 7.315050840377808 406.7652587890625 1.001178503036499 502.9648742675781 0.724558413028717 0.7345633 0.8542563915252686 True -10 21824 22.060638427734375 0.3812389373779297 373.76409912109375 0.8990898132324219 500.4650573730469 0.727063000202179 0.739717 0.8256429433822632 True -11 23808 22.328821420669556 8.450723648071289 417.6536560058594 1.0671950578689575 497.95947265625 0.7299832105636597 0.7446115 0.8059301972389221 True -12 25792 22.14559769630432 0.38452959060668945 372.9288330078125 0.6249966025352478 496.1807556152344 0.7316683530807495 0.74713683 0.8100615739822388 True -13 27776 22.066598176956177 0.3820216655731201 392.887939453125 0.6700505018234253 494.5848388671875 0.7333796620368958 0.75287485 0.7903850674629211 True -14 29760 22.014330863952637 0.37511277198791504 388.9764404296875 0.5892962217330933 492.6453552246094 0.7350187301635742 0.7609195 0.763869047164917 True -15 31744 22.015746355056763 0.5094540119171143 346.76544189453125 0.4620075523853302 492.4674377441406 0.7353737950325012 0.76295745 0.7635069489479065 True -16 33728 22.053065061569214 0.3771383762359619 387.60198974609375 0.7373860478401184 492.6142883300781 0.7352632880210876 0.76248306 0.773879885673523 False -17 35712 22.0259051322937 11.72618055343628 353.28631591796875 0.7154487371444702 493.3016357421875 0.7344275712966919 0.76322615 0.7971134185791016 True -18 37696 22.113045930862427 0.38161230087280273 359.11602783203125 0.4335799813270569 494.09979248046875 0.7336726188659668 0.7594832 0.8342398405075073 False -19 39680 21.62374472618103 0.37923622131347656 344.07440185546875 0.40615665912628174 494.4065856933594 0.7331097722053528 0.75760007 0.8458700180053711 False diff --git a/ENCSR915MTG/cherimoya.fold_2.performance.tsv b/ENCSR915MTG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index fbefdb8a7b0704ee5a7c4167550379b797ef3f71..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -493.3016357421875 0.22575317323207855 0.7344275712966919 0.33309537172317505 0.7632261514663696 0.7366916537284851 0.7971134185791016 \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_3.evaluate.json b/ENCSR915MTG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 275a6e5c87d3b25e88671bced903c690433e5619..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038DPP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_3.fit.json b/ENCSR915MTG/cherimoya.fold_3.fit.json deleted file mode 100644 index 2a8b8a1e0eaf9038cf44fc9418576a9b46012537..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF038DPP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_3.log b/ENCSR915MTG/cherimoya.fold_3.log deleted file mode 100644 index 62399b20d23a1c0151ff2246b41c2e1aeb2e33ff..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1916 24.965656042099 3.58984375 330.2594299316406 1.3393315076828003 763.1771240234375 0.5137340426445007 0.5720627 17.387775421142578 True -1 3832 21.269869565963745 0.5483567714691162 384.02081298828125 1.268864631652832 579.3021850585938 0.6450810432434082 0.639575 9.850703239440918 True -2 5748 21.60192084312439 0.39664793014526367 356.03668212890625 0.9662042260169983 532.3656005859375 0.692253053188324 0.64932 3.2222514152526855 True -3 7664 21.27693796157837 0.39141345024108887 385.8149108886719 1.0691297054290771 516.8989868164062 0.7041361331939697 0.6661277 1.8050990104675293 True -4 9580 21.284298419952393 1.203970193862915 472.41351318359375 1.1665501594543457 511.5173645019531 0.7088344097137451 0.6765053 1.412051796913147 True -5 11496 21.26248860359192 0.3937973976135254 321.8094482421875 1.1467647552490234 508.32244873046875 0.7122911214828491 0.6826077 1.2044230699539185 True -6 13412 21.27241039276123 1.0867345333099365 343.9555358886719 0.9637072682380676 505.343994140625 0.7153752446174622 0.69922155 1.0691604614257812 True -7 15328 21.24991774559021 0.3879563808441162 428.9991149902344 1.0695621967315674 503.8426818847656 0.7170712947845459 0.7051121 1.0276336669921875 True -8 17244 21.680384635925293 12.096188306808472 319.8317565917969 1.0098164081573486 500.82391357421875 0.7198641300201416 0.70584714 0.9758270978927612 True -9 19160 21.24540662765503 0.3937959671020508 390.25982666015625 0.6741848587989807 498.3483581542969 0.7226054668426514 0.7122291 0.9363438487052917 True -10 21076 21.246196508407593 9.846504926681519 434.93792724609375 1.3400428295135498 497.278564453125 0.7243190407752991 0.7165332 0.8973196148872375 True -11 22992 21.251726865768433 0.40088701248168945 410.7024230957031 0.7344892621040344 495.39459228515625 0.7265326976776123 0.7227988 0.8538410067558289 True -12 24908 21.252361536026 15.612017154693604 345.917724609375 0.8981107473373413 494.0588684082031 0.7279868721961975 0.72907156 0.8331966400146484 True -13 26824 21.455743312835693 0.3965771198272705 445.54547119140625 0.5412172675132751 492.1051025390625 0.7299226522445679 0.73642606 0.8195294737815857 True -14 28740 21.260656595230103 0.3970019817352295 361.7615966796875 0.7523428201675415 491.0317687988281 0.7308992743492126 0.74286085 0.8122989535331726 True -15 30656 21.267659902572632 0.39409422874450684 434.211181640625 0.6609780788421631 490.480224609375 0.7314507365226746 0.74718076 0.8255456686019897 True -16 32572 21.160823345184326 0.38608574867248535 394.9601745605469 0.7679922580718994 490.4568786621094 0.7311196327209473 0.7450666 0.8462609052658081 False -17 34488 20.79777431488037 0.3932318687438965 350.42999267578125 0.27594539523124695 491.0572814941406 0.7304198741912842 0.7429721 0.8904338479042053 False -18 36404 20.796613216400146 0.3854851722717285 330.44512939453125 0.26242032647132874 491.4573669433594 0.7296101450920105 0.7377863 0.9307155609130859 False -19 38320 20.828388452529907 0.38573217391967773 409.57568359375 0.45466524362564087 492.1782531738281 0.7291135787963867 0.7353668 0.9560079574584961 False diff --git a/ENCSR915MTG/cherimoya.fold_3.performance.tsv b/ENCSR915MTG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b6f6926aef99b0b3ec281ed3fe6a9f1193ffcf32..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -490.480224609375 0.22654347121715546 0.7314507365226746 0.3302541673183441 0.7471807599067688 0.7172853946685791 0.8255456686019897 \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_4.evaluate.json b/ENCSR915MTG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index c091b6a479fd762128d24dfd5d0e78acebc91ce0..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF038DPP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_4.fit.json b/ENCSR915MTG/cherimoya.fold_4.fit.json deleted file mode 100644 index b1883b559c53a5ab8a42950be385bfb84cce953a..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF038DPP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR915MTG/cherimoya.fold_4.log b/ENCSR915MTG/cherimoya.fold_4.log deleted file mode 100644 index b3d539a4508ab1f48a47b82eb1e45843ea82d369..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1910 24.82820177078247 3.267367362976074 364.6463623046875 1.5075966119766235 741.3397827148438 0.5048512816429138 0.59042704 14.77285099029541 True -1 3820 21.209943532943726 0.35402345657348633 447.54498291015625 1.2542822360992432 559.3235473632812 0.6369447112083435 0.66586506 9.076068878173828 True -2 5730 21.2498939037323 0.3410375118255615 406.64837646484375 1.5881673097610474 509.8797302246094 0.6900289058685303 0.65000695 3.577441930770874 False -3 7640 21.21060609817505 0.33682775497436523 408.9783020019531 1.067171335220337 495.2398681640625 0.7007591128349304 0.65108824 1.4918466806411743 False -4 9550 21.186402559280396 1.4473896026611328 425.419677734375 1.3465564250946045 489.1940612792969 0.7060169577598572 0.6765435 1.1110222339630127 True -5 11460 21.433096408843994 15.663614749908447 382.0151672363281 0.987764835357666 485.86834716796875 0.7099462747573853 0.6856446 0.9984049201011658 True -6 13370 21.194581985473633 0.34168052673339844 372.5042724609375 0.8684523701667786 482.91680908203125 0.7129393219947815 0.69171786 0.9388700127601624 True -7 15280 21.282652378082275 0.34233689308166504 360.5513610839844 0.8507043123245239 481.2576599121094 0.7155917286872864 0.69685066 0.911808967590332 True -8 17190 21.22142744064331 0.3408489227294922 400.7341613769531 1.014458179473877 479.00872802734375 0.7182468771934509 0.70612365 0.8557055592536926 True -9 19100 21.199466228485107 0.3431534767150879 443.29193115234375 0.7200420498847961 477.489013671875 0.7200398445129395 0.7113496 0.8476395010948181 True -10 21010 21.229350328445435 0.6452629566192627 353.62109375 1.1424044370651245 475.8571472167969 0.7222862243652344 0.7196518 0.8076200485229492 True -11 22920 21.287034034729004 0.3543846607208252 346.01434326171875 0.7090839147567749 473.6548767089844 0.7243653535842896 0.72993845 0.7796456217765808 True -12 24830 21.233430862426758 0.33988285064697266 410.5233459472656 0.8261339664459229 471.7843017578125 0.7261688113212585 0.7387596 0.7560293674468994 True -13 26740 21.19902729988098 0.34252190589904785 372.815673828125 0.7116827964782715 470.5635070800781 0.727562427520752 0.74412924 0.7427413463592529 True -14 28650 21.10835909843445 0.34193992614746094 305.3000793457031 0.7604124546051025 469.486572265625 0.7287774085998535 0.74892324 0.743687093257904 True -15 30560 20.78749704360962 0.3384559154510498 312.42315673828125 0.5944967269897461 469.2497253417969 0.7293471097946167 0.7549713 0.7366143465042114 True -16 32470 20.75915789604187 0.44065165519714355 310.65338134765625 0.6496533751487732 469.2681579589844 0.7287012934684753 0.751425 0.7640301585197449 False -17 34380 20.740352869033813 0.3309211730957031 350.2379150390625 0.5942028760910034 469.7530517578125 0.7280992865562439 0.7506314 0.7924483418464661 False -18 36290 20.814989805221558 0.34755706787109375 357.3040466308594 0.5644665956497192 470.3987121582031 0.7274143099784851 0.7456312 0.8335961699485779 False -19 38200 20.81823182106018 0.34906649589538574 365.0455322265625 0.3926004469394684 470.5558776855469 0.7270298004150391 0.74385494 0.8524637818336487 False diff --git a/ENCSR915MTG/cherimoya.fold_4.performance.tsv b/ENCSR915MTG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6477909aefa8b638b983e64ebc730b144e474476..0000000000000000000000000000000000000000 --- a/ENCSR915MTG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -469.2497253417969 0.2312278002500534 0.7293471097946167 0.32003724575042725 0.7549713253974915 0.712877631187439 0.7366143465042114 \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_0.evaluate.json b/ENCSR916MHX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6c6b7e9eac9d70c3f86f3d0b6fd946bedac339a4..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF281IYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_0.fit.json b/ENCSR916MHX/cherimoya.fold_0.fit.json deleted file mode 100644 index ec81c26142c4982d9e9302a5c485c6f6920241d9..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF281IYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_0.log b/ENCSR916MHX/cherimoya.fold_0.log deleted file mode 100644 index 3bb978ddbe04187e0f3274549d09e1d99d5ebc64..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 34.94413352012634 5.458257436752319 406.10675048828125 0.714364767074585 565.5348510742188 0.2537517547607422 0.7533976 3.856796979904175 True -1 5460 30.424060106277466 0.6313271522521973 402.1141357421875 0.27333924174308777 516.7659912109375 0.32441890239715576 0.8135406 1.1522631645202637 True -2 8190 30.435484170913696 0.589745044708252 434.0968322753906 0.426300585269928 508.5184631347656 0.33425775170326233 0.8177123 0.5081024765968323 True -3 10920 30.33008623123169 0.5957140922546387 421.8388366699219 0.3690524995326996 505.4852294921875 0.34022074937820435 0.8260921 0.383193701505661 True -4 13650 30.341405391693115 0.6003894805908203 439.4342346191406 0.5910766124725342 503.82110595703125 0.3418702781200409 0.83118975 0.30395981669425964 True -5 16380 30.266454219818115 0.5953149795532227 443.0115966796875 0.2797594666481018 502.0833435058594 0.3447835147380829 0.8328893 0.3109382688999176 True -6 19110 30.21284580230713 1.6844267845153809 403.7471923828125 0.3390502631664276 500.7213439941406 0.34760114550590515 0.83852756 0.2892858386039734 True -7 21840 30.18514919281006 1.742537260055542 485.048583984375 0.4139499068260193 498.26910400390625 0.35215482115745544 0.842168 0.27225300669670105 True -8 24570 29.607035636901855 0.5831112861633301 485.08868408203125 0.2890322506427765 498.0334167480469 0.3524613380432129 0.84903765 0.2537862956523895 True -9 27300 29.61926794052124 0.5847060680389404 434.23443603515625 0.31072378158569336 495.8214111328125 0.35687118768692017 0.8520089 0.24786639213562012 True -10 30030 29.614438772201538 0.5911850929260254 424.99224853515625 0.1937369704246521 494.3836364746094 0.3594909906387329 0.8539723 0.2375294268131256 True -11 32760 29.70002293586731 0.5778746604919434 490.4646911621094 0.32839763164520264 493.47283935546875 0.3607361316680908 0.85725164 0.22668525576591492 True -12 35490 29.632886171340942 0.5867154598236084 409.1949768066406 0.29374000430107117 491.99749755859375 0.3626769483089447 0.8586279 0.2213287204504013 True -13 38220 29.68565583229065 0.59090256690979 416.4431457519531 0.268656849861145 491.3612060546875 0.36419233679771423 0.864856 0.21312043070793152 True -14 40950 29.67322278022766 0.5822944641113281 422.42529296875 0.20511670410633087 491.234619140625 0.36419084668159485 0.8679642 0.20837344229221344 True -15 43680 29.646380186080933 0.5815551280975342 417.54608154296875 0.23134827613830566 490.1830139160156 0.3662271499633789 0.8707355 0.20533886551856995 True -16 46410 29.70305609703064 0.5879178047180176 403.76806640625 0.1551327109336853 490.4344177246094 0.3648448586463928 0.8710239 0.20218758285045624 True -17 49140 29.792043685913086 0.5756144523620605 461.0414733886719 0.18286244571208954 490.71136474609375 0.36461153626441956 0.8726657 0.2027273029088974 True -18 51870 29.70403027534485 1.3638315200805664 345.5816345214844 0.1712096929550171 490.6011047363281 0.36505627632141113 0.87130576 0.20388609170913696 False -19 54600 29.6237051486969 0.5809390544891357 384.0157775878906 0.25721293687820435 490.65386962890625 0.3648279905319214 0.87146616 0.2059122771024704 False diff --git a/ENCSR916MHX/cherimoya.fold_0.performance.tsv b/ENCSR916MHX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 373303e885e63a6b03f72634fb251f2acbbec807..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -490.71136474609375 0.40774640440940857 0.36461150646209717 0.1395346075296402 0.8726657032966614 0.8321729898452759 0.2027273029088974 \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_1.evaluate.json b/ENCSR916MHX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3c7ceb3854600b809a10f9235d4d35e228092d08..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF281IYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_1.fit.json b/ENCSR916MHX/cherimoya.fold_1.fit.json deleted file mode 100644 index 2f5ae19822f8b0b6a66b7c4fac59ef8632accd35..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF281IYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_1.log b/ENCSR916MHX/cherimoya.fold_1.log deleted file mode 100644 index a6c9a74fc9de1cbb44f1c73cc4e598f02afeb66a..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2710 34.73090958595276 4.887752056121826 476.11627197265625 0.4813823103904724 653.1757202148438 0.25677329301834106 0.74547535 4.528407573699951 True -1 5420 29.975891590118408 1.8742945194244385 488.02880859375 0.36786893010139465 595.102294921875 0.33614808320999146 0.8042713 1.0444655418395996 True -2 8130 30.061288595199585 0.7105162143707275 495.97613525390625 0.4087168574333191 580.9657592773438 0.3529602885246277 0.8183033 0.6923394799232483 True -3 10840 29.984355688095093 0.7282681465148926 464.70977783203125 0.3422453701496124 577.5018310546875 0.35651716589927673 0.8278422 0.5830200910568237 True -4 13550 30.01863431930542 0.6792521476745605 527.8974609375 0.5488173961639404 573.5592041015625 0.36435773968696594 0.8331408 0.4251483082771301 True -5 16260 30.013816833496094 0.7161118984222412 388.03643798828125 0.46170300245285034 570.5 0.37025347352027893 0.83514893 0.39711466431617737 True -6 18970 30.015731811523438 0.6716523170471191 414.02227783203125 0.32369428873062134 568.84228515625 0.37177619338035583 0.8391014 0.35727840662002563 True -7 21680 29.965925693511963 0.6911618709564209 387.36236572265625 0.26546865701675415 566.6550903320312 0.3750661313533783 0.8431327 0.3093462586402893 True -8 24390 29.34895372390747 0.7208170890808105 394.36187744140625 0.37969452142715454 565.4086303710938 0.37663331627845764 0.8476345 0.29307419061660767 True -9 27100 29.370246648788452 0.6798686981201172 445.2015380859375 0.3898625373840332 564.6658935546875 0.37767496705055237 0.85077584 0.2905484735965729 True -10 29810 29.685911417007446 20.06396460533142 455.9212646484375 0.3026104271411896 561.9546508789062 0.38219067454338074 0.85474455 0.2622631788253784 True -11 32520 29.39903473854065 15.048988342285156 370.99298095703125 0.27462518215179443 560.6384887695312 0.3837312161922455 0.85739064 0.2551906704902649 True -12 35230 29.45305347442627 0.6672992706298828 412.0489501953125 0.2984371781349182 559.995849609375 0.3840267062187195 0.86532557 0.2458813339471817 True -13 37940 29.433581113815308 0.6979541778564453 367.6085205078125 0.23315274715423584 558.4193115234375 0.38591378927230835 0.86924404 0.23720163106918335 True -14 40650 29.35404658317566 0.7008378505706787 394.97100830078125 0.2520754337310791 557.12451171875 0.38765543699264526 0.87367266 0.2282666563987732 True -15 43360 29.42424440383911 0.6879968643188477 392.4139404296875 0.27185720205307007 555.903076171875 0.38962873816490173 0.87810045 0.2231554388999939 True -16 46070 29.399179697036743 0.6757807731628418 404.6181640625 0.2105041742324829 555.5678100585938 0.3896844983100891 0.8803127 0.21904033422470093 True -17 48780 29.358816146850586 0.6475694179534912 408.12042236328125 0.12607626616954803 555.0047607421875 0.39058685302734375 0.88073975 0.21730470657348633 True -18 51490 29.375922441482544 0.6769218444824219 458.3855895996094 0.11189734935760498 555.3733520507812 0.38921764492988586 0.8810279 0.21950775384902954 True -19 54200 29.44683527946472 0.7016003131866455 418.9310302734375 0.2297605723142624 555.2637329101562 0.39016151428222656 0.88071716 0.22074705362319946 False diff --git a/ENCSR916MHX/cherimoya.fold_1.performance.tsv b/ENCSR916MHX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index b71fb6c0bb01b0fcb8f3a52851e396c9d0039afd..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -555.3733520507812 0.38734251260757446 0.38921764492988586 0.15677861869335175 0.88102787733078 0.8576680421829224 0.21950775384902954 \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_2.evaluate.json b/ENCSR916MHX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index d8b3d995b42a0724583e4f8fea5b9f80bd4a679b..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF281IYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_2.fit.json b/ENCSR916MHX/cherimoya.fold_2.fit.json deleted file mode 100644 index 3f39b8d4f6b3600fa58b4c3175e1d72d6d18a26b..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF281IYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_2.log b/ENCSR916MHX/cherimoya.fold_2.log deleted file mode 100644 index c10d07ff728bb6a5a014b3d731059711cf9a2ae0..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2867 36.276918172836304 4.0874786376953125 449.9984130859375 0.4273908734321594 586.8373413085938 0.2519989311695099 0.7451561 4.04123067855835 True -1 5734 31.75471067428589 1.559617280960083 416.1156005859375 0.43894678354263306 533.7765502929688 0.3251599967479706 0.80389607 0.6777024865150452 True -2 8601 31.80389165878296 0.5822494029998779 451.60076904296875 0.4094200134277344 523.462890625 0.33803194761276245 0.8185798 0.384560227394104 True -3 11468 31.741321325302124 1.0818004608154297 390.6734924316406 0.336397260427475 518.8264770507812 0.3454364836215973 0.82293266 0.39863717555999756 True -4 14335 31.763036727905273 0.5784196853637695 466.56866455078125 0.4191597104072571 518.452392578125 0.34577319025993347 0.8270024 0.3442857265472412 True -5 17202 31.776000499725342 0.5850763320922852 430.6456298828125 0.2869129180908203 517.4363403320312 0.3487376868724823 0.8274137 0.31200870871543884 True -6 20069 31.096496105194092 0.5570917129516602 391.08172607421875 0.19919142127037048 514.1341552734375 0.3529072701931 0.83419406 0.3085513114929199 True -7 22936 31.114243507385254 0.5685696601867676 399.75482177734375 0.5140611529350281 512.2105712890625 0.3568575382232666 0.8416895 0.29216983914375305 True -8 25803 31.145537853240967 0.5710203647613525 372.384521484375 0.23324544727802277 511.2266845703125 0.3580513298511505 0.8419442 0.28344109654426575 True -9 28670 31.128547191619873 0.6100995540618896 409.30853271484375 0.3169468641281128 509.5617980957031 0.36156508326530457 0.844581 0.26847636699676514 True -10 31537 31.16094994544983 0.600355863571167 447.4810485839844 0.23959827423095703 508.1108093261719 0.3638949394226074 0.8489817 0.25314760208129883 True -11 34404 31.116366624832153 0.5774767398834229 383.834228515625 0.3204084038734436 506.87359619140625 0.36505597829818726 0.85292035 0.24414733052253723 True -12 37271 31.109843492507935 0.5918517112731934 374.5960693359375 0.28045985102653503 505.92950439453125 0.36601442098617554 0.854461 0.2386605143547058 True -13 40138 31.22403597831726 0.575509786605835 442.11083984375 0.2758088707923889 505.0502014160156 0.3681296408176422 0.8582232 0.22827613353729248 True -14 43005 31.136417150497437 0.5743465423583984 420.9151611328125 0.38382411003112793 503.1774597167969 0.37138229608535767 0.86128646 0.22564570605754852 True -15 45872 31.12591814994812 0.575042724609375 380.79608154296875 0.18369077146053314 503.7472839355469 0.36992913484573364 0.8661492 0.21860428154468536 True -16 48739 31.07895851135254 0.5704078674316406 388.51495361328125 0.12926778197288513 503.2899475097656 0.37086570262908936 0.8675348 0.21513554453849792 True -17 51606 31.17455554008484 0.5728762149810791 448.30743408203125 0.19708827137947083 502.0504455566406 0.3734426498413086 0.86759466 0.21478281915187836 True -18 54473 31.20527744293213 0.5764796733856201 431.6908264160156 0.20778463780879974 502.99627685546875 0.3718003034591675 0.86708564 0.2155860960483551 False -19 57340 31.102120637893677 0.5743248462677002 432.2073059082031 0.13143882155418396 503.2198181152344 0.3711335062980652 0.8668906 0.2179664522409439 False diff --git a/ENCSR916MHX/cherimoya.fold_2.performance.tsv b/ENCSR916MHX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7b1c9d871bcedf105a005cbc685db617048144c2..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -502.0504455566406 0.4022260010242462 0.3734426498413086 0.1399402916431427 0.8675946593284607 0.8308751583099365 0.21478281915187836 \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_3.evaluate.json b/ENCSR916MHX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7e528bc5f8155396784510bac8b59da7cdfb4469..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF281IYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_3.fit.json b/ENCSR916MHX/cherimoya.fold_3.fit.json deleted file mode 100644 index 8329a0b617ac8314d8f5729e1e82d15974e46fc2..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF281IYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_3.log b/ENCSR916MHX/cherimoya.fold_3.log deleted file mode 100644 index a4c73fa47821087347590c4e9c73fee721a9ab15..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 35.45353031158447 4.821092128753662 449.713623046875 0.4859082102775574 554.6815185546875 0.25987735390663147 0.75259143 4.135151386260986 True -1 5498 30.501659870147705 0.5861797332763672 568.354248046875 0.4036630392074585 511.8166198730469 0.3181188702583313 0.8075886 0.9435595273971558 True -2 8247 30.423877477645874 0.5682919025421143 488.7632751464844 0.3354867100715637 501.7493896484375 0.3345597982406616 0.82217133 0.5617244243621826 True -3 10996 30.295833826065063 0.5515449047088623 416.32879638671875 0.503233790397644 496.6028747558594 0.34375959634780884 0.82674015 0.48211973905563354 True -4 13745 29.846041679382324 0.5509960651397705 459.96002197265625 0.43769222497940063 495.5023193359375 0.346052885055542 0.83308095 0.36983874440193176 True -5 16494 29.808537006378174 0.55224609375 446.0093994140625 0.3499772548675537 494.1216125488281 0.3478802442550659 0.8377199 0.3259409964084625 True -6 19243 29.84212350845337 0.5592801570892334 434.9992370605469 0.24746932089328766 491.9984130859375 0.3519671559333801 0.83765966 0.31720003485679626 False -7 21992 29.835388660430908 0.5453064441680908 428.5072326660156 0.27081331610679626 491.1056823730469 0.3528926372528076 0.8432653 0.3421664237976074 True -8 24741 29.841431856155396 0.5644962787628174 443.3540344238281 0.3234799802303314 489.0525207519531 0.3571276068687439 0.84513247 0.30512645840644836 True -9 27490 29.839071035385132 0.5531046390533447 431.4891357421875 0.2288631796836853 487.81549072265625 0.35887598991394043 0.85071766 0.26972562074661255 True -10 30239 29.840102434158325 0.5602636337280273 385.81121826171875 0.27675455808639526 486.6259460449219 0.360696405172348 0.8528608 0.26770615577697754 True -11 32988 29.84560227394104 0.5577609539031982 412.2625732421875 0.3180820643901825 486.24566650390625 0.36081549525260925 0.8573993 0.25702378153800964 True -12 35737 29.845836877822876 0.5446579456329346 347.1385803222656 0.40350770950317383 484.5942687988281 0.3635982573032379 0.8592688 0.24858172237873077 True -13 38486 29.837688446044922 0.5484089851379395 376.12493896484375 0.24055156111717224 483.6420593261719 0.36561816930770874 0.8620858 0.23810791969299316 True -14 41235 29.922146558761597 1.5488779544830322 424.6193542480469 0.21082265675067902 482.5029602050781 0.36731523275375366 0.8658185 0.23126220703125 True -15 43984 29.968610286712646 0.5745799541473389 405.4063720703125 0.2823939323425293 481.97515869140625 0.36752578616142273 0.86955166 0.2253705859184265 True -16 46733 29.89402413368225 0.5452797412872314 486.37188720703125 0.23864395916461945 481.2227783203125 0.3690970242023468 0.87230664 0.2204349935054779 True -17 49482 29.851415634155273 0.5503387451171875 416.90130615234375 0.18632769584655762 481.28155517578125 0.36915042996406555 0.87343115 0.21948634088039398 True -18 52231 29.811567783355713 0.5464298725128174 366.2109375 0.22320911288261414 481.7739562988281 0.36811232566833496 0.8728562 0.2192174196243286 False -19 54980 29.794811010360718 1.426405906677246 360.614013671875 0.14805568754673004 481.1835021972656 0.36951586604118347 0.8717251 0.22107630968093872 False diff --git a/ENCSR916MHX/cherimoya.fold_3.performance.tsv b/ENCSR916MHX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b4ee37be1825adbaeb1c1041c46121d7f035f046..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -481.28155517578125 0.40754130482673645 0.36915045976638794 0.14117443561553955 0.8734311461448669 0.8310562372207642 0.21948634088039398 \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_4.evaluate.json b/ENCSR916MHX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 77804bc1032b7f4d8394648ade33eed44e9e1d09..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF281IYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_4.fit.json b/ENCSR916MHX/cherimoya.fold_4.fit.json deleted file mode 100644 index 160fdd54289f9edf42c54451686c3c4aad4f7b5b..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF281IYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR916MHX/cherimoya.fold_4.log b/ENCSR916MHX/cherimoya.fold_4.log deleted file mode 100644 index addc7b1ff657bbe9920a74bc96586b734008974e..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2846 36.21198630332947 4.112149238586426 411.9263610839844 0.4109138250350952 537.91162109375 0.25607749819755554 0.7438061 4.097369194030762 True -1 5692 31.541373252868652 12.256282091140747 381.490966796875 0.7087633609771729 494.59149169921875 0.3210051357746124 0.8010893 0.8426622152328491 True -2 8538 31.67963981628418 14.336082220077515 374.4795227050781 0.4643986225128174 488.369140625 0.3289470672607422 0.8113152 0.45854610204696655 True -3 11384 32.08496689796448 0.5853896141052246 445.81854248046875 0.2611905336380005 484.1120300292969 0.33819490671157837 0.8174225 0.41712427139282227 True -4 14230 30.830403327941895 0.5837984085083008 321.099365234375 0.329501748085022 482.9384765625 0.3402370512485504 0.81629926 0.30626562237739563 False -5 17076 30.86888098716736 0.6049792766571045 436.98101806640625 0.2435910850763321 480.99755859375 0.34366852045059204 0.8214879 0.28284361958503723 True -6 19922 30.814812660217285 0.5623934268951416 360.6169738769531 0.319783091545105 480.212890625 0.34450429677963257 0.82672286 0.26942452788352966 True -7 22768 30.830824375152588 0.5790178775787354 414.4264221191406 0.3285559415817261 479.4460754394531 0.34600988030433655 0.83021307 0.2573958933353424 True -8 25614 30.837167501449585 0.6006588935852051 417.09075927734375 0.3521292805671692 477.56005859375 0.3493501842021942 0.83580345 0.23866601288318634 True -9 28460 30.83241295814514 1.2060234546661377 374.8450622558594 0.25790971517562866 476.33538818359375 0.3515920341014862 0.83938366 0.22882810235023499 True -10 31306 30.88773465156555 0.5805144309997559 405.7214660644531 0.2793503701686859 475.42645263671875 0.35321447253227234 0.84407604 0.22453583776950836 True -11 34152 30.88779091835022 0.6650571823120117 429.1366271972656 0.2951410412788391 474.53680419921875 0.35427728295326233 0.84924364 0.2149188220500946 True -12 36998 30.810668230056763 0.6097567081451416 451.928955078125 0.25512006878852844 473.7105407714844 0.3557215929031372 0.85315543 0.21149325370788574 True -13 39844 30.799317359924316 0.572246789932251 416.18658447265625 0.2840101420879364 473.0913391113281 0.3566741645336151 0.8581541 0.2041141539812088 True -14 42690 30.80219531059265 0.5701136589050293 397.8251953125 0.24087780714035034 471.41253662109375 0.3600940406322479 0.8619842 0.20032061636447906 True -15 45536 30.8260281085968 0.7967605590820312 350.251220703125 0.22200420498847961 471.8448791503906 0.3587762713432312 0.8642458 0.19678795337677002 True -16 48382 30.866064071655273 0.6013782024383545 422.876708984375 0.215534970164299 471.2697448730469 0.36035287380218506 0.86574113 0.19750788807868958 True -17 51228 30.885796546936035 0.6108829975128174 363.0902404785156 0.16423289477825165 471.4354553222656 0.35983094573020935 0.86857665 0.1978929340839386 True -18 54074 30.899908542633057 0.6040792465209961 430.52496337890625 0.29042017459869385 471.6713562011719 0.35913190245628357 0.86579156 0.19958895444869995 False -19 56920 30.89687204360962 0.5751240253448486 348.6382141113281 0.2689386010169983 471.5160217285156 0.35983049869537354 0.86607707 0.20052991807460785 False diff --git a/ENCSR916MHX/cherimoya.fold_4.performance.tsv b/ENCSR916MHX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7b7e7c557e86c64321b00e953ca9a81fa0fee537..0000000000000000000000000000000000000000 --- a/ENCSR916MHX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -471.4354553222656 0.41244974732398987 0.35983091592788696 0.13447785377502441 0.8685766458511353 0.8174753189086914 0.1978929340839386 \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_0.evaluate.json b/ENCSR918TVE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3dbae3d05f8e9b13a52b8d29aba564d726f14e47..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846JSP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_0.fit.json b/ENCSR918TVE/cherimoya.fold_0.fit.json deleted file mode 100644 index 3bc17d635569a2c63ebb1356516ece39fb3b7db9..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF846JSP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_0.log b/ENCSR918TVE/cherimoya.fold_0.log deleted file mode 100644 index 427effa2d9fa197f3a5ae473228bf87d6f4115b7..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2848 36.21166801452637 4.0252649784088135 477.8381652832031 0.945776641368866 716.9782104492188 0.5433237552642822 0.66961515 10.686324119567871 True -1 5696 31.740457773208618 0.9546787738800049 446.8247985839844 1.6147876977920532 602.2343139648438 0.6599298715591431 0.68032587 3.0396993160247803 True -2 8544 31.69810676574707 0.5865600109100342 509.42584228515625 0.8595119714736938 582.889404296875 0.6741458177566528 0.679459 1.5432113409042358 False -3 11392 31.428839206695557 0.5347452163696289 414.941650390625 1.4953210353851318 574.7142944335938 0.681376039981842 0.67938054 1.3686939477920532 False -4 14240 30.976056575775146 0.5442407131195068 442.58831787109375 1.2154868841171265 571.7594604492188 0.6847879886627197 0.6870535 1.224776268005371 True -5 17088 30.96132469177246 0.5439343452453613 418.03656005859375 1.2656340599060059 568.2608032226562 0.6884616613388062 0.69719434 1.1711664199829102 True -6 19936 31.04694366455078 0.5458247661590576 398.80950927734375 0.998266339302063 566.065673828125 0.6910677552223206 0.6978323 1.1175169944763184 True -7 22784 31.078969717025757 0.5538663864135742 588.6885986328125 0.999072790145874 563.4628295898438 0.6937779188156128 0.70040023 1.0729044675827026 True -8 25632 31.106660842895508 0.5475327968597412 517.7862548828125 1.0351728200912476 560.2343139648438 0.6964292526245117 0.70627785 0.9786341786384583 True -9 28480 31.128525495529175 0.5475773811340332 461.2535400390625 1.055527925491333 557.171875 0.6990771293640137 0.70956194 0.9070459008216858 True -10 31328 31.093996286392212 0.5488278865814209 483.5937805175781 0.7966516017913818 554.258056640625 0.70209139585495 0.7158346 0.8605754971504211 True -11 34176 31.076346397399902 0.5464675426483154 402.155517578125 0.889992356300354 551.6270141601562 0.7048894166946411 0.7267885 0.8050592541694641 True -12 37024 31.064699411392212 0.5583751201629639 452.23065185546875 0.5860339999198914 549.0848388671875 0.7073124647140503 0.73311937 0.7771129608154297 True -13 39872 31.024771213531494 0.5469417572021484 484.958251953125 0.7375401258468628 547.2495727539062 0.7091779708862305 0.7395257 0.7541237473487854 True -14 42720 31.133788108825684 0.5554952621459961 503.9922790527344 0.3138922154903412 545.7026977539062 0.7105355858802795 0.7440776 0.7654450535774231 True -15 45568 31.06521773338318 0.5554196834564209 467.17572021484375 0.5514399409294128 544.73388671875 0.7114033699035645 0.7485191 0.7267300486564636 True -16 48416 31.032081604003906 0.7793283462524414 330.9696044921875 0.888454020023346 544.5441284179688 0.7116385698318481 0.75070435 0.7272200584411621 True -17 51264 31.013498067855835 0.5559244155883789 428.6117248535156 0.6240670680999756 545.071533203125 0.7109816074371338 0.7484024 0.7402818202972412 False -18 54112 31.021605014801025 1.0020787715911865 396.41595458984375 0.4404643774032593 545.9305419921875 0.7102828621864319 0.7441883 0.7452132701873779 False -19 56960 30.980334281921387 0.611016035079956 455.79229736328125 0.3509896397590637 546.0185546875 0.7098731398582458 0.741291 0.7642203569412231 False diff --git a/ENCSR918TVE/cherimoya.fold_0.performance.tsv b/ENCSR918TVE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7b2aba14660425e8d4eb9db6280ca9546341f7a1..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -544.5441284179688 0.23434318602085114 0.7116386294364929 0.3410029709339142 0.7507043480873108 0.6946317553520203 0.7272200584411621 \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_1.evaluate.json b/ENCSR918TVE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d3a63d358c429294e492de209e15206e9a40969b..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846JSP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_1.fit.json b/ENCSR918TVE/cherimoya.fold_1.fit.json deleted file mode 100644 index 079298c9d4355880618e7a46021bbc4720adf15d..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF846JSP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_1.log b/ENCSR918TVE/cherimoya.fold_1.log deleted file mode 100644 index 034d761c8415c7d3bc7f669d941e41449e95f735..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 35.929720401763916 4.618783712387085 549.196533203125 1.0528268814086914 805.7725830078125 0.5619709491729736 0.6956228 7.904137134552002 True -1 5664 31.522082805633545 13.670921564102173 412.0185852050781 1.0853826999664307 671.0772705078125 0.6784391403198242 0.7078688 2.692760944366455 True -2 8496 31.63301110267639 0.9943835735321045 462.6366882324219 1.0204088687896729 651.565185546875 0.6922550201416016 0.7150568 1.3724948167800903 True -3 11328 31.554943323135376 0.8672797679901123 488.5491943359375 0.7863484025001526 640.908935546875 0.7000295519828796 0.71958274 1.19464111328125 True -4 14160 31.609288692474365 0.8750362396240234 500.1389465332031 1.2176845073699951 635.5580444335938 0.7042804956436157 0.72096765 1.1718672513961792 True -5 16992 31.674096822738647 0.7298321723937988 453.4512939453125 1.2787878513336182 632.6363525390625 0.7068512439727783 0.72670007 1.0858972072601318 True -6 19824 31.600574254989624 0.7215304374694824 429.09405517578125 1.527234673500061 630.3109741210938 0.7094066143035889 0.7277182 1.0685228109359741 True -7 22656 31.262406587600708 1.3023107051849365 526.6428833007812 0.6811057329177856 627.4179077148438 0.7120694518089294 0.72761685 1.0391985177993774 False -8 25488 30.858326196670532 0.7518177032470703 379.828125 0.9900126457214355 624.1138305664062 0.7148188352584839 0.73596776 0.970812201499939 True -9 28320 30.812153816223145 0.7589895725250244 386.9588317871094 0.9243789911270142 620.687744140625 0.7175836563110352 0.7393541 0.9237836003303528 True -10 31152 30.79848599433899 0.699904203414917 413.4582824707031 0.7272977828979492 616.5513305664062 0.7208595871925354 0.7506985 0.8408228158950806 True -11 33984 30.794435024261475 0.7030315399169922 400.2225341796875 0.5198479890823364 613.9015502929688 0.7232704758644104 0.75396603 0.839448094367981 True -12 36816 30.802489280700684 0.7081074714660645 408.8349914550781 0.8418338298797607 610.854248046875 0.7254015207290649 0.7607079 0.7936330437660217 True -13 39648 30.820249557495117 0.726783275604248 491.119873046875 0.8069202899932861 607.5857543945312 0.7277241349220276 0.76766014 0.742788553237915 True -14 42480 30.815040588378906 1.1244285106658936 439.3261413574219 0.9484127759933472 605.586181640625 0.7296549081802368 0.775216 0.7038744688034058 True -15 45312 30.8603036403656 0.7236254215240479 407.10931396484375 0.8383965492248535 604.6531982421875 0.7304676175117493 0.7779357 0.6909739375114441 True -16 48144 30.806541442871094 0.7153863906860352 388.7384338378906 0.7055755853652954 603.9612426757812 0.7307591438293457 0.7802644 0.6833334565162659 True -17 50976 30.802410125732422 0.7032263278961182 408.8548583984375 0.33221304416656494 604.7946166992188 0.7302150130271912 0.77890545 0.6907108426094055 False -18 53808 30.879907369613647 0.832575798034668 379.11907958984375 0.5153886675834656 605.4988403320312 0.7295557260513306 0.77385515 0.7038126587867737 False -19 56640 30.82353401184082 0.7159197330474854 435.8797607421875 0.33519336581230164 606.168701171875 0.7290891408920288 0.77138126 0.7207437753677368 False diff --git a/ENCSR918TVE/cherimoya.fold_1.performance.tsv b/ENCSR918TVE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a180f2102e056a706c3e206d00417bc29b2885f4..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -603.9612426757812 0.21778099238872528 0.7307591438293457 0.37411829829216003 0.7802643775939941 0.7628862261772156 0.6833334565162659 \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_2.evaluate.json b/ENCSR918TVE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5b3af0d21d7cd213f95c96651dad8946535da133..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846JSP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_2.fit.json b/ENCSR918TVE/cherimoya.fold_2.fit.json deleted file mode 100644 index e510828c60c16b20dc363a1d4cfe654dd156aa54..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF846JSP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_2.log b/ENCSR918TVE/cherimoya.fold_2.log deleted file mode 100644 index 65993dcae4e39aa3b642d465c2e7975e08f9b59b..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2992 38.18192386627197 3.89965558052063 428.2596130371094 1.0866469144821167 744.7791137695312 0.5555350184440613 0.6740385 8.015259742736816 True -1 5984 33.28442573547363 0.6402456760406494 477.7659912109375 1.4791911840438843 623.8974609375 0.6718377470970154 0.6837508 2.5941519737243652 True -2 8976 33.26162338256836 2.004441976547241 525.4434814453125 2.139293670654297 608.4390869140625 0.6826813817024231 0.69306314 1.3494226932525635 True -3 11968 33.22813630104065 0.5970683097839355 536.0333862304688 1.2588921785354614 602.2215576171875 0.6876801252365112 0.6969691 1.1504498720169067 True -4 14960 33.3061146736145 0.9759624004364014 419.38238525390625 1.329010248184204 597.5604248046875 0.6921225190162659 0.7053251 1.1126290559768677 True -5 17952 33.304741621017456 0.5757989883422852 449.2223815917969 0.9252433180809021 594.6826782226562 0.6960639953613281 0.7069403 1.1201475858688354 True -6 20944 33.23719906806946 0.5767176151275635 498.2389221191406 0.6835709810256958 592.2048950195312 0.6982712745666504 0.7087354 1.132804274559021 True -7 23936 33.29066443443298 0.5902917385101318 467.6672668457031 1.0167608261108398 589.4666137695312 0.7012518644332886 0.70935035 1.1057987213134766 True -8 26928 33.91433548927307 0.5760111808776855 403.80413818359375 0.948479175567627 586.8462524414062 0.7039719820022583 0.7108411 1.1483402252197266 True -9 29920 33.76756691932678 14.306291103363037 444.75579833984375 1.0478050708770752 584.392333984375 0.7058330178260803 0.7119667 1.155807375907898 True -10 32912 33.244285583496094 0.5831460952758789 384.110107421875 1.1851933002471924 580.9790649414062 0.7086067199707031 0.7185208 1.0177594423294067 True -11 35904 32.78535175323486 0.5726547241210938 403.0476379394531 0.9707892537117004 578.576171875 0.7111012935638428 0.72364026 0.9692122340202332 True -12 38896 32.51375985145569 0.5731010437011719 441.6175842285156 0.6793816685676575 575.7003173828125 0.7135825157165527 0.7303168 0.8999879956245422 True -13 41888 32.54104161262512 0.5717916488647461 414.8804626464844 0.778357982635498 573.5787963867188 0.7157389521598816 0.73688537 0.8526418805122375 True -14 44880 32.5280179977417 1.2843232154846191 387.0048828125 0.913189709186554 572.0581665039062 0.7171452045440674 0.7430538 0.8335767388343811 True -15 47872 32.55461931228638 1.1966941356658936 438.18341064453125 0.6073006391525269 570.8451538085938 0.7181004881858826 0.74587166 0.7899180054664612 True -16 50864 32.627421617507935 0.5680851936340332 386.7718200683594 0.6205441355705261 570.8690795898438 0.7182132601737976 0.746007 0.7892066240310669 True -17 53856 32.6984281539917 0.5919251441955566 469.4339599609375 0.43983131647109985 570.867431640625 0.7178931832313538 0.7449012 0.7906271815299988 False -18 56848 32.70284295082092 0.6441206932067871 411.8283386230469 0.46539634466171265 571.76171875 0.7173489928245544 0.7413893 0.8043171763420105 False -19 59840 32.63767862319946 0.6034646034240723 453.9438171386719 0.5271657705307007 572.5082397460938 0.7169712781906128 0.7382359 0.8153640031814575 False diff --git a/ENCSR918TVE/cherimoya.fold_2.performance.tsv b/ENCSR918TVE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9086a7fc4599457358a6de04ae48e810da6f1feb..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -570.8690795898438 0.22777484357357025 0.7182132005691528 0.3568353056907654 0.7460070252418518 0.706274688243866 0.7892066240310669 \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_3.evaluate.json b/ENCSR918TVE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 64f34d6f9cf5aa2250ce593c5e6b05ec20337319..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846JSP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_3.fit.json b/ENCSR918TVE/cherimoya.fold_3.fit.json deleted file mode 100644 index 5571f558c8bac2031a6aa3ad04c5bb87efadf057..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF846JSP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_3.log b/ENCSR918TVE/cherimoya.fold_3.log deleted file mode 100644 index 2310db1d8c969343da79a00cb7f7b99bad7a4834..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2904 37.05194616317749 4.058443307876587 373.14337158203125 1.088446021080017 719.5730590820312 0.5508298277854919 0.68624055 10.208086013793945 True -1 5808 32.250629901885986 1.8280045986175537 449.2257080078125 1.2432270050048828 608.0924682617188 0.6591225266456604 0.7036338 2.311915159225464 True -2 8712 31.65519070625305 2.117743492126465 406.67938232421875 0.9275494813919067 593.430908203125 0.6721092462539673 0.71081674 1.2762794494628906 True -3 11616 31.615654706954956 0.568824052810669 553.198974609375 0.8715329170227051 583.8325805664062 0.6795717477798462 0.7183921 1.3252198696136475 True -4 14520 31.604995012283325 3.8338398933410645 557.6235961914062 0.8310327529907227 580.4041137695312 0.6834490895271301 0.71904546 1.410028338432312 True -5 17424 31.583515644073486 0.5708043575286865 482.267333984375 1.142873764038086 577.2112426757812 0.6863298416137695 0.71981514 1.2189477682113647 True -6 20328 31.58486580848694 0.5815267562866211 480.08819580078125 1.3347134590148926 573.3574829101562 0.6901418566703796 0.7176601 1.1900609731674194 False -7 23232 31.66478443145752 0.5841975212097168 415.012939453125 0.8330560922622681 571.3221435546875 0.6918860673904419 0.7171974 1.12985360622406 False -8 26136 31.651071310043335 0.5860044956207275 444.2303466796875 0.6333730816841125 568.7240600585938 0.6950633525848389 0.72428036 1.0420283079147339 True -9 29040 31.594065189361572 0.5691995620727539 519.2567138671875 1.0713789463043213 565.8604736328125 0.6975367665290833 0.72636896 0.9762910008430481 True -10 31944 31.555688858032227 1.1898221969604492 482.17462158203125 0.6893743276596069 562.3854370117188 0.7003225684165955 0.729546 0.9263472557067871 True -11 34848 31.663225412368774 0.5739355087280273 377.43505859375 1.226511001586914 559.6646728515625 0.7032952904701233 0.73554826 0.9031550884246826 True -12 37752 31.583364248275757 0.5786194801330566 463.99920654296875 0.7699997425079346 557.2857666015625 0.7053497433662415 0.741416 0.8285437822341919 True -13 40656 31.595741987228394 0.5741074085235596 413.48016357421875 0.7525870203971863 555.446044921875 0.707251250743866 0.7465565 0.815053403377533 True -14 43560 31.616214513778687 0.5912351608276367 400.36846923828125 0.6882319450378418 553.5615234375 0.7090403437614441 0.7523431 0.7838762402534485 True -15 46464 31.61910915374756 1.1606841087341309 464.73870849609375 0.6867015957832336 552.6275024414062 0.7101868391036987 0.7574676 0.7466211318969727 True -16 49368 31.618630409240723 0.5760307312011719 405.1354675292969 0.9401100873947144 551.8226928710938 0.7106295228004456 0.7572368 0.7343111038208008 False -17 52272 31.5622820854187 0.5706183910369873 367.04730224609375 0.30320876836776733 552.4295654296875 0.7099810838699341 0.75498 0.7376729846000671 False -18 55176 31.583271980285645 0.5737593173980713 393.4143371582031 0.5675784945487976 553.177001953125 0.7092639207839966 0.75191355 0.7564161419868469 False -19 58080 31.576837301254272 0.5749607086181641 339.39117431640625 0.44863879680633545 553.447021484375 0.7088658809661865 0.7491494 0.7700873613357544 False diff --git a/ENCSR918TVE/cherimoya.fold_3.performance.tsv b/ENCSR918TVE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6ae963d1684cc2fda713839284b363d1d5ac8bd8..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -552.6275024414062 0.2323273867368698 0.7101868391036987 0.34502583742141724 0.7574676275253296 0.7158100008964539 0.7466211318969727 \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_4.evaluate.json b/ENCSR918TVE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6c74749c35069c62ce4d3ce7321f8f04608ebfcb..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF846JSP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_4.fit.json b/ENCSR918TVE/cherimoya.fold_4.fit.json deleted file mode 100644 index af616f7a5569a09c27e83dff523ec73a8ad7697e..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF846JSP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR918TVE/cherimoya.fold_4.log b/ENCSR918TVE/cherimoya.fold_4.log deleted file mode 100644 index 947f0eecd315f8b4144c26cd4a191f262dca8518..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2932 37.75393843650818 4.70867133140564 440.1762390136719 1.0440621376037598 687.4705810546875 0.5446012616157532 0.6651281 8.266300201416016 True -1 5864 31.957627773284912 0.6224594116210938 495.64447021484375 1.4934959411621094 584.29443359375 0.6564441919326782 0.6894455 1.9658719301223755 True -2 8796 32.556640625 12.159380435943604 442.18170166015625 0.95120769739151 569.9323120117188 0.6680719256401062 0.692556 1.4228641986846924 True -3 11728 31.957592487335205 0.5750415325164795 385.814453125 1.043440818786621 561.8929443359375 0.6760903000831604 0.6972294 1.118260145187378 True -4 14660 32.13892984390259 0.5770668983459473 425.7371826171875 1.064286708831787 558.70556640625 0.6795140504837036 0.70169705 1.1768581867218018 True -5 17592 31.883944034576416 0.5856006145477295 453.8646545410156 0.8090659379959106 555.9176025390625 0.6825876235961914 0.7027648 1.1512283086776733 True -6 20524 31.923991680145264 0.5652346611022949 455.31298828125 1.1792571544647217 552.837890625 0.6852631568908691 0.7073164 0.9303820729255676 True -7 23456 31.91326594352722 0.5698275566101074 505.53472900390625 1.007880449295044 550.5318603515625 0.6877086162567139 0.7117581 0.9339056611061096 True -8 26388 31.83793878555298 1.5805625915527344 503.6174621582031 1.572810173034668 548.4373168945312 0.6903413534164429 0.71364975 0.8914003372192383 True -9 29320 31.938049793243408 0.5683600902557373 492.0885314941406 1.0331482887268066 545.8648071289062 0.693259060382843 0.7173851 0.8458223342895508 True -10 32252 31.85832643508911 0.571619987487793 430.7596435546875 0.5180217623710632 543.375 0.6957423686981201 0.72371745 0.7940264940261841 True -11 35184 31.86215853691101 0.5657613277435303 440.6859436035156 0.7008206844329834 540.9921875 0.6984238028526306 0.73296225 0.749201774597168 True -12 38116 31.9044132232666 0.5681443214416504 448.755859375 0.8262525796890259 538.9900512695312 0.7001570463180542 0.7380793 0.7219152450561523 True -13 41048 31.94060969352722 0.5672376155853271 439.43658447265625 1.059086799621582 536.9090576171875 0.7021285891532898 0.7424188 0.7222990989685059 True -14 43980 31.87873649597168 0.5701041221618652 458.245849609375 0.573087215423584 535.8108520507812 0.7033984065055847 0.74606633 0.6976759433746338 True -15 46912 31.89578127861023 0.5689992904663086 425.445556640625 0.7075430750846863 535.1771850585938 0.7039434313774109 0.74767095 0.7018944025039673 True -16 49844 31.911130666732788 2.3613548278808594 304.08148193359375 0.7297410368919373 535.0321044921875 0.7041852474212646 0.74744904 0.7157871723175049 False -17 52776 32.04117941856384 2.062666654586792 440.8599853515625 0.88962721824646 535.5928955078125 0.7038692831993103 0.74579257 0.7353699207305908 False -18 55708 31.91919231414795 0.5793390274047852 431.10400390625 0.48352137207984924 536.3224487304688 0.7031719088554382 0.73868704 0.7566023468971252 False -19 58640 31.89773988723755 0.5660178661346436 444.09393310546875 0.43773654103279114 536.6075439453125 0.7028003334999084 0.73523515 0.7761940360069275 False diff --git a/ENCSR918TVE/cherimoya.fold_4.performance.tsv b/ENCSR918TVE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index fa531d44a99489a13ff3af0ca38ae9294879dd00..0000000000000000000000000000000000000000 --- a/ENCSR918TVE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -535.1771850585938 0.23804223537445068 0.7039434313774109 0.3361203670501709 0.7476709485054016 0.6954758763313293 0.7018944025039673 \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_0.evaluate.json b/ENCSR920FQJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 89dd3d1448a0cc978d152fc447295c47c3852029..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875ITC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_0.fit.json b/ENCSR920FQJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 69dae62b03b360d47a7e45411ef83da0247d881d..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF875ITC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_0.log b/ENCSR920FQJ/cherimoya.fold_0.log deleted file mode 100644 index c38bd7edc9ba68f24599eb2d62c14b10e8a162d0..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2266 29.832651615142822 3.9263973236083984 282.2362060546875 1.191394329071045 407.9403381347656 0.44056612253189087 0.51702625 8.22907829284668 True -1 4532 25.45253562927246 1.5546095371246338 321.47039794921875 0.9919637441635132 351.0947570800781 0.5611931085586548 0.594444 3.528050661087036 True -2 6798 25.28289818763733 0.461148738861084 248.1167755126953 0.70118647813797 340.9571228027344 0.5842680335044861 0.5953859 1.384663701057434 True -3 9064 25.28696584701538 0.4662301540374756 292.90380859375 0.7663989663124084 337.3841247558594 0.5912736654281616 0.61427563 0.9485098123550415 True -4 11330 24.994229078292847 0.4572770595550537 231.58396911621094 0.6821423768997192 336.2550048828125 0.5939606428146362 0.626308 0.8678449392318726 True -5 13596 24.79451298713684 10.881834745407104 236.8032684326172 0.6240213513374329 335.1596374511719 0.5965079665184021 0.63031423 0.8313139081001282 True -6 15862 25.068455696105957 0.47191667556762695 225.16586303710938 0.5315353274345398 334.01519775390625 0.5990374088287354 0.6360882 0.7904422283172607 True -7 18128 24.795839309692383 0.46088314056396484 253.3678741455078 0.8095670342445374 332.8934020996094 0.6019291877746582 0.6435112 0.7315340042114258 True -8 20394 24.760653734207153 0.4765584468841553 273.1602783203125 0.45513033866882324 332.120361328125 0.6039078235626221 0.6450708 0.7290335893630981 True -9 22660 24.899450302124023 4.406312704086304 251.4617919921875 0.556708812713623 331.23992919921875 0.6060726046562195 0.6544632 0.6852421164512634 True -10 24926 24.89756727218628 0.46941184997558594 279.8001708984375 0.44545602798461914 330.1145935058594 0.6086766123771667 0.6592182 0.6354458928108215 True -11 27192 24.932905435562134 0.4740009307861328 215.33670043945312 0.6915349960327148 329.3743896484375 0.6104422211647034 0.6681101 0.584809422492981 True -12 29458 24.900163412094116 1.5149314403533936 286.7716064453125 0.507389485836029 328.5850830078125 0.6121625304222107 0.6738447 0.5700393319129944 True -13 31724 24.807976722717285 0.4649496078491211 262.6329345703125 0.44833916425704956 327.9100646972656 0.6137807965278625 0.6786868 0.5390619039535522 True -14 33990 24.7645001411438 0.4646127223968506 258.41119384765625 0.5670409798622131 327.3307800292969 0.6147712469100952 0.68481624 0.5158874988555908 True -15 36256 24.708357572555542 0.4573659896850586 255.31231689453125 0.4517059326171875 327.15228271484375 0.6154899597167969 0.6905396 0.5120667219161987 True -16 38522 25.416043281555176 26.33008599281311 254.5079803466797 0.35216599702835083 327.0123596191406 0.6154317259788513 0.69218606 0.5141597390174866 True -17 40788 24.849971055984497 0.45899057388305664 268.9203186035156 0.48709797859191895 327.28485107421875 0.61485356092453 0.6884916 0.5167087912559509 False -18 43054 24.759834051132202 0.45588183403015137 264.5999755859375 0.33365947008132935 327.4353942871094 0.6143247485160828 0.6846798 0.5314096808433533 False -19 45320 24.735085010528564 0.45389223098754883 244.99607849121094 0.21066799759864807 327.6953430175781 0.6139459609985352 0.6807506 0.5362961888313293 False diff --git a/ENCSR920FQJ/cherimoya.fold_0.performance.tsv b/ENCSR920FQJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 34cc0b64d3320d2d6cbd562fdc88727e03fa3f49..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -327.0123596191406 0.3134021759033203 0.6154317259788513 0.21323475241661072 0.6921860575675964 0.6643040180206299 0.5141597390174866 \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_1.evaluate.json b/ENCSR920FQJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5c5c4980439c1006dc50b3322ab3c850119d7399..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875ITC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_1.fit.json b/ENCSR920FQJ/cherimoya.fold_1.fit.json deleted file mode 100644 index ed2e2c1c9cea9be08c77b6c68f5f7aed54e3e008..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF875ITC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_1.log b/ENCSR920FQJ/cherimoya.fold_1.log deleted file mode 100644 index 28a2f8c5ec4113a5dc603fe98808e4ddc453c7b5..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2309 30.864943265914917 4.681278944015503 271.9388732910156 1.0561109781265259 399.6038818359375 0.4444848299026489 0.4968951 7.539964199066162 True -1 4618 25.80457830429077 0.5397443771362305 265.50640869140625 0.8109575510025024 350.0536193847656 0.5537140369415283 0.60266066 2.418149709701538 True -2 6927 25.817085027694702 0.5264503955841064 254.65496826171875 0.6317082643508911 342.5436706542969 0.5723615884780884 0.6293249 0.8982353806495667 True -3 9236 25.21569800376892 0.9317245483398438 219.50698852539062 0.8142353296279907 339.2059020996094 0.5795286893844604 0.6406617 0.7117735743522644 True -4 11545 25.653000116348267 3.2039530277252197 311.045654296875 0.5222912430763245 338.0799255371094 0.5826961994171143 0.6465054 0.6234937906265259 True -5 13854 25.292802572250366 0.5257527828216553 293.66363525390625 0.5628292560577393 336.86724853515625 0.5860251784324646 0.65151554 0.6022243499755859 True -6 16163 25.242650747299194 0.5188090801239014 311.96923828125 0.7331025004386902 335.9381408691406 0.5882894396781921 0.660369 0.6019322276115417 True -7 18472 25.201953887939453 0.5135650634765625 294.24609375 0.3821902275085449 335.3038024902344 0.5897408127784729 0.66226846 0.594131350517273 True -8 20781 25.412330865859985 35.473816871643066 244.94195556640625 0.5162003040313721 333.865234375 0.5929474830627441 0.6672075 0.546527087688446 True -9 23090 25.34042978286743 0.5200619697570801 281.4671630859375 0.46025973558425903 333.2881164550781 0.5947082042694092 0.6717911 0.5239778161048889 True -10 25399 25.246439218521118 0.5122640132904053 294.6377258300781 0.6356909871101379 332.604248046875 0.5963765978813171 0.6800439 0.5075464248657227 True -11 27708 25.223851680755615 0.5152323246002197 232.14700317382812 0.6893463134765625 331.6710510253906 0.598427414894104 0.6867926 0.48710036277770996 True -12 30017 25.224361896514893 0.513756513595581 243.14178466796875 0.6142013072967529 331.04022216796875 0.6000308394432068 0.69563913 0.4651485085487366 True -13 32326 25.23196053504944 0.5161120891571045 231.0562744140625 0.43982017040252686 330.3306579589844 0.6014484167098999 0.70064765 0.4565942883491516 True -14 34635 25.177127838134766 0.5178067684173584 240.828369140625 0.493029922246933 329.925048828125 0.6025637984275818 0.70642203 0.4436601996421814 True -15 36944 25.29073929786682 0.5188086032867432 244.21005249023438 0.37260645627975464 329.6027526855469 0.6030897498130798 0.7103785 0.4421187937259674 True -16 39253 25.657525300979614 27.170156478881836 232.67318725585938 0.4662172198295593 329.5672607421875 0.6032806634902954 0.71550065 0.4351201355457306 True -17 41562 25.261399507522583 0.5228753089904785 227.18157958984375 0.5952626466751099 329.5746154785156 0.6029233932495117 0.7158079 0.4369194507598877 True -18 43871 25.275354623794556 1.6818304061889648 259.09759521484375 0.354027658700943 329.7981872558594 0.6022419929504395 0.7133197 0.4460269510746002 False -19 46180 25.27479910850525 0.5168180465698242 246.99295043945312 0.24547448754310608 329.8670654296875 0.6019318103790283 0.7109029 0.4523795545101166 False diff --git a/ENCSR920FQJ/cherimoya.fold_1.performance.tsv b/ENCSR920FQJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2eaffc34d5760bfe19c31c34962beab12a37e6e0..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -329.5746154785156 0.3170386552810669 0.6029233932495117 0.2119257152080536 0.7158079147338867 0.7099981307983398 0.4369194507598877 \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_2.evaluate.json b/ENCSR920FQJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index af09ca09e37969ee5c017fc5ac45c5378195f6c5..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875ITC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_2.fit.json b/ENCSR920FQJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 4d51e583d46435961c6e09b4e0c3e5c1f0669dd0..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF875ITC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_2.log b/ENCSR920FQJ/cherimoya.fold_2.log deleted file mode 100644 index c89cddd481eab8c63ee5bdd0c3af97c7eab70efa..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2403 31.318538427352905 3.3951656818389893 225.5821990966797 0.762232780456543 402.9049072265625 0.44741007685661316 0.52595675 5.9954657554626465 True -1 4806 26.789853811264038 0.45334672927856445 295.70062255859375 0.7140021920204163 353.19732666015625 0.5551186800003052 0.5955172 2.3616628646850586 True -2 7209 26.926628589630127 0.4448075294494629 256.6525573730469 0.9381704926490784 342.798583984375 0.5778616666793823 0.6180488 1.0322223901748657 True -3 9612 26.79319405555725 1.2248139381408691 311.7237243652344 0.835020899772644 339.4136962890625 0.585199773311615 0.631956 0.7451092600822449 True -4 12015 26.902825593948364 0.43988776206970215 230.96200561523438 0.4859686493873596 337.7480163574219 0.5898438096046448 0.63119394 0.6755855679512024 False -5 14418 26.799027919769287 0.43589019775390625 255.22015380859375 0.6151037216186523 336.70587158203125 0.5921758413314819 0.6392022 0.632283091545105 True -6 16821 26.879754304885864 0.43706345558166504 259.95355224609375 0.6787785291671753 335.46820068359375 0.5950795412063599 0.64354974 0.6211516857147217 True -7 19224 26.479970932006836 0.4375951290130615 228.40237426757812 0.3807370662689209 334.53668212890625 0.5973536968231201 0.65007496 0.5931719541549683 True -8 21627 26.222139596939087 0.43389129638671875 257.77313232421875 0.7390545606613159 333.80224609375 0.59896320104599 0.6541894 0.581466794013977 True -9 24030 26.220475912094116 0.5476641654968262 276.621826171875 0.6363276243209839 333.1376037597656 0.6007665395736694 0.6601548 0.564827561378479 True -10 26433 26.27957057952881 0.43201255798339844 236.62368774414062 0.45834416151046753 332.1094055175781 0.6028985381126404 0.66683036 0.5334978699684143 True -11 28836 26.237687587738037 21.063539505004883 223.6937255859375 0.442105770111084 331.3669128417969 0.6048117876052856 0.6729334 0.5185846090316772 True -12 31239 27.092596530914307 3.232210397720337 240.8248748779297 0.6471623778343201 330.5721435546875 0.6065532565116882 0.6793665 0.5103898048400879 True -13 33642 26.326966047286987 0.44226551055908203 245.51947021484375 0.4125646948814392 329.8379821777344 0.6082371473312378 0.6855172 0.5019711852073669 True -14 36045 26.307615280151367 1.075988531112671 265.1275634765625 0.4871392846107483 329.3482666015625 0.6093984842300415 0.6906115 0.5048779845237732 True -15 38448 26.31849479675293 0.4441406726837158 222.89297485351562 0.46520692110061646 329.2159118652344 0.609968364238739 0.69487643 0.49933764338493347 True -16 40851 26.29617977142334 0.4392256736755371 240.14639282226562 0.2962802052497864 329.1701965332031 0.6099171042442322 0.7002745 0.4997001886367798 True -17 43254 26.251190662384033 0.431488037109375 200.66014099121094 0.39579135179519653 329.3993835449219 0.6093044877052307 0.7000689 0.5034210681915283 False -18 45657 26.277958869934082 0.43175268173217773 249.72390747070312 0.3330956697463989 329.4794921875 0.6087581515312195 0.69911087 0.5049338936805725 False -19 48060 26.287116765975952 1.4798874855041504 252.87290954589844 0.20348313450813293 329.6114501953125 0.6083635091781616 0.69700164 0.5158632397651672 False diff --git a/ENCSR920FQJ/cherimoya.fold_2.performance.tsv b/ENCSR920FQJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9c41c1cfd5fda0423f2be8f18ff595a31880492d..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -329.1701965332031 0.31509077548980713 0.609917163848877 0.21525301039218903 0.7002745270729065 0.6777059435844421 0.4997001886367798 \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_3.evaluate.json b/ENCSR920FQJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a3eb5c727fbfc7301d756394a91de5d396fe4940..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875ITC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_3.fit.json b/ENCSR920FQJ/cherimoya.fold_3.fit.json deleted file mode 100644 index f9520cfdfce3e0e73bb09efd2d18c67f6a6b992e..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF875ITC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_3.log b/ENCSR920FQJ/cherimoya.fold_3.log deleted file mode 100644 index e78d4ee4184997ea2d61d27ec0f8618eb9346e28..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2365 32.29035544395447 31.85527014732361 307.2943115234375 0.8056403398513794 410.5144348144531 0.4494079351425171 0.5050689 7.279109001159668 True -1 4730 26.602020502090454 0.5124878883361816 302.2061767578125 0.871168851852417 353.7418518066406 0.5665546655654907 0.60246027 2.4038503170013428 True -2 7095 26.36798858642578 0.48751401901245117 228.80560302734375 0.5918572545051575 345.237060546875 0.5838106870651245 0.60899365 0.9510576725006104 True -3 9460 26.36547827720642 0.4879145622253418 248.24151611328125 0.5745805501937866 342.17034912109375 0.5895698666572571 0.61809224 0.849221408367157 True -4 11825 26.40230107307434 0.49558520317077637 248.27342224121094 0.9747858643531799 340.87786865234375 0.5924444794654846 0.6275417 0.7822450995445251 True -5 14190 26.39759922027588 28.367149114608765 244.47299194335938 0.7992796897888184 339.73602294921875 0.5949169993400574 0.63504916 0.753588855266571 True -6 16555 27.41248631477356 6.52189040184021 271.93804931640625 0.5861525535583496 338.517822265625 0.5979185700416565 0.6421497 0.6987303495407104 True -7 18920 26.391299962997437 1.0310773849487305 249.29067993164062 0.5858251452445984 337.3214416503906 0.6004779934883118 0.6473645 0.6673901677131653 True -8 21285 26.4038245677948 0.49851131439208984 241.627685546875 0.6183496713638306 336.505126953125 0.602418065071106 0.6580315 0.6070276498794556 True -9 23650 26.517401218414307 0.49083614349365234 240.24075317382812 0.5606050491333008 335.6219482421875 0.6043899655342102 0.66237384 0.6128435730934143 True -10 26015 26.469725370407104 27.9761905670166 247.39219665527344 0.5259208679199219 334.8714294433594 0.6065362691879272 0.66928667 0.5918149948120117 True -11 28380 27.025784730911255 0.49616289138793945 267.7173156738281 0.566317617893219 333.7640380859375 0.607943594455719 0.6761706 0.5666765570640564 True -12 30745 26.32431387901306 0.48283815383911133 254.93087768554688 0.47048962116241455 333.02374267578125 0.6097332835197449 0.6807696 0.5428565144538879 True -13 33110 25.85423517227173 0.4898834228515625 266.98681640625 0.43148401379585266 332.270263671875 0.611473798751831 0.6867605 0.5223574638366699 True -14 35475 25.824549198150635 0.4916834831237793 247.0274658203125 0.6473209261894226 331.875 0.6124873757362366 0.6954259 0.5032805800437927 True -15 37840 25.897141695022583 1.7918477058410645 206.38888549804688 0.31220802664756775 331.2384033203125 0.6130096912384033 0.7003185 0.500514805316925 True -16 40205 26.321785926818848 30.79717183113098 237.14663696289062 0.33938366174697876 331.46136474609375 0.613050639629364 0.70328444 0.49771779775619507 True -17 42570 26.059428930282593 0.5008285045623779 248.24118041992188 0.42783594131469727 331.3748779296875 0.6128184199333191 0.70061606 0.5032627582550049 False -18 44935 25.866865158081055 0.49392223358154297 255.40304565429688 0.49423715472221375 331.5697021484375 0.6122151017189026 0.698407 0.5127437710762024 False -19 47300 25.89443850517273 0.48512744903564453 273.09619140625 0.2734503149986267 331.80047607421875 0.6118449568748474 0.69444066 0.5224557518959045 False diff --git a/ENCSR920FQJ/cherimoya.fold_3.performance.tsv b/ENCSR920FQJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d06d32c77f015efd7fc9b7bf1311dc77c28dd289..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -331.46136474609375 0.31200408935546875 0.6130506992340088 0.2154201865196228 0.7032844424247742 0.6751235723495483 0.49771779775619507 \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_4.evaluate.json b/ENCSR920FQJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 38808b6b122eacb8d07a74be6ecb2aa7e0eb4e56..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF875ITC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_4.fit.json b/ENCSR920FQJ/cherimoya.fold_4.fit.json deleted file mode 100644 index 30c596042db365b6f5d7dae0d1d7b2807311b7fc..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF875ITC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR920FQJ/cherimoya.fold_4.log b/ENCSR920FQJ/cherimoya.fold_4.log deleted file mode 100644 index e60e8c33fa392023636c3044f9bfdf164227c86b..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2436 31.812017917633057 4.398409605026245 259.8507995605469 0.8185136318206787 407.0525817871094 0.44904565811157227 0.5549153 6.972496032714844 True -1 4872 27.193725109100342 0.4926180839538574 246.74456787109375 0.821997344493866 354.5499572753906 0.5646011233329773 0.58556 2.6453890800476074 True -2 7308 27.227641820907593 2.8631138801574707 312.237548828125 0.6886489391326904 345.4900207519531 0.5846490263938904 0.61386895 1.2125407457351685 True -3 9744 27.550081729888916 22.172356605529785 255.3907470703125 0.7101985216140747 342.0921325683594 0.5908024311065674 0.62677723 0.9765284061431885 True -4 12180 27.387591123580933 0.47391438484191895 244.36618041992188 0.6032648682594299 340.2755126953125 0.5956020355224609 0.6349336 0.8577209711074829 True -5 14616 27.23522400856018 0.4907047748565674 268.74224853515625 0.6354366540908813 339.2447814941406 0.5987160801887512 0.6367799 0.8140362501144409 True -6 17052 27.279242277145386 1.1844520568847656 256.1464538574219 0.6251015663146973 338.5289306640625 0.6001620888710022 0.6413911 0.7713980674743652 True -7 19488 27.2416512966156 0.47891759872436523 263.0704345703125 0.8050720691680908 337.02166748046875 0.6033154726028442 0.6487574 0.6926764249801636 True -8 21924 27.2318217754364 0.48845696449279785 268.2113037109375 0.5485935807228088 336.2453308105469 0.6050829291343689 0.6512504 0.669844925403595 True -9 24360 27.19505500793457 0.47939562797546387 255.82057189941406 0.6954951286315918 335.3934020996094 0.6071162223815918 0.6557708 0.6320847272872925 True -10 26796 27.256644010543823 0.4688987731933594 236.98760986328125 0.4190576374530792 334.4458923339844 0.6092913746833801 0.6661329 0.5999605059623718 True -11 29232 27.203728914260864 0.4787871837615967 307.2709045410156 0.326498419046402 333.6615905761719 0.6111104488372803 0.67443895 0.5692704319953918 True -12 31668 27.31559991836548 0.4708123207092285 221.05410766601562 0.5646561980247498 332.7953796386719 0.6131289601325989 0.68156725 0.5363061428070068 True -13 34104 27.259841918945312 0.47454333305358887 278.6473083496094 0.46161895990371704 332.0715637207031 0.6147779822349548 0.6887393 0.5101849436759949 True -14 36540 27.250744819641113 0.4875202178955078 276.49530029296875 0.3541231155395508 331.5028991699219 0.6158559322357178 0.6945706 0.5065938234329224 True -15 38976 27.36587882041931 0.4809117317199707 228.55868530273438 0.4022795855998993 331.03045654296875 0.6167455911636353 0.70090175 0.4977533221244812 True -16 41412 27.352365016937256 0.48218607902526855 257.2928466796875 0.3882240355014801 331.09429931640625 0.6165226101875305 0.70252013 0.4938162863254547 True -17 43848 27.09616780281067 0.4732840061187744 287.3520812988281 0.34428954124450684 331.3437194824219 0.6159136891365051 0.7016868 0.500827968120575 False -18 46284 26.814258813858032 27.20172429084778 247.616455078125 0.29654884338378906 331.4922180175781 0.6152331829071045 0.6975558 0.5070962309837341 False -19 48720 26.77186131477356 0.4800739288330078 231.21176147460938 0.2779947817325592 331.5941467285156 0.61482834815979 0.6958154 0.5111984610557556 False diff --git a/ENCSR920FQJ/cherimoya.fold_4.performance.tsv b/ENCSR920FQJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 03287b1a261707718a704d496f1df6ca0f04eb21..0000000000000000000000000000000000000000 --- a/ENCSR920FQJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -331.09429931640625 0.3117561638355255 0.6165225505828857 0.21851032972335815 0.7025201320648193 0.6672276258468628 0.4938162863254547 \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_0.evaluate.json b/ENCSR922YEW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3278615d239d9d83a26f61751813f7268fa321d3..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988RYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_0.fit.json b/ENCSR922YEW/cherimoya.fold_0.fit.json deleted file mode 100644 index 060c02205f6846ab12a81923cab6964aa2dfa583..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF988RYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_0.log b/ENCSR922YEW/cherimoya.fold_0.log deleted file mode 100644 index bd5f49826663793e83cbbccdd3e8fc8c408e3d74..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2745 34.54019021987915 3.5162341594696045 732.3356323242188 0.3572908043861389 1034.2257080078125 0.3000693619251251 0.6429857 7.6351141929626465 True -1 5490 30.317436456680298 0.5711586475372314 765.6619873046875 0.4600437581539154 926.7546997070312 0.37611764669418335 0.7036842 2.8273961544036865 True -2 8235 30.302774906158447 2.047351121902466 871.9920654296875 0.43472471833229065 900.2839965820312 0.3924062252044678 0.73151207 1.2527036666870117 True -3 10980 30.35616898536682 0.571784257888794 885.9754028320312 0.44949424266815186 889.812255859375 0.3940429985523224 0.74510545 1.0398999452590942 True -4 13725 30.301424741744995 16.84340238571167 704.8817138671875 0.4087345600128174 888.5745849609375 0.3950451612472534 0.7424092 1.2381560802459717 False -5 16470 31.646559476852417 0.5783736705780029 851.0418090820312 0.4104412794113159 878.8666381835938 0.403263658285141 0.7606478 0.7458308339118958 True -6 19215 29.735670566558838 0.5672461986541748 800.5507202148438 0.2906685769557953 884.2660522460938 0.39653095602989197 0.74595565 0.8049616813659668 False -7 21960 29.745418787002563 0.5665936470031738 822.8323974609375 0.30536386370658875 868.4022216796875 0.41063880920410156 0.7710608 0.6613843441009521 True -8 24705 29.74440860748291 0.5544934272766113 723.8792114257812 0.23446711897850037 862.2923583984375 0.41302964091300964 0.7861566 0.5783821940422058 True -9 27450 29.709917306900024 0.5573155879974365 771.79931640625 0.25543922185897827 857.19287109375 0.41756507754325867 0.79535675 0.5850188732147217 True -10 30195 29.653515338897705 0.5512850284576416 810.1295166015625 0.34909796714782715 854.0325927734375 0.4197978675365448 0.79749566 0.5019659399986267 True -11 32940 29.695232629776 0.55076003074646 750.30615234375 0.4203462600708008 851.6614379882812 0.42069655656814575 0.80528426 0.4501672387123108 True -12 35685 29.73387312889099 1.1752636432647705 705.6875 0.2298801839351654 847.5040283203125 0.42364412546157837 0.8144093 0.4054470360279083 True -13 38430 29.804355144500732 0.5582389831542969 691.1685791015625 0.1587633490562439 845.4880981445312 0.4229394197463989 0.8201984 0.3704022467136383 True -14 41175 33.53323531150818 16.527748346328735 765.3169555664062 0.21036192774772644 842.9475708007812 0.425826758146286 0.82422286 0.3369188904762268 True -15 43920 29.66738748550415 0.5655651092529297 742.0491943359375 0.1593557447195053 838.92626953125 0.42778685688972473 0.8296419 0.3080836534500122 True -16 46665 29.750792026519775 0.5494599342346191 808.51513671875 0.15386083722114563 838.2803955078125 0.428429514169693 0.8333272 0.29308000206947327 True -17 49410 29.748115301132202 0.5602703094482422 644.1016845703125 0.15980017185211182 837.8426513671875 0.4287879467010498 0.83323365 0.28527674078941345 False -18 52155 29.734419584274292 0.6241824626922607 693.770263671875 0.24776697158813477 837.8131713867188 0.42893698811531067 0.8323368 0.282694935798645 False -19 54900 29.663464546203613 1.9496212005615234 725.924072265625 0.33670204877853394 839.6268920898438 0.42649608850479126 0.834006 0.2824864685535431 True diff --git a/ENCSR922YEW/cherimoya.fold_0.performance.tsv b/ENCSR922YEW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7f794959624712548f91dc06f37632ef57e7a3c3..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -839.6268920898438 0.3463408052921295 0.42649611830711365 0.19889187812805176 0.8340060114860535 0.8013381361961365 0.2824864685535431 \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_1.evaluate.json b/ENCSR922YEW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6dcbd53c1321aca1fef6d003d525fe7828565235..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988RYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_1.fit.json b/ENCSR922YEW/cherimoya.fold_1.fit.json deleted file mode 100644 index 6475af8736ab8865216f92b720fe31574909a7ad..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF988RYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_1.log b/ENCSR922YEW/cherimoya.fold_1.log deleted file mode 100644 index 2a0f3fb132f1ca44908680844751b91607b5da98..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 34.79436731338501 3.599036693572998 666.2869262695312 0.4976293444633484 1219.150390625 0.30234387516975403 0.67290634 8.138551712036133 True -1 5468 30.21277093887329 0.6817834377288818 667.8704833984375 0.37342873215675354 1070.3990478515625 0.39569923281669617 0.7452182 3.169381856918335 True -2 8202 30.15449357032776 30.247450351715088 948.7225952148438 0.5361342430114746 1045.225830078125 0.41025054454803467 0.76565534 1.4362220764160156 True -3 10936 30.832157611846924 0.6674118041992188 911.3961181640625 0.5839928388595581 1028.230224609375 0.41902732849121094 0.7746962 1.1417585611343384 True -4 13670 30.67951798439026 35.63640999794006 755.2701416015625 0.470133900642395 1020.6985473632812 0.4223279058933258 0.78276813 0.9770646691322327 True -5 16404 30.227468967437744 0.6667044162750244 627.50732421875 0.40137505531311035 1015.1051025390625 0.4250776469707489 0.78798175 0.9874710440635681 True -6 19138 29.669641494750977 0.7518651485443115 740.1063232421875 0.31298989057540894 1012.0599365234375 0.42651844024658203 0.79078335 0.8263911008834839 True -7 21872 29.599812746047974 2.6427173614501953 771.876708984375 0.2604163885116577 1008.0451049804688 0.4294137954711914 0.7964361 0.7723661065101624 True -8 24606 29.564254760742188 5.40269923210144 837.2098999023438 0.3198382556438446 998.375 0.4362664222717285 0.803046 0.7345553040504456 True -9 27340 29.70157027244568 0.6657688617706299 648.2672119140625 0.23187896609306335 991.4658813476562 0.43962720036506653 0.81085384 0.6414273381233215 True -10 30074 29.667299270629883 0.6498138904571533 722.8114013671875 0.3286193609237671 987.1845092773438 0.4406357407569885 0.8178937 0.5869324803352356 True -11 32808 29.64723253250122 0.6612722873687744 672.6014404296875 0.2921493649482727 980.9345703125 0.4450294077396393 0.82481396 0.5416046977043152 True -12 35542 29.589648962020874 0.6516814231872559 726.2570190429688 0.33962517976760864 975.4841918945312 0.44791656732559204 0.8328754 0.4606465995311737 True -13 38276 29.636181831359863 0.6609663963317871 740.8248901367188 0.20510517060756683 967.6481323242188 0.45225369930267334 0.8404453 0.40814200043678284 True -14 41010 29.59632134437561 0.6524319648742676 632.37939453125 0.31264424324035645 964.1482543945312 0.45322003960609436 0.8492761 0.3644757866859436 True -15 43744 29.550780057907104 0.6607539653778076 671.8131713867188 0.15452143549919128 963.8388671875 0.4519699215888977 0.8523604 0.3267315626144409 True -16 46478 29.545518398284912 0.6587212085723877 657.1828002929688 0.2549326717853546 960.2891845703125 0.45458006858825684 0.85747945 0.30136412382125854 True -17 49212 29.53144407272339 0.6609501838684082 720.15380859375 0.23032225668430328 959.6583251953125 0.45519593358039856 0.8574789 0.2857667803764343 False -18 51946 29.60229992866516 0.6584358215332031 648.000244140625 0.26140040159225464 958.7267456054688 0.4558945894241333 0.85762143 0.27954867482185364 True -19 54680 29.595457315444946 0.6577446460723877 592.5654907226562 0.20882342755794525 958.4754638671875 0.45678508281707764 0.85862213 0.27944281697273254 True diff --git a/ENCSR922YEW/cherimoya.fold_1.performance.tsv b/ENCSR922YEW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f70fe80793c54a98621bd819fa01410b5979e29d..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -958.4754638671875 0.3243015706539154 0.45678505301475525 0.2252061367034912 0.858622133731842 0.8354713916778564 0.27944281697273254 \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_2.evaluate.json b/ENCSR922YEW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bc1431889601b59c47fcea2b704842b3302bfd87..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988RYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_2.fit.json b/ENCSR922YEW/cherimoya.fold_2.fit.json deleted file mode 100644 index b70bf37b74c8e94444e55004631a9b3b81f4c9cd..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF988RYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_2.log b/ENCSR922YEW/cherimoya.fold_2.log deleted file mode 100644 index 01e60de94638d24ac52885892c698b9d2809c0f6..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 38.128018617630005 3.6523349285125732 816.71533203125 0.396897554397583 1101.289794921875 0.30456194281578064 0.64380574 7.9795708656311035 True -1 5782 32.03538727760315 0.5900814533233643 749.8349609375 0.3604048490524292 984.8158569335938 0.38106974959373474 0.7101012 2.117553472518921 True -2 8673 32.02002477645874 0.5779135227203369 769.060302734375 0.33947885036468506 961.2080078125 0.3954779803752899 0.7288779 1.343094825744629 True -3 11564 31.892615795135498 0.6148653030395508 847.6719970703125 0.34408944845199585 944.114990234375 0.4050094485282898 0.74498516 1.0253630876541138 True -4 14455 31.967906713485718 0.5715405941009521 610.4071044921875 0.2854663133621216 949.4593505859375 0.40133124589920044 0.73595285 1.1805462837219238 False -5 17346 31.921634197235107 0.559542179107666 684.7008666992188 0.27738040685653687 938.0064086914062 0.4092276990413666 0.7539826 0.8604245781898499 True -6 20237 35.92565178871155 0.5669314861297607 762.9371948242188 0.3850705623626709 942.2578735351562 0.40642184019088745 0.7419661 0.9585660099983215 False -7 23128 31.718445539474487 0.5646352767944336 745.796875 0.2722075283527374 929.386474609375 0.4133266806602478 0.76249194 0.802237868309021 True -8 26019 31.340086698532104 0.5622138977050781 793.4149169921875 0.35726916790008545 921.1526489257812 0.41858115792274475 0.7744369 0.7098315358161926 True -9 28910 31.588334321975708 28.784796953201294 679.4622802734375 0.23451822996139526 918.4502563476562 0.419859915971756 0.7819803 0.6694169640541077 True -10 31801 31.261273622512817 0.5722627639770508 845.5861206054688 0.2853311002254486 911.8211059570312 0.4240633547306061 0.78784853 0.6222276091575623 True -11 34692 31.65999984741211 1.2829735279083252 664.2199096679688 0.23944933712482452 907.4812622070312 0.42639896273612976 0.7955625 0.5662813782691956 True -12 37583 31.266681909561157 0.5542130470275879 657.537109375 0.28973454236984253 903.1539306640625 0.4292644262313843 0.80618167 0.49720343947410583 True -13 40474 32.21870231628418 27.493407249450684 730.6605224609375 0.16526423394680023 898.4979858398438 0.43134605884552 0.81354046 0.4357145130634308 True -14 43365 33.636054277420044 0.6079537868499756 610.525634765625 0.21367023885250092 893.3167114257812 0.4345616102218628 0.8229432 0.3767538368701935 True -15 46256 31.264415502548218 1.239353895187378 808.7701416015625 0.4341350197792053 890.1356201171875 0.43699881434440613 0.8287943 0.33836641907691956 True -16 49147 31.29891347885132 0.5617473125457764 716.8416748046875 0.2428268939256668 890.5284423828125 0.4346863925457001 0.8327466 0.316338449716568 True -17 52038 31.275491952896118 0.5613701343536377 747.421142578125 0.27717092633247375 886.8621826171875 0.4371553063392639 0.8340456 0.30189844965934753 True -18 54929 31.32579731941223 0.5612099170684814 765.8502197265625 0.2234550416469574 889.4127197265625 0.43545159697532654 0.8348074 0.29804399609565735 True -19 57820 31.341918230056763 0.5512876510620117 770.4354248046875 0.19054390490055084 889.6382446289062 0.4355567991733551 0.8337163 0.2973593771457672 False diff --git a/ENCSR922YEW/cherimoya.fold_2.performance.tsv b/ENCSR922YEW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1fe5a2d754ab3619fdbd26e071772eeb38140bc2..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -889.4127197265625 0.33843427896499634 0.43545159697532654 0.20576529204845428 0.8348073959350586 0.8092610239982605 0.29804399609565735 \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_3.evaluate.json b/ENCSR922YEW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cce14dba53a9a31820751a15d1bfa8900cf1c4ba..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988RYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_3.fit.json b/ENCSR922YEW/cherimoya.fold_3.fit.json deleted file mode 100644 index 973cbe7b2fa06783051054a948b0e488914715f4..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF988RYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_3.log b/ENCSR922YEW/cherimoya.fold_3.log deleted file mode 100644 index 639ceb9d4ce4bdd52c56a6592b775f139f2a8f31..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2761 35.15581822395325 36.83576273918152 741.0095825195312 0.4470992088317871 1006.266845703125 0.3100808262825012 0.62874 7.824871063232422 True -1 5522 30.573650121688843 0.5853276252746582 707.261474609375 0.3947678804397583 899.4699096679688 0.3831644654273987 0.7097979 2.9310901165008545 True -2 8283 30.559483766555786 0.611879825592041 827.57275390625 0.4543016254901886 884.250244140625 0.3933054506778717 0.73037535 1.621427297592163 True -3 11044 30.5238778591156 0.5779280662536621 768.08154296875 0.30803540349006653 869.6270141601562 0.40296271443367004 0.74495256 1.2921161651611328 True -4 13805 30.4850652217865 0.5813844203948975 667.892333984375 0.3955097496509552 866.7560424804688 0.4060678482055664 0.7386519 1.1072901487350464 False -5 16566 30.53453755378723 0.571805477142334 674.8553466796875 0.2877148687839508 865.5121459960938 0.40672287344932556 0.73723966 0.9113898873329163 False -6 19327 30.569636583328247 0.5751349925994873 796.1961669921875 0.4147838354110718 855.8886108398438 0.41191935539245605 0.753315 0.8863310813903809 True -7 22088 30.71975612640381 0.5851380825042725 712.8125 0.3908883035182953 851.0214233398438 0.41414496302604675 0.7660784 0.7585556507110596 True -8 24849 30.60412049293518 0.5719645023345947 789.006591796875 0.34632712602615356 847.8980712890625 0.41634252667427063 0.7669991 0.7986143231391907 True -9 27610 30.487720489501953 0.5621838569641113 675.1571044921875 0.353982537984848 840.9097900390625 0.421738862991333 0.77868956 0.7352001667022705 True -10 30371 30.46657085418701 0.5623023509979248 729.1529541015625 0.3251710534095764 838.7874145507812 0.42144739627838135 0.7865424 0.6301280856132507 True -11 33132 31.470755577087402 0.561241865158081 705.9764404296875 0.35149335861206055 832.2626342773438 0.4275793135166168 0.7961958 0.5662717819213867 True -12 35893 30.85364580154419 26.751522541046143 861.83935546875 0.4582700729370117 829.3970947265625 0.4288623631000519 0.8041347 0.4913818836212158 True -13 38654 30.576054573059082 28.20309591293335 773.1204833984375 0.47312018275260925 828.0922241210938 0.4283877909183502 0.8113151 0.44598788022994995 True -14 41415 30.552968502044678 0.5688104629516602 615.6256103515625 0.232931986451149 822.5867919921875 0.43410587310791016 0.81972814 0.38948413729667664 True -15 44176 30.657601833343506 2.4587574005126953 637.5307006835938 0.19888055324554443 821.9920043945312 0.4333497881889343 0.82451075 0.35026389360427856 True -16 46937 30.60140633583069 0.5637836456298828 700.6586303710938 0.22474656999111176 817.5952758789062 0.43654921650886536 0.8308097 0.3141086995601654 True -17 49698 30.615739583969116 0.5723059177398682 665.7129516601562 0.2219795286655426 818.0648803710938 0.4358261227607727 0.831639 0.29618600010871887 True -18 52459 30.206254959106445 0.5659451484680176 697.9801635742188 0.24100205302238464 818.9982299804688 0.43504205346107483 0.8320037 0.2897772490978241 True -19 55220 30.495856046676636 0.5870568752288818 665.1309814453125 0.21673184633255005 819.4769287109375 0.435101717710495 0.83099884 0.28994253277778625 False diff --git a/ENCSR922YEW/cherimoya.fold_3.performance.tsv b/ENCSR922YEW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8eb68beeeea97e5cb720059ea86f21d788a63f7c..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -818.9982299804688 0.34253543615341187 0.43504205346107483 0.20180568099021912 0.8320037126541138 0.7959057092666626 0.2897772490978241 \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_4.evaluate.json b/ENCSR922YEW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b59592d236d9f1872f665c3b8b07cab5ec6d53a8..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF988RYR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_4.fit.json b/ENCSR922YEW/cherimoya.fold_4.fit.json deleted file mode 100644 index cd3cc932b1ac692e8148cc74f8cc499063f2a150..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF988RYR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR922YEW/cherimoya.fold_4.log b/ENCSR922YEW/cherimoya.fold_4.log deleted file mode 100644 index fc3573d2b192914ffb7ff7e96934241e3aea2563..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 35.41765069961548 3.521024465560913 882.32568359375 0.5638349056243896 983.7085571289062 0.29832401871681213 0.6401967 7.715948104858398 True -1 5554 30.70799493789673 0.5866968631744385 749.4769897460938 0.45655500888824463 878.6419067382812 0.3707965016365051 0.7187008 2.1115686893463135 True -2 8331 30.68280839920044 2.676607131958008 717.860595703125 0.37381798028945923 863.4500732421875 0.38215193152427673 0.7360966 1.1082347631454468 True -3 11108 30.698491096496582 0.5668339729309082 742.3297119140625 0.424385666847229 851.040771484375 0.3889956474304199 0.74857396 0.914359986782074 True -4 13885 30.694556951522827 0.5703125 773.8662719726562 0.354480504989624 844.04150390625 0.39252087473869324 0.7618558 0.973056972026825 True -5 16662 31.331607818603516 30.50697922706604 750.2139282226562 0.356160044670105 838.2439575195312 0.3967595100402832 0.7692507 0.7293499112129211 True -6 19439 31.346394062042236 0.6985962390899658 780.19189453125 0.3513883054256439 834.6815795898438 0.3983832895755768 0.7742505 0.6317551732063293 True -7 22216 30.63941192626953 0.8475232124328613 749.3408203125 0.3584918975830078 831.8623046875 0.4016217291355133 0.77918345 0.5988430976867676 True -8 24993 30.619530200958252 6.38630485534668 777.895751953125 0.3025209307670593 828.7095947265625 0.4029236137866974 0.7890836 0.5090967416763306 True -9 27770 31.512137174606323 10.466098070144653 951.2169799804688 0.4216025471687317 826.5952758789062 0.4044695198535919 0.7957571 0.47751709818840027 True -10 30547 30.69427752494812 3.2310075759887695 686.5703125 0.3535870909690857 823.1967163085938 0.4071708917617798 0.8018052 0.437858909368515 True -11 33324 30.652329921722412 0.5781798362731934 739.1373291015625 0.2794240117073059 820.5416259765625 0.4088820815086365 0.80692685 0.3938540816307068 True -12 36101 30.670350790023804 0.5791420936584473 657.7445068359375 0.36264610290527344 817.1790771484375 0.4102274477481842 0.8146355 0.356141060590744 True -13 38878 30.6321439743042 30.745527982711792 755.150390625 0.28406602144241333 812.0775756835938 0.41461509466171265 0.8212371 0.3251144587993622 True -14 41655 31.07854413986206 0.5851638317108154 596.2528686523438 0.2939665913581848 810.077880859375 0.41641658544540405 0.8256578 0.30361658334732056 True -15 44432 31.426090240478516 9.594287395477295 641.8026123046875 0.16913922131061554 809.9566650390625 0.4152614176273346 0.83189297 0.28016987442970276 True -16 47209 30.769152879714966 0.5834226608276367 757.1796875 0.23098048567771912 808.5883178710938 0.41613203287124634 0.8351836 0.2698115408420563 True -17 49986 30.703656435012817 0.5851621627807617 695.4681396484375 0.1890059858560562 807.4756469726562 0.41792991757392883 0.8373363 0.2634256184101105 True -18 52763 30.667816877365112 0.5749895572662354 710.11767578125 0.20177529752254486 808.1250610351562 0.4166260063648224 0.8369025 0.26238325238227844 False -19 55540 30.037808179855347 0.5562784671783447 776.2327880859375 0.24865387380123138 808.3508911132812 0.41716259717941284 0.8357763 0.2629006505012512 False diff --git a/ENCSR922YEW/cherimoya.fold_4.performance.tsv b/ENCSR922YEW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 872f147a37b4554c94fbf5ed618dff4292c9ca5b..0000000000000000000000000000000000000000 --- a/ENCSR922YEW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -807.4756469726562 0.3518673777580261 0.41792988777160645 0.19135530292987823 0.8373363018035889 0.7920064926147461 0.2634256184101105 \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_0.evaluate.json b/ENCSR923JYH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 46c225c42bf2a9dfba3e5e5a4bd42b1c6e90a459..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570NES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_0.fit.json b/ENCSR923JYH/cherimoya.fold_0.fit.json deleted file mode 100644 index b8effbf8468320dbc27fa3477c96e92a3019b6c1..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF570NES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_0.log b/ENCSR923JYH/cherimoya.fold_0.log deleted file mode 100644 index 8f0ce5ea1d2540c21f5cf989919ba6fb0b51d676..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2725 34.57635021209717 4.385301828384399 512.5227661132812 0.3808550238609314 640.0486450195312 0.24887503683567047 0.66233104 3.9343225955963135 True -1 5450 30.03770875930786 12.51190972328186 511.6484375 0.4111042618751526 599.3443603515625 0.30101069808006287 0.71630245 1.385886549949646 True -2 8175 30.52390718460083 0.7581214904785156 516.2117919921875 0.45217669010162354 586.7042236328125 0.3160216510295868 0.73407054 1.34244704246521 True -3 10900 29.51511836051941 0.63942551612854 498.7315673828125 0.4436047077178955 580.4476318359375 0.32236766815185547 0.7450528 0.5891868472099304 True -4 13625 29.491965770721436 0.8980343341827393 520.93408203125 0.3316632807254791 578.301025390625 0.32379746437072754 0.7519452 0.5551357269287109 True -5 16350 29.4686861038208 1.7338635921478271 547.695068359375 0.3997442126274109 576.0576171875 0.3281380236148834 0.75594777 0.5576189756393433 True -6 19075 29.46818995475769 0.6397535800933838 472.2845458984375 0.273663729429245 572.9140014648438 0.33239099383354187 0.7638215 0.5771742463111877 True -7 21800 29.481667518615723 0.6295092105865479 503.1882629394531 0.3645150661468506 570.7054443359375 0.3343014717102051 0.7704756 0.5393069386482239 True -8 24525 29.42968463897705 0.5880436897277832 454.047119140625 0.3567749261856079 569.4024047851562 0.33565154671669006 0.7763181 0.5228800773620605 True -9 27250 29.45551300048828 0.604362964630127 532.4788818359375 0.37638604640960693 568.6538696289062 0.33565187454223633 0.78216153 0.4900628626346588 True -10 29975 29.444667100906372 0.6039423942565918 530.013916015625 0.30276429653167725 566.6232299804688 0.3387371003627777 0.7893742 0.4278672933578491 True -11 32700 29.51636791229248 1.2175066471099854 464.29541015625 0.19993597269058228 565.0805053710938 0.3399849832057953 0.79520714 0.4029091000556946 True -12 35425 29.513460397720337 0.603632926940918 538.5888671875 0.32242441177368164 563.72412109375 0.3422347903251648 0.8000924 0.36537057161331177 True -13 38150 29.5421884059906 0.6075465679168701 526.1085205078125 0.3204357922077179 562.8976440429688 0.34352701902389526 0.8075601 0.31965145468711853 True -14 40875 29.48087787628174 0.621265172958374 558.496337890625 0.33002758026123047 561.5128784179688 0.34507521986961365 0.81231946 0.2779160439968109 True -15 43600 29.478405237197876 0.6005840301513672 504.6945495605469 0.19412186741828918 561.2512817382812 0.3447919189929962 0.8162966 0.25318455696105957 True -16 46325 29.470653533935547 0.5703957080841064 524.7205810546875 0.26255297660827637 559.9007568359375 0.34716325998306274 0.8200428 0.23432716727256775 True -17 49050 29.481752395629883 0.5706884860992432 486.7109069824219 0.18644586205482483 559.9788818359375 0.3466806709766388 0.8190374 0.2288064956665039 False -18 51775 29.48853635787964 1.3107237815856934 544.7565307617188 0.24924395978450775 559.7616577148438 0.34788766503334045 0.81687313 0.22770148515701294 False -19 54500 29.474371910095215 0.6201198101043701 465.28570556640625 0.19722780585289001 559.953369140625 0.3471792936325073 0.81638294 0.22826676070690155 False diff --git a/ENCSR923JYH/cherimoya.fold_0.performance.tsv b/ENCSR923JYH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 419a31a1f58fb81b115718be354e9864182e83b9..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -559.9007568359375 0.42598626017570496 0.34716325998306274 0.12591694295406342 0.8200427889823914 0.7861456871032715 0.23432716727256775 \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_1.evaluate.json b/ENCSR923JYH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4d4c4b9e373e488df73233022fa97691ca8be138..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570NES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_1.fit.json b/ENCSR923JYH/cherimoya.fold_1.fit.json deleted file mode 100644 index 9060bdc3f26fccad47b9632b44a632e4a91b2dc4..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF570NES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_1.log b/ENCSR923JYH/cherimoya.fold_1.log deleted file mode 100644 index 8d7fe11c2a6e6e17f88120bfd8cee38d882f2596..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2695 34.6883487701416 4.722239255905151 563.1546020507812 0.4804416298866272 751.2022094726562 0.25279420614242554 0.66542894 4.6138224601745605 True -1 5390 29.73473811149597 0.7616746425628662 443.69537353515625 0.26682573556900024 689.6824951171875 0.32319751381874084 0.73001844 1.4788753986358643 True -2 8085 29.695483922958374 0.7069158554077148 504.2730712890625 0.3215380609035492 675.42333984375 0.3391720950603485 0.7433346 0.8938105702400208 True -3 10780 29.70323348045349 0.7114622592926025 491.208740234375 0.2820114493370056 667.7596435546875 0.3456074595451355 0.75389284 0.8259558081626892 True -4 13475 29.75675940513611 0.7095086574554443 556.1124267578125 0.31139862537384033 665.396484375 0.34881463646888733 0.7573768 0.5668654441833496 True -5 16170 29.68099045753479 0.7104239463806152 478.68511962890625 0.4061813950538635 663.837646484375 0.3489745259284973 0.76481044 0.5622826814651489 True -6 18865 29.681368589401245 0.7102916240692139 487.0279541015625 0.35731080174446106 661.572021484375 0.35085242986679077 0.7718795 0.5255783200263977 True -7 21560 29.682090282440186 0.7744197845458984 583.7432250976562 0.5631468892097473 657.2844848632812 0.3569524884223938 0.7791987 0.469176322221756 True -8 24255 29.69979453086853 30.67289423942566 489.1783447265625 0.30866318941116333 653.9219360351562 0.3604038655757904 0.7868102 0.4543808698654175 True -9 26950 29.68799638748169 0.7454040050506592 469.88909912109375 0.3363039791584015 653.1163940429688 0.3602529764175415 0.7924403 0.4202902019023895 True -10 29645 29.48787784576416 0.7188849449157715 504.8865661621094 0.2483845055103302 650.802734375 0.36348697543144226 0.7975734 0.4001130163669586 True -11 32340 29.08543300628662 0.726412296295166 550.403564453125 0.28660300374031067 649.5476684570312 0.364146888256073 0.80240977 0.3734361529350281 True -12 35035 29.104732990264893 0.7187826633453369 457.8133544921875 0.1644950658082962 646.6658325195312 0.36917123198509216 0.80792516 0.3509756028652191 True -13 37730 29.07451581954956 0.7155907154083252 430.460693359375 0.1725049614906311 646.1032104492188 0.36824071407318115 0.8151917 0.32344773411750793 True -14 40425 29.173998594284058 0.7319996356964111 453.3929443359375 0.3095371127128601 643.116455078125 0.37305155396461487 0.82132566 0.3069250285625458 True -15 43120 29.211957454681396 0.7407689094543457 477.46295166015625 0.22214685380458832 641.1851806640625 0.3760244846343994 0.827646 0.281505823135376 True -16 45815 29.27215003967285 0.7172677516937256 486.47406005859375 0.2216625064611435 641.4094848632812 0.3747151792049408 0.8291155 0.26731806993484497 True -17 48510 29.35697078704834 0.7499692440032959 545.2723388671875 0.21009191870689392 641.8486328125 0.3740469813346863 0.83239025 0.25489696860313416 True -18 51205 29.209697723388672 0.7443592548370361 501.7169494628906 0.22360558807849884 641.6190795898438 0.3744919002056122 0.83192337 0.2517484128475189 False -19 53900 29.248891353607178 0.7342815399169922 457.887451171875 0.18552395701408386 641.64306640625 0.3746092617511749 0.8302455 0.2508929967880249 False diff --git a/ENCSR923JYH/cherimoya.fold_1.performance.tsv b/ENCSR923JYH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 26bb6fa22d6ee7e572e0fe9eb5e4868bef386e04..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -641.8486328125 0.40407639741897583 0.3740469515323639 0.14807632565498352 0.8323902487754822 0.8156591057777405 0.25489696860313416 \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_2.evaluate.json b/ENCSR923JYH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 699b091179afc0cf675d414e951c52657623bc3d..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570NES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_2.fit.json b/ENCSR923JYH/cherimoya.fold_2.fit.json deleted file mode 100644 index c6cad76c7d6e41ca3a40fa575169289514687120..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF570NES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_2.log b/ENCSR923JYH/cherimoya.fold_2.log deleted file mode 100644 index 2e207012959a69e3af8599b70d8823c749b3fc3a..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2875 36.257710218429565 3.8566887378692627 555.432861328125 0.3937034010887146 669.4050903320312 0.2496410459280014 0.6632061 3.8023810386657715 True -1 5750 31.7345769405365 0.5967288017272949 604.7230834960938 0.41851717233657837 619.6980590820312 0.31206822395324707 0.72686094 1.4333696365356445 True -2 8625 31.73753046989441 0.5671510696411133 497.8098449707031 0.3397611379623413 610.8583374023438 0.32057735323905945 0.73842627 0.7466363310813904 True -3 11500 31.736058950424194 0.564749002456665 600.8711547851562 0.3364418148994446 604.0105590820312 0.3282865881919861 0.75403875 0.5902349352836609 True -4 14375 31.756537199020386 0.5504016876220703 534.7701416015625 0.38606613874435425 601.9572143554688 0.32952383160591125 0.7588577 0.4600640535354614 True -5 17250 31.753421306610107 0.5629284381866455 453.31390380859375 0.31256115436553955 600.1257934570312 0.3313271403312683 0.7639964 0.4505704939365387 True -6 20125 31.720057249069214 2.318753719329834 521.9976196289062 0.392598032951355 598.2569580078125 0.33396828174591064 0.76942575 0.4664755165576935 True -7 23000 31.758963346481323 0.586540699005127 488.7283020019531 0.35697221755981445 597.953125 0.3352341651916504 0.7709579 0.5287116765975952 True -8 25875 31.74700617790222 0.6661756038665771 459.959228515625 0.3162137567996979 593.8075561523438 0.3399769067764282 0.7795394 0.4172970652580261 True -9 28750 31.766225337982178 0.6034996509552002 506.2220764160156 0.32410162687301636 592.780029296875 0.34044981002807617 0.78735 0.38097360730171204 True -10 31625 31.74417805671692 0.5600070953369141 443.45367431640625 0.21445520222187042 589.66796875 0.3452155590057373 0.79447305 0.383333683013916 True -11 34500 31.782812356948853 0.5645432472229004 474.8265075683594 0.2653566598892212 589.0941772460938 0.345573753118515 0.79787236 0.3616150915622711 True -12 37375 31.81318974494934 0.560478687286377 442.63665771484375 0.31111738085746765 587.425537109375 0.34802380204200745 0.8039946 0.33408352732658386 True -13 40250 31.774850606918335 0.5660955905914307 421.6218566894531 0.23626071214675903 586.0989379882812 0.34902700781822205 0.80886275 0.3093591630458832 True -14 43125 31.799561500549316 0.567296028137207 472.9560546875 0.2257090061903 584.98046875 0.35045039653778076 0.81377304 0.28528186678886414 True -15 46000 31.846015214920044 0.5746772289276123 548.251708984375 0.25562578439712524 584.7041625976562 0.3512723743915558 0.8184858 0.2582952380180359 True -16 48875 31.60106062889099 0.5581319332122803 474.7303466796875 0.2579776644706726 583.5213012695312 0.35233715176582336 0.8224275 0.24148674309253693 True -17 51750 31.080352544784546 0.5591757297515869 537.2685546875 0.26434946060180664 584.2832641601562 0.3503488302230835 0.8225164 0.235434427857399 True -18 54625 31.075469493865967 0.5540544986724854 602.7213134765625 0.2534843683242798 583.4607543945312 0.3522806763648987 0.82298315 0.2337425947189331 True -19 57500 31.064982414245605 18.04441738128662 495.410888671875 0.190436452627182 583.50634765625 0.35225507616996765 0.8232142 0.2344513088464737 True diff --git a/ENCSR923JYH/cherimoya.fold_2.performance.tsv b/ENCSR923JYH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4917c5f554e3dc593ed92333e1f265d412f4e5be..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -583.50634765625 0.4206794202327728 0.35225507616996765 0.13289852440357208 0.8232141733169556 0.7997347116470337 0.2344513088464737 \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_3.evaluate.json b/ENCSR923JYH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 800191e0090b5975fa4e188cfdf1fb81a5f31f62..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570NES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_3.fit.json b/ENCSR923JYH/cherimoya.fold_3.fit.json deleted file mode 100644 index 3ef6d1779c85cc8c07be173cfe93a69238b21237..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF570NES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_3.log b/ENCSR923JYH/cherimoya.fold_3.log deleted file mode 100644 index e4e19814fac8804b56e84a12343615968b538d82..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.84717869758606 4.127164125442505 555.91064453125 0.4163306653499603 643.1170043945312 0.24992014467716217 0.64750075 3.926464319229126 True -1 5498 30.95623469352722 0.6160142421722412 514.4707641601562 0.4433532655239105 593.408447265625 0.313597708940506 0.7261357 1.2939095497131348 True -2 8247 30.293691396713257 0.5829102993011475 486.9130859375 0.31128475069999695 581.9913330078125 0.32655391097068787 0.7385458 1.0938454866409302 True -3 10996 30.342857599258423 0.5712382793426514 520.637939453125 0.494293749332428 579.2610473632812 0.3286263048648834 0.7478365 0.708533525466919 True -4 13745 30.292258262634277 0.5752320289611816 522.304931640625 0.5238635540008545 576.6799926757812 0.33203738927841187 0.7495733 0.7134791612625122 True -5 16494 30.30697536468506 0.5794801712036133 478.2851257324219 0.5053614377975464 574.2147216796875 0.3351410925388336 0.7552099 0.6399418115615845 True -6 19243 30.271523475646973 0.57615065574646 507.97705078125 0.3603283762931824 571.4063110351562 0.33903607726097107 0.76168287 0.6289321780204773 True -7 21992 30.306573390960693 0.5795621871948242 464.68438720703125 0.43573158979415894 570.734130859375 0.33847421407699585 0.76692486 0.5957583785057068 True -8 24741 30.293779373168945 0.5809805393218994 576.4828491210938 0.4039776623249054 568.5042724609375 0.3418450653553009 0.770857 0.5641703605651855 True -9 27490 30.32726263999939 0.5707111358642578 501.1630554199219 0.2855297327041626 566.7946166992188 0.34362056851387024 0.7790083 0.5127530694007874 True -10 30239 30.321352243423462 0.5793423652648926 441.9411926269531 0.311804860830307 564.9305419921875 0.3464343845844269 0.78481996 0.4812130928039551 True -11 32988 30.34870481491089 0.602480411529541 569.8529052734375 0.3981139659881592 564.1215209960938 0.3464410901069641 0.78759176 0.4514198303222656 True -12 35737 30.353010416030884 0.597759485244751 490.338134765625 0.2944266200065613 562.1856079101562 0.34862279891967773 0.794422 0.3948169946670532 True -13 38486 30.333924293518066 0.5806283950805664 618.6646728515625 0.21733170747756958 559.9996337890625 0.3518046736717224 0.8022198 0.345305860042572 True -14 41235 30.269936084747314 0.5798790454864502 530.2186279296875 0.2837947905063629 559.5673828125 0.35189390182495117 0.80815846 0.30981045961380005 True -15 43984 30.282795429229736 0.58119797706604 555.9615478515625 0.24111972749233246 557.4118041992188 0.35524988174438477 0.81267184 0.28602316975593567 True -16 46733 30.290729761123657 1.2876191139221191 534.3218994140625 0.220161572098732 557.7435913085938 0.35367193818092346 0.8158788 0.2650376558303833 True -17 49482 30.368079662322998 7.78336238861084 472.49029541015625 0.15191173553466797 557.401123046875 0.3541564643383026 0.8173651 0.2514767348766327 True -18 52231 30.361238956451416 11.285603761672974 492.354248046875 0.23333275318145752 557.049072265625 0.3555719554424286 0.8167544 0.2463359385728836 False -19 54980 30.502641677856445 0.5946431159973145 473.511474609375 0.2163049727678299 557.083984375 0.35551249980926514 0.81692994 0.24649685621261597 False diff --git a/ENCSR923JYH/cherimoya.fold_3.performance.tsv b/ENCSR923JYH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 766ad115f9e73bd27b93b6190d2bbf751457ba53..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -557.401123046875 0.4224679172039032 0.3541564345359802 0.12992531061172485 0.8173651099205017 0.7773633003234863 0.2514767348766327 \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_4.evaluate.json b/ENCSR923JYH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 26217bdb226717f2261a965a9e2dc2d1491d63f5..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570NES.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_4.fit.json b/ENCSR923JYH/cherimoya.fold_4.fit.json deleted file mode 100644 index 97fc9e0d9fd9ffc3f5f1771fdd550a7c7cacda1e..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF570NES.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR923JYH/cherimoya.fold_4.log b/ENCSR923JYH/cherimoya.fold_4.log deleted file mode 100644 index 0c66d15bf0489319cc814ae410330a01fdd2f662..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2847 35.909287214279175 4.855386972427368 509.4375915527344 0.41716042160987854 614.9296875 0.24815073609352112 0.6350434 3.1565773487091064 True -1 5694 30.85563015937805 0.6672329902648926 484.7830810546875 0.24355238676071167 576.8488159179688 0.3008878529071808 0.69582486 1.0495598316192627 True -2 8541 31.4407696723938 0.6001913547515869 439.5189514160156 0.2775725722312927 566.19677734375 0.3169894516468048 0.7135463 0.5814279317855835 True -3 11388 31.448026418685913 0.5964865684509277 545.402099609375 0.4256930351257324 562.3289184570312 0.32117751240730286 0.7279391 0.5590048432350159 True -4 14235 30.913663148880005 0.5930285453796387 476.4608154296875 0.3418307602405548 559.9912109375 0.32322949171066284 0.7373885 0.4538101255893707 True -5 17082 30.767441034317017 0.5888240337371826 482.4781494140625 0.32254135608673096 558.8202514648438 0.3236500322818756 0.74154633 0.44581422209739685 True -6 19929 30.744115114212036 0.5907926559448242 524.4710083007812 0.4721793830394745 556.7947387695312 0.32667648792266846 0.7468048 0.42575326561927795 True -7 22776 30.811522722244263 0.6051077842712402 542.8380126953125 0.36784443259239197 554.9974975585938 0.32846546173095703 0.7559443 0.4054035544395447 True -8 25623 30.797675848007202 0.5936815738677979 517.7291259765625 0.4130755364894867 552.8333740234375 0.3323196768760681 0.7613329 0.4007517993450165 True -9 28470 30.806392669677734 0.5922336578369141 496.405029296875 0.39858829975128174 551.5232543945312 0.33390313386917114 0.77052855 0.3624249994754791 True -10 31317 30.759510278701782 0.6051654815673828 439.10125732421875 0.3611030578613281 550.6209716796875 0.33538368344306946 0.7746344 0.352061003446579 True -11 34164 30.7635395526886 0.6065211296081543 486.2505187988281 0.345901221036911 549.0487060546875 0.3371228575706482 0.78431344 0.31807443499565125 True -12 37011 30.74431586265564 0.5922799110412598 493.1480712890625 0.24780017137527466 548.6940307617188 0.3369986414909363 0.78936386 0.29440104961395264 True -13 39858 30.879863262176514 0.6022346019744873 495.3196105957031 0.21605876088142395 546.57763671875 0.34121188521385193 0.79668057 0.27607330679893494 True -14 42705 30.837076902389526 0.6034443378448486 465.72442626953125 0.2881205677986145 544.9010009765625 0.3442193269729614 0.8046014 0.2538580894470215 True -15 45552 30.817444562911987 0.6062281131744385 496.55804443359375 0.2494581639766693 544.6085815429688 0.34457623958587646 0.80743253 0.23805831372737885 True -16 48399 30.744125604629517 0.6049103736877441 524.7604370117188 0.19921272993087769 544.8132934570312 0.34344911575317383 0.81247324 0.2281922698020935 True -17 51246 30.812931776046753 0.6027376651763916 483.25927734375 0.21281427145004272 544.352783203125 0.3449174761772156 0.8144439 0.22191490232944489 True -18 54093 30.836591243743896 0.609351634979248 508.0005798339844 0.2716778814792633 544.5230102539062 0.3443900942802429 0.8154485 0.2181939333677292 True -19 56940 30.808889627456665 0.6057908535003662 454.8365783691406 0.1513039469718933 545.24365234375 0.34260573983192444 0.8138572 0.2184162586927414 False diff --git a/ENCSR923JYH/cherimoya.fold_4.performance.tsv b/ENCSR923JYH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 41740e51b30ca69820e755cb5c29f321e17198df..0000000000000000000000000000000000000000 --- a/ENCSR923JYH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -544.5230102539062 0.4289657175540924 0.3443900942802429 0.12384343147277832 0.815448522567749 0.7770756483078003 0.2181939333677292 \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_0.evaluate.json b/ENCSR924IHU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 04e6f09f7a519b33a510731bd98f218cf478bfdf..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF169QZM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_0.fit.json b/ENCSR924IHU/cherimoya.fold_0.fit.json deleted file mode 100644 index f2756022cf550ff3c040ed0edfc833e42aadefff..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF169QZM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_0.log b/ENCSR924IHU/cherimoya.fold_0.log deleted file mode 100644 index 075f35dd6e01fbc183873835d5901ca2e2e10d90..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 34.52996110916138 3.5920653343200684 403.993896484375 0.2065678834915161 492.5430908203125 0.30602404475212097 0.7895939 3.6270275115966797 True -1 5512 30.45732283592224 0.6003975868225098 364.13836669921875 0.23869869112968445 461.6646423339844 0.36553558707237244 0.8245471 0.7702160477638245 True -2 8268 30.566779136657715 0.569880485534668 326.0457763671875 0.31987160444259644 453.85467529296875 0.37750205397605896 0.8496529 0.42773595452308655 True -3 11024 30.441386222839355 0.5788693428039551 367.05078125 0.2119075357913971 450.94854736328125 0.38207539916038513 0.859013 0.28737565875053406 True -4 13780 30.380439281463623 0.7921373844146729 400.22918701171875 0.2345915287733078 448.425048828125 0.38772231340408325 0.86244565 0.2329370230436325 True -5 16536 30.443260431289673 1.9595894813537598 378.6103210449219 0.25280553102493286 448.6541748046875 0.3860333561897278 0.8652355 0.23364920914173126 True -6 19292 30.486315488815308 1.2953338623046875 384.40771484375 0.2435339242219925 446.4519958496094 0.39078110456466675 0.87090063 0.21657724678516388 True -7 22048 30.40255331993103 0.609611988067627 397.5470275878906 0.133070707321167 445.931640625 0.391451358795166 0.8743112 0.21029521524906158 True -8 24804 30.44700050354004 8.31705379486084 399.9477233886719 0.18630991876125336 444.46148681640625 0.39476826786994934 0.8780728 0.19646506011486053 True -9 27560 30.452698230743408 0.5810680389404297 377.94134521484375 0.1776117980480194 443.6897888183594 0.3961813449859619 0.8822978 0.1788240224123001 True -10 30316 30.441850423812866 0.5795719623565674 363.372802734375 0.12469123303890228 442.8592224121094 0.3976703882217407 0.88524204 0.1692928522825241 True -11 33072 30.188103914260864 0.5682246685028076 351.0408630371094 0.1947387456893921 441.9519958496094 0.3990756869316101 0.88827527 0.1558256298303604 True -12 35828 29.853681325912476 0.5681407451629639 356.284423828125 0.14372467994689941 441.74969482421875 0.3991889953613281 0.8906622 0.1466141939163208 True -13 38584 29.829508543014526 1.467468023300171 345.28973388671875 0.14372216165065765 440.7496337890625 0.40066298842430115 0.89343405 0.14166715741157532 True -14 41340 29.89309525489807 4.349945783615112 354.37225341796875 0.15198537707328796 440.13946533203125 0.40187376737594604 0.8977095 0.1350083202123642 True -15 44096 29.888091564178467 1.7467319965362549 376.27142333984375 0.23028284311294556 439.7514343261719 0.40336596965789795 0.9003212 0.12820477783679962 True -16 46852 29.890207052230835 1.6820104122161865 411.6586608886719 0.17430108785629272 439.3316650390625 0.40398550033569336 0.9020562 0.12361457943916321 True -17 49608 29.859964847564697 10.781757116317749 387.8819580078125 0.12780925631523132 439.2042236328125 0.4037794768810272 0.9051939 0.12172834575176239 True -18 52364 29.90169334411621 27.48355197906494 373.89923095703125 0.08842114359140396 439.64862060546875 0.4024991989135742 0.9042187 0.12177596986293793 False -19 55120 29.99708843231201 0.577277421951294 350.2431640625 0.12150029838085175 439.643798828125 0.40320372581481934 0.90201026 0.12168199568986893 False diff --git a/ENCSR924IHU/cherimoya.fold_0.performance.tsv b/ENCSR924IHU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1aa181e0003ada529f8565470280cad55e1641d7..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -439.2042236328125 0.3980310559272766 0.4037794768810272 0.1419752538204193 0.9051939249038696 0.8907868266105652 0.12172834575176239 \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_1.evaluate.json b/ENCSR924IHU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b08676e9215058f4c46e360f06b419d1de5bfd14..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF169QZM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_1.fit.json b/ENCSR924IHU/cherimoya.fold_1.fit.json deleted file mode 100644 index 18d9c9cd83ab46deed40d5281d3474efe9235f58..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF169QZM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_1.log b/ENCSR924IHU/cherimoya.fold_1.log deleted file mode 100644 index 2da0d96a75afdd62ee5cfac618fd2de7ee505105..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2704 33.690386056900024 4.065956354141235 413.67010498046875 0.26917028427124023 554.4302368164062 0.30090323090553284 0.7971995 4.0937724113464355 True -1 5408 29.821454763412476 0.7164115905761719 435.63525390625 0.47381389141082764 512.5243530273438 0.368967741727829 0.83337355 0.789156436920166 True -2 8112 29.859104871749878 0.7062933444976807 412.8218994140625 0.25002753734588623 500.893798828125 0.3862534165382385 0.8560672 0.4076826870441437 True -3 10816 29.864142656326294 0.6903254985809326 356.167724609375 0.20263388752937317 498.4009704589844 0.3889753520488739 0.8657843 0.3033222556114197 True -4 13520 30.435577392578125 0.7001197338104248 433.68646240234375 0.3157316744327545 495.76702880859375 0.39392340183258057 0.86748487 0.26011326909065247 True -5 16224 29.969974994659424 0.6978545188903809 421.98089599609375 0.28559327125549316 494.0096435546875 0.3963313400745392 0.87364364 0.24169921875 True -6 18928 29.66748595237732 0.688511848449707 344.4179992675781 0.2792850732803345 492.4029541015625 0.39969515800476074 0.8741305 0.24858206510543823 True -7 21632 29.292311668395996 0.6884012222290039 358.1298522949219 0.27330997586250305 490.9927062988281 0.40163347125053406 0.87910223 0.24164512753486633 True -8 24336 29.18437385559082 1.2455730438232422 385.0170593261719 0.17766183614730835 489.66082763671875 0.40326496958732605 0.8847106 0.21039463579654694 True -9 27040 29.277464866638184 2.668272018432617 359.48974609375 0.25253140926361084 488.7438049316406 0.40542665123939514 0.8875993 0.20047716796398163 True -10 29744 29.344106674194336 0.6971821784973145 432.44036865234375 0.1518174111843109 487.8746337890625 0.4055771231651306 0.8905918 0.1865101009607315 True -11 32448 29.22921061515808 0.6882913112640381 432.16143798828125 0.19740965962409973 486.81182861328125 0.4069649279117584 0.8931745 0.17819003760814667 True -12 35152 29.29461121559143 0.6908860206604004 355.4444580078125 0.1631413996219635 485.5874938964844 0.40944111347198486 0.8973579 0.17530807852745056 True -13 37856 29.22635793685913 0.6896343231201172 420.6971130371094 0.11989862471818924 484.25 0.4121280014514923 0.9004284 0.16027049720287323 True -14 40560 29.19909405708313 0.6908352375030518 407.78912353515625 0.1915569305419922 483.5359802246094 0.41262632608413696 0.90522045 0.14912597835063934 True -15 43264 29.223480701446533 0.6910731792449951 339.138916015625 0.12757378816604614 482.8339538574219 0.4131508469581604 0.90834206 0.14194798469543457 True -16 45968 29.254833698272705 0.6903860569000244 374.2091979980469 0.10123241692781448 483.7725524902344 0.410878986120224 0.91148156 0.13497769832611084 True -17 48672 29.283567428588867 0.6811766624450684 395.89007568359375 0.1607399582862854 482.95782470703125 0.4131247401237488 0.91450715 0.13070645928382874 True -18 51376 29.269598960876465 0.7161617279052734 399.85125732421875 0.09774933755397797 482.04144287109375 0.41628289222717285 0.9139441 0.12930114567279816 False -19 54080 29.356013536453247 0.6946744918823242 380.2957458496094 0.10583041608333588 482.9575500488281 0.4132018983364105 0.91516244 0.12898284196853638 True diff --git a/ENCSR924IHU/cherimoya.fold_1.performance.tsv b/ENCSR924IHU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9a57f93aa5c8ab07e72516d17ee70ee62c779a52..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -482.9575500488281 0.388470858335495 0.4132019281387329 0.15260782837867737 0.9151624441146851 0.912322461605072 0.12898284196853638 \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_2.evaluate.json b/ENCSR924IHU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7fe269e7ec99dff48e1b5a30fbf5544c9c147e0e..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF169QZM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_2.fit.json b/ENCSR924IHU/cherimoya.fold_2.fit.json deleted file mode 100644 index fb35d43287616da54220ad0b29f6b1e2e1660ce6..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF169QZM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_2.log b/ENCSR924IHU/cherimoya.fold_2.log deleted file mode 100644 index 3a96cb84ee67d5b48047272bcf363572657d355b..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2885 35.553112268447876 27.37337875366211 383.2596740722656 0.3070332407951355 518.6382446289062 0.3110051453113556 0.78158873 2.9271740913391113 True -1 5770 31.81625771522522 1.4326586723327637 476.3152160644531 0.32913637161254883 484.21759033203125 0.37141692638397217 0.8244124 0.6185914278030396 True -2 8655 31.94895076751709 0.5264418125152588 411.52679443359375 0.1415666937828064 477.6123046875 0.38045623898506165 0.8409713 0.28858113288879395 True -3 11540 31.29775333404541 0.6068589687347412 395.8604736328125 0.21660469472408295 474.0964660644531 0.385326087474823 0.8537508 0.26815512776374817 True -4 14425 31.282355070114136 0.8391036987304688 361.9255676269531 0.227688267827034 472.9529724121094 0.38669082522392273 0.85842425 0.19942371547222137 True -5 17310 31.24523115158081 1.0698611736297607 402.4906005859375 0.1775922179222107 471.2750244140625 0.39078930020332336 0.86281407 0.19413429498672485 True -6 20195 31.236361742019653 2.1071951389312744 358.726318359375 0.19075827300548553 470.2018737792969 0.3925947844982147 0.86446816 0.19226402044296265 True -7 23080 31.21667718887329 1.9891259670257568 403.4525146484375 0.15904530882835388 469.3735046386719 0.39345309138298035 0.8690462 0.18158824741840363 True -8 25965 31.20019817352295 0.7843489646911621 395.988525390625 0.29456132650375366 468.4577331542969 0.39513182640075684 0.87347156 0.17993386089801788 True -9 28850 31.227771520614624 0.5257587432861328 354.0892639160156 0.13185712695121765 466.996826171875 0.39800897240638733 0.8776664 0.16649259626865387 True -10 31735 31.258066177368164 0.5266296863555908 398.51568603515625 0.23727211356163025 466.2236328125 0.39924156665802 0.88130087 0.16446413099765778 True -11 34620 31.442383289337158 0.5158140659332275 375.84417724609375 0.1864749640226364 465.06854248046875 0.4011420011520386 0.88357383 0.15671832859516144 True -12 37505 31.22632122039795 0.5219461917877197 422.412353515625 0.17255108058452606 464.5350646972656 0.4015551507472992 0.88743514 0.14592397212982178 True -13 40390 31.197615146636963 0.5225539207458496 369.47283935546875 0.17951157689094543 463.0381164550781 0.40529975295066833 0.8902879 0.1447659581899643 True -14 43275 31.18983793258667 0.5245015621185303 431.67999267578125 0.12222017347812653 462.24969482421875 0.40642163157463074 0.89328486 0.13722284138202667 True -15 46160 31.20586895942688 0.5201032161712646 444.241455078125 0.1685173213481903 462.6986083984375 0.4044420123100281 0.89479065 0.134109765291214 True -16 49045 31.167150735855103 0.5211694240570068 333.58392333984375 0.18921831250190735 461.5101623535156 0.4079822897911072 0.8987963 0.13013598322868347 True -17 51930 31.230390548706055 0.5149197578430176 338.5919189453125 0.11455923318862915 461.80938720703125 0.4058511555194855 0.89900565 0.1273012012243271 True -18 54815 31.18219304084778 0.5205669403076172 428.119384765625 0.14239025115966797 461.89141845703125 0.4062466621398926 0.9001227 0.1268555223941803 True -19 57700 31.16247057914734 0.5207946300506592 362.7290954589844 0.1434163749217987 462.2466125488281 0.4058121144771576 0.89853036 0.12762171030044556 False diff --git a/ENCSR924IHU/cherimoya.fold_2.performance.tsv b/ENCSR924IHU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e770d7fd16208b5e6af0c353b6ccbc70be5e0f80..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -461.89141845703125 0.3939983546733856 0.4062466621398926 0.14780665934085846 0.9001227021217346 0.8921456933021545 0.1268555223941803 \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_3.evaluate.json b/ENCSR924IHU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 55795737c5df219cc0add3cb91068cf19e3a238e..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF169QZM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_3.fit.json b/ENCSR924IHU/cherimoya.fold_3.fit.json deleted file mode 100644 index 7eb5059e869c2659da8acad68e200690ac06c717..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF169QZM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_3.log b/ENCSR924IHU/cherimoya.fold_3.log deleted file mode 100644 index b276503e960d708b5efb4456875fda66a40b47f1..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 34.504424810409546 3.4847910404205322 427.97503662109375 0.3264405131340027 486.6844177246094 0.3163304626941681 0.7660805 3.471200466156006 True -1 5516 30.5448215007782 0.5516252517700195 390.48931884765625 0.3376599848270416 451.2407531738281 0.37538406252861023 0.8134987 0.7677310705184937 True -2 8274 30.549408435821533 0.5232870578765869 406.4730224609375 0.3796464800834656 446.26885986328125 0.382314532995224 0.8296544 0.3620092272758484 True -3 11032 30.477381467819214 0.5175769329071045 428.8541259765625 0.211787611246109 442.6346435546875 0.3877103924751282 0.8475753 0.29433879256248474 True -4 13790 30.463916778564453 0.5200009346008301 442.19110107421875 0.2227625846862793 440.9840087890625 0.39096009731292725 0.8508186 0.2478589117527008 True -5 16548 30.483866691589355 0.5243260860443115 378.5267333984375 0.20242047309875488 439.18890380859375 0.3945554494857788 0.86032933 0.22330638766288757 True -6 19306 30.487060546875 0.5245516300201416 417.8843688964844 0.14852498471736908 438.3440856933594 0.39547380805015564 0.8656722 0.2068248689174652 True -7 22064 30.519827365875244 0.5210225582122803 340.5088195800781 0.1385088413953781 437.1977233886719 0.39760035276412964 0.87014693 0.19640710949897766 True -8 24822 30.44009232521057 0.5169241428375244 415.1789245605469 0.2516336143016815 436.5194396972656 0.3984980285167694 0.87214166 0.18409521877765656 True -9 27580 30.461297750473022 0.5249125957489014 403.8514099121094 0.12631699442863464 435.5508117675781 0.3997413218021393 0.87718815 0.1774827539920807 True -10 30338 30.419196128845215 1.1470696926116943 394.7181091308594 0.2834435999393463 434.88323974609375 0.40144968032836914 0.879893 0.1736220121383667 True -11 33096 30.476113080978394 4.557301759719849 388.6693115234375 0.09621063619852066 433.57196044921875 0.40430310368537903 0.8806641 0.1697985976934433 True -12 35854 30.50722312927246 0.5809853076934814 423.8996887207031 0.11809016019105911 433.1805725097656 0.40405383706092834 0.88489425 0.15944185853004456 True -13 38612 30.654091596603394 0.5349645614624023 405.4979248046875 0.1651565432548523 432.4280090332031 0.40534281730651855 0.889296 0.15289585292339325 True -14 41370 29.854565382003784 0.5196161270141602 373.94256591796875 0.1690923124551773 431.8333435058594 0.40600764751434326 0.89140403 0.14684231579303741 True -15 44128 29.78829574584961 0.5166645050048828 342.8013916015625 0.16470623016357422 431.4343566894531 0.4070739448070526 0.89386004 0.1421705037355423 True -16 46886 29.805248022079468 27.60757303237915 347.76531982421875 0.09651611745357513 430.639892578125 0.40853309631347656 0.8983925 0.13616888225078583 True -17 49644 30.411282539367676 0.6425025463104248 376.0300598144531 0.10293999314308167 430.9705810546875 0.4077185392379761 0.8989554 0.13403956592082977 True -18 52402 29.76738429069519 0.512493371963501 392.42791748046875 0.20306484401226044 430.4808654785156 0.4088857173919678 0.8983585 0.13342536985874176 False -19 55160 29.795162439346313 0.5139296054840088 375.64349365234375 0.08254450559616089 431.3113098144531 0.40641656517982483 0.8990126 0.13340958952903748 True diff --git a/ENCSR924IHU/cherimoya.fold_3.performance.tsv b/ENCSR924IHU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b26958eb50c8c3a44cc4a71c72037f4761a87a38..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -431.3113098144531 0.3964231610298157 0.40641656517982483 0.14231732487678528 0.8990126252174377 0.8829244375228882 0.13340958952903748 \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_4.evaluate.json b/ENCSR924IHU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 57930d7d15b36c1cc0a04ff2e178806074a5c915..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF169QZM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_4.fit.json b/ENCSR924IHU/cherimoya.fold_4.fit.json deleted file mode 100644 index d80d7867a4f1beb1ce9974d37e26662777bfd275..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF169QZM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR924IHU/cherimoya.fold_4.log b/ENCSR924IHU/cherimoya.fold_4.log deleted file mode 100644 index b13995e909336b20d4e7d5b7e1933e916ed173ff..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2814 34.9816951751709 3.6062204837799072 392.18798828125 0.19942322373390198 448.776611328125 0.30495190620422363 0.7803925 3.095170736312866 True -1 5628 31.08206820487976 0.645052433013916 386.46240234375 0.1780375838279724 418.2372741699219 0.3618938624858856 0.82380646 0.5984202027320862 True -2 8442 31.293453454971313 0.6154839992523193 324.23297119140625 0.24722127616405487 412.18145751953125 0.3726440966129303 0.846448 0.259798139333725 True -3 11256 31.060729503631592 0.617647647857666 372.4163818359375 0.16094869375228882 409.5579528808594 0.376871794462204 0.85141885 0.2245924472808838 True -4 14070 31.09280490875244 0.6171267032623291 402.66668701171875 0.23825138807296753 408.45001220703125 0.3786982297897339 0.8578732 0.17563870549201965 True -5 16884 31.108198881149292 0.6166455745697021 458.6034851074219 0.2576628029346466 406.7775573730469 0.38353273272514343 0.86227655 0.18341268599033356 True -6 19698 31.201415061950684 0.6163427829742432 461.21087646484375 0.292955219745636 406.15301513671875 0.3835398256778717 0.87004596 0.163765549659729 True -7 22512 30.96075439453125 0.6127030849456787 419.92572021484375 0.21357858180999756 405.3039855957031 0.3846175968647003 0.87853825 0.14834347367286682 True -8 25326 30.47245216369629 0.6125791072845459 452.04949951171875 0.16563087701797485 405.0365905761719 0.3849748373031616 0.87969494 0.14443066716194153 True -9 28140 30.44101643562317 0.6112065315246582 384.18243408203125 0.14433541893959045 404.00518798828125 0.38825491070747375 0.8835679 0.13569322228431702 True -10 30954 30.439133405685425 0.6225185394287109 329.0987548828125 0.19090835750102997 403.3519287109375 0.38879573345184326 0.8883764 0.13041852414608002 True -11 33768 30.460782051086426 0.6085038185119629 373.366943359375 0.24260924756526947 402.88031005859375 0.39016836881637573 0.8895881 0.1301843822002411 True -12 36582 30.438069343566895 0.6024379730224609 370.69793701171875 0.1516191065311432 402.9354553222656 0.3897528648376465 0.8931287 0.12431716918945312 True -13 39396 30.423325538635254 0.6151793003082275 418.6468200683594 0.1228962391614914 401.7095031738281 0.39241844415664673 0.89421356 0.12172173708677292 True -14 42210 30.449337482452393 0.6506359577178955 319.3006896972656 0.12909004092216492 401.44171142578125 0.39287498593330383 0.898333 0.11702772229909897 True -15 45024 30.596694946289062 0.614487886428833 364.27691650390625 0.0993742123246193 401.06268310546875 0.3936505615711212 0.89980865 0.11391276121139526 True -16 47838 30.621843576431274 0.6196937561035156 417.7756652832031 0.14483515918254852 400.531494140625 0.39470428228378296 0.903367 0.11063457280397415 True -17 50652 30.484305143356323 0.6142559051513672 352.4842529296875 0.12532876431941986 400.3481750488281 0.39572247862815857 0.9054618 0.10842808336019516 True -18 53466 30.439062356948853 0.6137137413024902 388.95318603515625 0.10289514064788818 401.0450439453125 0.39352279901504517 0.90275866 0.109019435942173 False -19 56280 30.47841215133667 0.6066091060638428 383.1915588378906 0.14028611779212952 401.0418701171875 0.3936476707458496 0.90390444 0.10883350670337677 False diff --git a/ENCSR924IHU/cherimoya.fold_4.performance.tsv b/ENCSR924IHU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 33ed412e5cb5efc82f9859bf4b78e3a8908a1343..0000000000000000000000000000000000000000 --- a/ENCSR924IHU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -400.3481750488281 0.40887612104415894 0.3957224488258362 0.13261954486370087 0.9054617881774902 0.8873600959777832 0.10842808336019516 \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_0.evaluate.json b/ENCSR925LGW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d22ecd8ba0117a42cccb71a033b473ecd998b7f9..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF050HGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_0.fit.json b/ENCSR925LGW/cherimoya.fold_0.fit.json deleted file mode 100644 index 4cee6c176c589bb46186daf5af27e8d4cb96f3c4..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF050HGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_0.log b/ENCSR925LGW/cherimoya.fold_0.log deleted file mode 100644 index 6fb74d4839fa37ce1a2793abe07c748e3d09b9aa..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3391 42.47062349319458 3.98781156539917 559.475830078125 0.6600759029388428 701.3231201171875 0.6741946935653687 0.6789706 4.3406982421875 True -1 6782 37.808974266052246 19.16288709640503 413.41229248046875 0.6061908602714539 613.8245239257812 0.7460261583328247 0.7141047 1.0668134689331055 True -2 10173 37.389569997787476 6.978365659713745 485.2608642578125 0.7203823328018188 603.8165893554688 0.7542511820793152 0.7213789 0.5768308043479919 True -3 13564 37.01845073699951 1.33626389503479 536.570556640625 0.5318039655685425 598.5109252929688 0.7580296993255615 0.7262549 0.4783008098602295 True -4 16955 41.046018838882446 0.6743450164794922 512.499267578125 0.6020197868347168 595.7525634765625 0.7610117793083191 0.7250649 0.48895975947380066 False -5 20346 37.05339050292969 0.6763670444488525 548.849609375 0.46169212460517883 594.0082397460938 0.7625836730003357 0.7260431 0.4747609794139862 False -6 23737 37.07735848426819 0.6749515533447266 546.654296875 0.595084547996521 591.8439331054688 0.7647300958633423 0.7246535 0.48969289660453796 False -7 27128 37.023454666137695 0.6817338466644287 453.1911315917969 0.699446439743042 590.0245361328125 0.7666511535644531 0.7156752 0.5040647387504578 False -8 30519 37.09313344955444 0.6834456920623779 436.49322509765625 0.5633662343025208 587.1376953125 0.7693741321563721 0.7244639 0.4665721654891968 False -9 33910 37.32821249961853 19.696619033813477 479.29266357421875 0.5024043917655945 584.775634765625 0.7715091109275818 0.7316446 0.4606795608997345 True -10 37301 37.00428891181946 0.6880919933319092 577.0494384765625 0.6238988041877747 582.061767578125 0.7737572193145752 0.7374425 0.4515765905380249 True -11 40692 37.02099299430847 0.6841950416564941 450.2711181640625 0.5876122713088989 579.7898559570312 0.7759356498718262 0.7418771 0.4518522322177887 True -12 44083 37.00131392478943 0.6683928966522217 403.50390625 0.5658383965492249 577.2422485351562 0.7780263423919678 0.7475097 0.43666961789131165 True -13 47474 41.08282518386841 3.846783399581909 466.03436279296875 0.3839152157306671 574.7958374023438 0.7802039980888367 0.75615835 0.4256458878517151 True -14 50865 37.067606687545776 1.0031278133392334 397.4020690917969 0.5779480934143066 573.5030517578125 0.7814228534698486 0.76096326 0.4192575514316559 True -15 54256 37.11256980895996 0.6766800880432129 430.2987060546875 0.3807539939880371 572.5296020507812 0.7825475931167603 0.76713485 0.40642619132995605 True -16 57647 37.022995710372925 0.7080433368682861 547.5106201171875 0.48404693603515625 571.907958984375 0.7829909324645996 0.7709686 0.39382219314575195 True -17 61038 37.11941623687744 2.2987101078033447 447.1932678222656 0.23277220129966736 572.2332763671875 0.782900869846344 0.7708028 0.3915753662586212 False -18 64429 37.12963819503784 0.706892728805542 533.3976440429688 0.314713716506958 572.64990234375 0.7823760509490967 0.76941097 0.39556875824928284 False -19 67820 37.16193246841431 0.6842710971832275 524.4434814453125 0.2983776926994324 572.8101806640625 0.7821957468986511 0.7665863 0.3975943624973297 False diff --git a/ENCSR925LGW/cherimoya.fold_0.performance.tsv b/ENCSR925LGW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 51901cefff6defca5caec0e6c45f1a42b9f6e791..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -571.907958984375 0.18353424966335297 0.7829909324645996 0.39318186044692993 0.7709686160087585 0.6896369457244873 0.39382219314575195 \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_1.evaluate.json b/ENCSR925LGW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ee2b9a013d8f7892cc9a2a31fa497ae0fa5b8676..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF050HGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_1.fit.json b/ENCSR925LGW/cherimoya.fold_1.fit.json deleted file mode 100644 index 40386ac16e80d44694c1ff6c8eeabb7fe0d13793..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF050HGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_1.log b/ENCSR925LGW/cherimoya.fold_1.log deleted file mode 100644 index 12bf32b2602ee1d07b7915abcfa54bce499e78dc..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3375 42.45853233337402 4.608627796173096 550.8851928710938 0.7151432037353516 794.162109375 0.6859827637672424 0.7004262 4.804646015167236 True -1 6750 37.41559290885925 0.8887369632720947 543.7556762695312 0.5605038404464722 692.2333984375 0.7582287192344666 0.7275732 1.1280509233474731 True -2 10125 37.493019104003906 0.9020388126373291 570.3690185546875 0.5423206090927124 676.7003173828125 0.7677417397499084 0.7347131 0.5949824452400208 True -3 13500 37.508684396743774 0.8922266960144043 541.837646484375 0.7178266644477844 672.6043701171875 0.7706213593482971 0.7341732 0.6014604568481445 False -4 16875 37.80750584602356 46.05153250694275 511.654541015625 0.5956056714057922 667.7978515625 0.7734518647193909 0.7399986 0.5134531259536743 True -5 20250 37.58955001831055 2.0068488121032715 438.7471008300781 0.4673543870449066 664.4312744140625 0.7765985727310181 0.74399734 0.5033904910087585 True -6 23625 37.61301374435425 3.0674638748168945 539.9102172851562 0.6995989084243774 661.0703735351562 0.778719961643219 0.7504073 0.48457497358322144 True -7 27000 37.58760619163513 2.1840531826019287 517.178955078125 0.5403561592102051 659.5423583984375 0.7803347110748291 0.7528133 0.4608785808086395 True -8 30375 37.62047719955444 46.74725914001465 448.2298583984375 0.4639517664909363 655.7666625976562 0.7831259369850159 0.76175714 0.47303199768066406 True -9 33750 37.779990434646606 38.27126336097717 526.0609130859375 0.49584823846817017 653.3483276367188 0.7850566506385803 0.76203775 0.4477369487285614 True -10 37125 37.60482573509216 32.34855031967163 444.2142333984375 0.34366416931152344 650.826904296875 0.7871707677841187 0.76833546 0.4389055669307709 True -11 40500 37.816834688186646 0.8928663730621338 424.0674743652344 0.5031924247741699 648.3253784179688 0.7893723845481873 0.7749543 0.4235752820968628 True -12 43875 36.966054916381836 0.9171814918518066 489.518310546875 0.4806210994720459 645.9404907226562 0.7913684248924255 0.77834123 0.4242662191390991 True -13 47250 36.80759811401367 0.8711764812469482 465.8171081542969 0.44788026809692383 643.3406372070312 0.7934190034866333 0.78531176 0.41583919525146484 True -14 50625 36.92497253417969 0.8824195861816406 478.19805908203125 0.26306992769241333 640.7505493164062 0.795256495475769 0.7907714 0.40320658683776855 True -15 54000 36.88551592826843 34.790261030197144 515.7588500976562 0.3951118588447571 639.4690551757812 0.7964974045753479 0.79637855 0.4009215831756592 True -16 57375 36.98107552528381 0.9093773365020752 460.46051025390625 0.3370034694671631 638.9415283203125 0.7970564961433411 0.80011576 0.39535489678382874 True -17 60750 37.19202780723572 30.14672541618347 483.48114013671875 0.27619248628616333 639.0147094726562 0.7970798015594482 0.80195147 0.3919183611869812 True -18 64125 36.87450933456421 20.18767786026001 486.8145751953125 0.2921473979949951 639.4151000976562 0.7967483997344971 0.7986714 0.3949317932128906 False -19 67500 36.93220806121826 0.8857581615447998 488.2783508300781 0.3125787377357483 639.6513671875 0.7964674830436707 0.7993904 0.3956356942653656 False diff --git a/ENCSR925LGW/cherimoya.fold_1.performance.tsv b/ENCSR925LGW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f3205213511d991006affbcf1721c3cd41424b37..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -639.0147094726562 0.1692029982805252 0.7970798015594482 0.4303441345691681 0.8019514679908752 0.7566267848014832 0.3919183611869812 \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_2.evaluate.json b/ENCSR925LGW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a4cc5a9ad5528ab49219217d1fb58b89892c052c..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF050HGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_2.fit.json b/ENCSR925LGW/cherimoya.fold_2.fit.json deleted file mode 100644 index c626b0f8271581c2638f9bb8ecc91c1ca4080220..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF050HGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_2.log b/ENCSR925LGW/cherimoya.fold_2.log deleted file mode 100644 index a775a91e708bbfe1140212643f20880506361f52..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3589 44.27883744239807 3.6721677780151367 546.8440551757812 0.8250038623809814 721.4713134765625 0.6852472424507141 0.6923797 4.130079746246338 True -1 7178 39.771759033203125 0.7981398105621338 612.2777099609375 0.6413922309875488 631.193603515625 0.7553207874298096 0.7277907 0.6911719441413879 True -2 10767 39.784892082214355 0.7405645847320557 568.6427001953125 1.0165395736694336 623.6438598632812 0.7597125768661499 0.7295927 0.5175263285636902 True -3 14356 39.79313564300537 0.7333090305328369 537.2461547851562 0.5888816714286804 618.7394409179688 0.7640093564987183 0.7317951 0.5034089684486389 True -4 17945 39.81362843513489 0.7219922542572021 533.682861328125 0.451723575592041 616.192138671875 0.7655096650123596 0.73854816 0.4571465849876404 True -5 21534 39.85784339904785 0.7244412899017334 492.9482727050781 0.6604432463645935 614.0962524414062 0.7680625319480896 0.73705137 0.4379396140575409 False -6 25123 39.89095330238342 0.7224864959716797 527.26953125 0.5567383766174316 611.5321044921875 0.7705665826797485 0.7396567 0.4426254332065582 True -7 28712 39.79816150665283 0.7238948345184326 497.4751281738281 0.676581859588623 608.5322265625 0.7728767395019531 0.7394327 0.4556507170200348 False -8 32301 39.81757378578186 0.7190313339233398 507.47100830078125 0.5815788507461548 607.1888427734375 0.774384617805481 0.7418496 0.4516555368900299 True -9 35890 39.84982752799988 0.7256689071655273 466.0257568359375 0.4159129858016968 604.4107055664062 0.7764949798583984 0.7467002 0.44150224328041077 True -10 39479 39.861292123794556 0.7228736877441406 453.6310119628906 0.5100588798522949 602.0363159179688 0.7783535122871399 0.75317544 0.4334099590778351 True -11 43068 39.81439161300659 0.7244153022766113 509.6465148925781 0.7451426386833191 599.7108154296875 0.7804155349731445 0.7599945 0.4252523183822632 True -12 46657 39.784663915634155 0.7242147922515869 483.8955078125 0.3271804451942444 597.3529663085938 0.7825260758399963 0.763287 0.4211103618144989 True -13 50246 39.778082847595215 0.7284061908721924 517.1533203125 0.5070725679397583 595.6201782226562 0.7842558026313782 0.76831096 0.4215375781059265 True -14 53835 39.8365523815155 0.725588321685791 480.75146484375 0.5463496446609497 593.9984130859375 0.7857671976089478 0.77217394 0.4161713421344757 True -15 57424 39.76978540420532 0.7257719039916992 519.6905517578125 0.29373419284820557 592.9683837890625 0.7867580056190491 0.77739 0.41154786944389343 True -16 61013 39.81335473060608 0.7215802669525146 430.72247314453125 0.28708702325820923 591.9566650390625 0.7874433994293213 0.78204054 0.3959983289241791 True -17 64602 39.93321466445923 0.7221493721008301 470.5557861328125 0.28410065174102783 592.2723388671875 0.7872437238693237 0.78167254 0.3937830626964569 False -18 68191 39.79719924926758 0.721494197845459 486.59295654296875 0.31769004464149475 592.4591674804688 0.7869756817817688 0.7811865 0.3965549170970917 False -19 71780 39.85174226760864 0.7224259376525879 444.8412780761719 0.3312135934829712 592.7975463867188 0.7866887450218201 0.779166 0.39968419075012207 False diff --git a/ENCSR925LGW/cherimoya.fold_2.performance.tsv b/ENCSR925LGW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1c24404cc1dc2da9d005393ac34595f454e499d3..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -591.9566650390625 0.1790129691362381 0.7874433994293213 0.4058207869529724 0.782040536403656 0.7159367203712463 0.3959983289241791 \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_3.evaluate.json b/ENCSR925LGW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9ed1ce77e2d93a974a8be9796d1b03392bb6024f..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF050HGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_3.fit.json b/ENCSR925LGW/cherimoya.fold_3.fit.json deleted file mode 100644 index 613c0341b3fa8b295899bd002ade2f9d327ab21b..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF050HGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_3.log b/ENCSR925LGW/cherimoya.fold_3.log deleted file mode 100644 index 4fc5c62ebe532b2e86fc843429554bbe0174821c..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3456 43.161723136901855 3.6419596672058105 608.3175048828125 0.6261802315711975 683.2134399414062 0.6744930744171143 0.6932042 4.31361722946167 True -1 6912 38.354753494262695 0.7066366672515869 543.5858154296875 0.7873370051383972 609.667724609375 0.7370941638946533 0.72310907 0.7669694423675537 True -2 10368 38.771817445755005 15.118213176727295 547.76513671875 0.9163510799407959 592.9708251953125 0.7502509951591492 0.7298365 0.4708925187587738 True -3 13824 39.43406844139099 10.566442489624023 539.9974365234375 0.5212886333465576 588.2838745117188 0.7540223598480225 0.7346631 0.4509117007255554 True -4 17280 39.54934787750244 0.6674947738647461 465.88543701171875 0.6079868674278259 585.2891845703125 0.7568960189819336 0.7331173 0.41792845726013184 False -5 20736 38.359294176101685 0.6681172847747803 472.2723083496094 0.788034975528717 581.9287719726562 0.7595107555389404 0.7387195 0.41141214966773987 True -6 24192 38.256256341934204 0.6663510799407959 501.24359130859375 0.5014199018478394 580.2254638671875 0.7610580325126648 0.739564 0.4126361906528473 True -7 27648 37.56150269508362 0.6607861518859863 461.4739074707031 0.47626686096191406 577.5143432617188 0.7636210322380066 0.7450287 0.41426268219947815 True -8 31104 37.638458490371704 16.907171726226807 476.18560791015625 0.45228174328804016 575.8193969726562 0.7654640674591064 0.7436262 0.4163403809070587 False -9 34560 37.58523178100586 0.6688170433044434 519.400634765625 0.6390718221664429 573.5756225585938 0.7676646709442139 0.74931824 0.42471468448638916 True -10 38016 37.62688636779785 0.6689209938049316 492.90106201171875 0.6983458995819092 571.6820678710938 0.769706666469574 0.75096875 0.41060081124305725 True -11 41472 38.35593128204346 0.6669979095458984 485.2798767089844 0.7433180212974548 569.5369873046875 0.7715741395950317 0.75210524 0.41369709372520447 True -12 44928 37.90350103378296 30.13365077972412 483.56170654296875 0.6837648749351501 566.766845703125 0.7738593816757202 0.76240516 0.3969683349132538 True -13 48384 37.58168601989746 0.6748678684234619 522.5447998046875 0.37641939520835876 564.851318359375 0.7757430672645569 0.77151996 0.38753342628479004 True -14 51840 37.53490209579468 0.6568453311920166 550.1063232421875 0.42017507553100586 562.95849609375 0.777690589427948 0.77448165 0.3863566219806671 True -15 55296 37.614163875579834 0.6652567386627197 494.73272705078125 0.4286944270133972 562.0722045898438 0.7787010669708252 0.7795044 0.37948110699653625 True -16 58752 37.57858920097351 0.6569595336914062 467.65911865234375 0.35179051756858826 561.6559448242188 0.7792994379997253 0.78381395 0.37383177876472473 True -17 62208 37.557016372680664 0.7633016109466553 418.13909912109375 0.3513340950012207 561.6760864257812 0.7791829705238342 0.78330886 0.3759728968143463 False -18 65664 37.580257415771484 0.6743068695068359 463.16131591796875 0.2550814747810364 562.2128295898438 0.778745174407959 0.78116053 0.37997695803642273 False -19 69120 37.59765887260437 0.6651229858398438 441.4031066894531 0.4031798839569092 562.4880981445312 0.7784644365310669 0.7799825 0.38658270239830017 False diff --git a/ENCSR925LGW/cherimoya.fold_3.performance.tsv b/ENCSR925LGW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index cacd25f0318d11cbe059232dc6b50d48cb30721d..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -561.6559448242188 0.18652983009815216 0.7792993187904358 0.3844686448574066 0.7838139533996582 0.7027187347412109 0.37383177876472473 \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_4.evaluate.json b/ENCSR925LGW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 41223e4cb6c4c9d35f4a393b980cd4e015a927f6..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF050HGA.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_4.fit.json b/ENCSR925LGW/cherimoya.fold_4.fit.json deleted file mode 100644 index 03a3c0b58e3e20780fdbaf7146dd5508b514fbed..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF050HGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR925LGW/cherimoya.fold_4.log b/ENCSR925LGW/cherimoya.fold_4.log deleted file mode 100644 index 4b592294b9f2b48ee4a443f4ca09fe754148345d..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3531 43.77836561203003 3.5914499759674072 558.3713989257812 0.5933045148849487 665.7319946289062 0.679328441619873 0.67646116 4.172638893127441 True -1 7062 39.23123621940613 0.718430757522583 572.119140625 0.5543960332870483 594.6443481445312 0.7456895709037781 0.69687504 1.2336266040802002 True -2 10593 39.293278217315674 0.704524040222168 494.20013427734375 0.5987478494644165 583.6185302734375 0.7538192868232727 0.7039742 0.5962367653846741 True -3 14124 39.191208362579346 0.7064776420593262 593.131103515625 0.652754008769989 579.0526123046875 0.7577577829360962 0.7068157 0.6148349046707153 True -4 17655 38.527684450149536 0.6980082988739014 442.27325439453125 0.6119882464408875 576.3817138671875 0.7600219249725342 0.71375144 0.4600907266139984 True -5 21186 38.358420610427856 19.779672384262085 508.9161376953125 0.4735736548900604 575.0175170898438 0.7618983387947083 0.71398246 0.47687414288520813 True -6 24717 38.34897589683533 0.6929624080657959 484.5836486816406 0.5464301705360413 572.7684326171875 0.7639694213867188 0.7122245 0.48382434248924255 False -7 28248 38.45326805114746 0.7101411819458008 496.8453369140625 0.5460966229438782 570.99072265625 0.7653758525848389 0.7210417 0.4437277317047119 True -8 31779 38.4330952167511 0.6976635456085205 541.3794555664062 0.46941107511520386 569.5162963867188 0.7672093510627747 0.7220042 0.45504292845726013 True -9 35310 38.401395082473755 0.6917824745178223 469.5111083984375 0.45115798711776733 567.3329467773438 0.769293487071991 0.7242919 0.4312247335910797 True -10 38841 38.43583106994629 0.7504827976226807 450.66522216796875 0.5889784097671509 565.5591430664062 0.7713693976402283 0.7307899 0.4185559153556824 True -11 42372 38.46388506889343 0.6864118576049805 517.7162475585938 0.46787747740745544 563.9019775390625 0.7729337811470032 0.7396351 0.4061727523803711 True -12 45903 38.44510579109192 0.6818563938140869 437.8614501953125 0.5207294225692749 561.8817749023438 0.7751731276512146 0.74484825 0.3992941975593567 True -13 49434 38.42260718345642 0.6937923431396484 470.818115234375 0.3558502793312073 560.2169189453125 0.7770431041717529 0.75166154 0.3901784420013428 True -14 52965 38.363537073135376 0.6898787021636963 518.5540771484375 0.36671486496925354 558.79345703125 0.7783756852149963 0.7598837 0.38758528232574463 True -15 56496 38.38694739341736 2.10290265083313 463.96881103515625 0.37481656670570374 557.8377075195312 0.779414713382721 0.76231 0.3792003095149994 True -16 60027 38.506813764572144 0.6940436363220215 451.244873046875 0.28997647762298584 557.318359375 0.7799981832504272 0.76668316 0.37468913197517395 True -17 63558 38.46626138687134 0.6944394111633301 441.4313659667969 0.3409143388271332 557.3325805664062 0.7800149917602539 0.76607126 0.37684035301208496 False -18 67089 38.40633034706116 2.979785680770874 459.751708984375 0.44516003131866455 557.6784057617188 0.7797218561172485 0.7658522 0.38010337948799133 False -19 70620 38.38969397544861 2.465376377105713 491.188232421875 0.2637687027454376 557.8240356445312 0.7794525027275085 0.7641092 0.38404756784439087 False diff --git a/ENCSR925LGW/cherimoya.fold_4.performance.tsv b/ENCSR925LGW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c1f102489e8fa50312119033f8cafb1a76525492..0000000000000000000000000000000000000000 --- a/ENCSR925LGW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -557.318359375 0.1862352192401886 0.7799981832504272 0.385646790266037 0.7666831612586975 0.6739176511764526 0.37468913197517395 \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_0.evaluate.json b/ENCSR926SNI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 94d0221c4ff516f0f7f8d5f06732640ff11cd674..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416RWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_0.fit.json b/ENCSR926SNI/cherimoya.fold_0.fit.json deleted file mode 100644 index 48c8f8cb947cb92e21b36217dc14399621b07db6..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF416RWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_0.log b/ENCSR926SNI/cherimoya.fold_0.log deleted file mode 100644 index 716ccbe9322e0cba073ff677e8ad202a63ac0d86..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.76236319541931 3.4295012950897217 168.21295166015625 0.4387071430683136 185.80517578125 0.12800920009613037 0.7358877 2.5666310787200928 True -1 5484 30.36838173866272 0.6134161949157715 156.41116333007812 0.4892948567867279 175.39096069335938 0.15962208807468414 0.77879804 1.148073673248291 True -2 8226 31.200446605682373 20.611574172973633 119.81987762451172 0.4116722345352173 172.27259826660156 0.1634385734796524 0.80178225 0.5788799524307251 True -3 10968 30.81386399269104 0.4708709716796875 149.1301727294922 0.2809818983078003 171.91693115234375 0.1646696925163269 0.8053002 0.49855929613113403 True -4 13710 30.205429077148438 0.4856133460998535 166.81373596191406 0.364483118057251 170.88743591308594 0.16767627000808716 0.80929244 0.46735885739326477 True -5 16452 30.317250728607178 0.48143935203552246 167.97735595703125 0.37615853548049927 169.96763610839844 0.17104415595531464 0.8220236 0.44194093346595764 True -6 19194 30.317070245742798 0.47200679779052734 132.86688232421875 0.3392953872680664 169.63002014160156 0.17252245545387268 0.8244244 0.42685461044311523 True -7 21936 30.192874908447266 0.4710514545440674 125.84158325195312 0.44210535287857056 169.11203002929688 0.17452138662338257 0.82825065 0.4096216559410095 True -8 24678 30.167987823486328 1.7213678359985352 143.77442932128906 0.35698121786117554 168.884765625 0.17521320283412933 0.8341509 0.3871995806694031 True -9 27420 30.23832130432129 0.4726748466491699 148.1117706298828 0.31753867864608765 168.51031494140625 0.17631074786186218 0.8385047 0.3603013753890991 True -10 30162 30.226611375808716 0.46908020973205566 117.63607788085938 0.33807405829429626 168.1422576904297 0.17747686803340912 0.84548235 0.3415103256702423 True -11 32904 31.325199127197266 28.140886783599854 150.36708068847656 0.2951955795288086 167.66534423828125 0.1792464405298233 0.8530217 0.3136785328388214 True -12 35646 30.351123809814453 0.4731106758117676 129.41354370117188 0.18716681003570557 167.41436767578125 0.18010734021663666 0.86046135 0.2894022762775421 True -13 38388 30.32957100868225 0.472947359085083 155.37136840820312 0.3350907564163208 167.05604553222656 0.1809038668870926 0.86570895 0.26842793822288513 True -14 41130 30.362322568893433 0.4721705913543701 105.12216186523438 0.27618926763534546 166.82537841796875 0.1809101104736328 0.8702146 0.2542558014392853 True -15 43872 30.261663675308228 0.5911710262298584 140.82568359375 0.2405659258365631 166.5294647216797 0.18200629949569702 0.8751648 0.24202370643615723 True -16 46614 29.70105791091919 0.4665849208831787 121.15625762939453 0.29748785495758057 166.6218719482422 0.18175099790096283 0.8749096 0.2364889532327652 False -17 49356 29.796052932739258 0.4603114128112793 126.94758605957031 0.20072203874588013 166.5747833251953 0.1815008670091629 0.87630004 0.22980262339115143 True -18 52098 29.67349338531494 0.46584343910217285 122.03585052490234 0.16872340440750122 166.4076385498047 0.18263012170791626 0.87665087 0.23016119003295898 True -19 54840 29.66481328010559 0.46878480911254883 124.02261352539062 0.18395930528640747 166.57632446289062 0.18166287243366241 0.87506324 0.23008993268013 False diff --git a/ENCSR926SNI/cherimoya.fold_0.performance.tsv b/ENCSR926SNI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9ad7dc21d7e1f16b46e40cd44bd3a63682210506..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -166.4076385498047 0.5718854069709778 0.18263012170791626 0.045668479055166245 0.876650869846344 0.795023500919342 0.23016119003295898 \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_1.evaluate.json b/ENCSR926SNI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8941a7ef918d2089cb403da5452efd8822a1e4a4..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416RWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_1.fit.json b/ENCSR926SNI/cherimoya.fold_1.fit.json deleted file mode 100644 index 22882236c88a0c9ae768be7b2311b41548835d72..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF416RWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_1.log b/ENCSR926SNI/cherimoya.fold_1.log deleted file mode 100644 index e62bdfd8c120bb208edcb06e3eaf3385b5d21731..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2771 34.746366024017334 48.91574192047119 146.47088623046875 0.3686046004295349 205.2604217529297 0.13400310277938843 0.734761 3.0337436199188232 True -1 5542 30.60992980003357 47.27769947052002 101.82148742675781 0.4595094323158264 192.140380859375 0.1733371466398239 0.7929157 1.272183895111084 True -2 8313 30.68174719810486 0.7186992168426514 129.1954345703125 0.2514269948005676 189.79519653320312 0.17483285069465637 0.8046023 0.7997170090675354 True -3 11084 30.65417718887329 0.6909337043762207 118.21076202392578 0.22033289074897766 188.70367431640625 0.17607973515987396 0.8155397 0.6913784742355347 True -4 13855 30.61462378501892 2.5216405391693115 141.25662231445312 0.359531432390213 187.5802459716797 0.17791861295700073 0.82811177 0.6059781312942505 True -5 16626 30.543367862701416 6.89310622215271 121.06910705566406 0.18859036266803741 186.6814727783203 0.1807795614004135 0.83795357 0.5597754716873169 True -6 19397 30.786460399627686 0.6816282272338867 157.39501953125 0.5226424336433411 186.0448455810547 0.18337614834308624 0.84364545 0.49162477254867554 True -7 22168 30.270520448684692 0.8973395824432373 102.99771118164062 0.2326468974351883 185.3568115234375 0.1855364441871643 0.84636015 0.48921364545822144 True -8 24939 29.8876633644104 0.6836330890655518 142.2993927001953 0.2514297366142273 184.9217071533203 0.18677112460136414 0.8509637 0.45839157700538635 True -9 27710 29.892853260040283 2.9605038166046143 134.2564697265625 0.2597823739051819 184.4669189453125 0.18835055828094482 0.85577875 0.42842352390289307 True -10 30481 30.025304794311523 0.6759459972381592 116.08966827392578 0.3194655776023865 183.7349395751953 0.1909974366426468 0.8640658 0.3854873478412628 True -11 33252 30.00237512588501 0.6750099658966064 121.67776489257812 0.3632270097732544 183.48590087890625 0.1914709061384201 0.865805 0.36327698826789856 True -12 36023 29.94761323928833 0.688612699508667 111.10789489746094 0.20850762724876404 182.96311950683594 0.19313640892505646 0.8729467 0.33280131220817566 True -13 38794 30.017366409301758 0.6812024116516113 103.45514678955078 0.25932610034942627 182.35231018066406 0.19548562169075012 0.87967294 0.3062750995159149 True -14 41565 30.027710914611816 2.5057966709136963 123.78022766113281 0.2832946479320526 182.2095489501953 0.1949779987335205 0.8846965 0.2875365614891052 True -15 44336 29.987096786499023 0.6765894889831543 111.01412200927734 0.2537153959274292 182.19406127929688 0.1947951465845108 0.889927 0.26895013451576233 True -16 47107 30.015685319900513 0.71783447265625 114.6872329711914 0.19639721512794495 181.89898681640625 0.19586633145809174 0.8915044 0.2572745084762573 True -17 49878 30.108684301376343 0.6858742237091064 151.66769409179688 0.2933722734451294 182.01124572753906 0.1953892558813095 0.8932104 0.2495504468679428 True -18 52649 30.189868211746216 17.72767210006714 114.49417114257812 0.22061607241630554 182.01710510253906 0.19534936547279358 0.89214087 0.24851341545581818 False -19 55420 30.15409278869629 1.2244691848754883 139.21981811523438 0.18014131486415863 181.99378967285156 0.1954045593738556 0.8936109 0.24837630987167358 True diff --git a/ENCSR926SNI/cherimoya.fold_1.performance.tsv b/ENCSR926SNI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5679f0c1c8b73262708d77fa28b9f074212a2441..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -181.99378967285156 0.5626426935195923 0.1954045593738556 0.04611716419458389 0.8936108946800232 0.8320434093475342 0.24837630987167358 \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_2.evaluate.json b/ENCSR926SNI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 66eb4c0e9682291d36098f097a7da5fb8879247f..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416RWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_2.fit.json b/ENCSR926SNI/cherimoya.fold_2.fit.json deleted file mode 100644 index 6a517c10d40060fc71b6982a655466262c74437f..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF416RWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_2.log b/ENCSR926SNI/cherimoya.fold_2.log deleted file mode 100644 index 86c554ad9dfe31d0a1d0fdfa3100e0d631a016ca..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 36.21628284454346 3.784013271331787 142.17727661132812 0.3112058639526367 206.67861938476562 0.13698144257068634 0.7135676 2.680663824081421 True -1 5758 31.849143743515015 0.4616734981536865 168.2552490234375 0.43243032693862915 192.93833923339844 0.1741705685853958 0.7876486 1.0299626588821411 True -2 8637 31.822317361831665 23.856682062149048 152.4739990234375 0.4400002360343933 190.4422607421875 0.1800123155117035 0.7950647 0.7652014493942261 True -3 11516 32.3105046749115 0.4414677619934082 136.04135131835938 0.2574979364871979 189.0825653076172 0.18085463345050812 0.8073446 0.55511474609375 True -4 14395 31.797863006591797 0.444561243057251 138.96527099609375 0.291779100894928 187.9831085205078 0.18436120450496674 0.81561553 0.5509421825408936 True -5 17274 32.11645269393921 0.44355082511901855 143.91021728515625 0.38662463426589966 187.6495819091797 0.1852283775806427 0.8168355 0.5336564183235168 True -6 20153 35.176597356796265 0.43203043937683105 107.26507568359375 0.2899666428565979 187.50515747070312 0.18544577062129974 0.8177304 0.5029475092887878 True -7 23032 31.98490071296692 3.5513992309570312 148.9457244873047 0.37390172481536865 186.4001007080078 0.188700333237648 0.8242683 0.43073204159736633 True -8 25911 32.408663511276245 0.43624424934387207 163.108642578125 0.4528923034667969 185.79681396484375 0.1906619817018509 0.82892257 0.3972735106945038 True -9 28790 31.995273113250732 6.3410327434539795 114.55558776855469 0.29726749658584595 185.2198944091797 0.19247117638587952 0.8366163 0.38088691234588623 True -10 31669 34.02438044548035 26.484806537628174 181.7064208984375 0.414364755153656 184.40354919433594 0.19535772502422333 0.8460391 0.3433079421520233 True -11 34548 33.10718774795532 0.42830777168273926 180.43817138671875 0.1872248649597168 184.47219848632812 0.19487442076206207 0.8521036 0.32503312826156616 True -12 37427 31.987041234970093 0.43412208557128906 95.61599731445312 0.3643634617328644 184.03343200683594 0.1960587203502655 0.86012113 0.30045580863952637 True -13 40306 31.812129974365234 0.4396049976348877 133.10098266601562 0.3621206283569336 183.57740783691406 0.19777821004390717 0.86495715 0.28732460737228394 True -14 43185 31.77611804008484 0.8366684913635254 138.71755981445312 0.30122479796409607 183.280029296875 0.19875742495059967 0.8681251 0.2745043933391571 True -15 46064 31.423619508743286 0.4253406524658203 119.6142807006836 0.29189497232437134 183.19760131835938 0.19855564832687378 0.87195915 0.26502126455307007 True -16 48943 31.400580167770386 0.4252591133117676 126.40585327148438 0.20779761672019958 183.0938262939453 0.19914661347866058 0.8736229 0.2611657381057739 True -17 51822 31.605950832366943 0.4367706775665283 128.46536254882812 0.1214148998260498 183.11802673339844 0.19896982610225677 0.8737748 0.2585163712501526 True -18 54701 31.299039840698242 0.4382331371307373 102.62368774414062 0.16535484790802002 183.35162353515625 0.19801698625087738 0.87294704 0.2575887143611908 False -19 57580 31.235854625701904 0.42905735969543457 112.74125671386719 0.13414642214775085 183.10768127441406 0.19952982664108276 0.87376904 0.25881436467170715 False diff --git a/ENCSR926SNI/cherimoya.fold_2.performance.tsv b/ENCSR926SNI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0cb628277246c05c20bd3d330798008c1a654aa3..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -183.11802673339844 0.5598711967468262 0.19896982610225677 0.04848354682326317 0.8737748265266418 0.8184368014335632 0.2585163712501526 \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_3.evaluate.json b/ENCSR926SNI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 86f1bbdbff4248804dfd17763c91c658eed2252a..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416RWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_3.fit.json b/ENCSR926SNI/cherimoya.fold_3.fit.json deleted file mode 100644 index 2a627cb5f2eb11f3cb14794a41b8dfe996a90893..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF416RWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_3.log b/ENCSR926SNI/cherimoya.fold_3.log deleted file mode 100644 index 9aebf0dedcc0d72173eda208fef7ea7159f4448e..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 34.464706897735596 3.6485724449157715 138.00914001464844 0.4624951481819153 172.6669158935547 0.1296938955783844 0.69741946 2.6776680946350098 True -1 5404 29.79918384552002 0.58184814453125 153.18002319335938 0.46685856580734253 163.6209259033203 0.15643665194511414 0.76916444 0.9852036237716675 True -2 8106 29.778051376342773 0.6260221004486084 119.57599639892578 0.3276413381099701 161.8295440673828 0.15956954658031464 0.78236586 0.54648357629776 True -3 10808 29.793967485427856 1.753636121749878 145.53419494628906 0.6862050890922546 160.7416229248047 0.16263562440872192 0.791883 0.44885262846946716 True -4 13510 29.791020393371582 0.5726029872894287 150.37359619140625 0.21894274652004242 160.12359619140625 0.16372457146644592 0.80583763 0.42878323793411255 True -5 16212 29.753138780593872 0.5609924793243408 118.24836730957031 0.39996880292892456 159.5366668701172 0.16617263853549957 0.8102591 0.4412156939506531 True -6 18914 29.364205360412598 0.561164379119873 137.67465209960938 0.3212583363056183 159.19549560546875 0.1671300083398819 0.8156506 0.40967684984207153 True -7 21616 29.29558038711548 23.059616088867188 145.57308959960938 0.34130245447158813 158.6793670654297 0.1690702587366104 0.8206802 0.39811256527900696 True -8 24318 29.189993381500244 29.908419609069824 145.44287109375 0.3899666965007782 158.33265686035156 0.17017459869384766 0.8277798 0.3664852976799011 True -9 27020 29.3494291305542 0.5598893165588379 111.60092163085938 0.29312533140182495 158.0611114501953 0.17105844616889954 0.83444035 0.3350403904914856 True -10 29722 30.243200063705444 4.5232834815979 146.22203063964844 0.2247510552406311 157.84695434570312 0.17176951467990875 0.8411224 0.32476115226745605 True -11 32424 29.1804461479187 0.8925204277038574 141.97781372070312 0.5453633069992065 157.4293975830078 0.1735312044620514 0.8461464 0.30889031291007996 True -12 35126 29.15074133872986 2.3005549907684326 136.09793090820312 0.2995055913925171 157.18072509765625 0.17433644831180573 0.85107595 0.2918136417865753 True -13 37828 29.362595081329346 0.5544581413269043 111.19328308105469 0.41368210315704346 156.91769409179688 0.1755603849887848 0.8554215 0.2772054374217987 True -14 40530 29.358709573745728 0.5714001655578613 133.75350952148438 0.40153753757476807 156.80152893066406 0.17571885883808136 0.8626403 0.26595765352249146 True -15 43232 29.37936520576477 0.584789514541626 134.21566772460938 0.2789176106452942 156.57867431640625 0.17616941034793854 0.8658103 0.25417035818099976 True -16 45934 30.144283533096313 0.5713231563568115 123.78199768066406 0.21248608827590942 156.58248901367188 0.17602945864200592 0.8683244 0.247256338596344 True -17 48636 29.348965167999268 0.56813645362854 136.78146362304688 0.21601399779319763 156.64060974121094 0.1755271553993225 0.87221533 0.24186275899410248 True -18 51338 29.302739143371582 0.5561394691467285 153.926513671875 0.16087296605110168 156.55482482910156 0.17589136958122253 0.87333125 0.23952405154705048 True -19 54040 29.287903547286987 0.5671489238739014 116.38923645019531 0.3669915795326233 156.5405731201172 0.1759861707687378 0.87273836 0.23965904116630554 False diff --git a/ENCSR926SNI/cherimoya.fold_3.performance.tsv b/ENCSR926SNI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 39c098dc959a88349deb7874d3bbb3bc7245f6bd..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -156.55482482910156 0.5773736238479614 0.17589136958122253 0.03710946440696716 0.8733312487602234 0.7787743210792542 0.23952405154705048 \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_4.evaluate.json b/ENCSR926SNI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 5ff3f7f04f803f3e813e27ee4014efcf892323f7..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF416RWG.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_4.fit.json b/ENCSR926SNI/cherimoya.fold_4.fit.json deleted file mode 100644 index b3c7fd5333fd08f266f6ec469cbf516ef68dc74d..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF416RWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926SNI/cherimoya.fold_4.log b/ENCSR926SNI/cherimoya.fold_4.log deleted file mode 100644 index efbf9334a05f31675b35b42e2b7fdce7007f41e1..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 36.99124240875244 3.6726763248443604 144.76084899902344 0.2630939185619354 147.9766845703125 0.11868223547935486 0.71998113 1.6824746131896973 True -1 5782 31.92389440536499 0.6451294422149658 116.94935607910156 0.33541417121887207 140.73492431640625 0.1427428126335144 0.76463896 0.8363913297653198 True -2 8673 31.92523765563965 29.38259243965149 122.8084487915039 0.33503246307373047 139.46031188964844 0.14434613287448883 0.7809512 0.4494853615760803 True -3 11564 32.74380707740784 17.349399089813232 168.02186584472656 0.545906126499176 139.03240966796875 0.14482901990413666 0.7884489 0.403617262840271 True -4 14455 31.890457153320312 0.6445221900939941 105.58847045898438 0.2571445107460022 138.49769592285156 0.1462801694869995 0.8020285 0.38675379753112793 True -5 17346 31.936316967010498 0.6165390014648438 100.61436462402344 0.3964436650276184 138.15501403808594 0.14741790294647217 0.8052978 0.3903444707393646 True -6 20237 32.556987047195435 18.755492448806763 115.06338500976562 0.15073162317276 137.7071533203125 0.14965593814849854 0.80997324 0.3647501766681671 True -7 23128 31.884859323501587 2.8880081176757812 116.13597106933594 0.26871997117996216 137.31190490722656 0.15118633210659027 0.813927 0.33923542499542236 True -8 26019 31.63481640815735 0.6243665218353271 137.2272186279297 0.2569802403450012 137.23422241210938 0.15096236765384674 0.81992406 0.2949305772781372 True -9 28910 31.267866134643555 0.6156654357910156 131.33729553222656 0.33282914757728577 136.8851318359375 0.15240269899368286 0.8234026 0.27768099308013916 True -10 31801 31.360947608947754 34.21684002876282 148.8454132080078 0.29797792434692383 136.6868896484375 0.1526450365781784 0.82926303 0.26082396507263184 True -11 34692 31.406204223632812 0.6289463043212891 103.63619995117188 0.15823283791542053 136.5563507080078 0.1530911922454834 0.84086555 0.24314314126968384 True -12 37583 32.10960602760315 6.254161834716797 127.695068359375 0.2661493122577667 136.29904174804688 0.1542823165655136 0.84519464 0.2295924872159958 True -13 40474 31.292972803115845 1.8972985744476318 135.22821044921875 0.21905207633972168 135.91529846191406 0.15552932024002075 0.8530951 0.21217244863510132 True -14 43365 31.30645728111267 0.6235895156860352 93.94268798828125 0.214114710688591 135.83135986328125 0.15610185265541077 0.8581137 0.20000319182872772 True -15 46256 31.43279457092285 0.6377513408660889 117.1275863647461 0.17720633745193481 135.64166259765625 0.1567046344280243 0.86190456 0.19406995177268982 True -16 49147 31.553147077560425 0.6317057609558105 122.79529571533203 0.24107825756072998 135.7654571533203 0.15614911913871765 0.8643248 0.18781347572803497 True -17 52038 31.5260066986084 0.6308078765869141 112.1462631225586 0.19742479920387268 135.73191833496094 0.15552778542041779 0.86744976 0.1860639452934265 True -18 54929 31.48567295074463 0.6278488636016846 133.62649536132812 0.14918343722820282 135.79037475585938 0.15589044988155365 0.8659301 0.1851574033498764 False -19 57820 31.517366886138916 0.6364903450012207 165.0116729736328 0.1979200839996338 135.7406005859375 0.15640687942504883 0.866218 0.1857587844133377 False diff --git a/ENCSR926SNI/cherimoya.fold_4.performance.tsv b/ENCSR926SNI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index deddf5ae133f10802da5d45fc5376d243f04bee7..0000000000000000000000000000000000000000 --- a/ENCSR926SNI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -135.73191833496094 0.5922064781188965 0.1555277556180954 0.029667377471923828 0.8674497604370117 0.7456640005111694 0.1860639452934265 \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_0.evaluate.json b/ENCSR926TFY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e31f9492a4a1b58394faa2b6833a0414865c5466..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772DFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_0.fit.json b/ENCSR926TFY/cherimoya.fold_0.fit.json deleted file mode 100644 index 333b1af9ebb9761cc450740c800d19ac98747a7a..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF772DFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_0.log b/ENCSR926TFY/cherimoya.fold_0.log deleted file mode 100644 index 18ef2f3854fbf43755cbacb7087cb6771fd4cff5..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2082 27.325177431106567 3.7625319957733154 265.38134765625 0.608048677444458 426.51580810546875 0.4184960126876831 0.5378278 9.152969360351562 True -1 4164 23.04128360748291 0.45163607597351074 241.98696899414062 0.49447494745254517 355.8417663574219 0.5737457871437073 0.6196537 3.4686567783355713 True -2 6246 23.0372314453125 0.43406176567077637 283.9405517578125 0.5083661079406738 335.1569519042969 0.6157912611961365 0.63091326 0.9703867435455322 True -3 8328 22.99643087387085 0.43469953536987305 235.2581787109375 0.45608529448509216 329.4640808105469 0.6263693571090698 0.6373356 0.5699086785316467 True -4 10410 22.965455770492554 0.42873215675354004 246.40615844726562 0.5053197145462036 327.0137634277344 0.63125079870224 0.65157783 0.5314832329750061 True -5 12492 23.24438190460205 26.089494228363037 278.15252685546875 0.3383835554122925 325.76702880859375 0.633662760257721 0.6533985 0.4734361171722412 True -6 14574 23.258694410324097 0.9713344573974609 276.13671875 0.6149812936782837 324.4378356933594 0.6366908550262451 0.6589908 0.4584914445877075 True -7 16656 23.342951774597168 26.85964345932007 279.3397216796875 0.37116312980651855 323.36700439453125 0.6389691829681396 0.6709113 0.43077796697616577 True -8 18738 23.40999436378479 0.9556944370269775 311.6380615234375 0.6068054437637329 322.2069091796875 0.6412171125411987 0.6814678 0.4199545681476593 True -9 20820 23.25059461593628 8.2978355884552 245.51959228515625 0.3359009325504303 321.4661865234375 0.6428688764572144 0.6914464 0.4131869673728943 True -10 22902 22.979472637176514 1.6218152046203613 258.6397399902344 0.4075705111026764 320.47625732421875 0.6448955535888672 0.6993483 0.39551475644111633 True -11 24984 23.03723382949829 0.44997501373291016 247.07376098632812 0.44840824604034424 319.5848083496094 0.6466814875602722 0.709066 0.38789623975753784 True -12 27066 22.93027687072754 0.43674468994140625 263.5843505859375 0.34815269708633423 318.6602783203125 0.6483679413795471 0.7202281 0.37177255749702454 True -13 29148 22.55376648902893 0.44655632972717285 264.9934387207031 0.4291987121105194 317.6869201660156 0.6501021385192871 0.73146373 0.3601124584674835 True -14 31230 22.597617149353027 0.4358644485473633 250.98060607910156 0.2525103986263275 317.07708740234375 0.6511456370353699 0.73694116 0.35129088163375854 True -15 33312 22.548577308654785 0.4344217777252197 241.32363891601562 0.22016766667366028 316.6827697753906 0.6518440246582031 0.7415632 0.34841611981391907 True -16 35394 22.537588119506836 3.6447348594665527 289.97760009765625 0.23111283779144287 316.4291076660156 0.652249813079834 0.74799347 0.34714293479919434 True -17 37476 22.526904582977295 0.43221592903137207 221.60960388183594 0.2500576376914978 316.517333984375 0.6520737409591675 0.75015604 0.3463127911090851 True -18 39558 22.667295217514038 0.500025749206543 240.745361328125 0.22237998247146606 316.776123046875 0.6515815854072571 0.7491586 0.3525347113609314 False -19 41640 22.518736600875854 0.43712878227233887 279.2571105957031 0.3572176694869995 316.84844970703125 0.6513015031814575 0.74828434 0.3541679382324219 False diff --git a/ENCSR926TFY/cherimoya.fold_0.performance.tsv b/ENCSR926TFY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cf07cd72388db906ee997456022a7b53bd9bcdc4..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -316.517333984375 0.2965669333934784 0.6520738005638123 0.2050865739583969 0.750156044960022 0.7021074295043945 0.3463127911090851 \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_1.evaluate.json b/ENCSR926TFY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e756498bee1f05bb38f2f86161b851d467748164..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772DFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_1.fit.json b/ENCSR926TFY/cherimoya.fold_1.fit.json deleted file mode 100644 index d5c8337459bf0001c786739a473909aa563d816b..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF772DFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_1.log b/ENCSR926TFY/cherimoya.fold_1.log deleted file mode 100644 index 774ea0d76f4ce1d445f89535c0bf9342488ff117..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2079 27.713873147964478 3.470979928970337 278.7905578613281 0.6189470291137695 429.3839111328125 0.42377719283103943 0.5322528 8.947648048400879 True -1 4158 22.953113317489624 0.5577471256256104 224.1734619140625 0.49913930892944336 356.7202453613281 0.5830765962600708 0.6373882 2.7849531173706055 True -2 6237 22.951849460601807 0.5336410999298096 252.9870147705078 0.5114215016365051 341.0552062988281 0.617547869682312 0.6528286 0.6821687817573547 True -3 8316 23.036070346832275 0.5270261764526367 268.82080078125 0.3405649662017822 336.04327392578125 0.6256780624389648 0.66181934 0.4527502655982971 True -4 10395 23.094902992248535 0.535470724105835 321.38031005859375 0.4705227315425873 333.4599304199219 0.6312354207038879 0.66448635 0.42273613810539246 True -5 12474 22.529140949249268 0.5227596759796143 246.10281372070312 0.42445093393325806 331.9945068359375 0.634619951248169 0.67165947 0.40792611241340637 True -6 14553 22.575003147125244 0.5313713550567627 263.3516845703125 0.40004709362983704 331.1571960449219 0.6366903185844421 0.68015724 0.4051453769207001 True -7 16632 22.69729447364807 12.648983478546143 262.5242919921875 0.3434516191482544 329.6169128417969 0.6399444937705994 0.6899558 0.39360445737838745 True -8 18711 22.56020498275757 0.89455246925354 299.0965576171875 0.29470425844192505 328.67596435546875 0.6420530676841736 0.6970991 0.38347628712654114 True -9 20790 22.743266344070435 0.5284905433654785 211.50262451171875 0.39705705642700195 327.2853088378906 0.644696831703186 0.71275836 0.3744737505912781 True -10 22869 22.545687437057495 0.5276327133178711 278.99981689453125 0.3438955247402191 326.4576416015625 0.6465916037559509 0.7199022 0.36484837532043457 True -11 24948 22.541051149368286 0.5264432430267334 258.40191650390625 0.3663210868835449 325.33551025390625 0.6487635374069214 0.72994256 0.3481968641281128 True -12 27027 22.86198115348816 0.5250368118286133 216.5340576171875 0.27616384625434875 324.41656494140625 0.6507322788238525 0.73964 0.3399883806705475 True -13 29106 22.542603492736816 0.5193123817443848 241.89993286132812 0.41563743352890015 323.36541748046875 0.6525179743766785 0.75273347 0.32417023181915283 True -14 31185 22.496054887771606 0.5222699642181396 236.42193603515625 0.3074513077735901 322.7638244628906 0.6538371443748474 0.76031303 0.3161238431930542 True -15 33264 22.509179830551147 0.518160343170166 266.8478698730469 0.3588640093803406 322.14544677734375 0.6547148823738098 0.7643658 0.3135659694671631 True -16 35343 22.78527808189392 0.5192837715148926 233.97381591796875 0.3710782527923584 321.84088134765625 0.6549155116081238 0.768678 0.31075000762939453 True -17 37422 22.534895420074463 0.5174531936645508 240.09481811523438 0.28995001316070557 321.9048767089844 0.6544978618621826 0.7700539 0.3118979334831238 True -18 39501 22.48762798309326 0.5265703201293945 225.2335205078125 0.265727698802948 321.9944152832031 0.6540619134902954 0.7695345 0.3149263262748718 False -19 41580 22.48932671546936 0.5225367546081543 235.0682830810547 0.3019554018974304 322.0814208984375 0.6537646055221558 0.76955724 0.317361056804657 False diff --git a/ENCSR926TFY/cherimoya.fold_1.performance.tsv b/ENCSR926TFY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a8d0fb4fe50ea8d032005cebbcf1bff148587993..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -321.9048767089844 0.293660432100296 0.6544979810714722 0.20882482826709747 0.7700539231300354 0.7368300557136536 0.3118979334831238 \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_2.evaluate.json b/ENCSR926TFY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index fff99ad382e129bd1e00c2bbcd6a825e381cfec7..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772DFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_2.fit.json b/ENCSR926TFY/cherimoya.fold_2.fit.json deleted file mode 100644 index 7d30610835ee35df365dbcac774739be262c0853..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF772DFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_2.log b/ENCSR926TFY/cherimoya.fold_2.log deleted file mode 100644 index d00c8c3072b544abe4fe5e81ec962819b8e9d88c..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2224 29.094449043273926 3.31925630569458 260.7797546386719 0.5589597225189209 430.3215026855469 0.42895886301994324 0.53823507 6.756462574005127 True -1 4448 24.544950485229492 0.4056549072265625 255.01144409179688 0.45782098174095154 355.8484802246094 0.5872381925582886 0.66007614 2.375027656555176 True -2 6672 24.57351517677307 0.40613675117492676 242.26141357421875 0.515802264213562 342.7203063964844 0.6157026886940002 0.6425552 0.8620984554290771 False -3 8896 24.602426528930664 0.40962886810302734 252.24855041503906 0.4839630722999573 337.03875732421875 0.6262580156326294 0.65365505 0.6226814985275269 False -4 11120 24.513365983963013 0.41280436515808105 301.65966796875 0.4766365885734558 335.2134094238281 0.6300572156906128 0.65150255 0.5289707183837891 False -5 13344 24.51056671142578 0.4054136276245117 228.7033233642578 0.4627152681350708 333.4161376953125 0.634792685508728 0.6624656 0.504759669303894 True -6 15568 24.57110095024109 0.410686731338501 301.0129089355469 0.5150894522666931 332.08447265625 0.6372752785682678 0.673205 0.48278260231018066 True -7 17792 24.58171010017395 0.40012311935424805 268.803955078125 0.30598533153533936 330.7145690917969 0.640339732170105 0.68439627 0.44833773374557495 True -8 20016 24.546086072921753 28.93104600906372 280.33392333984375 0.5114957094192505 329.64031982421875 0.6423588395118713 0.69455105 0.43580830097198486 True -9 22240 24.89715075492859 0.4648160934448242 254.4266815185547 0.40394729375839233 328.680419921875 0.6445063352584839 0.70453 0.4128658175468445 True -10 24464 24.759456634521484 0.40438222885131836 301.50079345703125 0.4482630491256714 327.6173400878906 0.6465585231781006 0.713116 0.3951707184314728 True -11 26688 24.309805393218994 0.40376901626586914 300.62969970703125 0.45463913679122925 326.82275390625 0.6480227708816528 0.72438693 0.3901898264884949 True -12 28912 24.04988956451416 0.4002952575683594 259.26202392578125 0.2841950058937073 325.7207336425781 0.6499419808387756 0.7320761 0.37725067138671875 True -13 31136 24.08570098876953 0.4147207736968994 287.04498291015625 0.3884231150150299 324.6950378417969 0.6513344049453735 0.7415206 0.36511775851249695 True -14 33360 24.129257917404175 0.40305638313293457 241.7289276123047 0.34862497448921204 323.9431457519531 0.6526950597763062 0.749812 0.3542933166027069 True -15 35584 24.12009310722351 0.4055454730987549 239.70001220703125 0.32284191250801086 323.53668212890625 0.6534284353256226 0.7593519 0.34436604380607605 True -16 37808 24.179258346557617 0.40295934677124023 261.2067565917969 0.25397825241088867 323.4969177246094 0.6536117196083069 0.76121795 0.3447866439819336 True -17 40032 24.26227903366089 23.988579511642456 254.96514892578125 0.23583711683750153 323.57012939453125 0.653225302696228 0.7631116 0.34852665662765503 True -18 42256 24.376863956451416 0.4149918556213379 254.11537170410156 0.271915078163147 323.523193359375 0.6527943015098572 0.76247084 0.35060617327690125 False -19 44480 24.14728832244873 0.4052085876464844 202.30682373046875 0.2104087471961975 323.9510192871094 0.6525031328201294 0.76014733 0.3533446788787842 False diff --git a/ENCSR926TFY/cherimoya.fold_2.performance.tsv b/ENCSR926TFY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 35f8caed59eab4d98f6baffd7210bff2f014496f..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -323.57012939453125 0.2950771450996399 0.653225302696228 0.2099502831697464 0.7631115913391113 0.7210026979446411 0.34852665662765503 \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_3.evaluate.json b/ENCSR926TFY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5d49dfb922e275dfa395bab13092e3c9331a0afa..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772DFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_3.fit.json b/ENCSR926TFY/cherimoya.fold_3.fit.json deleted file mode 100644 index e13c9653247c04724222b117300d9a5b478be965..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF772DFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_3.log b/ENCSR926TFY/cherimoya.fold_3.log deleted file mode 100644 index cc751a9b964e3b2ef69516f16445c5da720369d3..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2149 28.508498668670654 3.325103998184204 272.44232177734375 0.6853262186050415 423.6827392578125 0.4243083596229553 0.54557085 8.588114738464355 True -1 4298 24.21469473838806 14.43872356414795 318.58099365234375 0.44661545753479004 351.2272033691406 0.5842577815055847 0.64597046 2.794921398162842 True -2 6447 23.960158348083496 0.44740843772888184 260.50286865234375 0.6213100552558899 336.00665283203125 0.6155030131340027 0.64524496 0.8784111142158508 False -3 8596 23.714794874191284 0.42885851860046387 265.02801513671875 0.3804633319377899 330.9747009277344 0.6232370138168335 0.64969736 0.6173759698867798 True -4 10745 23.70315170288086 0.4248795509338379 256.3099060058594 0.4945375919342041 328.7423400878906 0.627700686454773 0.65291935 0.495349258184433 True -5 12894 23.66019916534424 17.60090732574463 274.522705078125 0.5382764339447021 327.13531494140625 0.6310151815414429 0.6649664 0.4571568965911865 True -6 15043 23.811779975891113 0.44853687286376953 256.561279296875 0.4537122845649719 326.3880615234375 0.6329158544540405 0.6699505 0.4449932277202606 True -7 17192 23.742995023727417 0.4381415843963623 260.8855895996094 0.4017046093940735 325.13739013671875 0.6353960633277893 0.67873186 0.4436453580856323 True -8 19341 23.709797859191895 0.43686461448669434 272.9190673828125 0.36093172430992126 324.05316162109375 0.6374247074127197 0.69416964 0.41659459471702576 True -9 21490 23.67917823791504 0.42734193801879883 231.63702392578125 0.4464659094810486 323.25927734375 0.6392366290092468 0.6991608 0.40299415588378906 True -10 23639 23.691888570785522 0.4417130947113037 256.25042724609375 0.3329530358314514 322.0602111816406 0.6415891051292419 0.7101757 0.3909885883331299 True -11 25788 23.700746297836304 0.4381594657897949 263.29498291015625 0.41691696643829346 321.34320068359375 0.6430693864822388 0.71879154 0.37858811020851135 True -12 27937 23.754945278167725 0.43205928802490234 235.35745239257812 0.3671097755432129 320.2232666015625 0.6450508832931519 0.7302748 0.3662312924861908 True -13 30086 23.691643238067627 0.4308741092681885 250.8520965576172 0.4780656099319458 319.2359924316406 0.6466906070709229 0.7404636 0.3510340452194214 True -14 32235 24.346458435058594 12.273899555206299 304.1025085449219 0.2752319872379303 318.42041015625 0.6481940150260925 0.74777424 0.3416318893432617 True -15 34384 23.811342000961304 0.5645737648010254 256.6035461425781 0.2849350869655609 317.9002380371094 0.6488959789276123 0.7534693 0.3379712402820587 True -16 36533 23.71728253364563 0.43226099014282227 243.94769287109375 0.2864486575126648 317.672119140625 0.6490758061408997 0.7578187 0.3365767002105713 True -17 38682 23.31325340270996 0.42877912521362305 225.24314880371094 0.36157822608947754 317.6351013183594 0.6489042639732361 0.76203704 0.3363449275493622 True -18 40831 23.274317502975464 1.8452088832855225 263.91461181640625 0.2765871286392212 317.74151611328125 0.6485275030136108 0.7618507 0.339956670999527 False -19 42980 23.406909227371216 0.4247763156890869 224.23779296875 0.22530865669250488 317.7429504394531 0.648212194442749 0.7604705 0.34417903423309326 False diff --git a/ENCSR926TFY/cherimoya.fold_3.performance.tsv b/ENCSR926TFY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 60610806f52c99da2343e8d8885efba68fcb7a51..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.6351013183594 0.2965873181819916 0.6489042639732361 0.20648974180221558 0.7620370388031006 0.7145798802375793 0.3363449275493622 \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_4.evaluate.json b/ENCSR926TFY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 42648805c84e28d126a0e74896fd514bd217b20a..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF772DFI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_4.fit.json b/ENCSR926TFY/cherimoya.fold_4.fit.json deleted file mode 100644 index 0b6f1d60fdf3058140784e8dd84cf5a0db918601..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF772DFI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR926TFY/cherimoya.fold_4.log b/ENCSR926TFY/cherimoya.fold_4.log deleted file mode 100644 index e6aa448f7d448de9457018b2e47555d6009cf5ad..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2170 28.409729957580566 4.137519598007202 304.5704650878906 0.7611347436904907 422.1571350097656 0.4205450713634491 0.5723368 8.280263900756836 True -1 4340 23.881516933441162 1.5903398990631104 284.5340270996094 0.472739577293396 349.5707092285156 0.5829566717147827 0.66096354 2.9299471378326416 True -2 6510 23.985841512680054 0.42791128158569336 268.55645751953125 0.37720632553100586 332.3749084472656 0.6171757578849792 0.6711269 0.6983423233032227 True -3 8680 23.957266569137573 0.6095316410064697 290.94146728515625 0.49663737416267395 327.2072448730469 0.6254037618637085 0.67725253 0.5181373357772827 True -4 10850 23.921109199523926 0.425555944442749 276.13262939453125 0.6345710754394531 325.31121826171875 0.6286221146583557 0.68095136 0.43710586428642273 True -5 13020 23.905061721801758 2.6239635944366455 272.512451171875 0.4645915627479553 323.9114074707031 0.6317837834358215 0.6837241 0.4253987967967987 True -6 15190 23.896930932998657 0.7297682762145996 244.5867919921875 0.4139053225517273 322.8341369628906 0.6343162655830383 0.6975733 0.4087561368942261 True -7 17360 24.028111934661865 0.42188477516174316 233.45849609375 0.3849807381629944 321.6424560546875 0.6366357803344727 0.7055258 0.40537765622138977 True -8 19530 23.888969898223877 0.4273691177368164 277.7940979003906 0.46037405729293823 320.61529541015625 0.6389845609664917 0.70976174 0.39835330843925476 True -9 21700 23.91309905052185 0.4206535816192627 207.42201232910156 0.22613340616226196 319.66290283203125 0.6410911679267883 0.7203852 0.38451874256134033 True -10 23870 23.90102195739746 1.704153299331665 233.76039123535156 0.3460210859775543 318.72601318359375 0.6429250836372375 0.7282419 0.37352997064590454 True -11 26040 23.94943642616272 0.42259931564331055 232.85800170898438 0.40716052055358887 318.015625 0.6445720195770264 0.7356243 0.36230072379112244 True -12 28210 23.881808757781982 0.41773128509521484 271.7200622558594 0.2751358449459076 317.20391845703125 0.64637690782547 0.74380153 0.3518766462802887 True -13 30380 23.903706550598145 0.41667723655700684 298.47869873046875 0.36549195647239685 316.2185974121094 0.6478735208511353 0.755343 0.33650538325309753 True -14 32550 24.039421319961548 12.781129837036133 257.9586181640625 0.3471321761608124 315.888916015625 0.649264931678772 0.76194173 0.3289830982685089 True -15 34720 24.517715215682983 16.212865591049194 259.3289489746094 0.23109257221221924 315.5545349121094 0.6500484347343445 0.76803935 0.3275713622570038 True -16 36890 23.988176822662354 0.42281651496887207 269.84088134765625 0.2547849118709564 315.3284606933594 0.6500924825668335 0.77169836 0.32672131061553955 True -17 39060 23.93621826171875 0.42441463470458984 248.51443481445312 0.1819819211959839 315.159912109375 0.6500223278999329 0.7749865 0.326097309589386 True -18 41230 23.89431118965149 1.5293810367584229 221.72125244140625 0.32799750566482544 315.1641540527344 0.6497617959976196 0.7726814 0.3318941295146942 False -19 43400 23.953001737594604 0.42566466331481934 244.78082275390625 0.19183297455310822 315.428466796875 0.649442732334137 0.77252245 0.3338385820388794 False diff --git a/ENCSR926TFY/cherimoya.fold_4.performance.tsv b/ENCSR926TFY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c111c35229ca4a501ee8ccfc7f405c3be76a30b1..0000000000000000000000000000000000000000 --- a/ENCSR926TFY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -315.159912109375 0.2979907989501953 0.6500222682952881 0.20646467804908752 0.7749865055084229 0.7142717242240906 0.326097309589386 \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_0.evaluate.json b/ENCSR928PKL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 186123783bd1eafbbf337cc31a96b3cddaaf807c..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF125BCD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_0.fit.json b/ENCSR928PKL/cherimoya.fold_0.fit.json deleted file mode 100644 index dbbf87149037e1db72f0b70dfe5fc242092bf758..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF125BCD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_0.log b/ENCSR928PKL/cherimoya.fold_0.log deleted file mode 100644 index ff3a0da4bf4c2f6dbdc922ff8630ce228c9391bc..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2759 35.75575661659241 3.9390954971313477 343.6104736328125 0.44619888067245483 447.7745666503906 0.23239898681640625 0.78041786 3.6624538898468018 True -1 5518 30.98656964302063 0.8284645080566406 388.78839111328125 0.4832468628883362 423.6452331542969 0.2797928750514984 0.8269671 0.8984663486480713 True -2 8277 30.716575384140015 0.5772790908813477 488.9809265136719 0.33643752336502075 418.56158447265625 0.28798729181289673 0.8356052 0.48588231205940247 True -3 11036 30.50476908683777 0.6074790954589844 359.7706604003906 0.28582096099853516 414.8375244140625 0.29362887144088745 0.84665406 0.28283193707466125 True -4 13795 30.137109994888306 0.5902845859527588 371.915771484375 0.252044141292572 413.3185729980469 0.2966892123222351 0.85440874 0.26594629883766174 True -5 16554 30.16296696662903 0.5820250511169434 354.42364501953125 0.36087238788604736 413.2030944824219 0.2968509793281555 0.8556709 0.26611587405204773 True -6 19313 30.1593337059021 0.6086840629577637 374.09332275390625 0.22737304866313934 411.5577087402344 0.3001643121242523 0.8614897 0.24826429784297943 True -7 22072 30.165879487991333 1.7070667743682861 308.21710205078125 0.1748243272304535 410.76068115234375 0.3017895519733429 0.86669695 0.2225547432899475 True -8 24831 30.22696614265442 0.6071374416351318 323.3232421875 0.12967781722545624 410.27191162109375 0.3022992014884949 0.868608 0.21150490641593933 True -9 27590 30.165358781814575 0.5901021957397461 358.885498046875 0.2891659438610077 409.4688415527344 0.30432116985321045 0.87432957 0.19828931987285614 True -10 30349 30.147217750549316 0.5906162261962891 323.45318603515625 0.27615708112716675 408.7951354980469 0.30544784665107727 0.8767216 0.19044512510299683 True -11 33108 30.13711714744568 0.6005923748016357 321.0904846191406 0.17489537596702576 408.2515563964844 0.30691951513290405 0.8799129 0.19115106761455536 True -12 35867 30.12648844718933 0.6062965393066406 419.1047058105469 0.22073903679847717 407.0846862792969 0.3091984689235687 0.88604724 0.17816318571567535 True -13 38626 30.21378517150879 0.6080746650695801 343.60443115234375 0.10870452225208282 406.58221435546875 0.30965086817741394 0.8870731 0.1699913889169693 True -14 41385 30.163415908813477 0.6192169189453125 372.2167663574219 0.18203437328338623 405.861572265625 0.31167033314704895 0.89162004 0.16606345772743225 True -15 44144 30.16230297088623 0.6098692417144775 269.3216552734375 0.13157117366790771 405.856689453125 0.31148168444633484 0.8928039 0.16301371157169342 True -16 46903 30.334883451461792 0.613673210144043 309.15380859375 0.15441259741783142 405.5506286621094 0.3122860789299011 0.893919 0.16123704612255096 True -17 49662 30.279025554656982 0.6223642826080322 298.6746520996094 0.3617064356803894 405.4613037109375 0.31196701526641846 0.89595014 0.1591319739818573 True -18 52421 30.164968967437744 2.591118574142456 300.76885986328125 0.13928192853927612 405.3164367675781 0.31279343366622925 0.8945461 0.15921905636787415 False -19 55180 30.200063705444336 14.061909675598145 330.29754638671875 0.14401912689208984 406.1830139160156 0.3099841773509979 0.8947978 0.16073909401893616 False diff --git a/ENCSR928PKL/cherimoya.fold_0.performance.tsv b/ENCSR928PKL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d9cfd42f3296f9ea5b9d8deb5d98d624ceb7555a..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -405.4613037109375 0.45702865719795227 0.31196701526641846 0.10425204783678055 0.8959501385688782 0.87081378698349 0.1591319739818573 \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_1.evaluate.json b/ENCSR928PKL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 757cb0c2433d9009be74ae65a88ed8616d18f029..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF125BCD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_1.fit.json b/ENCSR928PKL/cherimoya.fold_1.fit.json deleted file mode 100644 index edb90a0c0eaa2f799f96d9b426f994dcef94260c..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF125BCD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_1.log b/ENCSR928PKL/cherimoya.fold_1.log deleted file mode 100644 index e6a932e4835a5e185c9ab47c0c779fdf34ad8ed0..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2712 35.380661487579346 4.6254894733428955 333.8732604980469 0.33825933933258057 500.05572509765625 0.23285779356956482 0.7773454 3.159029960632324 True -1 5424 30.320085048675537 0.7326161861419678 324.1315612792969 0.21897602081298828 468.4168701171875 0.28731846809387207 0.8362445 0.7696358561515808 True -2 8136 30.254286289215088 0.7544858455657959 351.95867919921875 0.36405646800994873 461.31634521484375 0.3007010221481323 0.84618884 0.43086615204811096 True -3 10848 30.30367875099182 0.7018043994903564 413.9013671875 0.3179219961166382 458.81170654296875 0.30252012610435486 0.8541264 0.3321465253829956 True -4 13560 30.211251735687256 0.7102982997894287 366.4408874511719 0.33381104469299316 457.3918151855469 0.30561354756355286 0.85808444 0.285159707069397 True -5 16272 29.621755361557007 0.6946520805358887 327.94891357421875 0.28540149331092834 455.6207580566406 0.3088085949420929 0.8614481 0.3025299310684204 True -6 18984 29.607282161712646 0.7066833972930908 338.12158203125 0.28882813453674316 454.0065612792969 0.3119528591632843 0.86430305 0.2994457185268402 True -7 21696 29.714494943618774 0.7018182277679443 365.32208251953125 0.2100626528263092 453.005859375 0.31358158588409424 0.8693972 0.28691601753234863 True -8 24408 29.672346115112305 0.7081584930419922 329.73162841796875 0.2922917604446411 452.8607177734375 0.3130429983139038 0.8741112 0.27978354692459106 True -9 27120 29.581122398376465 0.7078754901885986 370.31976318359375 0.3141430914402008 450.95208740234375 0.31687498092651367 0.8776309 0.24965214729309082 True -10 29832 29.5806941986084 0.7181575298309326 407.56866455078125 0.28248870372772217 449.69580078125 0.3190257251262665 0.88160795 0.23295266926288605 True -11 32544 29.635458946228027 0.6962018013000488 372.31610107421875 0.20473334193229675 449.29205322265625 0.3188663125038147 0.8844081 0.22542572021484375 True -12 35256 29.637418508529663 0.7386574745178223 378.61700439453125 0.29220545291900635 448.2232360839844 0.32102954387664795 0.8893936 0.20684979856014252 True -13 37968 29.672837257385254 0.7252440452575684 286.1396484375 0.16994138062000275 447.01727294921875 0.3227795958518982 0.8934795 0.19973263144493103 True -14 40680 29.67107391357422 0.7144875526428223 355.4228515625 0.2504528760910034 446.62762451171875 0.32295095920562744 0.8976253 0.1896396279335022 True -15 43392 29.660759210586548 0.720905065536499 312.60394287109375 0.18447601795196533 445.9925537109375 0.3242499828338623 0.90114945 0.1799052655696869 True -16 46104 29.65198254585266 0.7205810546875 314.6673583984375 0.1111849993467331 445.48895263671875 0.32524287700653076 0.9025917 0.1749051809310913 True -17 48816 29.76942491531372 0.7300429344177246 339.6901550292969 0.08232136070728302 445.69464111328125 0.3250586688518524 0.9044478 0.1728409379720688 True -18 51528 29.74887466430664 0.7409777641296387 359.7676086425781 0.15247930586338043 445.8224182128906 0.32482025027275085 0.9048345 0.17369820177555084 True -19 54240 29.74986433982849 1.1238031387329102 375.0360107421875 0.20181599259376526 445.80511474609375 0.3248823881149292 0.90244913 0.17488440871238708 False diff --git a/ENCSR928PKL/cherimoya.fold_1.performance.tsv b/ENCSR928PKL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7c0d82a3c978a14d4a9867297f3298296e9f8db7..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -445.8224182128906 0.4462251663208008 0.32482025027275085 0.11498718708753586 0.904834508895874 0.8946614861488342 0.17369820177555084 \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_2.evaluate.json b/ENCSR928PKL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f20ceba71f99c4de03ae3c3b1c0e1748c780fd93..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF125BCD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_2.fit.json b/ENCSR928PKL/cherimoya.fold_2.fit.json deleted file mode 100644 index 2966a7710faf1eb59a59c39fbed4d063d153ad89..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF125BCD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_2.log b/ENCSR928PKL/cherimoya.fold_2.log deleted file mode 100644 index ce81fb143b5f2899b311a6f75aea244d40124a78..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2856 36.398316860198975 3.901740074157715 381.46661376953125 0.2705032229423523 470.6335754394531 0.23522011935710907 0.77084655 2.835646152496338 True -1 5712 32.11955976486206 0.5844976902008057 390.51947021484375 0.48657071590423584 443.6926574707031 0.2819821536540985 0.8238612 0.7739999890327454 True -2 8568 31.84243679046631 0.5362157821655273 343.01690673828125 0.2653646767139435 437.54766845703125 0.2936713993549347 0.8376035 0.34712088108062744 True -3 11424 31.82162594795227 0.5480668544769287 319.1905822753906 0.2740461230278015 434.14605712890625 0.29856178164482117 0.84546185 0.2756492495536804 True -4 14280 31.452497482299805 1.7818334102630615 344.2510986328125 0.2354021817445755 432.8537902832031 0.3012464940547943 0.84829676 0.252103328704834 True -5 17136 31.24503779411316 0.5426108837127686 358.0517883300781 0.26449885964393616 431.9419250488281 0.3025538921356201 0.8517481 0.24637600779533386 True -6 19992 31.193960189819336 0.5421280860900879 323.9213562011719 0.21424272656440735 430.8865966796875 0.3040817081928253 0.8558492 0.23999455571174622 True -7 22848 31.170506954193115 0.5389511585235596 332.72998046875 0.3193908929824829 429.7705993652344 0.30645108222961426 0.86262083 0.22450600564479828 True -8 25704 31.19810962677002 0.769899845123291 305.91876220703125 0.23059451580047607 429.0564880371094 0.3075692057609558 0.865537 0.21931277215480804 True -9 28560 31.165740251541138 0.5463464260101318 329.177978515625 0.22487182915210724 428.7029724121094 0.3080894649028778 0.8702384 0.2150779813528061 True -10 31416 31.152225971221924 0.5255327224731445 346.504150390625 0.3030088245868683 427.3071594238281 0.3108096718788147 0.8726703 0.21159735321998596 True -11 34272 31.175589561462402 0.5419676303863525 312.61456298828125 0.1686367392539978 426.34747314453125 0.3128682076931 0.8758623 0.21238110959529877 True -12 37128 31.158482313156128 0.5452449321746826 304.5867919921875 0.16452601552009583 426.5036315917969 0.3118714690208435 0.8796877 0.20235112309455872 True -13 39984 31.242293119430542 0.550398588180542 338.10333251953125 0.19261980056762695 425.2247009277344 0.3142152428627014 0.88257056 0.19527998566627502 True -14 42840 31.1964373588562 0.5458433628082275 333.32318115234375 0.17903301119804382 425.29754638671875 0.3141706883907318 0.88625747 0.18693773448467255 True -15 45696 31.21629762649536 0.5443992614746094 276.94989013671875 0.22153043746948242 424.00048828125 0.31694480776786804 0.88931537 0.1773500293493271 True -16 48552 31.20651912689209 0.5421509742736816 364.0732421875 0.13207724690437317 423.7499694824219 0.31702038645744324 0.8918055 0.1727847307920456 True -17 51408 31.2790789604187 0.541447639465332 291.718994140625 0.11083321273326874 424.0283508300781 0.31714916229248047 0.89025694 0.17037831246852875 False -18 54264 31.188381671905518 0.542351245880127 338.5353088378906 0.15143170952796936 423.78326416015625 0.31802383065223694 0.89072734 0.169556125998497 False -19 57120 31.21142292022705 8.90406847000122 371.01483154296875 0.1465781033039093 424.5098571777344 0.3156336843967438 0.89246356 0.1702180951833725 True diff --git a/ENCSR928PKL/cherimoya.fold_2.performance.tsv b/ENCSR928PKL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f9c98d9b2d207a74f919ad42e3295c5ca093f23a..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -424.5098571777344 0.4528616666793823 0.3156336843967438 0.10792700946331024 0.8924635648727417 0.8713772892951965 0.1702180951833725 \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_3.evaluate.json b/ENCSR928PKL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 538802c181c22253bbe7880baf1c1a15e3a89214..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF125BCD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_3.fit.json b/ENCSR928PKL/cherimoya.fold_3.fit.json deleted file mode 100644 index 2625d1951540e311758c70f52da9c2944ac7d641..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF125BCD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_3.log b/ENCSR928PKL/cherimoya.fold_3.log deleted file mode 100644 index 6b19033d9fe7663f13b0e3a5c0b7b3f440f2a9cc..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 35.64345097541809 4.593891859054565 427.9654846191406 0.3954865634441376 439.0517272949219 0.2394368052482605 0.76430666 3.279752016067505 True -1 5524 30.944119930267334 0.5906887054443359 401.96514892578125 0.45409464836120605 413.4585876464844 0.28499069809913635 0.82641625 0.8341680765151978 True -2 8286 30.81221580505371 0.5554630756378174 379.32806396484375 0.260551393032074 407.42840576171875 0.29427987337112427 0.8443801 0.3343154489994049 True -3 11048 30.842040300369263 0.5487673282623291 459.49005126953125 0.27786508202552795 405.400634765625 0.2966941297054291 0.8482483 0.309089720249176 True -4 13810 30.915897846221924 0.5539727210998535 362.7694091796875 0.2459334135055542 404.17901611328125 0.29924020171165466 0.85327256 0.27036765217781067 True -5 16572 30.793052673339844 0.5221772193908691 360.3069152832031 0.14320826530456543 403.3052062988281 0.3012336194515228 0.8572278 0.2519870698451996 True -6 19334 30.43437170982361 0.58135986328125 384.6981506347656 0.29956868290901184 402.16119384765625 0.3033261001110077 0.8605703 0.2733035981655121 True -7 22096 30.385453462600708 0.5114624500274658 383.2746276855469 0.24665503203868866 401.16046142578125 0.3052225112915039 0.8657939 0.25104644894599915 True -8 24858 30.345160245895386 0.5218138694763184 361.6480712890625 0.2071273922920227 401.01873779296875 0.30558890104293823 0.8669436 0.24700812995433807 True -9 27620 30.339850425720215 0.5500342845916748 316.45611572265625 0.22042149305343628 400.16815185546875 0.30662208795547485 0.872008 0.232569620013237 True -10 30382 30.332414150238037 0.6924793720245361 321.2919006347656 0.22394874691963196 399.5264587402344 0.30802926421165466 0.8766339 0.2227233350276947 True -11 33144 30.333723306655884 0.538994312286377 330.4998779296875 0.22320881485939026 399.2063903808594 0.3085406720638275 0.88127965 0.21640241146087646 True -12 35906 30.219356298446655 0.5142171382904053 302.8337707519531 0.26450246572494507 398.3223876953125 0.3099709153175354 0.8833778 0.20661361515522003 True -13 38668 30.276323318481445 0.5162312984466553 427.7640075683594 0.2858450412750244 397.2350158691406 0.31237876415252686 0.8894444 0.1964576542377472 True -14 41430 30.303781509399414 0.527848482131958 411.478271484375 0.2541700601577759 396.95391845703125 0.3123907744884491 0.89215475 0.18302586674690247 True -15 44192 30.27047610282898 0.5262675285339355 334.57342529296875 0.16012725234031677 396.11151123046875 0.3148529529571533 0.8960204 0.1771584451198578 True -16 46954 30.272056102752686 0.5127780437469482 374.58319091796875 0.1446935534477234 395.96942138671875 0.3151549994945526 0.8966135 0.16849736869335175 True -17 49716 30.269861459732056 0.515064001083374 303.571533203125 0.12940514087677002 396.2777099609375 0.3140312433242798 0.8972621 0.1666414886713028 True -18 52478 30.272549390792847 0.5273480415344238 329.2290344238281 0.16376568377017975 396.5287170410156 0.3136062026023865 0.89902914 0.16569843888282776 True -19 55240 30.30677556991577 0.5389881134033203 364.32220458984375 0.09941031038761139 397.029541015625 0.31237682700157166 0.8987402 0.16672483086585999 False diff --git a/ENCSR928PKL/cherimoya.fold_3.performance.tsv b/ENCSR928PKL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index cb21d955f7fcc14e1d62be2f0196dffcb5387c92..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -396.5287170410156 0.4570317566394806 0.3136062026023865 0.10564351081848145 0.8990291357040405 0.8694483041763306 0.16569843888282776 \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_4.evaluate.json b/ENCSR928PKL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1b35e5da39207cc6cc2794492ae4038ac993b3d8..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF125BCD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_4.fit.json b/ENCSR928PKL/cherimoya.fold_4.fit.json deleted file mode 100644 index b23d0cb9fef23802dab8109809e873df5eff3f1b..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF125BCD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928PKL/cherimoya.fold_4.log b/ENCSR928PKL/cherimoya.fold_4.log deleted file mode 100644 index ac0bedef37ff8555c146eb25481686c293a9abd0..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2804 36.101683378219604 3.766817569732666 295.53533935546875 0.26931053400039673 405.9895935058594 0.22592328488826752 0.76380694 2.79106068611145 True -1 5608 31.30611801147461 1.0706477165222168 334.8709716796875 0.3154188394546509 385.6932373046875 0.2689445912837982 0.81740135 0.6073585152626038 True -2 8412 31.25010585784912 0.662663459777832 327.1365966796875 0.35238802433013916 381.468994140625 0.27636975049972534 0.82719755 0.2979762852191925 True -3 11216 31.237969160079956 0.6515865325927734 331.5450744628906 0.27746012806892395 378.6487731933594 0.28117355704307556 0.84173244 0.23835721611976624 True -4 14020 31.24998950958252 0.609428882598877 300.3045349121094 0.1489534080028534 377.6881103515625 0.2832033336162567 0.847793 0.21159057319164276 True -5 16824 31.412673950195312 10.452597618103027 358.7593078613281 0.2866674065589905 376.8968811035156 0.2844642996788025 0.85160434 0.2078985720872879 True -6 19628 30.940943241119385 1.3607237339019775 343.3625793457031 0.2886384129524231 376.01812744140625 0.2863444685935974 0.8542673 0.2026820033788681 True -7 22432 30.869529724121094 0.6419284343719482 354.730224609375 0.15822581946849823 374.9754333496094 0.2884894609451294 0.8572573 0.1954093873500824 True -8 25236 30.75909948348999 0.6212396621704102 410.0497741699219 0.2393769919872284 374.57977294921875 0.2887488305568695 0.8631306 0.1946161836385727 True -9 28040 30.745920181274414 0.6173126697540283 304.31640625 0.24228617548942566 373.4880065917969 0.29153716564178467 0.8679677 0.18174900114536285 True -10 30844 30.74335813522339 0.6120965480804443 344.4243469238281 0.23660320043563843 373.3904724121094 0.29167506098747253 0.8707933 0.17470188438892365 True -11 33648 30.72472071647644 0.6300818920135498 407.39923095703125 0.19159755110740662 372.9815673828125 0.2923567593097687 0.8774838 0.1684647500514984 True -12 36452 30.681886672973633 0.5987734794616699 376.689208984375 0.17684559524059296 372.64691162109375 0.2929914891719818 0.8790117 0.16777412593364716 True -13 39256 30.7288715839386 0.622166633605957 382.32061767578125 0.23695717751979828 371.6820983886719 0.2945782244205475 0.8842751 0.1600322425365448 True -14 42060 30.72816038131714 0.6170811653137207 324.40179443359375 0.29977044463157654 371.2418518066406 0.29589587450027466 0.88952714 0.1546158790588379 True -15 44864 30.84520936012268 0.634119987487793 280.62445068359375 0.21712711453437805 370.683349609375 0.2971900701522827 0.89216155 0.150249183177948 True -16 47668 30.670255661010742 0.6101164817810059 311.6573791503906 0.13748160004615784 370.4557800292969 0.2974091172218323 0.8947617 0.14682462811470032 True -17 50472 30.682790279388428 0.5970993041992188 354.242431640625 0.14114105701446533 370.9501953125 0.29638198018074036 0.8959561 0.14586223661899567 True -18 53276 30.65701937675476 0.5930590629577637 295.5361328125 0.12470608949661255 371.06231689453125 0.2964194118976593 0.8953075 0.14648638665676117 False -19 56080 30.619488954544067 0.591658353805542 323.11297607421875 0.30399084091186523 371.1314697265625 0.2962038218975067 0.89442766 0.14667755365371704 False diff --git a/ENCSR928PKL/cherimoya.fold_4.performance.tsv b/ENCSR928PKL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f0db98a60f44921ae3e14245c8ade2de1c4178e5..0000000000000000000000000000000000000000 --- a/ENCSR928PKL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -370.9501953125 0.47083452343940735 0.29638195037841797 0.09409557282924652 0.8959560990333557 0.8645294308662415 0.14586223661899567 \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_0.evaluate.json b/ENCSR928SYE/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2399b0a7114bbaa1857a3e4e54fa5a4198230675..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF850XNY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_0.fit.json b/ENCSR928SYE/cherimoya.fold_0.fit.json deleted file mode 100644 index f5615e7b2a42033bcfb1fc8dfa530bd754325979..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF850XNY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_0.log b/ENCSR928SYE/cherimoya.fold_0.log deleted file mode 100644 index 542b7fc3d2579f723a62f450ddffab7279e0ce81..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2770 34.32890725135803 3.483844757080078 230.1900177001953 0.631636381149292 298.78619384765625 0.15758726000785828 0.6294158 3.8714702129364014 True -1 5540 30.68081045150757 0.5815765857696533 200.66111755371094 0.9308304190635681 282.1790771484375 0.23210185766220093 0.67332876 1.12577486038208 True -2 8310 30.628133058547974 0.5709130764007568 209.77743530273438 0.8920361995697021 278.8550109863281 0.24042610824108124 0.6945895 0.6457136273384094 True -3 11080 30.568824529647827 0.5667915344238281 206.226806640625 0.7795277833938599 276.2650451660156 0.2493549883365631 0.70271474 0.5668196678161621 True -4 13850 30.58637046813965 0.5603866577148438 227.64317321777344 1.044511318206787 274.9585876464844 0.2556597888469696 0.69679767 0.5684177279472351 False -5 16620 30.589232921600342 0.5665853023529053 214.3279266357422 0.8552254438400269 274.1676330566406 0.2586342692375183 0.702992 0.6058666706085205 True -6 19390 30.542709827423096 3.6068482398986816 204.30197143554688 0.647561252117157 273.4832763671875 0.2611306309700012 0.7108749 0.6249051690101624 True -7 22160 30.62976574897766 0.6048972606658936 212.6797637939453 0.45730188488960266 272.81817626953125 0.2649172842502594 0.71372026 0.6310380101203918 True -8 24930 30.728652477264404 0.5869545936584473 264.60504150390625 0.6434335708618164 272.0066223144531 0.2685402035713196 0.71527195 0.5988379716873169 True -9 27700 30.710845947265625 0.5735313892364502 205.55093383789062 0.5711491107940674 271.91009521484375 0.26821884512901306 0.7186571 0.5858044028282166 True -10 30470 31.025429725646973 21.30900478363037 219.33514404296875 0.6236076951026917 271.0999755859375 0.27232182025909424 0.7187711 0.542890191078186 True -11 33240 30.788700103759766 0.5708587169647217 227.4193115234375 0.5708004236221313 270.3790283203125 0.2749912738800049 0.7227638 0.5382763743400574 True -12 36010 31.205780744552612 0.577606201171875 167.872802734375 0.997793436050415 269.81732177734375 0.27773579955101013 0.7292132 0.4985521733760834 True -13 38780 30.64515256881714 0.5759172439575195 190.17633056640625 0.6244912147521973 269.1325988769531 0.2797898054122925 0.7356729 0.4466494619846344 True -14 41550 30.57308840751648 0.5695359706878662 230.2803955078125 0.42506444454193115 268.7825622558594 0.28174304962158203 0.74173725 0.4099474549293518 True -15 44320 30.56171488761902 0.5742874145507812 262.5867004394531 0.3186095356941223 268.53399658203125 0.2813614308834076 0.74858075 0.38288259506225586 True -16 47090 30.598316192626953 1.546844244003296 227.3699951171875 0.3192332088947296 268.31121826171875 0.2832699418067932 0.7537715 0.37035804986953735 True -17 49860 30.617036819458008 0.5703988075256348 206.1403045654297 0.28087693452835083 268.2635192871094 0.2823978066444397 0.75866944 0.3479466140270233 True -18 52630 30.58069157600403 0.5686125755310059 192.62286376953125 0.4463666081428528 268.21368408203125 0.28320616483688354 0.7602838 0.3418956995010376 True -19 55400 30.640557765960693 0.5725729465484619 235.0522003173828 0.3864223062992096 268.0634765625 0.2843574583530426 0.7591749 0.342357337474823 False diff --git a/ENCSR928SYE/cherimoya.fold_0.performance.tsv b/ENCSR928SYE/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a98d3d876fa76ac85729a01f9d45ec3236efec98..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -268.21368408203125 0.4955999553203583 0.28320619463920593 0.07305439561605453 0.7602838277816772 0.723614513874054 0.3418956995010376 \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_1.evaluate.json b/ENCSR928SYE/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9ff435d3c5c0900f0ad5fba8b3aa6ff76104d2c6..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF850XNY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_1.fit.json b/ENCSR928SYE/cherimoya.fold_1.fit.json deleted file mode 100644 index 6a5558da299553f81b1bd4041d25b1d68a16caf6..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF850XNY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_1.log b/ENCSR928SYE/cherimoya.fold_1.log deleted file mode 100644 index eb4c9cf8954cbad6ca51012585a85ea7fdd03022..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 34.132293701171875 3.6712558269500732 204.13223266601562 1.011449933052063 346.1705322265625 0.16838961839675903 0.6359611 3.609346389770508 True -1 5472 30.550568103790283 0.7095379829406738 213.330078125 0.9240217804908752 325.0220947265625 0.2468404769897461 0.68116605 1.3229931592941284 True -2 8208 30.383442640304565 0.699476957321167 203.61851501464844 0.6586871147155762 318.5292663574219 0.26397812366485596 0.7219431 0.6842283606529236 True -3 10944 30.257071495056152 0.6924514770507812 228.68399047851562 0.6893947124481201 316.6994323730469 0.26778024435043335 0.73359334 0.5620426535606384 True -4 13680 30.251304388046265 2.806375741958618 271.2854919433594 1.0170496702194214 314.92596435546875 0.2742195427417755 0.73060364 0.5675843954086304 False -5 16416 30.255009174346924 0.6888806819915771 232.49954223632812 0.5212981700897217 314.1886901855469 0.2759256958961487 0.73458934 0.5957043766975403 True -6 19152 30.29596781730652 0.7319886684417725 228.4040069580078 0.5676788091659546 312.77679443359375 0.28113555908203125 0.74176365 0.5943995118141174 True -7 21888 30.210031270980835 10.843169212341309 182.4229736328125 0.6021063327789307 311.7032775878906 0.2853303551673889 0.7463544 0.6331709027290344 True -8 24624 30.28629779815674 0.7115607261657715 229.46180725097656 0.5536222457885742 311.1588134765625 0.2869262993335724 0.7488555 0.6499401330947876 True -9 27360 30.157188177108765 1.1965036392211914 194.67161560058594 0.7571570873260498 310.75762939453125 0.2881953716278076 0.7569105 0.5944858193397522 True -10 30096 30.386465311050415 0.7079880237579346 195.23716735839844 0.5573477149009705 309.4813537597656 0.2933819591999054 0.75786805 0.6091921925544739 True -11 32832 30.406294345855713 1.7808773517608643 209.31838989257812 0.414770245552063 309.1860656738281 0.29461589455604553 0.761526 0.5920864343643188 True -12 35568 30.492273569107056 0.7163293361663818 183.41836547851562 0.421833872795105 308.352294921875 0.29745760560035706 0.76443136 0.564187228679657 True -13 38304 30.329967975616455 0.7172350883483887 199.0284423828125 0.4214364290237427 307.87213134765625 0.2983752489089966 0.7661047 0.5157918930053711 True -14 41040 30.27949547767639 1.4056594371795654 181.55337524414062 0.5828417539596558 307.1133728027344 0.3005411922931671 0.77254444 0.4833110570907593 True -15 43776 30.26032066345215 0.7074034214019775 179.6902313232422 0.5319668650627136 306.6776123046875 0.30185163021087646 0.7798701 0.4438299536705017 True -16 46512 30.307939767837524 0.7062406539916992 181.42372131347656 0.5841754078865051 306.49896240234375 0.3031395971775055 0.7827248 0.41469526290893555 True -17 49248 30.337152004241943 0.7009813785552979 190.40675354003906 0.3790096938610077 305.66229248046875 0.3062427043914795 0.7849585 0.3911129832267761 True -18 51984 30.232712507247925 0.6983797550201416 196.43539428710938 0.466497004032135 305.79888916015625 0.3053138256072998 0.78602475 0.3820267915725708 True -19 54720 30.249279499053955 0.6966159343719482 214.1832733154297 0.37234410643577576 306.1984558105469 0.303027480840683 0.7851874 0.37946322560310364 False diff --git a/ENCSR928SYE/cherimoya.fold_1.performance.tsv b/ENCSR928SYE/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 989725e622273865925a12891eca268d6c946a81..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -305.79888916015625 0.4769696891307831 0.3053138554096222 0.08490055799484253 0.7860247492790222 0.759605348110199 0.3820267915725708 \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_2.evaluate.json b/ENCSR928SYE/cherimoya.fold_2.evaluate.json deleted file mode 100644 index aa4d83acd981ae422beae9d049b5ae1bb41c04ea..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF850XNY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_2.fit.json b/ENCSR928SYE/cherimoya.fold_2.fit.json deleted file mode 100644 index 6f653db7156507ce5363a6da3fa39fb443c684f0..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF850XNY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_2.log b/ENCSR928SYE/cherimoya.fold_2.log deleted file mode 100644 index 635932d70fd1d9cfdb349ef257f2c27720b8c8a8..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2895 35.94749069213867 3.433993339538574 215.29116821289062 0.9961318969726562 308.604736328125 0.16493920981884003 0.63055086 3.143355369567871 True -1 5790 32.08520746231079 0.5485942363739014 232.90093994140625 0.8465374708175659 289.8537902832031 0.23860594630241394 0.6839618 1.183093547821045 True -2 8685 32.05070924758911 0.5362625122070312 193.16403198242188 0.8391104936599731 285.68743896484375 0.251358300447464 0.7016027 0.5483273863792419 True -3 11580 31.926303148269653 0.5318708419799805 217.6451873779297 0.762507438659668 283.5394592285156 0.2583411633968353 0.7055536 0.5093355774879456 True -4 14475 31.942537784576416 0.5372061729431152 278.00970458984375 0.46330979466438293 282.508056640625 0.2608330249786377 0.71189654 0.49818873405456543 True -5 17370 31.966713666915894 0.5270798206329346 246.4825439453125 0.7209122180938721 281.77728271484375 0.26466649770736694 0.71085215 0.5942315459251404 False -6 20265 31.948212146759033 0.5305173397064209 187.7060089111328 0.5894882678985596 280.8427734375 0.26883891224861145 0.7120617 0.6783074140548706 True -7 23160 31.921326875686646 0.5288825035095215 232.35948181152344 0.7647533416748047 280.4896545410156 0.27027183771133423 0.716727 0.706950306892395 True -8 26055 31.993813037872314 0.5295305252075195 213.06358337402344 0.6202693581581116 279.5621643066406 0.27399933338165283 0.7153909 0.693071186542511 False -9 28950 32.02535438537598 0.5361886024475098 204.20272827148438 0.7919718623161316 279.5190734863281 0.2743588089942932 0.7142437 0.7049524784088135 False -10 31845 32.025838136672974 0.5350127220153809 255.73861694335938 0.31809335947036743 278.50103759765625 0.2775672972202301 0.7191003 0.6382632255554199 True -11 34740 31.9497230052948 0.5278124809265137 244.1625518798828 0.3587535619735718 277.85296630859375 0.28013476729393005 0.7245758 0.6114494204521179 True -12 37635 31.983760118484497 0.53507399559021 217.7449493408203 0.4623523950576782 276.9627990722656 0.28341376781463623 0.7273875 0.5678000450134277 True -13 40530 31.98719096183777 1.3160920143127441 226.5789794921875 0.38673895597457886 276.5284118652344 0.2858336567878723 0.73735344 0.5103988647460938 True -14 43425 32.185163736343384 0.5448930263519287 230.38287353515625 0.43813544511795044 275.93377685546875 0.28738802671432495 0.74466425 0.48100218176841736 True -15 46320 32.084311723709106 0.5391063690185547 212.29721069335938 0.788061261177063 275.5918884277344 0.2888481318950653 0.7514922 0.4430793523788452 True -16 49215 31.933369398117065 0.5380473136901855 261.2550048828125 0.5668654441833496 275.54833984375 0.2882857620716095 0.7569705 0.41077184677124023 True -17 52110 31.935962438583374 0.5390160083770752 221.69631958007812 0.39488041400909424 275.40789794921875 0.28894615173339844 0.75974697 0.3892839550971985 True -18 55005 32.0683057308197 1.5972795486450195 243.99636840820312 0.36644884943962097 275.08221435546875 0.29047730565071106 0.7618075 0.3793847858905792 True -19 57900 32.14673924446106 0.5437242984771729 236.410888671875 0.2602981925010681 275.27398681640625 0.2893773019313812 0.7603534 0.37916988134384155 False diff --git a/ENCSR928SYE/cherimoya.fold_2.performance.tsv b/ENCSR928SYE/cherimoya.fold_2.performance.tsv deleted file mode 100644 index db8c85e89e90847eb418ca0cffc58d4fd0df2b94..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -275.08221435546875 0.491140216588974 0.29047730565071106 0.07486957311630249 0.7618075013160706 0.7266033887863159 0.3793847858905792 \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_3.evaluate.json b/ENCSR928SYE/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3292d88c7becb2fcd12d45af6566289c87852b88..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF850XNY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_3.fit.json b/ENCSR928SYE/cherimoya.fold_3.fit.json deleted file mode 100644 index 0b6b4228f9f116c607a30934490fd353d5aba55f..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF850XNY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_3.log b/ENCSR928SYE/cherimoya.fold_3.log deleted file mode 100644 index 6ac16a74e7c8288c77f37357417275dbffae80f0..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2776 34.72581934928894 3.8264153003692627 216.0522003173828 0.6149702072143555 319.59381103515625 0.15808922052383423 0.6355967 3.531134605407715 True -1 5552 30.654816150665283 0.5794486999511719 219.37942504882812 0.8311333060264587 302.92315673828125 0.22835120558738708 0.6895931 1.4362115859985352 True -2 8328 30.71097469329834 10.220171213150024 212.83392333984375 0.6435308456420898 297.6058349609375 0.24469025433063507 0.70699286 0.6064722537994385 True -3 11104 30.996565341949463 0.5783488750457764 197.93646240234375 0.784546434879303 295.71649169921875 0.25069621205329895 0.71570325 0.6392599940299988 True -4 13880 30.68870234489441 0.5634164810180664 254.5281982421875 0.3877112567424774 295.0538024902344 0.2532351613044739 0.7158095 0.6935067772865295 True -5 16656 30.621230602264404 4.020215034484863 236.15887451171875 0.6560119390487671 294.1739807128906 0.2569534182548523 0.7152327 0.7174482345581055 False -6 19432 30.68895983695984 0.5757870674133301 202.21438598632812 0.6246399879455566 293.79052734375 0.2586199641227722 0.7188215 0.7253391742706299 True -7 22208 30.616925716400146 0.5643446445465088 248.561767578125 0.5431530475616455 292.79302978515625 0.26328524947166443 0.7224453 0.7635915279388428 True -8 24984 30.688870906829834 1.696331262588501 223.0373992919922 0.6934548020362854 292.426513671875 0.26526013016700745 0.7243331 0.7410889863967896 True -9 27760 30.67342209815979 0.5661060810089111 236.76902770996094 0.5196278095245361 292.1215515136719 0.2663617730140686 0.7257278 0.7621486186981201 True -10 30536 30.69250798225403 0.570645809173584 183.13302612304688 0.8045564293861389 291.4877624511719 0.2695052921772003 0.729873 0.674713134765625 True -11 33312 30.686789512634277 0.5698325634002686 217.05496215820312 0.3699799180030823 290.8397216796875 0.2714298665523529 0.7352938 0.6385260224342346 True -12 36088 30.66990613937378 0.5702238082885742 250.78652954101562 0.3986339271068573 290.7262268066406 0.2724956274032593 0.73916346 0.6327111124992371 True -13 38864 30.743382215499878 0.5699920654296875 192.7685089111328 0.4861307144165039 289.7052307128906 0.2762428820133209 0.7450328 0.583122730255127 True -14 41640 30.634387016296387 1.773169994354248 246.6418914794922 0.6539057493209839 288.8970642089844 0.27963876724243164 0.7545132 0.5015560984611511 True -15 44416 30.737715244293213 0.5650837421417236 251.9368133544922 0.4639163911342621 288.808837890625 0.2800297737121582 0.76091343 0.4499928057193756 True -16 47192 30.714747190475464 0.5608935356140137 192.03988647460938 0.3956983983516693 288.33428955078125 0.2812245786190033 0.7664608 0.41603168845176697 True -17 49968 30.677300214767456 0.5609316825866699 196.8175048828125 0.7200377583503723 288.5033264160156 0.28060978651046753 0.77036154 0.387890487909317 True -18 52744 30.82826566696167 0.5711610317230225 211.86016845703125 0.33617883920669556 288.12310791015625 0.2823222279548645 0.7717726 0.37484708428382874 True -19 55520 30.638336420059204 8.71289324760437 208.2042236328125 0.23497387766838074 288.2951965332031 0.28128287196159363 0.77109 0.3725646138191223 False diff --git a/ENCSR928SYE/cherimoya.fold_3.performance.tsv b/ENCSR928SYE/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 86f99ca10fc3b0e2bc131f79556fe35aa45a179a..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -288.12310791015625 0.49137887358665466 0.2823221981525421 0.07793384790420532 0.7717726230621338 0.7386196255683899 0.37484708428382874 \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_4.evaluate.json b/ENCSR928SYE/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fd2165cdc700bfd175f6494501e063e9ba273cd6..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF850XNY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_4.fit.json b/ENCSR928SYE/cherimoya.fold_4.fit.json deleted file mode 100644 index 0f59a72c55beeb95fb45c9ca9b6bb1858e2be4ca..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF850XNY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928SYE/cherimoya.fold_4.log b/ENCSR928SYE/cherimoya.fold_4.log deleted file mode 100644 index 39d86873f574f5f6f6b875d76ed1ef1ced39cafd..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2863 36.522823095321655 5.425171375274658 234.74288940429688 0.7569103837013245 302.14141845703125 0.16068655252456665 0.6196338 3.105962038040161 True -1 5726 31.714643478393555 4.492007255554199 223.60748291015625 0.7854518890380859 286.38885498046875 0.22747351229190826 0.6780921 1.2418010234832764 True -2 8589 31.62371850013733 8.23918080329895 214.99241638183594 0.5931519269943237 283.2494201660156 0.23725488781929016 0.69187135 0.7635525465011597 True -3 11452 31.73363423347473 0.6225950717926025 241.24050903320312 0.6802669763565063 281.3409729003906 0.2436368614435196 0.70111895 0.71614009141922 True -4 14315 31.65742325782776 13.534343004226685 238.84054565429688 0.40546929836273193 279.82769775390625 0.25018736720085144 0.7029573 0.7090178728103638 True -5 17178 32.07965278625488 0.612804651260376 222.445556640625 0.6636478900909424 279.1073913574219 0.25423359870910645 0.70239264 0.7828608155250549 False -6 20041 32.031842947006226 8.539217472076416 228.6561279296875 0.7994163632392883 278.6288757324219 0.2570742070674896 0.7029879 0.7732031345367432 True -7 22904 31.653650522232056 0.6028730869293213 234.96856689453125 0.5073237419128418 277.842041015625 0.2601989507675171 0.70905906 0.7294795513153076 True -8 25767 31.585912466049194 0.605463981628418 184.7935791015625 0.6225606799125671 277.36358642578125 0.2631046175956726 0.7092637 0.7494274377822876 True -9 28630 31.566558122634888 1.6412098407745361 216.78807067871094 0.6847219467163086 277.1236877441406 0.2635442018508911 0.70965624 0.6973927617073059 True -10 31493 31.60705828666687 0.6193697452545166 214.49769592285156 0.7345104217529297 276.57305908203125 0.2661510407924652 0.71235675 0.676024854183197 True -11 34356 31.644213914871216 0.6079764366149902 199.09564208984375 0.46398842334747314 276.09954833984375 0.2682592272758484 0.71912915 0.5800620317459106 True -12 37219 31.742765188217163 1.7582292556762695 187.7254638671875 0.601599931716919 275.2757873535156 0.27147021889686584 0.720961 0.5563073754310608 True -13 40082 31.72119665145874 0.6053190231323242 197.27642822265625 0.5661802291870117 274.62811279296875 0.27389320731163025 0.73311114 0.4960375428199768 True -14 42945 31.66706609725952 0.6008462905883789 246.342529296875 0.4242507219314575 274.1570129394531 0.27629613876342773 0.74170023 0.4508664309978485 True -15 45808 31.602381706237793 0.5992832183837891 218.01478576660156 0.3399893343448639 273.8877868652344 0.27674782276153564 0.74984425 0.4012506902217865 True -16 48671 31.587218523025513 0.6079564094543457 200.8680877685547 0.4341457188129425 273.5904846191406 0.27822285890579224 0.7556794 0.37288960814476013 True -17 51534 31.584235906600952 0.5915126800537109 209.38778686523438 0.3362354338169098 273.7306823730469 0.2779543101787567 0.75876373 0.35795843601226807 True -18 54397 31.57843279838562 0.6102139949798584 169.03334045410156 0.36858463287353516 273.765869140625 0.2768368124961853 0.7573407 0.35038554668426514 False -19 57260 31.58341884613037 0.6102004051208496 160.498291015625 0.3251228928565979 273.73699951171875 0.27745306491851807 0.7568103 0.3503618836402893 False diff --git a/ENCSR928SYE/cherimoya.fold_4.performance.tsv b/ENCSR928SYE/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8e510c3a148de5f3c3cdccc1a54b8286792cdb1f..0000000000000000000000000000000000000000 --- a/ENCSR928SYE/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -273.7306823730469 0.49639204144477844 0.2779543101787567 0.07495678216218948 0.7587637305259705 0.7179837226867676 0.35795843601226807 \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_0.evaluate.json b/ENCSR928WMU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4cc413d4155508343b7fd063b091f25fcbe25dd5..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093RNK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_0.fit.json b/ENCSR928WMU/cherimoya.fold_0.fit.json deleted file mode 100644 index a27ca4b77790abafcabb72d924d7915af07821c3..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF093RNK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_0.log b/ENCSR928WMU/cherimoya.fold_0.log deleted file mode 100644 index 18e234c1572e726dfbca82f935837861b85b0029..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2721 34.60388994216919 3.7699716091156006 554.6503295898438 0.4288593530654907 663.997802734375 0.25053271651268005 0.68510306 4.212411880493164 True -1 5442 29.680859804153442 0.6757011413574219 538.8280029296875 0.42300713062286377 607.2650756835938 0.3251068890094757 0.74978757 1.1845139265060425 True -2 8163 30.118094205856323 0.6021919250488281 463.783447265625 0.45609673857688904 599.2828979492188 0.33449065685272217 0.7637844 0.6022226214408875 True -3 10884 30.13819122314453 0.5681734085083008 490.57720947265625 0.5133112668991089 592.1688842773438 0.342398077249527 0.7700547 0.5538530945777893 True -4 13605 30.167521953582764 0.6187043190002441 490.62054443359375 0.2643851637840271 588.6903076171875 0.34792912006378174 0.78127396 0.3907187879085541 True -5 16326 29.70606231689453 0.5639355182647705 538.5966796875 0.4142719507217407 587.3438110351562 0.3498998284339905 0.78336334 0.36924830079078674 True -6 19047 29.495413064956665 1.066866159439087 467.6171875 0.25669920444488525 587.4835205078125 0.34907373785972595 0.7856906 0.5030010938644409 True -7 21768 29.44447135925293 0.5485258102416992 539.7203369140625 0.32607612013816833 584.501953125 0.352011501789093 0.79349273 0.3952694833278656 True -8 24489 29.458447456359863 0.5706162452697754 631.5789794921875 0.41711193323135376 582.8952026367188 0.35492709279060364 0.7977869 0.3573075532913208 True -9 27210 29.508766174316406 0.5799520015716553 496.47802734375 0.2894097864627838 579.9221801757812 0.3594513237476349 0.8016313 0.32372093200683594 True -10 29931 29.43606734275818 18.31792688369751 558.0010375976562 0.33689457178115845 578.3436889648438 0.36154597997665405 0.8061574 0.32046064734458923 True -11 32652 29.60495400428772 0.5699381828308105 575.7095336914062 0.3372214436531067 575.9197998046875 0.36444586515426636 0.8121524 0.30322569608688354 True -12 35373 29.553205251693726 0.5588386058807373 468.47857666015625 0.3466677665710449 574.6614990234375 0.36547040939331055 0.81897527 0.2960171103477478 True -13 38094 29.56510281562805 0.5554239749908447 489.5710754394531 0.44194695353507996 573.683349609375 0.36683860421180725 0.82439584 0.2757933437824249 True -14 40815 29.49894118309021 0.55517578125 460.5677490234375 0.19800224900245667 571.3638916015625 0.37097644805908203 0.83006656 0.2706608176231384 True -15 43536 29.492002248764038 0.5551047325134277 500.3802490234375 0.22061443328857422 570.0840454101562 0.3720991015434265 0.83212733 0.26009753346443176 True -16 46257 29.457424640655518 0.5598804950714111 535.1736450195312 0.30484750866889954 569.9807739257812 0.3708440065383911 0.8356266 0.2521708011627197 True -17 48978 29.5752694606781 0.7002661228179932 585.7816772460938 0.2104317843914032 570.2937622070312 0.3709418475627899 0.8371834 0.2484443038702011 True -18 51699 29.54909586906433 0.5604426860809326 427.93560791015625 0.17745572328567505 570.5590209960938 0.3703170418739319 0.8363918 0.24714626371860504 False -19 54420 29.557252168655396 0.561835765838623 479.87823486328125 0.22189320623874664 571.0040283203125 0.369573712348938 0.83560145 0.247515469789505 False diff --git a/ENCSR928WMU/cherimoya.fold_0.performance.tsv b/ENCSR928WMU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f051abd2c81ea58388eb9f0b0921533bc7f08fb7..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -570.2937622070312 0.40179798007011414 0.3709418475627899 0.14411737024784088 0.83718341588974 0.7810788750648499 0.2484443038702011 \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_1.evaluate.json b/ENCSR928WMU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 39ea51c2b5a8158650fa0f5a4aac4a499a32d639..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093RNK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_1.fit.json b/ENCSR928WMU/cherimoya.fold_1.fit.json deleted file mode 100644 index a53d477a6ca3bc84c03a61c04e241bb06f9911b0..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF093RNK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_1.log b/ENCSR928WMU/cherimoya.fold_1.log deleted file mode 100644 index 1c00ac1585aed3f01d2a58afd49e096e5c21df88..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 34.663835525512695 4.407469749450684 614.4105224609375 0.42542311549186707 787.614013671875 0.25736814737319946 0.685187 5.295456409454346 True -1 5404 29.879297733306885 0.789607048034668 487.75213623046875 0.38232123851776123 710.2340698242188 0.346214234828949 0.7559614 1.46745765209198 True -2 8106 29.980642318725586 0.6933071613311768 513.5106201171875 0.4126132130622864 697.29736328125 0.3561737835407257 0.7661786 0.8453128337860107 True -3 10808 29.928691864013672 0.6910815238952637 472.82061767578125 0.39416104555130005 688.912841796875 0.3635803461074829 0.7758653 0.7088788151741028 True -4 13510 29.880478620529175 0.7093296051025391 524.2864990234375 0.4814959764480591 683.20263671875 0.3686497211456299 0.787597 0.5337515473365784 True -5 16212 29.915841102600098 0.8146071434020996 453.2278137207031 0.27441543340682983 681.3818359375 0.3709415793418884 0.7920512 0.4667890965938568 True -6 18914 29.299672603607178 0.715378999710083 425.2124938964844 0.32481375336647034 676.650634765625 0.3771977722644806 0.7974897 0.4264315664768219 True -7 21616 29.385826587677002 0.7166306972503662 508.68707275390625 0.3015124201774597 675.1807250976562 0.3774167597293854 0.802362 0.4137841761112213 True -8 24318 29.340614080429077 0.7074325084686279 562.5431518554688 0.42515087127685547 672.5980834960938 0.3818705677986145 0.80573326 0.4041123390197754 True -9 27020 29.913583755493164 16.113673210144043 504.4259033203125 0.3740244507789612 671.3004760742188 0.3821536898612976 0.8106736 0.3772757053375244 True -10 29722 29.340630054473877 0.738853931427002 525.6075439453125 0.3921823501586914 668.572509765625 0.3861030042171478 0.81554365 0.3548981547355652 True -11 32424 29.273483753204346 0.7105600833892822 388.16815185546875 0.23059329390525818 665.8899536132812 0.3885733187198639 0.821483 0.34504497051239014 True -12 35126 29.334880828857422 0.7151026725769043 462.57611083984375 0.20895525813102722 665.405029296875 0.38741374015808105 0.82825786 0.3313829004764557 True -13 37828 29.535988569259644 29.30308246612549 549.1864624023438 0.3290754556655884 662.6278686523438 0.3915681838989258 0.83263576 0.3184684216976166 True -14 40530 29.56998634338379 0.7025175094604492 469.78948974609375 0.2101448029279709 660.6415405273438 0.3940297067165375 0.8400028 0.30522435903549194 True -15 43232 29.54666304588318 0.7040519714355469 441.3857116699219 0.2065732181072235 660.3677978515625 0.39330214262008667 0.84386164 0.2940372824668884 True -16 45934 29.4555401802063 0.702805757522583 565.1214599609375 0.29430440068244934 658.834716796875 0.3953813910484314 0.84699166 0.2845354974269867 True -17 48636 29.41531229019165 0.6996657848358154 513.3013305664062 0.1847338080406189 659.0972290039062 0.39485102891921997 0.84808904 0.28072357177734375 True -18 51338 29.425951719284058 0.6927766799926758 453.628173828125 0.15378163754940033 659.9199829101562 0.3940477669239044 0.84778756 0.2791742980480194 False -19 54040 29.429788827896118 1.829448938369751 510.1092529296875 0.2808098793029785 659.4330444335938 0.39473938941955566 0.8471023 0.27870967984199524 False diff --git a/ENCSR928WMU/cherimoya.fold_1.performance.tsv b/ENCSR928WMU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7fc42b58abacd5f6d82cb43245fb8ca31f637be2..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -659.0972290039062 0.37938499450683594 0.3948509991168976 0.16738654673099518 0.8480890393257141 0.8156460523605347 0.28072357177734375 \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_2.evaluate.json b/ENCSR928WMU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 32e740a9eaee9e90725d9d57219873c6ce53ead7..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093RNK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_2.fit.json b/ENCSR928WMU/cherimoya.fold_2.fit.json deleted file mode 100644 index 73633168247d25fbb020dfa053c2b5c226414957..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF093RNK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_2.log b/ENCSR928WMU/cherimoya.fold_2.log deleted file mode 100644 index 3e4e9d1bc4a1b2c3563bf14068765aeb97e93e95..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2887 36.494351863861084 3.4340240955352783 476.81597900390625 0.4929771423339844 697.0623779296875 0.25201326608657837 0.6871716 4.151428699493408 True -1 5774 31.982616424560547 2.3289942741394043 489.6006164550781 0.5737642049789429 631.4144287109375 0.33155909180641174 0.7569254 1.089485764503479 True -2 8661 31.45568537712097 0.547987699508667 530.90966796875 0.401090145111084 623.05908203125 0.34117862582206726 0.75921804 0.6484208703041077 True -3 11548 31.536676168441772 0.5567948818206787 541.0445556640625 0.5582932233810425 621.2515258789062 0.3408215045928955 0.76156914 0.5961345434188843 True -4 14435 31.396897077560425 0.5293922424316406 443.0334777832031 0.44470036029815674 616.3577270507812 0.346414715051651 0.771349 0.5179490447044373 True -5 17322 31.35867714881897 0.5393261909484863 523.6947631835938 0.37270134687423706 614.1622314453125 0.35026252269744873 0.77806747 0.5112838745117188 True -6 20209 31.41024422645569 0.5450294017791748 545.1858520507812 0.4896209239959717 610.4613647460938 0.354603111743927 0.78503144 0.5050029158592224 True -7 23096 31.33156180381775 0.5405917167663574 495.2586975097656 0.2469950020313263 608.7039184570312 0.356827050447464 0.79017377 0.4951251745223999 True -8 25983 31.36305856704712 0.5412979125976562 601.9397583007812 0.23885482549667358 607.23681640625 0.3585774302482605 0.7942441 0.4929957389831543 True -9 28870 31.44670581817627 0.5584259033203125 444.4471435546875 0.3453558683395386 604.63037109375 0.36203116178512573 0.80103076 0.4257950782775879 True -10 31757 31.45545196533203 0.5416295528411865 516.019775390625 0.3471490144729614 601.4332885742188 0.36624178290367126 0.80448955 0.392395943403244 True -11 34644 31.41201639175415 0.5412631034851074 498.5515441894531 0.3099455237388611 600.1279296875 0.36825352907180786 0.81148386 0.3632541298866272 True -12 37531 31.37011408805847 0.5408222675323486 443.69757080078125 0.2935291826725006 597.7778930664062 0.3709155023097992 0.81242573 0.332764595746994 True -13 40418 31.39458680152893 0.5405569076538086 501.1990966796875 0.2863177955150604 595.5629272460938 0.3737594187259674 0.81744254 0.319016695022583 True -14 43305 31.34192132949829 0.5443518161773682 450.12738037109375 0.24976080656051636 594.8695678710938 0.3742333650588989 0.8224269 0.2959613800048828 True -15 46192 31.349543809890747 0.5406796932220459 474.4366455078125 0.19624705612659454 594.5716552734375 0.37353047728538513 0.8261178 0.2811312675476074 True -16 49079 31.31778907775879 0.5411062240600586 424.0809326171875 0.25043773651123047 593.6755981445312 0.374671995639801 0.8297732 0.27421921491622925 True -17 51966 31.309587717056274 0.5424337387084961 474.50286865234375 0.1448194533586502 594.4058227539062 0.37324902415275574 0.8298697 0.27173933386802673 True -18 54853 31.514659881591797 1.6484177112579346 522.314453125 0.18652722239494324 593.6207885742188 0.37520986795425415 0.8275226 0.2725904881954193 False -19 57740 31.976242780685425 0.5546948909759521 496.1803283691406 0.148151695728302 593.75390625 0.3745619058609009 0.82794213 0.27356383204460144 False diff --git a/ENCSR928WMU/cherimoya.fold_2.performance.tsv b/ENCSR928WMU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index da70ae623f522694a249f149ebdea36bcfcbd662..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -594.4058227539062 0.39696595072746277 0.37324902415275574 0.14793746173381805 0.8298696875572205 0.7828015685081482 0.27173933386802673 \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_3.evaluate.json b/ENCSR928WMU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b570e4249a75fa4566f9ec1a5157afe360029057..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093RNK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_3.fit.json b/ENCSR928WMU/cherimoya.fold_3.fit.json deleted file mode 100644 index 9e7e03cba56dada71d290dc7f461d96aaebd6fa8..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF093RNK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_3.log b/ENCSR928WMU/cherimoya.fold_3.log deleted file mode 100644 index f223651b562e3e73d9971fd395b67f4d330000ea..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 35.37762999534607 4.082418441772461 544.8082885742188 0.40243980288505554 655.6279907226562 0.25609779357910156 0.6843569 4.350424289703369 True -1 5494 30.40473198890686 0.6243987083435059 557.6476440429688 0.5009967684745789 600.53369140625 0.32649996876716614 0.75427216 1.2018367052078247 True -2 8241 30.40581727027893 0.6314923763275146 509.513671875 0.44425106048583984 589.8173828125 0.3375285267829895 0.765289 0.7292754650115967 True -3 10988 30.410547733306885 0.5747730731964111 575.0969848632812 0.46349990367889404 584.7157592773438 0.3444085419178009 0.77120876 0.705915629863739 True -4 13735 29.891199588775635 0.6066145896911621 450.6048278808594 0.4110601544380188 582.7630004882812 0.34682005643844604 0.7750068 0.6341955065727234 True -5 16482 29.785606145858765 0.5735073089599609 468.91790771484375 0.25009089708328247 580.525146484375 0.34828171133995056 0.7826464 0.6149599552154541 True -6 19229 29.7911376953125 0.550966739654541 656.893798828125 0.4196632504463196 577.2066650390625 0.35335931181907654 0.7861017 0.49974924325942993 True -7 21976 29.79068875312805 0.5710883140563965 549.7410888671875 0.3855556845664978 574.0712890625 0.35782793164253235 0.79076505 0.4835454523563385 True -8 24723 29.77055811882019 1.4046308994293213 564.3134765625 0.5078452825546265 572.5064697265625 0.36001232266426086 0.7958137 0.45984911918640137 True -9 27470 29.832693576812744 0.5815961360931396 455.0629577636719 0.31589728593826294 571.4189453125 0.3605736494064331 0.80134815 0.42754143476486206 True -10 30217 29.784568548202515 0.5583982467651367 535.1668701171875 0.2531806528568268 569.6966552734375 0.36354032158851624 0.80542177 0.41160696744918823 True -11 32964 29.755547285079956 0.5682587623596191 518.6989135742188 0.31334710121154785 568.504638671875 0.3646310865879059 0.81152976 0.3903442621231079 True -12 35711 29.736313104629517 0.6282131671905518 485.5457458496094 0.25106072425842285 567.1024780273438 0.3661450743675232 0.81694347 0.3668586313724518 True -13 38458 29.818992137908936 0.5670709609985352 483.7607421875 0.2566238343715668 565.3858642578125 0.36781686544418335 0.8244789 0.3384391665458679 True -14 41205 29.738261461257935 0.5646305084228516 464.1614990234375 0.28363901376724243 564.35009765625 0.3690728545188904 0.8295934 0.31296631693840027 True -15 43952 29.771971940994263 0.5490732192993164 532.022705078125 0.30996400117874146 563.250732421875 0.3704972267150879 0.83348846 0.29005327820777893 True -16 46699 29.8252055644989 0.5705454349517822 489.0946044921875 0.29106417298316956 563.4620971679688 0.3693636655807495 0.8374736 0.2750236392021179 True -17 49446 29.842015266418457 0.5425899028778076 554.5726928710938 0.1556442379951477 562.6636352539062 0.37092557549476624 0.840986 0.26575472950935364 True -18 52193 29.768645763397217 0.7289049625396729 544.126220703125 0.2516328692436218 563.154541015625 0.37050533294677734 0.8376473 0.26423633098602295 False -19 54940 29.82188391685486 0.5653548240661621 553.2625732421875 0.227317675948143 563.2467041015625 0.37021952867507935 0.8372899 0.2654695212841034 False diff --git a/ENCSR928WMU/cherimoya.fold_3.performance.tsv b/ENCSR928WMU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b24eca56ec500396f56da5ba3c6a5302c10c890c..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -562.6636352539062 0.40284982323646545 0.37092557549476624 0.14774549007415771 0.8409860134124756 0.7755185961723328 0.26575472950935364 \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_4.evaluate.json b/ENCSR928WMU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fb686db6d441ccad3fb38b82d238a8daf66558ea..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF093RNK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_4.fit.json b/ENCSR928WMU/cherimoya.fold_4.fit.json deleted file mode 100644 index 6ef3dfbdd29a2a32a4724ace69d39cd4be27df2c..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF093RNK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR928WMU/cherimoya.fold_4.log b/ENCSR928WMU/cherimoya.fold_4.log deleted file mode 100644 index 033f30ca99427ae768d668c9b249d0c8205cc02c..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 36.06545424461365 3.558964252471924 601.3665161132812 0.5141487717628479 643.3053588867188 0.24826253950595856 0.6613798 3.3201229572296143 True -1 5664 31.460984468460083 1.1681327819824219 519.533447265625 0.3326795697212219 591.1658935546875 0.32201045751571655 0.71674854 1.2054319381713867 True -2 8496 31.006210327148438 0.5806622505187988 474.365478515625 0.29011017084121704 581.0560302734375 0.3346866965293884 0.7306966 0.6794869899749756 True -3 11328 30.73666262626648 20.63638424873352 495.7074890136719 0.36429882049560547 577.1112060546875 0.338826984167099 0.741955 0.6924632787704468 True -4 14160 30.9676730632782 0.6167516708374023 545.7794189453125 0.3572893738746643 573.7018432617188 0.342633992433548 0.7512101 0.5111533403396606 True -5 16992 30.71686577796936 0.5750381946563721 471.3040771484375 0.24352186918258667 572.0215454101562 0.34617671370506287 0.75566614 0.5399783849716187 True -6 19824 30.68446183204651 0.5853168964385986 518.972900390625 0.34365200996398926 571.0670166015625 0.34772345423698425 0.7560538 0.5051957964897156 True -7 22656 30.695587158203125 0.575955867767334 460.0638427734375 0.4418395757675171 569.1210327148438 0.35011982917785645 0.76464075 0.5295428037643433 True -8 25488 30.683393001556396 0.6015219688415527 513.0438232421875 0.25800594687461853 567.114013671875 0.3533796966075897 0.77147615 0.44293972849845886 True -9 28320 30.68879246711731 0.5850119590759277 531.0210571289062 0.3813183307647705 565.0977783203125 0.3559747636318207 0.780393 0.40835753083229065 True -10 31152 30.677090406417847 0.5848128795623779 473.15875244140625 0.2556079030036926 564.0073852539062 0.35737544298171997 0.7859984 0.3894804120063782 True -11 33984 30.6821448802948 0.5886993408203125 505.94622802734375 0.4077098071575165 562.3403930664062 0.3587164878845215 0.79156125 0.3638381063938141 True -12 36816 30.683292388916016 0.5730023384094238 420.6181640625 0.2964786887168884 561.7140502929688 0.35956984758377075 0.7977342 0.34055423736572266 True -13 39648 30.733166694641113 0.5880296230316162 445.7582092285156 0.29378771781921387 559.899169921875 0.362615168094635 0.8044962 0.31503450870513916 True -14 42480 30.841232776641846 0.5859425067901611 456.6332092285156 0.5062313079833984 558.43212890625 0.36479684710502625 0.8099689 0.2920015752315521 True -15 45312 30.743144989013672 0.5823330879211426 487.8473815917969 0.22827771306037903 557.92431640625 0.36529237031936646 0.815875 0.2792952060699463 True -16 48144 30.785008907318115 0.5874011516571045 431.89947509765625 0.2939123511314392 556.91015625 0.3670482039451599 0.81802773 0.2665753960609436 True -17 50976 30.716881275177002 0.5891256332397461 388.8764343261719 0.19129231572151184 556.3685302734375 0.3684594929218292 0.8216844 0.25922200083732605 True -18 53808 30.686612844467163 0.585155725479126 477.9350280761719 0.19964000582695007 557.35009765625 0.3658328354358673 0.819472 0.25881510972976685 False -19 56640 30.74083423614502 1.1807780265808105 437.76202392578125 0.16575974225997925 557.0399169921875 0.3668164014816284 0.81915575 0.25738996267318726 False diff --git a/ENCSR928WMU/cherimoya.fold_4.performance.tsv b/ENCSR928WMU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0726edc088d7a4637af58b197f552ba2c791d192..0000000000000000000000000000000000000000 --- a/ENCSR928WMU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -556.3685302734375 0.4038749933242798 0.3684594929218292 0.14280559122562408 0.8216844201087952 0.7552300095558167 0.25922200083732605 \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_0.evaluate.json b/ENCSR930PDT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index aa6ef5ffc63425e97114be687cde967a545dcafa..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957AKT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_0.fit.json b/ENCSR930PDT/cherimoya.fold_0.fit.json deleted file mode 100644 index 217997639a51ee28b944cc03a8194fe0440adf49..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF957AKT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_0.log b/ENCSR930PDT/cherimoya.fold_0.log deleted file mode 100644 index 80e6bea4901a33e2eabd16d27c27c122471710c8..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 35.56373357772827 3.6070828437805176 791.3096313476562 0.8485391139984131 1182.6549072265625 0.2618660628795624 0.59896827 7.6853790283203125 True -1 5524 30.533638954162598 0.586695671081543 681.7353515625 0.8020813465118408 996.63916015625 0.35553404688835144 0.7019073 3.3496177196502686 True -2 8286 30.509328842163086 0.5621569156646729 854.7012939453125 0.8716082572937012 981.0693969726562 0.36090952157974243 0.7030666 1.907610297203064 True -3 11048 30.462918996810913 0.5666031837463379 890.0804443359375 1.1908223628997803 961.0883178710938 0.3674796521663666 0.7182961 1.5749330520629883 True -4 13810 30.48801612854004 1.4648842811584473 888.2365112304688 0.9200350046157837 953.7626342773438 0.3700144588947296 0.72023255 1.1906864643096924 True -5 16572 30.47170376777649 0.5664739608764648 807.0645751953125 0.835199773311615 943.5849609375 0.37227970361709595 0.73132 1.0162657499313354 True -6 19334 30.53103470802307 30.721177339553833 687.9710693359375 0.5228322148323059 933.1458129882812 0.3798576891422272 0.738087 1.0069847106933594 True -7 22096 36.78269052505493 0.5733027458190918 705.7916259765625 0.5472370982170105 926.94970703125 0.3810921013355255 0.7485873 1.0016413927078247 True -8 24858 30.516439199447632 0.5645549297332764 830.8502197265625 1.0015113353729248 921.0640869140625 0.38458651304244995 0.7567843 0.9560132622718811 True -9 27620 30.634626150131226 0.5629737377166748 740.32861328125 0.5116135478019714 916.1491088867188 0.3872383236885071 0.7650327 0.8384323716163635 True -10 30382 30.435218572616577 0.5540182590484619 960.4273681640625 0.6954361200332642 909.31640625 0.391321063041687 0.7705082 0.827217161655426 True -11 33144 30.463889837265015 0.5649852752685547 789.7159423828125 0.5632299184799194 905.3425903320312 0.3927716612815857 0.7780358 0.7491746544837952 True -12 35906 30.647053003311157 0.5647437572479248 770.3073120117188 0.5011070370674133 895.5130004882812 0.39809417724609375 0.78679055 0.6574164628982544 True -13 38668 30.530462980270386 0.5598428249359131 721.0573120117188 0.5359584093093872 894.122314453125 0.3976927697658539 0.79100776 0.6044540405273438 True -14 41430 30.453406810760498 0.565540075302124 548.694580078125 0.38180291652679443 888.36376953125 0.40023812651634216 0.7980794 0.5617232918739319 True -15 44192 30.430383682250977 0.566645622253418 722.2514038085938 0.4028853178024292 884.4949951171875 0.40214961767196655 0.8032366 0.5161030292510986 True -16 46954 30.44231939315796 0.5620107650756836 760.5003662109375 0.40200886130332947 881.8119506835938 0.40393540263175964 0.8053134 0.5036335587501526 True -17 49716 30.511225938796997 0.5638015270233154 787.4385986328125 0.37127572298049927 883.874755859375 0.40198251605033875 0.80769396 0.48955273628234863 True -18 52478 30.510246515274048 3.1456894874572754 792.7539672851562 0.46703624725341797 885.1371459960938 0.40145331621170044 0.80848753 0.48383280634880066 True -19 55240 30.575673580169678 0.563068151473999 549.8004150390625 0.47202950716018677 884.125732421875 0.4035944640636444 0.8071773 0.48558375239372253 False diff --git a/ENCSR930PDT/cherimoya.fold_0.performance.tsv b/ENCSR930PDT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3d5b0e45327dcceec36134329da7f2026a755ed9..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -885.1371459960938 0.37122395634651184 0.40145331621170044 0.18718883395195007 0.8084875345230103 0.7438240647315979 0.48383280634880066 \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_1.evaluate.json b/ENCSR930PDT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 288cc320d2de9da2c9b72c02752310eb4f6c9c07..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957AKT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_1.fit.json b/ENCSR930PDT/cherimoya.fold_1.fit.json deleted file mode 100644 index b277ebf68b3b121285d80969038b4f79ff1a7e30..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF957AKT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_1.log b/ENCSR930PDT/cherimoya.fold_1.log deleted file mode 100644 index f83ad011bd16855aedf1b2aaa256e116a6272866..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2692 34.463823318481445 10.756724834442139 756.535400390625 0.7936922311782837 1450.0152587890625 0.2707972228527069 0.6118197 9.628885269165039 True -1 5384 29.722941875457764 0.7640254497528076 904.114990234375 0.8211106061935425 1204.32958984375 0.36933156847953796 0.72798645 3.1846628189086914 True -2 8076 29.840181827545166 0.7276692390441895 930.211181640625 0.8632827997207642 1177.64599609375 0.37810659408569336 0.7304322 1.8827643394470215 True -3 10768 29.81009864807129 0.74822998046875 887.440673828125 0.7851809859275818 1152.896728515625 0.3855927586555481 0.74407303 1.3911106586456299 True -4 13460 29.77043080329895 0.7478642463684082 752.3707885742188 0.6790002584457397 1139.29833984375 0.3923073410987854 0.7541044 1.2793993949890137 True -5 16152 29.922643423080444 7.904351711273193 819.0707397460938 0.5925277471542358 1134.8624267578125 0.39106395840644836 0.76301163 1.1852835416793823 True -6 18844 30.02050757408142 0.7436656951904297 776.0888061523438 0.5514335036277771 1124.1568603515625 0.39667463302612305 0.76709247 1.0972346067428589 True -7 21536 29.83769464492798 0.7382819652557373 866.8487548828125 0.5735496282577515 1111.5772705078125 0.4038536846637726 0.77765465 1.0207301378250122 True -8 24228 32.77772116661072 37.40538001060486 602.8674926757812 0.6350807547569275 1105.7271728515625 0.40568190813064575 0.78257 0.9451079368591309 True -9 26920 30.53520894050598 0.7793939113616943 705.9443359375 0.41182857751846313 1101.3760986328125 0.4066941440105438 0.78832936 0.957186758518219 True -10 29612 30.37067198753357 0.7538082599639893 673.6437377929688 0.6439038515090942 1088.94677734375 0.4139545261859894 0.79617715 0.9304286241531372 True -11 32304 30.483960151672363 1.1545517444610596 821.2911987304688 0.5106768608093262 1083.64501953125 0.4150124788284302 0.80418074 0.8340935707092285 True -12 34996 29.840717315673828 0.7504191398620605 685.9599609375 0.7231003046035767 1076.4190673828125 0.4170116186141968 0.80986494 0.7736890316009521 True -13 37688 29.80898642539978 0.7445893287658691 821.5269165039062 0.4503958821296692 1065.1741943359375 0.420359343290329 0.81788427 0.6832389235496521 True -14 40380 29.743590831756592 0.7292835712432861 632.7009887695312 0.40692436695098877 1061.8553466796875 0.42152130603790283 0.8240801 0.6109766960144043 True -15 43072 29.7490496635437 0.7387464046478271 659.9671630859375 0.4302140474319458 1057.053955078125 0.42281803488731384 0.82694495 0.5680484771728516 True -16 45764 29.66953206062317 0.7352111339569092 627.427490234375 0.3203423321247101 1057.41455078125 0.42215073108673096 0.82935065 0.534181535243988 True -17 48456 32.55595016479492 17.486018896102905 930.1187744140625 0.5063258409500122 1054.90576171875 0.423368364572525 0.8321468 0.5182799100875854 True -18 51148 29.785520315170288 0.7458548545837402 777.0316162109375 0.4954647123813629 1054.5096435546875 0.424048513174057 0.8312796 0.5104801654815674 False -19 53840 29.899269342422485 0.7518503665924072 880.0448608398438 0.45681652426719666 1055.619873046875 0.42356976866722107 0.8309855 0.5089449882507324 False diff --git a/ENCSR930PDT/cherimoya.fold_1.performance.tsv b/ENCSR930PDT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 541865f6480793f262382e8f61c7f9059415c2ff..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1054.90576171875 0.34951651096343994 0.42336830496788025 0.2155613899230957 0.8321468234062195 0.7954513430595398 0.5182799100875854 \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_2.evaluate.json b/ENCSR930PDT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 205714c182723f072432bc445a8af8c61a6f08b5..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957AKT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_2.fit.json b/ENCSR930PDT/cherimoya.fold_2.fit.json deleted file mode 100644 index 85d5e282be48b6b25034a832fbf2bfba7d90e00b..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF957AKT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_2.log b/ENCSR930PDT/cherimoya.fold_2.log deleted file mode 100644 index 2a8d1ebe3d7c237344e44db4a711fe7a79217320..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2880 36.400187969207764 3.633333921432495 901.4318237304688 0.7935259938240051 1223.84033203125 0.26340413093566895 0.59925866 6.257005214691162 True -1 5760 32.19735360145569 26.054983615875244 743.7750854492188 0.5200749039649963 1041.6181640625 0.34982553124427795 0.69978225 2.963897705078125 True -2 8640 32.21813988685608 0.5991158485412598 880.3435668945312 0.7035837173461914 1022.9312744140625 0.3569225072860718 0.7069014 2.192227363586426 True -3 11520 31.781054258346558 1.238715648651123 810.817138671875 0.5983834266662598 995.1734619140625 0.36363112926483154 0.726039 1.5981703996658325 True -4 14400 31.787198305130005 0.5884907245635986 979.8809814453125 0.6622459292411804 976.74169921875 0.3698990046977997 0.7376523 1.111229658126831 True -5 17280 31.706613302230835 16.578115701675415 720.1478271484375 0.6901033520698547 967.787353515625 0.3740465044975281 0.7442885 1.164044976234436 True -6 20160 31.793190002441406 24.56366467475891 823.2908935546875 0.771422803401947 959.6210327148438 0.3768322467803955 0.75485367 0.776205837726593 True -7 23040 32.59796214103699 4.872540473937988 728.5966796875 0.7194771766662598 956.3390502929688 0.37961772084236145 0.7643657 0.7695234417915344 True -8 25920 31.755140781402588 0.5822896957397461 863.9149169921875 0.8167842626571655 951.0232543945312 0.38019874691963196 0.77312934 0.7304165959358215 True -9 28800 31.84177565574646 0.5802168846130371 768.3840942382812 0.5086939930915833 944.311279296875 0.38486966490745544 0.778759 0.6593568921089172 True -10 31680 31.789506435394287 0.593064546585083 759.8284912109375 0.843166708946228 939.3447875976562 0.3877737820148468 0.7858169 0.645420491695404 True -11 34560 31.892412424087524 0.5878469944000244 1135.4888916015625 0.6770834922790527 935.005859375 0.3899626135826111 0.7908746 0.6412034630775452 True -12 37440 31.976379871368408 0.5839323997497559 745.9609985351562 0.37754732370376587 928.9089965820312 0.393811970949173 0.79666734 0.6092862486839294 True -13 40320 31.916602611541748 35.7012505531311 654.29150390625 0.423004686832428 924.836669921875 0.3959101736545563 0.8028888 0.5489522814750671 True -14 43200 32.07812809944153 0.5947437286376953 743.7875366210938 0.4444369077682495 920.3414306640625 0.3972552418708801 0.80725807 0.5230869650840759 True -15 46080 31.78715229034424 0.5871913433074951 625.4320068359375 0.5662280321121216 918.3989868164062 0.39766573905944824 0.811972 0.4971032440662384 True -16 48960 31.795298099517822 0.6136224269866943 743.8816528320312 0.48377323150634766 914.4664916992188 0.4002857804298401 0.81458855 0.47403818368911743 True -17 51840 31.80073881149292 0.5957403182983398 712.474609375 0.38088667392730713 914.9557495117188 0.39949023723602295 0.81462437 0.46839767694473267 True -18 54720 31.96824288368225 31.568382024765015 680.001708984375 0.5476478934288025 918.053466796875 0.3962430953979492 0.8149643 0.4687803089618683 True -19 57600 32.04239344596863 38.43034362792969 728.7503051757812 0.24174396693706512 916.3798828125 0.3983505666255951 0.81274027 0.4724656343460083 False diff --git a/ENCSR930PDT/cherimoya.fold_2.performance.tsv b/ENCSR930PDT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 09cdd31de70c410225b0be2f76c51675634552cb..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -918.053466796875 0.3690899610519409 0.3962430953979492 0.1915203034877777 0.8149642944335938 0.7615874409675598 0.4687803089618683 \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_3.evaluate.json b/ENCSR930PDT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 3be04fe49cc36e80fb2fe19317cbcb223cd23c63..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957AKT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_3.fit.json b/ENCSR930PDT/cherimoya.fold_3.fit.json deleted file mode 100644 index d2ecdf89de7feac22f1f097f0939920bd2f45a2f..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF957AKT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_3.log b/ENCSR930PDT/cherimoya.fold_3.log deleted file mode 100644 index 4666eed43d2f1f66d5bc5bf06f2906feac5f13fa..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 34.95991015434265 3.6055595874786377 1002.2257080078125 0.7889496088027954 1202.8309326171875 0.26460880041122437 0.601442 10.749249458312988 True -1 5512 30.45547366142273 0.5578782558441162 971.234619140625 0.9817748665809631 1022.315185546875 0.35004860162734985 0.7138275 3.0863215923309326 True -2 8268 30.528523206710815 0.5459113121032715 843.5685424804688 0.5272256731987 995.5095825195312 0.36259785294532776 0.72541124 1.6354522705078125 True -3 11024 30.419616222381592 0.5294532775878906 732.86767578125 0.5226454734802246 970.2350463867188 0.3716832995414734 0.7358851 1.4247512817382812 True -4 13780 30.414042472839355 0.5334937572479248 846.0653076171875 0.8016122579574585 956.59130859375 0.37530428171157837 0.74512 1.2584058046340942 True -5 16536 30.331308126449585 19.948126316070557 649.360107421875 0.6001457571983337 948.8950805664062 0.3785836398601532 0.7556745 1.0142967700958252 True -6 19292 31.226473808288574 25.5821795463562 669.278564453125 0.42903828620910645 943.4429931640625 0.38169530034065247 0.76203793 0.9479023814201355 True -7 22048 39.68059945106506 24.066237211227417 749.145751953125 0.7854498028755188 934.4788208007812 0.3857863247394562 0.7700137 0.922720193862915 True -8 24804 39.112459659576416 0.5569689273834229 873.9224853515625 0.7926839590072632 929.5411376953125 0.3880210816860199 0.777145 0.8477396368980408 True -9 27560 30.637505054473877 2.1860005855560303 829.9847412109375 0.6683884859085083 922.9926147460938 0.39082440733909607 0.7838121 0.8427997827529907 True -10 30316 30.60447931289673 0.5354878902435303 699.85693359375 0.7925487756729126 917.0532836914062 0.3944798409938812 0.7863381 0.7976981997489929 True -11 33072 30.546008825302124 0.5662012100219727 781.0996704101562 0.946539580821991 915.1000366210938 0.3943111300468445 0.790049 0.7381988167762756 True -12 35828 30.46967315673828 0.6304786205291748 944.46826171875 0.34124818444252014 909.2144775390625 0.39683717489242554 0.7943281 0.6962754130363464 True -13 38584 30.412280559539795 31.19084358215332 632.1908569335938 0.44782698154449463 904.7264404296875 0.3982018530368805 0.8029712 0.6381320953369141 True -14 41340 31.190675497055054 31.374813318252563 981.758544921875 0.5420448780059814 899.7181396484375 0.40083280205726624 0.8103557 0.5771296620368958 True -15 44096 30.756174564361572 0.5510671138763428 595.356689453125 0.48297804594039917 894.2620849609375 0.4038982391357422 0.8136456 0.5386685729026794 True -16 46852 30.594404935836792 0.5412578582763672 729.0953369140625 0.7192286252975464 892.872802734375 0.4044820964336395 0.81850004 0.5092589855194092 True -17 49608 30.4463894367218 0.5300881862640381 926.9425048828125 0.25820568203926086 894.6859741210938 0.4040467143058777 0.8194916 0.4972943961620331 True -18 52364 30.490108728408813 0.5364577770233154 669.6682739257812 0.3367871344089508 890.4984741210938 0.40638911724090576 0.8179853 0.49138322472572327 False -19 55120 30.422112703323364 1.0273017883300781 765.07666015625 0.35208532214164734 894.0274658203125 0.403175413608551 0.81718093 0.4946255683898926 False diff --git a/ENCSR930PDT/cherimoya.fold_3.performance.tsv b/ENCSR930PDT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fd021aa60a47f1276040fd44c2ce397b3b2f3db5..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -894.6859741210938 0.36991554498672485 0.4040467143058777 0.19254380464553833 0.8194916248321533 0.7625060081481934 0.4972943961620331 \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_4.evaluate.json b/ENCSR930PDT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 382eccc36a9df22aee08b3f8ffe30bc0d3ed3a8d..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF957AKT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_4.fit.json b/ENCSR930PDT/cherimoya.fold_4.fit.json deleted file mode 100644 index 8998ac1b376fe0fe18dc00796f4bd2592a796c5a..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF957AKT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930PDT/cherimoya.fold_4.log b/ENCSR930PDT/cherimoya.fold_4.log deleted file mode 100644 index 16c1f377ddd42f4f57297d5f8bafeb3cd5784327..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2781 35.766472816467285 5.186644792556763 859.6510009765625 0.6941080093383789 1089.12646484375 0.26373055577278137 0.5780449 6.350043773651123 True -1 5562 30.72523546218872 0.6991429328918457 817.1798095703125 0.9685437679290771 943.3313598632812 0.3462649881839752 0.6831357 2.8648152351379395 True -2 8343 30.646177291870117 0.5850682258605957 875.5130615234375 0.830333411693573 924.1946411132812 0.3536093831062317 0.6838905 1.4307405948638916 True -3 11124 30.62991428375244 1.5901179313659668 595.4951782226562 0.5538844466209412 911.2521362304688 0.3547022044658661 0.6945507 1.2579255104064941 True -4 13905 30.75866174697876 0.5957059860229492 852.448974609375 0.5505791902542114 894.7146606445312 0.36360976099967957 0.71172786 0.7929502129554749 True -5 16686 30.610641956329346 0.5799109935760498 752.0413818359375 0.5641176700592041 883.7354736328125 0.36922261118888855 0.7187185 0.7992060780525208 True -6 19467 30.627806901931763 0.5891029834747314 779.947021484375 0.7935177087783813 875.005615234375 0.37401339411735535 0.7306579 0.8946680426597595 True -7 22248 30.634478092193604 2.1715474128723145 972.519287109375 0.6269264817237854 871.132080078125 0.3753294050693512 0.7442153 0.7560033798217773 True -8 25029 30.680434942245483 0.5917129516601562 895.38671875 0.8205710053443909 862.3809814453125 0.3813704550266266 0.7511758 0.7950823307037354 True -9 27810 30.676651000976562 1.8832626342773438 861.01953125 0.5800801515579224 859.4358520507812 0.3827654719352722 0.75737554 0.7556477189064026 True -10 30591 30.692975997924805 0.584092378616333 752.0963745117188 0.6380190849304199 855.5450439453125 0.3852176368236542 0.7631053 0.7255971431732178 True -11 33372 30.67667841911316 0.5864255428314209 755.5899658203125 0.361657977104187 851.8656616210938 0.3870033919811249 0.77027595 0.6711065173149109 True -12 36153 30.69730520248413 0.5765161514282227 768.8743286132812 0.5856486558914185 849.0086059570312 0.3893498480319977 0.77332276 0.6550918221473694 True -13 38934 30.665607690811157 0.5956618785858154 728.2920532226562 0.48061174154281616 845.5693359375 0.390206515789032 0.78067654 0.6043973565101624 True -14 41715 30.6545991897583 0.5947582721710205 847.440185546875 0.5103873014450073 840.2837524414062 0.3937554657459259 0.7874907 0.5651207566261292 True -15 44496 30.733011484146118 2.458441972732544 788.8212280273438 0.4063630998134613 836.7891845703125 0.39496251940727234 0.79312474 0.5146938562393188 True -16 47277 30.88082218170166 1.8649044036865234 753.5811767578125 0.3499189615249634 836.5546264648438 0.39473414421081543 0.79742706 0.4862109422683716 True -17 50058 31.002944469451904 0.5917689800262451 659.683837890625 0.39621806144714355 833.6732177734375 0.3972037136554718 0.7987557 0.47286391258239746 True -18 52839 32.006348609924316 29.32760715484619 756.1990966796875 0.4027341902256012 838.1920776367188 0.39292600750923157 0.8011752 0.46646252274513245 True -19 55620 30.768237829208374 0.678809642791748 650.605224609375 0.34110403060913086 837.1403198242188 0.3948752284049988 0.8004633 0.46450531482696533 False diff --git a/ENCSR930PDT/cherimoya.fold_4.performance.tsv b/ENCSR930PDT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 311a586637d4f57f6c0c4e99894c46725e79af98..0000000000000000000000000000000000000000 --- a/ENCSR930PDT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -838.1920776367188 0.3766181766986847 0.39292603731155396 0.18233373761177063 0.8011751770973206 0.7410103678703308 0.46646252274513245 \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_0.evaluate.json b/ENCSR930USX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ab4ec680db7f36fbf04220bafb8650f4583f85c0..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570EXK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_0.fit.json b/ENCSR930USX/cherimoya.fold_0.fit.json deleted file mode 100644 index fba13dd81642360809960c908359051fbfcdb2fe..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF570EXK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_0.log b/ENCSR930USX/cherimoya.fold_0.log deleted file mode 100644 index 2a0084d3e159e1454b7a9d3a1858fb561686fa7b..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2161 28.474154472351074 4.6464011669158936 368.0318298339844 0.7955191731452942 554.4100952148438 0.15596498548984528 0.6134952 10.004289627075195 True -1 4322 23.778695583343506 0.4561648368835449 401.79486083984375 0.9822689294815063 460.5574951171875 0.23148396611213684 0.75088763 3.463254451751709 True -2 6483 23.750078678131104 0.44324755668640137 493.83514404296875 1.445011019706726 440.347412109375 0.24338068068027496 0.75367016 2.3254523277282715 True -3 8644 23.889559030532837 16.84044909477234 402.66961669921875 0.856515645980835 430.53863525390625 0.24608942866325378 0.77466416 1.4503787755966187 True -4 10805 23.69123125076294 0.4494047164916992 359.1015319824219 1.0463998317718506 421.2445068359375 0.2540242671966553 0.79172534 1.152468204498291 True -5 12966 23.796778440475464 0.47608447074890137 301.9859619140625 0.6348973512649536 418.1383056640625 0.2561509311199188 0.7979907 1.0246906280517578 True -6 15127 23.791074514389038 0.44897031784057617 498.29315185546875 0.8138832449913025 415.53070068359375 0.2597239315509796 0.804235 1.000413417816162 True -7 17288 23.76665735244751 0.44126152992248535 393.0950012207031 0.6598384976387024 413.0827331542969 0.26048970222473145 0.8130429 0.8751172423362732 True -8 19449 23.275051593780518 0.8214952945709229 340.8822326660156 0.5945839881896973 411.0137939453125 0.2632702589035034 0.8214623 0.7983015775680542 True -9 21610 23.29282522201538 0.46098995208740234 377.77337646484375 0.5548020601272583 407.2107238769531 0.2659928798675537 0.8305656 0.7284011244773865 True -10 23771 23.41378617286682 0.4499044418334961 490.56585693359375 0.8907555341720581 403.53692626953125 0.26997482776641846 0.8335592 0.669617235660553 True -11 25932 23.41404390335083 0.44402599334716797 378.9285583496094 0.6976714134216309 403.26995849609375 0.2696954011917114 0.8390328 0.6386295557022095 True -12 28093 23.348347425460815 0.44284486770629883 305.7587585449219 0.799727201461792 399.69317626953125 0.27433541417121887 0.84354055 0.616190493106842 True -13 30254 23.428334712982178 0.4434828758239746 373.7517395019531 0.6754407286643982 399.9394836425781 0.27321285009384155 0.8489201 0.5960457921028137 True -14 32415 23.324888467788696 0.45220136642456055 314.4746398925781 0.41077348589897156 398.2708435058594 0.27545320987701416 0.85351366 0.5738140940666199 True -15 34576 23.338444471359253 0.43662548065185547 409.5797119140625 0.5874898433685303 395.7188415527344 0.27743324637413025 0.8558017 0.5508338809013367 True -16 36737 23.275495052337646 0.45356059074401855 347.1935119628906 0.697770357131958 395.4812316894531 0.27738696336746216 0.8596395 0.5377025008201599 True -17 38898 23.26200580596924 0.4527420997619629 373.60455322265625 0.5267703533172607 394.9442138671875 0.27719345688819885 0.8602086 0.5280076265335083 True -18 41059 23.28061008453369 0.45221900939941406 342.55938720703125 0.3807217478752136 396.5187683105469 0.2759741544723511 0.859308 0.5260920524597168 False -19 43220 23.253337860107422 0.4648323059082031 300.5780029296875 0.3818243741989136 396.5942687988281 0.276566743850708 0.8592133 0.5301040410995483 False diff --git a/ENCSR930USX/cherimoya.fold_0.performance.tsv b/ENCSR930USX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fbba2bf61fc7de6e0ae0d8c600691a3101698e2d..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -394.9442138671875 0.4914079010486603 0.27719342708587646 0.10097534209489822 0.8602085709571838 0.7986273169517517 0.5280076265335083 \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_1.evaluate.json b/ENCSR930USX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3047a35d7ab47dc92be1080ca463bdcffca11671..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570EXK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_1.fit.json b/ENCSR930USX/cherimoya.fold_1.fit.json deleted file mode 100644 index 8035b5c6122877073f1d868f49fdc10579d17717..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF570EXK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_1.log b/ENCSR930USX/cherimoya.fold_1.log deleted file mode 100644 index 3edc2202eaf9f74b39887a00d0a281e8060838d5..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2099 27.836611032485962 3.8604838848114014 310.4810485839844 0.7009259462356567 705.4901123046875 0.1693599969148636 0.5961543 10.974983215332031 True -1 4198 23.194868326187134 0.8771324157714844 443.5887451171875 1.05695378780365 578.1869506835938 0.2572281062602997 0.7547369 4.992401123046875 True -2 6297 23.118838787078857 0.6083190441131592 369.17547607421875 0.8422607183456421 554.553955078125 0.2687304615974426 0.77292466 3.01763916015625 True -3 8396 23.118055820465088 0.6176919937133789 345.7732238769531 0.8669672012329102 537.3313598632812 0.27932098507881165 0.7804584 1.8920122385025024 True -4 10495 23.123693227767944 0.6282939910888672 359.27337646484375 1.003483772277832 527.9022216796875 0.28597161173820496 0.7904843 1.6116541624069214 True -5 12594 23.118056297302246 0.6308712959289551 367.95904541015625 0.6324761509895325 521.9034423828125 0.2903078496456146 0.79480094 1.5318260192871094 True -6 14693 23.162127017974854 0.6690528392791748 362.08026123046875 0.7026840448379517 518.3779296875 0.29309120774269104 0.8054188 1.3124349117279053 True -7 16792 23.10750722885132 0.6456649303436279 395.16387939453125 0.7936016321182251 513.573974609375 0.2971344292163849 0.8158025 1.1220307350158691 True -8 18891 23.129242658615112 1.9261293411254883 341.1565856933594 0.6221950054168701 509.3900451660156 0.2997320890426636 0.82668585 1.0251470804214478 True -9 20990 23.158499002456665 0.6355841159820557 315.16326904296875 0.9709706902503967 506.87054443359375 0.3016487658023834 0.8360915 0.8705539703369141 True -10 23089 23.173121452331543 0.6416976451873779 341.02740478515625 0.5094045400619507 505.2622375488281 0.3017716705799103 0.8423576 0.8472108840942383 True -11 25188 23.135305166244507 0.6156156063079834 325.6681823730469 0.6159114837646484 499.714599609375 0.3067598044872284 0.8495156 0.7809872627258301 True -12 27287 23.110685110092163 14.035731792449951 449.8123779296875 0.5107806921005249 497.18731689453125 0.30849501490592957 0.85480285 0.7402976155281067 True -13 29386 23.184559106826782 0.6417407989501953 377.25445556640625 0.7239768505096436 493.6332702636719 0.31157588958740234 0.8617408 0.6808058619499207 True -14 31485 23.24911093711853 0.6027305126190186 323.97015380859375 0.52513587474823 491.2134094238281 0.31323930621147156 0.8652818 0.6530434489250183 True -15 33584 23.157499074935913 0.6401891708374023 423.6609191894531 0.5695703625679016 489.864501953125 0.31301599740982056 0.86757034 0.6256237626075745 True -16 35683 23.159244298934937 0.6279854774475098 301.04376220703125 0.36846375465393066 491.56036376953125 0.310905396938324 0.8716373 0.6056146025657654 True -17 37782 23.121322870254517 0.6135900020599365 259.2804260253906 0.28282803297042847 492.3097229003906 0.31063711643218994 0.870402 0.6034243106842041 False -18 39881 22.716404676437378 0.632390022277832 342.9732666015625 0.319699227809906 492.2354431152344 0.31052446365356445 0.87079096 0.6058928966522217 False -19 41980 22.668440341949463 0.6201004981994629 314.951416015625 0.3724285662174225 492.7081298828125 0.31029003858566284 0.86991227 0.60921710729599 False diff --git a/ENCSR930USX/cherimoya.fold_1.performance.tsv b/ENCSR930USX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4b7c2c5f7fa9e0c37d075c44c6ee09ad9343297e..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -491.56036376953125 0.4613780677318573 0.31090542674064636 0.1246890276670456 0.8716372847557068 0.8398831486701965 0.6056146025657654 \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_2.evaluate.json b/ENCSR930USX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 585e7eb2f12cdfe877d63dd537bcc975879db7d9..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570EXK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_2.fit.json b/ENCSR930USX/cherimoya.fold_2.fit.json deleted file mode 100644 index 124c8dd2c0a0cca60ff0f262654e9cc1db233260..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF570EXK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_2.log b/ENCSR930USX/cherimoya.fold_2.log deleted file mode 100644 index da2e172827238d3767c042d8ee573f7e82082420..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2255 29.506433248519897 4.382103204727173 515.1922607421875 1.2201502323150635 568.6057739257812 0.15725697576999664 0.57549036 8.350883483886719 True -1 4510 24.493465185165405 0.8616988658905029 332.49755859375 1.1773854494094849 465.98956298828125 0.23439346253871918 0.7401903 3.554715156555176 True -2 6765 24.719874382019043 0.4820258617401123 482.13958740234375 0.886992871761322 444.5766906738281 0.24384941160678864 0.76221174 2.6265926361083984 True -3 9020 24.7857723236084 0.5290322303771973 374.79913330078125 0.8190191984176636 438.6583251953125 0.24760529398918152 0.7692466 1.6855766773223877 True -4 11275 24.785754442214966 0.4976658821105957 393.6978759765625 0.862353503704071 432.8571472167969 0.2524201273918152 0.778967 1.1916570663452148 True -5 13530 24.78623390197754 3.0384182929992676 426.41644287109375 0.9320054650306702 426.73712158203125 0.25696611404418945 0.79323995 0.9771653413772583 True -6 15785 24.78658890724182 0.46535301208496094 312.05633544921875 0.8559401631355286 422.0921630859375 0.2618224322795868 0.79926836 0.9056913256645203 True -7 18040 24.804002285003662 1.7805161476135254 410.38482666015625 0.6632574796676636 421.3534851074219 0.26179879903793335 0.8076835 0.8633549809455872 True -8 20295 24.70627498626709 0.4657258987426758 325.54217529296875 0.6542774438858032 417.1569519042969 0.2657356560230255 0.8142284 0.77350252866745 True -9 22550 24.769660234451294 0.4765737056732178 262.7469482421875 0.6586002111434937 415.13751220703125 0.2671361565589905 0.8236529 0.726996123790741 True -10 24805 24.742138862609863 0.476346492767334 398.27752685546875 0.8710874319076538 412.5531005859375 0.26899322867393494 0.83124113 0.6801431179046631 True -11 27060 24.713988304138184 0.4609851837158203 374.0645751953125 0.7842530012130737 410.1783752441406 0.27142494916915894 0.834832 0.6554011106491089 True -12 29315 24.771300315856934 0.4802064895629883 351.7052307128906 0.9381371736526489 407.8624572753906 0.27318063378334045 0.8404682 0.6117051839828491 True -13 31570 24.78588581085205 1.0117292404174805 397.49041748046875 0.6008108854293823 405.9852600097656 0.2743885815143585 0.84717566 0.5852797627449036 True -14 33825 24.76764154434204 0.4791738986968994 236.57225036621094 0.7639936804771423 404.48876953125 0.2754570543766022 0.8513502 0.563356876373291 True -15 36080 24.769649028778076 0.4777846336364746 291.4676513671875 0.4334227740764618 403.1825866699219 0.277165949344635 0.853885 0.5496013760566711 True -16 38335 24.790815591812134 0.47007250785827637 405.37689208984375 0.29910916090011597 402.1929016113281 0.27841922640800476 0.8564348 0.5455593466758728 True -17 40590 24.776596546173096 0.4497032165527344 301.71142578125 0.45741987228393555 403.3985595703125 0.2767045497894287 0.85626537 0.5456632375717163 False -18 42845 24.737105131149292 0.4517481327056885 313.607177734375 0.36167022585868835 404.47735595703125 0.2759677469730377 0.85329664 0.5516151189804077 False -19 45100 24.905881881713867 0.48411059379577637 263.266845703125 0.49772316217422485 404.2585144042969 0.27675729990005493 0.8525386 0.5553046464920044 False diff --git a/ENCSR930USX/cherimoya.fold_2.performance.tsv b/ENCSR930USX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1d643276f019b9f16bfb4b1459a99ccd0139b062..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -402.1929016113281 0.4887668490409851 0.27841922640800476 0.10395971685647964 0.8564348220825195 0.8046269416809082 0.5455593466758728 \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_3.evaluate.json b/ENCSR930USX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f9d90b05e0973e63b49fdaef2bcc6a7dbf59488d..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570EXK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_3.fit.json b/ENCSR930USX/cherimoya.fold_3.fit.json deleted file mode 100644 index 902209932d7824745c05c7dc02451f0e4821dfab..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF570EXK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_3.log b/ENCSR930USX/cherimoya.fold_3.log deleted file mode 100644 index c281d0062471826ebb8a95e1297c912e47a34a37..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2157 28.029818058013916 3.7110435962677 438.6419677734375 0.8421088457107544 592.12890625 0.17280471324920654 0.57616675 9.612909317016602 True -1 4314 23.719929933547974 0.7417912483215332 411.2222595214844 0.9742370843887329 499.5172119140625 0.24572670459747314 0.7219217 4.718608379364014 True -2 6471 23.72596001625061 0.47726964950561523 308.6189270019531 1.1161607503890991 481.177734375 0.2576879858970642 0.72519493 2.98982572555542 True -3 8628 23.571714639663696 0.5328550338745117 378.3270263671875 0.9232001304626465 466.2989196777344 0.26577210426330566 0.73851204 1.836077094078064 True -4 10785 23.22284483909607 1.1637449264526367 404.57275390625 0.5694828033447266 459.6702575683594 0.26985853910446167 0.76281714 1.4946898221969604 True -5 12942 23.193547010421753 0.4449610710144043 483.45758056640625 0.7898852825164795 453.9200439453125 0.2757259011268616 0.7757806 1.3855184316635132 True -6 15099 23.16661524772644 0.4556884765625 331.843017578125 0.7105613946914673 449.5423583984375 0.2789987623691559 0.78829616 1.2564932107925415 True -7 17256 23.169198751449585 0.43838953971862793 439.974853515625 1.025598406791687 447.6445007324219 0.2805917263031006 0.7944998 1.1709496974945068 True -8 19413 23.172266721725464 0.41187620162963867 406.91546630859375 0.5235179662704468 445.7199401855469 0.28085705637931824 0.8034215 1.0800641775131226 True -9 21570 23.202290773391724 0.43733835220336914 339.79302978515625 0.8209853768348694 443.40228271484375 0.28340592980384827 0.81175786 0.9709581732749939 True -10 23727 23.237806797027588 0.4008610248565674 384.7811279296875 0.8193187713623047 441.1181335449219 0.2861204743385315 0.8197813 0.9001939296722412 True -11 25884 23.22211003303528 0.40084290504455566 382.1919250488281 1.0463389158248901 438.2906494140625 0.2883124053478241 0.8241162 0.8407705426216125 True -12 28041 23.2675302028656 0.7784478664398193 342.6750793457031 0.6805905103683472 435.4238586425781 0.2915215790271759 0.8334265 0.7904275059700012 True -13 30198 23.29368758201599 0.46324801445007324 337.6935119628906 0.5192571878433228 432.6673278808594 0.29429540038108826 0.8401557 0.7070596218109131 True -14 32355 23.25846815109253 0.4223778247833252 234.506591796875 0.5874906778335571 430.0314636230469 0.2957284152507782 0.8449855 0.658170759677887 True -15 34512 23.182034254074097 10.982699394226074 375.0824279785156 0.7983803749084473 428.53863525390625 0.2967854142189026 0.849369 0.6333633065223694 True -16 36669 23.247500896453857 0.4418809413909912 473.25567626953125 0.4651537239551544 429.3313293457031 0.29532504081726074 0.8514135 0.61544269323349 True -17 38826 23.245161771774292 0.4194812774658203 420.5576477050781 0.5663838386535645 428.1365966796875 0.29682376980781555 0.85343313 0.6122387647628784 True -18 40983 23.19678235054016 0.4343891143798828 256.3168029785156 0.3506757915019989 428.9500732421875 0.29507896304130554 0.8528313 0.6120008826255798 False -19 43140 23.18379807472229 0.8838882446289062 340.7546081542969 0.466295063495636 429.7381591796875 0.2940066456794739 0.8516146 0.6154677271842957 False diff --git a/ENCSR930USX/cherimoya.fold_3.performance.tsv b/ENCSR930USX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1bdb22c1c75f237ade98bb97144145214d2b138c..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -428.1365966796875 0.4760069251060486 0.29682374000549316 0.11116264015436172 0.8534331321716309 0.8039488792419434 0.6122387647628784 \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_4.evaluate.json b/ENCSR930USX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index aa6fcf15b234bee85ce7548eb0f34523d32d6f5b..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF570EXK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_4.fit.json b/ENCSR930USX/cherimoya.fold_4.fit.json deleted file mode 100644 index ab487a4595d7465b25f56ee84781ca66d061b5de..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF570EXK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR930USX/cherimoya.fold_4.log b/ENCSR930USX/cherimoya.fold_4.log deleted file mode 100644 index 5629072a9ee12e8a2e440dafa81d62aebe5d548d..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2165 28.502068758010864 12.20520830154419 383.48748779296875 0.8962169885635376 489.5231628417969 0.1562797725200653 0.5694186 8.391989707946777 True -1 4330 23.77992820739746 0.48615360260009766 510.2884521484375 1.21758234500885 413.0042419433594 0.222794771194458 0.7403122 3.207778215408325 True -2 6495 23.845759868621826 0.4353475570678711 275.245849609375 0.6917954683303833 395.1834411621094 0.23436272144317627 0.75275314 2.150455951690674 True -3 8660 23.75243902206421 0.46056342124938965 377.2109375 1.0199989080429077 390.196044921875 0.23666787147521973 0.7611402 1.3536375761032104 True -4 10825 23.594942092895508 0.44788122177124023 268.550537109375 0.6282011866569519 382.9356384277344 0.24266739189624786 0.7709031 1.0779595375061035 True -5 12990 23.29917025566101 0.4323697090148926 313.26593017578125 0.509797990322113 379.5686950683594 0.2443237453699112 0.7845565 0.9628384709358215 True -6 15155 23.304468154907227 0.432936429977417 365.46075439453125 0.787100076675415 376.546142578125 0.2477797269821167 0.7885403 0.9389243721961975 True -7 17320 23.303176403045654 0.43473076820373535 325.1717529296875 0.8587130308151245 375.4774475097656 0.24867349863052368 0.7950931 0.9003643989562988 True -8 19485 23.29382872581482 0.44649267196655273 353.3334045410156 0.7488468289375305 371.80645751953125 0.25137126445770264 0.8041755 0.7791395783424377 True -9 21650 23.30551052093506 0.4326028823852539 312.51348876953125 0.5600252151489258 371.9013977050781 0.2524235248565674 0.80990154 0.7297264933586121 True -10 23815 23.329503059387207 0.4308960437774658 403.02764892578125 0.6106484532356262 369.80340576171875 0.2540070712566376 0.8164893 0.6694185137748718 True -11 25980 23.358625650405884 0.42984890937805176 244.53713989257812 0.551904559135437 367.850341796875 0.25665485858917236 0.82153064 0.6449151635169983 True -12 28145 23.298107624053955 0.4258308410644531 326.001708984375 0.7051411271095276 365.1768493652344 0.2597236633300781 0.8322263 0.5981662273406982 True -13 30310 23.348963260650635 0.4424710273742676 375.4952392578125 0.4939199686050415 363.1603088378906 0.2620447874069214 0.8327143 0.5713440775871277 True -14 32475 23.344414949417114 0.43584465980529785 347.76861572265625 0.4076724946498871 362.8815002441406 0.26151251792907715 0.8407066 0.5448736548423767 True -15 34640 23.330678939819336 3.1283559799194336 341.1383361816406 0.4459134340286255 362.4803771972656 0.26194408535957336 0.8423137 0.531821072101593 True -16 36805 23.309879064559937 0.46033573150634766 225.48556518554688 0.39566370844841003 361.83172607421875 0.26243269443511963 0.8453117 0.5246855020523071 True -17 38970 23.46942949295044 0.4404466152191162 385.59613037109375 0.44433316588401794 362.8523864746094 0.2611788213253021 0.8448862 0.5232226252555847 False -18 41135 23.383381605148315 1.7147057056427002 317.3699951171875 0.40436679124832153 362.91094970703125 0.2624146640300751 0.84463197 0.5243722796440125 False -19 43300 23.406227350234985 0.45078229904174805 279.44677734375 0.2803349792957306 362.38031005859375 0.26395606994628906 0.8436705 0.5285016298294067 False diff --git a/ENCSR930USX/cherimoya.fold_4.performance.tsv b/ENCSR930USX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e14f907eb2c41383d01dc7052b9e71cfedd9d1e5..0000000000000000000000000000000000000000 --- a/ENCSR930USX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -361.83172607421875 0.5018417835235596 0.26243269443511963 0.08869576454162598 0.84531170129776 0.7871169447898865 0.5246855020523071 \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_0.evaluate.json b/ENCSR933GMM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 290c06abaf064e04ee601d90de1b89dc20ee7382..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF632GRM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_0.fit.json b/ENCSR933GMM/cherimoya.fold_0.fit.json deleted file mode 100644 index e9c08ab9b0a2afe2ba754cc1839bfb454b967ad6..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF632GRM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_0.log b/ENCSR933GMM/cherimoya.fold_0.log deleted file mode 100644 index 2b2d7924acfa59f9a6a8cdf42f36878b1f9fc4e0..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 34.76087927818298 3.6895134449005127 741.5550537109375 0.47783738374710083 958.343994140625 0.30867838859558105 0.7121897 7.4925031661987305 True -1 5528 30.734281301498413 0.6380701065063477 728.192138671875 0.8973839282989502 826.708251953125 0.3918811082839966 0.7816775 1.7898859977722168 True -2 8292 30.816077947616577 14.753717184066772 640.4678955078125 0.5727697610855103 807.6869506835938 0.40273669362068176 0.7942996 1.0238081216812134 True -3 11056 30.688732624053955 0.6270351409912109 759.8602294921875 0.4354267418384552 800.4845581054688 0.4080612063407898 0.8026884 0.9891278743743896 True -4 13820 30.69954776763916 0.6099338531494141 668.0269775390625 0.516388475894928 791.98486328125 0.41213539242744446 0.807398 0.878115713596344 True -5 16584 30.723787784576416 0.6130032539367676 618.4940795898438 0.2875641882419586 785.0530395507812 0.41733670234680176 0.8150808 0.6918003559112549 True -6 19348 30.742015600204468 0.6126036643981934 780.960693359375 0.6891641616821289 781.8074340820312 0.41928717494010925 0.8175255 0.6009317636489868 True -7 22112 30.75158953666687 0.6143748760223389 704.554931640625 0.4023602306842804 781.1514282226562 0.42031869292259216 0.82375026 0.5583375692367554 True -8 24876 30.768348217010498 0.6089456081390381 654.19921875 0.6203548908233643 774.8926391601562 0.4241843521595001 0.8299078 0.5485421419143677 True -9 27640 30.77745246887207 1.9062504768371582 625.673583984375 0.47384029626846313 772.7046508789062 0.42590096592903137 0.8335456 0.5150677561759949 True -10 30404 30.937817096710205 0.6162872314453125 623.7259521484375 0.41087326407432556 769.7638549804688 0.4274066686630249 0.8384431 0.47770172357559204 True -11 33168 30.796072721481323 0.6187777519226074 733.2904663085938 0.4172738492488861 765.4479370117188 0.4312177002429962 0.84479046 0.4604567587375641 True -12 35932 30.766833066940308 0.6224305629730225 801.99169921875 0.4331473112106323 763.9681396484375 0.43163880705833435 0.8511168 0.4170088768005371 True -13 38696 30.73992156982422 0.605353832244873 575.24072265625 0.46237999200820923 760.2828369140625 0.4340900778770447 0.8573094 0.38415271043777466 True -14 41460 30.69547963142395 0.6025371551513672 715.688720703125 0.2037806510925293 756.3275756835938 0.4364229738712311 0.8646738 0.3506508767604828 True -15 44224 30.69223141670227 0.6040852069854736 614.6397705078125 0.27312135696411133 756.0941772460938 0.4369657635688782 0.8704405 0.3300210237503052 True -16 46988 30.680909872055054 0.6051464080810547 741.0230712890625 0.3686034381389618 753.1605224609375 0.43930584192276 0.87413234 0.31257128715515137 True -17 49752 30.70267653465271 0.614647388458252 663.2955322265625 0.3130338191986084 752.1273803710938 0.43955767154693604 0.8767728 0.3015569746494293 True -18 52516 30.796061277389526 3.092252492904663 669.791259765625 0.22843706607818604 754.2743530273438 0.4390830397605896 0.8767653 0.3011380434036255 False -19 55280 30.81329345703125 1.0009958744049072 661.1163940429688 0.24799633026123047 755.6795654296875 0.437710702419281 0.87462866 0.3013473451137543 False diff --git a/ENCSR933GMM/cherimoya.fold_0.performance.tsv b/ENCSR933GMM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7953d8dbe525727c51efd558448f893b0801b20d..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -752.1273803710938 0.3580779731273651 0.43955761194229126 0.18677160143852234 0.8767728209495544 0.8354436159133911 0.3015569746494293 \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_1.evaluate.json b/ENCSR933GMM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 66bad278d5ada20d37a141562205c680fd8e3ded..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF632GRM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_1.fit.json b/ENCSR933GMM/cherimoya.fold_1.fit.json deleted file mode 100644 index 3eeee3395ca822efa8e08573ee5f929f0dcfbce7..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF632GRM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_1.log b/ENCSR933GMM/cherimoya.fold_1.log deleted file mode 100644 index cfaca312f9c7b8be39c920cb86dee962ab48798e..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2691 33.57514762878418 3.6305277347564697 714.9505615234375 0.6001757383346558 1147.40576171875 0.30682826042175293 0.7164201 7.463325023651123 True -1 5382 29.915898323059082 0.7932169437408447 700.4652099609375 0.6322078704833984 987.9373168945312 0.4027785062789917 0.7906975 2.8258261680603027 True -2 8073 29.913155555725098 0.7653617858886719 699.3490600585938 0.5095906853675842 962.6516723632812 0.4143401086330414 0.8018298 1.3160558938980103 True -3 10764 29.912383317947388 0.7631776332855225 697.015625 0.5348498821258545 943.9276123046875 0.424869179725647 0.8123139 1.0336329936981201 True -4 13455 29.899564027786255 0.7674603462219238 878.2066040039062 0.5416256189346313 932.4432373046875 0.43144121766090393 0.82307905 1.0114277601242065 True -5 16146 29.943466186523438 0.7690989971160889 581.6412963867188 0.47861093282699585 928.8886108398438 0.43456947803497314 0.82658726 0.919001042842865 True -6 18837 29.894896984100342 1.4149224758148193 788.4614868164062 0.4855565130710602 919.9010620117188 0.43984857201576233 0.83293474 0.8205909729003906 True -7 21528 30.002695560455322 0.7863113880157471 714.9340209960938 0.43695032596588135 916.8641357421875 0.44067028164863586 0.835861 0.7359121441841125 True -8 24219 30.000752925872803 0.7749254703521729 637.7523803710938 0.47892454266548157 910.8212280273438 0.4432311952114105 0.84129405 0.7277588248252869 True -9 26910 29.950996160507202 0.7724571228027344 557.1729125976562 0.3987693786621094 908.3381958007812 0.44368913769721985 0.84814715 0.6756424903869629 True -10 29601 29.933217525482178 0.7664682865142822 663.1434936523438 0.466609388589859 903.945068359375 0.4467135965824127 0.8505252 0.5844762921333313 True -11 32292 30.000799655914307 0.777606725692749 773.4423828125 0.4109930396080017 899.4044799804688 0.44995346665382385 0.85733175 0.5349268913269043 True -12 34983 29.949894189834595 0.7753846645355225 694.1412353515625 0.4847506284713745 894.0011596679688 0.4531373679637909 0.86393803 0.486116498708725 True -13 37674 29.9366717338562 0.7718615531921387 579.5357666015625 0.3588016629219055 889.87353515625 0.45530691742897034 0.86806715 0.4385804533958435 True -14 40365 29.96878480911255 1.3246328830718994 663.057373046875 0.3601427674293518 886.1956176757812 0.4568597376346588 0.8726226 0.39740416407585144 True -15 43056 29.94826316833496 0.7609143257141113 611.865234375 0.2806406617164612 885.6156005859375 0.45555680990219116 0.8786713 0.3590335547924042 True -16 45747 29.936384916305542 0.7631824016571045 601.5565185546875 0.29838424921035767 883.8641967773438 0.4576907455921173 0.8816637 0.34440505504608154 True -17 48438 29.972344160079956 1.6764473915100098 618.0501708984375 0.32273969054222107 883.914306640625 0.45833703875541687 0.8831536 0.32983914017677307 True -18 51129 29.990561962127686 0.7890887260437012 539.3915405273438 0.42909759283065796 884.58447265625 0.4575996994972229 0.8830122 0.32582250237464905 False -19 53820 29.947819709777832 0.7646980285644531 667.1961669921875 0.26729097962379456 884.5302124023438 0.45770856738090515 0.8816929 0.3248694837093353 False diff --git a/ENCSR933GMM/cherimoya.fold_1.performance.tsv b/ENCSR933GMM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 9f198f94dbd641ba3062e7583a27084c89d471a9..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -883.914306640625 0.33901190757751465 0.45833709836006165 0.21423394978046417 0.8831536173820496 0.8599616289138794 0.32983914017677307 \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_2.evaluate.json b/ENCSR933GMM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index acfb09d09fad83b60f41a126e1f1f197e8cea467..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF632GRM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_2.fit.json b/ENCSR933GMM/cherimoya.fold_2.fit.json deleted file mode 100644 index 76ea61edcd1e1bc1155525b404ea6e7d60ad4613..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF632GRM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_2.log b/ENCSR933GMM/cherimoya.fold_2.log deleted file mode 100644 index 88ea5a73ede11670cb0e849bc436415c7a6a1b08..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2900 36.530564069747925 4.772324562072754 548.7657470703125 0.4871687889099121 1040.2913818359375 0.3122081756591797 0.7097955 6.848132133483887 True -1 5800 32.31613516807556 27.636831045150757 612.2352294921875 0.5061048865318298 897.301025390625 0.3972603380680084 0.7797938 2.2361457347869873 True -2 8700 32.24062490463257 23.647193908691406 658.2210693359375 0.6494845747947693 879.7271118164062 0.4074842631816864 0.7865032 1.1622872352600098 True -3 11600 32.26020693778992 14.827136039733887 530.43212890625 0.4434727430343628 866.1842041015625 0.41544273495674133 0.7991016 0.9884280562400818 True -4 14500 32.303505182266235 0.6172161102294922 709.0318603515625 0.7178400158882141 867.9945678710938 0.4120219945907593 0.8010105 0.8040989637374878 True -5 17400 32.23861026763916 0.6189537048339844 576.27490234375 0.27189844846725464 858.20263671875 0.4187289774417877 0.8134588 0.7290654182434082 True -6 20300 32.25044226646423 0.6184232234954834 491.94744873046875 0.5371992588043213 854.18798828125 0.4219041168689728 0.8146139 0.7063701152801514 True -7 23200 32.22015976905823 0.6186282634735107 664.4696655273438 0.3434526324272156 847.9696044921875 0.42685043811798096 0.8178407 0.642408013343811 True -8 26100 32.26545238494873 1.097254753112793 696.463623046875 0.4888249635696411 844.2711791992188 0.4279584586620331 0.8288896 0.5750672221183777 True -9 29000 32.31290555000305 0.6209449768066406 797.2598266601562 0.5106477737426758 838.0849609375 0.4318901598453522 0.8303002 0.541448712348938 True -10 31900 32.32650017738342 0.6153900623321533 635.44287109375 0.41418004035949707 839.0404663085938 0.43056219816207886 0.8359884 0.48627567291259766 True -11 34800 32.3363139629364 1.1921567916870117 545.4320068359375 0.26992303133010864 834.7807006835938 0.43366673588752747 0.8414879 0.46044373512268066 True -12 37700 32.30125403404236 0.6634929180145264 652.8992309570312 0.30175697803497314 830.1663208007812 0.43651142716407776 0.8475652 0.4183613657951355 True -13 40600 32.29333424568176 0.6317851543426514 534.2157592773438 0.3162359595298767 827.1554565429688 0.4380711019039154 0.85480934 0.3939446806907654 True -14 43500 32.385141372680664 0.6177277565002441 675.111572265625 0.3381304144859314 821.7459716796875 0.4423759877681732 0.8572063 0.3752254545688629 True -15 46400 32.31812882423401 0.6232280731201172 647.36474609375 0.38516905903816223 821.1781005859375 0.44264286756515503 0.86136264 0.3599119186401367 True -16 49300 32.331910371780396 0.62648606300354 606.1801147460938 0.25494080781936646 822.0869750976562 0.44128087162971497 0.8652902 0.3399467468261719 True -17 52200 32.364689111709595 0.6259994506835938 604.3521728515625 0.23472623527050018 822.5966186523438 0.44237464666366577 0.86897874 0.3307291269302368 True -18 55100 33.25624132156372 5.13595986366272 637.6948852539062 0.2742532193660736 821.156494140625 0.44318151473999023 0.8667541 0.32965290546417236 False -19 58000 32.66704988479614 0.6316220760345459 678.591796875 0.3467172682285309 822.5321655273438 0.44243428111076355 0.8679462 0.33068549633026123 False diff --git a/ENCSR933GMM/cherimoya.fold_2.performance.tsv b/ENCSR933GMM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f0b45ef3b7c12a2f52316fc1431849d21fe0eec3..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -822.5966186523438 0.3508848547935486 0.44237470626831055 0.19621171057224274 0.86897873878479 0.8378678560256958 0.3307291269302368 \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_3.evaluate.json b/ENCSR933GMM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 76c7dc88f96ec6187bd67d9219afb11882e47c54..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF632GRM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_3.fit.json b/ENCSR933GMM/cherimoya.fold_3.fit.json deleted file mode 100644 index 0accce5e0ceb256b82fa44cda465da43310307f6..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF632GRM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_3.log b/ENCSR933GMM/cherimoya.fold_3.log deleted file mode 100644 index 239c7ea2069469402c6d3cb5466dd6c8d098a238..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.40590572357178 3.540977954864502 658.5511474609375 0.6249922513961792 952.9110717773438 0.31121283769607544 0.6944532 7.7395405769348145 True -1 5494 30.483065366744995 0.5866425037384033 655.5079345703125 0.7879869937896729 826.7039794921875 0.39485663175582886 0.77655464 2.1989119052886963 True -2 8241 30.543795108795166 0.5699262619018555 614.9427490234375 0.635444700717926 803.1859741210938 0.40857672691345215 0.7951241 1.0835282802581787 True -3 10988 30.565433740615845 0.5727014541625977 768.6854248046875 0.4977138042449951 793.5396728515625 0.4136863350868225 0.80265266 0.902565598487854 True -4 13735 30.57090187072754 0.5669610500335693 471.71319580078125 0.3595947027206421 784.9904174804688 0.41840341687202454 0.80930126 0.8031811118125916 True -5 16482 30.602773666381836 0.5751051902770996 626.266357421875 0.4800681173801422 779.1450805664062 0.42120668292045593 0.814605 0.7798874378204346 True -6 19229 30.58977770805359 0.9708116054534912 907.5142822265625 0.4548887014389038 775.1764526367188 0.42475375533103943 0.819553 0.7110880017280579 True -7 21976 30.5986328125 0.5686261653900146 645.760498046875 0.513115406036377 770.24462890625 0.427825391292572 0.82432854 0.6363508701324463 True -8 24723 30.633520364761353 0.5852491855621338 568.9844360351562 0.3843803405761719 767.8878173828125 0.4291425943374634 0.8318227 0.6318594813346863 True -9 27470 30.649752616882324 0.5752832889556885 675.6073608398438 0.4357518255710602 767.7452392578125 0.4285414516925812 0.83590174 0.6089672446250916 True -10 30217 30.612714767456055 0.5786840915679932 714.7294311523438 0.5502690076828003 764.4495849609375 0.431119829416275 0.8403597 0.5870048999786377 True -11 32964 30.59236788749695 0.570549488067627 531.1344604492188 0.5141140818595886 757.427734375 0.4376276433467865 0.8478697 0.5193566083908081 True -12 35711 30.61147928237915 0.5671014785766602 445.1143798828125 0.41655948758125305 753.9140014648438 0.4387589991092682 0.85075676 0.4705601930618286 True -13 38458 30.577784299850464 0.7913558483123779 587.82470703125 0.32396769523620605 750.4714965820312 0.44244346022605896 0.85567296 0.42956918478012085 True -14 41205 30.54004716873169 0.890244722366333 555.7533569335938 0.41761767864227295 749.5882568359375 0.44263726472854614 0.86196244 0.39118123054504395 True -15 43952 30.650248050689697 0.9616503715515137 677.8099975585938 0.29438498616218567 749.3446044921875 0.4419369697570801 0.8676644 0.3621181845664978 True -16 46699 30.63081645965576 1.231205940246582 608.7305908203125 0.5257574319839478 748.0606689453125 0.4430620074272156 0.8697675 0.3450932204723358 True -17 49446 30.6909921169281 0.5764889717102051 643.3834838867188 0.2869768738746643 749.0 0.44117262959480286 0.8715638 0.3344494700431824 True -18 52193 30.705054998397827 0.5796310901641846 703.8544311523438 0.2642681896686554 749.9431762695312 0.4415628910064697 0.8720554 0.33054032921791077 True -19 54940 30.599902868270874 0.5763688087463379 502.30987548828125 0.20346224308013916 749.1577758789062 0.4422350227832794 0.86999255 0.33196255564689636 False diff --git a/ENCSR933GMM/cherimoya.fold_3.performance.tsv b/ENCSR933GMM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c07b5326cd8656473fa680f3f6bef4a70fc53d45..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -749.9431762695312 0.3566195070743561 0.4415628910064697 0.18816249072551727 0.8720554113388062 0.8261505365371704 0.33054032921791077 \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_4.evaluate.json b/ENCSR933GMM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9c72dc69f93dbf0ddbca7fec7a47cfe66940653d..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF632GRM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_4.fit.json b/ENCSR933GMM/cherimoya.fold_4.fit.json deleted file mode 100644 index 01691f7757512a3a0b7884f64668c48068ca1c19..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF632GRM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933GMM/cherimoya.fold_4.log b/ENCSR933GMM/cherimoya.fold_4.log deleted file mode 100644 index d1bae5dd4243ebfe3b1a66db5c7bf696bf840868..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 34.72070670127869 4.358584642410278 657.2330932617188 0.4736393690109253 891.1539306640625 0.3040415048599243 0.69719785 6.441030979156494 True -1 5524 30.724334716796875 0.6329512596130371 562.59619140625 0.6472365260124207 777.922119140625 0.3823217749595642 0.76854044 2.107651710510254 True -2 8286 30.724846839904785 0.6164116859436035 806.6791381835938 0.5054982900619507 757.201904296875 0.39389893412590027 0.7834471 0.906895101070404 True -3 11048 30.707051753997803 0.6210660934448242 733.587646484375 0.5860090851783752 748.1276245117188 0.3994002938270569 0.7915703 0.9147411584854126 True -4 13810 30.692230224609375 0.6111307144165039 619.1241455078125 0.4566497504711151 740.1964111328125 0.40575382113456726 0.801723 0.8463171124458313 True -5 16572 30.72822594642639 0.6095843315124512 604.5529174804688 0.4641844928264618 735.145751953125 0.40850093960762024 0.8132874 0.6988518238067627 True -6 19334 30.671658277511597 0.6050901412963867 651.6607666015625 0.4064902067184448 730.2654418945312 0.4130251407623291 0.8156666 0.6662505865097046 True -7 22096 30.6799054145813 1.0500848293304443 690.2736206054688 0.4827973246574402 727.1600341796875 0.4141027331352234 0.8237973 0.6393463611602783 True -8 24858 30.684253215789795 1.2125682830810547 567.9185791015625 0.33957672119140625 723.895751953125 0.4172165095806122 0.82575834 0.6079351902008057 True -9 27620 30.756176233291626 0.6160192489624023 844.818115234375 0.49940019845962524 719.6187744140625 0.42094919085502625 0.8290562 0.5437300205230713 True -10 30382 30.75331401824951 0.6188273429870605 602.8450927734375 0.36384424567222595 719.2686157226562 0.42066600918769836 0.837044 0.49769702553749084 True -11 33144 30.74382972717285 0.612839937210083 686.7406616210938 0.38510215282440186 714.513427734375 0.4243353605270386 0.8433646 0.4535140097141266 True -12 35906 30.791842222213745 0.6214156150817871 566.08056640625 0.47036099433898926 713.0465698242188 0.4258182644844055 0.8488088 0.4081301689147949 True -13 38668 30.757212162017822 1.923640489578247 612.2017822265625 0.32138633728027344 709.9978637695312 0.42742177844047546 0.8530273 0.3831104636192322 True -14 41430 30.80715823173523 0.6152727603912354 633.6985473632812 0.31803035736083984 708.587158203125 0.4283052086830139 0.86007 0.3496658205986023 True -15 44192 30.82532286643982 1.8455617427825928 522.63037109375 0.3004675805568695 706.8837890625 0.42956387996673584 0.86570203 0.3186221420764923 True -16 46954 30.803296089172363 0.6221580505371094 607.5744018554688 0.35190585255622864 706.4937133789062 0.43001729249954224 0.86992437 0.3009425401687622 True -17 49716 30.82208228111267 0.6291425228118896 712.1660766601562 0.32127970457077026 706.4288330078125 0.4310161769390106 0.87236094 0.2902953028678894 True -18 52478 30.903606414794922 0.64278244972229 669.1181640625 0.2043263465166092 706.1600952148438 0.43099960684776306 0.8726235 0.28838878870010376 True -19 55240 30.758159160614014 0.6934671401977539 564.0570068359375 0.2611682713031769 708.1756591796875 0.4287641644477844 0.8729326 0.2885453701019287 True diff --git a/ENCSR933GMM/cherimoya.fold_4.performance.tsv b/ENCSR933GMM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b89ece789ee758b138f27ff747c3db9e03e96718..0000000000000000000000000000000000000000 --- a/ENCSR933GMM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -708.1756591796875 0.36635416746139526 0.4287641644477844 0.17540766298770905 0.8729326128959656 0.8210912942886353 0.2885453701019287 \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_0.evaluate.json b/ENCSR933HFM/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9869f7d592f7b12e49447035022a90aa3a4f4e83..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF195QEI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_0.fit.json b/ENCSR933HFM/cherimoya.fold_0.fit.json deleted file mode 100644 index 684d23bae0e180f04eb871f37908fbcf6bb142f7..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF195QEI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_0.log b/ENCSR933HFM/cherimoya.fold_0.log deleted file mode 100644 index 55766f842052053c2bf5b677e5e3d57e5f5714a1..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2103 26.48303484916687 3.508366346359253 387.1701354980469 0.8166632652282715 610.2920532226562 0.1814541518688202 0.64935046 10.886896133422852 True -1 4206 23.375831365585327 0.4372713565826416 391.87811279296875 0.8458348512649536 519.689208984375 0.2662160396575928 0.7706861 3.686012029647827 True -2 6309 23.086787462234497 0.4024472236633301 346.238525390625 1.045572280883789 489.0449523925781 0.28518086671829224 0.7863443 1.828401803970337 True -3 8412 23.085971117019653 0.40874624252319336 332.1682434082031 0.8064054846763611 480.5593566894531 0.29085975885391235 0.7999453 1.4010688066482544 True -4 10515 23.067928075790405 0.40421104431152344 321.5534362792969 1.4140243530273438 476.0368347167969 0.2959634065628052 0.80594474 1.1948728561401367 True -5 12618 23.098336935043335 9.893207550048828 385.547119140625 0.613578200340271 471.3245849609375 0.301967054605484 0.8161576 1.007504940032959 True -6 14721 23.103610038757324 0.4152791500091553 408.0832824707031 0.6838630437850952 468.9952087402344 0.30561503767967224 0.82019764 0.9127830266952515 True -7 16824 23.114905834197998 0.41571807861328125 339.353271484375 0.5851526856422424 466.6655578613281 0.306640625 0.8275262 0.8331817388534546 True -8 18927 23.123748064041138 0.40851354598999023 322.7577209472656 0.8456704020500183 464.87823486328125 0.3091059923171997 0.8327343 0.7453908324241638 True -9 21030 23.141566038131714 0.41339898109436035 268.46484375 0.2868053615093231 461.9510192871094 0.31255772709846497 0.8362775 0.7127323746681213 True -10 23133 23.09639883041382 14.529874086380005 379.1673278808594 0.600833535194397 459.8941650390625 0.314428448677063 0.84261566 0.6522190570831299 True -11 25236 23.135853052139282 0.4196758270263672 374.77740478515625 0.5352342128753662 458.785888671875 0.3150864541530609 0.84694195 0.628694474697113 True -12 27339 23.11736822128296 0.41361379623413086 412.58343505859375 0.9572641849517822 456.31884765625 0.31849467754364014 0.8490755 0.6088354587554932 True -13 29442 22.82861351966858 0.4033842086791992 305.2171325683594 0.4795474410057068 454.162841796875 0.3200453817844391 0.8542146 0.5758007168769836 True -14 31545 22.650262594223022 0.407961368560791 405.6415100097656 0.4638848900794983 452.876708984375 0.3210727870464325 0.8585147 0.5530095100402832 True -15 33648 22.658676147460938 0.4029521942138672 476.43121337890625 0.3733974099159241 452.4342956542969 0.3212817907333374 0.8603306 0.535943329334259 True -16 35751 22.661673307418823 1.5638582706451416 314.819091796875 0.39650774002075195 451.8453063964844 0.32225483655929565 0.86092675 0.5309630632400513 True -17 37854 22.679765462875366 0.40018224716186523 257.3763427734375 0.500792920589447 452.7686767578125 0.32054027915000916 0.85929126 0.5393373370170593 False -18 39957 22.683650970458984 1.1601834297180176 416.6656494140625 0.349981427192688 453.6944274902344 0.31983596086502075 0.8587713 0.5469228625297546 False -19 42060 22.66345739364624 0.40877199172973633 380.78338623046875 0.4934527277946472 453.7683410644531 0.3202716112136841 0.85742205 0.5533356666564941 False diff --git a/ENCSR933HFM/cherimoya.fold_0.performance.tsv b/ENCSR933HFM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 99d5f403710834d5df7c680f401017c1d35fa7a8..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -451.8453063964844 0.45621371269226074 0.32225483655929565 0.11918187141418457 0.8609267473220825 0.8015758991241455 0.5309630632400513 \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_1.evaluate.json b/ENCSR933HFM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8d4c9757b529ae5bb092edb878928eac4fa0ace3..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF195QEI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_1.fit.json b/ENCSR933HFM/cherimoya.fold_1.fit.json deleted file mode 100644 index ac259b3923bad5e3d18e341693a278d4f2a42683..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF195QEI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_1.log b/ENCSR933HFM/cherimoya.fold_1.log deleted file mode 100644 index b5dc997ca3c3e11d529f90971ff515da03a5b2e8..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2046 26.02546215057373 3.5959372520446777 261.75567626953125 0.5327836275100708 728.7120971679688 0.19417499005794525 0.65267354 12.287947654724121 True -1 4092 22.611454486846924 0.8988995552062988 399.7187805175781 0.610032320022583 616.2891845703125 0.2876223027706146 0.77493477 5.019857406616211 True -2 6138 22.535884857177734 1.5875983238220215 373.545166015625 1.0402777194976807 577.980712890625 0.3072001338005066 0.7971689 2.8387131690979004 True -3 8184 22.505717515945435 0.5997142791748047 495.6309814453125 0.8449496030807495 565.7210083007812 0.31509479880332947 0.81425995 1.8324339389801025 True -4 10230 22.537286043167114 2.0868895053863525 362.02557373046875 0.8701170682907104 560.117919921875 0.3201560974121094 0.820873 1.4815828800201416 True -5 12276 22.493263006210327 0.6059787273406982 529.910888671875 1.086674451828003 556.2982788085938 0.32621803879737854 0.82338166 1.3275758028030396 True -6 14322 22.446616172790527 0.6015751361846924 365.3963928222656 0.8632091879844666 554.2476806640625 0.32704874873161316 0.8340206 1.1595007181167603 True -7 16368 22.541423082351685 0.6088781356811523 270.5028076171875 0.7391413450241089 550.5005493164062 0.32997721433639526 0.8459828 0.9921743869781494 True -8 18414 22.47623610496521 0.6117184162139893 459.4097900390625 0.8448463678359985 549.5134887695312 0.3312969505786896 0.8503283 0.9179632663726807 True -9 20460 22.466384887695312 0.6000864505767822 409.2685852050781 0.5479738712310791 545.0802001953125 0.33507809042930603 0.8582563 0.850385308265686 True -10 22506 22.458627223968506 0.5986766815185547 339.55364990234375 0.8324034214019775 541.8140869140625 0.33774882555007935 0.86294544 0.7763074040412903 True -11 24552 22.456809997558594 0.585822343826294 399.9679260253906 0.5353405475616455 540.5138549804688 0.33867913484573364 0.8674404 0.7063981294631958 True -12 26598 22.467962741851807 1.1762111186981201 361.3005065917969 0.809305727481842 538.3314208984375 0.3408571183681488 0.8713268 0.6454697847366333 True -13 28644 22.717710733413696 0.6015701293945312 299.95672607421875 0.5419130325317383 535.876953125 0.34223654866218567 0.874786 0.6049163937568665 True -14 30690 22.533274173736572 0.6047945022583008 296.38116455078125 0.4817063510417938 534.3878784179688 0.34267693758010864 0.879116 0.5777731537818909 True -15 32736 22.512157440185547 1.2739229202270508 297.0120849609375 0.27240070700645447 531.3416137695312 0.34596365690231323 0.880998 0.5593954920768738 True -16 34782 22.5447998046875 0.6014320850372314 299.7449645996094 0.4343392848968506 532.5386352539062 0.3450683355331421 0.88289577 0.5513896942138672 True -17 36828 22.557578563690186 0.6090898513793945 423.677490234375 0.5317366719245911 532.3436889648438 0.34555375576019287 0.8832745 0.5459040403366089 True -18 38874 22.61995005607605 1.9303734302520752 429.080810546875 0.5600431561470032 532.453369140625 0.345290869474411 0.8809014 0.5527641773223877 False -19 40920 22.552622079849243 0.6067149639129639 407.55133056640625 0.4089011251926422 532.8043212890625 0.3451194763183594 0.87998325 0.5576357841491699 False diff --git a/ENCSR933HFM/cherimoya.fold_1.performance.tsv b/ENCSR933HFM/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 28914a1b0bd8ada19490028da2ce4b03e0f84bb1..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -532.3436889648438 0.4341895878314972 0.34555375576019287 0.1441369652748108 0.883274495601654 0.8458336591720581 0.5459040403366089 \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_2.evaluate.json b/ENCSR933HFM/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 65398fe0c2f5fc9bc392fcd1bb641d347fb7bb74..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF195QEI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_2.fit.json b/ENCSR933HFM/cherimoya.fold_2.fit.json deleted file mode 100644 index 86d40466d26e5f9235f99c88d65dce840a4c7731..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF195QEI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_2.log b/ENCSR933HFM/cherimoya.fold_2.log deleted file mode 100644 index 37c0dce6215694d0dd9fd70f0e08c2090d188ddf..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2216 28.254308700561523 3.6478939056396484 478.91070556640625 1.0513755083084106 627.6485595703125 0.1870807707309723 0.6336536 8.779928207397461 True -1 4432 24.121022701263428 0.46513962745666504 332.185546875 0.9820551872253418 524.8765258789062 0.2715608775615692 0.76739943 3.7492523193359375 True -2 6648 24.467896461486816 0.4458606243133545 275.55364990234375 0.5795370936393738 497.82183837890625 0.2877160906791687 0.7886341 1.9879822731018066 True -3 8864 24.17515206336975 0.44302988052368164 445.739013671875 0.6549526453018188 486.51934814453125 0.29544103145599365 0.8042848 1.2617734670639038 True -4 11080 23.97453546524048 0.4499194622039795 448.31488037109375 1.0375767946243286 483.537109375 0.2991136610507965 0.8071551 1.1492860317230225 True -5 13296 23.963818788528442 0.45101308822631836 438.2615966796875 0.6202296018600464 481.0511779785156 0.30026957392692566 0.818277 1.0498756170272827 True -6 15512 24.012420654296875 0.44873619079589844 321.4093017578125 0.6531882882118225 476.9367370605469 0.30564984679222107 0.82462305 1.009617567062378 True -7 17728 23.982566833496094 0.4467792510986328 347.49676513671875 0.6544984579086304 474.35662841796875 0.3090164363384247 0.8298857 0.8894516229629517 True -8 19944 24.010783910751343 0.44740748405456543 447.6388854980469 0.9074806571006775 472.6685791015625 0.30949196219444275 0.83543426 0.8003154397010803 True -9 22160 23.99636936187744 0.45189857482910156 371.9749450683594 0.6083168387413025 471.57659912109375 0.31048819422721863 0.84073585 0.7470409274101257 True -10 24376 23.99799156188965 0.4473915100097656 430.6912841796875 0.5427688360214233 468.2522277832031 0.3141298294067383 0.84589165 0.6785227656364441 True -11 26592 23.9435772895813 0.44278502464294434 363.9004821777344 0.40690910816192627 466.5704040527344 0.3154992461204529 0.8478344 0.651239812374115 True -12 28808 24.002634286880493 0.44770216941833496 274.44512939453125 0.6303287744522095 464.83868408203125 0.3169611990451813 0.85133094 0.618295431137085 True -13 31024 24.050461530685425 0.7565696239471436 394.32891845703125 0.5625525712966919 464.68109130859375 0.31773456931114197 0.8534748 0.582468569278717 True -14 33240 23.988970041275024 0.44562649726867676 364.5104675292969 0.2723275125026703 462.2293701171875 0.32019931077957153 0.8577896 0.5633659362792969 True -15 35456 24.03178381919861 0.44465208053588867 416.90032958984375 0.35564666986465454 462.67877197265625 0.3188861608505249 0.8607612 0.5470095276832581 True -16 37672 24.00093960762024 0.44487953186035156 389.6649169921875 0.2880405783653259 462.9176940917969 0.3193143904209137 0.86093277 0.544243574142456 True -17 39888 23.919034719467163 0.44058823585510254 251.98492431640625 0.5355040431022644 461.968017578125 0.3205556571483612 0.8601219 0.5465664267539978 False -18 42104 23.919438123703003 0.4440131187438965 357.5940856933594 0.4615917205810547 462.0120849609375 0.3210265338420868 0.86056286 0.5514196157455444 False -19 44320 23.9295015335083 0.44373297691345215 431.24444580078125 0.3319008946418762 462.9232482910156 0.3198687434196472 0.85876954 0.5555305480957031 False diff --git a/ENCSR933HFM/cherimoya.fold_2.performance.tsv b/ENCSR933HFM/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9be9ff3288eaaefcc20583644a8b1a5c67f79e06..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -462.9176940917969 0.45517560839653015 0.3193143904209137 0.12320166081190109 0.8609327673912048 0.8077512979507446 0.544243574142456 \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_3.evaluate.json b/ENCSR933HFM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 47d45c15a68b8d10df8c6e4075a72e4e9af16df8..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF195QEI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_3.fit.json b/ENCSR933HFM/cherimoya.fold_3.fit.json deleted file mode 100644 index 034d33520ded87e7d6336646dbb003fff44f0768..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF195QEI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_3.log b/ENCSR933HFM/cherimoya.fold_3.log deleted file mode 100644 index b3c0afe162d60b8dcf2f37d2b35b6d92c4a417db..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2114 28.33606719970703 3.5451900959014893 397.8897705078125 0.9453461170196533 613.5357666015625 0.1972612589597702 0.62936515 10.61099910736084 True -1 4228 23.2267804145813 0.43886756896972656 331.3770751953125 0.4568086862564087 524.0486450195312 0.278656005859375 0.7619855 3.790860414505005 True -2 6342 23.26687240600586 1.2973463535308838 429.671875 1.0359922647476196 499.2415466308594 0.2956543564796448 0.78396434 2.515367269515991 True -3 8456 23.30987572669983 0.43097686767578125 468.044921875 0.7203279137611389 490.5419616699219 0.3026871979236603 0.78886634 1.4873244762420654 True -4 10570 23.232683420181274 0.4344358444213867 344.01397705078125 0.7656798362731934 486.3804016113281 0.3069024980068207 0.79582036 1.2592514753341675 True -5 12684 23.29481816291809 18.519516706466675 448.0469665527344 0.8698559999465942 484.9552917480469 0.3093772828578949 0.8023345 1.214385747909546 True -6 14798 23.463122129440308 0.4491748809814453 390.1243591308594 1.0243319272994995 482.70709228515625 0.3112640380859375 0.8095264 1.1717808246612549 True -7 16912 23.28400421142578 0.43197154998779297 304.9057922363281 0.568535327911377 479.8189697265625 0.31379884481430054 0.8176121 1.056997299194336 True -8 19026 23.275009632110596 0.4306485652923584 360.46173095703125 0.7096412181854248 478.9363708496094 0.3151642680168152 0.82282573 0.9826462268829346 True -9 21140 23.247548580169678 0.7928817272186279 500.63031005859375 0.7885845303535461 476.1783752441406 0.3173995614051819 0.83245474 0.8653078079223633 True -10 23254 23.275169134140015 0.42683935165405273 410.524169921875 0.682438850402832 473.127197265625 0.3201720714569092 0.83778405 0.7795119285583496 True -11 25368 22.786296129226685 0.4157700538635254 361.5889587402344 0.5627288818359375 471.1563720703125 0.3222622573375702 0.84083694 0.7365835309028625 True -12 27482 22.74960684776306 0.4148213863372803 633.3826904296875 0.6070249080657959 468.44927978515625 0.324336975812912 0.8471329 0.6830776333808899 True -13 29596 22.806182622909546 0.5211424827575684 349.6542053222656 0.6077858209609985 466.11627197265625 0.3267947733402252 0.8529529 0.6468066573143005 True -14 31710 22.79687523841858 0.4244992733001709 382.40899658203125 0.7483720183372498 465.2189636230469 0.32849109172821045 0.8577365 0.6068291664123535 True -15 33824 22.82566809654236 0.4290187358856201 299.7663879394531 0.4571984112262726 463.97979736328125 0.3290337920188904 0.8627575 0.5808367133140564 True -16 35938 22.799495458602905 0.4302685260772705 426.37322998046875 0.5879629850387573 462.2022399902344 0.3320888876914978 0.86425275 0.576846182346344 True -17 38052 22.71537947654724 0.41494059562683105 288.5575256347656 0.47169822454452515 464.0818786621094 0.3289388418197632 0.86421174 0.5722208619117737 False -18 40166 22.7518572807312 0.4204401969909668 306.1466064453125 0.5841237306594849 464.0143737792969 0.3289393484592438 0.862215 0.5787903070449829 False -19 42280 22.7599515914917 0.43139123916625977 354.4930114746094 0.5370519161224365 465.37451171875 0.3271966278553009 0.8633134 0.5819547772407532 False diff --git a/ENCSR933HFM/cherimoya.fold_3.performance.tsv b/ENCSR933HFM/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7b95181c47ff2be4243c2e04e3fa5ce6075e5f08..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -462.2022399902344 0.44880056381225586 0.3320888876914978 0.1272718757390976 0.8642527461051941 0.8067275881767273 0.576846182346344 \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_4.evaluate.json b/ENCSR933HFM/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b8a6ad566a8e6dc8ac020241a0b0da7b0c22c927..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF195QEI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_4.fit.json b/ENCSR933HFM/cherimoya.fold_4.fit.json deleted file mode 100644 index 066dc4f19326f536f8ee0218ac988e497d672261..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF195QEI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR933HFM/cherimoya.fold_4.log b/ENCSR933HFM/cherimoya.fold_4.log deleted file mode 100644 index 193da3023703b062f6047cc211e8825dcf4d0468..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2121 28.173189878463745 3.418299913406372 282.5576477050781 0.5265061259269714 547.0762939453125 0.1814577281475067 0.62083906 10.318011283874512 True -1 4242 23.352715253829956 0.4619140625 437.33709716796875 0.6513458490371704 477.9179992675781 0.25360217690467834 0.7461089 3.517347574234009 True -2 6363 23.315968990325928 7.250836372375488 457.7975158691406 1.0578508377075195 446.3102111816406 0.2744080424308777 0.7766479 1.689706563949585 True -3 8484 23.35698914527893 0.41756343841552734 420.89013671875 0.9504262208938599 438.2872314453125 0.28003817796707153 0.787428 1.31497061252594 True -4 10605 23.322853088378906 0.41061925888061523 383.131103515625 0.912632942199707 435.5282897949219 0.28281766176223755 0.7935218 1.166324496269226 True -5 12726 23.36459755897522 0.4116544723510742 472.74505615234375 0.5134243965148926 430.20428466796875 0.2896747589111328 0.8003839 1.048332691192627 True -6 14847 23.33003067970276 0.41811680793762207 414.7937316894531 0.748764157295227 428.7688293457031 0.2891225218772888 0.8089113 0.8641330003738403 True -7 16968 23.325689792633057 0.4127066135406494 279.90936279296875 0.7287556529045105 427.09063720703125 0.29140719771385193 0.8168192 0.7807692885398865 True -8 19089 23.98213815689087 0.4186093807220459 294.1112060546875 0.587148904800415 425.60223388671875 0.2929286062717438 0.82260436 0.7442310452461243 True -9 21210 23.335951328277588 0.5550458431243896 320.332275390625 0.6504636406898499 422.1858215332031 0.2973121404647827 0.82948774 0.6668446660041809 True -10 23331 25.742738008499146 0.414750337600708 344.42266845703125 0.6936119198799133 420.7718505859375 0.2990678548812866 0.8353755 0.6373150944709778 True -11 25452 23.295871019363403 0.41751551628112793 391.8007507324219 0.6064515113830566 419.3318786621094 0.29978933930397034 0.8399567 0.5904214978218079 True -12 27573 23.86039900779724 0.5564868450164795 345.47235107421875 0.5206390023231506 416.7242736816406 0.3041541874408722 0.84712464 0.5620239973068237 True -13 29694 23.30582618713379 0.4163665771484375 334.06585693359375 0.30821120738983154 416.9229736328125 0.30321064591407776 0.8490523 0.5435378551483154 True -14 31815 23.36057162284851 0.4174964427947998 401.13006591796875 0.484774112701416 415.01177978515625 0.3054114282131195 0.85428417 0.5239675045013428 True -15 33936 23.321386575698853 0.4104743003845215 423.2567138671875 0.412778377532959 414.32415771484375 0.30719226598739624 0.8573748 0.5111351013183594 True -16 36057 23.327690839767456 0.4156532287597656 342.73193359375 0.4050412178039551 414.8821716308594 0.3066561222076416 0.8610511 0.4983566403388977 True -17 38178 23.321665048599243 0.4117701053619385 389.5839538574219 0.39567363262176514 415.8952331542969 0.30531513690948486 0.86149687 0.4997900724411011 True -18 40299 23.320420742034912 0.40911340713500977 370.8507080078125 0.30359742045402527 415.7171630859375 0.30521970987319946 0.8605111 0.504699170589447 False -19 42420 23.339606761932373 0.41527295112609863 360.36224365234375 0.32280585169792175 416.6175537109375 0.3038923442363739 0.85831535 0.5070846676826477 False diff --git a/ENCSR933HFM/cherimoya.fold_4.performance.tsv b/ENCSR933HFM/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a2040f9f69ef1b58f3efcfda4407c250f319ec3a..0000000000000000000000000000000000000000 --- a/ENCSR933HFM/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -415.8952331542969 0.4683486521244049 0.30531516671180725 0.1159043163061142 0.8614968657493591 0.8005285263061523 0.4997900724411011 \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_0.evaluate.json b/ENCSR934AWQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9941e3d5580a2b17096a01cb018a31cda46a85b3..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF351SCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_0.fit.json b/ENCSR934AWQ/cherimoya.fold_0.fit.json deleted file mode 100644 index bf0f6182fd08bc4725077d4b879b7227d1dbf88b..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF351SCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_0.log b/ENCSR934AWQ/cherimoya.fold_0.log deleted file mode 100644 index 58d16023001774f43db18dbaa53b9314f9d5eb35..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1357 19.2949378490448 3.5551047325134277 422.09014892578125 0.9712976217269897 770.8858642578125 0.4414631128311157 0.62737733 22.5360164642334 True -1 2714 15.014838218688965 0.24881720542907715 327.1393737792969 1.2448749542236328 570.2650146484375 0.5664384365081787 0.711198 11.472808837890625 True -2 4071 14.98106861114502 0.2599220275878906 273.89849853515625 0.7925441265106201 489.0018615722656 0.6510902047157288 0.7387032 3.2761948108673096 True -3 5428 14.988508701324463 0.2461872100830078 332.635498046875 0.8441575765609741 459.24700927734375 0.675471305847168 0.7463801 1.1125792264938354 True -4 6785 14.964820384979248 0.2537105083465576 378.6800231933594 0.8391116857528687 449.8573303222656 0.6841344833374023 0.7528195 0.7579836249351501 True -5 8142 14.971937656402588 0.24700570106506348 289.0809326171875 1.0451338291168213 446.2028503417969 0.6875947713851929 0.7589028 0.6764515042304993 True -6 9499 15.042872667312622 10.94322156906128 301.2760009765625 1.251537561416626 444.293701171875 0.6906625032424927 0.75158685 0.6736541390419006 False -7 10856 15.175881385803223 0.25480079650878906 341.4652099609375 0.8846921920776367 442.2295227050781 0.6935765147209167 0.7537298 0.6698083281517029 False -8 12213 14.966259241104126 0.24846601486206055 305.059326171875 0.6559891700744629 439.7309875488281 0.6966807246208191 0.76054376 0.6507040858268738 True -9 13570 15.040397644042969 0.25073719024658203 285.4747314453125 0.4830350875854492 437.31317138671875 0.6998960375785828 0.75920856 0.6555840373039246 False -10 14927 15.004624843597412 0.24932122230529785 365.213134765625 0.7585843205451965 435.7622985839844 0.7020763158798218 0.77349895 0.6198697090148926 True -11 16284 15.020817756652832 0.2525448799133301 287.1756591796875 0.6264240145683289 434.3739929199219 0.7037346959114075 0.77798617 0.6118566393852234 True -12 17641 15.00446629524231 0.26484251022338867 286.56072998046875 0.7080177664756775 432.76220703125 0.7055232524871826 0.7813599 0.6069478988647461 True -13 18998 14.968900680541992 0.46807289123535156 298.27630615234375 0.4979811906814575 431.6060791015625 0.7068675756454468 0.78577894 0.5976106524467468 True -14 20355 15.001128435134888 0.24974632263183594 266.4831237792969 0.5524835586547852 431.1778564453125 0.7077500224113464 0.78921294 0.5943276286125183 True -15 21712 15.075160264968872 6.45708703994751 347.17840576171875 0.4046558141708374 431.06170654296875 0.707929790019989 0.79452443 0.5886785984039307 True -16 23069 15.023491859436035 0.25247907638549805 342.1016845703125 0.3531724214553833 431.5975341796875 0.7071536779403687 0.7944075 0.6057533621788025 False -17 24426 15.015524625778198 1.0789759159088135 270.4993896484375 0.3416025638580322 432.4598083496094 0.7062063813209534 0.7953615 0.6261035799980164 True -18 25783 15.012574672698975 0.24759411811828613 340.0117492675781 0.2815663814544678 433.2768859863281 0.7050222158432007 0.79363805 0.647332489490509 False -19 27140 15.00287389755249 0.2462000846862793 338.56854248046875 0.1601373553276062 433.7684020996094 0.7042573690414429 0.79303485 0.6589570641517639 False diff --git a/ENCSR934AWQ/cherimoya.fold_0.performance.tsv b/ENCSR934AWQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a9004afc311be285619ac5da17af750326a5ab1a..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -432.4598083496094 0.2459188550710678 0.7062063217163086 0.2879883944988251 0.7953615188598633 0.769343912601471 0.6261035799980164 \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_1.evaluate.json b/ENCSR934AWQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c85f6b0b4b7b75601d082787485ffa4a99b77a77..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF351SCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_1.fit.json b/ENCSR934AWQ/cherimoya.fold_1.fit.json deleted file mode 100644 index 7b64588105cda1ae9580b7d8b5881237e3444791..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF351SCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_1.log b/ENCSR934AWQ/cherimoya.fold_1.log deleted file mode 100644 index 1bd5f701168025ad7f0d58fcb2d1a043a71b87e8..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1322 19.096989154815674 3.290827989578247 433.01788330078125 1.3369171619415283 862.6948852539062 0.4496152698993683 0.56506145 24.759614944458008 True -1 2644 14.641812562942505 0.7812983989715576 352.57684326171875 0.8849294185638428 632.4146728515625 0.5773019194602966 0.6765115 11.89810848236084 True -2 3966 14.583730459213257 0.41967105865478516 447.3927001953125 1.0258561372756958 539.6670532226562 0.6694161295890808 0.692273 4.835203170776367 True -3 5288 14.58381462097168 0.4283161163330078 359.0882873535156 0.8556094169616699 502.0622253417969 0.6987372636795044 0.7064979 1.48414146900177 True -4 6610 14.561602354049683 0.42607784271240234 378.46484375 0.7473926544189453 489.8788757324219 0.7095301747322083 0.7288408 0.9201356768608093 True -5 7932 14.561083316802979 0.419666051864624 334.49359130859375 0.7264929413795471 484.76007080078125 0.7144231796264648 0.7375025 0.807447612285614 True -6 9254 14.565772294998169 0.427581787109375 363.7199401855469 0.7045291066169739 481.93536376953125 0.717366635799408 0.7429771 0.7322058081626892 True -7 10576 14.564595222473145 0.4284203052520752 330.6321716308594 0.5627679824829102 478.80926513671875 0.7204859256744385 0.75212616 0.6672545671463013 True -8 11898 14.568962574005127 0.41834139823913574 334.6076354980469 0.8815573453903198 476.17401123046875 0.7233094573020935 0.75914323 0.6448511481285095 True -9 13220 14.583061218261719 0.4177567958831787 328.53179931640625 0.6441401839256287 473.7862854003906 0.7259837985038757 0.766636 0.626409113407135 True -10 14542 14.582505941390991 0.421628475189209 334.21142578125 0.9422986507415771 471.5502014160156 0.7281022071838379 0.77949566 0.5984034538269043 True -11 15864 14.562957048416138 1.0985586643218994 349.94549560546875 0.7528039813041687 469.5755310058594 0.7302144765853882 0.7826597 0.5908495187759399 True -12 17186 14.61812448501587 0.4693942070007324 337.5738525390625 0.36975184082984924 468.3744201660156 0.7318208813667297 0.78839666 0.5770183205604553 True -13 18508 14.581537246704102 0.42048001289367676 307.31976318359375 0.5057907104492188 467.39117431640625 0.7328853011131287 0.7978147 0.5609888434410095 True -14 19830 14.587721347808838 0.4199535846710205 279.49310302734375 0.474973201751709 466.66729736328125 0.7338512539863586 0.8008385 0.5605519413948059 True -15 21152 14.60085153579712 0.4199178218841553 333.8313903808594 0.4650465250015259 466.83685302734375 0.7337409853935242 0.8049524 0.5712141394615173 True -16 22474 14.591780662536621 0.42781949043273926 334.63909912109375 0.3512885570526123 467.6222229003906 0.732830286026001 0.806529 0.5901965498924255 True -17 23796 14.654402017593384 0.4203498363494873 307.7740783691406 0.35383930802345276 468.43084716796875 0.7315910458564758 0.8032224 0.624156653881073 False -18 25118 14.605205774307251 0.4313502311706543 342.3560791015625 0.27183371782302856 469.4083557128906 0.7303913831710815 0.80039144 0.6467380523681641 False -19 26440 14.564407348632812 0.41981935501098633 311.60223388671875 0.20799653232097626 470.31402587890625 0.7295546531677246 0.7989763 0.66011643409729 False diff --git a/ENCSR934AWQ/cherimoya.fold_1.performance.tsv b/ENCSR934AWQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 57f27391119eab6187fd6cb23db1b7512c0a3ffd..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -467.6222229003906 0.2266508787870407 0.7328302264213562 0.3116516172885895 0.8065289855003357 0.7956927418708801 0.5901965498924255 \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_2.evaluate.json b/ENCSR934AWQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index a0c277be7abbf7117fd21bda40b3c01e093ec03f..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF351SCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_2.fit.json b/ENCSR934AWQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 6c163c3f7f5ea6ca9c20de013daa172aff3e91dc..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF351SCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_2.log b/ENCSR934AWQ/cherimoya.fold_2.log deleted file mode 100644 index 06900ff2e4e868c009962e2f37ac2a6c6b1b0ed2..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1421 20.485888481140137 3.247231960296631 398.8860778808594 1.1442017555236816 797.3607788085938 0.4489234685897827 0.56766963 22.053905487060547 True -1 2842 16.272308826446533 16.238881826400757 397.658447265625 0.8535221815109253 593.6365966796875 0.5752277374267578 0.66737545 11.925281524658203 True -2 4263 17.095795154571533 0.2768223285675049 352.0462646484375 0.7344003319740295 499.2406005859375 0.6619151830673218 0.69966847 4.2948198318481445 True -3 5684 15.702698707580566 0.8468592166900635 319.0565185546875 0.6864677667617798 470.3489074707031 0.6872000098228455 0.7175071 1.3874292373657227 True -4 7105 15.742180109024048 0.2836728096008301 330.6419677734375 0.6944977045059204 460.207763671875 0.6956853270530701 0.7441972 0.8456404805183411 True -5 8526 15.69206953048706 1.4005076885223389 362.6712646484375 0.5949746370315552 455.50592041015625 0.7007766366004944 0.7455519 0.76308673620224 True -6 9947 15.697910785675049 0.2801625728607178 422.2327880859375 0.922000527381897 452.8236999511719 0.7032381296157837 0.74823236 0.7054148316383362 True -7 11368 15.652939319610596 0.2831907272338867 380.11358642578125 0.7512600421905518 450.9715270996094 0.7058634161949158 0.7522317 0.6705830097198486 True -8 12789 15.675146102905273 0.28196096420288086 346.74163818359375 0.6023530960083008 448.4588623046875 0.7086384892463684 0.75926006 0.6529368758201599 True -9 14210 15.704627990722656 0.27460789680480957 340.3000183105469 0.7702809572219849 446.5469665527344 0.7111379504203796 0.7654215 0.6453410983085632 True -10 15631 15.684477090835571 0.2737278938293457 331.3468017578125 0.6015387773513794 444.7803039550781 0.7135204672813416 0.7739948 0.6241468191146851 True -11 17052 15.678050994873047 0.27262258529663086 288.5777282714844 0.4267715513706207 443.0430603027344 0.7155651450157166 0.78345424 0.6052531599998474 True -12 18473 15.654707670211792 0.9803619384765625 366.3084716796875 0.5329291224479675 441.56927490234375 0.7173427939414978 0.7871098 0.5998940467834473 True -13 19894 15.699145555496216 0.27204108238220215 373.4789733886719 0.6548760533332825 440.35888671875 0.7187405228614807 0.79255575 0.5881800651550293 True -14 21315 15.686981916427612 0.2788856029510498 376.54473876953125 0.47182777523994446 440.0584716796875 0.7190643548965454 0.79769224 0.5860532522201538 True -15 22736 15.656108856201172 1.8161988258361816 287.87860107421875 0.274888813495636 439.97998046875 0.7188781499862671 0.7992766 0.5966236591339111 True -16 24157 15.703608751296997 0.27574896812438965 303.44683837890625 0.3127480149269104 440.6507263183594 0.7181435227394104 0.79855835 0.6052607893943787 False -17 25578 15.711739301681519 0.27252626419067383 369.01641845703125 0.25372686982154846 441.7152404785156 0.7168442010879517 0.7958259 0.6341919898986816 False -18 26999 15.683274030685425 13.707843780517578 289.314208984375 0.2191902995109558 442.7963562011719 0.7154941558837891 0.79396826 0.6653707027435303 False -19 28420 17.989906549453735 8.542279958724976 288.0242919921875 0.2905466556549072 443.5171203613281 0.7148004770278931 0.7910836 0.679228663444519 False diff --git a/ENCSR934AWQ/cherimoya.fold_2.performance.tsv b/ENCSR934AWQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f4dd2c52bfc2cb5ac8a7b36ea970e15b0294da18..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -439.97998046875 0.23719795048236847 0.7188780307769775 0.29960572719573975 0.79927659034729 0.7853832840919495 0.5966236591339111 \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_3.evaluate.json b/ENCSR934AWQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 1b8992b7d0634166d82c9843cf885fd02966b65a..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF351SCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_3.fit.json b/ENCSR934AWQ/cherimoya.fold_3.fit.json deleted file mode 100644 index b362923398a46b307dff59383219a240f8e3631f..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF351SCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_3.log b/ENCSR934AWQ/cherimoya.fold_3.log deleted file mode 100644 index 7e9d52a72ea8610961f48d99ee02090a7f53240a..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1377 19.62649655342102 3.2207202911376953 413.7972412109375 0.8261604309082031 758.083740234375 0.4490070343017578 0.59303 21.940702438354492 True -1 2754 15.27530813217163 0.30544304847717285 455.9132385253906 1.302420735359192 565.2393798828125 0.5723127126693726 0.6660338 11.511119842529297 True -2 4131 15.219124555587769 0.28351330757141113 319.1800537109375 0.922087550163269 488.28955078125 0.6541885733604431 0.6335543 3.6997344493865967 False -3 5508 15.213526010513306 0.2724270820617676 294.8352355957031 0.528688907623291 463.6853332519531 0.6775168180465698 0.6539843 1.3609739542007446 False -4 6885 15.22248888015747 0.6163411140441895 375.3468933105469 0.8142029047012329 453.9353332519531 0.6861838102340698 0.68507814 1.0228888988494873 True -5 8262 15.239590883255005 0.2771627902984619 362.3914489746094 0.6571727991104126 450.6172180175781 0.69019615650177 0.7016578 0.856306254863739 True -6 9639 15.381784677505493 8.829211235046387 290.9970703125 0.6257181167602539 447.6162109375 0.6929771900177002 0.70509464 0.7875790596008301 True -7 11016 15.254098176956177 0.2777061462402344 379.3175048828125 0.5525864362716675 445.3600769042969 0.6955536007881165 0.71336967 0.7478278875350952 True -8 12393 15.188342332839966 19.226398229599 342.9870300292969 0.7136394381523132 443.2882080078125 0.6982391476631165 0.71443003 0.7313017249107361 True -9 13770 21.617133855819702 4.304810047149658 389.5939636230469 0.5708997249603271 441.9121398925781 0.7006454467773438 0.7186687 0.7296109795570374 True -10 15147 15.22962212562561 0.28711867332458496 335.7450256347656 0.5232632756233215 439.7784729003906 0.7031036019325256 0.7287573 0.7074546813964844 True -11 16524 15.42054533958435 12.917012929916382 300.6488952636719 0.5289809703826904 437.4347229003906 0.7055656313896179 0.7442932 0.6742309331893921 True -12 17901 16.31947898864746 8.333685159683228 314.8970947265625 0.8148251175880432 436.6917419433594 0.7071309685707092 0.7467716 0.6734991073608398 True -13 19278 15.281310558319092 0.29506897926330566 300.31585693359375 0.5892871618270874 435.7571716308594 0.7083678841590881 0.7583505 0.6575728058815002 True -14 20655 15.263535976409912 1.6157054901123047 306.88818359375 0.4069191515445709 435.43280029296875 0.7089508771896362 0.7692422 0.6376529335975647 True -15 22032 15.257136583328247 0.2777674198150635 297.5377197265625 0.4726567566394806 435.3451843261719 0.7087751030921936 0.7734789 0.6389911770820618 True -16 23409 15.265107154846191 0.29007959365844727 351.2431640625 0.3372841477394104 436.1678466796875 0.7081607580184937 0.7794334 0.6469277739524841 True -17 24786 15.317681074142456 1.1409859657287598 294.02191162109375 0.3979591727256775 436.8798828125 0.707152247428894 0.781439 0.6606486439704895 True -18 26163 15.401994228363037 0.2806718349456787 354.7281494140625 0.2514030933380127 437.71728515625 0.7061058282852173 0.77903205 0.6820085644721985 False -19 27540 15.287053108215332 0.2763800621032715 331.68743896484375 0.34531310200691223 438.1176452636719 0.7053295373916626 0.7792322 0.6969704031944275 False diff --git a/ENCSR934AWQ/cherimoya.fold_3.performance.tsv b/ENCSR934AWQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ae5791eca2384dfed8328ada71ba6fa61ab42616..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -436.8798828125 0.2431051880121231 0.7071521878242493 0.29487845301628113 0.7814390063285828 0.7666917443275452 0.6606486439704895 \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_4.evaluate.json b/ENCSR934AWQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 794a8372b2089b32d6693781f1492b83c50c2d15..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF351SCV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_4.fit.json b/ENCSR934AWQ/cherimoya.fold_4.fit.json deleted file mode 100644 index 20e4ee1e1ddd496cb7ffa21f7f3e6bfcb33ebe23..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF351SCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR934AWQ/cherimoya.fold_4.log b/ENCSR934AWQ/cherimoya.fold_4.log deleted file mode 100644 index 6d1082bae9661c5a38b8519c1206ef931f971ada..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1348 21.595728397369385 3.1435277462005615 435.6872253417969 1.1077075004577637 732.7036743164062 0.43376368284225464 0.59056866 21.489486694335938 True -1 2696 14.853217840194702 0.9189958572387695 402.2872314453125 0.8896667957305908 545.7182006835938 0.5567832589149475 0.68164253 11.846270561218262 True -2 4044 14.98682689666748 11.63341236114502 399.89111328125 0.7636364698410034 468.08428955078125 0.6388412714004517 0.7075306 3.9242522716522217 True -3 5392 15.011649370193481 0.24966931343078613 288.899169921875 0.693901777267456 438.5141296386719 0.6641066670417786 0.71288073 1.0520579814910889 True -4 6740 14.85933780670166 0.2552371025085449 290.0625915527344 0.7704923152923584 429.6980895996094 0.6732131242752075 0.72710836 0.7610645890235901 True -5 8088 14.880709648132324 0.24302077293395996 368.82305908203125 0.6684385538101196 426.2083435058594 0.6772043704986572 0.7390942 0.6837282180786133 True -6 9436 14.853068351745605 0.977710485458374 363.54742431640625 0.7579178810119629 423.1779479980469 0.6801450848579407 0.7426152 0.6694519519805908 True -7 10784 14.882991790771484 0.25411462783813477 347.7283630371094 0.4593280553817749 421.2323303222656 0.6834837198257446 0.7418952 0.6789623498916626 False -8 12132 14.866488456726074 0.24843430519104004 322.93072509765625 0.7480689287185669 419.54400634765625 0.6859480142593384 0.7433163 0.6847730875015259 True -9 13480 14.860483407974243 0.24562811851501465 335.48260498046875 0.7085607647895813 418.00555419921875 0.688215970993042 0.75221914 0.6660636067390442 True -10 14828 14.855531454086304 0.2500295639038086 322.3311767578125 0.6281651854515076 416.4706726074219 0.6900782585144043 0.7635801 0.641087532043457 True -11 16176 14.869441032409668 0.24625396728515625 312.48052978515625 0.7012991905212402 415.26690673828125 0.69150310754776 0.7689453 0.6309511661529541 True -12 17524 14.8555326461792 0.9241204261779785 301.34698486328125 0.41325345635414124 413.32562255859375 0.693345308303833 0.7761236 0.6101287603378296 True -13 18872 14.908539295196533 0.24258661270141602 276.41571044921875 0.5148251056671143 412.7896423339844 0.6945357322692871 0.7829877 0.5986716151237488 True -14 20220 14.872028350830078 0.248030424118042 296.1557312011719 0.44288527965545654 412.2950134277344 0.6951298117637634 0.78860223 0.5848585367202759 True -15 21568 14.919916152954102 0.2505650520324707 301.04705810546875 0.3138611912727356 412.522216796875 0.6952618360519409 0.79278255 0.5837160348892212 True -16 22916 14.867769956588745 0.23686861991882324 315.67645263671875 0.3541337251663208 413.11834716796875 0.6946084499359131 0.79323256 0.5969524383544922 True -17 24264 14.860433101654053 0.23635005950927734 318.13739013671875 0.3325190544128418 413.6120910644531 0.6939253211021423 0.793598 0.6198931336402893 True -18 25612 14.88740587234497 0.24369096755981445 302.70068359375 0.3064035475254059 414.6463317871094 0.6927303671836853 0.7897555 0.6440259218215942 False -19 26960 14.849652528762817 0.24425721168518066 330.49334716796875 0.1920003592967987 415.1498718261719 0.6919058561325073 0.7902572 0.6589104533195496 False diff --git a/ENCSR934AWQ/cherimoya.fold_4.performance.tsv b/ENCSR934AWQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 287955906a2df6a0dccd95fc98b2c118e2c3c1be..0000000000000000000000000000000000000000 --- a/ENCSR934AWQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -413.6120910644531 0.2547052502632141 0.6939253211021423 0.2771450877189636 0.7935979962348938 0.7642484903335571 0.6198931336402893 \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_0.evaluate.json b/ENCSR935EVZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c98eecb193f30eb2505958ac4d3dc83d921e5fb5..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF900VMZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_0.fit.json b/ENCSR935EVZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 428b68acb3448908f2554ce8cb7d76e506f28b17..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF900VMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_0.log b/ENCSR935EVZ/cherimoya.fold_0.log deleted file mode 100644 index 87d95e13a5c0a21df9a2b037c4d6a3ebf2a493b2..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 33.91386079788208 3.4721310138702393 334.8634033203125 1.057873010635376 661.4996337890625 0.21921776235103607 0.5280555 5.633908271789551 True -1 5456 30.20026183128357 0.5787758827209473 507.45037841796875 1.2162044048309326 567.13427734375 0.3594467043876648 0.61908656 3.0737900733947754 True -2 8184 29.956558227539062 0.5492761135101318 459.0799560546875 1.0839686393737793 558.2734375 0.3683921694755554 0.62490475 1.8995929956436157 True -3 10912 29.966171503067017 0.8441562652587891 554.93212890625 0.9615689516067505 551.7337036132812 0.3751407563686371 0.62885565 1.5639958381652832 True -4 13640 29.89174246788025 1.2250308990478516 524.427978515625 1.15473210811615 544.772216796875 0.38288724422454834 0.6356923 1.5053383111953735 True -5 16368 29.942238569259644 0.547252893447876 343.3055725097656 1.0838088989257812 540.1600341796875 0.3902202248573303 0.6360461 1.2103192806243896 True -6 19096 29.4361355304718 0.5493419170379639 371.81402587890625 0.9164419770240784 538.3164672851562 0.3925005793571472 0.63555336 1.1669434309005737 False -7 21824 29.396051168441772 0.5594887733459473 397.58868408203125 0.9970234632492065 534.5342407226562 0.39908504486083984 0.6394242 1.074668049812317 True -8 24552 29.369261503219604 0.5528686046600342 399.89190673828125 1.005232334136963 531.341552734375 0.40393322706222534 0.6413757 1.060188889503479 True -9 27280 29.428685665130615 0.5531060695648193 371.10797119140625 0.6853562593460083 527.7091674804688 0.4092859625816345 0.6516939 0.9095428586006165 True -10 30008 29.416074752807617 0.5435400009155273 310.9505615234375 1.3493764400482178 525.2373657226562 0.4127601981163025 0.65921146 0.8627397418022156 True -11 32736 29.40066957473755 0.5463056564331055 492.48199462890625 0.7924726605415344 522.0797119140625 0.4161341190338135 0.67454845 0.8068825602531433 True -12 35464 29.402408123016357 0.5530915260314941 371.06884765625 0.8739019632339478 518.5225219726562 0.42272427678108215 0.6848781 0.7523772716522217 True -13 38192 29.49846839904785 0.5519485473632812 389.0733642578125 0.8376824259757996 514.9136962890625 0.42721322178840637 0.6969169 0.687220573425293 True -14 40920 29.382411003112793 0.5415115356445312 460.39752197265625 0.7077758312225342 514.9771728515625 0.4264718294143677 0.70849246 0.6638672351837158 True -15 43648 29.41920018196106 0.5476713180541992 326.8270568847656 0.9355210065841675 512.216796875 0.4327508211135864 0.71679103 0.6273994445800781 True -16 46376 29.403825044631958 0.5483624935150146 446.9538879394531 0.5713624358177185 510.6709289550781 0.43451035022735596 0.7210687 0.6042079925537109 True -17 49104 29.50297784805298 0.5568196773529053 380.02850341796875 0.4823513329029083 509.7744140625 0.43518710136413574 0.72526646 0.5982186198234558 True -18 51832 29.53462553024292 0.5703179836273193 298.6980285644531 0.43762004375457764 510.7346496582031 0.4333224892616272 0.7264996 0.5945377945899963 True -19 54560 29.457178592681885 3.745006561279297 407.5141906738281 0.4374478757381439 510.92877197265625 0.43380406498908997 0.72736996 0.5965288877487183 True diff --git a/ENCSR935EVZ/cherimoya.fold_0.performance.tsv b/ENCSR935EVZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e2c2f409e2d81a419d5e20f8786583605e4704e9..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -510.92877197265625 0.384549617767334 0.4338040053844452 0.15556931495666504 0.7273699641227722 0.6689353585243225 0.5965288877487183 \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_1.evaluate.json b/ENCSR935EVZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 63557d2b478039a2c2a63dc97e5f02402c25e929..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF900VMZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_1.fit.json b/ENCSR935EVZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 6a3ee959f94a7ddb932b1f6513c8b84e15a195f5..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF900VMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_1.log b/ENCSR935EVZ/cherimoya.fold_1.log deleted file mode 100644 index 9e2ed5358ba7830bfd519a76432f49ef8347d8a5..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2716 33.80847930908203 3.5818264484405518 452.04180908203125 1.2290269136428833 766.0648193359375 0.2270897477865219 0.55806285 7.350200653076172 True -1 5432 29.561367988586426 1.248394250869751 517.9935302734375 1.842254400253296 651.6012573242188 0.37306544184684753 0.64677423 3.4774725437164307 True -2 8148 29.973586559295654 0.6714041233062744 382.0748596191406 1.3842693567276 633.5181274414062 0.3880455493927002 0.6444054 2.232616424560547 False -3 10864 29.93759799003601 0.681398868560791 527.9734497070312 1.287158727645874 625.09130859375 0.3933720588684082 0.6544852 1.824012041091919 True -4 13580 29.878857374191284 0.6805169582366943 452.98822021484375 0.958837628364563 618.6417846679688 0.4010281562805176 0.66230804 1.522102952003479 True -5 16296 29.878944158554077 1.4859633445739746 340.6700744628906 1.7463504076004028 615.3540649414062 0.40276098251342773 0.6661288 1.1933716535568237 True -6 19012 29.87740135192871 14.267544507980347 393.13372802734375 1.4724462032318115 608.9917602539062 0.4116671681404114 0.66875756 1.1039129495620728 True -7 21728 30.034000158309937 0.6848180294036865 446.66522216796875 1.1024136543273926 606.5017700195312 0.41453278064727783 0.6746714 1.0626757144927979 True -8 24444 29.935327529907227 0.6773898601531982 622.5223388671875 1.1184723377227783 602.6697998046875 0.42011067271232605 0.6778967 1.0391037464141846 True -9 27160 29.955526113510132 0.6889433860778809 423.4371337890625 0.9558476209640503 599.1870727539062 0.42514482140541077 0.6811151 0.9948902130126953 True -10 29876 30.016655683517456 1.5888214111328125 395.77142333984375 0.9210265874862671 596.4313354492188 0.4290502965450287 0.6880386 0.9524068236351013 True -11 32592 29.99999737739563 0.685528039932251 425.4325256347656 1.1799076795578003 591.57470703125 0.4354536831378937 0.6950706 0.8765546679496765 True -12 35308 29.95614504814148 0.6896648406982422 348.2250061035156 1.0357160568237305 590.0924682617188 0.4363701045513153 0.699994 0.820281445980072 True -13 38024 29.869792699813843 0.6740553379058838 430.8414001464844 0.7701865434646606 585.9669189453125 0.44161075353622437 0.71486956 0.7838780879974365 True -14 40740 29.411144495010376 0.6726870536804199 364.80963134765625 0.5812162160873413 583.1137084960938 0.4450480341911316 0.72454655 0.7357487082481384 True -15 43456 29.378950357437134 1.0179131031036377 415.9285888671875 0.7369057536125183 580.721435546875 0.4471096992492676 0.73547006 0.6926383376121521 True -16 46172 29.321159839630127 15.623355627059937 486.708740234375 0.5275657176971436 579.9540405273438 0.4478367269039154 0.7428931 0.6565645933151245 True -17 48888 29.40672469139099 0.6773064136505127 501.559814453125 0.7909516096115112 577.6908569335938 0.4513925611972809 0.74659497 0.6481481194496155 True -18 51604 29.359532117843628 0.6853468418121338 413.21710205078125 0.8738453984260559 577.3416748046875 0.4525361955165863 0.7492126 0.6335769295692444 True -19 54320 29.405001640319824 0.6804203987121582 385.0146484375 0.5928032398223877 579.0225830078125 0.4493672549724579 0.7477237 0.6357155442237854 False diff --git a/ENCSR935EVZ/cherimoya.fold_1.performance.tsv b/ENCSR935EVZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8fa7f4abfc9011b3c33547d6f34ba2ad93c13728..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -577.3416748046875 0.36689743399620056 0.4525361955165863 0.1717960387468338 0.7492126226425171 0.7066611051559448 0.6335769295692444 \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_2.evaluate.json b/ENCSR935EVZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7f336ad2b678464a47520202e71a6e0d9d6d0f80..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF900VMZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_2.fit.json b/ENCSR935EVZ/cherimoya.fold_2.fit.json deleted file mode 100644 index cee9d3828559acf319a6a4aca56ba93e35c99b99..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF900VMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_2.log b/ENCSR935EVZ/cherimoya.fold_2.log deleted file mode 100644 index 0c9efa54336101d12667bdd371ad8ecd39f667d0..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 35.61379861831665 3.520951271057129 381.94378662109375 1.4363434314727783 686.383056640625 0.2269839495420456 0.5279925 4.952018737792969 True -1 5764 31.92029857635498 0.5484745502471924 459.3173522949219 0.8891722559928894 583.5532836914062 0.3600274324417114 0.62810576 3.378237247467041 True -2 8646 31.77815556526184 0.5222043991088867 453.46612548828125 1.1809465885162354 571.5903930664062 0.3726086914539337 0.62933767 1.9587496519088745 True -3 11528 31.74438190460205 0.5247781276702881 396.3283996582031 1.6598448753356934 565.661865234375 0.37748292088508606 0.6370599 1.434789776802063 True -4 14410 31.760030508041382 0.5298202037811279 393.3419189453125 1.104907512664795 559.53369140625 0.3874180018901825 0.64427304 1.3141084909439087 True -5 17292 31.73613691329956 0.5299563407897949 471.6285705566406 0.9026413559913635 555.9869995117188 0.39382901787757874 0.64579535 1.2526915073394775 True -6 20174 31.761877059936523 7.500982284545898 394.78558349609375 1.0558767318725586 555.023681640625 0.39598211646080017 0.64421356 1.2385683059692383 False -7 23056 31.48875904083252 0.5281782150268555 477.1622619628906 0.7206568121910095 548.3995361328125 0.4058040678501129 0.6473603 1.1838257312774658 True -8 25938 31.178905487060547 0.6087973117828369 370.6720886230469 0.9321638941764832 546.0377197265625 0.40799468755722046 0.65151185 1.0641601085662842 True -9 28820 31.164718866348267 0.532773494720459 379.25408935546875 1.029670238494873 542.2579956054688 0.41442033648490906 0.6571131 1.080268383026123 True -10 31702 31.168014526367188 0.960766077041626 448.33819580078125 1.0217869281768799 538.2783813476562 0.4192398488521576 0.6655008 0.945953369140625 True -11 34584 31.1431941986084 0.5159082412719727 370.2686462402344 0.8437923192977905 536.2266845703125 0.42106300592422485 0.6709267 0.9474914073944092 True -12 37466 31.225513458251953 1.0567426681518555 372.714111328125 0.8454595804214478 533.6102294921875 0.4247371256351471 0.6773843 0.8528242707252502 True -13 40348 31.18890357017517 0.5267429351806641 365.017578125 0.5371934175491333 530.68505859375 0.42899081110954285 0.69143736 0.7795659899711609 True -14 43230 31.11508560180664 0.5245471000671387 475.8086853027344 0.7764300107955933 528.5934448242188 0.4306545555591583 0.6998013 0.7428489923477173 True -15 46112 31.18172597885132 1.6233775615692139 358.23211669921875 0.7024431228637695 525.8536987304688 0.43444445729255676 0.70999855 0.6779388785362244 True -16 48994 31.154290676116943 0.5274391174316406 350.9022216796875 0.5511445999145508 525.3805541992188 0.435034841299057 0.7181497 0.6651343703269958 True -17 51876 31.150837898254395 0.518841028213501 421.274658203125 0.6038615107536316 523.6387329101562 0.4376371502876282 0.721971 0.6402264833450317 True -18 54758 31.180843591690063 0.5236344337463379 404.74090576171875 0.47933143377304077 524.256591796875 0.435462087392807 0.72257155 0.6385025382041931 True -19 57640 31.1832435131073 0.8565559387207031 333.1736145019531 0.5978081822395325 524.1963500976562 0.4356047511100769 0.72384745 0.6400412917137146 True diff --git a/ENCSR935EVZ/cherimoya.fold_2.performance.tsv b/ENCSR935EVZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 70d22cdce69e460356a5f88bc12fb012d20072a0..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -524.1963500976562 0.38070908188819885 0.4356047511100769 0.15807411074638367 0.7238474488258362 0.675317108631134 0.6400412917137146 \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_3.evaluate.json b/ENCSR935EVZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 169eabed34017e8d6981e5c48ffefbc5c937e092..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF900VMZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_3.fit.json b/ENCSR935EVZ/cherimoya.fold_3.fit.json deleted file mode 100644 index 1c8e7d02573c42f06c17099c803e82b656265a53..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF900VMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_3.log b/ENCSR935EVZ/cherimoya.fold_3.log deleted file mode 100644 index 62d38b461265f445d98e448ab719d771adea76e0..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 34.58004927635193 11.996638774871826 521.2274780273438 0.9756767749786377 691.9829711914062 0.22050155699253082 0.55762875 6.051422119140625 True -1 5510 30.47576403617859 1.3350765705108643 491.7959899902344 1.0007104873657227 597.941162109375 0.3546748757362366 0.63971734 3.335305690765381 True -2 8265 30.010830402374268 1.088444471359253 474.8182373046875 1.2844549417495728 586.9278564453125 0.368155837059021 0.6391114 1.779597520828247 False -3 11020 29.765637636184692 0.5567665100097656 372.98504638671875 1.264631986618042 577.677734375 0.37869489192962646 0.6497885 1.53677237033844 True -4 13775 29.768582344055176 0.5579009056091309 372.1554870605469 1.1691112518310547 575.1167602539062 0.38051894307136536 0.654623 1.4595282077789307 True -5 16530 29.754347324371338 0.5554065704345703 422.0740051269531 1.1947171688079834 569.5230102539062 0.38987284898757935 0.6477067 1.3437248468399048 False -6 19285 29.805731534957886 0.5519492626190186 464.05999755859375 1.0611979961395264 565.6400146484375 0.39585793018341064 0.6429792 1.2054682970046997 False -7 22040 29.76849627494812 0.5556402206420898 412.1573486328125 0.9100377559661865 561.4234619140625 0.4017188847064972 0.65068865 1.1989047527313232 False -8 24795 29.818716526031494 0.5541598796844482 369.7840576171875 1.4860432147979736 559.4741821289062 0.4040822386741638 0.6549712 1.1831369400024414 True -9 27550 29.765000581741333 0.5531673431396484 434.37384033203125 1.454616665840149 554.0435180664062 0.41304051876068115 0.6619983 1.0900324583053589 True -10 30305 29.773725271224976 0.5577940940856934 513.7059936523438 0.8036515116691589 552.471923828125 0.41389375925064087 0.6712968 1.0215840339660645 True -11 33060 29.788224935531616 0.557476282119751 367.0248718261719 0.8446800708770752 550.0966186523438 0.4164658486843109 0.6756493 0.9789731502532959 True -12 35815 31.372145414352417 13.15338921546936 475.62298583984375 1.084717035293579 546.8819580078125 0.42114147543907166 0.6885961 0.8863264322280884 True -13 38570 29.901917457580566 1.3370559215545654 392.6297607421875 0.9040276408195496 544.5476684570312 0.42373865842819214 0.7012104 0.8052250146865845 True -14 41325 29.933214902877808 0.9832124710083008 540.4711303710938 0.7587360143661499 541.6123657226562 0.4281814694404602 0.7126488 0.7471821308135986 True -15 44080 29.905824184417725 0.5691232681274414 358.44610595703125 0.7860946655273438 539.991455078125 0.42929771542549133 0.72229135 0.6922940611839294 True -16 46835 29.93059515953064 0.5746922492980957 371.7412109375 0.5648699998855591 538.586181640625 0.4308154881000519 0.7317897 0.6586703658103943 True -17 49590 29.912373781204224 0.5618100166320801 383.52789306640625 0.6278953552246094 537.9591064453125 0.4310157895088196 0.73551875 0.6262317299842834 True -18 52345 29.954642057418823 0.5726380348205566 401.93768310546875 0.6255462765693665 538.778564453125 0.4291612505912781 0.73642695 0.6239818930625916 True -19 55100 29.91234302520752 0.5589783191680908 333.046142578125 0.4349038004875183 538.1295166015625 0.43118980526924133 0.7369798 0.6267374157905579 True diff --git a/ENCSR935EVZ/cherimoya.fold_3.performance.tsv b/ENCSR935EVZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b056950e82938a2f002bfe7a8ba01da6b215f1e6..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -538.1295166015625 0.38162893056869507 0.4311898350715637 0.1572786271572113 0.7369797825813293 0.6798909902572632 0.6267374157905579 \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_4.evaluate.json b/ENCSR935EVZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bd8fe586d4e64b7111012faa9ee1c9d800df5cc9..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF900VMZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_4.fit.json b/ENCSR935EVZ/cherimoya.fold_4.fit.json deleted file mode 100644 index 4616b9a3ffa04959c475f327d88041c059d566f8..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF900VMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935EVZ/cherimoya.fold_4.log b/ENCSR935EVZ/cherimoya.fold_4.log deleted file mode 100644 index d3f89cc40f0358655e68b56d0fad52f8eba69afb..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2826 35.03421092033386 3.698288917541504 467.1111755371094 0.8402718305587769 643.6287841796875 0.22359919548034668 0.5219167 5.84638786315918 True -1 5652 31.22438883781433 0.59423828125 382.756103515625 1.4629626274108887 555.3933715820312 0.35730189085006714 0.5905752 3.2855780124664307 True -2 8478 31.31105661392212 0.9073169231414795 449.0443115234375 0.6997379064559937 545.41357421875 0.36775562167167664 0.5888816 1.9625803232192993 False -3 11304 31.194259881973267 0.590827226638794 427.535400390625 1.3296958208084106 540.3785400390625 0.37525877356529236 0.5964347 2.146232843399048 True -4 14130 31.215089797973633 0.5831508636474609 445.0227355957031 0.6840325593948364 536.4461059570312 0.38103440403938293 0.6075616 1.6724969148635864 True -5 16956 31.17293882369995 0.584113359451294 386.2706604003906 1.0764451026916504 532.2991333007812 0.38698065280914307 0.6182689 1.53765869140625 True -6 19782 31.153565168380737 0.5860593318939209 432.98809814453125 1.2292444705963135 530.6373901367188 0.38894230127334595 0.6256184 1.2684177160263062 True -7 22608 31.16395902633667 0.5733580589294434 454.027587890625 0.7622772455215454 526.7259521484375 0.39901962876319885 0.62840694 1.347251534461975 True -8 25434 31.17116951942444 0.5771088600158691 438.80535888671875 0.8463171124458313 524.7476196289062 0.40152707695961 0.63433826 1.2824829816818237 True -9 28260 31.180527210235596 0.5715749263763428 333.6644287109375 0.751700758934021 520.2321166992188 0.40960121154785156 0.64177614 1.0930804014205933 True -10 31086 31.278095960617065 0.5848383903503418 509.06396484375 0.7964032292366028 518.838134765625 0.4105493128299713 0.64550024 1.0108102560043335 True -11 33912 31.240326166152954 0.5899515151977539 485.8776550292969 1.0645568370819092 515.9293212890625 0.4132726192474365 0.6571547 0.9241731762886047 True -12 36738 31.15420651435852 0.5845823287963867 524.1688232421875 1.0410099029541016 512.3948364257812 0.4205825924873352 0.6657202 0.8973138928413391 True -13 39564 31.038248300552368 0.5853481292724609 413.8946533203125 0.6138846278190613 509.75054931640625 0.422726035118103 0.67986107 0.8022775053977966 True -14 42390 30.68704605102539 0.5845468044281006 392.1772155761719 0.6600184440612793 507.34857177734375 0.4261683225631714 0.6907473 0.7281855940818787 True -15 45216 30.697089672088623 0.5826907157897949 356.88494873046875 0.6735654473304749 505.89739990234375 0.42851024866104126 0.69880235 0.6750046014785767 True -16 48042 30.57805895805359 0.5792694091796875 408.5965576171875 0.600644052028656 504.4187316894531 0.43020132184028625 0.7056459 0.647119402885437 True -17 50868 30.583796977996826 0.5704996585845947 393.3600769042969 0.7298298478126526 505.4613342285156 0.4277670085430145 0.7101688 0.6177378296852112 True -18 53694 30.609458923339844 0.5826685428619385 351.19525146484375 0.44745856523513794 505.1318054199219 0.4294178783893585 0.71249914 0.6087028384208679 True -19 56520 30.632845163345337 2.0206165313720703 291.54412841796875 0.412460595369339 504.1435546875 0.4310353398323059 0.71082026 0.6113362312316895 False diff --git a/ENCSR935EVZ/cherimoya.fold_4.performance.tsv b/ENCSR935EVZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 423a1a5a4b52a0c9ad07264e520ead27fb65a243..0000000000000000000000000000000000000000 --- a/ENCSR935EVZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -505.1318054199219 0.3858897387981415 0.42941784858703613 0.15013675391674042 0.7124991416931152 0.6639928817749023 0.6087028384208679 \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_0.evaluate.json b/ENCSR935HEI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 3e73b7f08681a8d6aeb5cbe9c157374df6e0f237..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124DXB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_0.fit.json b/ENCSR935HEI/cherimoya.fold_0.fit.json deleted file mode 100644 index 53be27f1b0b9e9d1b39c03cdb89228e898df8c34..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF124DXB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_0.log b/ENCSR935HEI/cherimoya.fold_0.log deleted file mode 100644 index 01f7f821ea72bc0a8a03ad12730c7c79314faf80..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2616 33.125977993011475 4.315469026565552 906.6429443359375 1.7018792629241943 1954.189697265625 0.2807394862174988 0.5597023 13.728006362915039 True -1 5232 28.695265531539917 0.5402965545654297 1181.919189453125 1.8308866024017334 1472.757568359375 0.42055752873420715 0.6782133 6.294732093811035 True -2 7848 29.770846843719482 0.5344386100769043 1375.568359375 1.2542914152145386 1429.627197265625 0.4313843846321106 0.6935762 4.252049446105957 True -3 10464 28.719539880752563 0.5229456424713135 1056.0185546875 1.261289358139038 1387.7698974609375 0.44265201687812805 0.6962765 3.5945687294006348 True -4 13080 28.94857168197632 0.5336661338806152 969.6620483398438 1.4026284217834473 1349.3973388671875 0.45380228757858276 0.7054053 2.739654064178467 True -5 15696 29.006053686141968 1.4833545684814453 1343.192626953125 1.0983798503875732 1329.69775390625 0.4621833860874176 0.7046601 2.217667579650879 False -6 18312 28.88048791885376 0.5424084663391113 1050.0701904296875 1.4003558158874512 1322.3218994140625 0.46438050270080566 0.70999366 2.1841111183166504 True -7 20928 29.118892908096313 0.5489859580993652 1546.095947265625 1.4591999053955078 1305.0963134765625 0.46937093138694763 0.7231511 1.916871190071106 True -8 23544 28.995959520339966 0.5703415870666504 1076.5614013671875 1.191607117652893 1300.7882080078125 0.4699968993663788 0.73159957 1.7689496278762817 True -9 26160 28.90329360961914 1.8494369983673096 1598.480712890625 1.3251309394836426 1291.09765625 0.473969966173172 0.73871446 1.505264401435852 True -10 28776 28.86992645263672 0.536259651184082 936.155517578125 0.7415129542350769 1284.557861328125 0.47641721367836 0.7425219 1.4456193447113037 True -11 31392 28.75292730331421 0.5355122089385986 948.7757568359375 0.8644608855247498 1266.5947265625 0.48220300674438477 0.75223297 1.2404148578643799 True -12 34008 28.76338028907776 1.9721951484680176 1122.89404296875 1.3686718940734863 1250.0181884765625 0.48695114254951477 0.7590212 1.0849474668502808 True -13 36624 28.79359245300293 0.5427234172821045 1179.0159912109375 0.904126763343811 1239.5145263671875 0.4899446964263916 0.76850694 0.9928741455078125 True -14 39240 28.988122701644897 21.751805067062378 858.2567749023438 0.591736376285553 1227.66015625 0.4952853322029114 0.77687365 0.8939311504364014 True -15 41856 29.49161696434021 0.5478107929229736 755.1593017578125 0.9484566450119019 1216.6185302734375 0.49606648087501526 0.78618115 0.8177363276481628 True -16 44472 28.895535469055176 1.7371563911437988 1068.128173828125 0.5551456212997437 1209.797119140625 0.4987172782421112 0.7901323 0.7786264419555664 True -17 47088 29.309950351715088 33.51776385307312 952.1702880859375 0.6111854910850525 1208.64599609375 0.4999658763408661 0.79153883 0.7590862512588501 True -18 49704 28.949384927749634 0.5594120025634766 913.1321411132812 0.6874187588691711 1210.351806640625 0.49846965074539185 0.79116166 0.7495966553688049 False -19 52320 28.968114376068115 0.5376541614532471 920.6795654296875 0.43151772022247314 1215.032470703125 0.4949450194835663 0.79197145 0.7520329356193542 True diff --git a/ENCSR935HEI/cherimoya.fold_0.performance.tsv b/ENCSR935HEI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 27d043bf60d6c90949ab76e5f9c78177c50a0475..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1215.032470703125 0.3093075454235077 0.4949450194835663 0.24701645970344543 0.7919714450836182 0.7206395268440247 0.7520329356193542 \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_1.evaluate.json b/ENCSR935HEI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ce6167385ae0dbc57835054c3e1d1deb4d18f7a7..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124DXB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_1.fit.json b/ENCSR935HEI/cherimoya.fold_1.fit.json deleted file mode 100644 index 338a53a16164eaee475cff711cf088893e3c5955..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF124DXB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_1.log b/ENCSR935HEI/cherimoya.fold_1.log deleted file mode 100644 index 27552696ac23ca75c65b098058d20fc47bfb5eac..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2557 33.40748715400696 3.700348138809204 1167.1572265625 1.2356528043746948 2358.627685546875 0.29086899757385254 0.56611544 15.72744083404541 True -1 5114 28.183598279953003 0.7559070587158203 1169.217529296875 1.076584815979004 1762.971435546875 0.4249626100063324 0.69969195 7.541772842407227 True -2 7671 28.09342312812805 3.362013339996338 1134.851806640625 1.2545104026794434 1687.4166259765625 0.44339457154273987 0.7147863 4.607927322387695 True -3 10228 28.13074278831482 0.7268679141998291 1113.3153076171875 1.5548501014709473 1643.26318359375 0.45472094416618347 0.7247831 3.6977622509002686 True -4 12785 28.104910373687744 0.7272167205810547 1235.2579345703125 1.4418538808822632 1622.6943359375 0.45630598068237305 0.73230433 3.0977132320404053 True -5 15342 27.500015020370483 0.713078498840332 1232.203369140625 1.4969186782836914 1587.2125244140625 0.4659350514411926 0.74546504 2.589461326599121 True -6 17899 27.517984867095947 30.772139072418213 861.49267578125 1.131270170211792 1567.6517333984375 0.47118622064590454 0.7520989 2.2078847885131836 True -7 20456 27.750290870666504 0.7430136203765869 1021.0263671875 1.162217378616333 1565.0628662109375 0.47296690940856934 0.7526345 2.1577706336975098 True -8 23013 27.599112033843994 0.7197694778442383 1094.833251953125 0.7465554475784302 1540.8551025390625 0.48077112436294556 0.7564302 1.7667497396469116 True -9 25570 27.508131980895996 2.4884893894195557 791.1181030273438 0.6501466035842896 1522.329345703125 0.4871005415916443 0.76582915 1.4717767238616943 True -10 28127 27.552023887634277 0.7352771759033203 838.6416015625 1.4282104969024658 1514.4071044921875 0.4887470006942749 0.77336323 1.3328052759170532 True -11 30684 27.52816677093506 0.7199463844299316 1071.060546875 0.8293711543083191 1497.642578125 0.49225321412086487 0.78037226 1.1678904294967651 True -12 33241 27.58183455467224 0.7271325588226318 834.7689208984375 0.7045341730117798 1474.030029296875 0.4996080696582794 0.7889379 1.1403371095657349 True -13 35798 27.506701231002808 0.7217023372650146 1148.2548828125 0.6272857785224915 1455.3587646484375 0.5034863948822021 0.7982178 0.9955421686172485 True -14 38355 27.69317317008972 0.7239387035369873 830.78564453125 0.819705605506897 1442.09033203125 0.5053389668464661 0.80694705 0.9268529415130615 True -15 40912 27.48819351196289 1.7950613498687744 1060.617431640625 0.6640098094940186 1437.7701416015625 0.5065239667892456 0.81409776 0.8392381072044373 True -16 43469 27.452577590942383 0.7330658435821533 836.24609375 0.6693565845489502 1431.223876953125 0.5068914890289307 0.8193518 0.7973370552062988 True -17 46026 27.54982089996338 0.7242696285247803 999.4298095703125 0.9793145060539246 1434.9771728515625 0.5060592293739319 0.82226723 0.7680023312568665 True -18 48583 27.479875326156616 0.7269463539123535 670.6510009765625 0.5731533765792847 1439.6839599609375 0.5033110976219177 0.8232688 0.7581390142440796 True -19 51140 27.479387998580933 0.7162067890167236 799.2821044921875 0.8140392303466797 1442.2952880859375 0.5022192001342773 0.8239061 0.75923752784729 True diff --git a/ENCSR935HEI/cherimoya.fold_1.performance.tsv b/ENCSR935HEI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ca9965a2bd3efc116b864581e1246f97a527a96c..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1442.2952880859375 0.2967780530452728 0.5022192001342773 0.27274763584136963 0.8239061236381531 0.7757917642593384 0.75923752784729 \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_2.evaluate.json b/ENCSR935HEI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0788bf8912e3124cb9df8d9fb4d29c96318cf04d..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124DXB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_2.fit.json b/ENCSR935HEI/cherimoya.fold_2.fit.json deleted file mode 100644 index 95d3a50545cb8da770a8479d74f1e1a87e8ef4ed..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF124DXB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_2.log b/ENCSR935HEI/cherimoya.fold_2.log deleted file mode 100644 index 6c5b725809eecf66e57dbfd890ce0943029d794f..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 35.36715769767761 4.252721309661865 1278.701904296875 1.077286958694458 2022.5877685546875 0.2888500988483429 0.5525028 14.548150062561035 True -1 5530 30.45864701271057 0.562950611114502 1412.9864501953125 1.2832468748092651 1485.5350341796875 0.4172340929508209 0.6885598 5.790151119232178 True -2 8295 30.35557270050049 0.5518884658813477 976.62255859375 1.4810723066329956 1463.0189208984375 0.426193505525589 0.6980047 3.5298924446105957 True -3 11060 30.420520782470703 0.540647029876709 1146.22802734375 1.0760314464569092 1415.8760986328125 0.438884437084198 0.71328366 2.8538849353790283 True -4 13825 30.465124368667603 0.5465776920318604 793.9747314453125 0.9714151620864868 1391.57275390625 0.44703876972198486 0.7220275 2.561568021774292 True -5 16590 30.355757474899292 0.6165473461151123 1073.9580078125 1.363433837890625 1376.5869140625 0.45236068964004517 0.72397715 2.1986076831817627 True -6 19355 30.53070878982544 0.5466279983520508 1235.5810546875 1.1681632995605469 1356.939208984375 0.4563119113445282 0.7337626 1.8579412698745728 True -7 22120 30.471464157104492 0.5432400703430176 1070.614990234375 1.2406387329101562 1348.1175537109375 0.45850908756256104 0.7451818 1.5854909420013428 True -8 24885 30.322454690933228 1.609004020690918 788.7686767578125 0.8713334202766418 1332.970458984375 0.46426260471343994 0.7506384 1.476667046546936 True -9 27650 30.352298974990845 0.5384371280670166 1207.197998046875 0.7557558417320251 1323.500732421875 0.46867719292640686 0.7563087 1.3049594163894653 True -10 30415 30.37878394126892 0.5465743541717529 1307.5078125 0.9586040377616882 1313.0599365234375 0.4704846143722534 0.76118565 1.1978884935379028 True -11 33180 30.345616102218628 0.546095609664917 894.5240478515625 0.8954694867134094 1295.157958984375 0.47514766454696655 0.7698036 1.0918675661087036 True -12 35945 30.061952829360962 0.5454084873199463 1200.8336181640625 0.74748694896698 1284.4498291015625 0.478920578956604 0.7769086 0.9644668102264404 True -13 38710 33.349684715270996 21.762861013412476 1343.67333984375 0.9527032375335693 1270.0269775390625 0.48480460047721863 0.7841461 0.9225680828094482 True -14 41475 29.92375946044922 1.5708622932434082 754.9853515625 0.6938173770904541 1263.8211669921875 0.4854792654514313 0.78967035 0.8483148813247681 True -15 44240 29.82001256942749 0.5383682250976562 770.2694091796875 0.6565173864364624 1256.3603515625 0.48741787672042847 0.7951257 0.7966602444648743 True -16 47005 30.207366704940796 24.328319311141968 1006.3323974609375 0.6642135381698608 1248.06640625 0.4891786277294159 0.7982387 0.764948844909668 True -17 49770 29.83786678314209 11.524833917617798 809.2308349609375 0.6560244560241699 1256.4986572265625 0.4854789674282074 0.8008182 0.7443910241127014 True -18 52535 31.179738998413086 0.6092753410339355 866.7186279296875 0.6248537302017212 1254.8770751953125 0.4867917597293854 0.80207485 0.7416958808898926 True -19 55300 29.900602102279663 0.532203197479248 1247.490234375 0.5526734590530396 1258.04736328125 0.48584723472595215 0.80086505 0.7411991953849792 False diff --git a/ENCSR935HEI/cherimoya.fold_2.performance.tsv b/ENCSR935HEI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4bd42a886d8c60e307d8a09f4b64c822ff41bbee..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1254.8770751953125 0.3116559386253357 0.4867917597293854 0.24854467809200287 0.8020748496055603 0.7398061752319336 0.7416958808898926 \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_3.evaluate.json b/ENCSR935HEI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index d2ae169888853e2a0b8619491e9334ea2f1aa5c2..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124DXB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_3.fit.json b/ENCSR935HEI/cherimoya.fold_3.fit.json deleted file mode 100644 index 57d15fe529fc28eed986d358265cd70d23e8c264..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF124DXB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_3.log b/ENCSR935HEI/cherimoya.fold_3.log deleted file mode 100644 index 69b6a79e98cc19b577cfbcc2fd8dd89ad3d9fd98..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2642 33.67933654785156 5.08995795249939 1039.400146484375 1.4391536712646484 1929.3489990234375 0.30593985319137573 0.56257635 17.258602142333984 True -1 5284 29.134387969970703 0.5525374412536621 1537.0318603515625 1.6243358850479126 1483.162841796875 0.4299388527870178 0.68838036 6.502502918243408 True -2 7926 29.205721855163574 20.8112154006958 1346.372314453125 1.3508050441741943 1436.3009033203125 0.4434696137905121 0.69494903 5.618744373321533 True -3 10568 29.377193927764893 0.5401926040649414 946.8704833984375 0.8399295210838318 1402.0465087890625 0.45342302322387695 0.70835245 4.210862636566162 True -4 13210 32.52729058265686 5.386997938156128 995.5015869140625 1.6090295314788818 1389.52197265625 0.4568721652030945 0.71370083 3.2964909076690674 True -5 15852 28.995683193206787 33.96025323867798 960.078369140625 1.2875698804855347 1370.583984375 0.4667259752750397 0.72362614 2.6849963665008545 True -6 18494 29.331717491149902 0.565131664276123 970.9871826171875 0.7520073652267456 1345.0343017578125 0.474985271692276 0.72742766 2.2754435539245605 True -7 21136 31.114609718322754 2.1023755073547363 1217.39208984375 1.096529245376587 1336.736083984375 0.47701141238212585 0.7274361 1.7485649585723877 True -8 23778 29.003611087799072 0.5392665863037109 1479.342041015625 1.0514390468597412 1323.7900390625 0.4822039306163788 0.7351954 1.5782959461212158 True -9 26420 29.067861557006836 0.5401778221130371 867.7371215820312 1.0412342548370361 1316.552001953125 0.48454466462135315 0.74200255 1.3982470035552979 True -10 29062 29.017603635787964 0.5371396541595459 961.4780883789062 0.7682234644889832 1307.1146240234375 0.4862034320831299 0.7479904 1.2282664775848389 True -11 31704 29.075326919555664 0.535383939743042 1121.408935546875 1.3049390316009521 1293.0714111328125 0.49169737100601196 0.7552241 1.165188193321228 True -12 34346 28.604236841201782 0.524437665939331 1146.30322265625 1.1482222080230713 1281.1822509765625 0.49722766876220703 0.75933266 1.0419785976409912 True -13 36988 28.424949884414673 0.5306415557861328 1021.1416015625 0.7608853578567505 1268.9034423828125 0.5008307099342346 0.7722347 0.9628167748451233 True -14 39630 28.469492197036743 0.5249361991882324 891.6118774414062 0.9479129910469055 1255.385986328125 0.5031564831733704 0.7815791 0.9083986878395081 True -15 42272 28.411962032318115 5.154256582260132 1040.94775390625 1.1596159934997559 1250.9744873046875 0.5026937127113342 0.78996307 0.8550720810890198 True -16 44914 28.408291339874268 0.9632301330566406 919.887451171875 0.6976876854896545 1243.862060546875 0.505944013595581 0.7967766 0.8171632885932922 True -17 47556 28.539564847946167 0.5228133201599121 1133.741455078125 0.6604520082473755 1245.1981201171875 0.5052472949028015 0.8016552 0.7910096645355225 True -18 50198 28.48857092857361 0.5211515426635742 1064.27783203125 0.7092186212539673 1245.3631591796875 0.5056053996086121 0.8019076 0.7810273170471191 True -19 52840 28.43548274040222 0.5201234817504883 952.50146484375 0.6787425875663757 1248.8863525390625 0.5041418671607971 0.8012186 0.7810736894607544 False diff --git a/ENCSR935HEI/cherimoya.fold_3.performance.tsv b/ENCSR935HEI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 80c7ac54318ca45aa6bce0bbdb2da0fe0dcc5f36..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1245.3631591796875 0.3015315532684326 0.5056053996086121 0.25802499055862427 0.8019075989723206 0.7412973046302795 0.7810273170471191 \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_4.evaluate.json b/ENCSR935HEI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a75c19ce96e80e583f7860847650b2b56df1e89c..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF124DXB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_4.fit.json b/ENCSR935HEI/cherimoya.fold_4.fit.json deleted file mode 100644 index 0c496dfd04bc2ef2a647712239694a8aa54cd754..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF124DXB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR935HEI/cherimoya.fold_4.log b/ENCSR935HEI/cherimoya.fold_4.log deleted file mode 100644 index 64fe53c6bf8260d350468cc6d146a60f7d750fc3..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2646 33.65460157394409 2.9883029460906982 930.8395385742188 1.2458746433258057 1829.460693359375 0.2918684184551239 0.54492414 14.411771774291992 True -1 5292 29.034417629241943 3.5097532272338867 1639.7066650390625 1.4427592754364014 1404.5101318359375 0.4180828928947449 0.66211134 6.073314666748047 True -2 7938 29.102123975753784 0.4438455104827881 723.9403076171875 1.1585667133331299 1364.8250732421875 0.4282228350639343 0.6702684 3.827078104019165 True -3 10584 29.03629994392395 0.4546985626220703 1075.3507080078125 1.1581867933273315 1325.6456298828125 0.4397641718387604 0.6815806 3.199979782104492 True -4 13230 29.026645183563232 0.44368815422058105 1397.4727783203125 1.6569652557373047 1297.2550048828125 0.4491916298866272 0.6918596 2.5096170902252197 True -5 15876 29.126887321472168 0.44739198684692383 971.2145385742188 1.9959626197814941 1285.49462890625 0.4540187120437622 0.69966793 1.9933373928070068 True -6 18522 29.227453470230103 0.46352076530456543 1597.822265625 1.406299352645874 1268.882568359375 0.4612239897251129 0.6985582 1.6695126295089722 False -7 21168 29.115301609039307 0.4510304927825928 1006.6454467773438 0.8811880350112915 1252.760498046875 0.4657083749771118 0.7090301 1.437988042831421 True -8 23814 29.335755586624146 23.88142228126526 1494.46728515625 1.042191505432129 1243.3350830078125 0.46943899989128113 0.7154901 1.4762308597564697 True -9 26460 29.092803716659546 0.4486711025238037 1031.6357421875 1.0833683013916016 1231.63330078125 0.4734359681606293 0.7235454 1.2640517950057983 True -10 29106 29.099576950073242 3.399935722351074 808.9998168945312 0.7925565242767334 1220.8502197265625 0.4785151779651642 0.73101664 1.1518568992614746 True -11 31752 29.011375427246094 0.5420427322387695 1086.272216796875 1.1423215866088867 1213.1204833984375 0.48019033670425415 0.74128574 1.0420576333999634 True -12 34398 28.99911880493164 0.4487178325653076 1177.2965087890625 0.7427090406417847 1203.7191162109375 0.48113322257995605 0.752841 0.9291117787361145 True -13 37044 28.455381870269775 0.4374997615814209 943.1156616210938 1.08937668800354 1188.2265625 0.48870590329170227 0.7590764 0.8961585164070129 True -14 39690 28.505178213119507 0.4508841037750244 816.0328369140625 0.62819504737854 1184.1087646484375 0.4891289472579956 0.76719767 0.8256444334983826 True -15 42336 28.53718900680542 0.4414041042327881 815.1340942382812 0.7600416541099548 1175.7559814453125 0.4921882450580597 0.7779384 0.7820899486541748 True -16 44982 28.436556100845337 0.4490389823913574 1065.3121337890625 0.46514952182769775 1172.83984375 0.4948813021183014 0.7817097 0.7561955451965332 True -17 47628 28.47828984260559 0.4498121738433838 1114.78271484375 0.7559136152267456 1171.00048828125 0.4948681890964508 0.784524 0.7416456937789917 True -18 50274 28.607255220413208 0.5015480518341064 1049.9615478515625 0.4202112555503845 1177.630126953125 0.4928877651691437 0.78468096 0.7367144227027893 True -19 52920 28.54686403274536 3.413252353668213 934.9254150390625 0.5344323515892029 1173.73291015625 0.49503636360168457 0.78717685 0.7371585369110107 True diff --git a/ENCSR935HEI/cherimoya.fold_4.performance.tsv b/ENCSR935HEI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f77552e078ee0e16f7c2ba30d0603aad350fa52a..0000000000000000000000000000000000000000 --- a/ENCSR935HEI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1173.73291015625 0.3102874457836151 0.49503639340400696 0.24347858130931854 0.7871768474578857 0.7163263559341431 0.7371585369110107 \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_0.evaluate.json b/ENCSR937UWI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2e9a0708309c9d66c05d7a73ffa2ee9634c5bb05..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702TNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_0.fit.json b/ENCSR937UWI/cherimoya.fold_0.fit.json deleted file mode 100644 index 77bff88dda7c87deefbf4e60ca0ef4fed8aac52b..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF702TNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_0.log b/ENCSR937UWI/cherimoya.fold_0.log deleted file mode 100644 index 62629e5b721f1d4bf80bc5713559e1688ceec9a0..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1888 25.318495512008667 4.192735433578491 1293.87548828125 1.0182596445083618 2160.585693359375 0.19327031075954437 0.53629017 22.626022338867188 True -1 3776 20.764714002609253 0.724407434463501 1626.412841796875 1.2877968549728394 1899.00634765625 0.31758636236190796 0.56623936 6.039618968963623 True -2 5664 20.743110179901123 0.38678741455078125 1561.968017578125 0.8036263585090637 1763.02978515625 0.35483318567276 0.5831972 3.000119686126709 True -3 7552 20.79042363166809 0.356065034866333 1253.4476318359375 0.6138489246368408 1644.8671875 0.377516508102417 0.61014646 2.4113950729370117 True -4 9440 20.71624517440796 0.3629326820373535 1401.02392578125 0.9357232451438904 1588.657470703125 0.39203909039497375 0.6316294 1.921730875968933 True -5 11328 20.741102695465088 0.35637998580932617 1594.68017578125 1.39857017993927 1545.544189453125 0.4026864469051361 0.6599158 1.612660527229309 True -6 13216 20.613024473190308 0.3470151424407959 1310.513671875 0.6969436407089233 1510.89794921875 0.4156392216682434 0.67224455 1.4092284440994263 True -7 15104 20.31553602218628 0.3463735580444336 1317.883056640625 0.9721671938896179 1488.3955078125 0.42018797993659973 0.69193155 1.1686934232711792 True -8 16992 20.30198836326599 0.3463292121887207 1121.3961181640625 0.3911455273628235 1469.75439453125 0.4257206916809082 0.69744956 1.0522676706314087 True -9 18880 20.379671096801758 0.34523606300354004 1018.9127807617188 0.6916648149490356 1456.2620849609375 0.43042781949043274 0.708922 0.9146891832351685 True -10 20768 20.361809253692627 0.3587300777435303 1275.81005859375 0.8658061623573303 1439.26123046875 0.4355613589286804 0.7178857 0.8334342241287231 True -11 22656 20.362144708633423 0.34720683097839355 890.8483276367188 0.7559309005737305 1426.7979736328125 0.4375889301300049 0.72834265 0.7736960649490356 True -12 24544 20.338388681411743 0.34971046447753906 965.8485107421875 0.5848740935325623 1414.1123046875 0.43974462151527405 0.7320666 0.7262582778930664 True -13 26432 20.301825761795044 0.34608030319213867 1124.072998046875 0.5039665102958679 1404.3919677734375 0.4416804015636444 0.7392063 0.6819701194763184 True -14 28320 20.409311294555664 1.4145305156707764 1018.0087280273438 0.42059120535850525 1394.3134765625 0.44618603587150574 0.7470879 0.6501680612564087 True -15 30208 20.35590171813965 0.35780978202819824 1184.63720703125 0.520416259765625 1388.882568359375 0.4465807378292084 0.7528531 0.6130595803260803 True -16 32096 20.31457757949829 0.34534549713134766 885.0369262695312 0.46885567903518677 1387.0736083984375 0.4457094967365265 0.75868344 0.5969518423080444 True -17 33984 20.37397789955139 0.35245609283447266 1128.230712890625 0.4915747046470642 1386.33251953125 0.4464857578277588 0.75844944 0.5914952158927917 False -18 35872 20.3458194732666 0.35787034034729004 1129.876708984375 0.39695462584495544 1396.4649658203125 0.44191619753837585 0.7566405 0.5929533243179321 False -19 37760 20.327375650405884 0.34949517250061035 1297.75341796875 0.25233107805252075 1393.6650390625 0.44383513927459717 0.75718564 0.5979426503181458 False diff --git a/ENCSR937UWI/cherimoya.fold_0.performance.tsv b/ENCSR937UWI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8cf1ae7baf40df5b9e860ccf32df761cdbe604d1..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1387.0736083984375 0.280335009098053 0.4457094371318817 0.24578917026519775 0.758683443069458 0.644638180732727 0.5969518423080444 \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_1.evaluate.json b/ENCSR937UWI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 260f6ed336ef440b7d73a4d664e03f32db1951f7..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702TNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_1.fit.json b/ENCSR937UWI/cherimoya.fold_1.fit.json deleted file mode 100644 index 1067ab62dc324501b020c91f136da6be23522948..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF702TNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_1.log b/ENCSR937UWI/cherimoya.fold_1.log deleted file mode 100644 index 3843e4ddc5f3b57ea0319b0b9d8d4a7cef28f7b5..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1885 25.180809259414673 3.9374489784240723 1495.383544921875 0.9315831661224365 2512.152587890625 0.19642454385757446 0.52370363 23.588634490966797 True -1 3770 20.705853700637817 0.6382632255554199 1693.061767578125 0.9773135185241699 2159.04931640625 0.3292485773563385 0.6083328 7.817611217498779 True -2 5655 20.694551706314087 0.5682744979858398 1178.585205078125 1.0319876670837402 2041.8983154296875 0.367203027009964 0.6055104 3.759775161743164 False -3 7540 20.742214918136597 0.5564494132995605 1371.785888671875 0.8862404823303223 1884.32275390625 0.39149072766304016 0.6493653 2.4917805194854736 True -4 9425 20.682145595550537 24.19022536277771 1443.2603759765625 0.9118819236755371 1794.4659423828125 0.4059064984321594 0.6792291 1.9843443632125854 True -5 11310 20.824304342269897 0.5651645660400391 1396.75390625 1.136491060256958 1755.2957763671875 0.4124571979045868 0.6957708 1.7616055011749268 True -6 13195 21.96488094329834 11.482526063919067 1072.140380859375 0.8993985056877136 1713.8531494140625 0.4235747456550598 0.7080702 1.5869728326797485 True -7 15080 20.685993432998657 0.5646061897277832 1341.1162109375 0.7806717157363892 1677.7342529296875 0.42924270033836365 0.7279423 1.3612736463546753 True -8 16965 20.690724849700928 0.5416483879089355 1297.73193359375 0.7144478559494019 1655.3792724609375 0.4351769685745239 0.73808736 1.2299690246582031 True -9 18850 20.69622778892517 0.5561635494232178 1221.99169921875 0.6625434160232544 1638.6717529296875 0.436661034822464 0.7501491 1.0383740663528442 True -10 20735 20.759577751159668 1.3344297409057617 1524.9150390625 0.7716329097747803 1616.14111328125 0.44384875893592834 0.7570635 0.9841174483299255 True -11 22620 20.759480714797974 0.5642216205596924 978.7075805664062 0.5855996608734131 1606.5894775390625 0.4456987679004669 0.7659555 0.9123407602310181 True -12 24505 20.70364475250244 0.5511488914489746 1179.0283203125 0.6096140146255493 1578.3631591796875 0.455008327960968 0.7737221 0.8187355995178223 True -13 26390 20.725754022598267 0.5448908805847168 1037.19677734375 0.8206695318222046 1572.470458984375 0.4538441300392151 0.7821501 0.7436181306838989 True -14 28275 20.69969916343689 0.5515828132629395 1158.9388427734375 0.3690432608127594 1558.0399169921875 0.4554324746131897 0.78820676 0.687953531742096 True -15 30160 20.63282537460327 0.5419571399688721 1054.162109375 0.5399562120437622 1554.829345703125 0.4553913176059723 0.7935508 0.638338565826416 True -16 32045 20.34803342819214 0.5477392673492432 1111.729248046875 0.41483527421951294 1554.3367919921875 0.4561183452606201 0.7958794 0.610056459903717 True -17 33930 20.3062686920166 0.545724630355835 1111.878173828125 0.6095274686813354 1556.205810546875 0.45491862297058105 0.7978966 0.5930420756340027 True -18 35815 20.341228723526 0.5598845481872559 896.8212890625 0.35434746742248535 1561.808349609375 0.4526882767677307 0.79780126 0.5905980467796326 False -19 37700 20.292357683181763 0.5414299964904785 1047.9227294921875 0.36245861649513245 1563.7274169921875 0.4519733786582947 0.796613 0.5894215106964111 False diff --git a/ENCSR937UWI/cherimoya.fold_1.performance.tsv b/ENCSR937UWI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8c267746e21605cd658ea8896b005381da169a89..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1556.205810546875 0.271744966506958 0.45491862297058105 0.2671498656272888 0.7978966236114502 0.7136659622192383 0.5930420756340027 \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_2.evaluate.json b/ENCSR937UWI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b0ca5f140b48ad3e7d5a4fb16a1fc164b8883d19..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702TNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_2.fit.json b/ENCSR937UWI/cherimoya.fold_2.fit.json deleted file mode 100644 index 10652ca7b5d9217e411c9631ae97808b52700aed..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF702TNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_2.log b/ENCSR937UWI/cherimoya.fold_2.log deleted file mode 100644 index 1bfe703d5e02d45530b82a003626ba5db7e807d0..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2005 26.444044828414917 3.916563034057617 1273.6451416015625 0.8100651502609253 2218.098388671875 0.20032477378845215 0.5278659 20.548702239990234 True -1 4010 22.199474334716797 0.4618370532989502 1228.3760986328125 0.5001301765441895 1891.7247314453125 0.3276826739311218 0.61545664 6.263619422912598 True -2 6015 21.978360176086426 0.3991434574127197 1307.77099609375 0.6104738712310791 1803.828369140625 0.3625450134277344 0.5738103 3.553245782852173 False -3 8020 21.9716579914093 0.440356969833374 1327.1771240234375 0.8401522636413574 1672.498046875 0.38304954767227173 0.62655634 2.594841480255127 True -4 10025 21.9639310836792 0.42191100120544434 1287.0355224609375 0.6992627382278442 1618.009033203125 0.3926011621952057 0.6557534 1.976295828819275 True -5 12030 21.96357536315918 0.39406299591064453 1081.4501953125 0.9705989360809326 1583.5965576171875 0.4030299782752991 0.66727483 1.66315495967865 True -6 14035 21.959738969802856 0.4117286205291748 1106.93701171875 0.8713379502296448 1552.0819091796875 0.412471204996109 0.6831548 1.4729222059249878 True -7 16040 21.963692903518677 0.3821377754211426 983.239501953125 0.6578561663627625 1531.567626953125 0.4172852635383606 0.6954078 1.3444576263427734 True -8 18045 22.020957946777344 0.39008283615112305 1208.7740478515625 0.5356976389884949 1504.484375 0.42680656909942627 0.7094674 1.2019537687301636 True -9 20050 21.972872257232666 0.4021008014678955 1351.24755859375 0.6808263063430786 1489.47216796875 0.42886170744895935 0.72092855 1.038489580154419 True -10 22055 21.972140550613403 2.148296356201172 1175.6693115234375 0.43653208017349243 1475.5589599609375 0.4332019090652466 0.7324956 0.8713811635971069 True -11 24060 22.013036251068115 0.4032282829284668 1301.044189453125 0.31533801555633545 1461.42724609375 0.43522536754608154 0.7400364 0.834365725517273 True -12 26065 21.9984233379364 0.39752793312072754 1040.14599609375 0.5502359867095947 1446.3265380859375 0.4379221498966217 0.7467637 0.7463081479072571 True -13 28070 22.050408601760864 0.39140748977661133 1010.9000854492188 0.5997622609138489 1432.385498046875 0.44252708554267883 0.7553799 0.6968473792076111 True -14 30075 22.031325340270996 0.39692234992980957 773.0694580078125 0.497316837310791 1422.5655517578125 0.44372138381004333 0.7604587 0.6554337739944458 True -15 32080 22.00398874282837 0.5205445289611816 1133.6240234375 0.5733770132064819 1413.404052734375 0.4474506974220276 0.7647148 0.6182156205177307 True -16 34085 22.018672227859497 0.3943748474121094 1116.9002685546875 0.4709627628326416 1407.1488037109375 0.4480192959308624 0.7695716 0.5950332283973694 True -17 36090 22.05114984512329 0.3904407024383545 1185.19873046875 0.39922285079956055 1414.3402099609375 0.4419977068901062 0.771852 0.5895497798919678 True -18 38095 22.06550931930542 0.3967781066894531 1037.684814453125 0.42938852310180664 1413.7918701171875 0.44526398181915283 0.7692938 0.595128059387207 False -19 40100 22.00503635406494 0.390078067779541 939.2171630859375 0.39355364441871643 1412.5706787109375 0.44544997811317444 0.76921886 0.5955743193626404 False diff --git a/ENCSR937UWI/cherimoya.fold_2.performance.tsv b/ENCSR937UWI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a649136995bde6c91854518e4ae824edb0b40220..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1414.3402099609375 0.2802084982395172 0.441997766494751 0.2517935335636139 0.7718520164489746 0.6706006526947021 0.5895497798919678 \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_3.evaluate.json b/ENCSR937UWI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0c50e772e2a7685b470a6eb1ba4e2e0310bac039..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702TNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_3.fit.json b/ENCSR937UWI/cherimoya.fold_3.fit.json deleted file mode 100644 index 3bed7256c3367feba39e557d525cfe6a9ba4fdfc..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF702TNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_3.log b/ENCSR937UWI/cherimoya.fold_3.log deleted file mode 100644 index fb019c1c4834211eaf212dd6a1e67f3b65653b51..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1955 25.93885850906372 3.5871357917785645 1747.7076416015625 1.1601064205169678 2216.30712890625 0.20000506937503815 0.52785474 21.27028465270996 True -1 3910 21.350744485855103 0.8816592693328857 1432.2266845703125 0.8547585010528564 1941.7691650390625 0.32403263449668884 0.51005495 7.174839496612549 False -2 5865 21.482304573059082 0.4086277484893799 1481.610107421875 0.8053476810455322 1851.51025390625 0.35555893182754517 0.51403457 3.5732741355895996 False -3 7820 21.481814861297607 0.39304661750793457 990.1824951171875 0.5000301599502563 1753.327880859375 0.3630012571811676 0.59415287 2.3745691776275635 True -4 9775 21.580622911453247 0.4045834541320801 1137.658203125 0.7570355534553528 1681.075439453125 0.38111382722854614 0.62608576 1.9674522876739502 True -5 11730 21.491267681121826 0.38605737686157227 1466.97216796875 1.0497024059295654 1631.07666015625 0.3954213261604309 0.641222 1.8934656381607056 True -6 13685 21.47019052505493 0.38585448265075684 1327.615478515625 0.7776930332183838 1596.7471923828125 0.405740350484848 0.65743965 1.559256672859192 True -7 15640 21.478212356567383 0.4008595943450928 1338.67578125 0.6515791416168213 1577.703125 0.4076002240180969 0.6747188 1.4277398586273193 True -8 17595 21.449398279190063 0.41367554664611816 1046.05908203125 0.7021644711494446 1544.673583984375 0.4204374849796295 0.68349147 1.2888834476470947 True -9 19550 21.20853281021118 0.39894533157348633 1045.26513671875 0.7324731349945068 1534.369140625 0.4218894839286804 0.6954347 1.1364938020706177 True -10 21505 21.07261610031128 0.39104390144348145 1146.65234375 0.6727368235588074 1517.250244140625 0.42946839332580566 0.7014479 1.09445321559906 True -11 23460 21.08465576171875 0.7936065196990967 917.4986572265625 0.7472659349441528 1510.1505126953125 0.42988699674606323 0.70898056 1.0241810083389282 True -12 25415 21.15461277961731 0.39063549041748047 1043.32568359375 0.48741766810417175 1498.408203125 0.43292251229286194 0.71618474 0.9291616082191467 True -13 27370 21.048564672470093 0.37696313858032227 1650.29736328125 0.9109666347503662 1491.698486328125 0.43468934297561646 0.7285718 0.8592075109481812 True -14 29325 21.073357105255127 0.3773207664489746 1115.588134765625 0.4406702220439911 1482.74853515625 0.4350522458553314 0.73703283 0.7786642909049988 True -15 31280 21.07876968383789 0.39070725440979004 873.4915771484375 0.4028540253639221 1472.138671875 0.4394170641899109 0.7474539 0.7195015549659729 True -16 33235 21.12221670150757 0.39911746978759766 884.0362548828125 0.4699186086654663 1470.3084716796875 0.43698441982269287 0.75418895 0.6646714806556702 True -17 35190 21.06328821182251 0.42264819145202637 1125.465087890625 0.44648611545562744 1469.4964599609375 0.43919044733047485 0.75677407 0.6426454782485962 True -18 37145 21.058059453964233 0.39008498191833496 1043.128662109375 0.3334982991218567 1473.6156005859375 0.4362713694572449 0.75836545 0.6379636526107788 True -19 39100 21.064393281936646 2.7671477794647217 1157.1455078125 0.29024943709373474 1473.18017578125 0.43768686056137085 0.75755286 0.634983479976654 False diff --git a/ENCSR937UWI/cherimoya.fold_3.performance.tsv b/ENCSR937UWI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 113612007a1c8fb8b7a2dd7c36de33e4d4e46e09..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1473.6156005859375 0.2779485881328583 0.4362713098526001 0.251889705657959 0.7583654522895813 0.6698079705238342 0.6379636526107788 \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_4.evaluate.json b/ENCSR937UWI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 51b1fbd7d42d41678087ec473af6c564ef9a7866..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF702TNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_4.fit.json b/ENCSR937UWI/cherimoya.fold_4.fit.json deleted file mode 100644 index a723a9cdd94e91c987728895961a4e1035834b59..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF702TNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR937UWI/cherimoya.fold_4.log b/ENCSR937UWI/cherimoya.fold_4.log deleted file mode 100644 index b5273895d56801ada91f3b772e4c193c963fdf43..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2014 26.688947200775146 3.7775778770446777 1641.035400390625 1.0256510972976685 2071.52099609375 0.2027994841337204 0.52386814 19.924619674682617 True -1 4028 22.138874292373657 0.4040822982788086 1603.473388671875 1.0224018096923828 1817.410888671875 0.32517555356025696 0.5926069 5.658406734466553 True -2 6042 22.15944766998291 0.34729623794555664 1375.94189453125 0.7329092025756836 1703.2137451171875 0.35750675201416016 0.55150974 3.846745729446411 False -3 8056 22.10991621017456 0.3460667133331299 1209.410888671875 0.9955105781555176 1606.6405029296875 0.3758206367492676 0.615239 2.709141492843628 True -4 10070 22.109578609466553 0.3464951515197754 1431.630859375 0.9490103721618652 1555.1795654296875 0.3886849880218506 0.63643175 2.1389732360839844 True -5 12084 22.106303215026855 0.3414456844329834 1170.792724609375 0.46857136487960815 1503.6729736328125 0.402779221534729 0.65656763 1.8656249046325684 True -6 14098 22.13901138305664 0.42897582054138184 1297.272705078125 0.36677688360214233 1480.8748779296875 0.4067227840423584 0.66956466 1.6579809188842773 True -7 16112 22.084890604019165 0.346264123916626 1011.319580078125 0.8494075536727905 1459.7374267578125 0.4129296839237213 0.6880252 1.4027994871139526 True -8 18126 22.09933376312256 0.3513157367706299 1097.174560546875 0.6662607789039612 1443.64697265625 0.4179682731628418 0.70233417 1.082412838935852 True -9 20140 22.14323878288269 0.348463773727417 1191.373046875 0.5923508405685425 1437.0438232421875 0.41516947746276855 0.7109792 1.002459168434143 True -10 22154 22.162015199661255 0.3460099697113037 922.8270263671875 0.458830326795578 1417.8953857421875 0.42465150356292725 0.71350306 0.9391086101531982 True -11 24168 22.121912240982056 0.35077333450317383 1094.89013671875 0.6658735275268555 1403.7403564453125 0.4300506114959717 0.7196999 0.9099969267845154 True -12 26182 22.12567663192749 0.3663492202758789 979.0394287109375 0.3884078860282898 1396.837158203125 0.43171197175979614 0.7233528 0.8207241892814636 True -13 28196 21.818114519119263 0.34630274772644043 1074.34423828125 0.5788986682891846 1385.4462890625 0.4353921711444855 0.73196787 0.7491397857666016 True -14 30210 21.686834573745728 0.3405289649963379 1177.523193359375 0.5013927221298218 1382.0128173828125 0.43488314747810364 0.7396012 0.6912387013435364 True -15 32224 21.694942951202393 0.34587883949279785 1131.1748046875 0.42301949858665466 1370.4718017578125 0.4403037130832672 0.7490614 0.6423457860946655 True -16 34238 21.684808015823364 0.3444967269897461 1130.46875 0.4700276851654053 1378.3245849609375 0.43440353870391846 0.75460553 0.6129838824272156 True -17 36252 21.686736583709717 0.3938117027282715 937.5481567382812 0.41120243072509766 1373.08984375 0.4381365180015564 0.75870866 0.5927414894104004 True -18 38266 21.682111263275146 0.33920955657958984 1050.7142333984375 0.32476142048835754 1370.953857421875 0.43849846720695496 0.75914985 0.588384747505188 True -19 40280 21.687358379364014 0.34494972229003906 1222.9493408203125 0.2709782123565674 1374.5875244140625 0.4365869462490082 0.75943744 0.5885002017021179 True diff --git a/ENCSR937UWI/cherimoya.fold_4.performance.tsv b/ENCSR937UWI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0812135ec425dd4b0f7e118a3da36d3412a21ddb..0000000000000000000000000000000000000000 --- a/ENCSR937UWI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1374.5875244140625 0.283668577671051 0.4365869164466858 0.2425212562084198 0.7594374418258667 0.6654003858566284 0.5885002017021179 \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_0.evaluate.json b/ENCSR938UOR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6571dbfcbf9642e6d0faf4bd0e35c3de7cb771d6..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF929KKH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_0.fit.json b/ENCSR938UOR/cherimoya.fold_0.fit.json deleted file mode 100644 index 616d4141a57fb051e3e0febe291b88a878edc0a5..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF929KKH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_0.log b/ENCSR938UOR/cherimoya.fold_0.log deleted file mode 100644 index 16fe8d231ae2ea6a6a9c5dba83cbac2287d27fdf..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2755 36.34366846084595 4.619947910308838 117.78191375732422 0.7028499245643616 173.82684326171875 0.11292325705289841 0.49012443 2.426778793334961 True -1 5510 30.611647129058838 1.3412551879882812 150.72377014160156 0.5479804873466492 168.8135223388672 0.1490795761346817 0.6342143 0.9823962450027466 True -2 8265 30.72233557701111 0.5886199474334717 143.92010498046875 0.5193589925765991 167.04893493652344 0.15693727135658264 0.65666306 0.4922187924385071 True -3 11020 30.70565366744995 0.5902974605560303 144.62356567382812 0.564872682094574 166.1927032470703 0.1612897664308548 0.67469627 0.4361850917339325 True -4 13775 30.642276287078857 0.5804336071014404 118.75077819824219 0.3361598253250122 166.01583862304688 0.16229014098644257 0.684187 0.4301583766937256 True -5 16530 30.66670536994934 0.6066672801971436 148.79592895507812 0.5408117771148682 165.57095336914062 0.1650741696357727 0.6897052 0.46783679723739624 True -6 19285 30.569617986679077 2.0764036178588867 143.0410919189453 0.4738580882549286 165.4812469482422 0.16555708646774292 0.69540024 0.4368261396884918 True -7 22040 30.590110778808594 0.5812058448791504 131.8430633544922 0.3642504811286926 165.20745849609375 0.16740477085113525 0.70220333 0.42387741804122925 True -8 24795 30.59357786178589 2.280261278152466 130.60183715820312 0.5489804148674011 164.9093475341797 0.16942542791366577 0.7093954 0.40264981985092163 True -9 27550 30.593977451324463 0.5789518356323242 146.15625 0.5765255093574524 164.67037963867188 0.17107941210269928 0.7162944 0.37759050726890564 True -10 30305 30.56443953514099 0.5792117118835449 125.60589599609375 0.389923632144928 164.52252197265625 0.17191021144390106 0.7197414 0.3629940152168274 True -11 33060 30.47967839241028 0.5714371204376221 133.9646453857422 0.4958520531654358 164.20774841308594 0.1742430180311203 0.72527534 0.3572748601436615 True -12 35815 30.80493974685669 0.5715053081512451 124.48532104492188 0.4787198603153229 164.2019500732422 0.173836812376976 0.7316599 0.3389880657196045 True -13 38570 30.69117522239685 0.5799188613891602 131.7835693359375 0.44481778144836426 164.09579467773438 0.17417144775390625 0.7357617 0.3322373032569885 True -14 41325 30.818309783935547 0.5715386867523193 139.6036834716797 0.28937485814094543 163.8726806640625 0.1760748028755188 0.74400884 0.3251056373119354 True -15 44080 30.588955640792847 0.8561544418334961 124.08367919921875 0.2811797857284546 163.79368591308594 0.17605528235435486 0.7479422 0.31795477867126465 True -16 46835 30.649858474731445 0.5917792320251465 117.53990173339844 0.26610279083251953 163.88262939453125 0.17586995661258698 0.7500515 0.319429486989975 True -17 49590 30.575472593307495 0.5705320835113525 129.10055541992188 0.38026857376098633 163.84996032714844 0.176072359085083 0.7520208 0.3227774202823639 True -18 52345 30.5666241645813 0.5718967914581299 115.25076293945312 0.2939096987247467 163.83175659179688 0.17587228119373322 0.7510823 0.32757025957107544 False -19 55100 30.60513925552368 0.5791306495666504 151.10992431640625 0.28173908591270447 163.98715209960938 0.17467132210731506 0.7485531 0.33258697390556335 False diff --git a/ENCSR938UOR/cherimoya.fold_0.performance.tsv b/ENCSR938UOR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9e5ac46f87b87db7268d2099aa5be81cd731d726..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -163.84996032714844 0.5729714632034302 0.176072359085083 0.039593204855918884 0.7520207762718201 0.7068707942962646 0.3227774202823639 \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_1.evaluate.json b/ENCSR938UOR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index d39a11341af5592f4f1000420b9e260a21bc0d02..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF929KKH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_1.fit.json b/ENCSR938UOR/cherimoya.fold_1.fit.json deleted file mode 100644 index 8dc7f8899940fce5518f057b4f12a1f8dfd47ea8..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF929KKH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_1.log b/ENCSR938UOR/cherimoya.fold_1.log deleted file mode 100644 index 35433d6865169389c96cd9faba80eeda5b784ed9..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 35.47303104400635 3.711958646774292 131.60208129882812 0.761151909828186 194.6739044189453 0.11983110755681992 0.5406133 2.5470097064971924 True -1 5492 30.29500150680542 0.7070631980895996 121.55931091308594 0.7190413475036621 188.52415466308594 0.158839151263237 0.677215 0.9979537129402161 True -2 8238 30.260181188583374 4.127157211303711 114.9611587524414 0.733651876449585 186.04644775390625 0.16911981999874115 0.70249474 0.5188394784927368 True -3 10984 30.327442407608032 0.6734774112701416 138.86276245117188 0.5578086376190186 185.36865234375 0.17048855125904083 0.72480553 0.4659336805343628 True -4 13730 30.298237800598145 0.6848063468933105 158.76654052734375 0.49526864290237427 185.04446411132812 0.1723480522632599 0.7293024 0.49804452061653137 True -5 16476 30.40647530555725 40.259164571762085 132.4085693359375 0.6576005816459656 184.6226806640625 0.17471937835216522 0.73891526 0.48277920484542847 True -6 19222 30.704505920410156 0.6840176582336426 141.13710021972656 0.3855656087398529 184.45855712890625 0.1754685342311859 0.74516034 0.4632304906845093 True -7 21968 30.28538966178894 0.6888740062713623 133.78411865234375 0.4807888865470886 184.14736938476562 0.1772896647453308 0.7509894 0.4472388029098511 True -8 24714 30.353806734085083 0.705634355545044 121.63502502441406 0.5879126787185669 183.87289428710938 0.17867250740528107 0.75320494 0.40931519865989685 True -9 27460 30.338046550750732 0.6999526023864746 135.03961181640625 0.5392171144485474 183.40277099609375 0.18179255723953247 0.76181394 0.4057532250881195 True -10 30206 30.378877878189087 2.4825146198272705 139.80650329589844 0.3996860682964325 183.1009979248047 0.18308360874652863 0.7649824 0.3840927481651306 True -11 32952 30.542664766311646 0.6893718242645264 147.1638641357422 0.37656494975090027 182.6990203857422 0.1856669783592224 0.7700779 0.3648757040500641 True -12 35698 30.465282440185547 0.6805448532104492 131.83059692382812 0.4310012757778168 182.6035614013672 0.18628625571727753 0.7760097 0.3516552448272705 True -13 38444 30.609854221343994 0.6773746013641357 113.98677825927734 0.4040840268135071 182.5249786376953 0.1867910921573639 0.7814089 0.3373046815395355 True -14 41190 30.759056568145752 0.6801624298095703 120.61308288574219 0.29843857884407043 182.2884063720703 0.1882629543542862 0.7841776 0.32724183797836304 True -15 43936 30.43879747390747 0.6786646842956543 131.88693237304688 0.4402598738670349 182.2624053955078 0.1879531890153885 0.78994286 0.3233027458190918 True -16 46682 31.183027029037476 35.380699157714844 139.09857177734375 0.34061941504478455 182.22145080566406 0.18817462027072906 0.79186577 0.3223305344581604 True -17 49428 30.482762813568115 2.554173707962036 111.03219604492188 0.34523576498031616 182.27281188964844 0.18858854472637177 0.7927851 0.32965707778930664 True -18 52174 30.371392011642456 2.4465651512145996 132.0362548828125 0.26364073157310486 182.2349853515625 0.18856610357761383 0.7906041 0.3357521891593933 False -19 54920 30.366774320602417 2.25537371635437 120.8792724609375 0.27604323625564575 182.27761840820312 0.18824486434459686 0.7900987 0.33844658732414246 False diff --git a/ENCSR938UOR/cherimoya.fold_1.performance.tsv b/ENCSR938UOR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8a71d99937820c874e1a4007d53e86d6bead6fb1..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -182.27281188964844 0.5622840523719788 0.18858852982521057 0.0409863255918026 0.792785108089447 0.7487046122550964 0.32965707778930664 \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_2.evaluate.json b/ENCSR938UOR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 49a6ac6a0bf3751195e6f7d04adab86eb66d2793..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF929KKH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_2.fit.json b/ENCSR938UOR/cherimoya.fold_2.fit.json deleted file mode 100644 index db654aba4712aba84b5b36f736c41606fc12142c..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF929KKH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_2.log b/ENCSR938UOR/cherimoya.fold_2.log deleted file mode 100644 index c5de4c21cd7696937a4952bd808097109110bf41..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2916 36.91366195678711 3.3488831520080566 136.50624084472656 0.6975270509719849 175.09942626953125 0.11571118235588074 0.514797 2.1301069259643555 True -1 5832 32.20739960670471 0.5064396858215332 138.34518432617188 0.5901349782943726 169.8197784423828 0.1519351303577423 0.64491445 0.699505627155304 True -2 8748 32.237133264541626 0.49605226516723633 150.67425537109375 0.676169753074646 167.72305297851562 0.16193263232707977 0.6749058 0.45209476351737976 True -3 11664 32.14391255378723 0.5033650398254395 141.36016845703125 0.3800342082977295 167.21693420410156 0.1643339842557907 0.68024516 0.44116365909576416 True -4 14580 32.14460730552673 0.5041971206665039 132.33888244628906 0.5748369097709656 166.7501678466797 0.16732646524906158 0.68442905 0.4318847358226776 True -5 17496 32.16956973075867 0.5005571842193604 153.5159454345703 0.6416122317314148 166.56504821777344 0.16832883656024933 0.68597525 0.41213417053222656 True -6 20412 32.05904269218445 0.5014266967773438 142.5679931640625 0.3989006280899048 166.4076690673828 0.16901174187660217 0.69343764 0.43576470017433167 True -7 23328 32.05942702293396 0.4996805191040039 155.89263916015625 0.48261046409606934 166.2596893310547 0.16923116147518158 0.69879514 0.4227069318294525 True -8 26244 32.06428408622742 0.5771372318267822 132.2899169921875 0.5128661394119263 165.82870483398438 0.1727646142244339 0.70472336 0.3980591297149658 True -9 29160 32.13356423377991 0.5026745796203613 145.48892211914062 0.6434357762336731 165.7739715576172 0.17254331707954407 0.7111424 0.39736834168434143 True -10 32076 32.113513231277466 2.505920171737671 136.71615600585938 0.3995288610458374 165.35801696777344 0.17506323754787445 0.71730644 0.3725779056549072 True -11 34992 32.149903297424316 0.5196027755737305 133.57896423339844 0.5028894543647766 165.2662811279297 0.17564502358436584 0.72412133 0.363142728805542 True -12 37908 32.17896056175232 19.95254945755005 125.55143737792969 0.48932135105133057 165.01629638671875 0.17752695083618164 0.7290368 0.355159193277359 True -13 40824 32.61708426475525 0.5039739608764648 139.32455444335938 0.33157941699028015 164.80477905273438 0.17840145528316498 0.73420674 0.3418246805667877 True -14 43740 32.14060926437378 0.7135813236236572 125.8241958618164 0.27270540595054626 164.739013671875 0.17842687666416168 0.739686 0.3367561995983124 True -15 46656 32.15185189247131 0.5125184059143066 143.33383178710938 0.34733298420906067 164.60543823242188 0.17943057417869568 0.7467161 0.33193203806877136 True -16 49572 32.153088092803955 0.5105850696563721 130.25802612304688 0.3129972815513611 164.5789337158203 0.17959226667881012 0.7493208 0.33134740591049194 True -17 52488 32.15433430671692 0.4998488426208496 129.24728393554688 0.30464017391204834 164.7897491455078 0.1779838502407074 0.7518142 0.33385875821113586 True -18 55404 32.13582468032837 2.017378091812134 126.1307373046875 0.22426006197929382 164.66036987304688 0.17936618626117706 0.75109816 0.34361374378204346 False -19 58320 32.18797206878662 0.5025293827056885 127.79103088378906 0.36551493406295776 164.6194610595703 0.17958714067935944 0.74954915 0.3483119606971741 False diff --git a/ENCSR938UOR/cherimoya.fold_2.performance.tsv b/ENCSR938UOR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index afdab38469348d0a9d49d53dd9ccc5e76927a1d5..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -164.7897491455078 0.5717455744743347 0.1779838502407074 0.0379992313683033 0.7518141865730286 0.7055063247680664 0.33385875821113586 \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_3.evaluate.json b/ENCSR938UOR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9c5cf37bf5ec64107da65c4ae701a545cbda2036..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF929KKH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_3.fit.json b/ENCSR938UOR/cherimoya.fold_3.fit.json deleted file mode 100644 index de4f073346f8e7ac74f91c8f6830fa2f6daf8d5e..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF929KKH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_3.log b/ENCSR938UOR/cherimoya.fold_3.log deleted file mode 100644 index 71ef6e955c7d84a6245f61550807cb0560fd0377..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 35.53414535522461 3.633885622024536 134.81288146972656 0.6087155938148499 185.36293029785156 0.11458482593297958 0.5100485 2.74812912940979 True -1 5544 30.63401770591736 0.5977675914764404 127.53800201416016 0.7957369089126587 179.7205047607422 0.15341933071613312 0.63657504 0.9552426934242249 True -2 8316 30.621896743774414 0.5987677574157715 123.09869384765625 0.6219715476036072 178.07215881347656 0.15975062549114227 0.6660572 0.4918777644634247 True -3 11088 30.529049396514893 0.5894374847412109 142.4533233642578 0.3640856146812439 177.42291259765625 0.16276191174983978 0.6774178 0.44609177112579346 True -4 13860 30.55402684211731 0.5811097621917725 122.36054992675781 0.5896856188774109 176.94358825683594 0.1655595600605011 0.68513185 0.4600529670715332 True -5 16632 30.505042552947998 0.585594654083252 144.10316467285156 0.7000443935394287 176.61074829101562 0.16790127754211426 0.688466 0.4629010558128357 True -6 19404 30.47997784614563 0.5811452865600586 121.94306182861328 0.5103452205657959 176.47607421875 0.16834019124507904 0.6940314 0.4457644820213318 True -7 22176 30.53601884841919 4.261921167373657 132.96572875976562 0.43593209981918335 176.17552185058594 0.17029109597206116 0.69944096 0.42312243580818176 True -8 24948 30.550382137298584 0.5866427421569824 122.51102447509766 0.3819959759712219 175.91650390625 0.17213770747184753 0.7010861 0.43164029717445374 True -9 27720 30.60436224937439 0.5824329853057861 137.81314086914062 0.45451369881629944 175.9377899169922 0.17163018882274628 0.7096237 0.40190738439559937 True -10 30492 30.919485330581665 35.46300506591797 136.15576171875 0.380980521440506 175.71005249023438 0.17335009574890137 0.71749675 0.40057137608528137 True -11 33264 30.56890606880188 38.49279975891113 103.2060775756836 0.3764787018299103 175.38194274902344 0.1753874570131302 0.7249831 0.38964971899986267 True -12 36036 30.90126132965088 0.5912497043609619 136.2235870361328 0.346278578042984 175.14239501953125 0.1765396147966385 0.7337084 0.3800922632217407 True -13 38808 30.626707553863525 0.5984840393066406 157.1678009033203 0.28012388944625854 175.0902862548828 0.17700962722301483 0.73850155 0.36904749274253845 True -14 41580 30.608006238937378 1.1152262687683105 109.42510986328125 0.38759350776672363 174.99462890625 0.17703931033611298 0.745525 0.3565356731414795 True -15 44352 30.633203983306885 0.5824382305145264 168.21466064453125 0.34533047676086426 174.8142852783203 0.17855656147003174 0.7497554 0.3471587896347046 True -16 47124 30.758026361465454 1.837021827697754 142.77432250976562 0.22468301653862 174.82411193847656 0.17825882136821747 0.75392735 0.34749531745910645 True -17 49896 30.579020023345947 0.6503710746765137 120.87071990966797 0.25504031777381897 174.810546875 0.17855940759181976 0.75412595 0.3537183105945587 True -18 52668 30.594032287597656 0.5898802280426025 135.6934814453125 0.25039148330688477 174.929931640625 0.17778146266937256 0.75074106 0.3611949384212494 False -19 55440 30.545244455337524 0.7888791561126709 125.07473754882812 0.17059382796287537 175.0414276123047 0.17699305713176727 0.75009793 0.3669319152832031 False diff --git a/ENCSR938UOR/cherimoya.fold_3.performance.tsv b/ENCSR938UOR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 124967f9240bafdd8795ef702e8fbe9d799b2c1d..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -174.810546875 0.568298876285553 0.17855940759181976 0.04213481768965721 0.7541259527206421 0.7105693221092224 0.3537183105945587 \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_4.evaluate.json b/ENCSR938UOR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9f8b0d8358c9887f40772ee9a37f23fe1499ad63..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF929KKH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_4.fit.json b/ENCSR938UOR/cherimoya.fold_4.fit.json deleted file mode 100644 index 449008a07f517492755355b8b94a87cc38daa2fa..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF929KKH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR938UOR/cherimoya.fold_4.log b/ENCSR938UOR/cherimoya.fold_4.log deleted file mode 100644 index 967a18443089934af11b57c3a1cd48b53782434e..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2865 36.26860785484314 3.8781614303588867 136.73931884765625 0.9268699884414673 177.27101135253906 0.11223475635051727 0.49674127 2.2053496837615967 True -1 5730 31.633636236190796 0.59889817237854 121.55087280273438 0.40675488114356995 171.71316528320312 0.15161967277526855 0.6382265 0.9425173997879028 True -2 8595 31.630425930023193 0.5966782569885254 141.4770965576172 0.49470946192741394 170.5402374267578 0.1570064276456833 0.66241527 0.4759292006492615 True -3 11460 31.65608048439026 0.592475175857544 134.97593688964844 0.415921688079834 169.72828674316406 0.16040034592151642 0.6764397 0.43503305315971375 True -4 14325 31.572620153427124 0.5951929092407227 113.15603637695312 0.8612602353096008 169.3788604736328 0.16281606256961823 0.6828435 0.4565412104129791 True -5 17190 31.632367372512817 0.5955755710601807 154.11953735351562 0.6513835191726685 169.1228790283203 0.1637192666530609 0.68644756 0.45696747303009033 True -6 20055 32.02394342422485 7.838305473327637 164.26419067382812 0.6602723598480225 168.84889221191406 0.16570743918418884 0.6905785 0.46505942940711975 True -7 22920 32.03489065170288 0.6710720062255859 124.86052703857422 0.5435871481895447 168.5560760498047 0.16771847009658813 0.6944185 0.422899067401886 True -8 25785 31.740593671798706 1.2230801582336426 115.22895812988281 0.4293593764305115 168.56246948242188 0.1672215312719345 0.70194423 0.4189358651638031 True -9 28650 31.774986267089844 0.6229045391082764 158.10166931152344 0.5048009753227234 168.24757385253906 0.16955269873142242 0.707568 0.4069185256958008 True -10 31515 31.677339792251587 0.6100585460662842 107.65446472167969 0.35571572184562683 168.06439208984375 0.1708432137966156 0.7148933 0.4038439691066742 True -11 34380 31.725360870361328 0.6200027465820312 116.30540466308594 0.3933233320713043 167.62168884277344 0.1738099753856659 0.7170465 0.3734401762485504 True -12 37245 31.801039934158325 28.896812438964844 112.26962280273438 0.3229387402534485 167.48829650878906 0.17430928349494934 0.726898 0.35368239879608154 True -13 40110 31.681740283966064 1.139585018157959 115.78839874267578 0.27893954515457153 167.29864501953125 0.1755545735359192 0.7368485 0.34660419821739197 True -14 42975 31.730374336242676 0.6043269634246826 135.7211456298828 0.39669090509414673 167.28990173339844 0.1752661168575287 0.7439114 0.3333055078983307 True -15 45840 31.88469672203064 24.101890087127686 132.27577209472656 0.30288538336753845 167.22581481933594 0.17546355724334717 0.7477867 0.3282982110977173 True -16 48705 31.939500093460083 0.6406989097595215 115.02550506591797 0.30233538150787354 167.21986389160156 0.17516262829303741 0.7497127 0.33141836524009705 True -17 51570 32.04823923110962 0.597475528717041 132.01173400878906 0.3196049630641937 167.31101989746094 0.17455072700977325 0.75283384 0.3344249725341797 True -18 54435 31.632048845291138 0.6022486686706543 139.11497497558594 0.2521769404411316 167.2230224609375 0.17526155710220337 0.7509003 0.3405654728412628 False -19 57300 32.40359377861023 0.5925140380859375 125.89713287353516 0.23428292572498322 167.39646911621094 0.17387868463993073 0.75054294 0.34460484981536865 False diff --git a/ENCSR938UOR/cherimoya.fold_4.performance.tsv b/ENCSR938UOR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index da3a678985cec151be83decf25efa40a1cb923b1..0000000000000000000000000000000000000000 --- a/ENCSR938UOR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -167.31101989746094 0.5722501873970032 0.17455072700977325 0.038839325308799744 0.7528338432312012 0.7105217576026917 0.3344249725341797 \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_0.evaluate.json b/ENCSR940CXU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 92057bc8cc26245a755c6e63e487e664f106b06a..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236EUW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_0.fit.json b/ENCSR940CXU/cherimoya.fold_0.fit.json deleted file mode 100644 index 74f001b7649d951f8ce68bd94a83966ba40a909d..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF236EUW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_0.log b/ENCSR940CXU/cherimoya.fold_0.log deleted file mode 100644 index bf03536a84796eb5ad8f87f22e59eb9ccf6b6d42..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 35.01999497413635 4.322680711746216 951.132080078125 0.208713561296463 1223.2001953125 0.295780211687088 0.8603913 6.246656894683838 True -1 5500 30.203486919403076 0.5855076313018799 924.6427001953125 0.20135079324245453 1117.5660400390625 0.3585644066333771 0.8989324 0.7379217147827148 True -2 8250 30.240088939666748 1.4266571998596191 1044.62548828125 0.18386194109916687 1096.55712890625 0.3695242404937744 0.9099152 0.25548607110977173 True -3 11000 30.32668924331665 0.5982751846313477 920.404052734375 0.11692143976688385 1086.095703125 0.37596434354782104 0.9153054 0.18619374930858612 True -4 13750 30.29244351387024 0.5827579498291016 900.439208984375 0.2715073227882385 1081.7890625 0.3790900409221649 0.91729295 0.17833369970321655 True -5 16500 30.121026039123535 0.5657238960266113 1054.2398681640625 0.22495189309120178 1077.1986083984375 0.3828522264957428 0.9194682 0.16506348550319672 True -6 19250 29.661423921585083 0.5649154186248779 855.0137329101562 0.16529959440231323 1075.546630859375 0.3841356635093689 0.92216057 0.1484338641166687 True -7 22000 29.824004888534546 0.5812928676605225 966.9443969726562 0.11242634057998657 1071.8548583984375 0.38642680644989014 0.9240741 0.13589602708816528 True -8 24750 29.771099090576172 0.5797638893127441 911.1533203125 0.15383033454418182 1067.4256591796875 0.3892088234424591 0.92503023 0.13151758909225464 True -9 27500 29.744070529937744 0.5785472393035889 888.6387939453125 0.16356928646564484 1067.396728515625 0.38942229747772217 0.9267869 0.13215571641921997 True -10 30250 29.679969787597656 0.5800108909606934 962.6756591796875 0.226657897233963 1063.938720703125 0.3916594684123993 0.92966306 0.119464211165905 True -11 33000 29.631696462631226 10.432456493377686 924.85205078125 0.152303084731102 1061.2237548828125 0.3934536576271057 0.9315058 0.11707854270935059 True -12 35750 29.68554186820984 0.5708281993865967 779.6697998046875 0.12121173739433289 1057.6170654296875 0.39651334285736084 0.9333954 0.10560408234596252 True -13 38500 29.646964073181152 0.571481466293335 944.9491577148438 0.09967140853404999 1055.634765625 0.39789146184921265 0.9352108 0.10167140513658524 True -14 41250 29.629444360733032 0.5884594917297363 831.2103271484375 0.14133697748184204 1054.9912109375 0.3976793587207794 0.9373889 0.09591547399759293 True -15 44000 31.0211501121521 1.5953516960144043 916.739990234375 0.0979016050696373 1053.858154296875 0.3980698585510254 0.9395927 0.09095596522092819 True -16 46750 29.730183362960815 0.5938889980316162 996.578125 0.06818237155675888 1054.22119140625 0.397958904504776 0.9402435 0.08827263861894608 True -17 49500 29.71412992477417 0.5797743797302246 858.156494140625 0.11690498888492584 1054.283935546875 0.39774659276008606 0.9428812 0.0866970419883728 True -18 52250 29.691855907440186 0.5721890926361084 935.4171142578125 0.07341372221708298 1053.53369140625 0.398111492395401 0.94276094 0.08637748658657074 False -19 55000 29.688512086868286 0.9287886619567871 866.6431274414062 0.1399611234664917 1054.484375 0.3971133828163147 0.94302326 0.08665252476930618 True diff --git a/ENCSR940CXU/cherimoya.fold_0.performance.tsv b/ENCSR940CXU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c23b4ee1b98cfc8736d3d939f3f06f1f089fa2d6..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1054.484375 0.35897693037986755 0.3971133828163147 0.19091130793094635 0.9430232644081116 0.918902575969696 0.08665252476930618 \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_1.evaluate.json b/ENCSR940CXU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index efdcaf84225e8f237dc50ce76cee42888b1b62e8..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236EUW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_1.fit.json b/ENCSR940CXU/cherimoya.fold_1.fit.json deleted file mode 100644 index b4eb3e977c228259d16f5441b77a07593e02c53f..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF236EUW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_1.log b/ENCSR940CXU/cherimoya.fold_1.log deleted file mode 100644 index 9410e6a898756cf9fc4597d05ddbf8ec02270583..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2702 34.58085370063782 6.039442777633667 1075.231689453125 0.5237461924552917 1422.79931640625 0.30357784032821655 0.84985304 6.84194803237915 True -1 5404 29.8193097114563 2.606423854827881 1041.807861328125 0.1500152349472046 1298.1590576171875 0.3744828999042511 0.8949606 0.9038324952125549 True -2 8106 30.06291127204895 0.7089443206787109 941.3404541015625 0.16391025483608246 1264.813232421875 0.38862407207489014 0.911864 0.29823195934295654 True -3 10808 30.24964213371277 0.7094371318817139 937.1920166015625 0.37395671010017395 1250.0501708984375 0.39789658784866333 0.9161069 0.1952497810125351 True -4 13510 29.763932943344116 0.869438648223877 917.9714965820312 0.16211774945259094 1250.162109375 0.39736035466194153 0.91776586 0.1959700584411621 True -5 16212 29.77687406539917 0.7187974452972412 920.7697143554688 0.2019830048084259 1242.486328125 0.40368184447288513 0.91948164 0.21267063915729523 True -6 18914 29.703444242477417 0.696885347366333 966.0801391601562 0.13472802937030792 1240.8309326171875 0.4033941626548767 0.92138857 0.14652056992053986 True -7 21616 29.67096209526062 0.7081291675567627 964.13671875 0.21448653936386108 1234.8372802734375 0.40801337361335754 0.92344826 0.1464763730764389 True -8 24318 29.680841207504272 0.7105996608734131 852.201171875 0.18071229755878448 1229.74462890625 0.41014066338539124 0.9268144 0.14130568504333496 True -9 27020 29.68507480621338 0.7191729545593262 1078.056884765625 0.17889738082885742 1228.2271728515625 0.41152673959732056 0.9280834 0.13817253708839417 True -10 29722 29.704737424850464 0.682497501373291 907.3617553710938 0.12341953068971634 1225.75048828125 0.4122326374053955 0.9304784 0.13105376064777374 True -11 32424 29.68544316291809 0.6853227615356445 823.9014282226562 0.17548200488090515 1220.6893310546875 0.41572609543800354 0.9314692 0.12294258177280426 True -12 35126 29.696537256240845 0.6796121597290039 947.243896484375 0.07131783664226532 1218.71923828125 0.41590428352355957 0.93430156 0.11610955744981766 True -13 37828 29.70195245742798 0.7950048446655273 970.1399536132812 0.12545660138130188 1215.7193603515625 0.4185136556625366 0.93531454 0.10949015617370605 True -14 40530 29.725372076034546 0.6896827220916748 915.8411865234375 0.1021619439125061 1213.6416015625 0.420489102602005 0.93849397 0.10493666678667068 True -15 43232 29.719669818878174 0.6973719596862793 844.6898193359375 0.15104147791862488 1211.1700439453125 0.421663373708725 0.9413527 0.10112284123897552 True -16 45934 29.707512855529785 0.7248001098632812 1047.0234375 0.08791188895702362 1210.9580078125 0.421413779258728 0.94275415 0.09793102741241455 True -17 48636 29.705855131149292 19.212377309799194 800.3729248046875 0.19210508465766907 1209.943603515625 0.42204076051712036 0.94270945 0.09647596627473831 False -18 51338 29.752540349960327 0.698176383972168 1005.453125 0.10430090129375458 1211.39892578125 0.42105886340141296 0.94288826 0.09674738347530365 True -19 54040 29.384875774383545 0.6791629791259766 968.2858276367188 0.07426747679710388 1213.424560546875 0.41904258728027344 0.9435218 0.09680540859699249 True diff --git a/ENCSR940CXU/cherimoya.fold_1.performance.tsv b/ENCSR940CXU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 08382f3f192c31bf2338aed215d17dfcc48b9e74..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1213.424560546875 0.3362060487270355 0.4190426170825958 0.2153635174036026 0.9435217976570129 0.9371265172958374 0.09680540859699249 \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_2.evaluate.json b/ENCSR940CXU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 584e746e77a5d209b5ad3c4094a85a4d6fc4fe11..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236EUW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_2.fit.json b/ENCSR940CXU/cherimoya.fold_2.fit.json deleted file mode 100644 index b6aa7f0c5ee006365202d3f1d6163ee083ae06c8..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF236EUW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_2.log b/ENCSR940CXU/cherimoya.fold_2.log deleted file mode 100644 index c0352e614126babc4695a9b724fb336831601389..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 36.261149883270264 4.884772539138794 864.5302734375 0.14345324039459229 1296.724609375 0.3005657196044922 0.8525001 6.077350616455078 True -1 5762 31.750255584716797 0.7397315502166748 988.377197265625 0.1641162931919098 1189.1746826171875 0.3597433567047119 0.89679253 0.7330705523490906 True -2 8643 31.79558277130127 0.5772311687469482 1022.3177490234375 0.24364367127418518 1161.5010986328125 0.37665724754333496 0.9062781 0.2606775462627411 True -3 11524 31.712334871292114 0.5756373405456543 986.4290161132812 0.1839616298675537 1153.8087158203125 0.38105398416519165 0.91185284 0.19734396040439606 True -4 14405 31.736536264419556 0.5754711627960205 840.1744384765625 0.10713358223438263 1150.39697265625 0.38161736726760864 0.91596806 0.19543515145778656 True -5 17286 31.748358249664307 0.5567662715911865 1053.011474609375 0.14231182634830475 1147.1817626953125 0.3836171329021454 0.91563267 0.19369253516197205 False -6 20167 31.68528461456299 0.5714845657348633 977.4825439453125 0.12912611663341522 1145.0833740234375 0.3851752281188965 0.91752493 0.14790549874305725 True -7 23048 31.62267231941223 0.5926692485809326 908.1907958984375 0.13935035467147827 1136.8143310546875 0.3916148543357849 0.92146987 0.1349247694015503 True -8 25929 31.628788232803345 0.58939528465271 914.4893798828125 0.19956035912036896 1135.5738525390625 0.3925207555294037 0.92412823 0.13047032058238983 True -9 28810 31.619163274765015 0.5665411949157715 938.5948486328125 0.2107183188199997 1133.00537109375 0.3933486342430115 0.92566454 0.13199089467525482 True -10 31691 31.599860668182373 0.5699641704559326 994.682373046875 0.10187703371047974 1130.42431640625 0.3951273262500763 0.9262829 0.13020193576812744 True -11 34572 31.6342031955719 0.5676813125610352 1010.3331298828125 0.10014379024505615 1127.824462890625 0.39592263102531433 0.92833835 0.12103848904371262 True -12 37453 31.652525901794434 0.5601723194122314 961.8466796875 0.10304749011993408 1127.2562255859375 0.39620551466941833 0.9304488 0.11329013109207153 True -13 40334 31.651519060134888 0.5598061084747314 1036.927734375 0.1226361021399498 1123.274169921875 0.39876875281333923 0.9338883 0.1094372421503067 True -14 43215 31.765923976898193 1.7258868217468262 814.7571411132812 0.13866809010505676 1121.8050537109375 0.3995824456214905 0.93447614 0.10398969799280167 True -15 46096 31.534767627716064 17.784713983535767 830.6932373046875 0.07345741987228394 1121.0838623046875 0.4005042016506195 0.93733466 0.09856710582971573 True -16 48977 31.117055892944336 9.412622690200806 1022.01171875 0.12102516740560532 1118.6221923828125 0.40153852105140686 0.9377251 0.09571726620197296 True -17 51858 31.171184301376343 0.5596010684967041 982.0656127929688 0.06467244774103165 1117.118896484375 0.4033854007720947 0.9388963 0.0936393141746521 True -18 54739 31.101659536361694 0.5599749088287354 918.9607543945312 0.09412351250648499 1117.7442626953125 0.4024518132209778 0.9368921 0.09364847838878632 False -19 57620 31.126379251480103 0.5555205345153809 820.6196899414062 0.12550067901611328 1119.9781494140625 0.4001290798187256 0.93807286 0.09421748667955399 False diff --git a/ENCSR940CXU/cherimoya.fold_2.performance.tsv b/ENCSR940CXU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8de945e1405233e9355f974a5f246b4d09d2d5e4..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1117.118896484375 0.3510059714317322 0.4033854007720947 0.19879354536533356 0.9388962984085083 0.9257069230079651 0.0936393141746521 \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_3.evaluate.json b/ENCSR940CXU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 27ccd44465b9363f59c46bd3fd1ace7b1f5588df..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236EUW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_3.fit.json b/ENCSR940CXU/cherimoya.fold_3.fit.json deleted file mode 100644 index 41737c6cd91cfc165a620a34676d6e6569361c53..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF236EUW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_3.log b/ENCSR940CXU/cherimoya.fold_3.log deleted file mode 100644 index d90fee188892df8f71bd48baa6a97bc5950cfacd..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2742 34.81041240692139 3.8723208904266357 998.4331665039062 0.2265024483203888 1183.2415771484375 0.30344781279563904 0.85193723 6.803904056549072 True -1 5484 30.151169538497925 1.7043228149414062 989.5076904296875 0.17852166295051575 1087.0445556640625 0.3631284832954407 0.89924735 0.7310179471969604 True -2 8226 30.124336004257202 0.5708217620849609 931.3261108398438 0.15829508006572723 1070.2872314453125 0.37143903970718384 0.90863234 0.27804598212242126 True -3 10968 30.105918884277344 0.5432872772216797 869.828125 0.17676496505737305 1063.8607177734375 0.37617090344429016 0.91124874 0.16972403228282928 True -4 13710 30.12716579437256 0.5348944664001465 1005.769287109375 0.2240290641784668 1061.1981201171875 0.3777134120464325 0.91620904 0.17483937740325928 True -5 16452 30.151227712631226 0.5400485992431641 886.5054321289062 0.20365262031555176 1059.228515625 0.3793819844722748 0.916098 0.17189094424247742 False -6 19194 30.11016583442688 0.5425186157226562 895.4090576171875 0.15168830752372742 1056.751220703125 0.3819045126438141 0.91950667 0.1422765851020813 True -7 21936 30.176841020584106 0.5496416091918945 959.5855712890625 0.11936715245246887 1052.32177734375 0.3854254484176636 0.92031944 0.1285785734653473 True -8 24678 30.149726629257202 0.536879301071167 924.16552734375 0.11670460551977158 1050.635009765625 0.38616228103637695 0.9231515 0.12548115849494934 True -9 27420 30.129533767700195 0.5840120315551758 1042.521728515625 0.1495344340801239 1049.1563720703125 0.38720616698265076 0.9235505 0.12734554708003998 True -10 30162 30.19812297821045 0.5459959506988525 1093.5655517578125 0.18242502212524414 1048.2904052734375 0.38733839988708496 0.92652905 0.11959867179393768 True -11 32904 30.206194162368774 0.5496654510498047 904.4957275390625 0.2306142896413803 1043.468994140625 0.3915777802467346 0.92813945 0.11553221940994263 True -12 35646 30.117115020751953 0.5482828617095947 1008.6593627929688 0.18492491543293 1042.5877685546875 0.39161092042922974 0.9330218 0.11074426770210266 True -13 38388 30.092505931854248 0.5364820957183838 885.0320434570312 0.09955272078514099 1040.831787109375 0.39254334568977356 0.93470895 0.10401824116706848 True -14 41130 30.140896320343018 0.5921406745910645 938.6806640625 0.16755692660808563 1038.5887451171875 0.3943879306316376 0.93605536 0.09979476779699326 True -15 43872 29.70469331741333 1.0664234161376953 899.024658203125 0.1349075436592102 1037.8343505859375 0.3948212265968323 0.9402342 0.0941750779747963 True -16 46614 29.565408945083618 1.547814130783081 986.3047485351562 0.0962105467915535 1037.7618408203125 0.3946894705295563 0.9411839 0.091265007853508 True -17 49356 29.592549324035645 0.7664487361907959 887.4718017578125 0.11396105587482452 1036.614990234375 0.3959951102733612 0.9426052 0.08969337493181229 True -18 52098 29.600995540618896 13.03837776184082 836.9036865234375 0.1300216019153595 1037.4849853515625 0.3955184817314148 0.9416415 0.08976197987794876 False -19 54840 29.7093346118927 1.7232913970947266 913.1882934570312 0.06563575565814972 1036.864990234375 0.3960384428501129 0.9399869 0.08930863440036774 False diff --git a/ENCSR940CXU/cherimoya.fold_3.performance.tsv b/ENCSR940CXU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 692cb63dd518c8908e5c6707b2aaf9e73e83436b..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1036.614990234375 0.3596198558807373 0.3959951102733612 0.18917985260486603 0.942605197429657 0.9200916290283203 0.08969337493181229 \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_4.evaluate.json b/ENCSR940CXU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index decbc7d32a3d9225eabc381daa1b6c30cbd558af..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF236EUW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_4.fit.json b/ENCSR940CXU/cherimoya.fold_4.fit.json deleted file mode 100644 index 2378202230918d116c2fd70490c98850ae178dcd..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF236EUW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940CXU/cherimoya.fold_4.log b/ENCSR940CXU/cherimoya.fold_4.log deleted file mode 100644 index b361caaa0a90e31be4cc503d26b6349cd6f80543..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2822 35.65086102485657 4.358731746673584 960.5279541015625 0.25181248784065247 1138.832763671875 0.2974812388420105 0.85699373 5.501840591430664 True -1 5644 31.030032634735107 0.6992142200469971 1004.3414306640625 0.1520199328660965 1060.005615234375 0.3496752381324768 0.89326507 0.597831666469574 True -2 8466 30.981557369232178 0.6581630706787109 924.4871826171875 0.25433918833732605 1040.180419921875 0.36209836602211 0.9066293 0.21619969606399536 True -3 11288 31.002182722091675 0.5999996662139893 967.9105224609375 0.1356511116027832 1035.6966552734375 0.3644017279148102 0.9102157 0.15304765105247498 True -4 14110 31.040980100631714 0.6223955154418945 1028.0472412109375 0.1619325876235962 1032.28173828125 0.3667873740196228 0.911867 0.13178621232509613 True -5 16932 30.97464871406555 0.8173894882202148 939.533935546875 0.16114847362041473 1029.839111328125 0.3685370087623596 0.9138624 0.143294557929039 True -6 19754 30.991540908813477 0.6998209953308105 1063.093017578125 0.1895751655101776 1025.040771484375 0.37261754274368286 0.9177597 0.12157607823610306 True -7 22576 31.015483379364014 0.6274070739746094 912.2321166992188 0.09302932769060135 1022.2666015625 0.37460950016975403 0.91798997 0.1185918003320694 True -8 25398 31.01346206665039 0.6426386833190918 1016.58056640625 0.1079188883304596 1020.9384765625 0.3764782249927521 0.9201804 0.11927098035812378 True -9 28220 30.963253259658813 0.6131048202514648 1011.2032470703125 0.0989297479391098 1019.1305541992188 0.3769538700580597 0.92302614 0.11893155425786972 True -10 31042 31.10482406616211 0.6197798252105713 1009.8784790039062 0.14002105593681335 1015.3195190429688 0.3808409571647644 0.9237136 0.111660897731781 True -11 33864 30.960252285003662 0.6061911582946777 941.7266845703125 0.5261449217796326 1013.0108032226562 0.3820060193538666 0.9260698 0.10546676814556122 True -12 36686 30.949980974197388 0.6366047859191895 938.2529296875 0.1227593719959259 1012.6705322265625 0.3808729350566864 0.9285311 0.10045141726732254 True -13 39508 31.05352234840393 1.1738858222961426 929.7756958007812 0.07689997553825378 1010.5574340820312 0.3822351098060608 0.9312382 0.09349831938743591 True -14 42330 30.63624906539917 0.6260213851928711 811.9202270507812 0.13123521208763123 1008.2098999023438 0.38502922654151917 0.933737 0.0908743292093277 True -15 45152 30.463624477386475 1.7282967567443848 1009.9580688476562 0.11570756137371063 1006.221923828125 0.38654258847236633 0.9346797 0.08595526963472366 True -16 47974 30.44240689277649 0.6258399486541748 763.5308227539062 0.1792130023241043 1006.5457763671875 0.38591834902763367 0.93821186 0.08327952027320862 True -17 50796 30.438196420669556 0.6253681182861328 974.9625244140625 0.0864180475473404 1006.1949462890625 0.3870106041431427 0.93681556 0.08136273175477982 False -18 53618 30.434263467788696 0.6211214065551758 833.5836791992188 0.07245441526174545 1008.1973266601562 0.38489532470703125 0.9368115 0.08129093050956726 False -19 56440 30.417155742645264 0.6249923706054688 908.06494140625 0.08984328806400299 1006.8827514648438 0.3865632712841034 0.9383726 0.08132123202085495 True diff --git a/ENCSR940CXU/cherimoya.fold_4.performance.tsv b/ENCSR940CXU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 73e220875383278937208505434985d504c6be6a..0000000000000000000000000000000000000000 --- a/ENCSR940CXU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1006.8827514648438 0.3663543164730072 0.3865632712841034 0.18135955929756165 0.9383726119995117 0.9116218686103821 0.08132123202085495 \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_0.evaluate.json b/ENCSR940QJU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 69695fab56764c93df1315f88701debbe08839de..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF084NMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_0.fit.json b/ENCSR940QJU/cherimoya.fold_0.fit.json deleted file mode 100644 index 29f4ea3e24b7dac2263dc3f35e1085dec69e9ce9..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF084NMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_0.log b/ENCSR940QJU/cherimoya.fold_0.log deleted file mode 100644 index 182bac5cd2f30e857d2fc02fbfc679deb827bdd1..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1089 17.362419605255127 3.1306631565093994 118.45246887207031 0.8613284826278687 164.0321044921875 0.23685090243816376 0.5333582 9.635954856872559 True -1 2178 11.878105163574219 0.2489619255065918 108.83497619628906 0.6243526935577393 145.48936462402344 0.2913084924221039 0.5962718 4.093605041503906 True -2 3267 12.026503801345825 0.8755006790161133 87.82138061523438 0.815396785736084 136.83836364746094 0.3455856740474701 0.61791414 2.3567628860473633 True -3 4356 11.861805438995361 0.2399005889892578 82.02330780029297 0.5436123609542847 131.57687377929688 0.3800155818462372 0.6791534 0.9138971567153931 True -4 5445 11.853532552719116 0.24504947662353516 109.04908752441406 0.5406336784362793 129.41387939453125 0.3914623558521271 0.69150215 0.5928739309310913 True -5 6534 12.799193382263184 13.067496538162231 99.83453369140625 0.40864062309265137 128.44461059570312 0.3966224193572998 0.69899946 0.49140453338623047 True -6 7623 14.17061710357666 10.159260272979736 115.23532104492188 0.6798456907272339 127.9263687133789 0.3999621272087097 0.70786434 0.44368666410446167 True -7 8712 11.883876323699951 0.24858903884887695 104.43846130371094 0.5220618844032288 127.56098175048828 0.4024437665939331 0.7138147 0.40416833758354187 True -8 9801 11.881652116775513 0.24922466278076172 106.07156372070312 0.47276821732521057 127.23533630371094 0.40447333455085754 0.7190018 0.38992270827293396 True -9 10890 11.89813232421875 0.2501237392425537 111.86558532714844 0.5205565690994263 126.84170532226562 0.40656206011772156 0.7274918 0.36041441559791565 True -10 11979 11.890208005905151 0.24932646751403809 100.00143432617188 0.4638897776603699 126.57302856445312 0.4083267152309418 0.73344 0.347469687461853 True -11 13068 11.886806726455688 9.862627744674683 111.88687896728516 0.20409025251865387 126.28958129882812 0.40987029671669006 0.7414419 0.33817487955093384 True -12 14157 14.965468406677246 18.37791085243225 90.24052429199219 0.35350924730300903 126.01000213623047 0.41118425130844116 0.7474876 0.3279866576194763 True -13 15246 12.788320064544678 0.2500488758087158 106.43230438232422 0.37086737155914307 125.79754638671875 0.4121946692466736 0.7529304 0.325920969247818 True -14 16335 11.896281480789185 0.5582804679870605 91.3235092163086 0.32133573293685913 125.66761779785156 0.41254886984825134 0.75837934 0.3223131000995636 True -15 17424 11.900414943695068 5.2588231563568115 127.85368347167969 0.2836776375770569 125.63720703125 0.4123583436012268 0.76217556 0.3220393657684326 True -16 18513 11.916978359222412 0.2510814666748047 84.89140319824219 0.252155065536499 125.75172424316406 0.4114435315132141 0.7655251 0.324127733707428 True -17 19602 11.916238069534302 0.5522968769073486 82.07414245605469 0.24385300278663635 125.89830017089844 0.41007867455482483 0.76609105 0.33078303933143616 True -18 20691 12.183682441711426 13.137687921524048 89.04303741455078 0.5256562232971191 126.07640838623047 0.4087558388710022 0.7671446 0.334687203168869 True -19 21780 12.009228706359863 0.2506706714630127 95.3470458984375 0.24581949412822723 126.19471740722656 0.40781694650650024 0.7665047 0.33900895714759827 False diff --git a/ENCSR940QJU/cherimoya.fold_0.performance.tsv b/ENCSR940QJU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2549898971b6d18c64394a4ff38925079b2b8a62..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -126.07640838623047 0.46398690342903137 0.4087558388710022 0.07364367693662643 0.7671446204185486 0.7501340508460999 0.334687203168869 \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_1.evaluate.json b/ENCSR940QJU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 11644fab4291d8be2224b95fc7f07639777c195b..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF084NMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_1.fit.json b/ENCSR940QJU/cherimoya.fold_1.fit.json deleted file mode 100644 index 17af3adaa5930025662e42ab8cdc6dc83d640d1f..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF084NMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_1.log b/ENCSR940QJU/cherimoya.fold_1.log deleted file mode 100644 index 190ff2b48fcdcee058f64dbfb72d6e548e448fa2..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1096 22.313481092453003 9.924049139022827 94.48685455322266 0.9344319105148315 165.4162139892578 0.23853497207164764 0.5080394 9.80838680267334 True -1 2192 11.99648666381836 0.2720460891723633 109.99507904052734 0.6798826456069946 147.18048095703125 0.29254674911499023 0.57868236 4.409444332122803 True -2 3288 11.9818856716156 0.26802849769592285 104.03163146972656 0.6497241854667664 138.51327514648438 0.34731581807136536 0.60846233 2.2310547828674316 True -3 4384 11.975403070449829 0.26151251792907715 111.08362579345703 0.4476615786552429 133.92037963867188 0.3759697377681732 0.6614319 0.901089608669281 True -4 5480 11.93944239616394 0.2629241943359375 80.36588287353516 0.40951961278915405 131.91209411621094 0.3863687813282013 0.691768 0.5031705498695374 True -5 6576 11.953698635101318 0.26256585121154785 91.88111114501953 0.3734215497970581 131.0121612548828 0.3911212980747223 0.70485795 0.42191895842552185 True -6 7672 11.962403774261475 0.2617495059967041 112.10027313232422 0.561286985874176 130.5868682861328 0.39366665482521057 0.7111078 0.4010474681854248 True -7 8768 11.991961479187012 10.14318561553955 82.68209838867188 0.3915969729423523 130.15457153320312 0.3963176906108856 0.7241963 0.3598001301288605 True -8 9864 12.945435285568237 0.2678360939025879 93.19236755371094 0.36228781938552856 129.783203125 0.3984053134918213 0.7311387 0.3530450165271759 True -9 10960 11.975525617599487 0.2640724182128906 107.15533447265625 0.2294602394104004 129.4198760986328 0.40055686235427856 0.7398079 0.3296554982662201 True -10 12056 11.965827226638794 0.26048898696899414 95.26531219482422 0.38737064599990845 129.16375732421875 0.402072548866272 0.74658376 0.318107545375824 True -11 13152 12.124125480651855 1.4809191226959229 106.67100524902344 0.33301642537117004 128.9390869140625 0.4034803509712219 0.75248355 0.3172473609447479 True -12 14248 12.140252113342285 8.112260818481445 92.5326156616211 0.24114958941936493 128.67530822753906 0.4048440456390381 0.76057315 0.3094102144241333 True -13 15344 12.00851821899414 1.909921646118164 102.84869384765625 0.32341426610946655 128.4889373779297 0.40596193075180054 0.76790816 0.30347245931625366 True -14 16440 11.973134994506836 0.267000675201416 92.34147644042969 0.4097056984901428 128.3248291015625 0.4064788222312927 0.7706521 0.3024495244026184 True -15 17536 11.962197065353394 0.262467622756958 81.98365783691406 0.29987287521362305 128.29673767089844 0.4061471223831177 0.77405494 0.3031780421733856 True -16 18632 11.991794109344482 0.26549744606018066 89.11967468261719 0.2718731462955475 128.458984375 0.4052788317203522 0.7767699 0.30535730719566345 True -17 19728 11.97882628440857 0.27797389030456543 112.74031066894531 0.24903738498687744 128.56712341308594 0.4036528468132019 0.7794294 0.30665451288223267 True -18 20824 12.1382155418396 0.2652571201324463 93.76811981201172 0.28183889389038086 128.78526306152344 0.4020683765411377 0.77958685 0.30840644240379333 True -19 21920 11.985581159591675 0.2613224983215332 98.34969329833984 0.2111627161502838 129.0065155029297 0.4008406400680542 0.7788478 0.31268784403800964 False diff --git a/ENCSR940QJU/cherimoya.fold_1.performance.tsv b/ENCSR940QJU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8368f1365c1bcd7d5a6aeb57905bf0709f7d2a97..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -128.78526306152344 0.46444928646087646 0.40206843614578247 0.07206790149211884 0.7795868515968323 0.7776485085487366 0.30840644240379333 \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_2.evaluate.json b/ENCSR940QJU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3171df4a21cc9acfd76fceceb4fceccaf5f361c4..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF084NMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_2.fit.json b/ENCSR940QJU/cherimoya.fold_2.fit.json deleted file mode 100644 index f7589a6170267dd1075cf54ed2aee2a847f91cd9..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF084NMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_2.log b/ENCSR940QJU/cherimoya.fold_2.log deleted file mode 100644 index 8706f64d76762e71b593b780958cb6d8f709f4a5..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1157 17.108452796936035 3.1146347522735596 110.41964721679688 0.8740841746330261 171.59112548828125 0.24261212348937988 0.4980849 9.591883659362793 True -1 2314 12.682413339614868 0.22071599960327148 107.93938446044922 0.5064743757247925 152.19973754882812 0.3016851246356964 0.590399 4.230979919433594 True -2 3471 12.672500133514404 0.2135176658630371 89.72240447998047 0.5284832119941711 143.47586059570312 0.3566383123397827 0.63517594 2.432299852371216 True -3 4628 12.648168802261353 0.21630382537841797 99.34666442871094 0.6355243921279907 138.06732177734375 0.38652142882347107 0.68676335 1.0887987613677979 True -4 5785 12.647761821746826 0.21879148483276367 109.70992279052734 0.5346279144287109 135.91249084472656 0.39675331115722656 0.708488 0.6918230056762695 True -5 6942 12.676466464996338 0.21484661102294922 96.13044738769531 0.5459911823272705 135.02114868164062 0.40151867270469666 0.71364266 0.5114935040473938 True -6 8099 12.62653636932373 0.2183396816253662 108.96141815185547 0.5056803226470947 134.44317626953125 0.4048299491405487 0.7218927 0.44100338220596313 True -7 9256 12.65112566947937 0.2196507453918457 120.5379638671875 0.5544984340667725 133.87904357910156 0.4078983664512634 0.7259006 0.4203563928604126 True -8 10413 13.63141655921936 14.899266004562378 85.44637298583984 0.43042320013046265 133.535400390625 0.40962788462638855 0.7315352 0.3942265510559082 True -9 11570 12.935949802398682 0.22584319114685059 91.84933471679688 0.319624125957489 133.192138671875 0.4113912284374237 0.7371652 0.3873136639595032 True -10 12727 12.691417932510376 0.22179031372070312 97.78823852539062 0.6380186676979065 132.91070556640625 0.41316571831703186 0.7437756 0.37776845693588257 True -11 13884 12.666491270065308 0.22395992279052734 103.73036193847656 0.5071314573287964 132.53152465820312 0.41498807072639465 0.74867177 0.3619914650917053 True -12 15041 13.374540567398071 4.396891117095947 104.06993103027344 0.4376561641693115 132.1947021484375 0.41678550839424133 0.7551014 0.347216933965683 True -13 16198 12.688245296478271 0.21934843063354492 102.25004577636719 0.3377324342727661 131.9362335205078 0.4181238114833832 0.76065177 0.3365694284439087 True -14 17355 12.674912214279175 0.22124528884887695 85.04930114746094 0.5110496282577515 131.7600860595703 0.41896548867225647 0.7638581 0.33353665471076965 True -15 18512 12.709408283233643 0.22268128395080566 101.0862808227539 0.29675745964050293 131.73780822753906 0.41872188448905945 0.76846343 0.3381253182888031 True -16 19669 12.690645694732666 0.22390270233154297 101.22898864746094 0.33367684483528137 131.82386779785156 0.4177907109260559 0.7712352 0.3407074511051178 True -17 20826 12.715245962142944 0.21898627281188965 95.71544647216797 0.2985244393348694 131.9915771484375 0.416362464427948 0.7722383 0.34634289145469666 True -18 21983 12.66758680343628 0.21599864959716797 86.6003189086914 0.25881972908973694 132.16329956054688 0.4150100350379944 0.77204657 0.3533046245574951 False -19 23140 12.673535346984863 12.48898434638977 79.92170715332031 0.21244141459465027 132.2783660888672 0.41400352120399475 0.7733484 0.358051061630249 True diff --git a/ENCSR940QJU/cherimoya.fold_2.performance.tsv b/ENCSR940QJU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 952fe85526d96f6b073aaf83fb4def377669be0d..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -132.2783660888672 0.45901575684547424 0.41400352120399475 0.07882402092218399 0.7733483910560608 0.7643994688987732 0.358051061630249 \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_3.evaluate.json b/ENCSR940QJU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index b05b674ff7e318e1d36fe30f7d000e6771562d55..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF084NMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_3.fit.json b/ENCSR940QJU/cherimoya.fold_3.fit.json deleted file mode 100644 index 78fdefe0127c33f286465f800837d64bb39a1c7b..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF084NMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_3.log b/ENCSR940QJU/cherimoya.fold_3.log deleted file mode 100644 index 05343e004797c382cb9044220ad5fdc21a86e546..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1116 16.964887857437134 3.1909563541412354 99.14395141601562 0.864023745059967 166.7318572998047 0.24121487140655518 0.52936554 9.781229972839355 True -1 2232 12.235085010528564 8.767770528793335 89.91338348388672 0.5390979647636414 147.6216278076172 0.29989129304885864 0.594089 4.491639614105225 True -2 3348 13.59614610671997 3.539721727371216 105.17034149169922 0.6398143172264099 140.07691955566406 0.3467444181442261 0.6223519 2.5872504711151123 True -3 4464 12.199491262435913 0.2348799705505371 100.52481842041016 0.47625356912612915 134.49208068847656 0.3811594843864441 0.6656102 1.1359426975250244 True -4 5580 12.206671237945557 0.24044299125671387 97.35298156738281 0.5100401639938354 132.16590881347656 0.39432790875434875 0.68435174 0.6495069861412048 True -5 6696 12.252948999404907 0.2446751594543457 109.5230712890625 0.5214852094650269 131.1802978515625 0.3997734487056732 0.6955091 0.5103559494018555 True -6 7812 12.216174840927124 0.2400040626525879 102.61695861816406 0.5825964212417603 130.70907592773438 0.40232589840888977 0.69837976 0.4678618907928467 True -7 8928 12.184092998504639 0.24093317985534668 102.90524291992188 0.6275496482849121 130.5032958984375 0.40407150983810425 0.703531 0.44060832262039185 True -8 10044 12.217539072036743 0.24646592140197754 104.40731048583984 0.41964343190193176 130.27142333984375 0.4056989252567291 0.71577996 0.4131915867328644 True -9 11160 12.176625728607178 0.24147558212280273 100.66697692871094 0.4044645428657532 129.96888732910156 0.407678484916687 0.7207468 0.3967346251010895 True -10 12276 12.229224920272827 0.24308991432189941 88.81709289550781 0.48453348875045776 129.52052307128906 0.40981611609458923 0.7305147 0.3704083263874054 True -11 13392 12.179556608200073 0.24166154861450195 96.50758361816406 0.3059210181236267 129.22891235351562 0.41137564182281494 0.7391563 0.3610835075378418 True -12 14508 12.185376405715942 0.2381913661956787 103.0572738647461 0.45420801639556885 128.9053955078125 0.4129602015018463 0.74532187 0.34795764088630676 True -13 15624 12.174963474273682 0.23851680755615234 110.38047790527344 0.3430621922016144 128.69805908203125 0.41380488872528076 0.74905956 0.3420571982860565 True -14 16740 12.168221950531006 0.23738956451416016 112.99859619140625 0.37971487641334534 128.5503387451172 0.4146013557910919 0.75799847 0.3329346477985382 True -15 17856 12.183366060256958 0.24274778366088867 91.21005249023438 0.3297783136367798 128.50326538085938 0.4144982397556305 0.76141894 0.3295421898365021 True -16 18972 12.165295839309692 0.23787760734558105 93.27569580078125 0.38281917572021484 128.57333374023438 0.4136866629123688 0.7641071 0.33049777150154114 True -17 20088 12.171301364898682 0.2373650074005127 108.06928253173828 0.21432386338710785 128.76100158691406 0.4121420681476593 0.7671769 0.3372097611427307 True -18 21204 12.196143865585327 0.24329829216003418 89.87284851074219 0.23708508908748627 128.95545959472656 0.4108535349369049 0.7670084 0.3422854542732239 False -19 22320 12.175478219985962 1.403437852859497 113.47532653808594 0.2792419493198395 129.1120147705078 0.4098474085330963 0.76636326 0.3474208116531372 False diff --git a/ENCSR940QJU/cherimoya.fold_3.performance.tsv b/ENCSR940QJU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4be81af98b85b904cb2741a5e18e9981abef1a17..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -128.76100158691406 0.4607170522212982 0.4121420383453369 0.07670839875936508 0.7671769261360168 0.7568123936653137 0.3372097611427307 \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_4.evaluate.json b/ENCSR940QJU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index cb6a5a7943ed7b35a826beed6d2db5e0d5b412dd..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF084NMQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_4.fit.json b/ENCSR940QJU/cherimoya.fold_4.fit.json deleted file mode 100644 index b5c00736de4e5df2166ce53419b654d7bc0f435a..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF084NMQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940QJU/cherimoya.fold_4.log b/ENCSR940QJU/cherimoya.fold_4.log deleted file mode 100644 index 47569b5734490a997d5e4ccd6fe78a57108cd1ed..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1135 17.09787917137146 15.88916563987732 95.68352508544922 0.8843948841094971 168.24346923828125 0.2400936335325241 0.56441647 9.56315803527832 True -1 2270 16.86689829826355 15.531021356582642 100.4383544921875 0.5246113538742065 149.0447235107422 0.2946377694606781 0.61159486 4.445771217346191 True -2 3405 13.804634809494019 11.508949995040894 106.13795471191406 0.5421754717826843 140.3011016845703 0.3508242964744568 0.62885076 2.9422147274017334 True -3 4540 14.187256097793579 10.252017736434937 91.44236755371094 0.5204811096191406 134.74847412109375 0.38652899861335754 0.7073763 1.1322931051254272 True -4 5675 12.782653331756592 0.24279546737670898 104.55889892578125 0.4574962258338928 132.419677734375 0.39729928970336914 0.733044 0.6073380708694458 True -5 6810 12.510360956192017 0.23859143257141113 107.98269653320312 0.3741646409034729 131.43463134765625 0.40130364894866943 0.73116714 0.4695039391517639 False -6 7945 12.539252996444702 0.2431333065032959 101.19468688964844 0.45342135429382324 130.89735412597656 0.40376678109169006 0.7353893 0.40643492341041565 True -7 9080 12.523244380950928 0.23794913291931152 89.62730407714844 0.5038718581199646 130.59361267089844 0.40540385246276855 0.7380671 0.3974913954734802 True -8 10215 12.508442401885986 0.24975919723510742 112.98783874511719 0.3958837389945984 130.07847595214844 0.4081694781780243 0.7407579 0.36894530057907104 True -9 11350 12.503873348236084 0.3398263454437256 113.27464294433594 0.4761524796485901 129.73231506347656 0.4101283848285675 0.74845153 0.3465162515640259 True -10 12485 12.525537967681885 0.2446451187133789 104.81768035888672 0.3423920273780823 129.44171142578125 0.4118410646915436 0.7539891 0.3416937291622162 True -11 13620 12.527627229690552 0.24114346504211426 105.315673828125 0.4629536271095276 129.13609313964844 0.413377583026886 0.7606531 0.32567963004112244 True -12 14755 12.519129037857056 0.2412266731262207 90.50241088867188 0.4973215162754059 128.87875366210938 0.41472774744033813 0.7649461 0.31842663884162903 True -13 15890 12.510642528533936 0.2365255355834961 87.77117156982422 0.44507697224617004 128.70132446289062 0.4155436158180237 0.7690412 0.3155840039253235 True -14 17025 12.494385004043579 0.31558728218078613 98.05001068115234 0.24580097198486328 128.56578063964844 0.4162251353263855 0.77411306 0.3153030574321747 True -15 18160 12.529672622680664 15.607871770858765 89.03087615966797 0.15324825048446655 128.54241943359375 0.4161035716533661 0.7785635 0.3191387951374054 True -16 19295 16.918170928955078 6.993894100189209 80.22773742675781 0.45522475242614746 128.64173889160156 0.4151972532272339 0.78109753 0.3253011107444763 True -17 20430 12.532590389251709 0.24697589874267578 106.14559173583984 0.46895161271095276 128.8562774658203 0.41358888149261475 0.78125316 0.33819061517715454 True -18 21565 12.52856183052063 0.2483046054840088 78.21638488769531 0.20447836816310883 129.0514678955078 0.41228511929512024 0.7805276 0.346515417098999 False -19 22700 12.514193058013916 0.24463319778442383 105.66130065917969 0.17279170453548431 129.201171875 0.41131842136383057 0.78101414 0.3540739417076111 False diff --git a/ENCSR940QJU/cherimoya.fold_4.performance.tsv b/ENCSR940QJU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 79d8d8dd3878ce7cbfcf138b17909e06b3632c6a..0000000000000000000000000000000000000000 --- a/ENCSR940QJU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -128.8562774658203 0.46094128489494324 0.41358888149261475 0.0767616257071495 0.7812531590461731 0.7683507204055786 0.33819061517715454 \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_0.evaluate.json b/ENCSR940YDN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d9eebf3b8822c48199ee6b1bda42d9b222f91cb4..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123JOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_0.fit.json b/ENCSR940YDN/cherimoya.fold_0.fit.json deleted file mode 100644 index b7281ac40658106ae16c9ff435bb93a9a2230acb..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF123JOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_0.log b/ENCSR940YDN/cherimoya.fold_0.log deleted file mode 100644 index d65b88bcfd4d97e208897b93779165852f2535d1..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2325 30.19564938545227 3.540452241897583 303.12799072265625 0.8346253633499146 486.5129089355469 0.47651058435440063 0.5290126 8.500377655029297 True -1 4650 25.526870250701904 1.041001319885254 323.1103515625 0.7022208571434021 410.7821960449219 0.6061787605285645 0.6226731 2.289897918701172 True -2 6975 25.51447343826294 0.46079254150390625 328.4439697265625 0.5080767869949341 400.08819580078125 0.6253324747085571 0.61953497 1.0900516510009766 False -3 9300 25.321810007095337 0.495863676071167 298.00018310546875 0.6359447836875916 396.1849670410156 0.6320789456367493 0.6282336 0.8670598268508911 True -4 11625 25.013000965118408 0.46761488914489746 309.5346374511719 0.48049771785736084 393.2459411621094 0.6377946138381958 0.63582677 0.7955358624458313 True -5 13950 25.024649381637573 0.46773338317871094 361.2156677246094 0.5468460917472839 391.8242492675781 0.6411843299865723 0.63732165 0.7571612596511841 True -6 16275 25.42916703224182 4.60313868522644 362.9689636230469 0.5852282047271729 390.4912109375 0.6439136266708374 0.6496216 0.7089675664901733 True -7 18600 25.06970191001892 0.48659825325012207 296.45367431640625 0.5859136581420898 389.9237976074219 0.6453726887702942 0.65084225 0.6868632435798645 True -8 20925 25.045905590057373 0.4639577865600586 350.59765625 0.5411737561225891 388.7572937011719 0.6476472616195679 0.65518534 0.6254364252090454 True -9 23250 25.089519262313843 1.2453820705413818 326.354736328125 0.5617263913154602 387.7239685058594 0.6495893001556396 0.6625421 0.5757505297660828 True -10 25575 25.113181114196777 0.4704709053039551 293.68359375 0.4994966983795166 386.61346435546875 0.6517137885093689 0.6724208 0.55162513256073 True -11 27900 25.07210350036621 0.48593759536743164 324.368408203125 0.5282126069068909 385.2442932128906 0.6536026000976562 0.6793324 0.5195362567901611 True -12 30225 25.047017812728882 0.510953426361084 285.1529846191406 0.4934157729148865 384.3059997558594 0.6556230187416077 0.6877936 0.5043795108795166 True -13 32550 25.053963899612427 11.599080801010132 302.3448486328125 0.46733206510543823 383.28436279296875 0.6573840975761414 0.6962853 0.476889967918396 True -14 34875 25.126347541809082 0.4917433261871338 282.778076171875 0.2558879256248474 382.53826904296875 0.6583746671676636 0.69944286 0.46192753314971924 True -15 37200 25.26376438140869 0.47203731536865234 249.0586395263672 0.4080919027328491 382.4850158691406 0.6590689420700073 0.70681256 0.44643181562423706 True -16 39525 25.08607053756714 0.46624159812927246 314.2325439453125 0.3364383280277252 382.4034729003906 0.6589223146438599 0.7074236 0.45086953043937683 True -17 41850 25.10098671913147 0.46144723892211914 266.1199645996094 0.25710320472717285 382.8231201171875 0.6585528254508972 0.70710605 0.4527590572834015 False -18 44175 25.088768243789673 0.4606282711029053 338.5661315917969 0.24328824877738953 382.82769775390625 0.6578664779663086 0.70140994 0.4649004638195038 False -19 46500 25.072559595108032 0.4725821018218994 297.97235107421875 0.2541780471801758 382.7076416015625 0.6575053930282593 0.69761014 0.47236594557762146 False diff --git a/ENCSR940YDN/cherimoya.fold_0.performance.tsv b/ENCSR940YDN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 85c6155e2fc03d9c537df3f775a116ce4bfb29ea..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -382.4034729003906 0.2802009880542755 0.6589223146438599 0.2507428824901581 0.7074236273765564 0.6678240895271301 0.45086953043937683 \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_1.evaluate.json b/ENCSR940YDN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 35bc17a6f3138a060b70fb62eb40816b1b36c5bb..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123JOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_1.fit.json b/ENCSR940YDN/cherimoya.fold_1.fit.json deleted file mode 100644 index 55f58f5232a96235c4ca0da1f7492634c201f0de..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF123JOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_1.log b/ENCSR940YDN/cherimoya.fold_1.log deleted file mode 100644 index 1ab61624ac22a03a501b75654d760da9d21e7ff2..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2378 31.0297794342041 3.962390422821045 316.40460205078125 0.5618726015090942 484.5028381347656 0.4928765594959259 0.53911865 6.5701375007629395 True -1 4756 26.181673765182495 0.5702643394470215 325.34063720703125 0.67738938331604 419.9783020019531 0.6071451902389526 0.61494255 2.4219284057617188 True -2 7134 26.215320825576782 0.5403211116790771 341.78204345703125 0.9365612268447876 409.29547119140625 0.625977635383606 0.620021 0.8774535655975342 True -3 9512 26.150198698043823 0.552405834197998 279.900146484375 0.6737616062164307 405.08428955078125 0.633861243724823 0.6400627 0.6161389946937561 True -4 11890 26.096768140792847 1.7234835624694824 313.75079345703125 0.5457457304000854 403.9395446777344 0.6370253562927246 0.64469373 0.5963538289070129 True -5 14268 25.73935031890869 0.5222082138061523 332.9833679199219 0.3867490291595459 402.51116943359375 0.6396852731704712 0.6500524 0.6053977608680725 True -6 16646 25.666335105895996 0.522768497467041 373.36773681640625 0.3898518681526184 401.7010803222656 0.641716480255127 0.6581285 0.6033118367195129 True -7 19024 25.632015466690063 14.631937503814697 364.0946044921875 0.6858159303665161 400.4891052246094 0.6441053152084351 0.66682434 0.5519381165504456 True -8 21402 25.69419026374817 0.5310394763946533 281.6097106933594 0.5015004277229309 399.0725402832031 0.6466098427772522 0.67088187 0.5416793823242188 True -9 23780 25.707109212875366 0.5263974666595459 288.45751953125 0.7010000944137573 398.4782409667969 0.6479825377464294 0.6759795 0.5020573735237122 True -10 26158 25.653557062149048 0.5272612571716309 308.40838623046875 0.49531081318855286 397.40521240234375 0.6500071287155151 0.6842293 0.4764605462551117 True -11 28536 25.642704010009766 0.5189220905303955 277.51531982421875 0.3302175998687744 396.6016845703125 0.6518351435661316 0.68866885 0.4647505283355713 True -12 30914 25.65696692466736 0.5320262908935547 307.11614990234375 0.5561061501502991 395.7864685058594 0.6535530686378479 0.69326043 0.4603763520717621 True -13 33292 25.70910620689392 0.5269114971160889 254.83010864257812 0.48994871973991394 394.7462463378906 0.6555670499801636 0.70419276 0.4369252026081085 True -14 35670 25.680849075317383 14.066084861755371 281.9326171875 0.47633516788482666 393.767333984375 0.6567681431770325 0.71237504 0.42191702127456665 True -15 38048 26.119980573654175 0.8845119476318359 287.189697265625 0.5747453570365906 393.4200134277344 0.6576743125915527 0.715563 0.4212636351585388 True -16 40426 25.669721126556396 0.5253770351409912 311.3277893066406 0.21982838213443756 393.12628173828125 0.6578607559204102 0.71917677 0.41366374492645264 True -17 42804 25.657127380371094 0.5270211696624756 285.09381103515625 0.27569252252578735 393.09515380859375 0.657588005065918 0.7158232 0.4174044728279114 False -18 45182 25.63748788833618 0.5178229808807373 269.0243225097656 0.29265010356903076 393.2935485839844 0.6570035815238953 0.71342313 0.4259195327758789 False -19 47560 25.61121678352356 0.5087125301361084 308.1078796386719 0.31745630502700806 393.4812316894531 0.6566166877746582 0.7106136 0.43017998337745667 False diff --git a/ENCSR940YDN/cherimoya.fold_1.performance.tsv b/ENCSR940YDN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 920be96c8dd1065f3040293668b7975a1ae7a7af..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -393.12628173828125 0.2776445150375366 0.6578608155250549 0.25859346985816956 0.7191767692565918 0.7063717246055603 0.41366374492645264 \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_2.evaluate.json b/ENCSR940YDN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8f2ae6976541cc12bc0c80c94f8c593479d3bd11..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123JOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_2.fit.json b/ENCSR940YDN/cherimoya.fold_2.fit.json deleted file mode 100644 index 6616251db9fc225a7d8a5cd79564a9b3cb2bd16b..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF123JOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_2.log b/ENCSR940YDN/cherimoya.fold_2.log deleted file mode 100644 index 6431fd19a40e0a3c3cd773d17399f0d682800c27..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2480 32.256526708602905 3.743558168411255 292.3619079589844 0.41437727212905884 476.9672546386719 0.489057719707489 0.5495841 7.861326694488525 True -1 4960 27.2795307636261 11.881718397140503 281.6730041503906 0.8569930791854858 410.9556884765625 0.6093001365661621 0.6258956 2.3428468704223633 True -2 7440 27.28521490097046 0.47110724449157715 292.751708984375 1.0025782585144043 401.4490661621094 0.6245872378349304 0.62705505 0.7913808226585388 True -3 9920 27.248403310775757 0.4871797561645508 325.45135498046875 0.6342251896858215 397.2741394042969 0.6315540671348572 0.6340841 0.6870477795600891 True -4 12400 27.2797634601593 0.46445751190185547 318.027099609375 0.6946760416030884 395.6760559082031 0.6344619989395142 0.64595085 0.7034513354301453 True -5 14880 27.368475675582886 0.9572193622589111 346.2300109863281 0.7835608720779419 394.864990234375 0.6363409757614136 0.6562986 0.6810452938079834 True -6 17360 27.387701272964478 0.4788064956665039 267.3531494140625 0.6500791311264038 393.35626220703125 0.6393371224403381 0.6597041 0.6535952091217041 True -7 19840 27.39889883995056 0.4516110420227051 289.1160583496094 0.4401710629463196 392.1636657714844 0.6414984464645386 0.6642296 0.6136481165885925 True -8 22320 27.4424467086792 0.46274375915527344 276.9227294921875 0.40100863575935364 391.0526123046875 0.6437121629714966 0.67261887 0.6007140278816223 True -9 24800 27.411194562911987 1.4144814014434814 318.48480224609375 0.7596149444580078 389.6424560546875 0.6462167501449585 0.67785394 0.5474411845207214 True -10 27280 26.912556648254395 0.44965434074401855 350.53839111328125 0.6517646908760071 388.35235595703125 0.6483993530273438 0.6872876 0.5210948586463928 True -11 29760 26.818013906478882 0.4374363422393799 296.78350830078125 0.44990643858909607 387.2998962402344 0.6504092812538147 0.6908839 0.5081032514572144 True -12 32240 26.790626287460327 0.4593019485473633 286.287353515625 0.32484865188598633 386.3547668457031 0.6521754264831543 0.69474286 0.48501214385032654 True -13 34720 26.77311062812805 0.45131897926330566 304.0805358886719 0.38260990381240845 385.5096435546875 0.6537348628044128 0.6983701 0.47645220160484314 True -14 37200 26.769951343536377 0.4450709819793701 298.9148864746094 0.34093862771987915 384.8199462890625 0.654666006565094 0.707279 0.4692217707633972 True -15 39680 26.857560873031616 0.4561142921447754 290.64093017578125 0.48367545008659363 384.3660583496094 0.6554384827613831 0.7093536 0.4561153054237366 True -16 42160 26.84481716156006 0.4367947578430176 308.2637939453125 0.3263530135154724 384.22222900390625 0.6554792523384094 0.7127604 0.4554450213909149 True -17 44640 26.750359296798706 0.44179248809814453 326.7688293457031 0.3041853904724121 384.2749328613281 0.6551445722579956 0.71188253 0.4563286006450653 False -18 47120 26.778145790100098 0.44684290885925293 336.077392578125 0.2145276665687561 384.58819580078125 0.654633104801178 0.7080847 0.4651869237422943 False -19 49600 26.785362005233765 0.45615077018737793 277.65032958984375 0.32609251141548157 384.76837158203125 0.6540694236755371 0.7046168 0.4738810360431671 False diff --git a/ENCSR940YDN/cherimoya.fold_2.performance.tsv b/ENCSR940YDN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 35c7832085265dca7290b3dfab06acc0eb3507ab..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -384.22222900390625 0.2813434898853302 0.6554792523384094 0.25583457946777344 0.7127603888511658 0.6813125610351562 0.4554450213909149 \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_3.evaluate.json b/ENCSR940YDN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0afd825365d0f87daaa8ea863bc7a4493467de52..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123JOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_3.fit.json b/ENCSR940YDN/cherimoya.fold_3.fit.json deleted file mode 100644 index 4e6fe2adf06654777cdd06713da21d4dc0c12154..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF123JOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_3.log b/ENCSR940YDN/cherimoya.fold_3.log deleted file mode 100644 index 53d4c191d47cf5256c1d259962d15812cf385db7..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2420 31.70608162879944 3.5108730792999268 255.61573791503906 0.7902871370315552 483.20233154296875 0.4887980818748474 0.52855974 8.195980072021484 True -1 4840 26.59866976737976 0.6238887310028076 350.2232666015625 0.8536249399185181 413.52545166015625 0.6117628812789917 0.60035545 2.5160176753997803 True -2 7260 26.62475085258484 0.5333924293518066 340.65704345703125 0.6013753414154053 403.69580078125 0.626226544380188 0.6055321 1.0740841627120972 True -3 9680 26.57292628288269 0.5139069557189941 331.93218994140625 0.6007390022277832 399.58502197265625 0.6335871815681458 0.621368 0.8788555264472961 True -4 12100 26.598721027374268 0.5164022445678711 309.2517395019531 0.5806840062141418 397.361328125 0.6375710368156433 0.6371888 0.7559017539024353 True -5 14520 26.62502884864807 0.523259162902832 257.55242919921875 0.5223057866096497 395.983154296875 0.6403286457061768 0.6431501 0.7237659692764282 True -6 16940 26.638477563858032 0.518322229385376 286.4206848144531 0.7064043283462524 394.9715576171875 0.642551064491272 0.64860165 0.7015224099159241 True -7 19360 26.617706537246704 0.5169448852539062 296.7519226074219 0.6842026114463806 394.0225830078125 0.6442628502845764 0.6544511 0.6416977047920227 True -8 21780 26.621970653533936 0.5115833282470703 288.7752990722656 0.4184723496437073 392.89642333984375 0.6460625529289246 0.6545576 0.6457188129425049 True -9 24200 26.616636514663696 0.5162458419799805 296.33740234375 0.4358136057853699 392.3256530761719 0.6481748819351196 0.6657195 0.6015545725822449 True -10 26620 26.607282161712646 0.5180175304412842 292.0831298828125 0.5236541032791138 390.7426452636719 0.6504910588264465 0.67362654 0.5583693385124207 True -11 29040 26.62778329849243 0.5195131301879883 310.8204345703125 0.4561833143234253 389.75189208984375 0.6524553894996643 0.6826353 0.5283344984054565 True -12 31460 26.363592386245728 0.588977575302124 302.37030029296875 0.2803497314453125 388.3092346191406 0.6543557047843933 0.68938047 0.4976014196872711 True -13 33880 26.04946780204773 0.9997730255126953 283.7005615234375 0.3819468915462494 387.9073181152344 0.6556422114372253 0.69662356 0.4755592942237854 True -14 36300 26.06496286392212 0.5133514404296875 269.7618408203125 0.3264349699020386 387.20196533203125 0.6569663882255554 0.70585555 0.45536646246910095 True -15 38720 26.05375385284424 0.5178031921386719 276.5334777832031 0.39613741636276245 386.01837158203125 0.6578355431556702 0.7119305 0.44488710165023804 True -16 41140 26.055321216583252 0.515103816986084 242.0789031982422 0.31805479526519775 386.95220947265625 0.6579293012619019 0.71387655 0.448115736246109 True -17 43560 26.089736700057983 0.5014283657073975 289.9460144042969 0.30567222833633423 386.80499267578125 0.6575612425804138 0.7141146 0.45154696702957153 True -18 45980 26.081602096557617 9.06779146194458 333.6617736816406 0.17346139252185822 386.7054443359375 0.6570693850517273 0.7107387 0.462636798620224 False -19 48400 26.106968641281128 0.5289313793182373 324.4040832519531 0.23384281992912292 387.06781005859375 0.6567023396492004 0.70699364 0.4667345881462097 False diff --git a/ENCSR940YDN/cherimoya.fold_3.performance.tsv b/ENCSR940YDN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4cdfd6408d6b4cedcb03c1f2bd866216d91dc59d..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -386.80499267578125 0.2793961763381958 0.6575612425804138 0.25432536005973816 0.7141146063804626 0.6830431222915649 0.45154696702957153 \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_4.evaluate.json b/ENCSR940YDN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index a67385bf7e3351278ad99502421b00f9b9b88963..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF123JOI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_4.fit.json b/ENCSR940YDN/cherimoya.fold_4.fit.json deleted file mode 100644 index 89ce60d7f4432b87e73c1caad51458f3594db02a..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF123JOI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR940YDN/cherimoya.fold_4.log b/ENCSR940YDN/cherimoya.fold_4.log deleted file mode 100644 index 1e13b860c609cd1a28ef154a1561931e5c3fe4a5..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2478 32.12844753265381 3.5495243072509766 306.6298828125 0.7493254542350769 484.4548034667969 0.48843881487846375 0.56623656 5.384922504425049 True -1 4956 27.25804901123047 0.5363152027130127 348.12078857421875 0.7102200984954834 416.0904846191406 0.6153945326805115 0.6064765 2.311253309249878 True -2 7434 27.206321954727173 0.47741103172302246 334.7500915527344 0.6245628595352173 405.4461975097656 0.6314699649810791 0.61653924 0.9101485013961792 True -3 9912 27.2276508808136 11.040572166442871 261.30328369140625 0.5229178667068481 401.689453125 0.638357937335968 0.63856786 0.7069951295852661 True -4 12390 27.205070734024048 0.47500157356262207 289.00732421875 0.6399601697921753 399.855224609375 0.6421487331390381 0.64373577 0.7140443921089172 True -5 14868 27.204150676727295 15.043750047683716 323.20782470703125 0.4199489951133728 398.7865905761719 0.6446399092674255 0.6479958 0.6517223119735718 True -6 17346 27.33752942085266 0.47649097442626953 338.821533203125 0.4094325304031372 397.5508117675781 0.6472622752189636 0.65379834 0.6412286758422852 True -7 19824 27.274384021759033 0.475250244140625 309.32171630859375 0.530571699142456 396.123291015625 0.649989128112793 0.659905 0.6085968613624573 True -8 22302 27.255078554153442 0.47554826736450195 309.015869140625 0.42599254846572876 394.945556640625 0.652101457118988 0.66369575 0.5700445175170898 True -9 24780 27.33448028564453 0.475161075592041 307.1719970703125 0.4925302565097809 393.9193115234375 0.6539391875267029 0.6682773 0.5138823986053467 True -10 27258 27.264262676239014 0.47300243377685547 326.7926330566406 0.5317715406417847 392.8590087890625 0.6562491059303284 0.6740684 0.5053321123123169 True -11 29736 27.29001808166504 0.6572844982147217 258.8255615234375 0.4349743127822876 392.0128479003906 0.6579374074935913 0.6840228 0.4942363500595093 True -12 32214 26.82175922393799 0.4648401737213135 376.25299072265625 0.6912171840667725 390.8833923339844 0.6599870920181274 0.6901177 0.4826675355434418 True -13 34692 26.784883975982666 0.46991848945617676 272.877197265625 0.4679304361343384 390.26806640625 0.6611396670341492 0.6947999 0.48004400730133057 True -14 37170 26.741291522979736 0.4745521545410156 295.1234130859375 0.2899472415447235 389.487548828125 0.6624327898025513 0.70383275 0.46731072664260864 True -15 39648 26.715559005737305 0.46877551078796387 324.2694091796875 0.32797956466674805 389.02423095703125 0.6631843447685242 0.70863605 0.451099693775177 True -16 42126 26.738925218582153 0.4691338539123535 315.32391357421875 0.3229376971721649 388.8101806640625 0.6630858182907104 0.71333766 0.44340434670448303 True -17 44604 26.786875009536743 0.47268056869506836 298.81280517578125 0.36701709032058716 388.8495178222656 0.6627534031867981 0.71191245 0.4489234685897827 False -18 47082 26.741851568222046 0.4677293300628662 273.5989685058594 0.23187357187271118 389.2165222167969 0.6620124578475952 0.707951 0.46021920442581177 False -19 49560 26.741878271102905 0.47623705863952637 262.98516845703125 0.268044650554657 389.35247802734375 0.6616368889808655 0.703745 0.46735215187072754 False diff --git a/ENCSR940YDN/cherimoya.fold_4.performance.tsv b/ENCSR940YDN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 55048bc8e5e99384419c6bd6350e9a1f78b9061d..0000000000000000000000000000000000000000 --- a/ENCSR940YDN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -388.8101806640625 0.2772740423679352 0.6630857586860657 0.25784754753112793 0.7133376598358154 0.6679521799087524 0.44340434670448303 \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_0.evaluate.json b/ENCSR941DTJ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e8a70d6d819390c9488dd29e0f799decb2bdcd74..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131SQK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_0.fit.json b/ENCSR941DTJ/cherimoya.fold_0.fit.json deleted file mode 100644 index 849c7f2d90a214dde52cba38951adeaafe14b4ad..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF131SQK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_0.log b/ENCSR941DTJ/cherimoya.fold_0.log deleted file mode 100644 index 43248634b5ea3e6c0c6300262190dd3b4b85fc6c..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.90868282318115 2.6400649547576904 240.36883544921875 0.6649600267410278 236.86260986328125 0.1454807072877884 0.72923225 2.5739128589630127 True -1 5514 30.26858425140381 0.5658106803894043 153.38307189941406 0.5684471130371094 226.22308349609375 0.19324439764022827 0.7821356 1.0084456205368042 True -2 8271 30.224265575408936 0.5558269023895264 193.09669494628906 0.4996947944164276 223.1936798095703 0.20392708480358124 0.7906771 0.6022655963897705 True -3 11028 30.213303089141846 0.5508170127868652 170.90736389160156 0.5391085147857666 221.31643676757812 0.21120363473892212 0.7958626 0.5766709446907043 True -4 13785 30.212164163589478 0.982194185256958 180.63272094726562 0.5988037586212158 220.63412475585938 0.21244485676288605 0.7960658 0.5502651929855347 True -5 16542 30.26162099838257 0.5249416828155518 178.43710327148438 0.49799466133117676 220.06910705566406 0.2152966558933258 0.7994949 0.5212185382843018 True -6 19299 29.63214898109436 0.5196537971496582 188.86289978027344 0.5000317096710205 219.56851196289062 0.21812212467193604 0.804522 0.5415141582489014 True -7 22056 29.697237491607666 0.5750460624694824 139.63101196289062 0.6626297235488892 218.95208740234375 0.22113360464572906 0.8074257 0.5274929404258728 True -8 24813 29.6140456199646 0.536142110824585 183.1695556640625 0.3684408664703369 218.1203155517578 0.22526706755161285 0.8128778 0.4966592490673065 True -9 27570 29.694055557250977 0.5062940120697021 186.8980712890625 0.2760505974292755 218.07872009277344 0.22535888850688934 0.81551594 0.5029043555259705 True -10 30327 29.656754732131958 0.531184196472168 190.8410186767578 0.5363841652870178 217.5241241455078 0.22676317393779755 0.81712 0.4623762369155884 True -11 33084 29.649927377700806 0.5064349174499512 177.54519653320312 0.3817363977432251 217.33091735839844 0.22794678807258606 0.820757 0.4467496871948242 True -12 35841 29.685596704483032 0.5255470275878906 164.50428771972656 0.4167380928993225 216.690185546875 0.2308458536863327 0.8257499 0.41481783986091614 True -13 38598 29.689777851104736 0.509864330291748 168.93771362304688 0.40663397312164307 216.32061767578125 0.23233158886432648 0.8304706 0.3808675706386566 True -14 41355 29.686350345611572 0.5318005084991455 185.2833251953125 0.3945125937461853 216.30564880371094 0.2327340841293335 0.83505565 0.34074676036834717 True -15 44112 29.691272258758545 0.5328829288482666 194.7515869140625 0.24291560053825378 215.8468475341797 0.2344163954257965 0.83933246 0.3162875473499298 True -16 46869 29.70016622543335 0.5097477436065674 165.04324340820312 0.3206416666507721 215.76199340820312 0.23505651950836182 0.840537 0.29709964990615845 True -17 49626 29.832738399505615 0.5377001762390137 137.2278594970703 0.29182854294776917 216.0982208251953 0.23264792561531067 0.8426513 0.2880445718765259 True -18 52383 29.7536563873291 0.6211996078491211 177.58934020996094 0.24452772736549377 216.2742462158203 0.23241083323955536 0.84060824 0.28411227464675903 False -19 55140 29.719713926315308 0.5348973274230957 151.48626708984375 0.21734696626663208 215.7714385986328 0.23552368581295013 0.8404535 0.2856859862804413 False diff --git a/ENCSR941DTJ/cherimoya.fold_0.performance.tsv b/ENCSR941DTJ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a68e7dfd39cb1e6cb35172faeb1a50a8d1e710db..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -216.0982208251953 0.5361141562461853 0.23264791071414948 0.05282937362790108 0.8426513075828552 0.761842668056488 0.2880445718765259 \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_1.evaluate.json b/ENCSR941DTJ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 836b4444281de0492e5bb04b3998693ba7e8ea7a..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131SQK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_1.fit.json b/ENCSR941DTJ/cherimoya.fold_1.fit.json deleted file mode 100644 index bf812b2f27e9e4b547e5957d7cb1f65904c2bbb2..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF131SQK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_1.log b/ENCSR941DTJ/cherimoya.fold_1.log deleted file mode 100644 index f02fd8bd1ed2853b6b5144a405ab1cbc84e1c5d8..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 34.07766103744507 4.73475456237793 169.1832733154297 0.622805118560791 281.2019958496094 0.15726308524608612 0.71852714 3.225893497467041 True -1 5410 29.707408905029297 0.7538635730743408 156.54833984375 0.48785242438316345 265.5898742675781 0.21524584293365479 0.7891216 1.0094717741012573 True -2 8115 29.72119903564453 0.7045958042144775 156.49285888671875 0.6903374791145325 261.9779968261719 0.2273196578025818 0.801905 0.6103259921073914 True -3 10820 29.90799379348755 4.153485536575317 154.63626098632812 0.547661542892456 260.0374755859375 0.23129910230636597 0.80599916 0.5685248970985413 True -4 13525 29.68530774116516 0.7689921855926514 180.63514709472656 0.5227146744728088 258.9315185546875 0.23438331484794617 0.806881 0.5687021613121033 True -5 16230 29.721806526184082 0.7129397392272949 169.71487426757812 0.5462309718132019 257.849365234375 0.23833297193050385 0.8097692 0.5654227137565613 True -6 18935 29.687073469161987 0.7117011547088623 162.44210815429688 0.3737363815307617 257.0548400878906 0.2412998080253601 0.81374586 0.5721346139907837 True -7 21640 29.733067274093628 8.426430940628052 171.8507843017578 0.4726572632789612 256.3456726074219 0.2439354956150055 0.8185203 0.5562163591384888 True -8 24345 29.427846431732178 0.6817741394042969 200.05792236328125 0.43818360567092896 255.57437133789062 0.24640345573425293 0.82153285 0.5136914849281311 True -9 27050 29.11576747894287 0.6912648677825928 116.05012512207031 0.44646546244621277 255.24630737304688 0.24788789451122284 0.82476 0.47457680106163025 True -10 29755 29.17550802230835 0.6942646503448486 192.07101440429688 0.2678889036178589 254.47511291503906 0.25068655610084534 0.8291506 0.4547790586948395 True -11 32460 29.13374137878418 2.68031907081604 177.92788696289062 0.4102107286453247 253.76414489746094 0.25335028767585754 0.8349017 0.4302442967891693 True -12 35165 29.121757984161377 0.7179875373840332 208.63726806640625 0.3818157911300659 253.4530029296875 0.2543399930000305 0.8399429 0.4013633728027344 True -13 37870 29.247960567474365 1.1767971515655518 160.69166564941406 0.3875437378883362 253.00071716308594 0.25577259063720703 0.8459357 0.36890077590942383 True -14 40575 29.160608291625977 0.6992554664611816 142.1535186767578 0.3127923011779785 252.68971252441406 0.25652197003364563 0.8487363 0.3578431308269501 True -15 43280 29.27032780647278 1.830733060836792 177.83531188964844 0.26817870140075684 252.07830810546875 0.25897496938705444 0.8515432 0.34114155173301697 True -16 45985 29.346466541290283 0.7226836681365967 190.57049560546875 0.29234471917152405 252.6612548828125 0.25647634267807007 0.8558634 0.318157821893692 True -17 48690 29.278162240982056 0.6840741634368896 166.16372680664062 0.20691657066345215 252.6008758544922 0.2570044994354248 0.8586655 0.3078063428401947 True -18 51395 29.28405523300171 0.7073380947113037 148.55125427246094 0.29129087924957275 252.61187744140625 0.2566547393798828 0.85762036 0.305221289396286 False -19 54100 29.250718593597412 1.4407532215118408 170.4156951904297 0.2398444414138794 252.49728393554688 0.25735753774642944 0.8551466 0.306048184633255 False diff --git a/ENCSR941DTJ/cherimoya.fold_1.performance.tsv b/ENCSR941DTJ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 89c0e82ee49fc33171376c7725b6562e7a84a0c0..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -252.6008758544922 0.5160152912139893 0.2570044994354248 0.06707870960235596 0.8586655259132385 0.8070813417434692 0.3078063428401947 \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_2.evaluate.json b/ENCSR941DTJ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 2fd475dbeb43dad60e97bd57dd8dd562e3468b04..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131SQK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_2.fit.json b/ENCSR941DTJ/cherimoya.fold_2.fit.json deleted file mode 100644 index 7da5a68fab9ad21cdf4ab1d3d9c5a84f8f7f6c47..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF131SQK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_2.log b/ENCSR941DTJ/cherimoya.fold_2.log deleted file mode 100644 index a4dbbdbd3942db93c6ce3dc61e3bb2348235b04e..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.13522434234619 4.1164491176605225 186.82049560546875 0.6083094477653503 247.9559326171875 0.15022778511047363 0.72331256 2.6288113594055176 True -1 5744 31.507619380950928 0.6067392826080322 204.6426239013672 0.7046434879302979 234.685546875 0.20041389763355255 0.7886238 0.9349366426467896 True -2 8616 31.512561321258545 0.5519917011260986 168.42971801757812 0.38559335470199585 231.73410034179688 0.2096458226442337 0.7977108 0.5149509906768799 True -3 11488 31.533974170684814 0.5498886108398438 146.16311645507812 0.4066201448440552 230.10940551757812 0.21569685637950897 0.8033124 0.42791786789894104 True -4 14360 31.53752589225769 0.5558197498321533 223.39181518554688 0.5574448108673096 229.32313537597656 0.21940450370311737 0.8071119 0.4500575363636017 True -5 17232 31.488353967666626 0.5475683212280273 163.83554077148438 0.5317966938018799 228.5967559814453 0.2221532016992569 0.808263 0.4201684892177582 True -6 20104 31.547585487365723 14.110787391662598 164.93154907226562 0.428609699010849 228.14013671875 0.22337734699249268 0.8099506 0.4011206328868866 True -7 22976 31.61972165107727 0.563758373260498 160.39840698242188 0.3929371237754822 227.2879180908203 0.2269952893257141 0.8148323 0.4026288390159607 True -8 25848 31.15132975578308 10.440986394882202 196.13787841796875 0.468678742647171 227.0142059326172 0.22879943251609802 0.8180489 0.3943677842617035 True -9 28720 30.920330047607422 0.5513782501220703 154.027099609375 0.48863840103149414 226.693359375 0.2295277714729309 0.8208932 0.3775297999382019 True -10 31592 30.918835163116455 0.5527899265289307 175.48533630371094 0.4260331988334656 225.8385772705078 0.2333754301071167 0.82313395 0.3687911629676819 True -11 34464 30.8898823261261 0.5533924102783203 147.05088806152344 0.4915179908275604 225.06893920898438 0.23668009042739868 0.8267275 0.3651357591152191 True -12 37336 30.897602558135986 0.5364458560943604 166.78982543945312 0.3433381915092468 225.18077087402344 0.2350788563489914 0.8312223 0.343603253364563 True -13 40208 30.92513632774353 0.5383479595184326 208.2692413330078 0.5048197507858276 224.65162658691406 0.23823241889476776 0.8348247 0.33722051978111267 True -14 43080 30.91362476348877 0.5472476482391357 158.02450561523438 0.3127426505088806 224.6664276123047 0.2373536080121994 0.83887106 0.32741042971611023 True -15 45952 30.965579986572266 0.5450942516326904 173.55455017089844 0.2963636815547943 224.21717834472656 0.23888786137104034 0.8423477 0.30786144733428955 True -16 48824 30.941776990890503 0.5514678955078125 161.49801635742188 0.18512201309204102 223.83583068847656 0.24049422144889832 0.8457599 0.2981199622154236 True -17 51696 30.91658067703247 0.5422625541687012 164.49746704101562 0.20857134461402893 224.00839233398438 0.23988725244998932 0.8462498 0.2938452661037445 True -18 54568 30.999653816223145 0.5510721206665039 176.1964569091797 0.25605154037475586 224.2360382080078 0.23842482268810272 0.8443026 0.294651597738266 False -19 57440 31.004045724868774 0.5497581958770752 148.82379150390625 0.19405794143676758 224.12705993652344 0.239426389336586 0.8448251 0.29642370343208313 False diff --git a/ENCSR941DTJ/cherimoya.fold_2.performance.tsv b/ENCSR941DTJ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index d9cfb0af98f2147431eb325f02191f6ae6689cef..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -224.00839233398438 0.5309990644454956 0.23988725244998932 0.06059524789452553 0.8462498188018799 0.7844459414482117 0.2938452661037445 \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_3.evaluate.json b/ENCSR941DTJ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cab5b7205b7977b047830601d125145455444f4b..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131SQK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_3.fit.json b/ENCSR941DTJ/cherimoya.fold_3.fit.json deleted file mode 100644 index 7e5105a4d12d4d83b7abb856b80a6c735d4d7ca3..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF131SQK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_3.log b/ENCSR941DTJ/cherimoya.fold_3.log deleted file mode 100644 index 7edf8a8e62825134a2007307a6ba36b982036c32..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.96385860443115 3.8125388622283936 183.75221252441406 0.4884951114654541 244.4370880126953 0.14769487082958221 0.7291913 2.1729886531829834 True -1 5492 30.141162633895874 0.6044683456420898 206.9597625732422 0.6047701835632324 232.3136444091797 0.19751134514808655 0.7829008 0.9646525382995605 True -2 8238 30.154139518737793 0.5523722171783447 181.6856689453125 0.5502444505691528 229.70278930664062 0.20751425623893738 0.79355776 0.6182606220245361 True -3 10984 30.140096187591553 0.5617918968200684 188.48428344726562 0.2932586073875427 227.61260986328125 0.21550874412059784 0.79809153 0.572520911693573 True -4 13730 30.566915035247803 1.8078436851501465 194.3648681640625 0.6875855922698975 227.38116455078125 0.21541517972946167 0.8024781 0.5978705286979675 True -5 16476 30.288344860076904 1.146965503692627 169.321044921875 0.4928930401802063 226.74790954589844 0.21729283034801483 0.8068851 0.5118983387947083 True -6 19222 30.206114768981934 0.5564537048339844 121.43348693847656 0.5721402168273926 226.04754638671875 0.22015705704689026 0.80638266 0.5045729875564575 False -7 21968 29.895877599716187 0.5511317253112793 113.6357421875 0.39364486932754517 225.27218627929688 0.2243480086326599 0.8099991 0.5169561505317688 True -8 24714 29.68147873878479 0.552241325378418 149.1868896484375 0.44834864139556885 224.97662353515625 0.22545216977596283 0.81533885 0.47764912247657776 True -9 27460 29.623920917510986 0.5368008613586426 184.359375 0.5304512977600098 224.64767456054688 0.22684429585933685 0.8181663 0.4397248327732086 True -10 30206 29.549063205718994 0.5542502403259277 159.39834594726562 0.37128061056137085 224.1977081298828 0.22839616239070892 0.8210992 0.4124520421028137 True -11 32952 29.56831431388855 0.5596020221710205 175.10882568359375 0.34888067841529846 223.76271057128906 0.22998395562171936 0.82535446 0.4065355658531189 True -12 35698 29.56118893623352 0.5532572269439697 174.8758544921875 0.2852708399295807 223.28182983398438 0.2320980429649353 0.82991135 0.37806636095046997 True -13 38444 29.64358687400818 0.5513956546783447 210.670654296875 0.3872809410095215 222.87188720703125 0.23454558849334717 0.83341974 0.36387714743614197 True -14 41190 29.644801378250122 0.5851268768310547 228.89437866210938 0.5834050178527832 222.63548278808594 0.23497377336025238 0.8371372 0.34470000863075256 True -15 43936 29.58367085456848 0.5369818210601807 157.82933044433594 0.3033595681190491 222.46485900878906 0.23554785549640656 0.84297514 0.32499298453330994 True -16 46682 29.59195590019226 0.5425143241882324 185.13275146484375 0.2909049391746521 222.58433532714844 0.23452024161815643 0.84546065 0.3171190321445465 True -17 49428 29.5908100605011 0.5563349723815918 160.80384826660156 0.30064457654953003 222.5800018310547 0.23483452200889587 0.8444431 0.3084932267665863 False -18 52174 29.62408208847046 0.5586497783660889 211.11453247070312 0.32840168476104736 222.4842987060547 0.23590274155139923 0.8441686 0.307000070810318 False -19 54920 29.63320827484131 0.5549156665802002 129.02552795410156 0.31913405656814575 222.51512145996094 0.2357000857591629 0.84186363 0.30743613839149475 False diff --git a/ENCSR941DTJ/cherimoya.fold_3.performance.tsv b/ENCSR941DTJ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index cf7fb3457cf7c0ace9d6be8d4c6d3e9d0f43d625..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -222.58433532714844 0.5338227152824402 0.23452024161815643 0.054597433656454086 0.8454606533050537 0.7571609616279602 0.3171190321445465 \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_4.evaluate.json b/ENCSR941DTJ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fc90683eb68cfb61b95a7bafcea956a807e2c893..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF131SQK.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_4.fit.json b/ENCSR941DTJ/cherimoya.fold_4.fit.json deleted file mode 100644 index d82afdd564ed9001d904c43001b2be2bbca3b32d..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF131SQK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR941DTJ/cherimoya.fold_4.log b/ENCSR941DTJ/cherimoya.fold_4.log deleted file mode 100644 index b7023c8dce13a26da038dd8eec4e01314cd1d375..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 35.61768388748169 3.9766461849212646 162.26023864746094 0.36129412055015564 228.07666015625 0.14244471490383148 0.7199883 2.495976686477661 True -1 5606 30.7801570892334 0.6357245445251465 193.19601440429688 0.7636326551437378 217.72828674316406 0.1885945200920105 0.77409035 0.7681809663772583 True -2 8409 30.772188425064087 0.6139209270477295 153.7015838623047 0.473891943693161 214.6344451904297 0.2005206197500229 0.7838863 0.6456882357597351 True -3 11212 30.769410848617554 0.5976400375366211 166.5646514892578 0.3416823744773865 213.39881896972656 0.20484760403633118 0.7920612 0.5327757596969604 True -4 14015 30.79843282699585 0.598952054977417 208.37100219726562 0.5653008222579956 212.9108428955078 0.20589780807495117 0.7899518 0.5072831511497498 False -5 16818 31.20706009864807 11.293473482131958 196.63314819335938 0.449616938829422 212.65176391601562 0.20749863982200623 0.79216105 0.4619666337966919 True -6 19621 30.793394804000854 1.2683053016662598 156.0695037841797 0.37143000960350037 211.53758239746094 0.21273991465568542 0.79709005 0.473400741815567 True -7 22424 30.369331121444702 0.591519832611084 153.78228759765625 0.3965158462524414 211.45462036132812 0.2129019945859909 0.79875267 0.438030868768692 True -8 25227 30.160470485687256 0.6073570251464844 201.20187377929688 0.38394230604171753 210.93675231933594 0.215399369597435 0.803646 0.4227534234523773 True -9 28030 30.1054584980011 0.6071250438690186 165.5306396484375 0.41329869627952576 210.61083984375 0.21642811596393585 0.80535173 0.42520013451576233 True -10 30833 30.164000272750854 0.608116626739502 183.3280487060547 0.412461519241333 210.63735961914062 0.2167409211397171 0.8117438 0.39358434081077576 True -11 33636 30.205939292907715 9.846503257751465 183.76931762695312 0.3169216513633728 210.17185974121094 0.21873678267002106 0.81585914 0.381514310836792 True -12 36439 30.195677280426025 0.606020450592041 134.35299682617188 0.34255450963974 209.56056213378906 0.2210630476474762 0.8198482 0.3718835711479187 True -13 39242 30.188196659088135 0.6096353530883789 143.1829833984375 0.31874266266822815 209.17953491210938 0.2227940708398819 0.82294106 0.3527480661869049 True -14 42045 30.17297077178955 0.615525484085083 143.5518035888672 0.3165472745895386 208.94395446777344 0.22424761950969696 0.82834107 0.3329702615737915 True -15 44848 30.175769805908203 0.5994267463684082 156.15594482421875 0.3419059216976166 208.8807830810547 0.22403773665428162 0.8335468 0.31358152627944946 True -16 47651 30.193657159805298 0.6143839359283447 154.90525817871094 0.3674701452255249 208.84715270996094 0.22409415245056152 0.836724 0.28960850834846497 True -17 50454 30.18693232536316 0.598747730255127 183.5977020263672 0.24052874743938446 208.76937866210938 0.22529719769954681 0.8375113 0.2797013819217682 True -18 53257 30.165555715560913 0.5931305885314941 171.63174438476562 0.2949694097042084 208.7977294921875 0.22514468431472778 0.83770764 0.2785433530807495 True -19 56060 30.132290363311768 0.6108145713806152 140.39015197753906 0.20705491304397583 208.8526153564453 0.2249029278755188 0.8346731 0.2792122960090637 False diff --git a/ENCSR941DTJ/cherimoya.fold_4.performance.tsv b/ENCSR941DTJ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 50496d613a879de639c95a1ca2051cbecd8932d6..0000000000000000000000000000000000000000 --- a/ENCSR941DTJ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -208.7977294921875 0.5415964126586914 0.22514469921588898 0.05587397515773773 0.8377076387405396 0.7453121542930603 0.2785433530807495 \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_0.evaluate.json b/ENCSR943BCO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 14c0d8d150085facf4fa86c381ab5fad1dcf0501..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498LOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_0.fit.json b/ENCSR943BCO/cherimoya.fold_0.fit.json deleted file mode 100644 index dd74ed52ebba01f349396fa9239c9b06ec11edee..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF498LOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_0.log b/ENCSR943BCO/cherimoya.fold_0.log deleted file mode 100644 index 496104f18de8f7ea6ce1d554ee2f4470b7abdab9..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2723 34.45863580703735 2.155564308166504 168.7119903564453 0.559178352355957 178.70169067382812 0.1280050128698349 0.7384247 2.7118802070617676 True -1 5446 30.093077898025513 0.5609636306762695 156.31912231445312 0.2842654585838318 166.21400451660156 0.16238512098789215 0.7996108 1.1584144830703735 True -2 8169 30.045149564743042 0.5103330612182617 124.58100891113281 0.4406405985355377 164.89096069335938 0.1649157702922821 0.78723496 0.7833431959152222 False -3 10892 29.99589776992798 0.5178096294403076 151.73228454589844 0.7353830337524414 162.9129638671875 0.1685454249382019 0.80570984 0.6135521531105042 True -4 13615 29.985575675964355 0.5184228420257568 141.78126525878906 0.45647621154785156 162.12289428710938 0.1701025813817978 0.8167561 0.5606032013893127 True -5 16338 30.09771180152893 0.5122666358947754 173.08828735351562 0.38961347937583923 161.4214324951172 0.17175377905368805 0.82490134 0.5020005702972412 True -6 19061 30.061864376068115 0.517221212387085 149.73876953125 0.32653146982192993 160.74755859375 0.17429481446743011 0.82925355 0.5057068467140198 True -7 21784 29.98843502998352 0.5156097412109375 142.77554321289062 0.33935028314590454 160.04617309570312 0.1763860434293747 0.8373745 0.45124101638793945 True -8 24507 30.013693809509277 0.6970868110656738 136.23248291015625 0.34618157148361206 159.7098846435547 0.17739726603031158 0.84373045 0.41668277978897095 True -9 27230 30.283127784729004 0.534360408782959 148.46331787109375 0.3688894808292389 159.2687530517578 0.1790572553873062 0.8464218 0.3877938687801361 True -10 29953 30.309824466705322 0.5208415985107422 157.19656372070312 0.2432945966720581 158.90496826171875 0.17992497980594635 0.85315794 0.34062430262565613 True -11 32676 30.28158926963806 0.765434980392456 145.52508544921875 0.43504634499549866 158.41758728027344 0.18207833170890808 0.8572535 0.32397186756134033 True -12 35399 30.315227031707764 0.5200316905975342 118.06111145019531 0.23977933824062347 158.12384033203125 0.18279962241649628 0.8627827 0.30004456639289856 True -13 38122 30.300323247909546 0.5139822959899902 137.27456665039062 0.2413983941078186 157.9537353515625 0.1829252690076828 0.86629695 0.27783292531967163 True -14 40845 30.304566860198975 0.6833009719848633 98.99298095703125 0.4091821312904358 157.42185974121094 0.18586450815200806 0.86979824 0.26180317997932434 True -15 43568 30.19907307624817 0.5204217433929443 122.07868957519531 0.303311824798584 157.19837951660156 0.1859261840581894 0.87320924 0.25049063563346863 True -16 46291 30.16579556465149 0.5139625072479248 170.38107299804688 0.3713994026184082 157.29010009765625 0.1854502558708191 0.87635225 0.24297840893268585 True -17 49014 34.83249545097351 27.726887702941895 145.46481323242188 0.28454604744911194 157.17471313476562 0.18571944534778595 0.87692857 0.2389647513628006 True -18 51737 30.485249757766724 0.524014949798584 135.60069274902344 0.24939654767513275 157.29078674316406 0.1848713457584381 0.8773577 0.23910775780677795 True -19 54460 30.125210523605347 1.7498962879180908 136.55645751953125 0.2813670039176941 157.3323211669922 0.1844789981842041 0.87733424 0.2393627017736435 False diff --git a/ENCSR943BCO/cherimoya.fold_0.performance.tsv b/ENCSR943BCO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c093e5f83de4d59ab4df53332358f7b6e0cc433c..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -157.29078674316406 0.5737141370773315 0.1848713457584381 0.04319288954138756 0.8773577213287354 0.7767452597618103 0.23910775780677795 \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_1.evaluate.json b/ENCSR943BCO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 888660504bdae68cac95e006c4ce5f15f3a49dd5..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498LOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_1.fit.json b/ENCSR943BCO/cherimoya.fold_1.fit.json deleted file mode 100644 index 94c160ea8fdc01d6c08df69017e0e9e0179940b1..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF498LOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_1.log b/ENCSR943BCO/cherimoya.fold_1.log deleted file mode 100644 index 6346c461e0855ff2075dcea073b038ed54e00c2b..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2716 35.23970437049866 34.08274865150452 123.74498748779297 0.6174076795578003 231.231201171875 0.14604397118091583 0.7258851 3.559218645095825 True -1 5432 30.22934603691101 0.6853561401367188 168.59173583984375 0.507146418094635 212.73402404785156 0.1908925622701645 0.794726 1.5466957092285156 True -2 8148 30.070317029953003 0.6834959983825684 156.00506591796875 0.7101854085922241 210.0105743408203 0.1953744739294052 0.81002975 0.8505106568336487 True -3 10864 30.017349004745483 0.672208309173584 134.9203338623047 0.35715341567993164 207.7583770751953 0.19984187185764313 0.8195033 0.6846041083335876 True -4 13580 30.364387273788452 2.8239941596984863 135.77899169921875 0.48912471532821655 207.1178741455078 0.2006504386663437 0.8283007 0.6620104312896729 True -5 16296 29.95337176322937 1.7579576969146729 112.3055191040039 0.38608336448669434 206.11480712890625 0.2041410654783249 0.8330574 0.6310033202171326 True -6 19012 30.064217567443848 1.7753405570983887 122.70384216308594 0.3394204378128052 205.85678100585938 0.20446352660655975 0.8403227 0.5922621488571167 True -7 21728 29.979784727096558 10.98086404800415 122.99210357666016 0.33151620626449585 205.07748413085938 0.20562297105789185 0.8467904 0.5606691241264343 True -8 24444 29.963247299194336 0.6818492412567139 143.73382568359375 0.4855327606201172 203.7450408935547 0.21044610440731049 0.8532766 0.5127432346343994 True -9 27160 29.970728874206543 0.6617341041564941 132.9235382080078 0.2792072594165802 203.7153778076172 0.21014267206192017 0.85568964 0.5008268356323242 True -10 29876 29.91141438484192 0.673417329788208 123.83939361572266 0.42423635721206665 202.91310119628906 0.21234442293643951 0.8663638 0.44404199719429016 True -11 32592 29.976996660232544 0.6673593521118164 162.2618408203125 0.3768728971481323 202.40145874023438 0.21407562494277954 0.8717581 0.4054315686225891 True -12 35308 29.951982975006104 0.6603922843933105 144.09884643554688 0.30998027324676514 202.0481414794922 0.21442656219005585 0.8770292 0.36991390585899353 True -13 38024 30.269585847854614 0.6692225933074951 115.6924819946289 0.31776806712150574 201.67169189453125 0.21536649763584137 0.8820298 0.3387269675731659 True -14 40740 30.060213088989258 18.120442867279053 113.24407196044922 0.4531058073043823 200.9309539794922 0.21763402223587036 0.8880702 0.31537172198295593 True -15 43456 30.031997442245483 1.726677656173706 147.25323486328125 0.3297719955444336 200.5906524658203 0.21810157597064972 0.8919245 0.30124473571777344 True -16 46172 30.003461837768555 0.6731929779052734 143.56829833984375 0.3302260637283325 200.13327026367188 0.2197386473417282 0.89191985 0.2939826548099518 False -17 48888 30.1654372215271 0.6662759780883789 117.24578094482422 0.2889114320278168 200.2718048095703 0.21914604306221008 0.8951047 0.291196346282959 True -18 51604 29.99279260635376 16.538809299468994 111.95549011230469 0.2773231863975525 200.46511840820312 0.21861305832862854 0.894137 0.29037392139434814 False -19 54320 30.014923572540283 20.222277879714966 136.101318359375 0.32170045375823975 200.61671447753906 0.2179768979549408 0.8921347 0.2944711744785309 False diff --git a/ENCSR943BCO/cherimoya.fold_1.performance.tsv b/ENCSR943BCO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e92a0b951e161cbffcf72a96c9f982c10c10e062..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -200.2718048095703 0.5469555258750916 0.21914605796337128 0.054431188851594925 0.895104706287384 0.8386797904968262 0.291196346282959 \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_2.evaluate.json b/ENCSR943BCO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1eebc7389c42b40bc0c751d2986ae0a3cee90488..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498LOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_2.fit.json b/ENCSR943BCO/cherimoya.fold_2.fit.json deleted file mode 100644 index 72ac7a8e7617302cf9b66bb7fcf472b5a1dd1abb..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF498LOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_2.log b/ENCSR943BCO/cherimoya.fold_2.log deleted file mode 100644 index d35bbc0d85c78f405e055fb0c50af27f796d359e..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.38308835029602 40.196892976760864 182.83673095703125 0.5310211181640625 190.22036743164062 0.1356157809495926 0.7299305 2.5014760494232178 True -1 5754 32.29670715332031 26.581701517105103 166.7462615966797 0.6820555925369263 175.1777801513672 0.1726495921611786 0.8029113 1.0341800451278687 True -2 8631 31.81578540802002 1.0443670749664307 166.12347412109375 0.4672669470310211 173.55897521972656 0.17490139603614807 0.8136232 0.6252566576004028 True -3 11508 31.92222762107849 0.543097734451294 139.04832458496094 0.5131667256355286 172.32920837402344 0.17676031589508057 0.82202464 0.47794076800346375 True -4 14385 31.70646071434021 0.5436828136444092 124.7662353515625 0.406909316778183 171.4217987060547 0.17905974388122559 0.82978725 0.466102659702301 True -5 17262 31.754205226898193 0.541799783706665 129.22018432617188 0.359737753868103 170.4274444580078 0.18252292275428772 0.83548874 0.43773189187049866 True -6 20139 31.64354968070984 0.5411384105682373 139.7629852294922 0.3816216289997101 170.28916931152344 0.1824769824743271 0.8390624 0.4338415265083313 True -7 23016 31.736847400665283 0.5444061756134033 110.46153259277344 0.3569195866584778 169.6524200439453 0.18486598134040833 0.84277254 0.4134269058704376 True -8 25893 31.74055051803589 0.5436384677886963 131.52685546875 0.4503345787525177 169.3006134033203 0.18582873046398163 0.8472557 0.3932514488697052 True -9 28770 31.782451629638672 0.998035192489624 122.95381164550781 0.34369415044784546 168.79376220703125 0.18746225535869598 0.85507995 0.35659846663475037 True -10 31647 31.785565853118896 0.6259129047393799 125.32869720458984 0.22663410007953644 168.46278381347656 0.1886644959449768 0.8585189 0.34258779883384705 True -11 34524 31.727474689483643 0.5407447814941406 140.53964233398438 0.3380725383758545 168.2407684326172 0.18922124803066254 0.8648705 0.3105725944042206 True -12 37401 31.756259202957153 0.5478086471557617 140.80078125 0.38884392380714417 167.82188415527344 0.19060921669006348 0.86864454 0.29058578610420227 True -13 40278 31.798927783966064 0.5407123565673828 160.07504272460938 0.3742195963859558 167.6040802001953 0.19069209694862366 0.8733323 0.27807798981666565 True -14 43155 31.759117603302002 2.046992540359497 118.31498718261719 0.4142378568649292 167.41436767578125 0.19201761484146118 0.87868345 0.26184481382369995 True -15 46032 31.957875728607178 0.5786592960357666 131.00209045410156 0.2614031434059143 167.08047485351562 0.1926218718290329 0.8791864 0.2527239918708801 True -16 48909 31.9004168510437 0.5471000671386719 120.00018310546875 0.2654946744441986 167.01136779785156 0.19321860373020172 0.8805266 0.24933141469955444 True -17 51786 31.73996925354004 0.5580065250396729 139.09860229492188 0.3256083130836487 167.1907196044922 0.19239716231822968 0.88217336 0.2485574334859848 True -18 54663 31.839269876480103 1.86507248878479 118.42864990234375 0.2348218560218811 167.08062744140625 0.19315947592258453 0.881128 0.25098782777786255 False -19 57540 31.939900636672974 0.5501444339752197 113.97052001953125 0.2728913426399231 166.92124938964844 0.19381795823574066 0.880028 0.25182414054870605 False diff --git a/ENCSR943BCO/cherimoya.fold_2.performance.tsv b/ENCSR943BCO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index c0c35b67f945535cae7c4c75772cf7f9e8c3bc6f..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -167.1907196044922 0.5670395493507385 0.19239714741706848 0.04586642235517502 0.8821733593940735 0.8061578869819641 0.2485574334859848 \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_3.evaluate.json b/ENCSR943BCO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 14afe14f8fd3afc932c6d07c59ef2e7a73b89d40..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498LOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_3.fit.json b/ENCSR943BCO/cherimoya.fold_3.fit.json deleted file mode 100644 index 3771c17e8ff74d24ddcb6a6c787917de9274e4c5..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF498LOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_3.log b/ENCSR943BCO/cherimoya.fold_3.log deleted file mode 100644 index 4606106c11e80df7edff1ee132b5a20fd36cf740..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.95401859283447 3.5768373012542725 146.91119384765625 0.32969966530799866 186.79510498046875 0.13789018988609314 0.68558973 3.1931684017181396 True -1 5492 30.359368562698364 5.629183292388916 117.37109375 0.3963184952735901 173.85409545898438 0.1706904172897339 0.7703196 1.2872231006622314 True -2 8238 30.53385043144226 0.5745301246643066 171.6928253173828 0.4766712784767151 172.4823455810547 0.1721183955669403 0.77077556 0.8494779467582703 True -3 10984 30.29624032974243 0.5793001651763916 160.58489990234375 0.3441309332847595 171.34353637695312 0.17443755269050598 0.7863854 0.6444410085678101 True -4 13730 30.430798053741455 0.5834715366363525 134.2365264892578 0.3225548565387726 170.38587951660156 0.17759746313095093 0.80168307 0.5912984013557434 True -5 16476 30.34912633895874 0.6627058982849121 113.13294982910156 0.2618032991886139 169.62237548828125 0.1802336722612381 0.80650944 0.5906736850738525 True -6 19222 30.27349352836609 0.570263147354126 153.26376342773438 0.4398629367351532 169.06788635253906 0.1818743795156479 0.8107153 0.589943528175354 True -7 21968 30.267900466918945 0.5804064273834229 135.80484008789062 0.27805832028388977 168.34237670898438 0.1843957155942917 0.81938225 0.5700626969337463 True -8 24714 30.313759088516235 0.5874629020690918 127.2856674194336 0.4587498605251312 168.0357666015625 0.18547557294368744 0.82400155 0.5251169204711914 True -9 27460 30.421172857284546 0.5723495483398438 138.40994262695312 0.33218568563461304 167.62014770507812 0.18670940399169922 0.82682234 0.47967201471328735 True -10 30206 30.40261960029602 0.5795435905456543 166.9473876953125 0.3985591530799866 167.06707763671875 0.18895144760608673 0.83386785 0.44045040011405945 True -11 32952 30.28975486755371 1.106151819229126 158.4837646484375 0.2878393530845642 166.8611297607422 0.18905508518218994 0.83993256 0.4111998677253723 True -12 35698 30.36237072944641 0.5795435905456543 130.3163299560547 0.22256867587566376 166.5887451171875 0.1899176388978958 0.8488282 0.38252466917037964 True -13 38444 30.288917064666748 0.5817973613739014 134.0248260498047 0.2838519513607025 166.0526580810547 0.19156840443611145 0.85633296 0.34681034088134766 True -14 41190 30.259971618652344 0.5778253078460693 159.72027587890625 0.330691933631897 165.63723754882812 0.192460298538208 0.86147493 0.32253164052963257 True -15 43936 30.257901906967163 0.5759716033935547 135.91641235351562 0.25154757499694824 165.5492706298828 0.19257837533950806 0.8691221 0.30344557762145996 True -16 46682 35.95905828475952 34.93204665184021 153.70864868164062 0.280282199382782 165.3306884765625 0.19315461814403534 0.8719159 0.2865557074546814 True -17 49428 31.195947647094727 11.956968545913696 156.55087280273438 0.38067710399627686 165.43057250976562 0.19283606112003326 0.8759774 0.2775641083717346 True -18 52174 30.33693265914917 0.6411566734313965 114.70874786376953 0.27863234281539917 165.50628662109375 0.19238533079624176 0.8772865 0.2744690477848053 True -19 54920 30.261850357055664 0.5705556869506836 120.92031860351562 0.27076810598373413 165.30184936523438 0.1935494840145111 0.8769812 0.2763359248638153 False diff --git a/ENCSR943BCO/cherimoya.fold_3.performance.tsv b/ENCSR943BCO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6d1eba8e887c187dd3cf911aa2ce105c3c2a5982..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -165.50628662109375 0.5676438808441162 0.19238531589508057 0.04790325090289116 0.8772864937782288 0.7763239741325378 0.2744690477848053 \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_4.evaluate.json b/ENCSR943BCO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 227355b2d1e1fa37b71c32f598ea23fa815822d3..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF498LOJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_4.fit.json b/ENCSR943BCO/cherimoya.fold_4.fit.json deleted file mode 100644 index 25b97e4805e904cb50e4ee3c191461220f886dc2..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF498LOJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943BCO/cherimoya.fold_4.log b/ENCSR943BCO/cherimoya.fold_4.log deleted file mode 100644 index 8ec20555131a658ae71bd84de027e425f45545a9..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2848 36.153751373291016 3.5156373977661133 118.11885070800781 0.2775479853153229 163.9203338623047 0.1278546303510666 0.72275573 1.9268978834152222 True -1 5696 31.509114503860474 0.5978569984436035 155.4547119140625 0.4723478853702545 153.9267120361328 0.15743471682071686 0.78176206 1.004349708557129 True -2 8544 31.491339921951294 0.5842547416687012 109.1243667602539 0.32878899574279785 152.81988525390625 0.15774989128112793 0.7916585 0.4420590102672577 True -3 11392 31.482255935668945 2.292919874191284 170.99496459960938 0.45610854029655457 151.25201416015625 0.16261865198612213 0.8041583 0.3953329920768738 True -4 14240 31.388896942138672 0.5876922607421875 154.71893310546875 0.4200224280357361 150.86488342285156 0.1633153259754181 0.80884516 0.4055759310722351 True -5 17088 31.41515803337097 2.5041723251342773 126.26042175292969 0.4273790121078491 150.3184356689453 0.16541603207588196 0.81451625 0.38805094361305237 True -6 19936 31.491863012313843 0.5953660011291504 125.29682922363281 0.38336965441703796 149.933837890625 0.16642709076404572 0.81964946 0.34994807839393616 True -7 22784 31.393704652786255 0.589256763458252 134.5730438232422 0.2623344957828522 149.3690948486328 0.1684958040714264 0.8279022 0.35739341378211975 True -8 25632 31.417842626571655 0.5851461887359619 133.86465454101562 0.3205365538597107 149.11212158203125 0.16899780929088593 0.83329946 0.34460511803627014 True -9 28480 31.368112802505493 0.583470344543457 145.34829711914062 0.4291303753852844 148.59719848632812 0.17146170139312744 0.8384518 0.3307582437992096 True -10 31328 31.42627716064453 1.536062479019165 124.95782470703125 0.2731388509273529 148.4014129638672 0.1720581203699112 0.8466955 0.2967808246612549 True -11 34176 33.94818687438965 20.057485580444336 158.14108276367188 0.36921408772468567 148.03958129882812 0.1734478771686554 0.84990895 0.2799854576587677 True -12 37024 31.692376136779785 29.65524411201477 169.7103729248047 0.2849072813987732 147.7933349609375 0.17372645437717438 0.8556715 0.25626811385154724 True -13 39872 31.60336947441101 1.5108428001403809 122.26886749267578 0.2724287509918213 147.61814880371094 0.17431825399398804 0.8635421 0.24353839457035065 True -14 42720 31.45540189743042 0.5926821231842041 136.0604248046875 0.2938743233680725 147.3162384033203 0.1752804070711136 0.866782 0.23136906325817108 True -15 45568 31.426021337509155 0.5846264362335205 130.78240966796875 0.24019363522529602 147.20416259765625 0.1756558120250702 0.8707648 0.2222563773393631 True -16 48416 31.435268878936768 0.5818727016448975 109.57159423828125 0.24201807379722595 147.08135986328125 0.1760905683040619 0.8718415 0.21837076544761658 True -17 51264 31.518948793411255 0.5821926593780518 126.7291259765625 0.2616767883300781 147.15914916992188 0.17621424794197083 0.8738073 0.21545587480068207 True -18 54112 31.568593978881836 0.5811464786529541 136.71893310546875 0.24217428267002106 147.26763916015625 0.1756034791469574 0.8737562 0.21461935341358185 False -19 56960 31.413025617599487 0.5821635723114014 121.53459167480469 0.34565556049346924 147.2030792236328 0.1761360615491867 0.87486994 0.21451467275619507 True diff --git a/ENCSR943BCO/cherimoya.fold_4.performance.tsv b/ENCSR943BCO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 014f4606230e8da1974d23a7c7d69e196ab7ba31..0000000000000000000000000000000000000000 --- a/ENCSR943BCO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -147.2030792236328 0.5799276828765869 0.1761360764503479 0.037830840796232224 0.8748699426651001 0.7598065137863159 0.21451467275619507 \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_0.evaluate.json b/ENCSR943MRO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 963dda676e3b101492a430f5132a5928626d1e99..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692WNI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_0.fit.json b/ENCSR943MRO/cherimoya.fold_0.fit.json deleted file mode 100644 index 852cd79d60c36eb06417730d61a7e4bde22d24ed..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF692WNI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_0.log b/ENCSR943MRO/cherimoya.fold_0.log deleted file mode 100644 index 6a6a5f6434de2f7b9d8cc1c6ced8dc42a8530e93..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 35.39258050918579 4.873921632766724 402.90380859375 0.5354935526847839 584.9529418945312 0.2828313410282135 0.68737954 4.327538013458252 True -1 5502 30.671103954315186 34.762418270111084 430.1029052734375 0.3496798276901245 532.63232421875 0.3589572608470917 0.74051714 0.9137822985649109 True -2 8253 30.908197164535522 1.7139737606048584 475.40191650390625 0.3964160680770874 520.85595703125 0.37439772486686707 0.7550243 0.544528067111969 True -3 11004 30.740699291229248 0.5850198268890381 419.72332763671875 0.5309413075447083 515.85595703125 0.3797817826271057 0.7683397 0.5419861674308777 True -4 13755 30.785288333892822 33.56298851966858 408.86798095703125 0.32268083095550537 511.8745422363281 0.38542768359184265 0.7743802 0.4310894310474396 True -5 16506 31.26834726333618 0.5974020957946777 445.7369079589844 0.36587217450141907 510.5268249511719 0.3863376975059509 0.77954847 0.3905940353870392 True -6 19257 30.62630343437195 1.1318690776824951 426.17071533203125 0.6178702116012573 507.3677978515625 0.3914321959018707 0.78595173 0.36865973472595215 True -7 22008 30.530352354049683 0.5975463390350342 458.8315124511719 0.42024099826812744 504.9932556152344 0.3971022367477417 0.78980994 0.35709115862846375 True -8 24759 30.058690547943115 0.588721752166748 393.69317626953125 0.2497330605983734 503.1336669921875 0.39953136444091797 0.79605895 0.35670343041419983 True -9 27510 30.10808491706848 0.5802929401397705 432.06658935546875 0.2744649052619934 503.046630859375 0.39815038442611694 0.80176884 0.33583447337150574 True -10 30261 30.071074724197388 1.1790826320648193 436.47906494140625 0.3516388535499573 500.9420471191406 0.4016883671283722 0.80626345 0.30200478434562683 True -11 33012 30.17713451385498 0.5881164073944092 379.596923828125 0.33370664715766907 499.73828125 0.4038323760032654 0.814025 0.27711188793182373 True -12 35763 30.167114973068237 0.5898854732513428 415.16033935546875 0.329073429107666 497.4486083984375 0.4076411724090576 0.8193107 0.2675710916519165 True -13 38514 30.11018419265747 0.589641809463501 440.54412841796875 0.30671605467796326 497.2693176269531 0.40709978342056274 0.82552826 0.25912711024284363 True -14 41265 30.078576803207397 0.5805342197418213 432.69915771484375 0.25468897819519043 496.2800598144531 0.4089229702949524 0.8280009 0.24368417263031006 True -15 44016 30.120241165161133 0.5865006446838379 468.49017333984375 0.37155354022979736 494.5042724609375 0.41199153661727905 0.8328608 0.23373135924339294 True -16 46767 30.101285934448242 0.588221549987793 412.07342529296875 0.1755605787038803 495.1878356933594 0.40971648693084717 0.8368988 0.22616831958293915 True -17 49518 30.081681966781616 28.782418251037598 430.5992431640625 0.22075685858726501 494.42767333984375 0.4104660749435425 0.8410102 0.22243638336658478 True -18 52269 30.67131233215332 0.5860416889190674 364.90631103515625 0.1874314546585083 494.84039306640625 0.41044870018959045 0.83964276 0.22230133414268494 False -19 55020 30.108654260635376 0.5818023681640625 378.2347106933594 0.2066659778356552 494.7827453613281 0.41053029894828796 0.8380624 0.2227659374475479 False diff --git a/ENCSR943MRO/cherimoya.fold_0.performance.tsv b/ENCSR943MRO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 13263e991a44507a2cdba5973c1eb1fd93d78bc6..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -494.42767333984375 0.38585466146469116 0.4104660749435425 0.15256068110466003 0.8410102128982544 0.8114187121391296 0.22243638336658478 \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_1.evaluate.json b/ENCSR943MRO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2d8a3bcac5c81ec22319268cfe3648b8c65ee0de..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692WNI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_1.fit.json b/ENCSR943MRO/cherimoya.fold_1.fit.json deleted file mode 100644 index 870750609926ad0818f0db887a19a58b5719c7cd..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF692WNI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_1.log b/ENCSR943MRO/cherimoya.fold_1.log deleted file mode 100644 index b812c80053a4fa159b277ca322224492cabd1f0a..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2698 34.71858286857605 4.394673824310303 482.62664794921875 0.5009870529174805 661.3390502929688 0.28354576230049133 0.6896316 4.806049346923828 True -1 5396 30.189823150634766 0.7188596725463867 451.77801513671875 0.3198429346084595 596.1328735351562 0.3663558065891266 0.75474274 1.3977162837982178 True -2 8094 30.06660485267639 17.222638368606567 335.689453125 0.3555220365524292 581.3823852539062 0.3828129768371582 0.7676302 0.5834964513778687 True -3 10792 30.763302087783813 36.976250886917114 466.655029296875 0.3851270377635956 573.3008422851562 0.3900429606437683 0.77836144 0.5154345035552979 True -4 13490 29.90107488632202 0.7054588794708252 406.6615295410156 0.35291147232055664 569.6981201171875 0.39463192224502563 0.7787962 0.4482516348361969 True -5 16188 29.442834854125977 0.712479829788208 433.56707763671875 0.2626333236694336 565.6183471679688 0.39882025122642517 0.78569967 0.34846019744873047 True -6 18886 29.494584321975708 1.1202070713043213 439.700927734375 0.38692641258239746 564.197021484375 0.3998057544231415 0.78968304 0.35966941714286804 True -7 21584 29.472256660461426 0.6912603378295898 386.21380615234375 0.3519326448440552 561.5460205078125 0.4027113914489746 0.80040973 0.3367183804512024 True -8 24282 30.16397452354431 40.34827256202698 372.48455810546875 0.21193920075893402 557.8270263671875 0.40867167711257935 0.8041548 0.3265310823917389 True -9 26980 29.49613881111145 0.6918261051177979 451.6219177246094 0.3305804133415222 556.6160888671875 0.4094211459159851 0.8117762 0.3267150819301605 True -10 29678 29.51101803779602 1.3296213150024414 430.7686767578125 0.33266764879226685 554.730224609375 0.41198813915252686 0.8184839 0.30087658762931824 True -11 32376 29.497320890426636 0.6785283088684082 456.3963317871094 0.2480148822069168 553.2407836914062 0.41334396600723267 0.824198 0.285288542509079 True -12 35074 29.93326735496521 36.26104927062988 381.0006408691406 0.2758125960826874 551.7699584960938 0.41451945900917053 0.83226544 0.2662080228328705 True -13 37772 29.54074239730835 0.6927609443664551 407.3936462402344 0.19532060623168945 549.270751953125 0.41786083579063416 0.83788174 0.25783616304397583 True -14 40470 29.53970170021057 0.6913547515869141 427.4115295410156 0.24773195385932922 548.3303833007812 0.4191029369831085 0.84484154 0.24670016765594482 True -15 43168 29.526121854782104 2.948915958404541 344.77496337890625 0.17752259969711304 547.1087646484375 0.42101773619651794 0.8510762 0.23830123245716095 True -16 45866 29.557292461395264 39.56329965591431 460.7798767089844 0.2299879491329193 546.3425903320312 0.4209044873714447 0.8530408 0.2340102195739746 True -17 48564 29.870208978652954 0.723057746887207 444.90533447265625 0.12964650988578796 546.0556030273438 0.4215100407600403 0.85687566 0.2304210215806961 True -18 51262 29.46899175643921 0.688234806060791 455.68548583984375 0.14896821975708008 545.8395385742188 0.4220999479293823 0.8567447 0.22989709675312042 False -19 53960 29.496958017349243 0.6875789165496826 400.98370361328125 0.22074079513549805 545.9978637695312 0.4220760762691498 0.85681415 0.23207150399684906 False diff --git a/ENCSR943MRO/cherimoya.fold_1.performance.tsv b/ENCSR943MRO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4e91dc42951df259f491363222d87658f82a61f6..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -546.0556030273438 0.3749884068965912 0.4215100407600403 0.16229839622974396 0.8568756580352783 0.8401638865470886 0.2304210215806961 \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_2.evaluate.json b/ENCSR943MRO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 15f4a5446360a63d35c26841731ba21dfe4d14f1..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692WNI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_2.fit.json b/ENCSR943MRO/cherimoya.fold_2.fit.json deleted file mode 100644 index e6bf2ed5cb0d26c53edbd6acf6d6631462cc9b7e..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF692WNI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_2.log b/ENCSR943MRO/cherimoya.fold_2.log deleted file mode 100644 index 959effac765bd818d737512cb40808fd687e6917..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2876 36.00410318374634 4.278258562088013 458.3864440917969 0.3982526957988739 614.9495239257812 0.28854453563690186 0.6826397 3.0745139122009277 True -1 5752 32.133484840393066 18.272072076797485 401.9040222167969 0.36546850204467773 553.4407958984375 0.37320220470428467 0.74649274 0.8749186992645264 True -2 8628 34.86445617675781 0.5692462921142578 428.91925048828125 0.31381118297576904 542.3508911132812 0.3872363865375519 0.7581395 0.6604679822921753 True -3 11504 32.14425992965698 2.8656258583068848 416.73486328125 0.49768030643463135 538.575439453125 0.3900778889656067 0.7651807 0.5805420279502869 True -4 14380 32.08538794517517 0.5571887493133545 415.1664123535156 0.31901317834854126 536.9618530273438 0.3921961486339569 0.7698099 0.49181443452835083 True -5 17256 32.128167152404785 1.479308843612671 440.2198486328125 0.4134311079978943 533.8206176757812 0.3966294825077057 0.7772542 0.39880913496017456 True -6 20132 32.08119773864746 0.9241302013397217 413.19189453125 0.4025466740131378 531.9257202148438 0.3978312015533447 0.783785 0.37640851736068726 True -7 23008 32.080158948898315 0.5554134845733643 519.7413330078125 0.2563357353210449 530.09765625 0.4005475640296936 0.7879955 0.3686603307723999 True -8 25884 32.064120054244995 0.5576794147491455 391.608154296875 0.28130054473876953 527.734619140625 0.4048910439014435 0.79335815 0.3381827175617218 True -9 28760 32.11283993721008 1.5686967372894287 389.70416259765625 0.2605507969856262 525.7830810546875 0.40755581855773926 0.7962888 0.32369476556777954 True -10 31636 32.1737494468689 0.5501112937927246 478.2107238769531 0.2700706720352173 525.53466796875 0.4067135453224182 0.8016036 0.2997279167175293 True -11 34512 32.12827229499817 0.5539798736572266 417.5058288574219 0.23749777674674988 523.0719604492188 0.4109117090702057 0.807545 0.2781433165073395 True -12 37388 32.06512904167175 0.5492002964019775 466.41650390625 0.31013011932373047 521.6826171875 0.4119037389755249 0.8124297 0.27112919092178345 True -13 40264 32.131582260131836 0.565157413482666 416.042236328125 0.2214282751083374 520.248291015625 0.41429489850997925 0.8170282 0.258283406496048 True -14 43140 32.08921527862549 0.6303994655609131 392.5106201171875 0.19208180904388428 519.838623046875 0.41386789083480835 0.8251419 0.2415153980255127 True -15 46016 39.49228048324585 0.5534729957580566 429.0662536621094 0.2423921674489975 518.2532958984375 0.41751518845558167 0.8293702 0.24046345055103302 True -16 48892 32.11136770248413 0.5455918312072754 453.1553649902344 0.27332398295402527 519.0823974609375 0.4154530167579651 0.8334144 0.235928475856781 True -17 51768 32.22276830673218 0.5497760772705078 424.16522216796875 0.17500761151313782 517.7349243164062 0.4180871546268463 0.8342212 0.23333078622817993 True -18 54644 32.61085510253906 0.540351390838623 471.533447265625 0.18567198514938354 517.9005737304688 0.4175429046154022 0.8331309 0.2340465933084488 False -19 57520 31.462507247924805 0.8710947036743164 404.5444030761719 0.18815557658672333 519.074951171875 0.4144919812679291 0.8317698 0.234593465924263 False diff --git a/ENCSR943MRO/cherimoya.fold_2.performance.tsv b/ENCSR943MRO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5ab2ee059d010274e7409328d3f9c91bd2dee46a..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -517.7349243164062 0.37920188903808594 0.41808709502220154 0.16231383383274078 0.8342211842536926 0.8085201382637024 0.23333078622817993 \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_3.evaluate.json b/ENCSR943MRO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 58273fa31b6676c536fd709b564a1ce4864589f0..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692WNI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_3.fit.json b/ENCSR943MRO/cherimoya.fold_3.fit.json deleted file mode 100644 index 42f213a855afe64dcb8fccf5eb9a041ed28fa47d..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF692WNI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_3.log b/ENCSR943MRO/cherimoya.fold_3.log deleted file mode 100644 index 062a7dbcecc34394a7c282ee6db80e1c2c137a15..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 35.29628038406372 7.3143393993377686 432.96826171875 0.37103402614593506 587.4091186523438 0.2891028821468353 0.6707441 4.249661445617676 True -1 5520 30.814215183258057 0.5184886455535889 425.4708251953125 0.461100697517395 529.63916015625 0.37034982442855835 0.7481316 1.321857213973999 True -2 8280 30.749342918395996 0.503211259841919 452.76251220703125 0.3929916024208069 521.0860595703125 0.38244929909706116 0.757085 0.8001896739006042 True -3 11040 30.807348012924194 0.502448558807373 512.7196044921875 0.5319651365280151 514.0369262695312 0.39055967330932617 0.77151865 0.7291166186332703 True -4 13800 30.80290651321411 0.5044345855712891 422.9337463378906 0.4340132474899292 511.2010192871094 0.3935880959033966 0.7775958 0.5099101662635803 True -5 16560 30.87248158454895 0.5037853717803955 492.14093017578125 0.5316798686981201 508.79632568359375 0.39554503560066223 0.7855251 0.3982877731323242 True -6 19320 30.793785333633423 0.5016829967498779 397.8582458496094 0.3994632959365845 506.2254943847656 0.399098664522171 0.79115963 0.39736804366111755 True -7 22080 30.79489231109619 0.5039372444152832 445.142822265625 0.4508936405181885 504.6667175292969 0.4009748697280884 0.7952358 0.38757991790771484 True -8 24840 30.74167537689209 0.5019485950469971 457.41204833984375 0.29130038619041443 502.03485107421875 0.4053836464881897 0.80043226 0.34597229957580566 True -9 27600 30.76934790611267 0.4965994358062744 473.0281982421875 0.32874757051467896 500.8594665527344 0.4064399003982544 0.8037601 0.33049604296684265 True -10 30360 30.76494073867798 0.5025858879089355 416.23944091796875 0.2648974657058716 499.52923583984375 0.4076779782772064 0.81065357 0.32010242342948914 True -11 33120 30.751604557037354 0.502810001373291 442.63214111328125 0.2934570908546448 496.9945068359375 0.41262444853782654 0.8139409 0.29351934790611267 True -12 35880 31.223248720169067 0.5030333995819092 425.6170959472656 0.3477190136909485 495.9766540527344 0.4128226339817047 0.81979245 0.28102031350135803 True -13 38640 30.841169834136963 0.5027358531951904 464.43853759765625 0.2726675868034363 494.4078674316406 0.41432541608810425 0.8247872 0.27229079604148865 True -14 41400 30.585307359695435 0.49723339080810547 377.09002685546875 0.25717949867248535 493.3185119628906 0.4163688123226166 0.8320916 0.25833860039711 True -15 44160 30.231723070144653 0.4965519905090332 410.60931396484375 0.2085857391357422 492.9770202636719 0.4158572852611542 0.8374364 0.24850063025951385 True -16 46920 30.169592142105103 4.001646280288696 411.5343017578125 0.1926255077123642 491.912109375 0.4178767502307892 0.8407588 0.2377927452325821 True -17 49680 30.808221578598022 0.4981093406677246 425.74481201171875 0.18834038078784943 491.6749267578125 0.41760939359664917 0.8435476 0.23579587042331696 True -18 52440 30.210580825805664 0.49884819984436035 412.3411865234375 0.1797879934310913 491.17779541015625 0.41865968704223633 0.8454326 0.23537440598011017 True -19 55200 30.42245626449585 0.5123796463012695 381.11773681640625 0.5446135997772217 491.8384704589844 0.4176401197910309 0.84597695 0.23671604692935944 True diff --git a/ENCSR943MRO/cherimoya.fold_3.performance.tsv b/ENCSR943MRO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 672aede2035358d6b154eef49ea1ffeab8552491..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -491.8384704589844 0.3821066915988922 0.4176401197910309 0.15947721898555756 0.8459769487380981 0.817157506942749 0.23671604692935944 \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_4.evaluate.json b/ENCSR943MRO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index dbdfab4228e6fa80ae1dc62e317576e51c2ec6cd..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF692WNI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_4.fit.json b/ENCSR943MRO/cherimoya.fold_4.fit.json deleted file mode 100644 index d7f9f0863ae91843c8d3aa1deff639e218d00757..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF692WNI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943MRO/cherimoya.fold_4.log b/ENCSR943MRO/cherimoya.fold_4.log deleted file mode 100644 index d761d2d3793abe1b555b76e7258443bdad4cbd64..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2824 36.32024526596069 3.679459810256958 426.364013671875 0.40762853622436523 546.262939453125 0.27668190002441406 0.66610473 2.609081983566284 True -1 5648 31.45539379119873 0.5962462425231934 440.69036865234375 0.37536951899528503 496.958740234375 0.35502201318740845 0.7374048 1.158556342124939 True -2 8472 31.603575706481934 0.5913801193237305 503.51776123046875 0.5812854170799255 487.91766357421875 0.36980560421943665 0.7484591 0.5527662634849548 True -3 11296 31.54340887069702 0.5899882316589355 418.67132568359375 0.5214207768440247 482.32275390625 0.37803223729133606 0.76185167 0.5189964771270752 True -4 14120 31.466215133666992 0.5899908542633057 389.4998779296875 0.5206823348999023 480.9566955566406 0.37869885563850403 0.7652427 0.38089895248413086 True -5 16944 31.542566299438477 0.583669900894165 421.79022216796875 0.42185378074645996 479.057373046875 0.38037875294685364 0.7714583 0.3580389618873596 True -6 19768 31.69268226623535 0.6070878505706787 396.37255859375 0.23327583074569702 476.9969177246094 0.383736252784729 0.77963114 0.32831844687461853 True -7 22592 31.580242156982422 0.5935192108154297 414.26202392578125 0.2864888608455658 475.4362487792969 0.38600605726242065 0.782952 0.3086053431034088 True -8 25416 31.634820699691772 1.3376011848449707 441.5757141113281 0.4026494026184082 474.3031311035156 0.3867672383785248 0.7892155 0.2953307330608368 True -9 28240 31.573461532592773 0.5887691974639893 373.1937255859375 0.33327236771583557 472.7095947265625 0.3902249038219452 0.79269826 0.26959535479545593 True -10 31064 32.05817127227783 0.6020400524139404 478.76202392578125 0.34720784425735474 470.7543640136719 0.393406480550766 0.80181575 0.2586771249771118 True -11 33888 30.99169945716858 0.5739896297454834 371.6571044921875 0.28205156326293945 469.2720031738281 0.3955051600933075 0.8101136 0.24141986668109894 True -12 36712 31.903557300567627 0.5851900577545166 477.3582458496094 0.24236558377742767 468.35467529296875 0.39647266268730164 0.8154494 0.23661772906780243 True -13 39536 31.047807931900024 1.55543851852417 438.70660400390625 0.24324734508991241 466.6449279785156 0.39962315559387207 0.8212499 0.23181267082691193 True -14 42360 31.01482391357422 0.5864598751068115 424.76910400390625 0.3280256390571594 466.321044921875 0.3991822302341461 0.8290205 0.2225549817085266 True -15 45184 30.89278793334961 0.5853040218353271 390.0041198730469 0.20101216435432434 465.633544921875 0.4005148112773895 0.83233947 0.21567745506763458 True -16 48008 31.05636429786682 15.265628576278687 437.2873840332031 0.19446885585784912 465.0901184082031 0.40115591883659363 0.83641 0.21289023756980896 True -17 50832 30.915553092956543 20.549908876419067 367.696044921875 0.1720111072063446 465.31707763671875 0.4013431668281555 0.83857787 0.211284339427948 True -18 53656 32.01641225814819 0.5900981426239014 397.75299072265625 0.25680381059646606 464.8100280761719 0.4025488495826721 0.84068084 0.2106597125530243 True -19 56480 30.885643243789673 29.52870202064514 403.222412109375 0.2147524654865265 464.9605407714844 0.40177422761917114 0.84098965 0.21099068224430084 True diff --git a/ENCSR943MRO/cherimoya.fold_4.performance.tsv b/ENCSR943MRO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 3c6bf4849a4d860e2b6d1ccc6b97c4f6b183b135..0000000000000000000000000000000000000000 --- a/ENCSR943MRO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -464.9605407714844 0.39421072602272034 0.40177422761917114 0.1437867432832718 0.8409896492958069 0.8097178936004639 0.21099068224430084 \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_0.evaluate.json b/ENCSR943SYS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e31493ef25d73e003dc7313f226fcc6728a83655..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MHM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_0.fit.json b/ENCSR943SYS/cherimoya.fold_0.fit.json deleted file mode 100644 index 0af21bf88ea1c9c5946a985e162faef5a2109d2d..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF671MHM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_0.log b/ENCSR943SYS/cherimoya.fold_0.log deleted file mode 100644 index 2db13c20c0183be06bd645a7f25411e70ef69b1f..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 34.88761520385742 4.021192312240601 1291.28369140625 0.40819698572158813 1659.2174072265625 0.3055189251899719 0.6417204 9.71817398071289 True -1 5474 30.337430715560913 0.5946967601776123 1216.34326171875 0.4549737572669983 1441.586181640625 0.43668147921562195 0.7460831 1.3863996267318726 True -2 8211 30.332298517227173 0.5627520084381104 1044.8778076171875 0.5254157781600952 1416.9014892578125 0.4468272030353546 0.77091944 0.5338801145553589 True -3 10948 30.31576657295227 0.9057798385620117 1172.938720703125 0.5170849561691284 1397.9176025390625 0.45753151178359985 0.7818583 0.4044169485569 True -4 13685 30.361443519592285 0.5488145351409912 1385.06005859375 0.3624081015586853 1389.55615234375 0.4619312286376953 0.78760386 0.35289210081100464 True -5 16422 30.39884042739868 1.5028188228607178 1148.2388916015625 0.40325456857681274 1386.7071533203125 0.4632611870765686 0.7886064 0.3584093451499939 True -6 19159 30.327786922454834 0.6122565269470215 1085.94580078125 0.48483675718307495 1381.7022705078125 0.4659039080142975 0.7904812 0.3650568723678589 True -7 21896 30.372180938720703 0.5835766792297363 1121.0401611328125 0.3338633179664612 1376.9046630859375 0.46914660930633545 0.79217756 0.30324503779411316 True -8 24633 30.362486362457275 0.594240665435791 1066.775390625 0.2496037632226944 1372.98486328125 0.4713568389415741 0.79484904 0.28415489196777344 True -9 27370 30.363659381866455 0.5892312526702881 1183.24072265625 0.28642016649246216 1369.4114990234375 0.47352033853530884 0.7978784 0.2870652973651886 True -10 30107 30.212501525878906 0.5477266311645508 1084.0843505859375 0.33206140995025635 1366.24072265625 0.4748508632183075 0.80170023 0.2658226788043976 True -11 32844 29.69382667541504 0.5574016571044922 1002.883544921875 0.304317831993103 1358.9713134765625 0.48092037439346313 0.80696326 0.2437591850757599 True -12 35581 29.64110279083252 0.5616016387939453 1172.683837890625 0.3064352869987488 1356.37841796875 0.4827757179737091 0.81452274 0.22402343153953552 True -13 38318 29.662445306777954 2.070270299911499 1087.425537109375 0.20318226516246796 1351.6683349609375 0.48482242226600647 0.8178346 0.21496208012104034 True -14 41055 29.740618467330933 0.57303786277771 1200.2122802734375 0.3037486672401428 1348.3416748046875 0.4869186282157898 0.8252929 0.20820090174674988 True -15 43792 29.663626194000244 0.5673346519470215 1057.06787109375 0.25349172949790955 1348.652099609375 0.4870276153087616 0.82914555 0.2024277299642563 True -16 46529 29.736940383911133 0.56256103515625 1036.36962890625 0.22116753458976746 1347.3699951171875 0.4870179295539856 0.8352647 0.1968313455581665 True -17 49266 29.75162935256958 0.5718317031860352 1027.22802734375 0.17980802059173584 1347.4351806640625 0.4872126579284668 0.8371612 0.1942623108625412 True -18 52003 29.7136173248291 0.5765628814697266 1103.6552734375 0.22692438960075378 1346.2642822265625 0.48806288838386536 0.8364228 0.19567090272903442 False -19 54740 29.717276334762573 0.5592608451843262 1092.5198974609375 0.16992995142936707 1347.2835693359375 0.48683494329452515 0.8374024 0.19613760709762573 True diff --git a/ENCSR943SYS/cherimoya.fold_0.performance.tsv b/ENCSR943SYS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 540a1432f004becfd14ae197c28e6be62dbc06a4..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1347.2835693359375 0.27537915110588074 0.48683497309684753 0.2722134292125702 0.8374024033546448 0.8118367791175842 0.19613760709762573 \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_1.evaluate.json b/ENCSR943SYS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 1ef9efe01a94f96d7ab92f9ebc6b37f25bd1b889..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MHM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_1.fit.json b/ENCSR943SYS/cherimoya.fold_1.fit.json deleted file mode 100644 index f76fc958bc1a90cdc3a9c179ca5783a48d0ebb00..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF671MHM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_1.log b/ENCSR943SYS/cherimoya.fold_1.log deleted file mode 100644 index 8a2c2d28ed019e4fe88dc6950c3dba88247323c4..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 35.04112529754639 4.224041223526001 1180.5126953125 0.43526798486709595 1850.8740234375 0.31047114729881287 0.6473557 8.253732681274414 True -1 5476 30.33618688583374 0.6776840686798096 1125.868408203125 0.45959728956222534 1597.8616943359375 0.4409337639808655 0.7608227 1.371055245399475 True -2 8214 30.334795236587524 0.6831114292144775 1231.4156494140625 0.39700034260749817 1551.3348388671875 0.46371975541114807 0.78129184 0.529960572719574 True -3 10952 30.42862844467163 0.693627119064331 1078.78271484375 0.37478429079055786 1538.82958984375 0.4684838056564331 0.7900843 0.4822520315647125 True -4 13690 30.315906763076782 0.6822288036346436 1219.1162109375 0.21893267333507538 1531.8402099609375 0.4715832769870758 0.79207355 0.43489351868629456 True -5 16428 30.317100048065186 1.8704335689544678 1081.111328125 0.27644431591033936 1525.8079833984375 0.47447437047958374 0.79522717 0.4515730142593384 True -6 19166 30.50634264945984 0.7171285152435303 1044.1705322265625 0.2566158175468445 1512.0015869140625 0.48372602462768555 0.79986715 0.3806919455528259 True -7 21904 30.457794427871704 0.6987178325653076 1067.0582275390625 0.35440945625305176 1506.921875 0.48589274287223816 0.80033547 0.3372446596622467 True -8 24642 30.482527256011963 0.7233078479766846 1272.337158203125 0.3653549253940582 1503.8218994140625 0.48833203315734863 0.8029631 0.3330087959766388 True -9 27380 30.470295429229736 0.7056195735931396 1062.1337890625 0.39217936992645264 1497.438232421875 0.49178802967071533 0.8058789 0.3217567503452301 True -10 30118 30.542826175689697 0.6976420879364014 1038.168701171875 0.4574400782585144 1492.3037109375 0.49423518776893616 0.808015 0.3138752579689026 True -11 32856 30.39635992050171 0.6977634429931641 1036.81591796875 0.3050832748413086 1487.0614013671875 0.49711617827415466 0.8128712 0.289927214384079 True -12 35594 29.923566818237305 1.423022985458374 1140.8699951171875 0.3023632764816284 1481.5947265625 0.49968060851097107 0.82034975 0.2782960832118988 True -13 38332 29.89970111846924 0.6947448253631592 1163.5257568359375 0.26509708166122437 1479.3671875 0.5003361701965332 0.82759094 0.2497832477092743 True -14 41070 29.906030416488647 0.6905009746551514 981.455810546875 0.2897397577762604 1475.9962158203125 0.5012950301170349 0.8340818 0.24389825761318207 True -15 43808 29.880894660949707 0.6976423263549805 1207.557861328125 0.2343301624059677 1474.6619873046875 0.5015144944190979 0.84210175 0.22540055215358734 True -16 46546 29.863526582717896 0.6843600273132324 1190.1744384765625 0.21038620173931122 1469.8994140625 0.504305899143219 0.84502256 0.21615728735923767 True -17 49284 29.77524733543396 0.6854841709136963 1085.6722412109375 0.2723393440246582 1472.9964599609375 0.5017764568328857 0.85051835 0.20843587815761566 True -18 52022 29.70984172821045 0.6796154975891113 894.6290283203125 0.17162665724754333 1472.693115234375 0.5022843480110168 0.8495159 0.20589610934257507 False -19 54760 29.77090835571289 0.6948480606079102 1163.146240234375 0.2243163138628006 1469.4837646484375 0.5048469305038452 0.85036033 0.20397646725177765 False diff --git a/ENCSR943SYS/cherimoya.fold_1.performance.tsv b/ENCSR943SYS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a59e45922d6c15dcf6f51372173c1b09a62b68c0..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1472.9964599609375 0.25985437631607056 0.5017764568328857 0.29693377017974854 0.8505183458328247 0.8418479561805725 0.20843587815761566 \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_2.evaluate.json b/ENCSR943SYS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cf098979220a45d68846c48a31d2276e17d4231f..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MHM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_2.fit.json b/ENCSR943SYS/cherimoya.fold_2.fit.json deleted file mode 100644 index bdce70f7148fda1aabfa0edd64ce159bf4a96b24..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF671MHM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_2.log b/ENCSR943SYS/cherimoya.fold_2.log deleted file mode 100644 index 79e065ae1371df6d97de61c4a669587034cd7a48..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 36.524412870407104 3.7149453163146973 1193.8466796875 0.43289339542388916 1693.7635498046875 0.31079721450805664 0.6336653 8.939495086669922 True -1 5742 32.13394021987915 16.54611587524414 1289.756103515625 0.5646263360977173 1469.9892578125 0.43822866678237915 0.74280554 0.9416720867156982 True -2 8613 32.18082547187805 17.447645902633667 1259.71923828125 0.39354556798934937 1436.93896484375 0.4543576240539551 0.75426567 0.4324330985546112 True -3 11484 31.77372908592224 15.802937507629395 1187.55224609375 0.42444702982902527 1423.5025634765625 0.4608897864818573 0.77138215 0.3617860972881317 True -4 14355 31.80649495124817 0.5333564281463623 1175.1407470703125 0.2760201692581177 1416.921630859375 0.46569812297821045 0.77373916 0.3892284631729126 True -5 17226 31.835716247558594 0.5265176296234131 1134.6612548828125 0.39178135991096497 1410.814208984375 0.4680642783641815 0.7736177 0.3540537357330322 False -6 20097 31.806057691574097 0.5453829765319824 1001.7440185546875 0.33404117822647095 1403.472412109375 0.4729417860507965 0.77762026 0.32444632053375244 True -7 22968 31.758219718933105 0.5371382236480713 1117.31103515625 0.5303350687026978 1398.8631591796875 0.4759930670261383 0.7812475 0.30012646317481995 True -8 25839 31.816028118133545 0.542447566986084 1002.20166015625 0.345041960477829 1395.6531982421875 0.47726982831954956 0.7850528 0.30015814304351807 True -9 28710 31.798404932022095 1.9850413799285889 1158.138427734375 0.3545190691947937 1391.4102783203125 0.47991251945495605 0.78613734 0.2869499921798706 True -10 31581 31.50219440460205 0.5370562076568604 1204.34619140625 0.33271723985671997 1387.48828125 0.481769323348999 0.7868466 0.2698403000831604 True -11 34452 31.20169425010681 0.548006534576416 1118.3974609375 0.1874639391899109 1385.0013427734375 0.48316293954849243 0.7950524 0.2645171284675598 True -12 37323 31.270161628723145 0.5423581600189209 1226.0302734375 0.42271968722343445 1376.5360107421875 0.48874807357788086 0.80067706 0.2536722421646118 True -13 40194 31.18113684654236 0.5424764156341553 1024.108154296875 0.22951531410217285 1378.5772705078125 0.4861452877521515 0.80709404 0.23707839846611023 True -14 43065 31.140098571777344 0.5291910171508789 1090.69091796875 0.22645491361618042 1373.2698974609375 0.48953166604042053 0.81541955 0.23460599780082703 True -15 45936 31.15293312072754 0.5475566387176514 1175.3232421875 0.21404871344566345 1370.447021484375 0.4916559159755707 0.8215547 0.22140814363956451 True -16 48807 31.102354526519775 1.523587942123413 1155.5927734375 0.22280964255332947 1369.0604248046875 0.4919986426830292 0.8247337 0.2143067717552185 True -17 51678 31.14467978477478 1.2252428531646729 1070.4600830078125 0.14543670415878296 1367.5986328125 0.492725133895874 0.8275333 0.21159467101097107 True -18 54549 31.201809644699097 22.06539559364319 1092.09326171875 0.29224860668182373 1368.2506103515625 0.4929637610912323 0.82904 0.21092171967029572 True -19 57420 31.45164704322815 0.9953293800354004 1018.0623779296875 0.16850945353507996 1369.2406005859375 0.49243855476379395 0.828152 0.21118921041488647 False diff --git a/ENCSR943SYS/cherimoya.fold_2.performance.tsv b/ENCSR943SYS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 47c556a433f5d83cdd33b8850005619be0cc9b8e..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1368.2506103515625 0.27063921093940735 0.4929637908935547 0.2809033691883087 0.829039990901947 0.8043943643569946 0.21092171967029572 \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_3.evaluate.json b/ENCSR943SYS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index efcc1a3e00c260b7f4dc758a7420f5a1bee2d71d..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MHM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_3.fit.json b/ENCSR943SYS/cherimoya.fold_3.fit.json deleted file mode 100644 index 49a072fefe84e11acba3acba4c6e994e9934ca14..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF671MHM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_3.log b/ENCSR943SYS/cherimoya.fold_3.log deleted file mode 100644 index eee3fad1e24f73614a72c421debed98f69296397..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2802 35.743781328201294 4.194456577301025 1305.5574951171875 0.6019877195358276 1689.05224609375 0.31634747982025146 0.6486279 9.269977569580078 True -1 5604 31.027603149414062 0.5825135707855225 1051.085205078125 0.5350618362426758 1496.534912109375 0.43119707703590393 0.7455595 1.1824456453323364 True -2 8406 31.162248611450195 0.5516293048858643 1353.0408935546875 0.5173736810684204 1465.6766357421875 0.4447549879550934 0.7643923 0.4578447937965393 True -3 11208 31.056727170944214 1.4709737300872803 1081.86767578125 0.4654191732406616 1445.704345703125 0.458181232213974 0.77481467 0.3427892029285431 True -4 14010 31.01768732070923 0.5651633739471436 1174.032958984375 0.2772914171218872 1441.493896484375 0.4600478410720825 0.7794801 0.3261256515979767 True -5 16812 31.04083824157715 0.5651161670684814 1288.37451171875 0.3218368887901306 1438.2413330078125 0.4621424078941345 0.7788517 0.363506555557251 False -6 19614 31.14622664451599 0.5633654594421387 1299.2735595703125 0.3885725736618042 1433.5135498046875 0.4659130871295929 0.7749617 0.3541664779186249 False -7 22416 31.275447368621826 1.104074478149414 1155.777099609375 0.2925584316253662 1431.2012939453125 0.46674853563308716 0.7786134 0.3637979030609131 False -8 25218 31.177430391311646 0.5590047836303711 1209.923828125 0.2744784355163574 1425.826416015625 0.4711359739303589 0.78462595 0.3467409312725067 True -9 28020 31.005976676940918 0.5458850860595703 1226.593017578125 0.2723584771156311 1424.088623046875 0.47139453887939453 0.78552073 0.3126600682735443 True -10 30822 30.558882474899292 0.5469114780426025 1102.4852294921875 0.36058279871940613 1419.1593017578125 0.47487369179725647 0.7890681 0.31060314178466797 True -11 33624 30.555749893188477 0.5464823246002197 1267.124755859375 0.20290032029151917 1413.4400634765625 0.4775959551334381 0.7978534 0.2836973965167999 True -12 36426 30.543675899505615 0.541724443435669 1246.551025390625 0.28819262981414795 1411.683837890625 0.47797632217407227 0.80334 0.27615708112716675 True -13 39228 30.550224542617798 0.5396416187286377 1106.9586181640625 0.236385315656662 1407.69287109375 0.4800319969654083 0.80814004 0.2618746757507324 True -14 42030 30.542804956436157 0.5433039665222168 1125.38916015625 0.1997828334569931 1408.1336669921875 0.4788002371788025 0.8198844 0.24502530694007874 True -15 44832 30.579110383987427 0.5434117317199707 965.13427734375 0.16212505102157593 1402.0416259765625 0.482928991317749 0.82744557 0.22648213803768158 True -16 47634 30.641698122024536 0.5406856536865234 975.9776611328125 0.3753346800804138 1401.468017578125 0.48363420367240906 0.83184075 0.21872471272945404 True -17 50436 30.61046004295349 0.5469355583190918 1039.3173828125 0.1522221565246582 1401.0067138671875 0.48338961601257324 0.8389233 0.21064724028110504 True -18 53238 30.531245946884155 0.5449292659759521 1090.347900390625 0.21106074750423431 1399.9923095703125 0.483670175075531 0.83990085 0.20687952637672424 True -19 56040 30.517893314361572 0.5596499443054199 1058.8572998046875 0.16131506860256195 1399.903564453125 0.4829183518886566 0.8404667 0.20641803741455078 True diff --git a/ENCSR943SYS/cherimoya.fold_3.performance.tsv b/ENCSR943SYS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 21268e483f27045a400f8e702feb42b20000836b..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1399.903564453125 0.27335143089294434 0.4829184114933014 0.27848580479621887 0.8404666781425476 0.8169538378715515 0.20641803741455078 \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_4.evaluate.json b/ENCSR943SYS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 450a700c9b2194e9fa25be1ad235e27b3cecf539..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF671MHM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_4.fit.json b/ENCSR943SYS/cherimoya.fold_4.fit.json deleted file mode 100644 index e7864dc90320f4d30e6331080877a065853335d4..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF671MHM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR943SYS/cherimoya.fold_4.log b/ENCSR943SYS/cherimoya.fold_4.log deleted file mode 100644 index 06887785514d82f4e9b8c9e278b3b31d743f24ae..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2812 36.241997718811035 4.836486339569092 1134.71142578125 0.48788997530937195 1594.003662109375 0.3109411597251892 0.63194555 8.55736255645752 True -1 5624 31.22982954978943 0.6210875511169434 1063.231201171875 0.38117095828056335 1402.7947998046875 0.42904195189476013 0.72822785 0.8267780542373657 True -2 8436 31.20335292816162 0.5363516807556152 1201.197265625 0.5564308166503906 1375.530029296875 0.44164565205574036 0.75596184 0.33822527527809143 True -3 11248 31.173882246017456 0.5304548740386963 1283.38427734375 0.4667912721633911 1361.9439697265625 0.4499996304512024 0.76226604 0.29170456528663635 True -4 14060 31.1544406414032 0.529496431350708 1197.3553466796875 0.5380890369415283 1354.302490234375 0.4545108675956726 0.76772535 0.2960785925388336 True -5 16872 31.20922040939331 1.2795836925506592 1269.380859375 0.31832122802734375 1349.649658203125 0.4585680067539215 0.7684455 0.3536064922809601 True -6 19684 31.188389539718628 1.417107105255127 1180.788330078125 0.24216902256011963 1346.7227783203125 0.46002641320228577 0.77259046 0.3130965232849121 True -7 22496 31.183695316314697 0.5264379978179932 1149.76025390625 0.2732616066932678 1343.920166015625 0.4619317948818207 0.76751167 0.3145636320114136 False -8 25308 31.294098377227783 0.5329935550689697 1156.3189697265625 0.2781795263290405 1338.4765625 0.4660037159919739 0.76705414 0.2913491129875183 False -9 28120 31.230268716812134 0.5295538902282715 1088.6265869140625 0.33240777254104614 1333.678466796875 0.4692578613758087 0.7815839 0.2580666244029999 True -10 30932 30.735746383666992 0.5292618274688721 1003.3295288085938 0.2648371160030365 1330.2371826171875 0.4713840186595917 0.78376025 0.25617772340774536 True -11 33744 30.523298740386963 0.5198736190795898 1177.9815673828125 0.24901632964611053 1324.090087890625 0.47577041387557983 0.787271 0.24127498269081116 True -12 36556 30.528488397598267 0.5299129486083984 1071.775634765625 0.381502628326416 1324.3289794921875 0.4737600088119507 0.7965658 0.23141804337501526 True -13 39368 30.505306243896484 0.5209751129150391 977.8443603515625 0.16196976602077484 1319.774658203125 0.47747814655303955 0.8042632 0.2259950041770935 True -14 42180 30.50123643875122 1.0804829597473145 1217.074951171875 0.2569285035133362 1319.014892578125 0.4774489402770996 0.8138057 0.21152029931545258 True -15 44992 30.45890164375305 0.5307161808013916 1122.978759765625 0.18375352025032043 1315.03759765625 0.47962450981140137 0.8210836 0.203330397605896 True -16 47804 30.492127656936646 0.5270791053771973 1145.5533447265625 0.2702260911464691 1311.7296142578125 0.48275473713874817 0.82575923 0.19510836899280548 True -17 50616 30.581727504730225 0.5292322635650635 1053.202880859375 0.21232271194458008 1312.16748046875 0.4817083179950714 0.82754624 0.19109031558036804 True -18 53428 30.494972467422485 0.5212581157684326 1122.33349609375 0.2617446184158325 1314.2843017578125 0.48022958636283875 0.83027 0.18909400701522827 True -19 56240 30.620766401290894 0.548879861831665 992.34375 0.16105997562408447 1314.330810546875 0.4802147150039673 0.83128256 0.18937039375305176 True diff --git a/ENCSR943SYS/cherimoya.fold_4.performance.tsv b/ENCSR943SYS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a7e1e00f0cd575f6ef8623041b4785451e60d2ce..0000000000000000000000000000000000000000 --- a/ENCSR943SYS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1314.330810546875 0.28070497512817383 0.48021477460861206 0.264843225479126 0.8312825560569763 0.80572110414505 0.18937039375305176 \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_0.evaluate.json b/ENCSR945JJB/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c2396e9b2b96340e441d3ef079aaace23f65c17e..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF545TYC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_0.fit.json b/ENCSR945JJB/cherimoya.fold_0.fit.json deleted file mode 100644 index 9eae82e2115a03976f88334137d01d10bee13c56..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF545TYC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_0.log b/ENCSR945JJB/cherimoya.fold_0.log deleted file mode 100644 index 0f1f20f729191b9a013d72f74bdbc56fb91d466d..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2736 35.075695753097534 4.165403842926025 564.20556640625 0.4649697542190552 719.74267578125 0.264376699924469 0.74096525 4.408185958862305 True -1 5472 30.564111471176147 0.6064093112945557 641.55712890625 0.2912066578865051 659.53662109375 0.3301377296447754 0.798268 1.0925003290176392 True -2 8208 30.51675820350647 0.6118240356445312 675.712890625 0.21108222007751465 647.4240112304688 0.34156736731529236 0.80825466 0.5630608201026917 True -3 10944 30.79891014099121 0.583449125289917 615.0875244140625 0.17694979906082153 641.9488525390625 0.3468833565711975 0.8165694 0.5846863389015198 True -4 13680 30.484593868255615 0.6125667095184326 534.3746948242188 0.22009170055389404 639.7686767578125 0.348760187625885 0.8227346 0.3938908576965332 True -5 16416 30.523121118545532 0.6014907360076904 539.826904296875 0.10768033564090729 636.6151733398438 0.3537822961807251 0.8286367 0.3927425742149353 True -6 19152 30.430843353271484 0.5913040637969971 718.0000610351562 0.2154044806957245 633.6532592773438 0.3578827381134033 0.83589685 0.3524211347103119 True -7 21888 30.409611701965332 0.5998761653900146 570.0597534179688 0.17191855609416962 632.4104614257812 0.3580001890659332 0.8420215 0.34285768866539 True -8 24624 30.476216554641724 0.6015920639038086 606.1351318359375 0.19783490896224976 631.3678588867188 0.35921964049339294 0.8465084 0.3273751437664032 True -9 27360 30.43936252593994 0.6041054725646973 519.3004150390625 0.11925100535154343 629.1433715820312 0.36227947473526 0.85044795 0.3280235230922699 True -10 30096 30.4476101398468 0.5831842422485352 489.055419921875 0.21411477029323578 627.1641845703125 0.36391088366508484 0.85801107 0.2743586003780365 True -11 32832 30.48585844039917 0.606926441192627 478.2923583984375 0.3342176079750061 625.3682250976562 0.3662720024585724 0.86183995 0.2501479387283325 True -12 35568 30.44240641593933 0.591524600982666 604.5372314453125 0.17574095726013184 623.2152709960938 0.3692057132720947 0.8647732 0.22549064457416534 True -13 38304 30.432836771011353 0.6002852916717529 557.3324584960938 0.1872509866952896 621.5728149414062 0.37067675590515137 0.8712229 0.2041698843240738 True -14 41040 30.415459394454956 1.0527713298797607 512.80859375 0.20054103434085846 620.8462524414062 0.370901882648468 0.8729104 0.18979817628860474 True -15 43776 30.528100967407227 15.358455181121826 549.9929809570312 0.10772347450256348 619.3555908203125 0.3739149868488312 0.8791094 0.17544938623905182 True -16 46512 30.680094242095947 0.6072611808776855 490.0137939453125 0.14311820268630981 620.35107421875 0.37104249000549316 0.8819149 0.16877786815166473 True -17 49248 30.57773995399475 0.59208083152771 518.8702392578125 0.14284491539001465 619.8026733398438 0.37173429131507874 0.88070816 0.16343989968299866 False -18 51984 30.4131441116333 0.5929367542266846 645.8970336914062 0.10531052201986313 620.1102294921875 0.3719654679298401 0.8808173 0.16196678578853607 False -19 54720 30.508506536483765 0.599231481552124 561.9573974609375 0.13833901286125183 619.5968627929688 0.3731699287891388 0.8815378 0.16223326325416565 False diff --git a/ENCSR945JJB/cherimoya.fold_0.performance.tsv b/ENCSR945JJB/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 04dc30eb3154265efb3c4f3027d7db76a46352b7..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -620.35107421875 0.3942471444606781 0.37104249000549316 0.1528838723897934 0.8819149136543274 0.8400468826293945 0.16877786815166473 \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_1.evaluate.json b/ENCSR945JJB/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2dcd53f31820d5b93324a4cb975aca019c75253a..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF545TYC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_1.fit.json b/ENCSR945JJB/cherimoya.fold_1.fit.json deleted file mode 100644 index 8d078eea91ce32b9031a37a9a3420ebb3c3e7801..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF545TYC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_1.log b/ENCSR945JJB/cherimoya.fold_1.log deleted file mode 100644 index 8d280fb3699315944a006658eb0b64d4980f338e..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2714 35.032272815704346 4.425916910171509 615.3062744140625 0.19800037145614624 853.7761840820312 0.2747015357017517 0.7432911 5.454987049102783 True -1 5428 30.31546664237976 0.8050899505615234 555.27783203125 0.32619768381118774 774.9454345703125 0.353719562292099 0.7991494 1.3186771869659424 True -2 8142 30.289885759353638 0.7183876037597656 610.4837036132812 0.213868647813797 758.7550659179688 0.3654539883136749 0.8127466 0.6609227061271667 True -3 10856 30.311817169189453 0.7130417823791504 563.8458251953125 0.21922090649604797 752.4884643554688 0.3704638183116913 0.8195341 0.7433764934539795 True -4 13570 30.292192459106445 0.7547788619995117 618.778564453125 0.2765900790691376 745.0297241210938 0.3778879940509796 0.8278206 0.49151721596717834 True -5 16284 30.20203161239624 0.7220649719238281 534.23974609375 0.28432902693748474 742.6774291992188 0.3812768757343292 0.8263419 0.4951319396495819 False -6 18998 30.159159660339355 0.7057609558105469 553.6654663085938 0.21364527940750122 740.288818359375 0.38373979926109314 0.8316014 0.48571714758872986 True -7 21712 30.242552757263184 0.7270467281341553 581.1846923828125 0.22415748238563538 737.0457153320312 0.38706502318382263 0.83813787 0.4508056342601776 True -8 24426 30.253944635391235 0.7212021350860596 592.191650390625 0.2795794606208801 732.9020385742188 0.3917343318462372 0.84121877 0.4360753893852234 True -9 27140 30.230167627334595 0.7896382808685303 607.552734375 0.16107326745986938 731.9915771484375 0.39189016819000244 0.8472615 0.3919515311717987 True -10 29854 30.28136157989502 0.7355449199676514 581.3388671875 0.22583411633968353 729.3977661132812 0.39537519216537476 0.8529161 0.364859014749527 True -11 32568 30.256176948547363 0.7247891426086426 552.1107788085938 0.22832569479942322 727.4090576171875 0.3967919647693634 0.86033005 0.32921651005744934 True -12 35282 30.257747650146484 0.703439474105835 624.2608642578125 0.18131142854690552 724.69775390625 0.3996776044368744 0.86359984 0.3043537735939026 True -13 37996 30.280080556869507 0.7205362319946289 505.8187255859375 0.15629078447818756 722.5790405273438 0.4012044072151184 0.8689838 0.2772020697593689 True -14 40710 30.251893043518066 0.7049877643585205 531.6402587890625 0.1020752415060997 720.8489379882812 0.4028075039386749 0.8743002 0.25279685854911804 True -15 43424 30.229661226272583 0.7335183620452881 544.7703247070312 0.12430038303136826 719.1739501953125 0.404705286026001 0.88057 0.2234056144952774 True -16 46138 30.2035551071167 0.7298722267150879 605.855224609375 0.12172501534223557 718.278564453125 0.4049180746078491 0.8842802 0.20651234686374664 True -17 48852 30.140177726745605 0.7076976299285889 456.2000732421875 0.11281965672969818 718.800537109375 0.4042547047138214 0.8845696 0.1951114535331726 True -18 51566 29.59986114501953 0.7162537574768066 509.0400085449219 0.08658838272094727 718.6597290039062 0.40445053577423096 0.88463914 0.1919064223766327 True -19 54280 29.56301188468933 2.4286515712738037 626.4512939453125 0.06928842514753342 718.958251953125 0.404573529958725 0.8847655 0.19128519296646118 True diff --git a/ENCSR945JJB/cherimoya.fold_1.performance.tsv b/ENCSR945JJB/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 52189b7f8c745d4fdd42e7d16549887a4f359610..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -718.958251953125 0.3685433268547058 0.404573529958725 0.18111057579517365 0.8847655057907104 0.86294025182724 0.19128519296646118 \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_2.evaluate.json b/ENCSR945JJB/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f259c53dbbb7783720fb60e7073a085ed3d99a9d..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF545TYC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_2.fit.json b/ENCSR945JJB/cherimoya.fold_2.fit.json deleted file mode 100644 index 080a9ae81bd63f5b4111d9392170888df17453f4..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF545TYC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_2.log b/ENCSR945JJB/cherimoya.fold_2.log deleted file mode 100644 index d59d00827f5d31e8ff3f3ecb7553020b41b6a2aa..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2902 36.829906940460205 4.551174640655518 600.194091796875 0.4715620279312134 755.8341064453125 0.2699047029018402 0.7415683 3.8152077198028564 True -1 5804 32.354740619659424 0.5965111255645752 609.4741821289062 0.36160266399383545 693.798583984375 0.3373264670372009 0.7969619 1.2212003469467163 True -2 8706 32.353718519210815 0.5973255634307861 554.977294921875 0.4342658221721649 681.6875610351562 0.3482593297958374 0.80353945 0.6506528854370117 True -3 11608 32.93242955207825 0.5687570571899414 617.8270263671875 0.37807345390319824 676.2083129882812 0.3529932498931885 0.81030726 0.6621220111846924 True -4 14510 32.36010384559631 0.8261399269104004 597.2125244140625 0.22980809211730957 674.2788696289062 0.355722576379776 0.8140956 0.5218996405601501 True -5 17412 32.3003466129303 0.5667953491210938 595.1487426757812 0.16232067346572876 671.6477661132812 0.35854142904281616 0.818865 0.4902834892272949 True -6 20314 32.2794086933136 0.563417911529541 551.1959228515625 0.24106228351593018 668.96923828125 0.3601011633872986 0.8266721 0.4224306046962738 True -7 23216 32.31349444389343 0.5595223903656006 550.5859985351562 0.13913723826408386 667.191162109375 0.3626475930213928 0.82995546 0.43487128615379333 True -8 26118 32.27266216278076 0.5620889663696289 682.5367431640625 0.2505539357662201 663.8128051757812 0.3664710521697998 0.83679396 0.36793217062950134 True -9 29020 32.27616095542908 0.5482816696166992 558.58740234375 0.203299880027771 662.2127685546875 0.3684467673301697 0.84047836 0.3505953550338745 True -10 31922 32.275521755218506 0.5520153045654297 599.6409912109375 0.188487708568573 659.1737670898438 0.37224021553993225 0.8459404 0.3317036032676697 True -11 34824 32.28290104866028 0.538933277130127 506.0062255859375 0.2474270462989807 657.3544921875 0.37354159355163574 0.8524915 0.3013697564601898 True -12 37726 31.621355295181274 0.9778902530670166 651.7725830078125 0.24148774147033691 656.6859741210938 0.374316930770874 0.85331327 0.2800227999687195 True -13 40628 31.636662244796753 0.5453677177429199 494.1114501953125 0.14400608837604523 654.5469360351562 0.37668782472610474 0.8602867 0.2537001073360443 True -14 43530 31.59770917892456 0.5526232719421387 485.31890869140625 0.16144248843193054 652.0543823242188 0.3796953558921814 0.86573523 0.2266225814819336 True -15 46432 31.582717418670654 0.5493354797363281 561.2769775390625 0.13418975472450256 650.5925903320312 0.38088592886924744 0.86888486 0.20649787783622742 True -16 49334 31.56748938560486 0.5500049591064453 549.5428466796875 0.23027941584587097 651.5265502929688 0.37978798151016235 0.87001723 0.194742351770401 True -17 52236 31.592286348342896 0.5555472373962402 498.1572265625 0.13182388246059418 650.523681640625 0.3813648521900177 0.87261695 0.18644508719444275 True -18 55138 31.694953441619873 20.498257875442505 474.41363525390625 0.13010302186012268 650.7803344726562 0.3803914785385132 0.87050235 0.18335875868797302 False -19 58040 31.688544750213623 0.550356388092041 529.21337890625 0.09788943827152252 650.5530395507812 0.38080114126205444 0.8712108 0.18377403914928436 False diff --git a/ENCSR945JJB/cherimoya.fold_2.performance.tsv b/ENCSR945JJB/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e85d3b72d435265d2aabdbe5a1cd0e31ab99e44d..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -650.523681640625 0.3865165710449219 0.3813648521900177 0.1613759845495224 0.8726169466972351 0.8445769548416138 0.18644508719444275 \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_3.evaluate.json b/ENCSR945JJB/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 264a1460848b562c9408a60f4ecce3a3010b6351..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF545TYC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_3.fit.json b/ENCSR945JJB/cherimoya.fold_3.fit.json deleted file mode 100644 index 6caa2f6147a46586b0e6946c0d90fddf38115617..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF545TYC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_3.log b/ENCSR945JJB/cherimoya.fold_3.log deleted file mode 100644 index d008c25ecc8c8fcd447422819a8105defda7ef59..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2762 35.21813416481018 3.763929605484009 583.9287109375 0.42929595708847046 724.36376953125 0.27259087562561035 0.73215115 4.571932792663574 True -1 5524 30.764171838760376 0.6267867088317871 569.5155029296875 0.28890469670295715 662.9691772460938 0.33559277653694153 0.79581016 1.1926369667053223 True -2 8286 30.750149488449097 0.5804271697998047 632.49853515625 0.33736786246299744 652.324462890625 0.34717845916748047 0.806358 0.6153086423873901 True -3 11048 30.185961723327637 0.5681533813476562 601.0468139648438 0.22682301700115204 646.0702514648438 0.3534065783023834 0.81458503 0.6345955729484558 True -4 13810 30.19821834564209 0.5662164688110352 626.7354125976562 0.269633412361145 644.123046875 0.35474082827568054 0.8185181 0.5507351756095886 True -5 16572 30.121432304382324 0.5727672576904297 459.94671630859375 0.24093061685562134 639.9013061523438 0.3601682484149933 0.8249767 0.4537653923034668 True -6 19334 30.110155820846558 0.5892281532287598 547.2266845703125 0.26988959312438965 638.4208374023438 0.3619902431964874 0.82810044 0.44538286328315735 True -7 22096 30.185996532440186 0.5802922248840332 508.6637878417969 0.20020651817321777 636.0430908203125 0.3642524480819702 0.8333122 0.42451080679893494 True -8 24858 30.062098503112793 0.5617706775665283 553.7537841796875 0.18879051506519318 634.2112426757812 0.3663438856601715 0.8381356 0.3993746042251587 True -9 27620 30.16650366783142 0.5724060535430908 592.8572998046875 0.2726697027683258 633.275146484375 0.36683985590934753 0.8397667 0.3764394223690033 True -10 30382 30.14248752593994 0.5705349445343018 625.8729248046875 0.24591124057769775 630.6411743164062 0.3698897361755371 0.8450801 0.3547061085700989 True -11 33144 30.099411725997925 0.5716428756713867 579.1695556640625 0.30156368017196655 628.4498291015625 0.37214064598083496 0.8522537 0.31191015243530273 True -12 35906 30.094050884246826 0.5717902183532715 486.1943359375 0.13306483626365662 627.0027465820312 0.3749813437461853 0.85893446 0.27779385447502136 True -13 38668 30.098381280899048 0.6350753307342529 518.7880249023438 0.32088011503219604 624.939697265625 0.37753891944885254 0.86272895 0.26197466254234314 True -14 41430 30.08642554283142 0.5719451904296875 617.5321044921875 0.11727990955114365 624.7701416015625 0.37566280364990234 0.8705787 0.2338205873966217 True -15 44192 30.12942337989807 0.5742835998535156 550.3624267578125 0.17558260262012482 622.1704711914062 0.3793465793132782 0.87319547 0.20925398170948029 True -16 46954 30.143900632858276 0.5724127292633057 564.0789184570312 0.14993014931678772 621.983154296875 0.37912020087242126 0.87751865 0.19600006937980652 True -17 49716 30.131226539611816 0.579721212387085 524.3109130859375 0.16159287095069885 622.8434448242188 0.3782835602760315 0.8792685 0.18640010058879852 True -18 52478 30.994284629821777 21.722535610198975 543.8318481445312 0.11025617271661758 622.4575805664062 0.3787829875946045 0.87732685 0.18184085190296173 False -19 55240 30.184456825256348 16.897926568984985 461.2368469238281 0.11788565665483475 621.5926513671875 0.38045090436935425 0.8788565 0.18157927691936493 False diff --git a/ENCSR945JJB/cherimoya.fold_3.performance.tsv b/ENCSR945JJB/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5d3a0502f031537acfe5d82a26770a4630b20535..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -622.8434448242188 0.3907330632209778 0.3782835304737091 0.15723782777786255 0.8792685270309448 0.8298475742340088 0.18640010058879852 \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_4.evaluate.json b/ENCSR945JJB/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0c1fdb0b4705326214063e774c8659df5784a790..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF545TYC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_4.fit.json b/ENCSR945JJB/cherimoya.fold_4.fit.json deleted file mode 100644 index 4734b8e6dc2163e438b9e9fb90ebe71f775656e9..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF545TYC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR945JJB/cherimoya.fold_4.log b/ENCSR945JJB/cherimoya.fold_4.log deleted file mode 100644 index 52fbd233b165fc2a849b1779a7db4752195a06e1..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2793 35.89899826049805 3.8301191329956055 674.5123291015625 0.34612730145454407 687.8861083984375 0.25996240973472595 0.73210907 3.797229290008545 True -1 5586 31.176310539245605 0.8145673274993896 563.1084594726562 0.24591705203056335 637.2570190429688 0.32330650091171265 0.7896003 1.0051521062850952 True -2 8379 31.210230588912964 0.5989284515380859 599.4420776367188 0.33069199323654175 628.4109497070312 0.32966503500938416 0.79834074 0.5297200679779053 True -3 11172 31.1213641166687 0.6071310043334961 546.023193359375 0.26376956701278687 622.4129028320312 0.33850619196891785 0.8058717 0.5381638407707214 True -4 13965 31.096404790878296 0.606945276260376 598.8756103515625 0.21466350555419922 617.9412231445312 0.34320828318595886 0.81331134 0.42716968059539795 True -5 16758 31.034592866897583 0.5984206199645996 548.1548461914062 0.19938203692436218 615.3170776367188 0.34682154655456543 0.81946236 0.4104628562927246 True -6 19551 31.049174547195435 0.6126656532287598 496.46240234375 0.2538621127605438 613.5059204101562 0.3488504886627197 0.8246533 0.37477225065231323 True -7 22344 31.112531661987305 0.5975594520568848 641.02880859375 0.30003622174263 611.650146484375 0.3515433371067047 0.8305564 0.3769553303718567 True -8 25137 31.099292278289795 0.5945870876312256 566.5302734375 0.23241665959358215 608.8841552734375 0.355250746011734 0.83659583 0.32972636818885803 True -9 27930 31.044151067733765 0.6034598350524902 511.20098876953125 0.1336776465177536 608.4067993164062 0.3554004430770874 0.8414469 0.3379358947277069 True -10 30723 31.08448624610901 0.5891604423522949 542.1536865234375 0.16526587307453156 605.6862182617188 0.3588601052761078 0.84638053 0.2956012785434723 True -11 33516 31.07461190223694 3.4271669387817383 643.7979736328125 0.19522175192832947 603.6049194335938 0.36182522773742676 0.8521034 0.27354562282562256 True -12 36309 30.455378770828247 0.5941503047943115 551.050537109375 0.18405678868293762 602.1998291015625 0.36272111535072327 0.85912716 0.23877432942390442 True -13 39102 30.40419030189514 0.6231014728546143 563.2742919921875 0.19934681057929993 600.6480712890625 0.36490100622177124 0.86330533 0.21093009412288666 True -14 41895 30.419914960861206 0.5922319889068604 538.80908203125 0.16193997859954834 600.4555053710938 0.36441370844841003 0.86773735 0.1951059252023697 True -15 44688 30.484095811843872 0.592393159866333 562.31591796875 0.1675850749015808 599.0765380859375 0.3672284185886383 0.8723598 0.1765134036540985 True -16 47481 30.470468044281006 0.5933792591094971 479.07275390625 0.0880914032459259 598.2716064453125 0.36810240149497986 0.87561834 0.16731172800064087 True -17 50274 30.41313147544861 0.5948381423950195 513.0235595703125 0.139170840382576 598.4525146484375 0.3675788640975952 0.87711984 0.1580854058265686 True -18 53067 30.364274263381958 0.5834283828735352 520.103271484375 0.0862579420208931 598.8482055664062 0.36735549569129944 0.8785911 0.15645252168178558 True -19 55860 30.41754150390625 0.6034700870513916 546.1585083007812 0.14023460447788239 599.1212768554688 0.3670068085193634 0.8765421 0.15628771483898163 False diff --git a/ENCSR945JJB/cherimoya.fold_4.performance.tsv b/ENCSR945JJB/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d0bfeaeabca9ba18cd982f4aed2a35b5f1041abf..0000000000000000000000000000000000000000 --- a/ENCSR945JJB/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -598.8482055664062 0.39869368076324463 0.3673555254936218 0.1495112180709839 0.8785911202430725 0.8288845419883728 0.15645252168178558 \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_0.evaluate.json b/ENCSR946BPA/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8af7c7fd8f5f0927287914e22088c869c6654277..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811OHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_0.fit.json b/ENCSR946BPA/cherimoya.fold_0.fit.json deleted file mode 100644 index 3ad34c12e9c55453bf053afb7cc6ae2f65fd7063..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF811OHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_0.log b/ENCSR946BPA/cherimoya.fold_0.log deleted file mode 100644 index fb51f35fb38b0d387412ac33274c5d16223c1639..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2511 32.44525909423828 3.4545371532440186 337.36865234375 0.6273899674415588 348.87896728515625 0.14441853761672974 0.72315854 4.344972610473633 True -1 5022 27.908045291900635 0.6286804676055908 250.74656677246094 0.35705286264419556 326.4994812011719 0.18397660553455353 0.7959196 1.196297526359558 True -2 7533 27.907615661621094 0.5857257843017578 341.9949035644531 0.4863602817058563 320.0671081542969 0.1901296228170395 0.8099987 0.7435277104377747 True -3 10044 27.920151948928833 0.5496437549591064 242.98123168945312 0.3602924346923828 317.5329895019531 0.19462472200393677 0.8173841 0.513381838798523 True -4 12555 27.894930601119995 1.4137344360351562 234.567138671875 0.4049891233444214 315.6251220703125 0.19819189608097076 0.8279622 0.4555143117904663 True -5 15066 27.917142629623413 0.5377652645111084 242.5635528564453 0.23357780277729034 314.8186950683594 0.19951914250850677 0.8315737 0.3992915749549866 True -6 17577 27.897526502609253 1.0998516082763672 285.7400207519531 0.3887210488319397 313.6481018066406 0.20207056403160095 0.83946455 0.3743659257888794 True -7 20088 27.875142097473145 0.5374484062194824 279.6832275390625 0.4339704215526581 312.5875244140625 0.20414012670516968 0.84254533 0.3894672989845276 True -8 22599 27.92804217338562 2.634918212890625 237.9077606201172 0.3019639849662781 312.0592346191406 0.2054370939731598 0.85081273 0.32609039545059204 True -9 25110 27.975529670715332 0.5449612140655518 265.2401123046875 0.36973074078559875 310.9350280761719 0.20786385238170624 0.85550386 0.2864408791065216 True -10 27621 27.925960302352905 0.5434749126434326 327.65496826171875 0.3809050917625427 310.48358154296875 0.20849691331386566 0.8597398 0.26604515314102173 True -11 30132 27.908796787261963 0.526932954788208 245.11398315429688 0.2826550602912903 310.1559143066406 0.20969201624393463 0.8639278 0.252798855304718 True -12 32643 28.015242338180542 0.5473239421844482 262.1905517578125 0.29084035754203796 309.66845703125 0.2103148251771927 0.8681347 0.2485545128583908 True -13 35154 27.971092700958252 0.5546884536743164 248.397216796875 0.2044072449207306 308.99151611328125 0.21159124374389648 0.8703243 0.2389349788427353 True -14 37665 27.862433671951294 0.5354275703430176 333.98834228515625 0.22936132550239563 308.9336853027344 0.21195460855960846 0.87336475 0.23524899780750275 True -15 40176 27.90508008003235 0.5348646640777588 290.0430603027344 0.23506799340248108 308.4229431152344 0.21325136721134186 0.8748074 0.2277885526418686 True -16 42687 27.906997203826904 0.8619821071624756 260.4935607910156 0.20457179844379425 308.1994323730469 0.21343129873275757 0.87463295 0.2246917486190796 False -17 45198 27.84913396835327 0.5361442565917969 266.1405029296875 0.1405317336320877 308.43988037109375 0.21253924071788788 0.87531435 0.22335068881511688 True -18 47709 27.825676202774048 0.5467534065246582 254.8486785888672 0.14033415913581848 308.58935546875 0.21222980320453644 0.8723528 0.22651037573814392 False -19 50220 27.543823957443237 0.5477557182312012 244.83741760253906 0.16949355602264404 308.30755615234375 0.2130475491285324 0.87089133 0.2281654179096222 False diff --git a/ENCSR946BPA/cherimoya.fold_0.performance.tsv b/ENCSR946BPA/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 8be448b8a1f105e1f4672ac125b70dd79bfa933c..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -308.43988037109375 0.5220098495483398 0.21253922581672668 0.07009369879961014 0.8753143548965454 0.7788344621658325 0.22335068881511688 \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_1.evaluate.json b/ENCSR946BPA/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ba95bd13ee4878a3b075b446e40c946a2bd988cd..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811OHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_1.fit.json b/ENCSR946BPA/cherimoya.fold_1.fit.json deleted file mode 100644 index 01a97ed7b8433fab18f82fc78f0f67a65fe770f9..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF811OHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_1.log b/ENCSR946BPA/cherimoya.fold_1.log deleted file mode 100644 index 2d3c35def890600a71ad2cba352e4a4fd87f3405..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2484 31.955079317092896 3.7470905780792236 264.5721130371094 0.39359015226364136 427.3580017089844 0.16202831268310547 0.7081173 5.266386032104492 True -1 4968 27.530952215194702 0.7540090084075928 275.771240234375 0.29570481181144714 395.8052062988281 0.21360348165035248 0.79444116 1.6369829177856445 True -2 7452 27.553974866867065 0.687018871307373 279.486328125 0.39887136220932007 389.0523681640625 0.21947281062602997 0.81142515 0.8699774742126465 True -3 9936 27.49978733062744 0.6525804996490479 274.52093505859375 0.3680921792984009 385.921630859375 0.22192758321762085 0.8192373 0.6514971256256104 True -4 12420 27.536123275756836 0.7157573699951172 262.5357666015625 0.3776744604110718 382.7261962890625 0.22742140293121338 0.8256387 0.5328865647315979 True -5 14904 27.545523405075073 0.6748993396759033 313.6501770019531 0.44199731945991516 380.66998291015625 0.23108425736427307 0.8300773 0.4870522916316986 True -6 17388 27.516889572143555 0.6631181240081787 260.5609436035156 0.3107965588569641 379.67242431640625 0.23247765004634857 0.8390701 0.5015910267829895 True -7 19872 27.504313707351685 0.6656134128570557 270.2138671875 0.2443442940711975 377.7903137207031 0.23641005158424377 0.8468551 0.4617414176464081 True -8 22356 27.478695392608643 0.691638708114624 214.26084899902344 0.19660687446594238 376.9652099609375 0.2381860464811325 0.8527834 0.46245071291923523 True -9 24840 27.483081340789795 0.6713666915893555 360.85064697265625 0.3413946330547333 375.8899841308594 0.24056102335453033 0.85984546 0.4029179513454437 True -10 27324 27.527205228805542 0.6538336277008057 293.2574462890625 0.3145087957382202 374.9159851074219 0.24220430850982666 0.8666026 0.37265023589134216 True -11 29808 27.525086641311646 0.6581096649169922 297.33447265625 0.2133294939994812 374.705322265625 0.24234384298324585 0.8724963 0.3514244258403778 True -12 32292 27.956454753875732 18.772593021392822 278.44622802734375 0.3637123107910156 374.10858154296875 0.24317605793476105 0.87383443 0.3353791832923889 True -13 34776 27.552653789520264 0.6648690700531006 283.943115234375 0.30296143889427185 373.0635681152344 0.24498946964740753 0.8784401 0.3146594166755676 True -14 37260 28.249595165252686 0.6638116836547852 331.6941833496094 0.2451019287109375 372.3328857421875 0.24569547176361084 0.8818052 0.29483968019485474 True -15 39744 27.62040901184082 1.2393314838409424 294.80712890625 0.2582119107246399 372.13641357421875 0.24598243832588196 0.88389957 0.28271088004112244 True -16 42228 27.48764395713806 0.6713495254516602 271.54217529296875 0.19675472378730774 372.2655334472656 0.2456134706735611 0.8856565 0.2726449966430664 True -17 44712 27.54345417022705 1.2347898483276367 299.84417724609375 0.21840260922908783 372.0752258300781 0.24542586505413055 0.8842111 0.27341628074645996 False -18 47196 27.53913712501526 0.67146897315979 267.6968994140625 0.2632361054420471 371.9202880859375 0.2461892068386078 0.88207567 0.2738581895828247 False -19 49680 27.48873543739319 0.6661102771759033 282.9552917480469 0.15296237170696259 371.60137939453125 0.24688799679279327 0.8812457 0.2759828269481659 False diff --git a/ENCSR946BPA/cherimoya.fold_1.performance.tsv b/ENCSR946BPA/cherimoya.fold_1.performance.tsv deleted file mode 100644 index d4daafeb41fa6fbd415de7567a9de0c337905280..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -372.2655334472656 0.49399900436401367 0.24561350047588348 0.08896921575069427 0.885656476020813 0.8360146284103394 0.2726449966430664 \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_2.evaluate.json b/ENCSR946BPA/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6137691811fc916e3fe79cdae1b9ac93cf671df4..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811OHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_2.fit.json b/ENCSR946BPA/cherimoya.fold_2.fit.json deleted file mode 100644 index e395bf963e193ce39b7c7ab975bf4e501c8309ac..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF811OHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_2.log b/ENCSR946BPA/cherimoya.fold_2.log deleted file mode 100644 index 7a718af759988fb912d04b53b0c0fe93607aa4cc..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2664 34.08235287666321 3.6184568405151367 277.38507080078125 0.3982960879802704 370.4645690917969 0.15235760807991028 0.69973266 4.03352165222168 True -1 5328 29.491573333740234 1.1777760982513428 219.6034393310547 0.5036519765853882 342.3648376464844 0.1981123983860016 0.7932799 1.0953712463378906 True -2 7992 29.507785081863403 0.8649399280548096 321.51239013671875 0.4066210389137268 338.38995361328125 0.20393963158130646 0.80318063 0.7060496211051941 True -3 10656 29.50382924079895 18.726249933242798 222.79505920410156 0.46585026383399963 334.7896423339844 0.2081284075975418 0.8143604 0.4804825186729431 True -4 13320 29.543237447738647 0.5199172496795654 282.2101135253906 0.2658952474594116 332.826904296875 0.2102132886648178 0.82318014 0.44892174005508423 True -5 15984 29.464224100112915 0.5129623413085938 272.7135925292969 0.2580089569091797 331.6329040527344 0.21156901121139526 0.8277239 0.45141375064849854 True -6 18648 29.519933223724365 0.5346107482910156 320.74951171875 0.27850306034088135 330.56640625 0.21349819004535675 0.83820194 0.3800780475139618 True -7 21312 29.47001051902771 0.520566463470459 233.2585906982422 0.45976901054382324 329.1039733886719 0.21627666056156158 0.84568864 0.3476787209510803 True -8 23976 29.43433165550232 0.5179924964904785 270.62469482421875 0.3619527220726013 328.3058776855469 0.21762052178382874 0.8507748 0.32705190777778625 True -9 26640 29.45595622062683 0.5216844081878662 284.0592956542969 0.31903159618377686 327.931640625 0.21825110912322998 0.85486907 0.32194289565086365 True -10 29304 29.43230128288269 0.500756025314331 277.97381591796875 0.22258633375167847 327.8055725097656 0.218425452709198 0.85894275 0.2869262099266052 True -11 31968 29.466323852539062 0.5203099250793457 313.62188720703125 0.26344674825668335 326.88934326171875 0.22028978168964386 0.8638323 0.2752983868122101 True -12 34632 29.53282380104065 0.5202605724334717 274.5777893066406 0.13922430574893951 326.6105041503906 0.2209024280309677 0.86690027 0.26487404108047485 True -13 37296 29.566505670547485 0.521686315536499 283.0964050292969 0.2613840401172638 325.820556640625 0.2220172882080078 0.8713414 0.25674426555633545 True -14 39960 29.47608709335327 0.5117013454437256 252.73553466796875 0.2024383842945099 325.5647888183594 0.22323140501976013 0.8725588 0.2503947615623474 True -15 42624 29.468645334243774 0.544867992401123 281.17034912109375 0.2690814733505249 324.98468017578125 0.2239076793193817 0.8751535 0.2411455661058426 True -16 45288 29.54073476791382 0.5194253921508789 278.3402404785156 0.30796220898628235 325.09552001953125 0.22319592535495758 0.87489843 0.2385822832584381 False -17 47952 29.52474856376648 0.5207686424255371 338.1177062988281 0.24017104506492615 324.7201843261719 0.22474133968353271 0.8727134 0.24078597128391266 False -18 50616 29.48641037940979 0.5115020275115967 248.8787078857422 0.16893889009952545 325.03387451171875 0.2244553118944168 0.87271 0.24352312088012695 False -19 53280 29.494248390197754 0.5197465419769287 222.78692626953125 0.1413111686706543 325.1265869140625 0.22384004294872284 0.8706657 0.2440587729215622 False diff --git a/ENCSR946BPA/cherimoya.fold_2.performance.tsv b/ENCSR946BPA/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5bb7773bf35edf5ed3f8e5a2fab8a1f18970c4c9..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.98468017578125 0.5125089883804321 0.2239076793193817 0.07508452236652374 0.8751534819602966 0.8078564405441284 0.2411455661058426 \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_3.evaluate.json b/ENCSR946BPA/cherimoya.fold_3.evaluate.json deleted file mode 100644 index be6e3b026befe63ba5a5d311f08606bc70f94209..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811OHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_3.fit.json b/ENCSR946BPA/cherimoya.fold_3.fit.json deleted file mode 100644 index 6944e6aa49ff82bb6a8b6729cf59437aa0f19929..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF811OHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_3.log b/ENCSR946BPA/cherimoya.fold_3.log deleted file mode 100644 index 627aa0c746cd6e7ab8d335965d950aaef51f2803..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2520 32.53898072242737 4.307403087615967 285.20501708984375 0.5888795852661133 363.5771484375 0.15740269422531128 0.6899693 4.8816328048706055 True -1 5040 27.95533847808838 0.5463807582855225 296.65911865234375 0.3985756039619446 342.35955810546875 0.19485466182231903 0.762505 1.4790796041488647 True -2 7560 27.425613164901733 12.100469589233398 296.140380859375 0.33653855323791504 337.45965576171875 0.19823941588401794 0.7749173 1.0674296617507935 True -3 10080 28.525497913360596 0.5151612758636475 275.33868408203125 0.27138859033584595 333.7913513183594 0.20414528250694275 0.7816433 0.684895932674408 True -4 12600 27.320855617523193 0.507756233215332 372.59674072265625 0.46351519227027893 331.38873291015625 0.20854370296001434 0.79983974 0.6156258583068848 True -5 15120 27.266856908798218 0.5101189613342285 290.53558349609375 0.4557766914367676 331.1660461425781 0.20870088040828705 0.8036584 0.6066823601722717 True -6 17640 27.293832302093506 0.7166242599487305 295.05865478515625 0.32771429419517517 329.9054260253906 0.2112383395433426 0.81082726 0.5329989790916443 True -7 20160 27.31934428215027 0.5087869167327881 267.08746337890625 0.32020169496536255 329.3903503417969 0.2119959592819214 0.82183737 0.48095837235450745 True -8 22680 27.394920825958252 0.5222816467285156 250.16502380371094 0.27959656715393066 328.17626953125 0.21487592160701752 0.8281543 0.42501431703567505 True -9 25200 27.342396020889282 0.5021367073059082 348.0717468261719 0.41555455327033997 327.8284606933594 0.21544967591762543 0.8314093 0.4104171097278595 True -10 27720 27.339028120040894 0.5059018135070801 236.5112762451172 0.2679479122161865 326.7962341308594 0.21787193417549133 0.8379561 0.3787866234779358 True -11 30240 27.33330750465393 0.509573221206665 258.2249755859375 0.321186900138855 325.706787109375 0.2204360067844391 0.84446764 0.35697686672210693 True -12 32760 27.34858751296997 0.523836612701416 259.18463134765625 0.3436664938926697 325.4773864746094 0.2207869589328766 0.8526022 0.32443752884864807 True -13 35280 27.412527799606323 0.6399028301239014 346.99200439453125 0.33379191160202026 325.2696533203125 0.22129248082637787 0.8575234 0.3064537048339844 True -14 37800 27.398842096328735 0.6336302757263184 255.78396606445312 0.2482050210237503 324.9095153808594 0.22117669880390167 0.86397976 0.2863089144229889 True -15 40320 27.40234398841858 0.5097360610961914 243.3992919921875 0.24671372771263123 324.5901794433594 0.2214316874742508 0.8675224 0.2692902088165283 True -16 42840 27.429874897003174 4.001526355743408 279.2165222167969 0.15942229330539703 323.9571533203125 0.22325387597084045 0.8718225 0.2628622353076935 True -17 45360 27.504624843597412 0.5317897796630859 241.80880737304688 0.19578590989112854 324.015869140625 0.22244668006896973 0.8726929 0.25675615668296814 True -18 47880 27.48112177848816 0.512336254119873 300.913330078125 0.10002419352531433 324.14483642578125 0.22219061851501465 0.87145704 0.2561894655227661 False -19 50400 27.452900409698486 0.5148017406463623 258.0607604980469 0.16410523653030396 324.62548828125 0.22087325155735016 0.87170297 0.25839680433273315 False diff --git a/ENCSR946BPA/cherimoya.fold_3.performance.tsv b/ENCSR946BPA/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 4ee53b9800fc21e7a18146c0add2dce2714aff5e..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.015869140625 0.5136774182319641 0.22244666516780853 0.07512763142585754 0.872692883014679 0.7948198318481445 0.25675615668296814 \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_4.evaluate.json b/ENCSR946BPA/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1c7bb1c86e5010f0890e48efd8154b629e143f29..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF811OHY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_4.fit.json b/ENCSR946BPA/cherimoya.fold_4.fit.json deleted file mode 100644 index 3a68a95099e721dc866e749f7ba21a304b581619..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF811OHY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946BPA/cherimoya.fold_4.log b/ENCSR946BPA/cherimoya.fold_4.log deleted file mode 100644 index 35f23afff0f991a3e3ceabf526819fb4c497d835..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2611 33.322864055633545 18.234874486923218 294.42059326171875 0.36136314272880554 323.9755859375 0.14501604437828064 0.693943 3.5280075073242188 True -1 5222 29.086519479751587 14.423416376113892 297.8150939941406 0.48815861344337463 305.268798828125 0.18023018538951874 0.7672974 0.9219298958778381 True -2 7833 29.018110990524292 0.5741398334503174 276.0474853515625 0.27765247225761414 301.9218444824219 0.18233804404735565 0.7830736 0.7685421705245972 True -3 10444 29.203309535980225 0.5501842498779297 263.9632568359375 0.5107479095458984 299.6885681152344 0.18588419258594513 0.79254544 0.43367093801498413 True -4 13055 29.016700744628906 0.5577883720397949 269.36907958984375 0.4078938961029053 297.8011779785156 0.1892312467098236 0.8073958 0.37450623512268066 True -5 15666 28.9273521900177 0.5570926666259766 343.91473388671875 0.3910560607910156 296.4263610839844 0.19223520159721375 0.8160502 0.37849947810173035 True -6 18277 28.4889018535614 0.5713112354278564 279.08477783203125 0.27885109186172485 295.8515625 0.19289584457874298 0.82169807 0.34832122921943665 True -7 20888 28.374951124191284 0.5416224002838135 230.3517303466797 0.3200550675392151 294.97198486328125 0.19482992589473724 0.8268748 0.33200541138648987 True -8 23499 28.43680167198181 0.539609432220459 214.6319580078125 0.3083367943763733 294.1861572265625 0.19629642367362976 0.834095 0.3104039430618286 True -9 26110 28.402236700057983 0.5228466987609863 212.6922607421875 0.22168807685375214 293.9624938964844 0.19725564122200012 0.83787006 0.2848178446292877 True -10 28721 28.413745403289795 0.5475509166717529 255.169189453125 0.20689848065376282 293.19219970703125 0.19860580563545227 0.8468573 0.27091264724731445 True -11 31332 28.409167766571045 0.5378742218017578 285.4377746582031 0.332884281873703 292.7591552734375 0.19956620037555695 0.85225683 0.2592499554157257 True -12 33943 28.44461703300476 0.5355205535888672 247.60321044921875 0.32458314299583435 292.1653137207031 0.20118442177772522 0.8557507 0.24474318325519562 True -13 36554 28.474625825881958 0.551889181137085 282.24053955078125 0.34712541103363037 291.7446594238281 0.20262226462364197 0.86216635 0.2310902178287506 True -14 39165 28.432504415512085 0.5229964256286621 221.49481201171875 0.3073723614215851 291.7481384277344 0.20270733535289764 0.8638723 0.21681341528892517 True -15 41776 28.43498730659485 0.527123212814331 265.57965087890625 0.17408545315265656 291.517333984375 0.20246835052967072 0.8676885 0.20943881571292877 True -16 44387 28.435850143432617 0.5251543521881104 209.50592041015625 0.18813811242580414 291.2591857910156 0.2031201422214508 0.8708966 0.20499689877033234 True -17 46998 28.468771934509277 0.5368993282318115 259.54925537109375 0.2510260343551636 291.679931640625 0.20194128155708313 0.8685425 0.20495165884494781 False -18 49609 28.363901615142822 0.5480000972747803 256.2589111328125 0.13743436336517334 291.2541198730469 0.20350782573223114 0.86859924 0.20674577355384827 False -19 52220 28.407734632492065 1.0098662376403809 205.12686157226562 0.17630887031555176 291.87713623046875 0.20170605182647705 0.86660546 0.20992790162563324 False diff --git a/ENCSR946BPA/cherimoya.fold_4.performance.tsv b/ENCSR946BPA/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b057314c9bb202b898756cde339e3ee4af0f96ef..0000000000000000000000000000000000000000 --- a/ENCSR946BPA/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -291.2591857910156 0.5286992192268372 0.2031201422214508 0.06341187655925751 0.870896577835083 0.7646032571792603 0.20499689877033234 \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_0.evaluate.json b/ENCSR946MAI/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 2dfb81385f55f4a6d6c5ed1946d7e40cac64efac..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF116NJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_0.fit.json b/ENCSR946MAI/cherimoya.fold_0.fit.json deleted file mode 100644 index 9bf92299dd5ef6c39daf42236174d9e251cf1c8e..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF116NJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_0.log b/ENCSR946MAI/cherimoya.fold_0.log deleted file mode 100644 index 4d41f9fb98462e3a65892f873cc44073ab7a34e9..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1270 17.68151617050171 3.4002628326416016 160.21878051757812 0.9642390012741089 231.73802185058594 0.3459615707397461 0.6364418 12.007025718688965 True -1 2540 14.112330913543701 0.2796766757965088 125.54053497314453 0.8921626210212708 195.5602569580078 0.42726168036460876 0.6699953 4.689666271209717 True -2 3810 14.104130506515503 0.2717783451080322 126.21126556396484 1.0436415672302246 182.7265167236328 0.4768899381160736 0.6801961 2.4410836696624756 True -3 5080 14.088724136352539 0.27460527420043945 138.93186950683594 0.7263984680175781 177.02529907226562 0.5006956458091736 0.7067794 0.9481452107429504 True -4 6350 14.140008687973022 0.29625368118286133 147.66026306152344 0.7420677542686462 174.76223754882812 0.5103037357330322 0.7089573 0.4821133613586426 True -5 7620 14.098108053207397 0.27404189109802246 125.76338195800781 0.6236814260482788 173.7462921142578 0.5155035257339478 0.71290374 0.3949021100997925 True -6 8890 14.153521060943604 0.310305118560791 141.63621520996094 0.7332620024681091 173.0752410888672 0.5188148617744446 0.71353394 0.3733486831188202 True -7 10160 14.13582992553711 0.2724921703338623 130.12771606445312 0.8294446468353271 172.65646362304688 0.5213336944580078 0.717255 0.3681837320327759 True -8 11430 14.136809587478638 0.2814671993255615 144.00927734375 0.4954574704170227 172.21246337890625 0.5236644744873047 0.7240879 0.35742104053497314 True -9 12700 14.138131618499756 0.28468751907348633 149.7208709716797 0.590798556804657 171.81350708007812 0.5255997776985168 0.7229627 0.36916372179985046 False -10 13970 14.151386499404907 0.280170202255249 133.74366760253906 0.616611123085022 171.47007751464844 0.5272961854934692 0.72478384 0.3622269034385681 True -11 15240 14.322339296340942 0.2922534942626953 131.69801330566406 0.46598580479621887 171.1947784423828 0.5285830497741699 0.7304779 0.3495485782623291 True -12 16510 14.18168568611145 0.27923083305358887 126.88265991210938 0.6420868039131165 170.8280487060547 0.5299551486968994 0.73100996 0.35530176758766174 True -13 17780 14.254886627197266 0.28937387466430664 126.13076782226562 0.43346846103668213 170.68722534179688 0.5309041738510132 0.73668295 0.34644806385040283 True -14 19050 14.19992709159851 0.2835218906402588 135.770751953125 0.6475113034248352 170.49960327148438 0.5318832993507385 0.7363954 0.35149335861206055 False -15 20320 14.126231908798218 0.28235554695129395 128.30752563476562 0.47601282596588135 170.3827362060547 0.5322305560112 0.7376427 0.3536606431007385 True -16 21590 14.127597093582153 0.2815124988555908 143.21080017089844 0.4249352812767029 170.39280700683594 0.5321505665779114 0.734105 0.36547696590423584 False -17 22860 14.10010290145874 0.7157015800476074 143.26739501953125 0.28368979692459106 170.61859130859375 0.5312358140945435 0.72908217 0.3816295266151428 False -18 24130 14.120155096054077 0.29572010040283203 117.81193542480469 0.39656832814216614 170.67311096191406 0.5300072431564331 0.7256816 0.40117424726486206 False -19 25400 14.182562351226807 0.28784847259521484 116.91621398925781 0.46971595287323 170.9240264892578 0.5293083786964417 0.72059643 0.4149383008480072 False diff --git a/ENCSR946MAI/cherimoya.fold_0.performance.tsv b/ENCSR946MAI/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f6ffae0238bba0086286d71ebf724839dcae9ac3..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -170.3827362060547 0.3850789964199066 0.5322305560112 0.11885375529527664 0.7376427054405212 0.707581639289856 0.3536606431007385 \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_1.evaluate.json b/ENCSR946MAI/cherimoya.fold_1.evaluate.json deleted file mode 100644 index fa678dba843f4668f45a40a83d7f2f29421cc866..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF116NJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_1.fit.json b/ENCSR946MAI/cherimoya.fold_1.fit.json deleted file mode 100644 index b2e5b9f48f1cbad2b03256a5f4f1d0afaec429f9..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF116NJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_1.log b/ENCSR946MAI/cherimoya.fold_1.log deleted file mode 100644 index 365b7df3ec37433d6bfb04bf6a61597167122bcd..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1266 17.506110429763794 3.3335418701171875 126.73539733886719 0.9196508526802063 261.7686767578125 0.3594769835472107 0.5987874 12.993977546691895 True -1 2532 14.050123453140259 0.38767337799072266 126.56681060791016 1.0194321870803833 218.78050231933594 0.44799700379371643 0.67269737 4.824949741363525 True -2 3798 14.085116863250732 0.37337446212768555 137.5096435546875 0.9507703185081482 205.67115783691406 0.49144047498703003 0.67123556 1.8638824224472046 False -3 5064 14.073710680007935 0.37277936935424805 144.47067260742188 0.8504599332809448 198.18470764160156 0.5187286734580994 0.70477563 0.6900765299797058 True -4 6330 14.106733560562134 0.3768351078033447 133.22804260253906 1.29339599609375 195.65309143066406 0.5280687808990479 0.71824634 0.4475545287132263 True -5 7596 14.053186416625977 0.3769700527191162 147.20565795898438 0.8755449056625366 194.4770050048828 0.5324274897575378 0.7251729 0.3778916299343109 True -6 8862 14.074817180633545 0.38536930084228516 131.36473083496094 0.7241889834403992 193.67539978027344 0.5368403792381287 0.72624815 0.3748154938220978 True -7 10128 14.083135843276978 0.3819851875305176 150.26792907714844 0.4794124662876129 192.89816284179688 0.5404702425003052 0.72893363 0.3721342384815216 True -8 11394 14.084179162979126 0.3841087818145752 137.26446533203125 0.8876985907554626 192.2563934326172 0.5431273579597473 0.73350126 0.3650774657726288 True -9 12660 14.091552495956421 0.382098913192749 128.55685424804688 0.8165575265884399 191.86573791503906 0.5452853441238403 0.7361207 0.3769640624523163 True -10 13926 14.149535417556763 6.523164510726929 130.18994140625 0.6899356842041016 191.45848083496094 0.5470660328865051 0.73839986 0.3743305504322052 True -11 15192 14.08918809890747 0.3811783790588379 135.98538208007812 0.46149301528930664 190.96096801757812 0.549200713634491 0.74626666 0.3627913296222687 True -12 16458 14.069224119186401 0.3793807029724121 135.4107666015625 0.31275150179862976 190.64559936523438 0.5508145093917847 0.75154805 0.35754185914993286 True -13 17724 14.076500654220581 0.43160009384155273 139.1085205078125 0.5046230554580688 190.3053741455078 0.5520905256271362 0.74964947 0.3705317974090576 False -14 18990 14.0611572265625 0.3708927631378174 117.05780029296875 0.6892011165618896 190.07952880859375 0.5531237721443176 0.7555852 0.3740383982658386 True -15 20256 14.051557302474976 0.3705718517303467 137.572998046875 0.470470666885376 190.00389099121094 0.5533453822135925 0.75664353 0.38056647777557373 True -16 21522 14.070872783660889 0.3768959045410156 133.13633728027344 0.6064034700393677 190.03976440429688 0.5530378222465515 0.7581863 0.3824542164802551 True -17 22788 14.07353401184082 0.3810255527496338 140.73995971679688 0.5541619062423706 190.14649963378906 0.5522842407226562 0.75586337 0.3972470760345459 False -18 24054 14.086867332458496 0.48300981521606445 150.73318481445312 0.4306023418903351 190.31080627441406 0.5513777136802673 0.7529237 0.4108307659626007 False -19 25320 14.079459428787231 0.381267786026001 147.790283203125 0.23969638347625732 190.43650817871094 0.5507957935333252 0.7495018 0.4246167838573456 False diff --git a/ENCSR946MAI/cherimoya.fold_1.performance.tsv b/ENCSR946MAI/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 3471259bbc81416cb195d2f9b0ade1f8ea583559..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -190.03976440429688 0.36885374784469604 0.5530378222465515 0.13107743859291077 0.7581862807273865 0.7561042904853821 0.3824542164802551 \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_2.evaluate.json b/ENCSR946MAI/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 86e9d2c68d31f10e8375348e5fbcb862175eaef8..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF116NJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_2.fit.json b/ENCSR946MAI/cherimoya.fold_2.fit.json deleted file mode 100644 index ef8dfbfa8d1def2813fd4312f1e78665ab42ac10..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF116NJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_2.log b/ENCSR946MAI/cherimoya.fold_2.log deleted file mode 100644 index 027c4a919caf5cd1bf2bf1a1b1169481c927a231..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1349 18.480079412460327 4.365312337875366 135.37841796875 1.0436890125274658 239.8024139404297 0.3535729944705963 0.6193345 11.749237060546875 True -1 2698 14.98908805847168 0.2975037097930908 113.10317993164062 1.374660849571228 201.54429626464844 0.4401603043079376 0.67851996 4.89109468460083 True -2 4047 14.978718519210815 0.27560949325561523 147.89688110351562 0.5207644701004028 189.6380157470703 0.48634135723114014 0.69192314 1.5302578210830688 True -3 5396 14.985013961791992 0.27185702323913574 148.15234375 0.4129447638988495 184.2403564453125 0.5090704560279846 0.7015749 0.6134994626045227 True -4 6745 14.993185758590698 0.2719399929046631 145.25392150878906 0.7653122544288635 182.3452606201172 0.5169088840484619 0.7117562 0.4679897129535675 True -5 8094 14.993033409118652 0.27522754669189453 157.11460876464844 0.6266832947731018 181.38983154296875 0.5217394232749939 0.72115 0.4164929687976837 True -6 9443 14.99556303024292 0.27169251441955566 140.79171752929688 0.7601656317710876 180.77052307128906 0.5250645875930786 0.7225114 0.4052495062351227 True -7 10792 15.012694835662842 0.27929091453552246 139.14862060546875 0.8418573141098022 180.1717529296875 0.5277913212776184 0.72303104 0.4008222818374634 True -8 12141 14.992592573165894 0.2754206657409668 124.42948913574219 0.6947489976882935 179.6825408935547 0.5303714871406555 0.7254679 0.3982756435871124 True -9 13490 14.992489099502563 0.28553032875061035 141.6475830078125 0.7058116793632507 179.18276977539062 0.5326958298683167 0.72811157 0.4044730067253113 True -10 14839 15.000172138214111 0.2856583595275879 136.33261108398438 0.5214896202087402 178.7097930908203 0.5349351763725281 0.72818357 0.410477876663208 True -11 16188 14.983484029769897 1.4330432415008545 136.7985076904297 0.3974478244781494 178.20912170410156 0.5370004773139954 0.73402506 0.4053017199039459 True -12 17537 15.04241943359375 0.2776505947113037 130.63150024414062 0.6650267243385315 177.8368377685547 0.5388321876525879 0.7369265 0.4065306484699249 True -13 18886 15.024302959442139 7.335270404815674 139.11181640625 0.5108047723770142 177.48573303222656 0.5406050682067871 0.7403121 0.4045749008655548 True -14 20235 16.24947500228882 10.912648677825928 116.93055725097656 0.6662222146987915 177.29122924804688 0.5413739681243896 0.741335 0.4091193675994873 True -15 21584 15.036506652832031 0.28339171409606934 135.16867065429688 0.6740978956222534 177.1447296142578 0.5420833230018616 0.74776196 0.40557947754859924 True -16 22933 15.036722660064697 10.374694585800171 120.40644836425781 0.43572714924812317 177.1246795654297 0.5419123768806458 0.74629855 0.4122229516506195 False -17 24282 15.08025336265564 0.27806758880615234 167.18692016601562 0.36943578720092773 177.1607666015625 0.5413042306900024 0.7427505 0.4264075756072998 False -18 25631 14.990215539932251 1.3258581161499023 142.2392578125 0.35874029994010925 177.30499267578125 0.5403609275817871 0.7398952 0.44273075461387634 False -19 26980 15.012409448623657 0.2762296199798584 128.21107482910156 0.4282108247280121 177.36473083496094 0.5398015975952148 0.7370932 0.45724162459373474 False diff --git a/ENCSR946MAI/cherimoya.fold_2.performance.tsv b/ENCSR946MAI/cherimoya.fold_2.performance.tsv deleted file mode 100644 index cb16433633880f31bce8ce8a8801e54623937c1c..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -177.1447296142578 0.3794371783733368 0.5420833230018616 0.12356444448232651 0.7477619647979736 0.719963550567627 0.40557947754859924 \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_3.evaluate.json b/ENCSR946MAI/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4a5e75bbaa75f5001f88a816be5dfbbe3779dc57..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF116NJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_3.fit.json b/ENCSR946MAI/cherimoya.fold_3.fit.json deleted file mode 100644 index ecf583414be6b95290355856beb3eedfd6dcc4fd..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF116NJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_3.log b/ENCSR946MAI/cherimoya.fold_3.log deleted file mode 100644 index 37a4e7111bc2761937d597dd3c9bc4dc98375207..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1318 18.165440559387207 3.7049052715301514 129.65884399414062 1.3009400367736816 231.50755310058594 0.35197651386260986 0.63798636 11.481029510498047 True -1 2636 14.680301666259766 0.3218834400177002 167.99461364746094 0.7975116968154907 195.78929138183594 0.43522366881370544 0.6942137 4.26194429397583 True -2 3954 14.642788171768188 0.26267290115356445 152.82806396484375 1.0530712604522705 183.6404571533203 0.47771039605140686 0.6754745 1.7885571718215942 False -3 5272 14.71010971069336 0.26966214179992676 144.5047607421875 1.1573832035064697 178.15469360351562 0.5027078986167908 0.6889736 0.6587944626808167 False -4 6590 14.620308876037598 0.25794363021850586 121.61808776855469 1.4036839008331299 176.43943786621094 0.5101375579833984 0.7138235 0.43599602580070496 True -5 7908 14.708869457244873 0.2626192569732666 149.6348876953125 0.6387292742729187 175.3167266845703 0.5154989957809448 0.726141 0.38151484727859497 True -6 9226 14.657320261001587 0.2578439712524414 144.57052612304688 0.8129744529724121 174.67637634277344 0.5183905363082886 0.7285549 0.393436461687088 True -7 10544 14.665375709533691 0.2671222686767578 131.192138671875 0.8183270692825317 174.03375244140625 0.5215458273887634 0.73016024 0.3912998139858246 True -8 11862 14.667588472366333 0.2583625316619873 160.41551208496094 0.5725102424621582 173.59437561035156 0.5239310264587402 0.7335472 0.3927863538265228 True -9 13180 14.66052770614624 0.2618587017059326 142.94137573242188 0.5476465225219727 173.2223663330078 0.5260311961174011 0.7401007 0.3745032846927643 True -10 14498 14.669455528259277 0.25301122665405273 144.13955688476562 0.7915676832199097 172.83038330078125 0.527676522731781 0.7394796 0.3812348544597626 False -11 15816 14.671215295791626 0.2709169387817383 163.6083984375 0.37677815556526184 172.5422821044922 0.529489278793335 0.7404361 0.3872525095939636 True -12 17134 14.618287324905396 0.25464582443237305 140.1810302734375 0.5341814160346985 172.2230682373047 0.5310306549072266 0.73605335 0.40344369411468506 False -13 18452 14.662372827529907 0.5667769908905029 133.6852569580078 0.5964594483375549 171.98818969726562 0.5322214365005493 0.7396018 0.397244393825531 False -14 19770 14.662635803222656 0.26035594940185547 129.62161254882812 0.477103590965271 171.76919555664062 0.5333619117736816 0.7390941 0.40438634157180786 False -15 21088 14.662871599197388 6.543168067932129 134.82418823242188 0.5028356909751892 171.6824951171875 0.5335233211517334 0.7397584 0.4072795510292053 False -16 22406 14.643767833709717 0.26378750801086426 135.424560546875 0.255795955657959 171.66758728027344 0.5332632660865784 0.7374768 0.40965890884399414 False -17 23724 14.638250827789307 1.1074936389923096 151.4012451171875 0.3883839547634125 171.83827209472656 0.5325679779052734 0.7382839 0.4199913740158081 False -18 25042 15.037351608276367 10.289880275726318 121.29129028320312 0.412753164768219 171.95578002929688 0.5315906405448914 0.73412585 0.434489905834198 False -19 26360 14.743948698043823 0.258530855178833 138.72235107421875 0.3172417879104614 172.06788635253906 0.5310385227203369 0.7319044 0.4471811354160309 False diff --git a/ENCSR946MAI/cherimoya.fold_3.performance.tsv b/ENCSR946MAI/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 94f6eb53a05049cf7f1061c5f592b40dd62560e1..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -172.5422821044922 0.38765397667884827 0.529489278793335 0.11739359050989151 0.7404360771179199 0.708207368850708 0.3872525095939636 \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_4.evaluate.json b/ENCSR946MAI/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b16b2352c33972fa6816ee138567b98c6995a0f4..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF116NJC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_4.fit.json b/ENCSR946MAI/cherimoya.fold_4.fit.json deleted file mode 100644 index 0a2641edf20a71a9113f697c2e5f5404e5159def..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF116NJC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MAI/cherimoya.fold_4.log b/ENCSR946MAI/cherimoya.fold_4.log deleted file mode 100644 index c88bde0b0d38d6a5278ab9daac7aed70531ee491..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1327 18.214558601379395 3.47446608543396 122.62135314941406 0.8629419803619385 227.02630615234375 0.34850701689720154 0.6404297 11.110047340393066 True -1 2654 14.93328046798706 9.388019800186157 142.88543701171875 0.8909310698509216 191.7810516357422 0.43302807211875916 0.67371285 4.619602203369141 True -2 3981 15.447073221206665 5.907221078872681 143.71157836914062 0.6496124267578125 181.43113708496094 0.4719788134098053 0.6703258 2.162230968475342 False -3 5308 14.75820803642273 0.2739126682281494 126.19164276123047 0.9245799779891968 175.75608825683594 0.49767473340034485 0.6821993 0.8193486928939819 True -4 6635 14.828886985778809 8.420532941818237 135.54095458984375 1.0251497030258179 173.77517700195312 0.5066465139389038 0.6912375 0.47300371527671814 True -5 7962 15.131362915039062 0.27179431915283203 148.2425994873047 0.7065788507461548 172.89891052246094 0.5111576318740845 0.6962794 0.45687806606292725 True -6 9289 14.751401662826538 0.27158212661743164 131.83731079101562 0.9548138380050659 172.33921813964844 0.5141286849975586 0.7119516 0.42652398347854614 True -7 10616 14.827291011810303 0.27291440963745117 141.64096069335938 0.8465460538864136 172.0291748046875 0.5166023969650269 0.719883 0.39343899488449097 True -8 11943 14.75768756866455 0.2790641784667969 130.64346313476562 0.8232441544532776 171.5914306640625 0.5183650851249695 0.7229865 0.3938198685646057 True -9 13270 14.729740858078003 0.27402377128601074 158.9429168701172 0.3989562690258026 171.2598876953125 0.5201179385185242 0.7255031 0.3875885009765625 True -10 14597 14.730452537536621 0.27314209938049316 129.91995239257812 0.6727068424224854 170.9128875732422 0.5220129489898682 0.73239714 0.38171541690826416 True -11 15924 14.742250204086304 0.27286839485168457 152.82449340820312 0.6062777042388916 170.53994750976562 0.5236563682556152 0.7370234 0.37438613176345825 True -12 17251 14.73653531074524 0.2832756042480469 114.77838134765625 0.7456268072128296 170.17884826660156 0.5252131223678589 0.7378556 0.37315550446510315 True -13 18578 14.746511459350586 0.2779865264892578 129.94383239746094 0.6861609816551208 169.87403869628906 0.5265576839447021 0.742893 0.37144404649734497 True -14 19905 14.785311937332153 0.27521347999572754 113.07083129882812 0.585155725479126 169.61582946777344 0.5279375910758972 0.7455239 0.365826278924942 True -15 21232 14.769360780715942 0.2765493392944336 144.11029052734375 0.5863345861434937 169.502685546875 0.5283005833625793 0.7450701 0.3795599639415741 False -16 22559 14.736268520355225 0.28127431869506836 134.58758544921875 0.2401590198278427 169.47079467773438 0.528204619884491 0.743666 0.3891872465610504 False -17 23886 14.759201288223267 0.281268835067749 141.9574432373047 0.662224531173706 169.56661987304688 0.5274699926376343 0.740782 0.40178418159484863 False -18 25213 14.765514612197876 0.2828493118286133 107.0147705078125 0.456560343503952 169.6231689453125 0.5266166925430298 0.73653674 0.4169265627861023 False -19 26540 14.72246789932251 0.46265745162963867 159.6736602783203 0.6107603907585144 169.74111938476562 0.5261328816413879 0.7353778 0.42618146538734436 False diff --git a/ENCSR946MAI/cherimoya.fold_4.performance.tsv b/ENCSR946MAI/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7410880c20aebbc0db7738e05b383cba86cc5d84..0000000000000000000000000000000000000000 --- a/ENCSR946MAI/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -169.61582946777344 0.38790541887283325 0.5279375910758972 0.11408022791147232 0.7455239295959473 0.6953731775283813 0.365826278924942 \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_0.evaluate.json b/ENCSR946MVP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 98185b8c44c02251ac8f50dd339e0f3f0ce51378..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OFE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_0.fit.json b/ENCSR946MVP/cherimoya.fold_0.fit.json deleted file mode 100644 index 8e94d2af65aa00a77351aaac7e05e76f5f686b3f..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF378OFE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_0.log b/ENCSR946MVP/cherimoya.fold_0.log deleted file mode 100644 index 973e85fb038b0d934f4c147561517fc85a4afcc3..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2774 34.55700349807739 4.135267019271851 1319.2030029296875 1.0112062692642212 1940.972412109375 0.34286749362945557 0.50218177 9.980271339416504 True -1 5548 30.56426215171814 1.8644206523895264 1173.5478515625 0.5229079723358154 1730.9703369140625 0.4365527629852295 0.59041345 3.92457914352417 True -2 8322 30.606395721435547 1.2854089736938477 1338.509765625 0.6019668579101562 1689.2581787109375 0.4464527368545532 0.60006624 2.3647665977478027 True -3 11096 30.579713106155396 0.7763047218322754 1375.0755615234375 0.5483863949775696 1636.23046875 0.4618696868419647 0.62239474 1.7693016529083252 True -4 13870 30.587459802627563 6.555280923843384 1118.671875 0.5411583185195923 1610.0057373046875 0.47168949246406555 0.6343571 1.4740999937057495 True -5 16644 30.600204467773438 0.5904438495635986 1168.803466796875 0.5878923535346985 1594.7093505859375 0.47634610533714294 0.6483876 1.211647391319275 True -6 19418 30.562992095947266 0.5930676460266113 1209.486083984375 0.5263199806213379 1593.64501953125 0.47418397665023804 0.6544235 1.1378031969070435 True -7 22192 30.26035165786743 0.5802152156829834 1289.1513671875 0.7846372127532959 1575.2314453125 0.48463964462280273 0.6605269 1.0679354667663574 True -8 24966 29.94548726081848 0.5857770442962646 1144.107177734375 0.5556908845901489 1567.38525390625 0.4888083338737488 0.6656709 1.0371133089065552 True -9 27740 29.940895080566406 1.9448378086090088 1230.119384765625 0.8686718940734863 1555.1920166015625 0.49490654468536377 0.67112666 1.0558185577392578 True -10 30514 29.99101448059082 4.274420738220215 1058.1949462890625 0.5256499648094177 1548.6383056640625 0.4976194202899933 0.67793167 0.9548153877258301 True -11 33288 30.047763109207153 1.6550564765930176 1443.733642578125 0.6299128532409668 1551.1456298828125 0.4935294985771179 0.68152803 0.8707497119903564 True -12 36062 30.029376983642578 1.5407938957214355 1234.14599609375 0.6245027184486389 1541.954833984375 0.49805769324302673 0.687298 0.8001833558082581 True -13 38836 30.073127269744873 10.16914677619934 1333.1046142578125 0.41816627979278564 1530.364013671875 0.5039095282554626 0.6929465 0.6978768706321716 True -14 41610 30.126877307891846 23.799296140670776 1488.7940673828125 0.5573952794075012 1524.16162109375 0.5049561262130737 0.69993275 0.6380279064178467 True -15 44384 30.820567846298218 0.6055505275726318 1214.9490966796875 0.439361035823822 1516.289306640625 0.5092618465423584 0.70905614 0.5893479585647583 True -16 47158 30.047313690185547 0.5971074104309082 1097.3660888671875 0.47388455271720886 1508.62744140625 0.5128955245018005 0.7113862 0.5411309003829956 True -17 49932 30.04041314125061 0.5883104801177979 1052.199951171875 0.3807269334793091 1506.470703125 0.5132858157157898 0.7112325 0.5092353224754333 False -18 52706 30.003992795944214 0.585451602935791 1198.3819580078125 0.5506374835968018 1510.7813720703125 0.5106272101402283 0.7110834 0.5027464032173157 False -19 55480 29.958356857299805 0.5833580493927002 918.2838134765625 0.2629243731498718 1508.7318115234375 0.5119822025299072 0.710053 0.502035915851593 False diff --git a/ENCSR946MVP/cherimoya.fold_0.performance.tsv b/ENCSR946MVP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 943181ea9cdbeada94bde39f9ce57e22dd7e65e9..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1508.62744140625 0.2354464828968048 0.5128955245018005 0.3162462115287781 0.7113862037658691 0.6321861743927002 0.5411309003829956 \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_1.evaluate.json b/ENCSR946MVP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 234bdb9d0a19cd6671f2bb8f22c13dc9a0acf15b..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OFE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_1.fit.json b/ENCSR946MVP/cherimoya.fold_1.fit.json deleted file mode 100644 index f5aa53d69546c5f484bba01159910d830b86d0b6..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF378OFE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_1.log b/ENCSR946MVP/cherimoya.fold_1.log deleted file mode 100644 index 6aa77b80cdcfa115f5a7f3e5b8cca65e39d87097..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2699 33.67765498161316 8.972841739654541 1094.9658203125 0.7055426836013794 2288.37353515625 0.3356483578681946 0.53074795 10.892149925231934 True -1 5398 29.828741788864136 1.6166892051696777 1467.066650390625 0.7595072984695435 2009.8074951171875 0.4396400451660156 0.6481554 4.170742988586426 True -2 8097 29.879651308059692 0.7904677391052246 1108.840087890625 0.7046244144439697 1945.3497314453125 0.45743635296821594 0.658105 2.436211347579956 True -3 10796 29.85988712310791 0.8083369731903076 1243.874267578125 0.61000657081604 1882.7701416015625 0.4681450128555298 0.6814224 1.9679948091506958 True -4 13495 29.548536777496338 0.7755262851715088 1117.621337890625 0.5008000135421753 1852.591552734375 0.4750826954841614 0.68730474 1.7240583896636963 True -5 16194 29.264458656311035 0.7743520736694336 1051.3858642578125 0.6426346302032471 1829.7064208984375 0.4831751883029938 0.69558465 1.659720778465271 True -6 18893 29.21260118484497 0.7819066047668457 1371.5572509765625 0.7087458372116089 1829.77294921875 0.48161208629608154 0.6971888 1.5536292791366577 True -7 21592 29.174886226654053 0.7747528553009033 1347.889404296875 0.8247843980789185 1798.0294189453125 0.4911320209503174 0.7051974 1.5921931266784668 True -8 24291 29.189571380615234 0.7697267532348633 1006.7059326171875 0.6381391286849976 1783.775146484375 0.49461570382118225 0.7091879 1.358060359954834 True -9 26990 29.196074962615967 0.7642273902893066 1201.886962890625 0.5433770418167114 1777.666015625 0.49452000856399536 0.71106225 1.0964645147323608 True -10 29689 29.203827142715454 0.7903883457183838 1145.664794921875 0.5494164228439331 1763.611572265625 0.4977176785469055 0.7266978 0.9943290948867798 True -11 32388 29.212346076965332 0.7985184192657471 1401.6842041015625 0.6504271626472473 1749.188232421875 0.5032522678375244 0.7299547 0.9087458848953247 True -12 35087 29.36051106452942 0.8166332244873047 1020.2963256835938 0.33404505252838135 1729.014892578125 0.5103246569633484 0.73509824 0.8627220988273621 True -13 37786 29.425501585006714 1.8942217826843262 1142.388671875 0.38740110397338867 1729.5262451171875 0.507388710975647 0.7455672 0.7493215799331665 True -14 40485 29.40850305557251 0.8086216449737549 1203.363525390625 0.7886000871658325 1720.5089111328125 0.5101641416549683 0.754268 0.6810457706451416 True -15 43184 29.38818049430847 0.7956697940826416 1175.1153564453125 0.3471767008304596 1712.987060546875 0.511260986328125 0.76241183 0.6249691843986511 True -16 45883 29.401600122451782 0.7846500873565674 1290.639404296875 0.36823225021362305 1705.9781494140625 0.5148162841796875 0.76554793 0.5709388256072998 True -17 48582 29.3830509185791 0.7866895198822021 1057.9283447265625 0.24456018209457397 1711.5328369140625 0.510953962802887 0.7672715 0.5447314381599426 True -18 51281 29.38764214515686 0.8011724948883057 1129.9263916015625 0.3892461359500885 1710.9140625 0.5128894448280334 0.7655058 0.5318371057510376 False -19 53980 29.368961095809937 31.925224542617798 1074.33203125 0.25017380714416504 1702.14794921875 0.5190520286560059 0.7643745 0.5336719155311584 False diff --git a/ENCSR946MVP/cherimoya.fold_1.performance.tsv b/ENCSR946MVP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index bb921c18a4cbacad495f43d92f5815590d6952b0..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1711.5328369140625 0.22753344476222992 0.5109539031982422 0.33026397228240967 0.7672715187072754 0.702781617641449 0.5447314381599426 \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_2.evaluate.json b/ENCSR946MVP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 8b5c7bc53364990ce02dc017c2463a9502e10257..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OFE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_2.fit.json b/ENCSR946MVP/cherimoya.fold_2.fit.json deleted file mode 100644 index 7e27fa2c2924fa1e785fd6fd0246c20252f6de17..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF378OFE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_2.log b/ENCSR946MVP/cherimoya.fold_2.log deleted file mode 100644 index 26c1b1b3aed1ccf801597ce68d719079d4005889..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2873 35.377108097076416 3.6685731410980225 1082.3223876953125 0.4889897108078003 1925.930419921875 0.34433385729789734 0.46286422 8.358716011047363 True -1 5746 31.78410506248474 0.6042690277099609 1441.80126953125 0.5671560168266296 1710.196044921875 0.44222986698150635 0.58815664 3.8003392219543457 True -2 8619 31.547924041748047 0.5861835479736328 1380.796142578125 1.1925967931747437 1681.64501953125 0.44445228576660156 0.59071285 2.0513439178466797 True -3 11492 31.117844581604004 0.5854165554046631 1015.718017578125 0.47722887992858887 1642.1676025390625 0.4576996862888336 0.60703194 1.928934931755066 True -4 14365 31.085264682769775 0.5843462944030762 1266.7528076171875 0.5432101488113403 1611.1011962890625 0.4681272804737091 0.63242996 1.4118740558624268 True -5 17238 31.069900512695312 0.5831830501556396 1155.1588134765625 0.6785873174667358 1595.0968017578125 0.47259390354156494 0.6434486 1.1111220121383667 True -6 20111 31.378252267837524 0.5870645046234131 1110.967041015625 0.6479604840278625 1580.91845703125 0.48006969690322876 0.65047836 0.988473117351532 True -7 22984 31.14244532585144 0.580125093460083 1371.3033447265625 0.5863178968429565 1569.1619873046875 0.48292091488838196 0.6618527 0.8065089583396912 True -8 25857 31.18157410621643 0.5756099224090576 1410.9931640625 0.6479119062423706 1557.8197021484375 0.4866098463535309 0.6674429 0.7754256129264832 True -9 28730 31.158233880996704 0.581085205078125 1134.9586181640625 0.6139206290245056 1544.0845947265625 0.494383841753006 0.6782831 0.7359353303909302 True -10 31603 31.1285138130188 0.5825870037078857 1418.8026123046875 0.7276908755302429 1538.0433349609375 0.4951823055744171 0.67998856 0.6817813515663147 True -11 34476 31.129937648773193 0.58516526222229 1275.710693359375 0.506971001625061 1525.3250732421875 0.5009094476699829 0.6874526 0.6502857804298401 True -12 37349 31.13276958465576 0.5840418338775635 1452.449951171875 0.7099063992500305 1523.0184326171875 0.49926459789276123 0.698065 0.631364107131958 True -13 40222 31.185022354125977 0.590240478515625 1046.6961669921875 0.37102439999580383 1516.1949462890625 0.5015630125999451 0.70322853 0.5960146188735962 True -14 43095 31.23120617866516 0.5874497890472412 1287.603759765625 0.5437783598899841 1509.4073486328125 0.5046833753585815 0.71393675 0.5622221827507019 True -15 45968 31.208619117736816 0.5866081714630127 1065.1317138671875 0.5469508171081543 1502.1759033203125 0.5073628425598145 0.71923435 0.5377184152603149 True -16 48841 31.213821411132812 0.5847518444061279 1146.5712890625 0.42873674631118774 1505.2728271484375 0.5047808885574341 0.72678167 0.5028792023658752 True -17 51714 31.20124888420105 0.5849626064300537 1240.2705078125 0.21552470326423645 1500.670166015625 0.5079975128173828 0.73012495 0.4788830876350403 True -18 54587 31.215075492858887 0.5884194374084473 1088.747802734375 0.25136125087738037 1500.140625 0.5087507367134094 0.72751063 0.4717772305011749 False -19 57460 31.206650733947754 0.5861246585845947 1112.1513671875 0.42283856868743896 1498.5400390625 0.5104137063026428 0.7264767 0.4731995463371277 False diff --git a/ENCSR946MVP/cherimoya.fold_2.performance.tsv b/ENCSR946MVP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 14df5abb332039223248e28629590b5856a69cd4..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1500.670166015625 0.2389964759349823 0.5079975128173828 0.3134596645832062 0.7301249504089355 0.6588876247406006 0.4788830876350403 \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_3.evaluate.json b/ENCSR946MVP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 898a3cc25efdda130d2ab56f7c70d55854b45db8..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OFE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_3.fit.json b/ENCSR946MVP/cherimoya.fold_3.fit.json deleted file mode 100644 index 49bf8b42e213dbe1cb5e301481ef99ce8d87fe19..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF378OFE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_3.log b/ENCSR946MVP/cherimoya.fold_3.log deleted file mode 100644 index aba5ab76a0e0bf3c8c70b727e9ab6bc4ae3e6e3c..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 34.676743030548096 3.7032389640808105 1076.049560546875 0.5662915110588074 1914.6444091796875 0.3446914851665497 0.46863687 9.163714408874512 True -1 5596 30.888397932052612 1.059436559677124 1163.905517578125 0.7584042549133301 1703.4134521484375 0.4428737759590149 0.57200086 3.104017734527588 True -2 8394 30.95909547805786 0.5281612873077393 1629.2169189453125 0.6298420429229736 1660.799072265625 0.4568978250026703 0.588885 2.208221912384033 True -3 11192 30.898610591888428 0.5279881954193115 1432.26123046875 0.8115790486335754 1621.855712890625 0.47144827246665955 0.60446686 1.8743555545806885 True -4 13990 30.902764797210693 0.521543025970459 917.7548217773438 0.6869305968284607 1610.257568359375 0.4761284291744232 0.60547644 1.652956247329712 True -5 16788 30.928010940551758 0.5204451084136963 1369.9329833984375 0.7030258774757385 1594.5224609375 0.48520752787590027 0.61878693 1.6706147193908691 True -6 19586 31.116111993789673 0.5198154449462891 1096.62353515625 0.5726658701896667 1584.8607177734375 0.48606282472610474 0.62727314 1.3740408420562744 True -7 22384 30.92623782157898 0.5225207805633545 1329.7352294921875 0.45283907651901245 1571.2779541015625 0.492744505405426 0.6339712 1.356742024421692 True -8 25182 31.153655529022217 0.5231924057006836 1162.2266845703125 0.581311821937561 1563.8804931640625 0.49410685896873474 0.63752854 1.2340540885925293 True -9 27980 30.913986682891846 0.5173301696777344 1260.1380615234375 0.7957066297531128 1556.1583251953125 0.497687965631485 0.6498806 1.0449585914611816 True -10 30778 30.891775131225586 0.5299811363220215 1105.0400390625 0.5193542242050171 1540.1641845703125 0.5046229958534241 0.6590062 0.984211266040802 True -11 33576 31.544615745544434 24.340693473815918 1353.5234375 0.5141304731369019 1531.6732177734375 0.5057145953178406 0.67104805 0.8920828700065613 True -12 36374 30.956607580184937 0.5295460224151611 1120.282958984375 0.4871261715888977 1530.89404296875 0.5039063692092896 0.6810174 0.7770121693611145 True -13 39172 30.92645788192749 0.5197765827178955 1158.275634765625 0.4462091624736786 1517.81982421875 0.5093736052513123 0.6933584 0.6987819075584412 True -14 41970 30.89962863922119 0.5242571830749512 1288.0013427734375 0.5839440226554871 1511.510009765625 0.5130248665809631 0.7052935 0.6263338923454285 True -15 44768 30.950827836990356 0.5114095211029053 1168.367919921875 0.34172773361206055 1502.7484130859375 0.5140325427055359 0.71677583 0.5724189281463623 True -16 47566 30.946288347244263 0.5207102298736572 1096.314697265625 0.3579883277416229 1497.421142578125 0.5175405144691467 0.72342294 0.5275431275367737 True -17 50364 30.681549310684204 0.5162093639373779 1211.874755859375 0.3145986795425415 1499.515380859375 0.5131333470344543 0.72565925 0.5032980442047119 True -18 53162 30.269413471221924 0.5202803611755371 1046.212890625 0.38144347071647644 1494.171630859375 0.5181305408477783 0.7243238 0.49632564187049866 False -19 55960 30.34684443473816 1.544358491897583 1046.66162109375 0.3873886466026306 1495.8658447265625 0.5178658962249756 0.7222018 0.4979890286922455 False diff --git a/ENCSR946MVP/cherimoya.fold_3.performance.tsv b/ENCSR946MVP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9e49074c6404e6ab29fc58d79b5380a87d486458..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1499.515380859375 0.2408873587846756 0.5131334066390991 0.31371739506721497 0.7256592512130737 0.6524884700775146 0.5032980442047119 \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_4.evaluate.json b/ENCSR946MVP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ee4e4c45e7c204bcb29df6782a320c30941cba29..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF378OFE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_4.fit.json b/ENCSR946MVP/cherimoya.fold_4.fit.json deleted file mode 100644 index 44635b288674f180ac6ca29daa6f010c68350006..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF378OFE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR946MVP/cherimoya.fold_4.log b/ENCSR946MVP/cherimoya.fold_4.log deleted file mode 100644 index 26a315124255e1d6988d8e3074553768ea3dd905..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2834 35.144593715667725 3.682786464691162 1203.3865966796875 0.5083943605422974 1844.9100341796875 0.3336399495601654 0.4788283 9.342228889465332 True -1 5668 31.289232969284058 0.5855000019073486 1202.700439453125 0.49294549226760864 1634.7772216796875 0.4344184994697571 0.5776909 3.1966733932495117 True -2 8502 31.264405727386475 0.569965124130249 1357.314208984375 0.9013316035270691 1589.34033203125 0.451588898897171 0.5887621 1.8440916538238525 True -3 11336 31.222689867019653 0.5637404918670654 1199.7215576171875 0.6911517381668091 1564.833984375 0.45599564909935 0.603016 1.3821760416030884 True -4 14170 31.217535972595215 0.564673662185669 1264.8531494140625 0.572246253490448 1545.7659912109375 0.462106317281723 0.6094477 1.1412616968154907 True -5 17004 31.1966233253479 0.5674896240234375 1305.496826171875 0.6438318490982056 1524.147705078125 0.470661461353302 0.62751734 0.9804735779762268 True -6 19838 31.19717264175415 0.5659801959991455 1525.6737060546875 0.8648313283920288 1515.5186767578125 0.4728870987892151 0.63725096 1.0983690023422241 True -7 22672 31.22938299179077 0.5661025047302246 1191.115234375 0.6264018416404724 1506.4720458984375 0.4767833352088928 0.64088404 0.9261195659637451 True -8 25506 31.238743543624878 0.5674936771392822 1537.1416015625 0.9187772274017334 1494.732421875 0.4817541241645813 0.6550029 0.8293034434318542 True -9 28340 31.216575622558594 1.7651066780090332 1474.050537109375 0.426770955324173 1478.7144775390625 0.4926629364490509 0.66281813 0.7914527654647827 True -10 31174 31.229990005493164 1.9020347595214844 1180.555419921875 0.6194134950637817 1477.4742431640625 0.49025729298591614 0.6681136 0.7462904453277588 True -11 34008 31.208173990249634 0.5723698139190674 1210.025634765625 0.5356979370117188 1470.7977294921875 0.49214670062065125 0.6743118 0.6612406373023987 True -12 36842 31.226433753967285 0.5718085765838623 1204.851806640625 0.5327929854393005 1459.60986328125 0.4992234408855438 0.6835433 0.6278634667396545 True -13 39676 31.10420846939087 0.5723958015441895 1145.148681640625 0.5040128231048584 1450.068115234375 0.5032630562782288 0.69104344 0.5826379060745239 True -14 42510 31.845816612243652 0.5622687339782715 1079.9462890625 0.4723946154117584 1444.2978515625 0.5058625340461731 0.6999897 0.5332512259483337 True -15 45344 30.79415488243103 0.5643177032470703 1188.8092041015625 0.5559716820716858 1442.3231201171875 0.5067026019096375 0.70826936 0.5020288228988647 True -16 48178 30.67091393470764 1.9014315605163574 1141.85205078125 0.25975850224494934 1438.6639404296875 0.5068454742431641 0.7166257 0.4718640446662903 True -17 51012 30.675204753875732 0.5620713233947754 1154.7747802734375 0.41994959115982056 1437.6063232421875 0.507240891456604 0.7171792 0.45903709530830383 True -18 53846 30.617531538009644 0.8651115894317627 1179.46630859375 0.34076744318008423 1441.7694091796875 0.5043324828147888 0.71813524 0.45923912525177 True -19 56680 30.677531957626343 0.5645537376403809 1012.7353515625 0.3184379041194916 1438.9068603515625 0.5071985721588135 0.71499515 0.4599372446537018 False diff --git a/ENCSR946MVP/cherimoya.fold_4.performance.tsv b/ENCSR946MVP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 014c45fef7bde9ce7c1218bf9e393210f38a1c33..0000000000000000000000000000000000000000 --- a/ENCSR946MVP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1441.7694091796875 0.24212047457695007 0.5043325424194336 0.30825918912887573 0.7181352376937866 0.6467165946960449 0.45923912525177 \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_0.evaluate.json b/ENCSR947POC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 430f617c640899f2378e38d22f97687b27585f9d..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863TMT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_0.fit.json b/ENCSR947POC/cherimoya.fold_0.fit.json deleted file mode 100644 index 52d1360fec8865303a654dfc855ed0e2dc3a6416..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF863TMT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_0.log b/ENCSR947POC/cherimoya.fold_0.log deleted file mode 100644 index bde79c2bbdbbcdf32840ba8f28b12a5694d29555..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2723 34.520581007003784 2.864821195602417 230.21096801757812 1.3066407442092896 324.7449035644531 0.1894332468509674 0.463694 5.17726469039917 True -1 5446 30.004122972488403 0.646418571472168 236.55038452148438 1.1524637937545776 283.80194091796875 0.31456848978996277 0.57298064 2.3869364261627197 True -2 8169 30.213700771331787 1.3237419128417969 164.09910583496094 0.8401108384132385 278.4130859375 0.3277199864387512 0.5824518 1.0566937923431396 True -3 10892 30.047390937805176 1.9880046844482422 215.97549438476562 0.6343587040901184 276.0016174316406 0.33469271659851074 0.5954579 0.897645115852356 True -4 13615 30.106398344039917 1.4273908138275146 277.005615234375 1.2757514715194702 274.2847900390625 0.34065765142440796 0.6079172 0.8465006351470947 True -5 16338 30.047959327697754 2.034930467605591 208.56460571289062 0.6844595074653625 274.40435791015625 0.3400290310382843 0.609575 0.8018717169761658 True -6 19061 30.068005561828613 1.1089296340942383 193.7584991455078 0.9897274971008301 272.87957763671875 0.3449673652648926 0.61542064 0.766751766204834 True -7 21784 30.032745838165283 1.2686471939086914 201.65518188476562 0.7548235058784485 272.1050720214844 0.34678545594215393 0.62539595 0.7495661973953247 True -8 24507 30.030630588531494 1.1465420722961426 203.09332275390625 0.8522415161132812 270.84442138671875 0.3509555160999298 0.6376381 0.6762046813964844 True -9 27230 30.041037559509277 0.6578207015991211 178.2392578125 0.8554888963699341 270.5110168457031 0.35167208313941956 0.64582384 0.6614841818809509 True -10 29953 30.072245836257935 0.549591064453125 160.30450439453125 0.6917669177055359 269.8948669433594 0.35356101393699646 0.6573908 0.6434430480003357 True -11 32676 30.071488857269287 0.5575234889984131 234.63626098632812 0.955973744392395 268.6833801269531 0.35538390278816223 0.67269 0.6010175943374634 True -12 35399 30.01466202735901 0.5499422550201416 172.501220703125 0.5252935886383057 268.074951171875 0.3577626049518585 0.68253464 0.5692101716995239 True -13 38122 29.986260175704956 1.5664820671081543 218.21658325195312 0.6354816555976868 267.5733642578125 0.35912689566612244 0.69842434 0.5357350707054138 True -14 40845 30.04075860977173 0.5421657562255859 188.90151977539062 0.6596237421035767 266.5988464355469 0.3623238205909729 0.71230805 0.5113707184791565 True -15 43568 29.49285387992859 0.5774414539337158 216.06671142578125 0.5156934857368469 265.9082336425781 0.36448436975479126 0.72013134 0.5010197758674622 True -16 46291 29.490493535995483 0.5448603630065918 206.1119384765625 0.44365525245666504 265.3619079589844 0.36659249663352966 0.73002255 0.48892879486083984 True -17 49014 29.48568606376648 0.5511689186096191 174.17242431640625 0.4386276602745056 265.33221435546875 0.36638838052749634 0.73220515 0.4858085811138153 True -18 51737 29.465718984603882 0.631014347076416 206.20101928710938 0.5388374924659729 265.9583740234375 0.3632531762123108 0.73467356 0.4865330159664154 True -19 54460 29.568503856658936 0.5386831760406494 231.0148468017578 0.5234256982803345 265.4294738769531 0.36565008759498596 0.7347106 0.49118754267692566 True diff --git a/ENCSR947POC/cherimoya.fold_0.performance.tsv b/ENCSR947POC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 0ee05096ff533a5254abdf121b29d13a63878c20..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -265.4294738769531 0.46077960729599 0.3656500577926636 0.08994623273611069 0.7347105741500854 0.6868495345115662 0.49118754267692566 \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_1.evaluate.json b/ENCSR947POC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 10b2f22e8b9af83870e60f077d7ff9630a9ed6b3..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863TMT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_1.fit.json b/ENCSR947POC/cherimoya.fold_1.fit.json deleted file mode 100644 index 402f158f44efc34401bc8b8585f8ccf7c05b29b9..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF863TMT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_1.log b/ENCSR947POC/cherimoya.fold_1.log deleted file mode 100644 index 1d0d8038ab077daf7551bcec7f22afe0194c0422..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2720 34.66245412826538 3.7791831493377686 224.2813720703125 0.8991281986236572 356.32489013671875 0.19389045238494873 0.5084623 5.257236003875732 True -1 5440 29.930676460266113 0.7105143070220947 263.4456481933594 0.881629228591919 311.17779541015625 0.3241990804672241 0.5995823 2.3088364601135254 True -2 8160 29.914736032485962 0.6493179798126221 204.90399169921875 1.1712162494659424 302.9837951660156 0.33822518587112427 0.6044189 1.1261500120162964 True -3 10880 30.34068489074707 0.7084541320800781 213.88702392578125 1.0220189094543457 300.2742614746094 0.3424331843852997 0.61983824 0.8687654137611389 True -4 13600 29.846312999725342 2.0877325534820557 180.58355712890625 1.0902976989746094 298.8017883300781 0.3466818928718567 0.6273967 0.8272301554679871 True -5 16320 29.880506992340088 0.6385889053344727 227.02670288085938 0.7190827131271362 297.6945495605469 0.34890061616897583 0.63945127 0.7713106870651245 True -6 19040 29.84419274330139 1.5897321701049805 162.71749877929688 0.8482638597488403 296.4278869628906 0.3530385494232178 0.64122695 0.7656484842300415 True -7 21760 29.953012943267822 0.6683022975921631 150.79095458984375 0.4754686653614044 295.1357727050781 0.35736697912216187 0.65878856 0.7188889980316162 True -8 24480 29.852062225341797 0.6472721099853516 215.5543975830078 0.8799015283584595 293.9992370605469 0.36070674657821655 0.66454023 0.6938860416412354 True -9 27200 29.833641052246094 0.6245579719543457 196.45571899414062 0.8708862066268921 293.15985107421875 0.3630131483078003 0.6739223 0.689582884311676 True -10 29920 29.831829071044922 0.6438131332397461 206.8194580078125 0.6771911978721619 292.11602783203125 0.36540988087654114 0.68348104 0.6591649651527405 True -11 32640 29.986176013946533 0.6659679412841797 189.7764129638672 0.8190560340881348 291.7159423828125 0.365151971578598 0.6902736 0.6286447048187256 True -12 35360 30.106956481933594 0.6496791839599609 186.48008728027344 0.6514416337013245 290.052978515625 0.37011075019836426 0.70545685 0.5899893045425415 True -13 38080 29.95354676246643 0.6510789394378662 206.6178436279297 0.5025906562805176 289.1341247558594 0.3733483850955963 0.7169146 0.576153576374054 True -14 40800 29.947039127349854 0.6522109508514404 198.27926635742188 0.49665093421936035 288.7512512207031 0.37221983075141907 0.72825557 0.5534180402755737 True -15 43520 30.001283884048462 0.6406278610229492 179.5992431640625 0.5867218375205994 288.0924072265625 0.37450769543647766 0.73745245 0.5300471782684326 True -16 46240 29.99761986732483 0.6564297676086426 193.68801879882812 0.4012449085712433 287.38226318359375 0.3772837817668915 0.7457826 0.5202627778053284 True -17 48960 29.524028301239014 0.641472578048706 215.0081787109375 0.3818117380142212 287.71148681640625 0.3758145868778229 0.75099206 0.5155210494995117 True -18 51680 29.53616189956665 0.6334371566772461 249.03639221191406 0.41303640604019165 287.78094482421875 0.37609580159187317 0.75107056 0.5191826820373535 True -19 54400 29.479928255081177 0.6337018013000488 192.19210815429688 0.4009430408477783 287.76171875 0.37594956159591675 0.7518336 0.5185286402702332 True diff --git a/ENCSR947POC/cherimoya.fold_1.performance.tsv b/ENCSR947POC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ac8ce79e96ca23042b7785f08f4d6f6d472f5b89..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -287.76171875 0.4512231945991516 0.37594956159591675 0.09733816981315613 0.7518336176872253 0.7186879515647888 0.5185286402702332 \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_2.evaluate.json b/ENCSR947POC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 6050ce1fb323a15f28d8083fce2103ba1ce7f349..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863TMT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_2.fit.json b/ENCSR947POC/cherimoya.fold_2.fit.json deleted file mode 100644 index 5a616b4e889c638c97353da1ced16e0bfe1887a8..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF863TMT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_2.log b/ENCSR947POC/cherimoya.fold_2.log deleted file mode 100644 index 3b86f94a65e8dce63f012f8602b99faf27f83760..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2869 36.49287271499634 5.910406827926636 224.1864013671875 0.9668079018592834 333.98876953125 0.18787835538387299 0.4715868 4.8570356369018555 True -1 5738 31.646133422851562 1.687324047088623 224.39083862304688 0.8051104545593262 291.0285949707031 0.3207796514034271 0.59416986 1.6981253623962402 True -2 8607 31.653589248657227 0.555497407913208 197.33062744140625 0.5895670652389526 285.2254333496094 0.33014827966690063 0.5962751 0.8435498476028442 True -3 11476 31.51886248588562 0.5884571075439453 233.31539916992188 0.8355585932731628 281.9709777832031 0.3398588299751282 0.6109697 0.7499833106994629 True -4 14345 31.508406162261963 0.6477048397064209 198.6270751953125 0.8231862783432007 281.01409912109375 0.3419307768344879 0.6156631 0.6900691390037537 True -5 17214 31.500734090805054 0.5498673915863037 230.748779296875 0.855215847492218 279.4922180175781 0.34588396549224854 0.62959063 0.667031466960907 True -6 20083 31.49893808364868 0.5500004291534424 227.12225341796875 0.7769042253494263 278.7029113769531 0.3483666777610779 0.6360013 0.6446252465248108 True -7 22952 31.496984243392944 0.5359230041503906 215.761962890625 0.6341041326522827 277.798583984375 0.35162898898124695 0.64373994 0.6309620141983032 True -8 25821 31.78047204017639 0.5591559410095215 196.18936157226562 0.631844162940979 276.490478515625 0.3550165593624115 0.65614325 0.608835756778717 True -9 28690 31.587358713150024 0.5517010688781738 211.08157348632812 0.45475298166275024 275.9888916015625 0.35709065198898315 0.6578488 0.6038761138916016 True -10 31559 31.52195906639099 0.531346321105957 237.5838165283203 0.6669498682022095 275.08856201171875 0.35907530784606934 0.6673772 0.592476487159729 True -11 34428 31.48644518852234 0.5371813774108887 222.29476928710938 0.49423083662986755 274.4966125488281 0.361078679561615 0.67855626 0.5769411325454712 True -12 37297 31.48159670829773 0.9958562850952148 210.6169891357422 0.5197382569313049 273.7912292480469 0.3607935905456543 0.68893415 0.5641351342201233 True -13 40166 31.512027740478516 4.444483280181885 213.06358337402344 0.5330893397331238 273.2551574707031 0.3631257116794586 0.7024196 0.5332614779472351 True -14 43035 31.569676876068115 0.5487666130065918 187.61521911621094 0.375563383102417 272.2869873046875 0.36616250872612 0.7120064 0.5245103240013123 True -15 45904 31.528149127960205 0.5479717254638672 171.59385681152344 0.4832719564437866 271.7610778808594 0.36838361620903015 0.7237915 0.5075453519821167 True -16 48773 31.394639015197754 0.5416698455810547 154.0880889892578 0.3243746757507324 271.790771484375 0.3667858839035034 0.7297341 0.5093177556991577 True -17 51642 30.865609884262085 0.5252895355224609 176.99227905273438 0.32436609268188477 271.5737609863281 0.36814141273498535 0.73442894 0.5032026767730713 True -18 54511 30.979896068572998 0.5335545539855957 197.70620727539062 0.4075464904308319 271.71514892578125 0.36764323711395264 0.73547703 0.508735716342926 True -19 57380 30.934035539627075 0.5412399768829346 223.29931640625 0.6129412651062012 271.4169006347656 0.3692263960838318 0.7364387 0.5097449421882629 True diff --git a/ENCSR947POC/cherimoya.fold_2.performance.tsv b/ENCSR947POC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e6946c1eed226c005ac181d0cf39a4664ff27323..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -271.4169006347656 0.4575223922729492 0.3692264258861542 0.09150318801403046 0.7364386916160583 0.6976073384284973 0.5097449421882629 \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_3.evaluate.json b/ENCSR947POC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 29e5bafff4c44d0c77855a8046c1908f0994a30d..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863TMT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_3.fit.json b/ENCSR947POC/cherimoya.fold_3.fit.json deleted file mode 100644 index 969f359e96701503e4ce60fccfe67dbc8cd1de80..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF863TMT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_3.log b/ENCSR947POC/cherimoya.fold_3.log deleted file mode 100644 index 538262ab67ae5c5ebebc41e87ad53b0afc018ef0..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.138683795928955 3.429704427719116 239.5538330078125 1.2734997272491455 331.8362731933594 0.19153456389904022 0.4874452 4.451079368591309 True -1 5516 30.386401414871216 0.8415982723236084 248.11509704589844 0.8460437655448914 291.43359375 0.3188537061214447 0.5888849 1.876579999923706 True -2 8274 30.298229932785034 0.6012747287750244 214.27536010742188 1.0501132011413574 287.2958679199219 0.32778462767601013 0.5877244 0.9616600871086121 False -3 11032 30.323870182037354 0.5456619262695312 205.2025146484375 1.0927931070327759 284.73785400390625 0.33459532260894775 0.606004 0.7954552173614502 True -4 13790 30.268755197525024 0.5515303611755371 214.60711669921875 0.9506085515022278 283.85711669921875 0.33824101090431213 0.614775 0.7219207882881165 True -5 16548 30.324275016784668 0.5436797142028809 223.08799743652344 1.1287152767181396 282.6054992675781 0.34146028757095337 0.6215507 0.6895264387130737 True -6 19306 30.378910779953003 11.726018905639648 201.4445037841797 0.7764365077018738 281.47735595703125 0.34448570013046265 0.6289625 0.667045533657074 True -7 22064 30.317573070526123 1.1741783618927002 247.5123291015625 1.072307825088501 280.5669250488281 0.34622451663017273 0.64069986 0.655820906162262 True -8 24822 30.344656705856323 0.6256282329559326 230.07363891601562 0.674414873123169 279.1688537597656 0.3523063063621521 0.64260834 0.6540156006813049 True -9 27580 30.360666513442993 0.5588798522949219 215.1529541015625 0.39997249841690063 278.7432556152344 0.3523777425289154 0.65910625 0.6323515176773071 True -10 30338 30.37386655807495 0.5496401786804199 185.7174835205078 0.657459557056427 277.8028869628906 0.3554399609565735 0.67146385 0.6167175769805908 True -11 33096 30.298134088516235 0.5449702739715576 195.51268005371094 1.084719181060791 277.39923095703125 0.35615867376327515 0.6737677 0.5909786224365234 True -12 35854 30.335627794265747 0.5384764671325684 203.4955596923828 0.4894619584083557 276.4236755371094 0.35901832580566406 0.68639505 0.5689189434051514 True -13 38612 30.361156225204468 0.5426976680755615 232.32431030273438 0.4598807692527771 275.1590881347656 0.36337339878082275 0.70146686 0.5482351183891296 True -14 41370 30.332053899765015 20.261418342590332 210.94229125976562 0.640897274017334 274.9678955078125 0.3623426854610443 0.7130573 0.5297679901123047 True -15 44128 30.640961170196533 0.5586342811584473 176.49514770507812 0.5149582624435425 273.6927795410156 0.36635538935661316 0.7228872 0.5153933167457581 True -16 46886 32.895665884017944 0.5479409694671631 204.94512939453125 0.5568580627441406 273.52093505859375 0.366519033908844 0.733698 0.5043964385986328 True -17 49644 29.7898051738739 0.5278043746948242 253.11038208007812 0.5155500173568726 273.5256042480469 0.36558130383491516 0.73775345 0.5027499794960022 True -18 52402 29.715826511383057 0.5297160148620605 252.7155303955078 0.3023219704627991 273.4367980957031 0.3657165467739105 0.737415 0.5074437260627747 False -19 55160 29.777092456817627 0.7055568695068359 202.08367919921875 0.5375990271568298 273.7585144042969 0.3638795018196106 0.73643124 0.5102201700210571 False diff --git a/ENCSR947POC/cherimoya.fold_3.performance.tsv b/ENCSR947POC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a055cc8929c64fe0a97b2f7b223b5d0eedfde041..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -273.5256042480469 0.4586228132247925 0.36558130383491516 0.09230505675077438 0.7377534508705139 0.6972755789756775 0.5027499794960022 \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_4.evaluate.json b/ENCSR947POC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9fefd0624d2b73ff28e38413105d480e679d4774..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF863TMT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_4.fit.json b/ENCSR947POC/cherimoya.fold_4.fit.json deleted file mode 100644 index f76170c055e2945cba2b8704789c74eb742c9a8a..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF863TMT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR947POC/cherimoya.fold_4.log b/ENCSR947POC/cherimoya.fold_4.log deleted file mode 100644 index 60b17a2a93808e076a38ac3bd64d290a6df0d6bd..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2864 36.00367283821106 3.5285403728485107 158.50701904296875 0.7414817810058594 308.1546630859375 0.18489329516887665 0.4691362 5.384261131286621 True -1 5728 31.53806161880493 1.2994980812072754 237.662353515625 0.8093582391738892 270.86138916015625 0.3086974024772644 0.5798148 1.4483537673950195 True -2 8592 31.553032636642456 0.688072919845581 220.68356323242188 0.9191032648086548 266.160400390625 0.3207581043243408 0.5744078 0.8977294564247131 False -3 11456 31.476685762405396 0.5969605445861816 173.53782653808594 0.9653292894363403 263.6926574707031 0.32595789432525635 0.5928343 0.693045437335968 True -4 14320 31.45746159553528 0.5790553092956543 205.1304931640625 0.8465574383735657 262.385986328125 0.33086907863616943 0.60225695 0.6698040962219238 True -5 17184 31.517553567886353 0.5795555114746094 224.90902709960938 0.9533289670944214 261.2408142089844 0.33505889773368835 0.60174644 0.6667322516441345 False -6 20048 31.461400032043457 0.5799148082733154 199.27761840820312 0.6051833033561707 260.5425720214844 0.3360646665096283 0.6115383 0.656245231628418 True -7 22912 31.501920700073242 0.5981044769287109 212.83958435058594 0.6383038759231567 260.3973083496094 0.3370469808578491 0.62135565 0.6200847625732422 True -8 25776 31.536460638046265 0.5814330577850342 168.21624755859375 0.9817631840705872 259.5019836425781 0.3398232161998749 0.6312044 0.6130266189575195 True -9 28640 31.454355239868164 1.7847011089324951 219.43890380859375 0.526228129863739 258.54022216796875 0.34297069907188416 0.6383622 0.5988965630531311 True -10 31504 31.4699068069458 0.6016807556152344 180.59738159179688 0.6259547472000122 257.75244140625 0.34549978375434875 0.64660895 0.5799331665039062 True -11 34368 31.53462791442871 0.6170425415039062 247.30783081054688 0.751887321472168 256.9543762207031 0.34765106439590454 0.6617841 0.5592169761657715 True -12 37232 31.50898313522339 0.6522369384765625 220.6656494140625 0.43040284514427185 256.2265319824219 0.34960249066352844 0.67634946 0.5434855818748474 True -13 40096 31.47518229484558 1.6048471927642822 185.79490661621094 0.7999999523162842 255.71697998046875 0.35168084502220154 0.689531 0.5219536423683167 True -14 42960 31.494553089141846 1.7875194549560547 216.80361938476562 0.41640859842300415 255.16348266601562 0.3534186780452728 0.70157045 0.5099131464958191 True -15 45824 31.64822506904602 1.2126762866973877 194.058837890625 0.42818862199783325 254.95687866210938 0.3529583513736725 0.7094492 0.4933626353740692 True -16 48688 31.26120662689209 0.6386864185333252 157.56362915039062 0.5482079386711121 254.57366943359375 0.3545627295970917 0.7182204 0.48326951265335083 True -17 51552 31.052339792251587 0.6187233924865723 173.62306213378906 0.48883193731307983 254.27684020996094 0.3558262586593628 0.7237224 0.47841882705688477 True -18 54416 31.05250835418701 0.610053300857544 214.4733428955078 0.29700469970703125 254.7422637939453 0.3543219566345215 0.7249632 0.4765200912952423 True -19 57280 31.027948141098022 0.6214277744293213 194.60841369628906 0.23576007783412933 254.6510467529297 0.3547579050064087 0.72543997 0.480063796043396 True diff --git a/ENCSR947POC/cherimoya.fold_4.performance.tsv b/ENCSR947POC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ae7f9c967f0a435f4edcc27f964e687efe213b08..0000000000000000000000000000000000000000 --- a/ENCSR947POC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -254.6510467529297 0.46852773427963257 0.35475796461105347 0.08630400151014328 0.7254399657249451 0.6774172186851501 0.480063796043396 \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_0.evaluate.json b/ENCSR948MQC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 80caef7647e25cb98ad4d7d1fedac15140d822aa..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF360EKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_0.fit.json b/ENCSR948MQC/cherimoya.fold_0.fit.json deleted file mode 100644 index 57331ae1dfad6f504b82df1ab231a280bf144b15..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF360EKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_0.log b/ENCSR948MQC/cherimoya.fold_0.log deleted file mode 100644 index d808eef5488da2b71989c4653322865ed4a94b10..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3397 41.69998812675476 3.9643101692199707 689.49365234375 0.520410418510437 864.7483520507812 0.7058019042015076 0.7316492 5.705469608306885 True -1 6794 36.730132818222046 0.7020485401153564 766.5548095703125 0.6015967726707458 751.8568115234375 0.7719447612762451 0.76242393 1.263952374458313 True -2 10191 37.2758584022522 16.974822521209717 608.279541015625 0.30265745520591736 729.4364013671875 0.7830585837364197 0.77123827 0.5960026979446411 True -3 13588 38.10186696052551 36.772913694381714 578.6409912109375 0.48335784673690796 722.8966064453125 0.7855426669120789 0.7762563 0.5357961058616638 True -4 16985 38.76233673095703 0.6507914066314697 580.392822265625 0.5131766200065613 720.78759765625 0.7885275483131409 0.774212 0.5377893447875977 False -5 20382 37.400391817092896 0.6608984470367432 623.587158203125 0.23467886447906494 716.3255615234375 0.7908012866973877 0.7809548 0.48140424489974976 True -6 23779 36.647866010665894 0.6606347560882568 634.16015625 0.5154487490653992 713.6036987304688 0.7920520901679993 0.7768433 0.4234546422958374 False -7 27176 40.076844692230225 0.6564788818359375 628.060546875 0.41638240218162537 709.4862670898438 0.7945747375488281 0.78348696 0.4172627031803131 True -8 30573 38.76456260681152 21.923529863357544 573.6177978515625 0.45490920543670654 705.3997802734375 0.7966892719268799 0.79077685 0.39762404561042786 True -9 33970 36.67810583114624 0.6446983814239502 526.9161376953125 0.36240437626838684 702.9384155273438 0.7986815571784973 0.787078 0.40343573689460754 False -10 37367 37.7982223033905 39.70029830932617 627.1611328125 0.3588191866874695 699.6970825195312 0.8004502058029175 0.7962056 0.38894709944725037 True -11 40764 38.22093963623047 16.671048879623413 650.513916015625 0.46244293451309204 696.3250732421875 0.8024663925170898 0.8010671 0.3641328811645508 True -12 44161 36.99361252784729 10.503157377243042 528.4703369140625 0.3191364109516144 693.2938842773438 0.8043688535690308 0.80738497 0.35515454411506653 True -13 47558 36.7029504776001 0.6422898769378662 571.29833984375 0.32384753227233887 690.8658447265625 0.8063453435897827 0.81497526 0.33755871653556824 True -14 50955 36.63368630409241 0.6548416614532471 542.2724609375 0.3317449688911438 688.616455078125 0.8077146410942078 0.8204792 0.32523390650749207 True -15 54352 36.767646074295044 0.6546924114227295 633.835205078125 0.45266222953796387 687.2060546875 0.8088288307189941 0.82521105 0.3164605498313904 True -16 57749 36.82913064956665 0.6509814262390137 590.399658203125 0.34295937418937683 686.5005493164062 0.809190571308136 0.8267908 0.3095325231552124 True -17 61146 36.68569278717041 1.089677095413208 648.300048828125 0.2560611367225647 686.9852294921875 0.809174120426178 0.8279268 0.309978723526001 True -18 64543 36.67569136619568 0.6430454254150391 541.5556640625 0.1902984082698822 687.495361328125 0.8090037107467651 0.82734984 0.31138768792152405 False -19 67940 36.654420375823975 0.6414587497711182 520.24169921875 0.30751556158065796 687.958740234375 0.8087877631187439 0.8250958 0.3153515160083771 False diff --git a/ENCSR948MQC/cherimoya.fold_0.performance.tsv b/ENCSR948MQC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cd5acd50e20a5f9d32c6ebb9ab1830a63014f8fd..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -686.9852294921875 0.15457968413829803 0.8091740608215332 0.4635126292705536 0.8279268145561218 0.7387924790382385 0.309978723526001 \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_1.evaluate.json b/ENCSR948MQC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5000fd7801a42d6fe370fc85163629389646c1fa..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF360EKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_1.fit.json b/ENCSR948MQC/cherimoya.fold_1.fit.json deleted file mode 100644 index 6d727d109b226387638d4fcb1619607b5a63fda1..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF360EKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_1.log b/ENCSR948MQC/cherimoya.fold_1.log deleted file mode 100644 index 11e7f54b3f9851c084419f26f42ee27f0c03a083..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3322 41.059661626815796 3.808255434036255 702.4617919921875 0.40439075231552124 949.665771484375 0.7148678302764893 0.7278856 4.9349846839904785 True -1 6644 36.59306335449219 0.9171669483184814 659.8862915039062 0.5045428276062012 812.4789428710938 0.7852541208267212 0.768963 1.4697786569595337 True -2 9966 36.5701584815979 0.8844962120056152 583.2894287109375 0.6122111082077026 794.939453125 0.7946064472198486 0.7793882 0.693683922290802 True -3 13288 36.536314725875854 4.643646717071533 694.2301025390625 0.4393814206123352 786.130615234375 0.797919511795044 0.783456 0.5851240158081055 True -4 16610 36.632638692855835 2.171312093734741 610.2286376953125 0.37534070014953613 780.2789916992188 0.8009774684906006 0.7857917 0.5532018542289734 True -5 19932 36.53095841407776 0.8931987285614014 616.0664672851562 0.4311044216156006 776.6136474609375 0.8035521507263184 0.7890287 0.5575329661369324 True -6 23254 36.549447774887085 8.100113868713379 600.339111328125 0.35765141248703003 772.9910888671875 0.8050565719604492 0.7882638 0.49961355328559875 False -7 26576 36.61675548553467 41.19498538970947 557.79345703125 0.3677099347114563 767.7982177734375 0.8076417446136475 0.7937912 0.4733436405658722 True -8 29898 36.72677159309387 0.9007120132446289 654.3057861328125 0.34683358669281006 764.6159057617188 0.8095090985298157 0.8009725 0.43526721000671387 True -9 33220 36.54067087173462 0.8930153846740723 602.1741943359375 0.3929961025714874 760.0023193359375 0.8116967678070068 0.8070358 0.4152669608592987 True -10 36542 36.59658694267273 0.9058079719543457 660.8687744140625 0.26158422231674194 755.7557983398438 0.8143081068992615 0.81269604 0.4153584837913513 True -11 39864 37.131662368774414 28.019539833068848 631.4956665039062 0.3103722035884857 752.3037719726562 0.8160470724105835 0.81929547 0.38432425260543823 True -12 43186 36.731992959976196 1.7740812301635742 611.12109375 0.25935569405555725 749.4277954101562 0.8179447054862976 0.8240022 0.3695642352104187 True -13 46508 36.676172494888306 1.7733652591705322 595.8502197265625 0.3600943684577942 746.5613403320312 0.8198146224021912 0.83259666 0.35753363370895386 True -14 49830 36.722756147384644 48.08494973182678 581.4689331054688 0.27119022607803345 744.6061401367188 0.8212569952011108 0.8349841 0.33019590377807617 True -15 53152 36.65065240859985 0.9131028652191162 645.2252197265625 0.20286202430725098 742.8765258789062 0.8222619295120239 0.8410606 0.32044991850852966 True -16 56474 36.173075914382935 0.8990435600280762 635.762939453125 0.1801176369190216 742.19384765625 0.8227891325950623 0.84091127 0.31317320466041565 False -17 59796 36.004064321517944 0.9046597480773926 608.0731201171875 0.22252148389816284 742.5752563476562 0.8226892948150635 0.84114903 0.3069005012512207 True -18 63118 36.06101059913635 0.9158802032470703 575.7774658203125 0.15821421146392822 743.381591796875 0.8221464157104492 0.84175664 0.30780029296875 True -19 66440 36.21005868911743 0.8948557376861572 549.5926513671875 0.24676531553268433 743.8546142578125 0.8218980431556702 0.84058875 0.30845707654953003 False diff --git a/ENCSR948MQC/cherimoya.fold_1.performance.tsv b/ENCSR948MQC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7b9c90cb13994f742bdd483ba871af61cb608992..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -743.381591796875 0.14315882325172424 0.8221463561058044 0.49478083848953247 0.8417566418647766 0.7911443114280701 0.30780029296875 \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_2.evaluate.json b/ENCSR948MQC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 80f8c647998cdc06983df91d26abf2d6149fe7e8..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF360EKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_2.fit.json b/ENCSR948MQC/cherimoya.fold_2.fit.json deleted file mode 100644 index ab7bd05f2766c87e69e13adbf3ca4d1a0b1c7b07..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF360EKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_2.log b/ENCSR948MQC/cherimoya.fold_2.log deleted file mode 100644 index 87839f76534559578ed16ccf9accb6a0a8fe6383..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3540 43.39060020446777 6.61139702796936 635.380859375 0.27998247742652893 872.869384765625 0.7107619047164917 0.71629137 4.252636909484863 True -1 7080 38.92058253288269 0.7041709423065186 604.3079223632812 0.2767070233821869 757.1512451171875 0.7762959599494934 0.76154196 1.0088529586791992 True -2 10620 38.899389028549194 1.4290220737457275 521.4744873046875 0.3175628185272217 736.6693115234375 0.7862730622291565 0.7780054 0.545928418636322 True -3 14160 39.40890192985535 28.09276247024536 527.43994140625 0.21079950034618378 728.39697265625 0.7909433841705322 0.78307575 0.5298879146575928 True -4 17700 39.35832762718201 40.402971029281616 640.1632080078125 0.37142258882522583 725.6658935546875 0.7929989099502563 0.7880631 0.5726050138473511 True -5 21240 39.32548761367798 0.6916224956512451 656.0992431640625 0.3324151933193207 723.1177368164062 0.7938012480735779 0.79162854 0.4792173504829407 True -6 24780 39.028146743774414 13.808736801147461 621.771240234375 0.39001229405403137 718.6985473632812 0.7966715097427368 0.794568 0.4695858657360077 True -7 28320 39.4236376285553 47.4745831489563 574.828125 0.3986646831035614 715.3427124023438 0.7988730669021606 0.7957193 0.45861077308654785 True -8 31860 42.880287408828735 41.1443145275116 607.244140625 0.4194032549858093 711.6585083007812 0.8008381128311157 0.79859173 0.4349775016307831 True -9 35400 44.63315963745117 0.6771013736724854 652.23486328125 0.432129830121994 709.0849609375 0.8027063608169556 0.80193096 0.40932926535606384 True -10 38940 38.9002001285553 0.681171178817749 581.9388427734375 0.30860573053359985 707.6615600585938 0.804121732711792 0.80773205 0.42037832736968994 True -11 42480 38.77156662940979 0.672816276550293 627.8460083007812 0.3418000340461731 703.819091796875 0.8061979413032532 0.81201047 0.38747596740722656 True -12 46020 38.32522130012512 1.563011884689331 524.1865844726562 0.25041675567626953 701.037841796875 0.8079648017883301 0.8160883 0.3663890063762665 True -13 49560 38.362892627716064 0.6924076080322266 603.3851318359375 0.2629247009754181 699.3177490234375 0.8091939687728882 0.8219775 0.35539963841438293 True -14 53100 38.338090896606445 0.6856484413146973 608.721923828125 0.2066943645477295 697.1348266601562 0.8108296990394592 0.82657045 0.32938268780708313 True -15 56640 38.30538058280945 0.6775438785552979 579.0814208984375 0.2312021553516388 695.9725341796875 0.811751663684845 0.830164 0.30841177701950073 True -16 60180 38.260435342788696 0.6817641258239746 609.9036254882812 0.2369362860918045 695.3925170898438 0.812085747718811 0.8327119 0.29791325330734253 True -17 63720 38.206934213638306 10.932102918624878 623.9212646484375 0.20050382614135742 695.9238891601562 0.811965823173523 0.83302075 0.29405418038368225 True -18 67260 38.286731243133545 0.6797680854797363 595.0343017578125 0.1787446141242981 696.4488525390625 0.8115909695625305 0.8307191 0.29442304372787476 False -19 70800 38.34504985809326 36.045520544052124 566.9373779296875 0.23474013805389404 696.9208984375 0.8113617300987244 0.82995886 0.2959992289543152 False diff --git a/ENCSR948MQC/cherimoya.fold_2.performance.tsv b/ENCSR948MQC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index bffdbeb6ffc668b15aa55612e74ef36cb0f0670a..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -695.9238891601562 0.1517636924982071 0.8119657635688782 0.47139260172843933 0.8330207467079163 0.7566348314285278 0.29405418038368225 \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_3.evaluate.json b/ENCSR948MQC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ec354c95b2ee9a3273d1457ee1cbe93378c2af95..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF360EKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_3.fit.json b/ENCSR948MQC/cherimoya.fold_3.fit.json deleted file mode 100644 index 39dd11a5b323c078ef9151bc24f7097ad6531b8f..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF360EKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_3.log b/ENCSR948MQC/cherimoya.fold_3.log deleted file mode 100644 index 2154d56f6ee197f8674fac736f84360d7e47c5d3..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3416 42.4965181350708 3.750790596008301 682.6788330078125 0.5310877561569214 858.5189819335938 0.7094782590866089 0.7007935 3.9485270977020264 True -1 6832 37.95106863975525 0.7185571193695068 660.4964599609375 0.4372703731060028 749.7392578125 0.7748194932937622 0.7423571 1.2198468446731567 True -2 10248 37.54265546798706 0.8417751789093018 698.991943359375 0.4867021441459656 729.3170166015625 0.7854008674621582 0.75367934 0.6493995785713196 True -3 13664 37.52558970451355 0.6847844123840332 623.2830810546875 0.36572983860969543 722.5673828125 0.7885351777076721 0.75665987 0.5687592625617981 True -4 17080 37.47798037528992 0.6967122554779053 642.8482666015625 0.5136196613311768 717.1171264648438 0.7917557954788208 0.7619399 0.585831880569458 True -5 20496 37.47999119758606 32.22096085548401 602.5435791015625 0.4271530508995056 716.1097412109375 0.7914446592330933 0.7627689 0.48463574051856995 True -6 23912 39.706464767456055 0.7017192840576172 622.2349853515625 0.37812718749046326 712.6337280273438 0.7941264510154724 0.76624066 0.4670119881629944 True -7 27328 37.51019740104675 0.6786520481109619 662.4995727539062 0.47776952385902405 708.343017578125 0.7963454723358154 0.77323264 0.4362924098968506 True -8 30744 36.75046396255493 0.6976733207702637 689.9447021484375 0.3526690900325775 706.4732666015625 0.7982312440872192 0.77598226 0.4511997699737549 True -9 34160 36.81532096862793 0.6870143413543701 735.2998046875 0.29839378595352173 703.1903076171875 0.8001520037651062 0.7806586 0.4222700595855713 True -10 37576 36.79595398902893 0.6787149906158447 609.5888671875 0.29893258213996887 700.35986328125 0.8018782734870911 0.7847368 0.4207478165626526 True -11 40992 41.11923265457153 5.235008716583252 635.7557373046875 0.375948041677475 696.8255615234375 0.8039864897727966 0.7905684 0.40346017479896545 True -12 44408 36.9810905456543 0.6990408897399902 568.020751953125 0.28064313530921936 694.7626953125 0.806171178817749 0.79485375 0.4074246883392334 True -13 47824 36.910035848617554 0.6793160438537598 605.11279296875 0.4157233238220215 692.1856689453125 0.807959258556366 0.8026109 0.3882674276828766 True -14 51240 37.25190472602844 0.672659158706665 549.2685546875 0.2541743218898773 689.7185668945312 0.809651792049408 0.80747414 0.36703431606292725 True -15 54656 36.86143660545349 4.652979135513306 498.5111389160156 0.1911497414112091 688.410888671875 0.8107770681381226 0.810195 0.35645586252212524 True -16 58072 36.8340048789978 0.6811957359313965 544.665283203125 0.2394121289253235 688.077392578125 0.8109369277954102 0.8118391 0.34516796469688416 True -17 61488 36.73832178115845 0.6895937919616699 526.5227661132812 0.1575874388217926 687.9522094726562 0.8109461069107056 0.811714 0.33881261944770813 False -18 64904 36.72737002372742 0.6803624629974365 654.60205078125 0.20634590089321136 688.8775024414062 0.8104363083839417 0.8097865 0.3389924168586731 False -19 68320 36.83071279525757 0.6782166957855225 554.3080444335938 0.21202880144119263 689.3388061523438 0.8100996017456055 0.8082566 0.33983638882637024 False diff --git a/ENCSR948MQC/cherimoya.fold_3.performance.tsv b/ENCSR948MQC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 8d219b8f8bd98c15b93a0e01f54037bd570a2532..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -688.077392578125 0.15273959934711456 0.8109369277954102 0.46452730894088745 0.8118391036987305 0.7231000065803528 0.34516796469688416 \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_4.evaluate.json b/ENCSR948MQC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e0385b9ff3d7691f17d67a31ce9c7cbc27c3e08e..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF360EKV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_4.fit.json b/ENCSR948MQC/cherimoya.fold_4.fit.json deleted file mode 100644 index d4ba693cef6cfff908bdbf1f278262c1dfcea33a..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF360EKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_4.log b/ENCSR948MQC/cherimoya.fold_4.log deleted file mode 100644 index 7a914dd3e65f0b72d73a623bf343e9fc123b9129..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3431 43.21000528335571 24.43463706970215 671.150634765625 0.3942035436630249 816.1490478515625 0.7037840485572815 0.7020532 4.151066303253174 True -1 6862 38.09120845794678 0.7273340225219727 564.3346557617188 0.3157085180282593 711.1915283203125 0.7702847123146057 0.7438262 1.1693856716156006 True -2 10293 38.02210235595703 0.6918761730194092 598.0817260742188 0.28674083948135376 694.6118774414062 0.779292106628418 0.75508124 0.6134806275367737 True -3 13724 37.89085555076599 0.68747878074646 595.3252563476562 0.3723110556602478 687.9820556640625 0.7828004360198975 0.75920445 0.5465729236602783 True -4 17155 38.87974524497986 5.576094388961792 659.3250732421875 0.6410760879516602 684.3162231445312 0.7849599719047546 0.7572488 0.5493472218513489 False -5 20586 38.265591621398926 24.694236516952515 632.428955078125 0.44392675161361694 682.1439819335938 0.7859006524085999 0.7560763 0.49619483947753906 False -6 24017 37.11229133605957 0.6687750816345215 594.1309204101562 0.3597252368927002 678.4612426757812 0.7883501052856445 0.7631477 0.44944047927856445 True -7 27448 37.06297588348389 0.6631419658660889 646.9778442382812 0.29804015159606934 674.4143676757812 0.7909103631973267 0.7703951 0.40925484895706177 True -8 30879 37.021361351013184 0.6634902954101562 602.8778076171875 0.28939640522003174 672.1803588867188 0.7928946614265442 0.7749614 0.41356542706489563 True -9 34310 37.058982849121094 36.11480402946472 640.08642578125 0.3514305055141449 669.9581909179688 0.7946645617485046 0.7764805 0.3989007771015167 True -10 37741 37.18217182159424 40.216174364089966 605.5404663085938 0.288460910320282 666.5380249023438 0.797095000743866 0.7836283 0.38669052720069885 True -11 41172 37.91578269004822 0.6694285869598389 614.1822509765625 0.34365516901016235 664.143798828125 0.7990449666976929 0.7913394 0.3569841682910919 True -12 44603 37.02699065208435 0.6857678890228271 622.39892578125 0.41834861040115356 661.87109375 0.8010783195495605 0.7995499 0.34467074275016785 True -13 48034 37.0276734828949 1.3423802852630615 593.0360107421875 0.25400835275650024 660.0213623046875 0.8027271032333374 0.80603874 0.3202672004699707 True -14 51465 37.17896008491516 0.6639716625213623 660.2684936523438 0.26975446939468384 658.310546875 0.8043415546417236 0.81303054 0.3146815896034241 True -15 54896 37.023550510406494 0.6814823150634766 570.1314697265625 0.2062474489212036 657.1259765625 0.805293083190918 0.8192019 0.2968311011791229 True -16 58327 37.10833406448364 1.3998048305511475 540.4591674804688 0.21351921558380127 657.1655883789062 0.805684506893158 0.8196858 0.2922830581665039 True -17 61758 38.728790283203125 38.98649001121521 545.8773193359375 0.2183595597743988 657.5181884765625 0.8054117560386658 0.8199071 0.289002925157547 True -18 65189 37.2282509803772 0.6643180847167969 563.6734619140625 0.1951199322938919 657.9591674804688 0.8051223158836365 0.8179184 0.2890614867210388 False -19 68620 37.983869791030884 29.731669425964355 563.6052856445312 0.12822698056697845 658.5409545898438 0.8048647046089172 0.8178319 0.2916426360607147 False diff --git a/ENCSR948MQC/cherimoya.fold_4.performance.tsv b/ENCSR948MQC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e364feb0b7bc32171ab24de06b67ea9beeb9a915..0000000000000000000000000000000000000000 --- a/ENCSR948MQC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -657.5181884765625 0.15842652320861816 0.805411696434021 0.45144855976104736 0.8199071288108826 0.7216423153877258 0.289002925157547 \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_0.evaluate.json b/ENCSR949JYS/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4f4d40313becd7af867106880125d0c688edf893..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF893NXR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_0.fit.json b/ENCSR949JYS/cherimoya.fold_0.fit.json deleted file mode 100644 index 155bdbead9572a57e57737590902ee527c02c68a..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF893NXR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_0.log b/ENCSR949JYS/cherimoya.fold_0.log deleted file mode 100644 index 8ea5c46492c571d2de70d563ab19f4f9beaffc35..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2751 35.59498834609985 18.94994282722473 220.9398651123047 0.7413257956504822 306.5559997558594 0.1526695042848587 0.5153815 3.7256112098693848 True -1 5502 30.680254220962524 0.5970306396484375 205.98150634765625 0.6667143106460571 299.74627685546875 0.18819983303546906 0.6147283 1.1417756080627441 True -2 8253 30.086766004562378 0.5737183094024658 222.17152404785156 0.8202372193336487 297.57861328125 0.1969025880098343 0.63497305 0.5610530376434326 True -3 11004 29.995160818099976 0.5697598457336426 233.2412109375 0.7177168130874634 296.483154296875 0.20147570967674255 0.6462234 0.48440468311309814 True -4 13755 30.02287983894348 3.024062156677246 251.70303344726562 0.5098521113395691 296.1083984375 0.2021985650062561 0.6560506 0.4382951855659485 True -5 16506 29.42440176010132 0.5602302551269531 224.13623046875 0.5347326397895813 295.3439636230469 0.20658570528030396 0.66078526 0.43110769987106323 True -6 19257 29.373085260391235 0.5564010143280029 234.8975830078125 0.4002194404602051 295.1866149902344 0.20662447810173035 0.66405946 0.4289049506187439 True -7 22008 29.3662850856781 0.5591475963592529 226.14151000976562 0.44973087310791016 294.1774597167969 0.21245898306369781 0.6666356 0.42553868889808655 True -8 24759 29.425538539886475 0.5576362609863281 258.22955322265625 0.5609495639801025 294.11932373046875 0.21216405928134918 0.6719866 0.4310149848461151 True -9 27510 29.452635049819946 0.5634398460388184 255.18182373046875 0.4326171875 293.7138977050781 0.21410052478313446 0.6773255 0.418364942073822 True -10 30261 29.40518879890442 0.5631260871887207 226.06973266601562 0.43640461564064026 293.55059814453125 0.21440847218036652 0.68511736 0.3970673680305481 True -11 33012 29.34721541404724 0.5630571842193604 269.67291259765625 0.37790822982788086 293.52154541015625 0.21451853215694427 0.68872297 0.37322095036506653 True -12 35763 29.37491250038147 0.5585026741027832 233.10824584960938 0.4870476722717285 293.0458984375 0.2165083885192871 0.6940014 0.3586403727531433 True -13 38514 29.383297204971313 0.5567333698272705 233.1092529296875 0.5749380588531494 292.9839172363281 0.21690085530281067 0.70305187 0.33677154779434204 True -14 41265 29.40776038169861 2.194051742553711 198.73635864257812 0.49679020047187805 292.74493408203125 0.21816717088222504 0.70883083 0.3231149911880493 True -15 44016 29.398792028427124 1.8291256427764893 237.0795440673828 0.2415505200624466 292.6396484375 0.21873170137405396 0.71376294 0.3168095648288727 True -16 46767 29.4133563041687 0.5720694065093994 258.0718994140625 0.31337106227874756 292.6932067871094 0.21857850253582 0.71727514 0.3122142255306244 True -17 49518 29.44203233718872 0.5581076145172119 238.51637268066406 0.35052698850631714 293.1368103027344 0.21600815653800964 0.7184922 0.3156045973300934 True -18 52269 29.433482885360718 0.8404862880706787 256.95794677734375 0.16489195823669434 293.0610656738281 0.2165318727493286 0.71736395 0.32523998618125916 False -19 55020 29.38357949256897 2.8786003589630127 232.51211547851562 0.3355872333049774 292.9142761230469 0.21759025752544403 0.7165015 0.33169615268707275 False diff --git a/ENCSR949JYS/cherimoya.fold_0.performance.tsv b/ENCSR949JYS/cherimoya.fold_0.performance.tsv deleted file mode 100644 index ad62ef2586ea329ad2e9924c9b555f7ef6ecf4f7..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -293.1368103027344 0.5113321542739868 0.21600815653800964 0.0732603669166565 0.7184922099113464 0.6996641755104065 0.3156045973300934 \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_1.evaluate.json b/ENCSR949JYS/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 22d84af00214af9b020222cb973f0d37fea019f5..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF893NXR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_1.fit.json b/ENCSR949JYS/cherimoya.fold_1.fit.json deleted file mode 100644 index cd6e4bfca189292f8000ee67bd16c12ded5c2297..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF893NXR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_1.log b/ENCSR949JYS/cherimoya.fold_1.log deleted file mode 100644 index 50b51193246686ffb15ede13a192eebec29cffc2..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 34.68375611305237 4.0528404712677 223.02926635742188 0.6359113454818726 336.4803161621094 0.16146254539489746 0.5743136 4.008554458618164 True -1 5516 30.025955200195312 0.6980485916137695 217.2822723388672 0.9327762126922607 328.9375 0.19750946760177612 0.66588277 0.9908229112625122 True -2 8274 30.026926040649414 0.6930327415466309 247.64486694335938 0.493607759475708 325.97503662109375 0.2072274386882782 0.67949176 0.5789856910705566 True -3 11032 30.002877712249756 0.6778140068054199 313.40869140625 0.4004930257797241 324.6396179199219 0.21211478114128113 0.6903605 0.47593751549720764 True -4 13790 29.949726343154907 0.6672298908233643 241.88543701171875 0.38492053747177124 323.9317626953125 0.21477580070495605 0.6980095 0.5078830122947693 True -5 16548 30.069327116012573 0.6817460060119629 229.50909423828125 0.4950586259365082 323.56719970703125 0.2157687544822693 0.70417184 0.5018028616905212 True -6 19306 30.122840881347656 36.72210955619812 221.4653778076172 0.861169695854187 323.0618896484375 0.21755991876125336 0.7080658 0.4869403839111328 True -7 22064 30.25764513015747 0.7465293407440186 216.3511962890625 0.532495379447937 322.66400146484375 0.21931564807891846 0.71206677 0.482963889837265 True -8 24822 29.4192852973938 0.7067794799804688 270.8167419433594 0.4379771947860718 321.9609375 0.22251996397972107 0.7174996 0.47362184524536133 True -9 27580 29.541765689849854 28.43437886238098 228.80760192871094 0.3549288809299469 321.33013916015625 0.22521013021469116 0.72644734 0.4287392795085907 True -10 30338 29.686688899993896 0.7772960662841797 229.73468017578125 0.6369674801826477 321.2647705078125 0.2252265065908432 0.7283409 0.4140684902667999 True -11 33096 30.77985715866089 4.315801382064819 245.27188110351562 0.5445284843444824 320.9870910644531 0.22667717933654785 0.7374821 0.39659804105758667 True -12 35854 29.47355341911316 4.2366697788238525 245.5804901123047 0.4078634977340698 320.54595947265625 0.22820128500461578 0.74306136 0.3729497194290161 True -13 38612 29.555166721343994 21.79791569709778 255.31597900390625 0.29665958881378174 320.3752746582031 0.2287936955690384 0.74742514 0.35162824392318726 True -14 41370 29.458088874816895 0.6842284202575684 193.41958618164062 0.33069366216659546 320.09521484375 0.2299850881099701 0.7528702 0.33394867181777954 True -15 44128 29.43301796913147 0.6810941696166992 255.29977416992188 0.2591835856437683 319.9767761230469 0.23062346875667572 0.7583361 0.321196049451828 True -16 46886 29.54440951347351 0.6995599269866943 225.380859375 0.23124800622463226 319.9602355957031 0.23004822432994843 0.7626692 0.31622815132141113 True -17 49644 29.471814155578613 0.6690397262573242 243.08795166015625 0.4668806195259094 320.2235412597656 0.22903385758399963 0.76206285 0.31885042786598206 False -18 52402 32.367308139801025 0.6716475486755371 278.57427978515625 0.19018621742725372 320.62646484375 0.22829848527908325 0.76092553 0.3266713619232178 False -19 55160 29.52121901512146 31.176036834716797 220.54754638671875 0.4773818254470825 320.1393737792969 0.2305019497871399 0.7611115 0.33274906873703003 False diff --git a/ENCSR949JYS/cherimoya.fold_1.performance.tsv b/ENCSR949JYS/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c5d29ae6d6b7d385102044397d06296a77b34f70..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -319.9602355957031 0.4986509084701538 0.23004822432994843 0.07704795151948929 0.7626692056655884 0.7590907216072083 0.31622815132141113 \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_2.evaluate.json b/ENCSR949JYS/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 586106ff14a1882d312fd99591d4e6598cf91047..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF893NXR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_2.fit.json b/ENCSR949JYS/cherimoya.fold_2.fit.json deleted file mode 100644 index fbb886392a57c90125500d5e0c116139159692bb..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF893NXR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_2.log b/ENCSR949JYS/cherimoya.fold_2.log deleted file mode 100644 index ef51691284a7474db2f65f7d8d5b729635f310b9..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2916 39.78802275657654 3.5241475105285645 274.40142822265625 0.6474583148956299 312.04327392578125 0.1577964425086975 0.54922396 2.9687366485595703 True -1 5832 31.810903549194336 0.5351641178131104 232.3017578125 0.6930292248725891 304.767822265625 0.19511617720127106 0.6299419 1.0487303733825684 True -2 8748 31.773552179336548 0.5115833282470703 262.0747375488281 0.5616640448570251 303.3442077636719 0.19874568283557892 0.64252716 0.542673647403717 True -3 11664 31.73498034477234 0.5025522708892822 199.36915588378906 0.739545464515686 302.0162048339844 0.2041333168745041 0.65365916 0.5690990090370178 True -4 14580 31.80271077156067 0.5082266330718994 201.09228515625 0.5938583016395569 301.1300048828125 0.20787791907787323 0.65437675 0.5774869322776794 True -5 17496 31.71999764442444 0.5068924427032471 182.33493041992188 0.5557777285575867 300.7925109863281 0.20916293561458588 0.6550654 0.5828115344047546 True -6 20412 31.736706256866455 0.4964439868927002 211.177001953125 0.5720123052597046 300.3118591308594 0.21144989132881165 0.6575515 0.5730153322219849 True -7 23328 31.348832607269287 5.126761436462402 239.77732849121094 0.698419988155365 300.0766296386719 0.21225661039352417 0.6568832 0.5605360269546509 False -8 26244 31.095438957214355 0.5063800811767578 248.5733642578125 0.5418386459350586 299.26220703125 0.21597963571548462 0.6621185 0.5457016229629517 True -9 29160 31.13812017440796 0.9427919387817383 259.220458984375 0.5530160069465637 298.91522216796875 0.2177661508321762 0.66901547 0.520656943321228 True -10 32076 31.190165042877197 0.5062785148620605 281.41900634765625 0.37542322278022766 298.41119384765625 0.22006894648075104 0.67857647 0.46641430258750916 True -11 34992 31.283052921295166 0.49858665466308594 179.2298583984375 0.5270242094993591 298.2535095214844 0.22021833062171936 0.6802875 0.4442542493343353 True -12 37908 31.129453420639038 0.4980189800262451 230.47335815429688 0.4050050973892212 298.3252258300781 0.21955031156539917 0.6912664 0.4021315574645996 True -13 40824 31.217686414718628 0.49811410903930664 222.6719512939453 0.43496066331863403 297.9462890625 0.22191545367240906 0.6969574 0.3831042945384979 True -14 43740 31.245306253433228 0.4907717704772949 282.40582275390625 0.45531895756721497 297.7542419433594 0.22317665815353394 0.70388967 0.36498722434043884 True -15 46656 31.185222148895264 0.49462056159973145 278.4647216796875 0.32187896966934204 297.40338134765625 0.2242926061153412 0.7121268 0.3425978720188141 True -16 49572 31.213254928588867 0.5005502700805664 217.23626708984375 0.24684032797813416 297.4216613769531 0.22412465512752533 0.718272 0.3364183306694031 True -17 52488 31.183401823043823 0.4988377094268799 237.9496612548828 0.3377833068370819 297.5516357421875 0.22310326993465424 0.72180396 0.33796608448028564 True -18 55404 31.09476399421692 0.9391934871673584 194.92568969726562 0.3205046057701111 297.6373291015625 0.22316080331802368 0.7202699 0.3439297378063202 False -19 58320 31.231483459472656 1.878960371017456 216.82135009765625 0.32658034563064575 297.74444580078125 0.2221706509590149 0.7202436 0.34605872631073 False diff --git a/ENCSR949JYS/cherimoya.fold_2.performance.tsv b/ENCSR949JYS/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 1ca0b1c6484e0d9dedd2fd24c8be99d67b2892b5..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -297.5516357421875 0.5078789591789246 0.22310324013233185 0.07405487447977066 0.7218039631843567 0.7099502086639404 0.33796608448028564 \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_3.evaluate.json b/ENCSR949JYS/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a2f1d4203eb7f6cee8925f5241e1fba3b78a4847..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF893NXR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_3.fit.json b/ENCSR949JYS/cherimoya.fold_3.fit.json deleted file mode 100644 index 73de5ef025a332b0d6b5d15c354388d15b8232cc..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF893NXR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_3.log b/ENCSR949JYS/cherimoya.fold_3.log deleted file mode 100644 index 22d57d4e6cac7e94ceae0f7b93a3c9a1131842e2..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2773 35.80329918861389 4.494806289672852 254.01681518554688 0.6055870652198792 324.8890686035156 0.15611623227596283 0.5516696 3.8269035816192627 True -1 5546 30.204479455947876 3.9370572566986084 231.99050903320312 0.7388378381729126 317.64739990234375 0.1937042474746704 0.6409104 0.998104989528656 True -2 8319 30.146967887878418 0.7865586280822754 249.19668579101562 0.6527233123779297 315.60986328125 0.20030303299427032 0.6618526 0.5760713815689087 True -3 11092 30.258075714111328 0.6031033992767334 238.78570556640625 0.6775995492935181 314.6082763671875 0.20426146686077118 0.6716689 0.6037046313285828 True -4 13865 30.18382740020752 0.5970220565795898 238.8009033203125 0.5042271614074707 313.73370361328125 0.20827272534370422 0.6772726 0.5094640254974365 True -5 16638 30.12137746810913 0.598717451095581 219.09848022460938 0.44335299730300903 313.37823486328125 0.20940929651260376 0.67449147 0.5808151364326477 False -6 19411 30.226205587387085 0.5994260311126709 191.85073852539062 0.6338284015655518 312.9023132324219 0.21126249432563782 0.679624 0.5311853289604187 True -7 22184 30.204472064971924 0.5963454246520996 215.8842315673828 0.4737761318683624 312.87200927734375 0.2113596498966217 0.6801124 0.552954912185669 True -8 24957 30.02401065826416 0.5941116809844971 221.99081420898438 0.6006813049316406 312.31805419921875 0.21380791068077087 0.6836902 0.5480768084526062 True -9 27730 29.645081520080566 0.5894227027893066 226.73941040039062 0.43250715732574463 312.0799865722656 0.21469959616661072 0.68678766 0.5309603810310364 True -10 30503 29.68701982498169 0.5857269763946533 212.14285278320312 0.44530588388442993 311.9789733886719 0.21532094478607178 0.68926877 0.5057937502861023 True -11 33276 29.601176023483276 0.5942933559417725 254.40896606445312 0.49981844425201416 311.4360046386719 0.21802203357219696 0.6968584 0.45821747183799744 True -12 36049 29.704821348190308 0.5914499759674072 201.668212890625 0.4469050168991089 311.3309326171875 0.21835170686244965 0.7049309 0.45114874839782715 True -13 38822 29.63988423347473 0.5942440032958984 238.31527709960938 0.3657929003238678 311.130615234375 0.21917392313480377 0.71018016 0.40337228775024414 True -14 41595 29.61397695541382 0.5855743885040283 249.8778076171875 0.34020888805389404 310.7308349609375 0.22091548144817352 0.71953744 0.38333526253700256 True -15 44368 29.65754508972168 0.5960993766784668 232.1217041015625 0.3915868103504181 310.53314208984375 0.22175125777721405 0.7258034 0.3665347695350647 True -16 47141 29.691040992736816 10.494917392730713 211.73214721679688 0.342780739068985 310.60455322265625 0.22095157206058502 0.73010546 0.3546166718006134 True -17 49914 29.667854070663452 0.5955853462219238 246.00555419921875 0.21465575695037842 311.2107238769531 0.2181522697210312 0.7322108 0.35701796412467957 True -18 52687 29.697250366210938 0.6081833839416504 228.24618530273438 0.38537490367889404 310.947509765625 0.2195172905921936 0.73041564 0.359502375125885 False -19 55460 29.69765067100525 0.5945127010345459 218.01837158203125 0.2541051506996155 311.0321044921875 0.21905170381069183 0.72998047 0.36523672938346863 False diff --git a/ENCSR949JYS/cherimoya.fold_3.performance.tsv b/ENCSR949JYS/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 1775dd0a439cdee39ee9cae4f035c344c5ad0672..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -311.2107238769531 0.5052236914634705 0.2181522399187088 0.07622592151165009 0.7322108149528503 0.7135795950889587 0.35701796412467957 \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_4.evaluate.json b/ENCSR949JYS/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 79f5a3c6abc743748f374d3521fd9caf9292f4c9..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF893NXR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_4.fit.json b/ENCSR949JYS/cherimoya.fold_4.fit.json deleted file mode 100644 index 52b7ab80d2bda7a1a830a36287a075f02423f35a..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF893NXR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR949JYS/cherimoya.fold_4.log b/ENCSR949JYS/cherimoya.fold_4.log deleted file mode 100644 index bfeab49a6294dc949e9a2be89ae3aff5c1da7f36..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 36.76567482948303 36.74153113365173 220.75912475585938 0.8115528225898743 310.6933288574219 0.15574413537979126 0.52582437 3.4838192462921143 True -1 5758 33.10025453567505 0.6543352603912354 224.090576171875 0.720090925693512 304.0757751464844 0.19049647450447083 0.61422044 0.9574376344680786 True -2 8637 31.424479246139526 0.6279201507568359 258.9692077636719 0.48064011335372925 301.692626953125 0.20107220113277435 0.63278276 0.5848773717880249 True -3 11516 31.609065294265747 0.6146588325500488 250.88275146484375 0.4684906005859375 300.8913879394531 0.20372995734214783 0.6424368 0.6193702220916748 True -4 14395 31.78916835784912 0.6107094287872314 184.7076416015625 0.4942355751991272 300.5835266113281 0.2037530541419983 0.6517591 0.516643226146698 True -5 17274 31.49064326286316 10.123666048049927 259.427001953125 0.6386781334877014 300.4130859375 0.20443211495876312 0.6550981 0.4550151228904724 True -6 20153 31.46197271347046 2.5120766162872314 212.1258544921875 0.5703001022338867 299.5799865722656 0.20816488564014435 0.6667916 0.4551575183868408 True -7 23032 31.460906744003296 1.054079294204712 196.86209106445312 0.3870387077331543 299.1732482910156 0.21026639640331268 0.67308855 0.4381040334701538 True -8 25911 31.82951593399048 0.610875129699707 236.95101928710938 0.39583590626716614 299.0491943359375 0.21054553985595703 0.67599046 0.4353139102458954 True -9 28790 31.025758743286133 0.6014974117279053 235.81155395507812 0.3596237599849701 298.60693359375 0.2128985971212387 0.6822491 0.42182621359825134 True -10 31669 30.941593885421753 0.6032054424285889 230.1749267578125 0.48226284980773926 298.4501037597656 0.21367254853248596 0.68600273 0.40343600511550903 True -11 34548 30.8788800239563 0.6005864143371582 217.82363891601562 0.4400245249271393 297.7962646484375 0.21692591905593872 0.6892885 0.39462247490882874 True -12 37427 30.911141633987427 0.6559886932373047 245.22314453125 0.3804197311401367 297.73333740234375 0.21722279489040375 0.69713384 0.3686266839504242 True -13 40306 30.84743618965149 0.5954318046569824 221.738525390625 0.36809176206588745 297.6347961425781 0.21787360310554504 0.70462924 0.3596024811267853 True -14 43185 30.852543830871582 0.5950462818145752 249.41226196289062 0.39306139945983887 297.6771240234375 0.2172616422176361 0.71003455 0.3442929685115814 True -15 46064 30.964210033416748 1.4921283721923828 225.39352416992188 0.28091350197792053 297.86163330078125 0.21622377634048462 0.71434003 0.3410942852497101 True -16 48943 30.81489324569702 2.4044182300567627 217.91775512695312 0.21284930408000946 297.5907897949219 0.21741321682929993 0.7179001 0.339687317609787 True -17 51822 30.81677532196045 2.9105172157287598 241.39547729492188 0.31380322575569153 297.6793518066406 0.21737651526927948 0.7182892 0.3428684175014496 True -18 54701 30.74881076812744 41.298964738845825 229.97470092773438 0.2654424011707306 297.7244567871094 0.21707668900489807 0.71654916 0.353193074464798 False -19 57580 31.024441719055176 0.6030185222625732 235.43283081054688 0.23534250259399414 297.926025390625 0.21584752202033997 0.7137817 0.3619307279586792 False diff --git a/ENCSR949JYS/cherimoya.fold_4.performance.tsv b/ENCSR949JYS/cherimoya.fold_4.performance.tsv deleted file mode 100644 index be33a7698bc2178b2b9d9fa481d0b6660c05eae2..0000000000000000000000000000000000000000 --- a/ENCSR949JYS/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -297.6793518066406 0.5096901059150696 0.2173765003681183 0.06843487173318863 0.7182891964912415 0.6970708966255188 0.3428684175014496 \ No newline at end of file diff --git a/ENCSR951MYM/cherimoya.fold_0.log b/ENCSR951MYM/cherimoya.fold_0.log deleted file mode 100644 index cc86f7e158bc582b8715cb758ac3328d3b575648..0000000000000000000000000000000000000000 --- a/ENCSR951MYM/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1593 21.494001150131226 6.070230722427368 289.7840576171875 0.7301355004310608 389.13421630859375 0.14868971705436707 0.6418938 10.894742965698242 True -1 3186 17.646634101867676 0.3358936309814453 223.99179077148438 0.5459721088409424 353.9978942871094 0.20935319364070892 0.7548453 5.391195297241211 True -2 4779 17.658365488052368 0.31980204582214355 278.06597900390625 0.696836531162262 321.7823791503906 0.24999509751796722 0.78652394 2.7264583110809326 True -3 6372 17.680281162261963 6.543564319610596 280.88232421875 0.6748216152191162 311.318603515625 0.26235100626945496 0.8082118 1.4488636255264282 True -4 7965 17.656269788742065 0.3247866630554199 225.48629760742188 0.6534503698348999 307.5917053222656 0.2675985097885132 0.8170672 1.0217716693878174 True -5 9558 17.7048237323761 0.3207533359527588 266.3662109375 0.5073153972625732 305.6337585449219 0.2716521918773651 0.8244618 0.8969846367835999 True -6 11151 17.660374641418457 0.3244290351867676 227.18896484375 0.66275954246521 304.0313415527344 0.2739889621734619 0.83192027 0.7633774876594543 True -7 12744 17.70659613609314 0.3189079761505127 279.7851257324219 0.3786218762397766 302.9477233886719 0.2757672071456909 0.8422053 0.6655789017677307 True -8 14337 17.648595333099365 0.6534209251403809 299.35662841796875 0.6539946794509888 301.9438171386719 0.27724406123161316 0.84920096 0.5746400356292725 True -9 15930 17.753355264663696 0.3215467929840088 275.1893310546875 0.6364911794662476 300.8728942871094 0.2786296606063843 0.85492426 0.5176677107810974 True -10 17523 17.69336485862732 0.668048620223999 305.98065185546875 0.5254224538803101 300.0181884765625 0.28039321303367615 0.8595856 0.4980262219905853 True -11 19116 17.67513418197632 0.32277989387512207 311.40966796875 0.6042768955230713 298.3653564453125 0.2834145724773407 0.8630984 0.4720326066017151 True -12 20709 17.661471605300903 0.3190603256225586 217.82318115234375 0.3652802109718323 296.8089904785156 0.2857603132724762 0.86818516 0.4399513602256775 True -13 22302 17.299632787704468 0.3138396739959717 247.03945922851562 0.35693496465682983 297.165771484375 0.28493160009384155 0.87279564 0.42142173647880554 True -14 23895 17.309633255004883 0.3196690082550049 292.48004150390625 0.29795974493026733 296.318115234375 0.2869608402252197 0.8741544 0.41224703192710876 True -15 25488 17.33216881752014 0.3122842311859131 222.32606506347656 0.2840854525566101 295.8594665527344 0.28692296147346497 0.8785835 0.3973565399646759 True -16 27081 17.400096893310547 0.315122127532959 301.19140625 0.30448010563850403 296.4413146972656 0.2853069305419922 0.87775165 0.3956626057624817 False -17 28674 17.351053953170776 0.31385159492492676 290.8043518066406 0.2606121897697449 296.1681213378906 0.2861267924308777 0.87939006 0.3971136212348938 True -18 30267 17.323608875274658 0.31339144706726074 182.56646728515625 0.2905971109867096 296.3899841308594 0.28539609909057617 0.87695336 0.4012986719608307 False -19 31860 17.325862646102905 0.31135058403015137 176.48904418945312 0.25583845376968384 296.7628479003906 0.2847648561000824 0.8770188 0.40570783615112305 False diff --git a/ENCSR951MYM/cherimoya.fold_0.performance.tsv b/ENCSR951MYM/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 4a6fb36d2b75c72dd4fd1e56360ebe49a9e0538d..0000000000000000000000000000000000000000 --- a/ENCSR951MYM/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -296.1681213378906 0.492571622133255 0.2861268222332001 0.09153292328119278 0.8793900609016418 0.8228832483291626 0.3971136212348938 \ No newline at end of file diff --git a/ENCSR951MYM/cherimoya.fold_1.evaluate.json b/ENCSR951MYM/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0c192cbe08df4163db2402531afff4475bbd140c..0000000000000000000000000000000000000000 --- a/ENCSR951MYM/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF389QEV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR951MYM/cherimoya.fold_1.log b/ENCSR951MYM/cherimoya.fold_1.log deleted file mode 100644 index c886bd26791bba9067cb2b2c3ddfe91379ed2026..0000000000000000000000000000000000000000 --- a/ENCSR951MYM/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1543 20.72840428352356 4.101603746414185 260.7060241699219 0.5067023634910583 478.9822692871094 0.16089190542697906 0.6090284 12.668072700500488 True -1 3086 16.98886275291443 0.4750654697418213 305.67816162109375 0.9508646726608276 441.97802734375 0.2228066474199295 0.7298146 6.325021743774414 True -2 4629 17.094640731811523 0.45438051223754883 277.4949951171875 0.6072326302528381 391.763671875 0.28238847851753235 0.80283326 3.099175453186035 True -3 6172 17.020076513290405 0.4528679847717285 259.58746337890625 0.7275928258895874 375.6602478027344 0.29511988162994385 0.8302733 1.5547239780426025 True -4 7715 16.999295234680176 0.44786882400512695 244.6340789794922 0.38438475131988525 370.0320129394531 0.3022891879081726 0.83802295 1.299835205078125 True -5 9258 16.98905086517334 0.44840049743652344 211.6830291748047 0.7572363615036011 368.05413818359375 0.3058408796787262 0.8381096 1.0418627262115479 True -6 10801 16.98169255256653 0.45136189460754395 231.20350646972656 0.7670533657073975 366.8544006347656 0.3075682520866394 0.8440763 0.9048471450805664 True -7 12344 16.980618715286255 0.44516682624816895 236.87319946289062 0.6912016272544861 365.5450134277344 0.3089566230773926 0.8544656 0.7696521282196045 True -8 13887 16.965835094451904 1.3903241157531738 205.90957641601562 0.5084334015846252 364.2095642089844 0.31179097294807434 0.863052 0.6505483984947205 True -9 15430 16.983863592147827 0.4477100372314453 249.25347900390625 0.4250751733779907 362.3492736816406 0.31437966227531433 0.8668445 0.575806736946106 True -10 16973 16.969684839248657 0.46465158462524414 286.8912658691406 0.3340967297554016 361.4301452636719 0.3155902922153473 0.8697362 0.5427551865577698 True -11 18516 17.0062313079834 0.4516103267669678 214.12416076660156 0.48732542991638184 360.4408264160156 0.3172067403793335 0.87365746 0.5242723822593689 True -12 20059 16.97089958190918 1.2248930931091309 264.23583984375 0.35966360569000244 360.14404296875 0.31776583194732666 0.87794095 0.4827810823917389 True -13 21602 16.997007608413696 0.4533090591430664 209.33370971679688 0.6104403138160706 358.040771484375 0.321416437625885 0.88288015 0.4620146155357361 True -14 23145 16.996472358703613 0.4532654285430908 247.6520233154297 0.4246625304222107 357.3565673828125 0.3223331868648529 0.88378084 0.44937682151794434 True -15 24688 16.982404947280884 0.4555647373199463 247.10693359375 0.2933018207550049 356.82794189453125 0.32318830490112305 0.8858028 0.43826210498809814 True -16 26231 16.96892213821411 0.4537017345428467 219.0 0.35203778743743896 356.571533203125 0.32342490553855896 0.8880251 0.4343930184841156 True -17 27774 16.959224224090576 0.4544668197631836 223.33615112304688 0.5052014589309692 357.538818359375 0.3208256959915161 0.88800794 0.43902847170829773 False -18 29317 16.974223136901855 0.4598088264465332 254.6224365234375 0.2892548441886902 356.8886413574219 0.3233059048652649 0.88696164 0.44414177536964417 False -19 30860 16.982661724090576 0.4545471668243408 207.2484130859375 0.23101018369197845 357.3671875 0.32199209928512573 0.88573354 0.4497842788696289 False diff --git a/ENCSR951MYM/cherimoya.fold_2.fit.json b/ENCSR951MYM/cherimoya.fold_2.fit.json deleted file mode 100644 index 43ec17bdd7c8edfc187f8f874f22304afed6afc7..0000000000000000000000000000000000000000 --- a/ENCSR951MYM/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF389QEV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR951MYM/cherimoya.fold_3.evaluate.json b/ENCSR951MYM/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 22738b09f29b0bf6c66346ec664ba3942d51a0c6..0000000000000000000000000000000000000000 --- a/ENCSR951MYM/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF389QEV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_0.evaluate.json b/ENCSR952SPO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c440b901a53f4f7d070927b7603be434cc300b61..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588LWH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_0.fit.json b/ENCSR952SPO/cherimoya.fold_0.fit.json deleted file mode 100644 index 14a45d0b23d4abe66004d977cad41c98eecf33d1..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF588LWH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_0.log b/ENCSR952SPO/cherimoya.fold_0.log deleted file mode 100644 index c9815a28344110560ef63729312e3e87f2c8d36d..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3835 47.48224425315857 4.375686168670654 849.8917846679688 0.9661507606506348 1274.0615234375 0.7106247544288635 0.6103678 9.309618949890137 True -1 7670 42.67731952667236 1.439993143081665 1000.0108642578125 0.9151854515075684 1073.1666259765625 0.7961246967315674 0.6591642 2.15744948387146 True -2 11505 42.53669500350952 23.852360486984253 788.12841796875 0.9386966824531555 1044.39892578125 0.8045554757118225 0.66238654 1.2717841863632202 True -3 15340 42.54919743537903 0.7901999950408936 753.1907958984375 0.7538841962814331 1028.07958984375 0.8097266554832458 0.66450346 0.9736770391464233 True -4 19175 42.26860523223877 0.7500975131988525 962.1109619140625 0.9121760129928589 1021.624755859375 0.8133189082145691 0.6722817 0.9368488192558289 True -5 23010 41.68667507171631 0.7585813999176025 914.5061645507812 0.8215906620025635 1016.6231079101562 0.8153320550918579 0.67375636 0.8584309220314026 True -6 26845 41.67456912994385 0.7443678379058838 860.4617919921875 0.9736459255218506 1009.780029296875 0.8185515403747559 0.6766714 0.8340296149253845 True -7 30680 41.79920673370361 0.7463531494140625 787.575927734375 0.5242695808410645 1000.9838256835938 0.8209468126296997 0.68400687 0.7317422032356262 True -8 34515 41.58611226081848 0.7332189083099365 849.393310546875 0.7371442317962646 995.3734741210938 0.8238080739974976 0.6854243 0.7074706554412842 True -9 38350 41.617605686187744 0.7310936450958252 854.2914428710938 0.675887405872345 989.867919921875 0.8262081146240234 0.6932529 0.6686222553253174 True -10 42185 41.6582396030426 0.7373309135437012 877.9688720703125 0.7843033075332642 983.0795288085938 0.8298456072807312 0.7029387 0.6376615762710571 True -11 46020 41.64191293716431 0.7580842971801758 703.7504272460938 0.6547024250030518 977.0591430664062 0.8322888016700745 0.7050407 0.6373301148414612 True -12 49855 41.65745496749878 0.7368977069854736 713.0260009765625 0.6865867376327515 968.981689453125 0.8350812792778015 0.71515113 0.594419002532959 True -13 53690 41.75459003448486 0.7717010974884033 816.098876953125 0.38282474875450134 962.3587646484375 0.8380693197250366 0.72558916 0.5695301294326782 True -14 57525 41.6279935836792 0.7302649021148682 760.486572265625 0.7692819237709045 957.0344848632812 0.840298056602478 0.7334458 0.5420474410057068 True -15 61360 41.666630029678345 1.9204277992248535 777.8216552734375 0.9722005724906921 952.888671875 0.8420422673225403 0.7394653 0.5338117480278015 True -16 65195 41.58372926712036 0.7363009452819824 849.9531860351562 0.6004659533500671 950.9054565429688 0.8429475426673889 0.74307096 0.5302074551582336 True -17 69030 41.58440804481506 0.7351202964782715 740.5067749023438 0.6534081697463989 951.43798828125 0.8431039452552795 0.74604714 0.5276239514350891 True -18 72865 41.64871287345886 0.7371184825897217 735.452880859375 0.5693163275718689 952.0772705078125 0.8428130149841309 0.74414796 0.532303512096405 False -19 76700 41.725611448287964 0.7317061424255371 768.8383178710938 0.4032924771308899 951.6480712890625 0.8425516486167908 0.7442581 0.5361767411231995 False diff --git a/ENCSR952SPO/cherimoya.fold_0.performance.tsv b/ENCSR952SPO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index d2e14359b627120ed244096b98d88f60e7b6dbb9..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -951.43798828125 0.12384725362062454 0.8431040048599243 0.5483008623123169 0.7460471391677856 0.6937090158462524 0.5276239514350891 \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_1.evaluate.json b/ENCSR952SPO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9dc648f42ffb0dfbcbeb8e83184b879b1788476e..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588LWH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_1.fit.json b/ENCSR952SPO/cherimoya.fold_1.fit.json deleted file mode 100644 index f3f00e0267adaee581779fec1d16daf032ae62cc..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF588LWH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_1.log b/ENCSR952SPO/cherimoya.fold_1.log deleted file mode 100644 index fea81d99e1eb7faec064568d81f1274650f928c2..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3793 46.774332761764526 4.773897171020508 804.4105224609375 0.9155483245849609 1363.0780029296875 0.7144003510475159 0.6335742 9.133040428161621 True -1 7586 42.03961706161499 1.073732614517212 1003.9466552734375 0.8721065521240234 1143.088134765625 0.8014199733734131 0.6798286 2.308419942855835 True -2 11379 42.033422231674194 1.0590896606445312 870.0413818359375 0.8445205688476562 1119.156494140625 0.8071737885475159 0.6944531 1.4707567691802979 True -3 15172 41.96980881690979 0.9728748798370361 931.8045654296875 1.392907977104187 1098.3839111328125 0.8127806782722473 0.70251507 1.0482629537582397 True -4 18965 42.017943382263184 1.00569486618042 803.7949829101562 0.6812637448310852 1089.9122314453125 0.8160604238510132 0.70104647 1.1250706911087036 False -5 22758 42.042460441589355 2.0832347869873047 991.4559326171875 0.8933601975440979 1081.990966796875 0.8177292346954346 0.7037917 0.830429196357727 True -6 26551 41.97998094558716 1.0098731517791748 820.132568359375 0.678030252456665 1073.052490234375 0.8205822110176086 0.7115735 0.774771511554718 True -7 30344 41.93478798866272 2.1905181407928467 951.9461669921875 0.8473169803619385 1063.619384765625 0.8239906430244446 0.71873283 0.7459982633590698 True -8 34137 42.04833436012268 1.0002198219299316 900.381103515625 0.368606299161911 1055.336669921875 0.826662003993988 0.72342765 0.7015311121940613 True -9 37930 41.987523317337036 0.9940853118896484 835.5506591796875 0.7734323143959045 1048.2227783203125 0.8294533491134644 0.7261344 0.6582507491111755 True -10 41723 41.93706178665161 0.9879803657531738 811.7584838867188 0.5051094889640808 1043.0780029296875 0.8320682644844055 0.731629 0.6518635749816895 True -11 45516 42.015310287475586 1.0002119541168213 746.117919921875 0.6029523611068726 1035.239013671875 0.8346224427223206 0.7366439 0.6112443804740906 True -12 49309 41.61196851730347 1.003652811050415 824.3265380859375 0.664553165435791 1026.7532958984375 0.8381747603416443 0.7477818 0.5821497440338135 True -13 53102 41.1247444152832 0.9759888648986816 875.5692749023438 0.8609583973884583 1019.536376953125 0.8407300710678101 0.7535672 0.5580793023109436 True -14 56895 41.13400745391846 0.9825620651245117 795.614501953125 0.5844904780387878 1013.0555419921875 0.8431903123855591 0.76040304 0.5372880697250366 True -15 60688 41.079752683639526 1.0036301612854004 859.5311279296875 0.613747775554657 1009.2928466796875 0.8446957468986511 0.7659108 0.5272475481033325 True -16 64481 41.12940001487732 0.9915571212768555 746.1494750976562 0.41707566380500793 1007.3699340820312 0.8455309867858887 0.7703359 0.5207785964012146 True -17 68274 41.20281624794006 1.0139422416687012 754.3739624023438 0.4434313178062439 1007.4121704101562 0.8455498218536377 0.76987743 0.5221637487411499 False -18 72067 41.24121952056885 1.0004594326019287 764.086669921875 0.516441285610199 1009.0103759765625 0.8451160788536072 0.7701859 0.5279390215873718 False -19 75860 41.20974779129028 1.0015637874603271 727.61376953125 0.5396246314048767 1009.5455322265625 0.8448326587677002 0.7695042 0.531207263469696 False diff --git a/ENCSR952SPO/cherimoya.fold_1.performance.tsv b/ENCSR952SPO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 810d708a0664cfaf770a0c13feae231e6fcf8a7f..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1007.3699340820312 0.11894502490758896 0.8455309867858887 0.5671102404594421 0.7703359127044678 0.7370008230209351 0.5207785964012146 \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_2.evaluate.json b/ENCSR952SPO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index feab3f096f0d907bde5f3e5c8c7eb4d267753687..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588LWH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_2.fit.json b/ENCSR952SPO/cherimoya.fold_2.fit.json deleted file mode 100644 index b75a241d4b14a3c8b0790ba38a529f9afa8f2365..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF588LWH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_2.log b/ENCSR952SPO/cherimoya.fold_2.log deleted file mode 100644 index 437993115353599c7adf8626ffb2f799e6ebc627..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 4035 49.534905672073364 5.7324159145355225 874.322265625 1.0200917720794678 1317.152587890625 0.7167121171951294 0.6131705 9.526908874511719 True -1 8070 44.651082277297974 0.7888243198394775 1138.543701171875 0.9634674787521362 1109.4132080078125 0.8031116724014282 0.6675134 2.3859195709228516 True -2 12105 44.68902611732483 0.812762975692749 865.1993408203125 0.9061239361763 1080.5914306640625 0.8103622794151306 0.68340266 1.150131106376648 True -3 16140 44.71446442604065 24.567699193954468 863.6685791015625 0.6555100679397583 1066.252197265625 0.8146834373474121 0.6936677 0.9856082797050476 True -4 20175 44.72738265991211 0.768890380859375 814.701171875 0.822350800037384 1058.6290283203125 0.8170087933540344 0.6936171 0.9223527908325195 False -5 24210 44.759626388549805 0.7721850872039795 884.461181640625 1.0585027933120728 1050.382080078125 0.8202616572380066 0.6933017 0.7198013067245483 False -6 28245 43.99245262145996 0.7768828868865967 817.2918090820312 0.6489670872688293 1043.9267578125 0.8226973414421082 0.6979418 0.6771683692932129 True -7 32280 43.761391162872314 0.7646608352661133 813.5586547851562 0.8779178857803345 1038.697998046875 0.825010359287262 0.70211834 0.672674834728241 True -8 36315 43.88801169395447 0.7688186168670654 843.3461303710938 0.6661906242370605 1033.3797607421875 0.8274312615394592 0.7081648 0.6530139446258545 True -9 40350 43.749884605407715 0.8439521789550781 712.9425048828125 0.6137665510177612 1026.233154296875 0.830383837223053 0.71658427 0.6109108924865723 True -10 44385 43.74108362197876 0.7809021472930908 779.1611938476562 0.5994311571121216 1019.8722534179688 0.8326634168624878 0.7175558 0.617088794708252 True -11 48420 43.97864484786987 0.7772121429443359 795.5078735351562 0.9453454613685608 1014.1740112304688 0.8356693983078003 0.72154504 0.6033071875572205 True -12 52455 44.13736581802368 0.7828073501586914 884.1405029296875 0.8462496995925903 1006.983154296875 0.8384757041931152 0.7291608 0.5918270349502563 True -13 56490 44.34315633773804 0.811863899230957 791.6990966796875 0.3260403871536255 999.8959350585938 0.8406850695610046 0.73851985 0.5523905158042908 True -14 60525 44.27530074119568 0.7780458927154541 844.624755859375 0.72044438123703 994.7404174804688 0.8431562185287476 0.74392295 0.5533836483955383 True -15 64560 43.96532416343689 0.7733819484710693 792.4428100585938 0.6598674058914185 991.1502075195312 0.8444151878356934 0.74662316 0.539600670337677 True -16 68595 44.03758668899536 0.7676565647125244 738.5732421875 0.4463154077529907 990.4466552734375 0.8450221419334412 0.7522977 0.5354244112968445 True -17 72630 43.840060234069824 0.7686939239501953 740.07861328125 0.3615877330303192 989.6980590820312 0.8451021313667297 0.75403243 0.5397916436195374 True -18 76665 43.840441942214966 0.7668285369873047 754.0809936523438 0.4297519326210022 990.2989501953125 0.8448997139930725 0.7527327 0.5448280572891235 False -19 80700 44.010051250457764 0.7655630111694336 877.5667724609375 0.28842729330062866 991.285400390625 0.8446114659309387 0.75122094 0.5477079153060913 False diff --git a/ENCSR952SPO/cherimoya.fold_2.performance.tsv b/ENCSR952SPO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b24461fff82095dc6ce2d5ae09433754ae2aa4c8..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -989.6980590820312 0.12040524184703827 0.8451021313667297 0.5610795617103577 0.7540324330329895 0.7133091688156128 0.5397916436195374 \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_3.evaluate.json b/ENCSR952SPO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f6f3045a242c8ae4cfd3c6267e88ebe4b9014468..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588LWH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_3.fit.json b/ENCSR952SPO/cherimoya.fold_3.fit.json deleted file mode 100644 index 7ffaa3b0fa05dce2c32e8c2b8c1f632dcd04627a..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF588LWH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_3.log b/ENCSR952SPO/cherimoya.fold_3.log deleted file mode 100644 index 6f3bd77903a15c5fa36b983278adb70e560372e8..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3906 47.33661961555481 4.429362058639526 1020.626708984375 1.133617639541626 1265.7613525390625 0.7115190625190735 0.6244611 8.33445930480957 True -1 7812 43.30092239379883 0.9883582592010498 874.0116577148438 1.114562749862671 1080.5341796875 0.7936329245567322 0.66314477 2.010646343231201 True -2 11718 43.19971442222595 0.8228423595428467 904.7723388671875 0.6696139574050903 1055.8631591796875 0.7997799515724182 0.67027235 1.2500511407852173 True -3 15624 42.342358112335205 0.74810791015625 825.5013427734375 0.7966594696044922 1039.3023681640625 0.8055869340896606 0.68353283 0.9519931077957153 True -4 19530 42.3983678817749 0.7764487266540527 790.0977783203125 0.6019999384880066 1033.1973876953125 0.8072083592414856 0.6782491 0.9292194247245789 False -5 23436 42.44469380378723 0.7626268863677979 855.3170776367188 0.7438098192214966 1027.62060546875 0.8099296689033508 0.68384826 0.8541188836097717 True -6 27342 45.03145670890808 12.793500423431396 707.768310546875 0.44565486907958984 1020.2777099609375 0.8130106329917908 0.68780327 0.8337502479553223 True -7 31248 42.61418032646179 1.9482483863830566 816.4829711914062 0.7638073563575745 1016.1632080078125 0.8154506683349609 0.68831235 0.8101058006286621 True -8 35154 43.83880591392517 6.176777362823486 833.947998046875 0.7476998567581177 1006.3439331054688 0.8191196918487549 0.6966687 0.7264816164970398 True -9 39060 42.412744760513306 0.7680468559265137 623.762451171875 0.5929504632949829 1000.9536743164062 0.8218482136726379 0.7067379 0.7378780841827393 True -10 42966 42.43751335144043 0.766165018081665 798.2420654296875 0.6185004711151123 992.2633056640625 0.8248439431190491 0.7098451 0.6514467597007751 True -11 46872 42.43719816207886 1.1275851726531982 727.0020141601562 0.7306771278381348 982.5033569335938 0.8282209038734436 0.7162068 0.631373941898346 True -12 50778 42.42933249473572 0.8720242977142334 828.2710571289062 0.6366963386535645 977.1275024414062 0.831221342086792 0.72397494 0.606616735458374 True -13 54684 42.42581391334534 0.7894189357757568 762.1624145507812 0.6693809032440186 971.296630859375 0.8340280652046204 0.73707646 0.568616509437561 True -14 58590 42.53188514709473 0.7899751663208008 786.9818725585938 0.675749659538269 964.896484375 0.8362964987754822 0.7447614 0.5494381785392761 True -15 62496 42.61246991157532 0.8478271961212158 777.825927734375 0.47055160999298096 960.9346923828125 0.8380495309829712 0.7518494 0.5323224663734436 True -16 66402 42.51748085021973 0.8255810737609863 708.9285888671875 0.609825611114502 958.538818359375 0.8389907479286194 0.75621897 0.5237265229225159 True -17 70308 42.55664610862732 0.77730393409729 723.45947265625 0.3684620261192322 959.7930297851562 0.8389570713043213 0.75761056 0.5271189212799072 True -18 74214 42.64018797874451 0.7912411689758301 737.8458251953125 0.46234628558158875 959.9286499023438 0.8385874629020691 0.7569162 0.5293048024177551 False -19 78120 42.55495071411133 1.3162779808044434 865.8641967773438 0.43522369861602783 960.9170532226562 0.8383340239524841 0.75514126 0.5366455316543579 False diff --git a/ENCSR952SPO/cherimoya.fold_3.performance.tsv b/ENCSR952SPO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index a6f6a7a95aecf7100960e08ea0fe47a50aa05e71..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -959.7930297851562 0.1252293735742569 0.8389570713043213 0.5465605854988098 0.757610559463501 0.7184129357337952 0.5271189212799072 \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_4.evaluate.json b/ENCSR952SPO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index b1b3ac33979fc2fc68b980a51391199c09241999..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588LWH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_4.fit.json b/ENCSR952SPO/cherimoya.fold_4.fit.json deleted file mode 100644 index 01c28085e5e729945acf1ebd298e0fccbeaf1877..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF588LWH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR952SPO/cherimoya.fold_4.log b/ENCSR952SPO/cherimoya.fold_4.log deleted file mode 100644 index e4dd7d0fff5ff720f64987d08edb640ee3738883..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3957 48.70869445800781 4.409575700759888 804.2465209960938 0.7870754599571228 1242.0146484375 0.7121205925941467 0.58877635 7.907392978668213 True -1 7914 45.53375840187073 0.7989022731781006 787.18505859375 1.0372891426086426 1052.5379638671875 0.7965829968452454 0.63934076 2.0783629417419434 True -2 11871 43.92610430717468 0.818256139755249 750.3662719726562 0.8786521553993225 1028.7977294921875 0.8029488325119019 0.64536047 1.1379594802856445 True -3 15828 43.923874855041504 0.7999804019927979 807.61474609375 0.8411558866500854 1012.0267333984375 0.8092639446258545 0.64557904 1.032305121421814 True -4 19785 43.86057376861572 0.7821307182312012 781.800537109375 0.8086153268814087 1008.6560668945312 0.8114615678787231 0.6451582 1.1302894353866577 False -5 23742 43.95016121864319 0.7814135551452637 843.451416015625 0.6707231998443604 1003.271728515625 0.8141655325889587 0.6512239 0.9293345212936401 True -6 27699 43.93571758270264 0.7968385219573975 927.1365966796875 0.7429822683334351 994.92529296875 0.8167644739151001 0.65737325 0.8284083008766174 True -7 31656 43.88125228881836 0.7833151817321777 763.5843505859375 0.5945374369621277 987.9910888671875 0.8203772902488708 0.66561073 0.799740195274353 True -8 35613 43.846482038497925 0.7826535701751709 830.7257080078125 0.611621618270874 982.1962280273438 0.8227291107177734 0.6699694 0.7261212468147278 True -9 39570 43.81243085861206 0.7835443019866943 708.003173828125 0.678807258605957 974.6615600585938 0.8253396153450012 0.674186 0.6937983632087708 True -10 43527 43.88950228691101 8.782352209091187 869.8465576171875 0.7366610169410706 970.7308349609375 0.8278260231018066 0.6801887 0.6832236647605896 True -11 47484 43.665887117385864 0.7908215522766113 836.2808227539062 0.7318795919418335 963.947509765625 0.8304662108421326 0.68797517 0.6588260531425476 True -12 51441 42.99575877189636 0.7912299633026123 828.0391845703125 0.5939964056015015 959.1246948242188 0.8325265645980835 0.69152164 0.6379169821739197 True -13 55398 43.02149200439453 0.7877788543701172 785.1973266601562 0.6285229325294495 952.488037109375 0.8353862762451172 0.7017011 0.6115034222602844 True -14 59355 42.94882082939148 0.7799286842346191 734.018310546875 0.4672855734825134 948.4368896484375 0.8372301459312439 0.71196854 0.5869281888008118 True -15 63312 43.00122356414795 0.7774863243103027 875.11328125 0.4851958155632019 945.0796508789062 0.8389036059379578 0.7182058 0.5690398812294006 True -16 67269 42.96256470680237 9.571568965911865 679.110107421875 0.4732521176338196 943.0029296875 0.8396502733230591 0.72246224 0.5623778700828552 True -17 71226 42.992563009262085 0.7842724323272705 776.373779296875 0.41048410534858704 943.839111328125 0.8397418856620789 0.72382796 0.5644229054450989 True -18 75183 42.93530225753784 0.7802152633666992 761.0836181640625 0.5652589797973633 945.0001220703125 0.8394461274147034 0.7232275 0.5713382959365845 False -19 79140 42.956900119781494 19.71384072303772 735.2819213867188 0.47386878728866577 945.552490234375 0.8393340110778809 0.7228579 0.5769666433334351 False diff --git a/ENCSR952SPO/cherimoya.fold_4.performance.tsv b/ENCSR952SPO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6182ccd24e5c516381e4ec8c832e65ffb0a4061b..0000000000000000000000000000000000000000 --- a/ENCSR952SPO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -943.839111328125 0.12494149059057236 0.8397419452667236 0.5469381213188171 0.7238279581069946 0.6789979338645935 0.5644229054450989 \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_0.evaluate.json b/ENCSR953XJU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6e081910690eb7a2bd6d1c5f9dedebd212222835..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588ZCP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_0.fit.json b/ENCSR953XJU/cherimoya.fold_0.fit.json deleted file mode 100644 index 7ad9fe1f163be2b9d6061fd33015b56e7ffbf582..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF588ZCP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_0.log b/ENCSR953XJU/cherimoya.fold_0.log deleted file mode 100644 index ec537fcca7c8765f19b2da31fefda6168f6e12b8..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2785 35.783610343933105 3.7319998741149902 217.0040283203125 0.5509727597236633 258.2537841796875 0.14005762338638306 0.72976965 3.2308859825134277 True -1 5570 30.920528411865234 0.6547496318817139 177.98593139648438 0.6324163675308228 249.07675170898438 0.18661271035671234 0.77769995 1.0534148216247559 True -2 8355 31.022986888885498 0.6047680377960205 223.8919677734375 0.7385801076889038 245.62046813964844 0.19985726475715637 0.7914343 0.6044415235519409 True -3 11140 30.97399139404297 0.7954757213592529 190.1476593017578 0.6154729723930359 244.58775329589844 0.20453804731369019 0.79896504 0.5066114068031311 True -4 13925 30.92299795150757 0.5748751163482666 239.46380615234375 0.4601471424102783 243.79962158203125 0.2083156257867813 0.80162245 0.49899575114250183 True -5 16710 30.630029439926147 0.5714852809906006 170.96139526367188 0.6953898668289185 243.79324340820312 0.20708416402339935 0.80269045 0.5345847010612488 True -6 19495 30.26291561126709 1.775848388671875 175.78533935546875 0.4116576015949249 243.67529296875 0.20794285833835602 0.8048335 0.49490779638290405 True -7 22280 30.300331592559814 0.5939586162567139 190.72305297851562 0.40757930278778076 243.23777770996094 0.21056699752807617 0.8072158 0.47657862305641174 True -8 25065 30.244449853897095 0.5604300498962402 191.66697692871094 0.6901265382766724 242.78823852539062 0.21314629912376404 0.80657786 0.4939931333065033 False -9 27850 30.23111653327942 0.6232428550720215 225.31024169921875 0.45368891954421997 242.44528198242188 0.21446870267391205 0.8107322 0.4600907564163208 True -10 30635 30.240556240081787 0.5745954513549805 171.42294311523438 0.333888441324234 242.1516571044922 0.21498237550258636 0.81292766 0.42482972145080566 True -11 33420 30.293907403945923 17.08061718940735 225.82398986816406 0.3390251398086548 241.61883544921875 0.2171168327331543 0.81590134 0.4045915901660919 True -12 36205 30.545585870742798 0.5731747150421143 225.86154174804688 0.5655033588409424 240.90911865234375 0.220672145485878 0.8193565 0.37328070402145386 True -13 38990 30.36821150779724 0.576167106628418 228.77249145507812 0.33928483724594116 240.52040100097656 0.2235478013753891 0.82390773 0.3565657138824463 True -14 41775 30.412177562713623 0.5801458358764648 171.82659912109375 0.3125154376029968 240.4216766357422 0.22375483810901642 0.8256706 0.3335612118244171 True -15 44560 30.251778841018677 0.5809810161590576 183.20242309570312 0.43848758935928345 240.2240753173828 0.22479499876499176 0.8294079 0.3197501003742218 True -16 47345 30.23462200164795 0.5735304355621338 167.97402954101562 0.3689194321632385 240.24227905273438 0.22382597625255585 0.8313941 0.3134019374847412 True -17 50130 30.24942684173584 0.548391580581665 198.16534423828125 0.48276135325431824 240.34703063964844 0.22298669815063477 0.83244264 0.3039516508579254 True -18 52915 30.278448343276978 0.5708422660827637 204.24163818359375 0.306999534368515 240.2666015625 0.2238597720861435 0.8314189 0.3060898184776306 False -19 55700 30.278428554534912 0.6483550071716309 187.18499755859375 0.37424519658088684 240.5712432861328 0.22179673612117767 0.83203703 0.30417928099632263 False diff --git a/ENCSR953XJU/cherimoya.fold_0.performance.tsv b/ENCSR953XJU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c42b2b08052a24579fcb866925716dd5747af816..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -240.34703063964844 0.5309339761734009 0.22298669815063477 0.05982287600636482 0.8324426412582397 0.7775214910507202 0.3039516508579254 \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_1.evaluate.json b/ENCSR953XJU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a15d2d743107f209cf0b8c31ec761f4824fb4521..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588ZCP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_1.fit.json b/ENCSR953XJU/cherimoya.fold_1.fit.json deleted file mode 100644 index df78e75290356d8256f7f8670d7124ff09b6314d..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF588ZCP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_1.log b/ENCSR953XJU/cherimoya.fold_1.log deleted file mode 100644 index 70bb4e30907ef9f7034132edcc20f4afbb0202c4..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 34.95118689537048 4.191238164901733 185.17666625976562 0.68971848487854 304.2657470703125 0.1496691107749939 0.7175916 3.9877076148986816 True -1 5462 30.339881420135498 3.8591389656066895 167.2303466796875 0.5113699436187744 292.1183166503906 0.20640194416046143 0.79185015 1.0022586584091187 True -2 8193 29.850471019744873 0.7311193943023682 157.7687225341797 0.7860130071640015 288.030517578125 0.2188747525215149 0.80046964 0.535281240940094 True -3 10924 29.674901723861694 0.7186853885650635 198.06137084960938 0.4489278197288513 286.44158935546875 0.22247639298439026 0.8093437 0.5187743306159973 True -4 13655 29.693263053894043 0.708437442779541 214.70387268066406 0.634272038936615 285.9621276855469 0.2243494987487793 0.81204695 0.48248738050460815 True -5 16386 29.694299459457397 0.7107915878295898 205.12014770507812 0.7118058204650879 285.4912414550781 0.22565801441669464 0.8154699 0.4984593093395233 True -6 19117 29.580564498901367 0.7089419364929199 184.33572387695312 0.6192692518234253 284.8639831542969 0.2284393310546875 0.815694 0.4934830367565155 True -7 21848 29.619918823242188 0.7218523025512695 198.607177734375 0.6942901015281677 284.41046142578125 0.22992107272148132 0.817897 0.47637003660202026 True -8 24579 29.601234436035156 0.7236227989196777 193.36436462402344 0.4699169099330902 283.3969421386719 0.23409593105316162 0.8222181 0.4436264634132385 True -9 27310 29.60053300857544 0.7268421649932861 172.380126953125 0.5359882116317749 282.6066589355469 0.2377723604440689 0.8264154 0.4033081829547882 True -10 30041 29.614928007125854 0.7149310111999512 193.4571990966797 0.3337496221065521 282.443603515625 0.2380785495042801 0.8307775 0.4023425877094269 True -11 32772 29.66197156906128 0.7002990245819092 191.75338745117188 0.5354427099227905 282.10833740234375 0.23967011272907257 0.83313704 0.3990512490272522 True -12 35503 29.606454372406006 0.7327380180358887 197.9474639892578 0.35750308632850647 281.9158935546875 0.23955699801445007 0.8370334 0.38407447934150696 True -13 38234 29.607541799545288 0.8046309947967529 222.028076171875 0.4367355704307556 280.9215087890625 0.2441701889038086 0.83845794 0.3740338683128357 True -14 40965 29.610339879989624 1.125368595123291 233.924560546875 0.3329709768295288 280.7654113769531 0.2447354942560196 0.84193933 0.36187729239463806 True -15 43696 29.659536600112915 1.65165376663208 181.41024780273438 0.3586076498031616 280.8601379394531 0.24425174295902252 0.8440347 0.3548402488231659 True -16 46427 29.684561491012573 2.5171515941619873 172.08566284179688 0.42638540267944336 280.9456481933594 0.24307523667812347 0.8481494 0.3409307897090912 True -17 49158 29.671409368515015 1.592503547668457 224.77914428710938 0.2654041647911072 280.932861328125 0.24356584250926971 0.8465471 0.3347419798374176 False -18 51889 29.70416808128357 2.172273635864258 165.99447631835938 0.50221848487854 280.9066467285156 0.2434702217578888 0.84905255 0.3343561887741089 True -19 54620 29.66940665245056 1.144043207168579 195.0848388671875 0.19146278500556946 280.9054260253906 0.24390558898448944 0.84758514 0.3330540657043457 False diff --git a/ENCSR953XJU/cherimoya.fold_1.performance.tsv b/ENCSR953XJU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 5399520158d9f9edfba3e094fd3e2a146a36a8c9..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -280.9066467285156 0.5109125971794128 0.2434702217578888 0.06824914366006851 0.8490525484085083 0.8180949091911316 0.3343561887741089 \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_2.evaluate.json b/ENCSR953XJU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4f6901f3ac6aa8dfdc3f63e707cc7704855a428a..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588ZCP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_2.fit.json b/ENCSR953XJU/cherimoya.fold_2.fit.json deleted file mode 100644 index 79da998a9ffb95f0bb6901a41642d413c1d3090c..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF588ZCP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_2.log b/ENCSR953XJU/cherimoya.fold_2.log deleted file mode 100644 index d1d5bcd2954f817ceba19330a8f5bfaf236ae9e3..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2903 37.108518838882446 3.8222813606262207 253.3602752685547 0.6865879893302917 270.86907958984375 0.14463385939598083 0.72964424 2.6605026721954346 True -1 5806 32.2479088306427 0.6529133319854736 215.0080108642578 0.685272753238678 260.2066955566406 0.19614100456237793 0.78550917 0.8866567611694336 True -2 8709 32.27607607841492 0.5422132015228271 216.75564575195312 0.6331701278686523 257.30078125 0.20426297187805176 0.7956172 0.6162316203117371 True -3 11612 32.223923683166504 0.5401389598846436 163.72149658203125 1.0144917964935303 256.21820068359375 0.2083483785390854 0.79932123 0.5690099000930786 True -4 14515 32.26195979118347 0.6020686626434326 160.46676635742188 0.4438062310218811 255.3922882080078 0.21292416751384735 0.8042075 0.4876229166984558 True -5 17418 32.22708344459534 0.5345301628112793 154.86688232421875 0.5646674036979675 255.15130615234375 0.21413516998291016 0.8037423 0.5153560638427734 False -6 20321 31.590929985046387 0.5339560508728027 204.62673950195312 0.36836743354797363 254.544189453125 0.21701441705226898 0.8044627 0.5277243852615356 True -7 23224 31.584177255630493 0.5531563758850098 173.22265625 0.5697770118713379 254.2899169921875 0.2179943323135376 0.80867857 0.4919307231903076 True -8 26127 31.650283813476562 1.1574172973632812 209.57798767089844 0.6059222221374512 254.12738037109375 0.2185690850019455 0.8104384 0.47755327820777893 True -9 29030 31.633119821548462 0.553459882736206 217.00572204589844 0.6499344110488892 253.36328125 0.22256426513195038 0.811217 0.45424357056617737 True -10 31933 31.571531295776367 0.7721354961395264 212.51516723632812 0.41605883836746216 252.65589904785156 0.22613243758678436 0.811904 0.44918209314346313 True -11 34836 31.588375329971313 0.5423562526702881 181.51913452148438 0.6308794617652893 252.44837951660156 0.22674891352653503 0.8131485 0.4132745862007141 True -12 37739 31.63204526901245 0.5681164264678955 196.3128662109375 0.39342838525772095 252.1667938232422 0.22786402702331543 0.81710994 0.39965614676475525 True -13 40642 31.804940938949585 0.5428001880645752 211.9470672607422 0.5447729229927063 252.11997985839844 0.22731058299541473 0.81763184 0.38517439365386963 True -14 43545 31.68224596977234 0.5600123405456543 244.52438354492188 0.36319097876548767 251.4043731689453 0.23068992793560028 0.82321244 0.3649597764015198 True -15 46448 31.687898635864258 0.5434226989746094 177.05010986328125 0.3669138252735138 251.65843200683594 0.2295435070991516 0.8297835 0.34536343812942505 True -16 49351 31.62538981437683 0.5322632789611816 211.1576690673828 0.2996523976325989 251.34231567382812 0.23118740320205688 0.83233875 0.3380662798881531 True -17 52254 31.66902995109558 0.5633196830749512 177.79739379882812 0.4771631062030792 251.7637939453125 0.22948473691940308 0.83308554 0.3281324803829193 True -18 55157 31.79455804824829 0.5472753047943115 236.09939575195312 0.2859419286251068 251.57611083984375 0.22970925271511078 0.8330324 0.3259959816932678 False -19 58060 31.72518801689148 0.5345497131347656 202.9375 0.20900791883468628 251.3878173828125 0.2310495227575302 0.8328029 0.32643717527389526 False diff --git a/ENCSR953XJU/cherimoya.fold_2.performance.tsv b/ENCSR953XJU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index febb2b2d360b29d15c1b243ea77f717fa56bdf89..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -251.7637939453125 0.5252172350883484 0.2294846922159195 0.06490857154130936 0.8330855369567871 0.7882387042045593 0.3281324803829193 \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_3.evaluate.json b/ENCSR953XJU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e1d2f5278bb51dfb9bb67cc49f9246c4a4b65050..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588ZCP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_3.fit.json b/ENCSR953XJU/cherimoya.fold_3.fit.json deleted file mode 100644 index 1f0839d5b263173f98fd4fb92eee78949f820c79..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF588ZCP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_3.log b/ENCSR953XJU/cherimoya.fold_3.log deleted file mode 100644 index 7533d5d2c2f310a4fa22f44d22051f9c561f79f9..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2785 56.870015382766724 68.6012909412384 198.8387451171875 0.5797392129898071 273.5861511230469 0.14409826695919037 0.7173593 3.5769565105438232 True -1 5570 31.023448944091797 0.6915979385375977 203.80679321289062 0.8308120965957642 264.0609130859375 0.19021867215633392 0.7922945 0.8771964311599731 True -2 8355 31.0359890460968 0.5801270008087158 156.00677490234375 0.604286789894104 261.65216064453125 0.19907638430595398 0.7990618 0.5795961618423462 True -3 11140 31.003392219543457 13.574588537216187 198.45565795898438 0.7656536102294922 260.5232849121094 0.20227687060832977 0.80291164 0.5299720764160156 True -4 13925 31.00971555709839 10.524272680282593 211.35128784179688 0.586992621421814 259.7825927734375 0.20511110126972198 0.80321586 0.5839072465896606 True -5 16710 30.97673797607422 0.5903730392456055 207.8973388671875 0.6648997068405151 259.6050109863281 0.20637184381484985 0.80283463 0.6152350902557373 False -6 19495 30.96865677833557 0.5839402675628662 207.75869750976562 0.6390978693962097 258.8807678222656 0.21007812023162842 0.80128837 0.6254088282585144 False -7 22280 31.0583713054657 21.65673851966858 176.76400756835938 0.4937002658843994 258.50799560546875 0.21101006865501404 0.80199796 0.6172980666160583 False -8 25065 31.093687772750854 0.5914139747619629 195.5670166015625 0.5142711400985718 258.1900939941406 0.2132229059934616 0.8036174 0.5644174218177795 True -9 27850 31.04081082344055 0.5943105220794678 192.23536682128906 0.6599500179290771 257.91827392578125 0.21469919383525848 0.8038235 0.5793737769126892 True -10 30635 30.984840154647827 2.6224098205566406 214.97756958007812 0.46532806754112244 257.5134582519531 0.21614903211593628 0.8059078 0.5273721814155579 True -11 33420 31.017379999160767 16.580273628234863 210.7261505126953 0.35942697525024414 257.2566223144531 0.21726536750793457 0.81140906 0.49935269355773926 True -12 36205 31.070967197418213 0.6082730293273926 184.64735412597656 0.556053638458252 257.0268249511719 0.2184971123933792 0.81289196 0.47477078437805176 True -13 38990 31.01511263847351 0.5898962020874023 160.2750244140625 0.477618932723999 256.5772399902344 0.22013969719409943 0.81862247 0.44517311453819275 True -14 41775 31.009384870529175 0.5972156524658203 213.89413452148438 0.4739236533641815 256.58831787109375 0.22001197934150696 0.824114 0.4119500517845154 True -15 44560 31.03467845916748 0.5856106281280518 201.2302703857422 0.4075900912284851 256.20819091796875 0.22145815193653107 0.8297604 0.37290158867836 True -16 47345 31.03307557106018 0.5938475131988525 198.65219116210938 0.34005892276763916 256.250732421875 0.22103822231292725 0.83392966 0.34790584444999695 True -17 50130 31.078778505325317 0.5917675495147705 205.23585510253906 0.4907858073711395 255.99998474121094 0.22214502096176147 0.8342677 0.33752721548080444 True -18 52915 31.036259651184082 0.5943236351013184 226.35745239257812 0.3670555651187897 256.1056213378906 0.2212079018354416 0.8340067 0.33505550026893616 False -19 55700 31.575496435165405 0.5919187068939209 186.8711700439453 0.25354018807411194 256.4840087890625 0.21962013840675354 0.8335799 0.3337625563144684 False diff --git a/ENCSR953XJU/cherimoya.fold_3.performance.tsv b/ENCSR953XJU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 84ba12148434e29a816e488b006099a03beeb4a6..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -255.99998474121094 0.5269098281860352 0.22214500606060028 0.0637589618563652 0.8342676758766174 0.7784839272499084 0.33752721548080444 \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_4.evaluate.json b/ENCSR953XJU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fcc8f0816bfa7b3f0caf904bd6f526dfbe7b3983..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF588ZCP.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_4.fit.json b/ENCSR953XJU/cherimoya.fold_4.fit.json deleted file mode 100644 index 8d4afe50f460ddc9aa9ad2e3dc46e17b57ba0387..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF588ZCP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR953XJU/cherimoya.fold_4.log b/ENCSR953XJU/cherimoya.fold_4.log deleted file mode 100644 index aef1affa9c383fafa88589926c6073cf85eff796..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2855 36.543731927871704 3.972370147705078 218.341796875 0.5409531593322754 256.4318542480469 0.14194674789905548 0.73217994 2.2679576873779297 True -1 5710 31.46524977684021 0.8021175861358643 202.0274658203125 0.8551725149154663 247.9232635498047 0.1854461133480072 0.7821702 0.8248043656349182 True -2 8565 31.90355086326599 0.6380670070648193 219.1663360595703 0.5157889127731323 245.5907745361328 0.19317233562469482 0.78700054 0.5502490401268005 True -3 11420 31.84791088104248 0.6547408103942871 197.49237060546875 0.5619242787361145 244.59230041503906 0.19660329818725586 0.7964717 0.5579264163970947 True -4 14275 31.876785278320312 0.6399264335632324 168.05014038085938 0.6204087734222412 243.9358673095703 0.19999846816062927 0.797301 0.546972930431366 True -5 17130 31.89917802810669 0.6255671977996826 215.58392333984375 0.42209622263908386 243.68130493164062 0.20108197629451752 0.80038565 0.5304101705551147 True -6 19985 31.833110570907593 2.020348072052002 208.7724151611328 0.8023282289505005 243.547119140625 0.20189234614372253 0.8014928 0.5017371773719788 True -7 22840 31.870342016220093 0.6601467132568359 165.28060913085938 0.6693814992904663 243.09291076660156 0.20434601604938507 0.8025416 0.5018773674964905 True -8 25695 31.777709245681763 0.6541080474853516 191.99362182617188 0.485323965549469 242.6712646484375 0.20610617101192474 0.806373 0.45000603795051575 True -9 28550 31.798665046691895 0.6452395915985107 209.66726684570312 0.3159405589103699 242.24386596679688 0.20830003917217255 0.80874306 0.43810293078422546 True -10 31405 31.7874174118042 0.648590087890625 180.31234741210938 0.4294672906398773 241.75157165527344 0.21064485609531403 0.8109689 0.4264160096645355 True -11 34260 31.822953701019287 0.6498045921325684 174.53753662109375 0.44587454199790955 241.47035217285156 0.21185186505317688 0.8130102 0.40458714962005615 True -12 37115 31.787872076034546 0.6387152671813965 187.04769897460938 0.37854236364364624 241.22015380859375 0.21283547580242157 0.81439114 0.3847908675670624 True -13 39970 31.804314851760864 0.6377959251403809 168.82742309570312 0.5168985724449158 240.98880004882812 0.21452763676643372 0.8170554 0.36839190125465393 True -14 42825 31.78333616256714 0.6484413146972656 206.8565673828125 0.45390570163726807 240.6111297607422 0.21672074496746063 0.82094437 0.3532572090625763 True -15 45680 31.84506845474243 0.6376791000366211 208.06399536132812 0.3839699923992157 240.69137573242188 0.21603946387767792 0.82665086 0.341579794883728 True -16 48535 31.82126498222351 1.7238521575927734 167.13314819335938 0.43861067295074463 240.5731964111328 0.21672965586185455 0.8286705 0.32316580414772034 True -17 51390 31.849454402923584 0.6653530597686768 178.90440368652344 0.3352411687374115 240.8961944580078 0.21523083746433258 0.82856935 0.3119010031223297 False -18 54245 31.98315453529358 0.7000625133514404 145.96484375 0.3088671565055847 240.8228302001953 0.21552535891532898 0.8270655 0.3116343319416046 False -19 57100 31.877843856811523 9.43038296699524 216.53018188476562 0.3148585259914398 240.8907470703125 0.21533605456352234 0.82647115 0.31105837225914 False diff --git a/ENCSR953XJU/cherimoya.fold_4.performance.tsv b/ENCSR953XJU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e27f34fe53e35d7fbfcbf302e12eccea4fb43373..0000000000000000000000000000000000000000 --- a/ENCSR953XJU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -240.5731964111328 0.5332908630371094 0.21672962605953217 0.05657355114817619 0.8286705017089844 0.7640946507453918 0.32316580414772034 \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_0.evaluate.json b/ENCSR956NOL/cherimoya.fold_0.evaluate.json deleted file mode 100644 index bb528e3c73dbb811f8864add26b7824ee6e1d937..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF931XMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_0.fit.json b/ENCSR956NOL/cherimoya.fold_0.fit.json deleted file mode 100644 index ba335c2a3e5df144c35706be69fce0f931604000..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF931XMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_0.log b/ENCSR956NOL/cherimoya.fold_0.log deleted file mode 100644 index 852ffbe8957ed50cb4a0b24370b60c5c3c52c298..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.40412950515747 19.521104335784912 150.50657653808594 0.9291777610778809 192.6254119873047 0.11667759716510773 0.54037637 2.7926366329193115 True -1 5492 30.51961922645569 21.680493116378784 147.95191955566406 0.5824432373046875 188.20172119140625 0.14898087084293365 0.6534207 0.830436646938324 True -2 8238 30.41050386428833 0.6215016841888428 166.26608276367188 0.7382251620292664 186.69775390625 0.15606534481048584 0.67868054 0.5987903475761414 True -3 10984 30.267679929733276 0.6032044887542725 127.95088958740234 0.5516214370727539 185.89999389648438 0.1596752405166626 0.6860332 0.5406078100204468 True -4 13730 30.15313220024109 0.5870633125305176 157.2032928466797 0.7471481561660767 185.42811584472656 0.16160406172275543 0.6949528 0.6014665365219116 True -5 16476 30.149906158447266 1.9141302108764648 162.9810791015625 0.5866784453392029 185.1010284423828 0.1636638194322586 0.69967204 0.5386329293251038 True -6 19222 30.137901782989502 1.276324987411499 138.5682830810547 0.5272420644760132 184.9295654296875 0.1646583080291748 0.70493066 0.5361400246620178 True -7 21968 30.146815299987793 1.0324585437774658 138.7444610595703 0.34879404306411743 184.78759765625 0.16550712287425995 0.7091465 0.503292977809906 True -8 24714 30.190485954284668 0.5871648788452148 160.78717041015625 0.5788532495498657 184.55931091308594 0.1666025072336197 0.71511966 0.5037676692008972 True -9 27460 30.21225643157959 19.476582765579224 164.00701904296875 0.4429616332054138 184.20343017578125 0.16863881051540375 0.7194293 0.4420525133609772 True -10 30206 30.188796043395996 0.6021285057067871 137.35093688964844 0.5061731338500977 184.19696044921875 0.16864022612571716 0.7254527 0.4335375428199768 True -11 32952 30.223132848739624 0.5810704231262207 150.55874633789062 0.5083461999893188 183.8701629638672 0.17103073000907898 0.7309566 0.41736969351768494 True -12 35698 30.153658628463745 0.5856592655181885 145.92855834960938 0.3464451730251312 183.5575408935547 0.17314627766609192 0.73604476 0.38952991366386414 True -13 38444 30.15517544746399 0.5743153095245361 125.06684875488281 0.32363393902778625 183.5947265625 0.17238478362560272 0.73980266 0.3719009757041931 True -14 41190 30.162384271621704 0.5721778869628906 185.64573669433594 0.4581448435783386 183.38624572753906 0.17384473979473114 0.74484676 0.3582778871059418 True -15 43936 30.14025354385376 0.574498176574707 138.4186248779297 0.5893436670303345 183.3922119140625 0.17390176653862 0.75048476 0.35047659277915955 True -16 46682 30.19851517677307 0.5844621658325195 156.80145263671875 0.34357815980911255 183.3973388671875 0.17407293617725372 0.7522449 0.34984710812568665 True -17 49428 30.182231187820435 0.5980198383331299 124.9852066040039 0.2562026381492615 183.56214904785156 0.17263028025627136 0.7518999 0.35410597920417786 False -18 52174 29.947803735733032 0.5906732082366943 160.48568725585938 0.3851766586303711 183.47434997558594 0.17372150719165802 0.7510023 0.36161449551582336 False -19 54920 29.653847455978394 0.589339017868042 162.00465393066406 0.2231651097536087 183.59071350097656 0.17286425828933716 0.7497108 0.36832520365715027 False diff --git a/ENCSR956NOL/cherimoya.fold_0.performance.tsv b/ENCSR956NOL/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c03da5731e94e5debda91c4f8f169c0bc6aa3ae3..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -183.3973388671875 0.5663919448852539 0.17407292127609253 0.045420486479997635 0.7522448897361755 0.7154927253723145 0.34984710812568665 \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_1.evaluate.json b/ENCSR956NOL/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 5c81463e302ec383550927ee825516ee5c93c853..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF931XMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_1.fit.json b/ENCSR956NOL/cherimoya.fold_1.fit.json deleted file mode 100644 index d7ed06f781448fd54263b496616cea9c1f3b6fd3..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF931XMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_1.log b/ENCSR956NOL/cherimoya.fold_1.log deleted file mode 100644 index b116a683753adce45fdc21d2baecdf1057b97933..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2750 34.70042061805725 3.7723870277404785 145.70321655273438 0.7209897041320801 222.2046661376953 0.12477868050336838 0.58783334 2.6802663803100586 True -1 5500 30.240044355392456 2.5122568607330322 164.44776916503906 0.618080735206604 217.02407836914062 0.15775471925735474 0.6957471 1.055171012878418 True -2 8250 30.271005868911743 0.7582125663757324 154.7317352294922 0.4691791534423828 214.95718383789062 0.1669616401195526 0.72168726 0.5598037838935852 True -3 11000 30.288750171661377 0.8107616901397705 181.51644897460938 0.5704566240310669 213.8788299560547 0.171830415725708 0.7357529 0.46439221501350403 True -4 13750 30.283294200897217 0.6750645637512207 149.83053588867188 0.67196124792099 213.00393676757812 0.1758786141872406 0.74015796 0.467273086309433 True -5 16500 31.191917657852173 0.6850881576538086 164.49264526367188 0.6840267181396484 212.7640380859375 0.17718786001205444 0.7468557 0.4714122414588928 True -6 19250 30.207417011260986 0.6850101947784424 152.78347778320312 0.3473038673400879 212.3573760986328 0.17959463596343994 0.75155383 0.4612204432487488 True -7 22000 30.19183611869812 0.6782824993133545 140.2989501953125 0.654522180557251 212.16635131835938 0.1804247945547104 0.75521755 0.45118704438209534 True -8 24750 30.23776149749756 0.6790928840637207 142.1196746826172 0.5633363127708435 211.51690673828125 0.1841430515050888 0.7604625 0.4471738040447235 True -9 27500 30.257168531417847 0.6970987319946289 121.69929504394531 0.3829832971096039 211.34738159179688 0.18462486565113068 0.7667193 0.42327484488487244 True -10 30250 30.218627214431763 0.6501684188842773 131.29330444335938 0.5663501620292664 211.09693908691406 0.1859326958656311 0.77218705 0.40080636739730835 True -11 33000 30.26826763153076 0.6622037887573242 112.26513671875 0.46015605330467224 210.84552001953125 0.18695947527885437 0.7752566 0.3926931619644165 True -12 35750 30.29192328453064 0.6972815990447998 122.17262268066406 0.45552143454551697 210.58892822265625 0.18823251128196716 0.7821801 0.374329149723053 True -13 38500 30.367379188537598 0.6911170482635498 150.99559020996094 0.3951886296272278 210.5116424560547 0.1882108896970749 0.7869116 0.3653561472892761 True -14 41250 30.231042861938477 0.6758871078491211 126.78019714355469 0.3996671140193939 210.26451110839844 0.1897767335176468 0.7938704 0.3543836772441864 True -15 44000 30.19532299041748 0.6701719760894775 146.94937133789062 0.3982114791870117 210.24705505371094 0.19043079018592834 0.7956783 0.344482421875 True -16 46750 29.75654363632202 1.4298834800720215 159.36569213867188 0.5918886661529541 210.24522399902344 0.19001615047454834 0.7973567 0.34294185042381287 True -17 49500 29.745889902114868 0.7394514083862305 136.45851135253906 0.2414352297782898 210.32984924316406 0.19001442193984985 0.79846334 0.34467315673828125 True -18 52250 29.723504543304443 0.7158498764038086 124.94277954101562 0.36201274394989014 210.5657958984375 0.1883823424577713 0.7980285 0.35426056385040283 False -19 55000 29.672428131103516 1.7317211627960205 121.96199035644531 0.3228318691253662 210.47152709960938 0.1892908662557602 0.79648775 0.35661035776138306 False diff --git a/ENCSR956NOL/cherimoya.fold_1.performance.tsv b/ENCSR956NOL/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 23f6060dde14d239fb5b4833003c820f9f5c2751..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -210.32984924316406 0.5515378713607788 0.19001443684101105 0.05148935317993164 0.7984633445739746 0.7773107290267944 0.34467315673828125 \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_2.evaluate.json b/ENCSR956NOL/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 0ef8e4946e05ef92084fdb61d757374db1f9c010..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF931XMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_2.fit.json b/ENCSR956NOL/cherimoya.fold_2.fit.json deleted file mode 100644 index c44339081f81fab34cebb5442a41102146829f75..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF931XMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_2.log b/ENCSR956NOL/cherimoya.fold_2.log deleted file mode 100644 index a496217566f5773947a1e1cf14f1de944aba813c..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2918 36.695868492126465 3.9453752040863037 143.8512725830078 0.552135705947876 195.69517517089844 0.12157268077135086 0.5618728 2.5472824573516846 True -1 5836 32.08160448074341 0.5454094409942627 172.614990234375 0.6375555992126465 190.75392150878906 0.15405826270580292 0.6682616 0.8820675015449524 True -2 8754 32.04679226875305 0.5212616920471191 140.21592712402344 0.5134917497634888 189.41421508789062 0.16024506092071533 0.68533945 0.5620577335357666 True -3 11672 32.099743366241455 0.5408637523651123 171.44003295898438 0.5322993993759155 188.70924377441406 0.16309544444084167 0.69468105 0.5496272444725037 True -4 14590 32.30742692947388 0.5269026756286621 139.75131225585938 0.5388664603233337 188.53280639648438 0.16405609250068665 0.7002623 0.6303610801696777 True -5 17508 32.21450209617615 0.5230212211608887 158.35366821289062 0.6803693771362305 188.13558959960938 0.1660650372505188 0.7049803 0.67416912317276 True -6 20426 32.164316177368164 1.7525477409362793 123.87672424316406 0.5690233707427979 188.00083923339844 0.16672776639461517 0.7096026 0.6458472013473511 True -7 23344 32.26660180091858 0.5224533081054688 157.21298217773438 0.49023735523223877 187.7225799560547 0.1687803715467453 0.71468824 0.6450799107551575 True -8 26262 32.188180685043335 0.5201253890991211 149.50949096679688 0.4634997248649597 187.34585571289062 0.17075157165527344 0.71972895 0.6036142110824585 True -9 29180 32.221827030181885 0.5255441665649414 153.18394470214844 0.45201238989830017 187.2305145263672 0.17137739062309265 0.72354233 0.5689306259155273 True -10 32098 32.190348625183105 0.5272712707519531 144.62496948242188 0.6705417633056641 187.05026245117188 0.17214417457580566 0.7271586 0.5168637633323669 True -11 35016 32.18194842338562 0.5208735466003418 137.99131774902344 0.6813036203384399 186.9038848876953 0.17254893481731415 0.73469436 0.4640844464302063 True -12 37934 32.260865211486816 0.5190920829772949 147.6048583984375 0.46510905027389526 186.42977905273438 0.1757674217224121 0.7387103 0.4456935226917267 True -13 40852 32.16786575317383 0.5582945346832275 128.92782592773438 0.3822406232357025 186.343017578125 0.17607194185256958 0.74292034 0.4179520606994629 True -14 43770 32.098007678985596 1.108293056488037 143.20065307617188 0.41186368465423584 186.30784606933594 0.17594636976718903 0.75057435 0.3968338370323181 True -15 46688 31.613896131515503 13.439163208007812 154.25311279296875 0.2514643967151642 186.17446899414062 0.1768089085817337 0.755421 0.379099041223526 True -16 49606 32.38762331008911 0.5281970500946045 132.5177764892578 0.3995744585990906 186.14202880859375 0.17660640180110931 0.75436944 0.3749382197856903 False -17 52524 31.713600397109985 0.5392568111419678 154.95330810546875 0.2346680611371994 186.1119842529297 0.17708013951778412 0.75579184 0.3742104768753052 True -18 55442 31.637149810791016 0.5226778984069824 131.28746032714844 0.259873628616333 186.20223999023438 0.17653609812259674 0.75412923 0.3813033699989319 False -19 58360 31.6172993183136 0.5152008533477783 158.82579040527344 0.32385313510894775 186.35415649414062 0.1752619445323944 0.75382376 0.3857097923755646 False diff --git a/ENCSR956NOL/cherimoya.fold_2.performance.tsv b/ENCSR956NOL/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 79e34bec73ed83ebd66daaee679b604116740e2a..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -186.1119842529297 0.564250111579895 0.17708013951778412 0.046562619507312775 0.7557918429374695 0.7203467488288879 0.3742104768753052 \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_3.evaluate.json b/ENCSR956NOL/cherimoya.fold_3.evaluate.json deleted file mode 100644 index ecfde689ab8fdcd48a566d90c20cc161ec1831e5..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF931XMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_3.fit.json b/ENCSR956NOL/cherimoya.fold_3.fit.json deleted file mode 100644 index a9ff555df991ab110efe6d745868ea701459f85d..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF931XMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_3.log b/ENCSR956NOL/cherimoya.fold_3.log deleted file mode 100644 index bfd980aa5542803c7bfe9b5c7d3da2f7b72277bb..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2773 35.437071800231934 5.1410651206970215 139.2295379638672 0.7050461769104004 206.3513946533203 0.12212368100881577 0.5690331 2.786017894744873 True -1 5546 30.527753353118896 0.6308472156524658 149.27870178222656 0.7260833382606506 201.91908264160156 0.15271446108818054 0.6725253 0.9148957133293152 True -2 8319 30.523463249206543 0.6295292377471924 167.0377655029297 0.7147275805473328 200.10203552246094 0.16157591342926025 0.6937015 0.5371010899543762 True -3 11092 30.555826663970947 0.6017355918884277 159.92803955078125 0.6745574474334717 199.61814880371094 0.16278034448623657 0.7045603 0.4727937579154968 True -4 13865 30.783905267715454 13.456975221633911 171.7581024169922 0.5899919271469116 199.261962890625 0.1643725335597992 0.70848113 0.4967803359031677 True -5 16638 30.535123586654663 0.8811221122741699 149.4272003173828 0.632152259349823 198.8883819580078 0.16696828603744507 0.71213955 0.5259947776794434 True -6 19411 30.548312187194824 0.5925285816192627 160.00311279296875 0.401288241147995 198.66485595703125 0.1677151322364807 0.7169621 0.5821117162704468 True -7 22184 30.472490549087524 0.6017765998840332 155.99069213867188 0.5571843385696411 198.47613525390625 0.1691027581691742 0.7212822 0.5385664701461792 True -8 24957 30.514143705368042 0.599562406539917 154.74171447753906 0.4420889616012573 198.2493438720703 0.1700941026210785 0.7235416 0.5087637305259705 True -9 27730 30.503576040267944 1.1561131477355957 155.66506958007812 0.35349977016448975 197.78372192382812 0.17298097908496857 0.73207146 0.4936598241329193 True -10 30503 30.57133936882019 0.6138887405395508 154.37814331054688 0.34320002794265747 197.7454833984375 0.17326118052005768 0.73543453 0.46069902181625366 True -11 33276 30.10339069366455 0.6017627716064453 155.57626342773438 0.38311102986335754 197.72207641601562 0.17360633611679077 0.7382943 0.45376208424568176 True -12 36049 29.859184503555298 0.5940067768096924 181.7093505859375 0.2431698739528656 197.6047821044922 0.17413575947284698 0.74156916 0.4195784330368042 True -13 38822 29.852776288986206 0.5921366214752197 144.69265747070312 0.53156578540802 197.3671875 0.17561952769756317 0.74910927 0.40295037627220154 True -14 41595 29.873040676116943 0.5949990749359131 174.67160034179688 0.3557261526584625 197.12167358398438 0.17725232243537903 0.75355524 0.39009907841682434 True -15 44368 29.89103627204895 0.6068174839019775 138.13134765625 0.4123644232749939 197.0841827392578 0.1771966964006424 0.75835055 0.3834017515182495 True -16 47141 29.88216543197632 0.578291654586792 164.4766845703125 0.25703704357147217 197.0989227294922 0.17701074481010437 0.7593181 0.3828679621219635 True -17 49914 29.8794846534729 0.5961027145385742 143.37425231933594 0.4579434096813202 197.19949340820312 0.17627063393592834 0.7603315 0.3866848647594452 True -18 52687 29.91074800491333 0.6113624572753906 140.6453857421875 0.24581491947174072 197.38063049316406 0.1751440316438675 0.7575718 0.3944540023803711 False -19 55460 29.906329870224 0.6045541763305664 155.369140625 0.35738974809646606 197.40969848632812 0.17494018375873566 0.75538254 0.40302136540412903 False diff --git a/ENCSR956NOL/cherimoya.fold_3.performance.tsv b/ENCSR956NOL/cherimoya.fold_3.performance.tsv deleted file mode 100644 index e383c3bcf1856a16c3cdc6472a7ba8fe442033aa..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -197.19949340820312 0.5607900023460388 0.17627063393592834 0.045260366052389145 0.7603315114974976 0.7214216589927673 0.3866848647594452 \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_4.evaluate.json b/ENCSR956NOL/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bd618128a89757175b07a15067ac3149500fe0a9..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF931XMM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_4.fit.json b/ENCSR956NOL/cherimoya.fold_4.fit.json deleted file mode 100644 index 629756fdc42e373171e28cf953c90c3194da2068..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF931XMM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR956NOL/cherimoya.fold_4.log b/ENCSR956NOL/cherimoya.fold_4.log deleted file mode 100644 index 433042004e633a40a837ab40bd5b22985f461f40..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 36.25940752029419 4.441253185272217 159.0555419921875 0.5322860479354858 198.86257934570312 0.11825419962406158 0.5359193 2.7987825870513916 True -1 5748 31.65375852584839 0.6171314716339111 113.02178955078125 0.432203471660614 194.35023498535156 0.1495823860168457 0.64168864 1.0382503271102905 True -2 8622 32.09868597984314 24.454176664352417 143.24456787109375 0.4991922378540039 192.79238891601562 0.15845027565956116 0.6634691 0.47583213448524475 True -3 11496 31.722219228744507 0.6169548034667969 132.68948364257812 0.6495418548583984 192.1029510498047 0.1614728569984436 0.673793 0.42581960558891296 True -4 14370 31.60161304473877 0.6579470634460449 122.31683349609375 0.6762655377388 191.58929443359375 0.16449551284313202 0.68072134 0.44044962525367737 True -5 17244 31.62465476989746 0.5852162837982178 164.48492431640625 0.7387843132019043 191.12603759765625 0.1674870103597641 0.6855677 0.4448823630809784 True -6 20118 32.61553692817688 20.578363180160522 134.62158203125 0.592176079750061 191.07379150390625 0.16773231327533722 0.68985415 0.47189053893089294 True -7 22992 31.582740783691406 1.708723545074463 107.71461486816406 0.44215869903564453 190.80712890625 0.1689658910036087 0.6961589 0.4656408131122589 True -8 25866 31.629172325134277 1.2818713188171387 139.22988891601562 0.5528039932250977 190.60919189453125 0.1698852777481079 0.70290476 0.4556185007095337 True -9 28740 31.62303352355957 1.551560401916504 148.075927734375 0.5622254610061646 190.57766723632812 0.16969412565231323 0.7089129 0.4300350248813629 True -10 31614 31.602458953857422 1.937382459640503 144.21316528320312 0.5071626901626587 190.29249572753906 0.17131057381629944 0.71355677 0.42879098653793335 True -11 34488 31.59646511077881 1.3408160209655762 160.9945526123047 0.38492870330810547 190.0916748046875 0.17253555357456207 0.7234819 0.4111422896385193 True -12 37362 31.42866587638855 0.8856165409088135 155.76206970214844 0.46179360151290894 189.7925567626953 0.17486093938350677 0.72637177 0.3947773575782776 True -13 40236 30.991124629974365 0.5830063819885254 149.46124267578125 0.22831347584724426 189.72689819335938 0.1752018928527832 0.73396313 0.3855849802494049 True -14 43110 30.99764084815979 0.6230056285858154 116.25006866455078 0.3679046034812927 189.4775848388672 0.17690278589725494 0.740121 0.3717709183692932 True -15 45984 31.196211099624634 0.6036019325256348 148.52993774414062 0.4650801718235016 189.5693359375 0.17614024877548218 0.74542683 0.3719249367713928 True -16 48858 31.129584312438965 0.6022143363952637 125.33879089355469 0.30599331855773926 189.6897735595703 0.1752062737941742 0.7499095 0.37070339918136597 True -17 51732 31.143814086914062 0.5995867252349854 168.07827758789062 0.31978878378868103 189.76876831054688 0.17480386793613434 0.74870217 0.3788890838623047 False -18 54606 31.05135416984558 0.5951967239379883 146.35028076171875 0.25329697132110596 189.83203125 0.1743471771478653 0.7465319 0.3877049386501312 False -19 57480 31.08210325241089 0.5898468494415283 119.23701477050781 0.26504629850387573 189.94313049316406 0.1736903190612793 0.7472046 0.39102640748023987 False diff --git a/ENCSR956NOL/cherimoya.fold_4.performance.tsv b/ENCSR956NOL/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 6a91c218a9d2f59a436eacd419d851ddcb60c579..0000000000000000000000000000000000000000 --- a/ENCSR956NOL/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -189.6897735595703 0.5635968446731567 0.1752062737941742 0.044517453759908676 0.749909520149231 0.7123278975486755 0.37070339918136597 \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_0.evaluate.json b/ENCSR959ZXU/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d158d692b363f07b842a440be8d720102113efcf..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF481TVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_0.fit.json b/ENCSR959ZXU/cherimoya.fold_0.fit.json deleted file mode 100644 index f6c6517d3925fb59a83d5875fd538f074c417bd3..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF481TVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_0.log b/ENCSR959ZXU/cherimoya.fold_0.log deleted file mode 100644 index 49bb4dbef09c97a9aed2d328d31b9476010493f1..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 34.57564973831177 3.6364023685455322 1038.19091796875 1.8172240257263184 1697.4385986328125 0.28102850914001465 0.35043657 11.811138153076172 True -1 5418 30.146944522857666 1.0708179473876953 1024.558837890625 1.687748908996582 1352.970947265625 0.4701476991176605 0.41101325 7.856423854827881 True -2 8127 30.12969470024109 0.5686683654785156 1114.8004150390625 1.4181907176971436 1323.16259765625 0.48383715748786926 0.42987475 4.955636501312256 True -3 10836 30.084473371505737 0.5470077991485596 857.8212890625 1.2611613273620605 1290.869140625 0.4976980984210968 0.4489117 3.8605735301971436 True -4 13545 30.08578062057495 0.5637423992156982 943.42333984375 1.458711862564087 1270.5994873046875 0.506525456905365 0.46758404 3.99359393119812 True -5 16254 30.12793779373169 0.5686707496643066 886.6351318359375 0.9763005971908569 1255.3466796875 0.5147290825843811 0.4787548 3.2769315242767334 True -6 18963 30.079957008361816 0.5714473724365234 931.4708862304688 0.9938414096832275 1244.7353515625 0.5201143622398376 0.49536777 2.954988956451416 True -7 21672 30.068936586380005 0.5659172534942627 1098.03564453125 1.0678327083587646 1236.0447998046875 0.5253251791000366 0.49630734 2.6904501914978027 True -8 24381 30.15436029434204 0.5667567253112793 892.0415649414062 1.1909239292144775 1230.609375 0.5257314443588257 0.5038405 2.6208863258361816 True -9 27090 30.07099485397339 0.5507798194885254 1013.9913330078125 1.256988525390625 1223.536376953125 0.5302123427391052 0.4999448 2.5717127323150635 False -10 29799 29.58105158805847 0.5626766681671143 1061.842041015625 1.0820066928863525 1207.412841796875 0.5414987206459045 0.49298257 2.2957077026367188 False -11 32508 29.55660057067871 0.9973721504211426 894.0904541015625 1.3367424011230469 1201.7353515625 0.5427998900413513 0.50485647 2.078552484512329 True -12 35217 29.672207832336426 1.6768064498901367 891.0726318359375 1.0274791717529297 1188.556640625 0.5470972657203674 0.5359752 1.724034070968628 True -13 37926 29.508291959762573 11.432650804519653 788.1441040039062 0.6911258697509766 1174.674560546875 0.5538095235824585 0.562407 1.4647915363311768 True -14 40635 29.568496704101562 0.566960334777832 845.5553588867188 0.8905551433563232 1168.1622314453125 0.5553358793258667 0.5857664 1.2594658136367798 True -15 43344 29.510960340499878 0.5469651222229004 932.512939453125 1.1028532981872559 1164.16552734375 0.5555230379104614 0.6078818 1.11342453956604 True -16 46053 29.538017988204956 0.5687131881713867 697.8578491210938 0.6947736144065857 1155.230224609375 0.5617179870605469 0.6232606 0.984443187713623 True -17 48762 29.566508769989014 0.5808789730072021 994.4840698242188 0.6485946178436279 1154.2642822265625 0.5604740381240845 0.63422364 0.9080521464347839 True -18 51471 29.533712148666382 1.3667755126953125 821.3576049804688 0.7369948625564575 1153.858642578125 0.5607733130455017 0.63631266 0.8725455403327942 True -19 54180 29.63656187057495 0.5749001502990723 785.7562866210938 0.5435816049575806 1155.764404296875 0.558903694152832 0.6382139 0.8673100471496582 True diff --git a/ENCSR959ZXU/cherimoya.fold_0.performance.tsv b/ENCSR959ZXU/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cbd9aec3d73e12c3a4463bac4985ea77a7638249..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1155.764404296875 0.262417197227478 0.558903694152832 0.297159343957901 0.6382138729095459 0.6058218479156494 0.8673100471496582 \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_1.evaluate.json b/ENCSR959ZXU/cherimoya.fold_1.evaluate.json deleted file mode 100644 index cdface570be7092c2c8ebc37b0246ccabc3299de..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF481TVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_1.fit.json b/ENCSR959ZXU/cherimoya.fold_1.fit.json deleted file mode 100644 index 1da59ce80d080b8126e8752c4c96a987b48cd305..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF481TVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_1.log b/ENCSR959ZXU/cherimoya.fold_1.log deleted file mode 100644 index be89a9767ed012d4772641f427c3572069f5bc4e..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 35.40078020095825 3.7478439807891846 995.8055419921875 1.0963847637176514 1784.18505859375 0.29371654987335205 0.39440027 12.564027786254883 True -1 5468 30.3521990776062 0.7225821018218994 730.54541015625 1.344364881515503 1443.3616943359375 0.4764513671398163 0.47629625 8.566914558410645 True -2 8202 30.653366088867188 1.8030061721801758 1072.9815673828125 1.1820414066314697 1425.8739013671875 0.4802577495574951 0.47041035 7.044938564300537 False -3 10936 29.818313598632812 1.9207310676574707 915.9306640625 1.0608437061309814 1384.718017578125 0.4942537844181061 0.5079807 4.973182678222656 True -4 13670 29.783019065856934 1.873983383178711 838.7010498046875 0.9537255167961121 1351.4439697265625 0.5109613537788391 0.51998204 4.2504801750183105 True -5 16404 29.791592836380005 1.908144235610962 811.9620361328125 1.194702386856079 1344.5916748046875 0.5171043872833252 0.52995217 3.7870187759399414 True -6 19138 29.778769731521606 1.582496166229248 961.7725219726562 1.1496442556381226 1346.572265625 0.5189001560211182 0.5276398 3.1996877193450928 False -7 21872 29.815744638442993 2.358266830444336 972.0850830078125 1.0281901359558105 1331.4075927734375 0.526330292224884 0.5359596 3.091975212097168 True -8 24606 29.818315744400024 1.6313071250915527 770.5716552734375 1.0259697437286377 1317.9454345703125 0.5308830738067627 0.5395187 2.8320839405059814 True -9 27340 29.81034564971924 2.2196550369262695 825.510498046875 1.071512222290039 1305.94677734375 0.5361698865890503 0.55175674 2.4963901042938232 True -10 30074 29.822306871414185 1.6312880516052246 829.86474609375 1.2046242952346802 1297.2974853515625 0.5392208099365234 0.56229395 2.253222942352295 True -11 32808 29.823039293289185 1.6681087017059326 991.4736328125 0.959778904914856 1284.1705322265625 0.5442159175872803 0.56769764 2.1558103561401367 True -12 35542 29.819509267807007 0.7139456272125244 935.055419921875 0.9324837923049927 1273.947265625 0.5474449396133423 0.5894082 1.8723161220550537 True -13 38276 29.860758304595947 0.7040920257568359 853.1567993164062 0.6693496704101562 1261.1385498046875 0.5512223243713379 0.6178939 1.4749966859817505 True -14 41010 29.82517981529236 0.7506334781646729 850.595458984375 0.8375773429870605 1251.045654296875 0.5553037524223328 0.63775784 1.2644060850143433 True -15 43744 29.90273904800415 0.6999893188476562 831.2420654296875 0.5905413031578064 1245.3282470703125 0.5571944713592529 0.6543837 1.0902764797210693 True -16 46478 29.954399585723877 0.7188777923583984 993.92626953125 0.9986867904663086 1238.3802490234375 0.5594469904899597 0.6651578 0.9580370783805847 True -17 49212 29.97484278678894 0.7612721920013428 889.5504760742188 1.0336391925811768 1240.02685546875 0.5567722916603088 0.6731819 0.8768102526664734 True -18 51946 29.916224241256714 0.7321410179138184 1052.086669921875 0.663097620010376 1236.55078125 0.5582373142242432 0.6727691 0.8455705642700195 False -19 54680 29.888134717941284 0.7222769260406494 896.0074462890625 0.5530050992965698 1233.8592529296875 0.5602748394012451 0.6727591 0.8401409387588501 False diff --git a/ENCSR959ZXU/cherimoya.fold_1.performance.tsv b/ENCSR959ZXU/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 324aa3e23dcfc5ea961a117deab305998dc68330..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1240.02685546875 0.2570877969264984 0.5567722916603088 0.30521056056022644 0.6731818914413452 0.6447318196296692 0.8768102526664734 \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_2.evaluate.json b/ENCSR959ZXU/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 78ec6bb30cffa50d2db1581bc42153bbb8537fd7..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF481TVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_2.fit.json b/ENCSR959ZXU/cherimoya.fold_2.fit.json deleted file mode 100644 index d6278678d6f59f5b0a59b8aeefd1e2d1098ebe08..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF481TVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_2.log b/ENCSR959ZXU/cherimoya.fold_2.log deleted file mode 100644 index b20afeb9dab95bd628608c2fbec70764b9a562cf..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2879 37.730334758758545 2.018172025680542 966.196533203125 1.337860345840454 1617.8697509765625 0.30028843879699707 0.32564297 11.58853816986084 True -1 5758 31.96023154258728 0.642266035079956 1034.8646240234375 1.9282472133636475 1321.1064453125 0.46704304218292236 0.4181425 7.00563383102417 True -2 8637 31.990398406982422 0.534001350402832 920.3057250976562 1.28916597366333 1295.8563232421875 0.4743148684501648 0.4288908 4.13153600692749 True -3 11516 31.921860933303833 1.065913438796997 1200.818603515625 1.2050024271011353 1251.111572265625 0.49483954906463623 0.4597062 2.877230405807495 True -4 14395 31.89723038673401 0.5243220329284668 883.1530151367188 1.3651652336120605 1233.4544677734375 0.5055484175682068 0.4723802 2.4677112102508545 True -5 17274 31.850265979766846 0.47260189056396484 974.2567138671875 1.0221747159957886 1217.5849609375 0.5160796642303467 0.48675123 2.288938283920288 True -6 20153 31.3534677028656 0.47296714782714844 802.50634765625 1.2732309103012085 1210.1527099609375 0.5202760696411133 0.49074426 2.4140663146972656 True -7 23032 31.320281744003296 0.44107651710510254 822.067138671875 1.1731313467025757 1204.3402099609375 0.5233740210533142 0.4979308 2.451507329940796 True -8 25911 31.319068431854248 0.4600403308868408 1091.2554931640625 1.17860746383667 1207.259765625 0.5225396752357483 0.49213743 2.2459189891815186 False -9 28790 31.33991265296936 0.4666006565093994 1157.52734375 1.1080176830291748 1195.0972900390625 0.5296707153320312 0.49845028 2.0493295192718506 True -10 31669 31.38202977180481 0.4774048328399658 1095.0068359375 1.225446105003357 1183.839111328125 0.5374687314033508 0.51058334 1.9384567737579346 True -11 34548 31.340158224105835 0.46401357650756836 878.8023681640625 0.8250356912612915 1172.51904296875 0.5409424304962158 0.5245269 1.687227725982666 True -12 37427 31.366955757141113 0.45903944969177246 968.8391723632812 1.0405361652374268 1160.7353515625 0.5455936789512634 0.5475519 1.4697762727737427 True -13 40306 31.313856840133667 0.4748268127441406 688.2764892578125 0.7517298460006714 1150.8438720703125 0.5495282411575317 0.57025236 1.2849762439727783 True -14 43185 31.331721782684326 0.47670698165893555 725.7677612304688 0.6445642113685608 1144.9508056640625 0.5490390062332153 0.6011105 1.1030962467193604 True -15 46064 31.398311138153076 1.319864273071289 834.0900268554688 0.9018205404281616 1134.0877685546875 0.5546483993530273 0.6226374 0.9615696668624878 True -16 48943 31.49122190475464 0.5134375095367432 813.9347534179688 0.6254535913467407 1129.451904296875 0.5558626651763916 0.63642126 0.8647034764289856 True -17 51822 31.387611627578735 0.48340702056884766 951.1300659179688 0.7831029891967773 1130.3270263671875 0.5550562143325806 0.6470188 0.8113795518875122 True -18 54701 31.35236382484436 0.4815230369567871 921.6443481445312 0.5778253078460693 1129.3348388671875 0.554751455783844 0.6507195 0.7928946018218994 True -19 57580 31.417956113815308 0.49039125442504883 801.2301025390625 0.6571495532989502 1126.8455810546875 0.5561944246292114 0.6510705 0.7947890162467957 True diff --git a/ENCSR959ZXU/cherimoya.fold_2.performance.tsv b/ENCSR959ZXU/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 14116c5da1b1a2ae28d0d1a8ed9ab281db4c964f..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1126.8455810546875 0.26391735672950745 0.5561944246292114 0.2926294207572937 0.6510704755783081 0.6234807968139648 0.7947890162467957 \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_3.evaluate.json b/ENCSR959ZXU/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 717389df62888f5991878bf3cd6f7880a0e071bf..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF481TVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_3.fit.json b/ENCSR959ZXU/cherimoya.fold_3.fit.json deleted file mode 100644 index 5c4b5aa20a8b71afaf9ea4f9fdda250ff4272d8b..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF481TVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_3.log b/ENCSR959ZXU/cherimoya.fold_3.log deleted file mode 100644 index 9fb80b14d5e6da48a831bcc8bd02f4298b1dc270..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2786 35.97121524810791 4.4207072257995605 983.87451171875 1.0489091873168945 1712.4752197265625 0.2970111668109894 0.3579803 11.633879661560059 True -1 5572 30.93839979171753 0.6139931678771973 1205.369873046875 1.2023311853408813 1389.4434814453125 0.47186383605003357 0.37379003 7.300840377807617 True -2 8358 30.920530796051025 0.7865025997161865 1007.004150390625 1.6741058826446533 1353.7923583984375 0.49137741327285767 0.402671 4.018453598022461 True -3 11144 30.89995574951172 1.186293601989746 920.9424438476562 1.319939374923706 1323.9110107421875 0.5026286840438843 0.43323967 3.6592674255371094 True -4 13930 30.918863773345947 0.5448026657104492 898.3637084960938 1.2719486951828003 1307.3514404296875 0.5145761370658875 0.44259873 3.767591714859009 True -5 16716 30.92667555809021 0.5476524829864502 850.78515625 1.1003186702728271 1299.8436279296875 0.5194795727729797 0.4406184 3.395359754562378 False -6 19502 30.879791498184204 0.5522294044494629 884.64453125 0.971183180809021 1284.167236328125 0.5261465907096863 0.46503702 3.1416544914245605 True -7 22288 30.927936792373657 0.67386794090271 912.3598022460938 1.2704517841339111 1276.7652587890625 0.5307531952857971 0.46010303 2.907907009124756 False -8 25074 30.910337924957275 0.8611526489257812 794.201416015625 1.234468698501587 1271.5355224609375 0.5338044762611389 0.45412174 2.912891149520874 False -9 27860 30.977973699569702 1.0085999965667725 899.8746948242188 0.812592089176178 1257.58740234375 0.5406895875930786 0.46641633 2.6094093322753906 True -10 30646 30.967010974884033 1.2437002658843994 841.3182373046875 0.8243257999420166 1254.5323486328125 0.5427804589271545 0.4607787 2.5507240295410156 False -11 33432 30.99042820930481 0.8191158771514893 961.7225341796875 1.064026117324829 1242.334716796875 0.5475065112113953 0.48262852 2.17817759513855 True -12 36218 30.951632738113403 1.14766263961792 855.5601806640625 0.6902503371238708 1228.59033203125 0.5540781021118164 0.51647395 1.9154002666473389 True -13 39004 30.939793825149536 2.009549140930176 935.5784912109375 0.9301227331161499 1217.7332763671875 0.5553113222122192 0.5531123 1.6396008729934692 True -14 41790 30.99053120613098 1.919412612915039 870.97216796875 1.0134880542755127 1210.0816650390625 0.5568618774414062 0.57852745 1.384946346282959 True -15 44576 31.078320503234863 1.7437033653259277 1015.1851806640625 0.668857991695404 1200.665283203125 0.559895396232605 0.6052294 1.1533249616622925 True -16 47362 31.145402193069458 2.0608413219451904 781.415771484375 0.7596113681793213 1193.5501708984375 0.5635986924171448 0.6263254 0.9976897835731506 True -17 50148 31.062970876693726 1.1468136310577393 806.0426025390625 0.6836682558059692 1188.4117431640625 0.5658579468727112 0.63566333 0.9164079427719116 True -18 52934 31.082737922668457 1.9595770835876465 947.74072265625 0.6582613587379456 1188.433349609375 0.5653595924377441 0.64027745 0.8859237432479858 True -19 55720 31.076897621154785 2.1879684925079346 792.46435546875 0.5889034271240234 1185.937744140625 0.5672664642333984 0.6403557 0.8784316182136536 True diff --git a/ENCSR959ZXU/cherimoya.fold_3.performance.tsv b/ENCSR959ZXU/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5ae2c199596dc301d40b87a129c8f0eb296478cb..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1185.937744140625 0.2574939429759979 0.5672664642333984 0.3050873279571533 0.6403557062149048 0.620997428894043 0.8784316182136536 \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_4.evaluate.json b/ENCSR959ZXU/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 0611a226383faf018382f373fb77f28de0ccd179..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF481TVB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_4.fit.json b/ENCSR959ZXU/cherimoya.fold_4.fit.json deleted file mode 100644 index e159b3b6ffe4ae3a90fa1f8821d50c6e19ca9366..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF481TVB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR959ZXU/cherimoya.fold_4.log b/ENCSR959ZXU/cherimoya.fold_4.log deleted file mode 100644 index 3c5aaa2cb12fe679541aecc414c944827b26304a..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2847 36.262163400650024 4.323606729507446 1087.07763671875 1.4079594612121582 1652.851318359375 0.28764355182647705 0.3443634 11.301681518554688 True -1 5694 31.642032623291016 0.6414196491241455 980.3504638671875 1.2319256067276 1330.8599853515625 0.47146350145339966 0.4039006 6.981478691101074 True -2 8541 31.686968564987183 0.5429201126098633 932.4235229492188 1.445083498954773 1303.2877197265625 0.48387405276298523 0.4247755 4.555960655212402 True -3 11388 31.59284281730652 0.527209997177124 1006.8924560546875 1.5647823810577393 1272.76123046875 0.49715951085090637 0.44638848 3.5365819931030273 True -4 14235 31.559322595596313 0.5293173789978027 921.18212890625 0.9915063381195068 1251.4146728515625 0.506136953830719 0.47467506 2.988206148147583 True -5 17082 31.547438144683838 0.5182678699493408 901.9794921875 1.2378984689712524 1236.1234130859375 0.5155919790267944 0.48501492 3.139666795730591 True -6 19929 31.576916217803955 0.5345630645751953 932.2138671875 1.2769114971160889 1225.6358642578125 0.522024929523468 0.49095038 2.6432039737701416 True -7 22776 31.621087312698364 0.5279726982116699 1022.9139404296875 0.9405776858329773 1214.5657958984375 0.5280392169952393 0.49488223 2.377190589904785 True -8 25623 31.573165893554688 0.5434885025024414 880.4413452148438 0.9193626046180725 1202.6304931640625 0.5347254872322083 0.49450195 2.1765341758728027 False -9 28470 31.591915607452393 0.5303213596343994 975.323974609375 1.1393885612487793 1195.8955078125 0.5361604690551758 0.49294105 1.9330260753631592 False -10 31317 31.657333850860596 0.5367922782897949 839.6129150390625 1.2232697010040283 1185.457763671875 0.541267991065979 0.50898457 1.7121548652648926 True -11 34164 31.644521951675415 0.5305469036102295 971.295166015625 1.1094125509262085 1175.4931640625 0.5466716885566711 0.5233615 1.557303547859192 True -12 37011 31.569990873336792 0.536186695098877 591.9888916015625 0.8104988932609558 1168.976318359375 0.5482991337776184 0.5462365 1.364787220954895 True -13 39858 31.596301794052124 0.5398843288421631 828.09765625 0.8569619655609131 1155.103759765625 0.5558233261108398 0.5700966 1.1738317012786865 True -14 42705 31.598833799362183 0.5223827362060547 1073.29736328125 0.9858046770095825 1150.2852783203125 0.5571072697639465 0.5899136 1.0881563425064087 True -15 45552 31.58662462234497 0.5357580184936523 793.0640869140625 1.0352120399475098 1146.7034912109375 0.5567379593849182 0.6094478 0.9720261096954346 True -16 48399 31.59572720527649 0.5240094661712646 825.22314453125 0.8645212054252625 1143.8983154296875 0.5555817484855652 0.6249984 0.9092692732810974 True -17 51246 31.604546308517456 0.5335302352905273 858.6793823242188 0.8484310507774353 1141.174072265625 0.5584301948547363 0.63408214 0.8683553338050842 True -18 54093 31.322885751724243 0.5303382873535156 741.4036254882812 0.5072777271270752 1142.3861083984375 0.5567141771316528 0.63626796 0.8579633831977844 True -19 56940 31.063048601150513 0.5300188064575195 859.0333251953125 0.6351125240325928 1141.18896484375 0.5579825639724731 0.6365087 0.855201780796051 True diff --git a/ENCSR959ZXU/cherimoya.fold_4.performance.tsv b/ENCSR959ZXU/cherimoya.fold_4.performance.tsv deleted file mode 100644 index f61ea16007e35de44d4a3aedce348b5cfb4853a4..0000000000000000000000000000000000000000 --- a/ENCSR959ZXU/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1141.18896484375 0.2637748420238495 0.5579825639724731 0.2965150475502014 0.6365087032318115 0.610953152179718 0.855201780796051 \ No newline at end of file diff --git a/ENCSR960EJV/cherimoya.fold_1.performance.tsv b/ENCSR960EJV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2116c1769a8a0acb747abf8c0026bf0203408ab5..0000000000000000000000000000000000000000 --- a/ENCSR960EJV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -341.0453796386719 0.47252464294433594 0.30082330107688904 0.09388378262519836 0.7238397598266602 0.6816983222961426 0.514260470867157 \ No newline at end of file diff --git a/ENCSR960EJV/cherimoya.fold_2.performance.tsv b/ENCSR960EJV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4a41285aa865ce01849fdbdf62101489ae5fd215..0000000000000000000000000000000000000000 --- a/ENCSR960EJV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -318.9734191894531 0.47922685742378235 0.2968769967556 0.08793853968381882 0.6922259330749512 0.6578781008720398 0.5155617594718933 \ No newline at end of file diff --git a/ENCSR960EJV/cherimoya.fold_4.evaluate.json b/ENCSR960EJV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 43b0f8cfd699a02ddfcf01422b7a25cf608360e4..0000000000000000000000000000000000000000 --- a/ENCSR960EJV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF613VVE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_0.evaluate.json b/ENCSR960KGO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index d2830e81b5c44e99c2938061a8f94bdf1bfbf12e..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF015MML.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_0.fit.json b/ENCSR960KGO/cherimoya.fold_0.fit.json deleted file mode 100644 index 4f6148e830d4eb42f47d6697db1b601fe3a56806..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF015MML.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_0.log b/ENCSR960KGO/cherimoya.fold_0.log deleted file mode 100644 index 23757562d98954a32dea7785ff4e1aa563ee8fa0..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2029 27.016622066497803 3.374967098236084 317.1876525878906 0.8115970492362976 511.7560119628906 0.47121483087539673 0.5487622 9.675107955932617 True -1 4058 22.403752326965332 0.41738009452819824 335.7228088378906 0.6116909980773926 435.5382080078125 0.5905824899673462 0.6400275 3.467772960662842 True -2 6087 22.477171182632446 0.41372203826904297 329.18109130859375 0.4160502552986145 415.9488220214844 0.6282249689102173 0.6543892 0.9920685291290283 True -3 8116 22.513813495635986 0.41274380683898926 328.27947998046875 0.6399050354957581 410.70343017578125 0.6375390887260437 0.66119283 0.6719009876251221 True -4 10145 22.420963048934937 0.7703351974487305 283.594482421875 0.6383755207061768 408.82794189453125 0.6404764652252197 0.6653499 0.6431106328964233 True -5 12174 22.36436676979065 0.4182884693145752 334.9884033203125 0.4334751069545746 407.3003845214844 0.6433482766151428 0.6693575 0.654632031917572 True -6 14203 22.346400022506714 0.40255260467529297 298.6485595703125 0.4006989002227783 405.9483642578125 0.6460554003715515 0.6748993 0.6062658429145813 True -7 16232 22.941965341567993 18.3313992023468 306.21630859375 0.5276840925216675 405.3104553222656 0.6477550268173218 0.6761595 0.58149254322052 True -8 18261 22.366894960403442 2.4913535118103027 365.3387756347656 0.5041001439094543 404.3406982421875 0.6494179368019104 0.68518096 0.5529839992523193 True -9 20290 22.370818614959717 0.4183981418609619 307.6682434082031 0.4312584698200226 403.5223388671875 0.6512389779090881 0.68664926 0.5362738966941833 True -10 22319 22.35295820236206 0.4111154079437256 270.238525390625 0.5529054403305054 402.52117919921875 0.6531640291213989 0.69384766 0.5086508989334106 True -11 24348 22.397343397140503 0.41016077995300293 373.8431091308594 0.42781639099121094 402.08203125 0.6547159552574158 0.69644296 0.4883407950401306 True -12 26377 22.366973876953125 0.473923921585083 326.5211181640625 0.758245050907135 400.80621337890625 0.656228244304657 0.70358473 0.4694363474845886 True -13 28406 22.390681266784668 0.40880656242370605 341.6319580078125 0.4238325357437134 399.7850036621094 0.6578526496887207 0.71071255 0.45381373167037964 True -14 30435 22.39895725250244 1.342428207397461 347.7187805175781 0.3030354380607605 399.4726257324219 0.6586971282958984 0.7095064 0.45312702655792236 False -15 32464 22.365010261535645 17.387015342712402 327.52178955078125 0.2688531279563904 399.3766174316406 0.659037709236145 0.71520585 0.4437978267669678 True -16 34493 23.11641550064087 0.4185924530029297 363.2713317871094 0.3220304846763611 399.3694763183594 0.6586703062057495 0.7155951 0.4451601505279541 True -17 36522 22.39789366722107 0.4174659252166748 313.21759033203125 0.15995243191719055 399.2354736328125 0.6578975915908813 0.71461165 0.4511335790157318 False -18 38551 22.37641978263855 0.40909743309020996 289.9404296875 0.23317044973373413 399.9526672363281 0.6573581695556641 0.7115345 0.45782411098480225 False -19 40580 22.380659341812134 0.41570138931274414 305.8092041015625 0.24990123510360718 399.8117980957031 0.6568896770477295 0.7086068 0.46326637268066406 False diff --git a/ENCSR960KGO/cherimoya.fold_0.performance.tsv b/ENCSR960KGO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index f42fc866eca1bec3b47175a87cbe8c458b3bee32..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -399.3694763183594 0.27794209122657776 0.6586703062057495 0.2636776268482208 0.7155951261520386 0.6692126989364624 0.4451601505279541 \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_1.evaluate.json b/ENCSR960KGO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index a6df72e3620d6da578f5ad5789a44643bf794934..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF015MML.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_1.fit.json b/ENCSR960KGO/cherimoya.fold_1.fit.json deleted file mode 100644 index 895af1b082aeabd36fc4fe03f632af97da000230..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF015MML.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_1.log b/ENCSR960KGO/cherimoya.fold_1.log deleted file mode 100644 index 694d216dc7071fe46e8346d9ee8c1625e0dd112c..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2061 27.434555053710938 3.44407057762146 379.8515625 0.7103309631347656 523.4751586914062 0.4849262535572052 0.5312308 9.76502513885498 True -1 4122 22.762012004852295 1.2132952213287354 365.04840087890625 0.5670609474182129 450.7203369140625 0.5965121984481812 0.657551 2.518895387649536 True -2 6183 22.760950326919556 0.4831860065460205 363.3332824707031 0.5972925424575806 435.68682861328125 0.6271413564682007 0.6657776 0.9337252974510193 True -3 8244 22.753653526306152 0.5310878753662109 352.86431884765625 0.6174132227897644 431.4346618652344 0.6337493062019348 0.6804949 0.7470096945762634 True -4 10305 22.718859672546387 0.485576868057251 341.93505859375 0.5715363621711731 429.3216552734375 0.6379122734069824 0.6822399 0.6746955513954163 True -5 12366 22.68805956840515 2.4839158058166504 292.7315673828125 0.7542015910148621 427.5709228515625 0.6407628059387207 0.6914359 0.5865994691848755 True -6 14427 22.78001117706299 30.872982501983643 316.4950256347656 0.5602070689201355 426.6875305175781 0.6426452994346619 0.6957125 0.559313178062439 True -7 16488 23.10610818862915 0.4923865795135498 291.21954345703125 0.5124456882476807 425.8470153808594 0.6446051597595215 0.7022936 0.5330044031143188 True -8 18549 22.80739426612854 0.49979448318481445 309.7333984375 0.323866605758667 424.8479309082031 0.6464466452598572 0.706274 0.5050069689750671 True -9 20610 22.73483967781067 0.4855465888977051 312.32513427734375 0.35715270042419434 423.2443542480469 0.6488745808601379 0.7144755 0.4623374938964844 True -10 22671 22.723833084106445 0.48256802558898926 323.95794677734375 0.3887491226196289 422.299072265625 0.650945782661438 0.7200373 0.4386855363845825 True -11 24732 22.905415058135986 23.94619607925415 382.5207214355469 0.5553182363510132 421.3433837890625 0.6524938941001892 0.72588044 0.4192658066749573 True -12 26793 23.245049953460693 0.4966707229614258 256.44000244140625 0.5303642749786377 420.49334716796875 0.653992235660553 0.73323065 0.4073864817619324 True -13 28854 22.864372730255127 0.5051364898681641 324.55322265625 0.4279928505420685 419.63714599609375 0.655669093132019 0.73925585 0.3921361565589905 True -14 30915 22.928120374679565 0.4966871738433838 292.7834167480469 0.41125863790512085 418.8487548828125 0.6567835807800293 0.74094385 0.38469812273979187 True -15 32976 22.884031534194946 0.5032100677490234 323.2525329589844 0.4846033751964569 418.5484619140625 0.6574467420578003 0.7486335 0.38149160146713257 True -16 35037 22.879859447479248 21.783406496047974 312.5743408203125 0.3138664662837982 418.4854431152344 0.6574200987815857 0.74749285 0.383912056684494 False -17 37098 25.400959968566895 0.49488258361816406 338.3572692871094 0.2588002681732178 418.51483154296875 0.6569214463233948 0.7447943 0.3903758227825165 False -18 39159 22.78878140449524 0.49596500396728516 291.665771484375 0.2630118727684021 418.73419189453125 0.656610906124115 0.74270856 0.39701908826828003 False -19 41220 22.764649391174316 1.746877670288086 331.2866516113281 0.22289890050888062 418.728515625 0.6562151312828064 0.7400942 0.4005446135997772 False diff --git a/ENCSR960KGO/cherimoya.fold_1.performance.tsv b/ENCSR960KGO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 8926b6a58dfec0d42cae2746439d5441d1976013..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -418.5484619140625 0.273049920797348 0.6574467420578003 0.27365487813949585 0.7486335039138794 0.7327299118041992 0.38149160146713257 \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_2.evaluate.json b/ENCSR960KGO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 726119adbadf1782eb953c9786b6a491eb66ed79..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF015MML.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_2.fit.json b/ENCSR960KGO/cherimoya.fold_2.fit.json deleted file mode 100644 index 3ac2a016a44fbaf3b4daf6468175086af6d43fa8..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF015MML.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_2.log b/ENCSR960KGO/cherimoya.fold_2.log deleted file mode 100644 index 30746c29f0da0f610d8ec52fca0906ea0d98fc4f..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2164 28.391947507858276 3.389002799987793 365.3492126464844 0.5179214477539062 511.5631408691406 0.4801957905292511 0.55978984 8.419328689575195 True -1 4328 23.85060691833496 0.4002819061279297 315.88153076171875 0.7039257287979126 437.93145751953125 0.5997000336647034 0.6506883 3.0273191928863525 True -2 6492 23.88438606262207 0.39443278312683105 304.84234619140625 0.5094234347343445 423.3686828613281 0.6261879205703735 0.65206987 0.876275360584259 True -3 8656 23.916234254837036 0.3979456424713135 316.1400146484375 0.4937801957130432 417.75225830078125 0.6347813010215759 0.67320156 0.600938081741333 True -4 10820 23.90942072868347 0.3977322578430176 339.2281494140625 0.56754469871521 416.0705871582031 0.6386113166809082 0.680713 0.6114345192909241 True -5 12984 23.86581802368164 1.1875948905944824 314.3220520019531 0.8087781667709351 414.8226318359375 0.6403492093086243 0.6839362 0.6132903695106506 True -6 15148 23.91372561454773 0.8395190238952637 362.109130859375 0.507877767086029 413.1540832519531 0.6431813836097717 0.68839455 0.5426777005195618 True -7 17312 23.879319429397583 0.39174389839172363 344.5416564941406 0.5841561555862427 412.284912109375 0.6449917554855347 0.6928686 0.5035045742988586 True -8 19476 23.838783025741577 0.3880953788757324 308.50970458984375 0.42213672399520874 411.2561340332031 0.6471147537231445 0.69570464 0.48634329438209534 True -9 21640 23.87100315093994 0.3979518413543701 319.690673828125 0.49690574407577515 410.1964111328125 0.6488978266716003 0.6980371 0.46943262219429016 True -10 23804 23.93623185157776 16.544071197509766 337.66571044921875 0.3657457232475281 409.12255859375 0.6508786082267761 0.70499367 0.4520432651042938 True -11 25968 23.97990655899048 0.3945350646972656 329.0736999511719 0.602713406085968 408.3001403808594 0.652603805065155 0.7118314 0.44657063484191895 True -12 28132 25.6445152759552 15.30203652381897 317.20263671875 0.4428735077381134 407.3987121582031 0.6543428301811218 0.71631116 0.4333628714084625 True -13 30296 23.888616800308228 0.7029225826263428 340.8316345214844 0.397907018661499 406.6283874511719 0.6555935740470886 0.7232953 0.4241792559623718 True -14 32460 23.98200488090515 0.3988609313964844 334.03839111328125 0.33305227756500244 406.14569091796875 0.6565718650817871 0.72813034 0.4183683693408966 True -15 34624 23.884419441223145 0.3986661434173584 312.549072265625 0.2673785984516144 405.8820495605469 0.656909704208374 0.7281854 0.4243108630180359 True -16 36788 23.905499935150146 0.3893613815307617 345.04132080078125 0.27195823192596436 405.6671447753906 0.6570007801055908 0.7321255 0.42061901092529297 True -17 38952 23.905038356781006 0.3931875228881836 356.53106689453125 0.3404256999492645 405.9084167480469 0.6563602685928345 0.7284775 0.4304283559322357 False -18 41116 23.901448011398315 0.39817023277282715 298.15301513671875 0.26108789443969727 406.31256103515625 0.6555405259132385 0.7276655 0.4398893713951111 False -19 43280 23.8339741230011 29.449098348617554 308.77984619140625 0.22833332419395447 406.5444641113281 0.6551656126976013 0.7246327 0.4473757743835449 False diff --git a/ENCSR960KGO/cherimoya.fold_2.performance.tsv b/ENCSR960KGO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6a3182ae0dde9337c63db9c5c526a34fa48757e9..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -405.6671447753906 0.27764472365379333 0.6570007801055908 0.2676909863948822 0.7321255207061768 0.6995978355407715 0.42061901092529297 \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_3.evaluate.json b/ENCSR960KGO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 5c7fd51cb42f77958b55c704e8931cb413ecdb5b..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF015MML.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_3.fit.json b/ENCSR960KGO/cherimoya.fold_3.fit.json deleted file mode 100644 index 5a3c2308555328ea0d5737769f07fe2d18aadc02..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF015MML.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_3.log b/ENCSR960KGO/cherimoya.fold_3.log deleted file mode 100644 index efc1f2a9560e7d806efe6d938c04281cb5ad4278..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2112 31.79724383354187 3.7857043743133545 375.4922790527344 0.8052871823310852 520.5869140625 0.48373907804489136 0.5535789 9.70280647277832 True -1 4224 23.37957501411438 2.289513111114502 290.7445068359375 0.7235671281814575 440.3788146972656 0.608485221862793 0.63503677 3.3744218349456787 True -2 6336 23.320178747177124 0.4447355270385742 317.2812805175781 0.5962263345718384 426.3089599609375 0.6329700946807861 0.62595916 1.1405667066574097 False -3 8448 23.289300441741943 0.4435694217681885 357.2413024902344 0.5575939416885376 422.0750427246094 0.6389428973197937 0.6356128 0.8941783905029297 True -4 10560 23.306300163269043 0.43988561630249023 323.8448486328125 0.7458906173706055 420.2139892578125 0.6419310569763184 0.6484841 0.7533631324768066 True -5 12672 23.28731918334961 0.442852258682251 347.68865966796875 0.7628170847892761 418.580078125 0.6447302103042603 0.6601514 0.6680113673210144 True -6 14784 23.30580449104309 0.4404871463775635 305.7781982421875 0.4772929549217224 418.2128601074219 0.6461551785469055 0.6650756 0.6711654663085938 True -7 16896 23.273492336273193 0.5990293025970459 300.6393127441406 0.6679995059967041 416.74798583984375 0.6486760377883911 0.6695176 0.6119478344917297 True -8 19008 23.332725524902344 0.9516003131866455 340.6028747558594 0.40513935685157776 415.3519287109375 0.6511104106903076 0.6778653 0.5765577554702759 True -9 21120 23.26615262031555 0.43953585624694824 358.7473449707031 0.5094501376152039 414.4126281738281 0.6532312035560608 0.68518806 0.5203165411949158 True -10 23232 23.27859878540039 0.4399094581604004 351.78131103515625 0.42445075511932373 413.503173828125 0.6548330187797546 0.68849045 0.5152522921562195 True -11 25344 23.800962209701538 0.44286513328552246 306.874755859375 0.527857780456543 412.71295166015625 0.6562376618385315 0.6960852 0.4968293011188507 True -12 27456 23.35132384300232 0.4432706832885742 323.2381591796875 0.4990770220756531 411.7389831542969 0.6580929160118103 0.7051915 0.47405532002449036 True -13 29568 23.33210587501526 0.4447758197784424 313.3105163574219 0.476556658744812 410.7310485839844 0.6597169637680054 0.7107953 0.4651648700237274 True -14 31680 23.345186471939087 0.4435546398162842 387.17340087890625 0.44811683893203735 410.0216369628906 0.6607972979545593 0.71572435 0.4498615562915802 True -15 33792 23.26540446281433 0.4388868808746338 341.51361083984375 0.3715950548648834 409.6314697265625 0.6614931225776672 0.71902436 0.45307356119155884 True -16 35904 23.266948461532593 0.444777250289917 355.4844055175781 0.26057302951812744 409.36138916015625 0.6616602540016174 0.7205655 0.45139750838279724 True -17 38016 23.896666526794434 30.700778007507324 288.0194091796875 0.2878618836402893 409.44940185546875 0.6615197062492371 0.7195553 0.45325660705566406 False -18 40128 25.27975106239319 0.4495251178741455 338.15509033203125 0.26690709590911865 409.76300048828125 0.6608328223228455 0.71418214 0.46536850929260254 False -19 42240 23.498943090438843 0.45592331886291504 291.48919677734375 0.2684521973133087 409.8043518066406 0.6604082584381104 0.7114097 0.47548797726631165 False diff --git a/ENCSR960KGO/cherimoya.fold_3.performance.tsv b/ENCSR960KGO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6ec8ccb0a9954c9cea62b825320f81b4016f808d..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -409.36138916015625 0.27354562282562256 0.6616602540016174 0.27155497670173645 0.7205654978752136 0.6845792531967163 0.45139750838279724 \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_4.evaluate.json b/ENCSR960KGO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 1f285f9a8207ebd3a8db6d60d4c3910bfce94a7b..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF015MML.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_4.fit.json b/ENCSR960KGO/cherimoya.fold_4.fit.json deleted file mode 100644 index ec061a33cbd8e7fc2b27e9d1babc833b1b95b6fc..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF015MML.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR960KGO/cherimoya.fold_4.log b/ENCSR960KGO/cherimoya.fold_4.log deleted file mode 100644 index d9f5581a0669d612ba43da1c0f26a5f8312aa52c..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2167 28.954824447631836 3.4013960361480713 349.60430908203125 0.6267008185386658 513.9160766601562 0.4794124662876129 0.5883603 9.476499557495117 True -1 4334 23.922741651535034 0.46477508544921875 314.462646484375 0.7620911598205566 440.80889892578125 0.5983510613441467 0.6265493 3.2383992671966553 True -2 6501 23.98948884010315 0.4132077693939209 301.0042724609375 0.5666741132736206 421.7555236816406 0.633693277835846 0.65685743 0.984603226184845 True -3 8668 23.919126987457275 0.40874552726745605 285.13214111328125 0.4228612184524536 417.128662109375 0.6405954957008362 0.6717683 0.7422232031822205 True -4 10835 23.868372440338135 0.4072294235229492 314.6802978515625 0.37496212124824524 415.143798828125 0.6449160575866699 0.66776747 0.6897080540657043 False -5 13002 23.95006823539734 0.40695691108703613 311.1741638183594 0.6246005296707153 413.4225769042969 0.6478763818740845 0.6754788 0.6443936824798584 True -6 15169 23.869491815567017 0.406872034072876 312.91912841796875 0.49436143040657043 412.5834655761719 0.6494866013526917 0.681602 0.6069610118865967 True -7 17336 23.855019330978394 0.6620786190032959 307.2259521484375 0.5238379240036011 411.43365478515625 0.6517488956451416 0.6845732 0.5719737410545349 True -8 19503 23.876882314682007 0.40610218048095703 324.94775390625 0.4652009606361389 410.3328552246094 0.6539868116378784 0.6936174 0.5250061750411987 True -9 21670 23.82667374610901 0.40975499153137207 334.0460205078125 0.5239776372909546 409.2386474609375 0.6555615663528442 0.7021217 0.48696455359458923 True -10 23837 23.851411819458008 15.941612005233765 322.69561767578125 0.49770790338516235 408.3185119628906 0.6573464870452881 0.70548046 0.4690144658088684 True -11 26004 24.459765195846558 6.690187931060791 346.6075134277344 0.5212363600730896 407.5415344238281 0.6591869592666626 0.7115435 0.45598605275154114 True -12 28171 23.920698404312134 0.41458868980407715 299.8052978515625 0.2911372780799866 406.7204895019531 0.6606267690658569 0.7170474 0.45000556111335754 True -13 30338 23.87621307373047 0.40544652938842773 363.40380859375 0.6618220806121826 406.08941650390625 0.6616697907447815 0.72337353 0.44150832295417786 True -14 32505 23.920886754989624 0.41046810150146484 336.6962585449219 0.37791508436203003 405.5320739746094 0.6627758741378784 0.72886884 0.42708227038383484 True -15 34672 23.908912658691406 0.40529489517211914 283.40899658203125 0.31462863087654114 405.17236328125 0.6630175709724426 0.73157716 0.4252972900867462 True -16 36839 23.898380041122437 17.639159202575684 325.81365966796875 0.3080710172653198 405.20721435546875 0.662882387638092 0.73222685 0.4278932809829712 True -17 39006 24.564051866531372 19.2306489944458 304.92730712890625 0.4213867783546448 405.38177490234375 0.6623421311378479 0.72939616 0.4369294047355652 False -18 41173 25.212494134902954 27.263015270233154 337.2493591308594 0.31613555550575256 405.5645751953125 0.6617987751960754 0.72821397 0.4406997561454773 False -19 43340 24.846980571746826 23.501129388809204 327.8340759277344 0.18047930300235748 405.8233337402344 0.6613719463348389 0.72504056 0.44747793674468994 False diff --git a/ENCSR960KGO/cherimoya.fold_4.performance.tsv b/ENCSR960KGO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index a07b05f78186d081f4d2eb48a91eefbe374a9093..0000000000000000000000000000000000000000 --- a/ENCSR960KGO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -405.20721435546875 0.2752881646156311 0.6628823280334473 0.2687039077281952 0.7322268486022949 0.6793859601020813 0.4278932809829712 \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_0.evaluate.json b/ENCSR962EAP/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0956d11702627d284c4cbad0cb31b0194933b3f9..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF820OTW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_0.fit.json b/ENCSR962EAP/cherimoya.fold_0.fit.json deleted file mode 100644 index 0f3fc228f4746c3dd9c6550d3b5e1fd9927c445d..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF820OTW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_0.log b/ENCSR962EAP/cherimoya.fold_0.log deleted file mode 100644 index e9fd42ec9b1766d62df95e8a76f1255d215b965c..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2372 30.531545400619507 3.4351646900177 236.22840881347656 0.7031024694442749 350.9248962402344 0.14820875227451324 0.6083129 5.432089805603027 True -1 4744 26.366274118423462 0.5060584545135498 227.2318572998047 0.910340428352356 328.91217041015625 0.22466987371444702 0.67876846 1.537695288658142 True -2 7116 26.362213134765625 1.0746045112609863 217.7648162841797 0.5758092403411865 320.978271484375 0.24254699051380157 0.70890176 0.8159458041191101 True -3 9488 26.374439477920532 0.4817178249359131 307.67474365234375 0.4925328195095062 318.5470275878906 0.24799233675003052 0.71961486 0.6080191731452942 True -4 11860 26.372287273406982 0.7219433784484863 265.5653076171875 0.7266024351119995 317.8617858886719 0.2482837289571762 0.7202374 0.5953957438468933 True -5 14232 26.349801063537598 0.4965507984161377 221.62680053710938 0.7871607542037964 317.0224609375 0.25195905566215515 0.72798026 0.5733392834663391 True -6 16604 26.36166501045227 2.0986201763153076 275.4034729003906 0.6846334934234619 316.5683898925781 0.25286439061164856 0.7372052 0.561018168926239 True -7 18976 26.389981746673584 0.5020668506622314 295.70379638671875 0.8600373268127441 315.86920166015625 0.25600752234458923 0.7421925 0.5287064909934998 True -8 21348 26.38881206512451 0.49582815170288086 317.0347900390625 0.7745834589004517 315.71435546875 0.2557404041290283 0.7509198 0.5112439393997192 True -9 23720 26.36459231376648 0.5035817623138428 224.62741088867188 0.7297993302345276 314.64093017578125 0.2592810392379761 0.75083375 0.5019075870513916 False -10 26092 26.41133689880371 0.5189847946166992 235.10877990722656 0.5708953738212585 314.1658935546875 0.2602407932281494 0.7533706 0.49931997060775757 True -11 28464 26.40562391281128 0.4983663558959961 258.1655578613281 0.4329054355621338 313.48297119140625 0.26291537284851074 0.75907457 0.4876403212547302 True -12 30836 26.40351891517639 0.4913010597229004 246.51242065429688 0.6634591817855835 312.47412109375 0.2657158672809601 0.7659083 0.47349995374679565 True -13 33208 26.377447843551636 0.5005815029144287 213.859619140625 0.434165358543396 312.4631042480469 0.2655479609966278 0.77172273 0.4591163694858551 True -14 35580 27.023759365081787 13.866209506988525 248.5524444580078 0.47771722078323364 312.1131286621094 0.26659008860588074 0.7767065 0.45923706889152527 True -15 37952 26.44187068939209 0.49578046798706055 314.30731201171875 0.5646883845329285 312.2326965332031 0.26608768105506897 0.77898496 0.45607423782348633 True -16 40324 26.373008012771606 0.4916672706604004 277.97515869140625 0.47977831959724426 311.676025390625 0.2683730125427246 0.77770936 0.46761852502822876 False -17 42696 26.402488708496094 0.49001455307006836 241.99195861816406 0.36492258310317993 312.2401428222656 0.2653796970844269 0.77792776 0.4764341115951538 False -18 45068 26.367894887924194 0.48738551139831543 234.67031860351562 0.2587081491947174 312.5985107421875 0.26453086733818054 0.77452534 0.48710039258003235 False -19 47440 26.378089904785156 0.8575100898742676 266.3525085449219 0.3353433310985565 312.6028747558594 0.26486366987228394 0.7741908 0.4970633089542389 False diff --git a/ENCSR962EAP/cherimoya.fold_0.performance.tsv b/ENCSR962EAP/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 1dba519853549df4c10c0e79c6d9f2151edd6ab6..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -312.2326965332031 0.4942142069339752 0.26608768105506897 0.08809395879507065 0.7789849638938904 0.7391736507415771 0.45607423782348633 \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_1.evaluate.json b/ENCSR962EAP/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 35b4a0d4a1952b9812f0f58e311f147cf037f439..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF820OTW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_1.fit.json b/ENCSR962EAP/cherimoya.fold_1.fit.json deleted file mode 100644 index 23eb5df9f82dca07cdcc94ce91e6e9a1241dbb1d..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF820OTW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_1.log b/ENCSR962EAP/cherimoya.fold_1.log deleted file mode 100644 index 5c33bc902a320b91c23e95350e5000379633b6fc..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2376 30.28624653816223 5.974074125289917 328.4370422363281 0.8827036619186401 418.2699279785156 0.1636713147163391 0.58943003 6.738692760467529 True -1 4752 26.47471308708191 0.6908543109893799 226.58383178710938 0.6536122560501099 389.2532043457031 0.24846617877483368 0.6543083 2.376810073852539 True -2 7128 26.487623929977417 0.6867837905883789 210.9258270263672 0.7191867232322693 378.6249694824219 0.26922646164894104 0.710032 1.0121245384216309 True -3 9504 26.518786668777466 0.6902766227722168 282.6708068847656 0.6583653688430786 375.3996887207031 0.2752092778682709 0.72637564 0.7172843217849731 True -4 11880 26.449329376220703 13.819336652755737 260.5048522949219 0.7478692531585693 373.8759765625 0.27904003858566284 0.7382402 0.6465440392494202 True -5 14256 27.2497456073761 0.6934390068054199 240.24267578125 0.6709201335906982 372.23040771484375 0.28270599246025085 0.750881 0.5701629519462585 True -6 16632 26.465293884277344 20.77316951751709 210.0316162109375 0.6052669286727905 371.0538635253906 0.2867545187473297 0.75017875 0.5724906921386719 False -7 19008 26.41709303855896 0.6937642097473145 251.4053955078125 0.6714826226234436 370.9008483886719 0.28684002161026 0.75678015 0.5435798168182373 True -8 21384 26.434966802597046 0.6764359474182129 327.5054016113281 0.6946903467178345 370.6760559082031 0.28649601340293884 0.76075065 0.5297380089759827 True -9 23760 26.457170248031616 0.6831872463226318 262.5109558105469 0.9868293404579163 370.17779541015625 0.28786253929138184 0.760713 0.5295851826667786 False -10 26136 26.443801879882812 0.6768913269042969 254.04623413085938 0.8629765510559082 369.25445556640625 0.29010435938835144 0.7659962 0.5186293721199036 True -11 28512 26.41753101348877 1.5552561283111572 312.53363037109375 0.5219022035598755 368.12823486328125 0.2934305667877197 0.7696347 0.5093539357185364 True -12 30888 26.4525887966156 0.6784842014312744 228.35498046875 0.7710685729980469 367.46795654296875 0.2957880198955536 0.77662903 0.5038476586341858 True -13 33264 26.429012775421143 0.6884942054748535 234.4788818359375 0.62380450963974 367.13360595703125 0.29496970772743225 0.7826309 0.4951536953449249 True -14 35640 26.451520442962646 0.6813962459564209 239.73153686523438 0.3043496012687683 366.92706298828125 0.2954792082309723 0.7826803 0.5055350661277771 True -15 38016 26.433783292770386 0.7560851573944092 196.737060546875 0.5934874415397644 366.74603271484375 0.29603299498558044 0.78808755 0.5009838342666626 True -16 40392 26.452625274658203 0.6744194030761719 226.65386962890625 0.23656117916107178 366.6492614746094 0.2971682548522949 0.78658193 0.5141301155090332 False -17 42768 26.385664463043213 0.6777925491333008 242.3094940185547 0.40425270795822144 366.88134765625 0.29604417085647583 0.78494614 0.5367452502250671 False -18 45144 26.420313358306885 0.7007145881652832 274.7366943359375 0.4174116253852844 367.1497802734375 0.2958856225013733 0.7805916 0.5623675584793091 False -19 47520 26.49722957611084 8.891311407089233 215.09750366210938 0.3863871097564697 367.6827697753906 0.29394063353538513 0.7792175 0.5714384913444519 False diff --git a/ENCSR962EAP/cherimoya.fold_1.performance.tsv b/ENCSR962EAP/cherimoya.fold_1.performance.tsv deleted file mode 100644 index da6ea5ba17bb2825cf78230acfadb96e0c2c7d8d..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -366.74603271484375 0.4688483476638794 0.29603299498558044 0.09849292784929276 0.7880875468254089 0.7558294534683228 0.5009838342666626 \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_2.evaluate.json b/ENCSR962EAP/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f8b132d6da6632ad238431d1e9f67d29f8cc7dd5..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF820OTW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_2.fit.json b/ENCSR962EAP/cherimoya.fold_2.fit.json deleted file mode 100644 index 585d5902581e2d34112cbf7fd1ef13272ab0f551..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF820OTW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_2.log b/ENCSR962EAP/cherimoya.fold_2.log deleted file mode 100644 index 3ec5c32ded8ed53202eeccd11f885035799f7acb..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2531 31.81685495376587 3.424309253692627 293.24114990234375 0.8508641719818115 368.6254577636719 0.15717796981334686 0.58415407 5.055751323699951 True -1 5062 28.1418673992157 0.5098330974578857 277.7579040527344 0.7917560935020447 343.4913635253906 0.23904600739479065 0.6565376 1.36836838722229 True -2 7593 28.123614072799683 2.5914618968963623 269.90032958984375 0.9407487511634827 336.5346984863281 0.2496209591627121 0.6987213 0.7272830009460449 True -3 10124 28.158814430236816 0.4941411018371582 306.95343017578125 0.7856712341308594 333.28900146484375 0.25673210620880127 0.7094867 0.5874423384666443 True -4 12655 28.549195528030396 0.4937407970428467 289.29168701171875 0.5243834257125854 332.2122497558594 0.2581321597099304 0.7236121 0.5365031361579895 True -5 15186 28.132527828216553 0.49395155906677246 213.8710479736328 0.6368228793144226 330.9705505371094 0.2615894377231598 0.7294013 0.5254883766174316 True -6 17717 28.21425175666809 0.49810075759887695 235.38592529296875 0.6763370037078857 330.4623107910156 0.26274362206459045 0.731268 0.5239382386207581 True -7 20248 28.36125111579895 0.6118950843811035 284.9970397949219 0.529380202293396 328.9646911621094 0.26761165261268616 0.7348421 0.5174711346626282 True -8 22779 28.29861617088318 1.4620001316070557 312.1228942871094 0.637709379196167 329.1513671875 0.2656967043876648 0.74113756 0.5102895498275757 True -9 25310 28.26656675338745 0.5025265216827393 269.1424865722656 0.661515474319458 327.6441650390625 0.2714294195175171 0.7416166 0.5102317929267883 True -10 27841 28.345774173736572 0.5099496841430664 182.0027618408203 0.8670077919960022 327.2336120605469 0.2719470262527466 0.74466825 0.5071680545806885 True -11 30372 28.290279626846313 0.4985072612762451 208.17715454101562 0.588962197303772 326.5089416503906 0.2735973298549652 0.7494299 0.5002999901771545 True -12 32903 28.233060836791992 0.501253604888916 244.84478759765625 0.4410356879234314 326.32513427734375 0.2743532359600067 0.7537663 0.49917396903038025 True -13 35434 28.244821786880493 1.5610017776489258 272.39154052734375 0.9553946256637573 325.589599609375 0.27674588561058044 0.75684875 0.5027039051055908 True -14 37965 28.228440284729004 0.5355803966522217 254.8918914794922 0.4103041887283325 325.53521728515625 0.27783486247062683 0.7606825 0.5003446340560913 True -15 40496 28.2439227104187 0.49630188941955566 242.52059936523438 0.5147910118103027 325.0802917480469 0.2788589298725128 0.76307154 0.502834677696228 True -16 43027 28.199262857437134 0.4965348243713379 287.80767822265625 0.472941130399704 325.5918273925781 0.2773541212081909 0.76459616 0.5088914632797241 True -17 45558 28.28021812438965 0.508821964263916 239.03341674804688 0.3377116620540619 325.9450988769531 0.2761370837688446 0.76380223 0.524528980255127 False -18 48089 28.27784490585327 0.5020067691802979 203.6523895263672 0.25512099266052246 325.5188293457031 0.27709248661994934 0.761671 0.5405116677284241 False -19 50620 28.213306427001953 0.5018332004547119 272.3282470703125 0.2666434645652771 326.0727844238281 0.2749534845352173 0.75879335 0.548329770565033 False diff --git a/ENCSR962EAP/cherimoya.fold_2.performance.tsv b/ENCSR962EAP/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ed2092ca1a48ea4fa864d35e054fe0745dbf981d..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -325.5918273925781 0.4869215488433838 0.2773541212081909 0.08797696977853775 0.764596164226532 0.7273098230361938 0.5088914632797241 \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_3.evaluate.json b/ENCSR962EAP/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cbf1bc079c3f9c0aac2f9103422228c570c2f437..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF820OTW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_3.fit.json b/ENCSR962EAP/cherimoya.fold_3.fit.json deleted file mode 100644 index 1268543e11e07a06e7a77572fce2e4a0396cd2b6..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF820OTW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_3.log b/ENCSR962EAP/cherimoya.fold_3.log deleted file mode 100644 index 6d9505e92bd497207e68854c3b485ede1578ee24..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2427 31.125911474227905 3.4692962169647217 228.36508178710938 0.7052486538887024 382.5328369140625 0.15770947933197021 0.59921813 5.6494059562683105 True -1 4854 27.029642343521118 3.3938117027282715 291.31884765625 0.7777851819992065 359.5003356933594 0.2329438477754593 0.66921043 1.8739542961120605 True -2 7281 27.01741075515747 0.8602514266967773 236.5161590576172 0.8479329943656921 352.98858642578125 0.24532848596572876 0.6839387 0.9350687265396118 True -3 9708 27.045079708099365 0.5510776042938232 243.8250732421875 0.46243560314178467 351.0946044921875 0.24707846343517303 0.710679 0.7624916434288025 True -4 12135 27.004720211029053 0.5432090759277344 283.48956298828125 1.0078107118606567 349.6682434082031 0.25058209896087646 0.7232098 0.7129698991775513 True -5 14562 27.02882480621338 0.5449159145355225 252.67947387695312 0.5778236389160156 348.9590759277344 0.2529769241809845 0.7305563 0.6495417952537537 True -6 16989 27.049463272094727 0.541562557220459 222.5164794921875 0.5866168141365051 348.5080261230469 0.25429806113243103 0.734532 0.6194495558738708 True -7 19416 27.133493900299072 1.0453574657440186 259.2001953125 0.8029804229736328 347.6239929199219 0.25673335790634155 0.742204 0.5932543277740479 True -8 21843 27.0720534324646 0.5481059551239014 243.8748779296875 0.6289910078048706 346.68609619140625 0.2600474953651428 0.74637717 0.5692957043647766 True -9 24270 27.07652735710144 0.5537574291229248 226.18014526367188 0.7291353344917297 346.0379943847656 0.2610286772251129 0.7515927 0.5559681057929993 True -10 26697 26.997946739196777 0.5500006675720215 228.74581909179688 0.4688456356525421 345.05316162109375 0.26435983180999756 0.7609206 0.534770667552948 True -11 29124 26.993272304534912 0.5412638187408447 289.4371032714844 0.54497891664505 344.4910888671875 0.26501941680908203 0.7639685 0.5229028463363647 True -12 31551 26.954962253570557 0.5440263748168945 303.75360107421875 0.589207649230957 343.9304504394531 0.2670794427394867 0.7696908 0.5107306241989136 True -13 33978 26.979480981826782 1.9996066093444824 333.451904296875 0.45785391330718994 343.33251953125 0.26853877305984497 0.7740446 0.503391683101654 True -14 36405 26.98037075996399 0.5432000160217285 204.7902069091797 0.25513485074043274 343.3205871582031 0.2677293121814728 0.7802506 0.4962702989578247 True -15 38832 26.991395235061646 0.5411901473999023 279.7023010253906 0.34278035163879395 343.04229736328125 0.2679387927055359 0.78422576 0.4960162937641144 True -16 41259 27.004457712173462 0.5394654273986816 243.93557739257812 0.2606610655784607 342.8330993652344 0.26951688528060913 0.7858895 0.500439465045929 True -17 43686 27.02299666404724 0.5419466495513916 312.4163513183594 0.3337949514389038 343.0445861816406 0.2684435546398163 0.78303975 0.5153710246086121 False -18 46113 27.050991535186768 0.5411994457244873 260.632080078125 0.47082650661468506 343.36279296875 0.2672596275806427 0.781021 0.5334556102752686 False -19 48540 27.034442901611328 0.5423479080200195 278.483154296875 0.2743946313858032 343.15399169921875 0.26816797256469727 0.77934396 0.5442911982536316 False diff --git a/ENCSR962EAP/cherimoya.fold_3.performance.tsv b/ENCSR962EAP/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9f3ba627204afe85a7be5bc226c9a09b76950d3c..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -342.8330993652344 0.48649492859840393 0.26951688528060913 0.09026404470205307 0.7858895063400269 0.7541236281394958 0.500439465045929 \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_4.evaluate.json b/ENCSR962EAP/cherimoya.fold_4.evaluate.json deleted file mode 100644 index be3a5e85818f17db20e0dd0c54a6c104c9a43d08..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF820OTW.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_4.fit.json b/ENCSR962EAP/cherimoya.fold_4.fit.json deleted file mode 100644 index 462b0f3a5212d7083d54c5cad5b3755446cd8d3f..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF820OTW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962EAP/cherimoya.fold_4.log b/ENCSR962EAP/cherimoya.fold_4.log deleted file mode 100644 index 9cab6e59b8f9fc27daa6cddd055fcd8dc52fa8f4..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2486 31.360684633255005 3.442394971847534 250.51303100585938 0.878472089767456 346.6590576171875 0.152001291513443 0.59002495 4.87291145324707 True -1 4972 27.630919456481934 0.5194110870361328 220.2930450439453 0.7466030120849609 325.1184997558594 0.22687053680419922 0.6531311 1.3405358791351318 True -2 7458 27.716596841812134 0.5027914047241211 232.14251708984375 0.6285195350646973 319.4429016113281 0.2371693104505539 0.692999 0.6209739446640015 True -3 9944 27.615999937057495 0.501776933670044 265.186767578125 0.7640291452407837 317.5428161621094 0.24080218374729156 0.71022934 0.558527410030365 True -4 12430 28.015950918197632 2.508852005004883 248.73648071289062 0.5573480129241943 316.01751708984375 0.24472519755363464 0.71588355 0.5435322523117065 True -5 14916 27.67989182472229 0.5101296901702881 326.56768798828125 0.823793888092041 315.3742370605469 0.2466496080160141 0.72201824 0.5364817380905151 True -6 17402 27.64265727996826 0.5072164535522461 264.6495361328125 0.8295234441757202 314.565185546875 0.24898256361484528 0.72484934 0.5288230776786804 True -7 19888 27.62827157974243 3.667675256729126 266.5816650390625 0.536618173122406 314.2109375 0.24891670048236847 0.7281328 0.5173656940460205 True -8 22374 27.65145778656006 0.510545015335083 220.93577575683594 0.6761899590492249 313.4691162109375 0.25208964943885803 0.7317971 0.5110681653022766 True -9 24860 27.677706003189087 0.5077106952667236 229.02328491210938 0.5670024156570435 312.6539306640625 0.25394633412361145 0.73321414 0.5114554166793823 True -10 27346 27.655784845352173 0.5070035457611084 321.72607421875 0.7390233278274536 312.4807434082031 0.2546001374721527 0.7368778 0.5067943334579468 True -11 29832 27.737743377685547 0.6914634704589844 236.5435028076172 0.43177706003189087 311.3935241699219 0.25872424244880676 0.74226916 0.4967714548110962 True -12 32318 27.71737837791443 0.5086288452148438 270.1460266113281 0.3522556722164154 311.146728515625 0.2589610517024994 0.7504315 0.48709556460380554 True -13 34804 27.664923667907715 0.5086770057678223 224.47421264648438 0.3511204421520233 311.3084716796875 0.2588043510913849 0.7527362 0.48607131838798523 True -14 37290 27.64913845062256 0.5029888153076172 266.1773986816406 0.5446405410766602 310.9749450683594 0.2601272761821747 0.75958425 0.4784020781517029 True -15 39776 27.615169525146484 0.5047447681427002 258.0994873046875 0.5238069295883179 310.6513977050781 0.2609044909477234 0.76380414 0.47751760482788086 True -16 42262 27.674635410308838 0.5088763236999512 225.46389770507812 0.23688185214996338 310.9128112792969 0.26020196080207825 0.7653334 0.4822053611278534 True -17 44748 27.694580554962158 2.037269353866577 254.88336181640625 0.3014991879463196 310.9288024902344 0.2599486708641052 0.7635637 0.4954596161842346 False -18 47234 27.693809509277344 0.507997989654541 239.17124938964844 0.41914132237434387 311.53216552734375 0.25811058282852173 0.76069343 0.5096083283424377 False -19 49720 27.71526288986206 0.5111196041107178 205.47503662109375 0.361364483833313 311.4582214355469 0.2583478093147278 0.7573479 0.518849790096283 False diff --git a/ENCSR962EAP/cherimoya.fold_4.performance.tsv b/ENCSR962EAP/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e3998c54e7fc3e93f634d3693c7898c282d46866..0000000000000000000000000000000000000000 --- a/ENCSR962EAP/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -310.9128112792969 0.49699676036834717 0.26020199060440063 0.08050098270177841 0.7653334140777588 0.7233895659446716 0.4822053611278534 \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_0.evaluate.json b/ENCSR962ITF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 187ee63854cd1b3eda3e8ad02e27e8434a40dcb0..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415KBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_0.fit.json b/ENCSR962ITF/cherimoya.fold_0.fit.json deleted file mode 100644 index 72d0ec3537f0290ce8c913f18b565833459a5a89..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF415KBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_0.log b/ENCSR962ITF/cherimoya.fold_0.log deleted file mode 100644 index 7e9d2cf000c0cc9d7351fcef4d50ddf27fec8404..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1928 25.89061737060547 3.770371913909912 310.47857666015625 1.008995771408081 436.2748718261719 0.4284413754940033 0.53067136 11.721345901489258 True -1 3856 21.3558566570282 0.43581485748291016 275.55609130859375 0.8415126800537109 371.91082763671875 0.5437899231910706 0.59888244 4.64678955078125 True -2 5784 21.281713008880615 0.3982386589050293 283.75775146484375 0.665130615234375 354.68621826171875 0.5839943885803223 0.616959 1.192200779914856 True -3 7712 21.245588541030884 0.4029409885406494 269.6505126953125 0.6659461259841919 348.6513977050781 0.5956107378005981 0.63626 0.779754102230072 True -4 9640 21.345683336257935 0.39155125617980957 275.22576904296875 0.6927894353866577 347.2500915527344 0.5992156267166138 0.6355828 0.7983851432800293 False -5 11568 21.300427436828613 0.38764142990112305 286.40985107421875 0.7675825357437134 346.262939453125 0.6018823385238647 0.6410084 0.7834180593490601 True -6 13496 21.08758306503296 0.38944315910339355 263.3420104980469 0.7633776068687439 344.8224792480469 0.6050835251808167 0.6509521 0.6948822140693665 True -7 15424 20.89087176322937 0.3886103630065918 282.0874328613281 0.6971613764762878 343.91546630859375 0.6073424220085144 0.65453273 0.724833071231842 True -8 17352 20.84666919708252 0.3814868927001953 283.6772766113281 0.7304486632347107 342.8111267089844 0.6097568273544312 0.65825826 0.6454620957374573 True -9 19280 20.85888934135437 0.379504919052124 310.5574645996094 0.7519240975379944 341.9676513671875 0.6119855642318726 0.65880674 0.6190523505210876 True -10 21208 20.851860523223877 0.3772110939025879 297.434326171875 0.6400924921035767 340.8182373046875 0.6141015887260437 0.6683161 0.5808016657829285 True -11 23136 20.96735119819641 0.37836360931396484 252.67367553710938 0.5599156618118286 339.748291015625 0.6164621114730835 0.67601603 0.5549701452255249 True -12 25064 20.9096839427948 0.38349485397338867 255.53175354003906 0.4005783796310425 339.17242431640625 0.6179396510124207 0.68383706 0.5407207012176514 True -13 26992 20.86388635635376 0.3809688091278076 297.10186767578125 0.5422264337539673 338.5903015136719 0.619136393070221 0.6886862 0.5297605395317078 True -14 28920 20.883135080337524 0.37787294387817383 274.34014892578125 0.5443230271339417 338.0345458984375 0.620214581489563 0.6953595 0.5215432047843933 True -15 30848 20.870479106903076 0.39272260665893555 285.7851867675781 0.5737208127975464 337.6595153808594 0.6209957599639893 0.695129 0.5225049257278442 False -16 32776 20.865511178970337 0.3874826431274414 274.6696472167969 0.28069019317626953 337.5928649902344 0.6210135221481323 0.6960284 0.5268590450286865 True -17 34704 20.870519161224365 0.38367271423339844 200.97900390625 0.46569645404815674 337.67108154296875 0.6206932663917542 0.6965696 0.5256415605545044 True -18 36632 20.871796131134033 0.38216638565063477 243.110595703125 0.37776780128479004 338.0700988769531 0.6200275421142578 0.6944517 0.5366605520248413 False -19 38560 20.850785970687866 0.38107824325561523 232.8474884033203 0.33809036016464233 338.1640625 0.6195713877677917 0.69255275 0.5459538102149963 False diff --git a/ENCSR962ITF/cherimoya.fold_0.performance.tsv b/ENCSR962ITF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 197d2234443faf4f9c9ed313fa124cc70939ff25..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -337.67108154296875 0.3097293972969055 0.6206932663917542 0.2198580950498581 0.6965696215629578 0.6584300994873047 0.5256415605545044 \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_1.evaluate.json b/ENCSR962ITF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index af430d9ea8d3cdfb79db019701dee8af9e2eeec2..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415KBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_1.fit.json b/ENCSR962ITF/cherimoya.fold_1.fit.json deleted file mode 100644 index 3e661f2bf90c3c2902f93566f989ecd9361cb09c..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF415KBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_1.log b/ENCSR962ITF/cherimoya.fold_1.log deleted file mode 100644 index d8255a08057b9130990a2292998751fdc5a8dac5..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1948 25.844161987304688 3.1002814769744873 297.5576171875 0.8900206685066223 442.4809875488281 0.4365021586418152 0.52356726 11.200114250183105 True -1 3896 21.545671939849854 0.6602566242218018 277.66180419921875 0.7138307094573975 379.523193359375 0.5501975417137146 0.6118291 4.7230706214904785 True -2 5844 21.47792410850525 0.5043849945068359 264.4160461425781 0.5921511650085449 364.87908935546875 0.5838117003440857 0.63016355 1.3777432441711426 True -3 7792 21.50117301940918 1.7850661277770996 270.39263916015625 0.9613078832626343 360.3454895019531 0.5933198928833008 0.6483642 0.7737756371498108 True -4 9740 21.502137184143066 0.4482252597808838 271.9542541503906 0.6479455232620239 358.4607849121094 0.5973935127258301 0.65860444 0.6930312514305115 True -5 11688 21.507323265075684 0.5785284042358398 273.1761169433594 0.6493876576423645 357.4217834472656 0.5997750759124756 0.67072225 0.6946094036102295 True -6 13636 21.472749710083008 0.8280775547027588 255.2286376953125 0.6142065525054932 356.376708984375 0.6023956537246704 0.67816377 0.6072554588317871 True -7 15584 21.51208209991455 0.42345619201660156 212.5098876953125 0.7937318086624146 355.6792297363281 0.6040537357330322 0.67859316 0.5912246108055115 True -8 17532 21.471713304519653 0.46181392669677734 312.5547180175781 0.5593611001968384 354.1286926269531 0.6072545647621155 0.69135576 0.5503391027450562 True -9 19480 21.41716194152832 16.895718574523926 256.27508544921875 0.5321760773658752 353.1884765625 0.6091213226318359 0.70006865 0.5114761590957642 True -10 21428 21.515852689743042 0.44565343856811523 231.22064208984375 0.6895115375518799 352.1688537597656 0.6112455129623413 0.707222 0.48126277327537537 True -11 23376 21.946712255477905 0.4328186511993408 244.55661010742188 0.38140159845352173 351.3018798828125 0.6131584048271179 0.7155666 0.47074782848358154 True -12 25324 21.484172105789185 0.44439125061035156 267.65533447265625 0.5241186022758484 350.2955017089844 0.6152268052101135 0.7244688 0.447160542011261 True -13 27272 21.51215362548828 0.44112229347229004 261.1943359375 0.5603879690170288 349.68505859375 0.6165699362754822 0.7278085 0.44757023453712463 True -14 29220 21.496898412704468 0.4248087406158447 233.5281982421875 0.4271094501018524 349.0678405761719 0.617765486240387 0.7302567 0.43780264258384705 True -15 31168 21.484435558319092 0.4283578395843506 289.86236572265625 0.4927068054676056 348.7119445800781 0.6180318593978882 0.73549604 0.43356773257255554 True -16 33116 21.478256225585938 0.42977023124694824 299.5423583984375 0.31448760628700256 348.7578430175781 0.6182178854942322 0.73729086 0.43325188755989075 True -17 35064 21.45580768585205 0.4327254295349121 237.81597900390625 0.34113773703575134 348.7151184082031 0.6178272366523743 0.73472166 0.44408324360847473 False -18 37012 21.450302600860596 0.5700798034667969 246.0864715576172 0.2516730725765228 349.016845703125 0.6173750162124634 0.73282516 0.45248231291770935 False -19 38960 21.5249924659729 0.4263947010040283 237.84500122070312 0.2624560296535492 348.9657897949219 0.6170238256454468 0.73122734 0.46256500482559204 False diff --git a/ENCSR962ITF/cherimoya.fold_1.performance.tsv b/ENCSR962ITF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4cbcce9cf94dc7965b5b6ee232cfdb3f7eabe963..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -348.7578430175781 0.3063528835773468 0.6182178258895874 0.22407549619674683 0.7372908592224121 0.7258874773979187 0.43325188755989075 \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_2.evaluate.json b/ENCSR962ITF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3d0997d5fed0e2bf82144c64eb2819b4c52b87d8..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415KBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_2.fit.json b/ENCSR962ITF/cherimoya.fold_2.fit.json deleted file mode 100644 index ac5248f098b66fc22963b9c7e8e51afaa73df088..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF415KBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_2.log b/ENCSR962ITF/cherimoya.fold_2.log deleted file mode 100644 index f7defc135b4a235e1b8925a9b77fb936a6e92126..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2058 27.243746519088745 3.501093864440918 335.24151611328125 0.6890742778778076 427.7040100097656 0.4340255558490753 0.5314221 8.786395072937012 True -1 4116 23.027663230895996 0.6082024574279785 302.2890319824219 0.7123183608055115 368.1807556152344 0.547020673751831 0.6236972 3.7055726051330566 True -2 6174 22.66407346725464 1.4778783321380615 266.2734680175781 0.6307313442230225 355.0981140136719 0.5793165564537048 0.637737 1.2398642301559448 True -3 8232 22.723910093307495 0.39690494537353516 255.62237548828125 0.8068180084228516 349.3740234375 0.5896835923194885 0.66003 0.8300352692604065 True -4 10290 22.266096353530884 0.4437124729156494 270.7730712890625 0.7387591004371643 347.09967041015625 0.5943045616149902 0.66820765 0.71808922290802 True -5 12348 22.326363801956177 0.38271141052246094 259.1654052734375 0.596957266330719 346.1303405761719 0.5967410802841187 0.6713095 0.7038040161132812 True -6 14406 22.328603744506836 0.3907787799835205 330.8326416015625 0.5060461759567261 345.1936340332031 0.5990837216377258 0.67367846 0.6793999075889587 True -7 16464 22.305403232574463 0.39615774154663086 229.76483154296875 0.381968230009079 344.1808166503906 0.6011741757392883 0.6785776 0.6416995525360107 True -8 18522 22.322232484817505 0.3770871162414551 245.5910186767578 0.5144231915473938 343.4486389160156 0.6029793620109558 0.68161416 0.6082179546356201 True -9 20580 22.35940957069397 0.4049720764160156 294.71893310546875 0.5884866118431091 342.5099792480469 0.605275571346283 0.6819195 0.5800937414169312 True -10 22638 22.265957593917847 0.3889439105987549 240.59170532226562 0.5213858485221863 341.5295715332031 0.6071746349334717 0.68803763 0.564054548740387 True -11 24696 22.267070055007935 0.40778422355651855 255.21087646484375 0.44208472967147827 340.60406494140625 0.6092279553413391 0.6944095 0.5345886945724487 True -12 26754 22.275470733642578 0.3998374938964844 246.2621612548828 0.5222527980804443 339.806640625 0.6110677719116211 0.6990204 0.5183700919151306 True -13 28812 22.359378576278687 0.4094116687774658 290.4266357421875 0.36328744888305664 339.14349365234375 0.6124410033226013 0.7035063 0.520726203918457 True -14 30870 22.377052068710327 0.4150240421295166 250.2943878173828 0.45767152309417725 338.5003662109375 0.613819420337677 0.70938337 0.504794180393219 True -15 32928 22.40038228034973 0.39656639099121094 244.70089721679688 0.407014936208725 338.1737060546875 0.6143487095832825 0.7117395 0.5015432238578796 True -16 34986 22.389156579971313 0.5298855304718018 239.4019775390625 0.27655744552612305 338.13446044921875 0.6144330501556396 0.71488196 0.5005595088005066 True -17 37044 22.371342182159424 0.3942265510559082 272.4563293457031 0.37363898754119873 338.1294860839844 0.6142768263816833 0.7131204 0.5057094097137451 False -18 39102 22.320306539535522 0.3763711452484131 289.6867980957031 0.4974716007709503 338.2850646972656 0.6137286424636841 0.71077794 0.5145663619041443 False -19 41160 22.337560892105103 0.42703866958618164 255.91064453125 0.2673884630203247 338.4112243652344 0.6133689880371094 0.7081528 0.5216190218925476 False diff --git a/ENCSR962ITF/cherimoya.fold_2.performance.tsv b/ENCSR962ITF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5b3118d46e7c4e89b7d45106fc1fad34e01f6576..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -338.13446044921875 0.31190255284309387 0.6144330501556396 0.21805977821350098 0.714881956577301 0.6843191981315613 0.5005595088005066 \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_3.evaluate.json b/ENCSR962ITF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 85a118615755d7ae6f61a121d53f90927f56ca02..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415KBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_3.fit.json b/ENCSR962ITF/cherimoya.fold_3.fit.json deleted file mode 100644 index 89463f59c186994fe5a239c890a37fd0495becd0..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF415KBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_3.log b/ENCSR962ITF/cherimoya.fold_3.log deleted file mode 100644 index 4e645d29b2e7af2f83667222973bc5b467ac6107..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1986 26.3647358417511 3.497737407684326 265.63311767578125 0.774869441986084 440.6946716308594 0.4364469647407532 0.5198258 11.435770988464355 True -1 3972 21.97109293937683 0.5156607627868652 311.6075439453125 0.7759896516799927 375.8509826660156 0.5546683669090271 0.60470796 4.773095607757568 True -2 5958 21.930503129959106 0.4441249370574951 303.40252685546875 0.9971545934677124 360.2547607421875 0.5883442759513855 0.5811906 1.2256641387939453 False -3 7944 21.891154050827026 0.40730738639831543 314.7516174316406 0.4793953597545624 354.71343994140625 0.5987434983253479 0.60886866 0.8560724258422852 True -4 9930 21.90292716026306 0.42100071907043457 243.13165283203125 0.42063361406326294 353.6438293457031 0.6019299030303955 0.6182583 0.8542593121528625 True -5 11916 21.8995418548584 0.4166276454925537 243.79205322265625 0.7442507743835449 352.38311767578125 0.6050332188606262 0.6191526 0.8582350611686707 True -6 13902 21.941716194152832 0.4203989505767822 329.1173095703125 0.4780104160308838 351.05780029296875 0.6078827977180481 0.62857264 0.8087972402572632 True -7 15888 21.917538166046143 0.41480183601379395 270.47369384765625 0.6593676805496216 350.23065185546875 0.6096326112747192 0.6359555 0.7842802405357361 True -8 17874 21.89451313018799 7.678847312927246 255.90249633789062 0.533805787563324 349.0819091796875 0.6120033264160156 0.64882666 0.7239118814468384 True -9 19860 21.7760591506958 0.43828582763671875 232.25271606445312 0.6441854238510132 348.31396484375 0.6138597726821899 0.65413374 0.6850467920303345 True -10 21846 21.482853651046753 0.4236271381378174 243.5222625732422 0.516108512878418 347.4168395996094 0.6160082817077637 0.65578765 0.6603140234947205 True -11 23832 21.487075567245483 0.43282508850097656 231.4099884033203 0.43565845489501953 346.3168640136719 0.6180362105369568 0.665813 0.6245905756950378 True -12 25818 21.477402210235596 0.423964262008667 319.42022705078125 0.6719098687171936 345.5098876953125 0.6197987198829651 0.67836356 0.5846931338310242 True -13 27804 21.520184993743896 0.4127006530761719 252.446044921875 0.5083402395248413 344.7939147949219 0.6213929057121277 0.6870637 0.5614446401596069 True -14 29790 21.522151470184326 0.43216800689697266 246.94625854492188 0.4655730724334717 344.1224365234375 0.6226077675819397 0.6984527 0.5456205606460571 True -15 31776 21.495802879333496 0.4197108745574951 265.10113525390625 0.5426897406578064 343.4801940917969 0.6237032413482666 0.7053984 0.5196837186813354 True -16 33762 21.49349617958069 4.261734962463379 215.13531494140625 0.42996710538864136 343.4039306640625 0.6237639784812927 0.70841914 0.5205614566802979 True -17 35748 21.52805495262146 9.976847171783447 202.91384887695312 0.3372713327407837 343.48553466796875 0.623193085193634 0.70793515 0.524946928024292 False -18 37734 22.06210732460022 0.42145204544067383 246.2342529296875 0.291087806224823 343.6768798828125 0.6225845217704773 0.7079655 0.5234095454216003 False -19 39720 21.47237515449524 0.41300320625305176 234.94760131835938 0.38296687602996826 343.85418701171875 0.6221800446510315 0.70334136 0.5321820378303528 False diff --git a/ENCSR962ITF/cherimoya.fold_3.performance.tsv b/ENCSR962ITF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c25023e099ee454ba25cb4f1e8223fb89e9cf54e..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -343.4039306640625 0.3054462671279907 0.6237639784812927 0.2243167757987976 0.708419144153595 0.6790394186973572 0.5205614566802979 \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_4.evaluate.json b/ENCSR962ITF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e7d841ef74656cb23f9686c33a4d04ae34f62063..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF415KBT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_4.fit.json b/ENCSR962ITF/cherimoya.fold_4.fit.json deleted file mode 100644 index 0db7abded36ec2f33767296f61dc38caed95b964..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF415KBT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962ITF/cherimoya.fold_4.log b/ENCSR962ITF/cherimoya.fold_4.log deleted file mode 100644 index b4c8afd1d5954a7d31043a673b10e23cc678fed8..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2026 26.827226638793945 3.610670804977417 311.5930480957031 0.844663143157959 431.353271484375 0.43252283334732056 0.54263836 9.977523803710938 True -1 4052 22.41554045677185 0.44410085678100586 279.54052734375 0.9026793837547302 370.5286560058594 0.5526713728904724 0.61980176 3.6845009326934814 True -2 6078 22.38473105430603 0.385908842086792 279.4996032714844 0.7558764219284058 354.6927490234375 0.5866392254829407 0.6230295 1.3226592540740967 True -3 8104 22.3848876953125 0.42380833625793457 273.5085144042969 1.0276589393615723 349.9494934082031 0.596296489238739 0.62191373 0.9138867259025574 False -4 10130 22.382988929748535 0.39371657371520996 269.2789611816406 1.0015883445739746 348.352294921875 0.6003003120422363 0.6300975 0.9002567529678345 True -5 12156 22.353973627090454 0.38452839851379395 283.6311950683594 0.4648069739341736 347.2714538574219 0.6037000417709351 0.63485265 0.8611025810241699 True -6 14182 22.332191228866577 0.5601792335510254 243.0963592529297 1.2171673774719238 345.922119140625 0.6066004037857056 0.64873475 0.7706922292709351 True -7 16208 22.34121060371399 0.3834376335144043 271.7485046386719 0.6287002563476562 345.09027099609375 0.6086812019348145 0.652864 0.6920722723007202 True -8 18234 22.357085466384888 0.38966846466064453 247.09768676757812 0.5623537302017212 344.04083251953125 0.6109600067138672 0.6609001 0.6456568837165833 True -9 20260 22.359397888183594 0.3910243511199951 226.220703125 0.6264722347259521 343.1792907714844 0.6127314567565918 0.6654732 0.6159867644309998 True -10 22286 22.41705846786499 0.39960241317749023 225.411376953125 0.5541987419128418 342.5480651855469 0.6144387722015381 0.66917384 0.6162429451942444 True -11 24312 22.407501935958862 0.39084434509277344 294.57891845703125 0.5654081702232361 341.57177734375 0.6162434816360474 0.6770978 0.5659414529800415 True -12 26338 24.00187087059021 22.023817777633667 247.65184020996094 0.39993995428085327 340.5448303222656 0.6184283494949341 0.6839245 0.5518466830253601 True -13 28364 22.47976517677307 0.7723760604858398 270.5799255371094 0.4376833438873291 339.88006591796875 0.6198974251747131 0.69483536 0.5285352468490601 True -14 30390 22.39596176147461 0.40340614318847656 282.5787658691406 0.45822492241859436 339.24505615234375 0.6213232278823853 0.6995977 0.520754873752594 True -15 32416 22.391525745391846 0.38424205780029297 212.9180908203125 0.470224529504776 338.7349853515625 0.6219515204429626 0.7068731 0.5119542479515076 True -16 34442 22.354158878326416 0.39383435249328613 269.8083801269531 0.31723523139953613 338.6839904785156 0.621793270111084 0.71018666 0.500084400177002 True -17 36468 22.378910541534424 0.39744043350219727 284.9884948730469 0.36541226506233215 338.6864318847656 0.6216050386428833 0.70781904 0.5104368329048157 False -18 38494 22.445695877075195 0.40032029151916504 269.5093994140625 0.26051777601242065 338.75152587890625 0.621162474155426 0.7041607 0.5206542015075684 False -19 40520 22.439713954925537 1.0156786441802979 277.4835205078125 0.3928681015968323 338.9696044921875 0.6207660436630249 0.70185816 0.5279982089996338 False diff --git a/ENCSR962ITF/cherimoya.fold_4.performance.tsv b/ENCSR962ITF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index eb6695450ada1a6cb2f9df2287f1d3ca15ffce02..0000000000000000000000000000000000000000 --- a/ENCSR962ITF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -338.6839904785156 0.3082337975502014 0.6217932105064392 0.2212338149547577 0.7101866602897644 0.6707698702812195 0.500084400177002 \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_0.evaluate.json b/ENCSR962VJO/cherimoya.fold_0.evaluate.json deleted file mode 100644 index cb90aa90d7c723acb0ac867ae6bc210ccdef8b9a..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277AZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_0.fit.json b/ENCSR962VJO/cherimoya.fold_0.fit.json deleted file mode 100644 index 7bc6d38d9be642ac21dc27fb6e5debefbc9ae05f..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF277AZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_0.log b/ENCSR962VJO/cherimoya.fold_0.log deleted file mode 100644 index d4e7d993da6d8cdcefc1f19b18e9aece0051f1d3..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2734 33.33716702461243 3.624567985534668 746.1864013671875 0.5200755596160889 886.9791870117188 0.29131659865379333 0.71615523 5.730416774749756 True -1 5468 30.550703763961792 5.136504888534546 685.7228393554688 0.4787687063217163 780.211669921875 0.3879444897174835 0.7879711 1.748435378074646 True -2 8202 30.249790906906128 0.8009097576141357 776.15576171875 0.40162163972854614 770.0899047851562 0.3978175222873688 0.78957105 0.972741961479187 True -3 10936 30.179769039154053 0.5682427883148193 645.7940673828125 0.44290122389793396 760.9923095703125 0.4076528549194336 0.7972278 0.6861073970794678 True -4 13670 30.095932245254517 0.5656313896179199 691.7166748046875 0.3714495003223419 758.5286865234375 0.40982136130332947 0.7962102 0.5829482674598694 False -5 16404 30.09821581840515 19.689823627471924 552.31884765625 0.3866767883300781 752.26123046875 0.41446182131767273 0.80624247 0.4732116758823395 True -6 19138 30.099157094955444 0.8027703762054443 505.40728759765625 0.38709181547164917 750.7708740234375 0.41604629158973694 0.8092622 0.6408571004867554 True -7 21872 30.15087127685547 0.575387716293335 630.6585693359375 0.28399646282196045 749.0725708007812 0.4168863892555237 0.81806326 0.5103621482849121 True -8 24606 30.068500757217407 1.622746229171753 571.4486083984375 0.36800527572631836 747.53564453125 0.41873985528945923 0.81689626 0.43135011196136475 False -9 27340 30.14940333366394 0.7435646057128906 586.538818359375 0.5464380979537964 743.8394165039062 0.42290177941322327 0.82072437 0.4083668291568756 True -10 30074 30.149377584457397 0.5715816020965576 625.6202392578125 0.3654714822769165 740.65576171875 0.42571672797203064 0.8278416 0.3985716700553894 True -11 32808 30.08288311958313 0.5633485317230225 611.044677734375 0.2710798978805542 739.6218872070312 0.4260527491569519 0.83309734 0.36698710918426514 True -12 35542 30.169206142425537 0.5707657337188721 639.261474609375 0.37392210960388184 735.832763671875 0.4298982620239258 0.8389484 0.3527716398239136 True -13 38276 30.08924698829651 0.5629081726074219 555.1014404296875 0.2253214716911316 733.1030883789062 0.43204641342163086 0.84430134 0.33393675088882446 True -14 41010 30.09875988960266 0.5717337131500244 632.2457275390625 0.2971000075340271 732.7048950195312 0.431791752576828 0.85118294 0.3122340142726898 True -15 43744 30.144368171691895 0.5716557502746582 597.8011474609375 0.21799048781394958 729.39453125 0.4349782466888428 0.85558516 0.2965005040168762 True -16 46478 30.104547023773193 7.371182680130005 588.9967041015625 0.17688944935798645 729.991455078125 0.4334884285926819 0.85731035 0.28593501448631287 True -17 49212 30.168187379837036 0.5709724426269531 596.1279296875 0.24955002963542938 729.3101806640625 0.4344269335269928 0.85797215 0.28558599948883057 True -18 51946 30.130021572113037 0.5759062767028809 576.8309936523438 0.2523255944252014 729.4131469726562 0.43376052379608154 0.8569504 0.2860102951526642 False -19 54680 29.763355016708374 0.5651767253875732 628.1298828125 0.35323840379714966 728.2300415039062 0.4361421465873718 0.8562978 0.286838561296463 False diff --git a/ENCSR962VJO/cherimoya.fold_0.performance.tsv b/ENCSR962VJO/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 03dc1225f18e31293e16bd5a380726cfda5c91ef..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -729.3101806640625 0.34447231888771057 0.4344269633293152 0.19841064512729645 0.8579721450805664 0.8049463033676147 0.28558599948883057 \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_1.evaluate.json b/ENCSR962VJO/cherimoya.fold_1.evaluate.json deleted file mode 100644 index cd18035f6f0504eeadcc8c3efabdab7a852aba63..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277AZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_1.fit.json b/ENCSR962VJO/cherimoya.fold_1.fit.json deleted file mode 100644 index 588eb956c48fcbd20c83ef892025c82467c05e89..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF277AZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_1.log b/ENCSR962VJO/cherimoya.fold_1.log deleted file mode 100644 index 43d94953c4e6387f208d7479202da129d1e6f8d9..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2692 33.482258319854736 5.889672756195068 696.3270874023438 0.4339599609375 1025.218017578125 0.2997819781303406 0.7178701 6.277472496032715 True -1 5384 29.72456932067871 0.7473115921020508 694.1009521484375 0.5021339654922485 908.9031372070312 0.3969841003417969 0.7842482 2.015904664993286 True -2 8076 29.703218936920166 0.7464408874511719 681.972900390625 0.8236448764801025 887.28125 0.41203832626342773 0.79432994 1.027984380722046 True -3 10768 29.63845467567444 0.733292818069458 620.40576171875 0.45783892273902893 870.0249633789062 0.42361465096473694 0.80773634 0.7899072170257568 True -4 13460 29.595051288604736 0.7358269691467285 764.1915283203125 0.45510435104370117 865.0437622070312 0.42509350180625916 0.81416243 0.6423318982124329 True -5 16152 29.68318510055542 7.0765368938446045 546.808837890625 0.3718181252479553 859.6721801757812 0.43047821521759033 0.81682825 0.531995952129364 True -6 18844 29.644322872161865 0.7598483562469482 705.8995361328125 0.4793243408203125 859.191162109375 0.4310506582260132 0.819321 0.5318233966827393 True -7 21536 29.7319016456604 0.7458479404449463 645.2206420898438 0.6233611702919006 854.3363647460938 0.4350852072238922 0.8228796 0.49889200925827026 True -8 24228 30.045178413391113 0.7434954643249512 574.792236328125 0.37352216243743896 850.9214477539062 0.4379419982433319 0.8298856 0.46434104442596436 True -9 26920 29.749979734420776 0.7494840621948242 557.588134765625 0.3536152243614197 847.4419555664062 0.4421268105506897 0.83311164 0.4675711691379547 True -10 29612 29.784436464309692 0.7655215263366699 639.9031982421875 0.39244985580444336 846.08935546875 0.4417593777179718 0.8399379 0.4329564571380615 True -11 32304 29.741352558135986 0.7465581893920898 677.6197509765625 0.3396425247192383 843.31298828125 0.443691611289978 0.8451768 0.40465816855430603 True -12 34996 29.331951141357422 0.7481210231781006 645.9447021484375 0.3301168382167816 838.9825439453125 0.44724324345588684 0.8502971 0.3860771656036377 True -13 37688 29.159292936325073 8.511881828308105 548.3121337890625 0.27742600440979004 837.1980590820312 0.4480817914009094 0.8560293 0.3643842339515686 True -14 40380 29.139754056930542 0.7660765647888184 601.42333984375 0.3029125928878784 835.1890869140625 0.4495446979999542 0.86219853 0.34047457575798035 True -15 43072 29.224642992019653 0.7435810565948486 621.11962890625 0.1760556399822235 831.7260131835938 0.4533174932003021 0.86740625 0.31831008195877075 True -16 45764 29.101985931396484 0.742638111114502 652.81005859375 0.19269053637981415 832.568359375 0.4509618878364563 0.8703421 0.3045165240764618 True -17 48456 29.127052783966064 0.7405176162719727 716.4609375 0.25524669885635376 832.5965576171875 0.4514187276363373 0.8710646 0.29761484265327454 True -18 51148 29.141993522644043 0.7381975650787354 573.32177734375 0.18902060389518738 833.0628662109375 0.45135900378227234 0.87169445 0.29574957489967346 True -19 53840 29.150823831558228 0.7530534267425537 701.2281494140625 0.3422999382019043 834.107421875 0.44972845911979675 0.8726595 0.2958869934082031 True diff --git a/ENCSR962VJO/cherimoya.fold_1.performance.tsv b/ENCSR962VJO/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 586bc28914f5810e9d638dbf2871bfbd5a4ca758..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -834.107421875 0.3252227306365967 0.44972845911979675 0.22308571636676788 0.8726595044136047 0.8433821201324463 0.2958869934082031 \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_2.evaluate.json b/ENCSR962VJO/cherimoya.fold_2.evaluate.json deleted file mode 100644 index e7ae9e8aa092cb29f4eb7386c1d3d3198e41f618..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277AZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_2.fit.json b/ENCSR962VJO/cherimoya.fold_2.fit.json deleted file mode 100644 index 8bb7a3403952e02fb15a796c7606e40d1d185870..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF277AZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_2.log b/ENCSR962VJO/cherimoya.fold_2.log deleted file mode 100644 index a4a50196632fff5b9a75acdfd2cacb11f67f9b1b..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2891 35.60367465019226 3.5625903606414795 764.4132080078125 0.5072606801986694 913.1038818359375 0.30168575048446655 0.7116228 4.711206912994385 True -1 5782 31.893032550811768 0.5812017917633057 779.4576416015625 0.6253559589385986 814.7324829101562 0.3885333240032196 0.7780874 1.3457008600234985 True -2 8673 31.863452911376953 0.5679666996002197 712.8493041992188 0.4212367534637451 796.2399291992188 0.4020445942878723 0.79519653 0.7331011295318604 True -3 11564 31.841810703277588 0.9798049926757812 513.9742431640625 0.4912146329879761 789.96142578125 0.4063485264778137 0.8005628 0.6269206404685974 True -4 14455 31.884016752243042 15.602205753326416 704.6583251953125 0.5204318165779114 785.2730712890625 0.4082689583301544 0.8015545 0.5111473202705383 True -5 17346 31.47033977508545 0.5850489139556885 644.2579956054688 0.518919825553894 781.773681640625 0.41241610050201416 0.8098665 0.5176652669906616 True -6 20237 31.297415256500244 0.5636963844299316 672.529296875 0.4719076156616211 778.9384765625 0.4146578311920166 0.81171674 0.5001346468925476 True -7 23128 31.23053216934204 1.6630170345306396 521.295166015625 0.38020244240760803 774.2832641601562 0.4192778468132019 0.81430584 0.4751817286014557 True -8 26019 31.238555669784546 0.5576508045196533 591.0228271484375 0.36989808082580566 770.3876953125 0.42283889651298523 0.8209529 0.45125308632850647 True -9 28910 31.240150451660156 0.5684587955474854 537.1603393554688 0.30843979120254517 769.5584106445312 0.42339882254600525 0.8247931 0.4353269934654236 True -10 31801 31.25542426109314 0.5655734539031982 628.8095092773438 0.45139265060424805 767.3482055664062 0.4251704812049866 0.83016247 0.4211716651916504 True -11 34692 31.23699140548706 0.5611600875854492 547.726318359375 0.4274648129940033 763.7052612304688 0.4281167984008789 0.8354186 0.3872756361961365 True -12 37583 31.34500479698181 0.5764153003692627 674.0843505859375 0.33276641368865967 762.3070068359375 0.4297674298286438 0.84247994 0.3659941256046295 True -13 40474 31.25887632369995 0.5747008323669434 713.5147094726562 0.3923143744468689 759.6580200195312 0.43087396025657654 0.8469313 0.3437499403953552 True -14 43365 31.24756121635437 0.5720829963684082 559.5765991210938 0.28941258788108826 756.6859130859375 0.43413782119750977 0.8519356 0.32258957624435425 True -15 46256 31.225695371627808 0.5603246688842773 615.3658447265625 0.33405473828315735 754.8302001953125 0.43635937571525574 0.8554956 0.3071424961090088 True -16 49147 31.211766242980957 0.5519075393676758 625.8531494140625 0.3152346611022949 757.879638671875 0.43262508511543274 0.8581964 0.292502760887146 True -17 52038 31.207294702529907 0.5566964149475098 619.7259521484375 0.23919755220413208 755.9464111328125 0.43516409397125244 0.8596124 0.28722652792930603 True -18 54929 31.216142177581787 0.5536272525787354 582.3193359375 0.19468849897384644 757.473388671875 0.43383800983428955 0.85889345 0.2884606420993805 False -19 57820 31.214967489242554 0.8455181121826172 590.0421752929688 0.13778477907180786 757.3504638671875 0.4336232542991638 0.85738826 0.2897508144378662 False diff --git a/ENCSR962VJO/cherimoya.fold_2.performance.tsv b/ENCSR962VJO/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7299a52e38238b7cc8b5d547e298e9edac8d5a3c..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -755.9464111328125 0.34141474962234497 0.43516409397125244 0.20321331918239594 0.8596124053001404 0.8162063360214233 0.28722652792930603 \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_3.evaluate.json b/ENCSR962VJO/cherimoya.fold_3.evaluate.json deleted file mode 100644 index c700a373f47d259873d19d5ff57148cabe02bbd9..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277AZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_3.fit.json b/ENCSR962VJO/cherimoya.fold_3.fit.json deleted file mode 100644 index fcef6aa9754cfca3c20fd6d4099d15734da19bc0..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF277AZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_3.log b/ENCSR962VJO/cherimoya.fold_3.log deleted file mode 100644 index e53778f3f1216d643dcef31770e6e4c3ad9faf2a..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 34.196040868759155 3.4850962162017822 633.043212890625 0.47516578435897827 860.5302734375 0.3043321669101715 0.6899204 4.702295303344727 True -1 5544 30.589396238327026 0.5523266792297363 795.0625 0.8830959796905518 762.1488037109375 0.3890331983566284 0.7785374 1.5136117935180664 True -2 8316 30.590372323989868 0.5359902381896973 717.14208984375 0.5601627826690674 749.3956298828125 0.39716678857803345 0.7892456 0.9446523189544678 True -3 11088 30.641008615493774 0.5335211753845215 618.0257568359375 0.3068057894706726 742.9877319335938 0.401326060295105 0.7945291 0.7087414860725403 True -4 13860 30.74317455291748 3.6875715255737305 658.22802734375 0.37444519996643066 738.133544921875 0.40626803040504456 0.80015373 0.6089848279953003 True -5 16632 30.76808500289917 1.6540002822875977 718.947509765625 0.4450494945049286 735.4756469726562 0.4081840217113495 0.8026499 0.5763240456581116 True -6 19404 30.682029962539673 1.8165624141693115 652.5655517578125 0.38954710960388184 730.8109741210938 0.4130062758922577 0.8113437 0.5122616291046143 True -7 22176 30.649431467056274 1.2037973403930664 606.9708251953125 0.3671497702598572 727.082763671875 0.41708990931510925 0.8163921 0.4853147566318512 True -8 24948 30.62499213218689 1.6253492832183838 691.820556640625 0.39053571224212646 724.6793212890625 0.4188680052757263 0.8213323 0.45028039813041687 True -9 27720 30.61274242401123 12.47813892364502 612.3465576171875 0.30699169635772705 722.420166015625 0.4208087623119354 0.8300663 0.4329496920108795 True -10 30492 30.658618688583374 0.5410287380218506 691.462158203125 0.36006781458854675 720.6184692382812 0.4223616421222687 0.8333806 0.4083407521247864 True -11 33264 30.526562929153442 0.9175457954406738 587.9725341796875 0.31372836232185364 715.4368286132812 0.4279344081878662 0.83978057 0.3874192237854004 True -12 36036 30.593257427215576 0.5375239849090576 608.1300048828125 0.20498624444007874 713.7269287109375 0.428668737411499 0.84718853 0.35491976141929626 True -13 38808 30.519983291625977 0.5330889225006104 698.5664672851562 0.30275145173072815 711.1729736328125 0.4316508173942566 0.85405815 0.33165064454078674 True -14 41580 30.557985067367554 0.6620731353759766 664.96923828125 0.27252715826034546 710.7426147460938 0.43041563034057617 0.8586356 0.31010857224464417 True -15 44352 30.52661895751953 16.365123748779297 650.867431640625 0.2178339958190918 711.0430297851562 0.43050524592399597 0.86086935 0.2955934405326843 True -16 47124 30.086534023284912 0.5276057720184326 692.78662109375 0.38298308849334717 708.3140258789062 0.4320198595523834 0.8648974 0.283666729927063 True -17 49896 30.039589881896973 0.5283136367797852 869.3161010742188 0.2271614521741867 709.3529052734375 0.43200528621673584 0.86547637 0.2805739939212799 True -18 52668 29.92337203025818 1.779531478881836 687.07958984375 0.21037857234477997 709.3856811523438 0.43186742067337036 0.86687905 0.2813049852848053 True -19 55440 29.975990772247314 0.526503324508667 695.8383178710938 0.2117748260498047 710.01513671875 0.4312216341495514 0.8663472 0.28245487809181213 False diff --git a/ENCSR962VJO/cherimoya.fold_3.performance.tsv b/ENCSR962VJO/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b6ddd30ae5cf42007d5145269eeddbde3db5fdcc..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -709.3856811523438 0.3479345738887787 0.43186745047569275 0.19604253768920898 0.8668790459632874 0.8101324439048767 0.2813049852848053 \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_4.evaluate.json b/ENCSR962VJO/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8b34d844127893b4f0c3365892b323a517eae6bd..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277AZC.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_4.fit.json b/ENCSR962VJO/cherimoya.fold_4.fit.json deleted file mode 100644 index be023c6ae5b3b661dd53f6ced173251073d7383e..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF277AZC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR962VJO/cherimoya.fold_4.log b/ENCSR962VJO/cherimoya.fold_4.log deleted file mode 100644 index 536e20ea12eb1d00ffdf40b167f6b35cb6056c1f..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2790 35.41349697113037 3.527672052383423 607.6640625 0.3717959523200989 822.888671875 0.2980175018310547 0.7037018 5.929283618927002 True -1 5580 30.87015986442566 18.85406231880188 609.216796875 0.5679029226303101 730.7249755859375 0.3859506845474243 0.7769615 1.4163087606430054 True -2 8370 33.04907274246216 0.5890777111053467 623.9786376953125 0.4213202893733978 718.8502807617188 0.39740344882011414 0.7847727 0.8246849775314331 True -3 11160 30.869882822036743 0.559758186340332 557.84716796875 0.3975986838340759 712.9265747070312 0.40371522307395935 0.78580266 0.6124513149261475 True -4 13950 30.866047143936157 0.5603139400482178 594.4730224609375 0.42762571573257446 710.849853515625 0.4057907462120056 0.78545934 0.5846143960952759 False -5 16740 30.732952117919922 0.5556173324584961 661.1010131835938 0.46787455677986145 709.1990356445312 0.40660059452056885 0.79285175 0.5112242698669434 True -6 19530 30.744137048721313 0.5616142749786377 586.7197265625 0.5173089504241943 706.6159057617188 0.40788179636001587 0.80195224 0.45402267575263977 True -7 22320 30.7469539642334 0.5625498294830322 670.228759765625 0.40500226616859436 704.4517822265625 0.4113801121711731 0.80442137 0.4483971893787384 True -8 25110 30.803788423538208 0.5554139614105225 650.3139038085938 0.3445729911327362 701.419921875 0.4145822525024414 0.80726755 0.4339265823364258 True -9 27900 30.482318878173828 0.5607962608337402 613.474609375 0.27572566270828247 699.176513671875 0.4171005189418793 0.8114318 0.41104936599731445 True -10 30690 30.164547204971313 0.5586328506469727 716.305908203125 0.4579814672470093 697.1239624023438 0.41790106892585754 0.81775635 0.39483642578125 True -11 33480 30.140592098236084 0.5619814395904541 540.603515625 0.4397086799144745 694.403564453125 0.4215727746486664 0.8241024 0.3660320043563843 True -12 36270 30.15747618675232 0.5604095458984375 542.120849609375 0.23047861456871033 692.5711669921875 0.4232821762561798 0.83344626 0.33999156951904297 True -13 39060 30.199801206588745 0.5603258609771729 558.380126953125 0.31765449047088623 691.2144775390625 0.4232838451862335 0.8412107 0.31435805559158325 True -14 41850 30.211443424224854 0.5531868934631348 581.4756469726562 0.24648898839950562 688.7000122070312 0.426750510931015 0.84634465 0.2937626838684082 True -15 44640 30.19527244567871 0.5599017143249512 635.60302734375 0.25267308950424194 688.9791870117188 0.42542898654937744 0.8530657 0.28231197595596313 True -16 47430 30.17991304397583 0.5677957534790039 581.860595703125 0.2496720850467682 687.1228637695312 0.4280805289745331 0.8554951 0.27139008045196533 True -17 50220 30.447336196899414 0.5560033321380615 544.6194458007812 0.2789158225059509 688.669189453125 0.4256613254547119 0.8568618 0.26744648814201355 True -18 53010 30.168453216552734 0.5529100894927979 553.0565795898438 0.24636346101760864 687.0816040039062 0.4280072748661041 0.85508883 0.2672334313392639 False -19 55800 30.15194010734558 0.5552177429199219 588.3960571289062 0.2709496021270752 688.09228515625 0.4270838499069214 0.8564428 0.26788145303726196 False diff --git a/ENCSR962VJO/cherimoya.fold_4.performance.tsv b/ENCSR962VJO/cherimoya.fold_4.performance.tsv deleted file mode 100644 index c88df9887564fd1106a9bb41b11cbbb6119593c8..0000000000000000000000000000000000000000 --- a/ENCSR962VJO/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -688.669189453125 0.35173356533050537 0.4256612956523895 0.19151972234249115 0.8568618297576904 0.7947782278060913 0.26744648814201355 \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_0.evaluate.json b/ENCSR963ALV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 0588126315ac60040ac7809bb315b2993e2f5896..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF352VPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_0.fit.json b/ENCSR963ALV/cherimoya.fold_0.fit.json deleted file mode 100644 index dde27a0057a220b69e247077f8681d038fe18d30..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF352VPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_0.log b/ENCSR963ALV/cherimoya.fold_0.log deleted file mode 100644 index f6b01a7ba3af6817399ea73f700af155a81b754a..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2747 34.39150834083557 4.663274765014648 1857.9012451171875 0.6650084853172302 2549.749267578125 0.3182436525821686 0.7397334 12.039934158325195 True -1 5494 30.347098112106323 0.7345869541168213 1876.4327392578125 0.41127458214759827 2100.789306640625 0.44281041622161865 0.77482927 3.6126298904418945 True -2 8241 29.719743013381958 0.5657546520233154 1394.057373046875 0.29370003938674927 2032.5426025390625 0.4581693410873413 0.80376995 1.1396774053573608 True -3 10988 29.690919876098633 0.5631279945373535 1415.99462890625 0.42336297035217285 1984.350341796875 0.4710463881492615 0.8202235 0.7006851434707642 True -4 13735 29.757686138153076 0.564908504486084 1638.755615234375 0.5120358467102051 1960.0404052734375 0.478963166475296 0.82114154 0.7233995199203491 True -5 16482 29.689225912094116 0.5615649223327637 1776.155029296875 0.6274439692497253 1942.5887451171875 0.4814368486404419 0.82933515 0.5622479915618896 True -6 19229 29.688441514968872 0.56192946434021 1417.65478515625 0.7001267671585083 1928.7501220703125 0.4847734272480011 0.82848746 0.4709259569644928 False -7 21976 29.735127449035645 0.5541443824768066 1643.61572265625 0.5727171897888184 1923.458251953125 0.48632195591926575 0.8341954 0.42839711904525757 True -8 24723 29.700658082962036 0.5656485557556152 1603.060302734375 0.4066486954689026 1901.2991943359375 0.49335137009620667 0.8359376 0.3845256567001343 True -9 27470 29.7233624458313 0.5658352375030518 1636.6729736328125 0.42800384759902954 1896.72802734375 0.49476173520088196 0.83383983 0.36369115114212036 False -10 30217 29.675782442092896 0.5623443126678467 1716.989501953125 0.20786216855049133 1881.2054443359375 0.49881699681282043 0.84071547 0.34751617908477783 True -11 32964 29.720591068267822 0.5620570182800293 1584.9771728515625 0.444504976272583 1872.326171875 0.5007972121238708 0.84514505 0.32567867636680603 True -12 35711 29.721227169036865 0.565772533416748 1637.468994140625 0.40184083580970764 1858.3773193359375 0.5057575702667236 0.8510662 0.31766167283058167 True -13 38458 29.804022550582886 0.5654139518737793 1494.6356201171875 0.2748960852622986 1852.8111572265625 0.5055455565452576 0.85722023 0.29763364791870117 True -14 41205 29.805009365081787 0.9964690208435059 1676.908203125 0.4473513066768646 1842.744384765625 0.5089978575706482 0.8628263 0.2887716591358185 True -15 43952 29.926822185516357 35.11313486099243 1435.5653076171875 0.2875906527042389 1836.227294921875 0.5111478567123413 0.86998564 0.27129167318344116 True -16 46699 29.82615637779236 1.0180225372314453 1502.381103515625 0.2000821828842163 1835.5284423828125 0.510490894317627 0.87300885 0.26752716302871704 True -17 49446 29.83932328224182 0.6649820804595947 1527.54052734375 0.17883092164993286 1829.0548095703125 0.5131208896636963 0.8764042 0.2629905641078949 True -18 52193 29.741918802261353 0.5627851486206055 1635.27099609375 0.28979063034057617 1833.058349609375 0.5119778513908386 0.87766975 0.2615760266780853 True -19 54940 29.757801294326782 0.5644400119781494 1455.6553955078125 0.15856751799583435 1825.9061279296875 0.5153244733810425 0.876456 0.26262831687927246 False diff --git a/ENCSR963ALV/cherimoya.fold_0.performance.tsv b/ENCSR963ALV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 053fdd44c13af4959cf7dbb97e6779ed105b3fce..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1833.058349609375 0.27617737650871277 0.5119778513908386 0.2871062159538269 0.8776697516441345 0.8310842514038086 0.2615760266780853 \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_1.evaluate.json b/ENCSR963ALV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index b84ac723f6ff1e696208cea13bdaf955e8533fd9..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF352VPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_1.fit.json b/ENCSR963ALV/cherimoya.fold_1.fit.json deleted file mode 100644 index c77582a4e1b8c3744fc7d6c63d0a8417e63cf8f9..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF352VPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_1.log b/ENCSR963ALV/cherimoya.fold_1.log deleted file mode 100644 index d7ed382b5665c766b27f59cb3a0b45bc84015522..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2718 34.59747362136841 3.7537014484405518 1714.422119140625 0.5580757856369019 3042.847412109375 0.3307496905326843 0.7231566 14.231731414794922 True -1 5436 30.02330446243286 6.907140016555786 1749.02880859375 0.5662657022476196 2466.92724609375 0.46196556091308594 0.7885633 3.0409624576568604 True -2 8154 29.584800481796265 0.7107164859771729 1360.76416015625 0.5886661410331726 2392.061767578125 0.47902122139930725 0.80677444 1.3191272020339966 True -3 10872 29.570114135742188 0.688054084777832 1569.2010498046875 0.5583154559135437 2336.635009765625 0.4887377917766571 0.8183671 0.812515377998352 True -4 13590 29.51066255569458 0.7006680965423584 1663.319091796875 0.5353795886039734 2303.296630859375 0.49646812677383423 0.82744557 0.6457330584526062 True -5 16308 29.455435514450073 0.711845874786377 1809.344482421875 0.45076924562454224 2271.360107421875 0.5035193562507629 0.83447695 0.575954020023346 True -6 19026 29.39845871925354 0.684316873550415 1750.92822265625 0.5745609998703003 2261.40283203125 0.5062308311462402 0.83863294 0.5221430063247681 True -7 21744 29.41087532043457 0.674614429473877 1581.9566650390625 0.4006146490573883 2251.810302734375 0.5085806250572205 0.8408281 0.4534528851509094 True -8 24462 29.414199113845825 0.677987813949585 1619.99951171875 0.38766998052597046 2226.1630859375 0.5145500302314758 0.8396808 0.4252854883670807 False -9 27180 29.48341941833496 0.6915929317474365 1472.168701171875 0.32168716192245483 2214.427001953125 0.5176666975021362 0.8425351 0.4017912447452545 True -10 29898 29.38133978843689 0.6686344146728516 1352.856201171875 0.3604201674461365 2193.189697265625 0.521834135055542 0.85096943 0.3638416528701782 True -11 32616 29.42834782600403 0.6896474361419678 1520.607421875 0.4549815058708191 2178.203369140625 0.5251119136810303 0.85466176 0.3407522141933441 True -12 35334 29.481484413146973 30.88019633293152 1685.9853515625 0.3544050455093384 2164.7900390625 0.5287750959396362 0.8602028 0.3260403871536255 True -13 38052 30.285563945770264 0.6839199066162109 1816.794189453125 0.3073399066925049 2157.425537109375 0.529351532459259 0.8656853 0.3172907829284668 True -14 40770 29.47795271873474 0.6846332550048828 1306.7855224609375 0.2935686409473419 2141.648193359375 0.5336255431175232 0.8710291 0.2982028126716614 True -15 43488 29.437439918518066 0.6970305442810059 1328.11083984375 0.32753318548202515 2134.130126953125 0.5339423418045044 0.87816787 0.2870262861251831 True -16 46206 29.514014720916748 0.6851644515991211 1411.2080078125 0.2534679174423218 2129.9638671875 0.535815954208374 0.8827578 0.27873173356056213 True -17 48924 29.571289777755737 0.6872820854187012 1244.9085693359375 0.3065805435180664 2132.193115234375 0.533993124961853 0.8841387 0.2766090929508209 True -18 51642 29.46864604949951 1.116670846939087 1324.5560302734375 0.14905470609664917 2132.61376953125 0.5345949530601501 0.88544333 0.2775263488292694 True -19 54360 29.46814465522766 0.6863634586334229 1352.707763671875 0.17684002220630646 2130.781982421875 0.5351830720901489 0.88742155 0.2777560353279114 True diff --git a/ENCSR963ALV/cherimoya.fold_1.performance.tsv b/ENCSR963ALV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 311016c0080cc59b797f0994a54ff2442e3c7658..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -2130.781982421875 0.2533918023109436 0.5351831316947937 0.32318103313446045 0.8874215483665466 0.8634719252586365 0.2777560353279114 \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_2.evaluate.json b/ENCSR963ALV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1465a02c08603817791e7b58f586d05e2ab00b37..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF352VPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_2.fit.json b/ENCSR963ALV/cherimoya.fold_2.fit.json deleted file mode 100644 index 6c17246ad7ed97ca7e109ac31a4ebbc17e93ab12..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF352VPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_2.log b/ENCSR963ALV/cherimoya.fold_2.log deleted file mode 100644 index 4f1c4b9a8a3e71246c9c94156d33789376b30ddd..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2872 36.02920413017273 3.507371664047241 1664.75830078125 0.4522227346897125 2630.7705078125 0.3280777633190155 0.72482204 13.1564302444458 True -1 5744 31.701776027679443 0.5519359111785889 1756.694580078125 0.6078882813453674 2142.316650390625 0.4523068964481354 0.7896544 2.7621243000030518 True -2 8616 31.435922861099243 0.5319967269897461 1605.4429931640625 0.6237555146217346 2083.4111328125 0.46842890977859497 0.8032989 0.9504629969596863 True -3 11488 31.342291116714478 0.5337958335876465 2044.0478515625 0.5176341533660889 2038.97607421875 0.4786807894706726 0.8148866 0.6601924300193787 True -4 14360 31.059487342834473 0.5319027900695801 1708.704833984375 0.5616674423217773 2027.6019287109375 0.48159343004226685 0.8158243 0.4976690113544464 True -5 17232 31.089502334594727 0.5389752388000488 1518.3564453125 0.6634031534194946 2018.71044921875 0.4830980896949768 0.82048774 0.4625062942504883 True -6 20104 31.11123538017273 0.5360667705535889 1683.5455322265625 0.44362732768058777 1998.760498046875 0.4885883927345276 0.8231947 0.4201262891292572 True -7 22976 31.179264068603516 0.7860748767852783 1624.6826171875 0.2559136152267456 1971.7296142578125 0.49691760540008545 0.82899255 0.3972223103046417 True -8 25848 31.234184503555298 7.8346874713897705 1737.9412841796875 0.3412231206893921 1971.2896728515625 0.4947251081466675 0.832019 0.4071699380874634 True -9 28720 31.271177768707275 17.05664563179016 1717.327392578125 0.34662172198295593 1952.5491943359375 0.5008595585823059 0.8348396 0.3551584780216217 True -10 31592 31.377277851104736 0.5445816516876221 1395.074951171875 0.5108577013015747 1941.9383544921875 0.5035532116889954 0.8395412 0.34508541226387024 True -11 34464 31.126470804214478 0.553657054901123 1468.6982421875 0.30969247221946716 1925.09521484375 0.509146511554718 0.8484494 0.335252583026886 True -12 37336 31.339205503463745 0.55661940574646 1899.099853515625 0.24028918147087097 1920.220703125 0.5101763606071472 0.8518251 0.33015361428260803 True -13 40208 31.28752613067627 0.5432403087615967 1495.8212890625 0.2744508385658264 1909.87109375 0.5131588578224182 0.8555606 0.3099920451641083 True -14 43080 31.278064966201782 0.5436735153198242 1457.119873046875 0.2017323225736618 1901.31591796875 0.515015184879303 0.86227715 0.2954995334148407 True -15 45952 31.252469301223755 0.5416679382324219 1480.208740234375 0.25725656747817993 1892.4566650390625 0.516147255897522 0.8675734 0.2841823101043701 True -16 48824 31.27295446395874 0.5458786487579346 1449.758056640625 0.18846824765205383 1889.5792236328125 0.5171809196472168 0.87313545 0.2779082655906677 True -17 51696 31.405040979385376 0.5585963726043701 1252.5626220703125 0.19399118423461914 1897.2935791015625 0.5138979554176331 0.87502533 0.2747274339199066 True -18 54568 31.186310529708862 0.5403304100036621 1501.860595703125 0.32632628083229065 1888.8060302734375 0.517787516117096 0.8748013 0.2740549147129059 False -19 57440 31.195060968399048 0.5339312553405762 1606.9130859375 0.20748788118362427 1895.4932861328125 0.5148927569389343 0.8748313 0.2742772102355957 False diff --git a/ENCSR963ALV/cherimoya.fold_2.performance.tsv b/ENCSR963ALV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a47d1e0924c8372578650caf3b2f3a6ce25b201e..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1897.2935791015625 0.2712485194206238 0.5138979554176331 0.29332900047302246 0.8750253319740295 0.8353273868560791 0.2747274339199066 \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_3.evaluate.json b/ENCSR963ALV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a85edf6bb190b3584e178827f2f2e1028e65d2c1..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF352VPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_3.fit.json b/ENCSR963ALV/cherimoya.fold_3.fit.json deleted file mode 100644 index 1730168f00629e8dfa9b2ebc7649c83b85ebc8bd..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF352VPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_3.log b/ENCSR963ALV/cherimoya.fold_3.log deleted file mode 100644 index 3bcbe772ca02ffb1fcf3890d14f97c765fc565c8..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 34.96157479286194 4.912392616271973 1856.1572265625 0.38409924507141113 2573.26171875 0.32308387756347656 0.7295338 13.001362800598145 True -1 5544 30.703389883041382 0.5876004695892334 1520.6824951171875 0.5185403227806091 2139.894775390625 0.4440748691558838 0.7849803 2.075965642929077 True -2 8316 30.239412784576416 0.6570289134979248 1793.739013671875 0.5769407749176025 2068.763671875 0.46309974789619446 0.798871 0.9688439965248108 True -3 11088 30.189033031463623 0.5373835563659668 1747.915283203125 0.419059157371521 2038.6915283203125 0.46879100799560547 0.8120106 0.6203051805496216 True -4 13860 30.09731411933899 0.5333473682403564 1711.2620849609375 0.4824759364128113 2015.1693115234375 0.47514665126800537 0.819073 0.5126645565032959 True -5 16632 29.93815588951111 0.526139497756958 1804.5562744140625 0.34802761673927307 1994.949951171875 0.48254716396331787 0.82311636 0.5095643997192383 True -6 19404 29.947322607040405 0.5223972797393799 1494.39697265625 0.23811280727386475 1979.2996826171875 0.4861707091331482 0.82534534 0.469656765460968 True -7 22176 29.950730562210083 0.5288386344909668 1787.43505859375 0.4954777956008911 1970.2977294921875 0.4884505867958069 0.82468015 0.4704279601573944 False -8 24948 29.97109365463257 0.5218150615692139 1615.4268798828125 0.3696816563606262 1957.7686767578125 0.4918411672115326 0.8230186 0.4215503931045532 False -9 27720 30.018005847930908 2.850756883621216 1505.1116943359375 0.3634074032306671 1943.5106201171875 0.4959198832511902 0.82803464 0.40566813945770264 True -10 30492 29.961202383041382 0.5242717266082764 1619.9822998046875 0.34824442863464355 1934.19677734375 0.49872711300849915 0.8328389 0.39469805359840393 True -11 33264 30.13958430290222 0.5429606437683105 1669.39794921875 0.46647560596466064 1926.5623779296875 0.4999556541442871 0.8386122 0.3856590688228607 True -12 36036 30.206481218338013 0.5291903018951416 1373.8321533203125 0.35160374641418457 1918.4012451171875 0.5016244053840637 0.84365183 0.36344781517982483 True -13 38808 30.310778379440308 0.5492854118347168 1549.1484375 0.4663446545600891 1909.646484375 0.5023339986801147 0.8514092 0.34454602003097534 True -14 41580 30.12586545944214 0.5349712371826172 1663.658935546875 0.332463800907135 1899.2347412109375 0.5063288807868958 0.85815376 0.3248918354511261 True -15 44352 30.1982741355896 26.191006422042847 1152.04248046875 0.15908104181289673 1892.558349609375 0.5072323083877563 0.86579865 0.3005589246749878 True -16 47124 31.6007182598114 0.5384550094604492 1477.5567626953125 0.29313600063323975 1892.7640380859375 0.5077479481697083 0.87177956 0.2897372841835022 True -17 49896 30.07926917076111 0.5372817516326904 1542.037841796875 0.21374540030956268 1886.3446044921875 0.5083390474319458 0.8746252 0.28025761246681213 True -18 52668 30.00576400756836 1.373579978942871 1386.163330078125 0.19540899991989136 1884.016845703125 0.5086812376976013 0.87671405 0.27503129839897156 True -19 55440 30.100764513015747 0.5358927249908447 1243.9622802734375 0.14323799312114716 1888.986083984375 0.5072158575057983 0.87844336 0.27401313185691833 True diff --git a/ENCSR963ALV/cherimoya.fold_3.performance.tsv b/ENCSR963ALV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index bcecb94961a62d28743507eeca0e7ad6629291e0..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1888.986083984375 0.27608755230903625 0.5072158575057983 0.28865891695022583 0.8784433603286743 0.8338049650192261 0.27401313185691833 \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_4.evaluate.json b/ENCSR963ALV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6e486ae8374f8671dfcdf9e5a5625200e8292771..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF352VPL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_4.fit.json b/ENCSR963ALV/cherimoya.fold_4.fit.json deleted file mode 100644 index fe5c29b21a0feafe2f743ab04f4f6004e859aa76..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF352VPL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR963ALV/cherimoya.fold_4.log b/ENCSR963ALV/cherimoya.fold_4.log deleted file mode 100644 index 785d1bfbc1e5bd465600596c52c1315ba8a4f119..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2822 35.849971294403076 3.6151323318481445 1828.650634765625 0.6916342973709106 2417.041259765625 0.321012020111084 0.72175735 10.652814865112305 True -1 5644 31.153502464294434 1.2544336318969727 1569.1873779296875 0.6742936968803406 1995.9522705078125 0.439595103263855 0.78171974 2.499429941177368 True -2 8466 30.82997488975525 0.5623519420623779 1588.994873046875 0.697502613067627 1942.713134765625 0.4578535854816437 0.80039674 0.8423845767974854 True -3 11288 30.535434246063232 0.5647218227386475 1574.367431640625 0.3719589412212372 1904.0810546875 0.46836817264556885 0.8122442 0.55510413646698 True -4 14110 31.13456153869629 35.82184982299805 1668.1641845703125 0.3730678856372833 1885.6260986328125 0.4745507538318634 0.8212766 0.42002856731414795 True -5 16932 30.63916850090027 0.5869505405426025 1592.892822265625 0.39388784766197205 1864.900390625 0.480739951133728 0.8203998 0.35742905735969543 False -6 19754 30.606436729431152 0.5560407638549805 1682.1219482421875 0.5137606859207153 1855.432373046875 0.483871728181839 0.8264463 0.33717164397239685 True -7 22576 30.509565591812134 0.9231092929840088 2147.298828125 0.4745464324951172 1845.74755859375 0.486541748046875 0.8278914 0.33220192790031433 True -8 25398 30.60968804359436 2.053109645843506 1660.340087890625 0.33092862367630005 1835.8570556640625 0.48927637934684753 0.83640146 0.326593279838562 True -9 28220 30.676188230514526 1.1217753887176514 1630.2113037109375 0.4549643099308014 1830.0462646484375 0.49142515659332275 0.837359 0.3231448233127594 True -10 31042 30.978147268295288 0.5886359214782715 1532.5009765625 0.38965511322021484 1824.16796875 0.49124035239219666 0.8413386 0.30825892090797424 True -11 33864 30.48786425590515 0.5459244251251221 1333.3446044921875 0.46042853593826294 1812.6463623046875 0.49498727917671204 0.8447598 0.29992449283599854 True -12 36686 30.514484882354736 0.5617127418518066 1518.84130859375 0.3436548709869385 1804.0765380859375 0.49700114130973816 0.8533998 0.28568539023399353 True -13 39508 30.481106996536255 1.4332475662231445 1467.730712890625 0.21803684532642365 1800.4913330078125 0.4984991252422333 0.85865396 0.271770715713501 True -14 42330 30.585937023162842 0.5601918697357178 1367.089599609375 0.23798270523548126 1794.9122314453125 0.4997480809688568 0.8652949 0.26669254899024963 True -15 45152 30.53124237060547 0.5632708072662354 1390.03271484375 0.18828412890434265 1781.61865234375 0.5040796399116516 0.86968094 0.2559378445148468 True -16 47974 30.569801568984985 0.5688571929931641 1175.5552978515625 0.1546413004398346 1786.479736328125 0.501875102519989 0.87435836 0.24924162030220032 True -17 50796 30.535964250564575 0.5564916133880615 1603.2412109375 0.2889859080314636 1783.086181640625 0.5031059980392456 0.87665284 0.24587160348892212 True -18 53618 30.532530784606934 0.5696580410003662 1465.2894287109375 0.2306670844554901 1781.5963134765625 0.5039533376693726 0.8770955 0.24371911585330963 True -19 56440 30.548627853393555 0.5597870349884033 1445.621337890625 0.29212820529937744 1786.5267333984375 0.5015259385108948 0.87629145 0.2446819692850113 False diff --git a/ENCSR963ALV/cherimoya.fold_4.performance.tsv b/ENCSR963ALV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index cb333599d748f0b14395c9e69a20f1f9c1e4561c..0000000000000000000000000000000000000000 --- a/ENCSR963ALV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1781.5963134765625 0.2803676128387451 0.5039533376693726 0.27986565232276917 0.8770955204963684 0.8240529298782349 0.24371911585330963 \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_0.evaluate.json b/ENCSR964MZQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index e4bbb94090672182b0b74723801bd05892c50338..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373KQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_0.fit.json b/ENCSR964MZQ/cherimoya.fold_0.fit.json deleted file mode 100644 index 6c8adafe11bc3aebc8bbe3e51d9dfc7e7a6a3b93..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF373KQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_0.log b/ENCSR964MZQ/cherimoya.fold_0.log deleted file mode 100644 index fa9366b16efa4132b1293e58a71c8ba6dca7c5d4..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2709 33.753761529922485 3.5546000003814697 1593.193115234375 0.7681368589401245 2244.672607421875 0.2708008587360382 0.49869573 13.312071800231934 True -1 5418 30.192201852798462 0.5607917308807373 1626.1058349609375 0.6520054340362549 1887.16162109375 0.42311909794807434 0.56952417 4.7504425048828125 True -2 8127 30.232537984848022 0.5444536209106445 1555.6949462890625 0.7384552359580994 1837.6181640625 0.4365391135215759 0.58634645 1.9883207082748413 True -3 10836 30.12774896621704 0.5396449565887451 1716.3450927734375 0.6433758735656738 1812.3577880859375 0.4452083110809326 0.5997801 1.5782088041305542 True -4 13545 30.09729790687561 0.8321547508239746 1285.566650390625 0.6629059910774231 1800.7801513671875 0.44860583543777466 0.6123027 1.1664320230484009 True -5 16254 30.116774797439575 0.5319557189941406 1547.65185546875 0.5564284324645996 1790.2532958984375 0.4540614187717438 0.616353 1.1966618299484253 True -6 18963 30.161186695098877 2.74834942817688 1363.033447265625 0.9900444746017456 1781.6883544921875 0.4579303562641144 0.6242768 1.1617095470428467 True -7 21672 30.160994052886963 23.348501205444336 1366.8048095703125 0.6637244820594788 1782.443115234375 0.45804452896118164 0.62691784 1.0545551776885986 True -8 24381 30.14125680923462 0.5468354225158691 1628.156005859375 0.4279325008392334 1772.2659912109375 0.46250295639038086 0.63374454 0.9833678007125854 True -9 27090 30.115110874176025 0.5495357513427734 1374.996826171875 0.5861042737960815 1764.869384765625 0.4656805396080017 0.6365239 0.8212785720825195 True -10 29799 30.158759355545044 0.5368797779083252 1459.5087890625 0.5197851657867432 1761.485595703125 0.46633392572402954 0.647426 0.7450687289237976 True -11 32508 30.24059748649597 0.547321081161499 1341.7978515625 0.36243095993995667 1747.7113037109375 0.4725266993045807 0.65752727 0.6574957370758057 True -12 35217 30.207066297531128 0.5430068969726562 1526.62353515625 0.3975480794906616 1746.1240234375 0.4710609018802643 0.6676582 0.5840145945549011 True -13 37926 30.14179229736328 0.5348937511444092 1448.5721435546875 0.36099767684936523 1737.802490234375 0.4748702049255371 0.6793412 0.5109570026397705 True -14 40635 30.085501194000244 0.5343632698059082 1303.229736328125 0.28107136487960815 1730.0035400390625 0.47752395272254944 0.6881906 0.45601242780685425 True -15 43344 30.138429641723633 0.541236400604248 1245.8336181640625 0.3339790999889374 1725.760498046875 0.4787101745605469 0.6995384 0.41267332434654236 True -16 46053 30.143315076828003 0.5443015098571777 1545.7587890625 0.26023659110069275 1722.1138916015625 0.4797925651073456 0.7096966 0.37459856271743774 True -17 48762 30.105714082717896 0.5429055690765381 1537.7637939453125 0.38222062587738037 1719.0526123046875 0.48150140047073364 0.71560746 0.35365474224090576 True -18 51471 30.168067455291748 0.5420622825622559 1397.9254150390625 0.28308773040771484 1719.82080078125 0.48108670115470886 0.7160581 0.3440270721912384 True -19 54180 30.121397972106934 0.5453135967254639 1273.7220458984375 0.3718488812446594 1719.0318603515625 0.4819518029689789 0.71637243 0.3400518298149109 True diff --git a/ENCSR964MZQ/cherimoya.fold_0.performance.tsv b/ENCSR964MZQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5a35b1cd5f5d698aabe5469197068a36ad7867d2..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1719.0318603515625 0.2818337678909302 0.4819518029689789 0.28059229254722595 0.7163724303245544 0.665546178817749 0.3400518298149109 \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_1.evaluate.json b/ENCSR964MZQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 8cb3f86a4dfa24b0ff0dbd2583d5b6c16c7c0f9b..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373KQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_1.fit.json b/ENCSR964MZQ/cherimoya.fold_1.fit.json deleted file mode 100644 index b741b61d9badb929fe47a1da3572463a0b61aac0..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF373KQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_1.log b/ENCSR964MZQ/cherimoya.fold_1.log deleted file mode 100644 index 64707d180d2dbd702bff2f0e2cc6074f6118ae32..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2725 34.53611874580383 4.11591649055481 1670.46142578125 1.194244146347046 2418.56005859375 0.2701733708381653 0.50938123 12.801490783691406 True -1 5450 30.37557578086853 6.279436826705933 1689.765380859375 0.725486695766449 2031.716796875 0.4297923445701599 0.60243624 3.8404786586761475 True -2 8175 30.37845540046692 35.39429521560669 1427.9915771484375 0.714521050453186 1978.7122802734375 0.4435974955558777 0.6102945 2.104713201522827 True -3 10900 30.396576404571533 22.081013917922974 1681.7281494140625 0.7795130610466003 1951.224365234375 0.4503917992115021 0.6235655 1.375443696975708 True -4 13625 30.438835382461548 0.7177262306213379 1457.01123046875 0.5986158847808838 1937.2196044921875 0.45579683780670166 0.6346613 1.3342726230621338 True -5 16350 30.37134838104248 0.7112720012664795 1629.740478515625 0.6291351318359375 1926.234130859375 0.45965614914894104 0.6503072 1.241001009941101 True -6 19075 30.263684272766113 7.173848867416382 1319.347900390625 0.3872819244861603 1915.1298828125 0.4635108411312103 0.6598984 0.9176539778709412 True -7 21800 31.47907543182373 0.7353346347808838 1376.51806640625 0.5448446273803711 1902.044677734375 0.46940627694129944 0.66285884 0.8746118545532227 True -8 24525 30.29629898071289 0.7043697834014893 1428.7139892578125 0.47991809248924255 1890.0667724609375 0.4732547402381897 0.668764 0.8009987473487854 True -9 27250 30.268516302108765 0.7047474384307861 1254.87744140625 0.4760845899581909 1886.8282470703125 0.4744970500469208 0.66812426 0.7886201739311218 False -10 29975 30.34539008140564 0.7021005153656006 1376.9317626953125 0.4789363443851471 1882.6922607421875 0.4752207398414612 0.67668647 0.7384265065193176 True -11 32700 30.333922386169434 0.6924962997436523 1344.8853759765625 0.4229736328125 1869.671630859375 0.48021334409713745 0.6848976 0.6494040489196777 True -12 35425 30.365717887878418 0.691216230392456 1491.6689453125 0.4788331091403961 1860.9625244140625 0.48271679878234863 0.69363475 0.6307976841926575 True -13 38150 30.305609226226807 0.6879289150238037 1384.962890625 0.3572648763656616 1852.937255859375 0.4856184124946594 0.7031125 0.5574581623077393 True -14 40875 30.28385090827942 0.7066879272460938 1348.48388671875 0.48071056604385376 1842.5556640625 0.4900366961956024 0.71502656 0.4971157908439636 True -15 43600 30.325734853744507 1.219391107559204 1185.8896484375 0.4703032970428467 1840.3563232421875 0.4890426695346832 0.7287525 0.4368748366832733 True -16 46325 30.335007905960083 0.706179141998291 1239.548583984375 0.3085857927799225 1835.9273681640625 0.490599125623703 0.73771507 0.38962700963020325 True -17 49050 30.340449810028076 1.4112586975097656 1356.280517578125 0.3682904839515686 1832.7041015625 0.4911993741989136 0.74166214 0.37060651183128357 True -18 51775 30.335870265960693 0.7083423137664795 1167.30322265625 0.2995303273200989 1828.749267578125 0.4936358332633972 0.74388117 0.3565599322319031 True -19 54500 30.321959495544434 0.6986010074615479 1467.73876953125 0.3988070785999298 1834.439453125 0.49037671089172363 0.74255574 0.3563888967037201 False diff --git a/ENCSR964MZQ/cherimoya.fold_1.performance.tsv b/ENCSR964MZQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c8b55aa6b3d37c8ee63ed49d2fd5db9ff91fe14d..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1828.749267578125 0.2735227644443512 0.4936358332633972 0.29463768005371094 0.7438811659812927 0.7083589434623718 0.3565599322319031 \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_2.evaluate.json b/ENCSR964MZQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index cc6b31bd90b0fc28fa16bb16bc29c2f9d82019d8..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373KQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_2.fit.json b/ENCSR964MZQ/cherimoya.fold_2.fit.json deleted file mode 100644 index 050d21e512a3f1e200f0a9b766eacebcb1bd7e71..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF373KQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_2.log b/ENCSR964MZQ/cherimoya.fold_2.log deleted file mode 100644 index d0a73ca823b0e78ddf75acbd702118e001c0b45a..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2869 35.62496280670166 3.7730143070220947 1361.327880859375 0.7002593278884888 2297.711181640625 0.2819526493549347 0.48983586 10.719101905822754 True -1 5738 31.951631784439087 0.5640337467193604 1630.177734375 1.0633976459503174 1941.5648193359375 0.4319654405117035 0.54005253 4.307916164398193 True -2 8607 31.919408559799194 0.5418140888214111 1486.66064453125 0.5554991960525513 1893.0150146484375 0.445209801197052 0.567678 1.9779767990112305 True -3 11476 31.93476176261902 0.5400621891021729 1369.4937744140625 0.7861591577529907 1877.78466796875 0.4493634104728699 0.5830062 1.3551403284072876 True -4 14345 31.904510974884033 0.5487949848175049 1517.091552734375 0.5612245798110962 1860.20068359375 0.4557217061519623 0.5965644 1.1648889780044556 True -5 17214 31.888989686965942 2.027066707611084 1325.5966796875 0.4362121820449829 1854.737060546875 0.4574034512042999 0.61104566 1.1302909851074219 True -6 20083 31.917312383651733 0.5362341403961182 1454.5537109375 0.5284627676010132 1840.76025390625 0.46477991342544556 0.61695206 1.2981791496276855 True -7 22952 31.84901189804077 0.5379898548126221 1492.5428466796875 0.5057394504547119 1831.071533203125 0.46691736578941345 0.62588745 0.905116081237793 True -8 25821 31.91456151008606 0.5358889102935791 1692.367919921875 0.39677801728248596 1825.2674560546875 0.4689033031463623 0.6336826 0.8664216995239258 True -9 28690 31.850257635116577 0.5645449161529541 1329.5888671875 0.4380459785461426 1817.3541259765625 0.47232428193092346 0.6412247 0.7947624325752258 True -10 31559 31.85028624534607 0.5455322265625 1200.403076171875 0.3699125349521637 1810.6602783203125 0.47517263889312744 0.64616627 0.7653940916061401 True -11 34428 31.841197967529297 0.542905330657959 1322.49658203125 0.48063984513282776 1807.2109375 0.4745018780231476 0.65202016 0.6683780550956726 True -12 37297 31.931209802627563 0.5479464530944824 1385.723388671875 0.4242161512374878 1797.8013916015625 0.4781435430049896 0.66264427 0.6120962500572205 True -13 40166 31.908392667770386 0.5628139972686768 1286.2186279296875 0.375659316778183 1787.1292724609375 0.48267948627471924 0.6738227 0.5634152889251709 True -14 43035 31.896075963974 0.5464351177215576 1439.321044921875 0.48980796337127686 1779.876953125 0.4841375946998596 0.6878536 0.4968962073326111 True -15 45904 31.975622415542603 0.5449719429016113 1376.2188720703125 0.3444010019302368 1775.2982177734375 0.4849836826324463 0.6986908 0.446872740983963 True -16 48773 31.93362283706665 0.5445656776428223 1296.00927734375 0.33356112241744995 1770.548095703125 0.48676878213882446 0.70981133 0.40355968475341797 True -17 51642 31.900728940963745 0.564528226852417 1475.264404296875 0.3374063968658447 1767.1099853515625 0.487843781709671 0.7149071 0.3755364418029785 True -18 54511 31.95194983482361 0.5516777038574219 1671.10986328125 0.20758333802223206 1770.39892578125 0.485650897026062 0.71876186 0.3634984791278839 True -19 57380 31.901108980178833 1.4336833953857422 1497.333740234375 0.28218957781791687 1769.3526611328125 0.4868243634700775 0.71816856 0.35945001244544983 False diff --git a/ENCSR964MZQ/cherimoya.fold_2.performance.tsv b/ENCSR964MZQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index fdf18a3562e3d883224b081649d3cd63deb890ae..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1770.39892578125 0.27812764048576355 0.4856509268283844 0.2908097505569458 0.7187618613243103 0.6761820316314697 0.3634984791278839 \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_3.evaluate.json b/ENCSR964MZQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2e90b89ecdbbe7a1a46e2d8f87166c46eb24ca02..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373KQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_3.fit.json b/ENCSR964MZQ/cherimoya.fold_3.fit.json deleted file mode 100644 index 4ee9107ef5b0839f69cf0f61ce14ee5ddc3237d8..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF373KQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_3.log b/ENCSR964MZQ/cherimoya.fold_3.log deleted file mode 100644 index 89fc506e36f3a06db4b2ac627170c380711c4f5b..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2799 35.43173813819885 3.5783958435058594 1620.06396484375 0.6937843561172485 2224.9716796875 0.28610506653785706 0.52006197 11.671219825744629 True -1 5598 31.254021167755127 0.589118480682373 1383.795654296875 0.9082257747650146 1896.556640625 0.4265168011188507 0.594573 4.475254535675049 True -2 8397 31.228355884552002 0.7368650436401367 1131.11669921875 0.5788974761962891 1857.600830078125 0.4410008192062378 0.5889354 2.4222726821899414 False -3 11196 31.297699213027954 2.177046060562134 1367.3487548828125 0.8968014717102051 1831.9774169921875 0.4486261010169983 0.60654557 1.4984147548675537 True -4 13995 31.203407287597656 0.5949525833129883 1604.545166015625 0.514050304889679 1821.6121826171875 0.452314168214798 0.61900055 1.1077543497085571 True -5 16794 31.16577911376953 0.5906383991241455 1543.7708740234375 0.49107685685157776 1811.4097900390625 0.4562166631221771 0.6250498 1.367504358291626 True -6 19593 31.32178258895874 17.33083486557007 1359.5255126953125 0.3611854910850525 1807.6182861328125 0.4577594995498657 0.62738323 0.8221360445022583 True -7 22392 31.26464295387268 0.5924081802368164 1303.4344482421875 0.7308489084243774 1802.39599609375 0.45911121368408203 0.62417424 0.7707470655441284 False -8 25191 31.31889533996582 0.5881030559539795 1748.03125 0.48875951766967773 1792.7769775390625 0.4640869200229645 0.628487 0.791922390460968 True -9 27990 31.248096466064453 0.5839681625366211 1643.56103515625 0.6712435483932495 1782.7198486328125 0.46867579221725464 0.6331039 0.6993961334228516 True -10 30789 31.105931282043457 0.5748443603515625 1387.45703125 0.46993488073349 1778.4613037109375 0.4695374071598053 0.64438546 0.665876030921936 True -11 33588 31.130478620529175 0.5649585723876953 1415.7626953125 0.6128954291343689 1767.5640869140625 0.4738943874835968 0.66142035 0.5947961807250977 True -12 36387 31.187833547592163 0.5724854469299316 1378.537353515625 0.6025411486625671 1758.2642822265625 0.47623583674430847 0.6805817 0.531147301197052 True -13 39186 31.133758306503296 0.5649192333221436 1475.166015625 0.3766007125377655 1750.0687255859375 0.4795432984828949 0.6888899 0.5006475448608398 True -14 41985 31.201760053634644 0.5717344284057617 1334.7720947265625 0.4398201107978821 1745.06494140625 0.48120352625846863 0.7058396 0.45466670393943787 True -15 44784 31.133832693099976 0.57059645652771 1233.6197509765625 0.41251713037490845 1738.64697265625 0.48318538069725037 0.7179773 0.40979620814323425 True -16 47583 31.128859281539917 0.5684630870819092 1366.33203125 0.3904348909854889 1736.3553466796875 0.4837227463722229 0.72603846 0.3799392580986023 True -17 50382 31.13539433479309 0.5627827644348145 1464.1563720703125 0.4959847629070282 1729.874267578125 0.48702356219291687 0.7321384 0.35905539989471436 True -18 53181 31.078320026397705 0.5729267597198486 1336.8262939453125 0.31202614307403564 1736.4755859375 0.4826439619064331 0.73270047 0.35010194778442383 True -19 55980 31.113723516464233 0.5709710121154785 1450.560302734375 0.29281124472618103 1731.3807373046875 0.48618191480636597 0.73425883 0.3483847975730896 True diff --git a/ENCSR964MZQ/cherimoya.fold_3.performance.tsv b/ENCSR964MZQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 68d08197334f2e68e3bdc63916f684484a882b65..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1731.3807373046875 0.2767738401889801 0.48618194460868835 0.2876419723033905 0.7342588305473328 0.6909165978431702 0.3483847975730896 \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_4.evaluate.json b/ENCSR964MZQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3c46ad0b6f7f35238c43061634a84f14b5f3a875..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF373KQQ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_4.fit.json b/ENCSR964MZQ/cherimoya.fold_4.fit.json deleted file mode 100644 index c4eb984e446d356c63f3fae8610c10a39cbb3850..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF373KQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964MZQ/cherimoya.fold_4.log b/ENCSR964MZQ/cherimoya.fold_4.log deleted file mode 100644 index 0a46b7bc439e40fdb26cf07bd0deae94f3e20bc0..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 35.19864296913147 3.6004106998443604 1403.97802734375 0.639918327331543 2185.169677734375 0.2710096836090088 0.5080662 10.520517349243164 True -1 5664 31.46714210510254 0.5454657077789307 1698.23388671875 0.775290846824646 1854.0948486328125 0.4211444854736328 0.56191295 4.231849193572998 True -2 8496 31.507503747940063 0.5387718677520752 1326.08642578125 0.46507036685943604 1812.6114501953125 0.43475574254989624 0.57317317 2.1072094440460205 True -3 11328 31.527697801589966 0.5336439609527588 1530.5673828125 0.4636462926864624 1788.5960693359375 0.4425821900367737 0.59411025 1.2757229804992676 True -4 14160 31.548829317092896 0.5332257747650146 1349.1375732421875 0.6797869801521301 1766.05419921875 0.45194578170776367 0.6109093 0.8891183137893677 True -5 16992 31.48995327949524 0.5286116600036621 1350.2412109375 0.4447556734085083 1762.69921875 0.452875018119812 0.6193928 0.902773916721344 True -6 19824 31.732734441757202 12.455865859985352 1588.753173828125 0.5800215005874634 1751.3218994140625 0.4569222927093506 0.6302069 0.8338532447814941 True -7 22656 31.548360109329224 1.5956366062164307 1524.806884765625 0.5214006900787354 1745.0633544921875 0.4590971767902374 0.6407652 0.7495967149734497 True -8 25488 31.518420219421387 0.5367486476898193 1541.461181640625 0.5167739987373352 1736.0325927734375 0.4645783603191376 0.6446405 0.7321546673774719 True -9 28320 31.47187614440918 0.5388779640197754 1425.2293701171875 0.3617987334728241 1728.840087890625 0.4666293263435364 0.6506128 0.6435961127281189 True -10 31152 31.530802965164185 0.5352089405059814 1407.078857421875 0.48707491159439087 1727.2159423828125 0.46644264459609985 0.65484214 0.5828539729118347 True -11 33984 31.55413055419922 0.5381908416748047 1485.225830078125 0.44999366998672485 1713.4791259765625 0.47302818298339844 0.66543543 0.5372079014778137 True -12 36816 31.48599648475647 0.537057638168335 1366.705078125 0.4661022424697876 1711.4285888671875 0.4723196029663086 0.6730903 0.5346387028694153 True -13 39648 31.54811120033264 0.5303761959075928 1367.53564453125 0.39752352237701416 1706.7315673828125 0.47503989934921265 0.68261963 0.4808988869190216 True -14 42480 31.602258920669556 0.5623295307159424 1392.988037109375 0.4132465720176697 1702.6119384765625 0.4756948947906494 0.6928357 0.4393480122089386 True -15 45312 31.755647897720337 0.5701582431793213 1332.1737060546875 0.34607160091400146 1695.845703125 0.4788365364074707 0.7074819 0.39028695225715637 True -16 48144 31.58230185508728 0.5478436946868896 1338.83642578125 0.2628551125526428 1690.331787109375 0.4809238016605377 0.71432054 0.35909411311149597 True -17 50976 31.47793197631836 0.5330102443695068 1451.3582763671875 0.36749589443206787 1691.6544189453125 0.4791887700557709 0.7214006 0.3389054834842682 True -18 53808 31.48559546470642 0.5389163494110107 1341.0233154296875 0.2550252079963684 1689.207763671875 0.48097553849220276 0.72330654 0.33038485050201416 True -19 56640 31.438302040100098 0.5368258953094482 1159.10888671875 0.34347519278526306 1690.1785888671875 0.48060154914855957 0.72402674 0.32757285237312317 True diff --git a/ENCSR964MZQ/cherimoya.fold_4.performance.tsv b/ENCSR964MZQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 2ade06987d7c4f6f1d42319865d0f428b0e9117a..0000000000000000000000000000000000000000 --- a/ENCSR964MZQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1690.1785888671875 0.28204217553138733 0.48060157895088196 0.28023388981819153 0.7240267395973206 0.6726403832435608 0.32757285237312317 \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_0.evaluate.json b/ENCSR964VVW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 485706d5a09dcebbffea282b59cd8a3499398aaf..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF902LTL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_0.fit.json b/ENCSR964VVW/cherimoya.fold_0.fit.json deleted file mode 100644 index 51c194b361e8199603cd9f1f2b14b2a3e3872f53..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF902LTL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_0.log b/ENCSR964VVW/cherimoya.fold_0.log deleted file mode 100644 index 2c84b245a61c8a75c6c34d998696239bff93271a..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2744 33.96639966964722 2.4729514122009277 263.5550537109375 0.7762671709060669 342.31298828125 0.16498824954032898 0.4564957 4.253211498260498 True -1 5488 30.29646110534668 0.7825570106506348 283.3304443359375 0.8607518672943115 327.2082214355469 0.2307695746421814 0.56381583 0.9633786678314209 True -2 8232 30.27549910545349 0.5245094299316406 245.23593139648438 0.6729183197021484 323.7428283691406 0.24040305614471436 0.5809942 0.5649887919425964 True -3 10976 30.298558473587036 0.5232453346252441 279.6463317871094 0.7543133497238159 321.36810302734375 0.2477324903011322 0.5912748 0.5089757442474365 True -4 13720 30.26012110710144 0.590369462966919 258.44635009765625 0.6664341688156128 320.4673156738281 0.25045064091682434 0.5965163 0.5227583646774292 True -5 16464 30.222269773483276 0.5229446887969971 222.26522827148438 0.7538001537322998 319.9300842285156 0.25200599431991577 0.6030734 0.5478699803352356 True -6 19208 30.245544910430908 0.5278005599975586 260.04437255859375 0.48478519916534424 319.62841796875 0.2530965209007263 0.6127949 0.5406956076622009 True -7 21952 30.249959230422974 0.5227344036102295 254.46392822265625 0.5131736993789673 318.50164794921875 0.25815320014953613 0.61831695 0.5283547043800354 True -8 24696 30.24852991104126 0.5207598209381104 263.9144592285156 0.6932966113090515 318.19232177734375 0.2593872547149658 0.62763286 0.5324292778968811 True -9 27440 30.294777870178223 0.5148048400878906 225.775146484375 0.5481497645378113 317.21636962890625 0.26303544640541077 0.63276756 0.5171428918838501 True -10 30184 30.257319927215576 0.5254571437835693 277.43658447265625 0.5938711166381836 316.91650390625 0.264958918094635 0.6391225 0.5246475338935852 True -11 32928 30.297394514083862 0.6110672950744629 229.25782775878906 0.43466880917549133 316.42047119140625 0.2661462724208832 0.6484165 0.48465266823768616 True -12 35672 30.273216485977173 1.8933966159820557 269.78839111328125 0.42468997836112976 315.9642333984375 0.268192857503891 0.65934753 0.4717244505882263 True -13 38416 30.323999881744385 0.5024464130401611 257.60455322265625 0.3196246922016144 315.4554748535156 0.27021270990371704 0.66771924 0.4380452632904053 True -14 41160 30.262255430221558 0.527928352355957 208.41319274902344 0.4983300566673279 314.8333740234375 0.273275762796402 0.67866504 0.41587910056114197 True -15 43904 30.23817753791809 0.5468518733978271 219.25381469726562 0.4973286986351013 314.5225524902344 0.27407413721084595 0.6832145 0.41475391387939453 True -16 46648 30.298807621002197 0.5248205661773682 265.1156005859375 0.3917717933654785 314.40338134765625 0.2740004360675812 0.6917544 0.39376869797706604 True -17 49392 30.937365770339966 9.59378433227539 239.3955841064453 0.27622294425964355 314.729736328125 0.27288714051246643 0.6960333 0.3877820074558258 True -18 52136 30.34963631629944 0.5864267349243164 194.44540405273438 0.4676781892776489 314.83642578125 0.27260622382164 0.69446045 0.3905707001686096 False -19 54880 30.34176254272461 0.5206620693206787 262.95068359375 0.31392785906791687 314.9097900390625 0.2718540132045746 0.69516414 0.391249418258667 False diff --git a/ENCSR964VVW/cherimoya.fold_0.performance.tsv b/ENCSR964VVW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index eafab1a3797120a5106ba04fa6f266c5f228a9e6..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -314.729736328125 0.4865196943283081 0.27288714051246643 0.08560565114021301 0.6960332989692688 0.6778097748756409 0.3877820074558258 \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_1.evaluate.json b/ENCSR964VVW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9522554a36d5acdee3e9e7bb9a985235e9dff051..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF902LTL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_1.fit.json b/ENCSR964VVW/cherimoya.fold_1.fit.json deleted file mode 100644 index c7ea983c9502b99c299c71e206461ca306ba3e5d..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF902LTL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_1.log b/ENCSR964VVW/cherimoya.fold_1.log deleted file mode 100644 index cddba92848c231ad5c55fcd1aee67024f6a4d908..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2754 33.99942183494568 6.546995162963867 254.3597412109375 0.8761501908302307 378.60107421875 0.16963112354278564 0.49804953 5.312148094177246 True -1 5508 30.43796443939209 1.0478947162628174 279.43731689453125 0.8876938819885254 359.5550231933594 0.244772270321846 0.6058671 1.4345595836639404 True -2 8262 30.45103693008423 0.6851918697357178 262.7777099609375 0.7371204495429993 355.8392333984375 0.25365421175956726 0.63487226 0.7495630383491516 True -3 11016 30.45420265197754 0.6718912124633789 281.3379211425781 0.8141049742698669 353.274658203125 0.26108863949775696 0.6534655 0.7216387391090393 True -4 13770 30.33894991874695 0.6680042743682861 227.29718017578125 0.9169149398803711 351.7381591796875 0.2665066421031952 0.6594513 0.8144348859786987 True -5 16524 30.371147394180298 0.702167272567749 309.9189453125 0.4936892092227936 351.06219482421875 0.26888230443000793 0.663837 0.7626650333404541 True -6 19278 30.413753271102905 0.6700413227081299 315.09002685546875 0.6906391978263855 350.5950622558594 0.2703503370285034 0.66929704 0.7239159345626831 True -7 22032 30.33557438850403 0.6831021308898926 239.60009765625 0.46504634618759155 349.8050537109375 0.2726181447505951 0.6751994 0.6633297801017761 True -8 24786 30.366069555282593 0.6602070331573486 196.7798614501953 0.38612622022628784 348.98779296875 0.27574485540390015 0.6804438 0.6110347509384155 True -9 27540 30.36146831512451 0.6907410621643066 219.962158203125 0.563152551651001 348.51727294921875 0.2773534655570984 0.6884908 0.5786383748054504 True -10 30294 30.485102891921997 0.7105791568756104 216.953857421875 0.6851573586463928 348.0139465332031 0.27934470772743225 0.6948654 0.5583880543708801 True -11 33048 30.55375027656555 0.6958189010620117 278.4444580078125 0.8024272322654724 347.4492492675781 0.28174617886543274 0.70095086 0.5335765480995178 True -12 35802 31.708625555038452 0.6835358142852783 270.50689697265625 0.8363775014877319 346.8576354980469 0.28298208117485046 0.7080821 0.49490392208099365 True -13 38556 30.588956832885742 1.894270420074463 281.1080322265625 0.48000288009643555 345.9775695800781 0.2861519157886505 0.717428 0.4568746089935303 True -14 41310 30.588374853134155 0.69199538230896 254.039306640625 0.3698907494544983 345.86767578125 0.28614315390586853 0.7234408 0.43650752305984497 True -15 44064 30.66367816925049 0.6865239143371582 221.38394165039062 0.6577116250991821 346.00811767578125 0.28587082028388977 0.7293532 0.4116044342517853 True -16 46818 30.65791606903076 0.6872255802154541 246.1182403564453 0.4629043638706207 345.2361145019531 0.28896278142929077 0.7327682 0.40420207381248474 True -17 49572 30.60294818878174 21.422718286514282 254.61666870117188 0.3819321393966675 345.47509765625 0.2881350517272949 0.7342226 0.3991401195526123 True -18 52326 31.92878532409668 1.3914768695831299 223.4866943359375 0.2686193585395813 345.7846984863281 0.2870933413505554 0.7334394 0.3996444642543793 False -19 55080 30.60603904724121 0.6908509731292725 259.9314880371094 0.3805161714553833 345.61761474609375 0.28686991333961487 0.73339313 0.4035808742046356 False diff --git a/ENCSR964VVW/cherimoya.fold_1.performance.tsv b/ENCSR964VVW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 07d5110474ead8b87e6a613191d3f0a1b95476b6..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -345.47509765625 0.4726066589355469 0.2881350517272949 0.09246361255645752 0.7342225909233093 0.7189637422561646 0.3991401195526123 \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_2.evaluate.json b/ENCSR964VVW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 096bed5ed6a7b637b96f1aba2e3557fd4c609257..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF902LTL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_2.fit.json b/ENCSR964VVW/cherimoya.fold_2.fit.json deleted file mode 100644 index e66ff52dbef871edc0727ec7a3e0eae125a80a27..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF902LTL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_2.log b/ENCSR964VVW/cherimoya.fold_2.log deleted file mode 100644 index cc0c2158d8bf66c491de363a993daa36d5a2d535..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2907 35.89890170097351 3.7688205242156982 235.5556640625 0.8887218236923218 345.89105224609375 0.16597889363765717 0.470674 3.8287291526794434 True -1 5814 32.18956995010376 0.5711615085601807 234.53289794921875 1.0890576839447021 328.9635314941406 0.23550494015216827 0.5686837 0.9130740165710449 True -2 8721 32.131653785705566 0.5166611671447754 227.5011444091797 0.7858704328536987 325.91253662109375 0.24554292857646942 0.5877268 0.6554787755012512 True -3 11628 32.052783727645874 0.534735918045044 247.5157012939453 0.6641103029251099 324.1824645996094 0.2501462996006012 0.6050226 0.6121892333030701 True -4 14535 32.12009000778198 0.5253722667694092 212.59652709960938 0.7355515956878662 322.9626770019531 0.2552556097507477 0.61133176 0.6623556017875671 True -5 17442 32.07993841171265 0.5298824310302734 235.8917236328125 0.55225670337677 323.0254821777344 0.25487834215164185 0.619411 0.6613911390304565 True -6 20349 32.09801197052002 0.5507028102874756 234.85418701171875 0.6705943942070007 322.3714599609375 0.25804468989372253 0.6196865 0.6702349781990051 True -7 23256 32.106430768966675 0.5280635356903076 273.42279052734375 1.064110279083252 321.9485168457031 0.25984781980514526 0.62634826 0.6490330100059509 True -8 26163 32.07684326171875 0.545987606048584 253.89645385742188 0.6242953538894653 321.4687194824219 0.26118290424346924 0.6270175 0.6732662916183472 True -9 29070 32.07819962501526 0.5309090614318848 227.96185302734375 0.44872328639030457 320.6695861816406 0.26417919993400574 0.63774794 0.6426871418952942 True -10 31977 32.092554569244385 0.5369374752044678 258.12432861328125 0.6007049083709717 319.8047790527344 0.267698734998703 0.6472654 0.5964697003364563 True -11 34884 32.12991428375244 0.5336236953735352 234.60281372070312 0.5399246215820312 319.6446228027344 0.26883646845817566 0.6527051 0.578879177570343 True -12 37791 32.17639398574829 0.5200903415679932 245.35922241210938 0.5402246713638306 318.6324768066406 0.2713989317417145 0.6638934 0.5169727206230164 True -13 40698 32.101953744888306 0.5275464057922363 204.6426544189453 0.6770762801170349 318.20355224609375 0.27309465408325195 0.67199755 0.4821299612522125 True -14 43605 32.056275606155396 0.5279006958007812 250.4608154296875 0.4549466669559479 317.78082275390625 0.2744574248790741 0.68011326 0.4532773196697235 True -15 46512 32.09385848045349 0.5190718173980713 252.0355224609375 0.46836069226264954 317.5802917480469 0.27578893303871155 0.6873249 0.4343906342983246 True -16 49419 32.092658281326294 0.520576000213623 265.8130187988281 0.554508626461029 317.62384033203125 0.2750556766986847 0.6924354 0.4186263382434845 True -17 52326 32.06997084617615 0.5296576023101807 265.0791931152344 0.3270692825317383 317.6749572753906 0.27531614899635315 0.69554687 0.41534537076950073 True -18 55233 32.35614538192749 0.5181412696838379 201.105224609375 0.5270810127258301 317.4160461425781 0.27610400319099426 0.69810885 0.4122786223888397 True -19 58140 32.17237997055054 1.2748064994812012 241.49887084960938 0.2970161736011505 317.7210693359375 0.27499786019325256 0.6966119 0.4181784689426422 False diff --git a/ENCSR964VVW/cherimoya.fold_2.performance.tsv b/ENCSR964VVW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 9aff569f8fcf1cc9339cd3b7277a433449a6fc07..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -317.4160461425781 0.48460400104522705 0.27610400319099426 0.08434730023145676 0.6981088519096375 0.6853461861610413 0.4122786223888397 \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_3.evaluate.json b/ENCSR964VVW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 6650c96907eb973063c8937654f97256eec58339..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF902LTL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_3.fit.json b/ENCSR964VVW/cherimoya.fold_3.fit.json deleted file mode 100644 index c267963dffed71fc836d6ce247dc966186dad593..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF902LTL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_3.log b/ENCSR964VVW/cherimoya.fold_3.log deleted file mode 100644 index c98fec1adef21aca421d1d8640132b4baa87ca97..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2789 34.76885795593262 3.7194743156433105 280.9848327636719 0.6062775254249573 365.10235595703125 0.16969159245491028 0.49830917 4.095108985900879 True -1 5578 30.779111623764038 0.6499733924865723 274.8779296875 1.2605681419372559 350.2509460449219 0.23014892637729645 0.5972329 1.1676297187805176 True -2 8367 30.807852745056152 0.6003341674804688 276.48406982421875 0.6411895155906677 345.759765625 0.244527205824852 0.61514705 0.6148592233657837 True -3 11156 30.772438526153564 0.5849530696868896 218.98635864257812 0.6704213619232178 344.7867736816406 0.24602116644382477 0.6212172 0.7177779078483582 True -4 13945 30.778971433639526 0.5861208438873291 289.2586975097656 0.7532923221588135 343.5212097167969 0.2506811320781708 0.63233376 0.7033643126487732 True -5 16734 30.802241563796997 0.5869371891021729 218.89773559570312 0.6498880386352539 342.9029235839844 0.25319942831993103 0.6391944 0.723598301410675 True -6 19523 30.754231929779053 0.587498664855957 231.5865478515625 0.7802563905715942 342.1905212402344 0.25591450929641724 0.6432701 0.7334296703338623 True -7 22312 30.745986461639404 0.5763375759124756 244.40380859375 0.7978223562240601 341.88238525390625 0.2570120394229889 0.6446098 0.7037443518638611 True -8 25101 30.731751441955566 0.5917580127716064 232.11376953125 0.8223324418067932 341.3009338378906 0.2590382993221283 0.65038776 0.6592112183570862 True -9 27890 30.764487266540527 1.9414501190185547 268.5516052246094 0.5449215173721313 340.8462219238281 0.26150357723236084 0.6535253 0.6402334570884705 True -10 30679 30.818798065185547 0.5849242210388184 239.229736328125 0.5793541669845581 340.5828552246094 0.2616204619407654 0.6619752 0.6199276447296143 True -11 33468 30.770779371261597 0.587421178817749 240.13133239746094 0.5750182867050171 340.017822265625 0.26383665204048157 0.6646468 0.600712239742279 True -12 36257 30.74085521697998 0.5916645526885986 250.6833038330078 0.3735809326171875 339.4046936035156 0.26595279574394226 0.67573917 0.5528191328048706 True -13 39046 30.746691942214966 0.5763747692108154 272.8526611328125 0.49951133131980896 338.86419677734375 0.26847851276397705 0.6852894 0.5165453553199768 True -14 41835 30.73861813545227 0.5722348690032959 277.86212158203125 0.384482204914093 338.1353759765625 0.27067258954048157 0.6936035 0.4578358829021454 True -15 44624 30.745434284210205 0.5777089595794678 204.877197265625 0.40749460458755493 338.0660705566406 0.271687388420105 0.70140046 0.4398018419742584 True -16 47413 30.736801862716675 0.579369068145752 238.91558837890625 0.46083563566207886 337.89581298828125 0.2709832787513733 0.70559394 0.4211808145046234 True -17 50202 30.75229263305664 0.5922214984893799 259.0237121582031 0.4455874562263489 337.9730224609375 0.27162814140319824 0.70701253 0.4140545427799225 True -18 52991 30.763028144836426 0.5748353004455566 240.22036743164062 0.37599536776542664 337.8948669433594 0.27122458815574646 0.7068101 0.4134882986545563 False -19 55780 30.803841829299927 0.5909066200256348 250.68975830078125 0.23540157079696655 338.47552490234375 0.2690599858760834 0.7049559 0.41871359944343567 False diff --git a/ENCSR964VVW/cherimoya.fold_3.performance.tsv b/ENCSR964VVW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index b2b652b2f745d7eb431c2c01f5bdd3582db2883b..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -337.9730224609375 0.4804763197898865 0.27162817120552063 0.08833208680152893 0.7070125341415405 0.6873776912689209 0.4140545427799225 \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_4.evaluate.json b/ENCSR964VVW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 9c540473f09070daad8e0f685a4c5e52f4444585..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF902LTL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_4.fit.json b/ENCSR964VVW/cherimoya.fold_4.fit.json deleted file mode 100644 index 0e3c104d76a8bd7c5907d68f82cb6325a5891843..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF902LTL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964VVW/cherimoya.fold_4.log b/ENCSR964VVW/cherimoya.fold_4.log deleted file mode 100644 index 02959bf44127bfe0939002318fcb87e85752c31e..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2881 35.92149543762207 4.227816343307495 245.75396728515625 0.9738640189170837 348.5147705078125 0.16973434388637543 0.47172767 3.7173542976379395 True -1 5762 31.81492018699646 0.6037964820861816 275.3670349121094 0.5552263259887695 333.88250732421875 0.23021529614925385 0.5611829 1.1505488157272339 True -2 8643 31.860610246658325 0.6098878383636475 227.93896484375 0.9644627571105957 331.26324462890625 0.23870287835597992 0.57828504 0.782916784286499 True -3 11524 31.819616556167603 0.5854527950286865 284.1007080078125 0.6143577098846436 329.1015319824219 0.2444063127040863 0.5817493 0.760984480381012 True -4 14405 31.775019645690918 0.5873656272888184 235.8811798095703 0.680220365524292 328.220458984375 0.24722854793071747 0.5884143 0.7378565073013306 True -5 17286 31.76165008544922 0.5885562896728516 234.63323974609375 1.2667547464370728 327.93798828125 0.24826502799987793 0.59619725 0.7323295474052429 True -6 20167 31.790772914886475 0.5971949100494385 243.8870086669922 0.5209187269210815 326.9908447265625 0.25316694378852844 0.6030052 0.7184807062149048 True -7 23048 31.796512126922607 0.5891811847686768 250.42242431640625 0.7086042165756226 326.60601806640625 0.25499677658081055 0.61023164 0.6973457336425781 True -8 25929 31.74066472053528 0.5954113006591797 226.12074279785156 0.5542757511138916 325.8533935546875 0.2580900192260742 0.6217626 0.6355674862861633 True -9 28810 31.76594090461731 0.6042029857635498 224.42660522460938 0.6212420463562012 325.61138916015625 0.259452223777771 0.6256889 0.6449831128120422 True -10 31691 32.08112287521362 0.5951945781707764 299.74468994140625 0.3106594681739807 324.8439025878906 0.26208674907684326 0.6334424 0.59050452709198 True -11 34572 31.817270755767822 0.84354567527771 262.447998046875 0.5227805376052856 324.1702575683594 0.26487383246421814 0.6379875 0.5969319343566895 True -12 37453 31.80979084968567 0.5910120010375977 257.3751525878906 0.4594571888446808 323.86016845703125 0.2654518485069275 0.6524641 0.5365208387374878 True -13 40334 31.79094099998474 0.6086602210998535 255.58242797851562 0.683417797088623 323.36260986328125 0.26782622933387756 0.6625673 0.48254451155662537 True -14 43215 31.873531818389893 0.5858063697814941 272.227783203125 0.31649506092071533 322.7218017578125 0.2704218327999115 0.671365 0.4566367268562317 True -15 46096 31.864049911499023 0.5907905101776123 249.49075317382812 0.5070176720619202 322.76641845703125 0.27036723494529724 0.6795843 0.43603166937828064 True -16 48977 31.84934711456299 0.5834064483642578 235.0712890625 0.3448909521102905 322.2860107421875 0.2723303735256195 0.6846364 0.4153405725955963 True -17 51858 31.902544260025024 1.0834712982177734 244.65335083007812 0.4125504791736603 322.65966796875 0.26973673701286316 0.6894795 0.4022558927536011 True -18 54739 31.879491806030273 0.5983667373657227 208.55369567871094 0.40819957852363586 322.5802307128906 0.27053019404411316 0.6884347 0.40379855036735535 False -19 57620 31.903241872787476 0.6046755313873291 284.9234313964844 0.3161523640155792 322.63677978515625 0.27054059505462646 0.6881961 0.4048905074596405 False diff --git a/ENCSR964VVW/cherimoya.fold_4.performance.tsv b/ENCSR964VVW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index e73ba586cf453e5c80d0430a9628c76a65fe4992..0000000000000000000000000000000000000000 --- a/ENCSR964VVW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -322.65966796875 0.4849095940589905 0.26973673701286316 0.08667682856321335 0.6894794702529907 0.6698623299598694 0.4022558927536011 \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_0.evaluate.json b/ENCSR964WHY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c59f285566f642bb2fdbc58cb71cd425f6aeb9aa..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF512VYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_0.fit.json b/ENCSR964WHY/cherimoya.fold_0.fit.json deleted file mode 100644 index 6980444f0894e9db0ee70ef8f79df19c4c1f605c..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF512VYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_0.log b/ENCSR964WHY/cherimoya.fold_0.log deleted file mode 100644 index d320773b885be054277cb9aa4497888bf48f6e5e..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 33.689751863479614 3.4970028400421143 991.54638671875 0.3953646421432495 1420.4990234375 0.27404752373695374 0.6771391 7.830654144287109 True -1 5470 30.574780225753784 0.5749249458312988 1169.281982421875 0.48518288135528564 1286.11669921875 0.3748951852321625 0.76193875 0.777577817440033 True -2 8205 30.100661039352417 0.5564813613891602 1025.444091796875 0.33319953083992004 1258.552001953125 0.3941723108291626 0.7762915 0.29121553897857666 True -3 10940 30.12206745147705 0.553685188293457 1011.856689453125 0.2799593210220337 1248.4981689453125 0.4003143906593323 0.7865532 0.274396151304245 True -4 13675 30.17590022087097 0.5497152805328369 938.1898193359375 0.47670555114746094 1246.87353515625 0.40173864364624023 0.7881969 0.26680833101272583 True -5 16410 30.186091661453247 0.5449934005737305 1052.186767578125 0.3220498859882355 1239.9320068359375 0.4072234332561493 0.79669464 0.241036057472229 True -6 19145 30.171680212020874 0.5493090152740479 980.705810546875 0.45541393756866455 1236.5518798828125 0.40970170497894287 0.7973548 0.23681841790676117 True -7 21880 30.202184915542603 3.2074410915374756 999.0328979492188 0.3076314926147461 1233.9320068359375 0.4116736948490143 0.7956708 0.21944721043109894 False -8 24615 30.23338747024536 0.5617499351501465 1034.877197265625 0.3640221655368805 1233.6263427734375 0.41216883063316345 0.7988605 0.2113959640264511 True -9 27350 30.15011501312256 0.6360337734222412 1151.2738037109375 0.23973330855369568 1231.4326171875 0.4140278697013855 0.79993105 0.21387524902820587 True -10 30085 30.219762325286865 0.5557396411895752 970.2275390625 0.20078164339065552 1226.1904296875 0.4187845289707184 0.803519 0.20786669850349426 True -11 32820 30.17887234687805 0.5539536476135254 1144.366943359375 0.2119649350643158 1223.6998291015625 0.42042645812034607 0.81074643 0.19404277205467224 True -12 35555 30.177863359451294 0.5562801361083984 1169.137939453125 0.20195341110229492 1222.4588623046875 0.42079225182533264 0.8155574 0.19220523536205292 True -13 38290 30.182204484939575 0.557861328125 975.3282470703125 0.2737191915512085 1221.65673828125 0.4210277795791626 0.8217949 0.18355290591716766 True -14 41025 30.210437774658203 0.5569193363189697 1063.943603515625 0.13659007847309113 1217.6832275390625 0.42497530579566956 0.82739073 0.17718413472175598 True -15 43760 30.10173225402832 0.5557527542114258 1074.91943359375 0.1756070852279663 1218.093994140625 0.4242793023586273 0.8324007 0.17449960112571716 True -16 46495 30.1654953956604 0.5588545799255371 1093.187744140625 0.16997000575065613 1216.18408203125 0.42599040269851685 0.83490413 0.17021381855010986 True -17 49230 30.18181848526001 0.5598258972167969 942.825927734375 0.22652629017829895 1215.9024658203125 0.42606213688850403 0.8355253 0.17063573002815247 True -18 51965 30.156278133392334 0.5398547649383545 1030.251953125 0.12629273533821106 1217.0501708984375 0.42520010471343994 0.8344528 0.17055034637451172 False -19 54700 30.144282341003418 0.5564999580383301 1075.290283203125 0.15401354432106018 1216.1646728515625 0.4262407720088959 0.8360121 0.1716984063386917 True diff --git a/ENCSR964WHY/cherimoya.fold_0.performance.tsv b/ENCSR964WHY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 78b67f49151abb4dbe8807176882ca8a6fff9453..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1216.1646728515625 0.317089319229126 0.4262407422065735 0.22336289286613464 0.8360121250152588 0.8071596622467041 0.1716984063386917 \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_1.evaluate.json b/ENCSR964WHY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e6ea027b281af1a70ccfea51967f1601d5b58f9b..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF512VYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_1.fit.json b/ENCSR964WHY/cherimoya.fold_1.fit.json deleted file mode 100644 index 6a33e230d5b419bab3789caab45523687db1928b..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF512VYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_1.log b/ENCSR964WHY/cherimoya.fold_1.log deleted file mode 100644 index 52391f1b6984c903540d9fba0270513220a441e0..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2727 33.94674301147461 3.7036609649658203 970.830810546875 0.34097597002983093 1580.2159423828125 0.28036510944366455 0.6784011 7.673873424530029 True -1 5454 30.09534001350403 0.6961526870727539 1081.216796875 0.40270543098449707 1411.6551513671875 0.39447301626205444 0.75507194 1.242170810699463 True -2 8181 30.055728673934937 0.7057080268859863 968.9015502929688 0.43852126598358154 1389.2457275390625 0.406194806098938 0.77751535 0.43385550379753113 True -3 10908 30.074960470199585 0.6842036247253418 946.9815673828125 0.5941867828369141 1374.84375 0.41556352376937866 0.7906624 0.3319193720817566 True -4 13635 30.111469507217407 0.8564190864562988 1054.67822265625 0.21997421979904175 1368.8936767578125 0.4200562834739685 0.795 0.3467556834220886 True -5 16362 30.14530062675476 0.7074103355407715 981.2169189453125 0.30432021617889404 1364.348876953125 0.42250555753707886 0.79720825 0.29536256194114685 True -6 19089 30.052653074264526 0.7067408561706543 1067.29052734375 0.27397266030311584 1361.890869140625 0.4231874942779541 0.8022731 0.26091673970222473 True -7 21816 30.018906593322754 0.6900081634521484 1281.593505859375 0.2912645936012268 1357.653564453125 0.4263705909252167 0.8059526 0.2611228823661804 True -8 24543 30.031755447387695 0.7048611640930176 978.368896484375 0.32044893503189087 1353.8662109375 0.42865291237831116 0.8075228 0.25059813261032104 True -9 27270 30.00240397453308 0.6827757358551025 1073.709228515625 0.1564352959394455 1351.0146484375 0.4306871294975281 0.80895394 0.236877903342247 True -10 29997 30.06728959083557 0.6923065185546875 908.4556884765625 0.3407939076423645 1347.479248046875 0.4323728680610657 0.8142655 0.22249892354011536 True -11 32724 30.0181667804718 0.6830933094024658 1058.629638671875 0.20969536900520325 1341.1402587890625 0.43738022446632385 0.8222185 0.20870964229106903 True -12 35451 30.089619874954224 0.7084672451019287 1028.5941162109375 0.22851057350635529 1342.276611328125 0.4349113702774048 0.83020526 0.1997559368610382 True -13 38178 30.084853172302246 0.6963560581207275 913.9698486328125 0.3836667239665985 1336.741943359375 0.4393860101699829 0.8351345 0.19267749786376953 True -14 40905 30.039320468902588 0.6918084621429443 941.8839721679688 0.1891520619392395 1334.5859375 0.4405665397644043 0.8414672 0.185003861784935 True -15 43632 30.095210552215576 1.3695790767669678 943.9022827148438 0.1566828191280365 1333.9971923828125 0.44036468863487244 0.848083 0.1768626570701599 True -16 46359 30.064545154571533 0.6797442436218262 867.2696533203125 0.2032226324081421 1332.1572265625 0.44186195731163025 0.8532677 0.17290042340755463 True -17 49086 30.136279821395874 0.7019557952880859 959.5657958984375 0.1497415453195572 1331.68603515625 0.4422925114631653 0.85322106 0.17291127145290375 False -18 51813 30.340495109558105 0.7283964157104492 963.9691772460938 0.1561904102563858 1332.7259521484375 0.4415614604949951 0.85483736 0.1734648197889328 True -19 54540 30.33131432533264 0.7088022232055664 1027.4324951171875 0.15369267761707306 1335.08935546875 0.4388762414455414 0.8528525 0.174162819981575 False diff --git a/ENCSR964WHY/cherimoya.fold_1.performance.tsv b/ENCSR964WHY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index de2241084c6b8c39c7d424f1876f631a73d230f1..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1332.7259521484375 0.3012793958187103 0.4415614902973175 0.245235875248909 0.8548373579978943 0.8432735800743103 0.1734648197889328 \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_2.evaluate.json b/ENCSR964WHY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f3ba7e300ac8222886ad9dc9292f316ec5e2393a..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF512VYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_2.fit.json b/ENCSR964WHY/cherimoya.fold_2.fit.json deleted file mode 100644 index a61450330cc5ba0ffdeec18271262b424e583183..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF512VYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_2.log b/ENCSR964WHY/cherimoya.fold_2.log deleted file mode 100644 index 3c3f064cea9f777957238bae6d1a21e079d8ef36..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2866 35.25696277618408 3.6939547061920166 1101.658203125 0.2926098108291626 1450.0521240234375 0.28321632742881775 0.6533276 5.960047245025635 True -1 5732 31.641846895217896 0.5658612251281738 1002.296630859375 0.5669828653335571 1313.9117431640625 0.3802014887332916 0.7480361 0.8533898591995239 True -2 8598 31.614235162734985 0.5473892688751221 1079.8731689453125 0.3267059922218323 1290.580810546875 0.39539429545402527 0.76418537 0.3722691833972931 True -3 11464 31.568634271621704 0.5438671112060547 1008.5960083007812 0.3574785590171814 1275.07177734375 0.40642303228378296 0.7760445 0.2993031442165375 True -4 14330 31.66651964187622 0.5410113334655762 994.9195556640625 0.2943822145462036 1273.4326171875 0.4071938991546631 0.77725434 0.35670778155326843 True -5 17196 31.626563549041748 0.5622093677520752 1055.6610107421875 0.331866979598999 1270.8399658203125 0.40867549180984497 0.7781465 0.3224632441997528 True -6 20062 31.603280782699585 0.5479114055633545 962.283935546875 0.2818130552768707 1267.3236083984375 0.41119185090065 0.78097564 0.289033979177475 True -7 22928 31.583993911743164 0.5401864051818848 930.9825439453125 0.2316880226135254 1264.4593505859375 0.41284796595573425 0.78604615 0.26270151138305664 True -8 25794 31.5884211063385 0.5477142333984375 999.3914794921875 0.2589661777019501 1259.658447265625 0.4169065058231354 0.7902972 0.2482360452413559 True -9 28660 31.6382155418396 0.5398552417755127 1073.498779296875 0.20322176814079285 1256.2579345703125 0.41952741146087646 0.7954587 0.2414809614419937 True -10 31526 31.66662335395813 0.5416250228881836 945.7979125976562 0.20421205461025238 1254.3680419921875 0.42045101523399353 0.80141115 0.2234930694103241 True -11 34392 31.686000108718872 1.0130279064178467 1148.180908203125 0.3058123290538788 1251.8349609375 0.42280113697052 0.80458504 0.21835987269878387 True -12 37258 31.67680287361145 0.5543372631072998 1158.8187255859375 0.16100984811782837 1248.958984375 0.4244006872177124 0.81106985 0.21495260298252106 True -13 40124 31.684082984924316 0.5565047264099121 1013.4872436523438 0.20129621028900146 1248.2569580078125 0.42541807889938354 0.81612074 0.2058372050523758 True -14 42990 31.639820098876953 0.5469703674316406 993.06103515625 0.17386041581630707 1246.94775390625 0.4260821044445038 0.82153267 0.19838860630989075 True -15 45856 31.61752986907959 0.5562973022460938 1045.67578125 0.2111814320087433 1243.0133056640625 0.4297746419906616 0.8246387 0.19169823825359344 True -16 48722 31.67546844482422 0.5502188205718994 1073.0050048828125 0.20777621865272522 1243.6717529296875 0.4283946752548218 0.8306452 0.18596328794956207 True -17 51588 31.651853322982788 0.5497736930847168 985.4611206054688 0.16688458621501923 1242.541259765625 0.42982217669487 0.8323186 0.1833929866552353 True -18 54454 31.63661479949951 0.5534801483154297 976.2899169921875 0.20835641026496887 1245.5355224609375 0.42637792229652405 0.8329517 0.18235857784748077 True -19 57320 31.75440526008606 0.5521790981292725 1031.223388671875 0.14584194123744965 1244.8197021484375 0.42734968662261963 0.8338741 0.18123666942119598 True diff --git a/ENCSR964WHY/cherimoya.fold_2.performance.tsv b/ENCSR964WHY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f6ae8c4fe1d046d5b8fe5ded8771cc63b949109c..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1244.8197021484375 0.31384575366973877 0.42734968662261963 0.22912007570266724 0.8338741064071655 0.808194637298584 0.18123666942119598 \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_3.evaluate.json b/ENCSR964WHY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 32415d9a5129fcb499e321d7d3da6ffeea983aab..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF512VYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_3.fit.json b/ENCSR964WHY/cherimoya.fold_3.fit.json deleted file mode 100644 index 9836654aae053de8ad634d0e3c33420bf53cd977..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF512VYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_3.log b/ENCSR964WHY/cherimoya.fold_3.log deleted file mode 100644 index ae43ad7daaf8f961748273c1f8df237f9cc917a9..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2812 34.6434645652771 4.060757160186768 988.532958984375 0.6801952123641968 1437.8721923828125 0.28591734170913696 0.67939156 6.799849033355713 True -1 5624 30.972922325134277 0.5686624050140381 1064.3365478515625 0.40192270278930664 1311.959228515625 0.38132935762405396 0.7610303 0.9578502774238586 True -2 8436 30.99389624595642 0.5393755435943604 1056.31005859375 0.3099665641784668 1297.648681640625 0.391364723443985 0.7648862 0.3769870102405548 True -3 11248 31.008814096450806 0.5364110469818115 957.4478149414062 0.4110378623008728 1288.54296875 0.3966648280620575 0.7764941 0.3156127333641052 True -4 14060 30.982726573944092 0.5422132015228271 1059.127685546875 0.3005965054035187 1279.3453369140625 0.40348583459854126 0.78892004 0.2574847638607025 True -5 16872 30.979732751846313 0.5406427383422852 1134.069580078125 0.3495170772075653 1274.0931396484375 0.40735724568367004 0.7949043 0.2655009627342224 True -6 19684 31.033125400543213 0.5420305728912354 947.4927368164062 0.3654024600982666 1272.9754638671875 0.40865299105644226 0.7959423 0.24472041428089142 True -7 22496 31.0503351688385 1.2551727294921875 1054.9420166015625 0.2827906608581543 1270.3277587890625 0.410277396440506 0.79004085 0.2436288744211197 False -8 25308 31.025099992752075 2.6809706687927246 1024.75732421875 0.2380543053150177 1268.3870849609375 0.4110870063304901 0.79315525 0.23824624717235565 False -9 28120 31.02873682975769 0.5496039390563965 1078.20458984375 0.22208666801452637 1264.505859375 0.41504237055778503 0.8011014 0.22098621726036072 True -10 30932 31.036784648895264 0.5433692932128906 1115.282470703125 0.2319520264863968 1262.6707763671875 0.4159006178379059 0.8043194 0.2142408788204193 True -11 33744 31.404749155044556 21.033715963363647 941.2755126953125 0.21621868014335632 1259.9981689453125 0.4186961352825165 0.8063246 0.2165985405445099 True -12 36556 31.404839754104614 0.5451228618621826 1058.2568359375 0.20420047640800476 1259.1575927734375 0.4188535511493683 0.81844735 0.1993461400270462 True -13 39368 31.039023637771606 0.5458803176879883 1043.912353515625 0.22690023481845856 1257.349365234375 0.41948965191841125 0.82573664 0.19014622271060944 True -14 42180 31.017767429351807 0.5431082248687744 1011.5321044921875 0.22849726676940918 1254.4449462890625 0.42250990867614746 0.8309167 0.1836249828338623 True -15 44992 31.01326012611389 0.5352623462677002 917.5716552734375 0.2483081817626953 1252.0234375 0.4237097203731537 0.8375631 0.1831318587064743 True -16 47804 31.00256609916687 0.5389404296875 1041.601806640625 0.11706767231225967 1252.2467041015625 0.423644095659256 0.84201753 0.1742716133594513 True -17 50616 31.00432825088501 0.53859543800354 908.8472290039062 0.28289592266082764 1251.7227783203125 0.4232286810874939 0.8460204 0.17194321751594543 True -18 53428 30.983059644699097 0.5408740043640137 1103.0850830078125 0.12244400382041931 1251.4132080078125 0.42408648133277893 0.84706926 0.17153745889663696 True -19 56240 31.013258934020996 0.5355300903320312 926.37353515625 0.11923769861459732 1253.0042724609375 0.42198944091796875 0.8449786 0.17194412648677826 False diff --git a/ENCSR964WHY/cherimoya.fold_3.performance.tsv b/ENCSR964WHY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 202078c07e221061b5d7898212827f7e663526f5..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1251.4132080078125 0.31385982036590576 0.4240865111351013 0.22746336460113525 0.847069263458252 0.8198392391204834 0.17153745889663696 \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_4.evaluate.json b/ENCSR964WHY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6bcb4fd003e6e0ef674ab79e7bac7dc8f4b4ba0a..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF512VYB.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_4.fit.json b/ENCSR964WHY/cherimoya.fold_4.fit.json deleted file mode 100644 index 6109a6b0f8528403e9d4ea58fba20a33e8bf6605..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF512VYB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR964WHY/cherimoya.fold_4.log b/ENCSR964WHY/cherimoya.fold_4.log deleted file mode 100644 index 6590081171818c4c9d8c4b74fb4d6d1cc824c74b..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2830 34.84138751029968 3.873246431350708 942.202392578125 0.2883080244064331 1366.49560546875 0.278122216463089 0.66647196 6.090185165405273 True -1 5660 31.2107675075531 1.1008567810058594 1026.88720703125 0.34886956214904785 1245.34716796875 0.37440237402915955 0.7380694 0.8884901404380798 True -2 8490 31.26720905303955 0.5197780132293701 1039.2908935546875 0.2676961421966553 1224.607666015625 0.38988927006721497 0.74513453 0.32427096366882324 True -3 11320 31.22520613670349 0.5050008296966553 1072.848388671875 0.40180259943008423 1213.804443359375 0.39722320437431335 0.75725424 0.2771185040473938 True -4 14150 31.188883543014526 0.49552035331726074 1092.3076171875 0.32691246271133423 1209.357177734375 0.4007100760936737 0.76280576 0.25529685616493225 True -5 16980 31.216269969940186 0.4979572296142578 999.25537109375 0.4218626916408539 1206.6424560546875 0.4028369188308716 0.7639936 0.2591468393802643 True -6 19810 31.245398998260498 0.49799370765686035 1077.3017578125 0.23191259801387787 1204.591552734375 0.40386754274368286 0.7723835 0.24372416734695435 True -7 22640 31.270962953567505 0.4995453357696533 981.3729248046875 0.18860779702663422 1202.169189453125 0.40658727288246155 0.771134 0.24442733824253082 False -8 25470 31.20622205734253 0.8933050632476807 969.7592163085938 0.2223564088344574 1198.955322265625 0.408374547958374 0.77441514 0.2327912598848343 True -9 28300 31.232481241226196 0.5494086742401123 914.1522216796875 0.28783392906188965 1196.113525390625 0.41121745109558105 0.77572566 0.22665360569953918 True -10 31130 31.244739532470703 3.1824915409088135 1011.1719970703125 0.23123672604560852 1196.147705078125 0.41079458594322205 0.7829892 0.21213148534297943 True -11 33960 31.219842433929443 0.510321855545044 979.90771484375 0.20342519879341125 1191.45458984375 0.4148217439651489 0.78883904 0.20436745882034302 True -12 36790 31.21698546409607 0.5073225498199463 1014.5159301757812 0.23094171285629272 1189.69970703125 0.41604185104370117 0.79494935 0.1980845034122467 True -13 39620 31.20703434944153 0.5021090507507324 1078.509765625 0.13559551537036896 1188.716552734375 0.41659870743751526 0.79799503 0.19625505805015564 True -14 42450 31.20244264602661 2.6016414165496826 1095.42578125 0.14941373467445374 1187.0032958984375 0.41805127263069153 0.8038857 0.18653970956802368 True -15 45280 31.21664571762085 1.2118110656738281 1054.6260986328125 0.1206129714846611 1185.119140625 0.42019420862197876 0.80964726 0.1825954169034958 True -16 48110 31.285109043121338 1.9549996852874756 1080.966552734375 0.17070217430591583 1183.9442138671875 0.4210663437843323 0.81614774 0.17820371687412262 True -17 50940 31.248292207717896 0.7594079971313477 1043.205078125 0.10150279849767685 1183.9752197265625 0.4203532636165619 0.81838036 0.17624475061893463 True -18 53770 31.346563816070557 0.5354776382446289 1054.322998046875 0.14556513726711273 1184.21826171875 0.4201858937740326 0.81940556 0.17659710347652435 True -19 56600 31.27340865135193 0.5107605457305908 1051.0550537109375 0.14258934557437897 1185.7158203125 0.4183982312679291 0.818503 0.17641626298427582 False diff --git a/ENCSR964WHY/cherimoya.fold_4.performance.tsv b/ENCSR964WHY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d97bdc2ecea3b9525dd7a5e6f9fdedc613adca48..0000000000000000000000000000000000000000 --- a/ENCSR964WHY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1184.21826171875 0.32201966643333435 0.4201858937740326 0.2187606245279312 0.8194055557250977 0.7894914150238037 0.17659710347652435 \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_0.evaluate.json b/ENCSR965JHW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7ba951c1acfff389ad1cac5d2f48d87209de95de..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791GZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_0.fit.json b/ENCSR965JHW/cherimoya.fold_0.fit.json deleted file mode 100644 index c0fb6594754b253f9efa7cd4cc4462593ac3fa2b..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF791GZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_0.log b/ENCSR965JHW/cherimoya.fold_0.log deleted file mode 100644 index 498ab0bee6171e91df2c67f44d12b2dfb2a4b213..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1845 24.44134759902954 3.502394914627075 403.8547668457031 1.0172079801559448 608.32373046875 0.15564917027950287 0.57813853 11.663251876831055 True -1 3690 20.615928411483765 0.38369321823120117 449.7935791015625 1.1922025680541992 520.5361328125 0.238011434674263 0.7328319 5.2515482902526855 True -2 5535 20.699650764465332 0.3940703868865967 401.6422119140625 1.1245481967926025 481.8606872558594 0.26526007056236267 0.7441387 3.1383137702941895 True -3 7380 20.650696516036987 0.3965418338775635 344.31103515625 0.7824448347091675 466.897216796875 0.2742403745651245 0.7648478 2.249342679977417 True -4 9225 20.631550312042236 0.3837251663208008 470.2015380859375 0.7101863622665405 458.52557373046875 0.27945342659950256 0.77493036 1.518003225326538 True -5 11070 20.63636803627014 0.3857991695404053 481.96441650390625 0.8264183402061462 454.041259765625 0.2846072316169739 0.7801408 1.2058576345443726 True -6 12915 20.645520448684692 0.3791184425354004 447.888671875 0.7227277159690857 450.0786437988281 0.2878596782684326 0.78709453 1.0489914417266846 True -7 14760 20.675583362579346 0.3854184150695801 370.7369689941406 0.8595288991928101 445.97698974609375 0.2916432321071625 0.7955951 0.9504233002662659 True -8 16605 20.645482301712036 0.3831460475921631 426.61932373046875 0.659232497215271 444.64703369140625 0.2920498251914978 0.8013539 0.8767219185829163 True -9 18450 20.630175352096558 0.37786102294921875 436.08819580078125 0.7953535914421082 441.9543762207031 0.29645898938179016 0.80570656 0.8043017983436584 True -10 20295 20.635682106018066 1.5222318172454834 455.9302978515625 0.6474809646606445 439.8157653808594 0.2980721890926361 0.81527597 0.755366325378418 True -11 22140 20.661362886428833 2.5324184894561768 408.0878601074219 0.4616082012653351 436.47967529296875 0.302041620016098 0.8192224 0.7169767022132874 True -12 23985 20.679669857025146 0.3896820545196533 437.9107360839844 0.9767884016036987 431.9148254394531 0.307936429977417 0.8259541 0.6840619444847107 True -13 25830 20.660121202468872 0.47512054443359375 386.11614990234375 0.6131327152252197 431.27252197265625 0.30731111764907837 0.8309787 0.6330081820487976 True -14 27675 20.658724784851074 0.38326263427734375 287.727783203125 0.7154171466827393 430.301513671875 0.30832722783088684 0.8381011 0.5916826725006104 True -15 29520 20.65215253829956 0.37745070457458496 347.84820556640625 0.6270215511322021 429.04241943359375 0.3093722462654114 0.84217274 0.5753147602081299 True -16 31365 20.65617537498474 0.38835620880126953 240.45123291015625 0.4097793698310852 428.28216552734375 0.3098614811897278 0.84456944 0.564988374710083 True -17 33210 20.657910108566284 0.37932395935058594 431.77716064453125 0.48331403732299805 428.7544250488281 0.30883386731147766 0.8437861 0.5622298717498779 False -18 35055 20.640732526779175 0.5273706912994385 379.8497619628906 0.44638127088546753 428.9503173828125 0.30890029668807983 0.8438327 0.5644803047180176 False -19 36900 20.73953676223755 0.3924837112426758 328.22802734375 0.4106171727180481 429.65478515625 0.308277428150177 0.8430665 0.5654338598251343 False diff --git a/ENCSR965JHW/cherimoya.fold_0.performance.tsv b/ENCSR965JHW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a3c5c2e8cb2dc4deb237785b26e8e101a44f32a7..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -428.28216552734375 0.4656825065612793 0.3098614811897278 0.10916554927825928 0.8445694446563721 0.7925893664360046 0.564988374710083 \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_1.evaluate.json b/ENCSR965JHW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9a0ba1dde1d6e059164ca7a5050800e21a14c84c..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791GZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_1.fit.json b/ENCSR965JHW/cherimoya.fold_1.fit.json deleted file mode 100644 index dd854aba8721d12eb61cc3de35b5811d736edea9..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF791GZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_1.log b/ENCSR965JHW/cherimoya.fold_1.log deleted file mode 100644 index 640d85e5d430fe0550b5e8006c80b6c8dbce91f4..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1806 23.896851062774658 3.5122718811035156 356.47125244140625 0.704345703125 740.21044921875 0.16467097401618958 0.5476112 14.174062728881836 True -1 3612 20.229586124420166 22.938211917877197 530.5697021484375 1.3019492626190186 638.6441650390625 0.24996669590473175 0.6940548 6.63519287109375 True -2 5418 20.66653299331665 0.59163498878479 458.54571533203125 1.0314748287200928 582.3775634765625 0.28492891788482666 0.7588487 3.3625364303588867 True -3 7224 20.175026416778564 0.5584621429443359 418.9539794921875 0.5115700960159302 559.1687622070312 0.29865628480911255 0.7775824 2.142260789871216 True -4 9030 20.180511236190796 0.5666062831878662 396.67950439453125 1.01267671585083 550.1417236328125 0.3048204779624939 0.7835127 1.5976346731185913 True -5 10836 20.203291654586792 1.0890412330627441 390.0990905761719 0.9467062950134277 544.2406616210938 0.3086615800857544 0.79471105 1.2460670471191406 True -6 12642 20.218011379241943 0.565852165222168 606.2158813476562 1.7446210384368896 537.8333129882812 0.31433865427970886 0.8049005 1.0807777643203735 True -7 14448 20.214070081710815 0.554126501083374 383.3399658203125 0.8843466639518738 535.3760986328125 0.31668621301651 0.8109895 1.0056077241897583 True -8 16254 20.275555849075317 0.5576028823852539 525.6800537109375 1.027721881866455 530.6285400390625 0.32007792592048645 0.8231403 0.9072871208190918 True -9 18060 20.194214582443237 0.752650260925293 299.9119567871094 0.5031290650367737 529.8438720703125 0.3225831389427185 0.82456046 0.9181724190711975 True -10 19866 20.211740970611572 0.562744140625 380.93572998046875 0.8045309782028198 522.95263671875 0.3290303349494934 0.83358186 0.7951672673225403 True -11 21672 20.239221572875977 0.5513057708740234 416.36663818359375 0.5306798219680786 522.2954711914062 0.3282516896724701 0.83801055 0.7506964206695557 True -12 23478 20.196266889572144 0.5506947040557861 350.78070068359375 0.7787184119224548 519.105224609375 0.32940366864204407 0.8441406 0.7033197283744812 True -13 25284 20.182089805603027 4.4021971225738525 373.72589111328125 0.4513961970806122 515.227294921875 0.33263692259788513 0.8488907 0.6684831976890564 True -14 27090 20.24680233001709 0.5740444660186768 235.14337158203125 0.4599911570549011 512.540283203125 0.33475589752197266 0.852456 0.6333337426185608 True -15 28896 20.268125772476196 0.5662860870361328 401.8091125488281 0.3929400146007538 511.703857421875 0.33446988463401794 0.85769653 0.6196319460868835 True -16 30702 20.191832780838013 0.5675148963928223 345.8931884765625 0.6657934188842773 512.2957153320312 0.3334559202194214 0.8593205 0.6116297841072083 True -17 32508 20.226072311401367 0.5589175224304199 358.5481872558594 0.33738964796066284 510.9934387207031 0.33572477102279663 0.85794795 0.6053345799446106 False -18 34314 20.47469711303711 25.96651577949524 264.1011962890625 0.37739914655685425 513.2831420898438 0.3325718939304352 0.85939276 0.6072701811790466 True -19 36120 20.184967041015625 0.580284595489502 376.775634765625 0.3780185580253601 513.444091796875 0.332577109336853 0.85663617 0.6142867207527161 False diff --git a/ENCSR965JHW/cherimoya.fold_1.performance.tsv b/ENCSR965JHW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 494a95c9d2ab1717c935863e71758f532c1668eb..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -513.2831420898438 0.4432491362094879 0.3325718939304352 0.13497868180274963 0.8593927621841431 0.8296562433242798 0.6072701811790466 \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_2.evaluate.json b/ENCSR965JHW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 3ddc1f0795685c23d6668b45fe647cb24796fe22..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791GZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_2.fit.json b/ENCSR965JHW/cherimoya.fold_2.fit.json deleted file mode 100644 index a5034e216f97c9fa39369deaf323538a6970a18b..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF791GZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_2.log b/ENCSR965JHW/cherimoya.fold_2.log deleted file mode 100644 index 57af7f4e3fed83738580bdc3d271a3c105aaa9fd..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1940 25.294215440750122 3.371638298034668 308.70086669921875 1.1836806535720825 615.8323364257812 0.15449140965938568 0.54533637 10.395221710205078 True -1 3880 21.694286108016968 0.4321746826171875 328.30450439453125 0.7249270677566528 522.7471923828125 0.23569177091121674 0.6981285 5.376852989196777 True -2 5820 21.706450700759888 0.4167060852050781 341.79248046875 1.2451622486114502 479.4097595214844 0.2660044729709625 0.7421664 2.8422884941101074 True -3 7760 21.716564893722534 0.41407036781311035 505.82672119140625 0.9312157034873962 464.9043884277344 0.27352768182754517 0.7621735 1.7593683004379272 True -4 9700 21.70139193534851 0.41601133346557617 506.6138610839844 1.3093571662902832 457.9848327636719 0.28030499815940857 0.77447236 1.2132997512817383 True -5 11640 21.688894987106323 0.41504502296447754 284.1231994628906 0.6189494729042053 454.130615234375 0.28392690420150757 0.78352606 1.133805274963379 True -6 13580 21.73683500289917 0.42176389694213867 365.0546875 0.9039788246154785 451.02734375 0.2867172062397003 0.78812015 1.0696159601211548 True -7 15520 21.666825771331787 5.253759860992432 413.28680419921875 0.6973052024841309 448.1824035644531 0.2897462248802185 0.79483294 0.9676823019981384 True -8 17460 21.752368688583374 0.41864728927612305 275.1668701171875 0.9104700088500977 445.8460693359375 0.2916591465473175 0.7993248 0.9141325950622559 True -9 19400 21.713576078414917 0.4137582778930664 364.91400146484375 0.7471902370452881 442.6318359375 0.29557061195373535 0.8107395 0.8170079588890076 True -10 21340 21.669636249542236 0.41502904891967773 295.9632568359375 0.6636740565299988 440.3984680175781 0.29715245962142944 0.8144062 0.7721688747406006 True -11 23280 21.715253114700317 0.41857242584228516 439.2595520019531 0.37455520033836365 437.50567626953125 0.3005850911140442 0.82297945 0.7142179012298584 True -12 25220 21.71396803855896 0.41420412063598633 486.9023742675781 0.5275484919548035 435.10699462890625 0.3032190501689911 0.82932526 0.6563327312469482 True -13 27160 21.769020318984985 0.4146153926849365 409.4505310058594 0.7453435063362122 433.6274108886719 0.30443766713142395 0.8339288 0.6236839294433594 True -14 29100 21.673909902572632 0.41881632804870605 395.67333984375 0.47502702474594116 430.5359802246094 0.30680927634239197 0.8403923 0.595742404460907 True -15 31040 21.688397884368896 0.41932177543640137 515.7357788085938 0.39353692531585693 429.52490234375 0.3086811900138855 0.8418618 0.5758593082427979 True -16 32980 21.67363691329956 0.4148216247558594 341.3269348144531 0.40786293148994446 428.793701171875 0.3086339831352234 0.8462365 0.5628129243850708 True -17 34920 21.67093539237976 0.4135100841522217 287.1225280761719 0.5180730223655701 428.385009765625 0.30807924270629883 0.8447283 0.5581465363502502 False -18 36860 21.69845676422119 0.4154202938079834 246.78994750976562 0.44306498765945435 429.8941345214844 0.30657529830932617 0.84674096 0.5599325299263 True -19 38800 21.755362033843994 0.4174056053161621 342.1936950683594 0.2965155839920044 430.5638122558594 0.30588117241859436 0.843639 0.5628111362457275 False diff --git a/ENCSR965JHW/cherimoya.fold_2.performance.tsv b/ENCSR965JHW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 6dcf8ecdac1ffd05aa67bf34187dab0b67dce285..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -429.8941345214844 0.4658016264438629 0.30657529830932617 0.11966193467378616 0.8467409610748291 0.7992358207702637 0.5599325299263 \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_3.evaluate.json b/ENCSR965JHW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 085cd05b5c078cbbaf9862a923b068fce4859fea..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791GZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_3.fit.json b/ENCSR965JHW/cherimoya.fold_3.fit.json deleted file mode 100644 index ad7a0b9bfdcdfb8ede85916084d7bdb809edb7a7..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF791GZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_3.log b/ENCSR965JHW/cherimoya.fold_3.log deleted file mode 100644 index 0d9504559680bc822f9fe8ea818d3fe626823b36..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1854 24.45513892173767 3.5210988521575928 566.8607177734375 1.221924066543579 633.722412109375 0.1693781316280365 0.5312079 11.628538131713867 True -1 3708 20.73935890197754 0.42920947074890137 320.65863037109375 0.8222188949584961 551.5086669921875 0.247381791472435 0.6980379 6.080869674682617 True -2 5562 20.78739857673645 0.40372657775878906 433.5233154296875 0.815595805644989 509.2069091796875 0.2745290994644165 0.7083936 3.4840588569641113 True -3 7416 20.799017429351807 0.9204769134521484 332.27447509765625 0.8312700390815735 490.6040954589844 0.2849207818508148 0.7341735 2.501340866088867 True -4 9270 20.770106077194214 0.40238094329833984 446.73651123046875 0.8575097918510437 485.63812255859375 0.28865811228752136 0.748236 1.9219111204147339 True -5 11124 20.778401613235474 1.1411933898925781 423.8722839355469 0.7854428291320801 479.72698974609375 0.2958650588989258 0.75769037 1.5804932117462158 True -6 12978 20.780479431152344 0.40661144256591797 377.33966064453125 0.5955297946929932 476.6260681152344 0.297940731048584 0.76272315 1.4222569465637207 True -7 14832 20.76901888847351 0.39871740341186523 324.2968444824219 1.1924057006835938 472.7454528808594 0.30123457312583923 0.77444774 1.18185293674469 True -8 16686 20.785686492919922 0.394381046295166 383.1935729980469 0.9248999357223511 471.4433288574219 0.301910400390625 0.7815573 1.0718672275543213 True -9 18540 20.75602889060974 1.5752699375152588 330.59332275390625 0.4806908369064331 466.5401916503906 0.30721911787986755 0.7886345 0.9468111395835876 True -10 20394 20.79555106163025 0.400357723236084 315.2055969238281 0.4370557963848114 464.0538330078125 0.30996283888816833 0.79756844 0.8685793876647949 True -11 22248 20.834601402282715 0.40672802925109863 468.56793212890625 0.6409195065498352 462.0223083496094 0.3115293085575104 0.80546147 0.8017306327819824 True -12 24102 20.892536401748657 18.987181663513184 353.6282958984375 0.7412213087081909 460.1888122558594 0.3118128180503845 0.8139861 0.7580279111862183 True -13 25956 20.927321195602417 0.40299248695373535 390.8880310058594 0.6425464153289795 458.41070556640625 0.31353074312210083 0.8193306 0.7218223810195923 True -14 27810 20.759302854537964 0.3975255489349365 308.5708312988281 0.5161343216896057 455.83062744140625 0.3157370388507843 0.82492644 0.696394681930542 True -15 29664 20.762195348739624 0.3963649272918701 310.6117248535156 0.5600661039352417 453.4962463378906 0.31867384910583496 0.83026075 0.6727825403213501 True -16 31518 20.76505970954895 0.39392518997192383 245.83566284179688 0.511243462562561 452.983154296875 0.31729796528816223 0.8331665 0.6497875452041626 True -17 33372 20.896888494491577 0.39269375801086426 393.14837646484375 0.37081965804100037 451.52532958984375 0.31983110308647156 0.8352485 0.6390529274940491 True -18 35226 20.744555711746216 0.38990116119384766 266.99835205078125 0.32266005873680115 453.71087646484375 0.3159629702568054 0.8365777 0.6356939673423767 True -19 37080 20.736021518707275 0.3876481056213379 399.70050048828125 0.6531777381896973 453.3669738769531 0.31693169474601746 0.83554715 0.6417386531829834 False diff --git a/ENCSR965JHW/cherimoya.fold_3.performance.tsv b/ENCSR965JHW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9a2e211080cf29662d0382fe8963fb4d07f9a79a..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -453.71087646484375 0.45729708671569824 0.3159629702568054 0.12064509093761444 0.8365777134895325 0.7893725037574768 0.6356939673423767 \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_4.evaluate.json b/ENCSR965JHW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 16de3dee15e5883b5e2e0b828aced489e9f67400..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF791GZF.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_4.fit.json b/ENCSR965JHW/cherimoya.fold_4.fit.json deleted file mode 100644 index 5aed83098cf42edf94a252266397cacdc7c87a1b..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF791GZF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR965JHW/cherimoya.fold_4.log b/ENCSR965JHW/cherimoya.fold_4.log deleted file mode 100644 index de8506c221f533912918a03d13d1741aa6d6b9f8..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1865 25.161336183547974 2.8716111183166504 343.0357666015625 1.0406544208526611 555.8886108398438 0.15702641010284424 0.54522467 11.560498237609863 True -1 3730 20.874340534210205 0.3596205711364746 476.47088623046875 1.0223478078842163 483.5019836425781 0.22957175970077515 0.6912858 4.866140365600586 True -2 5595 20.854936599731445 0.35603880882263184 488.1043701171875 0.8166091442108154 446.5402526855469 0.2554125487804413 0.72742116 2.3389580249786377 True -3 7460 20.86189103126526 0.350780725479126 349.7408447265625 0.900031328201294 436.672119140625 0.2634666860103607 0.7370218 1.7609853744506836 True -4 9325 20.854594469070435 0.3494284152984619 240.28451538085938 0.5657267570495605 426.7504577636719 0.2717550992965698 0.750388 1.2998970746994019 True -5 11190 20.877131700515747 0.36511707305908203 245.04034423828125 0.4935743510723114 425.13055419921875 0.27259987592697144 0.7614311 1.0800442695617676 True -6 13055 20.905126094818115 0.3670613765716553 253.77493286132812 0.8568942546844482 419.4342041015625 0.27744218707084656 0.7661259 0.9930528998374939 True -7 14920 20.921600103378296 0.3627469539642334 454.2730712890625 0.7091994881629944 415.8392333984375 0.2832696735858917 0.774785 0.9853259325027466 True -8 16785 20.93961787223816 0.41287827491760254 322.2957763671875 0.8133805990219116 413.7753601074219 0.2842561900615692 0.7804923 0.8881477117538452 True -9 18650 20.87206768989563 0.36559247970581055 420.7203063964844 1.5864968299865723 411.579833984375 0.28655552864074707 0.7905486 0.7873339056968689 True -10 20515 20.90421438217163 0.3599827289581299 355.8875732421875 0.8352089524269104 409.1616516113281 0.28865137696266174 0.79782283 0.7111725807189941 True -11 22380 20.860265970230103 1.199549913406372 421.52618408203125 0.5222450494766235 408.9606628417969 0.2875693738460541 0.8029073 0.6806439161300659 True -12 24245 20.906232357025146 0.3677709102630615 279.53814697265625 0.5907971858978271 406.68701171875 0.29023176431655884 0.80730534 0.6580907106399536 True -13 26110 20.95491933822632 1.1105146408081055 356.2677001953125 0.5596373081207275 404.666015625 0.29219377040863037 0.81485635 0.6283174157142639 True -14 27975 20.88083577156067 1.042020320892334 269.9547119140625 0.7641797065734863 403.2893371582031 0.292222261428833 0.8201923 0.6086710095405579 True -15 29840 20.8609721660614 0.36321043968200684 311.31463623046875 0.44732004404067993 402.3684387207031 0.29421958327293396 0.8242104 0.5869547128677368 True -16 31705 20.9240779876709 0.35447239875793457 311.9794921875 0.5897043943405151 401.0377502441406 0.29437991976737976 0.830008 0.5724918842315674 True -17 33570 20.864450454711914 15.187816858291626 349.72052001953125 0.42684274911880493 401.8384094238281 0.2938104569911957 0.83153456 0.5687692165374756 True -18 35435 20.931293964385986 0.35822391510009766 284.2305908203125 0.23517821729183197 402.7804870605469 0.29279428720474243 0.8298959 0.5685402154922485 False -19 37300 21.110456705093384 17.949357509613037 362.02203369140625 0.38839036226272583 403.21514892578125 0.292209655046463 0.8299887 0.5690064430236816 False diff --git a/ENCSR965JHW/cherimoya.fold_4.performance.tsv b/ENCSR965JHW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 99569d71d3f3a8267b1a28fa4c9f43bcb9cb7d3f..0000000000000000000000000000000000000000 --- a/ENCSR965JHW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -401.8384094238281 0.4753388464450836 0.2938104569911957 0.10884088277816772 0.8315345644950867 0.7752863168716431 0.5687692165374756 \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_0.evaluate.json b/ENCSR969QKG/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 01e4cf34f41cf3173f8105f5f7794393627f18de..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF141BVL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_0.fit.json b/ENCSR969QKG/cherimoya.fold_0.fit.json deleted file mode 100644 index 04811193d9c5b9262c5a4c1b092675ff1b031892..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF141BVL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_0.log b/ENCSR969QKG/cherimoya.fold_0.log deleted file mode 100644 index 69a3c044a53577da6d62ec828bc2221531d7ae39..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2743 36.35046863555908 4.547884941101074 457.9392395019531 0.453893780708313 582.7007446289062 0.19101348519325256 0.70889986 5.040737152099609 True -1 5486 30.813912391662598 2.3018558025360107 441.593017578125 0.5728172659873962 545.58251953125 0.23682820796966553 0.80314356 1.1721274852752686 True -2 8229 30.670063972473145 21.813871145248413 481.79400634765625 0.42597031593322754 540.0210571289062 0.23985865712165833 0.80561477 0.6376408934593201 True -3 10972 30.996614933013916 11.246357679367065 478.138671875 0.2900652289390564 535.6224975585938 0.2444823980331421 0.8124442 0.563082218170166 True -4 13715 30.51815962791443 22.25807237625122 639.2708740234375 0.4026010036468506 533.5674438476562 0.2462170273065567 0.8214028 0.43663787841796875 True -5 16458 30.52034282684326 7.034418344497681 502.5835876464844 0.3900471329689026 532.4279174804688 0.24760347604751587 0.82732093 0.4195612072944641 True -6 19201 30.487812757492065 1.0393071174621582 503.5353088378906 0.33633220195770264 530.999755859375 0.25018391013145447 0.8328799 0.4006457030773163 True -7 21944 30.47838258743286 1.0792901515960693 408.0777587890625 0.29794812202453613 529.5701904296875 0.25142547488212585 0.8386306 0.37715059518814087 True -8 24687 30.472848653793335 0.6675155162811279 496.925537109375 0.27487456798553467 528.6150512695312 0.25220057368278503 0.84565127 0.35591748356819153 True -9 27430 30.520887851715088 0.6906864643096924 501.6185302734375 0.33438533544540405 527.727783203125 0.253656268119812 0.8537547 0.32667991518974304 True -10 30173 30.468063831329346 11.295295715332031 438.4025573730469 0.34011346101760864 526.0883178710938 0.2561855912208557 0.8545798 0.31809112429618835 True -11 32916 30.470983028411865 0.7845571041107178 467.6449279785156 0.23498989641666412 524.8638916015625 0.25742092728614807 0.86075044 0.3001968264579773 True -12 35659 30.486915588378906 1.0664482116699219 462.93359375 0.39736831188201904 524.1875610351562 0.25785771012306213 0.8659022 0.29153162240982056 True -13 38402 30.456949949264526 0.5069665908813477 460.243408203125 0.3853652775287628 522.1484375 0.2603186368942261 0.86940116 0.2742251753807068 True -14 41145 30.48914098739624 0.5050184726715088 451.17352294921875 0.23888006806373596 521.6072387695312 0.2606034576892853 0.87251115 0.2605039179325104 True -15 43888 30.458521604537964 1.0854332447052002 370.59869384765625 0.20158372819423676 521.1171875 0.261088490486145 0.8768465 0.25162237882614136 True -16 46631 30.48039484024048 0.5141117572784424 392.8887939453125 0.2983822226524353 520.9918212890625 0.2617484927177429 0.87740517 0.25154802203178406 True -17 49374 30.453506469726562 0.5021555423736572 436.96978759765625 0.21048009395599365 521.100830078125 0.26124414801597595 0.8740903 0.2556496262550354 False -18 52117 30.45279836654663 0.5034036636352539 482.0126647949219 0.12949977815151215 521.9464721679688 0.2608393728733063 0.871842 0.26165810227394104 False -19 54860 30.466946601867676 0.5101988315582275 425.6347351074219 0.11851908266544342 521.942626953125 0.26084333658218384 0.8721237 0.2647418975830078 False diff --git a/ENCSR969QKG/cherimoya.fold_0.performance.tsv b/ENCSR969QKG/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 90d9c5ba07c0344e2be9651aa8707c1abc00e478..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -520.9918212890625 0.4590207040309906 0.2617484927177429 0.11348012089729309 0.8774051666259766 0.8350851535797119 0.25154802203178406 \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_1.evaluate.json b/ENCSR969QKG/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 0d95c779c3874b0ab21c4e8b6366d5b0744068ae..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF141BVL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_1.fit.json b/ENCSR969QKG/cherimoya.fold_1.fit.json deleted file mode 100644 index f8247b4d8893c7075235bc3327a9694da6bdaa11..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF141BVL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_1.log b/ENCSR969QKG/cherimoya.fold_1.log deleted file mode 100644 index 3c6bce74d536cdfa18e15c55009abfa10c5dac05..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2703 34.81094551086426 4.25475287437439 482.2767028808594 0.4052414000034332 647.3576049804688 0.20321308076381683 0.73966354 5.883443355560303 True -1 5406 30.091355800628662 0.8163838386535645 460.2765197753906 0.596024751663208 604.6775512695312 0.25255316495895386 0.81474125 1.513572096824646 True -2 8109 30.041555643081665 0.8258872032165527 372.35302734375 0.5654760599136353 597.8942260742188 0.25492170453071594 0.84051716 0.6958435773849487 True -3 10812 30.04064178466797 1.3838298320770264 431.977294921875 0.2638038396835327 593.9716796875 0.25840047001838684 0.8477576 0.5546419620513916 True -4 13515 30.025891065597534 16.306459188461304 355.39691162109375 0.33900395035743713 591.77783203125 0.259909063577652 0.8575641 0.565396249294281 True -5 16218 30.01999044418335 0.8021347522735596 399.4237976074219 0.26933878660202026 588.93701171875 0.26365482807159424 0.8631223 0.4726177453994751 True -6 18921 30.00196361541748 0.7996010780334473 393.023681640625 0.26841405034065247 587.11474609375 0.265944242477417 0.8658453 0.45860394835472107 True -7 21624 29.985772609710693 0.8060693740844727 411.47821044921875 0.41648223996162415 586.0588989257812 0.2678292691707611 0.87032443 0.4269474148750305 True -8 24327 30.011367082595825 0.8089466094970703 379.8150634765625 0.36452749371528625 584.8760986328125 0.2693672478199005 0.8761408 0.3993144631385803 True -9 27030 30.03933310508728 0.8090355396270752 609.9442749023438 0.22918257117271423 583.8690795898438 0.2707117199897766 0.8780965 0.3846190571784973 True -10 29733 30.054216146469116 0.8443243503570557 423.2293701171875 0.3723292648792267 582.7515869140625 0.2717021703720093 0.8828834 0.3640711307525635 True -11 32436 30.042246103286743 0.8039684295654297 384.6385498046875 0.3612693250179291 580.8655395507812 0.27416884899139404 0.88736093 0.3481660783290863 True -12 35139 30.049533367156982 0.8054678440093994 398.00152587890625 0.26492565870285034 579.8168334960938 0.2753606140613556 0.89035434 0.32640331983566284 True -13 37842 30.03325629234314 0.8012344837188721 385.4096984863281 0.380567729473114 578.3233032226562 0.27677983045578003 0.8952002 0.2955152690410614 True -14 40545 30.02121329307556 0.8051509857177734 386.87640380859375 0.35532671213150024 577.4668579101562 0.27771830558776855 0.8990797 0.2794957756996155 True -15 43248 30.01080870628357 0.8062653541564941 442.90283203125 0.20169931650161743 576.4052124023438 0.2789803147315979 0.9007484 0.2623923420906067 True -16 45951 30.035271167755127 1.1755964756011963 428.62890625 0.22725842893123627 576.7769165039062 0.2785489559173584 0.9025866 0.2529771029949188 True -17 48654 30.02847671508789 1.7817573547363281 389.0675964355469 0.16403520107269287 576.4061889648438 0.27907684445381165 0.90171546 0.24996978044509888 False -18 51357 30.05333161354065 25.546446561813354 421.73663330078125 0.1245265007019043 577.6988525390625 0.276412695646286 0.9025012 0.2519816756248474 False -19 54060 30.062241077423096 0.8445422649383545 462.08843994140625 0.0949743241071701 577.80419921875 0.27650776505470276 0.89970165 0.2555385231971741 False diff --git a/ENCSR969QKG/cherimoya.fold_1.performance.tsv b/ENCSR969QKG/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4e5c3a7477bf10e6bdd4194345f497b2d68fd68a..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -576.7769165039062 0.4422622621059418 0.278548926115036 0.12723687291145325 0.9025865793228149 0.880400538444519 0.2529771029949188 \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_2.evaluate.json b/ENCSR969QKG/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 81b78a8ace5035e3aea48b6a215f47ff3200d3ef..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF141BVL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_2.fit.json b/ENCSR969QKG/cherimoya.fold_2.fit.json deleted file mode 100644 index 64c8b767569a26bca5b06b0f506dcc5670e49b0c..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF141BVL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_2.log b/ENCSR969QKG/cherimoya.fold_2.log deleted file mode 100644 index 4706c61e9b5c2a24e0a5cf69095a9ab69569170d..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2884 36.93210172653198 3.892225980758667 457.41693115234375 0.5281227827072144 596.0053100585938 0.19202978909015656 0.7112279 4.202054023742676 True -1 5768 32.09827947616577 0.6144652366638184 536.0802612304688 0.45255404710769653 555.7327880859375 0.2407890409231186 0.8047892 1.3015143871307373 True -2 8652 32.117143630981445 0.6468887329101562 415.8788757324219 0.4654928743839264 551.8665161132812 0.24125315248966217 0.8153857 0.6118930578231812 True -3 11536 32.02151703834534 0.5702240467071533 414.0318603515625 0.48942863941192627 549.3472290039062 0.24300234019756317 0.8232328 0.5775858163833618 True -4 14420 31.96214485168457 0.59226393699646 577.0709228515625 0.37989404797554016 545.4652709960938 0.24912762641906738 0.8287202 0.4908292591571808 True -5 17304 32.136258363723755 0.5715293884277344 442.7235107421875 0.35534951090812683 544.751953125 0.249358668923378 0.83566284 0.41314008831977844 True -6 20188 32.186262130737305 0.578413724899292 462.55718994140625 0.34235620498657227 541.44384765625 0.2542007565498352 0.8429775 0.36960187554359436 True -7 23072 32.20999836921692 0.595628023147583 462.7300109863281 0.42030590772628784 541.3685302734375 0.2540915310382843 0.84420776 0.36399587988853455 True -8 25956 32.21750736236572 0.6358873844146729 529.036865234375 0.39818114042282104 539.1442260742188 0.2580955922603607 0.8519473 0.3371571898460388 True -9 28840 32.19021129608154 0.5782322883605957 435.226318359375 0.24325570464134216 538.3079223632812 0.2579825818538666 0.8587921 0.3196309208869934 True -10 31724 32.16496443748474 0.5932996273040771 421.9372253417969 0.27341383695602417 538.026123046875 0.2585344612598419 0.86226636 0.30617907643318176 True -11 34608 32.42859864234924 0.601982831954956 494.14874267578125 0.35623836517333984 536.6892700195312 0.26023709774017334 0.8677505 0.2790752649307251 True -12 37492 32.111271381378174 0.5897204875946045 419.6280212402344 0.20100277662277222 535.7919311523438 0.2616012990474701 0.87410986 0.26640787720680237 True -13 40376 32.16292643547058 0.5882914066314697 444.18505859375 0.36382022500038147 534.7086791992188 0.26250648498535156 0.8772373 0.25410476326942444 True -14 43260 32.06290888786316 0.5849711894989014 412.5660400390625 0.22182267904281616 533.81298828125 0.26453593373298645 0.87962216 0.25051045417785645 True -15 46144 32.06334209442139 0.5969724655151367 489.3260803222656 0.21547359228134155 533.5086059570312 0.26404649019241333 0.88089377 0.24426564574241638 True -16 49028 32.2406051158905 0.5915353298187256 423.3459167480469 0.2162192463874817 533.21923828125 0.26425936818122864 0.8826221 0.2417568862438202 True -17 51912 32.13164281845093 0.5785102844238281 414.48681640625 0.15544649958610535 533.822998046875 0.26356175541877747 0.8805936 0.24567943811416626 False -18 54796 32.172776222229004 0.590937614440918 380.0516052246094 0.16838648915290833 534.9790649414062 0.2614370286464691 0.8780892 0.25261953473091125 False -19 57680 32.18749690055847 0.5890672206878662 347.25146484375 0.14443233609199524 534.3544311523438 0.2628079652786255 0.87807333 0.25516900420188904 False diff --git a/ENCSR969QKG/cherimoya.fold_2.performance.tsv b/ENCSR969QKG/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 4087c91d1df9cf7535f61c11460e4b41c56154de..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -533.21923828125 0.455084890127182 0.26425936818122864 0.11903264373540878 0.8826221227645874 0.8478395938873291 0.2417568862438202 \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_3.evaluate.json b/ENCSR969QKG/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 11783650931d2b8a75f143c87fb55f8938499a0c..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF141BVL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_3.fit.json b/ENCSR969QKG/cherimoya.fold_3.fit.json deleted file mode 100644 index 6a86c307143e7c4306f01d44fb2f56f4e00f944e..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF141BVL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_3.log b/ENCSR969QKG/cherimoya.fold_3.log deleted file mode 100644 index 67e4391d5bc5ad5e357ac061aaf43cd965f5f4bc..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 35.13120627403259 4.054539680480957 407.77716064453125 0.28379085659980774 555.8544921875 0.192820206284523 0.68107086 4.187522888183594 True -1 5498 30.49005699157715 1.8680415153503418 445.8846435546875 0.3232322931289673 522.4669189453125 0.2338637113571167 0.7749021 1.1038358211517334 True -2 8247 30.56910014152527 0.6088101863861084 446.52264404296875 0.37481385469436646 518.1497802734375 0.23752492666244507 0.7961996 0.593594491481781 True -3 10996 30.654701471328735 0.6020944118499756 520.661865234375 0.19519561529159546 515.9130859375 0.2410375326871872 0.8054492 0.5460693836212158 True -4 13745 30.5050950050354 0.5697717666625977 458.7451171875 0.3719955086708069 514.1087646484375 0.24357552826404572 0.8056932 0.4898368716239929 True -5 16494 30.54727578163147 0.5887019634246826 464.78466796875 0.4351367652416229 512.4876708984375 0.24560117721557617 0.81115896 0.46854057908058167 True -6 19243 30.568025827407837 0.5770349502563477 441.79559326171875 0.3460351824760437 511.5153503417969 0.24702425301074982 0.8141876 0.46715328097343445 True -7 21992 30.49572777748108 1.1058828830718994 468.78582763671875 0.477672278881073 510.4027404785156 0.24840687215328217 0.8188075 0.4317165017127991 True -8 24741 30.52824091911316 0.5809290409088135 452.05169677734375 0.39343443512916565 509.27581787109375 0.24944883584976196 0.8228468 0.42866724729537964 True -9 27490 30.54157543182373 0.5798842906951904 472.1338195800781 0.41612809896469116 508.00909423828125 0.2526036202907562 0.8264027 0.4189463257789612 True -10 30239 30.508973121643066 0.5658810138702393 429.8146057128906 0.23714366555213928 506.4877014160156 0.25464344024658203 0.83170706 0.39277946949005127 True -11 32988 30.506269216537476 0.6006224155426025 397.794189453125 0.3101614713668823 506.9009094238281 0.2533003091812134 0.83917975 0.3600103259086609 True -12 35737 30.63321828842163 0.6227962970733643 416.0408935546875 0.3461754322052002 505.761962890625 0.2539219856262207 0.846261 0.3345138430595398 True -13 38486 30.629074096679688 2.805006265640259 442.9039001464844 0.2661009132862091 504.8516845703125 0.2552010118961334 0.848952 0.32715120911598206 True -14 41235 30.630775451660156 2.2839465141296387 420.075927734375 0.1795380711555481 504.1451416015625 0.25667718052864075 0.8545985 0.31729963421821594 True -15 43984 30.529463291168213 1.7890193462371826 428.0859375 0.23828117549419403 503.7496032714844 0.256452739238739 0.85798115 0.3049801290035248 True -16 46733 30.58133625984192 1.3254435062408447 453.88189697265625 0.282606840133667 503.79791259765625 0.25598353147506714 0.8611538 0.29713383316993713 True -17 49482 30.56442666053772 1.037278175354004 473.4716796875 0.14905627071857452 503.6430969238281 0.256533145904541 0.8594489 0.2982119917869568 False -18 52231 30.63410210609436 0.5752871036529541 454.1173400878906 0.2322688102722168 503.1002197265625 0.2578621506690979 0.85840476 0.3016357421875 False -19 54980 30.559335231781006 0.5842809677124023 508.4041442871094 0.13412843644618988 502.7742004394531 0.2583942413330078 0.8572862 0.30474379658699036 False diff --git a/ENCSR969QKG/cherimoya.fold_3.performance.tsv b/ENCSR969QKG/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 24cd6996def54bc760a8212deb2a1468f9d28714..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -503.79791259765625 0.4645933210849762 0.2559835612773895 0.1068112701177597 0.861153781414032 0.8162879347801208 0.29713383316993713 \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_4.evaluate.json b/ENCSR969QKG/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 492fc49b156af380719cdeafdb1f6cb6e730a5f5..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF141BVL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_4.fit.json b/ENCSR969QKG/cherimoya.fold_4.fit.json deleted file mode 100644 index 741a28fd3a7e1cc7b608709438fdda21da788921..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF141BVL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR969QKG/cherimoya.fold_4.log b/ENCSR969QKG/cherimoya.fold_4.log deleted file mode 100644 index 792f31265e0ad7acbe73bae6af00613cafccec85..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2795 36.09662222862244 3.98221492767334 457.8990783691406 0.3606971502304077 511.9783020019531 0.1840614229440689 0.70059776 3.798811197280884 True -1 5590 31.00824809074402 0.6724414825439453 403.39013671875 0.4489316940307617 482.8536071777344 0.22140449285507202 0.79100275 1.044251799583435 True -2 8385 31.057082653045654 0.5560662746429443 396.95556640625 0.22898165881633759 478.059814453125 0.22608967125415802 0.7965929 0.6149011850357056 True -3 11180 31.097633600234985 0.5562613010406494 367.44775390625 0.3852851986885071 476.7674255371094 0.22566816210746765 0.80451715 0.6370517015457153 True -4 13975 31.117721557617188 0.5687563419342041 492.79681396484375 0.47396546602249146 474.3446350097656 0.22766217589378357 0.81810945 0.453514039516449 True -5 16770 31.075359582901 0.5575852394104004 426.4197998046875 0.41386878490448 471.8786315917969 0.23182989656925201 0.8201821 0.4145306944847107 True -6 19565 31.024640560150146 0.5636534690856934 372.9146728515625 0.40561622381210327 470.3752746582031 0.23430363833904266 0.82542217 0.38236841559410095 True -7 22360 30.984795331954956 0.5547356605529785 394.4093933105469 0.1807798147201538 470.25579833984375 0.23412014544010162 0.83190763 0.365425169467926 True -8 25155 31.037888288497925 0.5577201843261719 441.28216552734375 0.2843484580516815 468.45068359375 0.23708517849445343 0.84001744 0.34100446105003357 True -9 27950 31.009680032730103 0.5545361042022705 391.1954345703125 0.17901723086833954 467.649169921875 0.23933649063110352 0.8441564 0.32448694109916687 True -10 30745 30.996612787246704 0.5604894161224365 486.8466796875 0.2845410704612732 466.6439208984375 0.2402477264404297 0.84955615 0.3082863688468933 True -11 33540 31.0135281085968 0.5974991321563721 383.7023010253906 0.15982484817504883 466.2275695800781 0.24086372554302216 0.85334384 0.28673678636550903 True -12 36335 31.03184962272644 0.551647424697876 416.946044921875 0.24579575657844543 465.2394714355469 0.24294914305210114 0.8563287 0.2751106917858124 True -13 39130 31.06463646888733 0.5603578090667725 424.61260986328125 0.2324628084897995 465.1141662597656 0.24193738400936127 0.8577178 0.2659167945384979 True -14 41925 31.091604948043823 0.5585794448852539 468.60113525390625 0.37074676156044006 464.8139953613281 0.2430589646100998 0.8631091 0.25428494811058044 True -15 44720 31.05573034286499 0.5605952739715576 493.16387939453125 0.18143630027770996 463.92138671875 0.2440161257982254 0.8677477 0.24521969258785248 True -16 47515 31.041144609451294 0.5586180686950684 424.6094665527344 0.22400450706481934 462.9161376953125 0.24518521130084991 0.8699968 0.23890036344528198 True -17 50310 31.071665048599243 0.5624616146087646 535.6831665039062 0.2114439606666565 465.0442199707031 0.24185222387313843 0.8708331 0.23943696916103363 True -18 53105 30.794356107711792 0.5556719303131104 465.1879577636719 0.22265878319740295 463.9494323730469 0.24438315629959106 0.86865264 0.24128100275993347 False -19 55900 30.41335654258728 0.5555272102355957 401.2955322265625 0.09204142540693283 464.724853515625 0.2426939606666565 0.86713314 0.24310898780822754 False diff --git a/ENCSR969QKG/cherimoya.fold_4.performance.tsv b/ENCSR969QKG/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 49ace4a28dafc4dfada0961370601f5617e90de8..0000000000000000000000000000000000000000 --- a/ENCSR969QKG/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -465.0442199707031 0.477726012468338 0.241852268576622 0.09696105122566223 0.8708330988883972 0.8148050904273987 0.23943696916103363 \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_0.evaluate.json b/ENCSR970UNF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 6188beb579ffdc0112435d131f2a784ae4875cc6..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF663BYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_0.fit.json b/ENCSR970UNF/cherimoya.fold_0.fit.json deleted file mode 100644 index 4799660da012de612a6769505cd05ab82d29f10a..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF663BYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_0.log b/ENCSR970UNF/cherimoya.fold_0.log deleted file mode 100644 index 14db6f74a025dc25a745ba99eb48a711ab6aa915..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3836 47.36859178543091 4.77621603012085 812.381591796875 0.9491466283798218 1440.23876953125 0.7504644989967346 0.6154573 10.920275688171387 True -1 7672 43.122798442840576 0.7656688690185547 896.0260009765625 1.0776704549789429 1156.169677734375 0.8378679156303406 0.6677012 1.3360044956207275 True -2 11508 42.72354793548584 0.7560989856719971 822.193603515625 0.8601152300834656 1124.7681884765625 0.8461806178092957 0.67445225 0.7752581834793091 True -3 15344 42.65581274032593 0.7617881298065186 939.4697875976562 0.7361992597579956 1103.0467529296875 0.852120041847229 0.6801364 0.6769060492515564 True -4 19180 42.731388568878174 2.9411380290985107 912.0581665039062 0.8532633781433105 1096.0853271484375 0.854055643081665 0.6799005 0.7106015086174011 False -5 23016 42.769487619400024 0.7555243968963623 948.3361206054688 0.6042935252189636 1088.965576171875 0.856162428855896 0.68344057 0.6705082654953003 True -6 26852 42.73181128501892 0.7506430149078369 756.891357421875 1.11741042137146 1082.100830078125 0.8584398031234741 0.69279337 0.6323717832565308 True -7 30688 42.5203959941864 0.7416605949401855 836.2034912109375 0.657695472240448 1073.2083740234375 0.8608338832855225 0.69292563 0.6146886944770813 True -8 34524 41.838979721069336 0.7397408485412598 936.2178344726562 0.5033725500106812 1066.9384765625 0.8632163405418396 0.6974738 0.6096233129501343 True -9 38360 41.81954884529114 0.7434611320495605 982.7359619140625 0.9407876133918762 1060.275390625 0.8653868436813354 0.6987107 0.6184812784194946 True -10 42196 41.80780053138733 1.280700445175171 863.365234375 0.763096272945404 1051.611328125 0.8676538467407227 0.706802 0.6042808294296265 True -11 46032 41.85371780395508 0.7471065521240234 891.572509765625 0.6627619862556458 1043.1119384765625 0.8700706958770752 0.71574306 0.5741486549377441 True -12 49868 41.90456676483154 0.7385542392730713 1085.1842041015625 0.5494710206985474 1036.1904296875 0.8721656203269958 0.72431797 0.5615456700325012 True -13 53704 41.90234875679016 0.7420992851257324 954.8651123046875 0.4377184510231018 1027.5994873046875 0.8746148943901062 0.73427695 0.5429086685180664 True -14 57540 41.894596099853516 0.739051342010498 930.8357543945312 0.7406302690505981 1021.1790771484375 0.8762063980102539 0.7419185 0.5228602886199951 True -15 61376 41.93306350708008 1.8111305236816406 894.240478515625 0.5210603475570679 1018.4699096679688 0.8774257898330688 0.7510919 0.5049002170562744 True -16 65212 41.839938163757324 27.61489748954773 833.4771118164062 0.653256356716156 1016.7113037109375 0.8778654336929321 0.75401235 0.4938555657863617 True -17 69048 42.086257219314575 0.7545647621154785 723.1421508789062 0.5127211809158325 1017.0588989257812 0.8779328465461731 0.7561581 0.49634870886802673 True -18 72884 41.86786675453186 0.7528886795043945 872.6082763671875 0.8538820147514343 1018.4142456054688 0.8774682283401489 0.755912 0.49890169501304626 False -19 76720 41.90376615524292 0.7383131980895996 818.2467041015625 0.35989928245544434 1019.3499145507812 0.8772513270378113 0.7551976 0.5027372241020203 False diff --git a/ENCSR970UNF/cherimoya.fold_0.performance.tsv b/ENCSR970UNF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7fd1e0579591c1ca532e4d8a07367011fd52278c..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1017.0588989257812 0.09948781132698059 0.8779327273368835 0.5918881297111511 0.7561581134796143 0.7167935371398926 0.49634870886802673 \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_1.evaluate.json b/ENCSR970UNF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 3ccb80b2603f4a55d05d9bf2300e47da40be5453..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF663BYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_1.fit.json b/ENCSR970UNF/cherimoya.fold_1.fit.json deleted file mode 100644 index c01066748fe3efa37d2e9fbcfb7eace03e4bf079..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF663BYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_1.log b/ENCSR970UNF/cherimoya.fold_1.log deleted file mode 100644 index d361e2048fc9854a2e05ecbf5653f18e961136dd..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3773 46.900394678115845 6.391474008560181 1035.20068359375 0.8784570693969727 1610.5347900390625 0.7583526968955994 0.62813467 10.592936515808105 True -1 7546 42.121830701828 19.216713190078735 861.295166015625 1.0341084003448486 1302.43701171875 0.842588484287262 0.67907983 2.188141345977783 True -2 11319 41.26606369018555 1.0682547092437744 993.9134521484375 0.8031092882156372 1258.95751953125 0.8512148261070251 0.69105947 0.8944054245948792 True -3 15092 41.14624643325806 1.0559172630310059 985.1705322265625 0.5895399451255798 1238.681396484375 0.8567498922348022 0.69801694 0.9443331360816956 True -4 18865 41.1525456905365 1.5656208992004395 1024.25634765625 0.8134000301361084 1224.4307861328125 0.8602274060249329 0.7005857 0.8486138582229614 True -5 22638 41.16655516624451 1.0831313133239746 1012.0535888671875 0.7357686161994934 1212.4898681640625 0.8626908659934998 0.70200384 0.8037174940109253 True -6 26411 41.13546657562256 1.0513465404510498 930.6396484375 0.8912317752838135 1206.068115234375 0.8647021651268005 0.7048333 0.7784351110458374 True -7 30184 41.26301455497742 1.0866825580596924 904.9579467773438 0.6297046542167664 1197.91455078125 0.8668431639671326 0.7084142 0.7849494814872742 True -8 33957 41.162928104400635 1.0445308685302734 907.904052734375 0.7146129608154297 1188.6470947265625 0.8689712882041931 0.71338373 0.7166508436203003 True -9 37730 41.132479429244995 1.2344660758972168 859.0208129882812 0.5133236050605774 1181.5380859375 0.8709258437156677 0.71985275 0.7038227319717407 True -10 41503 41.16996932029724 1.0335140228271484 859.1994018554688 0.6109155416488647 1172.5350341796875 0.8732789754867554 0.7252932 0.6797866225242615 True -11 45276 41.16750526428223 1.0457768440246582 953.5645751953125 1.0864518880844116 1162.5238037109375 0.8757335543632507 0.7363703 0.6583203673362732 True -12 49049 41.16654944419861 1.0615336894989014 852.305419921875 0.6115471720695496 1153.02783203125 0.8777070045471191 0.7452456 0.5919979214668274 True -13 52822 41.131497621536255 1.0438790321350098 794.55615234375 0.6121922731399536 1144.8121337890625 0.8797668218612671 0.7575382 0.557503342628479 True -14 56595 41.183955907821655 1.0304057598114014 1021.2560424804688 0.8006385564804077 1137.7225341796875 0.8816269636154175 0.76334554 0.5428324937820435 True -15 60368 41.175867557525635 1.4371750354766846 797.678466796875 0.739999532699585 1132.968505859375 0.8828914165496826 0.770651 0.5241492986679077 True -16 64141 41.22128129005432 1.0329005718231201 775.248046875 0.6514562368392944 1131.2806396484375 0.8835628628730774 0.77523106 0.5154560804367065 True -17 67914 41.15447235107422 1.0811948776245117 800.232177734375 0.42536336183547974 1130.79248046875 0.8834844827651978 0.7778791 0.501163899898529 True -18 71687 41.17351531982422 1.0493030548095703 738.7298583984375 0.40520530939102173 1132.247802734375 0.8831647038459778 0.779262 0.5021254420280457 True -19 75460 41.25716495513916 37.572914361953735 795.7669677734375 0.6137165427207947 1133.3446044921875 0.8828449845314026 0.7782927 0.505186140537262 False diff --git a/ENCSR970UNF/cherimoya.fold_1.performance.tsv b/ENCSR970UNF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index e442eb010be71abf9cc96e29b48427cd26bc7d8a..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1132.247802734375 0.09100430458784103 0.8831647634506226 0.6282235383987427 0.7792620062828064 0.766061007976532 0.5021254420280457 \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_2.evaluate.json b/ENCSR970UNF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 261cc34be56366a1e45dd660b936e538fe5b52cf..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF663BYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_2.fit.json b/ENCSR970UNF/cherimoya.fold_2.fit.json deleted file mode 100644 index e6a1f61ed29092835736571b5ce022da2c2ca01f..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF663BYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_2.log b/ENCSR970UNF/cherimoya.fold_2.log deleted file mode 100644 index 04afdb878135b948e63e4598c08aa161a18abd8a..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3997 49.39093017578125 5.33862829208374 1037.186279296875 0.7217621803283691 1487.28076171875 0.7621302008628845 0.6369128 9.668428421020508 True -1 7994 44.55368137359619 1.046435832977295 951.2351684570312 1.1387355327606201 1231.0787353515625 0.8374112248420715 0.67849094 1.8954346179962158 True -2 11991 44.53834414482117 0.8293709754943848 986.2507934570312 1.2874159812927246 1196.1529541015625 0.8453770875930786 0.6902157 0.9232507944107056 True -3 15988 44.56706213951111 0.8277440071105957 883.4512939453125 0.9440670013427734 1178.8486328125 0.8495239019393921 0.6897525 0.9787114858627319 False -4 19985 44.52226233482361 0.8177220821380615 972.1161499023438 0.8127254247665405 1170.746337890625 0.8528949618339539 0.6933539 1.022635579109192 True -5 23982 44.463746547698975 0.7843127250671387 902.2055053710938 0.6593614816665649 1161.6536865234375 0.8553311228752136 0.69573134 0.953798234462738 True -6 27979 44.622464179992676 0.7892272472381592 893.6822509765625 0.4858691096305847 1157.8819580078125 0.8560155034065247 0.6913792 0.8632338047027588 False -7 31976 44.51846408843994 0.7840938568115234 1163.565185546875 1.223952054977417 1140.949462890625 0.8600080013275146 0.70455587 0.8132661581039429 True -8 35973 44.64891982078552 0.8053007125854492 831.9241943359375 0.6785805821418762 1132.05859375 0.8629494309425354 0.70940363 0.750603437423706 True -9 39970 44.67077422142029 0.8023223876953125 951.37548828125 1.0605640411376953 1122.11865234375 0.86510169506073 0.7164672 0.70355224609375 True -10 43967 44.698216676712036 0.7908284664154053 966.3123168945312 0.7403719425201416 1111.03125 0.867474377155304 0.72807854 0.6343116164207458 True -11 47964 44.56271290779114 2.1096465587615967 850.6500244140625 0.41441985964775085 1101.8447265625 0.8702267408370972 0.73608905 0.6211092472076416 True -12 51961 44.56575894355774 0.7858388423919678 834.2107543945312 0.7154649496078491 1093.383544921875 0.872698187828064 0.7434292 0.5919811129570007 True -13 55958 44.20102858543396 0.7970442771911621 843.912841796875 0.4441000521183014 1084.6446533203125 0.8749307990074158 0.7500221 0.55845707654953 True -14 59955 43.67114305496216 0.777712345123291 760.8946533203125 0.4195865988731384 1077.4544677734375 0.8768354058265686 0.7575615 0.5356863141059875 True -15 63952 43.601619243621826 0.7796652317047119 951.31005859375 0.6324390172958374 1073.409912109375 0.8782376646995544 0.7638935 0.5075790882110596 True -16 67949 43.72988796234131 0.7865598201751709 825.8766479492188 0.3433776795864105 1069.6881103515625 0.8790748119354248 0.77048194 0.49607446789741516 True -17 71946 43.71152329444885 1.028965950012207 825.471923828125 0.4184631407260895 1069.8818359375 0.8790495991706848 0.77155143 0.49038755893707275 True -18 75943 43.76225423812866 0.7965047359466553 927.2223510742188 0.3359169661998749 1071.478515625 0.878656268119812 0.7729582 0.4899885058403015 True -19 79940 43.64311337471008 0.7978696823120117 793.2933349609375 0.35598522424697876 1072.779541015625 0.8784547448158264 0.77180105 0.4918676018714905 False diff --git a/ENCSR970UNF/cherimoya.fold_2.performance.tsv b/ENCSR970UNF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index f4b8bb60a51c7e0e0cbd2609f4e91993fbb887ff..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1071.478515625 0.0958404615521431 0.878656268119812 0.6097158789634705 0.7729582190513611 0.7445316910743713 0.4899885058403015 \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_3.evaluate.json b/ENCSR970UNF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7d4232fa262e51029b34fbe57d687229a9810185..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF663BYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_3.fit.json b/ENCSR970UNF/cherimoya.fold_3.fit.json deleted file mode 100644 index 19819714b49e26829d116e846d730aeb57093b21..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF663BYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_3.log b/ENCSR970UNF/cherimoya.fold_3.log deleted file mode 100644 index 45ff84d409e5789db8121b9a45bc342c59f59a3c..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3904 48.33391571044922 4.839508056640625 1049.935546875 0.7841068506240845 1444.7049560546875 0.7573766708374023 0.6006535 9.423955917358398 True -1 7808 43.62765693664551 1.2695248126983643 1080.77099609375 1.3823533058166504 1193.74609375 0.8366750478744507 0.6445798 1.886859655380249 True -2 11712 43.58479833602905 1.0270884037017822 980.0927734375 0.7925636768341064 1152.8740234375 0.8452609777450562 0.65344286 1.3009213209152222 True -3 15616 43.527130126953125 0.9182381629943848 860.9118041992188 0.6792987585067749 1134.876708984375 0.850002646446228 0.65174866 1.0601540803909302 False -4 19520 43.51564860343933 0.8184530735015869 930.9395751953125 0.8194890022277832 1123.855712890625 0.8523758053779602 0.6545115 0.9240508675575256 True -5 23424 43.475467920303345 0.8354628086090088 827.2142333984375 1.0936651229858398 1117.2451171875 0.8546764254570007 0.6592207 0.8471565842628479 True -6 27328 43.55255937576294 0.8734047412872314 944.827392578125 0.9245038628578186 1107.727783203125 0.8574042916297913 0.665935 0.7992919683456421 True -7 31232 43.58037829399109 0.8510310649871826 1065.58544921875 0.8499287366867065 1099.629150390625 0.8596274256706238 0.66882193 0.8090726733207703 True -8 35136 43.420554637908936 2.5071659088134766 1001.9429931640625 0.5553720593452454 1092.89111328125 0.8621281981468201 0.6801154 0.7845125794410706 True -9 39040 42.74516725540161 0.8448548316955566 807.8450927734375 1.4377609491348267 1086.1561279296875 0.8639769554138184 0.6806503 0.7140353322029114 True -10 42944 42.94498610496521 0.8517696857452393 986.04345703125 0.5453668832778931 1079.2205810546875 0.8664127588272095 0.691288 0.6934967041015625 True -11 46848 42.801921367645264 0.8946468830108643 850.623779296875 0.4748481512069702 1069.5504150390625 0.8685481548309326 0.7005458 0.6314750909805298 True -12 50752 42.871761083602905 0.8356397151947021 920.29345703125 0.5285377502441406 1061.99267578125 0.8712827563285828 0.71069735 0.6095693111419678 True -13 54656 42.82122302055359 0.8285825252532959 790.0642700195312 0.48140832781791687 1054.33056640625 0.8735365867614746 0.7247273 0.5823765397071838 True -14 58560 42.852978229522705 33.35669708251953 814.6483764648438 0.6556456685066223 1047.415771484375 0.8754198551177979 0.73409766 0.5534791350364685 True -15 62464 42.75075697898865 0.8363313674926758 930.0946044921875 0.5161314010620117 1043.3939208984375 0.876736044883728 0.742768 0.5333621501922607 True -16 66368 42.93429660797119 0.8588056564331055 725.482666015625 0.4480922222137451 1041.140869140625 0.8772521615028381 0.74664783 0.5241466760635376 True -17 70272 42.87743520736694 2.2972288131713867 991.0484619140625 0.6000249981880188 1042.4283447265625 0.8771239519119263 0.7483764 0.5245259404182434 True -18 74176 42.839176654815674 0.837979793548584 875.8372192382812 0.4063934087753296 1043.935791015625 0.8767343163490295 0.7489616 0.5313559174537659 True -19 78080 42.8309850692749 0.8726909160614014 830.3609619140625 0.46032947301864624 1044.4757080078125 0.876444399356842 0.7473022 0.5359891653060913 False diff --git a/ENCSR970UNF/cherimoya.fold_3.performance.tsv b/ENCSR970UNF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f96ccdecaee39d7985330ae7bede21aa25672be0..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1043.935791015625 0.09802521765232086 0.8767343163490295 0.5965354442596436 0.7489616274833679 0.7179361581802368 0.5313559174537659 \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_4.evaluate.json b/ENCSR970UNF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e187ab2a02c3d0400f52dc1d5bfe7edcaec243d4..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF663BYV.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_4.fit.json b/ENCSR970UNF/cherimoya.fold_4.fit.json deleted file mode 100644 index d430cabaec3c60c8aa49c0844038b032a4cc082b..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF663BYV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR970UNF/cherimoya.fold_4.log b/ENCSR970UNF/cherimoya.fold_4.log deleted file mode 100644 index 3e0282fa32fd09987a10bec07cb1a14fff91bf3c..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3929 48.56519627571106 4.449625492095947 941.2825317382812 0.9982308745384216 1387.954833984375 0.7517477869987488 0.59445417 10.122542381286621 True -1 7858 43.788816928863525 0.7897579669952393 1013.925537109375 0.8938994407653809 1138.705078125 0.8343030214309692 0.6523586 1.2652993202209473 True -2 11787 43.839422941207886 0.8019757270812988 930.3867797851562 1.1246665716171265 1098.56689453125 0.8445909023284912 0.6567625 0.812646210193634 True -3 15716 43.829314947128296 0.7569880485534668 881.726806640625 1.0340518951416016 1079.4288330078125 0.8500165343284607 0.66143054 0.7550964951515198 True -4 19645 43.4048855304718 2.281595230102539 1209.8868408203125 0.5480782985687256 1071.826904296875 0.8520999550819397 0.66663444 0.7441778182983398 True -5 23574 43.069908618927 0.8317463397979736 862.1636962890625 0.9488257169723511 1064.5875244140625 0.8550271391868591 0.6647074 0.7705608010292053 False -6 27503 43.020519733428955 0.7533297538757324 976.3201904296875 0.6930622458457947 1055.7811279296875 0.8577370047569275 0.673842 0.6590877771377563 True -7 31432 43.00571894645691 1.2940292358398438 903.05517578125 0.7798759937286377 1048.452880859375 0.8601870536804199 0.6739599 0.6548122763633728 True -8 35361 43.01245641708374 0.7584455013275146 936.366943359375 0.9895944595336914 1043.5535888671875 0.8621184229850769 0.683092 0.6662106513977051 True -9 39290 43.05799150466919 0.766768217086792 878.693603515625 0.6607722043991089 1036.702392578125 0.8639276623725891 0.6891654 0.6622834801673889 True -10 43219 43.017539739608765 0.7605772018432617 796.9136962890625 0.49553489685058594 1029.4471435546875 0.8664575815200806 0.6979259 0.6251935362815857 True -11 47148 43.09969711303711 0.7531592845916748 934.0804443359375 0.6957936882972717 1022.4755249023438 0.8682839870452881 0.71136856 0.5884732007980347 True -12 51077 43.04472827911377 0.7952942848205566 931.4569702148438 0.7958258986473083 1014.787353515625 0.8704997897148132 0.7164317 0.5708149671554565 True -13 55006 45.09147667884827 15.385197162628174 836.92333984375 0.5428934097290039 1009.3416137695312 0.8722958564758301 0.7287836 0.5424811840057373 True -14 58935 43.06993055343628 0.7554614543914795 890.5350952148438 0.45037534832954407 1003.0965576171875 0.874213695526123 0.7370622 0.5152891278266907 True -15 62864 44.15465831756592 24.415263414382935 782.758544921875 0.7002673149108887 998.5208740234375 0.8756290078163147 0.74596334 0.5021405220031738 True -16 66793 42.95532035827637 0.7579741477966309 976.688232421875 0.539175271987915 997.0948486328125 0.8761729598045349 0.7508458 0.4905836582183838 True -17 70722 42.94071841239929 0.7605106830596924 899.3192138671875 0.2694040834903717 998.3145141601562 0.8760778903961182 0.7527289 0.4921240508556366 True -18 74651 42.96217203140259 0.7561843395233154 798.8189697265625 0.6812599897384644 1000.0150756835938 0.8755888342857361 0.7501852 0.49667778611183167 False -19 78580 43.057159662246704 0.760296106338501 821.9644775390625 0.5452402234077454 1001.51806640625 0.8753107190132141 0.7507137 0.4998028576374054 False diff --git a/ENCSR970UNF/cherimoya.fold_4.performance.tsv b/ENCSR970UNF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 745ff7291dad1aa983c7a3c6c0792296a8b338ed..0000000000000000000000000000000000000000 --- a/ENCSR970UNF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -998.3145141601562 0.10082618147134781 0.8760778903961182 0.5860143303871155 0.7527288794517517 0.7055773735046387 0.4921240508556366 \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_0.evaluate.json b/ENCSR971MMF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index c86e5d3991a544ff4edbcbae80490ff49c40ddf6..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272CCY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_0.fit.json b/ENCSR971MMF/cherimoya.fold_0.fit.json deleted file mode 100644 index 42b71b618471ec92c5a4d97e946a2cb711920fb3..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF272CCY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_0.log b/ENCSR971MMF/cherimoya.fold_0.log deleted file mode 100644 index 95c8c65ebf0bf83016dca9d6a626821e035bf6b0..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2730 33.908414363861084 3.6565208435058594 300.66815185546875 0.44456610083580017 324.4117736816406 0.1687016636133194 0.7200851 2.937255620956421 True -1 5460 30.155576467514038 0.5542616844177246 213.31939697265625 0.2937157154083252 309.6675109863281 0.20890595018863678 0.7840224 0.9022960066795349 True -2 8190 30.119864463806152 0.5444343090057373 237.47933959960938 0.3921583890914917 306.57958984375 0.21383149921894073 0.7926548 0.5444267392158508 True -3 10920 30.11387801170349 2.598421335220337 240.66514587402344 0.38094401359558105 305.0845947265625 0.21691183745861053 0.80157113 0.38063982129096985 True -4 13650 30.155844688415527 0.5577020645141602 225.112060546875 0.3405178487300873 304.4345703125 0.21817362308502197 0.8115368 0.3828338086605072 True -5 16380 30.180763006210327 0.5526971817016602 296.9281921386719 0.25476694107055664 303.65753173828125 0.22143477201461792 0.8179051 0.4013473391532898 True -6 19110 30.18608331680298 0.5388872623443604 236.60800170898438 0.3036592900753021 303.2034606933594 0.2232210338115692 0.8206008 0.4211944043636322 True -7 21840 30.157780647277832 0.5467453002929688 241.5115966796875 0.29500043392181396 302.7779846191406 0.22353015840053558 0.82850647 0.3654750883579254 True -8 24570 30.151567459106445 0.5549540519714355 312.858154296875 0.3578772246837616 302.45416259765625 0.22495663166046143 0.83422095 0.34551215171813965 True -9 27300 29.678301572799683 0.5532441139221191 199.29722595214844 0.3590359091758728 302.0254821777344 0.22574292123317719 0.84150547 0.32132694125175476 True -10 30030 29.64698076248169 0.5492496490478516 260.762939453125 0.480401873588562 301.4992370605469 0.22774603962898254 0.8442322 0.30136632919311523 True -11 32760 29.637503623962402 0.5492110252380371 235.37841796875 0.24949334561824799 301.29498291015625 0.22851824760437012 0.85127264 0.28320831060409546 True -12 35490 29.641640186309814 1.1353838443756104 271.7508850097656 0.2854589521884918 300.71636962890625 0.23062752187252045 0.8521893 0.26977330446243286 True -13 38220 29.69992423057556 0.5410952568054199 253.22622680664062 0.29927659034729004 300.8734130859375 0.22938570380210876 0.8553131 0.2560899555683136 True -14 40950 29.544105052947998 0.5424947738647461 286.19952392578125 0.4198042154312134 300.603759765625 0.2300310581922531 0.858872 0.24612993001937866 True -15 43680 29.532240867614746 0.535991907119751 256.72711181640625 0.21548908948898315 300.12347412109375 0.23196463286876678 0.8596142 0.2401093691587448 True -16 46410 29.66506552696228 0.5347447395324707 292.5801086425781 0.2577563524246216 300.2997131347656 0.2311037927865982 0.8630128 0.23619310557842255 True -17 49140 29.6266667842865 0.5347611904144287 295.86248779296875 0.22198447585105896 300.1061096191406 0.2317545861005783 0.86202663 0.23808349668979645 False -18 51870 29.53550672531128 0.5326540470123291 222.03964233398438 0.16197934746742249 300.6810607910156 0.23009684681892395 0.8605471 0.23860852420330048 False -19 54600 29.564436197280884 0.5421402454376221 274.63983154296875 0.14027643203735352 300.5101318359375 0.2310461401939392 0.857804 0.24053855240345 False diff --git a/ENCSR971MMF/cherimoya.fold_0.performance.tsv b/ENCSR971MMF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fce2619d6885a62827c37930124505d7c88879ea..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -300.2997131347656 0.514062225818634 0.2311038076877594 0.0736381858587265 0.8630127906799316 0.8127949237823486 0.23619310557842255 \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_1.evaluate.json b/ENCSR971MMF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 27c382c9708cde73163ffba655bda0295b28b0a3..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272CCY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_1.fit.json b/ENCSR971MMF/cherimoya.fold_1.fit.json deleted file mode 100644 index 9ab2c7d5891f6d14371a0a71d3cb5f6cbd21b435..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF272CCY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_1.log b/ENCSR971MMF/cherimoya.fold_1.log deleted file mode 100644 index ea20ad7392d44b63d31e3d90f9665ac29949a2c2..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2687 33.54829740524292 3.6557910442352295 297.1007080078125 0.4896908402442932 370.00323486328125 0.17956297099590302 0.7374672 3.6469085216522217 True -1 5374 29.66658067703247 0.7546393871307373 273.68994140625 0.4871810972690582 350.22174072265625 0.2246377170085907 0.80579907 0.973753035068512 True -2 8061 29.59613347053528 0.7309565544128418 259.0867919921875 0.37801384925842285 347.71868896484375 0.2295699566602707 0.81335163 0.623872697353363 True -3 10748 29.58010983467102 0.7326979637145996 243.57757568359375 0.3872361183166504 347.06494140625 0.22849231958389282 0.82250196 0.42606887221336365 True -4 13435 29.60128903388977 0.7274277210235596 232.41363525390625 0.3927854895591736 345.91473388671875 0.2309732586145401 0.8241171 0.4153926372528076 True -5 16122 29.637457132339478 3.7089426517486572 233.59564208984375 0.45278263092041016 344.8660888671875 0.23426903784275055 0.8280883 0.4353858232498169 True -6 18809 29.63387703895569 0.7586672306060791 228.61172485351562 0.3242540657520294 344.22174072265625 0.23551912605762482 0.8356464 0.44044026732444763 True -7 21496 29.656802654266357 0.7518813610076904 320.810302734375 0.4028239846229553 343.3963928222656 0.2383202314376831 0.84127903 0.4162333309650421 True -8 24183 29.56831979751587 0.7430315017700195 255.18099975585938 0.361214280128479 342.9750061035156 0.23912575840950012 0.8496683 0.4039785861968994 True -9 26870 29.65512204170227 0.7667295932769775 314.87176513671875 0.3020288944244385 342.383056640625 0.2413831353187561 0.8555315 0.3822406530380249 True -10 29557 29.66496515274048 0.7747929096221924 268.664794921875 0.24624457955360413 342.0314025878906 0.2417725920677185 0.8614902 0.3749517500400543 True -11 32244 29.259809732437134 0.7419681549072266 278.6320495605469 0.414935827255249 341.469970703125 0.2440629005432129 0.8632734 0.3629832863807678 True -12 34931 29.190654516220093 0.7419900894165039 255.4860382080078 0.2700524628162384 340.6954040527344 0.24581147730350494 0.8692044 0.3264145851135254 True -13 37618 29.30494451522827 0.7518138885498047 238.92373657226562 0.3456805944442749 340.8397521972656 0.2450484037399292 0.87611866 0.3044651448726654 True -14 40305 29.23308777809143 0.7379240989685059 265.12982177734375 0.306125283241272 340.13519287109375 0.24675610661506653 0.87857753 0.2867093086242676 True -15 42992 29.183069944381714 0.7391526699066162 295.7265930175781 0.3854386806488037 339.6338195800781 0.2484743595123291 0.8795246 0.2716001868247986 True -16 45679 29.232625722885132 0.7427842617034912 253.59140014648438 0.24927330017089844 339.5858154296875 0.24802526831626892 0.8791747 0.2641853392124176 False -17 48366 29.258070707321167 0.7443718910217285 237.6052703857422 0.2127721905708313 339.973388671875 0.24710872769355774 0.8799196 0.2585153579711914 True -18 51053 29.208494186401367 0.736187219619751 267.91253662109375 0.21601411700248718 339.8468017578125 0.24769149720668793 0.87907875 0.2622823119163513 False -19 53740 29.213051557540894 0.7399046421051025 266.92047119140625 0.16460049152374268 339.9188537597656 0.2471403181552887 0.87662405 0.2640484869480133 False diff --git a/ENCSR971MMF/cherimoya.fold_1.performance.tsv b/ENCSR971MMF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 20ecf7247197d0968ef0290182e7ef8c1b63c0c5..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -339.973388671875 0.49814528226852417 0.24710875749588013 0.08502572774887085 0.8799195885658264 0.8514924049377441 0.2585153579711914 \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_2.evaluate.json b/ENCSR971MMF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index f437b31d4afcce46f2094ce39aed2fcbcf0335f6..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272CCY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_2.fit.json b/ENCSR971MMF/cherimoya.fold_2.fit.json deleted file mode 100644 index 6afbf93127390731c0f12bf33c446db6495bc26e..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF272CCY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_2.log b/ENCSR971MMF/cherimoya.fold_2.log deleted file mode 100644 index e8f997bd75b1cd859ac1ff97a562467de9300630..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2901 35.78254008293152 3.7746071815490723 290.7628173828125 0.40959686040878296 342.18719482421875 0.1709083765745163 0.70855194 2.7792067527770996 True -1 5802 32.185842752456665 0.5588953495025635 260.0710144042969 0.3351711630821228 324.76324462890625 0.21633684635162354 0.7789886 0.928187906742096 True -2 8703 31.674618005752563 0.5206465721130371 266.49053955078125 0.4636228680610657 321.5295715332031 0.2202659547328949 0.7905088 0.5893949270248413 True -3 11604 31.48784875869751 0.5290846824645996 262.47747802734375 0.2613929808139801 319.6258239746094 0.22357089817523956 0.8012495 0.4301719069480896 True -4 14505 31.369892358779907 0.521651029586792 282.9844970703125 0.3623109459877014 318.5774841308594 0.22597728669643402 0.809593 0.40935030579566956 True -5 17406 31.36499857902527 0.5247740745544434 253.94882202148438 0.404428094625473 317.6455993652344 0.2293214350938797 0.8166265 0.408198744058609 True -6 20307 31.437132358551025 2.3629698753356934 272.69464111328125 0.29436901211738586 317.2699890136719 0.23034465312957764 0.8173893 0.4271364212036133 True -7 23208 31.69013810157776 0.5192735195159912 265.24383544921875 0.37210071086883545 316.83905029296875 0.23113739490509033 0.82467663 0.39537233114242554 True -8 26109 31.416579484939575 0.5202383995056152 298.32244873046875 0.3679547905921936 316.30096435546875 0.23313631117343903 0.831512 0.37584760785102844 True -9 29010 31.450256824493408 21.592318773269653 243.2442626953125 0.4231221675872803 315.7694091796875 0.2338104099035263 0.83723205 0.34755656123161316 True -10 31911 31.488940477371216 0.5294559001922607 242.1316375732422 0.3685670793056488 315.3800964355469 0.2352946251630783 0.84248567 0.3367314338684082 True -11 34812 31.47953152656555 0.53299880027771 252.03521728515625 0.3094189167022705 314.8041687011719 0.23709943890571594 0.8472707 0.31342440843582153 True -12 37713 31.972392559051514 0.5311629772186279 268.3358459472656 0.2596833109855652 314.3165588378906 0.23869824409484863 0.8498043 0.2975262701511383 True -13 40614 31.550471544265747 0.5209646224975586 247.8287811279297 0.2051464319229126 314.325439453125 0.23837162554264069 0.8547292 0.27503839135169983 True -14 43515 31.461827993392944 0.5209333896636963 280.99420166015625 0.17662957310676575 313.8216857910156 0.23919935524463654 0.8561862 0.2668372690677643 True -15 46416 31.461917638778687 0.5259268283843994 245.85699462890625 0.21500703692436218 313.7910461425781 0.23983359336853027 0.85942173 0.2548816204071045 True -16 49317 31.46124005317688 0.5270445346832275 241.31100463867188 0.19956885278224945 313.6565246582031 0.23997749388217926 0.8608259 0.24846868216991425 True -17 52218 31.441373348236084 0.5259222984313965 251.45387268066406 0.2903949022293091 313.6709899902344 0.2398144155740738 0.8596999 0.24740280210971832 False -18 55119 31.7267644405365 14.090253353118896 231.39434814453125 0.18459098041057587 314.0289001464844 0.23841068148612976 0.8595786 0.24858593940734863 False -19 58020 31.559141635894775 0.8667812347412109 248.050537109375 0.15288513898849487 313.942138671875 0.23893481492996216 0.85813576 0.25007739663124084 False diff --git a/ENCSR971MMF/cherimoya.fold_2.performance.tsv b/ENCSR971MMF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 8129780db1ce90a635b73f792f4df5254fed64a8..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -313.6565246582031 0.507533609867096 0.23997749388217926 0.07662853598594666 0.8608258962631226 0.8218050003051758 0.24846868216991425 \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_3.evaluate.json b/ENCSR971MMF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7be0fc5e333d302b404239e3e5a4d2eb5893b29e..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272CCY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_3.fit.json b/ENCSR971MMF/cherimoya.fold_3.fit.json deleted file mode 100644 index 2fe92d2b890fa87df2776e0d026c0e6190100f8b..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF272CCY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_3.log b/ENCSR971MMF/cherimoya.fold_3.log deleted file mode 100644 index 7f0a8713523dee1278652b27c1baab105261c756..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 34.25071048736572 3.5118191242218018 269.00994873046875 0.3623250722885132 335.103759765625 0.1776224672794342 0.69114923 3.3763861656188965 True -1 5534 30.585825443267822 0.5555033683776855 255.96144104003906 0.4183765649795532 321.775146484375 0.21200776100158691 0.7612865 0.9762586355209351 True -2 8301 30.516846179962158 0.5451021194458008 273.66632080078125 0.329397976398468 318.9206848144531 0.21762679517269135 0.77594197 0.7130475044250488 True -3 11068 30.544334650039673 0.5432426929473877 338.17767333984375 0.38952702283859253 317.63427734375 0.22043393552303314 0.77839947 0.5405384302139282 True -4 13835 30.423760414123535 0.5416207313537598 269.63250732421875 0.3436379134654999 316.3829040527344 0.22478021681308746 0.7769654 0.5618504285812378 False -5 16602 30.470401525497437 0.5329680442810059 294.7251892089844 0.4395737946033478 316.1588439941406 0.22528265416622162 0.78798366 0.5437238812446594 True -6 19369 30.48262667655945 0.5298066139221191 215.10220336914062 0.38813525438308716 315.7987365722656 0.22622503340244293 0.7994257 0.5092085003852844 True -7 22136 30.156809091567993 0.5421772003173828 268.05023193359375 0.43129652738571167 315.3586730957031 0.22747169435024261 0.8033185 0.4934689402580261 True -8 24903 29.91926598548889 0.54593825340271 238.21371459960938 0.3527854382991791 314.6136169433594 0.2304064929485321 0.8129129 0.4428306818008423 True -9 27670 29.923113346099854 0.538848876953125 243.89183044433594 0.2973650395870209 313.7189636230469 0.23353725671768188 0.81819624 0.42145368456840515 True -10 30437 29.933325052261353 2.009455919265747 242.78237915039062 0.30180245637893677 314.2578125 0.23079153895378113 0.82168025 0.4101656675338745 True -11 33204 29.952587366104126 0.5453858375549316 254.91944885253906 0.33666443824768066 313.70465087890625 0.23274177312850952 0.829523 0.3702631890773773 True -12 35971 29.93433904647827 0.5393598079681396 252.0619354248047 0.23620645701885223 313.1907958984375 0.23477286100387573 0.83411837 0.34868961572647095 True -13 38738 29.93979239463806 2.30206561088562 262.8258972167969 0.19008097052574158 313.0711975097656 0.2345472276210785 0.8381326 0.33485954999923706 True -14 41505 29.94533395767212 0.548269510269165 224.434326171875 0.20626820623874664 312.9308166503906 0.23438552021980286 0.84145766 0.31540900468826294 True -15 44272 29.939793586730957 0.5409553050994873 243.1852569580078 0.13438045978546143 312.8306579589844 0.23491503298282623 0.84644103 0.30271050333976746 True -16 47039 29.969341278076172 0.5409440994262695 297.7023010253906 0.1594688445329666 312.40911865234375 0.235258087515831 0.8490112 0.29176032543182373 True -17 49806 29.943881511688232 0.5394270420074463 275.77685546875 0.2447250634431839 312.029296875 0.23679354786872864 0.84825253 0.286277174949646 False -18 52573 29.974303483963013 0.5412051677703857 316.2328796386719 0.26112276315689087 312.08221435546875 0.23654736578464508 0.847054 0.28966665267944336 False -19 55340 29.918267250061035 0.5367343425750732 299.35174560546875 0.13121755421161652 312.0725402832031 0.23651687800884247 0.84523386 0.29239094257354736 False diff --git a/ENCSR971MMF/cherimoya.fold_3.performance.tsv b/ENCSR971MMF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f6db3f6ac7da7f8bdce3b466a96460de03dd3f15..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -312.40911865234375 0.5086040496826172 0.235258087515831 0.0794161856174469 0.8490111827850342 0.8083110451698303 0.29176032543182373 \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_4.evaluate.json b/ENCSR971MMF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 944b81d3442c3a1db560f4f67bbdeb98346879d6..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF272CCY.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_4.fit.json b/ENCSR971MMF/cherimoya.fold_4.fit.json deleted file mode 100644 index 468638c3b6c18338425fed73b090811825dd905e..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF272CCY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_4.log b/ENCSR971MMF/cherimoya.fold_4.log deleted file mode 100644 index b9a86eb7600ed76479c193247fc3b2ef575a54a2..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2832 34.943130016326904 3.569197654724121 247.6552276611328 0.43221545219421387 288.5752868652344 0.16419678926467896 0.7078186 2.658352851867676 True -1 5664 31.251989603042603 0.6000199317932129 242.37986755371094 0.4171777367591858 275.9244079589844 0.1967751383781433 0.78305405 0.6798005700111389 True -2 8496 31.28100085258484 0.5796079635620117 250.07415771484375 0.43211519718170166 274.3513488769531 0.20000861585140228 0.79539204 0.4686832129955292 True -3 11328 31.229989767074585 0.5928678512573242 243.47097778320312 0.44536256790161133 273.87188720703125 0.1994916796684265 0.80302984 0.3477170169353485 True -4 14160 31.205644369125366 0.5818421840667725 261.84814453125 0.29815033078193665 273.2006530761719 0.20178668200969696 0.80868965 0.37766528129577637 True -5 16992 31.220172882080078 0.5733582973480225 316.9315185546875 0.5420401692390442 272.0601806640625 0.2061711549758911 0.8146894 0.3910316228866577 True -6 19824 31.24172067642212 0.5895030498504639 282.24029541015625 0.2860536277294159 271.9906311035156 0.20592986047267914 0.8219358 0.3860659599304199 True -7 22656 31.164276123046875 0.5933961868286133 270.716064453125 0.31525421142578125 271.646728515625 0.20707771182060242 0.8267963 0.3927721381187439 True -8 25488 31.232428073883057 0.8380005359649658 308.36376953125 0.37031203508377075 271.0628356933594 0.209265798330307 0.83134896 0.35700318217277527 True -9 28320 31.19317650794983 0.5949530601501465 261.9895324707031 0.23514807224273682 270.8340759277344 0.20962533354759216 0.8409842 0.31159284710884094 True -10 31152 31.218405961990356 0.5860435962677002 218.77337646484375 0.3001994490623474 270.7046203613281 0.2095046043395996 0.8453027 0.28853949904441833 True -11 33984 31.208577632904053 0.5793914794921875 264.8538513183594 0.23205019533634186 270.1864929199219 0.21163877844810486 0.84764 0.2716027796268463 True -12 36816 31.243881940841675 0.592172384262085 239.66787719726562 0.29761573672294617 269.79095458984375 0.21331645548343658 0.8539328 0.2451072633266449 True -13 39648 31.101884841918945 0.582848310470581 248.50155639648438 0.25629618763923645 269.71014404296875 0.21350984275341034 0.85840476 0.23425182700157166 True -14 42480 30.616122484207153 0.5855443477630615 207.04347229003906 0.304048627614975 269.51141357421875 0.21410273015499115 0.86056787 0.22170615196228027 True -15 45312 30.648428201675415 0.586686372756958 255.8340606689453 0.20041745901107788 269.5283508300781 0.21334005892276764 0.86241955 0.2143295407295227 True -16 48144 30.626956701278687 0.5851716995239258 246.59381103515625 0.16072401404380798 269.43902587890625 0.21359167993068695 0.86410046 0.21192814409732819 True -17 50976 30.603577375411987 0.5904674530029297 236.17776489257812 0.15840518474578857 269.7368469238281 0.21283583343029022 0.8628226 0.20984533429145813 False -18 53808 30.67182469367981 0.5811927318572998 225.34112548828125 0.2061648964881897 269.51715087890625 0.21334081888198853 0.862222 0.21349070966243744 False -19 56640 30.634082317352295 0.6009018421173096 284.50616455078125 0.18485739827156067 269.5481872558594 0.21361593902111053 0.86158633 0.2145349681377411 False diff --git a/ENCSR971MMF/cherimoya.fold_4.performance.tsv b/ENCSR971MMF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4c155f2f7443bfeb10e187e213788bbca754c892..0000000000000000000000000000000000000000 --- a/ENCSR971MMF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -269.43902587890625 0.5294126272201538 0.21359169483184814 0.06418660283088684 0.864100456237793 0.7948087453842163 0.21192814409732819 \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_0.evaluate.json b/ENCSR974TXT/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4af35bd0127135bfd1ad6b67f070550cc23e4d2a..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF747PDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_0.fit.json b/ENCSR974TXT/cherimoya.fold_0.fit.json deleted file mode 100644 index 6510b51221ec141ba8f01046dc1bebc9c108335f..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF747PDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_0.log b/ENCSR974TXT/cherimoya.fold_0.log deleted file mode 100644 index 9b36e8481091ceb73c38bd96f1d78b9adf0fe81e..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2784 35.64722752571106 3.7920925617218018 220.5108642578125 0.5046685934066772 313.2319030761719 0.16140009462833405 0.623421 3.6986351013183594 True -1 5568 30.955787658691406 1.3402535915374756 274.8471374511719 0.49085384607315063 304.3821105957031 0.20138852298259735 0.70039225 0.6483752131462097 True -2 8352 30.921422958374023 0.581071138381958 221.0455322265625 0.6802042722702026 301.7623596191406 0.20966239273548126 0.7070732 0.6166383624076843 True -3 11136 30.93053364753723 0.5624172687530518 267.19805908203125 0.6868829727172852 300.521728515625 0.21364694833755493 0.71731883 0.5638230443000793 True -4 13920 30.906150102615356 1.2664389610290527 219.5211944580078 0.4619775414466858 299.34039306640625 0.21912673115730286 0.72187436 0.47962042689323425 True -5 16704 31.147265195846558 0.7787637710571289 260.2542724609375 0.41426515579223633 298.712646484375 0.22166968882083893 0.72138304 0.5068632960319519 False -6 19488 30.87242555618286 0.5434403419494629 228.67605590820312 0.5170243382453918 298.5408935546875 0.222323939204216 0.7242294 0.5724595189094543 True -7 22272 30.802083015441895 0.5370073318481445 241.23422241210938 0.5304703712463379 298.1474914550781 0.22409842908382416 0.72932523 0.5783199071884155 True -8 25056 30.80455207824707 0.533390998840332 192.1215057373047 0.3725714385509491 298.09906005859375 0.22447569668293 0.7345076 0.5342936515808105 True -9 27840 30.801992893218994 0.5612478256225586 235.71337890625 0.33980539441108704 297.4910888671875 0.22773359715938568 0.73515993 0.49476662278175354 True -10 30624 30.8451828956604 0.5716056823730469 254.26394653320312 0.3712390661239624 297.2384033203125 0.2285923808813095 0.73955125 0.45568400621414185 True -11 33408 30.803850650787354 0.5352530479431152 269.600830078125 0.4602331519126892 296.4756774902344 0.23203808069229126 0.74465436 0.42176613211631775 True -12 36192 30.824098587036133 1.5055718421936035 241.1163787841797 0.32322749495506287 296.2132873535156 0.23347952961921692 0.74638134 0.37851133942604065 True -13 38976 30.884915828704834 0.5498247146606445 265.60003662109375 0.3626045286655426 295.8082275390625 0.2351783663034439 0.7499712 0.3602142035961151 True -14 41760 30.861714363098145 0.5350098609924316 206.00314331054688 0.3125295639038086 295.67333984375 0.23536324501037598 0.7562111 0.3276538848876953 True -15 44544 30.855350494384766 0.6783835887908936 244.53826904296875 0.21358783543109894 295.46624755859375 0.23670130968093872 0.7604528 0.3018115162849426 True -16 47328 30.85356569290161 0.8205738067626953 220.8991241455078 0.3660566210746765 295.498291015625 0.23631031811237335 0.76380247 0.28912752866744995 True -17 50112 30.38286781311035 0.5353372097015381 227.89291381835938 0.3338901996612549 295.5968933105469 0.23550960421562195 0.76523507 0.2820024788379669 True -18 52896 30.211691856384277 0.9432289600372314 210.23060607910156 0.36051198840141296 295.8739318847656 0.23355327546596527 0.7638653 0.28102415800094604 False -19 55680 30.245444297790527 0.5451056957244873 241.42877197265625 0.23675331473350525 295.7037048339844 0.23483766615390778 0.7637663 0.2843501567840576 False diff --git a/ENCSR974TXT/cherimoya.fold_0.performance.tsv b/ENCSR974TXT/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3100b435b29b4a53cc9fd8ff506700a4d4c6e506..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -295.5968933105469 0.506382405757904 0.23550958931446075 0.0723801851272583 0.7652350664138794 0.7498467564582825 0.2820024788379669 \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_1.evaluate.json b/ENCSR974TXT/cherimoya.fold_1.evaluate.json deleted file mode 100644 index fe36fef6806f6a2ed194761a3288722b70939e3d..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF747PDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_1.fit.json b/ENCSR974TXT/cherimoya.fold_1.fit.json deleted file mode 100644 index 4547f160f2ac79fc3946721b6a72b8730be3fb19..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF747PDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_1.log b/ENCSR974TXT/cherimoya.fold_1.log deleted file mode 100644 index b889e1e68770552bfc130eab4d92cb1ae4f01d40..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2738 35.22012233734131 4.6391074657440186 220.7801513671875 0.6872670650482178 347.7151184082031 0.16685278713703156 0.605413 4.792567729949951 True -1 5476 30.398128986358643 1.0771260261535645 231.447265625 0.8552069664001465 335.58953857421875 0.2169926017522812 0.71068764 0.9555507898330688 True -2 8214 30.420243740081787 1.0544986724853516 264.97998046875 0.6039862036705017 332.5929870605469 0.22641895711421967 0.7329656 0.678489625453949 True -3 10952 30.34125590324402 0.7265315055847168 243.06956481933594 0.5612442493438721 331.394287109375 0.2291201502084732 0.7430095 0.48922115564346313 True -4 13690 30.295767545700073 0.7270503044128418 210.53121948242188 0.37168407440185547 330.3863525390625 0.23326748609542847 0.75346833 0.4504936635494232 True -5 16428 30.305165767669678 0.716346025466919 247.0101776123047 0.5087630152702332 329.7901306152344 0.2345695197582245 0.7577082 0.4562353789806366 True -6 19166 30.336026430130005 0.7612807750701904 208.32345581054688 0.6571037769317627 329.3780212402344 0.23649953305721283 0.7595835 0.47783663868904114 True -7 21904 30.36306357383728 1.7081139087677002 281.0146789550781 0.5092567205429077 328.84735107421875 0.23839788138866425 0.7591626 0.4862942099571228 False -8 24642 30.406253576278687 0.7490284442901611 223.07476806640625 0.5083860158920288 328.4510803222656 0.2405066192150116 0.7640093 0.452821284532547 True -9 27380 30.340404748916626 0.7553188800811768 241.155029296875 0.5474646687507629 328.3227233886719 0.24058213829994202 0.7663562 0.4272439181804657 True -10 30118 30.405345678329468 0.7394208908081055 254.65475463867188 0.3754737377166748 327.7213134765625 0.24308599531650543 0.7696618 0.4146803319454193 True -11 32856 30.43321681022644 0.8619561195373535 215.514892578125 0.4698638916015625 327.1739196777344 0.24537448585033417 0.7750776 0.38378408551216125 True -12 35594 30.616775512695312 0.7278544902801514 190.64944458007812 0.3765711188316345 327.0296630859375 0.24566149711608887 0.7756693 0.3583572804927826 True -13 38332 30.496201753616333 0.7430648803710938 223.96896362304688 0.40525129437446594 326.4650573730469 0.24881400167942047 0.7815623 0.33913132548332214 True -14 41070 30.096019506454468 0.7488489151000977 235.98275756835938 0.4043978452682495 326.15167236328125 0.24897538125514984 0.7887478 0.32389792799949646 True -15 43808 29.67266583442688 0.7255978584289551 198.75479125976562 0.3154488801956177 325.91668701171875 0.2498132288455963 0.79092956 0.3100196123123169 True -16 46546 29.68445324897766 1.7724618911743164 195.406494140625 0.38793349266052246 325.81072998046875 0.2497505396604538 0.79519385 0.3023339509963989 True -17 49284 29.838900327682495 0.7435135841369629 217.9210968017578 0.3681848645210266 326.2803955078125 0.24866554141044617 0.79692304 0.2965924143791199 True -18 52022 29.836137294769287 0.7372498512268066 236.54425048828125 0.28630656003952026 325.90045166015625 0.25005924701690674 0.7965736 0.2999688982963562 False -19 54760 29.704376697540283 0.7442281246185303 245.95196533203125 0.2506116032600403 326.47869873046875 0.24759212136268616 0.7936275 0.3001495599746704 False diff --git a/ENCSR974TXT/cherimoya.fold_1.performance.tsv b/ENCSR974TXT/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c99e4be80891e75b8b24a223b9464c08372ed73c..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -326.2803955078125 0.49311545491218567 0.24866555631160736 0.08316661417484283 0.796923041343689 0.7887648344039917 0.2965924143791199 \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_2.evaluate.json b/ENCSR974TXT/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 83ececb9b41ec920815a6a1a989b7b70a350a4aa..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF747PDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_2.fit.json b/ENCSR974TXT/cherimoya.fold_2.fit.json deleted file mode 100644 index 000d1835d08af3cdf92e92dab0eec3bec1407155..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF747PDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_2.log b/ENCSR974TXT/cherimoya.fold_2.log deleted file mode 100644 index c181dcf78ddfe86e3a991ede98ef81ab595f58ed..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2906 37.03115940093994 3.790971279144287 228.5938262939453 0.8825319409370422 320.2189025878906 0.16358521580696106 0.62813014 3.0281155109405518 True -1 5812 32.263508796691895 0.6339855194091797 245.14633178710938 0.481648713350296 310.1767272949219 0.2095741629600525 0.71093965 0.8624903559684753 True -2 8718 32.21773958206177 0.5195343494415283 236.13656616210938 0.4552721381187439 307.4680480957031 0.21787001192569733 0.72491723 0.47060027718544006 True -3 11624 32.21248412132263 0.5114521980285645 235.65548706054688 0.6081138253211975 306.4176330566406 0.220781147480011 0.72788244 0.41520416736602783 True -4 14530 32.16429257392883 0.5125138759613037 261.5307922363281 0.6259889602661133 305.3791809082031 0.225091353058815 0.7306549 0.40814200043678284 True -5 17436 32.17155337333679 1.3920466899871826 211.93597412109375 0.7119140028953552 304.778564453125 0.22691385447978973 0.7331673 0.3888434171676636 True -6 20342 32.20898771286011 1.5634236335754395 254.89019775390625 0.7111915349960327 303.9887390136719 0.23040616512298584 0.736797 0.368752658367157 True -7 23248 32.195067405700684 0.5140120983123779 203.9896697998047 0.4629056751728058 304.5284423828125 0.22750256955623627 0.7424309 0.3642411530017853 True -8 26154 32.15378165245056 0.5214042663574219 226.97055053710938 0.6523798704147339 303.67767333984375 0.2310858517885208 0.74604714 0.3706842064857483 True -9 29060 32.14419913291931 0.513277530670166 188.16456604003906 0.4835663437843323 303.1095886230469 0.2343146800994873 0.74939036 0.35639819502830505 True -10 31966 32.156086921691895 0.5178592205047607 254.2001495361328 0.3240428566932678 302.7658996582031 0.23569607734680176 0.7521611 0.3545908033847809 True -11 34872 31.776443243026733 0.5081748962402344 238.78359985351562 0.5379726886749268 302.6070556640625 0.23642171919345856 0.75466156 0.34209731221199036 True -12 37778 31.519323348999023 0.5113985538482666 258.117919921875 0.4348917603492737 301.96588134765625 0.23925229907035828 0.75767004 0.3256591856479645 True -13 40684 31.569604873657227 1.2509300708770752 233.30978393554688 0.4235481023788452 301.8845520019531 0.23920440673828125 0.7626088 0.3188187777996063 True -14 43590 31.62460160255432 0.5283946990966797 265.49139404296875 0.4462078809738159 301.4908142089844 0.2413463294506073 0.764348 0.31169965863227844 True -15 46496 31.552801847457886 0.5247859954833984 217.1285400390625 0.5400190353393555 301.2947692871094 0.2421385496854782 0.7684243 0.2963697016239166 True -16 49402 31.597840547561646 0.512397050857544 298.0157165527344 0.29832708835601807 301.38177490234375 0.2420080006122589 0.7719665 0.29421117901802063 True -17 52308 31.549230337142944 0.512566089630127 222.1447296142578 0.4565266966819763 301.62713623046875 0.24058032035827637 0.77396315 0.2880633473396301 True -18 55214 31.603801250457764 0.5214648246765137 244.29489135742188 0.2902814447879791 301.6466369628906 0.2402353733778 0.7743061 0.2864420413970947 True -19 58120 31.553237438201904 0.5212533473968506 183.20040893554688 0.40400049090385437 302.02508544921875 0.2383507937192917 0.7725336 0.2917380928993225 False diff --git a/ENCSR974TXT/cherimoya.fold_2.performance.tsv b/ENCSR974TXT/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0296e1186951f7f76e959c5f024e81cf0562127f..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -301.6466369628906 0.502830982208252 0.24023540318012238 0.07368820905685425 0.7743061184883118 0.7597173452377319 0.2864420413970947 \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_3.evaluate.json b/ENCSR974TXT/cherimoya.fold_3.evaluate.json deleted file mode 100644 index efd3a98460d8f13a43d1ec6a6c7c55b3e3ac76e4..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF747PDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_3.fit.json b/ENCSR974TXT/cherimoya.fold_3.fit.json deleted file mode 100644 index ba59545f39fc862d1e21a6c1ec8e4110e88d7e70..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF747PDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_3.log b/ENCSR974TXT/cherimoya.fold_3.log deleted file mode 100644 index f1a1a976f485a0988914ae07264c181ab7549bca..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2789 37.370359659194946 4.183760643005371 232.33627319335938 0.7335835099220276 343.1858215332031 0.16130268573760986 0.6345851 3.552208662033081 True -1 5578 30.978464365005493 2.1804327964782715 251.1458282470703 0.604216456413269 331.6648864746094 0.21453191339969635 0.7028728 1.2136574983596802 True -2 8367 30.95446252822876 1.3018865585327148 241.76966857910156 0.5783660411834717 329.1700439453125 0.2214737832546234 0.7161595 0.6895673274993896 True -3 11156 30.99367618560791 9.425612211227417 293.24951171875 0.5837135314941406 327.9407958984375 0.2260570079088211 0.7315915 0.5375493764877319 True -4 13945 33.47738766670227 0.612541913986206 208.92901611328125 0.6404355764389038 327.4759521484375 0.2268407940864563 0.73940676 0.5429112911224365 True -5 16734 30.968353509902954 0.5437946319580078 222.24343872070312 0.6659208536148071 326.9272155761719 0.22913630306720734 0.74768156 0.5181652903556824 True -6 19523 31.005451917648315 0.5800414085388184 269.2294616699219 0.5055373907089233 326.6019592285156 0.23140189051628113 0.7443146 0.5565621256828308 False -7 22312 31.04705047607422 0.5742015838623047 244.49978637695312 0.5496845245361328 326.18341064453125 0.23242507874965668 0.74687195 0.5423004627227783 False -8 25101 31.031643867492676 0.5572021007537842 269.9407653808594 0.34680065512657166 326.08111572265625 0.23281140625476837 0.75084376 0.5361872911453247 True -9 27890 30.98296570777893 0.5572094917297363 208.14590454101562 0.4917007088661194 325.6853942871094 0.23442956805229187 0.7516017 0.5470655560493469 True -10 30679 30.96486234664917 0.5563335418701172 202.6232147216797 0.5504811406135559 325.1440124511719 0.23640863597393036 0.7576438 0.5036137700080872 True -11 33468 30.909857988357544 0.5397238731384277 247.94384765625 0.4336114525794983 324.95745849609375 0.23731529712677002 0.7624082 0.45978665351867676 True -12 36257 30.315014123916626 0.5413472652435303 225.32754516601562 0.7263253927230835 324.6397705078125 0.23813331127166748 0.76532507 0.43527892231941223 True -13 39046 30.30313730239868 0.5486268997192383 202.84397888183594 0.35640788078308105 324.2147521972656 0.2401202917098999 0.7712422 0.3951200544834137 True -14 41835 30.284076690673828 0.5451986789703369 276.5368347167969 0.2477131187915802 323.835205078125 0.24213886260986328 0.7748731 0.3645600974559784 True -15 44624 30.29546070098877 0.5525448322296143 225.86807250976562 0.1785208135843277 323.742431640625 0.24243882298469543 0.77834284 0.34015601873397827 True -16 47413 30.274411916732788 0.5463316440582275 219.44009399414062 0.2816580832004547 324.1308288574219 0.23987092077732086 0.7826288 0.31790441274642944 True -17 50202 30.265897274017334 0.5522522926330566 216.7362060546875 0.3815310001373291 323.9667663574219 0.24103231728076935 0.7838582 0.30428236722946167 True -18 52991 30.292938947677612 0.5517990589141846 231.21434020996094 0.18589353561401367 324.3526611328125 0.23924671113491058 0.7846984 0.3020437955856323 True -19 55780 30.32715129852295 0.5452601909637451 217.27569580078125 0.2827068567276001 324.3336486816406 0.23928509652614594 0.783157 0.3009450137615204 False diff --git a/ENCSR974TXT/cherimoya.fold_3.performance.tsv b/ENCSR974TXT/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 3d66798835b535757c8a855f7218aefc9a87efe6..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.3526611328125 0.49677661061286926 0.23924671113491058 0.08048225194215775 0.7846984267234802 0.7654688358306885 0.3020437955856323 \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_4.evaluate.json b/ENCSR974TXT/cherimoya.fold_4.evaluate.json deleted file mode 100644 index bfd658f564d37af0587801acb88d34519fe0cb35..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF747PDE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_4.fit.json b/ENCSR974TXT/cherimoya.fold_4.fit.json deleted file mode 100644 index 1a45bb9ce72e576746f79d765a3c817f7bfb3e94..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF747PDE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR974TXT/cherimoya.fold_4.log b/ENCSR974TXT/cherimoya.fold_4.log deleted file mode 100644 index b637df8f94ea21e23ad22699f689b8ef2b02c5a4..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2860 36.42056202888489 4.029039144515991 230.2685546875 0.47485050559043884 309.748779296875 0.15977680683135986 0.6376356 3.0051398277282715 True -1 5720 31.76016402244568 0.6384007930755615 278.8155517578125 0.5396720767021179 300.8396301269531 0.20331169664859772 0.6929344 0.6411505341529846 True -2 8580 31.787733554840088 0.6156859397888184 220.7770233154297 0.6302615404129028 298.7419128417969 0.21040505170822144 0.71456385 0.5379296541213989 True -3 11440 31.748565673828125 0.9183154106140137 247.70458984375 0.5116985440254211 297.3835144042969 0.21468447148799896 0.72749525 0.488979309797287 True -4 14300 31.73269772529602 0.6153385639190674 225.50448608398438 0.4356720745563507 296.6921081542969 0.2174680083990097 0.73071605 0.5305097103118896 True -5 17160 31.726112842559814 0.6083011627197266 239.5421142578125 0.9092416763305664 295.99658203125 0.22020238637924194 0.73375416 0.5555724501609802 True -6 20020 31.738495111465454 0.6143584251403809 241.74618530273438 0.42386263608932495 295.9132995605469 0.22007393836975098 0.73366594 0.5315079689025879 False -7 22880 31.774653911590576 1.7275176048278809 242.57249450683594 0.5197896361351013 295.54693603515625 0.22189150750637054 0.7390599 0.4548671543598175 True -8 25740 31.738778591156006 1.2051045894622803 261.1669921875 0.5444820523262024 295.1960754394531 0.22392402589321136 0.7444432 0.4516931176185608 True -9 28600 31.70122194290161 1.1388053894042969 224.75967407226562 0.3988936245441437 294.8072509765625 0.22548454999923706 0.74568623 0.43019014596939087 True -10 31460 31.67012882232666 0.6142001152038574 239.00616455078125 0.37392744421958923 294.5187072753906 0.22613681852817535 0.7482742 0.3867183327674866 True -11 34320 31.70841121673584 0.6014535427093506 204.65170288085938 0.48753342032432556 294.5688781738281 0.22543874382972717 0.7530186 0.3622628450393677 True -12 37180 31.671486616134644 0.6056184768676758 260.8478088378906 0.3538582921028137 294.11297607421875 0.22807829082012177 0.7551264 0.3477754592895508 True -13 40040 31.02463936805725 0.6004624366760254 220.1005859375 0.4182931184768677 293.8552551269531 0.22966063022613525 0.7592367 0.33150097727775574 True -14 42900 31.04775595664978 0.6103448867797852 265.6780700683594 0.4772745668888092 293.5439758300781 0.22962813079357147 0.7657991 0.3112313151359558 True -15 45760 31.09398579597473 0.6074724197387695 254.87091064453125 0.4248869717121124 293.6562805175781 0.23004016280174255 0.76685977 0.3002355694770813 True -16 48620 31.084880352020264 0.6187019348144531 276.4169616699219 0.22654470801353455 293.60882568359375 0.23088081181049347 0.7726149 0.28362518548965454 True -17 51480 31.097221612930298 1.483292818069458 229.25173950195312 0.25771504640579224 293.67547607421875 0.2301364243030548 0.77124035 0.2793145477771759 False -18 54340 31.031867504119873 0.6064755916595459 264.8099060058594 0.15620754659175873 293.8129577636719 0.22890402376651764 0.76839805 0.28028804063796997 False -19 57200 31.075926780700684 1.0308585166931152 206.6644287109375 0.2879367470741272 293.7873840332031 0.23013147711753845 0.7682816 0.28386130928993225 False diff --git a/ENCSR974TXT/cherimoya.fold_4.performance.tsv b/ENCSR974TXT/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 911e4d1fa4b5cae733fb5e8eb5e1849522b81424..0000000000000000000000000000000000000000 --- a/ENCSR974TXT/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -293.60882568359375 0.5093514323234558 0.23088081181049347 0.07552289217710495 0.7726148962974548 0.7501710653305054 0.28362518548965454 \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_0.evaluate.json b/ENCSR975LGK/cherimoya.fold_0.evaluate.json deleted file mode 100644 index f938e72c937531cceb4189d36a7e78917f973b4a..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF300RYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_0.fit.json b/ENCSR975LGK/cherimoya.fold_0.fit.json deleted file mode 100644 index 94c831eb60e68fdf28dcc79641d4e3fe20ec58c6..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF300RYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_0.log b/ENCSR975LGK/cherimoya.fold_0.log deleted file mode 100644 index 6f7ec206dd5c9c52019f560252672a03c90d8217..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.144033908843994 3.52492094039917 438.6951904296875 0.8468431234359741 652.0963745117188 0.19337274134159088 0.6908602 5.794659614562988 True -1 5492 30.327991008758545 0.5859246253967285 650.7371215820312 0.5029358863830566 600.6200561523438 0.23637981712818146 0.7659807 1.6979658603668213 True -2 8238 30.256975412368774 0.5694925785064697 532.9135131835938 0.38692229986190796 590.52490234375 0.24033957719802856 0.7805603 1.2076295614242554 True -3 10984 30.32099223136902 0.5743072032928467 465.29949951171875 0.5900450348854065 583.3055419921875 0.24486815929412842 0.7898418 1.0100198984146118 True -4 13730 30.29689311981201 0.5580220222473145 545.13330078125 0.4639790654182434 579.8513793945312 0.24651940166950226 0.8016416 0.7605811953544617 True -5 16476 30.291208267211914 0.554290771484375 458.80340576171875 0.312045156955719 578.5789794921875 0.24772270023822784 0.803102 0.6809507012367249 True -6 19222 30.259870052337646 0.5682413578033447 480.4819030761719 0.4324326813220978 576.2542114257812 0.2506472170352936 0.80858356 0.5553563237190247 True -7 21968 30.29150915145874 0.5604491233825684 514.4722900390625 0.2841310501098633 574.6062622070312 0.25123026967048645 0.8166335 0.5175615549087524 True -8 24714 30.287272930145264 0.5402638912200928 418.98211669921875 0.27819183468818665 572.09521484375 0.2539663314819336 0.825607 0.4938780963420868 True -9 27460 30.286508321762085 0.556483268737793 437.5216064453125 0.43991997838020325 569.3225708007812 0.2572042942047119 0.8320895 0.45798176527023315 True -10 30206 30.248515129089355 0.5468924045562744 462.26275634765625 0.5005946755409241 567.8965454101562 0.25860217213630676 0.83663285 0.43282461166381836 True -11 32952 30.23413920402527 0.5680713653564453 544.56201171875 0.4105204939842224 565.1923828125 0.2604491412639618 0.8446301 0.4021260440349579 True -12 35698 30.256343841552734 0.5533335208892822 436.00933837890625 0.29024267196655273 564.2294311523438 0.2609241008758545 0.85122305 0.37809839844703674 True -13 38444 30.25688338279724 0.5507137775421143 637.588134765625 0.44012191891670227 561.5897216796875 0.2644331157207489 0.8591701 0.34744274616241455 True -14 41190 30.276150941848755 0.5595028400421143 460.5374450683594 0.29347795248031616 562.4777221679688 0.26244381070137024 0.8650298 0.32462555170059204 True -15 43936 30.3437020778656 0.5564870834350586 673.1327514648438 0.27380526065826416 560.19091796875 0.26534900069236755 0.8694618 0.30544647574424744 True -16 46682 30.285537242889404 0.5707461833953857 389.9613342285156 0.1885983645915985 560.9669189453125 0.2635740637779236 0.87351483 0.2950361967086792 True -17 49428 30.270736694335938 0.5512349605560303 423.5180969238281 0.2616365849971771 559.9762573242188 0.26477697491645813 0.8742253 0.2916148900985718 True -18 52174 30.378679990768433 0.5676288604736328 489.5207214355469 0.2395283281803131 560.837158203125 0.2634434998035431 0.87341046 0.29292261600494385 False -19 54920 30.522067308425903 0.7223455905914307 463.1487121582031 0.11682478338479996 560.4725341796875 0.2646252512931824 0.87257403 0.2948993742465973 False diff --git a/ENCSR975LGK/cherimoya.fold_0.performance.tsv b/ENCSR975LGK/cherimoya.fold_0.performance.tsv deleted file mode 100644 index fa5e9995857e50515dc729d027c8f9af96c2aebf..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -559.9762573242188 0.4631657600402832 0.26477697491645813 0.11099071800708771 0.8742253184318542 0.8210394978523254 0.2916148900985718 \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_1.evaluate.json b/ENCSR975LGK/cherimoya.fold_1.evaluate.json deleted file mode 100644 index e19ecb88822337b09648ad121eca5e601c7baf7b..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF300RYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_1.fit.json b/ENCSR975LGK/cherimoya.fold_1.fit.json deleted file mode 100644 index 2749d4a3dd72096afbcc7ff2f58cdda121df94b1..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF300RYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_1.log b/ENCSR975LGK/cherimoya.fold_1.log deleted file mode 100644 index b754386cfc3eb8d8c7c2d8f6328c36b7e0798c45..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2701 33.73143291473389 3.761172294616699 479.55535888671875 0.3785901367664337 803.9417114257812 0.20725689828395844 0.69528544 6.980965614318848 True -1 5402 29.786511182785034 1.2049543857574463 473.5479431152344 0.5803520083427429 730.2207641601562 0.2586818337440491 0.7843352 2.182681083679199 True -2 8103 29.846878051757812 1.1538989543914795 482.0042724609375 0.5701698064804077 722.5297241210938 0.26145637035369873 0.7887099 1.524231195449829 True -3 10804 29.848354816436768 0.7881982326507568 405.390380859375 0.2727311849594116 712.3427124023438 0.26682788133621216 0.8015252 1.4217339754104614 True -4 13505 29.93217158317566 0.7491848468780518 528.88720703125 0.49663808941841125 705.1288452148438 0.27199995517730713 0.8130504 0.8847910165786743 True -5 16206 29.860310554504395 0.7513113021850586 494.57623291015625 0.44221100211143494 702.2559814453125 0.2739596366882324 0.8207302 0.8531873822212219 True -6 18907 29.821173429489136 0.8720052242279053 534.221923828125 0.5556578636169434 696.8453979492188 0.27703526616096497 0.8309498 0.7580524682998657 True -7 21608 29.782799005508423 0.7543647289276123 541.0010375976562 0.558689534664154 693.1483154296875 0.280784547328949 0.8402378 0.680404543876648 True -8 24309 29.927534103393555 0.7478811740875244 424.7330017089844 0.3706381916999817 690.0664672851562 0.28296780586242676 0.84357053 0.6322718858718872 True -9 27010 29.966278314590454 0.7319133281707764 450.08050537109375 0.3242700397968292 689.4963989257812 0.28321757912635803 0.8473833 0.5897822380065918 True -10 29711 29.920552730560303 0.7274365425109863 557.3203125 0.4652462601661682 684.2344970703125 0.2882370948791504 0.8577301 0.5390572547912598 True -11 32412 29.974806308746338 0.7317733764648438 499.30877685546875 0.38964903354644775 680.060546875 0.29164040088653564 0.86360794 0.4785709083080292 True -12 35113 29.949469566345215 0.7341666221618652 471.3380432128906 0.45041894912719727 681.0708618164062 0.28897950053215027 0.87335026 0.42771708965301514 True -13 37814 29.914512634277344 0.7271084785461426 501.29754638671875 0.2366151213645935 679.2264404296875 0.291059285402298 0.8774955 0.3918803036212921 True -14 40515 29.817312479019165 0.7277026176452637 402.96282958984375 0.3446768522262573 674.86767578125 0.29473915696144104 0.88382965 0.37355828285217285 True -15 43216 29.908666372299194 0.730865478515625 527.1041259765625 0.28637605905532837 674.9813232421875 0.2935062646865845 0.88504475 0.35575541853904724 True -16 45917 29.804504871368408 0.7218770980834961 444.27813720703125 0.21448343992233276 673.6840209960938 0.29467475414276123 0.8899031 0.34162917733192444 True -17 48618 29.824278593063354 0.7318916320800781 505.4094543457031 0.1827380359172821 674.3722534179688 0.29373273253440857 0.88801754 0.3393077254295349 False -18 51319 29.868711948394775 0.7319228649139404 407.613037109375 0.18382295966148376 673.7086791992188 0.29552197456359863 0.88638437 0.3429732322692871 False -19 54020 29.825762510299683 0.7292051315307617 525.859375 0.1600828766822815 676.3091430664062 0.29214924573898315 0.8849963 0.3471570611000061 False diff --git a/ENCSR975LGK/cherimoya.fold_1.performance.tsv b/ENCSR975LGK/cherimoya.fold_1.performance.tsv deleted file mode 100644 index cca50f5bb1eb70fe6cf7686024bdad647e1e6508..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -673.6840209960938 0.43533802032470703 0.2946747839450836 0.1362350881099701 0.8899031281471252 0.8666306138038635 0.34162917733192444 \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_2.evaluate.json b/ENCSR975LGK/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 1d6ac81dc98cf5bd67dc3cc26c8dc96b59ea971e..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF300RYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_2.fit.json b/ENCSR975LGK/cherimoya.fold_2.fit.json deleted file mode 100644 index 21294bee477f1ddc5560250ad8f8e9095bc823f1..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF300RYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_2.log b/ENCSR975LGK/cherimoya.fold_2.log deleted file mode 100644 index 4bb5d247e07b6062556b6be37909036dd26e596f..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 35.65564322471619 3.5985329151153564 661.3129272460938 0.7197564840316772 694.08984375 0.1946568638086319 0.68829954 4.615024566650391 True -1 5754 31.665500164031982 0.5782983303070068 477.14898681640625 0.6087146997451782 631.6491088867188 0.24327556788921356 0.77274454 1.8051776885986328 True -2 8631 31.756282329559326 0.5592899322509766 616.757568359375 0.5181653499603271 624.6098022460938 0.244729146361351 0.78553426 1.0708476305007935 True -3 11508 31.669040203094482 0.5751616954803467 601.5213623046875 0.44009923934936523 621.4974365234375 0.2463265359401703 0.7892177 1.0240970849990845 True -4 14385 31.654255628585815 0.5710840225219727 511.6282043457031 0.3822062015533447 612.8405151367188 0.25378215312957764 0.8020633 0.751082718372345 True -5 17262 31.707675218582153 0.5698812007904053 434.8623962402344 0.38151827454566956 609.3331909179688 0.25711333751678467 0.813852 0.60551518201828 True -6 20139 31.748153686523438 0.5745429992675781 577.0120849609375 0.5198571681976318 608.1821899414062 0.25728416442871094 0.8160981 0.5709536671638489 True -7 23016 31.710235118865967 0.5709781646728516 581.1624755859375 0.5705646276473999 605.4459838867188 0.2601291537284851 0.82349217 0.5210143327713013 True -8 25893 31.907773971557617 0.5717620849609375 523.04541015625 0.3634071946144104 604.7886962890625 0.2596511244773865 0.8280764 0.5159496068954468 True -9 28770 31.757137060165405 0.5744845867156982 425.85906982421875 0.20174375176429749 602.9108276367188 0.2619302570819855 0.83656603 0.46881672739982605 True -10 31647 31.69563913345337 0.5685667991638184 526.812744140625 0.31412753462791443 599.577880859375 0.26510319113731384 0.8445192 0.4209822714328766 True -11 34524 31.704054832458496 0.5710709095001221 604.7393798828125 0.3945050537586212 597.5453491210938 0.26651737093925476 0.85196096 0.3906620442867279 True -12 37401 31.755250215530396 0.5702283382415771 508.03619384765625 0.49684005975723267 597.288818359375 0.26588553190231323 0.8558719 0.3656337559223175 True -13 40278 31.681215286254883 0.6427099704742432 383.590576171875 0.3429270386695862 594.5784912109375 0.2687230408191681 0.8608599 0.3487064242362976 True -14 43155 31.780994176864624 0.5773870944976807 452.21868896484375 0.2843506336212158 593.1557006835938 0.26959431171417236 0.8676691 0.32547470927238464 True -15 46032 31.798094272613525 0.5812196731567383 410.3744201660156 0.26696377992630005 591.6704711914062 0.2715838551521301 0.87135434 0.31405407190322876 True -16 48909 31.777324199676514 0.5665864944458008 582.24853515625 0.2767690420150757 590.3687133789062 0.27258214354515076 0.87313247 0.30526918172836304 True -17 51786 31.727970123291016 0.5798475742340088 411.6015625 0.20478829741477966 591.1508178710938 0.27164146304130554 0.8748296 0.3028339445590973 True -18 54663 31.816967964172363 0.5674288272857666 462.47802734375 0.33099377155303955 593.5523681640625 0.26787102222442627 0.8735595 0.30530327558517456 False -19 57540 31.803639888763428 0.7964215278625488 527.5787963867188 0.1798395961523056 593.5648193359375 0.26873841881752014 0.8730203 0.3074911832809448 False diff --git a/ENCSR975LGK/cherimoya.fold_2.performance.tsv b/ENCSR975LGK/cherimoya.fold_2.performance.tsv deleted file mode 100644 index aa1021ed3ac57921d3e86f80acdd753a9665fd40..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -591.1508178710938 0.45554015040397644 0.27164146304130554 0.12111896276473999 0.8748295903205872 0.8380488753318787 0.3028339445590973 \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_3.evaluate.json b/ENCSR975LGK/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 4a95cc91626f0cabe6e2116d69b4fa7419b816b4..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF300RYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_3.fit.json b/ENCSR975LGK/cherimoya.fold_3.fit.json deleted file mode 100644 index 7927cf8dcfa4c17b6fd149dd473d90f1db9a8c8b..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF300RYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_3.log b/ENCSR975LGK/cherimoya.fold_3.log deleted file mode 100644 index ba8da61598220d83d77ef1ff9b0b08b8d91cfb08..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 36.45434021949768 4.090589761734009 442.846435546875 0.5259116888046265 649.1243896484375 0.19999632239341736 0.6552492 5.3102593421936035 True -1 5466 30.115359783172607 1.336402416229248 443.3707275390625 0.4690283536911011 602.536376953125 0.2376694530248642 0.71895534 1.7142369747161865 True -2 8199 30.1081485748291 1.020176649093628 550.2095336914062 0.3683927655220032 594.6041259765625 0.24178378283977509 0.7474685 1.2703680992126465 True -3 10932 30.064668655395508 0.6369483470916748 638.0606079101562 0.37963640689849854 587.939208984375 0.24831540882587433 0.76491034 1.1105153560638428 True -4 13665 30.119067668914795 0.5624172687530518 566.783935546875 0.6583234071731567 583.2174682617188 0.25227582454681396 0.77887326 0.7347537279129028 True -5 16398 30.115056037902832 0.5694313049316406 537.9378662109375 0.6204397678375244 580.7737426757812 0.2537536025047302 0.7904072 0.6407621502876282 True -6 19131 30.13350486755371 0.5900325775146484 367.8980712890625 0.2437058687210083 579.080810546875 0.2545973062515259 0.79227686 0.6275367736816406 True -7 21864 30.16555953025818 0.5794744491577148 492.7341003417969 0.38182157278060913 578.130126953125 0.25496742129325867 0.7948463 0.6404604315757751 True -8 24597 30.22469162940979 0.5758118629455566 533.9037475585938 0.5901937484741211 575.2323608398438 0.25815969705581665 0.805079 0.6077005863189697 True -9 27330 30.25617504119873 0.5814218521118164 447.7537536621094 0.2986742854118347 571.0693969726562 0.2629912197589874 0.8167792 0.5656824111938477 True -10 30063 30.436666011810303 0.5816395282745361 431.112060546875 0.34396523237228394 571.5748901367188 0.26197561621665955 0.82185227 0.5284398794174194 True -11 32796 30.27621841430664 0.5827605724334717 481.054443359375 0.30661243200302124 568.6991577148438 0.26460501551628113 0.83122206 0.48610347509384155 True -12 35529 30.40943145751953 0.5838627815246582 482.76287841796875 0.5237711668014526 567.3099975585938 0.26534536480903625 0.84069914 0.42739787697792053 True -13 38262 30.459471225738525 0.576185941696167 485.08935546875 0.3129897117614746 565.532958984375 0.26726022362709045 0.848371 0.39899083971977234 True -14 40995 30.369894981384277 0.5783069133758545 461.526123046875 0.26775071024894714 564.9656982421875 0.26731276512145996 0.8548991 0.3697882890701294 True -15 43728 30.313572883605957 0.585946798324585 374.47174072265625 0.15842851996421814 565.648193359375 0.265818327665329 0.85980403 0.34662574529647827 True -16 46461 30.534361600875854 1.4629039764404297 439.33428955078125 0.1140713021159172 563.5159912109375 0.2684670686721802 0.8624768 0.3352532982826233 True -17 49194 30.486451148986816 0.6027669906616211 485.6385498046875 0.20696841180324554 563.9961547851562 0.26793015003204346 0.8640729 0.3276156783103943 True -18 51927 30.416168689727783 0.5801901817321777 399.9581604003906 0.17449349164962769 563.7699584960938 0.2677996754646301 0.86467856 0.3253565728664398 True -19 54660 30.42153239250183 0.5752217769622803 419.19366455078125 0.2113206386566162 562.1699829101562 0.2699297070503235 0.86506027 0.3266174793243408 True diff --git a/ENCSR975LGK/cherimoya.fold_3.performance.tsv b/ENCSR975LGK/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7e21702e33c08552291e53db42b031a43783f4b4..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -562.1699829101562 0.46006569266319275 0.2699297368526459 0.11667793989181519 0.8650602698326111 0.8192312717437744 0.3266174793243408 \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_4.evaluate.json b/ENCSR975LGK/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ff35e50ef96ab4b1522186e06f0e2854cf121cf9..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF300RYU.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_4.fit.json b/ENCSR975LGK/cherimoya.fold_4.fit.json deleted file mode 100644 index 3abd9aef3d5bfb71f40db43dc44f5b433c204310..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF300RYU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR975LGK/cherimoya.fold_4.log b/ENCSR975LGK/cherimoya.fold_4.log deleted file mode 100644 index 22d700479640b31e7ccd0eb8ddf3bf2c8bdaf7f9..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 34.87821125984192 3.990384578704834 551.7531127929688 0.5807475447654724 594.941650390625 0.19585205614566803 0.6710248 4.663365840911865 True -1 5612 30.9304838180542 0.5971808433532715 512.2666625976562 0.48264575004577637 555.9448852539062 0.2272006869316101 0.7257147 1.5116945505142212 True -2 8418 30.93251943588257 0.5845019817352295 604.330322265625 0.48779651522636414 549.4559936523438 0.23125885426998138 0.74763185 0.9167191386222839 True -3 11224 30.992915391921997 1.340487003326416 504.91748046875 0.5321864485740662 544.9365844726562 0.2318764626979828 0.7619089 0.8177014589309692 True -4 14030 30.958965063095093 0.5877575874328613 459.92919921875 0.24224796891212463 540.978759765625 0.2355577051639557 0.7752347 0.7001804709434509 True -5 16836 31.427369117736816 0.5792391300201416 459.91839599609375 0.3612701892852783 535.7045288085938 0.24195075035095215 0.78581744 0.618046760559082 True -6 19642 30.882434844970703 0.5759365558624268 423.9617919921875 0.37445223331451416 535.3575439453125 0.24161994457244873 0.7911464 0.6118292808532715 True -7 22448 30.91797375679016 0.579047441482544 542.0684814453125 0.28656482696533203 532.9143676757812 0.24458274245262146 0.7964864 0.5446568131446838 True -8 25254 30.967894554138184 0.5799283981323242 475.6562805175781 0.27788305282592773 531.3916015625 0.24573099613189697 0.80291224 0.5129967927932739 True -9 28060 30.93496322631836 0.9505901336669922 392.95294189453125 0.25177454948425293 529.2493286132812 0.24832239747047424 0.8101515 0.48021963238716125 True -10 30866 31.054026126861572 2.8562660217285156 551.8186645507812 0.5206636786460876 529.3003540039062 0.24898327887058258 0.81674933 0.43983739614486694 True -11 33672 31.01510453224182 0.5921108722686768 356.44073486328125 0.26791343092918396 529.1044311523438 0.24785161018371582 0.8213646 0.414827436208725 True -12 36478 30.98718762397766 18.06924271583557 505.3069763183594 0.2951602041721344 526.229736328125 0.25188443064689636 0.82552695 0.39089828729629517 True -13 39284 30.96146297454834 0.607785701751709 425.2560119628906 0.16788148880004883 525.406005859375 0.25126558542251587 0.8355399 0.3691883683204651 True -14 42090 30.98669743537903 0.5797064304351807 415.95208740234375 0.2550841271877289 524.90869140625 0.25235408544540405 0.84357905 0.34570494294166565 True -15 44896 30.99976634979248 1.2202470302581787 455.41009521484375 0.24867194890975952 523.99267578125 0.25364822149276733 0.85064733 0.3218100965023041 True -16 47702 30.957148551940918 5.620028972625732 474.5677490234375 0.21906104683876038 523.37060546875 0.25348353385925293 0.8554448 0.30815234780311584 True -17 50508 30.98120951652527 0.6059210300445557 481.18194580078125 0.2322481870651245 523.7671508789062 0.25202256441116333 0.8576256 0.300687313079834 True -18 53314 30.98103380203247 0.7163069248199463 418.7921142578125 0.1398315131664276 523.5747680664062 0.2529204785823822 0.8563316 0.29935553669929504 False -19 56120 30.92122983932495 3.668458938598633 519.739990234375 0.15907523036003113 523.8645629882812 0.2525380551815033 0.8547333 0.3025432229042053 False diff --git a/ENCSR975LGK/cherimoya.fold_4.performance.tsv b/ENCSR975LGK/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 8e1ca1207c12e3b8b0eaf6b175981b51a03e62c6..0000000000000000000000000000000000000000 --- a/ENCSR975LGK/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -523.7671508789062 0.4724276661872864 0.25202256441116333 0.10536910593509674 0.8576256036758423 0.8119405508041382 0.300687313079834 \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_0.evaluate.json b/ENCSR976XOY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9c373a04f1428d2710fff178377c5bbab1090dac..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF086HLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_0.fit.json b/ENCSR976XOY/cherimoya.fold_0.fit.json deleted file mode 100644 index fb1d48cc70a53052e279c88379a9e15b824a9601..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF086HLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_0.log b/ENCSR976XOY/cherimoya.fold_0.log deleted file mode 100644 index 606883aeba6c058d75310171b36114f14b77d29c..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2764 35.93282198905945 4.315011262893677 760.0821533203125 0.453041672706604 841.0697021484375 0.20067694783210754 0.81535906 4.280040264129639 True -1 5528 30.13988208770752 0.5801775455474854 787.0736694335938 0.19114747643470764 805.6909790039062 0.23389773070812225 0.8621556 0.7461143732070923 True -2 8292 30.659074306488037 0.5582225322723389 737.50390625 0.3384435474872589 798.5159912109375 0.24079008400440216 0.87386554 0.24408425390720367 True -3 11056 30.691593170166016 0.5743589401245117 660.6585083007812 0.21817222237586975 795.3375244140625 0.2423226535320282 0.8816523 0.2674609124660492 True -4 13820 30.75165343284607 0.5648858547210693 740.273681640625 0.2309289574623108 792.8052978515625 0.24492715299129486 0.88563985 0.18636317551136017 True -5 16584 30.978315830230713 7.351586818695068 687.98193359375 0.17068597674369812 792.098388671875 0.24575722217559814 0.88766074 0.2042446881532669 True -6 19348 30.047744750976562 25.424575567245483 662.4393920898438 0.15553049743175507 788.6677856445312 0.2501322329044342 0.8934494 0.15817303955554962 True -7 22112 32.36285901069641 0.5678102970123291 677.4998779296875 0.20305532217025757 789.2908935546875 0.24824322760105133 0.8946859 0.1613205373287201 True -8 24876 30.28672456741333 0.5739009380340576 752.93408203125 0.1611563265323639 788.5748901367188 0.2489442229270935 0.8993059 0.1552133560180664 True -9 27640 30.194936513900757 0.5702672004699707 689.2916259765625 0.11972896009683609 786.5699462890625 0.25148138403892517 0.9032195 0.14404365420341492 True -10 30404 30.0777690410614 0.5683550834655762 629.8155517578125 0.13305237889289856 785.9755249023438 0.2515890896320343 0.90544283 0.1372179090976715 True -11 33168 30.127824068069458 0.5605101585388184 650.2130126953125 0.12675079703330994 785.5027465820312 0.2522653341293335 0.90994924 0.1355932354927063 True -12 35932 30.105279207229614 0.5599427223205566 755.4781494140625 0.18255960941314697 783.7637329101562 0.25432443618774414 0.9110607 0.13405515253543854 True -13 38696 30.140594005584717 0.5519671440124512 654.93994140625 0.20794452726840973 783.3157348632812 0.25488999485969543 0.91425097 0.12999731302261353 True -14 41460 30.050431966781616 0.5627396106719971 762.3568115234375 0.1153680831193924 783.2091674804688 0.25528448820114136 0.9179697 0.12641428411006927 True -15 44224 30.16768765449524 30.417703866958618 714.3577270507812 0.14212453365325928 781.8737182617188 0.25636550784111023 0.9175565 0.12386859208345413 False -16 46988 31.773519277572632 0.5994110107421875 783.8263549804688 0.11593683063983917 782.1474609375 0.25621113181114197 0.9213744 0.12122977524995804 True -17 49752 30.09976601600647 0.5703771114349365 664.5850830078125 0.09862849116325378 782.1375122070312 0.2565096616744995 0.9218908 0.12166376411914825 True -18 52516 30.115775108337402 0.5644810199737549 639.2777099609375 0.11891543865203857 782.5138549804688 0.25641006231307983 0.92099464 0.1220289096236229 False -19 55280 34.95588731765747 26.289006233215332 651.1361083984375 0.0891745388507843 782.7698364257812 0.25557535886764526 0.92114156 0.12235645204782486 False diff --git a/ENCSR976XOY/cherimoya.fold_0.performance.tsv b/ENCSR976XOY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 366a7908ecb3b59a035e22326b79959bf2d8f575..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -782.1375122070312 0.46534737944602966 0.2565096318721771 0.10686235874891281 0.9218907952308655 0.8956125974655151 0.12166376411914825 \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_1.evaluate.json b/ENCSR976XOY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index f32be73b11a6f4141a72c9d4fd33cd16cbf659c5..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF086HLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_1.fit.json b/ENCSR976XOY/cherimoya.fold_1.fit.json deleted file mode 100644 index 11acc8432a254aebebd88e7c6b6872d8bbade474..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF086HLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_1.log b/ENCSR976XOY/cherimoya.fold_1.log deleted file mode 100644 index 8a9878fba116b6c636077178dda76f5ad4236c02..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2698 35.265392780303955 3.78568434715271 562.197998046875 0.2161937654018402 968.9063720703125 0.2100008726119995 0.8132075 4.727843761444092 True -1 5396 29.955169439315796 2.144862174987793 724.6175537109375 0.26079875230789185 926.9912719726562 0.24904823303222656 0.86763746 0.6815246939659119 True -2 8094 29.414524793624878 0.6991190910339355 737.6380615234375 0.3539758324623108 916.0624389648438 0.255929559469223 0.88194513 0.29098427295684814 True -3 10792 29.378848791122437 0.6769363880157471 840.4164428710938 0.27851602435112 912.1309204101562 0.2586555480957031 0.8881089 0.2559206783771515 True -4 13490 29.34605097770691 0.6761572360992432 668.2138671875 0.3601222038269043 910.2135009765625 0.25987160205841064 0.89260554 0.23695053160190582 True -5 16188 29.35450577735901 0.6990389823913574 615.5301513671875 0.15452955663204193 907.323974609375 0.26314079761505127 0.8964143 0.2000378519296646 True -6 18886 29.39368510246277 0.6786899566650391 658.3422241210938 0.4478636085987091 904.6991577148438 0.26548367738723755 0.90324837 0.1740582138299942 True -7 21584 29.951602458953857 0.6810998916625977 740.9707641601562 0.1560095250606537 903.5172119140625 0.26689159870147705 0.90555775 0.17052900791168213 True -8 24282 30.07010245323181 25.583404302597046 711.916259765625 0.1864878386259079 899.5704345703125 0.27106913924217224 0.91033727 0.16589386761188507 True -9 26980 29.399017333984375 38.47721076011658 651.5763549804688 0.18418565392494202 899.7860107421875 0.2704964578151703 0.91020626 0.1777777373790741 False -10 29678 29.442269325256348 31.272209644317627 714.6087646484375 0.1376122385263443 897.2890014648438 0.27272745966911316 0.9146757 0.15825091302394867 True -11 32376 31.41455841064453 0.7932462692260742 619.5877685546875 0.3490290641784668 897.8546142578125 0.2716580927371979 0.9169793 0.14945068955421448 True -12 35074 31.35099172592163 23.5227370262146 663.2047119140625 0.22280827164649963 896.846435546875 0.27237874269485474 0.92108345 0.14539016783237457 True -13 37772 29.546496868133545 1.9566431045532227 664.2635498046875 0.17200902104377747 895.8584594726562 0.2735500633716583 0.92262936 0.13902731239795685 True -14 40470 29.415926456451416 0.695746898651123 738.4310302734375 0.1086764857172966 893.8754272460938 0.2755737006664276 0.9252195 0.13581569492816925 True -15 43168 29.395195960998535 0.6872053146362305 654.5390625 0.12090182304382324 893.5093383789062 0.2756207287311554 0.9271845 0.13226647675037384 True -16 45866 29.425223112106323 1.3625373840332031 740.694091796875 0.1540280282497406 894.4840087890625 0.27455800771713257 0.92832124 0.12959960103034973 True -17 48564 29.407649040222168 0.6781911849975586 724.4417724609375 0.12911313772201538 894.9151611328125 0.2746245861053467 0.9290295 0.1310446709394455 True -18 51262 29.366737842559814 0.6781435012817383 669.7682495117188 0.07181617617607117 895.2322387695312 0.27401629090309143 0.9292787 0.13107052445411682 True -19 53960 29.359302759170532 0.6841788291931152 720.964599609375 0.18428261578083038 895.9192504882812 0.27293211221694946 0.92819476 0.1319664865732193 False diff --git a/ENCSR976XOY/cherimoya.fold_1.performance.tsv b/ENCSR976XOY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index c311d30c4e1da78e81ed023c7293b95084138841..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -895.2322387695312 0.44531649351119995 0.27401629090309143 0.12411650270223618 0.9292786717414856 0.9219939112663269 0.13107052445411682 \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_2.evaluate.json b/ENCSR976XOY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4583ce1eaf913688a53f4b63792c2f90e57c1643..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF086HLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_2.fit.json b/ENCSR976XOY/cherimoya.fold_2.fit.json deleted file mode 100644 index 6df2d0e1c51a7819708827ff50900b43a52b19a1..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF086HLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_2.log b/ENCSR976XOY/cherimoya.fold_2.log deleted file mode 100644 index 6e508e372b3c02b5b29dbb2a8c8bc868f4769ff4..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2878 36.346725940704346 3.764111280441284 640.4235229492188 0.23180750012397766 895.8724975585938 0.20612190663814545 0.80351233 3.7554357051849365 True -1 5756 31.972875118255615 0.5496306419372559 705.7027587890625 0.2195071429014206 855.6646118164062 0.24135908484458923 0.8561483 0.6981024742126465 True -2 8634 31.911601066589355 0.5399720668792725 690.8491821289062 0.2467866688966751 848.4342041015625 0.24566812813282013 0.87253654 0.25783300399780273 True -3 11512 31.23082399368286 0.5380406379699707 710.7293701171875 0.16903698444366455 844.1657104492188 0.24975086748600006 0.87735784 0.2270383983850479 True -4 14390 31.286329984664917 0.5286667346954346 736.8887939453125 0.20637789368629456 842.7146606445312 0.25070279836654663 0.87983 0.2216102033853531 True -5 17268 31.287206172943115 0.530677080154419 654.601318359375 0.26104214787483215 840.31494140625 0.2536519467830658 0.8857907 0.18246927857398987 True -6 20146 31.30172085762024 0.5257768630981445 636.7288208007812 0.2656830847263336 839.7796630859375 0.25376585125923157 0.8886222 0.1689719259738922 True -7 23024 31.336370944976807 1.613525629043579 783.1298217773438 0.30048882961273193 837.9317016601562 0.2555011510848999 0.89077884 0.17560796439647675 True -8 25902 31.313668966293335 0.5304780006408691 750.452392578125 0.19651368260383606 837.5203247070312 0.2559976279735565 0.89435214 0.16256603598594666 True -9 28780 31.22696614265442 0.5238754749298096 817.4359741210938 0.2419019341468811 835.8590087890625 0.257785439491272 0.8975315 0.16258418560028076 True -10 31658 32.47224259376526 0.5290122032165527 666.4371337890625 0.1863918900489807 836.390625 0.25667721033096313 0.900561 0.15786443650722504 True -11 34536 32.348381996154785 11.242350816726685 662.92138671875 0.18774591386318207 834.2447509765625 0.2592977285385132 0.9026781 0.15517108142375946 True -12 37414 31.358806133270264 1.2034573554992676 726.6658935546875 0.1670697182416916 833.50439453125 0.25986677408218384 0.90396327 0.15276482701301575 True -13 40292 31.42564868927002 25.146448135375977 632.5633544921875 0.20199085772037506 831.82568359375 0.26215746998786926 0.90653485 0.1501046121120453 True -14 43170 31.97862219810486 0.5469369888305664 711.4528198242188 0.17618916928768158 831.6052856445312 0.2621053457260132 0.9087647 0.14273159205913544 True -15 46048 31.393335580825806 0.5352218151092529 669.3534545898438 0.15176056325435638 831.7203369140625 0.26231399178504944 0.9110372 0.1408330798149109 True -16 48926 31.286962747573853 0.5336480140686035 634.6275634765625 0.10747454315423965 830.8952026367188 0.2629198133945465 0.9115607 0.1365656852722168 True -17 51804 31.268638372421265 0.5417399406433105 680.772705078125 0.16829612851142883 832.957763671875 0.26062098145484924 0.9142874 0.13571250438690186 True -18 54682 31.27644181251526 0.5686233043670654 747.1968383789062 0.16469472646713257 832.787109375 0.26108023524284363 0.9138489 0.13574406504631042 False -19 57560 31.304306745529175 0.5443065166473389 605.10205078125 0.09276528656482697 833.4049072265625 0.26038262248039246 0.9129232 0.13658101856708527 False diff --git a/ENCSR976XOY/cherimoya.fold_2.performance.tsv b/ENCSR976XOY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7215379349c0e2a031ab29db87c651d62fd5264e..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -832.957763671875 0.45703643560409546 0.26062098145484924 0.11210078001022339 0.9142873883247375 0.8976194858551025 0.13571250438690186 \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_3.evaluate.json b/ENCSR976XOY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 7369e3367e442847eb42654ff93248e2778ddd98..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF086HLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_3.fit.json b/ENCSR976XOY/cherimoya.fold_3.fit.json deleted file mode 100644 index c1c7c62989ef0d6aa6ab7e8d457510a1d72b8827..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF086HLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_3.log b/ENCSR976XOY/cherimoya.fold_3.log deleted file mode 100644 index d22e6f27aad9c29cc1f50110b744067e2a8f56b1..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2739 35.46075367927551 1.9705305099487305 694.367431640625 0.2847397029399872 850.6141357421875 0.20594076812267303 0.79843646 4.102970123291016 True -1 5478 34.80357599258423 16.782952070236206 700.822265625 0.24103276431560516 815.9021606445312 0.23869062960147858 0.85592043 0.6747741103172302 True -2 8217 30.420249938964844 0.49432849884033203 712.5947875976562 0.33721742033958435 808.038330078125 0.24448515474796295 0.8672517 0.2396721988916397 True -3 10956 30.459671020507812 0.4911174774169922 576.7860107421875 0.25725996494293213 804.5570678710938 0.24807995557785034 0.8801226 0.20006375014781952 True -4 13695 29.92832350730896 0.4780447483062744 691.9903564453125 0.19131821393966675 802.327392578125 0.25007694959640503 0.8846317 0.24765779078006744 True -5 16434 29.705814599990845 0.48400354385375977 639.0951538085938 0.17099334299564362 801.5215454101562 0.25098416209220886 0.8892552 0.18926499783992767 True -6 19173 29.75980806350708 0.48812031745910645 686.5615234375 0.25333675742149353 800.3765258789062 0.25216880440711975 0.89102036 0.17472125589847565 True -7 21912 29.812872409820557 0.4897162914276123 742.9544677734375 0.1981213390827179 798.0074462890625 0.2550765573978424 0.89504457 0.16999730467796326 True -8 24651 29.90592122077942 0.4829418659210205 724.8614501953125 0.13526716828346252 797.6849975585938 0.2550068795681 0.8981465 0.17239238321781158 True -9 27390 29.82258653640747 0.496936559677124 691.3677368164062 0.15023058652877808 796.571044921875 0.2562500536441803 0.901258 0.17334626615047455 True -10 30129 29.770852088928223 0.49814939498901367 700.306884765625 0.21437287330627441 796.245849609375 0.25675660371780396 0.9029829 0.16594722867012024 True -11 32868 29.849067211151123 0.49036192893981934 684.0360107421875 0.17625771462917328 795.1441040039062 0.2580068111419678 0.90400356 0.1598890870809555 True -12 35607 30.06462574005127 9.594745635986328 661.470458984375 0.17815549671649933 794.3902587890625 0.25864657759666443 0.9064746 0.1594896912574768 True -13 38346 29.806973457336426 3.1299808025360107 746.9945678710938 0.16489064693450928 793.7933959960938 0.25888898968696594 0.90901977 0.15203221142292023 True -14 41085 29.99033498764038 3.1037046909332275 728.2579345703125 0.1269315779209137 793.3408203125 0.2602306008338928 0.9110269 0.149561807513237 True -15 43824 29.92383861541748 9.840065002441406 636.7990112304688 0.13173145055770874 792.12939453125 0.26118937134742737 0.9135432 0.14667686820030212 True -16 46563 29.904470920562744 2.5982024669647217 774.6495361328125 0.10501247644424438 792.4635620117188 0.26057860255241394 0.9156841 0.14143458008766174 True -17 49302 29.92246675491333 6.993014812469482 648.4320068359375 0.1536155343055725 793.19580078125 0.25991812348365784 0.91510344 0.14037199318408966 False -18 52041 29.862614393234253 20.41213345527649 648.3613891601562 0.10421853512525558 793.2943725585938 0.2604019045829773 0.91566324 0.1399620920419693 False -19 54780 31.376492738723755 0.4918332099914551 662.8798828125 0.07549016177654266 792.8192138671875 0.2610839307308197 0.91403794 0.14051467180252075 False diff --git a/ENCSR976XOY/cherimoya.fold_3.performance.tsv b/ENCSR976XOY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index f214d1c607e1b0da3a22070dd4873ae329d05e0e..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -792.4635620117188 0.4613077640533447 0.26057860255241394 0.10675406455993652 0.9156841039657593 0.8895605206489563 0.14143458008766174 \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_4.evaluate.json b/ENCSR976XOY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 8ee62a841c070ecda29de7cafdad1e883e32ccdf..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF086HLJ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_4.fit.json b/ENCSR976XOY/cherimoya.fold_4.fit.json deleted file mode 100644 index 2e7ea62f21a243943bdf8d2bf3cae87477aca76e..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF086HLJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR976XOY/cherimoya.fold_4.log b/ENCSR976XOY/cherimoya.fold_4.log deleted file mode 100644 index 9d97e2ccdf96bb2a101d5170a045b05ca7142417..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2811 36.0510835647583 3.5342490673065186 738.6538696289062 0.4622378945350647 795.4359741210938 0.19807472825050354 0.80942214 3.701667308807373 True -1 5622 31.24865698814392 0.6461622714996338 639.1181640625 0.2345891147851944 766.2357177734375 0.22864189743995667 0.8629428 0.41949060559272766 True -2 8433 31.340123891830444 0.6334733963012695 745.4650268554688 0.19621938467025757 759.5899658203125 0.23436041176319122 0.8696261 0.21665333211421967 True -3 11244 31.222718238830566 1.5739624500274658 736.5355834960938 0.18796952068805695 755.6912231445312 0.23813064396381378 0.873279 0.20214156806468964 True -4 14055 30.858882904052734 0.6304619312286377 701.5687255859375 0.1548134684562683 754.000732421875 0.24013900756835938 0.8805459 0.1919310986995697 True -5 16866 30.606735944747925 0.6319241523742676 739.6534423828125 0.14585648477077484 752.724853515625 0.24156171083450317 0.88719136 0.16251152753829956 True -6 19677 30.586371421813965 0.6258361339569092 657.54931640625 0.36205679178237915 752.8861694335938 0.24074609577655792 0.89027464 0.15635398030281067 True -7 22488 30.507675170898438 2.2558374404907227 725.7696533203125 0.2604352831840515 751.798095703125 0.24129432439804077 0.89436716 0.14777179062366486 True -8 25299 30.567325353622437 1.302915334701538 568.99951171875 0.3153805136680603 751.1475830078125 0.2421673685312271 0.8987455 0.13901111483573914 True -9 28110 31.083515167236328 0.7216989994049072 760.9030151367188 0.20506739616394043 750.2281494140625 0.2432938516139984 0.90112805 0.13527870178222656 True -10 30921 30.60107922554016 20.529335737228394 720.229248046875 0.09076105803251266 749.5607299804688 0.24387167394161224 0.90384847 0.13290590047836304 True -11 33732 30.601430416107178 21.060972452163696 824.9449462890625 0.2779256999492645 748.6093139648438 0.2452196478843689 0.9074682 0.13292808830738068 True -12 36543 31.111528396606445 0.6357226371765137 732.9219970703125 0.1448533684015274 747.6458740234375 0.24678172171115875 0.9097856 0.12814240157604218 True -13 39354 31.206116676330566 15.801213026046753 692.7880859375 0.15116490423679352 746.83984375 0.2475171536207199 0.91095763 0.12292208522558212 True -14 42165 30.81811261177063 1.156782865524292 736.3265380859375 0.10025008022785187 746.3660278320312 0.24801038205623627 0.9150069 0.11991894245147705 True -15 44976 30.76261043548584 0.7428538799285889 642.892822265625 0.2140175998210907 746.7577514648438 0.24741165339946747 0.91546667 0.11723479628562927 True -16 47787 30.61928653717041 0.6233808994293213 744.1929931640625 0.10414503514766693 745.6832885742188 0.24877169728279114 0.9172858 0.11663097143173218 True -17 50598 30.585038661956787 0.6213722229003906 710.2852172851562 0.16711008548736572 746.2669677734375 0.24823777377605438 0.91773397 0.11603985726833344 True -18 53409 30.55896019935608 1.4814774990081787 706.7261352539062 0.09854702651500702 746.4114379882812 0.2482282668352127 0.9188463 0.11635186523199081 True -19 56220 30.679256200790405 0.7239110469818115 616.9710083007812 0.16194604337215424 747.1958618164062 0.24672892689704895 0.91601354 0.11691860109567642 False diff --git a/ENCSR976XOY/cherimoya.fold_4.performance.tsv b/ENCSR976XOY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 9ceeeeb1386c4cedb95800e8a5c3e85df1f884e4..0000000000000000000000000000000000000000 --- a/ENCSR976XOY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -746.4114379882812 0.4729779362678528 0.2482282817363739 0.09909941256046295 0.9188463091850281 0.8879599571228027 0.11635186523199081 \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_0.evaluate.json b/ENCSR983HXF/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 4410e8b194246b0ab7b87f6e8a5563f61ee9aa21..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277ZXH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_0.fit.json b/ENCSR983HXF/cherimoya.fold_0.fit.json deleted file mode 100644 index 9003d67fd4a3e14f01c3644256eb625bb1a9d399..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF277ZXH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_0.log b/ENCSR983HXF/cherimoya.fold_0.log deleted file mode 100644 index 99cfc03ef4c71c82479d968c5acc0747a8e2f5f8..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1675 22.43386459350586 13.727416276931763 443.0830993652344 1.782691478729248 661.1124267578125 0.4676327407360077 0.582955 18.12442398071289 True -1 3350 18.553141117095947 0.34047985076904297 345.463623046875 0.8921789526939392 505.2601623535156 0.6027865409851074 0.6536529 9.506982803344727 True -2 5025 18.466041803359985 0.31736063957214355 322.85882568359375 1.4469224214553833 456.1412658691406 0.6668777465820312 0.66843563 2.2126262187957764 True -3 6700 18.48540496826172 1.2697482109069824 418.57952880859375 0.8345658779144287 441.8272399902344 0.6814929246902466 0.6811829 0.9454097151756287 True -4 8375 18.416341543197632 0.31265997886657715 307.0965270996094 1.3693870306015015 436.9100036621094 0.6879464387893677 0.6896587 0.8978025317192078 True -5 10050 18.42896556854248 1.1987826824188232 282.60400390625 0.8697651624679565 434.4606018066406 0.6910191178321838 0.688884 0.8435614109039307 False -6 11725 18.424471855163574 0.319232702255249 276.2085266113281 0.9576075077056885 432.4240417480469 0.6938326358795166 0.70106703 0.7835713028907776 True -7 13400 18.478773593902588 0.3206350803375244 337.1294250488281 0.9793456792831421 430.4087829589844 0.6964515447616577 0.69690627 0.7913328409194946 False -8 15075 18.437160968780518 0.31253623962402344 454.7868347167969 0.5371460914611816 428.22235107421875 0.6988504528999329 0.7059792 0.75570148229599 True -9 16750 18.445406198501587 1.0180084705352783 345.3355407714844 1.0885918140411377 426.44879150390625 0.7016945481300354 0.7142126 0.7471701502799988 True -10 18425 18.493767499923706 1.196528434753418 341.5020446777344 0.6422053575515747 424.45916748046875 0.7043581008911133 0.72098076 0.7237484455108643 True -11 20100 19.085846424102783 0.3203310966491699 292.56353759765625 0.9469268321990967 422.9168701171875 0.7065204381942749 0.7253709 0.7076920866966248 True -12 21775 18.458848237991333 0.31934523582458496 345.771728515625 0.7889934778213501 421.7227478027344 0.7081311941146851 0.7324107 0.6920998692512512 True -13 23450 18.45271873474121 0.3183126449584961 344.63275146484375 0.6537827253341675 420.58013916015625 0.7098065614700317 0.7390617 0.6825290322303772 True -14 25125 18.440690755844116 0.31491613388061523 316.6016845703125 0.7188456058502197 419.8329772949219 0.7106106877326965 0.74346095 0.6739084124565125 True -15 26800 18.445194959640503 0.3167698383331299 337.2685546875 0.5988653302192688 419.6501159667969 0.7108902335166931 0.75195855 0.6698653697967529 True -16 28475 18.45820927619934 0.31787681579589844 324.70050048828125 0.36726295948028564 419.7288818359375 0.7106931209564209 0.7559535 0.6748490929603577 True -17 30150 18.45677614212036 0.31353139877319336 284.551025390625 0.5171054601669312 420.0460510253906 0.7100109457969666 0.7533879 0.6977888941764832 False -18 31825 18.112817525863647 0.31326818466186523 332.87896728515625 0.4955585300922394 420.46826171875 0.7092217206954956 0.75048405 0.7233447432518005 False -19 33500 18.1841938495636 0.3134176731109619 258.12518310546875 0.4213317930698395 420.5955505371094 0.7087264657020569 0.7477041 0.7342754006385803 False diff --git a/ENCSR983HXF/cherimoya.fold_0.performance.tsv b/ENCSR983HXF/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 3510b045b1832f4c7f1a5ad402a9fb8bd4e96cde..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -419.7288818359375 0.24720439314842224 0.7106930613517761 0.28581851720809937 0.7559534907341003 0.7404015064239502 0.6748490929603577 \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_1.evaluate.json b/ENCSR983HXF/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 9fa7352db0fe9670c1a3086a5f43bad054667de7..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277ZXH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_1.fit.json b/ENCSR983HXF/cherimoya.fold_1.fit.json deleted file mode 100644 index 72b9a68e559a297fbf80135c06b92dc4980efdee..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF277ZXH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_1.log b/ENCSR983HXF/cherimoya.fold_1.log deleted file mode 100644 index 162f20c71d9a11774c6a739b97cfe94467f9983f..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1642 23.81213402748108 3.5347158908843994 383.8081359863281 1.5413434505462646 753.17138671875 0.48303288221359253 0.545261 20.255268096923828 True -1 3284 18.038392066955566 0.5220389366149902 365.58026123046875 1.3307113647460938 572.1784057617188 0.6152918934822083 0.64904857 11.019643783569336 True -2 4926 18.09835171699524 0.49512457847595215 372.1590270996094 1.0738635063171387 516.6685180664062 0.6829167008399963 0.64898956 3.202737331390381 False -3 6568 18.114807605743408 0.47947096824645996 265.11572265625 1.1925204992294312 494.23187255859375 0.7014127969741821 0.6893407 1.4050966501235962 True -4 8210 18.07719588279724 0.4885749816894531 341.0679931640625 1.0971134901046753 486.9815979003906 0.708599328994751 0.6966271 1.118141531944275 True -5 9852 18.083588123321533 0.48113226890563965 313.2980041503906 0.784791886806488 483.26397705078125 0.7128324508666992 0.709802 0.9673560261726379 True -6 11494 18.12315034866333 0.8706698417663574 334.9739990234375 1.071824550628662 481.1061706542969 0.7154553532600403 0.7181512 0.8308510780334473 True -7 13136 18.06976008415222 0.48667407035827637 263.6574401855469 1.012158751487732 478.02642822265625 0.7189471125602722 0.72539794 0.7804018259048462 True -8 14778 18.03854012489319 0.47998976707458496 356.72637939453125 1.4776065349578857 475.7704772949219 0.7219616770744324 0.7358585 0.7434767484664917 True -9 16420 18.04272985458374 0.4860725402832031 377.32550048828125 0.8496342897415161 473.8563537597656 0.7241736650466919 0.7405239 0.7019005417823792 True -10 18062 18.091556310653687 0.4857912063598633 308.71820068359375 1.069615125656128 471.10028076171875 0.7277264595031738 0.7439169 0.6780707240104675 True -11 19704 18.092954635620117 0.47958898544311523 319.779052734375 0.6340665221214294 469.1100158691406 0.7297819256782532 0.75124943 0.6636504530906677 True -12 21346 18.05043911933899 0.4853031635284424 310.26617431640625 0.5900853872299194 467.1253662109375 0.7320817112922668 0.7575702 0.6485477685928345 True -13 22988 18.08178210258484 0.49091100692749023 286.4248046875 0.5368268489837646 465.7550964355469 0.7337071895599365 0.7616126 0.647419810295105 True -14 24630 18.06071901321411 0.4797091484069824 340.59332275390625 0.868091881275177 465.0845031738281 0.7346802353858948 0.7693922 0.6386886239051819 True -15 26272 18.062159061431885 0.48464512825012207 295.8189697265625 0.47622033953666687 464.77813720703125 0.7349755764007568 0.7720981 0.6447887420654297 True -16 27914 18.07885241508484 0.48761725425720215 368.97503662109375 0.5185391902923584 464.9023742675781 0.7346174716949463 0.7746653 0.6648297309875488 True -17 29556 18.067676305770874 0.4982585906982422 282.71746826171875 0.26626700162887573 465.55731201171875 0.7335847616195679 0.77090913 0.6922491788864136 False -18 31198 18.05414390563965 0.4897651672363281 281.88916015625 0.28871482610702515 466.2240905761719 0.7327084541320801 0.76581454 0.7294809818267822 False -19 32840 18.044393301010132 0.4825150966644287 272.0806579589844 0.5105103254318237 466.63128662109375 0.7322388887405396 0.7630087 0.7456523776054382 False diff --git a/ENCSR983HXF/cherimoya.fold_1.performance.tsv b/ENCSR983HXF/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 738f3897d2a069ab9023481c96df7a531453b1f7..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -464.9023742675781 0.2279503494501114 0.7346174716949463 0.3159227967262268 0.7746652960777283 0.7704469561576843 0.6648297309875488 \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_2.evaluate.json b/ENCSR983HXF/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 14de9e24a5a0b68af2672a1e20a55b568728b89e..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277ZXH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_2.fit.json b/ENCSR983HXF/cherimoya.fold_2.fit.json deleted file mode 100644 index 4e80483dee19645aae22f55703bc8bf91ddbb436..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF277ZXH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_2.log b/ENCSR983HXF/cherimoya.fold_2.log deleted file mode 100644 index 3a0dc760387119616bab963e88e721b684e05edb..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1766 23.06037187576294 3.2634284496307373 412.23138427734375 1.1370983123779297 685.3082885742188 0.4801885783672333 0.5592402 16.775165557861328 True -1 3532 19.42119574546814 0.3437652587890625 302.81219482421875 1.1313893795013428 530.1139526367188 0.609470009803772 0.6470915 7.954663276672363 True -2 5298 19.446831226348877 0.3607468605041504 356.7646484375 1.197807788848877 473.28936767578125 0.6742339730262756 0.6793358 2.028040885925293 True -3 7064 19.43683934211731 0.3420827388763428 416.81512451171875 0.8141778707504272 457.8512878417969 0.689360499382019 0.6967141 1.0314315557479858 True -4 8830 19.436366081237793 0.341083288192749 327.67974853515625 1.2236194610595703 453.4057312011719 0.694629430770874 0.70547915 0.8708316087722778 True -5 10596 19.415919065475464 0.3410165309906006 326.41015625 1.069089651107788 450.6305236816406 0.6982585191726685 0.7147239 0.7956005334854126 True -6 12362 19.439408540725708 0.3448195457458496 366.4837646484375 0.8447723388671875 448.6539611816406 0.7008716464042664 0.7184268 0.7549512982368469 True -7 14128 19.23494052886963 0.386120080947876 309.0131530761719 1.0653468370437622 447.27850341796875 0.7035995125770569 0.72187406 0.7574489712715149 True -8 15894 19.03092932701111 0.3357212543487549 295.4897155761719 1.0549705028533936 445.52850341796875 0.7063201069831848 0.71973926 0.7518044710159302 False -9 17660 19.061870336532593 0.3431386947631836 353.42974853515625 0.7211387157440186 443.0399169921875 0.7095987200737 0.72680336 0.7234145998954773 True -10 19426 19.039864778518677 1.028756856918335 392.7547302246094 0.44413524866104126 441.0353698730469 0.7123427987098694 0.7345828 0.6941878199577332 True -11 21192 19.042815685272217 0.3330717086791992 310.0390625 1.0477577447891235 439.19281005859375 0.7146891951560974 0.7417687 0.6787562370300293 True -12 22958 19.093832969665527 7.61617112159729 355.9382019042969 0.47449302673339844 438.0933837890625 0.7166825532913208 0.7508335 0.6645248532295227 True -13 24724 19.06484079360962 0.33821964263916016 297.32965087890625 1.0801526308059692 437.1075134277344 0.7183510661125183 0.7539262 0.6618420481681824 True -14 26490 19.05764865875244 0.3388674259185791 353.8786315917969 1.0141489505767822 436.3181457519531 0.7195459604263306 0.7580666 0.657683253288269 True -15 28256 19.080950260162354 0.34644174575805664 374.7433166503906 0.498293399810791 436.2287292480469 0.7195298671722412 0.7584874 0.6733205318450928 True -16 30022 19.148231029510498 0.3417668342590332 354.66839599609375 0.4258577823638916 436.4535217285156 0.719249963760376 0.7622556 0.6818713545799255 True -17 31788 19.042941093444824 0.3450474739074707 300.0404357910156 0.3318292796611786 436.7424011230469 0.718352198600769 0.7630505 0.6957228183746338 True -18 33554 19.055304288864136 1.2168869972229004 308.6519470214844 0.30889809131622314 437.20758056640625 0.7175816893577576 0.7620054 0.7177562713623047 False -19 35320 19.090368509292603 0.6980407238006592 296.8896179199219 0.30769795179367065 437.4051513671875 0.717195451259613 0.75837034 0.7347129583358765 False diff --git a/ENCSR983HXF/cherimoya.fold_2.performance.tsv b/ENCSR983HXF/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e8aa4d14a84cd47f8eb19b94e9821577a744fb9b..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -436.7424011230469 0.24123550951480865 0.7183522582054138 0.29521510004997253 0.7630504965782166 0.7481355667114258 0.6957228183746338 \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_3.evaluate.json b/ENCSR983HXF/cherimoya.fold_3.evaluate.json deleted file mode 100644 index f9f1667f48a83236b60d0b9da3ec0654358e4437..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277ZXH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_3.fit.json b/ENCSR983HXF/cherimoya.fold_3.fit.json deleted file mode 100644 index 58444194cea1732c3727fa19a9cd7de7c6c6bbe2..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF277ZXH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_3.log b/ENCSR983HXF/cherimoya.fold_3.log deleted file mode 100644 index 9961680c56a470a213f1e8d86fe488c4ea5ae913..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1715 34.3302800655365 64.00621557235718 395.1238708496094 1.7466251850128174 675.6979370117188 0.4799448847770691 0.55942214 16.944398880004883 True -1 3430 18.879164218902588 0.9164590835571289 338.6167297363281 1.406964898109436 517.55322265625 0.608569324016571 0.6455819 8.82972240447998 True -2 5145 18.878660917282104 0.3539905548095703 310.20135498046875 1.6261487007141113 471.0693359375 0.6697134971618652 0.6198215 2.9103052616119385 False -3 6860 18.84628129005432 0.6023039817810059 391.52154541015625 0.9754218459129333 456.35894775390625 0.6832141876220703 0.63781905 1.3057944774627686 False -4 8575 18.841885566711426 0.3575432300567627 379.29998779296875 0.7865055799484253 451.64532470703125 0.6885205507278442 0.65213585 1.0593420267105103 True -5 10290 18.851435661315918 0.3565669059753418 309.038818359375 1.1849839687347412 447.9237060546875 0.6927841901779175 0.6684483 0.9498746395111084 True -6 12005 18.885044813156128 0.35318779945373535 343.6794128417969 1.0484607219696045 445.2864074707031 0.6962941288948059 0.6779005 0.9202550053596497 True -7 13720 18.871012926101685 0.35846948623657227 294.1811218261719 1.0696377754211426 443.8744201660156 0.6987444758415222 0.68381506 0.8451921343803406 True -8 15435 18.871220350265503 0.3587923049926758 398.6789245605469 1.0871963500976562 441.5091247558594 0.7017155289649963 0.6916049 0.8010936379432678 True -9 17150 18.89613699913025 0.3583967685699463 436.22796630859375 0.9199789762496948 440.2371826171875 0.7042211890220642 0.6959287 0.7879868149757385 True -10 18865 18.87115478515625 0.35349416732788086 360.32623291015625 0.7121415734291077 438.0911865234375 0.707013726234436 0.7024139 0.7589099407196045 True -11 20580 18.86589479446411 6.539804458618164 312.544921875 0.5754262208938599 436.7435302734375 0.7089239954948425 0.7085442 0.7520085573196411 True -12 22295 18.88427972793579 0.3555154800415039 344.50201416015625 0.6640037298202515 435.3443603515625 0.7105499505996704 0.7164854 0.7390645146369934 True -13 24010 18.894994020462036 0.3560664653778076 354.1540832519531 0.6803432106971741 434.3005065917969 0.7120226621627808 0.72390234 0.7263267040252686 True -14 25725 18.888748168945312 0.3614630699157715 314.3504943847656 0.981751561164856 433.9129943847656 0.7130457758903503 0.73523927 0.7152761816978455 True -15 27440 18.93861746788025 0.8105332851409912 320.5231018066406 0.4945201873779297 433.4337158203125 0.7134484052658081 0.74177015 0.7169803977012634 True -16 29155 18.60862684249878 0.35829901695251465 320.26507568359375 0.6606943607330322 433.7359924316406 0.7128706574440002 0.7457876 0.7281533479690552 True -17 30870 18.520073652267456 0.3553802967071533 345.5121154785156 0.6347118616104126 433.98883056640625 0.7120490670204163 0.74458206 0.7545414566993713 False -18 32585 18.5198872089386 0.3512997627258301 232.89044189453125 0.38979196548461914 434.0053405761719 0.7113261222839355 0.7441259 0.7790079712867737 False -19 34300 18.509936571121216 0.35457706451416016 301.59185791015625 0.5947480797767639 434.7889709472656 0.710848867893219 0.74192625 0.7967243790626526 False diff --git a/ENCSR983HXF/cherimoya.fold_3.performance.tsv b/ENCSR983HXF/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 7797132ccba73955deb34e90dcc790bbfba3cfe1..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -433.7359924316406 0.24310316145420074 0.712870717048645 0.2922649085521698 0.7457876205444336 0.7329707145690918 0.7281533479690552 \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_4.evaluate.json b/ENCSR983HXF/cherimoya.fold_4.evaluate.json deleted file mode 100644 index fc2cfaa9c464eb0204cefea65254f740c2c6872e..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF277ZXH.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_4.fit.json b/ENCSR983HXF/cherimoya.fold_4.fit.json deleted file mode 100644 index 8790d1b4886289fd1b8dc71a232f261175660e45..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF277ZXH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR983HXF/cherimoya.fold_4.log b/ENCSR983HXF/cherimoya.fold_4.log deleted file mode 100644 index 505cf201e7fdaccd0c56a3a0b4a602f7e789db0d..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1695 22.598490953445435 3.814441204071045 356.8759765625 1.138291358947754 662.5302124023438 0.4688427746295929 0.56137687 16.744083404541016 True -1 3390 18.735235452651978 0.31223058700561523 364.77093505859375 1.9376931190490723 506.31842041015625 0.6007144451141357 0.6279616 9.835192680358887 True -2 5085 18.735692024230957 0.29589056968688965 324.2107238769531 1.2434635162353516 457.0482482910156 0.6657640933990479 0.63021266 2.421358585357666 True -3 6780 18.703622341156006 0.29899024963378906 342.1032409667969 1.0987694263458252 440.6502685546875 0.681519627571106 0.65133625 1.008760929107666 True -4 8475 18.707958221435547 0.3090364933013916 313.9647216796875 0.901098370552063 436.1322937011719 0.6868235468864441 0.6613337 0.8870325684547424 True -5 10170 18.731167793273926 0.29481983184814453 310.8417663574219 0.8560852408409119 433.5123596191406 0.6911072731018066 0.6635794 0.9015835523605347 True -6 11865 18.754435062408447 0.2951014041900635 301.6456604003906 0.7737609148025513 431.098388671875 0.6940444111824036 0.67118925 0.8474191427230835 True -7 13560 18.738417148590088 0.3091592788696289 375.80322265625 0.684037446975708 429.3855895996094 0.6966932415962219 0.67228055 0.8265630602836609 True -8 15255 18.70646595954895 10.571412801742554 353.4495849609375 1.1324530839920044 428.01226806640625 0.6986182332038879 0.6771562 0.8290868997573853 True -9 16950 19.06982922554016 0.3253672122955322 358.5170593261719 0.9444026947021484 425.1604919433594 0.7015586495399475 0.68825597 0.798738956451416 True -10 18645 18.72047257423401 0.2997899055480957 381.7381591796875 0.7975074052810669 423.634033203125 0.7040420174598694 0.69902587 0.7668165564537048 True -11 20340 18.73814582824707 0.3089630603790283 309.15911865234375 0.8329977989196777 421.7460632324219 0.7063358426094055 0.70566374 0.7578365802764893 True -12 22035 18.7744300365448 0.3044130802154541 309.21234130859375 0.6142171621322632 420.2457580566406 0.7084094285964966 0.7157028 0.7334843277931213 True -13 23730 18.723565578460693 0.30135202407836914 329.1875 0.7073967456817627 419.2026672363281 0.7100910544395447 0.72282606 0.7199819684028625 True -14 25425 18.733335256576538 0.3044767379760742 311.7926940917969 0.5503125190734863 418.30828857421875 0.7111248970031738 0.73125595 0.7084028720855713 True -15 27120 18.77259135246277 0.2962017059326172 254.2539825439453 0.5626095533370972 418.0592346191406 0.7114322185516357 0.7351642 0.7090588808059692 True -16 28815 18.737180709838867 0.3010063171386719 299.0537109375 0.3578793406486511 418.1019287109375 0.7111354470252991 0.7412178 0.7123108506202698 True -17 30510 18.715298652648926 0.29520440101623535 303.6282958984375 0.5785239338874817 418.7881774902344 0.7098637819290161 0.74153394 0.7295398712158203 True -18 32205 18.71585726737976 0.29508399963378906 355.08172607421875 0.5440254211425781 419.40411376953125 0.7091391086578369 0.74149054 0.7437978982925415 False -19 33900 18.734968423843384 0.3016808032989502 278.0381164550781 0.5963737368583679 419.6978454589844 0.7085960507392883 0.7380699 0.7552476525306702 False diff --git a/ENCSR983HXF/cherimoya.fold_4.performance.tsv b/ENCSR983HXF/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 0f128f8f7599a06f9f1c34b6ce08bf7e02bffcfa..0000000000000000000000000000000000000000 --- a/ENCSR983HXF/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -418.7881774902344 0.24748992919921875 0.7098637819290161 0.28595513105392456 0.7415339350700378 0.7131707072257996 0.7295398712158203 \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_0.evaluate.json b/ENCSR986HEN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a4c21ea391a31cc672c3ef2ad2bc33084234afe8..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF648LNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_0.fit.json b/ENCSR986HEN/cherimoya.fold_0.fit.json deleted file mode 100644 index 23b71adca8155443d9ef7b1b0e054ae7a282a76c..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF648LNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_0.log b/ENCSR986HEN/cherimoya.fold_0.log deleted file mode 100644 index ce6dc8bedc069804c4dc2e9259f85033e11d31d7..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2765 35.257243156433105 3.661311149597168 164.64349365234375 0.36826950311660767 218.99314880371094 0.14220000803470612 0.6391052 2.444955587387085 True -1 5530 30.809977531433105 0.5836381912231445 180.0103759765625 0.6038025617599487 208.6020965576172 0.2003304660320282 0.7001682 0.7773587703704834 True -2 8295 30.81113624572754 0.5848798751831055 145.18995666503906 0.5600751638412476 205.25486755371094 0.21174059808254242 0.71768117 0.5139719843864441 True -3 11060 30.78151297569275 0.5628771781921387 169.45266723632812 0.5817703008651733 203.4677276611328 0.21779859066009521 0.7251061 0.4497230648994446 True -4 13825 30.893279314041138 0.5719983577728271 155.61331176757812 0.5556785464286804 202.70570373535156 0.22169016301631927 0.7286264 0.4319188892841339 True -5 16590 30.893507719039917 0.5786960124969482 185.48959350585938 0.6770310401916504 201.84365844726562 0.22686205804347992 0.7312592 0.43366527557373047 True -6 19355 30.91726589202881 0.5868520736694336 216.77102661132812 0.4533737003803253 201.35263061523438 0.2291429191827774 0.7379287 0.4572105407714844 True -7 22120 31.01582145690918 0.5767488479614258 160.28750610351562 0.5089704990386963 201.0664825439453 0.23007501661777496 0.7407356 0.4467197358608246 True -8 24885 31.01463532447815 0.5905792713165283 149.1586151123047 0.5347477197647095 200.3140106201172 0.2344934046268463 0.7440421 0.4066624939441681 True -9 27650 30.88524842262268 0.5971195697784424 169.33334350585938 0.3600315749645233 199.67259216308594 0.23897813260555267 0.7468101 0.3880407512187958 True -10 30415 30.874809503555298 1.0174295902252197 126.21021270751953 0.5008325576782227 199.4803924560547 0.23958392441272736 0.75059724 0.3878105878829956 True -11 33180 33.571858644485474 28.94426465034485 170.03941345214844 0.4066113829612732 199.06593322753906 0.2417149394750595 0.75002134 0.36863139271736145 False -12 35945 31.117027044296265 0.572134256362915 146.17739868164062 0.32486993074417114 198.7661590576172 0.24341754615306854 0.7588529 0.3584285080432892 True -13 38710 30.863101482391357 0.5732111930847168 161.36221313476562 0.3690548241138458 198.29029846191406 0.24587686359882355 0.76365006 0.34035244584083557 True -14 41475 30.90807008743286 0.5885179042816162 163.1368865966797 0.5643330812454224 198.1930694580078 0.24612340331077576 0.76947486 0.32331815361976624 True -15 44240 30.973918676376343 0.5882511138916016 167.81390380859375 0.4010681211948395 197.96044921875 0.24663180112838745 0.77676207 0.30120164155960083 True -16 47005 31.01467990875244 0.5872440338134766 174.7872772216797 0.307175874710083 197.60848999023438 0.2490011304616928 0.78038186 0.2863088548183441 True -17 49770 30.97102928161621 0.5856752395629883 155.81236267089844 0.27950289845466614 197.46365356445312 0.24958164989948273 0.78240496 0.2790294885635376 True -18 52535 30.97886562347412 0.5729718208312988 151.15597534179688 0.21353335678577423 197.5457000732422 0.24889862537384033 0.78292197 0.2798168957233429 True -19 55300 30.411614656448364 0.5723240375518799 147.66226196289062 0.3260420262813568 197.53819274902344 0.24880819022655487 0.7804119 0.28217360377311707 False diff --git a/ENCSR986HEN/cherimoya.fold_0.performance.tsv b/ENCSR986HEN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 5a1b2075c99f9d7eb5f54a300b24409e5c92f8e3..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -197.5457000732422 0.53252774477005 0.24889861047267914 0.05298107862472534 0.7829219698905945 0.7193746566772461 0.2798168957233429 \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_1.evaluate.json b/ENCSR986HEN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 4fa7bcf7c55fec97fd25246fd403aaef71af4172..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF648LNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_1.fit.json b/ENCSR986HEN/cherimoya.fold_1.fit.json deleted file mode 100644 index d4422e22685ed07446f6122b723dc13865008a42..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF648LNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_1.log b/ENCSR986HEN/cherimoya.fold_1.log deleted file mode 100644 index 91055164e91d09824a2f74f531e1b7d536ad66aa..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2733 36.230682134628296 4.546128988265991 173.14573669433594 0.5472675561904907 256.9273681640625 0.15277262032032013 0.636761 3.327382802963257 True -1 5466 30.492472648620605 0.7145888805389404 165.74127197265625 0.49978363513946533 242.43931579589844 0.21814218163490295 0.7185947 0.9539368152618408 True -2 8199 31.76986861228943 0.7057251930236816 146.2321319580078 0.41631990671157837 238.75241088867188 0.23045335710048676 0.73701674 0.5161026120185852 True -3 10932 30.448469161987305 2.9415063858032227 165.22372436523438 0.38138335943222046 236.56463623046875 0.2356599122285843 0.7493305 0.4536706209182739 True -4 13665 30.460254192352295 1.6213500499725342 182.42591857910156 1.0245059728622437 234.58250427246094 0.24291150271892548 0.75718725 0.4252174496650696 True -5 16398 30.474928379058838 1.3222873210906982 153.4272003173828 0.5182778835296631 233.70518493652344 0.24653437733650208 0.76268446 0.42321696877479553 True -6 19131 30.750832557678223 45.790706157684326 153.64288330078125 0.2714741826057434 233.0408172607422 0.2491525113582611 0.76755816 0.4414812922477722 True -7 21864 30.880022287368774 2.463099956512451 171.29983520507812 0.32013100385665894 232.61581420898438 0.25065863132476807 0.77166355 0.44324755668640137 True -8 24597 30.530070304870605 1.2300605773925781 154.31663513183594 0.4658436179161072 231.83126831054688 0.25420600175857544 0.77514946 0.46260523796081543 True -9 27330 30.64444613456726 0.7273991107940674 143.63128662109375 0.4346567690372467 231.42050170898438 0.2566097378730774 0.77812934 0.4744086265563965 True -10 30063 30.473774909973145 0.6979036331176758 152.57913208007812 0.3882892429828644 230.96817016601562 0.25819826126098633 0.7830756 0.47309407591819763 True -11 32796 30.46090006828308 0.7054998874664307 173.20008850097656 0.26378220319747925 230.3777313232422 0.2612830102443695 0.78624296 0.4529588222503662 True -12 35529 30.48976969718933 0.6954755783081055 129.9722442626953 0.5645526647567749 229.83779907226562 0.26416441798210144 0.7886929 0.44366589188575745 True -13 38262 30.495590925216675 0.7024290561676025 132.79324340820312 0.2525344491004944 229.46177673339844 0.2652853727340698 0.7937662 0.41134992241859436 True -14 40995 30.48040246963501 0.7781524658203125 147.9346466064453 0.35871103405952454 229.04571533203125 0.26720863580703735 0.79706067 0.3858739137649536 True -15 43728 30.412622213363647 0.7056045532226562 146.9239501953125 0.287123441696167 228.57296752929688 0.2693120539188385 0.8032264 0.3533485531806946 True -16 46461 30.43581509590149 0.7159929275512695 133.97439575195312 0.36194750666618347 228.25930786132812 0.26983270049095154 0.8077691 0.32755470275878906 True -17 49194 30.563958406448364 0.6987729072570801 153.01052856445312 0.24751845002174377 228.27862548828125 0.26955974102020264 0.8073893 0.3180094361305237 False -18 51927 30.549339056015015 1.2210581302642822 138.18026733398438 0.4020233154296875 228.78823852539062 0.26668453216552734 0.8068098 0.31053426861763 False -19 54660 30.589192152023315 34.751450300216675 160.78561401367188 0.20888133347034454 228.47486877441406 0.26848891377449036 0.8059296 0.3131043016910553 False diff --git a/ENCSR986HEN/cherimoya.fold_1.performance.tsv b/ENCSR986HEN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 687f7f8d6a1a20862c612f555cf4234cd9d955dc..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -228.25930786132812 0.5146564841270447 0.26983270049095154 0.06532668322324753 0.8077691197395325 0.7587922811508179 0.32755470275878906 \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_2.evaluate.json b/ENCSR986HEN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index bf42a8fc0f606ee513ab225a3ff714f9c8e252f1..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF648LNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_2.fit.json b/ENCSR986HEN/cherimoya.fold_2.fit.json deleted file mode 100644 index 4a808106fc5936e8c04bc1d8669607362fe25309..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF648LNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_2.log b/ENCSR986HEN/cherimoya.fold_2.log deleted file mode 100644 index cac4cf134c79b695f4e86a40401d73bada738036..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2888 36.757380962371826 3.6875643730163574 160.22610473632812 0.527911901473999 226.3236541748047 0.14827905595302582 0.63580006 1.9695796966552734 True -1 5776 32.216466665267944 12.511587381362915 147.81190490722656 0.702360212802887 214.3580322265625 0.2077433168888092 0.70870805 0.7278600931167603 True -2 8664 32.2987859249115 0.5443148612976074 130.5597686767578 0.6086258888244629 211.13140869140625 0.2184855043888092 0.72615075 0.49897706508636475 True -3 11552 32.21715998649597 0.5347139835357666 189.22720336914062 0.5588504076004028 209.01666259765625 0.22756792604923248 0.7325987 0.3943009674549103 True -4 14440 32.25558090209961 0.544558048248291 192.2333984375 0.6382727026939392 208.40835571289062 0.22973968088626862 0.7368932 0.3991747498512268 True -5 17328 32.15595841407776 0.5469348430633545 165.30026245117188 0.6295178532600403 208.00921630859375 0.2314382642507553 0.7362688 0.41332557797431946 False -6 20216 32.81389832496643 21.201171159744263 157.4088592529297 0.6674085855484009 207.20504760742188 0.23575104773044586 0.74121475 0.4485457241535187 True -7 23104 32.231868505477905 0.5546953678131104 179.10601806640625 0.6201391816139221 206.8087615966797 0.23734772205352783 0.74418426 0.4321751296520233 True -8 25992 32.26721262931824 0.5489740371704102 231.7759552001953 0.503692090511322 206.30535888671875 0.24000675976276398 0.7470084 0.4742909073829651 True -9 28880 32.359567403793335 0.5508913993835449 143.3019256591797 0.32705655694007874 205.8755645751953 0.2432059943675995 0.74722064 0.46289509534835815 True -10 31768 32.235342264175415 0.5595026016235352 177.7603759765625 0.2736344635486603 205.46449279785156 0.24431979656219482 0.7536461 0.4662955701351166 True -11 34656 32.22114944458008 0.5460879802703857 169.69285583496094 0.4226725697517395 205.0482177734375 0.2456253618001938 0.7561781 0.44650742411613464 True -12 37544 32.19918084144592 1.9250361919403076 161.91680908203125 0.26293686032295227 204.66346740722656 0.2482353001832962 0.7622765 0.4167231619358063 True -13 40432 32.22341847419739 7.712468147277832 153.09490966796875 0.2896237373352051 204.32606506347656 0.25001952052116394 0.7684743 0.38246074318885803 True -14 43320 32.204238414764404 1.1444942951202393 151.2045440673828 0.30942171812057495 203.61878967285156 0.2534686028957367 0.7775334 0.34899020195007324 True -15 46208 32.24962043762207 0.5478720664978027 160.8138885498047 0.2633957862854004 203.63133239746094 0.2527703046798706 0.78015715 0.33063602447509766 True -16 49096 32.28155207633972 1.1727821826934814 168.20541381835938 0.3282654881477356 203.42481994628906 0.25385960936546326 0.78662467 0.3142603635787964 True -17 51984 32.284202575683594 0.5455260276794434 143.20697021484375 0.28405091166496277 203.36241149902344 0.25379979610443115 0.78664416 0.3013424277305603 True -18 54872 32.251259565353394 0.5369436740875244 170.96067810058594 0.3360760807991028 203.18211364746094 0.2550431191921234 0.7874149 0.2974224090576172 True -19 57760 32.281951904296875 0.5442204475402832 151.2646484375 0.2514292299747467 203.404052734375 0.25328731536865234 0.7872547 0.29892322421073914 False diff --git a/ENCSR986HEN/cherimoya.fold_2.performance.tsv b/ENCSR986HEN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ed3138d01a8eef985209f0ab7bf6467aaf290a3d..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -203.18211364746094 0.5283010601997375 0.2550431191921234 0.05395875498652458 0.7874149084091187 0.7257384061813354 0.2974224090576172 \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_3.evaluate.json b/ENCSR986HEN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 42ad09172700e140130e79b7d7a209b20eac93b9..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF648LNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_3.fit.json b/ENCSR986HEN/cherimoya.fold_3.fit.json deleted file mode 100644 index 400dea97744ac5207c14fc054e7bed88b384eb93..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF648LNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_3.log b/ENCSR986HEN/cherimoya.fold_3.log deleted file mode 100644 index b1487a096297684f5711ab5165d13ec9fc3c6490..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2776 36.014193058013916 3.643453359603882 191.450927734375 0.9452911615371704 233.36993408203125 0.14464469254016876 0.6555316 2.692793607711792 True -1 5552 30.54413151741028 0.5829994678497314 146.14962768554688 0.6177163124084473 221.4502410888672 0.20469297468662262 0.71578264 0.8864175081253052 True -2 8328 31.015503406524658 0.5612454414367676 138.2283477783203 0.6452063322067261 218.36634826660156 0.21760837733745575 0.73559624 0.5528501272201538 True -3 11104 30.993329763412476 0.5585494041442871 179.4266815185547 0.42019569873809814 217.081787109375 0.22124934196472168 0.74131 0.5072334408760071 True -4 13880 30.96774911880493 0.5583233833312988 195.35659790039062 0.5579599142074585 216.40769958496094 0.22401437163352966 0.74243385 0.4927254021167755 True -5 16656 31.036176443099976 0.5487473011016846 193.05941772460938 0.49195757508277893 215.8118133544922 0.22712692618370056 0.74243605 0.512832760810852 True -6 19432 30.973746061325073 0.5567984580993652 157.51913452148438 0.4167183041572571 214.99752807617188 0.23171186447143555 0.7469162 0.5050845146179199 True -7 22208 30.955352783203125 0.5537045001983643 202.51107788085938 0.33971190452575684 214.55601501464844 0.23398318886756897 0.7462864 0.5282669067382812 False -8 24984 30.936110258102417 0.5572636127471924 161.5951690673828 0.3513101637363434 213.92437744140625 0.23740209639072418 0.75182366 0.48410850763320923 True -9 27760 30.923704147338867 1.014573574066162 181.68310546875 0.3312641382217407 213.6980438232422 0.2385406494140625 0.7503879 0.45944082736968994 False -10 30536 30.91873002052307 0.6430256366729736 152.30442810058594 0.3343545198440552 213.27207946777344 0.2404976487159729 0.7564039 0.4623829424381256 True -11 33312 30.964457750320435 0.5599339008331299 165.6516571044922 0.32409730553627014 212.9662322998047 0.24235929548740387 0.75710285 0.4586026072502136 True -12 36088 31.09390115737915 0.5578372478485107 147.292724609375 0.3821571469306946 212.2159423828125 0.24597550928592682 0.76334935 0.4328301250934601 True -13 38864 31.006132125854492 0.5666544437408447 128.44094848632812 0.28542637825012207 212.0398406982422 0.2466314285993576 0.77183115 0.4126608967781067 True -14 41640 30.956642627716064 27.223325967788696 165.9490966796875 0.42957454919815063 211.776123046875 0.24822206795215607 0.7817146 0.37269875407218933 True -15 44416 36.3491108417511 0.5955243110656738 162.2952880859375 0.372444748878479 211.59934997558594 0.24884653091430664 0.78683156 0.3426399827003479 True -16 47192 31.071702241897583 2.0516369342803955 170.17819213867188 0.5405806303024292 211.3693084716797 0.249604731798172 0.7896362 0.3228980600833893 True -17 49968 31.052215337753296 1.6994314193725586 140.5236358642578 0.3118181824684143 211.32627868652344 0.2501194477081299 0.7915781 0.3073086440563202 True -18 52744 31.28997826576233 0.5653436183929443 193.0218048095703 0.38384148478507996 211.45181274414062 0.2493341863155365 0.7943093 0.30274948477745056 True -19 55520 31.301249265670776 0.5754640102386475 141.91375732421875 0.2462213635444641 211.2398681640625 0.2508522868156433 0.79150105 0.30309557914733887 False diff --git a/ENCSR986HEN/cherimoya.fold_3.performance.tsv b/ENCSR986HEN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 47d275c56920d692597743012951c13e12928ed6..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -211.45181274414062 0.5282720327377319 0.24933423101902008 0.057791341096162796 0.7943093180656433 0.7308896780014038 0.30274948477745056 \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_4.evaluate.json b/ENCSR986HEN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 2d321bc23f351d38b0b35722fc8695f339365b1e..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF648LNL.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_4.fit.json b/ENCSR986HEN/cherimoya.fold_4.fit.json deleted file mode 100644 index 7916f5622fb0f56a797b9b1d5ae0db203f61473f..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF648LNL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986HEN/cherimoya.fold_4.log b/ENCSR986HEN/cherimoya.fold_4.log deleted file mode 100644 index 9e7575003e016ff73da0d9fd1d4c0b5ff950fb19..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 37.09065055847168 28.796220064163208 158.7668914794922 0.470991313457489 221.2935333251953 0.14429789781570435 0.63295394 2.427412271499634 True -1 5736 32.724186182022095 0.6447482109069824 158.0116729736328 0.4743538796901703 210.75489807128906 0.2016710340976715 0.6970085 0.7877219319343567 True -2 8604 31.966800212860107 0.6056737899780273 159.8001251220703 0.6511255502700806 207.82260131835938 0.21306630969047546 0.70359 0.49590498208999634 True -3 11472 31.330840826034546 0.6000993251800537 183.25909423828125 0.9130199551582336 206.61769104003906 0.21677909791469574 0.7154756 0.45207667350769043 True -4 14340 31.482293128967285 0.7905027866363525 167.1822509765625 0.457649290561676 205.92312622070312 0.22050483524799347 0.71726215 0.48586416244506836 True -5 17208 31.36795163154602 16.687241315841675 166.86720275878906 0.6539143323898315 205.4405975341797 0.2230077087879181 0.7247812 0.5134841203689575 True -6 20076 32.4866418838501 11.063802719116211 157.966064453125 0.41507279872894287 204.7113494873047 0.2270667403936386 0.7275735 0.5144075751304626 True -7 22944 31.405597448349 0.6185376644134521 134.71859741210938 0.41920414566993713 204.3988037109375 0.22856244444847107 0.73310167 0.48623940348625183 True -8 25812 31.314047813415527 0.6176438331604004 171.36666870117188 0.5052878856658936 204.0300750732422 0.23068231344223022 0.7386586 0.4390164613723755 True -9 28680 31.323596239089966 0.6032326221466064 187.12608337402344 0.6373230218887329 203.41195678710938 0.2346823662519455 0.740414 0.42572152614593506 True -10 31548 31.305021047592163 0.6002645492553711 155.63238525390625 0.3443742096424103 203.1226043701172 0.2358340620994568 0.7426245 0.4236004948616028 True -11 34416 31.485738039016724 39.729408740997314 179.6229248046875 0.34465646743774414 202.84103393554688 0.23834335803985596 0.74680805 0.40551239252090454 True -12 37284 31.557668209075928 0.597496509552002 191.60919189453125 0.4218360185623169 202.41998291015625 0.2399202138185501 0.75161046 0.3856215178966522 True -13 40152 31.381047010421753 0.6099381446838379 163.0830841064453 0.4775923490524292 202.16091918945312 0.2410801500082016 0.7544336 0.36790183186531067 True -14 43020 31.352187633514404 1.1646158695220947 187.324951171875 0.33476734161376953 201.7344970703125 0.24375756084918976 0.7651559 0.3368489444255829 True -15 45888 31.429553031921387 0.6155476570129395 163.70167541503906 0.2985386252403259 201.50628662109375 0.2442607581615448 0.76835984 0.31584471464157104 True -16 48756 31.591317415237427 38.89306879043579 150.09649658203125 0.23981820046901703 201.49986267089844 0.24376694858074188 0.7745364 0.3006640374660492 True -17 51624 33.42466855049133 1.1883296966552734 167.76025390625 0.29996153712272644 201.33102416992188 0.24529950320720673 0.77487254 0.28854772448539734 True -18 54492 31.650509357452393 0.6017410755157471 175.69522094726562 0.22592636942863464 201.66400146484375 0.24293266236782074 0.7753116 0.28716862201690674 True -19 57360 31.568450927734375 1.3157598972320557 140.75306701660156 0.19818994402885437 201.6004638671875 0.24376390874385834 0.7735446 0.28563445806503296 False diff --git a/ENCSR986HEN/cherimoya.fold_4.performance.tsv b/ENCSR986HEN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index be687d4917126cd67a8b2d6359e74c7d150626ad..0000000000000000000000000000000000000000 --- a/ENCSR986HEN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -201.66400146484375 0.5333678126335144 0.24293266236782074 0.05096771940588951 0.7753115892410278 0.7091934084892273 0.28716862201690674 \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_0.evaluate.json b/ENCSR986XLW/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 002b11fc876f0532ab2d90db4fe6e2f76df6dc61..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF057FQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_0.fit.json b/ENCSR986XLW/cherimoya.fold_0.fit.json deleted file mode 100644 index 06d586ce62c7ad8a91f60cb6d90e77d99ff0c550..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF057FQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_0.log b/ENCSR986XLW/cherimoya.fold_0.log deleted file mode 100644 index 8d5edeed737b9090b95472dd76fee82f011cd647..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2741 34.02712678909302 3.427199363708496 240.47186279296875 1.7001756429672241 294.94183349609375 0.20279131829738617 0.3753575 4.15854549407959 True -1 5482 30.591656923294067 0.5784766674041748 240.81602478027344 1.1743029356002808 262.5979309082031 0.30893608927726746 0.49866506 2.5237514972686768 True -2 8223 30.553470134735107 0.5622227191925049 171.9943084716797 1.5486551523208618 258.3674621582031 0.32022541761398315 0.5035711 1.5605436563491821 True -3 10964 30.579593658447266 0.5629396438598633 215.08346557617188 1.328961730003357 255.77224731445312 0.3271335959434509 0.50990725 1.3301726579666138 True -4 13705 30.588706254959106 0.5682122707366943 182.45509338378906 1.346332311630249 254.4049835205078 0.33095163106918335 0.51709986 1.399579644203186 True -5 16446 30.494511604309082 0.562335729598999 200.28346252441406 0.8398734331130981 252.25784301757812 0.3371172249317169 0.52482414 1.347123146057129 True -6 19187 30.49880337715149 0.5628912448883057 220.23199462890625 1.2842628955841064 251.1548309326172 0.3421240746974945 0.53503376 1.2143625020980835 True -7 21928 30.5378680229187 0.5628147125244141 153.7825164794922 1.2270451784133911 250.01602172851562 0.3466698229312897 0.5446099 1.1503700017929077 True -8 24669 30.5206139087677 0.5632710456848145 220.04966735839844 1.2208077907562256 248.62490844726562 0.3501013517379761 0.5534644 1.1242759227752686 True -9 27410 30.519052743911743 0.5899984836578369 175.09681701660156 0.8938699960708618 248.0341033935547 0.3529888391494751 0.5639204 1.0540956258773804 True -10 30151 30.569039344787598 0.5785164833068848 154.159912109375 0.8214671015739441 246.49615478515625 0.3568301796913147 0.5742085 0.9540743827819824 True -11 32892 30.58897590637207 0.5894355773925781 153.04319763183594 0.7213363647460938 245.8131866455078 0.3597407341003418 0.5800123 0.874365508556366 True -12 35633 30.56379246711731 9.270368337631226 217.3016357421875 0.7890844345092773 244.61256408691406 0.3622221350669861 0.59027267 0.8445858955383301 True -13 38374 30.518439769744873 19.16122317314148 191.5043487548828 1.0018903017044067 243.532470703125 0.3669987618923187 0.59974086 0.7872680425643921 True -14 41115 30.926478624343872 0.5720200538635254 186.21722412109375 0.8503694534301758 243.26002502441406 0.365895539522171 0.61431515 0.7136787176132202 True -15 43856 30.533971548080444 0.5777015686035156 202.76864624023438 0.7532960176467896 241.93704223632812 0.3722066581249237 0.6263685 0.6714080572128296 True -16 46597 30.530651330947876 0.7737622261047363 173.7598876953125 0.6016876697540283 241.776611328125 0.3705468773841858 0.6334777 0.6512418985366821 True -17 49338 30.632375717163086 0.5720312595367432 185.21676635742188 0.5755810737609863 241.41024780273438 0.3732166290283203 0.6401942 0.6239738464355469 True -18 52079 31.642849922180176 0.5671176910400391 159.2482452392578 0.7150331735610962 241.67816162109375 0.3715816140174866 0.64328027 0.6176802515983582 True -19 54820 30.633164405822754 0.5643801689147949 178.99844360351562 0.3725484013557434 241.99606323242188 0.3699553310871124 0.6422605 0.6229557991027832 False diff --git a/ENCSR986XLW/cherimoya.fold_0.performance.tsv b/ENCSR986XLW/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 06345771b6a81266f4084dbdf6864041c66e2a62..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -241.67816162109375 0.46406129002571106 0.3715816140174866 0.0843760222196579 0.6432802677154541 0.6033717393875122 0.6176802515983582 \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_1.evaluate.json b/ENCSR986XLW/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 71c5b4bf28bbf1a2ab2f1ba0274a2a52ff7b2df4..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF057FQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_1.fit.json b/ENCSR986XLW/cherimoya.fold_1.fit.json deleted file mode 100644 index aa25779b368e2ef63449cfd0f88fd8b1ba389901..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF057FQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_1.log b/ENCSR986XLW/cherimoya.fold_1.log deleted file mode 100644 index a1d9062191624931eb80f6a6f586a19809ccd36d..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2749 34.39150404930115 4.7571046352386475 155.77975463867188 1.3929733037948608 329.052978515625 0.20643547177314758 0.4417441 5.372078895568848 True -1 5498 30.89576816558838 0.686392068862915 205.1470947265625 1.4976251125335693 292.372802734375 0.31080883741378784 0.530723 2.899035692214966 True -2 8247 30.646435260772705 0.6803946495056152 166.40640258789062 1.3982672691345215 285.23712158203125 0.32731565833091736 0.53911567 1.4840604066848755 True -3 10996 30.58843493461609 1.2205994129180908 234.75955200195312 1.7789185047149658 282.8740539550781 0.3308210074901581 0.5545689 1.4359853267669678 True -4 13745 30.65704107284546 16.78587055206299 235.40057373046875 1.1220622062683105 280.3171081542969 0.33983567357063293 0.5654234 1.4823439121246338 True -5 16494 30.73328399658203 0.6737930774688721 176.22177124023438 1.1605205535888672 278.4221496582031 0.3459041118621826 0.5708169 1.5012012720108032 True -6 19243 30.836246252059937 0.6826648712158203 168.08456420898438 1.1893236637115479 277.0630187988281 0.34878093004226685 0.5809919 1.3542671203613281 True -7 21992 30.590442895889282 0.6763091087341309 218.65371704101562 1.098344326019287 275.2159729003906 0.35490089654922485 0.5884802 1.42247474193573 True -8 24741 30.9863760471344 0.658771276473999 168.30821228027344 1.1975618600845337 274.2587585449219 0.3551868200302124 0.59394836 1.2769640684127808 True -9 27490 30.55625295639038 0.7501206398010254 175.35812377929688 0.5839508771896362 272.81134033203125 0.36107805371284485 0.5989437 1.1936931610107422 True -10 30239 30.59536576271057 0.6630825996398926 199.62530517578125 0.8424417972564697 271.5689392089844 0.36520254611968994 0.60752285 1.090956687927246 True -11 32988 30.572929620742798 0.662468671798706 202.3369140625 0.86337810754776 271.0247802734375 0.3652447462081909 0.6182732 1.0059465169906616 True -12 35737 30.648397207260132 1.338059902191162 201.75955200195312 1.0874536037445068 269.1670227050781 0.37098127603530884 0.6284803 0.9281826615333557 True -13 38486 30.636183500289917 1.3983359336853027 191.90274047851562 0.7420022487640381 268.3727111816406 0.3715614080429077 0.6369103 0.8550363779067993 True -14 41235 30.62405014038086 0.6649301052093506 230.24722290039062 0.7872792482376099 267.2706298828125 0.3752261996269226 0.64809394 0.781753420829773 True -15 43984 30.610806465148926 0.6654207706451416 199.9951934814453 0.894345760345459 266.786865234375 0.37719571590423584 0.6601043 0.7243268489837646 True -16 46733 30.64198136329651 0.6633505821228027 193.03550720214844 0.5872997045516968 266.311767578125 0.3775985538959503 0.6686584 0.6941474676132202 True -17 49482 30.564900159835815 0.7341046333312988 191.63851928710938 0.5964451432228088 265.9100341796875 0.3792133331298828 0.67215455 0.6684274077415466 True -18 52231 30.632888317108154 21.503679990768433 157.1043701171875 0.5869555473327637 265.8370056152344 0.37887582182884216 0.6731515 0.6546255946159363 True -19 54980 30.64788317680359 0.6736710071563721 160.59033203125 0.3660728335380554 265.8116149902344 0.37964239716529846 0.6732122 0.660213828086853 True diff --git a/ENCSR986XLW/cherimoya.fold_1.performance.tsv b/ENCSR986XLW/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 2f14c0e2c421136fa5a378c99b3e5c54fddafdc0..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -265.8116149902344 0.4556182622909546 0.37964239716529846 0.09291970729827881 0.6732121706008911 0.6346839666366577 0.660213828086853 \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_2.evaluate.json b/ENCSR986XLW/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 51a4127bee03b39cc97062b48c287573250a5457..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF057FQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_2.fit.json b/ENCSR986XLW/cherimoya.fold_2.fit.json deleted file mode 100644 index 9dc59a0b5a5b538fb519e69d206c8c05e87a2ad1..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF057FQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_2.log b/ENCSR986XLW/cherimoya.fold_2.log deleted file mode 100644 index 859007aa6bea4625f720894c43bba40e85cb97b6..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2912 36.28722071647644 3.5665552616119385 175.46051025390625 1.18239164352417 305.84246826171875 0.21491186320781708 0.40646875 4.497039794921875 True -1 5824 32.4036328792572 0.5259597301483154 151.502197265625 2.06748104095459 273.09698486328125 0.31436827778816223 0.5060038 2.6868393421173096 True -2 8736 32.46046280860901 0.5070843696594238 208.2032012939453 1.2746837139129639 269.7555847167969 0.31756335496902466 0.5207935 1.6371536254882812 True -3 11648 32.43035626411438 0.49890804290771484 207.23565673828125 1.1705139875411987 266.1033020019531 0.32752200961112976 0.53345704 1.321301817893982 True -4 14560 32.389973878860474 0.5106461048126221 161.362060546875 0.8241029977798462 262.8685607910156 0.3384649157524109 0.5483592 1.2823107242584229 True -5 17472 32.43684196472168 0.4996216297149658 148.88002014160156 1.532644271850586 261.2576599121094 0.34628888964653015 0.553568 1.3629813194274902 True -6 20384 32.50035619735718 0.5060155391693115 183.20989990234375 0.84099942445755 260.38836669921875 0.3482382893562317 0.5611169 1.2856357097625732 True -7 23296 32.44070100784302 0.5000355243682861 168.736083984375 0.9642941951751709 259.7530212402344 0.34979453682899475 0.56563455 1.246139407157898 True -8 26208 32.41787362098694 0.49748682975769043 165.44290161132812 0.7834908962249756 258.5502014160156 0.3528718650341034 0.5715483 1.1804875135421753 True -9 29120 32.42503905296326 0.6927177906036377 158.52833557128906 1.00863516330719 257.3603515625 0.35749733448028564 0.5805024 1.1297065019607544 True -10 32032 32.410303831100464 0.5077404975891113 158.79437255859375 0.9659205675125122 256.0703125 0.360698401927948 0.5886904 0.9907364249229431 True -11 34944 32.4678738117218 0.4966089725494385 193.88165283203125 0.8254873752593994 254.47438049316406 0.3654411733150482 0.5967584 0.9448971748352051 True -12 37856 32.434075117111206 0.5086352825164795 228.155517578125 1.1129562854766846 253.60023498535156 0.3678775429725647 0.6107585 0.8440463542938232 True -13 40768 32.43131494522095 0.5071547031402588 179.27857971191406 1.1441924571990967 253.10397338867188 0.3691612482070923 0.6210798 0.8106629848480225 True -14 43680 32.420947790145874 8.36903429031372 178.36851501464844 0.5949137806892395 251.95936584472656 0.37366214394569397 0.6295296 0.7579625248908997 True -15 46592 32.46141219139099 0.5190176963806152 177.627197265625 0.7682220935821533 251.48175048828125 0.37385094165802 0.63903433 0.7194963693618774 True -16 49504 32.4894540309906 0.5558750629425049 175.05743408203125 0.7597724199295044 250.73178100585938 0.37570253014564514 0.6490447 0.6673887968063354 True -17 52416 32.537102699279785 0.5104539394378662 196.8878936767578 0.4903298616409302 250.83023071289062 0.37412986159324646 0.65243596 0.6525178551673889 True -18 55328 32.48881196975708 0.5062527656555176 167.83465576171875 0.8026828169822693 250.48876953125 0.3757050931453705 0.65418625 0.6421299576759338 True -19 58240 32.44681739807129 1.4496729373931885 199.45437622070312 0.5720295906066895 250.6680450439453 0.3746083080768585 0.6559357 0.6365970969200134 True diff --git a/ENCSR986XLW/cherimoya.fold_2.performance.tsv b/ENCSR986XLW/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 7224dd1bb0d065cc9d42f420bd7b51af71db87b5..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -250.6680450439453 0.45964619517326355 0.37460827827453613 0.08520887047052383 0.6559357047080994 0.6216830611228943 0.6365970969200134 \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_3.evaluate.json b/ENCSR986XLW/cherimoya.fold_3.evaluate.json deleted file mode 100644 index aaeef3623a0648b6aee559863e909c6d3ea89ddc..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF057FQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_3.fit.json b/ENCSR986XLW/cherimoya.fold_3.fit.json deleted file mode 100644 index ecce16b37c7b2fe2ed8b159ed5d6789359b152a7..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF057FQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_3.log b/ENCSR986XLW/cherimoya.fold_3.log deleted file mode 100644 index e62e5d8d434f8a1dfbbe96fcf51f1167c66ca1d9..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2790 35.180440187454224 4.394807577133179 197.6532745361328 1.3561921119689941 309.0794372558594 0.20569449663162231 0.43241298 4.45128870010376 True -1 5580 31.0988187789917 0.5787100791931152 217.98580932617188 1.3741834163665771 279.1531677246094 0.30338233709335327 0.5243833 2.9636170864105225 True -2 8370 31.075165510177612 1.6683640480041504 152.67752075195312 1.2154934406280518 272.8087463378906 0.3179672360420227 0.52620846 1.8401397466659546 True -3 11160 31.15046715736389 0.5578925609588623 205.46974182128906 0.8436129093170166 269.4936828613281 0.3306328058242798 0.5253442 1.8379333019256592 False -4 13950 31.086690187454224 1.959575891494751 183.468505859375 1.032652497291565 267.61236572265625 0.33616718649864197 0.5333163 1.7665023803710938 True -5 16740 31.09998083114624 0.562258243560791 166.45257568359375 0.8365602493286133 266.21185302734375 0.34172311425209045 0.5376315 1.7515872716903687 True -6 19530 31.029497861862183 0.5521252155303955 155.7753448486328 0.7823660373687744 264.57366943359375 0.34650418162345886 0.5437709 1.632304072380066 True -7 22320 31.038933515548706 0.5595531463623047 163.14105224609375 1.0016906261444092 263.4710998535156 0.35070762038230896 0.55764717 1.6011521816253662 True -8 25110 31.009479761123657 0.5616536140441895 197.5391082763672 0.9396928548812866 261.7221984863281 0.3568337857723236 0.5734089 1.5106871128082275 True -9 27900 31.043587923049927 0.5601990222930908 218.26541137695312 0.9028069376945496 261.3366394042969 0.35664039850234985 0.57650876 1.3383725881576538 True -10 30690 31.050108671188354 0.55977463722229 172.11459350585938 0.7499451041221619 259.8482360839844 0.36142098903656006 0.584212 1.2354463338851929 True -11 33480 31.087048053741455 0.5561730861663818 200.2581329345703 0.8030328154563904 258.9229431152344 0.36325010657310486 0.59643763 1.135992169380188 True -12 36270 31.084898471832275 0.5603411197662354 203.69776916503906 0.8429503440856934 257.4097595214844 0.3687984347343445 0.60835505 0.9683185815811157 True -13 39060 31.073163986206055 0.5543491840362549 216.2632293701172 0.7974590063095093 256.7225646972656 0.3696809709072113 0.6187406 0.8976621031761169 True -14 41850 31.12259602546692 0.5609927177429199 125.4073715209961 0.8764948844909668 255.73019409179688 0.3720219135284424 0.63144666 0.795997142791748 True -15 44640 31.099292516708374 0.5607681274414062 187.43255615234375 0.6337209343910217 254.96539306640625 0.37462466955184937 0.64321446 0.7253397107124329 True -16 47430 31.040953874588013 1.5648047924041748 196.45401000976562 0.7700395584106445 254.61178588867188 0.3754121959209442 0.65331036 0.6664820909500122 True -17 50220 31.072561264038086 0.5643560886383057 164.74713134765625 0.4797380566596985 254.1153564453125 0.37858250737190247 0.6581876 0.636565625667572 True -18 53010 31.05430841445923 1.317289113998413 190.39431762695312 0.3980507552623749 254.04356384277344 0.3774113953113556 0.65946317 0.6214698553085327 True -19 55800 31.08756160736084 0.5686845779418945 243.19384765625 0.7659144997596741 254.15142822265625 0.3778487741947174 0.65912473 0.6213032603263855 False diff --git a/ENCSR986XLW/cherimoya.fold_3.performance.tsv b/ENCSR986XLW/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 16febe019a1c41b8a7104e5fe7f55f73bb1fab91..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -254.04356384277344 0.458771288394928 0.3774113357067108 0.08619292825460434 0.6594631671905518 0.6226927042007446 0.6214698553085327 \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_4.evaluate.json b/ENCSR986XLW/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6fa143d92533642cec799bd85a3101f917f76afc..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF057FQT.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_4.fit.json b/ENCSR986XLW/cherimoya.fold_4.fit.json deleted file mode 100644 index c07e9d3496fc355452335b0ff269ce0096d7fcf0..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF057FQT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986XLW/cherimoya.fold_4.log b/ENCSR986XLW/cherimoya.fold_4.log deleted file mode 100644 index 1442b9ecd10c44d5fa79bd544a6b80dc4f25b55b..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2877 36.014814376831055 3.4537858963012695 214.94223022460938 1.2242727279663086 291.9994201660156 0.2059064358472824 0.39513308 4.128706455230713 True -1 5754 32.376646995544434 2.6412250995635986 194.46200561523438 1.1683318614959717 261.7720947265625 0.3068534731864929 0.48473564 2.35392427444458 True -2 8631 32.04615330696106 1.400163173675537 206.8520965576172 1.1554286479949951 258.2755126953125 0.3158864974975586 0.502293 1.8657901287078857 True -3 11508 31.9853777885437 0.5872526168823242 235.6236572265625 0.7392123937606812 255.6158447265625 0.3215419352054596 0.513934 1.942279577255249 True -4 14385 31.970213174819946 0.5865306854248047 180.20706176757812 1.475497841835022 252.79795837402344 0.33301979303359985 0.5240435 1.6440154314041138 True -5 17262 32.008827447891235 0.582735538482666 189.8951416015625 0.9797122478485107 251.95001220703125 0.33633938431739807 0.53239965 1.555468201637268 True -6 20139 31.952680826187134 1.8345720767974854 189.05526733398438 1.2976880073547363 251.05116271972656 0.3387198746204376 0.5372909 1.4582335948944092 True -7 23016 31.99117875099182 0.5898900032043457 206.58560180664062 0.9125820994377136 249.94737243652344 0.3418956696987152 0.54907787 1.305634617805481 True -8 25893 32.00458216667175 0.5961768627166748 231.1782989501953 0.8405638337135315 249.11146545410156 0.34363439679145813 0.55866563 1.2173986434936523 True -9 28770 31.97605538368225 0.5902726650238037 182.65286254882812 0.8501743078231812 247.4644775390625 0.3511388897895813 0.56195325 1.163327693939209 True -10 31647 32.01254653930664 0.6024060249328613 199.02426147460938 0.9239181280136108 246.2041778564453 0.35461974143981934 0.5665116 1.1311304569244385 True -11 34524 32.0107159614563 0.5930743217468262 159.14710998535156 1.0156629085540771 245.84959411621094 0.3536626696586609 0.57798934 1.0427558422088623 True -12 37401 32.01849865913391 1.2546114921569824 186.59420776367188 1.0617573261260986 244.5889434814453 0.3583418130874634 0.58682555 0.9388508200645447 True -13 40278 32.0693678855896 0.5950920581817627 202.4404754638672 1.0138431787490845 243.3363800048828 0.3628448247909546 0.60039794 0.8523606061935425 True -14 43155 32.096503257751465 0.595954418182373 171.84381103515625 1.100638747215271 242.39419555664062 0.36637526750564575 0.60874337 0.7972240447998047 True -15 46032 31.992568731307983 0.5836386680603027 156.2640380859375 0.788567841053009 242.04640197753906 0.3655376136302948 0.6197951 0.7320668697357178 True -16 48909 31.98519730567932 0.5880558490753174 179.77029418945312 0.6829673051834106 241.18423461914062 0.3695140779018402 0.6292691 0.6836032271385193 True -17 51786 31.98624587059021 0.5956284999847412 194.33407592773438 0.7824258804321289 241.55703735351562 0.3669075667858124 0.6379481 0.6529813408851624 True -18 54663 32.042561531066895 0.5881030559539795 179.0367431640625 0.7296366691589355 241.40736389160156 0.36816173791885376 0.64041156 0.6407656073570251 True -19 57540 32.05249786376953 0.5845978260040283 210.34385681152344 0.8239925503730774 241.22039794921875 0.36909812688827515 0.63914615 0.6457381248474121 False diff --git a/ENCSR986XLW/cherimoya.fold_4.performance.tsv b/ENCSR986XLW/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 76b486a59fbf0fbe659db573b0eb653a4e3e2646..0000000000000000000000000000000000000000 --- a/ENCSR986XLW/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -241.40736389160156 0.465686172246933 0.36816176772117615 0.08055397123098373 0.6404115557670593 0.602332353591919 0.6407656073570251 \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_0.evaluate.json b/ENCSR986YWZ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 7badb5c59cf8da7b11bd3189fe4b307e619213da..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215TNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_0.fit.json b/ENCSR986YWZ/cherimoya.fold_0.fit.json deleted file mode 100644 index 24898835d7d40b44c75d6cf26532597b25dc29eb..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF215TNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_0.log b/ENCSR986YWZ/cherimoya.fold_0.log deleted file mode 100644 index 2c94b65fba19826f1ef68245bafaff88a6309b6b..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2737 34.57613396644592 3.555497407913208 689.9525756835938 0.3991631865501404 843.5657348632812 0.25806349515914917 0.5263266 6.0483927726745605 True -1 5474 30.096835374832153 0.8121516704559326 603.683349609375 0.42735177278518677 795.65185546875 0.33356112241744995 0.55959505 0.7327962517738342 True -2 8211 30.101853370666504 0.5648922920227051 648.8309326171875 0.43842047452926636 782.0431518554688 0.351351797580719 0.5995674 0.37503230571746826 True -3 10948 30.160813331604004 0.6696643829345703 623.5667724609375 0.5918660759925842 777.1297607421875 0.3575080335140228 0.62697726 0.31933945417404175 True -4 13685 30.14975094795227 1.5457334518432617 604.9517822265625 0.7461622953414917 773.002197265625 0.3643900156021118 0.63649213 0.31589120626449585 True -5 16422 30.6231586933136 0.5656325817108154 638.49658203125 0.28371503949165344 771.1170654296875 0.3665139973163605 0.6472325 0.27571702003479004 True -6 19159 30.17684555053711 0.5674707889556885 639.1008911132812 0.36890608072280884 769.2540283203125 0.36960116028785706 0.64635503 0.2860468327999115 False -7 21896 30.138678312301636 0.5670528411865234 655.765869140625 0.2637362480163574 768.9984130859375 0.3692130446434021 0.6548752 0.26805588603019714 True -8 24633 30.226359605789185 0.56166672706604 605.3828735351562 0.4156304895877838 767.5263061523438 0.3734404742717743 0.65465206 0.28160884976387024 False -9 27370 29.637558460235596 0.612450122833252 655.9727783203125 0.2946605682373047 765.2064819335938 0.3777044117450714 0.6598549 0.26880210638046265 True -10 30107 29.587844610214233 0.5806002616882324 568.973388671875 0.3562430143356323 764.8446655273438 0.3771722912788391 0.6669956 0.25298434495925903 True -11 32844 29.577643156051636 23.492696285247803 644.4393310546875 0.28164470195770264 763.7530517578125 0.37884655594825745 0.67400974 0.25255802273750305 True -12 35581 35.14071488380432 18.04370665550232 641.1276245117188 0.361139178276062 762.233154296875 0.38175201416015625 0.6891795 0.22490651905536652 True -13 38318 29.537978172302246 0.5681569576263428 657.6259765625 0.2520047426223755 761.3651123046875 0.3829922676086426 0.6949979 0.21796607971191406 True -14 41055 29.56364154815674 0.5721263885498047 605.873779296875 0.4924863874912262 760.4710693359375 0.3841578960418701 0.70479953 0.20794788002967834 True -15 43792 29.56615400314331 0.5712461471557617 677.4107055664062 0.19083906710147858 759.571533203125 0.38603776693344116 0.7113914 0.20921756327152252 True -16 46529 29.454014778137207 0.571723461151123 649.4140625 0.2881343960762024 759.2108154296875 0.3856997489929199 0.71917963 0.2040233612060547 True -17 49266 29.900717973709106 0.6747488975524902 617.6489868164062 0.29131877422332764 758.8572387695312 0.3861936032772064 0.7206295 0.20368783175945282 True -18 52003 29.609267711639404 0.5747663974761963 583.5051879882812 0.2974868416786194 758.8975830078125 0.3865108788013458 0.71937627 0.2060682475566864 False -19 54740 29.64631152153015 0.9232001304626465 607.3831176757812 0.287593811750412 759.1143188476562 0.3862268030643463 0.72025 0.2063913196325302 False diff --git a/ENCSR986YWZ/cherimoya.fold_0.performance.tsv b/ENCSR986YWZ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index c86dad1c6dac262ac3d3e4e32dc3f19c7d34b8d0..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -758.8572387695312 0.3350813388824463 0.38619354367256165 0.19543077051639557 0.7206295132637024 0.6636229753494263 0.20368783175945282 \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_1.evaluate.json b/ENCSR986YWZ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index c7503cdae5ea4811fa86de490442cab3b3e10e8d..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215TNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_1.fit.json b/ENCSR986YWZ/cherimoya.fold_1.fit.json deleted file mode 100644 index 53d8974bb98a86304be6ba2c0f1b5a8179acb32e..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF215TNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_1.log b/ENCSR986YWZ/cherimoya.fold_1.log deleted file mode 100644 index afd347968960bc39885dfc43cb1e18bfbb5f3205..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2746 34.745235204696655 4.237163543701172 647.3418579101562 0.33137133717536926 904.8938598632812 0.2659047544002533 0.5585436 5.427713394165039 True -1 5492 30.183968782424927 1.5071954727172852 651.0106811523438 0.6824750900268555 844.7911376953125 0.34979337453842163 0.60008544 0.7974920868873596 True -2 8238 30.228899717330933 1.2320573329925537 646.5776977539062 0.39329811930656433 830.01708984375 0.36691814661026 0.6613779 0.6095190048217773 True -3 10984 30.25053071975708 0.7060017585754395 627.6909790039062 0.5393707156181335 822.8231811523438 0.37423911690711975 0.6815711 0.35094279050827026 True -4 13730 30.238025903701782 0.7163815498352051 687.7416381835938 0.5851376056671143 820.2633056640625 0.3773948848247528 0.68010765 0.33197009563446045 False -5 16476 30.591755151748657 0.706430196762085 701.194580078125 0.5853710174560547 817.3275756835938 0.38204312324523926 0.67903733 0.30847761034965515 False -6 19222 30.477259635925293 0.6991305351257324 759.54541015625 0.39055848121643066 814.2728881835938 0.3851923942565918 0.69170105 0.3049052655696869 True -7 21968 33.02753925323486 31.485883712768555 742.6099853515625 0.4873490035533905 812.410400390625 0.3873971104621887 0.69444126 0.28724205493927 True -8 24714 30.309184551239014 44.63593554496765 624.83154296875 0.3376684784889221 809.8739624023438 0.3926949203014374 0.6993455 0.26968914270401 True -9 27460 30.786887884140015 1.1859080791473389 593.52685546875 0.40375083684921265 809.0263061523438 0.3925560414791107 0.705649 0.26580339670181274 True -10 30206 29.61319327354431 1.417712688446045 641.0263671875 0.2457626461982727 806.6952514648438 0.3962455093860626 0.7152746 0.2548096179962158 True -11 32952 29.636746883392334 34.41408038139343 688.85791015625 0.3211645185947418 805.0836791992188 0.39784371852874756 0.7227062 0.24744738638401031 True -12 35698 30.69579839706421 43.52365779876709 643.485107421875 0.2638304829597473 803.8505249023438 0.3997567594051361 0.7288238 0.23643477261066437 True -13 38444 30.26684856414795 0.6949913501739502 549.255615234375 0.33500903844833374 801.906982421875 0.4026588797569275 0.7390342 0.23185917735099792 True -14 41190 35.71767282485962 21.19011664390564 676.2847900390625 0.3677675426006317 800.8692016601562 0.40390491485595703 0.7468717 0.22081466019153595 True -15 43936 29.71372365951538 0.7257754802703857 605.24560546875 0.31786781549453735 800.1613159179688 0.40465930104255676 0.7566214 0.21610845625400543 True -16 46682 29.666044235229492 0.6907310485839844 591.6891479492188 0.25395146012306213 799.3230590820312 0.4058682322502136 0.7625364 0.21313543617725372 True -17 49428 29.6839497089386 0.6843564510345459 680.3861083984375 0.3216988444328308 799.3235473632812 0.40592700242996216 0.7674227 0.21119889616966248 True -18 52174 29.62386202812195 0.6867032051086426 643.9847412109375 0.28944501280784607 800.0404052734375 0.40371227264404297 0.76827735 0.21176716685295105 True -19 54920 29.80087399482727 0.6822915077209473 587.94873046875 0.3540119528770447 799.1989135742188 0.4055066406726837 0.7665201 0.21430738270282745 False diff --git a/ENCSR986YWZ/cherimoya.fold_1.performance.tsv b/ENCSR986YWZ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f5268bdd2f45f44ba9eb81dd3a806fb82c8f1670..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -800.0404052734375 0.32485294342041016 0.40371227264404297 0.2057829350233078 0.7682773470878601 0.7188424468040466 0.21176716685295105 \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_2.evaluate.json b/ENCSR986YWZ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 48752ba591a1134594efc9288877a5a1ba0c4984..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215TNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_2.fit.json b/ENCSR986YWZ/cherimoya.fold_2.fit.json deleted file mode 100644 index 9e0c5cc3e19c9ebdf0425caa38e49eb789b63eda..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF215TNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_2.log b/ENCSR986YWZ/cherimoya.fold_2.log deleted file mode 100644 index 8bbcc1fc6fe979fd4a5719605a3eb2a05d38e036..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2890 36.44985866546631 3.6663577556610107 677.2916870117188 0.513825535774231 856.609130859375 0.2628823518753052 0.559131 5.064441204071045 True -1 5780 31.796870231628418 8.953367233276367 672.6068115234375 0.4381779432296753 800.0800170898438 0.3474540710449219 0.5897632 0.6313977241516113 True -2 8670 31.85938572883606 29.431416988372803 632.35400390625 0.4869871139526367 789.92431640625 0.3595620095729828 0.62392557 0.34946343302726746 True -3 11560 33.09989285469055 0.5807993412017822 650.6751098632812 0.5138776898384094 783.1873168945312 0.36749717593193054 0.64855003 0.3084879517555237 True -4 14450 31.882689237594604 0.5481829643249512 690.869140625 0.4079790711402893 780.6509399414062 0.36982807517051697 0.6615615 0.27187299728393555 True -5 17340 31.789424419403076 1.381519079208374 654.3045654296875 0.2851967215538025 778.0857543945312 0.3746162950992584 0.6721427 0.25437745451927185 True -6 20230 31.762930393218994 0.5484681129455566 616.651123046875 0.555638313293457 776.1412963867188 0.3780796229839325 0.6707622 0.24323974549770355 False -7 23120 31.7822265625 1.0152995586395264 658.0172119140625 0.3311446011066437 774.5857543945312 0.3794448971748352 0.68071735 0.2377181351184845 True -8 26010 31.19156575202942 0.5492119789123535 669.0194702148438 0.3765731155872345 772.5284423828125 0.38301268219947815 0.6845202 0.2386358231306076 True -9 28900 31.183317184448242 0.5375351905822754 617.9627685546875 0.30485057830810547 771.4611206054688 0.38485947251319885 0.6817997 0.24701756238937378 False -10 31790 31.079259395599365 1.6251943111419678 679.278564453125 0.3519139289855957 769.9893798828125 0.38686487078666687 0.690198 0.2317659854888916 True -11 34680 31.45322012901306 0.5530283451080322 520.0145874023438 0.3058420419692993 768.7800903320312 0.38796478509902954 0.6983745 0.22969521582126617 True -12 37570 31.372539281845093 0.5478758811950684 688.0576171875 0.5053186416625977 767.52734375 0.3902822732925415 0.7053355 0.21987149119377136 True -13 40460 31.381223678588867 35.19935464859009 561.9943237304688 0.25560492277145386 766.7601928710938 0.39092904329299927 0.71676683 0.2156703621149063 True -14 43350 33.16737222671509 0.5414903163909912 614.0543212890625 0.32478490471839905 765.3508911132812 0.39282143115997314 0.71968937 0.21714290976524353 True -15 46240 31.257200002670288 0.5340085029602051 590.7434692382812 0.2569734454154968 764.2911376953125 0.3946787118911743 0.72651196 0.2125425934791565 True -16 49130 31.605130672454834 0.5307133197784424 657.4681396484375 0.20217573642730713 764.27099609375 0.3939574658870697 0.73080385 0.21507850289344788 True -17 52020 31.124131441116333 1.1313447952270508 629.9442138671875 0.21400681138038635 762.7470092773438 0.397148996591568 0.73411363 0.21781225502490997 True -18 54910 31.19110679626465 0.5482938289642334 655.7156982421875 0.21441063284873962 763.8814697265625 0.3940536081790924 0.7353827 0.21916019916534424 True -19 57800 31.123002290725708 0.5371394157409668 633.8788452148438 0.3044317960739136 764.3450927734375 0.3933737277984619 0.7324614 0.2236308455467224 False diff --git a/ENCSR986YWZ/cherimoya.fold_2.performance.tsv b/ENCSR986YWZ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index a6621f5b798231b8f82faaa6aef94bd1ab512196..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -763.8814697265625 0.33324891328811646 0.3940536081790924 0.19754834473133087 0.7353826761245728 0.6810397505760193 0.21916019916534424 \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_3.evaluate.json b/ENCSR986YWZ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cde53b0b2aa29ef3f6e495fe679341987bd7fdc0..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215TNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_3.fit.json b/ENCSR986YWZ/cherimoya.fold_3.fit.json deleted file mode 100644 index baa31fb796897e43707a4c0bfd0f8608c9c1c7fa..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF215TNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_3.log b/ENCSR986YWZ/cherimoya.fold_3.log deleted file mode 100644 index 0fa91f20b683fd0038df5014ebf1f70dcf1d5718..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2798 35.74009585380554 3.638685941696167 706.6921997070312 0.3266955614089966 885.7153930664062 0.2652919590473175 0.56161463 5.183237552642822 True -1 5596 30.8690242767334 0.60563063621521 725.03466796875 0.6370893716812134 833.201416015625 0.34156936407089233 0.61794335 0.8747488260269165 True -2 8394 30.819363355636597 1.2605130672454834 673.40576171875 0.48072853684425354 822.9360961914062 0.3561881482601166 0.65068984 0.4453170895576477 True -3 11192 30.750077724456787 0.562711238861084 699.3438720703125 0.4219009280204773 817.9398193359375 0.3636201024055481 0.6518343 0.4042343199253082 True -4 13990 36.14894676208496 13.769989490509033 627.3873901367188 0.49968811869621277 814.8820190429688 0.3674823045730591 0.663459 0.29610687494277954 True -5 16788 30.831493377685547 0.9814574718475342 631.907958984375 0.42612969875335693 813.3414916992188 0.3699122965335846 0.66224366 0.2701984941959381 False -6 19586 30.7846519947052 1.1355807781219482 699.05615234375 0.5646991729736328 810.6652221679688 0.3734700381755829 0.6700176 0.2594251334667206 True -7 22384 30.802502393722534 4.349377393722534 726.9492797851562 0.5192528963088989 810.54248046875 0.37288805842399597 0.67252684 0.2575560510158539 True -8 25182 30.781963109970093 1.7442703247070312 619.9434204101562 0.35919076204299927 809.17578125 0.3752056658267975 0.67334414 0.2480316162109375 True -9 27980 30.27185082435608 0.5588870048522949 638.965576171875 0.34464311599731445 806.7382202148438 0.37929680943489075 0.6771553 0.2565024197101593 True -10 30778 30.038217782974243 2.1045005321502686 662.2906494140625 0.28167492151260376 805.9324951171875 0.3797737956047058 0.6782985 0.25516411662101746 True -11 33576 30.34837293624878 0.5725827217102051 645.02197265625 0.32899054884910583 805.360595703125 0.380249947309494 0.6887833 0.24807104468345642 True -12 36374 30.161092281341553 6.524524927139282 621.1236572265625 0.5292753577232361 803.4486694335938 0.38360580801963806 0.6953861 0.24193313717842102 True -13 39172 30.25441288948059 0.5730240345001221 655.0736083984375 0.4180043339729309 801.5108032226562 0.3870263695716858 0.70605415 0.23852163553237915 True -14 41970 30.128424406051636 0.5594832897186279 549.402099609375 0.3349418044090271 800.4091796875 0.38859403133392334 0.71564174 0.22257444262504578 True -15 44768 30.166608333587646 0.5549674034118652 659.3892822265625 0.43423178791999817 800.3134155273438 0.38817769289016724 0.72207433 0.22327108681201935 True -16 47566 30.153660535812378 0.5664718151092529 644.3760375976562 0.24502575397491455 800.239990234375 0.38786402344703674 0.7284478 0.2161249816417694 True -17 50364 30.136755228042603 0.5566189289093018 646.3394775390625 0.19353462755680084 798.8903198242188 0.39051109552383423 0.730877 0.21785852313041687 True -18 53162 30.211147785186768 0.5590994358062744 624.8424072265625 0.2479114830493927 799.4473266601562 0.38915300369262695 0.73133147 0.2195388823747635 True -19 55960 30.204025983810425 0.5659041404724121 592.9554443359375 0.334316611289978 799.129638671875 0.3898344933986664 0.7299318 0.22244325280189514 False diff --git a/ENCSR986YWZ/cherimoya.fold_3.performance.tsv b/ENCSR986YWZ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c2a57a636d21af82482aac9883b5057c88737545..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -799.4473266601562 0.32846519351005554 0.38915297389030457 0.20667065680027008 0.731331467628479 0.6908397078514099 0.2195388823747635 \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_4.evaluate.json b/ENCSR986YWZ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 7009444bdbca96d972cf5aaf13f6e1ec02807228..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF215TNM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_4.fit.json b/ENCSR986YWZ/cherimoya.fold_4.fit.json deleted file mode 100644 index d5534a8ff9f7071a16411345ee3406124defcaba..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF215TNM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR986YWZ/cherimoya.fold_4.log b/ENCSR986YWZ/cherimoya.fold_4.log deleted file mode 100644 index eb0f8be835c6fa7d23819bbcf2ded03bcd1f4886..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2913 36.79129934310913 3.5469579696655273 708.5574951171875 0.8541181087493896 844.6495361328125 0.2673380374908447 0.54231304 4.653454303741455 True -1 5826 32.14887762069702 0.6039175987243652 630.0880126953125 0.38261204957962036 795.74365234375 0.34502992033958435 0.60821974 0.505727231502533 True -2 8739 32.063859939575195 0.5630640983581543 687.5889282226562 0.32123562693595886 789.474853515625 0.3526591658592224 0.62800175 0.31630390882492065 True -3 11652 32.05573225021362 9.060589075088501 712.109619140625 0.36470311880111694 782.4479370117188 0.362856388092041 0.64043695 0.2920877933502197 True -4 14565 32.093618869781494 0.5624122619628906 615.2786254882812 0.3547067642211914 780.4527587890625 0.3644839823246002 0.6410741 0.2534598410129547 True -5 17478 32.08996939659119 0.5602805614471436 730.1757202148438 0.2827029824256897 779.6644287109375 0.365536093711853 0.64513636 0.24781008064746857 True -6 20391 32.06400680541992 0.5572483539581299 560.1280517578125 0.47991883754730225 777.5784301757812 0.36916837096214294 0.6479499 0.25889939069747925 True -7 23304 32.06966495513916 0.9892985820770264 690.1082763671875 0.4368274211883545 776.5814208984375 0.37054505944252014 0.652393 0.26781103014945984 True -8 26217 31.51387119293213 0.5743930339813232 673.9597778320312 0.2575889825820923 774.2706298828125 0.37496238946914673 0.6603084 0.24461378157138824 True -9 29130 31.36346745491028 0.5504682064056396 679.9742431640625 0.23857381939888 773.2454223632812 0.3759814202785492 0.6667171 0.24096626043319702 True -10 32043 31.546388626098633 0.5635523796081543 683.8841552734375 0.29334232211112976 772.1062622070312 0.3776553273200989 0.6745508 0.23235175013542175 True -11 34956 31.422305583953857 0.5559170246124268 713.867919921875 0.25456929206848145 772.4842529296875 0.3767130672931671 0.6797582 0.228288933634758 True -12 37869 31.43923592567444 2.600315570831299 645.7183837890625 0.4140409231185913 770.4533081054688 0.38032296299934387 0.6867677 0.22206977009773254 True -13 40782 31.590399265289307 0.5541822910308838 670.3109130859375 0.18552842736244202 768.5208740234375 0.3842838704586029 0.69621366 0.21331976354122162 True -14 43695 31.379740476608276 0.5487394332885742 575.8602905273438 0.25953051447868347 767.378662109375 0.38584187626838684 0.7048707 0.20465953648090363 True -15 46608 31.46164560317993 1.2206931114196777 635.5405883789062 0.22295215725898743 767.87353515625 0.38466396927833557 0.71019 0.20385931432247162 True -16 49521 31.586679220199585 0.7169528007507324 615.7406005859375 0.38728412985801697 767.8289794921875 0.38419604301452637 0.71799296 0.1992538571357727 True -17 52434 31.44835114479065 0.6264364719390869 675.6631469726562 0.20927585661411285 766.5215454101562 0.38669008016586304 0.7225978 0.19913747906684875 True -18 55347 31.531429767608643 1.2059693336486816 581.9266357421875 0.22493833303451538 765.824462890625 0.38895300030708313 0.72234035 0.2000461220741272 False -19 58260 31.4019992351532 2.1343443393707275 585.8823852539062 0.211281418800354 767.0556640625 0.38529324531555176 0.7217946 0.20123183727264404 False diff --git a/ENCSR986YWZ/cherimoya.fold_4.performance.tsv b/ENCSR986YWZ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d645c1438eb53c9c074abee8c4414af83a3aea99..0000000000000000000000000000000000000000 --- a/ENCSR986YWZ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -766.5215454101562 0.3332239091396332 0.38669008016586304 0.1984112709760666 0.7225977778434753 0.671891987323761 0.19913747906684875 \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_0.evaluate.json b/ENCSR987CQN/cherimoya.fold_0.evaluate.json deleted file mode 100644 index ad299d6e9bc2a8f2ee02db22700d71fe55b4ab5f..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF912SBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_0.fit.json b/ENCSR987CQN/cherimoya.fold_0.fit.json deleted file mode 100644 index 6e9b1099ea681efc96ff487d49af9ddd78db7d5f..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF912SBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_0.log b/ENCSR987CQN/cherimoya.fold_0.log deleted file mode 100644 index a1fa64d263992afcad2fe4b16a2c6055c53c4963..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2758 35.07670712471008 3.8846654891967773 526.4989013671875 0.45348456501960754 640.7526245117188 0.2876858711242676 0.70075756 5.332437515258789 True -1 5516 31.653502464294434 0.6405465602874756 427.32476806640625 0.5334470272064209 576.3345336914062 0.3619525730609894 0.7660393 1.5892258882522583 True -2 8274 30.584112405776978 0.6024346351623535 459.3004455566406 0.3395572900772095 563.99853515625 0.3745811879634857 0.7766851 0.6570295095443726 True -3 11032 30.39402174949646 0.597102165222168 495.9349365234375 0.5053274035453796 555.7922973632812 0.38272541761398315 0.78694373 0.6337282657623291 True -4 13790 30.394063711166382 0.5910453796386719 539.6856689453125 0.5226159691810608 553.4603881835938 0.38451650738716125 0.7954183 0.5292547345161438 True -5 16548 30.38563323020935 0.5941226482391357 441.4384765625 0.47101014852523804 549.0709228515625 0.3884190320968628 0.8013147 0.45428916811943054 True -6 19306 30.370866537094116 0.5876405239105225 392.8721618652344 0.45825499296188354 548.1602783203125 0.3883950710296631 0.80523807 0.4530247747898102 True -7 22064 30.382890939712524 0.5911815166473389 450.02252197265625 0.3328574299812317 544.5523681640625 0.3946889638900757 0.81310976 0.41611140966415405 True -8 24822 30.379026889801025 0.5918989181518555 486.51519775390625 0.49825355410575867 543.618408203125 0.3946879804134369 0.81670284 0.4350598454475403 True -9 27580 30.36896514892578 0.598217248916626 431.67413330078125 0.5665597915649414 540.4902954101562 0.3983447849750519 0.82075554 0.3903501331806183 True -10 30338 30.30419087409973 1.040696144104004 394.0137939453125 0.3773772120475769 538.3350219726562 0.4011687934398651 0.8272865 0.37870872020721436 True -11 33096 30.056904792785645 0.5907652378082275 433.8829650878906 0.3768043518066406 537.511962890625 0.4012107253074646 0.8326013 0.3596341013908386 True -12 35854 29.88750195503235 0.5883243083953857 478.4398193359375 0.42978376150131226 534.2904052734375 0.40573549270629883 0.8362176 0.34143775701522827 True -13 38612 29.753490447998047 0.5860931873321533 404.9198913574219 0.3284810781478882 533.6358642578125 0.40580329298973083 0.8422964 0.33139845728874207 True -14 41370 29.792670726776123 0.5905716419219971 472.6645202636719 0.3472602367401123 533.1975708007812 0.4059617519378662 0.847423 0.3195256292819977 True -15 44128 30.020167350769043 0.5943028926849365 373.01202392578125 0.513131856918335 531.895751953125 0.4074757993221283 0.8505689 0.30938971042633057 True -16 46886 29.96939444541931 1.4596977233886719 409.43182373046875 0.3085208535194397 531.1664428710938 0.40777814388275146 0.85362285 0.3021189570426941 True -17 49644 29.936622619628906 0.6011147499084473 477.4983215332031 0.27723243832588196 530.6640625 0.4090849459171295 0.85332376 0.29734498262405396 False -18 52402 29.885183572769165 0.603571891784668 435.7734375 0.4305323362350464 531.4888305664062 0.40848830342292786 0.8547384 0.2978385090827942 True -19 55160 29.866616010665894 1.5429043769836426 388.76934814453125 0.2380487620830536 532.2515869140625 0.4067688584327698 0.8542079 0.29924100637435913 False diff --git a/ENCSR987CQN/cherimoya.fold_0.performance.tsv b/ENCSR987CQN/cherimoya.fold_0.performance.tsv deleted file mode 100644 index cdfb5b8c239e9ccf9967ef7b2e693346d89ed7f7..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -531.4888305664062 0.3943925201892853 0.40848830342292786 0.14827293157577515 0.8547384142875671 0.8246358633041382 0.2978385090827942 \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_1.evaluate.json b/ENCSR987CQN/cherimoya.fold_1.evaluate.json deleted file mode 100644 index df017c29755e391c810e7a02f6d762785a9a611d..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF912SBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_1.fit.json b/ENCSR987CQN/cherimoya.fold_1.fit.json deleted file mode 100644 index 309d456b73e74c7523fbcc99f6be5f91fac2ea46..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF912SBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_1.log b/ENCSR987CQN/cherimoya.fold_1.log deleted file mode 100644 index 47c5eed29f4dcbced9590c64ec7170b1362a135a..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2695 34.19939374923706 4.050824403762817 605.5587158203125 0.47758299112319946 749.8125 0.2851901650428772 0.7016916 5.684637069702148 True -1 5390 29.66662287712097 1.3038232326507568 571.5580444335938 0.5365701913833618 667.7288208007812 0.3670583963394165 0.7632027 2.1619770526885986 True -2 8085 29.694771766662598 0.7938857078552246 499.8419189453125 0.4246450662612915 647.9296875 0.3825679123401642 0.7854768 1.0814930200576782 True -3 10780 29.696577072143555 0.7817995548248291 354.412109375 0.37508654594421387 637.0491333007812 0.39300814270973206 0.796101 0.7958082556724548 True -4 13475 29.691891193389893 1.4996066093444824 507.116943359375 0.407073050737381 634.31103515625 0.39365220069885254 0.79870635 0.6666181683540344 True -5 16170 29.686717748641968 11.89450192451477 378.19769287109375 0.3840944766998291 627.4163208007812 0.4008319675922394 0.8031163 0.5620259046554565 True -6 18865 29.737802028656006 0.748786211013794 474.68194580078125 0.7662700414657593 622.931396484375 0.40371760725975037 0.8111404 0.5365702509880066 True -7 21560 29.66165828704834 0.7215907573699951 405.2284240722656 0.40778595209121704 621.7780151367188 0.40429553389549255 0.8156935 0.5120463967323303 True -8 24255 29.672335147857666 0.7622284889221191 416.3804626464844 0.4758870303630829 619.9566040039062 0.4056134521961212 0.81979376 0.5166783928871155 True -9 26950 29.659465074539185 0.7172181606292725 357.0570068359375 0.4754908084869385 615.4642944335938 0.4105231463909149 0.82879925 0.48239684104919434 True -10 29645 29.57145047187805 0.7221887111663818 458.2698974609375 0.40137386322021484 612.3292236328125 0.4140724241733551 0.832445 0.4407336115837097 True -11 32340 29.081231594085693 0.7357685565948486 499.90411376953125 0.4981231093406677 609.1177978515625 0.4169216752052307 0.8416754 0.4163099527359009 True -12 35035 29.116363048553467 0.7192564010620117 352.76080322265625 0.3196322023868561 607.0451049804688 0.41908419132232666 0.8465039 0.3913654685020447 True -13 37730 29.101499319076538 0.702918291091919 378.17181396484375 0.5020289421081543 605.498046875 0.4190654456615448 0.85215735 0.3690294623374939 True -14 40425 29.12416696548462 8.12523889541626 361.43109130859375 0.3146413266658783 603.0096435546875 0.42226824164390564 0.8572818 0.3481275141239166 True -15 43120 29.094322204589844 1.2506980895996094 416.24053955078125 0.2778790295124054 601.2940063476562 0.423838347196579 0.8647768 0.3330252468585968 True -16 45815 29.10914921760559 0.726872444152832 429.52667236328125 0.410457968711853 602.1348266601562 0.4221287965774536 0.86766255 0.323072224855423 True -17 48510 29.169133186340332 0.7941250801086426 411.52301025390625 0.23990175127983093 601.4503784179688 0.4230767488479614 0.8688152 0.3139926493167877 True -18 51205 29.114763498306274 1.7754526138305664 430.907470703125 0.2620698809623718 602.35888671875 0.42104998230934143 0.8694236 0.3112236261367798 True -19 53900 29.148160696029663 0.7192344665527344 344.920166015625 0.3009442090988159 601.2994995117188 0.42344167828559875 0.8685432 0.31102848052978516 False diff --git a/ENCSR987CQN/cherimoya.fold_1.performance.tsv b/ENCSR987CQN/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 50c95362693c4537ef08713e1fb7deb2d5e8f0e4..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -602.35888671875 0.38187700510025024 0.4210500121116638 0.16888265311717987 0.8694236278533936 0.8513478636741638 0.3112236261367798 \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_2.evaluate.json b/ENCSR987CQN/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 675c1cd4cda999e683589a03119255c9c8e4961d..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF912SBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_2.fit.json b/ENCSR987CQN/cherimoya.fold_2.fit.json deleted file mode 100644 index 13e930297fd176787adbfe167fdf78c7394d455c..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF912SBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_2.log b/ENCSR987CQN/cherimoya.fold_2.log deleted file mode 100644 index b6d962c1d4f9989050fd5c50b00d592dbdd48286..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2874 36.08146524429321 4.078309774398804 511.343505859375 0.4457740783691406 675.7042236328125 0.28913813829421997 0.6976418 5.4806227684021 True -1 5748 31.77081847190857 20.42707872390747 481.8596496582031 0.43613606691360474 598.2766723632812 0.37243562936782837 0.7708458 1.3732655048370361 True -2 8622 31.679296016693115 1.9261605739593506 543.6165771484375 0.9390124082565308 589.0945434570312 0.37778544425964355 0.7814392 0.877627968788147 True -3 11496 31.680755376815796 0.9478325843811035 438.2061767578125 0.6057735681533813 581.7770385742188 0.38387343287467957 0.78922856 0.6264789700508118 True -4 14370 31.67964816093445 0.8485579490661621 389.6466369628906 0.4333689212799072 577.837158203125 0.3884212374687195 0.79294145 0.5222775340080261 True -5 17244 31.650784492492676 0.5644440650939941 488.6035461425781 0.3494342565536499 576.7575073242188 0.3886905610561371 0.7966456 0.5034541487693787 True -6 20118 31.691453218460083 0.5669257640838623 411.834716796875 0.5519038438796997 574.3772583007812 0.3904615640640259 0.8017225 0.46826788783073425 True -7 22992 31.68436026573181 0.5626397132873535 471.4028625488281 0.42956072092056274 571.0196533203125 0.3949712812900543 0.81053776 0.44335734844207764 True -8 25866 31.669156789779663 0.5571272373199463 440.07965087890625 0.4193754494190216 567.4005126953125 0.3992921710014343 0.8161875 0.43046149611473083 True -9 28740 31.708855628967285 0.5652444362640381 380.72930908203125 0.503002941608429 566.1708374023438 0.40050777792930603 0.82250005 0.39493682980537415 True -10 31614 31.682074069976807 0.561633825302124 518.4105834960938 0.49464452266693115 565.3001708984375 0.4006739556789398 0.8261846 0.40985196828842163 True -11 34488 33.796643018722534 28.302704334259033 368.79693603515625 0.374714732170105 561.9534301757812 0.4044862687587738 0.8295107 0.3745998740196228 True -12 37362 34.623274087905884 19.156883478164673 484.6700439453125 0.38159504532814026 560.5446166992188 0.40637484192848206 0.83630735 0.3543153703212738 True -13 40236 31.072632312774658 0.5504648685455322 413.6969299316406 0.30700424313545227 558.9669799804688 0.4087846577167511 0.8414192 0.3447466790676117 True -14 43110 31.028143644332886 0.5490133762359619 398.701416015625 0.3144601583480835 557.3710327148438 0.41036638617515564 0.84756756 0.3248251974582672 True -15 45984 31.08056879043579 0.5542185306549072 432.8421630859375 0.21877256035804749 555.1724853515625 0.4134470224380493 0.8512595 0.30982866883277893 True -16 48858 31.042280435562134 0.5532844066619873 440.21502685546875 0.23795312643051147 555.3796997070312 0.41187113523483276 0.85253406 0.30028945207595825 True -17 51732 31.063602685928345 0.5596272945404053 423.3328857421875 0.28247910737991333 555.035888671875 0.4126991629600525 0.8541383 0.2978266477584839 True -18 54606 31.05775284767151 0.5409655570983887 392.5625 0.19528710842132568 556.74609375 0.40967699885368347 0.85540086 0.29658517241477966 True -19 57480 31.076082229614258 0.5659675598144531 446.707275390625 0.25417351722717285 555.800537109375 0.412166565656662 0.854676 0.2976123094558716 False diff --git a/ENCSR987CQN/cherimoya.fold_2.performance.tsv b/ENCSR987CQN/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 3b3dd364beb1161bd1a7778e459e5f99916eaf5c..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -556.74609375 0.39081600308418274 0.4096769690513611 0.15480276942253113 0.8554008603096008 0.827354907989502 0.29658517241477966 \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_3.evaluate.json b/ENCSR987CQN/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 175a4762f23c4721c147c5ccb4393b43ecde5ff0..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF912SBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_3.fit.json b/ENCSR987CQN/cherimoya.fold_3.fit.json deleted file mode 100644 index a011631b2a07544b1ea63f6100c3cd6790a279e2..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF912SBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_3.log b/ENCSR987CQN/cherimoya.fold_3.log deleted file mode 100644 index c76de7affcfd0e10ab0932b4dd30cf8353eab73c..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2767 35.05339217185974 4.803600072860718 381.39801025390625 0.5536851286888123 642.572509765625 0.295920729637146 0.6972226 5.290921688079834 True -1 5534 30.50029230117798 0.5518269538879395 451.63482666015625 0.6980117559432983 566.97021484375 0.37345045804977417 0.78135943 1.668250560760498 True -2 8301 30.532559394836426 1.9306683540344238 484.3323669433594 0.5642303824424744 557.5868530273438 0.38295868039131165 0.78477013 1.0661858320236206 True -3 11068 30.549211740493774 0.4845890998840332 435.5791320800781 0.46274489164352417 550.1609497070312 0.3897819221019745 0.8013726 0.5989218950271606 True -4 13835 30.5318386554718 1.5085101127624512 452.90386962890625 0.5708145499229431 548.3450317382812 0.39135655760765076 0.800047 0.5437740087509155 False -5 16602 30.5269718170166 0.49080967903137207 454.605224609375 0.47962701320648193 545.3184814453125 0.39344504475593567 0.8058651 0.46031150221824646 True -6 19369 30.549366235733032 0.501474142074585 400.24774169921875 0.7223827838897705 543.1201782226562 0.39672350883483887 0.8054946 0.43890276551246643 False -7 22136 30.48611569404602 0.494800329208374 470.3170166015625 0.5289041996002197 540.811279296875 0.3978050947189331 0.81301814 0.41300928592681885 True -8 24903 30.4807026386261 0.4965951442718506 384.5296630859375 0.47224628925323486 538.4266357421875 0.40081775188446045 0.81730306 0.40451791882514954 True -9 27670 30.473498582839966 0.493833065032959 420.4450378417969 0.4143807291984558 536.9759521484375 0.40335115790367126 0.8242712 0.40048539638519287 True -10 30437 30.472662448883057 0.49355292320251465 491.74871826171875 0.44033557176589966 535.1651000976562 0.40473711490631104 0.82869256 0.39032480120658875 True -11 33204 30.492830514907837 0.49780964851379395 389.50927734375 0.4719599187374115 533.958740234375 0.40502744913101196 0.83261096 0.3829818367958069 True -12 35971 30.52685022354126 2.081376314163208 438.2115478515625 0.5072507858276367 531.1807250976562 0.40816831588745117 0.8385245 0.36129170656204224 True -13 38738 29.891515731811523 0.477431058883667 430.9934997558594 0.5025838613510132 530.2137451171875 0.4085419774055481 0.8466563 0.34332776069641113 True -14 41505 29.891233682632446 2.3930113315582275 381.07196044921875 0.3103172481060028 526.501953125 0.4140789210796356 0.85096914 0.3286000192165375 True -15 44272 29.945122003555298 0.4952375888824463 471.5528564453125 0.26190292835235596 526.1986083984375 0.4135681092739105 0.8567084 0.31887656450271606 True -16 47039 29.88381004333496 0.48372364044189453 465.2841796875 0.30451828241348267 524.7684936523438 0.41615402698516846 0.8600469 0.31169888377189636 True -17 49806 29.87210202217102 0.4868290424346924 425.02996826171875 0.2549797296524048 525.7047729492188 0.4142592251300812 0.8627711 0.30891716480255127 True -18 52573 29.8766348361969 0.4959557056427002 531.9276123046875 0.2757960855960846 525.2420654296875 0.4148823618888855 0.86294264 0.3081522285938263 True -19 55340 30.03863024711609 0.5761337280273438 400.9482421875 0.20928102731704712 526.2099609375 0.4132057726383209 0.86227167 0.3094523251056671 False diff --git a/ENCSR987CQN/cherimoya.fold_3.performance.tsv b/ENCSR987CQN/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 5dc0f054049caecfab2ea977e8da1f10b9bd1611..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -525.2420654296875 0.3913201689720154 0.4148823618888855 0.1511818915605545 0.862942636013031 0.8331764340400696 0.3081522285938263 \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_4.evaluate.json b/ENCSR987CQN/cherimoya.fold_4.evaluate.json deleted file mode 100644 index cfce8c8c7698c7d31fc23e02c926ff504c916896..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF912SBD.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_4.fit.json b/ENCSR987CQN/cherimoya.fold_4.fit.json deleted file mode 100644 index 13617a7607d46ff595bebf9b2d4fc579c723d807..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF912SBD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR987CQN/cherimoya.fold_4.log b/ENCSR987CQN/cherimoya.fold_4.log deleted file mode 100644 index 009ef3b256d8ef4682d798d86409d1873cb22a25..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 35.72295379638672 3.970790147781372 436.56689453125 0.5475842952728271 579.5408935546875 0.2829810380935669 0.6969421 4.016196250915527 True -1 5606 30.919942378997803 0.584721565246582 438.5845947265625 0.5538823008537292 520.6228637695312 0.35305488109588623 0.7524617 1.112233281135559 True -2 8409 30.88566017150879 0.6161065101623535 391.890380859375 0.5031180381774902 510.62225341796875 0.36397120356559753 0.7699487 0.6583263874053955 True -3 11212 30.896016836166382 0.5908334255218506 444.1796875 0.6192348599433899 505.9397277832031 0.3666827082633972 0.78208244 0.6370887756347656 True -4 14015 30.900644302368164 0.6766393184661865 484.9803161621094 0.7134214043617249 502.1946105957031 0.3712793290615082 0.79151773 0.45050203800201416 True -5 16818 30.92100238800049 0.5854346752166748 436.31683349609375 0.6008169054985046 499.43841552734375 0.3758446276187897 0.79539394 0.4068223834037781 True -6 19621 30.938600778579712 0.5914499759674072 407.3389892578125 0.506152868270874 497.8428039550781 0.37592071294784546 0.8002495 0.4056255519390106 True -7 22424 30.914276361465454 1.406135082244873 477.2171630859375 0.39845046401023865 495.7659606933594 0.37888333201408386 0.8049717 0.3885648250579834 True -8 25227 31.022648096084595 0.6266219615936279 355.3081359863281 0.3810642659664154 494.4625244140625 0.3804030120372772 0.81137276 0.3756062686443329 True -9 28030 30.901936054229736 0.5947341918945312 408.215087890625 0.6433931589126587 493.0192565917969 0.38175514340400696 0.81619054 0.36704951524734497 True -10 30833 30.93556499481201 0.6112895011901855 396.83538818359375 0.36039403080940247 490.91046142578125 0.38460758328437805 0.82294005 0.35512644052505493 True -11 33636 30.98765754699707 0.5978844165802002 398.2895812988281 0.3764403462409973 488.7592468261719 0.3881697952747345 0.83055246 0.3366447985172272 True -12 36439 30.89998435974121 0.9539453983306885 495.1817626953125 0.563503623008728 487.4432067871094 0.3894287943840027 0.83178973 0.3231180012226105 True -13 39242 30.52621293067932 1.6377050876617432 423.3796081542969 0.3537803888320923 484.7853088378906 0.39361634850502014 0.83946306 0.3106737732887268 True -14 42045 30.28761124610901 0.6189031600952148 442.5809326171875 0.31000053882598877 485.4497985839844 0.39178797602653503 0.84353966 0.29750770330429077 True -15 44848 30.362093687057495 0.6464393138885498 439.41839599609375 0.4223974943161011 483.870849609375 0.39437583088874817 0.84885603 0.28705543279647827 True -16 47651 30.33964204788208 0.607717752456665 511.4939880371094 0.27657651901245117 483.75384521484375 0.3943954110145569 0.8525194 0.2816697955131531 True -17 50454 30.2902672290802 0.5908694267272949 397.58563232421875 0.29082387685775757 484.1113586425781 0.3926461338996887 0.8568803 0.2777979373931885 True -18 53257 30.284295797348022 0.5895743370056152 375.8102111816406 0.33490654826164246 484.19317626953125 0.3929300904273987 0.8563419 0.2781433165073395 False -19 56060 30.238429307937622 0.6071534156799316 445.14404296875 0.24647484719753265 483.08135986328125 0.3958183228969574 0.8564746 0.27898094058036804 False diff --git a/ENCSR987CQN/cherimoya.fold_4.performance.tsv b/ENCSR987CQN/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 4acec940606fb7200a3135ed636a15806516e931..0000000000000000000000000000000000000000 --- a/ENCSR987CQN/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -484.1113586425781 0.40795060992240906 0.3926461338996887 0.13684076070785522 0.8568803071975708 0.8195785284042358 0.2777979373931885 \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_0.evaluate.json b/ENCSR988YKR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index fbf5abb942e7facb8e3a23190fb2c3f3281b83ba..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF664FOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_0.fit.json b/ENCSR988YKR/cherimoya.fold_0.fit.json deleted file mode 100644 index 8e64ba9455eefa36f4bf8d0a00579714fe38cb79..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF664FOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_0.log b/ENCSR988YKR/cherimoya.fold_0.log deleted file mode 100644 index 166fcf00ed554568568ebc714d361d99392571bb..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 34.00437045097351 3.7454493045806885 472.18133544921875 0.58697909116745 648.7140502929688 0.21581247448921204 0.41724062 4.898199081420898 True -1 5512 30.404138565063477 1.0855298042297363 438.0823974609375 0.6632410287857056 606.4341430664062 0.32526835799217224 0.5532366 1.2223984003067017 True -2 8268 30.37477469444275 1.232785701751709 470.01873779296875 0.7977223992347717 600.4652099609375 0.3358139395713806 0.5752481 0.4410756826400757 True -3 11024 30.452675580978394 0.5711514949798584 503.8310241699219 0.6163270473480225 598.2962036132812 0.3378240466117859 0.59455913 0.36737310886383057 True -4 13780 30.380852460861206 0.557105541229248 449.7807312011719 0.37014609575271606 596.382568359375 0.34225350618362427 0.6049905 0.3581081032752991 True -5 16536 30.38866376876831 0.5506153106689453 495.4053649902344 0.7158879637718201 595.4830322265625 0.34399327635765076 0.6076127 0.35868412256240845 True -6 19292 30.369901657104492 0.5444118976593018 462.3501281738281 0.35767149925231934 594.2840576171875 0.34669363498687744 0.61693394 0.35531869530677795 True -7 22048 30.399965286254883 0.5547833442687988 544.5 0.38493746519088745 593.112548828125 0.3497006297111511 0.62688553 0.3473351001739502 True -8 24804 30.34622025489807 0.5736041069030762 427.0023193359375 0.5355175733566284 592.2332153320312 0.3515138626098633 0.6339497 0.33851170539855957 True -9 27560 29.826724529266357 0.5432953834533691 482.1530456542969 0.32385867834091187 591.7232055664062 0.35244351625442505 0.6411287 0.33239462971687317 True -10 30316 29.841562509536743 0.5511770248413086 422.39703369140625 0.42827773094177246 590.8406982421875 0.3543781638145447 0.6522858 0.325732558965683 True -11 33072 29.773533582687378 0.5411536693572998 418.52423095703125 0.4168049097061157 590.2469482421875 0.3555833697319031 0.6617513 0.319210410118103 True -12 35828 29.770541429519653 0.5420985221862793 488.4500427246094 0.2622886896133423 589.8419799804688 0.3567641079425812 0.6723721 0.3112685978412628 True -13 38584 29.813230991363525 1.6238682270050049 545.6023559570312 0.4600474536418915 589.3145751953125 0.35755085945129395 0.6819364 0.30575791001319885 True -14 41340 29.888597011566162 0.5559084415435791 460.89190673828125 0.26906144618988037 587.82080078125 0.3614048361778259 0.692504 0.2978578805923462 True -15 44096 29.781452178955078 1.1610734462738037 475.1470947265625 0.23656359314918518 587.89208984375 0.36181578040122986 0.69985604 0.29690006375312805 True -16 46852 29.81762933731079 16.19825005531311 453.70550537109375 0.28845810890197754 587.781494140625 0.36154666543006897 0.70286036 0.3004309833049774 True -17 49608 29.915098428726196 0.5634613037109375 484.25872802734375 0.20732763409614563 587.978515625 0.36100780963897705 0.70546967 0.3030511140823364 True -18 52364 29.84667706489563 0.5544211864471436 468.5953063964844 0.20007380843162537 587.6856689453125 0.362040638923645 0.7042574 0.3101610541343689 False -19 55120 29.827686309814453 0.5503573417663574 481.1450500488281 0.3156411051750183 587.6687622070312 0.36192914843559265 0.7026266 0.31634286046028137 False diff --git a/ENCSR988YKR/cherimoya.fold_0.performance.tsv b/ENCSR988YKR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 32e7e4419177c0b94e19b656a8bc724a311ab173..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -587.978515625 0.38438570499420166 0.36100780963897705 0.1412218064069748 0.7054696679115295 0.6873819231987 0.3030511140823364 \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_1.evaluate.json b/ENCSR988YKR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 39014b941f2f8809f5a251b291ca717ec5222678..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF664FOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_1.fit.json b/ENCSR988YKR/cherimoya.fold_1.fit.json deleted file mode 100644 index 09af0ae1baf9c5c3605d4456a07f4b13dcc35907..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF664FOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_1.log b/ENCSR988YKR/cherimoya.fold_1.log deleted file mode 100644 index cd6714c7b527cecb337de27b7f1c2f8cdf28da8d..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2756 34.20727205276489 3.6217687129974365 477.0942687988281 0.6852767467498779 680.3369140625 0.21958880126476288 0.4506567 5.296560764312744 True -1 5512 30.37230658531189 0.7195494174957275 482.2413635253906 0.6019032597541809 637.3530883789062 0.33064964413642883 0.59011656 1.0430852174758911 True -2 8268 30.4111967086792 0.976083517074585 534.6022338867188 0.5951271057128906 630.455810546875 0.3404301702976227 0.63153917 0.5114971995353699 True -3 11024 30.43013834953308 0.7080042362213135 461.64166259765625 0.5071558952331543 626.6025390625 0.34533414244651794 0.643144 0.4098624289035797 True -4 13780 30.446163415908813 0.7080991268157959 458.981201171875 0.4841213822364807 624.8225708007812 0.34751856327056885 0.63262165 0.3912894129753113 False -5 16536 30.456273317337036 0.7063186168670654 550.85546875 0.46180856227874756 623.0781860351562 0.3518834412097931 0.6563323 0.37422364950180054 True -6 19292 30.43177366256714 0.7044401168823242 466.98095703125 0.5349420309066772 622.333740234375 0.35199353098869324 0.66875964 0.36964502930641174 True -7 22048 30.366257905960083 0.7067553997039795 523.7451171875 0.7647433280944824 620.873779296875 0.3552958071231842 0.67513925 0.3502570688724518 True -8 24804 30.358404636383057 0.7029368877410889 426.6091003417969 0.3793680667877197 619.488525390625 0.35874852538108826 0.6839865 0.34521275758743286 True -9 27560 30.434189319610596 0.7104616165161133 491.9515686035156 0.38904714584350586 618.2160034179688 0.3617546856403351 0.6887125 0.3347575068473816 True -10 30316 29.864643096923828 0.7009525299072266 478.2314453125 0.43935948610305786 618.06103515625 0.36128807067871094 0.6994837 0.32789885997772217 True -11 33072 29.813010215759277 3.287740468978882 384.7734375 0.4165152907371521 616.2352294921875 0.36574217677116394 0.70563495 0.3171873092651367 True -12 35828 29.845678567886353 0.7146439552307129 465.19488525390625 0.23401610553264618 615.9052124023438 0.36545076966285706 0.7137691 0.3134271502494812 True -13 38584 29.868980646133423 0.7037138938903809 470.6927795410156 0.3466702401638031 615.0442504882812 0.36794984340667725 0.7210116 0.3101445138454437 True -14 41340 29.846450090408325 0.7008278369903564 535.3758544921875 0.28788137435913086 614.998291015625 0.36805394291877747 0.72772354 0.3053357005119324 True -15 44096 29.809088945388794 0.7072978019714355 510.20404052734375 0.3590359389781952 614.2108764648438 0.36939316987991333 0.7337745 0.30029311776161194 True -16 46852 29.820555210113525 1.3958170413970947 500.8524475097656 0.19461117684841156 613.9072265625 0.369912713766098 0.7380533 0.29786601662635803 True -17 49608 30.1032555103302 30.93479895591736 481.502197265625 0.4861409664154053 614.167236328125 0.36931824684143066 0.73943424 0.3025256097316742 True -18 52364 29.825820207595825 0.7098608016967773 494.2381896972656 0.2057243287563324 614.4404907226562 0.36874210834503174 0.73728126 0.3054659366607666 False -19 55120 29.882349252700806 0.7074933052062988 422.588623046875 0.26862287521362305 614.3731689453125 0.36890801787376404 0.73589826 0.31089794635772705 False diff --git a/ENCSR988YKR/cherimoya.fold_1.performance.tsv b/ENCSR988YKR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f973cb358a5e4fd1460631049e417473c3d863f6..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -614.167236328125 0.3762122094631195 0.36931824684143066 0.15338550508022308 0.7394342422485352 0.7296029925346375 0.3025256097316742 \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_2.evaluate.json b/ENCSR988YKR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 4e523a0b9b4102afda386df8c30f8239e78a4e34..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF664FOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_2.fit.json b/ENCSR988YKR/cherimoya.fold_2.fit.json deleted file mode 100644 index cb77e1b30a49c2dc3630475c7dba00d77ae2420b..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF664FOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_2.log b/ENCSR988YKR/cherimoya.fold_2.log deleted file mode 100644 index 9a1a47f68d570d35d2abb78417bdabf30a4b057c..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2911 36.22129726409912 3.7643327713012695 510.878173828125 0.7903294563293457 644.3937377929688 0.2235226333141327 0.43261623 4.721456050872803 True -1 5822 32.034566164016724 0.5606975555419922 456.1688232421875 0.8166913390159607 604.0960083007812 0.3279881477355957 0.56623846 0.956709623336792 True -2 8733 32.07469868659973 0.5238924026489258 495.2119445800781 0.5407260656356812 597.9480590820312 0.33698388934135437 0.58598524 0.4518008530139923 True -3 11644 31.992833137512207 0.5253520011901855 491.35760498046875 0.5518944263458252 595.8724365234375 0.3396752178668976 0.5979845 0.38879749178886414 True -4 14555 31.974841594696045 0.527292013168335 526.9771118164062 0.4829639792442322 592.8910522460938 0.3450559377670288 0.6130198 0.3632708787918091 True -5 17466 31.57946753501892 0.5211071968078613 429.12109375 0.49866873025894165 592.03173828125 0.3472396433353424 0.61961985 0.3587661683559418 True -6 20377 31.36261773109436 0.5101301670074463 461.8815612792969 0.3489719033241272 590.7009887695312 0.34945884346961975 0.6290338 0.35624873638153076 True -7 23288 31.39101481437683 0.5212993621826172 511.80291748046875 0.7982308268547058 589.5303344726562 0.35312095284461975 0.63567287 0.3531535565853119 True -8 26199 31.353146076202393 0.5227518081665039 444.97265625 0.3920157849788666 588.8973999023438 0.3540275990962982 0.6400466 0.35115623474121094 True -9 29110 31.3351309299469 0.9743061065673828 462.0859375 0.2808617353439331 588.4392700195312 0.3544740378856659 0.6533365 0.3415195941925049 True -10 32021 31.35716676712036 0.5211279392242432 496.2461853027344 0.3677825331687927 587.539306640625 0.35659828782081604 0.65980905 0.34886690974235535 True -11 34932 31.346611261367798 0.72690749168396 457.3465576171875 0.493221640586853 586.5620727539062 0.3592052161693573 0.67073107 0.33534514904022217 True -12 37843 31.466928482055664 0.521787166595459 490.4795837402344 0.3084247410297394 585.3793334960938 0.3620850741863251 0.6778755 0.32203277945518494 True -13 40754 31.688404083251953 0.5265750885009766 513.3461303710938 0.2883337438106537 584.7376098632812 0.3635483682155609 0.69017446 0.3161216378211975 True -14 43665 31.354996919631958 0.5137083530426025 481.1486511230469 0.23219449818134308 584.9002685546875 0.36252403259277344 0.6966845 0.31221869587898254 True -15 46576 31.40820002555847 0.6424310207366943 516.434814453125 0.22170241177082062 584.1354370117188 0.3644360303878784 0.70507014 0.3025720715522766 True -16 49487 31.36983871459961 0.5090932846069336 500.76385498046875 0.3258206248283386 584.2017822265625 0.36454644799232483 0.7096277 0.30163493752479553 True -17 52398 31.346457481384277 0.5238451957702637 423.8825378417969 0.28595250844955444 584.2390747070312 0.36409780383110046 0.71160126 0.3053405284881592 True -18 55309 31.42735528945923 0.5154240131378174 466.05712890625 0.21458934247493744 583.8941040039062 0.36555278301239014 0.7110268 0.3113884925842285 False -19 58220 31.491811752319336 0.515362024307251 432.3194580078125 0.2850624620914459 584.2276611328125 0.3639160990715027 0.708652 0.3159390091896057 False diff --git a/ENCSR988YKR/cherimoya.fold_2.performance.tsv b/ENCSR988YKR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 5d56406c5ccfd2279430aa09b110d1b2beec829c..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -584.2390747070312 0.3843073844909668 0.36409780383110046 0.14537620544433594 0.7116012573242188 0.6939988136291504 0.3053405284881592 \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_3.evaluate.json b/ENCSR988YKR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index cf8d1a7e355aa14b126a1ebdcec8b0dfa51bc737..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF664FOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_3.fit.json b/ENCSR988YKR/cherimoya.fold_3.fit.json deleted file mode 100644 index bfbb82aa74107ffbf567372b659769e29f9db7e5..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF664FOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_3.log b/ENCSR988YKR/cherimoya.fold_3.log deleted file mode 100644 index 853568f117a5f287b8f3e8e2a3f144621369d977..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2817 34.75334692001343 3.6241841316223145 457.6029052734375 0.4735487699508667 663.638671875 0.21746116876602173 0.424381 5.6941423416137695 True -1 5634 31.329020738601685 0.5667533874511719 463.20904541015625 0.7374980449676514 623.5208129882812 0.32187619805336 0.56426316 0.9984832406044006 True -2 8451 30.578633546829224 0.530930757522583 489.6361083984375 0.4712693989276886 617.9075927734375 0.33218279480934143 0.58285785 0.4779220521450043 True -3 11268 30.358380556106567 0.5331735610961914 461.9736022949219 0.7343799471855164 613.925048828125 0.33870941400527954 0.59191763 0.40382909774780273 True -4 14085 30.352868795394897 0.5360593795776367 441.4053955078125 0.3912731409072876 612.3333740234375 0.340565025806427 0.6009494 0.40221163630485535 True -5 16902 30.344161987304688 1.2666447162628174 454.4371337890625 0.7121744155883789 610.8757934570312 0.343966007232666 0.610133 0.38519206643104553 True -6 19719 30.46547818183899 0.5440390110015869 408.62347412109375 0.41321858763694763 609.9732666015625 0.3459876775741577 0.6158279 0.3824988901615143 True -7 22536 30.384936571121216 0.5388855934143066 461.4824523925781 0.7182412147521973 609.37109375 0.3470273017883301 0.6184569 0.3804209530353546 True -8 25353 30.39386487007141 0.535670280456543 484.3453674316406 0.42054587602615356 608.54150390625 0.349025696516037 0.6290084 0.3674878776073456 True -9 28170 30.39948868751526 0.5342073440551758 454.141357421875 0.3539489507675171 608.3125 0.34885281324386597 0.63704634 0.3588266670703888 True -10 30987 30.46366596221924 0.5441980361938477 453.09832763671875 0.35385340452194214 607.3496704101562 0.35120588541030884 0.64600384 0.37237152457237244 True -11 33804 30.350536346435547 1.1845035552978516 427.89044189453125 0.3251767158508301 606.9202880859375 0.3520297110080719 0.66330945 0.347202867269516 True -12 36621 30.382318258285522 1.5796587467193604 549.7901611328125 0.4247034788131714 605.9590454101562 0.3542989492416382 0.6725873 0.3368659019470215 True -13 39438 30.367607593536377 0.539283037185669 442.75103759765625 0.4300588071346283 605.4298706054688 0.3553273379802704 0.68652815 0.33032262325286865 True -14 42255 30.436364889144897 0.5377919673919678 478.1036682128906 0.3121701180934906 604.7781372070312 0.3567281663417816 0.7003056 0.31244462728500366 True -15 45072 30.397766828536987 0.5396795272827148 567.665771484375 0.32607322931289673 604.14208984375 0.3586883246898651 0.71089035 0.3102661967277527 True -16 47889 30.45633578300476 0.545128345489502 444.0733642578125 0.2762755751609802 603.8302612304688 0.3591408133506775 0.7143301 0.3066132068634033 True -17 50706 30.373055934906006 0.5435953140258789 419.87274169921875 0.18196392059326172 603.8770141601562 0.35887396335601807 0.71706796 0.30742281675338745 True -18 53523 30.344568729400635 0.5401067733764648 466.3286437988281 0.19893327355384827 603.543701171875 0.35931986570358276 0.7158743 0.3134729266166687 False -19 56340 30.338615655899048 0.7380974292755127 474.85052490234375 0.2335425615310669 603.696044921875 0.3593929409980774 0.7150196 0.31596603989601135 False diff --git a/ENCSR988YKR/cherimoya.fold_3.performance.tsv b/ENCSR988YKR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index ac18734795aa0f137de93b0c10c90641693bd45d..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -603.8770141601562 0.3818568289279938 0.35887396335601807 0.14799226820468903 0.7170679569244385 0.7035151124000549 0.30742281675338745 \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_4.evaluate.json b/ENCSR988YKR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index ca34729e6f3740739b2de8825cf8d9aa4268b053..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF664FOZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_4.fit.json b/ENCSR988YKR/cherimoya.fold_4.fit.json deleted file mode 100644 index a0a3fe670660a91e534948c3b01129ceeea1173e..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF664FOZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR988YKR/cherimoya.fold_4.log b/ENCSR988YKR/cherimoya.fold_4.log deleted file mode 100644 index 4b454fead6abf3d4aaff759e37c43ae4cc70738b..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2871 35.5696804523468 3.8393659591674805 472.3945007324219 0.4837191700935364 633.2901000976562 0.21454325318336487 0.42406136 3.8569488525390625 True -1 5742 31.558764934539795 0.582744836807251 458.5362548828125 0.5216494202613831 593.8616943359375 0.32287389039993286 0.5673757 0.8952431678771973 True -2 8613 31.57891345024109 0.559899091720581 468.4107666015625 0.7719079852104187 589.8810424804688 0.32704782485961914 0.590031 0.42001354694366455 True -3 11484 31.616121292114258 0.5607476234436035 487.66802978515625 0.48247581720352173 587.770263671875 0.32915177941322327 0.60384387 0.3766835033893585 True -4 14355 31.645743131637573 0.5607695579528809 515.050537109375 0.5331342816352844 584.799560546875 0.3367556631565094 0.6171948 0.36741992831230164 True -5 17226 31.667656898498535 0.5632009506225586 495.9052734375 0.43741223216056824 584.1131591796875 0.33742910623550415 0.62332445 0.36771610379219055 True -6 20097 32.42443323135376 0.5617551803588867 474.91937255859375 0.38850656151771545 583.4053955078125 0.3394675552845001 0.63168323 0.3854646384716034 True -7 22968 31.621947288513184 0.5626096725463867 457.7421875 0.4424792230129242 582.2457275390625 0.34148019552230835 0.6385143 0.3635210394859314 True -8 25839 31.785311698913574 0.5664575099945068 436.214111328125 0.3694896101951599 581.4342651367188 0.34367769956588745 0.64474994 0.3586314022541046 True -9 28710 31.954444646835327 0.5728154182434082 512.0906982421875 0.3866668939590454 581.068115234375 0.34412074089050293 0.6502984 0.3473251760005951 True -10 31581 31.74329662322998 0.5705509185791016 432.6066589355469 0.478681743144989 580.1204833984375 0.34652966260910034 0.6612649 0.3549121022224426 True -11 34452 31.57837152481079 0.5635924339294434 508.9740295410156 0.3444441556930542 579.5532836914062 0.34758567810058594 0.66807103 0.3408266603946686 True -12 37323 31.616151094436646 1.029479742050171 511.8916320800781 0.49398618936538696 578.1678466796875 0.3516080379486084 0.6791055 0.33034881949424744 True -13 40194 31.671131134033203 0.8199658393859863 513.9137573242188 0.35259974002838135 577.6566772460938 0.3527110815048218 0.6873784 0.32341089844703674 True -14 43065 31.68288016319275 0.5619983673095703 466.21441650390625 0.2103152573108673 578.0152587890625 0.35178327560424805 0.6967222 0.319850891828537 True -15 45936 31.16433048248291 0.558788537979126 495.5024719238281 0.3162730932235718 577.4539184570312 0.35286301374435425 0.7041716 0.3096679747104645 True -16 48807 31.33161997795105 0.559711217880249 396.75921630859375 0.4589952230453491 577.426025390625 0.3525785505771637 0.70548654 0.30747246742248535 True -17 51678 31.244582176208496 0.5605916976928711 573.2108154296875 0.23809143900871277 577.38671875 0.3525558412075043 0.71057504 0.3068961203098297 True -18 54549 31.24911069869995 0.5810277462005615 530.943359375 0.19845892488956451 577.1160888671875 0.35345032811164856 0.7086772 0.31220635771751404 False -19 57420 31.10314393043518 0.5652065277099609 444.8866882324219 0.24591845273971558 577.6388549804688 0.35220903158187866 0.7072726 0.31743547320365906 False diff --git a/ENCSR988YKR/cherimoya.fold_4.performance.tsv b/ENCSR988YKR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 7f40d4f496172b38cebf14d5abd4bd429ad3a38f..0000000000000000000000000000000000000000 --- a/ENCSR988YKR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -577.38671875 0.3901769816875458 0.35255590081214905 0.13947850465774536 0.7105750441551208 0.6859748959541321 0.3068961203098297 \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_0.evaluate.json b/ENCSR989YIV/cherimoya.fold_0.evaluate.json deleted file mode 100644 index eb32fee5684bfc92ec4991123858fee564d3ee78..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482HCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_0.fit.json b/ENCSR989YIV/cherimoya.fold_0.fit.json deleted file mode 100644 index cfd74bb620036c4974f2c9735fcb943b43368b8c..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF482HCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_0.log b/ENCSR989YIV/cherimoya.fold_0.log deleted file mode 100644 index 55b3f62030b0e7d1a8ff630bd1a6cd3ffd5d0956..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2735 35.230395555496216 17.683784246444702 150.91314697265625 0.7671054601669312 245.74386596679688 0.14602789282798767 0.563168 3.883759021759033 True -1 5470 30.071163415908813 2.4429595470428467 178.9030303955078 0.6056674718856812 230.32484436035156 0.22136352956295013 0.6385442 1.9133269786834717 True -2 8205 30.148317098617554 4.886933326721191 146.29188537597656 0.6609398722648621 227.01101684570312 0.23179812729358673 0.6516925 1.0554338693618774 True -3 10940 29.551474809646606 0.5479006767272949 203.80816650390625 0.6589879989624023 225.2867431640625 0.23880043625831604 0.66475594 0.9426558017730713 True -4 13675 29.51946449279785 0.5493991374969482 186.15347290039062 0.8421875238418579 224.9370574951172 0.2391553521156311 0.67561287 0.9222471714019775 True -5 16410 29.55907917022705 1.7501227855682373 135.12173461914062 0.5656468868255615 224.48953247070312 0.24133314192295074 0.6804937 0.8755742311477661 True -6 19145 29.57249641418457 0.5460395812988281 190.27088928222656 0.5039688348770142 223.9793701171875 0.2441108226776123 0.6859305 0.8192885518074036 True -7 21880 29.64738655090332 21.262717485427856 182.4701690673828 0.4810972511768341 223.56918334960938 0.2455316036939621 0.6876932 0.7268429398536682 True -8 24615 30.518918991088867 6.232864618301392 176.118896484375 0.5558544397354126 223.01783752441406 0.24852365255355835 0.69247854 0.6789606809616089 True -9 27350 29.63294005393982 0.5475409030914307 169.46994018554688 0.6369353532791138 222.97425842285156 0.2478811889886856 0.69984055 0.6235564947128296 True -10 30085 29.63610315322876 0.5508081912994385 150.26768493652344 0.5206834077835083 222.0126190185547 0.2533148527145386 0.7049494 0.610541045665741 True -11 32820 29.599047422409058 0.5386738777160645 180.99276733398438 0.5580158233642578 222.0678253173828 0.25274744629859924 0.70660573 0.5852134227752686 True -12 35555 29.601481676101685 0.5469727516174316 197.2566680908203 0.4494384527206421 221.38099670410156 0.2559826970100403 0.7186796 0.526960015296936 True -13 38290 29.66512942314148 0.547966718673706 199.1420135498047 0.36841821670532227 221.028076171875 0.25726351141929626 0.7276817 0.4997820556163788 True -14 41025 29.650843143463135 0.5426084995269775 160.52398681640625 0.3486332595348358 220.7734832763672 0.25840598344802856 0.7355748 0.4651099741458893 True -15 43760 29.652434825897217 0.545539379119873 169.27362060546875 0.4029983878135681 220.8024444580078 0.2576583921909332 0.7410175 0.4382537603378296 True -16 46495 29.641528606414795 0.5412678718566895 153.5857391357422 0.2625107169151306 220.62203979492188 0.25889846682548523 0.7459919 0.4180281460285187 True -17 49230 30.16254734992981 25.29429292678833 143.18423461914062 0.39645659923553467 220.52792358398438 0.2590761184692383 0.747424 0.40939390659332275 True -18 51965 29.979586601257324 0.5421864986419678 169.94082641601562 0.3762633204460144 220.4232635498047 0.2598974108695984 0.74854666 0.4075508117675781 True -19 54700 29.651719570159912 0.5376811027526855 196.22369384765625 0.3198503255844116 220.41578674316406 0.2597494125366211 0.74770314 0.4110972583293915 False diff --git a/ENCSR989YIV/cherimoya.fold_0.performance.tsv b/ENCSR989YIV/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 7e60f69fcc31d7de5c5e80904fe10d9cac1e113b..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -220.4232635498047 0.5203128457069397 0.2598974108695984 0.06278818845748901 0.7485466599464417 0.6847867965698242 0.4075508117675781 \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_1.evaluate.json b/ENCSR989YIV/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 11fbbb39ae0ae4d687620a02ec8b4aad447db11f..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482HCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_1.fit.json b/ENCSR989YIV/cherimoya.fold_1.fit.json deleted file mode 100644 index 5f65bf13cbc2c8e4ac9cd20917b0a358dac96cfd..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF482HCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_1.log b/ENCSR989YIV/cherimoya.fold_1.log deleted file mode 100644 index 1fb32a3fa94d931d78a4e41280f7052474af7b45..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 34.53623652458191 3.670308828353882 167.860107421875 0.6464421153068542 270.2741394042969 0.15157602727413177 0.58176297 3.7787063121795654 True -1 5520 30.437469720840454 0.7175502777099609 177.62860107421875 1.139101266860962 252.02200317382812 0.2336551696062088 0.68662393 1.9812582731246948 True -2 8280 30.444144010543823 34.695064306259155 160.47201538085938 0.4587671458721161 249.09829711914062 0.24178963899612427 0.7069684 1.0593922138214111 True -3 11040 31.12052822113037 0.9956133365631104 152.12022399902344 0.7964975833892822 247.37918090820312 0.24654096364974976 0.7176682 0.8974937796592712 True -4 13800 30.496968030929565 35.358928203582764 176.26669311523438 0.7266750335693359 246.224853515625 0.25158387422561646 0.7215488 0.7750197052955627 True -5 16560 31.03194570541382 0.7344837188720703 130.360595703125 0.6003288626670837 245.483154296875 0.2546720504760742 0.7275099 0.7184873819351196 True -6 19320 31.010610342025757 0.7149040699005127 155.72146606445312 0.5513970851898193 245.02102661132812 0.25682583451271057 0.73442 0.6798044443130493 True -7 22080 30.482799530029297 0.7072701454162598 166.1886444091797 0.7228495478630066 244.72039794921875 0.2576386332511902 0.7405715 0.6439782381057739 True -8 24840 30.540278911590576 0.7060327529907227 163.91152954101562 0.5928842425346375 243.95538330078125 0.261553019285202 0.7454322 0.6471167206764221 True -9 27600 30.48843479156494 0.7080628871917725 186.53648376464844 0.43964308500289917 244.05059814453125 0.25993579626083374 0.7479802 0.5973138213157654 True -10 30360 30.57194232940674 0.7137470245361328 201.2667236328125 0.616487979888916 243.3020477294922 0.2637737989425659 0.75640565 0.5603653788566589 True -11 33120 30.608216047286987 0.718580961227417 154.6721649169922 0.5060707330703735 242.8922576904297 0.2654193341732025 0.7619612 0.5234496593475342 True -12 35880 30.94404888153076 20.931737899780273 180.37210083007812 0.39320889115333557 242.4868621826172 0.2664264440536499 0.7672253 0.49772909283638 True -13 38640 30.592345237731934 0.7426433563232422 150.04800415039062 0.598334789276123 241.9833221435547 0.26873841881752014 0.7742111 0.465935617685318 True -14 41400 30.96209216117859 0.7287333011627197 173.39227294921875 0.40844860672950745 241.61285400390625 0.2694961428642273 0.779796 0.4314989149570465 True -15 44160 30.605005979537964 0.7108292579650879 188.20394897460938 0.5827988386154175 241.279052734375 0.2711653709411621 0.784682 0.4110805094242096 True -16 46920 30.597153425216675 0.7090213298797607 174.6393280029297 0.4919508099555969 241.1160430908203 0.27170225977897644 0.7871887 0.3991234004497528 True -17 49680 30.553723573684692 43.93697452545166 154.607421875 0.37064146995544434 240.9061279296875 0.27320006489753723 0.7876133 0.38666436076164246 True -18 52440 30.62946343421936 0.7331364154815674 155.43649291992188 0.4528486430644989 241.38246154785156 0.2699723541736603 0.7862578 0.3858841061592102 False -19 55200 30.593876600265503 0.7401473522186279 156.89776611328125 0.26195967197418213 241.4716339111328 0.26967671513557434 0.7855506 0.38774988055229187 False diff --git a/ENCSR989YIV/cherimoya.fold_1.performance.tsv b/ENCSR989YIV/cherimoya.fold_1.performance.tsv deleted file mode 100644 index ab2a4371146fd7c38750490a2124b92f8ce01e3d..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -240.9061279296875 0.5089985728263855 0.27320006489753723 0.06558864563703537 0.7876132726669312 0.7424287796020508 0.38666436076164246 \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_2.evaluate.json b/ENCSR989YIV/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 56b00effd8eef165a711939cbbc4ee9fe1c6beb5..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482HCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_2.fit.json b/ENCSR989YIV/cherimoya.fold_2.fit.json deleted file mode 100644 index 5cc27118d3f182ce621ef68522155c98583be630..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF482HCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_2.log b/ENCSR989YIV/cherimoya.fold_2.log deleted file mode 100644 index af7d50de4731e710ae64fae8109256626eaed97b..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2907 38.01610088348389 45.787296295166016 198.59033203125 0.7336981892585754 249.6275634765625 0.1530444324016571 0.5533163 2.92301607131958 True -1 5814 32.183117628097534 31.399860620498657 187.66058349609375 0.7481590509414673 233.77944946289062 0.22520172595977783 0.6600609 1.6844205856323242 True -2 8721 32.73663806915283 23.287475109100342 176.39736938476562 0.6034518480300903 231.6819610595703 0.23279452323913574 0.6662531 1.1294194459915161 True -3 11628 32.47387337684631 0.563880443572998 169.54833984375 0.6526061296463013 230.12501525878906 0.23819001019001007 0.67867756 0.9597697854042053 True -4 14535 32.13155436515808 0.5666623115539551 200.50332641601562 0.49224787950515747 229.36305236816406 0.24012364447116852 0.69262356 0.7932626008987427 True -5 17442 32.15511703491211 0.5690791606903076 137.04122924804688 0.6072144508361816 228.69493103027344 0.24266798794269562 0.69860965 0.7736081480979919 True -6 20349 32.19321823120117 0.5529558658599854 236.51602172851562 0.6304998397827148 227.80694580078125 0.24725347757339478 0.70760906 0.7176252603530884 True -7 23256 32.22020649909973 0.5621616840362549 152.9658203125 0.5773900747299194 227.52427673339844 0.24800625443458557 0.7159885 0.6478517055511475 True -8 26163 32.12561368942261 21.53897476196289 168.34866333007812 0.4902236759662628 226.74099731445312 0.25235599279403687 0.72065353 0.6198795437812805 True -9 29070 32.25012278556824 0.5636329650878906 181.49871826171875 0.7671817541122437 226.49534606933594 0.2529699504375458 0.72365844 0.584087073802948 True -10 31977 32.141660928726196 1.233715295791626 185.670166015625 0.5095750093460083 225.81910705566406 0.2560533285140991 0.72912455 0.5645015835762024 True -11 34884 32.07344841957092 0.5549716949462891 178.67236328125 0.5149643421173096 225.4800262451172 0.2575460970401764 0.73567003 0.5123090744018555 True -12 37791 32.107420206069946 1.3499157428741455 204.14833068847656 0.4861140251159668 225.2333221435547 0.2586347460746765 0.74178296 0.4782389998435974 True -13 40698 32.14663648605347 2.506092071533203 166.1981201171875 0.49706435203552246 224.8397979736328 0.25977909564971924 0.7467685 0.4589959979057312 True -14 43605 32.1379611492157 0.5521254539489746 184.13339233398438 0.32222187519073486 224.4811248779297 0.2612825930118561 0.75398225 0.43425655364990234 True -15 46512 32.18492555618286 0.5536458492279053 182.27740478515625 0.3247465491294861 224.42434692382812 0.26133573055267334 0.7603599 0.4186334013938904 True -16 49419 32.10768222808838 0.5530223846435547 196.27133178710938 0.3568271994590759 224.38839721679688 0.2615453600883484 0.7623321 0.404258668422699 True -17 52326 32.11562752723694 0.9440615177154541 201.30311584472656 0.39627861976623535 224.12339782714844 0.26333925127983093 0.76503175 0.3945399820804596 True -18 55233 32.14798951148987 0.5480160713195801 159.17398071289062 0.4559885859489441 224.31932067871094 0.26191800832748413 0.7651681 0.396854430437088 True -19 58140 31.626312255859375 0.5497314929962158 191.46458435058594 0.21083110570907593 224.18719482421875 0.2628208100795746 0.76235014 0.4012914299964905 False diff --git a/ENCSR989YIV/cherimoya.fold_2.performance.tsv b/ENCSR989YIV/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 298b31582449154dcb34a6aab41456a3d669d5f7..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -224.31932067871094 0.5180790424346924 0.26191800832748413 0.06274958699941635 0.7651680707931519 0.709729015827179 0.396854430437088 \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_3.evaluate.json b/ENCSR989YIV/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 2214ed4db29acc69b6dd767990ed7fd3b06fffa8..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482HCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_3.fit.json b/ENCSR989YIV/cherimoya.fold_3.fit.json deleted file mode 100644 index 58872dff0289bc4069c901e59ddaf41a128f373f..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF482HCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_3.log b/ENCSR989YIV/cherimoya.fold_3.log deleted file mode 100644 index 078909c4059ff02a5ef1438ddf2c2fa281fd4f5a..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2806 40.43014717102051 3.82912540435791 227.75332641601562 0.9193063378334045 247.03138732910156 0.149123415350914 0.5775326 3.599280595779419 True -1 5612 31.023504972457886 0.620307445526123 162.21585083007812 0.6726515293121338 232.41310119628906 0.22367125749588013 0.6628942 1.9023224115371704 True -2 8418 31.03766942024231 0.5895471572875977 203.69468688964844 0.7371058464050293 229.6620635986328 0.23217898607254028 0.68086785 1.0544395446777344 True -3 11224 31.03950834274292 1.581418514251709 173.01129150390625 0.5639842748641968 227.7578887939453 0.24007096886634827 0.68968433 0.8768095970153809 True -4 14030 31.0664222240448 0.5877537727355957 121.40170288085938 0.9222900867462158 227.67356872558594 0.23913739621639252 0.6944664 0.8133655190467834 True -5 16836 31.00408387184143 0.5917410850524902 146.5891571044922 0.5424983501434326 227.17100524902344 0.241553395986557 0.7024701 0.7254412174224854 True -6 19642 30.985507011413574 0.5896682739257812 169.71282958984375 0.532844066619873 226.37742614746094 0.2454785257577896 0.710004 0.6601664423942566 True -7 22448 30.972758531570435 0.5812480449676514 208.85342407226562 0.5522423982620239 226.0300750732422 0.24705412983894348 0.71540266 0.6208580732345581 True -8 25254 31.020867824554443 0.5878372192382812 147.25904846191406 0.9154975414276123 225.7998504638672 0.2480161339044571 0.71891487 0.5840622782707214 True -9 28060 30.972370624542236 0.5793905258178711 207.37417602539062 0.4942057430744171 225.05345153808594 0.2518111765384674 0.72258866 0.529616117477417 True -10 30866 31.020548582077026 0.5827834606170654 170.61660766601562 0.47643014788627625 224.68173217773438 0.25359171628952026 0.72903144 0.5108150839805603 True -11 33672 31.081143856048584 0.5896544456481934 164.56631469726562 0.4197850525379181 224.31919860839844 0.2554200291633606 0.7338145 0.4828082025051117 True -12 36478 31.082420825958252 20.246337890625 139.26535034179688 0.44772565364837646 223.88499450683594 0.25743386149406433 0.7376036 0.474195271730423 True -13 39284 31.004339933395386 1.6503372192382812 201.87448120117188 0.5824717283248901 223.50962829589844 0.2591542899608612 0.7446431 0.4425468146800995 True -14 42090 31.099766492843628 21.178971529006958 157.94143676757812 0.4512127935886383 223.37937927246094 0.2589869499206543 0.75199914 0.423437237739563 True -15 44896 31.94133496284485 0.5878002643585205 170.7144012451172 0.5503484606742859 223.3103790283203 0.25923144817352295 0.75705963 0.41410472989082336 True -16 47702 31.23698616027832 0.6028008460998535 208.66864013671875 0.5193883180618286 223.23410034179688 0.2597295939922333 0.7624295 0.40318453311920166 True -17 50508 31.086349964141846 0.5909111499786377 170.09768676757812 0.2783315181732178 223.3691864013672 0.25852450728416443 0.764379 0.40031442046165466 True -18 53314 35.76102900505066 23.43786907196045 180.94482421875 0.35305503010749817 223.1518096923828 0.2597448527812958 0.7630436 0.39866575598716736 False -19 56120 30.47586679458618 0.5800416469573975 198.59727478027344 0.2416015863418579 223.0371551513672 0.26069334149360657 0.7613304 0.4051746129989624 False diff --git a/ENCSR989YIV/cherimoya.fold_3.performance.tsv b/ENCSR989YIV/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6079bd0a7155dc657191c51dea3ce53b0161eb89..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -223.3691864013672 0.5197460651397705 0.25852450728416443 0.05796702951192856 0.7643790245056152 0.7081526517868042 0.40031442046165466 \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_4.evaluate.json b/ENCSR989YIV/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 68143c1f46807364dda0040890eb8f0d91dcd449..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF482HCZ.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_4.fit.json b/ENCSR989YIV/cherimoya.fold_4.fit.json deleted file mode 100644 index c3c1cf450596e270d8ee81d6588e05f84238548b..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF482HCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_4.log b/ENCSR989YIV/cherimoya.fold_4.log deleted file mode 100644 index 7e635ba621ddbb05401f2e367bc90670f5765ddd..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2862 36.43203687667847 3.5025241374969482 143.74813842773438 0.8534210920333862 237.71273803710938 0.14973066747188568 0.5649321 3.7103888988494873 True -1 5724 31.643008708953857 0.5531082153320312 171.21080017089844 0.4817243218421936 224.1936798095703 0.21841108798980713 0.6504555 1.397447109222412 True -2 8586 31.579965114593506 0.5382957458496094 203.3438720703125 0.7621612548828125 220.88424682617188 0.22954010963439941 0.67015797 0.9121379852294922 True -3 11448 31.535409927368164 0.5344464778900146 182.17825317382812 0.6073980927467346 219.629150390625 0.23385898768901825 0.6868642 0.7480142712593079 True -4 14310 31.826022386550903 28.69748854637146 170.51995849609375 0.7324737310409546 218.96897888183594 0.23710228502750397 0.68764 0.6576847434043884 True -5 17172 31.77583622932434 0.5687711238861084 160.55804443359375 0.5777761340141296 218.65745544433594 0.23829856514930725 0.69165736 0.6986986398696899 True -6 20034 31.569121837615967 0.7879116535186768 152.31503295898438 0.7231007814407349 218.32376098632812 0.24015749990940094 0.6962531 0.7155720591545105 True -7 22896 31.68256163597107 0.5362520217895508 236.9920654296875 0.44085314869880676 217.9584503173828 0.24181343615055084 0.7000744 0.7116846442222595 True -8 25758 31.62211322784424 0.5449860095977783 204.72341918945312 0.6349809169769287 217.1393585205078 0.24613745510578156 0.7100998 0.6334221363067627 True -9 28620 31.59286332130432 0.541754961013794 192.35498046875 0.4792284071445465 216.92303466796875 0.24744559824466705 0.7096406 0.6371551752090454 False -10 31482 31.60231590270996 0.5501232147216797 199.3140869140625 0.48670828342437744 216.5849151611328 0.24877560138702393 0.7167715 0.5783362984657288 True -11 34344 31.632461071014404 0.59649658203125 161.5722198486328 0.4277423024177551 216.5435028076172 0.24844950437545776 0.72178215 0.5628588795661926 True -12 37206 31.657913208007812 0.5409364700317383 185.60934448242188 0.6027466058731079 216.15489196777344 0.25030460953712463 0.7313671 0.5185993313789368 True -13 40068 31.989341497421265 0.5349361896514893 190.63491821289062 0.4190329909324646 215.562744140625 0.2531026303768158 0.7364528 0.4741660952568054 True -14 42930 31.982221841812134 0.5414352416992188 176.51205444335938 0.3494155704975128 215.16737365722656 0.2550458610057831 0.74527085 0.4445265233516693 True -15 45792 31.785853624343872 0.5479931831359863 181.96664428710938 0.551030695438385 215.3688507080078 0.25315290689468384 0.75006807 0.42225298285484314 True -16 48654 31.77246880531311 0.5410888195037842 188.17086791992188 0.27122122049331665 215.1548309326172 0.25461405515670776 0.75593597 0.4003143608570099 True -17 51516 31.294939756393433 0.5321266651153564 171.7064666748047 0.3243666887283325 215.09628295898438 0.25534364581108093 0.75712943 0.39220255613327026 True -18 54378 31.189571380615234 0.5335261821746826 199.77244567871094 0.28571242094039917 215.2959747314453 0.2538750171661377 0.756334 0.38955527544021606 False -19 57240 31.25944232940674 0.5373332500457764 161.46240234375 0.30647730827331543 215.18309020996094 0.2549651861190796 0.75515 0.39119333028793335 False diff --git a/ENCSR989YIV/cherimoya.fold_4.performance.tsv b/ENCSR989YIV/cherimoya.fold_4.performance.tsv deleted file mode 100644 index b1bad06ebeb26d1e6f62f5b174a6db86fb9bec4c..0000000000000000000000000000000000000000 --- a/ENCSR989YIV/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -215.09628295898438 0.5239243507385254 0.2553436756134033 0.05649752914905548 0.757129430770874 0.6918281316757202 0.39220255613327026 \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_0.evaluate.json b/ENCSR990NNX/cherimoya.fold_0.evaluate.json deleted file mode 100644 index dcc0ce140d7eddd6ea488b8cf57bc40c594ce9cb..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF490GJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_0.fit.json b/ENCSR990NNX/cherimoya.fold_0.fit.json deleted file mode 100644 index 2dbcd8e205a71bd8fe1dba1aa18fe972b11514da..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF490GJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_0.log b/ENCSR990NNX/cherimoya.fold_0.log deleted file mode 100644 index 4418d87d864ea28333eb433696c0130397a6944a..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3425 41.72558307647705 3.5645487308502197 708.8450927734375 0.46235018968582153 1054.5184326171875 0.7442787885665894 0.74903804 5.546687126159668 True -1 6850 38.0163197517395 0.6870520114898682 854.4292602539062 0.6191898584365845 901.5973510742188 0.8088914752006531 0.7985339 1.0007853507995605 True -2 10275 38.06413960456848 0.6786105632781982 777.4901123046875 0.3418123722076416 874.8960571289062 0.8185338377952576 0.8046818 0.7224032282829285 True -3 13700 38.05393981933594 27.68125867843628 733.7471923828125 0.2900869846343994 860.5524291992188 0.8238431811332703 0.8122656 0.47841164469718933 True -4 17125 38.151853799819946 0.6723530292510986 893.9849243164062 0.5291217565536499 853.2159423828125 0.8259040713310242 0.81998086 0.3725517988204956 True -5 20550 38.14930272102356 1.3313446044921875 812.6397705078125 0.2976669371128082 850.0498046875 0.8276244401931763 0.8197133 0.38094404339790344 False -6 23975 38.11430907249451 0.6643075942993164 646.986083984375 0.45244720578193665 844.3040161132812 0.8299527168273926 0.82535505 0.3299207091331482 True -7 27400 38.057682514190674 0.6671106815338135 584.7593383789062 0.18242153525352478 838.9180297851562 0.8314931392669678 0.82633126 0.31862133741378784 True -8 30825 38.099493980407715 1.917764663696289 724.40087890625 0.30194687843322754 835.6162109375 0.8331669569015503 0.8300048 0.30063730478286743 True -9 34250 38.103761434555054 0.6703705787658691 766.052490234375 0.4571559429168701 831.3040771484375 0.8350329995155334 0.83274007 0.31988441944122314 True -10 37675 38.242034673690796 0.6709380149841309 692.7166748046875 0.35214728116989136 827.7421264648438 0.8371564149856567 0.83358115 0.3156723082065582 True -11 41100 38.184226274490356 0.9667825698852539 580.3402099609375 0.2165776491165161 820.9247436523438 0.8404881358146667 0.8406006 0.28815242648124695 True -12 44525 38.1882061958313 24.041237831115723 719.5540771484375 0.5249325037002563 816.7939453125 0.8426176905632019 0.84707904 0.2679138779640198 True -13 47950 38.254530906677246 0.6578121185302734 763.1072998046875 0.26095426082611084 810.6172485351562 0.8452081680297852 0.8524562 0.25023558735847473 True -14 51375 38.16491985321045 0.6740245819091797 726.6563110351562 0.18733736872673035 806.576904296875 0.8473815321922302 0.8573576 0.2421325147151947 True -15 54800 38.07430958747864 0.6706314086914062 649.1805419921875 0.2451128214597702 804.3203735351562 0.8487091660499573 0.86151624 0.23417264223098755 True -16 58225 37.82597303390503 0.6623668670654297 788.562255859375 0.27923300862312317 802.3867797851562 0.8496225476264954 0.8653036 0.22429180145263672 True -17 61650 37.26705288887024 0.650625467300415 722.7318725585938 0.2673739790916443 801.63818359375 0.8500317335128784 0.8687299 0.2217385321855545 True -18 65075 37.419620990753174 1.5270469188690186 643.48974609375 0.21004843711853027 801.7230224609375 0.8499230146408081 0.8683068 0.21980546414852142 False -19 68500 37.58271765708923 1.2778441905975342 648.36962890625 0.1541891247034073 802.26708984375 0.8497996926307678 0.868486 0.22071103751659393 False diff --git a/ENCSR990NNX/cherimoya.fold_0.performance.tsv b/ENCSR990NNX/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 2ed3c8d93ab1e1def50f2db2e655b944381b0cac..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -801.63818359375 0.12185274809598923 0.8500317931175232 0.5221337080001831 0.8687298893928528 0.7868958115577698 0.2217385321855545 \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_1.evaluate.json b/ENCSR990NNX/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 23196fee12e74362dbf0136ad2d676a9b1606399..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF490GJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_1.fit.json b/ENCSR990NNX/cherimoya.fold_1.fit.json deleted file mode 100644 index af50709fc80c87c464580f0f9f5a1ef898e7a65d..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF490GJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_1.log b/ENCSR990NNX/cherimoya.fold_1.log deleted file mode 100644 index 20996c06f110da1c5993384b8d69b73fefd717eb..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3370 41.178466796875 5.2363340854644775 802.4293212890625 0.5024041533470154 1212.3834228515625 0.7457056641578674 0.75971943 5.786906719207764 True -1 6740 37.51774191856384 0.922738790512085 710.25537109375 1.0974416732788086 1001.8370361328125 0.8172699213027954 0.8076574 1.285725712776184 True -2 10110 37.50207591056824 0.8988525867462158 660.97119140625 0.5194270610809326 971.2164916992188 0.826282799243927 0.8187777 0.7713887095451355 True -3 13480 37.59253692626953 0.8777518272399902 755.9618530273438 0.9631986618041992 954.325927734375 0.8324496150016785 0.82488376 0.5991637706756592 True -4 16850 37.539188385009766 2.5416653156280518 749.6334228515625 0.33887261152267456 944.3982543945312 0.8355932235717773 0.8294585 0.5157363414764404 True -5 20220 37.60236215591431 1.1845078468322754 776.1612548828125 0.529410719871521 941.6847534179688 0.8375744223594666 0.8307596 0.5364208221435547 True -6 23590 37.50940418243408 0.8766953945159912 852.36474609375 0.4013959467411041 935.8880004882812 0.8397719264030457 0.83262753 0.41582927107810974 True -7 26960 37.41188669204712 0.8963680267333984 616.2618408203125 0.34498700499534607 928.0167846679688 0.8421310782432556 0.8385246 0.38725998997688293 True -8 30330 37.34252429008484 0.8885476589202881 790.2733154296875 0.3240741789340973 922.7177734375 0.8439754247665405 0.8400528 0.3834720253944397 True -9 33700 37.3714325428009 0.868105411529541 622.4556884765625 0.3828009366989136 916.6781005859375 0.845832884311676 0.8430759 0.37472814321517944 True -10 37070 37.35861253738403 0.8675951957702637 757.7467041015625 0.24503524601459503 910.8536376953125 0.8478958606719971 0.8480844 0.3587214946746826 True -11 40440 37.418397188186646 0.8699679374694824 748.8027954101562 0.2853724956512451 903.470947265625 0.8510598540306091 0.855188 0.3508916199207306 True -12 43810 37.52257680892944 35.67721080780029 707.77099609375 0.4785909950733185 896.11767578125 0.8539120554924011 0.8625684 0.31559619307518005 True -13 47180 36.835681676864624 0.8740537166595459 677.9570922851562 0.3437100052833557 891.0219116210938 0.8561936616897583 0.8667086 0.28112274408340454 True -14 50550 36.75658988952637 8.474886894226074 642.7872314453125 0.22629690170288086 886.0552978515625 0.8581852316856384 0.8731378 0.2680661976337433 True -15 53920 36.67200803756714 0.872546911239624 605.1644287109375 0.2214321494102478 882.1409301757812 0.8595788478851318 0.8759769 0.2513623833656311 True -16 57290 36.661951303482056 0.8685989379882812 678.692138671875 0.20915007591247559 880.3202514648438 0.8603260517120361 0.8822733 0.2383524477481842 True -17 60660 36.666311264038086 9.575113773345947 629.9487915039062 0.5448791980743408 879.6134643554688 0.8607456088066101 0.88422835 0.23295018076896667 True -18 64030 37.42693114280701 0.8712587356567383 722.5664672851562 0.41394010186195374 879.7750244140625 0.8605083227157593 0.88401264 0.2308613359928131 False -19 67400 36.71323299407959 0.8725030422210693 664.5765991210938 0.21239925920963287 880.6743774414062 0.860378623008728 0.88212055 0.23181669414043427 False diff --git a/ENCSR990NNX/cherimoya.fold_1.performance.tsv b/ENCSR990NNX/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 1de06ce78945510d0597903ffc3bb474b0315328..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -879.6134643554688 0.11192271113395691 0.8607456088066101 0.5554826855659485 0.8842283487319946 0.8387538194656372 0.23295018076896667 \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_2.evaluate.json b/ENCSR990NNX/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 624604954d90e45bb0fcc62dec6fd4cd2540b409..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF490GJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_2.fit.json b/ENCSR990NNX/cherimoya.fold_2.fit.json deleted file mode 100644 index 8a65c1e411b0fa68e33ce21caac5fa9b7df6ada8..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF490GJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_2.log b/ENCSR990NNX/cherimoya.fold_2.log deleted file mode 100644 index 040f146b77c15cfbdc77078aa68141613aba0125..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3583 43.840752363204956 3.6900827884674072 762.4183349609375 0.7405315637588501 1085.9676513671875 0.7538349032402039 0.7450263 5.462287425994873 True -1 7166 39.913591623306274 0.7106904983520508 777.7118530273438 0.8845759034156799 927.6627197265625 0.8137012720108032 0.8019847 0.9802688360214233 True -2 10749 39.84117317199707 1.3675322532653809 868.0252075195312 0.45534706115722656 909.7507934570312 0.8191421627998352 0.81060517 0.6356057524681091 True -3 14332 39.77469778060913 0.7005774974822998 684.98291015625 0.3815460205078125 897.7037353515625 0.8235863447189331 0.81844115 0.4919619858264923 True -4 17915 39.818562746047974 0.7036879062652588 712.7908935546875 0.4181334376335144 885.1017456054688 0.8271192312240601 0.82563883 0.42015784978866577 True -5 21498 40.87558603286743 0.707237958908081 766.3049926757812 0.322878360748291 882.1495361328125 0.8277928829193115 0.8238707 0.40221932530403137 False -6 25081 42.623926639556885 0.6991901397705078 724.464599609375 0.28322649002075195 877.6334838867188 0.8292372822761536 0.8275266 0.32498282194137573 True -7 28664 39.75807309150696 0.7038650512695312 799.0030517578125 0.28007200360298157 871.6654663085938 0.8310543894767761 0.83105457 0.3011467754840851 True -8 32247 39.7189085483551 0.7027192115783691 816.3793334960938 0.36659467220306396 866.0540161132812 0.8331394195556641 0.83389676 0.29694920778274536 True -9 35830 39.75375938415527 0.7046065330505371 717.0806884765625 0.28939175605773926 861.0665283203125 0.8358128070831299 0.83780575 0.2963632047176361 True -10 39413 39.02588772773743 0.7051386833190918 715.0331420898438 0.3209371268749237 855.0643920898438 0.8379374146461487 0.84229064 0.28706300258636475 True -11 42996 38.891321897506714 1.105116844177246 706.7943115234375 0.29182952642440796 848.372802734375 0.8413199186325073 0.8495054 0.2793397903442383 True -12 46579 38.90333700180054 0.6959648132324219 743.2117919921875 0.4352254867553711 843.5801391601562 0.8442572355270386 0.85203576 0.2652932107448578 True -13 50162 38.973692893981934 0.6906189918518066 676.625 0.2544253170490265 839.5536499023438 0.846595048904419 0.85852754 0.2509576380252838 True -14 53745 38.90886616706848 0.6964304447174072 731.6993408203125 0.2631953954696655 834.8591918945312 0.8486446738243103 0.863671 0.2421518713235855 True -15 57328 38.98784255981445 0.700326681137085 665.2777709960938 0.17620989680290222 831.5044555664062 0.8501151204109192 0.86642987 0.23479166626930237 True -16 60911 38.944145917892456 0.6958317756652832 759.5438842773438 0.2100944221019745 829.6056518554688 0.8508741855621338 0.8685486 0.2303811013698578 True -17 64494 38.91689109802246 0.7028629779815674 739.8855590820312 0.2652013897895813 829.8394775390625 0.8511401414871216 0.86959153 0.22671477496623993 True -18 68077 38.910024881362915 0.7004199028015137 594.4832763671875 0.2432938665151596 829.7787475585938 0.8509030938148499 0.87041354 0.22742107510566711 True -19 71660 38.929932594299316 0.6976699829101562 671.18115234375 0.2171303778886795 829.9779663085938 0.850787341594696 0.86886394 0.22879120707511902 False diff --git a/ENCSR990NNX/cherimoya.fold_2.performance.tsv b/ENCSR990NNX/cherimoya.fold_2.performance.tsv deleted file mode 100644 index b01adb93c5b88af018c097f2950bb16448cfdcd9..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -829.7787475585938 0.11868695914745331 0.8509030938148499 0.5359703898429871 0.8704135417938232 0.8046347498893738 0.22742107510566711 \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_3.evaluate.json b/ENCSR990NNX/cherimoya.fold_3.evaluate.json deleted file mode 100644 index e89312eda2ef01e1e9e638619a5f757de13cb3f9..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF490GJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_3.fit.json b/ENCSR990NNX/cherimoya.fold_3.fit.json deleted file mode 100644 index 8f550b1188f17b73e1987ded00973b154af409ec..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF490GJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_3.log b/ENCSR990NNX/cherimoya.fold_3.log deleted file mode 100644 index 363d4a094db96e839c609bb4c7fd5b80e5bae46c..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3446 42.03859829902649 3.125356912612915 834.7244873046875 0.28671371936798096 1026.2591552734375 0.7456091046333313 0.7262247 7.522557258605957 True -1 6892 38.33812642097473 23.38970136642456 839.0537109375 0.5260583758354187 880.6823120117188 0.8090811371803284 0.7856711 1.2532436847686768 True -2 10338 38.37772750854492 0.7099132537841797 776.22900390625 0.4513130187988281 860.716552734375 0.815985918045044 0.79353535 0.6221595406532288 True -3 13784 38.23530888557434 0.6581757068634033 708.1198120117188 0.4167918860912323 852.743408203125 0.8197559118270874 0.79875016 0.5216324925422668 True -4 17230 38.319461822509766 0.6621248722076416 770.2841796875 0.2428285926580429 844.1736450195312 0.8231596350669861 0.8008556 0.5254501104354858 True -5 20676 38.18710112571716 3.587420701980591 792.7750244140625 0.6582526564598083 837.510498046875 0.8259742856025696 0.8042261 0.48008501529693604 True -6 24122 37.48715686798096 0.6274683475494385 795.3104248046875 0.3048846125602722 832.0988159179688 0.8275145292282104 0.80778927 0.4033663272857666 True -7 27568 37.442668199539185 15.30637502670288 716.966064453125 0.4179295599460602 828.3552856445312 0.8288851976394653 0.81157243 0.37333986163139343 True -8 31014 37.55379867553711 0.6373293399810791 644.2850952148438 0.583698034286499 823.3064575195312 0.8306097984313965 0.81478524 0.3600730299949646 True -9 34460 37.427627086639404 0.6234698295593262 767.131103515625 0.2891930043697357 819.2059326171875 0.8330488801002502 0.81843185 0.3590412139892578 True -10 37906 37.4084997177124 0.6280937194824219 679.2366333007812 0.41773921251296997 815.3040771484375 0.8346503376960754 0.82112736 0.3398834466934204 True -11 41352 37.96923089027405 0.6258301734924316 757.3571166992188 0.3772560954093933 809.0032958984375 0.8383882641792297 0.829951 0.3083605468273163 True -12 44798 37.491347789764404 2.5999252796173096 773.942138671875 0.2194550633430481 804.341064453125 0.8410041332244873 0.83693284 0.28214943408966064 True -13 48244 37.47658634185791 0.6285429000854492 624.723388671875 0.3593998849391937 799.944091796875 0.8432161808013916 0.84132236 0.2637408375740051 True -14 51690 37.44645833969116 0.61867356300354 746.517578125 0.7838201522827148 796.3551025390625 0.8452229499816895 0.84782803 0.2558494508266449 True -15 55136 37.42437505722046 0.6365566253662109 624.4923095703125 0.2327640950679779 794.2644653320312 0.8464445471763611 0.8522182 0.24985697865486145 True -16 58582 37.51590967178345 0.6239867210388184 671.6771240234375 0.10611303150653839 792.8663940429688 0.8473061919212341 0.85579264 0.2466418296098709 True -17 62028 37.44750785827637 0.6255481243133545 685.55712890625 0.136212557554245 792.189697265625 0.8474826812744141 0.8570123 0.24292241036891937 True -18 65474 37.49982213973999 0.6185762882232666 735.7273559570312 0.15527591109275818 792.3922729492188 0.8472830653190613 0.8540426 0.24608168005943298 False -19 68920 37.46582913398743 0.7156248092651367 736.209716796875 0.2531113624572754 792.8969116210938 0.8471426367759705 0.8544282 0.24599190056324005 False diff --git a/ENCSR990NNX/cherimoya.fold_3.performance.tsv b/ENCSR990NNX/cherimoya.fold_3.performance.tsv deleted file mode 100644 index d96c4c03377adddd95dcb8c0b50cabcf6c4a58ef..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -792.189697265625 0.12359760701656342 0.8474826812744141 0.513851523399353 0.8570122718811035 0.7753003835678101 0.24292241036891937 \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_4.evaluate.json b/ENCSR990NNX/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e154a2b1a8332c35a55e6ad3dbd081b8785e4c52..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF490GJM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_4.fit.json b/ENCSR990NNX/cherimoya.fold_4.fit.json deleted file mode 100644 index ab8660f9b053148ada7912ed3645b8d0dc267eda..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF490GJM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990NNX/cherimoya.fold_4.log b/ENCSR990NNX/cherimoya.fold_4.log deleted file mode 100644 index bbb3b05c6df4618cacaf6608fa9a46cccd820513..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3495 42.75512504577637 3.644882917404175 865.76318359375 0.5763046145439148 993.3265380859375 0.7458390593528748 0.73843884 5.318628311157227 True -1 6990 38.85743951797485 16.51846981048584 800.764404296875 0.355962872505188 862.216064453125 0.8025040030479431 0.7863426 0.9885903596878052 True -2 10485 38.19873285293579 0.7029144763946533 806.3277587890625 0.3176863193511963 845.6917114257812 0.8105308413505554 0.7885116 0.6068360805511475 True -3 13980 38.09582567214966 0.7074506282806396 832.8222045898438 0.560921311378479 831.6813354492188 0.8156164884567261 0.7974154 0.4754561185836792 True -4 17475 38.28746771812439 0.7149753570556641 801.8680419921875 0.3904053568840027 825.9646606445312 0.8185018301010132 0.7993327 0.4614429175853729 True -5 20970 38.32626938819885 25.63476276397705 694.9119873046875 0.28642332553863525 818.3633422851562 0.8216322064399719 0.8048598 0.37948766350746155 True -6 24465 38.26845955848694 0.7462990283966064 661.0550537109375 0.27481091022491455 812.730712890625 0.8244264125823975 0.8101788 0.36450818181037903 True -7 27960 38.10756278038025 0.7194790840148926 781.1873168945312 0.36294084787368774 810.0392456054688 0.8261421918869019 0.8114514 0.3650001287460327 True -8 31455 38.0576548576355 2.3680338859558105 739.0196533203125 0.33158549666404724 805.8796997070312 0.8275661468505859 0.813908 0.3800266981124878 True -9 34950 38.04327654838562 0.7178442478179932 666.6832275390625 0.3484344482421875 801.802734375 0.8291720747947693 0.8180891 0.36636072397232056 True -10 38445 37.99920582771301 1.0361299514770508 673.78076171875 0.3138393461704254 796.6972045898438 0.832036018371582 0.8224324 0.3499726951122284 True -11 41940 38.120012521743774 0.7096326351165771 774.5535888671875 0.31286895275115967 791.231201171875 0.8348079323768616 0.8266447 0.3013462424278259 True -12 45435 38.109143018722534 0.7040388584136963 800.642578125 0.218061625957489 785.4607543945312 0.8376701474189758 0.8374045 0.2748357057571411 True -13 48930 38.075783252716064 0.7204363346099854 636.666259765625 0.1804734319448471 781.2494506835938 0.8400269150733948 0.8454995 0.26332563161849976 True -14 52425 38.09114384651184 17.708394050598145 700.9344482421875 0.26732152700424194 776.7079467773438 0.8420665264129639 0.852723 0.2372545748949051 True -15 55920 38.180593729019165 0.7222769260406494 666.39013671875 0.27325472235679626 774.0526123046875 0.8431839942932129 0.8572641 0.22309841215610504 True -16 59415 38.20717978477478 3.8397045135498047 689.1397705078125 0.22428786754608154 772.1109008789062 0.8441145420074463 0.8626752 0.21111363172531128 True -17 62910 38.19583606719971 0.7177057266235352 707.8270263671875 0.11119973659515381 771.5814208984375 0.8444228172302246 0.8624141 0.21114341914653778 False -18 66405 38.02165198326111 0.7027790546417236 719.1713256835938 0.20333164930343628 771.9451904296875 0.8444157838821411 0.8640548 0.21096210181713104 True -19 69900 38.10076832771301 3.341214179992676 622.7882080078125 0.14074264466762543 772.0858764648438 0.8443054556846619 0.86196834 0.21234793961048126 False diff --git a/ENCSR990NNX/cherimoya.fold_4.performance.tsv b/ENCSR990NNX/cherimoya.fold_4.performance.tsv deleted file mode 100644 index d02ef17f5cced916de7274b6ff53083b01b88a44..0000000000000000000000000000000000000000 --- a/ENCSR990NNX/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -771.9451904296875 0.12620361149311066 0.8444157838821411 0.5101146697998047 0.864054799079895 0.7729621529579163 0.21096210181713104 \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_0.evaluate.json b/ENCSR990XXC/cherimoya.fold_0.evaluate.json deleted file mode 100644 index a25894325746a1a8bddc0c67d6849cfcf3edbe91..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF369IVI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_0.fit.json b/ENCSR990XXC/cherimoya.fold_0.fit.json deleted file mode 100644 index 0eaa3951bf74efd6c1d92c8c5581c2fbde32029b..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF369IVI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_0.log b/ENCSR990XXC/cherimoya.fold_0.log deleted file mode 100644 index 2aca3b871b49ece2ec0cafe54d8d7242d4a41640..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2748 34.55258321762085 3.776232957839966 263.94207763671875 0.7726890444755554 323.25738525390625 0.17145971953868866 0.6358895 3.705409049987793 True -1 5496 30.13024401664734 0.6047332286834717 243.68423461914062 0.533816397190094 307.0240478515625 0.23586268723011017 0.6878725 0.96373051404953 True -2 8244 30.167546272277832 0.54201340675354 254.4091033935547 0.7442498207092285 302.6589050292969 0.24937804043293 0.69468355 0.7006418108940125 True -3 10992 30.15489673614502 0.5531349182128906 242.53521728515625 0.46159014105796814 300.8665771484375 0.25568273663520813 0.7022003 0.5567763447761536 True -4 13740 30.16237759590149 0.5445263385772705 251.4048614501953 0.615681529045105 300.2023010253906 0.2579447329044342 0.70361465 0.5046026706695557 True -5 16488 30.15246820449829 0.5333783626556396 288.4644775390625 0.6884430646896362 299.36273193359375 0.26104044914245605 0.70229024 0.5713366270065308 False -6 19236 30.181366205215454 0.5835616588592529 218.87646484375 0.7182353734970093 298.3310241699219 0.26554790139198303 0.7086258 0.548517644405365 True -7 21984 30.175965070724487 0.5590951442718506 248.62525939941406 0.621513843536377 297.9915466308594 0.2669239938259125 0.71102387 0.5659859776496887 True -8 24732 29.686225652694702 0.5483498573303223 190.44573974609375 0.5281186699867249 297.0863952636719 0.270283967256546 0.7093908 0.5757945775985718 False -9 27480 29.54713010787964 1.2078211307525635 232.08078002929688 0.5151538848876953 296.3348083496094 0.2739464044570923 0.71595585 0.5461723804473877 True -10 30228 29.53285527229309 0.8276991844177246 247.9621124267578 0.6156656742095947 295.55059814453125 0.2770807147026062 0.7167133 0.523204505443573 True -11 32976 29.607074975967407 0.5467195510864258 210.3630828857422 0.40330371260643005 295.1541442871094 0.27819421887397766 0.7227765 0.48469895124435425 True -12 35724 29.572844982147217 0.5497276782989502 229.502197265625 0.44046562910079956 294.29327392578125 0.2812574803829193 0.73257977 0.430939257144928 True -13 38472 29.625640630722046 0.5532310009002686 216.4034423828125 0.4763616919517517 294.0410461425781 0.2818177044391632 0.73730385 0.4281759560108185 True -14 41220 29.57205319404602 0.5451054573059082 210.8200225830078 0.5405524969100952 293.78790283203125 0.28253838419914246 0.74628454 0.3906552493572235 True -15 43968 29.5713050365448 0.5431485176086426 205.01901245117188 0.45239484310150146 293.1540832519531 0.2848629653453827 0.7553121 0.36216452717781067 True -16 46716 29.578166961669922 0.9810559749603271 220.16986083984375 0.5211940407752991 292.907958984375 0.2852604389190674 0.75869346 0.34480640292167664 True -17 49464 29.58591079711914 0.5408725738525391 220.77987670898438 0.4476059079170227 292.65802001953125 0.28682953119277954 0.76197535 0.33715182542800903 True -18 52212 29.606027603149414 0.5580599308013916 246.01461791992188 0.3831813633441925 292.59942626953125 0.2871399521827698 0.7629388 0.336223840713501 True -19 54960 29.564215421676636 0.5383288860321045 268.40264892578125 0.3193798065185547 292.656005859375 0.28665634989738464 0.7603938 0.33794769644737244 False diff --git a/ENCSR990XXC/cherimoya.fold_0.performance.tsv b/ENCSR990XXC/cherimoya.fold_0.performance.tsv deleted file mode 100644 index b177a3140638301e9e20bf5f10cd189731039edc..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -292.59942626953125 0.48841506242752075 0.2871399521827698 0.07856504619121552 0.7629387974739075 0.7192747592926025 0.336223840713501 \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_1.evaluate.json b/ENCSR990XXC/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 460ecafa187dde1030faac6b17a44e522b027275..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF369IVI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_1.fit.json b/ENCSR990XXC/cherimoya.fold_1.fit.json deleted file mode 100644 index d92ab6199d3a40e87b3627d0b2284afe98126ad9..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF369IVI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_1.log b/ENCSR990XXC/cherimoya.fold_1.log deleted file mode 100644 index 03d17ff48180095abf2cf10bd22316a3ddce73ce..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2705 34.15676522254944 4.437050819396973 271.01263427734375 0.7598575949668884 361.4548645019531 0.1787116527557373 0.6383645 4.1355085372924805 True -1 5410 29.730159044265747 1.0340819358825684 207.54022216796875 0.6542125940322876 341.37164306640625 0.25039660930633545 0.7057251 1.2566512823104858 True -2 8115 29.744712829589844 0.7022974491119385 215.26092529296875 0.5634474754333496 335.5510559082031 0.2635914087295532 0.71057105 0.7678623199462891 True -3 10820 29.726946592330933 0.6976454257965088 275.70538330078125 0.7986458539962769 333.52191162109375 0.2697352468967438 0.72464395 0.6977338194847107 True -4 13525 29.798368215560913 0.7042868137359619 219.03076171875 0.6336857080459595 332.22320556640625 0.2734970152378082 0.72493464 0.735966145992279 True -5 16230 29.680307388305664 0.6934385299682617 264.667236328125 0.723909854888916 331.58770751953125 0.2757580578327179 0.72528607 0.8277196288108826 True -6 18935 29.752397537231445 0.7071895599365234 258.3134765625 0.5193004012107849 330.8664245605469 0.2780723571777344 0.72795504 0.88095623254776 True -7 21640 29.54476499557495 0.740816593170166 244.226806640625 0.45134538412094116 329.6432800292969 0.2830153703689575 0.72891927 0.9068636298179626 True -8 24345 29.066038370132446 0.6966891288757324 260.82489013671875 0.497437059879303 328.59661865234375 0.2863450050354004 0.7347001 0.7804893255233765 True -9 27050 29.086360931396484 0.6892027854919434 203.06317138671875 0.5457659959793091 327.8675842285156 0.28918856382369995 0.737366 0.7162862420082092 True -10 29755 29.112547636032104 0.6976771354675293 244.5530548095703 0.4942789375782013 327.4868469238281 0.2898898422718048 0.7367681 0.6601912379264832 False -11 32460 29.092273950576782 0.6936099529266357 218.41949462890625 0.45325833559036255 326.52099609375 0.29374685883522034 0.7430547 0.6271517872810364 True -12 35165 29.080734252929688 0.6993613243103027 231.11253356933594 0.43230774998664856 325.7171325683594 0.2949959337711334 0.7491653 0.6023284196853638 True -13 37870 29.07719659805298 0.6868913173675537 249.09423828125 0.44574570655822754 324.99700927734375 0.2974488139152527 0.7591328 0.5155469179153442 True -14 40575 29.143460750579834 2.8094892501831055 244.1548614501953 0.3719150424003601 324.5969543457031 0.29778555035591125 0.7656409 0.48414021730422974 True -15 43280 29.184109210968018 13.034905910491943 249.39927673339844 0.265080064535141 324.23394775390625 0.29934683442115784 0.7719208 0.4495756924152374 True -16 45985 29.117948293685913 0.7205755710601807 232.5703582763672 0.25765982270240784 323.7042236328125 0.3017421364784241 0.7770494 0.4084130823612213 True -17 48690 29.13948392868042 0.701923131942749 218.34152221679688 0.3368421792984009 323.8310546875 0.3002285063266754 0.778103 0.3912564814090729 True -18 51395 29.12705397605896 0.6995739936828613 219.45407104492188 0.39734020829200745 324.0726013183594 0.29926788806915283 0.7783783 0.38172975182533264 True -19 54100 29.182169198989868 0.6973874568939209 234.375 0.3839382827281952 323.9024963378906 0.30034294724464417 0.77750283 0.38161763548851013 False diff --git a/ENCSR990XXC/cherimoya.fold_1.performance.tsv b/ENCSR990XXC/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 4bb43bc8231da41d7868ddd566b7bb07235e8816..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -324.0726013183594 0.47487038373947144 0.29926785826683044 0.09163929522037506 0.7783783078193665 0.7553431987762451 0.38172975182533264 \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_2.evaluate.json b/ENCSR990XXC/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 5a2ea9d04c13df920db60691920c9cbef1ca04aa..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF369IVI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_2.fit.json b/ENCSR990XXC/cherimoya.fold_2.fit.json deleted file mode 100644 index c413c805b2de8afa2fd17b8b5ca1b9227938a476..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF369IVI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_2.log b/ENCSR990XXC/cherimoya.fold_2.log deleted file mode 100644 index 387dbd3c355d9d2756d88fce382e03b3abc03db1..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2868 36.34790658950806 3.990116596221924 235.47251892089844 0.7336010932922363 331.6300964355469 0.17649708688259125 0.6221122 2.6255922317504883 True -1 5736 31.790573835372925 0.6428959369659424 249.23193359375 0.9390272498130798 313.37371826171875 0.24543452262878418 0.68956745 0.9845534563064575 True -2 8604 31.78298854827881 0.8771812915802002 250.9789276123047 0.6902635097503662 309.2920837402344 0.256002813577652 0.6968095 0.6768737435340881 True -3 11472 31.73613667488098 0.5436828136444092 270.330078125 0.5793718695640564 307.3182067871094 0.26313912868499756 0.6951493 0.682923436164856 False -4 14340 31.55338168144226 0.5273208618164062 188.60874938964844 0.7052960395812988 306.76025390625 0.26332974433898926 0.70096827 0.6805833578109741 True -5 17208 31.08644723892212 0.5264689922332764 200.968017578125 0.8007341027259827 305.84881591796875 0.2669221758842468 0.7009568 0.6603597402572632 False -6 20076 31.128796577453613 0.5345098972320557 216.74180603027344 0.5692523717880249 305.2200012207031 0.2701718509197235 0.70739144 0.6734333634376526 True -7 22944 31.072716236114502 0.5091452598571777 263.6377258300781 0.5049281120300293 304.7347412109375 0.27198171615600586 0.7110464 0.6835947036743164 True -8 25812 31.066187143325806 2.4127864837646484 259.4442443847656 0.5877734422683716 303.8564758300781 0.2755468487739563 0.7155155 0.622002363204956 True -9 28680 31.138566493988037 0.5279667377471924 211.4574432373047 0.5708358287811279 303.4157409667969 0.2774331569671631 0.7170137 0.6042261719703674 True -10 31548 31.152270555496216 0.5290660858154297 242.39407348632812 0.43977537751197815 302.48870849609375 0.2806749641895294 0.7214724 0.5651291608810425 True -11 34416 31.153654098510742 0.5209500789642334 277.15350341796875 0.4411896765232086 301.6137390136719 0.28412961959838867 0.72437894 0.5385935306549072 True -12 37284 31.15120768547058 0.5250530242919922 224.8872528076172 0.6095961332321167 301.0312194824219 0.2861360013484955 0.7312192 0.5043768882751465 True -13 40152 31.12867283821106 0.5160069465637207 239.49656677246094 0.6024538278579712 300.78955078125 0.28744861483573914 0.7387167 0.4793010354042053 True -14 43020 31.091301918029785 0.5119953155517578 217.2335968017578 0.4484902024269104 299.8689270019531 0.2899906039237976 0.7446067 0.43854227662086487 True -15 45888 31.15874457359314 0.5267183780670166 258.1681823730469 0.49125197529792786 299.85443115234375 0.29011058807373047 0.75113136 0.40960222482681274 True -16 48756 31.211777687072754 1.564877986907959 257.31134033203125 0.3497803807258606 299.54888916015625 0.29089805483818054 0.75574046 0.38840341567993164 True -17 51624 31.151714324951172 0.5362792015075684 200.56224060058594 0.4076628088951111 299.2161865234375 0.29195669293403625 0.7575847 0.3716059625148773 True -18 54492 31.11637830734253 0.5756967067718506 250.66539001464844 0.42108961939811707 299.2651672363281 0.2919853627681732 0.75833017 0.3695584833621979 True -19 57360 31.128431797027588 0.5387623310089111 225.49314880371094 0.42829594016075134 299.2156982421875 0.29220113158226013 0.75763565 0.3690475523471832 False diff --git a/ENCSR990XXC/cherimoya.fold_2.performance.tsv b/ENCSR990XXC/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e63880b843c8c1168052d0da8ee6d3f1c41dd482..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -299.2651672363281 0.48427507281303406 0.2919853627681732 0.07893672585487366 0.7583301663398743 0.7251560091972351 0.3695584833621979 \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_3.evaluate.json b/ENCSR990XXC/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 77daf4c87ad7a4e8b9c4d73be97cfb3144d8c2a5..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF369IVI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_3.fit.json b/ENCSR990XXC/cherimoya.fold_3.fit.json deleted file mode 100644 index accd36a738f313032d9e3b19dab8307b035c7fba..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF369IVI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_3.log b/ENCSR990XXC/cherimoya.fold_3.log deleted file mode 100644 index 4231319df4ba6b5c13f347afc3dc7e9aa2a2f39d..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2760 34.84717679023743 4.880055904388428 232.91244506835938 0.6615130305290222 348.08251953125 0.17849357426166534 0.651616 3.451239824295044 True -1 5520 30.37818455696106 16.122960090637207 247.0854034423828 0.523213267326355 331.63372802734375 0.24023319780826569 0.71188813 1.3093702793121338 True -2 8280 30.352712631225586 0.566931962966919 263.6199035644531 0.6252462863922119 326.4931945800781 0.2556707262992859 0.7156504 0.766139566898346 True -3 11040 29.94725012779236 2.552717685699463 229.41348266601562 0.5808761715888977 324.66094970703125 0.25977909564971924 0.7231236 0.6470340490341187 True -4 13800 29.73825192451477 1.2808890342712402 229.5415496826172 0.8692820072174072 323.2388610839844 0.26541611552238464 0.7212604 0.5838385224342346 False -5 16560 29.784546613693237 1.1728417873382568 235.21127319335938 0.5020381212234497 322.4891357421875 0.26731568574905396 0.7258787 0.5925164818763733 True -6 19320 29.784591674804688 3.5523746013641357 245.59864807128906 0.6744423508644104 322.2336730957031 0.2684745192527771 0.72678643 0.5909450650215149 True -7 22080 29.791786670684814 0.8507413864135742 241.07077026367188 0.6741871237754822 322.1907043457031 0.26840072870254517 0.7285328 0.5978251695632935 True -8 24840 29.798014163970947 0.5458672046661377 215.71202087402344 0.7905177474021912 321.1708679199219 0.2728617191314697 0.7294285 0.6033653616905212 True -9 27600 29.775660037994385 18.623061180114746 211.66238403320312 0.5280887484550476 320.2577209472656 0.2767137289047241 0.73215944 0.6144111752510071 True -10 30360 29.740447521209717 0.5683853626251221 238.64495849609375 0.6347735524177551 319.8352355957031 0.27828502655029297 0.73540854 0.5943940877914429 True -11 33120 29.762709140777588 1.0380847454071045 208.19876098632812 0.4247155785560608 319.13916015625 0.28011107444763184 0.74150264 0.5670226216316223 True -12 35880 29.734333992004395 0.5499413013458252 196.39089965820312 0.6160979270935059 319.08123779296875 0.28015872836112976 0.74792635 0.5331562161445618 True -13 38640 29.771388053894043 0.5493350028991699 242.35568237304688 0.4802946448326111 318.0270080566406 0.2834755778312683 0.755696 0.4718468189239502 True -14 41400 29.758651733398438 0.5472152233123779 211.93385314941406 0.3567294180393219 317.8299865722656 0.2840977609157562 0.7607212 0.4625961184501648 True -15 44160 29.81402039527893 0.5399961471557617 248.57955932617188 0.29789629578590393 317.0797424316406 0.2861332893371582 0.7681316 0.43507981300354004 True -16 46920 29.769768953323364 0.5424134731292725 264.39312744140625 0.48874130845069885 317.118896484375 0.2862025797367096 0.7722768 0.39875832200050354 True -17 49680 29.781147718429565 0.5405113697052002 241.5364532470703 0.29457026720046997 317.44281005859375 0.28448373079299927 0.7764385 0.37857475876808167 True -18 52440 29.745080709457397 0.5469081401824951 224.28663635253906 0.33521318435668945 316.8684387207031 0.28700754046440125 0.7775739 0.36958950757980347 True -19 55200 29.692188501358032 0.5380196571350098 223.59066772460938 0.4403015971183777 316.85552978515625 0.28764837980270386 0.7765091 0.3687587082386017 False diff --git a/ENCSR990XXC/cherimoya.fold_3.performance.tsv b/ENCSR990XXC/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 6ea26307eadd3cdb9f9319535d1e3163f833cdc4..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -316.8684387207031 0.4817686378955841 0.28700754046440125 0.08733515441417694 0.7775738835334778 0.73984295129776 0.36958950757980347 \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_4.evaluate.json b/ENCSR990XXC/cherimoya.fold_4.evaluate.json deleted file mode 100644 index e748437428748e7df6ee266dd0049e42e4c0cccb..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF369IVI.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_4.fit.json b/ENCSR990XXC/cherimoya.fold_4.fit.json deleted file mode 100644 index a01cb91c9355ad67ec7add1ed100056a7311bd6c..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF369IVI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR990XXC/cherimoya.fold_4.log b/ENCSR990XXC/cherimoya.fold_4.log deleted file mode 100644 index 0ade31da11754ba7eab01ce720f61680d2244607..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2827 35.86921787261963 4.823768377304077 268.1226806640625 0.6454775333404541 316.8526306152344 0.17464545369148254 0.6260415 3.1689329147338867 True -1 5654 30.631768465042114 0.7063775062561035 235.91705322265625 0.5476154088973999 303.0870056152344 0.22970420122146606 0.68974036 1.0098137855529785 True -2 8481 31.053473949432373 0.5986175537109375 234.64401245117188 0.8481260538101196 298.2430419921875 0.24452897906303406 0.69687635 0.636198103427887 True -3 11308 31.098910331726074 0.6174914836883545 198.01690673828125 0.7844081521034241 296.789794921875 0.24836726486682892 0.70226467 0.6064867973327637 True -4 14135 30.815647840499878 0.6063685417175293 261.36083984375 0.6396040916442871 295.3670959472656 0.2543392777442932 0.70606214 0.6754527688026428 True -5 16962 30.420358657836914 0.6102848052978516 220.5546417236328 0.7647629380226135 294.88946533203125 0.2558479607105255 0.7108367 0.6562765836715698 True -6 19789 30.421767711639404 0.6172873973846436 243.60885620117188 0.5473611950874329 294.1936340332031 0.25899043679237366 0.70867 0.6444152593612671 False -7 22616 30.43102526664734 1.143864631652832 236.41259765625 0.7391802072525024 293.6962890625 0.26119154691696167 0.7129298 0.6263197064399719 True -8 25443 30.826102018356323 0.5872178077697754 226.09896850585938 0.37784284353256226 293.32415771484375 0.26232224702835083 0.71278715 0.5834671854972839 False -9 28270 30.434879302978516 0.6331713199615479 212.1208038330078 0.4928552210330963 292.5434265136719 0.2659192979335785 0.7174391 0.5644996762275696 True -10 31097 30.417139530181885 0.6346266269683838 283.9111328125 0.5149065852165222 291.8780212402344 0.2688942551612854 0.72333425 0.5497945547103882 True -11 33924 30.44944429397583 0.6135649681091309 201.3068389892578 0.41408291459083557 291.38458251953125 0.27083146572113037 0.7290361 0.5062122344970703 True -12 36751 30.482072353363037 0.6203954219818115 219.74708557128906 0.4584769606590271 290.92327880859375 0.2723928987979889 0.7336696 0.49257782101631165 True -13 39578 30.429810762405396 0.6175661087036133 194.48789978027344 0.49516260623931885 290.6357116699219 0.273145854473114 0.7390439 0.46015095710754395 True -14 42405 30.413398027420044 0.6002535820007324 229.50775146484375 0.42435821890830994 289.974365234375 0.2759970426559448 0.74671257 0.40152132511138916 True -15 45232 30.40631866455078 0.5912425518035889 212.43194580078125 0.4535299241542816 289.78167724609375 0.2765848934650421 0.7546716 0.37160199880599976 True -16 48059 30.430155992507935 0.6123800277709961 212.98715209960938 0.34633344411849976 289.6070861816406 0.2766200304031372 0.7561298 0.3545232117176056 True -17 50886 30.439539432525635 0.6040070056915283 203.79795837402344 0.5001304745674133 289.4581298828125 0.27718275785446167 0.7602381 0.34319522976875305 True -18 53713 30.417293310165405 0.5958425998687744 209.04014587402344 0.39595383405685425 289.6141662597656 0.2769789397716522 0.7606106 0.33890342712402344 True -19 56540 30.408118724822998 0.597968339920044 217.96771240234375 0.29198384284973145 289.6501770019531 0.2767241299152374 0.7596048 0.3390011787414551 False diff --git a/ENCSR990XXC/cherimoya.fold_4.performance.tsv b/ENCSR990XXC/cherimoya.fold_4.performance.tsv deleted file mode 100644 index de1282172455455f4a4f566cdd3a81647d6ea1a3..0000000000000000000000000000000000000000 --- a/ENCSR990XXC/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -289.6141662597656 0.4930751621723175 0.2769789397716522 0.08274900168180466 0.7606105804443359 0.7160313129425049 0.33890342712402344 \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_0.evaluate.json b/ENCSR993XED/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 45d1aaeb1240e9096f5a0ef1025fd9414ba5c07c..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF451RXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_0.fit.json b/ENCSR993XED/cherimoya.fold_0.fit.json deleted file mode 100644 index e79f3b593b4ee0d851ea08d2b534618deddc0afa..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF451RXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_0.log b/ENCSR993XED/cherimoya.fold_0.log deleted file mode 100644 index 5fa188c088197e4daebd823b1ef68f292dcdc47a..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1917 26.74045705795288 4.521697998046875 347.3774108886719 1.168414831161499 598.8685302734375 0.48131394386291504 0.60958153 13.691356658935547 True -1 3834 21.34099793434143 0.3906383514404297 343.59228515625 1.4651265144348145 470.5918884277344 0.613298237323761 0.6952711 5.6118388175964355 True -2 5751 21.12829303741455 13.569972276687622 332.3553466796875 0.5974051356315613 433.2290344238281 0.6577635407447815 0.7030972 1.5056171417236328 True -3 7668 20.886533737182617 0.36885738372802734 312.77685546875 1.1125248670578003 420.58380126953125 0.6699897646903992 0.71564484 0.850407063961029 True -4 9585 20.884211540222168 0.36991357803344727 274.92034912109375 0.9896852970123291 416.4565734863281 0.6751962900161743 0.7202311 0.7641027569770813 True -5 11502 20.894243240356445 0.37006187438964844 389.4259033203125 0.8044624924659729 415.0014343261719 0.6784988045692444 0.72353953 0.7515431046485901 True -6 13419 20.89523673057556 0.36611318588256836 313.4395751953125 0.7418621778488159 412.9311218261719 0.6809251308441162 0.7293368 0.7180114388465881 True -7 15336 20.893324375152588 0.3619365692138672 307.921630859375 0.636834979057312 410.9000549316406 0.6839250922203064 0.7341048 0.7047492861747742 True -8 17253 20.83624243736267 0.3665907382965088 348.2779541015625 1.0196336507797241 408.9118957519531 0.6863316893577576 0.73948824 0.6805120706558228 True -9 19170 21.085774660110474 0.36712026596069336 280.7738952636719 0.6951800584793091 406.9777526855469 0.6891030669212341 0.74765515 0.6551439762115479 True -10 21087 20.86397886276245 1.111302375793457 277.7655334472656 0.5183655023574829 405.3235778808594 0.6916162371635437 0.7535877 0.6386477947235107 True -11 23004 20.891218662261963 0.36148881912231445 306.23797607421875 0.5666429400444031 404.69635009765625 0.6928980946540833 0.7619766 0.6277504563331604 True -12 24921 20.856290102005005 0.37230396270751953 307.1264953613281 0.623989999294281 403.1850280761719 0.6952105164527893 0.76563007 0.6177870035171509 True -13 26838 20.858620643615723 0.36612892150878906 323.40087890625 0.665300726890564 401.92108154296875 0.6969515681266785 0.771817 0.5963482856750488 True -14 28755 20.8870849609375 0.36550235748291016 295.0438537597656 0.6799445748329163 401.2836608886719 0.6979535818099976 0.7770732 0.5880832076072693 True -15 30672 20.89429807662964 1.689399003982544 344.39288330078125 0.3686036765575409 401.3400573730469 0.6978809237480164 0.78064734 0.5883089303970337 True -16 32589 21.293179988861084 16.360938549041748 268.78631591796875 0.496657133102417 401.58355712890625 0.6973804831504822 0.78164154 0.5993839502334595 True -17 34506 21.2810001373291 0.3934366703033447 281.1672668457031 0.2627682089805603 401.98651123046875 0.6968116760253906 0.77919775 0.6223200559616089 False -18 36423 20.91721510887146 0.3634378910064697 286.438232421875 0.5393964052200317 402.48699951171875 0.696067214012146 0.7764294 0.6419870257377625 False -19 38340 20.862018585205078 0.36850929260253906 344.208984375 0.2541753649711609 402.6825866699219 0.6956424713134766 0.77625304 0.6526285409927368 False diff --git a/ENCSR993XED/cherimoya.fold_0.performance.tsv b/ENCSR993XED/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 10bfb050eab35125f54b3ac530a35812022a9524..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -401.58355712890625 0.2551736533641815 0.6973804831504822 0.27683669328689575 0.7816415429115295 0.7421858906745911 0.5993839502334595 \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_1.evaluate.json b/ENCSR993XED/cherimoya.fold_1.evaluate.json deleted file mode 100644 index afdeea7069c9aeb56b4876644b714ba6fc748561..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF451RXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_1.fit.json b/ENCSR993XED/cherimoya.fold_1.fit.json deleted file mode 100644 index a1dca3278d5e2ca8575b57127a26d7e74f606fdf..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF451RXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_1.log b/ENCSR993XED/cherimoya.fold_1.log deleted file mode 100644 index 011e7b997722b84afd745c4a9a4887d7a6b68265..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1888 25.374821424484253 3.933833599090576 351.0059509277344 1.1659929752349854 698.7241821289062 0.4943183362483978 0.5915219 15.041338920593262 True -1 3776 21.025012969970703 0.580237865447998 286.1007385253906 1.355943202972412 539.8776245117188 0.6313911080360413 0.7029104 6.679028034210205 True -2 5664 21.020031929016113 0.5372357368469238 254.9196319580078 0.9563944339752197 493.7474060058594 0.6855917572975159 0.70839727 2.0109851360321045 True -3 7552 21.195297718048096 0.5370519161224365 359.4484558105469 0.8464834690093994 477.5964660644531 0.6986560225486755 0.7316566 1.07369863986969 True -4 9440 21.08419394493103 0.5404543876647949 345.6158447265625 1.2115541696548462 472.6121826171875 0.7034890651702881 0.7308844 0.8974503874778748 False -5 11328 21.000574827194214 19.666533946990967 356.8270263671875 0.7812024354934692 469.5780944824219 0.7063989639282227 0.7381397 0.8041965365409851 True -6 13216 22.367520570755005 0.545630931854248 385.2389831542969 0.9484086632728577 467.3385009765625 0.7093385457992554 0.74150085 0.7602108120918274 True -7 15104 21.005507469177246 0.5441527366638184 294.6297912597656 0.8040741682052612 465.1026306152344 0.7121145129203796 0.74113464 0.764110267162323 False -8 16992 20.68717074394226 0.5352113246917725 305.19659423828125 0.865720808506012 463.07342529296875 0.714979350566864 0.7491719 0.7129610776901245 True -9 18880 20.549598217010498 0.5329558849334717 295.88616943359375 0.5827999711036682 460.7003479003906 0.7175975441932678 0.75407183 0.6766636967658997 True -10 20768 20.595372438430786 0.5377175807952881 343.50457763671875 0.7024656534194946 459.0762023925781 0.7197651863098145 0.7616839 0.6573993563652039 True -11 22656 20.57710599899292 0.5296037197113037 320.95880126953125 0.6724741458892822 457.1804504394531 0.7215915322303772 0.77195436 0.6330773234367371 True -12 24544 20.5899875164032 0.5334553718566895 279.8608093261719 0.7742382287979126 455.3365783691406 0.7237536311149597 0.7801774 0.6050724387168884 True -13 26432 20.600812435150146 0.5305912494659424 328.0892028808594 0.6200979948043823 453.8075866699219 0.72552889585495 0.7879763 0.5896246433258057 True -14 28320 20.661009550094604 0.5285599231719971 279.3153381347656 0.4471954107284546 453.09796142578125 0.7262855768203735 0.79397434 0.5775960087776184 True -15 30208 20.59205460548401 0.5362980365753174 303.4016418457031 0.5566472411155701 453.0027160644531 0.7266923189163208 0.7960525 0.5848343372344971 True -16 32096 20.595174074172974 0.536475658416748 271.57513427734375 0.429624080657959 452.8840637207031 0.7264580726623535 0.79889643 0.59650719165802 True -17 33984 20.585285186767578 0.5395233631134033 362.9600524902344 0.2925507128238678 453.5276184082031 0.7256390452384949 0.79709005 0.6253155469894409 False -18 35872 20.599626064300537 0.5281581878662109 293.7656555175781 0.4239746630191803 454.2701721191406 0.7247102856636047 0.7936033 0.6512772440910339 False -19 37760 20.607133626937866 0.527803897857666 274.1643371582031 0.4818042814731598 454.7419128417969 0.7242261171340942 0.7923739 0.6678901314735413 False diff --git a/ENCSR993XED/cherimoya.fold_1.performance.tsv b/ENCSR993XED/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 714a8a63db4077ad884282d1204277497d42e932..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -452.8840637207031 0.23254181444644928 0.7264580726623535 0.3087744116783142 0.7988964319229126 0.7844971418380737 0.59650719165802 \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_2.evaluate.json b/ENCSR993XED/cherimoya.fold_2.evaluate.json deleted file mode 100644 index b9a9e1bcdd936a0d3f11c6e31466a8e216009c3e..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF451RXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_2.fit.json b/ENCSR993XED/cherimoya.fold_2.fit.json deleted file mode 100644 index ab0f09f1d78a1158b1114aa6e0aa0c42eec172d4..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF451RXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_2.log b/ENCSR993XED/cherimoya.fold_2.log deleted file mode 100644 index 465b8bdde8fe7e765fcca7e388f8da7b3b201a22..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2032 26.950841903686523 5.368593454360962 355.4267578125 1.5006649494171143 628.4580078125 0.49470746517181396 0.58549047 12.723671913146973 True -1 4064 22.60930848121643 0.4171905517578125 379.4351806640625 0.931870698928833 487.1669921875 0.6313809156417847 0.699115 5.048534393310547 True -2 6096 22.63513994216919 0.3894195556640625 336.7718505859375 1.1639121770858765 453.685302734375 0.6687231659889221 0.7154583 1.5403964519500732 True -3 8128 22.619475603103638 0.40432310104370117 354.3146057128906 0.7164890766143799 442.64892578125 0.6786304712295532 0.7283239 1.0204932689666748 True -4 10160 22.620323657989502 0.3912961483001709 334.5492858886719 0.7511340379714966 439.0322265625 0.6828123331069946 0.7326587 0.8998449444770813 True -5 12192 22.57871127128601 26.916157960891724 375.341064453125 1.1668994426727295 436.96026611328125 0.6851884126663208 0.73418176 0.88368821144104 True -6 14224 25.16063094139099 0.4359264373779297 356.61956787109375 0.9868654608726501 435.3489685058594 0.6872285008430481 0.7341345 0.8643962740898132 False -7 16256 22.61800479888916 0.3888683319091797 329.36907958984375 0.8624792695045471 433.0678405761719 0.6897772550582886 0.73975176 0.7978077530860901 True -8 18288 22.689719438552856 0.3820953369140625 351.1444396972656 0.8869369029998779 431.2025451660156 0.6924158930778503 0.74680036 0.7813167572021484 True -9 20320 22.983243465423584 1.367868185043335 311.7703857421875 0.9068208932876587 429.4500732421875 0.6946500539779663 0.75048965 0.7707887291908264 True -10 22352 22.64030933380127 1.5435607433319092 316.5869140625 0.8276077508926392 427.3481140136719 0.6972131133079529 0.7589934 0.7276319265365601 True -11 24384 22.626463174819946 0.39681196212768555 291.5596923828125 0.9133222103118896 426.00738525390625 0.699141800403595 0.7608614 0.7024877071380615 True -12 26416 22.64103364944458 0.3882596492767334 338.4324951171875 0.5477789640426636 424.035888671875 0.7013980746269226 0.76889706 0.6588559746742249 True -13 28448 22.680218935012817 0.3812265396118164 318.227294921875 0.6549009084701538 423.09130859375 0.702739953994751 0.77527195 0.6483539342880249 True -14 30480 22.62643265724182 0.38506054878234863 346.22735595703125 0.951645016670227 421.9603576660156 0.7035874128341675 0.781513 0.6332016587257385 True -15 32512 22.59568428993225 0.4142270088195801 280.99224853515625 0.3717730641365051 421.5322265625 0.7042138576507568 0.7840769 0.6298007369041443 True -16 34544 22.58494544029236 1.844651222229004 307.2974548339844 0.4279043972492218 421.38861083984375 0.7042338848114014 0.7848559 0.6350767016410828 True -17 36576 23.066964864730835 29.72035002708435 356.29498291015625 0.47193074226379395 421.8095703125 0.7036131620407104 0.7831129 0.6496379375457764 False -18 38608 24.27740168571472 0.39866113662719727 236.9375 0.41860315203666687 422.45489501953125 0.7027537822723389 0.7803785 0.6651113629341125 False -19 40640 22.155990600585938 0.38358259201049805 331.01446533203125 0.35967013239860535 422.7947692871094 0.7024132609367371 0.77813774 0.6763347387313843 False diff --git a/ENCSR993XED/cherimoya.fold_2.performance.tsv b/ENCSR993XED/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 0758e957e02c0e2344378772dd7dd9384ccc2d3e..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -421.38861083984375 0.24883924424648285 0.7042338848114014 0.2870889902114868 0.7848559021949768 0.7589044570922852 0.6350767016410828 \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_3.evaluate.json b/ENCSR993XED/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 9f7a4c1292d4696a37208b6e181460f55960810e..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF451RXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_3.fit.json b/ENCSR993XED/cherimoya.fold_3.fit.json deleted file mode 100644 index d05c98c8c45f8aa8e9ce78250ea2684df1f68d60..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF451RXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_3.log b/ENCSR993XED/cherimoya.fold_3.log deleted file mode 100644 index 157a26eceba65379d50c9b29923e0ab537495b71..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1953 27.03091597557068 2.0665981769561768 327.1817321777344 1.2528190612792969 608.8549194335938 0.4872831106185913 0.5705949 13.166711807250977 True -1 3906 21.732368230819702 0.3728792667388916 352.5771484375 1.143075942993164 476.8056640625 0.619324803352356 0.6656252 5.129777431488037 True -2 5859 21.769255876541138 0.3738560676574707 393.9622802734375 0.87729412317276 438.3443298339844 0.6641712188720703 0.6694708 1.6821240186691284 True -3 7812 21.708962440490723 2.6286895275115967 422.70135498046875 0.8087130784988403 428.4841003417969 0.6735796332359314 0.68047 1.0818731784820557 True -4 9765 21.723932027816772 0.36855125427246094 349.4373474121094 0.9000136256217957 423.9361572265625 0.6787182688713074 0.69014627 0.9238789677619934 True -5 11718 21.733153343200684 0.3672051429748535 318.5943603515625 1.2309200763702393 422.4892883300781 0.6810860633850098 0.6960539 0.932152271270752 True -6 13671 21.736940622329712 0.3664274215698242 348.0211181640625 0.7250691652297974 420.33392333984375 0.6839767098426819 0.70254 0.8795667886734009 True -7 15624 21.969710111618042 0.3847057819366455 286.83770751953125 0.8646376132965088 418.7519836425781 0.6862181425094604 0.7016727 0.8303899168968201 False -8 17577 21.8438241481781 0.3678882122039795 309.75836181640625 0.985737681388855 417.2021484375 0.6883142590522766 0.710711 0.8329803943634033 True -9 19530 21.732781171798706 1.4738340377807617 263.4540710449219 0.9521271586418152 415.2210693359375 0.6913310885429382 0.7202272 0.7888821959495544 True -10 21483 21.807016372680664 2.2326114177703857 311.695068359375 0.7456861734390259 414.1767578125 0.6929397583007812 0.7238614 0.7735242247581482 True -11 23436 21.731043338775635 0.3656742572784424 267.84991455078125 0.6860707998275757 412.2673645019531 0.6955618262290955 0.7319042 0.7403542995452881 True -12 25389 21.742305755615234 0.37217020988464355 288.0058898925781 0.6761654615402222 410.5784606933594 0.6973083019256592 0.7410087 0.716167688369751 True -13 27342 21.81536340713501 0.3644278049468994 297.90325927734375 0.4467189908027649 409.8955993652344 0.6985898613929749 0.7456026 0.7118459939956665 True -14 29295 22.889541149139404 27.462903022766113 330.50531005859375 0.5366895198822021 408.8716125488281 0.6996403336524963 0.7528979 0.6949244141578674 True -15 31248 22.10520315170288 0.419238805770874 261.423828125 0.3992214798927307 408.3089294433594 0.7000783085823059 0.75502914 0.6944988369941711 True -16 33201 21.727057695388794 0.3693423271179199 261.3262023925781 0.6537588834762573 408.61651611328125 0.6996250152587891 0.7588917 0.7060648798942566 True -17 35154 21.73240351676941 0.3674449920654297 289.5581970214844 0.4322548508644104 408.9128112792969 0.6989179253578186 0.7591371 0.721253514289856 True -18 37107 21.863130807876587 6.5191240310668945 349.5388488769531 0.29364824295043945 409.2439270019531 0.6980663537979126 0.75535685 0.7418165802955627 False -19 39060 21.764012575149536 0.3625457286834717 339.7257080078125 0.5395040512084961 409.66400146484375 0.6976538896560669 0.75384915 0.7548133730888367 False diff --git a/ENCSR993XED/cherimoya.fold_3.performance.tsv b/ENCSR993XED/cherimoya.fold_3.performance.tsv deleted file mode 100644 index c85703dced918cfd2417b086a4819f83fd4e55f6..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -408.9128112792969 0.2510416507720947 0.6989178657531738 0.2820301055908203 0.7591370940208435 0.7307021617889404 0.721253514289856 \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_4.evaluate.json b/ENCSR993XED/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3f45265d995b52da7ae8fba4cdf9bd38cdb4a47c..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF451RXE.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_4.fit.json b/ENCSR993XED/cherimoya.fold_4.fit.json deleted file mode 100644 index 9223cc1b7f2d9f81c554f768027bf246e5b6f57a..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF451RXE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR993XED/cherimoya.fold_4.log b/ENCSR993XED/cherimoya.fold_4.log deleted file mode 100644 index 778ef679bda44ac40254b59cd84007b84adf5c43..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1935 25.943822860717773 3.316098690032959 355.54046630859375 0.8627648949623108 589.9722290039062 0.47664403915405273 0.5672327 12.82275104522705 True -1 3870 21.532792806625366 0.3657803535461426 344.88873291015625 1.130028247833252 461.12701416015625 0.6045761108398438 0.66927034 4.865912914276123 True -2 5805 21.550448656082153 0.7930901050567627 281.7661437988281 0.8075000047683716 425.2422180175781 0.6530806422233582 0.69491297 1.830741286277771 True -3 7740 21.491695165634155 0.35599470138549805 332.43194580078125 0.5976216793060303 414.6137390136719 0.6627302169799805 0.7047187 1.056280493736267 True -4 9675 21.565726280212402 1.0032742023468018 281.1573486328125 1.266784906387329 410.5375061035156 0.6667374968528748 0.7184198 0.8592032194137573 True -5 11610 21.51897096633911 15.948612928390503 341.44580078125 0.7140060663223267 407.95904541015625 0.6698678731918335 0.7225758 0.7925420999526978 True -6 13545 24.412885904312134 25.95389676094055 398.67034912109375 0.7494151592254639 406.0619812011719 0.672642707824707 0.72555405 0.7397234439849854 True -7 15480 23.897679805755615 22.494281768798828 334.60211181640625 0.9995394945144653 404.5607604980469 0.6750102043151855 0.72725844 0.7359678149223328 True -8 17415 24.99656057357788 26.012134075164795 297.338623046875 0.5659236907958984 402.7419738769531 0.6770694851875305 0.7312461 0.7249469757080078 True -9 19350 22.91076350212097 0.3582313060760498 329.41925048828125 0.7453560829162598 401.2288818359375 0.6792035102844238 0.7400518 0.6961576342582703 True -10 21285 21.10035753250122 0.35323095321655273 330.286865234375 0.6505091190338135 399.2569885253906 0.6813890337944031 0.7456406 0.6743034720420837 True -11 23220 21.09216594696045 0.35218334197998047 350.3029479980469 0.4853910207748413 397.823974609375 0.6835500001907349 0.74960816 0.6612974405288696 True -12 25155 21.06578302383423 0.351581335067749 347.5975341796875 0.5927928686141968 396.805908203125 0.6849589347839355 0.75548726 0.6450207829475403 True -13 27090 21.09527039527893 0.34868407249450684 356.3853759765625 0.8554601669311523 395.803466796875 0.6867281198501587 0.7624459 0.6345160007476807 True -14 29025 21.059190273284912 0.35382843017578125 291.6675109863281 0.6318619251251221 394.9550476074219 0.6882013082504272 0.77185076 0.6168195009231567 True -15 30960 21.09326410293579 1.070486068725586 329.6785583496094 0.6630082130432129 394.4119567871094 0.6885883212089539 0.7734768 0.6171457767486572 True -16 32895 21.073665857315063 0.35277533531188965 286.6305847167969 0.4311073124408722 394.6068420410156 0.6882791519165039 0.7754616 0.6185011863708496 True -17 34830 21.062061309814453 0.3499877452850342 299.86810302734375 0.5288556814193726 395.1669006347656 0.6876189112663269 0.7744249 0.6365697383880615 False -18 36765 21.094866275787354 0.34844422340393066 247.50108337402344 0.36375969648361206 395.57415771484375 0.6869916915893555 0.77100176 0.6573793888092041 False -19 38700 21.103480577468872 0.34966182708740234 245.78330993652344 0.43220579624176025 395.8985290527344 0.6865268349647522 0.7690605 0.6711500287055969 False diff --git a/ENCSR993XED/cherimoya.fold_4.performance.tsv b/ENCSR993XED/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ba85e200f9c3908b3294f5092c15a6c37a781b69..0000000000000000000000000000000000000000 --- a/ENCSR993XED/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -394.6068420410156 0.26030248403549194 0.6882791519165039 0.2718701660633087 0.7754616141319275 0.7353799939155579 0.6185011863708496 \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_0.evaluate.json b/ENCSR994KTY/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 8ed18104bceaa9e561036616384e9ed087bd61b7..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184EGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_0.fit.json b/ENCSR994KTY/cherimoya.fold_0.fit.json deleted file mode 100644 index 61d93d14e7da54b73f569da5ae1a19f6d5e8fe6b..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF184EGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_0.log b/ENCSR994KTY/cherimoya.fold_0.log deleted file mode 100644 index 6c6c563a50ff4f23825478b1e7854ed5e7bb5086..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2763 35.24293899536133 3.8098034858703613 526.96435546875 0.14198625087738037 629.1644287109375 0.2752707600593567 0.81772417 3.572676420211792 True -1 5526 30.43190860748291 0.6211645603179932 474.9754638671875 0.1536165028810501 594.80859375 0.31622520089149475 0.84726316 0.6858688592910767 True -2 8289 30.456114768981934 0.7109279632568359 569.2139892578125 0.1469149887561798 585.5264892578125 0.3253486156463623 0.87193394 0.29058292508125305 True -3 11052 30.33986234664917 0.5337364673614502 497.9747009277344 0.3437578082084656 583.8313598632812 0.32790324091911316 0.8750914 0.3165142834186554 True -4 13815 29.773010730743408 0.5435748100280762 521.2772827148438 0.1298673003911972 580.7431640625 0.3316250741481781 0.87777966 0.19589217007160187 True -5 16578 29.79025959968567 0.6121037006378174 490.7296142578125 0.11016468703746796 579.9437866210938 0.3331347107887268 0.88164973 0.18505844473838806 True -6 19341 29.835045099258423 0.5417141914367676 545.9151611328125 0.09647996723651886 578.527587890625 0.3352070152759552 0.8848634 0.18641643226146698 True -7 22104 29.84671449661255 0.5838398933410645 550.4907836914062 0.24410271644592285 577.0368041992188 0.3372580409049988 0.8875767 0.18074025213718414 True -8 24867 29.854491472244263 0.5386824607849121 538.4239501953125 0.21816283464431763 575.6365356445312 0.3390536308288574 0.8936925 0.163737952709198 True -9 27630 29.84371542930603 0.5761046409606934 593.4544067382812 0.15369540452957153 574.459228515625 0.3411846458911896 0.895927 0.15496115386486053 True -10 30393 29.835874557495117 0.5435183048248291 532.9429321289062 0.22605443000793457 573.39111328125 0.3426421284675598 0.8997726 0.14915838837623596 True -11 33156 29.769115924835205 0.729285717010498 520.911865234375 0.2083296775817871 572.0966796875 0.34435582160949707 0.9027955 0.14780837297439575 True -12 35919 29.83795475959778 0.6399531364440918 528.324951171875 0.11138435453176498 571.5758666992188 0.3452947735786438 0.90508544 0.13627594709396362 True -13 38682 29.857086658477783 0.5458905696868896 555.4832153320312 0.2016347348690033 570.1786499023438 0.347322553396225 0.9104088 0.12725947797298431 True -14 41445 29.806431531906128 0.581092119216919 506.587158203125 0.17125457525253296 568.952392578125 0.34952250123023987 0.9122597 0.11687736958265305 True -15 44208 29.852771997451782 0.553642749786377 563.9232177734375 0.08640672266483307 568.53173828125 0.34948521852493286 0.9158459 0.1060982197523117 True -16 46971 29.852334022521973 0.5440871715545654 472.87591552734375 0.07153697311878204 568.2717895507812 0.34988248348236084 0.9185555 0.09993407875299454 True -17 49734 29.804749727249146 0.5793015956878662 493.705078125 0.07746472954750061 567.9127807617188 0.35057610273361206 0.9204285 0.09646764397621155 True -18 52497 29.895151138305664 0.5672473907470703 502.79608154296875 0.09989526867866516 568.541259765625 0.349488228559494 0.9194182 0.09548886865377426 False -19 55260 29.83565878868103 0.5493166446685791 446.924560546875 0.09488993138074875 568.3445434570312 0.3500942289829254 0.92068547 0.0952899158000946 True diff --git a/ENCSR994KTY/cherimoya.fold_0.performance.tsv b/ENCSR994KTY/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e3a71920c305fca9552bc27dd76ba5222c7e9423..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -568.3445434570312 0.40222400426864624 0.3500942587852478 0.14192472398281097 0.9206854701042175 0.9029296040534973 0.0952899158000946 \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_1.evaluate.json b/ENCSR994KTY/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 2ae0723e890437b92229703b52c7f19ef6933607..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184EGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_1.fit.json b/ENCSR994KTY/cherimoya.fold_1.fit.json deleted file mode 100644 index 96e4f0eda2b171987c78e859c6f418dd11cbc513..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF184EGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_1.log b/ENCSR994KTY/cherimoya.fold_1.log deleted file mode 100644 index 7d4697f8f972f0f2b4b8c491c7916c8f2c92c008..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2731 34.90584921836853 4.088968515396118 477.8968811035156 0.14822274446487427 721.6043701171875 0.2768181562423706 0.8143187 3.9046614170074463 True -1 5462 30.027734756469727 0.6999225616455078 501.7624816894531 0.17762911319732666 681.3927001953125 0.3232470750808716 0.84465265 0.8541024923324585 True -2 8193 30.049508094787598 0.6842479705810547 522.734130859375 0.27585718035697937 666.8489379882812 0.3389398157596588 0.86803186 0.3298136293888092 True -3 10924 30.030911922454834 1.25612473487854 538.477294921875 0.17628148198127747 660.5958251953125 0.34471312165260315 0.8811309 0.23964054882526398 True -4 13655 30.070363521575928 1.3226733207702637 599.8646240234375 0.1683254837989807 657.0958862304688 0.34928005933761597 0.88511187 0.2982524633407593 True -5 16386 30.08693814277649 0.6855053901672363 458.3466796875 0.1526697725057602 656.8673095703125 0.3494798541069031 0.88676745 0.22413165867328644 True -6 19117 29.639862537384033 0.6736781597137451 498.18756103515625 0.16456860303878784 655.8018798828125 0.35142141580581665 0.8859409 0.22352170944213867 False -7 21848 29.445089101791382 0.661146879196167 498.6168212890625 0.13459447026252747 653.5818481445312 0.3541669249534607 0.88918024 0.2336791753768921 True -8 24579 29.449779510498047 0.6624009609222412 467.8265075683594 0.10512642562389374 651.7361450195312 0.356829434633255 0.8935469 0.21475471556186676 True -9 27310 29.457408905029297 0.6774170398712158 563.7825927734375 0.10099369287490845 649.999755859375 0.35912227630615234 0.89778006 0.19966037571430206 True -10 30041 29.50533962249756 0.6536238193511963 439.6814270019531 0.10030976682901382 648.4974365234375 0.36089667677879333 0.9027122 0.18711896240711212 True -11 32772 29.475444555282593 0.6491773128509521 634.811767578125 0.11844085156917572 646.8790283203125 0.36306121945381165 0.9048646 0.17572744190692902 True -12 35503 29.474250078201294 1.7754449844360352 586.6568603515625 0.130588561296463 644.9306640625 0.36550623178482056 0.9115925 0.15966492891311646 True -13 38234 29.558765649795532 23.9281644821167 533.3060302734375 0.13894972205162048 643.6793823242188 0.36685648560523987 0.9153695 0.1526607871055603 True -14 40965 29.500819206237793 15.566645622253418 510.8360290527344 0.0860590860247612 642.1976318359375 0.3694112300872803 0.9186945 0.1369997262954712 True -15 43696 29.51964497566223 0.6608283519744873 506.99560546875 0.11997951567173004 640.78173828125 0.37100598216056824 0.92112494 0.12419027835130692 True -16 46427 29.55960178375244 0.6634790897369385 515.256103515625 0.091734379529953 641.3903198242188 0.3699791729450226 0.92432046 0.116019107401371 True -17 49158 29.460521459579468 0.6662819385528564 518.7050170898438 0.07880058884620667 640.31787109375 0.3717607259750366 0.92684335 0.10912850499153137 True -18 51889 29.446539402008057 0.6548852920532227 471.76025390625 0.11721713095903397 640.4300537109375 0.37135589122772217 0.9263886 0.10673005878925323 False -19 54620 29.48824715614319 0.6534557342529297 538.2675170898438 0.07692410051822662 641.0963745117188 0.3701835870742798 0.9261865 0.10620692372322083 False diff --git a/ENCSR994KTY/cherimoya.fold_1.performance.tsv b/ENCSR994KTY/cherimoya.fold_1.performance.tsv deleted file mode 100644 index f01cdd0d787017cdb1511dbbf86ad56d5d5eab6c..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -640.31787109375 0.38421085476875305 0.371760755777359 0.16293613612651825 0.9268433451652527 0.9197932481765747 0.10912850499153137 \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_2.evaluate.json b/ENCSR994KTY/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7ce8be564e5c6db772126056b22d831ddfc7c4ad..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184EGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_2.fit.json b/ENCSR994KTY/cherimoya.fold_2.fit.json deleted file mode 100644 index 213e21a2786863f9f177656d86bee603a06dab8b..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF184EGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_2.log b/ENCSR994KTY/cherimoya.fold_2.log deleted file mode 100644 index 34afdb83edd9e831f9f4f44648e8f36b3f434cf9..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2897 36.46451663970947 4.845201730728149 567.488525390625 0.20902742445468903 668.8853149414062 0.2740497589111328 0.8064368 3.0095574855804443 True -1 5794 31.91560196876526 1.0724492073059082 497.7637023925781 0.22219815850257874 633.51123046875 0.3187064826488495 0.847789 0.6216422319412231 True -2 8691 31.92544198036194 0.5304529666900635 499.0238037109375 0.17083075642585754 624.9527587890625 0.32638752460479736 0.8648702 0.2697625458240509 True -3 11588 31.845789194107056 0.5250148773193359 537.63134765625 0.17992159724235535 620.3167724609375 0.3315538465976715 0.87347555 0.2714766561985016 True -4 14485 31.817999362945557 0.5172295570373535 571.3984375 0.24795591831207275 618.240478515625 0.3350931704044342 0.8759858 0.2252511978149414 True -5 17382 31.82574200630188 0.5246715545654297 554.9624633789062 0.09293191134929657 616.8738403320312 0.3370516896247864 0.8766186 0.2242647111415863 True -6 20279 31.86210036277771 0.5116205215454102 545.172119140625 0.14566290378570557 616.5606079101562 0.33745908737182617 0.87544143 0.22334478795528412 False -7 23176 31.3040509223938 0.5179646015167236 441.6232604980469 0.18563967943191528 615.3129272460938 0.33891478180885315 0.87946534 0.21603989601135254 True -8 26073 31.317410469055176 0.5204010009765625 415.74456787109375 0.1066754162311554 613.127197265625 0.34185105562210083 0.8837754 0.1947970688343048 True -9 28970 31.314022302627563 0.5169773101806641 578.6959228515625 0.08199985325336456 612.2914428710938 0.34336382150650024 0.8862388 0.18521332740783691 True -10 31867 31.350721836090088 0.5192289352416992 562.6600341796875 0.12183110415935516 610.8807983398438 0.3451084494590759 0.89122516 0.17578093707561493 True -11 34764 31.23229956626892 0.5214948654174805 575.9471435546875 0.19056227803230286 610.0157470703125 0.3460656702518463 0.8937452 0.1626104712486267 True -12 37661 31.29908275604248 0.5380589962005615 526.0927124023438 0.17118977010250092 608.2283935546875 0.34828028082847595 0.898999 0.15077918767929077 True -13 40558 31.29847502708435 0.5135316848754883 529.231201171875 0.10311977565288544 606.3915405273438 0.3510623276233673 0.9035211 0.1393568068742752 True -14 43455 31.307512760162354 0.52083420753479 486.56365966796875 0.1368713080883026 605.7364501953125 0.3518292009830475 0.90601766 0.12697818875312805 True -15 46352 31.266038417816162 0.5255692005157471 435.52056884765625 0.07950353622436523 605.2427978515625 0.3526172637939453 0.9083659 0.12014161795377731 True -16 49249 31.313855409622192 0.5219714641571045 498.1689453125 0.09109530597925186 604.9796142578125 0.3525947034358978 0.9109969 0.11289210617542267 True -17 52146 31.265607357025146 0.8259861469268799 457.5533142089844 0.22736254334449768 604.8321533203125 0.3530067801475525 0.9126985 0.10921815782785416 True -18 55043 31.30417013168335 0.5202076435089111 597.5780029296875 0.09549646079540253 605.1943359375 0.352439820766449 0.9125186 0.10796601325273514 False -19 57940 31.244612216949463 0.5181710720062256 493.74072265625 0.05993487685918808 605.2263793945312 0.35239094495773315 0.9133168 0.1077282577753067 True diff --git a/ENCSR994KTY/cherimoya.fold_2.performance.tsv b/ENCSR994KTY/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e306a8666887a66b9a333e879155a2f2cd43d769..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -605.2263793945312 0.3959255814552307 0.3523908853530884 0.14615033566951752 0.9133167862892151 0.9035147428512573 0.1077282577753067 \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_3.evaluate.json b/ENCSR994KTY/cherimoya.fold_3.evaluate.json deleted file mode 100644 index fa0496ce893fc68bc1ee36d2ae398b26a72d607b..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184EGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_3.fit.json b/ENCSR994KTY/cherimoya.fold_3.fit.json deleted file mode 100644 index ad6c9eb1c8fea92b07d79fa2d5374e2b00265482..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF184EGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_3.log b/ENCSR994KTY/cherimoya.fold_3.log deleted file mode 100644 index f584ea820a77dd949b81fcf09939844c20ccad4e..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2757 34.91021156311035 3.7226898670196533 497.8932189941406 0.13964341580867767 619.1011352539062 0.2812911868095398 0.7956447 3.637986898422241 True -1 5514 30.387487649917603 0.6319353580474854 526.874755859375 0.18948423862457275 590.0779418945312 0.3169998228549957 0.8283718 0.8684624433517456 True -2 8271 30.33000683784485 0.5710251331329346 569.7813720703125 0.278717964887619 579.2769775390625 0.3295416235923767 0.8533319 0.3469730019569397 True -3 11028 30.326854944229126 0.5450687408447266 510.20819091796875 0.0960492193698883 576.2246704101562 0.3329375982284546 0.8664512 0.30265316367149353 True -4 13785 30.32577109336853 0.5792129039764404 507.6441650390625 0.17310792207717896 574.2118530273438 0.33641648292541504 0.8672316 0.24631984531879425 True -5 16542 30.277599334716797 0.5553586483001709 509.494873046875 0.1327296495437622 571.9437866210938 0.34061676263809204 0.8674816 0.24399249255657196 True -6 19299 30.26637077331543 0.5452957153320312 566.2340087890625 0.1303369104862213 571.386474609375 0.3405424654483795 0.86991936 0.23750630021095276 True -7 22056 30.27497386932373 0.5451745986938477 527.8104248046875 0.18946397304534912 569.488037109375 0.34409967064857483 0.87414294 0.23612080514431 True -8 24813 29.76410484313965 0.5518383979797363 488.9764709472656 0.1115659847855568 568.8765869140625 0.3449212908744812 0.87646794 0.2286609262228012 True -9 27570 29.699512243270874 0.5528028011322021 518.1572265625 0.1264331042766571 566.9359741210938 0.34717926383018494 0.8822508 0.20632311701774597 True -10 30327 29.76331090927124 0.5646450519561768 489.7281188964844 0.1765022873878479 566.0429077148438 0.34850427508354187 0.88616854 0.19443345069885254 True -11 33084 29.83458638191223 0.5532011985778809 499.4928894042969 0.2140706330537796 564.7642211914062 0.35064494609832764 0.8893883 0.18665574491024017 True -12 35841 29.82388663291931 0.5972461700439453 467.12677001953125 0.14200422167778015 563.705078125 0.3518781363964081 0.8932522 0.17418621480464935 True -13 38598 29.85149073600769 0.5666191577911377 511.58404541015625 0.11675480753183365 563.5812377929688 0.35169821977615356 0.89763665 0.16274946928024292 True -14 41355 29.702030420303345 0.5964124202728271 480.26873779296875 0.06963430345058441 561.8624267578125 0.35461780428886414 0.90104675 0.14540687203407288 True -15 44112 29.818034172058105 0.5601241588592529 523.4346313476562 0.14009851217269897 561.2965698242188 0.35540589690208435 0.90505 0.12984676659107208 True -16 46869 29.894667863845825 0.5700769424438477 514.4955444335938 0.16971929371356964 560.516845703125 0.35637959837913513 0.9074069 0.12229349464178085 True -17 49626 29.868902921676636 0.5527303218841553 475.77056884765625 0.14117461442947388 560.8983154296875 0.3558187186717987 0.9083742 0.11779843270778656 True -18 52383 29.872928619384766 0.5489628314971924 560.115234375 0.07816900312900543 561.0298461914062 0.35532474517822266 0.9088032 0.11612098664045334 True -19 55140 29.816155195236206 0.5488207340240479 442.6337890625 0.10495171695947647 560.91357421875 0.35533207654953003 0.90788406 0.11599811166524887 False diff --git a/ENCSR994KTY/cherimoya.fold_3.performance.tsv b/ENCSR994KTY/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 98b82886b7d6d4a994b8d8cd49272d4e77865622..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -561.0298461914062 0.3996536433696747 0.35532474517822266 0.1442229300737381 0.9088032245635986 0.8903538584709167 0.11612098664045334 \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_4.evaluate.json b/ENCSR994KTY/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 3f6021309a83e9931dbc7543a894a7d45c480e4d..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF184EGS.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_4.fit.json b/ENCSR994KTY/cherimoya.fold_4.fit.json deleted file mode 100644 index 84840e387235a072c0dd949c484f881b0afc7467..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF184EGS.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR994KTY/cherimoya.fold_4.log b/ENCSR994KTY/cherimoya.fold_4.log deleted file mode 100644 index 23d69e67129efe5affe45a2de22c1e314bd7c826..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2777 35.51982045173645 5.5016560554504395 517.11669921875 0.1377134919166565 579.3043212890625 0.2704223692417145 0.8161141 3.004725217819214 True -1 5554 30.567495346069336 0.7101531028747559 555.9900512695312 0.25067681074142456 550.3287963867188 0.3102099895477295 0.85161096 0.5570021271705627 True -2 8331 30.535247564315796 0.6081621646881104 554.4622802734375 0.17143197357654572 542.8656616210938 0.3189004957675934 0.86852634 0.2448074221611023 True -3 11108 30.54328751564026 0.6118507385253906 576.6961669921875 0.21353739500045776 540.37890625 0.32165053486824036 0.87677294 0.1848088800907135 True -4 13885 30.518571138381958 0.6035666465759277 456.4053039550781 0.11147502809762955 540.1610717773438 0.3217502236366272 0.877836 0.19839732348918915 True -5 16662 30.474061965942383 0.615234375 501.1302490234375 0.15844964981079102 538.7175903320312 0.3240283131599426 0.8836558 0.17762361466884613 True -6 19439 30.475759506225586 0.617372989654541 486.8825378417969 0.11812479048967361 536.2508544921875 0.3278067111968994 0.8864953 0.15507464110851288 True -7 22216 30.831054210662842 0.6078190803527832 533.7638549804688 0.09711425751447678 535.9244995117188 0.327993780374527 0.8901427 0.1464296281337738 True -8 24993 30.844388484954834 18.447023153305054 524.03857421875 0.1037219688296318 535.2271118164062 0.32934778928756714 0.89318836 0.14774517714977264 True -9 27770 30.050848245620728 0.6132683753967285 564.1824951171875 0.1249803900718689 533.6723022460938 0.3317224681377411 0.8960993 0.1411592662334442 True -10 30547 29.915290355682373 0.6043457984924316 484.41064453125 0.0994751900434494 532.6248168945312 0.3334323763847351 0.8985578 0.13795742392539978 True -11 33324 29.969948291778564 0.6101155281066895 499.8496398925781 0.14981290698051453 532.4149780273438 0.33342260122299194 0.9013566 0.1274718940258026 True -12 36101 29.977909803390503 0.6043503284454346 476.70086669921875 0.0814787745475769 531.1650390625 0.3354041576385498 0.90375274 0.1183425784111023 True -13 38878 29.997316598892212 0.6138105392456055 513.179443359375 0.08136100322008133 530.416015625 0.33632922172546387 0.90951055 0.10810385644435883 True -14 41655 29.963399171829224 0.6079754829406738 575.0427856445312 0.12863996624946594 529.9266967773438 0.3374123275279999 0.91241485 0.10358346998691559 True -15 44432 30.07192373275757 0.6024794578552246 492.008544921875 0.13125857710838318 529.7931518554688 0.33705824613571167 0.91511464 0.09607966989278793 True -16 47209 30.079283714294434 0.619373083114624 529.3416137695312 0.09770410507917404 529.846435546875 0.33719977736473083 0.9181741 0.09030072391033173 True -17 49986 30.036397695541382 0.6247637271881104 507.8827819824219 0.11442548781633377 529.8018798828125 0.33738774061203003 0.9176552 0.08747316151857376 False -18 52763 30.035999059677124 0.6265065670013428 476.43267822265625 0.0913117378950119 529.5639038085938 0.3378583490848541 0.91966087 0.0865069329738617 True -19 55540 30.035106897354126 0.6086132526397705 509.18646240234375 0.04491061344742775 530.2535400390625 0.33638641238212585 0.91823214 0.08646298199892044 False diff --git a/ENCSR994KTY/cherimoya.fold_4.performance.tsv b/ENCSR994KTY/cherimoya.fold_4.performance.tsv deleted file mode 100644 index ff3a8682376d0b4b25f946122c4b223d7176608e..0000000000000000000000000000000000000000 --- a/ENCSR994KTY/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -529.5639038085938 0.4122450351715088 0.3378583490848541 0.1327003687620163 0.9196608662605286 0.8967592716217041 0.0865069329738617 \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_0.evaluate.json b/ENCSR996ZCR/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 5ed3e17bf2440d52bcb037ebb2467b9cb870f2e8..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF376ZAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_0.fit.json b/ENCSR996ZCR/cherimoya.fold_0.fit.json deleted file mode 100644 index f82cf8d552a05a752c938181bf566f35908f6946..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF376ZAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_0.log b/ENCSR996ZCR/cherimoya.fold_0.log deleted file mode 100644 index 57c0855714ecd7980d033a02a3b0e7229747d1aa..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3308 39.635398387908936 3.5318431854248047 542.3983154296875 0.4968078136444092 771.7355346679688 0.6957565546035767 0.7194338 3.644000768661499 True -1 6616 36.43067479133606 0.6515634059906006 573.2733764648438 0.34376686811447144 667.7276611328125 0.7668020725250244 0.77629685 0.8474040031433105 True -2 9924 36.55661058425903 0.6359426975250244 553.9039306640625 0.5291580557823181 656.6882934570312 0.7717677354812622 0.78325623 0.3976863920688629 True -3 13232 36.51688861846924 0.6328637599945068 513.4420776367188 0.3659892976284027 652.3009033203125 0.7739298939704895 0.78165364 0.39202433824539185 False -4 16540 36.410011529922485 0.634739875793457 604.5446166992188 0.24637311697006226 646.3588256835938 0.778716504573822 0.7796187 0.3528105318546295 False -5 19848 36.41818976402283 0.6340270042419434 483.9962158203125 0.41482654213905334 642.2113037109375 0.780829906463623 0.7862209 0.33286842703819275 True -6 23156 36.4138822555542 0.6325745582580566 595.4336547851562 0.316442608833313 640.9563598632812 0.782689094543457 0.78680193 0.3472857177257538 True -7 26464 36.38252663612366 0.6340823173522949 558.5159912109375 0.2862303853034973 637.8359375 0.7848381996154785 0.7913258 0.31519609689712524 True -8 29772 36.349597454071045 5.536421060562134 577.17626953125 0.46067744493484497 635.1785278320312 0.7870877981185913 0.7879075 0.3204192817211151 False -9 33080 36.44271421432495 0.6384978294372559 487.7247314453125 0.2328493446111679 632.219970703125 0.7891173958778381 0.7928394 0.3178659975528717 True -10 36388 36.408820152282715 0.6380085945129395 534.166259765625 0.3788941502571106 629.39306640625 0.7912333607673645 0.8027452 0.29978451132774353 True -11 39696 36.30597925186157 0.6364283561706543 501.083251953125 0.28324997425079346 626.8508911132812 0.7939136624336243 0.8101088 0.2925684154033661 True -12 43004 36.355228662490845 0.6286909580230713 532.7669677734375 0.29413267970085144 624.07568359375 0.79604172706604 0.8159023 0.28833842277526855 True -13 46312 36.379270792007446 1.0837266445159912 585.8378295898438 0.3266838788986206 622.4320678710938 0.7976106405258179 0.8218865 0.2807226777076721 True -14 49620 36.63170790672302 1.4366579055786133 552.763671875 0.24352967739105225 620.3508911132812 0.799479067325592 0.8289655 0.2716718912124634 True -15 52928 36.41675782203674 0.6380019187927246 615.7610473632812 0.23014220595359802 619.2476806640625 0.8004882335662842 0.83443797 0.26542940735816956 True -16 56236 36.435019969940186 0.641303300857544 606.8883056640625 0.2067568004131317 618.6439208984375 0.8009547591209412 0.8377292 0.26468807458877563 True -17 59544 36.40181016921997 0.6374285221099854 473.97265625 0.18132629990577698 619.287109375 0.8008055090904236 0.837085 0.2610930800437927 False -18 62852 36.39525389671326 0.6392824649810791 506.9794921875 0.20942112803459167 619.3280029296875 0.8004325032234192 0.8367954 0.2614680230617523 False -19 66160 36.39839053153992 0.6391465663909912 502.2557067871094 0.15984603762626648 619.7619018554688 0.8002288937568665 0.8359236 0.26340094208717346 False diff --git a/ENCSR996ZCR/cherimoya.fold_0.performance.tsv b/ENCSR996ZCR/cherimoya.fold_0.performance.tsv deleted file mode 100644 index e798e0f422f263caf8ace11b9131f86bc2bb67c3..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -618.6439208984375 0.16541549563407898 0.8009547591209412 0.4303463399410248 0.8377292156219482 0.7656587958335876 0.26468807458877563 \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_1.evaluate.json b/ENCSR996ZCR/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 6a927ecb13b44bf209a615a7d2d9ef9f28e11d62..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF376ZAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_1.fit.json b/ENCSR996ZCR/cherimoya.fold_1.fit.json deleted file mode 100644 index b819dfbd7c89e4eeb4f69a8f9f74f63541f05ad5..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF376ZAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_1.log b/ENCSR996ZCR/cherimoya.fold_1.log deleted file mode 100644 index 70cf860d5fc22e5526a55410e9314a48b0144446..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3245 39.368290185928345 3.8295958042144775 513.9268798828125 0.38095489144325256 892.24951171875 0.7033670544624329 0.7370124 4.4565205574035645 True -1 6490 35.71115326881409 1.442091464996338 667.348388671875 0.4284279942512512 753.5850219726562 0.7801803350448608 0.7880148 1.2801364660263062 True -2 9735 35.48043727874756 0.8755714893341064 548.4700927734375 0.33398517966270447 736.5056762695312 0.7891594171524048 0.7972715 0.5022736191749573 True -3 12980 35.03631353378296 0.8419194221496582 519.7850952148438 0.5189244151115417 730.8221435546875 0.7919284105300903 0.797223 0.47004395723342896 False -4 16225 35.01686358451843 1.5478875637054443 618.3394775390625 0.4217206537723541 727.0656127929688 0.7939828038215637 0.7988656 0.3971395194530487 True -5 19470 34.975499629974365 1.130049467086792 511.47412109375 0.3143036961555481 724.3190307617188 0.7960733771324158 0.80098915 0.4083257019519806 True -6 22715 35.00567030906677 2.4965693950653076 540.924072265625 0.3340268135070801 718.138916015625 0.7987196445465088 0.809306 0.387749046087265 True -7 25960 35.05464267730713 0.8597030639648438 516.8550415039062 0.4056961238384247 714.253662109375 0.8007364273071289 0.8164476 0.3766774833202362 True -8 29205 35.00267553329468 0.9152915477752686 563.4410400390625 0.2915393114089966 711.3760375976562 0.8021033406257629 0.81582475 0.35206329822540283 False -9 32450 35.040252447128296 0.857764720916748 522.6170654296875 0.2558545470237732 707.03759765625 0.8047282695770264 0.823248 0.3294360637664795 True -10 35695 34.977455854415894 0.8527617454528809 594.60546875 0.43284499645233154 702.9057006835938 0.8069331049919128 0.8286478 0.31434395909309387 True -11 38940 34.96141242980957 0.8492968082427979 528.4342041015625 0.22489239275455475 699.6989135742188 0.809211790561676 0.834809 0.3057958781719208 True -12 42185 35.03015613555908 0.8478827476501465 586.4141235351562 0.2936963438987732 696.392333984375 0.8115282654762268 0.84255356 0.2971622049808502 True -13 45430 34.996004819869995 0.8580422401428223 559.7181396484375 0.528239369392395 693.1737670898438 0.8136446475982666 0.8484717 0.28229448199272156 True -14 48675 34.98110604286194 0.8572039604187012 504.6503601074219 0.2675374746322632 690.6721801757812 0.8153812885284424 0.8542008 0.26989877223968506 True -15 51920 34.95667886734009 0.8611063957214355 549.9092407226562 0.18009647727012634 689.5570068359375 0.816352367401123 0.85961837 0.2574406862258911 True -16 55165 34.95606017112732 0.843707799911499 483.628662109375 0.2231837809085846 688.8099365234375 0.8170549869537354 0.86035955 0.25750112533569336 True -17 58410 34.954830169677734 0.849459171295166 642.617431640625 0.14264443516731262 689.0182495117188 0.8169854283332825 0.8615206 0.2548331618309021 True -18 61655 34.96012806892395 0.8406741619110107 484.7432556152344 0.1754656434059143 689.7982177734375 0.8165865540504456 0.8610798 0.25503143668174744 False -19 64900 34.93989372253418 0.8403809070587158 508.5323486328125 0.14977677166461945 690.2927856445312 0.8162946701049805 0.8590652 0.257284015417099 False diff --git a/ENCSR996ZCR/cherimoya.fold_1.performance.tsv b/ENCSR996ZCR/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 0d27c8b371810db52e585b7f5459aee1a0e53eaf..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -689.0182495117188 0.15024589002132416 0.816985547542572 0.46956077218055725 0.8615205883979797 0.828680157661438 0.2548331618309021 \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_2.evaluate.json b/ENCSR996ZCR/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 57f64321d23a95a43daf4a24cc1dde3f5afb1fe9..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF376ZAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_2.fit.json b/ENCSR996ZCR/cherimoya.fold_2.fit.json deleted file mode 100644 index 5f4dea9e6d081cb128d960a7849e29168eab2967..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF376ZAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_2.log b/ENCSR996ZCR/cherimoya.fold_2.log deleted file mode 100644 index a49758b836e48a2ab757f103f81ff25add8a87f0..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3439 41.87782096862793 3.647862672805786 549.397705078125 0.501181960105896 801.6832885742188 0.7036608457565308 0.7261785 3.6767783164978027 True -1 6878 37.86039733886719 0.715900182723999 558.054931640625 0.4104622006416321 696.2805786132812 0.7683359384536743 0.78332436 0.8645685315132141 True -2 10317 37.86375570297241 0.6888408660888672 555.5442504882812 0.4724726676940918 683.2435302734375 0.7767065763473511 0.7901673 0.38480547070503235 True -3 13756 37.36286020278931 0.6902625560760498 538.05224609375 0.3269524574279785 675.404052734375 0.7801789045333862 0.7986812 0.35223355889320374 True -4 17195 37.1295063495636 0.677990198135376 588.6481323242188 0.32117149233818054 672.2198486328125 0.7834682464599609 0.7955555 0.3256436586380005 False -5 20634 37.04432129859924 0.6792266368865967 612.00146484375 0.3567069470882416 667.8518676757812 0.7862937450408936 0.79927546 0.3423261046409607 True -6 24073 37.01159715652466 1.7942156791687012 539.972412109375 0.3879231810569763 664.6294555664062 0.7887961864471436 0.8008337 0.3345990478992462 True -7 27512 37.17728662490845 0.6907401084899902 576.536376953125 0.305040180683136 661.7568969726562 0.7903292775154114 0.805892 0.32451459765434265 True -8 30951 37.135364294052124 0.6777749061584473 566.4158935546875 0.3123783767223358 659.3364868164062 0.7922426462173462 0.80610347 0.3346608579158783 True -9 34390 37.13758373260498 0.682844877243042 475.8674011230469 0.32769912481307983 655.8121948242188 0.7942698001861572 0.8083056 0.32990211248397827 True -10 37829 37.213793992996216 0.6829104423522949 583.7176513671875 0.211800217628479 653.4240112304688 0.7961959838867188 0.81478524 0.31731152534484863 True -11 41268 37.202237129211426 0.677278995513916 509.56414794921875 0.29090362787246704 649.9772338867188 0.7984616756439209 0.823823 0.28971540927886963 True -12 44707 37.21711444854736 1.1538703441619873 574.9625854492188 0.3243228793144226 647.78857421875 0.8001821041107178 0.8282104 0.28868767619132996 True -13 48146 37.091795682907104 0.6813714504241943 598.5680541992188 0.22419752180576324 645.336181640625 0.8016039729118347 0.83593154 0.27217239141464233 True -14 51585 37.08201813697815 1.7853007316589355 491.52764892578125 0.15459957718849182 643.3304443359375 0.8032209873199463 0.8420043 0.2626636028289795 True -15 55024 37.181397438049316 0.6774814128875732 431.4162292480469 0.20306941866874695 642.630859375 0.8041011095046997 0.84669596 0.2567163407802582 True -16 58463 37.14800214767456 0.6850135326385498 612.8856201171875 0.16065481305122375 641.6401977539062 0.804583728313446 0.8482198 0.2520345449447632 True -17 61902 37.15285634994507 0.6790001392364502 610.8242797851562 0.15753494203090668 642.1832275390625 0.8044424057006836 0.84983355 0.24854248762130737 True -18 65341 37.18122982978821 0.6821162700653076 587.2667236328125 0.16332119703292847 642.6541137695312 0.8041698932647705 0.84943825 0.24860702455043793 False -19 68780 37.14346790313721 1.5477988719940186 499.4019470214844 0.12731871008872986 642.8779296875 0.8039137125015259 0.84787244 0.2499212622642517 False diff --git a/ENCSR996ZCR/cherimoya.fold_2.performance.tsv b/ENCSR996ZCR/cherimoya.fold_2.performance.tsv deleted file mode 100644 index ad92e7b4067b8a470448f464cc1ce50e1b932d3c..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -642.1832275390625 0.16060125827789307 0.8044424057006836 0.4448011815547943 0.8498335480690002 0.7913970351219177 0.24854248762130737 \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_3.evaluate.json b/ENCSR996ZCR/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 0f823a934232a62c4f2c70f967b1020ca0276e39..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF376ZAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_3.fit.json b/ENCSR996ZCR/cherimoya.fold_3.fit.json deleted file mode 100644 index b5b3f4e58e7f6343869d7a84bc3047c99753fdcb..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF376ZAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_3.log b/ENCSR996ZCR/cherimoya.fold_3.log deleted file mode 100644 index 5c759db783ad37150bd2bf483933c12b3c8b04a7..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3335 40.40389084815979 3.5596745014190674 610.8453979492188 0.6248632669448853 762.3392944335938 0.6954790949821472 0.72409314 4.122409820556641 True -1 6670 36.660900354385376 0.663719892501831 568.4627075195312 0.4239286780357361 666.9205322265625 0.7644860148429871 0.76885116 0.8774244785308838 True -2 10005 36.70473504066467 0.6513910293579102 569.181396484375 0.3693333864212036 653.0411987304688 0.7720544338226318 0.77790624 0.532640814781189 True -3 13340 36.745256185531616 0.6525897979736328 549.759521484375 0.32914814352989197 647.4300537109375 0.775053858757019 0.7763377 0.4694850444793701 False -4 16675 35.98947358131409 0.6358699798583984 613.7786865234375 0.32175126671791077 644.8387451171875 0.777593195438385 0.7743427 0.40224629640579224 False -5 20010 35.983792543411255 0.6388907432556152 636.2763061523438 0.3837911784648895 641.454345703125 0.7794938683509827 0.78550464 0.38248756527900696 True -6 23345 36.03803825378418 0.6408336162567139 526.8248291015625 0.3621845245361328 638.1690673828125 0.7816274166107178 0.78478026 0.37549278140068054 False -7 26680 36.15648031234741 0.6669626235961914 545.18994140625 0.27750295400619507 634.1156616210938 0.7840083241462708 0.7894147 0.36628231406211853 True -8 30015 36.19357347488403 0.6554555892944336 586.6022338867188 0.18341851234436035 631.980712890625 0.7864415645599365 0.79677576 0.35961881279945374 True -9 33350 36.012800216674805 0.6543498039245605 497.4579772949219 0.3019506335258484 629.734619140625 0.7878488302230835 0.79718417 0.34862032532691956 True -10 36685 36.05474543571472 23.282363653182983 554.85986328125 0.21172967553138733 627.019287109375 0.789874255657196 0.80223596 0.3529222905635834 True -11 40020 36.5852415561676 0.6452462673187256 520.904541015625 0.2936663031578064 624.2643432617188 0.7920823693275452 0.8077353 0.3346748650074005 True -12 43355 35.97429943084717 0.6381838321685791 526.44287109375 0.3368735909461975 621.7692260742188 0.7942383885383606 0.81644773 0.31722092628479004 True -13 46690 35.98087000846863 0.6444847583770752 578.5523681640625 0.2556349039077759 619.77294921875 0.7960770726203918 0.82123464 0.30633091926574707 True -14 50025 36.05899620056152 0.6367301940917969 517.4784545898438 0.17829808592796326 617.6220092773438 0.7976155877113342 0.82875466 0.2971179783344269 True -15 53360 36.064051389694214 0.6394467353820801 553.8271484375 0.20556429028511047 616.3802490234375 0.7987273335456848 0.8345135 0.28108081221580505 True -16 56695 36.012219190597534 0.6368968486785889 494.4279479980469 0.1985042691230774 615.7437133789062 0.7991721630096436 0.8373383 0.2735375165939331 True -17 60030 36.02100419998169 0.6371843814849854 546.8629760742188 0.21259962022304535 615.531982421875 0.7991824746131897 0.8370612 0.2730962038040161 False -18 63365 36.038219690322876 2.394399404525757 501.068359375 0.14094801247119904 615.9439086914062 0.7988926768302917 0.8361428 0.2745521664619446 False -19 66700 36.05472993850708 0.6374428272247314 508.381591796875 0.11734701693058014 616.572265625 0.7986050248146057 0.83556825 0.276437371969223 False diff --git a/ENCSR996ZCR/cherimoya.fold_3.performance.tsv b/ENCSR996ZCR/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 0a22b109c8cf5baae226db0b63e451bc92ffbeee..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -615.7437133789062 0.16649699211120605 0.7991721034049988 0.4250909984111786 0.8373383283615112 0.7679024934768677 0.2735375165939331 \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_4.evaluate.json b/ENCSR996ZCR/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6b0d99585a5c1386dda9ec3045466d422f2bc234..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF376ZAM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_4.fit.json b/ENCSR996ZCR/cherimoya.fold_4.fit.json deleted file mode 100644 index 74f5ccd34838833cf4460fd87b93674901dc9044..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF376ZAM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR996ZCR/cherimoya.fold_4.log b/ENCSR996ZCR/cherimoya.fold_4.log deleted file mode 100644 index 15f3906c5326d9acb678b385904c5777ba47de58..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 3334 42.64750599861145 4.669323921203613 544.4932861328125 0.4471731185913086 743.4295654296875 0.6901804208755493 0.71241957 3.8007256984710693 True -1 6668 36.74305057525635 0.682765007019043 536.0491333007812 0.36071768403053284 647.1434936523438 0.7599588632583618 0.76413256 0.8221379518508911 True -2 10002 36.711108446121216 0.6558074951171875 519.8333740234375 0.5091286301612854 631.6514282226562 0.7700861692428589 0.77727515 0.3522939682006836 True -3 13336 36.76713562011719 0.6695950031280518 603.6073608398438 0.4119793772697449 626.416748046875 0.773786723613739 0.7820865 0.33471086621284485 True -4 16670 36.799789905548096 0.6668567657470703 510.73797607421875 0.3203732371330261 623.2798461914062 0.7754066586494446 0.786827 0.31629058718681335 True -5 20004 36.173301219940186 0.6593711376190186 621.853271484375 0.36237475275993347 620.1985473632812 0.7782135605812073 0.79215103 0.325545996427536 True -6 23338 36.203932762145996 0.6545889377593994 591.8936767578125 0.3061462640762329 617.5145263671875 0.7803292870521545 0.79368037 0.29293373227119446 True -7 26672 36.2023983001709 0.6497402191162109 559.6521606445312 0.35201284289360046 615.3109741210938 0.7825074791908264 0.7923439 0.2889798581600189 False -8 30006 36.204307317733765 0.6588339805603027 542.6396484375 0.3335345983505249 612.59619140625 0.7846844792366028 0.8003416 0.2845351994037628 True -9 33340 36.15935659408569 0.6483273506164551 561.5233764648438 0.2455468773841858 609.5872192382812 0.7870850563049316 0.8035923 0.2797991633415222 True -10 36674 36.13183522224426 0.6532440185546875 521.9881591796875 0.3130747675895691 607.1163330078125 0.7888283133506775 0.8077756 0.2720508277416229 True -11 40008 36.11214733123779 0.6643874645233154 519.3606567382812 0.3185683786869049 605.340087890625 0.7908447980880737 0.8137421 0.26941078901290894 True -12 43342 36.213051557540894 0.6535344123840332 555.6660766601562 0.3035948574542999 603.2345581054688 0.792489767074585 0.8176892 0.26330313086509705 True -13 46676 36.30836749076843 0.6576473712921143 521.9486694335938 0.2526477575302124 600.9639282226562 0.7946328520774841 0.82232946 0.25767362117767334 True -14 50010 36.17884063720703 0.6498730182647705 542.1055908203125 0.22938573360443115 599.5554809570312 0.7960024476051331 0.8273739 0.25554051995277405 True -15 53344 36.18782925605774 0.6504862308502197 570.8433837890625 0.1833031177520752 598.673095703125 0.7970826029777527 0.83441657 0.24708768725395203 True -16 56678 36.18536376953125 2.019145965576172 508.3955383300781 0.22438818216323853 598.1568603515625 0.7976891398429871 0.83819634 0.24050816893577576 True -17 60012 36.09599852561951 2.067615032196045 493.6953125 0.24014750123023987 598.7969360351562 0.7974580526351929 0.8384662 0.24218735098838806 True -18 63346 36.15145826339722 0.6589441299438477 513.1380615234375 0.11950479447841644 599.17822265625 0.7971444725990295 0.8390634 0.24303452670574188 True -19 66680 36.14930081367493 1.4718713760375977 519.5647583007812 0.22661343216896057 599.4926147460938 0.7970147728919983 0.8385742 0.2428484559059143 False diff --git a/ENCSR996ZCR/cherimoya.fold_4.performance.tsv b/ENCSR996ZCR/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 80503788ae2ce9e57bd62cada7dbfb1951d85797..0000000000000000000000000000000000000000 --- a/ENCSR996ZCR/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -599.17822265625 0.16915446519851685 0.7971444725990295 0.4205054044723511 0.8390634059906006 0.7577423453330994 0.24303452670574188 \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_0.evaluate.json b/ENCSR998IXQ/cherimoya.fold_0.evaluate.json deleted file mode 100644 index b8a3a1a9c2da4e59a2639a9bde3879fdc9b83f0a..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637TOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_0.fit.json b/ENCSR998IXQ/cherimoya.fold_0.fit.json deleted file mode 100644 index cc2626128396a7ad2f4ab5f1df41915c46e97adc..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF637TOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_0.log b/ENCSR998IXQ/cherimoya.fold_0.log deleted file mode 100644 index fcc9eeabf1489940d932fc88cfe7e333554402ca..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1828 24.612337827682495 3.7910547256469727 295.533447265625 1.0794875621795654 428.3592834472656 0.14709225296974182 0.65416855 10.040220260620117 True -1 3656 20.101476192474365 0.37766313552856445 313.8226013183594 0.8529590368270874 379.420654296875 0.21026962995529175 0.77264196 4.542496681213379 True -2 5484 20.100000143051147 0.3999612331390381 232.97970581054688 0.9334056377410889 347.281494140625 0.2348870187997818 0.8050687 1.9025343656539917 True -3 7312 20.124743700027466 0.3854329586029053 299.8270263671875 0.7424190044403076 341.1363525390625 0.2411661297082901 0.8145842 1.2191987037658691 True -4 9140 20.071128606796265 0.3603332042694092 354.246337890625 1.0744622945785522 337.7294616699219 0.2457875907421112 0.8253328 0.871026873588562 True -5 10968 20.074997901916504 0.364349365234375 342.378662109375 0.7755037546157837 335.3243103027344 0.2484193593263626 0.835578 0.7997581958770752 True -6 12796 20.063806295394897 0.36852240562438965 265.3002624511719 0.7027401328086853 334.01019287109375 0.2508372366428375 0.8394185 0.7807876467704773 True -7 14624 20.09622359275818 0.3653123378753662 235.1990966796875 0.6851252317428589 331.3716735839844 0.2555210292339325 0.8460413 0.7174996137619019 True -8 16452 20.069267749786377 0.3649630546569824 276.828857421875 0.8200098276138306 330.43731689453125 0.2558620274066925 0.84973574 0.676536500453949 True -9 18280 20.073673725128174 0.3621950149536133 224.43601989746094 0.5659884810447693 329.5793762207031 0.2565527856349945 0.8558394 0.6157242059707642 True -10 20108 20.07762360572815 0.4190535545349121 284.22265625 0.9179580807685852 327.4784240722656 0.2602243721485138 0.86030126 0.5790058374404907 True -11 21936 20.102813482284546 0.3864564895629883 267.65130615234375 0.40789780020713806 327.0860595703125 0.2602134943008423 0.8650184 0.5388380289077759 True -12 23764 20.075752019882202 0.37294745445251465 220.58251953125 0.5582959055900574 325.66705322265625 0.2626659870147705 0.8701012 0.5079973936080933 True -13 25592 20.075103521347046 0.37032055854797363 236.71714782714844 0.5682445168495178 324.6551818847656 0.2636972963809967 0.8748936 0.48868173360824585 True -14 27420 20.09961462020874 0.3663332462310791 230.51797485351562 0.460796058177948 323.838134765625 0.26479747891426086 0.8765487 0.47655776143074036 True -15 29248 20.118118286132812 0.3615901470184326 274.4620056152344 0.3612273931503296 322.5243225097656 0.266879141330719 0.8777744 0.46720221638679504 True -16 31076 20.133028984069824 0.36976170539855957 288.081298828125 0.32366064190864563 322.7303771972656 0.2668861448764801 0.8785672 0.4649132490158081 True -17 32904 20.097376585006714 0.360579252243042 253.7078857421875 0.36419519782066345 323.1765441894531 0.26585716009140015 0.87754905 0.4673873484134674 False -18 34732 20.092848777770996 0.4057650566101074 283.91851806640625 0.22121453285217285 324.26513671875 0.26334822177886963 0.8761456 0.47414472699165344 False -19 36560 19.819263696670532 0.358839750289917 232.8272247314453 0.43492287397384644 325.0167541503906 0.2622087895870209 0.8774074 0.48187533020973206 False diff --git a/ENCSR998IXQ/cherimoya.fold_0.performance.tsv b/ENCSR998IXQ/cherimoya.fold_0.performance.tsv deleted file mode 100644 index 9543c4ee63e7a14c3ad0f583cac1e1318c68569c..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -322.7303771972656 0.5040085315704346 0.2668861448764801 0.09188520908355713 0.8785672187805176 0.821805477142334 0.4649132490158081 \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_1.evaluate.json b/ENCSR998IXQ/cherimoya.fold_1.evaluate.json deleted file mode 100644 index ff7dea6296ff6a7439ff9411bd547a742b3c69f1..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637TOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_1.fit.json b/ENCSR998IXQ/cherimoya.fold_1.fit.json deleted file mode 100644 index d18c7e16e36890fcf6cd723845566350ca459be1..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF637TOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_1.log b/ENCSR998IXQ/cherimoya.fold_1.log deleted file mode 100644 index ed29322908764a0d0ab461e1c16e2e9bb30d7460..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1771 23.87474012374878 5.005970478057861 197.15228271484375 0.8814657926559448 523.2897338867188 0.15882796049118042 0.6387275 11.939517974853516 True -1 3542 19.427168369293213 0.5337197780609131 245.68978881835938 0.9655517339706421 460.9906311035156 0.23175866901874542 0.7640021 5.897111415863037 True -2 5313 19.409071683883667 0.5160746574401855 258.218017578125 0.6802616119384766 422.1739501953125 0.2617471218109131 0.813296 2.83803129196167 True -3 7084 19.424839973449707 0.5284795761108398 316.65264892578125 0.6346036195755005 415.23931884765625 0.2695768177509308 0.81580484 2.174156665802002 True -4 8855 19.43411946296692 0.513460636138916 245.47775268554688 0.6419682502746582 410.6282043457031 0.2746187746524811 0.82683897 1.5706342458724976 True -5 10626 19.454185962677002 0.522197961807251 266.9895935058594 0.8423690795898438 406.72802734375 0.2795768082141876 0.83755857 1.2803103923797607 True -6 12397 19.44507122039795 0.532888650894165 330.69244384765625 0.583149254322052 403.96771240234375 0.2825806140899658 0.845658 1.080458641052246 True -7 14168 19.492088317871094 0.5125298500061035 258.23443603515625 0.7449830770492554 402.24237060546875 0.28420278429985046 0.85213417 0.9891257882118225 True -8 15939 19.509718894958496 0.5668900012969971 215.39370727539062 0.6200720071792603 400.4921569824219 0.28581053018569946 0.860635 0.833667516708374 True -9 17710 19.440986394882202 13.196322917938232 276.74658203125 0.652010440826416 398.04119873046875 0.2891724705696106 0.8662814 0.7584294080734253 True -10 19481 19.468361377716064 0.5384979248046875 246.22506713867188 0.672888994216919 395.968994140625 0.2907831370830536 0.8738655 0.6709282994270325 True -11 21252 19.78346037864685 14.289495468139648 207.99594116210938 0.8633140325546265 395.4852600097656 0.2913016676902771 0.8799739 0.6173995137214661 True -12 23023 19.717714071273804 0.5308103561401367 295.1751708984375 0.7328429222106934 392.9063720703125 0.2945886552333832 0.8814902 0.5844824314117432 True -13 24794 19.47139263153076 0.5282268524169922 289.1419982910156 0.5548797845840454 391.626953125 0.2957099974155426 0.888112 0.5309202075004578 True -14 26565 19.49090576171875 0.5173311233520508 237.76170349121094 0.5709586143493652 390.3445739746094 0.2971261143684387 0.8911317 0.5109978914260864 True -15 28336 19.481534004211426 0.5147361755371094 251.6596221923828 0.30018749833106995 390.4191589355469 0.2961566150188446 0.89425516 0.49258702993392944 True -16 30107 19.49146819114685 0.5251703262329102 208.19229125976562 0.40380334854125977 389.2839660644531 0.29804596304893494 0.89508396 0.48453134298324585 True -17 31878 19.48976731300354 0.509047269821167 243.40853881835938 0.5796258449554443 390.5599670410156 0.29587316513061523 0.8953886 0.48764652013778687 True -18 33649 19.485092163085938 0.508941650390625 258.42047119140625 0.6511414051055908 391.4976501464844 0.29381486773490906 0.8943918 0.4958311915397644 False -19 35420 19.4906964302063 0.5085947513580322 272.6038513183594 0.2638278305530548 391.4248352050781 0.29415571689605713 0.89385134 0.501254677772522 False diff --git a/ENCSR998IXQ/cherimoya.fold_1.performance.tsv b/ENCSR998IXQ/cherimoya.fold_1.performance.tsv deleted file mode 100644 index a9e735c00f458c6bd7cdb0b6373c2a16092da701..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -390.5599670410156 0.47773417830467224 0.29587316513061523 0.10808441042900085 0.8953886032104492 0.8594011664390564 0.48764652013778687 \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_2.evaluate.json b/ENCSR998IXQ/cherimoya.fold_2.evaluate.json deleted file mode 100644 index af9b094497b0342692be393948a82d446a3d1fdd..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637TOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_2.fit.json b/ENCSR998IXQ/cherimoya.fold_2.fit.json deleted file mode 100644 index c9afec9be4b5d5828d25287ff24ed34c6f66cb9e..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF637TOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_2.log b/ENCSR998IXQ/cherimoya.fold_2.log deleted file mode 100644 index 5560de2bcf69d793ecdf5bf246cf869d0bdb9e9d..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1909 25.51336407661438 3.6695444583892822 383.3853759765625 1.1500167846679688 425.81304931640625 0.1447620391845703 0.6248635 10.502365112304688 True -1 3818 20.970839977264404 0.4136319160461426 259.76507568359375 0.45306313037872314 369.8545837402344 0.21219022572040558 0.7547131 4.491589069366455 True -2 5727 20.964378356933594 0.3972806930541992 272.77874755859375 0.6469541192054749 343.6065979003906 0.23579567670822144 0.8079095 1.9449102878570557 True -3 7636 20.974353551864624 0.4544665813446045 277.9239501953125 0.6100889444351196 338.03582763671875 0.23943579196929932 0.8158334 1.3180357217788696 True -4 9545 20.956521034240723 0.3998265266418457 193.42376708984375 0.7636394500732422 333.1912841796875 0.24493135511875153 0.8262791 0.9546827077865601 True -5 11454 20.981268882751465 0.3951427936553955 261.22503662109375 0.6417715549468994 332.3540954589844 0.24653030931949615 0.83191353 0.8891950845718384 True -6 13363 20.983846426010132 0.395266056060791 275.1195068359375 0.8186759948730469 329.47650146484375 0.24969056248664856 0.8393935 0.7787814140319824 True -7 15272 20.614357471466064 0.39478492736816406 250.16799926757812 0.7408391237258911 328.28515625 0.25107115507125854 0.8471727 0.7536522746086121 True -8 17181 20.518235206604004 0.39690637588500977 244.31695556640625 0.5883675217628479 326.4439392089844 0.25342658162117004 0.85270506 0.672070324420929 True -9 19090 20.55379891395569 0.3813648223876953 312.9121398925781 0.8856921792030334 324.83251953125 0.2563959062099457 0.8565186 0.60489422082901 True -10 20999 20.52077007293701 0.3815944194793701 229.92428588867188 0.5585389137268066 323.6238708496094 0.25764384865760803 0.86230445 0.5463405251502991 True -11 22908 20.531257152557373 0.38726234436035156 222.63101196289062 0.8688859343528748 322.0090026855469 0.25979265570640564 0.8670266 0.5113533139228821 True -12 24817 20.55447292327881 0.38619351387023926 291.0869140625 0.6039613485336304 321.5074157714844 0.26065561175346375 0.86804956 0.5015155673027039 True -13 26726 20.5422203540802 0.4872126579284668 218.0747528076172 0.403133749961853 320.2652282714844 0.26206064224243164 0.872609 0.4919278919696808 True -14 28635 20.5559401512146 0.3902597427368164 345.5921630859375 0.5366926193237305 319.432861328125 0.2634565234184265 0.873172 0.4726715385913849 True -15 30544 20.550036907196045 0.3958144187927246 288.89013671875 0.3478567600250244 319.0533447265625 0.2640817165374756 0.87595224 0.4657381474971771 True -16 32453 20.578438758850098 0.39540863037109375 270.1658935546875 0.35826221108436584 319.3681335449219 0.26255136728286743 0.8766155 0.46464353799819946 True -17 34362 20.583543300628662 0.39676427841186523 283.3009033203125 0.5127255916595459 319.3192443847656 0.2623838782310486 0.87598634 0.46931007504463196 False -18 36271 20.581661224365234 0.39495420455932617 226.37545776367188 0.4135870933532715 320.364501953125 0.2609046399593353 0.8750111 0.4750538170337677 False -19 38180 20.514291286468506 0.39374208450317383 229.61705017089844 0.22645530104637146 320.183349609375 0.26167482137680054 0.87401205 0.4806690812110901 False diff --git a/ENCSR998IXQ/cherimoya.fold_2.performance.tsv b/ENCSR998IXQ/cherimoya.fold_2.performance.tsv deleted file mode 100644 index 381929fec099118a204f3639e657e89fcdfa285b..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -319.3681335449219 0.5055866241455078 0.2625513970851898 0.08953607827425003 0.8766155242919922 0.8231868147850037 0.46464353799819946 \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_3.evaluate.json b/ENCSR998IXQ/cherimoya.fold_3.evaluate.json deleted file mode 100644 index a213b718b6996efcfc39539be21ca2a4745a1819..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637TOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_3.fit.json b/ENCSR998IXQ/cherimoya.fold_3.fit.json deleted file mode 100644 index cf381fac9763be377ae67d0760926d8b80744897..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF637TOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_3.log b/ENCSR998IXQ/cherimoya.fold_3.log deleted file mode 100644 index 0ec7fae62059eafc476586ccdfb9a72ddc2b33bf..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1828 24.394575834274292 3.538443088531494 261.7314453125 0.7227455973625183 436.1346740722656 0.15951061248779297 0.61966527 10.596162796020508 True -1 3656 20.033158540725708 0.36494016647338867 312.6864318847656 0.7244164943695068 387.6609191894531 0.22506268322467804 0.745492 5.092762470245361 True -2 5484 20.095863342285156 0.4444129467010498 337.57489013671875 0.7689701318740845 361.9812927246094 0.2481774091720581 0.7896887 2.248427152633667 True -3 7312 20.075592041015625 0.400468111038208 258.7999267578125 0.7651669383049011 354.8731689453125 0.2548254132270813 0.8011497 1.4833543300628662 True -4 9140 20.054681539535522 0.35856199264526367 226.34579467773438 0.5567337274551392 351.6424560546875 0.2594878673553467 0.80497986 1.2242389917373657 True -5 10968 20.11705708503723 0.3571648597717285 284.11956787109375 0.665125846862793 349.83392333984375 0.2614513635635376 0.8101395 1.1679096221923828 True -6 12796 20.086718320846558 0.35645389556884766 220.3604736328125 0.4388299584388733 347.3956298828125 0.26557937264442444 0.81428397 1.109713077545166 True -7 14624 20.042171478271484 0.36099839210510254 228.52049255371094 0.6453298330307007 345.4641418457031 0.2684375047683716 0.8250907 0.9552372097969055 True -8 16452 20.030032634735107 0.3604440689086914 278.222412109375 0.5747650861740112 344.078125 0.2699781060218811 0.8311913 0.8614479899406433 True -9 18280 20.08249592781067 0.3597543239593506 224.38912963867188 0.7000873684883118 342.2169494628906 0.2730141580104828 0.83530736 0.7746362090110779 True -10 20108 20.07184410095215 1.3453667163848877 324.8856201171875 0.5288575291633606 341.6998596191406 0.2728341817855835 0.84355474 0.7152508497238159 True -11 21936 20.083872318267822 0.379730224609375 246.5127410888672 0.6067858934402466 339.96063232421875 0.2751593589782715 0.84992266 0.6643525958061218 True -12 23764 20.12335181236267 0.3686859607696533 320.1217041015625 0.6870729923248291 339.2590026855469 0.2755512595176697 0.85555756 0.613140881061554 True -13 25592 20.102924346923828 0.3682107925415039 276.7596435546875 0.4914066195487976 338.1133728027344 0.27767592668533325 0.8620438 0.5733447074890137 True -14 27420 20.070103406906128 0.40167975425720215 256.83282470703125 0.5384319424629211 335.935302734375 0.28074899315834045 0.86541855 0.5493318438529968 True -15 29248 20.101871252059937 0.37075257301330566 289.8642578125 0.6013473868370056 336.0247802734375 0.2799760103225708 0.8692707 0.5337226390838623 True -16 31076 20.111847400665283 0.369781494140625 216.24212646484375 0.6497743129730225 336.1310729980469 0.27932560443878174 0.8706669 0.5298874378204346 True -17 32904 20.035553693771362 12.019821882247925 312.53082275390625 0.4145648777484894 336.41632080078125 0.27862003445625305 0.87157255 0.5297576785087585 True -18 34732 22.302212476730347 0.3846704959869385 288.35955810546875 0.8235533237457275 337.10076904296875 0.2779932916164398 0.87082976 0.534020185470581 False -19 36560 19.717185497283936 0.3676412105560303 204.1790313720703 0.46340346336364746 337.0481262207031 0.27821049094200134 0.8707487 0.5377880334854126 False diff --git a/ENCSR998IXQ/cherimoya.fold_3.performance.tsv b/ENCSR998IXQ/cherimoya.fold_3.performance.tsv deleted file mode 100644 index 9d55f1c2bb533524d8d3768990cabe562d41b8a1..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -336.41632080078125 0.49347740411758423 0.27862003445625305 0.08852648735046387 0.8715725541114807 0.8238024115562439 0.5297576785087585 \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_4.evaluate.json b/ENCSR998IXQ/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 635e8f56eae0c1b5a125dc2f14c7355e379431ab..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF637TOM.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_4.fit.json b/ENCSR998IXQ/cherimoya.fold_4.fit.json deleted file mode 100644 index ae907a94ee024834b93e2eb56fed879268ad28eb..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF637TOM.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR998IXQ/cherimoya.fold_4.log b/ENCSR998IXQ/cherimoya.fold_4.log deleted file mode 100644 index db3090a43c989eb590e40c7c21b4ccabb7e3fc94..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 1825 24.59977102279663 3.9220733642578125 365.7699890136719 0.8142017126083374 384.5682678222656 0.14121660590171814 0.629605 8.935833930969238 True -1 3650 20.082671403884888 0.4483978748321533 186.26834106445312 0.898592472076416 346.4554748535156 0.19814397394657135 0.73879385 3.78225040435791 True -2 5475 20.138500928878784 0.46929454803466797 321.8510437011719 0.7328732013702393 321.174072265625 0.22222045063972473 0.7981444 1.7396595478057861 True -3 7300 20.040400505065918 0.658294677734375 248.2960205078125 0.9481263756752014 314.7105407714844 0.23013290762901306 0.80525887 1.2968802452087402 True -4 9125 20.02947759628296 0.38910698890686035 271.53173828125 0.6196165084838867 311.2311706542969 0.2330089956521988 0.81492823 0.9122771620750427 True -5 10950 20.052635431289673 0.36408543586730957 300.6966552734375 0.7186003923416138 308.79119873046875 0.23519092798233032 0.82345176 0.7864401340484619 True -6 12775 20.082738399505615 0.37715673446655273 351.8670349121094 0.5247204303741455 306.1274108886719 0.23908460140228271 0.8271716 0.7341687679290771 True -7 14600 20.080137968063354 0.3910048007965088 247.481201171875 0.8673048615455627 305.78704833984375 0.23823079466819763 0.8328273 0.6910569667816162 True -8 16425 20.094871044158936 0.380434513092041 306.63702392578125 0.7627447843551636 303.572998046875 0.24242623150348663 0.84064007 0.6383352279663086 True -9 18250 20.05433988571167 0.7567241191864014 293.9433898925781 0.5301131010055542 302.8921813964844 0.24384398758411407 0.8450164 0.5958859324455261 True -10 20075 20.076204299926758 0.38216161727905273 324.60205078125 0.7064129710197449 301.6129150390625 0.24544300138950348 0.84906864 0.5468432307243347 True -11 21900 20.040098428726196 0.38863635063171387 262.1640625 0.5354553461074829 299.9432373046875 0.24838024377822876 0.85267746 0.5307309627532959 True -12 23725 20.073120594024658 0.3661978244781494 272.49090576171875 0.6096217632293701 298.75921630859375 0.25042977929115295 0.85837066 0.5035859942436218 True -13 25550 20.043432235717773 0.36081528663635254 253.96266174316406 0.6763924956321716 298.2881774902344 0.250186949968338 0.8616544 0.48595255613327026 True -14 27375 20.02913475036621 0.36052823066711426 164.76051330566406 0.405225545167923 296.70916748046875 0.25313514471054077 0.86522317 0.46785596013069153 True -15 29200 20.032898426055908 0.3624122142791748 328.26434326171875 0.3692982792854309 297.08929443359375 0.25169673562049866 0.86910653 0.4574056565761566 True -16 31025 20.028775453567505 0.3648338317871094 174.5703125 0.3228001594543457 296.8531188964844 0.2523077428340912 0.87203574 0.4537738263607025 True -17 32850 20.070990800857544 0.3599696159362793 239.25006103515625 0.39297255873680115 297.09576416015625 0.2516190707683563 0.87079805 0.45552071928977966 False -18 34675 20.05277967453003 0.36503124237060547 284.4949951171875 0.31680870056152344 297.69830322265625 0.25027376413345337 0.87038976 0.4617031514644623 False -19 36500 20.026461601257324 0.3616952896118164 238.39207458496094 0.4281047582626343 298.0021057128906 0.2496694177389145 0.8690388 0.4644860029220581 False diff --git a/ENCSR998IXQ/cherimoya.fold_4.performance.tsv b/ENCSR998IXQ/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1f3ce3133f6ca3f3be82fcad0bb89f47de24dbbd..0000000000000000000000000000000000000000 --- a/ENCSR998IXQ/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -296.8531188964844 0.5144265294075012 0.2523077428340912 0.08269752562046051 0.8720357418060303 0.8099709749221802 0.4537738263607025 \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_0.evaluate.json b/ENCSR999VDH/cherimoya.fold_0.evaluate.json deleted file mode 100644 index 9d80cd0dda5aab4c553c5863593ad23ce55070cd..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_0.evaluate.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr8", - "chr20" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_0.bed", - "valid_peaks.fold_0.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_0.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_0", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_0.bed", - "valid_nonpeaks.fold_0.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_0.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653PIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr2", - "chr4", - "chr5", - "chr7", - "chr9", - "chr10", - "chr11", - "chr12", - "chr13", - "chr14", - "chr15", - "chr16", - "chr17", - "chr18", - "chr19", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr8", - "chr20" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_0.fit.json b/ENCSR999VDH/cherimoya.fold_0.fit.json deleted file mode 100644 index 2f93ed5903064abedbfdd4b3496d2870f3795858..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_0.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF653PIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_0.log b/ENCSR999VDH/cherimoya.fold_0.log deleted file mode 100644 index 5a4b7b8da7a859e74e44b70d2a99cd52fc5992ac..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_0.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2803 34.68797779083252 3.6120798587799072 758.28564453125 0.9379760026931763 1150.4061279296875 0.284054696559906 0.67033964 6.86047887802124 True -1 5606 31.063913822174072 0.5736575126647949 1010.7445068359375 1.1985511779785156 964.8505249023438 0.3730132281780243 0.74864143 3.3359882831573486 True -2 8409 31.099825143814087 0.5700869560241699 864.9720458984375 0.45498567819595337 942.7770385742188 0.3812756836414337 0.7569126 1.861952304840088 True -3 11212 32.36974549293518 9.892635822296143 616.725341796875 0.6171673536300659 936.6632080078125 0.3832315504550934 0.7590309 1.5063731670379639 True -4 14015 31.104281663894653 0.5662882328033447 783.1398315429688 0.7518950700759888 924.1713256835938 0.3866236209869385 0.7699294 1.073555827140808 True -5 16818 31.09101676940918 0.5646424293518066 961.9594116210938 0.9592845439910889 917.5736083984375 0.38678693771362305 0.7778504 0.8990476131439209 True -6 19621 31.061076402664185 2.80314040184021 708.7567138671875 0.8620180487632751 902.6947631835938 0.39447021484375 0.78670037 0.8650829195976257 True -7 22424 31.00637698173523 0.5551624298095703 604.6124267578125 0.8142072558403015 898.311279296875 0.3952380418777466 0.7936463 0.8312139511108398 True -8 25227 30.982543468475342 0.5634448528289795 890.0675048828125 0.5467556715011597 895.422119140625 0.3978933095932007 0.8002831 0.8352019786834717 True -9 28030 30.941545248031616 0.58978271484375 663.9486083984375 0.6341637969017029 888.66748046875 0.40176495909690857 0.80816394 0.7938549518585205 True -10 30833 31.036250829696655 0.5541143417358398 625.5269775390625 0.5571444034576416 882.4742431640625 0.40512245893478394 0.8127371 0.7530784606933594 True -11 33636 30.949201822280884 0.5600719451904297 650.5919189453125 0.3546103537082672 880.2823486328125 0.40482690930366516 0.8164285 0.7001785635948181 True -12 36439 31.001675844192505 0.5604305267333984 813.2713623046875 0.683285653591156 874.1052856445312 0.40787699818611145 0.826885 0.6288139820098877 True -13 39242 31.0276997089386 0.5562384128570557 611.670166015625 0.4406468868255615 871.6784057617188 0.40778106451034546 0.83095914 0.5789178609848022 True -14 42045 31.05174493789673 0.5561282634735107 825.5411376953125 0.562016487121582 865.7450561523438 0.410908579826355 0.8367858 0.5234230160713196 True -15 44848 31.03290629386902 0.5640442371368408 713.8284301757812 0.2627527117729187 864.7245483398438 0.41236600279808044 0.8448576 0.4828663170337677 True -16 47651 31.101457118988037 0.5551095008850098 649.6560668945312 0.4021713137626648 864.5297241210938 0.41196751594543457 0.8474813 0.45125383138656616 True -17 50454 31.05312991142273 0.5625486373901367 861.9129638671875 0.3012152314186096 861.742919921875 0.4143883287906647 0.8506689 0.4349552094936371 True -18 53257 30.960553884506226 0.5555503368377686 778.2623291015625 0.48176079988479614 864.273193359375 0.4128987491130829 0.8492222 0.4323284327983856 False -19 56060 31.09484624862671 0.5661990642547607 636.705322265625 0.36380791664123535 862.9213256835938 0.4145810902118683 0.84996676 0.4335033893585205 False diff --git a/ENCSR999VDH/cherimoya.fold_0.performance.tsv b/ENCSR999VDH/cherimoya.fold_0.performance.tsv deleted file mode 100644 index a07f730b33d29e0e6567277b04914740c52a070f..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_0.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -861.742919921875 0.37481606006622314 0.4143883287906647 0.17727920413017273 0.8506689071655273 0.8024683594703674 0.4349552094936371 \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_1.evaluate.json b/ENCSR999VDH/cherimoya.fold_1.evaluate.json deleted file mode 100644 index 23e9d89bab18fdf746f30443acf4e2ccf8d7dccb..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_1.evaluate.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr12", - "chr17" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_1.bed", - "valid_peaks.fold_1.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_1.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_1", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_1.bed", - "valid_nonpeaks.fold_1.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_1.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653PIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr3", - "chr4", - "chr5", - "chr6", - "chr7", - "chr10", - "chr11", - "chr13", - "chr14", - "chr15", - "chr18", - "chr19", - "chr20", - "chr21", - "chr22", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr12", - "chr17" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_1.fit.json b/ENCSR999VDH/cherimoya.fold_1.fit.json deleted file mode 100644 index 799c82900a8c2822d3f033ff19e3cd59729b2e01..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_1.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF653PIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_1.log b/ENCSR999VDH/cherimoya.fold_1.log deleted file mode 100644 index 32c4388ab438f64296950f6a4a92e06e38c84db1..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_1.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2685 33.765087366104126 3.792846918106079 647.9669189453125 0.606920063495636 1385.8375244140625 0.284148633480072 0.67005354 8.918843269348145 True -1 5370 29.711063146591187 0.7683262825012207 1066.21826171875 0.9133050441741943 1156.623291015625 0.38072633743286133 0.749825 3.345517158508301 True -2 8055 29.675748825073242 0.7378151416778564 682.0167236328125 0.8944126963615417 1119.7705078125 0.39271166920661926 0.76110333 1.823837399482727 True -3 10740 30.20447826385498 9.28403115272522 762.265380859375 0.876147985458374 1103.436279296875 0.3978176414966583 0.77544737 1.390284538269043 True -4 13425 29.742511510849 0.7636868953704834 768.09521484375 0.7178528308868408 1088.6527099609375 0.4023629426956177 0.7818377 1.3116378784179688 True -5 16110 29.828452348709106 0.7538073062896729 740.2425537109375 0.7017542123794556 1077.815673828125 0.40530696511268616 0.7919377 1.1754069328308105 True -6 18795 29.964784145355225 0.7628769874572754 1059.0245361328125 0.6203480958938599 1072.302001953125 0.406589150428772 0.79722595 1.0532387495040894 True -7 21480 29.79250979423523 0.9584884643554688 683.4962768554688 0.7458054423332214 1064.1337890625 0.40966901183128357 0.8033484 0.9116811752319336 True -8 24165 29.99916911125183 11.023133277893066 848.519775390625 0.4554454982280731 1052.9033203125 0.4148010313510895 0.8109199 0.9100511074066162 True -9 26850 30.039704084396362 1.28670072555542 824.3428344726562 0.6064901351928711 1048.7689208984375 0.41626614332199097 0.81821823 0.8710616827011108 True -10 29535 29.74259042739868 1.5254344940185547 719.4276123046875 0.4040873050689697 1043.299072265625 0.41683387756347656 0.8264254 0.8175541758537292 True -11 32220 29.723626613616943 1.131401538848877 918.06884765625 0.8380590677261353 1032.043212890625 0.42382675409317017 0.833918 0.7492198348045349 True -12 34905 29.798299312591553 12.17037582397461 644.4031372070312 0.3941824734210968 1026.187744140625 0.42518359422683716 0.8419694 0.6757275462150574 True -13 37590 29.906474828720093 0.7436521053314209 621.3864135742188 0.43558740615844727 1023.2557373046875 0.42526641488075256 0.8489855 0.6134780049324036 True -14 40275 29.76145601272583 0.7402641773223877 618.3201904296875 0.395969957113266 1018.3135375976562 0.4271107316017151 0.85478646 0.5708635449409485 True -15 42960 29.822905778884888 0.7499580383300781 746.951904296875 0.39317139983177185 1018.6467895507812 0.42619577050209045 0.85918164 0.5124339461326599 True -16 45645 29.74713945388794 0.7510519027709961 832.070556640625 0.455687940120697 1013.7474365234375 0.4298030436038971 0.8650004 0.4713785946369171 True -17 48330 29.839415311813354 0.7446269989013672 777.4344482421875 0.34725725650787354 1014.08935546875 0.4294642508029938 0.86586523 0.4493961036205292 True -18 51015 29.73643732070923 0.7444984912872314 592.6956787109375 0.2393961399793625 1014.0748291015625 0.42903560400009155 0.8637278 0.44725602865219116 False -19 53700 29.733996391296387 0.7427821159362793 729.0817260742188 0.3371620774269104 1015.0985717773438 0.42858412861824036 0.863539 0.4473573863506317 False diff --git a/ENCSR999VDH/cherimoya.fold_1.performance.tsv b/ENCSR999VDH/cherimoya.fold_1.performance.tsv deleted file mode 100644 index 7d2d38be159d089e48f115141cf216cf7c948c32..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_1.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -1014.08935546875 0.35754725337028503 0.4294642508029938 0.20402197539806366 0.8658652305603027 0.8448505401611328 0.4493961036205292 \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_2.evaluate.json b/ENCSR999VDH/cherimoya.fold_2.evaluate.json deleted file mode 100644 index 7ebacfae6d82b16533f619236c947922adfbbdcf..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_2.evaluate.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr22", - "chr7" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_2.bed", - "valid_peaks.fold_2.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_2.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_2", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_2.bed", - "valid_nonpeaks.fold_2.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_2.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653PIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr5", - "chr6", - "chr8", - "chr9", - "chr10", - "chr13", - "chr14", - "chr16", - "chr17", - "chr18", - "chr19", - "chr20", - "chr21", - "chrX" - ], - "validation_chroms": [ - "chr22", - "chr7" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_2.fit.json b/ENCSR999VDH/cherimoya.fold_2.fit.json deleted file mode 100644 index aaa85affe0e8baa18aa177af096674fa036678a5..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_2.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF653PIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_2.log b/ENCSR999VDH/cherimoya.fold_2.log deleted file mode 100644 index c43429e8c4d4163a6b3c52993c793750eafb5e53..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_2.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2882 35.61290431022644 3.5461361408233643 681.2313842773438 0.7849663496017456 1214.21240234375 0.28459998965263367 0.65994525 6.7761030197143555 True -1 5764 31.91686701774597 0.6252985000610352 839.089111328125 0.8981481790542603 1026.95947265625 0.36883583664894104 0.74218196 2.9145309925079346 True -2 8646 31.943400859832764 0.6148228645324707 678.3560180664062 0.5374679565429688 1001.8220825195312 0.37981978058815 0.75290114 1.6527185440063477 True -3 11528 31.96927809715271 0.616753101348877 795.3271484375 0.5041511058807373 991.1802978515625 0.38118961453437805 0.757114 1.3588221073150635 True -4 14410 31.96008610725403 0.6109693050384521 679.6387939453125 0.579614520072937 981.0156860351562 0.38520267605781555 0.76511675 1.3515853881835938 True -5 17292 31.867229223251343 0.6108691692352295 749.6303100585938 0.5188495516777039 972.9036254882812 0.38857048749923706 0.77002645 1.2363578081130981 True -6 20174 31.884560346603394 0.6169378757476807 457.7941589355469 0.4354645013809204 964.1835327148438 0.39195865392684937 0.7797203 0.9548788070678711 True -7 23056 32.23261380195618 17.033355951309204 868.1993408203125 0.5292319059371948 961.0048217773438 0.3935839533805847 0.78039676 0.9079484343528748 True -8 25938 31.95893430709839 2.3794949054718018 739.290283203125 0.5205948352813721 953.4722900390625 0.3964420258998871 0.7890065 0.8816951513290405 True -9 28820 31.885640144348145 0.7924377918243408 590.1304931640625 0.5133333802223206 946.8695678710938 0.3994874954223633 0.79811734 0.7811015248298645 True -10 31702 31.886325120925903 0.6388857364654541 818.3753662109375 0.6860148906707764 942.5877075195312 0.40193605422973633 0.80460095 0.7572229504585266 True -11 34584 31.903701066970825 0.6277225017547607 857.7478637695312 0.6372724175453186 934.816650390625 0.4055681824684143 0.8104502 0.7010648846626282 True -12 37466 31.918798446655273 0.6213278770446777 724.9171752929688 0.4446139335632324 931.4854125976562 0.406514436006546 0.8175113 0.6535157561302185 True -13 40348 31.91367745399475 0.6601545810699463 825.0350341796875 0.5888464450836182 927.0062866210938 0.4094141125679016 0.8251878 0.6124261617660522 True -14 43230 31.92537760734558 0.6179277896881104 844.8526611328125 0.4496835470199585 926.0335083007812 0.4089561104774475 0.82919014 0.5612277388572693 True -15 46112 32.015735387802124 0.6207571029663086 741.3745727539062 0.41592785716056824 919.8782958984375 0.411207914352417 0.8342661 0.5148745775222778 True -16 48994 31.897400856018066 0.6093647480010986 638.5082397460938 0.38484621047973633 919.95703125 0.41085171699523926 0.83828515 0.4786966145038605 True -17 51876 31.90632128715515 0.6204640865325928 640.1053466796875 0.3232724368572235 918.700439453125 0.4133096933364868 0.8385966 0.4648876190185547 True -18 54758 31.981975555419922 0.6131339073181152 668.7526245117188 0.5620513558387756 919.3380126953125 0.4122944474220276 0.8395923 0.45922011137008667 True -19 57640 31.9535813331604 0.6224198341369629 695.0999755859375 0.21345967054367065 922.5816040039062 0.40877071022987366 0.84020734 0.45957523584365845 True diff --git a/ENCSR999VDH/cherimoya.fold_2.performance.tsv b/ENCSR999VDH/cherimoya.fold_2.performance.tsv deleted file mode 100644 index e89fb69191ec0bd13b42988fe07e7a589a0e1b03..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_2.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -922.5816040039062 0.3725565969944 0.40877071022987366 0.1834551841020584 0.8402073383331299 0.8034428954124451 0.45957523584365845 \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_3.evaluate.json b/ENCSR999VDH/cherimoya.fold_3.evaluate.json deleted file mode 100644 index 65dea9efa8debf7cd86bc04b7b002a3110339088..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_3.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr6", - "chr21" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_3.bed", - "valid_peaks.fold_3.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_3.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_3", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_3.bed", - "valid_nonpeaks.fold_3.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_3.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653PIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr7", - "chr8", - "chr9", - "chr11", - "chr12", - "chr13", - "chr15", - "chr16", - "chr17", - "chr19", - "chrX", - "chrY" - ], - "validation_chroms": [ - "chr6", - "chr21" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_3.fit.json b/ENCSR999VDH/cherimoya.fold_3.fit.json deleted file mode 100644 index 9282ce728d863fc03524d13936c0eba2405ef142..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_3.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF653PIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_3.log b/ENCSR999VDH/cherimoya.fold_3.log deleted file mode 100644 index 69de6ed1c9a96b965ba57b98edd34070da59431f..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_3.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2772 34.444111347198486 3.475414276123047 1041.7681884765625 0.7983354330062866 1106.31201171875 0.2913295030593872 0.64772123 9.102352142333984 True -1 5544 30.617706298828125 0.5045351982116699 863.5615844726562 0.7416362762451172 938.5856323242188 0.37463322281837463 0.73812234 3.0384256839752197 True -2 8316 30.601406812667847 0.5407960414886475 789.2862548828125 0.5552579760551453 914.1764526367188 0.38408640027046204 0.7500175 1.6133912801742554 True -3 11088 30.71336007118225 1.1645770072937012 1008.0348510742188 0.768397331237793 906.796142578125 0.38546159863471985 0.7582969 1.3749544620513916 True -4 13860 30.685122966766357 0.9114217758178711 752.722412109375 0.5580152273178101 895.57861328125 0.38978734612464905 0.7656825 1.2461862564086914 True -5 16632 30.705714464187622 0.8293917179107666 793.3096313476562 0.7266658544540405 887.3599853515625 0.3939804136753082 0.7718633 1.0916829109191895 True -6 19404 30.64293122291565 0.4914224147796631 726.3414306640625 0.6502856612205505 881.8224487304688 0.39622944593429565 0.7804144 0.9903229475021362 True -7 22176 30.634750843048096 0.4926934242248535 825.5946044921875 0.6077476739883423 876.3018798828125 0.398160845041275 0.79052585 0.8502169251441956 True -8 24948 30.638567447662354 0.48856282234191895 772.2750244140625 1.2989566326141357 870.5281982421875 0.4016069769859314 0.7967497 0.8483063578605652 True -9 27720 30.65032434463501 0.4991734027862549 947.5045166015625 1.0063549280166626 867.4019165039062 0.40388157963752747 0.80066967 0.8385332226753235 True -10 30492 30.638619422912598 0.49432873725891113 802.0518188476562 0.6783519983291626 860.5105590820312 0.405772864818573 0.8090362 0.7875909209251404 True -11 33264 30.647972345352173 0.49582457542419434 611.4306640625 0.5604031682014465 856.4668579101562 0.4092505872249603 0.81369555 0.7491496801376343 True -12 36036 30.646395444869995 0.49641895294189453 655.356201171875 0.6480321884155273 855.6697387695312 0.4068720042705536 0.82480097 0.6798821687698364 True -13 38808 30.649903774261475 0.4906888008117676 849.8953857421875 0.7053089141845703 848.9262084960938 0.41178297996520996 0.8298525 0.6252270936965942 True -14 41580 30.71798276901245 0.496077299118042 752.6173706054688 0.32768136262893677 846.6106567382812 0.41300538182258606 0.83608884 0.5714495182037354 True -15 44352 30.70271921157837 0.5065920352935791 627.9550170898438 0.45556777715682983 843.1377563476562 0.415685772895813 0.843709 0.5176458954811096 True -16 47124 30.633543729782104 0.49549412727355957 850.89306640625 0.5194790363311768 842.614013671875 0.41485142707824707 0.84502494 0.47348347306251526 True -17 49896 30.704360008239746 0.49771904945373535 694.4468994140625 0.4238892197608948 842.7493286132812 0.4145217835903168 0.8461429 0.45521801710128784 True -18 52668 30.835431575775146 12.365867614746094 567.5213012695312 0.6433128714561462 844.1817626953125 0.4131830930709839 0.8476679 0.45012062788009644 True -19 55440 30.721811532974243 0.6110877990722656 783.952392578125 0.4534880816936493 843.5965576171875 0.4138767719268799 0.8449272 0.45121654868125916 False diff --git a/ENCSR999VDH/cherimoya.fold_3.performance.tsv b/ENCSR999VDH/cherimoya.fold_3.performance.tsv deleted file mode 100644 index fd2a3ff3ae20b3b4e3081d4592d14f992f9e0707..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_3.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -844.1817626953125 0.3749060034751892 0.41318315267562866 0.17540600895881653 0.8476678729057312 0.802689790725708 0.45012062788009644 \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_4.evaluate.json b/ENCSR999VDH/cherimoya.fold_4.evaluate.json deleted file mode 100644 index 6c4c369cfe41b4fcc84450b21a30ec3bad346f95..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_4.evaluate.json +++ /dev/null @@ -1,75 +0,0 @@ -{ - "adam_lr": 0.001, - "adam_wd": 0.0, - "batch_size": 64, - "chroms": [ - "chr10", - "chr18" - ], - "controls": null, - "device": "cuda", - "dtype": "bfloat16", - "early_stopping": 20, - "exclusion_lists": [ - "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" - ], - "expansion": 2, - "in_window": 2114, - "loci": [ - "train_peaks.fold_4.bed", - "valid_peaks.fold_4.bed" - ], - "lw_lr": 0.001, - "lw_momentum": 0.9, - "lw_wd": 0.0, - "max_epochs": 20, - "max_jitter": 0, - "model": "cherimoya.fold_4.torch", - "muon_lr": 0.025, - "muon_wd": 0.03, - "n_filters": 128, - "n_layers": 9, - "n_warmup_epochs": 2, - "name": "cherimoya.fold_4", - "negative_ratio": 0.25, - "negatives": [ - "train_nonpeaks.fold_4.bed", - "valid_nonpeaks.fold_4.bed" - ], - "num_workers": 1, - "out_window": 1000, - "performance_filename": "cherimoya.fold_4.performance.tsv", - "random_state": null, - "residual_scale": 0.15, - "reverse_complement": false, - "reverse_complement_average": false, - "sequences": "hg38.fa", - "signals": [ - "ENCFF653PIR.bigWig" - ], - "skip": false, - "summits": false, - "training_chroms": [ - "chr1", - "chr2", - "chr3", - "chr4", - "chr5", - "chr6", - "chr8", - "chr9", - "chr11", - "chr12", - "chr14", - "chr15", - "chr16", - "chr20", - "chr22", - "chrY" - ], - "validation_chroms": [ - "chr10", - "chr18" - ], - "verbose": true -} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_4.fit.json b/ENCSR999VDH/cherimoya.fold_4.fit.json deleted file mode 100644 index c767154e86fd9a45457f7135297c681654d51308..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_4.fit.json +++ /dev/null @@ -1 +0,0 @@ -{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF653PIR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR999VDH/cherimoya.fold_4.log b/ENCSR999VDH/cherimoya.fold_4.log deleted file mode 100644 index 839ea005a05ad93719e7a52ecd0a938024c647d2..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_4.log +++ /dev/null @@ -1,21 +0,0 @@ -Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? -0 2728 33.991100549697876 4.875023365020752 1059.5679931640625 1.0169907808303833 1005.7382202148438 0.2761397361755371 0.6490392 8.432656288146973 True -1 5456 30.206464290618896 0.7061731815338135 684.094482421875 0.80890291929245 859.0256958007812 0.3576038181781769 0.72946876 2.914076328277588 True -2 8184 30.23651647567749 0.6284580230712891 719.0353393554688 0.6791976094245911 836.6787719726562 0.3669998049736023 0.7421078 1.697348713874817 True -3 10912 30.136463165283203 0.5682129859924316 698.8296508789062 0.451302170753479 825.9851684570312 0.3698153793811798 0.74897337 1.3370728492736816 True -4 13640 30.12585949897766 0.9133362770080566 907.7799682617188 0.8071576952934265 816.233642578125 0.37489983439445496 0.75212044 1.3444384336471558 True -5 16368 30.08370852470398 0.5756187438964844 732.5120849609375 0.8735051155090332 810.927978515625 0.37717196345329285 0.7630665 1.0682750940322876 True -6 19096 30.10556936264038 0.5893819332122803 785.37841796875 0.4306706190109253 804.308837890625 0.37828880548477173 0.7697668 0.8732399940490723 True -7 21824 30.085058450698853 0.5770132541656494 938.34912109375 0.6392512321472168 796.2883911132812 0.3838709592819214 0.7778711 0.8157055974006653 True -8 24552 30.11651349067688 0.5793428421020508 850.70166015625 0.8130205869674683 796.0404052734375 0.3828575909137726 0.7821174 0.8074935674667358 True -9 27280 30.12019944190979 0.576958179473877 712.2423095703125 0.6278657913208008 789.8453369140625 0.38650253415107727 0.7924813 0.7835842370986938 True -10 30008 30.097829818725586 0.5769636631011963 703.89111328125 0.5112383961677551 786.8121948242188 0.38759052753448486 0.800944 0.710105299949646 True -11 32736 30.12006449699402 0.5677480697631836 574.691162109375 0.7098557949066162 780.7098999023438 0.39076393842697144 0.80551213 0.6756474375724792 True -12 35464 30.091846704483032 0.5775425434112549 639.5252685546875 0.5043169260025024 777.367431640625 0.3924385905265808 0.8124106 0.6262547373771667 True -13 38192 30.111031770706177 0.6099755764007568 671.4271850585938 0.5853623151779175 774.5757446289062 0.3938477039337158 0.81879854 0.5659612417221069 True -14 40920 30.253039360046387 0.5772926807403564 673.2389526367188 0.49258965253829956 771.5640258789062 0.3948960602283478 0.82470286 0.5181552171707153 True -15 43648 30.147717475891113 1.6674416065216064 718.5933837890625 0.44293707609176636 769.257568359375 0.3972713053226471 0.8329335 0.4734116494655609 True -16 46376 30.119767665863037 0.5723738670349121 732.7915649414062 0.41930386424064636 769.5618286132812 0.3963157534599304 0.8346476 0.44289863109588623 True -17 49104 30.144628524780273 0.5840435028076172 680.7364501953125 0.3826879560947418 770.5491943359375 0.39656156301498413 0.8368199 0.43257683515548706 True -18 51832 30.172903060913086 0.5776891708374023 811.1922607421875 0.22958582639694214 772.5250244140625 0.39489543437957764 0.83482486 0.43299996852874756 False -19 54560 30.33736824989319 0.5699481964111328 665.5143432617188 0.32923752069473267 770.9745483398438 0.39671218395233154 0.83413744 0.4343230128288269 False diff --git a/ENCSR999VDH/cherimoya.fold_4.performance.tsv b/ENCSR999VDH/cherimoya.fold_4.performance.tsv deleted file mode 100644 index 1b78e6c6be471abeafa002ab66b76e77cc87cc17..0000000000000000000000000000000000000000 --- a/ENCSR999VDH/cherimoya.fold_4.performance.tsv +++ /dev/null @@ -1,2 +0,0 @@ -profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse -770.5491943359375 0.3896101415157318 0.39656156301498413 0.16499435901641846 0.8368198871612549 0.7819376587867737 0.43257683515548706 \ No newline at end of file